# 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/Archaeoglobus_sulfaticallidus_PM70_1_uid201033/NC_021169.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/Archaeoglobus_sulfaticallidus_PM70_1_uid201033/NC_021169.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Archaeoglobus_sulfaticallidus_PM70_1_uid201033/NC_021169.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|488599559|ref|YP_007906030.1|  [L=355]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   88.8   0.2    6.5e-25   87.7   0.2    1.5  1  OrfB_IS605      Probable transposase
    4.4e-11   42.1   0.6    1.1e-10   40.9   0.6    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
      6e-05   22.9   0.0    0.00033   20.5   0.0    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.01   16.0   0.2      0.048   13.8   0.1    2.0  2  HEPN_RES_NTD1   HEPN/RES N-terminal domain 1
       0.72   10.6   4.9       0.28   11.9   0.5    2.1  2  Occludin_ELL    Occludin homology 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 !   87.7   0.2   1.8e-28   6.5e-25      10     117 ..     172     276 ..     154     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 1.8e-28
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +p ++++k++giD+G++ +++  +++    + ++ ++ +++k+ ++ ++ l++k+k+skn++k++ kla+ ++k+ +
  gi|488599559|ref|YP_007906030.1| 172 KPLAPTGKVVGIDVGVRYFLADTDGR---QVENPCFYEKTLKRIKRLQRDLSRKQKGSKNWEKCRIKLAKAYEKLVN 245
                                       78899*********************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r+++lhkl++  +++++ ++ve+L ++nm+
  gi|488599559|ref|YP_007906030.1| 246 QRNDFLHKLSRFYVDNYDVIAVEDLRIQNMV 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 !   40.9   0.6     3e-14   1.1e-10       1      47 []       1      46 [.       1      46 [. 0.96

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3e-14
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M l +yk+r+yP +  ++kl++ ++++R+ YN+ L+e ++a +e++k
  gi|488599559|ref|YP_007906030.1|  1 M-LISYKFRIYPSKAIQAKLNEQLEICRWLYNRLLEEVNKAKKEGRK 46
                                      8.99***********************************99999876 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 ?   -1.3   0.0      0.59   2.1e+03      10      23 ..      38      51 ..      19      53 .. 0.81
   2 !   20.5   0.0   9.3e-08   0.00033       1      29 [.     291     319 ..     291     320 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.59
                    OrfB_Zn_ribbon 10 ykakeyGikveevn 23
                                      +kak++G+k+++ +
  gi|488599559|ref|YP_007906030.1| 38 NKAKKEGRKIKQTD 51
                                      68999999988765 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 9.3e-08
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSk 29 
                                       ++k+++ l+yka+++G+ v+ v+p  TS 
  gi|488599559|ref|YP_007906030.1| 291 WGKFIQLLSYKAERAGRRVVRVSPKGTSE 319
                                       99*************************95 PP

>> HEPN_RES_NTD1  HEPN/RES N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.3e-05     0.048      35     111 ..      30     104 ..      16     109 .. 0.90
   2 ?   -1.6   0.0      0.83     3e+03     101     117 ..     285     301 ..     275     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                     HEPN_RES_NTD1  35 YedaanelpydsreggylvgetydtedlleevieleaendeLiediadaledkaWverdpyglsedealkysWeaFk 111
                                       Y++  +e+   ++eg  + ++t dt+ l+ ++ e++ + ++++ ++ ++++ + W++++ +++ +++  k +W ++k
  gi|488599559|ref|YP_007906030.1|  30 YNRLLEEVNKAKKEGRKI-KQT-DTQALIVKLKEENPSLNKVYSKVLQMVNYQLWANIKALAKLRENGKKVGWLRYK 104
                                       666677788888888888.888.9********9****************************************9997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.83
                     HEPN_RES_NTD1 101 ealkysWeaFkelvkhk 117
                                       + l  sW +F +l+ +k
  gi|488599559|ref|YP_007906030.1| 285 RILDASWGKFIQLLSYK 301
                                       567889****9999887 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.3      0.42   1.5e+03      24      43 ..      30      54 ..      16      98 .. 0.57
   2 ?   11.9   0.5   7.8e-05      0.28      32      82 ..     206     257 ..     202     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.42
                      Occludin_ELL 24 YkelhaeleevskkfseLe.....r 43
                                      Y++l +e+++++k+ ++++     +
  gi|488599559|ref|YP_007906030.1| 30 YNRLLEEVNKAKKEGRKIKqtdtqA 54
                                      5555555555555444444222221 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.8e-05
                      Occludin_ELL  32 eevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrc 82 
                                       e++ k++++L+r+l++ ++gsk+++k   ++ + y+kl +  +++++k  r+
  gi|488599559|ref|YP_007906030.1| 206 EKTLKRIKRLQRDLSRKQKGSKNWEKCRIKLAKAYEKLVNqRNDFLHKLSRF 257
                                       78899********************************987688899888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2012.46
//
Query:       gi|488599560|ref|YP_007906031.1|  [L=134]
Description: Transposase-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-40  137.0   1.8    3.7e-40  136.8   1.8    1.0  1  Y1_Tnp    Transposase IS200 like
  ------ inclusion threshold ------
      0.049   13.5   0.9          5    7.0   0.1    2.2  2  DUF559    Protein of unknown function (DUF559)


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 !  136.8   1.8   4.1e-44   3.7e-40       1     121 []      12     132 ..      12     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 4.1e-44
                            Y1_Tnp   1 vsnlkyhivlvtkyRrkvltge.veerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgass 76 
                                       v++l+yh+++v+kyRrkv+t++ + ++lk+ i+ei+e++ev++l++e++ DHvH+l++++p+l+i+k+++alk  +s
  gi|488599560|ref|YP_007906031.1|  12 VYSLHYHLIFVVKYRRKVFTNDrIIDFLKQKIHEISETFEVEVLAIECDVDHVHILFKAKPTLNIPKYINALKTITS 88 
                                       689************************************************************************** PP

                            Y1_Tnp  77 rlinkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                       r i+++fpe+kkk l+k+ +W+++Yf++t g+++l+++krY+e+q
  gi|488599560|ref|YP_007906031.1|  89 REIRRNFPEVKKK-LWKNVFWSPSYFLATSGQVTLDVLKRYVESQ 132
                                       *********9988.566**************************98 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0022        19      26      56 ..      16      46 ..       6      53 .. 0.81
   2 ?    7.0   0.1   0.00056         5       5      25 ..      86     106 ..      82     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0022
                                      GGGTTTT--EEEEEEETTEEEEEEETTTTEE CS
                            DUF559 26 rnrrlsglkfrRqkpigsYivDfvclkakli 56
                                      + + +  +k+rR++  ++ i+Df+ +k + i
  gi|488599560|ref|YP_007906031.1| 16 HYHLIFVVKYRRKVFTNDRIIDFLKQKIHEI 46
                                      55666779***************98876655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00056
                                       XXXXXXXXXX-HHHHHHHHHH CS
                            DUF559   5 anarklRreqteaekkLWqll 25 
                                        ++r++Rr+ +e  kkLW+ +
  gi|488599560|ref|YP_007906031.1|  86 ITSREIRRNFPEVKKKLWKNV 106
                                       579***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); 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: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 822.73
//
Query:       gi|488599561|ref|YP_007906032.1|  [L=120]
Description: hypothetical protein Asulf_00003 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   99.8   0.2      1e-28   99.6   0.2    1.1  1  DUF86     Protein of unknown function DUF86
  ------ inclusion threshold ------
      0.089   13.0   0.1       0.19   12.0   0.1    1.8  1  DUF4209   Domain of unknown function (DUF4209)


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 !   99.6   0.2   1.1e-32     1e-28       1     116 [.      13     107 ..      13     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 1.1e-32
                                       HHHHHHHHCCHH...T.STSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHH CS
                             DUF86   1 ikealeklkefteeld.eeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepe 76 
                                       ++ea+ek++++t +++  e+f+++ +  dav+rnl++igEaa++i+++                      +++++ e
  gi|488599561|ref|YP_007906032.1|  13 MLEAIEKIERYTSSIEdLEDFMREDMVVDAVLRNLEIIGEAAKNIPED----------------------LRSKYGE 67 
                                       89*************99*******************************......................******* PP

                                       HHHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHH CS
                             DUF86  77 epwrkmiglRNrLvHgYlgidpeivwsiikenlpdleefl 116
                                       +pw++++glRN+++HgY+ +d+e vw i+k++lp+l+e+l
  gi|488599561|ref|YP_007906032.1|  68 IPWKRVVGLRNVVIHGYFAVDLEVVWVIVKRQLPELKEVL 107
                                       *************************************987 PP

>> DUF4209  Domain of unknown function (DUF4209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.1e-05      0.19      40      70 ..      43      86 ..       6      97 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                           DUF4209 40 l..........geelalilrvllgp...prglNLRNvvwHGfis 70
                                      +          ++++   lr  +g+   +r + LRNvv+HG+++
  gi|488599561|ref|YP_007906032.1| 43 VlrnleiigeaAKNIPEDLRSKYGEipwKRVVGLRNVVIHGYFA 86
                                      444444444445555555666666544467788********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 805.22
//
Query:       gi|488599562|ref|YP_007906033.1|  [L=107]
Description: putative nucleotidyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-16   58.1   0.6    9.7e-16   57.8   0.6    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
    3.6e-11   43.0   0.1    4.9e-11   42.6   0.1    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.066   12.7   0.0      0.079   12.4   0.0    1.0  1  ROK           ROK 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 !   57.8   0.6   1.6e-19   9.7e-16       6      92 ..      25     104 ..      13     107 .] 0.86

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.6e-19
                                       HHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC. CS
                      NTP_transf_2   6 eelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled. 81 
                                       ++lke+++v+++ +fGS+ rG+ +++SDiD++v ++e+v         ++++   +fleellg++vd+vt++   + 
  gi|488599562|ref|YP_007906033.1|  25 RILKERFKVKSIGVFGSVTRGEQKETSDIDIIVEFSEPVG--------WEIVDLKEFLEELLGVRVDVVTKNAAMRk 93 
                                       68999*********************************76........*********************77665554 PP

                                       CTEEEEEECEE CS
                      NTP_transf_2  82 pllvksileer 92 
                                       pll ksi+ e 
  gi|488599562|ref|YP_007906033.1|  94 PLLWKSIEREV 104
                                       66666666555 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   8.2e-15   4.9e-11       5      82 ..      25     101 ..      14     107 .] 0.81

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 8.2e-15
                                       TTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT.TS-HHHHHHH CS
                           Polbeta   5 eilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln.eapplllyei 80 
                                        il+++ +++ + +FGS+ +g+++e SDiD+ v ++e     e ++l++ le++ lg +vD+v+ n + ++ ll + 
  gi|488599562|ref|YP_007906033.1|  25 RILKERFKVKSIGVFGSVTRGEQKETSDIDIIVEFSEP-VGWEIVDLKEFLEEL-LGVRVDVVTKNaAMRKPLLWKS 99 
                                       4677778*******************************.556679*********.99*******9965555555444 PP

                                       HH CS
                           Polbeta  81 lk 82 
                                       ++
  gi|488599562|ref|YP_007906033.1| 100 IE 101
                                       44 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05     0.079      37     103 ..      11      85 ..       3      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                       CHHHHHHHHHHCCCHCCHTEEEEE.EEEESSEE.......ETTCCEBSSGGC.GCCCCTTHHHHHHHHHTS-EEEE CS
                               ROK  37 etlvdaiaelvdeaerkadeliav.gigspGli.......sdksgkivstpn.itwenfdlvekleerlnvpveve 103
                                       + l+++i+ +++e +r ++e+ +v +ig++G +        ++   iv+  + ++we +dl+e lee l+v v v 
  gi|488599562|ref|YP_007906033.1|  11 KNLEEVIQ-ILKENDRILKERFKVkSIGVFGSVtrgeqkeTSDIDIIVEFSEpVGWEIVDLKEFLEELLGVRVDVV 85 
                                       56655555.55556688889997768*******99998875566667766664889*************9998664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 771.03
//
Query:       gi|488599563|ref|YP_007906034.1|  [L=72]
Description: hypothetical protein Asulf_00005 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   5.0    2.3e-17   63.5   5.0    1.2  1  VAPB_antitox  Putative antitoxin
    5.4e-06   25.6   0.0    8.3e-06   25.0   0.0    1.4  1  SeqA_N        SeqA protein N-terminal domain
  ------ inclusion threshold ------
       0.13   11.6   0.1       0.13   11.6   0.1    1.0  1  AAA_8         P-loop containing dynein motor region D4
       0.29   11.1   3.8        7.8    6.6   1.1    2.5  2  RHH_1         Ribbon-helix-helix protein, copG family


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 !   63.5   5.0     5e-21   2.3e-17       1      64 [.       3      60 ..       3      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 5e-21
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilseeeadeiekaskel 64
                                      KtI +sd+vYe L+k K +geSFsdvI+rLl+++k      + ++ +il+++ead+i++ +++ 
  gi|488599563|ref|YP_007906034.1|  3 KTIAVSDDVYEMLSKTKMKGESFSDVIKRLLKRQK------ISDIPKILDDSEADKIKELIERQ 60
                                      9******************************8666......9*****************99765 PP

>> SeqA_N  SeqA protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.9e-09   8.3e-06       2      34 ..       3      34 ..       1      36 [. 0.95

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.9e-09
                            SeqA_N  2 KtIevDeeLYrYIasntqaiGESaSdILRRLLn 34
                                      KtI v ++ Y   +s+t+  GES Sd+  RLL+
  gi|488599563|ref|YP_007906034.1|  3 KTIAVSDDVYE-MLSKTKMKGESFSDVIKRLLK 34
                                      9**********.68******************7 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 ?   11.6   0.1   2.8e-05      0.13      82     130 ..       9      60 ..       1      69 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                             AAA_8  82 kevvfllsdnqiieesfledinnlLnt...GevpnLfskeekeeiieelrke 130
                                        +v  +ls+++++ esf + i+ lL+     ++p+++++ e ++i e ++++
  gi|488599563|ref|YP_007906034.1|   9 DDVYEMLSKTKMKGESFSDVIKRLLKRqkiSDIPKILDDSEADKIKELIERQ 60 
                                       4566689******************86222568999**********999976 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 ?    4.7   0.1    0.0068        30       3      35 ..       4      35 ..       4      38 .. 0.75
   2 ?    6.6   1.1    0.0017       7.8       6      21 ..      45      60 ..      45      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0068
                                      EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                             RHH_1  3 sirldeellerLdelarrrgrSrSelIReAlre 35
                                      +i ++++++e L +  ++ g S S++I+++l++
  gi|488599563|ref|YP_007906034.1|  4 TIAVSDDVYEMLSK-TKMKGESFSDVIKRLLKR 35
                                      56777777777764.678889999999999976 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                                      EEHHHHHHHHHHHHHH CS
                             RHH_1  6 ldeellerLdelarrr 21
                                      ld+++++++ el++r+
  gi|488599563|ref|YP_007906034.1| 45 LDDSEADKIKELIERQ 60
                                      8************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); 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: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 453.22
//
Query:       gi|488599564|ref|YP_007906035.1|  [L=129]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   64.3   0.7    1.6e-17   64.2   0.7    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 !   64.2   0.7   8.8e-22   1.6e-17       2     121 ..       3     123 ..       2     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 8.8e-22
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTS...SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                               PIN   2 vlDTsvliallrgeekaeaarklleel...eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida 75 
                                       ++DTs++i+l++ ++ka + ++    +   +  ++s++++ E+l++l++    ++ +++l++ +  ls+++i+p + 
  gi|488599564|ref|YP_007906035.1|   3 LFDTSFVIDLFKHDKKALKKAEET--DsspSIKAISVVTAHEVLRGLHY----IGDEEKLKLGEASLSRFEIIPYTY 73 
                                       58*********6666664333333..3347*******************....************************ PP

                                       HHHHHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  76 eiaeeaaeialkyg.....llpnDaliaAtAkehgikliatfDedfrrvak 121
                                       eia++aaei + +      l   D +iaAtA+ ++++l+ t+ ++f+r+++
  gi|488599564|ref|YP_007906035.1|  74 EIAKRAAEIDASLIkkgemLPFPDVVIAATAITYDLSLV-TREDHFKRIEG 123
                                       *********99988899**********************.********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 797.28
//
Query:       gi|488599565|ref|YP_007906036.1|  [L=78]
Description: hypothetical protein Asulf_00007 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 492.71
//
Query:       gi|488599566|ref|YP_007906037.1|  [L=392]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   79.1   0.2    3.6e-22   78.1   0.2    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.026   13.9   0.6      0.056   12.9   0.6    1.5  1  zf-ribbon_3     zinc-ribbon domain
       0.14   11.7   0.8       0.32   10.5   0.8    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.15   12.3   7.3       0.25   11.6   0.8    2.5  2  OrfB_IS605      Probable transposase
       0.36   10.7   2.0       0.43   10.4   0.5    1.9  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
       0.46   10.5   3.2       0.53   10.3   1.7    1.9  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.86    9.3   5.9       0.23   11.2   1.8    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


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 !   78.1   0.2   1.4e-25   3.6e-22       3      69 .]     290     355 ..     289     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.4e-25
                    OrfB_Zn_ribbon   3 klkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       k+k++l yka ++Gi+v  vn+a+TSk+C +Cgs+n+  + +r fkC++Cg+e++rD+n+++Ni +r
  gi|488599566|ref|YP_007906037.1| 290 KVKHMLLYKALWAGIPVAIVNEAWTSKQCWRCGSTNTV-VRKRMFKCKDCGLEYNRDLNGSVNIGNR 355
                                       7899**********************************.*************************876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   2.2e-05     0.056       3      24 ..     316     340 ..     315     341 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                       zf-ribbon_3   3 vrCPnCGa.p..lssddnvCpyCGt 24 
                                       ++C++CG+ +  +++++ +C+ CG 
  gi|488599566|ref|YP_007906037.1| 316 KQCWRCGStNtvVRKRMFKCKDCGL 340
                                       68******9999************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 ?   10.5   0.8   0.00013      0.32       2      27 ..     317     340 ..     317     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                       EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                       +C  Cgstn+v+      + C+dCGl
  gi|488599566|ref|YP_007906037.1| 317 QCWRCGSTNTVVRKR--MFKCKDCGL 340
                                       6999*****888855..8*******8 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.9      0.03        78      53      85 ..      22      57 ..      13      59 .. 0.88
   2 ?   11.6   0.8   9.8e-05      0.25      14     105 ..     156     247 ..     137     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.03
                        OrfB_IS605 53 lakeiaelqsklkkskn...ykkasrklarlhrkrs 85
                                      l++e  +lq++l++++    y + +++ +r+++k++
  gi|488599566|ref|YP_007906037.1| 22 LTQEYENLQKFLQGDNSvklYSANKQQAKRYYKKVK 57
                                      6788899********9899***************86 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.8e-05
                        OrfB_IS605  14 kgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrk 89 
                                       + + +++iD+G  n ++ v+  g      + ++l ++ ++ +     + + + ++k+ k a + ++ l +k sr++ 
  gi|488599566|ref|YP_007906037.1| 156 ERTVVIAIDIGEANPIASVELWGFGmQRRNVKFLGKEIRAIRTHYNWVRKSVGRKKI-KHAVKWIKQLGNKESRKVA 231
                                       566667777775555544444443324455566666666666666677777777775.8888999************ PP

                        OrfB_IS605  90 hllhklathliktlke 105
                                       ++lhk++++++++  e
  gi|488599566|ref|YP_007906037.1| 232 DVLHKATRSIVDRAIE 247
                                       ***********98766 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 ?   -2.9   0.1       2.4   6.3e+03      13      20 ..     315     322 ..     312     324 .. 0.78
   2 ?   10.4   0.5   0.00017      0.43      15      26 ..     331     345 ..     319     347 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                         zf-C2H2_3  13 asqCkeCg 20 
                                       ++qC  Cg
  gi|488599566|ref|YP_007906037.1| 315 SKQCWRCG 322
                                       568*9998 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00017
                         zf-C2H2_3  15 q...CkeCgMvYnpg 26 
                                       +   Ck Cg++Yn++
  gi|488599566|ref|YP_007906037.1| 331 RmfkCKDCGLEYNRD 345
                                       1455*********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 ?   -3.4   0.0       3.9     1e+04      23      34 ..       8      19 ..       8      23 .. 0.80
   2 ?   10.3   1.7   0.00021      0.53      15      44 ..     313     339 ..     307     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.9
                     Zn_Tnp_IS1595 23 hCgsrkayrikt 34
                                      +C++ +++r+k+
  gi|488599566|ref|YP_007906037.1|  8 KCKVVHLTRVKR 19
                                      699999999986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00021
                     Zn_Tnp_IS1595  15 WpngfvCPhCgsrkayriktrglfqCkeCr 44 
                                       W +++ C +Cgs+   ++ + + f+Ck+C+
  gi|488599566|ref|YP_007906037.1| 313 WTSKQ-CWRCGST--NTVVRKRMFKCKDCG 339
                                       77777.*****55..44444479******7 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         1   2.6e+03      14      21 ..       3      10 ..       1      11 [. 0.78
   2 ?   11.2   1.8   8.9e-05      0.23       3      24 ..     318     339 ..     317     341 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                                      SSS----S CS
                    DNA_RNApol_7kD 14 kgdpiRCk 21
                                       + +i+Ck
  gi|488599566|ref|YP_007906037.1|  3 VQKVIKCK 10
                                      5679***9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.9e-05
                                       -SSS--B----SSS----SSS- CS
                    DNA_RNApol_7kD   3 CgeCgaevslkkgdpiRCkeCG 24 
                                       C +Cg+ +++ ++   +Ck+CG
  gi|488599566|ref|YP_007906037.1| 318 CWRCGSTNTVVRKRMFKCKDCG 339
                                       99******************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      722  (0.04027); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2443.05
//
Query:       gi|488599567|ref|YP_007906038.1|  [L=140]
Description: Transposase-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-42  144.6   0.0    1.6e-42  144.5   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 !  144.5   0.0   8.7e-47   1.6e-42       1     119 [.       8     126 ..       8     128 .. 0.99

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 8.7e-47
                            Y1_Tnp   1 vsnlkyhivlvtkyRrkvltgeveerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassr 77 
                                       v++++yhiv+++kyR++vl +ev+e+l+e ik+iae+k+++i+ele+mpDH+Hl++++pp  ++++ivk lkg++++
  gi|488599567|ref|YP_007906038.1|   8 VYEINYHIVWCPKYRKPVLVDEVREFLEEQIKTIAETKGWEIIELEVMPDHIHLFISAPPFEAPTNIVKILKGVTAK 84 
                                       6899************************************************************************* PP

                            Y1_Tnp  78 linkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIe 119
                                       +++++fpel++k l+++++W+++Y+v t+g++s+et+k+YIe
  gi|488599567|ref|YP_007906038.1|  85 RLFEKFPELREKELWGGHIWSPSYYVGTAGHVSAETIKKYIE 126
                                       *****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 898.81
//
Query:       gi|488599568|ref|YP_007906039.1|  [L=282]
Description: glutamate synthase (NADPH) GltB3 subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-38  132.7   6.2    1.7e-38  132.2   6.2    1.2  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 !  132.2   6.2   9.2e-43   1.7e-38      13     182 ..      62     236 ..      50     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 9.2e-43
                                       HHHHHHHHHHTTT--....-.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-G CS
                             GXGXG  13 ilsneiakrygeegl....pedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfka 85 
                                       ++ n++++ry+ + l    p  +++i+++G++G++lgafl +G ++ ++G+a+d vG+++++G+i+i++ +      
  gi|488599568|ref|YP_007906039.1|  62 RVINTVGQRYIGTRLhlpsPAPKLEIHIEGTPGNDLGAFL-DGHRIIVHGNAQDGVGNTMDDGEIIIHGRA------ 131
                                       56678888888877733223579*****************.******************************...... PP

                                       GGSB-S-SSTTTT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S-B........- CS
                             GXGXG  86 eeniivGnvvlygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLgkt........g 148
                                             G+vv+ +++gGk++ir+++g+R+a+++     +++++v++g+  d+ +eYm+GG+v++Lg t        +
  gi|488599568|ref|YP_007906039.1| 132 ------GDVVAMSMRGGKIYIRDNVGYRTAIHMkeyinKVPVLVIGGTsQDFFGEYMAGGRVILLGLTlkegekhkA 202
                                       ......***************************9999999********99*********************999999 PP

                                       SSBTTT--EEEEEEE-SSSTHHHHB-TTT-EEEE CS
                             GXGXG 149 rnfaaGmsgGiayvldedekfekklnkelvelek 182
                                        ++++Gm+gG++y++ + ek++   ++ +ve+ek
  gi|488599568|ref|YP_007906039.1| 203 YYIGTGMHGGVIYLRGKVEKYQLGKEVGIVEMEK 236
                                       99*************8777765555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1772.58
//
Query:       gi|488599569|ref|YP_007906040.1|  [L=508]
Description: glutamate synthase (NADPH) GltB2 subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-141  470.3   0.0   5.9e-141  469.9   0.0    1.2  1  Glu_synthase     Conserved region in glutamate synthase
    1.5e-15   57.4   0.0    2.7e-08   33.6   0.0    2.2  2  Glu_syn_central  Glutamate synthase central domain
    5.8e-09   35.4   4.3    2.3e-08   33.5   3.2    2.4  3  FMN_dh           FMN-dependent dehydrogenase
    1.9e-07   30.4   4.9    5.4e-06   25.6   3.4    2.2  2  IMPDH            IMP dehydrogenase / GMP reductase domain
    7.8e-07   28.7  19.6    6.7e-06   25.7   1.1    3.4  3  Fer4             4Fe-4S binding domain
    3.6e-06   27.0  16.1    7.6e-06   26.0   9.0    2.4  2  Fer4_9           4Fe-4S dicluster domain
      4e-06   27.3  22.9    0.00052   20.5   1.8    3.2  4  Fer4_7           4Fe-4S dicluster domain
      1e-05   25.6   7.8      1e-05   25.6   7.8    2.3  2  Fer4_21          4Fe-4S dicluster domain
      2e-05   24.6  18.6     0.0015   18.6   0.6    3.3  3  Fer4_10          4Fe-4S dicluster domain
    0.00017   22.4  11.4    0.00024   22.0   0.2    3.3  3  Fer4_16          4Fe-4S double cluster binding domain
    0.00024   20.6   2.6    0.00042   19.8   2.6    1.3  1  NMO              Nitronate monooxygenase
     0.0012   18.8  22.2       0.01   15.9   1.8    3.3  3  Fer4_6           4Fe-4S binding domain
      0.002   18.5  27.7      0.012   16.1   2.3    3.3  3  Fer4_4           4Fe-4S binding domain
     0.0043   17.1   2.6     0.0043   17.1   2.6    3.5  3  Fer4_2           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.044   14.2  17.7       0.98    9.9  13.4    3.0  3  Fer4_8           4Fe-4S dicluster domain
      0.057   14.0  18.9       0.91   10.1   1.1    3.3  5  Fer4_17          4Fe-4S dicluster domain
      0.072   12.5   0.3       0.16   11.4   0.0    1.6  2  His_biosynth     Histidine biosynthesis protein


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 !  469.9   0.0  5.6e-144  5.9e-141       3     368 .]     109     476 ..     107     476 .. 0.98

  Alignments for each domain:
  == domain 1  score: 469.9 bits;  conditional E-value: 5.6e-144
                                       S-HHHHHHHHHHHHH---HHHHHHHHHHHTS.-S-SGGGGEEE--SS--...--GGGS--HHHHHTTEE---B-TTT CS
                      Glu_synthase   3 neievikllqkavqveskesidkyrekleerevlkakrdlleldaaeeal..ikleevepalkikkriltsamSyGa 77 
                                       ++i++++l+ +a+qv +++sid +re++e r++l++k+d le++++e+ +  +  +e++p++ ++++i++samSyGa
  gi|488599569|ref|YP_007906040.1| 109 YRIYWDHLVLNASQV-TNPSIDPLREPMELRTFLGRKPDGLEIKYSEDYEdvEIATELHPNVMLETPIVFSAMSYGA 184
                                       67899**********.******************************99887667899******************** PP

                                       S-HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS--EE CS
                      Glu_synthase  78 lseeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnakaleikiaQGakpgeGgql 154
                                       +s +a ++la+a +++gt +ntGEGG+++  +++    ai+QvasgrFGv+++yLn ++ +eiki+QGakpg+Gg+l
  gi|488599569|ref|YP_007906040.1| 185 ISYNAFKSLAMASKEFGTLFNTGEGGLPKSLREEYGGNAIVQVASGRFGVDPDYLNVSAVVEIKIGQGAKPGIGGHL 261
                                       *****************************9998888778************************************** PP

                                       -GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-.TTSEEEEEEE-STTHHHHHHHHHHTT-SE CS
                      Glu_synthase 155 pgeKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevn.keakvsvKlvaeagvetiaagvakanadi 230
                                       pgeKvs +i+++R+i++g+d++SPap+hdiysiedl++li++Lke++ +e++vsvK++a ++v +ia+g+++a+adi
  gi|488599569|ref|YP_007906040.1| 262 PGEKVSIRISETRMIPEGTDALSPAPQHDIYSIEDLSMLIYALKEATnYEKPVSVKIAAVHNVAAIASGIVRAGADI 338
                                       **********************************************99***************************** PP

                                       EEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                      Glu_synthase 231 ilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaal 307
                                       ++idGl+GGTGA+pk +++++G+P+elala vdq+l+eeg+r++ s+ ++Gg++ +adv+ka+alGAdav+igt al
  gi|488599569|ref|YP_007906040.1| 339 VAIDGLRGGTGAAPKIIRDNVGIPIELALASVDQRLREEGIRHKASILVAGGFRNSADVLKAIALGADAVYIGTPAL 415
                                       ***************************************************************************** PP

                                       HHTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT-S CS
                      Glu_synthase 308 ialgCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgin 368
                                       ia+gC+ +++C+t++C++G++tqdp+L krl+ e + +r+ n++k +++e++e+l+ +gin
  gi|488599569|ref|YP_007906040.1| 416 IAMGCTLCQKCYTGKCAWGICTQDPYLTKRLNPEIASRRLYNLLKGWSNEIKEMLGGMGIN 476
                                       **********************************************************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 !   21.8   0.0     1e-07   0.00011      49      97 ..     114     161 ..      78     215 .. 0.77
   2 !   33.6   0.0   2.6e-11   2.7e-08     133     270 ..     317     484 ..     244     494 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                                       GGEEE----SSS----TTTTGGG-B--EEES----SSS--G.GGG-EEEE CS
                   Glu_syn_central  49 dYFkqlfAqVTNPpiDpiREelvmsletllGkegnlleeee.eqakrlkl 97 
                                       d++  + +qVTNP+iDp+RE   m l+t+lG++++ le +  e+ + +++
  gi|488599569|ref|YP_007906040.1| 114 DHLVLNASQVTNPSIDPLREP--MELRTFLGRKPDGLEIKYsEDYEDVEI 161
                                       55555679************6..89**********999554244455544 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2.6e-11
                                       HHHHHHHHHHHHHHHHHTT-SEEEEESS........--STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS-- CS
                   Glu_syn_central 133 leealerlceeaeeavregaeilvLsDr........kvseervpipslLavgavhhhLvrkglrtkvslvvesgear 201
                                         +a++++++ a+  vr+ga+i+ ++          k+ +++v ip  La+++v+++L ++g r+k+s++v  g  r
  gi|488599569|ref|YP_007906040.1| 317 KIAAVHNVAAIASGIVRAGADIVAIDGLrggtgaapKIIRDNVGIPIELALASVDQRLREEGIRHKASILVA-GGFR 392
                                       457899999999999******9999987788887777889****************************9996.669* PP

                                       SHHHHHHHHHTT-SEEE...EHHHHHHHHHHHTTT..........S-...........----HH....HHHHHHHHH CS
                   Glu_syn_central 202 evhhfavllgyGadavn...Pylaletieklveeg..........al...........aeeele....knyrkavek 250
                                       +  ++   +++Gadav+   P l+   + +l+++           ++                +     n+ k+ ++
  gi|488599569|ref|YP_007906040.1| 393 NSADVLKAIALGADAVYigtPALIAMGC-TLCQKCytgkcawgicTQdpyltkrlnpeI----AsrrlYNLLKGWSN 464
                                       ****************755455554433.233333333455544400455554444321....133569******** PP

                                       HHHHHHHHTT--BHHHHHHS CS
                   Glu_syn_central 251 GllKimskmGistlqSYkga 270
                                        +   +  mGi  ++S +g 
  gi|488599569|ref|YP_007906040.1| 465 EIKEMLGGMGINAIESVRGN 484
                                       ****************9986 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.5   1.6e+03      42      91 ..     155     204 ..     148     208 .. 0.70
   2 !   33.5   3.2   2.2e-11   2.3e-08     268     308 ..     379     419 ..     316     422 .. 0.84
   3 ?   -0.9   0.0      0.61   6.5e+02     317     342 ..     457     482 ..     452     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                                       S-SS-B--EEET.TEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-E CS
                            FMN_dh  42 dvskvdlsttll.GqklslPvliaPvglaklahpdgelalaraaakagipf 91 
                                       d ++v+++t+l     l++P++++++++  +   ++   la a +++g++f
  gi|488599569|ref|YP_007906040.1| 155 DYEDVEIATELHpNVMLETPIVFSAMSYGAISY-NAFKSLAMASKEFGTLF 204
                                       5566666666663446799*******9998876.66667777777777665 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 2.2e-11
                                       H..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHH CS
                            FMN_dh 268 vggrievlvDgGirrGsDvlkAlalGAdavllGRpflygla 308
                                       +++++ +lv gG+r+ +DvlkA+alGAdav +G p+l ++ 
  gi|488599569|ref|YP_007906040.1| 379 IRHKASILVAGGFRNSADVLKAIALGADAVYIGTPALIAMG 419
                                       35699*******************************99976 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHHHHT-SBHHHHH CS
                            FMN_dh 317 rvleilraelertmallGvksvaeld 342
                                       ++l+ +++e+++ +  +G++ +++++
  gi|488599569|ref|YP_007906040.1| 457 NLLKGWSNEIKEMLGGMGINAIESVR 482
                                       678899***************99885 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.021        22      19      43 ..     157     181 ..     149     197 .. 0.89
   2 !   25.6   3.4   5.1e-09   5.4e-06     156     237 ..     325     412 ..     295     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.021
                                       GGSB--EESSTTEEESSSEEE-SST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  19 kevdlktkltkkiklniPlvsaamd 43 
                                       ++v+++t+l  ++ l++P+v +am 
  gi|488599569|ref|YP_007906040.1| 157 EDVEIATELHPNVMLETPIVFSAMS 181
                                       689********************96 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 5.1e-09
                                       HHHHHHHHHTT-SEEEE.-SS-STTBHHHHHC.SB---HHHHHHHHHHHHCTCT....-EEEEES---SHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                             IMPDH 156 aegakaLieagadavkv.GiGpGsiCttrvva.gvGvpqltAvaevaeaakkag....vpviaDGGikysgdivkAl 226
                                       a+ a+ +++agad+v + G+  G     +++   vG+p   A+a+v +  ++ g      ++  GG ++s d+ kA+
  gi|488599569|ref|YP_007906040.1| 325 AAIASGIVRAGADIVAIdGLRGGTGAAPKIIRdNVGIPIELALASVDQRLREEGirhkASILVAGGFRNSADVLKAI 401
                                       34467799********989988888888888537**************9999984444579999************* PP

                                       HTT-SEEEESC CS
                                       xxxxxxxxxxx RF
                             IMPDH 227 aaGadavmlGs 237
                                       a+Gadav +G 
  gi|488599569|ref|YP_007906040.1| 402 ALGADAVYIGT 412
                                       *********96 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   2.9   8.1e-05     0.085       2      18 ..      14      30 ..      13      32 .. 0.91
   2 !   25.7   1.1   6.3e-09   6.7e-06       3      24 .]      46      67 ..      44      67 .. 0.91
   3 ?    0.3   1.4      0.69   7.2e+02       8      15 ..     420     427 ..     416     428 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.1e-05
                                      EEETTTSSS-THHHHHS CS
                              Fer4  2 videekCigCGaCvevC 18
                                      + d e+Ci+C  C+  C
  gi|488599569|ref|YP_007906040.1| 14 ERDDERCIRCRVCERQC 30
                                      5699***********99 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 6.3e-09
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                       de  C+gC +Cv  CP++A+t
  gi|488599569|ref|YP_007906040.1| 46 HDEYVCVGCQRCVVFCPTNALT 67
                                      58899***************86 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.69
                                       SSS-THHH CS
                              Fer4   8 CigCGaCv 15 
                                       C+ C +C+
  gi|488599569|ref|YP_007906040.1| 420 CTLCQKCY 427
                                       99999997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   9.0   7.2e-09   7.6e-06       1      50 [.      19      65 ..      19      72 .. 0.92
   2 ?    5.0   0.6     0.026        28       2      15 ..     420     434 ..     397     450 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.2e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      +C++C+ C+++C ++ +++d     + ++++    C+gC++Cv  Cp++a
  gi|488599569|ref|YP_007906040.1| 19 RCIRCRVCERQCSQEGHRYDPELDRMFHDEY---VCVGCQRCVVFCPTNA 65
                                      6****************99999999998776...7************997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                            Fer4_9   2 CtgCgaCvea.Cpag 15 
                                       Ct C++C +  C  g
  gi|488599569|ref|YP_007906040.1| 420 CTLCQKCYTGkCAWG 434
                                       666666633326544 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   4.1    0.0042       4.5      32      49 ..      14      31 ..       9      33 .. 0.76
   2 !   20.4  13.6   5.5e-07   0.00058       1      52 []      19      65 ..      19      65 .. 0.95
   3 !   20.5   1.8   4.9e-07   0.00052       2      22 ..      51      71 ..      50      89 .. 0.82
   4 ?    4.0   0.7      0.07        74      32      51 ..     414     434 ..     391     439 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0042
                            Fer4_7 32 eidpekClgCgaCvavCP 49
                                      e d e+C+ C++C++ C 
  gi|488599569|ref|YP_007906040.1| 14 ERDDERCIRCRVCERQCS 31
                                      567888888888888885 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.5e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      rCi C+ C++ C+++  ++d+e      +++ +d+  C+gC++Cv  CPt+a
  gi|488599569|ref|YP_007906040.1| 19 RCIRCRVCERQCSQEGHRYDPE-----LDRMFHDEYVCVGCQRCVVFCPTNA 65
                                      8******************998.....678999*****************97 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 4.9e-07
                            Fer4_7  2 CigCgaCvaaCpvkaieldee 22
                                      C+gC++Cv+ Cp++a++++++
  gi|488599569|ref|YP_007906040.1| 51 CVGCQRCVVFCPTNALTVRPH 71
                                      *****************9876 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.07
                            Fer4_7  32 eidpekClgCgaCva.vCPtg 51 
                                       ++ ++ C+ C++C +  C +g
  gi|488599569|ref|YP_007906040.1| 414 ALIAMGCTLCQKCYTgKCAWG 434
                                       566788999999988567666 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   7.8   9.5e-09     1e-05       4      57 ..      16      66 ..      13      68 .. 0.80
   2 ?    1.4   0.5      0.33   3.5e+02      43      49 ..     419     425 ..     398     433 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.5e-09
                           Fer4_21  4 dedkCigCgkCliaCedtshqaieidakt.vlkvvedeCvGCnlCssvCPvedci 57
                                      d+++Ci C  C   C++++h   ++d++  ++ + e  CvGC+ C+  CP+ +++
  gi|488599569|ref|YP_007906040.1| 16 DDERCIRCRVCERQCSQEGH---RYDPELdRMFHDEYVCVGCQRCVVFCPT-NAL 66
                                      789*************9888...567664144456779************7.666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.33
                           Fer4_21  43 GCnlCss 49 
                                       GC+lC +
  gi|488599569|ref|YP_007906040.1| 419 GCTLCQK 425
                                       3444332 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   4.2   0.00046      0.49       2      19 ..      13      30 ..      12      47 .. 0.78
   2 !   18.6   0.6   1.4e-06    0.0015       3      24 ..      45      82 ..      43     110 .. 0.72
   3 ?    5.0   0.6     0.025        26       8      19 ..     419     431 ..     414     468 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00046
                           Fer4_10  2 vvidddtCirCgkCvkaC 19
                                      +++dd++CirC+ C + C
  gi|488599569|ref|YP_007906040.1| 13 IERDDERCIRCRVCERQC 30
                                      6789************** PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.4e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadl................t 24
                                       +d+  C++C++Cv +CP+++                t
  gi|488599569|ref|YP_007906040.1| 45 FHDEYVCVGCQRCVVFCPTNAltvrphpstyrpnanwT 82
                                      678889*************8877777776666555552 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.025
                           Fer4_10   8 tCirCgkCvka.C 19 
                                        C+ C+kC +  C
  gi|488599569|ref|YP_007906040.1| 419 GCTLCQKCYTGkC 431
                                       5999999998657 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.8      0.05        53       1      12 [.      19      30 ..       9      39 .. 0.76
   2 !   22.0   0.2   2.2e-07   0.00024       2      33 ..      51      81 ..      50     100 .. 0.66
   3 ?    1.2   0.4      0.69   7.2e+02       2       9 ..     420     427 ..     413     468 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.05
                           Fer4_16  1 rCgtCgkCaevC 12
                                      rC++C+ C   C
  gi|488599569|ref|YP_007906040.1| 19 RCIRCRVCERQC 30
                                      467777776666 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.2e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisy 33
                                      C++C++C+  CPtna++ + +++  +r + ++
  gi|488599569|ref|YP_007906040.1| 51 CVGCQRCVVFCPTNALTVRPHPST-YRPNANW 81
                                      *****************8854443.2333334 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.69
                           Fer4_16   2 CgtCgkCa 9  
                                       C+ C+kC 
  gi|488599569|ref|YP_007906040.1| 420 CTLCQKCY 427
                                       66666664 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.6     4e-07   0.00042     141     232 ..     316     421 ..     298     426 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4e-07
                               NMO 141 ptissvkeark....vearGaDalivqGpeaG.GhqGtpevgdkglfaLvpqvldavd...........iPviAaGG 201
                                       + i++v+++ +    + ++GaD++ ++G  +G G  +  ++   +    ++ +l  vd             ++ aGG
  gi|488599569|ref|YP_007906040.1| 316 VKIAAVHNVAAiasgIVRAGADIVAIDGLRGGtGAAP--KIIRDNVGIPIELALASVDqrlreegirhkASILVAGG 390
                                       44555555444001155688********988744444..44433333334444444445566888888899****** PP

                               NMO 202 iidrrgvaaaLalGAsgvqigtrfLltkesd 232
                                       + +  +v  a+alGA +v+igt  L++  ++
  gi|488599569|ref|YP_007906040.1| 391 FRNSADVLKAIALGADAVYIGTPALIAMGCT 421
                                       **********************999987775 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   2.7   2.6e-05     0.027       1      20 [.      12      31 ..      12      35 .. 0.91
   2 !   15.9   1.8   9.7e-06      0.01       5      24 .]      47      66 ..      44      66 .. 0.87
   3 ?   -0.6   2.7       1.5   1.6e+03       9      17 ..     420     428 ..     420     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                            Fer4_6  1 vveidpdkCigCgdCvrvCP 20
                                      ++e d+++Ci C+ C+r C 
  gi|488599569|ref|YP_007906040.1| 12 IIERDDERCIRCRVCERQCS 31
                                      6899***************6 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.7e-06
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d+  C+gC +Cv+ CP++a+
  gi|488599569|ref|YP_007906040.1| 47 DEYVCVGCQRCVVFCPTNAL 66
                                      6666**************97 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.5
                            Fer4_6   9 CigCgdCvr 17 
                                       C+ C +C++
  gi|488599569|ref|YP_007906040.1| 420 CTLCQKCYT 428
                                       999999997 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   5.9     6e-05     0.063       2      16 ..      18      32 ..      17      33 .. 0.92
   2 !   16.1   2.3   1.1e-05     0.012       4      17 .]      51      64 ..      42      64 .. 0.91
   3 ?    0.1   3.9       1.5   1.6e+03       4      12 ..     420     428 ..     417     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      erCi+C++C++ C+q
  gi|488599569|ref|YP_007906040.1| 18 ERCIRCRVCERQCSQ 32
                                      89***********97 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.1e-05
                            Fer4_4  4 CigCgsCvaaCPqg 17
                                      C+gC +Cv +CP++
  gi|488599569|ref|YP_007906040.1| 51 CVGCQRCVVFCPTN 64
                                      ************86 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.5
                            Fer4_4   4 CigCgsCva 12 
                                       C+ C +C+ 
  gi|488599569|ref|YP_007906040.1| 420 CTLCQKCYT 428
                                       9******95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   2.4   0.00024      0.25       4      20 ..      14      30 ..      11      32 .. 0.84
   2 !   17.1   2.6   4.1e-06    0.0043       2      22 .]      43      63 ..      42      63 .. 0.92
   3 ?   -0.4   4.4       1.5   1.6e+03      10      20 ..     420     431 ..     414     438 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                            Fer4_2  4 vvdtdrCigCgaCvsaC 20
                                      + d +rCi+C+ C   C
  gi|488599569|ref|YP_007906040.1| 14 ERDDERCIRCRVCERQC 30
                                      56889********9888 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.1e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      +++ d+  C+gC  Cv  CP+
  gi|488599569|ref|YP_007906040.1| 43 RMFHDEYVCVGCQRCVVFCPT 63
                                      5789999*************7 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.5
                            Fer4_2  10 CigCgaCvsa.C 20 
                                       C+ C +C++  C
  gi|488599569|ref|YP_007906040.1| 420 CTLCQKCYTGkC 431
                                       999999987555 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  13.4   0.00093      0.98       3      64 ..      18      64 ..      16      65 .. 0.84
   2 ?    9.9   2.3   0.00094         1       5      19 ..      51      65 ..      47      96 .. 0.63
   3 ?    4.5   0.1     0.044        47      50      59 ..     419     428 ..     389     467 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00093
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      e+Ci+C  C+ +C    ++  h++d++ +++   +  ++       + C++c++C++ Cp++
  gi|488599569|ref|YP_007906040.1| 18 ERCIRCRVCERQC----SQEGHRYDPELDRMF--H--DE-------YVCVGCQRCVVFCPTN 64
                                      69***********....455788899999888..3..34.......56************87 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00094
                            Fer4_8  5 CieCgaCqsaCpvlr 19
                                      C++C++C   Cp+  
  gi|488599569|ref|YP_007906040.1| 51 CVGCQRCVVFCPTNA 65
                                      666666666665444 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.044
                            Fer4_8  50 sCttcgaCte 59 
                                        Ct c++C +
  gi|488599569|ref|YP_007906040.1| 419 GCTLCQKCYT 428
                                       4555555532 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.0     0.011        12      44      58 ..      18      32 ..       6      35 .. 0.81
   2 ?    6.0   4.9     0.017        18       1      14 [.      19      32 ..      19      50 .. 0.69
   3 ?    8.9   1.2    0.0021       2.2      46      59 ..      51      64 ..      35      66 .. 0.85
   4 ?   10.1   1.1   0.00087      0.91       2      31 ..      51      81 ..      50      96 .. 0.59
   5 ?    5.3   0.3     0.028        29      43      57 ..     417     432 ..     392     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      ++Ci C+ Cer+C q
  gi|488599569|ref|YP_007906040.1| 18 ERCIRCRVCERQCSQ 32
                                      678888888888876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                           Fer4_17  1 rCiqCgyClpeCps 14
                                      rCi+C+ C+++C++
  gi|488599569|ref|YP_007906040.1| 19 RCIRCRVCERQCSQ 32
                                      46666666666654 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0021
                           Fer4_17 46 CieCgeCerkCPqg 59
                                      C++C++C+  CP +
  gi|488599569|ref|YP_007906040.1| 51 CVGCQRCVVFCPTN 64
                                      99999999999976 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00087
                           Fer4_17  2 CiqCgyClpeCpsyeaydn.epkkllraakl 31
                                      C +C+ C+  Cp+++ +   +p +++ +a++
  gi|488599569|ref|YP_007906040.1| 51 CVGCQRCVVFCPTNALTVRpHPSTYRPNANW 81
                                      7777777777777777443245555555555 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.028
                           Fer4_17  43 aslCieCgeCe.rkCP 57 
                                       a  C+ C++C   kC 
  gi|488599569|ref|YP_007906040.1| 417 AMGCTLCQKCYtGKCA 432
                                       6789999999866775 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.5   3.7e+03     184     209 ..     316     341 ..     309     350 .. 0.73
   2 ?   11.4   0.0   0.00015      0.16      73     106 ..     382     415 ..     370     428 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.5
                                       HHHHHHHSSEEEEESS--SHHHHHHH CS
                      His_biosynth 184 kelaeavkipviasGGvgsledlkel 209
                                        ++a+  ++  iasG v+  +d+ ++
  gi|488599569|ref|YP_007906040.1| 316 VKIAAVHNVAAIASGIVRAGADIVAI 341
                                       56777778888888888888887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00015
                                       SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                      His_biosynth  73 fipvqvGGGIrsledveelleagadkviigtaav 106
                                       ++ + v GG r+  dv +++ +gad v igt a+
  gi|488599569|ref|YP_007906040.1| 382 KASILVAGGFRNSADVLKAIALGADAVYIGTPAL 415
                                       478999*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 2786.08
//
Query:       gi|488599570|ref|YP_007906041.1|  [L=378]
Description: glutamate synthase (NADPH) GltB1 subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.0    5.7e-11   41.8   0.0    2.1  2  GATase_2  Glutamine amidotransferases class-II
    9.2e-07   29.1   0.0    1.9e-06   28.1   0.0    1.4  1  GATase_6  Glutamine amidotransferase domain
    0.00056   19.8   0.0       0.08   12.9   0.0    2.3  2  GATase_7  Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   9.6e-15   5.7e-11     101     244 ..      93     228 ..      64     234 .. 0.80
   2 !   13.9   0.0   2.7e-06     0.016     274     377 ..     241     347 ..     235     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 9.6e-15
                                       T-EEEEEEE--B-GGGS-HHHHHH--EEEEEEEE-TT---HHHHHHHHHHHHHHHGGG.....-BTTBEEEEEESSE CS
                          GATase_2 101 glevlgwRevpvdksvlgeaakesePsieqvfvekkedlseeelerklyviRkriekeiakkkaekefYicslssrt 177
                                       +++++   e+p++ s+      +  P + + fv+ k+  +ee+l  + +v+ k ++ ++      ++ Y+ s  +  
  gi|488599570|ref|YP_007906041.1|  93 NFDIVHDEEIPTNPSA----DVSYPPLVWRYFVAPKN--TEEKLSDDDFVVEKVMHINTR----IEDAYVFSSGKDM 159
                                       5556666666666543....34566888899998887..788899999999998877654....689********** PP

                                       EEEEESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-SSE....EEEE--TTHHHHHHH CS
                          GATase_2 178 ivYkglltseqlkefykdlkdeelesalalvHsRfstntfPsWelaqPlRll....aHnGEintlrGnknw 244
                                        v+kg+  +e++ +f+  + de ++ ++   HsRf tnt   W  a+P+ +l     HnGEi     n+++
  gi|488599570|ref|YP_007906041.1| 160 GVFKGVGFPEDVADFF--MLDELYKGYMWTAHSRFPTNTPGWWGGAHPFSILdwtvVHNGEISSYGTNRRY 228
                                       ****************..589****************************97533338*****998888876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHHH.TT--HHHHHHHHS----TT-GGGTHHHHHHHHHHTTT----..-SSEE.EEEE-SSEEEEEE CS
                          GATase_2 274 Dsasldnvlellvl.sgrslaealmlliPeawennksldkekkafyeyasalmepW..DGPal.ivftdGkvvgavL 346
                                       D++ +  +++ll++ +g  ++    ++  + w++ ++++++kk++y    ++  p   +GP + iv   G++ g   
  gi|488599570|ref|YP_007906041.1| 241 DTEVMAYAVDLLMRrQGLPIEIVSKIFAAPMWDQIEHMEEKKKKLYTTLRMVYAPLliNGPFTvIVAHHGEMFGI-T 316
                                       888889999998862577777788899999************************95559**76156677888886.5 PP

                                       -TT--S--EEEEETT--EEEES.STTSS---G CS
                          GATase_2 347 DRnGLRPaRylvtkddlvvlas.EvGvldlee 377
                                       DR  LRP        d+v l+s E+G+  +++
  gi|488599570|ref|YP_007906041.1| 317 DRIRLRPITAGAK-GDFVFLSSeEAGIRAVSP 347
                                       *******986655.555555552689887766 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.1e-10   1.9e-06       2     102 ..     173     273 ..     172     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.1e-10
                          GATase_6   2 dasglaslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevll 78 
                                       d+  l++l+++ ++ aH R  ++      ga+Pf  +   +++vhNGei+ y++ r+ l+   g+ +   +Dtev++
  gi|488599570|ref|YP_007906041.1| 173 DFFMLDELYKGYMWTAHSRFPTNTPGWWGGAHPF--SILDWTVVHNGEISSYGTNRRYLEM-FGYYCTLFTDTEVMA 246
                                       5666777788889999***999999999999***..999**************99999998.99999********** PP

                          GATase_6  79 all....eelGeevl.erlrGmfafaiwd 102
                                        ++    ++ G  +  e +  +fa+ +wd
  gi|488599570|ref|YP_007906041.1| 247 YAVdllmRRQG--LPiEIVSKIFAAPMWD 273
                                       *9844442222..2223344455555555 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.3e-05      0.08      23      64 ..     210     251 ..     200     278 .. 0.81
   2 !    4.7   0.0    0.0045        27      74     119 ..     298     340 ..     279     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                          GATase_7  23 rlvivfnGeiyNykelreeLeakghrfrtksDtevllallea 64 
                                       + ++v+nGei  y   r+ Le  g+ ++  +Dtev++ +++ 
  gi|488599570|ref|YP_007906041.1| 210 DWTVVHNGEISSYGTNRRYLEMFGYYCTLFTDTEVMAYAVDL 251
                                       5799*******************************9877664 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0045
                          GATase_7  74 lnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelk 119
                                       +nG f +++ ++ e  ++ + Dr+  +P+  g + gd ++++Se  
  gi|488599570|ref|YP_007906041.1| 298 INGPFTVIVAHHGE--MFGITDRIRLRPITAGAK-GDFVFLSSEEA 340
                                       78888888877666..******************.77777788755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2239.26
//
Query:       gi|488599571|ref|YP_007906042.1|  [L=432]
Description: hypothetical protein Asulf_00013 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-59  201.6   0.1    2.1e-59  201.1   0.1    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.7e-18   65.8   1.7    3.7e-18   65.8   1.7    3.1  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.9e-10   39.4   5.4     0.0012   17.6   1.3    4.0  4  HI0933_like     HI0933-like protein
    1.9e-07   30.9   0.5    8.4e-07   28.8   0.3    2.2  2  Rubredoxin_C    Rubredoxin NAD+ reductase C-terminal domain
    3.6e-07   29.7   5.1    4.4e-07   29.4   2.8    2.4  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    3.8e-05   23.2   4.2     0.0037   16.6   0.3    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase
    5.9e-05   23.2   0.7    0.00017   21.7   0.0    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00017   20.6   5.3       0.03   13.2   0.1    2.3  2  Trp_halogenase  Tryptophan halogenase
    0.00026   20.4   0.1    0.00039   19.8   0.1    1.2  1  FAD_binding_3   FAD binding domain
    0.00047   20.2   3.4       0.17   11.9   0.1    3.4  4  NAD_binding_9   FAD-NAD(P)-binding
    0.00078   19.4   0.2     0.0014   18.6   0.2    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00082   18.7   0.5     0.0017   17.7   0.5    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0013   17.9   8.2       0.21   10.6   2.7    3.5  4  FAD_binding_2   FAD binding domain
     0.0068   15.7   6.2      0.074   12.3   0.1    3.4  5  Thi4            Thi4 family
     0.0069   16.0  10.9      0.028   14.0   1.8    3.1  3  DAO             FAD dependent oxidoreductase
     0.0075   15.4   5.9       0.33    9.9   0.1    2.8  3  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.023   13.8   0.0       0.13   11.3   0.0    1.9  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.031   13.8   0.0      0.052   13.0   0.0    1.4  1  Glu_dehyd_C     Glucose dehydrogenase C-terminus
      0.056   12.9   0.4       0.14   11.6   0.5    1.5  2  KdpD            Osmosensitive K+ channel His kinase sensor do
      0.077   12.9   0.9        2.6    7.9   0.1    2.7  2  LpxI_N          LpxI N-terminal domain
      0.086   13.3   0.4       0.32   11.4   0.4    2.0  2  NAD_binding_7   Putative NAD(P)-binding
      0.098   12.9   1.6        1.4    9.2   0.4    2.5  2  TrkA_N          TrkA-N domain
       0.12   12.0   0.3       0.25   10.9   0.3    1.5  1  Clenterotox     Clostridium enterotoxin
       0.89    8.6   7.4        3.6    6.6   0.1    3.0  3  GIDA            Glucose inhibited division protein A
        6.4    6.0   6.7        9.5    5.4   1.0    2.8  3  FAD_oxidored    FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.1   0.1     3e-62   2.1e-59       1     292 [.       3     301 ..       3     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 3e-62
                                       CSEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgiel 69 
                                       +dvvviG  ++G+ + + ++     + ++++++e+++ + + l+++ l g  ++++         e+      +++ 
  gi|488599571|ref|YP_007906042.1|   3 FDVVVIGNSAGGIGCIEAIRSrnRDLTIAVISEEEYHTYSKALIPYYLSGRISREKMYYrppdfyEK-----MDVTP 74 
                                       69*************98888865799999**999999999999999998888888766677755532.....35999 PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC....TTBEECCSECHHHHHHCCSS-T. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv...aenvgklvrtldsaealklkllp. 142
                                       +lg+ +v+i   +kkv l     +++e+i+y+kl++AtG++p++++++G     en++ +  t+d+a +++++l + 
  gi|488599571|ref|YP_007906042.1|  75 ILGKRAVSINVSEKKVIL-----DSGEEIEYGKLLIATGGKPFIPQMEGFdpkLENAFSF-VTMDDALGIEKELEDa 145
                                       99999*************.....8899***********************9988888777.9*********999999 PP

                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgnge.kle 217
                                       k++v+ GgG+iG+  A +la+ g ev+++e +dr+l + +d++ s+++++++ ++Gv +++g ++k++++ ++  ++
  gi|488599571|ref|YP_007906042.1| 146 KKAVILGGGVIGLMAAEVLAEKGLEVHVIELADRVLaPVVDERTSEIVQRVFDEHGVSIHTGLTIKKVNSSNNrVYS 222
                                       **********************************************************************9996666 PP

                                       EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxx RF
                       Pyr_redox_2 218 vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpela 287
                                       v+l+dg+ei++dl++vavGv p+ +l+ +++ +e+  ++givv+++++t+ +++ya+GD+a       ++++ + l+
  gi|488599571|ref|YP_007906042.1| 223 VTLTDGREIECDLMIVAVGVVPNIDLV-RDSEIEV--NRGIVVNRKMETSAKDVYACGDCAevydfmiDDRRLLPLW 296
                                       ***************************.*******..99**********************9999999999999999 PP

                                       HHHHH CS
                                       xxxxx RF
                       Pyr_redox_2 288 qaAvq 292
                                       ++A  
  gi|488599571|ref|YP_007906042.1| 297 PNAYY 301
                                       99975 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       2.3   1.6e+03       2      27 ..       5      30 ..       4      39 .. 0.58
   2 ?   -0.1   0.0         2   1.4e+03      51      78 ..      68      92 ..      65      95 .. 0.84
   3 !   65.8   1.7   5.2e-21   3.7e-18       1      80 [.     147     227 ..     147     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.3
                                      EEEECSSHHHHHHHHHHHHTTSEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtv 27
                                      vvv+G +  g+ + +a++  + + t+
  gi|488599571|ref|YP_007906042.1|  5 VVVIGNSAGGIGCIEAIRSRNRDLTI 30
                                      89999655555555555544444444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                                      HHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox 51 ekngievllntkveeiegsedgvesvkl 78
                                      ek+ ++ +l++++++i+ se++   v l
  gi|488599571|ref|YP_007906042.1| 68 EKMDVTPILGKRAVSINVSEKK---VIL 92
                                      7889999*************98...655 PP

  == domain 3  score: 65.8 bits;  conditional E-value: 5.2e-21
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesv 76 
                                       k+v++GgG+igl++A++lae g +V+v+e +d++l ++ De +s+i+q+ + ++g+ ++++ ++++++ s++ v+sv
  gi|488599571|ref|YP_007906042.1| 147 KAVILGGGVIGLMAAEVLAEKGLEVHVIELADRVLaPVVDERTSEIVQRVFDEHGVSIHTGLTIKKVNSSNNRVYSV 223
                                       689*****************************************************************99999**** PP

                                       EEET CS
                         Pyr_redox  77 klkd 80 
                                       +l+d
  gi|488599571|ref|YP_007906042.1| 224 TLTD 227
                                       *987 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.12        87       1      30 [.       3      34 ..       3      46 .. 0.69
   2 ?    4.0   0.0     0.023        16     131     166 ..      79     111 ..      67     122 .. 0.73
   3 !   17.6   1.3   1.7e-06    0.0012       2      35 ..     147     180 ..     146     185 .. 0.91
   4 !   15.0   0.1   1.1e-05    0.0077     115     163 ..     193     241 ..     183     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                                      -SEEEE--SHHHHHH..HHHHHHTT--EEEE- CS
                       HI0933_like  1 kdviviGgGaAGlma..AisaakrgkrVllle 30
                                      +dv+viG  a G+ +  Ai+ ++r+  ++++ 
  gi|488599571|ref|YP_007906042.1|  3 FDVVVIGNSAGGIGCieAIRSRNRDLTIAVIS 34
                                      59*****8777776622555566666666664 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.023
                                       -EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                       HI0933_like 131 evksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                       +  s++ +e+   +v ++s+ee+e  kl++AtGG+ 
  gi|488599571|ref|YP_007906042.1|  79 RAVSINVSEK---KVILDSGEEIEYGKLLIATGGKP 111
                                       5555544444...466678***************85 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.7e-06
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       + +++GgG  GlmaA+ +a++g +V ++e a+++
  gi|488599571|ref|YP_007906042.1| 147 KAVILGGGVIGLMAAEVLAEKGLEVHVIELADRV 180
                                       689**************************88876 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                        ++  +e gv++++  ++k+v+++++++++v++++++e+e+d +++A+G
  gi|488599571|ref|YP_007906042.1| 193 VQRVFDEHGVSIHTGLTIKKVNSSNNRVYSVTLTDGREIECDLMIVAVG 241
                                       4566789****************************************99 PP

>> Rubredoxin_C  Rubredoxin NAD+ reductase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.5   3.2e+03      24      42 ..      28      46 ..       7      47 .. 0.67
   2 !   28.8   0.3   1.2e-09   8.4e-07       6      70 .]     326     395 ..     322     395 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.5
                                      SEEEEEE-SS-..EEEEEE CS
                      Rubredoxin_C 24 aeelveedkekgkYkklfi 42
                                       ++ v +++e ++Y+k +i
  gi|488599571|ref|YP_007906042.1| 28 LTIAVISEEEYHTYSKALI 46
                                      6667778888889999776 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.2e-09
                                       EETTEEEEEES.....--TT---SEEEEEE-SS-..EEEEEEETTEEEEEEEES-HHHHHHHHHHHHTT- CS
                      Rubredoxin_C   6 kvsgidlfSvG.....dieeeekaeelveedkekgkYkklfikngklvGAiliGDtkesaklkkliekkt 70 
                                       +++++ ++ +G     +i e+e +e+l + d e++ Y+++ ik+g + G +l+G ++++ ++++l+++k+
  gi|488599571|ref|YP_007906042.1| 326 HFFDVYIINAGlnitdEIAEKEGYEVLIRFDPERKVYRRIAIKDGLIKGIVLVGKVDRAGIYLNLMKRKI 395
                                       56666666666322224555666********************************************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 ?   -0.2   0.0      0.65   4.6e+02     235     268 ..      80     110 ..       4     133 .. 0.46
   2 !   29.4   2.8   6.2e-10   4.4e-07     118     305 .]      93     277 ..      79     277 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.65
                       Pyr_redox_3 235 vkeikekeeeykvktedgkkvevkddvvlatGyk 268
                                       + +i+ +e+  kv  ++g+++e + + ++atG k
  gi|488599571|ref|YP_007906042.1|  80 AVSINVSEK--KVILDSGEEIE-YGKLLIATGGK 110
                                       333333222..22233333332.34444444444 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 6.2e-10
                       Pyr_redox_3 118 tsketyeAkkviiAtGefdkPnklnipGeek.lvkhyskv..kef....hkya.gqkvvViGgknSavDaAlelvrk 186
                                        s e++e  k++iAtG   kP  ++++G +  l   +s v  +++    ++++  +k v+ Gg+  +  aA  l++k
  gi|488599571|ref|YP_007906042.1|  93 DSGEEIEYGKLLIATGG--KPFIPQMEGFDPkLENAFSFVtmDDAlgieKELEdAKKAVILGGGVIGLMAAEVLAEK 167
                                       45568888889999997..888888888875233333333113331111233336899999**************** PP

                       Pyr_redox_3 187 gaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekee.eykvktedgkkvevkddvv 262
                                       g eV+v+   + + +        +  ++ + ++++ +e+ + +++  ++k+++ +++  y v+ +dg+++e  d ++
  gi|488599571|ref|YP_007906042.1| 168 GLEVHVIELADRVLAP------VVDERTSEIVQRVFDEHGVSIHTGLTIKKVNSSNNrVYSVTLTDGREIEC-DLMI 237
                                       *******998744333......355555555555555566************976651579********987.888* PP

                       Pyr_redox_3 263 latGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +a+G  p+++++++s +e    +r  + + ++et  ++++ +G
  gi|488599571|ref|YP_007906042.1| 238 VAVGVVPNIDLVRDSEIEV---NRGIVVNRKMETSAKDVYACG 277
                                       *************999988...4445556789********998 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.4    0.0024       1.7       3      26 ..     157     180 ..     157     180 .. 0.98
   2 !   16.6   0.3   5.1e-06    0.0037     211     261 ..     191     241 ..     186     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHHTTEEEEEEESSSSS CS
                     Amino_oxidase   3 GLaaArqLlsaGfdVtvlEardrv 26 
                                       GL+aA  L+++G++V v+E  drv
  gi|488599571|ref|YP_007906042.1| 157 GLMAAEVLAEKGLEVHVIELADRV 180
                                       9********************997 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHTTTTEEEETSEEEEEEEEETTC.EEEEETTSTEEEESEEEE-S- CS
                     Amino_oxidase 211 qlpealaeelrgldirlntrVkeikregdg.vtvtledgevveaDaVvvTvp 261
                                       ++++++ + ++g++i+++   k+++ +++  ++vtl+dg+++e+D  +v+v 
  gi|488599571|ref|YP_007906042.1| 191 EIVQRVFD-EHGVSIHTGLTIKKVNSSNNRvYSVTLTDGREIECDLMIVAVG 241
                                       66777777.9****************77776*******************96 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 ?   -2.2   0.1         7   5.1e+03       1      24 [.       7      30 ..       7      33 .. 0.82
   2 !   21.7   0.0   2.4e-07   0.00017       1      31 [.     150     180 ..     150     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7
                                      EE--SHHHHHHHHHHHCCTEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvll 24
                                      ++G  ++G  +  +++ +++d ++
  gi|488599571|ref|YP_007906042.1|  7 VIGNSAGGIGCIEAIRSRNRDLTI 30
                                      788889999999999999887765 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.4e-07
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       I+G+G+ Gl aA  La++g++v+++e +dr+
  gi|488599571|ref|YP_007906042.1| 150 ILGGGVIGLMAAEVLAEKGLEVHVIELADRV 180
                                       89**************************997 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   1.6     0.001      0.72       2      34 ..     148     177 ..     147     185 .. 0.88
   2 !   13.2   0.1   4.2e-05      0.03     157     208 ..     190     241 ..     184     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                                       EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlvese 34 
                                        vi+GGG  G +aA +la+ +   lev ++e +
  gi|488599571|ref|YP_007906042.1| 148 AVILGGGVIGLMAAEVLAEKG---LEVHVIELA 177
                                       59****************999...889999865 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SG CS
                    Trp_halogenase 157 akfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsG 208
                                        ++ +rv  ++Gv +  g   + +   ++rv s++l+dgre+e dl+i + G
  gi|488599571|ref|YP_007906042.1| 190 SEIVQRVFDEHGVSIHTGLTIKKVNSSNNRVYSVTLTDGREIECDLMIVAVG 241
                                       678899999*********999999999*********************8877 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   5.4e-07   0.00039       4      33 ..     148     177 ..     146     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.4e-07
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                        +I G+G  Glm+a +L+e+G +v+++e  
  gi|488599571|ref|YP_007906042.1| 148 AVILGGGVIGLMAAEVLAEKGLEVHVIELA 177
                                       589************************844 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.4   5.3e+03       2      34 ..       7      36 ..       6      52 .. 0.75
   2 ?    1.6   0.0      0.34   2.4e+02     122     155 ..      78     109 ..      64     110 .. 0.80
   3 ?    5.0   0.8      0.03        21       1      32 [.     149     175 ..     149     185 .. 0.83
   4 !   11.9   0.1   0.00024      0.17     102     154 ..     187     241 ..     179     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.4
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdps 34
                                      ++G  + G+ ++e++ +r    ++l+i ++ ++
  gi|488599571|ref|YP_007906042.1|  7 VIGNSAGGIGCIEAIRSR---NRDLTIAVISEE 36
                                      778888888888888888...588888888443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.34
                     NAD_binding_9 122 aevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       +++v+++ +++  +v+l++g+++++ ++ +A+G 
  gi|488599571|ref|YP_007906042.1|  78 KRAVSINVSEK--KVILDSGEEIEYGKLLIATGG 109
                                       56777776666..5899***************95 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.03
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfd 32 
                                       +i G+G+ Gl+++e L+++      le+++++
  gi|488599571|ref|YP_007906042.1| 149 VILGGGVIGLMAAEVLAEKG-----LEVHVIE 175
                                       699**************995.....7777776 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00024
                     NAD_binding_9 102 dlfeellarlpegvtvevhra.evvdleeradgq.avlladgaslaadaVvLAlG 154
                                       ++ +e+++r+ ++  v++h++ ++ +++ +++++  v+l+dg+++++d  ++A+G
  gi|488599571|ref|YP_007906042.1| 187 ERTSEIVQRVFDEHGVSIHTGlTIKKVNSSNNRVySVTLTDGREIECDLMIVAVG 241
                                       667888899877778999988688899999999648******************9 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.9e-06    0.0014       2      53 ..     148     200 ..     147     248 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTT CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek.sleklvekg 53 
                                         ++G G++G   a+v+a++gleV++++ +++ l+ + ++ ++  ++++  ++
  gi|488599571|ref|YP_007906042.1| 148 AVILGGGVIGLMAAEVLAEKGLEVHVIELADRVLAPVVDERTSeIVQRVFDEH 200
                                       5699*************************999999877666552445554444 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   0.5   2.4e-06    0.0017      29      71 ..     146     189 ..     130     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-06
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TT CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lg 71 
                                        k +++GgGv Gl A+++ ++ g +V v+++  ++l  + +   
  gi|488599571|ref|YP_007906042.1| 146 KKAVILGGGVIGLMAAEVLAEKGLEVHVIELADRVLAPVVDeRT 189
                                       4789**************************99999887665444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0064       4.6       1      37 [.       4      39 ..       4      52 .. 0.89
   2 !   10.6   2.7   0.00029      0.21       2      32 ..     148     178 ..     147     182 .. 0.92
   3 ?   -2.7   0.1       3.3   2.4e+03     151     186 ..     197     229 ..     190     243 .. 0.75
   4 ?    2.0   0.0      0.12        89     375     404 ..     259     281 ..     252     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0064
                                      SEEEE-..-SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  1 DviViG..sGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      Dv+ViG  +G+ G+  A++ +++ l++av++ e++   +
  gi|488599571|ref|YP_007906042.1|  4 DVVVIGnsAGGIGCIEAIRSRNRDLTIAVISEEEY---H 39
                                      9*****8878889999*****************98...4 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00029
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32 
                                       +++ G+G+ GL+AA  +ae+Gl+v v+e ++
  gi|488599571|ref|YP_007906042.1| 148 AVILGGGVIGLMAAEVLAEKGLEVHVIELAD 178
                                       69*************************9875 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.3
                                       HHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTC CS
                     FAD_binding_2 151 arkagvdfqerteadeLivedgrvtGavvenpesgr 186
                                       ++++gv +++ + +++++  ++rv+ ++++   +gr
  gi|488599571|ref|YP_007906042.1| 197 FDEHGVSIHTGLTIKKVNSSNNRVYSVTLT---DGR 229
                                       4678999999999****99999***99998...333 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.12
                                       EEEBETTSBESTTEEESSBTEEE-STCEES CS
                     FAD_binding_2 375 GvetdengrvldadgqpipGLYAaGevaag 404
                                       G++++ ++++        ++ YA+G +a  
  gi|488599571|ref|YP_007906042.1| 259 GIVVNRKMET------SAKDVYACGDCA-E 281
                                       9999999999......***********9.4 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.019        14      17      48 ..       2      34 ..       1      38 [. 0.86
   2 ?   -1.5   0.0       1.6   1.2e+03     187     210 ..      73      96 ..      67     108 .. 0.73
   3 !   12.3   0.1    0.0001     0.074      20      48 ..     148     175 ..     139     183 .. 0.90
   4 ?   -3.1   0.0       5.1   3.7e+03     100     132 ..     189     220 ..     186     245 .. 0.72
   5 ?   -3.5   0.0       6.9     5e+03     127     153 ..     250     278 ..     237     282 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.019
                                      EEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEE CS
                              Thi4 17 esDvvivGaGssGLtaayylakk.pdlkvaile 48
                                      + Dvv++G  + G+ +   +  +  dl +a++ 
  gi|488599571|ref|YP_007906042.1|  2 KFDVVVIGNSAGGIGCIEAIRSRnRDLTIAVIS 34
                                      67**************999976659*****996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                       S-----ECB-HHHHHHHHHHHECE CS
                              Thi4 187 ekvkgeksldaekaedaivkktre 210
                                         + g++++  +++e++++ ++ e
  gi|488599571|ref|YP_007906042.1|  73 TPILGKRAVSINVSEKKVILDSGE 96 
                                       567899999******999955544 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0001
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvaile 48 
                                        vi G+G  GL aa +la+k +l+v ++e
  gi|488599571|ref|YP_007906042.1| 148 AVILGGGVIGLMAAEVLAEK-GLEVHVIE 175
                                       589*****************.*******9 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5.1
                                       HHHHHHHHHTSTTEEEEESEEEEEEEEETBTEE CS
                              Thi4 100 tstllskvlqlanvkllnavaveDlivregegv 132
                                       ts+++ +v++  +v + +++++  +   + ++v
  gi|488599571|ref|YP_007906042.1| 189 TSEIVQRVFDEHGVSIHTGLTIKKVNSSN-NRV 220
                                       67788888888888888877777665444.444 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 6.9
                                       ET.B.TEEEEEEEEEHHHHTCTTTSS.-B CS
                              Thi4 127 re.g.egvaGvvinwtlvelahdtqscvD 153
                                       r+ + e  +G+v+n ++ + a d  +c D
  gi|488599571|ref|YP_007906042.1| 250 RDsEiEVNRGIVVNRKMETSAKDVYACGD 278
                                       44233444688888877777777777765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6      0.87   6.3e+02       1      29 [.       4      36 ..       4      44 .. 0.82
   2 !   14.0   1.8     4e-05     0.028       2      28 ..     148     176 ..     147     182 .. 0.91
   3 !    6.5   0.0    0.0075       5.4     154     205 ..     195     245 ..     186     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.87
                                      EEEEEC..TSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiG..GGiiGlstAyeLarrg..Vtllekg 29
                                      dvv+iG  +G iG+  A     r   ++++  +
  gi|488599571|ref|YP_007906042.1|  4 DVVVIGnsAGGIGCIEAIRSRNRDltIAVISEE 36
                                      8*************9999986666888888766 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4e-05
                                       EEEECTSHHHHHHHHHHHHTT..EEEEES CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllek 28 
                                        vi GGG+iGl +A  La++g  V ++e 
  gi|488599571|ref|YP_007906042.1| 148 AVILGGGVIGLMAAEVLAEKGleVHVIEL 176
                                       69*************************95 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0075
                                       HHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH CS
                               DAO 154 raaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd 205
                                       r + ++Gv i++g ++++++  +++v+ v + t+g++ ++d  ++a G+  +
  gi|488599571|ref|YP_007906042.1| 195 RVFDEHGVSIHTGLTIKKVNSSNNRVYSV-TLTDGREIECDLMIVAVGVVPN 245
                                       45889************99888899****.666677755699******7654 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.87   6.3e+02       1      30 [.       4      33 ..       4      41 .. 0.75
   2 !    6.6   1.0    0.0048       3.4       3      39 ..     149     183 ..     148     188 .. 0.89
   3 !    9.9   0.1   0.00046      0.33      92     159 ..     191     261 ..     184     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.87
                     Lycopene_cycl  1 DvvviG..aGpAglslAarlteakpglkvvli 30
                                      DvvviG  aG  g+  A r+   + +l + +i
  gi|488599571|ref|YP_007906042.1|  4 DVVVIGnsAGGIGCIEAIRS--RNRDLTIAVI 33
                                      9*****76788888889888..6666766666 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0048
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsllfp 39 
                                       v+ G+G  gl  A+ l  a++gl+v +ie ++ +l p
  gi|488599571|ref|YP_007906042.1| 149 VILGGGVIGLMAAEVL--AEKGLEVHVIELADRVLAP 183
                                       899*******999999..99********999988765 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00046
                     Lycopene_cycl  92 ellerlv.engvkllea.kvesveeeeageslvvleggrkirarlvvdarglaslk.karrlglQtfyGve 159
                                       e+ +r+  e+gv+ + + ++++v+ +++   +v+l +gr+i++ l ++a g+  +    r+  + + +G++
  gi|488599571|ref|YP_007906042.1| 191 EIVQRVFdEHGVSIHTGlTIKKVNSSNNRVYSVTLTDGREIECDLMIVAVGVVPNIdLVRDSEIEVNRGIV 261
                                       56667666899998887588999999998889******************953222245555555555555 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.13     135     212 ..      85     166 ..      69     212 .. 0.71
   2 ?    0.2   0.0      0.45   3.2e+02     118     162 ..     209     246 ..     190     254 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                       K_oxygenase 135 veskd.aegeeeelearnlvlgvGtepkiPev..le.klegkervvHsseylerkeellakkriaVvGsGqSaaeif 207
                                       v+ k+   ++ ee+e  +l++++G++p iP++  ++ kle+   +v  +++l  ++el+++k+ ++ G+G  +   +
  gi|488599571|ref|YP_007906042.1|  85 VSEKKvILDSGEEIEYGKLLIATGGKPFIPQMegFDpKLENAFSFVTMDDALGIEKELEDAKKAVILGGGVIGLMAA 161
                                       444444456677888899************98443325667778888999999999999**********86544444 PP

                       K_oxygenase 208 edllr 212
                                       e l++
  gi|488599571|ref|YP_007906042.1| 162 EVLAE 166
                                       44444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.45
                       K_oxygenase 118 eveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepki 162
                                       ++++v+ ++   +++++v+      + +e+e+  ++++vG  p+i
  gi|488599571|ref|YP_007906042.1| 209 TIKKVNSSN---NRVYSVTL----TDGREIECDLMIVAVGVVPNI 246
                                       344444333...34777776....245677888888888888776 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 ?   13.0   0.0   7.3e-05     0.052      31      68 ..     145     179 ..     133     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                       Glu_dehyd_C  31 pesalvlGaGslGLLalalleaeerglervyvlgrrdr 68 
                                        ++a++lG G +GL+a+ +l+   +gle v+v++  dr
  gi|488599571|ref|YP_007906042.1| 145 AKKAVILGGGVIGLMAAEVLAE--KGLE-VHVIELADR 179
                                       5789************999985..7887.999886665 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.1   5.1e+03      30      80 ..      23      77 ..      19      83 .. 0.53
   2 ?   11.6   0.5   0.00019      0.14      77     174 ..     162     259 ..     145     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.1
                              KdpD 30 eegvdvviglvethgrketeall..egl.eviprkeveykgkel.eeldldaila 80
                                      ++++d++i+++++++ +  ++ l    l   i r+++ y+   + e++d+  il 
  gi|488599571|ref|YP_007906042.1| 23 SRNRDLTIAVISEEEYHTYSKALipYYLsGRISREKMYYRPPDFyEKMDVTPILG 77
                                      5667777777766555444433312122124566666666544315577776665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00019
                              KdpD  77 ailarkpevvlvDelahtnapgsrhekryqdveelLe.agidVittvnvqhleslndvvekitgvrvretvPdevle 152
                                       ++la+k   v v ela +  +    e+  + v+++ + +g+++ t + +++++s n+ v ++t ++ re+  d ++ 
  gi|488599571|ref|YP_007906042.1| 162 EVLAEKGLEVHVIELADRVLAPVVDERTSEIVQRVFDeHGVSIHTGLTIKKVNSSNNRVYSVTLTDGREIECDLMIV 238
                                       567777777777788888888888888888888888537*******************************9999999 PP

                              KdpD 153 eAdevelvDltpeeLlerLkeg 174
                                       +   v  +Dl  ++ + ++++g
  gi|488599571|ref|YP_007906042.1| 239 AVGVVPNIDLVRDSEI-EVNRG 259
                                       9999999999776543.35555 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0037       2.6       3      35 ..     148     180 ..     146     200 .. 0.83
   2 ?    2.6   0.1      0.16   1.1e+02      61      82 ..     367     391 ..     360     406 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0037
                            LpxI_N   3 gliAGsGrlPllvaeaakaagrevvvvalegea 35 
                                       ++i G+G + l++ae + ++g ev+v+ l + +
  gi|488599571|ref|YP_007906042.1| 148 AVILGGGVIGLMAAEVLAEKGLEVHVIELADRV 180
                                       6899***********************998754 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                            LpxI_N  61 LkregvtevvmaGkvekpkll...d 82 
                                       +k+  ++ +v++Gkv +  ++    
  gi|488599571|ref|YP_007906042.1| 367 IKDGLIKGIVLVGKVDRAGIYlnlM 391
                                       67778999*********99996442 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 ?   -1.4   0.0       4.5   3.2e+03      10      40 ..       5      37 ..       2      88 .. 0.66
   2 ?   11.4   0.4   0.00045      0.32       7      40 ..     145     178 ..     142     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.5
                     NAD_binding_7 10 vlvvGg..GevAarkvrklleagakvtvvapev 40
                                      v+v+G   G ++   + +  + + ++ v+++e 
  gi|488599571|ref|YP_007906042.1|  5 VVVIGNsaGGIGCIEAIRSRNRDLTIAVISEEE 37
                                      677774225555555555555667777888883 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00045
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                        kk ++ GgG +++  ++ l+e+g +v+v+  + 
  gi|488599571|ref|YP_007906042.1| 145 AKKAVILGGGVIGLMAAEVLAEKGLEVHVIELAD 178
                                       5899*************************76553 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.32   2.3e+02       1      49 [.       5      54 ..       5      60 .. 0.70
   2 ?    9.2   0.4    0.0019       1.4       2      46 ..     149     193 ..     148     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.32
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE.EEES-T CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreegle.vvvgda 49
                                      +++iG +  G   +e ++++++d ++   +ee  +++++  ++ ++ g  
  gi|488599571|ref|YP_007906042.1|  5 VVVIGNSAGGIGCIEAIRSRNRDLTIAVISEEEYHTYSKALIPyYLSGRI 54
                                      57888888888888888887767888888888888888777662444555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEE CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvv 46 
                                       +i+G G +G   ae L e+g +v vi+  +++++ + +e +  +v
  gi|488599571|ref|YP_007906042.1| 149 VILGGGVIGLMAAEVLAEKGLEVHVIELADRVLAPVVDERTSEIV 193
                                       8*****************6645******99999888877755444 PP

>> Clenterotox  Clostridium enterotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00035      0.25      77     141 ..      34      97 ..      27     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                       Clenterotox  77 yikvYntYekYelieyqnGnisdkaeyYlpslgylevtdapslgaevvetpidedsliqtGpeee 141
                                       +   Y tY k  +  y  G is +  yY+p   y ++  +p lg   v +++ e+++i +   ee
  gi|488599571|ref|YP_007906042.1|  34 SEEEYHTYSKALIPYYLSGRISREKMYYRPPDFYEKMDVTPILGKRAVSINVSEKKVILDSG-EE 97 
                                       5567******9888999**************9998888899*************99986543.33 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   8.3e+02     123     150 ..      85     109 ..      72     117 .. 0.79
   2 ?    3.5   2.3     0.043        31       2      28 ..     148     174 ..     147     195 .. 0.82
   3 ?    6.6   0.1     0.005       3.6      98     150 ..     189     242 ..     177     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                                       ECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 123 veekkvkgvvtedgetikakavviatGt 150
                                       v   + k v++++ge+i+  +  iatG 
  gi|488599571|ref|YP_007906042.1|  85 V---SEKKVILDSGEEIEYGKLLIATGG 109
                                       4...4467999***************96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.043
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                        +++GgG  G+ AA  +a++G++v  i
  gi|488599571|ref|YP_007906042.1| 148 AVILGGGVIGLMAAEVLAEKGLEVHVI 174
                                       5899********************998 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.005
                                       HHHHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA  98 skevteklenepnleiiee.eveeliveekkvkgvvtedgetikakavviatGt 150
                                        +e+ +++ +e+ ++i ++ ++++++ ++++v  v+++dg++i+++ +++a G 
  gi|488599571|ref|YP_007906042.1| 189 TSEIVQRVFDEHGVSIHTGlTIKKVNSSNNRVYSVTLTDGREIECDLMIVAVGV 242
                                       4556666666788888887468999999***********************996 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.72   5.2e+02       1      29 [.       4      34 ..       4      38 .. 0.73
   2 ?    5.4   1.0     0.013       9.5       3      29 ..     149     175 ..     148     181 .. 0.91
   3 ?    2.4   0.0      0.11        79      88     138 ..     188     235 ..     176     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.72
                      FAD_oxidored  1 DvvVvGGgpaGvaA..AiaAaraGakvlLve 29
                                      DvvV+G  ++G+ +  Ai + +++ + ++++
  gi|488599571|ref|YP_007906042.1|  4 DVVVIGNSAGGIGCieAIRSRNRDLTIAVIS 34
                                      9********9997655666666666666665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLve 29 
                                       v+ GGg+ G++AA   a++G +v ++e
  gi|488599571|ref|YP_007906042.1| 149 VILGGGVIGLMAAEVLAEKGLEVHVIE 175
                                       89**********************999 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.11
                      FAD_oxidored  88 vakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkv 138
                                          ++++ + +e+gv + ++ ++++v+ +++r+ svt+ +   +++i++++
  gi|488599571|ref|YP_007906042.1| 188 RTSEIVQRVFDEHGVSIHTGLTIKKVNSSNNRVYSVTLTD---GREIECDL 235
                                       5678889999********************9*******76...56666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 2595.45
//
Query:       gi|488599572|ref|YP_007906043.1|  [L=148]
Description: Fe-S-cluster-containing hydrogenase components 2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-18   65.2  12.7    4.6e-18   65.2  12.7    1.5  2  Fer4_11   4Fe-4S dicluster domain
    6.6e-10   39.4  25.4    3.8e-05   24.2  11.0    3.4  4  Fer4_7    4Fe-4S dicluster domain
    3.1e-09   36.3  33.0    6.5e-08   32.1   1.6    5.3  5  Fer4      4Fe-4S binding domain
    5.6e-09   36.0  26.4      1e-05   25.6   8.5    3.0  4  Fer4_9    4Fe-4S dicluster domain
    3.6e-08   33.0  28.8    1.9e-05   24.5   1.3    4.4  4  Fer4_2    4Fe-4S binding domain
    4.2e-08   32.9  30.0    1.7e-06   27.8   1.1    4.7  4  Fer4_6    4Fe-4S binding domain
    1.5e-06   28.2  29.3    1.7e-05   24.9   9.8    3.3  3  Fer4_10   4Fe-4S dicluster domain
    0.00021   21.3  31.7    0.00091   19.3  11.1    3.4  3  Fer4_21   4Fe-4S dicluster domain
     0.0027   18.5  40.0      0.052   14.5   2.6    4.3  4  Fer4_3    4Fe-4S binding domain
      0.006   17.0   3.1      0.006   17.0   3.1    4.8  4  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.025   15.5  29.2       0.13   13.2   4.4    4.6  6  Fer4_16   4Fe-4S double cluster binding domain
       0.29   11.6  26.5        4.5    7.8   4.8    3.4  3  Fer4_8    4Fe-4S dicluster domain
        1.8    9.2  30.7         23    5.6  11.6    4.0  3  Fer4_17   4Fe-4S dicluster domain
        3.2    8.4  21.0       0.27   11.8   1.7    3.5  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


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 ?   -3.1   0.4       6.6   8.5e+03       7      14 ..       8      15 ..       4      33 .. 0.63
   2 !   65.2  12.7   3.6e-21   4.6e-18       6      95 ..      56     140 ..      53     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.6
                           Fer4_11  7 peqCrhCl 14
                                      pe C  C 
  gi|488599572|ref|YP_007906043.1|  8 PEVCIGCH 15
                                      55555553 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 3.6e-21
                           Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGl 82 
                                       ++ qCrhC ep Cv ++ s+a++kd etG Vl de+++  ++ ++v+acPy  +  + e++k+ kCd+c        
  gi|488599572|ref|YP_007906043.1|  56 FAIQCRHCDEPNCVFACISGALYKDTETGKVLHDESKCV-GCLSCVMACPYGSIVIDFEEKKIVKCDLCEGLE---- 127
                                       778***********************************7.*****************************7765.... PP

                           Fer4_11  83 lpacvescptgal 95 
                                        p+cv++cp +al
  gi|488599572|ref|YP_007906043.1| 128 FPTCVKMCPNNAL 140
                                       5********9876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   8.6   2.7e-06    0.0035       2      52 .]      11      76 ..      10      76 .. 0.68
   2 !   24.2  11.0     3e-08   3.8e-05       1      51 [.      59     106 ..      59     107 .. 0.93
   3 !   20.3  11.6   4.9e-07   0.00063       1      52 []      92     139 ..      92     139 .. 0.75
   4 !    8.0   1.7    0.0034       4.4       1      17 [.     119     140 ..     118     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                            Fer4_7  2 CigCgaCvaaCpvkaield......eeenekgtekveidpek.......ClgCga..CvavCPtga 52
                                      CigC+ C+  C v   +++      ++e++k+++++++d++        C +C++  Cv +C +ga
  gi|488599572|ref|YP_007906043.1| 11 CIGCHLCEIWCAVAHSRTRdilkafKYEKKKPVPRIVVDENLpecfaiqCRHCDEpnCVFACISGA 76
                                      ***********85555544244433566666667776665424444445999*9888*****9887 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 3e-08
                            Fer4_7   1 rCigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       +C +C   +Cv aC ++a++ d e     t kv +d++kC+gC +Cv +CP+g
  gi|488599572|ref|YP_007906043.1|  59 QCRHCDepNCVFACISGALYKDTE-----TGKVLHDESKCVGCLSCVMACPYG 106
                                       5****878************9987.....689*******************98 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 4.9e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCg..aCvavCPtga 52 
                                       +C+gC  Cv aCp++ i +d ee    ++ v  + + C g +   Cv+ CP +a
  gi|488599572|ref|YP_007906043.1|  92 KCVGCLSCVMACPYGSIVIDFEE----KKIV--KCDLCEGLEfpTCVKMCPNNA 139
                                       7******************9982....2333..344555443227******987 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0034
                            Fer4_7   1 rCigCg.....aCvaaCpvkai 17 
                                       +C  C+      Cv++Cp++a+
  gi|488599572|ref|YP_007906043.1| 119 KCDLCEglefpTCVKMCPNNAL 140
                                       5777866666689999999987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   1.2   0.00017      0.21       5      15 ..       8      18 ..       4      19 .. 0.87
   2 ?    2.9   0.1     0.084   1.1e+02      13      23 ..      67      77 ..      67      78 .. 0.86
   3 !   32.1   1.6   5.1e-11   6.5e-08       3      23 ..      88     108 ..      86     109 .. 0.92
   4 ?   -0.5   0.4      0.96   1.2e+03      10      15 ..     119     124 ..     118     125 .. 0.61
   5 !   12.0   0.4   0.00011      0.14      13      23 ..     130     140 ..     130     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                      TTTSSS-THHH CS
                              Fer4  5 eekCigCGaCv 15
                                      +e CigC +C+
  gi|488599572|ref|YP_007906043.1|  8 PEVCIGCHLCE 18
                                      899*******7 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.084
                                      HHHHHSTTTEE CS
                              Fer4 13 aCvevCPvgAI 23
                                      +Cv +C  gA+
  gi|488599572|ref|YP_007906043.1| 67 NCVFACISGAL 77
                                      5*****99997 PP

  == domain 3  score: 32.1 bits;  conditional E-value: 5.1e-11
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                        de+kC+gC  Cv++CP+g I
  gi|488599572|ref|YP_007906043.1|  88 HDESKCVGCLSCVMACPYGSI 108
                                       69****************988 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.96
                                       S-THHH CS
                              Fer4  10 gCGaCv 15 
                                       +C +C+
  gi|488599572|ref|YP_007906043.1| 119 KCDLCE 124
                                       566664 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00011
                                       HHHHHSTTTEE CS
                              Fer4  13 aCvevCPvgAI 23 
                                       +Cv++CP++A+
  gi|488599572|ref|YP_007906043.1| 130 TCVKMCPNNAL 140
                                       5*********8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   2.2    0.0074       9.4      35      47 ..      10      22 ..       4      25 .. 0.73
   2 !   11.1   9.6   0.00027      0.35       2      50 ..      11      76 ..      10      77 .. 0.79
   3 !   22.8   9.9   5.9e-08   7.6e-05       1      50 [.      59     107 ..      58     108 .. 0.88
   4 !   25.6   8.5     8e-09     1e-05       1      50 [.      92     139 ..      92     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0074
                            Fer4_9 35 aCigCgaCveaCp 47
                                       CigC+ C+  C 
  gi|488599572|ref|YP_007906043.1| 10 VCIGCHLCEIWCA 22
                                      4888888887775 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase...............eaCigCga..CveaCpkga 50
                                      C+gC+ C+  C   + + ++  +  ++++++                 +C +C +  Cv aC +ga
  gi|488599572|ref|YP_007906043.1| 11 CIGCHLCEIWCAVAHSRTRDILKAFKYEKKKPvprivvdenlpecfaIQCRHCDEpnCVFACISGA 76
                                      ***********66666666666666666655567777777788899999*****999*****8876 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 5.9e-08
                            Fer4_9   1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +C  C++  Cv aC +g+  +d  ++k+ +++    +C+gC +Cv aCp g 
  gi|488599572|ref|YP_007906043.1|  59 QCRHCDEpnCVFACISGALYKDTETGKVLHDES---KCVGCLSCVMACPYGS 107
                                       699998555******************998764...8************985 PP

  == domain 4  score: 25.6 bits;  conditional E-value: 8e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.....CveaCpkga 50 
                                       kC+gC +Cv aCp+g +v d  e+k+        +C  C+      Cv+ Cp++a
  gi|488599572|ref|YP_007906043.1|  92 KCVGCLSCVMACPYGSIVIDFEEKKIV-------KCDLCEGlefptCVKMCPNNA 139
                                       7*******************9999999.......5*****************997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   2.6   0.00014      0.18       1      20 [.       2      21 ..       2      23 .. 0.85
   2 ?    4.6   3.5     0.031        40       9      20 ..      59      72 ..      44      73 .. 0.72
   3 !   24.5   1.3   1.5e-08   1.9e-05       2      22 .]      85     105 ..      84     105 .. 0.91
   4 !    8.0   0.4    0.0026       3.4       8      22 .]     113     137 ..     106     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                            Fer4_2  1 apvvvdtdrCigCgaCvsaC 20
                                      ++vv+ ++ CigC  C   C
  gi|488599572|ref|YP_007906043.1|  2 PKVVAKPEVCIGCHLCEIWC 21
                                      57999***********7556 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.031
                            Fer4_2  9 rCigCg..aCvsaC 20
                                       C +C    Cv aC
  gi|488599572|ref|YP_007906043.1| 59 QCRHCDepNCVFAC 72
                                      69999789****** PP

  == domain 3  score: 24.5 bits;  conditional E-value: 1.5e-08
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       +v  d+ +C+gC +Cv aCP+
  gi|488599572|ref|YP_007906043.1|  85 KVLHDESKCVGCLSCVMACPY 105
                                       5788****************5 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0026
                            Fer4_2   8 d.....rCigCg.....aCvsaCPa 22 
                                       +     +C  C+     +Cv+ CP+
  gi|488599572|ref|YP_007906043.1| 113 EekkivKCDLCEglefpTCVKMCPN 137
                                       4456669****779999*******5 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   2.6    0.0023       2.9       1      19 [.       3      21 ..       3      25 .. 0.87
   2 !    7.2   2.7    0.0043       5.6       9      24 .]      60      77 ..      59      77 .. 0.90
   3 !   27.8   1.1   1.3e-09   1.7e-06       1      24 []      85     108 ..      85     108 .. 0.91
   4 ?    6.0   1.6     0.011        14       8      24 .]     119     140 ..     116     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                            Fer4_6  1 vveidpdkCigCgdCvrvC 19
                                      +v+ +p+ CigC  C++ C
  gi|488599572|ref|YP_007906043.1|  3 KVVAKPEVCIGCHLCEIWC 21
                                      68999**********9877 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0043
                            Fer4_6  9 CigCgd..CvrvCPegai 24
                                      C +C++  Cv +C  ga+
  gi|488599572|ref|YP_007906043.1| 60 CRHCDEpnCVFACISGAL 77
                                      99**889******99986 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 1.3e-09
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +v +d++kC+gC  Cv++CP+g i
  gi|488599572|ref|YP_007906043.1|  85 KVLHDESKCVGCLSCVMACPYGSI 108
                                       5789*****************965 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.011
                            Fer4_6   8 kCigC.gd....CvrvCPegai 24 
                                       kC+ C g     Cv+ CP +a+
  gi|488599572|ref|YP_007906043.1| 119 KCDLCeGLefptCVKMCPNNAL 140
                                       8****6669999******9986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  12.2     0.014        18       1      55 [.       3      72 ..       3      73 .. 0.73
   2 !   15.3  13.3   1.2e-05     0.016       8      56 .]      59     104 ..      52     104 .. 0.95
   3 !   24.9   9.8   1.3e-08   1.7e-05       2      56 .]      86     136 ..      85     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadl.............tsvgakgeaseeeavrk.kvekCtgcg..aCveaC 55
                                      kvv  ++ Ci+C  C   C a +             ++++  + +  +e   +    +C +c   +Cv aC
  gi|488599572|ref|YP_007906043.1|  3 KVVAKPEVCIGCHLCEIWC-AVAhsrtrdilkafkyEKKKPVPRIVVDENLPEcFAIQCRHCDepNCVFAC 72
                                      578999*************.4447**999998777655555555555555555566677778678999888 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.2e-05
                           Fer4_10   8 tCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +C +C   +Cv aC      +ga ++++e ++v ++ +kC gc +Cv aCP
  gi|488599572|ref|YP_007906043.1|  59 QCRHCDepNCVFAC-----ISGALYKDTETGKVLHDESKCVGCLSCVMACP 104
                                       6****9999*****.....69*****************************9 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 1.3e-08
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg.....aCveaCP 56 
                                       v +d+++C++C  Cv aCP+             ++ ++kk+ kC+ c+      Cv+ CP
  gi|488599572|ref|YP_007906043.1|  86 VLHDESKCVGCLSCVMACPY---------GSIVIDFEEKKIVKCDLCEglefpTCVKMCP 136
                                       7899****************.........333334444446668888556688******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 !   11.9   3.3   0.00015      0.19      38      53 ..       8      23 ..       2      29 .. 0.73
   2 !   14.4  12.6   2.5e-05     0.032       7      56 ..      59     107 ..      47     110 .. 0.71
   3 !   19.3  11.1   7.1e-07   0.00091       4      55 ..      89     138 ..      86     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                           Fer4_21 38 edeCvGCnlCssvCPv 53
                                       + C+GC+lC + C v
  gi|488599572|ref|YP_007906043.1|  8 PEVCIGCHLCEIWCAV 23
                                      4678888888888877 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.5e-05
                           Fer4_21   7 kCigCg..kCliaCedtshqaieidaktvlkv.vedeCvGCnlCssvCPvedc 56 
                                       +C +C   +C+ aC      a+ +d++t   +  e++CvGC  C+  CP  + 
  gi|488599572|ref|YP_007906043.1|  59 QCRHCDepNCVFACI---SGALYKDTETGKVLhDESKCVGCLSCVMACPY-GS 107
                                       466665334778887...366777766654441588*************5.54 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 7.1e-07
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCn..lCssvCPved 55 
                                       de+kC+gC +C++aC+   +  i id +++  v  d C G +   C+++CP  +
  gi|488599572|ref|YP_007906043.1|  89 DESKCVGCLSCVMACP---YGSIVIDFEEKKIVKCDLCEGLEfpTCVKMCPN-N 138
                                       799*************...566777767776788999*9988446******4.4 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.3     0.015        20       1      11 [.      11      21 ..      11      24 .. 0.93
   2 ?    5.8   3.7     0.025        32       1      15 []      60      76 ..      60      76 .. 0.87
   3 !   10.2   5.8   0.00094       1.2       1      14 [.      93     106 ..      93     107 .. 0.93
   4 !   14.5   2.6     4e-05     0.052       1      15 []     120     139 ..     120     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.015
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC +C+ +C
  gi|488599572|ref|YP_007906043.1| 11 CIGCHLCEIWC 21
                                      **********9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.025
                            Fer4_3  1 CtgCg..aCvevCPvgA 15
                                      C +C    Cv +C +gA
  gi|488599572|ref|YP_007906043.1| 60 CRHCDepNCVFACISGA 76
                                      99**7677*****9988 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00094
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gC  Cv +CP+g
  gi|488599572|ref|YP_007906043.1|  93 CVGCLSCVMACPYG 106
                                       ****88******98 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 4e-05
                            Fer4_3   1 CtgCg.....aCvevCPvgA 15 
                                       C+ C+     +Cv+ CP++A
  gi|488599572|ref|YP_007906043.1| 120 CDLCEglefpTCVKMCPNNA 139
                                       ****8899999*******98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   2.1    0.0031       3.9       1      14 [.       8      21 ..       8      24 .. 0.87
   2 ?    0.6   3.8      0.86   1.1e+03       4      14 ..      60      72 ..      50      74 .. 0.80
   3 !   17.0   3.1   4.7e-06     0.006       2      17 .]      91     106 ..      90     106 .. 0.91
   4 ?   -0.3   3.5       1.7   2.1e+03       8      15 ..     129     136 ..     118     139 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0031
                            Fer4_4  1 qerCigCgsCvaaC 14
                                      +e CigC  C++ C
  gi|488599572|ref|YP_007906043.1|  8 PEVCIGCHLCEIWC 21
                                      588*******9877 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.86
                            Fer4_4  4 CigCgs..CvaaC 14
                                      C +C+   Cv aC
  gi|488599572|ref|YP_007906043.1| 60 CRHCDEpnCVFAC 72
                                      8899977787666 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 4.7e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       ++C+gC sCv aCP+g
  gi|488599572|ref|YP_007906043.1|  91 SKCVGCLSCVMACPYG 106
                                       58************86 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.7
                            Fer4_4   8 gsCvaaCP 15 
                                       + Cv  CP
  gi|488599572|ref|YP_007906043.1| 129 PTCVKMCP 136
                                       26999998 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 ?    3.0   2.3      0.15   1.9e+02      53      65 ..      10      22 ..       5      24 .. 0.69
   2 ?   -2.3  13.4       7.1   9.1e+03       2      64 ..      11      72 ..      10      72 .. 0.58
   3 ?    6.1   1.1     0.017        22       1      22 [.      59      82 ..      59      91 .. 0.84
   4 ?   13.2   4.4    0.0001      0.13       1      24 [.      92     116 ..      92     126 .. 0.78
   5 ?    3.0   2.5      0.15     2e+02      58      67 .]     124     138 ..     110     138 .. 0.61
   6 ?    4.4   2.8     0.057        74       7      17 ..     130     140 ..     118     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                           Fer4_16 53 aitgCdiCqdvCP 65
                                       ++gC  C+  C 
  gi|488599572|ref|YP_007906043.1| 10 VCIGCHLCEIWCA 22
                                      4677777777774 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.1
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisy...ntaekkdlaedeekckkqeaitgCd..iCqdvC 64
                                      C++C+ C   C +++ +++     ++ + ++y   +   +  + e+  +c  + ++  Cd  +C+ +C
  gi|488599572|ref|YP_007906043.1| 11 CIGCHLCEIWCAVAHSRTR-----DILKAFKYekkKPVPRIVVDENLPECF-AIQCRHCDepNCVFAC 72
                                      ***********99998888.....666666661102222333444444444.4445555555565555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.017
                           Fer4_16  1 rCgtCgk..CaevCPtnaikekke 22
                                      +C  C +  C+ +C ++a+ +++e
  gi|488599572|ref|YP_007906043.1| 59 QCRHCDEpnCVFACISGALYKDTE 82
                                      599999888*********998844 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.0001
                           Fer4_16   1 rCgtCgkCaevCPtnaikek.keke 24 
                                       +C++C  C+++CP + i  + +ek+
  gi|488599572|ref|YP_007906043.1|  92 KCVGCLSCVMACPYGSIVIDfEEKK 116
                                       5***************987733444 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.15
                           Fer4_16  58 d.....iCqdvCPan 67 
                                             +C+++CP+n
  gi|488599572|ref|YP_007906043.1| 124 EglefpTCVKMCPNN 138
                                       344444788888887 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.057
                           Fer4_16   7 kCaevCPtnai 17 
                                        C+++CP na+
  gi|488599572|ref|YP_007906043.1| 130 TCVKMCPNNAL 140
                                       59999999987 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  17.9    0.0038       4.8       4      64 ..      10     106 ..       8     107 .. 0.72
   2 ?    7.8   4.8    0.0035       4.5       3      18 ..      91     106 ..      89     121 .. 0.74
   3 ?    2.6   1.4      0.15   1.9e+02      48      64 ..     117     138 ..     108     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0038
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaae.....................................dvqeeqvle 43 
                                        Ci+C +C+  C v++++ +++l+a +  ++                                     +        
  gi|488599572|ref|YP_007906043.1|  10 VCIGCHLCEIWCAVAHSRTRDILKAFKYEKKkpvprivvdenlpecfaiqcrhcdepncvfacisgalY-------- 78 
                                       5************99999966666655555558887777777777766666666666666665555552........ PP

                            Fer4_8  44 e.......eealwsCttcgaCtevCpvg 64 
                                       +        +   +C++c +C+ +Cp g
  gi|488599572|ref|YP_007906043.1|  79 KdtetgkvLHDESKCVGCLSCVMACPYG 106
                                       0444545577889*************75 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0035
                            Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                       +kC++C  C  aCp  
  gi|488599572|ref|YP_007906043.1|  91 SKCVGCLSCVMACPYG 106
                                       5777777777777743 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.15
                            Fer4_8  48 lwsCttcga.....CtevCpvg 64 
                                       + +C  c+      C++ Cp++
  gi|488599572|ref|YP_007906043.1| 117 IVKCDLCEGlefptCVKMCPNN 138
                                       5667777766667788888875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  11.5      0.17   2.2e+02       2      58 ..      11      74 ..      10      76 .. 0.63
   2 ?    5.6  11.6     0.018        23      41      59 ..      88     106 ..      58     108 .. 0.63
   3 ?    2.3   1.9      0.19   2.5e+02       2      15 ..     120     138 ..     118     144 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.17
                           Fer4_17  2 CiqCgyClpeCpsyea........ydnepkkllraaklglleeaekeekaslCieCge..CerkCPq 58
                                      Ci+C  C+  C              + e+kk++ ++ +   +e   e+ a +C +C e  C+ +C +
  gi|488599572|ref|YP_007906043.1| 11 CIGCHLCEIWCAVAHSrtrdilkaFKYEKKKPVPRIVV---DENLPECFAIQCRHCDEpnCVFACIS 74
                                      *********99975542222222233355556666433...45556689999999985449999976 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                           Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                       +  s+C++C  C+++CP+g
  gi|488599572|ref|YP_007906043.1|  88 HDESKCVGCLSCVMACPYG 106
                                       44589************97 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
                           Fer4_17   2 CiqCgy.....ClpeCpsy 15 
                                       C  C+      C+++Cp +
  gi|488599572|ref|YP_007906043.1| 120 CDLCEGlefptCVKMCPNN 138
                                       6666633334488899865 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 ?    6.7   2.8    0.0084        11       4      51 ..       9      63 ..       8      66 .. 0.79
   2 ?   11.8   1.7   0.00021      0.27       2      17 ..      89     104 ..      88     105 .. 0.95
   3 ?    0.2   1.8      0.86   1.1e+03      11      18 ..     130     137 ..     114     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0084
                           Fer4_13  4 dtCiacgaCvelaPdvFeeddeggasvvaeqpts.......eeekadaeeAadaC 51
                                      + Ci+c++C   +     +  +  +++ +e++++       e + ++   ++  C
  gi|488599572|ref|YP_007906043.1|  9 EVCIGCHLCEIWCAVAHSRTRDILKAFKYEKKKPvprivvdENLPECFAIQCRHC 63
                                      56***********999999999999999988776566666666666666666666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D+++C++c +Cv+++P
  gi|488599572|ref|YP_007906043.1|  89 DESKCVGCLSCVMACP 104
                                       789************9 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.86
                           Fer4_13  11 aCvelaPd 18 
                                       +Cv+++P+
  gi|488599572|ref|YP_007906043.1| 130 TCVKMCPN 137
                                       7*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 968.97
//
Query:       gi|488599573|ref|YP_007906044.1|  [L=165]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-06   25.9   0.1    1.8e-05   24.6   0.1    1.7  1  HTH_11          HTH domain
    0.00034   20.1   0.1    0.00059   19.3   0.1    1.4  1  RepL            Firmicute plasmid replication protein (RepL)
    0.00054   19.8   0.1     0.0011   18.8   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00087   19.3   0.0     0.0027   17.7   0.0    1.8  2  HTH_20          Helix-turn-helix domain
     0.0012   18.7   0.1     0.0028   17.6   0.0    1.6  1  HTH_36          Helix-turn-helix domain
     0.0013   18.2   0.0     0.0032   17.0   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0026   17.3   0.1     0.0061   16.1   0.1    1.6  1  GerE            Bacterial regulatory proteins, luxR family
     0.0048   17.0   0.0     0.0091   16.1   0.0    1.4  1  FUR             Ferric uptake regulator family
      0.006   16.3   0.0      0.012   15.3   0.0    1.5  1  DUF4423         Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.023   14.7   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      0.029   14.5   0.0      0.058   13.5   0.0    1.5  1  HTH_28          Helix-turn-helix domain
      0.037   14.0   0.0      0.074   13.0   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.044   13.2   0.0      0.059   12.8   0.0    1.1  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
      0.059   13.4   0.0       0.14   12.2   0.0    1.6  1  HTH_29          Winged helix-turn helix
      0.096   12.4   0.0        0.2   11.4   0.0    1.5  1  Sigma70_r4_2    Sigma-70, region 4
       0.13   12.1   0.2        1.7    8.6   0.0    2.3  2  HTH_5           Bacterial regulatory protein, arsR family
       0.19   11.2   0.0       0.31   10.5   0.0    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family


Domain annotation for each model (and alignments):
>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.7e-08   1.8e-05      17      45 ..      21      49 ..      11      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.7e-08
                            HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                      + +e+A  LnvS++tv++++k Le+ g+ 
  gi|488599573|ref|YP_007906044.1| 21 TQDEIAYDLNVSTKTVYNRMKLLESHGYI 49
                                      689**********************9954 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   5.6e-07   0.00059      76     115 ..      20      59 ..       2      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.6e-07
                              RepL  76 atnRelaeetgislktvsetlkileeanilkkkanGvlvi 115
                                       +t+ e+a + ++s+ktv + +k le  +++k   +Gv  +
  gi|488599573|ref|YP_007906044.1|  20 KTQDEIAYDLNVSTKTVYNRMKLLESHGYIKEVKKGVWKV 59 
                                       6999********************************9876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1     1e-06    0.0011      22      58 ..      19      55 ..      11      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      ++t deia +l+v+  +vY+ ++ Le+ G+++ +k+ 
  gi|488599573|ref|YP_007906044.1| 19 SKTQDEIAYDLNVSTKTVYNRMKLLESHGYIKEVKKG 55
                                      6899***************************999865 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.6e-06    0.0027      29      60 ..      24      55 ..      18      56 .. 0.93
   2 ?   -2.0   0.0       3.6   3.8e+03      40      48 ..      85      93 ..      83      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-06
                                      HHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 29 elaerldlskntlsyHLrvLeeagLvevvreg 60
                                      e+a  l +s +t++++++ Le++g+++ v+ g
  gi|488599573|ref|YP_007906044.1| 24 EIAYDLNVSTKTVYNRMKLLESHGYIKEVKKG 55
                                      99*************************99876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                                      HHHHHHHHH CS
                            HTH_20 40 tlsyHLrvL 48
                                      tl  HL++L
  gi|488599573|ref|YP_007906044.1| 85 TLIEHLKKL 93
                                      566799998 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.7e-06    0.0028      27      55 .]      21      49 ..      15      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +q+ +a +l++s +Tv++  k+Le +Gyi
  gi|488599573|ref|YP_007906044.1| 21 TQDEIAYDLNVSTKTVYNRMKLLESHGYI 49
                                      799*************************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 !   17.0   0.0     3e-06    0.0032      19      48 .]      21      50 ..      19      50 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +q e+A  l++S  tv  r+k Le+ G+Ik
  gi|488599573|ref|YP_007906044.1| 21 TQDEIAYDLNVSTKTVYNRMKLLESHGYIK 50
                                      899**************************8 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.7e-06    0.0061      10      38 ..      12      40 ..       9      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.7e-06
                                      HHHHHCTTS-HHHHHHHHTS-HHHHHHHH CS
                              GerE 10 vLrllaeGksnkeIAeelniSekTVkvhk 38
                                      + + + + k+  eIA++ln+S+kTV + +
  gi|488599573|ref|YP_007906044.1| 12 IIEGILNSKTQDEIAYDLNVSTKTVYNRM 40
                                      6677888899***************7765 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.6e-06    0.0091      37      64 ..      28      55 ..      18      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.6e-06
                                      TTT--HHHHHHHHHHHHHTTSEEEEEET CS
                               FUR 37 dpeislaTVYrtLklleeaglvkelefe 64
                                      d ++s  TVY+ +klle+ g +ke++  
  gi|488599573|ref|YP_007906044.1| 28 DLNVSTKTVYNRMKLLESHGYIKEVKKG 55
                                      579********************99865 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05     0.012      37      82 ..      20      63 ..      10      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                           DUF4423 37 adpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteks 82
                                      ++ +e+a  l+  +s++ v + +++L++ g +k+ ++g +++  ++
  gi|488599573|ref|YP_007906044.1| 20 KTQDEIAYDLN--VSTKTVYNRMKLLESHGYIKEVKKGVWKVDYAK 63
                                      67789******..***************************987665 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.1e-05     0.023      10      49 ..      80     120 ..      72     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                                       TTHHHHHHHHHHTSTTEEEEEEESS.SSSEEEEEEESSHHH CS
                    AsnC_trans_reg  10 peqleefeealaelpeVvecyrvtG.dydyllkvvvrdlea 49 
                                       +e +e+++e+l++l++V+ ++ + G +y++ ++v++r le+
  gi|488599573|ref|YP_007906044.1|  80 REGMETLIEHLKKLDYVENVFEIIGsEYNLCIIVRFRGLEE 120
                                       5779********************************98876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.5e-05     0.058       5      40 ..      12      47 ..      10      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.5e-05
                            HTH_28  5 iikllaaGhsvreaArelgisrrtvyrWikryeegG 40
                                      ii+ +++ ++++e+A  l++s  tvy  +k +e++G
  gi|488599573|ref|YP_007906044.1| 12 IIEGILNSKTQDEIAYDLNVSTKTVYNRMKLLESHG 47
                                      5555677789***********************999 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 ?   13.0   0.0     7e-05     0.074      23      55 ..      21      54 ..       5      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.rgr 55
                                      tq+e+A  l+++  tv   ++ L+ +g+i+  ++
  gi|488599573|ref|YP_007906044.1| 21 TQDEIAYDLNVSTKTVYNRMKLLESHGYIKeVKK 54
                                      9****************************96443 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05     0.059     106     136 ..      23      53 ..      14      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                                       HHHHHTTGXXHHHHHHHHHHHHHTTXXEEEE CS
                     RNA_pol_Rpc34 106 rtiksklnLhksvvkkcLksLeskkyiksvk 136
                                        +i + ln   + v + +k+Les +yik+vk
  gi|488599573|ref|YP_007906044.1|  23 DEIAYDLNVSTKTVYNRMKLLESHGYIKEVK 53 
                                       579999************************9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.14      14      40 ..      21      47 ..      11      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegG 40
                                      t  +iA  l++s +tvy+  k+ e +G
  gi|488599573|ref|YP_007906044.1| 21 TQDEIAYDLNVSTKTVYNRMKLLESHG 47
                                      889***************999999998 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019       0.2      25      47 ..      18      40 ..      11      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                      S---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 25 eglsykEIAellgisegtVksrl 47
                                      + ++++EIA  l++s +tV++r+
  gi|488599573|ref|YP_007906044.1| 18 NSKTQDEIAYDLNVSTKTVYNRM 40
                                      67899****************98 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0016       1.7      15      46 ..      19      50 ..      10      51 .. 0.89
   2 ?    1.0   0.1      0.37   3.9e+02      31      39 ..      85      93 ..      85      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                                      SEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 15 elcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +++  e+a +l++s  tv    k L+  G+++
  gi|488599573|ref|YP_007906044.1| 19 SKTQDEIAYDLNVSTKTVYNRMKLLESHGYIK 50
                                      566779***********************996 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.37
                                      HHHHHHHHH CS
                             HTH_5 31 tvShHLkkL 39
                                      t+ +HLkkL
  gi|488599573|ref|YP_007906044.1| 85 TLIEHLKKL 93
                                      6789****9 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00029      0.31      21      49 ..      13      41 ..       7      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                      HTH_Tnp_ISL3 21 lelllesrsvkavArqlgvSwtTVwrild 49
                                      +e  l+s++  ++A +l+vS++TV ++++
  gi|488599573|ref|YP_007906044.1| 13 IEGILNSKTQDEIAYDLNVSTKTVYNRMK 41
                                      5556788999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1058.67
//
Query:       gi|488599574|ref|YP_007906045.1|  [L=367]
Description: L-lysine 2,3-aminomutase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-10   41.4   0.2    6.9e-10   39.5   0.2    1.9  1  Radical_SAM  Radical SAM superfamily
      0.001   19.3   0.0     0.0023   18.2   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
     0.0049   17.0   0.0      0.013   15.7   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.12   12.8   0.0        6.6    7.1   0.0    2.3  2  HAD          haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.2   1.5e-13   6.9e-10       3     158 ..     102     254 ..     100     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.5e-13
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vp 76 
                                        t++C++ C++C r++     g +   ++e++   v++++++k +++v+++gg+p+l p +v + + ++  +   v+
  gi|488599574|ref|YP_007906045.1| 102 ATNACAMYCRHCFRKR---LVGIPTKETIERLDGAVEYIREHKEINNVLVSGGDPFLLPTEVIEEFLYKLTDiphVD 175
                                       689************7...9*******************97777***************999999999999899999 PP

                                       TEEEEEEECSSCHG.....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                                       xxxxxxxxxxxxxx.....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd.....eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvv 146
                                        +r+   t+ t pd     +e  e l ++     rv++  +  +++         +  ++  +a+++l +a+   ++
  gi|488599574|ref|YP_007906045.1| 176 FVRFGTRTPVTFPDrilmdPELPEVLQKYStrDRRVYIVTQFNHPR---------EITDKSTRAVDALIKANTI-IS 242
                                       9999999999999999999888888888776545555544444444.........2234555777888888766.88 PP

                                       EEEEEBTTTSHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 147 drivglpGende 158
                                       + +v+l+G+nd+
  gi|488599574|ref|YP_007906045.1| 243 NQTVLLKGVNDS 254
                                       888888888886 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.1e-07    0.0023       8      79 ..      99     168 ..      90     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.1e-07
                           Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllpenaeallelvkev 79 
                                       l+l ++ C + C+ Cf k +    +++ ++   l+ ++e + + ++i+ + ++GG+P+l   +e++ e+++++
  gi|488599574|ref|YP_007906045.1|  99 LILATNACAMYCRHCFRKRLVGIPTKETIE--RLDGAVEYIREhKEINNVLVSGGDPFL-LPTEVIEEFLYKL 168
                                       5677899*********99999888887776..445555555542788************.7788888888775 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.8e-06     0.013       4      74 ..     102     168 ..      99     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-06
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrl 74 
                                        ++ C + C+ C++k        +++t e l+  ++   +++  i+++ ++GG+P++   ++++ +++ +l
  gi|488599574|ref|YP_007906045.1| 102 ATNACAMYCRHCFRKRLV--GIPTKETIERLDGAVEYIREHKE-INNVLVSGGDPFL-LPTEVIEEFLYKL 168
                                       5899***********955..45556666777777765555555.588********95.4777777777666 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0081        36      83     119 ..     128     165 ..      94     174 .. 0.71
   2 ?    7.1   0.0    0.0015       6.6      57     109 ..     160     216 ..     157     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0081
                               HAD  83 pklldpgalellaahraaGdrvvvvSgg.....lrplvepll 119
                                       ++    ga+e++++h++ +   v+vSgg     + +++e++l
  gi|488599574|ref|YP_007906045.1| 128 ER--LDGAVEYIREHKEINN--VLVSGGdpfllPTEVIEEFL 165
                                       33..36*******9988888..******77777777777777 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0015
                               HAD  57 lleallaglseelaaelerfvaevirpk......lldpgalellaahraaGdrvvvvSg 109
                                       ++e++l  l++  + ++ rf+   ++p       l+dp++ e+l++   +  rv++v+ 
  gi|488599574|ref|YP_007906045.1| 160 VIEEFLYKLTDIPHVDFVRFG--TRTPVtfpdriLMDPELPEVLQKYSTRDRRVYIVTQ 216
                                       667778888888888899999..455555577879**********999*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2503.17
//
Query:       gi|488599575|ref|YP_007906046.1|  [L=383]
Description: butyryl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  182.4   0.1    1.6e-53  180.9   0.1    1.7  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.2e-36  124.4   0.2    5.6e-36  123.6   0.2    1.4  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    7.2e-27   93.4   0.0    1.1e-26   92.8   0.0    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.8e-25   88.7   0.0    6.2e-25   88.0   0.0    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.04   13.6   0.2       0.32   10.6   0.2    2.2  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.77   2.8e+03      86     107 ..      92     113 ..      78     114 .. 0.80
   2 !  180.9   0.1   4.6e-57   1.6e-53       3     149 ..     231     377 ..     229     378 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.77
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  86 aeasmaKlfaselaqevadlam 107
                                         + m+K+f++e   e + +a+
  gi|488599575|ref|YP_007906046.1|  92 LGCPMVKYFGTEEQKERYLRAV 113
                                       567899***9999988887776 PP

  == domain 2  score: 180.9 bits;  conditional E-value: 4.6e-57
                                       HHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--- CS
                     Acyl-CoA_dh_1   3 GfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaeald 79 
                                       Gf++ m+ +n +R++v+a +lg+a  a+e+al+ya++rkafgkpli+hq++++kla+m + +e+a+ll+++aa+++d
  gi|488599575|ref|YP_007906046.1| 231 GFYQLMRFFNESRILVGAIQLGIAIGAYERALQYAKERKAFGKPLIEHQAIQFKLADMFTAIESAKLLIFKAAYLVD 307
                                       9**************************************************************************** PP

                                       -----HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  80 agkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +g+p++a +s+aKl+ase+a +v+ +a+q++Gg+G+++ey ver+yrdarv +i+eGtseiqr+ii+r l
  gi|488599575|ref|YP_007906046.1| 308 KGEPNPALSSAAKLYASETAIKVTYEAVQVFGGYGFSKEYDVERYYRDARVGTIYEGTSEIQRLIIGRFL 377
                                       ******************************************************************9965 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   0.2   1.6e-39   5.6e-36       1     112 [.       6     116 ..       6     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 1.6e-39
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       +ee+++lrd+vrefae+e+ p+ +e+de++e+p+e+++++a+lG++g  +peeygGag+d+++  i++ el+rad+g
  gi|488599575|ref|YP_007906046.1|   6 NEEHRMLRDAVREFAEKEIMPYGREYDEKAEYPWEIFRRAAKLGFVGADIPEEYGGAGMDFISIPIICMELTRADSG 82 
                                       69*************************************************************************** PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasg 112
                                       +++++++ s+l++p++  fGteeqk+ryL+ +a+g
  gi|488599575|ref|YP_007906046.1|  83 IGSAIAA-STLGCPMVKYFGTEEQKERYLRAVAEG 116
                                       ***9977.56999********************99 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   3.2e-30   1.1e-26       1      97 []     121     217 ..     121     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.2e-30
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS-------EEEEEEE..GGGEE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpdrarglslflvprdapgvs 74 
                                       a+a+TEp+aGsdv+s+kt  ae+ +g+y+lnG+K++itn++i+++++v+ar   ++kp+ ++g+s ++v+++++g++
  gi|488599575|ref|YP_007906046.1| 121 AIAITEPDAGSDVNSIKT-RAEKVEGGYILNGSKTFITNGGISDWVVVIARtdlNAKPA-YKGFSALVVEKSMEGFE 195
                                       78****************.77777779************************87666677.***************** PP

                                       E-----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  75 vrrieeklGlrglptgelvfedv 97 
                                        ++i +k+Gl+ ++t+el+f +v
  gi|488599575|ref|YP_007906046.1| 196 TKPI-KKMGLNCHDTSELYFRNV 217
                                       ****.59*************997 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0   1.7e-28   6.2e-25       2     133 ..     245     366 ..     244     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 1.7e-28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       +++a+ lG+A +a++ ++++a+er+   +g++l +++a+q++la++ +++++A++l+ +aa+     +++g+++   
  gi|488599575|ref|YP_007906046.1| 245 LVGAIQLGIAIGAYERALQYAKERKA--FGKPLIEHQAIQFKLADMFTAIESAKLLIFKAAYL----VDKGEPN--- 312
                                       6899**********************..***********************************....******8... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                         a +++a+++a+e+ai+++ ++++++Gg++  ke+ ++R++RDa++++++++++
  gi|488599575|ref|YP_007906046.1| 313 -PALSSAAKLYASETAIKVTYEAVQVFGGYGFSKEYDVERYYRDARVGTIYEGTS 366
                                       .8999**********************************************9987 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   8.8e-05      0.32     128     205 ..     104     173 ..      86     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.8e-05
                                       HHHHHHHHHHHHHT--EEEEES--SS-TTS-GGGSSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---SS CS
                            HpaB_N 128 enfrkyleyvqendlvlthaitdpkgdRskrpseqedpdvyvrvveetddGivVrGakvlaTgaaladeilvlptra 204
                                       e+ ++yl+ v+e + + ++ait+p      +  +        r  e+ + G + +G k ++T++ ++d+++v+    
  gi|488599575|ref|YP_007906046.1| 104 EQKERYLRAVAEGKTTSAIAITEPDAGSDVNSIK-------TR-AEKVEGGYILNGSKTFITNGGISDWVVVIARTD 172
                                       6667899999999999999999988766644333.......22.466789*********************998744 PP

                                       - CS
                            HpaB_N 205 m 205
                                       +
  gi|488599575|ref|YP_007906046.1| 173 L 173
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2414.80
//
Query:       gi|488599576|ref|YP_007906047.1|  [L=121]
Description: hypothetical protein Asulf_00018 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0069   16.9   0.2        1.2    9.7   0.0    2.3  2  RNA_pol_Rpb5_N  RNA polymerase Rpb5, N-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_N  RNA polymerase Rpb5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   6.9e-05       1.2      16      32 ..      55      71 ..      50      80 .. 0.83
   2 !    5.5   0.0    0.0014        25      62      86 ..      81     105 ..      72     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.9e-05
                                      CCCCCCCEE--CCCCT- CS
                    RNA_pol_Rpb5_N 16 eMlkdRgYlvaeeelni 32
                                      ++lkdRgY+v+e+++  
  gi|488599576|ref|YP_007906047.1| 55 KILKDRGYKVSEAQIRL 71
                                      689*********99976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0014
                                       SS--EEEEEE-SSTTE-TCCCHHHC CS
                    RNA_pol_Rpb5_N  62 dpseqilVfFpeekkvgvktikkya 86 
                                       d +++ +++F+ +k++ + +++ky+
  gi|488599576|ref|YP_007906047.1|  81 DFDDTWWITFSRQKEIFISVVRKYI 105
                                       557899*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 837.57
//
Query:       gi|488599577|ref|YP_007906048.1|  [L=51]
Description: hypothetical protein Asulf_00019 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.6   0.1       0.07   13.5   0.1    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.9e-06      0.07      38      76 ..       3      42 ..       1      49 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-06
                   Acylphosphatase 38 sVeivaegeeekvekfleelksgppk.arvdeveveelee 76
                                       Ve+ +e  e+k+++++e +k+++p  a+ + ++ve+++ 
  gi|488599577|ref|YP_007906048.1|  3 AVEVPVEDLEDKINALIELVKRKKPDnAEFEAIKVEDYDG 42
                                      599999****************88888*********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 339.86
//
Query:       gi|488599578|ref|YP_007906049.1|  [L=206]
Description: hypothetical protein Asulf_00020 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-11   44.5   2.6      4e-11   43.2   0.2    2.4  2  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
       0.03   13.9   8.9       0.41   10.2   1.1    3.2  3  DUF761           Cotton fibre expressed protein
      0.036   14.1   0.8      0.036   14.1   0.8    2.3  2  DUF1664          Protein of unknown function (DUF1664)
      0.056   13.0   5.4      0.068   12.7   5.4    1.2  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.065   13.3  14.8       0.67   10.0  14.4    2.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.094   12.1   2.0       0.12   11.8   2.0    1.2  1  YjcZ             YjcZ-like protein
        0.2   11.4   5.3       0.34   10.7   2.7    2.6  2  DASH_Duo1        DASH complex subunit Duo1
       0.24   10.8   8.8       0.46    9.9   8.4    1.6  1  FliD_C           Flagellar hook-associated protein 2 C-termin
       0.25   11.1   4.4       0.37   10.6   3.1    1.7  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.28   11.4   2.8       0.34   11.2   1.1    1.9  2  DUF948           Bacterial protein of unknown function (DUF94
       0.37   11.1  12.6       0.73   10.2   4.8    2.6  2  KxDL             Uncharacterized conserved protein
       0.48   10.6   5.1       0.28   11.3   2.0    2.2  2  YojJ             Bacterial membrane-spanning protein N-termin
       0.61    9.4  11.5       0.99    8.7  11.5    1.4  1  FAM76            FAM76 protein
       0.63    9.9  20.7       0.17   11.7   5.7    3.2  3  CdvA             CdvA-like coiled-coil domain
       0.66   11.1  12.3        2.2    9.4   2.5    3.1  2  DUF5320          Family of unknown function (DUF5320)
       0.99    8.5   6.7          1    8.5   5.2    1.6  2  IF-2B            Initiation factor 2 subunit family
        1.3    8.4  20.8        3.9    6.8  20.8    1.8  1  GAS              Growth-arrest specific micro-tubule binding
        1.3    8.8  11.0        1.2    8.9   2.5    2.7  2  DivIC            Septum formation initiator
        1.8    8.2   9.5        2.2    8.0   9.5    1.1  1  AAA_11           AAA domain
        2.3    7.0  19.7        4.7    6.0  19.8    1.6  1  Spc7             Spc7 kinetochore protein
        2.3    8.3   7.8        2.6    8.2   1.5    2.5  2  DUF1192          Protein of unknown function (DUF1192)
          3    8.1   0.0          3    8.1   0.0    3.0  3  DUF2951          Protein of unknown function (DUF2951)
        3.2    7.3  10.9        1.9    8.0   7.2    2.0  2  Fzo_mitofusin    fzo-like conserved region
        3.3    6.7  10.5        4.3    6.3  10.5    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        4.5    6.7   5.6        6.8    6.1   5.5    1.4  1  Allexi_40kDa     Allexivirus 40kDa protein
        5.7    7.5   6.5         31    5.2   6.5    2.3  1  YtxH             YtxH-like protein
          6    7.1  14.0        5.6    7.1   7.4    2.3  2  Fib_alpha        Fibrinogen alpha/beta chain family
        7.3    6.7  18.2        2.9    7.9  15.3    1.7  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        8.6    7.1   9.2         32    5.2   9.2    2.1  1  DUF2203          Uncharacterized conserved protein (DUF2203)


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 !   43.2   0.2   6.4e-14     4e-11       1      83 [.       3      91 ..       3      96 .. 0.90
   2 ?    1.1   0.2      0.87   5.4e+02      44      68 ..     150     176 ..     137     202 .. 0.57

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 6.4e-14
                   Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGy.vrNlsdg...sVeivaegeeekvekfleelksgppk.arvdeveveel 74
                                      v++++tG+V++ g+R f+ ++A+ l +  + +rN + +    + +++ ge+e++e+fle++ks++p+ a v++++vee+
  gi|488599578|ref|YP_007906049.1|  3 VKITITGKVHNAGYRLFLLEEADYLFIPYFdARNVKINgreALVVLVDGEKEQIEEFLEFIKSNKPEnAVVEKIQVEEY 81
                                      589*************************9999998765577999*******************88888*********** PP

                   Acylphosphatase 75 eeeeef.kdF 83
                                      + + +  ++F
  gi|488599578|ref|YP_007906049.1| 82 TGRVRDiERF 91
                                      9988876666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.87
                   Acylphosphatase  44 egeeekvekfleelksgppk..arvde 68 
                                        g++e++++ ++e++++ ++  +++d+
  gi|488599578|ref|YP_007906049.1| 150 RGTREDLKSEIREVNKSVKEasSKIDK 176
                                       444444444444444433332344433 PP

>> DUF761  Cotton fibre expressed protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.1      0.02        13      20      34 ..     110     124 ..     110     125 .. 0.93
   2 ?   10.2   1.1   0.00066      0.41      16      30 ..     127     141 ..     127     146 .. 0.87
   3 ?   -2.3   0.0       5.6   3.5e+03      12      20 ..     149     157 ..     149     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.02
                            DUF761  20 kLQRqeSilryqeml 34 
                                       +L++q+S+l+ q+m+
  gi|488599578|ref|YP_007906049.1| 110 MLEKQDSMLQKQDMM 124
                                       69***********97 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00066
                            DUF761  16 reqlkLQRqeSilry 30 
                                       r++++L++q+S+l+ 
  gi|488599578|ref|YP_007906049.1| 127 RQDMMLEKQDSMLKK 141
                                       89**********875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.6
                            DUF761  12 IakFreqlk 20 
                                       I+  re+lk
  gi|488599578|ref|YP_007906049.1| 149 IRGTREDLK 157
                                       8999***99 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   9.0    0.0017       1.1      50     119 ..     110     176 ..      95     179 .. 0.64
   2 ?   14.1   0.8   5.8e-05     0.036      35      80 ..     152     197 ..     150     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       + + ++s+ + ++ +   ++r d  l++q  + k+ +e ++e+r+  +++++++++v++ v++  sk+++
  gi|488599578|ref|YP_007906049.1| 110 MLEKQDSMLQKQDMM---LERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDK 176
                                       333344444444444...4455556666666667777777777777788888999999999999888876 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.8e-05
                           DUF1664  35 TkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqke 80 
                                       T+  l++ + +v k++++ s+++ +t + L++r +r+++++++ k+
  gi|488599578|ref|YP_007906049.1| 152 TREDLKSEIREVNKSVKEASSKIDKTNELLENRFERLEEEIEKIKK 197
                                       999**************************************99876 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 ?   12.7   5.4   0.00011     0.068     149     236 ..     110     196 ..      45     204 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                      Exonuc_VII_L 149 leelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekl 225
                                       + e ++++ ++ + +le++  +lek +s lk+++e +++ r   ++l++++++ ++k++k++++++++++e l++++
  gi|488599578|ref|YP_007906049.1| 110 MLEKQDSMLQKQDMMLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIRE-VNKSVKEASSKIDKTNELLENRF 185
                                       12222222222233333333333333333333333333333333333333333.33334444444444443333334 PP

                      Exonuc_VII_L 226 eekkerlkklk 236
                                       e+ +e+++k+k
  gi|488599578|ref|YP_007906049.1| 186 ERLEEEIEKIK 196
                                       43333333332 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   2.7      0.55   3.4e+02      94     124 ..     111     141 ..      77     145 .. 0.53
   2 ?   10.0  14.4    0.0011      0.67      47     111 ..     137     198 ..     112     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.55
                        TPR_MLP1_2  94 weeqkeelekelselekriedlneqNklLhd 124
                                       +e+q ++l+k+   le++   l++q ++L +
  gi|488599578|ref|YP_007906049.1| 111 LEKQDSMLQKQDMMLERQDMMLEKQDSMLKK 141
                                       3444444444444444444444444444433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                        TPR_MLP1_2  47 relvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekr 111
                                       + l k+ e++ke++ +re   +lk+ei+e+++++++a++++++  e +e++ e+le+e+++++k 
  gi|488599578|ref|YP_007906049.1| 137 SMLKKQDETIKEIRGTRE---DLKSEIREVNKSVKEASSKIDKTNELLENRFERLEEEIEKIKKA 198
                                       456666666666666665...6799************************************9986 PP

>> YjcZ  YjcZ-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.0   0.00019      0.12      37     122 ..      89     177 ..      64     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                              YjcZ  37 tqlraseinaevnaalelrLkllekLsreldpghLALttiaqrlallsqtlaekasaapkl...aqalaalaeefaa 110
                                        + r+s ++a++++ +++ Lk+lek  ++l++ ++ L +    l + + +l+++ ++++++   ++ l+    e+++
  gi|488599578|ref|YP_007906049.1|  89 ERFRSSFNTAQLSKIVQVGLKMLEKQDSMLQKQDMMLERQDMMLEKQDSMLKKQDETIKEIrgtREDLKSEIREVNK 165
                                       46788999********************************************9999988761115677777788888 PP

                              YjcZ 111 rverkekaltqr 122
                                       +v+++  ++ ++
  gi|488599578|ref|YP_007906049.1| 166 SVKEASSKIDKT 177
                                       888888777654 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    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      16      34 ..      88     107 ..      85     131 .. 0.59
   2 ?   10.7   2.7   0.00055      0.34       2      45 ..     139     182 ..     138     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.4
                         DASH_Duo1  16 ienviesLkkak.sniervk 34 
                                       ie +++s+++a+ s+i +v 
  gi|488599578|ref|YP_007906049.1|  88 IERFRSSFNTAQlSKIVQVG 107
                                       55566666666655555553 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00055
                         DASH_Duo1   2 LekEleqLrkinevienviesLkkaksniervketvestntLLd 45 
                                       L+k+ e++++i+ + e+++++++++++ +++ ++++++tn+LL+
  gi|488599578|ref|YP_007906049.1| 139 LKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDKTNELLE 182
                                       789999************************************96 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 ?    9.9   8.4   0.00075      0.46     164     239 ..     121     196 ..      87     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00075
                                       ......SXSHHHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHH CS
                            FliD_C 164 ektvtsdsglatrlenllksyvkssngtlqtasknltkqikdldkkiedldkrletleerlkkqfaalekavskln 239
                                       ++ + + + ++ + ++++ +  + + + +++  + l+ +i++++k +++ ++++++++e l+++f++le+ ++k++
  gi|488599578|ref|YP_007906049.1| 121 QDMMLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDKTNELLENRFERLEEEIEKIK 196
                                       3334444444444444444444555578889999***********************************9999986 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   1.9e+03      10      41 ..      70     106 ..      63     114 .. 0.63
   2 ?   10.6   3.1    0.0006      0.37     106     164 ..     122     180 ..      96     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHH CS
                         MCPsignal  10 eAeeggkevanvvkqmeeieks.....skeisdiieV 41 
                                       +A  ++ +v++  +++++ie+      ++++s+i++V
  gi|488599578|ref|YP_007906049.1|  70 NAVVEKIQVEEYTGRVRDIERFrssfnTAQLSKIVQV 106
                                       4555566666666666666654444555666666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0006
                                       ....HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 106 vesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqa 164
                                         +le      e+  ++ ++  e++kei  + ++++++++e++++++e s+ i+++n+ 
  gi|488599578|ref|YP_007906049.1| 122 DMMLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDKTNEL 180
                                       44566666777888888999999999999999999999999999999999999998875 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 ?   -1.1   0.0       3.7   2.3e+03      40      61 ..      98     119 ..      70     138 .. 0.54
   2 ?   11.2   1.1   0.00055      0.34      20      72 ..     138     190 ..     130     199 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.7
                            DUF948  40 kqvdpilkevedllakvnelle 61 
                                        q+ +i++   ++l+k   +l+
  gi|488599578|ref|YP_007906049.1|  98 AQLSKIVQVGLKMLEKQDSMLQ 119
                                       3444444444444444444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00055
                            DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdp 72 
                                       +l+k  +t++e++ t e+l+++++++ k v+++ +k+ ++ e ++++ e++++
  gi|488599578|ref|YP_007906049.1| 138 MLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDKTNELLENRFERLEE 190
                                       57777888888888888888555555555555544444444444445555444 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.6    0.0092       5.7       1      71 [.      90     163 ..      90     165 .. 0.87
   2 ?   10.2   4.8    0.0012      0.73      12      75 ..     136     196 ..     128     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0092
                              KxDL   1 rltsavdsedldeilalQaqtsgr...lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkki 71 
                                       r+ s++++++l++i+++  +++ +   + +k+ ++le ++++ e+  ++ ++  + +k ++ +++dL+s  + +
  gi|488599578|ref|YP_007906049.1|  90 RFRSSFNTAQLSKIVQVGLKMLEKqdsMLQKQDMMLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREV 163
                                       6899******************8733355799999999*****************************9866555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0012
                              KxDL  12 deilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslk 75 
                                       d++l++Q +t +++  + + L+  + ++++ ++++++++ +  +ll +  + Le   +k   +k
  gi|488599578|ref|YP_007906049.1| 136 DSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDKTNELLENRFERLEEEIEK---IK 196
                                       67899999999999999999999999999999999999988888887655555544444...33 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       3.8   2.3e+03      37      37 ..     122     122 ..      94     150 .. 0.60
   2 ?   11.3   2.0   0.00045      0.28      10      54 ..     152     196 ..     141     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.8
                              YojJ  37 e 37 
                                       +
  gi|488599578|ref|YP_007906049.1| 122 D 122
                                       1 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00045
                              YojJ  10 lkeklkeeLeqiekeleevlkaldeedeClLcelesirekfaele 54 
                                        +e+lk e++++ k+++e   ++d+ +e l   +e + e++++++
  gi|488599578|ref|YP_007906049.1| 152 TREDLKSEIREVNKSVKEASSKIDKTNELLENRFERLEEEIEKIK 196
                                       589***************************9*******9999886 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  11.5    0.0016      0.99     209     297 ..     105     197 ..      49     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                             FAM76 209 sldsnssdhlvavtqLkeeiaslk.kqleqkdqellekdkkitelkaellekekelre...klkelekeakekiekl 281
                                       ++ +++ ++   + q ++ + +++  +le++d++l ++d +i e+++  ++ ++e+re    +ke  ++++++ e l
  gi|488599578|ref|YP_007906049.1| 105 QVGLKMLEKQDSMLQKQDMMLERQdMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREvnkSVKEASSKIDKTNELL 181
                                       33333333333333444444444414677777888888888888888887777776641114455555556666667 PP

                             FAM76 282 ekkirellkevaelsk 297
                                       e++ ++l  e+ +++k
  gi|488599578|ref|YP_007906049.1| 182 ENRFERLEEEIEKIKK 197
                                       7777777777777776 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.83   5.1e+02      95     117 ..      50      72 ..      43      82 .. 0.78
   2 ?    6.7   8.6    0.0098       6.1       8      61 ..     123     176 ..     109     177 .. 0.77
   3 ?   11.7   5.7   0.00028      0.17      25      68 ..     161     204 ..     152     206 .] 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.83
                              CdvA  95 leekeeikklleklskleleeee 117
                                         eke+i++ le +++ + e+  
  gi|488599578|ref|YP_007906049.1|  50 DGEKEQIEEFLEFIKSNKPENAV 72 
                                       57999999999999877776554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0098
                              CdvA   8 eLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslek 61 
                                        +++++d++ ++ +++ +k +e++k+++ ++++lk+++++  k++++  ++++k
  gi|488599578|ref|YP_007906049.1| 123 MMLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDK 176
                                       467778888888888888888888888888888888888888887777777665 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00028
                              CdvA  25 ekleealkklkekakelkeklkkrlkeledqikslekalanlki 68 
                                       +++++++k+   k ++ +e l++r + le++i++++kal+++ i
  gi|488599578|ref|YP_007906049.1| 161 REVNKSVKEASSKIDKTNELLENRFERLEEEIEKIKKALIKAGI 204
                                       45566666666677777899*******************99877 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   4.6      0.23   1.4e+02      64      93 ..     118     147 ..      76     170 .. 0.68
   2 ?    9.4   2.5    0.0036       2.2      65      96 ..     168     199 ..     149     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.23
                           DUF5320  64 aetaeaskeeekelLeeqaeaLeeeleaik 93 
                                        +++ +  e +  +Le+q ++L+++ e+ik
  gi|488599578|ref|YP_007906049.1| 118 LQKQDMMLERQDMMLEKQDSMLKKQDETIK 147
                                       344455556666666666666666666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0036
                           DUF5320  65 etaeaskeeekelLeeqaeaLeeeleaikkrl 96 
                                       + a+++ ++++elLe++ e Leee+e+ikk l
  gi|488599578|ref|YP_007906049.1| 168 KEASSKIDKTNELLENRFERLEEEIEKIKKAL 199
                                       45667778899******************987 PP

>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         1   6.4e+02      79     109 ..      84     115 ..      40     126 .. 0.55
   2 ?    8.5   5.2    0.0016         1      29     103 ..     128     205 ..     105     206 .] 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                                       HHHHHHHHHHH.HHHHHHHHHHHHHTTC-TTE CS
                             IF-2B  79 liekikelike.ieeadekigdiaaelikdgd 109
                                        ++ i+++ ++   ++  ki++++ + ++++d
  gi|488599578|ref|YP_007906049.1|  84 RVRDIERFRSSfNTAQLSKIVQVGLKMLEKQD 115
                                       44455555555444444566666666666555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                                       HHH.....HHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             IF-2B  29 aeL.....keelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikelikeieeadekigdi 100
                                       +++      + l+k+ +++k+ r t  +l + ir++ k+    + ss+ +++++ l ++ ++l +eie+++++ +++
  gi|488599578|ref|YP_007906049.1| 128 QDMmlekqDSMLKKQDETIKEIRGTREDLKSEIREVNKS--VKEASSKIDKTNELLENRFERLEEEIEKIKKALIKA 202
                                       333567767899**************************5..5599999*************************9999 PP

                                       HHT CS
                             IF-2B 101 aae 103
                                       ++e
  gi|488599578|ref|YP_007906049.1| 203 GIE 205
                                       987 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  20.8    0.0063       3.9      23     165 ..      58     199 ..      53     202 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0063
                               GAS  23 nNLelIkslKeeieelkkke.ernekelseisqenkrl.kepLkk.aeeeveeLrkqlknyekdkqslknlkarlke 96 
                                       + Le Iks K e +  +k + e+ + ++ +i+   ++  + +L k ++  ++ L+kq    +k+ + l+++ + l++
  gi|488599578|ref|YP_007906049.1|  58 EFLEFIKSNKPENAVVEKIQvEEYTGRVRDIERFRSSFnTAQLSKiVQVGLKMLEKQDSMLQKQDMMLERQDMMLEK 134
                                       55666666666666655544134455555555433333133343313444555555555555555555555555555 PP

                               GAS  97 lekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaql 165
                                       +++ lk+  +  +  +   e +++e+ e     +++++e++ k++  n lLe++ ++l+ee+Ek ++ l
  gi|488599578|ref|YP_007906049.1| 135 QDSMLKKQDETIKEIRGTREDLKSEIRE----VNKSVKEASSKIDKTNELLENRFERLEEEIEKIKKAL 199
                                       5555555555544444444444444444....355699999**********************988876 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.5     0.002       1.2      12      52 ..     125     165 ..     116     174 .. 0.88
   2 ?    4.2   2.4     0.059        36      22      51 ..     167     196 ..     164     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                       XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  12 gkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                       ++++ + + ++++ ++++ +++++++ ++e+L++e+++ ++
  gi|488599578|ref|YP_007906049.1| 125 LERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREVNK 165
                                       66777888999999***********************9865 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.059
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                       +k+   ++ ++++ l ++ e+Le+e+++ k
  gi|488599578|ref|YP_007906049.1| 167 VKEASSKIDKTNELLENRFERLEEEIEKIK 196
                                       666667888999999999999999999986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.5    0.0036       2.2      84     189 ..      84     200 ..      50     205 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0036
                            AAA_11  84 ekykp.............kivRvgneeeriseavksvsleekvekrlek.eekaqlakeiskeleklakelrafeee 146
                                       +++++             kiv vg +  + ++++ + + + ++e++  + e++ ++ k+ ++++++++ + ++ +  
  gi|488599578|ref|YP_007906049.1|  84 RVRDIerfrssfntaqlsKIVQVGLKMLEKQDSMLQKQ-DMMLERQDMMlEKQDSMLKKQDETIKEIRGTREDLK-- 157
                                       33333223333333333366666666633333333333.233333222202233333333333333333333332.. PP

                            AAA_11 147 eek..eklkkskekskskleqerrklkkerkelskeleeaeesle 189
                                         +  ++++ks ++ +sk  ++++ l++  ++l++e+e+++++l 
  gi|488599578|ref|YP_007906049.1| 158 --SeiREVNKSVKEASSKIDKTNELLENRFERLEEEIEKIKKALI 200
                                       ..2346788888888888888888888888888888888887765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  19.8    0.0077       4.7     185     273 ..     110     197 ..      49     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0077
                              Spc7 185 klqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                       +l++ ++++ + +   Le     l+++++ ++++ + ++e +  +e+l+++i e++++ +e+ ++i + +++le++ 
  gi|488599578|ref|YP_007906049.1| 110 MLEK-QDSMLQKQDMMLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDKTNELLENRF 185
                                       3333.333333344445555555566666666666666666666666666666666666666666666666666666 PP

                              Spc7 262 gwsesevsrlke 273
                                       +  e+e++++k+
  gi|488599578|ref|YP_007906049.1| 186 ERLEEEIEKIKK 197
                                       666666666555 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.6      0.15        93      22      46 ..     146     170 ..     143     175 .. 0.84
   2 ?    8.2   1.5    0.0042       2.6      25      44 ..     181     200 ..     177     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                           DUF1192  22 veELeerIalLeaEIaRleaaiakk 46 
                                       ++E++   ++L++EI  + + ++++
  gi|488599578|ref|YP_007906049.1| 146 IKEIRGTREDLKSEIREVNKSVKEA 170
                                       6899999********9988877665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0042
                           DUF1192  25 LeerIalLeaEIaRleaaia 44 
                                       Le+r + Le+EI+++++a+ 
  gi|488599578|ref|YP_007906049.1| 181 LENRFERLEEEIEKIKKALI 200
                                       89**************9975 PP

>> DUF2951  Protein of unknown function (DUF2951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0049         3       5      66 ..      10      71 ..       7     111 .. 0.91
   2 ?    1.6   7.7      0.52   3.2e+02      15      71 ..     110     169 ..      97     174 .. 0.74
   3 ?    1.0   2.0      0.82   5.1e+02      31      64 ..     161     194 ..     157     202 .. 0.41

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0049
                           DUF2951  5 kkheqewrlrrleendktmlekldeikdslktqekvyikldktleelrkekeideknkkknd 66
                                      k h+  +rl  lee d  ++  +d  +   + +e + + +d + e+++   e  + nk +n+
  gi|488599578|ref|YP_007906049.1| 10 KVHNAGYRLFLLEEADYLFIPYFDARNVKINGREALVVLVDGEKEQIEEFLEFIKSNKPENA 71
                                      77999*************************************99999999999999999987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.52
                           DUF2951  15 rleendktmlek....ldeikdslktqekvyikldktleelrkekeideknkkkndknird 71 
                                        le++d +ml+k    l++ +  l  q+ + +k d t++e+r  +e  + + ++ +k +++
  gi|488599578|ref|YP_007906049.1| 110 MLEKQD-SMLQKqdmmLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKE 169
                                       555555.566552222556677789999**************9999877777777777765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.82
                           DUF2951  31 kdslktqekvyikldktleelrkekeideknkkk 64 
                                       ++  k+ ++   k+dkt e l++  e  e + +k
  gi|488599578|ref|YP_007906049.1| 161 REVNKSVKEASSKIDKTNELLENRFERLEEEIEK 194
                                       4444444444555555544443332222222222 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   4.0     0.047        29      77     156 ..      82     164 ..      73     166 .. 0.76
   2 ?    8.0   7.2    0.0031       1.9      96     159 ..     135     199 ..     120     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.047
                     Fzo_mitofusin  77 tekLrlivsltsancshqvqqelsstfarlcqqvdet.eke..leeeikelekeiekleevqkkakllrnkaslles 150
                                       t ++r i ++ s+    q+ + ++  ++ l++q  +  +++  le++   lek+ ++l++  ++ k +r   + l+s
  gi|488599578|ref|YP_007906049.1|  82 TGRVRDIERFRSSFNTAQLSKIVQVGLKMLEKQDSMLqKQDmmLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKS 158
                                       567888888888888888888888888888766544303342266667778999999*******************9 PP

                     Fzo_mitofusin 151 eLekfe 156
                                       e+++ +
  gi|488599578|ref|YP_007906049.1| 159 EIREVN 164
                                       998876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0031
                     Fzo_mitofusin  96 qqelsstfarlcqqvdetekeleeeikelekeiekle.evqkkakllrnkaslleseLekfeeqy 159
                                       q  + +  ++  ++++ t+++l++ei+e++k++++   ++ k+ +ll n+ ++le+e+ek ++  
  gi|488599578|ref|YP_007906049.1| 135 QDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASsKIDKTNELLENRFERLEEEIEKIKKAL 199
                                       55677777888899999****************987615677788999**********9998865 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  10.5    0.0069       4.3      33     117 ..     109     187 ..      77     202 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0069
                             Atg14  33 klksekeslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakls 108
                                       k++++++s+ +k + +le+++   e++++ +k++ + ++e++ +++dl+++++e+++++++  ++i+++ + l+ + 
  gi|488599578|ref|YP_007906049.1| 109 KMLEKQDSMLQKQDMMLERQDmMLEKQDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDKTNELLENR- 184
                                       4455555555555555555553233333333333344444444444444444444444444444443333333333. PP

                             Atg14 109 dklkkRrsd 117
                                              ++
  gi|488599578|ref|YP_007906049.1| 185 ------FER 187
                                       ......222 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.5     0.011       6.8      66     139 ..     126     197 ..      99     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                      Allexi_40kDa  66 nklnpvsllsqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelss 139
                                       ++ + + l  q ++L +  +++++++ + ++lks  +++++s ++a +sk+ k+ e +e+++e+l ++++++ +
  gi|488599578|ref|YP_007906049.1| 126 ERQDMM-LEKQDSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEA-SSKIDKTNELLENRFERLEEEIEKIKK 197
                                       333333.556777777777888888888888888887777777655.455677777777777777777777655 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.5      0.05        31      26      74 ..     152     192 ..      38     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.05
                              YtxH  26 tRkdlkekaddlkekakelleeakekakekaedlkekvkekadelkekv 74 
                                       tR+dlk +  ++ +++ke+          k+++  e +++++++l e++
  gi|488599578|ref|YP_007906049.1| 152 TREDLKSEIREVNKSVKEASS--------KIDKTNELLENRFERLEEEI 192
                                       777777777777777777744........44444444444444444333 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.0     0.026        16      37     127 ..      78     169 ..      55     173 .. 0.80
   2 ?    7.1   7.4    0.0091       5.6      34      97 ..     136     199 ..     122     203 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                                       HCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH...HHCCHHHHHHHHHH CS
                         Fib_alpha  37 lekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlket...idaqesnirvLqnv 110
                                       +e+ + ++++i++  ++ ++   +++++++   k  +++d++++k   +le++ + l+++   +++q ++i++++++
  gi|488599578|ref|YP_007906049.1|  78 VEEYTGRVRDIERFRSSFNT--AQLSKIVQVGLKMLEKQDSMLQKQDMMLERQDMMLEKQdsmLKKQDETIKEIRGT 152
                                       55666677777776666654..5888888888888888999999999999999888876433377888********* PP

                                       HHHHHHHHHHHHHHHHH CS
                         Fib_alpha 111 lesneqkiqkLeqdidq 127
                                        e+++++i + ++ +++
  gi|488599578|ref|YP_007906049.1| 153 REDLKSEIREVNKSVKE 169
                                       *********99998865 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0091
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketi 97 
                                       +  l+k  ++++ei+ + ++ ++ ++e+++s++e+ ++ +++++++++  ++leeei+++k+ +
  gi|488599578|ref|YP_007906049.1| 136 DSMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIDKTNELLENRFERLEEEIEKIKKAL 199
                                       2334455566677777777777777777777777777777777777777777777777777765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   9.4    0.0059       3.6     114     187 ..      87     161 ..      32     165 .. 0.68
   2 ?    7.9  15.3    0.0047       2.9      65     140 ..     114     199 ..      87     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0059
                           UPF0242 114 rlkeenqqLq.ekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEik 187
                                         ++   +++  +l++i++   +++ + ++ L+++   l+    ++e+q s+l+k+++ i+++    +Dl+ Ei+
  gi|488599578|ref|YP_007906049.1|  87 DIERFRSSFNtAQLSKIVQVGLKMLEKQDSMLQKQDMMLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEIR 161
                                       34444444431477777777777777788889999999999999999999999999999**99999999999998 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0047
                           UPF0242  65 l......ekskleekeaklteldeglktkeealeelqeeeeeLkee....ldakeeelerlkeenqqLqekleaiae 131
                                              +  +le +  +l ++d  lk+++e+++e +   e+Lk e     ++ +e++ +  + n+ L+ + e   e
  gi|488599578|ref|YP_007906049.1| 114 QdsmlqkQDMMLERQDMMLEKQDSMLKKQDETIKEIRGTREDLKSEirevNKSVKEASSKIDKTNELLENRFERLEE 190
                                       122334477788888888888889999999999999999999999955544566788889999************** PP

                           UPF0242 132 dfeelklel 140
                                       ++e+ k++l
  gi|488599578|ref|YP_007906049.1| 191 EIEKIKKAL 199
                                       ****99975 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   9.2     0.052        32      10      75 ..     137     205 ..      43     206 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.052
                           DUF2203  10 alLpllkelleelralrkeleeleeeleeakaeaekse...aaeleaeleeleaeieelveeieelGve 75 
                                       ++L + +e+++e+r +r++l++  +e++++ +ea+++     + le+++e+le+eie++ + + + G+e
  gi|488599578|ref|YP_007906049.1| 137 SMLKKQDETIKEIRGTREDLKSEIREVNKSVKEASSKIdktNELLENRFERLEEEIEKIKKALIKAGIE 205
                                       566677777778875555555555555444444332223447788999999999999999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2930  (0.163422); expected 358.6 (0.02)
Passed bias filter:                      899  (0.0501422); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); 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):              29  [number of targets reported over threshold]
# CPU time: 0.77u 0.28s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 1315.14
//
Query:       gi|488599579|ref|YP_007906050.1|  [L=71]
Description: hypothetical protein Asulf_00021 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   31.3   0.3    2.3e-07   30.9   0.3    1.2  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 !   30.9   0.3   1.3e-11   2.3e-07       9      47 ..      14      53 ..      10      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.3e-11
                           DUF2283  9 DalYIyl..segpveeseevdddiilDfDedGrlvGIEiLn 47
                                       +l I++  ++++ +  eev+++iil  +++G+++GIE+L 
  gi|488599579|ref|YP_007906050.1| 14 ETLDIWFddPQEE-YVCEEVGEEIILKKSKEGKVIGIEVLY 53
                                      6899***977777.667778*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 490.79
//
Query:       gi|488599580|ref|YP_007906051.1|  [L=181]
Description: hypothetical protein Asulf_00022 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-07   30.9   0.0    4.7e-07   30.0   0.0    1.5  1  NTP_transf_2   Nucleotidyltransferase domain
    3.3e-07   30.3   0.1    6.1e-07   29.4   0.1    1.5  1  Polbeta        Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.035   13.9   0.0    1.4  1  HTH_IclR       IclR helix-turn-helix domain
      0.075   12.9   0.0       0.11   12.4   0.0    1.3  1  Adenyl_cycl_N  Adenylate cyclase NT domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0     1e-10   4.7e-07      15      64 ..      99     149 ..      83     177 .. 0.65

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1e-10
                                       SEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH.HHHEHHHHHHHHCCCEE CS
                      NTP_transf_2  15 akvvlfGSyarGtalkgSDiDllvvlpeevsre.kkeegleklaeiikfle 64 
                                       ++++++GS+a G + + SD+D+l++++ee        e +ekl ++i+ ++
  gi|488599580|ref|YP_007906051.1|  99 ISLAIYGSFASGNFDEMSDLDILIIGEEEDVNRdLILELQEKLGREIQLTV 149
                                       5789***********************993211222233333333333333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.4e-10   6.1e-07       9      69 ..      97     150 ..      90     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.4e-10
                                       HHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEET CS
                           Polbeta   9 kekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdl 69 
                                       +    + + ++GS+a+g++ e SD+D+ ++ +e+   +   +l  el++  lg+++ l +l
  gi|488599580|ref|YP_007906051.1|  97 NC---ISLAIYGSFASGNFDEMSDLDILIIGEEE---DVNRDLILELQEK-LGREIQLTVL 150
                                       33...66789************************...6666778888887.7788877766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.7e-06     0.035       5      39 ..      10      45 ..       9      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.7e-06
                                      HHHHHCT-CTTBSS.-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR  5 alaiLdalaeapqe.ltlselArrtglpkStvhRlL 39
                                      ++ +L+++ +++ + + l+el+rr+ +++ ++  ++
  gi|488599580|ref|YP_007906051.1| 10 GFKVLEYFITHQSAeVHLKELSRRLKISPGSAKTYC 45
                                      899****999999856***************98887 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05      0.11      90     134 ..      96     141 ..      57     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                     Adenyl_cycl_N  90 aaieglylmGStgsiaqsekSDlDiWvc.hrselsaeelelLekKl 134
                                        +  +l   GS++s  + e SDlDi ++  +++++++ + +L++Kl
  gi|488599580|ref|YP_007906051.1|  96 ENCISLAIYGSFASGNFDEMSDLDILIIgEEEDVNRDLILELQEKL 141
                                       345677778******************9788999999999***997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); 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:                         4  (0.000223102); expected 0.2 (1e-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: 1382.63
//
Query:       gi|488599581|ref|YP_007906052.1|  [L=95]
Description: putative conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-12   45.3   0.7    8.4e-12   45.3   0.7    1.0  1  HEPN           HEPN domain
  ------ inclusion threshold ------
      0.056   13.9   0.0       0.07   13.6   0.0    1.0  1  HEPN_SAV_6107  SAV_6107-like HEPN
       0.12   11.7   0.0       0.18   11.2   0.0    1.3  1  GatD_N         GatD N-terminal domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.7   1.4e-15   8.4e-12      30     116 ..       5      89 ..       1      92 [. 0.95

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.4e-15
                                       HHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHH CS
                              HEPN  30 haqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeLekayiesrYpdakeeyteedaeealk 106
                                       +a+ +a+++++All++kg+   ++ +l   l++l ke  ++ el++++++++  +++ +Y+   +  ++e+ae ++ 
  gi|488599581|ref|YP_007906052.1|   5 AAYNSAFHSARALLFAKGYVERSHYCLGLALKYLYKERDKILELINTFDKIRLSRHNIQYGGLLV--SREEAEFVVG 79 
                                       79*********************************99999*************************..********** PP

                                       HHHHHHHHHH CS
                              HEPN 107 daeevlelve 116
                                       +aee+l++++
  gi|488599581|ref|YP_007906052.1|  80 FAEEFLRVAR 89 
                                       ******9865 PP

>> HEPN_SAV_6107  SAV_6107-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05      0.07      13      96 ..       5      87 ..       4      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                     HEPN_SAV_6107 13 aahlaAlraAaAvLaargrperrrrrprsaWelLaevaPelaewaalFaagaarraaieaGieravtareaddllreae 91
                                      aa+ +A  +A A+L a+g  er++     a + L +   ++ e  + F++    r +i+ G    v+++ea+ ++  ae
  gi|488599581|ref|YP_007906052.1|  5 AAYNSAFHSARALLFAKGYVERSHYCLGLALKYLYKERDKILELINTFDKIRLSRHNIQYGGL-LVSREEAEFVVGFAE 82
                                      6999*********************************************************87.9************** PP

                     HEPN_SAV_6107 92 eFlrl 96
                                      eFlr+
  gi|488599581|ref|YP_007906052.1| 83 EFLRV 87
                                      ***86 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     3e-05      0.18       1      25 [.      49      73 ..      49      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                                      --TT-EEEEE-SS-EEEEEE----T CS
                            GatD_N  1 ievGDlikvekkgreyeGilmPrse 25
                                      i+++D+i++ + +++y G+l  r+e
  gi|488599581|ref|YP_007906052.1| 49 INTFDKIRLSRHNIQYGGLLVSREE 73
                                      5789****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 609.32
//
Query:       gi|488599582|ref|YP_007906053.1|  [L=103]
Description: hypothetical protein Asulf_00024 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   50.8   1.7    1.7e-13   50.6   1.7    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    1.5e-11   44.3   0.8    1.9e-11   43.9   0.8    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0013   19.0   0.1     0.0013   18.9   0.1    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.084   13.0   0.2       0.18   11.9   0.2    1.6  1  SMODS           Second Messenger Oligonucleotide or Dinucleot
       0.16   12.2   0.1       0.28   11.4   0.1    1.5  1  GrpB            GrpB protein


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   1.7   4.9e-17   1.7e-13       4      93 ..       9     100 ..       6     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4.9e-17
                                       HHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEE CS
                      NTP_transf_2   4 lleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrek 78 
                                       + +++ke+++  v ++vlfGSyarG++  +SDiD+lvv+++++ +++  +  +  ++i k l +++ l++d +t++k
  gi|488599582|ref|YP_007906053.1|   9 ISRKIKERFGdkVERIVLFGSYARGDYSAESDIDILVVVRDDSIENDIRKVIYSFIPIAKRLISVKILRIDRYTKMK 85 
                                       6777888888889*****************************76554445557788888888888899999998888 PP

                                       CCCCTEEEEEECEEE CS
                      NTP_transf_2  79 ledpllvksileerp 93 
                                         +++ ++s++ e++
  gi|488599582|ref|YP_007906053.1|  86 EMNLSFIRSVEREGI 100
                                       888888888877765 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.8   5.3e-15   1.9e-11       2      87 ..      12     102 ..       9     103 .] 0.81

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.3e-15
                                       STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS-.......--HHHHHHHHHHHHHH.SSSEEEEEE.TT CS
                           Polbeta   2 kikeilekekeielaylFGSrakgkareeSDiDlavllkek.......ldleeelelaaelediklgkkvDlvd.ln 70 
                                       kike + ++  +e ++lFGS+a+g++  eSDiD+ v+++++       + ++  + +a+ l ++ +  ++D  + ++
  gi|488599582|ref|YP_007906053.1|  12 KIKERFGDK--VERIVLFGSYARGDYSAESDIDILVVVRDDsiendirKVIYSFIPIAKRLISV-KILRIDRYTkMK 85 
                                       677777666..******************************88766655555577888888888.457777666488 PP

                                       TS-HHHHHHHHHS-EEE CS
                           Polbeta  71 eapplllyeilkegkll 87 
                                       e ++ +++++ +eg+++
  gi|488599582|ref|YP_007906053.1|  86 EMNLSFIRSVEREGIVI 102
                                       99999999999999987 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 !   18.9   0.1   3.6e-07    0.0013      19      67 ..      15      64 ..       3      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.6e-07
                                      HHH-TT-E.EEE-HHHHTT-SEE.SSEEEEEEBTTBSTTSS--HHHHHHHH CS
                    DNA_pol_B_palm 19 keldpeve.vivcGSYRRgaess.GDvDvlitkkdakseskklkklleklv 67
                                      +++ ++ve ++  GSY Rg  s+  D+D+l+  +d + e++  +k++ +++
  gi|488599582|ref|YP_007906053.1| 15 ERFGDKVErIVLFGSYARGDYSAeSDIDILVVVRDDSIEND-IRKVIYSFI 64
                                      5555565515678******988747**********999765.555555554 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   0.2   5.1e-05      0.18      30      84 ..       8      50 ..       2      91 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                             SMODS 30 aitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnev 84
                                      +i++++++ f   ++k+++ +l+GSyar+         d  +e+d+d+lvvv++ 
  gi|488599582|ref|YP_007906053.1|  8 EISRKIKERF---GDKVERIVLFGSYARG---------DYSAESDIDILVVVRDD 50
                                      6788888888...899***********97.........33347899999888653 PP

>> GrpB  GrpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   7.9e-05      0.28      18      59 ..       9      54 ..       3      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.9e-05
                                      HHHHHHHHH...E.EEEEESGGGSTT--B-S-EEEEEEES-SGGGG CS
                              GrpB 18 ekarlraal...i.sieHiGSTsvpglaAKpiiDilvvvedledee 59
                                      + +++++ +   + +i  +GS +  + +A   iDilvvv+d++ e+
  gi|488599582|ref|YP_007906053.1|  9 ISRKIKERFgdkVeRIVLFGSYARGDYSAESDIDILVVVRDDSIEN 54
                                      6677777777776689999*********************855443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 715.48
//
Query:       gi|488599583|ref|YP_007906054.1|  [L=123]
Description: putative conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-22   80.5   1.5    1.2e-22   80.2   1.5    1.0  1  HEPN           HEPN domain
  ------ inclusion threshold ------
      0.016   15.7   0.1      0.046   14.2   0.0    1.8  2  HEPN_SAV_6107  SAV_6107-like HEPN
      0.038   13.9   1.0      0.089   12.7   0.8    1.8  2  PaREP1         Archaeal PaREP1/PaREP8 family
       0.11   12.6   0.5         16    5.6   0.1    2.3  2  DUF357         Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   1.5   2.7e-26   1.2e-22       4     117 ..       7     119 ..       4     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.7e-26
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHH CS
                              HEPN   4 wlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeL 80 
                                        +++Ae+ l++Ae  l++g y+ +c+ a++a+++a KA++l+ g ++  + + + L+ + k++l+ +ee    l+++
  gi|488599583|ref|YP_007906054.1|   7 RIKKAEKLLRDAESELKMGMYERCCSTAYYAMFHASKAMILSVGEDSRTHRGTIFLIWKNKEKLGLNEEDCIRLSKA 83 
                                       799*******************************************************99999999*********** PP

                                       HCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  81 ekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                       ++++ es+Y+ + e  +ee a ++lkda+e++++++e
  gi|488599583|ref|YP_007906054.1|  84 FDLREESDYGIFQEI-SEETATDILKDAREFVKKAKE 119
                                       **************7.****************99775 PP

>> HEPN_SAV_6107  SAV_6107-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6     7e+03      81      92 ..       9      20 ..       5      24 .. 0.65
   2 ?   14.2   0.0     1e-05     0.046      13      96 ..      33     116 ..      26     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                     HEPN_SAV_6107 81 readdllreaee 92
                                      ++a++llr+ae+
  gi|488599583|ref|YP_007906054.1|  9 KKAEKLLRDAES 20
                                      567777777764 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1e-05
                     HEPN_SAV_6107  13 aahlaAlraAaAv.LaargrperrrrrprsaWelLaevaPelaewaalFaagaarraaieaGieravtareaddllr 88 
                                       +a+ a   a+ A+ L + ++++++r ++   W+  ++     +e    ++++ + r + + Gi +++++++a+d+l+
  gi|488599583|ref|YP_007906054.1|  33 TAYYAMFHASKAMiLSVGEDSRTHRGTIFLIWKNKEKLG-LNEEDCIRLSKAFDLREESDYGIFQEISEETATDILK 108
                                       677777777766514445555577888888887644332.22344555666668999******************** PP

                     HEPN_SAV_6107  89 eaeeFlrl 96 
                                       +a eF+++
  gi|488599583|ref|YP_007906054.1| 109 DAREFVKK 116
                                       *****985 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8     2e-05     0.089       2      43 ..       7      48 ..       6     117 .. 0.79
   2 ?   -1.2   0.0      0.41   1.8e+03       3      17 ..     107     121 ..     105     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                            PaREP1  2 rleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaek 43
                                      r++ aek+l+ Ae+ l+ G +   +  ay A+  + ka++ +
  gi|488599583|ref|YP_007906054.1|  7 RIKKAEKLLRDAESELKMGMYERCCSTAYYAMFHASKAMILS 48
                                      899*****************************9999999877 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.41
                            PaREP1   3 leeaekeleeAeell 17 
                                       l+ a+++++ A+e+l
  gi|488599583|ref|YP_007906054.1| 107 LKDAREFVKKAKEFL 121
                                       677888888888886 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0051        23      32      60 ..       9      37 ..       3      38 .. 0.91
   2 ?    5.6   0.1    0.0037        16      19      49 ..      88     118 ..      72     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0051
                                      HHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                            DUF357 32 emaesYleDakyflekgdlvnAlasfsYa 60
                                      + ae+ l+Da+  l+ g +++  +   Ya
  gi|488599583|ref|YP_007906054.1|  9 KKAEKLLRDAESELKMGMYERCCSTAYYA 37
                                      679999*****************999998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0037
                                       .TS---HHHHHHHHHHHHHHHHHHHHHHTT- CS
                            DUF357  19 eesplgeaaeevlemaesYleDakyflekgd 49 
                                       ees +g  +e   e a+  l+Da++f++k +
  gi|488599583|ref|YP_007906054.1|  88 EESDYGIFQEISEETATDILKDAREFVKKAK 118
                                       5566666666667778888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 982.64
//
Query:       gi|488599584|ref|YP_007906055.1|  [L=133]
Description: hypothetical protein Asulf_00026 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   41.2   0.4    1.5e-10   40.7   0.4    1.2  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
      0.021   15.3   1.1      0.041   14.4   1.1    1.5  1  DUF3899   Domain of unknown function (DUF3899)


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 !   40.7   0.4   1.6e-14   1.5e-10      32     128 ..       5      89 ..       2     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.6e-14
                              YdjM  32 vavlgAllPD.iDhpsstlgrklgllskklaklvgHRgftHSllflallalvlllllrlfgrsalrlglllllgvls 107
                                       ++++g+llPD iD     lg  l +l++        R f H+llf+++l l++l    ++++s     l l ++ ++
  gi|488599584|ref|YP_007906055.1|   5 LIFIGSLLPDiID---KPLGMILLPLNN-------GRVFGHTLLFILILLLIGL----KYRKS-----LFLSFASFL 62 
                                       689*******999...788888888889.......**********987766655....45554.....447799999 PP

                              YdjM 108 HlllDlltkyGvpllwPfsk......k 128
                                       Hl+ D l++ +  ++wP+ +      +
  gi|488599584|ref|YP_007906055.1|  63 HLIEDELWNEPETFFWPLLGdfpakeH 89 
                                       ******************975544431 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.1   4.6e-06     0.041       9      83 ..      38     125 ..      32     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                           DUF3899   9 lllliigillivlnsGfFdgfsygfrklkklflkk.............skkddsyyeykekkkesskkstrplliiG 72 
                                       l++li+ ++ + +++ +F  f+   + + + ++++              k+++s+yey e   ++ ++s+++++i+ 
  gi|488599584|ref|YP_007906055.1|  38 LFILILLLIGLKYRKSLFLSFASFLHLIEDELWNEpetffwpllgdfpAKEHSSFYEYIERIISEYTPSLSHIFISE 114
                                       4666777777778888999999999999999999999999999999999************9999************ PP

                           DUF3899  73 lllivlsivll 83 
                                       ++ iv+ +++l
  gi|488599584|ref|YP_007906055.1| 115 VIGIVIILIFL 125
                                       ******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 792.92
//
Query:       gi|488599585|ref|YP_007906056.1|  [L=364]
Description: Glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-36  125.6   0.0    3.4e-36  124.4   0.0    1.6  2  Glycos_transf_1  Glycosyl transferases group 1
    5.7e-31  107.7   0.0    9.4e-31  107.0   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.1e-22   78.4   0.1      1e-21   77.7   0.1    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.5e-14   53.4   0.0    6.6e-14   52.1   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
    1.7e-11   44.8   0.0    2.6e-11   44.2   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    5.9e-09   36.1   0.3      1e-08   35.3   0.3    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
       0.19   11.7   0.0       0.37   10.7   0.0    1.4  1  Med10            Transcription factor subunit Med10 of Mediat


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7   4.3e+03      66     112 ..      81     124 ..      77     127 .. 0.64
   2 !  124.4   0.0   1.3e-39   3.4e-36       9     171 ..     187     341 ..     182     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                       HHHHCTTCGGGEEECCH.SSSHHHHHHCESEEEEEESSBSS-HHHHHH CS
                   Glycos_transf_1  66 aeelelsdnviflgevs.redleellknadifvlpsisEgfGivllEA 112
                                       ++   + + + +++++s +++l  ++kn + +++     + G++  EA
  gi|488599585|ref|YP_007906056.1|  81 SKDFDIVHVHSYIFFMSnMTALARIFKNFKYVLHF----HGGLNYSEA 124
                                       55566666677777777777777777777766665....556655555 PP

  == domain 2  score: 124.4 bits;  conditional E-value: 1.3e-39
                                       TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
                   Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsred 85 
                                       + + ++ +++ +vg lek+Kg +ll ++f+++   + ++vk+ ++G+g+  ++lk+     +l   +++ g+v++++
  gi|488599585|ref|YP_007906056.1| 187 YSE-NDSRVVTYVGKLEKWKGAELLKDVFKTIHN-ELEDVKFMVVGDGSLAEKLKNS----NL--PIKLMGHVPHDK 255
                                       444.699*************************75.6***********9999999999....33..5688******** PP

                                       HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                   Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                       ++ ++++  + vlps++Eg+++ ++E++a+g+pv+a+++g  +e+v+dg+tG+lvkp++a+a+a ++++lled++lr
  gi|488599585|ref|YP_007906056.1| 256 MPDIYHKTAVSVLPSYMEGLPTICMESLACGVPVVATDVGDTREIVTDGKTGFLVKPGDAKAMASKVIELLEDDDLR 332
                                       ***************************************************************************** PP

                                       HHHHHHHHH CS
                   Glycos_transf_1 163 erlgenark 171
                                       + +g+++r+
  gi|488599585|ref|YP_007906056.1| 333 KTMGREGRR 341
                                       ******996 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.0   3.7e-34   9.4e-31       2     134 .]     193     328 ..     192     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 3.7e-34
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaad 74 
                                       +v+ +vG+l e++kg++ll + ++ ++++  dv++++vGdg+ +e+l+    +l   ++++G+v  +++++++++  
  gi|488599585|ref|YP_007906056.1| 193 RVVTYVGKL-EKWKGAELLKDVFKTIHNEleDVKFMVVGDGSLAEKLK-NS-NL--PIKLMGHVphDKMPDIYHKTA 264
                                       5899*****.777**************99745*********8545886.33.44..4*******9556********* PP

                                       EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       v v+Ps  eg++   +E++a+g+pvVatdvg ++e+v  g++g+lv+pgd++a+a ++++Lled
  gi|488599585|ref|YP_007906056.1| 265 VSVLPSymEGLPTICMESLACGVPVVATDVGDTREIVtdGKTGFLVKPGDAKAMASKVIELLED 328
                                       ******************************999*****************************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 !   77.7   0.1     4e-25     1e-21       3     169 ..      17     183 ..      15     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 4e-25
                    Glyco_transf_4   3 GverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHah 79 
                                       G + +++e+ar+La++G eV+v+t++++     e  +  +++   l+ +   +++ +f+  + +ll + ++D+vH+h
  gi|488599585|ref|YP_007906056.1|  17 GSGIYAYEVARRLADQGNEVHVYTSSVGNFDKVE--YPDNFHIHVLRAYTVVWNMNPFANVFTKLLSK-DFDIVHVH 90 
                                       899**************************99999..999***************************96.******** PP

                    Glyco_transf_4  80 spaalgaallalrr.rlgiplVltvHglye.krllkarlkplsrllralerrl....lrradrviavSeatadelre 150
                                       s+++++  + al+r  ++ ++Vl++Hg    + + k++ ++ ++ ++ + + l    ++ ad+v+ v ++    +++
  gi|488599585|ref|YP_007906056.1|  91 SYIFFMSNMTALARiFKNFKYVLHFHGGLNySEAKKFHPWRTWAKENIYDKTLglltVKIADKVLSVAKSDIPIIKR 167
                                       *****************************8844445555555555555555556668******************** PP

                    Glyco_transf_4 151 rygvppekitVipnGvDle 169
                                       ++gv++   + ipn v +e
  gi|488599585|ref|YP_007906056.1| 168 KFGVDA---EWIPNCVCTE 183
                                       *****8...99***99776 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 !   52.1   0.0   2.6e-17   6.6e-14      14      90 ..     278     356 ..     265     358 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 2.6e-17
                   Glyco_trans_1_2  14 rlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhrae 88 
                                          E +acG++++++d  + +e++t+gk+++l++  d + +a k+ +ll+++++r+ +++++r++v+++++yd  +e
  gi|488599585|ref|YP_007906056.1| 278 ICMESLACGVPVVATDVGDTREIVTDGKTGFLVKpgDAKAMASKVIELLEDDDLRKTMGREGRRHVEENFSYDVIVE 354
                                       568**********************************************************************9988 PP

                   Glyco_trans_1_2  89 ql 90 
                                       ++
  gi|488599585|ref|YP_007906056.1| 355 RV 356
                                       75 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 !   44.2   0.0     1e-14   2.6e-11       1     141 [.      16     162 ..      16     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1e-14
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       +G+g+y++e+ar+La++G eV+v+t++  + +  +  d  ++h l+++   +  ++  ++  +  ll   +  +d+v
  gi|488599585|ref|YP_007906056.1|  16 TGSGIYAYEVARRLADQGNEVHVYTSSVGNFDKVEYPDNFHIHVLRAYTVVW--NMNPFANVFTKLL---SKDFDIV 87 
                                       69***********************98888888677999*******998864..5556888999998...******* PP

                   Glyco_trans_4_4  78 hahspt...aglaarlarrrrgiplvvtlhglllrrgsgavrrlyraler.........rllrradavlvvseaea 141
                                       h+hs+    +++  +lar  ++ ++v+++hg l  +++   +++++++           ++++ ad vl+v  ++ 
  gi|488599585|ref|YP_007906056.1|  88 HVHSYIffmSNM-TALARIFKNFKYVLHFHGGLNYSEAKKFHPWRTWAKEniydktlglLTVKIADKVLSVAKSDI 162
                                       ****76443454.56888778*********9775555445555555553324445555577777888887776665 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.3     4e-12     1e-08       9     120 ..      18     134 ..      14     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4e-12
                   Glyco_trans_4_2   9 ssvhtlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvdrkg.pleylk.afkl.kklikkikPDvvhah 81 
                                       s ++ +++a+ La++g eVhv t+ +g  ++++  +++h+h l+   ++  + +++  + +  kl+ k  +D+vh+h
  gi|488599585|ref|YP_007906056.1|  18 SGIYAYEVARRLADQGNEVHVYTSSVGNfDKVEYPDNFHIHVLR---AYtVVWNMNpFANVfTKLLSK-DFDIVHVH 90 
                                       5678999*****************99999**************8...563344444444442777766.7******* PP

                   Glyco_trans_4_2  82 yakpygllgslaarlsgvipvvlsvwGldvlkfpkksk.....l 120
                                         +  +   +++ar+ +  ++vl ++G   ++++kk       +
  gi|488599585|ref|YP_007906056.1|  91 SYIFFMSNMTALARIFKNFKYVLHFHGGLNYSEAKKFHpwrtwA 134
                                       9987655556678966679*******988899888887644443 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 ?   10.7   0.0   0.00015      0.37      26      81 ..     205     266 ..     180     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                                       S-TTHHHHHHHHHHHHHHHHHHHHH........HH--EEEHHHHHHHHTTB-HHHHHHHHHH CS
                             Med10  26 ssqevlaqklktlvesLqelsktaskl......lqdikiPlelieyvenGrNPdiYtrefve 81 
                                       +  e+l++  kt+ ++L++++ +          l++ ++P+ l+ +v + + PdiY +  v 
  gi|488599585|ref|YP_007906056.1| 205 KGAELLKDVFKTIHNELEDVKFMVVGDgslaekLKNSNLPIKLMGHVPHDKMPDIYHKTAVS 266
                                       56677777788888888888777665577777799*********************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2259.72
//
Query:       gi|488599586|ref|YP_007906057.1|  [L=359]
Description: UDP-N-acetylglucosamine 2-epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-123  412.0   0.0   1.8e-123  411.8   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 !  411.8   0.0    1e-127  1.8e-123       3     346 ..      22     353 ..      20     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 411.8 bits;  conditional E-value: 1e-127
                                       HTTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHH CS
                       Epimerase_2   3 lkaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtne 79 
                                       ++++  l++ +++tGqH+++em++++feele+++p+y+l+++s+++a++tg+++ig+e++l++ekp +vlv+GDtn+
  gi|488599586|ref|YP_007906057.1|  22 CEKR-GLDYFVLHTGQHYSYEMDRIFFEELELPRPKYNLDVGSGTHAEQTGKIMIGVEKILMQEKPKIVLVQGDTNT 97 
                                       5555.799********************************************************************* PP

                                       HHHHHHHHHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHH CS
                       Epimerase_2  80 tlagalaAfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviD 156
                                       +lagalaA+kl+i+ +HveAGlRs+d++  mpeEinR+l+d++sd++fapte a++nL++e ++e++ifv+Gnt++D
  gi|488599586|ref|YP_007906057.1|  98 VLAGALAAAKLHIKAGHVEAGLRSYDKR--MPEEINRVLTDHISDFLFAPTEVAKQNLIRESISENSIFVTGNTIVD 172
                                       ****************************..*********************************************** PP

                                       HHHHHHHHHH...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHH CS
                       Epimerase_2 157 alllskeeieeklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkr 231
                                       a++++ e +++k+    +lke  lk k+y+lvt Hr+en+d  er+k i++ l+ +++e  ++v++p+h  prt+kr
  gi|488599586|ref|YP_007906057.1| 173 AVYQNLEIAKKKV---SVLKElnLKPKEYFLVTTHRQENVDVRERIKGIIRGLELIHNEFAIPVIFPIH--PRTQKR 244
                                       **********888...77788889***********************************99********..****** PP

                                       HHHHHHH-TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHH CS
                       Epimerase_2 232 lleeleelenvtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdkee 308
                                       ++e   +l+ vtli+plg+l+fl+l +naklvltdSgG+qeE+++lgvp+v+lR++teRpe++e g+nvl+gt++e+
  gi|488599586|ref|YP_007906057.1| 245 IEEFGFNLNGVTLINPLGFLEFLQLEANAKLVLTDSGGVQEETCVLGVPCVTLRDNTERPETLEVGSNVLAGTKPER 321
                                       *9988899********************************************************************* PP

                                       HHHHHHHHCT-..--......--TT-SS-HHHHHHHHH CS
                       Epimerase_2 309 IvaaleklledkkelekmanaknpYgdGkaseriveil 346
                                       I+  ++ +l++       +n+knp+gdGka eri++++
  gi|488599586|ref|YP_007906057.1| 322 ILGGVKLMLNK------RNNWKNPFGDGKAGERIINAI 353
                                       *********77......567889************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1999.26
//
Query:       gi|488599587|ref|YP_007906058.1|  [L=719]
Description: putative dehydrogenase-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-24   87.1   0.0    3.2e-22   79.6   0.0    2.6  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    2.3e-16   59.9   0.0    7.2e-16   58.4   0.0    1.8  1  ADH_zinc_N       Zinc-binding dehydrogenase
    2.6e-05   23.8   0.1     0.0038   16.7   0.0    2.9  3  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    0.00035   21.1   0.3       0.15   12.6   0.0    2.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00047   19.6   0.1     0.0012   18.2   0.0    1.7  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00076   18.8   0.1     0.0018   17.6   0.1    1.6  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0018   17.9   0.2     0.0051   16.4   0.0    1.9  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0074   16.9   0.0      0.023   15.3   0.0    1.9  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.042   14.0   0.0    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.023   14.6   0.1      0.082   12.8   0.0    2.0  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.029   15.1   0.1        1.2    9.8   0.0    3.4  4  Methyltransf_25  Methyltransferase domain
      0.035   14.7   0.0       0.53   11.0   0.0    2.6  2  Methyltransf_11  Methyltransferase domain
       0.12   12.2   0.0       0.31   10.9   0.0    1.7  1  ADH_N            Alcohol dehydrogenase GroES-like domain


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 ?    4.6   0.0      0.04        56       2      80 ..     173     254 ..     173     265 .. 0.77
   2 !   79.6   0.0   2.3e-25   3.2e-22       1     120 []     396     516 ..     396     516 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.04
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS......HHHHHTCT.TESEEEE-S- CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd......leelladp.eidavivatp 71 
                                       +v iiG+G +g   + ++ ++ ++++v ++ d ++++ + +a+++g++ +s+      ++++++d   +davi+   
  gi|488599587|ref|YP_007906058.1| 173 NVCIIGLGLLGLLAV-QIAKA-SGYNVLGV-DVSEPKLK-LAKELGADEVSNtkdaikVSRIFSDGyGMDAVIIFAS 245
                                       678999999999888.44444.57777775.66666665.7899999988888888889999999999******988 PP

                                       GGGHHHHHH CS
                      GFO_IDH_MocA  72 ngtheelak 80 
                                       +++ e +++
  gi|488599587|ref|YP_007906058.1| 246 TKSDEPIEL 254
                                       877666655 PP

  == domain 2  score: 79.6 bits;  conditional E-value: 2.3e-25
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngthe 76 
                                       ++v++iGaG++++  + p+ ++ +  ++v++      +ae +a++f+++ + +++ ++l+dp+id+v++at+ ++h+
  gi|488599587|ref|YP_007906058.1| 396 INVGLIGAGNFAKGTILPIIKKIPYVNLVGVATATGTSAEYMARKFDFDyCTTNYMKILEDPNIDCVVIATRHDLHA 472
                                       69***********************************************9*************************** PP

                                       HHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  77 elakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       ++  +ale+ k+v++EKP+a+t +e+k+++e+ ++++ +++vg+
  gi|488599587|ref|YP_007906058.1| 473 RISSEALEHDKDVFVEKPMALTSKELKRVIEAYNSSDGKIMVGF 516
                                       *****************************************996 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   5.2e-19   7.2e-16       2      95 ..     182     275 ..     182     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 5.2e-19
                                       HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   2 vGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaalk 77 
                                       +Gl+avq+Aka+G +v +vd+se kl+lak+lGadev n+k+a +++    +   g ++ ++f  + s + +e a +
  gi|488599587|ref|YP_007906058.1| 182 LGLLAVQIAKASGYNVLGVDVSEPKLKLAKELGADEVSNTKDAiKVSRIFSDGY-GMDAVIIFASTKSDEPIELASE 257
                                       7***************************************88766555555555.5566667777779********* PP

                                       CEEEEEEEEECSCTSSEE CS
                        ADH_zinc_N  78 llkpgGrlvvvGggkgee 95 
                                       +++++G++vv G+++ + 
  gi|488599587|ref|YP_007906058.1| 258 IARERGKIVVPGLVGLDI 275
                                       ************843333 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 !   16.7   0.0   2.7e-06    0.0038      30     104 ..     170     240 ..     156     266 .. 0.77
   2 ?    3.1   0.0     0.041        57     182     201 ..     336     355 ..     324     366 .. 0.86
   3 ?   -0.6   0.0      0.58   7.9e+02     115     206 ..     415     512 ..     407     515 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
                       Glu_dehyd_C  30 epesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsret..pvdeipeaseemdlv 104
                                         e ++++G G lGLLa+ + +   +g++   vlg  d  +p+++l +elGa  v + ++  +v++i +    md v
  gi|488599587|ref|YP_007906058.1| 170 PGENVCIIGLGLLGLLAVQIAK--ASGYN---VLGV-DVSEPKLKLAKELGADEVSNTKDaiKVSRIFSDGYGMDAV 240
                                       447899***********66665..47887...8885.889************9997665412566676666667665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.041
                       Glu_dehyd_C 182 ldelvtkvvdldeleeAfed 201
                                       ld+++t++ ++de+e+A+e+
  gi|488599587|ref|YP_007906058.1| 336 LDKIITHRFKIDEAEKAYEE 355
                                       89****************85 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.58
                       Glu_dehyd_C 115 feaiealapnGvaaLlGvped...sevevdggelhrelvleNkalvGsvNanrr..hfeaavdtLaalpesllde.l 185
                                       ++ i  ++  Gva+ +G +++   +++++d  + +   +le   +   v a r+  h + + ++L++ ++ ++++ +
  gi|488599587|ref|YP_007906058.1| 415 IKKIPYVNLVGVATATGTSAEymaRKFDFDYCTTNYMKILEDPNIDCVVIATRHdlHARISSEALEHDKDVFVEKpM 491
                                       55666677778888888886532247888888888888888888877777777622455567889998888887724 PP

                       Glu_dehyd_C 186 vtkvvdldeleeAfedddeti 206
                                         +  +l+++ eA++++d +i
  gi|488599587|ref|YP_007906058.1| 492 ALTSKELKRVIEAYNSSDGKI 512
                                       446678999999999999887 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.017        24       2      92 ..     174     267 ..     173     272 .. 0.76
   2 !   12.6   0.0   0.00011      0.15       2      81 ..     398     478 ..     397     488 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..........-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..........vkvtavdneeaaeeadvvvla 68 
                                       ++iiG G +g   ++ + a+g   ++++ + + ++ k+ +la+elg          +kv+         +a +++ +
  gi|488599587|ref|YP_007906058.1| 174 VCIIGLGLLGLLAVQIAKASG---YNVL-GVDVSEPKL-KLAKELGadevsntkdaIKVSRIFSDGYGMDAVIIFAS 245
                                       789*****9998888888888...9999.756666666.88899997777777777666666666666678888888 PP

                                       S-HHHHHHHHHHCGHHHHTTSEEE CS
                     F420_oxidored  69 vkpedveevlselakdalkgklvi 92 
                                        k     e++se+  +  +gk+v+
  gi|488599587|ref|YP_007906058.1| 246 TKSDEPIELASEI--ARERGKIVV 267
                                       8888888999998..667888887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S-HHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae..eadvvvlavkpedvee 76 
                                       +g+iGaGn++++ ++ ++++    + + va + +  +ae++a+++  + +++++ + +e  + d vv+a +   ++ 
  gi|488599587|ref|YP_007906058.1| 398 VGLIGAGNFAKGTILPIIKKIPYVNLVGVA-TATGTSAEYMARKFDFDYCTTNYMKILEdpNIDCVVIATRHDLHAR 473
                                       89******************5366666666.9999****************999****9888999***998877777 PP

                                       HHHHC CS
                     F420_oxidored  77 vlsel 81 
                                       + se+
  gi|488599587|ref|YP_007906058.1| 474 ISSEA 478
                                       77766 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.8e-07    0.0012      36      95 ..     171     231 ..     158     233 .. 0.86
   2 ?   -3.6   0.0       4.3   5.9e+03      37      49 ..     396     408 ..     384     411 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.8e-07
                                       TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEE CS
                      2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv.elvsleellaesDiv 95 
                                       g+ v+iiGlG +G  + +++ka g +v+++d+s+ k + ++elg+ e+ + +++++ s i 
  gi|488599587|ref|YP_007906058.1| 171 GENVCIIGLGLLGLLAVQIAKASGYNVLGVDVSEPKLKLAKELGAdEVSNTKDAIKVSRIF 231
                                       789******************************9988888888885666788888777765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.3
                                       SEEEEES-SHHHH CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGq 49 
                                         vG+iG+G+ ++
  gi|488599587|ref|YP_007906058.1| 396 INVGLIGAGNFAK 408
                                       5799999999765 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 !   17.6   0.1   1.3e-06    0.0018      30      77 ..     173     220 ..     154     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev 77 
                                       +v +iG G  Gl A+++ak+ g +V  +Dv++ +l+  ++lga  v+ 
  gi|488599587|ref|YP_007906058.1| 173 NVCIIGLGLLGLLAVQIAKASGYNVLGVDVSEPKLKLAKELGADEVSN 220
                                       699*************************************99996654 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 ?   -3.1   0.0       3.6     5e+03      77      90 ..      11      24 ..       7      46 .. 0.70
   2 !   16.4   0.0   3.7e-06    0.0051       2      39 ..     173     210 ..     172     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.6
                                      -SEEEE-----B-T CS
                    UDPG_MGDP_dh_N 77 advifiaVgTPskk 90
                                       ++ ++ V+TP  +
  gi|488599587|ref|YP_007906058.1| 11 GEIKLVNVPTPLVR 24
                                      67889999999766 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.7e-06
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdkl 39 
                                       ++++iGlG +Gl    +  + g +v+gvD++e k +  
  gi|488599587|ref|YP_007906058.1| 173 NVCIIGLGLLGLLAVQIAKASGYNVLGVDVSEPKLKLA 210
                                       79***********99999999***********998765 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       7.6     1e+04       5      37 ..     177     211 ..     176     246 .. 0.63
   2 !   15.3   0.0   1.7e-05     0.023      22     114 ..     421     512 ..     402     515 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.6
                                       HHHHHHHHHHH---S.SEEEEEEEEESS.EEE-TT CS
                     NAD_binding_3   5 iGsavleqlkrqqse.ielelvavadrd.sllskd 37 
                                       iG ++l +l+ q ++  ++++ +v +++ +l+ ++
  gi|488599587|ref|YP_007906058.1| 177 IGLGLLGLLAVQIAKaSGYNVLGVDVSEpKLKLAK 211
                                       56666666666665556788888888883332222 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.7e-05
                                       EEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CGGG-HH CS
                     NAD_binding_3  22 lelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaLkagkdvvtankgaladea 98 
                                       ++lv+va +    ++  ++++    +t++  ++++++++d vV ++ ++  a +  +aL+++kdv +    al+ ++
  gi|488599587|ref|YP_007906058.1| 421 VNLVGVATATGTSAEYMARKFDFDYCTTNYMKILEDPNIDCVVIATRHDLHARISSEALEHDKDVFVEKPMALT-SK 496
                                       688999999844444488999999**************************************************.56 PP

                                       HHHHHTSSSTTS--.E CS
                     NAD_binding_3  99 lyeeLreaaeangaki 114
                                         ++ +ea ++++ ki
  gi|488599587|ref|YP_007906058.1| 497 ELKRVIEAYNSSDGKI 512
                                       6666666666666655 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     3e-05     0.042       2      57 ..     174     229 ..     173     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCS CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasld 57 
                                       + +iGlG +G   ++  +++gy+v ++++++ k++ + + ga+ +++ +++++  +
  gi|488599587|ref|YP_007906058.1| 174 VCIIGLGLLGLLAVQIAKASGYNVLGVDVSEPKLKLAKELGADEVSNTKDAIKVSR 229
                                       789********9999999******************************99998763 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 ?   12.8   0.0   5.9e-05     0.082       1      54 [.     173     226 ..     173     262 .. 0.87
   2 ?   -1.8   0.0       1.8   2.4e+03       2     158 ..     398     435 ..     397     444 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.9e-05
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTS CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgk 54 
                                       +v +iG G++G    +++ ++g++V  vd+se +l+ a+e  ++++++ + + k
  gi|488599587|ref|YP_007906058.1| 173 NVCIIGLGLLGLLAVQIAKASGYNVLGVDVSEPKLKLAKELGADEVSNTKDAIK 226
                                       589*********999999999***************999988887777665544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavd 78 
                                       v+ iGaG   +g    ++++   V+lv ++                                               
  gi|488599587|ref|YP_007906058.1| 398 VGLIGAGNFAKGTILPIIKKIPYVNLVGVA----------------------------------------------- 427
                                       556666666555555555544445444444............................................... PP

                                       -SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT- CS
                           3HCDH_N  79 adlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekT 155
                                                                                                               +++ T
  gi|488599587|ref|YP_007906058.1| 428 ------------------------------------------------------------------------TATGT 432
                                       ........................................................................44444 PP

                                       -HH CS
                           3HCDH_N 156 see 158
                                       s e
  gi|488599587|ref|YP_007906058.1| 433 SAE 435
                                       444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.3   1.8e+03      22      44 ..      34      56 ..      26      75 .. 0.75
   2 ?    9.8   0.0    0.0009       1.2       9      44 ..     183     217 ..     174     260 .. 0.69
   3 ?   -1.4   0.0       2.9     4e+03      60      82 ..     436     459 ..     424     479 .. 0.58
   4 ?   -1.3   0.0       2.7   3.8e+03       3      70 ..     556     627 ..     554     650 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                                      SEEEEEESSHHHHHHHHHHHHHT CS
                   Methyltransf_25 22 akvtgvDiseemleaareraeee 44
                                       +v+ +   ++m++ ar++  ++
  gi|488599587|ref|YP_007906058.1| 34 ISVVSIGTEKNMIDFARKNTISK 56
                                      6889999999*******998654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0009
                                       SHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHT CS
                   Methyltransf_25   9 GrltlalakrlgkakvtgvDiseemleaareraeee 44 
                                       G l+ ++ak+ g ++v+gvD+se  l+ a+e  ++e
  gi|488599587|ref|YP_007906058.1| 183 GLLAVQIAKASG-YNVLGVDVSEPKLKLAKELGADE 217
                                       889999999976.*****************998654 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.9
                                       SSTTTEEEEEEEST.GGGSSHHHH CS
                   Methyltransf_25  60 fedgsfDlvvssga.lhhlsdedl 82 
                                       + +++fD+ +++ + + +l+d+++
  gi|488599587|ref|YP_007906058.1| 436 YMARKFDFDYCTTNyMKILEDPNI 459
                                       334455555555554555555544 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.7
                                       EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHH....HHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaar....eraeeegl..nvefvqgdaedlpfedgsfDlvvs 70 
                                       d + G Gr++ ++ + + +  ++ ++ s++++ a +    +  +++++  n++f++g++ ++ + +   D  +s
  gi|488599587|ref|YP_007906058.1| 556 DPAEGGGRILGEVCHFV-DLAIYFTESSPKYVYAQAidapHYSADDNVlvNISFENGSIASILYVS-NGDRAFS 627
                                       55667777777777665.577778888877763322122122222444578888888887765443.3455555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.88   1.2e+03      13      43 ..      28      58 ..      23      75 .. 0.76
   2 ?   11.0   0.0   0.00038      0.53       4      86 ..     178     260 ..     176     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.88
                                      HHHHTTSEEEEEES-HHHHHHHHHHCCHHT- CS
                   Methyltransf_11 13 alakrgarvvgvDlskemlklakekaseegl 43
                                       l k++ +vv + + k+m++ a++++  + l
  gi|488599587|ref|YP_007906058.1| 28 VLVKNVISVVSIGTEKNMIDFARKNTISKAL 58
                                      566677889999999*******999876654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00038
                                       T-T.TSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTS..S-TT.-EEEEEEES-CCC-C CS
                   Methyltransf_11   4 GcG.tGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklp..fedn.sfDlvvssevlhhve 75 
                                       G G  G+la ++ak+  ++v+gvD+s+  lklake + +e         da k+   f d+  +D+v+++ + +  +
  gi|488599587|ref|YP_007906058.1| 178 GLGlLGLLAVQIAKASgYNVLGVDVSEPKLKLAKELGADEVS----NTKDAIKVSriFSDGyGMDAVIIFAS-TKSD 249
                                       56656888888995555******************9999874....45566555334777635777776654.3345 PP

                                       CHHHHHHHHHH CS
                   Methyltransf_11  76 dpekalkeiaR 86 
                                       +p ++ +eiaR
  gi|488599587|ref|YP_007906058.1| 250 EPIELASEIAR 260
                                       66666666665 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.31      21      69 ..      80     127 ..      74     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                       HTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SS CS
                             ADH_N  21 lkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscge 69 
                                       +k+ ++ + + p  lG   +G+v +vg++  ++++GdrV++      ++
  gi|488599587|ref|YP_007906058.1|  80 YKQ-AKRRLASPEPLGYSSAGIVIDVGNSDAEFRKGDRVACTGSGFASH 127
                                       555.6778888999*************************9966555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 4387.76
//
Query:       gi|488599588|ref|YP_007906059.1|  [L=412]
Description: Glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   0.1    3.5e-19   69.0   0.0    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
    3.2e-16   60.0   0.1    6.9e-16   58.9   0.1    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
    8.6e-15   55.5   0.0    1.3e-14   55.0   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.4e-13   51.2   0.0    2.7e-13   50.3   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00063   20.1   0.0     0.0013   19.1   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0078   16.2   0.5       0.85    9.6   0.4    2.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.81   2.4e+03      69      98 ..     171     200 ..     168     202 .. 0.75
   2 !   69.0   0.0   1.2e-22   3.5e-19       4     170 ..     216     385 ..     213     387 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.81
                                       HCTTCGGGEEECCHSSSHHHHHHCESEEEE CS
                   Glycos_transf_1  69 lelsdnviflgevsredleellknadifvl 98 
                                       +elsd+++++ e +++ + e     +i+v+
  gi|488599588|ref|YP_007906059.1| 171 YELSDHITVHSEGNKQHIAEKVPEEKITVI 200
                                       899999999999997777776666666665 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 1.2e-22
                                       HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEEC CS
                   Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflge 80 
                                       + rkklg+  +k ++ + g +++ ++++++++a+allk+  +++++++++G+g+++  +++++e l+l dnv +l +
  gi|488599588|ref|YP_007906059.1| 216 EFRKKLGI-IDKFVVTYAGIMSYSQDIETIVDAAALLKD--KKDIVFLLVGDGPQKGDIERKVELLGL-DNVLMLPF 288
                                       66788888.6999************************97..5**************************.******** PP

                                       CHSSSHHHHHHCESEEEEEESS.....BSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTTSEEEE-TT-HHHHHH CS
                   Glycos_transf_1  81 vsredleellknadifvlpsis.....EgfGivllEAmaaglpviasn..aggpaevvkdgetGllvkpnnaealae 150
                                       +++e+   ll ++d+ +++           +  l   maag +via     g ++++v+++e G++++p+n+e l+e
  gi|488599588|ref|YP_007906059.1| 289 QPKEKYSMLLAASDVCLVTLDAnrvktPVVPRKLNDIMAAGRAVIANVplDGDVPKIVREAECGYCIEPKNPENLVE 365
                                       **8888888888*******9999999999*****************9989999************************ PP

                                       HHHHHHHSHHHHHHHHHHHH CS
                   Glycos_transf_1 151 airklledeelrerlgenar 170
                                       ai +l +++ l e++g+n+ 
  gi|488599588|ref|YP_007906059.1| 366 AILELYNNPHLVEKFGRNGA 385
                                       ******************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 !   58.9   0.1   2.3e-19   6.9e-16       3     134 .]     228     373 ..     226     373 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.3e-19
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaad 74 
                                       v+ + G +    + ++ +++a++ll++k d+ +++vGdgp++ ++e++++  gl ++v ++ f   e+ + llaa+d
  gi|488599588|ref|YP_007906059.1| 228 VVTYAGIM-SYSQDIETIVDAAALLKDKkDIVFLLVGDGPQKGDIERKVEllGL-DNVLMLPFQpkEKYSMLLAASD 302
                                       67888888.44589************8846**********55799999988999.7********86679999***** PP

                                       EEEE--...-....--SHHHHHHHHTT-EEEE-.TGGG.TTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  75 vfvaPs...e....gfglkllEamaaglpvVat.dvgg.iaevv..gengllvppgdpealaeailrLled 134
                                       v+++++   +     ++ kl + maag++v+a  ++ g ++++v   e g++++p++pe l+eail+L+++
  gi|488599588|ref|YP_007906059.1| 303 VCLVTLdanRvktpVVPRKLNDIMAAGRAVIANvPLDGdVPKIVreAECGYCIEPKNPENLVEAILELYNN 373
                                       ******9873555568****************98786559999997799*******************986 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 !   55.0   0.0   4.3e-18   1.3e-14       7     160 .]      21     203 ..      15     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 4.3e-18
                   Glyco_trans_4_4   7 vaelaraLaarGheVtvlt................papapgap.eleedgvrvhrlp...vprrpspladlaalral 63 
                                       ++e+a++L +rGh Vtv+t                +++ ++a+ ++  dg+ v+r++   +pr +  l+ l++ +  
  gi|488599588|ref|YP_007906059.1|  21 FYEFAEELTKRGHKVTVVTtfpreynlnkdelhlmSKYKRKAFlREKIDGINVIRVRslqAPRDSPILRGLEHFFVP 97 
                                       589****************9865555555555444333333443466889999888733355555555667777655 PP

                   Glyco_trans_4_4  64 rrll.rqrrerpdvvhahspt..aglaarlarrrrgiplvvtlhglllrrg.......sgavrrlyralerrllrra 130
                                        ++  +    + dv+++ sp+  +gla+++++  +++pl+v++++l ++         ++ +  ++r +e++++   
  gi|488599588|ref|YP_007906059.1|  98 LSVTlGGLFAKSDVIVVYSPPlpLGLAGWVLSKIKRVPLIVNIQDLYPQAAidlgllkNPILIEIFRVIEKLVYELS 174
                                       555445567999******9654699******9899*********8553322333256688888899*********** PP

                   Glyco_trans_4_4 131 davlvvseaeaeelralgvpadrvvvvpng 160
                                       d+++v se+  ++++++ vp ++++v+pn+
  gi|488599588|ref|YP_007906059.1| 175 DHITVHSEGNKQHIAEK-VPEEKITVIPNW 203
                                       **************999.899********8 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0     9e-17   2.7e-13       5     164 ..      18     202 ..      14     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 9e-17
                    Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleeev....................elvvrvprvplpllkrllrslafl 61 
                                           +e+a++L +rGh+Vtvvt  +++   +++                    ++v+rv++   p + + lr l ++
  gi|488599588|ref|YP_007906059.1|  18 SHLFYEFAEELTKRGHKVTVVTTFPREYNLNKDelhlmskykrkaflrekidgINVIRVRSLQAPRDSPILRGLEHF 94 
                                       55679****************888877777777789************9*988666666666666666555544443 PP

                    Glyco_transf_4  62 r.....rlrrllkrekpDvv.HahspaalgaallalrrrlgiplVltvHglye...krllkarlkplsrllralerr 129
                                       +      l  l+   k Dv+  +  p +lg+a++ l + +++pl++ + +ly+     l   ++  l  ++r +e+ 
  gi|488599588|ref|YP_007906059.1|  95 FvplsvTLGGLFA--KSDVIvVYSPPLPLGLAGWVLSKIKRVPLIVNIQDLYPqaaIDLGLLKNPILIEIFRVIEKL 169
                                       3100003444444..889883344456778899988889**************998556666777788888899999 PP

                    Glyco_transf_4 130 llrradrviavSeatadelrerygvppekitVipn 164
                                       ++  +d++++ Se  +++++e  +vp+ekitVipn
  gi|488599588|ref|YP_007906059.1| 170 VYELSDHITVHSEGNKQHIAE--KVPEEKITVIPN 202
                                       9********************..************ PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.4e-07    0.0013      14      81 ..     321     392 ..     303     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.4e-07
                   Glyco_trans_1_2  14 rlfEaaacGafaltdda..egleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaeh 81 
                                       +l +++a+G+ ++++ +   ++++++++ + + ++e  ++e+l+e+i +l +np + ++ ++++ e +++++
  gi|488599588|ref|YP_007906059.1| 321 KLNDIMAAGRAVIANVPldGDVPKIVREAECGYCIEpkNPENLVEAILELYNNPHLVEKFGRNGAEYARNNF 392
                                       7789***********88***********************************************99888876 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.4   0.00028      0.85      13      51 ..      21      58 ..      14     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                   Glyco_trans_4_2 13 tlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlk 51
                                       +++a+eL krg++V+v+t  +  + +l+ + +h+++  
  gi|488599588|ref|YP_007906059.1| 21 FYEFAEELTKRGHKVTVVTTFPR-EYNLNKDELHLMSKY 58
                                      478999************99777.555666667766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2339.36
//
Query:       gi|488599589|ref|YP_007906060.1|  [L=332]
Description: Nucleoside-diphosphate-sugar epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  183.5   0.0      5e-54  183.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    8.7e-45  153.6   0.0    1.7e-44  152.6   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.2e-17   61.1   0.0      4e-13   49.1   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    7.5e-15   54.7   0.0    1.9e-14   53.3   0.0    1.6  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.4e-09   36.7   0.0    4.1e-09   36.0   0.0    1.4  2  RmlD_sub_bind    RmlD substrate binding domain
    3.7e-05   23.3   0.0      7e-05   22.4   0.0    1.4  1  adh_short        short chain dehydrogenase
    0.00023   21.1   0.1    0.00074   19.5   0.1    1.8  1  KR               KR domain
    0.00044   20.2   0.0    0.00064   19.7   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
       0.01   15.0   0.0      0.053   12.7   0.0    1.9  2  NAD_binding_4    Male sterility protein
      0.012   15.9   0.0       0.02   15.1   0.0    1.3  1  TrkA_N           TrkA-N domain
      0.074   13.1   0.0       0.51   10.4   0.0    2.2  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.091   12.5   0.0       0.17   11.5   0.0    1.4  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
       0.13   11.6   1.3       0.47    9.8   0.7    1.9  2  ThiF             ThiF family


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 !  183.3   0.0   3.7e-57     5e-54       1     240 [.      13     250 ..      13     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 3.7e-57
                                       EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl..elveldltdrsalerlfkeeqpdavihlAav 74 
                                       +lVtG++G+iGs+l+k l e g + vi ld ls + +++       e+v+++++d+++l+++f e +pd+v+hlAa 
  gi|488599589|ref|YP_007906060.1|  13 VLVTGGAGCIGSNLCKVLSELGAKkVIILDDLSASYKWNIPVADniEFVQGNILDEEKLKQVFYE-KPDYVFHLAAH 88 
                                       79********************777*******88888877665588******************7.9********** PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEE.GGGGTSCSSSS.BSTCSTTS----SSHHHHHHHHH CS
                         Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsS.sevYGkdaeqp.keettltgplkpnspYaaaKlag 149
                                          ++s+e+p+  ++ n  gtl++le++r ++v r++++sS ++vYG++a+ p ke+ +   +l   +pY ++Kl+g
  gi|488599589|ref|YP_007906060.1|  89 FANQNSVEHPETDLMVNGLGTLKILEYCRLTDVSRVVYASSgCSVYGAQAPLPlKEDFV---SLDLDTPYQIHKLLG 162
                                       *****************************************999********9666667...8899*********** PP

                                       HHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHH CS
                         Epimerase 150 eklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvl 226
                                       e ++ ++ + y+l++   r+fn+yGp++ +g+ ++vip ++  +l+g  ++ + g+g++ Rdf yv+D++++ l+  
  gi|488599589|ref|YP_007906060.1| 163 ELYCNYFYNLYELQVARARYFNVYGPGEVPGRYRNVIPNFMYWALNGM-PLPITGTGEETRDFTYVSDIVDGTLRCG 238
                                       ************************************************.***********************99865 PP

                                       HHHTT-STTEEEEE CS
                         Epimerase 227 ehvdagdkgeiyni 240
                                           +++ ge++n+
  gi|488599589|ref|YP_007906060.1| 239 VV--KKAVGEAFNL 250
                                       54..3355667765 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 !  152.6   0.0   1.3e-47   1.7e-44       1     332 []      14     315 ..      14     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 152.6 bits;  conditional E-value: 1.3e-47
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aG iGs+l++ L e g + ++i ++ s+ + ++i          + +n+++++g++ D+++l++++ e  pd
  gi|488599589|ref|YP_007906060.1|  14 LVTGGAGCIGSNLCKVLSELGAKKVIILDDLSASYKWNIP---------VADNIEFVQGNILDEEKLKQVFYEK-PD 80 
                                       9********************9999998888888888883.........34589******************96.** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPY 153
                                        v++LAA  + ++s+e+Pe+ + vn+lGtl++Le +r + ++    +y +S   vYG ++  p +E+   ++   PY
  gi|488599589|ref|YP_007906060.1|  81 YVFHLAAHFANQNSVEHPETDLMVNGLGTLKILEYCRLTDVS--RVVYASSGCSVYGAQAPLPLKEDfVSLDLDTPY 155
                                       *************************************99875..3567777789************9446899**** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                        + Kl  +  +  +++ y+l++  +++fn ++p   +    + i++++  +++g  + ++ G ++++Rd+++v+D+v
  gi|488599589|ref|YP_007906060.1| 156 QIHKLLGELYCNYFYNLYELQVARARYFNVYGPGEVPGRYRNVIPNFMYWALNGM-PLPITGTGEETRDFTYVSDIV 231
                                       **********************************999999999999999988887.99999**************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-. CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdll. 306
                                       ++  +    +k      a ge +++ +  e ++++l + i+              +g  +  + +k +r  +   + 
  gi|488599589|ref|YP_007906060.1| 232 DGTLRCGVVKK------AVGEAFNLASETETKIIDLANWINEL------------TG-NKAGIVFKERRSWDRSIRr 289
                                       **988544444......56777777777777777776533321............11.2334445555555554432 PP

                                       -B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvsfeelvrem 332
                                        + ++kake Lg++pkv+++++++++
  gi|488599589|ref|YP_007906060.1| 290 KASIKKAKEMLGYEPKVDIKSGLKKT 315
                                       799*******************9986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   2.9e-16     4e-13       1     130 [.      13     131 ..      13     138 .. 0.85
   2 !   10.0   0.0   0.00025      0.35     167     250 ..     187     272 ..     154     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 2.9e-16
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G iGs+l++ + +  +kk+i+l+    + y+ +  +     ++++++    v g++ d+e+l++++   k
  gi|488599589|ref|YP_007906060.1|  13 VLVTGGAGCIGSNLCKVLSELGAKKVIILDDLS-ASYKWNIPV-----ADNIEF----VQGNILDEEKLKQVFY-EK 78 
                                       8****************************9654.445555554.....234544....48*************9.8* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGG CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDK 130
                                       +d+vfh AA+       e+p   +  N lgt +++e +  ++v++vv+ S+  
  gi|488599589|ref|YP_007906060.1|  79 PDYVFHLAAHFANQNSVEHPETDLMVNGLGTLKILEYCRLTDVSRVVYASSGC 131
                                       *********98887777788999999**********************99865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00025
                                       EE-EETTGTTSSHHHHHHHHHTTSSEEES-T.T-EEEEE-HHHHHHHHHHHHHH--.SS-EEEE--.-EEEHHHHHH CS
                   Polysacc_synt_2 167 RfGNVlgSrGSviplFkkqikeggpvtvTdp.emtRyfmtieeavqLvlqalalak.ggeifvldmGepvkivdlak 241
                                         G V g    vip F     +g p+++T + e tR f  +++ v+  l ++   k  ge f l     +ki+dla+
  gi|488599589|ref|YP_007906060.1| 187 GPGEVPGRYRNVIPNFMYWALNGMPLPITGTgEETRDFTYVSDIVDGTLRCGVVKKaVGEAFNLASETETKIIDLAN 263
                                       33555566678******************76489****************997654279*******9********** PP

                                       HH....... CS
                   Polysacc_synt_2 242 alielsgle 250
                                        + el+g +
  gi|488599589|ref|YP_007906060.1| 264 WINELTGNK 272
                                       *99999865 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 !   53.3   0.0   1.4e-17   1.9e-14       1     222 [.      14     231 ..      14     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.4e-17
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleeal.egvdvvihlasl 76 
                                       +vtGgaG +G++l+k L +l+ +k +   Dl  s ++  ++   +++++++g ++d++kl+++  e+ d v+hla+ 
  gi|488599589|ref|YP_007906060.1|  14 LVTGGAGCIGSNLCKVLSELGAKKVIILDDLSASYKW--NIPVADNIEFVQGNILDEEKLKQVFyEKPDYVFHLAAH 88 
                                       69*******************7555555568888888..667777777**************9736679*****998 PP

                         3Beta_HSD  77 vdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKal 152
                                          ++ + + ++   vn  GT ++le c+ ++v ++vY Ss   v++ +   +    +E+  +      +y+  K l
  gi|488599589|ref|YP_007906060.1|  89 FANQNsVEHPETDLMVNGLGTLKILEYCRLTDVSRVVYASSGCSVYGAQAPLP---LKED-FVSLDLDTPYQIHKLL 161
                                       766654888899999**************************888888333333...3343.3455567788888888 PP

                         3Beta_HSD 153 aEklvlkaNgrtlknggrlyTcaLRpagiyGegd.....kllvpllkqlaklglalfkigdeevlsdrvYvgNva 222
                                        E +    N   + n  +l     R   +yG+g+     + + p +   a +g+ l  +g  e + d++Yv  ++
  gi|488599589|ref|YP_007906060.1| 162 GELY---CNY--FYNLYELQVARARYFNVYGPGEvpgryRNVIPNFMYWALNGMPLPITGTGEETRDFTYVSDIV 231
                                       8844...555..777777888888888888887644333455666666677777888888888888888887665 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 !   36.0   0.0     3e-12   4.1e-09       2     108 ..      12     137 ..      11     191 .. 0.88
   2 ?   -3.0   0.0       2.2   3.1e+03     185     232 ..     226     270 ..     217     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3e-12
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE--- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAA 60 
                                       ++lvtG+ G +Gs+L k l+e g++ + +  +                  + ++ d+e++++++ e kpd v ++AA
  gi|488599589|ref|YP_007906060.1|  12 TVLVTGGAGCIGSNLCKVLSELGAKKVIILDDlsasykwnipvadniefvQGNILDEEKLKQVFYE-KPDYVFHLAA 87 
                                       68*******************998777664445899*****************************9.********** PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEG.GGS-S- CS
                     RmlD_sub_bind  61 ytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStD.yVFdGe 108
                                       + a  +  +++e +  vn  ++ ++ e+++ +++  +++ S+   V+ ++
  gi|488599589|ref|YP_007906060.1|  88 HFANQNSVEHPETDLMVNGLGTLKILEYCRLTDVSrVVYASSGcSVYGAQ 137
                                       ********************************985388888752355555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
                                       EHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHC CS
                     RmlD_sub_bind 185 sardlAevllqllekaaeekelagvyHlanegetswlefArailkeag 232
                                       ++ d+ + +l        +k++ + + la+e et   ++A+ i + +g
  gi|488599589|ref|YP_007906060.1| 226 YVSDIVDGTLRCGVV---KKAVGEAFNLASETETKIIDLANWINELTG 270
                                       555555555443322...334577888888888888888888877665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.1e-08     7e-05       2      68 ..      12      75 ..      11      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.1e-08
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealv 68
                                      +vlvtG+++ IG +++k l + Gak v++    ++    ++++   ++++ ++q+++ d+e++++++
  gi|488599589|ref|YP_007906060.1| 12 TVLVTGGAGCIGSNLCKVLSELGAKKVIILDDLSAS--YKWNIPV-ADNIEFVQGNILDEEKLKQVF 75
                                      79***********************99965555544..5666664.467**************9987 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   5.4e-07   0.00074       1     142 [.      11     135 ..      11     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.4e-07
                                       SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                                KR   1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77 
                                       +t+l+tGG+G +G  l++ l e ga+++++l   +a+ +    +i  +     ++e+v+  + d++++++++ e   
  gi|488599589|ref|YP_007906060.1|  11 ATVLVTGGAGCIGSNLCKVLSELGAKKVIILDDLSASYKW---NIP-V---ADNIEFVQGNILDEEKLKQVFYEKP- 79 
                                       689**************************99766332222...222.2...2367777777777777777776655. PP

                                       HSS---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH- CS
                                KR  78 eeppikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllg 142
                                              v+h A +++ ++ +e+ +++ + +       G+  + e+++ +++  +v+ SS  +++g
  gi|488599589|ref|YP_007906060.1|  80 -----DYVFHLAAHFAnQNSVEHPETDLMVNG-----LGTLKILEYCRLTDVSRVVYASSGCSVYG 135
                                       .....346666655541333333333333333.....35666666666666666666666666666 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 !   19.7   0.0   4.7e-07   0.00064       1     101 [.      17     132 ..      17     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.7e-07
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH..HHHCTTTCEEEE--TT-CCHHHHHH.TT-SEEEES---TCCH CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla..eleaeeglevvegdvtdvedlaeal.kgadaVvsalggggkd 74 
                                       G+ G +G+ l+k l + g  + +++  + +     +++ ++++e v+g+++d+e+l++++ +  d V+  +++ +++
  gi|488599589|ref|YP_007906060.1|  17 GGAGCIGSNLCKVLSELG-AKKVIILDDLSASYkwNIPVADNIEFVQGNILDEEKLKQVFyEKPDYVFHLAAHFANQ 92 
                                       899999*****9999996.5655666664433213577889*******************45669999999777774 PP

                                       HHH.............HHHHHHHHHHCT--EEEEEEETTT CS
                    NAD_binding_10  75 eeg.............aknivdaakeagvkRfvlvsaigv 101
                                       + +             + +i++ ++ ++v+R+v+ s+ ++
  gi|488599589|ref|YP_007906060.1|  93 NSVehpetdlmvnglgTLKILEYCRLTDVSRVVYASSGCS 132
                                       4445566778899999******************999654 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.47   6.5e+02       1      19 [.      15      33 ..      15      42 .. 0.73
   2 ?   12.7   0.0   3.8e-05     0.053      76     151 ..      66     146 ..      40     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.47
                                      EE-TTSHHHHHHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrt 19
                                      +TG+ G +G+ L + L + 
  gi|488599589|ref|YP_007906060.1| 15 VTGGAGCIGSNLCKVLSEL 33
                                      7*********998766554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.8e-05
                                       --HHHHHHH.HHH--EEEE--SS-...S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS-TTT CS
                     NAD_binding_4  76 Lseedlqel.aeevdviihsaAtv...nfdepykellrvNveGtrevlelakklkklkvllhvST..ayvngerege 146
                                       L+ee+l+++  e+ d ++h aA     n +e+ ++ l vN +Gt ++le ++ +     +++ S+  ++   +    
  gi|488599589|ref|YP_007906060.1|  66 LDEEKLKQVfYEKPDYVFHLAAHFanqNSVEHPETDLMVNGLGTLKILEYCRLTDVS-RVVYASSgcSVYGAQAPLP 141
                                       67788888878999*******97721145556667899**************77666.9999999766655555555 PP

                                       --SSS CS
                     NAD_binding_4 147 veekv 151
                                       ++e++
  gi|488599589|ref|YP_007906060.1| 142 LKEDF 146
                                       55555 PP

>> TrkA_N  TrkA-N 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      0.02       5      68 ..      18      84 ..      13      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                      S-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHH..HHTTSEEEES-TTSHHHHHHTTGGGESEEEE CS
                            TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkdeerveel..reeglevvvgdatdeevLeeagiekadavia 68
                                      G+G +G++l++ Lse g k+v++ d+  +  +     ++++e+v+g+  dee L++   ek d+v  
  gi|488599589|ref|YP_007906060.1| 18 GAGCIGSNLCKVLSElGAKKVIILDDLSASYKWNipVADNIEFVQGNILDEEKLKQVFYEKPDYVFH 84
                                      89*************998989999999988777622467799*************999999888865 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00037      0.51       5      42 ..       3      41 ..       1      50 [. 0.91
   2 ?   -0.3   0.0      0.77   1.1e+03     105     136 ..     145     176 ..     136     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                                      HHHS..TT-EEEEE.S-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH  5 kkleslkekkvlli.GaGemaelvakhLlakgvkkvvva 42
                                      + +e++++++vl+  GaG +++ ++k L++ g+kkv+++
  gi|488599589|ref|YP_007906060.1|  3 EMFEEYEGATVLVTgGAGCIGSNLCKVLSELGAKKVIIL 41
                                      57889999****9945*********************97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.77
                                       .EEEEE--SS-SB-TTGGGSTTCCCEEHHHHH CS
                      Shikimate_DH 105 plllvDiavPRdvepevaeledvrlytvDdLk 136
                                         + +D+  P  +++ ++el  ++ y++ +L+
  gi|488599589|ref|YP_007906060.1| 145 DFVSLDLDTPYQIHKLLGELYCNYFYNLYELQ 176
                                       55789**********************99987 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 ?   11.5   0.0   0.00013      0.17      28      64 ..       6      43 ..       1      51 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                      S-STTEEEEEE--.SHHHHHHHHHHHHCT-EEEEEEES CS
                     ELFV_dehydrog 28 dslegkrvaisGs.GnvgsyaallltelgakvvavsDs 64
                                      +++eg++v + G  G +gs+ ++ l+elgak v + D 
  gi|488599589|ref|YP_007906060.1|  6 EEYEGATVLVTGGaGCIGSNLCKVLSELGAKKVIILDD 43
                                      45788888776655*****************9999986 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7   0.00034      0.47      21      50 ..      13      43 ..       6      49 .. 0.86
   2 ?   -0.1   0.0      0.36     5e+02      89     123 ..      57      92 ..      44      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00034
                                      EEEE.--SHHHHHHHHHHHHHTTTEEEEEES CS
                                      xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 21 vllv.GaGglGsellknLalsGvgkltlvDn 50
                                      vl+  GaG +Gs+l+k L  +G +k+ + D+
  gi|488599589|ref|YP_007906060.1| 13 VLVTgGAGCIGSNLCKVLSELGAKKVIILDD 43
                                      555437**********************996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.36
                                       EEEEEES-CCG.CCS-HHHHTT-SEEEEESSSHHHH CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  89 eveavteritd.etvleellesvDlVvdalDniear 123
                                       ++e v+++i d e++ + ++e+ D+V++    ++ +
  gi|488599589|ref|YP_007906060.1|  57 NIEFVQGNILDeEKLKQVFYEKPDYVFHLAAHFANQ 92 
                                       789999999995558899*********998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2004.90
//
Query:       gi|488599590|ref|YP_007906061.1|  [L=392]
Description: Glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  132.2   0.1    6.9e-38  129.9   0.1    2.0  2  Glycos_transf_1  Glycosyl transferases group 1
    2.9e-29  102.2   0.0    4.3e-29  101.7   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.2e-26   92.9   0.0    5.7e-26   91.5   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.1e-16   61.7   0.0    1.4e-16   61.4   0.0    1.1  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      3e-10   40.3   0.0    7.2e-10   39.1   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
    1.2e-07   31.8   0.7    3.4e-07   30.4   0.3    1.9  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    0.00097   18.9   0.3        0.3   10.7   0.0    2.2  2  Glyco_transf_5   Starch synthase catalytic domain
      0.005   16.9   0.0      0.029   14.4   0.0    2.4  2  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
  ------ inclusion threshold ------
      0.043   12.4   4.8        1.8    7.0   0.7    2.7  2  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 ?   -0.5   0.0       0.4   7.9e+02     112     133 ..     116     137 ..      73     158 .. 0.80
   2 !  129.9   0.1   3.5e-41   6.9e-38       5     171 ..     199     363 ..     196     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.4
                                       HHHTT--EEEETTTTHCHHCHT CS
                   Glycos_transf_1 112 Amaaglpviasnaggpaevvkd 133
                                       A ++g+p +  ++g ++ ++++
  gi|488599590|ref|YP_007906061.1| 116 AKKYGVPYVLQAHGSLPRMIAK 137
                                       5566777777776666666654 PP

  == domain 2  score: 129.9 bits;  conditional E-value: 3.5e-41
                                       HHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..STTHHHHHHHHHHHCTTCGGGEEEC CS
                   Glycos_transf_1   5 krkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.ngeeekelkklaeelelsdnviflge 80 
                                        ++k+++  +k+iil++gr+ k+Kg+d lik+f +l+ + +++v+lviaG +  ++++l +l+  l++s+ v f+g+
  gi|488599590|ref|YP_007906061.1| 199 RKFKEKFHINKRIILFLGRIHKRKGIDFLIKSFFRLNIE-KKDVVLVIAGpDDGHKDKLIELVNRLKISNSVYFVGY 274
                                       5788888899**************************997.***********99999********************* PP

                                       CHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHH CS
                   Glycos_transf_1  81 vsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklle 157
                                       ++  d  + +  a ++v+psi E fG+v+ EA+ +g+pvia++ +g+ e++k+   G+lv  +n  +l+e+i+ lle
  gi|488599590|ref|YP_007906061.1| 275 LD--DNLSAYVDAEVLVYPSIHEIFGLVPFEAIMCGTPVIATDDCGCGEIIKETNCGFLVRYGNENDLKEKIKILLE 349
                                       *9..9999999****************************************************************** PP

                                       SHHHHHHHHHHHHH CS
                   Glycos_transf_1 158 deelrerlgenark 171
                                       ++e  e++ +++++
  gi|488599590|ref|YP_007906061.1| 350 KPEIGEKMVKKGKR 363
                                       *******9999975 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   0.0   2.1e-32   4.3e-29       1     169 [.      16     190 ..      16     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 2.1e-32
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.....elvvrvprvplpllkrl.lrslaflrrlrrllkre 71 
                                       +GG  r+++eL+++L ++GheVtv+t ++  +  +       ++++rv ++p +++k +  +++  ++++  ++k+ 
  gi|488599590|ref|YP_007906061.1|  16 YGGPVRVAYELSKRLVEKGHEVTVYTTDTLSKDSRVNkkvqeIDGIRVQYFPNLSNKLAwNHNIFLSPSMISIVKKR 92 
                                       69***********************6555444444444679999999999998877765156778889999999999 PP

                    Glyco_transf_4  72 ..kpDvvHahspaal..gaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeat 144
                                         ++D++H h + ++  ++++ ++++ +g+p+Vl +Hg+ +  +  a++++++ + + + +++l+ a +viavS+a+
  gi|488599590|ref|YP_007906061.1|  93 iqNFDIIHMHEYRTFqnIVVYNYAKK-YGVPYVLQAHGSLP--RMIAKQNLKKLFDFTWGYKILNDASKVIAVSKAE 166
                                       99*********988754677777776.*************8..5666777778888888899*************** PP

                    Glyco_transf_4 145 adelrerygvppekitVipnGvDle 169
                                        +++++ +g++++ki++ipnG D++
  gi|488599590|ref|YP_007906061.1| 167 VKQYKH-MGISKNKIVTIPNGLDVD 190
                                       ******.****************98 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.5     7e+03      90     109 ..     116     135 ..      69     142 .. 0.67
   2 !   91.5   0.0   2.9e-29   5.7e-26       2     133 ..     210     349 ..     209     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.5
                                       HHHTT-EEEE-TGGGTTT-- CS
                   Glyco_trans_1_4  90 amaaglpvVatdvggiaevv 109
                                       a  +g+p V  + g +++++
  gi|488599590|ref|YP_007906061.1| 116 AKKYGVPYVLQAHGSLPRMI 135
                                       34577787777776667766 PP

  == domain 2  score: 91.5 bits;  conditional E-value: 2.9e-29
                                       EEEEEES---GG.GTHHHHHHHHHHHH..H.HEEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllr.kk.dvrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaa 73 
                                       ++ilf+Gr+ +++kg+d+l++ + +l  +k dv lvi+G ++  +++l el++  +++++v f+G+++d  +++ +a
  gi|488599590|ref|YP_007906061.1| 210 RIILFLGRI-HKRKGIDFLIKSFFRLNiEKkDVVLVIAGPDDgHKDKLIELVNrlKISNSVYFVGYLDDNLSAYVDA 285
                                       68*******.566**********555535537*******766766788888876889999*******99999999** PP

                                       SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                        v+v Ps  e fgl+  Ea ++g+pv+atd  g+ e++   + g+lv  g++++l e+i  Lle
  gi|488599590|ref|YP_007906061.1| 286 EVLVYPSihEIFGLVPFEAIMCGTPVIATDDCGCGEIIkeTNCGFLVRYGNENDLKEKIKILLE 349
                                       ********99*******************655999*99844669***************99997 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 !   61.4   0.0   6.9e-20   1.4e-16       1     160 []      17     186 ..      17     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 6.9e-20
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgape.....leedgvrvhrlp.....vprrpspladlaalralrrll 67 
                                       gG  r+++el+++L++ GheVtv+t++   ++ +     +e dg+rv  +p     + +++  + +++++  ++  +
  gi|488599590|ref|YP_007906061.1|  17 GGPVRVAYELSKRLVEKGHEVTVYTTDTLSKDSRvnkkvQEIDGIRVQYFPnlsnkLAWNHNIFLSPSMISIVKKRI 93 
                                       8999*********************5444443332222344688888887764444444445555666666666665 PP

                   Glyco_trans_4_4  68 rqrrerpdvvhahspt...aglaarlarrrrgiplvvtlhglllrrg.sgavrrly.ralerrllrradavlvvsea 139
                                           +++d++h h++       +   a+ + g+p+v+ +hg l+r   +  ++ l+  ++ + +l+ a  v++vs a
  gi|488599590|ref|YP_007906061.1|  94 ----QNFDIIHMHEYRtfqNIVVYNYAK-KYGVPYVLQAHGSLPRMIaKQNLKKLFdFTWGYKILNDASKVIAVSKA 165
                                       ....**********86354558889999.************887644555566777456799*************** PP

                   Glyco_trans_4_4 140 eaeelralgvpadrvvvvpng 160
                                       e++++  +g+  +++v++png
  gi|488599590|ref|YP_007906061.1| 166 EVKQYKHMGISKNKIVTIPNG 186
                                       ********************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 !   39.1   0.0   3.6e-13   7.2e-10       5      90 ..     291     378 ..     284     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.6e-13
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervla 79 
                                       ps +e + l+ fEa +cG++++++d  g +e++++ + ++l++  ++++l eki+ ll+ pe  +++ +++++ + +
  gi|488599590|ref|YP_007906061.1| 291 PSIHEIFGLVPFEAIMCGTPVIATDDCGCGEIIKETNCGFLVRygNENDLKEKIKILLEKPEIGEKMVKKGKRYIVE 367
                                       8889999********************************************************************** PP

                   Glyco_trans_1_2  80 ehtydhraeql 90 
                                       ++ +++ a+++
  gi|488599590|ref|YP_007906061.1| 368 NLAWNKVAKKM 378
                                       *******9987 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 !   30.4   0.3   1.7e-10   3.4e-07      14     137 ..      24     161 ..      13     163 .. 0.70
   2 ?   -2.1   0.0       1.8   3.6e+03      20      41 ..     236     257 ..     215     274 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.7e-10
                   Glyco_trans_4_2  14 lrlakeLakrgyeVhvitpkkga......kdeleaegihvhrlkvdrkgpleylk.a..f.klkklikki..kPDvv 78 
                                       ++l k L ++g+eV+v t ++ +      k+++e +gi+v+ ++ + + +l +   +    ++++++kk+  ++D++
  gi|488599590|ref|YP_007906061.1|  24 YELSKRLVEKGHEVTVYTTDTLSkdsrvnKKVQEIDGIRVQYFP-NLSNKLAWNHnIflSpSMISIVKKRiqNFDII 99 
                                       567899***********987654111134556667777777776.3333333332232245999999995449**** PP

                   Glyco_trans_4_2  79 hahyakpy.gllgslaarlsgvipvvlsvwGldv..lkfpkksklkklllkl.alkkatkvis 137
                                       h+h+     +++ +  a++ g +p+vl ++G+    +++++ +kl+ ++  +  l+ a+kvi+
  gi|488599590|ref|YP_007906061.1| 100 HMHEYRTFqNIVVYNYAKKYG-VPYVLQAHGSLPrmIAKQNLKKLFDFTWGYkILNDASKVIA 161
                                       ***996655677777788888.9*********7676888888886666666545677777776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                   Glyco_trans_4_2  20 LakrgyeVhvitpkkgakdele 41 
                                       + k+++  +++ p++g+kd+l+
  gi|488599590|ref|YP_007906061.1| 236 IEKKDVVLVIAGPDDGHKDKLI 257
                                       4455556666667777766665 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 !   10.7   0.0   0.00015       0.3       2      56 ..       3      58 ..       2      75 .. 0.73
   2 !    5.9   0.1    0.0044       8.9     116     170 ..      79     128 ..      63     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                    Glyco_transf_5  2 ilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry.gaikeekkeleev 56
                                      il v + + p    GG  +v+++L+k L ++gh+v+v + +  ++ ++ +k+++e+
  gi|488599590|ref|YP_007906061.1|  3 ILQVIPYFVPAWGYGGPVRVAYELSKRLVEKGHEVTVYTTDTlSKDSRVNKKVQEI 58
                                      6666666677777888899*******************999844444433444444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0044
                    Glyco_transf_5 116 alfsraalelleklgw.kpdvihahDWhtalvpallkelykerglfkkiktvftiH 170
                                       +++s  ++ +++k     +d+ih+h + t    ++++ ++k+      +++v+  H
  gi|488599590|ref|YP_007906061.1|  79 IFLSPSMISIVKK-RIqNFDIIHMHEYRTFQNIVVYNYAKKY-----GVPYVLQAH 128
                                       4788889999999.5526**********99887777776543.....378888777 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 !   14.4   0.0   1.5e-05     0.029       6     113 ..      14     122 ..       9     157 .. 0.61
   2 ?   -2.2   0.0       1.9   3.8e+03      99     120 ..     306     327 ..     299     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                       -SSHHHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHH.HHCCT-EEEE---G...........HCTT..CHHHHCCH CS
                   Glyco_transf_28   6 gGTgGhvfPalAlakeLkkegheVrylgtkrgleerl.veeaglefepiage...........klrrklspknlkei 70 
                                        G gG v  a  l k+L ++gheV+ + t++ l +   v ++  e+  i ++            ++  lsp++++ +
  gi|488599590|ref|YP_007906061.1|  14 WGYGGPVRVAYELSKRLVEKGHEVT-VYTTDTLSKDSrVNKKVQEIDGIRVQyfpnlsnklawNHNIFLSPSMISIV 89 
                                       578999*******************.777777766663566666888899994444444444333332344444444 PP

                                       HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHCCCCCHCCCTTH CS
                   Glyco_transf_28  71 lkvlkavvkakkilkeakpdavvgtggyvslpaviaaplarip 113
                                                 kk ++++ + ++ ++ ++++++++  a++ ++p
  gi|488599590|ref|YP_007906061.1|  90 ----------KKRIQNFDIIHMHEYRTFQNIVVYNYAKKYGVP 122
                                       ..........444444444444444444444444444444443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                                       CCHCCCCCHCCCTTHCCCCCHC CS
                   Glyco_transf_28  99 vslpaviaaplaripviihEqn 120
                                         + +via+  ++ + ii E n
  gi|488599590|ref|YP_007906061.1| 306 MCGTPVIATDDCGCGEIIKETN 327
                                       5678999******999999988 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.7   0.00092       1.8     226     273 ..     161     212 ..     153     237 .. 0.68
   2 ?    6.0   0.2    0.0018       3.5     471     509 ..     287     325 ..     267     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00092
                                       ESSHHHHHHHHHHSS---SEE-.---B-GGGT--TTT...HHHHHHHHHHHH CS
                      Glycogen_syn 226 tvseitaleaehllkrkpdvvl.pnGlnvkkfsalhe...fqnlhalkkeki 273
                                       +vs+    + +h+   k  +v+ pnGl+v kf+ l e   f++   ++k  i
  gi|488599590|ref|YP_007906061.1| 161 AVSKAEVKQYKHMGISKNKIVTiPNGLDVDKFKVLPEnrkFKEKFHINKRII 212
                                       67777777889999999988855***********988222444444444444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0018
                                       EEE---SSBSS-HHHHHHHHTT--EEEETTBHHHHHHHH CS
                      Glycogen_syn 471 lGvfpsyyepwGytpaectvmGipsvttnlsGfGcfmee 509
                                       + v+ps +e +G  p e  + G p ++t+  G G  ++e
  gi|488599590|ref|YP_007906061.1| 287 VLVYPSIHEIFGLVPFEAIMCGTPVIATDDCGCGEIIKE 325
                                       559*****************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2269.01
//
Query:       gi|488599591|ref|YP_007906062.1|  [L=335]
Description: Glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-16   59.8   0.2    5.1e-16   58.7   0.2    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
      6e-12   46.2   0.0    9.7e-12   45.5   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00023   21.2   0.0       0.04   13.9   0.0    3.3  3  Glyco_transf_4   Glycosyltransferase Family 4
     0.0055   17.1   0.0      0.015   15.6   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.028   14.2   0.0    1.6  1  Rbsn             Rabenosyn Rab binding domain
       0.11   12.1   0.0       0.22   11.1   0.0    1.4  1  Glycos_transf_N  3-Deoxy-D-manno-octulosonic-acid transferase


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 !   58.7   0.2   1.7e-19   5.1e-16       3     163 ..     155     305 ..     154     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.7e-19
                                       HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEE CS
                   Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflg 79 
                                       +k r +++++e+k +il vg l+k+ +++ l ++++          +++i+   e++k  k+ ++ l+    +if g
  gi|488599591|ref|YP_007906062.1| 155 KKLRVRYNIDEEKFTILHVGHLTKKRNLKILGELARM-------GNQVIIVS-SEYLKVEKNIIQTLQKTGCIIFRG 223
                                       6788899***************************994.......34556665.7*********************** PP

                                       CCHSSSHHHHHHCESEEEEEESS...BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHH CS
                   Glycos_transf_1  80 evsredleellknadifvlpsis...EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeair 153
                                       + +   +ee+++++d++++p        f+++++EAma++lpv++ +  g+  ++++ge Gl++ ++   +++++++
  gi|488599591|ref|YP_007906062.1| 224 YFE--HIEEFYQMSDCYIFPVLEgdtILFPLSVIEAMACNLPVLTRKFDGL-SIFNEGE-GLIFVEK-ETEIIQGVE 295
                                       **9..9**************87776667*******************9996.6999999.9999999.99******* PP

                                       HHHHSHHHHH CS
                   Glycos_transf_1 154 klledeelre 163
                                       k+ ++++ r 
  gi|488599591|ref|YP_007906062.1| 296 KIKKNGDIRI 305
                                       *****95554 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   3.2e-15   9.7e-12       3     129 ..     169     295 ..     167     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.2e-15
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHH.TT-T.T..EEEE---THHHHHHHH-SEE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleela.agleer..veftGfvedlaellaaadvf 76 
                                       +il+vG l+ + k+   +l +++++ +   +++iv ++    ++e+ + + l+++  ++f G+ e ++e+++ +d++
  gi|488599591|ref|YP_007906062.1| 169 TILHVGHLT-K-KRNLKILGELARMGN---QVIIVSSEYL--KVEKNIiQTLQKTgcIIFRGYFEHIEEFYQMSDCY 238
                                       788888883.4.444444455555553...5889995433..344333233333335*******99*********** PP

                                       EE--.--....-SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHH CS
                   Glyco_trans_1_4  77 vaPs.eg....fglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeail 129
                                       ++P  eg    f+l+++Eama+ lpv + +  g   +  + +gl++  +++ ++++ ++
  gi|488599591|ref|YP_007906062.1| 239 IFPVlEGdtilFPLSVIEAMACNLPVLTRKFDG-LSIFnEGEGLIFV-EKETEIIQGVE 295
                                       *****8555559*******************99.4545544576653.24566666555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.3e-05      0.04     115     169 ..      94     144 ..      36     145 .. 0.78
   2 ?   -0.6   0.0      0.38   1.1e+03     144     163 ..     153     172 ..     148     177 .. 0.69
   3 ?    2.6   0.0      0.04   1.2e+02      13      36 ..     186     209 ..     180     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                    Glyco_transf_4 115 rlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                        + p+ + ++++ + l r+ d ++a S++ ++ +++ +g++      +pnGvD e
  gi|488599591|ref|YP_007906062.1|  94 MSTPYPKDINRFIKSLPRKPDLILAQSNTSKRMFKS-LGLK---TIYVPNGVDFE 144
                                       4567888899999999********************.**76...699******87 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                    Glyco_transf_4 144 tadelrerygvppekitVip 163
                                       +++ lr ry++++ek t+++
  gi|488599591|ref|YP_007906062.1| 153 LKKKLRVRYNIDEEKFTILH 172
                                       56667777777777777765 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.04
                    Glyco_transf_4  13 raLarrGheVtvvtpgddgpleee 36 
                                        +Lar+G +V +v++++ + + + 
  gi|488599591|ref|YP_007906062.1| 186 GELARMGNQVIIVSSEYLKVEKNI 209
                                       68***********99987766655 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 !   15.6   0.0   5.1e-06     0.015      15      89 ..     254     322 ..     247     325 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-06
                   Glyco_trans_1_2  15 lfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydhraeq 89 
                                       + Ea+ac+ ++lt + +gl  +f++g+ +i++e + e+++ +++  +n +    i++a r++  + +++++ a++
  gi|488599591|ref|YP_007906062.1| 254 VIEAMACNLPVLTRKFDGLS-IFNEGEGLIFVEKETEIIQGVEKIKKNGD----IRIATRRK-VTPYSWKNIAQR 322
                                       78************777765.77899999999***********9854433....44555555.345566666665 PP

>> Rbsn  Rabenosyn Rab binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.3e-06     0.028      16      36 ..      25      45 ..      20      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.3e-06
                              Rbsn 16 AkkarrfDEvatLeeNLkELq 36
                                      Ak+  ++D++++L++N+kE++
  gi|488599591|ref|YP_007906062.1| 25 AKELSKYDDLDILKANIKEIK 45
                                      88889**************97 PP

>> Glycos_transf_N  3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.4e-05      0.22     132     165 ..     101     134 ..      94     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.4e-05
                   Glycos_transf_N 132 rfkallrsllskfdlilaqseedaerlralgape 165
                                        ++++++sl +k dlilaqs+++++ +++lg++ 
  gi|488599591|ref|YP_007906062.1| 101 DINRFIKSLPRKPDLILAQSNTSKRMFKSLGLKT 134
                                       46889**************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1923.18
//
Query:       gi|488599592|ref|YP_007906063.1|  [L=220]
Description: Thymidylate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-15   56.4   1.1    1.3e-08   34.8   0.1    2.2  2  Thymidylate_kin  Thymidylate kinase
     0.0004   20.9   0.0     0.0012   19.3   0.0    1.8  2  AAA_18           AAA domain
    0.00072   19.5   0.0     0.0024   17.8   0.0    2.0  1  NACHT            NACHT domain
     0.0027   18.1   0.1      0.009   16.4   0.0    1.9  3  AAA              ATPase family associated with various cellul
     0.0034   17.3   0.0      0.006   16.5   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
     0.0035   17.2   0.0     0.0061   16.5   0.0    1.3  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0071   16.6   0.1      0.017   15.4   0.0    1.7  2  AAA_22           AAA domain
     0.0094   15.9   0.0      0.015   15.2   0.0    1.4  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.046   13.8   0.0    1.8  2  Torsin           Torsin
      0.018   14.3   0.0       0.03   13.5   0.0    1.4  1  NB-ARC           NB-ARC domain
      0.021   15.1   0.3      0.065   13.5   0.0    1.9  2  AAA_28           AAA domain
      0.031   14.5   0.0      0.053   13.7   0.0    1.4  1  AAA_33           AAA domain
      0.031   14.7   0.1      0.052   13.9   0.0    1.5  2  AAA_16           AAA ATPase domain
      0.076   13.4   0.0       0.16   12.4   0.0    1.5  1  RNA_helicase     RNA helicase
        0.1   12.0   0.0       0.15   11.4   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
       0.16   12.4   0.1         11    6.5   0.0    2.5  3  AAA_17           AAA domain
       0.17   10.8   0.2       0.27   10.2   0.2    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   2.2e-07   0.00023       2      26 ..      13      37 ..      12      85 .. 0.84
   2 !   34.8   0.1   1.2e-11   1.3e-08      57     183 ..      91     212 ..      63     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-07
                                      EESTTSSHHHHHHHHHHHHHHTTE. CS
                   Thymidylate_kin  2 EGlDGaGKttqaellkerlkeegik 26
                                       G+DG+GKtt a+ll+  l+e+gi 
  gi|488599592|ref|YP_007906063.1| 13 TGIDGTGKTTLAKLLVTSLREKGID 37
                                      5**********************97 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 1.2e-11
                                       HHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-HHHHHHHHHT.TTTTTCHHHHHHGGGTTS...E-SEEEEEESSHH CS
                   Thymidylate_kin  57 eallfaadriehleekikpalkqgktvivdRylfSslaYqga.kegvdldlvlslnedvll...kPdltflldvdpe 129
                                         l ++ d i ++  kik  l  gk +++dRy++ +++ + a   +   + +l l ++ +l   +Pd++fl+d ++e
  gi|488599592|ref|YP_007906063.1|  91 YTLILLCDYIIQVILKIKIPLMFGKNIVCDRYIYDTIITDIAiDMNYSEEYILDLLKKCFLlipEPDFVFLIDAPEE 167
                                       566777788899999**********************99988555667788999999988889************** PP

                                       HHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHH CS
                   Thymidylate_kin 130 valkRlakrdeldeeeeeqldflrkvrerylelakederiliidasksieevhe 183
                                       +a+ R  +  +        +++l+  r+ yl++ k ++ ++++d +k+i+e+ +
  gi|488599592|ref|YP_007906063.1| 168 IAYSRKDDVPS--------IEYLKARRQIYLKIGK-KCCMFVLDGTKNIKELLS 212
                                       ***99877666........99999**********7.************999865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06    0.0012       1      27 [.      10      34 ..      10      86 .. 0.75
   2 ?   -1.1   0.0       2.5   2.7e+03      96     110 ..     154     173 ..     114     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvn 27
                                      I+ tG+ G+GKttlak L  +l   ++
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSL--REK 34
                                      99****************6665..333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                            AAA_18  96 k.....vvLtaspeelleRl 110
                                             + ++a++e+ + R 
  gi|488599592|ref|YP_007906063.1| 154 PepdfvFLIDAPEEIAYSRK 173
                                       03444477788888888885 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06    0.0024       3      85 ..      10      93 ..       9     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelpe 81
                                      ++ +G  G GKTtL++ l++ ++e+  ++    +v+   + ++s++   +++ ++lf   ++++++ +e     l  ++
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLREKGIDA---HYVYARLVPRISKPV--MTIGRFLFLRNKDISKNYTE----YLHSKK 79
                                      68899*********************999...688888888888864..68999999999999999999....444444 PP

                                      CEE..........E CS
                             NACHT 82 rlL..........l 85
                                      rlL          l
  gi|488599592|ref|YP_007906063.1| 80 RLLrcqivskiytL 93
                                      44444433333341 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.5e-06     0.009       1      23 [.      10      32 ..      10      90 .. 0.77
   2 ?   -2.2   0.0         5   5.3e+03      58      74 ..     155     172 ..     135     195 .. 0.67
   3 ?   -1.9   0.0       3.9   4.1e+03      35      53 ..     196     214 ..     159     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.5e-06
                                      EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA  1 vllyGppGtGKTllakavakelg 23
                                      ++++G  GtGKT+lak ++++l 
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLR 32
                                      689****************9984 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5
                                       TS.EEEEEETGGGHHHHH CS
                               AAA  58 kp.silfiDEidalaksr 74 
                                       +p  +++iD  +++a sr
  gi|488599592|ref|YP_007906063.1| 155 EPdFVFLIDAPEEIAYSR 172
                                       444677777777777766 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.9
                                       SSSSTTHHHHHHHHHHHHH CS
                               AAA  35 lskyvgesekkirelfkea 53 
                                       + ++v ++ k+i+el++e+
  gi|488599592|ref|YP_007906063.1| 196 CCMFVLDGTKNIKELLSEL 214
                                       3356777777777777665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.7e-06     0.006       2      34 ..       7      39 ..       6      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.7e-06
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EE CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvy 34
                                      g+ + +tG+ g+GK+t+a+ l ++L+ekgi + 
  gi|488599592|ref|YP_007906063.1|  7 GFFICFTGIDGTGKTTLAKLLVTSLREKGIDAH 39
                                      68899************************8764 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   5.8e-06    0.0061       2      29 ..      10      37 ..       9      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-06
                              MobB  2 lgivgksgsGKTtLleklipelkarglr 29
                                      ++++g  g+GKTtL + l++ l+++g+ 
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLREKGID 37
                                      799**********************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.7e-05     0.017       7      32 ..       9      34 ..       4      93 .. 0.80
   2 ?   -2.0   0.0       3.8     4e+03     109     135 ..     179     209 ..     141     215 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldee 32
                                      +++ tG  GtGKTtl++ l+ +l e 
  gi|488599592|ref|YP_007906063.1|  9 FICFTGIDGTGKTTLAKLLVTSLREK 34
                                      7899****************999543 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.8
                            AAA_22 109 leeLrsllnl....srkgvqliLvGtpelrk 135
                                       +e+L+ +  +    ++k + ++L Gt ++ +
  gi|488599592|ref|YP_007906063.1| 179 IEYLKARRQIylkiGKKCCMFVLDGTKNIKE 209
                                       4444444333344444444455555555544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.015       2      39 ..      10      47 ..       9      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                      ++ TG  G+GKtTl k ++  l+++g+  + +y++ v 
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLREKGIDAHYVYARLVP 47
                                      578***********************999888877665 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-05     0.046      55      88 ..       9      42 ..       3      55 .. 0.89
   2 ?   -2.3   0.0       4.4   4.6e+03      69      77 ..      82      90 ..      60     110 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEE CS
                            Torsin 55 vlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvk 88
                                       + f G  GtGk  +a++++  l ++G+ ++yv 
  gi|488599592|ref|YP_007906063.1|  9 FICFTGIDGTGKTTLAKLLVTSLREKGIDAHYVY 42
                                      5889****************************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.4
                                      HHHHHHHHH CS
                            Torsin 69 vaeiiaenl 77
                                      +  +i+ ++
  gi|488599592|ref|YP_007906063.1| 82 LRCQIVSKI 90
                                      223333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.8e-05      0.03      18     124 ..       5     110 ..       1     119 [. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                                       SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS.-STTS. CS
                            NB-ARC  18 lqslvvalvGmgGvGKttlakqilnksdeveg.rFdsvawvvvsktdkseeiletilkeLslseddleek.eeves. 91 
                                        + +++ + G  G GKttlak  + ++ e       ++a +v      +++ + ti + L l+++d+++  +e  + 
  gi|488599592|ref|YP_007906063.1|   5 RGGFFICFTGIDGTGKTTLAKLLVTSLREKGIdAHYVYARLV----PRISKPVMTIGRFLFLRNKDISKNyTEYLHs 77 
                                       56699*****************99996665442222333332....2233333347777777777776541344444 PP

                                       HHHHHHHHCCCT.TEEEEEEEE-SHHHH.....H CS
                            NB-ARC  92 lkrklvrlLltk.rfllvlDDVweeedwdkigvv 124
                                       +kr l+  + +k  +l++l D   ++ + ki+++
  gi|488599592|ref|YP_007906063.1|  78 KKRLLRCQIVSKiYTLILLCDYIIQVIL-KIKIP 110
                                       4444555566666667777665555555.56665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.2e-05     0.065       2      25 ..      10      37 ..       9      54 .. 0.75
   2 ?   -1.1   0.1       1.8   1.9e+03      80      87 ..     121     128 ..     114     195 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                            AAA_28  2 ivitGgestGKTtlleaLa....argyp 25
                                      i++tG  +tGKTtl++ L     ++g+ 
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVtslrEKGID 37
                                      9**************9987433233554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                            AAA_28  80 rglldtla 87 
                                       r + dt++
  gi|488599592|ref|YP_007906063.1| 121 RYIYDTII 128
                                       44444443 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     5e-05     0.053       2      39 ..      10      47 ..       9      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg 39
                                      + + G  G+GK+tla+ l+  l    ++  +++ rl++
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLREKGIDAHYVYARLVP 47
                                      5689**************99998888888887777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.9e-05     0.052      27      61 ..      10      46 ..       2      92 .. 0.83
   2 ?   -2.8   0.0         7   7.4e+03     120     143 ..     143     164 ..     126     188 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekd..ggiflrgkcd 61
                                      + ++G  G+GK++l++ l ++l+++  ++++++++ +
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLREKgiDAHYVYARLV 46
                                      668999*******************554666776655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7
                            AAA_16 120 lellkrllallsrderplvlvlDd 143
                                       l+llk+++ l+++  + +v+++D 
  gi|488599592|ref|YP_007906063.1| 143 LDLLKKCFLLIPE--PDFVFLIDA 164
                                       5556666644444..337777774 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   0.00015      0.16       1      36 [.      10      43 ..      10      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                      i+++G  g+GK+tlak L+++l +k   + ++ vy+
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLREKG--IDAHYVYA 43
                                      7899****************999776..44456665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.15       4      40 ..      10      46 ..       9      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddesl 40
                                      + +tG+  +GK+t+ak L + l+e++++ +++    +
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLREKGIDAHYVYARLV 46
                                      789*************************999976666 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.01        11       1      19 [.      13      31 ..      13      44 .. 0.83
   2 ?    3.3   0.0     0.095     1e+02      89     118 ..     143     172 ..     119     179 .. 0.68
   3 ?   -2.3   0.0       5.3   5.6e+03      58      96 ..     185     218 ..     172     219 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                                      EE-TTSSHHHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklveky 19
                                      +G+ G GK+t+++ lv  +
  gi|488599592|ref|YP_007906063.1| 13 TGIDGTGKTTLAKLLVTSL 31
                                      699*********9999765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.095
                                       EESSHHHHHHHH..SEEEEEE--HHHHHHH CS
                            AAA_17  89 ldglpkevleelkpdaiilleadpeeiler 118
                                       ld l+k +l   +pd+++l++a++e  ++r
  gi|488599592|ref|YP_007906063.1| 143 LDLLKKCFLLIPEPDFVFLIDAPEEIAYSR 172
                                       44444444455589********99855544 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHH CS
                            AAA_17  58 qkeaaekiaeeakkkgvlvdghprikeqagfldglpkev 96 
                                       ++++  ki ++++   +++dg   i   +++l++l++ev
  gi|488599592|ref|YP_007906063.1| 185 RRQIYLKIGKKCC--MFVLDGTKNI---KELLSELESEV 218
                                       4445555666655..3888887665...44666666665 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   0.2   0.00025      0.27      32      57 ..      10      35 ..       2      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                                      EEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB 32 vGltGvPGaGkstlvealglelrrrG 57
                                      + +tG+ G+Gk tl + l+++lr++G
  gi|488599592|ref|YP_007906063.1| 10 ICFTGIDGTGKTTLAKLLVTSLREKG 35
                                      789*********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1405.52
//
Query:       gi|488599593|ref|YP_007906064.1|  [L=354]
Description: hypothetical protein Asulf_00035 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   18.6   0.0     0.0024   17.6   0.0    1.6  1  NTP_transf_5  Uncharacterised nucleotidyltransferase
  ------ inclusion threshold ------
       0.38   10.6   2.3        1.9    8.4   0.1    3.1  4  CDC4_D        Cell division control protein 4 dimerisation do


Domain annotation for each model (and alignments):
>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-07    0.0024      95     248 ..      99     263 ..      50     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-07
                      NTP_transf_5  95 gDiDllvk..redldraeelLeelGyelesdgsekhevyyre...............kkgveielhwrllppesprl 154
                                       +D+D+l+   +++++ + e L++ Gy   ++++++  vy  +                 +  i+l  +++    + +
  gi|488599593|ref|YP_007906064.1|  99 SDVDVLFFcsENKYRWIIEQLLNRGYYKIGEAPNQVVVYDLRggyenidkrtvggkqGGKYYIDLYKEVSAS--YII 173
                                       7888887544888999**********887774777666666689999999999998555677********65..777 PP

                      NTP_transf_5 155 epdfddlleerarpveiggksilvlspedlllylalHlakhfwnrglgLrwlvDiaallrk..lkdeldweallara 229
                                       + d d+l +  +++++i++ +++vl pe +l ++++H     +     L  l+D ++ l    +++  +   + ++ 
  gi|488599593|ref|YP_007906064.1| 174 YLDKDKLKN-YVTEIRIENEKVKVLKPEAELAVVLTHSIIPEL-----LFTLADYYTTLYYlkNMNRKEISSFTSIF 244
                                       777666665.59**************************98888.....88999998877762234455566677999 PP

                      NTP_transf_5 230 relglrralllaltlakel 248
                                       re ++++a++++l ++k+l
  gi|488599593|ref|YP_007906064.1| 245 RENNILTAAQASLSIIKRL 263
                                       9999999999999998886 PP

>> CDC4_D  Cell division control protein 4 dimerisation 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      13      26 ..      74      87 ..      66      89 .. 0.51
   2 ?    8.4   0.1   0.00021       1.9      30      48 ..     229     247 ..     226     258 .. 0.91
   3 ?   -0.1   0.1     0.094   8.5e+02      39      48 ..     287     296 ..     275     297 .. 0.67
   4 ?   -3.1   0.0      0.83   7.5e+03       8      28 ..     328     348 ..     324     348 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                            CDC4_D 13 lstsLsesnyknLi 26
                                      +s+ L+e    + i
  gi|488599593|ref|YP_007906064.1| 74 ISKVLNELTEEYVI 87
                                      45555555555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00021
                            CDC4_D  30 LsnlnRseLSDlntLikdn 48 
                                       L n+nR+e+S++ +  ++n
  gi|488599593|ref|YP_007906064.1| 229 LKNMNRKEISSFTSIFREN 247
                                       78**********9877665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.094
                            CDC4_D  39 SDlntLikdn 48 
                                       S +n+L+k+n
  gi|488599593|ref|YP_007906064.1| 287 SEINNLVKNN 296
                                       4455555555 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 0.83
                            CDC4_D   8 elitnlstsLsesnyknLiFk 28 
                                       ++i + + +L    +kn+i++
  gi|488599593|ref|YP_007906064.1| 328 QIIYMSNPRLANWVIKNIIWR 348
                                       566677777888888999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2371.47
//
Query:       gi|488599594|ref|YP_007906065.1|  [L=370]
Description: GDP-mannose 4,6-dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     1e-140  468.9   0.0   1.2e-140  468.7   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      3e-69  233.2   0.0    3.7e-69  232.8   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.9e-08   33.8   0.0    2.6e-08   33.3   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    4.1e-06   26.1   0.0    6.2e-06   25.6   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0011   18.1   0.0     0.0015   17.6   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0011   18.2   0.0     0.0027   16.9   0.0    1.7  1  NAD_binding_4    Male sterility protein
     0.0041   17.0   0.0     0.0075   16.2   0.0    1.6  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.052   13.1   0.0      0.094   12.3   0.0    1.5  1  NmrA             NmrA-like family
      0.068   12.6   0.0       0.68    9.4   0.0    2.2  2  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.7   0.0  5.8e-144  1.2e-140       1     332 []       5     343 ..       5     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 468.7 bits;  conditional E-value: 5.8e-144
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       LiTG++G++Gsyl+e+Ll+k+y+v+g++rr+ssfnt+ri+h+ +   ++  e++ +++gD+tD++sl+++l+++qpd
  gi|488599594|ref|YP_007906065.1|   5 LITGVTGQDGSYLVEFLLNKNYKVYGVIRRASSFNTSRIDHIIE---FHSPEKFDWFRGDMTDETSLIKILEKIQPD 78 
                                       9*****************************************96...67789************************* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       e+ynLAAqshV+vsfe P yt++v ++GtlrLLea+++lgl  ++++yqaS+sE++G+    pq+E+tpf+P+sPYa
  gi|488599594|ref|YP_007906065.1|  79 EIYNLAAQSHVQVSFEVPVYTFDVVATGTLRLLEAVKNLGL--DIKIYQASSSEMFGSSP-PPQNEETPFNPKSPYA 152
                                       ****************************************9..6**************97.9*************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       +aK++a++++vnyreayg+++ ngilfnhesprrgetfvtrkitrav+ria g q++l+lG ldakRdwg++ +yv+
  gi|488599594|ref|YP_007906065.1| 153 IAKVAAYHLCVNYREAYGMWIANGILFNHESPRRGETFVTRKITRAVSRIAFGVQDKLVLGYLDAKRDWGYAPEYVK 229
                                       ***************************************************************************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH.........................TTGGCCCEEC CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrak.............esgkvvvevdp 295
                                       amwlmlqqd+p+dyviatge hsvr+fve af+++g  iew+g+g ee+g+++             + g++vvev++
  gi|488599594|ref|YP_007906065.1| 230 AMWLMLQQDEPDDYVIATGEAHSVRKFVEEAFKHIGVIIEWRGEGIEEKGVVAeimdsefkdsmkiKPGDIVVEVSK 306
                                       *************************************************9665444445555555579********* PP

                                       GG--SS--SB--B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 296 kyfrpgevdlllgdaskakeeLgWkpkvsfeelvrem 332
                                       +yfrp+e+++llgd +ka+++LgW+pkv+f+elv+ m
  gi|488599594|ref|YP_007906065.1| 307 RYFRPAEAEFLLGDSTKARKKLGWEPKVKFKELVKIM 343
                                       **********************************987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.8   0.0   1.9e-72   3.7e-69       1     241 []       4     246 ..       4     246 .. 0.99

  Alignments for each domain:
  == domain 1  score: 232.8 bits;  conditional E-value: 1.9e-72
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.........EEEE--TT-HHHHHHHHHHHT-SEE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.........elveldltdrsalerlfkeeqpdav 68 
                                       +l+tG+tG++Gs+lv+ ll+k+y+v g+ r+ s++nt+r++++         ++ ++d+td+++l +++++ qpd++
  gi|488599594|ref|YP_007906065.1|   4 ALITGVTGQDGSYLVEFLLNKNYKVYGVIRRASSFNTSRIDHIiefhspekfDWFRGDMTDETSLIKILEKIQPDEI 80 
                                       59*************************************************************************** PP

                                       EE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHH CS
                         Epimerase  69 ihlAavggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqpkeettltgplkpnspYaa 144
                                       ++lAa+++v++s+e p ++++  + gtl+llea++  g++ +++++sSse++G +++ p++e+t   p++p spYa+
  gi|488599594|ref|YP_007906065.1|  81 YNLAAQSHVQVSFEVPVYTFDVVATGTLRLLEAVKNLGLDiKIYQASSSEMFGSSPP-PQNEET---PFNPKSPYAI 153
                                       *************************************9999****************.9*****...********** PP

                                       HHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHH CS
                         Epimerase 145 aKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaea 221
                                       aK+a+++l+ +y+++yg+ + +++lfn+++pr+ge++v+r+i++++++i+ g q+ ++lg ++a+Rd++y+ ++++a
  gi|488599594|ref|YP_007906065.1| 154 AKVAAYHLCVNYREAYGMWIANGILFNHESPRRGETFVTRKITRAVSRIAFGVQDKLVLGYLDAKRDWGYAPEYVKA 230
                                       ***************************************************************************** PP

                                       HHHHHHHHTT-STTEEEEES CS
                         Epimerase 222 illvlehvdagdkgeiyniG 241
                                       ++l+l++    d++++y+i+
  gi|488599594|ref|YP_007906065.1| 231 MWLMLQQ----DEPDDYVIA 246
                                       *******....889999996 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 !   33.3   0.0   1.3e-11   2.6e-08       3     131 ..       4     157 ..       1     178 [. 0.93

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.3e-11
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT........................T--TTSHHHHHHHHHHH--SEE CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre........................eldltdaeavaellkeakpdvv 55 
                                        l+tG +Gq Gs L++ l +++++v+++ r+                        + d+td++++ ++l++++pd +
  gi|488599594|ref|YP_007906065.1|   4 ALITGVTGQDGSYLVEFLLNKNYKVYGVIRRassfntsridhiiefhspekfdwfRGDMTDETSLIKILEKIQPDEI 80 
                                       69**************************8888********************************************* PP

                                       EE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT..-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHH CS
                     RmlD_sub_bind  56 vnaAAytavDkaEseeeaayavnaeavealAeaaaavg..alLihvStDyVFdGekkrpYeeddetsPlnvYGrtKl 130
                                       +n+AA   v    + +   + v a+++ +l ea ++ g  +++ + S+   F  + + p +e+ + +P++ Y+ +K+
  gi|488599594|ref|YP_007906065.1|  81 YNLAAQSHVQVSFEVPVYTFDVVATGTLRLLEAVKNLGldIKIYQASSSEMFGSS-PPPQNEETPFNPKSPYAIAKV 156
                                       ***********************************987335778899*****655.7889999**********9998 PP

                                       H CS
                     RmlD_sub_bind 131 a 131
                                       a
  gi|488599594|ref|YP_007906065.1| 157 A 157
                                       7 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   3.1e-09   6.2e-06       2     119 ..       5     118 ..       4     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.1e-09
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES.-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiiller.dElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       l+tG +G  Gs lv+ +l+k+ k   ++ r + ++  +i++ +e +  + k++ +     gd++d+++l k+le+++
  gi|488599594|ref|YP_007906065.1|   5 LITGVTGQDGSYLVEFLLNKNYKVYGVIRRaSSFNTSRIDHIIEFHSPE-KFDWF----RGDMTDETSLIKILEKIQ 76 
                                       8*******************99988766652678999999987544444.55444....8***************** PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieag 119
                                       +d +++ AA  hV +  e p+ +++   +gt  ++ea ++ g
  gi|488599594|ref|YP_007906065.1|  77 PDEIYNLAAQSHVQVSFEVPVYTFDVVATGTLRLLEAVKNLG 118
                                       *********************************999988766 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.7e-07    0.0015       1     153 [.       5     158 ..       5     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.7e-07
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrlee.lke.vrvlDlrespelleelskvnvkk...viegDvtdkdkleealegv..dvv 70 
                                       ++tG +G  G++lv+ L++ +  +   +r +   ++++  +++ +++  +      gD+td+ +l + le++  d +
  gi|488599594|ref|YP_007906065.1|   5 LITGVTGQDGSYLVEFLLNKNYkVYGvIRRA-SSFNTSRIDHIIEFHSPEkfdWFRGDMTDETSLIKILEKIqpDEI 80 
                                       6899999999****99999886433313433.3444444455555554444569****************9833467 PP

                         3Beta_HSD  71 ihlaslvdvagklted.eimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqday 146
                                         la+ + v+  ++      +v   GT  +lea ++ g+ + +Y  s + +++   + + +  +Ee++   +++++y
  gi|488599594|ref|YP_007906065.1|  81 YNLAAQSHVQVSFEVPvYTFDVVATGTLRLLEAVKNLGLDIKIYQASSSEMFG--SSPPPQ--NEETPF--NPKSPY 151
                                       888888888776554414679***********************999888888..344444..666655..455666 PP

                         3Beta_HSD 147 pesKala 153
                                       +  K  a
  gi|488599594|ref|YP_007906065.1| 152 AIAKVAA 158
                                       6666555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.4e-06    0.0027       1     152 [.       6     145 ..       6     198 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-06
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TG+TG  G++L+e LL+++   k+y ++R  s+   + R+ +++ ++          +e+     GD++++     
  gi|488599594|ref|YP_007906065.1|   6 ITGVTGQDGSYLVEFLLNKNY--KVYGVIRRASS-FNTSRI-DHIIEFHS--------PEKFDWFRGDMTDET---- 66 
                                       8*****************998..9******9988.678899.55444444........455567777777665.... PP

                                       HHHHHHHHHH-..-EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--..-EEEEEEGGGTTS-TTT-- CS
                     NAD_binding_4  78 eedlqelaeev..dviihsaAtvnfdepyke...llrvNveGtrevlelakklkkl.kvllhvSTayvngeregeve 148
                                         +l ++ e++  d i++ aA+ +++ + ++    ++v  +Gt ++le  k+l    k +   S+ ++      + e
  gi|488599594|ref|YP_007906065.1|  67 --SLIKILEKIqpDEIYNLAAQSHVQVSFEVpvyTFDVVATGTLRLLEAVKNLGLDiKIYQASSSEMFGSSPPPQNE 141
                                       ..233333332226777777777777777664334455556666666666654444233333444555555554555 PP

                                       SSS- CS
                     NAD_binding_4 149 ekvy 152
                                       e+++
  gi|488599594|ref|YP_007906065.1| 142 ETPF 145
                                       5555 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 !   16.2   0.0   3.8e-06    0.0075       1     130 [.       8     161 ..       8     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.8e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH........HHHCTTTCEEEE--TT-CCHHHHHHTT-..SEEEES CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla........eleaeeglevvegdvtdvedlaealkga..daVvsa 67 
                                       G tG+ G++lv+ ll++ +++v  ++R++++++        e+ + e+ + + gd+td+ +l + l+ +  d ++  
  gi|488599594|ref|YP_007906065.1|   8 GVTGQDGSYLVEFLLNK-NYKVYGVIRRASSFNtsridhiiEFHSPEKFDWFRGDMTDETSLIKILEKIqpDEIYNL 83 
                                       789**************.6********9988876666677778899*******************997733456655 PP

                                       ---TCC.............HHHHHHHHHHHHHHCT--.EEEEEEETTTTSGCGCH.HHHHHHHCCHHHHHHHHHHHH CS
                    NAD_binding_10  68 lggggk.............deegaknivdaakeagvk.Rfvlvsaigvgdevpge.fgewnkellkaylaakraaee 129
                                       +++++               ++g+ ++++a+k+ g   ++   s+  +  ++p +  +e+  +  ++y++ak aa +
  gi|488599594|ref|YP_007906065.1|  84 AAQSHVqvsfevpvytfdvVATGTLRLLEAVKNLGLDiKIYQASSSEMFGSSPPPqNEETPFNPKSPYAIAKVAAYH 160
                                       54444445554444444434444888888888877531344444444433333330222222333566666666666 PP

                                       H CS
                    NAD_binding_10 130 l 130
                                       l
  gi|488599594|ref|YP_007906065.1| 161 L 161
                                       5 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.7e-05     0.094       2      34 ..       5      37 ..       4      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.7e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-S CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtks 34
                                      l++G TG+ G+++v++ll++++kv  ++R  +s
  gi|488599594|ref|YP_007906065.1|  5 LITGVTGQDGSYLVEFLLNKNYKVYGVIRRASS 37
                                      799*************************98843 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00034      0.68       1      72 [.       2      76 ..       2      82 .. 0.85
   2 ?    0.3   0.0      0.21   4.2e+02      63     107 ..     252     295 ..     243     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00034
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee..gakalaiqvDvtdreevealvekav 72
                                      k++l+tG ++  G  +++ l+++++kv+  + r ++     ++++ e    +k+  +++D+td++++ +++ek++
  gi|488599594|ref|YP_007906065.1|  2 KTALITGVTGQDGSYLVEFLLNKNYKVYGvIRRASSFNTSRIDHIIEFhsPEKFDWFRGDMTDETSLIKILEKIQ 76
                                      79**************************9455555555556777766677889*****************99986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHSSESEEE..E---SS--SSGGGCSHHHHHHHHHH CS
                         adh_short  63 evealvekavkklgkldvLv..nNAGitgsgpfselseeewerviev 107
                                       +v+++ve+a   ++++ v++   + Gi+++g ++e+ ++e+++++++
  gi|488599594|ref|YP_007906065.1| 252 SVRKFVEEA---FKHIGVIIewRGEGIEEKGVVAEIMDSEFKDSMKI 295
                                       444555555...6666666511578889999999*999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2122.93
//
Query:       gi|488599595|ref|YP_007906066.1|  [L=311]
Description: Nucleoside-diphosphate-sugar epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-48  164.9   0.0    2.8e-48  164.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.2e-22   79.9   0.0    5.5e-17   62.2   0.0    3.0  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.1e-08   32.3   0.0    9.2e-08   31.5   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    0.00011   21.4   0.1     0.0028   16.8   0.0    2.6  3  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00029   19.9   0.2        1.9    7.4   0.3    3.1  3  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
       0.18   11.4   0.0          1    8.9   0.0    2.1  1  NmrA             NmrA-like family


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 !  164.5   0.0   9.2e-52   2.8e-48       2     241 .]       5     234 ..       4     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 9.2e-52
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---H CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vggv 77 
                                        V+G+ Gf+Gs++vk l++k+yev+ ++r+                +d++d + l  ++k+++p++vi+ Aa vgg+
  gi|488599595|ref|YP_007906066.1|   5 AVAGGFGFLGSNIVKVLKKKNYEVVPFSRR--------------SGIDIRDWKTLISFLKNVEPEIVINSAAhVGGI 67 
                                       69****************************..............58******************************* PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS--.--SSHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgpl.kpnspYaaaKlageklv 153
                                       a ++ +p +++e+nl++  nll a+++ gvk+++++   ++Y+ +ae+ +e++  +gp+ ++   Y++   a    +
  gi|488599595|ref|YP_007906066.1|  68 AYNALKPVEIYEDNLMMGFNLLRASFEVGVKKFVNIMPNCTYPGVAEIYREDKWWDGPMhETVLTYGMPRKALWVHA 144
                                       ***********************************************98999999********************** PP

                                       HHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTS....SSEEEETTST-EEEEEEHHHHHHHHHHH CS
                         Epimerase 154 eayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegk....qevtllgdgtalRdflyveDvaeaillv 225
                                       +a++++yg+n i l l nlyGp+ ++++ +s+ + ali+ki ++k    + v ++g+g+++R+++yveD+ae+i+l+
  gi|488599595|ref|YP_007906066.1| 145 WALKEKYGFNSIHLVLPNLYGPGdHFDPIRSHALGALIKKIVDAKfegkKIVEIWGTGNPVREWGYVEDAAEGIVLA 221
                                       *******************************************666665799************************* PP

                                       HHHHTT-STTEEEEES CS
                         Epimerase 226 lehvdagdkgeiyniG 241
                                       +e +++    ei+niG
  gi|488599595|ref|YP_007906066.1| 222 MEMYND---VEIMNIG 234
                                       ***666...5799998 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 !   13.1   0.0   1.6e-05     0.048       2      31 ..       6      35 ..       5      37 .. 0.93
   2 !   62.2   0.0   1.9e-20   5.5e-17      59     332 .]      37     297 ..      35     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEE CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrs 31
                                      + G+ Gf Gs++++ L +k+yev+ + rrs
  gi|488599595|ref|YP_007906066.1|  6 VAGGFGFLGSNIVKVLKKKNYEVVPFSRRS 35
                                      78**********************998886 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 1.9e-20
                                       --TT-HHHHHHHHHHHT-SEEEE--S---.HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG- CS
                     GDP_Man_Dehyd  59 gDltDssslerllaevqpdevynLAAqsh.VdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYG 134
                                        D++D + l++ l++v+p+ v+n AA    +++   kP + +e n++  ++LL a  ++g++   +f+ +     Y 
  gi|488599595|ref|YP_007906066.1|  37 IDIRDWKTLISFLKNVEPEIVINSAAHVGgIAYNALKPVEIYEDNLMMGFNLLRASFEVGVK---KFVNIMPNCTYP 110
                                       69************************9654******************************96...899999999999 PP

                                       S-SSSSB-TT...S----.-SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT.....SCCCHHHHHHH CS
                     GDP_Man_Dehyd 135 kvqevpqtEt...tpfyP.rsPYaaaKlyadwivvnyreayglfavngilfnhesprrget.....fvtrkitrava 202
                                        v+e+  +++    p++     Y++ + +    + + +e+yg+  +  +l n ++p  + +         +i ++v 
  gi|488599595|ref|YP_007906066.1| 111 GVAEIYREDKwwdGPMHEtVLTYGMPRKALWVHAWALKEKYGFNSIHLVLPNLYGPGDHFDpirshALGALIKKIVD 187
                                       9998887765444677652579******************************8887754331111145666666666 PP

                                       HHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH..... CS
                     GDP_Man_Dehyd 203 rialgkqevlylGnldakRdwghvkDyveamwlmlqq.dkpedyviatgethsvrefvelaflelgktiewegkgee 278
                                          +gk+ v + G ++++R wg+v+D +e+++l+++  +  e ++i++g+ +++re++ +     +   +w+g    
  gi|488599595|ref|YP_007906066.1| 188 AKFEGKKIVEIWGTGNPVREWGYVEDAAEGIVLAMEMyNDVEIMNIGEGKGYTIREIAYMI----KDAANWDG---- 256
                                       666676666666*********************9986366788999999999999988653....33334654.... PP

                                       .......TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 279 evgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvrem 332
                                                    e+ + + +p  + + + d++k+k+ LgW+pk++++e+++++
  gi|488599595|ref|YP_007906066.1| 257 -------------EFIFDRSKPDGAPKKILDIRKMKRILGWQPKTNIREGIKKT 297
                                       .............233556789999999***********************986 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   3.1e-11   9.2e-08       2      61 ..       3      63 ..       2      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.1e-11
                                      EEEEESTTSHHHHHHHHHCTTTSEEEEEE.-TTT--TTSHHHHHHHHHHH--SEEEE---- CS
                     RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlal.treeldltdaeavaellkeakpdvvvnaAAy 61
                                      k+ v G+ G lGs+++k l+++++ev+++  r+ +d++d +++ ++lk+++p++v+n AA+
  gi|488599595|ref|YP_007906066.1|  3 KVAVAGGFGFLGSNIVKVLKKKNYEVVPFsRRSGIDIRDWKTLISFLKNVEPEIVINSAAH 63
                                      6899*************************55669**************************8 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.13   3.9e+02       1      27 [.       4      29 ..       4      36 .. 0.73
   2 !   16.8   0.0   9.5e-07    0.0028      61     126 ..      37     103 ..      17     106 .. 0.85
   3 ?    0.7   0.0     0.078   2.3e+02     206     244 ..     211     249 ..     204     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                                      EEEETTTSHHHHHHHHHHHHHB-SEEE CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkii 27
                                      v v+G+ G +Gs++v+ + kk+  +++
  gi|488599595|ref|YP_007906066.1|  4 VAVAGGFGFLGSNIVKVLKKKN-YEVV 29
                                      6799**********98665554.4444 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 9.5e-07
                                       --TT-HHHHHHHTT..T-SEEEE-----.-HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEE CS
                   Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlK.hVPlveenpleaiktNvlgtenvieaaieagvkkvvli 126
                                        d+rd ++l + l+++++++v+++AA+   +     +p+e  + N +   n+++a+ e gvkk+v i
  gi|488599595|ref|YP_007906066.1|  37 IDIRDWKTLISFLKNVEPEIVINSAAHVgGIAYNALKPVEIYEDNLMMGFNLLRASFEVGVKKFVNI 103
                                       59***********************96414555556789999***********************87 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH. CS
                   Polysacc_synt_2 206 ieeavqLvlqalalakggeifvldmGepvkivdlakali 244
                                       +e+a++ ++ a+++ ++ ei+    G+ ++i+++a  + 
  gi|488599595|ref|YP_007906066.1| 211 VEDAAEGIVLAMEMYNDVEIMNIGEGKGYTIREIAYMIK 249
                                       79999999*************99999*******997664 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 !    7.4   0.3   0.00063       1.9       1      20 [.       5      24 ..       5      34 .. 0.85
   2 !    4.6   0.0    0.0045        13      52     112 ..      37     101 ..      23     105 .. 0.85
   3 !    4.2   0.0    0.0059        18     198     247 ..     190     240 ..     158     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00063
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrl 20
                                      +v Gg GFlG+++vk L + 
  gi|488599595|ref|YP_007906066.1|  5 AVAGGFGFLGSNIVKVLKKK 24
                                      599***********998655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0045
                         3Beta_HSD  52 gDvtdkdkleealegvdvvihlaslvdvag....kltedeimkvnvkGTrnvleacvkagvrvlv 112
                                        D++d ++l   l++v+  i++ s+  v g     l+  ei++ n+    n+l a ++ gv+++v
  gi|488599595|ref|YP_007906066.1|  37 IDIRDWKTLISFLKNVEPEIVINSAAHVGGiaynALKPVEIYEDNLMMGFNLLRASFEVGVKKFV 101
                                       69*************************99942222345689999999999************998 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0059
                         3Beta_HSD 198 klglalf.kigdeevlsdrvYvgNvawahilAaralqdpkkkssvagqayf 247
                                         g++++   g  + + ++ Yv+  a  ++lA+   +d + ++  +g+ y 
  gi|488599595|ref|YP_007906066.1| 190 FEGKKIVeIWGTGNPVREWGYVEDAAEGIVLAMEMYNDVEIMNIGEGKGYT 240
                                       3444444156889999****************9887777666666666665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00034         1       1      98 [.       4     101 ..       4     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00034
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S......-SHHHHHHHHSTTEEEES-TT-H.HHHHHHHTT-SEEEE CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt......kselakslkeaGvelvkgdlddk.eslvealkgvdvvfs 70 
                                       ++v G+ G +G+ +v++l k++++v    R +       + l+  lk+   e+v +++     +  +alk v+    
  gi|488599595|ref|YP_007906066.1|   4 VAVAGGFGFLGSNIVKVLKKKNYEVVPFSRRSgidirdWKTLISFLKNVEPEIVINSAAHVgGIAYNALKPVE---- 76 
                                       68999********************999999988888777778888888888885554444044456666665.... PP

                                       ---GGS-HHHHHHHHHHHHHHHS-SEEE CS
                              NmrA  71 vtgfyskeiedgkklvdAakeaGvkhfi 98 
                                          +y++++  g +l +A  e Gvk+f+
  gi|488599595|ref|YP_007906066.1|  77 ---IYEDNLMMGFNLLRASFEVGVKKFV 101
                                       ...4588999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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 0.32s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1994.48
//
Query:       gi|488599596|ref|YP_007906067.1|  [L=140]
Description: hypothetical protein Asulf_00038 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 955.27
//
Query:       gi|488599597|ref|YP_007906068.1|  [L=364]
Description: putative pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-90  303.1   0.0    3.4e-90  303.0   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.9e-08   31.8   0.1    3.3e-07   29.6   0.1    1.8  1  Aminotran_5      Aminotransferase class-V
    1.4e-07   31.1   0.0    2.3e-07   30.3   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    1.9e-05   23.4   0.2    3.5e-05   22.5   0.1    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.005   16.2   0.0      0.011   15.1   0.0    1.6  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  303.0   0.0   9.5e-94   3.4e-90       3     361 .]      12     357 ..      10     357 .. 0.95

  Alignments for each domain:
  == domain 1  score: 303.0 bits;  conditional E-value: 9.5e-94
                                       HHHHHHHHHHHHTSS.-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH CS
                   DegT_DnrJ_EryC1   3 keeeleaveevlksg.wltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatan 78 
                                        + e++av e lksg wlt+ +++eeFE+++++ l+ ++a+ v+sGtaAl l+L a+g+++gd+VIvp +t +at n
  gi|488599597|ref|YP_007906068.1|  12 SKGEIKAVVEYLKSGgWLTEFKKTEEFEERICELLNIDYAVVVTSGTAALYLSLLACGISKGDKVIVPNFTMIATPN 88 
                                       5678999******9989999********************************************************* PP

                                       HHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1  79 avlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       av ++ga++++vD+++dt+++d ++ie +i +  ka + V l G++ +md++ + + + ++++ieD+++A+ +t+++
  gi|488599597|ref|YP_007906068.1|  89 AVKWTGADVILVDIEKDTLCLDIKKIE-KIDRSVKALIYVSLNGRSGNMDKVVKFCYENDIILIEDSCQAFMSTWNN 164
                                       **************************8.59*********************************************** PP

                                       EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHH CS
                   DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAigla 232
                                       k++G++g ++v+S+ p K +ttG GG++vtnde + +k+++l+ + +++       +e  +Gyn++ t++qA igl+
  gi|488599597|ref|YP_007906068.1| 165 KYLGTFGIIGVYSLTPHKLITTGQGGIIVTNDESIYKKIKKLKDFCRVK--PGVDLHED-IGYNFKFTDLQAVIGLE 238
                                       **********************************************993..44555555.8**************** PP

                                       HHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGS CS
                   DegT_DnrJ_EryC1 233 qLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhyp 309
                                       qL+ +++ v+r++ei++ y + L+++e++  ++t+ +++  + + + +lvee+    rdel++ lk+++ig+r++yp
  gi|488599597|ref|YP_007906068.1| 239 QLKSIKWRVKRKKEIYKFYYNSLKNVEEIKFIPTDLNQT--VPWFIDILVEES---IRDELINYLKTKNIGSRPFYP 310
                                       ***************************987777777775..777788999987...79******************5 PP

                                       CHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 310 nplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVvealr 361
                                        ++++q+ y+ +k+     +  +++++++ l+Lp++ +l+ e++d++v+++r
  gi|488599597|ref|YP_007906068.1| 311 -AINTQKPYKVYKGH----FDISNTISKQGLWLPSSLGLKYEELDYIVNNVR 357
                                       .*********99755....99***************************9985 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   9.2e-11   3.3e-07      43     333 ..      33     303 ..      29     307 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9.2e-11
                                       HHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE CS
                       Aminotran_5  43 kaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi 119
                                       k+ ee +e++ el+n++  + +++tsGt+ a+ l +l+    +++gd+++v +    a+     ++ k tga+v  +
  gi|488599597|ref|YP_007906068.1|  33 KKTEEFEERICELLNID--YAVVVTSGTA-ALYLSLLAC--GISKGDKVIVPNFTMIATP----NAVKWTGADVILV 100
                                       57899***********9..6********9.444444444..369**********999988....6667899***999 PP

                                       EBETTSC.BEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS..---HHHHTE. CS
                       Aminotran_5 120 pldeege.ldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghi..pidvkklgv. 192
                                        ++++ + ld++++ ++++  +k++++   +  +G+++ v +++    +++++++ D++qa+++   + ++ ++g+ 
  gi|488599597|ref|YP_007906068.1| 101 DIEKDTLcLDIKKI-EKIDRSVKALIYVSLNGRSGNMDKVVKFC---YENDIILIEDSCQAFMSTwnNKYLGTFGIi 173
                                       99988763678888.78******************999888777...899************996224556666642 PP

                                       SEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEEEEHCTTGGGS.SS--HHHHHHHHHHHHH CS
                       Aminotran_5 193 DflafsghK.llgPtGiGvlyvrkellekleplllggemveevsl.eettfaeapskfeaGTpnvagiiglgaaley 267
                                        +++++ hK +   +G  ++   +++ +k+++l+    +   v+l e+++       ++      +++  l+a++ +
  gi|488599597|ref|YP_007906068.1| 174 GVYSLTPHKlITTGQGGIIVTNDESIYKKIKKLKDFCRVKPGVDLhEDIG-------YN------FKFTDLQAVIGL 237
                                       56778888843333332334444445556655555555555555522222.......33......334455555555 PP

                                       HHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTE CS
                       Aminotran_5 268 leeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegI 333
                                        +   ++   k++ke  +  ++ lk++++++++ +d ++  +  + + +++   +++ ++L++++I
  gi|488599597|ref|YP_007906068.1| 238 EQLKSIKWRVKRKKEIYKFYYNSLKNVEEIKFIPTDLNQTVPWFIDILVEESIRDELINYLKTKNI 303
                                       555555555666777777777777777777776666666666666666666666666666666666 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 !   30.3   0.0   6.3e-11   2.3e-07      46     156 ..      35     128 ..      15     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 6.3e-11
                                       HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEB CS
                     Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvrypl 122
                                         e+ee+++++l+         + avvv+sG+ al   l ++  + +gd+++vp+ t     n++++ g+ v+ + +
  gi|488599597|ref|YP_007906068.1|  35 TEEFEERICELLN--------IDYAVVVTSGTAALYLSLLACG-ISKGDKVIVPNFTMIATPNAVKWTGADVILVDI 102
                                       469**********........5668******************.********************************7 PP

                                       EETTTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
                     Aminotran_1_2 123 yseedfhldlealeealkeapegnkktkvilves 156
                                       + +++  ld++++e+ +++       +k ++  s
  gi|488599597|ref|YP_007906068.1| 103 E-KDTLCLDIKKIEK-IDR------SVKALIYVS 128
                                       7.7888899999988.666......456666555 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   9.7e-09   3.5e-05      54     257 ..      35     251 ..      30     270 .. 0.74
   2 ?   -3.8   0.0      0.96   3.4e+03     264     291 ..     295     322 ..     293     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.7e-09
                                       HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST..TSH CS
                   Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkklgievkfvdt..sdl 127
                                       ++ +eeri++L + + a++v+sG+aA+ +++la  +++Gd+++v +     t + +k +   + +     dt   d+
  gi|488599597|ref|YP_007906068.1|  35 TEEFEERICELLNIDYAVVVTSGTAALYLSLLACgISKGDKVIVPNFTMIATPNAVKWTGADVILVDIEKDTlcLDI 111
                                       5789***********************99999875899*********999999999988777533333333333577 PP

                                       HHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGT..TTHTTTS-GGGGT-SEEEEETT..TTT CS
                   Cys_Met_Meta_PP 128 eelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDnt..faspllqrplklgaDivvhSaT..Kyl 200
                                       +++ek  ++   l+y+        +   + k++k++ +++++++ D +  f+s  + + l     i v+S T  K +
  gi|488599597|ref|YP_007906068.1| 112 KKIEKIDRSVKALIYVSLN----GRSGNMDKVVKFCYENDIILIEDSCqaFMSTWNNKYLGTFGIIGVYSLTphKLI 184
                                       7777766666667777433....345567899*********999997544999999999965455999999943444 PP

                                       TCSSS--EEEEEESSCHHHHHHHHHHH............HHHT-B--HHH..HHHHHHHHTTHHHHHHHHH CS
                   Cys_Met_Meta_PP 201 gGhsdvvaGvivvkgkeelkkelkflq............nalGavlspfd..awlllrGlkTLslRlerhq 257
                                          ++  +G+iv+++ e++ k++k+l+            +++G   +  d  a + l  lk ++ R++r++
  gi|488599597|ref|YP_007906068.1| 185 ---TTGQGGIIVTND-ESIYKKIKKLKdfcrvkpgvdlhEDIGYNFKFTDlqAVIGLEQLKSIKWRVKRKK 251
                                       ...566689999999.9999999998877777777777777777766554113444455566666666665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.96
                                       HHHHHTSTTEEEEE-TTSTTSTTHHHHH CS
                   Cys_Met_Meta_PP 264 AefLekhpkvekvyYpglpshpqhelak 291
                                        ++L++++  ++  Yp++++++ +++ k
  gi|488599597|ref|YP_007906068.1| 295 INYLKTKNIGSRPFYPAINTQKPYKVYK 322
                                       57888888888999*****999999987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     3e-06     0.011      32     169 ..      33     155 ..      30     251 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-06
                                       HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHC.C--EEEEE-EBTT CS
                   Beta_elim_lyase  32 ktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiael.agvklrdlknkea 106
                                       k+++++e++++el+  ++a+ v++GtaA  ++l +    +g++viv   + ++  +  a++   a+v l+d++++  
  gi|488599597|ref|YP_007906068.1|  33 KKTEEFEERICELLNIDYAVVVTSGTAALYLSLLACGiSKGDKVIVP--NFTMIATPNAVKWTgADVILVDIEKDT- 106
                                       57899***********************9999977665888888774..344444445555555556666666666. PP

                                       TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 107 GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                         +d++k+e++ + v+a      li++    n   G      ++++v +++ +++i l+ D++
  gi|488599597|ref|YP_007906068.1| 107 LCLDIKKIEKIDRSVKA------LIYVSL--N---G---RSGNMDKVVKFCYENDIILIEDSC 155
                                       89999999987666444......555433..3...2...234566666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2157.42
//
Query:       gi|488599598|ref|YP_007906069.1|  [L=374]
Description: Glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-38  130.4   0.0    7.6e-38  129.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.7e-25   90.0   0.0    2.6e-25   89.4   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    7.5e-24   84.6   0.0    1.9e-23   83.3   0.0    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    3.2e-10   40.7   0.0    2.8e-09   37.6   0.0    2.0  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.1e-08   35.3   0.0      2e-08   34.5   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00069   19.6   0.2     0.0027   17.7   0.2    2.1  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.052   13.2   0.2        7.4    6.2   0.0    2.5  2  Glyco_transf_5   Starch synthase catalytic domain
       0.14   11.9   0.1       0.29   10.9   0.1    1.4  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-


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 !  129.7   0.0   3.4e-41   7.6e-38       3     171 ..     179     351 ..     177     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 3.4e-41
                                       HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES......STTHHHHHHHHHHHCTTCG CS
                   Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.....ngeeekelkklaeelelsdn 74 
                                       +++r+++g+n+++ ++l+v++l+++Kg+dlli+ ++ + k+  +n+kl+++G       ++++ l++++ +++l++ 
  gi|488599598|ref|YP_007906069.1| 179 DEIRERYGINHDDIVLLCVSALTPRKGQDLLIDCMRIVTKK-IQNIKLLLVGsvgktTIQYKQILRYMVRNAGLEKY 254
                                       6899**********************************998.**************999****************** PP

                                       GGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHH CS
                   Glycos_transf_1  75 viflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaea 151
                                       vif g++++e+l++++ ++di+v  s++E+fG++ +EAma+g p+i  +   ++e++ dg +G+ vk +++ +la +
  gi|488599598|ref|YP_007906069.1| 255 VIFCGHIPDEELPKYYAASDIYVSASTWESFGLPFVEAMACGRPAIGFDKTAISELIIDGYNGYKVKYPDINELAIK 331
                                       ***************************************************************************** PP

                                       HHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 152 irklledeelrerlgenark 171
                                       i+ l +d e+r+ +g n+rk
  gi|488599598|ref|YP_007906069.1| 332 IIHLANDVEKRKIFGLNGRK 351
                                       ******************98 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 !   89.4   0.0   1.2e-28   2.6e-25       3     134 .]     193     338 ..     191     338 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.2e-28
                                       EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---.......HHHHHHHT..T-T.TEEEE---..THHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprp.....eeleelaa..gleerveftGfv..edlae 68 
                                       v+l+v++l+ ++kg+dll++ +  + kk  +++l++vG+  +      + l+ +++  gle+ v+f+G++  e+l++
  gi|488599598|ref|YP_007906069.1| 193 VLLCVSALT-PRKGQDLLIDCMRIVTKKiqNIKLLLVGSVGKTtiqykQILRYMVRnaGLEKYVIFCGHIpdEELPK 268
                                       799*****5.66**************99845*******632223344344444454689*999*******8667*** PP

                                       HHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  69 llaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       ++aa+d++v  s  e+fgl  +Eama+g+p + +d  +i+e++  g ng+ v+  d ++la +i++L +d
  gi|488599598|ref|YP_007906069.1| 269 YYAASDIYVSAStwESFGLPFVEAMACGRPAIGFDKTAISELIidGYNGYKVKYPDINELAIKIIHLAND 338
                                       ***********************************99****99*********999************987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0   8.5e-27   1.9e-23       2     169 ..      14     170 ..      13     171 .. 0.89
   2 ?   -3.0   0.0       2.9   6.5e+03     146     160 ..     179     193 ..     178     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 8.5e-27
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                        G++r+v+e+ar L ++G++V +v+ + + ++          + + ++ +++  ++ ++++++ + +kre+pD+ H+
  gi|488599598|ref|YP_007906069.1|  14 SGIGRVVEEMARCLYEKGYDVKIVCGKCNIKS----------KVPVILCKYNETLYQTNILDIIKTIKREEPDIFHS 80 
                                       59***********************5544333..........3456677778889999******************* PP

                    Glyco_transf_4  79 hspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl.lrradrviavSeatadelrerygv 154
                                       h+++  +++++     ++ +++ + Hg  ++++  + ++pls ++  + ++l l+ + ++i+vS+++++ l++++++
  gi|488599598|ref|YP_007906069.1|  81 HYYPMDVCGAFINS--SKTKHIMHSHGVNHQSWRLSWKNPLSLVRADIGEFLgLHFSEKIICVSNYMKNALIRKHRI 155
                                       ******99987766..8************977777788888888888888889************************ PP

                    Glyco_transf_4 155 ppekitVipnGvDle 169
                                       +++ki+V++nGv+l+
  gi|488599598|ref|YP_007906069.1| 156 EKSKIEVVYNGVNLQ 170
                                       *************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                    Glyco_transf_4 146 delrerygvppekit 160
                                       de+reryg++ ++i+
  gi|488599598|ref|YP_007906069.1| 179 DEIRERYGINHDDIV 193
                                       7999*****999885 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 !   37.6   0.0   1.3e-12   2.8e-09       1     160 []      14     166 ..      14     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.3e-12
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvv 77 
                                       +Gigr+v+e+ar L + G++V +++  + +        +v+v+ ++   +         + +   ++  +re pd+ 
  gi|488599598|ref|YP_007906069.1|  14 SGIGRVVEEMARCLYEKGYDVKIVCG-KCNIKS-----KVPVILCKYNETLYQ----TNILDIIKTI--KREEPDIF 78 
                                       6************************9.455544.....7*****999988743....3455556666..899***** PP

                   Glyco_trans_4_4  78 hahsptaglaarlarrrrgiplvvtlhglllr.rgsgavrrly....ralerrllrradavlvvseaeaeelra.lg 148
                                       h+h+++    ++++    +++++ + hg  ++ ++ +++ +l     +  e + l+    +++vs+++  +l++ + 
  gi|488599598|ref|YP_007906069.1|  79 HSHYYPMDVCGAFIN-SSKTKHIMHSHGVNHQsWRLSWKNPLSlvraDIGEFLGLHFSEKIICVSNYMKNALIRkHR 154
                                       ***************.***********73322133455555432221555889*********************677 PP

                   Glyco_trans_4_4 149 vpadrvvvvpng 160
                                       +  ++++vv ng
  gi|488599598|ref|YP_007906069.1| 155 IEKSKIEVVYNG 166
                                       ***********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 !   34.5   0.0   8.9e-12     2e-08       5      91 ..     279     367 ..     271     368 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 8.9e-12
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervla 79 
                                        s  es+ l ++Ea+acG++a+  d +++ el+ +g  +  ++  d +ela ki +l ++ e+r+  + ++r++v++
  gi|488599598|ref|YP_007906069.1| 279 ASTWESFGLPFVEAMACGRPAIGFDKTAISELIIDGYNGYKVKypDINELAIKIIHLANDVEKRKIFGLNGRKFVEK 355
                                       45669999****************************999988899******************************** PP

                   Glyco_trans_1_2  80 ehtydhraeqll 91 
                                       ++++++ +++++
  gi|488599598|ref|YP_007906069.1| 356 NFDVRRNIKKII 367
                                       ******999885 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 !   17.7   0.2   1.2e-06    0.0027      16     108 ..      23     105 ..      16     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                   Glyco_trans_4_2  16 lakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkgpleylkafklkklikkikPDvvhahyakpygllgsl 92 
                                       +a+ L ++gy+V++++ k       +  ++ v+  k     +l   +++ ++k ik+++PD+ h hy + + + g++
  gi|488599598|ref|YP_007906069.1|  23 MARCLYEKGYDVKIVCGKCN-----IKSKVPVILCK--YNETLYQTNILDIIKTIKREEPDIFHSHYYP-MDVCGAF 91 
                                       56668899999999998877.....44556677776..4446666679*******************54.5567777 PP

                   Glyco_trans_4_2  93 aarlsgvipvvlsvwG 108
                                       +   s+  + ++  +G
  gi|488599598|ref|YP_007906069.1|  92 I-NSSK-TKHIMHSHG 105
                                       6.3333.677777775 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 ?    6.2   0.0    0.0033       7.4      16      43 ..      14      41 ..      12      57 .. 0.88
   2 ?    4.2   0.1     0.014        30     118     232 ..      59     152 ..      53     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0033
                    Glyco_transf_5 16 GGLadvvgaLpkaLaklghdvrvilPry 43
                                       G+++vv+++++ L ++g+dv+++  ++
  gi|488599598|ref|YP_007906069.1| 14 SGIGRVVEEMARCLYEKGYDVKIVCGKC 41
                                      59*********************98666 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                    Glyco_transf_5 118 fsraalelleklgw.kpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrfpkdelaalglpaedf 193
                                       ++  +l++++ ++  +pd+ h h +   + +a++++ +        +k +++ H   +q ++ +++   l l     
  gi|488599598|ref|YP_007906069.1|  59 YQTNILDIIKTIKReEPDIFHSHYYPMDVCGAFINSSK--------TKHIMHSHGVNHQSWRLSWKNP-LSLV---- 122
                                       56667777777766369999999999999999998876........8888888888888666533321.2222.... PP

                    Glyco_transf_5 194 ekldglefygkvnflk.agivyadavttVSptyakEiltp 232
                                                 + +  +  g+ ++ +++ VS+++++ ++++
  gi|488599598|ref|YP_007906069.1| 123 ----------RADIGEfLGLHFSEKIICVSNYMKNALIRK 152
                                       ..........122222278888888888888888777665 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 ?   10.9   0.1   0.00013      0.29      71     118 ..      59     105 ..      41     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHCTS---EEEEEE---SCCCTTTT--EEEE CS
                     GalP_UDP_tr_C  71 ekedlaailkklarkydnlfetsfeysmGlhqaplnaeednswlHaHf 118
                                        +++++ i+k + r   ++f  s  y+m + +a +n+ + ++ +H H 
  gi|488599598|ref|YP_007906069.1|  59 YQTNILDIIKTIKREEPDIFH-SHYYPMDVCGAFINSSKTKHIMHSHG 105
                                       5789****************8.567*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2266.39
//
Query:       gi|488599599|ref|YP_007906070.1|  [L=704]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-106  356.0  30.9   1.9e-106  356.0  30.9    2.2  2  DUF2206   Predicted membrane protein (DUF2206)
    1.5e-06   27.9  11.8    4.8e-06   26.2  11.8    1.9  1  DUF1616   Protein of unknown function (DUF1616)


Domain annotation for each model (and alignments):
>> DUF2206  Predicted membrane protein (DUF2206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.8   3.9       1.8   1.6e+04     185     185 ..     170     170 ..     101     243 .. 0.61
   2 !  356.0  30.9  2.1e-110  1.9e-106       1     373 [.     346     700 ..     346     701 .. 0.98

  Alignments for each domain:
  == domain 1  score: -5.8 bits;  conditional E-value: 1.8
                           DUF2206 185 l 185
                                       l
  gi|488599599|ref|YP_007906070.1| 170 L 170
                                       1 PP

  == domain 2  score: 356.0 bits;  conditional E-value: 2.1e-110
                           DUF2206   1 kklLlviFgfglvvSHYglsyivllllalayllliilrlyikedksqilnftyvlifvvlalaWYlyissssafkti 77 
                                       kk+Ll+iF+fgl++SHYgl+y++++l  la+++l+ilr     +ksq+ln++y++++++++laWY ++++ssaf+t+
  gi|488599599|ref|YP_007906070.1| 346 KKILLIIFSFGLLISHYGLTYYYMFLSSLAIVILHILR-----KKSQLLNHRYLILYLISVLAWYKHTGNSSAFNTL 417
                                       89************************************.....9********************************* PP

                           DUF2206  78 asivnkilssiateflnptttqglavitkqissllhtvskylhliiqfliviGvlsvlflrkkkyrlsieylaivlv 154
                                       ++++n+ils+++++f++ +t++++ v+++++ +llht++kyl++++qf+i+iG+++ l++++kk ++s+e++a+++ 
  gi|488599599|ref|YP_007906070.1| 418 TKLANHILSNLISTFWQLETREATIVLMRKELTLLHTITKYLNIMTQFFIFIGINQ-LLVKRKKREFSAEHIAFFIS 493
                                       ********************************************************.88899*************** PP

                           DUF2206 155 llvilvasivlpyfas.alntaRlyqilliflapffiiGgialiklikkv...ikksklkskdsiklkiisvflvvl 227
                                       ++++++a++++pyf++ a++++R yqi+l++lap++iiG+ a++++i+++   +kk+k+ s+d+i++kiis+fl+++
  gi|488599599|ref|YP_007906070.1| 494 TVIWMIALLIIPYFMQlAYHQSRSYQIILLTLAPVSIIGCEAVFNWIVSStkkLKKFKEFSTDDITIKIISLFLAIY 570
                                       ***********************************************988888************************ PP

                           DUF2206 228 lLfnsGfiyeivkdsptsialdetldyalfndsevtgakWlsksaseektiysdkersslllrsfgaydkaivtesa 304
                                       lLfnsGf+ye+++d++ +i++++t++ya+f+ ++ ++a W+ k++++++tiy+d ++++l+lr++          ++
  gi|488599599|ref|YP_007906070.1| 571 LLFNSGFVYELADDPYPTISFNNTIEYARFSGQQDRAAIWILKNMDNSQTIYTDPMTKYLFLRYL----------PG 637
                                       *************************************************************8888..........89 PP

                           DUF2206 305 elneeilsessqie.segYiYlgsanvkdnlvlielvkkasknlvyaeyndlkkliksknkiYdNggsqi 373
                                        +++++l+es+qi+ ++gYiYl+++++k+       + ++s+n++ + y ++ +l+++ + +Y+N+++qi
  gi|488599599|ref|YP_007906070.1| 638 FIAVWVLDESKQIQvTKGYIYLRTNKNKT-------PIYCSSNRMEYVYLKELELTNQFEVVYKNNDAQI 700
                                       ************************99998.......5568899**************************9 PP

>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  11.8   5.3e-10   4.8e-06       4     106 ..      19     125 ..      16     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.3e-10
                           DUF1616   4 lalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnv.... 76 
                                       ++++ ll+ lv  +   +lR ++g++ + f+PG+ ++ +L  + ++++  e+l LS glS+a+v++  +++n+    
  gi|488599599|ref|YP_007906070.1|  19 ILAIQLLLWLVIAFDVPILRQIIGFVYLTFIPGFLVVKIL--KLDELTFNEKLFLSAGLSLAVVMFSVWLINFllpl 93 
                                       5667778888899999************************..7889*******************988888872222 PP

                           DUF1616  77 ..tpwgirlepilvslslftlllalvAivrRs 106
                                             i+ +p+++++s ++l+l +v +++R 
  gi|488599599|ref|YP_007906070.1|  94 fdVLSPISVQPLVITISTIVLILLMVCYYKRV 125
                                       22235799999******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); 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:                         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: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 4102.96
//
Query:       gi|488599600|ref|YP_007906071.1|  [L=308]
Description: putative glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-26   92.3   0.1    4.1e-26   91.8   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    3.3e-15   56.6   0.0    5.4e-15   55.9   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
      5e-07   29.5   0.0    8.2e-07   28.8   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    1.2e-05   25.4   0.1    2.1e-05   24.5   0.1    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0013   19.2   0.0     0.0029   18.1   0.0    1.7  1  Glyco_tranf_2_4  Glycosyl transferase family 2
     0.0076   15.7   0.1        1.8    7.9   0.0    2.1  2  Anp1             Anp1
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.23   10.9   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.1   1.6e-29   4.1e-26       2     131 ..      13     141 ..      12     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.6e-29
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                       vv+p++N ++  +e+lesl++  +yp+++ii+vDDgStD+t+e+++ +   +p v++++ + n  +++a+n g+++a
  gi|488599600|ref|YP_007906071.1|  13 VVVPVHNNKEDTAEFLESLKSV-TYPNYKIIIVDDGSTDGTEEMIKTA---YPEVILLKGDGNLWWSRAVNLGIEKA 85 
                                       9*********************.*************************...89************************ PP

                                       -SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-S CS
                   Glycos_transf_2  79 tgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkr 131
                                             y+l++D D+++d ++ + lve + ++++++++ ++ +++  ++ +e    
  gi|488599600|ref|YP_007906071.1|  86 LEIcadYVLLIDNDCVVDSGFMSALVETALRNPRSIIVSKVLYYDHPNKIWEAGAD 141
                                       986666*************************8887777777666666655554444 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 !   55.9   0.0   2.1e-18   5.4e-15       4     214 ..      11     227 ..       9     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 2.1e-18
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnl.gstgksral 79 
                                       +av+Vp+ n+ ++  e lesl + +yp++++++v+d+s+++t e+++    a+p v   ++  + nl  s++   ++
  gi|488599600|ref|YP_007906071.1|  11 VAVVVPVHNNKEDTAEFLESLKSVTYPNYKIIIVDDGSTDGTEEMIKT---AYPEV--ILLKGDGNLwWSRAVNLGI 82 
                                       89********************************************97...89996..4455566664444444555 PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrstlvsalgal.efaerhlrflaar.. 152
                                       + al+++  d+vll+D D+vv+ ++  +l+ ++ + p+  +v    + +++++ + a  ++  f+ ++  +      
  gi|488599600|ref|YP_007906071.1|  83 EKALEIC-ADYVLLIDNDCVVDSGFMSALVETAlRNPRSIIVSKVLYYDHPNKIWEAGADInWFKGEYVPIGHGEid 158
                                       5555555.69***********************77777777777778889999987775443444444422222233 PP

                   Glyco_tranf_2_3 153 .....ralgvltlnGsgslirrevlkelegldp.lfllt.dDyelglrlrragfrtayvpgaavrevfp 214
                                            ++  v +++  g li+ +++ke ++ d  +f  +  D++ ++r+ ++g+ + y+p++ v++   
  gi|488599600|ref|YP_007906071.1| 159 kgqyqTERYVKCSTLVGALIDVTIFKEMGLMDYkNFPQFkADIDFTYRAYKRGYSIIYQPKSQVWHKVD 227
                                       333414444666555*************999998777668**************************844 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 !   28.8   0.0   3.2e-10   8.2e-07       2     126 ..      13     129 ..      12     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.2e-10
                   Glyco_tranf_2_2   2 vviplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrG 76 
                                       vv+p+++++e     e +  l+  +y  ++ ++i+vddgS++ + e +++       + lk         ++a N+G
  gi|488599600|ref|YP_007906071.1|  13 VVVPVHNNKED--TAEFLesLKSVTY--PNYKIIIVDDGSTDGTEEMIKTAYPEV--ILLKGD--GNLWWSRAVNLG 81 
                                       99****99999..7888843444455..***************999999866544..444444..344556789*** PP

                   Glyco_tranf_2_2  77 askae...sdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdl 126
                                       ++ka    +d+vl +D Dc + s  + ++++     +l +n+ + +v  v ++
  gi|488599600|ref|YP_007906071.1|  82 IEKALeicADYVLLIDNDCVVDSGFMSALVE----TAL-RNPRSIIVSKVLYY 129
                                       ***953348************9999999888....223.35566666555555 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 !   24.5   0.1   8.3e-09   2.1e-05       1     143 [.      92     243 ..      92     295 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.3e-09
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelas.pevaivqgpvlvmnvanwleelaalf.faedhgkdilvrealgrvvp.... 71 
                                       ++ll+D D v++  +   +++   + p+  iv+   +++  ++++e  a++  f+  +  +++     g   +    
  gi|488599600|ref|YP_007906071.1|  92 YVLLIDNDCVVDSGFMSALVETALRnPRSIIVSKVLYYDHPNKIWEAGADINwFKGEYVPIGHGEIDKGQYQTeryv 168
                                       79*****************997665266555555555668899*****99996244444444444344444444444 PP

                   Glyco_trans_2_3  72 ..svGsgaflrrsalqevggwd.gdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayG 143
                                         s+ +ga++++  ++e+g  d  ++     D d+  r++++Gy +++ p s+v+ k+ +t+r  l   +     
  gi|488599600|ref|YP_007906071.1| 169 kcSTLVGALIDVTIFKEMGLMDyKNFPQFKADIDFTYRAYKRGYSIIYQPKSQVWHKVDSTIRKKLPKTSSFRST 243
                                       44778899***********77755577999*******************************99877655544333 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0029      10      81 ..      27      99 ..      14     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                   Glyco_tranf_2_4 10 flahhlalgf..drilvydndstDgtrailkel.pevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                                      fl+ ++++ +   +i+++d++stDgt +++k   pev ll+ d++   + r+v+l  + + ++  ad+vl +D D
  gi|488599600|ref|YP_007906071.1| 27 FLESLKSVTYpnYKIIIVDDGSTDGTEEMIKTAyPEVILLKGDGNLW-WSRAVNLGIEKALEI-CADYVLLIDND 99
                                      56666666553235****************885599****9999874.667766555555454.68999999998 PP

>> Anp1  Anp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00069       1.8      22      58 ..      10      43 ..       2      64 .. 0.78
   2 !    5.8   0.0    0.0031       7.9     123     191 ..      75     145 ..      73     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00069
                              Anp1 22 kvLiltplrdaekflpeyfenllkltyphelidLafl 58
                                       v +++p++++++   e++e l+++typ+ +i    +
  gi|488599600|ref|YP_007906071.1| 10 LVAVVVPVHNNKEDTAEFLESLKSVTYPNYKII---I 43
                                      57799************************9983...3 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0031
                              Anp1 123 araRNsLlssaLkpehswvlwlDaDiv...etpktliedlishdkdvivpnvlrklpdelek..eqpYDlnsWv 191
                                       +ra N  + +aL+    +vl +D D v      + l+e+  +  + +iv +vl     + +k  e   D n W 
  gi|488599600|ref|YP_007906071.1|  75 SRAVNLGIEKALEICADYVLLIDNDCVvdsGFMSALVETALRNPRSIIVSKVLYYD--HPNKiwEAGADIN-WF 145
                                       5888999999***************9865555678999999999*******98744..3444335555554.55 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 ?   10.9   0.0   8.8e-05      0.23      30      80 ..      89     140 ..      76     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.8e-05
                   Glyco_transf_21  30 kydllvisDsdvrvkpdyLeellaa.ledpkvglVtslpvgsdakglaaale 80 
                                        +d++++ D d +v++ ++  l+++ l+ p+  +V+ + ++ ++++++ a +
  gi|488599600|ref|YP_007906071.1|  89 CADYVLLIDNDCVVDSGFMSALVETaLRNPRSIIVSKVLYYDHPNKIWEAGA 140
                                       579*******************98626669999***********99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1862.33
//
Query:       gi|488599601|ref|YP_007906072.1|  [L=276]
Description: hypothetical protein Asulf_00043 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-23   81.9   0.0      9e-23   80.7   0.0    1.6  2  Glycos_transf_1  Glycosyl transferases group 1
    1.3e-19   71.0   0.1    4.2e-19   69.3   0.0    1.8  2  Glyco_trans_1_4  Glycosyl transferases group 1
     0.0057   16.7   0.0      0.015   15.3   0.0    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.034   14.6   0.0    1.7  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
        0.1   13.0   0.0       0.21   12.0   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
       0.11   11.1   0.5       0.17   10.6   0.3    1.3  2  Glyco_transf_20  Glycosyltransferase family 20


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 ?   -1.3   0.0      0.46   1.4e+03      44      63 ..      66      86 ..      58      93 .. 0.63
   2 !   80.7   0.0     3e-26     9e-23       2     170 ..      87     251 ..      86     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.46
                                      HCSCEEEEEES..STTHHHHH CS
                   Glycos_transf_1 44 lnpnvklviaG.ngeeekelk 63
                                      ++ +++l+i+G + +++k l 
  gi|488599601|ref|YP_007906072.1| 66 KRIDLQLTIVGvDFDRFKPLN 86
                                      578999*****6433333333 PP

  == domain 2  score: 80.7 bits;  conditional E-value: 3e-26
                                       HHHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEE CS
                   Glycos_transf_1   2 kekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnvifl 78 
                                       ke+ ++  +++++kk+il+vgrl k Kg d +i+af++lkk  + +v l+++G  ++++ l k a +++     +++
  gi|488599601|ref|YP_007906072.1|  87 KERAKEIVRLPSQKKVILYVGRLYKLKGADIIIQAFKTLKK--KYDVELIMIG-YHQNDPLIKDARAAGA----RII 156
                                       6778889999*****************************97..6*********.8999***********9....999 PP

                                       ECCHSSSHHHHHHCESEEEEEESS......BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHH CS
                   Glycos_transf_1  79 gevsredleellknadifvlpsis......EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaeala 149
                                         +++e+l  ++++ad+fv  s         g G++++EA+a+++pv++   + +++  +d + ++ + p ++e+ a
  gi|488599601|ref|YP_007906072.1| 157 PVIPQEQLVPYYNAADVFVTASFEenvvapGGIGMAPIEALACNTPVVS---PSLRHFPQDDVEKVGKIPQSPEDVA 230
                                       999999******************9***********************7...56666667777777789999***** PP

                                       HHHHHHHHSHHHHHHHHHHHH CS
                   Glycos_transf_1 150 eairklledeelrerlgenar 170
                                       + i+ +led+  ++++++ ar
  gi|488599601|ref|YP_007906072.1| 231 KCIAGILEDPTPYHNCRRVAR 251
                                       ***************999887 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 ?   -1.4   0.0      0.97   2.9e+03      29      38 ..      66      76 ..      35      96 .. 0.65
   2 !   69.3   0.0   1.4e-22   4.2e-19       2     134 .]     101     239 ..     100     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.97
                                      .H.HEEEEEES CS
                   Glyco_trans_1_4 29 kk.dvrlvivG 38
                                      k+ d++l+ivG
  gi|488599601|ref|YP_007906072.1| 66 KRiDLQLTIVG 76
                                      22348899999 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 1.4e-22
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-S CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaad 74 
                                       +vil+vGrl+ + kg+d++++a++ l+kk dv+l+++G ++ +p  ++  a+   ++ ++   +  e+l ++++aad
  gi|488599601|ref|YP_007906072.1| 101 KVILYVGRLY-KLKGADIIIQAFKTLKKKyDVELIMIGYHQnDP-LIK-DARA--AGARIIPVIpqEQLVPYYNAAD 172
                                       89*******5.67**************9977*******775333.444.5542..3455555444388********* PP

                                       EEEE--..-......--SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  75 vfvaPs..e......gfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLled 134
                                       vfv  s  e      g+g++ +Ea+a+ +pvV+ ++  +++   ++ g  + p++pe+ a+ i+ +led
  gi|488599601|ref|YP_007906072.1| 173 VFVTASfeEnvvapgGIGMAPIEALACNTPVVSPSLRHFPQDDvEKVGK-I-PQSPEDVAKCIAGILED 239
                                       *******637788889*******************98776522245553.4.45899***999999987 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   5.1e-06     0.015      90     160 ..       6      69 ..       1      79 [. 0.86
   2 ?   -2.5   0.0       1.5   4.3e+03     103     108 ..     138     143 ..      97     178 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.1e-06
                    Glyco_transf_4  90 alrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekit 160
                                       a++  +++plV+t Hg       ++ l++l  ++  l r +++++d++++ ++a+++++ + +g + ++i 
  gi|488599601|ref|YP_007906072.1|   6 ACLS-KNMPLVITSHGGR-----YNPLMRLIDRIDLLARIAFKNVDCLLVDTQAEKEYFSRILG-DDKRID 69 
                                       5555.8************.....688888888888899999*******************9888.667775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                    Glyco_transf_4 103 vHglye 108
                                       +H  ++
  gi|488599601|ref|YP_007906072.1| 138 YHQNDP 143
                                       333332 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.034      91     154 ..       6      68 ..       2      70 .. 0.84
   2 ?   -2.5   0.0         2     6e+03      34      51 ..     147     162 ..     124     180 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                   Glyco_trans_4_4  91 arrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpadrv 154
                                       a + ++ plv+t hg  +++ + ++   ++ l r +++++d++lv ++ae e++ +  +++ r+
  gi|488599601|ref|YP_007906072.1|   6 ACLSKNMPLVITSHGGRYNPLM-RLIDRIDLLARIAFKNVDCLLVDTQAEKEYFSRILGDDKRI 68 
                                       5556789********9888775.445666789************************88888887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                   Glyco_trans_4_4  34 eleedgvrvhrlpvprrp 51 
                                       +++++g+r++  pv +++
  gi|488599601|ref|YP_007906072.1| 147 DARAAGARII--PVIPQE 162
                                       3566677774..333333 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 ?   12.0   0.0   7.1e-05      0.21      10      75 ..     188     252 ..     168     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                   Glyco_trans_1_2  10 spnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaare 75 
                                       ++ +   Ea+ac++++++    +l+ + +++ e +     ++e++a+ i+  l++p  ++  ++ ar+
  gi|488599601|ref|YP_007906072.1| 188 GIGMAPIEALACNTPVVSP---SLRHFPQDDVEKVGKIpqSPEDVAKCIAGILEDPTPYHNCRRVARR 252
                                       6778889************...466666555544432236***************9877766666555 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   5.5e-05      0.17     233     305 ..      63     129 ..      39     137 .. 0.81
   2 ?   -4.1   0.0       1.5   4.6e+03     362     381 ..     160     179 ..     159     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.5e-05
                                       ETTEEEEEEE------HHHHHHHCCSCHHHHHHHHHHHHT.TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH- CS
                   Glyco_transf_20 233 ykgrkvsvkalpigidverlesalkkesvsekvkelkerfenkkklilgvDrlDyikGvkqkllaferfLeey 305
                                        ++++++++ + +g+d +r++   k     e++ke+    ++ kk+il v rl ++kG +  ++af+++ ++y
  gi|488599601|ref|YP_007906072.1|  63 GDDKRIDLQLTIVGVDFDRFKPLNK-----ERAKEIVRLPSQ-KKVILYVGRLYKLKGADIIIQAFKTLKKKY 129
                                       57899999***********987665.....889999877766.6**********************9986655 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.5
                                       -HHHHHHHHHH-SEEEE--S CS
                   Glyco_transf_20 362 dfeeliallaaadvllvtsl 381
                                       ++e+l+ +++aadv++  s 
  gi|488599601|ref|YP_007906072.1| 160 PQEQLVPYYNAADVFVTASF 179
                                       678999999****9998776 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:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1744.95
//
Query:       gi|488599602|ref|YP_007906073.1|  [L=109]
Description: hypothetical protein Asulf_00044 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.7   0.1       0.12   12.3   0.1    1.2  1  TDRP      Testis development-related protein


Domain annotation for each model (and alignments):
>> TDRP  Testis development-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.8e-06      0.12      51      76 ..      27      52 ..      20      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-06
                              TDRP 51 WdslvlkqnvqskkldeieGWePPkl 76
                                      W  ++ kq+++  k  eie W P + 
  gi|488599602|ref|YP_007906073.1| 27 WHIVTAKQIIRQTKKYEIECWQPERT 52
                                      8889*******9999********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 762.99
//
Query:       gi|488599603|ref|YP_007906074.1|  [L=66]
Description: hypothetical protein Asulf_00045 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0013   18.4   3.9      0.043   13.6   0.1    2.6  2  UVR          UvrB/uvrC motif
     0.0019   18.4   1.5     0.0027   17.9   1.5    1.4  1  DUF4976      Domain of unknown function (DUF4976)
     0.0064   16.4   0.3      0.011   15.7   0.1    1.5  2  DUF4994      Domain of unknown function
  ------ inclusion threshold ------
      0.011   14.7   0.2      0.011   14.6   0.2    1.0  1  Imm65        Immunity protein 65
      0.026   15.3   0.2       0.03   15.0   0.2    1.1  1  Sulfatase_C  C-terminal region of aryl-sulfatase
      0.034   13.8   0.8      0.034   13.8   0.8    1.9  2  DUF2312      Uncharacterized protein conserved in bacteria (D


Domain annotation for each model (and alignments):
>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.5e-05     0.043      18      32 ..      24      38 ..      23      38 .. 0.88
   2 !    4.8   1.2     0.008        24      14      34 ..      42      61 ..      41      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                               UVR 18 edFEkAAklRDqina 32
                                       d+E A++lRD +++
  gi|488599603|ref|YP_007906074.1| 24 NDYEIAMELRDTLSK 38
                                      69*********9975 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.008
                               UVR 14 AaenedFEkAAklRDqinalk 34
                                       +en  FEkA k++ +i++l+
  gi|488599603|ref|YP_007906074.1| 42 HIENKKFEKA-KIKEKIKRLR 61
                                      6788999997.7888888887 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.5     9e-07    0.0027      62     100 ..       6      42 ..       2      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9e-07
                           DUF4976  62 welyDlkkDpkelknlyddpeyeevvkelkkkleelrkk 100
                                        ely+lk+Dp+e +n+++++   e++ el++ l++  ++
  gi|488599603|ref|YP_007906074.1|   6 EELYNLKEDPEEENNIIEND--YEIAMELRDTLSKWVEH 42 
                                       59***************876..46777777777766554 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.6e-06     0.011      68      98 .]       6      36 ..       3      36 .. 0.92
   2 ?   -2.2   0.0       1.3     4e+03      79      90 ..      49      56 ..      39      62 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                           DUF4994 68 pqLydlkkdegekenvaekhpekvkelkelL 98
                                      + Ly+lk+d+ e++n+ e+  e+  el++ L
  gi|488599603|ref|YP_007906074.1|  6 EELYNLKEDPEEENNIIENDYEIAMELRDTL 36
                                      68************************98765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                           DUF4994 79 ekenvaekhpek 90
                                      ek     k  ek
  gi|488599603|ref|YP_007906074.1| 49 EKA----KIKEK 56
                                      322....23333 PP

>> Imm65  Immunity protein 65
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   3.8e-06     0.011     277     320 ..      18      63 ..       5      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-06
                             Imm65 277 kfrimhndavyssdlrdslskrvryiynkgvydk..eerirrffkw 320
                                       +  i+ nd   + +lrd+lsk v +i nk       +e+i+r+  +
  gi|488599603|ref|YP_007906074.1|  18 ENNIIENDYEIAMELRDTLSKWVEHIENKKFEKAkiKEKIKRLRSF 63 
                                       46799***********************986432125777776544 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2     1e-05      0.03      56      98 ..       8      47 ..       5      63 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                                      EEETTT-TT--S-TTSTTCCHHHHHHHHHHHHHHHCCC----- CS
                       Sulfatase_C 56 lFdlerDpsEkyplsaespeykevlkeikkaveehkktlkpvp 98
                                      l++l++Dp+E++++ +++    e+  e+++ + ++ + +++ +
  gi|488599603|ref|YP_007906074.1|  8 LYNLKEDPEEENNIIEND---YEIAMELRDTLSKWVEHIENKK 47
                                      9**************655...4444555555555555555433 PP

>> DUF2312  Uncharacterized protein conserved in bacteria (DUF2312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4      0.25   7.5e+02      55      68 ..      14      27 ..       7      31 .. 0.52
   2 ?   13.8   0.8   1.1e-05     0.034       2      29 ..      33      60 ..      32      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.25
                           DUF2312 55 dereEeeallelYk 68
                                      d  eE++ + + Y 
  gi|488599603|ref|YP_007906074.1| 14 DPEEENNIIENDYE 27
                                      33344555555555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.1e-05
                           DUF2312  2 adqLrqfieRiErleeEkkaiaedikdv 29
                                      +d L + +e iE+ + Ek++i+e+ik +
  gi|488599603|ref|YP_007906074.1| 33 RDTLSKWVEHIENKKFEKAKIKEKIKRL 60
                                      57899*********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1415  (0.0789224); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 429.61
//
Query:       gi|488599604|ref|YP_007906075.1|  [L=69]
Description: hypothetical protein Asulf_00046 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.1   0.2      0.047   13.8   0.2    1.1  1  DUF5432   Family of unknown function (DUF5432)
      0.043   14.0   0.1      0.048   13.8   0.1    1.0  1  RTC4      RTC4-like domain


Domain annotation for each model (and alignments):
>> DUF5432  Family of unknown function (DUF5432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   5.3e-06     0.047      16      63 ..      17      63 ..       5      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-06
                           DUF5432 16 escssihllslhPlyv.imsPmdiiGfnkyfrsdtkilfvdvldlillc 63
                                      +    ih++ l+ l++ i   ++    n + r+++k+l+ +v  l ++ 
  gi|488599604|ref|YP_007906075.1| 17 NN--CIHSFVLKKLFInINEQLEQTNINTFKRYQKKVLYAEVAALCMVA 63
                                      44..59*********9566789*******************98887765 PP

>> RTC4  RTC4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.3e-06     0.048      41      92 ..      11      59 ..       3      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-06
                              RTC4 41 YYGlkgqriiseeilkkfkkelrkravkdklvsargvsdFvqaVLvPEvavr 92
                                      YY ++  ++i++ +lkk+  +++++ ++ +     + + + ++VL  Eva++
  gi|488599604|ref|YP_007906075.1| 11 YYAMRLNNCIHSFVLKKLFININEQLEQTN---INTFKRYQKKVLYAEVAAL 59
                                      *****************9888887665555...689*************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 416.60
//
Query:       gi|488599605|ref|YP_007906076.1|  [L=337]
Description: hypothetical protein Asulf_00047 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-49  167.3   0.0    6.2e-49  167.0   0.0    1.1  1  Sulfatase      Sulfatase
    2.3e-13   50.5   1.1    3.9e-06   26.7   0.0    2.2  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
     0.0009   18.0   0.1     0.0012   17.6   0.1    1.3  1  DUF229         Protein of unknown function (DUF229)
  ------ inclusion threshold ------
       0.09   12.1   0.6       0.15   11.4   0.6    1.3  1  Metalloenzyme  Metalloenzyme superfamily


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 !  167.0   0.0   1.4e-52   6.2e-49       1     284 [.       8     332 ..       8     337 .] 0.86

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 1.4e-52
                                       EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT.. CS
                         Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg.. 75 
                                       pn+++i++d l+a +l++yg++  t pn+d++a++g++f n+ys+++++ ps  ++++g+y  ++g+ +++   +  
  gi|488599605|ref|YP_007906076.1|   8 PNIIFIVIDALRARNLSCYGYSKLTSPNIDNIAKKGILFENAYSCTNTTDPSITTIFSGKYILSHGIIHHGTLVQks 84 
                                       9********************************************************************9988889* PP

                                       ...HHCTTTS-HHHHHHHHTT-EEEEEEES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCC... CS
                         Sulfatase  76 ...gglpqteatLpellkeaGYntaaigkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrv... 146
                                          + +   + +Lpe+lk+ GY t+a+      w+       +rg+d ++g p+gs+a  +       + +  +   
  gi|488599605|ref|YP_007906076.1|  85 einKLKESGTYFLPEILKSYGYVTCAFD-ILGRWH-------KRGYDFYIG-PSGSSAAVGGIIKRIKRTAS-Kfps 151
                                       **999999999*************6654.333333.......456664444.55555544433333332222.2456 PP

                                       .................TTTTCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCC CS
                         Sulfatase 147 .................ppeggysddrlldealefllarn.dkpfflylatlapHappeapdeyakkyatffddgse 205
                                                        +p  + + ++l+++a++f+ ++n +k+ffl++++  +H+ ++ p+ey +k++  ++ +se
  gi|488599605|ref|YP_007906076.1| 152 piykflkvlylkirgesEPVIYDDAKILTNKAIRFI-DQNlGKKFFLFIHYWDVHQ-YNPPKEYIGKFSIDDNIQSE 226
                                       677777779999999877778889999********5.7777**************6.9**********999998888 PP

                                       CCH..............................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSC CS
                         Sulfatase 206 aar..............................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgas 252
                                       ++                                 ++ y+ +++ vD+ igr+++ Le+++ ld+t+++ t+Dhg+s
  gi|488599605|ref|YP_007906076.1| 227 EEIlnqitypttlpsvkegllrhivsreiktvsDFIARYDEAIYFVDHEIGRLIEHLEKKKILDDTFIILTADHGES 303
                                       877889999999999999*********************************************************** PP

                                       CCGHHTTSSSCTTCSSSHHHHBEEEEEEETTT CS
                         Sulfatase 253 leesngplrggkganayeggtrvPllvwwpge 284
                                       l e  g + ++ g   y+  +++Pl+  +p++
  gi|488599605|ref|YP_007906076.1| 304 LFE-HGIFVDHHG--LYDVNIHIPLIFLYPEI 332
                                       *99.777777777..9**********999986 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   8.7e-10   3.9e-06       2      69 ..      11      80 ..      10     137 .. 0.89
   2 !   22.6   0.3   1.5e-08   6.7e-05     199     236 ..     267     304 ..     248     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 8.7e-10
                                      EEEEETT-BTTHHHHHG.S..TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEE CS
                      Phosphodiest  2 lvislDGlradlldrla.e..llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfy 69
                                      ++i++D lra+ l+ +     + pn++++ak+g+ ++n ++  +t T p+ +++ +G+y  +HGi++   +
  gi|488599605|ref|YP_007906076.1| 11 IFIVIDALRARNLSCYGySklTSPNIDNIAKKGILFENAYSCTNT-TDPSITTIFSGKYILSHGIIHHGTL 80
                                      79***********9987657999**************99999886.89******************96655 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EE CS
                      Phosphodiest 199 dalrrvDkaigdLlealderglsaetniilvSDHGmad 236
                                       +a+  vD+ ig+L+e l+++++ ++t iil++DHG + 
  gi|488599605|ref|YP_007906076.1| 267 EAIYFVDHEIGRLIEHLEKKKILDDTFIILTADHGESL 304
                                       67788******************************665 PP

>> DUF229  Protein of unknown function (DUF229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.6e-07    0.0012     303     344 ..     261     302 ..     175     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-07
                            DUF229 303 lshdkfnllealDedllkylkklekkgllentlvlllsDHGl 344
                                       ++ ++ + +  +D+++ +++ +lekk++l++t+++l +DHG 
  gi|488599605|ref|YP_007906076.1| 261 FIARYDEAIYFVDHEIGRLIEHLEKKKILDDTFIILTADHGE 302
                                       445555666678*****************************5 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   3.3e-05      0.15     153     187 ..     264     302 ..     257     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHHHHHHHHHTTS-T....TTEEEEEE-SSB- CS
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                     Metalloenzyme 153 atiaaieaaDeavkeildaieq....vdgilvvtADHgn 187
                                       ++ +ai  +D+ ++++++++e+    +d+ +++tADHg 
  gi|488599605|ref|YP_007906076.1| 264 RYDEAIYFVDHEIGRLIEHLEKkkilDDTFIILTADHGE 302
                                       56789999*************93333467899*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2086.20
//
Query:       gi|488599606|ref|YP_007906077.1|  [L=306]
Description: putative dehydrogenase-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   99.9   1.6    4.2e-28   98.6   0.3    2.0  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    8.4e-06   25.3   0.3    1.7e-05   24.3   0.1    1.6  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.4e-05   23.8   4.5    0.00048   19.5   4.3    2.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    3.9e-05   23.9   2.1    0.00048   20.3   0.1    2.3  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00057   19.9   0.0     0.0013   18.7   0.0    1.6  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    0.00066   20.3   0.3      0.002   18.7   0.3    1.8  1  CoA_binding     CoA binding domain
     0.0015   19.0   0.2      0.004   17.7   0.1    1.7  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.003   17.6   0.3      0.024   14.7   0.1    2.1  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.012   15.2   0.5      0.042   13.4   0.2    2.0  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.055   13.3   2.5       0.15   11.9   0.3    2.2  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.073   13.0   0.9        0.2   11.6   0.6    2.0  2  RuvC            Crossover junction endodeoxyribonuclease RuvC
       0.38   10.3   5.1       0.45   10.1   2.0    2.4  2  UDPG_MGDP_dh_N  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 !   98.6   0.3   2.8e-31   4.2e-28       1     120 []       7     123 ..       7     123 .. 0.98
   2 ?   -0.1   0.1         1   1.6e+03      83     110 ..     274     302 ..     268     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 2.8e-31
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthee 77 
                                       +rv++iG+G +g++h+r ++e   + e+v++ d d+er e+v++ +g  a+ +++ell+ ++idav++a+p++ h +
  gi|488599606|ref|YP_007906077.1|   7 IRVGVIGVGVMGKNHVRVYKEL--GCELVGIADVDKERVEEVSRLYGTRAFMSYKELLN-SRIDAVSIAVPTTFHGK 80 
                                       69**************999988..99*********************************.77*************** PP

                                       HHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  78 lakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       +a++a++ag++vl+EKP+a++v+ a e++e+a+k++++++vg+
  gi|488599606|ref|YP_007906077.1|  81 VALDAINAGVNVLVEKPIADSVKSALEIIEAAKKRSVKLMVGH 123
                                       *****************************************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                                       HHTT-.EEEEESSS-SSHHHHHHHHHHHH CS
                      GFO_IDH_MocA  83 leagk.hvllEKPlattveeakelvelae 110
                                       l a++ +++ +KP+  + e+  +++e ae
  gi|488599606|ref|YP_007906077.1| 274 LSAFVeSIIKDKPVPVSGEDGLKVLEVAE 302
                                       667788999*****999999999998875 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 !   24.3   0.1   1.1e-08   1.7e-05      33     104 ..       3      78 ..       1      87 [. 0.79
   2 ?   -3.0   0.0       2.6   3.9e+03      84      98 ..     133     147 ..     121     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.1e-08
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTC.EECSHHHHHH.H-SEEEE-S--STT CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgv.elvsleella.esDivslhlpltpe 104
                                        l++ +vG+iG+G +G++  ++ k++g++++++    k++     + +g   ++s +ell+ + D vs+++p t +
  gi|488599606|ref|YP_007906077.1|   3 GLENIRVGVIGVGVMGKNHVRVYKELGCELVGIADVDKERVeeVSRLYGTrAFMSYKELLNsRIDAVSIAVPTTFH 78 
                                       578899***********************99998877755543344556656779999995279********9866 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                       SHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C  84 sleellaesDivslh 98 
                                        ++e +a++D++s+ 
  gi|488599606|ref|YP_007906077.1| 133 VIKERIAHADVISIS 147
                                       567889999999986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   4.3   3.2e-07   0.00048      24      98 ..       2      75 ..       1     158 [. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.2e-07
                                      TCB---EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE- CS
                       AlaDh_PNT_C 24 pgvepakvlviGgGvaGlqAiatakglgak.VtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigt 98
                                      +g e+ +v viG+Gv G + +++ k+lg + V + Dv+++r e+++ l ++  ++ +s +ell++++  + + + t
  gi|488599606|ref|YP_007906077.1|  2 RGLENIRVGVIGVGVMGKNHVRVYKELGCElVGIADVDKERVEEVSRLYGT--RAFMSYKELLNSRIDAVSIAVPT 75
                                      5778899*********************9857899************5555..47777777777777777776655 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   3.2e-07   0.00048       1      68 [.       8      78 ..       8      92 .. 0.85
   2 ?    3.4   0.4     0.051        76      37      90 ..      92     147 ..      79     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.2e-07
                                      EEEEE--SHHHHHHHHHHHHTT-EEEE.E-SSHHHHHHHHHT.TEEE-SSHHHHHHHC.SEEEE-SSSHHH CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvav.ynrtkekveelvae.gakaaesieelvasl.dvvitmvkagka 68
                                      ++g+iG+GvMG+n ++  ++ g+++++  +++ke+vee+    g +a+ s +el++s  d+v + v+ + +
  gi|488599606|ref|YP_007906077.1|  8 RVGVIGVGVMGKNHVRVYKELGCELVGiADVDKERVEEVSRLyGTRAFMSYKELLNSRiDAVSIAVPTTFH 78
                                      58*********************98761679999**99998746999******999877***999998755 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.051
                                       HHHHTT.EEE-SSHHHHHHHC..SEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S CS
                     NAD_binding_2  37 elvaeg.akaaesieelvasl..dvvitmvkagkavdeviegllealkkgdilidgs 90 
                                        lv++  a+ ++s+ e+++++  + v +mv + +  + v+e ++e+++  d+ i  s
  gi|488599606|ref|YP_007906077.1|  92 VLVEKPiADSVKSALEIIEAAkkRSVKLMVGHVERFNPVVEVIKERIAHADV-ISIS 147
                                       455554456666667777777779999***9999999999999999877775.4444 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.9e-07    0.0013      39      69 ..     160     190 ..     153     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.9e-07
                                       STSHHHHTCHHHHHHHHHHHTSEEEEEEEEE CS
                    GFO_IDH_MocA_C  39 sgGvlgdlgiHdiDllqwLfGqppsvvaalg 69 
                                       + Gv+ dl++HdiDl+++L+ ++p++++   
  gi|488599606|ref|YP_007906077.1| 160 DVGVVLDLATHDIDLARYLTESEPVEIYSFI 190
                                       679*********************9998663 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   1.4e-06     0.002       3      91 ..       6      94 ..       5      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                                      TEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET..TEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding  3 dtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl..glpvyksvdeleektevdvavitvPaesaqeav 79
                                      + +v+viG+g +g+  + ++ ++l+++++ +++v+ + v +  +  g  ++ s +el ++  +d+  i+vP ++  +++
  gi|488599606|ref|YP_007906077.1|  6 NIRVGVIGVGVMGKNHV-RVYKELGCELVGIADVDKERVEEVSRlyGTRAFMSYKELLNS-RIDAVSIAVPTTFHGKVA 82
                                      568*********66655.566677*************888666688999**9******99.9***************** PP

                                      HHHHHTT-SEEE CS
                       CoA_binding 80 delveagikgiv 91
                                      +++++ag+++ v
  gi|488599606|ref|YP_007906077.1| 83 LDAINAGVNVLV 94
                                      ********9876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.7e-06     0.004       1      79 [.       8      83 ..       8      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.7e-06
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH.H-SEEEE-S-HHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae.eadvvvlavkpedveevl 78
                                      ++g+iG G mg+  ++   + g    e+v +++ ++e++ee  + +g +++  +++e+++ + d v +av+++ + +v+
  gi|488599606|ref|YP_007906077.1|  8 RVGVIGVGVMGKNHVRVYKELG---CELVGIADVDKERVEEVSRLYGTRAFM-SYKELLNsRIDAVSIAVPTTFHGKVA 82
                                      69********************...6666566*******************9.7777777699*********9998887 PP

                                      H CS
                     F420_oxidored 79 s 79
                                       
  gi|488599606|ref|YP_007906077.1| 83 L 83
                                      5 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.6e-05     0.024      10      80 ..       4      73 ..       1      88 [. 0.80
   2 ?    0.8   0.0      0.32   4.7e+02      66      84 ..     131     149 ..      92     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                      .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCG.HHHHHHT-SEEE CS
                      Shikimate_DH 10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealklee.lkellaeadvvi 80
                                      l++ +v +iG G m++  ++   + g++ v +a  + er++e+ + +++    +++++e l+++++++ + +
  gi|488599606|ref|YP_007906077.1|  4 LENIRVGVIGVGVMGKNHVRVYKELGCELVGIADVDKERVEEVSRLYGTR--AFMSYKElLNSRIDAVSIAV 73
                                      67889**************************************9988666..45555541455666666655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.32
                                       GCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH  66 leelkellaeadvvisata 84 
                                       +e +ke++a+adv+ ++t 
  gi|488599606|ref|YP_007906077.1| 131 VEVIKERIAHADVISISTV 149
                                       5668999******999986 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   2.8e-05     0.042       2      83 ..       4      88 ..       3     121 .. 0.83
   2 ?   -0.8   0.0      0.64   9.6e+02      27      66 ..     105     146 ..      99     148 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                                      HHTS-EEEES-SHHHHHHHHHHHHTT--EE.EEE-TT-HHHHHHHHTT-EE.EEHHHHHH.T-SEEEE-S-HHHHHHHH CS
                              IlvN  2 lkgkkiaviGyGsqGhaqalnlrdsgldvv.vglregsksvkkAkeegfev.ltvaeavk.kadvvmiliPDelqkevy 77
                                      l++ ++ viG G  G+++ +  ++ g+++v ++  ++++  +  +  g +  ++++e+ + + d v i +P +++ +v 
  gi|488599606|ref|YP_007906077.1|  4 LENIRVGVIGVGVMGKNHVRVYKELGCELVgIADVDKERVEEVSRLYGTRAfMSYKELLNsRIDAVSIAVPTTFHGKVA 82
                                      67889**********************955377777777778888888875378999875268************9998 PP

                                      HHHTGG CS
                              IlvN 78 eeeiep 83
                                       ++i+ 
  gi|488599606|ref|YP_007906077.1| 83 LDAINA 88
                                      888765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.64
                                       T--EEEEE-TT-HHHHHHHHTT-E..EEEHHHHHHT-SEEEE CS
                              IlvN  27 gldvvvglregsksvkkAkeegfe..vltvaeavkkadvvmi 66 
                                        l+++ + ++ s ++   + e f+  v  ++e +++adv+ i
  gi|488599606|ref|YP_007906077.1| 105 ALEIIEAAKKRSVKLMVGHVERFNpvVEVIKERIAHADVISI 146
                                       566666666666655555555554325678999999999987 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 ?   11.9   0.3    0.0001      0.15       2      41 ..       9      49 ..       8      85 .. 0.84
   2 ?    1.3   0.1      0.18   2.7e+02      15      67 ..      82     134 ..      76     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                      EEEE--SCCHHHHHHHHHHTT-E.EEEE-S-HHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagle.Vvlvdiseealekalek 41
                                      v+viG G+mG+    v  + g+e V + d+++e++e++ + 
  gi|488599606|ref|YP_007906077.1|  9 VGVIGVGVMGKNHVRVYKELGCElVGIADVDKERVEEVSRL 49
                                      9*********************9566899999999987665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.18
                                       HHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCE CS
                           3HCDH_N  15 aavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalari 67 
                                       a  +++ag++V +    ++++++ale ie+  ++ v+    + e ++ +++ i
  gi|488599606|ref|YP_007906077.1|  82 ALDAINAGVNVLVEKPIADSVKSALEIIEAAKKRSVKLMVGHVERFNPVVEVI 134
                                       66678889999999999999999999999877777765554455555555444 PP

>> RuvC  Crossover junction endodeoxyribonuclease RuvC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2   1.8e+03     107     122 ..      31      46 ..       7      74 .. 0.73
   2 ?   11.6   0.6   0.00013       0.2      78     128 ..      74     126 ..      41     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                                       HHTSSTT--HHHHHHH CS
                              RuvC 107 avtGigkaekeqvqal 122
                                        ++Gi++ +ke v+ +
  gi|488599606|ref|YP_007906077.1|  31 ELVGIADVDKERVEEV 46 
                                       5788888888888764 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHTTT--EEEE..EHHHHHHHHTSSTT--HHHHHHHHHHHTT CS
                              RuvC  78 laqarGvvilaalereisvaey..tpsqvkkavtGigkaekeqvqalvkrlLk 128
                                        + + G v+l a++ +++v      +  vk a+  i +a+k+ v+ +v ++ +
  gi|488599606|ref|YP_007906077.1|  74 PTTFHGKVALDAINAGVNVLVEkpIADSVKSALEIIEAAKKRSVKLMVGHVER 126
                                       45789***********998765115679********************98755 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 ?   10.1   2.0    0.0003      0.45       2      41 ..       8      48 ..       7     114 .. 0.90
   2 ?   -0.3   0.1      0.47     7e+02     102     127 ..     129     153 ..     118     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE.-S-HHHHHHHCT CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigv.Dideekvdklns 41
                                      ++ viG G +G  +  v+ e+g e++g+ D+d+e+v+++ +
  gi|488599606|ref|YP_007906077.1|  8 RVGVIGVGVMGKNHVRVYKELGCELVGIaDVDKERVEEVSR 48
                                      899*********************99987*******99865 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHCEEEEEE-S---TTH CS
                    UDPG_MGDP_dh_N 102 saarsiaealkkgkvvvvkSTvpvgt 127
                                        +++ i+e + + +v+ + STv vg 
  gi|488599606|ref|YP_007906077.1| 129 PVVEVIKERIAHADVISI-STVRVGP 153
                                       577788888888887655.8998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1730.65
//
Query:       gi|488599607|ref|YP_007906078.1|  [L=255]
Description: Acyl-(acyl carrier protein)--UDP-N-acetylglucosamine O-acyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   69.2  20.4    9.6e-10   37.8   0.7    4.7  5  Hexapep          Bacterial transferase hexapeptide (six repea
    1.6e-08   34.9   0.0    5.4e-08   33.2   0.0    1.9  1  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D
     0.0053   16.5   1.0     0.0053   16.5   1.0    4.2  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   1.0   3.8e-10   2.3e-06       2      35 ..      36      69 ..      35      70 .. 0.95
   2 !    9.0   1.0    0.0002       1.2      20      34 ..      88     102 ..      85     103 .. 0.70
   3 !   37.8   0.7   1.6e-13   9.6e-10       2      36 .]     110     144 ..     109     144 .. 0.97
   4 !   15.2   1.0   2.1e-06     0.013       5      29 ..     131     155 ..     130     162 .. 0.88
   5 !    7.0   0.2   0.00085       5.1       2      34 ..     146     178 ..     145     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.8e-10
                                      EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                      + I s +lI p+++i g V+IG n +Ig+++vig
  gi|488599607|ref|YP_007906078.1| 36 AEIKSSTLILPGCMIVGEVEIGGNNVIGPYTVIG 69
                                      7899*****************************8 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0002
                                       EEE-TTEEEETTEEE CS
                           Hexapep  20 VkIGdnvkIgagvvi 34 
                                       ++IG+n +I ++v++
  gi|488599607|ref|YP_007906078.1|  88 IVIGNNNIIREFVTV 102
                                       677777777777776 PP

  == domain 3  score: 37.8 bits;  conditional E-value: 1.6e-13
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       tvIG+n+++ +++++g++V++G+nv++ +++ igg
  gi|488599607|ref|YP_007906078.1| 110 TVIGDNCFLLAYVHLGHDVILGNNVTLSNNTQIGG 144
                                       89*****************************9997 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 2.1e-06
                                       ETTEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep   5 GsnvlIgpfaviggnVkIGdnvkIg 29 
                                       G+nv++ ++++igg+ +I dnv+ g
  gi|488599607|ref|YP_007906078.1| 131 GNNVTLSNNTQIGGHSTIKDNVITG 155
                                       9*********************977 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.00085
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       ++I +nv+ g ++ i+  +++G ++ Ig g+ +
  gi|488599607|ref|YP_007906078.1| 146 STIKDNVITGLNTCIHQYTTLGAYSMIGMGSIV 178
                                       788999999999999999999999999999876 PP

>> Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0     9e-12   5.4e-08       1      48 [.     181     226 ..     181     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 9e-12
                                       BB-TTEEEETTTTEEEEE-HHHHHHTT--HHHHHHHHHHHHHHHSSSS CS
                   Acetyltransf_11   1 DVpPfvlvagnparlrglNlvgLkRrgfseeeikalkkayrllyrsgl 48 
                                       DVpPfv+ +      + +N vgL+R+gf+ +ei+++kk y+ +   ++
  gi|488599607|ref|YP_007906078.1| 181 DVPPFVVYKN--FICYKINEVGLERAGFNTSEIEEIKKYYKEFLDIDK 226
                                       9*****9987..9****************************9987443 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.7      0.11   6.6e+02      18      28 ..      54      64 ..      46      70 .. 0.50
   2 ?   -2.7   0.7      0.88   5.3e+03       3       7 ..      89      93 ..      86      96 .. 0.51
   3 !   16.5   1.0   8.9e-07    0.0053       2      30 ..     110     140 ..     109     143 .. 0.84
   4 !    3.6   0.1    0.0093        56       6      32 ..     150     178 ..     147     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.11
                                      EEE-TT-EE-T CS
                         Hexapep_2 18 vslGdncvvga 28
                                      v++G n v+g+
  gi|488599607|ref|YP_007906078.1| 54 VEIGGNNVIGP 64
                                      55555555544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.88
                                      EE-TT CS
                         Hexapep_2  3 iIGdn 7 
                                       IG+n
  gi|488599607|ref|YP_007906078.1| 89 VIGNN 93
                                      44444 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 8.9e-07
                                       EEE-TT-EE-TT-EES..EEE-TT-EE-TT- CS
                         Hexapep_2   2 viIGdnCliGanagiG..vslGdncvvgaGv 30 
                                       + IGdnC++ a    G  v+lG+n++++++ 
  gi|488599607|ref|YP_007906078.1| 110 TVIGDNCFLLAYVHLGhdVILGNNVTLSNNT 140
                                       68******9777777666***********97 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.0093
                                       TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   6 dnCliGanagi..GvslGdncvvgaGvvi 32 
                                       dn++ G n +i   ++lG  + +g+G+++
  gi|488599607|ref|YP_007906078.1| 150 DNVITGLNTCIhqYTTLGAYSMIGMGSIV 178
                                       8999999988865599***9*****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1732.40
//
Query:       gi|488599608|ref|YP_007906079.1|  [L=255]
Description: 3-oxoacyl-(acyl-carrier-protein) reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-76  255.3   0.9    6.3e-76  255.0   0.9    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.2e-69  231.9   3.6    4.9e-69  231.7   3.6    1.0  1  adh_short        short chain dehydrogenase
    1.3e-20   74.1   0.3    1.6e-20   73.8   0.3    1.1  1  KR               KR domain
    0.00059   20.1   1.2     0.0012   19.1   0.5    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00088   18.8   0.3     0.0015   18.0   0.3    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0035   17.3   0.5     0.0047   16.8   0.5    1.2  1  NAD_binding_10   NAD(P)H-binding
     0.0043   16.4   0.1        0.1   11.9   0.0    2.5  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
     0.0091   15.4   0.0      0.054   12.8   0.0    2.0  1  DUF1776          Fungal family of unknown function (DUF1776)
  ------ inclusion threshold ------
      0.067   12.6   0.1       0.11   11.9   0.1    1.3  1  PALP             Pyridoxal-phosphate dependent enzyme


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 !  255.0   0.9   3.2e-79   6.3e-76       1     233 [.      20     253 ..      20     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 255.0 bits;  conditional E-value: 3.2e-79
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilv 74 
                                       G  +gIGra+A +la+eG +vv+++l++++ +++v+++ e++g++ + +++DV++ ++v+++ve+v +k+g++Dilv
  gi|488599608|ref|YP_007906079.1|  20 GSSRGIGRAVALSLAREGSDVVVSYLEKKEkAREVADMIEDMGRRaItIQVDVKNFNEVAHMVEHVIKKLGRIDILV 96 
                                       5679**************************99***********88448***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaale 149
                                       nnagi ++    + ++++ee+d+++++nl+++f+++ka++p+m+++  g+ivn+ssv +  +  +++ y+a+Ka+++
  gi|488599608|ref|YP_007906079.1|  97 NNAGIIRD--RTIKKMEKEEWDDVINTNLTGVFNCTKAVIPYMEKQggGKIVNISSVIGLAGNFGQTNYAASKAGVI 171
                                       ********..*******************************9998889***************************** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                       ++t++lA+el++kgi vNav+pg+++T + ++i+  +++++++ +r+plgr++tp+e+ ++++fLasd+a+yitGq+
  gi|488599608|ref|YP_007906079.1| 172 GFTKSLAKELARKGILVNAVAPGFVETGMLKAIP--NRIKKQILERIPLGRFATPDEISKVVVFLASDDANYITGQV 246
                                       *********************************9..89*************************************** PP

                                       EEESTTG CS
                      adh_short_C2 227 lvvDgGl 233
                                       ++vDgG+
  gi|488599608|ref|YP_007906079.1| 247 IIVDGGW 253
                                       ******6 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.7   3.6   2.5e-72   4.9e-69       1     191 [.      14     205 ..      14     209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 2.5e-72
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                       kv+lvtG s+GIGra+a  la+eG +vvv + +++ek++eva+ +++ g++a++iqvDv++ +ev  +ve+++kklg
  gi|488599608|ref|YP_007906079.1|  14 KVALVTGSSRGIGRAVALSLAREGSDVVVsYLEKKEKAREVADMIEDMGRRAITIQVDVKNFNEVAHMVEHVIKKLG 90 
                                       89*************************************************************************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       ++d+LvnNAGi ++++++++++eew++vi++Nltgvf++t+av+p+m kq +G+Ivn+sSv+g+ +++g++ Y+AsK
  gi|488599608|ref|YP_007906079.1|  91 RIDILVNNAGIIRDRTIKKMEKEEWDDVINTNLTGVFNCTKAVIPYMEKQGGGKIVNISSVIGLAGNFGQTNYAASK 167
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                       a+v+g+t+slakela++gi vnavaPG+v+T+m k++ 
  gi|488599608|ref|YP_007906079.1| 168 AGVIGFTKSLAKELARKGILVNAVAPGFVETGMLKAIP 205
                                       *********************************99875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.3   8.1e-24   1.6e-20       3     173 ..      16     191 ..      14     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 8.1e-24
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        l+tG   g+G+++a  la++g   +v    +   +e++++  + +e++g +  ++++Dv + ++v++++e++ ++ 
  gi|488599608|ref|YP_007906079.1|  16 ALVTGSSRGIGRAVALSLAREGSDVVVSYLEK---KEKAREVADMIEDMGRRAITIQVDVKNFNEVAHMVEHVIKKL 89 
                                       59********************9977665555...67788899999******************************* PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaa 152
                                       ++i   ++ Ag++rd+++++m++e+++ v++  ++G+ n  +++ +    +    +v +SS+ gl g++gq+nYaa 
  gi|488599608|ref|YP_007906079.1|  90 GRIDILVNNAGIIRDRTIKKMEKEEWDDVINTNLTGVFNCTKAVIPymekQGGGKIVNISSVIGLAGNFGQTNYAAS 166
                                       ***************************************9998766555477889*********************8 PP

                                       HH....HHHHHHHHHHHHHHTEEEE CS
                                KR 153 Na....flDalaeyrrsqglpavsi 173
                                        a    f  +la++ +++g  + ++
  gi|488599608|ref|YP_007906079.1| 167 KAgvigFTKSLAKELARKGILVNAV 191
                                       7644446777777777777666655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5   6.2e-07    0.0012       8      88 ..      24     110 ..      17     146 .. 0.79
   2 ?   -2.3   0.0       2.5     5e+03      61      79 ..     176     193 ..     173     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.2e-07
                                       HHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTS.......SEEE CS
                   Sacchrp_dh_NADP   8 svGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkeg.......dlvv 74 
                                       ++G+ava  lar+++    ++v   +k++ ++++a++    g r+++i++d++n  + +a ++++        d++v
  gi|488599608|ref|YP_007906079.1|  24 GIGRAVALSLAREGSD---VVVSYLEKKEKAREVADMiedMGRRAITIQVDVKNFNE-VAHMVEHVikklgriDILV 96 
                                       79***********987...5555444444445555556999****************.8888888888889****** PP

                                       E-SSGGGHHHHHHH CS
                   Sacchrp_dh_NADP  75 nlsppissldvlka 88 
                                       n ++ i ++++ k+
  gi|488599608|ref|YP_007906079.1|  97 NNAGIIRDRTIKKM 110
                                       ****9999998776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                       HHHHHHHTTSSEEEE-SSG CS
                   Sacchrp_dh_NADP  61 avLaallkegdlvvnlspp 79 
                                       + La+ l+ ++++vn++ p
  gi|488599608|ref|YP_007906079.1| 176 S-LAKELARKGILVNAVAP 193
                                       4.77888888999998765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   7.7e-07    0.0015       1     116 [.      16     151 ..      16     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.7e-07
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HH....HHHHHHHHH.T- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrs....alerlfkee.qp 65 
                                       +lVtG +  iG+a++  l+++g +v++   ++++++++  + +         +++d+++ +     +e ++k+  ++
  gi|488599608|ref|YP_007906079.1|  16 ALVTGSSRGIGRAVALSLAREGSDVVVSYLEKKEKAREVADMIedmgrraITIQVDVKNFNevahMVEHVIKKLgRI 92 
                                       59**********************9888888666666665555999***999999999998555556778888899* PP

                                       SEEEE--S.---...HHHHHHSHHHHHHHHTHHHHH....HHHHHHHHTCTEEEEEEEG CS
                         Epimerase  66 davihlAa.vgg...vaassedpadfieknlqgtln....lleaarkagvkrllflsSs 116
                                       d+ ++ A+ + +    + + e+  d+i++nl g+ n    ++ ++ k+g  +++++sS+
  gi|488599608|ref|YP_007906079.1|  93 DILVNNAGiIRDrtiKKMEKEEWDDVINTNLTGVFNctkaVIPYMEKQGGGKIVNISSV 151
                                       ******9965542112334455679999**99866522226777779999999999993 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 !   16.8   0.5   2.3e-06    0.0047       1     144 [.      20     194 ..      20     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH...CT..TTCEEEE--TT-CCHHHHHHT.......T-SEEE CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele...ae..eglevvegdvtdvedlaealk.......gadaVv 65 
                                       G + ++Gr+++  l+++g   v+ +  ++ek+ e++   ++   ++ ++++dv + +++a+ ++        +d+ v
  gi|488599608|ref|YP_007906079.1|  20 GSSRGIGRAVALSLAREGSDVVVSYLEKKEKAREVAdmiEDmgRRAITIQVDVKNFNEVAHMVEhvikklgRIDILV 96 
                                       78899************98889999******99776333232357778999****9999999997777776779988 PP

                                       ES---TCC....HHHH...................HHHHHHHHHHCT--EEEEEEE.TTTTSGCGCHHHHHHHHCCH CS
                    NAD_binding_10  66 salggggk....deeg...................aknivdaakeagvkRfvlvsa.igvgdevpgefgewnkellk 118
                                        ++g  ++    +  +                   +k+++  ++++g  ++v +s+ ig      g+fg++n+ + k
  gi|488599608|ref|YP_007906079.1|  97 NNAGIIRDrtikK--MekeewddvintnltgvfncTKAVIPYMEKQGGGKIVNISSvIGLA----GNFGQTNYAASK 167
                                       8885433324441..14445677778889999**********************9945555....788888887777 PP

                                       HHHHHHHH.HHHHHHHSSSEEEEEEE- CS
                    NAD_binding_10 119 aylaakra.aeellrasgldwTivrpg 144
                                       a ++  ++  +++l ++g+    v pg
  gi|488599608|ref|YP_007906079.1| 168 AGVIGFTKsLAKELARKGILVNAVAPG 194
                                       666553331444555556555555555 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 !   11.9   0.0   5.1e-05       0.1      30      70 ..       7      47 ..       2      66 .. 0.78
   2 ?    1.4   0.0     0.086   1.7e+02      69      99 ..     173     202 ..     140     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                                      CT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS CS
                     THF_DHG_CYH_C 30 tgielegkkvvvvGrsnivgkplallLleknatVtvchskt 70
                                      ++  l+gk ++v G s+ +g+++al L+++++ V v   + 
  gi|488599608|ref|YP_007906079.1|  7 ENLRLRGKVALVTGSSRGIGRAVALSLAREGSDVVVSYLEK 47
                                      67889************************966665543333 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.086
                                       TSCCHHHHHCCSSEEEE-SS-TT-B-GGGS- CS
                     THF_DHG_CYH_C  69 ktkdlaeitreadivvvavGkpelikaemvk 99 
                                        tk+la+ + +  i+v av  p++++  m+k
  gi|488599608|ref|YP_007906079.1| 173 FTKSLAKELARKGILVNAV-APGFVETGMLK 202
                                       69999***********999.58899888877 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.7e-05     0.054     107     189 ..     106     185 ..      12     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                           DUF1776 107 pietiplsswaselnerllspiltlqallplltsra.......................kqkakiivvnpsisssln 160
                                        i+++ +++w +++n++l   +  ++a +p ++++                          ka +i           
  gi|488599608|ref|YP_007906079.1| 106 TIKKMEKEEWDDVINTNLTGVFNCTKAVIPYMEKQGggkivnissviglagnfgqtnyaASKAGVI----------- 171
                                       5899*****************************955444444444444444444444444444444........... PP

                           DUF1776 161 lpfhapEalvssalsalfevLkrelrphn 189
                                                       ++++L++el++++
  gi|488599608|ref|YP_007906079.1| 172 ---------------GFTKSLAKELARKG 185
                                       ...............45555555554444 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.5e-05      0.11      48     124 ..       4      88 ..       1     104 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.5e-05
                                       HHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-..HHHHHHHHHTT-EEEEE...CCHHHHHHH CS
                              PALP  48 rlkeg...tgaktvveassGNhgralAaaaallGlkvtivvpadas..pekvallrllGaevvev...ggdydeava 116
                                       + +e+   +g+  +v++ss   gra+A+  a+ G +v++   +++    e +++++ +G + + +    ++++e + 
  gi|488599608|ref|YP_007906079.1|   4 AMRENlrlRGKVALVTGSSRGIGRAVALSLAREGSDVVVSYLEKKEkaREVADMIEDMGRRAITIqvdVKNFNEVAH 80 
                                       3333334468999**********************9999855555524488999*****998888444444777766 PP

                                       HHHHHHHH CS
                              PALP 117 aaaelaae 124
                                       +++ ++++
  gi|488599608|ref|YP_007906079.1|  81 MVEHVIKK 88 
                                       66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1690.09
//
Query:       gi|488599609|ref|YP_007906080.1|  [L=378]
Description: putative pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-139  463.7   0.0   5.2e-139  463.5   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.6e-08   34.2   0.2      4e-08   32.9   0.2    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
      5e-08   32.5   0.1    1.9e-07   30.6   0.1    1.9  2  Aminotran_1_2    Aminotransferase class I and II
    3.7e-07   29.0   0.0    5.5e-07   28.5   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    3.4e-06   26.2   0.0    6.1e-06   25.4   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.013   14.3   0.0      0.017   13.9   0.0    1.2  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
      0.079   11.9   0.0       0.13   11.2   0.0    1.4  1  SelA             L-seryl-tRNA selenium transferase


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 !  463.5   0.0    2e-142  5.2e-139       2     360 ..      25     366 ..      24     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 463.5 bits;  conditional E-value: 2e-142
                                       HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH CS
                   DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatan 78 
                                       i+eee++av evl+sg l++g++v+ FE++fa+y+g+++aiav+sGt+Alh+aL+ lg+g+gdeVI+++++Fv+ta+
  gi|488599609|ref|YP_007906080.1|  25 IGEEEIKAVVEVLRSGRLSQGDRVATFEEKFAQYVGTEYAIAVNSGTSALHVALSSLGIGKGDEVITTTFSFVSTAS 101
                                       689************************************************************************** PP

                                       HHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1  79 avlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       ++l  gakpvfvD+dp+tyni+p++ie  itertkaI+pVhlyGq+++++++ ++a+k++l+vieD+A+AlGa+y+g
  gi|488599609|ref|YP_007906080.1| 102 CILMQGAKPVFVDIDPKTYNIEPSQIEHRITERTKAIIPVHLYGQPCEINKIINVAEKYNLWVIEDCAQALGAEYHG 178
                                       ***************************************************************************** PP

                                       EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHH CS
                   DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAigla 232
                                       kkvG++gd+a+fSFyptK +ttGeGG++vtnde++ae+ar++rnhG++     +y +e+ lGynyr+t+i+AAig++
  gi|488599609|ref|YP_007906080.1| 179 KKVGTFGDVACFSFYPTKSITTGEGGMIVTNDERIAERARMIRNHGQR----VKYIHEI-LGYNYRMTDIAAAIGIV 250
                                       **********************************************99....5******.***************** PP

                                       HHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGS CS
                   DegT_DnrJ_EryC1 233 qLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhyp 309
                                       qLe+l+ ++++R  +ae+y+++L+  ++    t+  ++ +h++ ly+++v+     +r+ l+e+lk++ ig  ++yp
  gi|488599609|ref|YP_007906080.1| 251 QLEKLEGFIQKRISNAEYYNKNLKIKGK----TFVANNVRHVFNLYTIRVR-----NREGLIEHLKRNDIGYGIYYP 318
                                       ***********************98663....445555559**********.....89******************* PP

                                       CHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 310 nplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                       +plhrqp +++ + +   +lp aer++ +vls+p++p ltee+++rV++ +
  gi|488599609|ref|YP_007906080.1| 319 IPLHRQPKFMRFCRR---SLPEAERACGEVLSIPMHPTLTEEQLKRVCDVI 366
                                       ************966...69****************************976 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.2   1.6e-11     4e-08      33     234 ..      47     274 ..      41     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.6e-11
                                       HHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.T CS
                   Beta_elim_lyase  33 tvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.G 107
                                        v ++e+++a+++g+e+a+ v +Gt A +++l+ l   +g+evi t  +   f  t     ++g+k++ ++++ +  
  gi|488599609|ref|YP_007906080.1|  47 RVATFEEKFAQYVGTEYAIAVNSGTSALHVALSSLGiGKGDEVITTTFS---FVSTASCILMQGAKPVFVDIDPKtY 120
                                       57789***************************999879*****888755...6667777889999999888776658 PP

                                       BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHH CS
                   Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivke 184
                                       ++++ ++e  i+e+ +      +i+    + +  Gq+    e++++ ++a+ky++ ++ D A  + a      + k+
  gi|488599609|ref|YP_007906080.1| 121 NIEPSQIEHRITERTK------AIIP--VHLY--GQPC---EINKIINVAEKYNLWVIEDCAQALGAE----YHGKK 180
                                       9************555......4432..2445..8887...57889999************9988876....66788 PP

                                       HHTTSSEEEEES..SSTT--SS-EEEEE-HH.............................................. CS
                   Beta_elim_lyase 185 mfsyvDsvtmsl..kKdllanvGgvlafrddel..........................................ed 217
                                       +    D+ ++s+  +K +++  Gg+++++d+ +                                          e 
  gi|488599609|ref|YP_007906080.1| 181 VGTFGDVACFSFypTKSITTGEGGMIVTNDERIaerarmirnhgqrvkyiheilgynyrmtdiaaaigivqleklEG 257
                                       899999999997669****************6677777776666666666666666666666666666666666666 PP

                                       HHHHHHHHHHHHT---S CS
                   Beta_elim_lyase 218 ylaerveqrkylggglr 234
                                       ++++r+  ++y+ ++l+
  gi|488599609|ref|YP_007906080.1| 258 FIQKRISNAEYYNKNLK 274
                                       66666666666666555 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 !   30.6   0.1   7.4e-11   1.9e-07      46     188 ..      48     168 ..      24     177 .. 0.88
   2 ?   -3.2   0.0       1.4   3.7e+03     346     363 .]     348     366 ..     342     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 7.4e-11
                                       HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEB CS
                     Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvrypl 122
                                        +++ee+ a+++g        +e a+ v sG++al +al  l  + +gde++  + ++ s   ++ + g++ v + +
  gi|488599609|ref|YP_007906080.1|  48 VATFEEKFAQYVG--------TEYAIAVNSGTSALHVALSSLG-IGKGDEVITTTFSFVSTASCILMQGAKPVFVDI 115
                                       589**********........999*******************.********************************6 PP

                                       EETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                     Aminotran_1_2 123 yseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                       + ++++++   ++e  ++e      +tk i+   p +  G    + e+ k++++a+kynl+++ D 
  gi|488599609|ref|YP_007906080.1| 116 D-PKTYNIEPSQIEHRITE------RTKAII---PVHLYG---QPCEINKIINVAEKYNLWVIEDC 168
                                       6.*****************......999998...444444...45577777777999999998876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                                       EEC.TTS-HHHHHHHHHHH CS
                     Aminotran_1_2 346 itv.Aglteeeleelveal 363
                                       i + ++ltee+l+++++ +
  gi|488599609|ref|YP_007906080.1| 348 IPMhPTLTEEQLKRVCDVI 366
                                       557789999****999976 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.1e-10   5.5e-07      55     231 ..      49     224 ..      40     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.1e-10
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHH...TTCEEEEESTTSH CS
                   Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkk...lgievkfvdtsdl 127
                                        ++ee+ a+  g+e a+av+sG++A+++a+ +l + +Gde+++++  + +t + +     k   + i+ k ++  ++
  gi|488599609|ref|YP_007906080.1|  49 ATFEEKFAQYVGTEYAIAVNSGTSALHVALSSLgIGKGDEVITTTFSFVSTASCILMQGAKpvfVDIDPKTYNI-EP 124
                                       689****************************997789*************998765544443233444555555.89 PP

                                       HHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT..-SEEEEET..TTTT CS
                   Cys_Met_Meta_PP 128 eelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklg..aDivvhSa..TKyl 200
                                       +++e+ i+e+tk++    p     + + i+ki+++a k ++ v+ D + a ++  +  k g   D+ + S   TK +
  gi|488599609|ref|YP_007906080.1| 125 SQIEHRITERTKAII---PVHLYGQPCEINKIINVAEKYNLWVIEDCAQALGAEYHGKKVGtfGDVACFSFypTKSI 198
                                       9************96...7777888899************9999998888777776666664468888885447777 PP

                                       TCSSS--EEEEEESSCHHHHHHHHHHHHHHT CS
                   Cys_Met_Meta_PP 201 gGhsdvvaGvivvkgkeelkkelkflqnalG 231
                                           +  +G+iv+++ e+++++++++ ++ G
  gi|488599609|ref|YP_007906080.1| 199 T---TGEGGMIVTND-ERIAERARMI-RNHG 224
                                       4...44578888777.7777776654.5555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.4e-09   6.1e-06      45     182 ..      48     174 ..      38     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.4e-09
                                       HHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEB CS
                       Aminotran_5  45 veearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipl 121
                                       v + +ek+a+ +++e     i + ++t+a+ +++ sl+  + +gde+++t+    ++  ++  +   +gak +++ +
  gi|488599609|ref|YP_007906080.1|  48 VATFEEKFAQYVGTEY---AIAVNSGTSALHVALSSLG--IGKGDEVITTTFSFVSTASCI-LM---QGAKPVFVDI 115
                                       6778999999999996...566666666*********5..9***********999999333.33...5777777777 PP

                                       ETT.SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTT CS
                       Aminotran_5 122 dee.geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavgh 182
                                       d++  +++++++e+ ++e+tk+++  h     G   ++++i+++a k++ +v+ D aqa+g 
  gi|488599609|ref|YP_007906080.1| 116 DPKtYNIEPSQIEHRITERTKAIIPVHL---YGQPCEINKIINVAEKYNLWVIEDCAQALGA 174
                                       76416999****************9996...8***************************986 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 ?   13.9   0.0   6.5e-06     0.017      72     144 ..      52     124 ..      11     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-06
                                       HHHHHHHCT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--EB-TTS-BE CS
                          OKR_DC_1  72 qkyaarvfgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepernalgiig 144
                                       ++  a+  g++ +  v  GTs+   ++    + +gd v+       S +  +++ ga+Pv++  +   + i  
  gi|488599609|ref|YP_007906080.1|  52 EEKFAQYVGTEYAIAVNSGTSALHVALSSLGIGKGDEVITTTFSFVSTASCILMQGAKPVFVDIDPKTYNIEP 124
                                       445577889999999999***9999999999*******************************99988888753 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.1e-05      0.13      45      91 ..      44      92 ..      30     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.1e-05
                                      E--STHHHHHHHHHHHT-SEEEEES-HHHHHHHHHHHHHBTS..EEEEE CS
                              SelA 45 rgsrdalveellkeltgaedalvvnnnaaavllvLntlaagk..eviis 91
                                      +g+r a  ee++ + +g+e a+ vn   +a  ++L++l+ gk  evi++
  gi|488599609|ref|YP_007906080.1| 44 QGDRVATFEEKFAQYVGTEYAIAVNSGTSALHVALSSLGIGKgdEVITT 92
                                      699**********************************986663377765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2462.77
//
Query:       gi|488599610|ref|YP_007906081.1|  [L=73]
Description: hypothetical protein Asulf_00052 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 485.26
//
Query:       gi|488599611|ref|YP_007906082.1|  [L=459]
Description: hypothetical protein Asulf_00053 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-17   61.3  33.7    9.1e-17   61.3  33.7    2.0  2  Polysacc_synt    Polysaccharide biosynthesis protein
    5.8e-09   35.6  21.0    5.8e-09   35.6  21.0    2.0  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    4.2e-06   26.5  14.0    4.2e-06   26.5  14.0    4.0  3  MatE             MatE
     0.0017   18.4   8.5     0.0017   18.4   8.5    4.2  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
          8    6.4   8.2        1.8    8.5   1.0    3.6  2  PsbN             Photosystem II reaction centre N protein (ps


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 !   61.3  33.7   2.5e-20   9.1e-17       3     266 ..      58     321 ..      56     322 .. 0.86
   2 ?   -0.4  10.7      0.16   5.9e+02      72     183 ..     335     447 ..     327     456 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2.5e-20
                     Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslill 79 
                                       +++ +l+++ ++++ l++++ +++ari +p++ Gl ++++++v++l+ ++ lG+n+ lvr+  + ++k+ ++++ l 
  gi|488599611|ref|YP_007906082.1|  58 ENAYYLMAGSVVSASLGLIYWIVIARIYSPAEIGLASALISTVGMLSSFSLLGFNLGLVRFLPEDEDKNGTINSCLT 134
                                       7999************************************************************************* PP

                     Polysacc_synt  80 nvllvllvlvllfllllliaa...flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrv 153
                                       ++ l++++l+++f+   ++ +   ++ ++  ++ +l+ ++++    ++  ++r  f +++  k ++++q++ ++  +
  gi|488599611|ref|YP_007906082.1| 135 MSGLISMMLSIIFISGITLWMpklLFLKENMVFSLLFTFFAII--GSILFMQRYVFIAFRSVKFNFLQQIIANVLKI 209
                                       **************99999889877777766666666555555..999999999*********************** PP

                     Polysacc_synt 154 ilvliavflfldivaavlgavlaalvggivslavlrkkf..rprfvilslklvrellsfsapltisslaillytyid 228
                                        l + +++  + ++++ l++ +a l++ i++ +++r+++  + +  ++++k + ++l +s+   +  +++ ++++i 
  gi|488599611|ref|YP_007906082.1| 210 PLAI-VLISLG-VLGIFLAYGSALLLAVILGNVLIRIILpgYSPLPTIKKKVINDMLHYSFANYVAGIFGGISNFIL 284
                                       6655.555555.56666666677777777777777777764455555559*************************** PP

                     Polysacc_synt 229 sillglllgaeavGiYnaayqllvaisgllapivtaal 266
                                        ++  ++lgaea ++++ a + ++++  +  +i+t +l
  gi|488599611|ref|YP_007906082.1| 285 PLMVLSILGAEANAYFTIAFTASMMVFTVPCAIAT-SL 321
                                       ************************99877777777.55 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.16
                     Polysacc_synt  72 elvslillnvllvllvlvllfllllliaa....flglpelavlylilalmllllvgvasfrrglfqglermkyaavs 144
                                       + +++i+l+ +l++ +++l+fl+ + i       +++ ++ +l ++++++++  ++++ ++++  +  ++   ++v+
  gi|488599611|ref|YP_007906082.1| 335 NAIRSIKLSFILLIPLSILIFLFGDKILLlfgrAYSENAFKLLSIFIISAVP--ISIIETYVSVERVRRKVGNVLVT 409
                                       5678999***************955554422257777778877777777777..99999999999999********* PP

                     Polysacc_synt 145 qvveqlsrvilvliavflfldivaavlgavlaalvggiv 183
                                        v+  +s ++++ ++++ ++ +v++++g ++++ ++++v
  gi|488599611|ref|YP_007906082.1| 410 YVIMATSTIVMSYLLMTRIG-LVGVGIGWLIGTGIAALV 447
                                       ********************.******999998666555 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6  21.0   1.6e-12   5.8e-09       1     290 [.      80     371 ..      80     374 .. 0.75
   2 ?   -2.4   3.3      0.62   2.2e+03     118     144 ..     406     432 ..     372     457 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.6e-12
                   Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqke..dltee.dlstvftfnlvlgllialvlfl.laplia 73 
                                       v+AR+ sp++ G+ + ++  +++++ f+ +G++  l++    d +++  ++++ t++ +++++++++++  +  ++ 
  gi|488599611|ref|YP_007906082.1|  80 VIARIYSPAEIGLASALISTVGMLSSFSLLGFNLGLVRFLpeDEDKNgTINSCLTMSGLISMMLSIIFISgITLWMP 156
                                       79***********************************9753233333589999999999999888876651344555 PP

                   Polysacc_synt_3  74 s.fynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigt.ll 148
                                       + ++ ++++v  l    +  i+ ++  +q+  +      k  f  +++++v+ + +aivl  lg     L++g+ ll
  gi|488599611|ref|YP_007906082.1| 157 KlLFLKENMVFSLL-FTFFAIIGSILFMQRYVFIAFRSVKFNFLQQIIANVLKIPLAIVLISLGVLGIFLAYGSaLL 232
                                       52444444444444.44555666666666665544444455566677777777777777766654333344443122 PP

                   Polysacc_synt_3 149 ssll..slvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlasl 223
                                        +++  ++++ ++   + p ++++ k+++++++++    ++++   +++ +  l++ ++l+++a +++++a + +++
  gi|488599611|ref|YP_007906082.1| 233 LAVIlgNVLIRIILPGYSPLPTIKKKVINDMLHYSFANYVAGIFGGISNFILPLMVLSILGAEANAYFTIAFTASMM 309
                                       222211344445556788*****************************************************998887 PP

                   Polysacc_synt_3 224 pvaeitsviakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWle 290
                                       + +    v  +++++ +++ ++ ++klr +  ++++l+ ++ +P+ ++++++ + +  +l+G+ ++e
  gi|488599611|ref|YP_007906082.1| 310 VFT----VPCAIATSLFAEGSNVPEKLRINAIRSIKLSFILLIPLSILIFLFGDKI-LLLFGRAYSE 371
                                       765....344567888899999999****************************985.6789988876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.62
                   Polysacc_synt_3 118 tlvssvvgvivaivlAllglgvwALvi 144
                                        lv++v+++ ++iv+ +l+++   Lv 
  gi|488599611|ref|YP_007906082.1| 406 VLVTYVIMATSTIVMSYLLMTRIGLVG 432
                                       578888999999999998887777763 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   2.3         1   3.6e+03       9      49 ..      70     112 ..      63     120 .. 0.60
   2 ?   -4.7  10.5       4.7   1.7e+04     112     160 ..     184     227 ..     126     228 .. 0.70
   3 !   26.5  14.0   1.2e-09   4.2e-06      12     160 ..     280     422 ..     272     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                              MatE   9 esllslidtllvgrl.gskalAavsialsilsllfv.fllgls 49 
                                         +l+li  ++++r+ ++ +++ +s+ +s++ +l +  llg++
  gi|488599611|ref|YP_007906082.1|  70 SASLGLIYWIVIARIySPAEIGLASALISTVGMLSSfSLLGFN 112
                                       5566666666666666777766666666666655553445555 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 4.7
                              MatE 112 krylrililgipalalqlvlsgilrgagktkvplyislisl.llniplny 160
                                       +ry+ i++ ++ +++lq++++++l      k+pl+i+lisl +l+i l+y
  gi|488599611|ref|YP_007906082.1| 184 QRYVFIAFRSVKFNFLQQIIANVL------KIPLAIVLISLgVLGIFLAY 227
                                       455555555555666666666555......78999999999999999887 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 1.2e-09
                              MatE  12 lslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliia 87 
                                       +++i+ l+v ++ g++a A  +ia++ ++++f+++ +++t+l      a G++ +++++  + ++++l+++l ++++
  gi|488599611|ref|YP_007906082.1| 280 SNFILPLMVLSIlGAEANAYFTIAFTASMMVFTVPCAIATSL-----FAEGSNVPEKLRINAIRSIKLSFILLIPLS 351
                                       6788888988888***********************998887.....688*************************** PP

                              MatE  88 llvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplny 160
                                       +l++lf ++il lf+     +e a ++l+i i++++++++ +++ ++ r   k+  +l+ ++i +   i+++y
  gi|488599611|ref|YP_007906082.1| 352 ILIFLFGDKILLLFGRAY--SENAFKLLSIFIISAVPISIIETYVSVERVRRKVGNVLVTYVIMATSTIVMSY 422
                                       **************8766..7******************9988877766666666666666665555555555 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 ?   -7.5  16.0         5   1.8e+04      32     134 ..      60     182 ..      48     192 .. 0.48
   2 ?   -4.3  25.9       4.9   1.8e+04       5     119 ..     171     290 ..     164     320 .. 0.60
   3 ?   -4.8   6.6         5   1.8e+04      33      72 ..     272     311 ..     259     365 .. 0.55
   4 !   18.4   8.5   4.8e-07    0.0017       1      74 [.     376     449 ..     376     458 .. 0.93

  Alignments for each domain:
  == domain 1  score: -7.5 bits;  conditional E-value: 5
                   Polysacc_synt_C  32 lkalvigal..vklilnllli..plfgivGaaiatvlallvvavlnlyalrrllgikl..........ellrrll.k 93 
                                       +++l++g +  + l+l ++ +    ++   + +a++l  +v+++  + +l   lg+            +     +  
  gi|488599611|ref|YP_007906082.1|  60 AYYLMAGSVvsASLGLIYWIViaRIYSPAEIGLASALISTVGMLSSFSLLGFNLGLVRflpededkngT-----InS 131
                                       667777777233445555555443344444444444444444444444444444444445555443321.....223 PP

                   Polysacc_synt_C  94 pllaalvmgiv.....vylllllllglllla......alalllavlvgalvY 134
                                        l ++ +++++     + +++l++++ll+l       +l +++a+ +g +++
  gi|488599611|ref|YP_007906082.1| 132 CLTMSGLISMMlsiifISGITLWMPKLLFLKenmvfsLLFTFFAI-IGSILF 182
                                       333333333330111244555555555554465555322444444.444443 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 4.9
                   Polysacc_synt_C   5 lalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrll 81 
                                       +++ +i+ s+  +  +++++   +k+ ++  +i+ ++k+ l ++li ++g++G+ +a   all++ +l  +++r +l
  gi|488599611|ref|YP_007906082.1| 171 FTFFAIIGSILFMQRYVFIAFRSVKFNFLQQIIANVLKIPLAIVLI-SLGVLGIFLAYGSALLLAVILGNVLIRIIL 246
                                       4455555566666667777777777777777888888888888888.89********99999999999988888866 PP

                   Polysacc_synt_C  82 .gikl......ellrrllkpllaalvmgivvylllllllglllla 119
                                        g+++      ++++++l + +a  v gi    + +++l+l  l+
  gi|488599611|ref|YP_007906082.1| 247 pGYSPlptikkKVINDMLHYSFANYVAGIFGG-ISNFILPLMVLS 290
                                       24555775555334444444444444444422.333333322222 PP

  == domain 3  score: -4.8 bits;  conditional E-value: 5
                   Polysacc_synt_C  33 kalvigalvklilnllliplfgivGaaiatvlallvvavl 72 
                                       +a ++g + ++il l+ +  +g+   a+ t++  + ++v+
  gi|488599611|ref|YP_007906082.1| 272 VAGIFGGISNFILPLMVLSILGAEANAYFTIAFTASMMVF 311
                                       4556666666666666666666544333333333333322 PP

  == domain 4  score: 18.4 bits;  conditional E-value: 4.8e-07
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnl 74 
                                       +L+i+++s++++s++ ++ s+     ++  +l+  vi a   +++++ll+ ++g+vG+ i+++++  ++a++  
  gi|488599611|ref|YP_007906082.1| 376 LLSIFIISAVPISIIETYVSVERVRRKVGNVLVTYVIMATSTIVMSYLLMTRIGLVGVGIGWLIGTGIAALVVT 449
                                       599*****************************************************************999874 PP

>> PsbN  Photosystem II reaction centre N protein (psbN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4      0.37   1.3e+03       8      25 ..     138     155 ..     134     156 .. 0.84
   2 ?    8.5   1.0    0.0005       1.8       4      28 ..     204     228 ..     202     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.37
                              PsbN   8 sisiaavlvaiTgfsiYt 25 
                                        is++ +++ i+g+ +++
  gi|488599611|ref|YP_007906082.1| 138 LISMMLSIIFISGITLWM 155
                                       699999999999999885 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0005
                              PsbN   4 AtvlsisiaavlvaiTgfsiYtaFG 28 
                                       A vl i +a+vl+++  ++i++a+G
  gi|488599611|ref|YP_007906082.1| 204 ANVLKIPLAIVLISLGVLGIFLAYG 228
                                       789*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 2978.02
//
Query:       gi|488599612|ref|YP_007906083.1|  [L=40]
Description: hypothetical protein Asulf_00054 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         0  (0); expected 0.2 (1e-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: 273.10
//
Query:       gi|488599613|ref|YP_007906084.1|  [L=57]
Description: hypothetical protein Asulf_00055 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 440.90
//
Query:       gi|488599614|ref|YP_007906085.1|  [L=154]
Description: hypothetical protein Asulf_00056 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-06   27.6   9.1    5.1e-06   25.9   9.1    1.7  1  YdjM             LexA-binding, inner membrane-associated puta
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.018   15.1   0.1    1.2  1  Zn_dep_PLPC      Zinc dependent phospholipase C
       0.23   11.9  11.6       0.35   11.3   2.4    3.0  3  Caps_synth_CapC  Capsule biosynthesis CapC


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 !   25.9   9.1   8.5e-10   5.1e-06       3     168 ..       4     148 ..       1     153 [. 0.75

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 8.5e-10
                              YdjM   3 gltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgH....RgftHSllf 75 
                                        l+H+l++ +l+ +l+ + +   + + +a++++g+l+PD      ++g  + l+ +       H        H+  +
  gi|488599614|ref|YP_007906085.1|   4 WLAHVLFAYILCKVLGIRFKVFSN-ENTAIVIVGSLVPDTV----KVGLIFDLIDV-------HawdfIAPLHTPAG 68 
                                       568999999999999999987655.*************966....44444444444.......322224899***** PP

                              YdjM  76 lallalvlllllrlfgrsalrlglllllgvlsHlllDlltk...yGvpllwPfskkkvrlsllfiiidplltllsrr 149
                                        +l+a +++ll+  + +      lll+lg+ +H +lDll k    G+ ll+Pfs  +   +l +i +d+        
  gi|488599614|ref|YP_007906085.1|  69 SLLVAGLISLLFYEVYTV----FLLLILGFTTHYMLDLLLKhvsGGMLLLFPFS--WGGYQLGLIQVDD-------- 131
                                       ******999999999877....899***************999999*******9..6666666666666........ PP

                              YdjM 150 glvalelvllvlylviilv 168
                                           ++lv++vl++++  v
  gi|488599614|ref|YP_007906085.1| 132 YR--ITLVFVVLAVIVYAV 148
                                       22..345555544444444 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 ?   15.1   0.1     3e-06     0.018       2     108 ..       7     106 ..       6     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-06
                                       HHHHHHHHHHHH....HHH-HHHTHHHHHHHHHGGGG......-TT-GGG--BTTT.TB-HHHHS-HHHHHHHHHHH CS
                       Zn_dep_PLPC   2 HltlashalavlpalkkkrklklnkaalllGsvaPDl....eylfnasshsyktht.kagllgedhhweetgkflll 73 
                                       H ++a  + +vl++ +k    ++n a ++ Gs  PD+             ++ ++   ++++++  h      +++ 
  gi|488599614|ref|YP_007906085.1|   7 HVLFAYILCKVLGIRFKVFS-NENTAIVIVGSLVPDTvkvgLI-------FDLIDVhAWDFIAPL-HTPAGSLLVAG 74 
                                       99999999999998888665.8999999*********765422.......444444111111111.11444444555 PP

                                       HHHHHHC.....T-HHHHHHHHHHHHHHHHHHTS.H CS
                       Zn_dep_PLPC  74 likklrelyksegslklaafllGvlsHyvaDvft.H 108
                                       li+ l      e  ++ +  +lG+ +Hy+ D    H
  gi|488599614|ref|YP_007906085.1|  75 LISLLFY----EVYTVFLLLILGFTTHYMLDLLLkH 106
                                       5555544....44678899*************9999 PP

>> Caps_synth_CapC  Capsule biosynthesis CapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2    0.0095        57      44      74 ..       9      39 ..       4      58 .. 0.62
   2 ?   11.3   2.4   5.9e-05      0.35      15      57 ..      65     107 ..      54     116 .. 0.88
   3 ?    1.9   0.1      0.05     3e+02      30      51 ..     129     150 ..     121     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0095
                   Caps_synth_CapC 44 lltylivrllsrflilyGrrrfvavlllgvl 74
                                      l +y+++++l  ++ ++  + +++v++ +++
  gi|488599614|ref|YP_007906085.1|  9 LFAYILCKVLGIRFKVFSNENTAIVIVGSLV 39
                                      5566666666666666666666665555544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.9e-05
                   Caps_synth_CapC  15 lslgGlvvpGylalvldqplsllvtllialltylivrllsrfl 57 
                                         +g l+v G++ l+++++++++++l+  + t +++ ll +++
  gi|488599614|ref|YP_007906085.1|  65 TPAGSLLVAGLISLLFYEVYTVFLLLILGFTTHYMLDLLLKHV 107
                                       56799*****************************999976654 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.05
                   Caps_synth_CapC  30 ldqplsllvtllialltylivr 51 
                                       +d+    lv+++ a+++y+++r
  gi|488599614|ref|YP_007906085.1| 129 VDDYRITLVFVVLAVIVYAVTR 150
                                       4677778899999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 964.64
//
Query:       gi|488599615|ref|YP_007906086.1|  [L=147]
Description: hypothetical protein Asulf_00057 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.16   12.2   0.1       0.28   11.4   0.1    1.4  1  Peptidase_M23  Peptidase family M23
        5.3    7.1   8.0        1.2    9.1   2.9    2.5  2  TNFR_16_TM     Tumor necrosis factor receptor member 16 trans


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.2e-05      0.28      16      64 ..      37      87 ..      25      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                                      EEESSSEEEEEEEE..ETTT.EEEEEEEECTCEEEEEEEESEESS-TTEEE- CS
                     Peptidase_M23 16 VlAaadGtVvfagk..kegy.GnvviidhgdgystlyahlskisvkegqkVk 64
                                      ++   +G+V   g   +++y G +++i+hg +       ls+++v+ g++V+
  gi|488599615|ref|YP_007906086.1| 37 IIEGFEGKVSIYGVviNKSYdGFYILIEHGPK-NKAVKVLSDLDVENGDRVE 87
                                      555567888666665677888********998.788899***********97 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.12   1.1e+03      25      30 ..     103     108 ..     102     112 .. 0.87
   2 ?    9.1   2.9   0.00014       1.2      17      31 ..     119     133 ..     110     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                        TNFR_16_TM  25 vifKrw 30 
                                       +++K w
  gi|488599615|ref|YP_007906086.1| 103 IVYKKW 108
                                       89**** PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00014
                        TNFR_16_TM  17 VvvgLlaYvifKrwk 31 
                                       + + ++++++fK w+
  gi|488599615|ref|YP_007906086.1| 119 IAIPIVVFIFFKYWR 133
                                       55679*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1015.12
//
Query:       gi|488599616|ref|YP_007906087.1|  [L=295]
Description: Nucleoside-diphosphate-sugar epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-55  187.2   0.0    3.9e-54  184.3   0.0    2.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.8e-54  183.1   0.0    6.7e-54  182.9   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    8.2e-21   74.3   0.0      1e-20   74.0   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    7.4e-19   68.0   1.4    4.1e-16   59.0   1.4    2.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.8e-18   65.9   0.1    4.5e-18   65.2   0.1    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      6e-13   48.6   0.0    4.8e-10   39.0   0.0    2.3  2  NAD_binding_4    Male sterility protein
    2.2e-09   37.4   0.0    3.9e-09   36.7   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
     0.0052   16.4   0.3       0.02   14.5   0.1    2.0  2  NmrA             NmrA-like family


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   0.0   1.7e-57   3.9e-54       1     327 [.       4     286 ..       4     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 1.7e-57
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG +G+iGsy++e+++++  + +g++ r        i+ l++           + +gDl++ + ++++++++  d
  gi|488599616|ref|YP_007906087.1|   4 LVTGASGQIGSYVLERFVDN-CDAIGVDLRRCP-----IKDLRD----------LVLQGDLRNCEFVRKVVRDM--D 62 
                                       9*****************98.778898766544.....555543..........2579**************98..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       +v++LAAq  V++s+++P y a +n++ t++LL+a+ ++++    rf+ +S++ vYG++q vp++E++p +P sPY+
  gi|488599616|ref|YP_007906087.1|  63 AVVHLAAQVSVENSWSNPVYDAGNNIISTINLLKACSDVEV---SRFVYISSAAVYGNPQYVPVDEEHPKNPISPYG 136
                                       **************************************987...5******************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCC.HHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtr.kitravarialgkqevlylGnldakRdwghvkDyv 230
                                       ++Kl+ ++ ++ + +   +++v+ + fn  s r+ ++ +    i ++++r+++++ + +++G+++++Rd+ hv+D+v
  gi|488599616|ref|YP_007906087.1| 137 VSKLTGEYYCRVFSD--RIHTVTIRPFNVFSARMDPSNPYSgVIAKFISRVKQKL-PPVIYGDGNQTRDFIHVRDVV 210
                                       ************976..7899999**********99866543999*******988.55669**************** PP

                                       HHHHHHHHCSS-.--EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkp.edyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdll 306
                                       + +  +++++ +   y+++tg+++s++e++e+ ++ +g++                      +  + + rpg+ ++ 
  gi|488599616|ref|YP_007906087.1| 211 DFIEIAVKKGVNgGAYNVGTGRETSIQELAEIIMEIAGINS---------------------RPVFDKPRPGDIRRS 266
                                       *******9986536788899999999888887777776531.....................22255789******* PP

                                       -B-THHHHHHH----SS-HHH CS
                     GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvsfee 327
                                       ++d+ska+ +Lg++pk++++ 
  gi|488599616|ref|YP_007906087.1| 267 CADISKAR-KLGFEPKTDLRR 286
                                       *******9.9*******9976 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.9   0.0     3e-57   6.7e-54       1     241 []       3     229 ..       3     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 3e-57
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       ilVtGa+G+iGs++++++ ++  + ig+d ++   +  r+    + ++dl++ + ++++++  ++dav+hlAa+ +v
  gi|488599616|ref|YP_007906087.1|   3 ILVTGASGQIGSYVLERFVDN-CDAIGVDLRRCPIKDLRD---LVLQGDLRNCEFVRKVVR--DMDAVVHLAAQVSV 73 
                                       8******************95.8********666655444...589***************..8************* PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       ++s+++p + + +n++ t nll+a+++ +v r++++sS++vYG+++ +p +e+    p +p spY+++Kl+ge +++
  gi|488599616|ref|YP_007906087.1|  74 ENSWSNPVYDAGNNIISTINLLKACSDVEVSRFVYISSAAVYGNPQYVPVDEEH---PKNPISPYGVSKLTGEYYCR 147
                                       ***********************************************9*99999...99****************** PP

                                       HHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                        + +   ++++++r+fn++++r ++ +  s+vi+++i++++++  + +++gdg++ Rdf++v+Dv++ i  ++++  
  gi|488599616|ref|YP_007906087.1| 148 VFSDR--IHTVTIRPFNVFSARmDPSNPYSGVIAKFISRVKQKL-PPVIYGDGNQTRDFIHVRDVVDFIEIAVKK-- 219
                                       *9655..69*************777777****************.******************************.. PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                        g +g++yn+G
  gi|488599616|ref|YP_007906087.1| 220 -GVNGGAYNVG 229
                                       .9999*****9 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 !   74.0   0.0   4.5e-24     1e-20       1     283 [.       1     293 [.       1     295 [] 0.84

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 4.5e-24
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHHHHH--SEEEE------HH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaellkeakpdvvvnaAAytavD 65 
                                       mkilvtGa+Gq+Gs + +++  +++++++++ +            + dl++ e v++++++   d+vv++AA   v 
  gi|488599616|ref|YP_007906087.1|   1 MKILVTGASGQIGSYVLERFV-DNCDAIGVDLRrcpikdlrdlvlQGDLRNCEFVRKVVRD--MDAVVHLAAQVSVE 74 
                                       89*****************99.5679999976679**************************..889*********** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH..H CS
                     RmlD_sub_bind  66 kaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla..a 139
                                       +  s++  ++  n  ++ +l +a++ v++  ++++S+  V+   +  p  e+++++P++ YG +Kl GE   +   +
  gi|488599616|ref|YP_007906087.1|  75 NSWSNPVYDAGNNIISTINLLKACSDVEVsRFVYISSAAVYGNPQYVPVDEEHPKNPISPYGVSKLTGEYYCRVfsD 151
                                       ****************************846**************************************98776326 PP

                                       -SSEEEEEE-SEESS.......SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG- CS
                     RmlD_sub_bind 140 gkkalivRtswvyge.......kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekela 207
                                         +++ +R   v+++       +    ++++++++k++ +  +  D  q++   ++rd+ +++  +++k ++     
  gi|488599616|ref|YP_007906087.1| 152 RIHTVTIRPFNVFSArmdpsnpY-SGVIAKFISRVKQKLPPVIYGDgnQTRDFIHVRDVVDFIEIAVKKGVN----G 223
                                       6678899******9977544422.233444444444443333333333888899999999999999999998....9 PP

                                       EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHH CS
                     RmlD_sub_bind 208 gvyHlanegetswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlk 283
                                       g y ++  +ets  e+A+ i++ ag +s   +p+  +  p   +R   S+ d +k+++ +  + ++ r +l e+++
  gi|488599616|ref|YP_007906087.1| 224 GAYNVGTGRETSIQELAEIIMEIAGINS---RPVFDKPRPGDIRR---SCADISKARKLGFEPKTDLRRDLDEIFE 293
                                       ************************9966...88877777777776...6778888888877788888888877766 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   1.4   1.8e-19   4.1e-16       1     251 [.       3     251 ..       3     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.8e-19
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +lvtGa+G iGs ++++++++ +  i  ++     + ++++          l     ++ gd+r+ e ++k+++  +
  gi|488599616|ref|YP_007906087.1|   3 ILVTGASGQIGSYVLERFVDN-CDAIG-VDLRRCPIKDLRD----------L-----VLQGDLRNCEFVRKVVR--D 60 
                                       678888888888888887764.22222.2333333333333..........2.....3359*************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE..............GGGSS--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt..............DKAvnPtnvmGa 140
                                       +d+v+h AA   V    +np+    +N+++t n+++a+ + +v+++v+iS+                  nP++ +G+
  gi|488599616|ref|YP_007906087.1|  61 MDAVVHLAAQVSVENSWSNPVYDAGNNIISTINLLKACSDVEVSRFVYISSaavygnpqyvpvdeEHPKNPISPYGV 137
                                       **************************************************833333333333321234589****** PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT.......TSSHHHHHHHHHTT.SSEEES-TT-EEEEE-HHHH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvRfGNVlgSr.......GSviplFkkqikeg.gpvtvTdpemtRyfmtieea 209
                                       +K++ e ++  ++++      + v++R  NV+ +r         vi +F +++k++  pv   d + tR f+ +++ 
  gi|488599616|ref|YP_007906087.1| 138 SKLTGEYYCRVFSDRI-----HTVTIRPFNVFSARmdpsnpySGVIAKFISRVKQKlPPVIYGDGNQTRDFIHVRDV 209
                                       **********999998.....55667777777665333333346**********99889999*************** PP

                                       HHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH........ CS
                   Polysacc_synt_2 210 vqLvlqalalakggeifvldmGepvkivdlakalielsglee 251
                                       v+++  a++++ +g  + +  G  ++i++la+ ++e++g+++
  gi|488599616|ref|YP_007906087.1| 210 VDFIEIAVKKGVNGGAYNVGTGRETSIQELAEIIMEIAGINS 251
                                       *************************************99876 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 !   65.2   0.1     2e-21   4.5e-18       1     231 [.       4     219 ..       4     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 2e-21
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtG++G +G+++ +++v+  ++     +Dlr  p +  +l+      v++gD+++ + ++++++++d+v+hla+ v
  gi|488599616|ref|YP_007906087.1|   4 LVTGASGQIGSYVLERFVDNCDAI---GVDLRRCPIK--DLRD---L-VLQGDLRNCEFVRKVVRDMDAVVHLAAQV 71 
                                       69****************988633...3588887766..3333...3.899************************** PP

                         3Beta_HSD  78 dvagkltedeimkv.nvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        v +  ++  ++   n+  T n+l+ac + +v ++vY Ssa v g+    + +   dEe  +++++ ++y  sK   
  gi|488599616|ref|YP_007906087.1|  72 SVENSWSNPVYDAGnNIISTINLLKACSDVEVSRFVYISSAAVYGN---PQYVP-VDEE--HPKNPISPYGVSKLTG 142
                                       ****8888877653389**************************999...55555.6665..5678999********* PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyG.......egdkllvpllkqlaklglalfkigdeevlsdrvYvgNvaw 223
                                       E +     +       r+ T+ +Rp  ++        +++ ++ +++ ++ k++l  + +gd +++ d++ v  v++
  gi|488599616|ref|YP_007906087.1| 143 EYYCRVFSD-------RIHTVTIRPFNVFSarmdpsnPYSGVIAKFISRV-KQKLPPVIYGDGNQTRDFIHVRDVVD 211
                                       **9977666.......79***********833322223444555555554.55668899*****************9 PP

                         3Beta_HSD 224 ahilAara 231
                                        + +A+++
  gi|488599616|ref|YP_007906087.1| 212 FIEIAVKK 219
                                       99888875 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0011       2.6       1      23 [.       5      27 ..       5      35 .. 0.88
   2 !   39.0   0.0   2.2e-13   4.8e-10      81     250 ..      54     206 ..      48     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
                                      EE-TTSHHHHHHHHHHHHHS-.T CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev 23
                                      +TGa+G +G+++le+ +++++++
  gi|488599616|ref|YP_007906087.1|  5 VTGASGQIGSYVLERFVDNCDAI 27
                                      7*****************99854 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 2.2e-13
                                       HHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H. CS
                     NAD_binding_4  81 lqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyee 154
                                       ++++++ +d+++h aA+v+++++ ++       N+ +t ++l+ ++ ++    ++++S+a+v+g+ +  v       
  gi|488599616|ref|YP_007906087.1|  54 VRKVVRDMDAVVHLAAQVSVENSWSNpvyDAGNNIISTINLLKACSDVEVS-RFVYISSAAVYGNPQY-V------- 121
                                       5788999***************99994333578**************9999.*******999999994.3....... PP

                                       .....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-......-SSST---TTSHHHHHH CS
                     NAD_binding_4 155 gekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg......esktGwingsdlgirgl 225
                                                 ++++ k+    Y  sK  +E+ +r  +  +++ +v +Rp ++ +      ++ +G       +i+ +
  gi|488599616|ref|YP_007906087.1| 122 --------PVDEEHPKNPISPYGVSKLTGEYYCRVFS--DRIHTVTIRPFNVFSarmdpsNPYSG-------VIAKF 181
                                       ........345667788889*****************..67************965544444444.......44455 PP

                                       HHHHHH-EEES-SB---TT--EEEH CS
                     NAD_binding_4 226 lgliakgvlpeilgdkeavldlvpv 250
                                       ++ ++++  p i+gd +++ d++ v
  gi|488599616|ref|YP_007906087.1| 182 ISRVKQKLPPVIYGDGNQTRDFIHV 206
                                       5555555555555555555555555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   1.7e-12   3.9e-09       1     106 [.       7     118 ..       7     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.7e-12
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..HH CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..de 75 
                                       GA+G++G++++++ +++      a+  +  + + ++ + +  v++gd+ + e +++++++ daVv  +++ +     
  gi|488599616|ref|YP_007906087.1|   7 GASGQIGSYVLERFVDNC----DAIGVDLRRCP-IK-DLRDLVLQGDLRNCEFVRKVVRDMDAVVHLAAQVSVenS- 76 
                                       9***************95....35555666666.44.456679********************9988855444220. PP

                                       HH.............HHHHHHHHHHCT--EEEEEEETTTTSGCG CS
                    NAD_binding_10  76 eg.............aknivdaakeagvkRfvlvsaigvgdevp 106
                                                      ++n+++a+   +v+Rfv++s++ v+ + p
  gi|488599616|ref|YP_007906087.1|  77 -WsnpvydagnniisTINLLKACSDVEVSRFVYISSAAVYGN-P 118
                                       .13334555677899************************963.2 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   8.9e-06      0.02       1     101 [.       3     110 ..       3     119 .. 0.80
   2 ?   -2.5   0.0       1.3   2.9e+03     168     196 ..     192     219 ..     175     248 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.9e-06
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.. CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.. 75 
                                       Ilv+Ga+G++G++v + ++++   +     d+++  +k l +    +++gdl + e +++++++ d+v    +    
  gi|488599616|ref|YP_007906087.1|   3 ILVTGASGQIGSYVLERFVDNCDAIG---VDLRRCPIKDLRDL---VLQGDLRNCEFVRKVVRDMDAVVHLAAQVsv 73 
                                       8******************9765555...56666677777764...6699999999999999999988766654456 PP

                                       ...........S-HHHHHHHHHHHHHHHS-SEEEEEE CS
                              NmrA  76 ...........skeiedgkklvdAakeaGvkhfiySs 101
                                                  +++i    +l +A     v +f+y s
  gi|488599616|ref|YP_007906087.1|  74 enswsnpvydaGNNIISTINLLKACSDVEVSRFVYIS 110
                                       6667888888999999999999999999999999954 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                                       EEEESS-TTS-EE-HHHHHHHHHHHHHHH CS
                              NmrA 168 tllgpgnpkavlldaeeDiGafvikilkd 196
                                       ++ g+gn    ++ +++D+  f+  ++k+
  gi|488599616|ref|YP_007906087.1| 192 VIYGDGNQTRDFI-HVRDVVDFIEIAVKK 219
                                       5667777666666.777777777666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); 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:                         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 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2120.29
//
Query:       gi|488599617|ref|YP_007906088.1|  [L=164]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase-related enzymes [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-13   49.4   0.0    5.7e-13   48.9   0.0    1.2  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
    8.5e-07   28.6   0.1    1.6e-06   27.7   0.1    1.4  1  Cupin_2          Cupin domain
     0.0001   22.0   0.0    0.00013   21.7   0.0    1.1  1  FdtA             WxcM-like, C-terminal


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   9.6e-17   5.7e-13       5     148 ..       2     138 ..       1     150 [. 0.85

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 9.6e-17
                                       TTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEE CS
                   dTDP_sugar_isom   5 egvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaV 81 
                                       eg+l+   k+f+DeRGff+e  +e+      ++ e+vq+nls++  g++R  H +  +++q  +  +++G++  +a 
  gi|488599617|ref|YP_007906088.1|   2 EGILVKPLKRFADERGFFTEIMREDWN---VFQDEVVQANLSITYPGIVRAWHRH--ERGQVDYFVCIKGAIKICAY 73 
                                       678888899************998764...46678******************55..67****************** PP

                                       E-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-.SSEEEEEEEESS---GGGEEEE-..TT-TTT CS
                   dTDP_sugar_isom  82 DlRkgSptfgkwvgveLsaenkrqlyipegfahGflvl.sdeaevlYkvteyyapesergir..wnDpel 148
                                       D  ++ p+    +      en + + +p  + hGf ++ s+ a+++Y v++ y++es   ir  wnDp++
  gi|488599617|ref|YP_007906088.1|  74 DDETQEPNEIVST-----GENLQVVRVPGHYWHGFRAVgSEPAMLVYFVNRLYDHESPDEIRrpWNDPTV 138
                                       *988877655554.....566669***********8663788**************87777666999986 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   2.8e-10   1.6e-06       7      68 ..      44     114 ..      39     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.8e-10
                                       TTEEEEEECSSSEE.EEEEEEESEEEEE.ECTE....EEEEETTE...EEEE-TT-EEEEEE-SSS-EEEE CS
                           Cupin_2   7 pGesapshrHpged.effyVleGegelt.vdge....eveleaGd...svyfpagtpHrfrNtgdeparll 68 
                                       pG +  +hrH++ +  +f++++G +++  +d+e      ++++G+   +v +p + +H+fr  g+epa l+
  gi|488599617|ref|YP_007906088.1|  44 PGIVRAWHRHERGQvDYFVCIKGAIKICaYDDEtqepNEIVSTGEnlqVVRVPGHYWHGFRAVGSEPAMLV 114
                                       5556789***99999****************998888899****7444788999*************9986 PP

>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.1e-08   0.00013       6     117 ..       7     124 ..       2     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-08
                                       EEEEEEEETTEEEEEEEBT.TTBSS--SEEEEEES--TTTEEEEEEESS.--EEEEEEES-EEEEEE-SS-E..EEE CS
                              FdtA   6 ielpkikdergnLsvieee.kevpfeikrvyyvydvpegeerGeHahkk.leqllialsGsvevllddgkkk..kei 78 
                                       + l++++derg  + i +e ++v  +      ++ +  g++r  H h + +   +++++G++++++ d +++  +ei
  gi|488599617|ref|YP_007906088.1|   7 KPLKRFADERGFFTEIMREdWNVFQDEVVQANLSITYPGIVRAWHRHERgQVDYFVCIKGAIKICAYDDETQepNEI 83 
                                       56788889999888765541555444444445666778899******7625689**********9866655534566 PP

                                       EE-STT.EEEEE-TT-EEEEE---TT.-EEEEEESS---GG CS
                              FdtA  79 lldsps.kglyipkmiWrelinfsed.avllvlasesydee 117
                                       +    + + + +p   W+    + ++ a+l+ + ++ yd+e
  gi|488599617|ref|YP_007906088.1|  84 VSTGENlQVVRVPGHYWHGFRAVGSEpAMLVYFVNRLYDHE 124
                                       55544449999*******99998877688888999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 938.72
//
Query:       gi|488599618|ref|YP_007906089.1|  [L=65]
Description: hypothetical protein Asulf_00060 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.7   0.0    1.2e-14   54.5   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    3.4e-07   30.7   0.0    3.5e-07   30.7   0.0    1.0  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.012   15.4   0.0    1.0  1  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 !   54.5   0.0     2e-18   1.2e-14       1      57 [.       2      57 ..       2      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2e-18
                                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTT CS
                   NTP_transferase  1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqeh 57
                                      ka+IL+GG GtRL+PLt +++k+l+pv++k +++ + ++ ++++g+++i +++ +++
  gi|488599618|ref|YP_007906089.1|  2 KALILSGGHGTRLRPLTYSQQKQLIPVANK-PVLFYAIEDVIEAGVKDIGIIIGPNK 57
                                      79****************************.*****************999987765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   5.9e-11   3.5e-07       1      50 [.       3      57 ..       3      65 .] 0.84

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5.9e-11
                                      EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCH CS
                      NTP_transf_3  1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggdee 50
                                      a+iL GG+++R+      + K+l+p+++kp+l ++++ + +agv+++ ++ g+++
  gi|488599618|ref|YP_007906089.1|  3 ALILSGGHGTRLRpltysQQKQLIPVANKPVLFYAIEDVIEAGVKDIGIIIGPNK 57
                                      79**********6554436****************************99987743 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0     2e-06     0.012       2      58 ..       2      61 ..       1      65 [] 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-G.GGHHH CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvse.ddtee 58
                                       ++i   G+G+R++     + Kq++ ++++++l  +++ + +   v+ i +++ + +dt+e
  gi|488599618|ref|YP_007906089.1|  2 KALILSGGHGTRLRpltYSQQKQLIPVANKPVLFYAIEDVIE-AGVKDIGIIIGPnKDTKE 61
                                      6889999*****85332789*****************99998.567777776655055554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.35s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 369.26
//
Query:       gi|488599619|ref|YP_007906090.1|  [L=93]
Description: hypothetical protein Asulf_00061 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-05   24.9   0.5    1.1e-05   24.8   0.5    1.1  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.5   6.3e-10   1.1e-05     102     147 ..       1      61 [.       1      83 [. 0.79

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.3e-10
                              YdjM 102 llgvlsHlllDlltk...yGvpllwPfskkkvrlsllfiiidplltll.............s 147
                                       ++g+ +H +lDll k   +G+pll+Pfs ++ ++++  ++i+++l+ +             +
  gi|488599619|ref|YP_007906090.1|   1 MFGFTTHYMLDLLLKhvsSGIPLLFPFS-WEESWGWYRVMIAGWLLVVlavvvraatrngsK 61 
                                       7899**********9999*********7.8*************8877666666665554442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 527.88
//
Query:       gi|488599620|ref|YP_007906091.1|  [L=230]
Description: hypothetical protein Asulf_00062 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   0.3       0.41   10.6   0.1    1.8  2  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.08   1.4e+03      33      48 ..      46      59 ..      28      71 .. 0.73
   2 ?   10.6   0.1   2.3e-05      0.41     127     189 ..     127     188 ..      82     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.08
                            AbiEii 33 fSeDIDlsllrgdrke 48
                                      +++DID+++    r++
  gi|488599620|ref|YP_007906091.1| 46 ATKDIDIVV--LGREQ 59
                                      699****98..44444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 2.3e-05
                            AbiEii 127 l.....ggpafevpvysleellaeKllalldrgrdrsraRDlyDlalLleaeldaealaeallaylas 189
                                             + + fe+  +s e+++  K ++ +       r+RD+ Dl++L ea+ld e + + l++ l +
  gi|488599620|ref|YP_007906091.1| 127 VpgefsSHELFEIYLVSKEDIFLFKTITSI------ERVRDVEDLVMLVEAGLDFEIIIQELKNQLSM 188
                                       04444555899*****************66......99****************99977666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1408.42
//
Query:       gi|488599621|ref|YP_007906092.1|  [L=313]
Description: hypothetical protein Asulf_00063 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-10   39.0   0.6     0.0011   18.8   0.2    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.3e-09   37.8   0.9      4e-06   26.6   0.2    2.3  2  MarR_2           MarR family
    2.9e-05   24.5   1.7     0.0031   18.0   0.4    2.4  2  HTH_27           Winged helix DNA-binding domain
    5.2e-05   23.2   0.1      0.085   12.9   0.0    2.7  2  HTH_29           Winged helix-turn helix
    0.00019   21.3   1.2      0.014   15.3   0.4    2.5  2  MarR             MarR family
     0.0002   21.1   0.0     0.0062   16.3   0.0    2.3  2  FtsK_gamma       Ftsk gamma domain
    0.00022   20.7   1.0       0.26   10.9   0.3    2.4  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00057   19.9   0.0       0.12   12.5   0.0    2.5  2  HTH_7            Helix-turn-helix domain of resolvase
    0.00059   19.9   0.9      0.021   14.9   0.1    2.3  2  HTH_20           Helix-turn-helix domain
    0.00075   19.3   2.1       0.19   11.6   0.1    2.4  2  HTH_IclR         IclR helix-turn-helix domain
    0.00083   19.3   0.4       0.31   11.0   0.1    2.9  2  Cdc6_C           CDC6, C terminal winged helix domain
    0.00095   19.5   0.1       0.66   10.4   0.1    2.6  2  Penicillinase_R  Penicillinase repressor
     0.0032   17.8   0.7       0.24   11.8   0.2    2.6  2  Rrf2             Transcriptional regulator
     0.0046   16.0   0.0     0.0067   15.5   0.0    1.2  1  Glucokinase      Glucokinase
  ------ inclusion threshold ------
      0.026   14.4   0.7       0.48   10.3   0.2    2.4  2  HTH_5            Bacterial regulatory protein, arsR family
      0.033   14.0   0.1        3.1    7.7   0.0    2.7  2  HTH_23           Homeodomain-like domain
      0.034   14.1   0.6        3.9    7.5   0.0    2.6  2  HTH_36           Helix-turn-helix domain
      0.043   13.9   0.1        1.9    8.7   0.0    2.6  2  HTH_28           Helix-turn-helix domain
      0.054   13.5   0.6        4.4    7.4   0.2    2.5  2  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.21   11.6   1.5        4.4    7.3   0.2    2.9  3  HTH_11           HTH domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   1.2e-06    0.0011      14      64 ..      10      59 ..       2      63 .. 0.78
   2 !   18.2   0.0   1.9e-06    0.0017      18      62 ..      92     138 ..      88     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                                      CHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE CS
                              TrmB 14 YlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYra 64
                                          l  + + t++++a+el+++  ++   + sLe+kGlV++ k+   k+ ++
  gi|488599621|ref|YP_007906092.1| 10 L---LkLSRERTISQLAKELDISIYRASTLVTSLERKGLVKTGKKGkHKRVSP 59
                                      3...2346899******************************988551446555 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.9e-06
                                       H..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                              TrmB  18 l..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62 
                                       l   + p+ a ei  +++++rs+ Y ++ +L++ G+  ++k+++k++
  gi|488599621|ref|YP_007906092.1|  92 LavLKAPLGAHEICLRSNLSRSTFYHIVDRLSSYGILGKRKKERKYF 138
                                       4345899******************************9999886554 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.2   4.4e-09     4e-06       3      61 ..       2      56 ..       1      57 [. 0.91
   2 !    9.5   0.0   0.00097      0.87      10      54 ..      90     131 ..      85     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.4e-09
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      l++++  +L+ L r+     t+++la++l++s  ++s ++  L+++GLv + +   +kR
  gi|488599621|ref|YP_007906092.1|  2 LSRMEVTLLLKLSRER----TISQLAKELDISIYRASTLVTSLERKGLVKTGKKGKHKR 56
                                      5788889999999985....*******************************98888888 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00097
                                       HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       +L+a+  +p   l + e++ r +ls+s+   i++rL++ G + +r
  gi|488599621|ref|YP_007906092.1|  90 ALLAVLKAP---LGAHEICLRSNLSRSTFYHIVDRLSSYGILGKR 131
                                       677777777...889**********************98877555 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 !   18.0   0.4   3.5e-06    0.0031       2      66 ..       3      61 ..       2      62 .. 0.85
   2 ?    5.4   0.0     0.028        25      21      58 ..     101     136 ..      88     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.5e-06
                            HTH_27  2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTd 66
                                      +r+++ +L  +    r+ ++++l++ l+++   +s  +  L++kGLv +tg++  ++ krv+ +d
  gi|488599621|ref|YP_007906092.1|  3 SRMEVTLLLKLS---RERTISQLAKELDISIYRASTLVTSLERKGLV-KTGKK--GKHKRVSPSD 61
                                      566777777776...999*****************************.77776..8889998877 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
                            HTH_27  21 ladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58 
                                       + ++c r n++ s++  ++++L  +G + + ++e  r+
  gi|488599621|ref|YP_007906092.1| 101 AHEICLRSNLSRSTFYHIVDRLSSYGILGKRKKE--RK 136
                                       569*************************888887..33 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0051       4.6       4      48 ..       9      50 ..       7      61 .. 0.65
   2 !   12.9   0.0   9.5e-05     0.085      15      41 ..     101     127 ..      89     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0051
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rr 48
                                       ll+l+++  t+sq+Ak l++s     + +   e +G   l + ++
  gi|488599621|ref|YP_007906092.1|  9 LLLKLSRER-TISQLAKELDISIYRASTLVTSLERKG---LVKtGK 50
                                      689999999.9**********9555555555555555...444344 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.5e-05
                            HTH_29  15 vsqiAkllglsrrtvyrwlkrfeegGl 41 
                                         +i+ + +lsr+t+y++++r    G+
  gi|488599621|ref|YP_007906092.1| 101 AHEICLRSNLSRSTFYHIVDRLSSYGI 127
                                       569******************999886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   1.6e-05     0.014      18      48 ..      17      47 ..       2      57 .. 0.81
   2 ?    4.1   0.0      0.05        45      17      52 ..      98     133 ..      86     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlie 48
                                       ++s+Lak l +s+  ++++++ Le+kGl++
  gi|488599621|ref|YP_007906092.1| 17 RTISQLAKELDISIYRASTLVTSLERKGLVK 47
                                      47899************************96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.05
                                       TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  17 plsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                       pl  +e+  ++++s+st   ++drL   G + ++k+
  gi|488599621|ref|YP_007906092.1|  98 PLGAHEICLRSNLSRSTFYHIVDRLSSYGILGKRKK 133
                                       378889999****************99888877776 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.9e-06    0.0062      18      60 ..      15      57 ..       6      59 .. 0.89
   2 ?    2.2   0.0      0.18   1.6e+02      38      56 ..     117     135 ..     116     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.9e-06
                        FtsK_gamma 18 gkaStSllQRrlriGYnRAarlidqLeeeGiVgpaegskpReV 60
                                      ++  +S l ++l i   RA+ l+  Le++G+V   ++ k + V
  gi|488599621|ref|YP_007906092.1| 15 RERTISQLAKELDISIYRASTLVTSLERKGLVKTGKKGKHKRV 57
                                      56679****************************9998888776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                        FtsK_gamma  38 rlidqLeeeGiVgpaegsk 56 
                                       +++d+L + Gi g+ ++++
  gi|488599621|ref|YP_007906092.1| 117 HIVDRLSSYGILGKRKKER 135
                                       59***********988654 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   0.3   0.00029      0.26      19      48 .]      18      47 ..      11      47 .. 0.96
   2 !    8.1   0.0    0.0021       1.9      22      46 ..     103     127 ..      89     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++++LA++l++S+   ++ +  Le++Gl+k
  gi|488599621|ref|YP_007906092.1| 18 TISQLAKELDISIYRASTLVTSLERKGLVK 47
                                      899*************************97 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                            HTH_24  22 eLAerlglSpstvnrrlkrLeeeGl 46 
                                       e++ r++lS+st    ++rL + G+
  gi|488599621|ref|YP_007906092.1| 103 EICLRSNLSRSTFYHIVDRLSSYGI 127
                                       8999****************99887 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 ?    4.6   0.0     0.038        34      23      34 ..      18      29 ..       9      32 .. 0.92
   2 !   12.5   0.0   0.00013      0.12      20      41 ..      97     118 ..      90     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.038
                                      -STTTSSSS--- CS
                             HTH_7 23 siskIAkevnis 34
                                      +is++Ake++is
  gi|488599621|ref|YP_007906092.1| 18 TISQLAKELDIS 29
                                      7**********9 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00013
                                       TT--STTTSSSS---SSSS--S CS
                             HTH_7  20 eGisiskIAkevnisRsTvYRy 41 
                                       ++  + +I+ ++n+sRsT+Y +
  gi|488599621|ref|YP_007906092.1|  97 APLGAHEICLRSNLSRSTFYHI 118
                                       5566789*************76 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.4e-05     0.021      12      60 ..       4      52 ..       3      53 .. 0.93
   2 ?    3.4   0.0     0.087        78       7      58 ..      83     132 ..      78     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      R+++  +L+  +++t s+la++ld+s   +s  +  Le+ gLv++ + g
  gi|488599621|ref|YP_007906092.1|  4 RMEVTLLLKLSRERTISQLAKELDISIYRASTLVTSLERKGLVKTGKKG 52
                                      8999999999*********************************997766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.087
                                       HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58 
                                       +++   +++l+ L  +++l a e++ r  ls++t ++ ++ L++ g++  ++
  gi|488599621|ref|YP_007906092.1|  83 ILSGKTLALLAVL--KAPLGAHEICLRSNLSRSTFYHIVDRLSSYGILGKRK 132
                                       5555667888999..99999999999999*************9999986666 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 !    6.9   0.4    0.0059       5.2      17      49 ..      15      47 ..       8      49 .. 0.87
   2 !   11.6   0.1   0.00021      0.19       9      48 ..      89     128 ..      87     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0059
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +e t+s+lA++++++   ++ l+ +L++ G+v+
  gi|488599621|ref|YP_007906092.1| 15 RERTISQLAKELDISIYRASTLVTSLERKGLVK 47
                                      44499***************************8 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00021
                                       HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR   9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                       L +la    +l+  e++ r+ l++St ++++  L   G++
  gi|488599621|ref|YP_007906092.1|  89 LALLAVLKAPLGAHEICLRSNLSRSTFYHIVDRLSSYGIL 128
                                       6788888999*********************999998877 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 ?    5.3   0.0     0.022        20      41      70 ..      32      55 ..      16      60 .. 0.80
   2 !   11.0   0.1   0.00035      0.31      36      65 ..     109     136 ..     102     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                                      HHHHHHHHHHHTTSEEEEEEE-CC.C-EEE CS
                            Cdc6_C 41 evsdllseLemlgileleksskGrregrtr 70
                                      + s l++ Le +g++++ k+      g+++
  gi|488599621|ref|YP_007906092.1| 32 RASTLVTSLERKGLVKTGKK------GKHK 55
                                      78999************988......3344 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00035
                                       ---HHHHHHHHHHHHHTTSEEEEEEE-CC. CS
                            Cdc6_C  36 pltqrevsdllseLemlgileleksskGrr 65 
                                        l+++++++++++L+++gil  +k+ +  +
  gi|488599621|ref|YP_007906092.1| 109 NLSRSTFYHIVDRLSSYGILGKRKKER--K 136
                                       589*******************99944..4 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00073      0.66      24      64 ..      19      59 ..      10      83 .. 0.82
   2 ?    6.3   0.0     0.013        12      31      66 ..     108     140 ..     101     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00073
                                      HHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE- CS
                   Penicillinase_R 24 veeleeekelaysTVktllrrLvkKgllsrekegrafiYsp 64
                                      +++l++e + +     tl++ L++Kgl+++ k+g++ + sp
  gi|488599621|ref|YP_007906092.1| 19 ISQLAKELDISIYRASTLVTSLERKGLVKTGKKGKHKRVSP 59
                                      5677777777777789******************9876555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                                       G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE--- CS
                   Penicillinase_R  31 kelaysTVktllrrLvkKgllsrekegrafiYsplv 66 
                                       ++l++sT   ++ rL   g+l ++k++r++    l+
  gi|488599621|ref|YP_007906092.1| 108 SNLSRSTFYHIVDRLSSYGILGKRKKERKYF---LI 140
                                       4699*************************93...55 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.2   0.00027      0.24      22      57 ..      15      48 ..       4      56 .. 0.80
   2 ?    3.5   0.0       0.1        91      13      56 ..      88     129 ..      82     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +e   +++++a++ +is   ++ +++ L+++glvk+
  gi|488599621|ref|YP_007906092.1| 15 RE--RTISQLAKELDISIYRASTLVTSLERKGLVKT 48
                                      33..489***************************97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                                       HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56 
                                       +l+ La  +   p+ ++ei  r n+s+s   +i+ +L+  g++ 
  gi|488599621|ref|YP_007906092.1|  88 TLALLAVLKA--PLGAHEICLRSNLSRSTFYHIVDRLSSYGILG 129
                                       5666777666..7999**********************999975 PP

>> Glucokinase  Glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.5e-06    0.0067     155     199 ..      49      93 ..      34     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.5e-06
                       Glucokinase 155 asEGGhvdfapeseeevelleilrkklgrvsaErvlSGpGLvnly 199
                                          G h   +p++++ +el++ l++k++++  E +lSG+ L+ l+
  gi|488599621|ref|YP_007906092.1|  49 GKKGKHKRVSPSDAKPAELFRRLTHKFSHMPLEVILSGKTLALLA 93 
                                       55689**********************************999876 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 ?   10.3   0.2   0.00053      0.48       5      28 ..       5      29 ..       3      48 .. 0.79
   2 ?    1.9   0.0      0.22     2e+02       7      31 ..      90     114 ..      85     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                                      HHHHHHHTT.SSEEHHHHHHHHTS- CS
                             HTH_5  5 lkILklLae.gelcvcelaeelgls 28
                                       ++  lL   +e+++++la+el++s
  gi|488599621|ref|YP_007906092.1|  5 MEVTLLLKLsRERTISQLAKELDIS 29
                                      55566666689************99 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.22
                                       HHHHHTTSSEEHHHHHHHHTS-HHH CS
                             HTH_5   7 ILklLaegelcvcelaeelglsqst 31 
                                        L ++ + +l ++e++   +ls+st
  gi|488599621|ref|YP_007906092.1|  90 ALLAVLKAPLGAHEICLRSNLSRST 114
                                       5889999****************99 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.078        70      10      30 ..      10      29 ..       1      45 [. 0.78
   2 ?    7.7   0.0    0.0035       3.1      21      45 ..     102     126 ..      89     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.078
                            HTH_23 10 illllaeGlsvreIAreLgvs 30
                                       l+l +e  ++++ A+eL++s
  gi|488599621|ref|YP_007906092.1| 10 LLKLSRE-RTISQLAKELDIS 29
                                      4555665.8***********9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
                            HTH_23  21 reIAreLgvsrrTvyrwlkryreeG 45 
                                       +eI+ + + sr+T y+++ r    G
  gi|488599621|ref|YP_007906092.1| 102 HEICLRSNLSRSTFYHIVDRLSSYG 126
                                       68899999**********9975555 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.044        39      28      55 .]      19      46 ..       8      46 .. 0.89
   2 ?    7.5   0.0    0.0043       3.9      31      55 .]     104     128 ..     101     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.044
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                       + lak l +s   +s+ + +Le++G++
  gi|488599621|ref|YP_007906092.1| 19 ISQLAKELDISIYRASTLVTSLERKGLV 46
                                      5789**********************85 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0043
                            HTH_36  31 lakrlglsknTvsraikeLeqlGyi 55 
                                       ++ r++ls++T + +++ L  +G++
  gi|488599621|ref|YP_007906092.1| 104 ICLRSNLSRSTFYHIVDRLSSYGIL 128
                                       9**********************87 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.23     2e+02       8      25 ..      11      29 ..       4      37 .. 0.77
   2 ?    8.7   0.0    0.0021       1.9      17      48 ..     103     134 ..      98     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.23
                            HTH_28  8 lla.aGhsvreaArelgis 25
                                      l + + ++++++A+el is
  gi|488599621|ref|YP_007906092.1| 11 LKLsRERTISQLAKELDIS 29
                                      3342567*********997 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                            HTH_28  17 eaArelgisrrtvyrWikryeegGiagLvprr 48 
                                       e++ + ++sr+t y  + r+ ++Gi g +++ 
  gi|488599621|ref|YP_007906092.1| 103 EICLRSNLSRSTFYHIVDRLSSYGILGKRKKE 134
                                       6788889******************5555544 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0049       4.4      23      55 ..      18      50 ..       5      57 .. 0.84
   2 ?    3.8   0.0     0.064        58      21      54 ..      98     132 ..      79     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0049
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrgr 55
                                      t  +lA  l ++    s + + L+r+gl+++g+
  gi|488599621|ref|YP_007906092.1| 18 TISQLAKELDISIYRASTLVTSLERKGLVKTGK 50
                                      4579*************************9653 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.064
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.rg 54 
                                       pl   e+  + +l+r+t+  i  +L+  g++  r+
  gi|488599621|ref|YP_007906092.1|  98 PLGAHEICLRSNLSRSTFYHIVDRLSSYGILGkRK 132
                                       666778888999*******************9532 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0049       4.4       8      28 ..       9      29 ..       4      52 .. 0.79
   2 ?    2.0   0.0      0.22     2e+02      14      50 ..      97     131 ..      87     137 .. 0.78
   3 ?   -1.9   0.0       3.6   3.2e+03      19      28 ..     265     274 ..     250     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0049
                            HTH_11  8 lLleargpisgeeLAeeLnvS 28
                                      lLl+     ++++LA+eL++S
  gi|488599621|ref|YP_007906092.1|  9 LLLKLSRERTISQLAKELDIS 29
                                      455555558***********9 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
                            HTH_11  14 gpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesep 50 
                                        p+ + e+  + n+Sr+t +  +++L++ g  I +++
  gi|488599621|ref|YP_007906092.1|  97 APLGAHEICLRSNLSRSTFYHIVDRLSSYG--ILGKR 131
                                       457788899999*********999999999..55555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.6
                            HTH_11  19 eeLAeeLnvS 28 
                                        eL ++ +vS
  gi|488599621|ref|YP_007906092.1| 265 FELGKKYDVS 274
                                       4777788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1916.66
//
Query:       gi|488599622|ref|YP_007906093.1|  [L=92]
Description: putative metal-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-24   86.3   0.8    1.5e-24   86.1   0.8    1.0  1  UPF0058       Uncharacterised protein family UPF0058
  ------ inclusion threshold ------
      0.066   13.1   1.3      0.098   12.6   1.3    1.3  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.8   1.6e-28   1.5e-24       1      71 [.       1      71 [.       1      87 [. 0.92

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 1.6e-28
                                      --HHHHHHHHHHHHHHHHHHTSTT--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHC CS
                           UPF0058  1 MhKdeLieLHqllvevkkeleeeevekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekees 71
                                      MhK+eL+ LH +l+++k+ +ee+++++ +f +Y++L i+P+hih+sKaehk+Ai+ L++ i ++++e++++
  gi|488599622|ref|YP_007906093.1|  1 MHKEELVFLHLTLFHMKRFFEEAGIANGHFASYDKLGIQPVHIHKSKAEHKKAILTLCKGITDIFKESQPE 71
                                      ******************************************************************99887 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 ?   12.6   1.3   1.1e-05     0.098       8      19 ..      70      81 ..      67      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                      BCA_ABC_TP_C  8 PaEvrndPrVie 19
                                      P++v+++PrV+e
  gi|488599622|ref|YP_007906093.1| 70 PEDVVKNPRVRE 81
                                      9**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      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: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 606.16
//
Query:       gi|488599623|ref|YP_007906094.1|  [L=145]
Description: (SSU ribosomal protein S18P)-alanine acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   75.9   0.0    3.5e-21   75.6   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.5e-14   54.1   0.0    1.6e-14   54.0   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.7e-13   50.1   0.1    3.6e-13   49.7   0.1    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      9e-10   38.7   0.0    6.9e-09   35.9   0.0    1.9  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    7.6e-07   29.0   0.0    1.2e-06   28.4   0.0    1.3  1  FR47             FR47-like protein
    7.4e-05   23.4   0.0    0.00014   22.6   0.0    1.5  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00029   20.6   0.0    0.00031   20.5   0.0    1.1  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
    0.00033   20.8   0.1    0.00079   19.6   0.1    1.7  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00046   20.4   0.0    0.00061   20.0   0.0    1.2  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
    0.00087   19.4   0.0     0.0016   18.5   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0018   18.0   0.0     0.0035   17.0   0.0    1.6  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.071   13.1   0.0    1.7  2  Nudix_hydro      Nudix hydrolase domain
       0.14   11.6   0.1       0.25   10.8   0.1    1.3  1  Pho86            Inorganic phosphate transporter Pho86


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 !   75.6   0.0   2.6e-24   3.5e-21       3     117 .]      12     118 ..      10     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 2.6e-24
                                       HHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1   3 dlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGs 79 
                                       d+ e+++e f p n++ ++ + ++s   + + llva  +g+++G+i +   +      a i+s+aV++e+rg+G+G+
  gi|488599623|ref|YP_007906094.1|  12 DMLEIEKEAFQPANPSYDLFV-YIS---HSDDLLVADIGGRVVGYIAVMDMDS----SAKIISFAVKREFRGMGIGT 80 
                                       788999999999999999998.666...7789**************9999999....8******************* PP

                                       HHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  80 aLlealeerareegikkivlaveedndaairlYeklGF 117
                                        Ll++++ r+re+g k ++l+v+++n++a++lY+k GF
  gi|488599623|ref|YP_007906094.1|  81 ILLDKALVRCRERGKKSVYLEVRVSNERAQKLYKKKGF 118
                                       *********************************88**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   1.1e-17   1.6e-14      32     110 ..      39     122 ..       4     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.1e-17
                   Acetyltransf_10  32 lllvaeeggkivGvielrdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYek 103
                                        llva+ gg++vG+i+++d +   +i  ++V++e+rg Gig+ Ll++++ +++++g k   l+v+ s+  a+++Y+k
  gi|488599623|ref|YP_007906094.1|  39 DLLVADIGGRVVGYIAVMDMDssaKIISFAVKREFRGMGIGTILLDKALVRCRERGKKSvYLEVRVSNeRAQKLYKK 115
                                       589************995555579*****************************999999****************** PP

                   Acetyltransf_10 104 lGFkavg 110
                                        GFk ++
  gi|488599623|ref|YP_007906094.1| 116 KGFKIID 122
                                       ***9884 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.1   2.6e-16   3.6e-13       4      75 ..      39     119 ..      29     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2.6e-16
                                       EEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEE.EE.EEEETHHHHHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea...ae..kgii.le.qlelnaekaikfYek 71 
                                        ++Va+ +g++vG+ia++  d  a i+ +aV+ e+rg GiG+ Ll+    ++  +g + ++ ++++++e+a+k+Y+k
  gi|488599623|ref|YP_007906094.1|  39 DLLVADIGGRVVGYIAVMDMDssAKIISFAVKREFRGMGIGTILLDKalvRCreRGKKsVYlEVRVSNERAQKLYKK 115
                                       57899999********999999999999*****************9535521445522222234445569******* PP

                                       TTEE CS
                    Acetyltransf_7  72 lGFe 75 
                                        GF+
  gi|488599623|ref|YP_007906094.1| 116 KGFK 119
                                       ***8 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0     5e-12   6.9e-09       2     127 ..       2     120 ..       1     121 [. 0.93

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5e-12
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtg 78 
                                       ir++t+ d++++le+ k+aFq  ++ +      f ++  +++ l+a  +g++vg +a+++++ +        a + +
  gi|488599623|ref|YP_007906094.1|   2 IRSYTSRDVKDMLEIEKEAFQPANPSY----DLFVYISHSDDLLVADIGGRVVGYIAVMDMDSS--------AKIIS 66 
                                       89***********************96....6899**************************975........78*** PP

                                       EEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  79 VavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                        av+ e rg g+ + Ll++al ++re+g++ ++l       ++ ++Y+++G++i
  gi|488599623|ref|YP_007906094.1|  67 FAVKREFRGMGIGTILLDKALVRCRERGKKSVYLEVrvsneRAQKLYKKKGFKI 120
                                       **********************************99887666679******987 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   8.4e-10   1.2e-06      21      80 ..      61     121 ..      47     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 8.4e-10
                                       TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfeki 80 
                                       +  + +  v+ e+r++G g+ l  +   + +ergk+ v l v+ sN+++++ly+k Gf+ i
  gi|488599623|ref|YP_007906094.1|  61 SAKIISFAVKREFRGMGIGTILLDKALVRCRERGKKsVYLEVRVSNERAQKLYKKKGFKII 121
                                       46788999**************9999999999997625688*****************987 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   9.8e-08   0.00014      56     138 .]      40     119 ..       1     119 [. 0.74

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.8e-08
                    Acetyltransf_3  56 waivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvl 132
                                       +++ + +++v+G++ + d++ +     +++ ++++f+g G++t  +  +l  + +e g + ++ ++  +Ne+ ++++
  gi|488599623|ref|YP_007906094.1|  40 LLVADIGGRVVGYIAVMDMDSSA--KIISFAVKREFRGMGIGTILLDKALVRC-RERGKKSVYLEVRVSNERAQKLY 113
                                       3333344547**********996..6999************************.6777999**************** PP

                    Acetyltransf_3 133 eklGfe 138
                                       +k Gf+
  gi|488599623|ref|YP_007906094.1| 114 KKKGFK 119
                                       *****7 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.3e-07   0.00031      10      88 ..       5      88 ..       1     121 [. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.3e-07
                              PanZ 10 lsaqdkiDLakIy.....paqsaealeaalteegalfaarFNdRlLgAvkveledkeaelsdlcVRevTRrRGVgsyLl 83
                                       ++ d +D+  I      pa+ +  l   + ++  l++a    R  g ++v   d++a++ ++ V+++ R  G+g  Ll
  gi|488599623|ref|YP_007906094.1|  5 YTSRDVKDMLEIEkeafqPANPSYDLFVYISHSDDLLVADIGGRVVGYIAVMDMDSSAKIISFAVKREFRGMGIGTILL 83
                                      5667777777777777788888888999999************************************************ PP

                              PanZ 84 eearr 88
                                      ++a+ 
  gi|488599623|ref|YP_007906094.1| 84 DKALV 88
                                      99875 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   5.7e-07   0.00079      52     144 ..      40     128 ..       2     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.7e-07
                    Acetyltransf_4  52 flvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiq 127
                                       +lva+  +r+vGy ++  +++     + ++s+ ++ r  + +g+g  l+d    + +e + ++ + e+ ++ne +++
  gi|488599623|ref|YP_007906094.1|  40 LLVADiGGRVVGYIAVMDMDS----SAKIISFAVK-REFRGMGIGTILLDKALVRCRERGKKSVYLEVRVSNERAQK 111
                                       57888899********99999....8889*****8.78********9999888888********************* PP

                    Acetyltransf_4 128 fhkalGFelvgifkkci 144
                                       ++k+ GF++      ++
  gi|488599623|ref|YP_007906094.1| 112 LYKKKGFKIIDVIPSYY 128
                                       ********987665555 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.4e-07   0.00061      73     131 ..      40      98 ..      30     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.4e-07
                    Acetyltransf_6  73 lyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllweliedaaeeGlrrf 131
                                       l+v+  +gr+v++++++  +  +     ++ +e++++++g++ll +++ +++e+G +++
  gi|488599623|ref|YP_007906094.1|  40 LLVADIGGRVVGYIAVMDMDSSAKIISFAVKREFRGMGIGTILLDKALVRCRERGKKSV 98 
                                       678899************************************************97665 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 !   18.5   0.0   1.2e-06    0.0016      22      59 ..      59      96 ..      40     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                   Acetyltransf_CG 22 egvldfthTeVpeelrGkGiAkkLvkaalddareeglk 59
                                      +   ++    V+ e+rG Gi+  L ++al   re+g+k
  gi|488599623|ref|YP_007906094.1| 59 DSSAKIISFAVKREFRGMGIGTILLDKALVRCRERGKK 96
                                      4567788889**************************98 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.5e-06    0.0035      89     140 ..      71     121 ..      34     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                                       HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEE CS
                    Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfeke 140
                                        e+rg g++t ll + + ++ ++ + ++v +E +v+Nera +l++k Gf+  
  gi|488599623|ref|YP_007906094.1|  71 REFRGMGIGTILLDKALVRCRER-GKKSVYLEVRVSNERAQKLYKKKGFKII 121
                                       6899***********99999887.99***********************976 PP

>> Nudix_hydro  Nudix hydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.2   5.7e+03      52      65 ..      61      74 ..      59      75 .. 0.81
   2 ?   13.1   0.0   5.1e-05     0.071      29      68 ..      83     122 ..      80     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.2
                       Nudix_hydro 52 qselvpiavkeGFe 65
                                      ++++++ avk +F+
  gi|488599623|ref|YP_007906094.1| 61 SAKIISFAVKREFR 74
                                      57889999999996 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.1e-05
                       Nudix_hydro  29 LkaslsqwreegkrgvwlkvpieqselvpiavkeGFefHh 68 
                                       L++ l  +re+gk++v+l+v  ++ +  +   k+GF++ +
  gi|488599623|ref|YP_007906094.1|  83 LDKALVRCRERGKKSVYLEVRVSNERAQKLYKKKGFKIID 122
                                       889999******************************9865 PP

>> Pho86  Inorganic phosphate transporter Pho86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00018      0.25     197     267 ..      63     123 ..      57     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                             Pho86 197 kitglgvRkVylksgiledLidwallrtrellkeykkkkkgssikllidvYSfDkelkktLkkkgFkliss 267
                                       ki ++ v++ +   gi + L+d al+r re  k++          + ++v   +++ +k+ kkkgFk+i++
  gi|488599623|ref|YP_007906094.1|  63 KIISFAVKREFRGMGIGTILLDKALVRCRERGKKS----------VYLEVRVSNERAQKLYKKKGFKIIDV 123
                                       89999************************987775..........56777778999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1036.33
//
Query:       gi|488599624|ref|YP_007906095.1|  [L=131]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-38  131.0   0.0    2.6e-38  130.8   0.0    1.0  1  UPF0146          Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.022   14.6   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
      0.046   13.8   0.0      0.052   13.7   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase


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 !  130.8   0.0   4.4e-42   2.6e-38       6     128 ..       7     126 ..       2     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 4.4e-42
                                       HHHHHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HHHHTTEEEEEEES--TT CS
                           UPF0146   6 kkiaeenargkvvEvGiGrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPnleiYkgadliYslRpPae 82 
                                       + ++ +n+ gkvvEv  G ++dva +l+krg+++v +D+k  + +egv +  DD+ +P++eiY++ +liYs+RpP e
  gi|488599624|ref|YP_007906095.1|   7 TAFISKNYSGKVVEVCCGNRFDVALELSKRGFNIVCVDVKRFEPPEGVSFECDDIRNPRIEIYENSSLIYSIRPPYE 83 
                                       67899************************************************************************ PP

                                       SHHHHHHHHHHHT-EEEEE-BTTB-----TT-EEEEETTEEEEEEE CS
                           UPF0146  83 lqsaildvakkvgAaliikpLlgedvvvekelklvnykgalFyike 128
                                       l++ i++++++v A++iikpL+ge++     l lvn  g++Fy+++
  gi|488599624|ref|YP_007906095.1|  84 LYKHIIRLSDRVMADCIIKPLYGEHP---EGLELVNHLGDYFYLRQ 126
                                       *************************6...99************975 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.7e-06     0.022      17     108 ..      11      91 ..       2      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-06
                   Methyltransf_23  17 lpklraggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevl 92 
                                       +  ++ +g+v+++ cG    ++ +l+++gf+++ vD            ++ +++ +  ++++  + ++++  ++ ++
  gi|488599624|ref|YP_007906095.1|  11 S--KNYSGKVVEVCCGNRfDVALELSKRGFNIVCVDVK----------RFEPPEGVSFECDDIRNPRIEIYENSSLI 75 
                                       3..68899**********99*****************5..........67777777778888888888888888888 PP

                   Methyltransf_23  93 ehvpdppellrqiatl 108
                                       +++++p el ++i +l
  gi|488599624|ref|YP_007906095.1|  76 YSIRPPYELYKHIIRL 91 
                                       8888888888888775 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.7e-06     0.052      23      75 ..      16      66 ..       5     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.7e-06
                                      -EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSH CS
                              FtsJ 23 ktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpet 75
                                      ++vv++++  G+  +v+l+  + + ++v vD++  +p++gv++ + di++p+ 
  gi|488599624|ref|YP_007906095.1| 16 GKVVEVCC--GNRFDVALELSKRGFNIVCVDVKRFEPPEGVSFECDDIRNPRI 66
                                      46888887..778899999987789*************************976 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:                      398  (0.0221987); 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 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 885.35
//
Query:       gi|488599625|ref|YP_007906096.1|  [L=353]
Description: signal recognition particle-docking protein FtsY [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-74  247.2   1.0    1.7e-73  246.5   1.0    1.4  1  SRP54            SRP54-type protein, GTPase domain
    2.9e-11   43.4   2.9    2.9e-11   43.4   2.9    3.3  2  SRP54_N          SRP54-type protein, helical bundle domain
    2.1e-07   30.5   0.1    2.1e-07   30.5   0.1    1.7  2  Zeta_toxin       Zeta toxin
    8.3e-06   26.3   0.5    8.3e-06   26.3   0.5    2.3  2  AAA_17           AAA domain
    3.9e-05   23.8   4.2      6e-05   23.2   0.0    2.7  3  AAA_33           AAA domain
    8.2e-05   23.0   0.4    8.2e-05   23.0   0.4    2.9  2  AAA              ATPase family associated with various cellul
     0.0001   22.3   0.0    0.00019   21.3   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
     0.0001   22.1   2.6     0.0001   22.1   2.6    1.9  1  AAA_30           AAA domain
    0.00014   21.9   0.6    0.00014   21.9   0.6    2.0  2  ResIII           Type III restriction enzyme, res subunit
    0.00021   21.7   0.8    0.00044   20.7   0.1    2.0  2  AAA_16           AAA ATPase domain
    0.00028   20.6   0.4    0.00028   20.6   0.4    2.9  2  Thymidylate_kin  Thymidylate kinase
     0.0008   19.0   0.0     0.0017   17.9   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
    0.00089   18.6   0.3    0.00089   18.6   0.3    1.8  1  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00096   19.4   2.2      0.003   17.8   0.1    2.3  2  AAA_28           AAA domain
     0.0014   19.0   0.5     0.0014   19.0   0.5    1.8  1  AAA_19           AAA domain
     0.0051   16.9   0.3      0.013   15.5   0.3    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0069   15.7   0.0       0.01   15.1   0.0    1.3  1  VirC1            VirC1 protein
     0.0073   16.8   1.7      0.018   15.5   0.1    2.2  2  ABC_tran         ABC transporter
     0.0075   15.4   0.0      0.017   14.2   0.0    1.5  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
  ------ inclusion threshold ------
      0.013   15.4   0.3      0.013   15.4   0.3    3.1  4  MobB             Molybdopterin guanine dinucleotide synthesis
      0.015   14.3   0.9      0.015   14.3   0.9    1.8  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.015   15.5   0.8      0.056   13.7   0.0    2.2  2  AAA_22           AAA domain
       0.02   14.9   0.1       0.11   12.5   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
      0.021   14.9   1.0      0.094   12.7   0.0    2.5  2  AAA_14           AAA domain
      0.026   14.3   0.3      0.092   12.5   0.1    1.9  1  IstB_IS21        IstB-like ATP binding protein
      0.026   14.2   1.6      0.046   13.4   0.2    2.1  2  AAA_24           AAA domain
      0.029   13.5   3.5      0.095   11.8   0.0    2.7  3  DUF815           Protein of unknown function (DUF815)
       0.03   13.4   0.4      0.052   12.6   0.3    1.5  1  T2SSE            Type II/IV secretion system protein
      0.032   14.1   0.9      0.032   14.1   0.9    2.8  3  NTPase_1         NTPase
      0.054   14.5   0.5      0.054   14.5   0.5    2.1  1  LytR_C           LytR cell envelope-related transcriptional a
      0.073   12.0   0.1       0.14   11.0   0.1    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.14   10.7   5.1      0.072   11.7   0.2    2.4  3  DUF853           Bacterial protein of unknown function (DUF85
       0.14   11.5   1.7       0.15   11.5   0.0    1.9  3  KTI12            Chromatin associated protein KTI12
       0.15   11.9   0.2       0.15   11.9   0.2    1.9  2  Helicase_RecD    Helicase
       0.16   11.6   0.2       0.36   10.5   0.1    1.6  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.17   10.7   2.5       0.51    9.1   0.3    2.6  3  Fe-ADH           Iron-containing alcohol dehydrogenase
       0.19   12.3   0.1       0.19   12.3   0.1    2.7  2  AAA_18           AAA domain
       0.21   11.5   2.7       0.14   12.0   0.3    1.9  2  AAA_31           AAA domain
       0.84    9.4   0.0       0.84    9.4   0.0    2.4  1  AAA_11           AAA domain
        4.3    7.4   7.2       0.76    9.9   1.4    2.6  2  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 !  246.5   1.0   3.7e-76   1.7e-73       2     195 ..     159     352 ..     158     353 .] 0.99

  Alignments for each domain:
  == domain 1  score: 246.5 bits;  conditional E-value: 3.7e-76
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                         il+vG++G+GKTtt+aK+a++l+++g++v+++a DtfRa+A+eQL+++a++lgv++ik+k++adpaav+++a+++
  gi|488599625|ref|YP_007906096.1| 159 ANILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAGDTFRAGAIEQLEEHAKNLGVKIIKHKTGADPAAVIFDAIKH 235
                                       579************************************************************************** PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                       a++++id+vl DTaGr++++k+l+++l kik+v+kp+ +++v ++++g++a++ a+ F++avgi+g iltklD+d k
  gi|488599625|ref|YP_007906096.1| 236 AEAKGIDIVLSDTAGRMHTKKNLIDQLGKIKRVTKPALTIFVDESLAGNDAIERARMFNDAVGIDGSILTKLDADPK 312
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       gG+a+si++ +++P+ f+g+G++++dle+f++e+l+ r++
  gi|488599625|ref|YP_007906096.1| 313 GGTAISISYITGKPVLFVGTGQSYDDLEKFSSEWLIGRIF 352
                                       *************************************997 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8  10.9       4.2   1.9e+03      39      73 ..      39      72 ..       1      73 [. 0.78
   2 !   43.4   2.9   6.4e-14   2.9e-11      17      75 .]      76     133 ..      72     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.2
                                      --HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHH CS
                           SRP54_N 39 Vgvkvvkklienvkkkavgekklkpkqqvkkivkd 73
                                      V  +vv++ +++v+k +++++k++ k+++k +v++
  gi|488599625|ref|YP_007906096.1| 39 VEAEVVEEKRKEVEK-EAKKEKVSLKDKIKAVVFE 72
                                      899**********77.777799***********97 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 6.4e-14
                                       CGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHHH CS
                           SRP54_N  17 kideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkdeL 75 
                                        ide  le +l ele++Lle+DV+++vv+++++++k++ vg ++ k +q++ +iv deL
  gi|488599625|ref|YP_007906096.1|  76 IIDEGKLEGILSELEMILLESDVAFDVVDEITQKLKDSLVG-RRKKIGQKLSDIVIDEL 133
                                       48***************************************.66799***********8 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.9       7.8   3.5e+03     159     177 ..      40      55 ..      13      76 .. 0.40
   2 !   30.5   0.1   4.6e-10   2.1e-07      12     117 ..     153     262 ..     143     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.8
                        Zeta_toxin 159 hdeafeglresvealeeek 177
                                         e++e+ r++ve+   e 
  gi|488599625|ref|YP_007906096.1|  40 EAEVVEEKRKEVEK---EA 55 
                                       22222222222222...22 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 4.6e-10
                        Zeta_toxin  12 sq.erPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe.lhPeyeeilka.dpkkaseltqkdaselv 84 
                                       ++ ++P+ il +G  G GK++++++++++l+ ++ +vv+  +D++R+  + + ee+ k+  +k     t +d   + 
  gi|488599625|ref|YP_007906096.1| 153 RNvDKPANILFVGVNGTGKTTTIAKIAKRLTsQGYSVVVAAGDTFRAgAIEQLEEHAKNlGVKIIKHKTGADPAAVI 229
                                       4449***************************55556777789****8578899999998899999************ PP

                        Zeta_toxin  85 ekllqeaiengyniivegtlrspdvvkklaeal 117
                                         ++++a  +g++i++  t    ++ k+l+++l
  gi|488599625|ref|YP_007906096.1| 230 FDAIKHAEAKGIDIVLSDTAGRMHTKKNLIDQL 262
                                       *****************9999999999888766 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   4.4         2     9e+02      32     111 ..      23     103 ..      10     134 .. 0.52
   2 !   26.3   0.5   1.9e-08   8.3e-06       1     109 [.     164     278 ..     164     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2
                                       HHHHTTTSHSSHHHHC........TSHHHHHHHHHHHHHHHHHHHH.....HSSEEEEEE-SEEEETTEEEESSHHH CS
                            AAA_17  32 eeakrgglakardemr........klpleekkelqkeaaekiaeea.....kkkgvlvdghprikeqagfldglpke 95 
                                       ee+++          +        k++ e+ +e +ke++++ ++e+     k k v+++    i  ++g l+g+ +e
  gi|488599625|ref|YP_007906096.1|  23 EEVRQV---------EareakpepKVEAEVVEEKRKEVEKEAKKEKvslkdKIKAVVFEREVII--DEGKLEGILSE 88 
                                       333333.........2222222334555555555555555555554443212233444444433..34556666666 PP

                                       HHHHH..SEEEEEE-- CS
                            AAA_17  96 vleelkpdaiillead 111
                                        +  l  +  + +++ 
  gi|488599625|ref|YP_007906096.1|  89 LEMIL-LESDVAFDVV 103
                                       54444.4445555554 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.9e-08
                                       EE-TTSSHHHHHHHHHHHH...TEEE.EEHHHHHHHHHHTTTSHSSHHHHC..TSHHHHHHHHHHHHHHHHHHHHHS CS
                            AAA_17   1 lGgPGsGKgtqceklveky...gfth.lsaGdllreeakrgglakardemr..klpleekkelqkeaaekiaeeakk 71 
                                       +G+ G GK+t ++k+++++   g+++ + aGd +r+ a ++ l+++ +++     +++   +  + + ++i+++++k
  gi|488599625|ref|YP_007906096.1| 164 VGVNGTGKTTTIAKIAKRLtsqGYSVvVAAGDTFRAGAIEQ-LEEHAKNLGvkIIKHKTGADPAAVIFDAIKHAEAK 239
                                       79***************9999977751688*****998654.55566655532445555666666777777776544 PP

                                       ..SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                            AAA_17  72 ..kgvlvdghprikeqagfldglpkevleelkpdaiille 109
                                         + vl d+  r+ +++ ++d+l k +++  kp + i+++
  gi|488599625|ref|YP_007906096.1| 240 giDIVLSDTAGRMHTKKNLIDQLGK-IKRVTKPALTIFVD 278
                                       1256999******999998888875.89999999999987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.8       3.7   1.7e+03     100     139 ..      10      50 ..       1      53 [. 0.69
   2 ?   -0.7   0.0       3.1   1.4e+03      17      40 ..      83     117 ..      82     145 .. 0.55
   3 !   23.2   0.0   1.3e-07     6e-05       2     120 ..     161     291 ..     161     304 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.7
                            AAA_33 100 rivvvetdeetlkeRlakRaangddrs.evpeealdrqkar 139
                                       +i   ++dee+++e +++ +a++ ++  +v+ e++++ ++ 
  gi|488599625|ref|YP_007906096.1|  10 KIFRKKVDEEEAREEVRQVEAREAKPEpKVEAEVVEEKRKE 50 
                                       56666899999999999888877555436777777776665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.1
                            AAA_33  17 erllkklgavllssdt...........lrrrlfgt 40 
                                       e++l +l ++ll+sd+           l++ l+g+
  gi|488599625|ref|YP_007906096.1|  83 EGILSELEMILLESDVafdvvdeitqkLKDSLVGR 117
                                       56788999999999995555554444444444443 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.3e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrr.rlfgtdqqskt......dytrvldrlyqilnelarka 66 
                                       +l+vG++G+GK+t + +++k+l+     +v+ + dt+r  +++  +++ k+      + ++ +d +   +++ ++ a
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLTsqgysVVVAAGDTFRAgAIEQLEEHAKNlgvkiiKHKTGADPAA-VIFDAIKHA 236
                                       69************************97777788998885555544444445666544444555555.667999999 PP

                            AAA_33  67 lsagrnvil.datnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaa 120
                                        ++g++++l d   +++ +   +++l +   v   ++++ +de+++     +Ra+
  gi|488599625|ref|YP_007906096.1| 237 EAKGIDIVLsDTAGRMHTKKNLIDQLGKIKRVTKPALTIFVDESLAGNDAIERAR 291
                                       9*****9994455566677778888888888888888888888887766666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3       1.3     6e+02      45      74 ..     109     140 ..      81     155 .. 0.65
   2 !   23.0   0.4   1.8e-07   8.2e-05       1      97 [.     161     266 ..     161     342 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHTS..TSEEEEEETGGGHHHHH CS
                               AAA  45 kirelfkeakeka..kpsilfiDEidalaksr 74 
                                       k+++ +   ++k   k s ++iDE+ ++ k+ 
  gi|488599625|ref|YP_007906096.1| 109 KLKDSLVGRRKKIgqKLSDIVIDELKSILKDI 140
                                       44444433222225444779999999998765 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.8e-07
                                       EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSSSTTHHHHHHHHHHHHH.HHTS..TSEEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakel...gvefleisgsellskyvgesekkirelfkea.keka..kpsilfiDEidala 71 
                                       +l++G  GtGKT+++  +ak l   g +++   g +++   +++ e++ ++l  ++ k+k   +p  +++D i    
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLtsqGYSVVVAAGDTFRAGAIEQLEEHAKNLGVKIiKHKTgaDPAAVIFDAIKHAE 237
                                       69*******************95545778888888888777777777777765554143336688888888887665 PP

                                       HHH...TTCCCHHHHHHHHHHHHHHHHTT CS
                               AAA  72 ksr...sgseseeeervvnqLlteldgvk 97 
                                        +      s++  ++ + + L+ +l + k
  gi|488599625|ref|YP_007906096.1| 238 AKGidiVLSDTAGRMHTKKNLIDQLGKIK 266
                                       55555534444455555555555555555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.3e-07   0.00019       2      50 ..     158     206 ..     157     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.3e-07
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50 
                                       ++ +++ G+ g+GK+t   +++k+L+++g+sv++  Gd+ R g  ++L 
  gi|488599625|ref|YP_007906096.1| 158 PANILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAGDTFRAGAIEQLE 206
                                       67899***********999**********************99888775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   2.6   2.3e-07    0.0001      22      73 ..     162     212 ..     149     297 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.3e-07
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieasti 73 
                                       + +G+ GtGKtt+++++++ ++++g++v+++A     A +++ +l+ +a+++
  gi|488599625|ref|YP_007906096.1| 162 LFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAGDTFRAGAIE-QLEEHAKNL 212
                                       679*****************************8887777766.233333333 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 ?   -1.5   1.6       4.8   2.2e+03      85     110 ..      47      72 ..       3     133 .. 0.59
   2 !   21.9   0.6   3.1e-07   0.00014      21     109 ..     135     246 ..     101     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.8
                                       GEEEESSS-B--.......-SEEEEE CS
                            ResIII  85 igkkvsgdkkkakekdstnkkilvtt 110
                                       + k+v+++ kk+k + ++++k +v++
  gi|488599625|ref|YP_007906096.1|  47 KRKEVEKEAKKEKVSLKDKIKAVVFE 72 
                                       22222222222233334444444444 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 3.1e-07
                                       ......................TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII  21 s....................krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkf 77 
                                       s                    ++  ++l++   GtGKT ++ak+++rl+++g+    ++++ + +    ++e++++ 
  gi|488599625|ref|YP_007906096.1| 135 SilkdildrnrfdfdefvrnvDKPANILFVGVNGTGKTTTIAKIAKRLTSQGY---SVVVAAGDTFRAGAIEQLEEH 208
                                       2555566666677777777667888*************************988...599999999999999998888 PP

                                       TGG....GEEEESSS-B--.............-SEEEE CS
                            ResIII  78 lseaykeigkkvsgdkkka......kekdstnkkilvt 109
                                       +++   +i k ++g    a      k+ +++ ++i+++
  gi|488599625|ref|YP_007906096.1| 209 AKNLGVKIIKHKTGADPAAvifdaiKHAEAKGIDIVLS 246
                                       88876555555554444445666555555555555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       4.6   2.1e+03      80      80 ..      75      75 ..       7     150 .. 0.57
   2 !   20.7   0.1   9.9e-07   0.00044      24      63 ..     158     197 ..     114     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.6
                            AAA_16 80 e 80
                                       
  gi|488599625|ref|YP_007906096.1| 75 V 75
                                      1 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 9.9e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       p ++l++G  G+GK++ + +++++l+ +g  ++ +  d +
  gi|488599625|ref|YP_007906096.1| 158 PANILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAGDTF 197
                                       5799************************755555555555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.2      0.78   3.5e+02      19      74 ..       4      59 ..       1      76 [. 0.68
   2 !   20.6   0.4   6.2e-07   0.00028       3      56 ..     165     216 ..     163     295 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.78
                                      HHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTH...HHHH CS
                   Thymidylate_kin 19 rlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehle...ekik 74
                                      +lke+ +  ++++  ++ e +e +r++  +e + e++ ea      r +++e   +k k
  gi|488599625|ref|YP_007906096.1|  4 KLKEKLK--IFRKKVDEEEAREEVRQVEAREAKPEPKVEAEVVEEKR-KEVEkeaKKEK 59
                                      5555553..77788888889999999999999999999999998888.77763333333 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 6.2e-07
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqt 56 
                                       G++G+GKtt ++++++rl+++g++vv+    g+t  +  i +l +++++l  + 
  gi|488599625|ref|YP_007906096.1| 165 GVNGTGKTTTIAKIAKRLTSQGYSVVVA--AGDTFRAGAIEQLEEHAKNLGVKI 216
                                       9**********************96654..455666666666666666655555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.8e-06    0.0017      31      65 ..     156     190 ..     143     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.8e-06
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkekylsl 65 
                                       ++  ++l+vG  GtGKt++i ++ k+l ++ y+++
  gi|488599625|ref|YP_007906096.1| 156 DKPANILFVGVNGTGKTTTIAKIAKRLTSQGYSVV 190
                                       56679***********************9999876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3     2e-06   0.00089       4     106 ..     161     258 ..     158     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkka 80 
                                       +l  Gv GtGKt    +++ +l    ++ ++v++     +++   e+l++++  k+ + ++ k ++   ++    +a
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRL---TSQGYSVVVAAGDTFRAGAIEQLEEHA--KNLGVKIIKHKTGADPAAVIFDA 232
                                       5556******************...88888999999999999999***9999..77888888888888888766889 PP

                           DUF2075  81 eekkeepkedvvivDEAhrlltksdq 106
                                       ++++e + +d+v+ D A r+ tk++ 
  gi|488599625|ref|YP_007906096.1| 233 IKHAEAKGIDIVLSDTAGRMHTKKNL 258
                                       9*********************7765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.96   4.3e+02      29      79 ..      19      64 ..       3      91 .. 0.55
   2 !   17.8   0.1   6.8e-06     0.003       1      46 [.     160     209 ..     160     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.96
                            AAA_28 29 Eaareileeklakgedalpwvedllafaer.vleeqleeeaaaaankvlfcD 79
                                      E are +++  a++ +  p+      ++++ v+e+++e e++a+++kv + D
  gi|488599625|ref|YP_007906096.1| 19 EEAREEVRQVEAREAKPEPK------VEAEvVEEKRKEVEKEAKKEKVSLKD 64
                                      44444444444444432222......23220333333444555555444433 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.8e-06
                            AAA_28   1 kivitGgestGKTtlleaLaar....gypvvpEaareileeklakgedal 46 
                                       +i ++G  +tGKTt+++++a+r    gy+vv  a+ ++     ++ e+++
  gi|488599625|ref|YP_007906096.1| 160 NILFVGVNGTGKTTTIAKIAKRltsqGYSVVVAAGDTFRAGAIEQLEEHA 209
                                       5899************9999887888***997777777666665555554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   3.1e-06    0.0014      11     111 ..     159     280 ..     150     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.1e-06
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae................... 68 
                                        ++l ++  GtGKT+++ +i + l ++g  ++   +  +f   A ++l+e  ++lg++                   
  gi|488599625|ref|YP_007906096.1| 159 ANILFVGVNGTGKTTTIAKIAKRLTSQG-YSVVVAAGDTFRAGAIEQLEEHAKNLGVKiikhktgadpaavifdaik 234
                                       567788999**************99999.3333334446777789*******9999997776666666555544444 PP

                            AAA_19  69 ...atTiHrlal......ldfddlltealelleeaeeekklqeee.llivDEf 111
                                          a               d+ ++++++ +l+++  + k +++ + +++vDE+
  gi|488599625|ref|YP_007906096.1| 235 haeA-------KgidivlSDTAGRMHTKKNLIDQLGKIKRVTKPAlTIFVDES 280
                                       4443.......044444444555555555555555556666666669999996 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3     3e-05     0.013       9      37 ..     168     196 ..     165     310 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-05
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDp 37 
                                       G+GKTt+ a++a+ l  +g+ V++   D+
  gi|488599625|ref|YP_007906096.1| 168 GTGKTTTIAKIAKRLTSQGYSVVVAAGDT 196
                                       9*********************9976665 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.3e-05      0.01      12      96 ..     168     253 ..     161     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                             VirC1  12 GaGkttalmglcsalasdgkrvalfeadenrP..ltkwkenalrkgawddacevfvadelplleaayeeaegeGfdy 86 
                                       G+Gktt++  +   l+s+g  v +  +d  r   +++  e+a++ g          ad  +++ +a ++ae++G d+
  gi|488599625|ref|YP_007906096.1| 168 GTGKTTTIAKIAKRLTSQGYSVVVAAGDTFRAgaIEQLEEHAKNLGVKII-KHKTGADPAAVIFDAIKHAEAKGIDI 243
                                       89**************************9885337889999988776544.445689999***************** PP

                             VirC1  87 aladtrgGss 96 
                                       +l+dt g   
  gi|488599625|ref|YP_007906096.1| 244 VLSDTAGRMH 253
                                       *****98665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3       2.2   9.8e+02      68      80 ..      35      69 ..       3     119 .. 0.47
   2 !   15.5   0.1   4.1e-05     0.018      12      61 ..     159     212 ..     150     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.2
                                      --S-TTSB.HHHH.....................H CS
                                      xxxxxxxx.xxxx.....................x RF
                          ABC_tran 68 pqlfpelt.vren.....................e 80
                                      p+ + e + v+e+                      
  gi|488599625|ref|YP_007906096.1| 35 PEPKVEAEvVEEKrkevekeakkekvslkdkikaV 69
                                      22222222122222222222222223333333330 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.1e-05
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG...B-HHHCCHCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx...xxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke...qeleslrkei 61 
                                         + +vG nG+GK+t ++ +a+ l+ +  ++ +  g+ ++    ++le+  k++
  gi|488599625|ref|YP_007906096.1| 159 ANILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAaGDTFRAgaiEQLEEHAKNL 212
                                       56889******************9998888877645555545554444444443 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.8e-05     0.017      25      70 ..     149     191 ..     132     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                                       TTSS--B--SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEE CS
                              LpxK  25 agllkserlpvpVivVGNitvGGtGKTPlvialvkllqarglkvgv 70 
                                        ++++++  p+ ++ VG   v GtGKT +++ ++k+l+++g+ v+v
  gi|488599625|ref|YP_007906096.1| 149 DEFVRNVDKPANILFVG---VNGTGKTTTIAKIAKRLTSQGYSVVV 191
                                       45677778888888888...99*********************987 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 ?   -1.9   0.3       6.4   2.9e+03     103     119 ..       5      21 ..       2      30 .. 0.70
   2 ?   -1.7   0.3       5.6   2.5e+03      62      98 ..      43      80 ..      39      92 .. 0.67
   3 ?   15.4   0.3   2.9e-05     0.013       2      32 ..     161     191 ..     160     197 .. 0.92
   4 ?    0.0   0.2       1.6   7.3e+02      25      59 ..     209     242 ..     195     272 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.4
                              MobB 103 alpkievlraelgkeel 119
                                         +k++++r+++++ee 
  gi|488599625|ref|YP_007906096.1|   5 LKEKLKIFRKKVDEEEA 21 
                                       4689999**99998765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.6
                              MobB 62 vaskerlalikeleeaelsleellarl.sevDlvlvEG 98
                                      v+ ++r  + ke +++++sl++ ++ +  e  +++ EG
  gi|488599625|ref|YP_007906096.1| 43 VVEEKRKEVEKEAKKEKVSLKDKIKAVvFEREVIIDEG 80
                                      55566666666666667777777776644566666555 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2.9e-05
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgt 32 
                                       + +vg +g+GKTt + k+ + l+++g++v +
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLTSQGYSVVV 191
                                       579************************9965 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.6
                              MobB  25 arglrvgtiKhahhgfdvdkpgkDsyrhrkAGAke 59 
                                       a++l v +iKh++ g d      D+ +h++A    
  gi|488599625|ref|YP_007906096.1| 209 AKNLGVKIIKHKT-GADPAAVIFDAIKHAEAKGID 242
                                       4667778888875.456666667777777763333 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.4       7.8   3.5e+03     225     228 ..      44      47 ..       4      80 .. 0.49
   2 ?   14.3   0.9   3.4e-05     0.015      31     131 ..     160     250 ..     148     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.8
                                       HHHH CS
                              MeaB 225 ieeh 228
                                       +ee 
  gi|488599625|ref|YP_007906096.1|  44 VEEK 47 
                                       2222 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.4e-05
                                       EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-----HHHHH CS
                              MeaB  31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslpsrGalGGla 107
                                        + + Gv G+Gk t++ +++ +l+++G+ v v a D   +f  G+i     +lee+a++ gv i    ++      a
  gi|488599625|ref|YP_007906096.1| 160 NILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAGD---TFRAGAI----EQLEEHAKNLGVKIIKHKTGADP---A 226
                                       56688*************************998866...6777877....46777777777766665554433...4 PP

                                       HHHHHHHHHHHHTT-SEEEEEEES CS
                              MeaB 108 aktrevvllleaaGfDvvlietvG 131
                                       a   ++++  ea G D+vl +t G
  gi|488599625|ref|YP_007906096.1| 227 AVIFDAIKHAEAKGIDIVLSDTAG 250
                                       445666777777777777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3       2.5   1.1e+03      73     103 ..      80     110 ..      10     149 .. 0.58
   2 ?   13.7   0.0   0.00013     0.056       7      34 ..     160     187 ..     152     297 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.5
                            AAA_22  73 lsseellealeqalraravielliiDEaqh.l 103
                                       +++e +l+ le  l + +v ++ ++DE+   l
  gi|488599625|ref|YP_007906096.1|  80 GKLEGILSELEMILLESDV-AFDVVDEITQkL 110
                                       4444444444555555555.555555543323 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeak 34 
                                        ++ +G  GtGKTt++++++++l+ + +
  gi|488599625|ref|YP_007906096.1| 160 NILFVGVNGTGKTTTIAKIAKRLTSQGY 187
                                       68899*****************964422 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.8   1.2e+03      69      91 ..     128     143 ..      86     159 .. 0.70
   2 ?   12.5   0.0   0.00024      0.11       1      33 [.     160     193 ..     160     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.8
                                       EEEESGGG--HHHHHHHHHHHHS CS
                             AAA_5  69 lvlDEveraesevlnsLlsllee 91 
                                       +v+DE++ + +++       l++
  gi|488599625|ref|YP_007906096.1| 128 IVIDELKSILKDI-------LDR 143
                                       5666666544444.......444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00024
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE-- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqlt 33 
                                       ++l vG  GtgK++ + ++a++l  + + +v   
  gi|488599625|ref|YP_007906096.1| 160 NILFVGVNGTGKTTTIAKIAKRLtSQGYSVVVAA 193
                                       5899******************985555555444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3       2.4   1.1e+03      69      84 ..     102     138 ..      43     149 .. 0.52
   2 ?   12.7   0.0   0.00021     0.094       5      76 ..     161     236 ..     157     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.4
                            AAA_14  69 flDEiqev.....................pewekalk 84 
                                       + DEi +                      +e++++lk
  gi|488599625|ref|YP_007906096.1| 102 VVDEITQKlkdslvgrrkkigqklsdiviDELKSILK 138
                                       3344433334444444444444444444444455555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00021
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklkeekktylflDEiqev 76 
                                       ++ +G+  +GKTt + +++k+l  +  s++  + d+ r  ++++ e    +l   i ++ ++ +   +++D i+++
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAGDTFRAGAIEQLEehakNLGVKIIKHKTGADPAAVIFDAIKHA 236
                                       56789**************999988888888888887775555443223233344444434467889999999887 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 ?   12.5   0.1   0.00021     0.092      44      80 ..     155     191 ..     149     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlf 80 
                                       ++k +ni+++G  G+GK+   + ++++   +g+sv+ 
  gi|488599625|ref|YP_007906096.1| 155 VDKPANILFVGVNGTGKTTTIAKIAKRLTSQGYSVVV 191
                                       78899*****************************974 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       2.4   1.1e+03      59      80 ..     106     139 ..      45     143 .. 0.73
   2 ?   13.4   0.2    0.0001     0.046       2      91 ..     158     264 ..     157     278 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.4
                            AAA_24  59 l............aaeladyktlviDtideleel 80 
                                       +            ++  ++++ +viD +  + + 
  gi|488599625|ref|YP_007906096.1| 106 ItqklkdslvgrrKKIGQKLSDIVIDELKSILKD 139
                                       1333555555556777788888888888776665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.0001
                            AAA_24   2 klkiliyGpsgiGKTtlakel.......gpkplfi...........dtekGlksldadkfpdieswedfldevvel. 59 
                                       +++il +G +g+GKTt+++++       g+++++            ++e+ +k+l ++ ++                
  gi|488599625|ref|YP_007906096.1| 158 PANILFVGVNGTGKTTTIAKIakrltsqGYSVVVAagdtfragaieQLEEHAKNLGVKIIK--------------Hk 220
                                       6799*****************5554444444444344333333333333333333333333..............03 PP

                            AAA_24  60 ..............aaeladyktlviDtideleelclaevirqnek 91 
                                                      ae ++++++  Dt++ +  ++++++i+q +k
  gi|488599625|ref|YP_007906096.1| 221 tgadpaavifdaikHAEAKGIDIVLSDTAGRM--HTKKNLIDQLGK 264
                                       33334444445556677777777777777777..667777777666 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.4   6.3e+02     167     185 ..      48      65 ..      36      71 .. 0.71
   2 ?    1.2   0.4      0.37   1.7e+02     107     135 ..      89     117 ..      57     130 .. 0.78
   3 ?   11.8   0.0   0.00021     0.095      51      87 ..     156     192 ..     123     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                            DUF815 167 eeeihaseaveeklsLsdR 185
                                       ++e+ ++ea +ek+sL d+
  gi|488599625|ref|YP_007906096.1|  48 RKEV-EKEAKKEKVSLKDK 65 
                                       3444.579999****9997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                            DUF815 107 erfilfvDDLsFeeeeeeyksLksvLeGs 135
                                        ++il+  D++F+  +e  ++Lk  L G 
  gi|488599625|ref|YP_007906096.1|  89 LEMILLESDVAFDVVDEITQKLKDSLVGR 117
                                       4689999****************999886 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00021
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrliev 87 
                                        +  n+L++G  GtGK +++  + ++++++g  ++  
  gi|488599625|ref|YP_007906096.1| 156 DKPANILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVA 192
                                       35679************************99887755 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00012     0.052     116     160 ..     146     189 ..      33     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                        +++e++r+   +  +il+ G  g+GKtt++  + k + ++   +
  gi|488599625|ref|YP_007906096.1| 146 FDFDEFVRNV-DKPANILFVGVNGTGKTTTIAKIAKRLTSQGYSV 189
                                       5678888876.999*****************99999998884333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.3       6.7     3e+03     100     110 ..      76      85 ..      16     141 .. 0.62
   2 ?   14.1   0.9   7.1e-05     0.032       2      30 ..     161     189 ..     160     223 .. 0.91
   3 ?    0.6   0.1         1   4.6e+02      84     132 ..     228     276 ..     199     297 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.7
                                       EE---STTGGG CS
                          NTPase_1 100 viDEiGkmElk 110
                                       +iDE Gk+E  
  gi|488599625|ref|YP_007906096.1|  76 IIDE-GKLEGI 85 
                                       4444.444433 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.1e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       ++  G  G+GKtT + k+++ l s+g++v
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLTSQGYSV 189
                                       5667999*******************998 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1
                                       HHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE- CS
                          NTPase_1  84 lalealrkal.seadviviDEiGkmElkskkfkeaveevLksekpvlavi 132
                                       ++ +a+++a  ++ d+++ D  G+m  k k++++++ ++ +  kp l+++
  gi|488599625|ref|YP_007906096.1| 228 VIFDAIKHAEaKGIDIVLSDTAGRMHTK-KNLIDQLGKIKRVTKPALTIF 276
                                       5677888877788899999999999876.556667777777666666655 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 ?   14.5   0.5   0.00012     0.054       7      81 ..     166     245 ..     166     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00012
                            LytR_C   7 lNgtgvsGlAarvadaLeerGftvgevgnagnadeettivyreaaaaaakalaaalglgelqedsvkdas....... 76 
                                       +Ngtg++   a++a+ L+++G+ v+   +ag++      +  ++a ++ ++ a+ lg++ +++++ +d++       
  gi|488599625|ref|YP_007906096.1| 166 VNGTGKTTTIAKIAKRLTSQGYSVVV--AAGDT-----FR--AGAIEQLEEHAKNLGVKIIKHKTGADPAavifdai 233
                                       5*********************7776..24444.....33..33335666888888888877777777776666666 PP

                            LytR_C  77 .......vtvvl 81 
                                              +++vl
  gi|488599625|ref|YP_007906096.1| 234 khaeakgIDIVL 245
                                       666666666665 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00032      0.14      16      49 ..     159     192 ..     152     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                     TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdraivl 49 
                                       + il+vG  G+GKt+++ k+ + + ++g  ++v+
  gi|488599625|ref|YP_007906096.1| 159 ANILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVA 192
                                       5799************************999986 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 ?    0.2   1.1       0.5   2.2e+02     408     475 ..      14      65 ..       2     120 .. 0.43
   2 ?   11.7   0.2   0.00016     0.072      25      56 ..     162     193 ..     155     240 .. 0.84
   3 ?   -2.7   0.0       3.5   1.6e+03     244     266 ..     258     280 ..     254     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.5
                            DUF853 408 eeidresayevLakkvaeaaeaaeqaaaeeekeeesgllgalkdtalgaaakkaeergskketvveal 475
                                       +++d e a e + +  a+                e++ +++++++++ ++ k++e+ ++k+++  +  
  gi|488599625|ref|YP_007906096.1|  14 KKVDEEEAREEVRQVEAR----------------EAKPEPKVEAEVVEEKRKEVEKEAKKEKVSLKDK 65 
                                       334444443333222222................2222233333333322222222222222222222 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00016
                            DUF853  25 liaGatGtGktvtLqvlaeslseaGvpvflad 56 
                                       l  G  GtGkt t+ ++a+ l+++G +v++a 
  gi|488599625|ref|YP_007906096.1| 162 LFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAA 193
                                       56899**********************99984 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.5
                            DUF853 244 LfeeLPevGdldkPklvfffdea 266
                                       L ++L  +  + kP l +f de+
  gi|488599625|ref|YP_007906096.1| 258 LIDQLGKIKRVTKPALTIFVDES 280
                                       677888888899*********96 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3       6.1   2.8e+03      58      75 ..      45      62 ..      12      81 .. 0.57
   2 ?   -3.0   0.2       8.4   3.8e+03     201     214 ..     101     114 ..      50     139 .. 0.56
   3 ?   11.5   0.0   0.00034      0.15       4      41 ..     161     198 ..     159     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.1
                                      HHHHHHHHHHHTT.SEEE CS
                             KTI12 58 sslrsavkrdLskekvVI 75
                                      ++ r++v+++ +kekv  
  gi|488599625|ref|YP_007906096.1| 45 EEKRKEVEKEAKKEKVSL 62
                                      333333333333333333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.4
                                       HHHHHHHH....HT CS
                             KTI12 201 eivkeileaqksav 214
                                       ++v+ei +++k + 
  gi|488599625|ref|YP_007906096.1| 101 DVVDEITQKLKDSL 114
                                       33333333333333 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00034
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                       +++ G+  +GK+t  +++ak l+++++svvv   ++++
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAGDTFR 198
                                       7999***************************9999887 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.5       5.2   2.3e+03      49      91 ..      24      66 ..       4      89 .. 0.54
   2 ?   11.9   0.2   0.00033      0.15       6      57 ..     167     216 ..     163     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.2
                     Helicase_RecD 49 glealglkeeekkkkaekaelrvrkqrieyiapdellklkeqa 91
                                      ++++++ +e + + k e   ++ +++++e  a +e ++lk++ 
  gi|488599625|ref|YP_007906096.1| 24 EVRQVEAREAKPEPKVEAEVVEEKRKEVEKEAKKEKVSLKDKI 66
                                      4444444443333344444444444444444444444444333 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00033
                     Helicase_RecD   6 RGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke 57 
                                        G+GK++++++++++l+++g+ +++v+a +    +  +e+l++  ++lg+k 
  gi|488599625|ref|YP_007906096.1| 167 NGTGKTTTIAKIAKRLTSQGY-SVVVAAGDTF-RAGAIEQLEEHAKNLGVKI 216
                                       59******************9.5666665543.2334455555556666554 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00079      0.36      17      57 ..     161     201 ..     155     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00079
                                       EEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsddaiiyvgiGergneva 57 
                                       +l +g +g+Gkt+ +++++k  +s+ ++++v+ G   +  a
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAGDTFRAGA 201
                                       677899***************99999******999876543 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1         1   4.6e+02      28      70 ..      75     115 ..      55     129 .. 0.76
   2 ?    3.2   0.0      0.07        32      57      89 ..     162     194 ..     152     196 .. 0.91
   3 ?    9.1   0.3    0.0011      0.51       7      86 ..     168     245 ..     165     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1
                                       EEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHH CS
                            Fe-ADH  28 ivtdkgslkksglldkvlesleeagievtvfdgvepnptleev 70 
                                       ++ d+g  k +g+l++++  l e++++++v+d++++  +++ v
  gi|488599625|ref|YP_007906096.1|  75 VIIDEG--KLEGILSELEMILLESDVAFDVVDEITQKLKDSLV 115
                                       445555..34699999999999999999999999988777665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.07
                                       E.EEE-S---HHHHHHHHTTS-TT.--EEEEEE CS
                            Fe-ADH  57 vfdgvepnptleeveeaaalareegadvviavG 89 
                                       +f gv++  ++++++++a+++ ++g+ vv+a G
  gi|488599625|ref|YP_007906096.1| 162 LFVGVNGTGKTTTIAKIAKRLTSQGYSVVVAAG 194
                                       688999999**********************99 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0011
                                       ETTGGGGHHHHHTTT-....EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT. CS
                            Fe-ADH   7 gkgaleelgellkklgak..ralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareeg 81 
                                       g+g+++ +++ +k+l  +  ++++ ++   + ++g++++++e+ ++ g+++   +  ++  + + + +a++ a+++g
  gi|488599625|ref|YP_007906096.1| 168 GTGKTTTIAKIAKRLTSQgySVVVAAGDT-F-RAGAIEQLEEHAKNLGVKII--KHKTGADPAAVIFDAIKHAEAKG 240
                                       66666677777777754432555555555.4.799********966666666..55566667799************ PP

                                       --EEE CS
                            Fe-ADH  82 advvi 86 
                                       +d+v+
  gi|488599625|ref|YP_007906096.1| 241 IDIVL 245
                                       **997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.4       2.7   1.2e+03      45      66 ..      70      91 ..       4     146 .. 0.57
   2 ?   12.3   0.1   0.00042      0.19       1      32 [.     161     197 ..     161     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.7
                            AAA_18 45 aldeskrldedkldklldalee 66
                                       ++++ ++de+kl+ +l++le 
  gi|488599625|ref|YP_007906096.1| 70 VFEREVIIDEGKLEGILSELEM 91
                                      3333333333333333333333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00042
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdva 32 
                                       Il  G+ G+GKtt    ++krl +     +v  +d++
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLTSqgysvVVAAGDTF 197
                                       8999*****************8555666655555554 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       4.5     2e+03     100     100 ..      92      92 ..      37     148 .. 0.52
   2 ?   12.0   0.3   0.00032      0.14      12      88 ..     168     248 ..     164     279 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.5
                            AAA_31 100 l 100
                                       +
  gi|488599625|ref|YP_007906096.1|  92 I 92 
                                       1 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00032
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyevl..i.eeknikeaiiktkvenldli 84 
                                       G GKTTt  ++a+ l+++g+ v +   D+  + ++ +l+ + +++  ++++    +   + i +ai++++ + +d++
  gi|488599625|ref|YP_007906096.1| 168 GTGKTTTIAKIAKRLTSQGYSVVVAAGDTFRAGAIeQLEEHAKNLGVKIIKHKtgAdPAAVIFDAIKHAEAKGIDIV 244
                                       89**********************99998766655133334455555665554333344556677777777777777 PP

                            AAA_31  85 pssi 88 
                                        s++
  gi|488599625|ref|YP_007906096.1| 245 LSDT 248
                                       7665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0019      0.84      20      44 ..     161     185 ..     144     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                            AAA_11  20 tliqGPPGtgKTktivellsqllsr 44 
                                        l+ G  GtgKT+ti+++ ++l+s+
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRLTSQ 185
                                       5667778***************754 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4       6.1   2.7e+03      87      87 ..      79      79 ..      18     130 .. 0.63
   2 ?    9.9   1.4    0.0017      0.76       2      84 ..     161     278 ..     160     299 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.1
                                      T CS
                          MMR_HSR1 87 e 87
                                      e
  gi|488599625|ref|YP_007906096.1| 79 E 79
                                      1 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0017
                                       EEEEESTTSSHHHHHHHHHTS....TEEESSSTTSSSSE.EEEEEEETTEE.......................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge....kaivsdkpgtTrdi.negrvklkgke.......................... 47 
                                       +++vG   +GK+t i ++ ++       v   +g T      ++++++                             
  gi|488599625|ref|YP_007906096.1| 161 ILFVGVNGTGKTTTIAKIAKRltsqGYSVVVAAGDTFRAgAIEQLEEH--Aknlgvkiikhktgadpaavifdaikh 235
                                       899**************9985422122444444444444233333322..023444555555555566666666666 PP

                                       .......EEEEECGGCSSHHHHHHHHHHHHHHHHC.T.SEEEEEEE CS
                          MMR_HSR1  48 .......ielvDtpGliegaseekglgkaflalee.a.dlillvvd 84 
                                              i+l Dt+G     +++k+l +++ ++++ +  ++ + vd
  gi|488599625|ref|YP_007906096.1| 236 aeakgidIVLSDTAGR---MHTKKNLIDQLGKIKRvTkPALTIFVD 278
                                       6666666********4...456666777766666632233444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1888  (0.105304); expected 358.6 (0.02)
Passed bias filter:                      876  (0.0488594); expected 358.6 (0.02)
Passed Vit filter:                       167  (0.00931452); 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):              40  [number of targets reported over threshold]
# CPU time: 0.90u 0.39s 00:00:01.29 Elapsed: 00:00:00.57
# Mc/sec: 1878.87
//
Query:       gi|488599626|ref|YP_007906097.1|  [L=144]
Description: prefoldin, archaeal alpha subunit/eukaryotic subunit 5 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   66.6   5.1    1.8e-18   66.6   5.1    1.4  1  Prefoldin      Prefoldin subunit
     0.0029   17.5  15.1        0.2   11.7   3.7    2.5  2  Prefoldin_2    Prefoldin subunit
  ------ inclusion threshold ------
      0.031   14.5   3.6       0.14   12.4   0.2    2.1  2  CREPT          Cell-cycle alteration and expression-elevated 
       0.31    9.6   3.9       0.36    9.4   3.9    1.1  1  Peptidase_S46  Peptidase S46
       0.45   10.9   5.8        3.8    7.9   1.1    2.4  2  GAT            GAT domain
          1    9.9   7.7        3.4    8.2   2.7    2.2  2  UPF0449        Uncharacterised protein family UPF0449
        1.4    9.2  12.2        1.8    8.8   1.8    2.2  2  Cortex-I_coil  Cortexillin I, coiled coil
        1.5    8.5  10.6        1.5    8.5   4.4    2.1  2  Tex_N          Tex-like protein N-terminal domain
        1.5    9.3  16.3        0.9   10.1   0.9    2.4  2  APG6_N         Apg6 coiled-coil region
        2.3    9.0   8.3        4.5    8.1   0.9    2.3  2  RecG_N         RecG N-terminal helical domain
        4.8    7.5  13.6        2.5    8.4   4.9    3.0  3  DUF4164        Domain of unknown function (DUF4164)
        7.5    6.6   9.0         13    5.9   1.8    2.3  2  DUF1664        Protein of unknown function (DUF1664)


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 !   66.6   5.1   1.2e-21   1.8e-18       1     118 [.      22     139 ..      22     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.2e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHH CS
                         Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyvekslee 77 
                                       l++e+e++q+++ +++  + e+++t+etl+ ++k ++++ +l++lg+g+++++++k+ +k+lvd+Gag  +e+++ e
  gi|488599626|ref|YP_007906097.1|  22 LQSEAEEIQRKIFEVDVVQAEIDRTIETLEYFEKVEDDVDALINLGSGVFAYVDIKNSKKMLVDVGAGAVIEREVSE 98 
                                       5899************************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                         ++lkk++e+++k  + + + le  ++q+ +l++++a+l+
  gi|488599626|ref|YP_007906097.1|  99 VLDILKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAELS 139
                                       **************************************987 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   3.7   0.00013       0.2       1      67 [.      13      83 ..      13      86 .. 0.71
   2 !   11.0   3.7   0.00021      0.31      55     102 ..      91     138 ..      86     144 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHS-TT.--EEEEETTEEEEE-HHHHHHHH CS
                       Prefoldin_2  1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleel...ellded.tkvyklvGdvlvkqdkeevkeeL 67
                                      q++++ +qqlq++ ++++ +i +++    e++ ++e+l   e++++d +    l  +v+  +d ++ k++L
  gi|488599626|ref|YP_007906097.1| 13 QQKLALLQQLQSEAEEIQRKIFEVDVVQAEIDRTIETLeyfEKVEDDvDALINLGSGVFAYVDIKNSKKML 83
                                      899*****************988887777777777777222577777444444444666666666666665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
                                       EEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  55 lvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                        +++++ ev++ L++rke+++k  +++ + le +  + ++l++e+ ++
  gi|488599626|ref|YP_007906097.1|  91 VIEREVSEVLDILKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAEL 138
                                       58999*****************98888888888888888888877765 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 ?   12.4   0.2   9.2e-05      0.14      87     131 ..      14      58 ..       4      68 .. 0.79
   2 ?    3.4   0.3     0.054        80      82     123 ..      97     138 ..      79     144 .] 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.2e-05
                             CREPT  87 aqkellakaeekleelkeklekvksvrkelkshiqsLPdLtelpd 131
                                       ++ +ll++ ++++ee+++k+ +v+ v++e++++i+ L   +++ d
  gi|488599626|ref|YP_007906097.1|  14 QKLALLQQLQSEAEEIQRKIFEVDVVQAEIDRTIETLEYFEKVED 58 
                                       3345789****************************9976666555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.054
                             CREPT  82 edfleaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                       ++ l ++k++ +  ++  +++ + le v s+ ++l++ i  L
  gi|488599626|ref|YP_007906097.1|  97 SEVLDILKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAEL 138
                                       455555555555555555566666666666666666666554 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.9   0.00024      0.36     401     530 ..       4     143 ..       1     144 [] 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00024
                                       ..HH-HHHHHHHHHHHHHHCHHHHCS--.HHHHHHHHHHHHHHHHHHS-..GGG--S----SS.............. CS
                     Peptidase_S46 401 daereeeyqeralealekeleridkdld.aevdkavlaallkeyreklk..aerlpavdkvlgkes........kgd 466
                                       d+er ++  +++l+ l++  ++  ++++ + ++  v++a++++  e+l+  ++  ++vd++++  s        k++
  gi|488599626|ref|YP_007906097.1|   4 DEERIAQEAQQKLALLQQLQSEA-EEIQrKIFEVDVVQAEIDRTIETLEyfEKVEDDVDALINLGSgvfayvdiKNS 79 
                                       56666666666665554444333.33330334666677776666655542223346778888777777888885555 PP

                                       -S-SHHCCCCC-TTSSCHHHHHHT-SHHCHHHHCC-HHHHHHHHHHHHHHHTHHHHHHHHHHHH CS
                     Peptidase_S46 467 lealvdrlvakskladeakrkalleeakaaveaskDplielavaladaraalekaekelegkle 530
                                        + lvd    +   ++  ++  +l+++k+++++ kD+ i+l + ++ + ++l+k+ +el+++l+
  gi|488599626|ref|YP_007906097.1|  80 KKMLVDVGAGAVIEREVSEVLDILKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAELSSQLK 143
                                       5555666666666678899***********************************9999998876 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.1    0.0025       3.8      18      43 ..      11      36 ..       4      66 .. 0.76
   2 ?    5.4   0.3     0.015        22      21      47 ..     116     142 ..      94     144 .] 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0025
                               GAT 18 eellenellkeLyetckamqpriqkl 43
                                      e  ++  ll++L ++ +++q++i++ 
  gi|488599626|ref|YP_007906097.1| 11 EAQQKLALLQQLQSEAEEIQRKIFEV 36
                                      4567899****************985 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                               GAT  21 lenellkeLyetckamqpriqklieet 47 
                                          +ll+  y++ +++q+ i +l +++
  gi|488599626|ref|YP_007906097.1| 116 RYIQLLEGVYSQARQLQKEIAELSSQL 142
                                       45689999**************99885 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.7    0.0023       3.4      55     100 ..       3      48 ..       1      49 [. 0.92
   2 ?    4.7   0.2     0.028        42      44      90 ..     108     140 ..      74     144 .] 0.52

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                           UPF0449  55 aeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLeeeie 100
                                       ++ e++ +++++ l+l ++L+++ ee+++k  e  ++  e++++ie
  gi|488599626|ref|YP_007906097.1|   3 KDEERIAQEAQQKLALLQQLQSEAEEIQRKIFEVDVVQAEIDRTIE 48 
                                       678899999*********************************9997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                           UPF0449  44 kassseeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLkt 90 
                                       ++ ++ ++   +  e++Y q+r              +L+++  eL++
  gi|488599626|ref|YP_007906097.1| 108 ESIQKGKDRYIQLLEGVYSQAR--------------QLQKEIAELSS 140
                                       2222222233333455555554..............44444444433 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   3.1      0.01        15      33      75 ..       6      51 ..       2      65 .. 0.68
   2 ?    8.8   1.8    0.0012       1.8      25      69 ..     100     144 .]      88     144 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHH CS
                     Cortex-I_coil 33 eelikqkdelesllasleseaaerekrlrel...eakldealknle 75
                                      e++++  ++   ll+ l+sea+e ++++ e+   +a +d ++  le
  gi|488599626|ref|YP_007906097.1|  6 ERIAQEAQQKLALLQQLQSEAEEIQRKIFEVdvvQAEIDRTIETLE 51
                                      4445555555678999999999999999886222566666666665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Cortex-I_coil  25 lesekvsreelikqkdelesllasleseaaerekrlreleaklde 69 
                                       l+  k  +e + k kd+  +ll  + s+a + +k ++el ++l+e
  gi|488599626|ref|YP_007906097.1| 100 LDILKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAELSSQLKE 144
                                       6666888999*******************************9976 PP

>> 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 ?    8.5   4.4   0.00099       1.5      42      93 ..       6      58 ..       2      61 .. 0.90
   2 ?    4.0   0.4     0.024        36      32      69 ..     106     143 ..      86     144 .] 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00099
                             Tex_N 42 eql.reieerleylrelekrkeevlksieeqgklteeLkkkieaaktleeled 93
                                      e++ +e +++l  l++l++  ee+ ++i e + ++ e+ ++ie+ +  e++ed
  gi|488599626|ref|YP_007906097.1|  6 ERIaQEAQQKLALLQQLQSEAEEIQRKIFEVDVVQAEIDRTIETLEYFEKVED 58
                                      44425789999****************************************98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.024
                             Tex_N  32 Rkeatggldeeqlreieerleylrelekrkeevlksie 69 
                                       Rke +++ ++  ++ +e  ++++r+l+k  +e  ++++
  gi|488599626|ref|YP_007906097.1| 106 RKESIQKGKDRYIQLLEGVYSQARQLQKEIAELSSQLK 143
                                       99999999999999999999999999999888877776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   8.5     0.042        63      47      89 ..      10      52 ..       1      66 [. 0.54
   2 ?   10.1   0.9    0.0006       0.9      11      92 ..     100     143 ..      76     144 .] 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.042
                            APG6_N 47 eeleeleeeleklekeeeelleeLkelekereeleaelaalee 89
                                      +e ++    l++l++e ee ++++ e++  ++e+++ +++le 
  gi|488599626|ref|YP_007906097.1| 10 QEAQQKLALLQQLQSEAEEIQRKIFEVDVVQAEIDRTIETLEY 52
                                      2222233336666666666666666666666666666666654 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaal 87 
                                       l+                                       l+++ e ++k +++ ++ L+ + ++ ++l++e+a+l
  gi|488599626|ref|YP_007906097.1| 100 LDI--------------------------------------LKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAEL 138
                                       334......................................455555566666666666666666666666666666 PP

                            APG6_N  88 eeele 92 
                                       +++l+
  gi|488599626|ref|YP_007906097.1| 139 SSQLK 143
                                       66554 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.3     0.025        38      12      62 ..       8      56 ..       1      64 [. 0.66
   2 ?    8.1   0.9     0.003       4.5       3      49 ..      97     143 ..      95     144 .] 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                                      HHTS---TTT........HHHHHHH---GGGG-HHHH...HHHHHHHHHHTTS CS
                            RecG_N 12 llkkvlsgkleteelieeikkkleliddplleneevlk..eklskfldYikpi 62
                                      +++++ ++kl    l++ +++++e+i++++ e   v+   ++  + l+Y +++
  gi|488599626|ref|YP_007906097.1|  8 IAQEA-QQKL---ALLQQLQSEAEEIQRKIFEVDVVQAeiDRTIETLEYFEKV 56
                                      33333.4455...79999********999999877663113445556666665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH. CS
                            RecG_N   3 EeFLeelekllkkvlsgkleteelieeikkkleliddplleneevlk 49 
                                        e L+ l k ++++++gk    +l+e +++++ ++++++ e ++ lk
  gi|488599626|ref|YP_007906097.1|  97 SEVLDILKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAELSSQLK 143
                                       578999********************************999988776 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.9    0.0017       2.5      44      76 ..       1      33 [.       1      49 [. 0.93
   2 ?    0.8   0.0      0.41   6.2e+02      21      43 ..      40      62 ..      34      66 .. 0.60
   3 ?    2.9   0.8     0.091   1.4e+02      35      77 ..     101     143 ..      90     144 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                           DUF4164 44 lgedrsRLaeeLdqaearaarleevnrEvsrrL 76
                                      +++d++R+a+e  q++a +++l++ ++E++r++
  gi|488599626|ref|YP_007906097.1|  1 MDKDEERIAQEAQQKLALLQQLQSEAEEIQRKI 33
                                      799***************************987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.41
                           DUF4164 21 Ekavdrrleaerkrdeleaeiea 43
                                       + +dr +e+ +  +++e ++ a
  gi|488599626|ref|YP_007906097.1| 40 QAEIDRTIETLEYFEKVEDDVDA 62
                                      45566666666666666666655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.091
                           DUF4164  35 deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLk 77 
                                       d l+++ e +++ + R  + L ++   a++l++  +E+s++Lk
  gi|488599626|ref|YP_007906097.1| 101 DILKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAELSSQLK 143
                                       5677788888888888888899999999999999999988886 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.8    0.0084        13      71     114 ..       8      51 ..       2      66 .. 0.69
   2 ?    5.1   0.7     0.014        22      49      96 ..      95     142 ..      80     144 .] 0.57

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0084
                           DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       + ++ ++  ++ +++++e +e+++++ e++    ++++++e+le
  gi|488599626|ref|YP_007906097.1|   8 IAQEAQQKLALLQQLQSEAEEIQRKIFEVDVVQAEIDRTIETLE 51 
                                       55556666677777777777777777777777777777777776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredl 96 
                                       ++ +v + l++ k+ +++  dr  + l+ +   ++++++e++e++++l
  gi|488599626|ref|YP_007906097.1|  95 EVSEVLDILKKRKESIQKGKDRYIQLLEGVYSQARQLQKEIAELSSQL 142
                                       445555555555555555555555555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1796  (0.100173); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); 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: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 814.60
//
Query:       gi|488599627|ref|YP_007906098.1|  [L=60]
Description: LSU ribosomal protein LX [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   33.7   0.0    3.8e-08   33.4   0.0    1.1  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   2.1e-12   3.8e-08      73     119 ..       7      53 ..       2      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.1e-12
                                       ......TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEE CS
                    Ribosomal_L18A  73 lrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIek 119
                                        +++  + +++f+k +++ +e+ a e+v s +gs+h++kr+ I+Ie+
  gi|488599627|ref|YP_007906098.1|   7 GKFRNGEIWTKFRKVVEAHNENFAREKVLSLIGSNHKVKRNLIKIEE 53 
                                       577778889************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 362.78
//
Query:       gi|488599628|ref|YP_007906099.1|  [L=218]
Description: translation initiation factor 6 (aeIF-6) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-67  227.0   5.4    1.5e-67  226.8   5.4    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 !  226.8   5.4   8.5e-72   1.5e-67       2     197 .]       5     197 ..       4     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 226.8 bits;  conditional E-value: 8.5e-72
                                       E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHH CS
                             eIF-6   2 lsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeelek 78 
                                       lsi+g + +G+++r+ ++ya+v    +e++++++eeeL+v++++ttiags+lvG++v++Ns g +v ++v+++e+ek
  gi|488599628|ref|YP_007906099.1|   5 LSIQGVPLVGLYIRASEDYAVVGVR-DEKVIQIVEEELEVKAIRTTIAGSELVGAMVAMNSTGAVVCRHVRQKEIEK 80 
                                       57999*****************999.999************************************************ PP

                                       HHHHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE- CS
                             eIF-6  79 lkeslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvh 155
                                       ++++  ++v+++++++t+lGN il+ND++A+vhp+l+++ +e+i+d++g+++  gti+giktvG++a+vtnkg+lv+
  gi|488599628|ref|YP_007906099.1|  81 ISRY--IDVRVVDTNMTCLGNNILINDYGAIVHPELDRALIEEISDFFGIKILVGTIGGIKTVGMSACVTNKGALVN 155
                                       ***9..78888****************************************************************** PP

                                       TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 156 pkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       p++te+e+++l+++lkv+ve+gT+N+Gs++vg+g+vaN+kg+
  gi|488599628|ref|YP_007906099.1| 156 PNSTEWEMKRLSDILKVPVEKGTINFGSDMVGTGVVANTKGY 197
                                       ****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1525.30
//
Query:       gi|488599629|ref|YP_007906100.1|  [L=89]
Description: LSU ribosomal protein L31E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-13   50.2   0.2      3e-13   49.8   0.2    1.1  1  Ribosomal_L31e  Ribosomal protein L31e
     0.0028   16.6   0.0      0.003   16.5   0.0    1.0  1  YukC            WXG100 protein secretion system (Wss), protei


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 !   49.8   0.2   3.3e-17     3e-13       5      69 ..       8      74 ..       5      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 3.3e-17
                    Ribosomal_L31e  5 reytInihkrihgvgfkkraprAlkeikkfamkemg.tpdv.ridtrLnkavwakgirnvpyrirvr 69
                                      r y +++ ++++ + +  ra++A+k ++kf  ++m+  pd  ++dtrLn+ +w++gi+++p+rir+r
  gi|488599629|ref|YP_007906100.1|  8 RVYSVRLRQKLKPYPRWLRAKKAMKFLRKFLSRHMKaEPDNiKFDTRLNEKIWERGIQKPPARIRIR 74
                                      88999999999999999*******************889999***********************98 PP

>> YukC  WXG100 protein secretion system (Wss), protein YukC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.3e-07     0.003      51     108 ..      14      68 ..       5      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-07
                                       GGGGS-HHHHHHHHHH.GGGGGGGGGSSEE---SGGGEEE-TTS-EEES--EETTTBS- CS
                              YukC  51 eikkkekkeklrlaln.ikaleellssrltlilhPeNlvfdknlepkilhrgvkeslpp 108
                                         +k + + +++ a + +k+l+++ls   ++  +P+N+ fd  l+ ki  rg+++  pp
  gi|488599629|ref|YP_007906100.1|  14 LRQKLKPYPRWLRAKKaMKFLRKFLS--RHMKAEPDNIKFDTRLNEKIWERGIQK--PP 68 
                                       55677888999999999*********..7999*********************96..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 620.34
//
Query:       gi|488599630|ref|YP_007906101.1|  [L=50]
Description: LSU ribosomal protein L39E [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   65.7  12.8    2.3e-18   65.5  12.8    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5  12.8   1.3e-22   2.3e-18       1      42 []       8      49 ..       8      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.3e-22
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                      +K rLaK ++qNr+ P Wv+lkt+r+v ++pkrRhWRr+kLk
  gi|488599630|ref|YP_007906101.1|  8 VKFRLAKFYRQNRRAPLWVTLKTKRRVFSSPKRRHWRRKKLK 49
                                      59***************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); 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: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 320.97
//
Query:       gi|488599631|ref|YP_007906102.1|  [L=111]
Description: DNA-binding TFAR19-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-27   94.5  19.5      5e-27   94.4  19.5    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain


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 !   94.4  19.5   2.8e-31     5e-27       1     107 [.       7     109 ..       7     111 .] 0.93

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 2.8e-31
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       ir+++laelqaq +++ +  + ++qqe q+e   +++k+aiL+ iLepeAreRL+ri+l++pe +e++en+Li laq
  gi|488599631|ref|YP_007906102.1|   7 IRRRKLAELQAQRERELE--ELRRQQELQSE--IQAQKKAILRAILEPEARERLARIKLAHPEISESIENQLIALAQ 79 
                                       9**********9997766..45677777777..99****************************************** PP

                                       --SS-----HHHHHHHHHHHS---XXXXX. CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvaekkketkiv 107
                                       +G+lr+k+t+e L+e+L++   kk+etki 
  gi|488599631|ref|YP_007906102.1|  80 TGRLRQKITDEMLVEILKRALPKKRETKII 109
                                       ****************************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1733  (0.096659); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 738.75
//
Query:       gi|488599632|ref|YP_007906103.1|  [L=149]
Description: SSU ribosomal protein S19E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-56  188.0   0.0    6.5e-56  187.8   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
     0.0041   16.9   0.0       0.17   11.8   0.0    2.3  2  RuvB_C          RuvB C-terminal winged helix domain
     0.0072   16.3   0.0      0.012   15.6   0.0    1.4  1  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.053   13.5   0.0    1.8  2  HTH_12          Ribonuclease R winged-helix domain
      0.029   14.9   0.0      0.044   14.3   0.0    1.3  1  AAA_assoc_C     C-terminal AAA-associated domain
      0.033   13.8   0.1      0.079   12.6   0.0    1.6  2  GntR            Bacterial regulatory proteins, gntR family
      0.052   13.4   0.0       0.12   12.3   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.07   13.3   0.0       0.33   11.1   0.0    2.0  2  Mrr_N           Mrr N-terminal domain
       0.14   12.2   0.1       0.41   10.8   0.0    1.8  2  HemN_C          HemN C-terminal domain
       0.19   12.1   0.0       0.32   11.4   0.0    1.4  1  Rrf2            Transcriptional regulator


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 !  187.8   0.0   3.6e-59   6.5e-56       1     136 [.       3     137 ..       3     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 3.6e-59
                                       TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                    Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                       tv+dVpa+eli+ +a++L++ +++++Pewa++vKtg++k+++pe+++W+y R+A+i R+vy++gpvG++rlr+v+Gg
  gi|488599632|ref|YP_007906103.1|   3 TVYDVPANELIEYVAKKLEEMEEFKPPEWANFVKTGVHKQRSPEQPNWWYLRTAAIFRRVYTDGPVGIQRLRTVFGG 79 
                                       79*************************************************************************** PP

                                       -------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                    Ribosomal_S19e  78 kkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                       +krrg++p +f+k+sgs++rk+lqqLek+g+v+k ++ gr++t+kG+++ld+ a+e+++
  gi|488599632|ref|YP_007906103.1|  80 RKRRGSKPPRFAKGSGSIVRKALQQLEKAGFVEKVDG-GRIVTPKGRSFLDKSANELKE 137
                                       ********************************99977.*****************9875 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.053        96      15      34 ..      59      78 ..      52      83 .. 0.81
   2 !   11.8   0.0   9.4e-05      0.17      50      71 ..     107     128 ..     101     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.053
                                      HHHT.TT--B-HHHHHHHTT CS
                            RuvB_C 15 lkekfkggpvglktlaailg 34
                                      + + + +gpvg++ l ++ g
  gi|488599632|ref|YP_007906103.1| 59 FRRVYTDGPVGIQRLRTVFG 78
                                      56789********9987765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.4e-05
                                       HTTSEEEETTEEEE-HHHHHHH CS
                            RuvB_C  50 keglIertsrGRilTkkglkyl 71 
                                       k g++e+ + GRi+T+kg ++l
  gi|488599632|ref|YP_007906103.1| 107 KAGFVEKVDGGRIVTPKGRSFL 128
                                       689***************9998 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   6.8e-06     0.012      35      70 ..      97     132 ..      94     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.8e-06
                            HTH_45  35 llnkYLdmLvekglikkskekYvlTekGlelleklk 70 
                                       +++k L++L + g+++k ++   +T kG+ +l+k  
  gi|488599632|ref|YP_007906103.1|  97 IVRKALQQLEKAGFVEKVDGGRIVTPKGRSFLDKSA 132
                                       57889***************************9854 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 ?   -3.1   0.0       4.4   7.9e+03      40      45 ..      18      23 ..      11      26 .. 0.52
   2 ?   13.5   0.0     3e-05     0.053      35      65 ..      98     127 ..      93     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                            HTH_12 40 rkleer 45
                                      +klee+
  gi|488599632|ref|YP_007906103.1| 18 KKLEEM 23
                                      444443 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3e-05
                            HTH_12  35 vRyrLrkleergltrrvgyagreltEkGlee 65 
                                       vR  L+ le+ g++++v  +gr +t kG + 
  gi|488599632|ref|YP_007906103.1|  98 VRKALQQLEKAGFVEKVD-GGRIVTPKGRSF 127
                                       8***************97.56******9765 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 ?   14.3   0.0   2.5e-05     0.044      18      62 ..     102     146 ..      97     149 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                       AAA_assoc_C  18 veaaelLglveveegdielTelGrkfveadikerKeifreqllkl 62 
                                       ++ +e  g+ve  +g  ++T++Gr+f++++ +e Ke + e++ +l
  gi|488599632|ref|YP_007906103.1| 102 LQQLEKAGFVEKVDGGRIVTPKGRSFLDKSANELKEKLVEKIPAL 146
                                       55667779****************************999998765 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.4e-05     0.079      37      61 ..      94     118 ..      91     120 .. 0.87
   2 ?   -3.6   0.0         5   9.1e+03       5      11 ..     135     141 ..     132     144 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                       -HHHHHHHHHHHHHTTSEEEETTCE CS
                              GntR  37 srttvReALrrLeaeglverrqgrG 61 
                                       s + vR+AL++Le +g ve  +g+ 
  gi|488599632|ref|YP_007906103.1|  94 SGSIVRKALQQLEKAGFVEKVDGGR 118
                                       5678***************999876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5
                                       HHHHHHH CS
                              GntR   5 vyerLre 11 
                                       ++e+L e
  gi|488599632|ref|YP_007906103.1| 135 LKEKLVE 141
                                       3444444 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.6e-05      0.12      39      58 ..      98     117 ..      92     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHCTSEEEESST CS
                              TrmB  39 vYevLrsLedkGlVerekgr 58 
                                       v ++L++Le++G+Ve+++g 
  gi|488599632|ref|YP_007906103.1|  98 VRKALQQLEKAGFVEKVDGG 117
                                       789*************9976 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.88   1.6e+03      21      32 ..      10      25 ..       6      50 .. 0.65
   2 ?   11.1   0.0   0.00019      0.33      56      86 ..     100     129 ..      91     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.88
                             Mrr_N 21 keirervaerf....g 32
                                      +e++e+va+++    +
  gi|488599632|ref|YP_007906103.1| 10 NELIEYVAKKLeemeE 25
                                      6777777777632223 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                             Mrr_N  56 WartyLkkagllespkrgvwkiTekGrevlk 86 
                                        a+++L kag++e+   g   +T+kGr++l 
  gi|488599632|ref|YP_007906103.1| 100 KALQQLEKAGFVEKV-DGGRIVTPKGRSFLD 129
                                       5899***********.666789*****9985 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.3     6e+03      35      47 ..      13      25 ..      10      25 .. 0.71
   2 ?   10.8   0.0   0.00023      0.41      37      65 ..      97     125 ..      88     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.3
                            HemN_C 35 eellaaaleklqe 47
                                       e++a++le+++e
  gi|488599632|ref|YP_007906103.1| 13 IEYVAKKLEEMEE 25
                                      5667888998876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                            HemN_C  37 llaaaleklqeqGLLeldggrlrltprGr 65 
                                       ++++al++l+++G++e  +g+  +tp+Gr
  gi|488599632|ref|YP_007906103.1|  97 IVRKALQQLEKAGFVEKVDGGRIVTPKGR 125
                                       56899***********************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.32      39      60 ..      95     116 ..      90     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHTTSEEEETT CS
                              Rrf2  39 psylekilakLrkaglvksvrG 60 
                                        s+++k l++L+kag+v+ v G
  gi|488599632|ref|YP_007906103.1|  95 GSIVRKALQQLEKAGFVEKVDG 116
                                       6799**************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 963.34
//
Query:       gi|488599633|ref|YP_007906104.1|  [L=80]
Description: putative RNA-binding protein containing KH domain, possibly ribosomal protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-12   47.5   0.4    1.5e-12   47.5   0.4    1.0  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.4   8.3e-17   1.5e-12      18      81 ..      10      77 ..       1      80 [] 0.90

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 8.3e-17
                         CRS1_YhbY 18 pkvkiGkaGvtkevvdeiheklkteelvkvkc....egppalnmkrmaeiLeektgglviqrsgtsiv 81
                                      ++++iGk+G+t++v++ei+ +l+++ +vkvk+    ++ + +++k++a+++e++ +g +++ +g +++
  gi|488599633|ref|YP_007906104.1| 10 STINIGKNGLTENVIKEINFQLEKRGVVKVKLlrsfRESTGRDRKELAREVEKNINGRLVSLRGMVLT 77
                                      689*********************************6677888******************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 551.87
//
Query:       gi|488599634|ref|YP_007906105.1|  [L=504]
Description: hypothetical protein Asulf_00076 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-18   66.1  36.4    6.7e-18   64.7  28.2    1.8  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7  28.2   3.8e-22   6.7e-18      14     352 ..      26     361 ..      19     362 .. 0.83
   2 !   14.5   1.1   6.9e-07     0.012     105     186 ..     329     433 ..     328     474 .. 0.70

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 3.8e-22
                             MFS_1  14 ilgpalplalaedlg...ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll..fa... 82 
                                       + ++++p ++++ l    +sp  ig+++++ +l ++  ++p  +++++++r+++ l+  ll+ ++lll++  +a   
  gi|488599634|ref|YP_007906105.1|  26 FSLVTVP-IISSYLAlmkASPLLIGFVAGIPYLSQL-VQIPSVYIAEKYSRKKICLIYNLLSRISLLLIAiaLAidf 100
                                       3334444.66666555559*************9665.69**************888888887777455553444789 PP

                             MFS_1  83 .sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                        +s+ l+++l     ++  a+     ++++d+ p++ rg+ ++   a   + a+++ l  ++l  +lg +a  +++ 
  gi|488599634|ref|YP_007906105.1| 101 dNSVSLVVILFTAYTVFKEASSLPWSSWMRDLIPDNMRGKIYSKRIANGKFIALFAVLSFAVLFNYLGSPAFILLFM 177
                                       55555******************************************999999999888888888999877777777 PP

                             MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylq 235
                                        ++l ++v    l++ +  +   +++k +      ++l++++k +   +    l  +l l+ f+  + + ++ +y+ 
  gi|488599634|ref|YP_007906105.1| 178 TAFLAGAV---SLYFITGIDDVDVETKGK------RNLREPFKNINFVR----LTSSLSLWRFASGMSTPFFSVYII 241
                                       77777767...666666666666655444......55555566677666....8889999998889999999999** PP

                             MFS_1 236 evlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt....ssavllllvlv 308
                                       +vl+++ l+ + +l ++++l +  +  ++g+++d +g+++ ++l++++++laal++ ++ ++     ++++l+l+++
  gi|488599634|ref|YP_007906105.1| 242 SVLNYP-LWVVITLASVSQLSSTYFLRISGKMMDMFGNKPLTILSFSSFSLAALLFTFTTMPerhpLTPMILVLIYI 317
                                       ******.9*****************99***********************************888666666666777 PP

                             MFS_1 309 liGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                       + Gf + +  +++++++++ +p+ +++++++++n+a+sl galg
  gi|488599634|ref|YP_007906105.1| 318 IDGFYSNIPPIAVMNMIAKITPKGNSASYYAANNVASSLFGALG 361
                                       7777777779*******************************998 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.9e-07
                             MFS_1 105 agaaliadwfpkeergraigllsagfslGailgpllggllasslg..........................Wravfy 155
                                       a++ +ia+++pk + +++++  ++++sl  +lg l gg++as l                           +  +f+
  gi|488599634|ref|YP_007906105.1| 329 AVMNMIAKITPKGNSASYYAANNVASSLFGALGSLTGGIIASGLLylnfgikidiestigflqipaihlagYDFLFL 405
                                       6899********************88888888888888777433346666999999999998888888888888888 PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspke 186
                                       i a++s+l++    +l   e+++   ++ ++
  gi|488599634|ref|YP_007906105.1| 406 ISAFLSVLSVK---ILRKFEESNAVDEELVK 433
                                       88888888733...44444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3650.05
//
Query:       gi|488599635|ref|YP_007906106.1|  [L=765]
Description: Intein/homing endonuclease [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-22   78.1   0.4      2e-21   76.2   0.1    2.2  2  Rep_fac_C        Replication factor C C-terminal domain
    1.5e-18   67.0   0.0    3.5e-18   65.8   0.0    1.6  1  Intein_splicing  Intein splicing domain
    5.9e-14   52.6   0.2    3.1e-05   24.4   0.0    3.9  3  AAA              ATPase family associated with various cellul
    6.3e-14   52.1   0.1    2.5e-09   37.1   0.1    2.7  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
    3.7e-07   30.4   2.7      1e-05   25.7   0.0    3.0  2  LAGLIDADG_3      LAGLIDADG-like domain
    9.1e-07   29.4   0.2      0.011   16.1   0.0    3.3  3  AAA_16           AAA ATPase domain
    2.6e-06   27.3   0.1    2.6e-05   24.0   0.0    2.6  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.7e-05   24.6   0.3    6.9e-05   22.7   0.0    2.2  2  DNA_pol3_delta   DNA polymerase III, delta subunit
    6.8e-05   23.1   0.2    0.00027   21.2   0.0    2.3  1  AAA_assoc_2      AAA C-terminal domain
    0.00014   22.1   1.4        0.2   11.9   0.0    3.8  4  AAA_22           AAA domain
    0.00027   20.9   0.2     0.0011   18.9   0.0    2.1  2  Rad17            Rad17 P-loop domain
    0.00081   18.8   0.0      0.061   12.7   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.003   16.8   0.0     0.0084   15.3   0.0    1.7  2  TIP49            TIP49 P-loop domain
     0.0035   16.9   0.0     0.0083   15.7   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
     0.0051   16.8   0.0      0.048   13.7   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
      0.009   15.6   0.0       0.35   10.4   0.0    2.4  2  AAA_25           AAA domain
     0.0091   15.8   0.0      0.045   13.5   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.018   15.2   0.0       0.15   12.2   0.0    2.3  2  Hom_end          Homing endonuclease
      0.085   13.4   0.0       0.49   10.9   0.0    2.4  1  AAA_18           AAA domain
      0.086   12.8   0.1        1.8    8.6   0.0    2.8  3  AAA_5            AAA domain (dynein-related subfamily)
      0.087   12.5   0.0        5.5    6.7   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
       0.16   11.7   0.0       0.48   10.2   0.0    1.7  2  AAA_11           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 ?   -2.5   0.0       8.6     7e+03      14      36 ..     604     626 ..     596     631 .. 0.66
   2 !   76.2   0.1   2.5e-24     2e-21       2      87 ..     665     749 ..     664     749 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.6
                                       HHT-HHHHHHHHHHHHHHC---H CS
                         Rep_fac_C  14 lngdfeeaykklrellvekGysa 36 
                                       +++++ e+++k +++++e+G+ a
  gi|488599635|ref|YP_007906106.1| 604 MKKKLLEICEKENVEITEDGLQA 626
                                       35666666666667777777765 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 2.5e-24
                                       -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-H CS
                         Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGase 78 
                                       +p+e++++le +l+g+f ea++kl+ ll+e+G+s+ed+++ql++ ++++ +l+e++k+ ++++lgei++rl+eG++e
  gi|488599635|ref|YP_007906106.1| 665 RPEEVKDLLELALSGNFLEAREKLEHLLIEYGMSGEDVVNQLFKEIISS-SLDERLKVVLIDKLGEIDFRLTEGSNE 740
                                       79**********************************************5.7************************** PP

                                       HHHHHHHHH CS
                         Rep_fac_C  79 hlqlsalla 87 
                                       ++ql a la
  gi|488599635|ref|YP_007906106.1| 741 RIQLDAYLA 749
                                       *****9876 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   4.3e-21   3.5e-18      21     134 .]     120     514 ..      98     514 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 4.3e-21
                                       TEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCT.TEEEEEECCC--TT-EEEEE... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx... RF
                   Intein_splicing  21 eevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrd.egivEkradeLkegdliavp... 93 
                                        evl ++ e++++ +++v+k+i++k ++++++++e g  i +T++H ++ +++ + +v k+a+e+kegd+ +     
  gi|488599635|ref|YP_007906106.1| 120 LEVLTVD-EKYRVRWARVSKIIRHKARKILRVRVEGGGVIELTGNHAVMLLDKnGSLVAKKASEIKEGDFFISFvsk 195
                                       4566666.88999**************************************88899**************99779** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|488599635|ref|YP_007906106.1| 196 lggslnklsfsdylprsvtsrvrvidelevnelvswsfgayaaegavsirgdtsgqvvytfgsneleqigrikefse 272
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|488599635|ref|YP_007906106.1| 273 slglkiyetytssgfdrskysakqikvlstqlakfvrdnfydgygfkaknkripgfvyelpfeakmaflrgladgdg 349
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|488599635|ref|YP_007906106.1| 350 ygewanivrissaskdllidvawlsrmtgiessifdrevrliwkggmgyqksellpaeifvnfferisdkiegnwry 426
                                       ***************************************************************************** PP

                                       .............................................HSCEEEEEEEEEEEEECEEEEEEEEETTT-EE CS
                                       .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  94 .............................................dadvvwdkvksievedeeeyVYdltvednhNF 125
                                                                                    ++d+   +v++ie  d+++ VYd++v++n+ F
  gi|488599635|ref|YP_007906106.1| 427 emrhqlyenrktvskqtlkkildmvdvesltekekevlknlrnlvNSDLHVLRVREIEAVDYNDFVYDVSVPGNEMF 503
                                       ***************************************************************************** PP

                                       EE.CTTE.EE- CS
                                       xx.xxxx.xxx RF
                   Intein_splicing 126 va.ngii.vHN 134
                                       +a n  + +HN
  gi|488599635|ref|YP_007906106.1| 504 FAgNVPVlLHN 514
                                       *9865555999 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 !   19.5   0.0   1.2e-06     0.001       1      33 [.      41      78 ..      41     130 .. 0.86
   2 !   24.4   0.0   3.8e-08   3.1e-05      40     127 ..     521     594 ..     492     599 .. 0.83
   3 ?    3.8   0.1     0.088        72      37      94 ..     694     755 ..     670     762 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
                                      EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTT CS
                               AAA  1 vllyGppGtGKTllakavakel.....gvefleisgse 33
                                      +l+ GppGtGKT+ a a+ ++l       +f+e+++s 
  gi|488599635|ref|YP_007906106.1| 41 LLFAGPPGTGKTASAIALTRDLfgenwRDNFIEMNASV 78
                                      699******************86554458899999975 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 3.8e-08
                                       THHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGS CS
                               AAA  40 gesekkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkl 115
                                           +ki+e+ ++a    +p +i+f+DE+dal+ +            +++L + ++ ++k    + +i+ +n+++++
  gi|488599635|ref|YP_007906106.1| 521 DVVRHKIKEFARTAPIGDAPfKIIFLDEADALTADA-----------QAALRRTMEMYSK---ICRFILSCNYVSRI 583
                                       555666777776665555899***********9888...........*************...599*********** PP

                                       THHHHSTTSSEE CS
                               AAA 116 dpallrgRfdrk 127
                                        +++  +R+ + 
  gi|488599635|ref|YP_007906106.1| 584 IEPIQ-SRCAVF 594
                                       *****.9*9875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.088
                                       SSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHH CS
                               AAA  37 kyvgesekkirelfkeakeka...kpsilfiDEidalaksr.sgseseeeervvnqLlteld 94 
                                       +y   +e+ +++lfke+ +++   + ++++iD + ++  +  +gs+++ + ++  ++l+ + 
  gi|488599635|ref|YP_007906106.1| 694 EYGMSGEDVVNQLFKEIISSSldeRLKVVLIDKLGEIDFRLtEGSNERIQLDAYLAFLSTIA 755
                                       5777889999******8777789666******998884443444444455555555555555 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00018      0.14       1      50 [.      21      69 ..      21      82 .. 0.90
   2 !   37.1   0.1     3e-12   2.5e-09      81     162 ..     501     599 ..     431     600 .. 0.75
   3 ?   -2.5   0.0       4.7   3.8e+03      86     112 ..     701     727 ..     681     732 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                   DNA_pol3_delta2  1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallceekne 50
                                      gq+ +++ l++ +++ ++ h +Lf+G+ g+gk ++a +l + l+ e+ ++
  gi|488599635|ref|YP_007906106.1| 21 GQHAIVQRLKGYVEKRNIPH-LLFAGPPGTGKTASAIALTRDLFGENWRD 69
                                      689999*********99999.8**********************998765 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 3e-12
                   DNA_pol3_delta2  81 r...............sikldqirelieelsrkpre..skkkiiiiedaekmtksAaNalLktlEEPsenaifiLit 140
                                       +               +  +d +r+ i+e+ r++ +  +  kii +++a+ +t+ A+ al +t+E  s+   fiL  
  gi|488599635|ref|YP_007906106.1| 501 EmffagnvpvllhnsdERGIDVVRHKIKEFARTAPIgdAPFKIIFLDEADALTADAQAALRRTMEMYSKICRFILSC 577
                                       04555555555555556689****77777777766635778************************************ PP

                   DNA_pol3_delta2 141 sdtnklLktirSRcqelkfspl 162
                                       +  ++++++i+SRc ++kf+p+
  gi|488599635|ref|YP_007906106.1| 578 NYVSRIIEPIQSRCAVFKFRPI 599
                                       ********************97 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.7
                   DNA_pol3_delta2  86 dqirelieelsrkpreskkkiiiieda 112
                                       d +++l +e+  ++   + k+++i++ 
  gi|488599635|ref|YP_007906106.1| 701 DVVNQLFKEIISSSLDERLKVVLIDKL 727
                                       667899999999999999999999876 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2       0.1        83       9      50 ..     234     277 ..     232     309 .. 0.77
   2 !   25.7   0.0   1.3e-08     1e-05       2      62 ..     336     389 ..     335     417 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
                                       HHHHHCCECCECSTTTTS..EEEEES-HHHHHHHHHHHHHCT.H CS
                       LAGLIDADG_3   9 GlfdaDGsvskskkkgvs..isltssskelledvqrlLlrlGIe 50 
                                       G ++a+G vs +++++++   +++s+++e +  +++  + lG++
  gi|488599635|ref|YP_007906106.1| 234 GAYAAEGAVSIRGDTSGQvvYTFGSNELEQIGRIKEFSESLGLK 277
                                       6799*********9999977788888899899999988888875 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EEE-SC CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek.kkakgr 62 
                                        k afLrGl d+DG+ ++ +     ++++s+sk+ll dv+ l    GIes+i  +      r
  gi|488599635|ref|YP_007906106.1| 336 AKMAFLRGLADGDGYGEWANI----VRISSASKDLLIDVAWLSRMTGIESSIFDReV----R 389
                                       689*****************4....***************************99952....3 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-05     0.011       2      52 ..      19      66 ..      18     147 .. 0.79
   2 !    7.2   0.0    0.0075       6.1     116     160 ..     518     565 ..     411     573 .. 0.66
   3 ?    2.1   0.1      0.28   2.3e+02      75     149 ..     663     732 ..     628     757 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdg 52
                                      +vG  + +++L+ ++e+ +    + +l+ G++G+GK++ + +l r l +++
  gi|488599635|ref|YP_007906106.1| 19 VVGQHAIVQRLKGYVEKRNI---PHLLFAGPPGTGKTASAIALTRDLFGEN 66
                                      68899999999999995544...79**************988888887774 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0075
                            AAA_16 116 a..srllellkrllallsrderp.lvlvlDdlqwadeaslqllaaLlr 160
                                       +    +++++k++++ ++ ++ p  +++lD+++ + ++ +++l+ +++
  gi|488599635|ref|YP_007906106.1| 518 RgiDVVRHKIKEFARTAPIGDAPfKIIFLDEADALTADAQAALRRTME 565
                                       1446677888888888888888978***************99998775 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.28
                            AAA_16  75 alareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwade 149
                                       ++ r e +++ll+ a s ++ ++rekle  l    e   +++  +++l+k+++ + l   er  v+++D l  +d+
  gi|488599635|ref|YP_007906106.1| 663 TA-RPEEVKDLLELALSGNFLEAREKLEHLLI---EYGMSGEDVVNQLFKEIIsSSLD--ERLKVVLIDKLGEIDF 732
                                       33.44666777777777788888888887777...5555555999********44444..5546999998876665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.2e-08   2.6e-05       2      57 ..      12      62 ..      11      69 .. 0.89
   2 ?   -1.4   0.0       2.1   1.7e+03      86     111 ..     542     567 ..     539     570 .. 0.89
   3 ?   -2.0   0.0       3.3   2.7e+03     105     143 ..     629     667 ..     619     721 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.2e-08
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                                      rPk+l+e +gq+++ ++lk ++e     ++++ h+l++GpPG Gkt+ a  ++++l
  gi|488599635|ref|YP_007906106.1| 12 RPKTLDEVVGQHAIVQRLKGYVE-----KRNIPHLLFAGPPGTGKTASAIALTRDL 62
                                      9******************9997.....45689**************999888776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                            RuvB_N  86 dvlfideihrlsraveevlysamedf 111
                                       +++f+de   l+  ++  l  +me +
  gi|488599635|ref|YP_007906106.1| 542 KIIFLDEADALTADAQAALRRTMEMY 567
                                       699**************999999976 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.3
                            RuvB_N 105 ysamedfrldivigkGpsarsikldlpkftlvgattrag 143
                                       y +  dfr  i   +G+++   k+d +    ++at+r  
  gi|488599635|ref|YP_007906106.1| 629 YVSGGDFRKAINALQGAATFGEKIDAEVIFQITATARPE 667
                                       555556666666666666666666666666666665543 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 ?   -3.5   0.2       9.1   7.4e+03     112     130 ..     442     460 ..     432     476 .. 0.55
   2 !   22.7   0.0   8.5e-08   6.9e-05      59     170 ..     542     643 ..     522     644 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.1
                                       HHHTTTEEEEEE----TTT CS
                    DNA_pol3_delta 112 klLkkkatvveaktlkeee 130
                                       ++Lkk   +v+++ l+e+e
  gi|488599635|ref|YP_007906106.1| 442 QTLKKILDMVDVESLTEKE 460
                                       4455555555555554443 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 8.5e-08
                                       EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHH CS
                    DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwi 135
                                       +i++l+ +      + l+++ +++L ++++ +++ + +il ++       +++  ++++  v+++ + +ee +kk++
  gi|488599635|ref|YP_007906106.1| 542 KIIFLDEA------DALTADAQAALRRTMEMYSKICRFILSCN-YV---SRIIEPIQSRCAVFKFRPISEEAMKKKL 608
                                       66666666......67999************************.44...4799999********************* PP

                                       HHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 136 qkraqelglkiekealelLlelvennlsaikqele 170
                                        +++++++++i+++ l+ L++ ++++++ + ++l+
  gi|488599635|ref|YP_007906106.1| 609 LEICEKENVEITEDGLQALIYVSGGDFRKAINALQ 643
                                       ******************************99997 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 !   21.2   0.0   3.3e-07   0.00027       2      39 ..     614     651 ..     613     729 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.3e-07
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLElaaeaaea 39 
                                       ++++++++d l+al+ +++GD Rka+n+L+ aa+  e+
  gi|488599635|ref|YP_007906106.1| 614 KENVEITEDGLQALIYVSGGDFRKAINALQGAATFGEK 651
                                       6789**************************87776654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00025       0.2       7      66 ..      40      94 ..      35     157 .. 0.62
   2 ?    0.7   0.1      0.74     6e+02      87     120 ..     437     473 ..     405     485 .. 0.64
   3 ?    5.4   0.2     0.025        20      80     127 ..     525     575 ..     437     581 .. 0.71
   4 ?   -1.6   0.1       3.6     3e+03      54     100 ..     685     727 ..     650     758 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralgl 66
                                      +l+  G++GtGKT ++  l++ l    + e+ r+ ++++++++s+ ++ +   ++  a+++
  gi|488599635|ref|YP_007906106.1| 40 HLLFAGPPGTGKTASAIALTRDL----FGENWRDNFIEMNASVSKsTPVT--VRVNGAVER 94
                                      67889**************9998....44444666666666666633322..233333333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.74
                            AAA_22  87 rarav...ielliiDEaqhlr..seealeeLrsllnlsr 120
                                       ++ ++   +++l   +++ l+  ++e+l++Lr+l+n  +
  gi|488599635|ref|YP_007906106.1| 437 KTVSKqtlKKILDMVDVESLTekEKEVLKNLRNLVN--S 473
                                       444444333333333677786544999999999999..3 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.025
                            AAA_22  80 ealeqalrarav....ielliiDEaqhlrseealeeLrsllnlsrkgvqliL 127
                                       +++ + +r++       +++ +DEa+ l +++a   Lr+ ++  +k +++iL
  gi|488599635|ref|YP_007906106.1| 525 HKIKEFARTAPIgdapFKIIFLDEADAL-TADAQAALRRTMEMYSKICRFIL 575
                                       44444444444466677899********.88888888888776666666666 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.6
                            AAA_22  54 kdllrellralglelkaerlsseellealeqalraravielliiDEa 100
                                       ++ l++ll ++g ++++      +l++ +   + + +  ++++iD  
  gi|488599635|ref|YP_007906106.1| 685 REKLEHLLIEYGMSGED---VVNQLFKEIISSSLDERL-KVVLIDKL 727
                                       44445555555555555...777777777777777777.78888865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.4e-06    0.0011       6      77 ..       4      71 ..       2      89 .. 0.72
   2 ?   -3.0   0.3       7.4     6e+03      22      48 ..     438     464 ..     427     469 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-06
                             Rad17  6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel.giklrewl 77
                                       e W+eky+P++++e+      ++ +k ++     e+r+   LL +GP+G gk+     L++ l g + r++ 
  gi|488599635|ref|YP_007906106.1|  4 SEIWVEKYRPKTLDEVVGQHAIVQRLKGYV-----EKRNIPHLLFAGPPGTGKTASAIALTRDLfGENWRDNF 71
                                      799************976655555555544.....44445568***********9887777764255666654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.4
                             Rad17  22 avhkkkieevkewlkadvLesrkkriL 48 
                                        v k+ ++++ ++++ ++L +++k++L
  gi|488599635|ref|YP_007906106.1| 438 TVSKQTLKKILDMVDVESLTEKEKEVL 464
                                       577888999999999999988888776 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   7.5e-05     0.061      21      63 ..      37      80 ..      15      99 .. 0.71
   2 ?    3.3   0.0     0.057        46     109     137 ..     543     570 ..     531     590 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-05
                      Mg_chelatase 21 GgHnlllvGppGsGKtmlakrlp.sllpplseeealevakiasv 63
                                         +ll++GppG+GKt  a +l+  l+ +  +++ +e+++  s 
  gi|488599635|ref|YP_007906106.1| 37 NIPHLLFAGPPGTGKTASAIALTrDLFGENWRDNFIEMNASVSK 80
                                      4569**************99987257778888888888776654 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.057
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevti 137
                                       ++fLDE+  +++++  +LR+ +e  + +i
  gi|488599635|ref|YP_007906106.1| 543 IIFLDEADALTADAQAALRRTMEMYS-KI 570
                                       89********************9754.45 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05    0.0084      52      86 ..      40      77 ..      16      85 .. 0.77
   2 ?   -3.6   0.0       6.1     5e+03     281     304 ..     543     566 ..     542     578 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXX.XXX..XXXXXXXX CS
                             TIP49 52 avLlaGpsgtGktalaiaiskelg.edv..pfvalsgs 86
                                       +L+aGp+gtGkta aia++++l  e+    f+ +++s
  gi|488599635|ref|YP_007906106.1| 40 HLLFAGPPGTGKTASAIALTRDLFgENWrdNFIEMNAS 77
                                      68*******************99524432257777776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.1
                                       XXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 281 vlfiDevhmlDiecfsylnrales 304
                                       ++f+De+  l  ++ + l r++e 
  gi|488599635|ref|YP_007906106.1| 543 IIFLDEADALTADAQAALRRTMEM 566
                                       689*******99999999999994 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     1e-05    0.0083      35      75 ..      40      80 ..      26      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsa 75
                                      ++l+ Gp GtGKt+ +  l++ l  e++  ++i+++a+ s 
  gi|488599635|ref|YP_007906106.1| 40 HLLFAGPPGTGKTASAIALTRDLFGENWRDNFIEMNASVSK 80
                                      799*********************************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 !   13.7   0.0   5.9e-05     0.048       8      58 ..      22      72 ..      15      75 .. 0.85
   2 ?   -0.4   0.1       1.3     1e+03     127     160 ..     535     570 ..     427     578 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58
                                      Q  ++++l+  +++++  ++l++ + GtGKT  a++l++ l+ ++++++f+
  gi|488599635|ref|YP_007906106.1| 22 QHAIVQRLKGYVEKRNIPHLLFAGPPGTGKTASAIALTRDLFGENWRDNFI 72
                                      67777777777775556699************************9999986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                                       HHHTTT-SEEEEETGGGTTS...TTTHHHHHT---S CS
                            ResIII 127 ellrdrfdviiiDEaHrlgak..kswreilekfkea 160
                                         ++  f++i+ DEa  l+a+  ++ r+ +e++++ 
  gi|488599635|ref|YP_007906106.1| 535 PIGDAPFKIIFLDEADALTADaqAALRRTMEMYSKI 570
                                       333444558888888777776333555555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00043      0.35      37      65 ..      42      69 ..      28     129 .. 0.86
   2 ?    2.5   0.0      0.11        91     120     178 ..     697     757 ..     667     762 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                            AAA_25 37 llaGapgtGKttlaldlalavatGkpwlg 65
                                      l+aG+pgtGKt+ a+ l  ++  G++w +
  gi|488599635|ref|YP_007906106.1| 42 LFAGPPGTGKTASAIALTRDLF-GENWRD 69
                                      789***************9999.788877 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                            AAA_25 120 drggtlltadvdaleaaieevegvrlvviDplsralgg.densnsdv..galvealeriarr 178
                                       ++g+ ++++ +++++    + e++++v iD l ++     e sn+ +  +a ++ l  ia+r
  gi|488599635|ref|YP_007906106.1| 697 MSGEDVVNQLFKEIISSSLD-ERLKVVLIDKLGEIDFRlTEGSNERIqlDAYLAFLSTIAKR 757
                                       4677789999*****99999.99**********99988877777665557777777777766 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   5.5e-05     0.045      49      85 ..      40      76 ..      18      90 .. 0.83
   2 ?   -2.7   0.0         5   4.1e+03      72      93 ..     125     146 ..     120     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.5e-05
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrved 85
                                       +++ Gp+G+GK+  aial ++   ++++  f+ +++
  gi|488599635|ref|YP_007906106.1| 40 HLLFAGPPGTGKTASAIALTRDLFGENWRDNFIEMNA 76
                                      58899*******************9999999998875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5
                         IstB_IS21  72 vraglsvlfvrvedLveelkra 93 
                                       v + ++v++ rv++++++ +r+
  gi|488599635|ref|YP_007906106.1| 125 VDEKYRVRWARVSKIIRHKARK 146
                                       6788999999999998876555 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.5   1.2e+03      47      64 ..     265     282 ..     240     304 .. 0.79
   2 ?   12.2   0.0   0.00019      0.15       3      66 ..     326     387 ..     324     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                           Hom_end  47 egivklarsLGikasvkt 64 
                                        +i ++++sLG+k+  + 
  gi|488599635|ref|YP_007906106.1| 265 GRIKEFSESLGLKIYETY 282
                                       578999******996554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                           Hom_end   3 psflaseaievREaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktke 66 
                                       p f++   +e++ aFl GL d+dgy + +  + + +++ +k ++ ++  l+r  Gi+ s+ ++e
  gi|488599635|ref|YP_007906106.1| 326 PGFVYELPFEAKMAFLRGLADGDGYGEWA--NIVRISSASKDLLIDVAWLSRMTGIESSIFDRE 387
                                       55666666888999************999..79************************9987765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00061      0.49       3      44 ..      43      83 ..      41     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                       +G+pG+GKt  a +L + l fg+n rd++ e + + +   +
  gi|488599635|ref|YP_007906106.1| 43 FAGPPGTGKTASAIALTRDL-FGENWRDNFIEMNASVSKSTP 83
                                      79**************8887.899999999987766665555 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 ?    8.6   0.0    0.0022       1.8       1      36 [.      40      78 ..      40      92 .. 0.81
   2 ?   -1.8   0.1       3.5   2.8e+03      39      90 ..     418     472 ..     414     508 .. 0.61
   3 ?    0.3   0.0      0.79   6.4e+02      67      89 ..     542     564 ..     519     567 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0022
                                      EEEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT- CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal...nreveyvqltrdt 36
                                      ++l  GppGtgK+  a  l + l   n++ + + ++++ 
  gi|488599635|ref|YP_007906106.1| 40 HLLFAGPPGTGKTASAIALTRDLfgeNWRDNFIEMNASV 78
                                      68999*********9999988887777666666666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.5
                                       HHHH--B--.........--------G-SEEEE...ESGGG--HHHHHHHHHHHH CS
                             AAA_5  39 edlkgrreikngttslvdsplvraaregeilvl...DEveraesevlnsLlslle 90 
                                       +++ g ++++++++ +++ + v + + ++il +   + +++ e+evl+ L +l +
  gi|488599635|ref|YP_007906106.1| 418 DKIEGNWRYEMRHQLYENRKTVSKQTLKKILDMvdvESLTEKEKEVLKNLRNLVN 472
                                       5667777777777777777777666655554430003344445667777755554 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.79
                                       SEEEEESGGG--HHHHHHHHHHH CS
                             AAA_5  67 eilvlDEveraesevlnsLlsll 89 
                                       +i++lDE + +  +++++L + +
  gi|488599635|ref|YP_007906106.1| 542 KIIFLDEADALTADAQAALRRTM 564
                                       79*************99997665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0068       5.5      18      60 ..      32      78 ..      19      93 .. 0.75
   2 ?    3.1   0.0     0.085        69      96     118 ..     543     565 ..     532     572 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0068
                                      HCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETTT CS
                   Sigma54_activat 18 vaktd..lsvlitGesGtGKellaraihe..askrkekpfvavncaa 60
                                      +++++   ++l  G  GtGK+  a a+ +    ++ + +f+++n + 
  gi|488599635|ref|YP_007906106.1| 32 YVEKRniPHLLFAGPPGTGKTASAIALTRdlFGENWRDNFIEMNASV 78
                                      444443457899************99998666788889999999875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.085
                                       EEEEETGGGS-HHHHHHHHHHHH CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlq 118
                                       ++fLDe   l++++Q+ L r ++
  gi|488599635|ref|YP_007906106.1| 543 IIFLDEADALTADAQAALRRTME 565
                                       89****************99987 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   0.00058      0.48      19      42 ..      40      63 ..      23     110 .. 0.72
   2 ?   -2.7   0.0       4.8   3.9e+03     122     122 ..     425     425 ..     340     475 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                            AAA_11 19 itliqGPPGtgKTktivellsqll 42
                                        l+ GPPGtgKT   ++l + l 
  gi|488599635|ref|YP_007906106.1| 40 HLLFAGPPGTGKTASAIALTRDLF 63
                                      46899********99999988886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.8
                            AAA_11 122 k 122
                                       +
  gi|488599635|ref|YP_007906106.1| 425 R 425
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.49
# Mc/sec: 4667.15
//
Query:       gi|488599636|ref|YP_007906107.1|  [L=262]
Description: Enoyl-CoA hydratase/carnithine racemase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-50  170.1   0.0    6.2e-50  169.8   0.0    1.0  1  ECH_1          Enoyl-CoA hydratase/isomerase
    1.9e-33  116.3   0.0    1.1e-29  104.0   0.0    2.0  2  ECH_2          Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.059   13.1   0.0      0.097   12.4   0.0    1.3  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.8   0.0     1e-53   6.2e-50       4     248 ..      12     261 ..      10     262 .] 0.93

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 1e-53
                                       TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHH CS
                             ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlel 80 
                                       +gva i lnrP+++N ls ++ +El++al+ +e d  ++++++ G++  F+aG+++ke +e+   +q   ++++++l
  gi|488599636|ref|YP_007906107.1|  12 DGVARIILNRPKEHNPLSLKTAKELADALKLCERD-DIKVIIICGRGSSFCAGLNVKETLENL--EQIRDRKNFQDL 85 
                                       69*********************************.***********************9984..333444444443 PP

                                       ........HHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHH CS
                             ECH_1  81 ........wtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskA 149
                                                +k++++pkp+i   +G+ +g+Gl ++la+D++ia+++  f   +++lGl p+ g + +++r vG ++A
  gi|488599636|ref|YP_007906107.1|  86 gdvfnfgiIKKMRDLPKPIIVLTKGFTFGAGLSIVLAADYAIASEDTIFFSGFIRLGLSPDIGTSYFMPRHVGIKRA 162
                                       22222223789****************************************************************** PP

                                       HHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             ECH_1 150 eeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfes 226
                                        e++ lg+ +sa  a + G+v++vv  ++l++    +a+k ++++++a++ +k+ ln ++++ l+e l +e +  ++
  gi|488599636|ref|YP_007906107.1| 163 FELMCLGETFSARKAYECGIVNEVVKPDELESRGDVIAKKFLKAPKDAVARIKQLLNIAFDNPLEEHLRIEMEHTYQ 239
                                       ***************************************************************************** PP

                                       HCTSHHHHHHHHHHHTCSH--- CS
                             ECH_1 227 tfskddikeGlqaflEkrkpef 248
                                       t+ +dd++eGl a +E+r+p+f
  gi|488599636|ref|YP_007906107.1| 240 TMLSDDFEEGLRAVIERREPRF 261
                                       ********************99 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   1.9e-33   1.1e-29       2     187 ..      15     202 ..      14     222 .. 0.85
   2 !   11.7   0.0   2.2e-05      0.13     268     316 ..     214     260 ..     196     262 .] 0.78

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1.9e-33
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THH.....HHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkee.....eeff 73 
                                       ++i+Lnrpk+ N Lsl+ +++l++alk +e+dd +k++++ g g  +fCAG  v++  e+ ++ ++++      ++f
  gi|488599636|ref|YP_007906107.1|  15 ARIILNRPKEHNPLSLKTAKELADALKLCERDD-IKVIIICGRG-SSFCAGLNVKETLENLEQIRDRKnfqdlGDVF 89 
                                       689*************************98765.9*******88.9************9999976553221122233 PP

                                       HHHHHHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHH CS
                             ECH_2  74 reeYklnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGly 149
                                         ++ + + + ++pkp++ l  G++ G G+++ + + + +++e+t+f    +++Gl PD+G+syf++r  g + +  
  gi|488599636|ref|YP_007906107.1|  90 --NFGIIKKMRDLPKPIIVLTKGFTFGAGLSIVLAADYAIASEDTIFFSGFIRLGLSPDIGTSYFMPRHVGiKRAFE 164
                                       ..5889999***********************************************************977688888 PP

                                       HHHH---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT CS
                             ECH_2 150 lalTGarlkgadalaaglathyvpseklealeeaLael 187
                                       l   G++++++ a+++g+ + +v+ ++le+  + +a+ 
  gi|488599636|ref|YP_007906107.1| 165 LMCLGETFSARKAYECGIVNEVVKPDELESRGDVIAKK 202
                                       9999********************99998766655553 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------ CS
                             ECH_2 268 leqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPk 316
                                       ++ql + +  + l+e lr E++ + +++ ++Df eG ra++  +  +P+
  gi|488599636|ref|YP_007906107.1| 214 IKQLLNIAFDNPLEEHLRIEMEHTYQTMLSDDFEEGLRAVIERR--EPR 260
                                       5566666666679**************************97444..455 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.6e-05     0.097       8      41 ..      31      66 ..      28      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                                      SSHHHHHHHHHHHHHCTSCEE.EESSSTTEE.STTC CS
                     FAD_binding_4  8 eseeevaaalrlaneaglpvl.vrGgGssll.gqav 41
                                      ++++e+a+al+l+++ +++v+ + G Gss++ g +v
  gi|488599636|ref|YP_007906107.1| 31 KTAKELADALKLCERDDIKVIiICGRGSSFCaGLNV 66
                                      799****************66156889***988876 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:                      563  (0.0314016); 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 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1720.48
//
Query:       gi|488599637|ref|YP_007906108.1|  [L=468]
Description: Phytoene dehydrogenase-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-07   29.8   0.0    6.3e-07   29.0   0.0    1.4  1  Amino_oxidase  Flavin containing amine oxidoreductase
    1.4e-06   28.5   0.1    2.6e-06   27.5   0.1    1.5  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.6e-05   24.7   0.2    0.00011   21.9   0.2    2.2  1  DAO            FAD dependent oxidoreductase
     0.0044   16.3   0.2      0.018   14.3   0.2    1.9  2  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.064   12.5   0.1       0.77    9.0   0.0    2.6  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.083   12.0   0.3       0.13   11.3   0.3    1.3  1  FAD_binding_2  FAD binding domain
       0.14   11.3   0.1       0.25   10.6   0.1    1.3  1  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.4e-10   6.3e-07       1     450 [.      21     464 ..      21     466 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.4e-10
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCC.GCE CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellkelgledslslpdpg.apk 76 
                                       ++GLaa + L       +++E   r+GG  ++++++G  + +G+  f+     +  ll ++ + ++ + +++     
  gi|488599637|ref|YP_007906108.1|  21 ISGLAASSLLGKS----ILIEKLHRAGGTSYSFKREGCMFLTGPLGFSY-PELVRSLLSRFSVYTRFRRKSYRiK-- 90 
                                       6888888777777....99****************99999999999988.8888899999888888886666631.. PP

                                       EEEETTEECCTTEECHH.HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH..................HHHCCCCHH CS
                     Amino_oxidase  77 rvlskggrefpgdlspv.paewealleqgalsaellsleeklrlgleall..................qktldeldl 134
                                           +g+  f+ d  +v ++e+++l ++ ++     +  e +r+++ +l                    + l++l++
  gi|488599637|ref|YP_007906108.1|  91 ----AGEIDFRIDSLDVvERELKRLFPHQDVE----RAIEDIRRAIGLLSnrffwrgrffeidfdrigNGVLNSLRP 159
                                       ....2222224444444455555555544444....33333333333333444477777777777777777777777 PP

                                       HHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHH CS
                     Amino_oxidase 135 dskslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsq 211
                                       +++  + +   +++  +++ ++ + +++       +++s+l   + ++ s+ +   + +  +  ++++++p+ G++ 
  gi|488599637|ref|YP_007906108.1| 160 ANFEPDLEKTPSAKEFFSE-YIDNEILL-------NILSAL---G-PKDSEQSLASCILMWNIIDKGIWYPEIGFKG 224
                                       7777776666666666666.33333333.......344444...2.5555555555555556667899********* PP

                                       HHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSHHHHHHHHHS.EE CS
                     Amino_oxidase 212 lpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPplpdekaeairnl.gf 287
                                       +++ +a+  ++ +i  nt V++i+  gd+ +++++   v+ aD+ ++++++  l+      +  d ++++++ l + 
  gi|488599637|ref|YP_007906108.1| 225 IIDGMAA-DLKAKIVKNTAVRSIES-GDKFRIETS-RGVYFADKLISCMDPLKLS------EILDVRVKSLEDLkPG 292
                                       *******.****************7.888788764.4445***************......776788999999999* PP

                                       EEEEEEEEEESSGGSGCSTS.ECE.....CECCCEEETTTEEEEECC.ECCCSTTTEEEEEEEEECHHHHHHHTTS. CS
                     Amino_oxidase 288 gsvnkvilefdrkfwednal.gqg.....vlvseltttlgeafissd.fpsrappgkglvllvyvggdaanelesl. 356
                                       gs+  v+  +d k+  d++l +++      l ++   + + + +++   ++   pg+++ + + +  ++  ++es+ 
  gi|488599637|ref|YP_007906108.1| 293 GSTLTVYCLTDMKADSDHILyYPSldesnNLSENRFYDKEIEITFLHnLSDEFCPGSVM-IRAAMD-YDEFKFESKe 367
                                       **************444444524333465555555555555555544655555555655.555555.4455556665 PP

                                       -HHHHHHHHHHHHHHHHTGTSSTCSEEEEEECCTETTTSSSEEE.BTTH.HHHHHHHHHCH....HCSTTEEE.SGG CS
                     Amino_oxidase 357 sdeelvqavlrdLrklfgeevpepkatlvtrWhtdplargsysyvsvgp.ghedydplakp....egdprlffAGeh 428
                                          e +++v ++L +++++ + + ++++ +   + p+++ ++   + g+  ++d+ + +        +p+l++AG +
  gi|488599637|ref|YP_007906108.1| 368 EYNEFKKQVSEELVEVVKAVNIDKIKIVDS---STPITYEVWGGRYRGSvAGWDWSDAYPRclveTDIPGLYVAGLY 441
                                       88999*************555555554444...377777777777777753333333333355567**********9 PP

                                       GCT.TTTTSHHHHHHHHHHHHHH CS
                     Amino_oxidase 429 tsr.eypgtvegAilSGlraAar 450
                                         +  ++g+++  +lSG  aA+ 
  gi|488599637|ref|YP_007906108.1| 442 SFSiPLFGGFPTSLLSGFMAAEL 464
                                       87634678899999999999975 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1     1e-09   2.6e-06       1      54 [.      16      65 ..      16      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhg 54
                                      ++GaG+sGl+a +lL k      l+ek +r GG ++s++++g+ + +g+  f  
  gi|488599637|ref|YP_007906108.1| 16 VIGAGISGLAASSLLGKS----ILIEKLHRAGGTSYSFKREGCMFLTGPLGFSY 65
                                      8***************96....9*********************9999987755 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   4.4e-08   0.00011       1     213 [.      13     279 ..      13     442 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.4e-08
                                       EEEEECTSHHHHHHHHHHHHTT.EEEEESSSSTTSSGGGSSE....EEEESSS......STHHSTH..HHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg.VtllekgdiagsgaSgrns....gllhsgl......rylpeas..elarlslea 64 
                                       dv++iG+Gi Gl++   L   g  +l+ek ++ag g+S          +   l      +y++      l r+s ++
  gi|488599637|ref|YP_007906108.1|  13 DVAVIGAGISGLAASSLL---GkSILIEKLHRAG-GTSYSFKregcM-F---LtgplgfSYPEL-VrsLLSRFSVYT 80 
                                       8************99999...559******9999.888766533221.2...212235443333.133677999998 PP

                                       HHHHHHHHHHHSSTTSEEEEEEEEEESS................................................. CS
                               DAO  65 leelreleeelgididyrrtGllslaad................................................. 92 
                                       + +++ +  + g +id+r   l +++++                                                 
  gi|488599637|ref|YP_007906108.1|  81 RFRRKSYRIKAG-EIDFRIDSLDVVERElkrlfphqdveraiedirraigllsnrffwrgrffeidfdrigngvlns 156
                                       766666666645.6999988877777766667777677666666666666666666666666666666666666666 PP

                                       ..............HHHHHHHHHHHHHH......HHTTTTEEEEEHHHHHHHSTTST...........TTSEEEEET CS
                               DAO  93 ..............eeelealdkllall......leagldaelldaeevrelepalp...........gllgalfyp 138
                                                     +  +e + + +++       +++g++          +     +            + ++++yp
  gi|488599637|ref|YP_007906108.1| 157 lrpanfepdlektpS-AKEFFSEYIDNEillnilSALGPK----------DS----EqslascilmwnIIDKGIWYP 218
                                       666665544433321.122222333332222222222221..........11....122223222332455667777 PP

                                       TEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTT CS
                               DAO 139 dtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgllkel 213
                                       + g       + ++a   ++l ++i+++t v+++e   g+  ++  +t+ g  +a d+++ ++ +  +l+   ++l
  gi|488599637|ref|YP_007906108.1| 219 EIGF---KGIIDGMA---ADLKAKIVKNTAVRSIES--GDKFRI--ETSrGVYFA-DKLISCMDPL-KLS---EIL 279
                                       7444...55555555...555699**********65..446889..777798655.*******987.333...333 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   6.9e-06     0.018      11      55 ..       5      44 ..       2      56 .. 0.80
   2 ?   -1.5   0.0      0.46   1.2e+03     142     157 ..     260     275 ..     214     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.9e-06
                                      HHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 11 dllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                      +++ + e Dv+++GaG sGL+a+  l+k+     +++e+    GG
  gi|488599637|ref|YP_007906108.1|  5 MVMRMGEFDVAVIGAGISGLAASSLLGKS-----ILIEKLHRAGG 44
                                      66778899*******************99.....55665555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                                       HHTCTTTSS.-B-EEE CS
                              Thi4 142 velahdtqscvDPlvi 157
                                       v  a +  sc+DPl +
  gi|488599637|ref|YP_007906108.1| 260 VYFADKLISCMDPLKL 275
                                       4445556788888765 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 ?   -0.9   0.1      0.29   7.5e+02       2      18 ..      16      32 ..      15      58 .. 0.73
   2 ?    9.0   0.0    0.0003      0.77      90     129 ..     229     267 ..     226     271 .. 0.87
   3 ?   -1.3   0.0      0.41     1e+03     294     305 .]     428     439 ..     422     439 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.29
                       Pyr_redox_3  2 IiGaGPaGlaaaielkk 18
                                      +iGaG  Glaa   l k
  gi|488599637|ref|YP_007906108.1| 16 VIGAGISGLAASSLLGK 32
                                      8********99876655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0003
                       Pyr_redox_3  90 vaksfelpiklfeeVesvkkedegfevetsketyeAkkvi 129
                                       +a+  + +i +++ V+s+++  ++f++ets+++y A+k+i
  gi|488599637|ref|YP_007906108.1| 229 MAADLKAKIVKNTAVRSIESG-DKFRIETSRGVYFADKLI 267
                                       5667778999********986.68**************99 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.41
                       Pyr_redox_3 294 eetnvpglflaG 305
                                        et +pgl++aG
  gi|488599637|ref|YP_007906108.1| 428 VETDIPGLYVAG 439
                                       59*********9 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   5.2e-05      0.13       1      47 [.      13      57 ..      13      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.2e-05
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS..GGGG--S-EE- CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg..atawsqGgida 47
                                      Dv ViG+G++GLaA+  +   G+  +++ek ++ gg   ++  +G +++
  gi|488599637|ref|YP_007906108.1| 13 DVAVIGAGISGLAASSLL---GK-SILIEKLHRAGGtsYSFKREGCMFL 57
                                      9************99844...55.8899999999995555666777666 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   9.6e-05      0.25       2      34 ..      12      40 ..      11      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.6e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       dV+++GaG +Gl +++lL +     +l+ek  
  gi|488599637|ref|YP_007906108.1| 12 FDVAVIGAGISGLAASSLLGKS----ILIEKLH 40
                                      79*****************998....7777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3008.19
//
Query:       gi|488599638|ref|YP_007906109.1|  [L=928]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-40  136.7   0.0    1.1e-13   51.7   0.0    4.2  3  GAF_2     GAF domain
    4.1e-38  129.8   2.6    2.7e-17   62.9   0.0    4.1  3  PAS_9     PAS domain
    2.4e-36  124.1   0.3    1.1e-13   51.2   0.0    3.8  3  PAS       PAS fold
    1.7e-30  105.5   0.0      3e-11   43.6   0.0    3.8  3  PAS_4     PAS fold
    2.8e-22   79.8   0.0    5.8e-10   39.9   0.0    3.6  3  GAF       GAF domain
      1e-19   71.1   0.0    2.3e-08   34.4   0.0    3.8  3  GAF_3     GAF domain
    1.5e-19   69.6   0.0    4.2e-08   33.0   0.0    3.9  3  PAS_8     PAS domain
    7.4e-17   61.4   0.0    3.5e-05   24.0   0.0    4.6  4  PAS_3     PAS fold
    4.7e-08   33.2   0.0      0.012   15.8   0.0    4.0  3  PAS_7     PAS fold
     0.0002   21.9   0.4      0.048   14.3   0.0    4.0  4  PAS_10    PAS domain
    0.00031   20.8   0.0       0.98    9.6   0.0    3.5  3  PAS_11    PAS domain
     0.0014   18.8   0.0       0.14   12.3   0.0    2.4  2  MLTR_LBD  MmyB-like transcription regulator ligand binding do
     0.0076   16.3   3.4      0.018   15.1   0.0    3.4  4  HisKA     His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   1.2e-16   1.7e-13       3     138 .]     158     285 ..     156     285 .. 0.77
   2 !   51.7   0.0   7.8e-17   1.1e-13       3     137 ..     312     442 ..     310     443 .. 0.88
   3 !   28.8   0.0   9.3e-10   1.3e-06      67     138 .]     769     841 ..     713     841 .. 0.68

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.2e-16
                                       HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--......-TT.HHHHHHHHTS-EEE CS
                             GAF_2   3 dleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrpl......geg.lvgealrtgrpvil 71 
                                        ++ell+ +++ +v+  g ++++i++v +d+ ++ +a +++++     l+          eg     a++t++p++ 
  gi|488599638|ref|YP_007906109.1| 158 RENELLNKACQIIVDEgGYRFAWIGYVTPDD-IKPVAKAGEGDVELPDLSWNEdegqrdLEGtADSAAIKTKKPIL- 232
                                       579**********99846********99765.56555555555555555442222222234422237777777777. PP

                                       S-GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  72 ndleedpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                                     ++ +++s +++Pl+++++v+Gvln+ya +++ fde+++ lL+elae +a+ai+
  gi|488599638|ref|YP_007906109.1| 233 --------------RDTRYGSAVSLPLVYKDEVFGVLNIYAGEKDVFDEDEVNLLKELAENLAFAIA 285
                                       ..............8899***********889*********************************95 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 7.8e-17
                                       HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B..---TT.HHHHHHHHTS-EEES-GG CS
                             GAF_2   3 dleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldr..plgeg.lvgealrtgrpvilndle 75 
                                       d ++ll ++l+e+v+l ++ +g++++   ++++r ++w+++ +  + + +   ++++g l++ea+++g+ +i+n+  
  gi|488599638|ref|YP_007906109.1| 312 DTNTLLHEALNEVVKLtDSKYGFFGEFG-ADDFRALVWSRDVMAECRRNEIhfQVSKGsLWAEAIKEGKTLIINQ-- 385
                                       67899**********967******9944.5669999************9886566***99*************99.. PP

                                       G-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  76 edpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                             +lp gh+++++flavP++ ++ +  +++l ank ++++ +d el + +a  + +++
  gi|488599638|ref|YP_007906109.1| 386 ---GEFRLPKGHVPINNFLAVPVFKNN-TGFMIGL-ANKSSNYTKADAELTKFFAVNMQQIL 442
                                       ...77899***************9963.5558888.99*************99998777766 PP

  == domain 3  score: 28.8 bits;  conditional E-value: 9.3e-10
                                       S-EEES-GGG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  67 rpvilndleedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       +++ ++dl e    + l+  + +agl s l++Pl++++++vGvl+l+++++ af +e +e++  +++q+a+a++
  gi|488599638|ref|YP_007906109.1| 769 EKTRVDDLLELNEFSELEkqLLRAGLTSYLCMPLMAKDEPVGVLFLASKRRKAF-DEKMEFIVDISAQLAVALH 841
                                       45566674443333333335999*************889********9******.999**************95 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   1.9e-20   2.7e-17       3     104 .]      26     128 ..      24     128 .. 0.97
   2 !   19.3   0.0   7.5e-07     0.001       3     104 .]     461     559 ..     459     559 .. 0.77
   3 !   44.8   0.5   8.7e-15   1.2e-11       2     104 .]     583     684 ..     582     684 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.9e-20
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf....vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       +i++ + +g+i+++N++a++l+Gy +e+v+g++++ lf    v++ e +++l+ al++g    + +e v+ rk+g++
  gi|488599638|ref|YP_007906109.1|  26 AIFFLDANGKIISWNKSAEKLMGYRAEDVVGTHFSILFskedVESGEPDDELKIALREGM---YVKEGVMLRKDGSR 99 
                                       788888******************************************************...************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                       f++++  + ++d++g+l+g++ i+rDite
  gi|488599638|ref|YP_007906109.1| 100 FLAEIVTVSLRDSNGNLMGFAKIVRDITE 128
                                       ****9999********************8 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.5e-07
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfw 77 
                                       +++i+ +d +i yaN+ a++l+   +e +lgks+ ++ +++++++    + l++++    ++++ev li+ +g+  +
  gi|488599638|ref|YP_007906109.1| 461 AMIIVKEDTTISYANRIAEKLFALPKERLLGKSWIEFTAKEDREKILRYHKLRRIDPklAPKSYEVKLIDAKGRVKH 537
                                       68888899*999*********************9999933333333334444444448*9***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       vll +s +   + ++ +  + l+D+te
  gi|488599638|ref|YP_007906109.1| 538 VLLIISMM---NPNMSL--ISLIDMTE 559
                                       **999988...444444..56667665 PP

  == domain 3  score: 44.8 bits;  conditional E-value: 8.7e-15
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       dgi+i ++d ri+++Ne+al++l + +ee+ g+++t++   ++++   +++++++ ++ + +++    +r +ge  w
  gi|488599638|ref|YP_007906109.1| 583 DGIIIMDMDARIIDCNESALKILNTRREEITGRKFTEIGiIDEEDLPYFMERFYRGIS-EKKSEMELKVRVDGEIKW 658
                                       7999988*******************************9999****************.666777777999****** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                        ++ +  +  d g+  +i++i+rDite
  gi|488599638|ref|YP_007906109.1| 659 LEILLNLIEVD-GKPDMILSIIRDITE 684
                                       ********665.5666688*******8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   7.7e-17   1.1e-13       7     113 .]      19     126 ..      16     126 .. 0.93
   2 !   35.5   0.0   5.9e-12   8.1e-09       4      92 ..     452     541 ..     449     546 .. 0.92
   3 !   33.1   0.1   3.3e-11   4.6e-08       2     113 .]     573     682 ..     572     682 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 7.7e-17
                                       HHH.SSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS   7 les.lpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfkl 81 
                                       l++  + +if +D++g+i+ +N++ae+l G+++e+v+g ++++l++ ed +   ++  ++ ++   +   + + +++
  gi|488599638|ref|YP_007906109.1|  19 LDNlQDYAIFFLDANGKIISWNKSAEKLMGYRAEDVVGTHFSILFSKEDVEsGEPDDELKIALREGMYVKEGVMLRK 95 
                                       55535569****************************************988999999999999999999******** PP

                                       TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        dg+ + +e+ ++++rd  g++ gf  ++rdi
  gi|488599638|ref|YP_007906109.1|  96 -DGSRFLAEIVTVSLRDSNGNLMGFAKIVRDI 126
                                       .************************9999998 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 5.9e-12
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisf 79 
                                       r+i+es+ +++++v ed+ i+y+N+ ae+l+ l+ e +lgks +++   ed++ +l+ + ++++  +  ++++e+++
  gi|488599638|ref|YP_007906109.1| 452 RTIIESTGTAMIIVKEDTTISYANRIAEKLFALPKERLLGKSWIEFTAKEDREkILRYHKLRRIDPKLAPKSYEVKL 528
                                       78************************************************999989999999999999999999999 PP

                                       ECTTSSEEEEEEE CS
                               PAS  80 klrdgrpihlevr 92 
                                          +gr++h+++ 
  gi|488599638|ref|YP_007906109.1| 529 IDAKGRVKHVLLI 541
                                       9999999999876 PP

  == domain 3  score: 33.1 bits;  conditional E-value: 3.3e-11
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++ i+es+ d+i++ D d ri+ +N++a ++l+ +ree+ g+++  +i   d+++l+  +e+ ++  +e++++   
  gi|488599638|ref|YP_007906109.1| 573 RYKLIFESSMDGIIIMDMDARIIDCNESALKILNTRREEITGRKFT-EIGIIDEEDLPYFMERFYRGISEKKSEMEL 648
                                       6899*****************************************9.555566667999999988887777765554 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                         ++dg++++le+  + +   +g++ ++l ++rdi
  gi|488599638|ref|YP_007906109.1| 649 KVRVDGEIKWLEILLNLIE-VDGKPDMILSIIRDI 682
                                       4446*********999764.456677999999997 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.2e-14     3e-11       1     109 [.      19     130 ..      19     131 .. 0.84
   2 !   19.3   0.0   7.3e-07     0.001       3      54 ..     457     508 ..     455     520 .. 0.89
   3 !   38.2   0.0     1e-12   1.4e-09       1     109 [.     578     686 ..     578     687 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.2e-14
                             PAS_4   1 ldslpdalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.. 74 
                                       ld+l+d+ +++ d++g+++ +N++a++l+g+++e+++G ++  l+++ed +  e++++  ++ +e  +  e + l  
  gi|488599638|ref|YP_007906109.1|  19 LDNLQDYAIFFlDANGKIISWNKSAEKLMGYRAEDVVGTHFSILFSKEDVESGEPDDELKIALREGMYVKEGVMLrk 95 
                                       689999888888************************************66666666555555555555444444446 PP

                             PAS_4  75 pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +g++   e+  + lrd++G  +g+  i+rDiTerr
  gi|488599638|ref|YP_007906109.1|  96 DGSRFLAEIVTVSLRDSNGNLMGFAKIVRDITERR 130
                                       99999999**************************9 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.3e-07
                             PAS_4   3 slpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarler 54 
                                       s+  a +++ +d ++ yaN+ a++lf++p e+llGk++ e+  +ed++ + r
  gi|488599638|ref|YP_007906109.1| 457 STGTAMIIVKEDTTISYANRIAEKLFALPKERLLGKSWIEFTAKEDREKILR 508
                                       5666778899********************************9999988765 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 1e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlae..llpeedaarleralrrvlegeepiefleelllp 75 
                                       ++s+ d++++ d d r++++N++a +++  ++ee++G+++ e  +  eed + +++   r ++++++  +l ++++ 
  gi|488599638|ref|YP_007906109.1| 578 FESSMDGIIIMDMDARIIDCNESALKILNTRREEITGRKFTEigIIDEEDLPYFMERFYRGISEKKSEMELKVRVD- 653
                                       79***************************************88899999***************988888887777. PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ge +++e+ l+ + + +G+++ +l i+rDiTe +
  gi|488599638|ref|YP_007906109.1| 654 GEIKWLEILLNLI-EVDGKPDMILSIIRDITEKK 686
                                       *************.89****************76 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.5e-08   3.5e-05      79     133 .]     229     284 ..     200     284 .. 0.87
   2 !   11.3   0.0   0.00029      0.41       1     128 [.     312     437 ..     312     442 .. 0.65
   3 !   39.9   0.0   4.2e-13   5.8e-10       2     133 .]     715     840 ..     714     840 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.5e-08
                                       HHHHHHTTESEEEEEEEEETTEEEEEEEEEE.SSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  79 rdllenmgirsslvvPlvndgelwGllvlhn.psppftreelellqvladqvaval 133
                                       + +l+ + + s++++Plv ++e++G+l ++  +++ f+++e++ll++la+ +a a+
  gi|488599638|ref|YP_007906109.1| 229 KPILRDTRYGSAVSLPLVYKDEVFGVLNIYAgEKDVFDEDEVNLLKELAENLAFAI 284
                                       56788888999********************76669****************9987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00029
                                       SHHHHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC.............EEEETTSHHHH......HHHHH CS
                               GAF   1 dleelldtvveelrellgadrvalylpdydGlhydipqasrw.............lfmkngrgicg......qvlat 58 
                                       d  +ll+++++e+ +l++  ++ +    + G   d   a+ w              f++             +++++
  gi|488599638|ref|YP_007906109.1| 312 DTNTLLHEALNEVVKLTDSKYGFF---GEFGA--DDFRALVWsrdvmaecrrneiHFQV------SkgslwaEAIKE 377
                                       56799*************999999...34442..1223333322122211122323333......0334445***** PP

                                       SSSEEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEE..ETTEEEEEEEEEESSSCSHHHHHHHHHHHHHH CS
                               GAF  59 gqplvipdstpdprfaqynrrdllenmgirsslvvPlv..ndgelwGllvlhnpsppftreelellqvladq 128
                                       g++l+i+     + f         ++  i+++l+vP++  n+g ++Gl    +   ++t+++ el + +a  
  gi|488599638|ref|YP_007906109.1| 378 GKTLIIN----QGEFRL-----PKGHVPINNFLAVPVFknNTGFMIGLANKSS---NYTKADAELTKFFAVN 437
                                       *******....344444.....34678899********544888999877666...5899999998888865 PP

  == domain 3  score: 39.9 bits;  conditional E-value: 4.2e-13
                                       HHHHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC...EEEETTSHHHHHHHHHSSSEEESTGGTSTTHHT CS
                               GAF   2 leelldtvveelrellgadrvalylpdydGlhydipqasrw...lfmkngrgicgqvlatgqplvipdstpdprfaq 75 
                                       l e l+ vve++r+++ +d va++  ++dGl++ +  +s+      +k  ++         +  +++d+ + + f++
  gi|488599638|ref|YP_007906109.1| 715 LNESLKPVVESIRDFVRCDVVAILAYREDGLEA-VATSSNIksdEIDKILKM------VRIEKTRVDDLLELNEFSE 784
                                       678899*****************5445999655.444444432222222333......1234555556667777888 PP

                                       THHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  76 ynrrdllenmgirsslvvPlvndgelwGllvlhnpsppftreelellqvladqvaval 133
                                           ++l + g  s+l++Pl++++e +G+l l +++++  +e +e++  +++q+aval
  gi|488599638|ref|YP_007906109.1| 785 --LEKQLLRAGLTSYLCMPLMAKDEPVGVLFLASKRRKAFDEKMEFIVDISAQLAVAL 840
                                       ..889*****************************8886778889************97 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   6.3e-10   8.7e-07       4     128 ..     161     285 ..     159     286 .. 0.65
   2 ?    2.7   0.0      0.11   1.5e+02       5     120 ..     316     435 ..     312     438 .. 0.68
   3 !   34.4   0.0   1.7e-11   2.3e-08       5     127 ..     718     840 ..     715     842 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 6.3e-10
                             GAF_3   4 ellekllkllvkllgaevgalllldedgnklqvaagw..dgkpalse.....sldedsalarralssgevvsepsfa 73 
                                       ell+k+++ +v+  g  ++ ++ +++d  k ++ ag+   + p+ls+       d +  + ++a++++ ++      
  gi|488599638|ref|YP_007906109.1| 161 ELLNKACQIIVDEGGYRFAWIGYVTPDDIKPVAKAGEgdVELPDLSWnedegQRDLEGTADSAAIKTKKPI------ 231
                                       56777777777777777777777777733333333333223333344323222222233333444444444...... PP

                             GAF_3  74 eedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiataie 128
                                           ++ ++a+ +PLv +++v+Gvl ++  ++  fd++++ ll++lA  +a ai+
  gi|488599638|ref|YP_007906109.1| 232 -LRDTRYGSAVSLPLVYKDEVFGVLNIYAGEKDVFDEDEVNLLKELAENLAFAIA 285
                                       .333567999******************999888*******************96 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                             GAF_3   5 llekllkllvkllgaevgalllldedgnklqvaagw.dgkpalse.sld.edsalarralssgevvsepsfae...e 75 
                                       ll ++l ++vkl+++++g+++++ +d  ++ v +    ++ + +e ++   + +l+++a+++g  ++ ++++    +
  gi|488599638|ref|YP_007906109.1| 316 LLHEALNEVVKLTDSKYGFFGEFGADDFRALVWSRDvMAECRRNEiHFQvSKGSLWAEAIKEGKTLIINQGEFrlpK 392
                                       67788999999999999999999988444322222213333333366667889999999999999999887772222 PP

                             GAF_3  76 dglpdraalavPLvagrqviGvlalastkprafdaedlelleslA 120
                                          p ++ lavP+    +  G++    +k ++++ +d+el + +A
  gi|488599638|ref|YP_007906109.1| 393 GHVPINNFLAVPVFK--NNTGFMIGLANKSSNYTKADAELTKFFA 435
                                       335667779999998..6677777666666788888888876655 PP

  == domain 3  score: 34.4 bits;  conditional E-value: 1.7e-11
                             GAF_3   5 llekllkllvkllgaevgalllldedgnklqva.agw..dgkpalsesldedsalarralssgevvsepsfaeedgl 78 
                                        l  +++ + + ++++v+a+l ++edg +++++ +++  d+ +++ + ++++    + +l+  e+ se++  +  + 
  gi|488599638|ref|YP_007906109.1| 718 SLKPVVESIRDFVRCDVVAILAYREDGLEAVATsSNIksDEIDKILKMVRIEKTRVDDLLELNEF-SELE-KQLLRA 792
                                       566689999*****************999977734444444444444555555555566677775.5877.456778 PP

                             GAF_3  79 pdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                        ++++l++PL+a+++++Gvl+las++ +afd e +e++ ++++q+a a+
  gi|488599638|ref|YP_007906109.1| 793 GLTSYLCMPLMAKDEPVGVLFLASKRRKAFD-EKMEFIVDISAQLAVAL 840
                                       89**********************9988886.67999999999999887 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.7e-07   0.00038       5      42 ..      17      56 ..      14      81 .. 0.85
   2 !   11.2   0.0   0.00021      0.29       3      47 ..     451     492 ..     449     509 .. 0.79
   3 !   33.0   0.0   3.1e-11   4.2e-08       2      57 ..     573     633 ..     572     644 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.7e-07
                             PAS_8  5 alfesspd.giavvd.lgdrivdvNqaalellGys.adlkg 42
                                      +l+++++d +i+ +d +g+ i+ +N++a++l Gy+ +d+ g
  gi|488599638|ref|YP_007906109.1| 17 SLLDNLQDyAIFFLDaNGK-IISWNKSAEKLMGYRaEDVVG 56
                                      79*************6666.**************9777766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00021
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgq 47 
                                        r+++es   ++++v+++++i ++N+ a++l+ ++   k+ llg+
  gi|488599638|ref|YP_007906109.1| 451 QRTIIESTGTAMIIVKEDTTISYANRIAEKLFALP---KERLLGK 492
                                       599*************8888************988...4444443 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 3.1e-11
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg....qllpvlrplle 57 
                                       r++ +fess dgi++ d + ri+d+N++al++l  + +++ g ++     ++ ++l++ +e
  gi|488599638|ref|YP_007906109.1| 573 RYKLIFESSMDGIIIMDMDARIIDCNESALKILNTRrEEITGRKFTeigiIDEEDLPYFME 633
                                       9****************7778************9779999999994333444444444444 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.5e-08   3.5e-05       1      88 [.      36     122 ..      36     123 .. 0.87
   2 ?   -0.2   0.0      0.91   1.3e+03      25      41 ..     179     195 ..     174     197 .. 0.87
   3 !   10.8   0.0   0.00034      0.46       3      69 ..     473     539 ..     471     554 .. 0.82
   4 !   20.2   0.0     4e-07   0.00055       1      88 [.     594     678 ..     594     679 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-08
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervr..ealqealkkgepyegeyRirrkdGeyrwveararvi 75 
                                       ii+++++ e+++Gy++e++ g+  ++  l   eD e  +  ++l+ al++g  y  e  ++rkdG+ +  e  ++ +
  gi|488599638|ref|YP_007906109.1|  36 IISWNKSAEKLMGYRAEDVVGT--HFSILFSKEDVESGEpdDELKIALREGM-YVKEGVMLRKDGSRFLAEIVTVSL 109
                                       589*******************..99********666542278888888888.9************98888888888 PP

                             PAS_3  76 rdengkpvrvigv 88 
                                       rd+ng+   + ++
  gi|488599638|ref|YP_007906109.1| 110 RDSNGNLMGFAKI 122
                                       ******9998876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.91
                             PAS_3  25 swldlvhpeDrervrea 41 
                                        w+ +v p+D++ v +a
  gi|488599638|ref|YP_007906109.1| 179 AWIGYVTPDDIKPVAKA 195
                                       69********9999875 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00034
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealq.ealkkge.pyegeyRirrkdGeyrwve 69 
                                       y+++  e+++ + +e llgk  sw+++   eDre++ + ++ + ++ +  p + e++++ + G + +v 
  gi|488599638|ref|YP_007906109.1| 473 YANRIAEKLFALPKERLLGK--SWIEFTAKEDREKILRYHKlRRIDPKLaPKSYEVKLIDAKGRVKHVL 539
                                       788888999999********..*****************996555555557788888888888887775 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 4e-07
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvir 76 
                                       ii ++e+  +il  ++ee++g++ + + ++  eD+++++e + + +++++ ++e  +   r dGe+ w+e   + i 
  gi|488599638|ref|YP_007906109.1| 594 IIDCNESALKILNTRREEITGRKFTEIGIIDEEDLPYFMERFYRGISEKKsEMELKV---RVDGEIKWLEILLNLI- 666
                                       589*******************999999******************88884555555...45**************. PP

                             PAS_3  77 dengkpvrvigv 88 
                                         +gkp+ ++++
  gi|488599638|ref|YP_007906109.1| 667 EVDGKPDMILSI 678
                                       99***9987766 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.7e-06     0.012       7     113 ..      26     132 ..      19     134 .. 0.72
   2 ?    3.1   0.0     0.072        99       2      43 ..     456     496 ..     455     565 .. 0.73
   3 !    9.7   0.0   0.00064      0.88       4      44 ..     581     620 ..     578     690 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.7e-06
                             PAS_7   7 GisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererp 83 
                                       +i  +Da+++++ wN+   +l+++ +e v vg++++ l+       ++++g++++e++  l++    k+  + r+  
  gi|488599638|ref|YP_007906109.1|  26 AIFFLDANGKIISWNKSAEKLMGYRAEDV-VGTHFSILFSKE----DVESGEPDDELKIALREGMYVKEGVMLRKDG 97 
                                       7999*************************.*****9887654....4555555555555555555555666666655 PP

                             PAS_7  84 dgrvievrgnpl.....pdgGfVttytDiTerrra 113
                                       +    e+ +  l        Gf  +  DiTerr+ 
  gi|488599638|ref|YP_007906109.1|  98 SRFLAEIVTVSLrdsngNLMGFAKIVRDITERRKL 132
                                       55555555555532222668999999*****9986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.072
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvplee 43 
                                       e+   +++++ +d+ +   Nr   +l+ lp+e +  g++  e
  gi|488599638|ref|YP_007906109.1| 456 ESTGTAMIIVKEDTTISYANRIAEKLFALPKERL-LGKSWIE 496
                                       556677899999******************9988.6666544 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00064
                             PAS_7   4 msqGisvfDadlrLvawNrrylelldlpeelvqvgvpleel 44 
                                         +Gi+++D d r++ +N+  l++l+  +e + +g++++e+
  gi|488599638|ref|YP_007906109.1| 581 SMDGIIIMDMDARIIDCNESALKILNTRREEI-TGRKFTEI 620
                                       568************************99999.89988887 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.5e-05     0.048       9     106 .]      24     127 ..      16     127 .. 0.81
   2 ?   -0.7   0.0       1.6   2.2e+03       4      37 ..     454     487 ..     452     511 .. 0.86
   3 ?    1.7   0.0      0.28   3.8e+02       7      81 ..     580     657 ..     575     683 .. 0.70
   4 ?   -0.4   0.0       1.2   1.7e+03       2      32 ..     760     790 ..     759     792 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                            PAS_10   9 pieltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknv...eeviealrtgekdevevvvpkngkwv 81 
                                       + ++ flD n +i+ ++++a+kl+ ++++d vG + + + +k+ v++     e+  alr+g  +++ v+  k+g  +
  gi|488599638|ref|YP_007906109.1|  24 DYAIFFLDANGKIISWNKSAEKLMGYRAEDvVGTHFSILFSKEDVESGepdDELKIALREGMYVKEGVMLRKDGSRF 100
                                       57899****************99998877736999888888876666644456778999999999999999****** PP

                            PAS_10  82 lvrylpy..rdedgeiaGvvetfvDit 106
                                       l ++  +  rd +g+  G   ++ Dit
  gi|488599638|ref|YP_007906109.1| 101 LAEIVTVslRDSNGNLMGFAKIVRDIT 127
                                       9998754339***************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipa 37 
                                       +++st  +++ + ++  i + ++ a+klf l ++
  gi|488599638|ref|YP_007906109.1| 454 IIESTGTAMIIVKEDTTISYANRIAEKLFALPKE 487
                                       67899999***************99****99876 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.28
                            PAS_10   7 stpieltflDdnlqirrFtpaakklfk.lipadvGrpladi..hpkkavknveeviealrtgekdevevvvpkngkw 80 
                                       s   +++ +D + +i+  +++a k+++ ++++ +Gr+ ++i    ++ ++ + e + + ++++k e+e +v ++g++
  gi|488599638|ref|YP_007906109.1| 580 SSMDGIIIMDMDARIIDCNESALKILNtRREEITGRKFTEIgiIDEEDLPYFMERFYRGISEKKSEMELKVRVDGEI 656
                                       55557899999*********99777762666778*****99444667777777777777777778888888877776 PP

                            PAS_10  81 v 81 
                                        
  gi|488599638|ref|YP_007906109.1| 657 K 657
                                       4 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.2
                            PAS_10   2 nnlLnstpieltflDdnlqirrFtpaakklf 32 
                                       + +L+ + ie t +Dd l++  F++ +k+l+
  gi|488599638|ref|YP_007906109.1| 760 DKILKMVRIEKTRVDDLLELNEFSELEKQLL 790
                                       678999*****************99888875 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00071      0.98       7      50 ..      29      69 ..      24      85 .. 0.91
   2 ?    0.8   0.0      0.37   5.2e+02      30      56 ..     484     510 ..     468     516 .. 0.86
   3 ?    5.5   0.0     0.013        18       6      56 ..     586     635 ..     583     653 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00071
                            PAS_11  7 rldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdls 50
                                       ld +gkIis ++   +a+   g+  e++vg+ +  L++++d++
  gi|488599638|ref|YP_007906109.1| 29 FLDANGKIISWNK---SAEKLMGYRAEDVVGTHFSILFSKEDVE 69
                                      5899*********...*************************975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.37
                            PAS_11  30 lekeelvgrsiydLchpqdlstlkshl 56 
                                       l+ke l+g+s+ ++  ++d++++ + +
  gi|488599638|ref|YP_007906109.1| 484 LPKERLLGKSWIEFTAKEDREKILRYH 510
                                       68899**************88765554 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.013
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeelvgrsiydL..chpqdlstlkshl 56 
                                       ++ d+d +Ii++++saL     l+  +ee++gr + ++  + ++dl   ++ +
  gi|488599638|ref|YP_007906109.1| 586 IIMDMDARIIDCNESAL---KILNTRREEITGRKFTEIgiIDEEDLPYFMERF 635
                                       678***********665...456677777888777663225566666555555 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 !   12.3   0.0    0.0001      0.14       7      39 ..      17      49 ..      16      61 .. 0.90
   2 ?    3.8   0.0      0.04        55       5      42 ..     450     487 ..     447     499 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                          MLTR_LBD  7 rlLdalepvPAlVldrrwdvlaaNraaraLlgd 39
                                       lLd+l++++ + ld++  ++ +N+ a++L+g 
  gi|488599638|ref|YP_007906109.1| 17 SLLDNLQDYAIFFLDANGKIISWNKSAEKLMGY 49
                                      69*****************************98 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.04
                          MLTR_LBD   5 lrrlLdalepvPAlVldrrwdvlaaNraaraLlgdpaa 42 
                                       l+r +   + ++ +++  + ++  aNr+a++L++ p++
  gi|488599638|ref|YP_007906109.1| 450 LQRTIIESTGTAMIIVKEDTTISYANRIAEKLFALPKE 487
                                       6777777779999********************98655 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 ?   -2.9   0.1       5.4   7.5e+03      21      53 ..     117     144 ..     115     146 .. 0.68
   2 ?   -0.9   0.1       1.3   1.8e+03      43      65 ..     288     310 ..     269     311 .. 0.76
   3 ?   -3.3   0.0       7.2   9.9e+03      29      46 ..     712     728 ..     702     734 .. 0.74
   4 !   15.1   0.0   1.3e-05     0.018       7      66 ..     864     915 ..     859     916 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.4
                                       HHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHH CS
                             HisKA  21 lgnaeaLkregklteelkeyletiesearrldh 53 
                                       +g+a++ ++        ++ le++++  +r ++
  gi|488599638|ref|YP_007906109.1| 117 MGFAKIVRD-----ITERRKLEIAKRRMKRALR 144
                                       678888877.....5566667777777777665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA  43 tiesearrldhlvedlLdlsrie 65 
                                       +++++a+r+++  + lL ls++e
  gi|488599638|ref|YP_007906109.1| 288 RARENAERVNKAMQFLLKLSTME 310
                                       57788889999999999999987 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.2
                                       C..T-HSSCHHHHHHHHH CS
                             HisKA  29 regklteelkeyleties 46 
                                       r ++l+e+lk  +e+i++
  gi|488599638|ref|YP_007906109.1| 712 R-KPLNESLKPVVESIRD 728
                                       3.4788888888888765 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHHHHHHH.HC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   7 agvaHELrtPLsailgnaeaL.kregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       a +   +r+PL +i+g a+++ ++     e+ k   + i+++++r++++++ l d +++e+
  gi|488599638|ref|YP_007906109.1| 864 AILVDKIRNPLFGISGIADTMiSD-----ERAK---KLIKEQVDRILEIISAL-DEGWLES 915
                                       667788**************9344.....4444...69*************98.9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (928 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); 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:                        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 0.30s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 5813.11
//
Query:       gi|488599639|ref|YP_007906110.1|  [L=194]
Description: Kae1-associated kinase Bud32 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-11   41.9   0.0    1.3e-10   41.2   0.0    1.3  1  RIO1            RIO1 family
    1.2e-08   35.2   0.0    1.5e-07   31.6   0.0    2.0  2  APH             Phosphotransferase enzyme family
    6.2e-06   25.7   0.0    3.1e-05   23.4   0.0    2.1  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    1.3e-05   24.7   0.1      2e-05   24.1   0.1    1.4  1  Pkinase         Protein kinase domain
    0.00032   20.1   0.0    0.00047   19.6   0.0    1.2  1  Kinase-like     Kinase-like
     0.0032   17.1   0.1       0.15   11.7   0.1    2.1  2  Choline_kinase  Choline/ethanolamine kinase
     0.0055   16.3   0.1      0.009   15.6   0.1    1.3  1  WaaY            Lipopolysaccharide core biosynthesis protein 
  ------ inclusion threshold ------
      0.052   12.6   0.1      0.084   11.9   0.1    1.3  1  MCR_C           Methyl-coenzyme M reductase operon protein C
      0.092   12.0   0.0       0.14   11.4   0.0    1.3  1  Pkinase_Tyr     Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   6.7e-14   1.3e-10      24     150 ..      13     126 ..       8     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 6.7e-14
                                       SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHH CS
                              RIO1  24 eFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkd 100
                                        F+++ +++ + kr++ +k       l k  ++ E++++  +++ gvp P ++++    ++me i+  g++++++ +
  gi|488599639|ref|YP_007906110.1|  13 IFEDVVHKIRRRKRYRIEK---LDSILRKSRVKTEVNIIASARRCGVPTPIVLDVDGYTIIMERIK--GTPLKEIMN 84 
                                       5778888888888866552...334455667899********************************..999888877 PP

                                       CG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                              RIO1 101 veeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                        e       l +ev + + + +++ g++H+D+   N+++++++v++ID++
  gi|488599639|ref|YP_007906110.1|  85 EE-------LSREVGR-LTAKLHRKGIIHGDITPMNLIYKDGRVYFIDFG 126
                                       66.......4455555.5556779************************97 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0029       5.8      37     107 ..      41     100 ..      25     101 .. 0.77
   2 !   31.6   0.0   7.4e-11   1.5e-07     147     202 ..      86     134 ..      77     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHC CS
                               APH  37 irrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhq 107
                                       +  ev + +  ++ gvp+P vl+      + g+   ++e++ g++l +       +el +++g++ a+lh+
  gi|488599639|ref|YP_007906110.1|  41 VKTEVNIIASARRCGVPTPIVLD------VDGY-TIIMERIKGTPLKE----IMNEELSREVGRLTAKLHR 100
                                       56688888999999999999999......4553.67888888888888....2357788888888888886 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 7.4e-11
                                       HHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECC CS
                               APH 147 eleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgppl 202
                                       el +    +l a l+   +++++HgD+ p Nl+ +  dgrv ++iDf+++ + +++
  gi|488599639|ref|YP_007906110.1|  86 ELSR-EVGRLTAKLH---RKGIIHGDITPMNLIYK--DGRV-YFIDFGLSFYDDRI 134
                                       4555.5666777777...9****************..9**9.*********99875 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.6e-08   3.1e-05     115     166 ..      79     125 ..      14     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                               Kdo 115 laeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                       l+e ++++l ++vgrl aklhr g+ H+d+ + n+  + +     ++++iD+
  gi|488599639|ref|YP_007906110.1|  79 LKEIMNEELSREVGRLTAKLHRKGIIHGDITPMNLIYKDG-----RVYFIDF 125
                                       567788999*************************998887.....5999999 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1     1e-08     2e-05      72     145 ..      66     128 ..      15     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1e-08
                                       EEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTS CS
                           Pkinase  72 elylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGla 145
                                        +++++e ++g+ l++++           +++ +++ +  + lH+kgiiH D+ p N++++ +g +  +DFGl+
  gi|488599639|ref|YP_007906110.1|  66 GYTIIMERIKGTPLKEIM----------NEELSREVGRLTAKLHRKGIIHGDITPMNLIYK-DGRVYFIDFGLS 128
                                       445555555555555555..........45677788888889*****************99.**********98 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.4e-07   0.00047     140     189 ..      78     126 ..      67     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.4e-07
                       Kinase-like 140 kletiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggft 189
                                       +l++i    l  ++ rl a+L+ kg++hg++t+ nl+++ +g+++  +f+
  gi|488599639|ref|YP_007906110.1|  78 PLKEIMNEELSREVGRLTAKLHRKGIIHGDITPMNLIYK-DGRVYFIDFG 126
                                       566677777888899**********************96.7999998885 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.025        50      22      80 ..      43     100 ..      32     104 .. 0.69
   2 !   11.7   0.1   7.4e-05      0.15     149     179 ..     105     133 ..     102     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHTTS.SS-EEEEETTEEEEE--TCEE--TTGGGCHHHHHHHHHHHHHHTT CS
                    Choline_kinase  22 tElvvfallsergl.gpklygifenGrieefiesrtlstedlrepeiskkiAkklaelHs 80 
                                       tE++++a   + g+  p ++ ++    i e i++++l  +++ ++e+s+++++ +a+lH+
  gi|488599639|ref|YP_007906110.1|  43 TEVNIIASARRCGVpTPIVLDVDGYTIIMERIKGTPL--KEIMNEELSREVGRLTAKLHR 100
                                       5555555555555422344444445556677777776..5899****************7 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.4e-05
                                       -S--SGGGEEE.-CTTEEEE--GTT-EEEEH CS
                    Choline_kinase 149 HnDlqegNillnkeekklvlIDFEYagynyr 179
                                       H D+ + N+++  +++++++IDF  + y  r
  gi|488599639|ref|YP_007906110.1| 105 HGDITPMNLIY--KDGRVYFIDFGLSFYDDR 133
                                       99*********..**********99988765 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.5e-06     0.009     115     178 ..      64     125 ..      57     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.5e-06
                              WaaY 115 vkvyimiieyiegielvdmpeiddevkakikqsieklhqlgmvsgdphrgnfivkkdevriidl 178
                                       v+ y +i+e i+g  l ++  +++e+  ++ +   klh++g++ gd    n+i k++ v  id+
  gi|488599639|ref|YP_007906110.1|  64 VDGYTIIMERIKGTPLKEI--MNEELSREVGRLTAKLHRKGIIHGDITPMNLIYKDGRVYFIDF 125
                                       67899***********985..789**************************************96 PP

>> 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 ?   11.9   0.1   4.2e-05     0.084     201     258 ..      14      70 ..       7      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                             MCR_C 201 lveeveevldkkreelakDpllvsparvkkeieeqveeieevlsPapitlqldglrvk 258
                                         + v+++  +kr  ++k   ++  +rvk+e++  + + +++  P+pi+l++dg  + 
  gi|488599639|ref|YP_007906110.1|  14 FEDVVHKIRRRKRYRIEKLDSILRKSRVKTEVN-IIASARRCGVPTPIVLDVDGYTII 70 
                                       45678888889999******************9.899*****************8775 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.1e-05      0.14      99     150 ..      78     128 ..      26     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.1e-05
                                       TSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTH CS
                       Pkinase_Tyr  99 kltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLa 150
                                       +l+     +++ +v +  + L++k ++H d++  N + + +  v   DfGL+
  gi|488599639|ref|YP_007906110.1|  78 PLKEIMNEELSREVGRLTAKLHRKGIIHGDITPMNLIYK-DGRVYFIDFGLS 128
                                       55555555677888888889***************7666.7778888****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1172.63
//
Query:       gi|488599640|ref|YP_007906111.1|  [L=322]
Description: O-sialoglycoprotein endopeptidase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-87  292.8   0.0    3.6e-87  292.5   0.0    1.0  1  Peptidase_M22  Glycoprotease family
  ------ inclusion threshold ------
       0.12   12.1   0.0        5.7    6.7   0.0    2.2  2  Staygreen      Staygreen protein


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 !  292.5   0.0     4e-91   3.6e-87      10     270 ..      28     289 ..      23     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 292.5 bits;  conditional E-value: 4e-91
                                       EEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEE CS
                     Peptidase_M22  10 qkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvg 86 
                                       ++ +++k GG++P++a+ +Hse++  l+++++++  +++e++d+I +++gPG++++Lr+++++A+ lal l+kPlvg
  gi|488599640|ref|YP_007906111.1|  28 SDPYVPKEGGIHPREAALHHSEKIGNLLNRVFSK--INPEEIDVISFSQGPGMGPCLRIVATAARVLALRLKKPLVG 102
                                       45688999************************98..8899************************************* PP

                                       EEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHHC CS
                     Peptidase_M22  87 VnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkieklak 163
                                       Vnh+ ah++ +r +++ e+P++l+vsGg++q+++ ++ ry+++getld+ +g+aldk+ar++gl++pggpkie+la+
  gi|488599640|ref|YP_007906111.1| 103 VNHCLAHVEVGRWKTGAEDPIALYVSGGNSQIIAKRGSRYRVFGETLDIGLGNALDKLARYMGLKHPGGPKIEELAR 179
                                       ************999889*****************99**************************************** PP

                                       TC.S.......EETTEEE.CHHHHHHHHHHST.T.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXH CS
                     Peptidase_M22 164 eg.kkiefprplkgldfsfsGlktavlkelek.e.vedlaasfqeavvdhlvekteralklpkakelvilGGvaank 237
                                       +g +++e+p+++kg+dfsfsG+ t++ k++ + + +ed+a+sfqe+++++l+e++era+++ +++el+++GGv+an+
  gi|488599640|ref|YP_007906111.1| 180 KGkEYYELPYVVKGMDFSFSGMVTSAQKLFDTgRrMEDIAFSFQETAFAMLAEVSERAMAYLDKDELLLVGGVGANS 256
                                       **888*************************65536****************************************** PP

                                       HHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHH CS
                     Peptidase_M22 238 rLrealeeeaeelglkliiPplkyctdnaamia 270
                                       rL+e+l+ ++e++++++++Pp++++ dn+amia
  gi|488599640|ref|YP_007906111.1| 257 RLQEMLRVMCEDRNASFYAPPKHLMGDNGAMIA 289
                                       ********************************8 PP

>> Staygreen  Staygreen protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0    0.0089        79      17      51 ..      34      68 ..      22      74 .. 0.87
   2 ?    6.7   0.0   0.00064       5.7      73     103 ..     123     153 ..     107     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0089
                         Staygreen 17 ktepiipRrYtlthsDltaeLtLtigekfaldklq 51
                                      k+  i pR+  l hs++ ++L   + +k++ ++++
  gi|488599640|ref|YP_007906111.1| 34 KEGGIHPREAALHHSEKIGNLLNRVFSKINPEEID 68
                                      5667899********************99999886 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00064
                         Staygreen  73 vhvyvsggelllelaaelRyeiFrkeLplvL 103
                                       + +yvsgg+ ++  +   Ry++F + L++ L
  gi|488599640|ref|YP_007906111.1| 123 IALYVSGGNSQIIAKRGSRYRVFGETLDIGL 153
                                       679******99999************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2083.15
//
Query:       gi|488599641|ref|YP_007906112.1|  [L=49]
Description: SSU ribosomal protein S27AE [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   72.7   2.5    2.2e-20   72.6   2.5    1.0  1  Ribosomal_S27    Ribosomal protein S27a
    0.00013   21.8   4.0    0.00068   19.5   4.0    2.0  1  Nudix_N_2        Nudix N-terminal
    0.00026   20.6   2.9      0.011   15.4   0.2    2.3  2  zinc_ribbon_2    zinc-ribbon domain
    0.00082   19.5   1.8    0.00096   19.3   1.8    1.2  1  Ribosomal_L37e   Ribosomal protein L37e
     0.0015   18.8   0.3     0.0016   18.6   0.3    1.1  1  IBR              IBR domain, a half RING-finger domain
     0.0018   18.4   0.2     0.0018   18.3   0.2    1.2  1  MqsA_antitoxin   Antitoxin component of bacterial toxin-antit
     0.0045   17.0   1.1     0.0073   16.3   1.1    1.3  1  DZR              Double zinc ribbon
     0.0076   16.1   1.0     0.0081   16.0   1.0    1.1  1  C1_1             Phorbol esters/diacylglycerol binding domain
  ------ inclusion threshold ------
      0.011   15.5   3.3      0.029   14.3   3.3    1.6  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.021   14.5   7.1       0.11   12.2   7.1    1.9  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.021   15.2   1.2      0.075   13.4   0.0    1.9  2  GFA              Glutathione-dependent formaldehyde-activatin
      0.028   14.8   1.5      0.037   14.4   1.5    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.03   14.4   1.0      0.031   14.3   1.0    1.0  1  DUF1451          Zinc-ribbon containing domain
      0.042   13.8   3.3      0.088   12.8   3.0    1.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.06   13.4   0.3       0.06   13.4   0.3    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.066   12.9   1.7       0.58    9.9   1.7    2.1  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.073   13.0   1.0      0.083   12.8   1.0    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.11   12.7   6.0       0.18   12.0   0.7    2.1  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.14   11.7   1.9        6.9    6.3   0.1    2.1  2  zf_C2H2_10       C2H2 type zinc-finger
        0.2   11.1   6.5        2.6    7.6   6.5    2.1  1  zf-ribbon_3      zinc-ribbon domain
       0.23   11.6   4.5        0.3   11.3   0.5    2.3  3  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
        5.8    6.6   7.6        1.6    8.4   1.6    2.5  2  zf_UBZ           Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   2.5   2.6e-23   2.2e-20       1      45 []       3      45 ..       3      45 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 2.6e-23
                                      SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27  1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                      v k+Y++++ +k  r+rk Cpr CG+Gvf+AehkdR +CGkCg+T
  gi|488599641|ref|YP_007906112.1|  3 VSKFYEIKG-EKLIRKRKFCPR-CGEGVFLAEHKDRLSCGKCGYT 45
                                      68*******.9***********.*********************9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   4.0   8.4e-07   0.00068       1      32 [.      19      46 ..      19      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.4e-07
                                      -B-TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                         Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgtih 32
                                      kFC+ CG+ v l+    +++ Rl C +Cg++ 
  gi|488599641|ref|YP_007906112.1| 19 KFCPRCGEGVFLA----EHKDRLSCGKCGYTE 46
                                      9********8776....69**********975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.3e-05     0.011      12      22 ..      17      27 ..      11      28 .. 0.74
   2 ?    6.0   0.3     0.013        10      16      21 ..      39      44 ..      32      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                     zinc_ribbon_2 12 nakFCpyCGtp 22
                                      + kFCp+CG++
  gi|488599641|ref|YP_007906112.1| 17 KRKFCPRCGEG 27
                                      679******86 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|488599641|ref|YP_007906112.1| 39 CGKCGY 44
                                      888886 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.8   1.2e-06   0.00096      17      43 ..      19      48 ..       9      49 .] 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                    Ribosomal_L37e 17 ilCrrCgkrsy...hvqkktCascGypsak 43
                                       +C rCg+  +   h  + +C++cGy + k
  gi|488599641|ref|YP_007906112.1| 19 KFCPRCGEGVFlaeHKDRLSCGKCGYTEFK 48
                                      57*********655666669******7654 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   1.9e-06    0.0016       7      46 ..      10      44 ..       4      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                               IBR  7 klkkslesdpnlkwCprpdCeaiieksegcksvtCskCgf 46
                                      k +k +   +++k Cp   C+  +   e++++++C kCg+
  gi|488599641|ref|YP_007906112.1| 10 KGEKLI---RKRKFCP--RCGEGVFLAEHKDRLSCGKCGY 44
                                      444444...45899**..9**********999******97 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   2.3e-06    0.0018      23      57 ..      10      41 ..       2      49 .] 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.3e-06
                    MqsA_antitoxin 23 kgektvikavtgdfCarCGegvldeeeedrlseel 57
                                      kgek++    + +fC+rCGegv+ +e++drls   
  gi|488599641|ref|YP_007906112.1| 10 KGEKLIR---KRKFCPRCGEGVFLAEHKDRLSCGK 41
                                      5555543...358*****************98765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.1     9e-06    0.0073       8      36 ..      14      44 ..      11      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9e-06
                               DZR  8 lppdarfCseCgtklkavaa..edrCpsCge 36
                                      l  + +fC++Cg+ +  +++     C +Cg+
  gi|488599641|ref|YP_007906112.1| 14 LIRKRKFCPRCGEGVFLAEHkdRLSCGKCGY 44
                                      556789******9965444455999999997 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.0   9.9e-06    0.0081       9      37 ..      16      45 ..       9      49 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.9e-06
                                      SS--B-TTT-SB--S.SSS-EEEETTT--E CS
                              C1_1  9 kqptfCkhCgeflwg.kekqglkCswCkll 37
                                      ++ +fC  Cge ++  + k  l+C  C+++
  gi|488599641|ref|YP_007906112.1| 16 RKRKFCPRCGEGVFLaEHKDRLSCGKCGYT 45
                                      7899*********999***********986 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.3   3.5e-05     0.029       2      31 ..      19      46 ..      19      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                                      EBESTTTSBEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  2 kFCpkCgNlLlpkedkegknfeCrqCgYee 31
                                      kFCp Cg     +e k    + C +CgY e
  gi|488599641|ref|YP_007906112.1| 19 KFCPRCGEGVFLAEHKDR--LSCGKCGYTE 46
                                      7******97666666666..55******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 ?   12.2   7.1   0.00013      0.11       4      32 .]      19      47 ..      16      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                     zf-NADH-PPase  4 rFCgrCGaptepaeggwarvCpaCglehY 32
                                      +FC+rCG  + +ae+   + C  Cg+  +
  gi|488599641|ref|YP_007906112.1| 19 KFCPRCGEGVFLAEHKDRLSCGKCGYTEF 47
                                      7**************99999999998765 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.2e-05     0.075      47      64 ..      16      33 ..       2      38 .. 0.67
   2 ?    3.0   0.1      0.16   1.3e+02      46      59 ..      33      46 ..      30      49 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-05
                               GFA 47 vtrsfCpeCgsplysees 64
                                       +r+fCp+Cg  ++  e+
  gi|488599641|ref|YP_007906112.1| 16 RKRKFCPRCGEGVFLAEH 33
                                      3569*********98544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.16
                               GFA 46 kvtrsfCpeCgspl 59
                                      +++r  C +Cg + 
  gi|488599641|ref|YP_007906112.1| 33 HKDRLSCGKCGYTE 46
                                      678899****9765 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 ?   14.4   1.5   4.6e-05     0.037       4      36 ..      19      44 ..      16      49 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-05
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga 36
                                      k CP Cg+   l +++++        +C +Cg+
  gi|488599641|ref|YP_007906112.1| 19 KFCPRCGEGVFLAEHKDRL-------SCGKCGY 44
                                      66*************8876.......6****99 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.0   3.8e-05     0.031     107     144 ..      11      48 ..       4      49 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                           DUF1451 107 GevvglGtlvCekCgkelalkkteeippCpkCgateFr 144
                                       Ge     +  C +Cg+ + l + +    C kCg teF+
  gi|488599641|ref|YP_007906112.1|  11 GEKLIRKRKFCPRCGEGVFLAEHKDRLSCGKCGYTEFK 48 
                                       7777777889***************************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 ?   -0.4   0.0       1.4   1.1e+03      27      36 ..       4      13 ..       2      20 .. 0.67
   2 ?   12.8   3.0   0.00011     0.088      20      46 .]      20      45 ..      12      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                     Zn_Tnp_IS1595 27 rkayriktrg 36
                                      +k+y+ik+ +
  gi|488599641|ref|YP_007906112.1|  4 SKFYEIKGEK 13
                                      5889999943 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCrkq 46
                                       CP+Cg + ++  ++  ++ C +C+++
  gi|488599641|ref|YP_007906112.1| 20 FCPRCG-EGVFLAEHKDRLSCGKCGYT 45
                                      3*****.5555555589*******985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   7.3e-05      0.06      69      97 ..      17      47 ..       4      49 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                                      -EEEETTTS-EEECHH.H.HHS-TTTSSS-E CS
                              HypA 69 vkvrCreCgkefelee.k.alrCpkCgsadv 97
                                       +  C +Cg+ + l+e k +l+C+kCg +++
  gi|488599641|ref|YP_007906112.1| 17 KRKFCPRCGEGVFLAEhKdRLSCGKCGYTEF 47
                                      5668*****999977744699*****98765 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.065        53      23      28 ..      20      25 ..      10      26 .. 0.77
   2 ?    9.9   1.7   0.00071      0.58       6      31 ..      21      46 ..      17      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.065
                     A2L_zn_ribbon 23 vCieCg 28
                                      +C+ Cg
  gi|488599641|ref|YP_007906112.1| 20 FCPRCG 25
                                      9****8 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00071
                     A2L_zn_ribbon  6 CsvCggngilnseqgylvCieCgasf 31
                                      C  Cg  + l   ++ l+C +Cg+++
  gi|488599641|ref|YP_007906112.1| 21 CPRCGEGVFLAEHKDRLSCGKCGYTE 46
                                      6667655555578899********86 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 ?   12.8   1.0    0.0001     0.083      30      55 ..      20      45 ..       8      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                       C++Cg+ +  a +++++ C +Cg++
  gi|488599641|ref|YP_007906112.1| 20 FCPRCGEGVFLAEHKDRLSCGKCGYT 45
                                      5*******99999***********97 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7   0.00023      0.18      21      31 ..      16      26 ..       6      31 .. 0.85
   2 ?    4.6   0.4     0.045        36      19      36 ..      32      49 .]      27      49 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                      NOB1_Zn_bind 21 mtkkFCpkCGn 31
                                       ++kFCp+CG+
  gi|488599641|ref|YP_007906112.1| 16 RKRKFCPRCGE 26
                                      589*******7 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.045
                      NOB1_Zn_bind 19 kdmtkkFCpkCGnktLkr 36
                                      +++++  C kCG    k+
  gi|488599641|ref|YP_007906112.1| 32 EHKDRLSCGKCGYTEFKK 49
                                      5678899*****987765 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.019        16       5      10 ..      21      26 ..      19      28 .. 0.87
   2 ?    6.3   0.1    0.0085       6.9       4      10 ..      38      44 ..      36      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.019
                        zf_C2H2_10  5 CPKCqe 10
                                      CP+C+e
  gi|488599641|ref|YP_007906112.1| 21 CPRCGE 26
                                      ****98 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0085
                        zf_C2H2_10  4 sCPKCqe 10
                                      sC KC++
  gi|488599641|ref|YP_007906112.1| 38 SCGKCGY 44
                                      9*****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 ?    7.6   6.5    0.0032       2.6       3      24 ..      19      44 ..      17      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0032
                       zf-ribbon_3  3 vrCPnCGa.p.lss..ddnvCpyCGt 24
                                      ++CP+CG+ + l++  d   C +CG+
  gi|488599641|ref|YP_007906112.1| 19 KFCPRCGEgVfLAEhkDRLSCGKCGY 44
                                      68******998874337788999986 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.9   6.5e+03      23      29 ..       4      10 ..       2      16 .. 0.56
   2 ?    2.2   0.1      0.25   2.1e+02       2       8 ..      21      27 ..      20      35 .. 0.79
   3 ?   11.3   0.5   0.00037       0.3      36      46 ..      37      47 ..      31      49 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.9
                    zinc_ribbon_13 23 skifdvq 29
                                      sk++++ 
  gi|488599641|ref|YP_007906112.1|  4 SKFYEIK 10
                                      5555554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                    zinc_ribbon_13  2 CpKCgnt 8 
                                      Cp+Cg+ 
  gi|488599641|ref|YP_007906112.1| 21 CPRCGEG 27
                                      9999975 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00037
                    zinc_ribbon_13 36 vsCknCgYtel 46
                                       sC +CgYte+
  gi|488599641|ref|YP_007906112.1| 37 LSCGKCGYTEF 47
                                      59********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 ?    8.4   1.6     0.002       1.6       3      13 ..      19      29 ..      17      35 .. 0.71
   2 ?    1.0   1.0       0.4   3.2e+02       3       9 ..      37      43 ..      35      45 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                            zf_UBZ  3 ylCerCgkeip 13
                                       +C+rCg+ + 
  gi|488599641|ref|YP_007906112.1| 19 KFCPRCGEGVF 29
                                      69*****9876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.4
                            zf_UBZ  3 ylCerCg 9 
                                        C +Cg
  gi|488599641|ref|YP_007906112.1| 37 LSCGKCG 43
                                      67****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 331.76
//
Query:       gi|488599642|ref|YP_007906113.1|  [L=101]
Description: SSU ribosomal protein S24E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-26   90.1   0.1    7.7e-26   89.9   0.1    1.1  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.1   4.3e-30   7.7e-26       3      77 ..      22      96 ..      20      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 4.3e-30
                                      EEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS--- CS
                    Ribosomal_S24e  3 dvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekk 77
                                       v +++++tps++eirek+a +++++ + +vv  ++ +fG g++ +++kiY+s+e++kk+Epkh++aRn   e +
  gi|488599642|ref|YP_007906113.1| 22 RVKYQNSPTPSRNEIREKVAGLFNTELEKIVVSYIKPQFGHGEAICYVKIYNSVEDLKKTEPKHIIARNFESESE 96
                                      799******************************************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 783.11
//
Query:       gi|488599643|ref|YP_007906114.1|  [L=195]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-35  121.2   0.5    2.5e-35  120.9   0.5    1.1  1  DUF359           Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.049   13.7   0.1       0.15   12.2   0.1    1.8  1  Phage_head_chap  Head assembly gene product


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 !  120.9   0.5   2.8e-39   2.5e-35       1     126 []      51     177 ..      51     177 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 2.8e-39
                            DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikeal.eseekvlilVd 76 
                                       vt+++ kag++Pd++++D kt R+e++ee  + +++k++++ +++v Np+++it +l+e++ ea+    +kvli+V+
  gi|488599643|ref|YP_007906114.1|  51 VTYYIFKAGYNPDIVVIDFKTIRNEIDEEVISFIESKTEGYVRLDVVNPQAYITLDLVEKLIEAVsLLPKKVLIVVE 127
                                       8***********************9999655555789****************************8899******** PP

                            DUF359  77 GEEDLavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekfe 126
                                       GEEDLavlp+++++p +s+++YGqp+eG+v+v ++ee+k+ + ++l+++e
  gi|488599643|ref|YP_007906114.1| 128 GEEDLAVLPLVYMLPLNSLLLYGQPREGIVAVVISEEKKNIIPDILQRME 177
                                       ************************************************96 PP

>> Phage_head_chap  Head assembly gene product
   #    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      18      49 ..      54      85 ..      48      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                   Phage_head_chap 18 YiheleyddgklkvdfstpsedekdeLaphVe 49
                                      Yi+++ y+   +++df+t  ++  +e++  +e
  gi|488599643|ref|YP_007906114.1| 54 YIFKAGYNPDIVVIDFKTIRNEIDEEVISFIE 85
                                      9*******777**********99***999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1164.60
//
Query:       gi|488599644|ref|YP_007906115.1|  [L=62]
Description: DNA-directed RNA polymerase, subunit E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   57.2   0.7    1.5e-15   57.0   0.7    1.1  1  Spt4          Spt4/RpoE2 zinc finger
  ------ inclusion threshold ------
      0.053   13.5   0.5      0.062   13.3   0.5    1.2  1  HypA          Hydrogenase/urease nickel incorporation, metall
       0.14   10.9   1.2       0.15   10.8   1.2    1.0  1  NRDD          Anaerobic ribonucleoside-triphosphate reductase
       0.17   12.1   4.8       0.91    9.7   4.8    1.9  1  Zn-ribbon_8   Zinc ribbon domain
       0.21   11.1   0.4       0.21   11.1   0.4    2.4  2  TF_Zn_Ribbon  TFIIB zinc-binding
       0.22   11.0   5.6       0.46   10.0   5.7    1.5  1  zn-ribbon_14  Zinc-ribbon
       0.64    9.8   8.0        2.2    8.1   1.8    2.3  2  Rubredoxin_2  Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.7   5.8e-19   1.5e-15       3      77 .]       5      62 .]       3      62 .] 0.97

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 5.8e-19
                              Spt4  3 ACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      AC++Ck++ +e+      C+nC           +s+++++e+ G+v+i+dpekS++A++  l+ k+pg+YA+kv+
  gi|488599644|ref|YP_007906115.1|  5 ACKKCKYISHESV----VCKNC-----------GSSDLTKEWYGYVVIIDPEKSQIAEK--LGVKIPGKYAIKVD 62
                                      9*********999....*****...........**************************..************95 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   2.4e-05     0.062      70      98 ..       3      28 ..       1      37 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                      EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 70 kvrCreCgkefeleekalrCpkCgsadve 98
                                       + C++C++  +++   + C++Cgs+d++
  gi|488599644|ref|YP_007906115.1|  3 DYACKKCKYISHES---VVCKNCGSSDLT 28
                                      678*****777654...68******9876 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.2     6e-05      0.15     509     530 ..       5      27 ..       2      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6e-05
                                       EETT.--.EESSSB-TTT--BE. CS
                              NRDD 509 vCnecgy.kgeiekCpkCgseee 530
                                        C++c+y ++e   C +Cgs++ 
  gi|488599644|ref|YP_007906115.1|   5 ACKKCKYiSHESVVCKNCGSSDL 27 
                                       5*******999999*****7663 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.8   0.00036      0.91       5      38 ..       3      29 ..       3      31 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00036
                       Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                      +Y C++C+            + ++C++Cgs ++++
  gi|488599644|ref|YP_007906115.1|  3 DYACKKCKYISH--------ESVVCKNCGSsDLTK 29
                                      799****95544........2445******99987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   5.0      0.01        26      16      27 ..      13      24 ..       4      24 .. 0.63
   2 ?   11.1   0.4   8.4e-05      0.21       2      12 ..      18      28 ..      17      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.01
                                      STTCEEESSSSB CS
                      TF_Zn_Ribbon 16 ergelvCtdCGl 27
                                      ++  +vC++CG+
  gi|488599644|ref|YP_007906115.1| 13 SHESVVCKNCGS 24
                                      456789999985 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.4e-05
                                      EETTTTCEECH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                      +C+nCgs++l+
  gi|488599644|ref|YP_007906115.1| 18 VCKNCGSSDLT 28
                                      8******9964 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.7   0.00018      0.46       2      18 ..       5      22 ..       4      23 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                      zn-ribbon_14  2 kCerCGylSSqk.iCkAC 18
                                       C++C y+S  + +Ck C
  gi|488599644|ref|YP_007906115.1|  5 ACKKCKYISHESvVCKNC 22
                                      5********988469999 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.5    0.0062        16       1      11 [.       4      14 ..       4      16 .. 0.88
   2 ?    8.1   1.8   0.00087       2.2       2      15 ..      18      33 ..      18      34 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0062
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      Y C++C + s+
  gi|488599644|ref|YP_007906115.1|  4 YACKKCKYISH 14
                                      99****99887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00087
                      Rubredoxin_2  2 vCsqCGfe..sakwfG 15
                                      vC++CG++  +  w+G
  gi|488599644|ref|YP_007906115.1| 18 VCKNCGSSdlTKEWYG 33
                                      7*****9833455665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 411.45
//
Query:       gi|488599645|ref|YP_007906116.1|  [L=190]
Description: DNA-directed RNA polymerase, subunit E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-19   68.1   0.0    1.1e-18   67.4   0.0    1.4  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    2.1e-12   47.2   0.4    2.1e-12   47.2   0.4    1.8  2  S1             S1 RNA binding domain
  ------ inclusion threshold ------
      0.026   14.7   0.5       0.95    9.7   0.1    2.4  2  CSD2           Cold shock domain
       0.07   13.4   0.1        0.1   12.8   0.1    1.3  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   2.4e-22   1.1e-18       1      70 []       8      77 ..       8      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.4e-22
                                      EEEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  1 edtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      +dtvr++P  +++++e+ +++ l e++egk+++++G iv ++ i+e+++g++++g+G+vy++V+f+a+ F
  gi|488599645|ref|YP_007906116.1|  8 RDTVRVPPTRFEEDIEEVIEDLLWEQFEGKLDKEYGMIVGIESIEEIGDGRIIEGDGAVYFDVVFNAITF 77
                                      69******************************************************************98 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.3     1e+04      51      69 ..       6      24 ..       4      26 .. 0.65
   2 !   47.2   0.4   4.6e-16   2.1e-12       6      71 ..      83     147 ..      78     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.3
                                      ETTEEEEEEEEEEETTTTE CS
                                S1 51 kvGdevkvkvlkvdkdrrr 69
                                      k+ d+v+v  +++++d ++
  gi|488599645|ref|YP_007906116.1|  6 KIRDTVRVPPTRFEEDIEE 24
                                      6678888876666666655 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 4.6e-16
                                       CEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEE CS
                                S1   6 evveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrrii 71 
                                       ev+eGeV++++++GafV++g + +g+++ s++  d+ v+d + +  +G+e k+ +++ d  r+ri+
  gi|488599645|ref|YP_007906116.1|  83 EVIEGEVIEIVEFGAFVNIG-PLDGLIHMSQITEDYVVFDDKNKRLIGKETKKSLQEGDFVRARIV 147
                                       8*******************.***********************************9999998886 PP

>> CSD2  Cold shock domain
   #    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      22      50 ..      64      93 ..      54      95 .. 0.80
   2 ?    9.7   0.1   0.00021      0.95       1      38 [.     117     152 ..     117     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.026
                              CSD2 22 gakdGdkVvveiteypdkkn.peGevievL 50
                                      ga+  d+V   it  p  ++ +eGevie+ 
  gi|488599645|ref|YP_007906116.1| 64 GAVYFDVVFNAITFKPLMQEvIEGEVIEIV 93
                                      566668899999999954555*******85 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                              CSD2   1 FVvpddkrlkqdifipkeklkgakdGdkVvveiteyp.d 38 
                                       +Vv ddk+     +i ke +k +++Gd V ++i+    +
  gi|488599645|ref|YP_007906116.1| 117 YVVFDDKNKR---LIGKETKKSLQEGDFVRARIVALSlK 152
                                       7888888766...89*****************9986643 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 ?   12.8   0.1   2.3e-05       0.1       1      86 [.      79     161 ..      79     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE- CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifv 77 
                                       P+++ev++g + +  + g +v++g +d ++   +   ++  fd++++  +    +e++  l+ g+ +r r++  + +
  gi|488599645|ref|YP_007906116.1|  79 PLMQEVIEGEVIEIVEFGAFVNIGPLDGLIHMSQITEDYVVFDDKNKRLIG---KETKKSLQEGDFVRARIVALSLK 152
                                       899************************9887788888899******98775...5699999**************** PP

                                       ------HHH CS
                     RNA_pol_Rbc25  78 dvkpkspke 86 
                                       +++p+++k 
  gi|488599645|ref|YP_007906116.1| 153 EREPEKSKI 161
                                       ***998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1248.98
//
Query:       gi|488599646|ref|YP_007906117.1|  [L=844]
Description: hypothetical protein Asulf_00088 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.1e-35  121.6  31.3    3.1e-35  121.6  31.3    3.0  3  NosD        Periplasmic copper-binding protein (NosD)
    3.8e-19   68.3   1.3    1.9e-18   66.0   0.6    2.6  2  PKD         PKD domain
    1.7e-13   50.7  29.4    1.7e-13   50.7  29.4    3.2  4  Beta_helix  Right handed beta helix region
    8.4e-12   44.9   8.0     0.0011   18.9   0.0    5.1  5  Y_Y_Y       Y_Y_Y domain
  ------ inclusion threshold ------
       0.13   12.2   1.7       0.21   11.5   0.0    2.3  2  DUF2141     Uncharacterized protein conserved in bacteria (DU
       0.27   11.5   2.7         65    3.8   0.0    4.1  4  Big_3_2     Bacterial Ig-like domain
        1.3    9.3  10.3       0.55   10.5   3.3    3.4  3  Dockerin_1  Dockerin type I domain


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6  31.3   1.2e-38   3.1e-35      21     239 ..      38     268 ..      17     270 .. 0.83
   2 ?   -3.2   2.4       1.5     4e+03     130     206 ..     408     483 ..     308     484 .. 0.55
   3 ?   -0.6   1.0      0.26   6.6e+02     183     225 ..     733     802 ..     714     812 .. 0.68

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 1.2e-38
                              NosD  21 lensegseisnneisnsrdgilldnssnntitgn.tienlryGihlenses...ntiedntlssne.sGialmsssn 92 
                                        + + +s+ +    ++++d i   +  + +i g    +++ryGi + +s +   n+   n++  n+ +G++l++ s+
  gi|488599646|ref|YP_007906117.1|  38 ANDIVNSTATTCIWIKTSDVI--LDGRGYKIDGVsSSSSNRYGILVYKSGEsltNITLANITVTNWgMGVYLQNVSH 112
                                       333344444444444444544..88888899998455566*********999*98888888888888********** PP

                              NosD  93 ntlenNtisnnenyGillsdssnntisnNtisnnnkGiflens.ssntitgNriesnqkiGil...llsssegntiy 165
                                        tl n  +++n + Gi+l+ s+n ti+n  i +n+ Gi++     + t+ ++++ +n  iGi     ++++ +ntiy
  gi|488599646|ref|YP_007906117.1| 113 ITLINVHLIDNYGDGIILKSSNNITIKNCSIADNDVGITIGYYtRNLTLVDSEVVGN-YIGINyenTVEYYPNNTIY 188
                                       ****************************************8873555788*******.****95555666677**** PP

                              NosD 166 nNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydg.......eDadgDGigDtpYeindgviDyl 235
                                       nN+F nn++nv+ + +    Wnttk++gtniigg+ylgGN W +++         D dgDGi+DtpY+in+ ++Dyl
  gi|488599646|ref|YP_007906117.1| 189 NNIF-NNTKNVYSQVNFYSVWNTTKQAGTNIIGGSYLGGNAWFTPSRdgfsdtcIDDDGDGICDTPYNINAHSTDYL 264
                                       ****.********9977***************************99999**************************** PP

                              NosD 236 plvn 239
                                       pl++
  gi|488599646|ref|YP_007906117.1| 265 PLTY 268
                                       **97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                              NosD 130 iflensssntitgNriesnqkiGilllsssegntiynNy..Finnsenvkydgsn.nneWnttktsgtniiggpylg 203
                                       if++ +s++ +    +e n ++ i    ++ g + y N   + n   +++  g+    +Wn+t+  ++  i++p ++
  gi|488599646|ref|YP_007906117.1| 408 IFVNVTSNEPLATALLEWN-GVNIT--MNGRGTNWYLNMtgLSNGVYQFRVYGRDlAGNWNSTE-VRSVTISTPLVE 480
                                       4455555555555555555.33333..3333334444533356666666666666777777777.555555666666 PP

                              NosD 204 GNy 206
                                        Ny
  gi|488599646|ref|YP_007906117.1| 481 DNY 483
                                       665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.26
                              NosD 183 nneW.....nttktsgtniiggpylgGNyWsdydg......................eDadgDGigDtpY 225
                                       + +W     n t+t++  i+     +GNy  + +                       +D ++  igD++Y
  gi|488599646|ref|YP_007906117.1| 733 DYTWnfgdgNITTTNQPIITHVYSSSGNYTVTLTVidndgstnslskllvvavkgdfNDNNEVDIGDVSY 802
                                       5556555556666555555555556688887777777777777777777777777777888888888887 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.2   3.2e+03      49      67 ..     632     650 ..     618     652 .. 0.78
   2 !   66.0   0.6   7.6e-22   1.9e-18       5      70 ..     708     775 ..     702     776 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                                       EE-SSEEEEEEEEEE-SS- CS
                               PKD  49 tYlspGeYeVtvtasnavg 67 
                                       t+l +G Y +t+ +s +++
  gi|488599646|ref|YP_007906117.1| 632 TPLVEGGYILTLSLSSDFS 650
                                       67789*******9999877 PP

  == domain 2  score: 66.0 bits;  conditional E-value: 7.6e-22
                                       -S--BSSEEEEEEEES....-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                               PKD   5 ptvlvpgatvaftaav...pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                       p+++ ++++v+f+a++   pdg +v y+W+fgd ++ +++ +p +th+Y+s G+Y+Vt+t+ +++gs++
  gi|488599646|ref|YP_007906117.1| 708 PSPATINEEVEFNASLsydPDGFIVDYTWNFGD-GNITTTNQPIITHVYSSSGNYTVTLTVIDNDGSTN 775
                                       567889***************************.********************************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 !   50.7  29.4   6.5e-17   1.7e-13       5     143 ..      59     208 ..      48     227 .. 0.84
   2 ?   -2.7   0.9       1.8   4.7e+03      33      33 ..     384     384 ..     335     492 .. 0.62
   3 ?   -3.0   0.1       2.2   5.6e+03       7       7 ..     618     618 ..     555     646 .. 0.61
   4 ?   -1.4   1.0      0.74   1.9e+03      39      93 ..     717     773 ..     680     796 .. 0.65

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 6.5e-17
                                       E-SS-E.EEESEEEES-SS-SEEE-SSS-.....EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT-- CS
                        Beta_helix   5 ingssnvtiknntisnsggyGiylrgssn....vvienneiannsgsGiyilgssnntisnntisdnngggialfga 77 
                                       ++g +  +i+++  s+s++yGi ++ s+     +++ n +++n +g G+y++++s++t+ n +  dn+g+gi l+ +
  gi|488599646|ref|YP_007906117.1|  59 LDGRG-YKIDGVSSSSSNRYGILVYKSGEsltnITLANITVTN-WGMGVYLQNVSHITLINVHLIDNYGDGIILKSS 133
                                       33344.59999999***************77777777777777.********************************* PP

                                       S--EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT...---EEES-EEES-S.......SEEEE CS
                        Beta_helix  78 snnlienneitdnggsGiyln.yssnntienNiidnnagsGividdss...snvtvtnNtitnnk.......gaGia 143
                                       +n +i+n+ i dn+  Gi++  y+ n+t+ ++ + +n+  Gi ++++    +n+t+ nN+++n k        ++++
  gi|488599646|ref|YP_007906117.1| 134 NNITIKNCSIADNDV-GITIGyYTRNLTLVDSEVVGNY-IGINYENTVeyyPNNTIYNNIFNNTKnvysqvnFYSVW 208
                                       *************66.*****77***************.999999999***9**********998666666633333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.8
                                       - CS
                        Beta_helix  33 n 33 
                                       +
  gi|488599646|ref|YP_007906117.1| 384 D 384
                                       2 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.2
                                       S CS
                        Beta_helix   7 g 7  
                                       g
  gi|488599646|ref|YP_007906117.1| 618 G 618
                                       1 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.74
                                       -EEES...-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS- CS
                        Beta_helix  39 neian...nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggs 93 
                                        e++       +G+ + +++n+   n t ++      +++ +s+n     +++dn+gs
  gi|488599646|ref|YP_007906117.1| 717 VEFNAslsYDPDGFIVDYTWNFGDGNITTTNQP-IITHVYSSSGNYTVTLTVIDNDGS 773
                                       444444444667777777666655555555555.888888888888888888888765 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.5   6.3e+03       5      39 ..      72     104 ..      70     107 .. 0.70
   2 !   18.9   0.0   4.3e-07    0.0011      28      63 ..     434     474 ..     426     476 .. 0.84
   3 ?   -1.0   0.0      0.67   1.7e+03      40      65 ..     482     508 ..     476     508 .. 0.84
   4 !   17.7   0.0     1e-06    0.0026      28      63 ..     590     630 ..     582     656 .. 0.88
   5 !    8.9   0.2   0.00054       1.4      29      62 ..     748     782 ..     733     786 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.5
                                       CTTEEEEEEEETTESSEEEESSTS.EEEEES--SE CS
                             Y_Y_Y   5 perllYrYrlegidkeWveasdysqeasytnlppG 39 
                                       ++ ++Y   l+++++e  ++     +++ tn   G
  gi|488599646|ref|YP_007906117.1|  72 SSSNRYGI-LVYKSGESLTNITLA-NITVTNWGMG 104
                                       67788888.888888777777776.7888876655 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4.3e-07
                                       S.....EEEEES--SEEEEEEEEEEETTS-B-SS-.EEEEE CS
                             Y_Y_Y  28 sq....easytnlppGdYtlkVkakdndgqwnydi.tslsf 63 
                                       ++     +++t l+ G Y+++V+++d  g+wn+ + +s+++
  gi|488599646|ref|YP_007906117.1| 434 GRgtnwYLNMTGLSNGVYQFRVYGRDLAGNWNSTEvRSVTI 474
                                       4444667899************************9999987 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.67
                                       EEEEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y  40 dYtlkVkakdndgqwnydi.tslsfti 65 
                                       +Y+l++ ++ n ++ ++d    +++t+
  gi|488599646|ref|YP_007906117.1| 482 NYVLRILVTANPSDMEEDNgFVIDLTV 508
                                       8*************9999888888876 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 1e-06
                                       S.....EEEEES--SEEEEEEEEEEETTS-B-SS-.EEEEE CS
                             Y_Y_Y  28 sq....easytnlppGdYtlkVkakdndgqwnydi.tslsf 63 
                                       ++     +++t l+ G Y+++V+++d  g+wn+ + + +++
  gi|488599646|ref|YP_007906117.1| 590 GRgtnwYLNMTGLSNGVYQFRVYGRDLAGNWNSTEvRNVTI 630
                                       4444667899***********************98887776 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.00054
                                       ..EEEEES--SEEEEEEEEEEETTS-B-SS-EEEE CS
                             Y_Y_Y  29 q.easytnlppGdYtlkVkakdndgqwnyditsls 62 
                                       q  ++    ++G+Yt+++ ++dndg+ n+ ++ l 
  gi|488599646|ref|YP_007906117.1| 748 QpIITHVYSSSGNYTVTLTVIDNDGSTNSLSKLLV 782
                                       3478888889****************998765555 PP

>> DUF2141  Uncharacterized protein conserved in bacteria (DUF2141)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.2e-05      0.21      50      87 ..     324     355 ..     284     368 .. 0.74
   2 ?   -2.9   0.4       2.4   6.1e+03      58      70 ..     783     795 ..     727     801 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.2e-05
                           DUF2141  50 nlppGtYAvavfhDengngkldknllgiPkEgyGfSnn 87 
                                       n+ +G Y v++f D ngng+ d        E++G+  n
  gi|488599646|ref|YP_007906117.1| 324 NVTEGIYYVSAFMDVNGNGTYDEG------EPFGVAIN 355
                                       5789******************99......88888766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
                           DUF2141  58 vavfhDengngkl 70 
                                       vav  D n+n+++
  gi|488599646|ref|YP_007906117.1| 783 VAVKGDFNDNNEV 795
                                       4444555555555 PP

>> Big_3_2  Bacterial Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       4.9   1.2e+04      36      69 ..      64      95 ..      42     104 .. 0.63
   2 ?    3.8   0.0     0.026        65      95     121 ..     448     474 ..     443     476 .. 0.88
   3 ?    3.3   0.0     0.038        97      95     120 ..     604     629 ..     599     632 .. 0.87
   4 ?    1.4   0.1      0.14   3.7e+02      93     115 ..     757     778 ..     716     822 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.9
                           Big_3_2 36 lrlsGitddasGidsaklrvidsdgsvyssvnvs 69
                                       +++G+  ++s+ ++  + v++s+ s+ + + ++
  gi|488599646|ref|YP_007906117.1| 64 YKIDGV--SSSSSNRYGILVYKSGESLTNITLAN 95
                                      466777..44444556666666666666655555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.026
                           Big_3_2  95 deeytlefeiyDkAGNkteipsqkvvf 121
                                       ++ y+++++  D AGN ++++ ++v++
  gi|488599646|ref|YP_007906117.1| 448 NGVYQFRVYGRDLAGNWNSTEVRSVTI 474
                                       689**************9998888875 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.038
                           Big_3_2  95 deeytlefeiyDkAGNkteipsqkvv 120
                                       ++ y+++++  D AGN ++++ ++v+
  gi|488599646|ref|YP_007906117.1| 604 NGVYQFRVYGRDLAGNWNSTEVRNVT 629
                                       689*************9999888876 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.14
                           Big_3_2  93 sldeeytlefeiyDkAGNkteip 115
                                       s  ++yt+ ++++D+ G++++++
  gi|488599646|ref|YP_007906117.1| 757 S-SGNYTVTLTVIDNDGSTNSLS 778
                                       3.567777777777777777763 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.18   4.5e+02      35      45 ..     334     344 ..     325     346 .. 0.81
   2 ?   -2.8   0.1         3   7.6e+03      40      48 ..     769     777 ..     768     782 .. 0.70
   3 ?   10.5   3.3   0.00022      0.55       1      57 [.     786     837 ..     786     838 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.18
                                       GGGSTT-SSCE CS
                        Dockerin_1  35 kaaDvNgDGrv 45 
                                       ++ DvNg+G+ 
  gi|488599646|ref|YP_007906117.1| 334 AFMDVNGNGTY 344
                                       57899999975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3
                                       T-SSCESHH CS
                        Dockerin_1  40 NgDGrvnal 48 
                                       ++DG+ n+l
  gi|488599646|ref|YP_007906117.1| 769 DNDGSTNSL 777
                                       788888887 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00022
                                       TTETTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHHH CS
                        Dockerin_1   1 agDVNgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvinyL 57 
                                       +gD N++++V+  D+  +   ++     ++  +   aD Ng+ rv+  D++ +  yL
  gi|488599646|ref|YP_007906117.1| 786 KGDFNDNNEVDIGDVSYVAYIVL-----GKMPQDLRADFNGNRRVDIGDLAKIAYYL 837
                                       59****************99999.....666667789************99887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (844 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 5085.22
//
Query:       gi|488599647|ref|YP_007906118.1|  [L=118]
Description: hypothetical protein Asulf_00089 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.6   0.5     0.0033   16.4   0.5    1.0  1  Trep_dent_lipo   Treponema clustered lipoprotein (Trep_dent_l
  ------ inclusion threshold ------
      0.044   14.2   0.1       0.17   12.3   0.1    1.8  1  Cu_amine_oxidN3  Copper amine oxidase, N3 domain
      0.074   13.4   0.8       0.22   11.8   0.1    1.9  2  DUF5603          Domain of unknown function (DUF5603)


Domain annotation for each model (and alignments):
>> Trep_dent_lipo  Treponema clustered lipoprotein (Trep_dent_lipo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   5.5e-07    0.0033       6      92 ..       6     104 ..       2     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.5e-07
                    Trep_dent_lipo   6 ifiLiLavLLfsCskevkeqkeeetkvekeakiekksklieenei.lskeeededv.............ktPelike 68 
                                       +++L+La +L  Cs    e+k++e+k+e +++ ek  + ++e ei ++ + e+  v             k P    +
  gi|488599647|ref|YP_007906118.1|   6 VLLLFLAAFLPGCS--SVEHKATENKTEVSKVSEKVKQTVNETEIlKTAGVENASVtmltpqnltklakKYPAIYGN 80 
                                       57899********5..469999**********************965566677777665555555555555555555 PP

                    Trep_dent_lipo  69 leekkayeeslkklrleldkkdkv 92 
                                       l +k  y+ + ++l + +d  +k 
  gi|488599647|ref|YP_007906118.1|  81 LPNKTLYQIKTENLLIIVDAEEKK 104
                                       555577888888888888887765 PP

>> Cu_amine_oxidN3  Copper amine oxidase, N3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.9e-05      0.17       7      89 ..      31     106 ..      28     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHTGGGGHHHHHHHHTTT.T---EEEE--SS-SSST.T--EEEEEEEE--SSS-GCGSEEE.EEEEEE- CS
                   Cu_amine_oxidN3   7 elaeieevikelpqfkealkkrgienldkvvltpltvgyrgeksegkRllkalvyyrtesanlyahPiegLellvDl 83 
                                       e  +++e +k+  +  e lk+ g+en +  +ltp + +   +k        +++y +  ++ ly   +e+L ++vD 
  gi|488599647|ref|YP_007906118.1|  31 EVSKVSEKVKQTVNETEILKTAGVENASVTMLTPQNLTKLAKKY-------PAIYGNLPNKTLYQIKTENLLIIVDA 100
                                       66677777888888888888888888888888887777666666.......899*********************** PP

                                       -SSSGG CS
                   Cu_amine_oxidN3  84 eakkvi 89 
                                       e+kkv+
  gi|488599647|ref|YP_007906118.1| 101 EEKKVL 106
                                       ****97 PP

>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.18   1.1e+03      63      74 ..      29      40 ..      18      62 .. 0.61
   2 ?   11.8   0.1   3.7e-05      0.22       3      36 ..      74     108 ..      72     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.18
                                      HHHHHHHHHHHH CS
                           DUF5603 63 qkkvskvldkls 74
                                      +  vskv +k++
  gi|488599647|ref|YP_007906118.1| 29 KTEVSKVSEKVK 40
                                      344555555543 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.7e-05
                                       EEEEES-H.HHHHHHHHHTT---EE-TTHHHH... CS
                           DUF5603   3 ypaikgdl.nklleelkkeglrveedkekeeklkd 36 
                                       ypai g+l nk l ++k e l ++ d e++++l+ 
  gi|488599647|ref|YP_007906118.1|  74 YPAIYGNLpNKTLYQIKTENLLIIVDAEEKKVLRK 108
                                       9******989***************9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1392  (0.0776396); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 820.06
//
Query:       gi|488599648|ref|YP_007906119.1|  [L=476]
Description: hypothetical protein Asulf_00090 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-17   64.3  10.6      0.025   13.9   0.1    7.1  7  BNR_4            BNR repeat-containing family member
    1.8e-05   24.7  10.2         26    5.0   0.1    7.2  7  Phage_head_chap  Head assembly gene product
  ------ inclusion threshold ------
      0.055   13.5  21.4        9.1    6.4   0.9    7.9  7  SBBP             Beta-propeller repeat
       0.61   10.3   6.6       0.68   10.1   0.5    3.1  4  bMG6             Bacterial macroglobulin domain 6
       0.66    9.8   9.3         28    4.7   0.2    6.1  7  RCC1_2           Regulator of chromosome condensation (RCC1) 
        2.1    8.6   6.5         13    6.0   0.2    3.9  4  IBV_3B           IBV 3B protein


Domain annotation for each model (and alignments):
>> BNR_4  BNR repeat-containing family member
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1     1e-05     0.031     228     271 ..      35      81 ..      17      83 .. 0.82
   2 !    9.2   0.0   0.00024      0.71     229     259 ..      89     123 ..      83     140 .. 0.78
   3 !    8.5   0.0   0.00037       1.1     229     271 ..     151     190 ..     141     192 .. 0.86
   4 !    7.4   0.0   0.00083       2.5     229     258 ..     196     222 ..     195     235 .. 0.79
   5 !    7.5   0.0   0.00077       2.3     228     256 ..     244     273 ..     228     289 .. 0.74
   6 !   13.9   0.1   8.4e-06     0.025     228     270 ..     299     337 ..     278     340 .. 0.77
   7 !    5.1   0.0    0.0042        12     228     254 ..     346     370 ..     336     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                                       S-EEEE-TT--EEEEEEE--TT-....SS-EEEEEEE-SS-EEEEE-S CS
                             BNR_4 228 qesvavDkegnpvvlyskfddag....atqkyyyrkanggaWekrqva 271
                                        +s+a+D+++np+++y+++++      ++ ky ++  ++g+W+++ v 
  gi|488599648|ref|YP_007906119.1|  35 YTSIALDSNDNPHISYVYYPSVLnptnSELKYAWK-DSNGKWHIETVD 81 
                                       789****************9877787788999999.89999**98775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00024
                                       -EEEE-TT--EEEEEEE--TT-....SS-EEEEEE CS
                             BNR_4 229 esvavDkegnpvvlyskfddag....atqkyyyrk 259
                                       +s+a+D++gnp+++y++f+  +    ++ ky y +
  gi|488599648|ref|YP_007906119.1|  89 TSIALDSNGNPHISYHNFSWTFvgavGELKYTYPR 123
                                       799***************98888888777777764 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00037
                                       -EEEE-TT--EEEEEEE--TT-SS-EEEEEEE-SS-EEEEE-S CS
                             BNR_4 229 esvavDkegnpvvlyskfddagatqkyyyrkanggaWekrqva 271
                                       +sva+D+++np+++y +      +  y ++  ++g+W+++ v 
  gi|488599648|ref|YP_007906119.1| 151 TSVALDSNDNPHISYCNATF--LNLEYAWK-DSNGNWHTETVD 190
                                       799***********998855..5899****.89999**98876 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.00083
                                       -EEEE-TT--EEEEEEE--TT-SS-EEEEE CS
                             BNR_4 229 esvavDkegnpvvlyskfddagatqkyyyr 258
                                       +s+a+D++gnp+++ys+ ++   + ky y+
  gi|488599648|ref|YP_007906119.1| 196 TSIALDSNGNPHISYSYNNG---SIKYAYK 222
                                       689************99865...4777777 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.00077
                                       S-EEEE-TT--EEEEEEE--TT-.SS-EEE CS
                             BNR_4 228 qesvavDkegnpvvlyskfddag.atqkyy 256
                                        +s+a+D++gnp+++y ++ ++  ++ ky 
  gi|488599648|ref|YP_007906119.1| 244 YTSLALDSNGNPHISYCYYYNNTfGEIKYA 273
                                       5799***********987766554777765 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 8.4e-06
                                       S-EEEE-TT--EEEEEEE--TT-SS-EEEEEEE-SS-EEEEE- CS
                             BNR_4 228 qesvavDkegnpvvlyskfddagatqkyyyrkanggaWekrqv 270
                                         s+a+D++gnp+++y++  +     ky y+  +++ W+++ v
  gi|488599648|ref|YP_007906119.1| 299 HPSLALDSNGNPHISYYDATNG--DLKYAYK--DANGWHIETV 337
                                       56899***********999775..7899999..7778998776 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.0042
                                       S-EEEE-TT--EEEEEEE--TT-SS-E CS
                             BNR_4 228 qesvavDkegnpvvlyskfddagatqk 254
                                        +s+a+D++g p+++y++  + +   k
  gi|488599648|ref|YP_007906119.1| 346 YTSLALDSNGYPHISYYDATNGD--LK 370
                                       5799*************987753..34 PP

>> Phage_head_chap  Head assembly gene product
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0088        26       8      34 ..      40      69 ..      38      78 .. 0.78
   2 ?    3.0   0.0     0.038   1.1e+02       8      25 ..      93     109 ..      90     126 .. 0.73
   3 ?    0.9   0.0      0.16   4.9e+02       8      29 ..     155     184 ..     153     191 .. 0.60
   4 ?    4.3   0.0     0.015        45       8      33 ..     200     221 ..     197     224 .. 0.74
   5 ?    3.2   0.0     0.032        96       8      23 ..     249     264 ..     247     275 .. 0.76
   6 !    5.0   0.1    0.0087        26       8      34 ..     304     327 ..     302     333 .. 0.78
   7 ?    1.8   0.0     0.085   2.5e+02       8      20 ..     351     363 ..     349     375 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0088
                   Phage_head_chap  8 lledGekhlvYiheleyd...dgklkvdfs 34
                                      l+ ++++h++Y++  ++    +++lk++++
  gi|488599648|ref|YP_007906119.1| 40 LDSNDNPHISYVYYPSVLnptNSELKYAWK 69
                                      57899*******976654456888888887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.038
                   Phage_head_chap   8 lledGekhlvYiheleyd 25 
                                       l+ +G++h++Y h+ +++
  gi|488599648|ref|YP_007906119.1|  93 LDSNGNPHISY-HNFSWT 109
                                       6889******9.787776 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.16
                   Phage_head_chap   8 lledGekhlvYi....heleyd....dgkl 29 
                                       l+ ++++h++Y      +ley     +g++
  gi|488599648|ref|YP_007906119.1| 155 LDSNDNPHISYCnatfLNLEYAwkdsNGNW 184
                                       578999*****7222234444444445554 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.015
                   Phage_head_chap   8 lledGekhlvYiheleyddgklkvdf 33 
                                       l+ +G++h++Y     y++g +k+++
  gi|488599648|ref|YP_007906119.1| 200 LDSNGNPHISYS----YNNGSIKYAY 221
                                       6889*******5....5566666666 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.032
                   Phage_head_chap   8 lledGekhlvYihele 23 
                                       l+ +G++h++Y +  +
  gi|488599648|ref|YP_007906119.1| 249 LDSNGNPHISYCYYYN 264
                                       5889*******87554 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.0087
                   Phage_head_chap   8 lledGekhlvYiheleyddgklkvdfs 34 
                                       l+ +G++h++Y+   + ++g lk++++
  gi|488599648|ref|YP_007906119.1| 304 LDSNGNPHISYY---DATNGDLKYAYK 327
                                       5889*******8...456777777776 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.085
                   Phage_head_chap   8 lledGekhlvYih 20 
                                       l+ +G +h++Y+ 
  gi|488599648|ref|YP_007906119.1| 351 LDSNGYPHISYYD 363
                                       5889*******84 PP

>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.043   1.3e+02      14      25 ..      34      45 ..      25      45 .. 0.87
   2 ?    4.8   0.1    0.0092        28      16      25 ..      89      98 ..      81      98 .. 0.90
   3 ?    0.4   0.1      0.22   6.5e+02      15      25 ..     150     160 ..     142     160 .. 0.89
   4 ?    6.4   0.9     0.003       9.1      14      25 ..     194     205 ..     179     205 .. 0.86
   5 ?    3.1   0.0     0.032        96      15      25 ..     244     254 ..     242     254 .. 0.92
   6 ?    1.1   0.0      0.14   4.1e+02      17      25 ..     301     309 ..     300     309 .. 0.91
   7 ?    1.6   0.1     0.095   2.8e+02      14      25 ..     345     356 ..     338     356 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.043
                              SBBP 14 ygngIavDsnGN 25
                                      ++++Ia Dsn N
  gi|488599648|ref|YP_007906119.1| 34 KYTSIALDSNDN 45
                                      589*******98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0092
                              SBBP 16 ngIavDsnGN 25
                                      ++Ia DsnGN
  gi|488599648|ref|YP_007906119.1| 89 TSIALDSNGN 98
                                      89*******9 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.22
                              SBBP  15 gngIavDsnGN 25 
                                       ++++a Dsn N
  gi|488599648|ref|YP_007906119.1| 150 YTSVALDSNDN 160
                                       79*******98 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.003
                              SBBP  14 ygngIavDsnGN 25 
                                       +g++Ia DsnGN
  gi|488599648|ref|YP_007906119.1| 194 IGTSIALDSNGN 205
                                       499********9 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.032
                              SBBP  15 gngIavDsnGN 25 
                                       ++++a DsnGN
  gi|488599648|ref|YP_007906119.1| 244 YTSLALDSNGN 254
                                       689*******9 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.14
                              SBBP  17 gIavDsnGN 25 
                                       ++a DsnGN
  gi|488599648|ref|YP_007906119.1| 301 SLALDSNGN 309
                                       799*****9 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.095
                              SBBP  14 ygngIavDsnGN 25 
                                       +++++a DsnG+
  gi|488599648|ref|YP_007906119.1| 345 KYTSLALDSNGY 356
                                       589********6 PP

>> bMG6  Bacterial macroglobulin domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00023      0.68      44      85 ..      63     103 ..      60     109 .. 0.88
   2 ?    2.1   0.1      0.07   2.1e+02      45      63 ..     173     190 ..     167     216 .. 0.83
   3 ?   -2.4   0.0       1.7   5.1e+03      49      67 ..     324     342 ..     318     355 .. 0.73
   4 ?   -3.6   0.0         4   1.2e+04      27      44 ..     389     406 ..     386     412 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                              bMG6  44 erdyqWeyssdggwryestekdkpvasgtvdlsaegkaklsl 85 
                                       e +y W ++s+g+w+ e++++ k  ++ ++ l+++g+ ++s+
  gi|488599648|ref|YP_007906119.1|  63 ELKYAW-KDSNGKWHIETVDRAKDFRDTSIALDSNGNPHISY 103
                                       568***.99*************************99988887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.07
                              bMG6  45 rdyqWeyssdggwryeste 63 
                                        +y W ++s+g+w+ e+++
  gi|488599648|ref|YP_007906119.1| 173 LEYAW-KDSNGNWHTETVD 190
                                       58***.99*****999875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.7
                              bMG6  49 Weyssdggwryestekdkp 67 
                                       + y++ +gw+ e+++++  
  gi|488599648|ref|YP_007906119.1| 324 YAYKDANGWHIETVDSEGD 342
                                       4568888888888877655 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 4
                              bMG6  27 dgkkvatkelkvklyree 44 
                                       +g++v+t +++v++  ++
  gi|488599648|ref|YP_007906119.1| 389 NGNPVSTASMRVTVKNVD 406
                                       677777777777776654 PP

>> RCC1_2  Regulator of chromosome condensation (RCC1) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.56   1.7e+03       7      18 ..      33      44 ..      31      52 .. 0.83
   2 ?   -0.9   0.0      0.52   1.6e+03       9      18 ..      88      97 ..      87      98 .. 0.83
   3 ?    1.4   0.0     0.096   2.9e+02       4      18 ..     145     159 ..     137     166 .. 0.87
   4 ?   -1.0   0.1      0.55   1.6e+03      11      18 ..     197     204 ..     182     205 .. 0.75
   5 ?    0.5   0.0      0.18   5.5e+02       9      19 ..     244     254 ..     243     261 .. 0.82
   6 ?    4.7   0.2    0.0092        28       5      18 ..     294     308 ..     291     309 .. 0.88
   7 ?    1.3   0.0       0.1   3.1e+02       7      18 ..     344     355 ..     342     356 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.56
                            RCC1_2  7 GdyHscaLtedG 18
                                      G y s+aL++++
  gi|488599648|ref|YP_007906119.1| 33 GKYTSIALDSND 44
                                      77999****997 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.52
                            RCC1_2  9 yHscaLtedG 18
                                      + s+aL+++G
  gi|488599648|ref|YP_007906119.1| 88 DTSIALDSNG 97
                                      5699*****9 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.096
                            RCC1_2   4 vsaGdyHscaLtedG 18 
                                       +  G y s+aL++++
  gi|488599648|ref|YP_007906119.1| 145 IVVGEYTSVALDSND 159
                                       67899*******996 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.55
                            RCC1_2  11 scaLtedG 18 
                                       s+aL+++G
  gi|488599648|ref|YP_007906119.1| 197 SIALDSNG 204
                                       89****99 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.18
                            RCC1_2   9 yHscaLtedGe 19 
                                       y s+aL+++G+
  gi|488599648|ref|YP_007906119.1| 244 YTSLALDSNGN 254
                                       679******96 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.0092
                            RCC1_2   5 saGdyH.scaLtedG 18 
                                       s G++H s+aL+++G
  gi|488599648|ref|YP_007906119.1| 294 SGGGRHpSLALDSNG 308
                                       5689**********9 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.1
                            RCC1_2   7 GdyHscaLtedG 18 
                                       G y s+aL+++G
  gi|488599648|ref|YP_007906119.1| 344 GKYTSLALDSNG 355
                                       7799*******9 PP

>> IBV_3B  IBV 3B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.9   2.7e+03      24      52 ..      47      79 ..      37      85 .. 0.66
   2 ?    2.6   0.1     0.049   1.5e+02      41      54 ..     125     138 ..     113     145 .. 0.79
   3 ?    6.0   0.2    0.0043        13      37      54 ..     257     274 ..     245     277 .. 0.87
   4 ?   -0.5   0.0      0.47   1.4e+03      42      54 ..     326     338 ..     316     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.9
                            IBV_3B 24 hissvlntevfdp....fdycyyrGGnfweies 52
                                      his v    v++p    + y +      w ie+
  gi|488599648|ref|YP_007906119.1| 47 HISYVYYPSVLNPtnseLKYAWKDSNGKWHIET 79
                                      888888888888722223466666666677776 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.049
                            IBV_3B  41 yyrGGnfweiesae 54 
                                        y G  fw ie+ e
  gi|488599648|ref|YP_007906119.1| 125 DYLGDYFWHIETVE 138
                                       48899******998 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0043
                            IBV_3B  37 fdycyyrGGnfweiesae 54 
                                         ycyy    f ei+ ae
  gi|488599648|ref|YP_007906119.1| 257 ISYCYYYNNTFGEIKYAE 274
                                       57************9998 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.47
                            IBV_3B  42 yrGGnfweiesae 54 
                                       y+  n w ie+ +
  gi|488599648|ref|YP_007906119.1| 326 YKDANGWHIETVD 338
                                       7899*****9863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3378.30
//
Query:       gi|488599649|ref|YP_007906120.1|  [L=118]
Description: hypothetical protein Asulf_00091 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-05   22.5   0.0    0.00018   21.2   0.0    1.7  1  HTH_23        Homeodomain-like domain
    0.00055   20.0   0.4     0.0015   18.6   0.1    1.8  2  HTH_28        Helix-turn-helix domain
     0.0089   15.6   0.1      0.021   14.4   0.1    1.7  1  HTH_24        Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.018   14.5   0.0    1.3  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.029   14.4   0.0      0.046   13.7   0.0    1.3  1  HTH_29        Winged helix-turn helix


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 !   21.2   0.0   4.9e-08   0.00018      10      45 ..      28      63 ..      19      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.9e-08
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      i++   +G s+r+IA++ ++++r v ++ kry+  G
  gi|488599649|ref|YP_007906120.1| 28 IIREKEKGTSTRTIAEIENITPRRVNQIYKRYKDTG 63
                                      7777788*************************8777 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   4.2e-07    0.0015       5      46 ..      28      66 ..      22      75 .. 0.75
   2 ?   -1.1   0.0      0.62   2.2e+03      29      43 ..      83      97 ..      77     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.2e-07
                            HTH_28  5 iikllaaGhsvreaArelgisrrtvyrWikryeegGiagLvp 46
                                      ii++  +G s r +A++ +i++r+v +  kry   G     p
  gi|488599649|ref|YP_007906120.1| 28 IIREKEKGTSTRTIAEIENITPRRVNQIYKRYKDTGK---IP 66
                                      45556668999*********************99886...34 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.62
                            HTH_28 29 vyrWikryeegGiag 43
                                      ++    +yee+ +++
  gi|488599649|ref|YP_007906120.1| 83 IKAIKEAYEEYRCNA 97
                                      555566778777665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   5.9e-06     0.021      14      47 ..      32      65 ..      19      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.9e-06
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      k+ ++s r +Ae  +++p  vn+  kr ++ G I
  gi|488599649|ref|YP_007906120.1| 32 KEKGTSTRTIAEIENITPRRVNQIYKRYKDTGKI 65
                                      36779**********************9999977 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 ?   14.5   0.0     5e-06     0.018      18      51 ..      26      59 ..      22      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-06
                      HTH_Tnp_ISL3 18 ayilelllesrsvkavArqlgvSwtTVwrildry 51
                                       +i+++  ++ s +++A++ ++++++V+ i++ry
  gi|488599649|ref|YP_007906120.1| 26 KWIIREKEKGTSTRTIAEIENITPRRVNQIYKRY 59
                                      67777755669**********************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 ?   13.7   0.0   1.3e-05     0.046       9      62 ..      33      83 ..      25      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                            HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeqe 62
                                      ++G s ++ iA++ ++++r v+ + kr+  +G +   +++  grpr+ lsee++
  gi|488599649|ref|YP_007906120.1| 33 EKGTS-TRTIAEIENITPRRVNQIYKRYKDTG-KIPEPKKL-GRPRKELSEEEI 83
                                      45665.**************************.55666776.999998899986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1082  (0.0603492); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 867.30
//
Query:       gi|488599650|ref|YP_007906121.1|  [L=57]
Description: hypothetical protein Asulf_00092 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   30.7   0.0      3e-07   30.7   0.0    1.0  1  rve            Integrase core domain
     0.0023   18.2   0.0     0.0023   18.1   0.0    1.0  1  DDE_Tnp_IS240  DDE 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 !   30.7   0.0   3.3e-11     3e-07      24      74 ..       9      57 .]       2      57 .] 0.94

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.3e-11
                               rve 24 ayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDn 74
                                      a++++ +dd+srli+++ +  +++++++l++l++a++++g+  pe +l+D+
  gi|488599650|ref|YP_007906121.1|  9 ARIIAYLDDASRLIVGYEVFENATTENALQVLKEAIDNYGK--PESILTDR 57
                                      778999***********************************..9******7 PP

>> DDE_Tnp_IS240  DDE 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      24      65 ..      15      56 ..       4      57 .] 0.93

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-07
                     DDE_Tnp_IS240 24 vDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtD 65
                                      +D ++r i+++ v+++  t+ a ++l+ a++++ ++pe+i+tD
  gi|488599650|ref|YP_007906121.1| 15 LDDASRlIVGYEVFENATTENALQVLKEAIDNY-GKPESILTD 56
                                      6999999**************************.********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 370.51
//
Query:       gi|488599651|ref|YP_007906122.1|  [L=779]
Description: hypothetical protein Asulf_00093 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-19   68.2  30.9    1.7e-12   47.7   4.6    5.1  6  FtsX      FtsX-like permease family
    3.7e-06   27.4   3.0    2.7e-05   24.6   0.0    2.9  3  MacB_PCD  MacB-like periplasmic core domain
  ------ inclusion threshold ------
      0.029   14.4   0.4         13    5.9   0.1    3.3  3  NapD      NapD protein
       0.17   12.2   8.6        1.4    9.3   0.2    4.1  4  DUF4149   Domain of unknown function (DUF4149)


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 ?    2.1   0.1     0.059   2.6e+02      21      89 ..      29      53 ..      18      80 .. 0.52
   2 ?   -0.9   0.1      0.51   2.3e+03      65      77 ..     271     283 ..     241     293 .. 0.55
   3 !   32.3   3.9   2.2e-11     1e-07       3      94 ..     297     388 ..     295     390 .. 0.86
   4 ?   -2.4   0.1       1.5   6.8e+03      70      79 ..     444     453 ..     424     479 .. 0.63
   5 ?   -0.1   0.1       0.3   1.4e+03      67      94 ..     644     671 ..     623     673 .. 0.72
   6 !   47.7   4.6   3.7e-16   1.7e-12       1      91 [.     677     765 ..     677     770 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.059
                              FtsX 21 llteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsis 89
                                       ++      +v  v+ lg+ l+++ +                                         ++
  gi|488599651|ref|YP_007906122.1| 29 KWMF----LAVTVVLMLGIMLFLSFY----------------------------------------LSY 53
                                      3333....333333333333333222........................................222 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.51
                              FtsX  65 dlitvliiivlll 77 
                                        ++ + ii+v+++
  gi|488599651|ref|YP_007906122.1| 271 FPSFFMIIAVFAT 283
                                       2222222222222 PP

  == domain 3  score: 32.3 bits;  conditional E-value: 2.2e-11
                              FtsX   3 eigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllll 79 
                                        i++lra+G+++ +++l +lt  ++i++ a+++G++lg++ a +l + +  +++ +       + ++   iv+++l+
  gi|488599651|ref|YP_007906122.1| 297 NIAVLRAMGLRRSEIVLHYLTYPVIIGFTATPLGVILGFMSASILTSSYIDFLNLPYYVSLPHYDIFGYSIVVGVLT 373
                                       69*************************************************98866666666666677778888888 PP

                              FtsX  80 allagllsiskilkk 94 
                                        +++g++ +++++ +
  gi|488599651|ref|YP_007906122.1| 374 PIISGFFVARNASQI 388
                                       888888888887765 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.5
                              FtsX  70 liiivlllll 79 
                                        ii+ l+l++
  gi|488599651|ref|YP_007906122.1| 444 SIIASLILIM 453
                                       2222222222 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.3
                              FtsX  67 itvliiivlllllallagllsiskilkk 94 
                                         ++++i+++l++    g+ +i++ +++
  gi|488599651|ref|YP_007906122.1| 644 GFFYAFIFFSLFFGASLGFSAIFNTTNI 671
                                       4566667777777777778888777766 PP

  == domain 6  score: 47.7 bits;  conditional E-value: 3.7e-16
                              FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlll 77 
                                       +re+++lr++G+++++++  +++e+ +i+++++v+Gl ++++ a+  ++ +++++     ++ +++ t+li i++++
  gi|488599651|ref|YP_007906122.1| 677 RREFATLRMIGYTNREIAMSIFIENTVISIISIVVGLPIAYASAYGYYQSFQTEL--YYFPMVVYPRTYLISIIMIF 751
                                       79*************************************************9996..79999999999999999999 PP

                              FtsX  78 llallagllsiski 91 
                                        ++ la++ ++  i
  gi|488599651|ref|YP_007906122.1| 752 AIVYLALIPAVKYI 765
                                       99999955555555 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 ?    1.9   0.1     0.057   2.5e+02      18     189 ..      38     230 ..      32     235 .. 0.47
   2 ?   -1.8   0.2      0.73   3.3e+03       6      20 ..     329     343 ..     325     396 .. 0.79
   3 !   24.6   0.0     6e-09   2.7e-05      21     194 ..     458     622 ..     439     623 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.057
                          MacB_PCD  18 ivslgeglqasvlsqisdlgnlvtvtpgkgsges.....lsdpdvealrr..evp.veavapvv.....tvrgggsg 81 
                                       +++lg  l  s+  ++  l+++++ + +k + e+     ++ +dv al++  +++ v +v +++     ++ +g+  
  gi|488599651|ref|YP_007906122.1|  38 VLMLGIMLFLSFYLSYLYLSDTYQTFYTKTNFEDlsievMRVDDV-ALAKirKIDgVLEVERRIaidgeAIINGK-- 111
                                       333333333333333222344444333332222212122334445.33221234445556665433332111111.. PP

                          MacB_PCD  82 eeevtvvg.vdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl......kpftVvGvled 150
                                          v ++  ++ + +k++ l+++eG             + ++ e++ae +   vG t++l      ++ ++ G + +
  gi|488599651|ref|YP_007906122.1| 112 RIPVKIISiPE-SQPKINRLYISEGE----------YSSFLVLEKFAEYYGlNVGNTMELefggnrINPRIGGLVYS 177
                                       11133333244.55666666555553..........33467778888887788999999999998888999999633 PP

                          MacB_PCD 151 pp...........gsgsalgddavylp...lttl..qrrsitvrlkdgadleaaa 189
                                       p+            s +++g   v++    l++l  +++++ +r+ + ++ +++ 
  gi|488599651|ref|YP_007906122.1| 178 PEyimiveegsivTSPGSYG--VVFVKedlLKRLgyDYNEVKIRVVSEDTRDEVL 230
                                       32455665443332222222..466656664444335666777777777777665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.73
                          MacB_PCD   6 LGiaiGvaaviaivs 20 
                                       LG+++G+++ ++++s
  gi|488599651|ref|YP_007906122.1| 329 LGVILGFMSASILTS 343
                                       899999887776663 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 6e-09
                          MacB_PCD  21 lgeglqasvlsqisdl.gnlvtvtpgkgsgeslsdpdve...alrr..evp.veavapvv....tvrgggsgeeevt 86 
                                       +++++   ++ ++++  +  + +         +s +d+     l++  ++  v ++ pvv    ++  g+  +++v+
  gi|488599651|ref|YP_007906122.1| 458 FVDSMDYVMDLEFNKIlS--YDIK--------VSLEDYNgkeKLKEikKIKgVIEAHPVVeetiLIEKGK--TKAVM 522
                                       444444444444443321..2222........23333322221211122344666777777643224444..55565 PP

                          MacB_PCD  87 vvgvdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl......kpftVvGvled.ppgsg 155
                                       +v++  dy ++++++ + G  +        p+++++ + +a++l  + G++i++      ++++VvG+  + p    
  gi|488599651|ref|YP_007906122.1| 523 LVAT--DYNDLYNIYNERGEKL------LPPKGIILPSLIAKNLSiVEGEKIKIytdfgeREVEVVGIE-KlP-L-- 587
                                       5555..5*******76667444......3799***********88*99***********999******6.423.1.. PP

                          MacB_PCD 156 salgddavylplttlq.rrsitvrlkdgadleaaaaelek 194
                                            +  y++l+ ++ +++i+vr+k+g +le+++ ++e+
  gi|488599651|ref|YP_007906122.1| 588 ----MPVSYMSLEFYDgFNEIVVRVKEG-SLEEVKSKVER 622
                                       ....4678999665533799*******9.56999999987 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.25   1.1e+03      55      67 ..      84      96 ..      80      97 .. 0.87
   2 ?    3.9   0.0     0.013        58      53      73 ..     489     509 ..     483     510 .. 0.89
   3 ?    5.9   0.1    0.0029        13       6      28 ..     604     626 ..     604     636 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.25
                              NapD 55 ieaiealpgVlsa 67
                                      +++i++++gVl +
  gi|488599651|ref|YP_007906122.1| 84 LAKIRKIDGVLEV 96
                                      789********98 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                              NapD  53 dtieaiealpgVlsaslvyhy 73 
                                       +++++i++++gV+ a+ v ++
  gi|488599651|ref|YP_007906122.1| 489 EKLKEIKKIKGVIEAHPVVEE 509
                                       789*************99876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0029
                              NapD   6 lvVqarperlaavkaalaalpgv 28 
                                       +vV+++ ++l++vk ++++++gv
  gi|488599651|ref|YP_007906122.1| 604 IVVRVKEGSLEEVKSKVERIDGV 626
                                       79*******************98 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3     0.098   4.4e+02      67      89 ..      29      51 ..      16      61 .. 0.66
   2 ?    9.3   0.2   0.00031       1.4      36      63 ..     269     294 ..     264     312 .. 0.83
   3 ?   -2.0   0.1         1   4.5e+03      68      95 ..     437     464 ..     422     470 .. 0.63
   4 ?    3.9   0.0     0.015        68      37      60 ..     651     674 ..     601     690 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.098
                           DUF4149 67 eellqlllllvvllltllnafyl 89
                                      + +++++ ++++l + l+ +fyl
  gi|488599651|ref|YP_007906122.1| 29 KWMFLAVTVVLMLGIMLFLSFYL 51
                                      44666666666666666666666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00031
                           DUF4149  36 klFplyfglglalsvlllltevavgsek 63 
                                        lFp +f++ +++++++llt +++   +
  gi|488599651|ref|YP_007906122.1| 269 ILFPSFFMIIAVFATYILLTRMIRE--Q 294
                                       59*******************9876..4 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1
                           DUF4149  68 ellqlllllvvllltllnafyleprits 95 
                                       ++ + ++++++ l+  +n+ ++   +  
  gi|488599651|ref|YP_007906122.1| 437 RMIFSSFSIIASLILIMNSMVFVDSMDY 464
                                       4556666666666666666666665555 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.015
                           DUF4149  37 lFplyfglglalsvlllltevavg 60 
                                        F+l+fg +l++s++   t++ v 
  gi|488599651|ref|YP_007906122.1| 651 FFSLFFGASLGFSAIFNTTNISVI 674
                                       39*************999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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):               4  [number of targets reported over threshold]
# CPU time: 0.80u 0.36s 00:00:01.16 Elapsed: 00:00:00.55
# Mc/sec: 4281.80
//
Query:       gi|488599652|ref|YP_007906123.1|  [L=231]
Description: ABC-type antimicrobial peptide transport system, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-35  121.6   0.0    4.4e-35  121.2   0.0    1.2  1  ABC_tran      ABC transporter
    1.4e-05   24.7   0.0      0.014   14.8   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    3.1e-05   24.0   0.0    4.8e-05   23.4   0.0    1.6  1  ATPase_2      ATPase domain predominantly from Archaea
    4.5e-05   23.4   0.9     0.0038   17.1   0.4    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0001   22.7   0.0    0.00013   22.4   0.0    1.3  1  AAA_16        AAA ATPase domain
    0.00048   20.7   0.0    0.00076   20.0   0.0    1.3  1  AAA_23        AAA domain
    0.00053   19.9   0.0    0.00088   19.2   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
    0.00083   19.0   0.0     0.0015   18.3   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
     0.0038   17.2   0.4        2.5    8.0   0.1    2.2  2  NTPase_1      NTPase
      0.005   16.8   0.0     0.0083   16.1   0.0    1.4  1  Rad17         Rad17 P-loop domain
     0.0071   16.1   0.0       0.14   11.9   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
     0.0072   16.6   0.0      0.019   15.3   0.0    1.7  2  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.014   15.8   0.7       0.11   12.9   0.7    2.2  1  AAA           ATPase family associated with various cellular 
      0.014   15.6   0.1      0.034   14.4   0.1    1.6  1  AAA_28        AAA domain
      0.026   13.4   0.0      0.035   13.0   0.0    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
      0.028   14.3   0.1      0.068   13.1   0.1    1.6  1  NACHT         NACHT domain
      0.029   14.4   0.0      0.049   13.7   0.0    1.5  1  AAA_14        AAA domain
       0.03   14.0   0.1        0.1   12.3   0.0    1.7  2  AAA_15        AAA ATPase domain
      0.033   13.8   0.0       0.12   11.9   0.0    1.8  2  AAA_25        AAA domain
      0.089   12.5   0.0       0.26   11.0   0.0    1.7  2  AAA_30        AAA domain
        0.1   13.0   0.0       0.29   11.5   0.0    1.8  1  RNA_helicase  RNA helicase
        0.1   12.3   0.0       0.15   11.8   0.0    1.3  1  AAA_24        AAA domain
       0.12   12.4   0.2       0.69   10.0   0.0    2.0  2  MMR_HSR1      50S ribosome-binding GTPase
       0.13   11.5   0.0       0.24   10.5   0.0    1.4  1  NB-ARC        NB-ARC domain
       0.15   11.7   0.0       0.23   11.0   0.0    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
        0.2   11.3   0.0       0.26   10.9   0.0    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind


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 !  121.2   0.0   6.4e-38   4.4e-35       1     136 [.      21     164 ..      21     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 6.4e-38
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l++v+l++++ge v+i+G++G+GK+tLl+l+ gl kp +G+i ++g ++++    + + + r++ig+++q  +l p+
  gi|488599652|ref|YP_007906123.1|  21 LRDVTLEIERGEFVVILGPSGCGKTTLLNLIGGLDKPSKGRIFFNGIEVSSlseeELTMHRRQNIGFIFQFFNLIPT 97 
                                       689********************************************999998866677899*************** PP

                                       SBHHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       lt+ren        +  + ++++l+ +gl + +d+      s+LSgG++qrva+aral+k p+l+l+DEpt
  gi|488599652|ref|YP_007906123.1|  98 LTARENvmlasdlvDNPRSADEVLEIVGLGDRADHFP----SELSGGEQQRVAIARALVKSPPLILADEPT 164
                                       *******999988777777999999999999666665....*****************************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 !    8.0   0.0    0.0024       1.7      25      42 ..      32      49 ..      19      52 .. 0.78
   2 !   14.8   0.0   2.1e-05     0.014     134     210 ..     134     208 ..      66     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                      +f +i+Gp G+GK+ ll+
  gi|488599652|ref|YP_007906123.1| 32 EFVVILGPSGCGKTTLLN 49
                                      599***********9986 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.1e-05
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemlekadkl 208
                                       +++LSgGe++ va+a       vk  pl l De    +D++  k + ++++  ++++++ +i +++++ + e adk+
  gi|488599652|ref|YP_007906123.1| 134 PSELSGGEQQRVAIARA----LVKSPPLILADEPTGSMDFETGKMILKVMReiNRQERMVLILVTHNSIIAEIADKI 206
                                       458*******9998754....68999*************************5446667889999***9999999998 PP

                                       EE CS
                                       xx RF
                             SMC_N 209 vg 210
                                       v 
  gi|488599652|ref|YP_007906123.1| 207 VY 208
                                       75 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 !   23.4   0.0     7e-08   4.8e-05      15      74 ..      26      84 ..      19     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7e-08
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeee 74
                                      le e+ e+++i Gp g+GKt+Ll+ +i  l++ +k +i+++ ++ +s+s+ + +++  ++
  gi|488599652|ref|YP_007906123.1| 26 LEIERGEFVVILGPSGCGKTTLLN-LIGGLDKPSKGRIFFNGIEVSSLSEEELTMHRRQN 84
                                      6778899***************97.66777788999****99999999888777554444 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 !   17.1   0.4   5.5e-06    0.0038       1      74 [.      33      89 ..      33     102 .. 0.74
   2 ?    5.0   0.0     0.025        18     236     299 ..     136     197 ..     100     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryry 74
                                      + v+ Gp g+GK++LL ++ +l                  +++k + ++++++ ++ +e e++ +  q++ + +
  gi|488599652|ref|YP_007906123.1| 33 FVVILGPSGCGKTTLLNLIGGLD-----------------KPSKGRIFFNGIEVSSLSEEELTMHRRQNIGFIF 89
                                      689****************9992.................6666666666666666666666666666665555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.025
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       elS G ++  a++ al   +   +l+l DEp  +++ +  + +l++++e +r ++  +il+TH+ 
  gi|488599652|ref|YP_007906123.1| 136 ELSGGEQQRVAIARALVKSP---PLILADEPTGSMDFETGKMILKVMREINRqERMVLILVTHNS 197
                                       56777777655555555555...**************666666666644444244777*****95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.9e-07   0.00013      22      89 ..      29     106 ..      18     218 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.9e-07
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekd..ggiflrgkcdql..esaipy..sa.laqalareellrqllde... 88 
                                        r+e v++ G+sG+GK++l++ +   l k   g if++g  +++  e+++++   + +  ++ +  l+  l ++   
  gi|488599652|ref|YP_007906123.1|  29 ERGEFVVILGPSGCGKTTLLNLIG-GLDKPskGRIFFNGIEVSSlsEEELTMhrRQnIGFIFQFFNLIPTLTARenv 104
                                       45689***************9998.4555555466666666666443333334433355555555788888777555 PP

                            AAA_16  89 .a 89 
                                        +
  gi|488599652|ref|YP_007906123.1| 105 mL 106
                                       31 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.1e-06   0.00076      10      39 ..      21      51 ..       2      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-06
                            AAA_23 10 frdqeidFsk.gltlItGpNGaGKTTildAi 39
                                      +rd++++ ++  +++I Gp G+GKTT+l+ i
  gi|488599652|ref|YP_007906123.1| 21 LRDVTLEIERgEFVVILGPSGCGKTTLLNLI 51
                                      48889999773588**************987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.3e-06   0.00088      92     121 ..      23      53 ..       5      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +++ +++  +++v++G+SG GK+tL+n + +
  gi|488599652|ref|YP_007906123.1|  23 DVTLEIERgEFVVILGPSGCGKTTLLNLIGG 53 
                                       55555555599****************9876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.1e-06    0.0015      14      55 ..      23      65 ..      12      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      + t+ei++ +++++ GpsG GK+Tll  i  l  p+k ++ fN
  gi|488599652|ref|YP_007906123.1| 23 DVTLEIERGEFVVILGPSGCGKTTLLNLIGGLDKPSKgRIFFN 65
                                      5789999777****************88877777777777777 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0048       3.3       2      19 ..      34      51 ..      33      85 .. 0.90
   2 !    8.0   0.1    0.0036       2.5      84     152 ..     143     214 ..     110     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0048
                                      EEEE--TTSSHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkv 19
                                      v+i Gp+G GKtTl++ +
  gi|488599652|ref|YP_007906123.1| 34 VVILGPSGCGKTTLLNLI 51
                                      6899**********9876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0036
                                       HHHHHHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EE CS
                          NTPase_1  84 lalealrkalseadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkv 152
                                         +++ r  ++++ +i+ DE  G+m +++ k++ +v + ++ +e++vl+ + +++   ++ ++i   kd+ v
  gi|488599652|ref|YP_007906123.1| 143 QRVAIARALVKSPPLILADEpTGSMDFETGKMILKVMREINrQERMVLILVTHNSiIAEIADKIVYLKDGGV 214
                                       44555555558888******88******99998887777775665555555444448889999988888655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.2e-05    0.0083      35      66 ..      21      52 ..      12      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      l+  +Le ++ + ++i GPsGCgk+t ++ + 
  gi|488599652|ref|YP_007906123.1| 21 LRDVTLEIERGEFVVILGPSGCGKTTLLNLIG 52
                                      55567888888899************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 !   11.9   0.0    0.0002      0.14      44      68 ..      28      52 ..      13      84 .. 0.82
   2 ?    2.0   0.0      0.22   1.5e+02     102     172 ..     147     218 ..     136     220 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      ie+ e +v+lGpsG GK+ l   +g
  gi|488599652|ref|YP_007906123.1| 28 IERGEFVVILGPSGCGKTTLLNLIG 52
                                      78999*************9876665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
                         IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviek..ryerrs.iiitsnlpfaewdevlgdatlatAilDRlv 172
                                       ++++l+k+  lil d  +  +d +  +++++v+ +  r er   i++t n  +ae  + +    l +  +DR+v
  gi|488599652|ref|YP_007906123.1| 147 IARALVKSPPLILADEPTGSMDFETGKMILKVMREinRQERMVlILVTHNSIIAEIADKIV--YLKDGGVDRVV 218
                                       567788888899999999999999999****998632555554245788888888777766..56666666665 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   2.7e-05     0.019       4      25 ..      30      51 ..      27      85 .. 0.87
   2 ?   -1.9   0.0       5.4   3.7e+03      93      99 ..     156     162 ..     117     198 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                      +  ++v+ G+sG+GKTtll+ +
  gi|488599652|ref|YP_007906123.1| 30 RGEFVVILGPSGCGKTTLLNLI 51
                                      56799*************9876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.4
                            AAA_22  93 elliiDE 99 
                                       +l++ DE
  gi|488599652|ref|YP_007906123.1| 156 PLILADE 162
                                       3666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   0.00016      0.11       1      21 [.      34      54 ..      34     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                                      EEEESSTTSSHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavake 21
                                      v++ Gp G+GKT+l + +   
  gi|488599652|ref|YP_007906123.1| 34 VVILGPSGCGKTTLLNLIGGL 54
                                      5789**********9999776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.9e-05     0.034       2      18 ..      34      50 ..      33      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-05
                            AAA_28  2 ivitGgestGKTtllea 18
                                      +vi+G++++GKTtll+ 
  gi|488599652|ref|YP_007906123.1| 34 VVILGPSGCGKTTLLNL 50
                                      8*************986 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     5e-05     0.035      25      55 ..      31      61 ..      18      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5e-05
                              DLIC 25 gksvlvlGedgsGkttliaklqGveeekkGr 55
                                      g  v++lG +g+Gkttl+  + G++++ kGr
  gi|488599652|ref|YP_007906123.1| 31 GEFVVILGPSGCGKTTLLNLIGGLDKPSKGR 61
                                      6679**************************8 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.9e-05     0.068       3      18 ..      34      49 ..      32      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                                      EEEEC-TTTCHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlq 18
                                      v++ G++G+GKTtLl 
  gi|488599652|ref|YP_007906123.1| 34 VVILGPSGCGKTTLLN 49
                                      89************97 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.1e-05     0.049       3      38 ..      32      66 ..      30     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinl 38
                                      + +vi G+  +GKTtll+ +      +++  +++n 
  gi|488599652|ref|YP_007906123.1| 32 EFVVILGPSGCGKTTLLNLIGGLDK-PSKGRIFFNG 66
                                      679*************977654333.5555555554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015       0.1      14      50 ..      21      58 ..      20     107 .. 0.80
   2 ?   -0.6   0.0       1.2   8.4e+02     342     369 .]     173     200 ..     153     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      l+dv+++++   + v+ G+ ++GK+++l+++  + + +
  gi|488599652|ref|YP_007906123.1| 21 LRDVTLEIERGeFVVILGPSGCGKTTLLNLIGGLDKPS 58
                                      788888888878*****************996666555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                            AAA_15 342 kvlikllkelandnktQviitTHSphii 369
                                       k++ k ++e+ +++++ +i+ TH++ i+
  gi|488599652|ref|YP_007906123.1| 173 KMILKVMREINRQERMVLILVTHNSIIA 200
                                       677889999999999999******9985 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   0.00018      0.12      30      50 ..      28      48 ..      24      52 .. 0.92
   2 ?   -1.3   0.0       1.9   1.3e+03     166     188 ..     173     195 ..     162     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + +ge++++ G++g+GKttl+
  gi|488599652|ref|YP_007906123.1| 28 IERGEFVVILGPSGCGKTTLL 48
                                      579****************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                       +++++ +++i r+ +  ++lv H
  gi|488599652|ref|YP_007906123.1| 173 KMILKVMREINRQERMVLILVTH 195
                                       78899999999999999999999 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00038      0.26      18      45 ..      31      58 ..      22      73 .. 0.81
   2 ?   -1.5   0.0       2.5   1.7e+03      30      45 ..     172     186 ..     119     203 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                        ++v+ Gp G GKtt+l+ +  + + +
  gi|488599652|ref|YP_007906123.1| 31 GEFVVILGPSGCGKTTLLNLIGGLDKPS 58
                                      3589**************9987766655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                            AAA_30  30 GKttalkalreaweaa 45 
                                       GK ++lk++re+ +++
  gi|488599652|ref|YP_007906123.1| 172 GK-MILKVMREINRQE 186
                                       22.2333334443333 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   0.00042      0.29       1      17 [.      34      50 ..      34      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                      RNA_helicase  1 iwlyGpsgeGKStlake 17
                                      +++ Gpsg+GK+tl + 
  gi|488599652|ref|YP_007906123.1| 34 VVILGPSGCGKTTLLNL 50
                                      6899**********997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.15       5      29 ..      34      65 ..      30     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                            AAA_24  5 iliyGpsgiGKTtlakel.......gpkplfi 29
                                      ++i Gpsg GKTtl++ +       + +++f 
  gi|488599652|ref|YP_007906123.1| 34 VVILGPSGCGKTTLLNLIggldkpsKGRIFFN 65
                                      79************998877665555555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0     0.001      0.69       2      20 ..      34      52 ..      33      80 .. 0.88
   2 ?    0.1   0.0       1.2   8.4e+02      46      84 ..     155     194 ..     138     219 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                                      EEEEESTTSSHHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinalt 20
                                      v+i+G +  GK+tL+n + 
  gi|488599652|ref|YP_007906123.1| 34 VVILGPSGCGKTTLLNLIG 52
                                      89**************875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                                       EEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEE CS
                          MMR_HSR1  46 keielvDtpGliegaseekglgkaflalee.adlillvvd 84 
                                       ++++l+D p    + +++k++ k ++++++   ++l++v 
  gi|488599652|ref|YP_007906123.1| 155 PPLILADEPTGSMDFETGKMILKVMREINRqERMVLILVT 194
                                       5666666664221334555555555554442344444444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035      0.24      21      40 ..      32      51 ..      18      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       +v + G  G+GKttl++ i
  gi|488599652|ref|YP_007906123.1| 32 EFVVILGPSGCGKTTLLNLI 51
                                      4899************8765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.23       3      21 ..      34      52 ..      32     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      +v+ G+ G GKTtLln + 
  gi|488599652|ref|YP_007906123.1| 34 VVILGPSGCGKTTLLNLIG 52
                                      7999***********9775 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00038      0.26       6      36 ..      23      53 ..      19     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                                      HHHS-EBTT-EEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslsk 36
                                      D+ + i +G+ ++i+g +g+Gkt++++ +  
  gi|488599652|ref|YP_007906123.1| 23 DVTLEIERGEFVVILGPSGCGKTTLLNLIGG 53
                                      67778999*****************977654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1370.83
//
Query:       gi|488599653|ref|YP_007906124.1|  [L=480]
Description: hypothetical protein Asulf_00095 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-12   48.2   0.0     0.0074   16.5   0.0    3.6  4  CARDB            CARDB
    3.4e-07   30.4   0.0    6.3e-05   23.2   0.0    3.2  3  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
     0.0014   18.9   0.0      0.041   14.2   0.0    2.8  3  DUF11            Domain of unknown function DUF11
     0.0016   18.3   0.5     0.0038   17.1   0.5    1.6  1  Gram_pos_anchor  LPXTG cell wall anchor motif
     0.0031   16.4   0.1       0.23   10.3   0.0    2.5  3  BatD             Oxygen tolerance
     0.0092   17.1   3.5        7.9    7.7   0.0    4.1  4  PPC              Bacterial pre-peptidase C-terminal domain
  ------ inclusion threshold ------
      0.024   14.6   0.0        1.2    9.1   0.0    2.8  2  DUF2393          Protein of unknown function (DUF2393)


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 ?   -3.4   0.0       4.5   1.1e+04      54      71 ..      81      97 ..      68     108 .. 0.53
   2 !   13.0   0.0   3.6e-05     0.092      15      90 ..     145     221 ..     135     227 .. 0.91
   3 !   14.0   0.0   1.8e-05     0.046      11      87 ..     247     327 ..     240     334 .. 0.88
   4 !   16.5   0.0   2.9e-06    0.0074      10      84 ..     354     429 ..     347     433 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.5
                                      ESEE-CTEEEEEEEEEE- CS
                             CARDB 54 vpsLaagesttvsftwtt 71
                                      +  La+g++ + +++  +
  gi|488599653|ref|YP_007906124.1| 81 LGDLASGST-SAQVKAYA 97
                                      555655544.33444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.6e-05
                                       EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE.SEE-CTEEEEEEEEEE-S.-S-CEEEEEEEESTT-S CS
                             CARDB  15 afvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv.psLaagesttvsftwtte.ategevtltvvvDpdne 89 
                                        +++e+ + +v +kN G ++ g++++ +   +  v++++v  s +age++++sf   ++   +g++ l +v+D  ++
  gi|488599653|ref|YP_007906124.1| 145 ISANEDKEYRVRIKNLG-GDLGNIRIGFKTPEGIVADSSVfDSWKAGEEKEISFRLSANdVRAGNYGLYLVIDYVDT 220
                                       67899999********9.689*********99999999999******************9*************8776 PP

                                       S CS
                             CARDB  90 v 90 
                                        
  gi|488599653|ref|YP_007906124.1| 221 L 221
                                       5 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.8e-05
                                       C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEE CS
                             CARDB  11 npseafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtvpsLaagesttvsftwtte..ategevtltvv 83 
                                        p++ ++ +++ i+++++N+G+ + ++ +++l   +e v  ++  +   + ge++ +++++t++  a++g++ +++ 
  gi|488599653|ref|YP_007906124.1| 247 IPDKIYPDSDFVISIQIRNSGNCDLKNLRARLDFPDEFVgeKEKFLGYFEVGETKIINYSITAKdyAKPGSYRFSLR 323
                                       5778899999*****************************8777889******************9999****96665 PP

                                       ESTT CS
                             CARDB  84 vDpd 87 
                                        ++d
  gi|488599653|ref|YP_007906124.1| 324 LEAD 327
                                       5544 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 2.9e-06
                                       EC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEE CS
                             CARDB  10 lnpseafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtvpsLaagesttvsftwtteategevtltvvv 84 
                                       ++p+    g++++++++++N+G+ +++a+ v+l+l +     ++  +  L++g+s+t ++  ++  ++g +++++ +
  gi|488599653|ref|YP_007906124.1| 354 TSPQRILGGDNFKLSLQLENSGKRSAKAVYVKLTLPEGFEgkNSYFIGTLESGDSATANLDLKAG-KPGLHEVKAEI 429
                                       67889999***************************998887688889***************998.99999988865 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 ?    0.0   0.0      0.41     1e+03       5      72 ..     149     211 ..     145     217 .. 0.71
   2 ?    2.7   0.0     0.058   1.5e+02       3      74 ..     253     322 ..     251     326 .. 0.78
   3 !   23.2   0.0   2.5e-08   6.3e-05       4      78 ..     362     431 ..     360     432 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.41
                       NPCBM_assoc   5 etvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyev 72 
                                       e++++++ ++n g++ + n+++  ++PeG     ++   ++s ++Ge+ e  +++++++  a G y +
  gi|488599653|ref|YP_007906124.1| 149 EDKEYRVRIKNLGGD-LGNIRIGFKTPEGIV---ADSSVFDSWKAGEEKEISFRLSANDVRA-GNYGL 211
                                       667777888888776.778889999999877...7777777888888888888887765543.66655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.058
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevta 74 
                                       p+++  + + + n+g+  ++n++ +l++P++      + + +   + Get   +  +t+ + a++G y+  +
  gi|488599653|ref|YP_007906124.1| 253 PDSDFVISIQIRNSGNCDLKNLRARLDFPDEFV--GEKEKFLGYFEVGETKIINYSITAKDYAKPGSYRFSL 322
                                       677888889999999999999999999999876..5555555678888888888888888888888887655 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 2.5e-08
                       NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                       G+  +l l + n+g+++a++v+++l+lPeG +   +    + +l+ G++++a++++++++   +G +ev+a++++
  gi|488599653|ref|YP_007906124.1| 362 GDNFKLSLQLENSGKRSAKAVYVKLTLPEGFE--GKNSYFIGTLESGDSATANLDLKAGK---PGLHEVKAEISY 431
                                       888999**************************..88888899***************996...8999**999987 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.21   5.3e+02      55      85 ..     178     208 ..     153     215 .. 0.79
   2 ?   -1.7   0.0       1.5   3.8e+03      10      30 ..     204     229 ..     196     235 .. 0.68
   3 !   14.2   0.0   1.6e-05     0.041       9      78 ..     358     417 ..     353     424 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.21
                             DUF11  55 asaltsv.gsLeagesatlsftvrvtrtaasg 85 
                                         a++sv  s +age++ +sf+++++   a +
  gi|488599653|ref|YP_007906124.1| 178 V-ADSSVfDSWKAGEEKEISFRLSANDVRAGN 208
                                       4.3344458889************99887765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                             DUF11  10 vrpGd.....tvtytltvtNtgpasa 30 
                                       vr+G       ++y+ t+ N g++++
  gi|488599653|ref|YP_007906124.1| 204 VRAGNyglylVIDYVDTLNNEGTDKL 229
                                       55555555556778889999999877 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.6e-05
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78 
                                       ++  Gd+ +  l + N+g +sa+ v v+ tlP+g+++  +             g+Le g sat ++ +++
  gi|488599653|ref|YP_007906124.1| 358 RILGGDNFKLSLQLENSGKRSAKAVYVKLTLPEGFEGKNSYFI----------GTLESGDSATANLDLKA 417
                                       66779999999*************************5444444..........99*******99998876 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 !   17.1   0.5   1.5e-06    0.0038      16      42 ..     454     480 .]     453     480 .] 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  16 gnifltaaGllallggllLlvkrRKke 42 
                                       +++++ +aGl+all  + Ll+k+R+k+
  gi|488599653|ref|YP_007906124.1| 454 SSYIFGFAGLIALLIVAYLLKKKRRKK 480
                                       689****************99999986 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   8.8e-05      0.23     298     372 ..      52     124 ..      41     173 .. 0.83
   2 ?   -1.4   0.0      0.29   7.6e+02      17      87 ..     355     421 ..     352     427 .. 0.62
   3 ?    3.3   0.1     0.012        30     399     451 ..     418     479 ..     400     480 .] 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.8e-05
                              BatD 298 GNlkllqlPelnfpegfevYdpkpedntkktgnglsGsrteeyalvPrkaGkytipaiefsyFDtatkkyetatl 372
                                       G +k l+l   ++ ++f  Yd+k + + +   +  sGs + ++ ++++k+G y+i+ + ++y+D++    + +++
  gi|488599653|ref|YP_007906124.1|  52 GEVKGLELFLSESEKDFSFYDEKSSLDLRLG-DLASGSTSAQVKAYAKKPGIYQID-VDLKYYDVNLSAWKSINS 124
                                       556666666666889*********9999985.799********************8.6*******9888887776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.29
                              BatD  17 dknevevgetfrLtftvngasgepdfsapslekdfevlsg.sqssstqiinGkssssssktwtytLapkkeG 87 
                                       +++++  g++f+L+++++++ g+   +  ++  ++++ +g +  +s+  + G+ +s  s t ++ L++ k+G
  gi|488599653|ref|YP_007906124.1| 355 SPQRILGGDNFKLSLQLENS-GKRSAK--AVYVKLTLPEGfEGKNSY--FIGTLESGDSATANLDLKAGKPG 421
                                       68889999999999999999.666666..333455555554333333..33555554555566666666655 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.012
                              BatD 399 qkeevkllgkdirfik...geaslkkkgs.ff.....lfwlllllplllfvvllllwrkrrr 451
                                        k    + + +i+++    +++s++k+ + ++     ++ + ++ +++l++v++ll +krr+
  gi|488599653|ref|YP_007906124.1| 418 GKPGLHEVKAEISYMDmayKKHSVTKTFTlYVfpkdsSYIFGFAGLIALLIVAYLLKKKRRK 479
                                       55555555667777754555555555555422588877778888888888999999999887 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 ?    3.2   0.1     0.079     2e+02      15      68 ..      43     107 ..      36     109 .. 0.55
   2 !    7.7   0.0    0.0031       7.9       3      64 ..     141     209 ..     139     215 .. 0.80
   3 ?   -2.1   0.0       3.4   8.7e+03      14      39 ..     257     272 ..     219     285 .. 0.66
   4 ?    4.3   0.0     0.035        89       9      34 ..     339     375 ..     334     418 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.079
                                       EEEEES-TT..SE...EEEE-TT..-SS-EE-ST.........T-TTS-TTS-EE-SSSEEEEEEE CS
                               PPC  15 ltididggtidld...Lylldsngtsvaaydans.........apsgsdeyieftapqaGtYyvaV 68 
                                       ++idi++ ++ ++   L+l+ s+  + + yd  s         a+++ + +++  a ++G Y + V
  gi|488599653|ref|YP_007906124.1|  43 ISIDISNAGGEVKgleLFLSESE-KDFSFYDEKSsldlrlgdlASGSTSAQVKAYAKKPGIYQIDV 107
                                       77999999996666225555544.333333333334444455544445566666666777776666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0031
                                       EEEEEEE-TT-EEEEEES-TT..SE.EE..EE-TT..-SS-EE-STT-TTS-TTS-EE-....SSSEEE CS
                               PPC   3 Dvysfevpagdsltididggtidld.Ly..lldsngtsvaaydansapsgsdeyiefta....pqaGtY 64 
                                       D+++++++++ ++ + i ++++dl  ++    +++g ++++++  s++ g    i+f        aG+Y
  gi|488599653|ref|YP_007906124.1| 141 DYFEISANEDKEYRVRIKNLGGDLGnIRigFKTPEGIVADSSVFDSWKAGEEKEISFRLsandVRAGNY 209
                                       9*********************99997644777777788888888888888888887765555666665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.4
                                       E.EEEEES-TT..SEEEEE-TT..-SS CS
                               PPC  14 s.ltididggtidldLylldsngtsva 39 
                                         ++i+i + +           + ++ 
  gi|488599653|ref|YP_007906124.1| 257 FvISIQIRNSG-----------NCDLK 272
                                       32344444444...........33333 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.035
                                       E-TT-EEEEEES-TT...........SE..EEEE-TT CS
                               PPC   9 vpagdsltididggti.........dld..Lylldsn 34 
                                       v+  ++++idi g  +         +++  L+l +s 
  gi|488599653|ref|YP_007906124.1| 339 VKDPGRISIDIAGVYTspqrilggdNFKlsLQLENSG 375
                                       788999*****88888888888888777557777766 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00046       1.2      60     139 ..     254     337 ..     231     341 .. 0.65
   2 ?    2.3   0.0      0.06   1.5e+02      54      87 ..     356     389 ..     351     449 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00046
                           DUF2393  60 teafvvdgtitNeGkftikeCkleiklvnkshnk..kskellkklkp.lvsksevikedlkpgesk.eFrviidyfp 132
                                       +++fv++++i+N G+ ++k+   ++++ ++   +  k+  +++   + + ++s++ k+  kpg+++ + r+ +d+f 
  gi|488599653|ref|YP_007906124.1| 254 DSDFVISIQIRNSGNCDLKNLRARLDFPDEFVGEkeKFLGYFEVGETkIINYSITAKDYAKPGSYRfSLRLEADDFA 330
                                       678*****************999999988887774433333332222145666666666666665435666666666 PP

                           DUF2393 133 yfknysv 139
                                       + ++++v
  gi|488599653|ref|YP_007906124.1| 331 QTSDIEV 337
                                       6666665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.06
                           DUF2393  54 qkrllyteafvvdgtitNeGkftikeCkleiklv 87 
                                        +r+l  + f ++++  N Gk+  k ++++++l 
  gi|488599653|ref|YP_007906124.1| 356 PQRILGGDNFKLSLQLENSGKRSAKAVYVKLTLP 389
                                       56788889999*****************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2910.54
//
Query:       gi|488599654|ref|YP_007906125.1|  [L=182]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   53.1   0.0    3.9e-14   52.2   0.0    1.5  1  TetR_N    Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.033   14.0   0.0      0.077   12.8   0.0    1.6  1  HTH_10    HTH DNA binding domain
       0.19   11.9   0.0       0.28   11.4   0.0    1.3  1  TetR_C_6  BetI-type transcriptional repressor, C-terminal


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 !   52.2   0.0   6.5e-18   3.9e-14       1      44 [.      13      56 ..      13      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 6.5e-18
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLl 44
                                      Il++A+e+   +  +++tv+eIAk+AGvskg+++++F++K  L 
  gi|488599654|ref|YP_007906125.1| 13 ILEVALEVYTAKPPHEVTVDEIAKKAGVSKGLIFYHFKNKYNLE 56
                                      9***************************************9885 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   1.3e-05     0.077      20      44 ..      25      49 ..      24      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                            HTH_10 20 yPRrvtlkeLAkelGIskstlsehL 44
                                       P++vt++e+Ak+ G+sk  + +h 
  gi|488599654|ref|YP_007906125.1| 25 PPHEVTVDEIAKKAGVSKGLIFYHF 49
                                      59***************98777775 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 ?   11.4   0.0   4.7e-05      0.28      70      93 ..     135     158 ..     111     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                                       STHHHHHHHHHHHHHHHHHHHHHT CS
                          TetR_C_6  70 adaeaaAerlaAlidGLwlraala 93 
                                       ad++ +A +++Al dGL++ ++ +
  gi|488599654|ref|YP_007906125.1| 135 ADPKKVAIAIMALFDGLSIYSLFY 158
                                       79****************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1207.01
//
Query:       gi|488599655|ref|YP_007906126.1|  [L=278]
Description: DNA repair photolyase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-11   44.0   0.1    3.8e-11   43.6   0.1    1.2  1  Radical_SAM  Radical SAM superfamily
    1.1e-07   31.9   7.2     0.0043   16.8   0.1    2.9  3  DUF1848      Domain of unknown function (DUF1848)
  ------ inclusion threshold ------
      0.014   15.6   0.3      0.042   14.1   0.2    1.9  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 !   43.6   0.1   6.4e-15   3.8e-11       2     164 ..      24     183 ..      23     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 6.4e-15
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.... 74 
                                       +++ gC+++C++C+ ++       +  +++ ++++ v++  ++   + +i+++   + yp  +++le  +k+     
  gi|488599655|ref|YP_007906126.1|  24 NPYTGCSHKCTYCYSTY---IPNFYSLRTKKDVIKRVEKDLEKIPENSIISMSNSSDPYPGVERKLEITRKILellk 97 
                                       6789************9...69999***************6555488888887777777555555555555557777 PP

                                       CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                       + ++r+ ++t    +  + +++l e++   vs+++ ++  +++ +++    ++e +++a++ l++++i+++    ++
  gi|488599655|ref|YP_007906126.1|  98 EYDMRVLIVTKSDIV-ARDVDLLSEMR-CAVSVSISTLKFFRTFEPN--AVDPEMRIRAMKVLKDNNIPVILRLDPV 170
                                       79*************.***********.************9555555..69******************77777799 PP

                                       BTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleell 164
                                       +p  ++ e++ +l
  gi|488599655|ref|YP_007906126.1| 171 IPFKTENEIDSIL 183
                                       9999999988876 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.7   1.9e-06     0.011     239     264 ..      12      37 ..       4      38 .. 0.90
   2 ?    0.9   0.0     0.051   3.1e+02     127     177 ..      45      99 ..      40     115 .. 0.69
   3 !   16.8   0.1   7.2e-07    0.0043      60     206 ..     111     266 ..      91     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-06
                           DUF1848 239 rkeCgCveskDiGayntClhgCvYCY 264
                                        k C+C e   +  y  C+h+C+YCY
  gi|488599655|ref|YP_007906126.1|  12 SKLCTCPEKFSLNPYTGCSHKCTYCY 37 
                                       577*********************** PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.051
                           DUF1848 127 ltvelhlekfeklaeelkgytekvviSfvdl...ykkvkrnlkkk.lelrelsee 177
                                       ++ +++ + ++++ ++l+++ e+ +iS+ +    y  v+r+l+ +   l+ l+e 
  gi|488599655|ref|YP_007906126.1|  45 YSLRTKKDVIKRVEKDLEKIPENSIISMSNSsdpYPGVERKLEITrKILELLKEY 99 
                                       5667778889999999999999999999765556999999996431233333444 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 7.2e-07
                           DUF1848  60 pllkkleelkergiklyfqfTltdyekelepnvpsleerietfkelseklgkerviwRyDPilltek.ltvelhlek 135
                                        + + ++ l+e+++ + + ++  ++ +++epn  + e ri+++k l ++     vi+R DP++  ++  +++  l++
  gi|488599655|ref|YP_007906126.1| 111 IVARDVDLLSEMRCAVSVSISTLKFFRTFEPNAVDPEMRIRAMKVLKDNN--IPVILRLDPVIPFKTeNEIDSILNS 185
                                       4556778888877777777777788899******************9975..67********976653333433333 PP

                           DUF1848 136 fe....klaeelk...gytekvviSfvdl..ykkvkrnlkkk.lelrelseeekeelaeelaeiakklglelatCae 202
                                        +     ++++lk   +  ++v+ S  +l  ++++  nl +k  +   l ++ +++++++++e ++++g++ a C e
  gi|488599655|ref|YP_007906126.1| 186 CDfvdhVVSSTLKlryDSLKRVISSNPELsfFRNIYLNLGEKiQNSFYLPAQIRRDILNAVKEKCEEMGISYAFCRE 262
                                       22001122333334356666666665444446666666655434455566666789999999999999999999998 PP

                           DUF1848 203 kedl 206
                                         ++
  gi|488599655|ref|YP_007906126.1| 263 GFRF 266
                                       7655 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2     7e-06     0.042      13      57 ..      27      71 ..      20     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7e-06
                           Fer4_12 13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esieglt 57
                                      +gC+++C +C+ + +    ++  ++k++++++ +dl+k ++++ ++
  gi|488599655|ref|YP_007906126.1| 27 TGCSHKCTYCYSTYI-PNFYSLRTKKDVIKRVEKDLEKiPENSIIS 71
                                      7**********5555.555788888999999999998755555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1609.65
//
Query:       gi|488599656|ref|YP_007906127.1|  [L=180]
Description: inosine/xanthosine triphosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-50  171.3   0.0    1.5e-50  171.2   0.0    1.0  1  NTPase_I-T  Protein of unknown function DUF84


Domain annotation for each model (and alignments):
>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.0   8.5e-55   1.5e-50       1     163 []       6     167 ..       6     167 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 8.5e-55
                                       S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET.... CS
                        NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleek 77 
                                       gS+Np Kve+vk+afe +f+dv+ve+ sv+sgv++qP++ + t++GAinRa n +++  e+d++vG+E+G++ ++++
  gi|488599656|ref|YP_007906127.1|   6 GSRNPLKVEGVKQAFELYFDDVTVESRSVDSGVESQPFN-NRTIEGAINRALNSYSE--EFDFAVGVEAGLFSFKNT 79 
                                       8**************************************.9***************9..79***************9 PP

                                       ...TEEEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHH CS
                        NTPase_I-T  78 ...lldvawaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedly 151
                                           +d+++ av+d+ +rvs+g++++fe+P+ vveev++g+e+g+vmdel+g +n+++k+Gai +lTkg+++R dl+
  gi|488599656|ref|YP_007906127.1|  80 itgFIDFQVSAVYDG-SRVSIGFGPGFEYPPFVVEEVLKGREVGDVMDELTGIKNLGEKTGAIYFLTKGKISRVDLT 155
                                       9999***********.8************************************************************ PP

                                       HHHHHHHTHHHH CS
                        NTPase_I-T 152 eqavilAlipfl 163
                                       + +vi Alip++
  gi|488599656|ref|YP_007906127.1| 156 RISVINALIPWI 167
                                       **********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1067.34
//
Query:       gi|488599657|ref|YP_007906128.1|  [L=779]
Description: putative P-loop ATPase fused to an acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-53  181.0   0.0    3.9e-53  179.9   0.0    1.6  1  Helicase_RecD    Helicase
    8.4e-43  146.4   0.1      3e-28   98.8   0.0    2.4  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
    5.7e-28   96.7   0.0    2.3e-27   94.7   0.0    2.1  1  DUF1726          Domain of unknown function (DUF1726)
    7.2e-06   25.9   1.6    1.3e-05   25.0   0.7    1.9  2  tRNA_bind_2      Possible tRNA binding domain
     0.0001   22.7   0.2     0.0025   18.2   0.2    2.7  2  AAA_19           AAA domain
    0.00011   22.0   0.0    0.00039   20.2   0.0    1.8  2  AAA_30           AAA domain
    0.00034   20.9   0.1        0.4   11.0   0.1    3.6  3  AAA_22           AAA domain
    0.00052   19.9   0.1     0.0012   18.8   0.1    1.5  1  DUF5420          Family of unknown function (DUF5420)
  ------ inclusion threshold ------
      0.053   13.3   0.0       0.13   12.1   0.0    1.6  1  MerR             MerR family regulatory protein
      0.068   13.6   0.1         18    5.6   0.0    2.6  2  AAA_16           AAA ATPase domain
       0.12   12.7   0.0       0.28   11.4   0.0    1.8  1  Acetyltransf_1   Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.9   0.0   2.4e-56   3.9e-53       1     177 []     248     431 ..     248     431 .. 0.97

  Alignments for each domain:
  == domain 1  score: 179.9 bits;  conditional E-value: 2.4e-56
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk......snilvtapskenvktlfeflakglealglke.eekkkkaekaelr 70 
                                       v+tAdRGRGK+a+lG+++ +li++ +       +i+v+a ++++v+t f+fl+ +l++ g+ + + k++++  + ++
  gi|488599657|ref|YP_007906128.1| 248 VITADRGRGKTAILGILTPHLISRMQrvlkraIRIMVVAQTPQSVQTYFRFLTIALKRHGFVDhKIKESSGMITVVT 324
                                       79********************99999999999***************************98867778888889999 PP

                     Helicase_RecD  71 vrkqrieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkr 147
                                        ++ r+ey+ p++++++ + ad+++vDEAA+i++++l ++l++ +  ++++T+hGYEG+Gr+fs++flk+l+ +++ 
  gi|488599657|ref|YP_007906128.1| 325 GKHLRVEYVVPRRAIAEARYADVVIVDEAASIDVNTLFEILKDTRYAIFSSTIHGYEGSGRSFSVRFLKRLEMDESV 401
                                       99*************************************************************************** PP

                     Helicase_RecD 148 elreleleepiRyaegdplEkwlndlLlLd 177
                                       e+++++leepiRya+gdp+E+wl+++LlLd
  gi|488599657|ref|YP_007906128.1| 402 EIQKISLEEPIRYAKGDPIERWLYKTLLLD 431
                                       ****************************97 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   0.0   1.9e-31     3e-28       3     123 ..     471     583 ..     469     588 .. 0.91
   2 !   46.0   0.0   2.5e-15   4.1e-12     177     226 ..     586     635 ..     581     636 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 1.9e-31
                   GNAT_acetyltr_2   3 vallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlipw 79 
                                       ++++v +HY+n P DL +l D P+h  f    +        + +c ++va+EG+i+++ v +++s+g +++G++ip+
  gi|488599657|ref|YP_007906128.1| 471 FGIYVLAHYRNRPSDLVILFDMPNHIAFRVSVNG-------KTVCSLHVAIEGSIEED-VIAKMSEGYKPKGQIIPD 539
                                       789**********************999876633.......579***********998.556788999********* PP

                   GNAT_acetyltr_2  80 tlsqqfqdeefaslsGaRivRiAvhpelqkmGYGsralelleky 123
                                       ++ +++ d +f++++G+R+vRiA+hp+++ mG G+ al++l ++
  gi|488599657|ref|YP_007906128.1| 540 VVLKHHWDYSFPKYKGLRVVRIATHPDVMDMGIGTFALKNLLEW 583
                                       ***************************************99765 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 2.5e-15
                   GNAT_acetyltr_2 177 pekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                       +e  d++g +fG++seLl+FW+r+gf pv++  ++ne++GE+++++++ l
  gi|488599657|ref|YP_007906128.1| 586 TEGYDWVGSGFGVSSELLRFWSRTGFIPVHITPQRNEISGEYTVVVIQGL 635
                                       5778******************************************9865 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.0   1.4e-30   2.3e-27       1      93 []      92     185 ..      92     185 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 1.4e-30
                           DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplt.eevkkrfn 76 
                                       +kese+vLG+ty++lv+dl+e ++Pn+lg ++et++ GG+ii+l pp+++++++++++hk+lv+ep++ e v +rf 
  gi|488599657|ref|YP_007906128.1|  92 FKESENVLGETYSALVIDLTEGFNPNDLGIIIETIEKGGIIIVLSPPVDKWNNFISKWHKELVSEPYSiESVIPRFY 168
                                       69*************************************************************************** PP

                           DUF1726  77 krfirklkehegilivd 93 
                                       +rfi+   e++g++i+d
  gi|488599657|ref|YP_007906128.1| 169 RRFIAHTLEAKGTIIYD 185
                                       **************998 PP

>> tRNA_bind_2  Possible tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.5   5.7e+03      43      79 ..      14      50 ..       5      69 .. 0.67
   2 !   25.0   0.7   8.2e-09   1.3e-05       6     127 ..     647     755 ..     643     778 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.5
                                      -------------------HHHHHHHHHHHHS---HH CS
                       tRNA_bind_2 43 ekseekkeltkeeldellspfDlkRLesYannllDYh 79
                                      +k++ek+  +++    +l + D  RL   ++++ +Y 
  gi|488599657|ref|YP_007906128.1| 14 KKATEKSIKNNHRFMVFLCSEDHDRLINLSKKIFEYY 50
                                      3344444455566677777778888877777777774 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 8.2e-09
                                       HHHHHHHHHHHHHHHSS------S--------------------------------HHHHHHHHHHHHS---HHHHH CS
                       tRNA_bind_2   6 akdFrkRflsLLsyqFrkfeavlaLsilesknkgeklekseekkeltkeeldellspfDlkRLesYannllDYhvil 82 
                                        +dF kR+++ Ls + ++++  +a  +l+s +k  ++e             +  l++ D+ R+e+Y + +  Y+ + 
  gi|488599657|ref|YP_007906128.1| 647 NSDFVKRVVEYLSDELKDLDFETAYLLLHSLHKSYDAE-------------KPKLTETDVSRMEKYIEGISLYEYVS 710
                                       68***********************9999988543222.............2348899******************* PP

                                       SSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHHHH CS
                       tRNA_bind_2  83 DllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddleke 127
                                       D+   + + y+    +++vkL+++++ +L+   LQ ks  + e+ 
  gi|488599657|ref|YP_007906128.1| 711 DIARPIVRYYYLLSDSNRVKLDELEERVLIQKCLQLKSWWEFEEL 755
                                       ***********999999********************97666553 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.5e-06    0.0025       8     124 ..     242     367 ..     236     372 .. 0.66
   2 ?    1.1   0.0      0.28   4.6e+02     105     127 ..     656     679 ..     570     683 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp...eeillvaftgrAakelrerlaalgaeatTiHrlalldfd 81 
                                        ++kv ++ta  G GKT +l     +l+++ ++ +    +i++va t ++++     l      a   H++  +  d
  gi|488599657|ref|YP_007906128.1| 242 REKKVAVITADRGRGKTAILGILTPHLISRMQRVLkraIRIMVVAQTPQSVQTYFRFL----TIALKRHGF--V--D 310
                                       6789***************987777777666554433378999999999998877655....333334444..2..2 PP

                            AAA_19  82 dlltealelle.............eaeeekklqeeellivDEfqdvd.elqyrLlka 124
                                       ++++e  +++               ++   + + ++++ivDE+  +d  + +++lk 
  gi|488599657|ref|YP_007906128.1| 311 HKIKESSGMITvvtgkhlrveyvvPRRAIAEARYADVVIVDEAASIDvNTLFEILKD 367
                                       222233333333344455566554333334443556***********9999999986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.28
                            AAA_19 105 llivDEfqdvd.elqyrLlkallg 127
                                         + DE  d+d e++y Ll+ l +
  gi|488599657|ref|YP_007906128.1| 656 EYLSDELKDLDfETAYLLLHSLHK 679
                                       4466**************999875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.4e-07   0.00039      17     112 ..     243     368 ..     226     377 .. 0.72
   2 ?   -1.8   0.0       1.3   2.1e+03      22      42 ..     376     396 ..     370     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.4e-07
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaag.......grviglAptgkaAkvLaeelgieastiakllkrlk..... 81 
                                       +++vav+t+  G GKt +l+ l+ ++ ++         r++++A t +  ++         + +   lkr++     
  gi|488599657|ref|YP_007906128.1| 243 EKKVAVITADRGRGKTAILGILTPHLISRMqrvlkraIRIMVVAQTPQSVQT-------YFRFLTIALKRHGfvdhk 312
                                       6789******************999888862455555455555555555544.......333333334444444444 PP

                            AAA_30  82 .........................grarlepgtllivDEagmvdtkqlaallkaa 112
                                                                + a+ + ++++ivDEa+ +d ++l ++lk  
  gi|488599657|ref|YP_007906128.1| 313 ikessgmitvvtgkhlrveyvvprrAIAEARYADVVIVDEAASIDVNTLFEILKDT 368
                                       445555555666666666789*98866677888***************99999876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                            AAA_30  22 vltGpAGtGKttalkalreaw 42 
                                       +++G+ G+G +++++ l+++ 
  gi|488599657|ref|YP_007906128.1| 376 TIHGYEGSGRSFSVRFLKRLE 396
                                       789***********9998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.44   7.2e+02      93     133 ..      29      72 ..       6      76 .. 0.74
   2 !   11.0   0.1   0.00024       0.4       4     114 ..     243     367 ..     240     372 .. 0.75
   3 ?    4.5   0.0     0.025        40       9      29 ..     376     396 ..     373     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.44
                            AAA_22  93 elliiDEaqhlr..seealeeL.rsllnlsrkgvqliLvGtpel 133
                                       ++l  ++ ++l+  s++++e+  +++ ++  kg++l+L+G + +
  gi|488599657|ref|YP_007906128.1|  29 VFLCSEDHDRLInlSKKIFEYYlKICPDCIPKGFRLLLAGRTRF 72 
                                       666667778877788999987658888889**********9866 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelka....... 70 
                                       ++++ v+t+  G GKT  l  l+  l  +    +   +r+  + v ++ + s ++ +r l  al++ +         
  gi|488599657|ref|YP_007906128.1| 243 EKKVAVITADRGRGKTAILGILTPHLISRM---QrvlKRAIRIMVVAQTPQSVQTYFRFLTIALKRHGFVdhkikes 316
                                       7899*******************9995444...144599999999999999*************9766669988888 PP

                            AAA_22  71 .........erlsseellealeqalraravielliiDEaqhlrseealeeLrs 114
                                                + l+ e ++ + + a  ++a   ++i+DEa  ++ ++++e L++
  gi|488599657|ref|YP_007906128.1| 317 sgmitvvtgKHLRVEYVVPRRAIAEARYA--DVVIVDEAASIDVNTLFEILKD 367
                                       88886666555555555544333333333..69********953666666655 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.025
                            AAA_22   9 vvtGesGtGKTtllrrlleql 29 
                                       +++G  G+G+++++r l++  
  gi|488599657|ref|YP_007906128.1| 376 TIHGYEGSGRSFSVRFLKRLE 396
                                       79*************999865 PP

>> DUF5420  Family of unknown function (DUF5420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   7.4e-07    0.0012      41     152 ..     166     272 ..     142     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.4e-07
                           DUF5420  41 pfyecwigdersvfgivcsadndvskvkevkgykfdevkdekvvvkpdkRykeGKelnkklqaireilkklpdFsty 117
                                       +fy+ +i++    +g ++  d   +k k vk ++ ++++dek +v p++R  +  +l  kl a ++ ++ l +F+t+
  gi|488599657|ref|YP_007906128.1| 166 RFYRRFIAHTLEAKGTIIY-D--ADKSKIVKRFQEGQREDEKEIVIPERRNIKK-KL-YKLCATQDQVNALYEFETF 237
                                       6888888888888887663.3..4688999********************8764.44.479999************* PP

                           DUF5420 118 mlkkLnllllvfgvssgrsylavsgvaedalivki 152
                                         +k +  + v+ +  gr+  a+ g+   +li ++
  gi|488599657|ref|YP_007906128.1| 238 FDRKREKKVAVITADRGRGKTAILGILTPHLISRM 272
                                       **************************999999876 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   7.8e-05      0.13       9      32 ..     596     622 ..     595     625 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                                       HTTTHHHHHHHHHTTSST...SEEETT CS
                              MerR   9 tGvsprtLRyYEreGLip...ppeRte 32 
                                       +Gvs+  LR++ r G ip   +p+R+e
  gi|488599657|ref|YP_007906128.1| 596 FGVSSELLRFWSRTGFIPvhiTPQRNE 622
                                       59***************8777777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.013        21      21      74 ..     241     300 ..     218     367 .. 0.72
   2 ?    5.6   0.0     0.011        18      28      76 ..     376     424 ..     355     492 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.013
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekd.........ggiflrgkcdqlesaipysalaq 74 
                                       + +  + +++ ++G GK++++  l  +l  +         ++ +++++ ++     +y  +++
  gi|488599657|ref|YP_007906128.1| 241 KREKKVAVITADRGRGKTAILGILTPHLISRmqrvlkraiRIMVVAQTPQSV---QTYFRFLT 300
                                       23338999*************9888877777677776655555555555555...55555444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                            AAA_16  28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipy...salaqal 76 
                                        ++G+ G+G s  vr l+r le d+   ++ +  +le+ i+y   +++ + l
  gi|488599657|ref|YP_007906128.1| 376 TIHGYEGSGRSFSVRFLKR-LEMDES--VEIQKISLEEPIRYakgDPIERWL 424
                                       49************99985.544421..444444444445554444444444 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00017      0.28      55      95 ..     545     590 ..     459     611 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                       T.....TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTES CS
                    Acetyltransf_1  55 d.....ekggvayieslaVspeyrgkGlGsaLlealeerareegik 95 
                                       +     +k++   + ++a +p+   +G+G+  l+ l+e+a  eg++
  gi|488599657|ref|YP_007906128.1| 545 HwdysfPKYKGLRVVRIATHPDVMDMGIGTFALKNLLEWAYTEGYD 590
                                       044778999999999*************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 4663.83
//
Query:       gi|488599658|ref|YP_007906129.1|  [L=103]
Description: hypothetical protein Asulf_00100 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-13   48.7   0.1    1.1e-12   48.5   0.1    1.0  1  ASCH         ASCH domain
  ------ inclusion threshold ------
      0.065   13.1   0.1       0.11   12.4   0.1    1.3  1  FTP          Fungalysin/Thermolysin Propeptide Motif
       0.12   12.9   0.0       0.17   12.4   0.0    1.3  1  Tox-REase-5  Restriction endonuclease fold toxin 5


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.1   1.8e-16   1.1e-12       2     106 ..       5     102 ..       4     103 .] 0.89

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.8e-16
                                       EE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCH CS
                              ASCH   2 sfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.slee 77 
                                        f+ ++++ i  G+K+ +ir + + + k   + +++ +l+++gr +g++++ kv vk+++e+ ee+a+++g+ s ee
  gi|488599658|ref|YP_007906129.1|   5 NFDSKFVEMIRLGRKKSTIRRGIKIFSK---G-SVV-NLTSDGRVFGKARIIKVIVKRLDEIGEEDAKLDGFeSREE 76 
                                       6888999*************77777555...4.444.4899************************************ PP

                                       HHHHHHCCHHHHHCCEEEEEEEEEEEEEE CS
                              ASCH  78 wrevheefyeeeseeyedelvvveefelv 106
                                       + ++++++y++  e   +e +++++fe++
  gi|488599658|ref|YP_007906129.1|  77 LFSELKRIYGSIDE---KEFFTIIHFEVI 102
                                       ***********876...9*********97 PP

>> FTP  Fungalysin/Thermolysin Propeptide Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.8e-05      0.11      25      45 ..      25      45 ..      24      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                                      TTEEEEEEEEEEEE-TTSSEE CS
                               FTP 25 nGipVfggdlvvhvdkdGkvt 45
                                      +Gi++f    vv++++dG+v+
  gi|488599658|ref|YP_007906129.1| 25 RGIKIFSKGSVVNLTSDGRVF 45
                                      5*******************8 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 ?   12.4   0.0   2.8e-05      0.17      27      50 ..      64      87 ..      46     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                       Tox-REase-5 27 ldvdfDGfksaeclllEaKagYdq 50
                                       d + DGf+s e+l+ E K  Y++
  gi|488599658|ref|YP_007906129.1| 64 EDAKLDGFESREELFSELKRIYGS 87
                                      46899***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 706.63
//
Query:       gi|488599659|ref|YP_007906130.1|  [L=377]
Description: radical SAM protein, BA_1875 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-17   63.8   0.1    2.5e-16   60.5   0.1    2.1  2  Radical_SAM  Radical SAM superfamily
    4.3e-08   33.5   0.0    7.6e-08   32.7   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    8.4e-07   29.1   0.0    1.7e-06   28.2   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
    2.1e-05   25.0   0.0    6.3e-05   23.4   0.0    1.9  1  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
      0.094   12.8   0.1       0.17   12.0   0.1    1.3  1  DUF2243      Predicted membrane protein (DUF2243)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.1   7.1e-20   2.5e-16       3     150 ..      16     158 ..      14     173 .. 0.87
   2 ?    1.1   0.0      0.13   4.7e+02     119     150 ..     218     249 ..     206     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 7.1e-20
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlaklavpgi 78 
                                        tr+C l+C++C  +   +r +++ +l  ee+++ + ++  ++k    v+++gg+pl++ d  +++++ + +   g+
  gi|488599659|ref|YP_007906130.1|  16 LTRACKLACKHCRAKA--QRKRHPDELNFEEVKKVIGQITeFSKPYPLVVITGGDPLMREDVFDIVREGVSK---GL 87 
                                       79*************9..5*********************88888*************88776666666665...** PP

                                       EEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd.eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdriv 150
                                       ri++  +gt +  e  le+l+++gv rv+++++   +  v++ ++  ++tf   ++ le++r+  +  + ++++
  gi|488599659|ref|YP_007906130.1|  88 RIAIAFSGTDLAdESTLEELKRAGVARVAISIDGSEK--VHDSFRgIKGTFRMSMDILENARNISLS-TQINTT 158
                                       ************9********************9888..788888899***************9877.444433 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                                       HHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 119 klmnrghtfeevlealeklreagikrvvdriv 150
                                       k +n + +    l+ +e+ r++gik v+d+++
  gi|488599659|ref|YP_007906130.1| 218 KNLNVKSSAATHLRRIEIQRKKGIKYVSDFYF 249
                                       5566788889999************9999986 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.1e-11   7.6e-08      12     120 ..      17     124 ..       7     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.1e-11
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi..egltllGGEPllpenaeallelvkevkeekpek 86 
                                       +  C+l+Ck C   ++++ ++ +e ++e  +++i ++ + s+  + ++++GG+Pl+   +e++ ++v+e  ++++  
  gi|488599659|ref|YP_007906130.1|  17 TRACKLACKHCR-AKAQRKRHPDELNFEEVKKVIGQITEFSKpyPLVVITGGDPLM---REDVFDIVREGVSKGL-R 88 
                                       678*******99.66777777788887777888888877555569***********...9***************.5 PP

                           Fer4_12  87 diwlytgytleelskk..ekeellkeidvlvdGkfe 120
                                         ++++g+ l + s+    k+  ++ + + +dG  +
  gi|488599659|ref|YP_007906130.1|  89 IAIAFSGTDLADESTLeeLKRAGVARVAISIDGSEK 124
                                       899*****9998874444556667777778887655 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   4.7e-10   1.7e-06       6      92 ..      18      98 ..      13     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.7e-10
                           Fer4_14  6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84
                                        C+l+Ck C  k++ k +  + + ee+ + i + ++ s+     +v+tGG+PL+    ++++++v++ + ++  + i 
  gi|488599659|ref|YP_007906130.1| 18 RACKLACKHCRAKAQRKRHPDELNFEEVKKVIGQITEFSKP-YPLVVITGGDPLMR---EDVFDIVREGVSKGLRIAIA 92
                                      57*********999888877777766666444432333333.345*********55...88889999999888555554 PP

                           Fer4_14 85 letngtle 92
                                      +  +gt  
  gi|488599659|ref|YP_007906130.1| 93 F--SGTDL 98
                                      4..44433 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.7e-08   6.3e-05       4      67 ..     288     344 ..     286     345 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.7e-08
                             SPASM   4 psrslfInsdGdVvpCcvdkktyveelklGnireesleeIw.nseeyqefrkskkfplielCrnC 67 
                                       ++ ++fI++ G+V+p  +       +++ Gnire+sl+eI+ +se ++++++   + l   C +C
  gi|488599659|ref|YP_007906130.1| 288 GRGMFFISHIGEVYPSGFL------PINAGNIREMSLKEIYcKSEIFTQLKN--PDLLKGKCGRC 344
                                       56799***********333......6***************45557888882..33345569999 PP

>> DUF2243  Predicted membrane protein (DUF2243)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.8e-05      0.17      97     124 ..     158     188 ..     153     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.8e-05
                           DUF2243  97 gvvdHkllgiHqvre...geelllydlvfla 124
                                       +v +H+++++H++     ++e++l+d+ f++
  gi|488599659|ref|YP_007906130.1| 158 TVTNHNIMHLHEIARiaiENEVTLWDVFFVV 188
                                       6889*********999999999*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2388.99
//
Query:       gi|488599660|ref|YP_007906131.1|  [L=312]
Description: tRNA pseudouridine synthase B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-26   92.6   0.4    4.1e-22   79.2   0.4    3.2  1  TruB_N           TruB family pseudouridylate synthase (N term
    1.3e-24   86.1   0.0    2.2e-24   85.4   0.0    1.4  1  TruB_C_2         tRNA pseudouridylate synthase B C-terminal d
    5.1e-16   58.4   4.6    6.6e-16   58.0   2.8    2.0  2  PUA              PUA domain
    2.9e-13   49.7   0.0    1.2e-11   44.4   0.1    2.4  2  DKCLD            DKCLD (NUC011) domain
    3.5e-06   27.2   0.3      2e-05   24.7   0.0    2.4  3  UPF0113          UPF0113 PUA domain
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.51   10.4   0.0    2.1  2  Phage_terminase  Phage terminase small subunit


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.4   1.4e-25   4.1e-22       1     149 []      40     153 ..      40     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.4e-25
                                       HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHH CS
                            TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekl 77 
                                       +++l++++ Gh+GtLDp++tGvL+v +++aTkl+++l+++ KeY+a +rl+ + +                  e+++
  gi|488599660|ref|YP_007906131.1|  40 RKILEVSRTGHAGTLDPKVTGVLPVFIENATKLVRFLQTSGKEYVALMRLHGDAS------------------EKRI 98 
                                       899***********************************************86443..................3469 PP

                                       HHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                            TruB_N  78 eevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                       +e+++ f+G+i+q+pp  SAvk                    r  +iye e+lev+ ++v ++v+ ++GtYi
  gi|488599660|ref|YP_007906131.1|  99 REAFNLFKGKIYQRPPLKSAVK-----------------KVLRIREIYESEILEVDGRDVLFRVRTEAGTYI 153
                                       99********************.................457899**************************8 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   7.4e-28   2.2e-24       1      63 [.     154     219 ..     154     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 7.4e-28
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H..HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee..LdrlllPlesal 63 
                                       R+Lc+DiGe++g+gAh++eLRRt++g fde+ ++tl+dL da+ +yke  + e  L+++++P+e a+
  gi|488599660|ref|YP_007906131.1| 154 RKLCTDIGEVIGTGAHMQELRRTKTGLFDENSAFTLHDLLDAYVIYKEtgE-EryLREIIKPMEIAV 219
                                       9***********************************************854.35**********998 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.53   1.6e+03       8      30 ..     117     139 ..     116     170 .. 0.69
   2 !   58.0   2.8   2.2e-19   6.6e-16       1      74 []     223     296 ..     223     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.53
                                       HHHHHHHTT-EEEGGGEEEEETT CS
                               PUA   8 gAvkallsgasLlapGvvevegd 30 
                                       +Avk++l+ + ++   ++ev+g 
  gi|488599660|ref|YP_007906131.1| 117 SAVKKVLRIREIYESEILEVDGR 139
                                       78889988888888888888874 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 2.2e-19
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                       ++vvv+d Av a+++ga+L a G+  +e+ +++gd Vai++ ++e+va+G+a+ +se +  +k g+ ve+erv+
  gi|488599660|ref|YP_007906131.1| 223 KKVVVKDTAVSAICYGADLSARGICYIEKGIKAGDDVAIFTLKNEVVAIGKALADSERMLNAKSGIMVETERVI 296
                                       58*********************************************************************985 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.1   4.2e-15   1.2e-11      26      58 .]       4      36 ..       2      36 .. 0.96
   2 ?    2.5   0.0     0.052   1.6e+02       5      42 ..     216     252 ..     213     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.2e-15
                                      SS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                             DKCLD 26 aGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                                      +G  P+k pi++yi+ Gv+ +DKPs+P+SHEVV
  gi|488599660|ref|YP_007906131.1|  4 MGAIPTKDPIQDYIRNGVVCIDKPSGPTSHEVV 36
                                      6999****************************9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.052
                                       X....XXX-EEESS-----TTSS--GGG--HHHHHHTE CS
                             DKCLD   5 pllLknydkllvrtehytplpaGssPlkRpieeyikyG 42 
                                       ++  k+++k++v+ ++   + +G +   R i  yi+ G
  gi|488599660|ref|YP_007906131.1| 216 EIAVKDMKKVVVKDTAVSAICYGADLSARGIC-YIEKG 252
                                       677899*****************998888873.66665 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   3.9e+03       8      27 ..     118     137 ..     116     148 .. 0.79
   2 ?   -1.7   0.0       1.2   3.5e+03      59      76 .]     138     155 ..     128     155 .. 0.72
   3 !   24.7   0.0   6.8e-09     2e-05       1      65 [.     224     291 ..     224     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                           UPF0113   8 aeklFLYGrdvlkesilkit 27 
                                       a k++L  r++++++il+++
  gi|488599660|ref|YP_007906131.1| 118 AVKKVLRIREIYESEILEVD 137
                                       66777777999999999886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                           UPF0113  59 pgkivvknlaDiGeYlRr 76 
                                        ++++++  +  G+Y+R+
  gi|488599660|ref|YP_007906131.1| 138 GRDVLFRVRTEAGTYIRK 155
                                       556666777788999996 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 6.8e-09
                           UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.aspgkivvk 65 
                                       kvvvk  a + + YG d+   +i +i++++k ++ v+++  ++e+++iGk+  d+      +++i+v+
  gi|488599660|ref|YP_007906131.1| 224 KVVVKDTAVSAICYGADLSARGICYIEKGIKAGDDVAIFTLKNEVVAIGKALADSerMlNAKSGIMVE 291
                                       79*************************************************99998533455556655 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         3   8.9e+03       9      32 ..     139     164 ..     138     166 .. 0.63
   2 ?   10.4   0.0   0.00017      0.51      12      46 ..     195     229 ..     192     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3
                   Phage_terminase   9 RDkAyelykEsggt..lklkdIAkvL 32 
                                       RD  +++  E g    +++ dI +v+
  gi|488599660|ref|YP_007906131.1| 139 RDVLFRVRTEAGTYirKLCTDIGEVI 164
                                       66667777777764114688888776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00017
                   Phage_terminase  12 AyelykEsggtlklkdIAkvLdvsestvrkWKakD 46 
                                       Ay +ykE g    l++I k ++++ + ++k  +kD
  gi|488599660|ref|YP_007906131.1| 195 AYVIYKETGEERYLREIIKPMEIAVKDMKKVVVKD 229
                                       9************************9999988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2085.57
//
Query:       gi|488599661|ref|YP_007906132.1|  [L=187]
Description: cytidylate kinase, putative [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   79.7   0.7    9.3e-20   71.5   0.7    2.1  1  Cytidylate_kin2  Cytidylate kinase-like family
    2.9e-16   60.2   0.0    9.6e-16   58.5   0.0    1.7  2  AAA_18           AAA domain
    8.1e-13   48.6   3.0    1.6e-05   24.8   0.9    2.2  2  Cytidylate_kin   Cytidylate kinase
      3e-11   43.9   0.1    5.6e-11   43.0   0.1    1.4  1  AAA_17           AAA domain
    6.4e-05   23.1   0.1    7.5e-05   22.9   0.1    1.1  1  SKI              Shikimate kinase
    0.00016   22.0   0.1     0.0003   21.1   0.0    1.6  1  AAA_28           AAA domain
    0.00062   19.9   0.1     0.0026   17.9   0.0    1.9  2  ADK              Adenylate kinase
      0.007   15.7   0.3      0.011   15.1   0.3    1.3  1  DUF2226          Uncharacterized protein conserved in archaea
  ------ inclusion threshold ------
      0.031   14.7   0.0      0.061   13.7   0.0    1.6  1  AAA              ATPase family associated with various cellul
       0.05   13.3   0.0      0.096   12.4   0.0    1.5  1  CoaE             Dephospho-CoA kinase
      0.058   13.1   0.4       0.59    9.8   0.0    2.1  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.068   13.3   0.2       0.34   11.1   0.1    2.1  2  DNA_pol_B_thumb  DNA polymerase beta thumb
        0.1   12.8   0.1       0.54   10.4   0.1    2.0  1  AAA_33           AAA domain
       0.19   11.8   0.8       0.81    9.8   0.1    2.1  2  DUF3195          Protein of unknown function (DUF3195)


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.7   7.3e-23   9.3e-20       2     178 ..       5     157 ..       4     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 7.3e-23
                   Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekl 77 
                                       ITIs+  G+g +ti++ L+e+L+lp+++  ++++++a+e g++ +e+ ++ ++++    +                 
  gi|488599661|ref|YP_007906132.1|   5 ITISGAPGTGTSTIAKLLSERLNLPVISAgMMFRKLARERGMTLDEFGRYADSNP---EI----------------- 61 
                                       9****************************999***************99999444...22................. PP

                   Cytidylate_kin2  78 ddelfeaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrra 154
                                       d  + ++q+   +e+++ +s+++ GR +  +++d +  l+v+l a +++r +r+a+re+   e ar +  ++++ + 
  gi|488599661|ref|YP_007906132.1|  62 DMLIDRTQK---EEAVKRDSCIVEGRLSGWMVEDAD--LKVLLFAKDDVRFQRIASREKKPFEVARDETLRREQIEM 133
                                       222222332...2344566***************77..*************************************** PP

                   Cytidylate_kin2 155 kyykkytgqdwgdaenYdlvlnts 178
                                       ++y ky+g d+ d + Yd+v+n++
  gi|488599661|ref|YP_007906132.1| 134 ERYLKYYGIDIRDYSIYDVVINSA 157
                                       **********************96 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   7.5e-19   9.6e-16       1     122 [.       5     124 ..       5     137 .. 0.81
   2 ?   -0.7   0.0       1.5   1.9e+03      91     113 ..     161     183 ..     144     187 .] 0.72

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 7.5e-19
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I ++G+pG+G +t+ak Ls+rl++     g   r++a+e+g+ l+++          ++d+   + ++ +e +    
  gi|488599661|ref|YP_007906132.1|   5 ITISGAPGTGTSTIAKLLSERLNLpvisaGMMFRKLARERGMTLDEFGR--YADSNPEIDM--LIDRTQKEEA---V 74 
                                       89********************99*************************..3333333333..3344444432...4 PP

                            AAA_18  73 egknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik..e 122
                                       + ++++++g+l+ +  e+a d+k v L a+++++++R++ R++++ + +  e
  gi|488599661|ref|YP_007906132.1|  75 KRDSCIVEGRLSGWMVEDA-DLK-VLLFAKDDVRFQRIASREKKPFEVArdE 124
                                       679************9977.578.9*****************9998877542 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                            AAA_18  91 akdikkvvLtaspeelleRlekR 113
                                       ak+i+ ++Lta +++l  R +++
  gi|488599661|ref|YP_007906132.1| 161 AKEIVEIILTALDQKLNARESNQ 183
                                       45555599999999988886655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.2e-08   2.8e-05       1      37 [.       5      41 ..       5      44 .. 0.96
   2 !   24.8   0.9   1.2e-08   1.6e-05      96     209 ..      59     172 ..      47     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.2e-08
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                      i+i G  g+G s++a++l+e+l+l ++++g+++R la
  gi|488599661|ref|YP_007906132.1|  5 ITISGAPGTGTSTIAKLLSERLNLPVISAGMMFRKLA 41
                                      89********************************987 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHHHHHH.TT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHH CS
                    Cytidylate_kin  96 pavRailvkklr.elvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRD 171
                                       p++   + + ++ e+vk+++++veGR ++  ++ da+lK+ l A+ ++R +R ++  ++k     +e    e  +R 
  gi|488599661|ref|YP_007906132.1|  59 PEIDMLIDRTQKeEAVKRDSCIVEGR-LSGWMVEDADLKVLLFAKDDVRFQRIASR-EKKP----FEVARDETLRRE 129
                                       56666666666525788*********.5566779****************987666.5554....555555666788 PP

                                       HHHHCT..SSS-S---TT-...EEEETTTS-HHHHHHHHHHHH CS
                    Cytidylate_kin 172 klDker..evgpLklaeda...liidtskltieevvekileli 209
                                       +  +er  +++++ + +     ++i++ + +++e+ve il+++
  gi|488599661|ref|YP_007906132.1| 130 QIEMERylKYYGIDIRDYSiydVVINSANFGAKEIVEIILTAL 172
                                       8888773334555554433111679999999999999998765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1   4.4e-14   5.6e-11       2     135 ..       9     126 ..       8     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.4e-14
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea.kkkgvlvd 77 
                                       G PG G +t+++ l e+++++++saG ++r+ a+++g+  + de+ +   +  + ++ ++ ++ +eea k++  +v+
  gi|488599661|ref|YP_007906132.1|   9 GAPGTGTSTIAKLLSERLNLPVISAGMMFRKLARERGM--TLDEFGRYADSNPE-IDMLIDRTQKEEAvKRDSCIVE 82 
                                       9************************************8..78888776644444.5555555556666777889999 PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHH CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesi 135
                                       g  +         g   +++e++  d+ +ll a++++ ++r ++++++  +    e++
  gi|488599661|ref|YP_007906132.1|  83 GRLS---------G---WMVEDA--DLKVLLFAKDDVRFQRIASREKKPFEVARDETL 126
                                       9985.........3...666788..888899999999999999998887777666666 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   5.9e-08   7.5e-05       1     135 [.      11     143 ..      11     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.9e-08
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlsee 77 
                                       +G+G st++kll+++l+l++i +  ++ k ++ +    ++e g  ++ + E ++l + +++e++V     ++v+ + 
  gi|488599661|ref|YP_007906132.1|  11 PGTGTSTIAKLLSERLNLPVISAGMMFRKLAR-ERGMTLDEFGRYADSNPEIDMLIDRTQKEEAVKRD-SCIVEGRL 85 
                                       69*************************99999.788999**********************8777655.88999999 PP

                                       HHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSS CS
                               SKI  78 nrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaa 135
                                       + +++++  + ++L ++ ++ ++r+++++++P+  ++++ + ++e+++ er   y  ++
  gi|488599661|ref|YP_007906132.1|  86 SGWMVEDADLKVLLFAKDDVRFQRIASREKKPFEVARDE-TLRREQIEmERYLKYYGID 143
                                       *********************************999999.6667777767877776653 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.3e-07    0.0003       1      39 [.       4      45 ..       4     100 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.3e-07
                            AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileekl 39
                                      ki i+G+++tG++t+++ L++r + pv+    ++r++ +e++
  gi|488599661|ref|YP_007906132.1|  4 KITISGAPGTGTSTIAKLLSERlNLPVIsaGMMFRKLARERG 45
                                      799******************999999943334444444443 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     2e-06    0.0026       1      36 [.       7      42 ..       7      50 .. 0.90
   2 ?    0.3   0.0      0.52   6.7e+02      73     102 ..      42      71 ..      39     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevk 36
                                      + GaPg+G  t a+ l ++++l+ +s+G ++R+  +
  gi|488599661|ref|YP_007906132.1|  7 ISGAPGTGTSTIAKLLSERLNLPVISAGMMFRKLAR 42
                                      57******************************8665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.52
                                       TTTEEEEESB-SSHHHHHHHHHHHHHHTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  73 kkkgfllDGfPRtveqaealeelleeekvk 102
                                       +++g  lD f R  + + +++ l+++++++
  gi|488599661|ref|YP_007906132.1|  42 RERGMTLDEFGRYADSNPEIDMLIDRTQKE 71 
                                       567788999999999999998887766544 PP

>> DUF2226  Uncharacterized protein conserved in archaea (DUF2226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   8.4e-06     0.011     110     220 ..      48     172 ..      33     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.4e-06
                           DUF2226 110 isekrdiveklleikleieldnliean.kgyiiykgqipiaaayEcdleel.lgkdayekleevlkepet....... 177
                                       ++e     +  +ei++ i+  + +ea  ++  i +g ++   ++++dl++l ++kd++ +     +e          
  gi|488599661|ref|YP_007906132.1|  48 LDEFGRYADSNPEIDMLIDRTQKEEAVkRDSCIVEGRLSGWMVEDADLKVLlFAKDDVRFQRIASREKKPfevarde 124
                                       555555666778899999888888886257789999999999******99636899887665544444445567777 PP

                           DUF2226 178 ......vsReelLkKlGikepdeesietiledvfepsdeelaeddleel 220
                                             ++ e  Lk +Gi+  d++  + +++ +  +++e + e  l  l
  gi|488599661|ref|YP_007906132.1| 125 tlrreqIEMERYLKYYGIDIRDYSIYDVVINSANFGAKEIV-EIILTAL 172
                                       766666777777****************9998877666655.5555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.8e-05     0.061       3      46 ..       7      48 ..       5      81 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekki 46
                                      ++G pGtG +++ak + + l+ ++++  +  ++ k+  e+ + +
  gi|488599661|ref|YP_007906132.1|  7 ISGAPGTGTSTIAKLLSERLNLPVIS--AGMMFRKLARERGMTL 48
                                      79*****************9887754..3334445444443333 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.5e-05     0.096       3      48 ..       5      51 ..       3      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.5e-05
                                      EEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHHH CS
                              CoaE  3 vgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkki 48
                                      + ++G  ++G st+a+l+++ l++p++ a ++ r++  +   +l++ 
  gi|488599661|ref|YP_007906132.1|  5 ITISGAPGTGTSTIAKLLSErLNLPVISAGMMFRKLARERGMTLDEF 51
                                      7899****************9*************9999888888765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00046      0.59       2      45 ..       5      58 ..       4      80 .. 0.67
   2 ?    1.7   0.2      0.15   1.9e+02     128     152 ..      91     115 ..      64     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00046
                               PRK  2 IgvagsSGaGkttvarklekifgrekvkaaei...........egdsflrldrae 45
                                      I ++g+ G G++t+a+ l ++++   +  a++           ++d+f r+   +
  gi|488599661|ref|YP_007906132.1|  5 ITISGAPGTGTSTIAKLLSERLNLPVIS-AGMmfrklarergmTLDEFGRYADSN 58
                                      89*********************54444.44435555555555555555555555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                               PRK 128 elldlkiyvdisidlelarklqRDi 152
                                       e +dlk+ + +++d+++ r  +R +
  gi|488599661|ref|YP_007906132.1|  91 EDADLKVLLFAKDDVRFQRIASREK 115
                                       4589***********9998777765 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 ?   11.1   0.1   0.00027      0.34      16      34 ..      38      65 ..      35     120 .. 0.75
   2 ?   -0.1   0.0      0.84   1.1e+03      13      34 ..     131     158 ..     130     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                      HHHHHCTTEEEETTEEE........... CS
                   DNA_pol_B_thumb 16 RrlakkkglkLnssglrd.........e 34
                                      R+la+++g++L++ g +           
  gi|488599661|ref|YP_007906132.1| 38 RKLARERGMTLDEFGRYAdsnpeidmlI 65
                                      9****************54333333220 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.84
                                       HHHHHHHHCTTEEEETTEEE........ CS
                   DNA_pol_B_thumb  13 rdlRrlakkkglkLnssglrd......e 34 
                                       +++ r+ k  g  + ++ ++d      +
  gi|488599661|ref|YP_007906132.1| 131 IEMERYLKYYGIDIRDYSIYDvvinsaN 158
                                       6789999999999999999975444430 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00043      0.54       4      75 ..       7      81 ..       5     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                            AAA_33  4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldr..lyqilnelarkalsagrn.vil 75
                                      + G+pG+G st a+ l ++l   ++s   ++r+l+ +   ++ +  r +d+   +++l ++ +k  + +r+ +i+
  gi|488599661|ref|YP_007906132.1|  7 ISGAPGTGTSTIAKLLSERLNLPVISAGMMFRKLARERGMTLDEFGRYADSnpEIDMLIDRTQKEEAVKRDsCIV 81
                                      57**************************99999999888888755553333234445555555555555553554 PP

>> DUF3195  Protein of unknown function (DUF3195)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.81     1e+03       8      19 ..      68      79 ..      62      82 .. 0.84
   2 ?    9.8   0.1   0.00063      0.81      43      76 ..     124     157 ..     105     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.81
                                      CCGHHHHHCHHH CS
                           DUF3195  8 gkkerivardlc 19
                                      ++ke++v rd c
  gi|488599661|ref|YP_007906132.1| 68 TQKEEAVKRDSC 79
                                      589*******99 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00063
                                       EE-.HHHHHHHHTSHHHHTTECEEEEESEE..ES CS
                           DUF3195  43 etsrletlekclslkyfkklvkrieiyekvvrst 76 
                                       et r+e++e+   lky+   ++   iy+ v+ s+
  gi|488599661|ref|YP_007906132.1| 124 ETLRREQIEMERYLKYYGIDIRDYSIYDVVINSA 157
                                       6789*************************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1229.14
//
Query:       gi|488599662|ref|YP_007906133.1|  [L=194]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-43  148.1  13.3    3.1e-43  147.4  13.3    1.3  1  EMC3_TMCO1   Integral membrane protein EMC3/TMCO1-like
     0.0004   20.8  11.6      0.017   15.5  11.6    2.4  1  DUF4199      Protein of unknown function (DUF4199)
  ------ inclusion threshold ------
      0.023   14.1   2.7      0.032   13.6   2.7    1.1  1  Helo_like_N  Fungal N-terminal domain of STAND proteins
      0.031   14.4   0.7      0.049   13.8   0.7    1.3  1  OSTbeta      Organic solute transporter subunit beta protein
      0.065   12.9   0.8       0.12   12.1   0.8    1.4  1  BAG6         BCL2-associated athanogene 6
        0.1   11.9   3.3       0.14   11.4   3.3    1.1  1  DUF3450      Protein of unknown function (DUF3450)
       0.13   12.4   2.4       0.21   11.7   2.4    1.2  1  Cep57_CLD_2  Centrosome localisation domain of PPC89
       0.88    9.4  12.6        1.9    8.4  12.6    1.7  1  60KD_IMP     60Kd inner membrane protein


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 !  147.4  13.3   1.4e-46   3.1e-43       3     167 ..      38     193 ..      36     194 .] 0.94

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 1.4e-46
                        EMC3_TMCO1   3 vldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqee 79 
                                       +ldpl +   ++Pi+ vil+++++t+ +s+++qk+++d ++++++qk+++++qk++ e++k+++k+klk+le+++ee
  gi|488599662|ref|YP_007906133.1|  38 FLDPLAK---IMPIYEVILILSVVTASYSTIIQKFTVDTNRLKEMQKKMAKFQKEYMEAMKQDNKFKLKQLESEREE 111
                                       6899999...******************************************************************* PP

                        EMC3_TMCO1  80 lmedqsemmmdqmkpmivtmipqiliffwlnsffs.gfvvaklpfpltgrfksllqrglesldvrfvssiswYflcs 155
                                       +++ qsemm +qmkpm++tm+++++if+wl+++++ + ++ ++pf  + +++      + + ++ f+++i+wY+lcs
  gi|488599662|ref|YP_007906133.1| 112 INKIQSEMMGMQMKPMFYTMVVTLPIFMWLYAKVKvENILINVPFA-AEKIH------IGDPVLFFPWWIFWYLLCS 181
                                       **********************************976677777775.55666......48***************** PP

                        EMC3_TMCO1 156 fglsqiirklLg 167
                                       + + q+irk+L+
  gi|488599662|ref|YP_007906133.1| 182 IVVGQVIRKVLR 193
                                       **********96 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  11.6   7.8e-06     0.017      38     168 .]      10     190 ..       3     190 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.8e-06
                           DUF4199  38 llllllvpflvylalk.kyrkknlgG.fisfgqafgfgflislvagllsavfq...yiyfnfi.dpd....fienyi 104
                                       +l+l + +f++ +++  ++r++  g+ + +f   +   + i+ v+ +ls+v+     i+ +f  d +    + ++++
  gi|488599662|ref|YP_007906133.1|  10 FLSLGI-VFFIGIFISpEFRREL-GNlVSPFLDPLAKIMPIYEVILILSVVTAsysTIIQKFTvDTNrlkeMQKKMA 84 
                                       444455.5555555555999998.44455565555555554433333333332222555555555556666999*** PP

                           DUF4199 105 aeilekleeakeesae.eenaemseeeike...ale..sls.................................... 139
                                       + ++e++e++k++++   ++ e+++eei++   +++  +++                                    
  gi|488599662|ref|YP_007906133.1|  85 KFQKEYMEAMKQDNKFkLKQLESEREEINKiqsEMMgmQMKpmfytmvvtlpifmwlyakvkvenilinvpfaaeki 161
                                       ****************************6643322223333555555555555555555555555555554444433 PP

                           DUF4199 140 piiv.alqsflgnliiGlilsliiAlilkk 168
                                         i   + +f + ++++l+ s++++ +++k
  gi|488599662|ref|YP_007906133.1| 162 H-IGdPVLFFPWWIFWYLLCSIVVGQVIRK 190
                                       2.3337788888888888888888888776 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.7   1.4e-05     0.032     147     203 ..      58     114 ..      50     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                       Helo_like_N 147 vleeykeliedttsdLeehLedideklealtek.seeaseedeaelqrlkeEresteq 203
                                       v  +y+++i++ t d  ++L+++++k+++++++  e+++++++ +l++l+ Ere++++
  gi|488599662|ref|YP_007906133.1|  58 VTASYSTIIQKFTVDT-NRLKEMQKKMAKFQKEyMEAMKQDNKFKLKQLESEREEINK 114
                                       5678***********5.79***********96615566778889**********9875 PP

>> OSTbeta  Organic solute transporter subunit beta protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   2.2e-05     0.049      38     110 ..      52     119 ..      47     131 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                           OSTbeta  38 iLvLsavvvvisvvLLarsiqanRnrKiqpqeketpealyleeakakennslnilretllsekpklaevevel 110
                                       iL+Ls+v +  s+++ +  + +nR + +q   k++++ + +    +k++n+  +l+  l se +++ +++ e+
  gi|488599662|ref|YP_007906133.1|  52 ILILSVVTASYSTIIQKFTVDTNRLKEMQ---KKMAKFQKEYMEAMKQDNKF-KLK-QLESEREEINKIQSEM 119
                                       9************************9999...44444333333334555555.333.3456666666666555 PP

>> BAG6  BCL2-associated athanogene 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   5.2e-05      0.12       7      48 ..      75     116 ..      73     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
                              BAG6   7 elrevqerlePfleryieileedptfeesdntegreeaqril 48 
                                       +l+e+q++++ f + y+e +++d +f+ ++ +++ree ++i 
  gi|488599662|ref|YP_007906133.1|  75 RLKEMQKKMAKFQKEYMEAMKQDNKFKLKQLESEREEINKIQ 116
                                       899***************************999999988775 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.3   6.5e-05      0.14      56     110 ..      77     136 ..      64     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.5e-05
                           DUF3450  56 lkeeleslevyneqlerlvasqeqeiasleeqieeieeie.....relvpllekmidrLe 110
                                        + +++ +++++e++e++ ++ + ++++le + eei++i+     ++++p++++m+ +L 
  gi|488599662|ref|YP_007906133.1|  77 KEMQKKMAKFQKEYMEAMKQDNKFKLKQLESEREEINKIQsemmgMQMKPMFYTMVVTLP 136
                                       4557888899999***********************999832222467899999999886 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.4   9.2e-05      0.21      10      53 ..      74     118 ..      72     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.2e-05
                       Cep57_CLD_2  10 nrLdsltrklqvheeel.krLnkERdsalrqLgvAyeelneLkae 53 
                                       nrL+ ++ k ++ + e+ +++ +++   l+qL + +ee+n+ ++e
  gi|488599662|ref|YP_007906133.1|  74 NRLKEMQKKMAKFQKEYmEAMKQDNKFKLKQLESEREEINKIQSE 118
                                       9*************665167888*******************999 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  12.6   0.00085       1.9       5      89 ..      51     147 ..      47     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00085
                          60KD_IMP   5 IilltiivrlillpltlkqlkssakmqelqPelkeiqekyk...........kdkqklqqemmklYkkegvnpla.G 69 
                                       +il+  +v +    + +k +  +++++e+q+++++ q+ y            k+ +   +e+ k++++     ++  
  gi|488599662|ref|YP_007906133.1|  51 VILILSVVTASYSTIIQKFTVDTNRLKEMQKKMAKFQKEYMeamkqdnkfklKQLESEREEINKIQSEMMGMQMKpM 127
                                       56666667777777778888888999999999999999998888765444332225566777777777543333324 PP

                          60KD_IMP  70 clplLiqlpifialyrvlrs 89 
                                       + +++++lpif+ ly  ++ 
  gi|488599662|ref|YP_007906133.1| 128 FYTMVVTLPIFMWLYAKVKV 147
                                       77899999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2890  (0.161191); expected 358.6 (0.02)
Passed bias filter:                     1094  (0.0610185); expected 358.6 (0.02)
Passed Vit filter:                       148  (0.00825478); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1259.50
//
Query:       gi|488599663|ref|YP_007906134.1|  [L=491]
Description: protein translocase subunit secY/sec61 alpha [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-70  238.3  23.6    1.4e-70  238.0  23.6    1.1  1  SecY             SecY translocase
    1.3e-10   40.9   0.8    1.3e-10   40.9   0.8    2.3  2  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.0  23.6   1.6e-74   1.4e-70       1     306 []      74     469 ..      74     469 .. 0.81

  Alignments for each domain:
  == domain 1  score: 238.0 bits;  conditional E-value: 1.6e-74
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC......... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg......... 65 
                                       si++LGI+P++tasIilqLl ++      ++k +  ++++r++++ ++r+l++v+++v+a+  +++ g         
  gi|488599663|ref|YP_007906134.1|  74 SILTLGIGPIVTASIILQLLvGA-----GIIKlDLtNPDDRATYQDFQRFLVFVMIAVEAIPQIVG-Gllkpnldia 144
                                       89******************999.....4555444489************************7765.46889***** PP

                                       ........HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHC.CHSS..............-HHH CS
                              SecY  66 ........lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlp.kals..............glie 119
                                               ++ +li+lql++g+vl+++++E+++++GiG+G+sl+i+agi+++++ + ++              +   
  gi|488599663|ref|YP_007906134.1| 145 nalgvspgVISFLIFLQLFIGGVLIVYMDEVVSKWGIGSGVSLFILAGISQSIIiGLFNwispagemppgiipR--- 218
                                       ********889*******************************************66666777777666655440... PP

                                       H...........SS..........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S-EEEEETTCC CS
                              SecY 120 l...........ale........gilallllllvtllvillvvyveeaerripvqya.krgrkggqssylPlklnya 176
                                       +                       i   +l+l++t+++i+lvv+ e ++++ip+ ++  r    g+++++P+kl+y+
  gi|488599663|ref|YP_007906134.1| 219 WvwiaqnipadqL-LtlsgisylLINGGILALITTIIIIFLVVFAEGTRVEIPLAHQmVR----GARGRFPIKLVYT 290
                                       2444434444441.1344554442237899***************************788....9************ PP

                                       CSCHHHHHHHHHH..........................................HHHCCCCS.......TCCCS.. CS
                              SecY 177 gviPiIfasslla..........................................lpstiaqfl......lalls.. 203
                                       +v+P+If+++l+a                                          +ps     l      +   +  
  gi|488599663|ref|YP_007906134.1| 291 SVLPMIFVRALQAnivvmgmvlynngitflgeyvggtpinglmyllspvrgpqnwIPS-----LvkqnpyF---Adl 359
                                       *************887777777777777766666666666655555444433333233.....23443331...135 PP

                                       THHH...HHHHHHHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHH CS
                              SecY 204 psvl...yvvlyvlliif....Fayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalf 271
                                       p+++   ++v+ ++++i+    Fa+f+++++ +++k va+++ +sg++ipg+r + + ++++L+++++++t++G+++
  gi|488599663|ref|YP_007906134.1| 360 PDWFillHLVIDATILIVggilFAMFWAQTSgMDAKTVANQIARSGMQIPGFRkSPQILERFLNRYIPKVTILGGAL 436
                                       3333444888888887777888*******************************9999******************** PP

                                       HHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                              SecY 272 laliavlpdllgasligafggtslLivVgvaletv 306
                                       ++l+++++++lg+  ig+++gt+lL++V++a++++
  gi|488599663|ref|YP_007906134.1| 437 IGLLTLIANMLGT--IGNVSGTGLLLAVSIAYRLY 469
                                       *************..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 !   40.9   0.8   1.5e-14   1.3e-10       1      35 []      40      73 ..      40      73 .. 0.98
   2 ?   -1.2   0.1      0.21   1.9e+03      11      25 ..     190     204 ..     186     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.5e-14
                                      HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      +lY++ls iP++G+s ++s+D+f+++Ra fA+++G
  gi|488599663|ref|YP_007906134.1| 40 ILYFILSGIPVFGLS-PDSIDIFEHYRAFFAGASG 73
                                      89************9.****************998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                                       -TT--SSS-TCCHTT CS
                   Plug_translocon  11 LyGissssssDpfyw 25 
                                       L Gis+s ++ +f w
  gi|488599663|ref|YP_007906134.1| 190 LAGISQSIIIGLFNW 204
                                       89***9988888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2896.00
//
Query:       gi|488599664|ref|YP_007906135.1|  [L=172]
Description: LSU ribosomal protein L15P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-24   87.1   0.2    2.2e-24   86.6   0.2    1.3  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.2   1.2e-28   2.2e-24       1     128 []      26     171 ..      26     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.2e-28
                                       GGGGTSSTTTTTTTTT-S--.......S--.........---.GGG..---.......................... CS
                    Ribosomal_L27A   1 kGktgGrGhkGqkkrsgvkk.kpgfeGGqmplyrrlpkrGfk.nskfkkey.......................... 49 
                                       +G++gG G++G  k+++ k  k+g+e G++         Gf+  ++ k ey                          
  gi|488599664|ref|YP_007906135.1|  26 RGSRGGAGNAGILKHKYLKAiKEGYEIGKH---------GFRrPENIKLEYrlkkdlfetlrelkddgklddyayly 93 
                                       59***************9988999******.........99973344455577888899****************** PP

                                       ....EEEEHHHHHHTTTTGTTS.--...----EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHH CS
                    Ribosomal_L27A  50 ....kvvnlkdLdelideerle.la...deaeeidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAke 117
                                           +++n++dL+++i+++++  la   ++a  idl+++          g+ K+lg+g ++kk+kvk++++++kA+e
  gi|488599664|ref|YP_007906135.1|  94 lksrPELNVGDLNNIIEKLNELgLAekeEDAFSIDLSTI----------GYyKLLGRGIVNKKMKVKVEYATPKAVE 160
                                       *******************998777888899********..........999************************* PP

                                       HHHHTT-EEEE CS
                    Ribosomal_L27A 118 kIeaaGGkvel 128
                                       kIea+GG+v++
  gi|488599664|ref|YP_007906135.1| 161 KIEAVGGAVVT 171
                                       ********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1207.51
//
Query:       gi|488599665|ref|YP_007906136.1|  [L=153]
Description: LSU ribosomal protein L30P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   49.5   0.3      5e-13   48.7   0.3    1.4  1  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.095   13.2   0.1       0.33   11.4   0.0    1.9  2  CBS            CBS domain


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 !   48.7   0.3   5.5e-17     5e-13       1      51 []       4      54 ..       4      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 5.5e-17
                                      EEEEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhlV 51
                                      ++V+r r+  ++   +r+tL++L+L+k   ++ v++n  ++ GmL+kVk++V
  gi|488599665|ref|YP_007906136.1|  4 YAVVRLRGRHDIRRSIRDTLKMLRLHKKYhCVIVPEN-ETYIGMLRKVKDYV 54
                                      57***************************55555555.99999********9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.7e-05      0.33      17      46 ..      18      47 ..      14      49 .. 0.90
   2 ?   -3.4   0.0       1.6   1.4e+04      16      25 ..      59      68 ..      53      74 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                                      BHHHHHHHHH.HHTSSEEEEEETTTBEEEEE CS
                               CBS 17 tleealelmr.ekgvsrlPVVdedgklvGiv 46
                                      ++++ l+++r +k+++++ +V+e++ ++G++
  gi|488599665|ref|YP_007906136.1| 18 SIRDTLKMLRlHKKYHCV-IVPENETYIGML 47
                                      79999****98888****.***9999***97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.6
                                      SBHHHHHHHH CS
                               CBS 16 ttleealelm 25
                                       t e +++l+
  gi|488599665|ref|YP_007906136.1| 59 ITAESLARLI 68
                                      3444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1242.04
//
Query:       gi|488599666|ref|YP_007906137.1|  [L=199]
Description: SSU ribosomal protein S5P [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-26   90.0   0.1    1.7e-25   88.7   0.1    1.7  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
      7e-23   79.9   0.1    1.4e-22   78.9   0.1    1.5  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.1   1.9e-29   1.7e-25       1      65 []      47     111 ..      47     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.9e-29
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                       l+++vl+i+ vq++t++Grrtsf+++++vG+++G++G+G gka++va Ai+kAi++Ak+n+++v+
  gi|488599666|ref|YP_007906137.1|  47 LEDEVLEINLVQRMTDSGRRTSFRVTAIVGNRDGYIGIGSGKASQVAPAIQKAIKDAKLNIFKVN 111
                                       799************************************************************96 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 !   78.9   0.1   1.6e-26   1.4e-22       1      63 [.     132     195 ..     132     199 .] 0.96

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.6e-26
                                       EEEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTT CS
                    Ribosomal_S5_C   1 tgkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklr 63 
                                       tg  g+v+v+l+p p+G Gi+ag+ +r+vlelaG++Dv++ ++g +r++in++kAt+eALk++ 
  gi|488599666|ref|YP_007906137.1| 132 TGSAGSVRVTLIPGPKGLGIVAGDMARKVLELAGVSDVWTFTRGnTRTTINFAKATYEALKQTM 195
                                       6899*********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1370.34
//
Query:       gi|488599667|ref|YP_007906138.1|  [L=187]
Description: LSU ribosomal protein L18P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-35  121.6   0.3    1.3e-23   83.8   0.2    2.2  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
    2.8e-09   37.4   0.0    3.5e-09   37.0   0.0    1.1  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.2   1.5e-27   1.3e-23       2      98 ..       6      95 ..       5      99 .. 0.95
   2 !   36.9   0.0   3.7e-13   3.3e-09     125     163 .]      95     133 ..      91     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.5e-27
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvglt 80
                                      r++v +rrrregkt+Y++r +l+        + k RlvVr+tnk +i+qi++ + egd+v+a+a+s el+k+g k   +
  gi|488599667|ref|YP_007906138.1|  6 RYRVPLRRRREGKTNYRKRLKLLL-------SRKPRLVVRITNKMVIAQIIEYSPEGDRVIAHADSYELQKLGWKGDAN 77
                                      9*********************98.......5688******************************************** PP

                     Ribosomal_L5e 81 nyaaaYatglllarrllk 98
                                      n  aaY+tgll+++++ k
  gi|488599667|ref|YP_007906138.1| 78 NTPAAYLTGLLIGKKAQK 95
                                      *************99765 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 3.7e-13
                     Ribosomal_L5e 125 ekrafkaiLdvGLartttgakvfgalkgavdgglsiphs 163
                                       + +  +a+Ld+GL++ t+g++vf++l+gav++gl++phs
  gi|488599667|ref|YP_007906138.1|  95 KAGVSEAVLDIGLKTPTRGSRVFAVLRGAVESGLEVPHS 133
                                       4566789*******************************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 !   37.0   0.0   3.9e-13   3.5e-09       8     115 ..      13     129 ..       7     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3.9e-13
                                       CHH..HHHHTTT--.TTSSS-EEEEEE-SS-EEEEEE-TT..T--EEEEECS-SCCCT..S-SSSCHHHHHHHHHHH CS
                    Ribosomal_L18p   8 krR..hkRirkkls.gtaerprlvvfrsnrhiyaQviddv..kgktlasastlekelk..lkstknkeaakkvgeli 77 
                                       +rR  ++  rk+l+   + +prlvv  +n+ + aQ+i+ +   ++++a+a++ e +    +  ++n+ aa   g li
  gi|488599667|ref|YP_007906138.1|  13 RRRegKTNYRKRLKlLLSRKPRLVVRITNKMVIAQIIEYSpeGDRVIAHADSYELQKLgwKGDANNTPAAYLTGLLI 89 
                                       44422455677777667889*****************96522789*******997654467788899999999**** PP

                                       HHHHCHHCHTC-EE--TTSS..S-CHHHHHHHHHHCTSSB CS
                    Ribosomal_L18p  78 AerakekgiekvvfDrggyk..YhGrvaalAdaaReaGlk 115
                                        ++a+++g++++v D g ++     rv a+  +a e Gl+
  gi|488599667|ref|YP_007906138.1|  90 GKKAQKAGVSEAVLDIGLKTptRGSRVFAVLRGAVESGLE 129
                                       ***************9865421456788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1215.80
//
Query:       gi|488599668|ref|YP_007906139.1|  [L=150]
Description: LSU ribosomal protein L19E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-56  189.8  14.0    2.7e-56  189.6  14.0    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
     0.0029   17.4   0.0     0.0039   17.0   0.0    1.0  1  Sin3a_C         C-terminal domain of Sin3a protein
  ------ inclusion threshold ------
      0.015   14.7   5.0      0.016   14.6   5.0    1.0  1  Nop53           Nop53 (60S ribosomal biogenesis)


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 !  189.6  14.0   4.6e-60   2.7e-56       1     143 [.       2     144 ..       2     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 4.6e-60
                                       -THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGG CS
                    Ribosomal_L19e   1 dlklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsG 77 
                                       +lk q+rla+svlk+G+n vwldp++le+iaeA t+e+ir+li++g+I++kp+kg srarar+r+ +++kgrrrg+G
  gi|488599668|ref|YP_007906139.1|   2 NLKIQRRLASSVLKCGENAVWLDPDQLESIAEASTKEEIRELIESGAIKRKPVKGVSRARARKRALQRKKGRRRGHG 78 
                                       5899************************************************************************* PP

                                       G--S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                    Ribosomal_L19e  78 krkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                       +rkG+k+aR+++k++Wi riRalRr Lkel+ ++k+d++tYr+lYrkakGgef+++a+L+ yie++
  gi|488599668|ref|YP_007906139.1|  79 RRKGRKGARMSRKRKWIIRIRALRRRLKELKVEGKLDTRTYRMLYRKAKGGEFRSVAHLELYIETN 144
                                       ***************************************************************976 PP

>> Sin3a_C  C-terminal domain of Sin3a protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.5e-07    0.0039     182     280 ..      22     125 ..      18     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.5e-07
                           Sin3a_C 182 lldkddetldddeveaeerwkeYves.YvlveptegvereklkkvfLkRnlkaerkeeekkeeeeqekaekee.... 253
                                       +ld d+ ++  ++ +++e+ +e +es  + ++p +gv+r++ +k  L+R   ++r + ++k ++ ++ + k++    
  gi|488599668|ref|YP_007906139.1|  22 WLDPDQLESIAEA-STKEEIRELIESgAIKRKPVKGVSRARARKRALQRKKGRRRGHGRRKGRKGARMSRKRKwiir 97 
                                       7888888888888.789*********55588********************88887777777665555545459*** PP

                           Sin3a_C 254 ..eaekeleveekleiriclnsyklvyvp 280
                                           + +l+ e k+e + ++++y+++y +
  gi|488599668|ref|YP_007906139.1|  98 irALRRRLK-ELKVEGKLDTRTYRMLYRK 125
                                       *74444444.678999***********86 PP

>> Nop53  Nop53 (60S ribosomal biogenesis)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   5.0   2.7e-06     0.016     257     336 ..      35     115 ..       5     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                             Nop53 257 eeeeeeeeeeesee.eeklnapvkkkpkrKTkaqRnkekrrkeeekeekeekkekkkeaqlerlkeikkevaekeke 332
                                       +++ee +e  es++ + k  + v+++  rK   qR+k +rr + +++ ++ +++ +k++ + r+++++++++e + e
  gi|488599668|ref|YP_007906139.1|  35 STKEEIRELIESGAiKRKPVKGVSRARARKRALQRKKGRRRGHGRRKGRKGARMSRKRKWIIRIRALRRRLKELKVE 111
                                       222333455566667455555667777********************************************998877 PP

                             Nop53 333 raea 336
                                        +  
  gi|488599668|ref|YP_007906139.1| 112 GKLD 115
                                       6654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 998.92
//
Query:       gi|488599669|ref|YP_007906140.1|  [L=134]
Description: LSU ribosomal protein L32E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-36  124.8   0.2    2.4e-36  124.5   0.2    1.1  1  Ribosomal_L32e  Ribosomal protein L32
  ------ inclusion threshold ------
        1.3    7.6   6.9        1.5    7.4   6.9    1.1  1  TT_ORF1         TT viral orf 1


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 !  124.5   0.2   2.6e-40   2.4e-36       1     108 []      25     130 ..      25     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 2.6e-40
                                       ------TTTTT-TTS-S.S------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTT CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklke.swrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmen 76 
                                       +++F+r++s+++ +l++ swr+prG+dn++r r+ g++  + +G++sp+++rg++psG+ +vlVhn+keLe+++ e+
  gi|488599669|ref|YP_007906140.1|  25 KPEFRRYESHKKLRLRRkSWRRPRGMDNKMRLRIAGKK-PVMVGFASPAEVRGYHPSGYIEVLVHNPKELENVDAET 100
                                       689*************77*****************975.589*********************************** PP

                                       E..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  77 ksyaaeiahsVsskkrkeiverAaelgikVtN 108
                                       +  a++ia+ V+ kkr +i+++A+elgik++N
  gi|488599669|ref|YP_007906140.1| 101 Q--AIRIASCVGLKKRLMIEDKAKELGIKILN 130
                                       *..***************************99 PP

>> TT_ORF1  TT viral orf 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.9   0.00017       1.5      14      83 ..      18      87 ..       8     107 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00017
                           TT_ORF1 14 rrrrrrrrrrvrrrrrrrrvRRRrrgrrrrr.rrrrrrrr.rrrkrkklilkqwqPetirkckIkGllplvi 83
                                      rrr++ r+ ++rr++  ++ R Rr  + +rr r    + r r   +k + +    P+ +r  +  G++ +++
  gi|488599669|ref|YP_007906140.1| 18 RRRQKARKPEFRRYESHKKLRLRR--KSWRRpRGMDNKMRlRIAGKKPVMVGFASPAEVRGYHPSGYIEVLV 87
                                      222223444455555555543344..3455555555555544556666677777888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 887.15
//
Query:       gi|488599670|ref|YP_007906141.1|  [L=180]
Description: LSU ribosomal protein L6P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-28   99.4   9.4    3.4e-16   59.7   3.8    2.1  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
       0.14   12.2   0.1       0.52   10.3   0.0    2.1  2  TubC_N        TubC N-terminal docking domain


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 !   59.7   3.8   3.8e-20   3.4e-16       1      76 []      10      87 ..      10      87 .. 0.96
   2 !   43.4   0.3   4.7e-15   4.2e-11       1      76 []      99     173 ..      99     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.8e-20
                                      CSTTEEEEEET....TTEEEEEESSEEEEEE-CTT.SEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6  1 iPvgvrvsikg....gqlvlvlGpkgeltreipeg.vtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVt 74
                                      iP+gv+vsi+g    g++++ +G kge +r ++   v++   +e+ kv+v + +g+ k+k+ ++gt+ ++i+n ikGVt
  gi|488599670|ref|YP_007906141.1| 10 IPEGVEVSIEGddvkGYTIKAKGQKGENSRYLKFRgVKIV--KEDSKVRVYTEDGKIKQKA-MVGTFAAHIRNLIKGVT 85
                                      8********************************9857777..99*****************.***************** PP

                                      TC CS
                      Ribosomal_L6 75 eg 76
                                      eg
  gi|488599670|ref|YP_007906141.1| 86 EG 87
                                      98 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 4.7e-15
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +Pv+ rv++ ++ ++++lG+k++++ +i    +v+++     +++i+v+gidke      A+++++++++n + + +
  gi|488599670|ref|YP_007906141.1|  99 FPVKLRVEGREVVIENFLGEKHPRRSKIVGRCEVKIQ-----GNDIIVTGIDKEECgqtaANLEQTTRIKNLDQRIF 170
                                       79*********************************99.....*******************************9999 PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                       ++g
  gi|488599670|ref|YP_007906141.1| 171 QDG 173
                                       997 PP

>> TubC_N  TubC N-terminal docking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.47   4.2e+03      12      21 ..      13      22 ..      12      24 .. 0.84
   2 ?   10.3   0.0   5.8e-05      0.52      12      40 ..      54      82 ..      41      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.47
                            TubC_N 12 gIkLwleggr 21
                                      g+++++eg+ 
  gi|488599670|ref|YP_007906141.1| 13 GVEVSIEGDD 22
                                      899*****96 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.8e-05
                            TubC_N 12 gIkLwleggrLrfrApkgaltpelraklk 40
                                       +++++e+g+ + +A  g++ + +r+ +k
  gi|488599670|ref|YP_007906141.1| 54 KVRVYTEDGKIKQKAMVGTFAAHIRNLIK 82
                                      699**********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1063.67
//
Query:       gi|488599671|ref|YP_007906142.1|  [L=130]
Description: SSU ribosomal protein S8P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-27   96.0   0.0    1.9e-27   95.7   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 !   95.7   0.0   1.1e-31   1.9e-27       1     127 []       5     130 .]       5     130 .] 0.85

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.1e-31
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEE CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklk 73 
                                       D++++++ +i+Naeka+ + +ev paskl  ++lkv+k+ Gyik+fe+  ++k     i+++ ++n+  +++i+   
  gi|488599671|ref|YP_007906142.1|   5 DTLSNTMIAIKNAEKAGYDVCEVrPASKLVGNVLKVFKDYGYIKEFEYIdDHKGGAfrITLTKRIND--CGAIRPRM 79 
                                       89**********************************************8544444444666666666..9**99655 PP

                                       E-SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  74 rvskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                         +k     Y k ++     + +Gi++vsT kGvm+++eAr+k++GG +layv+
  gi|488599671|ref|YP_007906142.1|  80 SAKKTE---YEKFEKRFLPGKDFGILVVSTVKGVMSQREAREKGLGGVLLAYVY 130
                                       444443...6666666666789*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 822.64
//
Query:       gi|488599672|ref|YP_007906143.1|  [L=50]
Description: SSU ribosomal protein S14P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-13   49.2   5.1    3.6e-13   49.1   5.1    1.0  1  Ribosomal_S14  Ribosomal protein S14p/S29e
     0.0079   16.2   0.2     0.0081   16.2   0.2    1.0  1  DUF1451        Zinc-ribbon containing domain
  ------ inclusion threshold ------
      0.043   13.5   0.6      0.056   13.1   0.6    1.2  1  zf-P11         P-11 zinc finger
      0.076   13.3   0.9      0.093   13.1   0.9    1.1  1  C1_2           C1 domain
      0.088   12.7   0.1       0.14   12.1   0.1    1.5  1  DUF4428        Domain of unknown function (DUF4428)


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 !   49.1   5.1     1e-16   3.6e-13      11      53 ..       8      49 ..       1      49 [. 0.91

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1e-16
                                      .CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE- CS
                     Ribosomal_S14 11 ptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKa 53
                                       +r+ n Cr +Gr  G++rk++L  +R+cfRe A +    G+kK+
  gi|488599672|ref|YP_007906143.1|  8 FGRGANECRRCGRKAGLVRKYRLylCRQCFREIAPE---LGFKKY 49
                                      49**********************************...*****8 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   2.3e-06    0.0081     106     138 ..       4      36 ..       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.3e-06
                           DUF1451 106 sGevvglGtlvCekCgkelalkkteeippCpkC 138
                                       s  v g G  +C++Cg++  l +  ++  C +C
  gi|488599672|ref|YP_007906143.1|   4 SEKVFGRGANECRRCGRKAGLVRKYRLYLCRQC 36 
                                       567899*************************** PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   1.6e-05     0.056       1      28 [.      11      37 ..      11      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                      -SSSBTTTSS--SSEEE-SSSEEEHHHH CS
                            zf-P11  1 GplsCksCWfkdksLveCsdHYLClrCl 28
                                      G   C+ C   + +Lv+    YLC++C+
  gi|488599672|ref|YP_007906143.1| 11 GANECRRCGR-KAGLVRKYRLYLCRQCF 37
                                      6678999975.579*************7 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9   2.6e-05     0.093      16      38 ..      10      36 ..       3      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                              C1_2 16 sesfnCsaCgrk...idgff.YsCseC 38
                                       +  +C+ Cgrk   + +++ Y C +C
  gi|488599672|ref|YP_007906143.1| 10 RGANECRRCGRKaglVRKYRlYLCRQC 36
                                      56789*******987666669****99 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     4e-05      0.14       2      30 ..      15      40 ..      14      50 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                           DUF4428  2 CaiCgkKigllkrlkleDgyvCkdClkKl 30
                                      C  Cg K gl         y+C  C+ ++
  gi|488599672|ref|YP_007906143.1| 15 CRRCGRKAGLVR---KYRLYLCRQCFREI 40
                                      777*******99...4445*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 325.35
//
Query:       gi|488599673|ref|YP_007906144.1|  [L=166]
Description: LSU ribosomal protein L5P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-22   80.1   0.0    2.1e-22   79.1   0.0    1.5  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    3.8e-19   68.8   0.2    6.2e-19   68.1   0.2    1.4  1  Ribosomal_L5    Ribosomal protein L5
  ------ inclusion threshold ------
      0.018   14.1   0.1      0.036   13.1   0.1    1.5  1  RELT            Tumour necrosis factor receptor superfamily m
        2.2    8.0  10.1          4    7.3   5.1    2.3  2  Cas9-BH         Bridge helix of CRISPR-associated endonucleas


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 !   79.1   0.0   4.6e-26   2.1e-22       1      94 []      59     157 ..      59     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 4.6e-26
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       piG+kvtLrgek++efl+++l v++++l+      ++++ + G +sfGi+e+i++p+++yd+d gifGmd+++ +++
  gi|488599673|ref|YP_007906144.1|  59 PIGLKVTLRGEKAEEFLKRALVVKENKLK------RKQV-NAGEFSFGIHEHIDLPGVDYDPDVGIFGMDVCVSLRR 128
                                       8****************************......6655.56*********************************** PP

                    Ribosomal_L5_C  78 k...tde.........earallkelgipf 94 
                                       +   +++         + + ++ke++i+f
  gi|488599673|ref|YP_007906144.1| 129 RgyrVKRrrisrskigKNHLITKEETIEF 157
                                       *8774446788888886666899988887 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.2   1.4e-22   6.2e-19       1      57 []       2      55 ..       2      55 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 1.4e-22
                                      SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      N+M++  ++K+vinmg+Ge+ge+   l++a k L+e+  QkP +t+a k+i+nF+iR
  gi|488599673|ref|YP_007906144.1|  2 NPMRELMIDKVVINMGIGESGER---LQRASKLLEELIEQKPAITHAVKTIKNFGIR 55
                                      9**********************...******************************9 PP

>> RELT  Tumour necrosis factor receptor superfamily member 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.1e-06     0.036      13      33 ..     115     135 ..     115     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-06
                              RELT  13 mGLlGvLiChvLkkKGYrCtt 33 
                                       +G +G+ +C  L+++GYr++ 
  gi|488599673|ref|YP_007906144.1| 115 VGIFGMDVCVSLRRRGYRVKR 135
                                       699***************975 PP

>> Cas9-BH  Bridge helix of CRISPR-associated endonuclease Cas9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.015        67      16      31 ..      23      38 ..      22      39 .. 0.91
   2 ?    7.3   5.1   0.00089         4       1      13 [.     128     140 ..     128     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.015
                                      HHHHHHHHHHHHHHHH CS
                           Cas9-BH 16 eRLhlLqelFaeeikk 31
                                      eRL++  +l++e+i++
  gi|488599673|ref|YP_007906144.1| 23 ERLQRASKLLEELIEQ 38
                                      8*************86 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00089
                                       HHHHHHHHHHHHH CS
                           Cas9-BH   1 RRlfRgsRRRleR 13 
                                       RR++R +RRR+ R
  gi|488599673|ref|YP_007906144.1| 128 RRGYRVKRRRISR 140
                                       9**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1017.14
//
Query:       gi|488599674|ref|YP_007906145.1|  [L=232]
Description: SSU ribosomal protein S4E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   75.5   0.6    1.1e-20   73.3   0.5    2.0  2  Ribosomal_S4e  Ribosomal family S4e
    4.8e-11   42.2   0.4    3.1e-10   39.6   0.2    2.2  2  S4             S4 domain
      1e-09   38.3   2.4    2.1e-09   37.3   2.4    1.5  1  RS4NT          RS4NT (NUC023) domain
    0.00036   20.4   0.1    0.00084   19.2   0.1    1.7  1  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.5   2.5e-24   1.1e-20       2      75 .]      89     159 ..      88     159 .. 0.96
   2 ?   -0.8   0.0      0.33   1.5e+03      31      50 ..     184     203 ..     179     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 2.5e-24
                                       TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                     Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                       +++yr+++d+kgr+ + +I  e+++ KL+Ki++kt+ k+g++ql++ dG++i+  ++  k++D+++++++++kI
  gi|488599674|ref|YP_007906145.1|  89 DKSYRIVFDEKGRYIPREI--EDSDRKLYKITGKTLLKGGKVQLNLFDGTNIIATNE-FKTKDSLLLEIPSKKI 159
                                       799****************..777889*****************************9.***************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                                       EECEEEEECCCEEEEEETTS CS
                     Ribosomal_S4e  31 KikkkttvkkgipqlvthdG 50 
                                       + k+ ++v++  p lvt  G
  gi|488599674|ref|YP_007906145.1| 184 RLKSYKVVRGSAPNLVTVEG 203
                                       77888999999999999887 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.2   6.9e-14   3.1e-10       2      48 .]      36      83 ..      35      83 .. 0.91
   2 ?   -0.1   0.0      0.18     8e+02      20      31 ..     120     131 ..     118     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 6.9e-14
                                      EHHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4  2 RLdkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      +L +v+   lgla   reAr++I  G +lV+Gkv+kd++++V+  Dv+
  gi|488599674|ref|YP_007906145.1| 36 PLLIVVrDFLGLADNAREARRIIASGDILVDGKVRKDYKFPVGLFDVV 83
                                      5667777669*********************************99987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.18
                                       HHHHHTTTEEET CS
                                S4  20 rqlIehGrVlVN 31 
                                       + l ++G+V++N
  gi|488599674|ref|YP_007906145.1| 120 KTLLKGGKVQLN 131
                                       67999****998 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   2.4   4.7e-13   2.1e-09       6      34 ..       2      30 ..       1      32 [. 0.97

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 4.7e-13
                                      -EETTTS-TTS---SSSSSEE----SSSS CS
                             RS4NT  6 HLKrlaAPkhWpldkkegvfavkPspGPH 34
                                      H Krl+APk+  +++k ++++vk spGPH
  gi|488599674|ref|YP_007906145.1|  2 HQKRLSAPKTLKIARKVKKWTVKASPGPH 30
                                      ***************************** PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.9e-07   0.00084       2      25 ..     168     191 ..     167     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.9e-07
                                       TSEEEESSSTTTTCEEEEEEEETT CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqh 25 
                                       G  V++++G+h+G++G+ ++    
  gi|488599674|ref|YP_007906145.1| 168 GALVMIIGGTHAGEIGRLKSYKVV 191
                                       999*************99876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1546.53
//
Query:       gi|488599675|ref|YP_007906146.1|  [L=122]
Description: LSU ribosomal protein L24P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-26   91.4   1.7    5.2e-26   90.9   1.7    1.2  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    7.9e-09   35.2   1.7    2.1e-08   33.8   1.7    1.7  1  KOW            KOW motif
  ------ inclusion threshold ------
      0.036   14.8   0.5      0.069   13.9   0.3    1.6  1  DUF4162        Domain of unknown function (DUF4162)
      0.061   13.1   1.5       0.11   12.3   1.2    1.7  1  eIF-1a         Translation initiation factor 1A / IF-1
       0.11   12.2   0.2       0.18   11.5   0.2    1.5  1  PSI_PsaE       Photosystem I reaction centre subunit IV / Psa
        1.1    9.7   7.5       0.76   10.2   0.3    2.6  2  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   1.7   1.8e-29   5.2e-26       1      81 [.       5     119 ..       5     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 1.8e-29
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................x RF
                     Ribosomal_L26   1 sssrrkqrKahfn.apshirrklmsapLskeLrekygvrslpir................................g 44 
                                       s+++rkqr+ +++  ++h+r++l++a LskeLr+kyg+r+++i+                                g
  gi|488599675|ref|YP_007906146.1|   5 SKQPRKQRRWLYKtSKLHERHRLLNATLSKELRKKYGRRTIRIKkgdkvrimrgefagqegkvievdmkrlrikvdG 81 
                                       89**********84679************************************************************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                     Ribosomal_L26  45 vtrekangttvpvgihpSkvvItklkl.DkdrkkiLer 81 
                                       vt +k +gt+v v+ihpS+v+I++l   D+ rk+ Le+
  gi|488599675|ref|YP_007906146.1|  82 VTTTKVDGTEVAVPIHPSNVMIVSLGEvDDVRKRKLEK 119
                                       *************************988********96 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   1.7     7e-12   2.1e-08       1      32 []      49      80 ..      49      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 7e-12
                                      TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                      +Gd V++++G ++G++GkV +vd ++ r+ vd
  gi|488599675|ref|YP_007906146.1| 49 KGDKVRIMRGEFAGQEGKVIEVDMKRLRIKVD 80
                                      7*************************999886 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   2.3e-05     0.069       4      47 ..      34      83 ..      33     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                                      HHHHTTS-SSEEEEE.--.....-----..--.-EEEE-TTS-EEEEE--.- CS
                           DUF4162  4 eeiKrsygknrieve.ad.....aeelleepg.veeveeeggelelkled.e 47
                                      +e++++yg+++i+++ +d      +e++ ++g v ev+ +  +l++k+++ +
  gi|488599675|ref|YP_007906146.1| 34 KELRKKYGRRTIRIKkGDkvrimRGEFAGQEGkVIEVDMK--RLRIKVDGvT 83
                                      79*************8443344455555667777777654..4888888622 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.2   3.7e-05      0.11      32      62 ..      37      68 ..      26      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                      -HHHH.CT----TT-EEEEEE-TT-TTEEEEE CS
                            eIF-1a 32 pgkfR.nkiwikrGdyVlVelspydltkGrIv 62
                                      ++k   ++i+ik+Gd+V +   +++ + G+++
  gi|488599675|ref|YP_007906146.1| 37 RKKYGrRTIRIKKGDKVRIMRGEFAGQEGKVI 68
                                      5555449**********998888777777776 PP

>> PSI_PsaE  Photosystem I reaction centre subunit IV / PsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2     6e-05      0.18       1      32 [.      47      76 ..      47      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                                      --TT-EEEE--TT-TTBTSEEEEEEE---T-S CS
                          PSI_PsaE  1 ikrgskVrilRkeSYWyndvGtvasvdksgik 32
                                      ik+g+kVri R e     + G+v+ vd + ++
  gi|488599675|ref|YP_007906146.1| 47 IKKGDKVRIMRGE--FAGQEGKVIEVDMKRLR 76
                                      79**********9..57899999999988665 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 ?    2.4   2.0      0.07   2.1e+02      43      59 ..      42      57 ..      29      87 .. 0.78
   2 ?   10.2   0.3   0.00025      0.76      21      35 ..      91     105 ..      88     122 .] 0.71

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.07
                     ribosomal_L24 43 rvgfrlkedgkkvRvsk 59
                                      r  +r+k +g kvR+ +
  gi|488599675|ref|YP_007906146.1| 42 RRTIRIK-KGDKVRIMR 57
                                      4445555.9999**986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                     ribosomal_L24  21 ekEapIhvSnVmlvd 35 
                                       e   pIh SnVm+v 
  gi|488599675|ref|YP_007906146.1|  91 EVAVPIHPSNVMIVS 105
                                       5678*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 756.25
//
Query:       gi|488599676|ref|YP_007906147.1|  [L=132]
Description: LSU ribosomal protein L14P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-36  125.1   0.3    1.7e-36  125.0   0.3    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e
  ------ inclusion threshold ------
       0.11   13.2   0.1       0.16   12.6   0.1    1.4  1  Imm1           Immunity protein Imm1


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 !  125.0   0.3   1.9e-40   1.7e-36       4     122 .]      14     132 .]      11     132 .] 0.94

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 1.9e-40
                                       SS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-E CS
                     Ribosomal_L14   4 lktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsv 76 
                                       +++rl + DN+ga+e+e+i+v g+k    + +aa vGdi+vvsvkk++p   + +++v++av+vr++ke+rr+dG+ 
  gi|488599676|ref|YP_007906147.1|  14 TGARLVCTDNTGARELEIIAVKGYKgvrrRYPAAGVGDIVVVSVKKGTP---EIRKQVHYAVIVRQRKEFRRPDGTR 87 
                                       6799******************99987544499****************...899********************** PP

                                       EEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                     Ribosomal_L14  77 irfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                       ++f+dnaaV+ + +g+p+G++i g+vare++e+ f++i +lA  ++
  gi|488599676|ref|YP_007906147.1|  88 VKFEDNAAVITDPNGNPKGSEIRGAVAREAAER-FSRIGTLAAAIV 132
                                       ********************************9.********9875 PP

>> Imm1  Immunity protein Imm1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.8e-05      0.16      66     117 ..      76     126 ..      24     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                              Imm1  66 ddgpvsssngdppdseevvydyvggqtefPadsevpleqvraAlkeFlatge 117
                                       ++  +++++g+  ++e+ +  + +++   P++se+  +++r+A++ F + g+
  gi|488599676|ref|YP_007906147.1|  76 QRKEFRRPDGTRVKFEDNAA-VITDPNGNPKGSEIRGAVAREAAERFSRIGT 126
                                       35579999999999999988.55666699******************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 923.48
//
Query:       gi|488599677|ref|YP_007906148.1|  [L=109]
Description: SSU ribosomal protein S17P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-24   85.1   2.0    3.3e-24   84.8   2.0    1.1  1  Ribosomal_S17    Ribosomal protein S17
  ------ inclusion threshold ------
      0.052   13.9   0.2       0.15   12.5   0.0    1.9  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   2.0   3.7e-28   3.3e-24       1      68 []      35     102 ..      35     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 3.7e-28
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                       G+Vv++  +k++v+++e+  ++pky++y+k+r+k++ah+++++ +kvGD+V+i ecrPlSktk+fv+ve
  gi|488599677|ref|YP_007906148.1|  35 GKVVKT-YEKSAVIQREHIRYIPKYERYMKKRSKLHAHNPPCInAKVGDTVTIIECRPLSKTKSFVIVE 102
                                       788886.78*********************************************************996 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 ?   12.5   0.0   1.6e-05      0.15      35      69 .]       3      33 ..       1      33 [. 0.75
   2 ?   -1.4   0.1      0.36   3.2e+03      30      34 ..      59      63 ..      37      71 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                      ---TT----GGGGS-----TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 35 nvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                      ++g   k P++  +    D  CPF G+  +rG++L
  gi|488599677|ref|YP_007906148.1|  3 DIGYDVKPPEKECD----DENCPFHGKLPVRGQML 33
                                      56666666655544....99************987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                                      ----- CS
                   Ribosomal_S17_N 30 kryvk 34
                                      +ry+k
  gi|488599677|ref|YP_007906148.1| 59 ERYMK 63
                                      34444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 698.10
//
Query:       gi|488599678|ref|YP_007906149.1|  [L=104]
Description: ribonuclease P protein subunit Rpp29 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-21   74.1   0.0    7.5e-21   73.9   0.0    1.1  1  UPF0086   Domain of unknown function UPF0086
  ------ inclusion threshold ------
      0.041   13.3   0.0      0.047   13.1   0.0    1.3  1  PIN_5     PINc domain ribonuclease


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 !   73.9   0.0   8.3e-25   7.5e-21       3      84 .]       5      84 ..       3      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 8.3e-25
                                      HCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHH CS
                           UPF0086  3 LlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadR 81
                                      ++ ++l+G+e eVv+s n+  vg++G +v+Et++tl i+t +++ k++ K++  F+++v +   ve+dG+ + yrp++R
  gi|488599678|ref|YP_007906149.1|  5 IIAHELIGLECEVVDSPNRYEVGLAGEIVDETMKTLLIRT-DRGYKRIAKADRKFKLRV-GDSCVELDGNLIAYRPEER 81
                                      789*************************************.99****************.7899*************** PP

                                      HCH CS
                           UPF0086 82 aer 84
                                      ++r
  gi|488599678|ref|YP_007906149.1| 82 IKR 84
                                      *97 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.3e-06     0.047      77     111 ..      17      52 ..       5      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-06
                             PIN_5  77 vkkspdryevkipaeilyeyveevrerinkGlr.va 111
                                       v+ sp+ryev +  ei+ e ++++  r ++G + +a
  gi|488599678|ref|YP_007906149.1|  17 VVDSPNRYEVGLAGEIVDETMKTLLIRTDRGYKrIA 52 
                                       4579***************************75144 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 797.17
//
Query:       gi|488599679|ref|YP_007906150.1|  [L=65]
Description: LSU ribosomal protein L29P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-16   58.2   3.8    7.1e-16   57.9   3.8    1.0  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
      0.044   13.9   0.9      0.049   13.7   0.3    1.4  2  Mito_fiss_reg  Mitochondrial fission regulator
       0.17   11.9   0.2        0.2   11.8   0.2    1.3  1  Bromodomain    Bromodomain


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 !   57.9   3.8   1.2e-19   7.1e-16       1      56 [.       4      60 ..       4      60 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.2e-19
                                      HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlre 56
                                      +e+r++s ee  +kl el++eL++ r q ++g ++enp+ +r++RkdIAR+k  lre
  gi|488599679|ref|YP_007906150.1|  4 NEIRKMSREEKIKKLRELENELLRVRTQVRSGgSIENPGIVRAIRKDIARVKLALRE 60
                                      69******************************9**********************98 PP

>> Mito_fiss_reg  Mitochondrial fission regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   8.1e-06     0.049     111     136 ..       7      32 ..       1      34 [. 0.86
   2 ?   -2.8   0.0      0.87   5.2e+03     240     247 ..      49      56 ..      46      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.1e-06
                     Mito_fiss_reg 111 dlkaneeAlkkiaaLedELakLRaQI 136
                                       +++  ee +kk  +Le+EL++ R+Q+
  gi|488599679|ref|YP_007906150.1|   7 RKMSREEKIKKLRELENELLRVRTQV 32 
                                       56778999*****************7 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.87
                     Mito_fiss_reg 240 KDlnkvkL 247
                                       KD+ +vkL
  gi|488599679|ref|YP_007906150.1|  49 KDIARVKL 56 
                                       99999998 PP

>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   3.3e-05       0.2      37      67 ..       1      31 [.       1      48 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                                      --HHHHHHHHHTT--SSHHHHHHHHHHHHHH CS
                       Bromodomain 37 ldLstIkkklesnkYksladfeadlkllfsN 67
                                      +++++I+k  +++k+k+l ++e++l ++ + 
  gi|488599679|ref|YP_007906150.1|  1 MKMNEIRKMSREEKIKKLRELENELLRVRTQ 31
                                      79***********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 414.69
//
Query:       gi|488599680|ref|YP_007906151.1|  [L=246]
Description: SSU ribosomal protein S3P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-23   81.7   0.7    4.1e-23   81.7   0.7    1.9  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
      2e-12   46.7   0.2      7e-12   45.0   0.1    2.0  2  KH_2            KH domain
  ------ inclusion threshold ------
      0.015   15.1   1.1      0.035   13.9   0.1    2.1  3  KH_1            KH domain
      0.065   13.3   0.2       0.46   10.6   0.0    2.4  3  KH_5            NusA-like KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.39   1.7e+03       6      32 ..       9      35 ..       5      37 .. 0.76
   2 !   81.7   0.7   9.1e-27   4.1e-23       1      83 []      98     181 ..      98     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.39
                                      HTT--HHHHHHHHHHHHHHCC-SEEEE CS
                    Ribosomal_S3_C  6 ekrvsfRramkkairramkagakGiki 32
                                      e+r++  r+ + + +++ +ag  G+ i
  gi|488599680|ref|YP_007906151.1|  9 EERLKKFRVKEWMAQEVRNAGFGGVDI 35
                                      666666677888899999999999988 PP

  == domain 2  score: 81.7 bits;  conditional E-value: 9.1e-27
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       +a++le+++ fR+a ++++ r+m+agakG++i++sG+L+ +e+ar+ek+ +G++ +  +++ + +++++  a  k G
  gi|488599680|ref|YP_007906151.1|  98 LARALERGWYFRKAGYRFLYRIMEAGAKGCEIEISGKLT-GERARTEKFLAGTMVHtgEPAISAVKTGFDVAIKKLG 173
                                       689************************************.9************************************ PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                       ++G+kV+I
  gi|488599680|ref|YP_007906151.1| 174 VMGIKVRI 181
                                       ******98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.1   1.6e-15     7e-12       2      77 ..      17      88 ..      16      89 .. 0.89
   2 ?   -2.5   0.0         1   4.6e+03      11      21 ..     120     130 ..     116     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.6e-15
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTG CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpe 77
                                      ++e+ a+e+++ag ++v+I rt+ ++ i++ +++pg+vIGkgG++i++++++l++    + + +V+  + +++kpe
  gi|488599680|ref|YP_007906151.1| 17 VKEWMAQEVRNAGFGGVDITRTPLGTQITLFVERPGLVIGKGGRRIRNLTEKLKEFG--IDNPQVS--VDEIEKPE 88
                                      678899***********************************************5554..8999999..56777765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1
                                       ECETEEEEEEE CS
                              KH_2  11 kkagvskveIe 21 
                                        +ag++++eIe
  gi|488599680|ref|YP_007906151.1| 120 MEAGAKGCEIE 130
                                       57889999995 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   7.8e-06     0.035      12      28 ..      52      68 ..      42      85 .. 0.87
   2 ?   -1.9   0.0      0.67     3e+03      30      52 ..     126     133 ..     117     142 .. 0.61
   3 ?   -3.6   0.0       2.3     1e+04      32      40 ..     178     186 ..     176     204 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.8e-06
                                      HHHHTGGGHHHHHHHHH CS
                              KH_1 12 griIGkgGsnIkeIree 28
                                      g++IGkgG++I+++ e+
  gi|488599680|ref|YP_007906151.1| 52 GLVIGKGGRRIRNLTEK 68
                                      89************996 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.67
                                       T-EEEEESSTT...T.-EEEEEE CS
                              KH_1  30 gakIkvpksedegsderevtisG 52 
                                       g+ I +               sG
  gi|488599680|ref|YP_007906151.1| 126 GCEIEI---------------SG 133
                                       555554...............44 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.3
                                       EEEEESSTT CS
                              KH_1  32 kIkvpksed 40 
                                       k++++++++
  gi|488599680|ref|YP_007906151.1| 178 KVRIIPPDA 186
                                       555553222 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.76   3.4e+03      52      65 ..       5      18 ..       3      19 .. 0.85
   2 ?   10.6   0.0    0.0001      0.46      20      39 ..      52      71 ..      47     101 .. 0.83
   3 ?   -1.7   0.0      0.73   3.3e+03      29      45 ..     157     182 ..     147     205 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.76
                              KH_5 52 aefianalsPaevl 65
                                      ++f+++ l++++v+
  gi|488599680|ref|YP_007906151.1|  5 RKFVEERLKKFRVK 18
                                      68999999999997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                              KH_5 20 GaivgkkGsrikavsseLkg 39
                                      G ++gk+G+ri+++ ++Lk+
  gi|488599680|ref|YP_007906151.1| 52 GLVIGKGGRRIRNLTEKLKE 71
                                      789***************85 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.73
                              KH_5  29 rikavsseLk.........gekidvv 45 
                                        i+av+  ++         g k++++
  gi|488599680|ref|YP_007906151.1| 157 AISAVKTGFDvaikklgvmGIKVRII 182
                                       45555544444444444555566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1644.65
//
Query:       gi|488599681|ref|YP_007906152.1|  [L=153]
Description: LSU ribosomal protein L22P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-29  100.3   0.6    8.8e-29   99.8   0.6    1.3  1  Ribosomal_L22   Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
      0.045   14.2   0.1      0.052   14.0   0.1    1.3  1  Peptidase_S8_N  N-terminal of Subtilase family


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 !   99.8   0.6   9.8e-33   8.8e-29       1     101 [.      19     149 ..      19     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 9.8e-33
                                       EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST............................THHHHHHHH CS
                     Ribosomal_L22   1 akgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk............................aakfvlklL 47 
                                       a+g ++++sfk++ e++  I+gmk++eA+++L++  + k+                            aa+++lk++
  gi|488599681|ref|YP_007906152.1|  19 AMGYEMPISFKHAVEICSEIKGMKIDEAIRFLEEvaEMKRavrfkkyykkvghksgldkwfagrypqkAARYILKVI 95 
                                       578899****************************9877779************************************ PP

                                       HHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  48 knaeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievv 101
                                       kn eana++kg ++d+l+I+++q++kg+ lkr+t+rA Gr++p  k  + +e v
  gi|488599681|ref|YP_007906152.1|  96 KNLEANADYKGIEKDRLIITHAQAKKGRVLKRFTPRAFGRATPKFKTLTTVEFV 149
                                       ***********************************************9999987 PP

>> Peptidase_S8_N  N-terminal of Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.8e-06     0.052      32      98 ..      42     111 ..      16     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                    Peptidase_S8_N  32 sldevlaelg.avelervfpvdgkfeertrkaGLhlWYdvkfdesvdl..seaaeelkslagvevveyvr 98 
                                       ++de+++ l+ + e++r ++ ++ +++  +k GL++W+  ++ +++     ++ ++l++ a+ + +e  r
  gi|488599681|ref|YP_007906152.1|  42 KIDEAIRFLEeVAEMKRAVRFKKYYKKVGHKSGLDKWFAGRYPQKAARyiLKVIKNLEANADYKGIEKDR 111
                                       56777777761458************************99998876432245555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1086.13
//
Query:       gi|488599682|ref|YP_007906153.1|  [L=133]
Description: SSU ribosomal protein S19P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-29  100.5   0.6    5.1e-29  100.0   0.6    1.2  1  Ribosomal_S19  Ribosomal protein S19


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 !  100.0   0.6   2.8e-33   5.1e-29       3      81 .]      43     116 ..      38     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 2.8e-33
                                       HHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS-- CS
                     Ribosomal_S19   3 lkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkp 78 
                                       + +g +  +e+ll+k++      kk++++th+Rd+++lPemvg  + V+nGk+fv+ve+k+em+Gh+LgEF+ Tr++
  gi|488599682|ref|YP_007906153.1|  43 ILRGfTEQEEKLLRKLK------KKDAVRTHCRDMIVLPEMVGKIIMVHNGKDFVRVEVKPEMIGHRLGEFAQTRTF 113
                                       45555556666666554......56689************************************************* PP

                                       --S CS
                     Ribosomal_S19  79 vkh 81 
                                        kh
  gi|488599682|ref|YP_007906153.1| 114 IKH 116
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 912.25
//
Query:       gi|488599683|ref|YP_007906154.1|  [L=236]
Description: LSU ribosomal protein L2P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-47  159.8   0.9    1.4e-46  157.8   0.9    1.8  2  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    2.7e-20   72.1   0.0    2.5e-19   69.0   0.0    2.5  3  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 ?   -0.7   0.0      0.17   1.5e+03      46      61 ..      53      68 ..      37      78 .. 0.75
   2 !  157.8   0.9   1.5e-50   1.4e-46       2     121 ..      89     219 ..      88     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.17
                                      SEEEEEETTS-EEEEE CS
                    Ribosomal_L2_C 46 kkvtvklpSgevrkvs 61
                                        ++vklp g+ r++ 
  gi|488599683|ref|YP_007906154.1| 53 PIAKVKLPDGSERYII 68
                                      5688999999999875 PP

  == domain 2  score: 157.8 bits;  conditional E-value: 1.5e-50
                                       SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT CS
                    Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehke 78 
                                       +Gn++ lknipeG+ v+nie++pg+ggk++r++Gt+a vv++e++++ v++pSg  ++++ +crA+iGvv++g++++
  gi|488599683|ref|YP_007906154.1|  89 PGNITYLKNIPEGSPVCNIESNPGDGGKFVRASGTFALVVSHEETRTLVQMPSGVLKWFNPNCRAMIGVVAGGGRTD 165
                                       8**************************************************************************** PP

                                       ----STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SSSST CS
                    Ribosomal_L2_C  79 kklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksrkap 121
                                       k+++kAg+k+++      ++p vrGvamn+vdHp+GGG+    Gk  t+sr+ap
  gi|488599683|ref|YP_007906154.1| 166 KPFVKAGKKYHKykskaAKWPVVRGVAMNAVDHPFGGGKhqhtGKpkTVSRNAP 219
                                       ****************99*********************888866656667666 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 !   69.0   0.0   2.8e-23   2.5e-19       1      76 [.      11      80 ..      11      81 .. 0.96
   2 ?   -1.0   0.0      0.19   1.7e+03      48      68 ..     122     142 ..     103     145 .. 0.76
   3 ?   -2.2   0.0      0.47   4.2e+03      43      64 ..     148     170 ..     147     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 2.8e-23
                                      TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                      G++++ +r+++++++       + i+f   ++ vk+kV++ie+Dp+R+ApiA vk+ dg++ryiia+eg+ +G +++
  gi|488599683|ref|YP_007906154.1| 11 GKGTPtYRAPSHKYKA----DLKHINF---EGLVKAKVIDIEHDPARNAPIAKVKLPDGSERYIIATEGMGTGHIIE 80
                                      99************99....9999999...788******************************************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.19
                                       S-EEEEEETTTEEEEEE--SS CS
                      Ribosomal_L2  48 ApiAlvkyedgekryiiapeg 68 
                                       +  Alv+  + +++++ +p g
  gi|488599683|ref|YP_007906154.1| 122 GTFALVVSHEETRTLVQMPSG 142
                                       456888888888888888877 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.47
                                       -TT-SS-EEEEEETT.TEEEEEE CS
                      Ribosomal_L2  43 DpgRsApiAlvkyed.gekryii 64 
                                       +p+  A i+ v+ +   +k ++ 
  gi|488599683|ref|YP_007906154.1| 148 NPNCRAMIGVVAGGGrTDKPFVK 170
                                       68888888888877744444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1588.44
//
Query:       gi|488599684|ref|YP_007906155.1|  [L=81]
Description: LSU ribosomal protein L23P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   51.2   7.8    6.3e-13   48.9   7.8    1.8  1  Ribosomal_L23  Ribosomal protein L23
     0.0017   18.5   0.1     0.0022   18.1   0.1    1.2  1  Mrr_N          Mrr N-terminal domain
  ------ inclusion threshold ------
      0.015   15.4   0.2      0.016   15.3   0.2    1.2  1  ASL_C          Adenylosuccinate lyase C-terminal
      0.075   13.3   0.1       0.11   12.7   0.1    1.4  1  DUF2551        Protein of unknown function (DUF2551)


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 !   48.9   7.8   1.4e-16   6.3e-13       3      75 ..       3      62 ..       1      73 [. 0.86

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.4e-16
                                      EEEE--SHHHHHHHTTE.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEE CS
                     Ribosomal_L23  3 ilkPvitEkstklaeknkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkai 75
                                      i++ ++tEk+ +  +kn ++  V+k+anK +ik+ +ek F+VkVekVntl+ ++ +k+             a+
  gi|488599684|ref|YP_007906155.1|  3 IKCFIVTEKTSTEIDKNILTAIVDKRANKKQIKEEIEKRFEVKVEKVNTLITPKGEKK-------------AY 62
                                      77889*********999**********************************9996665.............33 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   4.9e-07    0.0022       4      48 ..      16      60 ..      14      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.9e-07
                             Mrr_N  4 lmlplLealadgsehrlkeirervaerfglseeeraell.psgkqt 48
                                      + + +L a+ d+++ + k+i+e++++rf+++ e+++ l+ p+g+++
  gi|488599684|ref|YP_007906155.1| 16 IDKNILTAIVDKRANK-KQIKEEIEKRFEVKVEKVNTLItPKGEKK 60
                                      56789***********.********************997777654 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   3.6e-06     0.016      29      75 ..      19      65 ..       7      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
                                      HHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-TTHHHHH CS
                             ASL_C 29 sllkglsklevneealaedLdenwevlaEaiqtvlrregiekpYekl 75
                                      ++l+++   ++n+++++e++++  ev  E + t++  +g +k+Y kl
  gi|488599684|ref|YP_007906155.1| 19 NILTAIVDKRANKKQIKEEIEKRFEVKVEKVNTLITPKGEKKAYIKL 65
                                      56677777789*********************************887 PP

>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.5e-05      0.11       9      50 ..      13      53 ..       4      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                           DUF2551  9 ksGiRrevLklfleakkltveeiyeklkekfdvsykgvasmv 50
                                      ++ i +++L+ ++++ +   ++i e+++++f+v++++v +++
  gi|488599684|ref|YP_007906155.1| 13 STEIDKNILTAIVDK-RANKKQIKEEIEKRFEVKVEKVNTLI 53
                                      567889999999975.56789*****************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2096  (0.116906); expected 358.6 (0.02)
Passed bias filter:                      901  (0.0502538); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 588.40
//
Query:       gi|488599685|ref|YP_007906156.1|  [L=252]
Description: LSU ribosomal protein L4P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-50  171.2   0.8    2.3e-50  171.0   0.8    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.0   0.8   1.3e-54   2.3e-50       1     190 [.      16     248 ..      16     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 171.0 bits;  conditional E-value: 1.3e-54
                                       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++a+ + ++ rrq+++ ++ a+   s+  +++++  G+G ARv++++       +p+a+g
  gi|488599685|ref|YP_007906156.1|  16 IEL-PSVFDTEYRPDIIRKAIHSLQSRRRQPYGPSPlAGINYSA--ENWGP--GHGYARVPRLKtgsravkVPQAVG 87 
                                       789.***********************************99999..6****..************************ PP

                                       ---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES--.-..-S.........S--HHHHHHHHHHTT-. CS
                      Ribosomal_L4  70 GgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvdnl.e.ple.........esktkelvellkklgl. 134
                                       G++ah+pk+++ +++k+nkK+ r+Al+sa++a+++++l+  + ++ + +l+          +ktke+ve+lk++g+ 
  gi|488599685|ref|YP_007906156.1|  88 GRRAHPPKVQKIWEEKINKKEMRKALCSAIAATVNAQLVSERPHIfSgELPkivvddlqnLKKTKEVVEALKAIGVy 164
                                       *******************************************765766778889999999************9999 PP

                                       .........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEE CS
                      Ribosomal_L4 135 .........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvit 182
                                                                 +ksvLiv++e +++++ +arnl+gv+v+ +++lnv+ l++++k    +v+t
  gi|488599685|ref|YP_007906156.1| 165 edveraksrkryragkgkmrgrryiVKKSVLIVAGE-KSDILNSARNLAGVDVVVARNLNVELLAPGAKagrlTVWT 240
                                       9999999999999999999999999999*******7.99************************************** PP

                                       HHHHHHHH CS
                      Ribosomal_L4 183 ksavekle 190
                                       ksa+e le
  gi|488599685|ref|YP_007906156.1| 241 KSAIEALE 248
                                       ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1637.45
//
Query:       gi|488599686|ref|YP_007906157.1|  [L=329]
Description: LSU ribosomal protein L3P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-91  304.7   3.0    8.3e-90  301.4   3.0    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 !  301.4   3.0   4.6e-94   8.3e-90       7     369 .]       4     328 ..       1     328 [. 0.94

  Alignments for each domain:
  == domain 1  score: 301.4 bits;  conditional E-value: 4.6e-94
                                       XXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC-- CS
                      Ribosomal_L3   7 eaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetpp 83 
                                       ++pr+gs+ f+prkRa++  ++++++P+  ++kp+   +f+GyKaGmth+V ++d+ +s++ ++e+v++vtv+etpp
  gi|488599686|ref|YP_007906157.1|   4 HRPRRGSMAFSPRKRAKSIIPRIRAWPEHSETKPL---GFAGYKAGMTHVVIVDDRRNSPTYGEEIVVPVTVLETPP 77 
                                       68******************************997...89************************************* PP

                                       EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCE CS
                      Ribosomal_L3  84 mvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvv 160
                                       ++++g ++y +tp+G   + ++wae+l +++ rr+             +  kk +++      + dl+++ +     
  gi|488599686|ref|YP_007906157.1|  78 LKVAGFRAYRKTPYGFEIMSEIWAENLDNQLGRRI-------------NIPKKVNGN----ADDIDLDKVDH----F 133
                                       ***********************************.............233344222....22457888887....9 PP

                                       EEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT CS
                      Ribosomal_L3 161 rviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWg 237
                                       r+i++t+  k++++ +K ++++E +v gG +   + + +e+l   + v +vF++g +iDv+++tkGkGf+G+vkRWg
  gi|488599686|ref|YP_007906157.1| 134 RLITYTQPYKITGVPKKTPEIMEQKV-GGDVETAFGYVKEKLGGEIRVFEVFEEGSIIDVTSITKGKGFQGPVKRWG 209
                                       ***********************887.799*********************************************** PP

                                       ----STTTSSS..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TT CS
                      Ribosomal_L3 238 vkklprkthrg..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmG 312
                                       v  l +k++r+  +R+++++g+w+p +V++tv++aGq+G+h+Rte+nk+i+++g+              ++e+tP G
  gi|488599686|ref|YP_007906157.1| 210 VITLNAKHARSskHRRIGNLGPWNPHHVRPTVPQAGQMGFHQRTEFNKRIIKMGE-------------NGEEVTPNG 273
                                       **********999******************************************.............6899***** PP

                                       TCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                      Ribosomal_L3 313 GfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                       GfvhyG+v++d+++v GsvpG  krlv++r ++++       + v+  +++t+sk+g
  gi|488599686|ref|YP_007906157.1| 274 GFVHYGVVRGDYVMVSGSVPGSVKRLVRFRYAVRPPSAA--YDGVNVIYVSTTSKQG 328
                                       **********************************98765..5566669*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2178.76
//
Query:       gi|488599687|ref|YP_007906158.1|  [L=251]
Description: hypothetical protein Asulf_00129 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-53  180.1   0.0    7.8e-53  179.8   0.0    1.1  1  Methyltrn_RNA_3  Putative RNA methyltransferase


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 !  179.8   0.0   4.4e-57   7.8e-53       3     284 ..       2     244 ..       1     246 [. 0.91

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 4.4e-57
                   Methyltrn_RNA_3   3 siaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFpl 79 
                                        iaiPss + n ++++ k+y++ qIAR +aiF+V++i++++d+ ++      +s ++  +L+YletP+YLrk+lFp+
  gi|488599687|ref|YP_007906158.1|   2 NIAIPSSSLINENDEKIKAYKVWQIARYCAIFRVEKIYIYHDPRKD------DSGYIKDILEYLETPQYLRKSLFPI 72 
                                       69****************************************9966......579********************** PP

                   Methyltrn_RNA_3  80 hkelkyaglLppldaphhlrsse.egeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVklssee 155
                                       +k+l yag Lppl +p h  ++   ge+r Gvv ++ ++++    +V++Gl++ + ++   + p+g RVtV++ s  
  gi|488599687|ref|YP_007906158.1|  73 KKSLSYAGALPPLAIPSHKPKHLkIGELRDGVVRKVGPDGTL---WVDVGLPALALMKG--DKPKGARVTVRVCS-- 142
                                       ******************977766**************9887...*******9998777..99**********55.. PP

                   Methyltrn_RNA_3 156 sveakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtsergekveeklaelekkkefkhllivfG 232
                                        ++  vV+++epr     ywGY+V+ + +l +++++s         ++ s+rg++++e+l+e+     +++ +++fG
  gi|488599687|ref|YP_007906158.1| 143 -KTPLVVEEAEPR----EYWGYRVEKV-KLGRILDNS---------VILSRRGKPISESLEEI-----NQNSTLLFG 199
                                       .8999*******8....8*********.9****9987.........889**************.....58999**** PP

                   Methyltrn_RNA_3 233 g.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLa 284
                                       + ++g+ +++++    k++ + +       +n +pnqg++t+r+EEa++++La
  gi|488599687|ref|YP_007906158.1| 200 NpEEGVHEIARRL---KIKLDGIP-----SINSIPNQGTETVRLEEAIIATLA 244
                                       *9********433...33333333.....4888*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1639.88
//
Query:       gi|488599688|ref|YP_007906159.1|  [L=216]
Description: GMP synthase - Glutamine amidotransferase domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-20   71.2   0.0    1.2e-19   70.8   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    0.00024   20.9   0.1    0.00069   19.4   0.0    1.9  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.021   14.4   0.0      0.032   13.8   0.0    1.3  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 !   70.8   0.0     2e-23   1.2e-19      17     176 ..      21     171 ..       7     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2e-23
                                       HHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.......TTTHHHHHHHHCTSTS-EEEETHHHHHHHH CS
                            GATase  17 lvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.......vegkieaikearenkiPiLGICLGmQllai 86 
                                       + +++++ + v  ++ +ee   +  ++++ ++ gGp  ++        ++++e+i+ + + k+P+LG+CLG Ql+a+
  gi|488599688|ref|YP_007906159.1|  21 FEARNIEFDYVMAKE-IEEVS-EYLDYTHFIILGGPQGVYeddkhpyLKKEMELIRLVDG-KKPVLGVCLGAQLIAN 94 
                                       555666666666553.34442.5789**********999989999999999****99999.**************** PP

                                       HTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTT CS
                            GATase  87 efgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknp 163
                                       +fg++v+k k  +++g+ +  +          ++e+ + ++H++++n     p++ ++++k ++  e+ ++i +kn 
  gi|488599688|ref|YP_007906159.1|  95 AFGADVYKYK--KELGWYSVRKV----ADLPFPDEMVVFQWHQDTFN----IPEDAKIVFKGDNV-ENQGFILRKN- 159
                                       *******999..45666555444....2277899*************....6*********9776.9********9. PP

                                       EEEESSBTTSTTS CS
                            GATase 164 fvgvQFHPEstst 176
                                        v+vQFH E+t  
  gi|488599688|ref|YP_007906159.1| 160 -VAVQFHLEVTKD 171
                                       .********9976 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.2e-07   0.00069      94     129 ..      69     103 ..       6     131 .. 0.80
   2 ?   -3.4   0.0       1.1   6.5e+03     209     216 .]     160     167 ..     157     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-07
                     Peptidase_C26  94 elaLiraalergvPilgiCrGlqllnvalGGtlyqd 129
                                       e+ Lir  ++ ++P+lg+C+G ql++ a+G ++y+ 
  gi|488599688|ref|YP_007906159.1|  69 EMELIR-LVDGKKPVLGVCLGAQLIANAFGADVYKY 103
                                       455554.56889******************999875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                     Peptidase_C26 209 lgvQwHPE 216
                                       ++vQ+H E
  gi|488599688|ref|YP_007906159.1| 160 VAVQFHLE 167
                                       79****76 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 ?   13.8   0.0   5.4e-06     0.032      35      97 ..      41     102 ..      17     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-06
                          GATase_3  35 eslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei.edpeg 97 
                                       e l +  +++il+G + + +d ++    + + ++ +++  ++pvlg+C G q+  + + +d ++
  gi|488599688|ref|YP_007906159.1|  41 EYL-DYTHFIILGGPQGVYEDDKHPYL-KKEMELIRLVDGKKPVLGVCLGAQLIANAFgADVYK 102
                                       455.34889***************999.778899999****************99988666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1385.04
//
Query:       gi|488599689|ref|YP_007906160.1|  [L=461]
Description: Single-stranded DNA-specific exonuclease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-18   65.6   5.0    3.6e-17   63.1   0.8    3.0  3  DHHA1     DHHA1 domain
     0.0018   18.5   0.1     0.0035   17.5   0.1    1.5  1  DHH       DHH family
     0.0095   15.6   0.0        1.5    8.6   0.0    2.7  2  UPF0181   Uncharacterised protein family (UPF0181)


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.035   2.1e+02      24      76 ..       7      58 ..       4      70 .. 0.77
   2 ?    0.1   0.0      0.17   9.9e+02       1      44 [.     227     279 ..     227     302 .. 0.71
   3 !   63.1   0.8   6.1e-21   3.6e-17      53     138 .]     365     454 ..     323     454 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.035
                                      HHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG.BTTCEEEEE CS
                             DHHA1 24 klkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl.kkpvivfva 76
                                      +lk++e+++++ +   + vl++    ++d  + g++a   +++l  + ++vfv 
  gi|488599689|ref|YP_007906160.1|  7 MLKRAEYISSLIKR-SDEVLIVTH-IDADGITSGSIARITLDRLgIENEVVFVK 58
                                      67888899988887.777777777.78888888888888888886668888875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                                       HHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC..........TCEEEE CS
                             DHHA1   1 leslneerkelekeleelkealaklkaeellekaeevk..........gvkvlv 44 
                                       l+sl+ e +e +k+++ l+e++ k + +e+++ +  +           g ++++
  gi|488599689|ref|YP_007906160.1| 227 LDSLGIEVSEWKKWID-LSEEERKRAVNEIVKLCISAGipfksikrivGETYIL 279
                                       6899999999999995.9999999999988877655545555555555555555 PP

  == domain 3  score: 63.1 bits;  conditional E-value: 6.1e-21
                                       HHHHHHHHHHHHTHG..BTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEE CS
                             DHHA1  53 agalgiaadklkskl..kkpvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagip 123
                                        +++gi+a++  sk   +kp+i+++ ++eg  +kvsar++++    gv++++++k +++k+gg+GGGH  AaGa ip
  gi|488599689|ref|YP_007906160.1| 365 DTIVGIVAGMCFSKAnlNKPIIALARNDEG--IKVSARATQRlvdrGVNLAKAIKLVSEKIGGKGGGHSIAAGALIP 439
                                       458888888887755437799999998886..********99*********************************** PP

                                       HCHHHHHHHHHHHHH CS
                             DHHA1 124 aekleealealeeai 138
                                       +++++ +l++l+++i
  gi|488599689|ref|YP_007906160.1| 440 ESEVDRFLKELDRVI 454
                                       ***********9876 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.9e-07    0.0035       2      58 ..      24     107 ..      23     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.9e-07
                                       EEEE-ECSSSHHHHHH.HHHHHHC..............ECS--TCGGCGCCH..............HCCCSEEEEEE CS
                                       xxxxxxxxxxxxxxxx.xxxxxxx..............xxxxxxxxxxxxxx..............xxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigS.aialanl..............lvDhneksqavege..............akeeaedviii 49 
                                       +li  + + D+D+i+S +ia   l              l D ++++ a e++              +++++ d +i+
  gi|488599689|ref|YP_007906160.1|  24 VLI--VTHIDADGITSgSIARITLdrlgienevvfvkqLSDSEIEKIADENKftwftdlgsgqinsIIDKKIDFVIT 98 
                                       677..899********9998888555555666555555666666666666668888888888888899********* PP

                                       E-S---SS- CS
                                       xxxxxxxxx RF
                               DHH  50 DHHrlgeef 58 
                                       DHH +  ++
  gi|488599689|ref|YP_007906160.1|  99 DHHLPVMDN 107
                                       ***986533 PP

>> UPF0181  Uncharacterised protein family (UPF0181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0068        41       4      23 ..     239     258 ..     237     265 .. 0.84
   2 !    8.6   0.0   0.00024       1.5      21      41 ..     403     423 ..     399     429 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0068
                           UPF0181   4 nllsLtHeqQQqAVEkIqeL 23 
                                       +++ L+ e+ ++AV++I +L
  gi|488599689|ref|YP_007906160.1| 239 KWIDLSEEERKRAVNEIVKL 258
                                       5889*************998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00024
                           UPF0181  21 qeLmaqGmssgeAIalVAqel 41 
                                       q L+ +G++ + AI+lV++++
  gi|488599689|ref|YP_007906160.1| 403 QRLVDRGVNLAKAIKLVSEKI 423
                                       99****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3385.15
//
Query:       gi|488599690|ref|YP_007906161.1|  [L=251]
Description: putative membrane-associated protein/domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   32.7   0.5    6.4e-08   32.0   0.5    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00011   22.1   0.0    0.00017   21.4   0.0    1.3  1  MarR_2           MarR family
    0.00022   21.0   0.1    0.00039   20.3   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00037   20.4   0.1    0.00069   19.5   0.1    1.4  1  MarR             MarR family
    0.00039   20.6   0.0    0.00088   19.5   0.0    1.6  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0018   18.0   0.0     0.0029   17.4   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
     0.0024   17.8   0.0     0.0066   16.4   0.0    1.7  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0036   17.2   0.1     0.0057   16.6   0.1    1.3  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.004   16.1   0.1     0.0058   15.5   0.1    1.1  1  HTH_micro        HTH-like
     0.0085   16.0   0.4      0.014   15.3   0.4    1.4  1  HTH_11           HTH domain
  ------ inclusion threshold ------
      0.011   16.2   0.1      0.023   15.2   0.1    1.4  1  HTH_27           Winged helix DNA-binding domain
      0.027   14.5   0.2      0.047   13.8   0.2    1.3  1  FeoC             FeoC like transcriptional regulator
      0.068   13.4   0.1       0.13   12.5   0.1    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.09   12.6   0.2       0.17   11.7   0.2    1.5  1  fn3_3            Polysaccharide lyase family 4, domain II
       0.11   12.6   0.0       0.26   11.5   0.0    1.6  1  HTH_34           Winged helix DNA-binding domain
       0.12   12.5   0.1       0.24   11.6   0.1    1.5  1  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
       0.14   12.4   0.0       0.31   11.3   0.0    1.5  1  SdrD_B           SdrD B-like domain
       0.29   12.0   0.7       0.48   11.2   0.7    1.3  1  DMAP_binding     DMAP1-binding Domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.5   6.5e-11   6.4e-08       6      48 .]     189     232 ..     188     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 6.5e-11
                            HTH_24   6 rkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       +++L++L+k+++ i+q+eL ++lg S + v+  +  Le+ G+++
  gi|488599690|ref|YP_007906161.1| 189 KEVLNILMKEGGrITQKELRKKLGYSEAKVSLMIADLERRGIVE 232
                                       579******8877*****************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.7e-07   0.00017      10      54 ..     191     234 ..     190     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                                       HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       vL+ L  ++gr +t++el ++lg+s + vs ++++L+++G ve+ 
  gi|488599690|ref|YP_007906161.1| 191 VLNILMKEGGR-ITQKELRKKLGYSEAKVSLMIADLERRGIVEKI 234
                                       67777777776.9*****************************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 !   20.3   0.1   3.9e-07   0.00039      12      57 ..     190     236 ..     179     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.9e-07
                                       CHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  12 kvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                       +v   L+ + g+ t +e+ ++lg +++kv  ++  Le++G+Ve++k+
  gi|488599690|ref|YP_007906161.1| 190 EVLNILMkEGGRITQKELRKKLGYSEAKVSLMIADLERRGIVEKIKK 236
                                       6777888566788*******************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1     7e-07   0.00069      12      51 ..     195     235 ..     190     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7e-07
                                       HHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  12 lyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       l  +g+ ++++eL kklg s + v+ ++  Le++G +e+ k
  gi|488599690|ref|YP_007906161.1| 195 LMKEGGrITQKELRKKLGYSEAKVSLMIADLERRGIVEKIK 235
                                       5555555*******************************976 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.8e-07   0.00088       2      81 ..      38     116 ..      37     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.8e-07
                   CarboxypepD_reg   2 isGrVtd.asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv..sapGyatatreevtltagqtt 75 
                                       i+G++ + ++ +p+ ga V++     ++  + +  ++G++ ++++ pg+y++++    +G   ++ e++t+  +++ 
  gi|488599690|ref|YP_007906161.1|  38 IHGKIFSwENFKPLDGAVVEIN----TKPVQKKVTENGSYIFESILPGNYTIKAyyWQDGELLYWEENITIVSEGKY 110
                                       889998856889**********....6778888899******************77788888888889998888877 PP

                   CarboxypepD_reg  76 tlditL 81 
                                        ld++L
  gi|488599690|ref|YP_007906161.1| 111 VLDMVL 116
                                       777766 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   2.9e-06    0.0029       8      50 ..     191     233 ..     190     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.9e-06
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       +L++l +++++ t +el +++g + ++v+ +++ L+++G+ve+
  gi|488599690|ref|YP_007906161.1| 191 VLNILMKEGGRITQKELRKKLGYSEAKVSLMIADLERRGIVEK 233
                                       9****************************************96 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.6e-06    0.0066       1      52 [.      38      89 ..      38      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.6e-06
                   CarbopepD_reg_2  1 isGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsy 52
                                      i+G++++ e+ +pl ga V ++ + ++    enG++ ++++ +g+yt+++ y
  gi|488599690|ref|YP_007906161.1| 38 IHGKIFSWENFKPLDGAVVEINTKPVQKKVTENGSYIFESILPGNYTIKAYY 89
                                      78********************9999998899****************9765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.7e-06    0.0057      21      63 ..     201     247 ..     182     251 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TEE.EEES-HH CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis..r.grr.irildle 63 
                                       ++tq+el   lG +   vs ++++L+r+g+++  + gr+ i+ l  e
  gi|488599690|ref|YP_007906161.1| 201 RITQKELRKKLGYSEAKVSLMIADLERRGIVEkiKkGRGnIIFLRDE 247
                                       68******************************853356577766555 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.8e-06    0.0058      95     151 ..     190     245 ..     184     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.8e-06
                         HTH_micro  95 kivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeakivikin 151
                                       +++++l+k   +++++elr+kl     k++ +i  L+++g++e k+k++   +i ++
  gi|488599690|ref|YP_007906161.1| 190 EVLNILMKEGGRITQKELRKKLGYSEAKVSLMIADLERRGIVE-KIKKGRGNIIFLR 245
                                       699****************************************.9999887776655 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   1.4e-05     0.014       3      48 ..     189     233 ..     187     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                            HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48 
                                       + +l +L+++ g i+ +eL ++L+ S++ v   I++Le  g  +e+
  gi|488599690|ref|YP_007906161.1| 189 KEVLNILMKEGGRITQKELRKKLGYSEAKVSLMIADLERRG-IVEK 233
                                       67899**9*******************************99.3333 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.3e-05     0.023       8      54 ..     191     237 ..     189     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54 
                                       vL+ ++ +++r ++++l+++l ++ + +s ++  L+++G ve+ ++ 
  gi|488599690|ref|YP_007906161.1| 191 VLNILMKEGGRITQKELRKKLGYSEAKVSLMIADLERRGIVEKIKKG 237
                                       89999999999999***************************988765 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.7e-05     0.047       8      50 ..     195     237 ..     188     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                              FeoC   8 yleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50 
                                       +++e gr+  keL +++  s++ +  m++ ++r+G vek +++
  gi|488599690|ref|YP_007906161.1| 195 LMKEGGRITQKELRKKLGYSEAKVSLMIADLERRGIVEKIKKG 237
                                       567889********************************98775 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00013      0.13      11      56 ..     189     235 ..     185     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                       HHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress  11 etIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56 
                                       + ++ +   e++ +++k+l + L+ s + Vs m+  Le+ G ve  k
  gi|488599690|ref|YP_007906161.1| 189 KEVLNILMkEGGRITQKELRKKLGYSEAKVSLMIADLERRGIVEKIK 235
                                       5555555559999*****************************98655 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 ?   11.7   0.2   0.00017      0.17      31      69 ..      67     106 ..      64     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                             fn3_3  31 adssgsftipnVkpGtYrlt..vYadglfgdykqdsvtVta 69 
                                       ++++gs+ ++++ pG+Y+     ++dg +  y ++++t+ +
  gi|488599690|ref|YP_007906161.1|  67 VTENGSYIFESILPGNYTIKayYWQDGEL-LYWEENITIVS 106
                                       6789*************986215666665.66689999864 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.26       4      49 ..     190     236 ..     189     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                            HTH_34   4 avlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdke 49 
                                       +vl +L++   +++ +el+++l+ ++++ s  +  Le  g +e  k+
  gi|488599690|ref|YP_007906161.1| 190 EVLNILMKeGGRITQKELRKKLGYSEAKVSLMIADLERRGIVEKIKK 236
                                       589999997789****************************9986665 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00024      0.24      10      44 ..     198     237 ..     190     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                           AbiEi_4  10 qvGlfttrelea.aGispsa....lrrLvrkGwLvrlrrG 44 
                                       ++G +t +el++ +G s+      ++ L r+G ++++++G
  gi|488599690|ref|YP_007906161.1| 198 EGGRITQKELRKkLGYSEAKvslmIADLERRGIVEKIKKG 237
                                       5566777899999*****557******************9 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.31      28      65 ..      55      88 ..      46     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                            SdrD_B 28 tVtLkdakgevvatttTdasGkYkFtnltpGeYkVeft 65
                                       V++   +++ v++ +T ++G+Y F+++ pG+Y+++  
  gi|488599690|ref|YP_007906161.1| 55 VVEI---NTKPVQKKVT-ENGSYIFESILPGNYTIKAY 88
                                      5555...4555555666.68**************9975 PP

>> DMAP_binding  DMAP1-binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   0.00048      0.48       4      33 ..     183     210 ..     180     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                      DMAP_binding   4 sLPkdvrerLaeLeldlseGdiTeKgyekk 33 
                                        LP+d++e L+ L ++   G iT+K+  kk
  gi|488599690|ref|YP_007906161.1| 183 DLPDDLKEVLNILMKEG--GRITQKELRKK 210
                                       69**************9..66*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      862  (0.0480785); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1589.90
//
Query:       gi|488599691|ref|YP_007906162.1|  [L=219]
Description: hypothetical protein Asulf_00133 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   60.4  26.1    1.7e-14   54.3  26.1    2.1  1  DsbD      Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3  26.1   9.3e-19   1.7e-14       1     210 [.       7     186 ..       7     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 9.3e-19
                              DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkev 77 
                                       af +Gl+s lsPC+lp+iP+ ++  s       +++      +++a++ +l ++ +f+ lg+ ++ +       +  
  gi|488599691|ref|YP_007906162.1|   7 AFIGGLISALSPCVLPVIPVVFAV-S-------RAN------IVRAFVTALSMTATFSILGFFFGLI-------EGQ 62 
                                       699*****************9984.4.......232......3556666778899999999877654.......566 PP

                              DsbD  78 irrvaglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskesl 154
                                       +r++ +li  ++G  +l  ++i+ ++ l l ++ +   +  v+g++llG   +++wsPCigP+l++vl la+s+   
  gi|488599691|ref|YP_007906162.1|  63 LRVISSLILAIFGAMLL--LNINPFQSLPLGITNRIYLTGGVVGSILLGAGLGVIWSPCIGPILGAVLSLASSSS-- 135
                                       79999999999998887..8899999999998888888999*******************************988.. PP

                              DsbD 155 akgallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvl 210
                                         g++++l+y+ G+++ +  +++l+  lk + ++++  +   +i g+++lv+  vl
  gi|488599691|ref|YP_007906162.1| 136 --GLTVMLAYSSGFGMAI--ASILFLGLKATERVVRVSKASNRIFGAIILVF-VVL 186
                                       ..9***********9875..66666666644444444444444455555544.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1512.89
//
Query:       gi|488599692|ref|YP_007906163.1|  [L=376]
Description: Aspartate/tyrosine/aromatic aminotransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-70  237.8   0.0    2.3e-70  237.6   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
      4e-05   22.3   0.0    5.6e-05   21.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00065   18.8   0.0     0.0011   18.0   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.023   14.0   0.0      0.037   13.3   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.037   12.9   0.1       0.33    9.8   0.0    2.1  2  Alliinase_C      Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.6   0.0   6.5e-74   2.3e-70       2     363 .]      30     371 ..      29     371 .. 0.93

  Alignments for each domain:
  == domain 1  score: 237.6 bits;  conditional E-value: 6.5e-74
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       +vi+++++e+++     t+  +++a+ +  +++++  +y+p++g pel +a+ + l+++++l++ +e ++++++Ga+
  gi|488599692|ref|YP_007906163.1|  30 PVIDMSVGEPDFP----TPSFIIEAAYK--AMKEGKVFYTPTRGIPELLSAISEKLKNENGLDYAPE-NIITTPGAK 99 
                                       69**********9....*********99..8999999******************************.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        +i  +i++  ++ gde+++ dp++  y+ +++++gg+vv +p  ++e+f      +e+ +++      ktk+i+++
  gi|488599692|ref|YP_007906163.1| 100 YAIYEAIMAV-VEEGDEVILLDPSWVTYEACIKMAGGKVVWVP--HAEGF--EDAPVEDYITS------KTKLIIIN 165
                                       **********.9*******************************..22333..33345555666......8******* PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                       sp+NP G+v+++  l+k+ dla  +n+l+++De+Y++  f+ + + + +a+++   + +++ ++lsK ++++G+R+G
  gi|488599692|ref|YP_007906163.1| 166 SPSNPLGVVYPESFLKKIRDLAVDRNILVMSDEVYEKIIFDGK-HKS-IAEFDGMLErTILINGLSKTYSMTGWRLG 240
                                       ****************************************965.445.9999999999******************* PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       y++++++++++++k++++  s  +s +q+a++aa++ ++    +l+em++++++rr+ + d+L++lg+k+ ++++++
  gi|488599692|ref|YP_007906163.1| 241 YAASTEEIIKAMTKIQSHSVShpTSFVQYAAVAAIKSDQS---FLNEMVSEFKARRDIIMDGLDRLGIKYAPPKGAF 314
                                       **********************888888888888888775...9********************************* PP

                                       EEEEEETHHCHHHHHHH.HHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsaetakelskk.Lleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       + ++d+++   ++++++ L++e  v+ tpg+ f++  ++++R+++ ++++e++ee + +l
  gi|488599692|ref|YP_007906163.1| 315 YIFMDVKQD-SMKFCEEfLAKE-YVATTPGSAFGLkySTWVRVSY-ATSRENIEEMLVRL 371
                                       *******99.899999956666.**********************.********998775 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.6e-08   5.6e-05      71     175 ..      92     199 ..      39     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-08
                                       EEESSH.HHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS CS
                   Cys_Met_Meta_PP  71 lavssG.maAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtp 146
                                       ++++ G   Ai  ai+a++++Gde+++ d  +  t++ + k++    + v + +  + + +e  i+++tkl+ + +p
  gi|488599692|ref|YP_007906163.1|  92 IITTPGaKYAIYEAIMAVVEEGDEVILLDPSWV-TYEACIKMAGGKVVWVPHAEGFEDAPVEDYITSKTKLIIINSP 167
                                       444444146999*****************9995.7888888888888999999999********************* PP

                                       -TTTT----...HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 147 tnpllkvvD...iekiaklakkagvlvvvDnt 175
                                       +npl  v     ++ki +la ++++lv+ D +
  gi|488599692|ref|YP_007906163.1| 168 SNPLGVVYPesfLKKIRDLAVDRNILVMSDEV 199
                                       ***97664323388999999999999998875 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     3e-07    0.0011      62     176 ..      90     198 ..      68     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-07
                                       GGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--T CS
                       Aminotran_5  62 eeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllne 138
                                       e+ii t G+  ai  +++++   +++gde+++ +        + ++  k  g kv+++p  +eg  d  ++e++++ 
  gi|488599692|ref|YP_007906163.1|  90 ENIITTPGAKYAIYEAIMAV---VEEGDEVILLDPSWV----TYEACIKMAGGKVVWVPH-AEGFED-APVEDYITS 157
                                       67888888888888888888...99****999875433....44455556699*****99.666666.89******* PP

                                       TEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE- CS
                       Aminotran_5 139 ktklvaithvsnvtGtiqp...veeigklakkkgalvlvDa 176
                                       ktkl++i+  sn +G++ p   +++i +la ++++lv+ D 
  gi|488599692|ref|YP_007906163.1| 158 KTKLIIINSPSNPLGVVYPesfLKKIRDLAVDRNILVMSDE 198
                                       ****************8774447899999999999999886 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     1e-05     0.037      54     144 ..     105     197 ..      89     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                       HHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB--.. CS
                   DegT_DnrJ_EryC1  54 aLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVhlyGqva.. 125
                                       a++a  v++gdeVI    ++v+  +++  +g k+v v         + a +e  it++tk I+   p + +G v   
  gi|488599692|ref|YP_007906163.1| 105 AIMA-VVEEGDEVILLDPSWVTYEACIKMAGGKVVWVPHA---EGFEDAPVEDYITSKTKLIIinsPSNPLGVVYpe 177
                                       4444.3678***************************9554...5568899************933335566666532 PP

                                       .-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 126 .dmdalkaiaakhglkvieD 144
                                         +++++++a + ++ v++D
  gi|488599692|ref|YP_007906163.1| 178 sFLKKIRDLAVDRNILVMSD 197
                                       24677777777777777666 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2     0.058   2.1e+02     183     218 ..     219     253 ..     110     277 .. 0.63
   2 ?    9.8   0.0   9.2e-05      0.33     304     361 ..     315     373 ..     304     375 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.058
                                       B--SEEEEEHHHHHS-GGG-EEEEEES-HHHHHHHH CS
                       Alliinase_C 183 adedimLftlskltGhaGsrlGWalvkdkevakklv 218
                                        +  i +  lsk+   +G rlG+a   + e+ k ++
  gi|488599692|ref|YP_007906163.1| 219 LERTILINGLSKTYSMTGWRLGYAASTE-EIIKAMT 253
                                       3456677778888888888888886544.4444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 9.2e-05
                                       EEEEEESSSS..-HHHHHHTTTEEEEEGGGGTS-.TTEEEEESSS-HHHHHHHHHHHHT CS
                       Alliinase_C 304 yaWlkcekeededcaevlrekkiltrsGevfeae.sryvrlsllkrdddfdvllerlkk 361
                                       y ++ +++++ + c+e+l ++ + t  G+ f+ + s +vr+s   + ++ + +l rl++
  gi|488599692|ref|YP_007906163.1| 315 YIFMDVKQDSMKFCEEFLAKEYVATTPGSAFGLKySTWVRVSYATSRENIEEMLVRLER 373
                                       67889999999*********************763679****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2527.17
//
Query:       gi|488599693|ref|YP_007906164.1|  [L=142]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-32  110.1   0.4    8.5e-32  109.9   0.4    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.014   14.7   0.4      0.058   12.7   0.3    1.9  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.4   9.5e-36   8.5e-32       2     135 ..       4     133 ..       3     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 9.5e-36
                                       EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCH CS
                     DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetph 78 
                                       +++++Vva+fn++it  +   a+++++ +g+  e +d+++VPG+f+ p+a+k+++e++  +dav+++G+vi+G+t+h
  gi|488599693|ref|YP_007906164.1|   4 IKLGLVVAEFNRDITYMMEILAKEHADFLGA--EITDIIRVPGVFDTPIAVKRILEKG-DVDAVVTVGTVIEGDTEH 77 
                                       799***************************7..59*********************64.46**************** PP

                                       HHHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHH CS
                     DMRL_synthase  79 feyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaale 135
                                       +e+va+++++++m++sl++++Pv+ g+  +   +  a+er+     ++G eaa   ++
  gi|488599693|ref|YP_007906164.1|  78 DEIVAQHAARKIMDLSLEYNKPVTLGIAGPGmGRIAAQERVD--YAKRGVEAAVKLVR 133
                                       *******************************66777789993..36777777776665 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   6.5e-06     0.058      24      61 ..      51      88 ..      32      98 .. 0.79
   2 ?   -0.9   0.0      0.09   8.1e+02     151     174 ..     115     138 ..     103     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-06
                                      HHHHHHHH.--SEEEEES-----HHHHHHHHHHHHTT-- CS
                     Metallophos_3 24 lveviedk.dpDllvlvGdlvkaeakadeyesaqeerre 61
                                       v+ i +k d+D++v vG +++++++ de   aq + r+
  gi|488599693|ref|YP_007906164.1| 51 AVKRILEKgDVDAVVTVGTVIEGDTEHDEIV-AQHAARK 88
                                      467777777********************99.5555553 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.09
                                       SSS-EEEHHHHHHHGGGGGGS--- CS
                     Metallophos_3 151 efrLkYPaweveyrLkvlkelkdr 174
                                       + r+ Y ++ ve ++k+++ l+++
  gi|488599693|ref|YP_007906164.1| 115 QERVDYAKRGVEAAVKLVRRLREY 138
                                       567889999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 960.06
//
Query:       gi|488599694|ref|YP_007906165.1|  [L=153]
Description: riboflavin synthase alpha chain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   44.0   0.0    2.1e-11   43.8   0.0    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
        0.1   12.9   0.0       0.15   12.4   0.0    1.3  1  HAD_SAK_2      HAD domain in Swiss Army Knife RNA repair prot
       0.12   12.1   0.1       0.33   10.6   0.0    1.7  2  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   3.5e-15   2.1e-11       4     137 ..       3     127 ..       1     131 [. 0.75

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 3.5e-15
                                       EEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHH CS
                     DMRL_synthase   4 iaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfe 80 
                                       ++i  ++f      ++ + a++el++       ++++tVPG  +lp+aakkl++++++ d vi++G v   e ++  
  gi|488599694|ref|YP_007906165.1|   3 VGIADTTF---SRINMGKIAINELRKICS--LPYERYTVPGIKDLPIAAKKLIDERGC-DIVITCGWVGATENDKLS 73 
                                       55555555...234677778888888764..4799*******************6445.*********999999999 PP

                                       HHHHHHHHHHHHHHHHCTS-EEEEEEEESSHHCCHHCCTSTCCCHHHHHHHHHHHHH CS
                     DMRL_synthase  81 yvaeavskglmrvsldtgvPvifgvltvdteeqaleraggkagnkGeeaaeaalema 137
                                       y++ ++s +l  v+l tg+ vi   +  d+ e+ +e   + a+n+ +e++++a++++
  gi|488599694|ref|YP_007906165.1|  74 YIVLSMSLQL--VQLMTGKHVIDVTIHEDEAEDEQELL-VVAENRVREHVRNAVDLL 127
                                       9998777666..56677766776655555444444444.4469**********9986 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.4e-05      0.15      35      93 ..      46     117 ..      40     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                         HAD_SAK_2  35 lkriveatgakiVlsstWrrred.........eelkallkaag...rpriigvtpdlpeeeseeekk....sRaq 93 
                                        k+++++ g++iV++  W    +         ++  +l    +    + +i+vt + +e+e+e+e      +R++
  gi|488599694|ref|YP_007906165.1|  46 AKKLIDERGCDIVITCGWVGATEndklsyivlSMSLQLV---QlmtGKHVIDVTIHEDEAEDEQELLvvaeNRVR 117
                                       689***************999888777443332233333...2556999*******9999876654465554444 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.5e-05      0.33      39      75 ..      39      73 ..      15      94 .. 0.73
   2 ?   -0.8   0.0      0.18   1.1e+03      29      52 ..      88     111 ..      77     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.5e-05
                                      E-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HH CS
                     MoCF_biosynth 39 vpDdeeeikeallaaleeadviittGGtGptpdDvtp 75
                                      ++D + + k+ + ++ ++ d++it+G +G+t+ D   
  gi|488599694|ref|YP_007906165.1| 39 IKDLPIAAKKLI-DE-RGCDIVITCGWVGATENDKLS 73
                                      556665555555.66.888***************765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.18
                                       TSEEEEEEEEE-SSHHHHHHHHHH CS
                     MoCF_biosynth  29 lgvevskytvvpDdeeeikealla 52 
                                        g +v+++t+  D+ e+ +e l  
  gi|488599694|ref|YP_007906165.1|  88 TGKHVIDVTIHEDEAEDEQELLVV 111
                                       467888899999998888877733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 983.32
//
Query:       gi|488599695|ref|YP_007906166.1|  [L=373]
Description: L-aspartate aminotransferase apoenzyme /phosphoserine aminotransferase apoenzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-37  126.8   0.0    1.2e-36  126.5   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.016   14.4   0.0      0.021   14.0   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
      0.043   13.1   0.0      0.064   12.5   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.0   1.9e-40   1.2e-36      17     365 ..      21     342 ..       6     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 1.9e-40
                                       HHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEE CS
                       Aminotran_5  17 dalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalslarslkpgdeiv 92 
                                       +a           +   ++h++ e+++++++++  ++el++++   +++ +sG+++ ++++++ s+    ++  +i 
  gi|488599695|ref|YP_007906166.1|  21 NA----------MAKPLIGHRTPEFSDIMKNCTLGLKELFGTDG--DVYLISGSGTaGMEAAISSF----SKVSRIT 81 
                                       33..........33336899***********************6..99999998885777777777....8899999 PP

                                       EETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT CS
                       Aminotran_5  93 vteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkg 169
                                         ++++ + +    ++a  +  +v+ ++++++ ++dl+++++ l++  ++va+ h++++tG+++p  ei+k+akk+ 
  gi|488599695|ref|YP_007906166.1|  82 CIDNGKFGDR--LCRIAS-RYTEVDALRFEWGESIDLEKVKESLENGSEAVAFVHNETSTGILNPAREIAKIAKKHS 155
                                       99********..455663.45899***************************************************** PP

                                       -EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS....SS.STTSEEEEETTEEEEHC CS
                       Aminotran_5 170 alvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekl..eplllggemveevsleettfae 243
                                       alv++D+ ++vg  +++++++g+D++ ++++K l  P+G+ ++ v ++++e +  +   +   m  +++l++++   
  gi|488599695|ref|YP_007906166.1| 156 ALVIMDGITSVGGDEVKMDEWGIDVAIVGSQKcLGIPPGLAAVAVNERAWEFYneKAPFYLDLMAYKKKLKDWQ--- 229
                                       ********************************6666*****************433333444444444445554... PP

                                       TTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES..-B-CTCBSEEEEEE.TT CS
                       Aminotran_5 244 apskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlyg.pdkaerrasivsfnf.kg 318
                                       +p+     Tp v+ +++l++a+e+++e gle+  +++++ + +++e   + +   +    +    +++++++++ +g
  gi|488599695|ref|YP_007906166.1| 230 TPY-----TPAVPLFVALNEAIEMIKEEGLENRIQRHRKFSRAVREWAVNAGLELFPRlNEYSSYSNTVTAIKMpEG 301
                                       777.....************************999999999988876666554444221245578889999999889 PP

                                       CSHHHHHHHHHHT.TEEEEEE-TTTHHHHHHTT.S-EEEEE.--TTS-H CS
                       Aminotran_5 319 vhaedvatlLdee.gIavrsGhhcaqplmkrlalegtvRaS.lyiynte 365
                                       +  ++++  L++e  I +++G++++          +++R++ +++  ++
  gi|488599695|ref|YP_007906166.1| 302 ITDKELRGTLKQEySITISGGQEHL--------KGKIFRIGtMGNIGKR 342
                                       99999999999999*********99........6677777666655555 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-06     0.021     128     348 ..     111     335 ..      53     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-06
                                       TEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHH CS
                     Aminotran_1_2 128 fhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatr 204
                                        ++dle+++e l++ +        +++      tG + +  e+ k+   akk+ +l++ D + +++  +       +
  gi|488599695|ref|YP_007906166.1| 111 ESIDLEKVKESLENGS------EAVAFVHNETSTGILNPAREIAKI---AKKHSALVIMDGITSVGGDE-------V 171
                                       5799999999999933......355555555679************...*************9999988.......6 PP

                                       GGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH.................HHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                     Aminotran_1_2 205 anveeepnllivgslsKafGlaGeRvGyilgna.................avvsqlrklsrpflsssllqaavaaal 264
                                          e +++++ivgs  K +G++   ++++++n+                 a+++ l+++++p++   +l  a+++a+
  gi|488599695|ref|YP_007906166.1| 172 KMDEWGIDVAIVGSQ-KCLGIPP-GLAAVAVNErawefynekapfyldlmAYKKKLKDWQTPYTPAVPLFVALNEAI 246
                                       666678889999997.****975.3778888889****************************877777777777777 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH.......CHHHHHHHHHHTCTEEEEE CS
                     Aminotran_1_2 265 sdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae.......takelskkLleevgvyvtp 334
                                       +  +++   le++ qr+ k ++ +r+   ++gl+ ++  + + +++ +  +       t+kel   L +e+ + ++ 
  gi|488599695|ref|YP_007906166.1| 247 EMIKEE--GLENRIQRHRKFSRAVREWAVNAGLELFPRLNEYSSYSNTVTAikmpegiTDKELRGTLKQEYSITISG 321
                                       776654..67777777777777777666666777777666666666666666677779******************* PP

                                       GGGGTSTTEEEEEC CS
                     Aminotran_1_2 335 gtsftvpgrlRitv 348
                                       g++  + + +Ri  
  gi|488599695|ref|YP_007906166.1| 322 GQEHLKGKIFRIGT 335
                                       99999888899865 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.1e-05     0.064      40     168 ..      45     162 ..      15     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                                       HHHHHTT-SEEEEES-..HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHH CS
                   Beta_elim_lyase  40 avaelfgkeaalfvpq..GtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekl 114
                                        ++elfg+++ +++ +  Gta+ + +++ +  + + + + +++ +  + ++ ++ + +v +  ++  e   +dlek+
  gi|488599695|ref|YP_007906166.1|  45 GLKELFGTDGDVYLISgsGTAGMEAAISSFS-KVSRITCIDNGKFGDRLCRIASRYTEVDALRFEWGE--SIDLEKV 118
                                       5789******999885337888888888887.778999999999999999*********999999888..9****** PP

                                       HHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                   Beta_elim_lyase 115 eaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                       ++ +++ g+  e ++++  ++ + +       l+  re+a+iakk+   +++Dg
  gi|488599695|ref|YP_007906166.1| 119 KESLEN-GS--EAVAFVHNETSTGI-------LNPAREIAKIAKKHSALVIMDG 162
                                       ******.66..89999998888886.......77789****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2290.22
//
Query:       gi|488599696|ref|YP_007906167.1|  [L=652]
Description: 3-hydroxyacyl-CoA dehydrogenase /Enoyl-CoA hydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-67  225.3   2.4      5e-67  225.3   2.4    2.2  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    3.5e-55  187.0   0.0    5.4e-55  186.4   0.0    1.3  1  ECH_1            Enoyl-CoA hydratase/isomerase
      1e-52  176.7   0.6      2e-26   92.4   0.1    2.5  2  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    1.1e-40  140.2   0.9      9e-35  120.7   0.0    3.1  3  ECH_2            Enoyl-CoA hydratase/isomerase
    1.2e-08   35.3   0.0      4e-08   33.6   0.0    2.0  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    4.3e-07   30.4   0.8    5.6e-06   26.9   0.3    2.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    8.1e-06   26.1   0.6      2e-05   24.9   0.6    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    2.1e-05   23.9   2.4    0.00014   21.3   0.8    2.2  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    2.7e-05   23.6   0.8      6e-05   22.4   0.8    1.6  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    4.9e-05   23.3   0.3      0.025   14.6   0.0    3.7  4  ADH_zinc_N       Zinc-binding dehydrogenase
    5.5e-05   23.2   0.1    0.00015   21.8   0.1    1.7  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    6.6e-05   23.4   4.0     0.0016   19.0   0.7    3.4  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00022   20.9   1.1    0.00041   20.0   0.6    1.7  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00042   20.4   0.4     0.0013   18.8   0.4    1.9  1  OTCace           Aspartate/ornithine carbamoyltransferase, As
    0.00051   20.4   0.8     0.0017   18.7   0.8    1.9  1  NAD_binding_7    Putative NAD(P)-binding
     0.0067   15.9   0.3      0.012   15.1   0.3    1.5  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.025   14.7   0.1    1.6  1  DUF3479          Domain of unknown function (DUF3479)
      0.013   15.7   0.2      0.063   13.5   0.2    2.2  1  TrkA_N           TrkA-N domain
      0.015   15.7   1.2      0.015   15.7   1.2    1.9  1  Rubrerythrin     Rubrerythrin
      0.028   14.1   0.0      0.058   13.0   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.035   13.9   0.1      0.077   12.8   0.1    1.5  1  DFP              DNA / pantothenate metabolism flavoprotein
      0.048   14.1   0.3        0.2   12.1   0.3    2.1  1  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
      0.063   12.6   2.8       0.32   10.3   0.4    2.3  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.064   13.8   0.0       0.17   12.4   0.0    1.8  1  XdhC_C           XdhC Rossmann domain
      0.073   12.6   0.2       0.14   11.7   0.2    1.4  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
       0.11   12.3   1.0       0.42   10.4   1.0    2.0  1  DUF4116          Domain of unknown function (DUF4116)
       0.12   12.4   6.9        1.1    9.3   1.0    2.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.17   12.6   0.1       0.63   10.8   0.1    2.1  1  Methyltransf_25  Methyltransferase domain
       0.31   10.6   2.6         12    5.4   2.6    2.7  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi


Domain annotation for each model (and alignments):
>> 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 !  225.3   2.4   8.1e-70     5e-67       1     179 [.       3     182 ..       3     183 .. 0.98
   2 ?    0.3   0.1      0.93   5.8e+02      70     117 ..     589     634 ..     578     646 .. 0.80

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 8.1e-70
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77 
                                       +v viGaGtmG+gia+v+a ag++V++vdi++e+leka +ki  sl+kl++k+k+k e++e++l+ri++tt+leea+
  gi|488599696|ref|YP_007906167.1|   3 NVLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEFLEKAVKKIGWSLKKLESKKKIK-ENAEDVLKRIKTTTNLEEAA 78 
                                       588*****************************************************.99****************** PP

                                       .C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-T CS
                           3HCDH_N  78 .dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrge 153
                                        +ad+viEav+E++++K+++f++l++ +k+ +i+++nTS+++i+++++a++rpe viglHFfnPp+l+kLvE++rge
  gi|488599696|ref|YP_007906167.1|  79 kEADFVIEAVIEDTDVKKDIFKRLDENCKEGVIFSTNTSTIPITDISSATRRPESVIGLHFFNPPTLIKLVEIIRGE 155
                                       ***************************************************************************** PP

                                       T--HHHHHHHHHHHHHTT-EEEEE.CS CS
                           3HCDH_N 154 kTseetvatvvelakkigktpvvv.kd 179
                                       +Ts+etv++++e+ak ig   v v kd
  gi|488599696|ref|YP_007906167.1| 156 RTSDETVEKTKEFAKTIGMDYVLVeKD 182
                                       **********************99777 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.93
                                       ES-HHHHHC-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS CS
                           3HCDH_N  70 ttdleeavdadlviEavvEnlelKrkvfaelekiakpdailasnTSsl 117
                                        ++++++  a l + a+ E+++  rk+f+e  ++ k + ++   TS +
  gi|488599696|ref|YP_007906167.1| 589 VEKVSRL--APLSVKAIKESVNAVRKTFTEALELSKREIVMLIPTSDF 634
                                       4444444..7788999******************99999999888865 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.4   0.0   8.7e-58   5.4e-55       4     250 ..     406     651 ..     403     652 .] 0.94

  Alignments for each domain:
  == domain 1  score: 186.4 bits;  conditional E-value: 8.7e-58
                                       TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC..HHHHHHHCCHH CS
                             ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek..akqallkeevl 78 
                                       ++ a+i+++rP+++N+l++e+ t l+qa++k+e+dk vrav +tG +kaF+aG d+  m   +k     + +++  l
  gi|488599696|ref|YP_007906167.1| 406 HNYALITMRRPDKLNSLNEEMWTGLNQAFKKAEEDKDVRAVLITGEGKAFCAGDDISVMGSWKKftDGRDFFEKVAL 482
                                       66799*******************************************************99887566677888899 PP

                                       HHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHH CS
                             ECH_1  79 elwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilll 155
                                        l   l++  kp+i+ vnG+a+gGG+el l  Divia+++asf+ +e ++G +p+  ++ i +  +G+++ ++ +l+
  gi|488599696|ref|YP_007906167.1| 483 PLVATLMEYTKPTISLVNGYAFGGGMELNLLFDIVIASEKASFAVPEGLIGAMPPI-ASTIGVAMLGRKFIKY-CLT 557
                                       ******************************************************65.56677779***99976.89* PP

                                       T-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHH CS
                             ECH_1 156 gkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskdd 232
                                       g+++ ++ea++ G vd vvp++ql+   +e +ek+ + +p++++++ke++na ++++ +e+le+ ++    ++ + d
  gi|488599696|ref|YP_007906167.1| 558 GDQLDPEEAEELGFVDVVVPHDQLEMAGIEYVEKVSRLAPLSVKAIKESVNA-VRKTFTEALELSKREIVMLIPTSD 633
                                       *************************************************996.88999******************* PP

                                       HHHHHHHHHTCSH----- CS
                             ECH_1 233 ikeGlqaflEkrkpefed 250
                                       + eG+ af+ k+ p +++
  gi|488599696|ref|YP_007906167.1| 634 FAEGMMAFVKKKRPVWKG 651
                                       ****************96 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 !   92.4   0.1   3.3e-29     2e-26       1      96 [.     185     277 ..     185     278 .. 0.95
   2 !   82.1   0.0   5.3e-26   3.3e-23       6      97 .]     299     390 ..     297     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 3.3e-29
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF vnR+  ++++ea+r+veeg  +pe+iD+a++++lGlpmG++e++d  g+d++ ++++ ++++    +++ps+l+
  gi|488599696|ref|YP_007906167.1| 185 GFLVNRINLRVFTEAIRMVEEG-FKPEEIDSAVKYRLGLPMGILEVVDFSGVDIVFYVTHEMMKRGV--NVKPSKLV 258
                                       9*********************.************************************98888844..56788*** PP

                                       HHHHHTT--BGGGTBSSSB CS
                             3HCDH  78 eklveagrlgrktgkgfyk 96 
                                       e+++++grlg k+g+gfy+
  gi|488599696|ref|YP_007906167.1| 259 EEMIKEGRLGMKSGRGFYE 277
                                       ******************8 PP

  == domain 2  score: 82.1 bits;  conditional E-value: 5.3e-26
                                       HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHH CS
                             3HCDH   6 RvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklve 82 
                                       R+lap +nea +l+ +g+a+ ediD+am lg+G+p G +e++d +g+d++   le+ a+e+g ++y p pll ++ve
  gi|488599696|ref|YP_007906167.1| 299 RILAPAINEASWLLRNGIATREDIDKAMVLGMGYPKGLLEMADDFGIDMVVETLEARAKETGLDEYSPDPLLVEMVE 375
                                       9**************************************************************************** PP

                                       TT--BGGGTBSSSBC CS
                             3HCDH  83 agrlgrktgkgfyky 97 
                                       a++lg+k+g+gfy++
  gi|488599696|ref|YP_007906167.1| 376 AKKLGKKSGEGFYTW 390
                                       *************87 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.041        26     159     243 ..      24     107 ..      19     182 .. 0.79
   2 !  120.7   0.0   1.5e-37     9e-35       2     178 ..     409     582 ..     408     585 .. 0.95
   3 !   12.4   0.1   0.00013     0.081     253     318 ..     589     650 ..     584     651 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.041
                                       HHHHHHTTS--EE--GGGHHHHHHHHHTT..........--------......----SHHHHHHHHHHHT.-S-T.T CS
                             ECH_2 159 gadalaaglathyvpseklealeeaLaelessd..eeaveevleelaeeaeeeeeeselaekreaidrlfsadsv.e 232
                                       g ++  +++ + +++++ ++++  +L++les++  +e+ e+vl++++++++    e++ +e    i++++++++v +
  gi|488599696|ref|YP_007906167.1|  24 GYNVTIVDIKDEFLEKA-VKKIGWSLKKLESKKkiKENAEDVLKRIKTTTNL---EEAAKEADFVIEAVIEDTDVkK 96 
                                       55666677777777655.7788888888887777788888999888866655...3455666789999998887526 PP

                                       THHHHHH.T.. CS
                             ECH_2 233 eiveaLekaea 243
                                       +i+++L+++ +
  gi|488599696|ref|YP_007906167.1|  97 DIFKRLDENCK 107
                                       89999986443 PP

  == domain 2  score: 120.7 bits;  conditional E-value: 1.5e-37
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHH.HH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffre.eY 77 
                                       ++it+ rp++lN+L+ em + l++a+k+ e+d++v++v+++g+g kafCAG D+  + + +k ++ +  +ff++   
  gi|488599696|ref|YP_007906167.1| 409 ALITMRRPDKLNSLNEEMWTGLNQAFKKAEEDKDVRAVLITGEG-KAFCAGDDISVMGSWKKFTDGR--DFFEKvAL 482
                                       579***************************************88.**********999999987765..68877368 PP

                                       HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH- CS
                             ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTG 154
                                        l +++ +y+kp+++l++G++ GgG+ l +   + +++e++ fA+PE  IG +P ++ +   + l  ++ +y +lTG
  gi|488599696|ref|YP_007906167.1| 483 PLVATLMEYTKPTISLVNGYAFGGGMELNLLFDIVIASEKASFAVPEGLIGAMPPIASTIGVAMLGRKFIKY-CLTG 558
                                       9****************************************************************9999999.6*** PP

                                       --B-HHHHHHTTS--EE--GGGHH CS
                             ECH_2 155 arlkgadalaaglathyvpsekle 178
                                       ++l+ ++a ++g+ + +vp+++le
  gi|488599696|ref|YP_007906167.1| 559 DQLDPEEAEELGFVDVVVPHDQLE 582
                                       *********************986 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00013
                                       HHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------S CS
                             ECH_2 253 letlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWk 318
                                       +e++++ +P+s+k++ e+++  rk+  ++e+l+   r ++ l+ ++Df+eG  a +  k+k+P Wk
  gi|488599696|ref|YP_007906167.1| 589 VEKVSRLAPLSVKAIKESVNAVRKT--FTEALELSKREIVMLIPTSDFAEGMMAFV--KKKRPVWK 650
                                       6788899****************99..9************************9986..55799997 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   6.5e-11     4e-08       2      97 ..       4     124 ..       3     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 6.5e-11
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......................EEE-SSHHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......................akaaesieelvas 55 
                                       + +iG G+MG+ +a+ ++ agy+v++++ + e +e++v++                        +k+++++ee++++
  gi|488599696|ref|YP_007906167.1|   4 VLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEFLEKAVKKIgwslkkleskkkikenaedvlkrIKTTTNLEEAAKE 80 
                                       569***********************************9967999******************************** PP

                                       CSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE.-S---HHHH CS
                     NAD_binding_2  56 ldvvitmvkagkavdevieg.llealkkgdilid.gstsspedt 97 
                                       +d+vi  v ++++v++ i++ l e++k+g i+   +st+ ++d 
  gi|488599696|ref|YP_007906167.1|  81 ADFVIEAVIEDTDVKKDIFKrLDENCKEGVIFSTnTSTIPITDI 124
                                       ***************99999899999999998541455555554 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 !   26.9   0.3   9.1e-09   5.6e-06       3      69 ..       5      88 ..       3     114 .. 0.91
   2 ?   -0.2   0.0       2.4   1.5e+03      26      60 ..     406     439 ..     401     449 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 9.1e-09
                                      EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......................-EEECECHHHHH CS
                     F420_oxidored  3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......................vkvtavdneeaa 59
                                       +iGaG mg+++a+ ++ ag   ++++++ + + e +e++ +++g                      +k+t+ + eeaa
  gi|488599696|ref|YP_007906167.1|  5 LVIGAGTMGHGIAEVCAIAG---YNVTIV-DIKDEFLEKAVKKIGwslkkleskkkikenaedvlkrIKTTT-NLEEAA 78
                                      58******************...****88.***********************************9888888.99**** PP

                                      HH-SEEEE-S CS
                     F420_oxidored 60 eeadvvvlav 69
                                      +ead+v+ av
  gi|488599696|ref|YP_007906167.1| 79 KEADFVIEAV 88
                                      *******887 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.4
                                       GCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH CS
                     F420_oxidored  26 heivvansrnpekaeelaeelgvkvtavdneeaae 60 
                                       h+  +++ r p+k+++l ee+  ++ + + ++a e
  gi|488599696|ref|YP_007906167.1| 406 HNYALITMRRPDKLNSLNEEMWTGLNQ-AFKKAEE 439
                                       45555679*********9998755555.5555544 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 !   24.9   0.6   3.2e-08     2e-05       1      77 [.       4      88 ..       4      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.2e-08
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..........TTTCEEEEE--T...TTHHHHHHHH CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..........lgvrfeaialda...enyeavLaal 66
                                      vl+iGaG +G+++ae++a  + +  ++t++d ++e le++++k+          +  +++  a d+    + +  L+++
  gi|488599696|ref|YP_007906167.1|  4 VLVIGAGTMGHGIAEVCAIAG-Y--NVTIVDIKDEFLEKAVKKIgwslkkleskK--KIKENAEDVlkrIKTTTNLEEA 77
                                      89*****************97.6..8***************999**888888442..3333333330012233337888 PP

                                      HTTSSEEEE-S CS
                   Sacchrp_dh_NADP 67 lkegdlvvnls 77
                                       ke+d+v+ ++
  gi|488599696|ref|YP_007906167.1| 78 AKEADFVIEAV 88
                                      88889999876 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   0.8   2.2e-07   0.00014     143     214 ..       2      73 ..       1      99 [. 0.82
   2 ?    1.7   0.0       0.2   1.2e+02     189     214 ..     241     266 ..     234     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.2e-07
                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge 214
                                       k+++v+G+G  G  +A + a +g++vt+v+  d++l++  k+++  l++   k++++   + + k+i+  ++
  gi|488599696|ref|YP_007906167.1|   2 KNVLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEFLEKAVKKIGWSLKKLESKKKIKENAEDVLKRIKTTTN 73 
                                       689*********************************999999999988888888999888888888886665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.2
                                       HHHHHHHTTEEEEESCEEEEEEETTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 189 leealekeGvevklgtsvkeidgnge 214
                                       +++++ k+Gv+vk  + v+e++++g+
  gi|488599696|ref|YP_007906167.1| 241 VTHEMMKRGVNVKPSKLVEEMIKEGR 266
                                       78899****************99986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.8   9.7e-08     6e-05      30      99 ..       3      88 ..       1      93 [. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.7e-08
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE................HCHHHHHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev................lksqeellaeavke 91
                                      +vlviG+G+ G   +++++  g +Vt++D++ + le+  + +g + ++                 + ++  +l+ea+ke
  gi|488599696|ref|YP_007906167.1|  3 NVLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEFLEKAVKkIGWS-LKKleskkkikenaedvlkRIKTTTNLEEAAKE 80
                                      69*******************************999876655544.33335599*********9999999********* PP

                                      -SEEEE-- CS
                       AlaDh_PNT_C 92 advvigtv 99
                                      ad vi +v
  gi|488599696|ref|YP_007906167.1| 81 ADFVIEAV 88
                                      *****987 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     4e-05     0.025       2      70 ..      12      92 ..      11     152 .. 0.76
   2 ?   -0.3   0.0       1.6   9.9e+02      26      43 ..     165     182 ..     158     249 .. 0.74
   3 ?   -2.0   0.0       5.3   3.2e+03      27      41 ..     337     351 ..     333     365 .. 0.71
   4 ?    3.6   0.0     0.097        60      28      81 ..     564     623 ..     546     629 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                                      HHHHHHHHHHHTT-EEEEEESSHHHHHHH.HHTT.ESEEEET.....TTC.HHHHHHHHHT....TTSSEEEEEESSCS CS
                        ADH_zinc_N  2 vGlaavqlAkalGaeviavdsseeklela.kklG.adeviny.....kea.dlverikelt....ggegvdvvfecvGs 68
                                      +G+   ++++++G +v+ vd+++e le+a kk+G     + +     ++a d+ +rik  t      + +d+v+e+v  
  gi|488599696|ref|YP_007906167.1| 12 MGHGIAEVCAIAGYNVTIVDIKDEFLEKAvKKIGwSLKKLESkkkikENAeDVLKRIKTTTnleeAAKEADFVIEAVIE 90
                                      79999*******************997661569965555555788887777999999999999875789******9984 PP

                                      HH CS
                        ADH_zinc_N 69 ga 70
                                       +
  gi|488599696|ref|YP_007906167.1| 91 DT 92
                                      33 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                                       HHHHHHHTTESEEEETTT CS
                        ADH_zinc_N  26 klelakklGadevinyke 43 
                                         e+ak +G+d+v+ +k+
  gi|488599696|ref|YP_007906167.1| 165 TKEFAKTIGMDYVLVEKD 182
                                       447889999999988844 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.3
                                       HHHHHHTTESEEEET CS
                        ADH_zinc_N  27 lelakklGadeviny 41 
                                       le+a ++G d v+ +
  gi|488599696|ref|YP_007906167.1| 337 LEMADDFGIDMVVET 351
                                       688889999999988 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.097
                                       HHHHHTT.ESEEEET....TTC.HHHHHHHHHTTTSSEEEEEESSC.SHHHHHHHHHCEEE CS
                        ADH_zinc_N  28 elakklG.adeviny....kea.dlverikeltggegvdvvfecvG.sgatleaalkllkp 81 
                                       e a++lG +d+v+ +        ++ve++ +l  +  v+++ e v+ + +t+++al+l k+
  gi|488599696|ref|YP_007906167.1| 564 EEAEELGfVDVVVPHdqleMAGiEYVEKVSRLA-PLSVKAIKESVNaVRKTFTEALELSKR 623
                                       789****9999999977653333699******9.99*********98999******99876 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   2.3e-07   0.00015       2      93 ..       4     106 ..       3     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.3e-07
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H....HHHHHHH...HHSSBTTTBTT..----TTEEEES-HHHHHTT CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree....elieein...eehenvkyLpg..iklpenlvattdlaealkg 69 
                                       + v+GaG  G  +A v+a +g +v++   ++    + +++i    ++ e +k +++   ++ + ++ tt+l+ea+k+
  gi|488599696|ref|YP_007906167.1|   4 VLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDefleKAVKKIGwslKKLESKKKIKEnaEDVLKRIKTTTNLEEAAKE 80 
                                       78*************************9998788844444432224455555555522357799************* PP

                                       --EEEE---..HHHHHHHHHHHCCC- CS
                    NAD_Gly3P_dh_N  70 adiivlvvP..sqalrevlkklkgll 93 
                                       ad+++ +v   + + ++++k+l++  
  gi|488599696|ref|YP_007906167.1|  81 ADFVIEAVIedTDVKKDIFKRLDENC 106
                                       *****999511345555666666555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.7   2.5e-06    0.0016       1      68 [.       3      70 ..       3      79 .. 0.75
   2 ?    0.4   0.0       1.6   9.8e+02      38      67 ..      90     122 ..      83     129 .. 0.85
   3 ?    2.1   0.0      0.46   2.9e+02      45      70 ..     240     265 ..     230     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeieg 68
                                      +v+v+G+G+ g   A++ a  g +Vt+v+ +d++l +  ++++  l++  +k++i+   + ++++i++
  gi|488599696|ref|YP_007906167.1|  3 NVLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEFLEKAVKKIGWSLKKLESKKKIKENAEDVLKRIKT 70
                                      599********************************555555554455444555666655555555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                                       SSHHHHHHHHHHHHHT...TEEEECSEEEEEEE CS
                         Pyr_redox  38 lDeeaskilqeklekn...gievllntkveeie 67 
                                       +D ++ k + ++l +n   g+ + +nt++  i+
  gi|488599696|ref|YP_007906167.1|  90 EDTDVKKDIFKRLDENckeGVIFSTNTSTIPIT 122
                                       7999999999999999999*******9987776 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.46
                                       HHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox  45 ilqeklekngievllntkveeiegse 70 
                                       +++ ++ k+g++v  ++ vee+ +++
  gi|488599696|ref|YP_007906167.1| 240 YVTHEMMKRGVNVKPSKLVEEMIKEG 265
                                       7999*************999988776 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 !   20.0   0.6   6.6e-07   0.00041       2      84 ..       3      88 ..       2     108 .. 0.82
   2 ?   -3.3   0.0       9.5   5.8e+03      78     105 ..     568     594 ..     563     602 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.6e-07
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH.HCTTS-SS--TTHHHHHHHHCHT..TTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdk.lnsgkipiyepgLeelvkkaves..grlsfttdvekaveea 77
                                      ++ viG+G +G   a v a +g +v++vDi +e  +k +++   ++   + ++ +k+++e+  +r++ tt++e+a++ea
  gi|488599696|ref|YP_007906167.1|  3 NVLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEFLEKaVKKIGWSLKKLESKKKIKENAEDvlKRIKTTTNLEEAAKEA 81
                                      789***************************99877662444456666666666667666653489************** PP

                                      SEEEE-- CS
                    UDPG_MGDP_dh_N 78 dvifiaV 84
                                      d ++ aV
  gi|488599696|ref|YP_007906167.1| 82 DFVIEAV 88
                                      *998777 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.5
                                       SEEEE-----B-TTTTCB-THHHHHHHH CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaar 105
                                       ++ f+ V  P ++ ++ a ++yve+++r
  gi|488599696|ref|YP_007906167.1| 568 ELGFVDVVVPHDQLEM-AGIEYVEKVSR 594
                                       6778899999999555.59999999976 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 !   18.8   0.4   2.2e-06    0.0013       4      94 ..       3     103 ..       1     110 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-06
                                       EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TT..SSH..........-HHHHHHHHHHHHHHT-EEEEESSCHHH CS
                            OTCace   4 kiafvGdkknnvanslikllarlgmdvvlvaPkg..lep..........dkevleeakknakksggsititedleea 68 
                                       ++  +G   + + ++ ++++a+ g +v++v  k+  le+          + e  +++k+na+   ++i+ t++leea
  gi|488599696|ref|YP_007906167.1|   3 NVLVIG--AGTMGHGIAEVCAIAGYNVTIVDIKDefLEKavkkigwslkKLESKKKIKENAEDVLKRIKTTTNLEEA 77 
                                       566677..36899*********************9766689999999877777788888888888************ PP

                                       HTT-SEEEE--SSETTCCGGHHHHHH CS
                            OTCace  69 vkgaDvvytdvwvsmgeekereerlk 94 
                                       +k+aD+v+  v+     +k+ ++rl 
  gi|488599696|ref|YP_007906167.1|  78 AKEADFVIEAVIEDTDVKKDIFKRLD 103
                                       *********99998888887777765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.8   2.8e-06    0.0017       8      82 ..       2     102 ..       1     117 [. 0.67

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.8e-06
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele................elvklaeee.............. 54 
                                       k+vlv+G+G+++   ++  + ag +vt+v+ +  e+le                +       +              
  gi|488599696|ref|YP_007906167.1|   2 KNVLVIGAGTMGHGIAEVCAIAGYNVTIVDIK-DEFLEkavkkigwslkkleskK-------Kikenaedvlkrikt 70 
                                       79****************************99.7888844434444333332221.......123333333333333 PP

                     NAD_binding_7  55 ...lekdlegadlvi.aatddrelneriaeaa 82 
                                          le+  ++ad+vi a+++d+++++ i +  
  gi|488599696|ref|YP_007906167.1|  71 ttnLEEAAKEADFVIeAVIEDTDVKKDIFKRL 102
                                       33345558889977747789999999998854 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.9e-05     0.012       1      46 [.       2      46 ..       2     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelke 46
                                      k vlv+Ga+  +G+ ia+ +a +G++v++vd+++e le+++k+++ 
  gi|488599696|ref|YP_007906167.1|  2 KNVLVIGAG-TMGHGIAEVCAIAGYNVTIVDIKDEFLEKAVKKIGW 46
                                      789****99.9*******************************9975 PP

>> DUF3479  Domain of unknown function (DUF3479)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     4e-05     0.025       8     102 ..      34     124 ..      26     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                           DUF3479   8 esfnasalkraaaelnrelpelelsvfadeelrekpealeelaaavaeAdifiasllfdedqvealrealeaarekl 84 
                                       ++f+++a+k+   +l++  ++ +++  a   l++  +++++l++a +eAd++i +++ d d  + + ++l++   ++
  gi|488599696|ref|YP_007906167.1|  34 DEFLEKAVKKIGWSLKKLESKKKIKENAEDVLKR-IKTTTNLEEAAKEADFVIEAVIEDTDVKKDIFKRLDE---NC 106
                                       4555555555555665555555666555544444.47899********************************...79 PP

                           DUF3479  85 davlvfeSapelmrltkv 102
                                       +  ++f  +++ + +t +
  gi|488599696|ref|YP_007906167.1| 107 KEGVIFSTNTSTIPITDI 124
                                       999999999998888766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2    0.0001     0.063       1      39 [.       4      42 ..       4      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelre 39
                                      +++iG+G++G  +ae     g+ +v+++d ++e +e++ +
  gi|488599696|ref|YP_007906167.1|  4 VLVIGAGTMGHGIAEVCAIaGY-NVTIVDIKDEFLEKAVK 42
                                      68****************9777.6**********999855 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   1.2   2.5e-05     0.015      47     102 ..      35      91 ..      34     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHCSTTHH..B.SSBBS-------TTGGHHHHHHHHHHHHHHHHHCHHHH CS
                      Rubrerythrin  47 kilnklleklepele.levkekvreyaeakpkflttaknLeeaiegayaeeeemyrf 102
                                       ++l+k+++k+ ++l+ le k+k++e ae   k ++t++nLeea++ a  + e +++ 
  gi|488599696|ref|YP_007906167.1|  35 EFLEKAVKKIGWSLKkLESKKKIKENAEDVLKRIKTTTNLEEAAKEADFVIEAVIED 91 
                                       79********************************************99998888765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.3e-05     0.058       1      75 [.       4      87 ..       4     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEEETT.CEEEEEECEEECCH.......SCCCCS-E CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrltseg.geeilrppealsae.......ekselepi 69
                                      ++++GaG +G  +a   a ag++vt+++ ++  le+ +kk G +l++ + + ++++++++   +        ++ ++++
  gi|488599696|ref|YP_007906167.1|  4 VLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDeFLEKaVKKIGWSLKKLEsK-KKIKENAEDVLKriktttnLEEAAKEA 81
                                      68************99999*********999988888********999952.333333322222244444456666777 PP

                                      SEEEE- CS
                              ApbA 70 dlvivt 75
                                      d vi +
  gi|488599696|ref|YP_007906167.1| 82 DFVIEA 87
                                      777755 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013     0.077      28     102 ..       9      90 ..       7     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                       --HHHHHHHHHHHHTT-EEEEEE-S-S.S--..-T.T-EEEE--SHHHHHHHHHHHH...TT-SEEEE---S--EEE CS
                               DFP  28 SGkmGyalAeaaaarGaeVtlvsgpvs.let..pe.gvevvkvesaeemleaveeal...keadivimaAAvaDyrp 97 
                                        G+mG+ +Ae +a +G +Vt+v  + + le+  ++ g ++ k es ++++e++e+ l   k++  +  aA  aD+ +
  gi|488599696|ref|YP_007906167.1|   9 AGTMGHGIAEVCAIAGYNVTIVDIKDEfLEKavKKiGWSLKKLESKKKIKENAEDVLkriKTTTNLEEAAKEADFVI 85 
                                       69********************9885324433222366788888888887777665511155556666777899988 PP

                                       S---- CS
                               DFP  98 keaae 102
                                       + + e
  gi|488599696|ref|YP_007906167.1|  86 EAVIE 90 
                                       76543 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 ?   12.1   0.3   0.00032       0.2      50      99 ..      55     114 ..      15     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                                       G.........BTCCEEES-CHHHHTT-SEEEE-S.--GGGGGS-HHHHHHCCSS-EEEES CS
                    UDPG_MGDP_dh_C  50 e.........ekgvevvdsleealkgadaivilt.ehdefkeldlaklkelmkpavvfDg 99 
                                       +         +k+++++++leea+k+ad ++ ++ e  + k+  +++l e++k+ v+f +
  gi|488599696|ref|YP_007906167.1|  55 KkikenaedvLKRIKTTTNLEEAAKEADFVIEAViEDTDVKKDIFKRLDENCKEGVIFST 114
                                       033334446689*******************99977788999779999999999999976 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00052      0.32      37      72 ..       2      37 ..       1      57 [. 0.80
   2 ?    2.1   0.1      0.17   1.1e+02      77     123 ..      66     112 ..      53     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00052
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72
                                      k v +iG+G +G+ +a++++  g +v+++d + +  
  gi|488599696|ref|YP_007906167.1|  2 KNVLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEFL 37
                                      6899**************************996633 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.17
                                       HHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEE CS
                      2-Hacid_dh_C  77 elgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgail 123
                                       +   + ++lee+ +e+D+v+ ++    + ++ i ++  + +k+g+i+
  gi|488599696|ref|YP_007906167.1|  66 KRIKTTTNLEEAAKEADFVIEAVIEDTDVKKDIFKRLDENCKEGVIF 112
                                       33336789***********9888877777777767666777777665 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00027      0.17       1      35 [.       4      42 ..       4     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG....- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa....t 35
                                      ++++Gag +++ +a++ a +g++vt+vd ++ef     +
  gi|488599696|ref|YP_007906167.1|  4 VLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEFLekavK 42
                                      689***************************998844440 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00023      0.14       6      73 ..      12      84 ..       8     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTT...SEE.EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2  6 IGraiAkalaeeGaevvltdlneea.kkrveelaeelg...aev.lecDVtdeeqvealveevvekfgklDil 73
                                      +G++iA+ +a +G++v ++d+++e  +k+v+++  +l+   ++  ++ +++d  +  ++  +++e  ++ D++
  gi|488599696|ref|YP_007906167.1| 12 MGHGIAEVCAIAGYNVTIVDIKDEFlEKAVKKIGWSLKkleSKKkIKENAEDVLKRIKTTTNLEEAAKEADFV 84
                                      89***********************999999987665522122235555555555555555555555555555 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   1.0   0.00067      0.42       3      35 ..      35      69 ..      34     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00067
                           DUF4116  3 Eivleavkkngsalkyl..seeLknDkeivlkAvk 35
                                      E+  +avkk g++lk+l   +++k + e vlk +k
  gi|488599696|ref|YP_007906167.1| 35 EFLEKAVKKIGWSLKKLesKKKIKENAEDVLKRIK 69
                                      89**************864577*****99999777 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.0    0.0018       1.1      13      42 ..       2      30 ..       1      45 [. 0.85
   2 ?    5.5   0.8     0.028        17      31      88 ..      36      93 ..      28     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                                      -EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvva 42
                                      k+vl+iGaG m++ +a+  + +g++ v+++
  gi|488599696|ref|YP_007906167.1|  2 KNVLVIGAGTMGHGIAEVCAIAGYN-VTIV 30
                                      79**************998888887.7776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.028
                                      HHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                      Shikimate_DH 31 LlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseep 88
                                      +l+k vkk+      le  k++ e+ +++  ++++ ++l+e+ +ead vi a+   + 
  gi|488599696|ref|YP_007906167.1| 36 FLEKAVKKIGWSLKKLESKKKIKENAEDVLKRIKTTTNLEEAAKEADFVIEAVIEDTD 93
                                      566666666666677888889999999999999*****************99876654 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1     0.001      0.63       1      43 [.       4      46 ..       4     109 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                                      EEEET-TT.SHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH CS
                   Methyltransf_25  1 vLdlGcGt.GrltlalakrlgkakvtgvDiseemleaareraee 43
                                      vL +G+Gt G+ ++++ +  g ++vt vDi +e+le+a +++  
  gi|488599696|ref|YP_007906167.1|  4 VLVIGAGTmGHGIAEVCAIAG-YNVTIVDIKDEFLEKAVKKIGW 46
                                      677888886777777776657.****************988743 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 ?    5.4   2.6      0.02        12       5      88 ..       2     109 ..       1     118 [. 0.59

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.02
                                       S-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-................HHHHHHHHTT-EE.......EEHHHHH CS
                              IlvN   5 kkiaviGyGsqGhaqalnlrdsgldvvvglregs................ksvkkAkeegfev.......ltvaeav 58 
                                       k++ viG G+ Gh  a+    +g +v++   +++                +s kk ke++ +v       ++++ea+
  gi|488599696|ref|YP_007906167.1|   2 KNVLVIGAGTMGHGIAEVCAIAGYNVTIVDIKDEflekavkkigwslkklESKKKIKENAEDVlkrikttTNLEEAA 78 
                                       77889999999999999999999999888777775555566666666555233333333322211111114467777 PP

                                       HT-SEEE.E-S-HH.HHHHHHHHHTGGG--TT CS
                              IlvN  59 kkadvvm.iliPDe.lqkevyeeeiepnlkeg 88 
                                       k+ad+v+  +i D+ ++k+++ +++ +n keg
  gi|488599696|ref|YP_007906167.1|  79 KEADFVIeAVIEDTdVKKDIF-KRLDENCKEG 109
                                       777765524555542455555.6666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      827  (0.0461264); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.83u 0.37s 00:00:01.20 Elapsed: 00:00:00.52
# Mc/sec: 3754.43
//
Query:       gi|488599697|ref|YP_007906168.1|  [L=172]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00015   21.6   0.3    0.00079   19.3   0.0    2.2  2  HTH_11          HTH domain
    0.00038   20.5   0.0    0.00078   19.5   0.0    1.5  1  HTH_20          Helix-turn-helix domain
    0.00082   19.3   0.0     0.0016   18.3   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.001   19.3   0.3     0.0036   17.5   0.4    1.8  2  HigB_toxin      HigB_toxin, RelE-like toxic component of a to
     0.0011   18.9   0.0     0.0026   17.7   0.0    1.6  1  MarR            MarR family
     0.0013   18.2   0.0     0.0025   17.3   0.0    1.5  1  GerE            Bacterial regulatory proteins, luxR family
     0.0043   16.9   0.4      0.046   13.6   0.0    2.5  3  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0069   16.3   0.0      0.012   15.4   0.0    1.4  1  MarR_2          MarR family
     0.0073   16.1   0.0      0.012   15.5   0.0    1.3  1  CAAD            CAAD domains of cyanobacterial aminoacyl-tRNA
  ------ inclusion threshold ------
      0.015   15.4   0.1       0.19   11.9   0.0    2.3  2  HTH_17          Helix-turn-helix domain
      0.019   14.7   0.0        0.2   11.5   0.0    2.2  2  LacI            Bacterial regulatory proteins, lacI family
      0.021   14.8   0.0      0.062   13.3   0.0    1.7  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      0.028   14.3   0.1       0.29   11.1   0.0    2.0  2  DUF4294         Domain of unknown function (DUF4294)
      0.029   14.5   0.0      0.048   13.8   0.0    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.032   14.0   0.1      0.086   12.6   0.0    1.7  1  HTH_38          Helix-turn-helix domain
      0.035   13.7   0.0      0.076   12.6   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.04   13.9   0.0       0.11   12.5   0.0    1.8  1  HTH_29          Winged helix-turn helix
      0.045   14.0   0.0      0.068   13.4   0.0    1.4  1  NIPSNAP         NIPSNAP
       0.08   12.7   0.0       0.14   12.0   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
        0.1   12.5   0.0        0.2   11.5   0.0    1.5  1  HTH_10          HTH DNA binding domain
       0.12   12.3   0.0       0.31   10.9   0.0    1.7  1  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.3e-07   0.00079      13      45 ..      22      53 ..      11      59 .. 0.81
   2 ?   -1.1   0.0       2.1   1.8e+03      31      37 ..      78      84 ..      77      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.3e-07
                            HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                      +g ++ ee+A + +vS +t  ++IkaLe+ g+ 
  gi|488599697|ref|YP_007906168.1| 22 KG-FTLEEIANYAGVSPKTAFNRIKALESRGIV 53
                                      33.9*************************9954 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                            HTH_11 31 tvrrdIk 37
                                      ++++dIk
  gi|488599697|ref|YP_007906168.1| 78 AIHNDIK 84
                                      79****8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.1e-07   0.00078      14      58 ..      15      57 ..       4      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.1e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      +il  +  a+g+t++e+a   ++s++t+ +++++Le+ g+v  +r
  gi|488599697|ref|YP_007906168.1| 15 KILEGI--AKGFTLEEIANYAGVSPKTAFNRIKALESRGIVLKER 57
                                      577777..9*******************************88777 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.9e-06    0.0016      22      58 ..      24      61 ..       8      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-06
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisrgrr.ir 58
                                      +t ee+A++ G+++ t    +++L+ +g++ ++rr  +
  gi|488599697|ref|YP_007906168.1| 24 FTLEEIANYAGVSPKTAFNRIKALESRGIVLKERRtWK 61
                                      799**************************996443354 PP

>> HigB_toxin  HigB_toxin, RelE-like toxic component of a toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   4.2e-06    0.0036      12      57 ..      78     120 ..      74     132 .. 0.90
   2 ?   -2.0   0.0       5.2   4.4e+03      35      44 ..     155     165 ..     145     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-06
                                       HHHS--SSHHHHHHH-TT-EE-SSTEEEEEETTTTEEEEEEEETTT CS
                        HigB_toxin  12 vkkaewksladvkqtfpsadavgnnrvvFnIkgNkyRLivaieyer 57 
                                       + +++ k  ++v ++ +++d+v+n   +Fn+ g +y L+v+++y++
  gi|488599697|ref|YP_007906168.1|  78 AIHNDIKGYKKVVEALKKLDFVEN---IFNLIGSNYNLLVIVRYKD 120
                                       567888999999************...*****************75 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.2
                                       S.TEEEEEETT CS
                        HigB_toxin  35 n.nrvvFnIkg 44 
                                       + +r+ F++++
  gi|488599697|ref|YP_007906168.1| 155 EhKRTLFDVSQ 165
                                       34799999976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     3e-06    0.0026      18      52 ..      24      58 ..      21      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-06
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                       ++ e+a+  gvs+ t+ + +++Le +G + +++ 
  gi|488599697|ref|YP_007906168.1| 24 FTLEEIANYAGVSPKTAFNRIKALESRGIVLKERR 58
                                      5789**************************98875 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     3e-06    0.0025       5      33 ..      11      39 ..      10      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                                      HHHHHHHHHHCTTS-HHHHHHHHTS-HHH CS
                              GerE  5 kRErevLrllaeGksnkeIAeelniSekT 33
                                      kR +++L+ +a+G++ +eIA   ++S+kT
  gi|488599697|ref|YP_007906168.1| 11 KRMVKILEGIAKGFTLEEIANYAGVSPKT 39
                                      67789***********************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.4e-05     0.046      21      58 ..      22      59 ..      14      67 .. 0.88
   2 ?    0.1   0.0      0.91   7.8e+02      41      54 ..      88     101 ..      81     104 .. 0.77
   3 ?   -1.5   0.0       2.8   2.4e+03      49      66 ..     119     136 ..     110     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      +  t +eia+ +gv+  ++ + ++ Le++G+V +e+++
  gi|488599697|ref|YP_007906168.1| 22 KGFTLEEIANYAGVSPKTAFNRIKALESRGIVLKERRT 59
                                      56899***************************999887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.91
                                       HHHHHHHHCTSEEE CS
                              TrmB  41 evLrsLedkGlVer 54 
                                       +v++ L++ ++Ve 
  gi|488599697|ref|YP_007906168.1|  88 KVVEALKKLDFVEN 101
                                       67888888888875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.8
                                       CTSEEEESSTTTEEEE-- CS
                              TrmB  49 kGlVerekgrpklYravd 66 
                                       k+l e +k+r k+Y+ +d
  gi|488599697|ref|YP_007906168.1| 119 KDLKEASKEREKFYEWLD 136
                                       555566777777777665 PP

>> MarR_2  MarR family
   #    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      18      54 ..      22      56 ..       9      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       g  +t  e+a + g+s+ ++ +++k L+++G v ++
  gi|488599697|ref|YP_007906168.1| 22 KG--FTLEEIANYAGVSPKTAFNRIKALESRGIVLKE 56
                                      45..99****************************655 PP

>> CAAD  CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.4e-05     0.012      10      62 ..      64     118 ..      57     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                              CAAD  10 yerk.lkviglilaaiva.lklalavldaiddiPllpplleLvGlgytgwFvyry 62 
                                       y+++ l +ig++l+ai   +k + +v++a++++ ++++++ L+G  y    ++ry
  gi|488599697|ref|YP_007906168.1|  64 YQKAgLDTIGVLLIAIHNdIKGYKKVVEALKKLDFVENIFNLIGSNYNLLVIVRY 118
                                       45533999999988887548999*************************9999998 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.19       3      39 ..      25      63 ..      24      65 .. 0.77
   2 ?    0.8   0.0      0.65   5.5e+02      15      28 ..     128     141 ..     127     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                            HTH_17  3 tveEaAelLgvsrstvyrlir...rgelpaakiGrrwrip 39
                                      t eE+A++ gvs++t+ + i+   +  + ++k  r w+i+
  gi|488599697|ref|YP_007906168.1| 25 TLEEIANYAGVSPKTAFNRIKaleSRGI-VLKERRTWKID 63
                                      99*************9887855557777.77765667776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.65
                            HTH_17  15 rstvyrlirrgelp 28 
                                       r + y++++r  ++
  gi|488599697|ref|YP_007906168.1| 128 REKFYEWLDREGIK 141
                                       67889999999885 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024       0.2       1      16 [.      25      40 ..      25      44 .. 0.93
   2 ?    0.6   0.0      0.59     5e+02      32      46 .]      87     101 ..      84     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                      -HHHHHHHCTS-HHHH CS
                              LacI  1 tikDVArlAGVSkaTV 16
                                      t+ ++A  AGVS  T+
  gi|488599697|ref|YP_007906168.1| 25 TLEEIANYAGVSPKTA 40
                                      89**********9995 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.59
                                       HHHHHHHHHTTB-TT CS
                              LacI  32 erVeaameelnYiPn 46 
                                       ++V +a+++l+++ n
  gi|488599697|ref|YP_007906168.1|  87 KKVVEALKKLDFVEN 101
                                       79********99866 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.3e-05     0.062      12      51 ..      85     125 ..      77     133 .. 0.90
   2 ?   -2.2   0.0       5.1   4.3e+03      47      61 ..     142     156 ..     141     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHHHTSTTEEEEEEESS.SSSEEEEEEESSHHHHH CS
                    AsnC_trans_reg  12 qleefeealaelpeVvecyrvtG.dydyllkvvvrdleale 51 
                                        ++++ eal++l+ V+ ++ + G  y++l++v+ +dl++ +
  gi|488599697|ref|YP_007906168.1|  85 GYKKVVEALKKLDFVENIFNLIGsNYNLLVIVRYKDLKEAS 125
                                       4899*******************99************9865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                                       HHHHHHHHHHTTTTS CS
                    AsnC_trans_reg  47 lealerflreklasl 61 
                                       ++++ +f+ e+l ++
  gi|488599697|ref|YP_007906168.1| 142 VDSYAEFIGETLKEH 156
                                       689999999988765 PP

>> DUF4294  Domain of unknown function (DUF4294)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.47     4e+02     110     142 ..      13      45 ..      11      52 .. 0.83
   2 ?   11.1   0.0   0.00034      0.29      12      62 ..     115     166 ..     107     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.47
                           DUF4294 110 likelrggfkAffyqtvAklfgisLkkeYdpek 142
                                       ++k l+g  k f  +++A+  g+s k+ ++  k
  gi|488599697|ref|YP_007906168.1|  13 MVKILEGIAKGFTLEEIANYAGVSPKTAFNRIK 45 
                                       688899999999999999999999999998766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00034
                           DUF4294  12 yvf.kklkfknkkerkrylrlrrkvkkvyPyaklaaerlieleeeletlkdk 62 
                                       +v  k lk  +k+ +k y +l r+  kv  ya+++ e+l+e +++l  ++++
  gi|488599697|ref|YP_007906168.1| 115 IVRyKDLKEASKEREKFYEWLDREGIKVDSYAEFIGETLKEHKRTLFDVSQD 166
                                       333488899999*******************************999877654 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.6e-05     0.048      12      53 ..      21      58 ..      10      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                    B-block_TFIIIC 12 assRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                      a    +G t  ++a++ + +p+  f r+k+Le+ g + k   
  gi|488599697|ref|YP_007906168.1| 21 A----KGFTLEEIANYAGVSPKTAFNRIKALESRGIVLKERR 58
                                      4....79******************************99865 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.086      12      36 ..      15      39 ..      14      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            HTH_38 12 eIerllaeGlslreIArrLgrspsT 36
                                      +I  ++a+G +l eIA + g+sp T
  gi|488599697|ref|YP_007906168.1| 15 KILEGIAKGFTLEEIANYAGVSPKT 39
                                      6999*******************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 ?   12.6   0.0     9e-05     0.076      20      47 ..      26      53 ..      10      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-05
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGlI 47
                                        e+A   g+Sp t   r+k Le+ G++
  gi|488599697|ref|YP_007906168.1| 26 LEEIANYAGVSPKTAFNRIKALESRGIV 53
                                      56899999******************98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.11       3      47 ..      15      57 ..      14      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                            HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldr 47
                                      ++l  +a+G  t  +iA   g+s++t ++ +k+ e  G+  l++r
  gi|488599697|ref|YP_007906168.1| 15 KILEGIAKGF-TLEEIANYAGVSPKTAFNRIKALESRGI-VLKER 57
                                      68889999*9.9*************************97.44444 PP

>> NIPSNAP  NIPSNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.9e-05     0.068      40      70 ..     103     133 ..      81     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-05
                                       EEEESBSSEEEEEEEES-HHHHHHHHHHHHH CS
                           NIPSNAP  40 aseiGalnqvlhlwaydslaarearraalaa 70 
                                       ++ iG+++++l++++y++l +  ++r+++++
  gi|488599697|ref|YP_007906168.1| 103 FNLIGSNYNLLVIVRYKDLKEASKEREKFYE 133
                                       5689************************975 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.14      18      48 ..      23      53 ..      11      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyv 48
                                      + tl e+A+ +g+++ t+++ ++ L+ +G+v
  gi|488599697|ref|YP_007906168.1| 23 GFTLEEIANYAGVSPKTAFNRIKALESRGIV 53
                                      568**************************99 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024       0.2      22      49 ..      22      49 ..      20      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrkaes 49
                                      +  tl+e+A+  G+s+ t+ +++++ es
  gi|488599697|ref|YP_007906168.1| 22 KGFTLEEIANYAGVSPKTAFNRIKALES 49
                                      6789***************999998887 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.31      12      45 ..      18      51 ..       9      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                            HTH_23 12 lllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                         a+G + +eIA   gvs+ T  + +k+ +  G
  gi|488599697|ref|YP_007906168.1| 18 EGIAKGFTLEEIANYAGVSPKTAFNRIKALESRG 51
                                      44567*******************9999975455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1217.82
//
Query:       gi|488599698|ref|YP_007906169.1|  [L=139]
Description: hypothetical protein Asulf_00140 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0057   17.2   1.9       0.12   13.0   1.9    2.4  1  DUF1735        Domain of unknown function (DUF1735)
     0.0083   16.6   0.1        1.6    9.3   0.0    2.1  2  Cadherin-like  Cadherin-like beta sandwich domain
  ------ inclusion threshold ------
      0.031   14.3   0.4      0.075   13.1   0.4    1.6  1  DUF916         Bacterial protein of unknown function (DUF916)


Domain annotation for each model (and alignments):
>> DUF1735  Domain of unknown function (DUF1735)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.9     2e-05      0.12      73     109 ..      96     132 ..      13     139 .] 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                       EEE.GCGCEEECC.GGTEEEEEEEEE-.-TT--TTEEEE CS
                           DUF1735  73 ytlpsstvtikaG.eessasveiklkp.lekldgktYal 109
                                       y  +s+++ti+aG ++s a+v+++++  +++ ++++Y +
  gi|488599698|ref|YP_007906169.1|  96 Y--SSNKLTIPAGsSDSPAEVKVNVHIsADESANGSYTI 132
                                       2..6799******99999999999999544444888876 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00026       1.6      32      74 ..      16      62 ..      12      71 .. 0.67
   2 !    5.5   0.0    0.0041        24      56      87 ..     100     134 ..      76     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                     Cadherin-like 32 tataedsvatvtvngvaveeg...stetkdvsLneGrnk.ieikvta 74
                                      ta a+++ ++++vn +  e++   s+++++++L+ G+++  ei++++
  gi|488599698|ref|YP_007906169.1| 16 TALASEYIFSMKVNVKISESKidiSPKSFNLNLQSGTEYvREITIKN 62
                                      6677766666666666666666668***********99975555543 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0041
                     Cadherin-like  56 tkdvsLneGrnk..ieikv...taedgsttrtYtltv 87 
                                       + +++   G ++   e+kv   +++d s + +Yt+ +
  gi|488599698|ref|YP_007906169.1| 100 KLTIPA--GSSDspAEVKVnvhISADESANGSYTIYI 134
                                       334444..555556666666688999999999*9998 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 ?   13.1   0.4   1.2e-05     0.075       3     103 ..      28     134 ..      26     139 .] 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                            DUF916   3 VepilpenqidkkksYFdLkvkpgqeqelevkikNssdkeitveitvntAvTndnGvidYs...kskekkdkslkvs 76 
                                       V+ +++e+ id + + F+L+++ g+e   e++ikN  ++   +  ++ +  T +   +++     ++  + ++l+++
  gi|488599698|ref|YP_007906169.1|  28 VNVKISESKIDISPKSFNLNLQSGTEYVREITIKNYGESREIYFESFIEGETPEMMDVEFHdtfGNTIYSSNKLTIP 104
                                       88999******************************988776666677778888888888884443333344445554 PP

                            DUF916  77 lsel...vkipkeitlpakesktvklkikm 103
                                         +    ++++ ++++ a es + + +i +
  gi|488599698|ref|YP_007906169.1| 105 AGSSdspAEVKVNVHISADESANGSYTIYI 134
                                       433300134446666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 922.68
//
Query:       gi|488599699|ref|YP_007906170.1|  [L=132]
Description: putative aconitase subunit 2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-31  106.1   0.1    7.4e-31  105.8   0.1    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 !  105.8   0.1   4.1e-35   7.4e-31       1      80 []      24     103 ..      24     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 4.1e-35
                                       --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT- CS
                            DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadi 77 
                                       +Sflg+vdpe+G v  k+++++g++i+gki+++p+g+GStvg+yvll ++k g+aP A+i++++++i+a+Gai++di
  gi|488599699|ref|YP_007906170.1|  24 FSFLGDVDPESGLVKAKDSDIYGKNISGKIFAFPTGRGSTVGTYVLLRMKKAGSAPLAIINEKTEAIIAVGAIISDI 100
                                       7**************************************************************************** PP

                                       -EE CS
                            DUF126  78 Plv 80 
                                       Plv
  gi|488599699|ref|YP_007906170.1| 101 PLV 103
                                       *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 838.92
//
Query:       gi|488599700|ref|YP_007906171.1|  [L=434]
Description: uracil-xanthine permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-98  330.0  41.3      2e-98  329.7  41.3    1.1  1  Xan_ur_permease  Permease family


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.7  41.3  1.1e-102     2e-98       2     387 ..      17     393 ..      16     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: 329.7 bits;  conditional E-value: 1.1e-102
                                       HHHHHHHHHHHHHHHHHHHHHHTTTS-..........H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHHHHHG CS
                   Xan_ur_permease   2 qllllglQhllamfaalvvvPllvgdalgl.aeelrqlisatllasGiatllqllifgirlpillgssfafvtalmi 77 
                                       +++llglQh+lamf+a+v+vPl+vg a+gl ++ ++ +i+a ll+ Giatllq++ +g+r pi++gssfaf++  +i
  gi|488599700|ref|YP_007906171.1|  17 KAVLLGLQHVLAMFGATVTVPLVVGTAIGLeSNAIALMIQAVLLTMGIATLLQTT-IGSRYPIVQGSSFAFIP-GLI 91 
                                       789***************************999**********************.*****************.9** PP

                                       GG-....HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..BTT.B CS
                   Xan_ur_permease  78 alGsaedieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaaveglt 154
                                        +G     + +la++ gal+v g+l  li+ +g++g++ rl+ P+vtg++++liG+sla +avk   +  a+ +g  
  gi|488599700|ref|YP_007906171.1|  92 SIGK----GLGLAAVEGALIVGGILEALIGGLGIVGKVKRLFSPLVTGVTIMLIGFSLAHVAVKYTFNFFADPSG-- 162
                                       ***5....*************************************************************977555.. PP

                                       ---HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHHHHS-SS-----------HH..H CS
                   Xan_ur_permease 155 vvslkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmgivnlspevseapwfqlpsplkfgtplfnl 231
                                          +k + +a+++ ++++ ++  ++g ++ +p+ +g i+g+l+++ +g+v+ls  v+e+p+f++p+pl++g p f++
  gi|488599700|ref|YP_007906171.1| 163 ASIPKAFFIALITFATTVYVALKARGPLRAMPVIVGAIVGYLISIPLGMVDLSL-VNELPVFSIPKPLPWGIPIFEA 238
                                       78999*************************************************.********************** PP

                                       .HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TIIIIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB-- CS
                   Xan_ur_permease 232 gliltvlavalvavvesvGdiravakvvgrslkpkpdlrralladGlatllsgllGalpvttyaeniGvvaltkvas 308
                                        +i+t+l+ ++v+++esvGd++a++ ++g +++ + +++r+++ +Gla+ ++g+lGa ++t+y+eniG+valtkvas
  gi|488599700|ref|YP_007906171.1| 239 TAIITLLFAFMVSIIESVGDYHAISAISGAKIT-DRNINRGIMSEGLACSIAGFLGACGTTSYSENIGLVALTKVAS 314
                                       *****************************9999.******************************************* PP

                                       HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHH.TTS-SHHHHHHHHHHHHHHHH-- CS
                   Xan_ur_permease 309 rrvmvtagvilillglipklaallssIPepvlgGvllvvfgmiaasgvsnlqt.vdldsarnllivavslvlGlgva 384
                                       r+v++++gvili l+lipk++  l+sIP+pvlgG +++++gmi ++g++ +++ v++   rn+li+a +l++Glg++
  gi|488599700|ref|YP_007906171.1| 315 RYVVQIGGVILIFLSLIPKFSGILASIPAPVLGGLTVALYGMISVTGLRLIKEkVEF-TDRNMLIIASALIVGLGAP 390
                                       *************************************************77651455.5*****************9 PP

                                       --- CS
                   Xan_ur_permease 385 tvp 387
                                       ++p
  gi|488599700|ref|YP_007906171.1| 391 QLP 393
                                       987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2673.60
//
Query:       gi|488599701|ref|YP_007906172.1|  [L=222]
Description: uracil phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-52  176.6   0.0    4.8e-52  176.4   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    2.8e-11   43.2   0.6    3.8e-11   42.7   0.6    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0018   17.8   0.0     0.0062   16.1   0.0    1.7  2  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0     8e-56   4.8e-52       3     206 ..      15     217 ..      13     218 .. 0.97

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 8e-56
                           UPRTase   3 shpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysgelldeekialVpilRaGe 79 
                                       ++p+l   lt lRd++t++  fr+ + +++r++++e+++  +++e+ +v+tpl++++    +d+++i+++ +lRa  
  gi|488599701|ref|YP_007906172.1|  15 DSPFLMEVLTELRDKNTDSIAFRKGLVKLGRYMGYELTKT-MEFEKIKVETPLEETKGVIAKDRKNIVIITVLRAAI 90 
                                       6789999********************************8.************************************ PP

                           UPRTase  80 gmeealrellpearvghlglqr.eeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIl 155
                                       +++e+l + l +arvg +   r ++ + e    y k+P+   e+tv+++Dp+iaTG+++ a+iq +k+ + + ++I+
  gi|488599701|ref|YP_007906172.1|  91 PLMEGLIKTLEHARVGIISASRgKPPEFEIDVKYVKIPEIKPEDTVIITDPMIATGSTLTAVIQEIKKYN-PPKRIV 166
                                       *******************9995557889999*******99***************************77.789*** PP

                           UPRTase 156 vlsvlaseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRlFg 206
                                       vl vla++eg++++ ++fp+v+++++++D+el+ kgyi+pGlGD+GDR Fg
  gi|488599701|ref|YP_007906172.1| 167 VLGVLAAPEGIEKIKKKFPEVEIFITKIDRELNSKGYILPGLGDAGDRAFG 217
                                       **************************************************8 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.6   6.4e-15   3.8e-11      27     137 ..      76     184 ..      64     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 6.4e-15
                                       -GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHH CS
                      Pribosyltran  27 ngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTl 103
                                       ++k+ v+++++r ++p+   l++ Le   + + + ++ +++  e+  + ++    +e++   +V+i D +++tG+Tl
  gi|488599701|ref|YP_007906172.1|  76 DRKNIVIITVLRAAIPLMEGLIKTLEHARVGIISASRGKPPEFEIDVKYVK---IPEIKPEDTVIITDPMIATGSTL 149
                                       689**********************99999888888888888888777766...78888899*************** PP

                                       HHHHHHHHCC-BS.EEEEEEEEE-HHHHHHHHHH- CS
                      Pribosyltran 104 laalelLkekgpe.evriavlvdkpateeevdkna 137
                                       +a+++ +k+++p  ++ +  +++ p++ e+ +k++
  gi|488599701|ref|YP_007906172.1| 150 TAVIQEIKKYNPPkRIVVLGVLAAPEGIEKIKKKF 184
                                       *****999998764555555667888888877765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.15   8.8e+02      49      86 ..      74     112 ..      41     125 .. 0.64
   2 !   16.1   0.0     1e-06    0.0062     119     161 ..     131     173 ..     122     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.15
                          PRTase_2  49 eelpepvlvigfAEtAtaLghgvadal.eeealylhtTR 86 
                                       ++ ++++++i +  +A+ L +g+ ++l ++++ ++ + R
  gi|488599701|ref|YP_007906172.1|  74 AKDRKNIVIITVLRAAIPLMEGLIKTLeHARVGIISASR 112
                                       466778888888888888888888888444666666666 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-06
                          PRTase_2 119 aaakelvLvDDEistGktalnliralqeklprkryvvvslvdw 161
                                       + ++++++ D  i+tG+t++++i+++++ +p kr+vv+ ++  
  gi|488599701|ref|YP_007906172.1| 131 KPEDTVIITDPMIATGSTLTAVIQEIKKYNPPKRIVVLGVLAA 173
                                       5678999******************************998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1519.15
//
Query:       gi|488599702|ref|YP_007906173.1|  [L=101]
Description: hypothetical protein Asulf_00145 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.17   11.1   7.9       0.18   10.9   7.9    1.0  1  Bac_export_2  FlhB HrpN YscU SpaS Family
       0.37   10.5  12.8       0.49   10.1  12.8    1.2  1  Yip1          Yip1 domain
          2    8.6   5.7        2.1    8.5   1.7    2.1  2  DUF2407_C     DUF2407 C-terminal domain
        3.5    7.1  15.7        3.8    7.0   1.5    2.0  2  DUF3169       Protein of unknown function (DUF3169)
        3.9    7.8  10.7        1.4    9.2   4.1    2.1  2  DUF5056       Domain of unknown function (DUF5056)


Domain annotation for each model (and alignments):
>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   7.9   5.1e-05      0.18      30     122 ..       4      98 ..       1     100 [. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Bac_export_2  30 alvllaglllllllgpslveelaellrevlsa..lelllelllallllllplllvlllaallanllqvgflfstkal 104
                                       ++v+++g+++ +l+g s +++l +++++v+++  ++l + ++ ++l ll++ +++++ + +l++l+ + ++ ++ ++
  gi|488599702|ref|YP_007906173.1|   4 TTVTIIGVIVGFLFGLSGIATLFNMMSTVITEasTQLSQVSAASTLVLLVIAIILVIKVRILSSLIVGAIIGAVLNF 80 
                                       4567777788888888888899999999999964333344444444445555666666789999999999999999* PP

                                       XXXXXXXXXXXXXXXXXX CS
                      Bac_export_2 105 kpklsklnplkglkrifs 122
                                        ++++ +++++++  i+s
  gi|488599702|ref|YP_007906173.1|  81 ILQMNGIDIVNQVFSIIS 98 
                                       ********9999877776 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  12.8   0.00014      0.49      64     150 ..       6      89 ..       3      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                              Yip1  64 gaiiggylglllgllllalllhliakllggkgsfkqtlsvvgyallPlilgaliaillllllgtllllvgllaliWs 140
                                       ++iig ++g+l+gl  +a l++ ++ +     +  q+ +v++ ++l+l++ a+i+++ + +l   l++  +++++  
  gi|488599702|ref|YP_007906173.1|   6 VTIIGVIVGFLFGLSGIATLFNMMSTVITEAST--QLSQVSAASTLVLLVIAIILVIKVRILSS-LIVGAIIGAVLN 79 
                                       578999999999999999999999999998888..89999999999999999998888887776.333355666666 PP

                              Yip1 141 lvllylglka 150
                                       ++l ++g+ +
  gi|488599702|ref|YP_007906173.1|  80 FILQMNGIDI 89 
                                       6666666655 PP

>> DUF2407_C  DUF2407 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.7   0.00057       2.1      91     115 ..       5      29 ..       1      59 [. 0.75
   2 ?    3.1   0.2     0.028     1e+02      86     106 ..      61      81 ..      30      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00057
                         DUF2407_C  91 edlliGlliGfflglfalllllkee 115
                                       +  +iG+++Gf++gl ++  l++  
  gi|488599702|ref|YP_007906173.1|   5 TVTIIGVIVGFLFGLSGIATLFNMM 29 
                                       5689***********9887766543 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.028
                         DUF2407_C  86 eskanedlliGlliGfflglf 106
                                       + + +  l++G++iG +l ++
  gi|488599702|ref|YP_007906173.1|  61 KVRILSSLIVGAIIGAVLNFI 81 
                                       556677888888888887664 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.6    0.0019       6.8      15      69 ..       7      60 ..       4      68 .. 0.58
   2 ?    7.0   1.5    0.0011       3.8      11      40 ..      64      93 ..      60     101 .] 0.57

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0019
                           DUF3169 15 gliGgiiGfllgafeaekgleelsaalkelllligskilpllliiavlvviisvv 69
                                       +iG i+Gfl+g+   +  ++ +s+++ e+++ ++++ +    ++ ++++ii+v+
  gi|488599702|ref|YP_007906173.1|  7 TIIGVIVGFLFGLSGIATLFNMMSTVITEASTQLSQVSAAS-TLVLLVIAIILVI 60
                                      57788888888777777777777777777777777743333.3333333333322 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0011
                           DUF3169 11 mliggliGgiiGfllgafeaekgleelsaa 40
                                      +l + ++G+iiG++l ++ + +g++ + ++
  gi|488599702|ref|YP_007906173.1| 64 ILSSLIVGAIIGAVLNFILQMNGIDIVNQV 93
                                      455667777777777776666666633333 PP

>> DUF5056  Domain of unknown function (DUF5056)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.1   0.00038       1.4      43      91 ..       5      53 ..       3      58 .. 0.76
   2 ?    2.9   0.5     0.036   1.3e+02      42      66 ..      69      95 ..      59     101 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00038
                           DUF5056 43 vcavlavvL.F.vvldGlelllevlrevftsaiqslasidldpkSlliavv 91
                                      ++++++v+  F + l G+++l+++++ v+t+a ++l   +++  S l++ v
  gi|488599702|ref|YP_007906173.1|  5 TVTIIGVIVgFlFGLSGIATLFNMMSTVITEASTQLS--QVSAASTLVLLV 53
                                      4556666652314578****************99988..999999887765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.036
                           DUF5056 42 avcavlavvLFvv..ldGlelllevlr 66
                                      +v a++++vL ++  ++G++++ +v++
  gi|488599702|ref|YP_007906173.1| 69 IVGAIIGAVLNFIlqMNGIDIVNQVFS 95
                                      456788888854412789999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1651  (0.0920854); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 726.51
//
Query:       gi|488599703|ref|YP_007906174.1|  [L=148]
Description: cytidyltransferase-related domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-18   66.5   0.0    3.1e-18   66.3   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.049   13.5   0.0    1.5  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 !   66.3   0.0   3.5e-22   3.1e-18       2     142 ..       5     138 ..       4     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 3.5e-22
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlk 78 
                                       +gGtF p+H GH +l+++a +l+++++++g++sde ++   +++ +   R e+++++  +++ ++++  +++  + +
  gi|488599703|ref|YP_007906174.1|   5 LGGTFEPLHEGHKKLIDVAIQLGGKEVMIGITSDEMARLRIRSVLPFRIRAENVRRYVLSKYGFEPSIVKIDSPYGR 81 
                                       69*************************************9************************************* PP

                                       HTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  79 klkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                        l++d  ylv++ ++ + ++  ++ ++ lg++++ +v+++       ++ +++ ++iSst+i++
  gi|488599703|ref|YP_007906174.1|  82 TLDVDFDYLVVSPETCKMAELINRKRRELGKKEIRIVKVD-------FLLAEDGKPISSTRIKR 138
                                       **996559*****************************998.......***************97 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.5e-06     0.049      13      79 ..       7      70 ..       1      76 [. 0.76
   2 ?   -2.0   0.0      0.33     3e+03     137     157 ..     113     134 ..      86     135 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.5e-06
                           FAD_syn 13 GnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvda 79
                                      G F  +H GH++l++ a+++  ++   ++ +t ++  r  ++ +  p+r+   + +  +l+++g++ 
  gi|488599703|ref|YP_007906174.1|  7 GTFEPLHEGHKKLIDVAIQLGGKEV--MIGITSDEMARLRIR-SVLPFRIRAENVRRYVLSKYGFEP 70
                                      79*****************986553..344677777777777.788888888888888888888775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.33
                           FAD_syn 137 lgfevevvpkv.eleeekisst 157
                                        ++++ +v+ +  ++++ isst
  gi|488599703|ref|YP_007906174.1| 113 KEIRIVKVDFLlAEDGKPISST 134
                                       3355555554446667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 978.58
//
Query:       gi|488599704|ref|YP_007906175.1|  [L=376]
Description: geranylgeranyl reductase family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   40.1   0.0    3.5e-05   22.9   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    1.5e-07   31.0   0.1      0.012   14.8   0.0    2.8  2  FAD_binding_3   FAD binding domain
    2.7e-05   23.9   0.1    4.1e-05   23.3   0.1    1.3  1  DAO             FAD dependent oxidoreductase
    9.9e-05   21.5   0.3     0.0067   15.5   0.0    2.1  2  Lycopene_cycl   Lycopene cyclase protein
     0.0005   19.2   0.0    0.00085   18.5   0.0    1.3  1  SE              Squalene epoxidase
     0.0033   17.6   0.3      0.007   16.6   0.3    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.021   14.1   0.0    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.032   12.9   0.0      0.047   12.4   0.0    1.2  1  HI0933_like     HI0933-like protein
      0.066   12.3   0.9      0.091   11.8   0.9    1.2  1  FAD_binding_2   FAD binding domain


Domain annotation for each model (and alignments):
>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   4.3e-06    0.0086       1      35 [.       2      32 ..       2      42 .. 0.87
   2 !   22.9   0.0   1.7e-08   3.5e-05     183     380 ..     116     314 ..     102     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      +i+ivGGG+aG+l+A++l+k      ev +ve  +
  gi|488599704|ref|YP_007906175.1|  2 RILIVGGGIAGSLSAIHLGKEN----EVVVVEEHQ 32
                                      69*****************999....788888765 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.7e-08
                                       TTS-EEEEEETTS-E.EE-SEEEE-SGGG-IIIIIIT---EEE-TTT----EEEEEEEE--H---SSEEEEE-SSEE CS
                    Trp_halogenase 183 edgrveslrledgre.veadlfiDcsGfrgllieqaLktgfedwsdvLltdrAlavqveseelvepytrataekaGW 258
                                        +g+ ++lr ++g+  +e+d+ i + G  +++ ++    gf++      +     +++  e+ ve y ++   +   
  gi|488599704|ref|YP_007906175.1| 116 SNGKKAKLRSDSGEMfLEYDFLIGADGTYSRVSSEY---GFRKPEVLSAIQFEANFECLDENMVELYFGSEYSSGFF 189
                                       567778899988765379999999999999999995...77765544444555566777778999999999888888 PP

                                       EEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--TTTS-.EEEE---EE....ES-SEETTEEE-CCCTEE-- CS
                    Trp_halogenase 259 tWkiPLqhrlgn.GyvyssahadddeAlaellaeldgkleaep.rkirfttGr....rkqawvknvvalGlasgfve 329
                                          iPL  ++   G+v   + +++ + l++l+++ + ++ +      ++++G      +++ ++nv ++G+++g   
  gi|488599704|ref|YP_007906175.1| 190 AYAIPLDSTTARiGVVTKASEINAVHYLKNLIEKHPSASIRFGkAITELNAGSipvgLNEIVRENVCLIGDSAGMTK 266
                                       99******99999***99999988888888888877665444426667888888888899***************** PP

                                       CCCS-HHHHHHHHHHHHHHT--BTT--HHHHHHHHHHHHHHHHHHHHHHHH CS
                    Trp_halogenase 330 PlestsihliqaalrrLlallpdksdepaaiaefnrevarelervrdfiil 380
                                       P  + +i+ + +a++ L + +p+    +   +e+ +++ +e+e   ++ +l
  gi|488599704|ref|YP_007906175.1| 267 PYTGGGIYYLLKAVECLSENFPSL---NRFKQEYLNRMGKEYEFGMKIYRL 314
                                       **********************75...344456666666666655555555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   4.5e-05     0.089       4      36 ..       3      34 ..       1      55 [. 0.88
   2 !   14.8   0.0   6.2e-06     0.012     136     303 ..     117     272 ..      87     274 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                      +lIVG+G aG ++a  L +   +vv+ve ++++
  gi|488599704|ref|YP_007906175.1|  3 ILIVGGGIAGSLSAIHLGKE-NEVVVVEEHQSA 34
                                      89******************.9******99875 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.2e-06
                                       CCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTC..CEEEEECC CS
                     FAD_binding_3 136 egvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdivep..lvlilsae 210
                                       +g +a++r+  +ge   ++ ++l+GaDG  S+v ++ g++   +       +  + f+a+++ + e+  + + +s+ 
  gi|488599704|ref|YP_007906175.1| 117 NGKKAKLRSD-SGEM-FLEYDFLIGADGTYSRVSSEYGFR--KP-----EVLSAIQFEANFECLDENmvELYFGSEY 184
                                       4556666665.3555.8999******************88..22.....2345566777777555556545555555 PP

                                       TTEE..EEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEE..EEEEEEEEEEEEEEESSSEE CS
                     FAD_binding_3 211 srgv..mviPlentlerfyvqvearaekeersekfteeevkarlreivgektldv..eieevsawtvaqrvaekyrk 283
                                       s+g+    iPl++t  r+ v+         +  +++  ++ ++l e + ++ ++    i+e +a  +     ++  +
  gi|488599704|ref|YP_007906175.1| 185 SSGFfaYAIPLDSTTARIGVVT--------KASEINAVHYLKNLIEKHPSASIRFgkAITELNAGSIPV-GLNEIVR 252
                                       5555577889999333333322........223334444444444433333333322344444333333.3344445 PP

                                       TTEEE-GGGTEEE-STTSHH CS
                     FAD_binding_3 284 grvflaGDAaHihpPtgGqG 303
                                       ++v+l+GD+a ++ P +G G
  gi|488599704|ref|YP_007906175.1| 253 ENVCLIGDSAGMTKPYTGGG 272
                                       56788888887777777776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   2.1e-08   4.1e-05       2      33 ..       3      35 ..       2      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.1e-08
                                      EEEECTSHHHHHHHHHHHHTT.EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg.Vtllekgdiag 33
                                      ++i+GGGi+G+  A +L +++ V+++e +  ag
  gi|488599704|ref|YP_007906175.1|  3 ILIVGGGIAGSLSAIHLGKENeVVVVEEHQSAG 35
                                      99***************88879******95544 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.2    0.0096        19       2      36 ..       3      34 ..       2      41 .. 0.82
   2 !   15.5   0.0   3.4e-06    0.0067     187     273 ..     188     270 ..     141     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0096
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      ++++G+G Ag + A +l    ++ +vv++e  +s 
  gi|488599704|ref|YP_007906175.1|  3 ILIVGGGIAGSLSAIHL---GKENEVVVVEEHQSA 34
                                      78***************...667788888876665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.4e-06
                     Lycopene_cycl 187 tFlYalPldsdrllvEeTelaskpeLpadalkkrlaaylralglk.vkevveeEqgviPvtlggslprleqkvlaiG 262
                                        F Ya+Plds+++ +      ++ e+ a  + k l ++     ++  k + e   g iPv   g  + + ++v+ iG
  gi|488599704|ref|YP_007906175.1| 188 FFAYAIPLDSTTARIGV--VTKASEINAVHYLKNLIEKHPSASIRfGKAITELNAGSIPV---GLNEIVRENVCLIG 259
                                       599*********99975..4455556777777777777777777625789999*******...777777888***** PP

                     Lycopene_cycl 263 aaaglvhPaTG 273
                                         ag+++P TG
  gi|488599704|ref|YP_007906175.1| 260 DSAGMTKPYTG 270
                                       **********9 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.3e-07   0.00085       6     172 ..     138     295 ..     135     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.3e-07
                                SE   6 vvcDGifsklRkelsdnkvevtssfvGlvlknaelpkknkghvilgk..pspvllYqi..sstetRilveikskklP 78 
                                       + +DG++s++  e    k+ev s        n e  ++n  ++ +g+  +s  + Y i   st +Ri v  k++++ 
  gi|488599704|ref|YP_007906175.1| 138 IGADGTYSRVSSEYGFRKPEVLSAI--QFEANFECLDENMVELYFGSeySSGFFAYAIplDSTTARIGVVTKASEIN 212
                                       6688999999999888888888865..34567777788888888887666777888762256777777766666554 PP

                                SE  79 siangelkeylkeevaPqlPkelrksfkkaleegklrsmpnkflpasknekkGlillGDalnmRHPltggGmtvaln 155
                                               +ylk+ +  +   ++   f ka+ e +  s+p      ++  ++ ++l+GD+  m  P tggG+   l+
  gi|488599704|ref|YP_007906175.1| 213 A------VHYLKNLIEKHPSASI--RFGKAITELNAGSIPVGL---NEIVRENVCLIGDSAGMTKPYTGGGIYYLLK 278
                                       4......6788888776654555..599999998888888654...44455779*********************** PP

                                SE 156 Divllskllkpledlsd 172
                                        +  ls+    l+ +++
  gi|488599704|ref|YP_007906175.1| 279 AVECLSENFPSLNRFKQ 295
                                       **999998888866654 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   3.5e-06     0.007       1      32 [.       5      35 ..       5      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      IvG+G++G++ A +L k+  +v+++e +++ G
  gi|488599704|ref|YP_007906175.1|  5 IVGGGIAGSLSAIHLGKE-NEVVVVEEHQSAG 35
                                      9****************8.89******99998 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     1e-05     0.021       2     106 ..       2     140 ..       1     158 [. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE..TTHCHHHCSHHH..HCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx..xxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve..legtclnggcll..skallgvaedaeias................. 57 
                                       +++++GgG+AG   a++l++ + +v++ve  +   ++ + c    s+++ ++ ++ + +                  
  gi|488599704|ref|YP_007906175.1|   2 RILIVGGGIAGSLSAIHLGK-ENEVVVVEehQSAGFPVQ-CAGliSEECYNILSNFSKRCyinkidgafffspngdy 76 
                                       799****************9.888899965433333333.3322455555555444433355557777777777777 PP

                                       ...................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE- CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ...................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlA 106
                                                          + ++k +++   l+++++++  +gk k kl+ ++   e  ++yd l+ A
  gi|488599704|ref|YP_007906175.1|  77 lelygkrrgvvierkildfDLISKASENANILMKTKYISS-NGK-KAKLRSDS--GEMFLEYDFLIGA 140
                                       7777777777777777777666666666666666445554.233.44443333..3345566666555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.4e-05     0.047       2      43 ..       2      42 ..       1      59 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      +++++GgG AG + Ai+++k+ ++V+++e+ +++g  ++ +G
  gi|488599704|ref|YP_007906175.1|  2 RILIVGGGIAGSLSAIHLGKE-NEVVVVEEHQSAGFPVQCAG 42
                                      689***************765.56777888888887666666 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.9   4.6e-05     0.091       2      35 ..       3      35 ..       2      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.6e-05
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      ++++G+G+AG  +A+ + +++  v+vve  q+ g
  gi|488599704|ref|YP_007906175.1|  3 ILIVGGGIAGSLSAIHLGKENE-VVVVEEHQSAG 35
                                      79*************9977776.99999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2455.11
//
Query:       gi|488599705|ref|YP_007906176.1|  [L=69]
Description: hypothetical protein Asulf_00148 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-33  113.6   3.5      4e-33  113.4   3.5    1.0  1  DUF5371        Family of unknown function (DUF5371)
  ------ inclusion threshold ------
      0.013   16.2   0.0      0.017   15.9   0.0    1.1  1  PSK_trans_fac  Rv0623-like transcription factor
      0.052   13.9   0.1      0.058   13.7   0.1    1.2  1  PIN_9          PIN like domain
      0.082   13.1   0.0      0.082   13.1   0.0    1.1  1  DUF4253        Domain of unknown function (DUF4253)


Domain annotation for each model (and alignments):
>> DUF5371  Family of unknown function (DUF5371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   3.5   8.9e-37     4e-33       1      64 [.       1      62 [.       1      63 [. 0.99

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 8.9e-37
                           DUF5371  1 mvKivHAqtvLaeeeLeeLKkKtnesstkdAlsiAveHYleCeYtdlneemwtkKlEkvvqKKk 64
                                      mvKivHAqtvL+e +LeeLKkKt+es+tkdA+++AveHYl C+Yt+  e+++ kKlE+v++KKk
  gi|488599705|ref|YP_007906176.1|  1 MVKIVHAQTVLPESVLEELKKKTGESATKDAIAKAVEHYLSCPYTH--EDPLGKKLEEVLKKKK 62
                                      89********************************************..***************9 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   3.7e-06     0.017      14      57 ..      16      59 ..      13      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.7e-06
                                      XXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX--HHHHHHHHHH CS
                     PSK_trans_fac 14 areLarltgeskt.eAvrrAleerlerlrreraepllerllallr 57
                                       +eL + tges t +A+ +A+e++l+     +++pl ++l ++l+
  gi|488599705|ref|YP_007906176.1| 16 LEELKKKTGESATkDAIAKAVEHYLSCPY-THEDPLGKKLEEVLK 59
                                      589*******98857**********9754.478888877777766 PP

>> PIN_9  PIN like 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     0.058      28      62 ..       6      40 ..       2      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                             PIN_9 28 svelvvpkavleELerlakagkgkertaakvalsL 62
                                      + ++v+p++vleEL++ + + + k++ a  v   L
  gi|488599705|ref|YP_007906176.1|  6 HAQTVLPESVLEELKKKTGESATKDAIAKAVEHYL 40
                                      5689************9888888888877776655 PP

>> DUF4253  Domain of unknown function (DUF4253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05     0.082      64     106 ..      26      66 ..       6      69 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                           DUF4253  64 kteeealalAaEhyafCpdlvdqgvgtl.edlaealkkskawff 106
                                       +  ++a a A Ehy  Cp + ++    l ++l+e lkk+k  f+
  gi|488599705|ref|YP_007906176.1|  26 SATKDAIAKAVEHYLSCPYTHEDP---LgKKLEEVLKKKKDKFL 66 
                                       4455799**************955...45667778877776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 485.44
//
Query:       gi|488599706|ref|YP_007906177.1|  [L=90]
Description: hypothetical protein Asulf_00149 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0027   18.1   2.5     0.0032   17.8   2.5    1.2  1  MgtE             Divalent cation transporter
     0.0063   16.7  16.3     0.0069   16.5  16.3    1.1  1  DUF5518          Family of unknown function (DUF5518)
  ------ inclusion threshold ------
      0.027   14.5   6.0      0.037   14.0   6.0    1.2  1  CarS-like        CDP-archaeol synthase
       0.91    9.8   6.5        1.3    9.3   6.5    1.3  1  DUF2304          Uncharacterized conserved protein (DUF2304)
        2.5    8.3   9.3          2    8.6   0.2    2.1  2  Bacteriocin_IIc  Bacteriocin class II with double-glycine lea
        2.5    6.8   7.3          3    6.5   7.3    1.2  1  DUF2207          Predicted membrane protein (DUF2207)
        4.9    7.3   9.4       0.22   11.6   4.3    1.3  2  DUF2614          Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.5   1.3e-06    0.0032      33      97 ..      25      88 ..       4      90 .] 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHHHHHH..HHHHHHHHHH CS
                              MgtE 33 kkvllkelrvvlllgvilgllifllalllgwslllalvvglalvlvllaaallilgvllplllwk 97
                                       ++l k ++ ++++g+ilgll++++    g ++  a +vg++++++++a+ ++ +g+++  +l +
  gi|488599706|ref|YP_007906177.1| 25 INILKKAVIFGIVVGIILGLLVGIIFPPAGILVAGAGMVGFTIITLYFAVFFV-VGTIIGDFLER 88
                                      56788889999999999999999883333334445556999888888888888.77777666555 PP

>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  16.3   2.7e-06    0.0069      32     117 ..       8      85 ..       1      86 [. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                           DUF5518  32 lvgGlvaGylaggd..skdgavaGalaGligaipvlvlllvlllglvaaigglagfvallvalllvvllllvvllvi 106
                                       l+ G++ Gy+  g+  + + +  +++ G++++i++++l+++++        ++ag+++++++++ +  +++ +++++
  gi|488599706|ref|YP_007906177.1|   8 LLLGMIYGYINPGRedRINILKKAVIFGIVVGIILGLLVGIIF--------PPAGILVAGAGMVGF--TIITLYFAV 74 
                                       66799*****866511567899*************99999999........455555555555444..455666666 PP

                           DUF5518 107 lgaiGGaiGgl 117
                                       + ++G +iG  
  gi|488599706|ref|YP_007906177.1|  75 FFVVGTIIGDF 85 
                                       66777777765 PP

>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   6.0   1.4e-05     0.037      52     111 ..      31      89 ..      25      90 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                         CarS-like  52 GtvaGvlvGvlvgliqglleklsilaldss.gsvlefvilalllafGallGdavGsfikrr 111
                                        +++G++vG++ gl+ g++  +    + +    ++ f i++l++a+  ++G ++G f+ r+
  gi|488599706|ref|YP_007906177.1|  31 AVIFGIVVGIILGLLVGII--FPPAGILVAgAGMVGFTIITLYFAVFFVVGTIIGDFLERK 89 
                                       6899**************9..55544444404577889999****************9986 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.5   0.00051       1.3       4      78 ..       3      81 ..       1      88 [. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00051
                           DUF2304  4 iiliivsvllllliirlvrkkklkleysllwllla....lilivlslfpqiltvlanllGvgrgtnllfllgivfllvi 78
                                      i l+++++ +++ +i+  r++++++ ++ +++ ++    l+l+v ++fp +   +a +  vg+++  l++++++++  i
  gi|488599706|ref|YP_007906177.1|  3 IELLALLLGMIYGYINPGREDRINILKKAVIFGIVvgiiLGLLVGIIFPPAGILVAGAGMVGFTIITLYFAVFFVVGTI 81
                                      668899999999999999****999777766655401114567889***999999999999999888888888776555 PP

>> Bacteriocin_IIc  Bacteriocin class II with double-glycine leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00076         2      32      62 .]       8      50 ..       3      50 .. 0.79
   2 ?    2.7   4.3     0.052   1.3e+02      31      59 ..      55      83 ..      51      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00076
                   Bacteriocin_IIc 32 alaGaatGaa............tlgilgaavGavvGavvGail 62
                                       l G++ G++             + i+g +vG ++G +vG+i+
  gi|488599706|ref|YP_007906177.1|  8 LLLGMIYGYInpgredrinilkKAVIFGIVVGIILGLLVGIIF 50
                                      56677777777777777777777889999**********9986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.052
                   Bacteriocin_IIc 31 galaGaatGaa..tlgilgaavGavvGavvG 59
                                        +aGa++  +  t ++l+ av +vvG++ G
  gi|488599706|ref|YP_007906177.1| 55 ILVAGAGM--VgfTIITLYFAVFFVVGTIIG 83
                                      45566654..3347999***********998 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.3    0.0012         3     373     425 ..      18      78 ..       3      89 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0012
                           DUF2207 373 dkkgkkklkklsalglgliilglilillallllvll........lvfllilllillliaii 425
                                       +   + ++++l  + +++i++g+il+ll+ + + ++        +v++ i++l +++++++
  gi|488599706|ref|YP_007906177.1|  18 NPGREDRINILKKAVIFGIVVGIILGLLVGIIFPPAgilvagagMVGFTIITLYFAVFFVV 78 
                                       5555556666666666666666666665555544445553333333333333333333333 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2       4.2   1.1e+04      39      46 ..       6      13 ..       3      17 .. 0.53
   2 ?   11.6   4.3   8.5e-05      0.22       3      61 ..      22      81 ..      20      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.2
                           DUF2614 39 lflllGll 46
                                      l lllG++
  gi|488599706|ref|YP_007906177.1|  6 LALLLGMI 13
                                      44455554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.5e-05
                           DUF2614  3 sskinkirtfalllvfigliv.myigllfkeselllvlflllGlllvlastvvyfwiGll 61
                                      +++in +++  ++ + +g+i+ + +g++f  + +l++   ++G+ ++ + ++v+f++G++
  gi|488599706|ref|YP_007906177.1| 22 EDRINILKKAVIFGIVVGIILgLLVGIIFPPAGILVAGAGMVGFTIITLYFAVFFVVGTI 81
                                      5789999998888888888874789*********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 565.47
//
Query:       gi|488599707|ref|YP_007906178.1|  [L=339]
Description: de-hypoxanthine futalosine cyclase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-14   52.4   0.5    2.3e-13   50.9   0.1    2.0  3  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.039   13.4   0.0      0.069   12.6   0.0    1.4  1  KdpD         Osmosensitive K+ channel His kinase sensor domai


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   2.6e-17   2.3e-13       2     161 ..      41     203 ..      40     212 .. 0.82
   2 ?   -3.1   0.0         1     9e+03     124     135 ..     243     254 ..     225     280 .. 0.64
   3 ?   -1.7   0.0      0.37   3.3e+03      22      41 ..     303     322 ..     295     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2.6e-17
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpg 77 
                                       + t  C  +C+ Ca++     ++  + ls++eil++vk + +e+g +++ i+gg +p    ++ e++++ +k   + 
  gi|488599707|ref|YP_007906178.1|  41 NYTDICVSKCPLCAFS-----NRENYLLSTREILKLVKDA-VERGaTEVHIVGGHNPEIGIEYFEDVFKSIKDMFDV 111
                                       67899***********.....7******************.89999************************9985222 PP

                                       EEEEEEECSSCHG..........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxx..........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd..........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagi 142
                                          ++++ ++  d          +e+l rl+ +g       g+e++ d+ v+k++   + + e++le++++++e gi
  gi|488599707|ref|YP_007906178.1| 112 TIKALTATEV--DfysrkekmsvKEFLSRLKLAGmDAMPGGGAEILVDD-VRKIIApNKINSERWLEVMRIAHETGI 185
                                       2222222222..2457888888************666678899999999.*************************** PP

                                       ETEEEEEEEBTTTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 143 krvvdrivglpGendeele 161
                                       k +  +++ ++ e+ +++ 
  gi|488599707|ref|YP_007906178.1| 186 K-SNATMLFGHVESYKDRS 203
                                       *.55666666666666554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1
                                       TSHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 124 ghtfeevleale 135
                                       + ++e+vl+++ 
  gi|488599707|ref|YP_007906178.1| 243 KSSPEDVLKTIA 254
                                       445555555554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  22 regrgrslsveeileevkel 41 
                                         +++ sl ve+i+++++ +
  gi|488599707|ref|YP_007906178.1| 303 GAETPTSLEVERIVKIARNA 322
                                       55677788888888888766 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-06     0.069      86     139 ..     154     208 ..     124     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-06
                              KdpD  86 vlvDelahtnapgsrhekryqdveelL.eagidVittvnvqhleslndvvekitg 139
                                       +lvD++ +  ap+  +++r+ +v ++  e gi+  +t+   h+es +d  e++ +
  gi|488599707|ref|YP_007906178.1| 154 ILVDDVRKIIAPNKINSERWLEVMRIAhETGIKSNATMLFGHVESYKDRSEHLYK 208
                                       8************************97367*****************98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2154.95
//
Query:       gi|488599708|ref|YP_007906179.1|  [L=259]
Description: futalosine synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-46  157.5   0.0      5e-46  157.4   0.0    1.0  1  VitK2_biosynth  Menaquinone biosynthesis


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.4   0.0   2.8e-50     5e-46       2     265 ..      17     254 ..      16     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 2.8e-50
                                       EEEEESSHHHHHHHHHHHTTSS..SGCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEE CS
                    VitK2_biosynth   2 rlGhspylNdlflfyaLvegkvdsegleveivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalG 78 
                                       r+G   +lN + ++y L      ++++++eiv ++p ++ ++ll++++ +a+++ +a ++  + +  ++ +++++ +
  gi|488599708|ref|YP_007906179.1|  17 RIGKFGFLNNFLPYYFL------EKSKKYEIVETNPRNMVNMLLRKQIHYAPVPLFASLK--NGLKNYS-FCVASND 84 
                                       89***************......44789*****************************999..6677776.89***** PP

                                       SSSSEEEEESS-CCC-SSS.T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTSSEEEEECCHH CS
                    VitK2_biosynth  79 rvygvllvskvpleelegelgkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlegedagLlIgesa 155
                                       rv++v++vsk+  +eleg+    +a++++s Tsv+Ll+++l+e+ gl++rl+e + +     +l+++d +L+Ig++a
  gi|488599708|ref|YP_007906179.1|  85 RVLSVVVVSKK--KELEGD----IAITNQSLTSVNLLKIILKEK-GLENRLREFD-SGSAWDLLKECDNALVIGDEA 153
                                       *********77..677777....*********************.9*********.8888889999*********** PP

                                       HTGGGGTTEEEEEHHHHHHHHHSS-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS.HH CS
                    VitK2_biosynth 156 ltyaeeglkkvlDLgelWeeltglPlvlglwvvrrdlaaeaakeleealreSveyalahldevaeyaaeraqemdde 232
                                       ++ +     +v+DLge+W++ tglP+v+g+ +  + +    a +++++l eS e ++++++ ++e+a+++ +++   
  gi|488599708|ref|YP_007906179.1| 154 IKAR-MVFRVVMDLGEEWYDITGLPMVFGISASLNGF---DASKIDRDLLESTEKGYKNIHLIIEEAEKHFKMP--- 223
                                       *955.67*****************************9...4567******************************... PP

                                       HHHHHHHHHCSHHHHS-CHHHHHHHHHHHHHHH CS
                    VitK2_biosynth 233 vlekhlelYvnelsydlgeegragleeflelaa 265
                                          ++le+Y+++l+++lg ++r+++e f e+++
  gi|488599708|ref|YP_007906179.1| 224 --VEFLEEYFKTLKFKLGGKERRSIELFEEYCR 254
                                       ..****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 00:00:00.39
# Mc/sec: 1989.47
//
Query:       gi|488599709|ref|YP_007906180.1|  [L=340]
Description: menaquinone biosynthesis protein, SCO4550 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   73.9   0.0    3.3e-20   73.1   0.0    1.4  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 !   73.1   0.0   1.8e-24   3.3e-20       1     165 [.      43     211 ..      43     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.8e-24
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavp 76 
                                       ++ t+ C  +C+fCa++     +++g +ls ++il+ +  + +++g + ++++gg++p+l  +  e l+rl+k +  
  gi|488599709|ref|YP_007906180.1|  43 INYTNICVSKCKFCAFY-----RDDGFVLSYDDILDRISDA-VKHGvTQVMLQGGMNPDLGIEWFEGLFRLIKSKFQ 113
                                       57899************.....69*****************.99**999**************************99 PP

                                       TEEEEEEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagi 142
                                       +i+++  +++  +          +e+le+l+++g       g+e+++d+ v++++  ++ + +e++e+++ ++++g+
  gi|488599709|ref|YP_007906180.1| 114 NIHLHSLSPPEIVFlseleglsyREVLEKLKNAGlDSLPGGGAEILSDR-VRRKLSpKKCSADEWIEVMREAHRLGM 189
                                       99999999888877889999999***********666678899999999.******9******************** PP

                                       ETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 143 krvvdrivglpGendeeleelle 165
                                       k ++ +++ ++ e++e+++e+l 
  gi|488599709|ref|YP_007906180.1| 190 K-TTATMMFGHVESHEDIVEHLF 211
                                       *.9***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2442.93
//
Query:       gi|488599710|ref|YP_007906181.1|  [L=209]
Description: hypothetical protein Asulf_00153 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.34   10.5   7.7        2.1    7.9   5.4    2.2  2  Saf_2TM          SAVED-fused 2TM effector domain
          2    8.0  14.1      0.047   13.3   3.4    2.1  2  Wzy_C            O-Antigen ligase


Domain annotation for each model (and alignments):
>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.4   0.00023       2.1       4      85 ..      13      95 ..      11     104 .. 0.66
   2 ?    2.7   0.0    0.0095        85      73     114 ..     106     148 ..     101     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00023
                           Saf_2TM  4 ldyvirklidwlfRkrsaelllftigvalllailgt.dwalkialklaggslevsfssseipeivlaiilvigvllivv 81
                                      ++ +++++ +++fR   ++++ + +++++ll++l t +++ k+ +     s   ++    ++ +    i++ +++li++
  gi|488599710|ref|YP_007906181.1| 13 ISVFVANFLSLFFRIEGPAMVYLALAISILLSSLYTlTKSEKLTAIHIAVSAATALTLIAVIRFSPSAIILFAIILIAG 91
                                      57899***************************99986333333333334445555555555544444444444455555 PP

                           Saf_2TM 82 Gavl 85
                                      +++l
  gi|488599710|ref|YP_007906181.1| 92 SIIL 95
                                      4443 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0095
                           Saf_2TM  73 vigvllivvGavllilryvn.eakrqskkkvivIEgrgLrdts 114
                                       +  ++l+v+G+++++  ++   a     +k i +E +g+ + s
  gi|488599710|ref|YP_007906181.1| 106 AANSFLTVLGVIIAFMALIGySAHEHYNAKYISVEKIGDAECS 148
                                       5568899999999998887624567778999999999998765 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   3.0      0.05   4.5e+02      19      67 ..       5      50 ..       2      63 .. 0.53
   2 ?   13.3   3.4   5.3e-06     0.047       7      59 ..      69     132 ..      63     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.05
                             Wzy_C 19 iigllvalivlliifykrripfllllgilvgvilliilfvlstnletlk 67
                                      +i++++++i ++++ +  ++   ++ g +++ ++l+i ++ls+ l+tl+
  gi|488599710|ref|YP_007906181.1|  5 LISFIAGFISVFVANFLSLF--FRIEGPAMVYLALAISILLSS-LYTLT 50
                                      46666666666666666666..555554443333333333333.33333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.3e-06
                             Wzy_C   7 llalflstsRsgiigllvalivlliifykrri........pfllllgilvgvilliilfv...l 59 
                                        l+ ++  s s+ii ++++li++ ii+ ++r         +fl +lg++++ ++li +++    
  gi|488599710|ref|YP_007906181.1|  69 TLIAVIRFSPSAIILFAIILIAGSIILGRNRKeevsiaanSFLTVLGVIIAFMALIGYSAhehY 132
                                       345567899***********************99987666666666666656555555553331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); 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):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 1392.85
//
Query:       gi|488599711|ref|YP_007906182.1|  [L=395]
Description: HD superfamily phosphohydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   31.7   1.1    1.4e-07   31.7   1.1    2.2  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 !   31.7   1.1   7.9e-12   1.4e-07       1     120 [.      51     160 ..      51     162 .. 0.70
   2 ?   -0.9   0.1       0.1   1.8e+03     103     120 ..     234     251 ..     208     253 .. 0.57

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 7.9e-12
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH.......HHHCTCCHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk.......eeefekflaHekvgaeilre 69 
                                       r+eHsl+V +++++l e+l+   + +  +l+ a++HD ++ pf+++ e++       + e+  f+  +++ + +++e
  gi|488599711|ref|YP_007906182.1|  51 RFEHSLGVFYITKKLTEKLEIsKDSEMEILISAIIHDSAHAPFSHSSERIikrylgkTHERIDFYLKSTELEDVIKE 127
                                       79*****************88855555688********************765544322244555555555555555 PP

                                       HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                                HD  70 vekrlgldledvaklirehheswegkkrprglaerqlslearivklaDrla 120
                                       ++ +l     dva+  +e +                + + +++++++D+l 
  gi|488599711|ref|YP_007906182.1| 128 LGFSL----RDVARHLSEESY--------------GIVSGEIDADRMDYLV 160
                                       55555....334444444444..............4457888888888875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.1
                                       CCTSCHHHHHHHHHHHHH CS
                                HD 103 erqlslearivklaDrla 120
                                       ++   lear++ ++D ++
  gi|488599711|ref|YP_007906182.1| 234 IELGELEARDLVRMDDYD 251
                                       334456777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2797.07
//
Query:       gi|488599712|ref|YP_007906183.1|  [L=507]
Description: 2-isopropylmalate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-91  304.6   0.7    1.1e-90  303.8   0.7    1.4  1  HMGL-like     HMGL-like
    4.1e-32  110.9   2.3    8.5e-32  109.8   2.3    1.6  1  LeuA_dimer    LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
      0.086   12.7   0.6        0.2   11.5   0.0    1.8  2  MogR_DNAbind  DNA binding domain of the motility gene repress
          1    9.8   4.9       0.22   12.0   0.9    1.9  2  CelTOS        Cell-traversal protein for ookinetes and sporoz


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 !  303.8   0.7   2.4e-94   1.1e-90       2     264 .]       4     261 ..       3     261 .. 0.99

  Alignments for each domain:
  == domain 1  score: 303.8 bits;  conditional E-value: 2.4e-94
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       + ++dttLRDGeq++++++ ++ k++iak+Ld++gvd+iE+gfp+as+++fe+v++i++   +++i++l+r +++di
  gi|488599712|ref|YP_007906183.1|   4 ISVFDTTLRDGEQTPGVSFPINYKIQIAKQLDKLGVDYIEAGFPVASKGEFEAVKTIVNLDLDSKICGLARIVKEDI 80 
                                       789************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       + a +     g++ vh+fi+ts++++ + +kk+ree+++ ++eav++++++g ++ +s++da+rt++++l e+++a+
  gi|488599712|ref|YP_007906183.1|  81 DSALD----SGVDLVHIFISTSKIQIDYTIKKSREEIINDSVEAVEYIKDHGRECMFSAMDATRTEIDYLKEIYKAV 153
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       eeaG+++in++DtvGv+tP+ +++li++l+e++k  v++ vHcHnd+GlAvant aAv aGad+v +tvnG+GeraG
  gi|488599712|ref|YP_007906183.1| 154 EEAGVDIINVPDTVGVATPFRFHNLIKELREHLK--VPIDVHCHNDFGLAVANTHAAVLAGADQVQVTVNGIGERAG 228
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealg.vdtgldlqklrsiaalv 264
                                       na+l e+v+ l+ l+ ++t++ ++ l ++++lv
  gi|488599712|ref|YP_007906183.1| 229 NASLAEVVMILKSLEgIETNIRTEYLVETSRLV 261
                                       ************9988**************997 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   2.3   1.9e-35   8.5e-32       2     132 ..     359     491 ..     337     492 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1.9e-35
                                       XXXXXXXXXXXXXXXX...XX--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHHT CS
                        LeuA_dimer   2 vtdedlealvkdelle...aeerlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgvd 75 
                                       vtd dl ++++ +++e   + + + +++++v +g++ ++ta+++++v  +  ++ sa+G+GpvdA+l+A+r+++g+ 
  gi|488599712|ref|YP_007906183.1| 359 VTDLDLFTIAEVVIGElrkEDRAIVVDEITVLTGNKITPTAVINANV-FNDSRVKSAIGVGPVDAALKAVRELVGET 434
                                       78888888888777777746699************************.77888************************ PP

                                       -EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  76 ikLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                       ik+++++++ait+g+da+aev+V++e d gk+++++++ +div+AS+ A+i+a+n+l
  gi|488599712|ref|YP_007906183.1| 435 IKITEFKMDAITGGSDALAEVYVTVEDDSGKSFTARAAGPDIVMASIDAVINAVNYL 491
                                       **************************888**************************98 PP

>> MogR_DNAbind  DNA binding domain of the motility gene repressor (MogR)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.5e-05       0.2      21      92 ..      99     167 ..      87     175 .. 0.85
   2 ?   -2.5   0.1      0.99   4.4e+03      18      42 ..     325     351 ..     322     355 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                                       HHHHHHT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHTSSEEE-HHHHHHHHHHHHHHHHTT--HHHHHHHH CS
                      MogR_DNAbind  21 kiekeaqvdeeelvelynllvlfqidvekhGGirkyeksaiswlkielellsevyqiailedlkvldiskyl 92 
                                       ki+ ++ ++ +  +e+ n  v+    +++hG  r+ + sa+   ++e++ l e+y+     +++++++ + +
  gi|488599712|ref|YP_007906183.1|  99 KIQIDYTIK-KSREEIINDSVEAVEYIKDHG--RECMFSAMDATRTEIDYLKEIYKAVEEAGVDIINVPDTV 167
                                       444455554.4568999999**********9..89999*****************************98876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.99
                                       HHHHHHHHHT..--HHHHHHHHHHHHH CS
                      MogR_DNAbind  18 eikkiekeaq..vdeeelvelynllvl 42 
                                       +ikk+ ++a+  v+ee+l ++++++ +
  gi|488599712|ref|YP_007906183.1| 325 QIKKMLEDAGyiVNEEDLTKIFEKVKE 351
                                       689998887655889999999988765 PP

>> CelTOS  Cell-traversal protein for ookinetes and sporozoites
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   4.8e-05      0.22      14      87 ..      54     124 ..      47     127 .. 0.91
   2 ?   -3.1   0.2       2.4   1.1e+04      18      48 ..     347     379 ..     337     387 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.8e-05
                            CelTOS  14 ssklseiiradldskgdelvdliandlekelqknslvaasfLqsgfdvkkkaKeiiKkvllevlksllpvveki 87 
                                        ++++ i+  dldsk   l+ ++ +d+ ++l+    +   f+ ++   k ++  +iKk   e++   ++ ve i
  gi|488599712|ref|YP_007906183.1|  54 FEAVKTIVNLDLDSKICGLARIVKEDIDSALDSGVDLVHIFISTS---KIQIDYTIKKSREEIINDSVEAVEYI 124
                                       5778999*************************9987888899998...99********************9965 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                            CelTOS  18 seiiradldskgdelvd....liandlekelqkns 48 
                                       ++   ++l +kg  + d    +ia+ ++ el+k++
  gi|488599712|ref|YP_007906183.1| 347 EK--VKELGDKGKKVTDldlfTIAEVVIGELRKED 379
                                       33..3456666666666333346666777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3356.77
//
Query:       gi|488599713|ref|YP_007906184.1|  [L=246]
Description: hydrolase, TatD family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  191.9   0.0    1.4e-56  191.7   0.0    1.0  1  TatD_DNase    TatD related DNase
     0.0015   18.4   0.0      0.012   15.4   0.0    2.4  1  Amidohydro_2  Amidohydrolase
      0.005   16.2   0.3      0.016   14.5   0.3    1.9  1  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
       0.11   12.8   0.9       0.54   10.6   0.1    2.3  2  Mur_ligase    Mur ligase family, catalytic domain
       0.13   12.1   0.0       0.24   11.2   0.0    1.4  1  CAP_assoc_N   CAP-associated N-terminal


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 !  191.7   0.0   3.9e-60   1.4e-56       1     254 [.       5     242 ..       5     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 3.9e-60
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHH CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleel 77 
                                       iD+HcH++ k+f++dr+e+++ra  +gv  +vv g +  ++ ++l+l ++  n ++a+lG+ P+  ++ +e+++ ++
  gi|488599713|ref|YP_007906184.1|   5 IDSHCHIQIKNFDRDRQEVIRRAISNGVVGIVVSGYDISSNHKALNLKSS--N-IFATLGFSPTMNTKGHEHVISQI 78 
                                       8*************************************999999999865..5.9********87777777776666 PP

                                       HHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEE CS
                        TatD_DNase  78 kelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvl 154
                                        e     ++++va+Ge+G+D   +   + ++q+++Fe +lrlA+e+++p+viH+r+ae + ++++++++    k ++
  gi|488599713|ref|YP_007906184.1|  79 MEH----QNEIVAVGEVGIDR-VKGRLPFDEQKKIFESFLRLASEMDKPVVIHARDAEIEAIDLASRYGV---KAMI 147
                                       555....899***********.5666*****************************************954...68** PP

                                       TT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHH CS
                        TatD_DNase 155 HsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvvekl 231
                                       H+f+gs +  + + + g+ +s+s ++tf  + +l+++v++++l++++iETD+P+l+p  +r  rnepan+ y v+++
  gi|488599713|ref|YP_007906184.1| 148 HCFNGSLKAFRLAKDSGAIVSISTMVTF--SDRLKRVVREMDLENVVIETDSPFLSP--KR-GRNEPANLVYAVNEI 219
                                       ****************************..669************************..44.79************* PP

                                       HHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 232 aelkaltleelaeitaeNakrlf 254
                                       ++l +++ ee+a+it+ Na+ ++
  gi|488599713|ref|YP_007906184.1| 220 SKLIEEDKEEVARITKRNAEDFY 242
                                       ********************998 PP

>> Amidohydro_2  Amidohydrolase
   #    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     221     291 .]     167     244 ..      21     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-06
                                       SEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH........SSHHHHHHHHTHHHHHHC CS
                      Amidohydro_2 221 lyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlval........lsdeerekilggNAarly 289
                                        +  + +++  +l+r++ + + ++++  +D P+ ++++ + + a+l              ++ee+++i + NA+ +y
  gi|488599713|ref|YP_007906184.1| 167 VSISTMVTFSDRLKRVVREMDLENVVIETDSPFLSPKRGRNEPANLVYA-VneisklieEDKEEVARITKRNAEDFY 242
                                       445677889999********************************77433.246*****99***************** PP

                                       TB CS
                      Amidohydro_2 290 gl 291
                                       g+
  gi|488599713|ref|YP_007906184.1| 243 GI 244
                                       96 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   4.6e-06     0.016       6     189 ..       4     158 ..       4     198 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                                       EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH..................HHH CS
                      Amidohydro_1   6 lIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst..................gie 64 
                                       lID+H H+ q  ++++      + +e ++ a+ +g++  + sG  +  ++ a + +                  +  
  gi|488599713|ref|YP_007906184.1|   4 LIDSHCHI-QIKNFDR------DRQEVIRRAISNGVVGIVVSGYDISSNHKALNLKssnifatlgfsptmntkgH-- 71 
                                       79999999.5777777......77777777777777777777777777777755554444444432222222221.. PP

                                       HHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHH CS
                      Amidohydro_1  65 alleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealke 140
                                              e ++ + ++  + ++   ++e+ +++++  ++  +e +k++++ +   ++++ +   ++ d+e+ ea+++
  gi|488599713|ref|YP_007906184.1|  72 -------EHVISQIMEHQNEIV--AVGEVGIDRVKGRLPF-DEQKKIFESFLRLaSEMDKPVVIHARDAEI-EAIDL 137
                                       .......111121121111111..2222222222222222.222233333333335555555555555555.44455 PP

                                       HHHHTTEEEEEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCC CS
                      Amidohydro_1 141 akkrdlpvaiHa..letkgevedaeaafgetiehgthlevaeslglldeik 189
                                       a++++++ +iH+  +++k++                              +
  gi|488599713|ref|YP_007906184.1| 138 ASRYGVKAMIHCfnGSLKAF------------------------------R 158
                                       55555555555554444333..............................3 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00015      0.54      23      73 ..      34      95 ..      23     100 .. 0.90
   2 ?   -0.1   0.1      0.34   1.2e+03      48      70 ..     209     237 ..     204     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                      TSEEEEEESSHC.....HHHTT-EEEES-HGGGG......EE-TS-TTCHHHHHHHHTTEEE CS
                        Mur_ligase 23 GykvdGsdfies.....lialGaaavvghdaani......vvssiskdnpeleaakepgipv 73
                                      G  v+G d+  +     l+ +++ a +g+++ +       v+s+i + + e++a++e+gi  
  gi|488599713|ref|YP_007906184.1| 34 GIVVSGYDISSNhkalnLKSSNIFATLGFSPTMNtkghehVISQIMEHQNEIVAVGEVGIDR 95
                                      88899999999999999***************889*********9999999*****999975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.34
                                       GGGG.....EE-T.S-TTCHHHHHHHHTT CS
                        Mur_ligase  48 aani.....vvss.iskdnpeleaakepg 70 
                                       +an+      +s+ i +d++e+++ ++++
  gi|488599713|ref|YP_007906184.1| 209 PANLvyavnEISKlIEEDKEEVARITKRN 237
                                       55666777788999999999999877765 PP

>> CAP_assoc_N  CAP-associated N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.6e-05      0.24      24      97 ..      10      81 ..       3      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.6e-05
                       CAP_assoc_N 24 gyewwvYnedykeyiqvgvedgkVvtlytngeeiaikpfkigesleevekklgipeeveveikkgsyrfelsee 97
                                       +++  +++d +e i  ++++g Vv++++ g +i+++  +++ ++++++ +lg++++++ + ++  +   ++e 
  gi|488599713|ref|YP_007906184.1| 10 HIQIKNFDRDRQEVIRRAISNG-VVGIVVSGYDISSNHKALNLKSSNIFATLGFSPTMNTKGHEHVISQ-IMEH 81
                                      6678889999999999999876.89*********************************98888766554.4433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1469.63
//
Query:       gi|488599714|ref|YP_007906185.1|  [L=195]
Description: Uncharacterized protein containing a Zn-finger-like domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-21   75.6   7.8    3.6e-21   74.9   7.8    1.3  1  zf-like   Cysteine-rich small domain


Domain annotation for each model (and alignments):
>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   7.8     2e-25   3.6e-21       9      68 ..      25      85 ..      20      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 2e-25
                           zf-like  9 eCeyyPCHktedenClfCyCPlYaledeel.Gefveteng.kvkdCskCllvHkkevadell 68
                                      eC+yyPCH+ ++++C+fCyCP+Y++ +  + Ge++ t++g  v++C++C l+H++e  ++++
  gi|488599714|ref|YP_007906185.1| 25 ECKYYPCHF-AGQDCSFCYCPFYPCLNYDMgGELKVTSDGsYVWSCMNCDLIHDREFSENVI 85
                                      8********.9*************98755439************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1294.38
//
Query:       gi|488599715|ref|YP_007906186.1|  [L=284]
Description: hypothetical protein Asulf_00158 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  161.8   0.5    2.5e-47  161.6   0.5    1.0  1  DUF89     Protein of unknown function DUF89
  ------ inclusion threshold ------
      0.022   14.3   0.9      0.045   13.3   0.0    2.0  2  DUF761    Cotton fibre expressed protein


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 !  161.6   0.5   2.8e-51   2.5e-47       2     352 ..       4     279 ..       3     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 2.8e-51
                                       HHTHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHH CS
                             DUF89   2 leerlpciltqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrlle 78 
                                        +++  c+l++v  ++++++d+  e+  +++e   ++++e + +k ++++                ++++++r+++e
  gi|488599715|ref|YP_007906186.1|   4 SPKCPSCLLNRVYMEARMSTDD-AEKIDRAVELALKILAEEYPKKGINAV----------------IATRIHRKVYE 63 
                                       689*******************.9**************************................*********** PP

                                       HHTHSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHH CS
                             DUF89  79 lfglskelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllateediqkdqeee 155
                                       +++      ++Dp++e+K+++n+ +lk+++e+++ + +  d    f+   k+s++ N++D+++ + +e+  +     
  gi|488599715|ref|YP_007906186.1|  64 VLE------DEDPYREVKKRANEVSLKYLPEIKRIVYR-DD---AFRSTAKASIIANTFDYGVMG-HEVNDSAFLDY 129
                                       ***......***********************997433.33...59*******************.99999999*** PP

                                       HHHHHHCTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHH CS
                             DUF89 156 arkaleknilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeD 232
                                       + +++++++ +d+lek+ + +    ++rv++++DN+G E+v+D l+++e+++  ++++  ++v++ P ++sD+t+eD
  gi|488599715|ref|YP_007906186.1| 130 FIRKFRESLKIDNLEKIRSLC----KGRVVYLTDNCG-EIVYDALFMKEIKK--ICERLSVVVRGRP-IISDATYED 198
                                       *********************....9***********.**************..*************.********* PP

                                       HHHHHHHHH-TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHHC-SEEEEEHHHHHHHHT CS
                             DUF89 233 fewlleqladsksfelsalgagldellkegklvlrgssfwttglsysempeapelyeelekadLvifKGdlNyrkLt 309
                                       +                   ag+d+   +++++++g+    +g+  +e+  +++  + +e+ad++i+KG++Ny++L+
  gi|488599715|ref|YP_007906186.1| 199 AV-----------------IAGVDK--IADEVLDNGDG---IGIIDEEL--PEKTKDRIENADIIIAKGMANYECLS 251
                                       **.................9*****..88999999999...999999**..*************************8 PP

                                       TSCTTTTTSEHHHHTGTSS--EEEEEE--SHHHHHHH.STTTHE CS
                             DUF89 310 gdrkwppttpfttalgfspvpvlaLrtvKadvvagll.egegek 352
                                       + ++                 + +L+t+K+++va+ + +++g++
  gi|488599715|ref|YP_007906186.1| 252 DSAYT----------------IGFLLTAKCEPVAKSIgVEVGDM 279
                                       76664................99*************99999886 PP

>> DUF761  Cotton fibre expressed protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     5e-06     0.045       3      27 ..     120     146 ..     118     154 .. 0.74
   2 ?   -2.3   0.1      0.38   3.4e+03       3      10 ..     203     210 ..     202     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-06
                            DUF761   3 evDakA..EeFIakFreqlkLQRqeSi 27 
                                       ev+  A  + FI+kFre lk+  +e i
  gi|488599715|ref|YP_007906186.1| 120 EVNDSAflDYFIRKFRESLKIDNLEKI 146
                                       6666666688**********8666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.38
                            DUF761   3 evDakAEe 10 
                                        vD+ A+e
  gi|488599715|ref|YP_007906186.1| 203 GVDKIADE 210
                                       59****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1836.00
//
Query:       gi|488599716|ref|YP_007906187.1|  [L=461]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   1.2    1.5e-14   53.7   1.2    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.1e-06   27.9   1.8    2.1e-06   27.9   1.8    3.2  3  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.012   14.6   1.8      0.025   13.6   1.8    1.4  1  DUF3987         Protein of unknown function (DUF3987)
      0.042   14.2   2.9       0.08   13.3   2.9    1.4  1  C1_2            C1 domain
      0.051   13.7   0.6        0.1   12.7   0.6    1.5  1  DUF2318         Predicted membrane protein (DUF2318)
      0.063   13.0   4.5          2    8.1   0.1    2.5  3  EMC3_TMCO1      Integral membrane protein EMC3/TMCO1-like
       0.31   10.6   5.5       0.67    9.5   5.5    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.84   10.3   7.2        5.6    7.6   2.5    2.7  2  Hemerythrin     Hemerythrin HHE cation binding domain
        1.1    9.4   5.9         11    6.2   1.8    2.5  2  DASH_Dad3       DASH complex subunit Dad3
          2    7.2  10.7       0.13   11.1   1.1    2.1  2  Mitofilin       Mitochondrial inner membrane protein
          2    8.6  10.4       0.12   12.5   4.0    2.1  2  DUF1090         Protein of unknown function (DUF1090)
        4.5    7.3   5.3         10    6.1   0.0    3.3  3  DUF1967         Domain of unknown function (DUF1967)


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 !   53.7   1.2   9.7e-18   1.5e-14       1      68 [.     343     409 ..     343     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 9.7e-18
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       f+++  +l  k ke   + + v + y+ ktC +Cgs+n+  +++r f+C+nC +++drD nA+ Nil 
  gi|488599716|ref|YP_007906187.1| 343 FKEFGDILILKLKENENHAIFVGEVYSTKTCCVCGSTNTI-VEDRSFYCKNCDTKLDRDENASTNILL 409
                                       89999***********************************.*************************97 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       8.4   1.3e+04      68      82 ..      15      29 ..       6      35 .. 0.53
   2 ?    3.4   6.8     0.055        82      40      88 ..      82     129 ..      67     131 .. 0.86
   3 !   27.9   1.8   1.4e-09   2.1e-06      12     108 ..     219     313 ..     209     322 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.4
                        OrfB_IS605 68 knykkasrklarlhr 82
                                        ++ ++rkl r+ r
  gi|488599716|ref|YP_007906187.1| 15 VSHEITKRKLDRIER 29
                                      445566666666544 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.055
                        OrfB_IS605  40 lykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrr 88 
                                       l   r++k+  ++++k+  el + l++++  k+ ++ +++l rk++r +
  gi|488599716|ref|YP_007906187.1|  82 LEMYRSYKRLHEKWKKRVEELKKSLERARA-KENKNGIRKLERKLKRMM 129
                                       5555889999******************85.99***********99987 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 1.4e-09
                        OrfB_IS605  12 kpkgnkaagiDlGinnLatvv.tedgtw.flykg....rrlksdykylakeiaelqsklkksknykkasrklarlhr 82 
                                       ++  +  agiDlG+++La v  +++g+   l  +     +++++  +l+++ia+lq+++k         + l++l +
  gi|488599716|ref|YP_007906187.1| 219 EVHVKGYAGIDLGMKRLAYVKqVSEGENrVLSIPkedhHHFFRRMHELNNRIARLQRLKKI--------KVLKKLKN 287
                                       5566779***********8852455555444444113345666667777777777777444........469***** PP

                        OrfB_IS605  83 krsrrrkhllhklathliktlkevgv 108
                                       kr+++ +++ +kla++++ +  ++ v
  gi|488599716|ref|YP_007906187.1| 288 KRRNIARDFRRKLAKDVASHITNTIV 313
                                       *****************998877764 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.8   1.6e-05     0.025      62     120 ..      72     137 ..      61     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                           DUF3987  62 eieaelreeyeeelkeyeaekkaweaelealekkaakak.......eakaeealaeleaeepeePk 120
                                       ++ + +r++  e+ ++y++ +++w+++ e+l+k++++a+        +k e++l+ + ++ep +P 
  gi|488599716|ref|YP_007906187.1|  72 AFIQCARDRALEMYRSYKRLHEKWKKRVEELKKSLERARakenkngIRKLERKLKRMMDREPSPPS 137
                                       444556666677777777777777777777777777777666666689999999999999999885 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.9   5.4e-05      0.08      14      44 ..     366     399 ..     352     400 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                              C1_2  14 dssesfnCsaCgrk...idgff.YsCseCdfslhv 44 
                                       + +++++C +Cg +   + +++ ++C+ Cd +l+ 
  gi|488599716|ref|YP_007906187.1| 366 EVYSTKTCCVCGSTntiV-EDRsFYCKNCDTKLDR 399
                                       56889*********9955.4446********9995 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6     7e-05       0.1      33      64 ..     369     400 ..     336     405 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                           DUF2318  33 aldaCevCekkgYvqegeelvCknCgvrfald 64 
                                          +C vC+++  + e+ +  CknC+++++ d
  gi|488599716|ref|YP_007906187.1| 369 STKTCCVCGSTNTIVEDRSFYCKNCDTKLDRD 400
                                       5679***********************99876 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.6   6.8e+03     139     155 ..      29      45 ..      15      62 .. 0.56
   2 ?    5.3   1.1    0.0099        15      40      83 ..      88     131 ..      69     144 .. 0.82
   3 ?    8.1   0.1    0.0013         2      39     103 ..     251     315 ..     247     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.6
                        EMC3_TMCO1 139 sldvrfvssiswYflcs 155
                                        l  r  ++is+Y+ ++
  gi|488599716|ref|YP_007906187.1|  29 RLSARLTYAISLYLDIV 45 
                                       55555555555555443 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0099
                        EMC3_TMCO1  40 dkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmed 83 
                                       +k   ek +kr +el+k  ++++ + +k+   kle++ +++m+ 
  gi|488599716|ref|YP_007906187.1|  88 YKRLHEKWKKRVEELKKSLERARAKENKNGIRKLERKLKRMMDR 131
                                       34446777999999999999999999999999999999999875 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0013
                        EMC3_TMCO1  39 idkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsemmmdqmkpmivtmipqi 103
                                       i k+  +++ +r+ el +r  +lq+ ++ + lkkl++++  ++ d +  + +   + i++ i+++
  gi|488599716|ref|YP_007906187.1| 251 IPKEDHHHFFRRMHELNNRIARLQRLKKIKVLKKLKNKRRNIARDFRRKLAKDVASHITNTIVFV 315
                                       55676777889**********************************99999999999999999887 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.5   0.00045      0.67       2      30 ..     372     398 ..     372     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00045
                                       EETTTTCEE.CHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDpergelvCtdCGlVle 30 
                                       +C +Cgstn +veD +   ++C++C + l+
  gi|488599716|ref|YP_007906187.1| 372 TCCVCGSTNtIVEDRS---FYCKNCDTKLD 398
                                       699******9999977...******55554 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.5    0.0038       5.6      65     123 ..      77     132 ..      13     134 .. 0.84
   2 ?    4.3   0.2     0.039        58      72     121 ..     248     309 ..     234     312 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                                       .CCC.HHHHHHHHHHHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHHHH CS
                       Hemerythrin  65 drpggravldvlereHdeirelleelrellkgleepsaaafaelleeladllreHiakE 123
                                       +r+++ +++++ +r H+   +++eel++ l+++    a +++  +++l++ l++++++E
  gi|488599716|ref|YP_007906187.1|  77 ARDRALEMYRSYKRLHEKWKKRVEELKKSLERAR---AKENKNGIRKLERKLKRMMDRE 132
                                       6899999********************9999999...999999**************99 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHHHCHTCG............GSTCHHHHHHHHHHHHHHHHHHH CS
                       Hemerythrin  72 vldvlereHdeirelleelrellkgle............epsaaafaelleeladllreHia 121
                                       vl+  +++H+ + ++++el+  +++l+            +   + +++  ++la+++++Hi+
  gi|488599716|ref|YP_007906187.1| 248 VLSIPKEDHHHFFRRMHELNNRIARLQrlkkikvlkklkNKRRNIARDFRRKLAKDVASHIT 309
                                       55555788888888899888666666646666666555555555555577777777777775 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.8    0.0075        11      11      48 ..      87     125 ..      81     129 .. 0.80
   2 ?    4.5   0.1     0.025        38      16      43 ..     260     287 ..     242     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0075
                         DASH_Dad3  11 eYerLaenlktLasel.keLasnsteeildgLReLErki 48 
                                        Y+rL e+ k+  +el k+L ++ ++e  +g+R+LErk+
  gi|488599716|ref|YP_007906187.1|  87 SYKRLHEKWKKRVEELkKSLERARAKENKNGIRKLERKL 125
                                       699999998875555516789999**************8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.025
                         DASH_Dad3  16 aenlktLaselkeLasnsteeildgLRe 43 
                                        + +++L++++++L++ ++ ++l++L++
  gi|488599716|ref|YP_007906187.1| 260 FRRMHELNNRIARLQRLKKIKVLKKLKN 287
                                       5789********************9986 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   2.7      0.12   1.7e+02     327     363 ..      92     128 ..      50     133 .. 0.70
   2 ?   11.1   1.1   8.7e-05      0.13     296     346 ..     258     309 ..     256     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                         Mitofilin 327 keelekqeealsarleeerakeerqlrlelereleei 363
                                       +e+ +k  e+l+++le +rake++   ++ler+l+++
  gi|488599716|ref|YP_007906187.1|  92 HEKWKKRVEELKKSLERARAKENKNGIRKLERKLKRM 128
                                       3334555566666666666666666666666666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.7e-05
                         Mitofilin 296 hAkteidqlskelaelkkeeekkieralekqkee.lekqeealsarleeera 346
                                       h+ ++++ l+ ++a+l++  + k+ ++l++++ +  ++++++l++ ++++++
  gi|488599716|ref|YP_007906187.1| 258 HFFRRMHELNNRIARLQRLKKIKVLKKLKNKRRNiARDFRRKLAKDVASHIT 309
                                       999********************************************99987 PP

>> DUF1090  Protein of unknown function (DUF1090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.0   8.1e-05      0.12      53     103 ..      74     127 ..      45     131 .. 0.70
   2 ?   -1.1   0.4       1.4   2.1e+03      72     101 ..     263     292 ..     250     301 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-05
                           DUF1090  53 anCtdek...lkaerqekveekeeeVaereaeLaeakekgdkdkiakrqekLae 103
                                        +C+ ++   + + +++  e+ ++ V+e ++ L+ a++k++k+ i+k ++kL+ 
  gi|488599716|ref|YP_007906187.1|  74 IQCARDRaleMYRSYKRLHEKWKKRVEELKKSLERARAKENKNGIRKLERKLKR 127
                                       4555444111445566667888999***************************86 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                           DUF1090  72 eeeVaereaeLaeakekgdkdkiakrqekL 101
                                        +e+++r a L+  k+ +  +k + +++ +
  gi|488599716|ref|YP_007906187.1| 263 MHELNNRIARLQRLKKIKVLKKLKNKRRNI 292
                                       445555555555555555445554444444 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.45   6.7e+02      29      44 ..     113     128 ..      82     129 .. 0.74
   2 ?    0.3   0.4      0.46   6.8e+02      39      52 ..     274     287 ..     261     289 .. 0.82
   3 ?    6.1   0.0    0.0069        10      27      55 ..     398     426 ..     393     431 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.45
                                       -TGGGHHHHHHHHHHT CS
                           DUF1967  29 eneeavrrfarrLkkl 44 
                                       en+ ++r+++r+Lk++
  gi|488599716|ref|YP_007906187.1| 113 ENKNGIRKLERKLKRM 128
                                       5778889999999887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.46
                                       HHHHHTTHHHHHHT CS
                           DUF1967  39 rrLkklGvedaLrk 52 
                                       +rLkk+ v ++L++
  gi|488599716|ref|YP_007906187.1| 274 QRLKKIKVLKKLKN 287
                                       479*********97 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0069
                                       EE-TGGGHHHHHHHHHHTTHHHHHHTTT- CS
                           DUF1967  27 nfeneeavrrfarrLkklGvedaLrkaGa 55 
                                       + +++ + + + + Lkk G+++a+ +aGa
  gi|488599716|ref|YP_007906187.1| 398 DRDENASTNILLKGLKKTGLDEAMLRAGA 426
                                       5567778899******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1593  (0.0888505); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 2812.85
//
Query:       gi|488599717|ref|YP_007906188.1|  [L=249]
Description: TIM-barrel protein, putative [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-08   33.6   0.1    3.1e-08   33.1   0.1    1.2  1  Dus           Dihydrouridine synthase (Dus)
     0.0004   19.9   0.1     0.0012   18.4   0.0    1.7  2  His_biosynth  Histidine biosynthesis protein
     0.0015   17.8   0.0      0.062   12.5   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.023   14.8   0.3      0.099   12.8   0.1    2.2  3  DUF211        Uncharacterized ArCR, COG1888


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   6.9e-12   3.1e-08      68     228 ..      91     235 ..      59     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 6.9e-12
                                       HHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHH CS
                               Dus  68 laeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalela 144
                                         + A+ vad +  +I++N+ C ++++ + g G aLl + + ++ iv+++ +      +vkir g d    +   la
  gi|488599717|ref|YP_007906188.1|  91 YIDVAEAVAD-YNGIIEINAHCRQPEMMELGCGQALLFDIERLCAIVEKTSEICT--TSVKIRGGLD---IDYAALA 161
                                       5678999999.999**********************************9998876..689*******...66779** PP

                                       HHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTT CS
                               Dus 145 kiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPw 221
                                       +++++ G+++l v     a    g+ad++ I+e+     i  i+N  +++++da++++e  Ga+ v ++r+ l++ +
  gi|488599717|ref|YP_007906188.1| 162 EKLKEHGCDMLHV----DAMIVGGKADLDLIRELSGI--IFTIGNNSVTSVDDARKMIEC-GAELVSCARAVLRDEN 231
                                       **********998....4567777*****99998643..789***************998.************9988 PP

                                       HHHHHHH CS
                               Dus 222 lfaesta 228
                                       +f    +
  gi|488599717|ref|YP_007906188.1| 232 FFT---K 235
                                       886...3 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.38   1.7e+03      61      81 ..     132     152 ..     114     155 .. 0.68
   2 !   18.4   0.0   2.6e-07    0.0012      30     118 ..     156     239 ..     153     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHH-SSEEEEESS CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGG 81 
                                         ++ve++ e ++  v + GG
  gi|488599717|ref|YP_007906188.1| 132 LCAIVEKTSEICTTSVKIRGG 152
                                       456677777777777777777 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.6e-07
                                       SHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS.SSSHHHHHHHHHCT-SEEEESHHH CS
                      His_biosynth  30 dpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG.Irsledveelleagadkviigtaa 105
                                       d ++la++++e+g+d+lhv   da   g +a+ldl++e+       +++G   + s++d+++++e ga+ v+ + a+
  gi|488599717|ref|YP_007906188.1| 156 DYAALAEKLKEHGCDMLHV---DAMIVGGKADLDLIRELSGI---IFTIGNNsVTSVDDARKMIECGAELVSCARAV 226
                                       56789*************7...88999**********99987...77888756************************ PP

                                       HH-THHHHHHHHH CS
                      His_biosynth 106 vknpelikelaek 118
                                       +++ +++++l+e 
  gi|488599717|ref|YP_007906188.1| 227 LRDENFFTKLLED 239
                                       ******9999874 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0076        34     112     197 ..      89     176 ..      61     187 .. 0.65
   2 !   12.5   0.0   1.4e-05     0.062     240     295 .]     190     245 ..     185     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0076
                                       HHHHHHHHHHGGGESEEEEES-SCTCCTSCCCGCHHHHH...HHHHHHHHHHHSS.EEEEEE-SSSSHHHHHHHHHH CS
                            DHO_dh 112 ddyvevvrkigpfadilelNvSsPntpglrdlqekeelk...aillkvvkevskv.pvlvKlaPdltdeekkdiadv 184
                                         y+ v++ ++ +++i+e+N  +   p   +l+  ++l    + l++ v+++s++    vK+     d++ ++ a++
  gi|488599717|ref|YP_007906188.1|  89 RGYIDVAEAVADYNGIIEINAHCR-QPEMMELGCGQALLfdiERLCAIVEKTSEIcTTSVKIRG-GLDIDYAALAEK 163
                                       469999**************9994.345555555555541113445555555544145678877.447777777777 PP

                                       HHHHTECEEEE.. CS
                            DHO_dh 185 llelkldgiivtN 197
                                       l+e++ d++ v  
  gi|488599717|ref|YP_007906188.1| 164 LKEHGCDMLHVDA 176
                                       7777777776555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.4e-05
                                       HTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       +l++ i  Ig   ++s +Da  +ie+GA lv    a+  ++ +  k +++el + +
  gi|488599717|ref|YP_007906188.1| 190 ELSGIIFTIGNNSVTSVDDARKMIECGAELVSCARAVLRDENFFTKLLEDELLSQM 245
                                       566678889999*************************9999999999999998765 PP

>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.44     2e+03      17      35 ..      91     109 ..      81     119 .. 0.77
   2 ?   12.8   0.1   2.2e-05     0.099      37      83 ..     135     182 ..     104     186 .. 0.79
   3 ?   -2.1   0.0      0.99   4.4e+03      70      77 ..     201     208 ..     178     221 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.44
                                       HHHHHHHHHTSTTEEEEEE CS
                            DUF211  17 ivelakklaelegvdgvni 35 
                                        +++a+++a+ +g+  +n+
  gi|488599717|ref|YP_007906188.1|  91 YIDVAEAVADYNGIIEINA 109
                                       6788888888888877776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.2e-05
                                       EEEE-SSEEEEEEEEEE.SSE-HHHHHHHHHCTT-EEEEEEEEEEESS CS
                            DUF211  37 vkevDketenlkitieG.enidyeeieeaieelggvihSiDevvaGkk 83 
                                       ++e   e+ ++++ i G  +idy ++ e+++e g+ +  +D +++G k
  gi|488599717|ref|YP_007906188.1| 135 IVEKTSEICTTSVKIRGgLDIDYAALAEKLKEHGCDMLHVDAMIVGGK 182
                                       4556678888999998627***********************999865 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.99
                                       -EEEEEEE CS
                            DUF211  70 gvihSiDe 77 
                                        ++ S+D+
  gi|488599717|ref|YP_007906188.1| 201 NSVTSVDD 208
                                       35566664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1384.80
//
Query:       gi|488599718|ref|YP_007906189.1|  [L=281]
Description: diaminopimelate epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-64  215.8   1.4      1e-39  135.5   0.3    2.1  2  DAP_epimerase  Diaminopimelate epimerase
    0.00055   19.5   0.0      0.001   18.6   0.0    1.4  2  PhzC-PhzF      Phenazine biosynthesis-like protein
     0.0042   16.2   0.0      0.041   12.9   0.0    2.0  2  Pro_racemase   Proline racemase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.3   1.7e-43     1e-39       1     119 [.       6     127 ..       6     129 .. 0.96
   2 !   79.7   0.0   3.2e-26   1.9e-22       1     121 []     153     268 ..     153     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 1.7e-43
                                       EEEECSSEEEEEEECCTTCSSHHH...HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCCHH CS
                     DAP_epimerase   1 fakshGnpndvvvvddveaelvle...aelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnGvr 74 
                                       f+k hGn+nd+v+vd++ ++ + e   +e+v+a+c+r++g+gadg lfv+ s+++d+++ryfn+dgseaemCGnG+r
  gi|488599718|ref|YP_007906189.1|   6 FVKLHGNGNDFVLVDEFSGTIIPEdrkPEFVRAVCHRRFGVGADGALFVQRSEKADVRFRYFNSDGSEAEMCGNGIR 82 
                                       799****************99998899************************************************** PP

                                       HHHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSS.EEEEEE--E CS
                     DAP_epimerase  75 vfaaylreggletkkevtvetlgGeleievkddgek.vkvdmGkas 119
                                       +f +yl ++g + ++ v+vetl+G le+ev + ++  vkv+mG+++
  gi|488599718|ref|YP_007906189.1|  83 CFTRYLVDEGYA-NDIVKVETLAGVLELEVSNGEKFlVKVNMGRVR 127
                                       **********77.******************99877*******987 PP

  == domain 2  score: 79.7 bits;  conditional E-value: 3.2e-26
                                       EEEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEE.EEETTTEEESTTHCC.HHH CS
                     DAP_epimerase   1 fakshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvkpsgeediklr.yfnrdgseaemCGnG.vrv 75 
                                       +a++ G+p++v++vd++++ ++     ++++  +e +p +++v+fv ++ge+++++r y++++++e+ +CG+G v+ 
  gi|488599718|ref|YP_007906189.1| 153 YAVNSGVPHAVIFVDEIDHMDIIP--PARKIRYHELFPHGINVNFVSVAGENELRIRtYERGVEDETLSCGTGsVAS 227
                                       589*********************..99*****************************7777889*********6666 PP

                                       HHHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--EEE CS
                     DAP_epimerase  76 faaylreggletkkevtvetlgGeleievkddgekvkvdmGkaslv 121
                                       + ++   g     ++v+v t+gGel ie   d   + ++ G+a++v
  gi|488599718|ref|YP_007906189.1| 228 AFVAKELG--YVSDPVRVITKGGELIIEFDGD---IAYMSGSANRV 268
                                       55554444..469**********999999888...57*****9986 PP

>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.7e-07     0.001      41     175 ..      52     178 ..      45     234 .. 0.79
   2 ?   -2.0   0.0      0.33     2e+03      63     101 ..     216     252 ..     192     258 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.7e-07
                                       EEEE--SSTTSSEEEEEE-S.SSEES--HHHHHHHHHHHHHHCT-S-SCEEEEEETTEEEEE.EEEEETCEECCEEE CS
                         PhzC-PhzF  41 aFllkpsdekarfrlRyFTP.vaEvdlcGHatlasahalaekglvasaetveletkaGilpvkslkekddgeellie 116
                                        F+ +  +eka++r RyF    +E ++cG      ++ l+ +g   +++ v++et aG l +    e  +ge++l++
  gi|488599718|ref|YP_007906189.1|  52 LFVQR--SEKADVRFRYFNSdGSEAEMCGNGIRCFTRYLVDEGY--ANDIVKVETLAGVLEL----EVSNGEKFLVK 120
                                       57777..599********65279********************7..5**************9....68899999999 PP

                                       EE-SEEEEEE-HHHHHHHHHHCCTSGG-TTS-BEEEESSSEEEEEEBSTCCHHHH---- CS
                         PhzC-PhzF 117 lkfPvikteevssedlallakllklaaqkalpiavkstglekvivplsseeavaelspd 175
                                       +++  + +++ +     + +   ++   + +++ + ++g  + ++ + +  +++ + p 
  gi|488599718|ref|YP_007906189.1| 121 VNMGRVRKRAEDVPVNTEKEFFWGER-IGSMEVYAVNSGVPHAVIFVDEIDHMDIIPPA 178
                                       99999999998888777766655555.77888888888888888888777766665554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.33
                                       EES--HHHHHHHHHHHHHHCT-S-SCEEEEEETTEEEEE CS
                         PhzC-PhzF  63 EvdlcGHatlasahalaekglvasaetveletkaGilpv 101
                                       E   cG   +asa +  e g v  ++ v + tk G+l +
  gi|488599718|ref|YP_007906189.1| 216 ETLSCGTGSVASAFVAKELGYV--SDPVRVITKGGELII 252
                                       4445888888888887777765..777777777777765 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   6.9e-06     0.041      59     149 ..      52     136 ..      36     145 .. 0.71
   2 ?    1.0   0.0      0.03   1.8e+02      80     104 ..     217     241 ..     212     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-06
                                       EE--SSTTSSEEEEEEESSSB-.SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTSTSEEEEEE CS
                      Pro_racemase  59 lvppkepdadlgvifletsgyl.pmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrdgkvervsl 134
                                       l+  ++++ad+ + +++++g    mcG++  + ++ l+++G  +       +++et aG++e ++++ ++   +v++
  gi|488599718|ref|YP_007906189.1|  52 LFVQRSEKADVRFRYFNSDGSEaEMCGNGIRCFTRYLVDEGYAND-----IVKVETLAGVLELEVSNGEKFLVKVNM 123
                                       344567899999999999987527*****************7543.....245677777777777776666666665 PP

                                       E-S-BEEEEEEEEEE CS
                      Pro_racemase 135 envpsfvyaldveve 149
                                         v     a+dv v+
  gi|488599718|ref|YP_007906189.1| 124 GRVR--KRAEDVPVN 136
                                       5554..344444444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.03
                                       -SSTHHHHHHHHHHHHHTTSS-SEE CS
                      Pro_racemase  80 lpmcGsntigvvtvlletGlvevqe 104
                                       + +cG ++++ + v+ e G v+ + 
  gi|488599718|ref|YP_007906189.1| 217 TLSCGTGSVASAFVAKELGYVSDPV 241
                                       568****************998664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.33s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1702.52
//
Query:       gi|488599719|ref|YP_007906190.1|  [L=212]
Description: orotidine-5-phosphate decarboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.8e-35  121.2   0.0    5.9e-35  120.9   0.0    1.0  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
  ------ inclusion threshold ------
      0.018   14.4   0.1      0.031   13.6   0.1    1.3  1  TMP-TENI   Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.0   6.6e-39   5.9e-35       3     224 ..       4     202 ..       3     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 6.6e-39
                                       EEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHST CS
                         OMPdecase   3 LclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatag 79 
                                       L+lalDv+++++++ la++v +++++lK++y+lv + g      ++++++ +  +++++D+K+aDI++t +++a+  
  gi|488599719|ref|YP_007906190.1|   4 LILALDVMDRNRAIWLAREVSEYVDYLKVNYPLVLSAG-----IEIIRELSEI-KPVIADFKIADIPYTSSLIAR-- 72 
                                       89************************************.....99*****999.5*******************9.. PP

                                       CHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEE CS
                         OMPdecase  80 sarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfv 156
                                         +++  a +v++h++aG++++ka++++ +++g   +++++++ss+ ++ ++     ++++  ar+        G++
  gi|488599719|ref|YP_007906190.1|  73 -KAFENSAFAVICHGMAGSDTLKAVLDVSDEFG-GEVYVVTELSSESEFLRKF---SDEIAMLARDIGC----HGII 140
                                       .789****************************8.8*************98887...9999999999885....5*** PP

                                       CCCHTHHHHHHTTCSCEEEHHHTT.EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 157 aqetlnateedaddfihltpgigl.eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       a +t++      + + +l++ +g  +  + g g q   +e+ i+ agad+iivGR+I+++++p++ a+ 
  gi|488599719|ref|YP_007906190.1| 141 APATRA------ERVAQLRKIVGSmKILSPGVGAQGGSVEETIK-AGADYIIVGRSIYTSDEPKAVARD 202
                                       ****99......45555555555555577777778888899999.89******************9997 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.5e-06     0.031      68     134 ..     130     198 ..     124     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-06
                          TMP-TENI  68 lalavgadgvHlgq.ddlpvaearellgpdliiGlSvhslee.aeeaealgadYigvGpifpTdtKkda 134
                                       la ++g++g+     +   va++r+++g+ +i+   v  +   +ee  ++gadYi vG    T+  ++a
  gi|488599719|ref|YP_007906190.1| 130 LARDIGCHGIIAPAtRAERVAQLRKIVGSMKILSPGVGAQGGsVEETIKAGADYIIVGRSIYTSDEPKA 198
                                       67777777777777344589*************9999999888***************98888766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 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:                        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 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1311.58
//
Query:       gi|488599720|ref|YP_007906191.1|  [L=590]
Description: Uncharacterized metal-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-89  298.5   0.1    4.9e-89  297.8   0.1    1.3  1  RACo_C_ter      C-terminal domain of RACo the ASKHA domain
      1e-46  158.6   0.3    2.1e-46  157.6   0.1    1.6  2  Raco_middle     RACo middle region
    1.7e-11   43.9   0.2    3.9e-11   42.7   0.2    1.6  1  Fer2            2Fe-2S iron-sulfur cluster binding domain
     0.0047   16.9   0.1      0.012   15.6   0.1    1.7  1  Fer2_4          2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
       0.13   12.4   0.1       0.26   11.5   0.1    1.4  1  VP4_haemagglut  Outer Capsid protein VP4 (Hemagglutinin) Conc


Domain annotation for each model (and alignments):
>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.8   0.1   1.4e-92   4.9e-89       2     258 ..     337     584 ..     336     586 .. 0.96

  Alignments for each domain:
  == domain 1  score: 297.8 bits;  conditional E-value: 1.4e-92
                                       -EEEEEESSSEEEEEE-SS-EEEEEEE--SCCCTTTSTTBE-SSTTEEEEEEEEGGGSSEEEEECTSS--SEEEHHH CS
                        RACo_C_ter   2 lslliDiGTNaEivlgnkdellaasaaaGPAlEGaeikcGmrAapgAIedveidpetlevelkvigdekakGicGsG 78 
                                       +sll+D+GTN+Eivlg++ +l+++s a+GPA+EG ei++G rA +gAI++v+i+  +  +e++vig++k+  icGsG
  gi|488599720|ref|YP_007906191.1| 337 ISLLVDLGTNGEIVLGSEGWLISTSVASGPAFEGYEIEHGSRAVEGAIDHVRIKGGN--LEYTVIGNTKPASICGSG 411
                                       89***************************************************9998..99**************** PP

                                       HHHHHHHHHHTTSB-TTS-B-GGG-TTTEEEETTCEEEEEE-GGGSSS.S-EEEEHHHHHHHHHHHHHHHHHHHHHH CS
                        RACo_C_ter  79 iidliaelleagiidkkgklnkelkserireeeetleyvlakaeetet.kdivitekDieelikakaAiyagiktLl 154
                                       +idl+ael+++gi+d +g+l+++   er+    +  ++++a aeet+t kdi++t++Di++lik+kaA++agi++Ll
  gi|488599720|ref|YP_007906191.1| 412 LIDLLAELFKNGIVDFTGSLQDN---ERV----KDGKFIVAYAEETSTgKDIFLTQNDIDTLIKSKAAVCAGIAVLL 481
                                       ********************554...444....6789999********99*************************** PP

                                       HHTT--GGG--EEEEESSGGGCEEHHHHHHHTSS-SS-GGGEEEECSHHHHHHHHHHCBHHHHHHHHHHHHHEEE-- CS
                        RACo_C_ter 155 eevglevediekvylAGafGsyidaekAitiGllPdlelekvvqvGNtslagAreallseealeeleeiarkityie 231
                                       +++gl+v+di+k+y+AGafG yi++e+++ iGl+P++++++vvq+GN+slagA++a++se++++ +e+iar  ty++
  gi|488599720|ref|YP_007906191.1| 482 KKAGLSVDDITKFYIAGAFGYYINIENSTIIGLFPEFPNAEVVQIGNGSLAGAYMAMTSERKRKIVERIARVFTYFD 558
                                       ***************************************************************************** PP

                                       TTSSSHHHHHHHHHSSSS-SSGGG-ST CS
                        RACo_C_ter 232 lateeeFqeeyvaalflphtdlelfps 258
                                       l+t+++F+eey +al+lp  + elfp+
  gi|488599720|ref|YP_007906191.1| 559 LSTDPNFMEEYNSALSLPG-NPELFPT 584
                                       ******************9.5558887 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.6   0.1   5.8e-50   2.1e-46       1     160 [.     174     331 ..     174     334 .. 0.97
   2 ?   -3.1   0.0       1.5   5.5e+03      69      91 ..     476     498 ..     465     499 .. 0.85

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 5.8e-50
                       Raco_middle   1 yGlavDiGtTtvvaaLvdletgkelaeasalNpQikyGeDvlsRiayakeeeegleklqkavveeinelieelleea 77 
                                       +GlavD+GtTtvv+aL++l +g+++++ s++N Qi yGe+vlsR+++ +++++glek+++a++++in+li e++ + 
  gi|488599720|ref|YP_007906191.1| 174 FGLAVDVGTTTVVGALINLGDGSIVDVRSDYNGQIIYGEEVLSRVEFVRSRKDGLEKINRAIIDTINRLIGEIMGNL 250
                                       7************************************************************************9876 PP

                       Raco_middle  78 giekeeiyevvvagNttMlhlllgldpkslakapyvpvvseavelkakelglkinpeakvyvlpnvssyvGgDivag 154
                                         ++++iy++v+agNt M+h++++ d ++l+++   ++ ++a +  ak+lg++ np+a+v+ +p+v++yvGgDiva+
  gi|488599720|ref|YP_007906191.1| 251 --SSKRIYDIVIAGNTLMTHFFFKKDIEYLFTTSNPKIERKAFVDYAKNLGINSNPNAMVFGFPSVGKYVGGDIVAD 325
                                       ..899****************************9999999999999******************************* PP

                       Raco_middle 155 ilasgl 160
                                       ilas +
  gi|488599720|ref|YP_007906191.1| 326 ILASTI 331
                                       ***987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                       Raco_middle  69 lieelleeagiekeeiyevvvag 91 
                                        i+ ll++ag++ ++i++  +ag
  gi|488599720|ref|YP_007906191.1| 476 GIAVLLKKAGLSVDDITKFYIAG 498
                                       57789999999999999999998 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 !   42.7   0.2   1.1e-14   3.9e-11       4      76 ..      16      85 ..      12      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.1e-14
                                      TTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSS.SSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSE CS
                              Fer2  4 dgkevevevadgettlldaaeenggidipysCgggg.CgtClvevlegevqsdetelegeeldegklrlaCqti 76
                                       gk+v+v   +g t +l+ a+e+ g +i+  Cgg+g Cg C+v +++gev+++ +++e+  +  gk +laCq++
  gi|488599720|ref|YP_007906191.1| 16 SGKRVTV--RKGST-ILESAQEA-GEGIRSICGGKGsCGKCRVVLNKGEVEKNLEAHEKFLKLLGKQILACQSR 85
                                      4555555..56777.88888888.999999****888*************98977777777777788*****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 !   15.6   0.1   3.5e-06     0.012       3      56 ..      10      54 ..       8      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-06
                            Fer2_4  3 pvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClV 56
                                      +vt+   Gk+vtv++G+t+++ ++++g  ++  c            g+C +C V
  gi|488599720|ref|YP_007906191.1| 10 TVTFLPSGKRVTVRKGSTILESAQEAGEGIRSICGG---------KGSCGKCRV 54
                                      5888889***********************999987.........333333333 PP

>> VP4_haemagglut  Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.1e-05      0.26      92     155 ..     231     294 ..     216     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
                                       EEEE.ECCTTSSEEEEEEEEEETTCEEEEEEECCEETTCEEEECCEECCEE.SSTTEEEECXS-E CS
                    VP4_haemagglut  92 lekq.vvtangsvGGilikplsssklrivmkgneklnadsanyettnyefprsnpsvnitaytey 155
                                       +++  + t+n  +G i+   lss +++ ++   + l ++ +  ++ +y f  snp ++ +a+++y
  gi|488599720|ref|YP_007906191.1| 231 INRAiIDTINRLIGEIM-GNLSSKRIYDIVIAGNTLMTHFFFKKDIEYLFTTSNPKIERKAFVDY 294
                                       55541458999999888.99*******88888888999999999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 3304.09
//
Query:       gi|488599721|ref|YP_007906192.1|  [L=257]
Description: hypothetical protein Asulf_00164 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-19   70.1   0.6    3.8e-15   56.2   0.6    2.5  2  Hist_deacetyl  Histone deacetylase domain
  ------ inclusion threshold ------
       0.14   11.6   0.0        0.4   10.0   0.0    1.7  2  Peripla_BP_1   Periplasmic binding proteins and sugar binding
       0.26   11.4   1.1       0.64   10.1   0.1    2.1  3  Lambda_CIII    Lambda Phage CIII


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 !   56.2   0.6   6.3e-19   3.8e-15      93     179 ..      72     154 ..      16     164 .. 0.84
   2 !   11.8   0.0   2.1e-05      0.12     240     306 ..     190     255 ..     158     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 6.3e-19
                                       HHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SSS--HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  93 lavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDvHhGnGtee 169
                                        ++ +v +av+++ +  ++ a+v+  + gH a++++  G++++N+v +ai  +++  +++r+a++D D+HhG+G+ e
  gi|488599721|ref|YP_007906192.1|  72 KSAWCVYTAVKLLDE--YDLAIVATAGTGHNAMRDRFRGYSFINDVNLAISIMKD--SMPRIAVIDTDIHHGDGVFE 144
                                       445556666666664..59999999****************************99..789***************99 PP

                                       HCTT-TTEEE CS
                                       xxxxxxxxxx RF
                     Hist_deacetyl 170 afysdpdvlt 179
                                       ++ +++++ +
  gi|488599721|ref|YP_007906192.1| 145 YAAYNDNISI 154
                                       8888877755 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.1e-05
                                       SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G..EEEEE-S---HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 240 dlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvk.kvvllleGGYnlealaravtavlsa 306
                                       d+++  +G Da +  +l+e + +++ ++++ +k++el  k++ k++++l GG + e ++r  ++++s+
  gi|488599721|ref|YP_007906192.1| 190 DALIWYLGQDAFE--ELHEQSFDEKCLERIARKIRELGTKTRiKTLIILSGGVDSEVTERISKKIFSV 255
                                       7788888888886..578888899*****************55***********99999998888776 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 ?   10.0   0.0   6.8e-05       0.4     127     162 ..      11      46 ..       6      53 .. 0.91
   2 ?   -2.1   0.0      0.34     2e+03     214     249 ..     194     226 ..     178     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.8e-05
                                       EE-TTSHHHHHHHHHHHHHHHTT-GGGEEEEE-SSS CS
                      Peripla_BP_1 127 gpesaltakervqGflaalaeaGlevkdvhvalgsn 162
                                       ++es+l++ +r  Gf+ al+e G e k++++++ ++
  gi|488599721|ref|YP_007906192.1|  11 MKESNLAVCRRLYGFEKALKELGIEYKEPEILEFDE 46 
                                       6799***************************99876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.34
                                       EESSGGGHHHHTSSS--SEEEEEEE-HHHH....HH CS
                      Peripla_BP_1 214 fiesvvvydgLkkaqdtilelsplaviqlprellGr 249
                                        +++++++++L    ++ ++++ l  i  + ++lG 
  gi|488599721|ref|YP_007906192.1| 194 WYLGQDAFEEL---HEQSFDEKCLERIARKIRELGT 226
                                       56667777777...6666666666655555555554 PP

>> Lambda_CIII  Lambda Phage CIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.3   1.4e+04      27      32 ..      17      22 ..      17      23 .. 0.82
   2 ?   10.1   0.1   0.00011      0.64      15      27 ..     211     223 ..     207     233 .. 0.84
   3 ?   -2.8   0.0       1.1   6.8e+03      19      25 ..     246     252 ..     239     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.3
                       Lambda_CIII 27 egwkrl 32
                                      ++++rl
  gi|488599721|ref|YP_007906192.1| 17 AVCRRL 22
                                      689998 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00011
                       Lambda_CIII  15 ESlLdRitrklRe 27 
                                       E  L+Ri+rk+Re
  gi|488599721|ref|YP_007906192.1| 211 EKCLERIARKIRE 223
                                       778*********9 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.1
                       Lambda_CIII  19 dRitrkl 25 
                                       +Ri++k+
  gi|488599721|ref|YP_007906192.1| 246 ERISKKI 252
                                       7898887 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:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1629.07
//
Query:       gi|488599722|ref|YP_007906193.1|  [L=192]
Description: 3-hexulose-6-phosphate isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   70.6   0.2    1.3e-19   70.3   0.2    1.2  1  SIS              SIS domain
      5e-06   26.6   2.6     0.0029   17.6   0.4    2.3  2  SIS_2            SIS domain
  ------ inclusion threshold ------
      0.053   13.0   0.0      0.094   12.2   0.0    1.4  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
       0.14   11.3   0.9       0.19   10.9   0.9    1.1  1  Vert_IL3-reg_TF  Vertebrate interleukin-3 regulated transcrip


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 !   70.3   0.2   2.9e-23   1.3e-19       2     106 ..      39     138 ..      38     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.9e-23
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelake 78 
                                       + ++++i+++GaG+s+++ak +a+ l+++g++v++v ++++      + i++ddl+i is sget+++v+   +ak+
  gi|488599722|ref|YP_007906193.1|  39 IVSSRSIFIMGAGRSGFVAKSFAMRLMHLGYNVYVVGETTT------PKIKKDDLLITISGSGETSSVVNITMKAKS 109
                                       67899************************************......88***************************9 PP

                                       TT.SEEEEEESSTTSHHHHHSSEEEEEEE CS
                               SIS  79 rg.akiiaITdskgsplareadlalyina 106
                                           ki +IT+s++s+la+++d+++ i  
  gi|488599722|ref|YP_007906193.1| 110 MVgSKIAVITSSPNSSLAKMSDVVVVIKG 138
                                       874889****************9998765 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00028       1.3      22      59 ..      30      66 ..      11      78 .. 0.73
   2 !   17.6   0.4   6.5e-07    0.0029     100     138 .]      81     120 ..      69     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00028
                                      HHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT- CS
                             SIS_2 22 ekaaeliadslenggkvlvfGsGhSaalaeelaaragg 59
                                      e +   + +s+ + + ++++G+G S   a+ +a r+  
  gi|488599722|ref|YP_007906193.1| 30 ESV-GKLIESIVSSRSIFIMGAGRSGFVAKSFAMRLMH 66
                                      333.34568899999*******************9875 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.5e-07
                                       T--TT-EEEEE-SS--SHHHHHHHHHHHHH.T-EEEEEE- CS
                             SIS_2 100 rlkpgDvLlviSnsGnnavvveaaeaaker.gmkviAlts 138
                                       ++k+ D+L+ iS sG+  +vv++ ++ak++ g k+ ++ts
  gi|488599722|ref|YP_007906193.1|  81 KIKKDDLLITISGSGETSSVVNITMKAKSMvGSKIAVITS 120
                                       689*************************854999999987 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 ?   12.2   0.0   2.1e-05     0.094      30      74 ..      41      85 ..      34     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                       Glu_dehyd_C 30 epesalvlGaGslGLLal.alleaeerglervyvlgrrdrpdptid 74
                                      + +s +++GaG  G++a   ++++++ g++ vyv+g + +p+ + d
  gi|488599722|ref|YP_007906193.1| 41 SSRSIFIMGAGRSGFVAKsFAMRLMHLGYN-VYVVGETTTPKIKKD 85
                                      56899***********96257889999998.*****9999987654 PP

>> Vert_IL3-reg_TF  Vertebrate interleukin-3 regulated transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9   4.2e-05      0.19      39      67 ..     107     135 ..      91     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.2e-05
                   Vert_IL3-reg_TF  39 psvvassCisvikhsPqsslsdvsevssv 67 
                                       +  + +s i+vi  sP+ssl+ +s+v  v
  gi|488599722|ref|YP_007906193.1| 107 AKSMVGSKIAVITSSPNSSLAKMSDVVVV 135
                                       34455778*****************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1438.98
//
Query:       gi|488599723|ref|YP_007906194.1|  [L=351]
Description: Cellulase M-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   7.5e-104  346.8   3.0   9.1e-104  346.6   3.0    1.1  1  Peptidase_M42  M42 glutamyl aminopeptidase
    1.6e-09   37.8   0.4    2.5e-09   37.1   0.4    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
     0.0044   15.9   0.0     0.0087   14.9   0.0    1.5  1  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.6   3.0  1.5e-107  9.1e-104       1     292 []      45     336 ..      45     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 346.6 bits;  conditional E-value: 1.5e-107
                                       S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGC CS
                     Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHll 77 
                                       Gn+i++k+g  +e   mia+H+DeiGf+Vk I++ G +rf+++GG+ ++++ +qrv ++++kg+++Gvig+kppHl+
  gi|488599723|ref|YP_007906194.1|  45 GNIICVKNG--NEFTEMIASHIDEIGFIVKYIDDRGYIRFAALGGWFDQTALNQRVVLHGSKGNVYGVIGCKPPHLM 119
                                       9********..99**************************************************************** PP

                                       HHHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS- CS
                     Peptidase_M42  78 keeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeel 154
                                       +++erkk ++ik++fiD+ga skee++elGi++G+++++d+ef+el+n+k+++ka+D+rag av++e+lk+ +++  
  gi|488599723|ref|YP_007906194.1| 120 RDDERKKVIQIKDMFIDVGAGSKEEVQELGIDIGTPITIDREFRELGNNKVTGKAFDNRAGTAVMIEALKNTESK-- 194
                                       **********************************************************************99887.. PP

                                       SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT...CCSHHHHH CS
                     Peptidase_M42 155 eatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas...giyhpklr 226
                                        at+++v+tvqEEvGl+Ga++sa+ i+pd+aia Dv++a d pg++++ ++  lg+Gp+i+v+Das   +i+++++ 
  gi|488599723|ref|YP_007906194.1| 195 -ATIFAVGTVQEEVGLKGARISAFAIEPDVAIATDVCVAVDFPGTESAYMDvkLGNGPAITVVDASgrgLIASKRVI 270
                                       .7*******************************************99987788************99989******* PP

                                       HHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                     Peptidase_M42 227 kkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                       ++l+ +A++++ipyq+ev++gg+tDA+aihlt++g+pt+++s+p+ryiHspvev++++d+ + +kL
  gi|488599723|ref|YP_007906194.1| 271 EWLKGTAERYEIPYQMEVAEGGTTDATAIHLTKSGIPTGVVSVPARYIHSPVEVIDVNDVVNSAKL 336
                                       **************************************************************9987 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 !   37.1   0.4   4.2e-13   2.5e-09      29     206 ..     169     342 ..     157     343 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.2e-13
                                       EEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  29 klyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgil 105
                                       k+ G  a d+ +g + ++eal++ +      k ti  + ++ EE+g +Ga+  +  +e + ++   + + +  pg  
  gi|488599723|ref|YP_007906194.1| 169 KVTGK-AFDNRAGTAVMIEALKNTES-----KATIFAVGTVQEEVGLKGARISAFAIEPDVAIATDVCVAVDFPGTE 239
                                       55565.89*************98444.....67***********887999444443332344444444445545554 PP

                                       CHSTETEEEEE.EEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH....TTTEEEEEEE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....xxxxxxxxxx RF
                     Peptidase_M20 106 eagklaigvvk.vevelleggapvtlndsplvkalaeaaeelfgekveli.vsgpggtdarff....agiptvmifg 176
                                       +   +++++++   ++ + ++    + +++++++l+ +ae++    ++++ + g g+tda  +     gipt ++ +
  gi|488599723|ref|YP_007906194.1| 240 S-AYMDVKLGNgPAITVVDASGRGLIASKRVIEWLKGTAERY-EIPYQMEvAEG-GTTDATAIhltkSGIPTGVVSV 313
                                       4.77888888445555444444445555*************6.66644444899.********9988888***9999 PP

                                       SSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 177 pgsglaHspnEyvdledlekgikvlarlle 206
                                       p    +Hsp E +d++d+++ +k++ar le
  gi|488599723|ref|YP_007906194.1| 314 PA-RYIHSPVEVIDVNDVVNSAKLVARSLE 342
                                       99.9*********************99875 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-06    0.0087     311     427 ..     223     336 ..     196     339 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-06
                                       EEEEE--EE---TTSGGGS-TTTS--TTSEEEEEE.ETTSS.STT-HHHHHHHHHHHHHHC-EEEEEEE-TTS---- CS
                     Peptidase_M18 311 lliSaDvahaihPnysskheenhapllnkGvvikv.nanqr.yatnsagaallkevaqkanvklQelvvrndspcGs 385
                                       + i  Dv+ a++  ++         +l++G+ i v +a  r   ++++ ++ lk  a++ +++ Q      + ++G+
  gi|488599723|ref|YP_007906194.1| 223 VAIATDVCVAVD--FPGTESAYMDVKLGNGPAITVvDASGRgLIASKRVIEWLKGTAERYEIPYQME----VAEGGT 293
                                       667888888885..6666666677899***999863555556999*******************974....457787 PP

                                       H.CHHHHHHHHT-EEEEEE-EEBSTTSSSEEEECCHHHHHHHH CS
                     Peptidase_M18 386 t.igpilaaktGirtiDlGaaqlsmHSireltgskdveeavkl 427
                                       t   +i  +k Gi t  +  +   +HS+ e+++ +dv +  kl
  gi|488599723|ref|YP_007906194.1| 294 TdATAIHLTKSGIPTGVVSVPARYIHSPVEVIDVNDVVNSAKL 336
                                       7467899******************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2351.02
//
Query:       gi|488599724|ref|YP_007906195.1|  [L=483]
Description: archaeosine tRNA-ribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-83  281.1   0.0    1.6e-83  280.7   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.7   0.0   9.1e-88   1.6e-83       3     349 ..      12     338 ..       9     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 280.7 bits;  conditional E-value: 9.1e-88
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EE CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpil 79 
                                       +R+G+l++p g++etPa+mpv  ++++  +  ++lk  +ga+i+++n+y+++ +   + va+ +g+h++++ d p++
  gi|488599724|ref|YP_007906195.1|  12 GRIGRLKTPSGVVETPALMPV-INPNIDFIPVKDLK-RIGAEIVITNSYIIYRSRDLREVAESKGVHRLINSDLPVM 86 
                                       8********************.999**********5.99*************9999999****************** PP

                                       EE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHH CS
                               TGT  80 tdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwld 156
                                       tdsg++q++               + G+ v+++++++ie+q++++sDi+++ld +  ++ +++++e+ +e Tl++ +
  gi|488599724|ref|YP_007906195.1|  87 TDSGSYQLMV--------------Y-GD-VEVDNRTIIEFQNRIKSDIVVPLDIPSLPDIDREKAERDLEITLKREK 147
                                       *******664..............5.**.*************************999999***************** PP

                                       HHHHHH......SEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-E CS
                               TGT 157 rcleah......qalfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkpr 224
                                       ++++ h        + +++qG++y dlr++saee +k+++d y+igG +++ +  + +++++++ +v++ lp + p+
  gi|488599724|ref|YP_007906195.1| 148 EAIDLHseigddRLISAPIQGSTYLDLRRKSAEECSKLNADFYPIGGvVPLLDayRFQDVVRIILEVKSALPPSAPV 224
                                       ***********666*********************************7788887888******************** PP

                                       EETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHH CS
                               TGT 225 ylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhl 301
                                       +l+G+g+P+ ++ avalG+D fd+++++++a++gr+lt +g+ +l++ +y     p    C+C++C++yt+ +++++
  gi|488599724|ref|YP_007906195.1| 225 HLFGAGHPMVFAMAVALGCDFFDSAAYALYAKDGRYLTVNGTKKLEELQYF----P----CKCPVCSDYTPREVKSM 293
                                       **********************************************99999....9....***************** PP

                                       HHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 302 lktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                        k ++    iLl  HNl++ +e++++i++aI+e+++ e+ve+++r+++
  gi|488599724|ref|YP_007906195.1| 294 EKRDR---EILLGKHNLYVCFEEINTIKQAIRENNLFELVETRVRSHP 338
                                       ***99...***********************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3117.90
//
Query:       gi|488599725|ref|YP_007906196.1|  [L=536]
Description: Queuine tRNA-ribosyltransferase, containing PUA domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  157.2   0.0    5.5e-46  156.2   0.0    1.5  1  DUF5591   Domain of unknown function (DUF5591)
    9.6e-09   35.1   0.0    1.9e-08   34.1   0.0    1.5  1  PUA       PUA domain
    2.1e-06   27.1   0.1    1.5e-05   24.3   0.2    2.4  3  TGT       Queuine tRNA-ribosyltransferase


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 !  156.2   0.0   9.3e-50   5.5e-46       1     154 []     242     389 ..     242     389 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 9.3e-50
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT------- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqY 77 
                                       v+ f +r++e Yep+  +kv +LlPc+akkPys s++h+++ +++++  ++v+e+i++sPl v Pre+e++YPa++Y
  gi|488599725|ref|YP_007906196.1| 242 VSYFLQRIKEVYEPE--TKVALLLPCTAKKPYSLSRTHKTILSHLGNLIKRVDEIIISSPL-VLPREFELCYPAMNY 315
                                       6789**********9..6*******************************************.*************** PP

                                       ---------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHHH CS
                           DUF5591  78 diavtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvvedkptskeslknLkeaL 154
                                       d++vtg+ws eeiefvae+l++ +++++y  +iah+e++y+e+v+e+ +++g+++ +t+ e+ +tsk+s+++Lke+L
  gi|488599725|ref|YP_007906196.1| 316 DTPVTGHWSGEEIEFVAEHLSSLIDSFDY--IIAHVEGGYKEVVREALDATGKDASFTA-ENGVTSKKSMERLKEEL 389
                                       *************************7766..****************************.999***********987 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   3.2e-12   1.9e-08      18      72 ..     477     529 ..     468     531 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.2e-12
                                       EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA  18 sLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                        ++ +G+  ++++++++dvV   +   e+++vG+a++s+ e+++ ++g +v ++r
  gi|488599725|ref|YP_007906196.1| 477 TIFSAGIEWADEKIRPNDVVIFRNS--EFIGVGRALMSGREMMESNKGYAVSVKR 529
                                       6899****************99988..*************************997 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.3   1.8e+03       3      21 ..      14      32 ..      11      38 .. 0.84
   2 !   24.3   0.2   2.6e-09   1.5e-05     205     340 ..      81     192 ..      50     202 .. 0.73
   3 ?   -2.6   0.0      0.38   2.3e+03     155     182 ..     335     361 ..     324     403 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.3
                                      EEEEEEEETTEEEEESEEE CS
                               TGT  3 aRlGklelphgtietPafm 21
                                      aR++++  ++++++tP ++
  gi|488599725|ref|YP_007906196.1| 14 ARIAEFDFNGEKFQTPFVI 32
                                      9*********99****876 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.6e-09
                                       HHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBS CS
                               TGT 205 eellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspl 281
                                       ++++e++ +++++    kp +   + tP+++  +   GvD fd ++++  a +g ++ +   ln      + d  p 
  gi|488599725|ref|YP_007906196.1|  81 SKVVELLIEIRQKS-LTKPMIATAIATPQNIPLLCYFGVDFFDNAMAIASAHKGLYFHE-RVLNFD----SLDELP- 150
                                       44555555554444.489***************************************95.567876....456668. PP

                                       SSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHH CS
                               TGT 282 degCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeef 340
                                          CsC +C+n                g  Ll+ HN+  + e    +R+ I+++++ + 
  gi|488599725|ref|YP_007906196.1| 151 ---CSCEACRNLE--------------GLELLKRHNTIKLEEQALLVRQLIRNESLRNH 192
                                       ...*******432..............45566666666666666666666666666555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.38
                                       HHHHHHHHSEEEEEE--TT-HHHHHHHH CS
                               TGT 155 ldrcleahqalfgivqGglyedlreesa 182
                                       l   +++++ +++ v+Gg++e +re  +
  gi|488599725|ref|YP_007906196.1| 335 LSSLIDSFDYIIAHVEGGYKEVVREA-L 361
                                       44455555778888889888766654.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); 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: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3286.38
//
Query:       gi|488599726|ref|YP_007906197.1|  [L=263]
Description: putative sugar phosphatases of the HAD superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-23   81.1   0.0    2.1e-22   79.1   0.0    2.0  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase
    1.4e-17   63.5   0.0    2.9e-17   62.5   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
    4.5e-06   26.9   0.3    3.5e-05   24.0   0.1    2.4  3  HAD_2           Haloacid dehalogenase-like hydrolase
    1.3e-05   25.6   0.0    2.1e-05   24.9   0.0    1.4  1  Hydrolase       haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   4.7e-26   2.1e-22       1      99 [.      10     108 ..      10     110 .. 0.98
   2 ?   -1.1   0.0      0.48   2.1e+03      52      77 ..     197     222 ..     185     250 .. 0.47

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 4.7e-26
                                       EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr 77 
                                       f++D+dGv+ rg+k+i+ a  a++ l +++k+vv+++Nns++s++ y  ++++ g++++e+q++ + +a+a+y+k++
  gi|488599726|ref|YP_007906197.1|  10 FILDVDGVIGRGKKPIKPAISAVKKLIEMEKKVVFVSNNSTRSRRIYTRRFRDYGLEVDEDQMILTTYATAQYIKEN 86 
                                       799************************************************************************** PP

                                       SXXXEEEEESXHHHHHHHHHTT CS
                       Hydrolase_6  78 kadkkvlvigeeglreelkeag 99 
                                       +++ +++ +ge gl eel+ ag
  gi|488599726|ref|YP_007906197.1|  87 YGKMRIFTTGEIGLIEELELAG 108
                                       ******************9888 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
                                       HHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6  52 eklgvditeeqvvtsataaaeylkkr 77 
                                       e lg+++++  vv     +  +  k 
  gi|488599726|ref|YP_007906197.1| 197 EYLGLEAKDVVVVGDQIDVDVIAGKS 222
                                       55555555444444333333333333 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   6.4e-21   2.9e-17       2      74 ..     184     260 ..     183     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 6.4e-21
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHH....HHHHHT---SEEES CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedlee....pehkptyvaddlae 74 
                                       +gKPe++++  ale lg++ ++v+++GD+++ D+++++ + ++++LVl+Gvt+++ le        kp+yv++dl +
  gi|488599726|ref|YP_007906197.1| 184 CGKPEKVIMLKALEYLGLEAKDVVVVGDQIDVDVIAGKSINAETLLVLSGVTTRDNLENmikkYGVKPDYVLEDLSK 260
                                       9*****************************************************999988865557********986 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.15   6.6e+02      79     106 ..      23      50 ..      10     110 .. 0.66
   2 !   24.0   0.1   7.9e-09   3.5e-05     134     178 .]     185     230 ..     179     230 .. 0.93
   3 ?   -3.5   0.0       2.1   9.5e+03     143     153 ..     242     252 ..     237     261 .. 0.44

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsksr 106
                                       kp++ +++++++L e++ k+  v+++s+
  gi|488599726|ref|YP_007906197.1|  23 KPIKPAISAVKKLIEMEKKVVFVSNNST 50 
                                       3444444455555555555555555443 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 7.9e-09
                             HAD_2 134 kKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                        KP+  +++kale l+l++++v++vGD++  D++a+k ++ +++ v
  gi|488599726|ref|YP_007906197.1| 185 GKPEKVIMLKALEYLGLEAKDVVVVGDQIdVDVIAGKSINAETLLV 230
                                       69**************************************998865 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.1
                             HAD_2 143 kaleklklkke 153
                                       ++++k+++k++
  gi|488599726|ref|YP_007906197.1| 242 NMIKKYGVKPD 252
                                       33333333333 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.6e-09   2.1e-05       2     209 ..       8     223 ..       7     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.6e-09
                                       SEEEEESBTTTBCHHHHHHHHHHHH....CHHHHHHHHHH......HHCHHHHHHHHHHHHH...HHHHHHHHHETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx......xxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa....alalaaaletg......sehpigkalvaaakar...sgaltgfatfig 65 
                                       k +++D+dG++ +g++ ++ +i  +    +++ ++++  +      s++ +++++  +  ++   +  lt +at   
  gi|488599726|ref|YP_007906197.1|   8 KGFILDVDGVIGRGKKPIKPAISAVkkliEMEKKVVF--VsnnstrSRRIYTRRFRDYGLEVdedQMILTTYAT--- 79 
                                       67899**********5555555555221122222222..13455556666666666666666654333355555... PP

                                       TEHHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHH.HHHHHHHHTTEEEEEE CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                         Hydrolase  66 rgayaigkpewltal.dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaa.eavasLkaagievvll 140
                                           a   +e   ++  +++     i++++ +g++ +    ++ +++ +  ++++  e+  +a++   ++  + +++
  gi|488599726|ref|YP_007906197.1|  80 ----AQYIKENYGKMrIFTTGEIGLIEELELAGHEIVDY--EEAEMLVVGSNREINFELItKALRMCLSK--KPYIA 148
                                       ....33333344444445888899999999999999999..66666666655555555555888886655..89*** PP

                                       ESSEHHHHHHHHHHTT.....GGGESEEEEHHCES......STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHH CS
                                       xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                         Hydrolase 141 tgdnpetaeraanqlG.....ddyfdaviasdiet......vakpspegkvaaireLqgkpeevamVGDgvn.Daaa 205
                                       t+ ++ ++ +     G        ++ +      +      ++kp++ ++++a++ L+ + ++v++VGD +  D+ a
  gi|488599726|ref|YP_007906197.1| 149 TNPDRIFPSEDGPIPGtgmiiGALYWMT------GrmpdciCGKPEKVIMLKALEYLGLEAKDVVVVGDQIDvDVIA 219
                                       *****99999999988644422222333......1334567************************************ PP

                                       HHHT CS
                                       xxxx RF
                         Hydrolase 206 laaA 209
                                       ++  
  gi|488599726|ref|YP_007906197.1| 220 GKSI 223
                                       9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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: 2001.87
//
Query:       gi|488599727|ref|YP_007906198.1|  [L=394]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-32  110.4   0.1    1.2e-31  109.9   0.1    1.2  1  Acyl-CoA_dh_1    Acyl-CoA dehydrogenase, C-terminal domain
    2.1e-30  105.7   0.4    4.2e-30  104.7   0.4    1.5  1  Acyl-CoA_dh_N    Acyl-CoA dehydrogenase, N-terminal domain
    1.3e-23   83.0   0.0    2.8e-23   81.9   0.0    1.6  1  Acyl-CoA_dh_M    Acyl-CoA dehydrogenase, middle domain
    2.1e-19   70.1   0.0    3.3e-19   69.5   0.0    1.2  1  Acyl-CoA_dh_2    Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.053   13.6   0.1        5.6    7.2   0.0    2.4  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.1   3.4e-35   1.2e-31       2     147 ..     235     383 ..     234     386 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 3.4e-35
                                       BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                     Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaeal 78 
                                        G++  + tln eR++   aa+g+a++a+  a+ey+++rk f  p++++q +++ lae +a le arl++++a  ++
  gi|488599727|ref|YP_007906198.1| 235 GGWYNLLDTLNPERMCFTTAAIGIAKAAIKKAVEYSKQRKVFVDPVGSYQGLQFPLAEAYATLETARLMNFKASTLF 311
                                       6**************************************************************************** PP

                                       ------...HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                     Acyl-CoA_dh_1  79 dagkpd...raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                       d+++p    ++ a+maK++a e+  +++  amq +Gg+Gy++ey ver++r++ + r++  t+++ +  i++
  gi|488599727|ref|YP_007906198.1| 312 DKNAPYrevGKYANMAKVVAVEAGLKAVYWAMQCFGGYGYAKEYDVERWWREINLIRLAPVTQQMALAYIGE 383
                                       *****999*********************************************9999887777777766665 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.4   1.2e-33   4.2e-30       1     113 []       6     120 ..       6     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 1.2e-33
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       +eeq+++  ++r+ a++  +++ +e de+gef +e+wk+l ++G++gi +peeygGag++++e +i++eel + ++g
  gi|488599727|ref|YP_007906198.1|   6 NEEQKMIASSARDIAKDFPPEYWREKDEKGEFAEEFWKALSDAGFTGIVIPEEYGGAGMGMTELLIAIEELCANGCG 82 
                                       69***************9999****************************************************9998 PP

                                       HHH.HHHHHHHTTH.HHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  78 lal.llgvhsslva.pailrfGteeqkrryLpklasge 113
                                       +a   + v + + +  +i+r+Gteeqk++yLp +a+ge
  gi|488599727|ref|YP_007906198.1|  83 MAGnWYLVLTEVFGgMTIVRHGTEEQKEKYLPGIAKGE 120
                                       8888777766666559*********************8 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   7.8e-27   2.8e-23       1      96 [.     124     221 ..     124     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 7.8e-27
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS---.----EEEEEEE..GGGE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpd.rarglslflvprdapgv 73 
                                       ++alTEp+aG+++ s+kt  ae+dg+e+v+nG+Ki+i++a  a+ +l++ar    ek++ +++g++lfl +  +p v
  gi|488599727|ref|YP_007906198.1| 124 CMALTEPDAGTNTLSIKT-RAEKDGDEWVINGNKIFISGADRAKGMLIVARttpREKAEkKTHGITLFLADLPDPAV 199
                                       9*****************.88999999************************8664444489**************** PP

                                       EE-----BSS-TTS-EEEEEEE. CS
                     Acyl-CoA_dh_M  74 svrrieeklGlrglptgelvfed 96 
                                       +v++i +k+G++  +t+e+ +++
  gi|488599727|ref|YP_007906198.1| 200 KVNPI-PKHGINYSKTCEVSINN 221
                                       *****.69***********9987 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   9.1e-23   3.3e-19       2     126 ..     250     367 ..     249     370 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 9.1e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       +++++a+G+A+aa++++ve+ ++r+   + +++   + +q+ laea a l++Ar++  +a +      ++++++  e
  gi|488599727|ref|YP_007906198.1| 250 CFTTAAIGIAKAAIKKAVEYSKQRKV--FVDPVGSYQGLQFPLAEAYATLETARLMNFKASTL----FDKNAPY-RE 319
                                       899***********************..*******************************9999....8888887.89 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaa 126
                                         + a +a+++ave   +av ++++ +Gg++++ke+ ++R wR+++ +
  gi|488599727|ref|YP_007906198.1| 320 VGKYANMAKVVAVEAGLKAVYWAMQCFGGYGYAKEYDVERWWREINLI 367
                                       99*******************************************976 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 ?    3.9   0.0     0.016        57      27      43 ..      50      66 ..      27      80 .. 0.84
   2 ?    7.2   0.0    0.0015       5.6      40      72 ..     257     289 ..     255     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.016
                   Acetyltransf_CG 27 fthTeVpeelrGkGiAk 43
                                      ft +++pee++G G+++
  gi|488599727|ref|YP_007906198.1| 50 FTGIVIPEEYGGAGMGM 66
                                      78899**********97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0015
                   Acetyltransf_CG  40 GiAkkLvkaalddareeglkvvptCsyvaayle 72 
                                       GiAk+ +k+a+++ ++++  v p+ sy   +++
  gi|488599727|ref|YP_007906198.1| 257 GIAKAAIKKAVEYSKQRKVFVDPVGSYQGLQFP 289
                                       9*************************9766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2604.06
//
Query:       gi|488599728|ref|YP_007906199.1|  [L=153]
Description: putative nucleic-acid-binding protein containing a Zn-ribbon [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-10   39.2   0.0    6.9e-10   38.8   0.0    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    1.5e-09   37.5   0.0    2.2e-09   37.0   0.0    1.2  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.036   14.0   2.6      0.036   14.0   2.6    1.6  2  zf-C2HC_2      zinc-finger of a C2HC-type
       0.12   11.9   0.8       0.24   11.0   0.8    1.5  1  TF_Zn_Ribbon   TFIIB zinc-binding


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 !   38.8   0.0   1.5e-13   6.9e-10       2      64 ..      71     134 ..      70     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.5e-13
                                       EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT.....-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLde..gvrimarlvgvdpdevriGmrVravf 64 
                                       ve+sg+G v +ftv +   ++++ e+P +++++++d+  g+ +++ l +v p++v iGm+V+ v 
  gi|488599728|ref|YP_007906199.1|  71 VEISGEGYVRAFTVARLDGDENPMEEPEIYAIIDMDGtdGC-LIHLLGEVKPEDVYIGMKVKPVL 134
                                       89***********************************7555.999999999**********9885 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 !   37.0   0.0     5e-13   2.2e-09       2      34 ..      35      67 ..      34      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 5e-13
                           DUF35_N  2 daaaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                      + ++e ++++++C++CG+ +fPPr +C + +sd
  gi|488599728|ref|YP_007906199.1| 35 KKLKEDKFIASKCKKCGRTFFPPRIYCEYDFSD 67
                                      6799***********************999998 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.6     8e-06     0.036       4      14 ..      46      56 ..      45      59 .. 0.87
   2 ?   -3.9   0.0       3.3   1.5e+04      15      20 ..     109     114 ..     108     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-06
                         zf-C2HC_2  4 pCpkCgRsFnp 14
                                      +C+kCgR+F+p
  gi|488599728|ref|YP_007906199.1| 46 KCKKCGRTFFP 56
                                      7********99 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.3
                         zf-C2HC_2  15 drlekH 20 
                                       d + +H
  gi|488599728|ref|YP_007906199.1| 109 DGCLIH 114
                                       678889 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   5.3e-05      0.24       2      21 ..      46      71 ..      45      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.3e-05
                                      EETTTTCEEC......HEETSTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnl......veDpergelv 21
                                      kC++Cg t++      ++D++ +e+v
  gi|488599728|ref|YP_007906199.1| 46 KCKKCGRTFFppriycEYDFSDTEFV 71
                                      8********9**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 941.81
//
Query:       gi|488599729|ref|YP_007906200.1|  [L=176]
Description: putative nucleic-acid-binding protein containing a Zn-ribbon [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-13   51.0   0.1      2e-13   50.1   0.1    1.4  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    2.8e-05   23.9   0.1    6.9e-05   22.6   0.1    1.6  2  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !   50.1   0.1   2.2e-17     2e-13       1      65 []      89     156 ..      89     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.2e-17
                                       EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT.......-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLde.gvr...imarlvgvdpdevriGmrVravfr 65 
                                       wv ++++Gtv +f++ +  p++++ ++P +v+v+  d+       im+ l +v p++v iGm+V+av++
  gi|488599729|ref|YP_007906200.1|  89 WVYVKDTGTVQTFSISYIDPDAKPLPEPIIVAVIAIDGaS-PnmgIMHILGEVKPEDVYIGMKVKAVWK 156
                                       9*************************************53.2588**********************96 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 !   22.6   0.1   7.6e-09   6.9e-05       4      31 ..      55      82 ..      52      86 .. 0.92
   2 ?   -2.4   0.0      0.53   4.7e+03      15      21 ..      93      99 ..      91      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.6e-09
                           DUF35_N  4 aaegrLvgqrCpdCGtvqfPPravCphC 31
                                      ++ g+L++ +C +C +  fPPr +C  C
  gi|488599729|ref|YP_007906200.1| 55 LKKGKLIAVKCNKCHRIMFPPRMFCELC 82
                                      789**********************877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.53
                           DUF35_N 15 pdCGtvq 21
                                      +d+Gtvq
  gi|488599729|ref|YP_007906200.1| 93 KDTGTVQ 99
                                      79***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1044.85
//
Query:       gi|488599730|ref|YP_007906201.1|  [L=400]
Description: Acetyl-CoA acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.2e-09   35.4   0.0    2.1e-07   30.5   0.0    2.4  2  Thiolase_N  Thiolase, N-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 !   30.5   0.0   1.2e-11   2.1e-07       1     186 [.      17     189 ..      17     208 .. 0.79
   2 !    2.3   0.0    0.0051        91     243     257 ..     218     232 ..     213     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.2e-11
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSE CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevp 77 
                                       v+iv+a +t   +      + + +eL+  a+k++le+ag++  +++ v++G    +++g  ++ +  l+     + p
  gi|488599730|ref|YP_007906201.1|  17 VAIVGAGMTTWKR----RLNETGKELSYLAVKQALEEAGLEIGDIEMVVMGSAPDTFDGLHMKGEYLLDGSGGSDRP 89 
                                       79********999....7788899*********************************************9999**** PP

                                       EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSE CS
                        Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneeh 154
                                        ++v    + g+ a +++   +a+g adv++++  E+ms           sg k+  + + d  ++  l        
  gi|488599730|ref|YP_007906201.1|  90 YMRVFVGGGTGVFAPIAGYWHVASGLADVCLVVCEEKMSSCHPHP----QSGFKYIWDPILDRPLNPNLIW-----I 157
                                       **************************************9754333....3444444444444333332222.....2 PP

                                       HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHH CS
                        Thiolase_N 155 mGltaenlakkykisReeqdefAvkshqkaaa 186
                                        +l  +++ + ++i  e+ + + vk++++a +
  gi|488599730|ref|YP_007906201.1| 158 FALEMRRYMHVHNIKHEDIALVSVKNKANALD 189
                                       35666666666666666666666666666655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0051
                                       SB--BEEEEEEEEEE CS
                        Thiolase_N 243 nasqisDGaaavllm 257
                                       ++s+ sDGaaa++++
  gi|488599730|ref|YP_007906201.1| 218 DVSPPSDGAAALIMV 232
                                       67999*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 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:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2705.29
//
Query:       gi|488599731|ref|YP_007906202.1|  [L=380]
Description: Acetyl-CoA acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-05   23.1   0.0    0.00011   21.8   0.0    1.6  1  Thiolase_C   Thiolase, C-terminal domain
  ------ inclusion threshold ------
        0.1   12.1   0.0        7.1    6.3   0.0    2.3  2  SLC3A2_N     Solute carrier family 3 member 2 N-terminus
       0.13   12.1   0.3       0.71    9.8   0.1    2.1  2  ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase 


Domain annotation for each model (and alignments):
>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.9e-08   0.00011      28     112 ..     256     360 ..     232     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-08
                                       HHHHHHHHT--..GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTT CS
                        Thiolase_C  28 ikkvlkkaglt..vedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGa 84 
                                       +k++ k ag+t   ++id+ E+++ Fa + L+ ++al+l +                    vN+ GG + +G  l a
  gi|488599731|ref|YP_007906202.1| 256 AKMAYKLAGITnpAKEIDFAEVDDRFAFKELQHLEALQLSKryetatlmqegyfardgaLPVNISGGNLGIGNLLEA 332
                                       456788999997789************************999**************99989**************** PP

                                       HHHHHHHHHHHHHHHCTTSEEEEEEEET CS
                        Thiolase_C  85 sGaRivvtllselkkeggklgvaalCig 112
                                       +G   +  ++ +l+   gk  ++ +  g
  gi|488599731|ref|YP_007906202.1| 333 TGGQKALEVVLQLRGLAGKRQLSDVEVG 360
                                       ********99999987777666655555 PP

>> SLC3A2_N  Solute carrier family 3 member 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0012       7.1       9      32 ..     108     131 ..     101     133 .. 0.80
   2 ?    3.4   0.0    0.0095        57      14      32 ..     213     231 ..     199     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0012
                          SLC3A2_N   9 ekdkftGltkeeLlklandPfWvr 32 
                                       +++++  lt  +++k+a dP+W+r
  gi|488599731|ref|YP_007906202.1| 108 HSKASDILTFGNVIKFAMDPIWLR 131
                                       5566667888899*********98 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0095
                          SLC3A2_N  14 tGltkeeLlklandPfWvr 32 
                                       + l  + + k a+dP+Wv+
  gi|488599731|ref|YP_007906202.1| 213 FVLASDKIAKEAEDPVWVK 231
                                       4466777778888888886 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 ?    9.8   0.1   0.00012      0.71       7      41 ..      81     115 ..      78     123 .. 0.86
   2 ?   -1.0   0.0      0.28   1.7e+03      52      64 ..     206     218 ..     191     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                                       GGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS CS
                       ACP_syn_III   7 CsgfvyalsvAdaliesgaakrvLvigaetlskil 41 
                                       C  f+y++++A   iesg a  ++v +  + s+il
  gi|488599731|ref|YP_007906202.1|  81 CGDFLYGIATAYMHIESGLADVAVVEAHSKASDIL 115
                                       999***************99998887777777765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.28
                                       B-EEEEEEEEEEE CS
                       ACP_syn_III  52 fGDGAgAvvleas 64 
                                        +DGA  +vl  +
  gi|488599731|ref|YP_007906202.1| 206 RADGAIVFVLASD 218
                                       589**99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2548.55
//
Query:       gi|488599732|ref|YP_007906203.1|  [L=268]
Description: Acyl CoA:acetate/3-ketoacid CoA transferase, beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   88.2   0.0    6.6e-25   87.8   0.0    1.1  1  CoA_trans  Coenzyme A transferase


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   3.7e-29   6.6e-25       7     215 ..      16     220 ..      10     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 3.7e-29
                                       HHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEEEEESCTTBBCEHHHHH CS
                         CoA_trans   7 avakeikdGmtvavGGFgligiPealiaalarsgvkdltviiseagvlglgplllngsvkkviasyggetvnprfgk 83 
                                       a+ + ++d+ t++vG     giP + +a la++ +++++v   e g+  +gpl ++   +  +    ++  + r  +
  gi|488599732|ref|YP_007906203.1|  16 AA-RLLEDNKTIFVG----WGIP-QVVAILAEKLYTPNIVQVFEFGA--IGPLSRTPFLRGTMG-GPSN--TYRSLQ 81 
                                       45.59**********....****.***********************..*******99988887.3344..777777 PP

                                       HHHTTSSEEEEHHHHHHHHHHHHHHHTEETTEEEESTTTT.SHGGTTESEEEEETTEEEEEEESSSEEEEEEECCEE CS
                         CoA_trans  84 qflsgelefellpqgtlaerlraGgaglpelgfltntgig.tlvapklkkvpgfgGaeyilepalkadvalikaska 159
                                       +  s  l f  + q + ++  ++G+a+++++g++++t+ig ++++pk  ++pg gG +++++++  ++++++ ++k+
  gi|488599732|ref|YP_007906203.1|  82 W-CSMNLAFS-YAQAGYIDYGMLGAAQIDRYGNINSTMIGdDYEKPK-VRFPGSGGGNEVASYCW-KTIIVMAHEKR 154
                                       7.8899****.************************************.6***************9.6********** PP

                                       ETTCSEESSGGGHTTHSHHHHH..........HEEEEEEEEEEEECTTSSECCCESBTGGGHSEEE CS
                         CoA_trans 160 deegnlvfeksagnfnkpaiae..........aakvtileveeivekgkldpekvliPgvlvdavv 215
                                       +++++ +f++s g++ +++ +            +++t ++ + ++ek+k++++  ++ g++vd+v 
  gi|488599732|ref|YP_007906203.1| 155 RFVERCDFITSPGYMIDGKSRDevglpaetgpYRVITSMGMFGFDEKTKELKLIGVMKGLTVDEVL 220
                                       ***************99998889*****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1759.11
//
Query:       gi|488599733|ref|YP_007906204.1|  [L=325]
Description: Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-32  110.6   0.0    8.4e-32  110.3   0.0    1.1  1  CoA_trans  Coenzyme A transferase


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.0   4.7e-36   8.4e-32       5     216 ..      42     251 ..      38     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 4.7e-36
                                       HHHHCTT--TTEEEEE-SBTTBT.HHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEEEEESCTTBBCEHH CS
                         CoA_trans   5 aeavakeikdGmtvavGGFglig.iPealiaalarsgvkdltviiseagvlglgplllngsvkkviasyggetvnpr 80 
                                       +eav+k++kdG+++a   F +    P++li++++r+  k+l ++ + + +    +l+ +g+v+k  +++ g    p 
  gi|488599733|ref|YP_007906204.1|  42 KEAVKKFVKDGDYLAYD-FSSLTrGPQSLIREIIRQRKKNLWILAKFTLL-ESVLLAGAGCVDKIDVGFLGF--GPY 114
                                       79*************98.765544**********************9999.999***************999..9** PP

                                       HHHHHHTTSSEEEEHHHHHHHHHHHHHHHTEETTEEEESTTTTSHGGTTESEE.EEETTEEEEEEESSSEEEEEEEC CS
                         CoA_trans  81 fgkqflsgelefellpqgtlaerlraGgaglpelgfltntgigtlvapklkkv.pgfgGaeyilepalkadvalika 156
                                       ++k++ +g+++++++++g+ ++rl+aG++g+p+++ +   g++tl++ + + v + f G+++ l+pal++dv +i+ 
  gi|488599733|ref|YP_007906204.1| 115 IAKKVQEGAVKVYDWSNGSVTYRLVAGAMGIPFIPARDLLGTDTLKHSGAIVVkDPFSGKPVALMPALNPDVSVIHV 191
                                       *************************************************444415699******************* PP

                                       CEEETTCSEESSGGGHTTHSHHHHHHEEEEEEEEEEEE..CTTSSECCCESBTGGGHSEEEE CS
                         CoA_trans 157 skadeegnlvfeksagnfnkpaiaeaakvtileveeiv..ekgkldpekvliPgvlvdavve 216
                                       + ad +gn++  + +  + + a+a   k++i + e+iv   + +++p+ ++iP+++vdavv+
  gi|488599733|ref|YP_007906204.1| 192 QEADVYGNARVYGPTVATLETAMA--SKRVIISAERIVetIEFREHPNWTTIPYYCVDAVVH 251
                                       ************977777766666..9***********43345789***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2581.62
//
Query:       gi|488599734|ref|YP_007906205.1|  [L=281]
Description: Metal-dependent hydrolases of the beta-lactamase superfamily II [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   39.9   0.0    5.9e-10   39.5   0.0    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    4.2e-05   23.1   0.0    5.9e-05   22.7   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.039   13.4   0.0      0.058   12.8   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   9.9e-14   5.9e-10      13      89 ..      42     115 ..      30     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 9.9e-14
                                       ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHH CS
                       Lactamase_B  13 gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeadd 89 
                                       +++  +L DtG + + +  ++   +  l +++v +++l+H H+DH+Ggl ++ ++t++p++a++   +  f + +++
  gi|488599734|ref|YP_007906205.1|  42 DEEIGVLLDTGAGYAIEHNWE---QFSLCWDEVNYIVLSHRHFDHTGGLLKVLDKTNAPIIAHPNLFKPSFLWVRGR 115
                                       567779*************96...****************************************9999988888744 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 !   22.7   0.0   9.9e-09   5.9e-05       3      66 ..      47     104 ..      46     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9.9e-09
                                       EEES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHH CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgv 66 
                                       +L+D+g + +   +   ++ +  +d   +++ ++l+h H+DH+ gll +     +++p++a++ +
  gi|488599734|ref|YP_007906205.1|  47 VLLDTGAGYAIEHNW--EQFSlCWD---EVNYIVLSHRHFDHTGGLLKVLDK--TNAPIIAHPNL 104
                                       577777774433222..22332344...69*******************995..45899999875 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 ?   12.8   0.0   9.7e-06     0.058       5      61 ..      43      96 ..      39     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-06
                     Lactamase_B_6  5 dnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfks 61
                                      +++ +LlD G       +e+  ++ +   ++v+ i+Lsh   +h G++  ++ k ++
  gi|488599734|ref|YP_007906205.1| 43 EEIGVLLDTGAGYA---IEHNWEQFSLCWDEVNYIVLSHRHFDHTGGLLKVLDKTNA 96
                                      4799******9975...577899999999******************9877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1861.82
//
Query:       gi|488599735|ref|YP_007906206.1|  [L=207]
Description: hypothetical protein Asulf_00178 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-19   67.9   0.1    2.2e-18   66.6   0.0    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.3e-13   48.8   0.1    1.4e-12   47.9   0.1    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.7e-12   45.7   0.0      1e-11   44.8   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.9e-12   46.0   0.0      1e-11   45.6   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    9.2e-09   35.6   0.1    1.5e-08   34.9   0.0    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.8e-08   34.3   0.0    3.5e-08   33.3   0.0    1.4  1  FR47             FR47-like protein
    9.8e-06   25.3   0.0    1.2e-05   25.1   0.0    1.3  1  GNAT_acetyltran  GNAT acetyltransferase
    7.2e-05   22.9   0.0        0.2   11.7   0.0    2.3  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.037   13.7   0.0      0.097   12.4   0.0    1.6  2  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.062   13.4   0.0       0.11   12.6   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.071   13.3   0.0      0.081   13.1   0.0    1.2  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
      0.095   12.1   0.0       0.13   11.7   0.0    1.2  1  Glyco_hydro_85   Glycosyl hydrolase family 85


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 !   66.6   0.0   1.5e-21   2.2e-18      29     117 .]      85     170 ..      61     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.5e-21
                                       HSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTE CS
                    Acetyltransf_1  29 sleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedn 105
                                          +++ lvae+dg++iG++ + +  d  g++a i  ++++ +++++G+G+ L++++++ +r+ g++ i+l +e +n
  gi|488599735|ref|YP_007906206.1|  85 LAKNGFALVAEKDGRIIGHVVIVPTED--GKKADI-TIFIHQDFQNRGVGQILMKTMIDLCRKIGFDGIMLVTERTN 158
                                       446678889***********9999999..777777.9**********************************99999* PP

                                       HHHHHHHHHTTE CS
                    Acetyltransf_1 106 daairlYeklGF 117
                                        +ai++Y+klGF
  gi|488599735|ref|YP_007906206.1| 159 ARAIHVYKKLGF 170
                                       *******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 !   47.9   0.1   9.2e-16   1.4e-12       4      75 ..      90     171 ..      85     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 9.2e-16
                                       EEEEEEETTEEEEEEEEEEES...TCTEE...EEE-GGGTTSSHHHHHHHH......TT..SEEEEEEEEETHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitr...laVdpeyrgkGiGraLlea......ae..kgiileqlelnaekai 66 
                                         +Vae+dg+i+G +++++++           ++++++++++G+G+ L++       ++   gi l++ ++na +ai
  gi|488599735|ref|YP_007906206.1|  90 FALVAEKDGRIIGHVVIVPTEdgkK---AditIFIHQDFQNRGVGQILMKTmidlcrKIgfDGIMLVTERTNA-RAI 162
                                       5689***********9999986443...1456******************64555432255553333223333.9** PP

                                       HHHHHTTEE CS
                    Acetyltransf_7  67 kfYeklGFe 75 
                                       + Y+klGFe
  gi|488599735|ref|YP_007906206.1| 163 HVYKKLGFE 171
                                       ********9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   6.9e-15     1e-11      22     111 ..      78     175 ..      65     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6.9e-15
                   Acetyltransf_10  22 lrerie..egealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltv 91 
                                       ++++i+  +++ + lvae++g+i+G++ +  +++       +f++++++ +G+g+ L++++++ ++k g     l  
  gi|488599735|ref|YP_007906206.1|  78 IENWIDylAKNGFALVAEKDGRIIGHVVIvPTEDgkkADITIFIHQDFQNRGVGQILMKTMIDLCRKIGFDGiMLVT 154
                                       4555544489999**************776555555433346*************************9999886666 PP

                   Acetyltransf_10  92 nasp.yavpfYeklGFkavge 111
                                       + ++  a+ +Y+klGF++v++
  gi|488599735|ref|YP_007906206.1| 155 ERTNaRAIHVYKKLGFEVVSP 175
                                       666679***********9987 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   6.9e-15     1e-11       3     138 .]      41     171 ..      40     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 6.9e-15
                    Acetyltransf_3   3 lLrpl.teeDlealfelrsdpe.vmry.lpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdlee 76 
                                       ++r++  eeD e+l +++++ +   r  + +p t+ + e w++ ++a+    +g+ ++  +kd+++iG v + + e+
  gi|488599735|ref|YP_007906206.1|  41 TIRKYiHEEDREKLIQMYENFDpSLRClGLPPITRVAIENWID-YLAK----NGFALVA-EKDGRIIGHVVIVPTED 111
                                       6788867789999999999777666765666899999999*99.3443....6754444.466657*******9999 PP

                    Acetyltransf_3  77 edeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                         + a++ + ++++f+++G+++  ++ +++++ ++ g + ++ v++ +N + i v++klGfe
  gi|488599735|ref|YP_007906206.1| 112 GKK-ADITIFIHQDFQNRGVGQILMKTMIDLC-RKIGFDGIMLVTERTNARAIHVYKKLGFE 171
                                       877.****************************.9999************************7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0     1e-11   1.5e-08      36     137 ..      77     173 ..      42     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1e-11
                    Acetyltransf_4  36 efekflealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnie 112
                                        +e ++++l +++ + + +++++ri+G   ++  ++    +ka +++++ ++d +++g+g+ l++ +++  ++ ++ 
  gi|488599735|ref|YP_007906206.1|  77 AIENWIDYL-AKNGFALVAEKDGRIIGHVVIVPTED---GKKADITIFI-HQDFQNRGVGQILMKTMIDLCRKIGFD 148
                                       467999998.66666666666***********8877...99********.59************************* PP

                    Acetyltransf_4 113 nllaeiaspnensiqfhkalGFelv 137
                                        ++  +  +n+ +i ++k+lGFe+v
  gi|488599735|ref|YP_007906206.1| 149 GIMLVTERTNARAIHVYKKLGFEVV 173
                                       ***********************98 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   2.3e-11   3.5e-08      27      80 ..     119     173 ..     117     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.3e-11
                                       EEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  27 lqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfeki 80 
                                       + +++++++rG g+ l k ++   ++ g + ++lv+  +N ++i++y+klGfe+ 
  gi|488599735|ref|YP_007906206.1| 119 IFIHQDFQNRGVGQILMKTMIDLCRKIGfDGIMLVTERTNARAIHVYKKLGFEVV 173
                                       66899*********************66367999999***************975 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   7.8e-09   1.2e-05     150     242 ..      81     178 ..      10     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.8e-09
                   GNAT_acetyltran 150 yedfk.kkGlGvvilkngeivsgasSys.vyekgieieidTkedyrrkgLAtivaaalileclkrg...lyPsWDaa 221
                                       + d++ k+G+  v+ k+g+i+  ++ +     k++ i i  ++d++++g  +i+ + +i+ c k g   ++      
  gi|488599735|ref|YP_007906206.1|  81 WIDYLaKNGFALVAEKDGRIIGHVVIVPtEDGKKADITIFIHQDFQNRGVGQILMKTMIDLCRKIGfdgIMLVTERT 157
                                       4566669**************999877625567899****************************7611144445555 PP

                   GNAT_acetyltran 222 neaSvaLaekLGYefekeYkv 242
                                       n  ++++++kLG+e +++Y  
  gi|488599735|ref|YP_007906206.1| 158 NARAIHVYKKLGFEVVSPYIE 178
                                       ******************975 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00014       0.2      30      62 ..      77     109 ..      69     111 .. 0.88
   2 !    8.6   0.0    0.0013       1.9      81     127 ..     121     172 ..     117     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEE CS
                    Acetyltransf_9  30 eireyfrklleesrvlgaedngelvgqlallpl 62 
                                        i+++ ++l +++ +l+ae++g+++g++ ++p 
  gi|488599735|ref|YP_007906206.1|  77 AIENWIDYLAKNGFALVAEKDGRIIGHVVIVPT 109
                                       478999***********************9996 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                                       E-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  81 vapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                        + + ++rgv + L++++++ +r+ g   ++l+      ++i++Y+++G+e+
  gi|488599735|ref|YP_007906206.1| 121 IHQDFQNRGVGQILMKTMIDLCRKIGFDGIMLVTertnaRAIHVYKKLGFEV 172
                                       578899**************************9988887889********98 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.1   4.7e+03     126     142 ..      79      95 ..      74      97 .. 0.76
   2 ?   12.4   0.0   6.5e-05     0.097      89     140 ..     123     173 ..     111     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.1
                                       HHHHHHHHHTT-EEEEE CS
                    Acetyltransf_8 126 erairllekaGfekeke 142
                                       e+ i +l+k Gf+ + e
  gi|488599735|ref|YP_007906206.1|  79 ENWIDYLAKNGFALVAE 95 
                                       67789999999988765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.5e-05
                                       HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEE CS
                    Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfeke 140
                                       +++ ++g+++ l++++++++ +  + + +++  + +N+rai++++k+Gfe +
  gi|488599735|ref|YP_007906206.1| 123 QDFQNRGVGQILMKTMIDLCRKI-GFDGIMLVTERTNARAIHVYKKLGFEVV 173
                                       67899*************99876.9************************976 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   7.6e-05      0.11       9      57 ..      98     146 ..      85     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                   Acetyltransf_CG   9 geevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeg 57 
                                       g  ++++    +++g+ +   +++++ ++ +G+++ L+k+++d  r+ g
  gi|488599735|ref|YP_007906206.1|  98 GRIIGHVVIVPTEDGKKADITIFIHQDFQNRGVGQILMKTMIDLCRKIG 146
                                       55666666654555544455699********************999876 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.4e-05     0.081      46     135 ..      66     154 ..       6     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.4e-05
                    Acetyltransf_6  46 pdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgd.rlyywlggydpelaklspgllllwelie 121
                                        ++  +p tr  +++ ++ l  + ++  +v++ dgr+++ ++++  +d       + ++ ++   ++g++l+  +i+
  gi|488599735|ref|YP_007906206.1|  66 RCLGLPPITRVAIENWIDYL--AKNGFALVAEKDGRIIGHVVIVPTEDgKKADITIFIHQDFQNRGVGQILMKTMID 140
                                       46777788888888888888..7888899**********9977766662666677777******************* PP

                    Acetyltransf_6 122 daaeeGlrrfdlgg 135
                                        ++  G++ + l++
  gi|488599735|ref|YP_007906206.1| 141 LCRKIGFDGIMLVT 154
                                       ****9999888776 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 ?   11.7   0.0   8.4e-05      0.13      53     107 ..      99     158 ..      74     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.4e-05
                                       -EEEEEEEEEE--H..HHHHHHT---TTS-...-HHHHHHHHHHHHHT--EEEEEEEE-. CS
                    Glyco_hydro_85  53 kvlGtlifeedesg..edleellekdeege...fpvadkLielAkyygFdGwliNiEtal 107
                                       +++G +++ ++e g  +d+  ++++d +++   +++ + +i+l+++ gFdG ++  E + 
  gi|488599735|ref|YP_007906206.1|  99 RIIGHVVIVPTEDGkkADITIFIHQDFQNRgvgQILMKTMIDLCRKIGFDGIMLVTERTN 158
                                       467766555555554677778888865555446779***************999999873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1353.11
//
Query:       gi|488599736|ref|YP_007906207.1|  [L=593]
Description: Chloride channel protein EriC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-97  327.4  34.7    2.1e-97  326.6  29.8    2.0  2  Voltage_CLC      Voltage gated chloride channel
    4.6e-26   91.0   6.8    2.9e-15   56.4   0.2    3.0  3  CBS              CBS domain
  ------ inclusion threshold ------
        0.1   12.9   0.0       0.22   11.8   0.0    1.5  1  GAF_2            GAF domain
        3.7    7.4   6.7        7.1    6.5   0.0    3.5  3  PspC             PspC 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 !    3.6   0.2    0.0074        33     164     192 ..      13      41 ..       3      51 .. 0.84
   2 !  326.6  29.8  4.6e-101   2.1e-97       1     352 [.      77     432 ..      77     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC 164 lilfvllGilgGllgalfvrlllkverlf 192
                                       ++l++++G+++G+ + +f  ll  ++++f
  gi|488599736|ref|YP_007906207.1|  13 ILLAIIVGVISGIGAFVFYTLLEISTKFF 41 
                                       6789999********99999998888776 PP

  == domain 2  score: 326.6 bits;  conditional E-value: 4.6e-101
                                       HHHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC   1 lggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsr 77 
                                       +ggl++g++v+++apea+g+G++ v++a+++ kg+++ rv +vk++as++t+gsG+s+GreGp+ qiGA +gs l++
  gi|488599736|ref|YP_007906207.1|  77 IGGLISGFIVYRFAPEAEGHGTDAVIKAFHRLKGNVRGRVPIVKTIASAITIGSGGSAGREGPIAQIGAGFGSFLGN 153
                                       689************************************************************************** PP

                                       HTT.--SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTT.TSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S..-. CS
                       Voltage_CLC  78 llklsrndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEe.vsrefslrallpvfvasvvaalvlrlllgeepa..fg 151
                                       ll+ls++d +r+l+++G+++Gi+++F++P+gG+lf++E+ ++r+++++al+p+f++s+va+ v +lllg +++  fg
  gi|488599736|ref|YP_007906207.1| 154 LLNLSDRD-RRILLLCGVSGGIGSIFQSPMGGALFGIEVlYRRDYEVEALVPSFTSSIVAYTVYNLLLGFTNQihFG 229
                                       ****9888.888***************************999***************************99887866 PP

                                       T.....---...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC. CS
                       Voltage_CLC 152 e.....veslfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpas 223
                                       +      +++   s+ +l++ +++++++G++g ++++ +++++++f+k+   +i+++++p+++gll+gl+++ +p+ 
  gi|488599736|ref|YP_007906207.1| 230 TlrifsTPAVRINSPADLLICLVIAVFAGIIGLIYIKAFYTTHEYFKKV---RIPNYFKPMIGGLLTGLIAIYIPE- 302
                                       6444335555699**********************************99...9999********************. PP

                                       CSSSSCCHHHHHCTT-S-....HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CT CS
                       Voltage_CLC 224 vlgggyeliasllegstl....llsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpg 296
                                       ++g+gy+ ++ +++g+ l     l+ll++++++++k+lat++t+gsg +gG+faPs viG+++G++vg +++++  g
  gi|488599736|ref|YP_007906207.1| 303 AMGMGYGIVQLAIDGKILsiygNLTLLFIFIFIFAKILATSFTIGSGGSGGVFAPSVVIGGMIGAFVGYAFQSF--G 377
                                       *************9987699998999999*********************************************..3 PP

                                       SSC...HHHHHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHH CS
                       Voltage_CLC 297 aassdpgafalvGmaaflagvtrapltaiviviEltgdlelllplmlavliAkava 352
                                        ++++p++f+lvGma+f+++v+++p+++i++v+E+tg+++ll+ lm+++++A+ ++
  gi|488599736|ref|YP_007906207.1| 378 -VVEEPAFFVLVGMASFVSAVAKTPIASIIMVLEMTGGYNLLPALMISSILAYKIT 432
                                       .45589***********************************************886 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.66     3e+03      18      36 ..     101     119 ..      96     122 .. 0.71
   2 !   36.5   1.0   1.1e-12     5e-09       1      51 [.     465     516 ..     465     519 .. 0.88
   3 !   56.4   0.2   6.5e-19   2.9e-15       1      54 [.     529     583 ..     529     586 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.66
                                       HHHHHHHHHHHT.SS.EEEEE CS
                               CBS  18 leealelmrekg.vs.rlPVV 36 
                                       + +a+ ++  kg v+ r+P+V
  gi|488599736|ref|YP_007906207.1| 101 VIKAFHRL--KGnVRgRVPIV 119
                                       66788899..44464499*99 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 1.1e-12
                                       HHHH..SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   1 Vgdi..mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       Vgd   + ++vvtv+p++ l e++++++e+g+ ++PV+ e+gk+vGi+t +D+
  gi|488599736|ref|YP_007906207.1| 465 VGDAmvPAEKVVTVTPEMKLIEVMKMIEETGHMGYPVM-ENGKIVGIITFEDV 516
                                       566423777******************999966*****.9**********997 PP

  == domain 3  score: 56.4 bits;  conditional E-value: 6.5e-19
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllra 54 
                                       V+d+mt+d++  +pd+tle+al+++++++++rlPV+  +d klvG++t++D++ra
  gi|488599736|ref|YP_007906207.1| 529 VADVMTKDIIATYPDETLEDALKKLASRNIGRLPVLsRDDSKLVGLITRSDIMRA 583
                                       89***********************9999******9844557***********98 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.9e-05      0.22      93     126 ..     496     529 ..     458     534 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
                                       EEEEEE-TTS---EEEEES......--HHHHHHH CS
                             GAF_2  93 flavPlisegrvvGvlnlyankppafdeedlelL 126
                                       +++ P++++g++vG++++   ++ +f+e+++  +
  gi|488599736|ref|YP_007906207.1| 496 HMGYPVMENGKIVGIITFEDVERVPFEERNVKTV 529
                                       499***************9999999***998765 PP

>> PspC  PspC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.7      0.03   1.4e+02      11      22 ..      17      28 ..      15      30 .. 0.88
   2 ?    6.5   0.0    0.0016       7.1       5      24 ..     160     179 ..     159     182 .. 0.85
   3 ?   -3.8   0.2       2.6   1.2e+04      11      19 ..     287     295 ..     286     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.03
                              PspC 11 vlgGVcaGlAey 22
                                      ++ GV++G+++ 
  gi|488599736|ref|YP_007906207.1| 17 IIVGVISGIGAF 28
                                      899******985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0016
                              PspC   5 RspdnkvlgGVcaGlAeyfg 24 
                                       R+++  +l+GV +G++  f+
  gi|488599736|ref|YP_007906207.1| 160 RDRRILLLCGVSGGIGSIFQ 179
                                       67777789********9986 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.6
                              PspC  11 vlgGVcaGl 19 
                                       ++gG + Gl
  gi|488599736|ref|YP_007906207.1| 287 MIGGLLTGL 295
                                       789998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3644.90
//
Query:       gi|488599737|ref|YP_007906208.1|  [L=599]
Description: Aldehyde:ferredoxin oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-56  191.7   1.8    3.1e-56  190.4   0.8    2.0  2  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma
    2.4e-41  142.0   0.3      3e-41  141.7   0.3    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3


Domain annotation for each model (and alignments):
>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.4   0.8   3.4e-60   3.1e-56       1     197 [.       5     195 ..       5     196 .. 0.97
   2 ?   -0.8   0.0      0.13   1.2e+03     123     156 ..     250     280 ..     221     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 190.4 bits;  conditional E-value: 3.4e-60
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       gk l+++Ls+ k+e+ e++++++ek+ G  g+a+++  + +  ++dplspen +++++G+lt t++pg++++++v+k
  gi|488599737|ref|YP_007906208.1|   5 GKALEINLSDMKYEEIEIDDHVYEKHAGIIGIAYEFAEK-LAGRYDPLSPENFVILSAGILTNTGIPGATKTIAVTK 80 
                                       689********************************9999.6799********************************* PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTSEEEE CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgdkvav 154
                                        Pl +t+g +  Gg f+ ++kraGyd+++++Gka++pv++ i+++ +ei++a ++wg+d+ ett+ l+++   +v++
  gi|488599737|ref|YP_007906208.1|  81 NPLNNTYGPAVGGGAFARNMKRAGYDMVILKGKAKHPVWIDINSK-IEINKA-NFWGKDIVETTKLLNSN---SVLA 152
                                       ******************************************666.*****8.78************995...9*** PP

                                       E-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 155 iGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                       iG+aGen+v++A   +d+ +++g+gGlGav+gsKn+kai vrg
  gi|488599737|ref|YP_007906208.1| 153 IGKAGENRVPIALALIDAIHHIGKGGLGAVLGSKNVKAIRVRG 195
                                       *************99**************************99 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.13
                                       EEEEEE-TTTTTS-HHHHHHHHHHHHTSEEEEE- CS
                            AFOR_N 123 kveiedaedlwgldtyettealkeelgdkvaviG 156
                                       k e+ da+ l++ ++ + +e++k++   ++ ++G
  gi|488599737|ref|YP_007906208.1| 250 KSEVVDADTLKEFGVEKYKERIKKR---STGCVG 280
                                       5688899999999999999999996...556666 PP

>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   0.3   3.3e-45     3e-41       2     372 ..     210     599 .]     209     599 .] 0.83

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 3.3e-45
                                       HHHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS-.-TTGGGGSHHHHHHHTEEEE.E-TT-SS-- CS
                            AFOR_C   2 lgkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegt.fekaekisgealeekylvknegCfsCpiaC 77 
                                       +++++++++ks++ vt+ +++ G ++  ++  + g l  +  +e +  ++ ++ + e+++e+++++  gC++Cp +C
  gi|488599737|ref|YP_007906208.1| 210 VVREFKNKVKSDK-VTKIYSDIGIMSAWDAWAKLGYLTRRMKSEVVdADTLKEFGVEKYKERIKKRSTGCVGCPARC 285
                                       5678899999999.777******************998887777663444477888*****99999999******** PP

                                       EEEEE.......ET.EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHH CS
                            AFOR_C  78 grevkveegkk.vk.vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedt 152
                                       +++++ve   k v+       + ++ +G ++g+++ e+ + + +l++++G+D ++++++   +  l e G  +    
  gi|488599737|ref|YP_007906208.1| 286 KSVLEVEVDGKkVEsLASLYLGVAYEFGVKCGVESAEKAVLCHDLANRMGIDAMTFAELFDILATLKESGKTDI--- 359
                                       *****998877677877778889999********************************************9964... PP

                                       TS----TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HH.HHHHHHH-TTS CS
                            AFOR_C 153 dglelefgdaeallellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakg.malaYatsnrG 228
                                          ++   +ae +++ l+ +A+regig+ +++G+k l+  ++ e++ +  kG+e p  dpr + g  a +  t++rG
  gi|488599737|ref|YP_007906208.1| 360 ---DI-ERSAECVMKYLKLVANREGIGEYIGKGIKGLKGLCEFEDYFI--KGIE-PIFDPRISFGsEAFGLLTNPRG 429
                                       ...44.46899**************************99999999996..7744.89****87764799******** PP

                                       S-SGG.G-THHHH.....................S---TT.....--H..HHHHHHHHHHHHHHHHHHHT--GGGG- CS
                            AFOR_C 229 acHlr.ayliale.....................ekvdpl.....ete..gkaelvkwfqdltalvdslglCkftse 276
                                       a+                                e    l     + +  + a +++ ++++  l++ +glC+  s 
  gi|488599737|ref|YP_007906208.1| 430 AQEGPvTI----TvipgrkkesiirymrsigasdE----LieatfR-NgfNSALYTISAENWLWLLNGMGLCRRES- 496
                                       *9555333....33356888777666666655541....1554223.2469*************************. PP

                                       HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---.......SSTTTT CS
                            AFOR_C 277 aeerldlelyakllsavtGidvteeellkaGeRiynleRlfnlreGltrkddtlperlleeplk.......egpakg 346
                                       +   l+++ + ++++ +tG+++++ee++ka+   + + R +n  eG t kdd  p+++++  ++        +   +
  gi|488599737|ref|YP_007906208.1| 497 IARSLNIDTVRDMFNYATGFNLSNEEMIKASAEAFGVARKLNCSEGYTYKDDLPPKKFFTPLQTwvgkkvwRDYLTN 573
                                       8889*******************************************************433322222222222224 PP

                                       ---...-HHHHHHHHHHHHT--TTS-- CS
                            AFOR_C 347 kvl.edeleemldeyYelrGWdetGvP 372
                                       +++ +d++ +ml +yY +rGW+ +G+P
  gi|488599737|ref|YP_007906208.1| 574 ETVdYDHVMKMLGDYYSMRGWK-NGCP 599
                                       5555788**************9.9*99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 3277.06
//
Query:       gi|488599738|ref|YP_007906209.1|  [L=790]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-36  125.0   2.3    6.4e-16   58.5   0.2    3.7  3  PAS_9     PAS domain
    2.1e-33  114.7   0.4    1.3e-14   54.1   0.1    3.5  3  PAS       PAS fold
    2.9e-29  101.5   0.0      9e-11   42.0   0.0    3.4  3  PAS_4     PAS fold
    6.9e-29  100.9   0.0    1.9e-21   76.8   0.0    3.0  2  GAF_2     GAF domain
      5e-21   74.3   0.0    5.1e-07   29.6   0.0    4.1  4  PAS_8     PAS domain
    4.2e-20   71.8   0.1    8.2e-09   35.6   0.0    3.5  3  PAS_3     PAS fold
    6.2e-18   65.7   0.0    7.4e-09   36.3   0.0    2.6  2  GAF       GAF domain
      5e-11   43.1   0.0    9.1e-05   22.8   0.0    2.7  2  GAF_3     GAF domain
    4.3e-08   33.2   1.1     0.0006   19.9   0.1    3.9  3  SpoVT_C   Stage V sporulation protein T C-terminal, transcrip
    4.7e-05   23.3   0.1    0.00028   20.8   0.1    2.4  1  HisKA     His Kinase A (phospho-acceptor) domain
    0.00068   19.3   0.1       0.63    9.7   0.0    2.7  2  PAS_12    UPF0242 C-terminal PAS-like domain
     0.0073   16.5   0.1        4.6    7.5   0.0    4.1  4  PAS_7     PAS fold


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.2   4.3e-19   6.4e-16       2     104 .]      22     127 ..      21     127 .. 0.94
   2 !   29.7   0.1   3.9e-10   5.9e-07       3     104 .]     324     422 ..     322     422 .. 0.81
   3 !   34.6   0.0   1.2e-11   1.7e-08       2     104 .]     446     546 ..     445     546 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 4.3e-19
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf.....vtdpeanerlraaleqgrkkerevevvlirkng 73 
                                       d+++i+n  g+il++N+ ++r++G+++eev+gk +t l       +d   +e + +++e g   +r+ve   +r++g
  gi|488599738|ref|YP_007906209.1|  22 DAVVITNIAGKILFVNKEFERITGFKREEVVGKAVTGLEirpeeMKDRVVKEIMPELMEKGY--VRNVEGLVRRRDG 96 
                                       8999*9*********************************98888888888888888888888..************* PP

                             PAS_9  74 etfwvlltaspvkdddgelvgiivilrDite 104
                                       ++++vl+++s ++d+dg+ ++ + ++rDit+
  gi|488599738|ref|YP_007906209.1|  97 TEVHVLISLSLMRDADGKPTHTVRVIRDITD 127
                                       *****************************96 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 3.9e-10
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirknget 75 
                                       + +i+++d ++ +aN  a++l+G+s+ee++gks+ +++  ++e+ erl ++ +  +      + ++e+ +++ +g+ 
  gi|488599738|ref|YP_007906209.1| 324 ALVIIDEDTTVKFANHEAEKLYGQSKEELVGKSWMEFI--PEEEIERLMRYHKLRQIdptlAPSRYETKIVDVKGNV 398
                                       567777999777**************************..6666666666666666566998888888888888888 PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                         v +tas v  ++     +i+ ++Dite
  gi|488599738|ref|YP_007906209.1| 399 KNVFITASMVSAEQ-----CILSIIDITE 422
                                       88889999995554.....7799999997 PP

  == domain 3  score: 34.6 bits;  conditional E-value: 1.2e-11
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf.vtdpeanerlraaleqgrkkerevevvl.irkngetf 76 
                                        g++++ +d ++l++Ne+al+++G++ ++v+g+++ dl   ++++  + l+++++  ++  + +e+ l ++ +g++ 
  gi|488599738|ref|YP_007906209.1| 446 IGVVLTGTDMTVLDCNESALKIFGMD-RDVIGRKWPDLGiFHHEDLPRILEEFYRGVQD--KIFELKLkVTVEGREK 519
                                       6899999*****************99.559*******99899****************5..4555443134457888 PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w+++  + +  +dg+  ++++ ++Dite
  gi|488599738|ref|YP_007906209.1| 520 WIKVLSVLIE-KDGKPYAFLSMIHDITE 546
                                       *999888885.46777889********8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   8.8e-18   1.3e-14       8     113 .]      18     125 ..      11     125 .. 0.83
   2 !   34.9   0.0     8e-12   1.2e-08       5      64 ..     316     377 ..     313     418 .. 0.77
   3 !   21.9   0.0     9e-08   0.00013       3     113 .]     437     544 ..     435     544 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 8.8e-18
                                       HHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC... CS
                               PAS   8 eslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl... 81 
                                       e + d++++++  g+il+vN+++e+++G++reev+gk + +l + +++  +++++ + +    +++++ ++++    
  gi|488599738|ref|YP_007906209.1|  18 EVMNDAVVITNIAGKILFVNKEFERITGFKREEVVGKAVTGLEIRPEE--MKDRVVKEIMPELMEKGYVRNVEGlvr 92 
                                       6689************************************99888765..666655555555555555555555555 PP

                                       .TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  82 .rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        rdg+++h+++  s +rda+g++++ + v+rdi
  gi|488599738|ref|YP_007906209.1|  93 rRDGTEVHVLISLSLMRDADGKPTHTVRVIRDI 125
                                       5******************************98 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 8e-12
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH..HHHHHHHH CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda..elaelleq 64 
                                       +i+e++ ++ +++Ded+ + ++N++ae+l G s ee++gks +++i+ee+ +   ++ +l+q
  gi|488599738|ref|YP_007906209.1| 316 TIVENTGTALVIIDEDTTVKFANHEAEKLYGQSKEELVGKSWMEFIPEEEIErlMRYHKLRQ 377
                                       79*********************************************996444444444444 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 9e-08
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGG..BSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldl..iheeddaelaelleqlleqgeesragei 77 
                                       +++++e +p +++++  d  +l +N++a +++G +r +v+g++  dl  +h+ed   l+++le+ ++  +++  + +
  gi|488599738|ref|YP_007906209.1| 437 YKTLFEKSPIGVVLTGTDMTVLDCNESALKIFGMDR-DVIGRKWPDLgiFHHED---LPRILEEFYRGVQDKIFELK 509
                                       88999******************************9.68999999886455555...**********9999888777 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                          ++ gr++++ v  + +    g++  fl +++di
  gi|488599738|ref|YP_007906209.1| 510 LKVTVEGREKWIKVLSVLIEKD-GKPYAFLSMIHDI 544
                                       6666**********98877666.56679******98 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0     6e-14     9e-11       1     107 [.      17     127 ..      17     130 .. 0.95
   2 !   29.0   0.0   6.5e-10   9.7e-07       2      55 ..     319     372 ..     318     424 .. 0.86
   3 !   26.6   0.0   3.6e-09   5.4e-06       1     107 [.     441     546 ..     441     548 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 6e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla..ellpee.daarleralrrvlegeepiefleelll 74 
                                       ++ ++da+++ +  g++l++N++++++ g+ +ee++Gk +   e+ pee   + + +++ +++e + +   +  +++
  gi|488599738|ref|YP_007906209.1|  17 FEVMNDAVVITNIAGKILFVNKEFERITGFKREEVVGKAVTglEIRPEEmKDRVVKEIMPELMEKGYVRNVEGLVRR 93 
                                       67899********************************************66666899*************9999999 PP

                             PAS_4  75 .pgeerhyelrllPlrdesGevigvlvisrDiTe 107
                                        +g e+h++++l+ +rd++G++ +++ ++rDiT+
  gi|488599738|ref|YP_007906209.1|  94 rDGTEVHVLISLSLMRDADGKPTHTVRVIRDITD 127
                                       *********************************7 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 6.5e-10
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarlera 55 
                                       +++  al+++d+d +v +aN +a++l+g + eel+Gk++ e+ pee  +rl+r+
  gi|488599738|ref|YP_007906209.1| 319 ENTGTALVIIDEDTTVKFANHEAEKLYGQSKEELVGKSWMEFIPEEEIERLMRY 372
                                       77888999**************************************99999986 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 3.6e-09
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       ++++p +++  ++d++vl++N++a ++fg++  +++G+++ +l    + ++l r+l++  +g +  +f+  l+   +
  gi|488599738|ref|YP_007906209.1| 441 FEKSPIGVVLTGTDMTVLDCNESALKIFGMD-RDVIGRKWPDL-GIFHHEDLPRILEEFYRGVQDKIFELKLKVtvE 515
                                       799***********************99997.579******94.33388888888888888866666666665579* PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTe 107
                                       g+e+++ +  + + + +G++ ++l +++DiTe
  gi|488599738|ref|YP_007906209.1| 516 GREKWIKVLSVLI-EKDGKPYAFLSMIHDITE 546
                                       *************.68***************9 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   1.3e-24   1.9e-21       3     138 .]     157     299 ..     155     299 .. 0.88
   2 !   20.8   0.0   2.6e-07   0.00038      85     138 .]     651     702 ..     574     702 .. 0.83

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 1.3e-24
                                       HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEE....EEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-G CS
                             GAF_2   3 dleelldlvldelvel.gaalgyillvdddgglrla....awgeaeeefgaaldrplgeglvgealrtgrpvilndl 74 
                                       d++ell++v++ +ve  g a+ +i++ + d+ +r +      g+a+       ++  g+g++g a+r+g+p i+ d+
  gi|488599738|ref|YP_007906209.1| 157 DEKELLERVCKVIVEEgGYAYTWIGYAESDKTVRPVakagIDGYADVIKVTWDESETGKGPTGSAIRMGKPAIVRDI 233
                                       789**********99846**********99997766555344444444444444466******************** PP

                                       GG-S-HHHHH..HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  75 eedpdkkglp..aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       e+dp   +++  a ++g++s++a+Pli+++ v+G+ln+y+++++afd  + elL+ l+e ++ ai+
  gi|488599738|ref|YP_007906209.1| 234 ETDPVFTPWRdfALKRGFASSIALPLIHGDSVFGALNIYSSERDAFDGGETELLKKLSENLSYAIA 299
                                       ****************************999********************************995 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.6e-07
                                       HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHHH CS
                             GAF_2  85 aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiaie 138
                                       + + g++s +++Pli++++ +G l l+++k    +++d e++++l +q aia++
  gi|488599738|ref|YP_007906209.1| 651 LLKNGMKSYIVLPLIARDERIGSLMLASKK--IISDDDFEFVKSLVNQFAIALH 702
                                       678899999*******899******95444..489*****************96 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.1e-08   3.1e-05       6      53 ..      16      60 ..      15      78 .. 0.75
   2 !   15.5   0.0     9e-06     0.013       5      57 ..     316     365 ..     313     376 .. 0.80
   3 !   29.6   0.0   3.4e-10   5.1e-07       2      54 ..     436     484 ..     436     502 .. 0.75
   4 ?   -3.0   0.0       5.3     8e+03       2      17 ..     723     738 ..     722     757 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.1e-08
                             PAS_8  6 lfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlr 53
                                      +fe ++d++++++ +g+ i++vN+ +++++G++ +++ g+ +    ++l+
  gi|488599738|ref|YP_007906209.1| 16 VFEVMNDAVVITNiAGK-ILFVNKEFERITGFKrEEVVGKAV----TGLE 60
                                      8************8888.*************77666655555....3222 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9e-06
                             PAS_8   5 alfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrplle 57 
                                       +++e+   +++++d+++++ ++N  a++l+G    +k+el+g+ + ++ p++e
  gi|488599738|ref|YP_007906209.1| 316 TIVENTGTALVIIDEDTTVKFANHEAEKLYG-Q--SKEELVGKSWMEFIPEEE 365
                                       7999999*******8888*************.4..788888866666655555 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 3.4e-10
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrp 54 
                                       ++++lfe sp g++++ ++ +++d+N++al+++G    ++++++g+ +p+l  
  gi|488599738|ref|YP_007906209.1| 436 KYKTLFEKSPIGVVLTGTDMTVLDCNESALKIFG----MDRDVIGRKWPDLGI 484
                                       69************8543347*************....999999955555443 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 5.3
                             PAS_8   2 rlralfesspdgiavv 17 
                                       ++  l++++++++a +
  gi|488599738|ref|YP_007906209.1| 723 KFAILVDHIRNPLAAI 738
                                       5666899999999973 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   5.5e-12   8.2e-09       2      86 ..      34     119 ..      33     122 .. 0.95
   2 !   19.0   0.0   8.5e-07    0.0013       3      43 ..     336     374 ..     334     415 .. 0.84
   3 !   13.2   0.0   5.3e-05     0.079       2      87 ..     458     539 ..     457     541 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 5.5e-12
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealq.ealkkgepyegeyRirrkdGeyrwveararvird 77 
                                       ++v++++e+i+G+ +ee+ gk  + l++   e+ +rv ++++ e+++kg + ++e  +rr+dG+ ++v  + + +rd
  gi|488599738|ref|YP_007906209.1|  34 LFVNKEFERITGFKREEVVGKAVTGLEIRPEEMKDRVVKEIMpELMEKGYVRNVEGLVRRRDGTEVHVLISLSLMRD 110
                                       89***************************************98999999999************************* PP

                             PAS_3  78 engkpvrvi 86 
                                        +gkp++ +
  gi|488599738|ref|YP_007906209.1| 111 ADGKPTHTV 119
                                       *****9877 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 8.5e-07
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealq 43 
                                       +++ + e+++G s+eel gk  sw++++  e++er+++ ++
  gi|488599738|ref|YP_007906209.1| 336 FANHEAEKLYGQSKEELVGK--SWMEFIPEEEIERLMRYHK 374
                                       78999***************..***************9987 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 5.3e-05
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrk.dGeyrwveararvird 77 
                                       + ++e+  +i+G ++ +++g++   l + h eD++r+ e++ + ++++  +  e +++    G   w++   + i  
  gi|488599738|ref|YP_007906209.1| 458 LDCNESALKIFGMDR-DVIGRKWPDLGIFHHEDLPRILEEFYRGVQDKI-F--ELKLKVTvEGREKWIKVLSVLI-E 529
                                       689**********86.677773444789**************9996666.5..44444444*************9.* PP

                             PAS_3  78 engkpvrvig 87 
                                       ++gkp+ +++
  gi|488599738|ref|YP_007906209.1| 530 KDGKPYAFLS 539
                                       *****98875 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0     5e-12   7.4e-09       4     133 .]     160     298 ..     157     298 .. 0.77
   2 !   26.9   0.0     4e-09     6e-06       3     133 .]     578     701 ..     576     701 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5e-12
                                       HHHHHHHHHHHHHHTESEEEE.EE....EEETTEEE...........CEEEEECCEEEETTSHHHHHHHHHSSSEEE CS
                               GAF   4 elldtvveelrellgadrval.yl....pdydGlhy...........dipqasrwlfmkngrgicgqvlatgqplvi 64 
                                       ell++v++ + e  g+ +  + y     +      +                 +w + ++g+g  g +++ g+p ++
  gi|488599738|ref|YP_007906209.1| 160 ELLERVCKVIVEEGGYAYTWIgYAesdkT------VrpvakagidgyADVIKVTWDESETGKGPTGSAIRMGKPAIV 230
                                       77788888888888887766633332220......1223333222223334556688888888899*********** PP

                                       STGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE.SSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  65 pdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhn.psppftreelellqvladqvaval 133
                                        d+ +dp f +  +rd++   g+ ss+++Pl++++ ++G+l +++ +++ f+  e ell+ l++ ++ a+
  gi|488599738|ref|YP_007906209.1| 231 RDIETDPVFTP--WRDFALKRGFASSIALPLIHGDSVFGALNIYSsERDAFDGGETELLKKLSENLSYAI 298
                                       ***********..********************************76669************99998876 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 4e-09
                                       HHHHHHHHHHHHHHHTESEEEEEEEEETTEEE...CEEEEECCEEEET.TSHHHHHHHHHSSSEEESTGGTSTTHHT CS
                               GAF   3 eelldtvveelrellgadrvalylpdydGlhy...dipqasrwlfmkn.grgicgqvlatgqplvipdstpdprfaq 75 
                                       +++l++ ++ lre++++d +++    y+G+++     p+ s+ + +   +r+i  +  + + +l ++        ++
  gi|488599738|ref|YP_007906209.1| 578 DKILKESLRGLREIVDYDLACIAV--YSGSEVktlAEPEISQNIQRLFaDRNIEVEMKKVDGILELE------TLSR 646
                                       7899***************99955..88855545533333333222222333212222223344444......3333 PP

                                       THHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  76 ynrrdllenmgirsslvvPlvndgelwGllvlhnpsppftreelellqvladqvaval 133
                                             l   g++s++v+Pl++++e +G l l +++   ++++ e++++l +q a+al
  gi|488599738|ref|YP_007906209.1| 647 --LEVELLKNGMKSYIVLPLIARDERIGSLMLASKKI-ISDDDFEFVKSLVNQFAIAL 701
                                       ..33345568************************766.8*****************97 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   6.1e-08   9.1e-05      80     127 ..     251     298 ..     158     300 .. 0.80
   2 !   17.5   0.0   2.6e-06    0.0039       4     127 ..     579     701 ..     577     703 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.1e-08
                             GAF_3  80 draalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                        ++ +a+PL++g+ v+G l ++s++  afd  ++ell+ l+  ++ ai
  gi|488599738|ref|YP_007906209.1| 251 FASSIALPLIHGDSVFGALNIYSSERDAFDGGETELLKKLSENLSYAI 298
                                       4889**************************************999998 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.6e-06
                             GAF_3   4 ellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesldedsalarralssgevvse..........p 70 
                                       ++l ++l+ l ++++ + + + ++   g+++++ a       +s+++    + a+r ++ ++  +           +
  gi|488599738|ref|YP_007906209.1| 579 KILKESLRGLREIVDYDLACIAVYS--GSEVKTLAEP----EISQNIQ--RLFADRNIEVEMKKVDgileletlsrL 647
                                       5666666666666666666666666..3355555544....2222222..122222222222221111111111003 PP

                             GAF_3  71 sfaeedglpdraalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       +++      + +++++PL+a+++ iG l+las+k   ++++d e+++sl +q a+a+
  gi|488599738|ref|YP_007906209.1| 648 EVELLK-NGMKSYIVLPLIARDERIGSLMLASKK--IISDDDFEFVKSLVNQFAIAL 701
                                       322211.245899*******99**********77..47*****************98 PP

>> SpoVT_C  Stage V sporulation protein T C-terminal, transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.11   1.6e+02      76     116 ..     250     289 ..     229     297 .. 0.83
   2 !    6.4   0.4    0.0057       8.6      12     101 ..     316     423 ..     306     439 .. 0.56
   3 !   19.9   0.1     4e-07    0.0006      20     101 ..     588     680 ..     574     698 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                           SpoVT_C  76 eysaqviaPIiaeGdviGaVillskeekkklgelekklaet 116
                                        + ++++ P+i    v Ga  + s+e+++ ++  e++l++ 
  gi|488599738|ref|YP_007906209.1| 250 GFASSIALPLIHGDSVFGALNIYSSERDA-FDGGETELLKK 289
                                       5678999****************999886.77777777765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0057
                           SpoVT_C  12 slaetlghivlitDrdqiiava........gaskkellekei.....skeleklmeerktvlakk.....eekklv. 69 
                                       ++ e +g + +i+D+d+ +  a        g+sk el++k+      ++e+e+lm   k   ++      +      
  gi|488599738|ref|YP_007906209.1| 316 TIVENTGTALVIIDEDTTVKFAnheaeklyGQSKEELVGKSWmefipEEEIERLMRYHKLRQIDPtlapsR----Ye 388
                                       78899***************995444444455555555554311112345666666666555544433211....11 PP

                           SpoVT_C  70 ...veeekeeysaqviaPIiaeGdviGaVillske 101
                                          v+ + +  +  + a+ ++++++i ++i ++++
  gi|488599738|ref|YP_007906209.1| 389 tkiVDVKGNVKNVFITASMVSAEQCILSIIDITEM 423
                                       23223333333446666666666666666655444 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 4e-07
                           SpoVT_C  20 ivlitDrd.qiiav.agaskkellekeiskeleklmeerktvlakkeekklv.........veeekeeysaqviaPI 85 
                                          i+D d  +iav +g++ k l e eis+++++l  +r++ ++ k+ + +          ve  k+ ++++++ P+
  gi|488599738|ref|YP_007906209.1| 588 LREIVDYDlACIAVySGSEVKTLAEPEISQNIQRLFADRNIEVEMKKVDGILeletlsrleVELLKNGMKSYIVLPL 664
                                       55577777556777358888********************977766433333445443333233347899******* PP

                           SpoVT_C  86 iaeGdviGaVillske 101
                                       ia  + iG+ +l sk+
  gi|488599738|ref|YP_007906209.1| 665 IARDERIGSLMLASKK 680
                                       *************886 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 !   20.8   0.1   1.9e-07   0.00028       7      66 ..     725     776 ..     722     777 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.9e-07
                                       HHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   7 agvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       a +   +r+PL+ai+g ae+  r      + +e  e i s+++r+ + ve+l d +++e+
  gi|488599738|ref|YP_007906209.1| 725 AILVDHIRNPLAAISGLAET--R-----VDDEETRELILSQVERIVDTVERL-DRGWLES 776
                                       677889**************..3.....566777778888888888888887.7777665 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 !    9.7   0.0   0.00042      0.63      60      89 ..      24      53 ..      17      61 .. 0.85
   2 !    6.5   0.0     0.004       5.9      54      89 ..     319     354 ..     311     367 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                            PAS_12 60 lvysqkenkllfaNaqirallGwssdkflq 89
                                      +v ++ + k+lf+N+++++++G+  ++++ 
  gi|488599738|ref|YP_007906209.1| 24 VVITNIAGKILFVNKEFERITGFKREEVVG 53
                                      67778899*****************99875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.004
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflq 89 
                                       En+g+ lv    +  + faN++ ++l G s+++++ 
  gi|488599738|ref|YP_007906209.1| 319 ENTGTALVIIDEDTTVKFANHEAEKLYGQSKEELVG 354
                                       899999999999********************9985 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.19   2.9e+02       2      40 ..      18      55 ..      17     133 .. 0.83
   2 !    7.5   0.0     0.003       4.6       1      45 [.     318     361 ..     318     428 .. 0.75
   3 ?    2.1   0.0      0.14   2.1e+02       5      35 ..     445     475 ..     441     489 .. 0.86
   4 ?   -3.2   0.0         6     9e+03     100     113 ..     537     550 ..     516     552 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                             PAS_7  2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvp 40
                                      e m++++++ + +++++++N+++ ++ ++ +e v vg+ 
  gi|488599738|ref|YP_007906209.1| 18 EVMNDAVVITNIAGKILFVNKEFERITGFKREEV-VGKA 55
                                      6799999999999999*****9999999888777.5554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.003
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleell 45 
                                       +en   +++++D+d+ + + N++  +l++ ++e + vg++  e++
  gi|488599738|ref|YP_007906209.1| 318 VENTGTALVIIDEDTTVKFANHEAEKLYGQSKEEL-VGKSWMEFI 361
                                       5888999**********************999988.787766555 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                             PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelv 35 
                                       + G+++   d+ ++ +N+  l+++++ ++++
  gi|488599738|ref|YP_007906209.1| 445 PIGVVLTGTDMTVLDCNESALKIFGMDRDVI 475
                                       679999999*****************99987 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 6
                             PAS_7 100 fVttytDiTerrra 113
                                       f+++ +DiTe  ++
  gi|488599738|ref|YP_007906209.1| 537 FLSMIHDITEDMAT 550
                                       7888999*998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (790 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 4884.92
//
Query:       gi|488599739|ref|YP_007906210.1|  [L=454]
Description: Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase-related deacylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-20   74.1   0.3      4e-17   62.6   0.1    2.2  2  Peptidase_M20  Peptidase family M20/M25/M40
    9.5e-19   67.3   0.0    1.7e-18   66.5   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
    4.2e-09   35.9   0.2    2.8e-07   29.9   0.0    2.7  3  Peptidase_M42  M42 glutamyl aminopeptidase
  ------ inclusion threshold ------
      0.013   15.2   0.0       0.04   13.6   0.0    1.8  2  DUF1353        Protein of unknown function (DUF1353)
      0.019   14.7   0.0          4    7.1   0.0    2.4  2  Peptidase_M28  Peptidase family M28
       0.16   11.1   0.0       0.25   10.5   0.0    1.2  1  FTR1           Iron permease FTR1 family


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 !    9.6   0.0   0.00023      0.69       2      29 ..      84     110 ..      83     118 .. 0.85
   2 !   62.6   0.1   1.3e-20     4e-17      23     206 ..     144     449 ..     133     450 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00023
                                       EEEES-BSSTTCGGGSSS.TTSEEETTTE CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGk 29 
                                       + +H+D+V +++  +w t pf ++  +G+
  gi|488599739|ref|YP_007906210.1|  84 FSAHMDTVSAGDYGKWLTdPFGAE--EGV 110
                                       89*******999999******999..464 PP

  == domain 2  score: 62.6 bits;  conditional E-value: 1.3e-20
                                       EEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHH.TTTCESEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                     Peptidase_M20  23 lteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegle.erekvdavfelh 98 
                                        ++e+  +yGrG+ d+k++v+++l +l  l d     +g+i  +f++ EE+  +G+k++++ ++ + +k++  ++++
  gi|488599739|ref|YP_007906210.1| 144 KEKEKKIIYGRGSFDNKASVAILLFLLDILGDIEM--DGKIYAVFTVREEVDAEGIKHFIKTYKrDFDKFRERYAVV 218
                                       3445568***********************99975..99***********988********8886666666666554 PP

                                       EESSSBTCHSTETEEEE............................................................ CS
                                       xxxxxxxxxxxxxxxxx............................................................ RF
                     Peptidase_M20  99 ieepgileagklaigvv............................................................ 115
                                       +e ++++         v                                                            
  gi|488599739|ref|YP_007906210.1| 219 LE-GSYSFMP------Viahrgvcwayirtygkrchastphlgrnavvemcrivdyleankrriidelyehsedrll 288
                                       44.6666623......22355558999999999999999999999999999999*********************** PP

                                       ...................................................................EEEEEEEEEE CS
                                       ...................................................................xxxxxxxxxx RF
                     Peptidase_M20 116 ...................................................................kvevellegg 125
                                                                                                          +++ve++  +
  gi|488599739|ref|YP_007906210.1| 289 gkptfsitsivgggirkvvggkidridlnvipdfcessvdirygrgitaelihdfftreikkvsqdfEFTVEEETFY 365
                                       ****************************************************************9885666655444 PP

                                       SHEEEC...CHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH..TTTEEEEEEESSGGCTTSTTTEEEHHHHHH CS
                                       xxxxxx...xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 126 apvtln...dsplvkalaeaaeelfgekveli.vsgpggtdarff..agiptvmifgpgsglaHspnEyvdledlek 196
                                       +++ +    d+++ + + +a+ e  g   +++ + + g+++ +f+  ag +t++ fgp ++ +H  +Eyv+++++++
  gi|488599739|ref|YP_007906210.1| 366 PSAGIGnsfDDAMEDDFVKAVMESSG--INQVgIAP-GASEGAFLhsAGFKTLVEFGPAGAFSHDAHEYVEIDEIKR 439
                                       44444444888887777777777557..33443666.9*******8888899999**888***************** PP

                                       HHHHHHHHHH CS
                                       xxxxxxxxxx RF
                     Peptidase_M20 197 gikvlarlle 206
                                       g+kv + ll+
  gi|488599739|ref|YP_007906210.1| 440 GVKVTTTLLN 449
                                       ****999986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   5.8e-22   1.7e-18       1     104 [.     229     351 ..     229     356 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 5.8e-22
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC............TCCTCCCCCEECCE-C... CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.......eerslprttlnvtgiegGs... 67 
                                       i+h+G++++ i++ gk +H++ p+ g+NA+ +++r+++ le+++++i        e+r l+++t+++t+i gG    
  gi|488599739|ref|YP_007906210.1| 229 IAHRGVCWAYIRTYGKRCHASTPHLGRNAVVEMCRIVDYLEANKRRIIdelyehsEDRLLGKPTFSITSIVGGGirk 305
                                       69*********************************************9***************************** PP

                                       .........CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSC CS
                         M20_dimer  68 .........aknvipdeaeakidiRllpgedpeevleeieeileke 104
                                                  nvipd +e ++diR   g ++e + + ++  ++k+
  gi|488599739|ref|YP_007906210.1| 306 vvggkidriDLNVIPDFCESSVDIRYGRGITAELIHDFFTREIKKV 351
                                       *************************988888887777777777665 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.019        58       4      26 ..      72      92 ..      69      94 .. 0.73
   2 !   29.9   0.0   9.4e-11   2.8e-07     128     181 ..     151     205 ..     139     208 .. 0.85
   3 ?   -1.4   0.0       0.3     9e+02     133     168 ..     327     363 ..     322     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.019
                                      EEEEESSTTSSEEEEEEE--B-E CS
                     Peptidase_M42  4 iakkkgkekepkvmiaAHmDeiG 26
                                      +++  +   e  ++++AHmD++ 
  gi|488599739|ref|YP_007906210.1| 72 VCEVGE--GERCIVFSAHMDTVS 92
                                      444444..788899*******96 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 9.4e-11
                                       EEET.THHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHHHHHH- CS
                     Peptidase_M42 128 ivsk.alDdragvavllellkelkeeeleatvylvatvqEEvGlrGaktsaekik 181
                                       i ++  +D++a+va+ll ll  l + e++ ++y+v+tv EEv   G k + +++k
  gi|488599739|ref|YP_007906210.1| 151 IYGRgSFDNKASVAILLFLLDILGDIEMDGKIYAVFTVREEVDAEGIKHFIKTYK 205
                                       5665469***************************************998877665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHCTSS-S.SEEEEEEESTCTT CS
                     Peptidase_M42 133 lDdragvavllellkelkeeele.atvylvatvqEEv 168
                                       +D r+g  + +el++ + ++e++ +   + +tv+EE 
  gi|488599739|ref|YP_007906210.1| 327 VDIRYGRGITAELIHDFFTREIKkVSQDFEFTVEEET 363
                                       68899999********999999999999*******96 PP

>> DUF1353  Protein of unknown function (DUF1353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         2     6e+03      34      49 ..     235     250 ..     234     252 .. 0.83
   2 ?   13.6   0.0   1.3e-05      0.04      23      62 ..     312     352 ..     300     395 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                           DUF1353  34 lwaliptegrylkAav 49 
                                        wa+i t+g+  +A+ 
  gi|488599739|ref|YP_007906210.1| 235 CWAYIRTYGKRCHAST 250
                                       69999****9999985 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.3e-05
                           DUF1353  23 frtDlASiPrllwali.ptegrylkAavvHDwlyretklvs 62 
                                        r+Dl  iP +  + +  ++gr + A ++HD++ re k+vs
  gi|488599739|ref|YP_007906210.1| 312 DRIDLNVIPDFCESSVdIRYGRGITAELIHDFFTREIKKVS 352
                                       689***********99779***************7666663 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0054        16       2      30 ..      71      95 ..      70     109 .. 0.73
   2 ?    7.1   0.0    0.0014         4      34      88 ..     155     212 ..     140     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0054
                                      EEEEESTTCESEEEEEEEE--B-TTTTCC CS
                     Peptidase_M28  2 viatlegkatdevlllgAHyDsvgvgrgp 30
                                      ++ ++ g+  ++ ++++AH+D+v+ g  +
  gi|488599739|ref|YP_007906210.1| 71 IVCEV-GEG-ERCIVFSAHMDTVSAG--D 95
                                      55555.444.689**********984..3 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0014
                                       -TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH...HHC...CC CS
                     Peptidase_M28  34 GAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak...akp...el 88 
                                       G  Dn ++va+lL l+ +l +   + + ++  +f+  EE    G k+f+k   + +    +
  gi|488599739|ref|YP_007906210.1| 155 GSFDNKASVAILLFLLDILGD--IEMDGKIYAVFTVREEVDAEGIKHFIKtykR-DfdkFR 212
                                       888*****************9..689***********************86422.134344 PP

>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.4e-05      0.25      92     146 ..     119     190 ..     110     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.4e-05
                              FTR1  92 lwmrrvgkklkeeveqklakavaeiknrekaa.qkgekgsekwalfilsF................livlRE 146
                                       ++  + gk+++++++++++++ ++ k++ek+   +   + +k +++il F                ++++RE
  gi|488599739|ref|YP_007906210.1| 119 VEVEVCGKRVRGKIRDQMDRIWKMRKEKEKKIiYGRGSFDNKASVAILLFlldilgdiemdgkiyaVFTVRE 190
                                       5556669*************************9999**************7666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3029.20
//
Query:       gi|488599740|ref|YP_007906211.1|  [L=287]
Description: hypothetical protein Asulf_00183 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.5   0.0        0.3   11.3   0.0    1.6  1  LigA      Aromatic-ring-opening dioxygenase LigAB, LigA subun


Domain annotation for each model (and alignments):
>> LigA  Aromatic-ring-opening dioxygenase LigAB, LigA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.7e-05       0.3      17      62 ..     140     185 ..     133     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                                       HHHSHHHHHHHS---HHHHHHHHTT-HHHHHHHT--HHHHHHHHHH CS
                              LigA  17 FladeeayldeygLteeqkeavlardwlkllalGgniyyLaKlaav 62 
                                       F +++ + l +y L+e++ e+vl+    kll+  g++y+L+++  +
  gi|488599740|ref|YP_007906211.1| 140 FTKEKFSQLIDYILSEKEVEVVLNYHTSKLLDPNGKFYFLERIIEF 185
                                       777777788899*****************************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1579.23
//
Query:       gi|488599741|ref|YP_007906212.1|  [L=439]
Description: Glutamine synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-101  338.4   0.0   5.4e-101  338.0   0.0    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    7.2e-16   58.0   0.0    1.3e-15   57.1   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 !  338.0   0.0    6e-105  5.4e-101       2     345 .]     110     435 ..     109     435 .. 0.97

  Alignments for each domain:
  == domain 1  score: 338.0 bits;  conditional E-value: 6e-105
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR +lk+    l+e ++++  ++E EF+lfd++++                 p +++ +f ++++++ +++  ++
  gi|488599741|ref|YP_007906212.1| 110 ADPRPILKQK---LSELDFEIKSAFETEFYLFDSNSK-----------------PYDDALCFATPAMNASNEFAIRV 166
                                       79*****976...56779***************8866.................457799***************** PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                        e+le + + ve +  E+++gQ+Ei +k+a  +++aDn ++++++v+ vA+  glta+FmpKp ++ +Gsg+H+h+S
  gi|488599741|ref|YP_007906212.1| 167 KEYLEMQDVFVEHFYPEYGPGQYEIAVKPACGITSADNQIILRETVRGVAQGLGLTASFMPKPSNELPGSGVHIHIS 243
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-. CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa. 231
                                       lw kdg+nlfad +   +ls+la+hfigG+lkh+kal+a+ta+tvnSYkRl p+ +a++++++g +NR+a++Rip  
  gi|488599741|ref|YP_007906212.1| 244 LW-KDGENLFADGS---DLSDLAYHFIGGILKHMKALLAFTASTVNSYKRLLPHNWASAYACYGFENREAAIRIPLp 316
                                       **.**********8...6*********************************************************99 PP

                                       ...TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHH CS
                        Gln-synt_C 232 ...skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlea 303
                                          ++++  ++E++ +d+  NPYL+l  ++aAg+dGi+nk++pg+pv+kd +++s++er   g+e+ P++l eA+ +
  gi|488599741|ref|YP_007906212.1| 317 ihkKEKETLHLEIKPVDGCNNPYLVLGSIIAAGVDGIKNKIDPGDPVDKDPADMSEAERdrYGVERFPQNLGEAIAE 393
                                       9866777889************************************************9999*************** PP

                                       HHCSHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 304 leedellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       le+d +++e+ g++++e+yl++k+ E+e+++++v+dwe+++y
  gi|488599741|ref|YP_007906212.1| 394 LEKDRMFEEFWGRTLYEEYLKTKKFEWEAFCQHVTDWEINKY 435
                                       ***************************************988 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 !   57.1   0.0   1.5e-19   1.3e-15       6     103 ..       6     104 ..       1     108 [. 0.92

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.5e-19
                                       .....------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGG.GG--TTS---TT-S-SSS--EEEEE-GG CS
                      Gln-synt_N_2   6 vveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkat.lalserdlidevedlgpvGelrLvpdPa 81 
                                       +++ +eek +e i++ly+d  Gv+rGk     + +  L+sG+ ++  + +a+  +dl+ + + +g vGel+ +pd +
  gi|488599741|ref|YP_007906212.1|   6 ILKLIEEKGIEYIRYLYIDNDGVVRGKMGNAKNAKSDLVSGVTYVSCMqSAFGALDLLTPNSIYGCVGELKHIPDLN 82 
                                       66778999*************************************998356899*********************** PP

                                       G-EEE---SSTTSEEEEEE-TT CS
                      Gln-synt_N_2  82 savalpyaPdaaallgdlvevd 103
                                       ++  +pya ++a ++gd++  d
  gi|488599741|ref|YP_007906212.1|  83 TFRIVPYAEKTAMVIGDFYTRD 104
                                       *****************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2856.07
//
Query:       gi|488599742|ref|YP_007906213.1|  [L=440]
Description: 4-aminobutyrate aminotransferase-related aminotransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-94  314.6   0.0    9.6e-94  314.3   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.3   0.0   5.4e-98   9.6e-94      10     406 .]      20     421 ..      14     421 .. 0.95

  Alignments for each domain:
  == domain 1  score: 314.3 bits;  conditional E-value: 5.4e-98
                                       CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                       Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                       +l++++ eG ++ d dgk+y+D+ +s+av+n+G+ + k+++av eq  k+s  s+  + +e+++klae ll+l+p++
  gi|488599742|ref|YP_007906213.1|  20 PLIVDRCEGYRIRDIDGKEYIDFNASWAVANVGYGNKKIIDAVCEQFSKTSSFSLTSYYHEKSIKLAELLLSLVPES 96 
                                       3899************************************************************************7 PP

                                       .S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-T CS
                       Aminotran_3  87 ld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlky 162
                                        + kv++  sGs+ + + +Kl         at+k+kii+f g++HG+t+g+ s++g+    ++++ + + +vv+++y
  gi|488599742|ref|YP_007906213.1|  97 ENkKVIFGHSGSDINDGIFKLLPY------ATKKNKIITFLGSYHGQTYGSFSLSGH---KAEGWLNPAGGVVKVPY 164
                                       6689********************......***************************...67899999********* PP

                                       TBGGGTB-HHHHHHHHHHHHHHHH......CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE- CS
                       Aminotran_3 163 pdeevlkeneeeeaalleeleale......kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDE 233
                                       p+++++++  e  ++ +++++ +e       + +++v+ v +Epiq++gG++v+++ef  +l +lck++++   vDE
  gi|488599742|ref|YP_007906213.1| 165 PYCYRCPFSLEYPECKIHCVRFIEeyifetVAPAEDVSIVFLEPIQSDGGDIVPPEEFHDRLYKLCKRNGIYYGVDE 241
                                       **********99998888888777666876567889999************************************** PP

                                       TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS.B--TTTT-HHHHHHHHHHHHHHH CS
                       Aminotran_3 234 vqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs.hgsTfgGnplacavalavleiie 309
                                       v++Gf+rTGk+f+ eh+g++pD++t++K ++gG+p+sa ++ +ev +    g  h sT +G p  c++++a++e i+
  gi|488599742|ref|YP_007906213.1| 242 VKVGFARTGKFFGFEHYGIKPDFITVGKPMGGGFPISACIGVREVLDYP--GAfHLSTIAGHPAGCSASIATIEYIK 316
                                       **********************************************988..555*********************** PP

                                       HTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETT. CS
                       Aminotran_3 310 eekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGd. 379
                                       e+kl +na+++g++l +gL+e++++ + i++vRgkGl++++el+ ++e ke      + ++ +  e G+++  +G  
  gi|488599742|ref|YP_007906213.1| 317 ENKLDRNAEKMGDRLIKGLKEIAENRDIIGDVRGKGLIVGVELVRDRESKEpaskecAMLTYRCWELGLVLAYVGLy 393
                                       ************************************************9999**9998899**************88 PP

                                       .TEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 380 .nvirllppliitdeeidelleilkkal 406
                                        nv+ ++ppl+i +e ide+l+i+ +al
  gi|488599742|ref|YP_007906213.1| 394 sNVVEITPPLVIDEEGIDEGLNIFDQAL 421
                                       8***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2995.51
//
Query:       gi|488599743|ref|YP_007906214.1|  [L=441]
Description: Gamma-aminobutyrate permease-related permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-50  170.9  44.3    4.9e-50  170.5  44.3    1.1  1  AA_permease    Amino acid permease
    1.3e-41  142.8  48.5    1.6e-41  142.5  48.5    1.0  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5  44.3   5.5e-54   4.9e-50       1     430 [.      13     410 ..      13     438 .. 0.88

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 5.5e-54
                       AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfv 77 
                                       hv  i +g v+G g+f+ +g  +  aGp +al+ay +ag++++++m+s+ge+a+ +p +g+  ++ +r+lg  +Gf 
  gi|488599743|ref|YP_007906214.1|  13 HVWAIGVGAVVGDGIFLLIGEGAKIAGP-AALVAYTIAGLFLLFIMISMGEMAVGMPDAGAMWVWNKRTLGGLAGFL 88 
                                       88899***********************.899********************************************* PP

                       AA_permease  78 iGlnylfswitvlaleltaasiliqfwel...vtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaii 151
                                       +G +y + wi++ +   + a+ +i+ w +    ++++   ++++++l+v++++nlvgv   + ++++l l ++  ++
  gi|488599743|ref|YP_007906214.1|  89 TGTSYAIGWIIAGGSV-GLAIGTITSWFFqigSPEIS-VVIWAIIWLTVFMLLNLVGVIPAANTQLVLVLGLVGLML 163
                                       ***********98876.67777777774433456777.8888***********************999999999999 PP

                       AA_permease 152 afiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdP 228
                                        f i+g+   a+gk  +       ++       ++p+g        f++ + ++++   a++G + +a+ ++Ev+dP
  gi|488599743|ref|YP_007906214.1| 164 LFGIFGF---ASGKIDPS------NYT-----PFMPNG--------FSSLFPAIAFGTYAYMGALTLATSGSEVRDP 218
                                       9999984...22222222......122.....358888........******************************* PP

                       AA_permease 229 eksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssan 305
                                       + ++P+a     i+ +i+Y+++++++  lvp++ l++ +      spf  + + +    +a +in++  +aa  +++
  gi|488599743|ref|YP_007906214.1| 219 R-DLPRALWASSITFLIIYTIAMAAMLGLVPYSELSVSE------SPFTKAAEVAFGTSAAYIINFAAWLAAATCLL 288
                                       6.8*******************************99999......9*******************999888888888 PP

                       AA_permease 306 ss.lysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivw 380
                                       ++ ly+a+R+lys+ +d+++P  + k+++k++ P++ai++++i+s  ++ll + n++  iv+  l+ +  ++ +++w
  gi|488599743|ref|YP_007906214.1| 289 GGtLYAAPRLLYSMGEDRILPsVFSKVHEKHKTPHVAIIFTWIASIGLVLLGYQNPD--IVYVHLSLLLVFAWVVTW 363
                                       6538*****************66678899****************************..****************** PP

                       AA_permease 381 lliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillila 430
                                       l++++s + +R+++ ++ +    l+ k +l+pl++il+l+ + ii+  ++
  gi|488599743|ref|YP_007906214.1| 364 LISLISAVQYRRKFPEEVK---NLPWKQPLYPLFPILGLIGIAIIFYGTF 410
                                       *************777666...89*************9976666654433 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5  48.5   1.8e-45   1.6e-41       1     420 [.       9     426 ..       9     431 .. 0.85

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 1.8e-45
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       ls+  + a+ +g+v+g gif     +a  +gpa+++ + ia l + l  ++ + E++  +p+ g + v+ k++ g +
  gi|488599743|ref|YP_007906214.1|   9 LSFKHVWAIGVGAVVGDGIFLLIgeGAKIAGPAALVAYTIAGLFL-LFIMISMGEMAVGMPDAGAMWVWNKRTLGGL 84 
                                       79999***********99999865455559999988888877776.6777799999966****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                       ++fl++ +++++++++  +++ +a++++ +++++ + ++   +++ ai+ l++++l+n++g+   a+ q +l++  +
  gi|488599743|ref|YP_007906214.1|  85 AGFLTGTSYAIGWIIAG-GSVGLAIGTITSWFFQIGSPEI-SVVIWAIIWLTVFMLLNLVGVIPAANTQLVLVLGLV 159
                                       ***************76.77788999****9999888875.55555999999*******************999999 PP

                     AA_permease_2 153 llpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk.kdvpkaifigll 228
                                        ++++++ i+g++ ++++ ++      + f+png ++ + +++  ++++ G  + a   +ev+  +d+p+a+  + +
  gi|488599743|ref|YP_007906214.1| 160 -GLMLLFGIFGFASGKIDPSN-----YTPFMPNGFSSLFPAIAFGTYAYMGALTLATSGSEVRDpRDLPRALWASSI 230
                                       .799**************999.....569***********************************9************ PP

                     AA_permease_2 229 ivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintav.igssrvlealar 304
                                       + l++y+  + a+lg vp +e++++++   ++++ +e ++g+ +a+i++++++l+++ ++++ + ++++r+l+++++
  gi|488599743|ref|YP_007906214.1| 231 TFLIIYTIAMAAMLGLVPYSELSVSES---PFTKAAEVAFGTSAAYIINFAAWLAAATCLLGGTlYAAPRLLYSMGE 304
                                       ***********************9776...7******************************98626789******** PP

                     AA_permease_2 305 dgvlPrffakvn.kfgspiraiiltaivslillllfllas.saaynfllsvsslgliisyllliigalilrkkrphl 379
                                       d++lP++f+kv+ k+++p +aii+t+i s i l+l+ + + +  y  l+ + +++ ++ +l+ +i+a+ +r+k p++
  gi|488599743|ref|YP_007906214.1| 305 DRILPSVFSKVHeKHKTPHVAIIFTWIAS-IGLVLLGYQNpDIVYVHLSLLLVFAWVVTWLISLISAVQYRRKFPEE 380
                                       ****************************9.8777777666788888999999999********************99 PP

                     AA_permease_2 380 kr..pgk....ilvaiigalfllfllvalffppkgpatqssliytii 420
                                        +  p+k    +l+ i+g++++ ++++ +f  +++ ++  +++y ++
  gi|488599743|ref|YP_007906214.1| 381 VKnlPWKqplyPLFPILGLIGIAIIFYGTF-QGAETSVIIGIAYVVL 426
                                       444755522222333333333333332222.2333334444455444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 2723.99
//
Query:       gi|488599744|ref|YP_007906215.1|  [L=311]
Description: hypothetical protein Asulf_00188 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  134.6   0.1    5.2e-39  134.1   0.1    1.2  1  Thioredoxin_4  Thioredoxin
    9.3e-22   77.7   0.6      4e-19   69.2   0.6    2.2  1  DSBA           DSBA-like thioredoxin domain
    8.1e-10   39.1   0.7      2e-09   37.9   0.2    2.0  2  Thioredoxin_2  Thioredoxin-like domain
    0.00072   19.5   0.1          1    9.5   0.0    3.1  3  Thioredoxin_3  Thioredoxin domain
     0.0043   17.3   0.5      0.016   15.5   0.5    2.2  1  Thioredoxin_8  Thioredoxin-like
     0.0097   15.6   0.4      0.093   12.4   0.0    2.2  2  Thioredoxin_5  Thioredoxin
  ------ inclusion threshold ------
      0.019   15.1   0.5        1.6    9.0   0.1    3.1  3  Glutaredoxin   Glutaredoxin
      0.023   14.7   0.2       0.17   11.9   0.0    2.5  3  Thioredoxin    Thioredoxin
      0.059   12.7   0.1        1.1    8.6   0.0    2.2  2  DUF929         Domain of unknown function (DUF929)
       0.34   11.3   5.3         10    6.5   3.9    3.0  2  FtsH_ext       FtsH Extracellular


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1   0.1   2.9e-42   5.2e-39       3     166 .]     142     307 ..     140     307 .. 0.92

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 2.9e-42
                                       SSSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHH CS
                     Thioredoxin_4   3 etdiviGnpdApvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpldkekeslkaamaarcageespe 79 
                                       ++d++ G++dA+vt+ie++d++Cp+Cakfe+ + ++ ++y    ++k+++rdfp++++  s+ aa aa+ca+e++  
  gi|488599744|ref|YP_007906215.1| 142 DDDPYRGKEDAKVTIIEFSDYACPYCAKFEKVLSEIEKKY---PDIKIVFRDFPIHGNV-SIIAAKAANCANEQN-- 212
                                       67999***********************************...***************7.************998.. PP

                                       HHHHHHHHHHTHHHHTTS-HHH........HH.....HHHHHTS-------HHHHHHHHHHHHHHT--SS-EEEETT CS
                     Thioredoxin_4  80 aflaikallysqqeewaeslke........laaealdkdekfeacleeekldalveaeskeakkagiestPtfiing 148
                                       +f+++++ll+++q ew e+lk+        +a+e + + ++f++cl++ k+d +++++  +  +ag+++tPt+++ng
  gi|488599744|ref|YP_007906215.1| 213 RFWEYHDLLFEKQNEWIEALKNgdkqklylYAEELGLNLTEFKSCLNSNKYDSEIQKDYFDGLTAGVSGTPTVFLNG 289
                                       *******************7764444444444446677999************************************ PP

                                       EEE-TT--HHHHHHHHT- CS
                     Thioredoxin_4 149 ekveepqtyeelkalida 166
                                        kve+  t e+l ++i++
  gi|488599744|ref|YP_007906215.1| 290 IKVEGLATQEALAEIIEQ 307
                                       ****************85 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.6   2.2e-22     4e-19       1     192 [.     155     305 ..     155     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 2.2e-22
                                       EEEEEEBTTBHHHHHHHHHHHHHHHHCCTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT.... CS
                              DSBA   1 tvdeffDvlCPyCylgkerleklaarspdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplr 77 
                                       t++ef+D+ CPyC  ++++l+++++++pd+k+v+r+f++ g+                                   
  gi|488599744|ref|YP_007906215.1| 155 TIIEFSDYACPYCAKFEKVLSEIEKKYPDIKIVFRDFPIHGN----------------------------------- 196
                                       79****************************************................................... PP

                                       GGSSHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHTSSS......-TSSHHHHHHHHHHTTS.HHHHHHHHTSHH CS
                              DSBA  78 fpkdklknstraarlllaagaeglaekvvrelfealwsegq......aitddqellevaekaGldaeeldealesea 148
                                               s  aa+++  a++++     ++e+++ l++++       + +d+q+l   ae++Gl+ +e++  l+s++
  gi|488599744|ref|YP_007906215.1| 197 -------VSIIAAKAANCANEQN----RFWEYHDLLFEKQNewiealKNGDKQKLYLYAEELGLNLTEFKSCLNSNK 262
                                       .......7899999999999996....566666666665541111116789999*********************** PP

                                       HHHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHHH CS
                              DSBA 149 vkeavrentaaaqslgvtGvPtvvvdgkrmvfGadrldtladal 192
                                       + ++++++   +   gv+G+Ptv+++g   v G   ++ la+ +
  gi|488599744|ref|YP_007906215.1| 263 YDSEIQKDYFDGLTAGVSGTPTVFLNGI-KVEGLATQEALAEII 305
                                       ***************************8.9*****999999876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.5   9.8e+03      25      36 ..      83      94 ..      55     111 .. 0.59
   2 !   37.9   0.2   1.1e-12     2e-09       3     108 ..     150     304 ..     148     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.5
                     Thioredoxin_2 25 kelkelddvtvr 36
                                       e+k+++++ v+
  gi|488599744|ref|YP_007906215.1| 83 VEVKDIKKLDVY 94
                                      233333333333 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 1.1e-12
                     Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkel....ddvtvrvllfplkpsfepk.avaiwcakekkkafkd......... 65 
                                       ++ k +++ f+d  CpyC+k++k+l+e+    +d+++  ++fp++ +++++ a a  ca+e+++ ++          
  gi|488599744|ref|YP_007906215.1| 150 EDAKVTIIEFSDYACPYCAKFEKVLSEIekkyPDIKIVFRDFPIHGNVSIIaAKAANCANEQNRFWEYhdllfekqn 226
                                       678999***********************99************8888665516678999999866666888888888 PP

                     Thioredoxin_2  66 ........................................ieenvelarkygvrgtPtivfldgkeivarlpGyvpa 102
                                                                               i++ +  + + gv+gtPt+++   k     ++G+ ++
  gi|488599744|ref|YP_007906215.1| 227 ewiealkngdkqklylyaeelglnltefksclnsnkydseIQKDYFDGLTAGVSGTPTVFLNGIK-----VEGLATQ 298
                                       88889999*************************988887766666666666******97665444.....7888888 PP

                     Thioredoxin_2 103 eeleal 108
                                       e l+++
  gi|488599744|ref|YP_007906215.1| 299 EALAEI 304
                                       887765 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.82   1.5e+03      20      41 ..      72      93 ..      67     101 .. 0.73
   2 !    6.1   0.0    0.0065        12       8      27 ..     162     181 ..     152     191 .. 0.75
   3 !    9.5   0.0   0.00056         1      38      76 .]     270     306 ..     252     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.82
                                      HHHHCHCCTCECEEECCTTHHH CS
                     Thioredoxin_3 20 vkeaaaekgikaevekvtdfee 41
                                      +++++ ++g+k+ev+++++++ 
  gi|488599744|ref|YP_007906215.1| 72 INRYLLKPGVKVEVKDIKKLDV 93
                                      5667778899999988877654 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0065
                                       SSSTTCHHHHHHHHHHCHCC CS
                     Thioredoxin_3   8 pgCakCpklekavkeaaaek 27 
                                         C++C k+ek++ e+ ++ 
  gi|488599744|ref|YP_007906215.1| 162 YACPYCAKFEKVLSEIEKKY 181
                                       45**********99987776 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00056
                                       THHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHHH CS
                     Thioredoxin_3  38 dfeeiekygVmsvPalvidgkvvvsGkvpseeeirklle 76 
                                       d+ +    gV  +P+++++g ++v+G + ++e +++++e
  gi|488599744|ref|YP_007906215.1| 270 DYFDGLTAGVSGTPTVFLNG-IKVEG-LATQEALAEIIE 306
                                       555556789**********9.899**.999999999985 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   8.8e-06     0.016       2      50 ..     153     211 ..     151     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                                       SEEEEEE--SSSHHHHHHHHHHHHHHHHHH........H..TTSEEEEEEE-SS-HHHH CS
                     Thioredoxin_8   2 kvvlLyfgaswcppckaftpklkelyeklk........k..kkkveivyvsldkkeeef 50 
                                       kv+++ f+++ cp c++f + l+e+++k+            + +v i++ +  +  +e+
  gi|488599744|ref|YP_007906215.1| 153 KVTIIEFSDYACPYCAKFEKVLSEIEKKYPdikivfrdFpiHGNVSIIAAKAANCANEQ 211
                                       899**************************866666654145677777766665443333 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.23     4e+02       3      26 ..     159     182 ..     157     192 .. 0.82
   2 !   12.4   0.0   5.2e-05     0.093      77     178 ..     198     295 ..     190     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
                     Thioredoxin_5   3 FidPlcseCweiEpelkklkveyg 26 
                                       F d  c+ C ++E+ l  + ++y 
  gi|488599744|ref|YP_007906215.1| 159 FSDYACPYCAKFEKVLSEIEKKYP 182
                                       67778***********99988874 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.2e-05
                     Thioredoxin_5  77 aslaiKAAelQgkkkg....rkFLrklqealflekkniskeellleiaekaglDveefkeDlesklakkafqcDlkl 149
                                       +++a KAA+   +++     +++L + q++ ++  kn +k + l+  ae+ gl+++efk  l+s+      q+D   
  gi|488599744|ref|YP_007906215.1| 198 SIIAAKAANCANEQNRfweyHDLLFEKQNEWIEALKNGDK-QKLYLYAEELGLNLTEFKSCLNSNKYDSEIQKDYFD 273
                                       5788888888776653222268889999999888888888.88999*****************************99 PP

                     Thioredoxin_5 150 akemgvtevPtlvffneneeeeglkvegl 178
                                           gv+ +Pt+ f n      g+kvegl
  gi|488599744|ref|YP_007906215.1| 274 GLTAGVSGTPTV-FLN------GIKVEGL 295
                                       9999******95.555......5555555 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.1     2e+03      17      34 ..      74      91 ..      70     103 .. 0.82
   2 ?    9.0   0.1   0.00088       1.6       8      28 ..     163     183 ..     156     190 .. 0.81
   3 ?    2.2   0.0      0.12   2.1e+02      45      57 ..     276     289 ..     244     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                                      HHHHHTTGGEEEEEGCCS CS
                      Glutaredoxin 17 rlLkelgvkfeeidvdkd 34
                                      r+L + gvk+e+ d+ k 
  gi|488599744|ref|YP_007906215.1| 74 RYLLKPGVKVEVKDIKKL 91
                                      678889999999999886 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00088
                                       SSHHHHHHHHHHHHTTGGEEE CS
                      Glutaredoxin   8 tCpyCkkakrlLkelgvkfee 28 
                                        CpyC+k  ++L e   k+  
  gi|488599744|ref|YP_007906215.1| 163 ACPYCAKFEKVLSEIEKKYPD 183
                                       7***********999888754 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.12
                                       H.TSSSSSEEEETT CS
                      Glutaredoxin  45 s.gvrtvPqvfidg 57 
                                       + gv+  P+vf +g
  gi|488599744|ref|YP_007906215.1| 276 TaGVSGTPTVFLNG 289
                                       2699********98 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.7   6.6e+03      60      76 ..      59      75 ..      53     100 .. 0.63
   2 ?   11.9   0.0   9.3e-05      0.17      17      53 ..     151     188 ..     127     204 .. 0.83
   3 ?   -0.9   0.0      0.89   1.6e+03      68     101 ..     277     305 ..     254     307 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.7
                                      TSHHHHHHTT-SSSSEE CS
                       Thioredoxin 60 enedlakkyevegiPtl 76
                                      e +++a +y+v++i   
  gi|488599744|ref|YP_007906215.1| 59 EINKTAVDYSVKYINRY 75
                                      45566666777666443 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.3e-05
                                       TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEE CS
                       Thioredoxin  17 ekklvlveFyApwCghCkalaPeleklaeelkd.kvkl 53 
                                       ++k  ++eF    C+ C +++ +l ++ +++ d k+++
  gi|488599744|ref|YP_007906215.1| 151 DAKVTIIEFSDYACPYCAKFEKVLSEIEKKYPDiKIVF 188
                                       46889***************************666665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.89
                                       TT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHH CS
                       Thioredoxin  68 yevegiPtlklfkngkevkkyegarekeklaafl 101
                                        +v+g Pt+  f ng    k+eg +++e+la+ +
  gi|488599744|ref|YP_007906215.1| 277 AGVSGTPTV--FLNGI---KVEGLATQEALAEII 305
                                       578888887..44554...455556666666555 PP

>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.066   1.2e+02     105     130 ..      44      75 ..      30      91 .. 0.66
   2 ?    8.6   0.0   0.00059       1.1      56      80 ..     150     174 ..     113     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.066
                            DUF929 105 niPgLiFknftp......nskvefysiYiyne 130
                                        i g+ F n++       +  v+++++Yi  +
  gi|488599744|ref|YP_007906215.1|  44 AIVGFAFSNMQKseteinKTAVDYSVKYINRY 75 
                                       45566666665556666666677777777544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00059
                            DUF929  56 sngkvevyfvswegCPvgaaesWaL 80 
                                       ++ kv +++ s + CP++a     L
  gi|488599744|ref|YP_007906215.1| 150 EDAKVTIIEFSDYACPYCAKFEKVL 174
                                       56799**************866555 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.9    0.0058        10       2      82 ..      32     117 ..      31     142 .. 0.72
   2 ?    1.8   0.0      0.17     3e+02      36      87 ..     229     293 ..     211     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0058
                          FtsH_ext   2 llwlllallllllllslfggsgtgstkeisyseF....ledle...........qgnvekvvvqestisalirrptg 63 
                                       +l++l+a++l++++  ++ +s+ +++++    +     +++++            ++++k +v+  +++        
  gi|488599744|ref|YP_007906215.1|  32 ILFALIAGVLIGAIVGFA-FSNMQKSETEINKTAvdysVKYINryllkpgvkveVKDIKKLDVYALNVE-------- 99 
                                       89999**********999.55555555444444435553333344455555555888999999955555........ PP

                          FtsH_ext  64 dgvsttkkgnstttystpt 82 
                                        +vs++++ + +++y t +
  gi|488599744|ref|YP_007906215.1| 100 -FVSKNSTLGEDYVYITSD 117
                                       .888888888888887765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.17
                          FtsH_ext  36 ledleqgnvekvvvqestis.................alirrptgdgvsttkkgnstttystptlgsve 87 
                                       +e l++g+ +k +++    +                 + ++   +d + + + g s t +++ +  +ve
  gi|488599744|ref|YP_007906215.1| 229 IEALKNGDKQKLYLY----AeelglnltefksclnsnKYDSEIQKDYFDGLTAGVSGTPTVFLNGIKVE 293
                                       68899*********9....32333444444444444444444446666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2126.16
//
Query:       gi|488599745|ref|YP_007906216.1|  [L=123]
Description: hypothetical protein Asulf_00189 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-15   57.5   0.4      2e-15   56.8   0.4    1.3  1  SepF        Cell division protein SepF
  ------ inclusion threshold ------
      0.034   14.5   0.2      0.072   13.4   0.0    1.6  2  Npun_R1517  Npun R1517


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 !   56.8   0.4   2.2e-19     2e-15       1      72 []      39     112 ..      39     112 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.2e-19
                                       EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                              SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                       ++v+e++ +++++ei ++++eg+iVi+++  l++   ++ ri++ l++++ +++Gdi+ +g+++f++tP++++i
  gi|488599745|ref|YP_007906216.1|  39 IKVAEVTGLSEVPEIRRQIYEGNIVIIDVAFLKHdkLTLDRILKDLRQLAEDVKGDIVGLGDDYFIVTPTGIRI 112
                                       89***************************999997799*********************************998 PP

>> Npun_R1517  Npun R1517
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     8e-06     0.072      40      71 ..      26      57 ..      12      60 .. 0.88
   2 ?   -2.6   0.0       0.8   7.2e+03      27      43 ..      84     101 ..      69     107 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8e-06
                        Npun_R1517 40 eGedeylesleasvkiqevaelkasPemrrql 71
                                      e e e l+  e+ +k+ ev+ l   Pe+rrq+
  gi|488599745|ref|YP_007906216.1| 26 EYESEILDEAETVIKVAEVTGLSEVPEIRRQI 57
                                      55789999***********************7 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.8
                        Npun_R1517  27 realle.vlldalseGed 43 
                                         +l e v  d +  G+d
  gi|488599745|ref|YP_007906216.1|  84 LRQLAEdVKGDIVGLGDD 101
                                       344433122344445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 940.79
//
Query:       gi|488599746|ref|YP_007906217.1|  [L=192]
Description: ZPR1-related zinc finger protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  117.2   0.3    7.8e-34  116.8   0.3    1.2  1  zf-ZPR1   ZPR1 zinc-finger domain


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   0.3   4.3e-38   7.8e-34       2     158 ..       3     154 ..       2     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 4.3e-38
                           zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatv 78 
                                       +Cp+Cg ++ +   ++ ++Pyf++v+i+s++Ce Cg+k+++  +++ +++  +r+  k++ +++l ++v++S+++t+
  gi|488599746|ref|YP_007906217.1|   3 SCPACG-REIKILSTVHDVPYFGKVLITSISCE-CGFKHSDSIITEIKDP--VRYISKIN-KDNLFTKVIRSTSGTI 74 
                                       7****8.6566666666****************.********99999999..*******8.689************* PP

                           zf-ZPR1  79 eipeleleippg.tlegrlttvEGlLeqikeele.keegdqaeredeekekieeflekleeliegeepftlildDpa 153
                                       ++pel+++i+pg ++++++t+ EG+L+++++ ++  ++ +++++  e+ e ++++lek++++i+g+e++t+i++Dp 
  gi|488599746|ref|YP_007906217.1|  75 RFPELGVDIEPGpASNAFITNFEGVLSKVEDIVKlAKSWNSENQ--EKVEICDKILEKISNTINGDEELTIIIEDPY 149
                                       *********************************74333333333..679**************************** PP

                           zf-ZPR1 154 gnSfi 158
                                       gnS+i
  gi|488599746|ref|YP_007906217.1| 150 GNSAI 154
                                       ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1505.06
//
Query:       gi|488599747|ref|YP_007906218.1|  [L=367]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-16   58.9   1.8    5.4e-16   58.3   0.5    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.06   13.4   0.1       0.13   12.3   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.065   13.1   0.1       0.15   11.9   0.1    1.6  1  Cys_rich_CPCC   Cysteine-rich CPCC


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 ?   -2.3   0.0      0.73   4.4e+03       1      17 [.      28      44 ..      28      48 .. 0.86
   2 !   58.3   0.5   9.1e-20   5.4e-16       4      66 ..     288     350 ..     285     351 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.73
                    OrfB_Zn_ribbon  1 frklkeqleykakeyGi 17
                                      +r+l ++l + +k+ Gi
  gi|488599747|ref|YP_007906218.1| 28 YRRLAMFLIECCKKTGI 44
                                      68899999999999998 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 9.1e-20
                    OrfB_Zn_ribbon   4 lkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNi 66 
                                       ++  + +ka ++ i v++ + +y+S++C++C ++++++++gr+fkC +Cgfe d Dv+A +N+
  gi|488599747|ref|YP_007906218.1| 288 IHSAIVEKALWEEIAVQTRKAYYSSQKCPVCKYVSSKNRKGRRFKCLKCGFEEDVDVVAGMNL 350
                                       5678999*******************************************************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 ?   12.3   0.1   2.2e-05      0.13      69     105 ..     311     350 ..     285     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                                       -EEEETTTS-EEECHHH..HHS-TTTSSS.-EEEEESSSE CS
                              HypA  69 vkvrCreCgkefeleek..alrCpkCgsa.dveivsGeel 105
                                        + +C +C++  ++++k  +++C kCg + dv++v+G +l
  gi|488599747|ref|YP_007906218.1| 311 SSQKCPVCKYVSSKNRKgrRFKCLKCGFEeDVDVVAGMNL 350
                                       4679*****999977745699******7659****99887 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.5e-05      0.15       2      30 ..     314     342 ..     313     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                     Cys_rich_CPCC   2 qCpcCgyltleeeegsydiCpvCfWedDl 30 
                                       +Cp+C y++ ++++g    C  C  e+D+
  gi|488599747|ref|YP_007906218.1| 314 KCPVCKYVSSKNRKGRRFKCLKCGFEEDV 342
                                       8*************99999*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2692.68
//
Query:       gi|488599748|ref|YP_007906219.1|  [L=187]
Description: putative hydrolases of HD superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-17   63.5   0.5    4.6e-17   62.4   0.5    1.5  1  HD_3           HD domain
    1.4e-12   47.8   2.2    2.6e-12   46.9   2.2    1.5  1  HD_2           HD containing hydrolase-like enzyme
    0.00059   20.0   1.8    0.00081   19.6   1.1    1.6  1  Alpha_Helical  Alpha helical domain
  ------ inclusion threshold ------
       0.36   11.1   2.6        1.8    8.8   2.6    2.3  1  HD             HD domain


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.5     1e-20   4.6e-17       1     157 [.      13     161 ..      13     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1e-20
                              HD_3   1 vekLKfqkRqgwlqtgrvreesvaeHmwrvalmalllseelkekvdiarvikmf.LiHDlvEiltgDiispdelake 76 
                                       v++LK+++R+gwl++g+ + esvaeH+ r+a++a++++    ++ ++a       LiHD++E+ t D+     la++
  gi|488599748|ref|YP_007906219.1|  13 VGELKRVPRSGWLRFGIGNVESVAEHSMRTAFIAFIVAFIETSSYEVATKSAFYaLIHDMAEARTTDLHK---LARK 86 
                                       689**********************************998886666554444337*************55...7788 PP

                              HD_3  77 ekeeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllqalekegdslaaf.eaklsqvygv 152
                                       + + + ++a ++ l+llp++lae++l+       + ++  k++kd Dkle+l+qa+e+++ + + +  a+  ++ + 
  gi|488599748|ref|YP_007906219.1|  87 YMDVDTERAFRDQLSLLPSNLAEKILE-------ERDDVKKYVKDADKLELLFQAMEYSKINSETLlYAENLSFETD 156
                                       888888888888899*****9998874.......45667799****************9988877755555555555 PP

                              HD_3 153 sskel 157
                                       + ke+
  gi|488599748|ref|YP_007906219.1| 157 AAKEI 161
                                       55555 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   2.2   5.8e-16   2.6e-12      10     150 ..      17     143 ..      10     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 5.8e-16
                              HD_2  10 kyieRwalmrn..treenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpe 84 
                                       k + R +  r    + e+vaeHs+++a+ia ++a ie   +  ++ a + a  al+HD++E+ t Dl         +
  gi|488599748|ref|YP_007906219.1|  17 KRVPRSGWLRFgiGNVESVAEHSMRTAFIAFIVAFIETSSY--EV-ATKSAFYALIHDMAEARTTDLH--------K 82 
                                       55555544443225779*********************997..44.4566789*************95........7 PP

                              HD_2  85 ireaykevEee.aeekllelLpeelreeyeelladeeaeeeekklvkaaDklsalikcleelkagnk 150
                                       ++++y +v +e a +  l+lLp++l e+   +l   e+++++kk+vk aDkl+ l +++e  k + +
  gi|488599748|ref|YP_007906219.1|  83 LARKYMDVDTErAFRDQLSLLPSNLAEK---IL---EERDDVKKYVKDADKLELLFQAMEYSKINSE 143
                                       88999999988899999********976...55...2234689***************998776554 PP

>> Alpha_Helical  Alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.1   1.8e-07   0.00081      28     104 ..     111     186 ..      90     187 .] 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.8e-07
                     Alpha_Helical  28 klrgkwnkkkalelakemeselqslkysylepedLakseevkklkekaeeiiealggeewsekfleeaekeekekte 104
                                        l  + + kk ++ a ++e  +q+++ys +++e+L  +e+++  ++ a+ei++a+ ++ w   f ee ++++++k e
  gi|488599748|ref|YP_007906219.1| 111 ILEERDDVKKYVKDADKLELLFQAMEYSKINSETLLYAENLSFETDAAKEIARAIKPDSWWIYF-EELNHNKHKKHE 186
                                       5666678899999************************************************999.777777777755 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.6    0.0004       1.8       2     115 ..      36     124 ..      35     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH..........HHHCTCCHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk..........eeefekflaHekvgaeil 67 
                                       +eHs+++a +a   a  +    e   +  + aL+HD+++ ++ d  + k          e                 
  gi|488599748|ref|YP_007906219.1|  36 AEHSMRTAFIAFIVAFIETSsYEVATKSAFYALIHDMAEARTTD--LHKlarkymdvdtE----------------- 93 
                                       79******9999998776668677778889***********988..22222332222210................. PP

                                       HHHHHHHHHH.HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHH CS
                                HD  68 revekrlgld.ledvaklirehheswegkkrprglaerqlslearivkl 115
                                                  + d + l  +++  +  +         + +   + vk+
  gi|488599748|ref|YP_007906219.1|  94 ---------RaFRDQLSLLPSNLAEKILE---------ERDDVKKYVKD 124
                                       .........11222233333333333222.........33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1294.88
//
Query:       gi|488599749|ref|YP_007906220.1|  [L=153]
Description: hypothetical protein Asulf_00193 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-31  109.9   0.2    1.3e-31  109.7   0.2    1.0  1  Mut7-C      Mut7-C RNAse domain
  ------ inclusion threshold ------
      0.038   13.7   0.0       0.11   12.3   0.0    1.8  2  DUF5615     Domain of unknown function (DUF5615)
      0.071   12.8   0.0      0.085   12.6   0.0    1.1  1  Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
       0.13   12.1   0.4       0.34   10.7   0.1    1.7  2  zf_C2HC_14  C2HC Zing finger domain


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 !  109.7   0.2   2.9e-35   1.3e-31       8     145 ..       1     146 [.       1     147 [. 0.81

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 2.9e-35
                            Mut7-C   8 mlgklakyLRllGydalyasdv.....edeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlrevi 77 
                                       mlgkl+++LR+ Gyd++y  d      ++e+    ++ ++rillTrdreL++r   +++  ++++s+ ++eq++e+ 
  gi|488599749|ref|YP_007906220.1|   1 MLGKLTTWLRISGYDTVYVGDLnimnrRKEDTFLVTSFKDRILLTRDRELYERCISSNRevIFINSNTIAEQIKEL- 76 
                                       8****************77766667774444444456789*************99999898999************. PP

                            Mut7-C  78 arlglklslkpelsrCvaCngeleevekeevker.....vpekvyeeadeftrCekCrkvfWkGshwerveel 145
                                       ++ g++   + +++rC  Cn+ l++ ++ee+ +      +pe  + +  ef+ Ce+C k++W Gshw+++ ++
  gi|488599749|ref|YP_007906220.1|  77 SEKGFEF--RIVMDRCSVCNNLLRRPSEEEILDVlrkegLPEDFK-TRYEFWYCENCVKLYWMGSHWRNMVKF 146
                                       6666666..6668******************98843333444433.3444********************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 ?   12.3   0.0   2.5e-05      0.11      13      62 ..       5      55 ..       3      67 .. 0.82
   2 ?   -1.4   0.0      0.45     2e+03      14      27 ..      73      86 ..      61     113 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                           DUF5615 13 lvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFgel.l 62
                                      l ++lr  g+d+++v +l+  +   e+ + + + +dri++T+D+  +e+ +
  gi|488599749|ref|YP_007906220.1|  5 LTTWLRISGYDTVYVGDLNIMNRRKEDTFLVTSFKDRILLTRDRELYERcI 55
                                      789****************8887777788888899********98877743 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.45
                           DUF5615 14 vellreaghdvlhv 27
                                      +++l+e+g+++  v
  gi|488599749|ref|YP_007906220.1| 73 IKELSEKGFEFRIV 86
                                      45555555554433 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05     0.085      90     164 ..      21      95 ..      16     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                        Hydant_A_N  90 lleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhSylnp 164
                                       +l+i + +++d f  +  k+ +l ++  e+ er     +++  ++ + + e++k+l+++g+e  +v+   S++n+
  gi|488599749|ref|YP_007906220.1|  21 DLNIMNRRKEDTFLVTSFKDRILLTRDRELYERCISSNREVIFINSNTIAEQIKELSEKGFEFRIVMDRCSVCNN 95 
                                       688999999999999999********************************************9999988888776 PP

>> zf_C2HC_14  C2HC Zing finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.68     3e+03       6      12 ..      89      95 ..      86      97 .. 0.77
   2 ?   10.7   0.1   7.6e-05      0.34       9      24 ..     126     141 ..     123     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.68
                        zf_C2HC_14  6 nCkgCek 12
                                       C+ C++
  gi|488599749|ref|YP_007906220.1| 89 RCSVCNN 95
                                      6999986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.6e-05
                        zf_C2HC_14   9 gCekqVcLSkMRaHia 24 
                                       +Ce+ V+L++M +H +
  gi|488599749|ref|YP_007906220.1| 126 YCENCVKLYWMGSHWR 141
                                       7*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1062.11
//
Query:       gi|488599750|ref|YP_007906221.1|  [L=530]
Description: histone acetyltransferase, ELP3 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-26   89.9   0.2    2.1e-25   88.6   0.2    1.7  1  Radical_SAM_C    Radical_SAM C-terminal domain
    2.8e-19   70.1   0.3    2.3e-18   67.2   0.0    2.6  3  Radical_SAM      Radical SAM superfamily
    2.6e-09   37.3   0.2    5.7e-09   36.2   0.2    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      3e-05   24.0   0.1    0.00018   21.5   0.1    2.1  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0023   18.3   0.0     0.0067   16.8   0.0    1.8  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.2   5.8e-29   2.1e-25       1      81 [.     301     380 ..     301     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 5.8e-29
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd +K+yp+lv+ gTeL+e+y+sgey+p+++ee+ +l+a+++++ p+++rv+R+++dip +l i g  ++nlr++++
  gi|488599750|ref|YP_007906221.1| 301 PDYLKIYPTLVVDGTELYEMYRSGEYRPYTTEEVAELIARAKRFFPKWVRVQRIQRDIPVKLAI-GLDKGNLRQIVH 376
                                       89*********************************************************99877.8889******** PP

                     Radical_SAM_C  78 krlk 81 
                                       ++lk
  gi|488599750|ref|YP_007906221.1| 377 QKLK 380
                                       *997 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.68   2.4e+03      86     133 ..      26      69 ..       5      78 .. 0.54
   2 !   67.2   0.0   6.3e-22   2.3e-18       3     158 ..      90     284 ..      88     292 .. 0.90
   3 ?   -2.2   0.0       1.4   4.8e+03     123     140 ..     327     344 ..     313     354 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.68
                                       SSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  86 gtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlea 133
                                       g+ +++  +e ++++    ++l+    +++ ++k +   +++e++++ 
  gi|488599750|ref|YP_007906221.1|  26 GIELTRSDIEIIKKRIAKKYNLSRIPSNPD-IRKFI---PDNERIKKM 69 
                                       333344445555555555555555555555.55555...455555555 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 6.3e-22
                                       EESEESS--TTTSCCTT..............HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHH CS
                                       xxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet..............vrregrgrslsveeileevkelkaekgvkevilgggepllypdfve 65 
                                       + ++ ++rC+ C+ + +                ++g+  +++v   l e+ke+ +  ++ e+i++gg+  +++++++
  gi|488599750|ref|YP_007906221.1|  90 PAPCPHGRCVPCPGGIKtpqsytgrepaamrAIQHGYDPFRQVTARLGELKEIGHAVDKVEIIVMGGTFPARDKEYR 166
                                       66778888*******99**************9**********************9999**************77777 PP

                                       HHHHHHHTC.......................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHH CS
                                       xxxxxxxxx.......................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  66 llerlakla.......................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddek 116
                                       + + l                           +++ r+   t +t+pd      ++++l +g + v+lg++++ d+ 
  gi|488599750|ref|YP_007906221.1| 167 DHFILNIYNalnsfdsdpsisstieeakeineKAKARCIGMTFETRPDycgLGEIKEMLSYGGTKVELGVQSIYDD- 242
                                       7777777777777788888888888888888889******************************************. PP

                                       HHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 117 vlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                       vl++++rgh+++++++a+++l+++ +k+ +++++glp   +e
  gi|488599750|ref|YP_007906221.1| 243 VLEIIKRGHGVDATVKATKLLKNSAFKVGYHIMPGLPSSDFE 284
                                       ***************************999999999976654 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.4
                                       CTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 123 rghtfeevlealeklrea 140
                                       r++t eev e++ ++++ 
  gi|488599750|ref|YP_007906221.1| 327 RPYTTEEVAELIARAKRF 344
                                       556666666666666655 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.2   1.6e-12   5.7e-09      28     117 .]     417     518 ..     392     518 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.6e-12
                                       HHSTTC.EEEE.EEETTEEEEEEEEEEEET...TSTTEEEEEEEEE...........SGGGTTSSHHHHHHHHHHHH CS
                    Acetyltransf_1  28 fsleae.gllv.aeedgeliGfisllkipd...ekggvayieslaV...........speyrgkGlGsaLlealeer 88 
                                        +  ++ ++++ +e ++ l+Gfi+l+       e +++a i++l+V           s++ +++G+Gs+Ll a+ee+
  gi|488599750|ref|YP_007906221.1| 417 YRASDGvEYFIsYETEDFLAGFIRLRFCEAaleEIENHALIRELHVygislplglkdSSSPQHRGIGSKLLSAAEEI 493
                                       233344455554777777***************999********************99999**************** PP

                                       HHHTTESEE.EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  89 areegikki.vlaveedndaairlYeklGF 117
                                       a +e +++i v+    + ++a+++Y+k+G+
  gi|488599750|ref|YP_007906221.1| 494 AIQE-FDRIaVI----SGVGAREYYRKHGY 518
                                       ***9.9998455....99*******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 ?   -0.7   0.0      0.35   1.3e+03      27      49 ..     420     442 ..     399     464 .. 0.79
   2 !   21.5   0.1     5e-08   0.00018      64     109 ..     478     521 ..     474     527 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.35
                   Acetyltransf_10  27 eegealllvaeeggkivGvielr 49 
                                       ++g  +++ +e ++ ++G+i+lr
  gi|488599750|ref|YP_007906221.1| 420 SDGVEYFISYETEDFLAGFIRLR 442
                                       47778888899999999***996 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5e-08
                   Acetyltransf_10  64 rgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkav 109
                                       +++Gig++Ll a+ee a ++    ++ v +   a+++Y+k+G+k++
  gi|488599750|ref|YP_007906221.1| 478 QHRGIGSKLLSAAEEIAIQE-FD-RIAVISGVGAREYYRKHGYKKL 521
                                       9***************9655.55.8******************987 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.9e-06    0.0067      37      76 .]     478     520 ..     474     520 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                                       TTSSHHHHHHHHTT....SEEEEEEEEETHH.....HHHHHHHHTTEEE CS
                    Acetyltransf_7  37 rgkGiGraLleaae....kgiileqlelnae.....kaikfYeklGFee 76 
                                       + +GiG++Ll aae    +    +  +          a+++Y+k+G+++
  gi|488599750|ref|YP_007906221.1| 478 QHRGIGSKLLSAAEeiaiQE---F-DRI--AvisgvGAREYYRKHGYKK 520
                                       7899******9722222222...1.111..0122347999*******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3403.19
//
Query:       gi|488599751|ref|YP_007906222.1|  [L=295]
Description: Malate/lactate dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-39  133.4   0.1    8.5e-39  132.9   0.1    1.3  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
    1.2e-22   80.6   0.0    1.9e-22   80.0   0.0    1.3  1  Ldh_1_C          lactate/malate dehydrogenase, alpha/beta C-t
    0.00037   20.1   1.2     0.0011   18.5   0.2    2.1  2  Glyco_hydro_4    Family 4 glycosyl hydrolase
  ------ inclusion threshold ------
       0.06   13.9   0.1       0.39   11.3   0.1    2.4  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.14   12.4   0.1       0.35   11.1   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.1   2.4e-42   8.5e-39       1     141 []       1     141 [.       1     141 [. 0.97

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 2.4e-42
                                       EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE- CS
                           Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvit 76 
                                       +k+  vGa G iG++ a++ ++++ +de+a++Di ++ + G+a+dl h+++ l    ++++ ++++ lk +d++v+ 
  gi|488599751|ref|YP_007906222.1|   1 MKIGFVGA-GRIGATSAFTCLQHMDVDEIAIVDIMEDLAVGEAMDLAHAAAGLDKYPNIKGgSDYSLLKRSDIIVVS 76 
                                       6999****.**************99**************************99887777776*************** PP

                                       -S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                           Ldh_1_N  77 agvprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                       ag  rkpG+tR+dL  +Na+I+k+i+ +i+++ap+ ++lvv+NP+d+++++++k +g p+++v+g
  gi|488599751|ref|YP_007906222.1|  77 AGLARKPGMTRLDLATKNAGIIKDIAGKIMEYAPESKILVVTNPMDVMNYIMWKETGKPRNEVFG 141
                                       ***************************************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   5.3e-26   1.9e-22       3     162 ..     146     292 ..     145     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 5.3e-26
                                       HHHHHHHHHHHHHHTS-GGGEE--EEBSSSTETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHHTTSSSS- CS
                           Ldh_1_C   3 LDivRaktflaekagvtprsvkvtViGgHsgvtiipllsqvkellklsekqleeliervqnggdevvkakkGagsat 79 
                                       LD+ R+k  l      + + +k++ +G+H++     + s +++   ++e + ++  e++++ ++ev+k+k   g++ 
  gi|488599751|ref|YP_007906222.1| 146 LDSSRLKERLYA--HGARNIRKAYMLGEHGDSMFLAK-SLADF---DNEVDWAKVEEETRFVAAEVIKRK---GATI 213
                                       666666665533..34567889*********997777.66666...7788999999**************...9*** PP

                                       HHHHHHHHHHHHHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHHHHHH CS
                           Ldh_1_C  80 lsmAvAgakfveallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleksvkeL 156
                                        + Av++ ++v+a+++dtke+++++v+ldge+g+kd   + ++vP++lgknGvekv+e    +++e e ++ s++ L
  gi|488599751|ref|YP_007906222.1| 214 FGPAVSIFRMVRAVVEDTKEEIPTSVILDGEYGIKD---VALGVPAILGKNGVEKVVE-YDFSEEELEGFKRSASIL 286
                                       ************************************...9******************.9***************** PP

                                       HHHHHH CS
                           Ldh_1_C 157 kkeiek 162
                                       k+ +++
  gi|488599751|ref|YP_007906222.1| 287 KERLKE 292
                                       *98875 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.18   6.6e+02       1      38 [.       2      35 ..       2      75 .. 0.72
   2 !   18.5   0.2   3.1e-07    0.0011     121     159 ..      95     133 ..      84     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.18
                                      EEEEETTTSSSHHHHHHHHHHTTTTCTEEEEEEE-SSH CS
                     Glyco_hydro_4  1 kiviiGgGStifaklllgdlkkteelsvselaLvDide 38
                                      ki+++G+G    +       +  ++++v e+a+vDi e
  gi|488599751|ref|YP_007906222.1|  2 KIGFVGAGRIGATS----AFTCLQHMDVDEIAIVDIME 35
                                      67777777654432....23344567788888888765 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.1e-07
                                       HHHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHST CS
                     Glyco_hydro_4 121 ipvlleIakdieelcPdawvlnytNPaavvteallrlvp 159
                                        +++ +Ia +i e++P++ +l  tNP+ v+  ++ + ++
  gi|488599751|ref|YP_007906222.1|  95 AGIIKDIAGKIMEYAPESKILVVTNPMDVMNYIMWKETG 133
                                       57899*************************999998876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.39       1      69 [.       2      77 ..       2      98 .. 0.81
   2 ?   -1.7   0.0       1.3   4.5e+03      14      22 ..     151     159 ..     129     195 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE-S CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvlav 69
                                      kig++GaG++g++ a  +l++ ++  ei ++ + +++ a   a +l          +++++++   +++++d++v++ 
  gi|488599751|ref|YP_007906222.1|  2 KIGFVGAGRIGATSAFTCLQH-MDVDEIAIV-DIMEDLAVGEAMDLAhaaagldkyPNIKGGSDYSLLKRSDIIVVSA 77
                                      7*****************999.488888876.6666655544444445566788889999999999999999999985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                                       HHHHHHHTT CS
                     F420_oxidored  14 lasgllaag 22 
                                       l ++l a+g
  gi|488599751|ref|YP_007906222.1| 151 LKERLYAHG 159
                                       333333333 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   9.9e-05      0.35       1      35 [.       3      36 ..       3      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.9e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHH CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrske 35
                                      + ++GaG++G   a  +++h dvd ei+++d  ++
  gi|488599751|ref|YP_007906222.1|  3 IGFVGAGRIGATSAFTCLQHMDVD-EIAIVDIMED 36
                                      5689*******************8.9999997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1768.38
//
Query:       gi|488599752|ref|YP_007906223.1|  [L=261]
Description: Transcriptional regulator/sugar kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  101.5   0.9    2.7e-28   99.3   0.9    1.9  1  ROK          ROK family
    7.1e-07   29.1   1.5    1.2e-06   28.3   1.5    1.4  1  Hydant_A_N   Hydantoinase/oxoprolinase N-terminal region
    6.3e-05   22.1   0.2     0.0096   15.0   0.0    2.6  3  Glucokinase  Glucokinase


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.9   4.5e-32   2.7e-28       2     269 ..       4     238 ..       3     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 4.5e-32
                                       EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEBSSG CS
                               ROK   2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeliavgigspGlisdksgkivst 78 
                                       +g+d+Ggt++ + l+d +++  + + v   t ++ +++ d i++++ +   +  ++ avgig+++ i   +gki  +
  gi|488599752|ref|YP_007906223.1|   4 LGLDVGGTNTDVVLLD-DSTFHHIKTV--KTRDIIDGISDLISDFILDIIPEK-DVKAVGIGIAAWI--RDGKIFRA 74 
                                       69**************.7778888888..7889999**********9986655.589**********..899***** PP

                                       GCGCC.CCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT- CS
                               ROK  79 pnitw.enfdlvekleerlnvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvage 154
                                       pn+ +  n++        +n+  ++enD+n++a+  +   ++ + +++i +t+gtG+G G+i++gkl++G++ +age
  gi|488599752|ref|YP_007906223.1|  75 PNLPViPNIN--------INLNHIIENDANCFAFFAS---KEFGFKDMIGITIGTGIGSGIILEGKLYRGKG-LAGE 139
                                       **98877775........58889********997544...5889**************************86.**** PP

                                       GGGSBS-TTS-B-TTS-BSBHHHCCSHHHHHHCHTCCGTTS-HHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHH CS
                               ROK 155 lGHiqldpegekcgCGnqgClEtlasgralekraqqkgekleakeiiklaekgdevaeevverlaeylakaiadlin 231
                                       +GH  + ++ + c CG+ g lE+   g a+e++ ++  ekl+++            +    +    +  +a+a ++ 
  gi|488599752|ref|YP_007906223.1| 140 IGHAVVSDD-KTCVCGEVGHLEAHFGGWAIERDFSKPAEKLDIDI----------HSLSGFD----RFCRAVAFAVM 201
                                       ****99988.99************************999999875..........2233333....34566667788 PP

                                       HH--SEEEEEH..CCCTSTTHHHHHHHHHHHCCTTTTCCC CS
                               ROK 232 lfdpqaivlgG..gvseadklleairklvkkylnkklevp 269
                                       ++d + +v+gG  g+s ++k+l   +k +++yl+ ++  +
  gi|488599752|ref|YP_007906223.1| 202 MMDFEGVVVGGriGMSLSEKVL---KKRISEYLMPEFDPE 238
                                       8999999999955556666666...777888887766544 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 !   28.3   1.5     2e-10   1.2e-06       2      63 ..       4      61 ..       3      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2e-10
                        Hydant_A_N  2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmG 63
                                      +g DvGGT+TD+v+ld+   +++ +K++ t ++++ gi +++++ +   ip ++++++v +G
  gi|488599752|ref|YP_007906223.1|  4 LGLDVGGTNTDVVLLDD--STFHHIKTVKT-RDIIDGISDLISDFILDIIP-EKDVKAVGIG 61
                                      689*************5..58*********.9************9999888.8888888766 PP

>> Glucokinase  Glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.6e-06    0.0096       4      77 ..       7      77 ..       4      81 .. 0.83
   2 !    4.3   0.1    0.0029        17     133     167 ..     114     149 ..      93     173 .. 0.78
   3 ?   -1.6   0.0      0.17     1e+03     248     270 ..     198     220 ..     187     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-06
                       Glucokinase  4 DiGGTkarlalveaeeeelelleiekyasady.asleealqaflaeaeaevkrpksavlAvAgpvegdev.eltNl 77
                                      D+GGT++ + l+++++ +    +i++++++d  +++++++++f+ +  +  k++k++ +++A  ++++++ +  Nl
  gi|488599752|ref|YP_007906223.1|  7 DVGGTNTDVVLLDDSTFH----HIKTVKTRDIiDGISDLISDFILD-IIPEKDVKAVGIGIAAWIRDGKIfRAPNL 77
                                      *************99988....9******996378*********97.56677778899*****9998765155665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0029
                       Glucokinase 133 lGaGTGLGvallipekerrv.vlasEGGhvdfapes 167
                                       +  GTG+G +++++ k  r   la+E Gh+  +  +
  gi|488599752|ref|YP_007906223.1| 114 ITIGTGIGSGIILEGKLYRGkGLAGEIGHAVVSDDK 149
                                       567*********9999877669*******9877655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.17
                       Glucokinase 248 laLkllargGvyiaGGiapkile 270
                                        a++++ ++Gv ++G i   + e
  gi|488599752|ref|YP_007906223.1| 198 FAVMMMDFEGVVVGGRIGMSLSE 220
                                       678899999*9999988666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1640.03
//
Query:       gi|488599753|ref|YP_007906224.1|  [L=313]
Description: ribose 1,5-bisphosphate isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-93  311.3   0.2    6.2e-93  311.1   0.2    1.0  1  IF-2B         Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.077   12.6   0.0       0.35   10.5   0.0    2.1  3  Phage_endo_I  Phage endonuclease I


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 !  311.1   0.2   6.9e-97   6.2e-93       1     282 []      17     284 ..      17     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: 311.1 bits;  conditional E-value: 6.9e-97
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakk 77 
                                       +vrG+ +ia   ++vl+e++ ++k    +++ ee++ka++ L ++rPtavsl n+i +++       s ++++e ++
  gi|488599753|ref|YP_007906224.1|  17 EVRGAGRIAKFCAKVLMEYAMEIK----KNFDEEMKKAAEILLNTRPTAVSLYNSIYYVMD-----YSGESDEEKRE 84 
                                       589********************9....99*******************************.....7899******* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHH CS
                             IF-2B  78 sliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeL 154
                                       sl++++ke+i+++ +a++ ig+i++ +ik+g tilT+cns ++l+v+++a +++k+++V+++EsrPr qG+ltakeL
  gi|488599753|ref|YP_007906224.1|  85 SLVKRAKEFIEWVDTAQKEIGRIGSRRIKSGSTILTHCNSASALSVIKEAYRKGKDIEVFATESRPRYQGHLTAKEL 161
                                       ***************************************************************************** PP

                                       HHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGG CS
                             IF-2B 155 vqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlded 231
                                       + +gipvtli+dsav+y+++e +d+vivGAd+i+ nG+++nkiGTs++A++Ake+++p++v+ae++kfs+++ l+e 
  gi|488599753|ref|YP_007906224.1| 162 SAEGIPVTLIVDSAVRYFIRE-IDYVIVGADAITVNGSLVNKIGTSQIALIAKEARVPFMVAAETYKFSPKTLLGES 237
                                       *********************.******************************************************* PP

                                       SSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 232 ifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       i+ieerdp+e+++ + +      +k++npafD+tP+++I+liITe+G++pp
  gi|488599753|ref|YP_007906224.1| 238 IVIEERDPAEVAPEELRSL----VKIRNPAFDITPRHYIDLIITEIGAIPP 284
                                       *************999886....99************************98 PP

>> Phage_endo_I  Phage endonuclease I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.3   2.7e+03     106     122 ..      21      37 ..       6      54 .. 0.72
   2 ?   -2.1   0.0      0.28   2.5e+03      24      68 ..     158     204 ..     155     209 .. 0.69
   3 ?   10.5   0.0   3.9e-05      0.35      37      90 ..     213     266 ..     188     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.3
                                       SSBHHHHHHHCT-EEEE CS
                      Phage_endo_I 106 pttyaewceknGikfad 122
                                           a++c k  +++a 
  gi|488599753|ref|YP_007906224.1|  21 AGRIAKFCAKVLMEYAM 37 
                                       45568899999888885 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.28
                                       HHHHHHTT---EES.-EEEEEEE--EEEEE.--SEE-TTSEEEEEES CS
                      Phage_endo_I  24 akqleakGlkveye.slvvpyviPasdhky.tPdfllpnGiivetkG 68 
                                       ak l a+G++v+      v y i + d+     d +  nG +v+  G
  gi|488599753|ref|YP_007906224.1| 158 AKELSAEGIPVTLIvDSAVRYFIREIDYVIvGADAITVNGSLVNKIG 204
                                       67788888888864145678877777765415688888888887655 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 3.9e-05
                                       S-EEEEEEE--EEEEE--SEE-TTSEEEEEESS--HHHHHHHHHHHHH-TTSEE CS
                      Phage_endo_I  37 eslvvpyviPasdhkytPdfllpnGiivetkGlfesedrkkhllireqhPeldi 90 
                                       ++ +vp+++ a+++k++P  ll + i++e +   e+   + + l++ + P +di
  gi|488599753|ref|YP_007906224.1| 213 KEARVPFMVAAETYKFSPKTLLGESIVIEERDPAEVAPEELRSLVKIRNPAFDI 266
                                       5779****************************9999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1926.60
//
Query:       gi|488599754|ref|YP_007906225.1|  [L=299]
Description: hypothetical protein Asulf_00198 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   57.5   5.9    5.2e-10   39.2   0.4    2.6  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0011   18.8   0.3      0.048   13.4   0.1    2.2  2  CDC24_OB3        Cell division control protein 24, OB domain 
     0.0023   18.1   0.2        1.4    9.2   0.0    2.3  2  tRNA_anti_2      OB-fold nucleic acid binding domain
     0.0079   16.3   0.5       0.49   10.5   0.1    2.7  2  DNA_pol_D_N      DNA polymerase delta subunit OB-fold domain
  ------ inclusion threshold ------
       0.07   12.8   4.8       0.24   11.1   0.0    2.7  3  DUF5088          Domain of unknown function (DUF5088)
      0.076   13.1   0.0       0.27   11.3   0.0    1.9  2  YobH             YobH-like protein
       0.99    9.3   4.6       0.33   10.9   0.7    2.2  2  SF3a60_bindingd  Splicing factor SF3a60 binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.8   1.6e-07   0.00041       1      61 [.      70     132 ..      69     148 .. 0.83
   2 !   39.2   0.4     2e-13   5.2e-10       1      64 [.     220     282 ..     220     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.6e-07
                                       EEEEEEEEEEE.EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-.....TTSEEEEEEEEEEC CS
                   tRNA_anti-codon   1 VtvaGrvtsis.drsggkvifidlrDgtgriqvvlfreeatklaenlk.....eGdvvrvtGrvkrr 61 
                                       V+v G v  i+    +g v+ ++l+D++g + v +++    + ae +k     eG++++++G +k  
  gi|488599754|ref|YP_007906225.1|  70 VRVSGVVEEIEyFYTKGMVAKLKLKDESGVVGVKFWK----DCAELVKvgdvfEGCIIEIKGFLKQN 132
                                       789999999999888899*******************....66666665556699999999999865 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 2e-13
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTS CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpgg 64 
                                       V++ Grv+ i   + g+++++ l D++gri+vvl++ ++ ++++++++Gd++ +  G+vk  ++ 
  gi|488599754|ref|YP_007906225.1| 220 VNLIGRVSGIG-IKRGNYADMYLSDDSGRIRVVLWD-SKVEIFKEIDIGDHIVILrGYVKNGEKS 282
                                       7899******7.8889********************.***********************98665 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 ?    3.3   0.0     0.022        56      11      67 ..      72     125 ..      66     150 .. 0.73
   2 !   13.4   0.1   1.9e-05     0.048       9      68 ..     220     272 ..     216     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.022
                         CDC24_OB3  11 LlGrvvaifreknsekkkmdryslrieDttGaidatlweeagklhfk.rlrvGhlvll 67 
                                       + G+v +i ++  +  k m    l+++D++G + +  w+  ++l++  ++  G ++ +
  gi|488599754|ref|YP_007906225.1|  72 VSGVVEEI-EYFYT--KGMV-AKLKLKDESGVVGVKFWKDCAELVKVgDVFEGCIIEI 125
                                       55666666.22222..2344.79***************99999887766666665555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.9e-05
                         CDC24_OB3   9 vtLlGrvvaifreknsekkkmdryslrieDttGaidatlweeagklhfkrlrvGhlvlls 68 
                                       v L+Grv +i   ++ ++       + + D++G i+++lw+  ++  +  + +G+ +++ 
  gi|488599754|ref|YP_007906225.1| 220 VNLIGRVSGIG--IKRGN----YADMYLSDDSGRIRVVLWDSKVEIFKE-IDIGDHIVIL 272
                                       7899******4..44444....23688***************8877666.****877664 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 !    6.7   0.1    0.0031         8       8      69 ..      57     120 ..      46     135 .. 0.75
   2 !    9.2   0.0   0.00054       1.4      18      74 ..     216     271 ..     211     284 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                       tRNA_anti_2   8 raikelleaelkkavwvrGeisnlkr.kasg.hvYftLkDekakisavifrsraaklkft.ledG 69 
                                       ++i+++++ +  + v v G + +++   ++g  + ++LkDe+  + + +++  a+ +k+  + +G
  gi|488599754|ref|YP_007906225.1|  57 QKISDVVNGSN-RVVRVSGVVEEIEYfYTKGmVAKLKLKDESGVVGVKFWKDCAELVKVGdVFEG 120
                                       56777775544.6699********84456774679***************987776664335555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00054
                       tRNA_anti_2  18 lkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlv 74 
                                       l ++v + G +s +  k+  ++ + L+D++ +i++v++ s+++    +++ G+++++
  gi|488599754|ref|YP_007906225.1| 216 LGQRVNLIGRVSGIGIKRGNYADMYLSDDSGRIRVVLWDSKVEIF-KEIDIGDHIVI 271
                                       556788999999995333557778899************999554.46888887664 PP

>> DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00019      0.49      80     125 ..      83     135 ..      28     138 .. 0.88
   2 ?    3.2   0.0     0.035        90      85      99 ..     238     252 ..     232     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                       DNA_pol_D_N  80 vse..kdellLEDesgrvrLs.....gsgieseklvtGvvvavlGvetengdf 125
                                       +++    +l L Desg v ++      + ++++ +  G+++ ++G +++n  f
  gi|488599754|ref|YP_007906225.1|  83 YTKgmVAKLKLKDESGVVGVKfwkdcAELVKVGDVFEGCIIEIKGFLKQNEIF 135
                                       3444688999***********9999877899****************999988 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.035
                       DNA_pol_D_N  85 ellLEDesgrvrLsg 99 
                                        ++L D+sgr+r++ 
  gi|488599754|ref|YP_007906225.1| 238 DMYLSDDSGRIRVVL 252
                                       589*********983 PP

>> DUF5088  Domain of unknown function (DUF5088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.83   2.1e+03     105     134 ..       8      38 ..       2      52 .. 0.78
   2 ?    3.2   0.2     0.026        66      26      80 ..      93     151 ..      67     196 .. 0.76
   3 ?   11.1   0.0   9.3e-05      0.24      21      59 ..     236     275 ..     219     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.83
                           DUF5088 105 keiFttvvGkveYlsvllrks.angkyeeYv 134
                                       ke ++ ++ +ve+   l r+  +++++ +Y+
  gi|488599754|ref|YP_007906225.1|   8 KEYYKPISEEVEFEDFLKRYDeIKEHFGDYI 38 
                                       4557888889999999999987788888885 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.026
                           DUF5088  26 lstsaglvkvvvWke..alrkysslkvGDiivikkfrkkkki..ealskidrntfsetk 80 
                                       l+ ++g+v v +Wk   +l k   + +G ii ik+f k+++i  ++ + +++  f e++
  gi|488599754|ref|YP_007906225.1|  93 LKDESGVVGVKFWKDcaELVKVGDVFEGCIIEIKGFLKQNEIfvSSAENVEIKGFEEME 151
                                       55678899999**96336778888889999******98887522556677777777765 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 9.3e-05
                           DUF5088  21 fffiilstsaglvkvvvWkealrkysslkvGDiivi.kkf 59 
                                       +  + ls ++g ++vv+W  ++  +  +++GD ivi +++
  gi|488599754|ref|YP_007906225.1| 236 YADMYLSDDSGRIRVVLWDSKVEIFKEIDIGDHIVIlRGY 275
                                       556678899999********************99872555 PP

>> YobH  YobH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.27      32      63 ..      72     103 ..      61     113 .. 0.82
   2 ?   -1.9   0.0       1.4   3.5e+03      45      61 ..     233     249 ..     227     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                              YobH  32 aaGlGLqCqyltargvvtaqylhtdsGviGvt 63 
                                       ++G+  + +y+ ++g+v++  l ++sGv+Gv 
  gi|488599754|ref|YP_007906225.1|  72 VSGVVEEIEYFYTKGMVAKLKLKDESGVVGVK 103
                                       566677889*********************95 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                              YobH  45 rgvvtaqylhtdsGviG 61 
                                       rg  +  yl +dsG i 
  gi|488599754|ref|YP_007906225.1| 233 RGNYADMYLSDDSGRIR 249
                                       67778899999999875 PP

>> SF3a60_bindingd  Splicing factor SF3a60 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.96   2.5e+03      18      23 ..       7      12 ..       6      12 .. 0.70
   2 ?   10.9   0.7   0.00013      0.33       7      21 ..      19      33 ..      13      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.96
                   SF3a60_bindingd 18 IKdyHr 23
                                      +K+y++
  gi|488599754|ref|YP_007906225.1|  7 LKEYYK 12
                                      688886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                   SF3a60_bindingd  7 pFseFYkrLkeIKdy 21
                                      +F+ F kr++eIK++
  gi|488599754|ref|YP_007906225.1| 19 EFEDFLKRYDEIKEH 33
                                      8*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1758.81
//
Query:       gi|488599755|ref|YP_007906226.1|  [L=351]
Description: histidinol phosphate aminotransferase apoenzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-42  143.6   0.0    9.8e-42  143.4   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
     0.0067   15.4   0.0     0.0094   14.9   0.0    1.2  1  Alliinase_C    Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.0   1.1e-45   9.8e-42       2     353 ..      27     337 ..      26     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 1.1e-45
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       ++i L+sne++ +    ++++v++a ++   a+  +n+y+++  +++l+e + +++       ++++  + vg+Ga+
  gi|488599755|ref|YP_007906226.1|  27 KIISLSSNENPLL----PPDDVKEAYIR---AFDRINRYPHPF-YDDLKELISEYVD------VEKD-MIAVGNGAS 88 
                                       789**********....*********88...************.*************......7777.9******** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       +++ ++  +  l++ d++++p p y++y+    l+++ ++ +++   +++++d+ ++e+            k+i+++
  gi|488599755|ref|YP_007906226.1|  89 EILKMICEVN-LEAFDKVIIPMPGYTMYIVFSMLMDASIRLVEF---PEYKVDAGKIED--------G---KLIFLC 150
                                       **********.******************999998888777773...4889**999999........2...59**** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp+NPtG  +++ e++ +    ++   l+++DeaYa+f  +s      + +v+e  nl++v+s+sK f++aG RvGy
  gi|488599755|ref|YP_007906226.1| 151 SPNNPTGNSIPEREVRRI---LESFSGLVVIDEAYAEFSKKSF-----LRLVDEFENLIVVRSFSKFFSMAGARVGY 219
                                       ******************...99999***************54.....778999889******************** PP

                                       EEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmfl 308
                                       ++gn + +s+++k+  pf++s +  a++ a l++ +    ++ + r+++ ++r+ l+ eL++   lkv++s+++++l
  gi|488599755|ref|YP_007906226.1| 220 AVGNYETISAIEKVRLPFNISYISVAVAKACLDNLD----YFIKVRDEIVREREWLYRELKKFdSLKVYPSDANFIL 292
                                       *********************999999999999977....9*******************8889**********999 PP

                                       EEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-H CS
                     Aminotran_1_2 309 ltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglte 353
                                       + +++ +++++      e +g++++ +t        + Ritv g  e
  gi|488599755|ref|YP_007906226.1| 293 V-RFDDLSDSQEVSRYFESKGIILRDVTGLIGldGVHYRITV-GRRE 337
                                       8.5555544444444555558877775544335444677777.4444 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     1e-06    0.0094      66     209 ..      78     223 ..      65     250 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-06
                                       TSEEEEECHHHHHHHHHHHHHHHH..SSSSSEEEEE-SS--THHHHHTTTT-BTTEEEEEESTT-.--S..S-EEEE CS
                       Alliinase_C  66 dryivvGtGstqLlqalvyalspeasseskpvkvvaavPyysvykeqtslldsklykweGdaaayvkkknpeefiel 142
                                       +  i vG+G++++l+ +   +       +   kv+  +P y++y   + l+d +    e    +    k  +  + +
  gi|488599755|ref|YP_007906226.1|  78 KDMIAVGNGASEILKMI-CEVN-----LEAFDKVIIPMPGYTMYIVFSMLMDASIRLVEFPEYKVDAGKIEDGKLIF 148
                                       55677777777776643.3333.....34567899999999999988877776544333322222233333445568 PP

                                       EESS-TTT--.-..-..-----TT-EEEEEE-TT-...STTTS---S-B--SEEEEEHHHHHS-GGG-EEEEEES CS
                       Alliinase_C 143 vtsPnnPdgl.l..r..eavvkgseakviyDlayY...WPhytpitskadedimLftlskltGhaGsrlGWalvk 209
                                         sPnnP g+ +  r  + ++++ ++ v+ D ay       +  +  + ++ i++ ++sk+   aG+r+G+a+  
  gi|488599755|ref|YP_007906226.1| 149 LCSPNNPTGNsIpeRevRRILESFSGLVVIDEAYAefsKKSFLRLVDEFENLIVVRSFSKFFSMAGARVGYAVGN 223
                                       89*****997333222246889***********96211234666667777789999***************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2308.18
//
Query:       gi|488599756|ref|YP_007906227.1|  [L=105]
Description: hypothetical protein Asulf_00200 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 765.23
//
Query:       gi|488599757|ref|YP_007906228.1|  [L=482]
Description: L-glutamine synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-122  408.7   0.0     2e-122  408.5   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    2.4e-22   78.5   0.1    5.1e-22   77.4   0.1    1.6  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.5   0.0  2.3e-126    2e-122       2     345 .]     107     479 ..     106     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 408.5 bits;  conditional E-value: 2.3e-126
                                       T-HHH.HHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCE.SSEEEEEEE.T...................B...B. CS
                        Gln-synt_C   2 rdPRs.vlkralarlaeeGltvvvgpElEFflfdkeedke.asksllevdse...................ekgrpa 57 
                                       +dPR  v+k  +++l + G++v++gpE+EFf+f+  + ++ a++++++++                      +   +
  gi|488599757|ref|YP_007906228.1| 107 CDPRAyVAKSLEKKLGDDGMSVIFGPEIEFFVFEGIDPTRlAWDMWVSPNGGagdswgpprvmpesseiepGGFFIR 183
                                       69**7689999999*********************999999999999999999****************9988899* PP

                                       TSS-TTBHCCCCCTCCHHHHHHHHHHHTT--EECCEEECCCT.EEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT- CS
                        Gln-synt_C  58 ekggyfsvapvdeaedlrreivealealgieveashhEvatg.QvEinlkfadalkaaDnvvtfKrvvkevArkhgl 133
                                        k+gyf+ +p d+++++r+e+  +le+lg+ ve +hhEvat+ QvE++++++++++  D ++++K ++k++A+++gl
  gi|488599757|ref|YP_007906228.1| 184 PKEGYFRPPPEDTTMEYRNELSYYLEKLGVFVEYHHHEVATAgQVELDFRPKTLVDVSDAFYLYKFAAKNIAAMNGL 260
                                       *****************************************99********************************** PP

                                       EEE-SSSSSTTS---BEEEEEEEEEC...TTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCS CS
                        Gln-synt_C 134 tatFmpKplegdnGsgmHvhlSlwdk...dgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlv 207
                                        atFmpKpl+ dn+sgmH+++Slw+    +g+++f d+dde +ls+ ar++igGll+hakalta++apt+nSYkRlv
  gi|488599757|ref|YP_007906228.1| 261 LATFMPKPLYLDNASGMHINQSLWEGkpfEGNPVFGDADDEFMLSQKARYYIGGLLEHAKALTAICAPTINSYKRLV 337
                                       ************************7667789********************************************** PP

                                       SSTTSSSBEEEESS-TTCSEEEE-..TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS CS
                        Gln-synt_C 208 pgyeaPvalawgarNRsallRipa..skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyel 282
                                       pg+eaP++++w+ rNRsal+R+p+  ++++a r+E+R +d+s+NPYLa+Aa +aAgldGi++k+epg+pv +d+yel
  gi|488599757|ref|YP_007906228.1| 338 PGFEAPIYICWSPRNRSALVRVPMyvKSPSAVRLEYRGADPSCNPYLAFAAQVAAGLDGIKKKIEPGDPVMEDVYEL 414
                                       ***************************************************************************** PP

                                       -TTTH..TSS-B--SSHHHHHHHHHCSHHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 283 speer..kgieelPasleeAlealeedellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       sp +r  +gi elP++l++Al++l++de+l ++lg+++++a+++lk +E+++++ ++++we+ +y
  gi|488599757|ref|YP_007906228.1| 415 SPMKRkeLGIGELPTTLRDALDHLASDEVLIKTLGSHIFDAFMSLKYDEWNQYCLYITPWEILKY 479
                                       **999999*****************************************************9876 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.1   5.7e-26   5.1e-22       1      83 []      14      99 ..      14      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 5.7e-26
                                      T--EEEEEEE-SSS-EEEEEEEHHHH.HHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-...EEEE CS
                        Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadel.sedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek..ktarv 76
                                      +v++v + F Di+g l++++ipa+ + +++++e g++FDGSsi+gf +ie+SD++ +Pd+ t+ ++P+ +++  kta++
  gi|488599757|ref|YP_007906228.1| 14 NVRWVLCAFSDIRGFLQTFSIPAKVFmENSVFERGIGFDGSSIRGFRSIEKSDLVWMPDPATLKVIPWIDDPiqKTAIM 92
                                      689*******************999855999***************************************99*9***** PP

                                      EEEEE-T CS
                        Gln-synt_N 77 icdvydp 83
                                      + dv++p
  gi|488599757|ref|YP_007906228.1| 93 FGDVHEP 99
                                      ****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3087.59
//
Query:       gi|488599758|ref|YP_007906229.1|  [L=187]
Description: polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-29  102.0   0.0    3.1e-29  101.8   0.0    1.0  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.0   1.7e-33   3.1e-29       1     125 [.       2     163 ..       2     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 1.7e-33
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS....TCSSHHHHHHCT...........TES CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaaredpilhielrr...........wad 66 
                                       kki+++iTG+++ i++l+ll+kLk+ ++e++v++++ A  +++ e ++l++++d   h                ++d
  gi|488599758|ref|YP_007906229.1|   2 KKIVVAITGASGQIYGLRLLQKLKELDVETHVIVSNPAIITMKYEGVDLEDIKDLSDHFYSTSdissrlasgsfKHD 78 
                                       79*******************************************999999888888887755788889999***** PP

                                       EEEEEEEEHHHHHHHHTT--SSHH...........................HHHHHTHCCTTEEEEE.--HHCCTCS CS
                      Flavoprotein  67 llviaPasantlakianGiadnll...........................tlilratakkpiliaPamnpamyenp 116
                                       ++viaP++ nt + ia+Giadnl+                           + +l+  ++++++i+P + pa+y +p
  gi|488599758|ref|YP_007906229.1|  79 GMVIAPCTVNTASSIAYGIADNLIvrsadvtlkekrklillvretplheghLETLLKLSRMGTIIMP-PVPAFYIKP 154
                                       ***************************************************444544599*******.********* PP

                                       TCHHHHHHH CS
                      Flavoprotein 117 qtlknlekl 125
                                       + l +++++
  gi|488599758|ref|YP_007906229.1| 155 KHLTDIVDH 163
                                       ******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1329.05
//
Query:       gi|488599759|ref|YP_007906230.1|  [L=901]
Description: PGF-CTERM archaeal protein-sorting signal [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-09   37.8   5.6    2.6e-09   36.7   5.6    1.6  1  PGF-CTERM    PGF-CTERM motif
    0.00014   21.8  15.5    0.00027   20.9  15.5    1.4  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)
  ------ inclusion threshold ------
      0.019   15.1   0.3       0.68   10.1   0.0    3.3  3  V-set        Immunoglobulin V-set domain
      0.024   14.6   4.4        4.7    7.2   0.2    4.3  3  Y_Y_Y        Y_Y_Y domain
          2    7.4  17.8      0.051   12.7   0.3    3.8  4  DUF945       Bacterial protein of unknown function (DUF945)


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   5.6   7.4e-13   2.6e-09       2      23 .]     880     901 .]     879     901 .] 0.97

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 7.4e-13
                         PGF-CTERM   2 PGFGavlAlaGLLaaalLaRRr 23 
                                       PGF+a++A+aGLLa+a+L+RRr
  gi|488599759|ref|YP_007906230.1| 880 PGFEAIFAVAGLLAVAYLLRRR 901
                                       *********************9 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9  15.5   7.5e-08   0.00027      57     126 ..     827     895 ..     814     898 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.5e-08
                       Trypan_PARP  57 tdpepepepepepepepepepepetepeeepepepepepepepepepepepepepgaatlksvalpfaia 126
                                       t+p p p pe  p p p pe  p + pee+p p p  e  p p p  + ep+p pg  ++ +va  +a+a
  gi|488599759|ref|YP_007906230.1| 827 TKPTPTPTPEETPTPTPTPEKTPTPTPEETPTPTPTKEVTPTPTPT-KEEPQPGPGFEAIFAVAGLLAVA 895
                                       4444333333333333333333344666666666666666666665.569**********9**9999988 PP

>> V-set  Immunoglobulin V-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.1   7.4e+03      68      81 ..     322     335 ..     293     360 .. 0.62
   2 ?    0.8   0.0      0.16   5.6e+02      79      94 ..     359     374 ..     356     396 .. 0.77
   3 ?   10.1   0.0   0.00019      0.68      59      91 ..     532     564 ..     469     577 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.1
                                       GTTTEEEEEESSES CS
                             V-set  68 pskgdfsltiqnlt 81 
                                       +++g+fs+++++ +
  gi|488599759|ref|YP_007906230.1| 322 DDSGKFSVKFTDSE 335
                                       34566666666633 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                                       SESGGG-EEEEEEEEC CS
                             V-set  79 nltlsDsGtYtCavvp 94 
                                       nl++sD+++Y+ + v+
  gi|488599759|ref|YP_007906230.1| 359 NLKYSDEAVYNIEFVN 374
                                       899*******998533 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00019
                                       TTTEEEEEEGTTTEEEEEESSESGGG-EEEEEE CS
                             V-set  59 kgrfslrkdpskgdfsltiqnltlsDsGtYtCa 91 
                                        +++ l++++++ df +++++++  D+GtY++ 
  gi|488599759|ref|YP_007906230.1| 532 YNAYALPDNDNNLDFKIKVSDASGVDAGTYYLY 564
                                       57889999***********************87 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 ?    0.3   0.1      0.19   6.8e+02      37      50 ..     340     353 ..     313     363 .. 0.80
   2 ?    7.2   0.2    0.0013       4.7      35      65 ..     669     699 ..     667     700 .. 0.90
   3 ?    4.9   0.0    0.0071        25      30      47 ..     762     779 ..     735     783 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.19
                                       -SEEEEEEEEEEET CS
                             Y_Y_Y  37 ppGdYtlkVkakdn 50 
                                       + G Y++k++a++ 
  gi|488599759|ref|YP_007906230.1| 340 STGYYKIKIEAISY 353
                                       57899999999874 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                                       S--SEEEEEEEEEEETTS-B-SS-EEEEEEE CS
                             Y_Y_Y  35 nlppGdYtlkVkakdndgqwnyditslsfti 65 
                                        l+ G YtlkVk   n+++ ++ ++++ ++i
  gi|488599759|ref|YP_007906230.1| 669 KLSVGIYTLKVKLYYNNSEVDSATKTIPIEI 699
                                       5889***********9999999999999988 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0071
                                       EEEEES--SEEEEEEEEE CS
                             Y_Y_Y  30 easytnlppGdYtlkVka 47 
                                       +++   l +G+Yt++V+ 
  gi|488599759|ref|YP_007906230.1| 762 TFETLGLAAGKYTFYVRD 779
                                       555556899*******96 PP

>> DUF945  Bacterial protein of unknown function (DUF945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.13   4.5e+02     117     189 ..      36     112 ..      21     126 .. 0.78
   2 ?    3.5   1.2    0.0085        30     181     275 ..     252     357 ..     205     363 .. 0.85
   3 ?    0.9   0.7     0.054   1.9e+02     130     245 ..     390     516 ..     365     554 .. 0.60
   4 ?   12.7   0.3   1.4e-05     0.051     135     241 ..     599     717 ..     576     741 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.13
                            DUF945 117 deatkklfdklkgksP.....ltlttrvgysgstsseltlpafelkeeggklewsggkvkvdlskdlkklsgegnld 188
                                       d+a k  ++kl ++sP     l++++  +y  +++++ +++ +e++  + ++  + +++++d +k l+++++ ++l 
  gi|488599759|ref|YP_007906230.1|  36 DTALKVDLAKLSDDSPsygddLSIDVQWSYLDKVTGTRRIAVVEYTVYNSSIY-NATTGQIDTAKLLDEAKYVVSLS 111
                                       5556666777789999999999***********************33333333.68888999888888888877766 PP

                            DUF945 189 g 189
                                       +
  gi|488599759|ref|YP_007906230.1| 112 E 112
                                       5 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0085
                            DUF945 181 lsgegnldglkleadndeslelkgltlssdlkrgkeglyl......Gdsslkiasltvssedqega.....elknls 246
                                       +++++ ++ ++  +   + +++++l++s+ ++ +k+g  +      G++ + +  l+++++++ ++     +  ++s
  gi|488599759|ref|YP_007906230.1| 252 VTFQVVSPAIESVDIPATYVKFTDLKFSGVTNLQKTGSSYdmqvaeGQNIVVVRILDLNDNEKINKtvfvdDSGKFS 328
                                       45555555554333338999********9999999998888899******************9999999******** PP

                            DUF945 247 ldsssteegdllnstlkyslkslklngkd 275
                                       ++++ +e g + +++ k +++ +++n+ +
  gi|488599759|ref|YP_007906230.1| 329 VKFTDSEVGAFSTGYYKIKIEAISYNNVT 357
                                       *************************9865 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.054
                            DUF945 130 ksP.ltlttrvgysgstsseltlpafel..keeggklews.......ggkvkvdls..kdlkklsgegnldglklea 194
                                       +s  +t++t+++ +  +++ ++ p++     ++  ++           ++v ++++  + l++++++++++g ++++
  gi|488599759|ref|YP_007906230.1| 390 QSIkFTIDTNLKINKIVNFIIENPKIIGdtVNATRTF--VyavdalgDATVSITVAndAPLTTYTFKAEIPGTSVKD 464
                                       4444555555555555555555555555222222222..13355544344455555558899*************87 PP

                            DUF945 195 dndeslelkgltlssdlkrgkeglylGds.....slkiasltvssedqegaelknl 245
                                       +  +s+e+ + tl+++l +  + +  G+s     + + +++ ++ ++++++ +   
  gi|488599759|ref|YP_007906230.1| 465 E--VSVEVVKQTLNVSLDK--NVVTKGSSiritgTTTADRVYIYADEDDVFLFGTT 516
                                       7..9999999999988864..33444777777666667777777777776644444 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 1.4e-05
                            DUF945 135 lttrvgysgstsseltlpafelkeeggklewsggkvkvdlskdlkklsgegnldglkleadn......deslelkgl 205
                                        tt + y+g+++++++++ +++++++++++ +g+++kv  ++    + +++++dg++  + +       ++l+++  
  gi|488599759|ref|YP_007906230.1| 599 STTKIPYQGKVDIDVKVNVGDTSKAQVTFTLEGMNIKVGPADFGMAAFTSVDSDGIASFSLSlrdytgSSKLSVGIY 675
                                       6899*********************************9888555555555555555432222222445666666666 PP

                            DUF945 206 tlssdlkrgkeglylGds....slkiasltvssedqega..e 241
                                       tl+++l  ++++++  ++    ++   ++tv+ ++++++  +
  gi|488599759|ref|YP_007906230.1| 676 TLKVKLYYNNSEVDSATKtipiEIVKPEMTVTIKPDQPVtgD 717
                                       666666666665543333333333355666666666665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (901 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); 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:                         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: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 5352.65
//
Query:       gi|488599760|ref|YP_007906231.1|  [L=407]
Description: hypothetical protein Asulf_00204 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-06   27.0   0.8      2e-05   24.6   0.2    2.5  3  DUF357           Protein of unknown function (DUF357)
    6.1e-05   23.0   2.9       0.18   11.7   0.1    2.7  3  YfdX             YfdX protein
     0.0041   17.4   0.1     0.0041   17.4   0.1    3.3  3  PG_binding_4     Putative peptidoglycan binding domain
  ------ inclusion threshold ------
      0.012   15.4   1.3      0.023   14.5   1.3    1.4  1  SH3BP5           SH3 domain-binding protein 5 (SH3BP5)
      0.027   14.2   5.7      0.025   14.3   4.2    1.8  2  Tex_N            Tex-like protein N-terminal domain
      0.043   13.4   3.8      0.052   13.1   1.6    2.2  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.053   13.4   0.4       0.14   12.0   0.4    1.7  1  TarH             Tar ligand binding domain homologue
       0.12   12.6   2.2          8    6.7   0.1    2.6  2  TrbC             TrbC/VIRB2 family
        3.1    8.4  14.0       0.19   12.4   3.2    3.1  3  Com_YlbF         Control of competence regulator ComK, YlbF/Y
        4.6    7.1   6.9    1.4e+02    2.2   6.9    2.5  1  PCRF             PCRF domain
        5.5    7.5  10.8         15    6.0   0.7    3.9  4  FlaC_arch        Flagella accessory protein C (FlaC)
        6.1    5.6   7.5         21    3.9   3.8    2.2  2  LMBR1            LMBR1-like membrane protein


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 !   24.6   0.2   1.3e-08     2e-05       2      55 ..     166     222 ..     165     228 .. 0.76
   2 ?   -1.6   0.0       1.9   2.9e+03      30      51 ..     298     312 ..     271     321 .. 0.59
   3 ?   -2.2   0.0       3.1   4.6e+03       4      39 ..     333     367 ..     331     371 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHHHHH.......TS--.-HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                            DUF357   2 Yirlleealekvk.iap.deespl.geaaeevlemaesYleDakyflekgdlvnAla 55 
                                       Yi  l++++++++  a+  e+  + ++ a+++l++aesY++D+k+f++++++++A  
  gi|488599760|ref|YP_007906231.1| 166 YITSLTQKISELRkRADgLEKAGVsTATAKKYLDIAESYINDGKRFFNNEKYIEANT 222
                                       88888999999884344433444404556************************9965 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHTT-HH CS
                            DUF357  30 vlemaesYleDakyflekgdlv 51 
                                        +e+       ak ++++g ++
  gi|488599760|ref|YP_007906231.1| 298 KIEL-------AKDYIAQGLFE 312
                                       3444.......45555555555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHH.....TS---HHHHHHHHHHHHHHH CS
                            DUF357   4 rlleealekvkiapdeesplgeaaeevlemaesYle 39 
                                       ++l++ le +   ++ ++ + +   ++l+ + s+l+
  gi|488599760|ref|YP_007906231.1| 333 NNLKKELEGLM-PTPTKTAVATPTPNTLDKISSFLR 367
                                       67888888888.336667777777777777777775 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00012      0.18     103     147 ..     191     235 ..     178     237 .. 0.81
   2 !    9.1   0.2   0.00078       1.2      71     107 ..     295     331 ..     239     335 .. 0.60
   3 !   10.7   0.1   0.00025      0.37       4      46 ..     298     338 ..     296     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                       EEEEEEEHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHT-EEEE CS
                              YfdX 103 ittallPLatypaavkkAaelleegkyyeAkeaLkealntlvfvs 147
                                       + ta+  L+  +  +++  ++ +++ky eA++ L++a+++l+  +
  gi|488599760|ref|YP_007906231.1| 191 TATAKKYLDIAESYINDGKRFFNNEKYIEANTTLTNAEDNLIQAE 235
                                       4445555666788999************************99765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00078
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHTT-EEEEEEEE CS
                              YfdX  71 kkaaikkanellkkgdtqaArelLkllgseidittal 107
                                       k+++i+ a++ +++g +++A+ + + +++e+d  t+ 
  gi|488599760|ref|YP_007906231.1| 295 KNKKIELAKDYIAQGLFEDAIVIINSANNEVDKLTTD 331
                                       4455666666666666666666666666666655543 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-S-- CS
                              YfdX   4 diqkArlaldqgdtkeAkkllekAqgkleaaladdpklvkkap 46 
                                       +i+ A   ++qg  ++A+  +++A+++ +++ +d ++l k  +
  gi|488599760|ref|YP_007906231.1| 298 KIELAKDYIAQGLFEDAIVIINSANNEVDKLTTDVNNLKK--E 338
                                       7999********************************9933..2 PP

>> PG_binding_4  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.7e-06    0.0041      26      89 ..      38     102 ..      26     102 .. 0.94
   2 ?   -1.5   1.6         2   2.9e+03      18      43 ..     198     226 ..     184     266 .. 0.43
   3 ?    2.6   0.5      0.11   1.6e+02       2      61 ..     281     341 ..     280     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                      PG_binding_4  26 rkgnelerlsetiaawkevdlrvsldeeklkeyldeiakeidtepkdasfkl.kggsvkvspeky 89 
                                        k+n +++ se+++ ++e++++ + d  kl+e+  e+++e   +   a++++ +ggsv+ ++++y
  gi|488599760|ref|YP_007906231.1|  38 PKFNDFYKASEQVQFSIEIKPKTENDAVKLDERTYEFSTELTSPKIRATINYrNGGSVSYEGGEY 102
                                       589999*********99*****************************************9998875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                      PG_binding_4  18 vaealtygrkgnelerlsetiaawk...e 43 
                                       ++ a +y ++g+ + +  + i a+    +
  gi|488599760|ref|YP_007906231.1| 198 LDIAESYINDGKRFFNNEKYIEANTtltN 226
                                       55555555555554444444443322221 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.11
                      PG_binding_4   2 tikseelglay.di.eeyvaealtygrkgnelerlsetiaawkevd.lrvsldeeklkeylde 61 
                                        ik ee + +y  i +++++ a++y ++g  ++ ++++++a  +++ ++++ d + lk+ l+ 
  gi|488599760|ref|YP_007906231.1| 281 DIKFEEFKDTYkEIkNKKIELAKDYIAQGLFEDAIVIINSA--NNEvDKLTTDVNNLKKELEG 341
                                       5777888888865536889999*********9999999999..56668888888888887765 PP

>> SH3BP5  SH3 domain-binding protein 5 (SH3BP5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.3   1.5e-05     0.023      52     204 ..     186     338 ..     161     344 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                            SH3BP5  52 klgksvekarpYyearekakeaqkeaqkaaekferansahaaAketvalaeqslleeeertldkawqemLnhatqkV 128
                                       k g s  +a+ Y +  e   +  k+     ek+  an+ ++ A +++ +ae++l++ + ++   ++ + Ln+   k+
  gi|488599760|ref|YP_007906231.1| 186 KAGVSTATAKKYLDIAESYINDGKRFF-NNEKYIEANTTLTNAEDNLIQAENELNRIDAMNRLYKVEDKLNKVLDKI 261
                                       566777778888886655554444444.3689********************************************* PP

                            SH3BP5 129 neaeeekkeaeeehqrktkkleeaekkvqqlekklk.rsikkskpYfelk..aklnkqleeqkekveelekevkeaK 202
                                       ne ++     e  +++ t+k+    +++++  k++k ++i+ +k Y  +   +    ++++ +++v++l  +v++ K
  gi|488599760|ref|YP_007906231.1| 262 NEIDAI--LVELRKTTPTTKYDIKFEEFKDTYKEIKnKKIELAKDYIAQGlfEDAIVIINSANNEVDKLTTDVNNLK 336
                                       *87655..556666777888888888899999998878999999998765114444567999999999999999999 PP

                            SH3BP5 203 ae 204
                                       +e
  gi|488599760|ref|YP_007906231.1| 337 KE 338
                                       87 PP

>> 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 ?   -2.1   0.0       1.7   2.5e+03     113     151 ..     183     228 ..     175     240 .. 0.53
   2 ?   14.3   4.2   1.7e-05     0.025      47     150 ..     241     342 ..     225     371 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                             Tex_N 113 GLeplAelileqkslaeeeaakyvn........kevksaeealegar 151
                                       GLe+      + k+   + a++y+n        ++  +a+++l++a+
  gi|488599760|ref|YP_007906231.1| 183 GLEKAGVSTATAKKY-LDIAESYINdgkrffnnEKYIEANTTLTNAE 228
                                       555554444443332.4666666666644444434444444444444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.7e-05
                             Tex_N  47 ieerleylrelekrkeevlksieeqgklteeLkkkieaak...tleeledlylpYkpkrkTkatiArekGLeplAel 120
                                       i + +++l ++e++ ++vl++i+e + +  eL+k+  ++k   + ee +d y++ k+k+   a+  +++GL + A +
  gi|488599760|ref|YP_007906231.1| 241 I-DAMNRLYKVEDKLNKVLDKINEIDAILVELRKTTPTTKydiKFEEFKDTYKEIKNKKIELAKDYIAQGLFEDAIV 316
                                       4.5689999**************************9999822244555566666666666666666789******** PP

                             Tex_N 121 ileqkslaeeeaakyvnkevksaeealega 150
                                       i++  s+ ++e+ k  + +v++ +++leg+
  gi|488599760|ref|YP_007906231.1| 317 IIN--SA-NNEVDKL-TTDVNNLKKELEGL 342
                                       ***..43.5677777.67888888888876 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 ?   -2.2   0.0       1.9   2.8e+03     110     140 ..     152     182 ..     142     187 .. 0.69
   2 ?   13.1   1.6   3.5e-05     0.052      29      91 ..     276     340 ..     247     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.9
                     PI3K_P85_iSH2 110 dlkqqkeeereleReinalkpellqLqkrkd 140
                                       dlk ++ + +++   i++l   + +L+kr d
  gi|488599760|ref|YP_007906231.1| 152 DLKIKVVNPKLFGNYITSLTQKISELRKRAD 182
                                       6666777777777777788888888887766 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.5e-05
                     PI3K_P85_iSH2  29 kskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaq..ehEieklqenle 91 
                                        +++yd + ee++ + +ei+ k+  l     a  +Fe+ i ++++ ++e++   +++++l++ le
  gi|488599760|ref|YP_007906231.1| 276 PTTKYDIKFEEFKDTYKEIKNKKIELAKDYIAQGLFEDAIVIINSANNEVDklTTDVNNLKKELE 340
                                       4679**********************99999*************977766322444444444444 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   9.6e-05      0.14      48     150 ..     218     317 ..     208     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.6e-05
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHHHHHHHHHHHHHHTS---GGGHH.HHHHHHHH CS
                              TarH  48 lqqqaaLaearvsllqaRltLnragiaaladeaedakellaraeeslaqseeawkaYlalprtaeeeealaaelkak 124
                                       +++ ++L++a+++l qa + Lnr     +++   ++++ l+++ + ++++++   + ++++ t+ + +   +e+k+ 
  gi|488599760|ref|YP_007906231.1| 218 IEANTTLTNAEDNLIQAENELNR---IDAMNRLYKVEDKLNKVLDKINEIDAILVELRKTTPTT-KYDIKFEEFKDT 290
                                       567899*****************...77888888889999999999999**9999999999999.778899999999 PP

                                       HHH.HHHHHHHHHHHHHTT-HHHHHHS CS
                              TarH 125 yka.lqdglapliaaleagnleaffdl 150
                                       yk+  ++ ++ + +++++g +e+++ +
  gi|488599760|ref|YP_007906231.1| 291 YKEiKNKKIELAKDYIAQGLFEDAIVI 317
                                       999556666666678888888887754 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.019        29      10      33 ..       3      26 ..       1      40 [. 0.63
   2 ?    6.7   0.1    0.0054         8      28      65 ..     347     382 ..     341     396 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.019
                              TrbC 10 rlllalalalvllllaspalAqaa 33
                                      + +++l++++v++l+as ++A+++
  gi|488599760|ref|YP_007906231.1|  3 KITRVLITIAVIMLSASLSFAAET 26
                                      455666667777777777777655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0054
                              TrbC  28 alAqaaggdpvetvlqnivdfltgplakviatiaiiva 65 
                                          + a  +p+ + l++i +fl+ ++ k+++  +iiv+
  gi|488599760|ref|YP_007906231.1| 347 TKTAVA--TPTPNTLDKISSFLRENARKIAIYTGIIVL 382
                                       445555..8999************99888887666654 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 ?   12.4   3.2   0.00013      0.19      56      99 ..     222     264 ..     170     266 .. 0.87
   2 ?    2.0   1.0       0.2   3.1e+02      16      50 ..     289     323 ..     282     343 .. 0.62
   3 ?   -0.9   0.0       1.7   2.5e+03      30      49 ..     321     340 ..     318     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                       ----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  56 eelkeeekkelqelkeeldknplvkeyleaeqelnellqevnki 99 
                                         l+++e+ +l ++++el+ ++ ++++++ e++ln++l+++n+i
  gi|488599760|ref|YP_007906231.1| 222 TTLTNAED-NLIQAENELNRIDAMNRLYKVEDKLNKVLDKINEI 264
                                       57889999.*********************************97 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  16 eeykeykeaeealeedeelqklikefkklqkelqe 50 
                                       + yke k+ + +l +d  +q l+++   + +++++
  gi|488599760|ref|YP_007906231.1| 289 DTYKEIKNKKIELAKDYIAQGLFEDAIVIINSANN 323
                                       56888888888888888888888776655554444 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.7
                                       CSHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  30 edeelqklikefkklqkelq 49 
                                       ++ e+ kl +++++l+kel+
  gi|488599760|ref|YP_007906231.1| 321 ANNEVDKLTTDVNNLKKELE 340
                                       67777788888888887775 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   6.9     0.094   1.4e+02      29      90 ..     249     343 ..     166     352 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.094
                                       HHHHHTHHHHHHHHHHHHHTTTHHH...HT.......-S-..-GG..............................GT CS
                              PCRF  29 kelaeleeivealeeleealedleeakelleed...eelaelaee..............................el 72 
                                       k   +l++++++++e+++ l +l++++   + d   ee+++  +e                              e+
  gi|488599760|ref|YP_007906231.1| 249 KVEDKLNKVLDKINEIDAILVELRKTTPTTKYDikfEEFKDTYKEiknkkielakdyiaqglfedaiviinsannEV 325
                                       44444444444444444444444443333322200011111111122222222333333333333444443333377 PP

                                       HHHHHHHHHH..HHHHHT CS
                              PCRF  73 eelekeleeleeelkklL 90 
                                       ++l++++++l++el+ l+
  gi|488599760|ref|YP_007906231.1| 326 DKLTTDVNNLKKELEGLM 343
                                       777777777777777665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.7   4.1e+03      25      39 ..     120     134 ..     112     148 .. 0.66
   2 ?   -1.2   0.0       1.9   2.8e+03      16      34 ..     167     185 ..     163     187 .. 0.70
   3 ?    6.0   0.7      0.01        15       6      35 ..     235     266 ..     231     273 .. 0.90
   4 ?    5.9   0.1     0.011        17       3      26 ..     319     342 ..     318     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.7
                         FlaC_arch  25 elsksveelkenVkd 39 
                                       e+s +v e+++++++
  gi|488599760|ref|YP_007906231.1| 120 EVSGKVPEVDKRIEE 134
                                       555556666666544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                         FlaC_arch  16 letvkkeneelsksveelk 34 
                                       ++++ ++++el+k  + l+
  gi|488599760|ref|YP_007906231.1| 167 ITSLTQKISELRKRADGLE 185
                                       5667777788887777666 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.01
                         FlaC_arch   6 Enklsklst..eletvkkeneelsksveelke 35 
                                       En+l++++   +l  v+++++++ ++++e++ 
  gi|488599760|ref|YP_007906231.1| 235 ENELNRIDAmnRLYKVEDKLNKVLDKINEIDA 266
                                       9*******9899***************99985 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.011
                         FlaC_arch   3 delEnklsklsteletvkkeneel 26 
                                       ++  n+++kl t ++++kke+e l
  gi|488599760|ref|YP_007906231.1| 319 NSANNEVDKLTTDVNNLKKELEGL 342
                                       556799999999999999999866 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.8     0.014        21     221     328 ..     179     289 ..     162     323 .. 0.64
   2 ?    2.8   0.1      0.03        44     160     197 ..     367     401 ..     347     407 .] 0.63

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.014
                             LMBR1 221 reledllkevkklrksisesdplrkyleeilkkvPeeiaeklksnenkteeslaklekql..ikalqkrertekqwk 295
                                       ++ + l k+   + + +++ d  ++y+++  + +++e   +++++ +++e++l++ e++l  i a+++  + e++++
  gi|488599760|ref|YP_007906231.1| 179 KRADGLEKAGVSTATAKKYLDIAESYINDGKRFFNNEKYIEANTTLTNAEDNLIQAENELnrIDAMNRLYKVEDKLN 255
                                       333322233333333333333345666666667777777777779999999*9999988722568************ PP

                             LMBR1 296 rllekalelediiknksskekefksses.srrge 328
                                       + l+k+ e+ +i+ +  ++    k   + ++ + 
  gi|488599760|ref|YP_007906231.1| 256 KVLDKINEIDAILVELRKTTPTTKYDIKfEEFKD 289
                                       ******9999888665555544444444444444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.03
                             LMBR1 160 lpilislantwGlvllilllGyGlvelPrslwreiksd 197
                                        + +  +a   G+++l++ +Gy+l ++ ++ +r  k++
  gi|488599760|ref|YP_007906231.1| 367 RENARKIAIYTGIIVLLIAIGYALSRI-IKAYR--KRK 401
                                       444444455568888888888888888.66666..444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1762  (0.0982765); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); 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):              12  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 2402.85
//
Query:       gi|488599761|ref|YP_007906232.1|  [L=199]
Description: iron (metal) dependent repressor, DtxR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-25   86.7   1.0      3e-24   85.0   1.3    1.8  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    2.9e-19   68.9   1.3    7.3e-19   67.6   0.5    2.1  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    0.00014   21.7   0.0    0.00029   20.7   0.0    1.5  1  MarR            MarR family
    0.00035   20.2   0.1    0.00087   18.9   0.1    1.7  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
    0.00077   19.0   0.1     0.0029   17.1   0.0    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0008   19.2   0.0      0.003   17.4   0.0    1.9  2  MarR_2          MarR family
     0.0012   19.1   0.0     0.0036   17.6   0.0    1.8  1  Rrf2            Transcriptional regulator
     0.0013   18.7   0.0      0.017   15.1   0.1    2.5  2  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
     0.0031   17.7   0.3      0.035   14.3   0.2    2.2  2  Rio2_N          Rio2, N-terminal
     0.0059   16.6   0.6       0.01   15.8   0.6    1.4  1  HTH_45          Winged helix-turn-helix
     0.0067   16.2   0.0      0.015   15.1   0.0    1.6  2  HTH_IclR        IclR helix-turn-helix domain
     0.0096   15.0   0.1      0.014   14.4   0.1    1.2  1  Topoisom_bac    DNA topoisomerase
  ------ inclusion threshold ------
      0.027   14.3   0.1       0.19   11.5   0.0    2.3  2  HTH_10          HTH DNA binding domain
      0.027   14.3   0.8      0.051   13.4   0.1    1.8  2  TFIIE_alpha     TFIIE alpha subunit
      0.028   14.2   0.7      0.054   13.2   0.7    1.4  1  DUF2284         Predicted metal-binding protein (DUF2284)
      0.037   14.1   0.8       0.12   12.5   0.2    2.2  3  Sigma70_r3      Sigma-70 region 3
      0.039   13.9   1.2      0.067   13.1   0.2    2.1  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.057   13.4   0.0       0.17   11.9   0.0    1.8  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.058   13.3   0.0       0.16   11.9   0.0    1.7  1  CtsR            CtsR N-terminal HTH domain
      0.084   12.5   0.0       0.17   11.6   0.0    1.6  1  GntR            Bacterial regulatory proteins, gntR family
       0.11   13.0   0.0       0.22   12.0   0.0    1.5  1  HTH_27          Winged helix DNA-binding domain
        0.3   11.0   0.0        0.3   11.0   0.0    2.5  3  HTH_5           Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   1.3   3.7e-27     3e-24       3      60 .]       5      63 ..       4      63 .. 0.98
   2 ?   -2.6   0.0       8.2   6.7e+03      28      41 ..     155     168 ..     144     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 3.7e-27
                                      -HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  3 vestEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      ve+ E+YLe+IY+++e ++  vkt++la+ L+v+pssV+em+ kL++ Gyv+y++y+g+
  gi|488599761|ref|YP_007906232.1|  5 VERVEEYLEAIYDIQEsSNRLVKTTELAKKLDVKPSSVTEMILKLKDSGYVDYQPYRGV 63
                                      689******************************************************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.2
                                       HHHHHTS-HHHHHH CS
                    Fe_dep_repress  28 laerLnvspssVse 41 
                                       + + L+++p ++ +
  gi|488599761|ref|YP_007906232.1| 155 IVRNLGIAPNTIIQ 168
                                       66789999998766 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 !   67.6   0.5     9e-22   7.3e-19       1      64 [.      66     131 ..      66     136 .. 0.91
   2 ?   -1.9   0.0       4.4   3.6e+03      39      52 ..     178     191 ..     175     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 9e-22
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT..-.SB-TT CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellg..fpeecPh 64 
                                       T+kG  +Akr++++h++ e+f++++lg+++ee h+ +++lEh++s+e++e+++ +++   ++ c +
  gi|488599761|ref|YP_007906232.1|  66 TKKGYDVAKRIKKYHKIFETFFTEFLGLNEEESHNLSCELEHHVSDEVAEKICMIVSssDCKICEE 131
                                       99****************************************************998555555654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                                       CCGGGS-HHHHHHH CS
                     Fe_dep_repr_C  39 rlEhalseelierl 52 
                                        +E  ls+el  ++
  gi|488599761|ref|YP_007906232.1| 178 DMEFELSDELKSKI 191
                                       69999999997776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.6e-07   0.00029      19      48 ..      27      56 ..      11      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.6e-07
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 19 svseLakklgvskstvtrvldrLekkGlie 48
                                      + +eLakkl v++s+vt+++ +L + G+++
  gi|488599761|ref|YP_007906232.1| 27 KTTELAKKLDVKPSSVTEMILKLKDSGYVD 56
                                      678************************996 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.1e-06   0.00087       7      72 ..       9      72 ..       5      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                      HrcA_DNA-bdg  7 keilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayea 72
                                      +e l+a+ ++++ ++r vK++e+A++l+ ++  v  ++  Lk  g v+ +  P  G + t k y++
  gi|488599761|ref|YP_007906232.1|  9 EEYLEAIYDIQESSNRLVKTTELAKKLDVKPSSVTEMILKLKDSGYVDYQ--PYRGVMLTKKGYDV 72
                                      678999***************************************99976..45666667666665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.5e-06    0.0029      20      47 ..      28      55 ..      18      56 .. 0.91
   2 ?   -2.4   0.0       4.6   3.8e+03      25      34 ..     157     166 ..     155     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.5e-06
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGlI 47
                                       +eLA++l++ ps v++ + +L+++G++
  gi|488599761|ref|YP_007906232.1| 28 TTELAKKLDVKPSSVTEMILKLKDSGYV 55
                                      68*************************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                            HTH_24  25 erlglSpstv 34 
                                       + lg+ p+t+
  gi|488599761|ref|YP_007906232.1| 157 RNLGIAPNTI 166
                                       6799999997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.7e-06     0.003      23      55 ..      27      59 ..      11      62 .. 0.87
   2 ?   -1.5   0.0       2.8   2.3e+03      22      37 ..     150     165 ..     138     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverrp 55
                                        +ela++l++++s+v+ ++ +L + G+v ++p
  gi|488599761|ref|YP_007906232.1| 27 KTTELAKKLDVKPSSVTEMILKLKDSGYVDYQP 59
                                      568**************************9886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                                       EEHHHHHHHHTSSHHH CS
                            MarR_2  22 ltvgelarrlglsksa 37 
                                       l++  ++r lg+ + +
  gi|488599761|ref|YP_007906232.1| 150 LAAPTIVRNLGIAPNT 165
                                       5888899999998866 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.4e-06    0.0036      11      59 ..      12      59 ..       5      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      l a++++++ +++  v+++e+a++ +++ps +  ++ kL+ +g+v  + 
  gi|488599761|ref|YP_007906232.1| 12 LEAIYDIQESSNRL-VKTTELAKKLDVKPSSVTEMILKLKDSGYVDYQP 59
                                      56777777777765.******************************8775 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.1e-05     0.017       7      44 ..       5      42 ..       3      43 .. 0.95
   2 ?   -0.0   0.0       1.1   9.2e+02       6      19 ..      72      85 ..      71      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHHHHHHHHHHTT--EE-HHHHHHHCTS-HHHH CS
                    Put_DNA-bind_N  7 ikRLplYlryLeelkeegveriSSteLaealgvtaaqv 44
                                      ++R   Yl+++ +++e+    +  teLa++l+v+++ v
  gi|488599761|ref|YP_007906232.1|  5 VERVEEYLEAIYDIQESSNRLVKTTELAKKLDVKPSSV 42
                                      7999*******************************987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                                      HHHHHHHHHHHHHH CS
                    Put_DNA-bind_N  6 tikRLplYlryLee 19
                                      + kR   Y+++ e+
  gi|488599761|ref|YP_007906232.1| 72 VAKRIKKYHKIFET 85
                                      789******99876 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   4.3e-05     0.035      21      73 ..      22      72 ..      11      74 .. 0.90
   2 ?    0.9   0.0      0.66   5.4e+02       9      56 ..     147     194 ..     143     199 .] 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                            Rio2_N 21 nhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDy 73
                                      + ++V t+++++   +k ++v++ + +l + + + ++  +y G  Lt +GyD+
  gi|488599761|ref|YP_007906232.1| 22 SNRLVKTTELAKKLDVKPSSVTEMILKLKDSGYVDYQ--PYRGVMLTKKGYDV 72
                                      567899999999999********************99..8************7 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.66
                            Rio2_N   9 frvLtavEmgmrnhevVptelieeisr.lkeeevkkrlsrllkaklisr 56 
                                       + vL a  +  rn  + p + i+++   ++ ++++  ls+ lk k++++
  gi|488599761|ref|YP_007906232.1| 147 YEVLAA-PTIVRNLGIAPNTIIQKVGDtVRVNDMEFELSDELKSKILVK 194
                                       556544.466799999999999999862558899999999888888766 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   1.2e-05      0.01       6      75 ..      13      82 ..      10      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                            HTH_45  6 eIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlelleklkeleel 75
                                      e i+dI e+  +   k T++ +k + + + + +++ +L + g+++       +lT+kG ++ +++k+++++
  gi|488599761|ref|YP_007906232.1| 13 EAIYDIQESS-NRLVKTTELAKKLDVKPSSVTEMILKLKDSGYVDYqPYRGVMLTKKGYDVAKRIKKYHKI 82
                                      6788998876.889999***************************65388999***************9987 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   1.9e-05     0.015      19      52 .]      26      59 ..      17      59 .. 0.87
   2 ?   -3.2   0.0       9.5   7.8e+03      23      34 ..     154     165 ..     147     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      ++ +elA+++++ +S+v  ++  L   Gyv +++
  gi|488599761|ref|YP_007906232.1| 26 VKTTELAKKLDVKPSSVTEMILKLKDSGYVDYQP 59
                                      4789**************************9875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.5
                                       HHHHHHTS-HHH CS
                          HTH_IclR  23 elArrtglpkSt 34 
                                        + r++g+++ t
  gi|488599761|ref|YP_007906232.1| 154 TIVRNLGIAPNT 165
                                       578899988776 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.7e-05     0.014     343     392 ..      39      89 ..      27      92 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                      Topoisom_bac 343 paTraeiieklvergYverkk.kslvptelGkalvellekfkdlvspelTa 392
                                       p++  e+i kl+++gYv+ +  + ++ t++G  +++ ++k++++ +  +T 
  gi|488599761|ref|YP_007906232.1|  39 PSSVTEMILKLKDSGYVDYQPyRGVMLTKKGYDVAKRIKKYHKIFETFFTE 89 
                                       8999****************99*****************9****9998885 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.19      22      46 ..      24      48 ..      21      52 .. 0.88
   2 ?   -0.6   0.0       1.5   1.2e+03      32      41 ..     158     167 ..     154     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrk 46
                                      R v++ eLAk+l++++s+++e + k
  gi|488599761|ref|YP_007906232.1| 24 RLVKTTELAKKLDVKPSSVTEMILK 48
                                      7799****************98865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                            HTH_10  32 elGIskstls 41 
                                        lGI+++t+ 
  gi|488599761|ref|YP_007906232.1| 158 NLGIAPNTII 167
                                       69*****985 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.3e-05     0.051      26      63 ..      24      61 ..       7      85 .. 0.85
   2 ?   -2.1   0.0       4.2   3.4e+03      19      47 ..     167     195 ..     153     198 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                                      TSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEE CS
                       TFIIE_alpha 26 gevteedlakelkidlnelrklLnrLyearlvkykrrr 63
                                        v+  +lak+l +++  + +++ +L++ + v+y+  r
  gi|488599761|ref|YP_007906232.1| 24 RLVKTTELAKKLDVKPSSVTEMILKLKDSGYVDYQPYR 61
                                      458889****************************8665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.2
                                       HHHHHCTTSEBHHHHHHHHTS-HHHHHHH CS
                       TFIIE_alpha  19 ldvLlekgevteedlakelkidlnelrkl 47 
                                       ++ +   + v++ + +   +++ ++l kl
  gi|488599761|ref|YP_007906232.1| 167 IQKVGDTVRVNDMEFELSDELKSKILVKL 195
                                       44455555555555555555555555555 PP

>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   6.6e-05     0.054      60     111 ..      72     133 ..      56     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                           DUF2284  60 ledeedd.........keemkevkeelekillelekeafeagypk.alalsagsCtlCetCa 111
                                       ++++ ++         +e +   +ee +++++ele+++ ++  +k ++++s+  C++Ce+C 
  gi|488599761|ref|YP_007906232.1|  72 VAKRIKKyhkifetffTEFLGLNEEESHNLSCELEHHVSDEVAEKiCMIVSSSDCKICEECD 133
                                       4444444445555554455556678899**********9998888357788899*******7 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.53   4.3e+02      30      43 ..       1      14 [.       1      19 [. 0.86
   2 ?   12.5   0.2   0.00015      0.12       2      46 ..       7      51 ..       6      58 .. 0.86
   3 ?   -2.4   0.0       6.3   5.1e+03      16      31 ..     104     118 ..      96     121 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.53
                                      HTXXHHHHHHHHHH CS
                        Sigma70_r3 30 LglseekVrevlea 43
                                      + +s+e+V+e+lea
  gi|488599761|ref|YP_007906232.1|  1 MTWSVERVEEYLEA 14
                                      5689********97 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00015
                                      HHHHHHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXX CS
                        Sigma70_r3  2 klnkikraqreLeqelgrePtpeEiAeeLglseekVrevleaare 46
                                      +  ++ +a+  +++  +r  +++E+A++L++ ++ V e++   ++
  gi|488599761|ref|YP_007906232.1|  7 RVEEYLEAIYDIQESSNRLVKTTELAKKLDVKPSSVTEMILKLKD 51
                                      5677889999999999**********************9876655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.3
                                       HHSSXXXHHHHHHHHT CS
                        Sigma70_r3  16 elgrePtpeEiAeeLg 31 
                                       el+++ + +E+Ae+  
  gi|488599761|ref|YP_007906232.1| 104 ELEHHVS-DEVAEKIC 118
                                       5555544.57888765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   8.2e-05     0.067      24      58 ..      27      61 ..      17      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-05
                                      HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      +++e+a++l+v  s+v e++ +L+d G+V+ ++ r
  gi|488599761|ref|YP_007906232.1| 27 KTTELAKKLDVKPSSVTEMILKLKDSGYVDYQPYR 61
                                      689**************************988755 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   0.0    0.0002      0.17      22      55 ..      26      60 ..       6      69 .. 0.79
   2 ?   -2.2   0.0       5.1   4.1e+03      50      63 ..     166     180 ..     163     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis.rgr 55
                                      +  +elA  l + +++v+ ++ +Lk+ g+++ + +
  gi|488599761|ref|YP_007906232.1| 26 VKTTELAKKLDVKPSSVTEMILKLKDSGYVDyQPY 60
                                      56789*************************95323 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                                       SEE.ETEEEEES-HH CS
                         HTH_Crp_2  50 lis.rgrririldle 63 
                                       +i+  g ++r++d+e
  gi|488599761|ref|YP_007906232.1| 166 IIQkVGDTVRVNDME 180
                                       7885473399*9997 PP

>> CtsR  CtsR N-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.16       4      41 ..       6      43 ..       4      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                              CtsR  4 dlieeyikelleeseeeeveikRnelaekfecvPsQin 41
                                      + +eey++ + + +e+++  +k +ela+k+++ Ps ++
  gi|488599761|ref|YP_007906232.1|  6 ERVEEYLEAIYDIQESSNRLVKTTELAKKLDVKPSSVT 43
                                      679********99999999****************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 ?   11.6   0.0   0.00021      0.17      28      62 ..      29      63 ..       7      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                       eLa++++V+ ++v e + +L+  g+v  ++ rG+
  gi|488599761|ref|YP_007906232.1| 29 TELAKKLDVKPSSVTEMILKLKDSGYVDYQPYRGV 63
                                      69**************************9999997 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   0.00027      0.22      16      52 ..      23      59 ..      10      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                      +r +k ++l+++l+v  s++ +++ kL   G+v  ++
  gi|488599761|ref|YP_007906232.1| 23 NRLVKTTELAKKLDVKPSSVTEMILKLKDSGYVDYQP 59
                                      344556***************************4433 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037       0.3      17      47 .]      27      57 ..      22      57 .. 0.93
   2 ?   -2.7   0.5       6.9   5.6e+03       7      20 ..     117     130 ..     115     133 .. 0.74
   3 ?   -3.2   0.1       9.8   7.9e+03       1      12 [.     185     196 ..     185     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVek 47
                                      + +ela++l++ +s v +   kL+++G+V++
  gi|488599761|ref|YP_007906232.1| 27 KTTELAKKLDVKPSSVTEMILKLKDSGYVDY 57
                                      578**************************86 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.9
                                       HHHHHTTSSEEHHH CS
                             HTH_5   7 ILklLaegelcvce 20 
                                       I ++++++ +++ce
  gi|488599761|ref|YP_007906232.1| 117 ICMIVSSSDCKICE 130
                                       55667778888887 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 9.8
                                       SHHHHHHHHHHT CS
                             HTH_5   1 dptRlkILklLa 12 
                                       d+ ++kIL  L 
  gi|488599761|ref|YP_007906232.1| 185 DELKSKILVKLI 196
                                       677889998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1472.38
//
Query:       gi|488599762|ref|YP_007906233.1|  [L=393]
Description: hypothetical protein Asulf_00206 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-93  312.3   0.0    4.4e-93  312.0   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    2.9e-31  107.6   0.0    7.5e-31  106.3   0.0    1.7  2  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 !  312.0   0.0     5e-97   4.4e-93       2     270 .]      13     277 ..      12     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 312.0 bits;  conditional E-value: 5e-97
                             Nre_N   2 cglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediik 78 
                                       cg+k+cp+l+k++ +++   +  + ele  +pPsvfVGr gYPkV vgpl++ + +++++ldsp kw + +++d+i+
  gi|488599762|ref|YP_007906233.1|  13 CGRKECPLLKKFSFLKSFDIR--EGELEKPTPPSVFVGRIGYPKVFVGPLIALNPENPEYLDSPWKW-SGKVDDVIA 86 
                                       **************9996555..5*******************************************.6789***** PP

                             Nre_N  79 lrlslvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkv 154
                                       lr+sl+rg k+++v++ak +d++l++iqe++ s kpvd+++e+ +   +k  fd++++P+G+sa+++ l++aenpk+
  gi|488599762|ref|YP_007906233.1|  87 LRMSLLRGMKTMSVDSAKnPDRFLTNIQEMTASIKPVDLSTEVGRV-VRKEVFDDTVQPMGMSARIKALELAENPKI 162
                                       *****************999***********************999.78889************************* PP

                             Nre_N 155 prkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpei 231
                                       pr+ve+l++D dl+A++av +L+++g+++y++q++LS+G+LG +++rr+VPTrWsITA++di+g+++k+ei++++++
  gi|488599762|ref|YP_007906233.1| 163 PRRVENLYYD-DLSAANAVRYLFDHGFSTYYLQKILSIGMLGYQSRRRIVPTRWSITAIHDILGEQIKREIAEFESL 238
                                       **********.****************************************************************** PP

                             Nre_N 232 devevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       dev +fs+e++gN+f +i+ Pg++sf+l+E+w+++s+w+
  gi|488599762|ref|YP_007906233.1| 239 DEVLLFSYEHFGNHFEIIISPGDYSFQLIEIWMRKSFWS 277
                                       **************************************6 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.1   9.4e+03      63      78 ..     228     243 ..     222     252 .. 0.76
   2 !  106.3   0.0   8.4e-35   7.5e-31       3     110 .]     290     392 ..     288     392 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                             Nre_C  63 lekkpkefesleeale 78 
                                       ++++ +efesl+e+l 
  gi|488599762|ref|YP_007906233.1| 228 IKREIAEFESLDEVLL 243
                                       5677889999999875 PP

  == domain 2  score: 106.3 bits;  conditional E-value: 8.4e-35
                             Nre_C   3 yegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealee 79 
                                         ++++ys+++G+Yyaarl+vle+L+ki+r+ +++v+reitpeY+aP+GvW+v e+vrka++ +p +f+s+ +a+e 
  gi|488599762|ref|YP_007906233.1| 290 LARKRGYSPLSGGYYAARLPVLEYLRKIRRKGRILVIREITPEYYAPLGVWVVEEGVRKAMN-NPVRFDSFPSAVEV 365
                                       67899********************************************************7.799*********** PP

                             Nre_C  80 vseklklplkkllkkskllkelkkqktLddF 110
                                       +++++k+p + +  k ++++++  q +L++F
  gi|488599762|ref|YP_007906233.1| 366 ACKRIKTPYNFW--KDRIVRSF--QVSLENF 392
                                       *********999..55677776..6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2306.06
//
Query:       gi|488599763|ref|YP_007906234.1|  [L=398]
Description: methionine adenosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-180  599.9   4.7   2.1e-180  599.7   4.7    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.044   13.8   0.0       0.13   12.3   0.0    1.7  1  DUF3963          Protein of unknown function (DUF3963)


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 !  599.7   4.7  2.3e-184  2.1e-180       1     396 []       2     394 ..       2     394 .. 0.99

  Alignments for each domain:
  == domain 1  score: 599.7 bits;  conditional E-value: 2.3e-184
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       +ni +ee+ ++p+eeq++EivErKGiGHPDs+aDgiaea+sralskeyl+++g +lhhn+D++++vaG+s+p+fgGG
  gi|488599763|ref|YP_007906234.1|   2 KNIFIEEIVHTPIEEQQIEIVERKGIGHPDSLADGIAEAMSRALSKEYLKRCGYVLHHNTDETQIVAGRSNPQFGGG 78 
                                       69*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BE CS
                   AdoMet_Synthase  78 eviepieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevpla 154
                                       e+iepi++ll+gratk+++g  ip+++i+l+aakey+k+++++l++e+d+++dv++g+gs+dLkdvf+r+k  vp++
  gi|488599763|ref|YP_007906234.1|  79 EIIEPIYVLLVGRATKQFDGVYIPADRIVLKAAKEYVKNSMQNLNPETDIVFDVRIGEGSTDLKDVFQRSKG-VPHS 154
                                       *********************************************************************877.9*** PP

                                       SSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHH CS
                   AdoMet_Synthase 155 NDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevke 231
                                       NDtSfg+g+aplse+e++v+++er + + e++kk+p++GeD+KvmglRek+ i+lT+a+a+vdr+v d++eY+++ke
  gi|488599763|ref|YP_007906234.1| 155 NDTSFGIGFAPLSETERVVYNVERRIYN-EFRKKNPAIGEDVKVMGLREKDMINLTIACAFVDRYVGDIREYIAIKE 230
                                       **************************95.9*********************************************** PP

                                       HHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-T CS
                   AdoMet_Synthase 232 eikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNP 308
                                       e+++ ve++++++t+ r+v v++NtaD++++++vyltvtGtsaE+gDdGsvGRGNR+nGlitp+rpms+EA++GKNP
  gi|488599763|ref|YP_007906234.1| 231 ELQQFVEDIITEYTE-RKVVVNINTADDYDNKVVYLTVTGTSAENGDDGSVGRGNRANGLITPSRPMSMEATSGKNP 306
                                       ***************.************************************************************* PP

                                       TT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-H CS
                   AdoMet_Synthase 309 vsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideeleki 385
                                       ++HvGKiYn+lan+ia+++v+ veg+ke+yv++lsqiGkpid+P ++s+qvi+ekg+sl+++e++++ +++e+l++i
  gi|488599763|ref|YP_007906234.1| 307 INHVGKIYNLLANRIANDCVSAVEGIKEIYVKILSQIGKPIDDPYALSIQVIPEKGYSLDKMESRIRFVAEEWLSDI 383
                                       ***************************************************************************** PP

                                       HHHHHHHTTT- CS
                   AdoMet_Synthase 386 eeiteeliegk 396
                                       ++ite++i+g+
  gi|488599763|ref|YP_007906234.1| 384 TKITEMVINGE 394
                                       ********996 PP

>> DUF3963  Protein of unknown function (DUF3963)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05      0.13       2      20 ..     208     226 ..     207     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                           DUF3963   2 LsiyaiFiEkYFgDiqKWi 20 
                                       L+i  +F+++Y gDi  +i
  gi|488599763|ref|YP_007906234.1| 208 LTIACAFVDRYVGDIREYI 226
                                       8**************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2437.23
//
Query:       gi|488599764|ref|YP_007906235.1|  [L=85]
Description: hypothetical protein Asulf_00208 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.8   3.0      0.039   14.0   3.0    1.4  1  Mst1_SARAH  C terminal SARAH domain of Mst1


Domain annotation for each model (and alignments):
>> Mst1_SARAH  C terminal SARAH domain of Mst1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.0   2.2e-06     0.039       1      29 [.      48      76 ..      48      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-06
                        Mst1_SARAH  1 fefLkflsvdeLqqrlasLDpeMEqEiee 29
                                      +e++ +l+++e ++r++++ ++ E+Eie+
  gi|488599764|ref|YP_007906235.1| 48 YEIVEELTLEEIEKRVKEIEKKVEKEIEK 76
                                      688999*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2182  (0.121702); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 551.56
//
Query:       gi|488599765|ref|YP_007906236.1|  [L=243]
Description: hypothetical protein Asulf_00209 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-34  119.5   0.0    1.9e-34  119.3   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 !  119.3   0.0     1e-38   1.9e-34       3     234 ..       6     241 ..       4     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 1e-38
                                       STCTSSSCTTSSSE..E...EEEEEEEEEEE-HHHHHTTSBTTEEECSTSEEEEEEEEEEEECTTTC.......... CS
                               ADC   3 Plaitpsgksalvp..y...naealtvsyrtdpeaaaallPepLelaerplvavyfaeypdssfggg.......... 64 
                                       Pl  t+ g+salvp  +     +a+ v+   +p++++ +    L+ +  ++ ++yfa++ ++s ++           
  gi|488599765|ref|YP_007906236.1|   6 PL--TKFGRSALVPegPwsyAFDAIAVHAVANPDRLKNI--TELKTD--GEMWIYFADIISHSPNFPqlnyetpqlv 76 
                                       66..788999999976366799*************9999..789999..8***************99********** PP

                                       EEEEEEEEEEEEETTEEEEEEEEEEESSHHHHHHHHHHTT--EEE-EEEEEE.....ETTEEEEEEEETTEEEEEEE CS
                               ADC  65 qYneagivvpvryggkegayilvlwvdkeaalaaGRElwGfPKklAditltr.....egdtlggtverggkrlaelt 136
                                       qY+e++++++ +++gk++ay+++++vd++ +l++G  + GfPKk+A+i +tr     +++ +g+++ r g+ l++++
  gi|488599765|ref|YP_007906236.1|  77 QYKEVAFFIKIEFEGKSYAYCPFMYVDNDVSLMRGY-IVGFPKKIASIGITRdhplmKQKIFGANAMRAGYSLIRAK 152
                                       ************************************.**************************************** PP

                                       EEEEEEE-HHHHHHHHHTS.EEEEEEEEE-TTSTSEEEEEEEEEEEEEEEEEEEEEEEEEEEE-SSTTCCGGGSCCS CS
                               ADC 137 velkerapddeealpslka.ptfllkiipsvdggkadvtelvryelsdtrvgeawtGpaslelepsaddpladlpvl 212
                                       ve++e+a    ++lp +++ +++l ++i +  g    + el++   + ++   +++G+a+le+++ ++d+l+ ++++
  gi|488599765|ref|YP_007906236.1| 153 VEVEEKA----KSLPLDNFgTWILRRYI-GLMG----IDELIEFVPEVEYE-YIYRGKATLEIGGGINDELEFFKPE 219
                                       *******....9****999555555555.4344....9*********9998.************************* PP

                                       EEEEEEEEEEEEEEEEEEEEEE CS
                               ADC 213 evlsayyikadltvgggevled 234
                                       ++l +y ++a l+v++++vl++
  gi|488599765|ref|YP_007906236.1| 220 KILEGYRYSALLKVKDIRVLKS 241
                                       ******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1674.21
//
Query:       gi|488599766|ref|YP_007906237.1|  [L=780]
Description: replicative DNA polymerase I [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-78  264.5   0.0    2.4e-78  263.9   0.0    1.3  1  DNA_pol_B       DNA polymerase family B
    3.9e-37  128.2   1.3    1.5e-17   63.7   0.1    2.7  2  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    2.9e-13   50.0   0.0    5.9e-13   49.0   0.0    1.4  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
    1.7e-08   34.6   0.0    4.6e-08   33.2   0.0    1.7  1  RNase_H_2       RNase_H superfamily
      0.003   16.5   0.2      0.063   12.1   0.0    2.6  3  DNA_pol_B_2     DNA polymerase type B, organellar and viral


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 !  263.9   0.0   6.8e-82   2.4e-78       5     457 ..     353     758 ..     349     760 .. 0.90

  Alignments for each domain:
  == domain 1  score: 263.9 bits;  conditional E-value: 6.8e-82
                                       HHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-ST CS
                         DNA_pol_B   5 rvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcy 81 
                                        v   g+  +v  lLl++a + g i+p  + +  ++   Y+Ga+VleP++gl+++ v+ lDFaS+YPsi++a+N+++
  gi|488599766|ref|YP_007906237.1| 353 DVTRMGRGKQVDWLLLNEAYKLGEIAP-NPAE-ISQP--YEGAFVLEPERGLHEN-VVCLDFASMYPSIMIAFNISP 424
                                       5667788899999**************.5555.5666..*************986.6789***************** PP

                                       TTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHH..CS--HHHHHHHHHHH CS
                         DNA_pol_B  82 ttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelk..eekdefekalldkqQ 156
                                        tl +   + ++ ++            +++f+k+    g + ++Lk l+ kRk+ikk +k  + +++ + ++ld++Q
  gi|488599766|ref|YP_007906237.1| 425 DTLAKGPCDCHTAPEV-----------GHRFLKS--PDGFFKRILKMLIGKRKEIKKIMKtlDYNSP-DYRVLDIRQ 487
                                       ******9998876653...........4567655..57**********************6333444.999****** PP

                                       HHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEE CS
                         DNA_pol_B 157 lalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSv 233
                                       +alKv+ Ns+YG+tG +  r +c + A+  T+ GR+ ++k  e+  ++                 ++ v YGDTDS+
  gi|488599766|ref|YP_007906237.1| 488 QALKVLTNSFYGYTGWNMARWYCRECAEATTAWGRHFIKKSAEIARNM-----------------GFTVLYGDTDSI 547
                                       **********************************************99.................9*********** PP

                                       EEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTSEEEEESSGGGSTTS CS
                         DNA_pol_B 234 fielkvkdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskanklliKGvdlvRrdn 310
                                       f++ ++ +++e+ +  k l  ++se   + p+++e+++ yk + +++KK+Yag + +     +++++KG+++ R d+
  gi|488599766|ref|YP_007906237.1| 548 FVKKDGLSIDEMRAEVKRLIMKLSE---ELPIQIEVDEYYKTIFFVEKKRYAGYTED-----GRIIVKGLEVRRGDW 616
                                       ************9988888888888...889***********************999.....9************** PP

                                       -HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHH CS
                         DNA_pol_B 311 cklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphleva 387
                                       c+l+k+v k v+e llk+    r++e++l+ +ks++    e+++++++ +e++v+ k+++++ + y+s + +h+++a
  gi|488599766|ref|YP_007906237.1| 617 CELAKKVQKMVIEILLKE----RDPEKALKTVKSVI----EKINSGSFGIEEYVIYKSITRKISRYESVQ-AHVKAA 684
                                       ******************....**************....9***************************99.999999 PP

                                       HHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEH..HHHHHCC...SEB-HHHHHH.TTHHHHHHHHT CS
                         DNA_pol_B 388 krlkkrneeapevgdrisYvivekkkevkkknllaseraedp..eyvlekn...lpidieyYls.qllkevarlle 457
                                        r +k  +  ++vg ++ Yviv  +   +      ++++e+   e+ + ++    +id eyY++ q+l+ v+r+le
  gi|488599766|ref|YP_007906237.1| 685 MRAEKM-GIHYSVGSKVGYVIVRGAG-NIGDRAYPYDLIESFdgEIIRGSDggvYRIDKEYYIEnQILPSVMRILE 758
                                       988777.799**************97.4677777888888665477776544569*******************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 !   63.2   0.2   6.2e-21   2.2e-17       7     192 ..      34     190 ..      28     195 .. 0.75
   2 !   63.7   0.1   4.3e-21   1.5e-17     231     337 .]     195     288 ..     189     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 6.2e-21
                                       EEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHH CS
                    DNA_pol_B_exo1   7 svcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelk 83 
                                        v+++   f+pyfY+      e+  vk      +e+ +k+++ ++++e  +k++++g ek+   ++kv+ ++p++++
  gi|488599766|ref|YP_007906237.1|  34 FVAYD-RTFEPYFYVISD--YEP-YVK------VEDGKKTIA-VERIE-RVKRKILGKEKD---VFKVFAKHPQHVP 95 
                                       44444.466666665433..112.222......222233344.66777.899*********...************* PP

                                       HHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTCCS-EE CS
                    DNA_pol_B_exo1  84 kirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkesepplr 160
                                       k+r+ +   +++ dv+e+d+++  r+lid+++  f+ + ++       + + ++  e+++++ + ++  + + p+l+
  gi|488599766|ref|YP_007906237.1|  96 KLRESI---SKFADVREADIPFVYRYLIDKDLACFDGIALS------GKLVGKNFREFEVESVERVR--ENGYPDLK 161
                                       *****8...789*****************************......33333444467765555555..4445**** PP

                                       EEEEEEEETEETTSEETTTT..--EEEEEEEE CS
                    DNA_pol_B_exo1 161 vlsFDIeckskkgkfpdaensedpiiqIscvl 192
                                       +++FD e  s  g +pd+e+  dpii I + +
  gi|488599766|ref|YP_007906237.1| 162 IMAFDCEMLSSFG-MPDPER--DPIIVIGVKS 190
                                       *************.******..******9877 PP

  == domain 2  score: 63.7 bits;  conditional E-value: 4.3e-21
                                       EEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEEEEC CS
                    DNA_pol_B_exo1 231 kvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskqare 307
                                       ++++ d+E+e++++f++++k++dPd+i+gYN ++FDlpY+++Ra++l +       +l + gr  +se +     r+
  gi|488599766|ref|YP_007906237.1| 195 EIINGDNEREVIKRFVQVVKEIDPDIIVGYNQNSFDLPYLKKRATKLGI-------KL-DLGRD-GSELTL----RG 258
                                       899******************************************5555.......22.33432.444444....48 PP

                                       EEEETTSEEEEHHHHHHHHSSSSG-SHHHH CS
                    DNA_pol_B_exo1 308 kvkisgrihlDlyrvvkrklklpsYkLnav 337
                                       + ki+gr+++Dly++v r++  +  kL++v
  gi|488599766|ref|YP_007906237.1| 259 NPKIAGRLNVDLYDIVLRTIDVKVKKLENV 288
                                       *********************999999987 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 !   49.0   0.0   1.6e-16   5.9e-13      35     169 ..     200     332 ..     190     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.6e-16
                    DNA_pol_B_exo2  35 ssekelikkffegvekkkpq.lVsfngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsrystr.hlDLm 109
                                       ++e+e+ik+f ++v++  p  +V++n ++fDlp l+ ra k g++     d ++   + + n    +   r  +DL+
  gi|488599766|ref|YP_007906237.1| 200 DNEREVIKRFVQVVKEIDPDiIVGYNQNSFDLPYLKKRATKLGIKLDLGRDGSE--LTLRGN---PKIAGRlNVDLY 271
                                       689***************98358**********************986666555..344444...34445559**** PP

                    DNA_pol_B_exo2 110 dllseygaranakLdelakllglPGK.lgvdGskVaelyqegklkeireYcetDvlnTYlv 169
                                       d++ +    + +kL+++a+ lg      ++ ++++a+ ++egk k++ +Y   Dvl TY +
  gi|488599766|ref|YP_007906237.1| 272 DIVLRTIDVKVKKLENVAEFLGKRIEiADITAKDIAKRWKEGKRKDVLNYSLQDVLHTYYI 332
                                       *99999899999*********98765269******************************87 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.3e-11   4.6e-08      12     165 ..     178     336 ..     173     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.3e-11
                         RNase_H_2  12 pkknliyliGvldvdekeiekltqllaeepeeekailelf.lellekkkalvtfngksFDvpflkrlfkkyklde.. 85 
                                       p+++ i++iGv   d +ei+       ++ +e++ i++++ + +  + + +v +n +sFD+p+lk+++ k  ++   
  gi|488599766|ref|YP_007906237.1| 178 PERDPIIVIGVKSGDYEEII-------NGDNEREVIKRFVqVVKEIDPDIIVGYNQNSFDLPYLKKRATKLGIKLdl 247
                                       67888999999876666554.......4667777777755333445568899****************776666666 PP

                         RNase_H_2  86 ...............eefrhiDLlkel.rkkklesysLksvekelgierreedlsGsqavklyqeylrtgdeellek 146
                                                        +  +DL+ ++ r+ +++  +L++v+++lg + +  d+  ++++k ++e        + + 
  gi|488599766|ref|YP_007906237.1| 248 grdgseltlrgnpkiAGRLNVDLYDIVlRTIDVKVKKLENVAEFLGKRIEIADITAKDIAKRWKE-------GKRKD 317
                                       889998999887666666899***9774777777779***********************98765.......56788 PP

                         RNase_H_2 147 ilaYNedDvralatlyekl 165
                                       +l Y  +Dv+ ++++ e+l
  gi|488599766|ref|YP_007906237.1| 318 VLNYSLQDVLHTYYIAEEL 336
                                       9*************99876 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.063   2.3e+02     136     166 ..     314     344 ..     281     362 .. 0.78
   2 !   12.1   0.0   1.8e-05     0.063     209     246 ..     384     420 ..     377     429 .. 0.84
   3 ?   -1.2   0.0       0.2   7.1e+02     371     390 ..     487     506 ..     484     582 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.063
                       DNA_pol_B_2 136 ivketleYckqDvlvlaklllklkesideff 166
                                        +k+ l+Y  qDvl ++ ++++l  +++e  
  gi|488599766|ref|YP_007906237.1| 314 KRKDVLNYSLQDVLHTYYIAEELLPMYYELS 344
                                       4678899****************99999754 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.8e-05
                       DNA_pol_B_2 209 iRkayrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthy 246
                                       i + y G ++ +p   + + en+++ D+ S+YPs+m  +
  gi|488599766|ref|YP_007906237.1| 384 ISQPYEGAFVlEPE--RGLHENVVCLDFASMYPSIMIAF 420
                                       66778899997777..6688****************876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.2
                       DNA_pol_B_2 371 rsiaKlllNsLYGrFatnpd 390
                                       ++  K l Ns YG  + n+ 
  gi|488599766|ref|YP_007906237.1| 487 QQALKVLTNSFYGYTGWNMA 506
                                       56679999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (780 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.48
# Mc/sec: 4888.89
//
Query:       gi|488599767|ref|YP_007906238.1|  [L=129]
Description: hypothetical protein Asulf_00211 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-16   58.9   3.6    2.8e-07   30.5   0.3    2.0  2  DrsE_2          DsrE/DsrF/DrsH-like family
    1.8e-09   38.0   0.2    2.1e-09   37.7   0.2    1.1  1  DrsE            DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.015   15.3   0.1       0.02   15.0   0.1    1.3  1  Haem_degrading  Haem-degrading
       0.15   11.3   0.0       0.22   10.8   0.0    1.2  1  Herpes_UL69     Herpesvirus transcriptional regulator family
        1.5    9.3   4.6        2.6    8.5   0.0    2.8  3  G0-G1_switch_2  G0/G1 switch protein 2


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.3   1.1e-10   3.8e-07       4      55 ..       3      56 ..       1      67 [. 0.84
   2 !   30.5   0.3   7.9e-11   2.8e-07      90     150 ..      64     126 ..      56     129 .] 0.85

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.1e-10
                                      EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GG..G---T CS
                            DrsE_2  4 klaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkee..kkkvk 55
                                      klai++ +g+l+k  aa i++s+Aa lg+ev +F t  GL +++k+   kk+ k
  gi|488599767|ref|YP_007906238.1|  3 KLAIVLASGELEKLQAASIIGSVAATLGTEVLVFATMDGLMAFKKDVveKKAWK 56
                                      899******************************************952144444 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 7.9e-11
                                       HHHCT---HHHHHHHHHHTT.-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-SE CS
                            DrsE_2  90 mkekgvasleeLleaakeag.vklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeeadv 150
                                       m +++++   +  ++ake g  kl+aC m md++gl+ +e++d      g++++l+  e a+v
  gi|488599767|ref|YP_007906238.1|  64 MLQANAPLFIDTFKQAKETGnLKLYACGMVMDMLGLSMDEFVDVFdDKLGVTAFLGMTEGAQV 126
                                       5667777777888999988659***********************99********98888776 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.2     6e-13   2.1e-09       3      91 ..       4     109 ..       2     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 6e-13
                                       EEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS.............---TGGGTS---GGGGGG CS
                              DrsE   3 vfilvtggpygseaarealelalaaaalghevsvffygdGvllllk.............gqtanpadeknlaellka 66 
                                       ++i+  +g  + e+ ++a  +  +aa+lg ev vf ++dG  +++k             g+   +a+ + +++++k+
  gi|488599767|ref|YP_007906238.1|   4 LAIVLASG--ELEKLQAASIIGSVAATLGTEVLVFATMDGLMAFKKdvvekkawkagelGKGMLQANAPLFIDTFKQ 78 
                                       55666655..67778999*********************************99999999666677777889****** PP

                                       CGGGT.-EEEEEHHHHHHTT--GGG.....E CS
                              DrsE  67 lkeyg.vklyvCgqaakargldede.....d 91 
                                       +ke g  kly+Cg+ ++  gl+ de     d
  gi|488599767|ref|YP_007906238.1|  79 AKETGnLKLYACGMVMDMLGLSMDEfvdvfD 109
                                       ***888****************987442221 PP

>> Haem_degrading  Haem-degrading
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   5.5e-06      0.02      20      65 ..      19      63 ..       3      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.5e-06
                    Haem_degrading 20 kgkpvviaivdaggqllffarmdgaspdnedwaerKantaarfgks 65
                                      ++   ++a ++ g ++l+fa mdg ++ ++d++e+Ka+ a  +gk 
  gi|488599767|ref|YP_007906238.1| 19 ASIIGSVAATL-GTEVLVFATMDGLMAFKKDVVEKKAWKAGELGKG 63
                                      34444444444.779***********************99988865 PP

>> Herpes_UL69  Herpesvirus transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.2e-05      0.22     159     190 ..      71     102 ..      63     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.2e-05
                       Herpes_UL69 159 klvqyirdfdteealeeYrPGavsallleale 190
                                        +++++++  +++ l+ Y +G+v+++l   ++
  gi|488599767|ref|YP_007906238.1|  71 LFIDTFKQAKETGNLKLYACGMVMDMLGLSMD 102
                                       5788999999***************9976665 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 ?    1.8   0.3      0.09   3.2e+02      28      43 ..      21      36 ..       7      57 .. 0.58
   2 ?    8.5   0.0   0.00073       2.6       9      38 ..      70      99 ..      64     108 .. 0.86
   3 ?   -3.1   0.1       2.9   1.1e+04      31      41 ..     113     123 ..     113     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.09
                    G0-G1_switch_2 28 vlGsvLallGvviglv 43
                                      ++Gsv a lG+ + + 
  gi|488599767|ref|YP_007906238.1| 21 IIGSVAATLGTEVLVF 36
                                      5666666666543333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00073
                    G0-G1_switch_2  9 PfakemlsqkpsrklvklYvlGsvLallGv 38
                                      P+  + ++q  + + +klY  G v+ +lG+
  gi|488599767|ref|YP_007906238.1| 70 PLFIDTFKQAKETGNLKLYACGMVMDMLGL 99
                                      6777788999999****************7 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.9
                    G0-G1_switch_2  31 svLallGvvig 41 
                                       +v a+lG+  g
  gi|488599767|ref|YP_007906238.1| 113 GVTAFLGMTEG 123
                                       5789***9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 867.82
//
Query:       gi|488599768|ref|YP_007906239.1|  [L=75]
Description: putative redox protein, regulator of disulfide bond formation [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-23   82.3   0.0    1.7e-23   82.2   0.0    1.0  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0   9.5e-28   1.7e-23       1      70 []       4      73 ..       4      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 9.5e-28
                                      EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                              TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                      i++D+rG  CP+Pl++l k+++ +e g ++evl++d+++ +dip+++kk ghelv ve+++++++iv++k
  gi|488599768|ref|YP_007906239.1|  4 IVVDARGSFCPGPLMELVKTIKDAEVGTEIEVLSSDESSAKDIPEWVKKAGHELVGVEKKGDYWSIVVKK 73
                                      589*****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 00:00:00.42
# Mc/sec: 530.47
//
Query:       gi|488599769|ref|YP_007906240.1|  [L=379]
Description: hypothetical protein Asulf_00213 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-20   72.8   0.0    1.4e-19   70.4   0.0    1.8  1  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
     0.0037   17.8   0.4        2.9    8.5   0.0    2.4  2  Pyr_redox    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.032   14.5   0.0    1.8  1  Phage_CI_C   Bacteriophage CI repressor 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 !   70.4   0.0   2.4e-23   1.4e-19       2     278 ..       3     290 ..       2     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 2.4e-23
                                       SEEEE--SHHHHHHHHHHHH........HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCC CS
                                       xxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq........agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgiell 70 
                                       ++v+iGgG++G+ ++ +l++         + k+tl+++++  l++ + l + + + +e++e ++e         ++l
  gi|488599769|ref|YP_007906240.1|   3 NIVIIGGGVGGTLVSNYLSHklkeeireGKTKITLISDRDKQLYE-PGLLYMIFNRMEEGELFKEL--------TYL 70 
                                       89*****************99999998779******777777777.66667888888888877764........444 PP

                                       HCCT.CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T...S CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                       Pyr_redox_2  71 lgee.vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp...k 143
                                       l+    +ki+++ k v +e+ +e ++ +++yd+lv+AtGs+     +pG+ e+++    +++ a++l+++l +    
  gi|488599769|ref|YP_007906240.1|  71 LDPMiDLKIERATKIVADENYVETEKGRYDYDYLVIATGSRIVPEEVPGLVEGGH-WFYNVEGARRLRDELARfkgG 146
                                       4422235555666666666666677789***********988777*****55555.4499*************9994 PP

                                       EEEE..ES....-SHHHHHHHHHHHHHT-......EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEE CS
                                       xxxx..xx....xxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivv..vG....gGyiGvElAaalaklgk......evtlveardrllraldkelsaaleealekeGvevklgtsvke 208
                                       +ivv   G      +  +E++ +l+++ k      +v +++  ++    + +++++ + e+++++G++ k+  ++ e
  gi|488599769|ref|YP_007906240.1| 147 KIVVsiMGiphkCPVAPIEVTFMLHDFFKlhrlrdKVEILYTYPINRVFTLENVTEVVVEYFNERGIKYKTFFNPIE 223
                                       4443114422211233466666654443344444499999999988655569******************9999999 PP

                                       EEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BES.STTEEE-GGGC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxx RF
                       Pyr_redox_2 209 idgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdefl.rtn.vpgiyaiGDva 278
                                       +d++++  + ++ +gee+++dl++     + s+ ++  ++gl  d++g++ +d++  +++  ++iya+GD +
  gi|488599769|ref|YP_007906240.1| 224 VDAKNK--KIITLEGEEEPYDLLIAIPPHKGSQLII--DSGLG-DRDGWVPTDRYTlKVEgYDNIYAVGDAT 290
                                       999998..99************99988888888775..88886.7*********9878988*********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 !    8.5   0.0   0.00049       2.9       1      35 [.       3      45 ..       3      61 .. 0.77
   2 !    7.2   0.1    0.0013       7.6      40      77 ..     198     233 ..     175     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00049
                                      EEEEECSSHHHHHHHHHH.......HHTT...SEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgal.......aelg...kkVtvversdkll 35
                                      ++v++GgG+ g  + ++l          +    k+t++  +dk l
  gi|488599769|ref|YP_007906240.1|  3 NIVIIGGGVGGTLVSNYLshklkeeI--RegkTKITLISDRDKQL 45
                                      59****************76555441..25558999999999977 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox  40 eeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       e + +++ e++ ++gi+  +  ++ e++ ++++   ++
  gi|488599769|ref|YP_007906240.1| 198 ENVTEVVVEYFNERGIKYKTFFNPIEVDAKNKK--IIT 233
                                       678899**********************99987..244 PP

>> Phage_CI_C  Bacteriophage CI repressor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.4e-06     0.032      15      96 ..      81     166 ..      69     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-06
                        Phage_CI_C  15 esglvlldkkllkkelkep...lvieeekklylvdkkeadvsdGkwLvdieGrlsir.elariPvkklrvsgdevsf 87 
                                        + +++ d++++++e  +     ++ +  ++ + ++    v+ G+w  ++eG+  +r elar+ ++k+ vs  +++ 
  gi|488599769|ref|YP_007906240.1|  81 RATKIVADENYVETEKGRYdydYLVIATGSRIVPEEVPGLVEGGHWFYNVEGARRLRdELARFKGGKIVVSIMGIPH 157
                                       55555556665555544333443444444444555555667889************846****************** PP

                        Phage_CI_C  88 ecklddikv 96 
                                        c +  i+v
  gi|488599769|ref|YP_007906240.1| 158 KCPVAPIEV 166
                                       **9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2723.06
//
Query:       gi|488599770|ref|YP_007906241.1|  [L=155]
Description: hypothetical protein Asulf_00214 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   57.2   0.1    2.8e-15   55.9   0.1    1.7  1  DUF1641   Protein of unknown function (DUF1641)
  ------ inclusion threshold ------
      0.058   12.6   0.0      0.079   12.1   0.0    1.2  1  SOG2      RAM signalling pathway protein
      0.067   12.6   0.0      0.083   12.3   0.0    1.1  1  FAM92     FAM92 protein
       0.12   12.4   0.0       0.69   10.0   0.1    2.2  2  DnaB      DnaB-like helicase N terminal domain


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.1   6.3e-19   2.8e-15       5      39 .]     119     153 ..     116     153 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 6.3e-19
                           DUF1641   5 epkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                       e++pvGlfgLl+aLr P+Vq++LG+l+++++++Gk
  gi|488599770|ref|YP_007906241.1| 119 EAEPVGLFGLLKALREPEVQKALGMLVKIAREMGK 153
                                       79********************************8 PP

>> SOG2  RAM signalling pathway protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.8e-05     0.079     401     485 ..       3      81 ..       1      92 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                              SOG2 401 lteelakkirdLtdtcrqameltkaLrerLsllklkedlsekgsttsektklwedinaFlksivsilaliKelslmh 477
                                       ltee  kk+++L  ++++   l++ L+e L++l+ ++   +   +   ++  w +    l si  ++aliK  + + 
  gi|488599770|ref|YP_007906241.1|   3 LTEEEIKKLKELANNADALISLSSGLGEILKNLA-EN---KDDINGVIDKLVWLEKSGNLESILGFAALIK--IFQD 73 
                                       689999***************************3.22...3444444555667777788999999999999..8888 PP

                              SOG2 478 elPnevrp 485
                                       +l+ ev++
  gi|488599770|ref|YP_007906241.1|  74 TLSDEVVA 81 
                                       88888875 PP

>> FAM92  FAM92 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05     0.083      55     148 ..       7     102 ..       2     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                             FAM92  55 lvkevkayaddeeineklcqGlksfadevaklqdyrdieverl...e.akvveelktyetlvkskrddlklaliard 127
                                        +k++k  a++ +   +l  Gl +  +++a  +d  +  +++l   e +  +e +  +  l+k  +d l   ++a++
  gi|488599770|ref|YP_007906241.1|   7 EIKKLKELANNADALISLSSGLGEILKNLAENKDDINGVIDKLvwlEkSGNLESILGFAALIKIFQDTLSDEVVAKN 83 
                                       56888889999999999999999999999988888887777763324134689999********************* PP

                             FAM92 128 kevkrlrqleelkskfsadrs 148
                                        e+     l  + skfs+d+s
  gi|488599770|ref|YP_007906241.1|  84 AEMISNIGL--IASKFSSDNS 102
                                       999876555..6799***998 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 ?   10.0   0.1   0.00015      0.69      65     102 ..      51      88 ..       6      89 .. 0.84
   2 ?   -0.5   0.0      0.29   1.3e+03      33      50 ..      95     112 ..      91     151 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                                       HSCSSS-GGHGT.HHHHHHHHHC-S-CCCHHHHHHHHH CS
                              DnaB  65 elekkgkledvggaaylaelvaavpsaanieeyaeivk 102
                                       +lek+g+le++ g+a l+++++++ s++ + + ae++ 
  gi|488599770|ref|YP_007906241.1|  51 WLEKSGNLESILGFAALIKIFQDTLSDEVVAKNAEMIS 88 
                                       45************************999999999885 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                                       GGSSSHHHHHHHHHHHHH CS
                              DnaB  33 edFyepahrliFeailel 50 
                                         F++++  ++F+ai + 
  gi|488599770|ref|YP_007906241.1|  95 SKFSSDNSLKLFNAIGDA 112
                                       567777777777777653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 957.12
//
Query:       gi|488599771|ref|YP_007906242.1|  [L=302]
Description: formylmethanofuran-tetrahydromethanopterin formyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-56  189.1   0.0    5.8e-56  188.6   0.0    1.2  1  FTR_C     FTR, proximal lobe
    5.8e-46  156.0   0.0    9.9e-46  155.2   0.0    1.4  1  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 !  188.6   0.0   6.5e-60   5.8e-56       1     149 []     151     297 ..     151     297 .. 0.99

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 6.5e-60
                                       EEEEEES-EEEEEEEEEEEEEEEESSHHHHHHHHHHHHHHHHTSTTEE--SGGGEESS-EEES-S-TT-SEEE-GGG CS
                             FTR_C   1 geflieeklgvvkgvaGgnllilaedqeaaleaaeaaveaikkvegvitpFpGgivrsgSKvgskykflkastNeaf 77 
                                       gef+ie+ +g+++gvaGgn++++++++e+alea+e avea+k+++gvit+F  gi+++gSK+++ky+++ ++tN+ f
  gi|488599771|ref|YP_007906242.1| 151 GEFIIERYIGYAEGVAGGNIWYFCDSEESALEAGELAVEALKEIDGVITSF--GICSAGSKPETKYPEIGPTTNHYF 225
                                       8**************************************************..************************ PP

                                       -TTSTT....----TT--EEEEEEEEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS-SEEEEGGGG CS
                             FTR_C  78 cptlkekveeselpedveavlEiVidgldeeavaeamkagieaavkvegvlkisAgNygGkLGkykfkLkel 149
                                       cptlk+k+ +s++p++v++++EiVi+g++ + +++am +++e a kv+gvl+is gNy+GkLG++k++L+++
  gi|488599771|ref|YP_007906242.1| 226 CPTLKNKIPDSKVPDGVKSIPEIVINGINLDVLKKAMYVCMEVASKVDGVLRISSGNYDGKLGQHKIYLRDI 297
                                       *********************************************************************996 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.2   0.0   1.1e-49   9.9e-46       1     142 []       3     148 ..       3     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 1.1e-49
                                       -EETTEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-EEEESEEB-GGGSTTSS-EEEEEEE CS
                               FTR   1 leingveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaEagiervlspeetpDgRpGvailif 77 
                                       le+ngv ++dt++EaF+  ++r+iiTa+++ ++k+aa+ at+++++v+g e E+gi+r+lsp+etpDgR G++ +++
  gi|488599771|ref|YP_007906242.1|   3 LELNGVPVDDTYCEAFDGIYSRFIITAKHRWLLKSAAYGATALPSTVFG-ESEGGIDRWLSPSETPDGRHGAIAQVW 78 
                                       689**********************************************.*************************** PP

                                       ....ESSHHHHHHHHHHHHHHHTTTSTT-EEEE--.GG-SEEHHHHHHGGGTT--EEEEETTEEEEEEEE CS
                               FTR  78 ....aaskkklekqlleRigqcvLtapttavfngl.aeekiklgkklrffgDgyeiekelggrkvwriPv 142
                                           ++ ++ l++++++Ri+q vL++ptt+vfn++ +e+k++ + +++ +gDgye+e+e++grkv+r+P+
  gi|488599771|ref|YP_007906242.1|  79 vqksKKFMDVLTREMSKRIRQGVLVVPTTRVFNATdSETKFDAELNIGRCGDGYEWEEEMWGRKVIRVPI 148
                                       6544444566889**********************55699*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2091.14
//
Query:       gi|488599772|ref|YP_007906243.1|  [L=155]
Description: O-6-methylguanine DNA methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  100.0   0.0    1.1e-28   99.2   0.0    1.4  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b
  ------ inclusion threshold ------
      0.054   13.0   0.0      0.067   12.6   0.0    1.1  1  AviRa          RRNA methyltransferase AviRa


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 !   99.2   0.0   1.2e-32   1.1e-28       2      81 .]      76     153 ..      75     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 1.2e-32
                                       HHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHH CS
                     DNA_binding_1   2 fqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLea 78 
                                       f+ +V++++++IpyGk+ tY+++A++++  +a raVg+al++np+++++PcHRVv+++g +ggy++g+e+k++lL+ 
  gi|488599772|ref|YP_007906243.1|  76 FASEVLKVVSEIPYGKTLTYSQVADRIN-SRAYRAVGKALRNNPVPVIIPCHRVVAKNG-IGGYSSGIEIKKYLLRL 150
                                       889*************************.9*****************************.***************** PP

                                       TTS CS
                     DNA_binding_1  79 Egv 81 
                                       Egv
  gi|488599772|ref|YP_007906243.1| 151 EGV 153
                                       *97 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.5e-06     0.067     127     211 ..      41     123 ..      24     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.5e-06
                             AviRa 127 aealesaerleellakkgeekeievfkadite.keeeaekevdivitDlPYGelvswqgeseepvkqlleslaavld 202
                                       + +l+s +rle+ l++    + +++   d++e +++  ++ev  v+ ++PYG++ ++++ +++  ++  +++ ++l 
  gi|488599772|ref|YP_007906243.1|  41 RARLKSESRLENALRSYFDGEVVDL--SDLVEiESDGFASEVLKVVSEIPYGKTLTYSQVADRINSRAYRAVGKAL- 114
                                       4567777777777733333333332..33333034455555889***************99999999999999999. PP

                             AviRa 203 peesvvavi 211
                                        ++ v ++i
  gi|488599772|ref|YP_007906243.1| 115 RNNPVPVII 123
                                       556665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1121.27
//
Query:       gi|488599773|ref|YP_007906244.1|  [L=196]
Description: nicotinamide-nucleotide adenylyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-16   61.1   0.0    1.8e-16   60.6   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.0     1e-20   1.8e-16       1     143 []       5     138 ..       5     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 1e-20
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.kevdevisvdpweltrev 76 
                                       ++ G+F+p H+GH ++++++  +++e li+g+ s+++++   +++++a eR+ m+  a  e ++ + +++ +l + +
  gi|488599773|ref|YP_007906244.1|   5 FFIGRFQPYHYGHHEVIRNIITKVDE-LIIGIGSAQESHEL-ENPFTAGERILMISSAlDELKDELGDKKVYLIP-L 78 
                                       589***********************.************99.****************97777778888888887.8 PP

                                       HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
                   CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                        + ++     +v   +++        ++ +++n++lvv+ ++e  ++v+   ++++ ++ +t+ir+r
  gi|488599773|ref|YP_007906244.1|  79 EDIYRNS--LWVSHVISMVP-----PFDVVFSNNPLVVRLFTEAGKKVVNTSMYNRDEYQGTEIRRR 138
                                       8888888..99999999998.....6***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1240.50
//
Query:       gi|488599774|ref|YP_007906245.1|  [L=521]
Description: putative Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-24   87.0   0.1    3.2e-24   86.2   0.1    1.5  1  Radical_SAM  Radical SAM superfamily
    2.9e-07   30.6   0.4    4.8e-06   26.7   0.0    2.5  2  Fer4_14      4Fe-4S single cluster domain
    9.1e-07   29.2   0.1    2.8e-06   27.7   0.1    1.9  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.24   11.6   0.3        1.7    8.8   0.2    2.5  2  DUF4287      Domain of unknown function (DUF4287)


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 !   86.2   0.1   7.1e-28   3.2e-24       1     166 [.     106     264 ..     106     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 7.1e-28
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklav 75 
                                       +v t+ C l+C++C ++ +  r g++++ ++++i e v+ ++  ++  ++ v l+ggep+l+ d+v+++++++++  
  gi|488599774|ref|YP_007906245.1| 106 IVLTNRCDLACWYCFFYAK--RAGYVYEPTIDQIREMVRTARsLKPVpANAVQLTGGEPTLREDLVDIIKAIKEE-- 178
                                       6889*************96..*********************955555***************************.. PP

                                       CTEEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                          +i + tng+++   +e  ++ + +g+++v+l+ + +d++     +n+ ++  e+ + le++r+a +  +v + +
  gi|488599774|ref|YP_007906245.1| 179 GIDHIQLNTNGIRLAldPELPKKVRLAGCNTVYLSFDGVDEK-----TNP-KNHNEIPKILENCRRAELG-IVLVPT 248
                                       9****************************************9.....745.7888888************.****** PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                       +++G+nd++l +++++
  gi|488599774|ref|YP_007906245.1| 249 VIKGVNDHQLGDIIRF 264
                                       **********999987 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3       0.1   4.5e+02       6      20 ..      85      99 ..      82     103 .. 0.81
   2 !   26.7   0.0   1.1e-09   4.8e-06       3      90 ..     107     190 ..     106     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
                           Fer4_14  6 sgCnlsCkgCdnket 20
                                      ++C++ C  C ++ +
  gi|488599774|ref|YP_007906245.1| 85 AKCPFTCGLCKDHMS 99
                                      79********97765 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.1e-09
                           Fer4_14   3 vrlsgCnlsCkgCdnketwkselgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                       v +++C l+C  C+  ++ +  + +p   +++ ++++   + + + ++ + ltGGeP +    ++l++++k +kee+
  gi|488599774|ref|YP_007906245.1| 107 VLTNRCDLACWYCFFYAKRAGYVYEPT-IDQIREMVRtARSLKPVPANAVQLTGGEPTLR---EDLVDIIKAIKEEG 179
                                       4589**********8774444433333.333334443245555666799********955...99************ PP

                           Fer4_14  79 pekkiwletngt 90 
                                          +i+l+tng 
  gi|488599774|ref|YP_007906245.1| 180 -IDHIQLNTNGI 190
                                       .567******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 !   27.7   0.1   6.2e-10   2.8e-06       9      97 ..     106     193 ..      73     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.2e-10
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeft...kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkee 82 
                                       ++++++C+l+C +Cf  + ++  +  e t      + +  ++lk    + + l+GGEP l   +e+l++++k +kee
  gi|488599774|ref|YP_007906245.1| 106 IVLTNRCDLACWYCFFYA-KRAGYVYEPTidqIREMVRTARSLKPVPANAVQLTGGEPTL---REDLVDIIKAIKEE 178
                                       67899**********444.44443333331122333344555555666************...************** PP

                           Fer4_12  83 kpekdiwlytgytle 97 
                                       +++   + ++g  l 
  gi|488599774|ref|YP_007906245.1| 179 GIDHIQLNTNGIRLA 193
                                       **8888888887765 PP

>> DUF4287  Domain of unknown function (DUF4287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.7   1.6e+04       9      16 ..     331     338 ..     327     343 .. 0.72
   2 ?    8.8   0.2   0.00039       1.7       5      22 ..     485     502 ..     482     518 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.7
                           DUF4287   9 iekkTGkt 16 
                                       +e+ TG++
  gi|488599774|ref|YP_007906245.1| 331 VEAITGHP 338
                                       67888887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00039
                           DUF4287   5 yldniekkTGktldewla 22 
                                       y d+i++k+G +ldew +
  gi|488599774|ref|YP_007906245.1| 485 YRDKIQAKYGIPLDEWEK 502
                                       7799************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3242.23
//
Query:       gi|488599775|ref|YP_007906246.1|  [L=183]
Description: hypothetical protein Asulf_00219 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-63  212.0   8.2    7.4e-63  211.7   8.2    1.0  1  CarS-like     CDP-archaeol synthase
    5.7e-06   26.3   4.8    5.7e-06   26.3   4.8    1.8  1  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   8.2   8.3e-67   7.4e-63       1     175 []       4     183 .]       4     183 .] 0.97

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 8.3e-67
                         CarS-like   1 lldlilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsila 77 
                                       ++ li+k+i+ll+pay++n++av++GGG p+d+ k+++dG+r++GdG+t rG+v+Gv++G+l g+iq+ +e +  l 
  gi|488599775|ref|YP_007906246.1|   4 IIALIIKTIWLLIPAYTPNNFAVVFGGGMPIDFRKKFIDGKRILGDGKTIRGFVFGVMGGILCGMIQYKIEPIFNLN 80 
                                       6889************************************************************************* PP

                         CarS-like  78 ldssgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp.....vkllpieliil 149
                                       l ss+s+ + + l + l+fG+l Gd+ Gsfikrr +ierG  +++ dql f+ ++ll+ay        l++ e+i+ 
  gi|488599775|ref|YP_007906246.1|  81 LFSSLSIFDAFCLIFALSFGSLSGDVFGSFIKRRAGIERGGVFPVFDQLTFLAVSLLFAYLisphfSSLFTREVIVT 157
                                       ***********************************************************87444545789******* PP

                         CarS-like 150 ivlitlvlhlsaniiayklglkdvwy 175
                                        +++t+vlhl aniia+klglk+v++
  gi|488599775|ref|YP_007906246.1| 158 GLIVTPVLHLIANIIAFKLGLKNVPW 183
                                       *************************9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   4.8   6.3e-10   5.7e-06     170     250 ..      50     127 ..      47     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.3e-10
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS.....---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-SSS-S-SSS CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal.....alsllhllllslllslvavfGDLveSglKRafgiKDsGkliPG 241
                                       +KT+ Gf+ G+++ ++ g++ +++ + +      +ls++ ++ l + ls+ +  GD++ S +KR++gi         
  gi|488599775|ref|YP_007906246.1|  50 GKTIRGFVFGVMGGILCGMIQYKIEPIFNlnlfsSLSIFDAFCLIFALSFGSLSGDVFGSFIKRRAGIE-------- 118
                                       6**********************999877999999********************************94........ PP

                                       SS-HHHHHH CS
                      CTP_transf_1 242 hGGilDRlD 250
                                       +GG++  +D
  gi|488599775|ref|YP_007906246.1| 119 RGGVFPVFD 127
                                       455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1146.52
//
Query:       gi|488599776|ref|YP_007906247.1|  [L=181]
Description: orotate phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   57.5   0.3    1.6e-15   57.0   0.3    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.034   13.6   0.0      0.049   13.1   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
       0.11   12.6   0.0       0.19   11.8   0.0    1.3  1  DUF3276       Protein of unknown function (DUF3276)


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 !   57.0   0.3   2.7e-19   1.6e-15       6     133 ..      42     158 ..      37     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.7e-19
                                       TT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE- CS
                      Pribosyltran   6 lenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrll 82 
                                       +  p +l  + + + ++ e+ + + d +++i+ gGvp+a +l+   + p+ + rk+k++ +++++ +          
  gi|488599776|ref|YP_007906247.1|  42 T-DPDFLTLISKTMLRLAEDCRLNFDKIACIELGGVPLAVALSITSNKPYIIFRKKKKEYGVTSDLI---------- 107
                                       3.4899999999999999**********************************************997.......... PP

                                       ---TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHH CS
                      Pribosyltran  83 edpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeev 133
                                       +++ g++ ++V+D+ +tG++ l ++e++ e+g +++++ v+vd+ +++e+v
  gi|488599776|ref|YP_007906247.1| 108 GEINGERFVVVEDVTTTGSSALSVVERVMERGGKVLGVLVVVDREEGAEDV 158
                                       799********************************************9998 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.2e-06     0.049     111     172 ..     102     161 ..      85     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-06
                           UPRTase 111 yynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaee 172
                                       + + L  +i+ ++ ++++ v  TG+sa ++++++ erg +     vl v+  eeg++ + +e
  gi|488599776|ref|YP_007906247.1| 102 VTSDLIGEINGERFVVVEDVTTTGSSALSVVERVMERGGK--VLGVLVVVDREEGAEDVFKE 161
                                       556677778888999*********************9975..45677788899999888765 PP

>> DUF3276  Protein of unknown function (DUF3276)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05      0.19      17      57 ..      25      67 ..      20      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                           DUF3276 17 lkAG.kRiYflDvkktkkddyyltitEskkvt..nddgsvsfek 57
                                      l  G k  Y++Dvkk+  d  +lt+  sk +    +d +++f+k
  gi|488599776|ref|YP_007906247.1| 25 LSSGkKSSYYVDVKKSLTDPDFLTLI-SKTMLrlAEDCRLNFDK 67
                                      56673457****************97.55555478999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1219.90
//
Query:       gi|488599777|ref|YP_007906248.1|  [L=325]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-05   23.2   0.0      0.048   13.1   0.0    2.2  2  SBP_bac_3       Bacterial extracellular solute-binding protei
    0.00028   20.7   0.0      0.011   15.4   0.0    2.1  1  NMT1_2          NMT1-like family
     0.0008   19.3   0.1     0.0017   18.2   0.1    1.5  1  MarR_2          MarR family
     0.0034   16.8   0.6     0.0081   15.6   0.3    1.7  2  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
     0.0048   16.2   0.1     0.0093   15.2   0.0    1.6  1  DUF3834         Protein of unknown function (DUF3834)
     0.0093   15.8   0.2      0.026   14.4   0.2    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.014   14.9   1.2      0.014   14.9   1.2    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.019   15.1   0.1      0.043   14.0   0.1    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.034   13.5   0.2      0.096   12.0   0.2    1.8  2  DUF1670         Protein of unknown function (DUF1670)
      0.053   13.4   0.3       0.15   12.0   0.3    1.8  1  HTH_5           Bacterial regulatory protein, arsR family
      0.072   13.4   0.0       0.16   12.3   0.0    1.5  1  Cul7            Mouse development and cellular proliferation 
       0.12   12.3   0.1       0.29   11.1   0.1    1.6  1  MarR            MarR family
       0.15   12.3   0.2       0.61   10.3   0.1    2.0  2  B-block_TFIIIC  B-block binding subunit of TFIIIC


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 !   13.1   0.0   3.5e-05     0.048     112     156 ..      75     119 ..      54     152 .. 0.83
   2 !    8.5   0.0    0.0009       1.2     100     173 ..     147     222 ..     131     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                                       EEEEETTSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 112 kvgvqagstaeellkeelkkgaeivefdtleealqaLkngrvdav 156
                                       +vgv +++ ++ l+k++l  g+ +++fd+  e+++aL++grvd +
  gi|488599777|ref|YP_007906248.1|  75 RVGVLKSTEYAYLIKSALDCGMIVRVFDDAIELTKALSQGRVDLA 119
                                       8**********8899876669999*******************75 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0009
                                       CCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC...TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 100 ssiksladLkgkkvgvqagstaeellkeelkk...gaeivefdtleealqaLkngrvdavvadspvlaylvkknpdk 173
                                       s+i+ ++ L +   g++  st +  l++++ k   + ++++f++ e +++  ++ ++d ++  +p l  l+kk  d 
  gi|488599777|ref|YP_007906248.1| 147 SGIA-IKALRNAIFGASEMSTMDRNLRRYMDKkdiSGRVIYFKSPEKMIESFEKCQIDGIAIWEPYLTILAKKGYDV 222
                                       4554.669999999**************9998988778899**************************9999998765 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.3e-06     0.011     126     227 ..     159     254 ..      89     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.3e-06
                            NMT1_2 126 iavtfpgsthdlllrywLaaaGldpeadvklvvvpp.pqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqel 201
                                       +++ +++st d  lr++++++++      +++  ++ ++m++ +++ +idg +  eP+  + +a+  G+ +   +e 
  gi|488599777|ref|YP_007906248.1| 159 FGA-SEMSTMDRNLRRYMDKKDISG----RVIYFKSpEKMIESFEKCQIDGIAIWEPY-LTILAK-KGYDVEYFNEC 228
                                       454.889999999999999999998....7777777699*******************.444444.46899999999 PP

                            NMT1_2 202 wkdhPekvlgvredfveknpntaral 227
                                       + d+ ++ l+v+ d +  n+++ + +
  gi|488599777|ref|YP_007906248.1| 229 LGDFLCCTLAVNTDSYRLNKDLFNEF 254
                                       9*********9999887777666655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.2e-06    0.0017       7      54 ..       7      51 ..       4      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + r+L ++g  +   + ++e+   l+lsks+vs il  L+++  ++r+
  gi|488599777|ref|YP_007906248.1|  7 IIRLLEEVGEKG---ILQSEIPSILDLSKSTVSEILSNLESKRKIVRE 51
                                      579999999998...9*************************9988887 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   5.9e-06    0.0081      93     133 ..       9      49 ..       2      66 .. 0.85
   2 ?   -1.9   0.0       1.2   1.7e+03      15      60 ..     138     182 ..     132     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.9e-06
                                       HHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXE CS
                     RNA_pol_Rpc34  93 siIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyik 133
                                          ee G +GI + +i s l L ks v  +L +Lesk+ i 
  gi|488599777|ref|YP_007906248.1|   9 RLLEEVGEKGILQSEIPSILDLSKSTVSEILSNLESKRKIV 49 
                                       678999********************************995 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       HHHHHHCSSSSSHCCHHHHHHH.STTSHHHHHHHHHHHHHHCTSEEC CS
                     RNA_pol_Rpc34  15 lleelrkaseqklfsqqdLqdd.ipslslklllsavqeLldkkllvl 60 
                                       + ++++++    ++  + L +  + + +++++ + +++ +dkk +++
  gi|488599777|ref|YP_007906248.1| 138 IVSAIAQN--GSGIAIKALRNAiFGASEMSTMDRNLRRYMDKKDISG 182
                                       55566666..7778888888887888888888889999999988765 PP

>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.8e-06    0.0093      48     153 ..     135     243 ..     123     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.8e-06
                           DUF3834  48 glridlvvikkllviipkigkekIavwrkGsaaDvllrilldlkkikaevvyaddpeevlkllnegevdsavv.... 120
                                       ++ri+  + ++ + i  k  ++ I      s  D +lr ++d+k+i++ v+y   pe++++  ++ ++d + +    
  gi|488599777|ref|YP_007906248.1| 135 NIRIVSAIAQNGSGIAIKALRNAIFGASEMSTMDRNLRRYMDKKDISGRVIYFKSPEKMIESFEKCQIDGIAIwepy 211
                                       666666666666666666666677777777999************************************98652211 PP

                           DUF3834 121 .aselkkgeafedllkklgvyvpGsCgaavkene 153
                                        ++  kkg  +e + + lg ++   C  av++++
  gi|488599777|ref|YP_007906248.1| 212 lTILAKKGYDVEYFNECLGDFLC--CTLAVNTDS 243
                                       14556777777777777777777..777777664 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   1.9e-05     0.026      26      65 ..      22      61 ..      10      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                      CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                              TrmB 26 deiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                      +ei ++l++++s+v e+L++Le+k  + re+ + + Yr+ 
  gi|488599777|ref|YP_007906248.1| 22 SEIPSILDLSKSTVSEILSNLESKRKIVREQVSSRSYRVW 61
                                      79999**************************999999875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.2     1e-05     0.014       6      44 ..       5      45 ..       3      49 .. 0.92
   2 ?   -1.8   0.1       1.7   2.3e+03       6      20 ..     136     151 ..     134     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                            HTH_24  6 rkILelLqk..nprisqreLAerlglSpstvnrrlkrLeee 44
                                       +I++lL++  + +i q+e+   l+lS+stv++ l +Le++
  gi|488599777|ref|YP_007906248.1|  5 ERIIRLLEEvgEKGILQSEIPSILDLSKSTVSEILSNLESK 45
                                      589************************************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                            HTH_24   6 rkILelLqknpr.isq 20 
                                       ++I +++ +n++ i +
  gi|488599777|ref|YP_007906248.1| 136 IRIVSAIAQNGSgIAI 151
                                       6899999999975655 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.1e-05     0.043      16      48 ..      11      44 ..       5      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                                      HHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                    Fe_dep_repress 16 lse.ekkvvktkdlaerLnvspssVsemlkkLek 48
                                      l+e ++k + ++++ ++L+ s+s+Vse l+ Le+
  gi|488599777|ref|YP_007906248.1| 11 LEEvGEKGILQSEIPSILDLSKSTVSEILSNLES 44
                                      5668888999*********************986 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2     7e-05     0.096      87     136 ..       2      49 ..       1      54 [. 0.87
   2 ?   -3.7   0.0       4.6   6.3e+03      87     108 ..      92     113 ..      88     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                           DUF1670  87 lrkkrivRlfnEAyeqealltqsDlalllgvstrtvskqvkeyqeeegiv 136
                                       l ++ri+Rl +E  e++ l  qs++ ++l  s++tvs+  +++  +++iv
  gi|488599777|ref|YP_007906248.1|   2 LAEERIIRLLEEVGEKGIL--QSEIPSILDLSKSTVSEILSNLESKRKIV 49 
                                       6789*********998855..99********************7666665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.6
                           DUF1670  87 lrkkrivRlfnEAyeqealltq 108
                                       l    ivR+f++A e    l+q
  gi|488599777|ref|YP_007906248.1|  92 LDCGMIVRVFDDAIELTKALSQ 113
                                       5556789999999886666665 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   0.3   0.00011      0.15       6      40 ..       6      43 ..       6      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      HHHHHHTT.SSEEH..HHHHHHHTS-HHHHHHHHHHHH CS
                             HTH_5  6 kILklLae.gelcv..celaeelglsqstvShHLkkLr 40
                                      +I++lL+e ge+ +  +e+  +l+ls+stvS+ L+ L+
  gi|488599777|ref|YP_007906248.1|  6 RIIRLLEEvGEKGIlqSEIPSILDLSKSTVSEILSNLE 43
                                      588888888777665599**************999997 PP

>> Cul7  Mouse development and cellular proliferation protein Cullin-7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.16       7      34 ..      81     108 ..      76     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                              Cul7   7 rdeYaeYvrenlkpGMrVrlledyeevs 34 
                                       + eYa  ++ +l+ GM+Vr+ +d  e++
  gi|488599777|ref|YP_007906248.1|  81 STEYAYLIKSALDCGMIVRVFDDAIELT 108
                                       679******************9987765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00021      0.29      17      49 ..      18      50 ..       3      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieR 49
                                      ++ +se+ + l +skstv+++l  Le k  i R
  gi|488599777|ref|YP_007906248.1| 18 GILQSEIPSILDLSKSTVSEILSNLESKRKIVR 50
                                      36789*********************9865555 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 ?   10.3   0.1   0.00044      0.61       8      59 ..      11      58 ..       7      68 .. 0.84
   2 ?   -1.6   0.0       2.3   3.2e+03      55      69 ..     173     187 ..     133     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00044
                    B-block_TFIIIC  8 LelIassRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatk 59
                                      Le+++   ++Gi+qs++ ++++ +++ +  +l  Le+k  Iv+ ++ +s  +
  gi|488599777|ref|YP_007906248.1| 11 LEEVG---EKGILQSEIPSILDLSKSTVSEILSNLESKRKIVREQV-SSRSY 58
                                      55554...68***********************************9.55554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                    B-block_TFIIIC  55 dsatkksistsllvl 69 
                                       ++++kk is+ ++++
  gi|488599777|ref|YP_007906248.1| 173 RYMDKKDISGRVIYF 187
                                       566666677766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2192.58
//
Query:       gi|488599778|ref|YP_007906249.1|  [L=197]
Description: phosphatidylserine decarboxylase precursor-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-31  108.7   1.8    3.2e-28   98.6   0.4    2.1  2  PS_Dcarbxylase   Phosphatidylserine decarboxylase
    4.4e-06   26.8   0.3      0.025   14.8   0.0    3.3  3  Peptidase_M23    Peptidase family M23
    2.2e-05   24.2   2.0        2.1    8.2   0.0    3.5  4  Biotin_lipoyl    Biotin-requiring enzyme
    0.00023   20.9   5.2      0.052   13.4   0.1    3.5  4  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0014   18.6   0.6       0.26   11.3   0.0    3.1  3  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.014   15.4   0.0       0.26   11.3   0.0    2.2  2  Apocytochr_F_C   Apocytochrome F, C-terminal
      0.027   14.2   0.8         23    4.8   0.0    3.7  3  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
       0.22   12.2   0.4        8.7    7.1   0.1    2.8  3  HlyD_3           HlyD family secretion protein
       0.91    9.4   5.8        2.7    7.9   5.8    1.8  1  PsbT             Photosystem II reaction centre T protein
        2.3    8.0   5.0       0.69    9.6   0.4    2.3  2  TCR_zetazeta     T-cell surface glycoprotein CD3 zeta chain


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   0.1   0.00025      0.45       4      35 ..      45      73 ..      43      76 .. 0.83
   2 !   98.6   0.4   1.8e-31   3.2e-28      71     199 ..      75     194 ..      70     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                    PS_Dcarbxylase  4 ffvrklkdgaRpidddpgaivsPaDgrilqig 35
                                      f   +++d+ R i  ++g ivsPaDgr+  +g
  gi|488599778|ref|YP_007906249.1| 45 FTLLFFRDPPRDI--GEG-IVSPADGRVDFVG 73
                                      677899*******..665.********97765 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 1.8e-31
                    PS_Dcarbxylase  71 yfvviyLspgdyHryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlvie.wkGkvavvpvGatnvgs 146
                                         + i++sp+d+H+++aPvsg+ve++ + +G ++++     ++        eR+ + i+ +kG + v++++++++++
  gi|488599778|ref|YP_007906249.1|  75 RRIEIFMSPFDCHVNRAPVSGVVEKVVYKKGSFIPAYRR--NDF------SERNEIFIRnEKGLFRVIQIAGFFARR 143
                                       5689****************************9976443..333......679999999449*************** PP

                    PS_Dcarbxylase 147 ivlnvlkgdelkkGeelGyFqfGStvvlvfeagkfieslvekgqkvkmGeklg 199
                                       i+++v++gd+++kG+++G+++fGS+vvl ++ g  + + v++g+k+k+G++++
  gi|488599778|ref|YP_007906249.1| 144 INCYVKEGDFVEKGQKIGIIKFGSRVVLEIPDG--YAFVVKEGEKIKAGRTIA 194
                                       *********************************..9999***********986 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.034        60      13      30 ..      58      75 ..      52      82 .. 0.86
   2 !   14.8   0.0   1.4e-05     0.025      18      72 ..      91     163 ..      84     170 .. 0.66
   3 ?    4.3   0.1     0.026        46      55      70 ..     179     194 ..     175     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.034
                                      T-EEEESSSEEEEEEEEE CS
                     Peptidase_M23 13 gtpVlAaadGtVvfagkk 30
                                      g+ ++++adG+V f+g++
  gi|488599778|ref|YP_007906249.1| 58 GEGIVSPADGRVDFVGER 75
                                      888*********999985 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       ESSSEEEEEEEEET............TTEEEEEEEECTCEEEEEEE....ESEES..S-TTEEE-TTCEEEEE CS
                     Peptidase_M23  18 AaadGtVvfagkke............gyGnvviidhgdgystlyah....lskis..vkegqkVkaGqvIGtv 72 
                                       A+ +G+V ++ +k+            +  n + i+ ++g++ ++        +i+  vkeg++V++Gq+IG +
  gi|488599778|ref|YP_007906249.1|  91 APVSGVVEKVVYKKgsfipayrrndfSERNEIFIRNEKGLFRVIQIagffARRINcyVKEGDFVEKGQKIGII 163
                                       666666655555334555666666645578888888888554443322223445577**************86 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.026
                                       ESS-TTEEE-TTCEEE CS
                     Peptidase_M23  55 isvkegqkVkaGqvIG 70 
                                       + vkeg+k+kaG +I+
  gi|488599778|ref|YP_007906249.1| 179 FVVKEGEKIKAGRTIA 194
                                       469***********98 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.6   6.5e+03      45      54 ..      61      70 ..      60      72 .. 0.82
   2 !    6.9   0.0    0.0031       5.6      47      63 ..      91     107 ..      88     110 .. 0.89
   3 !    8.2   0.0    0.0012       2.1      17      36 ..     144     163 ..     134     165 .. 0.84
   4 !    6.6   0.0    0.0038       6.7      18      34 ..     178     194 ..     168     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                                      EEBSSSEEEE CS
                     Biotin_lipoyl 45 ieapkaGvvk 54
                                      i +p++G+v 
  gi|488599778|ref|YP_007906249.1| 61 IVSPADGRVD 70
                                      7899999985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0031
                                       BSSSEEEEEESSTTTEE CS
                     Biotin_lipoyl  47 apkaGvvkeilvkeGdt 63 
                                       ap++Gvv+++++k+G+ 
  gi|488599778|ref|YP_007906249.1|  91 APVSGVVEKVVYKKGSF 107
                                       89************985 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0012
                                       CSESSSTTCEE-TTSEEEEE CS
                     Biotin_lipoyl  17 vevlvkvGdkVkagqvlaev 36 
                                       ++ +vk+Gd V++gq + ++
  gi|488599778|ref|YP_007906249.1| 144 INCYVKEGDFVEKGQKIGII 163
                                       6789***********98776 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0038
                                       SESSSTTCEE-TTSEEE CS
                     Biotin_lipoyl  18 evlvkvGdkVkagqvla 34 
                                       ++ vk+G+k+kag ++a
  gi|488599778|ref|YP_007906249.1| 178 AFVVKEGEKIKAGRTIA 194
                                       57899999999999887 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.7   8.4e+03       7      13 ..      63      69 ..      61      70 .. 0.79
   2 !    5.5   0.0    0.0087        16       7      23 ..      91     107 ..      90     110 .. 0.89
   3 !   13.4   0.1   2.9e-05     0.052      17      33 ..     147     163 ..     145     164 .. 0.91
   4 ?    3.0   0.0     0.052        93      18      31 ..     181     194 ..     178     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.7
                   Biotin_lipoyl_2  7 apvsGrV 13
                                      +p +GrV
  gi|488599778|ref|YP_007906249.1| 63 SPADGRV 69
                                      8999*99 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0087
                   Biotin_lipoyl_2   7 apvsGrVaqlnVkdGqr 23 
                                       apvsG+V+++  k G  
  gi|488599778|ref|YP_007906249.1|  91 APVSGVVEKVVYKKGSF 107
                                       89***********9976 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 2.9e-05
                   Biotin_lipoyl_2  17 nVkdGqrVkaGdvLael 33 
                                       +Vk+G+ V++G+ + ++
  gi|488599778|ref|YP_007906249.1| 147 YVKEGDFVEKGQKIGII 163
                                       8************9887 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.052
                   Biotin_lipoyl_2  18 VkdGqrVkaGdvLa 31 
                                       Vk+G  +kaG ++a
  gi|488599778|ref|YP_007906249.1| 181 VKEGEKIKAGRTIA 194
                                       9*********8887 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 ?    0.5   0.1      0.32   5.7e+02      71      80 ..      91     100 ..      81     107 .. 0.85
   2 !   11.3   0.0   0.00014      0.26      40      59 ..     142     161 ..     104     171 .. 0.81
   3 ?    3.3   0.0     0.042        76      44      59 ..     179     194 ..     172     197 .] 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.32
                            RnfC_N  71 asvsGtVkai 80 
                                       a+vsG V ++
  gi|488599778|ref|YP_007906249.1|  91 APVSGVVEKV 100
                                       9******988 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00014
                            RnfC_N  40 apakplvkvgdkVlkGqkia 59 
                                        + ++ vk+gd V+kGqki+
  gi|488599778|ref|YP_007906249.1| 142 RRINCYVKEGDFVEKGQKIG 161
                                       566899*************9 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.042
                            RnfC_N  44 plvkvgdkVlkGqkia 59 
                                        +vk+g+k++ G  ia
  gi|488599778|ref|YP_007906249.1| 179 FVVKEGEKIKAGRTIA 194
                                       69************98 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 ?    2.2   0.0     0.098   1.8e+02       6      60 ..      90     160 ..      86     163 .. 0.65
   2 ?   11.3   0.0   0.00015      0.26      33      61 ..     166     194 ..     155     197 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.098
                                       B-SSSEEEEEEEEEES............SEEEEEEETSTSEEE-EEEE....SSS-BS--ST-EE-TT-BS CS
                    Apocytochr_F_C   6 kasaaGtiskiekeek............ggtevtietedgeavvetip....aGpelivsegqevkageal 60 
                                       +a+++G ++k+  ++             + +e+ i++e+g   v +i+       +  v+eg+ v++g+++
  gi|488599778|ref|YP_007906249.1|  90 RAPVSGVVEKVVYKKGsfipayrrndfsERNEIFIRNEKGLFRVIQIAgffaRRINCYVKEGDFVEKGQKI 160
                                       67888888887766663444444443434888999999997766666421113456679999999999876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                                       SEEE-EEEESSS-BS--ST-EE-TT-BSC CS
                    Apocytochr_F_C  33 geavvetipaGpelivsegqevkagealt 61 
                                       g+ vv +ip G  ++v+eg+++kag +++
  gi|488599778|ref|YP_007906249.1| 166 GSRVVLEIPDGYAFVVKEGEKIKAGRTIA 194
                                       778999*******************9876 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 ?    0.7   0.0      0.22     4e+02      39      53 ..      60      74 ..      53      88 .. 0.78
   2 ?    4.8   0.0     0.013        23      84     101 ..     144     161 ..     116     170 .. 0.87
   3 ?    4.3   0.0     0.018        33      82     100 ..     175     193 ..     162     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.22
                                      EEEES--EEEEE--S CS
                        PTS_EIIA_1 39 kvvapvdGkvekvfp 53
                                       +v+p+dG+v  v +
  gi|488599778|ref|YP_007906249.1| 60 GIVSPADGRVDFVGE 74
                                      489999999988765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
                                       EEES----SEE-SEEEEE CS
                        PTS_EIIA_1  84 FellvkegdkVkagdklv 101
                                        +++vkegd V++g+k+ 
  gi|488599778|ref|YP_007906249.1| 144 INCYVKEGDFVEKGQKIG 161
                                       5789***********985 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.018
                                       TTEEES----SEE-SEEEE CS
                        PTS_EIIA_1  82 egFellvkegdkVkagdkl 100
                                       +g+   vkeg+k+kag ++
  gi|488599778|ref|YP_007906249.1| 175 DGYAFVVKEGEKIKAGRTI 193
                                       78999***********987 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   2.6e+03       2      13 ..      61      72 ..      60      78 .. 0.83
   2 ?    7.1   0.1    0.0048       8.7       3      23 ..      90     110 ..      88     112 .. 0.93
   3 ?    1.7   0.0      0.23   4.2e+02      15      31 ..     148     164 ..     143     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                            HlyD_3  2 lrApvdGvvvel 13
                                      + +p dG+v ++
  gi|488599778|ref|YP_007906249.1| 61 IVSPADGRVDFV 72
                                      789******987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0048
                            HlyD_3   3 rApvdGvvvelnveegevvqa 23 
                                       rApv+Gvv ++ +++g++++a
  gi|488599778|ref|YP_007906249.1|  90 RAPVSGVVEKVVYKKGSFIPA 110
                                       8*****************987 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.23
                            HlyD_3  15 veegevvqagdelleii 31 
                                       v+eg++v++g+++  i 
  gi|488599778|ref|YP_007906249.1| 148 VKEGDFVEKGQKIGIIK 164
                                       68999999999998775 PP

>> PsbT  Photosystem II reaction centre T protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.8    0.0015       2.7       8      28 ..      34      55 ..      32      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                              PsbT  8 lllvltL.gvlFFAIaFRePPr 28
                                      +l +l L  +lF   +FR+PPr
  gi|488599778|ref|YP_007906249.1| 34 FLIILSLfSLLFTLLFFRDPPR 55
                                      555555515778889******9 PP

>> TCR_zetazeta  T-cell surface glycoprotein CD3 zeta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.5       0.7   1.3e+03      14      24 ..      10      22 ..       6      24 .. 0.70
   2 ?    9.6   0.4   0.00039      0.69      10      26 ..      36      52 ..      35      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.7
                      TCR_zetazeta 14 iYgiI..iTaLFl 24
                                      iY+ I  iT LFl
  gi|488599778|ref|YP_007906249.1| 10 IYAEItmITVLFL 22
                                      6664444999996 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00039
                      TCR_zetazeta 10 giLliYgiIiTaLFlRe 26
                                      +iL ++++ +T+LF+R+
  gi|488599778|ref|YP_007906249.1| 36 IILSLFSLLFTLLFFRD 52
                                      69*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1352.21
//
Query:       gi|488599779|ref|YP_007906250.1|  [L=259]
Description: archaeosortase A, PGF-CTERM-specific [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   44.6  19.3    1.7e-11   44.1  19.3    1.2  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1  19.3   9.5e-16   1.7e-11      96     250 ..      46     226 ..       3     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 9.5e-16
                   Exosortase_EpsH  96 G...............................lralrlllfpllllllalPlpavlvaqlslpLqllvaavagflls 141
                                       G                                  l l +f+ l  ++++P   ++   l  +L+  +a++++ l +
  gi|488599779|ref|YP_007906250.1|  46 GdyfnsviivsafilftligiaiiaerdvsrlNTFLNLSAFSALSAIFYFP--FAMNGFLGDFLISKTAQLTVMLAN 120
                                       022222222222222222335666666888888888888889999999999..3444555669************** PP

                   Exosortase_EpsH 142 llgipvereGnviql.ptgqveVaeaCsGlrsllallalglllallfrrrlwkrklllllaavpiaflaNlvRilll 217
                                       +lg+++++ G  i   +   ve+  aC+G++s+    ++g+ l   +r  ++ rkl  ++++vp+++++Nl+R++++
  gi|488599779|ref|YP_007906250.1| 121 FLGYNIQMYGDRILYlNGKCVEIILACTGIESIAL--FAGATL--GMRADWS-RKLKAFMVSVPVIYVLNLLRNVFI 192
                                       **********6555525555*********776643..333332..2555555.66********************** PP

                   Exosortase_EpsH 218 vllayh..ygpeaaegllHeiaGwllfgvalllll 250
                                       ++ +++  +g++++   +H i+  +l  +al+l+ 
  gi|488599779|ref|YP_007906250.1| 193 TVSFGYswFGENSF-YIAHHIISKILATLALILIS 226
                                       99987633689999.78887766666655544432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1487.94
//
Query:       gi|488599780|ref|YP_007906251.1|  [L=213]
Description: Histidinol phosphatase and related hydrolases of the PHP family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   37.2   0.9    1.6e-08   35.1   0.9    1.9  1  PHP           PHP domain
      0.009   15.5   0.3        2.1    7.7   0.1    2.2  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.024   14.6   0.0    1.7  1  DUF1027       Protein of unknown function (DUF1027)
      0.055   13.2   0.0       0.39   10.5   0.0    2.3  2  PHP_C         PHP-associated
       0.09   12.6   0.0       0.17   11.8   0.0    1.4  1  SIS           SIS domain


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.9   4.4e-12   1.6e-08       1     166 [.       3     161 ..       3     162 .. 0.55

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 4.4e-12
                                       EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT.......HHHHHHHHHHH.HTTTTSEEEEEEE... CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlf.......gyvefykaakk.kykagikpiiGleayv 68 
                                       dlH+H++ys ++ +++   +++kkake++lk iai Dh+  +       ++v+   +++k + + +i+++  +e+ +
  gi|488599780|ref|YP_007906251.1|   3 DLHIHSNYSdGS-SPI--RDIAKKAKERNLKVIAIADHSMEHkfgldeaKAVKRQLEIEKySSAYNIEILSAVECGI 76 
                                       89*******444.666..********************988877777774555544554433446899999999665 PP

                                       .........................E....EHHHHHHHHHHHHH..........HHHHHH......S.......... CS
                                       xxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxx RF
                               PHP  69 addse..........kerpshltllaknqeGyknllkllskaylegfyrkpridkellek......hsegLivlsgc 129
                                         d+e                                 +++a +++ +++ r+ k + +       h          
  gi|488599780|ref|YP_007906251.1|  77 LADGEimipdfdfdiI--------------------LASIHANISFKEYNLRVRKCIEKYdvdviaH---------- 123
                                       5555433322222220....................2222222222233333332222222222222.......... PP

                                       ........TTGG..HHHHHHHHHHHHHHHC.T-EEEEEG CS
                                       xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 130 lkGevfealdli..eveekaeealeelakifgdyiEint 166
                                       l +e+f  +d    +  e a + +++++++ +++iE+nt
  gi|488599780|ref|YP_007906251.1| 124 LYSEMFHPFDFQlnDCVEDALDLIDFIKDN-DVAIELNT 161
                                       445555544333334434455566666665.66666665 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 !    6.0   0.0     0.002       7.1      27      69 ..      14      57 ..       1      77 [. 0.74
   2 !    7.7   0.1    0.0006       2.1     121     164 ..     114     163 ..     104     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.002
                                      HHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHH CS
                      AP_endonuc_2 27 deelrelrkaldelglriaslslftrfgypdederear.reesv 69
                                       + +r+++k ++e++l++ ++  ++  +  + de +a+ r+  +
  gi|488599780|ref|YP_007906251.1| 14 SSPIRDIAKKAKERNLKVIAIADHSMEHKFGLDEAKAVkRQLEI 57
                                      4679*****************99999998888755555555444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0006
                                       HHHTSEEEEE--TTTTSSSTC......HHHHHHHHHHTTTTEEEEEEHHH CS
                      AP_endonuc_2 121 ekegvklalEtlagsgvelgd......eelarlldavdspnvgvclDtgH 164
                                       ek++v ++++   + ++ +        e++++l+d +++  v + l+t+H
  gi|488599780|ref|YP_007906251.1| 114 EKYDVDVIAHLYSEMFHPFDFqlndcvEDALDLIDFIKDNDVAIELNTAH 163
                                       678888888888888876666888899**********************9 PP

>> DUF1027  Protein of unknown function (DUF1027)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.7e-06     0.024       6      59 ..     104     158 ..      99     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.7e-06
                           DUF1027   6 kyel.iknykdafdeeeleeryseildkydYivGDigyekLRLkGFykdenkkak 59 
                                       +y+l +++  + +d + +++ yse+++ +d+ + D   + L L  F+kd+   ++
  gi|488599780|ref|YP_007906251.1| 104 EYNLrVRKCIEKYDVDVIAHLYSEMFHPFDFQLNDCVEDALDLIDFIKDNDVAIE 158
                                       5665345667899***********************************9966554 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.32   1.2e+03       2      19 ..     104     121 ..     103     122 .. 0.83
   2 ?   10.5   0.0   0.00011      0.39      20      34 ..     181     195 ..     171     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.32
                             PHP_C   2 eaNrrArrfAeklglpgt 19 
                                       e N r+r+  ek+++ ++
  gi|488599780|ref|YP_007906251.1| 104 EYNLRVRKCIEKYDVDVI 121
                                       6799*********98665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                             PHP_C  20 gGSDAHrleeVGray 34 
                                        GSDAH+l+ +G + 
  gi|488599780|ref|YP_007906251.1| 181 IGSDAHSLARIGDVR 195
                                       59**********876 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.7e-05      0.17      62      91 ..      10      39 ..       3      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                                      SSSHHHHHHHHHHHHHHTTSEEEEEESSTT CS
                               SIS 62 fsgetkdlvaaaelakergakiiaITdskg 91
                                      +s+ +++  + a++aker+ k+iaI+d+++
  gi|488599780|ref|YP_007906251.1| 10 YSDGSSPIRDIAKKAKERNLKVIAIADHSM 39
                                      899999999*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1274.35
//
Query:       gi|488599781|ref|YP_007906252.1|  [L=137]
Description: ADP-ribose pyrophosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-20   72.4   0.0    4.1e-20   72.2   0.0    1.0  1  NUDIX     NUDIX domain
    0.00016   21.2   0.0      0.019   14.5   0.0    2.1  2  DUF4916   Domain of unknown function (DUF4916)
  ------ inclusion threshold ------
       0.19   11.3   0.0       0.28   10.8   0.0    1.1  1  dCache_3  Double sensory domain of two-component sensor kinas


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   6.9e-24   4.1e-20       9     128 ..      13     123 ..       6     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 6.9e-24
                                       EEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   9 vllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdehei 84 
                                       v +++   ++l+rr++ pf+g ++lPgG ve+gE++e A++REl+EEtGl+ +  +l+g    +++++ ++++ h++
  gi|488599781|ref|YP_007906252.1|  13 VPYRGG--IVLIRRKNEPFKGyYALPGGIVEYGESVESAVLRELKEETGLDGKIYKLVG----VYSDPNRDPRGHFV 83 
                                       366666..*************778**************************999999999....7788888888**** PP

                                       EEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHH CS
                             NUDIX  85 lyvfleevegelepndenevsevrwvpleellkeklaaesrkll 128
                                       +++f  + +g+l+ +   + +ev  ++l+el  ++la +++k++
  gi|488599781|ref|YP_007906252.1|  84 SVCFIVKGKGRLKAG--SDAREVGVFSLDEL--PELAFDHKKMI 123
                                       *****8888888887..66668888******..78888888776 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0027        16      55      79 ..      35      59 ..      15      62 .. 0.83
   2 !   14.5   0.0   3.2e-06     0.019     106     149 ..      74     117 ..      68     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0027
                                      -EEEE--TT--HHHHHHHHHHHHH- CS
                           DUF4916 55 lvsGrvlyhetvreallrhiekdlG 79
                                      l  G v y e+v  a+lr+++++ G
  gi|488599781|ref|YP_007906252.1| 35 LPGGIVEYGESVESAVLRELKEETG 59
                                      66799**************998876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.2e-06
                                       SEE-TT-EEEEEEEEEEB-S-----TTEEEEEEE-HHHHTSHHH CS
                           DUF4916 106 eytdprqhavslayvvpvaGdceprqdaleleWltpeealseev 149
                                       +  dpr h vs++++v  +G  ++ +da e+  ++ +e  + ++
  gi|488599781|ref|YP_007906252.1|  74 PNRDPRGHFVSVCFIVKGKGRLKAGSDAREVGVFSLDELPELAF 117
                                       568****************************9999888765554 PP

>> dCache_3  Double sensory domain of two-component sensor kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.8e-05      0.28     134     160 ..      38      64 ..      36      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.8e-05
                          dCache_3 134 GavvfgvsLnndllrelkeatgadiai 160
                                       G+v++g+s ++++lrelke+tg+d  i
  gi|488599781|ref|YP_007906252.1|  38 GIVEYGESVESAVLRELKEETGLDGKI 64 
                                       99********99**********99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 957.10
//
Query:       gi|488599782|ref|YP_007906253.1|  [L=102]
Description: DNA-directed RNA polymerase, subunit M [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   65.6   3.2    2.5e-18   65.6   3.2    3.1  3  TFIIS_C         Transcription factor S-II (TFIIS)
    2.6e-10   40.0  14.9    1.1e-09   38.0   3.4    3.1  3  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
    5.4e-06   26.3  12.2    0.00014   21.8   1.0    3.2  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
    3.1e-05   23.8   6.1     0.0042   17.0   0.1    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00014   21.3  10.6      0.023   14.2   1.6    3.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00041   20.3   9.8      0.026   14.6   1.4    2.7  2  DZR             Double zinc ribbon
    0.00097   18.5  12.0        1.7    8.2   0.1    4.1  4  zf-ribbon_3     zinc-ribbon domain
     0.0038   16.9  17.4        2.4    8.0   0.1    4.2  4  zinc_ribbon_2   zinc-ribbon domain
      0.005   17.0   6.1       0.24   11.6   0.6    2.3  2  DUF2387         Probable metal-binding protein (DUF2387)
     0.0087   15.7   6.8      0.012   15.3   0.4    2.6  2  TackOD1         Thaumarchaeal output domain 1
     0.0093   15.8   9.7        3.6    7.6   0.1    4.0  4  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.021   15.0   2.1         19    5.6   0.1    3.4  3  zf-RING_7       C4-type zinc ribbon domain
      0.026   13.8   2.7       0.44    9.8   0.1    2.6  3  Gmx_para_CXXCG  Protein of unknown function (Gmx_para_CXXCG)
      0.038   14.1  11.1       0.75    9.9   0.1    3.8  4  UPF0547         Uncharacterised protein family UPF0547
      0.057   13.4  10.4       0.14   12.2   1.4    2.8  3  zinc-ribbons_6  zinc-ribbons
      0.063   13.1   0.4      0.063   13.1   0.4    2.0  2  FdhE            Protein involved in formate dehydrogenase for
      0.065   13.3   8.2          2    8.5   0.0    3.9  4  Rubredoxin      Rubredoxin
      0.067   13.2   9.4      0.079   13.0   0.4    3.0  3  HypA            Hydrogenase/urease nickel incorporation, meta
       0.09   12.9  16.5        2.1    8.5   0.2    4.1  4  Zn-ribbon_8     Zinc ribbon domain
       0.13   12.3   0.5       0.13   12.3   0.5    3.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.14   12.0   3.6       0.35   10.7   0.0    2.3  2  zf-ZPR1         ZPR1 zinc-finger domain
       0.21   11.3   0.1       0.21   11.3   0.1    3.0  2  Baculo_LEF5_C   Baculoviridae late expression factor 5 C-term
       0.24   11.2  15.8        0.3   10.9   3.5    3.6  3  A2L_zn_ribbon   A2L zinc ribbon domain
       0.65   10.1   8.7        3.2    7.8   1.1    3.5  3  CpXC            CpXC protein
       0.75    9.8   7.9       0.47   10.5   0.6    2.8  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.75   10.1  12.9       0.68   10.2   3.2    2.9  2  IBR             IBR domain, a half RING-finger domain
       0.88    9.5   5.9       0.35   10.8   0.1    2.2  2  eIF-5_eIF-2B    Domain found in IF2B/IF5
          1    9.7   6.0        2.9    8.2   0.1    3.4  3  zinc_ribbon_9   zinc-ribbon
        1.4    8.8   9.2        9.3    6.1   3.4    3.2  3  PADR1           PADR1 (NUC008) domain
        1.4    8.6  12.0         19    4.9   0.1    4.0  4  zf_UBZ          Ubiquitin-Binding Zinc Finger
        1.7    9.1   9.0          9    6.7   0.5    3.1  3  Opy2            Opy2 protein
        1.7    8.8   9.0         33    4.7   9.0    2.4  1  FYVE            FYVE zinc finger
        2.5    8.3  17.7         28    4.9   0.4    4.3  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        2.5    8.1  17.3        0.3   11.0   0.9    4.0  4  zinc_ribbon_4   zinc-ribbon domain
        2.7    8.0  16.6        2.3    8.2   2.7    3.8  2  Nudix_N_2       Nudix N-terminal
        2.7    8.0  12.1         22    5.1   0.2    4.0  4  Zn_ribbon_SprT  SprT-like zinc ribbon domain
          3    7.6  18.3        5.6    6.8   0.3    4.1  4  Rubredoxin_2    Rubredoxin metal binding domain
        3.6    7.8  13.0         22    5.3   0.2    3.6  3  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        4.6    8.0  16.1        7.3    7.4   1.4    4.1  3  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        4.8    7.3   7.7         13    5.9   2.1    3.0  3  zf-BED          BED zinc finger
        5.9    6.7  14.5         16    5.3   0.4    3.6  3  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        6.5    6.2  14.2        1.7    8.1   3.0    3.3  2  zf-TFIIB        Transcription factor zinc-finger
        6.5    6.8  11.8        8.8    6.4   0.0    3.8  3  YhfH            YhfH-like protein
        6.8    6.5  10.2         11    5.7   0.3    3.9  4  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
        9.9    6.4  12.7       0.71   10.1   2.7    2.7  3  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        9.9    6.2  16.9        2.5    8.1   0.3    4.1  4  DUF1936         Domain of unknown function (DUF1936)


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 ?    5.8   0.3     0.031        12       3      13 ..       4      14 ..       2      17 .. 0.84
   2 ?    2.9   0.7      0.26     1e+02       2       9 ..      19      26 ..      18      29 .. 0.59
   3 !   65.6   3.2   6.4e-21   2.5e-18       2      39 .]      62      99 ..      61      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.031
                           TFIIS_C  3 CpkCgsreayf 13
                                      CpkC+s  +y+
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIYY 14
                                      *****988887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.26
                           TFIIS_C  2 kCpkCgsr 9 
                                       C kCg +
  gi|488599782|ref|YP_007906253.1| 19 VCRKCGYE 26
                                      46666654 PP

  == domain 3  score: 65.6 bits;  conditional E-value: 6.4e-21
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                       Cp+Cg+reay++ +Q+R+aDE++++f++CtkCg++Wr
  gi|488599782|ref|YP_007906253.1| 62 ICPECGNREAYWWLRQLRAADESEVRFFRCTKCGKTWR 99
                                      6************************************8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   3.4   2.9e-12   1.1e-09       1      34 [.       1      30 [.       1      32 [. 0.95
   2 ?    5.2   0.6     0.051        20       4       9 ..      63      68 ..      62      69 .. 0.96
   3 ?    4.3   0.1     0.092        36      16      28 ..      82      95 ..      78      97 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.9e-12
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepad 34
                                      ++FCpkC++ +++ + k +    Cr+CgYe++ +
  gi|488599782|ref|YP_007906253.1|  1 MEFCPKCKSIMIYYQNKAV----CRKCGYEKEVG 30
                                      99*****************....********986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.051
                                      ESTTTS CS
                    RNA_POL_M_15KD  4 CpkCgN 9 
                                      Cp+CgN
  gi|488599782|ref|YP_007906253.1| 63 CPECGN 68
                                      *****9 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.092
                                      CSCCCE.EEESSSS CS
                    RNA_POL_M_15KD 16 dkegkn.feCrqCg 28
                                      d++ ++ f C +Cg
  gi|488599782|ref|YP_007906253.1| 82 DESEVRfFRCTKCG 95
                                      555556799***97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.5      0.17        65      21      27 ..       4      10 ..       2      15 .. 0.77
   2 !    8.4   0.1    0.0054       2.1      15      28 ..      14      27 ..      11      33 .. 0.82
   3 !   21.8   1.0   3.5e-07   0.00014      19      46 .]      61      97 ..      56      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                     Zn_Tnp_IS1595 21 CPhCgsr 27
                                      CP+C+s 
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSI 10
                                      ****986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0054
                     Zn_Tnp_IS1595 15 WpngfvCPhCgsrk 28
                                      + n+ vC +Cg++k
  gi|488599782|ref|YP_007906253.1| 14 YQNKAVCRKCGYEK 27
                                      6799*******983 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 3.5e-07
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt........rglfqCkeCrkq 46
                                       +CP Cg+r  ++ +++         + f+C +C+k+
  gi|488599782|ref|YP_007906253.1| 61 AICPECGNReAYWWLRQlraadeseVRFFRCTKCGKT 97
                                      68*******55555555999**************985 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   1.9    0.0039       1.5      31      55 ..       4      26 ..       2      28 .. 0.94
   2 !   17.0   0.1   1.1e-05    0.0042      27      56 ..      59      98 ..      34     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0039
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe 55
                                      C++C s++ +   +++ +C++Cg+e
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIY--YQNKAVCRKCGYE 26
                                      **********..***********97 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.1e-05
                    OrfB_Zn_ribbon 27 TSktCseCgsknke..........alsgrtfkCpnCgfea 56
                                      T   C+eCg +  +          + + r f+C++Cg ++
  gi|488599782|ref|YP_007906253.1| 59 TTAICPECGNREAYwwlrqlraadESEVRFFRCTKCGKTW 98
                                      7889******************99999**********986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.5   0.00059      0.23       3      27 ..       4      25 ..       2      30 .. 0.82
   2 !   14.2   1.6   5.9e-05     0.023       2      26 ..      62      95 ..      61     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00059
                                      ETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGl 27
                                      CP+C+s ++++    +  vC +CG+
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIYYQ---NKAVCRKCGY 25
                                      ******887554...679******7 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.9e-05
                                      EETTTTCEE.C.......HEETSTTCE.EESSSS CS
                      TF_Zn_Ribbon  2 kCPnCgstn.l.......veDpergel.vCtdCG 26
                                      +CP+Cg+++ +         D+++  + +Ct+CG
  gi|488599782|ref|YP_007906253.1| 62 ICPECGNREaYwwlrqlrAADESEVRFfRCTKCG 95
                                      6********77*****998887777777*****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.4   6.6e-05     0.026      13      37 ..       2      26 ..       1      33 [. 0.82
   2 !    9.7   1.7    0.0021      0.82       8      37 ..      56      97 ..      51     102 .] 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-05
                               DZR 13 rfCseCgtklkavaaedrCpsCgek 37
                                      +fC++C++ +  ++++ +C +Cg++
  gi|488599782|ref|YP_007906253.1|  2 EFCPKCKSIMIYYQNKAVCRKCGYE 26
                                      5999999999988999999999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0021
                               DZR  8 lppdarfCseCgtk.....lkavaa.......edrCpsCgek 37
                                      lp     C+eCg++     l++  a         rC +Cg+ 
  gi|488599782|ref|YP_007906253.1| 56 LPTTTAICPECGNReaywwLRQLRAadesevrFFRCTKCGKT 97
                                      566778999999998888844443456688888899999875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0044       1.7       2      10 ..       1       9 [.       1      13 [. 0.78
   2 ?    5.3   0.2     0.035        14      18      24 ..      19      25 ..      15      26 .. 0.88
   3 !    8.1   0.2    0.0047       1.8       4      10 ..      62      68 ..      58      69 .. 0.66
   4 ?    3.0   0.2      0.18        70      19      24 ..      91      96 ..      88      97 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0044
                       zf-ribbon_3  2 tvrCPnCGa 10
                                      + +CP+C++
  gi|488599782|ref|YP_007906253.1|  1 MEFCPKCKS 9 
                                      678999987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.035
                       zf-ribbon_3 18 vCpyCGt 24
                                      vC +CG+
  gi|488599782|ref|YP_007906253.1| 19 VCRKCGY 25
                                      8*****8 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0047
                       zf-ribbon_3  4 rCPnCGa 10
                                       CP+CG+
  gi|488599782|ref|YP_007906253.1| 62 ICPECGN 68
                                      5666664 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.18
                       zf-ribbon_3 19 CpyCGt 24
                                      C++CG+
  gi|488599782|ref|YP_007906253.1| 91 CTKCGK 96
                                      666664 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.3     0.051        20      15      19 ..       3       7 ..       2       9 .. 0.73
   2 ?    6.4   0.4     0.019       7.3       2       8 ..      20      26 ..      16      32 .. 0.73
   3 !    8.0   0.1    0.0061       2.4      15      20 ..      62      67 ..      54      69 .. 0.58
   4 !    7.5   0.3    0.0087       3.4       1       7 [.      90      96 ..      85      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.051
                     zinc_ribbon_2 15 FCpyC 19
                                      FCp+C
  gi|488599782|ref|YP_007906253.1|  3 FCPKC 7 
                                      77777 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                     zinc_ribbon_2  2 CpnCGae 8 
                                      C +CG+e
  gi|488599782|ref|YP_007906253.1| 20 CRKCGYE 26
                                      6666665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0061
                     zinc_ribbon_2 15 FCpyCG 20
                                       Cp+CG
  gi|488599782|ref|YP_007906253.1| 62 ICPECG 67
                                      566666 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0087
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +C++CG+
  gi|488599782|ref|YP_007906253.1| 90 RCTKCGK 96
                                      5888887 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.6    0.0065       2.5      11      45 ..       4      32 ..       2      55 .. 0.74
   2 !   11.6   0.6    0.0006      0.24       9      37 ..      61      95 ..      58     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0065
                           DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsek 45
                                      CP+C++   i+++ +++     C +Cg+  e  ek
  gi|488599782|ref|YP_007906253.1|  4 CPKCKS---IMIYYQNKAV---CRKCGYEKEVGEK 32
                                      999985...9999999864...8889999888777 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0006
                           DUF2387  9 avCPrCsemD......kirmweedeveyrECvsCg 37
                                      a+CP C +        ++r+ +e ev++  C++Cg
  gi|488599782|ref|YP_007906253.1| 61 AICPECGNREaywwlrQLRAADESEVRFFRCTKCG 95
                                      9*******99999999999999999*********9 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4     3e-05     0.012      88     114 ..       2      28 ..       1      39 [. 0.87
   2 ?    2.7   1.1      0.22        87      96     110 ..      81      95 ..      53     102 .] 0.43

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                           TackOD1  88 evCpkCkSidieeqelihhftCgnvgp 114
                                       e CpkCkSi i  q+   + +Cg+ ++
  gi|488599782|ref|YP_007906253.1|   2 EFCPKCKSIMIYYQNKAVCRKCGYEKE 28 
                                       789**********99999****99765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.22
                           TackOD1  96 idieeqelihhftCg 110
                                       +d +e  ++ + +Cg
  gi|488599782|ref|YP_007906253.1|  81 ADESEVRFFRCTKCG 95 
                                       222333333333333 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.36   1.4e+02      27      33 ..       3       9 ..       1       9 [. 0.78
   2 ?    2.8   0.1      0.29   1.1e+02      13      18 ..      19      24 ..      13      25 .. 0.67
   3 !    7.6   0.1    0.0092       3.6      23      34 ..      57      69 ..      55      71 .. 0.80
   4 ?    7.4   0.1      0.01       4.1       3      19 ..      80      96 ..      78      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.36
                           DUF35_N 27 vCphCgs 33
                                      +Cp+C s
  gi|488599782|ref|YP_007906253.1|  3 FCPKCKS 9 
                                      8999965 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.29
                           DUF35_N 13 rCpdCG 18
                                       C++CG
  gi|488599782|ref|YP_007906253.1| 19 VCRKCG 24
                                      355555 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0092
                           DUF35_N 23 PPr.avCphCgsd 34
                                      P + a+Cp Cg +
  gi|488599782|ref|YP_007906253.1| 57 PTTtAICPECGNR 69
                                      66669*****976 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.01
                           DUF35_N  3 aaaegrLvgqrCpdCGt 19
                                      aa+e ++++ rC++CG+
  gi|488599782|ref|YP_007906253.1| 80 AADESEVRFFRCTKCGK 96
                                      7888889999******7 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 ?    3.1   0.0      0.28   1.1e+02      25      32 ..       3      10 ..       1      11 [. 0.83
   2 ?    5.6   0.1     0.047        19      24      30 ..      61      67 ..      51      67 .. 0.87
   3 ?    4.5   0.0       0.1        40      14      30 ..      75      95 ..      74      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.28
                                      E-TTT--E CS
                         zf-RING_7 25 tCpeCGRI 32
                                      +Cp C  I
  gi|488599782|ref|YP_007906253.1|  3 FCPKCKSI 10
                                      9****998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.047
                                      EE-TTT- CS
                         zf-RING_7 24 vtCpeCG 30
                                      + CpeCG
  gi|488599782|ref|YP_007906253.1| 61 AICPECG 67
                                      68****9 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.1
                                      HHHHCCSTB....-EE-TTT- CS
                         zf-RING_7 14 lselragde....vvtCpeCG 30
                                      l++lra+de     ++C  CG
  gi|488599782|ref|YP_007906253.1| 75 LRQLRAADEsevrFFRCTKCG 95
                                      56789998877666******9 PP

>> Gmx_para_CXXCG  Protein of unknown function (Gmx_para_CXXCG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0011      0.44     167     212 ..      14      59 ..       3      65 .. 0.89
   2 ?    1.4   0.1      0.41   1.6e+02     169     182 ..      59      72 ..      56      90 .. 0.79
   3 ?    3.6   0.1     0.088        34      15      38 ..      76      99 ..      67     102 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                    Gmx_para_CXXCG 167 edreppCetCGreslrlpeepiLdaaslpadlDvFrledfatliva 212
                                        ++++ C +CG e+    ++++L +++  +d+ v   e+++tl  +
  gi|488599782|ref|YP_007906253.1|  14 YQNKAVCRKCGYEKEVGEKSVVLVTKTNREDVPVIEGENIKTLPTT 59 
                                       567899*****************************99999998655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.41
                    Gmx_para_CXXCG 169 reppCetCGreslr 182
                                       +++ C++CG+++++
  gi|488599782|ref|YP_007906253.1|  59 TTAICPECGNREAY 72 
                                       57789999998765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.088
                    Gmx_para_CXXCG 15 GsldaahkwslpgveCptcgatws 38
                                       +l+aa++ ++   +C++cg tw 
  gi|488599782|ref|YP_007906253.1| 76 RQLRAADESEVRFFRCTKCGKTWR 99
                                      567888888888889999*99996 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4      0.23        89      15      20 ..       2       7 ..       1      10 [. 0.67
   2 ?    6.1   0.1      0.03        12      16      23 ..      19      26 ..      16      26 .. 0.88
   3 ?    9.9   0.1    0.0019      0.75       9      21 ..      55      67 ..      54      68 .. 0.89
   4 ?   -0.6   0.1       3.8   1.5e+03      17      21 ..      91      95 ..      90     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.23
                           UPF0547 15 qfCphC 20
                                      +fCp C
  gi|488599782|ref|YP_007906253.1|  2 EFCPKC 7 
                                      667766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.03
                           UPF0547 16 fCphCGyv 23
                                      +C+ CGy+
  gi|488599782|ref|YP_007906253.1| 19 VCRKCGYE 26
                                      7******7 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0019
                           UPF0547  9 kvPvaaqfCphCG 21
                                      ++P+ + +Cp+CG
  gi|488599782|ref|YP_007906253.1| 55 TLPTTTAICPECG 67
                                      6899999*****9 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 3.8
                           UPF0547 17 CphCG 21
                                      C  CG
  gi|488599782|ref|YP_007906253.1| 91 CTKCG 95
                                      88899 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4   0.00035      0.14       3      25 ..       4      26 ..       2      34 .. 0.84
   2 ?    4.5   0.2     0.086        33      29      37 ..      60      68 ..      54      74 .. 0.81
   3 ?    4.1   2.1      0.12        46       2      24 ..      62      96 ..      61     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00035
                                      -SSS-S--EE-SSEEE-TTT--E CS
                    zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqed 25
                                      Cp+C++ +   ++++ C++C  +
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIYYQNKAVCRKCGYE 26
                                      99999999999999999999865 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.086
                                      EEE-SSS-S CS
                    zinc-ribbons_6 29 ealCpeCeq 37
                                      +a+CpeC++
  gi|488599782|ref|YP_007906253.1| 60 TAICPECGN 68
                                      689999986 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.12
                                      --SSS-S--E.E-S...........SEEE-TTT-- CS
                    zinc-ribbons_6  2 kCpeCqqele.krg...........eqyhCeaCqe 24
                                      +CpeC +    +             + ++C +C +
  gi|488599782|ref|YP_007906253.1| 62 ICPECGNREAyWWLrqlraadesevRFFRCTKCGK 96
                                      68888776554433366677776666677777766 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 ?   -0.3   1.2         2   7.7e+02     197     215 ..       4      24 ..       1      44 [. 0.56
   2 ?   13.1   0.4   0.00016     0.063     156     205 ..      48      99 ..      31     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                                       ETTT--E..EE--TTS-TTT- CS
                              FdhE 197 CslCete..WhvvRvkCsnCe 215
                                       C  C++   +   ++ C +C+
  gi|488599782|ref|YP_007906253.1|   4 CPKCKSImiYYQNKAVCRKCG 24 
                                       333333211233344455555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00016
                                       --TTSSS-.-TT-SS-TTT---EEEEEEE---..----EEEEEETTT--EEE CS
                              FdhE 156 ldakalaelaeekglCPvCgsaPvasvvrigg..eaeglRylhCslCeteWh 205
                                       ++ ++++ l +++++CP Cg       +r+    +++ +R+  C+ C   W+
  gi|488599782|ref|YP_007906253.1|  48 IEGENIKTLPTTTAICPECGNREAYWWLRQLRaaDESEVRFFRCTKCGKTWR 99 
                                       6678888899999********999888876541146789************7 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3      0.99   3.8e+02      37      41 ..       4       8 ..       3      11 .. 0.85
   2 ?    8.5   0.0    0.0052         2       3      32 ..      19      46 ..      17      48 .. 0.89
   3 ?    5.1   0.1     0.059        23      35      43 ..      61      69 ..      49      73 .. 0.72
   4 ?    0.9   0.3       1.2   4.7e+02       2       9 ..      89      96 ..      88     102 .] 0.61

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.99
                                      BTTTB CS
                        Rubredoxin 37 CPdCg 41
                                      CP+C+
  gi|488599782|ref|YP_007906253.1|  4 CPKCK 8 
                                      ****7 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0052
                                      EETTT-BEEETTTBBGGGTB-TT--GGGS- CS
                        Rubredoxin  3 eCkvCgyvYdpakGdpdegiapgTkFedlP 32
                                       C+ Cg  Y+ ++G+++  +  +T+ ed+P
  gi|488599782|ref|YP_007906253.1| 19 VCRKCG--YEKEVGEKSVVLVTKTNREDVP 46
                                      799999..5799***************999 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.059
                                      -BBTTTB-B CS
                        Rubredoxin 35 WvCPdCgve 43
                                       +CP+Cg +
  gi|488599782|ref|YP_007906253.1| 61 AICPECGNR 69
                                      47****976 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.2
                                      EEETTT-B CS
                        Rubredoxin  2 yeCkvCgy 9 
                                      ++C+ Cg 
  gi|488599782|ref|YP_007906253.1| 89 FRCTKCGK 96
                                      56777764 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       1.1   4.5e+02      89      97 ..       4      12 ..       1      17 [. 0.76
   2 ?   13.0   0.4    0.0002     0.079      69      96 ..      16      70 ..      11      76 .. 0.86
   3 ?    4.4   0.2     0.095        37      70      81 ..      88      99 ..      75     102 .] 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
                                      -TTTSSS-E CS
                              HypA 89 CpkCgsadv 97
                                      CpkC+s  +
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMI 12
                                      999998765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0002
                                      -EEEETTTS-EEECHHHHH...........................S-TTTSSS- CS
                              HypA 69 vkvrCreCgkefeleekal...........................rCpkCgsad 96
                                       k+ Cr+Cg+e e+ ek++                            Cp+Cg+++
  gi|488599782|ref|YP_007906253.1| 16 NKAVCRKCGYEKEVGEKSVvlvtktnredvpviegeniktlptttaICPECGNRE 70
                                      5789********98765335689999*******************99****9876 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.095
                                      EEEETTTS-EEE CS
                              HypA 70 kvrCreCgkefe 81
                                       +rC++Cgk+++
  gi|488599782|ref|YP_007906253.1| 88 FFRCTKCGKTWR 99
                                      468999998886 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.5       0.3   1.2e+02      29      34 ..       4       9 ..       1      13 [. 0.81
   2 ?    5.3   0.5     0.055        21       8      17 ..      20      29 ..      11      46 .. 0.77
   3 ?    8.5   0.2    0.0053       2.1      25      34 ..      58      68 ..      49      71 .. 0.77
   4 ?    6.4   0.3     0.024       9.5       6      14 ..      89      97 ..      88     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.3
                       Zn-ribbon_8 29 CPeCgs 34
                                      CP+C+s
  gi|488599782|ref|YP_007906253.1|  4 CPKCKS 9 
                                      ****87 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.055
                       Zn-ribbon_8  8 CeeCghefev 17
                                      C++Cg e ev
  gi|488599782|ref|YP_007906253.1| 20 CRKCGYEKEV 29
                                      9999998884 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0053
                       Zn-ribbon_8 25 plta.CPeCgs 34
                                        ta CPeCg 
  gi|488599782|ref|YP_007906253.1| 58 TTTAiCPECGN 68
                                      46788****97 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.024
                       Zn-ribbon_8  6 YrCeeCghe 14
                                      +rC++Cg++
  gi|488599782|ref|YP_007906253.1| 89 FRCTKCGKT 97
                                      89*****86 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   0.00033      0.13       5      28 ..       4      26 ..       3      27 .. 0.88
   2 ?    6.1   0.8     0.028        11      21      27 ..      62      68 ..      58      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                    PhnA_Zn_Ribbon  5 CplCaSeytY.edgallvCpeCahE 28
                                      Cp+C+S+  Y +++a  vC +C++E
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIYyQNKA--VCRKCGYE 26
                                      **********66666..7****998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.028
                    PhnA_Zn_Ribbon 21 vCpeCah 27
                                      +CpeC++
  gi|488599782|ref|YP_007906253.1| 62 ICPECGN 68
                                      9****85 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.9      0.87   3.4e+02      30      40 ..      17      27 ..       2      42 .. 0.72
   2 ?   10.7   0.0    0.0009      0.35       2      42 ..      62     100 ..      61     102 .] 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.87
                           zf-ZPR1 30 sfeCehCgykn 40
                                        +C++Cgy++
  gi|488599782|ref|YP_007906253.1| 17 KAVCRKCGYEK 27
                                      46799999976 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0009
                           zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknne 42 
                                        Cp+Cg  n e + +l ++    e  +  f+C +Cg + +e
  gi|488599782|ref|YP_007906253.1|  62 ICPECG--NREAYWWLRQLRAADESEVRFFRCTKCGKTWRE 100
                                       6****8..569999999*******************87665 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5      0.26     1e+02      36      41 ..      19      24 ..      15      25 .. 0.88
   2 ?   11.3   0.1   0.00053      0.21      22      41 ..      76      95 ..      75      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.26
                     Baculo_LEF5_C 36 yCskCg 41
                                      +C+kCg
  gi|488599782|ref|YP_007906253.1| 19 VCRKCG 24
                                      6****9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00053
                     Baculo_LEF5_C 22 iQnRagDEi.vsfvryCskCg 41
                                      +Q+Ra DE  v f r C kCg
  gi|488599782|ref|YP_007906253.1| 76 RQLRAADESeVRFFR-CTKCG 95
                                      7*******7477776.****9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.5   0.00076       0.3       6      31 ..       4      27 ..       1      29 [. 0.87
   2 ?    6.0   0.1     0.025       9.7      23      32 ..      62      71 ..      61      72 .. 0.81
   3 ?    0.9   1.0       1.1   4.1e+02       6      11 ..      91      96 ..      90      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00076
                     A2L_zn_ribbon  6 CsvCggngilnseqgylvCieCgasf 31
                                      C +C++ +i++++++  vC +Cg++ 
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIYYQNKA--VCRKCGYEK 27
                                      999*******88876..******986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.025
                     A2L_zn_ribbon 23 vCieCgasfp 32
                                      +C+eCg+ ++
  gi|488599782|ref|YP_007906253.1| 62 ICPECGNREA 71
                                      7*****9665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.1
                     A2L_zn_ribbon  6 CsvCgg 11
                                      C++Cg+
  gi|488599782|ref|YP_007906253.1| 91 CTKCGK 96
                                      888885 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.6      0.11        43      36      52 ..      16      32 ..       5      47 .. 0.78
   2 ?    7.8   1.1    0.0082       3.2       3      47 ..      20      70 ..      18      74 .. 0.71
   3 ?    4.2   0.1      0.11        42      34      46 ..      85      97 ..      77     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                              CpXC 36 featCpkCgatakleap 52
                                      ++a+C kCg++ ++  +
  gi|488599782|ref|YP_007906253.1| 16 NKAVCRKCGYEKEVGEK 32
                                      67899999998877655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0082
                              CpXC  3 CpaCgkefeaeiwtsidadedpelkeklldgs......lfeatCpkCgata 47
                                      C +Cg e e+    ++ +++++     +++g+       ++a Cp+Cg++ 
  gi|488599782|ref|YP_007906253.1| 20 CRKCGYEKEVGEKSVVLVTKTNREDVPVIEGEniktlpTTTAICPECGNRE 70
                                      9999999999888888887777766666666522222267889*****875 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                              CpXC 34 slfeatCpkCgat 46
                                      +++ ++C kCg+t
  gi|488599782|ref|YP_007906253.1| 85 EVRFFRCTKCGKT 97
                                      67789******97 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2       0.2        76       2       9 ..       4      11 ..       3      15 .. 0.87
   2 ?   10.5   0.6    0.0012      0.47       2      34 ..      63      95 ..      62     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.2
                         Ogr_Delta  2 CPhCgapa 9 
                                      CP+C++ +
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIM 11
                                      ****9977 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                         Ogr_Delta  2 CPhCgapaaartsrnlskdvre..ryyqCsnfeCg 34
                                      CP+Cg++ a +  r+l +      r++ C+   Cg
  gi|488599782|ref|YP_007906253.1| 63 CPECGNREAYWWLRQLRAADESevRFFRCTK--CG 95
                                      *******999999999874433689999998..77 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.2    0.0017      0.68      20      47 ..       3      26 ..       1      27 [. 0.84
   2 ?    3.7   2.3      0.19        75      38      46 ..      84      96 ..      39     101 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0017
                               IBR 20 wCprpdCeaiieksegcksvtCskCgfe 47
                                       Cp  +C++i+   +++  + C+kCg+e
  gi|488599782|ref|YP_007906253.1|  3 FCP--KCKSIMIYYQNK--AVCRKCGYE 26
                                      7*9..******998884..56*****97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.19
                               IBR 38 s....vtCskCgf 46
                                      s     +C+kCg+
  gi|488599782|ref|YP_007906253.1| 84 SevrfFRCTKCGK 96
                                      1333445666665 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.8       1.1   4.1e+02      90     115 ..       4      24 ..       3      28 .. 0.67
   2 ?   10.8   0.1   0.00089      0.35      89     116 ..      62      96 ..      30      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.1
                                       TSSSTSTCEEECCSSSCEEEEESSST CS
                      eIF-5_eIF-2B  90 CkeCkspetelekeerllvlkCkaCg 115
                                       C++Cks    +  +++ +   C++Cg
  gi|488599782|ref|YP_007906253.1|   4 CPKCKSIM--IYYQNKAV---CRKCG 24 
                                       88998864..34456666...78887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00089
                                       STSSSTSTCEEECC.......SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  89 lCkeCkspetelek.......eerllvlkCkaCga 116
                                       +C+eC++ e            e+++ +++C++Cg+
  gi|488599782|ref|YP_007906253.1|  62 ICPECGNREAYWWLrqlraadESEVRFFRCTKCGK 96 
                                       7*******9865444466687899**********7 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.45   1.7e+02      23      29 ..       3       9 ..       1      12 [. 0.85
   2 ?    8.2   0.1    0.0075       2.9      19      29 ..      58      68 ..      50      69 .. 0.71
   3 ?   -0.5   0.0         4   1.6e+03      20      28 ..      84      95 ..      76      97 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.45
                     zinc_ribbon_9 23 lCPhCgg 29
                                      +CP C++
  gi|488599782|ref|YP_007906253.1|  3 FCPKCKS 9 
                                      5****86 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0075
                     zinc_ribbon_9 19 dsdvlCPhCgg 29
                                      +  ++CP+Cg+
  gi|488599782|ref|YP_007906253.1| 58 TTTAICPECGN 68
                                      34456****97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4
                     zinc_ribbon_9 20 sdv...lCPhCg 28
                                      s+v    C  Cg
  gi|488599782|ref|YP_007906253.1| 84 SEVrffRCTKCG 95
                                      442233488897 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.4     0.024       9.3      14      29 ..       2      17 ..       1      28 [. 0.74
   2 ?    3.6   0.0      0.15        57      15      22 ..      62      69 ..      59      77 .. 0.80
   3 ?    0.9   0.1         1   4.1e+02      15      21 ..      90      96 ..      87     102 .] 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.024
                             PADR1 14 ekCpeCkegqlvfdss 29
                                      e Cp+Ck+  ++++++
  gi|488599782|ref|YP_007906253.1|  2 EFCPKCKSIMIYYQNK 17
                                      67*****888888776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.15
                             PADR1 15 kCpeCkeg 22
                                       CpeC++ 
  gi|488599782|ref|YP_007906253.1| 62 ICPECGNR 69
                                      6****975 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1
                             PADR1 15 kCpeCke 21
                                      +C +C++
  gi|488599782|ref|YP_007906253.1| 90 RCTKCGK 96
                                      6999985 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.078        30       4      10 ..       3       9 ..       1      12 [. 0.81
   2 ?    0.6   0.1       1.1   4.2e+02       4       9 ..      19      24 ..      16      31 .. 0.85
   3 ?    4.9   0.1      0.05        19       2      10 ..      60      68 ..      59      71 .. 0.82
   4 ?    4.9   0.3     0.052        20       3      11 ..      89      97 ..      87     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.078
                            zf_UBZ  4 lCerCgk 10
                                      +C++C++
  gi|488599782|ref|YP_007906253.1|  3 FCPKCKS 9 
                                      8****97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                            zf_UBZ  4 lCerCg 9 
                                      +C +Cg
  gi|488599782|ref|YP_007906253.1| 19 VCRKCG 24
                                      8****8 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.05
                            zf_UBZ  2 tylCerCgk 10
                                      t +C++Cg 
  gi|488599782|ref|YP_007906253.1| 60 TAICPECGN 68
                                      568****96 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.052
                            zf_UBZ  3 ylCerCgke 11
                                      + C +Cgk+
  gi|488599782|ref|YP_007906253.1| 89 FRCTKCGKT 97
                                      78*****96 PP

>> Opy2  Opy2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5     0.023         9      11      30 ..       4      23 ..       2      26 .. 0.92
   2 ?    5.1   0.6     0.076        30       5      17 ..      57      69 ..      57      71 .. 0.81
   3 ?    1.2   0.1       1.2   4.8e+02      27      33 ..      91      97 ..      86      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.023
                              Opy2 11 CPsCpsgeeCvltaqtCtsC 30
                                      CP+C+s  +  +    C +C
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIYYQNKAVCRKC 23
                                      *******9999999999999 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.076
                              Opy2  5 pdsapsCPsCpsg 17
                                      p+++  CP+C + 
  gi|488599782|ref|YP_007906253.1| 57 PTTTAICPECGNR 69
                                      678999****875 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.2
                              Opy2 27 CtsCakt 33
                                      Ct+C kt
  gi|488599782|ref|YP_007906253.1| 91 CTKCGKT 97
                                      8888665 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   9.0     0.086        33      11      33 ..       3      25 ..       1     100 [. 0.69

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.086
                                      B-TTT--B--SSS--EE-TTT-- CS
                              FYVE 11 kCeiCakkFsllrrrhhCrlCGk 33
                                       C++C++   + + +  Cr CG 
  gi|488599782|ref|YP_007906253.1|  3 FCPKCKSIMIYYQNKAVCRKCGY 25
                                      6*********************5 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.2     0.077        30       4      26 .]       4      23 ..       4      23 .. 0.75
   2 ?    3.2   0.7      0.24        93       4       8 ..      63      67 ..      62      68 .. 0.72
   3 ?    4.9   0.4     0.073        28       1       9 [.      88      96 ..      88      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.077
                            zf-ACC  4 CpsCgemlykkeLernlyVCPkC 26
                                      Cp+C++++ +    +n+ VC+kC
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIYY---QNKAVCRKC 23
                                      99999976543...588899988 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.24
                            zf-ACC  4 CpsCg 8 
                                      Cp+Cg
  gi|488599782|ref|YP_007906253.1| 63 CPECG 67
                                      77777 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.073
                            zf-ACC  1 WtKCpsCge 9 
                                      +++C++Cg 
  gi|488599782|ref|YP_007906253.1| 88 FFRCTKCGK 96
                                      689****96 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3       0.3   1.2e+02       5       9 ..       4       8 ..       3      11 .. 0.68
   2 ?    1.9   0.4      0.56   2.2e+02      25      32 ..      17      24 ..      15      26 .. 0.73
   3 ?    2.6   0.2      0.33   1.3e+02       5       9 ..      63      67 ..      58      69 .. 0.63
   4 ?   11.0   0.9   0.00077       0.3      26      36 .]      89      99 ..      83      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.3
                     zinc_ribbon_4 5 CpsCk 9
                                     Cp+Ck
  gi|488599782|ref|YP_007906253.1| 4 CPKCK 8
                                     77776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.56
                     zinc_ribbon_4 25 kvrCskCg 32
                                      k+ C kCg
  gi|488599782|ref|YP_007906253.1| 17 KAVCRKCG 24
                                      55688887 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.33
                     zinc_ribbon_4  5 CpsCk 9 
                                      Cp+C+
  gi|488599782|ref|YP_007906253.1| 63 CPECG 67
                                      66664 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00077
                     zinc_ribbon_4 26 vrCskCghvFr 36
                                       rC+kCg+++r
  gi|488599782|ref|YP_007906253.1| 89 FRCTKCGKTWR 99
                                      69********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 ?    0.1   6.2       2.1   8.1e+02       2      29 ..       3      24 ..       2      26 .. 0.51
   2 ?    8.2   2.7    0.0059       2.3       3      30 ..      63      96 ..      62      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.1
                                      B-TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCg 29
                                      FC++C + + +          +vC +Cg
  gi|488599782|ref|YP_007906253.1|  3 FCPKCKSIMIYYQ------NKAVCRKCG 24
                                      5555544433332......236777777 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0059
                                      -TTT--B-E.....EE--TT-SS-EE.EETTTTE CS
                         Nudix_N_2  3 CsqCGtpve.....lripdgDnreRl.vCpaCgt 30
                                      C++CG++ +     +   +++++ R+ +C++Cg 
  gi|488599782|ref|YP_007906253.1| 63 CPECGNREAywwlrQLRAADESEVRFfRCTKCGK 96
                                      ******9655676345558888899648****97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.67   2.6e+02      27      31 ..       4       8 ..       3      13 .. 0.69
   2 ?    2.9   0.4      0.26     1e+02      25      31 ..      18      24 ..      14      29 .. 0.73
   3 ?    5.1   0.2     0.056        22       4      13 ..      60      69 ..      60      74 .. 0.82
   4 ?    4.4   0.1      0.09        35       6      11 ..      90      95 ..      76      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.67
                    Zn_ribbon_SprT 27 CrrCk 31
                                      C++Ck
  gi|488599782|ref|YP_007906253.1|  4 CPKCK 8 
                                      66666 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.26
                    Zn_ribbon_SprT 25 YrCrrCk 31
                                        Cr+C+
  gi|488599782|ref|YP_007906253.1| 18 AVCRKCG 24
                                      4788886 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.056
                    Zn_ribbon_SprT  4 vYrCtgCgre 13
                                      ++ C+ Cg++
  gi|488599782|ref|YP_007906253.1| 60 TAICPECGNR 69
                                      578*****54 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.09
                    Zn_ribbon_SprT  6 rCtgCg 11
                                      rCt Cg
  gi|488599782|ref|YP_007906253.1| 90 RCTKCG 95
                                      577776 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.6      0.59   2.3e+02      17      22 ..       4       9 ..       3       9 .. 0.90
   2 ?    6.8   0.3     0.014       5.6       2       9 ..      19      26 ..      19      28 .. 0.89
   3 ?    5.3   0.5     0.041        16       3      13 ..      63      73 ..      62      74 .. 0.65
   4 ?    5.4   0.4     0.038        15       1       9 [.      89      97 ..      89     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.59
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp C+s
  gi|488599782|ref|YP_007906253.1|  4 CPKCKS 9 
                                      ****96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                      Rubredoxin_2  2 vCsqCGfe 9 
                                      vC++CG+e
  gi|488599782|ref|YP_007906253.1| 19 VCRKCGYE 26
                                      7******8 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.041
                      Rubredoxin_2  3 CsqCGfesakw 13
                                      C +CG++ a w
  gi|488599782|ref|YP_007906253.1| 63 CPECGNREAYW 73
                                      77777777766 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.038
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      ++C +CG +
  gi|488599782|ref|YP_007906253.1| 89 FRCTKCGKT 97
                                      89*****76 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.3     0.079        31      10      31 ..       3      25 ..       1      55 [. 0.76
   2 ?    5.3   0.2     0.056        22      21      32 ..      58      69 ..      51      72 .. 0.81
   3 ?    1.8   0.1       0.7   2.7e+02      10      17 ..      90      97 ..      81     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.079
                      NOB1_Zn_bind 10 rChaCfkvtkd.mtkkFCpkCGn 31
                                       C  C +++   ++k  C kCG 
  gi|488599782|ref|YP_007906253.1|  3 FCPKCKSIMIYyQNKAVCRKCGY 25
                                      58889998854499999999997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.056
                      NOB1_Zn_bind 21 mtkkFCpkCGnk 32
                                      +t   Cp+CGn+
  gi|488599782|ref|YP_007906253.1| 58 TTTAICPECGNR 69
                                      56778*****96 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.7
                      NOB1_Zn_bind 10 rChaCfkv 17
                                      rC+ C k+
  gi|488599782|ref|YP_007906253.1| 90 RCTKCGKT 97
                                      55555554 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   3.9       1.2   4.6e+02       3       3 ..      18      18 ..       2      42 .. 0.60
   2 ?    7.4   1.4     0.019       7.3       3      14 ..      61      72 ..      59      91 .. 0.73
   3 ?    2.5   0.6       0.6   2.3e+02       4      12 ..      90      99 ..      87     102 .] 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.2
                           zf-ISL3  3 h 3 
                                       
  gi|488599782|ref|YP_007906253.1| 18 A 18
                                      2 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.019
                           zf-ISL3  3 hrCPnCgsktvv 14
                                        CP+Cg++ ++
  gi|488599782|ref|YP_007906253.1| 61 AICPECGNREAY 72
                                      67******9773 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.6
                           zf-ISL3  4 rCPnCgsk.t 12
                                      rC +Cg++  
  gi|488599782|ref|YP_007906253.1| 90 RCTKCGKTwR 99
                                      8*****9855 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.1     0.034        13      14      23 ..      15      24 ..       4      33 .. 0.89
   2 ?   -0.7   0.0       3.9   1.5e+03      15      24 ..      59      68 ..      53      71 .. 0.81
   3 ?    3.4   0.1      0.21        80      16      25 ..      88      97 ..      81     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.034
                                      SS--EETTTT CS
                            zf-BED 14 eqkavCryCg 23
                                       +kavCr Cg
  gi|488599782|ref|YP_007906253.1| 15 QNKAVCRKCG 24
                                      589******9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.9
                                      S--EETTTTE CS
                            zf-BED 15 qkavCryCgk 24
                                      + a+C  Cg+
  gi|488599782|ref|YP_007906253.1| 59 TTAICPECGN 68
                                      6799999997 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.21
                                      --EETTTTEE CS
                            zf-BED 16 kavCryCgki 25
                                      + +C  Cgk+
  gi|488599782|ref|YP_007906253.1| 88 FFRCTKCGKT 97
                                      679*****97 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.1     0.078        30       3      25 ..       4      25 ..       3      26 .. 0.69
   2 ?    5.3   0.4     0.041        16      19      26 ..      62      69 ..      43      72 .. 0.85
   3 ?    4.6   0.4     0.068        27      19      24 ..      90      95 ..      85      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.078
                                      -SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGh 25
                                      C +C++ +   ++ ++ C++CG+
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIMIYYQNKAV-CRKCGY 25
                                      6677766665555555.*****8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.041
                                      --SSS--- CS
                    DNA_RNApol_7kD 19 RCkeCGhR 26
                                       C eCG R
  gi|488599782|ref|YP_007906253.1| 62 ICPECGNR 69
                                      59999988 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.068
                                      --SSS- CS
                    DNA_RNApol_7kD 19 RCkeCG 24
                                      RC++CG
  gi|488599782|ref|YP_007906253.1| 90 RCTKCG 95
                                      9****9 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   3.5      0.41   1.6e+02       2       9 ..       4      11 ..       3      24 .. 0.75
   2 ?    8.1   3.0    0.0043       1.7       2      26 ..      63      95 ..      62      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.41
                          zf-TFIIB  2 CPkCqdel 9 
                                      CPkC++ +
  gi|488599782|ref|YP_007906253.1|  4 CPKCKSIM 11
                                      99999866 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0043
                          zf-TFIIB  2 CPkCqd.ele....eser...ggveidyCpqCr 26
                                      CP C++ e      +++    ++v +++C++C+
  gi|488599782|ref|YP_007906253.1| 63 CPECGNrEAYwwlrQLRAadeSEVRFFRCTKCG 95
                                      9999985666777644446669**********8 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.1      0.62   2.4e+02      15      21 ..      19      25 ..       8      33 .. 0.82
   2 ?    4.8   0.1     0.072        28      16      21 ..      63      68 ..      51      70 .. 0.80
   3 ?    6.4   0.0     0.023       8.8      16      25 ..      91     100 ..      84     102 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.62
                              YhfH 15 kCteCGk 21
                                      +C +CG 
  gi|488599782|ref|YP_007906253.1| 19 VCRKCGY 25
                                      6999*95 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.072
                              YhfH 16 CteCGk 21
                                      C+eCG+
  gi|488599782|ref|YP_007906253.1| 63 CPECGN 68
                                      *****7 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.023
                              YhfH  16 CteCGkeieE 25 
                                       Ct+CGk   E
  gi|488599782|ref|YP_007906253.1|  91 CTKCGKTWRE 100
                                       *****98665 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 ?    1.1   0.0      0.82   3.2e+02       5      16 ..       2      14 ..       1      16 [. 0.72
   2 ?    1.7   0.2      0.56   2.2e+02      23      28 ..      19      24 ..      17      28 .. 0.87
   3 ?    5.7   0.3     0.029        11       6      13 ..      62      69 ..      62      72 .. 0.75
   4 ?    2.1   0.2      0.42   1.6e+02       6      12 ..      90      96 ..      88     102 .] 0.66

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.82
                           zf-RRN7  5 ppCgvCgc.rsft 16
                                      + C+ C +   ++
  gi|488599782|ref|YP_007906253.1|  2 EFCPKCKSiMIYY 14
                                      569***8865655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.56
                           zf-RRN7 23 yCrrCh 28
                                      +Cr C+
  gi|488599782|ref|YP_007906253.1| 19 VCRKCG 24
                                      799998 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.029
                           zf-RRN7  6 pCgvCgcr 13
                                      +C++Cg+r
  gi|488599782|ref|YP_007906253.1| 62 ICPECGNR 69
                                      58888886 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.42
                           zf-RRN7  6 pCgvCgc 12
                                      +C  Cg 
  gi|488599782|ref|YP_007906253.1| 90 RCTKCGK 96
                                      7888886 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 ?   10.1   2.7    0.0018      0.71      17      40 .]       3      24 ..       1      24 [. 0.87
   2 ?    2.9   0.2      0.32   1.3e+02      16      22 ..      61      67 ..      56      69 .. 0.71
   3 ?   -1.4   0.2       7.2   2.8e+03      18      22 ..      91      95 ..      89      97 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0018
                     Auto_anti-p27 17 tCpvCgvPLmrdrkggkvyCvaCd 40
                                       Cp+C++++    +++k +C  C+
  gi|488599782|ref|YP_007906253.1|  3 FCPKCKSIMIY--YQNKAVCRKCG 24
                                      6**********..56889*****6 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.32
                     Auto_anti-p27 16 etCpvCg 22
                                      + Cp+Cg
  gi|488599782|ref|YP_007906253.1| 61 AICPECG 67
                                      4577776 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 7.2
                     Auto_anti-p27 18 CpvCg 22
                                      C +Cg
  gi|488599782|ref|YP_007906253.1| 91 CTKCG 95
                                      77775 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5     0.082        32       2       7 ..       4       9 ..       3      12 .. 0.86
   2 ?    0.4   0.4       1.6   6.1e+02       2       6 ..      20      24 ..      19      27 .. 0.61
   3 ?    2.9   0.3      0.27     1e+02       1       6 [.      62      67 ..      62      70 .. 0.89
   4 ?    8.1   0.3    0.0065       2.5      16      27 ..      82      93 ..      81      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.082
                                     -TTTSS CS
                           DUF1936 2 CPKCnv 7
                                     CPKC +
  gi|488599782|ref|YP_007906253.1| 4 CPKCKS 9
                                     ****87 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                                      -TTTS CS
                           DUF1936  2 CPKCn 6 
                                      C KC+
  gi|488599782|ref|YP_007906253.1| 20 CRKCG 24
                                      66776 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.27
                                      B-TTTS CS
                           DUF1936  1 lCPKCn 6 
                                      +CP C+
  gi|488599782|ref|YP_007906253.1| 62 ICPECG 67
                                      8****8 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0065
                                      TTS-EEEEEES- CS
                           DUF1936 16 ekGEIKvFRCdr 27
                                      ++ E+++FRC +
  gi|488599782|ref|YP_007906253.1| 82 DESEVRFFRCTK 93
                                      678*******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                        70  (0.00390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 615.11
//
Query:       gi|488599783|ref|YP_007906254.1|  [L=204]
Description: thymidylate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-49  165.9   0.0    8.7e-49  165.7   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    7.8e-11   42.2   0.3    1.2e-09   38.3   0.3    2.0  1  dNK              Deoxynucleoside kinase
    4.7e-09   36.9   0.7    2.1e-08   34.8   0.2    2.2  2  AAA_18           AAA domain
    1.1e-07   32.2   0.0    2.4e-07   31.1   0.0    1.6  1  AAA_28           AAA domain
    1.6e-06   28.4   0.0    2.6e-06   27.6   0.0    1.4  1  AAA_33           AAA domain
    0.00064   20.1   0.1     0.0018   18.7   0.1    1.9  1  AAA_17           AAA domain
     0.0055   16.6   0.0      0.012   15.5   0.0    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0095   16.1   0.4      0.015   15.4   0.4    1.3  1  DUF2052          Coiled-coil domain containing protein (DUF20
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.036   13.5   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
      0.023   15.0   0.1       0.09   13.1   0.0    1.9  2  AAA_22           AAA domain
      0.025   14.5   0.0      0.053   13.4   0.0    1.5  1  NACHT            NACHT domain
      0.037   13.5   0.0       0.31   10.5   0.0    2.3  2  PPK2             Polyphosphate kinase 2 (PPK2)
       0.04   13.1   0.0      0.071   12.3   0.0    1.4  1  NB-ARC           NB-ARC domain
      0.042   13.7   0.0      0.067   13.1   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.098   13.2   0.0       0.15   12.6   0.0    1.5  1  ABC_tran         ABC transporter
       0.14   10.7   0.0       0.17   10.4   0.0    1.3  1  Cytochrom_D1     Cytochrome D1 heme 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 !  165.7   0.0   7.8e-52   8.7e-49       1     182 [.       5     181 ..       5     184 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 7.8e-52
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpal 77 
                                       iEG+DG+GKt+ a++l+e+lke g+ ++l +ep++++ G+ki+e+ +   +l+++ e+ lf+ dr + + ++i+pal
  gi|488599783|ref|YP_007906254.1|   5 IEGIDGSGKTSLARFLVEKLKELGYDAILLKEPTDSKWGKKIKESYK--SRLSPEEELRLFLLDREYDVKNNIIPAL 79 
                                       8********************************************77..9*************************** PP

                                       HTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHH CS
                   Thymidylate_kin  78 kqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrk 154
                                       ++gk+vi+dRy+fS++aYqga +  d d ++++ne++ +kPdl ++ld+ pe+al+R++ rde   +e+e++++l +
  gi|488599783|ref|YP_007906254.1|  80 ESGKIVIMDRYYFSTIAYQGALG-FDPDELKRMNEEIAPKPDLLIILDLNPEKALERIKNRDE--PNEFERKEYLSR 153
                                       ********************877.9************99************************..99********** PP

                                       HHHHHHHHHHTTSTEEEEETTS-HHHHH CS
                   Thymidylate_kin 155 vrerylelakederiliidasksieevh 182
                                       vre +l++ +ed  il++da++  +e++
  gi|488599783|ref|YP_007906254.1| 154 VREIFLSIEDEDVDILVVDANRDQDEIR 181
                                       *********9***********9988876 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.3   1.1e-12   1.2e-09       1     188 [.       3     177 ..       3     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.1e-12
                                       EEEEESTTSSHHHHHHHHHCCST.....CEEEE-HHH.HCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCH CS
                               dNK   1 ivveGnIgaGKstlvklLskklg.....vkvfeEpvd.kwtnvqknlLekfYkdpsrwsfalqtyvllsrlkqqlea 71 
                                       i++eG  g+GK++l+ +L +kl+        ++Ep d kw    ++ ++  Yk       +l  ++l   +++ +++
  gi|488599783|ref|YP_007906254.1|   3 IAIEGIDGSGKTSLARFLVEKLKelgydAILLKEPTDsKW----GKKIKESYKSRLSPEEELRLFLLDREYDVKNNI 75 
                                       89**************998776443333445688887367....799******98888899***************9 PP

                                       H...SSS-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTT CS
                               dNK  72 l...atkqvvvleRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgr 145
                                       +   + +++v+++R  +s       a      +++ elk ++   + +    +kpdlli L++++e+ lerik+R++
  gi|488599783|ref|YP_007906254.1|  76 IpalESGKIVIMDRYYFSTI-----AYQGALGFDPDELKRMN---EEIA---PKPDLLIILDLNPEKALERIKNRDE 141
                                       99889999999999988887.....22223335666655444...3333...67*********************** PP

                                       CCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTH CS
                               dNK 146 eeekkieldYlekLhekyeewlkklnevpvlvidveeldlvae 188
                                        +e +  ++Yl ++ e + +  ++   v +lv+d+++    ++
  gi|488599783|ref|YP_007906254.1| 142 PNEFE-RKEYLSRVREIFLSIEDE--DVDILVVDANR----DQ 177
                                       *9876.689******999887776..89999999998....33 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.2   1.9e-11   2.1e-08       1     127 [.       3     149 ..       3     153 .. 0.71
   2 ?   -0.5   0.1       1.5   1.7e+03      53      88 ..     163     194 ..     147     202 .. 0.54

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.9e-11
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe....aldeskrldedkldklldaleenss.... 69 
                                       I++ G+ G+GKt+la+ L ++l   +   d +  +++ ++ + +     +++ +  +e+ +  lld      +    
  gi|488599783|ref|YP_007906254.1|   3 IAIEGIDGSGKTSLARFLVEKL--KELGYDAILLKEPTDSKWGKkikeSYKSRLSPEEELRLFLLDREYDVKNniip 77 
                                       89*******************9..44444444444444444444344644444444444444444333333225666 PP

                            AAA_18  70 aleegknlvidghlaeleseaakdikk..................vvLtaspeelleRlekRgyeeakikeneeae 127
                                       ale+gk +++d      + ++   +                    ++L+++pe+ leR+++R++ +    e e+ e
  gi|488599783|ref|YP_007906254.1|  78 ALESGKIVIMDRYYFSTIAYQGALGFDpdelkrmneeiapkpdllIILDLNPEKALERIKNRDEPN----EFERKE 149
                                       9******9999988888888888766699999999****************************665....555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                            AAA_18  53 dedkldklldaleenssaleegknlvidghlaeles 88 
                                       ded++  ++da++ +    +e  +lv+d +l++l +
  gi|488599783|ref|YP_007906254.1| 163 DEDVDILVVDANRDQ----DEIRSLVLDRVLVDLSK 194
                                       333333333333333....34555666666666554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   2.1e-10   2.4e-07       2     144 ..       3     157 ..       2     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.1e-10
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv..pEaareileeklakgedalpwv.edllafaervleeqleeeaaa. 70 
                                       i+i G  ++GKT+l++ L ++    gy  +  +E+    + +k ++  +   +  e+l  f   ++   + +   a 
  gi|488599783|ref|YP_007906254.1|   3 IAIEGIDGSGKTSLARFLVEKlkelGYDAIllKEPTDSKWGKKIKESYKSRLSPeEELRLFLLDREYDVKNNIIPAl 79 
                                       8999***********88886666679997778********9999666654444448888888888877777766667 PP

                            AAA_28  71 aankvlfcDrglldtlaYarayggeaeaelea..aarekrydlvfllppap..eidddgeRre.dleereaiderlr 142
                                       +++k++++Dr ++ t+aY  a+g + + el++  ++ + + dl ++l+ +p   +++ ++R+e  + er+++  r+r
  gi|488599783|ref|YP_007906254.1|  80 ESGKIVIMDRYYFSTIAYQGALGFD-PDELKRmnEEIAPKPDLLIILDLNPekALERIKNRDEpNEFERKEYLSRVR 155
                                       9***********************9.888888544447888998888865532447777776645556666666666 PP

                            AAA_28 143 ea 144
                                       e+
  gi|488599783|ref|YP_007906254.1| 156 EI 157
                                       54 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   2.4e-09   2.6e-06       1     123 [.       2     144 ..       2     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.4e-09
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdt.......lrrrlfgtdqqsktdytr..vldrlyqilnela 63 
                                       l+ + G  GsGK+ la+ l++kl+     a+ll ++t       +++ ++ +   s+++  r  +ldr y+  n+++
  gi|488599783|ref|YP_007906254.1|   2 LIAIEGIDGSGKTSLARFLVEKLKelgydAILLKEPTdskwgkkIKESYKSRL--SPEEELRlfLLDREYDVKNNII 76 
                                       67889**************99999999**********8885555333333233..3333333448899**9998888 PP

                            AAA_33  64 rkalsagrnvildatnls...........rrerarflkl.arrlgvpvrivvvetdeetlkeRlakRaangd 123
                                         al++g+ vi d  ++s           ++e +r+ +  a+    p+++++++  +e++ eR++ R ++++
  gi|488599783|ref|YP_007906254.1|  77 -PALESGKIVIMDRYYFStiayqgalgfdPDELKRMNEEiAP---KPDLLIILDLNPEKALERIKNRDEPNE 144
                                       .79*********998666454455555547888887654144...489*******************99864 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.6e-06    0.0018       2     124 ..       7     141 ..       6     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-06
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHH.......HHHHHHHHHHH.H CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelq.......keaaekiaeea.k 70 
                                       G+ GsGK+ +++ lvek++   +    +l +e ++++ +k+ +e  k  l++++el+         ++++i  +  +
  gi|488599783|ref|YP_007906254.1|   7 GIDGSGKTSLARFLVEKLKELGYD--AILLKEPTDSKWGKKIKESYKSRLSPEEELRlflldreYDVKNNIIPALeS 81 
                                       899*************99766666..688899999998888888889888888888844444333444555554445 PP

                                       SSEEEEEE-S.EEEETTEEE...ESSHHHHHHHH....SEEEEEE--HHHHHHHHHHHTT CS
                            AAA_17  71 kkgvlvdghp.rikeqagfl...dglpkevleel..kpdaiilleadpeeilerrlkdrt 124
                                        k v++d ++ ++ + +g+l   ++  k + ee+  kpd++i+l+ +pe+ ler +++++
  gi|488599783|ref|YP_007906254.1|  82 GKIVIMDRYYfSTIAYQGALgfdPDELKRMNEEIapKPDLLIILDLNPEKALERIKNRDE 141
                                       56799999862445555554222333355677773457****************999854 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.1e-05     0.012       2      52 ..       3      52 ..       2      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrh 52
                                      ++i g  gsGKT+L   l+++lk+ g+   ++K  + + +  k+ k sy+ 
  gi|488599783|ref|YP_007906254.1|  3 IAIEGIDGSGKTSLARFLVEKLKELGYDAILLKEPT-DSKWGKKIKESYKS 52
                                      78999***********************99999755.55677777777775 PP

>> DUF2052  Coiled-coil domain containing protein (DUF2052)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   1.3e-05     0.015     137     184 ..     134     181 ..     106     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                           DUF2052 137 eaevlseeereelreeFtsimrerFLsGeDeefDYsavDeneelDdlk 184
                                       e+ + ++e  e  r+e+ s +re FLs eDe++D   vD+n++ D+++
  gi|488599783|ref|YP_007906254.1| 134 ERIKNRDEPNEFERKEYLSRVREIFLSIEDEDVDILVVDANRDQDEIR 181
                                       4455556668899********************************965 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   0.0   3.2e-05     0.036       1      78 [.       1      89 [.       1      98 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                      E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.....TTSSS-.-GGGHHHHH.......HHHHHHHHHH CS
                             KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvviddeslg....iekdsyk.dsakekalR.......sslrsavkrd 67
                                      M L+ + G+  sGK+++a+ L ++l+e +++ +++++ +        k+syk   + e++lR        ++++++  +
  gi|488599783|ref|YP_007906254.1|  1 M-LIAIEGIDGSGKTSLARFLVEKLKELGYDAILLKEPTDSkwgkKIKESYKsRLSPEEELRlflldreYDVKNNIIPA 78
                                      4.999*****************************996544334343345577345678888822222222345555667 PP

                                      HTT.SEEEE-S CS
                             KTI12 68 LskekvVIvDs 78
                                      L+  k+VI+D 
  gi|488599783|ref|YP_007906254.1| 79 LESGKIVIMDR 89
                                      88888888886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     8e-05      0.09       7      32 ..       2      27 ..       1      64 [. 0.82
   2 ?   -0.5   0.0       1.2   1.3e+03      71      98 ..     143     172 ..     119     199 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldee 32
                                      ++++ G  G+GKT l+r l+e+l+e 
  gi|488599783|ref|YP_007906254.1|  2 LIAIEGIDGSGKTSLARFLVEKLKEL 27
                                      58999*****************9754 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                            AAA_22  71 erlsseellealeqalrarav..ielliiD 98 
                                       ++ +++e+l+++++ + +  +  + +l++D
  gi|488599783|ref|YP_007906254.1| 143 NEFERKEYLSRVREIFLSIEDedVDILVVD 172
                                       455667777777777766666666666666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.7e-05     0.053       2      27 ..       2      27 ..       1      34 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                      l++++G  GsGKT L++ l+++++e 
  gi|488599783|ref|YP_007906254.1|  2 LIAIEGIDGSGKTSLARFLVEKLKEL 27
                                      689*******************9975 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00028      0.31      33      94 ..       2      63 ..       1      74 [. 0.91
   2 ?    0.0   0.0      0.44     5e+02      88     122 ..      81     114 ..      72     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                                      EEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--HHHHTS-TTHHHHTT---TT-EEEE CS
                              PPK2 33 vvifegrDaAGKgGaikrvtealnprvarvvalkaPteeEksqwylqRyvehlPakgeivlF 94
                                      ++ +eg D+ GK    + ++e+l+  ++    lk+Pt+   +++    y ++l ++ e+ lF
  gi|488599783|ref|YP_007906254.1|  2 LIAIEGIDGSGKTSLARFLVEKLKELGYDAILLKEPTDSKWGKKIKESYKSRLSPEEELRLF 63
                                      6779****************************************999999999999998887 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.44
                                       TT-EEEEES-GGGGGTHHHHHTSS-HHHHHHHHHH CS
                              PPK2  88 kgeivlFdRswYnragvervmgfctdkeaerflre 122
                                       +g+iv+ dR ++     +   gf +++e +r+ +e
  gi|488599783|ref|YP_007906254.1|  81 SGKIVIMDRYYFSTIAYQGALGF-DPDELKRMNEE 114
                                       58888888888887777777776.34445554444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.4e-05     0.071      22     108 ..       2      87 ..       1      88 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.4e-05
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS.HHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeves.lkrklv 97 
                                       ++a+ G  G+GKt la+  ++k++e+   +d +     +++   ++i e+   +Ls +e+ +    ++e   k+++ 
  gi|488599783|ref|YP_007906254.1|   2 LIAIEGIDGSGKTSLARFLVEKLKEL--GYDAILLKEPTDSKWGKKIKESYKSRLSPEEELRLFLLDREYdVKNNII 76 
                                       689*******************5554..7999999999999999999999999999998877766655555889999 PP

                                       HHCCCTTEEEE CS
                            NB-ARC  98 rlLltkrfllv 108
                                        +L++ + +++
  gi|488599783|ref|YP_007906254.1|  77 PALESGKIVIM 87 
                                       99998887764 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.9e-05     0.067       5      37 ..       3      35 ..       1      72 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                        APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLd 37
                                      + + G+ gsGK+++a+ l +kL+e g+ ++lL 
  gi|488599783|ref|YP_007906254.1|  3 IAIEGIDGSGKTSLARFLVEKLKELGYDAILLK 35
                                      6789***********************999885 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013      0.15      14      80 ..       3     110 ..       1     200 [. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                       EEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS....--S-TTSBHHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx....xxxxxxxxxxxx.. RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkp.teGeilldgkdlke....qeleslrkeigvlpqe....pqlfpeltvren.. 79 
                                       +ai G  G+GK++L++ l ++lk    + ill+ +++++    + +es++++++  p+e      l++e+ v++n  
  gi|488599783|ref|YP_007906254.1|   3 IAIEGIDGSGKTSLARFLVEKLKElGYDAILLK-EPTDSkwgkKIKESYKSRLS--PEEelrlFLLDREYDVKNNii 76 
                                       7999***************99987344455444.33333334333333333333..333235444555555666666 PP

                                       .................................H CS
                                       .................................x RF
                          ABC_tran  80 .................................e 80 
                                                                         
  gi|488599783|ref|YP_007906254.1|  77 palesgkivimdryyfstiayqgalgfdpdelkR 110
                                       6666666666666666666666666655555551 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.17     288     347 ..     115     175 ..      72     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                       T-SSHT-EEEEETTBT-EEE-HHHHHT--.EEEEEE-TTSSEEEEEEE--SSEEEEEETTT CS
                      Cytochrom_D1 288 lnpdndsvaviDkktlekvltlaesaglk.vvhvEfnkdGdevwlSvwdgkdalvvyDdkt 347
                                       + p+ d + ++D++  +  +++++  + +   + E+ ++ +e++lS+ d + ++ v+D+++
  gi|488599783|ref|YP_007906254.1| 115 IAPKPDLLIILDLNPEKALERIKNRDEPNeFERKEYLSRVREIFLSIEDEDVDILVVDANR 175
                                       556666777777777777777766555445899*************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); 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:                        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 0.32s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1272.47
//
Query:       gi|488599784|ref|YP_007906255.1|  [L=397]
Description: amino acid/amide ABC transporter substrate-binding protein, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-30  107.0   0.4    2.1e-30  106.6   0.4    1.1  1  Peripla_BP_6  Periplasmic binding protein
    1.5e-13   50.6   0.2      3e-06   26.6   0.0    2.1  2  ANF_receptor  Receptor family ligand binding region
    4.1e-05   22.7   0.7      0.019   14.0   0.2    2.3  2  Peripla_BP_5  Periplasmic binding protein domain


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 !  106.6   0.4   3.5e-34   2.1e-30       2     329 ..      38     362 ..      37     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 3.5e-34
                                       EEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BS CS
                      Peripla_BP_6   2 ikiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgpls 78 
                                       +kiG+l p +G +++sg  +++ a++a ++i ++    G k+elv +D + +++++ +a+ +l  +d v a+vg+ s
  gi|488599784|ref|YP_007906255.1|  38 LKIGVLIPKTGKFQTSGVVMENSARLAKKHIEEE---MGIKVELVFADCGDSAEKTKSAFLEL--SDSVLAVVGAYS 109
                                       69*****************************888...689***********************..57********** PP

                                       HHHHHHHHHHHHHHT-EEEESS-HH....C..CTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEE..ESSHH CS
                      Peripla_BP_6  79 savaaavaevlakdgvpvigpaglt....g..ekcspyvfslgpsysaqasalveylakelggkkvalvy..adyaf 147
                                       s  a a+a+++ +++ p+i  ++++    +  +++++yvf+ ++++  +++ +ve+l+   ++   ++ +  + + f
  gi|488599784|ref|YP_007906255.1| 110 STQAIAAADTAMETKTPYIVSVASAgiieQkvNEGNRYVFRNAYNTTYWGELAVEFLKL-SKAEGYYFQGfqPLSTF 185
                                       ********************665552333123599********************9763.34333444331044666 PP

                                       HHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTT..T-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEE CS
                      Peripla_BP_6 148 gregiaalkaaakaaGgevvgeepvplgttdfsaqvlqikaa..gadavllagtgadlaallkaaaeaGldakrill 222
                                        + + + +k++ +   +    ++  +++  d++  + ++++a    d+++l+  g   ++ lk+++++G ++  + +
  gi|488599784|ref|YP_007906255.1| 186 NQGMLNVIKKYKEPVAVS---YYNPSVDPKDVQKKAVEAANAvgEHDVLILGDPGRLSISYLKEYRQNGGKGIVYSI 259
                                       666666666665533333...333344444544444444444558999***********************988888 PP

                                       ECCC-CHHHHHHHHHHHHTTEEEEESCSTCCC.SHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTH CS
                      Peripla_BP_6 223 vswsgseedlkalggeaaegvlavtpyfpdld.npavrafvaayeaayggapppsqfaaggyiaadlllealkaags 298
                                       ++  + +++lk l+  +ae++ + ++  +    ++ ++++ ++y++ +g++ + +++++ +y+a+++l++a +++g 
  gi|488599784|ref|YP_007906255.1| 260 GGVLALPQTLKNLE--SAEYTAFQSAALDKIKvTEYTEKYFEDYRKEFGED-ANNYAGVLTYDAILILAKAFEKSG- 332
                                       88888899999997..69********9997654899**************8.7999******************99. PP

                                       CCHHHHHHHHHHS-BECCCTCCBEECTTSBE CS
                      Peripla_BP_6 299 ltreavraaleslgfdgllgplkftaedhqa 329
                                        + e +++ le+ +f+g++g +kf  e+hqa
  gi|488599784|ref|YP_007906255.1| 333 DDKEMLIKVLEEGEFTGACGVYKFN-ENHQA 362
                                       99******************97755.88886 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 !   22.4   0.0   9.6e-09   5.8e-05       4     114 ..      59     166 ..      56     170 .. 0.83
   2 !   26.6   0.0     5e-10     3e-06     234     340 ..     277     361 ..     187     366 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.6e-09
                                       HHHHHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEE.. CS
                      ANF_receptor   4 eAmklAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvi.. 78 
                                       ++++lA ++i +      gik+++   d  ++ ++++ a+l+++   v av+G++ss +++a+a  a + k P i  
  gi|488599784|ref|YP_007906255.1|  59 NSARLAKKHIEEE----MGIKVELVFADCGDSAEKTKSAFLELSDS-VLAVVGAYSSTQAIAAADTAMETKTPYIvs 130
                                       5677777777777....4789999999999****************.**************************9976 PP

                                       ..ESS---GGGG-TTTTTTEEESS--CHHHHHHHHHHH CS
                      ANF_receptor  79 ..sygstspelsdknryptflrtvpsdtsqaqAivdil 114
                                         s g   +++++ nry   +r ++++t+ ++  v+ l
  gi|488599784|ref|YP_007906255.1| 131 vaSAGIIEQKVNEGNRYV--FRNAYNTTYWGELAVEFL 166
                                       665566888888888866..888888888777666665 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 5e-10
                                       -EEEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHHC CS
                      ANF_receptor 234 vlgfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlkp 310
                                        + f+ +  ++ k++e++   ek  + ++ +e  +  + +y+  l+Yda+ +la+A++k +                
  gi|488599784|ref|YP_007906255.1| 277 YTAFQSAALDKIKVTEYT---EKYFE-DYRKEFGEDAN-NYAGVLTYDAILILAKAFEKSG---------------- 332
                                       346666666777777777...33322.44455666665.8888899***************................ PP

                                       CHHHHHHHHHHHT-EEEETTSCEEB-TTSB CS
                      ANF_receptor 311 weggqkllrylrnvnfeGltGdvkfdengd 340
                                        +++++l + l++ +f+G  G +kf+en +
  gi|488599784|ref|YP_007906255.1| 333 -DDKEMLIKVLEEGEFTGACGVYKFNENHQ 361
                                       .89************************987 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 !   14.0   0.2   3.2e-06     0.019       1      79 [.      38     111 ..      38     123 .. 0.88
   2 !    7.2   0.0   0.00035       2.1     254     328 ..     291     363 ..     184     388 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-06
                      Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwt 77 
                                       +k+GvL  ++G   +s   + + a+la ++i ++ G    k+e v +d+   +e+   k+  l  +d v +v+G++ 
  gi|488599784|ref|YP_007906255.1|  38 LKIGVLIPKTGKFQTSGVVMENSARLAKKHIEEEMG---IKVELVFADCGDSAEKT--KSAFLELSDSVLAVVGAYS 109
                                       59********************************96...68********8877764..555566689*********9 PP

                      Peripla_BP_5  78 Sa 79 
                                       S+
  gi|488599784|ref|YP_007906255.1| 110 ST 111
                                       97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00035
                      Peripla_BP_5 254 tpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvreallgqelkapeGevkidpenhhl 328
                                       t+  +++ +++++++ged+  n     +y ++ ++a+A ek g ++ e + + l + e++   G  k++++ + l
  gi|488599784|ref|YP_007906255.1| 291 TEYTEKYFEDYRKEFGEDA-NNYAGVLTYDAILILAKAFEKSGDDK-EMLIKVLEEGEFTGACGVYKFNENHQAL 363
                                       6678899999999999976.56777889**************9765.6677788888999999999998844444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2150.34
//
Query:       gi|488599785|ref|YP_007906256.1|  [L=251]
Description: hypothetical protein Asulf_00229 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-16   60.8  25.7    1.5e-16   60.4  25.7    1.1  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4  25.7   8.5e-21   1.5e-16       5     237 ..       7     242 ..       5     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 8.5e-21
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl..lllallvallvgaavglllgllvlr 79 
                                       l ++a+ l i+A +++l f+i+  +nl+ g+++a Gay++  l +l +    ++ ++++++l+g+++g+ l++l+ r
  gi|488599785|ref|YP_007906256.1|   7 LFSSAIFLSIFATCISLNFRISKFLNLALGSVYASGAYISYHLYHLSQTGfgFISSIALSMLAGIVLGVTLYILIKR 83 
                                       5678999************************************9999988999999********************9 PP

                      BPD_transp_2  80 lkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv....llalllvlavllllrrt 152
                                        +   l +t++  s+ +g+++   ++i + + ++     + + +++++       +    +++++lv++ l l++ +
  gi|488599785|ref|YP_007906256.1|  84 IGSSMLEATII--SLGFGIAV---EEILRITHSSGYYLIIEDLNYTIFGIRL---WelseIILFILVFLSLALIYLS 152
                                       99999888876..56667776...7777887777777777777777765554...3345899999************ PP

                      BPD_transp_2 153 rfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGga.... 225
                                       +fG +++ v +++ +a+  G++v+++ l+  ++++    + Ga+ +++l+++p +ig    +++i+++ l+ +    
  gi|488599785|ref|YP_007906256.1| 153 KFGIRVKFVEDDPLLAEIYGVDVEKYSLICIALTSSAICVLGAMSSFSLAVSP-SIGYLPLMSGIVIASLASIfrsv 228
                                       ****************************************************9.*************9999996665 PP

                      BPD_transp_2 226 ..gsllgtviGali 237
                                          + + + i ++ 
  gi|488599785|ref|YP_007906256.1| 229 giMHYIKIAIISIS 242
                                       55555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1454.97
//
Query:       gi|488599786|ref|YP_007906257.1|  [L=305]
Description: ABC-type branched-chain amino acid transport system, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-27   94.6  17.3    5.4e-27   94.6  17.3    1.6  2  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.5   0.3    0.0075   1.3e+02       6      33 ..      17      44 ..      15      44 .. 0.90
   2 !   94.6  17.3     3e-31   5.4e-27       5     266 ..      39     291 ..      35     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.0075
                      BPD_transp_2  6 ltlaailaiaAlGlalvfgiaGvinlgh 33
                                      +++aa+l ++A++l l f +  +inl++
  gi|488599786|ref|YP_007906257.1| 17 AAQAALLSLLAIALLLPFHLKWLINLAI 44
                                      6899**************9999999985 PP

  == domain 2  score: 94.6 bits;  conditional E-value: 3e-31
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlk 81 
                                       l++la+++ i+ l++ ++ +++G i+lgh   ++l++y +a+l  +++  ++++ + +++++ ++   + +l  ++ 
  gi|488599786|ref|YP_007906257.1|  39 LINLAILYSILTLSWVFMERYSGRISLGHTIPFGLAGYFSAILNFYFGDFFYAGWIPGFVASSII---FFILMEKTE 112
                                       67899*******************************************96666666666666554...455668888 PP

                      BPD_transp_2  82 vdeliitllllsvlvgltlllltgitsg.vkgqssvkellgfagallsflsavivllalllvlavllllrrtrfGra 157
                                          +++ + +l vl++++  l t  ++g ++g +++  ++ ++++ +   s    ll+ll+++ ++  +  + +G++
  gi|488599786|ref|YP_007906257.1| 113 RTGFVFITFILGVLIWIISPLITITKNGeIYGGEEGFSMIHISRDCIYLTS----LLILLMLFSFMKYFEISHYGLR 185
                                       888999999999999999877665555416777777777777777766665....9********************* PP

                      BPD_transp_2 158 lravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsllgtvi 233
                                        +a ++ne+ ar+lGi+  rvk++t +is+++A +aG l++l +++++p  ++v l + +++a v      + g+++
  gi|488599786|ref|YP_007906257.1| 186 FKAFRDNEDSARVLGIRSHRVKAVTSLISAFFASVAGNLYVLHFNHASPeLFSVHLAIFPFIATVFFRE-PITGAIA 261
                                       ******************************************************************999.******* PP

                      BPD_transp_2 234 Galiigvvksllltllgiptelarvllgallil 266
                                       G++ii+++++ l +++   ++++ +l  ++lil
  gi|488599786|ref|YP_007906257.1| 262 GSFIIVLLSDYLNSIF---PQFHLMLYAIILIL 291
                                       **********666666...77999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1881.45
//
Query:       gi|488599787|ref|YP_007906258.1|  [L=215]
Description: ABC-type branched-chain amino acid transport systems, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    3.5e-32  111.8   0.0    1.2  1  ABC_tran     ABC transporter
    6.4e-09   36.0   2.1    3.3e-05   23.9   0.2    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.1e-07   30.6   0.2     0.0019   17.7   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    4.6e-05   23.3   0.1    5.5e-05   23.0   0.1    1.2  1  AAA_15       AAA ATPase domain
    5.4e-05   23.8   0.8    0.00014   22.5   0.1    1.8  2  AAA_23       AAA domain
    0.00019   21.4   0.5     0.0084   16.0   0.1    2.1  2  ATPase_2     ATPase domain predominantly from Archaea
     0.0021   18.2   0.0     0.0045   17.2   0.0    1.6  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0049   16.8   0.2      0.015   15.2   0.0    1.8  2  Rad17        Rad17 P-loop domain
     0.0082   15.9   0.0      0.018   14.8   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.014   14.1   0.2      0.026   13.2   0.0    1.5  2  AAA_13       AAA domain
      0.015   15.3   0.1       0.19   11.7   0.0    2.1  2  AAA_14       AAA domain
       0.03   14.6   1.0       0.19   12.0   1.0    2.0  1  AAA_22       AAA domain
      0.032   14.7   0.4       0.28   11.6   0.4    2.2  1  AAA          ATPase family associated with various cellular a
      0.044   12.6   0.0       0.07   11.9   0.0    1.3  1  Adeno_IVa2   Adenovirus IVa2 protein
      0.045   12.9   0.4       0.13   11.4   0.4    1.9  1  NB-ARC       NB-ARC domain
      0.051   14.1   2.5       0.28   11.8   2.5    2.1  1  AAA_18       AAA domain
      0.085   12.9   0.1       0.14   12.3   0.1    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
       0.11   12.4   0.1       0.21   11.5   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.14   12.5   0.1        0.2   12.0   0.1    1.7  1  AAA_16       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.0   3.7e-35   3.5e-32       1     136 [.      17     161 ..      17     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 3.7e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l++++l++ +ge+++i+G+nG+GKStLl++++g +kp  G+i ++gk+++    +++++  i++ +q p+ f+ ltv
  gi|488599787|ref|YP_007906258.1|  17 LREINLEIDRGEVIGIFGPNGCGKSTLLRIISGFEKPSCGKIIMEGKNITGfSVERRAEIGISYAFQIPKPFESLTV 93 
                                       6789***********************************************9999999******************* PP

                                       HHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        en            e+ ++++++l+k++++++ ++++    + LS+G+ + ++l++++ ++p+llllDEp+
  gi|488599787|ref|YP_007906258.1|  94 FENvlagfllrydekEAARKASDLLRKFDIDHISNRKA----TYLSQGELKLLELCKSVSTEPELLLLDEPF 161
                                       ***********998888888*****************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 !   23.9   0.2   3.4e-08   3.3e-05       2      55 ..      30      71 ..      29      96 .. 0.61
   2 !   12.1   0.1   0.00014      0.13     190     279 ..     119     173 ..      95     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.4e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpe 55
                                       ++ GpNg+GKS+LL++++++            e+++ g+i++  + +++ + e
  gi|488599787|ref|YP_007906258.1| 30 IGIFGPNGCGKSTLLRIISGF------------EKPSCGKIIMEGKNITGFSVE 71
                                      689***************988............333333333333333333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00014
                            AAA_21 190 rslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEp 266
                                       r+++ +                                +  ++ a+ lS+G ++ll l  ++   +    lll+DEp
  gi|488599787|ref|YP_007906258.1| 119 RKFDID--------------------------------HISNRKATYLSQGELKLLELCKSVSTEP---ELLLLDEP 160
                                       333333................................3334444456***************999...9******* PP

                            AAA_21 267 EngLHPkllrrll 279
                                        + L+ +  + ++
  gi|488599787|ref|YP_007906258.1| 161 FSALDRENSKNVM 173
                                       ****977666666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00018      0.17      26      43 ..      29      46 ..      16      53 .. 0.81
   2 !   17.7   0.0     2e-06    0.0019     124     211 ..     115     206 ..      57     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                      EEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldA 43
                                      +  i GpNG+GKs ll  
  gi|488599787|ref|YP_007906258.1| 29 VIGIFGPNGCGKSTLLRI 46
                                      6679*********99865 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2e-06
                                       HHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEE CS
                                       xxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                             SMC_N 124 sellesagiske......lLSgGektLvalaLlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkekskn.aQf 192
                                       s+ll++ +i+        +LS Ge +L+ l        v+ +p l llDe  +aLD +n k+v + ++  +++   +
  gi|488599787|ref|YP_007906258.1| 115 SDLLRKFDIDHIsnrkatYLSQGELKLLELCKS-----VSTEPeLLLLDEPFSALDRENSKNVMKKVRLMRDDgIAM 186
                                       444444444432444555899999999887543.....333333899*********************77766599* PP

                                       EEE-SSHHHCCC-.SCEEEE CS
                                       xxxxxxxxxxxxx.xxxxxx RF
                             SMC_N 193 ivislreemleka.dklvgv 211
                                       +++++++++le+  d+++ +
  gi|488599787|ref|YP_007906258.1| 187 LITAHKKRILERIsDRIFSI 206
                                       **********9985666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   5.9e-08   5.5e-05      17     126 ..      20     141 ..      16     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.9e-08
                            AAA_15  17 veidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef......... 83 
                                       + ++++   +  + G+N++GKS++l+++  F + +    + +i  e +++  f   s +++ +I + +         
  gi|488599787|ref|YP_007906258.1|  20 INLEIDRGeVIGIFGPNGCGKSTLLRIISGFEKPS----CGKIIMEGKNITGF---SVERRAEIGISYafqipkpfe 89 
                                       44444444599999*******************99....77777777777777...444444444444446666667 PP

                            AAA_15  84 ..................aekekakeyektlkskekkkadlllkkkesdlkktikdkklkl 126
                                                         +         +++++  +  ++++++++++++ +++ + +lkl
  gi|488599787|ref|YP_007906258.1|  90 sltvfenvlagfllrydeK---------EAARKASDLLRKFDIDHISNRKATYLSQGELKL 141
                                       7777666655554433220.........233334445555566666666666666665555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.5e-07   0.00014      14      39 ..      19      47 ..       2      49 .. 0.70
   2 ?   -0.4   0.1       1.5   1.4e+03     124     151 ..     120     147 ..      80     208 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.5e-07
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAi 39
                                      ei++      +  I+GpNG+GK+T+l+ i
  gi|488599787|ref|YP_007906258.1| 19 EINLeidRGEVIGIFGPNGCGKSTLLRII 47
                                      4555554447999*************987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                            AAA_23 124 llgskkiilnlilflgqerfeefelkdk 151
                                       +++++ i+++   +l q++ + +el + 
  gi|488599787|ref|YP_007906258.1| 120 KFDIDHISNRKATYLSQGELKLLELCKS 147
                                       3444444556666666666544444332 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   8.9e-06    0.0084      16      39 ..      23      46 ..      16      59 .. 0.83
   2 ?    3.8   0.0      0.05        47      41     132 ..      70     165 ..      65     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.9e-06
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlke 39
                                      e ++ e++ i+Gp g+GK++Ll+ 
  gi|488599787|ref|YP_007906258.1| 23 EIDRGEVIGIFGPNGCGKSTLLRI 46
                                      555689999*************85 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.05
                          ATPase_2  41 ienledkdkyviyyialreesiskldefie...eeeekkklekalgiavpkaeleeilkeksklvfkaielllekik 114
                                       +e++ + +    + i+   es++ +++ ++     +++k++++++++ ++k+ +++i+++k +++ +   +lle  k
  gi|488599787|ref|YP_007906258.1|  70 VERRAEIGISYAFQIPKPFESLTVFENVLAgflLRYDEKEAARKASDLLRKFDIDHISNRKATYLSQGELKLLELCK 146
                                       556666666666666666666666666666777678888899999999*********99888888888778888888 PP

                          ATPase_2 115 kkgkk.iiiiiDelqklid 132
                                          ++   +++De + + d
  gi|488599787|ref|YP_007906258.1| 147 SVSTEpELLLLDEPFSALD 165
                                       8888845888999888874 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.8e-06    0.0045      61      86 ..     149     174 ..     125     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-06
                           SbcCD_C  61 epalrlvfLDEAFsklDeesiatlle 86 
                                       ++ ++l++LDE Fs lD e+++++++
  gi|488599787|ref|YP_007906258.1| 149 STEPELLLLDEPFSALDRENSKNVMK 174
                                       6789******************9997 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   1.6e-05     0.015      40      67 ..      22      49 ..       3      69 .. 0.83
   2 ?   -0.8   0.0       1.3   1.3e+03     122     159 ..     141     176 ..     108     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                             Rad17 40 LesrkkriLLisGPsGCgkstvvkvLsk 67
                                      Le  + +++ i GP GCgkst ++++s 
  gi|488599787|ref|YP_007906258.1| 22 LEIDRGEVIGIFGPNGCGKSTLLRIISG 49
                                      66666678999**************985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                             Rad17 122 lqklGddlrtdkklilvedlPnkfyrdsdalrevirky 159
                                       l  l + + t+ +l+l+++  +   r  ++ ++v++k+
  gi|488599787|ref|YP_007906258.1| 141 LLELCKSVSTEPELLLLDEPFSALDR--ENSKNVMKKV 176
                                       44456666666666666664444433..3344555544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-05     0.018      17      39 ..      22      44 ..      16      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      +eid+ +++ + Gp+G GKSTll
  gi|488599787|ref|YP_007906258.1| 22 LEIDRGEVIGIFGPNGCGKSTLL 44
                                      6788666999************8 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05     0.026      21      47 ..      32      58 ..      24      95 .. 0.84
   2 ?   -1.9   0.1         1   9.6e+02     179     541 ..     132     166 ..     103     194 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepk 47
                                      i+G NG GK+tL r+++ +e+ +  + 
  gi|488599787|ref|YP_007906258.1| 32 IFGPNGCGKSTLLRIISGFEKPSCGKI 58
                                      9******************98665544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                            AAA_13 179 ellsdeelkakletvesenlpelaplslssidldalekaeilkkkvvgkdseieeLienldladWVkqGlelheass 255
                                       + ls+ elk  +  ++ ++ pel                                                      
  gi|488599787|ref|YP_007906258.1| 132 TYLSQGELKLLELCKSVSTEPEL------------------------------------------------------ 154
                                       33333333333333333333333...................................................... PP

                            AAA_13 256 dtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaea 332
                                                                                                                    
  gi|488599787|ref|YP_007906258.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                            AAA_13 333 leeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeles 409
                                                                                                                    
  gi|488599787|ref|YP_007906258.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                            AAA_13 410 eldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgeleLkfeeekkgY 486
                                                                                                                    
  gi|488599787|ref|YP_007906258.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                            AAA_13 487 rivrkggsqaaetLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDs 541
                                                                                    +D P S LD 
  gi|488599787|ref|YP_007906258.1| 155 -------------------------------------------LLLDEPFSALDR 166
                                       ...........................................333444444433 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.19       3      43 ..      28      75 ..      26     125 .. 0.64
   2 ?    2.2   0.1      0.18   1.7e+02      36      83 ..     121     176 ..     102     205 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell.......vkkesilyinldderd 43
                                      +++ i G+  +GK+tll+ +   +        ++ ++i  +++++  +
  gi|488599787|ref|YP_007906258.1| 28 EVIGIFGPNGCGKSTLLRIISGFEKpscgkiiMEGKNITGFSVERRAE 75
                                      7899************97664333355666666666777776666666 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                            AAA_14  36 inldderdkkladpe....kllelileklkeekktylflDEiqev......pewekal 83 
                                       +++d+ +++k++  +    kllel+++ +++ + ++l+lDE   +      +++ k +
  gi|488599787|ref|YP_007906258.1| 121 FDIDHISNRKATYLSqgelKLLELCKS-VST-EPELLLLDEPFSAldrensKNVMKKV 176
                                       566666665544332233345555555.445.88999***965554444444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.0    0.0002      0.19       7      29 ..      29      51 ..      24     199 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                            AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                      ++ ++G+ G+GK+tllr +    
  gi|488599787|ref|YP_007906258.1| 29 VIGIFGPNGCGKSTLLRIISGFE 51
                                      6779************9776654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00029      0.28       3      21 ..      32      50 ..      30     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      ++Gp G+GK++l + +   
  gi|488599787|ref|YP_007906258.1| 32 IFGPNGCGKSTLLRIISGF 50
                                      68************99765 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.4e-05      0.07      82     106 ..      23      46 ..       4      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.4e-05
                        Adeno_IVa2  82 nyglqPviGviyGPtGsGksqllrn 106
                                       ++++  viG i+GP G+Gks llr 
  gi|488599787|ref|YP_007906258.1|  23 EIDRGEVIG-IFGPNGCGKSTLLRI 46 
                                       445567999.58***********95 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   0.4   0.00014      0.13      21      40 ..      28      47 ..      16     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       v+++ G  G+GK+tl++ i
  gi|488599787|ref|YP_007906258.1| 28 EVIGIFGPNGCGKSTLLRII 47
                                      59**************9865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.5   0.00029      0.28       1     113 [.      30     202 ..      30     208 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                            AAA_18   1 IlltGtpGvGKttlakeL......skrlgf..................................gvnlrdvakengl 37 
                                       I++ G+ G+GK+tl + +      s    +                                  +  + +++  + l
  gi|488599787|ref|YP_007906258.1|  30 IGIFGPNGCGKSTLLRIIsgfekpS----CgkiimegknitgfsverraeigisyafqipkpfeSLTVFENVLAGFL 102
                                       89***************95554330....133344444445556666666666777777777776666666666666 PP

                            AAA_18  38 llevdpealdeskrldedkldklldaleenss.............aleegknlvidghlaeleseaakdikk..... 96 
                                       l ++++ea ++   l ++++  ++++ ++ +               ++e++ l++d   + l  e+ k   k     
  gi|488599787|ref|YP_007906258.1| 103 LRYDEKEAARKASDLLRKFDIDHISNRKATYLsqgelkllelcksVSTEPELLLLDEPFSALDRENSKNVMKkvrlm 179
                                       66666665666666666666666666666665666666666666666666666666555555544444433366666 PP

                            AAA_18  97 ......vvLtaspeelleRlekR 113
                                             + +ta+++  leR+++R
  gi|488599787|ref|YP_007906258.1| 180 rddgiaMLITAHKKRILERISDR 202
                                       66666677777777777777766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00015      0.14       2      30 ..      30      59 ..      29     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                      EEEEESTTSSHHHHHHHHHTS.TEEESSST CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkp 30
                                      ++i+G    GKStL++ ++g  k   +++ 
  gi|488599787|ref|YP_007906258.1| 30 IGIFGPNGCGKSTLLRIISGFeKPSCGKII 59
                                      89**************99984344445444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00023      0.21      96     130 ..      23      58 ..       4      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       +++  +++ + G+ G GKStL+  + + ++ + g++
  gi|488599787|ref|YP_007906258.1|  23 EIDRgEVIGIFGPNGCGKSTLLRIISGFEKPSCGKI 58 
                                       5554488899************99998666666655 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   0.00022       0.2      22      45 ..      25      48 ..      16     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                            AAA_16 22 grpelvllsGesGvGKsslvrell 45
                                      +r+e++ + G+ G+GKs+l+r + 
  gi|488599787|ref|YP_007906258.1| 25 DRGEVIGIFGPNGCGKSTLLRIIS 48
                                      566888999***********8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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 0.33s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1266.40
//
Query:       gi|488599788|ref|YP_007906259.1|  [L=224]
Description: ABC-type branched-chain amino acid transport systems, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   97.9   0.0    1.3e-27   97.0   0.0    1.4  1  ABC_tran        ABC transporter
    5.6e-07   29.7   0.1    2.3e-05   24.4   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    3.8e-05   23.3   0.1    7.5e-05   22.4   0.1    1.5  1  AAA_29          P-loop containing region of AAA domain
    4.8e-05   23.9   0.4    9.8e-05   22.9   0.2    1.6  2  AAA_23          AAA domain
    0.00021   20.8   0.1       0.02   14.3   0.0    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
     0.0015   18.3   0.0     0.0038   17.0   0.0    1.6  2  AAA_30          AAA domain
     0.0019   16.9   0.2      0.027   13.2   0.0    2.4  3  AAA_13          AAA domain
     0.0064   16.1   0.1      0.043   13.4   0.0    2.0  2  AAA_25          AAA domain
     0.0093   15.7   0.0       0.01   15.6   0.0    1.2  1  AAA_15          AAA ATPase domain
  ------ inclusion threshold ------
      0.016   15.5   0.1      0.098   12.9   0.0    2.1  2  AAA_22          AAA domain
      0.019   15.4   0.1      0.028   14.8   0.1    1.6  1  AAA_16          AAA ATPase domain
      0.023   13.8   0.1      0.053   12.6   0.0    1.7  2  T2SSE           Type II/IV secretion system protein
      0.026   14.6   0.0       0.14   12.2   0.0    2.2  2  AAA_14          AAA domain
      0.032   14.0   0.3       0.18   11.5   0.3    2.1  1  Cytidylate_kin  Cytidylate kinase
      0.034   13.7   0.1      0.085   12.4   0.0    1.6  2  AAA_27          AAA domain
       0.05   13.5   0.0       0.11   12.4   0.0    1.6  2  Rad17           Rad17 P-loop domain
      0.072   13.1   0.0       0.31   11.0   0.0    2.0  2  AAA_5           AAA domain (dynein-related subfamily)
      0.084   12.1   0.0       0.14   11.4   0.0    1.3  1  Zeta_toxin      Zeta toxin
      0.097   12.7   0.1        0.2   11.7   0.1    1.5  1  MutS_V          MutS domain V
        0.2   11.9   0.0        6.2    7.1   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 !   97.0   0.0   1.4e-30   1.3e-27       2     136 ..      19     152 ..      18     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 1.4e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++v++ +k+ge+  ++G+nG+GKSt+++++agl+k  +G+i ldg d+++  +++++r  i   p++ ++ ++ltv+
  gi|488599788|ref|YP_007906259.1|  19 QDVDFFIKRGEINLLTGPNGSGKSTVFRTMAGLVKAHSGSIYLDGVDITDyPPHQRYRMGIVLAPEKMRVAENLTVE 95 
                                       799**********************************************9999************************ PP

                                       HH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en     + e+++++  kl+   l+++++    ++LSgG++q+v+  ra++++pk lllDEp+
  gi|488599788|ref|YP_007906259.1|  96 ENirigGEIERVYDLFPKLR--RLRNHKA----KNLSGGERQMVVFGRAIASNPKYLLLDEPF 152
                                       ***55444444555555554..3446666....*****************************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 !   24.4   0.0   2.5e-08   2.3e-05       1      24 [.      30      53 ..      30     123 .. 0.68
   2 ?    3.6   0.0     0.055        49     237     271 ..     125     156 ..     113     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.5e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      +n+l+GpNgsGKS++++++ +l  
  gi|488599788|ref|YP_007906259.1| 30 INLLTGPNGSGKSTVFRTMAGLVK 53
                                      79*****************99944 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.055
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLH 271
                                       lS G +++  +  a+++ ++  + ll+DEp  gLH
  gi|488599788|ref|YP_007906259.1| 125 LSGGERQMVVFGRAIAS-NP--KYLLLDEPFQGLH 156
                                       56667777333334444.44..45*********** 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 !   22.4   0.1   8.4e-08   7.5e-05      17      42 ..      23      48 ..      16      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.4e-08
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAi 42
                                      + i++ ++ lltGp+GsGKST++  +
  gi|488599788|ref|YP_007906259.1| 23 FFIKRGEINLLTGPNGSGKSTVFRTM 48
                                      55665559*************98655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   1.1e-07   9.8e-05      13      37 ..      19      46 ..      13      50 .. 0.84
   2 ?   -1.7   0.0       3.9   3.5e+03     160     160 ..     169     169 ..      89     221 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                            AAA_23 13 qeidF...skgltlItGpNGaGKTTild 37
                                      q++dF      ++l+tGpNG+GK+T+++
  gi|488599788|ref|YP_007906259.1| 19 QDVDFfikRGEINLLTGPNGSGKSTVFR 46
                                      56788886668**************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.9
                            AAA_23 160 k 160
                                       +
  gi|488599788|ref|YP_007906259.1| 169 R 169
                                       1 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 !   14.3   0.0   2.2e-05      0.02      25      44 ..      29      48 ..      15      57 .. 0.86
   2 ?    4.6   0.0     0.021        19     132     198 ..     120     182 ..      79     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      +++ ++GpNGSGKs ++  +
  gi|488599788|ref|YP_007906259.1| 29 EINLLTGPNGSGKSTVFRTM 48
                                      6899***********99766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.021
                                       -STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 132 iskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislr 198
                                        + ++LSgGe+++v     +A    +p    llDe  + L      +v e +++ +k+a + vis++
  gi|488599788|ref|YP_007906259.1| 120 HKAKNLSGGERQMVVFGRAIAS---NP-KYLLLDEPFQGLHGDAGDIVLEEIQRIKKRAGIAVISHE 182
                                       45679*******9865544332...22.234678888888888888888888888888888888876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.2e-06    0.0038      18      67 ..      28      97 ..      21     151 .. 0.71
   2 ?   -1.7   0.0       2.3   2.1e+03     145     163 ..     158     177 ..     149     192 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-06
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaa.g..................grviglAptg.kaAkvLaeelg 67
                                        + +ltGp G+GK+t+ ++++ +++a+ g                  +  i+lAp++ ++A++L+ e +
  gi|488599788|ref|YP_007906259.1| 28 GEINLLTGPNGSGKSTVFRTMAGLVKAHsGsiyldgvditdypphqryRMGIVLAPEKmRVAENLTVEEN 97
                                      4599**********************99668888888888888888863345556544267777775444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                            AAA_30 145 gigtaeLtevvRqke.seer 163
                                       ++g + L+e++R+k+ + ++
  gi|488599788|ref|YP_007906259.1| 158 DAGDIVLEEIQRIKKrAGIA 177
                                       56677889999998733333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0     3e-05     0.027      16      84 ..      28     107 ..      22     111 .. 0.65
   2 ?    0.7   0.0      0.18   1.6e+02     489     510 ..     115     135 ..     111     136 .. 0.80
   3 ?   -1.8   0.1      0.99   8.8e+02     205     237 ..     189     221 ..     161     223 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                            AAA_13  16 kriNliYGwNGaGKTtLSrllrslelgetepkfangsi..............eitnge.......eldirVfNrdFv 71 
                                       ++iNl+ G NG+GK+t+ r ++ l +        +gsi              +            ++++rV  +  v
  gi|488599788|ref|YP_007906259.1|  28 GEINLLTGPNGSGKSTVFRTMAGLVKA------HSGSIyldgvditdypphqR----YrmgivlaPEKMRVAENLTV 94 
                                       689*******************99543......34444344444454444432....03333444777777777777 PP

                            AAA_13  72 eenlseqgelkpv 84 
                                       een++  ge++ v
  gi|488599788|ref|YP_007906259.1|  95 EENIRIGGEIERV 107
                                       7777766666655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                            AAA_13 489 vrkggsqaaetLSeGEktaIaf 510
                                        r ++ ++a++LS GE+ ++ f
  gi|488599788|ref|YP_007906259.1| 115 RRLRN-HKAKNLSGGERQMVVF 135
                                       55555.799********99977 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.99
                            AAA_13 205 slssidldalekaeilkkkvvgkdseieeLien 237
                                       ++ss+    +  ++i  ++++++d++i++L+e 
  gi|488599788|ref|YP_007906259.1| 189 EISSRITLMISGKVIHSREITSSDEVIKKLREY 221
                                       454444455556888888888889999988875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   4.8e-05     0.043      29      50 ..      24      45 ..      12      58 .. 0.82
   2 ?    0.0   0.0       0.6   5.4e+02     165     184 ..     159     179 ..     156     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                            AAA_25 29 llpagelallaGapgtGKttla 50
                                      ++ +ge++ll+G+ g+GK+t+ 
  gi|488599788|ref|YP_007906259.1| 24 FIKRGEINLLTGPNGSGKSTVF 45
                                      899*****************86 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.6
                            AAA_25 165 v.galvealeriarrtgaavl 184
                                       + + ++e ++ri++r g+av+
  gi|488599788|ref|YP_007906259.1| 159 AgDIVLEEIQRIKKRAGIAVI 179
                                       4488999**********9997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05      0.01      23      84 ..      29     116 ..      17     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                            AAA_15  23 eeltvliGkNnsGKSsilealdlFlnnkekkn...................kkvikiekedleifeniseskdikId 80 
                                       e +++l G+N+sGKS++ + +  + +     +                    + i+++ e++++ en   + +i+I 
  gi|488599788|ref|YP_007906259.1|  29 E-INLLTGPNGSGKSTVFRTMAGLVKAH---SgsiyldgvditdypphqryRMGIVLAPEKMRVAENLTVEENIRIG 101
                                       4.99*****************9999955...3447889999999999999988899999999999999999999999 PP

                            AAA_15  81 vef...........a 84 
                                        e            +
  gi|488599788|ref|YP_007906259.1| 102 GEIervydlfpklrR 116
                                       998555554444440 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.098       6      30 ..      29      53 ..      25      96 .. 0.83
   2 ?    0.2   0.1      0.96   8.6e+02      95     116 ..     162     191 ..     116     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                       i ++tG+ G+GK+t+ r+++   +
  gi|488599788|ref|YP_007906259.1| 29 EINLLTGPNGSGKSTVFRTMAGLVK 53
                                      56789*************9987664 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.96
                            AAA_22  95 liiDEaqhlr...s.....eealeeLrsll 116
                                       ++++E+q++          +e +e+L +++
  gi|488599788|ref|YP_007906259.1| 162 IVLEEIQRIKkraGiavisHERVEDLIEIS 191
                                       788899998654404444477777776655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.1e-05     0.028      23      51 ..      27      54 ..      14     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                      r+e+ ll+G+ G+GKs++ r+ +  l k+
  gi|488599788|ref|YP_007906259.1| 27 RGEINLLTGPNGSGKSTVFRTMAG-LVKA 54
                                      55888**************99985.4444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.9e-05     0.053     130     160 ..      29      59 ..       8      96 .. 0.86
   2 ?   -1.9   0.1       1.5   1.4e+03      36      64 ..     164     192 ..     156     213 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                             T2SSE 130 glilvsGgTgsGKttllyallkeinksderi 160
                                        + l++G+ gsGK+t+  ++   +++++  i
  gi|488599788|ref|YP_007906259.1|  29 EINLLTGPNGSGKSTVFRTMAGLVKAHSGSI 59 
                                       45599****************9999997776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                             T2SSE  36 lreveelekaalerlisriaalakldise 64 
                                       l+e+++++k+a  ++is+  +    +is+
  gi|488599788|ref|YP_007906259.1| 164 LEEIQRIKKRAGIAVISHERVEDLIEISS 192
                                       44444444444444444433333333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.14       3      90 ..      29     121 ..      27     136 .. 0.63
   2 ?    0.2   0.0      0.79   7.1e+02      64      72 ..     142     150 ..     114     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd....kkladpe.......kllelileklkeekktyl 68 
                                       +i ++tG+  +GK+t+ ++++      ++  +y++  d +d    +++   +       + +++  + l+  ++++ 
  gi|488599788|ref|YP_007906259.1|  29 EINLLTGPNGSGKSTVFRTMAGLV-KAHSGSIYLDGVDITDypphQRY---RmgivlapEKMRVAEN-LT-VEENIR 99 
                                       7899************99988444.47788889988887773333112...1222211122222222.22.356666 PP

                            AAA_14  69 flDEiqevpewekalkslvdeg 90 
                                       +  Ei +v +++  l++l +++
  gi|488599788|ref|YP_007906259.1| 100 IGGEIERVYDLFPKLRRLRNHK 121
                                       7777777777777777777765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.79
                            AAA_14  64 kktylflDE 72 
                                       + +yl+lDE
  gi|488599788|ref|YP_007906259.1| 142 NPKYLLLDE 150
                                       566777776 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3    0.0002      0.18       4      33 ..      34      60 ..      32     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                      E-STTSSHHHHHHHHHHHHT-EEEEHHHHH CS
                    Cytidylate_kin  4 DGPagsGKssvaralaeklglkyldtgalY 33
                                       GP gsGKs+v r++a  ++++   +g++Y
  gi|488599788|ref|YP_007906259.1| 34 TGPNGSGKSTVFRTMAGLVKAH---SGSIY 60
                                      6**************9766553...55555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.5e-05     0.085      19      49 ..      21      51 ..      18      53 .. 0.86
   2 ?   -2.6   0.0       3.8   3.4e+03      66      93 ..      96     123 ..      89     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.5e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +df  ++ ++ l+ GpN +GKst++r +  l
  gi|488599788|ref|YP_007906259.1| 21 VDFFIKRGEINLLTGPNGSGKSTVFRTMAGL 51
                                      67777888999***************99766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
                            AAA_27  66 kkLrigavleeadgeelefaRrkgrkkt 93 
                                       +++rig+ +e+  +   +++R +++k++
  gi|488599788|ref|YP_007906259.1|  96 ENIRIGGEIERVYDLFPKLRRLRNHKAK 123
                                       6789999998877777777777766654 PP

>> Rad17  Rad17 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      0.11      45      66 ..      28      49 ..      10      73 .. 0.81
   2 ?   -2.5   0.0       4.6   4.2e+03     126     149 ..     136     159 ..     119     194 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                             Rad17 45 kriLLisGPsGCgkstvvkvLs 66
                                       +i L++GP G gkstv + ++
  gi|488599788|ref|YP_007906259.1| 28 GEINLLTGPNGSGKSTVFRTMA 49
                                      4699*************99876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.6
                             Rad17 126 GddlrtdkklilvedlPnkfyrds 149
                                       G  + ++ k +l+++  +  ++d+
  gi|488599788|ref|YP_007906259.1| 136 GRAIASNPKYLLLDEPFQGLHGDA 159
                                       444445555555544333334333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00035      0.31       3      24 ..      32      53 ..      31      65 .. 0.88
   2 ?   -1.4   0.0       2.3   2.1e+03      69      79 ..     162     172 ..     129     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                                      EEE--SSSSHHHHHHHGGGGBS CS
                             AAA_5  3 lLvGppGtgKselaerlaaaln 24
                                      lL Gp G+gKs++ + +a +++
  gi|488599788|ref|YP_007906259.1| 32 LLTGPNGSGKSTVFRTMAGLVK 53
                                      89***************99885 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                                       EEEESGGG--H CS
                             AAA_5  69 lvlDEveraes 79 
                                       +vl+E++r+++
  gi|488599788|ref|YP_007906259.1| 162 IVLEEIQRIKK 172
                                       78999999875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.14      18      61 ..      30      73 ..      21      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPey 61
                                      + ll G  G+GKs++ + ++  ++++++ + ld+ d+  + P+ 
  gi|488599788|ref|YP_007906259.1| 30 INLLTGPNGSGKSTVFRTMAGLVKAHSGSIYLDGVDITDYPPHQ 73
                                      66999*****************************9999999985 PP

>> MutS_V  MutS domain V
   #    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       2      21 ..      32      51 ..      31      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                      EEE-STTSSHHHHHHHHHHH CS
                            MutS_V  2 litGpnmaGkstylrqvali 21
                                      l+tGpn +Gkst +r +a +
  gi|488599788|ref|YP_007906259.1| 32 LLTGPNGSGKSTVFRTMAGL 51
                                      79*************98854 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 ?    7.1   0.0     0.007       6.2      27      42 ..     119     134 ..     112     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.007
                           SbcCD_C  27 srssgtlSGGekqfla 42 
                                       ++++++lSGGe+q+++
  gi|488599788|ref|YP_007906259.1| 119 NHKAKNLSGGERQMVV 134
                                       5677889999997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.50
# Mc/sec: 1360.75
//
Query:       gi|488599789|ref|YP_007906260.1|  [L=264]
Description: rRNA biogenesis protein Nop56/Nop58 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-35  121.7   1.2      4e-35  121.4   1.2    1.2  1  Nop       snoRNA binding domain, fibrillarin
     0.0067   16.9   4.1       0.01   16.3   3.1    1.8  1  FadA      Adhesion protein FadA
  ------ inclusion threshold ------
       0.03   14.8   0.9       0.12   12.8   0.1    2.0  2  eIF3_N    eIF3 subunit 6 N terminal domain
       0.11   12.9   4.0        0.5   10.7   1.6    2.6  2  TcdB_N    TcdB toxin N-terminal helical domain
        0.2   12.1   2.0       0.41   11.1   2.0    1.5  1  UPF0184   Uncharacterised protein family (UPF0184)
       0.23   11.6   3.4        3.2    7.9   0.3    2.7  2  ArnB_C    Archaellum regulatory network B, C-terminal domain
        4.7    7.6   7.6        1.5    9.2   1.6    2.8  3  GAT       GAT domain


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 !  121.4   1.2   1.5e-38     4e-35      75     224 ..      99     251 ..      44     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 1.5e-38
                                       -SSS-S-H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHH CS
                               Nop  75 smgaelse.edlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPasti 150
                                       ++ ++l++  d   + el + + + ++lrk++++ ++s+ +++ PN+s+++G  +a rLi+  GgL+++a++Pasti
  gi|488599789|ref|YP_007906260.1|  99 EKLRDLEDvRDTIICDELKELIKSTKQLRKKVEDEINSNSRKLIPNMSEILGGVIAVRLIERGGGLKRIAELPASTI 175
                                       444455552355556677777888899999999999999************************************** PP

                                       TTTT-HHHHCCCHHT--......-SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHH CS
                               Nop 151 qilGaekalfralkkkn......tpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklr 221
                                       qilGaek+lf+al++ +      tpk+G+i+++++++ ++p+++++k+aR++a K+a+a+RiD f   +g+l ++l 
  gi|488599789|ref|YP_007906260.1| 176 QILGAEKSLFKALSRIKkgrkakTPKHGIIFQHPYIR-TLPKSMRGKMARFMAGKLAIASRIDFF---RGELNEDLV 248
                                       *************9552245677*************9.88***********************76...344444444 PP

                                       HHH CS
                               Nop 222 eei 224
                                       e +
  gi|488599789|ref|YP_007906260.1| 249 ETV 251
                                       444 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.1   4.1e-06      0.01      14      89 ..      67     141 ..      60     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-06
                              FadA  14 kkeeqrykkekakaeaaaaklakkkelkakieeklakleadsevrfykdeYkellkeyksllkelekeikekekki 89 
                                       kk ++++++ +  + a  ++l++     + ++ekl++le  +++ +  de kel+k+ k+l+k++e ei+++++k+
  gi|488599789|ref|YP_007906260.1|  67 KKVDEELRSDEKYLIALLKTLDELDLTINLLSEKLRDLEDVRDTII-CDELKELIKSTKQLRKKVEDEINSNSRKL 141
                                       556677777788888888999999999999*************988.69**********************99875 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.6e-05      0.12      60     119 ..      32      93 ..      11     102 .. 0.81
   2 ?    0.1   0.1      0.39   9.9e+02      42      74 ..     108     141 ..      96     150 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                            eIF3_N  60 eeevpeelekkreevleeleeleeeaekvlelledeevvsnlrsdkkqnlefLk..eehgit 119
                                       + ++p ++++   +v++  +e+ ++ +kv   + +++v ++lrsd+k+++++Lk  +e ++t
  gi|488599789|ref|YP_007906260.1|  32 NPKIPFSVKDAGLKVFKSEKEYYNTLRKVSIAVAEKKVDEELRSDEKYLIALLKtlDELDLT 93 
                                       4457889999999****************************************944455555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.39
                            eIF3_N  42 kkTnmvdyaadlykeleg.eeevpeelekkreev 74 
                                       ++T ++d +++l k++++  ++v +e++ + +++
  gi|488599789|ref|YP_007906260.1| 108 RDTIICDELKELIKSTKQlRKKVEDEINSNSRKL 141
                                       4566666666666666654444555666555555 PP

>> TcdB_N  TcdB toxin N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6   0.00019       0.5       4      49 ..      91     136 ..      88     147 .. 0.91
   2 ?    1.7   0.0      0.13   3.3e+02      18      34 ..     248     263 ..     231     264 .] 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHHHHSTT-TTH CS
                            TcdB_N   4 dlilenleeklnklseeqskkkyellkklkkeidnYnnlykkekns 49 
                                       dl+++ l ekl++l++ + +   ++lk+l k+++  +++ + e ns
  gi|488599789|ref|YP_007906260.1|  91 DLTINLLSEKLRDLEDVRDTIICDELKELIKSTKQLRKKVEDEINS 136
                                       9************************************999999888 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                                       TTS-HHHHHHHHHHHHH CS
                            TcdB_N  18 seeqskkkyellkklkk 34 
                                       +e+    kye+lkklkk
  gi|488599789|ref|YP_007906260.1| 248 VETVRL-KYEELKKLKK 263
                                       444444.4999999997 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.0   0.00016      0.41      36      75 ..      95     135 ..      63     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                           UPF0184  36 DqinsaLDalEernDdln.skLrELlesnRqiRlefaeqld 75 
                                       + ++  L +lE+  D +    L+EL++s +q R++++++ +
  gi|488599789|ref|YP_007906260.1|  95 NLLSEKLRDLEDVRDTIIcDELKELIKSTKQLRKKVEDEIN 135
                                       557788999***999976168**************999865 PP

>> ArnB_C  Archaellum regulatory network B, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0013       3.2       5      27 ..      49      71 ..      46      79 .. 0.89
   2 ?    3.7   0.2     0.026        68      45      69 ..     117     135 ..      98     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                                      HHHHHHHHHHHHHHHHHTT-HHH CS
                            ArnB_C  5 nEyrYyellkkysealeagnlke 27
                                      +E +Yy++l+k+s a+++++++e
  gi|488599789|ref|YP_007906260.1| 49 SEKEYYNTLRKVSIAVAEKKVDE 71
                                      599****************9998 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.026
                                       HHHHHHHTT--S-HHH.......HH CS
                            ArnB_C  45 ieliEaTrrLsrdlesteklskedl 69 
                                        eli +T++L +++e+      e++
  gi|488599789|ref|YP_007906260.1| 117 KELIKSTKQLRKKVED------EIN 135
                                       5899999999999988......222 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.28   7.1e+02      45      68 ..      71      94 ..      51      96 .. 0.62
   2 ?    9.2   1.6   0.00058       1.5       4      46 ..      94     136 ..      91     149 .. 0.84
   3 ?    0.1   0.0      0.39     1e+03      60      76 ..     243     260 ..     241     261 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.28
                               GAT 45 eet.adeedllaelLqlNDeLnnvl 68
                                      ee+ +de+  l  lL++ DeL  ++
  gi|488599789|ref|YP_007906260.1| 71 EELrSDEK-YLIALLKTLDELDLTI 94
                                      33356666.9999999999998776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00058
                               GAT   4 aklLsemLsstepd.eellenellkeLyetckamqpriqkliee 46 
                                       ++lLse L  +e d ++    + lkeL ++ k++++++ + i++
  gi|488599789|ref|YP_007906260.1|  94 INLLSEKLRDLE-DvRDTIICDELKELIKSTKQLRKKVEDEINS 136
                                       789********9.44788899*****************998887 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.39
                               GAT  60 lNDeLn.nvlerYerlkk 76 
                                       lN++L  +v ++Ye+lkk
  gi|488599789|ref|YP_007906260.1| 243 LNEDLVeTVRLKYEELKK 260
                                       677665156689999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1358  (0.0757432); expected 358.6 (0.02)
Passed bias filter:                      747  (0.0416643); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1623.15
//
Query:       gi|488599790|ref|YP_007906261.1|  [L=221]
Description: rRNA 2-O-methyltransferase fibrillarin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  237.3   0.2    1.3e-70  237.1   0.2    1.0  1  Fibrillarin  Fibrillarin


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 !  237.1   0.2   7.2e-75   1.3e-70       7     221 ..      13     218 ..       8     221 .] 0.94

  Alignments for each domain:
  == domain 1  score: 237.1 bits;  conditional E-value: 7.2e-75
                                       STTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSH CS
                       Fibrillarin   7 legvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGt 83 
                                        +  y+++ +g+++++t++ +p +  YgEk i      yR+W p+rsKl+a+ +kg + + ik++ kvLYlGaasGt
  gi|488599790|ref|YP_007906261.1|  13 ANKTYLAEINGKETIVTESRNPPH--YGEKKIG----KYREWIPYRSKLSAMFMKGHR-IDIKPEWKVLYLGAASGT 82 
                                       566789997788889999998875..****985....6******************76.****************** PP

                                       HHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHH CS
                       Fibrillarin  84 tvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilakn 160
                                       tvsH+sDi++  g +ya+e+s + +++++e+a +R+ni+Pil+DA kPe+Y+ +vekvD i++D+aq +q++i++ n
  gi|488599790|ref|YP_007906261.1|  83 TVSHISDILD-YGYIYAIEYSAKPFKKFLELAIERQNIIPILDDAGKPENYSGIVEKVDFIYQDIAQKNQIEIFTAN 158
                                       *********9.9***************************************************************** PP

                                       HHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEE CS
                       Fibrillarin 161 aklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvv 221
                                       +++flk+gg+ li++karsid+t+epe+vf++ +++lke+ ++++++  lepy+kdh+++ 
  gi|488599790|ref|YP_007906261.1| 159 VDFFLKDGGHGLIMVKARSIDSTAEPESVFERVIDELKEK-FRIVKSGGLEPYHKDHIFIH 218
                                       *************************************975.*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1608.17
//
Query:       gi|488599791|ref|YP_007906262.1|  [L=215]
Description: putative GTPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-18   64.3   0.0    1.8e-17   63.4   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
    7.1e-12   45.1   0.2    1.8e-10   40.6   0.2    2.1  1  FeoB_N       Ferrous iron transport protein B
    0.00039   20.4   0.0      0.051   13.5   0.0    2.4  2  RsgA_GTPase  RsgA GTPase
    0.00045   19.7   0.0     0.0033   16.9   0.0    1.9  2  Arf          ADP-ribosylation factor family
     0.0025   17.4   0.0       0.53    9.8   0.0    2.2  2  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0036   17.5   0.1       0.01   16.1   0.1    1.7  1  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0085   15.4   0.1      0.019   14.3   0.1    1.7  1  Septin       Septin
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.036   14.1   0.1    1.7  1  Dynamin_N    Dynamin family
      0.029   13.8   0.0      0.034   13.6   0.0    1.3  1  SRPRB        Signal recognition particle receptor beta subuni
      0.086   12.6   0.0       0.19   11.5   0.0    1.5  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.14   11.7   0.2          1    8.9   0.1    2.0  2  Ras          Ras 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 !   63.4   0.0   1.1e-20   1.8e-17       1     114 []      13     141 ..      13     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.1e-20
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH.HHHHHHHHHHCT CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek.glgkaflaleea 76 
                                       e+++vGr+NvGKStL+++l+g++++ +++pgtT+++n+  +k    ++ ++D+pG +        g++++f +  + 
  gi|488599791|ref|YP_007906262.1|  13 EIIFVGRSNVGKSTLFSRLFGKEVKKGKRPGTTIKPNTLVYK----DLLVTDLPG-YG----YIhGVRRDFNERVK- 79 
                                       689************************************776....6********.86....34499999998777. PP

                                       SEEEEEEETT.........................TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  77 dlillvvdas.........................eeklkpldeeleelleeakkplilvlnk 114
                                       d i++ ++++                         + +  p+d e+ ++l+e + +++l++nk
  gi|488599791|ref|YP_007906262.1|  80 DFIVHYIESNaeriicgihvvdgksfleiverwesR-GEIPIDIEMYDFLNEFDFQVFLAVNK 141
                                       999999996665665555555555555554444421.22456666666666666666666665 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.2   1.1e-13   1.8e-10       2     135 ..      13     160 ..      12     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.1e-13
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHH..HHHHHHHHH. CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsaysee..ekvardfll. 75 
                                       ++++vG  nvGk+tlf +l g++ k g  pG+t++ ++  +k    ++ ++DlPG   ++ + ++  e+v +df++ 
  gi|488599791|ref|YP_007906262.1|  13 EIIFVGRSNVGKSTLFSRLFGKEVKKGKRPGTTIKPNTLVYK----DLLVTDLPGYGYIHGVRRDfnERV-KDFIVh 84 
                                       6899********************************999999....9********977866665532555.444443 PP

                                       ...CTSSSEE..EEEEEGGGH....HH.........HHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHH CS
                            FeoB_N  76 ...eeepdvv..vnvvdatnl....er.........nLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekL 134
                                          ++   ++  ++vvd +++    er         ++ +   l e++ +v la+n++d++ekk +++++  +sekL
  gi|488599791|ref|YP_007906262.1|  85 yieSNAERIIcgIHVVDGKSFleivERwesrgeipiDIEMYDFLNEFDFQVFLAVNKMDKVEKKDYTLNA--ISEKL 159
                                       4423333333447899987632222443333422223455555778999***************999874..56666 PP

                                       T CS
                            FeoB_N 135 g 135
                                       g
  gi|488599791|ref|YP_007906262.1| 160 G 160
                                       5 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   3.1e-05     0.051     102     124 ..      14      36 ..       6      66 .. 0.81
   2 ?    4.7   0.0     0.016        26      44      72 ..     130     159 ..     125     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                                       EEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpele 124
                                       +++vG S vGKStL  +l +++ 
  gi|488599791|ref|YP_007906262.1|  14 IIFVGRSNVGKSTLFSRLFGKEV 36 
                                       68****************99843 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.016
                                       HTT-EEEEEEE-GGG--HHH.HHHHHHHHH CS
                       RsgA_GTPase  44 ekgiepvivlnKiDlleeee.eleelkeel 72 
                                       e + ++ +++nK+D +e+++ +l++++e+l
  gi|488599791|ref|YP_007906262.1| 130 EFDFQVFLAVNKMDKVEKKDyTLNAISEKL 159
                                       5567999***********996444444443 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06    0.0033      11      92 ..       8      89 ..       1     104 [. 0.81
   2 ?    0.7   0.0      0.19   3.1e+02     117     162 ..     134     181 ..     120     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                                      .TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTE.SEEEE CS
                               Arf 11 kkkelrilllGLDnaGKtTilkklkleelvt.tvPTigfnveeleiknlkftvwDvGGqeklRplWknYfekt.davif 87
                                      kk +l i+++G  n GK+T+  +l  +e+++   P +  + ++l +k+l   v D+ G   +  + +++ e++ d +++
  gi|488599791|ref|YP_007906262.1|  8 KKIKLEIIFVGRSNVGKSTLFSRLFGKEVKKgKRPGTTIKPNTLVYKDLL--VTDLPGYGYIHGVRRDFNERVkDFIVH 84
                                      4556789*********************999789*9999999*****875..569999988888888888877345666 PP

                                      EEETT CS
                               Arf 88 vvDsa 92
                                       ++s+
  gi|488599791|ref|YP_007906262.1| 85 YIESN 89
                                      66665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.19
                                       EEEEEEE-TTSTT..SS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTB CS
                               Arf 117 allvlaNKqDlpe..alseeelrellgleelkgkrkleiqkcsavkge 162
                                       ++ +  NK+D  e  + + + ++e+lg+    ++ k  i+ +sa kge
  gi|488599791|ref|YP_007906262.1| 134 QVFLAVNKMDKVEkkDYTLNAISEKLGMIPPWTNWKHRIFPVSAKKGE 181
                                       466678999987611456788899988877556777788888888776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0057       9.3       5      29 ..      13      37 ..       9      53 .. 0.81
   2 !    9.8   0.0   0.00032      0.53     117     179 ..     127     181 ..      90     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0057
                                      EEEEEESTTSSHHHHHHHHHHHTTS CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktga 29
                                       i+++g  + GK+TL  rL  k  +
  gi|488599791|ref|YP_007906262.1| 13 EIIFVGRSNVGKSTLFSRLFGKEVK 37
                                      68999*************9865544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00032
                                       HHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTB CS
                          GTP_EFTU 117 lalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkge 179
                                        +++ + ++++++NKmD+++++ + + +++++kl      +   +++   +  ++++Sa+kge
  gi|488599791|ref|YP_007906262.1| 127 FLNEFDFQVFLAVNKMDKVEKK-DYTLNAISEKL-----GMIPPWTNW--KHRIFPVSAKKGE 181
                                       5667788999*********544.33445555555.....222223332..4556666666655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   6.1e-06      0.01       2      31 ..      14      43 ..      13      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.1e-06
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETT CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekst 31
                                      +++vG s+vGK++l++r+  +++++ +++ 
  gi|488599791|ref|YP_007906262.1| 14 IIFVGRSNVGKSTLFSRLFGKEVKKGKRPG 43
                                      89*******************999877654 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.2e-05     0.019       2      33 ..       9      40 ..       8      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                      EEEEEEEEEEBTTSSCCCCCCTTSSSS----- CS
                            Septin  2 gieftlmvvGesglGkttlintlfetdlieee 33
                                       i++ ++ vG+s +Gk+tl+  lf +++++ +
  gi|488599791|ref|YP_007906262.1|  9 KIKLEIIFVGRSNVGKSTLFSRLFGKEVKKGK 40
                                      6899*********************9998764 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.2e-05     0.036       1      41 [.      14      71 ..      14     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE.................C CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql.................g 41
                                      i++vG  + GKS++   L g+++   +   tT +p++l +                 +
  gi|488599791|ref|YP_007906262.1| 14 IIFVGRSNVGKSTLFSRLFGKEVKKGKRPGTTIKPNTLVYkdllvtdlpgygyihgvR 71
                                      799*******************888778889999999999555555555554444443 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.1e-05     0.034       5      33 ..      13      41 ..       9     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                                      EEEEE-STTSSHHHHHHHHHHSS---B-- CS
                             SRPRB  5 avllvGlsdsGKTslftrLttdsvkktvt 33
                                       +++vG s+ GK +lf rL  ++vkk   
  gi|488599791|ref|YP_007906262.1| 13 EIIFVGRSNVGKSTLFSRLFGKEVKKGKR 41
                                      79******************999988653 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.19       3      30 ..      13      40 ..      11      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                         PduV-EutP  3 killiGkvgsGKttLtqalkgeelkYkk 30
                                      +i+++G++++GK tL  +l g+e+k  k
  gi|488599791|ref|YP_007906262.1| 13 EIIFVGRSNVGKSTLFSRLFGKEVKKGK 40
                                      69*******************9998666 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00064         1       2      27 ..      14      39 ..      13      55 .. 0.82
   2 ?    0.7   0.0      0.21   3.4e+02      71     120 ..      89     148 ..      75     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00064
                                      EEEEESTTSSHHHHHHHHHHSSCSSS CS
                               Ras  2 lvlvGdsavGKtslllrfvkdkFkee 27
                                      +++vG s+vGK++l  r   ++ k+ 
  gi|488599791|ref|YP_007906262.1| 14 IIFVGRSNVGKSTLFSRLFGKEVKKG 39
                                      799************99887776665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.21
                                       TESEEEEEEETTBHHHHHTHH.HHHH..HHHHHST.......TTSEEEEEEETTTGGGG- CS
                               Ras  71 daegillvyditsresfenvk.kwve..eikrvae.......envpivLvGnKvDleekr 120
                                       +ae i++   + + +sf ++  +w +  ei    e        ++++ L  nK+D  ek+
  gi|488599791|ref|YP_007906262.1|  89 NAERIICGIHVVDGKSFLEIVeRWESrgEIPIDIEmydflneFDFQVFLAVNKMDKVEKK 148
                                       566667767777777776655366541223222224445555457788888888876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1409.30
//
Query:       gi|488599792|ref|YP_007906263.1|  [L=54]
Description: Preprotein translocase subunit Sec61beta [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   62.5   0.2      3e-17   62.3   0.2    1.0  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.2   1.7e-21     3e-17       1      41 []      13      53 ..      13      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.7e-21
                                      XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS- CS
                        Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhila 41
                                      SsaG++ry+ee++++iki+Pk V +++++++a+V++++i++
  gi|488599792|ref|YP_007906263.1| 13 SSAGIMRYFEEEKTQIKINPKSVFAFGLIIGAVVFIMNIFY 53
                                      9**************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 333.28
//
Query:       gi|488599793|ref|YP_007906264.1|  [L=391]
Description: Permease, similar to cation transporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  127.8  25.3    3.4e-21   75.9   8.6    3.7  4  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.21   3.7e+03      70      91 ..      16      36 ..       8      47 .. 0.53
   2 !   65.7   8.8   2.8e-22   5.1e-18       2     123 ..      55     180 ..      54     181 .. 0.90
   3 ?    0.5   1.6      0.04   7.2e+02      72     102 ..     190     217 ..     181     257 .. 0.57
   4 !   75.9   8.6   1.9e-25   3.4e-21       1     123 [.     259     384 ..     259     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.21
                                      HHHHHHHHHHHHHHHH..HHHH CS
                              MgtE 70 vvglalvlvllaaallilgvll 91
                                      ++++ +++v+++  ++ +g++l
  gi|488599793|ref|YP_007906264.1| 16 LISFPFLIVCVVLDFF-AGAFL 36
                                      3444444444444443.34443 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 2.8e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHTTSS-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHH CS
                              MgtE   2 PvilglgGnlgaqlasristalhlgelekk..lkkvllkelrvvlllgvilgllifllalllgwslllalvvglalv 76 
                                       P ++gl+Gn+   +a r st l lge+e++   ++ + +++ + l+l++++++++ ++  l   ++ +a+vv l  +
  gi|488599793|ref|YP_007906264.1|  55 PGLMGLRGNIFGAMANRFSTLLYLGEMEPRirKNRRISSNIFLSLILSMLPVVILWAVGSLKVMDFSIAIVVFLIAI 131
                                       99*************************999877*********************99997776667888887777777 PP

                                       HHHHHHHHH....HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  77 lvllaaall..ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                          ++a+l+  + ++l++++ +++g DP ++a P++t+++Dl+++ llv
  gi|488599793|ref|YP_007906264.1| 132 SSTIFASLIlaYSTALVTVIPFRKGTDPNSIAPPVITSIADLVTIPLLV 180
                                       7777777777999**********************************98 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHH..HHHHHHHHHHTTS-G CS
                              MgtE  72 glalvlvllaaallilgvllplllwklglDP 102
                                       g+++  + l+a +l ++++  l++ klg+D 
  gi|488599793|ref|YP_007906264.1| 190 GITFYSLTLSAFML-FAYM--LIAVKLGMDE 217
                                       33444333333333.2222..2555555554 PP

  == domain 4  score: 75.9 bits;  conditional E-value: 1.9e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekklkkvllkelrvvlllgvilgllifllalllgwslllalvvglalvl 77 
                                       +P+il+ +Gn g++  + +st+lhlge+ k l++ ++ e+++  ++g+ l++++ +la l+ + + l+ +vgl  ++
  gi|488599793|ref|YP_007906264.1| 259 YPAILDSSGNYGSIIGAKTSTMLHLGEIGKPLDRKIVYEILIYSMTGIPLAVIMNSLATLIVK-VTLGKTVGLVPIF 334
                                       59**************************8889*************************998777.3344444444444 PP

                                       HHHHHHHH......HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  78 vllaaall....ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       +ll  ++l     +++l+++++ k+g+DPdn ++P++t+++D++gt++ v
  gi|488599793|ref|YP_007906264.1| 335 LLLYPIFLlfvmTIAHLIAIVSEKVGFDPDNTTVPVITTIADMIGTAFTV 384
                                       444433334445669*******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2305.40
//
Query:       gi|488599794|ref|YP_007906265.1|  [L=203]
Description: uncharacterized protein, PH0010 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-53  179.2   0.0    5.3e-53  179.0   0.0    1.0  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.0   0.0   2.9e-57   5.3e-53       1     166 []      14     184 ..      14     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 179.0 bits;  conditional E-value: 2.9e-57
                                       HHHHHHHHHHHTTSS-S-HH---HHHHSEEEEEEEEEEE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS--- CS
                           AMMECR1   1 lklareaieealkeekkleeeakeelkekaglFVtlkekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFspv 77 
                                       +klar+aie +lke+k+++++++  + ek+g+FVtl+ k++eLRGCiG+  p ++L e+++e A++aA++DpRF+p+
  gi|488599794|ref|YP_007906265.1|  14 VKLARNAIEVYLKEKKVIDTRYDGVFAEKRGVFVTLR-KNKELRGCIGFPYPYKRLDEAIIESAISAATQDPRFRPL 89 
                                       689*********************************9.77************************************* PP

                                       -HHHHTTEEEEEEEE---EE-...-...GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-T CS
                           AMMECR1  78 taeElpeleveVsvLtepepi...v...ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrp 148
                                       + +El+ ++veV++Lt+pe+i   v    e++e+g+hGl+i++g +s++lLPqva e + d eefl+++++Kagl+p
  gi|488599794|ref|YP_007906265.1|  90 STKELDVVTVEVTILTPPEKIevdVrkiSEQVEIGRHGLLIKRGIFSGLLLPQVAIEFNFDSEEFLSQTCMKAGLPP 166
                                       *********************6551566888********************************************** PP

                                       TCCCSTTSEEEEE-EEEE CS
                           AMMECR1 149 dewkdseikltryevekf 166
                                       d+w  + ++++r+e+++f
  gi|488599794|ref|YP_007906265.1| 167 DCWLMDGTEIYRFEGQIF 184
                                       **999*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1427.07
//
Query:       gi|488599795|ref|YP_007906266.1|  [L=156]
Description: thioredoxin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  108.2   0.0    2.6e-31  107.6   0.0    1.3  1  Thioredoxin    Thioredoxin
    3.4e-10   40.3   0.7    1.4e-08   35.1   0.1    2.8  2  Thioredoxin_2  Thioredoxin-like domain
    1.1e-08   35.3   0.1    2.9e-05   24.3   0.0    2.8  3  Thioredoxin_8  Thioredoxin-like
    1.8e-05   24.2   0.0    2.4e-05   23.8   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
    3.6e-05   23.5   0.2    4.9e-05   23.1   0.2    1.2  1  Thioredoxin_9  Thioredoxin
      5e-05   23.2   0.0    9.9e-05   22.3   0.0    1.5  2  HyaE           Hydrogenase-1 expression protein HyaE
    9.1e-05   22.4   0.0    0.00013   21.9   0.0    1.3  1  AhpC-TSA       AhpC/TSA family
    0.00059   19.7   0.0    0.00086   19.2   0.0    1.3  1  TraF           F plasmid transfer operon protein
     0.0017   18.3   0.0       0.01   15.7   0.0    1.8  1  Thioredoxin_6  Thioredoxin-like domain
      0.004   17.2   0.2      0.023   14.7   0.0    2.1  2  Thioredoxin_3  Thioredoxin domain
     0.0047   16.6   0.0      0.011   15.4   0.0    1.7  2  Redoxin        Redoxin
  ------ inclusion threshold ------
      0.013   15.7   0.1      0.039   14.1   0.1    1.8  2  Thioredoxin_7  Thioredoxin-like
       0.02   13.8   0.0      0.029   13.3   0.0    1.3  1  Phosducin      Phosducin
      0.084   12.6   0.3       0.13   12.0   0.3    1.2  1  Rep_fac-A_C    Replication factor-A C terminal domain
       0.11   11.7   0.0       0.15   11.3   0.0    1.2  1  RuBisCO_large  Ribulose bisphosphate carboxylase large chain,


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 !  107.6   0.0   2.2e-34   2.6e-31       3     103 .]      55     153 ..      53     153 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 2.2e-34
                                       EESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEE CS
                       Thioredoxin   3 lvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklf 79 
                                       +++t++nF+e +++  + v+++F+A+wC++Ck++aP +++la+e+ +kv++ kv+++e++ +a+++++++iPtl++f
  gi|488599795|ref|YP_007906266.1|  55 VNVTQSNFNEILKN--RYVVLDFWADWCAPCKMIAPIIDDLAREYDGKVVFGKVNTTEEQAIANRFAITAIPTLIFF 129
                                       57899*****9999..************************************************************* PP

                                       ETTEEEEEEESS-HHHHHHHHHHH CS
                       Thioredoxin  80 kngkevkkyegarekeklaaflkk 103
                                       +ngk v+k++ga +k +l+++++k
  gi|488599795|ref|YP_007906266.1| 130 RNGKPVDKIVGAMPKGELIRWINK 153
                                       *********************985 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.58   6.9e+02      19      59 ..      11      49 ..       2      69 .. 0.72
   2 !   35.1   0.1   1.2e-11   1.4e-08       4     108 ..      67     150 ..      64     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.58
                     Thioredoxin_2 19 yCkklkkelkel...ddvtvrvllfplkpsfepkavaiwcakek 59
                                      yC+ +kk + +l   d+++++      k++ ++k++++ ++k +
  gi|488599795|ref|YP_007906266.1| 11 YCETFKKLIGKLgfmDELEII-----RKKKLMEKMERMMGEKME 49
                                      888888888888777777777.....667777777776666655 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 1.2e-11
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrg 80 
                                       ++++v+++f++++C  Ck +   +++l   ++      ++ +   ++ ++ +++e+           + a+++ +++
  gi|488599795|ref|YP_007906266.1|  67 KNRYVVLDFWADWCAPCKMIAPIIDDL--ARE------YDGK--VVFGKVNTTEEQ-----------AIANRFAITA 122
                                       689*******************99999..222......4444..566666666665...........59******** PP

                     Thioredoxin_2  81 tPtiv.fldgkeivarlpGyvpaeeleal 108
                                        Pt++ f +gk +v++++G++p+ el  +
  gi|488599795|ref|YP_007906266.1| 123 IPTLIfFRNGK-PVDKIVGAMPKGELIRW 150
                                       ***55388888.***********999876 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.2   1.4e+03      33      65 ..      45      54 ..       3      69 .. 0.55
   2 !   24.3   0.0   2.4e-08   2.9e-05       1      31 [.      68      98 ..      67     108 .. 0.89
   3 !    8.3   0.0    0.0024       2.9      66      90 ..     106     130 ..      99     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                                      TTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.E CS
                     Thioredoxin_8 33 kkkveivyvsldkkeeefekylkknkkpwlsvp 65
                                      + k                       ++ +++p
  gi|488599795|ref|YP_007906266.1| 45 GEK-----------------------MEKINYP 54
                                      222.......................2333333 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.4e-08
                                      .SEEEEEE--SSSHHHHHHHHHHHHHHHHHH CS
                     Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelyeklk 31
                                      +++v+L f+a+wc+pck + p +++l +++ 
  gi|488599795|ref|YP_007906266.1| 68 NRYVVLDFWADWCAPCKMIAPIIDDLAREYD 98
                                      69************************99996 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0024
                                       E-TT-HHHHTT-S--TT-SEEEEE- CS
                     Thioredoxin_8  66 fddkkrnklkkkynvkaiPtlvvld 90 
                                       ++  + +++++++ ++aiPtl+  +
  gi|488599795|ref|YP_007906266.1| 106 VNTTEEQAIANRFAITAIPTLIFFR 130
                                       5667899**************9876 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0     2e-08   2.4e-05      10     105 ..      50     132 ..      42     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2e-08
                         OST3_OST6  10 s.ngviklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegk 85 
                                       + n  ++++++n++e+lk   + +vv+ + a      C++C+ ++p ++ +a+ ++ +       ++F+kv+  e +
  gi|488599795|ref|YP_007906266.1|  50 KiNYPVNVTQSNFNEILK---NRYVVLDFWAD----WCAPCKMIAPIIDDLAREYDGK-------VVFGKVNTTEEQ 112
                                       3368999*********95...88999999998....7****************99888.......9*********** PP

                         OST3_OST6  86 dvFqklglnsaPhlllfppk 105
                                        + +++ ++ +P l++f   
  gi|488599795|ref|YP_007906266.1| 113 AIANRFAITAIPTLIFFRNG 132
                                       *****************883 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   4.1e-08   4.9e-05       4     109 ..      33     134 ..      30     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.1e-08
                                       HHHHHHTS-HHHHHHHHHHHHHHHHH---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE- CS
                     Thioredoxin_9   4 feeyleemtkenkermlrvykkvelseeteekiksiekklkilvltedwCgDaavnvPvlakia.elnpnievkill 79 
                                        ++ +e+m+++  e+m+++   v++++   ++i  +++++ +l + +dwC  + ++ P+++ +a e+  ++ +  + 
  gi|488599795|ref|YP_007906266.1|  33 KKKLMEKMERMMGEKMEKINYPVNVTQSNFNEI--LKNRYVVLDFWADWCAPCKMIAPIIDDLArEYDGKVVFGKVN 107
                                       577899******************999998877..677889**********************94566678888888 PP

                                       HHHHHHHTTTTTT-SS--SSEEEEE-TT-- CS
                     Thioredoxin_9  80 rdenlelmdqyltngaraiPtliildeege 109
                                         e++ + +++      aiPtli++ ++  
  gi|488599795|ref|YP_007906266.1| 108 TTEEQAIANRFA---ITAIPTLIFFRNGKP 134
                                       888888889885...59*******988754 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.3   8.7e+03      67      81 ..      58      72 ..      48      75 .. 0.66
   2 !   22.3   0.0   8.3e-08   9.9e-05      49     101 ..      89     140 ..      82     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.3
                                      ETHHHHHHHHHCCT- CS
                              HyaE 67 adreqeealaerfgv 81
                                       +++ +e l++r+ v
  gi|488599795|ref|YP_007906266.1| 58 TQSNFNEILKNRYVV 72
                                      445666777777766 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 8.3e-08
                                       HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEES CS
                              HyaE  49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvlak 101
                                       ++ +l +++        v+ + +e+a+a+rf ++  P+l+f+r+g+ +  + +
  gi|488599795|ref|YP_007906266.1|  89 IIDDLAREYDGKVVFGKVN-TTEEQAIANRFAITAIPTLIFFRNGKPVDKIVG 140
                                       7888999998888888888.899**********************98877655 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.1e-07   0.00013      16      60 ..      58     100 ..      44     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-07
                                       EEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTE CS
                          AhpC-TSA  16 etvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergv 60 
                                       ++ +++++ k+++vvl f++  wc +C+  +p + +l+ e++    
  gi|488599795|ref|YP_007906266.1|  58 TQSNFNEIlKNRYVVLDFWAD-WCAPCKMIAPIIDDLAREYDG--K 100
                                       56777888799**********.****************99983..3 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.2e-07   0.00086     127     205 ..      66     135 ..      38     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.2e-07
                              TraF 127 lakeygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpks 203
                                       l+++y  l F +  c  c++ api++++a++y  +v++ +v+ +  + ++n         r+ ++ +P+l++++  +
  gi|488599795|ref|YP_007906266.1|  66 LKNRYVVLDFWADWCAPCKMIAPIIDDLAREYDGKVVFGKVNTTEEQAIAN---------RFAITAIPTLIFFRNGK 133
                                       789999******************************997777776655777.........************99886 PP

                              TraF 204 qk 205
                                         
  gi|488599795|ref|YP_007906266.1| 134 PV 135
                                       44 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.7e-06      0.01      81     183 ..      56     152 ..      47     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.7e-06
                                       E-SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEE CS
                     Thioredoxin_6  81 eltpenaeelfeeglppllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivi 157
                                        +t+ n++e+ +++   ++l f        + +  +i  +a+e+ +k+ f  +++++ + + +++ ++  ++P++++
  gi|488599795|ref|YP_007906266.1|  56 NVTQSNFNEILKNR--YVVLDFWADWCAPCKMIAPIIDDLAREYDGKVVFGKVNTTEEQAIANRFAIT--AIPTLIF 128
                                       57899999999999..5688888644556677777789999999999999999999999999999999..9999997 PP

                                       EESSSS-EEEET.TSS--HHHHHHHHH CS
                     Thioredoxin_6 158 vdsashkykypp.kdefspeklkeFlk 183
                                       +    + + + +  + +++++l ++++
  gi|488599795|ref|YP_007906266.1| 129 FR---NGKPVDKiVGAMPKGELIRWIN 152
                                       66...4444444567777777777776 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.83     1e+03      19      27 ..      39      47 ..       9      74 .. 0.55
   2 !   14.7   0.0   1.9e-05     0.023      10      72 ..      80     149 ..      75     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.83
                                      HHHHHCHCC CS
                     Thioredoxin_3 19 avkeaaaek 27
                                       +++++ ek
  gi|488599795|ref|YP_007906266.1| 39 KMERMMGEK 47
                                      333333333 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                                       STTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEE..ECTTCE..EEESS---CCHHH CS
                     Thioredoxin_3  10 CakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPal..vidgkv..vvsGkvpseeeir 72 
                                       Ca C+ ++ ++  +a e + k+ + kv  t+ + i +++ ++++P+l  + +gk   +++G++p++e ir
  gi|488599795|ref|YP_007906266.1|  80 CAPCKMIAPIIDDLAREYDGKVVFGKVntTEEQAIaNRFAITAIPTLifFRNGKPvdKIVGAMPKGELIR 149
                                       ******************999988888657778889***********76679997336999999998876 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.95   1.1e+03      50      89 ..      11      55 ..       5      61 .. 0.71
   2 !   15.4   0.0   9.5e-06     0.011      19      66 ..      58     104 ..      43     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.95
                                      HHHTHHHHHHCSTTTEEEEEESSSHH...HHHHHHH..TT-TSEE CS
                           Redoxin 50 yleklaellkekgvdvvavvadndaf...vkefwgk..eglkfpv 89
                                      y e++++l+++ g+     ++ +  +   + +++g+  e++++pv
  gi|488599795|ref|YP_007906266.1| 11 YCETFKKLIGKLGFMDELEIIRKKKLmekMERMMGEkmEKINYPV 55
                                      888888888888887777777777776667777777666666665 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 9.5e-06
                                       EEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEE CS
                           Redoxin  19 nsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvv 66 
                                       ++ +  e +k++ vv+ f++  +c +C+  +p +++la+++ ++ v + 
  gi|488599795|ref|YP_007906266.1|  58 TQSNFNEiLKNRYVVLDFWAD-WCAPCKMIAPIIDDLAREY-DGKVVFG 104
                                       555667789************.*******999*****9995.4445554 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.8   4.6e+03      21      37 ..       1      17 [.       1      19 [. 0.79
   2 ?   14.1   0.1   3.3e-05     0.039      17      81 ..      68     129 ..      66     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.8
                                      EEEE--TT-HHHHHHHH CS
                     Thioredoxin_7 21 lvffgaswcftCqaler 37
                                      ++++ a   ++C ++++
  gi|488599795|ref|YP_007906266.1|  1 MIYINAVITHYCETFKK 17
                                      67777888899999987 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.3e-05
                                       T--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                     Thioredoxin_7  17 gkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafl 81 
                                       ++ v ++f a+wc +C+ ++    +    ++ +++k+v+ +v+ te++a   ++  + +P+++f+
  gi|488599795|ref|YP_007906266.1|  68 NRYVVLDFWADWCAPCKMIAPIIDDL--ARE-YDGKVVFGKVNTTEEQAIANRFAITAIPTLIFF 129
                                       567899************98766554..777.************999993334444779999998 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.4e-05     0.029     145     214 ..      67     138 ..      16     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                       TT-EEEEEEE-TTSTTHHHHHHHHHHHHHH-T.TSEEEEEEHHHH--.TTSS-TTT-SEEEEEETTEEEEEE CS
                         Phosducin 145 kitlivvhiyedgvkgtealnssliclaaeyp.tvkfckvkasviga.sdrfsrdvlpallvykagellsnf 214
                                       k   +v+  + d    ++ +   +  la ey   v f kv+++   a ++rf+  ++p+l+ ++ g+ +  +
  gi|488599795|ref|YP_007906266.1|  67 KNRYVVLDFWADWCAPCKMIAPIIDDLAREYDgKVVFGKVNTTEEQAiANRFAITAIPTLIFFRNGKPVDKI 138
                                       44567888999999999999999999*****6479*****9987655389***************9877665 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00011      0.13      68     133 ..       7      74 ..       4      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       EEEEEHHHHHHHHSS-..HHHHHHHCCC-HHHHHHHHHHTTT-EEEEEEEEE----------EEEEEE CS
                       Rep_fac-A_C  68 wvtlFneaaekllgls..aeelkklkeedeeefekiiekvklkeflfrlrvkeesyndesrvrytvvk 133
                                        +t + e+ +kl+g+    +el+ +++++ +e  + +   k++++++ + v++ ++n+  ++ry v++
  gi|488599795|ref|YP_007906266.1|   7 VITHYCETFKKLIGKLgfMDELEIIRKKKLMEKMERMMGEKMEKINYPVNVTQSNFNEILKNRYVVLD 74 
                                       68999999999999863369************9999****************************9975 PP

>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.15      66     109 ..      34      77 ..      26      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHSS--EEEEE---SSHHHHHHHHHHHHHHHG CS
                     RuBisCO_large  66 eavaeaikraqdetGekklyalnitaddleemlrraefvketgg 109
                                       ++ +e ++r++ e  ek  y +n+t ++ +e+l++   v++  +
  gi|488599795|ref|YP_007906266.1|  34 KKLMEKMERMMGEKMEKINYPVNVTQSNFNEILKNRYVVLDFWA 77 
                                       6789******************************9988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); 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:                        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 0.34s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 969.25
//
Query:       gi|488599796|ref|YP_007906267.1|  [L=449]
Description: phosphoglucosamine mutase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-38  130.5   0.1    7.6e-38  129.3   0.1    1.6  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.2e-31  109.4   0.1    3.4e-31  107.9   0.0    1.9  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.1e-26   92.4   0.0    3.6e-26   91.6   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.4e-13   50.8   0.0    7.1e-13   48.5   0.0    2.2  2  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
     0.0067   16.6   0.0      0.024   14.8   0.0    2.0  2  CinA_KH      Damage-inducible protein CinA KH domain
  ------ inclusion threshold ------
      0.036   14.2   0.0      0.065   13.4   0.0    1.3  1  Laminin_G_3  Concanavalin A-like lectin/glucanases superfamil
       0.14   12.0   0.1       0.24   11.2   0.1    1.3  1  DUF1572      Protein of unknown function (DUF1572)
       0.21   11.6   0.0       0.86    9.6   0.0    1.9  2  Borealin     Cell division cycle-associated protein 8


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 !  129.3   0.1   3.4e-41   7.6e-38       2     135 ..       9     136 ..       8     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 3.4e-41
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       ++fgt+G+Rg+++ +elt+e++++lg+ i++  k      +++++ D+R+ss++l+ a++ag+++ G +vi+lg++p
  gi|488599796|ref|YP_007906267.1|   9 ELFGTNGVRGVAN-EELTAEMALNLGRVIGSLRKG-----RIAIATDARISSQMLKCAVIAGITSVGSDVIDLGVAP 79 
                                       58***********.77**************98875.....9************************************ PP

                                       HHHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                         PGM_PMM_I  79 tPavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                       tPa++++++  ++ +g+++taSHnp eyngiK++ s+G ++++e++e+ e+ +++++
  gi|488599796|ref|YP_007906267.1|  80 TPALQYYVKMRDVTGGVIVTASHNPREYNGIKFVHSDGTEFTREMDEESERVYKSKD 136
                                       *********************************************999888888766 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 !  107.9   0.0   1.5e-34   3.4e-31       3     103 .]     157     256 ..     155     256 .. 0.99
   2 ?   -3.2   0.0       5.8   1.3e+04      31      45 ..     306     320 ..     292     351 .. 0.66

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 1.5e-34
                                       HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGG CS
                        PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvk 79 
                                       Yi+++k++vd+  i+k++++vvid+++Ga+  ++++llkelg++v+++na+pd++fp+++++p e e+++ll ++vk
  gi|488599796|ref|YP_007906267.1| 157 YIDGIKSRVDQGLIAKKKFRVVIDCGNGAAVFTTPQLLKELGCEVISINAHPDGTFPQRSSEPVE-ENVELLKKVVK 232
                                       *****************************************************************.*********** PP

                                       GGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  80 kegadlglafDgDaDRlgvvderG 103
                                       +++adlg+a+DgDaDR  +vde+G
  gi|488599796|ref|YP_007906267.1| 233 ETSADLGIAHDGDADRATFVDENG 256
                                       **********************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.8
                                       TTHHHHHHHHHHTT- CS
                        PGM_PMM_II  31 aggeilkellkelgv 45 
                                       +g+ ++ +++ke+++
  gi|488599796|ref|YP_007906267.1| 306 VGSPVVVKVMKEINA 320
                                       566666666666555 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 !   91.6   0.0   1.6e-29   3.6e-26       3     112 ..     262     368 ..     260     370 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 1.6e-29
                                       HHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTT CS
                       PGM_PMM_III   3 dqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiiflde 79 
                                       d +lal+a+y+ ++   +g+ vv+++++s+ +e+++ ++g+++v t+vG+  v++ mke +av+GgE +g++if+++
  gi|488599796|ref|YP_007906267.1| 262 DVMLALMAEYYVRS--FGGK-VVTPISSSKCVEDAVLRAGGEIVYTAVGSPVVVKVMKEINAVFGGEGNGGLIFPEF 335
                                       889********884..6565.******************************************************** PP

                                       BSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
                       PGM_PMM_III  80 attkDGilaallvleilaetgkslselleellk 112
                                       + t+DG+++a++vle++a++++++sel++++++
  gi|488599796|ref|YP_007906267.1| 336 QLTRDGAMSAAKVLELMAKEDRPISELVKDIPR 368
                                       ****************************88654 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 ?   -2.4   0.0       2.4   5.5e+03      24      39 ..     105     120 ..      76     123 .. 0.74
   2 !   48.5   0.0   3.2e-16   7.1e-13      12      73 ..     384     444 ..     353     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                                       HCCCCCCCCGCCEEEE CS
                        PGM_PMM_IV  24 sikeglkilledGrrl 39 
                                       ++ +g+k+++ dG+ +
  gi|488599796|ref|YP_007906267.1| 105 REYNGIKFVHSDGTEF 120
                                       4568999999999866 PP

  == domain 2  score: 48.5 bits;  conditional E-value: 3.2e-16
                                       ..EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHHH CS
                        PGM_PMM_IV  12 vvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevaell 73 
                                        ++ l++ + +a++ +g++i++ dG++l +RpSGTep +r+ +Ea++++++++l +e ++++
  gi|488599796|ref|YP_007906267.1| 384 LLDGLRKEFPDANFTDGARIDYDDGWIL-IRPSGTEPIVRIFAEATTKSRAEELIKEGMDAV 444
                                       44555555555689**************.**********************99988877765 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.3   7.4e+03      21      44 ..      75     100 ..      68     106 .. 0.67
   2 !   14.8   0.0   1.1e-05     0.024      33      68 ..     414     449 .]     406     449 .] 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                                       GS-BSSSEEEEEEETTEEE..EEEE. CS
                           CinA_KH  21 lidrenptlAiyakegevt..vRlta 44 
                                       l     p l +y+k  +vt  v +ta
  gi|488599796|ref|YP_007906267.1|  75 LGVAPTPALQYYVKMRDVTggVIVTA 100
                                       44456788999999988864455555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.1e-05
                                       EETTEEEEEEE...EEHHHHHHHHH....HHHHHTT CS
                           CinA_KH  33 akegevtvRltakaaneeeaealiapveeeirerlg 68 
                                       ++  e  vR+ a+a ++  ae+li++ ++++r++lg
  gi|488599796|ref|YP_007906267.1| 414 PSGTEPIVRIFAEATTKSRAEELIKEGMDAVRRILG 449
                                       5667888***************************98 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 ?   13.4   0.0   2.9e-05     0.065      24     103 ..      86     163 ..      80     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                       Laminin_G_3  24 Wvkpdslpsaaqiiissssdg..rgfelgldgsgrlrfsvnagngaeesvtsgasvpageWtHvavtydggtlrlYv 98 
                                       +vk++++++  ++i+++s  +   + ++++  s+  +f+   ++ ++e+v  ++++ + +W+ v  +++++  rlY+
  gi|488599796|ref|YP_007906267.1|  86 YVKMRDVTG--GVIVTAS-HNprEYNGIKFVHSDGTEFTREMDE-ESERVYKSKDFMLAKWNEVGQVFEDDCRRLYI 158
                                       678888887..4555334.3446666788888889999999886.7899**************************** PP

                       Laminin_G_3  99 NGvev 103
                                       +G + 
  gi|488599796|ref|YP_007906267.1| 159 DGIKS 163
                                       **876 PP

>> DUF1572  Protein of unknown function (DUF1572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.24      61     111 ..     111     161 ..     100     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                           DUF1572  61 dfltsdGekpdRnRDaefedalkskeelleaweeGWelllsaldslkeedl 111
                                        f+ sdG   +R+ D+e e  +ksk+ +l+ w+e  +++ +   +l  + +
  gi|488599796|ref|YP_007906267.1| 111 KFVHSDGTEFTREMDEESERVYKSKDFMLAKWNEVGQVFEDDCRRLYIDGI 161
                                       5889******************************99999888777766655 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 ?   -1.7   0.0       1.2   2.6e+03      66      97 ..     170     201 ..     163     204 .. 0.77
   2 ?    9.6   0.0   0.00038      0.86      31      68 ..     281     317 ..     273     340 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                          Borealin  66 vteevanvniPvgdGevlslqakeldevdeel 97 
                                       +++++  v i  g+G  +  +++ l+e+  e+
  gi|488599796|ref|YP_007906267.1| 170 IAKKKFRVVIDCGNGAAVFTTPQLLKELGCEV 201
                                       566788899999***99999999998876555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00038
                          Borealin  31 itpkvdprlpkt.llRtpkagErvlslsGSPlaegvvte 68 
                                       +tp  +++     +lR    gE v++  GSP++++v++e
  gi|488599796|ref|YP_007906267.1| 281 VTPISSSKCVEDaVLRA--GGEIVYTAVGSPVVVKVMKE 317
                                       55555555555546664..48**************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 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:                         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 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3243.18
//
Query:       gi|488599797|ref|YP_007906268.1|  [L=418]
Description: tRNA pseudouridine synthase, TruD family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-135  451.0   0.0   3.9e-135  450.9   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)
     0.0089   15.6   0.0      0.013   15.1   0.0    1.2  1  DUF3053   Protein of unknown function (DUF3053)


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 !  450.9   0.0  4.4e-139  3.9e-135       2     416 .]       7     415 ..       6     415 .. 0.95

  Alignments for each domain:
  == domain 1  score: 450.9 bits;  conditional E-value: 4.4e-139
                              TruD   2 lgielyvtdtegigGrlrespeDFiVeEieef.sgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfa 77 
                                       +gi+ y+t+t gigG ++e+p+ F V+E++++        eg++l+lrv krnwdt++++r l+++lgis+kr+g+a
  gi|488599797|ref|YP_007906268.1|   7 VGIRGYITSTGGIGGLIKEEPDYFKVTEVADVaI-----GEGKHLILRVAKRNWDTINFARVLSNKLGISQKRIGYA 78 
                                       89***************************77743.....46************************************ PP

                              TruD  78 GtKDkrAvTtQlisirkvep..eelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeile 152
                                       GtKDkrA T+Q+ si+++++  e+le l+ikd+e+ev+g ++r+l+lGdL+GN+Feir+++ +++  +++ ++e++e
  gi|488599797|ref|YP_007906268.1|  79 GTKDKRAFTVQYYSIANAREvaEKLEGLHIKDAEIEVIGWSNRALKLGDLIGNEFEIRITE-SDA--DSEIIDETIE 152
                                       ***************88654227799***********************************.444..468******* PP

                              TruD 153 eleekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpk 229
                                       el+ kg  PN+fG+QRFG++r +th+vG++i+k+d+ +A+++yv+kpf +e+e++r++re ++e++d + +l+elpk
  gi|488599797|ref|YP_007906268.1| 153 ELKVKG-SPNFFGTQRFGTIRYITHIVGLHILKRDYGAAFWTYVAKPFVSENEEVRKIREELWESRDPKFGLRELPK 228
                                       ****98.********************************************************************** PP

                              TruD 230 slryErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer.lpdt 305
                                       +lryEr+ll++L+e +++ +kAl +lpknL+++FvhAyqSy+FNr+ls+R+++  +l+e++++D+v f + r    t
  gi|488599797|ref|YP_007906268.1| 229 HLRYERTLLQKLIE-ENSEEKALLSLPKNLKMMFVHAYQSYVFNRILSDRIAEFKTLREICDEDIVDFIRIRnGRLT 304
                                       **************.9****************************************************988867788 PP

                              TruD 306 drlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRail 382
                                        + + v+ +n ++++ li+ gra++++pl+G++te+ +g+v++   ++l+e++++ edF+ ++ +e+ss+G++R++ 
  gi|488599797|ref|YP_007906268.1| 305 IAGNPVEVRNRKRIDFLISVGRAVLCLPLPGYKTEV-KGWVKDRLLDILAEDDISFEDFRHEH-KEFSSSGEFRSAE 379
                                       89999******************************9.8**********************655.7************ PP

                              TruD 383 lrve..dlelsaeedeltleFsLpkGsYATvvlrEi 416
                                       ++++  +l ++ +++++ ++F+LpkG+YAT++lrE+
  gi|488599797|ref|YP_007906268.1| 380 IPIDfdELYYEIDGRDVFMKFFLPKGCYATSFLREF 415
                                       **99989999999999*******************7 PP

>> DUF3053  Protein of unknown function (DUF3053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.5e-06     0.013      93     193 ..     214     316 ..     183     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-06
                           DUF3053  93 ltrrd...elrqaagalneleqqlqnakaqadkaraaLkqpddlkavydkayektVtq..panaltpllplaeallq 164
                                        + rd    lr+  ++l   ++ lq+  +++ +++a L +p++lk ++ +ay+  V +   ++++++   l+e + +
  gi|488599797|ref|YP_007906268.1| 214 WESRDpkfGLRELPKHLRYERTLLQKLIEENSEEKALLSLPKNLKMMFVHAYQSYVFNriLSDRIAEFKTLREICDE 290
                                       445553225888888999999999********************************862235566665555555555 PP

                           DUF3053 165 qlvqvgdflqkqgnqvefegngvqfktqq 193
                                       ++v   df++ +  + ++ gn v++++ +
  gi|488599797|ref|YP_007906268.1| 291 DIV---DFIRIRNGRLTIAGNPVEVRNRK 316
                                       555...89999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2800.81
//
Query:       gi|488599798|ref|YP_007906269.1|  [L=115]
Description: peptidyl-tRNA hydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-38  129.1   0.2      1e-37  129.0   0.2    1.0  1  PTH2           Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
      0.063   12.1   0.4      0.078   11.8   0.4    1.1  1  Pox_ATPase-GT  mRNA capping enzyme N-terminal, ATPase and gua


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 !  129.0   0.2   1.2e-41     1e-37       1     117 []       3     114 ..       3     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 1.2e-41
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-S CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglp 77 
                                       +k+v+vvr DLk+s+Gk+ +q+ahA++  +++  k     +++++W+++gqkkivlkv++ +e++ ++ ka+++gl+
  gi|488599798|ref|YP_007906269.1|   3 YKQVIVVRDDLKLSRGKLSVQVAHASILGYEASNK-----KIVDAWRKSGQKKIVLKVKDLQEMMMVKYKAEKEGLV 74 
                                       79****************************96555.....59*********************************** PP

                                       EEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                              PTH2  78 aalirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                       +al+rDag t+i+pgt+T+laigP +++++d+vtg+L ll
  gi|488599798|ref|YP_007906269.1|  75 TALVRDAGLTEIPPGTVTALAIGPDEEKKIDRVTGNLPLL 114
                                       *************************************997 PP

>> Pox_ATPase-GT  mRNA capping enzyme N-terminal, ATPase and guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   8.7e-06     0.078      48     103 ..      17      71 ..       6      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.7e-06
                                       SEEEEEEEEGGG--SSS--HHHHHHT----EEEEEEEEEEEEEETTEEEEEEEEEE CS
                     Pox_ATPase-GT  48 ksKlRtklklskvhgldvkNvqlvdkldniiWEkKtlvsekkikeeillrhstEek 103
                                       + Kl  ++  + + g +  N ++vd+  +    kK +++ k+++e +++++  E++
  gi|488599798|ref|YP_007906269.1|  17 RGKLSVQVAHASILGYEASNKKIVDAWRK-SGQKKIVLKVKDLQEMMMVKYKAEKE 71 
                                       67899999999****************99.89999999999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 709.18
//
Query:       gi|488599799|ref|YP_007906270.1|  [L=91]
Description: hypothetical protein Asulf_00244 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 575.65
//
Query:       gi|488599800|ref|YP_007906271.1|  [L=213]
Description: phospholactate guanylyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-62  210.4   2.8      2e-62  210.2   2.8    1.0  1  CofC          Guanylyl transferase CofC like
    4.7e-06   27.0   0.0    2.6e-05   24.6   0.0    1.9  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 !  210.2   2.8   2.2e-66     2e-62       1     199 [.       1     198 [.       1     212 [. 0.90

  Alignments for each domain:
  == domain 1  score: 210.2 bits;  conditional E-value: 2.2e-66
                              CofC   1 mkviiPvsainsaktrlseilseeerkellkamlldvidalkrld..vlvvsedeev..ley.aldelgvevvkeke 72 
                                       m +++P++  n +ktrl++ils +erk+l+ +ml dv  al+++d   +vv +de v  + + + + +++evv ++ 
  gi|488599800|ref|YP_007906271.1|   1 MIAVVPFKYRN-PKTRLAKILSLDERKKLAMTMLRDVLSALSGVDrvTVVVPDDESVkaCSFiNAKFENAEVVMDD- 75 
                                       6789****999.*********************************95577888888743555234568999**999. PP

                              CofC  73 kdlntavekafeeieekeviiipsdiPlikkedvkdllelekradvviaPargGGtnllllrksalevkyedfsflk 149
                                       ++l++ v+   +   + ev+++++d+Pl++++ +++++e+++  dvviaP+r+GGtn+ll+r+++++v+y+ +sf+k
  gi|488599800|ref|YP_007906271.1|  76 RNLDDLVNYF-I-DSHGEVAVVMADLPLLNEKILSKFFETDG--DVVIAPGRKGGTNMLLVRNRMFRVSYHYGSFMK 148
                                       *****99986.4.47889************************..********************************* PP

                              CofC 150 hleearkrglkvkiydsfylsvdinteedlgeillhGegtkakeylrklg 199
                                       hl  a+ r lkv ++dsfy+s+di++e+d++e+l+hGeg++++++l ++ 
  gi|488599800|ref|YP_007906271.1| 149 HLAIAKSRKLKVVVFDSFYSSIDIDDESDILELLIHGEGKESYKFLSSIM 198
                                       **********************************************9983 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.9e-09   2.6e-05      25     139 ..      31     138 ..      19     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.9e-09
                                       CHHHHHHHHHCTT.-CEEEEECSHCHHHHHH.....TTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT- CS
                      NTP_transf_3  25 pllervldalraagvdevvvvggdeevlaal.....arlgvrvvededpgkgplaslaaalraaadadavlvlacDm 96 
                                       ++l+ vl al+ +  d+v+vv++d+e  +a+     +  +++vv d+      l  l      + +   v+v+++D+
  gi|488599800|ref|YP_007906271.1|  31 TMLRDVLSALSGV--DRVTVVVPDDESVKACsfinaKFENAEVVMDD----RNLDDLVNYF--IDSHGEVAVVMADL 99 
                                       99*********65..9********98887763333123356677776....3444444444..44689********* PP

                                       TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHH CS
                      NTP_transf_3  97 Plltpelverllaaaaasgadvvvptyegerghpllfrarlls 139
                                       Pll+++++ ++++    +g+ v++p ++g+  + ll r+r+++
  gi|488599800|ref|YP_007906271.1| 100 PLLNEKILSKFFET---DGDVVIAPGRKGGT-NMLLVRNRMFR 138
                                       *************7...56666666666555.88888888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1483.99
//
Query:       gi|488599801|ref|YP_007906272.1|  [L=603]
Description: hypothetical protein Asulf_00246 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   56.7   1.0    2.3e-15   56.7   1.0    3.0  4  T2SSF       Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.3      0.52   9.3e+03      94     110 ..     172     188 ..     163     192 .. 0.44
   2 ?   -6.4   4.3         1   1.8e+04     107     121 ..     259     273 ..     256     275 .. 0.58
   3 ?   -6.0   2.2         1   1.8e+04     107     118 ..     294     305 ..     289     308 .. 0.43
   4 !   56.7   1.0   1.3e-19   2.3e-15       1     119 [.     403     524 ..     403     529 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHTTXXXXX CS
                             T2SSF  94 lrrkllaallepllllv 110
                                        r  ll+a+l+ l+ +v
  gi|488599801|ref|YP_007906272.1| 172 KRLSLLLASLSILFAIV 188
                                       33334444443333333 PP

  == domain 2  score: -6.4 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXX CS
                             T2SSF 107 lllvvallvllilla 121
                                       ++++++ l+l+il++
  gi|488599801|ref|YP_007906272.1| 259 FIIILLTLILSILII 273
                                       555666666666554 PP

  == domain 3  score: -6.0 bits;  conditional E-value: 1
                                       XXXXXXXXXXXX CS
                             T2SSF 107 lllvvallvlli 118
                                       ++l++a+++l++
  gi|488599801|ref|YP_007906272.1| 294 ASLIFASIILIL 305
                                       333344444333 PP

  == domain 4  score: 56.7 bits;  conditional E-value: 1.3e-19
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqliragee 73 
                                       fl  la   + G+pl +a+++++  + +g l++ + ++  +++aG ++ eale    + +s+ +++ v+ +i+a ++
  gi|488599801|ref|YP_007906272.1| 403 FLIDLAESRRVGMPLGQAIKRASGGD-YGLLTPYIVKMSYQMSAGLTFIEALEkfaaSIKSKIIKRGVALIIEAFRS 478
                                       66778899999***************.**************************88876666566************* PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllil 119
                                       gg+++e+Le  a ++ e+  l+++++++++ +ll+++va++v+l+ 
  gi|488599801|ref|YP_007906272.1| 479 GGSISEALEVSAMHITEMKYLEKERRSNMTVYLLVIYVAFFVFLFT 524
                                       ******************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 4178.93
//
Query:       gi|488599802|ref|YP_007906273.1|  [L=291]
Description: hypothetical protein Asulf_00247 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   63.3   1.9      2e-17   63.3   1.9    2.6  4  T2SSF     Type II secretion system (T2SS), protein F
     0.0031   16.3   9.2     0.0041   16.0   1.7    2.1  2  DUF2207   Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.068   12.6   9.1        0.2   11.1   9.1    1.8  1  SfLAP     Sap, sulfolipid-1-addressing protein
        0.6    9.7   7.6        3.1    7.4   0.4    2.8  2  NapE      Periplasmic nitrate reductase protein NapE


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.3       1.8   8.2e+03     107     125 .]      51      69 ..      36      69 .. 0.65
   2 ?   -3.8   1.1       2.6   1.2e+04     102     119 ..      76      93 ..      72      99 .. 0.48
   3 !   63.3   1.9   4.5e-21     2e-17       2     124 ..     118     246 ..     117     247 .. 0.94
   4 ?   -1.3   1.7      0.44     2e+03     108     122 ..     264     278 ..     254     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.8
                                       XXXXXXXXXXXXXXXXXXX CS
                             T2SSF 107 lllvvallvllillaillp 125
                                       +l+ ++  ++++ll++llp
  gi|488599802|ref|YP_007906273.1|  51 FLAGIITSLSSLLLFFLLP 69 
                                       4555555566666666665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.6
                                       HHTTXXXXXXXXXXXXXX CS
                             T2SSF 102 llepllllvvallvllil 119
                                       l   l+ ++++ + ++  
  gi|488599802|ref|YP_007906273.1|  76 LVPILVAFPMITITFVYA 93 
                                       344444444444444444 PP

  == domain 3  score: 63.3 bits;  conditional E-value: 4.5e-21
                                       HHHHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.....SHHHHHCT-TT.TS-HHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.....slsealertpssefpelvvqlirage 72 
                                       l  +a l saGv++v  +++la++++ +  ++ e ++i++++   g     +l+++ er+ps  ++e+++ +i+++ 
  gi|488599802|ref|YP_007906273.1| 118 LSFMAALASAGVTPVGLFRALANQKSaYESISSEASKIYTDVTLYGmdiitALKNSAERSPSARYREVIQGIISTIT 194
                                       6789**************************************9988866666666666******************* PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       +gg+L e+L r a++l++e++++ k++ ++l++l++ +v+l v+++l++++l
  gi|488599802|ref|YP_007906273.1| 195 AGGSLKEYLFREAQELMRENRTKMKSFFETLSVLAESYVVLGVAFPLFMMIL 246
                                       **************************************************98 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.44
                                       XXXXXXXXXXXXXXX CS
                             T2SSF 108 llvvallvllillai 122
                                       +l+v+++++l++++i
  gi|488599802|ref|YP_007906273.1| 264 VLYVIIFIVLPVISI 278
                                       688999999999887 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   1.0    0.0017       7.4     381     435 ..      41      99 ..       9     120 .. 0.56
   2 !   16.0   1.7   9.1e-07    0.0041     350     435 ..     204     289 ..     139     291 .] 0.62

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0017
                           DUF2207 381 kklsalglgliilglilillallllvll....lvfllilllillliaiivlllfsrllg 435
                                       +++  +++ ++++g+i +l +lll++ll       l+ +l+++++i i +++ f ++ +
  gi|488599802|ref|YP_007906273.1|  41 YYVARIYFSCFLAGIITSLSSLLLFFLLpenmKARLVPILVAFPMITITFVYAFGYFYP 99 
                                       33333344444444444444444433334433555555555555555555555444444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.1e-07
                           DUF2207 350 akkfkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvll......lvfllilllill 420
                                        ++ ++ +++ +     k + +f++  +  + ++ +lg+++ ++++il+ + +ll+++        v+++i++++l+
  gi|488599802|ref|YP_007906273.1| 204 FREAQELMRENRT----KMKSFFETL-SVLAESYVVLGVAFPLFMMILFSV-MLLIQTSglvlsiQVLYVIIFIVLP 274
                                       2222222222222....233344444.566666666666666666665543.3444433799999************ PP

                           DUF2207 421 liaiivlllfsrllg 435
                                       +i+i++++l+++ ++
  gi|488599802|ref|YP_007906273.1| 275 VISIAYAILLKISMP 289
                                       ********9988876 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.1   4.4e-05       0.2      31     169 ..     113     283 ..     105     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                             SfLAP  31 llaFlvgwlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlllllaaveavrr................. 90 
                                        l + +  +++l+ +g+ ++ ++r+l+++ sa +s + +a +i + v l  + +  a++                  
  gi|488599802|ref|YP_007906273.1| 113 QLPYALSFMAALASAGVTPVGLFRALANQKSAYESISSEASKIYTDVTLYGMDIITALKNsaerspsaryreviqgi 189
                                       57788888999999999999999999987777777777777777777664444444444455558999999999999 PP

                             SfLAP  91 .................pkassrselprllsrleslleggalwvA..lvlgllsakplllylaalaaigasgasvgt 148
                                                        +    ++ ++   ++++s+ e+ ++++   +vlg++ +  +++ + ++++i++sg+  + 
  gi|488599802|ref|YP_007906273.1| 190 istitaggslkeylfreA----QELMRENRTKMKSFFETLSVLAEsyVVLGVAFPLFMMILFSVMLLIQTSGLVLSI 262
                                       999999999888744433....44444444444444444444433114677777777888999************** PP

                             SfLAP 149 qvvalvvFvvvalavveipll 169
                                       qv+ +++F+v+ + +++  +l
  gi|488599802|ref|YP_007906273.1| 263 QVLYVIIFIVLPVISIAYAIL 283
                                       ***********9998887766 PP

>> NapE  Periplasmic nitrate reductase protein NapE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4   0.00068       3.1      21      40 ..      77      96 ..      70      97 .. 0.83
   2 ?    4.6   1.6    0.0053        24      17      33 ..     263     279 ..     261     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00068
                              NapE 21 fltvvlfPiLsValVggYGf 40
                                      + ++v fP++++++V ++G+
  gi|488599802|ref|YP_007906273.1| 77 VPILVAFPMITITFVYAFGY 96
                                      557899************97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0053
                              NapE  17 kaflfltvvlfPiLsVa 33 
                                       +++ +++++++P++s+a
  gi|488599802|ref|YP_007906273.1| 263 QVLYVIIFIVLPVISIA 279
                                       6799***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1082  (0.0603492); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1761.80
//
Query:       gi|488599803|ref|YP_007906274.1|  [L=524]
Description: Type IV secretory pathway, VirB11 component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  164.0   0.0    5.4e-48  163.4   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
     0.0013   19.3   2.8      0.034   14.6   0.0    2.8  3  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.058   12.5   0.0        0.1   11.7   0.0    1.3  1  Parvo_NS1     Parvovirus non-structural protein NS1
      0.067   13.4   0.0        0.4   10.9   0.0    2.3  1  DUF1858       Domain of unknown function (DUF1858)
       0.12   12.2   0.0       0.28   11.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
       0.14   11.5   0.0       0.42    9.9   0.0    1.7  2  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.84    9.8   3.3        2.1    8.5   0.1    3.2  4  DUF1500       Protein of unknown function (DUF1500)


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 !  163.4   0.0   2.1e-51   5.4e-48      35     252 ..     161     388 ..     130     405 .. 0.87

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 2.1e-51
                             T2SSE  35 elreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvag..ealviRkksakeltlddlg 109
                                       +l++    e+ +l  ++ ++a+ a+++is   p++da+lp +g rl++     v +   +++iRk ++  +t+ dl+
  gi|488599803|ref|YP_007906274.1| 161 HLKTNIVFEEYELDSFVIKLAQKAGKHISVADPILDAALP-DGSRLQATYGREVTAsgSTFTIRKFQEIPFTVLDLI 236
                                       56666666777788888899********************.******9987655544699***************** PP

                             T2SSE 110 aeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak.... 182
                                       + ++ ++++a+     v+++++i+++GgT sGKtt+l+a+  +i+ +  +iv +ED++E+ l ++n ++ +++    
  gi|488599803|ref|YP_007906274.1| 237 KYNTINPQMAAYYWLMVENKMNIVFAGGTASGKTTMLNAICLFIPFN-VKIVSIEDTREVSLPHPNWIKSVTRegsg 312
                                       **********************************************9.*********************99999*** PP

                             T2SSE 183 .......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeqlgaevea 252
                                               ++v++ dllraaLR+rP  i+vGEiR+ke++ + +A+ TGH +  +T+Ha+s+ ++++rLe    ++++
  gi|488599803|ref|YP_007906274.1| 313 eivggrrIGEVDMYDLLRAALRQRPEYIIVGEIRGKEAVVAFQAMATGHVV-YTTMHADSVSSVIHRLESEPINIPR 388
                                       *****9999******************************************.****************975544554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.026        67      39     113 ..       7     107 ..       5     172 .. 0.56
   2 !   14.6   0.0   1.3e-05     0.034      22      41 ..     259     278 ..     222     286 .. 0.84
   3 ?   -1.2   0.1      0.95   2.4e+03      69     167 ..     457     473 ..     396     515 .. 0.40

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.026
                            AAA_23  39 iklaLygetprlsrks.......grgfeksdveiesegkvkayveltfenkdgry...................... 86 
                                       ik aL g++++   k+       g     + ve  + +k+ + ve+ f +++++y                      
  gi|488599803|ref|YP_007906274.1|   7 IKDALLGKKTKPMVKRgfqidveG-----RLVEAYDIEKGFSKVEILFDDENDEYfykviepelsdrdlyilefikd 78 
                                       566666655332222224333331.....333333333333346666666666665444444444334444444444 PP

                            AAA_23  87 ..trsiererelskkkgkttkkaklelle 113
                                          ++i+ ++e++++k +t  +   ++++
  gi|488599803|ref|YP_007906274.1|  79 tmLKTIHVDIEKAENKVETLWEIFQKIIT 107
                                       34444444444444444444333333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-05
                            AAA_23  22 tlItGpNGaGKTTildAikl 41 
                                        ++ G + +GKTT l+Ai+l
  gi|488599803|ref|YP_007906274.1| 259 IVFAGGTASGKTTMLNAICL 278
                                       4789***************8 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.95
                            AAA_23  69 gkvkay.veltfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfe 144
                                       +kvk++ ve  fe                                                                
  gi|488599803|ref|YP_007906274.1| 457 AKVKGVsVEEIFEE--------------------------------------------------------------- 470
                                       22222222222222............................................................... PP

                            AAA_23 145 efelkdkkerleelekeleeled 167
                                                            e+
  gi|488599803|ref|YP_007906274.1| 471 --------------------MEN 473
                                       ....................222 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     4e-05       0.1      85     146 ..     232     289 ..     212     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4e-05
                         Parvo_NS1  85 iykllslngynpvevgqvllawlskqlgkrntvwfyGpantGktnlaeaIakavp.lygcvnw 146
                                       +++l++ n  np+ ++   + wl+ +  k+n v + G+a+ Gkt + +aI+  +p ++++v++
  gi|488599803|ref|YP_007906274.1| 232 VLDLIKYNTINPQMAA---YYWLMVE-NKMNIVFAGGTAS-GKTTMLNAICLFIPfNVKIVSI 289
                                       67899999********...9999999.9***998888875.**********998834666655 PP

>> DUF1858  Domain of unknown function (DUF1858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016       0.4       7      58 ..     416     467 ..     412     468 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                       HHHHHHH-GGGHHHHHHT..TGGGGGSCCHHTTHHHHSBHHHHHHHHT--HHHH CS
                           DUF1858   7 IgelleeyPelaevLvel..GfhclgcpsllktvakvetleqaakvhgidldeL 58 
                                       I+e++  +P +++vLv+   ++++  +       ++   le +akv+g++++e+
  gi|488599803|ref|YP_007906274.1| 416 IAEIIGIDPATKDVLVNTvfKYDESINDF--IFSGRSYLLENIAKVKGVSVEEI 467
                                       99****************77777777775..56699999***********9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.28      22      43 ..     256     277 ..     244     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                            AAA_29  22 kgatlltGpsGsGKSTllDAiq 43 
                                       k +++++G + sGK+T+l Ai 
  gi|488599803|ref|YP_007906274.1| 256 KMNIVFAGGTASGKTTMLNAIC 277
                                       33799*************9985 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00016      0.42      38      59 ..     255     276 ..     238     282 .. 0.84
   2 ?   -2.7   0.0       1.1   2.9e+03     109     124 ..     464     479 ..     459     505 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                                       S-.SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  38 mashllvaGatgsGKStalntL 59 
                                       +  +++ aG+t sGK+t+ln++
  gi|488599803|ref|YP_007906274.1| 255 NKMNIVFAGGTASGKTTMLNAI 276
                                       4469****************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHH CS
                      FtsK_SpoIIIE 109 leeLvkemeeryalfr 124
                                       +ee+ +eme+r+++++
  gi|488599803|ref|YP_007906274.1| 464 VEEIFEEMENRARVLQ 479
                                       5678889999986654 PP

>> DUF1500  Protein of unknown function (DUF1500)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.87   2.2e+03      18      36 ..     117     135 ..     106     139 .. 0.65
   2 ?   -2.8   0.0       2.8   7.1e+03      22      53 ..     254     284 ..     238     294 .. 0.63
   3 ?   -1.1   0.0      0.81   2.1e+03       6      18 ..     322     334 ..     320     357 .. 0.82
   4 ?    8.5   0.1    0.0008       2.1      25      74 ..     443     485 ..     423     506 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.87
                           DUF1500  18 lrhyynkrfivygrsnail 36 
                                       + +y  + fi yg+   ++
  gi|488599803|ref|YP_007906274.1| 117 IFYYIRRDFIEYGKITVLM 135
                                       33566777999*9977665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.8
                           DUF1500  22 ynkrfivygrsnailhniyrlftrcavipfdd 53 
                                        nk  iv+    a  +    l + c  ipf+ 
  gi|488599803|ref|YP_007906274.1| 254 ENKMNIVFAGGTASGK-TTMLNAICLFIPFNV 284
                                       4666666665555433.345667788888864 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.81
                           DUF1500   6 dvdiydavrafll 18 
                                       +vd+yd +ra l 
  gi|488599803|ref|YP_007906274.1| 322 EVDMYDLLRAALR 334
                                       69*******9875 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0008
                           DUF1500  25 rfivygrsnailhniyrlftrcavipfddivrtmpnesrvkqwvmdtlng 74 
                                        fi  grs  +l ni +    +  + +++i   m n +rv qw+m    g
  gi|488599803|ref|YP_007906274.1| 443 DFIFSGRSY-LLENIAK----VKGVSVEEIFEEMENRARVLQWMMHK--G 485
                                       467777764.5677654....4567899****************973..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 3349.57
//
Query:       gi|488599804|ref|YP_007906275.1|  [L=168]
Description: hypothetical protein Asulf_00249 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00055   19.7   6.1    0.00097   19.0   6.1    1.4  1  DrrA_P4M         DrrA phosphatidylinositol 4-phosphate bindin
    0.00068   19.3  14.1    0.00094   18.8  14.1    1.3  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
    0.00071   19.0   2.5    0.00093   18.6   2.5    1.2  1  DUF3450          Protein of unknown function (DUF3450)
     0.0016   18.5   9.6     0.0034   17.4   9.6    1.6  1  BRE1             BRE1 E3 ubiquitin ligase
  ------ inclusion threshold ------
      0.012   14.5   8.0      0.014   14.3   8.0    1.1  1  VPS38            Vacuolar protein sorting 38
      0.035   14.6   1.6      0.058   13.9   1.6    1.3  1  DUF3698          Protein of unknown function (DUF3698)
      0.044   13.8   5.4      0.066   13.2   5.4    1.4  1  Dzip-like_N      Iguana/Dzip1-like DAZ-interacting protein N-
      0.072   13.5   9.0       0.14   12.6   9.0    1.5  1  CENP-H           Centromere protein H (CENP-H)
      0.076   12.3   2.2        0.1   11.8   2.2    1.3  1  TMPIT            TMPIT-like protein
      0.089   11.6   0.7        0.1   11.4   0.7    1.1  1  MreB_Mbl         MreB/Mbl protein
       0.18   10.9  11.9       0.21   10.6  11.9    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.18   11.9  16.0       0.22   11.6  16.0    1.2  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.22   10.3   4.0       0.24   10.1   4.0    1.1  1  O-antigen_lig    O-antigen ligase like membrane protein
       0.23   10.2   9.9       0.37    9.5   8.9    1.5  2  HAUS5            HAUS augmin-like complex subunit 5
       0.24   10.0   8.1        0.3    9.7   8.1    1.1  1  AAA_13           AAA domain
       0.25   11.5   6.0       0.39   10.8   6.0    1.3  1  DUF4337          Domain of unknown function (DUF4337)
        0.3   10.4   2.8       0.39   10.0   2.8    1.1  1  DUF4407          Domain of unknown function (DUF4407)
       0.92   10.2  15.0      0.044   14.4   9.0    1.9  2  YabA             Initiation control protein YabA
          1    8.5   6.8        1.5    8.0   6.8    1.2  1  Tho2             Transcription factor/nuclear export subunit 
        1.1    8.8  15.4        1.9    8.1  15.3    1.5  1  GrpE             GrpE
        1.3    9.1   4.9        2.1    8.4   4.9    1.3  1  DUF1664          Protein of unknown function (DUF1664)
        1.7    8.5  13.7         14    5.5  13.7    2.6  1  DivIC            Septum formation initiator
        2.9    8.4   6.7        5.2    7.6   6.3    1.8  1  DUF4140          N-terminal domain of unknown function (DUF41
          4    6.7   8.5        4.5    6.5   8.5    1.2  1  FAM76            FAM76 protein
          4    8.0  25.7        1.4    9.5  21.2    2.4  2  APG6_N           Apg6 coiled-coil region
        4.6    7.7  11.2          7    7.1  11.2    1.5  1  DUF3740          Sulfatase protein
        7.3    6.1   8.0         17    4.9   7.9    1.7  1  Fzo_mitofusin    fzo-like conserved region


Domain annotation for each model (and alignments):
>> DrrA_P4M  DrrA phosphatidylinositol 4-phosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   6.1   1.5e-06   0.00097      19      80 ..      52     115 ..      42     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                                       -GGGTT--HHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHTSHHHHHHH..S-SSHHHHHHT- CS
                          DrrA_P4M  19 kekyqklkGDaLKtkILkdfKdkleeistkeeLeklvkefkkseeykilk..tgQglftrlfgl 80 
                                       k++  k k D+LK++IL+  ++kle  ++ e L++ +k+++k +e ki+k  ++Q+++ rl+gl
  gi|488599804|ref|YP_007906275.1|  52 KKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKvkKKQRFLKRLLGL 115
                                       555566688***************************************8532778888888776 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 !   18.8  14.1   1.4e-06   0.00094      84     149 ..      40     105 ..       1     113 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                     PI3K_P85_iSH2  84 eklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrkdkylewLktk 149
                                        +l+  +  l+++ +e+++++++L++++     e++eleRei +lk e+ +L+k+k+  + + k+k
  gi|488599804|ref|YP_007906275.1|  40 LTLSRVIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKK 105
                                       46677777899999*********************************************9999987 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.5   1.4e-06   0.00093      21     104 ..      49     134 ..      37     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                           DUF3450  21 alkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasle..eqieeieeie 95 
                                       +++++e++ +++ q  k+i ++++ek el++e+++lkee+++l++++e     v++ ++ +++l    +++eie  e
  gi|488599804|ref|YP_007906275.1|  49 LEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQRFLKRLLglGRKNEIEIPE 125
                                       567899999*************************************9999999999998888885225788888888 PP

                           DUF3450  96 relvpllek 104
                                       +el  +l +
  gi|488599804|ref|YP_007906275.1| 126 EELRLVLAE 134
                                       888777765 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   9.6   5.2e-06    0.0034       8      70 ..      49     111 ..      42     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.2e-06
                              BRE1   8 lekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsK 70 
                                       le+ +ee +e+ ++++ke+ + e +kl le e+++ ++++++++++k+a   ++kk ++ l++
  gi|488599804|ref|YP_007906275.1|  49 LEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQRFLKR 111
                                       8999**********************************************9999998876665 PP

>> VPS38  Vacuolar protein sorting 38
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   8.0   2.1e-05     0.014     172     246 ..      33     107 ..       6     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             VPS38 172 sfsFnslLKLnklleYtsqveeElqeisekveelikseekkelwslkelqkaieqlkksiekkklklkrLessle 246
                                       +++  ++L L++++ Y +  +eE++e s ++ ++i + e+++l   +e+++ +e++k+  ++k++k+ +++++++
  gi|488599804|ref|YP_007906275.1|  33 MLKIEDALTLSRVIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQR 107
                                       5667789************************************9999*****************99999998766 PP

>> DUF3698  Protein of unknown function (DUF3698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.6   8.8e-05     0.058      10      74 ..      43     108 ..      35     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.8e-05
                           DUF3698  10 pdivhfleneead.alktpeilfevGdYktenycleqGleelkvaikdfkqklkekLksieeedlf 74 
                                       + ++++le ++++ + k  +  +e+ dY+ e+  le+ +e lk  ik+ +++++ k+ + ++++ f
  gi|488599804|ref|YP_007906275.1|  43 SRVIGYLEAKKEEiKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQRF 108
                                       556777765555414466777889**************************9998898888888777 PP

>> Dzip-like_N  Iguana/Dzip1-like DAZ-interacting protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.4    0.0001     0.066      67     117 ..      45      95 ..       4      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                       Dzip-like_N  67 vieYLlhsqelLakslekleerlqeaqaeaeelekelakqeeelkklkkes 117
                                       vi YL   +e +++++ +l++++ + ++e  ele+e+++++ee+k+l+ke 
  gi|488599804|ref|YP_007906275.1|  45 VIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEK 95 
                                       699*********************************************995 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   9.0   0.00021      0.14       4      74 ..      35     105 ..      32     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                            CENP-H   4 lieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleae 74 
                                       +ie   +ls  +  l+++ +e++e+ ++++ke+l+ +r++ el +e+++l++e ++ ++++++++ k++++
  gi|488599804|ref|YP_007906275.1|  35 KIEDALTLSRVIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKK 105
                                       6788889999999999999****************************999999999998888888888876 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.2   0.00015       0.1       9      73 ..      44     104 ..      36     141 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                             TMPIT   9 kefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelke 73 
                                       + +  le++++e+k+k+++l+k + +  +e  + ++++++lk+++k+l+k+++     ++ ++k+
  gi|488599804|ref|YP_007906275.1|  44 RVIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKE----AKIVKVKK 104
                                       55556777788888888888888888888888888888888888888877633....22222222 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7   0.00015       0.1     171     256 ..      54     134 ..      29     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                       EEES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHHEEEEEEEET....TTTCEE..EEEEEHHH CS
                          MreB_Mbl 171 ksvrvaGdeldeaiikyirkkynlliGertaekikieigsavkeeeeekmeikGrdl....vtglpk..evevssee 241
                                       + ++   d+l ++i++y r+k +l   er+ e++k ei ++ ke+e++ +++k ++     + gl +  e+e+ +ee
  gi|488599804|ref|YP_007906275.1|  54 EEIKEKSDQLKKEILDYEREKLEL---EREIERLKEEIKNLRKEKEAKIVKVKKKQRflkrLLGLGRknEIEIPEEE 127
                                       6688889**************999...79*******************99988765311112344441134444555 PP

                                       HHHHHHHHHHHHHHH CS
                          MreB_Mbl 242 vrealkepvsaivea 256
                                       +r +l+        +
  gi|488599804|ref|YP_007906275.1| 128 LRLVLA--------E 134
                                       554444........3 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  11.9   0.00032      0.21      36     117 ..      27     108 ..       4     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                             Atg14  36 sekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk 112
                                        e + l  kie+al+  +  + le+k +  k+k ++lk++i d ++++ el+  +++lk+ei++ +k+ +++  k+k
  gi|488599804|ref|YP_007906275.1|  27 VEDANLMLKIEDALTLSRVIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVK 103
                                       56677788999999999988888888888888888888888888888888888888888888888888887777777 PP

                             Atg14 113 kRrsd 117
                                       k+++ 
  gi|488599804|ref|YP_007906275.1| 104 KKQRF 108
                                       65544 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  16.0   0.00033      0.22      66     152 ..      16     107 ..       1     130 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                           UPF0242  66 ekskleekeaklteld.....eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelk 137
                                        ++++++++ ++ + +     e+  t    +  l++++ee ke+ d+ ++e+  +++e+ +L+ + e  +e++++l+
  gi|488599804|ref|YP_007906275.1|  16 PEEEIPSEKPLVEDANlmlkiEDALTLSRVIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLR 92 
                                       23334444444444447777777777777999999****************************************** PP

                           UPF0242 138 leleeqLaekqellq 152
                                       +e e+++ + +++  
  gi|488599804|ref|YP_007906275.1|  93 KEKEAKIVKVKKKQR 107
                                       ****99977666554 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 ?   10.1   4.0   0.00036      0.24     295     371 ..      23     125 ..       1     136 [. 0.58

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00036
                     O-antigen_lig 295 e...........................ikenykseglk..eavleqyeyandkqfsqellkeeveslllsnRdlql 342
                                       e                            k++  +e  k  +  +e+ +y+ +k + +    e++++++ + R+ ++
  gi|488599804|ref|YP_007906275.1|  23 EkplvedanlmlkiedaltlsrvigyleAKKEEIKE--KsdQLKKEILDYEREKLELER-EIERLKEEIKNLRKEKE 96 
                                       355555555555555555555544442222222222..132444444555544444333.4445555667999**** PP

                     O-antigen_lig 343 kvlkqvyknadisekLfGigYsrrtnikn 371
                                       +   +v k+++++++L+G+g +++++i +
  gi|488599804|ref|YP_007906275.1|  97 AKIVKVKKKQRFLKRLLGLGRKNEIEIPE 125
                                       ********************999776655 PP

>> HAUS5  HAUS augmin-like complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.36   2.4e+02     335     395 ..       2      66 ..       1      71 [. 0.73
   2 ?    9.5   8.9   0.00056      0.37      78     121 ..      70     113 ..      48     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.36
                             HAUS5 335 qkLlkrLqglkdeveleslgagetsqndsllrq....vleleleaaglkaslntLrsevqrLekl 395
                                       qk +++L+   +e+  e +++++ + +d++l      +l+l + +  l+a+ + + ++  +L+k 
  gi|488599804|ref|YP_007906275.1|   2 QKSKQKLELEDEEMPEEEIPSEKPLVEDANLMLkiedALTLSRVIGYLEAKKEEIKEKSDQLKKE 66 
                                       55677777778888888887777776666655447778888888888888888888888888876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00056
                             HAUS5  78 aaaereelekeverLraeirrldkeleareeelsreeaevkral 121
                                         +e+ ele+e+erL++ei++l+ke ea+  +++++ + +kr l
  gi|488599804|ref|YP_007906275.1|  70 YEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQRFLKRLL 113
                                       346788999********************999999998888876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   8.1   0.00045       0.3     406     474 ..      48     117 ..      30     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00045
                            AAA_13 406 eleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf.Glge 474
                                        le++ +e k+k ++l+k+i + e+e+ e e+e++ l+eeik+L+k+ + +   +++  + Lk+  Glg+
  gi|488599804|ref|YP_007906275.1|  48 YLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQRFLKRLlGLGR 117
                                       345555578899999********************************99999999999999999988876 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.0   0.00058      0.39      58     115 ..      38      96 ..      30     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00058
                           DUF4337  58 eqlelllkak.aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneasd 115
                                       + l+l +  +  e++++++++k +++kk+i  y++ek e++++ ++l++e +++ ++++
  gi|488599804|ref|YP_007906275.1|  38 DALTLSRVIGyLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKE 96 
                                       5566666666778889999*****************************99999888765 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.8   0.00059      0.39     115     166 ..      51     105 ..      47     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                           DUF4407 115 eqqeeakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqke 166
                                        ++ee+ke ++ql+++   ++ e  ele++i++l++ei++++++ +a+  +++k+
  gi|488599804|ref|YP_007906275.1|  51 AKKEEIKEKSDQLKKEildYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKK 105
                                       5667777777777777777777777777777777777777777777776666654 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   9.0   6.6e-05     0.044       9      77 ..      45     113 ..      37     118 .. 0.91
   2 ?   -1.5   0.0       5.9   3.9e+03      46      53 ..     126     143 ..     115     166 .. 0.39

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlY 77 
                                        +  le + ee++e+ ++lk+e+ +   e  eLe e e+l+e++++ +k++++k  ++++ ++ L+rl 
  gi|488599804|ref|YP_007906275.1|  45 VIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQRFLKRLL 113
                                       567799999*******************************************************99985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.9
                                       HHHHHHH..........X CS
                              YabA  46 eklrerl..........e 53 
                                       e+lr  l           
  gi|488599804|ref|YP_007906275.1| 126 EELRLVLaevdrllgflP 143
                                       333333322222222222 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   6.8    0.0022       1.5      31      89 ..      53     111 ..      45     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0022
                              Tho2  31 ieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLke 89 
                                        e++k+++++l+k+  d ++++ + ++e++rlke i++L++Ek+++i +v+k ++ Lk+
  gi|488599804|ref|YP_007906275.1|  53 KEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQRFLKR 111
                                       55677777777666667678888899********************9999998888876 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  15.3    0.0029       1.9       5      69 ..      51     113 ..      11     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                                       ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE   5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLL 69 
                                        ++ee +++ ++l++e+ + e+e  el+ +++rl++e++nlrk  eke++ +k +++++f+k LL
  gi|488599804|ref|YP_007906275.1|  51 AKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRK--EKEAKIVKVKKKQRFLKRLL 113
                                       5677778899999999999999999***************988..56777777777899999998 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.9    0.0031       2.1      64     124 .]      42     106 ..      33     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0031
                           DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl....esklerieekQ 124
                                       Ls+ i  +++k +e ke s ++k+e+ + +++  e+++++e +ke +++l    e+k+ ++++kQ
  gi|488599804|ref|YP_007906275.1|  42 LSRVIGYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLrkekEAKIVKVKKKQ 106
                                       77788899999999999999999999999999999999999999999988444455677777766 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  13.7     0.021        14      20      56 ..      61      97 ..      38     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.021
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                             DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedy 56
                                       qlk+ei + ++e  +l  e+e+L++e+k+L++++++
  gi|488599804|ref|YP_007906275.1| 61 DQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEA 97
                                      5899***************************998886 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.3    0.0079       5.2      58      97 ..      51      90 ..       8      97 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0079
                           DUF4140 58 pnreaeeeelkalraeleeledelaaledelaaaearlaf 97
                                      + +e+ +e+ ++l++e+   e+e+ +le+e+++++++++ 
  gi|488599804|ref|YP_007906275.1| 51 AKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKN 90
                                      3333333347778888888888888888888887777764 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.5    0.0067       4.5     222     274 ..      54     106 ..       2     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0067
                             FAM76 222 tqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekea 274
                                       +++ke+  +lkk++   + e le +++i  lk e  + +ke + k+ +++k+ 
  gi|488599804|ref|YP_007906275.1|  54 EEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQ 106
                                       46788888888888888888888888888888888888888888888777764 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  21.2    0.0021       1.4      50     113 ..      47     110 ..       1     114 [. 0.82
   2 ?   -0.3   0.1       2.1   1.4e+03      18      33 ..     128     143 ..     118     166 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0021
                            APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlell 113
                                         le + e+++++ ++l +e+ + e+e+ ele+e++ l+ee ++l +e+e+++ + +++q+ l+
  gi|488599804|ref|YP_007906275.1|  47 GYLEAKKEEIKEKSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEAKIVKVKKKQRFLK 110
                                       457788999******************************************9999999887665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.1
                            APG6_N  18 leqaekerdaYeeflk 33 
                                       l+ + +e d ++ fl 
  gi|488599804|ref|YP_007906275.1| 128 LRLVLAEVDRLLGFLP 143
                                       4444444444444443 PP

>> DUF3740  Sulfatase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  11.2      0.01         7      96     134 ..      59      97 ..       2     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.01
                           DUF3740  96 CsdviyesekaWkdsklqiDkeIelLkdKiknLkevkgh 134
                                       +sd+++++   + ++kl+++ eIe Lk+ iknL+  k+ 
  gi|488599804|ref|YP_007906275.1|  59 KSDQLKKEILDYEREKLELEREIERLKEEIKNLRKEKEA 97 
                                       78999999999**********************988864 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   7.9     0.026        17      98     150 ..      55     111 ..      39     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                     Fzo_mitofusin  98 elsstfarlcqqv...detekeleeeikelekeiekleevqk.kakllrnkaslles 150
                                       e+++  ++l++++   ++ + ele+ei++l++ei++l + ++ k  ++++k  +l++
  gi|488599804|ref|YP_007906275.1|  55 EIKEKSDQLKKEIldyEREKLELEREIERLKEEIKNLRKEKEaKIVKVKKKQRFLKR 111
                                       56666666766652225566789**************87654145556677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2909  (0.162251); expected 358.6 (0.02)
Passed bias filter:                     1158  (0.0645881); expected 358.6 (0.02)
Passed Vit filter:                       217  (0.0121033); 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):              27  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 1080.90
//
Query:       gi|488599805|ref|YP_007906276.1|  [L=448]
Description: hypothetical protein Asulf_00250 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3052.63
//
Query:       gi|488599806|ref|YP_007906277.1|  [L=453]
Description: MiaB-like tRNA modifying enzyme, archaeal-type [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-24   87.0   0.1    2.8e-23   83.1   0.1    2.3  2  Radical_SAM  Radical SAM superfamily
    6.7e-17   61.4   0.0    1.4e-16   60.3   0.0    1.5  1  UPF0004      Uncharacterized protein family UPF0004
    1.2e-09   38.0   0.2      3e-09   36.8   0.2    1.7  1  TRAM         TRAM domain
  ------ inclusion threshold ------
      0.068   13.6   4.2       0.25   11.7   4.2    1.9  1  Rhodanese_C  Rhodanase C-terminal


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 ?    1.6   0.0     0.069   3.1e+02     123     144 ..      76      97 ..      17     139 .. 0.75
   2 !   83.1   0.1   6.2e-27   2.8e-23       1     167 []     167     339 ..     167     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.069
                                       CTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 123 rghtfeevlealeklreagikr 144
                                         +t  ++l+ ++ l+++g ++
  gi|488599806|ref|YP_007906277.1|  76 VEYTERKILRRVQELKSSGKRV 97 
                                       4555555555555555555543 PP

  == domain 2  score: 83.1 bits;  conditional E-value: 6.2e-27
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlak 72 
                                       v++++gC ++Cs+Ca+++    +gr +s  +e+i++ev+ + +e g ke+ l++++ ++y      +++ell ++++
  gi|488599806|ref|YP_007906277.1| 167 VSISEGCLGKCSYCATRF---ARGRLKSFKPENIVDEVRLA-VESGFKEIQLTSQDTSAYgrdmnTNLAELLMMISE 239
                                       5799**************...8*******************.9*************99999999999********** PP

                                       TCCCTEEEEEEECSSCHG....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  73 lavpgiritvetngtlpd....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                       ++  ++r++v    + ++    e+ +  ++    +  +++++++++d  vl++mnr +t+ee+ e + klr+  +++
  gi|488599806|ref|YP_007906277.1| 240 ID-GEFRVRVGMMNPNHMldilEDLIYSFKSEKiFKFFHIPVQSGSDA-VLRRMNREYTVEEFEEIIVKLRKE-FED 313
                                       *7.555555555555555669999999999988***************.************************.*** PP

                                       ...EEEEEEEBTTTSHHHHHHHHHHH CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 ...vvdrivglpGendeeleellell 167
                                          ++d+ivg p e  ee+ e ++ll
  gi|488599806|ref|YP_007906277.1| 314 ivlSTDIIVGYPQEGLEEFMESYRLL 339
                                       *********************99986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   3.1e-20   1.4e-16       1      82 [.      31     107 ..      31     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.1e-20
                                       XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEH CS
                           UPF0004   1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGC 77 
                                       kv+iet+GC+ N++ds+++ +l++ke ++l ++ ++Advv++n+C+v+e +e+k++++++elk+     k+v+++GC
  gi|488599806|ref|YP_007906277.1|  31 KVYIETYGCTSNQADSDIMRGLIAKE-FTL-SSIDDADVVVINSCGVVEYTERKILRRVQELKSSG---KRVILAGC 102
                                       89*******************99875.666.5568********************99999999877...89****** PP

                                       HHHS- CS
                           UPF0004  78 maqre 82 
                                       ++   
  gi|488599806|ref|YP_007906277.1| 103 LPRIA 107
                                       98765 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.2   6.6e-13     3e-09       3      61 ..     393     448 ..     391     449 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.6e-13
                                       XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                                        vG+ ++Vlv++++ +  ++++rtd +++v+v++   +IG f  V +++++++yL+G+ 
  gi|488599806|ref|YP_007906277.1| 393 HVGKRYTVLVTKKG-KGNTFLARTDSYRPVIVED--VEIGNFYSVFVEDCTFNYLKGKK 448
                                       69************.*******************..458******************85 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.2   5.6e-05      0.25       1      48 [.     135     180 ..     135     193 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                       Rhodanese_C   1 rGklfVFDkRlalksevvgkCieCgkpvdelrkrnCanedCnelvlvC 48 
                                       +Gk+ VFD+R ++ ++   +C+ C    + +  +   +e C  +  +C
  gi|488599806|ref|YP_007906277.1| 135 EGKNVVFDERRKV-DKSEFRCVKCRLRENAIAIVSI-SEGCLGKCSYC 180
                                       6**********99.3455556666555443322222.23343333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2996.93
//
Query:       gi|488599807|ref|YP_007906278.1|  [L=345]
Description: hydrogenase expression/formation protein HypE [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   93.4   1.0    3.1e-26   92.4   1.0    1.5  1  AIRS_C         AIR synthase related protein, C-terminal domai
    2.6e-14   53.7   0.0    6.8e-14   52.3   0.0    1.8  2  AIRS           AIR synthase related protein, N-terminal domai
  ------ inclusion threshold ------
      0.025   15.1   0.0       0.19   12.4   0.0    2.2  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
        0.1   12.9   0.0       0.32   11.3   0.0    1.8  1  PAS_3          PAS fold


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 !   92.4   1.0     7e-30   3.1e-26       2     150 ..     175     319 ..     174     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 7e-30
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHH CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalae 78 
                                       +Gdv+i  gs+  ++++++ +r++le++        ++dv+ +   +   + +    g+++a++D T+GG++ +l+e
  gi|488599807|ref|YP_007906278.1| 175 DGDVIIINGSIAEHASAIMVIREGLEFQMDV-----KSDVYPV---WMFLKDAMNV-GGISAMKDPTRGGIAASLNE 242
                                       6**************************9854.....7788877...5555555555.89****************** PP

                                       HHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                            AIRS_C  79 mapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakee 150
                                       +a++sgvg+ i++d++pi+d ++     ++l+++ ++n+G++++av pe a++vl++l++ g ++aa+IG++t + +
  gi|488599807|ref|YP_007906278.1| 243 IAEKSGVGILIEEDAIPIRDDVKsfcdvLGLDPFSMANEGKVVMAVHPEMAEEVLKALRKSGQKDAAIIGHATSEFS 319
                                       *********************9999999********************************************98765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   1.5e-17   6.8e-14       6      93 ..      49     145 ..      12     146 .. 0.90
   2 ?   -3.4   0.0       3.5   1.6e+04      56      71 ..     234     249 ..     214     252 .. 0.59

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.5e-17
                                       EEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-E CS
                              AIRS   6 vvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvp 72 
                                       ++ttd    +++v+p  f    iG +a++++ +Dla+ GA+P ++++sl l+      +l+ +++++++ a+e+gv+
  gi|488599807|ref|YP_007906278.1|  49 LLTTD----SYVVDPPVFpggsIGSLAICGTSNDLAVKGAKPSFMSMSLVLQdgfeieKLRTILEDMERWAREIGVK 121
                                       68999....7777887778********************************************************** PP

                                       EEEEEEEEESS...EEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne...ptisvtavGl 93 
                                       +++Gdt++ ++   ++i+++ vG+
  gi|488599807|ref|YP_007906278.1| 122 IITGDTKVVDSgvgVIINTSGVGV 145
                                       *******99888999999999996 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHHTT- CS
                              AIRS  56 eevvrglaeaaeelgv 71 
                                        +++++l+e ae+ gv
  gi|488599807|ref|YP_007906278.1| 234 GGIAASLNEIAEKSGV 249
                                       3455666666666665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.35   1.6e+03      37      56 ..     109     128 ..      93     140 .. 0.78
   2 ?   12.4   0.0   4.1e-05      0.19      62      92 ..     281     311 ..     234     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                                       CCHHHHHHHHC-EEECECHH CS
                     F420_oxidored  37 ekaeelaeelgvkvtavdne 56 
                                       e +e +a+e+gvk++++d++
  gi|488599807|ref|YP_007906278.1| 109 EDMERWAREIGVKIITGDTK 128
                                       67899999*****9996654 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.1e-05
                                       -SEEEE-S-HHHHHHHHHHCGHHHHTTSEEE CS
                     F420_oxidored  62 advvvlavkpedveevlselakdalkgklvi 92 
                                          vv av+pe++eevl++l+k+ +k+  +i
  gi|488599807|ref|YP_007906278.1| 281 EGKVVMAVHPEMAEEVLKALRKSGQKDAAII 311
                                       445899**************99999998887 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     7e-05      0.32       7      48 ..     266     306 ..     264     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                             PAS_3   7 rveeilGyspeellgkveswldlvhpeDrervrealqealkk 48 
                                       +++++lG++p ++ +   ++ ++vhpe+ e+v +al ++ +k
  gi|488599807|ref|YP_007906278.1| 266 SFCDVLGLDPFSMANE-GKVVMAVHPEMAEEVLKALRKSGQK 306
                                       799***********99.9*****************9987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 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:                        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 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2176.78
//
Query:       gi|488599808|ref|YP_007906279.1|  [L=767]
Description: (NiFe) hydrogenase maturation protein HypF [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  126.1   0.0    2.3e-36  125.0   0.0    1.6  2  Sua5_yciO_yrdC   Telomere recombination
    4.3e-25   87.2  16.1    4.1e-13   48.9   3.4    2.7  3  zf-HYPF          HypF finger
    4.4e-25   88.3   0.0    4.4e-24   85.1   0.0    2.4  2  HypF_C           HypF Kae1-like domain
    9.7e-21   74.0   0.1    5.4e-20   71.6   0.0    2.2  2  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.044   14.0   0.1       0.43   10.8   0.0    2.5  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
      0.046   13.8   2.0        3.1    7.9   0.3    2.3  2  DZR              Double zinc ribbon
      0.049   13.7   9.2      0.081   13.1   0.7    2.8  2  Zn-ribbon_8      Zinc ribbon domain
      0.054   13.0   0.0        0.1   12.1   0.0    1.4  1  BcrAD_BadFG      BadF/BadG/BcrA/BcrD ATPase family
      0.063   13.7   2.8        5.9    7.3   0.1    2.5  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   12.5   1.4          3    7.9   0.3    2.7  3  HypA             Hydrogenase/urease nickel incorporation, met
       0.51   10.8   1.8        1.1    9.7   1.8    1.5  1  DUF4379          Probable Zinc-ribbon domain
          1    8.8   3.4        1.2    8.5   1.7    1.9  2  NMD3             NMD3 family
          1    9.3   2.6         22    5.0   0.1    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
        5.8    6.9   6.1         16    5.5   0.1    3.0  3  zinc_ribbon_4    zinc-ribbon domain


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 !  125.0   0.0   1.8e-39   2.3e-36       2     178 ..     205     372 ..     204     373 .. 0.93
   2 ?   -3.7   0.0       5.6   7.2e+03       6      24 ..     687     705 ..     686     708 .. 0.83

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 1.8e-39
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSC CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpi 78 
                                       ++++ + +a++++++Y++ac +t++++v +lr+  +r+ ++p+a++++++e+lk++a  + e++ l++  r    pi
  gi|488599808|ref|YP_007906279.1| 205 LIDSSHFIAVKGIGGYHIAC-ITDDDVVFELRKKLRRE-QQPFAIMARNMEKLKEIAVVNAEANELESYIR----PI 275
                                       5777889*************.89************999.******************98888888999999....** PP

                                       EEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-.EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS CS
                    Sua5_yciO_yrdC  79 tlllkrskeklpkevapglktvGvrlPdtplarlLlealgep.lvaTSanlsgepsitdaeeveeelgeivdlildg 154
                                       ++l+k+ +++   +vap+l+t+Gv+lP++p ++lL+e++++  +v+TSanl+gep+ +d   +e +    +d++l +
  gi|488599808|ref|YP_007906279.1| 276 VVLKKK-NRDAFYAVAPELDTIGVMLPYSPAHYLLFENMKADfIVMTSANLPGEPMFIDDGVFELD----LDYYLVH 347
                                       *****7.555999*************************98656****************9988666....69***** PP

                                       -.--SSS---EEEETTSSTSSECEX CS
                    Sua5_yciO_yrdC 155 g.eiavgvdstVvdltegkpkilRr 178
                                       + +i++++d++V+++++g+  i+R+
  gi|488599808|ref|YP_007906279.1| 348 NlRINNRIDDSVIKFVNGRRMIIRK 372
                                       ************************7 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.6
                                       TSEEEEE-SSSEEEEEETT CS
                    Sua5_yciO_yrdC   6 GgivaiptetvYgLacdat 24 
                                       G+i+a+  e+   +ac+  
  gi|488599808|ref|YP_007906279.1| 687 GEIIAYLAEGLAEIACRFA 705
                                       9999999999999999865 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.5   7.2e-16   9.2e-13       1      33 [.     102     134 ..     102     135 .. 0.97
   2 !   48.9   3.4   3.2e-16   4.1e-13       1      32 [.     152     183 ..     152     185 .. 0.95
   3 ?   -3.1   0.4       5.5   7.1e+03       4      15 ..     671     682 ..     671     682 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 7.2e-16
                                       --HHHHHHHC-TTSTTTT-TT---TTTS--EEE CS
                           zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsl 33 
                                       +C +Cl+E++d +dRR+ + fisCt+CG r+s+
  gi|488599808|ref|YP_007906279.1| 102 ICGKCLEELFDESDRRYLYSFISCTDCGARFSV 134
                                       7******************************96 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 3.2e-16
                                       --HHHHHHHC-TTSTTTT-TT---TTTS--EE CS
                           zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrls 32 
                                       lCe+C++Ey++ +dRR++aq i+C++CGP + 
  gi|488599808|ref|YP_007906279.1| 152 LCEECRNEYENVMDRRYYAQSIACPKCGPDYL 183
                                       7****************************985 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.5
                                       HHHHHHC-TTST CS
                           zf-HYPF   4 dClrEykdpldR 15 
                                       +Cl+ y d +dR
  gi|488599808|ref|YP_007906279.1| 671 ECLERYADGEDR 682
                                       7*******9998 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   3.5e-27   4.4e-24       6     102 .]     389     487 ..     384     487 .. 0.93
   2 ?   -0.0   0.0       1.1   1.4e+03      27      51 ..     553     577 ..     550     591 .. 0.82

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 3.5e-27
                            HypF_C   6 vLAlGaelkntfalakggqallsqhlGdlenletle.ayeealeeleklleik.pevivcDlhpdylstklaeelae 80 
                                        +AlGael n+++++k++ ++ sq++G+ ++++t++ +++++l+ ++++l+++  +++ cDlhp y+++++ae+l+e
  gi|488599808|ref|YP_007906279.1| 389 GVALGAELYNSICFLKDSMIIQSQYIGNTADFRTFNeFFKKSLNFFQNFLSMDsVDFVFCDLHPLYNTSQFAEKLVE 465
                                       58*******************************986157999*********96489********************* PP

                            HypF_C  81 keklelievqHHhAHllavlae 102
                                       k +++li++qHH AH ++v+ e
  gi|488599808|ref|YP_007906279.1| 466 KINARLIRIQHHFAHGMSVMNE 487
                                       ********************87 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                            HypF_C  27 lsqhlGdlenletleayeealeele 51 
                                       +  +lGd + l+ +e+y ++ e++e
  gi|488599808|ref|YP_007906279.1| 553 VYDYLGDYDLLRGYEKYLRENENFE 577
                                       6689*************99888776 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   4.2e-23   5.4e-20       1      79 [.       2      78 ..       2      82 .. 0.92
   2 ?   -1.3   0.0       2.4   3.1e+03      12      28 ..     722     738 ..     714     742 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 4.2e-23
                   Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppk.arvdeveveeleeee 78
                                      ++l+v+G VQgvgFR+fv+rlAk++glkGyvrN+ +g+Veiv+  ++   e f+e++k ++p+ +r+dev ve++e e 
  gi|488599808|ref|YP_007906279.1|  2 YKLTVKGVVQGVGFRPFVYRLAKSMGLKGYVRNMGNGTVEIVIDRNP---ELFIERMKDEKPPiSRIDEVFVETVEFEA 77
                                      6899***************************************8877...78*******99999*******99988776 PP

                   Acylphosphatase 79 e 79
                                      e
  gi|488599808|ref|YP_007906279.1| 78 E 78
                                      6 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                   Acylphosphatase  12 vgFRkfvrrlAkelglk 28 
                                         F ++v+++A+e g+k
  gi|488599808|ref|YP_007906279.1| 722 TIFNRHVYKKAEEYGVK 738
                                       56999********9986 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 ?   10.8   0.0   0.00033      0.43      14      42 ..      99     129 ..      95     131 .. 0.88
   2 ?   -0.7   0.0       1.3   1.6e+03       2       6 ..     175     179 ..     162     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                    zinc_ribbon_13  14 evaatGsglskifdvqnkkfi..tvsCknCg 42 
                                       +va++G  l  +fd   ++++  ++sC++Cg
  gi|488599808|ref|YP_007906279.1|  99 DVAICGKCLEELFDESDRRYLysFISCTDCG 129
                                       5899***********999975338******8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                    zinc_ribbon_13   2 CpKCg 6  
                                       CpKCg
  gi|488599808|ref|YP_007906279.1| 175 CPKCG 179
                                       77777 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.021        27       9      38 ..      97     132 ..      94     138 .. 0.83
   2 ?    7.9   0.3    0.0025       3.1      14      35 ..     152     179 ..     141     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.021
                               DZR   9 ppdarfCseCgtklkavaa......edrCpsCgekv 38 
                                       ppd   C++C ++l  +++       + C  Cg+  
  gi|488599808|ref|YP_007906279.1|  97 PPDVAICGKCLEELFDESDrrylysFISCTDCGARF 132
                                       577789999999998777799999999999999865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                               DZR  14 fCseCgtklkavaa......edrCpsCg 35 
                                        C+eC+++ ++v +      +++Cp+Cg
  gi|488599808|ref|YP_007906279.1| 152 LCEECRNEYENVMDrryyaqSIACPKCG 179
                                       7*******988777899999*******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 ?    5.8   0.1     0.011        14       4      20 ..     120     137 ..     118     146 .. 0.72
   2 ?   13.1   0.7   6.3e-05     0.081       8      33 ..     153     179 ..     149     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                       Zn-ribbon_8   4 YeYr.CeeCghefevlqs 20 
                                       Y +  C++Cg +f v  +
  gi|488599808|ref|YP_007906279.1| 120 YSFIsCTDCGARFSVAIT 137
                                       55556********97655 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.3e-05
                       Zn-ribbon_8   8 CeeCghefevlqsis.dapltaCPeCg 33 
                                       CeeC +e+e ++     a  +aCP+Cg
  gi|488599808|ref|YP_007906279.1| 153 CEECRNEYENVMDRRyYAQSIACPKCG 179
                                       *********6666675777888****9 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.8e-05       0.1     185     253 ..     680     745 ..     669     753 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                                       HHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--G CS
                       BcrAD_BadFG 185 lsggekaedIlaglhraialrvialisrsggvtdevtltGGvakneaavkelrklvkenygevkininp 253
                                       + +g +a +I+a l++ +a+ +  +++r g     v+l GGva n  + + + k  +e   +v in+  
  gi|488599808|ref|YP_007906279.1| 680 EDRGVIAGEIIAYLAEGLAEIACRFAERKGLP---VVLSGGVAYNTIFNRHVYKKAEEYGVKVHINEYT 745
                                       44555666666666666666666666666666...**********777777766666666666666544 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0046       5.9      15      36 ..     110     130 ..      99     147 .. 0.64
   2 ?    6.0   0.4     0.012        15       6      55 ..     153     199 ..     148     204 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0046
                   Lar_restr_allev  15 lersqrvvaeigqcvyCadCga 36 
                                       l+ + ++++ ++ +++C+dCga
  gi|488599808|ref|YP_007906279.1| 110 LFDESDRRYLYS-FISCTDCGA 130
                                       444445555444.9******** PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCgastpwfkiaedeaeaekeai 55 
                                       C  C ++ + + + r +a+    ++C +Cg     f++ +++ ++  eai
  gi|488599808|ref|YP_007906279.1| 153 CEECRNEYENVMDRRYYAQ---SIACPKCGPDYLLFNHKKERLAEGYEAI 199
                                       6666666666666666554...9999999985555555555555555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.12   1.6e+02      70      95 ..     100     131 ..      64     139 .. 0.76
   2 ?    7.9   0.3    0.0023         3      73      95 ..     153     181 ..     145     194 .. 0.75
   3 ?   -3.3   0.0       7.2   9.2e+03      33      58 ..     595     620 ..     591     629 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                                       EEEETTTS-EEECHHH.HH.....S-TTTSSS CS
                              HypA  70 kvrCreCgkefeleek.al.....rCpkCgsa 95 
                                       ++ C +C +e   e++ ++     +C +Cg++
  gi|488599808|ref|YP_007906279.1| 100 VAICGKCLEELFDESDrRYlysfiSCTDCGAR 131
                                       67788998887755432234666799999875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0023
                                       ETTTS-EEECHH..HHH.....S-TTTSSS CS
                              HypA  73 CreCgkefelee..kal.....rCpkCgsa 95 
                                       C+eC++e+e     + +      CpkCg  
  gi|488599808|ref|YP_007906279.1| 153 CEECRNEYENVMdrR-YyaqsiACPKCGPD 181
                                       *********554231.234556*****965 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.2
                                       EETTCT--HHHHHHHHHHHHCC.TTT CS
                              HypA  33 vGelsgvepeaLefafellaegtvle 58 
                                        G++      +Le +f+   eg+++ 
  gi|488599808|ref|YP_007906279.1| 595 TGRMLDAASAMLEVCFRRTYEGEPAM 620
                                       57777788889999999888888744 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.8   0.00084       1.1      32      56 .]     153     178 ..     152     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00084
                           DUF4379  32 CakCgheWeasvsnrtkgssk.CpkC 56 
                                       C++C +e+e  ++ r   +s  CpkC
  gi|488599808|ref|YP_007906279.1| 153 CEECRNEYENVMDRRYYAQSIaCPKC 178
                                       ***************9555556**** PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.065        83      14      45 ..     101     132 ..      94     141 .. 0.87
   2 ?    8.5   1.7   0.00094       1.2       1      43 [.     125     180 ..     125     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.065
                              NMD3  14 glCedCllkevditegiekievevCkeCgryl 45 
                                       ++C +Cl + +d ++    +++  C +Cg+ +
  gi|488599808|ref|YP_007906279.1| 101 AICGKCLEELFDESDRRYLYSFISCTDCGARF 132
                                       49**********9999888**********865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00094
                              NMD3   1 CcrCGkei...........eeling......lCedCllkevditegiekievevCkeCgr 43 
                                       C +CG++            +    +      lCe+C  +  ++++    ++   C++Cg 
  gi|488599808|ref|YP_007906279.1| 125 CTDCGARFsvaitlpydreN----TtfsefpLCEECRNEYENVMDRRYYAQSIACPKCGP 180
                                       99999999777777764331....2567789**************9999*********94 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 ?    5.0   0.1     0.017        22      28      38 ..     122     132 ..     119     133 .. 0.89
   2 ?   -1.5   0.1       1.8   2.3e+03      31      37 ..     153     159 ..     148     161 .. 0.65
   3 ?    2.7   0.0     0.088   1.1e+02       2      14 ..     174     186 ..     173     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                           TFIIS_C  28 fykCtkCghrW 38 
                                       f+ Ct+Cg r+
  gi|488599808|ref|YP_007906279.1| 122 FISCTDCGARF 132
                                       99*******98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                           TFIIS_C  31 CtkCghr 37 
                                       C +C ++
  gi|488599808|ref|YP_007906279.1| 153 CEECRNE 159
                                       6666665 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.088
                           TFIIS_C   2 kCpkCgsreayff 14 
                                        CpkCg +   f 
  gi|488599808|ref|YP_007906279.1| 174 ACPKCGPDYLLFN 186
                                       7****98877775 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.013        16       3      15 ..     123     135 ..     122     138 .. 0.89
   2 ?    0.5   2.9      0.45   5.8e+02      24      32 ..     171     179 ..     152     181 .. 0.56
   3 ?    2.4   0.3      0.12   1.5e+02       3      11 ..     173     181 ..     172     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                     zinc_ribbon_4   3 itCpsCkakyeid 15 
                                       i+C  C+a+++++
  gi|488599808|ref|YP_007906279.1| 123 ISCTDCGARFSVA 135
                                       99********986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.45
                     zinc_ribbon_4  24 vkvrCskCg 32 
                                       +++ C+kCg
  gi|488599808|ref|YP_007906279.1| 171 QSIACPKCG 179
                                       467788886 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.12
                     zinc_ribbon_4   3 itCpsCkak 11 
                                       i Cp+C+  
  gi|488599808|ref|YP_007906279.1| 173 IACPKCGPD 181
                                       778888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.54
# Mc/sec: 4266.48
//
Query:       gi|488599809|ref|YP_007906280.1|  [L=109]
Description: hydrogenase nickel insertion protein HypA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   86.4   0.6    1.4e-24   86.2   0.6    1.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0042   17.1   0.7      0.008   16.2   0.7    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.047   13.5   0.2      0.065   13.1   0.2    1.3  1  MCM_OB          MCM OB domain
      0.078   12.7   1.5        1.4    8.6   0.1    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.13   12.6   1.1       0.19   12.1   1.1    1.3  1  C1_2            C1 domain
       0.15   12.4   0.0        0.3   11.4   0.0    1.4  1  DUF2949         Protein of unknown function (DUF2949)
        0.3   10.9   4.1        0.8    9.5   4.1    1.7  1  zinc_ribbon_2   zinc-ribbon domain
        1.3    8.5   4.7        4.9    6.7   4.7    1.9  1  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.6   6.4e-28   1.4e-24       4     112 .]       1     106 [.       1     106 [. 0.96

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 6.4e-28
                                       HHHHHHHHHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EE CS
                              HypA   4 lsiaesivevveeeakeaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCgkef 80 
                                       +s a++ive + + a++++a+kv++++v vGel  ++p++Lef+++++++gt+le+++L ie  +++++C +Cg+++
  gi|488599809|ref|YP_007906280.1|   1 MSFASAIVENALKLAEKHNAKKVNSITVIVGELLLINPDQLEFCYSVASKGTILENSKLIIEVSKAEIKCVNCGERY 77 
                                       68999**********99************************************************************ PP

                                       ECHHHHHS-TTTSSS-EEEEESSSEEEEEEEE CS
                              HypA  81 eleekalrCpkCgsadveivsGeellvksiev 112
                                       ++    + C+kCg+  v++ +G+++ +k+ie+
  gi|488599809|ref|YP_007906280.1|  78 DSP--IYLCEKCGG-FVSVNGGKDMILKKIEM 106
                                       977..458******.59*************96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.7   3.6e-06     0.008      12      49 .]      41      88 ..      34      88 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.6e-06
                               DZR 12 arfCseCgtk...lkavaa..........edrCpsCgekvdpearfCpeCG 49
                                       +fC+   +k   l+   +          e++C++Cge  d+    C +CG
  gi|488599809|ref|YP_007906280.1| 41 LEFCYSVASKgtiLE---NskliievskaEIKCVNCGERYDSPIYLCEKCG 88
                                      555555555533322...133555566679********************9 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.9e-05     0.065      14      60 ..      47      88 ..      37     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                      EEEEEEEEEE---EEEEEEEEEEETTT-.-EEES----S.B-..TTT- CS
                            MCM_OB 14 vkveGivtrasevkpklkkavfeckkcgktveveleePr.kCeekeCe 60
                                      v  +G++ + s++  +++ka ++c +cg+    ++ +P   C  ++C+
  gi|488599809|ref|YP_007906280.1| 47 VASKGTILENSKLIIEVSKAEIKCVNCGE----RYDSPIyLC--EKCG 88
                                      5679************************8....577887467..6676 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 ?    8.6   0.1   0.00064       1.4      15      26 ..      65      76 ..      59      77 .. 0.88
   2 ?    3.2   0.1     0.031        70       1      12 [.      82      93 ..      82     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00064
                                      SS----SSS--- CS
                    DNA_RNApol_7kD 15 gdpiRCkeCGhR 26
                                      ++ i+C +CG R
  gi|488599809|ref|YP_007906280.1| 65 KAEIKCVNCGER 76
                                      688*******88 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.031
                                      -B-SSS--B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevsl 12
                                      Y C +Cg  vs+
  gi|488599809|ref|YP_007906280.1| 82 YLCEKCGGFVSV 93
                                      899999977765 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.1   8.4e-05      0.19      13      39 ..      62      88 ..      39      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-05
                              C1_2 13 edssesfnCsaCgrkidgffYsCseCd 39
                                      e s+++ +C  Cg+  d+  Y C++C 
  gi|488599809|ref|YP_007906280.1| 62 EVSKAEIKCVNCGERYDSPIYLCEKCG 88
                                      489999*********88888******5 PP

>> DUF2949  Protein of unknown function (DUF2949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014       0.3      13      50 ..       6      43 ..       4      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                           DUF2949 13 aiseasialalrqseqdpspLpmvLWqYGLvtleqLdk 50
                                      ai e++++la++++ ++ +++ ++   + L++ +qL+ 
  gi|488599809|ref|YP_007906280.1|  6 AIVENALKLAEKHNAKKVNSITVIVGELLLINPDQLEF 43
                                      68899******************************985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.1   0.00036       0.8       1      20 [.      69      88 ..      69      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCG 20
                                      +C nCG+  +     C++CG
  gi|488599809|ref|YP_007906280.1| 69 KCVNCGERYDSPIYLCEKCG 88
                                      8******************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.7    0.0022       4.9       2      24 ..      67      89 ..      66      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
                       zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCGt 24
                                      +++C nCG+   +s    C +CG+
  gi|488599809|ref|YP_007906280.1| 67 EIKCVNCGErY-DSPIYLCEKCGG 89
                                      799******77.999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 713.89
//
Query:       gi|488599810|ref|YP_007906281.1|  [L=215]
Description: hydrogenase accessory protein HypB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   97.5   2.2    8.6e-28   97.1   2.2    1.1  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
    2.7e-06   26.6   4.2    3.7e-06   26.1   1.6    1.9  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00095   19.1   0.1       0.38   10.7   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
     0.0073   16.2   0.3       0.33   10.8   0.1    2.4  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
  ------ inclusion threshold ------
      0.011   15.4   1.3        1.6    8.5   0.0    2.5  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.021   14.8   0.1      0.056   13.4   0.0    1.7  2  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
      0.048   14.1   0.0      0.068   13.5   0.0    1.3  1  AAA_16       AAA ATPase domain
       0.13   11.8   1.3        2.6    7.5   0.2    2.2  2  GTP_EFTU     Elongation factor Tu GTP binding domain
       0.16   12.2   0.1       0.66   10.2   0.2    2.1  2  AAA_22       AAA domain
       0.31   10.9   3.4       0.33   10.9   0.1    2.4  3  NTPase_1     NTPase


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 !   97.1   2.2   4.8e-31   8.6e-28       2     176 ..      34     191 ..      33     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 4.8e-31
                                       EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealee 78 
                                       ++++ G +GsGKT L++++l+   ++++ vi++++   + D e++++ +v++  +++G+ C+  ++ ++ +++++  
  gi|488599810|ref|YP_007906281.1|  34 AINIMGAIGSGKTLLIEKTLQS-VDYRVGVILGDVI-CKADYERVKKYDVSVEPINTGKECHLDAHLISHVIQSF-- 106
                                       6899****************76.9************.**************************444444444444.. PP

                                       HHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHC CS
                              cobW  79 reerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlld 154
                                        + ++d+iliE++G l++P            dl +d  v++v++    +e+++  ek ++ +  ad++++nK+Dl++
  gi|488599810|ref|YP_007906281.1| 107 -S-DVDLILIENVGnLVCPVDF---------DLGEDYRVVMVSV----TEGDDVVEKHPEIFRLADVIIINKIDLAE 168
                                       .4.799****************.........*************....9**************************** PP

                                       HC...HHHHHHHHHHHHTTS-EE CS
                              cobW 155 ee.allekleerlrqlnpeakvl 176
                                       ++ a+++k+ ++++++n +a+++
  gi|488599810|ref|YP_007906281.1| 169 AVeADVDKMVRDAKRINGSARII 191
                                       **9***************99987 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.065   1.2e+02      30      63 ..      33      63 ..      15      72 .. 0.79
   2 !   26.1   1.6     2e-09   3.7e-06     121     225 ..     108     208 ..      55     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.065
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                      + + + G  G+Gk  l+e+    l++  +rv+v+
  gi|488599810|ref|YP_007906281.1| 33 TAINIMGAIGSGKTLLIEKT---LQSVDYRVGVI 63
                                      46789999********9985...45556677766 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 2e-09
                                       T-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCS CS
                              MeaB 121 GfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgikkGileiaDiivvnkaDkkeaekaarelraalelee 197
                                         D +lie vG     vd     d  vv++    GD++      i+ +aD+i++nk D++ea +a   + +++   +
  gi|488599810|ref|YP_007906281.1| 108 DVDLILIENVGNLVCPVDFDLGEDYRVVMVSVTEGDDVVEKHPEIFRLADVIIINKIDLAEAVEAD--VDKMV--RD 180
                                       469****************9999******99***************************98886654..44443..34 PP

                                       TTBTTB--EEEEEBCCCTBSHHHHHHHH CS
                              MeaB 198 ekekeWrpkvlktsavegeGidelvdai 225
                                        k+ + +++++k+  + g+G de ++ +
  gi|488599810|ref|YP_007906281.1| 181 AKRINGSARIIKMDLKSGKGFDEWLEFL 208
                                       4556667899999999999999877655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0048       8.7      88     130 ..      18      63 ..       3      67 .. 0.73
   2 !   10.7   0.0   0.00021      0.38      48     101 ..     156     212 ..     148     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0048
                                       TTHHHHHHHCTT...SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  88 egleelkellkd...ktsvlvGqSGvGKStLinallpelelktgev 130
                                       + +e+ +e+lk+     + ++G  G GK+ Li++ l++ + ++g +
  gi|488599810|ref|YP_007906281.1|  18 RLAEKNREYLKSkgiTAINIMGAIGSGKTLLIEKTLQSVDYRVGVI 63 
                                       44555566666531234458**************999999999876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00021
                                       EEEEEEE-GGG--HHH.HHHHHHHHHHHTT..SEEEE--TTTHTTHHHHHHHCTTSE CS
                       RsgA_GTPase  48 epvivlnKiDlleeee.eleelkeelealg..yevllvsaktkegleelkellkdkt 101
                                         vi++nKiDl+e  e +++++  + ++++   ++++++ k+++g++e  e l+d +
  gi|488599810|ref|YP_007906281.1| 156 ADVIIINKIDLAEAVEaDVDKMVRDAKRINgsARIIKMDLKSGKGFDEWLEFLRDAV 212
                                       669**********99988999999999998556788889999999999999988876 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00019      0.33       2      33 ..      35      63 ..      34      68 .. 0.82
   2 ?    3.1   0.0     0.047        84      81      97 ..      99     115 ..      83     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                      ++i+g  gsGKT L+ek ++   + ++rvg+i
  gi|488599810|ref|YP_007906281.1| 35 INIMGAIGSGKTLLIEKTLQ---SVDYRVGVI 63
                                      7899************9765...556777776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.047
                              MobB  81 leellarlsevDlvlvE 97 
                                       ++++++ +s+vDl+l+E
  gi|488599810|ref|YP_007906281.1|  99 ISHVIQSFSDVDLILIE 115
                                       5678899999******9 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2    0.0061        11       4      20 ..      35      51 ..      32     117 .. 0.75
   2 ?    8.5   0.0   0.00089       1.6      87     142 ..     152     209 ..     131     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0061
                         PduV-EutP  4 illiGkvgsGKttLtqa 20
                                      i ++G++gsGKt L ++
  gi|488599810|ref|YP_007906281.1| 35 INIMGAIGSGKTLLIEK 51
                                      668*********99765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00089
                         PduV-EutP  87 vfnkeviGiitkidlaed.eeni.eaveelLksaGaekifevsavekegieellkyle 142
                                       +f+   + ii kidlae  e+++ ++v++  +  G ++i++++  + +g++e l++l+
  gi|488599810|ref|YP_007906281.1| 152 IFRLADVIIINKIDLAEAvEADVdKMVRDAKRINGSARIIKMDLKSGKGFDEWLEFLR 209
                                       555555569******986345564689999999*******************999886 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   3.1e-05     0.056       8      71 ..      17      96 ..      10     126 .. 0.66
   2 ?   -1.4   0.0       1.3   2.3e+03      68      90 ..     149     171 ..     121     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                                      HHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT--.......----TTTTSEEEEEE..SS.....EEEEE CS
                              TsaE  8 ealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve.......evkSPTFtlveeYelekeg.....lyHfD 70
                                      ++l++k  + l     ++i + G +G+GKT l+ + +++++++        +    +  v++Y+ + e       +H+D
  gi|488599810|ref|YP_007906281.1| 17 KRLAEKNREYLkskgITAINIMGAIGSGKTLLIEKTLQSVDYRvgvilgdVICKADYERVKKYDVSVEPintgkECHLD 95
                                      45555555544443345699*****************998664433334334555566666665544444555555555 PP

                                      - CS
                              TsaE 71 l 71
                                      +
  gi|488599810|ref|YP_007906281.1| 96 A 96
                                      5 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                                       EEE-TT-SSTHHHHHCTTCCCCS CS
                              TsaE  68 HfDlYRledeeeleelgleeyle 90 
                                       H  ++Rl+d   +++++l e++e
  gi|488599810|ref|YP_007906281.1| 149 HPEIFRLADVIIINKIDLAEAVE 171
                                       77788888877777777777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.8e-05     0.068      25      58 ..      33      65 ..      15     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrg 58
                                       ++ + G+ G+GK+ l+++ l+++  + + ++ g
  gi|488599810|ref|YP_007906281.1| 33 TAINIMGAIGSGKTLLIEKTLQSVDYR-VGVILG 65
                                      78889****************999999.555443 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 ?    3.2   0.1     0.032        57       3      25 ..      32      54 ..      30      60 .. 0.85
   2 ?    7.5   0.2    0.0015       2.6      97     147 ..     133     182 ..     130     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.032
                                      EEEEEEEESTTSSHHHHHHHHHH CS
                          GTP_EFTU  3 irnigiighvDhGKtTLtdrLly 25
                                      i  i i+g + +GKt L+++ l+
  gi|488599810|ref|YP_007906281.1| 32 ITAINIMGAIGSGKTLLIEKTLQ 54
                                      56789*************98775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0015
                                       EEEEEETTTB..STHHHHHHHHHHHHTTTEEEEEEESCGST...HHHHHHHHHHHH CS
                          GTP_EFTU  97 avlvvdaveG..vepqteevlrlalkegvpiivfiNKmDrl...kaelkeiveevk 147
                                        v++v+++eG  v ++  e++rla       +++iNK+D +   +a+++++v+++k
  gi|488599810|ref|YP_007906281.1| 133 RVVMVSVTEGddVVEKHPEIFRLAD------VIIINKIDLAeavEADVDKMVRDAK 182
                                       5666666666444444444444444......99*******9777777777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00037      0.66       8      43 ..      35      63 ..      26     130 .. 0.74
   2 ?   -2.3   0.0       2.7   4.8e+03      39      58 ..     187     209 ..     164     213 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43
                                      + ++G  G+GKT+l+++ l++ d        r++v+
  gi|488599810|ref|YP_007906281.1| 35 INIMGAIGSGKTLLIEKTLQSVDY-------RVGVI 63
                                      6689************99998753.......55555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                            AAA_22  39 rpevvfvtlpsst...sskdllr 58 
                                       ++++++++l+s++   ++ ++lr
  gi|488599810|ref|YP_007906281.1| 187 SARIIKMDLKSGKgfdEWLEFLR 209
                                       55666777766664444444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00018      0.33       2      60 ..      35      94 ..      34     101 .. 0.85
   2 ?    1.1   0.0      0.18   3.2e+02      70     107 ..      75     120 ..      69     122 .. 0.59
   3 ?   -1.3   0.2      0.97   1.7e+03      91     119 ..     151     179 ..     130     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                      EEEE--TTSSHHHHHHHHHHHH....GGGEEEEEEEEE-------EEEEEET.T--EEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss.gvkvgGfyteevreggrrigFkivdlasgeegiL 60
                                      + i G  G+GKt l++k l+ ++ + gv +g ++++   e+ ++   ++  +++g+e  L
  gi|488599810|ref|YP_007906281.1| 35 INIMGAIGSGKTLLIEKTLQSVDYRvGVILGDVICKADYERVKKYDVSVEPINTGKECHL 94
                                      6688******************87769999999999988888888888888888887665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                                       EETTEEE-HHH........HHHHHHHHHHHHHHHH-EEEE---STT CS
                          NTPase_1  70 rvgkyvvdves........feelalealrkalseadviviDEiGkm 107
                                       rv+ky v ve         ++   ++ + +++s+ d+i+i  +G++
  gi|488599810|ref|YP_007906281.1|  75 RVKKYDVSVEPintgkechLDAHLISHVIQSFSDVDLILIENVGNL 120
                                       5666666655433333333333333334445799999999999976 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.97
                                       HHHHHH-EEEE---STTGGG-HHHHHHHH CS
                          NTPase_1  91 kalseadviviDEiGkmElkskkfkeave 119
                                       + ++ advi+i  i   E   + + ++v+
  gi|488599810|ref|YP_007906281.1| 151 EIFRLADVIIINKIDLAEAVEADVDKMVR 179
                                       44577888888887766666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1219.23
//
Query:       gi|488599811|ref|YP_007906282.1|  [L=74]
Description: hydrogenase assembly chaperone HypC/HupF [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   87.2   0.2    6.6e-25   87.0   0.2    1.1  1  HupF_HypC     HupF/HypC family
  ------ inclusion threshold ------
      0.025   14.5   1.0      0.032   14.2   1.0    1.1  1  PDDEXK_10     PD-(D/E)XK nuclease superfamily
      0.046   13.7   0.0       0.05   13.6   0.0    1.1  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.2   1.1e-28   6.6e-25       1      64 [.       1      64 [.       1      65 [. 0.97

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.1e-28
                                      CCEEEEEEEEEEETTEEEEECTTEEEEEEGTTCTTB-TT-EEEEETTEEEEEE-HHHHHHHHHH CS
                         HupF_HypC  1 MCLaiPgkvveiedelAlvdvgGvrrevslalveevkvGdyVLvhvGfAiekideeeaeetlel 64
                                      MCLaiP++v+e++  +A+v++gG+r+ev+++l+++v+vGdyVLvhvG+Ai+k+d +e ee  ++
  gi|488599811|ref|YP_007906282.1|  1 MCLAIPAEVEEVNFPIAIVNFGGTRKEVRIDLLPDVRVGDYVLVHVGYAIQKVDVKEVEELAAI 64
                                      **********************************************************998765 PP

>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0   5.3e-06     0.032       2      43 ..      27      70 ..      26      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-06
                         PDDEXK_10  2 evelDvv..vkdgkvilvEiksslkrgDlavikrkkelYekakg 43
                                      ev +D++  v+ g  +lv +  ++++ D+++++  + +Y+k+++
  gi|488599811|ref|YP_007906282.1| 27 EVRIDLLpdVRVGDYVLVHVGYAIQKVDVKEVEELAAIYQKLQE 70
                                      6777777668999****************************987 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.4e-06      0.05      37      79 ..      25      67 ..       8      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-06
                      MMR_HSR1_Xtn 37 redvtvDdlidviegnrvYipclyvlNKiDlisleeldelare 79
                                      r++v +D l dv  g+ v +++ y++ K+D  + eel +++++
  gi|488599811|ref|YP_007906282.1| 25 RKEVRIDLLPDVRVGDYVLVHVGYAIQKVDVKEVEELAAIYQK 67
                                      79999********************************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 486.93
//
Query:       gi|488599812|ref|YP_007906283.1|  [L=357]
Description: hydrogenase expression/formation protein HypD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-136  453.0   0.0   7.8e-136  452.8   0.0    1.0  1  HypD      Hydrogenase formation hypA family
  ------ inclusion threshold ------
       0.04   14.4   0.0       0.14   12.7   0.0    2.0  1  NYN       NYN domain


Domain annotation for each model (and alignments):
>> HypD  Hydrogenase formation hypA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.8   0.0  8.7e-140  7.8e-136       2     350 ..       6     352 ..       5     353 .. 0.97

  Alignments for each domain:
  == domain 1  score: 452.8 bits;  conditional E-value: 8.7e-140
                                       HHHHHHHHHHHHHHTSS-EEEEE--HHHHHHHHHTTHHHHS-TTEEEEE-S--TTTTS-HHHHHHHHHHHHH--EEE CS
                              HypD   2 lakkllekikkeakkerelkimevCGghthaivryglrslLpenielisGPGCpVCvtpeeeidkaielaekeevil 78 
                                       l++k+ eki++eak+  ++kim++CG+h+ +i++y lrslLp+ni+l+sGPGCpVC++p+e+++k+++l eke++i+
  gi|488599812|ref|YP_007906283.1|   6 LISKISEKIHEEAKDAGKIKIMHLCGTHEDTITKYNLRSLLPDNIKLLSGPGCPVCIIPDEDLQKVFHLIEKENIIF 82 
                                       68899************************************************************************ PP

                                       EE-CCHHG---TT--HHHHHHTT-EEEE-SSHHHHHHHHHH-TTSEEEEEEEE-HHHHHHHHHHHHHHHHHT-SSEE CS
                              HypD  79 atfgDmlrvpgskksLleakaegadvrivyspldalkiakenpdkevvflavGFEttapatalalleakkeglknfs 155
                                       +tfgDm rvp + ksL+  ka+g d+rivys++da+kia+++ +++vv++++GFEtt+p+tala+l+     ++nf+
  gi|488599812|ref|YP_007906283.1|  83 TTFGDMARVPHNGKSLFYYKAKGYDIRIVYSIFDAIKIARNS-SRTVVHFGIGFETTMPSTALAILD----APENFC 154
                                       ***************************************998.9**********************9....89**** PP

                                       EEEEEE-HHHHHHHHHHTT.---SEEEEEHHHHHHHTTHHHHHHHHHH---EEEE-SSHHHHHHHHHHHHHHHHTT- CS
                              HypD 156 vlsshklvppalealleseelkidgfiapghvstviGlkayeelaeeykvpvvvaGFepldilqailmlvkqleege 232
                                       v+ssh++ +pa+e+l++   ++++gfi pghvst++G+kaye++ ++y++p++++GFep d++ +il+l+k +++g+
  gi|488599812|ref|YP_007906283.1| 155 VFSSHRYFIPAMEHLISLG-VEVNGFINPGHVSTITGIKAYEKI-KKYGIPQIISGFEPEDVMLSILKLIKAIKRGD 229
                                       ****************886.9*********************98.69****************************** PP

                                       --EEETTTTT--TT--HHHHHHHHHHEEEEEEEETTTEEEEEEEEEE-GGGGGGBGGGT---.....-S---SS-TT CS
                              HypD 233 aeveneYkrvvkeegnkkaqklieevfevrdaewRglgvipksglklreeyaefdaekkfel.....ekeeekekka 304
                                       aev neY+r+v+ +gn+ aqk++++vf+v d ewRglgv+p+sg  ++eey+efd+ k fe         e+k+kka
  gi|488599812|ref|YP_007906283.1| 230 AEVFNEYTRAVTYDGNVMAQKVMDDVFSVDDWEWRGLGVVPRSGAVIKEEYSEFDVVKVFEDafsdfVPVEDKAKKA 306
                                       ************************************************************77677667789999*** PP

                                       --HHHHHTTS--GGGSTTBTTTB-SSS-SSHHHHSTT-HHHHHHHT CS
                              HypD 305 ckcgevlkGkakPedCklFgkaCtpenpvGacmvSsEGaCaayyky 350
                                       c+cg+vl+G+++P dC+lF+k+Ctp++pvGacmvS EG+C+++ k+
  gi|488599812|ref|YP_007906283.1| 307 CRCGDVLRGIITPLDCPLFNKRCTPKDPVGACMVSFEGTCNIWAKF 352
                                       *******************************************998 PP

>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.5e-05      0.14      90     132 ..     144     185 ..      67     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                               NYN  90 laydnkydtivLvsgDgDFaplveklrergkrVevllaeeast 132
                                       la+ +++++++++s+ + F+p++e+l ++g++V+++   ++++
  gi|488599812|ref|YP_007906283.1| 144 LAILDAPENFCVFSSHRYFIPAMEHLISLGVEVNGFI-NPGHV 185
                                       5666999***************************998.44555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2465.94
//
Query:       gi|488599813|ref|YP_007906284.1|  [L=215]
Description: putative hydrocarbon binding protein (contains V4R domain) [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-17   61.2   0.1      1e-16   60.6   0.1    1.3  1  V4R             V4R domain
    6.1e-13   48.6   0.2    1.4e-12   47.5   0.0    1.7  1  HTH_20          Helix-turn-helix domain
    6.1e-13   48.4   1.1    1.1e-12   47.6   1.1    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    1.5e-07   30.8   1.0    3.9e-07   29.5   1.0    1.8  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.2e-05   25.1   0.0    2.2e-05   24.3   0.0    1.4  1  MarR_2          MarR family
    4.5e-05   23.2   0.0     0.0001   22.0   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    5.5e-05   23.0   1.3     0.0001   22.1   1.3    1.4  1  HTH_11          HTH domain
    6.1e-05   22.7   0.0    0.00019   21.2   0.0    1.8  1  HTH_38          Helix-turn-helix domain
    0.00015   21.3   0.5    0.00035   20.1   0.2    1.8  1  GerE            Bacterial regulatory proteins, luxR family
    0.00028   20.6   0.1     0.0007   19.4   0.1    1.7  1  HTH_10          HTH DNA binding domain
    0.00043   20.0   0.0     0.0034   17.1   0.0    2.1  2  HTH_23          Homeodomain-like domain
    0.00063   19.6   0.1     0.0012   18.7   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0011   19.3   0.3     0.0026   18.2   0.3    1.6  1  HTH_40          Helix-turn-helix domain
     0.0033   16.9   0.2      0.012   15.1   0.1    2.1  2  Sigma70_r4      Sigma-70, region 4
     0.0047   17.1   0.1     0.0079   16.4   0.1    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0076   16.4   0.7      0.013   15.7   0.7    1.4  1  HTH_34          Winged helix DNA-binding domain
     0.0077   16.2   0.2      0.017   15.1   0.2    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0082   16.1   0.1       0.11   12.5   0.0    2.1  2  Dimerisation2   Dimerisation domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.036   14.4   0.0    1.9  1  FaeA            FaeA-like protein
      0.012   15.6   0.6      0.023   14.6   0.6    1.6  1  MarR            MarR family
      0.013   15.4   0.9      0.031   14.3   0.6    1.8  1  HTH_45          Winged helix-turn-helix
      0.015   15.3   0.0      0.025   14.6   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.017   14.9   0.2      0.044   13.6   0.1    1.8  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.018   15.1   0.0      0.032   14.3   0.0    1.5  1  KorB            KorB domain
      0.024   14.6   0.1      0.046   13.7   0.1    1.4  1  HTH_36          Helix-turn-helix domain
      0.027   14.6   0.1      0.049   13.8   0.1    1.5  1  Trp_repressor   Trp repressor protein
      0.029   14.0   0.1       0.28   10.9   0.0    2.3  2  Sigma70_r4_2    Sigma-70, region 4
      0.046   13.4   0.1      0.074   12.8   0.1    1.3  1  DUF4423         Domain of unknown function (DUF4423)
      0.051   13.4   0.4       0.08   12.8   0.4    1.3  1  TFIIE_alpha     TFIIE alpha subunit
      0.059   13.3   0.0       0.11   12.5   0.0    1.3  1  HTH_1           Bacterial regulatory helix-turn-helix protein
       0.06   13.5   0.3       0.11   12.5   0.3    1.5  1  SpoIIID         Stage III sporulation protein D
      0.063   12.9   0.6          1    9.0   0.1    2.4  2  HTH_50          Helix-turn-helix domain
      0.075   13.0   0.2       0.17   11.9   0.1    1.6  1  MetOD1          Metanogen output domain 1
      0.079   13.2   0.1       0.65   10.2   0.1    2.3  2  HTH_17          Helix-turn-helix domain
      0.093   13.1   0.3       0.21   12.0   0.3    1.6  1  Rrf2            Transcriptional regulator
       0.11   12.5   0.1       0.65   10.0   0.1    2.2  2  PuR_N           Bacterial purine repressor, N-terminal
       0.14   12.0   0.0       0.28   11.0   0.0    1.5  1  LexA_DNA_bind   LexA DNA binding domain
       0.17   11.7   0.0       0.32   10.8   0.0    1.3  1  TetR_N          Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.1   2.2e-19     1e-16       3      61 ..     154     212 ..     152     213 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2.2e-19
                                       EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEE CS
                               V4R   3 lsieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFeve 61 
                                       + +e++  +++lp++++  C   +G+++g+l +++gkr+ v+Ev+C+++G++ CeFe++
  gi|488599813|ref|YP_007906284.1| 154 FVVEDCYMCRDLPNINDTYCKTDEGIIEGILLGKTGKRYLVKEVKCWGTGDEVCEFEIK 212
                                       569******************************************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0     3e-15   1.4e-12       9      59 ..       6      54 ..       5      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 3e-15
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +++R++il  L  +++ t +e+a++l+lsk+t+s+HL++L+e  Lv+vv++
  gi|488599813|ref|YP_007906284.1|  6 DETRLKILEIL--DKPKTTTEIAKTLGLSKSTISHHLKILSELKLVKVVKT 54
                                      79*********..***********************************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 !   47.6   1.1   2.3e-15   1.1e-12       1      46 [.       6      50 ..       6      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.3e-15
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      d+tRlkIL +L +++++ +e+a+ lgls+st+ShHLk+L e+ LV+
  gi|488599813|ref|YP_007906284.1|  6 DETRLKILEIL-DKPKTTTEIAKTLGLSKSTISHHLKILSELKLVK 50
                                      89*******99.78***************************99996 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   1.0   8.2e-10   3.9e-07       1      47 [.       5      49 ..       5      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 8.2e-10
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ldet++kILe+L k    + +e+A+ lglS+st++ +lk L e  l+
  gi|488599813|ref|YP_007906284.1|  5 LDETRLKILEILDK--PKTTTEIAKTLGLSKSTISHHLKILSELKLV 49
                                      79************..9999*******************99887766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   4.6e-08   2.2e-05      13      54 ..      14      52 ..       9      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.6e-08
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      ++ + p    t +e+a++lglsks++s +lk L++  Lv  +
  gi|488599813|ref|YP_007906284.1| 14 EILDKPK---TTTEIAKTLGLSKSTISHHLKILSELKLVKVV 52
                                      6677776...99***************************876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.1e-07    0.0001      15      49 ..      16      50 ..      10      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.1e-07
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                       + + t +e+A+ +gl+kSt +++L+ L el++v+
  gi|488599813|ref|YP_007906284.1| 16 LDKPKTTTEIAKTLGLSKSTISHHLKILSELKLVK 50
                                      4444567**************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   1.3   2.2e-07    0.0001       2      46 ..       9      51 ..       8      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.2e-07
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpI 46
                                      +l+ile+L ++    +  e+A+ L++S++t+  ++k+L+el  v++
  gi|488599813|ref|YP_007906284.1|  9 RLKILEIL-DKP--KTTTEIAKTLGLSKSTISHHLKILSELKlVKV 51
                                      68999999.555..59**********************88754665 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.9e-07   0.00019      10      42 ..       9      41 ..       6      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.9e-07
                            HTH_38 10 ReeIerllaeGlslreIArrLgrspsTIsRElk 42
                                      R +I   l++ ++  eIA+ Lg s+sTIs +lk
  gi|488599813|ref|YP_007906284.1|  9 RLKILEILDKPKTTTEIAKTLGLSKSTISHHLK 41
                                      89999999**********************997 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   7.3e-07   0.00035       3      39 ..       5      41 ..       3      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.3e-07
                                      S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHH CS
                              GerE  3 LskRErevLrllaeGksnkeIAeelniSekTVkvhks 39
                                      L++  +++L+ l + k+++eIA+ l++S+ T++ h++
  gi|488599813|ref|YP_007906284.1|  5 LDETRLKILEILDKPKTTTEIAKTLGLSKSTISHHLK 41
                                      6667788999999**********************97 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.5e-06    0.0007      24      45 ..      20      41 ..      16      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-06
                            HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                       t+ e+Ak+lG+skst+s hL+
  gi|488599813|ref|YP_007906284.1| 20 KTTTEIAKTLGLSKSTISHHLK 41
                                      5789*****************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.2e-06    0.0034       5      39 ..       7      41 ..       4      46 .. 0.88
   2 ?   -0.0   0.0       1.8   8.4e+02      13      26 ..     122     137 ..     120     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.2e-06
                            HTH_23  5 reRlrillllaeGlsvreIAreLgvsrrTvyrwlk 39
                                      + Rl+il  l++ ++++eIA+ Lg s++T+++ lk
  gi|488599813|ref|YP_007906284.1|  7 ETRLKILEILDKPKTTTEIAKTLGLSKSTISHHLK 41
                                      57999999999989****************98776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.8
                            HTH_23  13 llae..GlsvreIAre 26 
                                       l+++  G +++ IA++
  gi|488599813|ref|YP_007906284.1| 122 LADKveGETYEGIADL 137
                                       4554679999999997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.6e-06    0.0012      20      59 ..      17      61 ..      10      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-06
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....T CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....p 59
                                       +p+t++eia+ lg+++s++   L+ L++  lV+++k +      
  gi|488599813|ref|YP_007906284.1| 17 DKPKTTTEIAKTLGLSKSTISHHLKILSELKLVKVVKTEiernfI 61
                                      5799*******************************9987666663 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   5.4e-06    0.0026       6      58 ..      13      61 ..       8      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.4e-06
                            HTH_40  6 lelleeglsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIe 58
                                      le l + ++  eIAk  gl++sTI  HL  l e +    l ++v++e+e++ +
  gi|488599813|ref|YP_007906284.1| 13 LEILDKPKTTTEIAKTLGLSKSTISHHLKILSELK----LVKVVKTEIERNFI 61
                                      67788999*******************97766663....45556666665554 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.5e-05     0.012      18      41 ..      17      40 ..       1      43 [. 0.78
   2 ?   -2.1   0.0         6   2.8e+03      18      28 ..     126     136 ..     119     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                                      TTT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVrqie 41
                                      +++ T  EI+++lg+S+++++ ++
  gi|488599813|ref|YP_007906284.1| 17 DKPKTTTEIAKTLGLSKSTISHHL 40
                                      6788****************9776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6
                                       TTT--HHHHHH CS
                        Sigma70_r4  18 geglTleEIge 28 
                                       +eg T+e I++
  gi|488599813|ref|YP_007906284.1| 126 VEGETYEGIAD 136
                                       7999***9997 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 !   16.4   0.1   1.7e-05    0.0079      21      56 ..      18      53 ..       2      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-05
                                      SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                      k+ +t+++a+ L+ s+s++s  lk L++  +v+++k
  gi|488599813|ref|YP_007906284.1| 18 KPKTTTEIAKTLGLSKSTISHHLKILSELKLVKVVK 53
                                      556799***********************9999987 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 !   15.7   0.7   2.7e-05     0.013       2      53 ..       9      58 ..       8      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-05
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53
                                      Rl++l +L +    + +e+ ++l+++++ +s hlk+L + + ++v k+  ++
  gi|488599813|ref|YP_007906284.1|  9 RLKILEILDK--PKTTTEIAKTLGLSKSTISHHLKILSELKLVKVVKTEIER 58
                                      7888888854..45678****************************9998877 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   3.7e-05     0.017      19      54 ..      17      53 ..       1      61 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglis.rg 54
                                      + p t +e+A  lGl+ +t+s  l+ L++ +l++  +
  gi|488599813|ref|YP_007906284.1| 17 DKPKTTTEIAKTLGLSKSTISHHLKILSELKLVKvVK 53
                                      4477999************************999534 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00023      0.11      20      69 ..       9      56 ..       7      69 .. 0.88
   2 ?    1.3   0.0      0.72   3.4e+02       4      32 ..      79     107 ..      78     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                     Dimerisation2 20 eLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkee 69
                                      +L++ ++L +  p+++ e+a++lg+s + ++  l+ +  L+L ++ k+e 
  gi|488599813|ref|YP_007906284.1|  9 RLKILEILDK--PKTTTEIAKTLGLSKSTISHHLKILSELKLVKVVKTEI 56
                                      6999999988..9******************************9887654 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.72
                     Dimerisation2   4 ellnGFlaSkaLftAceLgvFdlLkeeep 32 
                                       e+++GF+ S+  f  + L+ F lL+ e++
  gi|488599813|ref|YP_007906284.1|  79 EVFKGFRLSNREFLRALLRSFTLLNLENK 107
                                       6799******9999999999999987554 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.6e-05     0.036       6      46 ..      13      50 ..       6      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.6e-05
                                      HHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA  6 leylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                      le    +  p +T+eiA+ lgls   + + L+ L   + +k
  gi|488599813|ref|YP_007906284.1| 13 LEI---LDKPKTTTEIAKTLGLSKSTISHHLKILSELKLVK 50
                                      333...4569***********************99888776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   4.9e-05     0.023       3      43 ..       7      45 ..       5      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-05
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLek 43
                                      +t+++iL+il+   p + +e+ak lg+skst++  l+ L +
  gi|488599813|ref|YP_007906284.1|  7 ETRLKILEILD--KPKTTTEIAKTLGLSKSTISHHLKILSE 45
                                      57777777776..588999******************9965 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   6.5e-05     0.031       9      52 ..      10      52 ..       3      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-05
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikks 52
                                      + ILe++ ++ ++ T+i +   Ls ++++  L++L e +l+k  
  gi|488599813|ref|YP_007906284.1| 10 LKILEIL-DKPKTTTEIAKTLGLSKSTISHHLKILSELKLVKVV 52
                                      689**99.99******************************9533 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.3e-05     0.025       1      34 [.       9      41 ..       9      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.3e-05
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlk 34
                                      R+++l  l++   t+ +iAk lgls++t+ ++lk
  gi|488599813|ref|YP_007906284.1|  9 RLKILEILDKPK-TTTEIAKTLGLSKSTISHHLK 41
                                      778888888877.9***************99987 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.4e-05     0.044       1      34 [.       5      36 ..       5      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.4e-05
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestv 34
                                      LDe+ +kILe+L  d   + +e+A+ +GlS st+
  gi|488599813|ref|YP_007906284.1|  5 LDETRLKILEIL--DKPKTTTEIAKTLGLSKSTI 36
                                      799999999999..6899**************98 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.7e-05     0.032       5      30 ..      21      46 ..      17      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.7e-05
                              KorB  5 kqadIAkaLGksksfvslylklldvp 30
                                      + ++IAk LG sks +s +lk+l   
  gi|488599813|ref|YP_007906284.1| 21 TTTEIAKTLGLSKSTISHHLKILSEL 46
                                      679******************98644 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   9.8e-05     0.046      28      54 ..      22      48 ..      19      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.8e-05
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGy 54
                                         +ak lglsk+T+s ++k L +l +
  gi|488599813|ref|YP_007906284.1| 22 TTEIAKTLGLSKSTISHHLKILSELKL 48
                                      568*******************99865 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1    0.0001     0.049      37      68 ..       8      38 ..       3      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                     Trp_repressor 37 qRlqvvkeLLkeelsqreIaeelgvSiAtItR 68
                                      +Rl++++ +L++ ++ +eIa+ lg S  tI+ 
  gi|488599813|ref|YP_007906284.1|  8 TRLKILE-ILDKPKTTTEIAKTLGLSKSTISH 38
                                      7******.**********************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00059      0.28      27      47 ..      20      40 ..       1      41 [. 0.83
   2 ?    0.4   0.0       1.2   5.4e+02      21      34 ..     123     136 ..     121     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00059
                                      --HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 27 lsykEIAellgisegtVksrl 47
                                      +++ EIA+ lg+s +t+ ++l
  gi|488599813|ref|YP_007906284.1| 20 KTTTEIAKTLGLSKSTISHHL 40
                                      5788*************9998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                                       HHHTS---HHHHHH CS
                      Sigma70_r4_2  21 lryleglsykEIAe 34 
                                          +eg +y+ IA 
  gi|488599813|ref|YP_007906284.1| 123 ADKVEGETYEGIAD 136
                                       5679********97 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00016     0.074      29      73 ..      12      54 ..       8      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                           DUF4423 29 llplkdfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                      +l++ d+ +++ e+ak l+  +s++ +++ l++L +l+l+k  + 
  gi|488599813|ref|YP_007906284.1| 12 ILEILDKPKTTTEIAKTLG--LSKSTISHHLKILSELKLVKVVKT 54
                                      6777888899*********..*******************97765 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   0.00017      0.08      13      79 ..       7      70 ..       1      83 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECC CS
                       TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinye 79
                                      e   ++l++L  k ++t  ++ak l++ +  + + L  L e +lvk+++    e +  k y+  + +
  gi|488599813|ref|YP_007906284.1|  7 ETRLKILEILD-KPKTT-TEIAKTLGLSKSTISHHLKILSELKLVKVVKTE-IERNFIKKYYISTLN 70
                                      56678888887.55544.46***************************9975.555666666665555 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022      0.11       3      39 ..       9      45 ..       8      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                                      HHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1  3 qlrlfvavaeegsftrAAeeLglsqpavsrqikrLEe 39
                                      +l++++ + + ++ t+ A+ Lgls +++s+++k L e
  gi|488599813|ref|YP_007906284.1|  9 RLKILEILDKPKTTTEIAKTLGLSKSTISHHLKILSE 45
                                      68888888889999999***************98865 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   0.00024      0.11      15      45 ..      15      44 ..       5      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                           SpoIIID 15 iveskatvRkaakvfgvskstvhkDvterLk 45
                                      i+++ +t  ++ak++g+skst+ + + ++L+
  gi|488599813|ref|YP_007906284.1| 15 ILDKPKTTTEIAKTLGLSKSTISHHL-KILS 44
                                      78899999**************7654.3444 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0022         1      25      45 ..      21      41 ..       8      42 .. 0.79
   2 ?    1.6   0.0      0.46   2.2e+02      10      20 ..      55      65 ..      50      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                            HTH_50 25 StRklAkrLGvShtaianklr 45
                                       t  +Ak LG+S+++i   l+
  gi|488599813|ref|YP_007906284.1| 21 TTTEIAKTLGLSKSTISHHLK 41
                                      55679***********87765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.46
                            HTH_50 10 efErelikkay 20
                                      e+Er+ ikk+y
  gi|488599813|ref|YP_007906284.1| 55 EIERNFIKKYY 65
                                      79********9 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00036      0.17     111     154 ..     169     213 ..     156     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                            MetOD1 111 nPifCllcraivsrsf.twtglkgsveqkktlgngdekCvFeikv 154
                                       n  +C   ++i++ ++  +tg +  v++ k+ g gde C+Feik 
  gi|488599813|ref|YP_007906284.1| 169 NDTYCKTDEGIIEGILlGKTGKRYLVKEVKCWGTGDEVCEFEIKN 213
                                       7778888899998875268999*********************86 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0014      0.65       3      20 ..      21      38 ..      21      66 .. 0.86
   2 ?    0.1   0.0       2.1   9.7e+02      19      40 ..     172     196 ..     168     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0014
                            HTH_17  3 tveEaAelLgvsrstvyr 20
                                      t+ E+A+ Lg+s+st+  
  gi|488599813|ref|YP_007906284.1| 21 TTTEIAKTLGLSKSTISH 38
                                      899************975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.1
                            HTH_17  19 yrlirrgelpaa...kiGrrwripr 40 
                                       y   ++g +      k G+r+++++
  gi|488599813|ref|YP_007906284.1| 172 YCKTDEGIIEGIllgKTGKRYLVKE 196
                                       6667888888888878999999875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00045      0.21      24      58 ..      18      52 ..      10      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00045
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksv 58
                                      +p +++eia+  ++s+s +++ l+ L++ +lvk+v
  gi|488599813|ref|YP_007906284.1| 18 KPKTTTEIAKTLGLSKSTISHHLKILSELKLVKVV 52
                                      467899**************************987 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0014      0.65      22      46 ..      21      45 ..      10      57 .. 0.84
   2 ?   -0.8   0.0       3.2   1.5e+03      38      59 ..     162     183 ..     152     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                             PuR_N 22 sltyfaerfeaAKSsiSeDlaiike 46
                                      + t++a+ ++ +KS+iS  l+i++e
  gi|488599813|ref|YP_007906284.1| 21 TTTEIAKTLGLSKSTISHHLKILSE 45
                                      567899***************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.2
                             PuR_N  38 SeDlaiikealekeglGkletv 59 
                                       + Dl  i+++  k++ G +e +
  gi|488599813|ref|YP_007906284.1| 162 CRDLPNINDTYCKTDEGIIEGI 183
                                       6799999999999999999854 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 ?   11.0   0.0   0.00059      0.28      25      52 ..      19      45 ..      11      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00059
                                      ---HHHHHHHHTS-.HHHHHHHHHHHHH CS
                     LexA_DNA_bind 25 pPsireiaralglkSpsaveehLkaLer 52
                                      p +  eia+ lgl+  s++ +hLk L+ 
  gi|488599813|ref|YP_007906284.1| 19 PKTTTEIAKTLGLS-KSTISHHLKILSE 45
                                      66889********7.9********9975 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   0.00067      0.32      18      36 ..      21      39 ..      20      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00067
                                      -HHHHHHHHTSSHHHHHHH CS
                            TetR_N 18 tvreIAkrAGvskgalYry 36
                                      t+ eIAk +G+sk+++ ++
  gi|488599813|ref|YP_007906284.1| 21 TTTEIAKTLGLSKSTISHH 39
                                      688***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1349.40
//
Query:       gi|488599814|ref|YP_007906285.1|  [L=140]
Description: Rubrerythrin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.7   6.0    1.9e-12   47.7   5.9    2.0  1  Rubrerythrin     Rubrerythrin
    5.6e-06   26.3   4.0    0.00031   20.7   4.0    2.1  1  Ferritin         Ferritin-like domain
    0.00021   20.2   1.0       0.14   11.0   0.1    2.0  2  FA_desaturase_2  Fatty acid desaturase
     0.0015   18.6   1.4       0.73    9.8   0.2    2.3  2  DUF892           Domain of unknown function (DUF892)
     0.0087   16.3   0.4       0.98    9.6   0.0    2.1  2  Ferritin_2       Ferritin-like domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   5.9   5.3e-16   1.9e-12       4     136 ..      24     135 ..      21     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 5.3e-16
                                       HHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTG CS
                      Rubrerythrin   4 ekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkfl 79 
                                       ++ ++gE ++  lY ++a++a+ egyp+ia++++++A +E+ Ha ++++l + ++ +l+                  
  gi|488599814|ref|YP_007906285.1|  24 TNEFRGETMEVGLYLAMARQAErEGYPEIARVLRDIAMDEAYHASRFAELNGMIKDTLK------------------ 82 
                                       56699**************************************************9999.................. PP

                                       GHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  80 ttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                          ++Le ++eg+ +++    r+ +  a++ g +ea+++ ++++++E +H+e l+ l
  gi|488599814|ref|YP_007906285.1|  83 ---ESLEYMLEGERKANVHK-RKIAVKAKELGLDEAHDIWDEASRDEYRHAEALKGL 135
                                       ...89**9999999999998.999999999***********************9987 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   4.0   8.6e-08   0.00031      17     138 ..      36     138 ..      21     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.6e-08
                                       HHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCSSHHHHHHHHHHHHH CS
                          Ferritin  17 qylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefgsveevleaalehek 93 
                                       +ylama+ ++ +g++++a  +++ a +e  ha ++ae    l+g          +       ++++e le +le e+
  gi|488599814|ref|YP_007906285.1|  36 LYLAMARQAEREGYPEIARVLRDIAMDEAYHASRFAE----LNG--------MIK-------DTLKESLEYMLEGER 93 
                                       6********************************9998....566........333.......499************ PP

                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  94 kvteslrelielaeeegDpatadfledfleeqeeheweleallek 138
                                       k++ + r+++  a+e g +  +d+ ++  +++ +h++ l+ lle+
  gi|488599814|ref|YP_007906285.1|  94 KANVHKRKIAVKAKELGLDEAHDIWDEASRDEYRHAEALKGLLER 138
                                       *****************************************9985 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   3.8e-05      0.14     172     205 ..      40      73 ..      37      89 .. 0.88
   2 !    8.7   0.1   0.00019      0.68     157     209 ..      87     139 ..      73     140 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.8e-05
                   FA_desaturase_2 172 taklakeagdellakicgaiaadEkrHeaaYtrv 205
                                       +a++a+++g + +a++++ ia dE+ H+  ++++
  gi|488599814|ref|YP_007906285.1|  40 MARQAEREGYPEIARVLRDIAMDEAYHASRFAEL 73 
                                       79*************************9988765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00019
                   FA_desaturase_2 157 YtsfQErATkvsHrntaklakeagdellakicgaiaadEkrHeaaYtrvvekl 209
                                       Y    Er  +v  r++a  ake g + ++ i    + dE rH+ a + ++e+ 
  gi|488599814|ref|YP_007906285.1|  87 YMLEGERKANVHKRKIAVKAKELGLDEAHDIWDEASRDEYRHAEALKGLLERY 139
                                       5556699999*9********************************998887765 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2    0.0002      0.73     100     147 ..      24      71 ..       6      86 .. 0.82
   2 !    8.0   0.1   0.00075       2.7     117     152 ..     103     138 ..     100     140 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
                                       .HHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892 100 aaaqavehyEiAsYgtLialAeqlgekeaaklLeqtleeekatdeklt 147
                                       +   + e +E+  Y  +++ Ae+ g++e+a++L+++   e   +++  
  gi|488599814|ref|YP_007906285.1|  24 TNEFRGETMEVGLYLAMARQAEREGYPEIARVLRDIAMDEAYHASRFA 71 
                                       55667799***************************9988877666554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00075
                                       HHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF892 117 ialAeqlgekeaaklLeqtleeekatdekltelaes 152
                                       +  A++lg +ea ++ ++    e++ +e l+ l+e+
  gi|488599814|ref|YP_007906285.1| 103 AVKAKELGLDEAHDIWDEASRDEYRHAEALKGLLER 138
                                       678*****************************9986 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00027      0.98      97     134 ..      34      74 ..      25      76 .. 0.76
   2 !    5.2   0.1    0.0065        23      36      61 ..     111     136 ..      83     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                        Ferritin_2  97 vsAYlgaaplls...nkelltaaasIlsvEArHaavirtll 134
                                       v  Yl  a++ +    +e++++   I+ +EA+Ha+ +++l 
  gi|488599814|ref|YP_007906285.1|  34 VGLYLAMARQAEregYPEIARVLRDIAMDEAYHASRFAELN 74 
                                       5567777776664456789999999********99998875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0065
                        Ferritin_2  36 daevrevaeeiakheeaHveflkaal 61 
                                        +e +++  e+  +e  H+e+lk+ l
  gi|488599814|ref|YP_007906285.1| 111 LDEAHDIWDEASRDEYRHAEALKGLL 136
                                       46678999***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 835.00
//
Query:       gi|488599815|ref|YP_007906286.1|  [L=506]
Description: cytochrome bd-I ubiquinol oxidase subunit 1 apoprotein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-74  249.5  22.2    1.5e-71  241.2  22.2    2.6  1  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
  ------ inclusion threshold ------
       0.24   11.8   6.1       0.32   11.4   1.3    2.5  2  Herpes_UL20     Herpesvirus egress protein UL20


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.2  22.2   1.7e-75   1.5e-71       3     408 ..      15     501 ..      14     506 .] 0.89

  Alignments for each domain:
  == domain 1  score: 241.2 bits;  conditional E-value: 1.7e-75
                    Cyt_bd_oxida_I   3 RlqfaltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseys 79 
                                       R+   + + +H++++   lGl+ll +++e+++l+t++e++ k+ ++++k f+i FavG++ G+  ef ++++W++ +
  gi|488599815|ref|YP_007906286.1|  15 RVLSMIGIEIHWIILQYILGLSLLAVVAEVIWLKTKKEEWAKISRTIAKGFIIVFAVGAAMGTASEFGLVLLWPNLI 91 
                                       677788999******************************************************************** PP

                    Cyt_bd_oxida_I  80 rfvGdifgapLaiEgllAFflEstflglmlfgwdrvskklhllatwlvaigtllSalwIlaanswmqtPvG...... 150
                                       +++G  +  pL+ E ++AF++E +f+ +++++w+++++k+h+++ +l++ g+++Sa +I+++ns+mq P G      
  gi|488599815|ref|YP_007906286.1|  92 EAAGRYIYFPLYAE-IFAFLMEVIFIYMFWYAWKKLPTKAHIVVGILAITGAWFSASMIMSVNSYMQAPPGiipayd 167
                                       **************.7************************************************************* PP

                    Cyt_bd_oxida_I 151 ............................................................................. 150
                                                                                                                    
  gi|488599815|ref|YP_007906286.1| 168 ngwrfdegypkltlfvpneivsaldvevlqslgtdvlgktdnsvivalpvsivkqlisdafsgktvgesllyvaltd 244
                                       *************************************************************************9999 PP

                    Cyt_bd_oxida_I 151 ................aelnpdtgraeltdflavlfnpsalakflHtvlaalltaaffvagvsawyllrrekefark 211
                                                       a ++++t   e+  +   + +p+ +a++lHt++aa+++++f vag +a+ + r++ + a+ 
  gi|488599815|ref|YP_007906286.1| 245 aaknslkdvpalnvvdA-IVANT-VKEVGVYTVTFKSPTYFASLLHTLFAAITVSSFTVAGGYALSYSRKNVKHAKL 319
                                       99999999999777532.23233.5566677777889**************************************** PP

                    Cyt_bd_oxida_I 212 slkialvvalvaallqal.lGdlsgkevaetqpaKlAAmeglweteeaplslfgipdeeeeknefaieiPgllslla 287
                                        lk +l +a++++++q + +G+++g  vae +p+K+AAme+++           +             +  + ++l+
  gi|488599815|ref|YP_007906286.1| 320 GLKYGLYFAIASLAFQGIvTGHEMGVAVAEWNPEKFAAMEANTPA---------F-------------LERIVAYLS 374
                                       ****************887**********************9942.........2.............3458999** PP

                    Cyt_bd_oxida_I 288 tgsldgevkGlndlpkeevPpvalvfwsfrimvglgvlllllallalll.....rwllrllllaipl.pfiaveaGW 358
                                       +g++++e++ + ++p + +Pp +l+++ +++ +++  +l ++alla+++     + + +  l+++p+ + + + +GW
  gi|488599815|ref|YP_007906286.1| 375 YGNFNAEIPDYYQIPDDLRPP-LLIHYLYYVKITVAAVLGIMALLAAYMlyrdrE-VSYGYLIILPIvAQVVSFLGW 449
                                       ********************9.788888999999999998888888877788954.555555555544999999*** PP

                    Cyt_bd_oxida_I 359 ivtevGRqPWivygllrtadavsp..vsagevllslilflllylvLlvvevy 408
                                       +v+e+GR+PW++yg++ +  a +    + ge ++  + f+ + +vL   +++
  gi|488599815|ref|YP_007906286.1| 450 AVREIGRKPWTIYGVMDVGTAHTInpPTLGEAAIISLYFVGILAVLTYSTYK 501
                                       *****************99997322255555555555555555555554444 PP

>> Herpes_UL20  Herpesvirus egress protein UL20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.3   3.5e-05      0.32      27      78 ..     102     156 ..      91     164 .. 0.74
   2 ?    2.1   0.2     0.025   2.3e+02      39      67 ..     397     423 ..     390     444 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                       Herpes_UL20  27 llstlvlkpiccli.fllya..kaltgrlllvagllaltvlyyvtlllellvvYv 78 
                                       l + +++  +++++ +++++  k+l ++  +v+g+la+t++++ ++++++   Y+
  gi|488599815|ref|YP_007906286.1| 102 LYAEIFAFLMEVIFiYMFWYawKKLPTKAHIVVGILAITGAWFSASMIMSVNSYM 156
                                       445666666666651445553467788999*******************988776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.025
                       Herpes_UL20  39 lifllyakaltgrlllvagllaltvlyyv 67 
                                       li +ly+  ++  +++v+g++al ++y +
  gi|488599815|ref|YP_007906286.1| 397 LIHYLYY--VKITVAAVLGIMALLAAYML 423
                                       4566777..56667778888888887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); 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:                         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: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3101.13
//
Query:       gi|488599816|ref|YP_007906287.1|  [L=388]
Description: hypothetical protein Asulf_00261 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-23   80.6  24.0    5.7e-20   71.3  14.5    2.0  2  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
  ------ inclusion threshold ------
       0.15   11.8   2.1       0.78    9.5   0.0    2.9  3  TMEM132D_C      Mature oligodendrocyte transmembrane protein,


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3  14.5   6.4e-24   5.7e-20       7     239 ..       7     233 ..       4     253 .. 0.91
   2 !   15.0   1.9   7.8e-07     0.007     314     407 ..     258     374 ..     251     381 .. 0.63

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 6.4e-24
                    Cyt_bd_oxida_I   7 altavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseysrfvG 83 
                                       al   +H+++v l+++++  + +l+ +  ++g+ +y k+ k +++ +a ++a+G v G+   + +   +++++ ++G
  gi|488599816|ref|YP_007906287.1|   7 ALVFGLHIVLVNLGIAFSTAIPLLKRRGEKEGNYAYIKTSKQLMNFYAATYALGGVFGTAFTVFLLSFYPSFIGLAG 83 
                                       778899*********************************************************************** PP

                    Cyt_bd_oxida_I  84 difgapLaiEgllAFflEstflglmlfgwdrvskklhllatwlvaigtllSalwIlaanswmqtPvGaelnpdtgra 160
                                       +    p+ + + lA +l    +  +++gwdr+s  +h ++ +++ ++ +l  +   a+ ++++ P+G  l p+    
  gi|488599816|ref|YP_007906287.1|  84 HLTFVPFGLAV-LAIVLHFFAITAYWYGWDRWSSDVHYTLGLILLVSVYLIPIGFRAVSAFLNVPEGLILTPKP--- 156
                                       *********95.9*********************************************************9775... PP

                    Cyt_bd_oxida_I 161 eltdflavlfnpsalakflHtvlaalltaaffvagvsawyllrrekefarkslkialvvalvaallqallGdlsgke 237
                                          d++a+++np++l  +l  ++aal+t+ f + + +++++ r  ++ a + ++  + +a++a++++++lG   ++ 
  gi|488599816|ref|YP_007906287.1| 157 -HLDVIAAFLNPTFLPLYLKSITAALATGFFTISSAYMLKYGRG-ENEAIEIVNKFMPLAAIAFIATLVLGAVYAEV 231
                                       .46****************************9999999999863.45566777777888888888888888877776 PP

                    Cyt_bd_oxida_I 238 va 239
                                       + 
  gi|488599816|ref|YP_007906287.1| 232 LN 233
                                       65 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 7.8e-07
                    Cyt_bd_oxida_I 314 wsfrimvglgvlllllallalll...rwllrllllaiplpfiaveaGWivtevGRqPWivy................ 371
                                       w f i v++ v+ +l++++ l +     + r+++la+p+++ia+ aG ++  +   P+ v+                
  gi|488599816|ref|YP_007906287.1| 258 WLFTIKVVMFVIQALAIIAFLKIrknPGYSRAIVLAGPASMIAIFAGEMLNSFSQYPYFVAklgddafvssipepir 334
                                       77777777777776666664433899669*******************************96666666655555544 PP

                    Cyt_bd_oxida_I 372 ....gllrtadavsp..vsagevllslilflllylvLlvvev 407
                                           + l  + +  +   ++ e+ + +++fl+  l+ ++v++
  gi|488599816|ref|YP_007906287.1| 335 tflaERLSLELS--NplATSYELYIITLVFLVPLLISACVFL 374
                                       333222222222..2224444444444444444444444444 PP

>> TMEM132D_C  Mature oligodendrocyte transmembrane protein, TMEM132D, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   8.8e-05      0.78      15      52 ..      35      73 ..      27      78 .. 0.83
   2 ?   -3.0   0.5      0.71   6.4e+03      42      54 ..      90     102 ..      88     106 .. 0.79
   3 ?   -0.1   0.1     0.092   8.3e+02      38      50 ..     266     278 ..     251     285 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 8.8e-05
                        TMEM132D_C 15 ek.sesdlvqasraltdLEiGmYaLlgvfClAilvflin 52
                                      ek ++   +++s++l +   + YaL gvf  A  vfl++
  gi|488599816|ref|YP_007906287.1| 35 EKeGNYAYIKTSKQLMNFYAATYALGGVFGTAFTVFLLS 73
                                      33245558999**************************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.71
                        TMEM132D_C  42 fClAilvflincv 54 
                                       f lA+l+++++  
  gi|488599816|ref|YP_007906287.1|  90 FGLAVLAIVLHFF 102
                                       7899999999865 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.092
                        TMEM132D_C  38 LlgvfClAilvfl 50 
                                       +  +  lAi++fl
  gi|488599816|ref|YP_007906287.1| 266 MFVIQALAIIAFL 278
                                       3345567777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 2348.85
//
Query:       gi|488599817|ref|YP_007906288.1|  [L=144]
Description: hypothetical protein Asulf_00262 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  116.7   6.7    5.4e-17   62.0   1.5    2.1  2  CBS         CBS domain
  ------ inclusion threshold ------
       0.05   13.7   0.1        2.7    8.1   0.0    2.1  2  sCache_3_2  Single cache domain 3


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 !   57.9   0.3   1.1e-19     1e-15       1      53 [.       9      60 ..       9      63 .. 0.96
   2 !   62.0   1.5     6e-21   5.4e-17       1      56 [.      81     136 ..      81     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.1e-19
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      V+d+mt+dv+++++++++ +a++l ++k++++lPV+ ++gkl+Giv+++Dl++
  gi|488599817|ref|YP_007906288.1|  9 VKDFMTEDVLSIDEEMSVDDAMNLVIDKKYNALPVT-KNGKLIGIVSRMDLIK 60
                                      89**********************88**********.9*************97 PP

  == domain 2  score: 62.0 bits;  conditional E-value: 6e-21
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V++im++ vvtv+pd+t++ a++l++e+++++lPVVd++++lvGi+t  D+lra +
  gi|488599817|ref|YP_007906288.1|  81 VKHIMRKAVVTVTPDDTIKAAADLIVEYRIRSLPVVDKEKNLVGIITVGDVLRAFM 136
                                       899**************************************************986 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 ?    3.6   0.0    0.0073        66     108     123 ..      40      54 ..      34      55 .. 0.92
   2 ?    8.1   0.0    0.0003       2.7     100     125 ..     104     129 ..      88     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0073
                        sCache_3_2 108 klPvfdadgrviGivs 123
                                       +lPv + +g++iGivs
  gi|488599817|ref|YP_007906288.1|  40 ALPVTK-NGKLIGIVS 54 
                                       68*999.*******97 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0003
                        sCache_3_2 100 tlgpslrvklPvfdadgrviGivsvG 125
                                       +++++    lPv+d++  ++Gi+ vG
  gi|488599817|ref|YP_007906288.1| 104 LIVEYRIRSLPVVDKEKNLVGIITVG 129
                                       578999999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 950.72
//
Query:       gi|488599818|ref|YP_007906289.1|  [L=67]
Description: archaeal histone [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.2    8.8e-22   77.2   0.2    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    9.6e-10   38.9   0.1      1e-09   38.8   0.1    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    2.4e-05   24.7   0.1    2.6e-05   24.6   0.1    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
    3.4e-05   23.9   0.1    3.7e-05   23.8   0.1    1.0  1  TAF            TATA box binding protein associated factor (TA
    8.2e-05   22.7   0.0    8.4e-05   22.6   0.0    1.0  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00032   20.8   0.0    0.00034   20.7   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
     0.0004   20.3   0.1    0.00042   20.3   0.1    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
     0.0016   18.8   0.0     0.0017   18.7   0.0    1.1  1  CENP-S         CENP-S protein
  ------ inclusion threshold ------
      0.014   15.5   0.3      0.015   15.4   0.3    1.0  1  Sipho_Gp157    Siphovirus Gp157
      0.016   15.2   0.0      0.017   15.1   0.0    1.1  1  Bromo_TP       Bromodomain associated
       0.08   13.3   1.0      0.096   13.0   1.0    1.1  1  CENP-X         CENP-S associating Centromere protein X


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.2   5.4e-25   8.8e-22       2      65 .]       3      65 ..       2      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 5.4e-25
                                      XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                     CBFD_NFYB_HMF  2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                      eLPia+v+++++++ +a+++++dAk+++ae +ee ++e+a++A+ei+k+ +rKt+kae+i lA+
  gi|488599818|ref|YP_007906289.1|  3 ELPIAPVERLIRNA-GAERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLAL 65
                                      7*************.***********************************************97 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.1   6.4e-13     1e-09      63     129 ..       5      66 ..       1      67 [] 0.89

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 6.4e-13
                                       XHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                           Histone  63 qklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                       + +p++R++r+         r+s +a ++l+e lE   +e+++ A  +akh  R+T+ ++Di lA+r
  gi|488599818|ref|YP_007906289.1|   5 PIAPVERLIRNAG-----AERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLALR 66 
                                       5567777777665.....59*********************************************99 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.6e-08   2.6e-05      15      63 ..      18      66 ..       9      67 .] 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.6e-08
                                      S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH CS
                       TFIID_20kDa 15 etkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhle 63
                                       +++ ed + +L+e+ +++ +++ k+a+++akh   +++ + Di+l l+
  gi|488599818|ref|YP_007906289.1| 18 AERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLALR 66
                                      577899****************************************985 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 !   23.8   0.1   2.3e-08   3.7e-05      16      66 .]      16      66 ..       2      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.3e-08
                                      TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                               TAF 16 lGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                       G + +s++a  +Lae +e+   ei+++a+   +h  R++  ++D++ ALr
  gi|488599818|ref|YP_007906289.1| 16 AGAERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLALR 66
                                      688999********************************************9 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 !   22.6   0.0   5.2e-08   8.4e-05       8      75 ..       4      66 ..       1      67 [] 0.87

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.2e-08
                          CENP-T_C  8 lPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                      lP a v +l +++       ++++++a  +l + ++++   +++     akH gRKt++++D+ l ++
  gi|488599818|ref|YP_007906289.1|  4 LPIAPVERLIRNA-----GAERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLALR 66
                                      6667777766665.....5679*****************************************98877 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 !   20.7   0.0   2.1e-07   0.00034      11      68 ..       9      66 ..       5      67 .] 0.94

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.1e-07
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiq 68
                                      ++ ++++ g + ++e+    L +    + +++ + A  +a+h ++k+v+++d++lA+ 
  gi|488599818|ref|YP_007906289.1|  9 VERLIRNAGAERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLALR 66
                                      67899999************************************************85 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.6e-07   0.00042      23      65 ..      24      66 ..       9      67 .] 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.6e-07
                                      HHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXX CS
                       TFIID-18kDa 23 etvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliR 65
                                      ++  +l + ++++ +e+ ++a+++ak+ g++ ++ ED+  ++R
  gi|488599818|ref|YP_007906289.1| 24 DAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLALR 66
                                      455678899999***************************9999 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     1e-06    0.0017      26      71 ..      21      66 ..       7      67 .] 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1e-06
                            CENP-S 26 atkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71
                                      +++++   l+e   + + ++ak     akH +R+t++++D+ L +R
  gi|488599818|ref|YP_007906289.1| 21 VSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLALR 66
                                      566666677777778888999999999****************998 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   8.9e-06     0.015      12      61 ..      12      62 ..       7      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.9e-06
                       Sipho_Gp157 12 llell.eeedvdeeeeeikdtLesleeeieeKaeniakviknleaeaeaik 61
                                      l+ ++  e   + ++ +++++Le+++ ei++Ka +iak +   + +ae i+
  gi|488599818|ref|YP_007906289.1| 12 LIRNAgAERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDIN 62
                                      55566344444445568899********************99999988876 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     1e-05     0.017      17      68 ..      14      65 ..       8      67 .] 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                                      HHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHH CS
                          Bromo_TP 17 eeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltL 68
                                      ++aG +++ e a   L e ++++ +e++++a + a h gR +++ +D+ l+L
  gi|488599818|ref|YP_007906289.1| 14 RNAGAERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKTVKAEDINLAL 65
                                      566666666777777999999****************************998 PP

>> CENP-X  CENP-S associating Centromere protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.0   5.9e-05     0.096      17      63 ..      19      60 ..       9      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.9e-05
                                      -EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SE.....EECHH CS
                            CENP-X 17 tkItkdalelvaeylklFvrEavaRaaeeaeeegkeesekskleved 63
                                       ++++da  ++aeyl+   +E +  a+e a+  g ++     +  ed
  gi|488599818|ref|YP_007906289.1| 19 ERVSEDAKVVLAEYLEEWATEIAKKAVEIAKHVGRKT-----VKAED 60
                                      599***************************9998887.....44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 500.39
//
Query:       gi|488599819|ref|YP_007906290.1|  [L=176]
Description: hypothetical protein Asulf_00264 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-06   28.8   0.1    1.9e-06   28.1   0.1    1.3  1  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
    3.5e-05   24.8   0.0    5.6e-05   24.2   0.0    1.4  1  Cytochrom_C      Cytochrome c


Domain annotation for each model (and alignments):
>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   2.1e-10   1.9e-06      13      67 .]      97     172 ..      92     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.1e-10
                   Cytochrome_CBB3  13 nCasCHgkggag................pslagrdwepdalvdiiknGk..g.....aMpafggqlsdeelwalvaY 66 
                                       +C+ CHg +g g                 +l ++++++d+++++i++G+  +      Mp +  q+ +++l++l+ Y
  gi|488599819|ref|YP_007906290.1|  97 SCVNCHGRDGTGgfvpmmcdekspdirySALVEEGMSEDEIKTAITKGVheNetlnyCMPRW--QMGERDLNDLISY 171
                                       8******66666699********555555555779999**********7441334458****..69*********** PP

                   Cytochrome_CBB3  67 l 67 
                                       l
  gi|488599819|ref|YP_007906290.1| 172 L 172
                                       7 PP

>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   6.2e-09   5.6e-05      11      91 ..      97     175 ..      78     176 .] 0.87

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.2e-09
                                       TGGGTB-SSSBSSS.........--HHHHHHHTTT-HHHHHHHHTTSS--SSSHHHHHHHGGGGGGG.TT--HHHHH CS
                       Cytochrom_C  11 nCaaCHgvegggakqgg.....gptlsgaaerasaasigasvanpaavsaprddfekkkltaemparkerlteqeia 82 
                                        C++CHg +g+g    +     +p+++  a  + + s+++++++      ++   e+++l++ mp +  ++ e +++
  gi|488599819|ref|YP_007906290.1|  97 SCVNCHGRDGTGGFVPMmcdekSPDIRYSALVEEGMSEDEIKTAI-----TKGVHENETLNYCMPRW--QMGERDLN 166
                                       7*****999999987778999999998888888888888888877.....68889999999999998..******** PP

                                       HHHHHHHTT CS
                       Cytochrom_C  83 dlaaYLksl 91 
                                       dl++YLk+l
  gi|488599819|ref|YP_007906290.1| 167 DLISYLKKL 175
                                       ******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1292.54
//
Query:       gi|488599820|ref|YP_007906291.1|  [L=104]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-12   44.9   3.3      8e-12   44.5   3.3    1.2  1  SHOCT            Short C-terminal domain
     0.0026   18.2   1.3     0.0031   18.0   1.3    1.2  1  DUF4199          Protein of unknown function (DUF4199)
     0.0074   15.4   5.9     0.0094   15.0   5.9    1.1  1  Acyl_transf_3    Acyltransferase family
  ------ inclusion threshold ------
      0.012   15.4   0.1       0.02   14.8   0.1    1.2  1  VbhA             Antitoxin VbhA
       0.05   13.7   0.1      0.065   13.3   0.1    1.1  1  DUF3278          Protein of unknown function (DUF3278)
      0.055   13.5   0.8      0.074   13.1   0.8    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.078   13.2   2.3        0.1   12.8   2.3    1.1  1  VKOR             Vitamin K epoxide reductase family
       0.08   11.8   2.6       0.09   11.6   2.6    1.0  1  DUF2142          Predicted membrane protein (DUF2142)
      0.094   11.5   0.6      0.099   11.4   0.6    1.2  1  DUF2207          Predicted membrane protein (DUF2207)
       0.15   12.0   0.1       0.15   12.0   0.1    1.1  1  Wzy_C_2          Virulence factor membrane-bound polymerase, 
       0.18   12.0   4.8       0.27   11.5   4.8    1.3  1  DUF3784          Domain of unknown function (DUF3784)
        0.5   10.8   3.5       0.61   10.5   1.0    1.9  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
        2.3    8.7   5.8        4.9    7.6   5.8    1.5  1  DUF805           Protein of unknown function (DUF805)
        7.7    5.5   8.4        3.6    6.6   0.0    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein


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 !   44.5   3.3   6.3e-15     8e-12       1      27 [.      76     102 ..      76     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 6.3e-15
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakL 27 
                                       ++Le+Lke+ya+GeIt+EE+ ++K++L
  gi|488599820|ref|YP_007906291.1|  76 TPLEILKERYAKGEITKEEYLRMKKEL 102
                                       58************************9 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.3   2.4e-06    0.0031       2      56 ..      16      72 ..      15      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                           DUF4199  2 fGlilglvwilifll.ilyllglhqi.lstgpllglla.llllllvpflvylalkkyr 56
                                      fG+ +  +w+l++++ +l + + +    ++gpl+ +l+ l ++ +v++l+y+ +++ +
  gi|488599820|ref|YP_007906291.1| 16 FGFGMLFWWLLFIVIgFLVYRDAN-ErGMNGPLWFILViLPMIGIVFLLLYIVIRESK 72
                                      79999999******8777777775.556788777677658888888888888888553 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   5.9   7.4e-06    0.0094     181     241 ..       8      67 ..       3      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 181 lfgpatsvgllplpsvlallfflfGalladaddrdrnlsrglkislllsllllalillalf 241
                                       + ++ ++++  ++  ++ llf+++G+l+++   +++ +   + i+++l ++++++ ll++ 
  gi|488599820|ref|YP_007906291.1|   8 MDWFGFPFFGFGMLFWW-LLFIVIGFLVYRDANERGMNGPLWFILVILPMIGIVFLLLYIV 67 
                                       33444444444444444.**********************************999999875 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.5e-05      0.02      27      42 ..      82      97 ..      78      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                              VbhA 27 leayvrGeIdadElvr 42
                                       e+y++GeI+ +E++r
  gi|488599820|ref|YP_007906291.1| 82 KERYAKGEITKEEYLR 97
                                      59************87 PP

>> DUF3278  Protein of unknown function (DUF3278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.1e-05     0.065      40     105 ..      20      87 ..      17      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                           DUF3278  40 llwlyllilslvalllakktp...eselilglvltnlllvvlvsglYiliaskklglatkeveakdyek 105
                                       +l+++ll + + +l+   + +   +  l+ +++++  +++++   lYi+i+ +k++ +  e+ ++ y k
  gi|488599820|ref|YP_007906291.1|  20 MLFWWLLFIVIGFLVYRDANErgmNGPLW-FILVILPMIGIVFLLLYIVIRESKAEKTPLEILKERYAK 87 
                                       67788777777777776554411145566.44446667899999**********999999998887765 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 ?   13.1   0.8   5.8e-05     0.074      45      98 ..      15      78 ..      10      86 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-05
                   Phage_holin_3_6 45 vlallalllllvalalal.....aa.....lwlaalivaavllvlagvlalvglkklkkakplp 98
                                      ++++ +l+ +l+++++++     a        l++++v + ++ +  +l+++ +++ k++k+++
  gi|488599820|ref|YP_007906291.1| 15 FFGFGMLFWWLLFIVIGFlvyrdANergmnGPLWFILVILPMIGIVFLLLYIVIRESKAEKTPL 78
                                      34444444444444444444544114455788899999999**999999999999999877644 PP

>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.3   7.9e-05       0.1      51      97 ..      10      68 ..       6      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-05
                                      ETTEEHHHHHHHHHHHHHHHHHS-.............HHHHHHHHHHHHHHHHHHHHHH CS
                              VKOR 51 ilgvplsllGllayalvlllalapl............lwlllllgslagvvfslyLiyl 97
                                       +g+p   +G+l+  l++++  +              lw++l+++ ++g+vf l  i++
  gi|488599820|ref|YP_007906291.1| 10 WFGFPFFGFGMLFWWLLFIVIGFLVyrdanergmngpLWFILVILPMIGIVFLLLYIVI 68
                                      599*******998887777655555699*****99877777777766666666655544 PP

>> DUF2142  Predicted membrane protein (DUF2142)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.6   7.1e-05      0.09     306     368 ..       4      67 ..       1      76 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                           DUF2142 306 figdlgwldvplPswlifawivllllllfaalvlgelr.lkekllvllvvlaivilivlalyls 368
                                       fi++++w+ +p  ++ +++w++l++++ f + +    r +   l ++lv+l  +++++l ly++
  gi|488599820|ref|YP_007906291.1|   4 FIHSMDWFGFPFFGFGMLFWWLLFIVIGFLVYRDANERgMNGPLWFILVILPMIGIVFLLLYIV 67 
                                       68999*******9999999999999999987666666645666666666666667777777765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   7.7e-05     0.099     392     432 ..      20      66 ..       5     104 .] 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.7e-05
                           DUF2207 392 ilglilillallllvll............lvfllilllillliaiivlllfsr 432
                                       +l++ l+++++     +            + +l ++l+il++i+i++lll+ +
  gi|488599820|ref|YP_007906291.1|  20 MLFWWLLFIVI-----GflvyrdanergmNGPLWFILVILPMIGIVFLLLY-I 66 
                                       12222221111.....12234466777776666666666666665555554.3 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 ?   12.0   0.1   0.00012      0.15      23      81 ..      20      76 ..       4      97 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                           Wzy_C_2 23 spfllaaflvlglldsksrsrrlrlrpklvlrvvalvlallglalllsilhdyqrleql 81
                                      + f +++f+v+g l    r  + r    ++ ++++++ ++ +++lll+i++  +++e+ 
  gi|488599820|ref|YP_007906291.1| 20 MLFWWLLFIVIGFLVY--RDANERGMNGPLWFILVILPMIGIVFLLLYIVIRESKAEKT 76
                                      6788888888866666..34444444555555666666666666677777776666665 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.8   0.00021      0.27      45      90 ..      15      66 ..      13      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                           DUF3784 45 fmgivllligilflllgll.....saiesealliiali.viiiiviylivya 90
                                      f g ++l++ +lf+++g+l     +  +++  l+++l+ + +i++++l++y+
  gi|488599820|ref|YP_007906291.1| 15 FFGFGMLFWWLLFIVIGFLvyrdaNERGMNGPLWFILViLPMIGIVFLLLYI 66
                                      6899*******************95555555555555537777777777776 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 ?    0.1   0.1      0.84   1.1e+03       8      19 ..      25      36 ..      23      40 .. 0.78
   2 ?   10.5   1.0   0.00047      0.61       3      27 ..      50      74 ..      49      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.84
                   FeoB_associated  8 iiaaavafvirr 19
                                      +++++++f+++r
  gi|488599820|ref|YP_007906291.1| 25 LLFIVIGFLVYR 36
                                      567778888886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00047
                   FeoB_associated  3 iIVgliiaaavafvirrlikkkkkG 27
                                      i+V+l  +++v+++++ +i+++k++
  gi|488599820|ref|YP_007906291.1| 50 ILVILPMIGIVFLLLYIVIRESKAE 74
                                      89*******************9975 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.8    0.0038       4.9      45      96 ..      20      73 ..       5      77 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0038
                            DUF805 45 vvlallllvpslavtvRRlHDtgrsgw....llllllvplialllll.vllllpgtp 96
                                      +++++ll+++   ++ R   D +  g+    +++l+++p+i++++ll ++++++++ 
  gi|488599820|ref|YP_007906291.1| 20 MLFWWLLFIVIGFLVYR---DANERGMngplWFILVILPMIGIVFLLlYIVIRESKA 73
                                      44444444444444444...6666666666788888889998877661555555554 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   7.3      0.87   1.1e+03     227     251 ..       8      33 ..       3      35 .. 0.66
   2 ?    6.6   0.0    0.0028       3.6       4      39 ..      48      83 ..      46     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.87
                   ABC2_membrane_3 227 l.afglgipfgnlglll..llfllfgla 251
                                       + +fg  +pf+++g l+  llf++ g++
  gi|488599820|ref|YP_007906291.1|   8 MdWFG--FPFFGFGMLFwwLLFIVIGFL 33 
                                       35899..999999999977444444443 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0028
                   ABC2_membrane_3  4 liitlllPiilvlllglifsnsveddentpiavvde 39
                                      ++i ++lP+i +++l+l + +  +++e+tp+ ++ e
  gi|488599820|ref|YP_007906291.1| 48 WFILVILPMIGIVFLLLYIVIRESKAEKTPLEILKE 83
                                      788999999999988888888888999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 751.28
//
Query:       gi|488599821|ref|YP_007906292.1|  [L=673]
Description: copper-(or silver)-translocating P-type ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  180.5   6.6    2.1e-53  180.5   6.6    2.2  3  E1-E2_ATPase  E1-E2 ATPase
    5.6e-46  157.5   2.4    5.6e-46  157.5   2.4    1.6  2  Hydrolase     haloacid dehalogenase-like hydrolase
    4.5e-07   29.9   0.5    0.00076   19.3   0.5    2.6  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
    4.5e-06   27.2   0.0    1.2e-05   25.8   0.0    1.7  1  HAD           haloacid dehalogenase-like hydrolase
     0.0087   15.4   1.0        1.3    8.3   0.1    2.4  2  PFK           Phosphofructokinase
     0.0099   16.0   0.8      0.048   13.8   0.0    2.4  2  HAD_2         Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.058   13.3   2.2        2.9    7.8   0.4    2.5  2  DUF1980       Domain of unknown function (DUF1980)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       3.6   9.3e+03     122     136 ..     107     121 ..      91     135 .. 0.59
   2 !  180.5   6.6   8.3e-57   2.1e-53       2     180 ..     168     346 ..     167     347 .. 0.99
   3 ?   -2.9   0.1       1.6   4.2e+03     100     157 ..     608     664 ..     590     667 .. 0.57

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHHS CS
                      E1-E2_ATPase 122 lvpvvlliallvfli 136
                                       +++++++i+++ f  
  gi|488599821|ref|YP_007906292.1| 107 MTLIAVAISVAYFYS 121
                                       344444444444433 PP

  == domain 2  score: 180.5 bits;  conditional E-value: 8.3e-57
                                       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++g ++++ +k l++GD vl+k+g+++p+Dg+++eg + v+e++LTGEs+pv+k++gd+v++G+++ +
  gi|488599821|ref|YP_007906292.1| 168 IMPSQAHLIKNGDVVDVSVKMLKVGDKVLVKPGEKIPVDGVVLEGVTAVNEAMLTGESKPVTKKAGDKVIGGSINGE 244
                                       6899************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralall 155
                                       g+++++V +tg+dt+l+++++lv++a+++k+++q  ++k + +l++++l+++ ++++++l +gk+ ++a+ ra++++
  gi|488599821|ref|YP_007906292.1| 245 GSIVVKVEKTGKDTYLNQVIELVRQAQETKSRTQDLANKAAFILTILALTVGTITLIVWLAYGKEFVFAIERAVTVM 321
                                       ***************************************************************************** PP

                                       HHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 156 vaaiPcaLplavplalalgarrlak 180
                                       v+++P aL+la+pl++a++++ +ak
  gi|488599821|ref|YP_007906292.1| 322 VITCPHALGLAIPLVVAVSTSLAAK 346
                                       ********************99997 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.6
                                       TS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHH CS
                      E1-E2_ATPase 100 lveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallva 157
                                       +++ ++++ +++ ++l   +++ ++++ l+a +++ + +ll+  +  all +l+++++
  gi|488599821|ref|YP_007906292.1| 608 VIKLSRKTYSKMFQNLLWATGYNFFAIPLAAGVLYGYGILLTPAA-GALLMSLSTVIV 664
                                       444455555555555555555555555555555555555555544.566665555555 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.3   1.1e+04     139     182 ..     220     259 ..     216     266 .. 0.59
   2 !  157.5   2.4   2.2e-49   5.6e-46       2     210 .]     364     577 ..     363     577 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.3
                                       EEESSEHHHHHHHHHH.TTGGGESEEEEHHCES....STTTSHHHHHHH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx....xxxxxxxxxxxx RF
                         Hydrolase 139 lltgdnpetaeraanq.lGddyfdaviasdiet....vakpspegkvaa 182
                                       +ltg ++   ++a ++ +G         ++i++    v k+++ gk   
  gi|488599821|ref|YP_007906292.1| 220 MLTGESKPVTKKAGDKvIG---------GSINGegsiVVKVEKTGKDTY 259
                                       5666665555544444444.........555554555888888777655 PP

  == domain 2  score: 157.5 bits;  conditional E-value: 2.2e-49
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH...HHHHHHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.. RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar...sgaltgfatfigrg.. 67 
                                        +vvfDk+GTLt+ge  v+d+i+ a++++++++e++      sehpi++ +v+ ak++     ++++f++++grg  
  gi|488599821|ref|YP_007906292.1| 364 QAVVFDKTGTLTKGEFGVTDIIPLADIEENKIMEIAasleanSEHPIAEGIVNSAKKMgveITNVEDFRAIPGRGie 440
                                       69***********************99999999999999999****************7766666************ PP

                                       ......HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEE CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ......ayaigkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagie 136
                                             +y + +p +l++l   +  ++++++  +qg+tv++l    + +a +++ad   +++e +ea+++L+++g++
  gi|488599821|ref|YP_007906292.1| 441 gtinnaKYKVVSPGYLKEL-GVEVDNEEVEKVKQQGKTVVFLveGSKPVAAIALADI--IREESKEAIKKLREMGLR 514
                                       *******************.999999999************988779**********..****************** PP

                                       EEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 137 vvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         +ltgdn+  a+ +a+++G           +e +a+++p  k  +i+e q++   vamVGDgvnDa+ala+A+
  gi|488599821|ref|YP_007906292.1| 515 CMMLTGDNRFVAKWVAEEIG----------LDEYFAEVLPHEKADKIKEVQERY-TVAMVGDGVNDAPALAQAD 577
                                       ********************..........7888****************8665.7*****************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 !    7.8   0.0   0.00098       2.5      16      58 ..     497     539 ..     494     542 .. 0.93
   2 !   19.3   0.5     3e-07   0.00076     205     252 ..     559     606 ..     545     609 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00098
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                       i e++keaikkl+e g   +  TG +   ++ v+ee+gld ++
  gi|488599821|ref|YP_007906292.1| 497 IREESKEAIKKLREMGLRCMMLTGDNRFVAKWVAEEIGLDEYF 539
                                       7799***********************************9876 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 3e-07
                                       GEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHH CS
                       Hydrolase_3 205 eviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVa 252
                                        v+ +GDg ND + L +a++g+A+g +++ + + Ad +  +n+   V+
  gi|488599821|ref|YP_007906292.1| 559 TVAMVGDGVNDAPALAQADVGIAIGAGTDVAVETADIILVKNDPRDVV 606
                                       57889**********************************999874444 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   4.5e-09   1.2e-05      79     187 ..     490     573 ..     466     574 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.5e-09
                               HAD  79 evirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkv 155
                                       ++++  +++++ +e++++ r+ G r+ +++g +r++++ +++e g    l++      ++             ++k+
  gi|488599821|ref|YP_007906292.1| 490 AIALADIIREESKEAIKKLREMGLRCMMLTGDNRFVAKWVAEEIG----LDE------YFAEV--------LPHEKA 548
                                       4445557889***********************************....***......44444........444555 PP

                               HAD 156 aalrewlaaegegidleevvayGDspsDlpll 187
                                       ++++e   +e       +v  +GD+++D p+l
  gi|488599821|ref|YP_007906292.1| 549 DKIKE--VQER-----YTVAMVGDGVNDAPAL 573
                                       55555..2223.....235555********98 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1   0.00051       1.3     141     202 ..     254     320 ..     247     330 .. 0.91
   2 !    5.3   0.1     0.004        10      37     101 ..     437     522 ..     410     541 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00051
                                       EEHHHHHHHHHHHHHHHHHHHHHH.....T-EEEEEES-TT-THHHHHHHHHHT-SEEE-TTS---H CS
                               PFK 141 iGfdTAlntiveaidklkstaksh.....krvfvvEvmGrncGwlAlmaglaggadvilipEepfdi 202
                                        G dT ln+++e ++++++t + +     k +f++ +     G ++l+  la g ++++  E+ +++
  gi|488599821|ref|YP_007906292.1| 254 TGKDTYLNQVIELVRQAQETKSRTqdlanKAAFILTILALTVGTITLIVWLAYGKEFVFAIERAVTV 320
                                       599****************999888888899*******************************98865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.004
                                       THHHHHHTT.-EE............EE-SGGGTT-TT--S-TT---.--GGG.......GSHHHHHHHHHHHHHHT- CS
                               PFK  37 eGfeGliee.eie............kltledvsgilsegGtiLgsa.Rskef.......keregrkkaaenlkklgi 92 
                                       +G+eG i++ +++            +++ e+v++++++g t+      sk+          re++k+a+++l++ g+
  gi|488599821|ref|YP_007906292.1| 437 RGIEGTINNaKYKvvspgylkelgvEVDNEEVEKVKQQGKTVVFLVeGSKPVaaialadIIREESKEAIKKLREMGL 513
                                       57777766653332222222222225568899999999999987762455545555543234559************ PP

                                       -EEEEEESH CS
                               PFK  93 daLvviGGd 101
                                       ++++  G++
  gi|488599821|ref|YP_007906292.1| 514 RCMMLTGDN 522
                                       ****99987 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5      0.81   2.1e+03      61      97 ..       7      44 ..       2      50 .. 0.58
   2 !   13.8   0.0   1.9e-05     0.048      82     145 ..     499     562 ..     492     582 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.81
                             HAD_2 61 kieellrkyneekkk.kevkpydgvkelLeeLkeagyk 97
                                      ++ee  ++++e +++ +e k  d+   +L++ k++ + 
  gi|488599821|ref|YP_007906292.1|  7 MHEEKEHEMHEPQHEtHEHKTHDHHARMLQDFKKRFIV 44
                                      55555555666666656666777777777777666555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.9e-05
                             HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekal 145
                                       ++ ke++++L+e+g+++   T  +r +++   e++g+++yF  ++  e++ k K  +e +  a+
  gi|488599821|ref|YP_007906292.1| 499 EESKEAIKKLREMGLRCMMLTGDNRFVAKWVAEEIGLDEYFAEVLPHEKADKIKEVQERYTVAM 562
                                       6789********************************************9999986666666665 PP

>> DUF1980  Domain of unknown function (DUF1980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4    0.0011       2.9      54      85 ..      19      55 ..       7      58 .. 0.83
   2 ?    4.5   0.1     0.011        29      38     108 ..     284     354 ..     275     408 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                           DUF1980 54 qkkk..ecghdHe...eksfikkllsylilviPlllg 85
                                      q+++  +++hdH+    + f k++++ +il +P+l++
  gi|488599821|ref|YP_007906292.1| 19 QHETheHKTHDHHarmLQDFKKRFIVSSILTVPILVL 55
                                      44445348899999999*****************985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                           DUF1980  38 amvvllilalvq....liraqkkkecghdHeeksf.ikkllsylilviPlllglllptkvl.dssiakakGfnfsla 108
                                       a+++l ilal+     li +          +e  f i++++ ++++  P  lgl +p +v+  +s+a+++G  +   
  gi|488599821|ref|YP_007906292.1| 284 AAFILTILALTVgtitLIVWLAYG------KEFVFaIERAVTVMVITCPHALGLAIPLVVAvSTSLAAKYGLLIRDR 354
                                       455555555555554455555555......13344599*******************88761557899999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1336  (0.0745161); expected 358.6 (0.02)
Passed bias filter:                      787  (0.0438954); 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: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 4225.90
//
Query:       gi|488599822|ref|YP_007906293.1|  [L=404]
Description: putative GTPase or GTP-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-22   78.7   0.0    1.3e-21   77.2   0.0    1.7  2  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.034   13.9   0.0    1.5  1  AAA_24    AAA domain
       0.12   12.8   0.0       0.21   12.0   0.0    1.3  1  AAA_16    AAA ATPase domain


Domain annotation for each model (and alignments):
>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   2.2e-25   1.3e-21       1     187 [.      93     258 ..      93     259 .. 0.89
   2 ?   -2.2   0.0      0.51   3.1e+03     116     142 ..     316     342 ..     311     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2.2e-25
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnp 77 
                                       G++dsGKS++a++L N++     k v+vDlD+Gq ++s P+++++ + +  i++ ++++      +f+G+ sp +  
  gi|488599822|ref|YP_007906293.1|  93 GESDSGKSSIAAYLSNRL---DGKKVIVDLDIGQASVSHPASMGIGITDGRITSISDVRVVD--GAFVGSISPVGRE 164
                                       899**************7...77889***************************988887666..68*********** PP

                            CLP1_P  78 slylalvkelareveekleenkkakasgliIntpGwvkgl.gaellleliealepdvvvvldqeellnelkrdlpls 153
                                       ++++++v e+ ++++ kl       ++  iI+++Gw++g  + e++l++i++lep+++++ +    l ++  d    
  gi|488599822|ref|YP_007906293.1| 165 TRCINAVMEIRKKIR-KL-------EGWKIIDSTGWIRGRrANEYKLAKISILEPTAIIAFKTPPFLDFIDCD---- 229
                                       **************9.34.......5679**********8456*******************97666666555.... PP

                            CLP1_P 154 kvkvvklpkspgvvqrsreerrelreerireYFy 187
                                          v+ l+++ g   rs+ +r+ +r e++ ++++
  gi|488599822|ref|YP_007906293.1| 230 ---VFMLESFAGK--RSKNQRSSYRAEKYSKFLE 258
                                       ...5599999997..**************99987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.51
                            CLP1_P 116 glgaellleliealepdvvvvldqeel 142
                                       ++g+e+  ++ e++ ++ +++l++++l
  gi|488599822|ref|YP_007906293.1| 316 EVGREVVRSIKEMFGIEDLLMLSKDDL 342
                                       579999***********9999999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.7e-06     0.034       4      38 ..      88     126 ..      85     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-06
                            AAA_24   4 kiliyGpsgiGKTtlakel....gpkplfidtekGlksl 38 
                                       +++iyG+s +GK+++a+ l      k +++d++ G +s+
  gi|488599822|ref|YP_007906293.1|  88 SFFIYGESDSGKSSIAAYLsnrlDGKKVIVDLDIGQASV 126
                                       789****************99999999******998876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.5e-05      0.21      19      55 ..      81     117 ..      73     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggif 55 
                                        r  + e+ +++Ges +GKss++  l ++l ++++i+
  gi|488599822|ref|YP_007906293.1|  81 FRNKSNESFFIYGESDSGKSSIAAYLSNRLDGKKVIV 117
                                       45555599**********************9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2598.59
//
Query:       gi|488599823|ref|YP_007906294.1|  [L=315]
Description: putative conserved protein related to dihydrodipicolinate reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0046   17.5   0.0      0.058   14.0   0.0    2.4  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.024   15.0   0.3        0.1   13.0   0.1    2.2  2  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
       0.12   13.0   0.0       0.31   11.8   0.0    1.7  1  CoA_binding    CoA binding domain


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 !   14.0   0.0   9.7e-06     0.058       3      69 ..       3      67 ..       3      92 .. 0.87
   2 ?    0.6   0.0      0.14   8.6e+02      37      52 ..     107     122 ..     104     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.7e-06
                                      EEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH.H-SEEEE-S CS
                     F420_oxidored  3 gii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae.eadvvvlav 69
                                      ++i G+G +g+ +a+ ++++g    ++v a + np+ + +  +++g++ +a + +  ++ e dvv+l+ 
  gi|488599823|ref|YP_007906294.1|  3 AVIyGFGPIGRLIAECCVKKG---INVVGAVDINPNLIGKRLSDFGIDSSA-EISSKLDfEGDVVFLST 67
                                      6788*****************...****999***************99999.444444459*****985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.14
                                       CCHHHHHHHHC-EEEC CS
                     F420_oxidored  37 ekaeelaeelgvkvta 52 
                                       ek+++la+e+gv+v +
  gi|488599823|ref|YP_007906294.1| 107 EKIDALAKEYGVTVLG 122
                                       899999****998876 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 ?   13.0   0.1   1.7e-05       0.1       3      32 ..       3      31 ..       1      49 [. 0.80
   2 ?   -2.5   0.0       1.1   6.5e+03      87      99 ..      59      71 ..      44      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                      EEEESTSHHHHHHHHHHHHHTTCEEEEEE- CS
                           Gp_dh_N  3 vainGfGRIGrlvlralleekelevvaind 32
                                       +i+GfG IGrl++  ++++  ++vv   d
  gi|488599823|ref|YP_007906294.1|  3 AVIYGFGPIGRLIAECCVKK-GINVVGAVD 31
                                      68************999965.677776555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                      TSSEEEE-SSS-- CS
                           Gp_dh_N 87 gvdlVvestGvft 99
                                      + d+V+ stG f 
  gi|488599823|ref|YP_007906294.1| 59 EGDVVFLSTGSFV 71
                                      5689999999986 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.1e-05      0.31       6      75 ..       3      70 ..       1      90 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                      EEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHH CS
                       CoA_binding  6 viviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesa 75
                                       +++G+g  g+ ++ + +k+  +++++ ++++np+ +g+  ++  +  s +e++ k++ +  v++++  s 
  gi|488599823|ref|YP_007906294.1|  3 AVIYGFGPIGRLIAeCCVKK--GINVVGAVDINPNLIGKRLSDFGID-SSAEISSKLDFEGDVVFLSTGSF 70
                                      57999999988877666665..5669********************9.********998888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1826.55
//
Query:       gi|488599824|ref|YP_007906295.1|  [L=430]
Description: pyridoxal-phosphate dependent TrpB-like enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-40  137.9   0.0    5.6e-40  137.6   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 !  137.6   0.0   3.1e-44   5.6e-40       5     294 .]      75     410 ..      71     410 .. 0.84

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 3.1e-44
                                       SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallG 78 
                                        +pTPl+r++rl+k+l++p  +++K+E+  p gS+K ++a+   ++  keg   +  +e+++G++g al +a +l+ 
  gi|488599824|ref|YP_007906295.1|  75 WRPTPLIRAERLEKALKTParIYFKYEGVSPPGSHKPNTAVAQAYYnMKEG-VERLTTETGAGQWGSALCFATKLFD 150
                                       68***************************************9888878888.8999999999*************** PP

                                       -EEEEEEETTS-...HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHHSTTCEE--TT CS
                              PALP  79 lkvtivvpadas...pekvallrllGaevvev..................ggdydeavaaaaelaaegegaylvsqf 134
                                       lk+t+++ + +    p+++ +++ +G evv +                  +g+   a + a e aa++++  +   +
  gi|488599824|ref|YP_007906295.1| 151 LKCTVFMVRISYeqkPYRRVMMETWGGEVVPSpsdrtefgrkilkehpdtPGSLGIAISEAIESAASDDKTKYSLGS 227
                                       ******7777665559****************666666666666555555555666666655666664554444444 PP

                                       TSHHHHHHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHHHSTT..-EEEEEEECTTCGGTTCC...S CS
                              PALP 135 dnptviegygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglkerrpd..vrvigvepegsdalarsl...r 203
                                          +v + ++ iglE ++ql    +k d ++ +vGgG+++aG+++++ ++  +   ++i+vep+ +++l+++    +
  gi|488599824|ref|YP_007906295.1| 228 VLNHVLLHQTVIGLETKKQLEkvdEKADILIGCVGGGSNFAGLCFPFVKDSEKdgSKIIAVEPTACPTLTKGDyryD 304
                                       46678888*********88877779999********************95555579****************93332 PP

                                       ..S.SS..B...................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB- CS
                              PALP 204 agrrvtvpvs..................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregiv 262
                                              +++                  +  a gl+ + +++    l++  + e+ +v++  ++ a  l+a++egi+
  gi|488599824|ref|YP_007906295.1| 305 -----FGDTAgltpllkmytlghdftppPIHAGGLRYHGDAPALCMLVKHGIIEARAVDQVSTFNAGLLFAKTEGII 376
                                       .....22222667779999999999999**********77777777999**************************** PP

                                       B-HHHHHHHHHH..HHHHHHCCTTCEEEEEEE-B CS
                              PALP 263 vepssaaalaal..klreagelkegdrvvviltg 294
                                       + p + +a+ ++  ++++a+e +e+ ++v+ ++g
  gi|488599824|ref|YP_007906295.1| 377 PAPETTHAIRVAidEALKAKEANEERVIVFNFSG 410
                                       ***7777777777*99999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 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:                         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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2897.29
//
Query:       gi|488599825|ref|YP_007906296.1|  [L=553]
Description: anthranilate--CoA ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-92  308.6   0.0    6.4e-92  308.3   0.0    1.0  1  AMP-binding    AMP-binding enzyme
      3e-19   69.8   0.7    1.9e-18   67.2   0.1    2.5  3  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.3   0.0   7.1e-96   6.4e-92       7     422 ..      47     454 ..      40     455 .. 0.90

  Alignments for each domain:
  == domain 1  score: 308.3 bits;  conditional E-value: 7.1e-96
                                       HSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                       AMP-binding   7 ktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                        +  k+a+++   ++++TYr+l++ +nr+A++L+ +Gv+k drV++ ++n+pe +++ ++i+kaGa++vplnp + +
  gi|488599825|ref|YP_007906296.1|  47 GRGRKTAVYF--MDRRVTYRDLYRLSNRIANFLKGIGVEKYDRVGFRMRNMPEAIAVNFGIMKAGAIPVPLNPMWAK 121
                                       45699***99..99********************99***************************************** PP

                                       HHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTT CS
                       AMP-binding  84 eelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpd 159
                                       +e+ ++ +++e+k+++    +e+   +++e  ++ ++ ++viv+d+++l++   + ++e  +e+a  + ++++l+  
  gi|488599825|ref|YP_007906296.1| 122 KEIVHVSNNAEVKAIF-VSGDEKtFGAVKESVPEIKTLSKVIVTDQEDLEDP-FVSFSEIYNESA--KFDPVPLEIG 194
                                       ****************.33345568999999**************9988766.444444444444..557889**** PP

                                       SEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-T CS
                       AMP-binding 160 dlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGatvvllp 235
                                        +a++++TSGTTG PKG+ +  +n++++v+ +   ++ +kl+eddvv   +p+++++g+  ++l+++++Ga v ++p
  gi|488599825|ref|YP_007906296.1| 195 KPAVVLFTSGTTGLPKGCAHFVENVLSAVYLV--GKYvWKLREDDVVGGPAPVSFAMGYGNGCLIPYFHGAGVSIWP 269
                                       ****************************9996..566699*9*********************************** PP

                                       TCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEE CS
                       AMP-binding 236 kdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevl 312
                                        ++      +++++e++++t++ + P++++ +l +++l++  k++dlsslrl+  gge+l +e++ +++++fg  ++
  gi|488599825|ref|YP_007906296.1| 270 MFSVE---NFFKFVEDHGITIFSSLPTAYRLILVNPNLDEYLKKYDLSSLRLCTGGGEALGAETAIKWKEKFGLDIY 343
                                       88873...478*******************997777777445667********9*********************** PP

                                       EEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-.....HHH CS
                       AMP-binding 313 egYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkk.....pea 384
                                       e+ G TE+ ++++  ++  +k+++gs+G+p+pg  +ki+D+et+e+++ ge+G l+++gp+    Y+++     +e+
  gi|488599825|ref|YP_007906296.1| 344 ESLGATEMVHICV-SNTCAPKPVAGSIGWPVPGYIAKIIDPETKEECKAGEVGNLYIKGPTGI-RYWNHptrplDEK 418
                                       ************9.77788889**************************************655.6***955555466 PP

                                       HHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 385 taeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       ++++++  ++w   GD +r de+Gy+++v R +dlik+
  gi|488599825|ref|YP_007906296.1| 419 QKKSVV--DGWNVLGDFVRKDENGYIYFVSRDDDLIKS 454
                                       777777..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 ?   -2.3   0.0       1.1   9.6e+03      32      51 ..       7      28 ..       4      35 .. 0.63
   2 ?   -0.8   0.0      0.37   3.3e+03      47      68 ..     145     166 ..     124     170 .. 0.74
   3 !   67.2   0.1   2.2e-22   1.9e-18       1      76 []     463     544 ..     463     544 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                      EEEE---.---..HHHHHHHHHH CS
                     AMP-binding_C 32 fVvlkdg.sea..leeeLkahvr 51
                                      + v++d  + +  +++e+++++ 
  gi|488599825|ref|YP_007906296.1|  7 YLVPEDTwP-EviIPDEVREYIG 28
                                      778864433.2478888888873 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.37
                                       HHHHHHHT-TTTS-SEEEE-S- CS
                     AMP-binding_C  47 kahvrkelgpyavpkkvvfvde 68 
                                          v++ ++++++ +kv+++d+
  gi|488599825|ref|YP_007906296.1| 145 FGAVKESVPEIKTLSKVIVTDQ 166
                                       5578999999999999998875 PP

  == domain 3  score: 67.2 bits;  conditional E-value: 2.2e-22
                                       HHHHHHHSSTTEEEEEEE-----..TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S-.--B CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpde..vkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvde.lpk 71 
                                       e+E+ l++hpaV e+aV+Gvpd+  v+G++++a++ lk+g+e+   l++++ ++++ ++++y+ p+ ++f +e lp+
  gi|488599825|ref|YP_007906296.1| 463 EIEQPLSQHPAVLECAVIGVPDPegVRGQVVKAVIRLKEGYEPsedLKKDILKYLEGQIAKYKLPRIIEFREEpLPR 539
                                       8**********************99999**********99533346*************************888*** PP

                                       -TTS- CS
                     AMP-binding_C  72 trsGK 76 
                                       t++GK
  gi|488599825|ref|YP_007906296.1| 540 TATGK 544
                                       ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3454.91
//
Query:       gi|488599826|ref|YP_007906297.1|  [L=332]
Description: hypothetical protein Asulf_00271 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00031   20.4   0.0    0.00064   19.3   0.0    1.5  1  RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
     0.0063   16.2   0.3       0.45   10.2   0.0    2.2  2  tRNA_m1G_MT   tRNA (Guanine-1)-methyltransferase


Domain annotation for each model (and alignments):
>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.2e-08   0.00064      52     106 ..     137     186 ..     101     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.2e-08
                      RNA_Me_trans  52 akleleke.sveellkelkevkkekvclLDpkaekelspedaeefdvflfGGIlGd 106
                                       +++e   + s  +++ke+   + ++v+lLDp+ae+  s   +e++d+f++GGI+  
  gi|488599826|ref|YP_007906297.1| 137 QEFERFYSeSTASFIKEK---NFDRVILLDPNAEEVYS---GEKADCFIIGGIVDK 186
                                       444444432666677664...579**********9766...66799*******855 PP

>> tRNA_m1G_MT  tRNA (Guanine-1)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0     5e-05      0.45      81     119 ..     154     191 ..     126     200 .. 0.79
   2 !    4.0   0.1     0.004        36     160     192 ..     237     269 ..     230     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5e-05
                                       GG..GEEEEETTTSSBECCGGTTSSEEEEEESSSSTTCSTT CS
                       tRNA_m1G_MT  81 ke..klvylcgdyegvdervdddkvdeysIGdfVlkggekg 119
                                       k+  ++++l + +e+v    + d+   ++IG++V+k g k+
  gi|488599826|ref|YP_007906297.1| 154 KNfdRVILLDPNAEEVYSGEKADC---FIIGGIVDKTGNKK 191
                                       3344999999***99999988888...*********99876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.004
                                       EHHTEHHHHHHHHHCCCTTTHHHHHHHHHHHSC CS
                       tRNA_m1G_MT 160 tlrglkVpeiLlsgnhakienWrlkealertvp 192
                                        l+g++V e  + ++ +  ++Wrlk++l + ++
  gi|488599826|ref|YP_007906297.1| 237 VLDGIEVEEAIRRVQSNLVARWRLKKELPKITK 269
                                       5799***********************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2215.50
//
Query:       gi|488599827|ref|YP_007906298.1|  [L=252]
Description: CO dehydrogenase maturation factor [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-26   91.1   0.0    7.3e-26   90.7   0.0    1.1  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    1.9e-13   50.4   0.1    2.1e-12   47.1   0.1    2.1  1  ParA          NUBPL iron-transfer P-loop NTPase
    1.1e-10   41.7   0.0    3.1e-10   40.3   0.0    1.7  1  AAA_31        AAA domain
    1.6e-08   34.1   0.3      2e-06   27.2   0.0    2.2  2  ArsA_ATPase   Anion-transporting ATPase
    1.3e-07   31.3   0.0    0.00022   20.8   0.0    2.1  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
    8.2e-06   25.4   0.1    0.00081   18.9   0.0    2.2  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    0.00031   20.5   0.0     0.0013   18.5   0.0    1.9  2  AAA_24        AAA domain
     0.0026   17.6   0.4       0.34   10.7   0.0    2.2  2  AAA_26        AAA domain
     0.0035   17.0   0.5     0.0068   16.1   0.5    1.5  1  SRP54         SRP54-type protein, GTPase domain
     0.0064   16.9   0.0      0.011   16.1   0.0    1.5  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.025   14.4   0.0    1.6  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
      0.014   15.3   0.1      0.037   14.0   0.1    1.7  1  NTPase_1      NTPase
      0.019   13.9   0.0      0.028   13.4   0.0    1.2  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.025   13.9   0.2       0.11   11.7   0.2    1.9  2  MipZ          ATPase MipZ
      0.036   14.0   0.0       0.14   12.1   0.0    1.8  2  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do
      0.057   13.3   0.0       0.11   12.5   0.0    1.4  1  NACHT         NACHT domain
      0.058   13.3   0.0       0.11   12.4   0.0    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.09   11.9   0.6       0.34   10.1   0.6    1.9  2  NB-ARC        NB-ARC domain
        0.1   12.3   0.4       0.94    9.2   0.1    2.0  2  AAA_30        AAA domain
        0.1   12.5   0.1        4.9    7.0   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
       0.12   11.9   0.0       0.17   11.3   0.0    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.12   13.0   0.1       0.37   11.3   0.0    1.8  2  AAA_18        AAA domain
       0.12   12.8   0.3       0.44   11.0   0.0    2.1  3  ABC_tran      ABC transporter
       0.17   11.7   0.0       0.31   10.8   0.0    1.5  1  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.17   11.9   0.0       0.82    9.6   0.0    2.0  2  Mur_ligase_M  Mur ligase middle 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 !   90.7   0.0     1e-28   7.3e-26       2     126 ..       4     228 ..       3     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 1e-28
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +++s+kGGvGKTtl+a La ++a++g++V ++D+D   n+ + + g+e++i+p                        
  gi|488599827|ref|YP_007906298.1|   4 IAVSGKGGVGKTTLTAMLAYLFAKDGYNVTAIDCDSSINLPT-VLGVEEEIKPiseledvieervrgplgtyklnpk 79 
                                       579*************************************99.99******************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|488599827|ref|YP_007906298.1|  80 vddvfeahskknehgirvlalgtiekggegcfcpqnaflrailrhaifkrkdvllldmeagiehlgrgtargvdlli 156
                                       ***************************************************************************** PP

                                       ...........CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...........dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavae 120
                                                  +lkr+ +l+e++g+k       +gvvln++  ++++++l++++ e     +  +lg ip++e +++
  gi|488599827|ref|YP_007906298.1| 157 avvepgmrsfeTLKRIQKLAEDIGIK------KIGVVLNKYIDNESSRKLIDMISE-----RYALLGRIPYNECFIK 222
                                       ************************76......7*********************99.....78************** PP

                                       CCHHTS CS
                                       xxxxxx RF
                              CbiA 121 aparge 126
                                       a+ ++ 
  gi|488599827|ref|YP_007906298.1| 223 ADLENI 228
                                       *99886 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 !   47.1   0.1   2.9e-15   2.1e-12       8     173 ..       5     189 ..       1     210 [. 0.83

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.9e-15
                              ParA   8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee........................ekpeq 60 
                                        +SgKGGVGK+t+++ lA+ +ak g++v  +D D    ++p++lgvee                         +p++
  gi|488599827|ref|YP_007906298.1|   5 AVSGKGGVGKTTLTAMLAYLFAKDGYNVTAIDCD-SSINLPTVLGVEEeikpiseledvieervrgplgtykLNPKV 80 
                                       47********************************.5699*********************99999998876522333 PP

                              ParA  61 sekkliPvea...kgikvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl 134
                                       + + +   ++   +gi+v+ +g++ +   e         +++++ +l+++ ++  D+L++D+  G   e+l      
  gi|488599827|ref|YP_007906298.1|  81 D-DVFEAHSKkneHGIRVLALGTIEK-GGEGCF---CPQNAFLRAILRHAIFKRKDVLLLDMEAGI--EHLGRGTAR 150
                                       3.2333333345699*******9988.555544...3468899*******************7665..899999999 PP

                              ParA 135 plagaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                        ++  + V  p   +++  k+  ++++++ +k +Gvv N
  gi|488599827|ref|YP_007906298.1| 151 GVDLLIAVVEPGMRSFETLKRIQKLAEDIGIKKIGVVLN 189
                                       9999*********************************98 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   4.3e-13   3.1e-10       8     162 ..       7     174 ..       1     184 [. 0.64

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 4.3e-13
                            AAA_31   8 nqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne.iektlyevlieeknikeaiiktkvenldl 83 
                                         KGGvGKTT + +la+ +ak g+ v  +D+D+  n+ t lg+e++    ++l +v+ e+++     +k + +  d+
  gi|488599827|ref|YP_007906298.1|   7 SGKGGVGKTTLTAMLAYLFAKDGYNVTAIDCDSSINLPTVLGVEEEIkPISELEDVIEERVRGPLGTYKLNPKVDDV 83 
                                       57****************************************96554233455555433333333333333333355 PP

                            AAA_31  84 ipssidLaeaeielvelekk...........eeilkell.ekvkdeYDyiiiDcpPsLglltenaLvasdsviipvq 148
                                         ++ +  e  i+++ l +            +  l+ +l +++ ++ D+ ++D+   ++ l +      d +i +v+
  gi|488599827|ref|YP_007906298.1|  84 FEAHSKKNEHGIRVLALGTIekggegcfcpqNAFLRAILrHAIFKRKDVLLLDMEAGIEHLGRGTARGVDLLIAVVE 160
                                       55555555444444433333224555555533335666633466677777777777777777777777777777777 PP

                            AAA_31 149 aeayaleGleqllk 162
                                       +  ++ e+l+++ k
  gi|488599827|ref|YP_007906298.1| 161 PGMRSFETLKRIQK 174
                                       77777777766655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.9e-09     2e-06       4      51 ..       4      51 ..       1      65 [. 0.88
   2 ?    5.2   0.1     0.014        10     210     252 ..     156     198 ..     151     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.9e-09
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS-- CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqkl 51
                                      i v+GKGGVGKtt+ a +a+  ++ g++v  i  D   +l  ++  + 
  gi|488599827|ref|YP_007906298.1|  4 IAVSGKGGVGKTTLTAMLAYLFAKDGYNVTAIDCDSSINLPTVLGVEE 51
                                      889********************************9999988877765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                                       EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSSS CS
                       ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivNkllpeeeqe 252
                                       ++Vv p   s++  +R  k  + +gik   v+ Nk++++e++ 
  gi|488599827|ref|YP_007906298.1| 156 IAVVEPGMRSFETLKRIQKLAEDIGIKKIGVVLNKYIDNESSR 198
                                       67899999999888888888889**************998775 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     3e-07   0.00022       1      41 [.       1      40 [.       1      52 [. 0.87
   2 !    8.5   0.0    0.0017       1.2      97     158 ..     110     172 ..      81     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3e-07
                          CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlspd 41
                                      m  +a++G +GGvG+t+l+a+La+ + + g++v +iD  ++
  gi|488599827|ref|YP_007906298.1|  1 MVKIAVSG-KGGVGKTTLTAMLAYLFAKDGYNVTAIDCDSS 40
                                      66788888.8***************************8665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0017
                          CBP_BcsQ  97 qlaekaeallaalkelk.eqyrwillDlpagasaltrellaladlvllvvepdanchvrLhqq 158
                                       ++++++  l a l++   ++ + +llD+ ag ++l r + +  dl ++vvep + +   L++ 
  gi|488599827|ref|YP_007906298.1| 110 CFCPQNAFLRAILRHAIfKRKDVLLLDMEAGIEHLGRGTARGVDLLIAVVEPGMRSFETLKRI 172
                                       566666666666654334999*******************************99998888775 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 !   18.9   0.0   1.1e-06   0.00081       2      39 ..       3      40 ..       2      68 .. 0.91
   2 ?    4.6   0.0     0.026        19     163     222 ..     170     228 ..     138     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                         Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPk 39
                                      kia+ GkGG+Gk+t ++ l+  +a++g  v  + CD  
  gi|488599827|ref|YP_007906298.1|  3 KIAVSGKGGVGKTTLTAMLAYLFAKDGYNVTAIDCDSS 40
                                      89**********************************75 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.026
                         Fer4_NifH 163 kgiekyaksggvrlgGliinsrkvdde..reliekfaeelgtkvlevvPrdeivrkaelrkk 222
                                       k i+k a+  g++  G++ n + +d+e  r+li+ + e+    +l  +P +e   ka+l++ 
  gi|488599827|ref|YP_007906298.1| 170 KRIQKLAEDIGIKKIGVVLN-KYIDNEssRKLIDMISER--YALLGRIPYNECFIKADLENI 228
                                       6799999*************.767776224566666665..568999999999999988764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.8e-06    0.0013       3      77 ..       2     106 ..       1     112 [. 0.71
   2 ?   -0.5   0.0       1.2   8.6e+02      24      40 ..     130     146 ..     121     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-06
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfp.dieswedfldevvel............ 59 
                                       +ki++ G+ g+GKTtl ++l       g+++  id++ + +   +  ++ +i+ + ++ d ++e             
  gi|488599827|ref|YP_007906298.1|   2 VKIAVSGKGGVGKTTLTAMLaylfakdGYNVTAIDCDSSINLPTVLGVEeEIKPISELEDVIEERvrgplgtyklnp 78 
                                       699*****************9****************9874322222210233444444444444666888888888 PP

                            AAA_24  60 ..........aaeladyktlviDtidel 77 
                                                 +++++++++l + ti++ 
  gi|488599827|ref|YP_007906298.1|  79 kvddvfeahsKKNEHGIRVLALGTIEKG 106
                                       8888888888788888888877777765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                            AAA_24  24 pkplfidtekGlkslda 40 
                                       +++l++d+e+G  +l  
  gi|488599827|ref|YP_007906298.1| 130 KDVLLLDMEAGIEHLGR 146
                                       78999*****9988765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.028        20      11      32 ..      11      32 ..       4      34 .. 0.86
   2 !   10.7   0.0   0.00048      0.34     133     192 ..     157     218 ..     151     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.028
                            AAA_26 11 gvGKTvvslgLvralkrkgvkv 32
                                      gvGKT+++++L++ + + g++v
  gi|488599827|ref|YP_007906298.1| 11 GVGKTTLTAMLAYLFAKDGYNV 32
                                      8************998888877 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00048
                            AAA_26 133 lVargglgtinqllltiealrqknvrvlGvilNkvrnpenvetlekksg..ipvlGvvPylp 192
                                        V+ +g ++++ l    +++ + +++ +Gv+lNk  + e  ++l  +++  + +lG++Py++
  gi|488599827|ref|YP_007906298.1| 157 AVVEPGMRSFETLKRIQKLAEDIGIKKIGVVLNKYIDNESSRKLIDMISerYALLGRIPYNE 218
                                       577777788888888888888999**********99998777777776634699******97 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   9.5e-06    0.0068       4      38 ..       4      38 ..       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.5e-06
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      i++ G  G+GKTt +a La l+ k+g++v  + +D
  gi|488599827|ref|YP_007906298.1|  4 IAVSGKGGVGKTTLTAMLAYLFAKDGYNVTAIDCD 38
                                      788999***********************998888 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-05     0.011      27      63 ..       4      40 ..       3     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      + +sG  GvGK++l  +l+  + kdg  +++ +cd++
  gi|488599827|ref|YP_007906298.1|  4 IAVSGKGGVGKTTLTAMLAYLFAKDGYNVTAIDCDSS 40
                                      579****************888888777799999998 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 ?   14.4   0.0   3.5e-05     0.025       1      46 [.       8      50 ..       8      68 .. 0.80
   2 ?   -3.3   0.0       9.3   6.6e+03      10      36 ..     117     143 ..     116     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtisla 46
                                      G+  +GK+Tl+++L+   ++ g++++ +D+D   s+i +P ++++ 
  gi|488599827|ref|YP_007906298.1|  8 GKGGVGKTTLTAMLAYLFAKDGYNVTAIDCD---SSINLPTVLGVE 50
                                      66789*************************9...566666666665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.3
                            CLP1_P  10 larlLlNyalrkgrkpvyvDlDvGqse 36 
                                       + r +l  a+ k + ++++D+  G  +
  gi|488599827|ref|YP_007906298.1| 117 FLRAILRHAIFKRKDVLLLDMEAGIEH 143
                                       678888889999999999999888655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.1e-05     0.037       1      35 [.       3      37 ..       3      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-05
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                      k++++G+ GvGKtTl   ++ l +++g++v+ + +
  gi|488599827|ref|YP_007906298.1|  3 KIAVSGKGGVGKTTLTAMLAYLFAKDGYNVTAIDC 37
                                      689**************************987665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.9e-05     0.028      31      72 ..       3      42 ..       1      62 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspft 72
                                      ++ + G  G+Gk tl+  l+  +++ G+ v+   +D  s+++
  gi|488599827|ref|YP_007906298.1|  3 KIAVSGKGGVGKTTLTAMLAYLFAKDGYNVTA--IDCDSSIN 42
                                      58899***********************9875..55555554 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00016      0.11       8      39 ..       8      39 ..       2      43 .. 0.91
   2 ?   -0.5   0.0      0.85   6.1e+02      95     143 ..     125     173 ..     114     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                      SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                              MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldl 39
                                       kGG Gk+t +  +a  ++k G +v+aid d 
  gi|488599827|ref|YP_007906298.1|  8 GKGGVGKTTLTAMLAYLFAKDGYNVTAIDCDS 39
                                      69***************************996 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.85
                                       HHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHCCCEEE- CS
                              MipZ  95 dleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdfdllgkvd 143
                                       ++ ++ d++++d     ++l r ++   d l++ +   +  f+ l +++
  gi|488599827|ref|YP_007906298.1| 125 AIFKRKDVLLLDMEAGIEHLGRGTARGVDLLIAVVEPGMRSFETLKRIQ 173
                                       4567889999999999999999999999999988888888888777776 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 ?   12.1   0.0   0.00019      0.14       5      77 ..      12      84 ..       3      88 .. 0.76
   2 ?   -1.0   0.0       1.9   1.4e+03     146     176 ..     155     187 ..     154     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                      E--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N  5 iGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77
                                      +G  t+ a +a++fa+ g++V+ +d+++++       +e++++   e + + ee v+  l + + + +++++ 
  gi|488599827|ref|YP_007906298.1| 12 VGKTTLTAMLAYLFAKDGYNVTAIDCDSSINLPTVLGVEEEIKPISELEDVIEERVRGPLGTYKLNPKVDDVF 84
                                      3444555679*****************9999999999999999888888888888888887777777777665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.9
                                       EEEEEE-TT--HHHHHHHHHHHHHT..T-EEEE CS
                           3HCDH_N 146 LvEvvrgekTseetvatvvelakki..gktpvv 176
                                       L+ vv+    s et++++++la++i  +k  vv
  gi|488599827|ref|YP_007906298.1| 155 LIAVVEPGMRSFETLKRIQKLAEDIgiKKIGVV 187
                                       566777777788999999999999933455555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.11       3      30 ..       4      31 ..       3      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                      +++ G+ G+GKTtL + la + a++ ++
  gi|488599827|ref|YP_007906298.1|  4 IAVSGKGGVGKTTLTAMLAYLFAKDGYN 31
                                      6899*****************9998766 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 ?   12.4   0.0   0.00015      0.11       2      33 ..       4      35 ..       3      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                      +++ gk g GKTtL   l   +++ g++v +i
  gi|488599827|ref|YP_007906298.1|  4 IAVSGKGGVGKTTLTAMLAYLFAKDGYNVTAI 35
                                      67899************************988 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6   0.00048      0.34      23      38 ..       4      19 ..       1      27 [. 0.88
   2 ?   -0.8   0.0         1   7.1e+02     194     249 ..     149     204 ..     127     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                                      EEEEESTTSSHHHHHH CS
                            NB-ARC 23 valvGmgGvGKttlak 38
                                      +a++G+gGvGKttl +
  gi|488599827|ref|YP_007906298.1|  4 IAVSGKGGVGKTTLTA 19
                                      899***********86 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                                       CTT-HHHHHHHHHHHC-TCSCCHHHHHHHHHHCTGCCTS--SSSSSSSHHHHHHHH CS
                            NB-ARC 194 ckGlPlalkvlggllstkktveewkkvlekleskllevekstskslesvasilqls 249
                                        +G  l ++v+   +++ +t+++ +k++e +  k+++v  ++  + es ++++ ++
  gi|488599827|ref|YP_007906298.1| 149 ARGVDLLIAVVEPGMRSFETLKRIQKLAEDIGIKKIGVVLNKYIDNESSRKLIDMI 204
                                       57888888888888888899999999999999999997666666666666666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0013      0.94      22      51 ..       5      34 ..       2      41 .. 0.91
   2 ?    1.2   0.0      0.37   2.7e+02      91     118 ..     155     182 ..     122     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggrvig 51
                                      ++ G  G GKtt+ + l+ +++++g++v +
  gi|488599827|ref|YP_007906298.1|  5 AVSGKGGVGKTTLTAMLAYLFAKDGYNVTA 34
                                      57899*********************9975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                            AAA_30  91 llivDEagmvdtkqlaallkaaekagak 118
                                       l+ v E gm ++++l+++ k ae+ g+k
  gi|488599827|ref|YP_007906298.1| 155 LIAVVEPGMRSFETLKRIQKLAEDIGIK 182
                                       5568899***************998865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0068       4.9     103     120 ..       5      22 ..       2      39 .. 0.86
   2 ?    3.3   0.0     0.094        67      22      76 ..     155     212 ..     127     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0068
                                       EEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase 103 vlvGqSGvGKStLinall 120
                                       ++ G+ GvGK+tL  +l+
  gi|488599827|ref|YP_007906298.1|   5 AVSGKGGVGKTTLTAMLA 22 
                                       678**********98875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.094
                                       EEESTTTT-.-HHHHHHHHHHHHHTT-.EEEEEEE-.GGG--HHHHHHHHHHHHHHTT CS
                       RsgA_GTPase  22 vvslkepel.slnlldrfLvlaeekgi.epvivlnK.iDlleeeeeleelkeelealg 76 
                                       +++++ep + s ++l+r+  lae+ gi ++ +vlnK iD  ++++ ++ ++e+++ lg
  gi|488599827|ref|YP_007906298.1| 155 LIAVVEPGMrSFETLKRIQKLAEDIGIkKIGVVLNKyIDNESSRKLIDMISERYALLG 212
                                       44555565514578999999*******66779****5577777776666666666554 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.17      64     143 ..     158     246 ..     134     252 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                                       S...HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT...SEEEEE--TT CS
                      AP_endonuc_2  64 r...reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekeg...vklalEtlag 134
                                       +     +s++ lkr  +la+++G++ + +      + +++s +  ++ + e+   l+++  +++   +k  lE++++
  gi|488599827|ref|YP_007906298.1| 158 VvepGMRSFETLKRIQKLAEDIGIKKIGVVLN--KYIDNESSRKLIDMISERYALLGRI--PYNecfIKADLENIPP 230
                                       444556789*********************88..999**********************..777767********** PP

                                       TTSSSTC.......HH CS
                      AP_endonuc_2 135 sgvelgd.......ee 143
                                        + e+         ee
  gi|488599827|ref|YP_007906298.1| 231 YELECEFesfkkikEE 246
                                       **99998444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00051      0.37       1      21 [.       4      24 ..       4      65 .. 0.82
   2 ?   -1.4   0.0       4.5   3.2e+03      24      44 ..     194     216 ..     172     243 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00051
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      I+++G+ GvGKttl+  L+ +
  gi|488599827|ref|YP_007906298.1|  4 IAVSGKGGVGKTTLTAMLAYL 24
                                      89*************999665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.5
                            AAA_18  24 f..gvnlrdvakenglllevdpe 44 
                                       +  +++l+d+++e++ ll++ p+
  gi|488599827|ref|YP_007906298.1| 194 NesSRKLIDMISERYALLGRIPY 216
                                       13466777777777777766666 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   0.00062      0.44      13      38 ..       3      28 ..       2      96 .. 0.86
   2 ?   -1.8   0.1       5.7   4.1e+03     118     133 ..     121     136 ..     118     139 .. 0.84
   3 ?   -2.3   0.0       8.4     6e+03      52      70 ..     192     210 ..     169     230 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00062
                                      EEEEEESTTSSHHHHHHHHTTSS--S CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpt 38
                                      k+a+ G+ G GK+tL ++la l  ++
  gi|488599827|ref|YP_007906298.1|  3 KIAVSGKGGVGKTTLTAMLAYLFAKD 28
                                      58999**************9887654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.7
                                       HHHHHHHHTSSEEEEE CS
                                       xxxxxxxxxxxxxxxx RF
                          ABC_tran 118 alarallkkpkllllD 133
                                        l  a++k++++lllD
  gi|488599827|ref|YP_007906298.1| 121 ILRHAIFKRKDVLLLD 136
                                       5667999********9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.4
                                       B-HHHCCHCEEEE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  52 qeleslrkeigvlpqepql 70 
                                       ++ es+rk i ++++   l
  gi|488599827|ref|YP_007906298.1| 192 IDNESSRKLIDMISERYAL 210
                                       5666677777776666544 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   0.00043      0.31       1      36 [.       6      41 ..       6      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      v G  G+GKtt++  l+ ++ + g++v  +  D   
  gi|488599827|ref|YP_007906298.1|  6 VSGKGGVGKTTLTAMLAYLFAKDGYNVTAIDCDSSI 41
                                      78999***********************99998754 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0011      0.82       3      40 ..      10      52 ..       9      65 .. 0.72
   2 ?   -0.6   0.0       1.5   1.1e+03      52      77 ..     135     159 ..     120     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                      SSS-HHHHHHHHHHHHHCT.EEEEETTC....SS-THHHHHHH CS
                      Mur_ligase_M  3 GtnGKTTtteliaaileka.gkvigtvg....ttnneiglpkt 40
                                      G  GKTT t ++a +++k  ++v+++      ++++ +g+ + 
  gi|488599827|ref|YP_007906298.1| 10 GGVGKTTLTAMLAYLFAKDgYNVTAIDCdssiNLPTVLGVEEE 52
                                      778*************999344444444666666666666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                                       EEEE--HCHHHCTTTCCHCBESEEEE CS
                      Mur_ligase_M  52 avlEvsshglgekrlegllkpdvavi 77 
                                       + +E++ ++lg +  +g ++  +av+
  gi|488599827|ref|YP_007906298.1| 135 LDMEAGIEHLGRGTARG-VDLLIAVV 159
                                       55777777777776666.66666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1741.79
//
Query:       gi|488599828|ref|YP_007906299.1|  [L=84]
Description: hypothetical protein Asulf_00273 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-05   25.2   0.0    1.6e-05   24.8   0.0    1.1  1  HTH_45       Winged helix-turn-helix
    5.4e-05   23.0   0.0    6.3e-05   22.8   0.0    1.1  1  tRNA_bind_2  Possible tRNA binding domain
    0.00026   21.0   0.0    0.00037   20.5   0.0    1.2  1  HTH_20       Helix-turn-helix domain
    0.00086   19.3   0.3     0.0014   18.7   0.3    1.4  1  HemN_C       HemN C-terminal domain
  ------ inclusion threshold ------
      0.034   14.2   0.1      0.047   13.8   0.1    1.2  1  DUF5457      Family of unknown function (DUF5457)
      0.055   13.1   0.1      0.073   12.7   0.1    1.3  1  HTH_53       Zap  helix turn helix N-terminal domain
       0.13   12.7   0.0       0.18   12.3   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 !   24.8   0.0   6.2e-09   1.6e-05      24      67 ..      39      82 ..      24      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.2e-09
                            HTH_45 24 kimykanLsykllnkYLdmLvekglikkskekYvlTekGlelle 67
                                       + ++ nLs  +l+  Ld L+++g++ ++++k +lTe G elle
  gi|488599828|ref|YP_007906299.1| 39 DLKKELNLSEFQLKFNLDWLIKEGFVVEEEGKLRLTEDGIELLE 82
                                      567899************************************97 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 !   22.8   0.0   2.5e-08   6.3e-05      98     135 ..      15      51 ..       5      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.5e-08
                                       STTTS-SSSSSSHHHHHHTT---HHHHHHHHT--SSHH CS
                       tRNA_bind_2  98 keevkLsavqsaiLlaiGLQrksvddlekeLnlpsnQv 135
                                         + ++s  ++ i+ aiG+Q k ++dl+keLnl++ Q+
  gi|488599828|ref|YP_007906299.1|  15 F-KASMSPYRRQIVAAIGVQGKALEDLKKELNLSEFQL 51 
                                       4.6899****************************9997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.4e-07   0.00037       2      56 ..      13      66 ..      12      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.4e-07
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ++++A  +P Rr i +a+ + +g  +++l+++l ls  +l ++L+ L + g+v  
  gi|488599828|ref|YP_007906299.1| 13 RLFKASMSPYRRQIVAAI-GVQGKALEDLKKELNLSEFQLKFNLDWLIKEGFVVE 66
                                      689***************.******************************999754 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   5.4e-07    0.0014      23      65 ..      37      78 ..      32      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.4e-07
                            HemN_C 23 laafeqrfgldleellaaaleklqeqGLLeldggrlrltprGr 65
                                      l++++ + +l+    l+++l++l+++G+++ ++g+lrlt+ G+
  gi|488599828|ref|YP_007906299.1| 37 LEDLKKELNLSEF-QLKFNLDWLIKEGFVVEEEGKLRLTEDGI 78
                                      5677777777723.3499**********************997 PP

>> DUF5457  Family of unknown function (DUF5457)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.8e-05     0.047      35      67 ..      42      74 ..      33      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                           DUF5457 35 kdlkvtErqvrevLdwLVkkkkvleklgkYqld 67
                                      k+l+++E+q++  LdwL+k+  v+e+ gk  l 
  gi|488599828|ref|YP_007906299.1| 42 KELNLSEFQLKFNLDWLIKEGFVVEEEGKLRLT 74
                                      6789**********************9998775 PP

>> HTH_53  Zap  helix turn helix N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.9e-05     0.073      18      51 ..      36      69 ..      25      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                            HTH_53 18 aLeeLlgeveLseaqLkevLeeAGpeRFllletg 51
                                      aLe+L++e++Lse qLk  L     e F++ e+g
  gi|488599828|ref|YP_007906299.1| 36 ALEDLKKELNLSEFQLKFNLDWLIKEGFVVEEEG 69
                                      79***************99998888888887766 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 ?   12.3   0.0   7.2e-05      0.18      11      68 .]      29      77 ..      20      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-05
                            HTH_27 11 lirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       i+  + +k+l+dl + ln++  +   +l+ L++ G+v++++ +       +rlT+ G
  gi|488599828|ref|YP_007906299.1| 29 AIG--VQGKALEDLKKELNLSEFQLKFNLDWLIKEGFVVEEEGK-------LRLTEDG 77
                                      555..78999****************************877776.......9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 516.92
//
Query:       gi|488599829|ref|YP_007906300.1|  [L=285]
Description: succinyl-CoA synthetase (ADP-forming) alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  100.6   4.6    7.7e-29  100.2   0.3    2.7  3  CoA_binding    CoA binding domain
    1.1e-15   57.6   0.1    3.4e-15   56.0   0.0    1.9  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.9e-14   53.7   0.2    3.5e-14   52.9   0.2    1.4  1  Ligase_CoA     CoA-ligase
    4.9e-05   23.8   0.0     0.0003   21.3   0.0    2.1  2  CoA_binding_2  CoA binding domain
  ------ inclusion threshold ------
      0.092   13.6   0.0        0.4   11.5   0.0    2.1  4  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.3   2.1e-32   7.7e-29       1      96 []       6      98 ..       6      98 .. 0.98
   2 ?    1.5   0.2      0.14     5e+02      35      94 ..     176     232 ..     144     234 .. 0.53
   3 ?   -2.5   0.0       2.4   8.4e+03      44      51 ..     265     272 ..     246     282 .. 0.52

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 2.1e-32
                                      CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding  1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeav 79
                                      d++t+viv+G++g   +g +++k++l+yg+k+v+gv+p+k+g+ev g+pv+++++e++ + ++++++i+vPa++a++a+
  gi|488599829|ref|YP_007906300.1|  6 DENTRVIVQGITGF--QGSFQTKRMLDYGTKIVGGVSPGKGGQEVYGVPVFNTMEEAMVT-DPNTSIIYVPARFAYDAI 81
                                      689***********..******************************************99.****************** PP

                                      HHHHHTT-SEEEEESST CS
                       CoA_binding 80 delveagikgiviiteg 96
                                      +e+++agi  +v++teg
  gi|488599829|ref|YP_007906300.1| 82 LEALDAGIGFVVCVTEG 98
                                      ***************97 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.14
                                       EC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES..-HHHHHHHHHHHHHTT-SEEEEES CS
                       CoA_binding  35 gvnprkvgtevlglpvyksvdeleektevdvavitv..Paesaqeavdelveagikgiviit 94 
                                       g++    g+ + gl+   +v ++ e+ +++  v+++     +a+e++ e +++  k++ ++ 
  gi|488599829|ref|YP_007906300.1| 176 GIG----GDPIPGLTFV-DVLQMFEEDKETKRVVLIgeIGGNAEEVASEYIKEMSKPVYAFL 232
                                       333....4566666666.33333333233333333323556777777777777777777765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.4
                                       EETTEEEE CS
                       CoA_binding  44 evlglpvy 51 
                                       e  g+ v 
  gi|488599829|ref|YP_007906300.1| 265 EKAGVRVA 272
                                       33344444 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   4.2e+03      43      59 ..      55      71 ..      53      72 .. 0.80
   2 !   56.0   0.0   9.5e-19   3.4e-15       1     135 [.     144     282 ..     144     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                      Succ_CoA_lig 43 adlleylaedpetkvil 59
                                      + + e++ +dp+t++i 
  gi|488599829|ref|YP_007906300.1| 55 NTMEEAMVTDPNTSIIY 71
                                      556689999****9996 PP

  == domain 2  score: 56.0 bits;  conditional E-value: 9.5e-19
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsirdgrkfls.a 74 
                                       pG+++++s SG+l  ++++ +++ g+g s+vv +G      +++ d+l++++ed+etk ++l  E  +++++ +s  
  gi|488599829|ref|YP_007906300.1| 144 PGDVGVVSRSGTLTYQVAENMTKAGIGQSTVVGIGGdpIPGLTFVDVLQMFEEDKETKRVVLIGEIGGNAEEVASeY 220
                                       79*********************************933458****************************99887515 PP

                      Succ_CoA_lig  75 arraarkkpvvvlksGrseagaraaashtgal....agsdavvdaafrqaGvlrvdsleelfdaa 135
                                       +++++  kpv ++ +Gr++   +  + h ga+    +g  +  ++a+++aGv ++++leel+d++
  gi|488599829|ref|YP_007906300.1| 221 IKEMS--KPVYAFLAGRTAPRGKR-MGHAGAIiegfSGTAESKTEALEKAGVRVAKTLEELIDLL 282
                                       66666..**********7654433.456666522227899999*******************987 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.2   9.7e-18   3.5e-14       1     152 [.     150     269 ..     150     270 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 9.7e-18
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++++GtL+y  ++ +++a              g +q++++++G+d  +         + ++ + l+ + +d+e+k +
  gi|488599829|ref|YP_007906300.1| 150 VSRSGTLTYQVAENMTKA--------------GIGQSTVVGIGGDPIP---------GLTFVDVLQMFEEDKETKRV 203
                                       689***************..............***************9.........******************** PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraaka 152
                                       +l +++G g++e++a+e++k++++        pv a++aG +a+ ++++++a+a+ e+   +a+sk++al+ a++
  gi|488599829|ref|YP_007906300.1| 204 VLIGEIG-GNAEEVASEYIKEMSK--------PVYAFLAGRTAPRGKRMGHAGAIIEGFSGTAESKTEALEKAGV 269
                                       *******.**********998754........799***********************************99875 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   8.4e-08    0.0003      32     114 ..      38     127 ..      20     129 .. 0.88
   2 ?   -0.2   0.0      0.38   1.4e+03       6      35 ..     147     177 ..     147     228 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.4e-08
                                       EESSS-..SEETTEES----T.....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHT CS
                     CoA_binding_2  32 pVnpke..eeilgekvyaslaed.pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeea 101
                                        V p +  +e+ g++v+ +++e+ ++++ +  +++p+  + + + eal++g+  v++  +     e+ ++  +++++
  gi|488599829|ref|YP_007906300.1|  38 GVSPGKggQEVYGVPVFNTMEEAmVTDPNTSIIYVPARFAYDAILEALDAGIGFVVCVTEgvplYEEMKLSWIVRDY 114
                                       58888888*************956***********************************99*988899999999999 PP

                                       T-EEE.ES-HHHH CS
                     CoA_binding_2 102 girvvgdrCilve 114
                                       +  ++g++C++v+
  gi|488599829|ref|YP_007906300.1| 115 NAMLLGPNCPGVI 127
                                       999********97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.38
                                       ET--S-TTSHHHHHHHHHHHHT.--EEEESS CS
                     CoA_binding_2   6 vGasdnpgkfgykvlryllehg.lpvvpVnp 35 
                                       vG+ +++g   y+v++++ ++g  + ++V  
  gi|488599829|ref|YP_007906300.1| 147 VGVVSRSGTLTYQVAENMTKAGiGQSTVVGI 177
                                       6888888888899999998866224444444 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011       0.4       5      90 ..      13      93 ..       9      95 .. 0.75
   2 ?   -3.0   0.0       3.6   1.3e+04      68      87 ..     149     169 ..     147     175 .. 0.72
   3 ?   -3.0   0.0       3.5   1.2e+04      27      43 ..     201     217 ..     186     233 .. 0.56
   4 ?   -3.0   0.0       3.5   1.3e+04      35      56 ..     257     277 ..     236     280 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                      EETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHH CS
                      GFO_IDH_MocA  5 iiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaa 82
                                      + G+ G+ gs + + + +   ++++v+ ++p++  +e     +gv++++ +ee +  ++++  i+ +p++  ++ +++a
  gi|488599829|ref|YP_007906300.1| 13 VQGItGFQGSFQTKRMLDY--GTKIVGGVSPGKGGQEV----YGVPVFNTMEEAMV-TDPNTSIIYVPARFAYDAILEA 84
                                      5555344466666555555..77888888888866663....8*******996555.4899****************** PP

                                      HHTT-.EEE CS
                      GFO_IDH_MocA 83 leagk.hvl 90
                                      l ag+  v+
  gi|488599829|ref|YP_007906300.1| 85 LDAGIgFVV 93
                                      ****96555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                                       E-S-G.GGHHHHHHHHHHTT- CS
                      GFO_IDH_MocA  68 vatpn.gtheelakaaleagk 87 
                                       v++++ ++ +++a+++++ag+
  gi|488599829|ref|YP_007906300.1| 149 VVSRSgTLTYQVAENMTKAGI 169
                                       666663558889999988887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.5
                                       EEEEEECSSHHHHHHHH CS
                      GFO_IDH_MocA  27 evvalldpdaeraeava 43 
                                       + v l+ +   +ae+va
  gi|488599829|ref|YP_007906300.1| 201 KRVVLIGEIGGNAEEVA 217
                                       33333333334444443 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3.5
                                       SHHHHHHHHHHTTHEEESSHHH CS
                      GFO_IDH_MocA  35 daeraeavaesfgveaysdlee 56 
                                        +++ ea+ e+ gv + + lee
  gi|488599829|ref|YP_007906300.1| 257 AESKTEAL-EKAGVRVAKTLEE 277
                                       33333333.5556666555555 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:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1840.54
//
Query:       gi|488599830|ref|YP_007906301.1|  [L=381]
Description: succinyl-CoA synthetase (ADP-forming) beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-65  218.4   4.7    1.2e-64  217.6   4.7    1.4  1  ATP-grasp_2  ATP-grasp domain
    2.5e-17   63.1   0.8    5.5e-17   62.0   0.8    1.6  1  Ligase_CoA   CoA-ligase
      1e-14   54.6   1.0      1e-14   54.6   1.0    1.5  2  ATP-grasp_5  ATP-grasp domain
      2e-07   31.0   1.7      2e-07   31.0   1.7    2.3  3  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
      1e-05   25.2   0.7    2.3e-05   24.0   0.7    1.5  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
    2.4e-05   24.0   0.3    5.4e-05   22.8   0.3    1.5  1  ATP-grasp    ATP-grasp domain
  ------ inclusion threshold ------
      0.015   14.9   0.2      0.026   14.1   0.2    1.3  1  TRIC         TRIC channel
        0.4   10.7   5.7        3.1    7.9   0.1    3.7  4  RRM_3        RNA binding motif


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.6   4.7   5.4e-68   1.2e-64       1     201 [.       2     191 ..       2     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.6 bits;  conditional E-value: 5.4e-68
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellg 77 
                                       +lhEyqakei++++g++vpeg v++s +ea ea+kklg+   v+KaQvl+GGRGKagGvk+v+++e a+e+a+++lg
  gi|488599830|ref|YP_007906301.1|   2 KLHEYQAKEIFKEHGIPVPEGYVVRSVDEAVEAVKKLGKA--VIKAQVLVGGRGKAGGVKVVDDAESAREVASQMLG 76 
                                       69***********************************976..5********************************** PP

                                       SEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB- CS
                       ATP-grasp_2  78 kelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl 154
                                       + ++       G+kve++lve+a+d++kElYl++++D++++k+++i+S+ GG++iEe+a ++Pe i+kv+ dp  gl
  gi|488599830|ref|YP_007906301.1|  77 SMIK-------GHKVEALLVEKAIDVEKELYLAYIVDKTERKPTIIFSKIGGINIEELAREHPESIFKVSYDPLIGL 146
                                       ****.......****************************************************************** PP

                                       -HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                       ATP-grasp_2 155 keeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                       +++++r++++k+g+e+  +k++ + ikk+ ++  +++a+lvEiNP+v
  gi|488599830|ref|YP_007906301.1| 147 QDYHIRKLLFKAGVED--FKEFFSLIKKINEIAWKYEAELVEINPIV 191
                                       **************97..9**************************98 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.8   2.5e-20   5.5e-17       2     152 ..     251     374 ..     250     375 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 2.5e-20
                                       ESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEE CS
                        Ligase_CoA   2 vnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvil 78 
                                        nG++La+ +md+i                 g+++++++d G++           Dp+k+ ++l  +++d++vkv+ 
  gi|488599830|ref|YP_007906301.1| 251 ANGAGLAMTTMDMIAYM--------------GGKPANFLDTGGGLA---------DPEKMKNCLLHVVKDEKVKVVY 304
                                       69***************..............**************9.........9********************* PP

                                       EEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHHH CS
                        Ligase_CoA  79 ldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraaka 152
                                       ++i+  + ++e++a++++ka+ e++   r++++v+ ++G ++d  +++  +k +ee g+ei+  ++ ++ a+ka
  gi|488599830|ref|YP_007906301.1| 305 INIFAEITRCEKVAEGIVKALDEMD---RKVVLVVKLVGVNED-IGREILKKYMEEKGAEIYFVNTLEEGARKA 374
                                       ************************9...***************.7889999**********9999988887776 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   1.0   4.5e-18     1e-14      10     220 ..       3     204 ..       1     205 [. 0.91
   2 ?   -3.7   0.0       2.9   6.5e+03      35      51 ..     318     334 ..     307     339 .. 0.71

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 4.5e-18
                       ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeile 86 
                                       L e++ake+++  gipv+e  +++s++eavea++++g + v+K ++  +  + ++gGv++ ++dae+ r+ a+++l 
  gi|488599830|ref|YP_007906301.1|   3 LHEYQAKEIFKEHGIPVPEGYVVRSVDEAVEAVKKLG-KAVIKAQVL-VGGRGKAGGVKV-VDDAESAREVASQMLG 76 
                                       89**********************************9.778998864.7899********.**************** PP

                       ATP-grasp_5  87 rvkekspeariegvlVqemakrggrElivgvteDpv.FGpvilfGl.GGtavevlkdvavalpplnstlareliert 161
                                       ++ +   ++++e +lV++  +  + El + +  D++   p i+f   GG+ +e l+  + +     s +    ++  
  gi|488599830|ref|YP_007906301.1|  77 SMIK---GHKVEALLVEKAID-VEKELYLAYIVDKTeRKPTIIFSKiGGINIEELAREHPESIFKVSYDPLIGLQDY 149
                                       *977...99**********99.8999999998887626899999977********9999777766666666677*** PP

                       ATP-grasp_5 162 kaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDari 220
                                       ++ kll +   e   d +++ +l+ ++ +++ +  e + ++inP++ ++eg+ a+Da+i
  gi|488599830|ref|YP_007906301.1| 150 HIRKLLFKAGVE---DFKEFFSLIKKINEIAWK-YEAELVEINPIVKTKEGLYAVDAVI 204
                                       *******98888...*****************9.577999*****************98 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.9
                       ATP-grasp_5  35 aeeaveaaeeigypvvl 51 
                                       ae  v+a +e++ +vvl
  gi|488599830|ref|YP_007906301.1| 318 AEGIVKALDEMDRKVVL 334
                                       55677888888888876 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 !   31.0   1.7   8.8e-11     2e-07       6     106 ..       8     111 ..       4     117 .. 0.87
   2 ?   -3.0   0.0       2.4   5.3e+03      41      60 ..     189     209 ..     153     211 .. 0.64
   3 ?   -0.8   0.4      0.51   1.1e+03      30      62 ..     322     355 ..     293     379 .. 0.61

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 8.8e-11
                                       HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT....-EEEESSHHHHHHHHHHHCTS-TTCC CS
                            GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagK....gvivakseeealkavkeilekkkfGe 78 
                                       ak+++k++gip +e  ++ +++ea e ++++++   V+Ka+ l +g+    gv+v++++e a ++++++l +   G+
  gi|488599830|ref|YP_007906301.1|   8 AKEIFKEHGIPVPEGYVVRSVDEAVEAVKKLGKA--VIKAQVLVGGRgkagGVKVVDDAESAREVASQMLGSMIKGH 82 
                                       79***************************99875..6*******99744556************************* PP

                                       CCSSEEEEE---SE.EEEEEEEECTTEEE CS
                            GARS_A  79 agekvviEelleGe.Evsllalvdgktvk 106
                                         e +++E+ ++ e E+ l  +vd ++ k
  gi|488599830|ref|YP_007906301.1|  83 KVEALLVEKAIDVEkELYLAYIVDKTERK 111
                                       *********99864277777777776655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                                       EEEE.ESC-GGGT-EEEESSH CS
                            GARS_A  41 lVvK.adglaagKgvivakse 60 
                                        +vK  +gl a   vi+a+++
  gi|488599830|ref|YP_007906301.1| 189 PIVKtKEGLYAVDAVIIADDN 209
                                       344414688888888887765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.51
                                       HHHHHHHSSSE.EEEEESC-GGGT-EEEESSHHH CS
                            GARS_A  30 keyieeataka.lVvKadglaagKgvivakseee 62 
                                        + ++e++ k+ lVvK +g+    g  + k+ +e
  gi|488599830|ref|YP_007906301.1| 322 VKALDEMDRKVvLVVKLVGVNEDIGREILKKYME 355
                                       3445555555446677666666665555544443 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 !   24.0   0.7     1e-08   2.3e-05       4     104 ..       7     108 ..       5     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-08
                                       HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTT....EEEESSHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   4 sakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkG....mrvarneeelaelvkkalaeaka 76 
                                       +ake+ k+ ++pv ++  +  ++++ea++++k++g  v ika + +GG+G     +v+++ e  +e++++ l     
  gi|488599830|ref|YP_007906301.1|   7 QAKEIFKEHGIPVPEGYVV--RSVDEAVEAVKKLGKAV-IKAQVLVGGRGkaggVKVVDDAESAREVASQMLGSMIK 80 
                                       689999**********999..**************876.7********96333369****************99999 PP

                                       HHSTS-EEEEE--SSSEEEEEEEEEETT CS
                       CPSase_L_D2  77 afgnkqvlvekslkgpkeiEvevlrDak 104
                                           + +lvek ++  ke+ +  + D++
  gi|488599830|ref|YP_007906301.1|  81 GHKVEALLVEKAIDVEKELYLAYIVDKT 108
                                       9****************99888888776 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.3   2.4e-08   5.4e-05       2      81 ..      13     102 ..      12     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.4e-08
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTT..TEEEECTCCGHHCHHHHC........GTTCEEE CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGk..Gqsvvrseedleqaleal........keekviv 68 
                                       +++g+pvp+ ++v+s +e+ ea+++lg  v+  +  +g  Gk  G +vv ++e+++++++++        k e ++v
  gi|488599830|ref|YP_007906301.1|  13 KEHGIPVPEGYVVRSVDEAVEAVKKLGKAVIKAQVLVGGRGKagGVKVVDDAESAREVASQMlgsmikghKVEALLV 89 
                                       799************************76544455668888877899**********999999****9988999*** PP

                                       EE----SEEEEEE CS
                         ATP-grasp  69 EefvpfekElsvl 81 
                                       E+ ++ ekEl + 
  gi|488599830|ref|YP_007906301.1|  90 EKAIDVEKELYLA 102
                                       *********8554 PP

>> TRIC  TRIC channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.2e-05     0.026      74     125 ..     299     352 ..     288     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                       HHHHH.HHHHHHHHHHHHHHHHHHHHHHHS.TT-HHHHHHHHHHHHHTHHHHHH CS
                              TRIC  74 pvklv.laalkevtrakkieaGvshaakvy.pnallvmvlvglvkGaGaellkn 125
                                        vk+v ++   e+tr++k+++G+ +a + + ++ +lv+ lvg+ +  G e+lk+
  gi|488599830|ref|YP_007906301.1| 299 KVKVVyINIFAEITRCEKVAEGIVKALDEMdRKVVLVVKLVGVNEDIGREILKK 352
                                       55554267889*******************4455677789***99999999986 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.21   4.7e+02      54      81 ..      28      55 ..       3      69 .. 0.80
   2 ?    2.3   0.1     0.077   1.7e+02      48      94 ..      62     111 ..      52     118 .. 0.75
   3 ?   -1.3   0.0         1   2.2e+03      15      33 ..     160     178 ..     157     187 .. 0.74
   4 ?    7.9   0.1    0.0014       3.1       2      38 ..     334     371 ..     333     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                                      HHHHHHC-B-CCTSSEEEEE--HHHHHH CS
                             RRM_3 54 lekateaklkikdaevtlelLeGeeEke 81
                                      +++a+ea +k+ +a +++++L G + k 
  gi|488599830|ref|YP_007906301.1| 28 VDEAVEAVKKLGKAVIKAQVLVGGRGKA 55
                                      5678888888999999999999977665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.077
                                       HHHHHHHHHHHHC.-B-CCTSSEEEEE--H..HHHHHHHHHHHHHHHHCC CS
                             RRM_3  48 eeakkalekatea.klkikdaevtlelLeG..eeEkeywkkiledkqkkk 94 
                                       ++a+ a e a ++   +ik ++v++ l+e   + Eke +   ++dk ++k
  gi|488599830|ref|YP_007906301.1|  62 DDAESAREVASQMlGSMIKGHKVEALLVEKaiDVEKELYLAYIVDKTERK 111
                                       34555666555555669*********999766899999888888888876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                                       HHHHHHHCHCCS-ECEEEE CS
                             RRM_3  15 redikellsklgevayvdy 33 
                                       +ed+ke++s + +++ +++
  gi|488599830|ref|YP_007906301.1| 160 VEDFKEFFSLIKKINEIAW 178
                                       5899999998887765555 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0014
                                       -EEEEEE-SSS--HHHHHHHCHCCS.-ECEEEE-TTSS CS
                             RRM_3   2 vilklsGlnkelsredikellsklg.evayvdyekgdk 38 
                                       +++kl G+n+++ re +k+ +++ g e+ +v+  ++ +
  gi|488599830|ref|YP_007906301.1| 334 LVVKLVGVNEDIGREILKKYMEEKGaEIYFVNTLEEGA 371
                                       589********************9999****9766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2442.02
//
Query:       gi|488599831|ref|YP_007906302.1|  [L=395]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  118.9   0.1    4.5e-33  114.3   0.0    2.3  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
      2e-31  109.3   0.1    2.7e-31  108.8   0.1    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.7e-23   82.6   0.1    3.4e-23   81.7   0.1    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    6.3e-05   23.3   0.0    8.5e-05   22.8   0.0    1.2  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.25   10.2   0.0       0.38    9.6   0.0    1.2  1  RdRP_4         Viral RNA-directed RNA-polymerase


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0   1.2e-36   4.5e-33       1     113 []      16     130 ..      16     130 .. 0.95
   2 ?    2.3   0.0     0.073   2.6e+02      37      78 ..     215     256 ..     189     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 1.2e-36
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGH...HHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefp...relwkklaelGllgitvpeeygGagldyleaaivaeelara 74 
                                       tee++ +r +vref+e+e+ p +a++ +++e p   re+  k++elGllg  +peeyg+ g++y+e  ++++e++r+
  gi|488599831|ref|YP_007906302.1|  16 TEEEKLVRNSVREFMENEILPLVADAFHNEE-PlnmREIAPKMGELGLLGAFLPEEYGCPGASYTEFGLICQEVERV 91 
                                       89************************97775.3246899************************************** PP

                                       -HHHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  75 daglalllgvhsslvapailrfGteeqkrryLpklasge 113
                                       d++++++++v s+lv+++i r+G+eeqkr+yLpkla+ge
  gi|488599831|ref|YP_007906302.1|  92 DSSMRSFVAVTSGLVMYPIWRYGSEEQKRKYLPKLAKGE 130
                                       **************************************8 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.073
                                       HHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N  37 wkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                          ++elGl++  vpee    +++ l a + +   ar+++++
  gi|488599831|ref|YP_007906302.1| 215 AGDVGELGLVNCRVPEENRLPEAKSLGAPLSCLNQARYGISW 256
                                       55679**********997666666666666666666655555 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.1   7.5e-35   2.7e-31       8     148 ..     244     384 ..     240     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 7.5e-35
                                       TTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH-------- CS
                     Acyl-CoA_dh_1   8 metlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd 84 
                                       ++ ln+ R ++ ++a+g+a+ ++e+al+y ++rk+fg pl+++qlv+ekl++m  e++  +l +yr+ +++d+gk +
  gi|488599831|ref|YP_007906302.1| 244 LSCLNQARYGISWGAIGAAMDCFETALNYTKDRKQFGVPLASFQLVQEKLVKMFMEITKGQLVAYRLGRLMDEGKAT 320
                                       578************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                     Acyl-CoA_dh_1  85 raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                       + ++s aK     +a+++a+ a +llG++G++ +y+  r++ ++ +   +eGt++i+ +i++r 
  gi|488599831|ref|YP_007906302.1| 321 TEQISFAKKNNVAVARYCARVARELLGANGISLDYSPIRHMANIESVYTYEGTDDIHTLILGRY 384
                                       ************************************************************9985 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.1   9.4e-27   3.4e-23       1      94 [.     134     223 ..     134     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 9.4e-27
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrr 77 
                                       +f+lTEp++Gsd  s++t +a+rdg+e++lnG+K+wi+ a+ia++a+v+ar  + d +++++ f+++r+++g++ ++
  gi|488599831|ref|YP_007906302.1| 134 CFGLTEPNHGSDPGSMET-TAKRDGDEWILNGTKTWISEAGIADIAVVWAR--DVD-DGKVKGFIIERGTKGFQQNE 206
                                       9*****************.99999999************************..666.89****************** PP

                                       ---BSS-TTS-EEEEEE CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvf 94 
                                       i++k  +r  + gel +
  gi|488599831|ref|YP_007906302.1| 207 IKRKGSMRAGDVGELGL 223
                                       *******9999998865 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.4e-08   8.5e-05       2     123 ..     253     364 ..     252     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.4e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       gi+  a+GaA  +++ ++ ++++r++  +g++la ++ +q +l ++ +++   +++ +r  +      ++gk+ t e
  gi|488599831|ref|YP_007906302.1| 253 GISWGAIGAAMDCFETALNYTKDRKQ--FGVPLASFQLVQEKLVKMFMEITKGQLVAYRLGRL----MDEGKA-TTE 322
                                       567779********************..**********************************9....777777.567 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHH CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDa 123
                                       +   a+ + +++++ +++++++l    G++++  ++   R++ ++
  gi|488599831|ref|YP_007906302.1| 323 QISFAKKNNVAVARYCARVAREL---LGANGISLDYSPIRHMANI 364
                                       77777778888888888887766...4666666666555555555 PP

>> RdRP_4  Viral RNA-directed RNA-polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00011      0.38     171     209 ..      13      53 ..       9      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00011
                            RdRP_4 171 qlv.nvnremydsykefvkeeivwlvegs.hddkkledsrl 209
                                       +l+ + ++ + +s++ef+++ei+ lv ++ h+ ++l++ ++
  gi|488599831|ref|YP_007906302.1|  13 ELLtEEEKLVRNSVREFMENEILPLVADAfHNEEPLNMREI 53 
                                       4555778999**************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2611.08
//
Query:       gi|488599832|ref|YP_007906303.1|  [L=324]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-64  216.0   2.0    5.7e-64  215.6   2.0    1.1  1  NRD1_2          NrpR regulatory domains NRD1 and 2
    4.1e-19   68.3   0.5    9.8e-19   67.1   0.1    1.9  2  HTH_12          Ribonuclease R winged-helix domain
     0.0002   21.2   0.2    0.00092   19.0   0.2    2.1  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00038   20.5   0.1      0.013   15.6   0.1    2.9  2  Mrr_N           Mrr N-terminal domain
     0.0027   17.7   0.0     0.0059   16.6   0.0    1.6  1  HTH_20          Helix-turn-helix domain
     0.0059   16.5   0.0      0.019   14.8   0.0    1.9  1  Type2_restr_D3  Type-2 restriction enzyme D3 domain
     0.0066   16.4   0.2       0.45   10.5   0.0    2.9  2  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
      0.037   13.6   0.6       0.86    9.2   0.1    3.0  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.078   13.5   0.0       0.22   12.0   0.0    1.7  1  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
      0.084   12.6   0.0       0.16   11.7   0.0    1.4  1  Ribosomal_S19e  Ribosomal protein S19e
      0.095   12.7   0.2       0.88    9.6   0.0    2.6  2  HTH_11          HTH 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 !  215.6   2.0   3.5e-67   5.7e-64       2     238 .]      82     319 ..      81     319 .. 0.99

  Alignments for each domain:
  == domain 1  score: 215.6 bits;  conditional E-value: 3.5e-67
                                       --HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE..........E CS
                            NRD1_2   2 gfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek..elevpegkv 76 
                                       g +++++e+++++++f +++ kG++ +N++++dk+++e+a++il+ev +s+++vsd++++++e+e+   le+p++k+
  gi|488599832|ref|YP_007906303.1|  82 GEFSERVEYNVFMSNFSIDEFKGTIPTNIAILDKKHYEKAMTILNEVSQSRFIVSDLITVIDESERagYLEIPKNKF 158
                                       7899***************************************************************999******* PP

                                       EEEEE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEE CS
                            NRD1_2  77 giatvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilA 153
                                       ++ +v+++ +d++L k G++++p+ +Gll++e+k p++F+elIsY+gt+++P  +f++++lTsv ++ ++g g ++A
  gi|488599832|ref|YP_007906303.1| 159 AVGIVSNTIFDVILRKYGVVLTPEASGLLHVEKKVPQGFSELISYSGTTLSPGWLFVKSRLTSVFRAEKKGYGDVIA 235
                                       ***************************************************************************** PP

                                       EEEEEETTTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEE CS
                            NRD1_2 154 nlReipvsarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsgl 230
                                       ++R+++v+  + v++ +++++++gi+g+++i+ p e+ +  +++  k+++++++G+n++a+l+e+g++ ei+++++l
  gi|488599832|ref|YP_007906303.1| 236 TIRSFNVHLIDVVKRRVSEIEEKGIRGIISISYPLENHIIQSIN-FKANLIIYAGVNYLAPLQEKGLNPEIHINEQL 311
                                       **************************************999988.99****************************** PP

                                       EEGGGSEE CS
                            NRD1_2 231 idiselkk 238
                                       i+ise+kk
  gi|488599832|ref|YP_007906303.1| 312 IEISEFKK 319
                                       *****985 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.1     6e-22   9.8e-19       1      66 []       7      72 ..       7      72 .. 0.97
   2 ?   -3.8   0.0       7.8   1.3e+04      40      62 ..     253     259 ..     247     261 .. 0.49

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 6e-22
                            HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                      veIL++l+e++ p+++k ia++Lk++g ++  r++Ry+L k+++ glt++  + +r +t kG e L
  gi|488599832|ref|YP_007906303.1|  7 VEILRVLSEAESPLSSKDIADSLKEKGINLEPRTIRYHLSKMDKAGLTQKPVKYKRIITPKGKEVL 72
                                      79************************************************99999*******9876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.8
                            HTH_12  40 rkleergltrrvgyagreltEkG 62 
                                                        e+ EkG
  gi|488599832|ref|YP_007906303.1| 253 S----------------EIEEKG 259
                                       3................455555 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 !   19.0   0.2   5.7e-07   0.00092       4      44 ..       6      53 ..       3      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.7e-07
                                      HHHHHHHHTT..SSEEHHHHHHHHT.....S-HHHHHHHHHHHHHTTS CS
                             HTH_5  4 RlkILklLae..gelcvcelaeelg.....lsqstvShHLkkLreaGL 44
                                       ++IL+ L+e  ++l++ ++a+ l+     l + t+++HL+k+ +aGL
  gi|488599832|ref|YP_007906303.1|  6 VVEILRVLSEaeSPLSSKDIADSLKekginLEPRTIRYHLSKMDKAGL 53
                                      589*******9999*******9985555559****************9 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   7.9e-06     0.013      31      86 ..      17      73 ..       8      74 .. 0.83
   2 ?   -1.4   0.0       1.6   2.6e+03      65      82 ..     243     260 ..     239     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.9e-06
                             Mrr_N 31 f.glseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwkiTekGrevlk 86
                                         ls ++ a  l++   ++  + +++ ++++ kagl ++p + +  iT+kG+evl+
  gi|488599832|ref|YP_007906303.1| 17 EsPLSSKDIADSLKEKGINLEPRTIRYHLSKMDKAGLTQKPVKYKRIITPKGKEVLR 73
                                      4477888888888777677888999******************************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                             Mrr_N  65 gllespkrgvwkiTekGr 82 
                                        l++  kr v +i ekG 
  gi|488599832|ref|YP_007906303.1| 243 HLIDVVKRRVSEIEEKGI 260
                                       6899999******99996 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   3.6e-06    0.0059      13      53 ..       7      53 ..       1      55 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.6e-06
                                      HHHHHHH.STCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTT CS
                            HTH_20 13 rrilraL.araegltaselaerl.....dlskntlsyHLrvLeeagL 53
                                       +ilr L   + +l+ +++a+ l      l + t++yHL ++ +agL
  gi|488599832|ref|YP_007906303.1|  7 VEILRVLsEAESPLSSKDIADSLkekgiNLEPRTIRYHLSKMDKAGL 53
                                      579999989999***********766555*************99**9 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.2e-05     0.019      18      62 ..       9      53 ..       4      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                    Type2_restr_D3 18 ilkylleskkrrsleeikayLklagleEdveTIkDDiqgliniGl 62
                                      il++l+e+++++s ++i   Lk +g++ +  TI+  +  + + Gl
  gi|488599832|ref|YP_007906303.1|  9 ILRVLSEAESPLSSKDIADSLKEKGINLEPRTIRYHLSKMDKAGL 53
                                      9*********************************98888888877 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   0.00027      0.45       7      70 ..       5      76 ..       2      83 .. 0.71
   2 ?    2.5   0.0     0.091   1.5e+02      24      48 ..     277     301 ..     271     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                            HTH_45  7 IiadILeaisegeakkTk..im.....ykanLsykllnkYLdmLvekglikk.skekYvlTekGlelleklk 70
                                      I+++IL+++se e+  ++  i      +  nL+ ++++  L+++ + gl +k  k k  +T kG+e+l++  
  gi|488599832|ref|YP_007906303.1|  5 IVVEILRVLSEAESPLSSkdIAdslkeKGINLEPRTIRYHLSKMDKAGLTQKpVKYKRIITPKGKEVLRRSL 76
                                      66666666665544433212332222256899999**************988688999*********99765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.091
                            HTH_45  24 kimykanLsykllnkYLdmLvekgl 48 
                                       +i  kanL      +YL  L+ekgl
  gi|488599832|ref|YP_007906303.1| 277 SINFKANLIIYAGVNYLAPLQEKGL 301
                                       5778999999999***********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 ?    9.2   0.1   0.00053      0.86       6      46 ..       7      53 ..       3      53 .. 0.79
   2 ?   -1.2   0.1      0.97   1.6e+03      34      46 ..     248     260 ..     247     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00053
                            HTH_24  6 rkILelLqk.nprisqreLAerl.....glSpstvnrrlkrLeeeGl 46
                                       +IL++L + ++ +s +++A+ l     +l p t++++l ++ ++Gl
  gi|488599832|ref|YP_007906303.1|  7 VEILRVLSEaESPLSSKDIADSLkekgiNLEPRTIRYHLSKMDKAGL 53
                                      589999*996777*******875333338999999999999999986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.97
                            HTH_24  34 vnrrlkrLeeeGl 46 
                                       v+rr+ + ee+G+
  gi|488599832|ref|YP_007906303.1| 248 VKRRVSEIEEKGI 260
                                       89*********97 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 ?   12.0   0.0   0.00013      0.22      33      73 ..      21      61 ..      19      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      -HHHHHHHHHHHT-----GGGEE-TT.T-SBSSEEEEEEESS CS
                    Ribosomal_L9_C 33 takdIaealkkklgieidkkkielee.piktlGeyevtvkLh 73
                                      ++kdIa+ lk+k gi+++ + i+ +  ++ + G ++ +vk +
  gi|488599832|ref|YP_007906303.1| 21 SSKDIADSLKEK-GINLEPRTIRYHLsKMDKAGLTQKPVKYK 61
                                      79**********.**********9763488888888777765 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.9e-05      0.16      94     129 ..      39      74 ..      21      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.9e-05
                                       HTTSSS--SSS---SS-HHHHHTHHHHH--SS--S- CS
                    Ribosomal_S19e  94 svirkilqqLeklglvkkekkkgrrltkkGqrlldr 129
                                       + ir+ l +++k+gl +k+ k +r++t+kG++ l r
  gi|488599832|ref|YP_007906303.1|  39 RTIRYHLSKMDKAGLTQKPVKYKRIITPKGKEVLRR 74 
                                       689*************999999*********99976 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00054      0.88       5      25 ..       9      29 ..       7      62 .. 0.74
   2 ?   -1.3   0.0       1.3   2.1e+03      32      44 ..     248     260 ..     246     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00054
                            HTH_11  5 ilelLleargpisgeeLAeeL 25
                                      il+ L ea++p+s++++A+ L
  gi|488599832|ref|YP_007906303.1|  9 ILRVLSEAESPLSSKDIADSL 29
                                      9*****************998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                            HTH_11  32 vrrdIkaLeelgv 44 
                                       v r++ ++ee+g+
  gi|488599832|ref|YP_007906303.1| 248 VKRRVSEIEEKGI 260
                                       8899******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1970.22
//
Query:       gi|488599833|ref|YP_007906304.1|  [L=258]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   34.0   0.1    3.1e-08   33.0   0.1    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
    8.7e-06   25.5   0.0    1.5e-05   24.8   0.0    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
    1.5e-05   24.7   0.0    2.7e-05   24.0   0.0    1.3  1  MarR_2         MarR family
    9.4e-05   22.3   0.0    0.00023   21.1   0.0    1.6  1  HTH_45         Winged helix-turn-helix
    0.00018   21.3   0.0    0.00045   20.1   0.0    1.6  1  MarR           MarR family
     0.0011   18.9   0.0     0.0021   18.0   0.0    1.4  1  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0016   18.6   0.0     0.0033   17.6   0.0    1.6  1  HTH_34         Winged helix DNA-binding domain
     0.0031   17.3   0.0     0.0058   16.4   0.0    1.4  1  LexA_DNA_bind  LexA DNA binding domain
     0.0083   16.2   0.0      0.014   15.4   0.0    1.3  1  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   16.1   0.0       0.02   15.4   0.0    1.4  1  HTH_27         Winged helix DNA-binding domain
      0.012   15.7   0.0      0.027   14.6   0.0    1.5  1  AbiEi_4        Transcriptional regulator, AbiEi antitoxin
      0.014   15.4   0.0      0.025   14.6   0.0    1.4  1  HemN_C         HemN C-terminal domain
      0.019   15.1   0.0      0.038   14.1   0.0    1.5  1  HTH_28         Helix-turn-helix domain
      0.029   14.5   0.1       0.38   10.9   0.0    2.2  2  Mrr_N          Mrr N-terminal domain
       0.03   14.8   0.1      0.055   13.9   0.1    1.5  1  HTH_40         Helix-turn-helix domain
      0.033   14.1   0.0      0.073   13.0   0.0    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.048   13.4   0.0      0.091   12.5   0.0    1.6  1  DUF4364        Domain of unknown function (DUF4364)
      0.076   13.4   0.0       0.17   12.3   0.0    1.6  1  Rrf2           Transcriptional regulator
      0.087   13.1   0.1        5.5    7.4   0.0    3.1  3  Mnd1           Mnd1 HTH domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   3.3e-11   3.1e-08       5      48 .]      12      55 ..       8      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 3.3e-11
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++ I+++L     ++qr++A++ +l+p++++++ k+L++eG+I+
  gi|488599833|ref|YP_007906304.1| 12 RLLIISELVLRKETNQRDIARKFNLTPQAISEHFKELVDEGYIR 55
                                      67788888889999*****************************7 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.6e-08   1.5e-05       4      46 ..      12      55 ..       9      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.6e-08
                                      HHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  4 RlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      Rl I++ L   +e+   ++a++++l++ ++S+H+k L ++G+++
  gi|488599833|ref|YP_007906304.1| 12 RLLIISELVLrKETNQRDIARKFNLTPQAISEHFKELVDEGYIR 55
                                      9999998888799*****************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.9e-08   2.7e-05      10      52 ..      15      55 ..       9      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.9e-08
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      ++ +L  r +   +++++ar+++l+++a+s + k+Lv+ G+++
  gi|488599833|ref|YP_007906304.1| 15 IISELVLRKE--TNQRDIARKFNLTPQAISEHFKELVDEGYIR 55
                                      5666777777..79****************************8 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.5e-07   0.00023      14      68 ..      19      74 ..      11      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.5e-07
                            HTH_45 14 aisegeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlellek 68
                                       + ++e+++  i  k nL+ + +++  + Lv++g+i+  +k+ Y++TekG e l k
  gi|488599833|ref|YP_007906304.1| 19 LVLRKETNQRDIARKFNLTPQAISEHFKELVDEGYIRViHKGFYEVTEKGTEWLTK 74
                                      45588999999*************************666************99875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.7e-07   0.00045      15      49 ..      22      56 ..      11      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.7e-07
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      + + ++ ++a+k+++++ ++++  ++L+++G+i+ 
  gi|488599833|ref|YP_007906304.1| 22 RKETNQRDIARKFNLTPQAISEHFKELVDEGYIRV 56
                                      567899***************************96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-06    0.0021      21      55 ..      24      59 ..       3      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgr 55
                                        +q+++A+  +lt++ +s  ++eL +eg+i+  ++
  gi|488599833|ref|YP_007906304.1| 24 ETNQRDIARKFNLTPQAISEHFKELVDEGYIRvIHK 59
                                      5689***************************96443 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 !   17.6   0.0   3.5e-06    0.0033       2      52 ..      12      63 ..      11      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-06
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev.dkefkg 52
                                      Rl ++s L+  +e + +++  + ++t  ++s h k L + gYi v +k+f +
  gi|488599833|ref|YP_007906304.1| 12 RLLIISELVLRKETNQRDIARKFNLTPQAISEHFKELVDEGYIRViHKGFYE 63
                                      99*****************************************862565554 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.2e-06    0.0058      29      59 ..      28      57 ..      23      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                                      HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyierd 59
                                      r+iar+++l+ p+a+ eh k L   Gyi++ 
  gi|488599833|ref|YP_007906304.1| 28 RDIARKFNLT-PQAISEHFKELVDEGYIRVI 57
                                      99********.*****************975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.5e-05     0.014      12      57 ..      12      57 ..       9      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      R+ i ++L  +++    ++a+ + l+++ +s H+++L++ g+++v 
  gi|488599833|ref|YP_007906304.1| 12 RLLIISELVLRKETNQRDIARKFNLTPQAISEHFKELVDEGYIRVI 57
                                      666777777777777789*************************996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.1e-05      0.02      15      68 .]      21      68 ..       5      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                            HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       r +  ++d++++ n++ ++is+  k+L+  G++   ++       ++++T+kG
  gi|488599833|ref|YP_007906304.1| 21 LRKETNQRDIARKFNLTPQAISEHFKELVDEGYIRVIHK------GFYEVTEKG 68
                                      4566677***************************55555......7*******9 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.8e-05     0.027      17      48 ..      28      64 ..      26      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                           AbiEi_4 17 relea.aGispsa....lrrLvrkGwLvrlrrGvYal 48
                                      r++++  +++p+a      +Lv++G +  +++G+Y +
  gi|488599833|ref|YP_007906304.1| 28 RDIARkFNLTPQAisehFKELVDEGYIRVIHKGFYEV 64
                                      789999*****************************75 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.6e-05     0.025       1      64 [.       5      68 ..       5      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                            HemN_C  1 lspedrleEeiilgLRlreGldlaafeqrfgldleellaaaleklqeqGLL.eldggrlrltprG 64
                                      ls++d+++ +ii  L lr++ + ++++ +f+l+ +++ +   ++l ++G++ ++++g + +t++G
  gi|488599833|ref|YP_007906304.1|  5 LSRKDAMRLLIISELVLRKETNQRDIARKFNLTPQAISEH-FKELVDEGYIrVIHKGFYEVTEKG 68
                                      89*******************************9999777.*********944788999999988 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     4e-05     0.038       2      30 ..      12      42 ..      11      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                            HTH_28  2 Rleii.kllaaGh.svreaArelgisrrtvy 30
                                      Rl ii +l+++ + ++r++Ar+++++++ ++
  gi|488599833|ref|YP_007906304.1| 12 RLLIIsELVLRKEtNQRDIARKFNLTPQAIS 42
                                      66666255778888**************985 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.38   3.6e+02      23      40 ..      26      43 ..      13      47 .. 0.77
   2 ?   10.9   0.0    0.0004      0.38      60      86 ..      47      73 ..      44      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.38
                             Mrr_N 23 irervaerfglseeerae 40
                                       ++ +a++f+l++++ +e
  gi|488599833|ref|YP_007906304.1| 26 NQRDIARKFNLTPQAISE 43
                                      47889********99887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0004
                             Mrr_N 60 yLkkagllespkrgvwkiTekGrevlk 86
                                      +L+ +g++    +g++++TekG e+l 
  gi|488599833|ref|YP_007906304.1| 47 ELVDEGYIRVIHKGFYEVTEKGTEWLT 73
                                      78999*******************996 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.8e-05     0.055       9      44 ..      21      55 ..      15      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-05
                            HTH_40  9 leeglsieeIAkerglkesTIegHLaelieegeeid 44
                                      l++  +  +IA++ +l+++ I +H+ el+ eg+ i 
  gi|488599833|ref|YP_007906304.1| 21 LRKETNQRDIARKFNLTPQAISEHFKELVDEGY-IR 55
                                      467778899**********************98.44 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.8e-05     0.073      17      57 ..      19      59 ..      15      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.8e-05
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      L+ +++ + ++ia++ ++  + + e  ++L+d G+++++++
  gi|488599833|ref|YP_007906304.1| 19 LVLRKETNQRDIARKFNLTPQAISEHFKELVDEGYIRVIHK 59
                                      8999*********************************9975 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.7e-05     0.091      36      71 ..      41      73 ..      30     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.7e-05
                           DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketle 71
                                      +++ ++eLv++g+i++    +k +y++TekG e l 
  gi|488599833|ref|YP_007906304.1| 41 ISEHFKELVDEGYIRV---IHKGFYEVTEKGTEWLT 73
                                      67899**********9...679**********9875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.17      13      57 ..      13      56 ..       1      60 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +l++ ++  ++e  + ++ia+++n+ p+ ++  +++L  +g++++
  gi|488599833|ref|YP_007906304.1| 13 LLIISELVLRKE-TNQRDIARKFNLTPQAISEHFKELVDEGYIRV 56
                                      444333333333.7899**************************97 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0058       5.5      23      46 ..      33      55 ..      26      59 .. 0.85
   2 ?   -1.1   0.0       2.6   2.4e+03      12      33 ..      82     104 ..      78     122 .. 0.71
   3 ?    1.6   0.0      0.38   3.6e+02      11      44 ..     209     247 ..     201     249 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0058
                              Mnd1 23 kekgivsqsVkdvlqsLvdDglve 46
                                      k  + ++q + ++ ++Lvd+g ++
  gi|488599833|ref|YP_007906304.1| 33 K-FNLTPQAISEHFKELVDEGYIR 55
                                      4.67899**************997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                              Mnd1  12 ytlKeleklapk.ekgivsqsVk 33 
                                       ++   ++kl++k    i s  +k
  gi|488599833|ref|YP_007906304.1|  82 FSEELIKKLYSKsIVAIASGDIK 104
                                       55555677777755556655555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.38
                              Mnd1  11 fytlKeleklapk.ekgivs....qsVkdvlqsLvdDgl 44 
                                       f+  Ke+  +a+   +g+++         +l sLvd+gl
  gi|488599833|ref|YP_007906304.1| 209 FFGSKEVCIEASHhGAGVIAvcteSLLDNLLVSLVDEGL 247
                                       677777777777655666541111445567778888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1491.45
//
Query:       gi|488599834|ref|YP_007906305.1|  [L=288]
Description: Deacetylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-36  126.5   1.9    7.2e-25   88.1   0.7    2.8  3  Hist_deacetyl  Histone deacetylase domain
  ------ inclusion threshold ------
      0.048   13.7   0.0       0.22   11.5   0.0    2.0  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 ?    1.8   0.0     0.015   1.3e+02      15      52 ..      37      70 ..      13      74 .. 0.69
   2 !   88.1   0.7   8.1e-29   7.2e-25      85     179 ..      72     165 ..      68     172 .. 0.92
   3 !   34.6   0.0   1.5e-12   1.4e-08     221     305 ..     192     276 ..     181     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.015
                                      HHHT.THHHHCCE.......EE-----HHHHTTTS-HHHHHHHH CS
                                      xxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 15 laesvglldelel......liqpseatkeellkvHskeYlelle 52
                                      l+          +      ++++++++++ +lkvHs e le ++
  gi|488599834|ref|YP_007906305.1| 37 LK----------KkysnieIFESEPVSEDLILKVHSLELLEGVK 70
                                      33..........12233447899*************99998776 PP

  == domain 2  score: 88.1 bits;  conditional E-value: 8.1e-29
                                       TTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  85 pktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDv 161
                                       +++ ++a +++g+v++a ++v+++++++af+++  +gHHa +++  GFC +N+v++a  ++ +k++  r+ai+D D+
  gi|488599834|ref|YP_007906305.1|  72 DTLCSTAWHSAGGVVTATEKVYKSEIRNAFCFIGAGGHHAGRKTFWGFCCFNDVVLAMTNIWEKYGDVRFAIIDTDA 148
                                       56778999**********************************************************88********* PP

                                       S--HHHHHHCTT-TTEEE CS
                                       xxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 162 HhGnGteeafysdpdvlt 179
                                       HhG+Gt e++++++ + +
  gi|488599834|ref|YP_007906305.1| 149 HHGDGTRELIEDKEVL-H 165
                                       ********99876544.3 PP

  == domain 3  score: 34.6 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHHCHHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxx RF
                     Hist_deacetyl 221 eylkvfeeilrpvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnlea 295
                                       ey +++e +  + +++fkPdli    G D+++gd +g++ l+v+ y ++ + l++la+++ + k+v++l+GG +++ 
  gi|488599834|ref|YP_007906305.1| 192 EYPQLVEDFD-RKARNFKPDLIFWYFGHDTHEGD-YGDIGLTVKEYVKIAEILKNLAEEIcNgKLVVVLGGGSSPSI 266
                                       6666666554.55699*****************9.699***********************99*********99998 PP

                                       HHHHHHHHHH CS
                                       xxxxxxxxxx RF
                     Hist_deacetyl 296 laravtavls 305
                                       + ++  av++
  gi|488599834|ref|YP_007906305.1| 267 ATESCLAVIE 276
                                       8888888776 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.5e-05      0.22      30     100 ..     182     273 ..     172     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                       B12-binding  30 eVqllganven.....edivaairaekpdvvglSal.............ltsqleavkelvel.lkrirp..rvkvv 85 
                                       + +++g+n +      ed+ +++r +kpd++   +                +++ +++e+++  +++i +   v v+
  gi|488599834|ref|YP_007906305.1| 182 DASYIGLNPDEypqlvEDFDRKARNFKPDLIFWYFGhdthegdygdiglTVKEYVKIAEILKNlAEEICNgkLVVVL 258
                                       6678999998899999**************88733344446666666666677777777777775555441146667 PP

                       B12-binding  86 vGGahpsldpeetle 100
                                        GG  ps++ e +l+
  gi|488599834|ref|YP_007906305.1| 259 GGGSSPSIATESCLA 273
                                       789999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1784.90
//
Query:       gi|488599835|ref|YP_007906306.1|  [L=81]
Description: hypothetical protein Asulf_00280 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.8   0.8     0.0026   17.7   0.8    1.0  1  DUF4252         Domain of unknown function (DUF4252)
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.013   15.5   0.1    1.1  1  DUF3558         Protein of unknown function (DUF3558)
      0.015   16.0   1.0      0.018   15.8   1.0    1.0  1  DUF2203         Uncharacterized conserved protein (DUF2203)
      0.029   13.3   0.4      0.037   13.0   0.4    1.0  1  PA26            PA26 p53-induced protein (sestrin)
      0.032   13.2   3.1      0.033   13.1   3.1    1.0  1  Trep_dent_lipo  Treponema clustered lipoprotein (Trep_dent_li
       0.07   11.9   0.3      0.077   11.7   0.3    1.0  1  Sarcoglycan_2   Sarcoglycan alpha/epsilon
      0.075   12.9   0.6      0.084   12.8   0.6    1.1  1  Utp13           Utp13 specific WD40 associated domain
        2.6    7.9   7.7       0.35   10.8   4.3    1.3  2  DUF5090         Domain of unknown function (DUF5090)


Domain annotation for each model (and alignments):
>> DUF4252  Domain of unknown function (DUF4252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.8   1.1e-06    0.0026       3      80 ..       4      80 ..       2      81 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                           DUF4252  3 illlllllllslpaaaqsaqaksldklfdkyednenvtsvniskkmlkllsklddeeddkelkellkklksikvltte 80
                                      +l+l+l+l+ +l++++q  ++ + +k  +  e  e+vt+ +++++  k+ +  ++e++ ke+++l+++lks+  lt+e
  gi|488599835|ref|YP_007906306.1|  4 LLALVLMLSILLAGCTQTTETTETQKEVKPAETSEKVTEEKVTEEIQKINDT-AIEQTLKEIEDLTTQLKSLDNLTFE 80
                                      6788888888888888*****************************9999976.6778888************999987 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1     6e-06     0.013       2      35 ..      14      45 ..      13      66 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6e-06
                           DUF3558  2 llaGCssttdGtapaasssassssttsssaapav 35
                                      llaGC++tt++t  +++ +  ++ t+++ ++ +v
  gi|488599835|ref|YP_007906306.1| 14 LLAGCTQTTETT--ETQKEVKPAETSEKVTEEKV 45
                                      8***********..33333333333333333333 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   1.0   7.9e-06     0.018      24      81 ..      19      76 ..       3      80 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.9e-06
                           DUF2203 24 alrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdlea 81
                                      ++++e +e+++e++ a+++++ +e++  e+  +  ++ ie++++eie+l  ++k+l++
  gi|488599835|ref|YP_007906306.1| 19 TQTTETTETQKEVKPAETSEKVTEEKVTEEIQKINDTAIEQTLKEIEDLTTQLKSLDN 76
                                      455666677778888888766665555555555556789****************986 PP

>> PA26  PA26 p53-induced protein (sestrin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   1.6e-05     0.037     159     231 ..       4      75 ..       3      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                              PA26 159 llahfhslasfvfgcglepeldlesskklksasasanekedsseeeeeelerkaaaeaeaevealmermkklq 231
                                       lla +  l+ +  gc  ++e+ ++++ ++k+a +s++ +e++ +ee ++++++a++++ +e+e l++++k+l 
  gi|488599835|ref|YP_007906306.1|   4 LLALVLMLSILLAGCTQTTETTETQK-EVKPAETSEKVTEEKVTEEIQKINDTAIEQTLKEIEDLTTQLKSLD 75 
                                       7999999********99999887776.566666666788899999999******************9999875 PP

>> Trep_dent_lipo  Treponema clustered lipoprotein (Trep_dent_lipo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.1   1.5e-05     0.033       4      86 ..       4      81 .]       1      81 [] 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                    Trep_dent_lipo  4 klifiLiLavLLfsCskevkeqkeeetkvekeakiekksklieeneils..keeededvktPelikeleekkayeeslk 80
                                       l ++L+L++LL  C++      +e t+++ke+k  + s  + e++++   ++ +d+ ++    +ke+e+  +  +sl 
  gi|488599835|ref|YP_007906306.1|  4 LLALVLMLSILLAGCTQ-----TTETTETQKEVKPAETSEKVTEEKVTEeiQKINDTAIEQT--LKEIEDLTTQLKSLD 75
                                      5789***********54.....4444444444444444444466666440033456666655..999999999999999 PP

                    Trep_dent_lipo 81 klrlel 86
                                      +l +e+
  gi|488599835|ref|YP_007906306.1| 76 NLTFEI 81
                                      998876 PP

>> Sarcoglycan_2  Sarcoglycan alpha/epsilon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   3.5e-05     0.077     308     366 ..       5      74 ..       2      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                     Sarcoglycan_2 308 llLlgiLsail..Clqhekl.........keessvekdnpatsdvqlvqysaedkstkkLkslkdpplll 366
                                       l L+++Ls++l  C q  +           e s   +++ +t+++q ++ +a+++++k++ +l      l
  gi|488599835|ref|YP_007906306.1|   5 LALVLMLSILLagCTQTTETtetqkevkpAETSEKVTEEKVTEEIQKINDTAIEQTLKEIEDLTTQLKSL 74 
                                       5678888888766888888899999999878888889999**************9999999998755444 PP

>> Utp13  Utp13 specific WD40 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   3.7e-05     0.084      42      81 ..      24      73 ..       4      76 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                      -..........-STSSSSSHHHHHHHHC--HHHHHHHHHHHHHHHTSTTT CS
                             Utp13 42 e..........eeesitgskevdevlkslskeqleklLkyirdWntnart 81
                                      +          e++++  +++v e +++++++ +e+ Lk i+d  t+ ++
  gi|488599835|ref|YP_007906306.1| 24 TtetqkevkpaETSEKVTEEKVTEEIQKINDTAIEQTLKEIEDLTTQLKS 73
                                      12233445665555555556************************999876 PP

>> DUF5090  Domain of unknown function (DUF5090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       4.5     1e+04     150     154 ..       7      11 ..       2      17 .. 0.40
   2 ?   10.8   4.3   0.00016      0.35       4      41 ..      24      61 ..      18      74 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.5
                           DUF5090 150 liyll 154
                                       l+ +l
  gi|488599835|ref|YP_007906306.1|   7 LVLML 11 
                                       22222 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                           DUF5090  4 entenskekaleekvkkveekvkeqiekieeSklGkkl 41
                                      +++ +++ k +e   k +eekv+e+i+ki+++++ + l
  gi|488599835|ref|YP_007906306.1| 24 TTETQKEVKPAETSEKVTEEKVTEEIQKINDTAIEQTL 61
                                      332233333444556668***************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3435  (0.191589); expected 358.6 (0.02)
Passed bias filter:                     1327  (0.0740142); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 490.57
//
Query:       gi|488599836|ref|YP_007906307.1|  [L=392]
Description: hypothetical protein Asulf_00281 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   11.0   0.1       0.42   11.0   0.1    3.4  4  V-SNARE          Vesicle transport v-SNARE protein N-terminus


Domain annotation for each model (and alignments):
>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3      0.13   2.3e+03      50      75 ..     135     161 ..     111     164 .. 0.67
   2 ?   -1.0   5.2      0.13   2.4e+03      49      76 ..     157     183 ..     153     184 .. 0.85
   3 ?   11.0   0.1   2.4e-05      0.42      54      78 ..     319     343 ..     286     344 .. 0.84
   4 ?   -1.8   0.0      0.23   4.2e+03      47      69 ..     353     375 ..     352     383 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                           V-SNARE  50 nlps.serasykaklreykselkklkk 75 
                                       n+ + +++a++k+  +  k +l+ ++k
  gi|488599836|ref|YP_007906307.1| 135 NMNKnQVKAQFKTAGKMHKVRLQDIQK 161
                                       332247888888888888888887776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.13
                           V-SNARE  49 rnlpsserasykaklreykselkklkke 76 
                                       ++++ + r +y +  r y  +++klkk+
  gi|488599836|ref|YP_007906307.1| 157 QDIQ-KKREQYENEYRYYSENYEKLKKK 183
                                       5665.89*******************95 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 2.4e-05
                           V-SNARE  54 serasykaklreykselkklkkelk 78 
                                       s   syk++l++ ks+l+ +k+el+
  gi|488599836|ref|YP_007906307.1| 319 SLLESYKTRLEDAKSKLEDVKDELN 343
                                       66789******************96 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.23
                           V-SNARE  47 Evrnlpsserasykaklreykse 69 
                                       E+r+   s+ras+ + l+++k  
  gi|488599836|ref|YP_007906307.1| 353 EIREYTLSARASLGEILKDIKIA 375
                                       78888889999999888888855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3071  (0.171287); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 2313.00
//
Query:       gi|488599837|ref|YP_007906308.1|  [L=337]
Description: pyridoxal phosphate synthase yaaD subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-97  322.9  11.0      6e-94  313.6   9.9    2.2  2  SOR_SNZ         SOR/SNZ family
    1.1e-08   34.8  10.0    1.1e-06   28.2   0.2    2.8  3  ThiG            Thiazole biosynthesis protein ThiG
    0.00013   21.2   0.5      0.092   11.8   0.0    2.3  2  Dus             Dihydrouridine synthase (Dus)
     0.0044   16.2   0.9       0.17   11.0   0.0    2.6  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
  ------ inclusion threshold ------
       0.02   13.9   0.5        1.7    7.6   0.0    2.3  2  FMN_dh          FMN-dependent dehydrogenase
      0.031   13.7   5.1       0.11   11.9   0.0    2.4  2  NMO             Nitronate monooxygenase
      0.037   14.2   0.0       0.29   11.4   0.0    2.2  2  Chaperone_III   Type III secretion chaperone domain
      0.041   13.0   0.1       0.43    9.7   0.0    2.4  2  IGPS            Indole-3-glycerol phosphate synthase
      0.085   13.0   0.1        7.4    6.8   0.1    2.3  2  Importin_rep_6  Importin repeat 6
       0.14   12.7   0.0       0.51   10.9   0.0    2.0  2  Peptidase_S66C  LD-carboxypeptidase C-terminal domain


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.6   9.9   3.4e-97     6e-94       3     198 ..      15     211 ..      13     218 .. 0.96
   2 !    8.4   0.0   0.00095       1.7     180     207 .]     228     255 ..     212     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 313.6 bits;  conditional E-value: 3.4e-97
                                       HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
                           SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                                        +k+g+a+m+kgGvimdv+naeqa +ae+aGavavmal++vpadir++ggvarm+dpk+i+ei++av+ipvmak+ri
  gi|488599837|ref|YP_007906308.1|  15 LIKRGFAKMQKGGVIMDVTNAEQAGVAEDAGAVAVMALHKVPADIRAAGGVARMADPKKIEEIMDAVTIPVMAKCRI 91 
                                       68*************************************************************************** PP

                                       T-HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHH CS
                           SOR_SNZ  80 GhfveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveav 156
                                       Gh++ea+ lealgvd+iDesevltpad  +hidk+kf+vpfvcGar+lgea+rri eGaamirtkGeagtG+vveav
  gi|488599837|ref|YP_007906308.1|  92 GHVAEAKALEALGVDMIDESEVLTPADIFFHIDKTKFTVPFVCGARSLGEAVRRIFEGAAMIRTKGEAGTGNVVEAV 168
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHTTS-HHHHHHHHHHHHGGG.HHHHHHHHHT CS
                           SOR_SNZ 157 rhvrkikeeirklkslseeelvalakelkapl.elvkevaelg 198
                                       +h+r i++ i++lk++ e+e++++a++++ ++  l++ v+e++
  gi|488599837|ref|YP_007906308.1| 169 KHIRLINKAISELKRMVETEITRVAENYASAYtRLLTAVREEQ 211
                                       ***************************9887736777777665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00095
                                       HHHHHHGGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 180 lakelkaplelvkevaelgrlpvvnfaa 207
                                       l++ ++  ++++ e+++++rlpvvnfaa
  gi|488599837|ref|YP_007906308.1| 228 LTEIIDGIYKILLEIKDMQRLPVVNFAA 255
                                       5566677899****************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   3.1   0.00029      0.51     119     201 ..      15     108 ..       6     118 .. 0.75
   2 ?   -1.3   0.0      0.59   1.1e+03      70     100 ..     159     191 ..     135     214 .. 0.70
   3 !   28.2   0.2   5.9e-10   1.1e-06     169     225 ..     241     299 ..     234     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00029
                                       HHHTT-EEEEE..E-S-HHHHHH...HHHTT-SEBEEBS...SSTTS----...S-HHHHHHHHHH-SS-BEEES-- CS
                              ThiG 119 LvkeGFevlpY..vsdDlvlarr...leevGcaavmPla...apiGsglGl...lnkealkiiieeakvPvivDAGi 184
                                       L+k GF+ +    v  D+  a++    e++G+ avm l    a i ++ G+   +++++++ i++ +++Pv+    i
  gi|488599837|ref|YP_007906308.1|  15 LIKRGFAKMQKggVIMDVTNAEQagvAEDAGAVAVMALHkvpADIRAAGGVarmADPKKIEEIMDAVTIPVMAKCRI 91 
                                       6666666665322556666666522259********97533378988888622156899****************** PP

                                       -SHHHHHHHHHTT-SEE CS
                              ThiG 185 gspsdaaqamelGadav 201
                                       g+  +a +   lG+d +
  gi|488599837|ref|YP_007906308.1|  92 GHVAEAKALEALGVDMI 108
                                       ****9988888999865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.59
                                       TT-SSHHHHHHHHHHHHHTT..S-SEEEE--BC CS
                              ThiG  70 aGaktaeeAvriarlarevl..etdliklEvia 100
                                       aG+ ++ eAv+  rl  +++   + ++  E+  
  gi|488599837|ref|YP_007906308.1| 159 AGTGNVVEAVKHIRLINKAIseLKRMVETEITR 191
                                       778888888888887666653334566666554 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 5.9e-10
                                       HHHHH-SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 169 iiieeakvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                        i +  ++Pv+  A  G+ +p daa  m+lG+d+v++ + + ++++p + A+a+  av+
  gi|488599837|ref|YP_007906308.1| 241 EIKDMQRLPVVNFAagGVATPADAAFMMQLGMDGVFVGSGIFKSSNPPEYAKAIVEAVQ 299
                                       45666689998654449****************************************97 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0012       2.1      99     200 ..      63      99 ..      31     111 .. 0.55
   2 !   11.8   0.0   5.1e-05     0.092     180     218 ..     246     283 ..     229     321 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                                       EGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHH CS
                               Dus  99 aGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalelakiveaaGaqaltvHgRtraqnyegtadweaI 175
                                       +G a                                                                   ad ++I
  gi|488599837|ref|YP_007906308.1|  63 GGVAR-----------------------------------------------------------------MADPKKI 74 
                                       33333.................................................................4444555 PP

                                       HHHHHH-SS-EEEESS--SHHHHHH CS
                               Dus 176 kevkqavsipviaNGdIkdaedaqa 200
                                       +e+ +av+ipv+a   I ++ +a+a
  gi|488599837|ref|YP_007906308.1|  75 EEIMDAVTIPVMAKCRIGHVAEAKA 99 
                                       5555555555555544444444443 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.1e-05
                                       HH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCC CS
                               Dus 180 qavsipviaNGdIkdaedaqaileetGadgvmigrgalg 218
                                       q+++++ +a G++ ++ da  +++  G+dgv +g g  +
  gi|488599837|ref|YP_007906308.1| 246 QRLPVVNFAAGGVATPADAAFMMQL-GMDGVFVGSGIFK 283
                                       566677789**************99.********99754 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.026        47     132     170 ..      69     108 ..      16     120 .. 0.65
   2 !   11.0   0.0   9.7e-05      0.17     138     179 ..     243     284 ..     226     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.026
                                       --HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEE CS
                              NanE 132 pDfalvkalsea.glkviaeGrintPekakkaieiGvdav 170
                                        D + ++++++a  + v+a  ri   ++ak    +Gvd++
  gi|488599837|ref|YP_007906308.1|  69 ADPKKIEEIMDAvTIPVMAKCRIGHVAEAKALEALGVDMI 108
                                       3444455555542455777777777777777777777665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.7e-05
                                       HHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-H CS
                              NanE 138 kalseaglkviaeGrintPekakkaieiGvdavvvGsaitrl 179
                                       k+++   +   a G + tP+ a+ ++++G+d v vGs i + 
  gi|488599837|ref|YP_007906308.1| 243 KDMQRLPVVNFAAGGVATPADAAFMMQLGMDGVFVGSGIFKS 284
                                       5666666677899************************99764 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2    0.0092        17     200     242 ..      66     109 ..      17     112 .. 0.79
   2 ?    7.6   0.0   0.00092       1.7     207     243 ..     241     277 ..     183     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0092
                                       -TC--HHHHHHHHHHHSSEEEEEE.E-SHHHHHHHHHTTESEEE CS
                            FMN_dh 200 dpsltwddikwlreqtklplvvKG.vltaedakraveaGvdgiv 242
                                        +  + ++i+++ +++ +p++ K  + ++++ak + ++Gvd i 
  gi|488599837|ref|YP_007906308.1|  66 ARMADPKKIEEIMDAVTIPVMAKCrIGHVAEAKALEALGVDMID 109
                                       34558899***************8699**************995 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00092
                                       HHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE CS
                            FMN_dh 207 dikwlreqtklplvvKGvltaedakraveaGvdgivv 243
                                       +ik +++   +++   Gv t++da  ++++G+dg+ v
  gi|488599837|ref|YP_007906308.1| 241 EIKDMQRLPVVNFAAGGVATPADAAFMMQLGMDGVFV 277
                                       56666666667777889*****************998 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   2.8     0.078   1.4e+02     183     210 ..      72      99 ..      20     108 .. 0.58
   2 ?   11.9   0.0   5.9e-05      0.11     180     231 ..     234     285 ..     209     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.078
                               NMO 183 aLvpqvldavdiPviAaGGiidrrgvaa 210
                                       + +++++dav iPv+A   i    + +a
  gi|488599837|ref|YP_007906308.1|  72 KKIEEIMDAVTIPVMAKCRIGHVAEAKA 99 
                                       4478899999999999765555554444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.9e-05
                               NMO 180 glfaLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltkes 231
                                       g  +++ +++d   +Pv+  AaGG+ +  + a ++ lG  gv +g+       s
  gi|488599837|ref|YP_007906308.1| 234 GIYKILLEIKDMQRLPVVnfAAGGVATPADAAFMMQLGMDGVFVGSGIFKS--S 285
                                       55667777888888***877*************************986543..4 PP

>> Chaperone_III  Type III secretion chaperone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.73   1.3e+03      56      84 ..      29      57 ..      23      62 .. 0.85
   2 ?   11.4   0.0   0.00016      0.29       7      52 ..     100     145 ..      95     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.73
                     Chaperone_III 56 ilslnyaskvtlaadaeksvllalyrlpa 84
                                      i+ +  a++  +a da   +++al+++pa
  gi|488599837|ref|YP_007906308.1| 29 IMDVTNAEQAGVAEDAGAVAVMALHKVPA 57
                                      566777899999************99987 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00016
                     Chaperone_III   7 yealGldPlddpallidddlevyfdesdeslellcPlialPddied 52 
                                        ealG+d  d+  +l   d+  ++d+++ ++ ++c  ++l + + +
  gi|488599837|ref|YP_007906308.1| 100 LEALGVDMIDESEVLTPADIFFHIDKTKFTVPFVCGARSLGEAVRR 145
                                       69***********************************999988766 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.15   2.7e+02      61      88 ..      25      52 ..      20     108 .. 0.82
   2 ?    9.7   0.0   0.00024      0.43     201     248 ..     241     288 ..     198     294 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                                      TEESBSS--HHHHHHHHTTT.-SEEEEE CS
                              IGPS 61 kgliredfdpaeiAkkyeeagAsaiSVL 88
                                      kg + +d+  ae+A + e+agA a+  L
  gi|488599837|ref|YP_007906308.1| 25 KGGVIMDVTNAEQAGVAEDAGAVAVMAL 52
                                      7888899999999999999999988655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00024
                                       HHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHH CS
                              IGPS 201 eLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedve 248
                                       e++++ +  v+  a  G++t++d+  + + g++++ vG+ + ++++  
  gi|488599837|ref|YP_007906308.1| 241 EIKDMQRLPVVNFAAGGVATPADAAFMMQLGMDGVFVGSGIFKSSNPP 288
                                       344444455788899**************************9998865 PP

>> Importin_rep_6  Importin repeat 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0041       7.4      31      81 ..     190     242 ..     164     252 .. 0.74
   2 ?    3.8   0.0     0.034        61      51      84 ..     287     320 ..     282     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0041
                    Importin_rep_6  31 kgvsanlsdvyervkereneddeyn..edvdddyddytdedlldeinkslaai 81 
                                         v++n +  y r+     e+  +    + d+ ++dyt  +++d i k l  i
  gi|488599837|ref|YP_007906308.1| 190 TRVAENYASAYTRLLTAVREEQGFAgiSNRDKVFEDYTLTEIIDGIYKILLEI 242
                                       458889999999987766666555422788999**************988766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.034
                    Importin_rep_6  51 ddeynedvdddyddytdedlldeinkslaailka 84 
                                         ey   + + +++y + +++ e++k+l  ++k 
  gi|488599837|ref|YP_007906308.1| 287 PPEYAKAIVEAVQHYDEPEVVAEVSKGLGDAMKG 320
                                       5699************************999985 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00029      0.51      48     113 ..      33      97 ..      26     107 .. 0.75
   2 ?   -2.8   0.0       4.9   8.9e+03      60      94 ..     273     302 ..     271     309 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                       HHHCTSTTGGG--EEEEEE--..G......CC...---HHHHHHHHHT-GGGTTS-EEEEESESSSBS- CS
                    Peptidase_S66C  48 tqlkeagvldkvkGivlGrftkpeek...eeeeekeeykealeevlaeiledlkiPvlynldiGHtspn 113
                                       t+ ++agv +++ ++++   +k++ +   +  +++    + +ee++    +  +iPv++++ iGH  + 
  gi|488599837|ref|YP_007906308.1|  33 TNAEQAGVAEDAGAVAVMALHKVPADiraAGGVARMADPKKIEEIM----DAVTIPVMAKCRIGHVAEA 97 
                                       6778899999999999998888833334555556666677788887....5888***********8765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.9
                                       -EEEEEE--..G...CC...---HHHHHHHHHT-G CS
                    Peptidase_S66C  60 kGivlGrftkpeekeeeeekeeykealeevlaeil 94 
                                        G+ +G+   +    ++++  ey++a+ e+++++ 
  gi|488599837|ref|YP_007906308.1| 273 DGVFVGS--GI---FKSSNPPEYAKAIVEAVQHYD 302
                                       5777773..23...223345677777888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2110.61
//
Query:       gi|488599838|ref|YP_007906309.1|  [L=196]
Description: pyridoxal phosphate synthase yaaE subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-54  184.8   0.1    1.6e-54  184.6   0.1    1.0  1  SNO            SNO glutamine amidotransferase family
    9.1e-11   41.7   0.0      1e-10   41.5   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    3.6e-06   26.9   0.0    7.1e-06   25.9   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    1.6e-05   24.7   0.0    2.2e-05   24.2   0.0    1.2  1  Peptidase_S51  Peptidase family S51
    0.00014   21.8   0.2    0.00021   21.1   0.1    1.5  2  DJ-1_PfpI      DJ-1/PfpI family
  ------ inclusion threshold ------
      0.074   12.8   0.2        1.3    8.7   0.2    2.7  1  Peptidase_C26  Peptidase C26
       0.17   11.6   0.0       0.29   10.8   0.0    1.4  1  ThiJ_like      ThiJ/PfpI family-like
       0.22   10.0   0.0       0.25    9.8   0.0    1.0  1  Ribophorin_II  Oligosaccharyltransferase subunit Ribophorin I


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 !  184.6   0.1   7.3e-58   1.6e-54       1     186 [.       5     195 ..       5     196 .] 0.90

  Alignments for each domain:
  == domain 1  score: 184.6 bits;  conditional E-value: 7.3e-58
                                       EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--E CS
                               SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvv 71 
                                       v+++qG+veehv a+k++             ++   + + da+iiPGGest++skli r  + e++l+ +k++ k+v
  gi|488599838|ref|YP_007906309.1|   5 VVGVQGDVEEHVLAVKRAFDRLgingevEATRKYGIVSNSDAVIIPGGESTTISKLIFRESISEEILDLAKDG-KPV 80 
                                       789**************9866556656555666677899*********************************9.*** PP

                                       EEETHHHHHHCCEETTB....SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTC CS
                               SNO  72 lGtCaGlillskelene....lvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeav 144
                                       +GtCaGlillsk+ +++      + lell+v+v+rnafGrq +sf+ +l++k+++ +f avfiraPvi e++  e v
  gi|488599838|ref|YP_007906309.1|  81 MGTCAGLILLSKHGDEQvektGTQLLELLDVHVRRNAFGRQRESFQVRLEIKGIG-EFDAVFIRAPVITEVG--ERV 154
                                       ***********96544433336778*****************************9.9***************..999 PP

                                       EEEEECTTEEEEEEETTEEEESS-GGGSTTHCHHHHHHHHHH CS
                               SNO 145 kvlyeldgeivvakqkkilatsfhPelaeddirvhdyfveev 186
                                       +vl   d +iv+++ ++il++sfhPel+ d +rvh+yf++++
  gi|488599838|ref|YP_007906309.1| 155 DVLARYDNHIVAVREDNILGLSFHPELTSD-TRVHEYFIKMI 195
                                       9*****99********************98.********986 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   4.7e-14     1e-10      39     122 ..      42     121 ..      22     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.7e-14
                          GATase_3  39 edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglLdiet 115
                                       ++ d+vi+pGg++t+ ++ + re ++ e+i ++a++g+pv+g C+Gl++L+++  +  +v  e++  + l lLd+++
  gi|488599838|ref|YP_007906309.1|  42 SNSDAVIIPGGESTTISKLIFRE-SISEEILDLAKDGKPVMGTCAGLILLSKHGDE--QV--EKTGTQLLELLDVHV 113
                                       669*********99888777777.8***************************9633..23..34599********99 PP

                          GATase_3 116 efek.ekl 122
                                       + +   ++
  gi|488599838|ref|YP_007906309.1| 114 RRNAfGRQ 121
                                       87664344 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   3.2e-09   7.1e-06      31     183 ..      30     191 ..       7     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.2e-09
                                       SHHHHHHH..THHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE....... CS
                            GATase  31 asaeeile..llknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvv....... 93 
                                        + e +++  + +n d+++++gG  +       +e   e i  +++ ++P++G C G+ ll +   ++v+       
  gi|488599838|ref|YP_007906309.1|  30 GEVEATRKygIVSNSDAVIIPGGESTTIsklifRESISEEILDLAKDGKPVMGTCAGLILLSKHGDEQVEktgtqll 106
                                       4455555554689**********998878999877777788888889***********9999999998887777777 PP

                                       .......EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTT CS
                            GATase  94 .......kekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknp 163
                                              +++ ++ +  + +++     +++g   e+++ +    ++++   + + ++v+a+  d+ ++++++e++  
  gi|488599838|ref|YP_007906309.1| 107 elldvhvRRNAFGRQRESFQVRL----EIKGI-GEFDAVFIRAPVITE---VGERVDVLARY-DN-HIVAVREDN-- 171
                                       77777676666788888888887....88999.778888888888898...89999998888.43.699998887.. PP

                                       EEEESSBTTSTTSTTHHHHH CS
                            GATase 164 fvgvQFHPEststpegpell 183
                                       + g+ FHPE ts ++ +e++
  gi|488599838|ref|YP_007906309.1| 172 ILGLSFHPELTSDTRVHEYF 191
                                       9***********99988876 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     1e-08   2.2e-05      41     135 ..       8      96 ..       4     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1e-08
                                       GG-S--HHHHHHHHHHHHTT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT- CS
                     Peptidase_S51  41 vsgdddeyvekvrkaleklglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqgl 117
                                       v gd++e v +v++a+  lg++ ++   ++++   + +    +d++++ GG+   + kl+ ++ + + +++  ++g+
  gi|488599838|ref|YP_007906309.1|   8 VQGDVEEHVLAVKRAFDRLGINGEV--EATRKYGIVSN----SDAVIIPGGESTTISKLIFRESISEEILDLAKDGK 78 
                                       5678888999999999999987654..33455666666....*********************************** PP

                                       EEEEETHHHHTTSSB-GG CS
                     Peptidase_S51 118 vyiGvSAGaivagesiet 135
                                       +++G+ AG i  ++ +  
  gi|488599838|ref|YP_007906309.1|  79 PVMGTCAGLILLSKHGDE 96 
                                       ********9999988765 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 !   21.1   0.1   9.5e-08   0.00021      60     115 ..      42      98 ..       2     113 .. 0.82
   2 ?   -3.7   0.0       4.2   9.4e+03      15      34 ..     149     168 ..     148     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.5e-08
                                       CG-SEEEE--BHHHH.HHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
                         DJ-1_PfpI  60 aeyDalvlpGGragp.erlrenekvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                                       ++ Da+++pGG++    +l   e + e + + a++gk+v   Cag +lL+++g  + 
  gi|488599838|ref|YP_007906309.1|  42 SNSDAVIIPGGESTTiSKLIFRESISEEILDLAKDGKPVMGTCAGLILLSKHGDEQV 98 
                                       567********9843266777889999999**********************97555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.2
                                       HHHHHHHHHHHTTEEEEEEE CS
                         DJ-1_PfpI  15 Elivpvdvlkragikvdvvs 34 
                                       E+ + vdvl+r + ++++v 
  gi|488599838|ref|YP_007906309.1| 149 EVGERVDVLARYDNHIVAVR 168
                                       66677888888888887776 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0006       1.3     102     216 .]      74     180 ..      25     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0006
                     Peptidase_C26 102 lergvPilgiCrGlqllnvalGGtlyqdiee.qsgltdhreheqsaashavkvekgsllaellgseeievnslHhqa 177
                                        + g+P++g+C Gl ll    G + +++  +   +l d +  ++ + +++ +++    ++   g  e++   +    
  gi|488599838|ref|YP_007906309.1|  74 AKDGKPVMGTCAGLILL-SKHGDEQVEKTGTqLLELLDVHVRRNAFGRQRESFQVRLEIK---GIGEFDAVFIRAPV 146
                                       57789999999999999.444444444433213344444333333333333333222222...23446666666778 PP

                     Peptidase_C26 178 ikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       i+e++e++ v A+  D+ i a++  +    +lg+ +HPE
  gi|488599838|ref|YP_007906309.1| 147 ITEVGERVDVLARY-DNHIVAVREDN----ILGLSFHPE 180
                                       88999999988875.77777887776....889999998 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.29      84     143 ..      43      95 ..      23     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                         ThiJ_like  84 eydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakp 143
                                       + d+v +pGG+  ++ +l+  e++++ + +      ++    k +  +c g + l++  +
  gi|488599838|ref|YP_007906309.1|  43 NSDAVIIPGGESTTISKLIFRESISEEILDLA----KD---GKPVMGTCAGLILLSKHGD 95 
                                       349***********************999877....33...3555556777777766555 PP

>> Ribophorin_II  Oligosaccharyltransferase subunit Ribophorin II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00011      0.25     209     301 ..      85     182 ..      51     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                     Ribophorin_II 209 rGilklakavkkkpaiteeqvvkLanyllsrksvqsvkdafnl...vealkvLssnkfsiPvvvslegka..slstk 280
                                       +G++ l+k+ +++ + t  q+++L ++ ++r  ++  ++ f++   ++++  ++   + +Pv+ +  +++    + +
  gi|488599838|ref|YP_007906309.1|  85 AGLILLSKHGDEQVEKTGTQLLELLDVHVRRNAFGRQRESFQVrleIKGIGEFDAVFIRAPVITEVGERVdvLARYD 161
                                       6899999**********************************9977789999999999******77777775477789 PP

                     Ribophorin_II 281 kpllkvrvtnvlgkplpaelt 301
                                       + ++ vr  n+lg +  +elt
  gi|488599838|ref|YP_007906309.1| 162 NHIVAVREDNILGLSFHPELT 182
                                       99***********99988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 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:                        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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1123.31
//
Query:       gi|488599839|ref|YP_007906310.1|  [L=251]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-48  163.6   0.0    6.2e-48  163.4   0.0    1.0  1  DUF169    Uncharacterised ArCR, COG2043


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.0   3.5e-52   6.2e-48       2     206 .]      10     212 ..       9     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 3.5e-52
                            DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklks 78 
                                       +++ lr++t+P++  f+++k+e+pek   i++   +Cq+ +lar++g+tv+f+ +t+ Cp G +a+Gf e++e + s
  gi|488599839|ref|YP_007906310.1|  10 IERYLRVQTFPLGFRFVKSKEEVPEKARVIPD-IAICQAYNLARKYGWTVYFDINTT-CPLGIVAYGFAEPDELYNS 84 
                                       7889********************99875443.3**********************9.******************* PP

                            DUF169  79 g.....egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvs 150
                                       g     +gy +++++a +f +++p+l a+ ++++vvapL++++ e+d+vv+++np+q++rLv+++l+d+gg  ++ +
  gi|488599839|ref|YP_007906310.1|  85 GklaydAGYAETMDVAPAFEDAVPKL-AERFEGCVVAPLNRCS-EVDFVVVYGNPAQILRLVHAVLHDKGG-AFETK 158
                                       ************************99.7889***********9.5************************99.9**** PP

                            DUF169 151 fpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemven 206
                                       + g   aCa++   +y e++p++ ++++g+r f+ ++dde+af++Pye+ ++++en
  gi|488599839|ref|YP_007906310.1| 159 ILG-RGACAEFL-EAYIEKKPRLVIPCYGDRLFGLTQDDEIAFSFPYEMGQKIAEN 212
                                       ***.7******9.***************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 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:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1615.34
//
Query:       gi|488599840|ref|YP_007906311.1|  [L=151]
Description: Deoxycytidylate deaminase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  107.2   1.6    3.8e-31  107.0   1.6    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.8e-23   82.8   0.5    2.4e-23   82.4   0.5    1.1  1  MafB19-deam      MafB19-like deaminase
    3.8e-05   23.8   0.5    7.5e-05   22.8   0.5    1.6  1  Bd3614-deam      Bd3614-like deaminase
     0.0076   16.1   1.6      0.097   12.5   1.6    2.5  1  Inv-AAD          Invertebrate-AID/APOBEC-deaminase
      0.009   15.9   0.4      0.017   15.0   0.4    1.5  1  APOBEC_N         APOBEC-like N-terminal domain
  ------ inclusion threshold ------
      0.046   13.8   0.0      0.072   13.2   0.0    1.3  1  XOO_2897-deam    Xanthomonas XOO_2897-like deaminase
      0.048   13.8   0.2      0.094   12.8   0.2    1.6  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
      0.052   13.7   0.2       0.21   11.7   0.2    1.9  1  APOBEC3          APOBEC3
      0.088   12.9   0.3       0.14   12.3   0.3    1.3  1  NAD1             Novel AID APOBEC clade 1


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   1.6   1.9e-34   3.8e-31       4     100 ..       9     126 ..       6     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.9e-34
                                       HHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.......................TTB-HHHH CS
                   dCMP_cyt_deam_1   4 dekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.......................ktiHAEvn 57 
                                       d +++++a+++a+++ +c + +VGavivk+++i+stgyng p+g                         + +HAE+n
  gi|488599840|ref|YP_007906311.1|   9 DTYFMSIAKLVASRS-TCLRQNVGAVIVKDKRILSTGYNGAPTGLAhcldigclreelniasgerhelcRAVHAEQN 84 
                                       789************.*****************************9******************************* PP

                                       HHHHHHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  58 AilkaaknggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                       Ai++aa   g+++ gatly+t++PC mCak+ii+++ikkv++g
  gi|488599840|ref|YP_007906311.1|  85 AIIQAAVH-GVSIAGATLYTTHQPCIMCAKMIINAKIKKVIYG 126
                                       ******88.899*****************************98 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.5   1.2e-26   2.4e-23       4     109 ..       9     137 ..       6     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 1.2e-26
                       MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsn.........................ekelnakataHaEi 55 
                                       + +f++++++v  ++ +  + +gavivkdk+++ +g+n                         ++  +     HaE 
  gi|488599840|ref|YP_007906311.1|   9 DTYFMSIAKLVASRSTCLRQNVGAVIVKDKRILSTGYNgaptglahcldigclreelniasgeRH--ELCRAVHAEQ 83 
                                       689**************************************************777777764322..3445569999 PP

                       MafB19-deam  56 aalqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks..lnk 109
                                       +a+ qAa  + s+   +atly+t++pC mCa++i++a++kk++yg ++p+   l+ 
  gi|488599840|ref|YP_007906311.1|  84 NAIIQAAVHGVSI--AGATLYTTHQPCIMCAKMIINAKIKKVIYGKKYPDErgLQF 137
                                       ******7766666..*********************************99766443 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.5   3.8e-08   7.5e-05      76      99 ..      97     120 ..      60     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.8e-08
                       Bd3614-deam  76 egarllvtlqcCkmCAalvvaaad 99 
                                       +ga+l+ t+q+C mCA ++++a  
  gi|488599840|ref|YP_007906311.1|  97 AGATLYTTHQPCIMCAKMIINAKI 120
                                       79*****************98765 PP

>> Inv-AAD  Invertebrate-AID/APOBEC-deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   1.6   4.9e-05     0.097       2     114 ..      32     145 ..      31     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-05
                           Inv-AAD   2 avlvdadkneilatGytlel...................eGnthaeqccliklaekhevaeeklaevlpkntvlYtt 59 
                                       av+v+  +++il+tGy                        G+ h  + c +  ae++++ +  ++ v  + + lYtt
  gi|488599840|ref|YP_007906311.1|  32 AVIVK--DKRILSTGYNGAPtglahcldigclreelniaSGERH--ELCRAVHAEQNAIIQAAVHGVSIAGATLYTT 104
                                       55553..4578888887666455666666666666665556655..45666678888888999****99******** PP

                           Inv-AAD  60 mepCskRlsGnlpCveRilklkeaiktvyvGvkePekfvaenkgrkkleeagiev 114
                                         pC         C + i++   +ik+v  G k P+     ++g + l++a+ie+
  gi|488599840|ref|YP_007906311.1| 105 HQPCI-------MCAKMIINA--KIKKVIYGKKYPD-----ERGLQFLKDANIEI 145
                                       ****6.......577777654..4777777777775.....35666666666665 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   0.4   8.7e-06     0.017      35      96 ..      58     119 ..      46     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.7e-06
                                       EEEEEEE-..SS........TBCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHHHHH CS
                          APOBEC_N  35 kGvLrnqsgaaa........skHaEelflediedqelrepkkkyeitlYvswsPChessdeCaeklaafl 96 
                                        G+Lr++   a+          HaE+     i ++++    +    tlY++ +PC      Ca+++ ++ 
  gi|488599840|ref|YP_007906311.1|  58 IGCLREELNIASgerhelcrAVHAEQNA---IIQAAVH-GVSIAGATLYTTHQPCIM----CAKMIINAK 119
                                       4555555444335555555589999983...3333444.6899999***********....****98765 PP

>> XOO_2897-deam  Xanthomonas XOO_2897-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.6e-05     0.072      28      70 ..      78     116 ..      65     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                     XOO_2897-deam  28 vmHsEekllqqleeagvepakvlelytErepClpgneCakllk 70 
                                         H+E++ + q++ +gv+ a    lyt  +pC     Cak++ 
  gi|488599840|ref|YP_007906311.1|  78 AVHAEQNAIIQAAVHGVSIAG-ATLYTTHQPC---IMCAKMII 116
                                       56*********9999987665.57********...9**99974 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   4.7e-05     0.094      22      63 ..      78     118 ..      62     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-05
                             SNAD4  22 e.haEllflekikseldpsqeyrvtwylswsPCaeCaekiaef 63 
                                         haE + + +    ++       t+y++  PC  Ca+ i++ 
  gi|488599840|ref|YP_007906311.1|  78 AvHAEQNAIIQA--AVHGVSIAGATLYTTHQPCIMCAKMIINA 118
                                       359998888777..6666677889**************99875 PP

>> APOBEC3  APOBEC3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00011      0.21      30      72 ..      78     117 ..      60     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                           APOBEC3  30 kkHAEerfidkirslnldslkqykitcylswsPcpkCaeelve 72 
                                         HAE+ +i + +   ++       t+y +  Pc  Ca+ +++
  gi|488599840|ref|YP_007906311.1|  78 AVHAEQNAIIQAAVHGVSIAG---ATLYTTHQPCIMCAKMIIN 117
                                       579**9999887776666555...8**************9997 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   6.8e-05      0.14      49      92 ..      79     118 ..      53     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                              NAD1  49 cHaEllflnkikslklldpsqkykvtwylswSPCseCasklaef 92 
                                       +HaE+  + +       +  ++   t+y+++ PC  Ca+ +++ 
  gi|488599840|ref|YP_007906311.1|  79 VHAEQNAIIQAAV----HGVSIAGATLYTTHQPCIMCAKMIINA 118
                                       4888877555533....45578899**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1134.77
//
Query:       gi|488599841|ref|YP_007906312.1|  [L=307]
Description: Inorganic pyrophosphatase/exopolyphosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-29  100.2   0.1    1.1e-28   99.5   0.1    1.4  1  DHH       DHH family
    3.8e-24   85.5   0.2    6.3e-24   84.8   0.2    1.4  1  DHHA2     DHHA2 domain
     0.0072   16.2   0.9        1.2    9.0   0.1    2.4  2  DUF2100   Uncharacterized protein conserved in archaea (DUF21


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 !   99.5   0.1   1.8e-32   1.1e-28       2     101 .]       3     143 ..       2     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 1.8e-32
                                       EEEE-ECSSSHHHHHHHHHHHH............................................CECS--TCGGC CS
                                       xxxxxxxxxxxxxxxxxxxxxx............................................xxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan............................................llvDhneksqa 34 
                                       +++vghk+pDtDs++Saia+a+                                            +lvDh+e +q+
  gi|488599841|ref|YP_007906312.1|   3 VYVVGHKSPDTDSVCSAIAYAElkkkvgvdavparqgdlnpettfvlekfgfdvpelvtdatgkrvILVDHSEVAQS 79 
                                       89********************777777777777777777777777777777777777777777777********** PP

                                       GCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  35 vegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                        ++   +++e+v+i+DHH++g +++t +pi++ln pvgsta++v +l+e+ ++eiskeia++ll+ i
  gi|488599841|ref|YP_007906312.1|  80 LDN--LDKGEIVEIVDHHKIG-DVTTPNPIFYLNMPVGSTATVVKKLYEDAGVEISKEIAGILLASI 143
                                       ***..****************.***************************************999876 PP

>> DHHA2  DHHA2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.2     1e-27   6.3e-24       1     142 [.     180     303 ..     180     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 1e-27
                                       HHHHHHHT-STTS-HHHHTTTTEEEEE.ETTEEEEEEEEEES-HHHHHT.THHHHHHHHHHHH.HHT-SEEEEEEE. CS
                             DHHA2   1 kelkkaksdlsglsledllrrDyKeftgeggvkvgiasvpvslsewleekrkgellaalekfaeerkldllvlmttf 77 
                                       +e++k+ks l+g+s++dll rD+K f+ ++g kvgi++++v+  + l++  k++l ++++k +e+++++ ++lm+t 
  gi|488599841|ref|YP_007906312.1| 180 MEMFKRKSELEGKSAKDLLFRDFKNFD-MSGNKVGIGQIEVVSLSLLDN-FKDALYEEMQKLKEAEGYHSIFLMLT- 253
                                       59*************************.***********9999967777.99***********9999*********. PP

                                       ....ETTT..EEEEEE...STTHHHHHT---B.T.EEET...............T---HHHHTHHHHHH CS
                             DHHA2  78 eeegdirr..elllaaldaaeklaealekase.e.leLeewkegaewrrvykqgnvkasRKqvaPllre 142
                                           di +  ++ll+++d  e +++a++k+ e   ++L+               +v++++Kqv+P  ++
  gi|488599841|ref|YP_007906312.1| 254 ----DIIQegTELLCVTDDPEVVKKAFDKEIEgRsVWLP---------------GVMSRKKQVVPNFEK 303
                                       ....77777988888744444499****9988766****...............***********8766 PP

>> DUF2100  Uncharacterized protein conserved in archaea (DUF2100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0002       1.2      93     151 ..      48     105 ..      42     136 .. 0.79
   2 !    5.6   0.1    0.0021        12      46      83 ..     133     170 ..     115     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0002
                                       HHHTTT---XX..XXXXSSSEEEESXHHHHHHHHHHXSSSXEEEXSSXSSSHHHHTT.. CS
                           DUF2100  93 vLeefgveeeedieeldkdalyivsnkkvlKaLkeinvdlniisteGvLeieDmkeiNP 151
                                       vLe+fg++  e ++++  + +++v  + v  +L +++   +i+ +    +i D+ + NP
  gi|488599841|ref|YP_007906312.1|  48 VLEKFGFDVPELVTDATGKRVILVDHSEVAQSLDNLD-KGEIVEIVDHHKIGDVTTPNP 105
                                       9**********************************95.445555555555555555555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHTHHHHHTTTT-EE-HHHHHHHHHHH CS
                           DUF2100  46 eelkkavyelieadeylykkaPehelkkeeAeefckil 83 
                                       +e+  ++   i +d+ + k+a + +++++ Aee++ki 
  gi|488599841|ref|YP_007906312.1| 133 KEIAGILLASILSDTVILKSATTTDIDRKAAEELAKIA 170
                                       5666777788899**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2366.11
//
Query:       gi|488599842|ref|YP_007906313.1|  [L=137]
Description: hypothetical protein Asulf_00287 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-45  154.7   0.1    1.6e-45  154.5   0.1    1.0  1  DUF523    Protein of unknown function (DUF523)
  ------ inclusion threshold ------
      0.068   12.9   0.0      0.089   12.5   0.0    1.1  1  DUF3334   Protein of unknown function (DUF3334)


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 !  154.5   0.1   1.8e-49   1.6e-45       3     137 .]       4     136 ..       3     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 1.8e-49
                            DUF523   3 vSaCLlgekvrydgkakksevleeelkelvke.elvpvCPEvaggLptPRepael.akr.vlkkegedvtealekga 76 
                                        SaCLlg ++rydg++k+    ++++ el+++  l+pvCPE++ggLptPRe+ el + + v++++g+d+te+l++ga
  gi|488599842|ref|YP_007906313.1|   4 CSACLLGINCRYDGRSKP----SKKVLELARKeVLIPVCPEQLGGLPTPREQSELrG-EsVVTRSGKDITENLVRGA 75 
                                       69****************....5667777777467********************64.55***************** PP

                            DUF523  77 eealeelkeeeikgailkekSPSCGvekiYdgtfskklvegeGvfaallkeegievpseee 137
                                       +++l+++k  ++k ailk++SPSCG+++iYdgtf+++ ++g+Gv++allk++gi+v+see+
  gi|488599842|ref|YP_007906313.1|  76 KQVLKIAKLFDVKEAILKQRSPSCGCGQIYDGTFTGTVIRGDGVTTALLKKHGIKVVSEED 136
                                       **********************************************************986 PP

>> DUF3334  Protein of unknown function (DUF3334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     1e-05     0.089       7      64 ..      64     115 ..      57     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                           DUF3334   7 tddillklcesvskvlssatasqvsysamvqkitktslkPdlgcfvlfdGgfsGlvvi 64 
                                        +di  +l +  ++vl+ a   +v+ + + q+       P  gc  ++dG+f+G v+ 
  gi|488599842|ref|YP_007906313.1|  64 GKDITENLVRGAKQVLKIAKLFDVKEAILKQR------SPSCGCGQIYDGTFTGTVIR 115
                                       56777778888888888888888877766665......699***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 909.25
//
Query:       gi|488599843|ref|YP_007906314.1|  [L=369]
Description: DNA primase, eukaryotic-type, small subunit, putative [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-22   77.9   0.3    1.8e-21   77.0   0.3    1.4  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.045   13.5   0.6       0.13   12.1   0.6    1.8  1  SAP            SAP domain
       0.14   12.2   0.1       0.26   11.3   0.1    1.5  1  Phasin         Poly(hydroxyalcanoate) granule associated prot


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.3   2.9e-25   1.8e-21       1     172 [.      96     299 ..      96     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.9e-25
                                       EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                     DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                       FDiD+d+ +  ++++  e      +++v++  ell++dfg    ++ +vfsg+rG+H++v d+    l+++er++iv
  gi|488599843|ref|YP_007906314.1|  96 FDIDADHIPA-KSKDMDELIDIAKKEIVRLS-ELLSKDFGVSdsEMRIVFSGGRGYHLHVYDEGLSILGSAERREIV 170
                                       9********8.99999999776666666665.8********999********************************* PP

                                       HH..................................................HCHHHHCT--------......... CS
                     DNA_primase_S  76 nylnlyrp...............lhpflsrs.mlkivkpvveeiileeqdpfeikkllrllpdkslre.......kk 129
                                       +y+ l +p               + +fl ++ +++++k++ ++  +  ++++ i+++lr+l ++s+++       ++
  gi|488599843|ref|YP_007906314.1| 171 DYILLTQPdmyadslqsrrlrvcFISFLRNLmKKDKLKEYLKSLGI--RKTDIIESDLRRLVEDSRAFirgdyriED 245
                                       *999994455455555555666677777777666666666665544..23349999999999999999988888866 PP

                                       ...........................-----------------....------ CS
                     DNA_primase_S 130 kw...........eakedivlvllyprldeqvtkgikhllkapfcihgktgnvc 172
                                       k+           e   +   ++l + +d +vt++ik+l+++p++ihgk+g  +
  gi|488599843|ref|YP_007906314.1| 246 KVrskskklnsmiEQIVSSCISKLSIHIDAPVTADIKRLIRLPGSIHGKSGLKA 299
                                       667777777877755556667788999***********************9655 PP

>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   2.1e-05      0.13       2      21 ..     200     219 ..     200     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                                       TT--HHHHHHHHHHTT--TT CS
                               SAP   2 skltVaeLKeeLkkrGLpts 21 
                                       ++++ ++LKe+Lk++G++ +
  gi|488599843|ref|YP_007906314.1| 200 NLMKKDKLKEYLKSLGIRKT 219
                                       68**************9875 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 ?   11.3   0.1   4.3e-05      0.26      72     117 ..     242     287 ..     204     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.3e-05
                            Phasin  72 evkekaeeqwdklekafdervakaLsrlgvpsredveaLsarvdeL 117
                                       ++++k+ ++ +kl++++++ v++ +s+l ++    v a  +r+ +L
  gi|488599843|ref|YP_007906314.1| 242 RIEDKVRSKSKKLNSMIEQIVSSCISKLSIHIDAPVTADIKRLIRL 287
                                       7999**************************9888888777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2714.04
//
Query:       gi|488599844|ref|YP_007906315.1|  [L=191]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.01   16.3   3.9       0.01   16.3   3.9    2.1  2  Sld5          GINS complex protein
      0.022   14.3   0.4      0.028   13.9   0.4    1.2  1  Allexi_40kDa  Allexivirus 40kDa protein
      0.039   14.3   0.3         10    6.5   0.0    2.4  2  DUF5601       Domain of unknown function (DUF5601)
      0.066   13.2   2.4       0.23   11.4   1.7    2.3  2  RPT           A repeated domain in UCH-protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   3.9   2.3e-06      0.01      33     104 ..       9      90 ..       1      98 [. 0.68
   2 ?   -0.2   0.0       0.3   1.4e+03      62      78 ..     126     141 ..      96     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.3e-06
                                       CCCHHTTSSSSTTTTTTHHHHH....HHHHHHHT..............HCHHHHHHHHHHHHHHHHHHHTHCHHHHH CS
                              Sld5  33 iledetkssdlpslpphflela....vkllelard.............ldelkrllrdllevRlakirkfaenleda 92 
                                       ile+++++  l+++ ++f+        kl +++ d             ++ l+r+l++++e+R +ki  +a++    
  gi|488599844|ref|YP_007906315.1|   9 ILEKNRTK--LTKIDDDFYDRIkdeiRKLEKMR-DraddeeisrindnIRTLRRILKKIFETRTSKIIRIAWSMVCG 82 
                                       55555555..88888888888855543344444.2344567777778899999*******************98777 PP

                                       HHTS-TCCHCCS CS
                              Sld5  93 agggggellsgl 104
                                       +    +e  ++l
  gi|488599844|ref|YP_007906315.1|  83 N----SESTENL 90 
                                       7....3444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.3
                                       T.HCHHHHHHHHHHHHH CS
                              Sld5  62 rdldelkrllrdllevR 78 
                                       r+ +++ ++ +d++ vR
  gi|488599844|ref|YP_007906315.1| 126 RE-EKIEKIENDYVLVR 141
                                       22.44555555555555 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   6.4e-06     0.028      54     157 ..      17     125 ..       3     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-06
                      Allexi_40kDa  54 Lthishdv.dsi...inklnpvsllsqttlLselrdalrtltklldklksvekklelsaetasdskllkklesiets 126
                                       Lt i+ d  d+i   i kl+++   ++  ++s++ d++rtl+++l+k+ ++ +++ +++   +     ++ e ++  
  gi|488599844|ref|YP_007906315.1|  17 LTKIDDDFyDRIkdeIRKLEKMRDRADDEEISRINDNIRTLRRILKKIFETRTSKIIRIAWSMVCGNSESTENLNSG 93 
                                       7777777435553336778888888899*********************9999999888877777777777777777 PP

                      Allexi_40kDa 127 leelhakldelsssetse.segPsssptkass 157
                                        +el  +l e++++ ++   + P++  + ++ 
  gi|488599844|ref|YP_007906315.1|  94 EKELLFRLVEVIKNYKERiMSYPEKDVHYEQV 125
                                       77888888777766555414457766655554 PP

>> DUF5601  Domain of unknown function (DUF5601)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0022        10      21      56 ..      18      54 ..       7      72 .. 0.86
   2 ?    5.8   0.1    0.0037        17      20      54 ..     101     135 ..      86     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0022
                           DUF5601 21 SemVqdFyqnlaerlnktplykt.vsseavedlldei 56
                                       ++  dFy  ++++++k +  ++ +++e+++++ d i
  gi|488599844|ref|YP_007906315.1| 18 TKIDDDFYDRIKDEIRKLEKMRDrADDEEISRINDNI 54
                                      56667************99888779999999888776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0037
                           DUF5601  20 lSemVqdFyqnlaerlnktplyktvsseavedlld 54 
                                       l+e+++++ + +    +k+ +y+ v +e++e++ +
  gi|488599844|ref|YP_007906315.1| 101 LVEVIKNYKERIMSYPEKDVHYEQVREEKIEKIEN 135
                                       7899999999999999***************9865 PP

>> RPT  A repeated domain in UCH-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.7   5.2e-05      0.23      28      55 ..      50      74 ..      32      75 .. 0.86
   2 ?   -1.4   0.0      0.53   2.4e+03      33      48 ..      93     108 ..      86     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
                               RPT 28 leddpsqkdklrrALkvIAeeRkSelLl 55
                                      +   ++++++lrr Lk+I e R S++++
  gi|488599844|ref|YP_007906315.1| 50 I---NDNIRTLRRILKKIFETRTSKIIR 74
                                      3...45*******************997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.53
                               RPT  33 sqkdklrrALkvIAee 48 
                                       ++k++l r ++vI ++
  gi|488599844|ref|YP_007906315.1|  93 GEKELLFRLVEVIKNY 108
                                       6666666666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1539  (0.0858386); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1369.54
//
Query:       gi|488599845|ref|YP_007906316.1|  [L=91]
Description: LSU ribosomal protein L44E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-25   89.1   4.3      2e-25   89.1   4.3    1.5  2  Ribosomal_L44  Ribosomal protein L44
    0.00032   21.1   4.8      0.083   13.3   1.9    2.4  2  Ribosomal_L33  Ribosomal protein L33
  ------ inclusion threshold ------
      0.035   14.4   1.6      0.049   13.9   1.6    1.3  1  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
      0.063   13.5   3.7       0.07   13.3   0.4    2.1  2  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like


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 ?   -1.7   0.2      0.93   4.2e+03      52      60 ..       7      15 ..       4      16 .. 0.76
   2 !   89.1   4.3   4.4e-29     2e-25       1      76 []      16      91 .]      16      91 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.93
                                      EEEEETTT- CS
                     Ribosomal_L44 52 lrleCteCk 60
                                      +r  C+ C+
  gi|488599845|ref|YP_007906316.1|  7 VRTYCKYCG 15
                                      678899998 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 4.4e-29
                                      EEEEEEEEE-------SSSHHHHHHHH.H-SSS..GGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                     Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgyg..GqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                      +Ht+h+ve++ kg++s+l++++R+++r + ++g  G++++v+++ +K+tK++++r++CteCkk+++++++Rak+felv
  gi|488599845|ref|YP_007906316.1| 16 RHTIHEVEKVSKGRQSSLRWINRQKAR-RGKVGnlGKFSKVPGG-DKPTKRVNIRFRCTECKKAEHRPTWRAKRFELV 91
                                      6************************99.5566678*********.*******************************96 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.9   1.9e-05     0.083      30      44 ..       7      21 ..       4      24 .. 0.86
   2 !    8.5   0.1    0.0006       2.7       1      13 [.      65      77 ..      65      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                      EEEEETTTTEEEEEE CS
                     Ribosomal_L33 30 lkKYcprcrkhtlhk 44
                                      ++ Yc++c +ht+h+
  gi|488599845|ref|YP_007906316.1|  7 VRTYCKYCGRHTIHE 21
                                      567***********7 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0006
                                      .EEEEEET..... CS
                     Ribosomal_L33  1 ekvtLeCtecksr 13
                                      ++++ +Cteck+ 
  gi|488599845|ref|YP_007906316.1| 65 VNIRFRCTECKKA 77
                                      5799*******94 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.6   1.1e-05     0.049      44      90 .]       7      75 ..       1      75 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                      CCTB-TTT--B--CTTTEEEEEE-SSS-E................................EEEEETTTT CS
                              Rpr2 44 krtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka.......................dvlvvtClaCg 90
                                       rt+Ck Cg   i +v+   + +++s +   +++ka                         + ++C++C+
  gi|488599845|ref|YP_007906316.1|  7 VRTYCKYCGRHTIHEVEKVSKGRQSSLR-WINRQKArrgkvgnlgkfskvpggdkptkrVNIRFRCTECK 75
                                      49*************9999998664433.22333335677888899999999999998855679*****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 ?   13.3   0.4   1.6e-05      0.07      20      62 ..       5      45 ..       2      54 .. 0.67
   2 ?    1.3   0.2     0.086   3.8e+02       9      19 ..      69      79 ..      62      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                      NOB1_Zn_bind 20 dmtkkFCpkCGnktLkrvavsvdengelklhlkknfqlnlrGt 62
                                      ++ + +C+ CG +t++ v+ + + +  ++     n+q   rG+
  gi|488599845|ref|YP_007906316.1|  5 KKVRTYCKYCGRHTIHEVEKVSKGR--QSSLRWINRQKARRGK 45
                                      67799***********998655443..3333334445555665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.086
                      NOB1_Zn_bind  9 lrChaCfkvtk 19
                                       rC+ C k  +
  gi|488599845|ref|YP_007906316.1| 69 FRCTECKKAEH 79
                                      68999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 667.31
//
Query:       gi|488599846|ref|YP_007906317.1|  [L=56]
Description: SSU ribosomal protein S27E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-25   86.1   0.7      1e-24   86.0   0.7    1.0  1  Ribosomal_S27e  Ribosomal protein S27
  ------ inclusion threshold ------
       0.03   13.9   1.3        0.2   11.3   0.0    2.1  2  Sgf11           Sgf11 (transcriptional regulation protein)
      0.033   13.7   1.6      0.064   12.8   1.6    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.11   12.4   1.8        0.2   11.6   1.8    1.6  1  zf-DNL          DNL zinc finger


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 !   86.0   0.7   2.3e-28     1e-24       2      54 ..       3      55 ..       2      56 .] 0.97

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 2.3e-28
                                      S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  2 rskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                      +skF++vkCpdCen +v+F+h++  vkC++Cg++L+e tGGk+ +ka+i+e+l
  gi|488599846|ref|YP_007906317.1|  3 KSKFIRVKCPDCENLQVIFDHPSIDVKCLICGRTLAEHTGGKGEIKAEIVEVL 55
                                      8*************************************************997 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   0.3     0.046   2.1e+02       5      11 ..       9      15 ..       7      16 .. 0.85
   2 ?   11.3   0.0   4.4e-05       0.2       2      15 ..      25      38 ..      24      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.046
                                      EE-TTTS CS
                             Sgf11  5 vtCpnCg 11
                                      v+Cp C+
  gi|488599846|ref|YP_007906317.1|  9 VKCPDCE 15
                                      79**995 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.4e-05
                                      C-EEE-TTTSSEEE CS
                             Sgf11  2 seyvtCpnCgRqia 15
                                      s +v+C++CgR+ a
  gi|488599846|ref|YP_007906317.1| 25 SIDVKCLICGRTLA 38
                                      5689*******987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.6   1.4e-05     0.064       2      31 ..      10      39 ..       9      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                                      EETTTTCEECHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVled 31
                                      kCP+C + ++++D+ + ++ C  CG  l +
  gi|488599846|ref|YP_007906317.1| 10 KCPDCENLQVIFDHPSIDVKCLICGRTLAE 39
                                      9******99***************987765 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.8   4.5e-05       0.2      28      45 ..       8      25 ..       3      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-05
                            zf-DNL 28 ivqCpgCknrHliaDnLg 45
                                       v+Cp+C+n  +i D+ +
  gi|488599846|ref|YP_007906317.1|  8 RVKCPDCENLQVIFDHPS 25
                                      59*************955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 403.45
//
Query:       gi|488599847|ref|YP_007906318.1|  [L=210]
Description: Thermostable 8-oxoguanine DNA glycosylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.9   0.0       0.44   11.0   0.0    2.0  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 ?   11.0   0.0   2.4e-05      0.44      39      91 ..      73     166 ..      44     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHTT..STTHHHHHHHHHHHHHHHH.........................................S-SSS- CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxx.........................................xxxxxx RF
                           HhH-GPD  39 ekLrelire..lGfyrrKakyikelArilv.........................................gkpdvl 72 
                                       ekL e ++   ++fy+++a+yi  lAr +                                          g+ + +
  gi|488599847|ref|YP_007906318.1|  73 EKLSERLKDlgHRFYNKRAEYIV-LARRFRnikdiiqdivhssgefearewlvrnvkglgykeashfmrnvGYLN-F 147
                                       55544444444**********96.777777788888888888888888888888888888888888888887766.7 PP

                                       -TTSHHHHHHHHHHTTSSS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  73 ivvDvhvrrilkrlrsike 91 
                                        + D h+ ++l+  ++i++
  gi|488599847|ref|YP_007906318.1| 148 AILDRHILKLLSSEGIIEK 166
                                       7788888888777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1451.84
//
Query:       gi|488599848|ref|YP_007906319.1|  [L=300]
Description: putative transcriptional regulator, contains C-terminal CBS domains [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-37  127.0   0.4    2.7e-37  126.3   0.4    1.4  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
    4.7e-22   78.2   7.4    4.5e-12   46.2   1.8    3.2  3  CBS           CBS domain
    8.7e-08   32.4   0.1    1.7e-07   31.5   0.1    1.4  1  Rrf2          Transcriptional regulator
      6e-07   29.3   0.1    1.4e-06   28.1   0.1    1.7  1  HTH_11        HTH domain
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.055   13.5   0.0    1.6  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.027   14.2   0.0      0.072   12.8   0.0    1.7  1  Sigma70_r4_2  Sigma-70, region 4
       0.03   14.2   0.0      0.079   12.9   0.0    1.8  1  TrmB          Sugar-specific transcriptional regulator TrmB
       0.04   13.7   0.0      0.084   12.7   0.0    1.5  1  HTH_38        Helix-turn-helix domain
      0.044   13.8   0.0      0.089   12.9   0.0    1.5  1  HTH_20        Helix-turn-helix domain
      0.048   13.2   1.8      0.051   13.1   0.1    2.0  2  HTH_24        Winged helix-turn-helix DNA-binding
       0.05   13.5   0.0       0.15   11.9   0.0    1.8  2  HTH_5         Bacterial regulatory protein, arsR 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 !  126.3   0.4   1.7e-40   2.7e-37       1      77 [.       4      81 ..       4      83 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 1.7e-40
                      HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkk.kravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqt 77
                                      eLt++qk+il aLi+ly+kk + ++KgeeiAe+++rn+GtvRNq+q+L+algLvegvpGPkGGYkPt+kaye l++++
  gi|488599848|ref|YP_007906319.1|  4 ELTQIQKDILYALITLYKKKiGLSIKGEEIAELINRNPGTVRNQMQALRALGLVEGVPGPKGGYKPTAKAYELLSVTK 81
                                      69******************99****************************************************9986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         1   1.6e+03      27      41 ..      83      95 ..      68      98 .. 0.61
   2 !   33.4   0.1   2.8e-11   4.6e-08       2      56 ..     177     230 ..     173     231 .. 0.92
   3 !   46.2   1.8   2.8e-15   4.5e-12       1      55 [.     238     291 ..     238     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1
                                      HHTSSEEEEEETTTB CS
                               CBS 27 ekgvsrlPVVdedgk 41
                                      e++v r+PV+  +++
  gi|488599848|ref|YP_007906319.1| 83 EEAV-RVPVI-RNDE 95
                                      4458.9***9.4544 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 2.8e-11
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       g+ m+++++tv+ d+ +++a +++ ek++ + PV  +dg l+Gi+tl++ ++a++
  gi|488599848|ref|YP_007906319.1| 177 GEHMSSPLITVDKDMIVRDATKILSEKKIYCAPV-KSDGSLIGIFTLEHAVKAIA 230
                                       667*********************999966****.69***************997 PP

  == domain 3  score: 46.2 bits;  conditional E-value: 2.8e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+++m++++vt+  dt ++ea++lmr+++v r+++V + g+++Gi+t+  +l  l
  gi|488599848|ref|YP_007906319.1| 238 VEEVMRPKIVTAEKDTKIREAIRLMRDEDV-RVLIVTDRGNPIGIITDQKVLTRL 291
                                       89***********************9999*.8878889***********999887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1     1e-10   1.7e-07      10      66 ..      12      68 ..       3      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1e-10
                                      HHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                              Rrf2 10 alhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                       l al+ L k++ + +++ eeiae  n +p  ++  ++ Lr  glv+ v G++GGy+
  gi|488599848|ref|YP_007906319.1| 12 ILYALITLYKKKIGLSIKGEEIAELINRNPGTVRNQMQALRALGLVEGVPGPKGGYK 68
                                      578999****999999****************************************7 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   8.8e-10   1.4e-06       5      55 .]      16      68 ..      12      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 8.8e-10
                            HTH_11  5 ilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GYr 55
                                      +++l +++ g  i gee+Ae +n+   tvr+ ++aL++lg  +e++pg+  GY+
  gi|488599848|ref|YP_007906319.1| 16 LITLYKKKIGLsIKGEEIAELINRNPGTVRNQMQALRALG-LVEGVPGPkgGYK 68
                                      5666666667789***************************.*********9996 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 ?   13.5   0.0   3.3e-05     0.055       8      52 ..      17      58 ..      10      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                                      HHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  8 lrlaeraggeielpltqeelAsmlGltretvsrilseLkreglis 52
                                      + l+++   +i l++  ee+A++++ ++ tv   +++L+  gl++
  gi|488599848|ref|YP_007906319.1| 17 ITLYKK---KIGLSIKGEEIAELINRNPGTVRNQMQALRALGLVE 58
                                      445443...48899*****************************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.4e-05     0.072      30      48 ..      31      49 ..      27      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 30 kEIAellgisegtVksrls 48
                                      +EIAel++ ++gtV+++++
  gi|488599848|ref|YP_007906319.1| 31 EEIAELINRNPGTVRNQMQ 49
                                      8***************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 ?   12.9   0.0   4.8e-05     0.079      24      65 ..      29      70 ..       2      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-05
                                      HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                              TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                      + +eiae +++   +v + ++ L   GlVe ++g +  Y+++
  gi|488599848|ref|YP_007906319.1| 29 KGEEIAELINRNPGTVRNQMQALRALGLVEGVPGPKGGYKPT 70
                                      579******************************998888775 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.1e-05     0.084      18      39 ..      23      46 ..      16      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.1e-05
                            HTH_38 18 aeGlslr..eIArrLgrspsTIsR 39
                                      + Gls++  eIA +++r+p+T+ +
  gi|488599848|ref|YP_007906319.1| 23 KIGLSIKgeEIAELINRNPGTVRN 46
                                      457888899************986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.5e-05     0.089      28      58 ..      31      61 ..      31      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 28 selaerldlskntlsyHLrvLeeagLvevvr 58
                                      +e+ae++   + t+++++++L+  gLve+v 
  gi|488599848|ref|YP_007906319.1| 31 EEIAELINRNPGTVRNQMQALRALGLVEGVP 61
                                      69**************************986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3       2.9   4.7e+03       2      12 ..       6      16 ..       5      17 .. 0.79
   2 ?   13.1   0.1   3.1e-05     0.051      22      48 .]      32      58 ..      27      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.9
                            HTH_24  2 detdrkILelL 12
                                       +++++IL +L
  gi|488599848|ref|YP_007906319.1|  6 TQIQKDILYAL 16
                                      68999999887 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.1e-05
                            HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlIk 48
                                      e+Ae ++  p+tv+ +++ L   Gl++
  gi|488599848|ref|YP_007906319.1| 32 EIAELINRNPGTVRNQMQALRALGLVE 58
                                      9************************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 ?   -3.5   0.0       6.3     1e+04       6      12 ..      11      17 ..       8      25 .. 0.80
   2 ?   11.9   0.0   9.5e-05      0.15      20      46 ..      32      58 ..      27      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.3
                                      HHHHHHT CS
                             HTH_5  6 kILklLa 12
                                      +IL++L 
  gi|488599848|ref|YP_007906319.1| 11 DILYALI 17
                                      6999996 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.5e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 20 elaeelglsqstvShHLkkLreaGLVe 46
                                      e+ae ++ +++tv+ +  +Lr +GLVe
  gi|488599848|ref|YP_007906319.1| 32 EIAELINRNPGTVRNQMQALRALGLVE 58
                                      89************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); 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:                        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 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1710.00
//
Query:       gi|488599849|ref|YP_007906320.1|  [L=805]
Description: copper-(or silver)-translocating P-type ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-55  186.4   3.7    3.3e-55  186.4   3.7    2.1  2  E1-E2_ATPase     E1-E2 ATPase
      2e-44  152.4   7.2      2e-44  152.4   7.2    1.8  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.8e-31  108.4  14.8    1.2e-16   60.9   0.5    3.7  3  HMA              Heavy-metal-associated domain
    4.5e-06   26.6   3.6     0.0039   17.0   0.1    3.7  4  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00036   21.0   0.0     0.0018   18.7   0.0    2.1  1  HAD              haloacid dehalogenase-like hydrolase
    0.00074   19.5   0.0        1.9    8.6   0.0    2.7  2  RRM_3            RNA binding motif
     0.0032   17.6   0.2      0.029   14.5   0.0    2.8  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
     0.0037   17.4   0.2        2.7    8.2   0.0    2.6  2  Tox-PL-2         Papain fold toxin 2
  ------ inclusion threshold ------
      0.011   15.2   0.1      0.031   13.8   0.1    1.7  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      0.021   14.9   0.6       0.12   12.5   0.6    2.3  1  HAD_2            Haloacid dehalogenase-like hydrolase
      0.062   13.5   0.2         12    6.2   0.0    3.0  2  DUF3213          Protein of unknown function (DUF3213)
      0.069   12.9   0.1       0.86    9.3   0.0    2.5  2  CT_C_D           Carboxyltransferase domain, subdomain C and 
      0.084   13.1   7.4        3.6    7.8   0.1    4.1  5  FeS_assembly_P   Iron-sulfur cluster assembly protein
       0.12   11.8   1.3          5    6.7   0.1    2.6  2  DUF2688          Protein of unknown function (DUF2688)
       0.12   12.2   0.1       0.29   11.1   0.1    1.6  1  Ribosomal_S4e    Ribosomal family S4e
       0.16   11.4   0.0       0.48    9.8   0.0    1.8  2  AP_endonuc_2     Xylose isomerase-like TIM barrel
        1.2    9.2   5.5        3.9    7.5   0.1    3.3  3  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc


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 !  186.4   3.7   3.1e-58   3.3e-55       2     179 ..     285     463 ..     284     465 .. 0.98
   2 ?   -1.6   0.1       1.5   1.6e+03      94     156 ..     723     786 ..     717     790 .. 0.76

  Alignments for each domain:
  == domain 1  score: 186.4 bits;  conditional E-value: 3.1e-58
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l+++ta v+rdg+e  + ++++++GDiv++k+g+++p+Dg+++eg++ vdes++TGE +p  k+  d+v++ t++++
  gi|488599849|ref|YP_007906320.1| 285 LQAKTAVVVRDGREIVVSVEDVKVGDIVIVKPGEKIPVDGVVIEGESYVDESMITGEPTPNLKKVSDEVIAATINKN 361
                                       7899************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralal 154
                                         +k+++t++g+dt l++i++lveea  +k+p+q+ +dk++ +++p+vl+ia+  f++++++ + +a +a++  +a+
  gi|488599849|ref|YP_007906320.1| 362 SFLKIRATRVGKDTLLAQIIKLVEEAVGSKPPIQRLADKIVTYFIPAVLTIAVGSFVYWYFIADAPAiFAFTTLVAV 438
                                       ****************************************************************9999********* PP

                                       HHHHS-TTHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 155 lvaaiPcaLplavplalalgarrla 179
                                       lv+a+Pca++la+p+al++g+++ a
  gi|488599849|ref|YP_007906320.1| 439 LVIACPCAFGLATPTALTVGMGKGA 463
                                       *********************9987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                                       TTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHHHH CS
                      E1-E2_ATPase  94 lgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralallv 156
                                       l  ++++++ ++++  +++++l   + + ++++ ++a l++ i+ +++++ +  a + + ++ v
  gi|488599849|ref|YP_007906320.1| 723 LRDVVAAIQLSEKTLNKIKQNLFWAMIYNSMLIPAAAGLLYPIFGVVFRPEWaGAAMAMSSVSV 786
                                       5667888999999999999999999999999999999999999988888766544444444444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   7.2   1.9e-47     2e-44       3     210 .]     483     698 ..     481     698 .. 0.93

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.9e-47
                                       EEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH...HHHHHETTTE.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.... RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsa.....alalaaaletgsehpigkalvaaakarsgal...tgfatfigrg.... 67 
                                        vvfDk+GTLt+g+p+v+dv++        l++aa+ e  sehp+++a+v++a+a+++++   ++f+ ++g+g    
  gi|488599849|ref|YP_007906320.1| 483 IVVFDKTGTLTKGRPEVTDVTAFDgsekeVLKIAAIAEKRSEHPLAEAIVRKAEAEKISVeepEKFEIIAGKGvvas 559
                                       79**********************7765555555555555****************777777899999********* PP

                                       ....HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEE CS
                                       ....xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ....ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagie 136
                                           ++++g+++++ ++   + +++++a ++++ +++t++l+  ++r+++v+ iad+  +k+ a ea+ +L+++g +
  gi|488599849|ref|YP_007906320.1| 560 fngnRILVGSRKLMVENglAVDKKVEDALQKLEMEAKTAILVasNDRIVGVIGIADT--LKESALEAIDELHKMGKK 634
                                       *******************************************999***********..****************** PP

                                       EEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 137 vvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       v+++tgdn++ta  +a++lG           i+   a+ +p +k + +++Lq+++e va+VGDg+nDa+ala+A+
  gi|488599849|ref|YP_007906320.1| 635 VAMITGDNKRTATVIAKKLG-----------IDFvLAEILPHQKAEEVKRLQESGEIVAFVGDGINDAPALAQAD 698
                                       ********************...........5555*****************99999*****************8 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.5   1.2e-19   1.2e-16       3      61 ..       7      65 ..       5      66 .. 0.97
   2 !   57.1   0.3   1.7e-18   1.8e-15       1      61 [.      75     135 ..      75     136 .. 0.98
   3 ?   -2.5   0.4         7   7.3e+03      18      44 ..     277     305 ..     273     312 .. 0.68

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.2e-19
                               HMA  3 rvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61
                                      ++ gm Ca+C++++e +L +l+gVe+v+v+lat ++ Ve+d+++++l+k ie+i+++gy
  gi|488599849|ref|YP_007906320.1|  7 KITGMSCASCVKAIETALRKLEGVENVSVNLATESAYVEYDPSKISLEKMIETIKSIGY 65
                                      788*******************************************************9 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 1.7e-18
                               HMA   1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       tv++ gm Ca Ca+++e ++s+lpgV+sv+v+l t ++ + +d + t+l++i++aie+ gy
  gi|488599849|ref|YP_007906320.1|  75 TVKIGGMSCAMCAKSIETTVSKLPGVKSVSVNLSTESARIIFDSSTTSLEDIKQAIESVGY 135
                                       799*******************************************************999 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7
                               HMA  18 kvLselpgV..esvkvdlatktvtVegda 44 
                                       +++++l g   ++++v  + ++ +V++++
  gi|488599849|ref|YP_007906320.1| 277 EAIKKLMGLqaKTAVVVRDGREIVVSVED 305
                                       56777777666777777777777777654 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.2   3.4e+03     112     161 ..      81     130 ..      23     133 .. 0.56
   2 ?   -0.1   0.0       0.6   6.4e+02      56     106 ..     555     607 ..     541     616 .. 0.78
   3 !    7.8   0.0    0.0023       2.4      15      58 ..     616     658 ..     610     662 .. 0.91
   4 !   17.0   0.1   3.7e-06    0.0039     197     242 ..     672     717 ..     665     730 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.2
                                       .THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEEEES-HHHHHHHHHHH CS
                       Hydrolase_3 112 eksekkkkeeektkkkkeeidseeeledeeiakililkdkekldelekel 161
                                        +     k++e+t +k + ++s + + ++e a i+++ + ++l+++++++
  gi|488599849|ref|YP_007906320.1|  81 MSCAMCAKSIETTVSKLPGVKSVSVNLSTESARIIFDSSTTSLEDIKQAI 130
                                       33344445555555666666666666666666666666666666666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.6
                                       SEEEEGGGTEEECTTTEEEEE--B-.HHHHHHHHHHHHHTT.CEEEEEESSEE CS
                       Hydrolase_3  56 lpvialNGaliddekgkilykstis.kedvkeiikllkenn.veillytedkv 106
                                         v ++NG  i   ++k++ ++ +   ++v++ ++ l+ +    il+ ++d++
  gi|488599849|ref|YP_007906320.1| 555 GVVASFNGNRILVGSRKLMVENGLAvDKKVEDALQKLEMEAkTAILVASNDRI 607
                                       467789*****888889999999986778999999998777466666666665 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0023
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                       +++e++ eai +l++ g kv+  TG + r++  ++++lg+d +v
  gi|488599849|ref|YP_007906320.1| 616 TLKESALEAIDELHKMGKKVAMITGDNKRTATVIAKKLGID-FV 658
                                       578999*********************************99.44 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 3.7e-06
                                       HHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEE CS
                       Hydrolase_3 197 kelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyv 242
                                       k+l+ s e v+ +GDg ND + L +a+lg+A+g++++ +++    v
  gi|488599849|ref|YP_007906320.1| 672 KRLQESGEIVAFVGDGINDAPALAQADLGIAIGSGTDIAIESGEIV 717
                                       6677788889999************************998866555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06    0.0018      85     187 ..     616     694 ..     578     695 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                               HAD  85 lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrew 161
                                       +l++ ale++++ ++ G +v++++g +++ +  ++++lg+d vla+       l  +         +++ v++l+e 
  gi|488599849|ref|YP_007906320.1| 616 TLKESALEAIDELHKMGKKVAMITGDNKRTATVIAKKLGIDFVLAE------ILPHQ---------KAEEVKRLQE- 676
                                       57789******999*************************9999998......44444.........4455566666. PP

                               HAD 162 laaegegidleevvayGDspsDlpll 187
                                           + +i    v ++GD+++D p+l
  gi|488599849|ref|YP_007906320.1| 677 ----SGEI----VAFVGDGINDAPAL 694
                                       ....3333....7777********98 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0018       1.9       4      60 ..       6      63 ..       5      75 .. 0.80
   2 !    8.2   0.0    0.0023       2.4       3      59 ..      75     131 ..      73     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                                      EEEEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHH.HHHHHHHHHHC CS
                             RRM_3  4 lklsGlnkelsredikellsklgevayvdyekgdkegevrFkedee.akkalekatea 60
                                      +k++G++ +++++ i ++l+kl+ v+ v ++   ++++v ++ ++   +k++e  + +
  gi|488599849|ref|YP_007906320.1|  6 IKITGMSCASCVKAIETALRKLEGVENVSVNLATESAYVEYDPSKIsLEKMIETIKSI 63
                                      6899*************************************98854345555554444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                                       EEEEEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHH CS
                             RRM_3   3 ilklsGlnkelsredikellsklgevayvdyekgdkegevrFkedeeakkalekate 59 
                                        +k+ G++ +++ ++i +++skl  v+ v ++   +++ + F+++  + + +++a e
  gi|488599849|ref|YP_007906320.1|  75 TVKIGGMSCAMCAKSIETTVSKLPGVKSVSVNLSTESARIIFDSSTTSLEDIKQAIE 131
                                       58999**************************************99765555555544 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.1   3.3e+03      18      39 ..     583     604 ..     577     620 .. 0.81
   2 !   14.5   0.0   2.8e-05     0.029       7      51 ..     609     653 ..     606     691 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.1
                                       THHHHHHHHHHTT-EEEEEE-- CS
                       Hydrolase_6  18 gaaealnalraagkpvvllTNn 39 
                                       ++++al+ l+ + k+ +l+  n
  gi|488599849|ref|YP_007906320.1| 583 KVEDALQKLEMEAKTAILVASN 604
                                       6889999999998888888665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.8e-05
                                       TTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                       Hydrolase_6   7 GvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                       Gv+   d++ + a ea++ l+++gk+v+++T  ++++   +akkl
  gi|488599849|ref|YP_007906320.1| 609 GVIGIADTLKESALEAIDELHKMGKKVAMITGDNKRTATVIAKKL 653
                                       88888899999**************************88888776 PP

>> Tox-PL-2  Papain fold toxin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.1    0.0082       8.6      12      46 ..       7      42 ..       1      63 [. 0.83
   2 !    8.2   0.0    0.0026       2.7       7      58 ..      72     120 ..      66     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0082
                          Tox-PL-2 12 rfklleCveCAaalekyLke.qgisGkrlklktksa 46
                                      +++ ++C +C +a+e++L++ +g++   ++l t+sa
  gi|488599849|ref|YP_007906320.1|  7 KITGMSCASCVKAIETALRKlEGVENVSVNLATESA 42
                                      678899************975788888888888876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                          Tox-PL-2   7 geivkrfklleCveCAaalekyLke.qgisGkrlklktksaedaasfilserl 58 
                                       ++i++++  ++C  CA+ +e+ + +  g++   ++l+t+sa+     i++ ++
  gi|488599849|ref|YP_007906320.1|  72 KAITVKIGGMSCAMCAKSIETTVSKlPGVKSVSVNLSTESARI----IFDSST 120
                                       67999999************98865369999999999999985....444443 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     3e-05     0.031      67     120 ..      35      88 ..      25     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                                       HHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECT CS
                       CPSase_L_D2  67 vkkalaeakaafgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlr 120
                                       v+ a++ a + +  +++ +ek+++  k i + vl D+k  ++ ++ + + +  +
  gi|488599849|ref|YP_007906320.1|  35 VNLATESAYVEYDPSKISLEKMIETIKSIGYSVLEDEKAITVKIGGMSCAMCAK 88 
                                       5678889999999************************************98763 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   0.00011      0.12      81     164 ..     618     690 ..     580     702 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                             HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviy 157
                                        + + e+++eL+++g k++ +T  ++++++   ++lgi+ ++  i+  +++e+ K           +l+ + e v +
  gi|488599849|ref|YP_007906320.1| 618 KESALEAIDELHKMGKKVAMITGDNKRTATVIAKKLGIDFVLAEILPHQKAEEVK-----------RLQESGEIVAF 683
                                       567889********************************99999999888888876...........56666666666 PP

                             HAD_2 158 vGDsptD 164
                                       vGD ++D
  gi|488599849|ref|YP_007906320.1| 684 VGDGIND 690
                                       6666666 PP

>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.011        12      18      71 ..      23      77 ..       6      82 .. 0.86
   2 ?    3.7   0.0     0.067        71      27      57 ..     102     132 ..      87     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                                      TTTTTTTB------TTSS--EEE--B-S-SHHHHHHHT...TT-SS-.------S CS
                           DUF3213 18 elekdervyrvflngyakvaevvideekvnieelkkkleelkgevve.ekeltlq 71
                                       l k e v  v +n  +  a+v +d +k++ e++ + ++ +   v+e ek +t++
  gi|488599849|ref|YP_007906320.1| 23 ALRKLEGVENVSVNLATESAYVEYDPSKISLEKMIETIKSIGYSVLEdEKAITVK 77
                                      567778888899999999*********************9999999658999985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.067
                                       -----TTSS--EEE--B-S-SHHHHHHHT.. CS
                           DUF3213  27 rvflngyakvaevvideekvnieelkkklee 57 
                                        v +n  +  a +++d +  + e++k+++e 
  gi|488599849|ref|YP_007906320.1| 102 SVSVNLSTESARIIFDSSTTSLEDIKQAIES 132
                                       5677888899******************976 PP

>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00081      0.86      26      76 ..      16      66 ..       8      78 .. 0.80
   2 ?    0.0   0.0      0.57   6.1e+02      29      76 ..      89     136 ..      68     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00081
                                      HHHHHHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHHHH CS
                            CT_C_D 26 rvlalaaalrakalpgvvelvpayrsllvefdpealdaaellaalkallee 76
                                       v+a+++alr+ +  + v +  a +s  ve+dp +++ +++++++k++  +
  gi|488599849|ref|YP_007906320.1| 16 CVKAIETALRKLEGVENVSVNLATESAYVEYDPSKISLEKMIETIKSIGYS 66
                                      58899999*996655566777899*********************988655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.57
                                       HHHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHHHH CS
                            CT_C_D  29 alaaalrakalpgvvelvpayrsllvefdpealdaaellaalkallee 76 
                                       ++++++++ +  + v +  + +s  + fd  +++ +++++a++++  +
  gi|488599849|ref|YP_007906320.1|  89 SIETTVSKLPGVKSVSVNLSTESARIIFDSSTTSLEDIKQAIESVGYR 136
                                       444445553344445556677777777888888888888888776544 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 ?    7.1   0.0    0.0059       6.2      53      72 ..      16      35 ..       6      37 .. 0.76
   2 ?    7.8   0.1    0.0034       3.6      38      73 ..      74     106 ..      66     107 .. 0.78
   3 ?   -1.8   0.0       3.3   3.5e+03      38      66 ..     364     393 ..     339     395 .. 0.77
   4 ?   -2.6   0.2         6   6.3e+03      53      71 ..     580     598 ..     579     601 .. 0.70
   5 ?   -3.1   0.0       8.7   9.2e+03      52      65 ..     718     731 ..     712     735 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0059
                                      HHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P 53 iradaeaalralpgvevveV 72
                                        +++e alr+l+gve v+V
  gi|488599849|ref|YP_007906320.1| 16 CVKAIETALRKLEGVENVSV 35
                                      5689**********666666 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0034
                                       EEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEEE CS
                    FeS_assembly_P  38 vditltypacslaeairadaeaalralpgvevveVe 73 
                                       +++ ++ + c+   + ++++e  + +lpgv++v+V+
  gi|488599849|ref|YP_007906320.1|  74 ITVKIGGMSCA---MCAKSIETTVSKLPGVKSVSVN 106
                                       45555555555...999************8887775 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.3
                                       EEE--SSTT-T.THHHHHHHHHHHHC.STT CS
                    FeS_assembly_P  38 vditltypacs.laeairadaeaalralpg 66 
                                       ++i+ t+ ++  l+++i + +e+a+++ p+
  gi|488599849|ref|YP_007906320.1| 364 LKIRATRVGKDtLLAQIIKLVEEAVGSKPP 393
                                       688889999988999999999999987665 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 6
                                       HHHHHHHHHC.STT--EEE CS
                    FeS_assembly_P  53 iradaeaalralpgvevve 71 
                                       + +++e+al++l+   ++ 
  gi|488599849|ref|YP_007906320.1| 580 VDKKVEDALQKLEMEAKTA 598
                                       5678999999888755555 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHC.ST CS
                    FeS_assembly_P  52 airadaeaalralp 65 
                                       ++r+d+++ ++a+ 
  gi|488599849|ref|YP_007906320.1| 718 LMRDDLRDVVAAIQ 731
                                       79999999999876 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0048         5       1      34 [.       4      37 ..       4      39 .. 0.92
   2 ?    3.2   0.1     0.056        59       6      33 ..      79     106 ..      75     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0048
                           DUF2688  1 kkieiVtTqCrRCGkslstlsrSLlGldeLkqkl 34
                                      k i+i    C  C k++ t  r L G+++  ++l
  gi|488599849|ref|YP_007906320.1|  4 KNIKITGMSCASCVKAIETALRKLEGVENVSVNL 37
                                      68999999********************998876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.056
                           DUF2688   6 VtTqCrRCGkslstlsrSLlGldeLkqk 33 
                                           C  C ks+ t+   L G+    ++
  gi|488599849|ref|YP_007906320.1|  79 GGMSCAMCAKSIETTVSKLPGVKSVSVN 106
                                       5568***********9999998877665 PP

>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00027      0.29      33      69 ..     279     315 ..     265     320 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                       CEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEE CS
                     Ribosomal_S4e  33 kkkttvkkgipqlvthdGrtirypdpdikvnDtvkid 69 
                                        kk ++ ++++ +v  dGr i ++ +d+kv+D v ++
  gi|488599849|ref|YP_007906320.1| 279 IKKLMGLQAKTAVVVRDGREIVVSVEDVKVGDIVIVK 315
                                       58899999************************99876 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 ?    9.8   0.0   0.00046      0.48      12      93 ..     105     178 ..      99     217 .. 0.79
   2 ?   -3.4   0.0       5.1   5.4e+03      77     102 ..     648     670 ..     644     686 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00046
                                       EEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHHHTBSEE CS
                      AP_endonuc_2  12 vElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraielaaaLGapll 87 
                                       v l++ +++ + + s + l+++++a+++ g+r         f +++ +e +++  e+++ ++kr + +aaa Ga ll
  gi|488599849|ref|YP_007906320.1| 105 VNLSTESARIIFDSSTTSLEDIKQAIESVGYR---------FLGVEGEEKSKEeGEDHITQMKRRLFFAAATGAVLL 172
                                       55666666666666999***************.........44443333344478999******************* PP

                                       EEEBCC CS
                      AP_endonuc_2  88 vlhpGt 93 
                                       +l  G+
  gi|488599849|ref|YP_007906320.1| 173 ILTYGR 178
                                       999885 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.1
                                       HHHHHHTBSEEEEEBCCGBCTTTSGH CS
                      AP_endonuc_2  77 elaaaLGapllvlhpGtagagpkgse 102
                                        +a++LG++++   +     ++k +e
  gi|488599849|ref|YP_007906320.1| 648 VIAKKLGIDFVLAEIL---PHQKAEE 670
                                       5788888888877766...3444333 PP

>> Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0037       3.9      63     121 ..      18      76 ..      14      77 .. 0.87
   2 ?    0.5   0.0      0.56   5.9e+02      62     106 ..      87     131 ..      84     133 .. 0.81
   3 ?    1.2   0.4      0.34   3.6e+02      83     145 ..     561     623 ..     556     651 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0037
                   Spore_YhcN_YlaJ  63 qniaqrverlegVedarvlvtgndvlVavqtdesdnekvkkkVketVekvvddiknVyV 121
                                       ++i+  +++legVe+++v    ++++V +++ +   ek+ +++k    +v  d k+++V
  gi|488599849|ref|YP_007906320.1|  18 KAIETALRKLEGVENVSVNLATESAYVEYDPSKISLEKMIETIKSIGYSVLEDEKAITV 76 
                                       6799999*************************988899999999888888877777766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.56
                   Spore_YhcN_YlaJ  62 aqniaqrverlegVedarvlvtgndvlVavqtdesdnekvkkkVk 106
                                       a+ i+  v++l+gV+ ++v    +++ +  +  ++  e++k+ ++
  gi|488599849|ref|YP_007906320.1|  87 AKSIETTVSKLPGVKSVSVNLSTESARIIFDSSTTSLEDIKQAIE 131
                                       7789999************88888888888877777777777665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.34
                   Spore_YhcN_YlaJ  83 tgndvlVavqtde.sdnekvkkkVketVekvvddiknVyVvtdpdvvdrirtmddrlrtgaaie 145
                                       +gn++lV+ +     +   v+kkV+++ +k+  + k+ + v+ +d +  +  ++d l+++a  e
  gi|488599849|ref|YP_007906320.1| 561 NGNRILVGSRKLMvENGLAVDKKVEDALQKLEMEAKTAILVASNDRIVGVIGIADTLKESA-LE 623
                                       5777888777444677778889999999999888888888888888888888888888875.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (805 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.68u 0.26s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5450.09
//
Query:       gi|488599850|ref|YP_007906321.1|  [L=67]
Description: Copper chaperone [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.7   1.0      0.017   15.6   1.0    2.1  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 !   15.6   1.0   9.4e-07     0.017       3      22 ..       7      26 ..       5      62 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.4e-07
                               HMA  3 rvsgmhCagCaakvekvLse 22
                                        sg+ C+gC++ v+ +L++
  gi|488599850|ref|YP_007906321.1|  7 ELSGLSCGGCVGVVKAALEN 26
                                      679***************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 394.53
//
Query:       gi|488599851|ref|YP_007906322.1|  [L=209]
Description: Methylase involved in ubiquinone/menaquinone biosynthesis [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-23   83.7   0.0    1.8e-23   83.0   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    6.9e-22   77.9   0.0    2.6e-21   76.0   0.0    1.8  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.1e-19   69.5   0.0      5e-19   68.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.3e-17   64.1   0.0    1.6e-17   63.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.3e-15   57.6   0.0    1.7e-15   57.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.2e-14   52.5   0.0    1.7e-13   51.1   0.0    1.7  2  Methyltransf_12  Methyltransferase domain
      0.001   18.1   0.0     0.0014   17.6   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0055   16.5   0.0     0.0081   15.9   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0081   16.0   0.0      0.017   15.0   0.0    1.6  2  Methyltransf_8   Hypothetical methyltransferase
     0.0093   15.3   0.0      0.012   14.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.026   14.2   0.0      0.036   13.7   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      0.046   13.3   0.0      0.067   12.8   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   1.2e-26   1.8e-23       1      96 []      53     146 ..      53     146 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.2e-26
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       L++G+GtG+++ ++   g ++++vD+s++m+  ake+++++   v+++v+dae+lpf+d+ fD+v+ ++v++ ve+p
  gi|488599851|ref|YP_007906322.1|  53 LEIGVGTGKNVPYYR-DG-HYIAVDISEKMIFKAKERVRNSTKDVQLIVSDAESLPFKDDVFDIVFTTFVFCSVENP 127
                                       89************9.55.9*********************999********************************* PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                        k lke++RvLkp+G+ ++
  gi|488599851|ref|YP_007906322.1| 128 IKGLKEAYRVLKPDGRAFF 146
                                       ***************9986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   1.8e-24   2.6e-21      12     168 ..      13     163 ..       3     181 .. 0.90
   2 ?   -0.6   0.0      0.45   6.7e+02     205     225 ..     180     200 ..     173     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.8e-24
                                       XXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHH CS
                   Ubie_methyltran  12 vfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvg 88 
                                        ++++a  y+   + + l   ++W+k++ ++ ++ +g ++l++  Gtg           + g+ + +Di+e+m+  +
  gi|488599851|ref|YP_007906322.1|  13 RYNRIAAIYEIAEAPMELFLSKKWRKYLFERINPCEGDRILEIGVGTGKNVPY-----YRDGHYIAVDISEKMIFKA 84 
                                       58999*******************************************86544.....467999************* PP

                                       HHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHH CS
                   Ubie_methyltran  89 ekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqa 165
                                       +++++++ ++++++++++ae Lpf+dd fD+v  +f +  v +  k+Lkeayrvlkp Gr + le   +++ l++  
  gi|488599851|ref|YP_007906322.1|  85 KERVRNS-TKDVQLIVSDAESLPFKDDVFDIVFTTFVFCSVENPIKGLKEAYRVLKPDGRAFFLEHMLPKNRLIQPI 160
                                       ****986.569******************************************************999999888777 PP

                                       HHH CS
                   Ubie_methyltran 166 yel 168
                                       ++l
  gi|488599851|ref|YP_007906322.1| 161 FHL 163
                                       665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.45
                                       HHHHHHTTEEEEEEEEEGGGT CS
                   Ubie_methyltran 205 keliedaGfksveyesltgGv 225
                                       +e i++aGf+ v+ e+l g v
  gi|488599851|ref|YP_007906322.1| 180 DENIRKAGFSIVKEEHLLGTV 200
                                       56699*******988876655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   3.3e-22     5e-19       1      97 []      52     142 ..      52     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 3.3e-22
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +L++G GtG+++ +  +    +++++vDise+m+ +a+er++++  +v++++ dae+lpf+d+ fD+v+ +++++ +
  gi|488599851|ref|YP_007906322.1|  52 ILEIGVGTGKNVPYYRD----GHYIAVDISEKMIFKAKERVRNSTKDVQLIVSDAESLPFKDDVFDIVFTTFVFCSV 124
                                       8*********9998863....69******************99999************************8776665 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +  +  k lke++rvLkp+G
  gi|488599851|ref|YP_007906322.1| 125 E--NPIKGLKEAYRVLKPDG 142
                                       5..6679************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   1.1e-20   1.6e-17      13     164 ..      37     192 ..      12     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.1e-20
                   Methyltransf_23  13 lerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgk 82 
                                       ++ l+++    +g r+L+iG GtG + +++r+   ++++vD+s++++ +a+     ++k  q    d+++ +++++ 
  gi|488599851|ref|YP_007906322.1|  37 RKYLFERinPCEGDRILEIGVGTGKNVPYYRDG--HYIAVDISEKMIFKAKervrnSTKDVQLIVSDAESLPFKDDV 111
                                       34444443234566****************888..9**************99999877777777888899999**** PP

                   Methyltransf_23  83 fdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldw.lylvpagrhisffsarslkelleea 158
                                       fd++  ++v+++v++p + l+ +++ lkp+G+++++e+   l+ +rl++ + ++l+p  r +     r   e  ++a
  gi|488599851|ref|YP_007906322.1| 112 FDIVFTTFVFCSVENPIKGLKEAYRVLKPDGRAFFLEH--MLPKNRLIQPIfHLLNPIARMMGPEINRKTDENIRKA 186
                                       **************************************..6899999999989999998888444448889999999 PP

                   Methyltransf_23 159 Glevve 164
                                       G+++v+
  gi|488599851|ref|YP_007906322.1| 187 GFSIVK 192
                                       999986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.1e-18   1.7e-15       4     112 ..      49     149 ..      47     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.1e-18
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g r+l++G GtG+ +         +++++ +Dise++i +A+e+ + +  + v++ ++d+e+l+  ++d+ fD++++
  gi|488599851|ref|YP_007906322.1|  49 GDRILEIGVGTGKNVPYYR-----DGHYIAVDISEKMIFKAKERVR-NSTKDVQLIVSDAESLP--FKDDVFDIVFT 117
                                       5689999999988877666.....99*****************988.55667************..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedp 112
                                         v++ + +p k l+e+ rvlkp+g+    ++
  gi|488599851|ref|YP_007906322.1| 118 TFVFCSVENPIKGLKEAYRVLKPDGRAFFLEH 149
                                       *************************9776665 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   1.2e-16   1.7e-13       1      98 [.      53     143 ..      53     144 .. 0.85
   2 ?   -1.3   0.0       2.5   3.7e+03      74      95 ..     145     166 ..     143     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.2e-16
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       LeiG GtG ++ + ++     +y++vDis+++i     k ++r +n+++ v+l + d+++l+ + + fD+v+  +v+
  gi|488599851|ref|YP_007906322.1|  53 LEIGVGTGKNVPYYRDG----HYIAVDISEKMI----FKAKERVRNSTKDVQLIVSDAESLPFKdDVFDIVFTTFVF 121
                                       8************9777....************....555555555556777777777666666789********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGr 98 
                                       + ++++ + l++++++Lkp+Gr
  gi|488599851|ref|YP_007906322.1| 122 CSVENPIKGLKEAYRVLKPDGR 143
                                       *********************7 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                   Methyltransf_12  74 nvlhhlkdirevldnirklLkp 95 
                                       ++l+h+ +++++++ i +lL+p
  gi|488599851|ref|YP_007906322.1| 145 FFLEHMLPKNRLIQPIFHLLNP 166
                                       5799999999999999999998 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   9.3e-07    0.0014     102     215 ..      34     144 ..      20     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.3e-07
                                       HHHHH.HGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS CS
                    Methyltransf_9 102 wkWdr.vlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieql 177
                                        kW + + + +++ +g +il++G g+G  +     +g  ++v i   e   + f+a +++ ++++ ++l+    e l
  gi|488599851|ref|YP_007906322.1|  34 KKWRKyLFERINPCEGDRILEIGVGTGKNVP-YYRDGHYIAVDIS--EK--MIFKAKERVRNSTKDVQLIVSDAESL 105
                                       58876356899****************8763.3456666666555..54..468999*************9****** PP

                                       -T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEE CS
                    Methyltransf_9 178 pe.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGel 215
                                       p   + fd+vf+  v+   + P+  l +    l+ +G  
  gi|488599851|ref|YP_007906322.1| 106 PFkDDVFDIVFTTFVFCSVENPIKGLKEAYRVLKPDGRA 144
                                       *86889************************999999964 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.4e-06    0.0081      73     134 ..      48     103 ..      23     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.4e-06
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       +g+r+Le+G G+G +         ++g+ ++++ +++++ +ak++++++  ++v+++v+D +
  gi|488599851|ref|YP_007906322.1|  48 EGDRILEIGVGTGKNVPY-----YRDGHYIAVDISEKMIFKAKERVRNST-KDVQLIVSDAE 103
                                       799**********98654.....578999*****************9976.56888888865 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.017     105     155 ..      94     145 ..      71     182 .. 0.85
   2 ?   -1.7   0.0       1.4   2.1e+03     170     198 ..     180     209 .]     153     209 .] 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                       STTEEES-TTS-S--TT-EEEEEEES--.-SS-HHHHHHHHHHHEEEEEEEE CS
                    Methyltransf_8 105 nervvacdlakvPledesvdvavfclsl.mgtnladflkeanrvlkvGGllk 155
                                       + ++++ d   +P +d+  d++   + +  ++n  + lkea+rvlk+ G  +
  gi|488599851|ref|YP_007906322.1|  94 DVQLIVSDAESLPFKDDVFDIVFTTFVFcSVENPIKGLKEAYRVLKPDGRAF 145
                                       5577899**************98776651579999***********999755 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                                       HHHHHCTTEEEEE.EE--STTEEEEEEEE- CS
                    Methyltransf_8 170 araltklGfevks.kdlsnkqfvlfefkkv 198
                                        +++ k Gf +++  +l  + f l+e +kv
  gi|488599851|ref|YP_007906322.1| 180 DENIRKAGFSIVKeEHLLGTVFRLVEAEKV 209
                                       567888899875515567788888887775 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   8.2e-06     0.012      35     164 ..      20     146 ..      11     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.2e-06
                                       --SSTT--HHHHHHHHH.HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-S CS
                              CMAS  35 yferddmtLeeAqlaKl.dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldl 110
                                       ++e +++ +e   ++K  + ++e+++  +G+++L+iG G G+ v +     d + +++ +S++   +ak+rv +   
  gi|488599851|ref|YP_007906322.1|  20 IYEIAEAPMELFLSKKWrKYLFERINPCEGDRILEIGVGTGKNVPYYR---DGHYIAVDISEKMIFKAKERVRNST- 92 
                                       555555555555556641567899999**************9988754...679******************9987. PP

                                       SS-EEEEES-GGG-..--.--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                              CMAS 111 erkvevklldyedl..de.kvdrvvsvgafehvgkenydtffkklkkllkedGllll 164
                                        ++v++ ++d e l  ++  +d v +   f    +en  +  k+++++lk+dG+   
  gi|488599851|ref|YP_007906322.1|  93 -KDVQLIVSDAESLpfKDdVFDIVFT--TFVFCSVENPIKGLKEAYRVLKPDGRAFF 146
                                       .5566666666655114534454444..45556678888889999999999997544 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.4e-05     0.036      69     141 ..      72     143 ..      48     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                              NodS  69 tvvdvveeaiararervkes.shiswivsdvqqfs.tdekfdlivvaevlyyiedvaelraavrnlvsllapdgq 141
                                         vd+ e+ i +a+erv++s  +++ ivsd + +  +d+ fd++  + v+  +e+  +    +++  ++l+pdg+
  gi|488599851|ref|YP_007906322.1|  72 IAVDISEKMIFKAKERVRNStKDVQLIVSDAESLPfKDDVFDIVFTTFVFCSVENPIK---GLKEAYRVLKPDGR 143
                                       579**************986268**********97357789*9999999887776432...34455556666665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.5e-05     0.067      13     101 ..      48     137 ..      38     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-05
                              MetW  13 pgsrvldlGcGdGellellkeek....qvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtl 85 
                                       +g r+l++G G G+ + + ++ +    +++ + + + +e v ++ +k +++i  d+++    f+d+ fd+v  +  +
  gi|488599851|ref|YP_007906322.1|  48 EGDRILEIGVGTGKNVPYYRDGHyiavDISEKMIFKAKERVRNS-TKDVQLIVSDAES--LPFKDDVFDIVFTTFVF 121
                                       4789***************9977111134445555555555544.5778888887765..579************** PP

                              MetW  86 qatrnpkevldellri 101
                                        ++ np + l+e  r+
  gi|488599851|ref|YP_007906322.1| 122 CSVENPIKGLKEAYRV 137
                                       *************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1413.96
//
Query:       gi|488599852|ref|YP_007906323.1|  [L=177]
Description: hypothetical protein Asulf_00298 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   29.8   0.0    8.2e-07   28.9   0.0    1.5  1  MarR             MarR family
    1.2e-05   24.8   0.0    2.2e-05   23.9   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    7.1e-05   22.6   0.0    0.00012   21.9   0.0    1.3  1  MarR_2           MarR family
    9.2e-05   22.2   0.0    0.00046   20.0   0.0    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00029   21.3   0.0    0.00071   20.0   0.0    1.6  1  HTH_27           Winged helix DNA-binding domain
      0.007   16.3   0.0      0.013   15.4   0.0    1.4  1  TBPIP            TBPIP/Hop2 winged helix domain
     0.0078   16.3   0.0      0.012   15.6   0.0    1.3  1  HTH_20           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.7   0.0       0.02   15.1   0.0    1.4  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.017   15.1   1.3      0.059   13.4   0.2    2.2  2  HTH_19           Helix-turn-helix domain
      0.032   14.6   0.0      0.057   13.8   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
      0.056   12.8   1.0      0.098   12.0   1.1    1.4  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
      0.082   12.6   0.0       0.09   12.5   0.0    1.1  1  Tetraspanin      Tetraspanin family
       0.14   11.8   0.9        4.7    6.8   0.2    2.1  2  TerC             Integral membrane protein TerC family
       0.16   12.3   0.3       0.21   11.9   0.3    1.1  1  Pro-rich         Proline-rich


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 !   28.9   0.0   6.4e-10   8.2e-07       1      51 [.     108     158 ..     108     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.4e-10
                                       --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR   1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       l+  + +iLri+++++++++  L  + g s+s ++ + ++Le+++li R++
  gi|488599852|ref|YP_007906323.1| 108 LNDDEAKILRIIHDNEGITQDSLHFRTGFSQSKISMIMKKLEERDLIVRER 158
                                       5677899*****************************************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 !   23.9   0.0   1.7e-08   2.2e-05       7      47 ..     114     154 ..     112     155 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.7e-08
                            HTH_24   7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       kIL+++ +n +i+q  L  r+g S+s ++  +k+Lee  lI
  gi|488599852|ref|YP_007906323.1| 114 KILRIIHDNEGITQDSLHFRTGFSQSKISMIMKKLEERDLI 154
                                       8*************************************999 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   9.2e-08   0.00012       7      55 ..     112     158 ..     108     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.2e-08
                                       HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       +a +L  +++++g  +t+  l  r+g s+s +s i k+L+++ L++r++
  gi|488599852|ref|YP_007906323.1| 112 EAKILRIIHDNEG--ITQDSLHFRTGFSQSKISMIMKKLEERDLIVRER 158
                                       7899*********..*******************************985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.2   1.5e+03      15      34 ..      66      85 ..      62      88 .. 0.82
   2 !   20.0   0.0   3.6e-07   0.00046       6      62 ..     108     166 ..     108     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                                      HHHHHHCCCHHCHHCCCTTS CS
                              TrmB 15 laLlklgpatadeiaeelgv 34
                                      l L+k  +++++ + +++++
  gi|488599852|ref|YP_007906323.1| 66 LSLVKTSSSEVSNLERDTNL 85
                                      67999999999999988876 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.6e-07
                                       HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.ST.TTEE CS
                              TrmB   6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.gr.pklY 62 
                                       L++ Eak+   +  ++  t d ++ ++g ++sk+  ++++Le+++l+ re+ g+ +k+Y
  gi|488599852|ref|YP_007906323.1| 108 LNDDEAKILRIIHDNEGITQDSLHFRTGFSQSKISMIMKKLEERDLIVRERfGKtYKIY 166
                                       7899*********************************************9964446666 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 !   20.0   0.0   5.6e-07   0.00071       4      52 ..     111     158 ..     104     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.6e-07
                            HTH_27   4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52 
                                        +a +L+ i   +++ ++  l++r+ +++s is ++kkL+e++L++r++
  gi|488599852|ref|YP_007906323.1| 111 DEAKILRIIH-DNEGITQDSLHFRTGFSQSKISMIMKKLEERDLIVRER 158
                                       5777899999.66666669**************************7764 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05     0.013      28      60 ..     134     167 ..     127     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                             TBPIP  28 kklgKtavqkaLdeLvdegkiieKeyGKq.kiYl 60 
                                        +++   +  ++ +L++ ++i+   +GK+ kiYl
  gi|488599852|ref|YP_007906323.1| 134 TGFSQSKISMIMKKLEERDLIVRERFGKTyKIYL 167
                                       4788889999***********************8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.6e-06     0.012      13      60 ..     113     160 ..     102     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.6e-06
                                       HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       ++ilr ++++eg t   l+ r + s++ +s  +++Lee +L+ ++r g
  gi|488599852|ref|YP_007906323.1| 113 AKILRIIHDNEGITQDSLHFRTGFSQSKISMIMKKLEERDLIVRERFG 160
                                       79*******************************************988 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.5e-05      0.02      17      53 ..     123     159 ..     110     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                    B-block_TFIIIC  17 sGitqsdLakeskqdprslfyrlksLekkgLIvkqsi 53 
                                       +Gitq +L+  ++ + +++  ++k+Le+  LIv+   
  gi|488599852|ref|YP_007906323.1| 123 EGITQDSLHFRTGFSQSKISMIMKKLEERDLIVRERF 159
                                       8********************************9876 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.54   6.9e+02      22      35 ..      69      82 ..      62     112 .. 0.81
   2 ?   13.4   0.2   4.6e-05     0.059       5      43 ..     117     157 ..     113     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.54
                            HTH_19 22 lgisrskisaiEng 35
                                      +++s s  s++E +
  gi|488599852|ref|YP_007906323.1| 69 VKTSSSEVSNLERD 82
                                      68889999999987 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.6e-05
                            HTH_19   5 keaReelgltqeelaerlgisrskisaiEng..kkdvpsae 43 
                                       + +  + g+tq+ l  r+g+s+skis+i +   ++d + +e
  gi|488599852|ref|YP_007906323.1| 117 RIIHDNEGITQDSLHFRTGFSQSKISMIMKKleERDLIVRE 157
                                       5566789*********************8776666555555 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.5e-05     0.057       3      61 ..     110     164 ..     108     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                                       -S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEE CS
                   Penicillinase_R   3 elEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafi 61 
                                       + Ea++++i+++++ +t ++++ +       ++s +  ++++L++++l+ re+ g+++ 
  gi|488599852|ref|YP_007906323.1| 110 DDEAKILRIIHDNEGITQDSLHFRT----GFSQSKISMIMKKLEERDLIVRERFGKTYK 164
                                       679**************88877554....46799*********************9983 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1   7.6e-05     0.098      83     133 ..     107     155 ..      62     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                                       TSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXE CS
                     RNA_pol_Rpc34  83 slsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyik 133
                                        l+ de+ ++ iI++  neGI +  +  +++  +s +  ++k Le + +i 
  gi|488599852|ref|YP_007906323.1| 107 LLNDDEAKILRIIHD--NEGITQDSLHFRTGFSQSKISMIMKKLEERDLIV 155
                                       466788899999997..9****************************99985 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05      0.09      46     132 ..      16      97 ..       2     147 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                                       .......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX--HHH.........HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Tetraspanin  46 pailaillivvGvllfllgflGcigalkenkcllltfs.llllvlfllelaagilgfvfsdkargkvsei.innaie 120
                                       + ++   l++ G+++++++fl ++  l+   ++   ++  l ++l ll la++il +v +++  ++vs+   +++++
  gi|488599852|ref|YP_007906323.1|  16 AEFV---LLIGGAFFLFTSFL-LFPNLHHYMMMGPYYMsYLPFILGLLGLAMIILSLVKTSS--SEVSNLeRDTNLK 86 
                                       3333...55555555555555.5555655554444444344466677777777788888888..6776653677776 PP

                                       HHHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Tetraspanin 121 vkyrddldlkkc 132
                                       ++ +++++ +k+
  gi|488599852|ref|YP_007906323.1|  87 NH-EENQNERKD 97 
                                       66.444444443 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0037       4.7      52      79 ..      10      36 ..       5      46 .. 0.79
   2 ?    3.8   0.0     0.032        41      50     106 ..      43     105 ..      38     109 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0037
                              TerC 52 avallelfdlilligglfLlytavkell 79
                                      ++ l ++ +++lligg+f l+t++ ++ 
  gi|488599852|ref|YP_007906323.1| 10 ISELNNA-EFVLLIGGAFFLFTSFLLFP 36
                                      5556666.9*************998775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.032
                              TerC  50 llavallelfdlilligglfLlytavkellekr.....le.nklvkeekkkkkktkstllavv 106
                                       +++ + ++++++il + gl ++++++    +++      + n +++ee+++++k +++l +++
  gi|488599852|ref|YP_007906323.1|  43 MMGPYYMSYLPFILGLLGLAMIILSLVKTSSSEvsnleRDtNLKNHEENQNERKDNEKLSVAL 105
                                       555566777789999999888888877777666788763334455555555555555565555 PP

>> Pro-rich  Proline-rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00016      0.21       3      46 ..      56      99 ..      54     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                          Pro-rich  3 liLLsvaLLaLssaqsseedvsqeeslsllseeleeqsqqggek 46
                                      l LL  a+++Ls ++ s+ +vs+ e  ++l++++e+q++ ++++
  gi|488599852|ref|YP_007906323.1| 56 LGLLGLAMIILSLVKTSSSEVSNLERDTNLKNHEENQNERKDNE 99
                                      66999****************************99999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1220.90
//
Query:       gi|488599853|ref|YP_007906324.1|  [L=113]
Description: hypothetical protein Asulf_00299 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   5.2      0.027   14.6   5.2    1.1  1  Keratin_2_head  Keratin type II head
        4.3    7.7   7.5        6.1    7.2   7.5    1.2  1  DUF1190         Protein of unknown function (DUF1190)


Domain annotation for each model (and alignments):
>> Keratin_2_head  Keratin type II head
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   5.2   3.1e-06     0.027      81     130 ..      26      67 ..       4      87 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-06
                    Keratin_2_head  81 ggfgl.GfggGvglgfgagggvGggfGgggglvGgggfGgggfGggGfGgp 130
                                         fg+ G+g G+ +g+  gg +G     g+ ++Gg+ +G  g+G  G+G+p
  gi|488599853|ref|YP_007906324.1|  26 TPFGWrGYGYGMPMGM--GGMMG----YGMPMMGGPMMG--GYG-AGYGMP 67 
                                       3333334444433333..33333....333333333333..333.334432 PP

>> DUF1190  Protein of unknown function (DUF1190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.5   0.00068       6.1      71     119 ..      37      93 ..      28     100 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00068
                           DUF1190  71 mPlmaGfmlgrll........sggg..gyrsqPlyrsrsrestlsgkeafvsasgkny.g 119
                                       mP+ +G m+g  +        +  g  + + +P y  ++++ + +++ + +++++++y +
  gi|488599853|ref|YP_007906324.1|  37 MPMGMGGMMGYGMpmmggpmmG--GygAGYGMPAYDYQYPQDPSNQN-QNINETSEQYpQ 93 
                                       5555555555544433333221..12234689*****9999998888.667777777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 854.22
//
Query:       gi|488599854|ref|YP_007906325.1|  [L=74]
Description: hypothetical protein Asulf_00300 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   74.5   1.7      7e-21   74.1   1.7    1.3  1  YHS              YHS domain
     0.0036   17.6   0.7     0.0085   16.4   0.7    1.7  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
      0.066   13.2   1.5       0.88    9.6   1.5    2.3  1  DUF2116          Uncharacterized protein containing a Zn-ribb


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   1.7   1.2e-24     7e-21       2      47 ..      19      64 ..      18      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 1.2e-24
                               YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYata 47
                                      +dPvcgm +d+eka +kseY+Gk+YyFcS  Ck  F+++PekY+++
  gi|488599854|ref|YP_007906325.1| 19 KDPVCGMVIDREKAVSKSEYMGKTYYFCSLDCKKTFDENPEKYLKK 64
                                      7******************************************976 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.7   1.4e-06    0.0085       4      35 ..      23      56 ..      22      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                   Arc_trans_TRASH  4 CGkeivgePivyklk..nkvYyvCCktCkselkk 35
                                      CG +i  e  v k+    k+Yy+C   Ck+ + +
  gi|488599854|ref|YP_007906325.1| 23 CGMVIDREKAVSKSEymGKTYYFCSLDCKKTFDE 56
                                      999999999998865227************9976 PP

>> 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 ?    9.6   1.5   0.00015      0.88      16      39 ..      42      65 ..      20      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                           DUF2116 16 desfCsekCqeeyekkrkkvarsq 39
                                      +  fCs +C++ ++++  k  + +
  gi|488599854|ref|YP_007906325.1| 42 TYYFCSLDCKKTFDENPEKYLKKR 65
                                      5579**********9999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 514.28
//
Query:       gi|488599855|ref|YP_007906326.1|  [L=662]
Description: hypothetical protein Asulf_00301 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-08   32.5  13.3    1.6e-06   27.9   5.7    5.9  6  Fer4_5    4Fe-4S binding domain
    0.00039   20.3   0.0     0.0009   19.1   0.0    1.6  1  COX2      Cytochrome C oxidase subunit II, periplasmic domain
  ------ inclusion threshold ------
      0.031   15.2   0.7      0.031   15.2   0.7    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
       0.84    9.9   7.1        1.8    8.8   2.6    2.1  2  Fer4_9    4Fe-4S dicluster domain
        1.4    9.0  11.1       0.37   10.9   4.1    2.6  2  Fer4_10   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.7      0.07   2.5e+02       6      21 ..     220     235 ..     216     236 .. 0.85
   2 !   27.9   5.7   4.6e-10   1.6e-06       2      46 ..     245     286 ..     244     296 .. 0.90
   3 ?   -2.5   1.4       1.5   5.3e+03       8      18 ..     306     316 ..     302     323 .. 0.50
   4 !   17.9   0.8   6.3e-07    0.0022       2      29 ..     328     356 ..     327     358 .. 0.77
   5 ?   -4.0   0.7       4.3   1.5e+04       3      18 ..     510     525 ..     508     526 .. 0.75
   6 ?   -3.7   3.4       3.4   1.2e+04       6      15 ..     559     568 ..     554     590 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.07
                            Fer4_5   6 lilflaivlvtllfGR 21 
                                        i+f+++v+v+++fG 
  gi|488599855|ref|YP_007906326.1| 220 SIFFFTLVIVAGFFGN 235
                                       59999********995 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 4.6e-10
                            Fer4_5   2 allllilflaivlvtllfGRafCgWiCPfGalqellakllrrklg 46 
                                       a++++++f+++ ++ l+ GR++C  +CP+ +l e++a+  rr++g
  gi|488599855|ref|YP_007906326.1| 245 AVVWILWFAIVEFTILFAGRFWCA-ACPIPVLGEWIAR--RRIVG 286
                                       67999999999999999*******.************9..77665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.5
                            Fer4_5   8 lflaivlvtll 18 
                                        ++++++++l+
  gi|488599855|ref|YP_007906326.1| 306 SVIGFFVLSLF 316
                                       34444444444 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 6.3e-07
                            Fer4_5   2 allllilfl.aivlvtllfGRafCgWiCP 29 
                                       a+++l l++ a +l tl+ GR+fC +iCP
  gi|488599855|ref|YP_007906326.1| 328 AVVFLTLVIaATLLYTLYPGRYFCRHICP 356
                                       567888888455555555*********** PP

  == domain 5  score: -4.0 bits;  conditional E-value: 4.3
                            Fer4_5   3 llllilflaivlvtll 18 
                                       ++ll+  la+v+ +++
  gi|488599855|ref|YP_007906326.1| 510 WALLVSTLALVAYPAV 525
                                       7888888888888776 PP

  == domain 6  score: -3.7 bits;  conditional E-value: 3.4
                            Fer4_5   6 lilflaivlv 15 
                                       l+ ++a+ + 
  gi|488599855|ref|YP_007906326.1| 559 LFVWIAFAVS 568
                                       4444433332 PP

>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.5e-07    0.0009      53     116 ..      79     148 ..      64     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.5e-07
                              COX2  53 etkirllvtaedvlhsfavpslg.....vkvdavpGrlnqvs.llidreGvfyGqcselcGvnhssmpiv 116
                                         ++ + v + dv h f +  ++      k+ + pGr+ +v  ++ dreG f  +cs  cG +h +m + 
  gi|488599855|ref|YP_007906326.1|  79 GDRVLFRVISRDVTHGFYIDGYTpspsdQKIFVLPGRVLEVGpITFDREGKFKLRCSVTCGPLHPFMVMD 148
                                       567899999*******99865532222378999****988853789******************997543 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.4       1.2   4.3e+03       8      15 ..     351     358 ..     349     410 .. 0.62
   2 ?   15.2   0.7   8.7e-06     0.031       2      20 ..     413     431 ..     412     454 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                           Fer4_16   8 CaevCPtn 15 
                                       C  +CP++
  gi|488599855|ref|YP_007906326.1| 351 CRHICPAS 358
                                       67777764 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.7e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       Cg+C +C+++CP n ++ k
  gi|488599855|ref|YP_007906326.1| 413 CGECFECIKSCPKNNMTVK 431
                                       ***************9988 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.2    0.0014       4.9       8      49 ..     351     426 ..     348     428 .. 0.83
   2 ?    8.8   2.6    0.0005       1.8       1      19 [.     412     430 ..     412     435 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0014
                            Fer4_9   8 CveaCpagvvvedaaerkarlraase..................................eaCigCgaCveaCpkg 49 
                                       C + Cpa  +++ +++  +   + ++                                  + C +C +C++ Cpk+
  gi|488599855|ref|YP_007906326.1| 351 CRHICPASGYIGYHSNVSILSVRSRDreicrshkskdcikgnskgygcpwklypggncenTYCGECFECIKSCPKN 426
                                       88899988887777766666666666689999999999999999999999999999999989************96 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0005
                            Fer4_9   1 kCtgCgaCveaCpagvvve 19 
                                       +C +C +C+++Cp++ ++ 
  gi|488599855|ref|YP_007906326.1| 412 YCGECFECIKSCPKNNMTV 430
                                       5888888999998888765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2  11.7      0.23   8.1e+02       7      56 .]     411     424 ..     349     424 .. 0.57
   2 ?   10.9   4.1    0.0001      0.37       6      27 ..     410     431 ..     406     449 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.23
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                         C +                                    c++C+++CP
  gi|488599855|ref|YP_007906326.1| 411 TYCGE------------------------------------CFECIKSCP 424
                                       23444....................................666666666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvg 27 
                                          C +C +C k+CP ++ +v+
  gi|488599855|ref|YP_007906326.1| 410 NTYCGECFECIKSCPKNNMTVK 431
                                       568************9553333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 3978.61
//
Query:       gi|488599856|ref|YP_007906327.1|  [L=128]
Description: hypothetical protein Asulf_00302 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-12   47.1   0.1    2.4e-12   46.8   0.1    1.2  1  COX2          Cytochrome C oxidase subunit II, periplasmic do
    8.2e-09   35.5   0.0      1e-08   35.2   0.0    1.1  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.15   12.5   0.2        1.7    9.2   0.2    2.2  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.1     4e-16   2.4e-12      46     114 ..      53     122 ..      37     128 .] 0.91

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 4e-16
                              COX2  46 nrvvlpvetkirllvtaedvlhsfavpslgvkvdav.pGrlnqvsllidreGvfyGqcselcGvnhssmp 114
                                       n vv+   +k+rl+v + dv+h f++pslg+ +  +  G+ + + +++++eG+++  cs  c   h +m 
  gi|488599856|ref|YP_007906327.1|  53 NLVVVEKGQKVRLIVESMDVVHGFTIPSLGINTGPIdVGKRKVIEFVAEKEGIYFFGCSVRCSPYHFFMR 122
                                       6699999*************************987626999999***********************996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.7e-12     1e-08       8     104 .]      21     127 ..      10     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.7e-12
                      Cupredoxin_1   8 llllsskaa..aaaektveit...vkdggfePskievkagekvklkiknkdktpeefesedlgee.kvlapgkttti 78 
                                       l+lls +++  a+++ tv+i    ++ ggf+P+ + v++g+kv+l ++  d  ++ f++++lg++   ++ gk ++i
  gi|488599856|ref|YP_007906327.1|  21 LALLSMDREflAEENGTVVIRayiAEAGGFKPNLVVVEKGQKVRLIVESMD-VVHGFTIPSLGINtGPIDVGKRKVI 96 
                                       2333333334677777777752224689*****************999887.58*********99458********* PP

                      Cupredoxin_1  79 tiaplkpGeYeftcd.....mhmdakGkliV 104
                                       ++ ++k+G Y f c      +h +++G +iV
  gi|488599856|ref|YP_007906327.1|  97 EFVAEKEGIYFFGCSvrcspYHFFMRGIIIV 127
                                       **************98877777789**9998 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00028       1.7      66      99 .]      90     128 .]      43     128 .] 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00028
                                       TTEEEEEEEE.SSEE.EEE....EETT.TTTTTSEEEEEEE CS
                       Copper-bind  66 gGekdsvtfd.eagt.Ykf....fCsP.HaaagMkgkvtve 99 
                                        G+ + ++f  e+++ Y f     CsP H+  +M+g ++v+
  gi|488599856|ref|YP_007906327.1|  90 VGKRKVIEFVaEKEGiYFFgcsvRCSPyHF--FMRGIIIVK 128
                                       466667777642333465511115789998..89***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 845.97
//
Query:       gi|488599857|ref|YP_007906328.1|  [L=46]
Description: hypothetical protein Asulf_00303 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 307.67
//
Query:       gi|488599858|ref|YP_007906329.1|  [L=124]
Description: transcriptional regulator, ArsR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-16   58.7   1.5    5.3e-16   58.2   1.5    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    2.6e-08   33.8   0.1    4.2e-08   33.1   0.1    1.3  1  HTH_20           Helix-turn-helix domain
     0.0013   18.6   0.1     0.0023   17.7   0.1    1.4  1  TFIIE_alpha      TFIIE alpha subunit
     0.0019   17.7   0.8     0.0046   16.5   0.8    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.018   15.0   0.2      0.035   14.1   0.2    1.7  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.027   14.4   0.2      0.043   13.7   0.2    1.3  1  MarR_2           MarR family
       0.05   14.0   0.1      0.096   13.1   0.1    1.5  1  Penicillinase_R  Penicillinase repressor
      0.052   13.4   0.1      0.076   12.9   0.1    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.081   13.1   0.0       0.15   12.2   0.0    1.4  1  DpnI_C           Dam-replacing HTH 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 !   58.2   1.5   2.7e-19   5.3e-16       1      47 []      44      90 ..      44      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 2.7e-19
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      d+ R+kIL  L+++elc c++++++gls s+vSh+L++Lr+  LV++
  gi|488599858|ref|YP_007906329.1| 44 DSSRIKILLTLSKRELCTCDISAITGLSVSAVSHQLRILRDKKLVKY 90
                                      789**************************************999975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   2.1e-11   4.2e-08       2      61 .]      37      95 ..      36      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.1e-11
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      + +eA+++ +R +il  L ++++l+  ++ +  +ls + +s++Lr+L++  Lv+ +regr
  gi|488599858|ref|YP_007906329.1| 37 EFLEAFGDSSRIKILLTL-SKRELCTCDISAITGLSVSAVSHQLRILRDKKLVKYRREGR 95
                                      679***************.***************************************98 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.2e-06    0.0023       8      92 ..      40     117 ..      34     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                                       HHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCC CS
                       TFIIE_alpha   8 rkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdv 84 
                                         f + + +++l  L  k e+   d++  +++    + + L  L++++lvky+r+       +++y+ +++e++  +
  gi|488599858|ref|YP_007906329.1|  40 EAFGDSSRIKILLTLS-KRELCTCDISAITGLSVSAVSHQLRILRDKKLVKYRRE------GRNVYYSLDDEHVAAI 109
                                       4444477889998887.9999999*****************************96......47899*******9999 PP

                                       HHHHHHHH CS
                       TFIIE_alpha  85 vkrkleev 92 
                                       +   le++
  gi|488599858|ref|YP_007906329.1| 110 LDTALEHI 117
                                       99888876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.8   2.3e-06    0.0046       4      48 .]      46      89 ..      44      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-06
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       ++kIL +L k   ++  +++  +glS+s+v+ +l+ L ++ l+k
  gi|488599858|ref|YP_007906329.1| 46 SRIKILLTLSK-RELCTCDISAITGLSVSAVSHQLRILRDKKLVK 89
                                      56788888888.5566669*********************99986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.7e-05     0.035      26      55 ..      63      94 ..      31     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.E CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.rg.r 55
                                      +++++ Gl+ + vs  l+ L++++l++ r+ +
  gi|488599858|ref|YP_007906329.1| 63 DISAITGLSVSAVSHQLRILRDKKLVKyRReG 94
                                      899************************75423 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.2e-05     0.043      26      56 ..      63      93 ..      46      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                                      HHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 26 elarrlglsksavsrilkrLvaaGLverrpg 56
                                      ++ + +gls savs  l+ L ++ Lv +r+ 
  gi|488599858|ref|YP_007906329.1| 63 DISAITGLSVSAVSHQLRILRDKKLVKYRRE 93
                                      89************************99964 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.8e-05     0.096      32      63 ..      69     100 ..      57     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                                       ---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
                   Penicillinase_R  32 elaysTVktllrrLvkKgllsrekegrafiYs 63 
                                        l+ s V   lr L +K+l++ ++egr   Ys
  gi|488599858|ref|YP_007906329.1|  69 GLSVSAVSHQLRILRDKKLVKYRREGRNVYYS 100
                                       5778899999******************9886 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   0.1   3.8e-05     0.076      19      65 ..      55     101 ..      48     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                                       HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                              TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65 
                                       ++ ++ + +i+ ++g++ s v   Lr L dk lV+ +++ +++Y  +
  gi|488599858|ref|YP_007906329.1|  55 SKRELCTCDISAITGLSVSAVSHQLRILRDKKLVKYRREGRNVYYSL 101
                                       677778889*****************************999999765 PP

>> DpnI_C  Dam-replacing HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.5e-05      0.15      47      67 ..      75      95 ..      72      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                                      HHHHHHHHHHTTSEEE-STTE CS
                            DpnI_C 47 irqqLqvlRDkglieFlgrGk 67
                                      ++ qL +lRDk l+++  +G+
  gi|488599858|ref|YP_007906329.1| 75 VSHQLRILRDKKLVKYRREGR 95
                                      678*************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 876.77
//
Query:       gi|488599859|ref|YP_007906330.1|  [L=686]
Description: heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-51  174.3   0.4    1.7e-51  174.3   0.4    1.9  2  E1-E2_ATPase  E1-E2 ATPase
    1.7e-42  146.1   1.6    3.3e-42  145.2   1.6    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
    3.6e-10   40.1   2.9    3.6e-10   40.1   2.9    2.9  3  HMA           Heavy-metal-associated domain
    4.5e-07   29.9   0.5      0.017   14.9   0.4    3.0  3  Hydrolase_3   haloacid dehalogenase-like hydrolase
    2.5e-05   24.8   0.1    0.00013   22.4   0.1    2.2  1  HAD           haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.026   14.6   0.0    1.6  1  HAD_2         Haloacid dehalogenase-like hydrolase
      0.047   13.1   0.0      0.082   12.3   0.0    1.3  1  TssN          Type VI secretion system, TssN
        2.4    7.7   3.7       0.56    9.7   0.2    1.7  2  CD34_antigen  CD34/Podocalyxin 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 !  174.3   0.4   7.6e-55   1.7e-51       3     181 .]     194     373 ..     192     373 .. 0.97
   2 ?   -3.4   0.1       2.7   6.1e+03      93     121 ..     620     648 ..     608     681 .. 0.47

  Alignments for each domain:
  == domain 1  score: 174.3 bits;  conditional E-value: 7.6e-55
                                       S--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE- CS
                      E1-E2_ATPase   3 lpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsg 79 
                                       +p+ a++  dg++++ + +++++GD++++++g+++p+Dg++v+g++ vd+saLTGEs+p ++ +gd+v sG+v++sg
  gi|488599859|ref|YP_007906330.1| 194 KPTFANLKVDGKTVRAKPEDVKVGDLIVVRPGEKIPLDGVVVKGTSVVDTSALTGESKPSSVAEGDEVLSGMVNMSG 270
                                       577788889******************************************************************** PP

                                       EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHHH CS
                      E1-E2_ATPase  80 eakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralall 155
                                        ++++Vt+  +d+++++i +lveea s+k++ +k++++++++++p+v+++a+ ++++ +l+ ++++ ++++ral+ll
  gi|488599859|ref|YP_007906330.1| 271 LLTVRVTKPFSDSTVSRILQLVEEAGSRKARAEKFITRFARYYTPAVIAMAVSIAALPPLILGEPFtTWIYRALVLL 347
                                       *********************************************************9998888888********** PP

                                       HHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 156 vaaiPcaLplavplalalgarrlakk 181
                                       v+++PcaL+l vpl+++++++++a++
  gi|488599859|ref|YP_007906330.1| 348 VISCPCALVLSVPLSYFASIGKAARE 373
                                       ***********************985 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.7
                                       TTTTTSTTS--------HHHHHHHHHHHH CS
                      E1-E2_ATPase  93 elgkiarlveeakskktplqkkldklgkv 121
                                       + +k+ar+++ +++++  + ++++   +v
  gi|488599859|ref|YP_007906330.1| 620 KPSKVARSIRLSQRTQRIVWQNISFALAV 648
                                       44555555555553333333333332222 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.2   1.6   1.5e-45   3.3e-42       2     210 .]     390     595 ..     389     595 .. 0.91

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 1.5e-45
                                       SEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakarsgaltgfatfigrg..... 67 
                                       + v+fDk+GTLt+g+ +v +v++++       l+ aa  e+ s+hpi+k ++ a+ +++g+++++ +++grg     
  gi|488599859|ref|YP_007906330.1| 390 RIVAFDKTGTLTKGSFRVAEVVAKNgfskenVLKFAALVEMHSNHPIAKSIIDAYGEIGGSVKSYKELAGRGvraei 466
                                       579**********************66655555555555555*********************************** PP

                                       ...HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH.TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEE CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ...ayaigkpewltaldippdlgaaigsaqsqgrtvall.qaralavftiadplkvkpeaaeavasLkaagievvll 140
                                          ++  g+  +++++      + + +s+  +g  v +  ++ + +++ ++d+  +k++a+eav+ Lk+ g++vv++
  gi|488599859|ref|YP_007906330.1| 467 ddyTIIAGNDALMHEM------NIEHDSCDVEGTVVHVAvNGVYAGYIIVSDQ--LKDDAREAVEDLKELGCRVVMV 535
                                       ****************......66667777777766666679***********..********************** PP

                                       ESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 141 tgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       tgd++e aer+a+qlG           +e  a+ +pe+kv++i+ L+++   va+ GDg+nDa+ +a+A+
  gi|488599859|ref|YP_007906330.1| 536 TGDSREIAERVASQLG----------VDEYYAELLPEDKVRVIEGLKAEDGIVAFAGDGINDAPVIARAD 595
                                       ****************..........5555*****************99999****************98 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   2.9   1.6e-13   3.6e-10       5      58 ..       7      56 ..       4      60 .. 0.90
   2 ?   -0.7   0.0      0.89     2e+03      24      60 ..     259     296 ..     253     297 .. 0.70
   3 ?   -3.7   0.1       7.6   1.7e+04      31      46 ..     482     497 ..     481     500 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.6e-13
                               HMA  5 sgmhCagCaakvekvLselpgVesvkvdlatktvtVeg.daestklrkiieaiek 58
                                      ++++Ca+Ca k+e+ L++l+gV+ ++v++ t++++V++ d+e+     +ie+i+k
  gi|488599859|ref|YP_007906330.1|  7 KNLDCASCAVKIEEELKKLEGVRFASVNFSTSELVVDTeDIEK-----VIETIKK 56
                                      69************************************77777.....8888876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.89
                               HMA  24 pgVesvkvdlatktvtVeg.daes.tklrkiieaiekag 60 
                                       ++V s  v++  + +tV++ ++ s  ++++i++ +e+ag
  gi|488599859|ref|YP_007906330.1| 259 DEVLSGMVNMS-GLLTVRVtKPFSdSTVSRILQLVEEAG 296
                                       66667777777.788888874444455699*99999987 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 7.6
                               HMA  31 vdlatktvtVegdaes 46 
                                       ++ + +++ Veg++ +
  gi|488599859|ref|YP_007906330.1| 482 MNIEHDSCDVEGTVVH 497
                                       6888899999998766 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         1   2.3e+03      71      99 ..     408     436 ..     382     464 .. 0.73
   2 !   11.6   0.0   7.6e-05      0.17      14      59 ..     512     557 ..     488     559 .. 0.84
   3 !   14.9   0.4   7.4e-06     0.017     200     251 ..     572     624 ..     565     628 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                                       TEEEEE--B-HHHHHHHHHHHHHTTCEEE CS
                       Hydrolase_3  71 gkilykstiskedvkeiikllkennveil 99 
                                        ++++k+ +ske+v ++ +l++ +  + +
  gi|488599859|ref|YP_007906330.1| 408 AEVVAKNGFSKENVLKFAALVEMHSNHPI 436
                                       56777888888888888877777765555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.6e-05
                                       S---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEE CS
                       Hydrolase_3  14 kkisektkeaikklkekgikvviATGRslravlpvleelgldlpvi 59 
                                        ++++ ++ea++ lke g+ vv  TG s + +++v+ +lg+d ++ 
  gi|488599859|ref|YP_007906330.1| 512 DQLKDDAREAVEDLKELGCRVVMVTGDSREIAERVASQLGVDEYYA 557
                                       5788999***********************************8875 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 7.4e-06
                                       T--GGGEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE--GGGTHH CS
                       Hydrolase_3 200 nisleeviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtksnnedGV 251
                                       + +   v+  GDg ND + + +a++g+Amg  +se ++++Ad v+ + + + V
  gi|488599859|ref|YP_007906330.1| 572 KAEDGIVAFAGDGINDAPVIARADVGIAMGGlGSEAAIEVADVVIMDDKPSKV 624
                                       5555567788*******************75499*********9987765555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   5.9e-08   0.00013      88     185 ..     516     589 ..     504     591 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.9e-08
                               HAD  88 pgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaa 164
                                        +a+e+++  ++ G rvv+v+g  r+++e+++ +lg+de +a+                     e+kv++++    +
  gi|488599859|ref|YP_007906330.1| 516 DDAREAVEDLKELGCRVVMVTGDSREIAERVASQLGVDEYYAE----------L--------LPEDKVRVIEG--LK 572
                                       589999**999*************************4444444..........3........44455666666..33 PP

                               HAD 165 egegidleevvayGDspsDlp 185
                                       ++ gi    v + GD+++D p
  gi|488599859|ref|YP_007906330.1| 573 AEDGI----VAFAGDGINDAP 589
                                       33333....555577777765 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-05     0.026      80     131 ..     514     565 ..     508     587 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                             HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedv 131
                                       + d+++e++e+Lke g ++  vT  sre +e+  +qlg+++y+   + +++v
  gi|488599859|ref|YP_007906330.1| 514 LKDDAREAVEDLKELGCRVVMVTGDSREIAERVASQLGVDEYYAELLPEDKV 565
                                       6799**************************************9998887776 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.7e-05     0.082      23     104 ..      74     154 ..      70     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                              TssN  23 kknkllkkkkliiyiLlaglvlalpgllgflknefvpygyillqilylllGilhlylllkkffkelkekkilfeill 99 
                                       +k + ++kk++i ++++a+l++  + l gfl+  +   +y +l  +yl++G   l+ + +++ k + +++ +   l 
  gi|488599859|ref|YP_007906330.1|  74 EKDEGVSKKEIIPIVVSAILFILGVTLEGFLHP-IPAAEYTVLLSAYLIVGWRVLWKAARNLTKGIVSDENFLLSLA 149
                                       566678899999999999999999999999986.6669******************************994444444 PP

                              TssN 100 tlivi 104
                                       t+ +i
  gi|488599859|ref|YP_007906330.1| 150 TIGAI 154
                                       44333 PP

>> CD34_antigen  CD34/Podocalyxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00025      0.56      62     124 ..      39      99 ..       7     102 .. 0.73
   2 ?   -4.0   0.4         4   8.9e+03     108     127 ..     344     363 ..     342     365 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                      CD34_antigen  62 t...etkevlellkdkrsdLeklgIqnltsvkeaqeedirseqdyskkllialvtsglllaiLlva 124
                                       +   +t++++++++ +++   +++I +l   ++ +e++  + +  skk +i +v+s++l +iL+v+
  gi|488599859|ref|YP_007906330.1|  39 ElvvDTEDIEKVIETIKKVEPEVEIIDLD--EDGKERE--KDEGVSKKEIIPIVVSAIL-FILGVT 99 
                                       24556677777777777777888899888..5555555..7889***********7775.677776 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4
                      CD34_antigen 108 lialvtsglllaiLlvagyY 127
                                       l++lv+s  ++ +L v + Y
  gi|488599859|ref|YP_007906330.1| 344 LVLLVISCPCALVLSVPLSY 363
                                       899****9999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 4247.82
//
Query:       gi|488599860|ref|YP_007906331.1|  [L=393]
Description: hypothetical protein Asulf_00306 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-57  193.9  30.4    1.4e-28   99.9  14.8    2.0  2  MFS_1       Major Facilitator Superfamily
    5.6e-11   42.0  29.5      8e-07   28.3   0.8    3.5  3  Sugar_tr    Sugar (and other) transporter
      3e-08   32.9  23.7    4.7e-07   29.0  23.7    2.7  1  MFS_1_like  MFS_1 like family
    5.7e-08   32.4  11.6    1.4e-07   31.2   1.7    2.8  3  MFS_4       Uncharacterised MFS-type transporter YbfB
  ------ inclusion threshold ------
       0.15   10.5  11.0       0.15   10.5   0.9    2.6  3  TRI12       Fungal trichothecene efflux pump (TRI12)
        1.5    7.0   9.6        1.7    6.8   0.8    2.7  3  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4  11.6   1.3e-31   3.8e-28       5     232 ..      21     232 ..      17     240 .. 0.83
   2 !   99.9  14.8   4.7e-32   1.4e-28       2     167 ..     216     379 ..     212     388 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.3e-31
                             MFS_1   5 aflsalarsilgpalplalaedlg....ispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgl 76 
                                        +  al+ +++++alpl l  + +     ++   g+++++ ++ a + +++lG+++dr+Gr + +l+ glll+ l l
  gi|488599860|ref|YP_007906331.1|  21 RLSDALGGGAVYFALPL-LIAEINeteiPNAFLSGIVIAIWGIIATLVQPVLGFFIDRYGRVKkILFSGLLLTTLVL 96 
                                       56667888899999995.555655455555666999*************************999************6 PP

                             MFS_1  77 llllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       +  +f+  l  l+ +rv  G+++++++ +++++ia +++k++rg  +gl+++ + +G+++ p+l+g+l++ +g+  v
  gi|488599860|ref|YP_007906331.1|  97 YSYTFVRDLLSLISVRVALGFTEAMVMVSSVVIIASISKKSNRGENFGLFYTVTDIGFAVSPVLAGFLLEFYGFNEV 173
                                       66669555559****************************************************************** PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltll 230
                                       f+  a+++l+++vl+l l+p  ++ + ++++ e+          p      ++     +++++l+ ff + +l++++
  gi|488599860|ref|YP_007906331.1| 174 FVSGALLTLVSAVLVLKLVPKVDKINVNDRGNEK----------P------SPE----IFVISLSLFFTICALSSYV 230
                                       *************977777666666666666666..........3......344....5555555555666677777 PP

                             MFS_1 231 pl 232
                                       pl
  gi|488599860|ref|YP_007906331.1| 231 PL 232
                                       76 PP

  == domain 2  score: 99.9 bits;  conditional E-value: 4.7e-32
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +l++f++++a s + p+      +   ++p ++g+ +++y ++  +++ p+G lsd++Gr++++++g +l++l+ ++
  gi|488599860|ref|YP_007906331.1| 216 SLSLFFTICALSSYVPLEE-SFFKYMALTPLTFGITYSAYIITRTFFNTPAGNLSDKIGRKKIFVIGTILLGLS-TI 290
                                       4666777777777777776.66677889**********************************************.88 PP

                             MFS_1  79 ll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       ++ f+ ++  +++lr lqG+  +++++ + al+ad + + + g+++++ +++  lG ++gp+++g+l  ++g++++f
  gi|488599860|ref|YP_007906331.1| 291 AVpFCKNFEQFVILRTLQGVLVAFVYSPATALVADKSEQ-NLGLGMSITNSSLTLGLAFGPIIAGFLGGYIGFQSPF 366
                                       888889988*****************************9.************************************* PP

                             MFS_1 155 yilaivsllafvl 167
                                       yi++++ +l+++l
  gi|488599860|ref|YP_007906331.1| 367 YIFGFLIVLSGIL 379
                                       **********997 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5  11.1   3.9e-06     0.012      44     187 ..      49     191 ..       2     197 .. 0.84
   2 !   28.3   0.8   2.7e-10     8e-07      44     130 ..     243     326 ..     211     332 .. 0.82
   3 !   10.8   2.4   5.2e-05      0.16      44      94 ..     331     381 ..     321     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-06
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                        + lsg++ +i  ++a++ + ++g+++dr+GR k +l++++l+    + +++    + +  li  Rv +G+   ++ 
  gi|488599860|ref|YP_007906331.1|  49 NAFLSGIVIAIWGIIATLVQPVLGFFIDRYGRVKKILFSGLLLTTLVLYSYTFV--RDLLSLISVRVALGFTEAMVM 123
                                       56799*************************************999999999888..68******************* PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.TTHHHHHHHCCHHHHHHHHHH CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn.adgwrillglqlvpallllil 187
                                       v + + i+ i++k+ Rg   +l+ + + +G+ v+ ++  +l ++ + ++ +     l+lv+a+l+l l
  gi|488599860|ref|YP_007906331.1| 124 VSSVVIIASISKKSNRGENFGLFYTVTDIGFAVSPVLAGFLLEFYGfNEVFVSGALLTLVSAVLVLKL 191
                                       ********************************998887777555553555666666666666666555 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 2.7e-10
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       + ++ g++ s++++ +++    ag l+d++GRkk+++i+++l+  +++   ++k   ++e++++ R l G+ v +++
  gi|488599860|ref|YP_007906331.1| 243 TPLTFGITYSAYIITRTFFNTPAGNLSDKIGRKKIFVIGTILLGLSTIAVPFCK---NFEQFVILRTLQGVLVAFVY 316
                                       5567899***********************************************...****************9999 PP

                                       HHHHHHHHTT CS
                          Sugar_tr 121 vlvPmyisEi 130
                                         ++ +++  
  gi|488599860|ref|YP_007906331.1| 317 SPATALVADK 326
                                       8888877765 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 5.2e-05
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqa 94 
                                       + + ++++ s++ +G ++G ++ag+lg ++G ++ + i+++l v +++l+ 
  gi|488599860|ref|YP_007906331.1| 331 LGLGMSITNSSLTLGLAFGPIIAGFLGGYIGFQSPFYIFGFLIVLSGILSQ 381
                                       456789999*************************************99975 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 !   29.0  23.7   1.6e-10   4.7e-07      35     381 ..      52     367 ..      42     371 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.6e-10
                        MFS_1_like  35 eigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektf 111
                                        +gi+ +i  +++ l +p++g+  Dr+g+ kk++  +lll ++++ s +f+                        ++
  gi|488599860|ref|YP_007906331.1|  52 LSGIVIAIWGIIATLVQPVLGFFIDRYGRVKKILFSGLLLTTLVLYSYTFVR-----------------------DL 105
                                       689***************************************9999999766.......................55 PP

                        MFS_1_like 112 wilfllvvlasfflaailvlldaatlkel...gedrkdyGrqrlfGsvGyaifafitGilidhysvnllpysallyv 185
                                        +l+ ++ +a  f++a++++  ++++  +   +++ +++G       +G+a++ ++ G+l+++y +n      +++ 
  gi|488599860|ref|YP_007906331.1| 106 LSLISVR-VALGFTEAMVMVSSVVIIASIskkSNRGENFGLFYTVTDIGFAVSPVLAGFLLEFYGFNE-----VFVS 176
                                       5555554.455677888888888888888543444556****************************85.....3333 PP

                        MFS_1_like 186 laallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYLkelgasntll 262
                                        a+l ++s +  l+l+   k +k++v     +  n    pe++++ l +++   + + +    + ++k +  +  + 
  gi|488599860|ref|YP_007906331.1| 177 GALLTLVSAV--LVLKLVPKVDKINVN----DRGNEKPSPEIFVISLSLFFTICALSSYVPLEESFFKYMALTPLTF 247
                                       3333333333..345555555555555....23444455665555555555555555555555556666699***** PP

                        MFS_1_like 263 GslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvs 339
                                       G++     +    +   a +l +k+G  k+ +i+ ++  l  + + +++n+   +++ +L+g+ ++ +++ a+  v+
  gi|488599860|ref|YP_007906331.1| 248 GITYSAYIITRTFFNTPAGNLSDKIGRKKIFVIGTILLGLSTIAVPFCKNFEQFVILRTLQGVLVAFVYSPATALVA 324
                                       ***********9999**********************************************************9999 PP

                        MFS_1_like 340 kiapksleatgqgllsglyfglGralGsliGGll..w.dlksaif 381
                                       +  +++  + g+++ ++ +  lG a+G +i+G+l  + + +s+++
  gi|488599860|ref|YP_007906331.1| 325 DK-SEQNLGLGMSITNS-SLTLGLAFGPIIAGFLggYiGFQSPFY 367
                                       44.44555666666655.589***********9833224444444 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   1.7   4.6e-11   1.4e-07      58     176 ..      80     199 ..      65     242 .. 0.82
   2 ?   -1.6   0.1      0.42   1.3e+03     197     215 ..     244     262 ..     232     268 .. 0.80
   3 !    7.5   0.4   0.00074       2.2      58     109 ..     274     326 ..     265     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4.6e-11
                             MFS_4  58 Rlr..llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiav 132
                                       R++  l  gll+t+l+l    +++ ++ ++ +R+++G + A+v+v    ++ + +++++r++  +l++    +G av
  gi|488599860|ref|YP_007906331.1|  80 RVKkiLFSGLLLTTLVLYSYTFVRDLLSLISVRVALGFTEAMVMVSSVVIIASISKKSNRGENFGLFYTVTDIGFAV 156
                                       34344899**************************************9999999999********************* PP

                             MFS_4 133 sgllvllllqlglsasslWlalavlsavllllvalllpraalre 176
                                       s +l+ +ll++   ++ + +  a+l +v  +lv+ l+p+  + +
  gi|488599860|ref|YP_007906331.1| 157 SPVLAGFLLEFYGFNE-VFVSGALLTLVSAVLVLKLVPKVDKIN 199
                                       ****998887655444.788999999999999999998554443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.42
                             MFS_4 197 llaYglaGfGYiitatFlv 215
                                        l++g+   +Yiit tF  
  gi|488599860|ref|YP_007906331.1| 244 PLTFGITYSAYIITRTFFN 262
                                       478999999*******975 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00074
                             MFS_4  58 Rlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlah 109
                                       R +   +g+++  l+++a+ + ++f  f+++R l Gv  A+v   +++lv  +
  gi|488599860|ref|YP_007906331.1| 274 RKKiFVIGTILLGLSTIAVPFCKNFEQFVILRTLQGVLVAFVYSPATALVADK 326
                                       555467899999****************************9988888887766 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.22   6.5e+02      80     112 ..      53      85 ..      29     117 .. 0.59
   2 ?   10.5   0.9     5e-05      0.15      57     124 ..     120     187 ..      93     196 .. 0.86
   3 ?    5.4   1.6    0.0017       4.9      99     208 ..     266     378 ..     253     386 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.22
                             TRI12  80 sslfstlwttgqavsilvmgrltdrfgrrpfvi 112
                                       s+++ ++w +  ++   v+g + dr+gr   ++
  gi|488599860|ref|YP_007906331.1|  53 SGIVIAIWGIIATLVQPVLGFFIDRYGRVKKIL 85 
                                       344445555555555556666666666654443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5e-05
                             TRI12  57 yfvlqasasalpnilqdvgqsensslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaiv 124
                                        +v+ +s   +  i +   + en +lf t+  +g avs ++ g l + +g   + +   +l lv a++
  gi|488599860|ref|YP_007906331.1| 120 AMVMVSSVVIIASISKKSNRGENFGLFYTVTDIGFAVSPVLAGFLLEFYGFNEVFVSGALLTLVSAVL 187
                                       467788888999999999***********************************99*********9985 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0017
                             TRI12  99 grltdrfgrrp.fvilthilglvgaivgctatkfntllaamtllgvaagpagasplfvgelmsnktkflgllivsip 174
                                       g l+d++gr+  fvi t +lgl    v   +++f+ ++   tl gv      +    +    s++   lg+ i    
  gi|488599860|ref|YP_007906331.1| 266 GNLSDKIGRKKiFVIGTILLGLSTIAVP-FCKNFEQFVILRTLQGVLVAFVYSPATALVADKSEQNLGLGMSITNSS 341
                                       89******975499999999*9876665.456788888888888887655544433333334444444555443333 PP

                             TRI12 175 vvvtsglsp....ylgqrlaiqgswrwifyiyiitsai 208
                                            + +p    +lg  +  q  + +if   i++s i
  gi|488599860|ref|YP_007906331.1| 342 LTLGLAFGPiiagFLGGYIGFQSPF-YIFGFLIVLSGI 378
                                       2222223331111344444444333.455555666655 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 ?    6.8   0.8   0.00057       1.7     137     195 ..     110     168 ..      92     176 .. 0.90
   2 ?   -1.9   0.1      0.25   7.4e+02      29      81 ..     238     290 ..     212     294 .. 0.67
   3 ?    5.6   0.2    0.0014         4     456     520 ..     295     356 ..     286     357 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00057
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 137 laqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkly 195
                                          + lG+ +++++   +  i   +kk+n    +g++y+++ +G a+  +l+++ll++y
  gi|488599860|ref|YP_007906331.1| 110 SVRVALGFTEAMVMVSSVVIIASISKKSNRGENFGLFYTVTDIGFAVSPVLAGFLLEFY 168
                                       55678999999999999****************************************99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.25
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP  29 krFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsl 81 
                                       k   l+  t g+  s++ i+ +++ +  + + ++  r ++  ig++l++l+++
  gi|488599860|ref|YP_007906331.1| 238 KYMALTPLTFGITYSAYIITRTFFNTPAGNLSDKIGRKKIFVIGTILLGLSTI 290
                                       44556666778888888888888888888888888888888888888887765 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0014
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                              OATP 456 CkkklllflillflvsflgalgrvpallvilRcVkkedksfalGlqlllir.llgliPgPiifGai 520
                                       C k++  f+il +l  +l+a+   pa+ ++    +k++  + lG++++  + +lgl  gPii G++
  gi|488599860|ref|YP_007906331.1| 295 C-KNFEQFVILRTLQGVLVAFVYSPATALV---ADKSEQNLGLGMSITNSSlTLGLAFGPIIAGFL 356
                                       8.56999********************999...89***************9889*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2546.90
//
Query:       gi|488599861|ref|YP_007906332.1|  [L=469]
Description: putative FAD-dependent dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-18   66.9   0.4    7.4e-06   25.4   0.0    3.2  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.9e-07   30.1   0.3    0.00018   20.4   0.2    2.1  2  HI0933_like    HI0933-like protein
    5.9e-06   25.6   0.3       0.21   10.6   0.0    3.0  3  GIDA           Glucose inhibited division protein A
      2e-05   24.4   0.1       0.02   14.5   0.0    2.5  2  DAO            FAD dependent oxidoreductase
    0.00011   22.7   0.1       0.15   12.6   0.0    3.2  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00035   20.7   0.6     0.0021   18.2   0.1    2.5  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00062   19.0   0.6     0.0037   16.4   0.2    2.2  2  FAD_binding_2  FAD binding domain
      0.003   16.8   0.1      0.007   15.6   0.1    1.6  1  Thi4           Thi4 family
     0.0037   16.6   0.7       0.17   11.1   0.3    2.3  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.019   14.2   1.2      0.021   14.1   0.0    1.7  2  FAD_binding_3  FAD binding domain
      0.025   14.6   0.4        4.4    7.3   0.0    2.5  3  NAD_binding_9  FAD-NAD(P)-binding
      0.052   12.8   0.0      0.088   12.1   0.0    1.3  1  Amino_oxidase  Flavin containing amine oxidoreductase
       0.18   10.8   0.1       0.29   10.1   0.1    1.3  1  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 !   21.3   0.0   9.4e-08   0.00013       1      41 [.       3      42 ..       3      50 .. 0.87
   2 !   25.4   0.0   5.3e-09   7.4e-06     184     252 ..     156     224 ..     131     243 .. 0.81
   3 !   16.8   0.0   2.3e-06    0.0031     257     279 ..     421     443 ..     402     456 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.4e-08
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcl 41
                                      +dv++iG+Gp+G+ aa++la  +a v+++e ++++  ++c+
  gi|488599861|ref|YP_007906332.1|  3 FDVIIIGAGPGGMFAAHKLAS-KASVAIFEMGRNIDKRKCP 42
                                      69******************9.99*****977777666664 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 5.3e-09
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle..eklglel 252
                                       ++ + +e++l  +Gv++ ++++v++i++n++  +  + dgee+++d ++++vG+   + l e   k g++l
  gi|488599861|ref|YP_007906332.1| 156 KVIKNIEDYLLGNGVKIFTNKTVVDINPNEK--KIYTADGEEYEYDKLIIGVGRGGAKWLEEwaVKYGMKL 224
                                       566778999*********************9..999******************98876654655556555 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 2.3e-06
                                       EEE--TTSBESSTTEEE-GGGCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 257 givvdeflrtnvpgiyaiGDvag 279
                                       +++vd+ +rtn ++iyaiGD ag
  gi|488599861|ref|YP_007906332.1| 421 KLEVDSEMRTNLKDIYAIGDGAG 443
                                       579*****************993 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   1.3e-07   0.00018       1      36 [.       3      37 ..       3      41 .. 0.87
   2 !    7.8   0.0   0.00084       1.2     110     163 ..     156     206 ..     134     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +dvi+iG+G+ G++aA ++a  +++V+++e ++++ 
  gi|488599861|ref|YP_007906332.1|  3 FDVIIIGAGPGGMFAAHKLA-SKASVAIFEMGRNID 37
                                      59****************95.6789*****998775 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       ++++ ++  l  +gvk+ ++++v +++ +e++   + t ++ee+e dkl++ +G
  gi|488599861|ref|YP_007906332.1| 156 KVIKNIEDYLLGNGVKIFTNKTVVDINPNEKK---IYTADGEEYEYDKLIIGVG 206
                                       6788888888999*************766666...556689*********9976 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00036       0.5       1      28 [.       4      30 ..       4      64 .. 0.79
   2 ?    2.0   0.0     0.064        88     109     166 ..     168     221 ..     153     235 .. 0.71
   3 !   10.6   0.0   0.00016      0.21     324     386 ..     393     464 ..     376     468 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00036
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dvi+iG+G  G+ AA ++a   a+v+++
  gi|488599861|ref|YP_007906332.1|  4 DVIIIGAGPGGMFAAHKLAS-KASVAIF 30
                                      8****************997.4677776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.064
                                       TTEEEE.ES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESS CS
                              GIDA 109 pnleii.eeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaG 166
                                       + ++i+ +++v ++++   + k ++t+dge+++ ++ +i  G    g  ++ e +++ G
  gi|488599861|ref|YP_007906332.1| 168 NGVKIFtNKTVVDINP---NEKKIYTADGEEYEYDKLIIGVGR--GGAKWLEEWAVKYG 221
                                       5566651457889988...556789**************9998..66666555555555 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00016
                                       -TT--EEE--EEEEEEEE-GGGB-T.........TSBBSSSBTEEE-CGGGTB.-SHHHHHHHHHHHHHHHHH CS
                              GIDA 324 LenaeivrpGyaieydyvdprqlln.........tLetkkvkgLflAGqinGt.eGYeEaaaqGllAGinaar 386
                                       Le+++ v pG+a + + + +++++          +++t+  k++++ G+  G+  G + aa +Gl+AG  + +
  gi|488599861|ref|YP_007906332.1| 393 LEQLDKVIPGVADDSTLLYAPEIKFyslklevdsEMRTN-LKDIYAIGDGAGVsRGIVGAAVTGLIAGESILK 464
                                       555555555555555555555554330100000145554.799**********99*************87765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.5e-05      0.02       1      31 [.       4      35 ..       4      39 .. 0.89
   2 !    7.4   0.0     0.002       2.8     147     201 ..     156     206 ..     146     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                                      EEEEECTSHHHHHHHHHHHHTT.EEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekgdi 31
                                      dv+iiG+G  G+++A+ La +  V+++e+g+ 
  gi|488599861|ref|YP_007906332.1|  4 DVIIIGAGPGGMFAAHKLASKAsVAIFEMGRN 35
                                      9*****************96646*****9975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--G CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaG 201
                                       k+++ + + +  +Gv+i+++ +v++++ +++k+++     +ge+ ++d++++  G
  gi|488599861|ref|YP_007906332.1| 156 KVIKNIEDYLLGNGVKIFTNKTVVDINPNEKKIYTA----DGEEYEYDKLIIGVG 206
                                       566777888999**************5555776666....366655688777666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.012        16       2      44 ..       5      47 ..       4      50 .. 0.88
   2 ?   -1.7   0.0       3.3   4.5e+03       5      57 ..      86     141 ..      84     146 .. 0.46
   3 !   12.6   0.0   0.00011      0.15      42      72 ..     157     187 ..     148     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeask 44
                                      v+++G+G  g+ +A  la  + +V ++e++ ++  r+++ ++++
  gi|488599861|ref|YP_007906332.1|  5 VIIIGAGPGGMFAAHKLASKA-SVAIFEMGRNIDkRKCPSDLAE 47
                                      89***************9988.9******999988888888775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                                       ECSSHHHHHHHHHHHHTTSEE.EEEESSSSSS..TTSSHHHHHHHHHHHHHTTEEE CS
                         Pyr_redox   5 vGgGyiglElAgalaelgkkV.tvversdkll..rllDeeaskilqeklekngiev 57 
                                       vGg+++gl    +l +  ++V +++  +  +    ++D++  + + +k    gie+
  gi|488599861|ref|YP_007906332.1|  86 VGGDFLGLIDPDYLLKKMDEVdSIFLENGAPDevYGMDDDKLTKFLRKANSAGIEF 141
                                       56666665444444444444433332222222223455555555555555556666 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegsedg 72 
                                       + k+++++l  ng+++ +n++v+ i+ +e++
  gi|488599861|ref|YP_007906332.1| 157 VIKNIEDYLLGNGVKIFTNKTVVDINPNEKK 187
                                       66899************************98 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.5e-06    0.0021       1      30 [.       7      35 ..       7      36 .. 0.92
   2 ?   -3.6   0.0       9.7   1.3e+04      41      52 ..     235     246 ..     225     250 .. 0.67
   3 ?   -1.1   0.1       1.7   2.3e+03       1      13 [.     448     460 ..     448     467 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                      I+GaG +G+ aA+ La + ++v ++e+++ 
  gi|488599861|ref|YP_007906332.1|  7 IIGAGPGGMFAAHKLASK-ASVAIFEMGRN 35
                                      9***************95.9******9976 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.7
                                       TTCEECTS---E CS
                     NAD_binding_8  41 pgvrvdygahif 52 
                                        gvrv+++a+i+
  gi|488599861|ref|YP_007906332.1| 235 VGVRVEVPASIM 246
                                       368888888876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.7
                                       EE--SHHHHHHHH CS
                     NAD_binding_8   1 IvGaGlsGlvaAy 13 
                                       IvGa ++Gl a  
  gi|488599861|ref|YP_007906332.1| 448 IVGAAVTGLIAGE 460
                                       9********9875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   2.7e-06    0.0037       1      30 [.       4      32 ..       4      37 .. 0.86
   2 ?   -0.1   0.0      0.27   3.7e+02     382     403 ..     422     443 ..     419     453 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.7e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                      Dvi+iG+G +G+ AA+++a +   va+ e 
  gi|488599861|ref|YP_007906332.1|  4 DVIIIGAGPGGMFAAHKLASKAS-VAIFEM 32
                                      9*****************98765.877765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.27
                                       SBESTTEEESSBTEEE-STCEE CS
                     FAD_binding_2 382 grvldadgqpipGLYAaGevaa 403
                                       ++v+++  +++++ YA+G  a+
  gi|488599861|ref|YP_007906332.1| 422 LEVDSEMRTNLKDIYAIGDGAG 443
                                       556666666*********9883 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.1e-06     0.007      17      48 ..       2      31 ..       1      36 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-06
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvaile 48
                                      + Dv+i+GaG+ G+ aa+ la k    vai+e
  gi|488599861|ref|YP_007906332.1|  2 KFDVIIIGAGPGGMFAAHKLASK--ASVAIFE 31
                                      67*******************99..6777777 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.3   0.00012      0.17       1      31 [.       6      34 ..       6      38 .. 0.87
   2 ?    3.2   0.0      0.03        42     218     264 ..     161     204 ..     141     222 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      iIiGaGP G+ aa++l  +    + i E g+
  gi|488599861|ref|YP_007906332.1|  6 IIIGAGPGGMFAAHKLASKAS--VAIFEMGR 34
                                      8***************99886..78999884 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.03
                       Pyr_redox_3 218 leelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvla 264
                                       +e+++  + +k+ +n++v +i+ +e+  k+ t+dg++ e +d+ ++ 
  gi|488599861|ref|YP_007906332.1| 161 IEDYLLGNGVKIFTNKTVVDINPNEK--KIYTADGEEYE-YDKLIIG 204
                                       44444444455555555555555433..45555555543.2333333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.5e-05     0.021       2      28 ..       3      28 ..       2      40 .. 0.85
   2 ?   -3.7   0.8       3.8   5.3e+03       6      18 ..     448     460 ..     446     463 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvv 28
                                       dV+I+GaGp G+ +a+ L+++  +v 
  gi|488599861|ref|YP_007906332.1|  3 FDVIIIGAGPGGMFAAHKLASK-ASVA 28
                                      69*****************987.5555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.8
                                       EE--SHHHHHHHH CS
                     FAD_binding_3   6 IVGaGpaGlmlal 18 
                                       IVGa  +Gl+++ 
  gi|488599861|ref|YP_007906332.1| 448 IVGAAVTGLIAGE 460
                                       9*********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 ?    7.3   0.0    0.0032       4.4       2      27 ..       7      26 ..       6      44 .. 0.83
   2 ?    5.1   0.0     0.015        20     119     155 ..     173     207 ..     119     208 .. 0.83
   3 ?   -3.4   0.2       6.2   8.6e+03       2      18 ..     448     464 ..     447     466 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0032
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkksple 27
                                      i+GaGp G+ ++ +L+++a      +
  gi|488599861|ref|YP_007906332.1|  7 IIGAGPGGMFAAHKLASKA------S 26
                                      9**************9996......3 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                     NAD_binding_9 119 vhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       + +++vvd+++++++  + +adg+++++d++++ +G 
  gi|488599861|ref|YP_007906332.1| 173 FTNKTVVDINPNEKK--IYTADGEEYEYDKLIIGVGR 207
                                       457899999988776..789*************9995 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.2
                     NAD_binding_9   2 ivGaGprGlavlerLla 18 
                                       ivGa ++Gl + e +l+
  gi|488599861|ref|YP_007906332.1| 448 IVGAAVTGLIAGESILK 464
                                       9*********9999987 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.4e-05     0.088     215     274 ..     157     224 ..      87     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                                       HHHH.....TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHH.....SSEEESCC CS
                     Amino_oxidase 215 alae.....elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlk.....ailfsPpl 274
                                        + +        g++i +n+ V +i+   ++ ++ + dge++e+D+ ++ v  g +k     a+++  +l
  gi|488599861|ref|YP_007906332.1| 157 VIKNiedylLGNGVKIFTNKTVVDINP--NEKKIYTADGEEYEYDKLIIGVGRGGAKwleewAVKYGMKL 224
                                       444443333336889999****99998..88889999********************7665555555566 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00021      0.29       1      27 [.       4      27 ..       4      38 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkv 27
                                      Dv++iGaGp g+  A++l ++k+   v
  gi|488599861|ref|YP_007906332.1|  4 DVIIIGAGPGGMFAAHKL-ASKAS--V 27
                                      9*****************.44443..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 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:                        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: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2934.12
//
Query:       gi|488599862|ref|YP_007906333.1|  [L=71]
Description: hypothetical protein Asulf_00308 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.7   1.6       0.15   12.3   1.6    1.1  1  DPM3      Dolichol-phosphate mannosyltransferase subunit 3 (D


Domain annotation for each model (and alignments):
>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.6   8.2e-06      0.15       7      64 ..       7      59 ..       4      69 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.2e-06
                              DPM3  7 tlalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGayslatlgygvltf 64
                                      ++++ l+l+  w+al+  l      +   +++p++P+w  +++G +++  l+++++ f
  gi|488599862|ref|YP_007906333.1|  7 VFWISLVLFYGWTALCWILE----ATAGINHIPLAPFWYAAVVGTFLIP-LIMSIISF 59
                                      56666777777777776655....4567889**************9765.55556555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 489.54
//
Query:       gi|488599863|ref|YP_007906334.1|  [L=529]
Description: putative symporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-49  167.6  35.1    5.2e-49  167.2  35.1    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 !  167.2  35.1   2.9e-53   5.2e-49       1     402 [.      34     448 ..      34     452 .. 0.90

  Alignments for each domain:
  == domain 1  score: 167.2 bits;  conditional E-value: 2.9e-53
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylsk 77 
                                       y++agr+++++v+gl+l ++++s as++Gl++ ++  G+   +    ++ ++ ++ ll a  lr++    ++dy   
  gi|488599863|ref|YP_007906334.1|  34 YYVAGRQIGSVVNGLALESTYLSPASMLGLPAYIFILGYPFWWAMAAIIAGMPVATLLTASALRKYAPTSFADYYVD 110
                                       9**************************************87666666667899************************ PP

                               SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlm 154
                                       R++++r l++l  +++++  +l+++  +vg a ++  +lG+ y  +++++ ++++lY+v GG++A++++   qa lm
  gi|488599863|ref|YP_007906334.1| 111 RYNDER-LRWLVGVVTIIGSILYITLSIVGMALFLLAILGVPYIYGIIIGTIIVMLYVVWGGMIATSWNAAFQAALM 186
                                       ******.********************************************************************** PP

                               SSF 155 lvgalilliivllevGgleslveklkeaapkv.vdlltpdslkllrdpltalslw.lglvlGvaglphilvRflaak 229
                                        ++a+i +i  + ++Ggl ++ + +++ +pk       p+  +ll     a++ w   + +G a +p ++vRf+++ 
  gi|488599863|ref|YP_007906334.1| 187 TIAAVIAAIAIVGKLGGLGAFYDAVAANNPKFwNTPSDPNPPHLLSGSWIAIIGWfFVWHYGFATMPYTVVRFFTTM 263
                                       ******************************884444558888888877777776625799***************** PP

                               SSF 230 dakailkgvlkltivlilvligmisiilfaiklagavp................kavgtevgvsniaypeLvvkllp 290
                                       d k+++++++  t   ++++i    ii  a k++   +                 a   + g +++ ++  v +l +
  gi|488599863|ref|YP_007906334.1| 264 DIKTARRSIFWCTLAAGIFYIAL-EIIGAASKVMIETGpmateganavvilknyMAQYGVGGWTDYSMVAAVEALQN 339
                                       ********************994.44444444444444599999987777754322233446689************ PP

                               SSF 291 nllaGlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvl 367
                                       ++++G+l a  lA  mst ++ +++   ++t+D    +++++ ake   v ++ri++++   + +++av+++   vl
  gi|488599863|ref|YP_007906334.1| 340 PFVLGILAAGGLAIAMSTAAGWVMVVNVMMTRDWGDMLLKSKFAKENP-VLLARIVSVIFLLIGLIVAVNPPGL-VL 414
                                       ******************************************998876.5688999****************99.** PP

                               SSF 368 klvelafaglasavlavillalfwkrvneqGAlag 402
                                       +l   af ++ sa ++ ++l+l+wkr+++  A++ 
  gi|488599863|ref|YP_007906334.1| 415 DLSGWAFVVIISALGPGLILGLWWKRATRA-AMWT 448
                                       **************************9975.7876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1261  (0.070333); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.27s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 3353.30
//
Query:       gi|488599864|ref|YP_007906335.1|  [L=285]
Description: hypothetical protein Asulf_00310 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.5     0.0017   18.5   0.0    2.0  2  DUF1724       Domain of unknown function (DUF1724)
     0.0098   15.9   0.2      0.079   13.0   0.0    2.4  2  HTH_45        Winged helix-turn-helix
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.035   13.9   0.0    1.5  1  HTH_IclR      IclR helix-turn-helix domain
      0.083   12.8   0.0       0.31   11.0   0.0    2.0  2  TrmB          Sugar-specific transcriptional regulator TrmB
      0.099   11.6   0.0       0.22   10.5   0.0    1.5  2  Topoisom_bac  DNA topoisomerase


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.89   3.2e+03      19      31 ..      58      70 ..      57      75 .. 0.82
   2 !   18.5   0.0   4.7e-07    0.0017      12      62 .]     215     264 ..     208     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.89
                           DUF1724 19 Dkflslslfdkdg 31
                                      ++++sl+l +kd 
  gi|488599864|ref|YP_007906335.1| 58 NNMFSLGLIRKDD 70
                                      5899****99985 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.7e-07
                           DUF1724  12 plsltvtDkflslslfdkdgkydhkdlisfdesAlkWGeeLFeyYlkrSep 62 
                                       pl l v D  + + +f kd+ +     i  d++A++W    F+yY++++ep
  gi|488599864|ref|YP_007906335.1| 215 PLQLGVIDERIGVIMFLKDKYFTP-IFITEDKKAVRWMDSVFDYYWDMAEP 264
                                       788889999999999999975544.58999*******************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 !   13.0   0.0   2.2e-05     0.079      34      75 ..      51      92 ..      19      94 .. 0.83
   2 ?   -0.1   0.0      0.26   9.3e+02      21      60 ..     129     170 ..     118     176 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                            HTH_45 34 kllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                      +++ + L+ + + gli+k+++k +lT  G  l++ ++++++l
  gi|488599864|ref|YP_007906335.1| 51 STFYRSLNNMFSLGLIRKDDDKIYLTPIGTLLIDAIQCINDL 92
                                      6777889*******************************9987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.26
                            HTH_45  21 kkTkimykanLsykllnkYLdmLvekgl..ikkskekYvlTe 60 
                                       + ++++y+     +   kY+d +++ +l  +  +k k + Te
  gi|488599864|ref|YP_007906335.1| 129 ETSRLVYDLIAGVEKGGKYIDRIIDPDLyaLMLKKRKECATE 170
                                       455677777777777789999999988844344555555555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.7e-06     0.035      26      52 .]      44      70 ..      17      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                                      HHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR 26 rrtglpkStvhRlLqtLvelGyveqdg 52
                                      + +glp+St +R L+ +  lG++++d+
  gi|488599864|ref|YP_007906335.1| 44 NGLGLPPSTFYRSLNNMFSLGLIRKDD 70
                                      469*********************995 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   8.7e-05      0.31      28      58 ..      42      72 ..      34      81 .. 0.86
   2 ?   -2.8   0.0       1.6   5.9e+03      31      47 ..     192     208 ..     188     210 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.7e-05
                                      HCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 28 iaeelgvprskvYevLrsLedkGlVerekgr 58
                                      + + lg+p s+ Y++L+++ + Gl+++ + +
  gi|488599864|ref|YP_007906335.1| 42 VKNGLGLPPSTFYRSLNNMFSLGLIRKDDDK 72
                                      56679********************998765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                                       CTTSSCHCHHHHHHHHH CS
                              TrmB  31 elgvprskvYevLrsLe 47 
                                       +++ +r ++ e  ++Le
  gi|488599864|ref|YP_007906335.1| 192 KTNFDRDTIEELEEKLE 208
                                       55555555555444444 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     6e-05      0.22     332     387 ..      38      94 ..       5      98 .. 0.86
   2 ?   -2.5   0.0      0.55     2e+03     357     380 ..     117     139 ..     115     171 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6e-05
                      Topoisom_bac 332 ikamekagiGt.paTraeiieklvergYverkkkslvptelGkalvellekfkdlvs 387
                                       ++++ k+g+G  p+T+   ++++++ g ++++  +++ t+ G+ l+++++ ++dl +
  gi|488599864|ref|YP_007906335.1|  38 LNELVKNGLGLpPSTFYRSLNNMFSLGLIRKDDDKIYLTPIGTLLIDAIQCINDLLE 94 
                                       5677788999637******************9999**************98888776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.55
                      Topoisom_bac 357 gYverkkkslvptelGkalvelle 380
                                       +Y+++  k++  te+++ +++l+ 
  gi|488599864|ref|YP_007906335.1| 117 RYIKEC-KKVDITETSRLVYDLIA 139
                                       577774.47888888888887763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1598.60
//
Query:       gi|488599865|ref|YP_007906336.1|  [L=400]
Description: argininosuccinate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-169  562.2   0.1   7.7e-169  562.0   0.1    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    0.00026   20.6   0.0    0.00058   19.4   0.0    1.6  2  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
       0.18   10.7   0.0       0.29   10.1   0.0    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 


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 !  562.0   0.1  1.3e-172  7.7e-169       1     387 [.       5     386 ..       5     387 .. 0.99

  Alignments for each domain:
  == domain 1  score: 562.0 bits;  conditional E-value: 1.3e-172
                   Arginosuc_synth   1 vLaysGGlDtsviikllkeklg.eeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikana 76 
                                       vL+ysGGlDt+v+i+llkek+g +evi+v+vd+Gq+e+++ e++e+++++++ k+++vDake+fv   +f+ ikan+
  gi|488599865|ref|YP_007906336.1|   5 VLSYSGGLDTTVCIPLLKEKYGfDEVITVTVDIGQPEKEVLEAEERGKRYAD-KHYTVDAKEDFV-SALFRLIKANG 79 
                                       89************************************************99.************.789******** PP

                   Arginosuc_synth  77 lYedrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeiey 153
                                        Ye+ Y+lgta+aRP+iakk ve+a ke+a a+ahGctGkGnDq+Rfe+++ +    + viaP+R+l+ltRe+eiey
  gi|488599865|ref|YP_007906336.1|  80 DYEG-YILGTAIARPIIAKKTVEIALKENAVAIAHGCTGKGNDQLRFENVFLQYG--FRVIAPMRDLNLTREWEIEY 153
                                       ****.***********************************************999..******************** PP

                   Arginosuc_synth 154 akekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeel 230
                                       akek+i++++tk+kpysiDenl++rs+e+g+Le+p++ ppe+iye+t dp+kapde+e+++i+fekG+Pv++++e++
  gi|488599865|ref|YP_007906336.1| 154 AKEKNIDIKATKDKPYSIDENLWSRSVEGGKLENPSFIPPEEIYEWTVDPKKAPDEEEIIKIDFEKGIPVSINDEKM 230
                                       ***************************************************************************** PP

                   Arginosuc_synth 231 svlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvY 307
                                       + +eli+ lnei+gkhGvGR+D++edR++glk+Re+Ye+paa++L++ah+dlekl+l+r+++kfk++vee++aelvY
  gi|488599865|ref|YP_007906336.1| 231 KGYELIRMLNEIGGKHGVGRTDMMEDRVLGLKARENYEHPAATILLTAHRDLEKLVLSRRELKFKRFVEEEWAELVY 307
                                       ***************************************************************************** PP

                   Arginosuc_synth 308 kGlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqa 384
                                       +Gl ++Pl++al+afi+ktqervtG+v++kl+kGsv+ ++R s+++lY+eel+s+d ++++dqk aeG+ ++hglq 
  gi|488599865|ref|YP_007906336.1| 308 YGLTNDPLYNALNAFIDKTQERVTGWVKLKLYKGSVIPVARYSDYALYSEELTSFD-TTSIDQKLAEGYSAFHGLQG 383
                                       ********************************************************.99*****************9 PP

                   Arginosuc_synth 385 kly 387
                                       +ly
  gi|488599865|ref|YP_007906336.1| 384 RLY 386
                                       988 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   9.7e-08   0.00058       2      50 ..       4      54 ..       3      78 .. 0.79
   2 ?   -3.2   0.0      0.81   4.8e+03     151     179 ..     133     163 ..     127     165 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.7e-08
                                      EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHH CS
                              QueC  2 avvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiake 50
                                      +v+  SGGlD t+++ l k+++  +ev+++t+d gq +k+ lea ++  + 
  gi|488599865|ref|YP_007906336.1|  4 VVLSYSGGLDTTVCIPLLKEKYgfDEVITVTVDIGQPEKEVLEAEERGKRY 54
                                      57778**********9999987669***********999888877665444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.81
                                       --EEE-TTTT--HHHHH..HHHHHTTHHHHH CS
                              QueC 151 kieieaPlidlsKaeiv..klgkelgvplee 179
                                        +++ aP+ dl+ +  +  + +ke +++++ 
  gi|488599865|ref|YP_007906336.1| 133 GFRVIAPMRDLNLTREWeiEYAKEKNIDIKA 163
                                       5778888877665555411456666666655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   4.8e-05      0.29     113     142 ..      18      47 ..       7      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHTT-SEEEEEEESSTTHHHHHHTT CS
                              MeaB 113 vvllleaaGfDvvlietvGvGqsevdvaev 142
                                       + ll e  GfD v+  tv +Gq e +v e+
  gi|488599865|ref|YP_007906336.1|  18 IPLLKEKYGFDEVITVTVDIGQPEKEVLEA 47 
                                       44577999*****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2966.35
//
Query:       gi|488599866|ref|YP_007906337.1|  [L=141]
Description: hypothetical protein Asulf_00312 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 844.37
//
Query:       gi|488599867|ref|YP_007906338.1|  [L=98]
Description: hypothetical protein Asulf_00313 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-13   50.5   6.1    8.6e-10   38.0   2.3    2.3  2  Fer4      4Fe-4S binding domain
    2.1e-12   46.6   6.5    5.8e-09   35.7   2.2    2.2  2  Fer4_6    4Fe-4S binding domain
    2.3e-11   44.1   8.8    1.4e-08   35.2   5.6    2.0  2  Fer4_7    4Fe-4S dicluster domain
    1.2e-10   41.3  11.5    5.8e-09   35.9   6.4    1.7  2  Fer4_10   4Fe-4S dicluster domain
    6.2e-10   39.9   0.7    7.3e-05   23.6   0.6    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    7.5e-09   35.6   3.3    1.1e-08   35.1   3.3    1.3  1  Fer4_9    4Fe-4S dicluster domain
    9.5e-09   35.3   4.3    1.3e-08   34.9   4.3    1.2  1  Fer4_21   4Fe-4S dicluster domain
    1.3e-08   34.4   6.9    6.5e-07   29.1   2.0    2.3  2  Fer4_2    4Fe-4S binding domain
    1.5e-07   31.4   5.1    2.1e-05   24.6   1.2    2.2  2  Fer4_4    4Fe-4S binding domain
    4.3e-06   27.4   6.6    0.00027   21.6   1.0    2.2  2  Fer4_15   4Fe-4S single cluster domain
    5.9e-06   26.9  13.4      0.002   18.9   4.9    2.2  2  Fer4_3    4Fe-4S binding domain
    8.5e-06   26.5   4.8      0.001   19.9   1.6    2.2  2  Fer4_22   4Fe-4S dicluster domain
    1.3e-05   25.6   4.0     0.0059   17.1   1.6    2.1  2  Fer4_17   4Fe-4S dicluster domain
    3.8e-05   24.1   6.5     0.0026   18.2   6.5    2.2  1  Fer4_8    4Fe-4S dicluster domain
    5.9e-05   23.5   4.7    0.00099   19.6   0.5    2.2  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.003   17.7   0.7     0.0038   17.3   0.7    1.1  1  Fer4_11   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.032   14.3   6.0       0.16   12.0   6.0    2.4  1  Fer4_19   Divergent 4Fe-4S mono-cluster
      0.048   13.9   6.8       0.66   10.2   2.0    2.1  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   2.3   8.6e-13   8.6e-10       2      24 .]       8      30 ..       7      30 .. 0.92
   2 !   14.2   0.1   2.9e-05     0.029       4      24 .]      40      60 ..      38      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 8.6e-13
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       +dee+CigCG+Cv+ CP+ A++
  gi|488599867|ref|YP_007906338.1|  8 AVDEELCIGCGRCVNSCPTSALY 30
                                      69*****************9985 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.9e-05
                                      ETTTSSS-THHHHHSTTTEEE CS
                              Fer4  4 deekCigCGaCvevCPvgAIt 24
                                      de +C g G C+ vCP  A++
  gi|488599867|ref|YP_007906338.1| 40 DEKLCDGFGSCIAVCPSHALY 60
                                      78888888*********9985 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   2.2   5.8e-12   5.8e-09       1      24 []       6      29 ..       6      29 .. 0.95
   2 !   13.2   0.1   7.2e-05     0.072       5      24 .]      40      59 ..      38      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.8e-12
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++++d+++CigCg+Cv+ CP+ a+
  gi|488599867|ref|YP_007906338.1|  6 IIAVDEELCIGCGRCVNSCPTSAL 29
                                      689******************996 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.2e-05
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d+ +C+g g C++vCP  a+
  gi|488599867|ref|YP_007906338.1| 40 DEKLCDGFGSCIAVCPSHAL 59
                                      8899************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 !   35.2   5.6   1.4e-11   1.4e-08       2      52 .]      14      58 ..      13      58 .. 0.85
   2 !   15.8   0.1   1.6e-05     0.016       2      25 ..      44      67 ..      43      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.4e-11
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekvei.dpekClgCgaCvavCPtga 52
                                      CigCg+Cv+ Cp++a++l+++       k+++ d+  C g g+C+avCP+ a
  gi|488599867|ref|YP_007906338.1| 14 CIGCGRCVNSCPTSALYLEND-------KAKLrDEKLCDGFGSCIAVCPSHA 58
                                      ******************776.......344416778************976 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.6e-05
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeene 25
                                      C g g C a+Cp++a++++e+e e
  gi|488599867|ref|YP_007906338.1| 44 CDGFGSCIAVCPSHALYIEEREAE 67
                                      88889*************998655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   6.4   5.8e-12   5.8e-09       3      56 .]       8      55 ..       6      55 .. 0.78
   2 !   14.1   0.2   3.8e-05     0.038       4      24 ..      39      62 ..      35      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.8e-12
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       +d++ Ci+Cg+Cv++CP+         + ++++a+  + + C+g g+C+++CP
  gi|488599867|ref|YP_007906338.1|  8 AVDEELCIGCGRCVNSCPT------SALYLENDKAKLRDEKLCDGFGSCIAVCP 55
                                      6799***************......44444444444445678***********9 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.8e-05
                           Fer4_10  4 idddtCirCgkCvkaCPadl...t 24
                                      +d++ C + g C ++CP+++   +
  gi|488599867|ref|YP_007906338.1| 39 RDEKLCDGFGSCIAVCPSHAlyiE 62
                                      688899999999999999554332 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 !   23.6   0.6   7.3e-08   7.3e-05       2      21 ..      14      33 ..      13      42 .. 0.81
   2 !   14.8   0.0     4e-05      0.04       2      21 ..      44      63 ..      43      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.3e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekk 21
                                      C++Cg+C+++CPt+a+  ++
  gi|488599867|ref|YP_007906338.1| 14 CIGCGRCVNSCPTSALYLEN 33
                                      ***************98873 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikekk 21
                                      C + g C+ vCP++a+  ++
  gi|488599867|ref|YP_007906338.1| 44 CDGFGSCIAVCPSHALYIEE 63
                                      9999***********76542 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   3.3   1.1e-11   1.1e-08       2      50 ..      14      58 ..      13      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.1e-11
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      C+gCg+Cv++Cp+ +   ++ + k r ++     C g g+C+++Cp++a
  gi|488599867|ref|YP_007906338.1| 14 CIGCGRCVNSCPTSALYLENDKAKLRDEK----LCDGFGSCIAVCPSHA 58
                                      ************************99876....6************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 !   34.9   4.3   1.3e-11   1.3e-08       3      53 ..       9      56 ..       7      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.3e-11
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53
                                      +de+ CigCg+C+ +C+   + a+ +++++     e+ C G   C++vCP 
  gi|488599867|ref|YP_007906338.1|  9 VDEELCIGCGRCVNSCP---TSALYLENDKAKLRDEKLCDGFGSCIAVCPS 56
                                      89***************...578888777776778999************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 !   29.1   2.0   6.5e-10   6.5e-07       3      22 .]       7      26 ..       5      26 .. 0.94
   2 !    7.9   0.2    0.0036       3.6       9      21 ..      43      55 ..      37      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.5e-10
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      ++vd++ CigCg Cv++CP+
  gi|488599867|ref|YP_007906338.1|  7 IAVDEELCIGCGRCVNSCPT 26
                                      789****************7 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                            Fer4_2  9 rCigCgaCvsaCP 21
                                       C g g+C+ +CP
  gi|488599867|ref|YP_007906338.1| 43 LCDGFGSCIAVCP 55
                                      555559******* PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   1.2   2.2e-08   2.1e-05       2      16 ..      12      26 ..      11      33 .. 0.92
   2 !    8.5   0.1    0.0031       3.1       8      15 ..      48      55 ..      41      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e CigCg+Cv++CP+
  gi|488599867|ref|YP_007906338.1| 12 ELCIGCGRCVNSCPT 26
                                      67************6 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0031
                            Fer4_4  8 gsCvaaCP 15
                                      gsC+a+CP
  gi|488599867|ref|YP_007906338.1| 48 GSCIAVCP 55
                                      79****** PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.0   2.7e-07   0.00027       1      32 [.       7      38 ..       7      42 .. 0.83
   2 !    9.8   0.5    0.0013       1.3       4      20 ..      40      56 ..      38      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.7e-07
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasv 32
                                      + vD+++Cigcg+Cv  +p+     e+++a++
  gi|488599867|ref|YP_007906338.1|  7 IAVDEELCIGCGRCVNSCPTSALYLENDKAKL 38
                                      78****************99777777777755 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0013
                           Fer4_15  4 DrdaCigcglCvaeape 20
                                      D+++C+g g C+a++p 
  gi|488599867|ref|YP_007906338.1| 40 DEKLCDGFGSCIAVCPS 56
                                      899************85 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   4.9   2.1e-06     0.002       1      15 []      14      28 ..      14      28 .. 0.94
   2 !   13.3   1.3   0.00013      0.13       1      15 []      44      58 ..      44      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg+Cv++CP+ A
  gi|488599867|ref|YP_007906338.1| 14 CIGCGRCVNSCPTSA 28
                                      ************976 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00013
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+g g C  vCP++A
  gi|488599867|ref|YP_007906338.1| 44 CDGFGSCIAVCPSHA 58
                                      99999********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 !   19.9   1.6     1e-06     0.001      76      94 ..       8      26 ..       2      28 .. 0.84
   2 !    7.8   0.1    0.0059       5.9      76      94 ..      38      56 ..      30      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-06
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                       ++e+ C+GCgRC+++cp+
  gi|488599867|ref|YP_007906338.1|  8 AVDEELCIGCGRCVNSCPT 26
                                      56899************97 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0059
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                        +e+ C G g Ci++cp+
  gi|488599867|ref|YP_007906338.1| 38 LRDEKLCDGFGSCIAVCPS 56
                                      458899***********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 !   17.1   1.6   5.9e-06    0.0059       2      23 ..      14      35 ..      13      43 .. 0.73
   2 !    8.8   0.0    0.0023       2.3       2      23 ..      44      65 ..      43      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.9e-06
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepk 23
                                      Ci+Cg C+++Cp+ + y ++ k
  gi|488599867|ref|YP_007906338.1| 14 CIGCGRCVNSCPTSALYLENDK 35
                                      9999999999998888776544 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepk 23
                                      C + g C+++Cps++ y +e++
  gi|488599867|ref|YP_007906338.1| 44 CDGFGSCIAVCPSHALYIEERE 65
                                      7777889999999888766554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   6.5   2.6e-06    0.0026       5      64 ..      14      57 ..      11      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.6e-06
                            Fer4_8  5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      Ci+Cg+C ++Cp+     +     +++a+   ++  +       + C + g+C  vCp +
  gi|488599867|ref|YP_007906338.1| 14 CIGCGRCVNSCPTSALYLE-----NDKAKL--RD--E-------KLCDGFGSCIAVCPSH 57
                                      ************6655532.....233222..22..2.......4699999999999986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.5   9.9e-07   0.00099       1      18 [.       9      26 ..       9      38 .. 0.85
   2 ?    5.9   0.3     0.019        19       2      19 ..      40      57 ..      40      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.9e-07
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD++ Ci+cg Cv+ +P 
  gi|488599867|ref|YP_007906338.1|  9 VDEELCIGCGRCVNSCPT 26
                                      9****************6 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                           Fer4_13  2 DrdtCiacgaCvelaPdv 19
                                      D++ C + g+C +++P +
  gi|488599867|ref|YP_007906338.1| 40 DEKLCDGFGSCIAVCPSH 57
                                      67789999********86 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.7   3.8e-06    0.0038       9      65 ..      13      65 ..       5      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.8e-06
                           Fer4_11  9 qCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneet 65
                                       C  C    Cv+s+p++a++ ++ + a l dek ++ ++ +++ +cP ++ + +e++
  gi|488599867|ref|YP_007906338.1| 13 LCIGCG--RCVNSCPTSALYLEN-DKAKLRDEKLCD-GFGSCIAVCPSHALYIEERE 65
                                      566664..6***********998.9999*******8.**********9999988765 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 ?   12.0   6.0   0.00016      0.16       3      61 ..       2      61 ..       1      64 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                           Fer4_19  3 geeitiednrelCihsgnCvkglpe..vFdpkrkpwikpdeasteeiievverCPSGALsy 61
                                      g+ + i  ++elCi+ g Cv+  p+  ++  ++k     de+  +   + ++ CPS AL +
  gi|488599867|ref|YP_007906338.1|  2 GKRMIIAVDEELCIGCGRCVNSCPTsaLYLENDK-AKLRDEKLCDGFGSCIAVCPSHALYI 61
                                      88999****************7664326766666.44578888999**********99976 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.0   0.00066      0.66      59      74 ..      12      27 ..       3      33 .. 0.84
   2 ?    6.8   0.1    0.0075       7.5      51      74 ..      34      57 ..      27      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00066
                           Fer4_18 59 gdcidcescvkvcPtg 74
                                        ci c+ cv+ cPt 
  gi|488599867|ref|YP_007906338.1| 12 ELCIGCGRCVNSCPTS 27
                                      56999********995 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0075
                           Fer4_18 51 eerkekgagdcidcescvkvcPtg 74
                                      ++ k +++  c   +sc++vcP +
  gi|488599867|ref|YP_007906338.1| 34 DKAKLRDEKLCDGFGSCIAVCPSH 57
                                      555556667788899*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 678.78
//
Query:       gi|488599868|ref|YP_007906339.1|  [L=142]
Description: archease family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   1.1    1.5e-36  125.7   1.1    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 !  125.7   1.1   8.2e-41   1.5e-36       1     138 []       4     142 .]       4     142 .] 0.95

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 8.2e-41
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       y++++htAD+++ea+G slee+fe+a +a++++++ l++v  ++e+ ie+e +d+e+l+f++L+ellylfdt+ f+ 
  gi|488599868|ref|YP_007906339.1|   4 YRLINHTADIAFEAYGYSLEELFENATRAFYDAFAVLESVGIDREQIIEMEDSDIEMLFFRYLNELLYLFDTDFFAG 80 
                                       899************************************************************************** PP

                                       ---EEEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEE...ETTEEEEEEEEE- CS
                          Archease  78 kevkvdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelriee...eddgweayvvvDi 138
                                       kev+v+ e+ e+el+l+a+++g k+++e    +te KA+T+h++ ie+   e++ w+a+vvvDi
  gi|488599868|ref|YP_007906339.1|  81 KEVNVSIEDVEDELRLKAKLKGGKISPEIV--KTEPKAITLHKFMIEKvknEKEFWKAFVVVDI 142
                                       ***997777899*************99965..5*************995556677********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 985.92
//
Query:       gi|488599869|ref|YP_007906340.1|  [L=277]
Description: 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   97.0   0.0    1.4e-27   96.4   0.0    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.7e-17   61.9   0.2    8.3e-17   61.1   0.2    1.4  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit
  ------ inclusion threshold ------
       0.34   10.5   1.5       0.64    9.6   1.5    1.5  1  Lsm_interact  Lsm interaction motif


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 !   96.4   0.0   2.3e-31   1.4e-27       2     153 .]      47     194 ..      46     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 2.3e-31
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+             +++++ +g+++ +G+++p+A+G+kl +p+ +v++  GDG++l i   +++   r+n++it
  gi|488599869|ref|YP_007906340.1|  47 IGCSGK----------IPHFVNvNGVHTLHGRAIPFAVGIKLSNPELTVMVNGGDGDLLGIgAGHFVSLGRKNVDIT 113
                                       666666..........7899999**************************************99************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       v+++nN++yg+t+gq   +  +g k+k+  + + l+p+++  la   G + +ar    ++e+l+e++k+ ++++g+a
  gi|488599869|ref|YP_007906340.1| 114 VILHNNGVYGLTKGQaspTLDYGLKTKALAEANRLYPLNPITLAIVSGYTfVARSYALKPEHLKEIIKKGINHRGSA 190
                                       ***************9966666777777777668****************9998788889***************** PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       liev
  gi|488599869|ref|YP_007906340.1| 191 LIEV 194
                                       **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 !   61.1   0.2   1.4e-20   8.3e-17       1      58 [.     198     252 ..     198     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.4e-20
                                       XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT-----EEEEEEEETTS--HH CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgdkiplGifYkeekptye 58 
                                       Cvt+N+++T+++Y er+y+le d     d+++A+ek+ e +++ip+GifY e+k+ +e
  gi|488599869|ref|YP_007906340.1| 198 CVTYNNIHTWKYYSERIYELESD--SGLDFSEAIEKSKE-KERIPIGIFYMEKKKVLE 252
                                       **********************8..457899********.***********9998876 PP

>> Lsm_interact  Lsm interaction motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.5   0.00011      0.64       5      17 ..     257     269 ..     255     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00011
                      Lsm_interact   5 akPmSNDDFRKMF 17 
                                         ++SN+DF ++F
  gi|488599869|ref|YP_007906340.1| 257 RAKLSNEDFKNLF 269
                                       579******9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1798.31
//
Query:       gi|488599870|ref|YP_007906341.1|  [L=613]
Description: 2-oxoacid:acceptor oxidoreductase, alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  204.7   0.0    2.2e-60  204.3   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    2.5e-33  115.6   0.0    4.3e-33  114.9   0.0    1.4  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.8e-10   40.8   0.0    4.1e-10   39.6   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
    5.2e-08   33.1   0.0    1.4e-07   31.7   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
  ------ inclusion threshold ------
       0.09   12.4   0.0       0.18   11.4   0.0    1.4  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.3   0.0   6.2e-64   2.2e-60       2     231 .]     240     474 ..     239     474 .. 0.89

  Alignments for each domain:
  == domain 1  score: 204.3 bits;  conditional E-value: 6.2e-64
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a+i ag+d++++YPITP+ +    l++++        +v+qme+Ei+ai+ +iG+a++Gar+ T TSg+G++Lm+e+
  gi|488599870|ref|YP_007906341.1| 240 AKIVAGMDFQSYYPITPAGDESLFLEKHMS-------NVYQMEDEISAICSAIGSALTGARSSTSTSGPGFSLMVEA 309
                                       67889***************5555555553.......6779************************************ PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       lg+a+++e+Pvvi++++Ra+pstg+++r++qsDl++a+     +++ iv+as++++eaf +++ AfnlA k+++Pvi
  gi|488599870|ref|YP_007906341.1| 310 LGWAGMNEVPVVITYYQRAGPSTGMPTRGSQSDLLFALfashgEFPRIVIASGDHEEAFYDTISAFNLADKYQLPVI 386
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC-SGG..G..S-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSX CS
                             POR_N 151 vlfDgfllshevekvelpdee.de..lklikekleeyerkey........aldpekpiargtaanpdtglehrekgn 216
                                       +l+D++l+ ++++++ lpd    e  + li e  +e+e+ ++         ++p+++i  g+  +++tg+eh+e g+
  gi|488599870|ref|YP_007906341.1| 387 HLLDKHLA-NSISTISLPDISkIEidRGLIAESDVESEEGYQrfsfgdtyPVSPRSFI--GKSVMWYTGSEHDEFGH 460
                                       ********.*********9884331134666766666666668999977667777765..9**************** PP

                                       BXXXXHHHHHHHHHH CS
                             POR_N 217 eaedaaekvveevek 231
                                        +ed  e +++++ek
  gi|488599870|ref|YP_007906341.1| 461 VTED-PEFRIRMYEK 474
                                       ****.9999999985 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.0   1.2e-36   4.3e-33       2     173 ..      10     204 ..       7     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 1.2e-36
                                       TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEE CS
                               POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkp 78 
                                       G G+++ag il++a+a  Gy v++nrey s+i+G+hsy+h ++s+ +   s++  ++dl+ ++dae+++ h++++k+
  gi|488599870|ref|YP_007906341.1|  10 GSGLESAGTILTRAFALMGYSVLSNREYYSNIKGRHSYIHTKVSENS--LSLS-LPVDLVAVMDAESVFFHYSDVKE 83 
                                       99******************************************983..5555.67********************* PP

                                       EEEEEEECTCGTT-CCHHHCTS-HHHHHHH.....................T-EEEEE-HHHHHHHCCC........ CS
                               POR  79 ggiiiynseelkpdelkkakeeerelkerl.....................gvrvygvdatkiakeiggn....... 127
                                       gg++iy+   +++++l+  k + r+++er                      +v+v+g+d++k++ e++ +       
  gi|488599870|ref|YP_007906341.1|  84 GGYFIYDL-STNDRTLDSIKTMGRKERERTsrklkelglddvesvidyigkKVNVVGIDFKKVFLELKSKysiqpkk 159
                                       ********.5799999999999999998889**********************************999889999999 PP

                                       .CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHH CS
                               POR 128 .eraaNtvmlGalaallglplealeeaikkrfpkkkeviekNlkafr 173
                                        +++++ +++G +a+++gl++  lee ik+rf++   ++e+N+  ++
  gi|488599870|ref|YP_007906341.1| 160 aSKYVSSILIGSIAGITGLEMSVLEESIKARFKGV--LAEHNIFIVE 204
                                       9********************************95..9****97766 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.2e-13   4.1e-10       2      71 ..     491     560 ..     491     580 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.2e-13
                                       EEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEE CS
                   Transketolase_C   2 kaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeav 71 
                                       ka++  eg+d++l+++G +   +++A+++L+++gisa+ +++  ++p+  ++i+++++ + ++v+vee++
  gi|488599870|ref|YP_007906341.1| 491 KARVYGEGSDLLLIGWGFTKGACVDAVKDLKEKGISASYLSIKLLSPFPSRLIESVIRDYSEVVLVEENY 560
                                       6788899*************************************************************98 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 !   31.7   0.0     4e-11   1.4e-07       2      70 ..     500     567 ..     499     593 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4e-11
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HH CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGql 70 
                                       + ++++ G + g + +av+ l+e+gi++ +l +++l PFP++ ++++++++++vv ++ n+ + + G l
  gi|488599870|ref|YP_007906341.1| 500 DLLLIGWGFTKGACVDAVKDLKEKGISASYLSIKLLSPFPSRLIESVIRDYSEVVLVEENY-LAQLGKL 567
                                       7789999******************************************************.4444554 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 ?   11.4   0.0     5e-05      0.18      40     123 ..     269     351 ..     260     389 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5e-05
                                       SEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH..S..TC--T CS
                      TPP_enzyme_N  40 irvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg..qgvlqqel 114
                                        +v+++ +E +a+  A g a           tsgpG+  ++ al  A  + +P+++   +r+  ++g  + + q   
  gi|488599870|ref|YP_007906341.1| 269 SNVYQMEDEISAICSAIGSALTGA--RSSTSTSGPGFSLMVEALGWAGMNEVPVVITYYQRAGPSTGmpTRGSQ-SD 342
                                       67899999**********998764..3456789************************99999888884433333.22 PP

                                       -CCHHHCCC CS
                      TPP_enzyme_N 115 dqlalfrpv 123
                                          alf+++
  gi|488599870|ref|YP_007906341.1| 343 LLFALFASH 351
                                       344555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3669.38
//
Query:       gi|488599871|ref|YP_007906342.1|  [L=100]
Description: hypothetical protein Asulf_00317 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.4   0.3     0.0042   17.4   0.3    1.7  2  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 ?   -1.3   0.1      0.16   2.9e+03      30      36 ..       7      13 ..       6      22 .. 0.70
   2 !   17.4   0.3   2.3e-07    0.0042       8      55 ..      25      83 ..      24      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.16
                   Lar_restr_allev 30 yCadCga 36
                                      +C++C  
  gi|488599871|ref|YP_007906342.1|  7 ICKKCAK 13
                                      5888876 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.3e-07
                   Lar_restr_allev  8 fCggravlersqrvvaeigq..............cvyCadCgastpwfkiaedeaeaekeai 55
                                      fC +r+v +r ++v ++  +              +vyC+ C +    +   e+ +e+e+++i
  gi|488599871|ref|YP_007906342.1| 25 FCVERKVTVRFHDVCEDFTHfdfetksreifekgWVYCMTCRM---PIFSVEELEEHEDDII 83
                                      9999999999999998776699999999***************...5556666777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 638.76
//
Query:       gi|488599872|ref|YP_007906343.1|  [L=155]
Description: hypothetical protein Asulf_00318 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1028.03
//
Query:       gi|488599873|ref|YP_007906344.1|  [L=259]
Description: putative sugar kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-48  164.0   0.0    1.2e-47  162.5   0.0    1.4  2  NAD_kinase  ATP-NAD kinase
     0.0028   17.3   0.0     0.0051   16.4   0.0    1.4  1  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.11   9.8e+02       2      36 ..       3      36 ..       2      40 .. 0.70
   2 !  162.5   0.0   1.4e-51   1.2e-47      78     290 ..      41     242 ..      34     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.11
                                      EEEEESSCGGTCSHHHHHHHHHHHCT.-...EEEEEC CS
                        NAD_kinase  2 vgivvnpikkeaieraeevarwLlda.ls.rvlevtv 36
                                      v+iv +     +i +a+eva++L d+    + ++++v
  gi|488599873|ref|YP_007906344.1|  3 VAIVYKYG---SIGLAREVASFLEDNgVYtDLYHLPV 36
                                      55665555...6899**********943356666655 PP

  == domain 2  score: 162.5 bits;  conditional E-value: 1.4e-51
                                       SSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE. CS
                        NAD_kinase  78 gvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskge 154
                                       + d+ii +GGDGT+l++ + l++  +P+ g+n G++g lt  ep++++  l+++l+g+++ve+ ++ld++i+ +   
  gi|488599873|ref|YP_007906344.1|  41 DYDFIISIGGDGTILQILQSLEN-PPPIFGINKGRIGILTHAEPDNFRDGLRRILDGDMKVESFMRLDCIINSERT- 115
                                       78********************7.********************************************99987666. PP

                                       .....EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEE CS
                        NAD_kinase 155 ediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivp 231
                                                +++lne+ +    ++ li + + vd+  +e++++dg++ stP+Gstay+ls Ggp+++P +  ili+p
  gi|488599873|ref|YP_007906344.1| 116 ---------HTALNEIAVLSSEPARLIGMRVLVDGVEIEDLRADGMLFSTPIGSTAYALSTGGPIVDPYLFSILITP 183
                                       .........899***************************************************************** PP

                                       ESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEE CS
                        NAD_kinase 232 icPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfkli 290
                                       i P++l  +p +v  +s++++++  +++ l++ dG++++e+sp+  ++++ s++++++ 
  gi|488599873|ref|YP_007906344.1| 184 IAPFKLGWKPWIVKRDSRISVELYPDRNSLIIADGQKRVEVSPDAKIEIVESEHPARFF 242
                                       **********************99999****************************9986 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.7e-07    0.0051      54      83 ..      40      66 ..      14      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.7e-07
                                      CC-SEEEEEESHHHHHHHHHHHCTHHCTTS CS
                          DAGK_cat 54 egvdlivvaGGDGtvsevlnglleelatkp 83
                                      +++d+i+ +GGDGt+ ++l++l +    +p
  gi|488599873|ref|YP_007906344.1| 40 SDYDFIISIGGDGTILQILQSLEN---PPP 66
                                      469******************998...433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1479.51
//
Query:       gi|488599874|ref|YP_007906345.1|  [L=259]
Description: D-fructose 1,6-bisphosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   71.8   0.0    3.9e-19   69.2   0.0    1.8  1  Inositol_P  Inositol monophosphatase family
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.035   14.1   0.1    1.5  1  DUF4298     Domain of unknown function (DUF4298)
      0.043   13.3   0.0      0.073   12.5   0.0    1.4  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   6.4e-23   3.9e-19      40     266 ..      38     256 ..      13     259 .] 0.79

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 6.4e-23
                                       HHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEETT CS
                        Inositol_P  40 edlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigllveg 116
                                         + +++d+++e++ ++ l+e + + ki++ee++  ge      d  ++ +DP+DGT n +r+ip +++s ++ + +
  gi|488599874|ref|YP_007906345.1|  38 GTPTKKVDKVAEDVAISILKE-Y-DFKIVSEEAGVVGE-----GD-IFVALDPVDGTFNATRKIPLYCISMCFSKSD 106
                                       4578899******99998765.4.69*********999.....45.8****************************99 PP

                                       EEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCH.EEEB CS
                        Inositol_P 117 kpvlGviaqPllgqlysaakgkGaflngeklplsrappiseallvtlfavssrkdtseasllekvesavsae.gvrs 192
                                       +   ++ a + +  ++  +  +G +++g  +  +++++i+         vs+++d+s  +    +  ++    ++r 
  gi|488599874|ref|YP_007906345.1| 107 RLSDAFFAYVSNLATLDEYYAEGEWSSG--FAYKNEQKIK---------VSNKEDISICNAVFYYPDRNYGFkRIRI 172
                                       9988888888777777777788999999..5555555222.........3334444443334444333333345789 PP

                                       ESSHHHHHHHHHHTSTSEEEEEC......EBHHHHHHHHHHHHHTTEEEEESSSC....SSSTTSS..EEEEESCHH CS
                        Inositol_P 193 vgssalklaavaeGkadaylefg.....rekkWDhAAGeaileeaGGvvtdakge....grlllar..giiaanqke 258
                                       +gssa++l++va+ ++d +++ +      + ++D+ AG +i + aG++ td++g+    +r  ++   ++++an ++
  gi|488599874|ref|YP_007906345.1| 173 FGSSAIELCLVADSSMDCFIDTRgnvkgMLRIYDVSAGLFIAKSAGAKATDLRGNpldsKRISMDErlTLVVAN-PV 248
                                       9*********************9999999**************************8877555555422334444.88 PP

                                       HHHHHHHH CS
                        Inositol_P 259 laellaaa 266
                                       l+++++ +
  gi|488599874|ref|YP_007906345.1| 249 LHTKIINL 256
                                       88888865 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.9e-06     0.035      28      62 ..     115     149 ..     101     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-06
                                       THHHHHHHHHHHTSHHHHHHHTS--SS.....--S CS
                           DUF4298  28 lqkklakLdeYYqseqwredleasnkgelpqelky 62 
                                         ++la+LdeYY+  +w++ + + n+++++ ++k 
  gi|488599874|ref|YP_007906345.1| 115 YVSNLATLDEYYAEGEWSSGFAYKNEQKIKVSNKE 149
                                       567899********************999877665 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 ?   12.5   0.0   1.2e-05     0.073      56     120 ..      36      92 ..       3     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                            FBPase  56 vtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSnidtn 120
                                        +G   kk+D +a+++ i  lk+ +    +vSEE     v+    eg + va+DP+DG  n   +
  gi|488599874|ref|YP_007906345.1|  36 KDGTPTKKVDKVAEDVAISILKEYD--FKIVSEEA---GVV---GEGDIFVALDPVDGTFNATRK 92 
                                       478899***************9884..56899986...466...79************9886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1842.58
//
Query:       gi|488599875|ref|YP_007906346.1|  [L=291]
Description: pyruvate ferredoxin oxidoreductase, beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   93.1   0.6    2.1e-26   92.5   0.6    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
       0.05   13.1   0.1       0.08   12.4   0.1    1.5  1  DUF3335       Peptidase_C39 like family


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.6   2.4e-30   2.1e-26       2     153 .]      37     200 ..      36     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 2.4e-30
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH.....ST.TSEEEEEEEHHHHHHT.GGGHHHHHHT CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla.....kp.drevvaivGDGgflmi.lqelatavrr 71 
                                       +Gcl++  +++    + + +  +++++ + ++ ++A G++la     +  + +vv+++GDG++++i +  l+ ++ r
  gi|488599875|ref|YP_007906346.1|  37 TGCLEIISSQY----ERSAWGVPYIHSLFENAGAVAAGIELAlkalkRTdEGKVVVFAGDGATADIgIGTLSGMMDR 109
                                       79999977777....4555666*******************44556433357************************* PP

                                       T-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHH CS
                      TPP_enzyme_C  72 nlpitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleeal 139
                                       n+++++++l+Ne+y++tg+q    +p+g++++++pag      +++++d+  +a a+G + +a+ ++a  +++++++
  gi|488599875|ref|YP_007906346.1| 110 NHDVIYICLDNEAYQNTGNQqsgLTPMGSNTTTTPAGAimlgkTGRKKDMISIAVAHGLPyVASASVAFHADIRRKV 186
                                       ********************88889************9****879999************9998889999******* PP

                                       HHHHCSSSEEEEEE CS
                      TPP_enzyme_C 140 kealekkgpaliev 153
                                       k+a e +g  +i++
  gi|488599875|ref|YP_007906346.1| 187 KKAAEIEGAKYIQI 200
                                       ****9999998875 PP

>> DUF3335  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   8.9e-06      0.08      46      65 ..       3      22 ..       1      88 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.9e-06
                           DUF3335 46 fmtsGhggceplGLalaaar 65
                                      + +sGhg+c   GLa+a+++
  gi|488599875|ref|YP_007906346.1|  3 YFASGHGACPGCGLAIAVRN 22
                                      789**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1933.38
//
Query:       gi|488599876|ref|YP_007906347.1|  [L=391]
Description: pyruvate ferredoxin oxidoreductase, alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-74  248.8   0.1    7.2e-74  248.4   0.1    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.1e-32  110.5   0.1    7.1e-32  109.8   0.1    1.4  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    2.7e-08   33.7   0.0    5.2e-08   32.8   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.17   12.1   0.0       0.33   11.2   0.0    1.4  1  Gp5_OB           Gp5 N-terminal OB 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 !  248.4   0.1   1.6e-77   7.2e-74       2     227 ..      14     235 ..      13     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 248.4 bits;  conditional E-value: 1.6e-77
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       a++ ++++viaaYPITP++ei+e+la+++ +ge++  e+v++esE+ga+s  +GA+aaGar++TaT++qGl+Lm+e 
  gi|488599876|ref|YP_007906347.1|  14 AVKLCKPNVIAAYPITPQTEIVENLAKMYSNGELEGCEYVTAESEFGAASILVGASAAGARTFTATCSQGLILMSEV 90 
                                       78899*****************************99***************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlf 153
                                       l  aag++lP+v+v+++Ral+++ lsi++d++D m +rd gli++++e++qea+d++  Af++Ae+  v++P+++ +
  gi|488599876|ref|YP_007906347.1|  91 LLNAAGMRLPIVLVNTNRALSAP-LSIWNDHQDSMVLRDGGLIQIHVETNQEAHDMVPLAFKVAENskVMLPFMINM 166
                                       ***********************.******************************************99********* PP

                                       EHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHH CS
                             POR_N 154 Dgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvve 227
                                       Dgf l+h++e+v+l+d++    +++++l++y++   ++++++p+++g++a+p+++ e+r  +++a+++a  v e
  gi|488599876|ref|YP_007906347.1| 167 DGFKLTHAYEPVDLLDQD----TVDSFLPPYNPPV-YMTTKNPLTFGCYAPPHCYTEFRVVMQRAMMRALDVLE 235
                                       ******************....***********88.***************************99998766655 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 !  109.8   0.1   1.6e-35   7.1e-32       1     101 [.     261     361 ..     261     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1.6e-35
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Ae +iv mGs+ g ++++v+elR++g+kvGll++rt+rPFP++++ke+lk+++k++v++r++sfg+eG+++ evk+a
  gi|488599876|ref|YP_007906347.1| 261 AELAIVSMGSLTGMVRDVVKELRKNGVKVGLLKIRTFRPFPAKQVKEALKNANKILVFERAVSFGYEGPVGIEVKSA 337
                                       89*************************************************************************** PP

                                       TGGGTSEEEEEE--GGG----HHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditved 101
                                       l + +++ ++f  glgGrd+  e+
  gi|488599876|ref|YP_007906347.1| 338 LFGLNPEFYSFAVGLGGRDVPREE 361
                                       *******************97776 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.2e-11   5.2e-08      10      74 ..     261     325 ..     256     348 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.2e-11
                                       SSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTT CS
                   Transketolase_C  10 kdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrg 74 
                                        ++++v++Gs   ++ ++++eL+k+g+++ ++ +rt++p+  + ++e++k+ ++++v+e av +g
  gi|488599876|ref|YP_007906347.1| 261 AELAIVSMGSLTGMVRDVVKELRKNGVKVGLLKIRTFRPFPAKQVKEALKNANKILVFERAVSFG 325
                                       6899******************************************************9988754 PP

>> Gp5_OB  Gp5 N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.3e-05      0.33      42      75 ..     245     278 ..     242     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.3e-05
                            Gp5_OB  42 tGiveGthvyGfflDkfkqdgvilGtlpgiykek 75 
                                       tG   G hv+G flD+ ++  v +G+l+g++++ 
  gi|488599876|ref|YP_007906347.1| 245 TGRDWGGHVVGEFLDDAELAIVSMGSLTGMVRDV 278
                                       6667799**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2346.81
//
Query:       gi|488599877|ref|YP_007906348.1|  [L=96]
Description: 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   47.9  20.5      1e-07   31.4   4.8    2.2  2  Fer4        4Fe-4S binding domain
      1e-11   44.8  30.2    7.5e-10   38.8  15.4    1.5  2  Fer4_21     4Fe-4S dicluster domain
    6.6e-09   35.8  10.4    8.7e-09   35.4  10.4    1.3  1  Fer4_9      4Fe-4S dicluster domain
    9.2e-09   35.3  24.1    3.7e-05   23.7  15.8    2.1  2  Fer4_10     4Fe-4S dicluster domain
    1.8e-08   34.0  17.1    7.7e-05   22.6   4.3    2.4  2  Fer4_2      4Fe-4S binding domain
    3.7e-08   33.1  19.0    3.7e-05   23.6   4.1    2.3  2  Fer4_6      4Fe-4S binding domain
    3.9e-08   33.8  29.5    7.9e-07   29.6  15.6    1.9  2  Fer4_7      4Fe-4S dicluster domain
    1.9e-06   28.7  12.9    0.00011   23.1   1.0    2.2  2  Fer4_16     4Fe-4S double cluster binding domain
    2.2e-05   24.6  15.0     0.0031   17.9   2.1    2.3  2  Fer4_4      4Fe-4S binding domain
    3.6e-05   24.1   7.2      0.035   14.5   0.5    2.2  2  Fer4_8      4Fe-4S dicluster domain
     0.0002   21.8   8.1       0.12   12.9   2.4    2.2  2  Fer4_17     4Fe-4S dicluster domain
    0.00083   19.8  16.5      0.021   15.4   7.4    2.2  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
       0.25   12.4  17.6       0.25   12.4   5.7    2.4  2  Fer4_3      4Fe-4S binding domain
        1.1   10.1  15.3        2.4    9.1   4.1    2.1  3  Fer4_22     4Fe-4S dicluster domain
        1.6    9.6  18.2        3.8    8.3   3.9    2.8  2  Fer4_15     4Fe-4S single cluster domain
        5.2    7.3  13.4        6.3    7.0   2.0    2.1  2  Fer4_18     4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   7.7   5.5e-08   6.2e-05       1      23 [.      29      51 ..      29      52 .. 0.94
   2 !   31.4   4.8   9.3e-11     1e-07       2      24 .]      63      85 ..      62      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.5e-08
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +v+deekC++C++C+  CP  +I
  gi|488599877|ref|YP_007906348.1| 29 PVVDEEKCTACKTCEHLCPDACI 51
                                      69*****************9998 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 9.3e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v d++ C gCG C +vCP +AI+
  gi|488599877|ref|YP_007906348.1| 63 VPDYDYCKGCGVCFSVCPADAIK 85
                                      679*******************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   6.8   2.5e-06    0.0028      33      57 ..      28      51 ..      21      53 .. 0.80
   2 !   38.8  15.4   6.7e-13   7.5e-10       2      59 .]      30      86 ..      29      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                           Fer4_21 33 vlkvvedeCvGCnlCssvCPvedci 57
                                      +  v e++C++C+ C + CP + ci
  gi|488599877|ref|YP_007906348.1| 28 YPVVDEEKCTACKTCEHLCP-DACI 51
                                      3345699*************.8998 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 6.7e-13
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      ++de+kC  C+ C   C+d+++  +e+ + +v+    d C GC +C svCP  d+i+m
  gi|488599877|ref|YP_007906348.1| 30 VVDEEKCTACKTCEHLCPDACIVIVEKGDTKVAVPDYDYCKGCGVCFSVCPA-DAIKM 86
                                      69*****************888877776666666689**************5.***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 !   35.4  10.4   7.7e-12   8.7e-09       1      51 []      35      84 ..      21      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7.7e-12
                            Fer4_9  1 kCtgCgaCveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kCt C++C++ Cp   + + +++ +k+++  +++  C gCg C+ +Cp +ai
  gi|488599877|ref|YP_007906348.1| 35 KCTACKTCEHLCPDACIvIVEKGDTKVAVPDYDY--CKGCGVCFSVCPADAI 84
                                      7***********9877725666666677766666..*************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 !   23.7  15.8   3.3e-08   3.7e-05       3      56 .]      30      80 ..      28      80 .. 0.95
   2 !   22.5   1.2   8.3e-08   9.3e-05       4      29 ..      64      89 ..      61      96 .] 0.74

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.3e-08
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+d+++C+ C++C   CP    +  ++ e+ + ++   +++ C gcg C ++CP
  gi|488599877|ref|YP_007906348.1| 30 VVDEEKCTACKTCEHLCPD---ACIVIVEKGDTKVAVPDYDYCKGCGVCFSVCP 80
                                      789****************...9999999999999999***************9 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 8.3e-08
                           Fer4_10  4 idddtCirCgkCvkaCPadltsvgak 29
                                       d d C +Cg C ++CPad+ +++ k
  gi|488599877|ref|YP_007906348.1| 64 PDYDYCKGCGVCFSVCPADAIKMELK 89
                                      5889**************66444443 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   4.3   6.9e-08   7.7e-05       2      21 ..      28      47 ..      27      48 .. 0.94
   2 !   19.3   2.9   7.7e-07   0.00087       6      22 .]      65      81 ..      60      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.9e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++vvd+++C++C++C + CP
  gi|488599877|ref|YP_007906348.1| 28 YPVVDEEKCTACKTCEHLCP 47
                                      79*****************9 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.7e-07
                            Fer4_2  6 dtdrCigCgaCvsaCPa 22
                                      d d C gCg C s+CPa
  gi|488599877|ref|YP_007906348.1| 65 DYDYCKGCGVCFSVCPA 81
                                      7889************8 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   7.0   1.2e-05     0.013       2      23 ..      29      50 ..      28      53 .. 0.91
   2 !   23.6   4.1   3.3e-08   3.7e-05       5      24 .]      65      84 ..      61      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      +++d++kC+ C  C+  CP + 
  gi|488599877|ref|YP_007906348.1| 29 PVVDEEKCTACKTCEHLCPDAC 50
                                      89*****************875 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 3.3e-08
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d+d C gCg C++vCP++ai
  gi|488599877|ref|YP_007906348.1| 65 DYDYCKGCGVCFSVCPADAI 84
                                      899***************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   5.9   1.3e-05     0.014      27      50 ..      25      48 ..      11      50 .. 0.82
   2 !   29.6  15.6     7e-10   7.9e-07       1      52 []      35      83 ..      35      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                            Fer4_7 27 gtekveidpekClgCgaCvavCPt 50
                                      gte++++d+ekC+ C+ C+  CP 
  gi|488599877|ref|YP_007906348.1| 25 GTEYPVVDEEKCTACKTCEHLCPD 48
                                      668889*****************5 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 7e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+ C+ C+  Cp  +i + e+ +   t+ ++ d+++C gCg+C +vCP++a
  gi|488599877|ref|YP_007906348.1| 35 KCTACKTCEHLCPDACIVIVEKGD---TKVAVPDYDYCKGCGVCFSVCPADA 83
                                      7******************99843...3446679***************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 !   10.6   5.0   0.00075      0.84       1      20 [.      35      54 ..      35      65 .. 0.81
   2 !   23.1   1.0   9.5e-08   0.00011       2      20 ..      69      87 ..      68      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00075
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C+ C+ C   CP ++i   
  gi|488599877|ref|YP_007906348.1| 35 KCTACKTCEHLCPDACIVIV 54
                                      5**************98754 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 9.5e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg C +vCP++aik++
  gi|488599877|ref|YP_007906348.1| 69 CKGCGVCFSVCPADAIKME 87
                                      *****************98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   5.3   0.00019      0.21       2      16 ..      34      48 ..      33      56 .. 0.93
   2 !   17.9   2.1   2.7e-06    0.0031       2      16 ..      67      81 ..      66      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e+C+ C+ C+  CP+
  gi|488599877|ref|YP_007906348.1| 34 EKCTACKTCEHLCPD 48
                                      89************6 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.7e-06
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C gCg+C ++CP 
  gi|488599877|ref|YP_007906348.1| 67 DYCKGCGVCFSVCPA 81
                                      89************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   1.2   7.1e-05     0.079      49      62 ..      34      47 ..      10      60 .. 0.84
   2 !   14.5   0.5   3.1e-05     0.035       3      17 ..      67      81 ..      65      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.1e-05
                            Fer4_8 49 wsCttcgaCtevCp 62
                                      ++Ct+c+ C+  Cp
  gi|488599877|ref|YP_007906348.1| 34 EKCTACKTCEHLCP 47
                                      57999999999998 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.1e-05
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      ++C +Cg C+s Cp+
  gi|488599877|ref|YP_007906348.1| 67 DYCKGCGVCFSVCPA 81
                                      679999999999983 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.4   0.00011      0.12      44      58 ..      34      48 ..      12      50 .. 0.86
   2 !   12.7   0.3   0.00013      0.14       2      58 ..      69      81 ..      54      92 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      ++C+ C+ Ce+ CP 
  gi|488599877|ref|YP_007906348.1| 34 EKCTACKTCEHLCPD 48
                                      68***********96 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                      C +Cg C  +Cp                                            +
  gi|488599877|ref|YP_007906348.1| 69 CKGCGVCFSVCP--------------------------------------------A 81
                                      555555555555............................................4 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   7.4   1.9e-05     0.021       1      18 [.      31      48 ..      31      50 .. 0.96
   2 !    9.9   1.6   0.00096       1.1       2      17 ..      65      80 ..      61      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD+++C+ac++C +l+Pd
  gi|488599877|ref|YP_007906348.1| 31 VDEEKCTACKTCEHLCPD 48
                                      9****************9 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00096
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D d C +cg+C +++P
  gi|488599877|ref|YP_007906348.1| 65 DYDYCKGCGVCFSVCP 80
                                      6688************ PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.1     0.031        35       1      12 [.      36      47 ..      36      52 .. 0.91
   2 ?   12.4   5.7   0.00022      0.25       1      15 []      69      83 ..      69      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.031
                            Fer4_3  1 CtgCgaCvevCP 12
                                      Ct C +C+  CP
  gi|488599877|ref|YP_007906348.1| 36 CTACKTCEHLCP 47
                                      999999999999 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00022
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gCg C+ vCP +A
  gi|488599877|ref|YP_007906348.1| 69 CKGCGVCFSVCPADA 83
                                      9***********887 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   6.1      0.11   1.3e+02       1      13 [.      35      47 ..      18      50 .. 0.64
   2 ?    5.4   5.6     0.031        34       1      20 [.      35      53 ..      35      64 .. 0.74
   3 ?    9.1   4.1    0.0021       2.4      72      94 ..      59      81 ..      50      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                           Fer4_22  1 rClsCgaCtlvCp 13
                                      +C +C +C  +Cp
  gi|488599877|ref|YP_007906348.1| 35 KCTACKTCEHLCP 47
                                      3555555555555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.031
                           Fer4_22  1 rClsCgaCtlvCptCsCfdv 20
                                      +C +C +C  +Cp   C+ +
  gi|488599877|ref|YP_007906348.1| 35 KCTACKTCEHLCPDA-CIVI 53
                                      7***********963.4444 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0021
                           Fer4_22 72 efkekfgesgCvGCgRCieacpv 94
                                      + ++  +   C GCg C ++cp+
  gi|488599877|ref|YP_007906348.1| 59 TKVAVPDYDYCKGCGVCFSVCPA 81
                                      4555557889***********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 ?    6.0   6.4     0.019        21       2      21 ..      30      49 ..      30      63 .. 0.83
   2 ?    8.3   3.9    0.0034       3.8       4      19 ..      65      80 ..      61      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                           Fer4_15  2 vvDrdaCigcglCvaeapev 21
                                      vvD+++C+ c  C  ++p+ 
  gi|488599877|ref|YP_007906348.1| 30 VVDEEKCTACKTCEHLCPDA 49
                                      69***************974 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0034
                           Fer4_15  4 DrdaCigcglCvaeap 19
                                      D d C gcg+C  ++p
  gi|488599877|ref|YP_007906348.1| 65 DYDYCKGCGVCFSVCP 80
                                      899***********98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.3     0.013        15      57      73 ..      32      48 ..      12      57 .. 0.81
   2 ?    7.0   2.0    0.0056       6.3      58      74 ..      66      82 ..      51      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                           Fer4_18 57 gagdcidcescvkvcPt 73
                                      ++ +c++c++c ++cP 
  gi|488599877|ref|YP_007906348.1| 32 DEEKCTACKTCEHLCPD 48
                                      5678***********96 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0056
                           Fer4_18 58 agdcidcescvkvcPtg 74
                                         c  c++c +vcP +
  gi|488599877|ref|YP_007906348.1| 66 YDYCKGCGVCFSVCPAD 82
                                      45699**********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 655.29
//
Query:       gi|488599878|ref|YP_007906349.1|  [L=189]
Description: pyruvate ferredoxin oxidoreductase, gamma subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  138.1   0.1    3.6e-40  137.9   0.1    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   0.1     2e-44   3.6e-40       1     176 [.      14     180 ..      14     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 2e-44
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldg 75 
                                       GGqGvvta+ +la a ++ Gyy ++++++g+e+rG ++ s +r+sdepiv++ e++++d++v++d++ +   ++ +g
  gi|488599878|ref|YP_007906349.1|  14 GGQGVVTAADMLAVAGFKDGYYTLSFPTFGAEKRGTPVASFLRLSDEPIVSRDEIYYPDYVVVMDPTVIGpvKVDAG 90 
                                       9********************************************************************98899999 PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleale 151
                                       +k +g ii+n ++  p+elk++           +v+vy+++at++a e++g ++++Nt+m+Ga+++++g +++++++
  gi|488599878|ref|YP_007906349.1|  91 IKSDGKIIANYPK-GPEELKESMGV--------DVEVYTINATRMAMEHLG-RPITNTAMVGAFVGATGiIKIDSVL 157
                                       ***********54.55555554443........378***************.************************* PP

                                       HHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 152 eaikkrfpkkkeviekNlkafragy 176
                                       e +++ f +  e++ekN k + ++y
  gi|488599878|ref|YP_007906349.1| 158 ETVREWFSG--ELAEKNAKLITEAY 180
                                       ********9..8************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 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:                        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 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1236.22
//
Query:       gi|488599879|ref|YP_007906350.1|  [L=270]
Description: hypothetical protein Asulf_00325 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        0.4   11.1   4.1       0.17   12.3   0.5    2.2  3  Uteroglobin  Uteroglobin family
        2.3    8.1   8.8        1.2    9.0   0.2    2.6  2  CLTH         CTLH/CRA C-terminal to LisH motif domain


Domain annotation for each model (and alignments):
>> Uteroglobin  Uteroglobin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.53   4.8e+03      48      84 ..       7      43 ..       3      48 .. 0.65
   2 ?   -2.7   0.0      0.85   7.6e+03      64      79 ..     152     168 ..     130     176 .. 0.59
   3 ?   12.3   0.5   1.9e-05      0.17      29      87 ..     209     268 ..     203     270 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.53
                                      TT---HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                       Uteroglobin 48 kynpdpeaeealaelKqcvdklsnetkenvaklleki 84
                                       ++++pe+++  +++    + l+  ++e+++  l+ +
  gi|488599879|ref|YP_007906350.1|  7 AFQEHPEINKKELNITMTLLVLTMRNLEDFERELKGV 43
                                      5777777777777777777777777777776665555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.85
                                       HHHT.TS-HHHHHHHHH CS
                       Uteroglobin  64 qcvd.klsnetkenvak 79 
                                       q ++ ++ + +k+++ak
  gi|488599879|ref|YP_007906350.1| 152 QVILkNIRKWEKDEIAK 168
                                       33343445555555555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 1.9e-05
                                       HHHHHHH.HS-HHHHHHHHHTT---HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHTS CS
                       Uteroglobin  29 evvekfl.egseeeYkeeLqkynpdpeaeealaelKqcvdklsnetkenvakllekilss 87 
                                       e+ve+++ ++se+e  + ++   + +   e + +lK  +d+l+  ++ +++k++e+ l+ 
  gi|488599879|ref|YP_007906350.1| 209 EEVEELIsVESESEMLNIFKAILEGDYSDERVSKLKDLIDNLTVSERLAIMKTIEAFLNY 268
                                       6788888666999999999999999999**************************998875 PP

>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2   0.00014       1.2      66     107 ..       2      46 ..       1      67 [. 0.73
   2 ?    1.3   3.8     0.031   2.8e+02      45      95 ..      89     178 ..      85     256 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00014
                              CLTH  66 renlefend...ehlkelekamsLLafsdpeskelssplknlldp 107
                                       r +++++++    ++kel+ +m+LL+  + + ++   +lk +ld 
  gi|488599879|ref|YP_007906350.1|   2 RSHFRAFQEhpeINKKELNITMTLLVLTMRNLEDFERELKGVLDE 46 
                                       67886555568899*************998874444455555554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.031
                              CLTH  45 lqfielirgktkd......ieealeyare..nl.efend..ehlkelekamsLLafsdpes................ 94 
                                        +++e++r   ++      ++++ e++r+  ++ +++ +  ++ + le+ m   ++++ +                 
  gi|488599879|ref|YP_007906350.1|  89 IELVEMFRT--RKeflqidYNTINEFIRRlwYFeSKREKgySFSQSLEDFMYI-VYRMKDVqnkidqvilknirkwe 162
                                       689999994..333455559999999999886633333368999999998864.46653224555555555555555 PP

                              CLTH  95 ...............k 95 
                                                       
  gi|488599879|ref|YP_007906350.1| 163 kdeiakmyfimiktfI 178
                                       5555555555555551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2008.52
//
Query:       gi|488599880|ref|YP_007906351.1|  [L=433]
Description: 3-hexulose-6-phosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   4.2    4.1e-43  147.1   4.2    1.9  2  RraA-like     Aldolase/RraA
    6.4e-24   84.8   4.9    1.3e-23   83.8   4.9    1.5  1  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
    1.3e-07   31.3   6.4    0.00016   21.2   0.3    2.9  3  His_biosynth  Histidine biosynthesis protein
      2e-06   27.5   5.0     0.0043   16.7   0.9    2.6  3  HMGL-like     HMGL-like
    1.9e-05   24.1   2.5    0.00012   21.5   2.5    2.5  1  TMP-TENI      Thiamine monophosphate synthase
    0.00013   21.2   1.6    0.00021   20.6   1.6    1.3  1  IGPS          Indole-3-glycerol phosphate synthase
    0.00015   21.3   4.2    0.00034   20.1   4.2    1.8  1  NMO           Nitronate monooxygenase
    0.00067   18.6   4.0      0.016   14.1   1.6    2.8  3  Trp_syntA     Tryptophan synthase alpha chain
    0.00085   18.6   2.9     0.0017   17.6   1.1    2.4  2  DUF561        Protein of unknown function (DUF561)
    0.00089   18.6   1.6     0.0029   16.9   1.6    1.8  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0051   16.3   2.3      0.024   14.1   0.1    2.6  3  PEP_mutase    Phosphoenolpyruvate phosphomutase
      0.009   15.8   0.2      0.012   15.4   0.2    1.2  1  DUF2855       Protein of unknown function (DUF2855)
  ------ inclusion threshold ------
       0.06   12.9   2.3       0.18   11.3   2.4    1.7  1  Peripla_BP_4  Periplasmic binding protein domain
      0.074   12.5   0.5       0.13   11.6   0.5    1.5  1  PALP          Pyridoxal-phosphate dependent enzyme


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   0.0       2.1   2.7e+03      37      50 ..      79     104 ..      45     119 .. 0.54
   2 !  147.1   4.2   3.2e-46   4.1e-43       1     150 []     240     386 ..     240     386 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                                       .............BGHHHHHHHTS-- CS
                         RraA-like  37 a............dnslvkealeeag 50 
                                       +            dns+++ea+ +a+
  gi|488599880|ref|YP_007906351.1|  79 KsgadiviilaasDNSTIEEAIRAAR 104
                                       23333333333338888888887554 PP

  == domain 2  score: 147.1 bits;  conditional E-value: 3.2e-46
                                       HHHHHHHCEE-SSBST.B.TT.EE.S.EEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSECE-HHH CS
                         RraA-like   1 tadvsDalkklggrsg.girpler.s.fvGpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraallGgll 74 
                                       t+++sDa+++       +i+p++r + +vG+avTv+++++d+++  ea++ ag g+v+V++++g  +++a++ G+l 
  gi|488599880|ref|YP_007906351.1| 240 TPNISDAMHRARA--MmDIHPVNRgKkIVGKAVTVSTMDGDWAKPVEAIDVAGMGEVIVIKCSG--DTTAVW-GELA 311
                                       789******3333..2579**99966899***********************************..548888.**** PP

                                       HHHHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSEEEEETTEEEE CS
                         RraA-like  75 ataakangvaGvvvdGavRDvaelreldfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdlivaDedGvvv 150
                                       ++++ ++g++Gv++dGavRDv+++r+l++pvfa+  +p++ + k g ge+nv++ +gg+ v+pgd+ivaD++Gv+v
  gi|488599880|ref|YP_007906351.1| 312 TRSCLNKGIEGVIIDGAVRDVDDIRKLGYPVFAKREVPNAGEPK-GFGEINVKIVCGGIEVNPGDWIVADDNGVMV 386
                                       ***************************************96666.*****************************87 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   4.9     1e-26   1.3e-23       3     225 .]       6     206 ..       4     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1e-26
                                       EEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHH CS
                         OMPdecase   3 LclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqa 76 
                                       L++alD+ + ++++e+a ++ +  +++++++++l++++g     ++++++++k+   ++i++D+K+ D G+++ ++a
  gi|488599880|ref|YP_007906351.1|   6 LQVALDLLELKRAIEIASEAIEgGADWIEVGTPLIKSEG-----MDAVRELKKRYrdHKIVADMKTIDTGAIEVEMA 77 
                                       9*******************999****************.....99*****999989******************** PP

                                       HSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHHH CS
                         OMPdecase  77 tagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehkae 149
                                             +k++adiv++ a+ + ++++++++aa+k+g    +++++++ ++  ++++  +  g+++   +   +++  
  gi|488599880|ref|YP_007906351.1|  78 ------AKSGADIVIILAASDNSTIEEAIRAARKYG--SEIMVDMINVTNPVERAKelEelGVDYINCHIGIDQQ-- 144
                                       ......69***************************9..9****************95424666666666666666.. PP

                                       TTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                         OMPdecase 150 dfvmGfvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                         +mG+   e           ++ + + + +   + ++g++ ++    i  +ga+i+ivG  I+k+++  e a+++
  gi|488599880|ref|YP_007906351.1| 145 --MMGMDPIEL----------LKEIAKAVSI-PVAGAGGLNAEKSALCIT-KGAKIVIVGSNIVKSRNVTESARKI 206
                                       ..566655554..........5678888998.999999999987666666.99*******************9986 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.4   1.8e-07   0.00023      86     222 ..      20     192 ..      17     196 .. 0.64
   2 !   21.2   0.3   1.2e-07   0.00016      28     116 ..     117     204 ..     101     238 .. 0.75
   3 ?   -1.7   0.1       1.2   1.6e+03     192     208 ..     321     337 ..     262     340 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.8e-07
                                       HHHHHHHHCT-SEEEESHHHHH-..THHHHHHHHHHCGGGEEEEEEEEE..........C................. CS
                      His_biosynth  86 edveelleagadkviigtaavkn..pelikelaekfgsqkivvaiDarr..........g................. 133
                                       e + e++e gad + +gt  +k+   + ++el +++ + kiv+   + +          +                 
  gi|488599880|ref|YP_007906351.1|  20 EIASEAIEGGADWIEVGTPLIKSegMDAVRELKKRYRDHKIVADMKTIDtgaievemaaKsgadiviilaasdnsti 96 
                                       55666667777777777776665224557777777777777766555444434444433044455555555555665 PP

                                       ....EEEEETTTTEE.........EEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---H.HHHHHHHHHHSSEEEE CS
                      His_biosynth 134 ....ykvaikgwree.........tgldavelakkleelgageilltdidrdGtlsGpdl.eltkelaeavkipvia 196
                                              a k                 ++ve ak+leelg+   +   i  d  ++G+d  el+ke+a+av+ipv  
  gi|488599880|ref|YP_007906351.1|  97 eeaiR-AARK----YgseimvdmiNVTNPVERAKELEELGVDY-INCHIGIDQQMMGMDPiELLKEIAKAVSIPVAG 167
                                       55531.2222....122223444445589999********977.566799999******659*************99 PP

                                       ESS--SHHHHHHHHHTTCSEEEESHH CS
                      His_biosynth 197 sGGvgsledlkelksegvdavivgsa 222
                                       +GG    e  +   ++g++ vivgs 
  gi|488599880|ref|YP_007906351.1| 168 AGGLN-AEKSALCITKGAKIVIVGSN 192
                                       99995.55556666899999999985 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.2e-07
                                       TTSHHHHHHHHHHHT-SEEEE.EEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESH CS
                      His_biosynth  28 agdpvelakryeeegadelhv.vDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigt 103
                                         +pve ak++ee g+d++   + +d  + g    ++l++eia++v+ipv   GG +  +  +  +  ga+ vi+g+
  gi|488599880|ref|YP_007906351.1| 117 VTNPVERAKELEELGVDYINChIGIDQQMMGM-DPIELLKEIAKAVSIPVAGAGGLNAEK-SALCITKGAKIVIVGS 191
                                       56788888888888888875425676666444.456788888888888888888887766.5667778888888888 PP

                                       HHHH-THHHHHHH CS
                      His_biosynth 104 aavknpelikela 116
                                         vk+ ++ +++ 
  gi|488599880|ref|YP_007906351.1| 192 NIVKSRNVTESAR 204
                                       8888887766654 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.2
                                       SEEEEESS--SHHHHHH CS
                      His_biosynth 192 ipviasGGvgsledlke 208
                                         vi+ G v++++d+++
  gi|488599880|ref|YP_007906351.1| 321 EGVIIDGAVRDVDDIRK 337
                                       33444444444444444 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.9   3.3e-06    0.0043      14     124 ..       7     116 ..       3     119 .. 0.80
   2 !   13.1   0.1     4e-05     0.051      19      93 ..     114     189 ..     107     222 .. 0.67
   3 ?   -2.5   0.0       2.3     3e+03      70      95 ..     271     296 ..     235     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
                                       HTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHH.HHHHHHH....TT CS
                         HMGL-like  14 qalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarek.dikaavealkgag 89 
                                       q + + l++++ ++ia +  e g d iEvg p    + +++vr+++k   + +i+a ++  +   i++ +  + + g
  gi|488599880|ref|YP_007906351.1|   7 QVALDLLELKRAIEIASEAIEGGADWIEVGTPLIKSEGMDAVRELKKRYRDHKIVADMKTIDTgAIEVEM--AAKSG 81 
                                       566677899999****************************************987766654441444433..36689 PP

                                       -SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHH CS
                         HMGL-like  90 akrvhvfiatselhlkaklkkdreevakkaeeavk 124
                                       a++v +  a  +  ++  ++  r++  ++++++++
  gi|488599880|ref|YP_007906351.1|  82 ADIVIILAASDNSTIEEAIRAARKYGSEIMVDMIN 116
                                       98888887777777888888888888888887775 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4e-05
                                       ---HHHHHHHHHHHHHHT-SEE--....TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-S CS
                         HMGL-like  19 alsveeklaiakaLdeagvdeiEv....gfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagak 91 
                                        ++v + ++ ak+L+e+gvd+i +       +++ d++e +++iakav ++ + +   ++ +  +  +   kga+ +
  gi|488599880|ref|YP_007906351.1| 114 MINVTNPVERAKELEELGVDYINChigiDQQMMGMDPIELLKEIAKAVSIP-VAGAGGLNAEKSALCIT--KGAKIV 187
                                       5677777888**************774334679***************887.54444444444333333..444444 PP

                                       EE CS
                         HMGL-like  92 rv 93 
                                       +v
  gi|488599880|ref|YP_007906351.1| 188 IV 189
                                       44 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.3
                                       EE-SSHHHHHHHHH....TT-SEEEE CS
                         HMGL-like  70 lvrarekdikaavealkgagakrvhv 95 
                                        v   + d ++ vea+ +ag+ +v v
  gi|488599880|ref|YP_007906351.1| 271 TVSTMDGDWAKPVEAIDVAGMGEVIV 296
                                       44455566677788888888888765 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.5   9.2e-08   0.00012      93     181 .]     106     193 ..      10     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.2e-08
                          TMP-TENI  93 lgpdliiGl.Svhslee.aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaev 167
                                        g++ ++ +  v ++ e a+e+e+lg+dYi + +i      ++  +  +e+lke+a+a++iPv   GG+++e+ a +
  gi|488599880|ref|YP_007906351.1| 106 YGSEIMVDMiNVTNPVErAKELEELGVDYINC-HI--GIDQQMMGMDPIELLKEIAKAVSIPVAGAGGLNAEKSALC 179
                                       555555543234444445************86.44..4555666777899*************************** PP

                          TMP-TENI 168 leagadgvavvsai 181
                                       + +ga+ v v s i
  gi|488599880|ref|YP_007906351.1| 180 ITKGAKIVIVGSNI 193
                                       ********998876 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.6   1.6e-07   0.00021      70     253 ..      18     205 ..      11     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHTTT.-SEEEEE--CCCC---C..CHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-H CS
                              IGPS  70 paeiAkkyeeagAsaiSVLteekyFqGsl..edLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvled 144
                                       + eiA++  e+gA+ i V t     +G +   +L++  +  ++ + +K       ++e a + gad+++ i+++ ++
  gi|488599880|ref|YP_007906351.1|  18 AIEIASEAIEGGADWIEVGTPLIKSEGMDavRELKKRYRDHKIVADMKTIDTGAIEVEMAAKSGADIVI-ILAASDN 93 
                                       5677777778888888887777777775311456666666667777777777788999********885.6777899 PP

                                       HHHHHHHHHHCCTT-EEEEEESS.HHHHHHHHHTT-SEEEEESEETT....TTEE-CHHHHHHCHCC-TT.SEEEEE CS
                              IGPS 145 eeleelaeaakslglevLvEvhd.eeeleralklgakiiGvNnRnLk....tlevdlntteeLaklvpkd.vllvae 215
                                       +++ee  +aa+++g e++v++ + ++ +era +l+   +Gv   n +    +  + ++   eL k++ k  ++ va 
  gi|488599880|ref|YP_007906351.1|  94 STIEEAIRAARKYGSEIMVDMINvTNPVERAKELEE--LGVDYINCHigidQQMMGMDP-IELLKEIAKAvSIPVAG 167
                                       99*****************987725679***99987..788877766222123333444.456666665658999*9 PP

                                       SSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                              IGPS 216 SGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                        G  ++e+   + ++g++ ++vG+ ++++ +v+++ r+
  gi|488599880|ref|YP_007906351.1| 168 AGGLNAEKSALCITKGAKIVIVGSNIVKSRNVTESARK 205
                                       9999999999999999***************9998876 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   4.2   2.7e-07   0.00034     100     232 ..      68     200 ..      33     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.7e-07
                               NMO 100 vrfyrkvevvldekvevvsfgfglpteevva.....rlkeagvv..liptissvkearkvearGaDalivqGpeaGG 169
                                       ++    ve+ ++ ++++v++ ++  +   ++     r+  ++++  +i ++  v+ a+++e++G D +         
  gi|488599880|ref|YP_007906351.1|  68 DTGAIEVEMAAKSGADIVIILAASDNSTIEEairaaRKYGSEIMvdMINVTNPVERAKELEELGVDYINC------- 137
                                       33344688888888888887777664443321111122223333114666778999********999855....... PP

                               NMO 170 hqG.tpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesd 232
                                       h+G + ++ + + ++L++++++av+iPv  aGG++ ++  a  ++ GA+ v +g+  +   + +
  gi|488599880|ref|YP_007906351.1| 138 HIGiDQQMMGMDPIELLKEIAKAVSIPVAGAGGLNAEKS-ALCITKGAKIVIVGSNIVKSRNVT 200
                                       566544444467799*******************98876.667899********9987665543 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.02        25      22      47 ..      14      39 ..       5      46 .. 0.86
   2 ?    0.2   0.1      0.22   2.8e+02     112     166 ..      52     106 ..      39     126 .. 0.75
   3 !   14.1   1.6   1.2e-05     0.016     145     246 ..     113     212 ..      74     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.02
                                      -HHHHHHHHHHHHHCT-SSEEEE--- CS
                         Trp_syntA 22 dleqsleilkalekagadviElGlpf 47
                                      +l++ +ei ++  ++gad iE+G p 
  gi|488599880|ref|YP_007906351.1| 14 ELKRAIEIASEAIEGGADWIEVGTPL 39
                                      678899999999***********995 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.22
                                       HHCTEEEEEETTSBCCCHHHH.HHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S- CS
                         Trp_syntA 112 keagvdglivpDlPleeaeel.veaakkkglelvflvapttsderlkevveqaegf 166
                                       k+   d  iv+D+ + +   + ve+a k g ++v ++a  +++++++e +++a+ +
  gi|488599880|ref|YP_007906351.1|  52 KKRYRDHKIVADMKTIDTGAIeVEMAAKSGADIVIILAA-SDNSTIEEAIRAARKY 106
                                       555556668888887777776356778888888888887.8888888888887765 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.2e-05
                                       EEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-S CS
                         Trp_syntA 145 flvapttsderlkevveqaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqvakvad 221
                                        ++  t + er ke+ e +  ++      G+   ++ + ++  el++++ k+   Pva   G+++++ +  ++k+a 
  gi|488599880|ref|YP_007906351.1| 113 DMINVTNPVERAKELEELGVDYI--NCHIGI--DQQMMGMDPIELLKEIAKAVSIPVAGAGGLNAEKSALCITKGAK 185
                                       45555555555566555544443..345555..345555666789*************999**************** PP

                                       EEEE-HHHHHH..HHCTTTSHHHHHHH CS
                         Trp_syntA 222 GvivGSalvkk..ieeeaeekeqalek 246
                                        vivGS +vk   + e+a++ ++a+++
  gi|488599880|ref|YP_007906351.1| 186 IVIVGSNIVKSrnVTESARKIRKAIDE 212
                                       *********852255566666665555 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.7   2.1e+03      75      88 ..      23      36 ..      17      38 .. 0.83
   2 !   17.6   1.1   1.3e-06    0.0017     129     233 ..     115     209 ..     108     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
                            DUF561 75 leavkaGadlveiG 88
                                       ea+  Gad +e+G
  gi|488599880|ref|YP_007906351.1| 23 SEAIEGGADWIEVG 36
                                      689999*******9 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.3e-06
                            DUF561 129 LkleeqvkLakkLeslgvdliqteGkitsiskakkvndliekslstlastyeiskkvslPvicasGlsdvtvplals 205
                                       +++ + v+ ak+Le+lgvd+i    +i +     +  d ie          ei+k+vs+Pv  a Gl+   + l ++
  gi|488599880|ref|YP_007906351.1| 115 INVTNPVERAKELEELGVDYINCHIGIDQQ---MMGMDPIE-------LLKEIAKAVSIPVAGAGGLNAEKSALCIT 181
                                       566777888899999999999876544333...33344444.......4568************************* PP

                            DUF561 206 lgasGiGigsavsklndeeemvallsei 233
                                        ga  + +gs++ k ++ +e    +++ 
  gi|488599880|ref|YP_007906351.1| 182 KGAKIVIVGSNIVKSRNVTESARKIRKA 209
                                       *************999988877766654 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.6   2.3e-06    0.0029     111     226 ..      98     212 ..      73     228 .. 0.83
   2 ?   -2.2   0.0       1.6   2.1e+03     193     214 ..     315     336 ..     311     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHHHTT-EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SH CS
                              ThiG 111 etlkaaeiLvkeGFevlpYvsdDlvlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigsp 187
                                       e ++aa+   +e  + +  v++ +  a+ lee+G+  +          +G+   e lk i + +++Pv   AG  ++
  gi|488599880|ref|YP_007906351.1|  98 EAIRAARKYGSEIMVDMINVTNPVERAKELEELGVDYINCHIGIDQQMMGMDPIELLKEIAKAVSIPVA-GAGGLNA 173
                                       56677777777777777888888999**********9987766666778999999999999999***86.5555578 PP

                                       HHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHH CS
                              ThiG 188 sdaaqamelGadavllntavaeakdpvamArafklavea 226
                                       ++ a  +  Ga+ v++ + + ++++  + Ar +++a++ 
  gi|488599880|ref|YP_007906351.1| 174 EKSALCITKGAKIVIVGSNIVKSRNVTESARKIRKAIDE 212
                                       889999******************************964 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                                       HHHTT-SEEEESHHHHTSSSHH CS
                              ThiG 193 amelGadavllntavaeakdpv 214
                                        ++ G+++v+++ av   +d+ 
  gi|488599880|ref|YP_007906351.1| 315 CLNKGIEGVIIDGAVRDVDDIR 336
                                       5788***********9998875 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         2   2.6e+03     155     175 ..      15      35 ..      12      73 .. 0.71
   2 !   14.1   0.1   1.9e-05     0.024     164     228 ..      76     146 ..      65     150 .. 0.78
   3 ?    1.6   0.2      0.12   1.6e+02      58     132 ..     151     212 ..     140     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
                        PEP_mutase 155 leeaieRaraYaeAGAdgvfv 175
                                       l++aie a    e GAd + v
  gi|488599880|ref|YP_007906351.1|  15 LKRAIEIASEAIEGGADWIEV 35 
                                       678899999999999998866 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.9e-05
                        PEP_mutase 164 aYaeAGAdgvfvpglqkdaeiaelvaavd......vplnvvplkgtlsvaelaelGvarislgnhllraal 228
                                       + a+ GAd v++  ++++++i+e ++a +      +  ++ ++++    +el+elGv  i ++  + ++++
  gi|488599880|ref|YP_007906351.1|  76 MAAKSGADIVIILAASDNSTIEEAIRAARkygseiMVDMINVTNPVERAKELEELGVDYINCHIGIDQQMM 146
                                       6789******************999999547765422222223445899***********99877666555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.12
                        PEP_mutase  58 laavraiaevvslPlivDledGygespeevaetvrrliaaGvvgvniEDkkkndaerqlldieefaekiaaaraa 132
                                       ++++++ia++vs+P+     +G g ++e+ a  +++ +++ +vg ni  + +        +++e a+ki++a ++
  gi|488599880|ref|YP_007906351.1| 151 IELLKEIAKAVSIPVAG---AG-GLNAEKSALCITKGAKIVIVGSNIVKS-R--------NVTESARKIRKAIDE 212
                                       57788888999999863...55.556888888888888888888888777.2........344444444444443 PP

>> DUF2855  Protein of unknown function (DUF2855)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   9.4e-06     0.012     139     305 ..      77     250 ..      50     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.4e-06
                           DUF2855 139 adlsgakvvvllsASsKTAlslayllrkrrkaeegplklvglTSaknr..........afveslglydkvvsYddle 205
                                       a  sga++v++l+AS    +  a  ++++  + e  + ++++T   +r              ++g+ ++++  d +e
  gi|488599880|ref|YP_007906351.1|  77 AAKSGADIVIILAASDNSTIEEAIRAARKYGS-EIMVDMINVTNPVERakeleelgvdYINCHIGIDQQMMGMDPIE 152
                                       44589****************99998888876.677***********998888888875566788888888999999 PP

                           DUF2855 206 sleaakkvvivDfagrdelleklhealkdkgklvlsvavGsthkvksseelqeakaaaaala.kpvqffapevidkr 281
                                        l++ +k+v + +ag ++l+++  +   +  k  ++v vGs+   ks + +++a++ ++a++ + +    ++v +k 
  gi|488599880|ref|YP_007906351.1| 153 LLKEIAKAVSIPVAGAGGLNAEKSALCIT--KGAKIVIVGSNIV-KSRNVTESARKIRKAIDeAWEKGSVSGVKKKS 226
                                       99999*****************9999999..8999999**9996.67777777777777777545666777777777 PP

                           DUF2855 282 ieelgaeeyferlaaawkrfleea 305
                                        +e+ +e +++ ++ ++++ +++a
  gi|488599880|ref|YP_007906351.1| 227 LDEEIRELFMKVSTPNISDAMHRA 250
                                       777777666666666666666544 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 ?   11.3   2.4   0.00014      0.18      48     152 ..      74     214 ..      46     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       HHHHHHTT-S.EEEE--SSHHHHHHHHHHHHHTT-EEEE........ESTTGCTTT-CEE............EEEC- CS
                      Peripla_BP_4  48 iedaiakgvd.giivapvdstalapalkkakaaGIpVva........fdsddapsgerla............yvgfd 103
                                       +e a ++g+d +ii+a+ d +++++a+ +a++ G  +++        + ++                     ++g+d
  gi|488599880|ref|YP_007906351.1|  74 VEMAAKSGADiVIILAASDNSTIEEAIRAARKYGSEIMVdminvtnpVERA--------KeleelgvdyincHIGID 142
                                       56778899**9999*********************8666665554444444........344444455566688899 PP

                                       HHHHHHHHHHHHHHHCTTH......................EEEEEE.TSCCCHHHHHHHHHHHHHHHHH.- CS
                      Peripla_BP_4 104 neaaGelqaeylaeklggk.....................kgkvvil.aGspgdpnaeeriegfrkvlke.y 152
                                       ++ +G    e+l+e  ++                       +k+vi+ +    ++n +e +  +rk+++e +
  gi|488599880|ref|YP_007906351.1| 143 QQMMGMDPIELLKEIAKAVsipvagagglnaeksalcitkGAKIVIVgSNIVKSRNVTESARKIRKAIDEaW 214
                                       999888888888888887755555555555555555555556777774444446666666666666666653 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5    0.0001      0.13      63     253 ..      66     248 ..      40     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                       SSHHHHHHHHHHHHHT-EEEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTS CS
                              PALP  63 sGNhgralAaaaallGlkvtivvpadas...pekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdn 136
                                       + ++g+    +aa+ G + +i + a+++   +e +++ r +G e+++   ++++ v++a+el++ g ++++++ + +
  gi|488599880|ref|YP_007906351.1|  66 TIDTGAIEVEMAAKSGADIVIILAASDNstiEEAIRAARKYGSEIMVDMINVTNPVERAKELEELGVDYINCHIGID 142
                                       5578888889************9999996556***************999***************999999998855 PP

                                       HHHHHH.HHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHH.HSTT-EEEEEEECTTCGGTTCCS..S.SS.. CS
                              PALP 137 ptvieg.ygtiglEileqlggkpdavvvpvGgGgliaGiaaglke.rrpdvrvigvepegsdalarslragrrvtvp 211
                                          +            e l++  +av  pv g+g + +   +l   ++ ++ ++g + + s  +++s+r+ r     
  gi|488599880|ref|YP_007906351.1| 143 QQMMGMdPI-------ELLKEIAKAVSIPVAGAGGLNAEKSALCItKGAKIVIVGSNIVKSRNVTESARKIR----- 207
                                       444443333.......44444456788888888777777666665355556666666668888888882222..... PP

                                       B.SSS.CCSTCSCGTTCCHHHHSEEEE.EEEEEEHHHHHHHHH CS
                              PALP 212 vsdtiadglavgspselafelldrlvd.eivtvsdeealeamr 253
                                         + i ++ + gs+s    + ld+ +   ++ vs+  + +am 
  gi|488599880|ref|YP_007906351.1| 208 --KAIDEAWEKGSVSGVKKKSLDEEIReLFMKVSTPNISDAMH 248
                                       ..22223333332222222222222221444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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):              14  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2521.63
//
Query:       gi|488599881|ref|YP_007906352.1|  [L=480]
Description: cysteinyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-129  429.6   0.8     1e-128  428.9   0.3    1.5  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
      1e-16   60.7   1.6    4.6e-09   35.5   0.1    2.2  2  tRNA-synt_1g    tRNA synthetases class I (M)
      3e-12   45.6   0.0    1.5e-10   40.0   0.0    2.2  2  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    3.2e-12   46.8   0.0    8.8e-12   45.3   0.0    1.8  1  DALR_2          DALR domain
    1.8e-08   33.7   1.2    6.5e-06   25.3   0.2    2.5  2  tRNA-synt_1f    tRNA synthetases class I (K)
      0.007   15.8   0.4      0.032   13.7   0.2    2.1  2  BAR_3_WASP_bdg  WASP-binding domain of Sorting nexin protein
  ------ inclusion threshold ------
      0.016   15.2   0.2       0.05   13.6   0.2    1.8  1  IL15            Interleukin 15
      0.053   13.7   1.8        1.3    9.3   0.0    2.7  2  SRP54_N         SRP54-type protein, helical bundle domain
       0.17   12.1   2.0        2.1    8.6   0.1    3.3  3  YozE_SAM_like   YozE SAM-like fold
        0.2   10.9   4.4         14    4.9   0.1    3.1  3  HEPN_LA2681     LA2681-like HEPN
       0.37   10.7   1.5        7.4    6.5   0.0    2.9  3  eIF-5_eIF-2B    Domain found in IF2B/IF5
        1.6    9.4   5.5       0.81   10.3   0.2    3.1  4  DUF643          Protein of unknown function (DUF643)


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.9   0.3  6.9e-132    1e-128       8     300 ..      20     317 ..      14     318 .. 0.97
   2 ?   -2.6   0.0       1.8   2.6e+03     102     118 ..     383     399 ..     348     445 .. 0.49

  Alignments for each domain:
  == domain 1  score: 428.9 bits;  conditional E-value: 6.9e-132
                                       TEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHH CS
                      tRNA-synt_1e   8 kkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefk 84 
                                       ++v++YvCG+t+yd+sh+GhaRs+v+fD lrr+l +lg  v +vqn+tD+dDkii+ra++e+k++ke+ae+fiee+ 
  gi|488599881|ref|YP_007906352.1|  20 DTVKIYVCGITAYDYSHIGHARSAVVFDTLRRYLMYLGKRVVYVQNFTDVDDKIIRRAVSEGKTQKEIAERFIEEYL 96 
                                       579************************************************************************** PP

                                       HHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TT..S-EEE-GGG-TTTTTTTT--HHHHHHT----S- CS
                      tRNA-synt_1e  85 kdleaLnvlkptleprvsekvdeiielvekliekgyaYavsd..gdvyfdvskkeeYgklskqnleelelgaegevs 159
                                       kd+++Lnv +++++p+v+e++++ii  v+k+iekgyaY+v d   dvyf+v +++eYgkls  +leel++++ +   
  gi|488599881|ref|YP_007906352.1|  97 KDMAELNVIPADYHPKVTENIPDIIAAVKKIIEKGYAYEVGDnnKDVYFHVPSFSEYGKLSGMSLEELNKHRIEPD- 172
                                       ***************************************9987789************************999877. PP

                                       -S-SSTT-EEEEEE--TTS....--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHH CS
                      tRNA-synt_1e 160 eekkdkkDfaLWkaskege....pswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaa 232
                                        +kkd kDfaLWka+ke++      +dsPwgkGRPGWhieCsv+a+k+lg  +dih+GG+DL+fPhhene aqs a+
  gi|488599881|ref|YP_007906352.1| 173 PRKKDVKDFALWKAAKEEDikaeSVFDSPWGKGRPGWHIECSVLATKFLGAPFDIHGGGKDLIFPHHENERAQSYAL 249
                                       79**************998555477**************************************************** PP

                                       SSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 233 fdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                       fd + v+y++hn++++i+gekmsksL+n+i+i+dv++k+ +++lR++llsahyrs ld++e+++e+a 
  gi|488599881|ref|YP_007906352.1| 250 FDVEPVRYWIHNDFVTINGEKMSKSLGNIIKIRDVIEKYGGEVLRYFLLSAHYRSSLDYSEKAMERAS 317
                                       ****************************************************************9985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                                       GGGHHHHHHHHHHHHHT CS
                      tRNA-synt_1e 102 sekvdeiielvekliek 118
                                       s ++++++   + +   
  gi|488599881|ref|YP_007906352.1| 383 STYINNLVTRCQSIDTL 399
                                       44444444443333333 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 !   24.4   0.2   7.5e-09   1.1e-05      13     115 ..      34     135 ..      26     145 .. 0.87
   2 !   35.5   0.1   3.1e-12   4.6e-09     312     385 ..     255     329 ..     231     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 7.5e-09
                                       ---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEE CS
                      tRNA-synt_1g  13 klHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkyg 89 
                                         H+Gh+++++  D + Ry    g+ v++v        +i  +A +eg t +e++e++ ee+ +++++ln+   +y+
  gi|488599881|ref|YP_007906352.1|  34 YSHIGHARSAVVFDTLRRYLMYLGKRVVYVQNFTDVDDKIIRRAVSEGKTQKEIAERFIEEYLKDMAELNVIPADYH 110
                                       57*****************************9999999********************************9999888 PP

                                       ETTSHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1g  90 rttseehkelvqeifkklkekgliye 115
                                          +e+  ++ ++ +kk+ ekg+ ye
  gi|488599881|ref|YP_007906352.1| 111 PKVTENIPDIIAA-VKKIIEKGYAYE 135
                                       7766666666554.466666777665 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 3.1e-12
                                       -S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHH.HS-TTS-EEE-HHHHHHHHHHHCCCHHHH CS
                      tRNA-synt_1g 312 pkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaa.eapekkDldfswedfvervNseLadklgn 385
                                       ++  + ++++t++g+K+SkS g+++k+++++e++  ++lRY+l++ +   + D + +  +   +  + L ++l n
  gi|488599881|ref|YP_007906352.1| 255 VRYWIHNDFVTINGEKMSKSLGNIIKIRDVIEKYGGEVLRYFLLSaHYRSSLDYSEKAMERASKSYESLKNALEN 329
                                       55566789***********************************99344444444444444445555666666666 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.011        16      37      67 ..      34      64 ..       5     104 .. 0.80
   2 !   40.0   0.0   9.9e-14   1.5e-10     514     598 ..     222     305 ..     151     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                       tRNA-synt_1 37 slHiGhalaktlkdivirykrmkGkevlyvp 67
                                        HiGha   ++ d++ ry    Gk+v yv 
  gi|488599881|ref|YP_007906352.1| 34 YSHIGHARSAVVFDTLRRYLMYLGKRVVYVQ 64
                                      57************************99975 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 9.9e-14
                       tRNA-synt_1 514 ffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltl 590
                                         p+d+   G D i+   ++   +s al++ eP +  + + +v+  +G KmSKslgN+i+  dvi+kyg ++lR++l
  gi|488599881|ref|YP_007906352.1| 222 GAPFDIHGGGKDLIFPHHENERAQSYALFDVEPVRYWIHNDFVT-INGEKMSKSLGNIIKIRDVIEKYGGEVLRYFL 297
                                       469999999*********************************98.58****************************** PP

                       tRNA-synt_1 591 ilsdvgrd 598
                                       +++++ + 
  gi|488599881|ref|YP_007906352.1| 298 LSAHYRSS 305
                                       *9988765 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   5.9e-15   8.8e-12       1      57 [.     361     418 ..     361     429 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5.9e-15
                                       HHHHHHTBT--HHHHHHHHHHHHHHHHH.HHHTT-HHHHHHHHHHHHHHHGGGT-S-S CS
                            DALR_2   1 kFeeaMdDDFNTaeAiavlFelakeiNr.alkeedkaaasalkallrelaevLGllqe 57 
                                       +F+eaMdDD+NT++ +a l+e +  iN    + +++++++++ ++++ + +vLGl+++
  gi|488599881|ref|YP_007906352.1| 361 RFREAMDDDLNTPKVLAILHEFSTYINNlVTRCQSIDTLETAFETFKRVCGVLGLFEK 418
                                       7***************************766777999999999*************97 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0025       3.7      23      90 ..      21      96 ..       5     124 .. 0.71
   2 !   25.3   0.2   4.3e-09   6.5e-06     272     340 ..     262     328 ..     226     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0025
                      tRNA-synt_1f 23 devvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDg..lRk.vpe.....nlpekllekyl 90
                                         +   Gi++    HiG +r  +  d ++r l  +g++v  +    d+D   +R+ v e     ++ e+ +e+yl
  gi|488599881|ref|YP_007906352.1| 21 TVKIYVCGITAYDYSHIGHARSAVVFDTLRRYLMYLGKRVVYVQNFTDVDDkiIRRaVSEgktqkEIAERFIEEYL 96
                                      3445568999999**************************9999988888853334314444333344444444444 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 4.3e-09
                      tRNA-synt_1f 272 elillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                                       ++++++g+ kms+S Gn++ ++d++e +  evlr+++l+++ +++++ + +  + r+   Y++l++++ 
  gi|488599881|ref|YP_007906352.1| 262 DFVTINGE-KMSKSLGNIIKIRDVIEKYGGEVLRYFLLSAHYRSSLDYSEK-AMERASKSYESLKNALE 328
                                       56666666.******************************999999999999.9**********999885 PP

>> BAR_3_WASP_bdg  WASP-binding domain of Sorting nexin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.71   1.1e+03     174     225 ..      12      67 ..       5      77 .. 0.71
   2 !   13.7   0.2   2.1e-05     0.032     104     159 ..      75     130 ..      57     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.71
                    BAR_3_WASP_bdg 174 seekeklkkrvsvisyalla....einhfhserieDfksvmqlyLkqqvkfyqkia 225
                                       +ee+ kl++ v++  + + a     i h  s  + D  +   +yL ++v + q+ +
  gi|488599881|ref|YP_007906352.1|  12 QEEELKLSDTVKIYVCGITAydysHIGHARSAVVFDTLRRYLMYLGKRVVYVQNFT 67 
                                       55666777888877777766433357777777888888888889999998888766 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.1e-05
                    BAR_3_WASP_bdg 104 nealaatgktYeeigevfaeqpkkDleflletleeYkGll.anfPDiigvhkgalek 159
                                        +a++  gkt +ei+e f e+  kD+  l  + + Y+  + +n+PDii + k+ +ek
  gi|488599881|ref|YP_007906352.1|  75 RRAVS-EGKTQKEIAERFIEEYLKDMAELNVIPADYHPKVtENIPDIIAAVKKIIEK 130
                                       44554.599***************************9877369*********99998 PP

>> IL15  Interleukin 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.3e-05      0.05      71     126 ..     310     362 ..     291     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                              IL15  71 eeeiekeeeikeevenliknanknlkslkdeskteseCkeCEeleeknfkeFlqsl 126
                                       e+ +e+ ++ +e+++n+++n +++++    +++ es  k C + eek+++eF   +
  gi|488599881|ref|YP_007906352.1| 310 EKAMERASKSYESLKNALENLDMEISA---LKTFESYSKNCGAEEEKEIREFEIRF 362
                                       667788888899999999999999998...6677888899999999*****97666 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 ?    9.3   0.0   0.00085       1.3       5      57 ..      74     125 ..      72     140 .. 0.80
   2 ?    2.6   0.5      0.11   1.6e+02      45      73 ..     426     456 ..     422     457 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00085
                                       HHHHHHHHCCSSCGHHHHHHHHHHHHHH.HHHHTT--HHHHHHHHHHHHHHHHC CS
                           SRP54_N   5 lnsalkklsgkskideedleealkelee.aLleaDVgvkvvkklienvkkkavg 57 
                                       +++a++  +++++i e ++ee lk++ e   + aD   kv++++ + +   av+
  gi|488599881|ref|YP_007906352.1|  74 IRRAVSEGKTQKEIAERFIEEYLKDMAElNVIPADYHPKVTENIPDII-A-AVK 125
                                       678888889999*************96526999999999999876655.2.444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHCTTS..S-HHHHHHHHHHH CS
                           SRP54_N  45 kklienvkkkavgekk..lkpkqqvkkivkd 73 
                                       k++++ +++++  +k+   ++++++++++k+
  gi|488599881|ref|YP_007906352.1| 426 KEFVDLIREREQARKEknFRRADEIRDLLKE 456
                                       78999999887665554577*******9997 PP

>> YozE_SAM_like  YozE SAM-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.43   6.4e+02      39      61 ..     291     313 ..     286     322 .. 0.85
   2 ?   -1.2   0.0       1.6   2.4e+03      33      59 ..     316     342 ..     315     345 .. 0.86
   3 ?    8.6   0.1    0.0014       2.1      20      65 ..     362     407 ..     350     408 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.43
                                       HHHHHHHTSHHHHTTHHHHHHHH CS
                     YozE_SAM_like  39 eisdYLelnaeylssmeifdeaw 61 
                                       e+++Y+ l+a+y+ss++  ++a 
  gi|488599881|ref|YP_007906352.1| 291 EVLRYFLLSAHYRSSLDYSEKAM 313
                                       899************99877765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                       T---HHHHHHHHHTSHHHHTTHHHHHH CS
                     YozE_SAM_like  33 qstdydeisdYLelnaeylssmeifde 59 
                                        s++y+++ + Le+   + s++++f++
  gi|488599881|ref|YP_007906352.1| 316 ASKSYESLKNALENLDMEISALKTFES 342
                                       689999999999999999999999975 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0014
                                       HHHHHHT-TTS-TT---HHHHHHHHHTSHHHHTTHHHHHHHHHHHH CS
                     YozE_SAM_like  20 lAenafkDksFPkqstdydeisdYLelnaeylssmeifdeaweeYl 65 
                                       + e + +D + Pk     +e s+Y+++  +  +s+++++ a+e ++
  gi|488599881|ref|YP_007906352.1| 362 FREAMDDDLNTPKVLAILHEFSTYINNLVTRCQSIDTLETAFETFK 407
                                       66789999999*******************************9987 PP

>> HEPN_LA2681  LA2681-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.011        16     126     194 ..     257     324 ..     256     330 .. 0.74
   2 ?    3.1   0.5     0.034        51     122     186 ..     298     359 ..     295     367 .. 0.80
   3 ?    4.9   0.1    0.0092        14     133     164 ..     429     464 ..     416     477 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                       HEPN_LA2681 126 ywlskDlvelkekliepeakelkeiRnaleHrylkiteegaskesessdelaytisreeleektlkllk 194
                                       yw+++D+v+++ + +++   ++ +iR+ +e  + ++  +   + +   ++l+y+ +  e  +k+++ lk
  gi|488599881|ref|YP_007906352.1| 257 YWIHNDFVTINGEKMSKSLGNIIKIRDVIEKYGGEVLRYFLLSAHY-RSSLDYSEKAMERASKSYESLK 324
                                       9*****9998888999999***********9999998877765553.3555555555555555555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.034
                       HEPN_LA2681 122 LrgLywlskDlvelkekliepeakelkeiRnaleHrylkiteegaskesessdelaytisreele 186
                                       L++ y+ s D   ++ek++e  +k ++++ nale   ++i   +  ++ +++   +++ +++e+e
  gi|488599881|ref|YP_007906352.1| 298 LSAHYRSSLD---YSEKAMERASKSYESLKNALENLDMEISALKTFESYSKNCGAEEEKEIREFE 359
                                       6667888888...8889******************999999988888877776666555555555 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0092
                       HEPN_LA2681 133 ve....lkekliepeakelkeiRnaleHrylkitee 164
                                       v+     +++ +e+++++ +eiR+ l  r+++++++
  gi|488599881|ref|YP_007906352.1| 429 VDlireREQARKEKNFRRADEIRDLLKERGIHLIDT 464
                                       4442234555999*******************9985 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.18   2.6e+02      47      88 ..      54      96 ..      46      98 .. 0.65
   2 ?    6.5   0.0    0.0049       7.4      10      82 ..     256     329 ..     251     330 .. 0.89
   3 ?   -1.1   0.1       1.1   1.7e+03      80     102 ..     382     405 ..     371     412 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.18
                                      HHHHHHHTSEEEESETTEEEESSSSSCCHHHHHH.HHHHHHHT CS
                      eIF-5_eIF-2B 47 kyllkelgtqgsidengrlilngkfeakklekll.dkyieeyV 88
                                       yl+k +   +++ + +  i++ ++++ k +k + +++ieey+
  gi|488599881|ref|YP_007906352.1| 54 MYLGKRVVYVQNFTDVDDKIIRRAVSEGKTQKEIaERFIEEYL 96
                                      5666666666666666666777777766666555267888885 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0049
                                       --SSTT--EEEETT..EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHH CS
                      eIF-5_eIF-2B  10 rykmpklqvkvegkk.ktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldk 82 
                                       ry + +  v+++g+k    + N+ +i + +++    vl+y+l     ++s+d +++++ + + + ++l+++l++
  gi|488599881|ref|YP_007906352.1| 256 RYWIHNDFVTINGEKmSKSLGNIIKIRDVIEKYGGEVLRYFLLSAHYRSSLDYSEKAMERASKSYESLKNALEN 329
                                       666667778888998888999*******************************9999999999999999999875 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHTS.TSSSTSTCEEECC CS
                      eIF-5_eIF-2B  80 ldkyieeyVl.CkeCkspetelek 102
                                       +++yi++ V+ C++ +  et +e+
  gi|488599881|ref|YP_007906352.1| 382 FSTYINNLVTrCQSIDTLETAFET 405
                                       567888888546666666666655 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.1   3.1e+03      43      74 ..      49      79 ..      41     101 .. 0.55
   2 ?   10.3   0.2   0.00054      0.81      13      72 ..     122     181 ..     112     194 .. 0.82
   3 ?   -3.3   0.0         9   1.4e+04      67      82 ..     273     288 ..     259     295 .. 0.64
   4 ?   -0.9   0.0       1.7   2.5e+03      17      61 ..     314     358 ..     297     385 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                            DUF643 43 iqeykiktGksveeiindiiepekefikdvlk 74
                                      +++y +  Gk v   ++++ + + ++i+  + 
  gi|488599881|ref|YP_007906352.1| 49 LRRYLMYLGKRV-VYVQNFTDVDDKIIRRAVS 79
                                      555666666666.4555566666666654443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00054
                            DUF643  13 kdtkkeinklyeteqltleqkkqlysavkkiqeykiktGksveeiindiiep..ekefikdv 72 
                                         +kk i+k y  e    ++ k++y  v +  ey++ +G s+ee+ ++ iep   k+ +kd 
  gi|488599881|ref|YP_007906352.1| 122 AAVKKIIEKGYAYE--VGDNNKDVYFHVPSFSEYGKLSGMSLEELNKHRIEPdpRKKDVKDF 181
                                       56899999999876..456789***********************99999752268888885 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9
                            DUF643  67 efikdvlkdknlikky 82 
                                       + + +++k + +i+ky
  gi|488599881|ref|YP_007906352.1| 273 KSLGNIIKIRDVIEKY 288
                                       3344566667777776 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.7
                            DUF643  17 keinklyeteqltleqkkqlysavkkiqeykiktGksveeiindi 61 
                                          +k ye  + +le+     sa+k+ + y++  G   e+ i ++
  gi|488599881|ref|YP_007906352.1| 314 ERASKSYESLKNALENLDMEISALKTFESYSKNCGAEEEKEIREF 358
                                       446778888888888777777888888888888887777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      813  (0.0453455); 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):              12  [number of targets reported over threshold]
# CPU time: 0.77u 0.34s 00:00:01.11 Elapsed: 00:00:00.54
# Mc/sec: 2655.33
//
Query:       gi|488599882|ref|YP_007906353.1|  [L=274]
Description: putative archaeal kinase (sugar kinase superfamily) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   33.3   0.0    1.3e-07   31.7   0.0    1.8  2  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 !   31.7   0.0   7.4e-12   1.3e-07       2      66 .]      73     137 ..      72     137 .. 0.88
   2 ?   -2.2   0.0      0.28     5e+03       3      14 ..     206     217 ..     191     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 7.4e-12
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee..aklaleaerlaqggngsggDvaasvyGg 66 
                                       ++++s iPvg+G+G S+A+++a++  +++     l++  ++l+   +++ +  +++ gDv +  yGg
  gi|488599882|ref|YP_007906353.1|  73 LKLESQIPVGCGFGFSGAACLAAAFEINKKMK--LKKgyFELTDIVHECEVESRTGLGDVVCQSYGG 137
                                       6799*******************999999774..544569999999977777**************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.28
                                       EEEESSHTTSSS CS
                    GHMP_kinases_N   3 vikseiPvgaGL 14 
                                       +i++e+ v++GL
  gi|488599882|ref|YP_007906353.1| 206 RISKEFAVKTGL 217
                                       455666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1705.39
//
Query:       gi|488599883|ref|YP_007906354.1|  [L=400]
Description: Phosphopantothenate-cysteine ligase /Phosphopantothenoylcysteine decarboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.1    3.2e-47  160.8   0.0    2.2  2  DFP           DNA / pantothenate metabolism flavoprotein
    3.5e-38  130.8   1.1    2.6e-37  128.0   0.6    2.4  3  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
      0.022   14.3   0.5       0.11   12.0   0.0    2.3  3  DUF166        Domain of unknown function
      0.084   12.0   0.0       0.83    8.7   0.0    2.1  2  NAD_synthase  NAD synthase


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 !    5.4   0.1    0.0033        15      33      55 ..      33      55 ..      30     101 .. 0.80
   2 !  160.8   0.0   7.1e-51   3.2e-47       2     186 .]     192     372 ..     191     372 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0033
                                      HHHHHHHHHTT-EEEEEE-S-SS CS
                               DFP 33 yalAeaaaarGaeVtlvsgpvsl 55
                                      ++lA+++++rGaeV  v ++++ 
  gi|488599883|ref|YP_007906354.1| 33 VKLARELIRRGAEVIAVMSESAR 55
                                      689**************998543 PP

  == domain 2  score: 160.8 bits;  conditional E-value: 7.1e-51
                                       TT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-.SS---TT-EEEE--SHHHHHHHHH CS
                               DFP   2 egkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpv.sletpegvevvkvesaeemleave 77 
                                       +g+kv+vt+GpT E+iDp+RfisNrSSG mGy++A ++++rGae+++++++   l+ p  +e + v s+eemle+  
  gi|488599883|ref|YP_007906354.1| 192 SGRKVVVTSGPTFEQIDPIRFISNRSSGMMGYEIALELWRRGAEIKIITSKPrGLSLP-DFEEIFVWSVEEMLEKSL 267
                                       799*********************************************9995377777.8999************** PP

                                       HHHTT-SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HHH CS
                               DFP  78 ealkeadivimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....elle 150
                                       e ++++d++++aAA aD++++  ae+Kik    +eel l+l+  p+il++++e  +    ++GF+aet     +l +
  gi|488599883|ref|YP_007906354.1| 268 EYVRDCDLFVSAAAAADFTIE-MAESKIKT---QEELVLHLKAAPKILHKVREIYDG--EVIGFKAETGvgedRLYN 338
                                       ********************8.5899**96...568***************665544..59******955788999* PP

                                       HHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                               DFP 151 nareklerkgldlivaNdvskeeagfgsdenevtll 186
                                        a ek+ +++l ++vaNdv ++  g+g+++++v+++
  gi|488599883|ref|YP_007906354.1| 339 IAYEKMLDDRLSMVVANDVISK--GMGTADTKVLVI 372
                                       ********************76..9****9999875 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.6   5.9e-41   2.6e-37       1     155 [.      17     183 ..      17     186 .. 0.93
   2 ?   -0.7   0.0      0.23     1e+03      17      36 ..     223     242 ..     217     243 .. 0.84
   3 ?   -1.1   0.0      0.31   1.4e+03      25      61 ..     268     306 ..     256     346 .. 0.74

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 5.9e-41
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadl 67 
                                       k+i+lg+TGs+aa+++++l ++L+++g+ev  v++++A+k+i++  l++a+       ++++++h+el   +  adl
  gi|488599883|ref|YP_007906354.1|  17 KRIVLGVTGSIAAVETVKLARELIRRGAEVIAVMSESARKIIHPYALEFATdnrviteITGKVEHVELlgeNGIADL 93 
                                       79*****************************************9999998899***************998889*** PP

                                       EEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT.............. CS
                      Flavoprotein  68 lviaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigk 141
                                       l+iaPa+ant++kianGi d+++t+++    ++ k i+iaPam+ +m +n+++ +n+e l + gv +++P   d+ k
  gi|488599883|ref|YP_007906354.1|  94 LLIAPATANTVSKIANGIDDTPVTTMATTalGSGKHIIIAPAMHESMIKNEAVRRNIEYLkNLGVDFVEPR-YDEYK 169
                                       ***********************999944489****************************77*********.88888 PP

                                       ..GHHHHHHHHHHC CS
                      Flavoprotein 142 gkmaeieeivgkil 155
                                       +k+a+ie+i   + 
  gi|488599883|ref|YP_007906354.1| 170 AKFADIETICLHVE 183
                                       99999999976665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.23
                                       HHHHHHHHHTTEEEEEEESC CS
                      Flavoprotein  17 lellekLkkegievqvvltk 36 
                                        e+  +L+++g+e++++ +k
  gi|488599883|ref|YP_007906354.1| 223 YEIALELWRRGAEIKIITSK 242
                                       578889***********997 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.31
                                       H..TTEEEEEEESCHHHHCCHHGGS....TCSSHHHHHH CS
                      Flavoprotein  25 k..egievqvvltkaAkkfiskeklklaaredpilhiel 61 
                                       +  +++++ v + +aA  +i+  ++k++++e+ +lh + 
  gi|488599883|ref|YP_007906354.1| 268 EyvRDCDLFVSAAAAADFTIEMAESKIKTQEELVLHLKA 306
                                       345567777777777777777777777777777777654 PP

>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   5.9e+03      77     103 ..     126     152 ..     117     163 .. 0.65
   2 ?   12.0   0.0   2.6e-05      0.11      39      98 ..     254     315 ..     217     328 .. 0.80
   3 ?   -0.9   0.1      0.23     1e+03      74     104 ..     362     394 ..     354     398 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                            DUF166  77 kkvkalivpaeapkaglrkelkeklee 103
                                       ++ +++i pa ++++  ++ +++++e 
  gi|488599883|ref|YP_007906354.1| 126 SGKHIIIAPAMHESMIKNEAVRRNIEY 152
                                       677788888888886666666666654 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.6e-05
                            DUF166  39 efiedpeelLpe....lkeaDiviaytlhpDlllelaekakekkvkalivpaeapkaglrkelk 98 
                                        f+  +ee+L++    ++++D++++  +  D ++e+ae   +++ ++++  + apk  + ++++
  gi|488599883|ref|YP_007906354.1| 254 IFVWSVEEMLEKsleyVRDCDLFVSAAAAADFTIEMAESKIKTQEELVLHLKAAPK--ILHKVR 315
                                       4666677888877777*********************9877788888888888787..444554 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.23
                            DUF166  74 akekkvkalivpaeapk..aglrkelkekleel 104
                                       +  ++ k+l++ +++++  +gl++e+ ek+ ++
  gi|488599883|ref|YP_007906354.1| 362 MGTADTKVLVITKKRKEwyEGLKSEVAEKIVKA 394
                                       566788999999999998888888888887664 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.054   2.4e+02      15      50 ..      13      49 ..       6      82 .. 0.77
   2 ?    8.7   0.0   0.00019      0.83      21      83 ..     103     167 ..      87     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.054
                                      HCTTSEEEEEE-SSHHHHHHHHHHHHHHTC.GEEEEE CS
                      NAD_synthase 15 kagakgvvlGlSGGvDSslvaalavkalgk.envlal 50
                                      k + k +vlG+ G +    + +la++++ + ++v+a+
  gi|488599883|ref|YP_007906354.1| 13 KLEGKRIVLGVTGSIAAVETVKLARELIRRgAEVIAV 49
                                      556689*********999999***9999441345554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00019
                                       EEEEE-SSHHHHHHHHHHHHHHTCGEEE..EEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                      NAD_synthase  21 vvlGlSGGvDSslvaalavkalgkenvl..alllPssvsseedvedalalaenlgievktidikp 83 
                                        v  +  G+D + v ++a +alg+ +++  a  + +s+ ++e v+  ++  +nlg+++ +   ++
  gi|488599883|ref|YP_007906354.1| 103 TVSKIANGIDDTPVTTMATTALGSGKHIiiAPAMHESMIKNEAVRRNIEYLKNLGVDFVEPRYDE 167
                                       5666889***************7777651155688899999999**********99887655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.36s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 2132.84
//
Query:       gi|488599884|ref|YP_007906355.1|  [L=438]
Description: formylmethanofuran dehydrogenase, subunit F [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-44  146.8  76.6    3.9e-08   32.8   2.6    8.3  8  Fer4       4Fe-4S binding domain
    9.2e-32  109.4  56.8    4.4e-09   36.8   8.5    4.9  5  Fer4_7     4Fe-4S dicluster domain
    1.6e-25   88.1  78.2    1.5e-05   24.8   2.3    8.3  8  Fer4_6     4Fe-4S binding domain
    1.7e-25   88.9  51.7    2.3e-05   24.4  10.1    6.5  6  Fer4_10    4Fe-4S dicluster domain
    6.3e-25   87.1  54.1      4e-07   30.1   5.9    5.5  6  Fer4_9     4Fe-4S dicluster domain
    5.3e-24   82.8  67.1    5.8e-05   23.0   1.4    8.3  8  Fer4_2     4Fe-4S binding domain
    1.6e-21   76.2  57.0      2e-05   24.6   8.6    5.8  5  Fer4_21    4Fe-4S dicluster domain
      2e-20   73.5  62.1    0.00018   22.4  11.5    7.8  7  Fer4_16    4Fe-4S double cluster binding domain
    5.8e-10   39.5  60.5      0.032   14.7   0.2    7.3  7  Fer4_8     4Fe-4S dicluster domain
    4.4e-09   36.1  80.6     0.0036   17.7   3.5    8.3  8  Fer4_4     4Fe-4S binding domain
    7.2e-08   32.9  66.7      0.057   14.0   0.1    7.6  6  Fer4_17    4Fe-4S dicluster domain
    5.5e-05   23.8  88.7      0.049   14.6   3.0    8.3  8  Fer4_3     4Fe-4S binding domain
  ------ inclusion threshold ------
      0.066   13.2   3.5       0.19   11.7   3.4    1.8  1  Flu_C_NS1  Influenza C non-structural protein (NS1)
      0.091   13.5   0.7      0.091   13.5   0.7    8.3  6  Fer4_15    4Fe-4S single cluster domain
        0.1   13.2  66.6       0.62   10.6   2.6    8.1  8  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 !   32.8   2.6   3.3e-11   3.9e-08       4      24 .]      30      50 ..      27      50 .. 0.91
   2 !   21.7   5.1     1e-07   0.00012       1      23 [.      66      88 ..      66      89 .. 0.93
   3 !   24.3   1.0   1.6e-08   1.9e-05       4      24 .]     113     133 ..     110     133 .. 0.92
   4 !   19.8   5.1   4.1e-07   0.00048       1      19 [.     154     172 ..     154     173 .. 0.92
   5 !   31.3   3.4   9.6e-11   1.1e-07       2      24 .]     193     215 ..     192     215 .. 0.94
   6 !   25.4   1.9     7e-09   8.4e-06       1      22 [.     232     253 ..     232     255 .. 0.94
   7 !    6.7   1.5    0.0056       6.7       9      21 ..     277     289 ..     277     289 .. 0.89
   8 !   27.2   2.7   1.9e-09   2.3e-06       1      23 [.     301     323 ..     301     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.3e-11
                                      ETTTSSS-THHHHHSTTTEEE CS
                              Fer4  4 deekCigCGaCvevCPvgAIt 24
                                      ++ kC gCG+Cv +CPv+AI+
  gi|488599884|ref|YP_007906355.1| 30 HYKKCNGCGICVYACPVNAIE 50
                                      688*****************6 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1e-07
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      v++d  kC +CG+C++ CP+++ 
  gi|488599884|ref|YP_007906355.1| 66 VIVDHTKCAYCGICYSFCPFNCF 88
                                      689******************96 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 1.6e-08
                                       ETTTSSS-THHHHHSTTTEEE CS
                              Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                        e+kC  C +C+++CP+ AI+
  gi|488599884|ref|YP_007906355.1| 113 FEDKCKDCTLCYKACPTSAIK 133
                                       59*****************96 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 4.1e-07
                                       EEEETTTSSS-THHHHHST CS
                              Fer4   1 vvideekCigCGaCvevCP 19 
                                       v+id ekC +CG+C+e C 
  gi|488599884|ref|YP_007906355.1| 154 VEIDFEKCNYCGICAEFCE 172
                                       68****************5 PP

  == domain 5  score: 31.3 bits;  conditional E-value: 9.6e-11
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        i+eekC +C++C++vCP +AI+
  gi|488599884|ref|YP_007906355.1| 193 LINEEKCDYCKLCEQVCPEDAIK 215
                                       59********************6 PP

  == domain 6  score: 25.4 bits;  conditional E-value: 7e-09
                                       EEEETTTSSS-THHHHHSTTTE CS
                              Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                       ++id+e+C +C +C+++CP++A
  gi|488599884|ref|YP_007906355.1| 232 IEIDQELCSHCSYCEKICPYDA 253
                                       68*******************9 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.0056
                                       SS-THHHHHSTTT CS
                              Fer4   9 igCGaCvevCPvg 21 
                                       +gC aC+++C ++
  gi|488599884|ref|YP_007906355.1| 277 VGCSACIKICKYN 289
                                       79********876 PP

  == domain 8  score: 27.2 bits;  conditional E-value: 1.9e-09
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       v+++e+ C++CGaC++ CP++ I
  gi|488599884|ref|YP_007906355.1| 301 VEFNEDFCVYCGACENSCPYDLI 323
                                       579*****************966 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   8.5   3.7e-12   4.4e-09       1      51 [.      33      86 ..      33      87 .. 0.91
   2 !   25.3  13.2   1.5e-08   1.8e-05       1      52 []      72     131 ..      72     131 .. 0.79
   3 !   26.5   9.4   6.1e-09   7.3e-06       1      49 [.     116     172 ..     116     175 .. 0.81
   4 !   35.7   7.3     8e-12   9.5e-09       1      52 []     198     253 ..     198     253 .. 0.90
   5 !   26.7   9.4   5.4e-09   6.4e-06       3      51 ..     277     321 ..     273     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 3.7e-12
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek...gtekveidpekClgCgaCvavCPtg 51
                                      +C gCg Cv aCpv+aiel ++++ +    ++ v +d++kC +Cg C + CP++
  gi|488599884|ref|YP_007906355.1| 33 KCNGCGICVYACPVNAIELGPVHDIAlglDIPPVIVDHTKCAYCGICYSFCPFN 86
                                      7*********************88886555588899****************98 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.5e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt.......ekveid.pekClgCgaCvavCPtga 52 
                                       +C  Cg C + Cp +++e++ + +e ++        k++++ ++kC +C+ C ++CPt a
  gi|488599884|ref|YP_007906355.1|  72 KCAYCGICYSFCPFNCFEFRIDGVEVEKsslpisfVKYTYRfEDKCKDCTLCYKACPTSA 131
                                       79****************99665555443455555666766489*************986 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 6.1e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaield........eeenekgt.ekveidpekClgCgaCvavCP 49 
                                       +C  C  C +aCp++ai+ +        +++ne  +  kveid ekC +Cg C++ C 
  gi|488599884|ref|YP_007906355.1| 116 KCKDCTLCYKACPTSAIKRNviitrqdiPVKNEG-IsGKVEIDFEKCNYCGICAEFCE 172
                                       7*****************9866655544343333.2589*****************96 PP

  == domain 4  score: 35.7 bits;  conditional E-value: 8e-12
                            Fer4_7   1 rCigCgaCvaaCpvkaield....eeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C  C+ C+++Cp +ai+++    ++e +++++++eid+e C++C  C++ CP++a
  gi|488599884|ref|YP_007906355.1| 198 KCDYCKLCEQVCPEDAIKVEgkliDFELPEKIAEIEIDQELCSHCSYCEKICPYDA 253
                                       7*****************986665566677889********************997 PP

  == domain 5  score: 26.7 bits;  conditional E-value: 5.4e-09
                            Fer4_7   3 igCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       +gC aC + C+++ + +  +     + +ve++++ C++CgaC++ CP++
  gi|488599884|ref|YP_007906355.1| 277 VGCSACIKICKYNRVWYVSR----NKSRVEFNEDFCVYCGACENSCPYD 321
                                       59************999887....34679******************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 !   21.8   3.0   1.1e-07   0.00014       7      24 .]      32      49 ..      28      49 .. 0.91
   2 !    7.7   5.5    0.0032       3.8       2      22 ..      66      86 ..      65      88 .. 0.89
   3 !   24.1   1.8   2.2e-08   2.7e-05       6      24 .]     114     132 ..     111     132 .. 0.94
   4 !    6.2   2.9    0.0095        11       1      20 [.     153     172 ..     153     177 .. 0.89
   5 !   18.4   3.3   1.3e-06    0.0016       3      24 .]     193     214 ..     192     214 .. 0.94
   6 !   24.8   2.3   1.3e-08   1.5e-05       2      23 ..     232     253 ..     231     254 .. 0.94
   7 !    9.0   3.1    0.0012       1.5       8      22 ..     273     289 ..     270     291 .. 0.89
   8 !   18.7   2.3   1.1e-06    0.0013       2      24 .]     301     323 ..     300     323 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                       kC+gCg Cv +CP +ai
  gi|488599884|ref|YP_007906355.1| 32 KKCNGCGICVYACPVNAI 49
                                      69**************98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0032
                            Fer4_6  2 veidpdkCigCgdCvrvCPeg 22
                                      v +d  kC  Cg C++ CP++
  gi|488599884|ref|YP_007906355.1| 66 VIVDHTKCAYCGICYSFCPFN 86
                                      568999*************97 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 2.2e-08
                            Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                       +dkC +C  C+++CP+ ai
  gi|488599884|ref|YP_007906355.1| 114 EDKCKDCTLCYKACPTSAI 132
                                       89**************998 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0095
                            Fer4_6   1 vveidpdkCigCgdCvrvCP 20 
                                       +veid +kC+ Cg C+  C 
  gi|488599884|ref|YP_007906355.1| 153 KVEIDFEKCNYCGICAEFCE 172
                                       689999**********9996 PP

  == domain 5  score: 18.4 bits;  conditional E-value: 1.3e-06
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                        i+++kC+ C  C+ vCPe+ai
  gi|488599884|ref|YP_007906355.1| 193 LINEEKCDYCKLCEQVCPEDAI 214
                                       59******************98 PP

  == domain 6  score: 24.8 bits;  conditional E-value: 1.3e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       +eid+++C +C  C+++CP++a
  gi|488599884|ref|YP_007906355.1| 232 IEIDQELCSHCSYCEKICPYDA 253
                                       89*****************987 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.0012
                            Fer4_6   8 kCi..gCgdCvrvCPeg 22 
                                       +C+  gC +C+++C ++
  gi|488599884|ref|YP_007906355.1| 273 RCDpvGCSACIKICKYN 289
                                       799889********987 PP

  == domain 8  score: 18.7 bits;  conditional E-value: 1.1e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       ve+++d C+ Cg+C++ CP++ i
  gi|488599884|ref|YP_007906355.1| 301 VEFNEDFCVYCGACENSCPYDLI 323
                                       89*****************9876 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   5.4e-06    0.0065       5      22 ..      30      47 ..      26      60 .. 0.78
   2 !   13.1   2.0   6.4e-05     0.076       2      24 ..      66      91 ..      65     112 .. 0.77
   3 !   24.4  10.1   1.9e-08   2.3e-05       6      55 ..     114     171 ..     109     172 .. 0.84
   4 !   17.2   0.4   3.4e-06    0.0041       2      28 ..     192     218 ..     191     227 .. 0.81
   5 !   20.5   8.1   3.2e-07   0.00038       2      55 ..     232     286 ..     231     287 .. 0.77
   6 !   19.2   0.1     8e-07   0.00095       2      28 ..     301     327 ..     300     365 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.4e-06
                           Fer4_10  5 dddtCirCgkCvkaCPad 22
                                        ++C +Cg Cv aCP++
  gi|488599884|ref|YP_007906355.1| 30 HYKKCNGCGICVYACPVN 47
                                      567899999999999984 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.4e-05
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl...t 24
                                      v++d  +C  Cg C ++CP++    +
  gi|488599884|ref|YP_007906355.1| 66 VIVDHTKCAYCGICYSFCPFNCfefR 91
                                      678999*************9655552 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 1.9e-08
                           Fer4_10   6 ddtCirCgkCvkaCPadl.......tsvgakgeas.eeeavrkkvekCtgcgaCveaC 55 
                                       +d+C  C+ C kaCP+++       t+++   +++ ++++v+++ ekC  cg C+e C
  gi|488599884|ref|YP_007906355.1| 114 EDKCKDCTLCYKACPTSAikrnviiTRQDIPVKNEgISGKVEIDFEKCNYCGICAEFC 171
                                       69**************99******9666665555505667777*************** PP

  == domain 4  score: 17.2 bits;  conditional E-value: 3.4e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvga 28 
                                       + i++++C  C+ C ++CP d+ +v++
  gi|488599884|ref|YP_007906355.1| 192 ILINEEKCDYCKLCEQVCPEDAIKVEG 218
                                       5799****************7655554 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 3.2e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaC 55 
                                       ++id++ C +C  C k CP+   ++  k+++ + +  +  +++C+   c aC+++C
  gi|488599884|ref|YP_007906355.1| 232 IEIDQELCSHCSYCEKICPY-DAAKTIKPFDGKLSLFEARMYRCDPvgCSACIKIC 286
                                       689*****************.3334445555555556669****975588****** PP

  == domain 6  score: 19.2 bits;  conditional E-value: 8e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvga 28 
                                       v++++d C+ Cg+C ++CP+dl +v+ 
  gi|488599884|ref|YP_007906355.1| 301 VEFNEDFCVYCGACENSCPYDLINVER 327
                                       67899***************8844433 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   5.9   3.3e-10     4e-07       1      49 [.      33      86 ..      33      88 .. 0.93
   2 !   19.8  12.2   5.3e-07   0.00064       1      51 []      72     132 ..      72     132 .. 0.84
   3 !   24.1   8.7   2.4e-08   2.9e-05       1      51 []     160     214 ..     160     214 .. 0.92
   4 !   22.5   7.2     8e-08   9.6e-05       2      49 ..     239     289 ..     238     291 .. 0.92
   5 !   19.5   8.7   6.7e-07    0.0008       3      50 ..     277     322 ..     277     323 .. 0.76
   6 !   15.9   1.2   9.2e-06     0.011       2      24 ..     308     330 ..     307     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.3e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkg 49
                                      kC+gCg Cv+aCp ++++   ++ +a            ++C  Cg C+  Cp +
  gi|488599884|ref|YP_007906355.1| 33 KCNGCGICVYACPVNAIELGPVHDIALGLDIPPvivdhTKCAYCGICYSFCPFN 86
                                      7*************************99777669******************76 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 5.3e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase............eaCigCgaCveaCpkgai 51 
                                       kC+ Cg C + Cp++ ++ +  + +++                  ++C +C  C++aCp+ ai
  gi|488599884|ref|YP_007906355.1|  72 KCAYCGICYSFCPFNCFEFRIDGVEVEKSS--LpisfvkytyrfeDKCKDCTLCYKACPTSAI 132
                                       7**************998777776666433..345789999****9**************987 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 2.4e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51 
                                       kC+ Cg C e C+   +ve++++ ++ +  ++     e+C  C+ C+++Cp++ai
  gi|488599884|ref|YP_007906355.1| 160 KCNYCGICAEFCEVFNMVEKEVQPYDIMPYEGIlineEKCDYCKLCEQVCPEDAI 214
                                       7**********************99999766559999***************997 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 8e-08
                            Fer4_9   2 CtgCgaCveaCpagvv.vedaaerkarlraaseeaC..igCgaCveaCpkg 49 
                                       C  C +C++ Cp++++ + + + +k +l +a++ +C  +gC aC+++C+ +
  gi|488599884|ref|YP_007906355.1| 239 CSHCSYCEKICPYDAAkTIKPFDGKLSLFEARMYRCdpVGCSACIKICKYN 289
                                       **************99789999***999999999**9999********975 PP

  == domain 5  score: 19.5 bits;  conditional E-value: 6.7e-07
                            Fer4_9   3 tgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +gC aC++ C+++ v + + ++ +   ++  + C+ CgaC++ Cp + 
  gi|488599884|ref|YP_007906355.1| 277 VGCSACIKICKYNRVWYVSRNKSRVEFNE--DFCVYCGACENSCPYDL 322
                                       59********9998865555555444333..36************985 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 9.2e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaer 24 
                                       C+ CgaC+++Cp+++++ ++++ 
  gi|488599884|ref|YP_007906355.1| 308 CVYCGACENSCPYDLINVERKTI 330
                                       999************99988765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.4   4.8e-08   5.8e-05       4      21 ..      28      45 ..      25      46 .. 0.86
   2 !   13.4   3.3   5.3e-05     0.064       2      21 ..      65      84 ..      64      85 .. 0.90
   3 !   15.1   1.7   1.5e-05     0.018       7      22 .]     114     129 ..     109     129 .. 0.93
   4 !   14.9   1.7   1.8e-05     0.021       2      20 ..     153     171 ..     152     173 .. 0.92
   5 !   18.2   1.0   1.6e-06    0.0019       3      22 .]     192     211 ..     190     211 .. 0.92
   6 !   16.8   1.2   4.4e-06    0.0052       3      22 .]     232     251 ..     230     251 .. 0.92
   7 ?    2.4   2.8      0.16   1.9e+02      11      21 ..     277     287 ..     272     288 .. 0.86
   8 !   19.6   2.3   5.8e-07    0.0007       2      22 .]     300     320 ..     299     320 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.8e-08
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      ++   +C+gCg+Cv aCP
  gi|488599884|ref|YP_007906355.1| 28 FYHYKKCNGCGICVYACP 45
                                      566789************ PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.3e-05
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      pv vd  +C  Cg+C+s CP
  gi|488599884|ref|YP_007906355.1| 65 PVIVDHTKCAYCGICYSFCP 84
                                      7889999************* PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.5e-05
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       +d+C  C  C++aCP+
  gi|488599884|ref|YP_007906355.1| 114 EDKCKDCTLCYKACPT 129
                                       79*************7 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 1.8e-05
                            Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                       +v++d ++C+ Cg+C   C
  gi|488599884|ref|YP_007906355.1| 153 KVEIDFEKCNYCGICAEFC 171
                                       6899**************9 PP

  == domain 5  score: 18.2 bits;  conditional E-value: 1.6e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       + +++++C  C+ C ++CP+
  gi|488599884|ref|YP_007906355.1| 192 ILINEEKCDYCKLCEQVCPE 211
                                       689****************5 PP

  == domain 6  score: 16.8 bits;  conditional E-value: 4.4e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       +++d + C +C+ C + CP+
  gi|488599884|ref|YP_007906355.1| 232 IEIDQELCSHCSYCEKICPY 251
                                       789****************5 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.16
                            Fer4_2  11 igCgaCvsaCP 21 
                                       +gC+aC++ C 
  gi|488599884|ref|YP_007906355.1| 277 VGCSACIKICK 287
                                       69*******95 PP

  == domain 8  score: 19.6 bits;  conditional E-value: 5.8e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       +v++++d C+ CgaC ++CP+
  gi|488599884|ref|YP_007906355.1| 300 RVEFNEDFCVYCGACENSCPY 320
                                       689*****************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 !   18.2   1.1   1.7e-06     0.002      36      58 ..      29      50 ..      15      51 .. 0.81
   2 !   24.6   8.6   1.7e-08     2e-05       3      57 ..      68     132 ..      66     134 .. 0.68
   3 !   23.9   9.0   2.8e-08   3.3e-05       2      58 ..     155     215 ..     154     216 .. 0.78
   4 !   16.4   8.8   6.2e-06    0.0074       2      51 ..     233     286 ..     230     291 .. 0.80
   5 !   16.8   8.3   4.7e-06    0.0056       9      58 ..     277     324 ..     269     325 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                           Fer4_21 36 vvedeCvGCnlCssvCPvedcie 58
                                      +  ++C GC +C+  CPv ++ie
  gi|488599884|ref|YP_007906355.1| 29 YHYKKCNGCGICVYACPV-NAIE 50
                                      45689************9.9987 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.7e-08
                           Fer4_21   3 idedkCigCgkCliaCedtshqa.i...eidaktvl.......kvv.edeCvGCnlCssvCPvedci 57 
                                       +d+ kC  Cg C+  C+ ++ +  i   e+++++ l       +++ ed+C  C+lC++ CP+  +i
  gi|488599884|ref|YP_007906355.1|  68 VDHTKCAYCGICYSFCPFNCFEFrIdgvEVEKSS-LpisfvkyTYRfEDKCKDCTLCYKACPT-SAI 132
                                       899**************77765423333333332.133334334434***************7.666 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 2.8e-08
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai.......eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                        id +kC  Cg C+  Ce    + +       +i + + + + e++C  C+lC +vCP ed+i+
  gi|488599884|ref|YP_007906355.1| 155 EIDFEKCNYCGICAEFCEV--FNMVekevqpyDIMPYEGILINEEKCDYCKLCEQVCP-EDAIK 215
                                       5999**************5..5555332233355566666888***************.89997 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 6.2e-06
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaie.idakt.vlkvvedeC..vGCnlCssvC 51 
                                        id++ C +C  C + C+  + + i+ +d+k   ++ +  +C  vGC  C+++C
  gi|488599884|ref|YP_007906355.1| 233 EIDQELCSHCSYCEKICPYDAAKTIKpFDGKLsLFEARMYRCdpVGCSACIKIC 286
                                       59***********************7577775234444444444********** PP

  == domain 5  score: 16.8 bits;  conditional E-value: 4.7e-06
                           Fer4_21   9 igCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +gC  C++ C+ + +  ++  +k++++  ed Cv C  C + CP  d i+
  gi|488599884|ref|YP_007906355.1| 277 VGCSACIKICKYNRVWYVSR-NKSRVEFNEDFCVYCGACENSCPY-DLIN 324
                                       89*********877777765.56677999***************6.7775 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 !   19.8   0.6   9.4e-07    0.0011       1      20 [.      33      52 ..      33      62 .. 0.87
   2 !   12.6   1.9   0.00017      0.21      52      67 .]      71      86 ..      64      99 .. 0.75
   3 !   22.4  11.5   1.5e-07   0.00018       1      64 [.     116     171 ..     116     175 .. 0.75
   4 !    7.0   2.5    0.0096        11       1      20 [.     160     179 ..     160     189 .. 0.78
   5 !   15.6  10.9     2e-05     0.024       1      66 [.     198     251 ..     198     252 .. 0.68
   6 ?    0.4  12.8       1.1   1.3e+03       2      66 ..     239     288 ..     238     289 .. 0.63
   7 !   18.1   0.2   3.2e-06    0.0039       1      29 [.     307     334 ..     307     367 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.4e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C +Cg C+ +CP+nai+  
  gi|488599884|ref|YP_007906355.1| 33 KCNGCGICVYACPVNAIELG 52
                                      5****************976 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                           Fer4_16 52 eaitgCdiCqdvCPan 67
                                      +++++C+iC   CP+n
  gi|488599884|ref|YP_007906355.1| 71 TKCAYCGICYSFCPFN 86
                                      5667777777777766 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 1.5e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                       +C++C+ C ++CPt+aik +   +i +r++i     ++++++ + e +   e++ +C+iC++ C
  gi|488599884|ref|YP_007906355.1| 116 KCKDCTLCYKACPTSAIKRN---VIITRQDIPV---KNEGISGKVEIDF--EKCNYCGICAEFC 171
                                       5*******************...6766666655...3444444444443..6777********* PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0096
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C  Cg Cae C +  + ek
  gi|488599884|ref|YP_007906355.1| 160 KCNYCGICAEFCEVFNMVEK 179
                                       59999999999998888777 PP

  == domain 5  score: 15.6 bits;  conditional E-value: 2e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek.kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       +C  C+ C +vCP++aik + k   +e +e+i        ++++d+e       +  C  C+++CP+
  gi|488599884|ref|YP_007906355.1| 198 KCDYCKLCEQVCPEDAIKVEgKLIDFELPEKI-------AEIEIDQEL------CSHCSYCEKICPY 251
                                       5*****************99222222333332.......234444444......669*********8 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.1
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C  C  C ++CP +a k+   k ++ +            ++ +  +c+      gC +C ++C +
  gi|488599884|ref|YP_007906355.1| 239 CSHCSYCEKICPYDAAKTI--KPFDGK---------LSLFEARMYRCD----PVGCSACIKICKY 288
                                       99***********998776..333322.........223445555555....5666666666665 PP

  == domain 7  score: 18.1 bits;  conditional E-value: 3.2e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeieare 29 
                                       +C+ Cg+C ++CP + i+ + +k+i ++e
  gi|488599884|ref|YP_007906355.1| 307 FCVYCGACENSCPYDLINVE-RKTIFSKE 334
                                       6*****************99.44444443 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   2.7e-05     0.032       3      17 ..      32      46 ..      21      60 .. 0.81
   2 !    8.2   1.0    0.0029       3.4       3      17 ..      71      85 ..      69     111 .. 0.85
   3 !   13.8  10.9   4.9e-05     0.058       3      63 ..     115     173 ..     114     175 .. 0.78
   4 !   13.6  11.0   5.8e-05     0.069       1      64 [.     157     212 ..     157     213 .. 0.81
   5 ?    0.8  11.8      0.58   6.9e+02       3      62 ..     237     287 ..     235     290 .. 0.65
   6 ?    2.8  11.1      0.13   1.6e+02      41      63 ..     307     320 ..     270     322 .. 0.57
   7 !   13.9   1.0   4.7e-05     0.056       5      17 ..     308     325 ..     304     367 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      +kC++Cg C  aCpv
  gi|488599884|ref|YP_007906355.1| 32 KKCNGCGICVYACPV 46
                                      578888888888886 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                       kC  Cg C s Cp+
  gi|488599884|ref|YP_007906355.1| 71 TKCAYCGICYSFCPF 85
                                      68********99994 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 4.9e-05
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       +kC  C +C +aCp+   +++ + + ++   + ++   + + e  +++C+ cg C+e C v
  gi|488599884|ref|YP_007906355.1| 115 DKCKDCTLCYKACPTSAIKRNVIITRQDIPVK-NEGISG-KVEIDFEKCNYCGICAEFCEV 173
                                       59************888888877777777666.444333.236779*************87 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 5.8e-05
                            Fer4_8   1 elekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ++ekC+ Cg C + C v++   k+ +    +  e      +       ++C  c+ C++vCp++
  gi|488599884|ref|YP_007906355.1| 157 DFEKCNYCGICAEFCEVFNMVEKEVQPYDIMPYE-GILINE-------EKCDYCKLCEQVCPED 212
                                       589*************999998887766666666.444444.......79************86 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.58
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsC..ttcgaCtevCp 62 
                                       e C +C++C++ Cp   ++   ++d +         e +      +++C  ++c aC + C+
  gi|488599884|ref|YP_007906355.1| 237 ELCSHCSYCEKICPYDAAKTIKPFDGKLSLF-----EAR------MYRCdpVGCSACIKICK 287
                                       56***********954444333344333333.....344......68887778888888886 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.13
                            Fer4_8  41 vleeeealwsCttcgaCtevCpv 63 
                                                 C+ cgaC++ Cp 
  gi|488599884|ref|YP_007906355.1| 307 F---------CVYCGACENSCPY 320
                                       3.........6666666666664 PP

  == domain 7  score: 13.9 bits;  conditional E-value: 4.7e-05
                            Fer4_8   5 CieCgaCqsaCp.....v 17 
                                       C+ CgaC+++Cp     v
  gi|488599884|ref|YP_007906355.1| 308 CVYCGACENSCPydlinV 325
                                       ***********9664330 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   3.5     3e-06    0.0036       2      17 .]      32      47 ..      31      47 .. 0.91
   2 ?    6.3   6.5     0.013        16       3      17 .]      72      86 ..      71      89 .. 0.89
   3 !   11.0   2.8   0.00043      0.51       2      16 ..     115     129 ..     114     135 .. 0.93
   4 ?    6.5   1.7     0.012        14       2      15 ..     159     172 ..     158     181 .. 0.92
   5 ?    6.0   3.0     0.017        20       2      16 ..     197     211 ..     196     217 .. 0.90
   6 !   10.9   3.7   0.00044      0.52       1      16 [.     236     251 ..     236     252 .. 0.92
   7 !    6.8   2.9    0.0096        12       3      17 .]     273     289 ..     271     289 .. 0.86
   8 !   13.2   2.2   8.4e-05       0.1       4      16 ..     308     320 ..     298     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C+gCg Cv+aCP++
  gi|488599884|ref|YP_007906355.1| 32 KKCNGCGICVYACPVN 47
                                      89************75 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C  Cg C+++CP++
  gi|488599884|ref|YP_007906355.1| 72 KCAYCGICYSFCPFN 86
                                      6888*********85 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00043
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++C +C  C+ aCP+
  gi|488599884|ref|YP_007906355.1| 115 DKCKDCTLCYKACPT 129
                                       89************6 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.012
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       e+C+ Cg C  +C+
  gi|488599884|ref|YP_007906355.1| 159 EKCNYCGICAEFCE 172
                                       89***********8 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.017
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C  C+ C+ +CP 
  gi|488599884|ref|YP_007906355.1| 197 EKCDYCKLCEQVCPE 211
                                       78999*********5 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.00044
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       qe C +C  C+ +CP+
  gi|488599884|ref|YP_007906355.1| 236 QELCSHCSYCEKICPY 251
                                       789************8 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.0096
                            Fer4_4   3 rC..igCgsCvaaCPqg 17 
                                       rC  +gC +C+ +C+++
  gi|488599884|ref|YP_007906355.1| 273 RCdpVGCSACIKICKYN 289
                                       88778*********975 PP

  == domain 8  score: 13.2 bits;  conditional E-value: 8.4e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C+ Cg+C+++CP+
  gi|488599884|ref|YP_007906355.1| 308 CVYCGACENSCPY 320
                                       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 !   13.0   1.0   9.5e-05      0.11      43      58 ..      31      46 ..      11      51 .. 0.78
   2 ?    3.1  15.0      0.12   1.4e+02       1      58 [.      72     129 ..      72     132 .. 0.67
   3 !    9.0  12.0    0.0017         2       1      57 [.     116     172 ..     116     173 .. 0.71
   4 ?    5.7  14.3     0.018        22       1      59 [.     160     212 ..     160     214 .. 0.71
   5 !   14.0   0.1   4.8e-05     0.057       2      15 ..     239     252 ..     219     269 .. 0.75
   6 ?    5.1  10.9     0.027        33      41      60 ..     303     322 ..     273     323 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.5e-05
                           Fer4_17 43 aslCieCgeCerkCPq 58
                                       ++C++Cg C+++CP 
  gi|488599884|ref|YP_007906355.1| 31 YKKCNGCGICVYACPV 46
                                      6788888888888885 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                           Fer4_17   1 rCiqCgyClpeCps....yeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       +C+ Cg C   Cp+    +++ + e +k    +++  +++  + +  ++C  C +C ++CP 
  gi|488599884|ref|YP_007906355.1|  72 KCAYCGICYSFCPFncfeFRIDGVEVEKSSLPISF--VKY--TYRFEDKCKDCTLCYKACPT 129
                                       6*********8886322244455444444444444..333..3568899************6 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0017
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaeke..ekaslCieCgeCerkCP 57 
                                       +C  C  C ++Cp+ ++ +n    +++++ + ++e+++ +    +++C+ Cg C++ C 
  gi|488599884|ref|YP_007906355.1| 116 KCKDCTLCYKACPTSAIKRNV-IITRQDIPV-KNEGISGKveIDFEKCNYCGICAEFCE 172
                                       6*************9998882.222333333.3444444432699***********995 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.018
                           Fer4_17   1 rCiqCgyClpeCpsyeaydne..pkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       +C+ Cg C++ C  ++  ++e  p  ++        e++    + ++C  C++Ce++CP++
  gi|488599884|ref|YP_007906355.1| 160 KCNYCGICAEFCEVFNMVEKEvqPYDIMPY------EGI--LINEEKCDYCKLCEQVCPED 212
                                       6***********999987764113333333......222..234479************97 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 4.8e-05
                           Fer4_17   2 CiqCgyClpeCpsy 15 
                                       C++C+yC++ Cp+ 
  gi|488599884|ref|YP_007906355.1| 239 CSHCSYCEKICPYD 252
                                       55666666666554 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.027
                           Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                        + + C+ Cg Ce +CP++l
  gi|488599884|ref|YP_007906355.1| 303 FNEDFCVYCGACENSCPYDL 322
                                       34578*************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 !   14.4   6.7   4.5e-05     0.054       1      15 []      34      48 ..      34      48 .. 0.98
   2 ?   -1.7   6.4       6.6   7.9e+03       1      14 [.      73      86 ..      72      87 .. 0.84
   3 !    8.1   3.5     0.005       5.9       1      15 []     117     131 ..     117     131 .. 0.89
   4 ?   -0.6   4.4       2.8   3.4e+03       1      11 [.     161     171 ..     161     173 .. 0.93
   5 !   14.6   3.0   4.1e-05     0.049       1      15 []     199     213 ..     199     213 .. 0.96
   6 !   14.5   2.6   4.3e-05     0.051       1      15 []     239     253 ..     239     253 .. 0.97
   7 ?    7.1   2.8      0.01        12       1      13 [.     274     288 ..     274     289 .. 0.82
   8 !   11.0   4.3   0.00056      0.67       1      14 [.     308     321 ..     308     321 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.5e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv +CPv+A
  gi|488599884|ref|YP_007906355.1| 34 CNGCGICVYACPVNA 48
                                      *************99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.6
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C  Cg C   CP +
  gi|488599884|ref|YP_007906355.1| 73 CAYCGICYSFCPFN 86
                                      55699*******87 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.005
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  C +C ++CP+ A
  gi|488599884|ref|YP_007906355.1| 117 CKDCTLCYKACPTSA 131
                                       888*********976 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.8
                            Fer4_3   1 CtgCgaCvevC 11 
                                       C+ Cg C e C
  gi|488599884|ref|YP_007906355.1| 161 CNYCGICAEFC 171
                                       999******99 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 4.1e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C +C++vCP++A
  gi|488599884|ref|YP_007906355.1| 199 CDYCKLCEQVCPEDA 213
                                       99**********998 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 4.3e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C +C+ C++ CP++A
  gi|488599884|ref|YP_007906355.1| 239 CSHCSYCEKICPYDA 253
                                       9************98 PP

  == domain 7  score: 7.1 bits;  conditional E-value: 0.01
                            Fer4_3   1 Ct..gCgaCvevCPv 13 
                                       C+  gC+aC + C +
  gi|488599884|ref|YP_007906355.1| 274 CDpvGCSACIKICKY 288
                                       66669********87 PP

  == domain 8  score: 11.0 bits;  conditional E-value: 0.00056
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ CgaC+++CP++
  gi|488599884|ref|YP_007906355.1| 308 CVYCGACENSCPYD 321
                                       999*********85 PP

>> Flu_C_NS1  Influenza C non-structural protein (NS1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.4   0.00016      0.19      49     115 ..     254     322 ..     241     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                         Flu_C_NS1  49 spcipnfdgn..vweatmyhhrgatltktmncncfqrtiwchpnpsrmrlsyafvlycrntkkicgyli 115
                                       +  i  fdg+  ++ea my+      +  ++   ++r  ++  n sr+ ++  f +yc   ++ c y +
  gi|488599884|ref|YP_007906355.1| 254 AKTIKPFDGKlsLFEARMYRCDPVGCSACIKICKYNRVWYVSRNKSRVEFNEDFCVYCGACENSCPYDL 322
                                       56788999973369*****************999*******************************9944 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0032       3.8       6      19 ..      32      45 ..      28      54 .. 0.87
   2 ?   13.5   0.7   7.6e-05     0.091       1      30 [.      66      96 ..      66     108 .. 0.88
   3 ?    3.5   1.3      0.11   1.3e+02       6      20 ..     115     129 ..     114     135 .. 0.85
   4 ?    5.2  12.4      0.03        36       1      66 []     154     216 ..     154     216 .. 0.89
   5 ?    5.6   0.8     0.022        26       1      19 [.     232     250 ..     232     258 .. 0.92
   6 ?    2.8   0.7      0.16     2e+02       1      19 [.     301     319 ..     301     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0032
                           Fer4_15  6 daCigcglCvaeap 19
                                      ++C gcg Cv ++p
  gi|488599884|ref|YP_007906355.1| 32 KKCNGCGICVYACP 45
                                      68**********98 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.6e-05
                           Fer4_15  1 VvvDrdaCigcglCvaea.pevfeldedgla 30
                                      V vD+++C  cg C+  +  + fe+  dg+ 
  gi|488599884|ref|YP_007906355.1| 66 VIVDHTKCAYCGICYSFCpFNCFEFRIDGVE 96
                                      78****************5589999999987 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.11
                           Fer4_15   6 daCigcglCvaeape 20 
                                       d+C  c lC++++p+
  gi|488599884|ref|YP_007906355.1| 115 DKCKDCTLCYKACPT 129
                                       899999999999985 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.03
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaeg.evpddeeeaaqeAaraCPvdAIrv 66 
                                       V++D ++C  cg C++ + evf + e+ ++  ++      eg  +++++ +  +   ++CP+dAI v
  gi|488599884|ref|YP_007906355.1| 154 VEIDFEKCNYCGICAEFC-EVFNMVEKEVQPYDIM---PYEGiLINEEKCDYCKLCEQVCPEDAIKV 216
                                       89***************9.6*****9999978874...456779999999999************87 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.022
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       +++D+++C  c  C + +p
  gi|488599884|ref|YP_007906355.1| 232 IEIDQELCSHCSYCEKICP 250
                                       79************99987 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.16
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V++++d C  cg+C   +p
  gi|488599884|ref|YP_007906355.1| 301 VEFNEDFCVYCGACENSCP 319
                                       78999*********98886 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.1     0.013        15       5      17 ..      33      45 ..      31      48 .. 0.92
   2 ?   10.6   2.6   0.00052      0.62       1      21 [.      68      89 ..      68     100 .. 0.84
   3 ?   10.0   2.4   0.00081      0.97       4      18 ..     115     129 ..     113     133 .. 0.92
   4 ?    7.7   1.9    0.0043       5.1       1      25 [.     156     179 ..     156     188 .. 0.88
   5 ?    5.8   2.8     0.017        20       1      18 [.     194     211 ..     194     215 .. 0.95
   6 ?    7.7   1.6    0.0044       5.2       1      17 [.     234     250 ..     234     251 .. 0.96
   7 ?   -1.6   0.6       3.4   4.1e+03       8      16 ..     278     286 ..     275     288 .. 0.84
   8 ?    5.0   1.2      0.03        36       3      17 ..     305     319 ..     303     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                           Fer4_13  5 tCiacgaCvelaP 17
                                      +C +cg+Cv ++P
  gi|488599884|ref|YP_007906355.1| 33 KCNGCGICVYACP 45
                                      8***********9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00052
                           Fer4_13  1 VDrdtCiacgaCvelaP.dvFe 21
                                      VD  +C  cg+C++++P ++Fe
  gi|488599884|ref|YP_007906355.1| 68 VDHTKCAYCGICYSFCPfNCFE 89
                                      899**************55565 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00081
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       d+C +c++C++++P 
  gi|488599884|ref|YP_007906355.1| 115 DKCKDCTLCYKACPT 129
                                       89************6 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0043
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeedde 25 
                                       +D ++C  cg+C+e++ +vF + ++
  gi|488599884|ref|YP_007906355.1| 156 IDFEKCNYCGICAEFC-EVFNMVEK 179
                                       7889***********9.89999876 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.017
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +++++C  c++C +++P+
  gi|488599884|ref|YP_007906355.1| 194 INEEKCDYCKLCEQVCPE 211
                                       789**************7 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0044
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D++ C+ c  C +++P
  gi|488599884|ref|YP_007906355.1| 234 IDQELCSHCSYCEKICP 250
                                       89**************9 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 3.4
                           Fer4_13   8 acgaCvela 16 
                                       +c aC +++
  gi|488599884|ref|YP_007906355.1| 278 GCSACIKIC 286
                                       799999998 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.03
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                       +d C+ cgaC + +P
  gi|488599884|ref|YP_007906355.1| 305 EDFCVYCGACENSCP 319
                                       688***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 2341.49
//
Query:       gi|488599885|ref|YP_007906356.1|  [L=781]
Description: CoB--CoM heterodisulfide reductase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-48  162.8   5.9    2.7e-47  159.8   0.0    3.4  3  FlpD            Methyl-viologen-reducing hydrogenase, delta s
    2.4e-22   79.5   0.0    3.4e-21   75.8   0.0    2.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      7e-21   73.1  38.4    1.1e-07   31.3   2.2    5.9  4  Fer4            4Fe-4S binding domain
    2.3e-14   53.7  31.9    4.4e-07   30.4  11.7    5.4  5  Fer4_7          4Fe-4S dicluster domain
    3.1e-14   52.4  45.3    1.3e-05   25.0   4.7    5.6  5  Fer4_6          4Fe-4S binding domain
    1.5e-12   47.5  42.4    4.8e-10   39.4  11.2    4.6  3  Fer4_21         4Fe-4S dicluster domain
    7.8e-12   44.5  47.0    4.4e-05   23.3   2.6    5.3  4  Fer4_2          4Fe-4S binding domain
    3.8e-11   43.8  19.7     0.0014   19.5   0.7    5.1  4  Fer4_16         4Fe-4S double cluster binding domain
    5.3e-11   42.5  32.7    1.2e-07   31.8  10.6    3.8  3  Fer4_9          4Fe-4S dicluster domain
    2.3e-08   34.0  33.7    5.9e-05   23.1  12.5    4.7  4  Fer4_10         4Fe-4S dicluster domain
    3.5e-08   33.1   0.5    0.00054   19.3   0.0    2.8  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.8e-08   32.8   0.1    1.1e-07   31.6   0.0    1.6  2  FAD_oxidored    FAD dependent oxidoreductase
    5.9e-07   28.9   0.6    8.1e-06   25.2   0.2    2.4  2  GIDA            Glucose inhibited division protein A
    8.7e-07   29.4   1.9     0.0002   21.9   0.4    3.1  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.2e-06   28.7   0.0    2.5e-06   27.6   0.0    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.9e-06   27.2   1.2    3.2e-06   26.5   1.2    1.3  1  FAD_binding_2   FAD binding domain
      2e-06   27.7   2.0     0.0054   16.4   1.4    2.4  2  DAO             FAD dependent oxidoreductase
      1e-05   25.9  23.7       0.13   12.7   1.1    4.9  4  Fer4_8          4Fe-4S dicluster domain
    7.4e-05   23.0  33.7       0.02   15.3   1.7    5.0  4  Fer4_4          4Fe-4S binding domain
    0.00011   22.2   0.6       0.06   13.3   0.0    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
    0.00021   21.8  30.2     0.0015   19.0   4.3    4.3  2  Fer4_17         4Fe-4S dicluster domain
     0.0014   17.4   1.4     0.0044   15.8   0.8    2.1  3  HI0933_like     HI0933-like protein
     0.0021   17.2   0.1       0.16   11.0   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein
     0.0036   16.6   0.0     0.0085   15.4   0.0    1.6  1  Thi4            Thi4 family
     0.0059   17.3  26.8       0.15   12.8   1.5    4.8  4  Fer4_15         4Fe-4S single cluster domain
     0.0095   15.1   0.3       0.26   10.4   0.0    2.5  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.056   12.7   0.0    2.0  2  Amino_oxidase   Flavin containing amine oxidoreductase
      0.013   14.8   0.0      0.026   13.8   0.0    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.019   15.5  30.9      0.083   13.4   2.5    4.6  4  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
      0.023   14.0   0.4      0.038   13.2   0.4    1.3  1  FAD_binding_3   FAD binding domain
      0.046   13.8   0.4       0.26   11.4   0.0    2.5  2  B12-binding     B12 binding domain
      0.059   14.2  23.7        2.5    9.0   2.5    4.8  4  Fer4_22         4Fe-4S dicluster domain
       0.15   10.9   1.1        5.4    5.7   0.2    2.1  2  Trp_halogenase  Tryptophan halogenase


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 ?    4.3   0.0     0.069        37      31      63 ..      39      71 ..      27      97 .. 0.90
   2 ?   -1.9   0.0       5.7   3.1e+03       5      52 ..     396     446 ..     395     449 .. 0.74
   3 !  159.8   0.0   4.9e-50   2.7e-47       1     123 []     647     769 ..     647     769 .. 1.00

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.069
                              FlpD 31 irvpCsgrvdpefilkalekGadgVlvlgChpg 63
                                      i+  Cs++ ++e+i    e++ d ++v++C p+
  gi|488599885|ref|YP_007906356.1| 39 IKYSCSDSAQEEIINAIKEHNLDRIVVSACSPK 71
                                      7899**********9999************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.7
                              FlpD   5 lCnwcayaaadlagvsrlqyppn...vriirvpCsgrvdpefilkalekGa 52 
                                       + + c+ a++++a + + +yp++   v  i ++  gr+ +ef  +  ekG+
  gi|488599885|ref|YP_007906356.1| 396 CSRVCCMATLKNAFTIKERYPDSeiyVYYIDIRAFGRMYEEFFRRVQEKGV 446
                                       566788899999999999999854447888888888888888777666665 PP

  == domain 3  score: 159.8 bits;  conditional E-value: 4.9e-50
                              FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerr 77 
                                       il+F+C +c+y a+dlag+++lqy+pn+r+ir+ Csgrvdpe+il al++G+dgV+v+gC+ g+Ch++ Gn+ka++r
  gi|488599885|ref|YP_007906356.1| 647 ILVFACWYCSYGAIDLAGTTKLQYEPNIRVIRTLCSGRVDPEWILFALKSGIDGVMVSGCRMGECHFKYGNYKASDR 723
                                       89*************************************************************************** PP

                              FlpD  78 veklkelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                       v++++e+l+e+gi+p+Rv++++ sa+e++++++ +++fv+ki+eLG
  gi|488599885|ref|YP_007906356.1| 724 VNAIREALKEVGINPDRVATSWHSAGEAKEIVSDFNDFVRKIRELG 769
                                       *********************************************8 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 !   75.8   0.0   6.2e-24   3.4e-21       3     284 ..     143     540 ..     141     550 .. 0.75

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 6.2e-24
                                       EEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx........ RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias........ 57 
                                        +viGgG+AG++aal++a +g+kv+lve           l++ +++++c++   ++++ +v  +++i+         
  gi|488599885|ref|YP_007906356.1| 143 ALVIGGGIAGIEAALNIADSGIKVYLVEkrptigghmatLNEVFPTNDCSIcilAPKMSEVWNHPNIEVitsaevks 219
                                       68*************************888888899999*********988666888888888888888****9999 PP

                                       .....................................HHHHCHHHHCCCCHC........CT.CEEEEESCEEEEET CS
                                       .....................................xxxxxxxxxxxxxxx........xx.xxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .....................................evvkklnqgielllg........ee.vvkidpgkkkvkle 88 
                                                                            ev +++   i ++++        ++ + +id ++ ++ + 
  gi|488599885|ref|YP_007906356.1| 220 vtgssgdfrvsvikypryvdtskckgciddcssvcpvEVPNEFDYTIGTRKAiyipipqsTPlYASIDWEH-CIGC- 294
                                       99888888888888888887777777777777777774433444444444445555555555566666555.3333. PP

                                       EEEC................TCEEEEEESEEEE---EEE-BC..TCT.TC....................TTBEECC CS
                                       xxxx................xxxxxxxxxxxxxxxxxxxxxx..xxx.xx...................xxxxxxxx RF
                       Pyr_redox_2  89 kkke................gdeekiaydklvlAtGssprdl..gip.Gv...................aenvgklv 127
                                          +                 +e +i  +++++AtG++++d   +++ G                    ++++g l+
  gi|488599885|ref|YP_007906356.1| 295 ---RlcekacepeaidfnqkAEEIEINVGTIIVATGFKAFDArkKTEyGYgrypnvitslelerllsasGPTQGILL 368
                                       ...0334456799999998778888999**************54333544778888888888888888878888888 PP

                                       SECHHHHHHCCSS-T......SEEEEES-SHHHHHHHHHHHHHT-.........EEEEEESSSSSSTTS-HHHHHHH CS
                                       xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 128 rtldsaealklkllp......krivvvGgGyiGvElAaalaklgk.........evtlveardrllraldkelsaal 189
                                       r++ds+ + + +  +      +++++    y++ ++++a  k +          e+ +v+  d+  ra++++ +++ 
  gi|488599885|ref|YP_007906356.1| 369 RPSDSKIPKRIAFIQcvgsrdENTNR----YCSRVCCMATLKNAFtikerypdsEI-YVYYIDI--RAFGRMYEEFF 438
                                       88888888888888877777666665....99999999942222223334444432.3333333..56887777776 PP

                                       HHHHHHTTEEEEESCEEEEEEETTE.....EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEE.E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Pyr_redox_2 190 eealekeGvevklgtsvkeidgnge.....kle.vvledgeeidadlvvvavGvrpstelleeklglelderggi.v 259
                                       +++ +++Gv+++ +++v +i++ ++     ++e +  ++ ee + dlvv+avG+++++el+  klg+ + e+g+   
  gi|488599885|ref|YP_007906356.1| 439 RRV-QEKGVRFV-RARVADIIEVEDgnlllNYEnTLSGEYEEKEFDLVVLAVGMEANNELA-TKLGISVGEDGFYeA 512
                                       655.555*****.99999999999999877666888899999*******************.*************88 PP

                                       --TTS...BESSTTEEE-GGGCTECCSS CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 260 vdefl...rtnvpgiyaiGDvaggkggp 284
                                       v ++l   +tnv gi+++G   g++++ 
  gi|488599885|ref|YP_007906356.1| 513 VHPKLrpsETNVRGIFLAGTSSGPRDIQ 540
                                       9999977779*********877444444 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   5.4       0.1        54       2      22 ..     237     258 ..     236     260 .. 0.89
   2 !   23.1   3.1   7.9e-08   4.3e-05       2      23 ..     285     306 ..     284     307 .. 0.92
   3 !   31.3   2.2   2.1e-10   1.1e-07       2      24 .]     570     592 ..     569     592 .. 0.94
   4 !   30.0   4.4   5.3e-10   2.9e-07       2      24 .]     599     621 ..     598     621 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                                       EEETTTSSS-.THHHHHSTTTE CS
                              Fer4   2 videekCigC.GaCvevCPvgA 22 
                                       ++d++kC gC   C +vCPv++
  gi|488599885|ref|YP_007906356.1| 237 YVDTSKCKGCiDDCSSVCPVEV 258
                                       79********999999999986 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 7.9e-08
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        id+e CigC +C+++C  +AI
  gi|488599885|ref|YP_007906356.1| 285 SIDWEHCIGCRLCEKACEPEAI 306
                                       69***************99999 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 2.1e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        +d +kCigCG+C  vC ++AI+
  gi|488599885|ref|YP_007906356.1| 570 FVDRDKCIGCGICRRVCRFNAIS 592
                                       59*******************96 PP

  == domain 4  score: 30.0 bits;  conditional E-value: 5.3e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        +d + C+ CG+Cv++CPv+AI+
  gi|488599885|ref|YP_007906356.1| 599 FVDSNSCVMCGICVSACPVDAID 621
                                       5899*****************95 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.2   0.00074       0.4      32      52 .]     237     258 ..     190     258 .. 0.73
   2 !   21.1   0.4   6.6e-07   0.00036       1      25 [.     290     314 ..     290     340 .. 0.85
   3 ?    1.1   0.2       1.1   6.1e+02       6      25 ..     394     417 ..     382     440 .. 0.65
   4 !   30.4  11.7   8.1e-10   4.4e-07       1      52 []     575     619 ..     575     619 .. 0.95
   5 !   19.7   3.2   1.8e-06   0.00098       1      27 [.     604     630 ..     604     683 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00074
                            Fer4_7  32 eidpekClgCga.CvavCPtga 52 
                                       ++d +kC gC   C +vCP+++
  gi|488599885|ref|YP_007906356.1| 237 YVDTSKCKGCIDdCSSVCPVEV 258
                                       67899*****766******975 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 6.6e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeene 25 
                                       +CigC+ C++aC  +ai+++++++e
  gi|488599885|ref|YP_007906356.1| 290 HCIGCRLCEKACEPEAIDFNQKAEE 314
                                       6******************998655 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.1
                            Fer4_7   6 gaCvaaCp....vkaieldeeene 25 
                                       ++C ++C      +a++++e+  +
  gi|488599885|ref|YP_007906356.1| 394 RYCSRVCCmatlKNAFTIKERYPD 417
                                       599999963344666666665444 PP

  == domain 4  score: 30.4 bits;  conditional E-value: 8.1e-10
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +CigCg C ++C  +ai++ ++       k+ +d+++C+ Cg Cv++CP++a
  gi|488599885|ref|YP_007906356.1| 575 KCIGCGICRRVCRFNAISMVDK-------KAFVDSNSCVMCGICVSACPVDA 619
                                       7******************886.......6899*****************97 PP

  == domain 5  score: 19.7 bits;  conditional E-value: 1.8e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekg 27 
                                       +C+ Cg Cv+aCpv+ai++  +++ + 
  gi|488599885|ref|YP_007906356.1| 604 SCVMCGICVSACPVDAIDMGFFSDSQI 630
                                       5*****************998755542 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   4.0   4.2e-05     0.023       4      22 ..     238     257 ..     237     259 .. 0.91
   2 !   13.3   2.2   0.00012     0.065       9      24 .]     291     306 ..     285     306 .. 0.89
   3 ?   -2.1   1.1       8.7   4.7e+03      14      21 ..     395     402 ..     393     405 .. 0.79
   4 !   22.8   3.1   1.2e-07   6.8e-05       1      24 []     568     591 ..     568     591 .. 0.94
   5 !   25.0   4.7   2.4e-08   1.3e-05       1      24 []     597     620 ..     597     620 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-05
                            Fer4_6   4 idpdkCigC.gdCvrvCPeg 22 
                                       +d +kC gC +dC +vCP  
  gi|488599885|ref|YP_007906356.1| 238 VDTSKCKGCiDDCSSVCPVE 257
                                       89****************86 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       CigC+ C+++C   ai
  gi|488599885|ref|YP_007906356.1| 291 CIGCRLCEKACEPEAI 306
                                       ***********87665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 8.7
                            Fer4_6  14 dCvrvCPe 21 
                                        C rvC +
  gi|488599885|ref|YP_007906356.1| 395 YCSRVCCM 402
                                       59***975 PP

  == domain 4  score: 22.8 bits;  conditional E-value: 1.2e-07
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       ++ +d+dkCigCg C rvC ++ai
  gi|488599885|ref|YP_007906356.1| 568 FAFVDRDKCIGCGICRRVCRFNAI 591
                                       578*****************9998 PP

  == domain 5  score: 25.0 bits;  conditional E-value: 2.4e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       ++ +d ++C+ Cg Cv++CP +ai
  gi|488599885|ref|YP_007906356.1| 597 KAFVDSNSCVMCGICVSACPVDAI 620
                                       578******************998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   1.0   0.00019       0.1      36      54 ..     238     257 ..     217     259 .. 0.85
   2 !   17.6   1.7   5.5e-06     0.003       1      31 [.     284     311 ..     284     320 .. 0.82
   3 !   39.4  11.2   8.8e-13   4.8e-10       1      59 []     569     622 ..     569     622 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                           Fer4_21  36 vvedeCvGC.nlCssvCPve 54 
                                       v +++C GC + CssvCPve
  gi|488599885|ref|YP_007906356.1| 238 VDTSKCKGCiDDCSSVCPVE 257
                                       5689*****779******95 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.5e-06
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidak 31 
                                       A id ++CigC +C +aCe    +ai++++k
  gi|488599885|ref|YP_007906356.1| 284 ASIDWEHCIGCRLCEKACEP---EAIDFNQK 311
                                       78*****************5...77766655 PP

  == domain 3  score: 39.4 bits;  conditional E-value: 8.8e-13
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       A++d+dkCigCg C  +C+    +ai++ +k+   v +++Cv C +C+s CPv d+i+m
  gi|488599885|ref|YP_007906356.1| 569 AFVDRDKCIGCGICRRVCR---FNAISMVDKKA-FVDSNSCVMCGICVSACPV-DAIDM 622
                                       799****************...89999886655.7999**************9.99998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   3.3   0.00018     0.097       3      21 ..     236     255 ..     234     256 .. 0.90
   2 !   16.6   1.0   1.2e-05    0.0063       4      20 ..     285     301 ..     282     304 .. 0.87
   3 !   23.0   2.1     1e-07   5.5e-05       3      20 ..     569     586 ..     566     588 .. 0.92
   4 !   23.3   2.6     8e-08   4.4e-05       2      21 ..     597     616 ..     596     617 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                            Fer4_2   3 vvvdtdrCigC.gaCvsaCP 21 
                                        +vdt +C gC   C s+CP
  gi|488599885|ref|YP_007906356.1| 236 RYVDTSKCKGCiDDCSSVCP 255
                                       689*********99****** PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.2e-05
                            Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                        +d ++CigC+ C +aC
  gi|488599885|ref|YP_007906356.1| 285 SIDWEHCIGCRLCEKAC 301
                                       6899************* PP

  == domain 3  score: 23.0 bits;  conditional E-value: 1e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       ++vd+d+CigCg+C+ +C
  gi|488599885|ref|YP_007906356.1| 569 AFVDRDKCIGCGICRRVC 586
                                       689*************** PP

  == domain 4  score: 23.3 bits;  conditional E-value: 8e-08
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       +++vd+++C+ Cg+CvsaCP
  gi|488599885|ref|YP_007906356.1| 597 KAFVDSNSCVMCGICVSACP 616
                                       579***************** 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 ?    7.2   0.1     0.018       9.8      52      66 ..     241     256 ..     206     272 .. 0.80
   2 !   13.9   0.3   0.00014     0.077       1      29 [.     290     319 ..     290     344 .. 0.70
   3 !   14.6   0.2   8.8e-05     0.048       1      18 [.     575     592 ..     556     603 .. 0.69
   4 !   19.5   0.7   2.5e-06    0.0014       2      30 ..     605     633 ..     604     657 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                           Fer4_16  52 eaitgC.diCqdvCPa 66 
                                        +++gC d C  vCP+
  gi|488599885|ref|YP_007906356.1| 241 SKCKGCiDDCSSVCPV 256
                                       5666774467777775 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00014
                           Fer4_16   1 rCgtCgkCaevCPtnaikek.kekeieare 29 
                                       +C++C+ C ++C  +ai+ + k++eie++ 
  gi|488599885|ref|YP_007906356.1| 290 HCIGCRLCEKACEPEAIDFNqKAEEIEINV 319
                                       7*****************884555566554 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 8.8e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       +C++Cg C  vC  nai+
  gi|488599885|ref|YP_007906356.1| 575 KCIGCGICRRVCRFNAIS 592
                                       366666666666666665 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 2.5e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearec 30 
                                       C+ Cg C+++CP++ai++      +++++
  gi|488599885|ref|YP_007906356.1| 605 CVMCGICVSACPVDAIDMGFFSDSQIKAE 633
                                       ****************9884444444444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   5.4   1.7e-07   9.3e-05       1      51 []     242     306 ..     242     306 .. 0.88
   2 ?   -2.0   0.6         8   4.3e+03       6      15 ..     394     403 ..     382     417 .. 0.66
   3 !   31.8  10.6   2.1e-10   1.2e-07       1      51 []     575     620 ..     575     620 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.7e-07
                            Fer4_9   1 kCtgC.gaCveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCpkgai 51 
                                       kC gC + C ++Cp +v +e + +   r  ++               e CigC+ C++aC+ +ai
  gi|488599885|ref|YP_007906356.1| 242 KCKGCiDDCSSVCPVEVPNEFDYTIGTRKAIYIPipqstplyasidwEHCIGCRLCEKACEPEAI 306
                                       7****557*********999999888887666558999********999***********98876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8
                            Fer4_9   6 gaCveaCpag 15 
                                       ++C ++C + 
  gi|488599885|ref|YP_007906356.1| 394 RYCSRVCCMA 403
                                       5799987443 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 2.1e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC+gCg C ++C ++++++ +++ ++  +     +C++Cg Cv aCp +ai
  gi|488599885|ref|YP_007906356.1| 575 KCIGCGICRRVCRFNAISMVDKKAFVDSN-----SCVMCGICVSACPVDAI 620
                                       7******************9999999985.....6*************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 !   11.2   0.7   0.00056       0.3       4      23 ..     238     258 ..     236     280 .. 0.78
   2 !   13.1   0.5   0.00014     0.077       3      34 ..     285     311 ..     283     326 .. 0.68
   3 !   23.1  12.5   1.1e-07   5.9e-05       4      56 .]     571     616 ..     568     616 .. 0.93
   4 !   17.3   2.8   7.1e-06    0.0039       3      24 ..     599     631 ..     597     657 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                           Fer4_10   4 idddtCirCg.kCvkaCPadl 23 
                                       +d+++C +C  +C ++CP+ +
  gi|488599885|ref|YP_007906356.1| 238 VDTSKCKGCIdDCSSVCPVEV 258
                                       6899*****989******943 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                           Fer4_10   3 vidddtCirCgkCvkaC.Padltsvgakgease 34 
                                        id + Ci+C+ C kaC P       a++++ +
  gi|488599885|ref|YP_007906356.1| 285 SIDWEHCIGCRLCEKACePE------AIDFNQK 311
                                       688899***********232......3333333 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 1.1e-07
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d+d+Ci+Cg C+++C       + +++ + +++  +++ +C +cg Cv+aCP
  gi|488599885|ref|YP_007906356.1| 571 VDRDKCIGCGICRRVC-------RFNAISMVDKKAFVDSNSCVMCGICVSACP 616
                                       799*************.......56999999999999***************9 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 7.1e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadl...........t 24 
                                        +d+++C+ Cg Cv+aCP+d+           +
  gi|488599885|ref|YP_007906356.1| 599 FVDSNSCVMCGICVSACPVDAidmgffsdsqiK 631
                                       6799***************88777776444331 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.9e-07   0.00054     159     247 ..     135     229 ..     107     237 .. 0.77
   2 !   11.0   0.0   0.00034      0.18     215     305 .]     435     531 ..     428     531 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.9e-07
                       Pyr_redox_3 159 fhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdi.......enrleelvkeekik 228
                                       ++k  ++  +ViGg+  +++aAl++++ g +V +v ++ +i  + ++ + ++ p++        +++ e++++ +i+
  gi|488599885|ref|YP_007906356.1| 135 VDKPVKKSALVIGGGIAGIEAALNIADSGIKVYLVEKRPTIGGHMATLN-EVFPTNdcsicilAPKMSEVWNHPNIE 210
                                       455567899******************************9999865544.566655111111256778888887899 PP

                       Pyr_redox_3 229 vlfnaevkeikekeeeykv 247
                                       v++ aevk+++ ++  ++v
  gi|488599885|ref|YP_007906356.1| 211 VITSAEVKSVTGSSGDFRV 229
                                       9999999999988887776 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00034
                       Pyr_redox_3 215 enrleelvkeekikvlfnaevkeikekeeeykvktedgkkvev....kddvvlatGykpdlsflkkslfeldedg.r 286
                                       e+ ++++++++ ++++    ++ i+ ++ +  ++ e++ + e      d vvla+G + + ++ +k +++  edg +
  gi|488599885|ref|YP_007906356.1| 435 EEFFRRVQEKG-VRFVRARVADIIEVEDGNLLLNYENTLSGEYeekeFDLVVLAVGMEANNELATKLGISVGEDGfY 510
                                       55566665555.777777777788888888777766543322211225668899*****************999944 PP

                       Pyr_redox_3 287 pvlte..eteetnvpglflaG 305
                                        ++++     etnv g+flaG
  gi|488599885|ref|YP_007906356.1| 511 EAVHPklRPSETNVRGIFLAG 531
                                       4555534678**********9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0     2e-10   1.1e-07       3      39 ..     144     180 ..     143     235 .. 0.94
   2 ?   -3.4   0.0       8.4   4.6e+03      54      69 ..     428     443 ..     379     456 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2e-10
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39 
                                       +V+GGg+aG+ AA+  a +G kv Lve+r+ +GG ++
  gi|488599885|ref|YP_007906356.1| 144 LVIGGGIAGIEAALNIADSGIKVYLVEKRPTIGGHMA 180
                                       7*********************************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.4
                      FAD_oxidored  54 qvvtgiareflerlrq 69 
                                       ++ +++++ef++r+++
  gi|488599885|ref|YP_007906356.1| 428 RAFGRMYEEFFRRVQE 443
                                       5667778888888765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.2   1.5e-08   8.1e-06       3      32 ..     144     172 ..     142     189 .. 0.83
   2 ?    1.4   0.0      0.24   1.3e+02     244     385 ..     408     555 ..     310     562 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.5e-08
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkl 32 
                                        ViGgG AG+eAAl++a +G+kv L+  k 
  gi|488599885|ref|YP_007906356.1| 144 LVIGGGIAGIEAALNIADSGIKVYLVE-KR 172
                                       6************************93.33 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.24
                                       HHHHHCTCC.C-T.T----B--S-CCC-SSTCC...CCCCSTT-S--EEEEEESSTT--EEEEET----S-HHHHHH CS
                              GIDA 244 hkiikenlk.ksaklfegcieelgprycpsied...kivrladkeshqvfLepegleteliylvgfstslpeevqke 316
                                         +ike    +++ ++  +i   g+ y++  +    k vr+ +   +   +e e+ +  l y + +s +++e++ + 
  gi|488599885|ref|YP_007906356.1| 408 AFTIKERYPdSEIYVYYIDIRAFGRMYEEFFRRvqeKGVRFVRARVAD-IIEVEDGNLLLNYENTLSGEYEEKEFDL 483
                                       334444444133334444488888888888887777888886444444.3677777777788888888888888877 PP

                                       HHTTSTT-TT--..EEE--EEEEEEEE-GGGB-TTSB..BSSSBTEEE-CGGGTB-SHHHHHH.HHHHHHHHHH CS
                              GIDA 317 vlrsipGLenae..ivrpGyaieydyvdprqllntLe..tkkvkgLflAGqinGteGYeEaaa.qGllAGinaa 385
                                       v+  + G+e  +   +++G ++ +d + +  + ++L+    +v+g+flAG  +G     +++a  Gl A   ++
  gi|488599885|ref|YP_007906356.1| 484 VVLAV-GMEANNelATKLGISVGEDGFYEA-VHPKLRpsETNVRGIFLAGTSSGPRDIQDSIAsAGLSASKAIH 555
                                       77777.777443124567777776666554.4444431123488999999999987777776656666665555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.4   3.6e-07    0.0002       2      35 ..     143     176 ..     142     185 .. 0.91
   2 ?    4.7   0.0     0.082        45      54      72 ..     208     226 ..     195     233 .. 0.80
   3 ?   -0.9   0.0       4.6   2.5e+03      44      71 ..     435     462 ..     430     467 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.6e-07
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       ++v+GgG  g+E+A ++a+ g kV++ve ++++ 
  gi|488599885|ref|YP_007906356.1| 143 ALVIGGGIAGIEAALNIADSGIKVYLVEKRPTIG 176
                                       79*****************************998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.082
                                       TEEEECSEEEEEEEEETTS CS
                         Pyr_redox  54 gievllntkveeiegsedg 72 
                                       +iev+++++v++++gs+  
  gi|488599885|ref|YP_007906356.1| 208 NIEVITSAEVKSVTGSSGD 226
                                       9*************99876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.6
                                       HHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsed 71 
                                       +++ ++++++g++++  +++  ie ++ 
  gi|488599885|ref|YP_007906356.1| 435 EEFFRRVQEKGVRFVRARVADIIEVEDG 462
                                       5677899*******99888877776654 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   4.6e-09   2.5e-06       1      39 [.     145     183 ..     145     200 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.6e-09
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39 
                                       ++G+G++G  aA  +a+ g++v l+ekr+ +GG++a+ +
  gi|488599885|ref|YP_007906356.1| 145 VIGGGIAGIEAALNIADSGIKVYLVEKRPTIGGHMATLN 183
                                       8**********************************9964 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.2   5.9e-09   3.2e-06       2      39 ..     143     180 ..     142     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.9e-09
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                       ++ViG+G+AG  AAl++a+ G kv +vek +  gg+ a
  gi|488599885|ref|YP_007906356.1| 143 ALVIGGGIAGIEAALNIADSGIKVYLVEKRPTIGGHMA 180
                                       69*********************************976 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.4     1e-05    0.0054       3      35 ..     144     177 ..     142     182 .. 0.92
   2 !    9.4   0.0    0.0013      0.71     151     208 ..     436     498 ..     421     531 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                                       EEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO   3 viiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                       ++iGGGi+G+ +A+  a  g  V l+ek++ +g g
  gi|488599885|ref|YP_007906356.1| 144 LVIGGGIAGIEAALNIADSGikVYLVEKRPTIG-G 177
                                       8***************9999*********9999.3 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                                       HHHHHHHHTT-EEEESECEEEE.EEEETCEEEEE...EECT.EEE..EEEEEEEE--GGGHH.HH.H CS
                               DAO 151 alaraaealGveilegtevtgl.eeedgkvwgve...rttp.gen..daadavVnaaGawsd.ll.g 208
                                        + r+++++Gv++++  +v ++ e edg +       + t  ge   +++d vV+a G  ++ +l  
  gi|488599885|ref|YP_007906356.1| 436 EFFRRVQEKGVRFVRA-RVADIiEVEDGNLL--LnyeN-TLsGEYeeKEFDLVVLAVGMEANnELaT 498
                                       567999*********9.88886266664422..24544.4446553347799********9985533 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.052        28      49      64 ..     241     257 ..     200     259 .. 0.80
   2 !    9.6   3.2    0.0022       1.2       3      17 ..     289     322 ..     287     403 .. 0.67
   3 !   10.0   1.0    0.0016       0.9       3      16 ..     574     587 ..     572     600 .. 0.80
   4 !   12.7   1.1   0.00024      0.13       3      17 ..     603     617 ..     601     656 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.052
                            Fer4_8  49 wsCttcga.CtevCpvg 64 
                                        +C +c   C++vCpv+
  gi|488599885|ref|YP_007906356.1| 241 SKCKGCIDdCSSVCPVE 257
                                       56777744488888876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0022
                            Fer4_8   3 ekCieCgaCqsaC.p..................v 17 
                                       e+Ci+C +C++aC p                  +
  gi|488599885|ref|YP_007906356.1| 289 EHCIGCRLCEKACePeaidfnqkaeeieinvgtI 322
                                       79***********524444334444444444433 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0016
                            Fer4_8   3 ekCieCgaCqsaCp 16 
                                       +kCi+Cg C+  C 
  gi|488599885|ref|YP_007906356.1| 574 DKCIGCGICRRVCR 587
                                       69********9995 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00024
                            Fer4_8   3 ekCieCgaCqsaCpv 17 
                                       ++C+ Cg C saCpv
  gi|488599885|ref|YP_007906356.1| 603 NSCVMCGICVSACPV 617
                                       678888888888885 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   3.6         7   3.8e+03       4      15 ..     243     255 ..     240     258 .. 0.52
   2 !   13.4   1.6   0.00016     0.085       2      15 ..     289     302 ..     287     311 .. 0.88
   3 !   11.1   4.2   0.00083      0.45       2      16 ..     574     588 ..     573     589 .. 0.90
   4 !   15.3   1.7   3.7e-05      0.02       1      16 [.     602     617 ..     602     623 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 7
                            Fer4_4   4 CigCgs.CvaaCP 15 
                                       C gC   C ++CP
  gi|488599885|ref|YP_007906356.1| 243 CKGCIDdCSSVCP 255
                                       4444322555566 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00016
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       e CigC+ C+ aC+
  gi|488599885|ref|YP_007906356.1| 289 EHCIGCRLCEKACE 302
                                       56***********8 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00083
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++CigCg C+++C +
  gi|488599885|ref|YP_007906356.1| 574 DKCIGCGICRRVCRF 588
                                       89***********76 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 3.7e-05
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +++C+ Cg Cv+aCP+
  gi|488599885|ref|YP_007906356.1| 602 SNSCVMCGICVSACPV 617
                                       589************6 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.011         6       2      41 ..     145     179 ..     144     188 .. 0.86
   2 !   13.3   0.0   0.00011      0.06      95     155 ..     429     490 ..     423     491 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrv 41 
                                       ++G+G++G+ ++ +++++      +++ l++++++ g g++
  gi|488599885|ref|YP_007906356.1| 145 VIGGGIAGIEAALNIADS-----GIKVYLVEKRPTiG-GHM 179
                                       8***************99.....5********98845.655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00011
                     NAD_binding_9  95 lyGrYlrdlfeellarlpegvtvevhraevvdleeradg.....qavlladg.aslaadaVvLAlGh 155
                                        +Gr  +++f++++++      v+++ra+v d+ e +dg     ++ +l+++ ++ ++d VvLA+G+
  gi|488599885|ref|YP_007906356.1| 429 AFGRMYEEFFRRVQEKG-----VRFVRARVADIIEVEDGnlllnYENTLSGEyEEKEFDLVVLAVGM 490
                                       57777788888877665.....99***********999954444444444444668**********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 !   19.0   4.3   2.8e-06    0.0015       1      57 [.     242     302 ..     242     307 .. 0.78
   2 ?    3.7  13.0      0.17        92       1      58 [.     575     617 ..     575     620 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.8e-06
                           Fer4_17   1 rCiqCgy.ClpeCpsyeaydnepk.kllraakl..glleeaekeekaslCieCgeCerkCP 57 
                                       +C +C   C  +Cp    ++++    +++a+++   + +   ++  ++ Ci+C++Ce++C 
  gi|488599885|ref|YP_007906356.1| 242 KCKGCIDdCSSVCPVEVPNEFDYTiGTRKAIYIpiPQSTPLYASIDWEHCIGCRLCEKACE 302
                                       69999866999***9999997644267777777554555567789***************5 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.17
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       +Ci+Cg C+++C ++++   ++k ++                 ++C+ Cg C+++CP 
  gi|488599885|ref|YP_007906356.1| 575 KCIGCGICRRVCRFNAISMVDKKAFVDS---------------NSCVMCGICVSACPV 617
                                       69********999988866655555544...............79***********96 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   8.1e-06    0.0044       3      37 ..     143     177 ..     141     182 .. 0.92
   2 ?   -1.7   0.0       1.6   8.7e+02      96     147 ..     180     231 ..     175     237 .. 0.79
   3 ?   -3.0   0.0       4.1   2.2e+03     116     164 ..     438     490 ..     435     502 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.1e-06
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                        +viGgG AG+ aA+++a+ g +V l+ek +++g 
  gi|488599885|ref|YP_007906356.1| 143 ALVIGGGIAGIEAALNIADSGIKVYLVEKRPTIGG 177
                                       68****************************99985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                                       -STTEEEETT.-CHHHHHHHHHHH.HHHT-EEE-S--EEEEECETTE.EEEEE CS
                       HI0933_like  96 edsgrlFpvsdkaedivdallkel.keagvklrletevksvekeedgkfrvkt 147
                                        +   +Fp++d +  i+   ++e+ ++ ++++ ++ evksv+ +++  frv++
  gi|488599885|ref|YP_007906356.1| 180 ATLNEVFPTNDCSICILAPKMSEVwNHPNIEVITSAEVKSVTGSSGD-FRVSV 231
                                       566789****999999987666652779*************765544.88876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.1
                                       HHHHHHHT-EEE-S--EEEEECETTE.EEEEE......TTEEEEESEEEE---- CS
                       HI0933_like 116 lkelkeagvklrletevksvekeedgkfrvktk.....seeeleadklvlAtGG 164
                                        ++++e+gv++ ++ +v+++ + edg++ ++++     + ee e d +vlA+G 
  gi|488599885|ref|YP_007906356.1| 438 FRRVQEKGVRF-VRARVADIIEVEDGNLLLNYEntlsgEYEEKEFDLVVLAVGM 490
                                       56788888887.577889998889999999885344444566777888888885 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   0.1    0.0003      0.16       3      64 ..     144     206 ..     143     224 .. 0.73
   2 ?    4.0   0.0      0.04        22      88     121 ..     432     465 ..     417     495 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsl...lfpnnyvWsdefedlgaleecvehsWsg 64 
                                       +viG+G Ag+  A ++  a  g+kv l+e  p +   + + n v    +  +  l+  ++ +W++
  gi|488599885|ref|YP_007906356.1| 144 LVIGGGIAGIEAALNI--ADSGIKVYLVEKRPTIgghMATLNEVFPTNDCSICILAPKMSEVWNH 206
                                       69**************..99*********998762224444555555555555577777777765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.04
                     Lycopene_cycl  88 rlkeellerlvengvklleakvesveeeeagesl 121
                                       r+ ee  +r+ e+gv++++a+v+ + e+e+g+ l
  gi|488599885|ref|YP_007906356.1| 432 RMYEEFFRRVQEKGVRFVRARVADIIEVEDGNLL 465
                                       68889999********************998765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.6e-05    0.0085      12      58 ..     135     180 ..     125     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                                       HHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                              Thi4  12 llkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58 
                                       ++k ++   +++G+G +G+ aa  +a + ++kv ++e++ ++GG + 
  gi|488599885|ref|YP_007906356.1| 135 VDKPVKKSALVIGGGIAGIEAALNIADS-GIKVYLVEKRPTIGGHMA 180
                                       56667777899*****************.***************875 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 ?   -0.2   0.9       3.2   1.7e+03       2      19 ..     237     255 ..     237     264 .. 0.67
   2 !   11.3   0.5   0.00083      0.45       3      25 ..     286     309 ..     285     326 .. 0.85
   3 !   12.8   1.5   0.00027      0.15       3      18 ..     571     586 ..     570     597 .. 0.87
   4 ?    6.6   3.6     0.024        13       2      19 ..     599     616 ..     598     635 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.2
                           Fer4_15   2 vvDrdaCigcg.lCvaeap 19 
                                       +vD ++C gc   C  ++p
  gi|488599885|ref|YP_007906356.1| 237 YVDTSKCKGCIdDCSSVCP 255
                                       5889999998424555554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00083
                           Fer4_15   3 vDrdaCigcglCvaea.pevfeld 25 
                                       +D++ Cigc lC +++ pe + ++
  gi|488599885|ref|YP_007906356.1| 286 IDWEHCIGCRLCEKACePEAIDFN 309
                                       9**************977777665 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00027
                           Fer4_15   3 vDrdaCigcglCvaea 18 
                                       vDrd+Cigcg C +++
  gi|488599885|ref|YP_007906356.1| 571 VDRDKCIGCGICRRVC 586
                                       9***********9988 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.024
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       +vD + C +cg Cv ++p
  gi|488599885|ref|YP_007906356.1| 599 FVDSNSCVMCGICVSACP 616
                                       59**************98 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.19     1e+02     143     213 ..      71     162 ..      42     178 .. 0.67
   2 ?   -2.7   0.0       4.7   2.6e+03     322     341 ..     310     329 ..     306     330 .. 0.78
   3 !   10.4   0.0   0.00047      0.26     279     340 ..     432     490 ..     421     492 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.19
                       K_oxygenase 143 eeeelearnlvlgvGtepkiPevleklegkervvHsseylerkee......................llakkriaVv 197
                                       + +e++ rn+ l  G +p++  +++  +++  +vHs +    + +                      +  kk+ +V+
  gi|488599885|ref|YP_007906356.1|  71 KLHEHTFRNVALRAGINPYMVVMANI-REQCSWVHSRTPQLATIKakdlirmavakarelkplervdKPVKKSALVI 146
                                       55666777777777777777666554.33566777764333222224666677777777777776666778999999 PP

                       K_oxygenase 198 GsGqSaaeifedllrr 213
                                       G+G  + e + +++++
  gi|488599885|ref|YP_007906356.1| 147 GGGIAGIEAALNIADS 162
                                       9999999999888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.7
                       K_oxygenase 322 esgeeetlevdavvlATGYr 341
                                       ++ ee +++v ++++ATG++
  gi|488599885|ref|YP_007906356.1| 310 QKAEEIEINVGTIIVATGFK 329
                                       556677888999******97 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00047
                       K_oxygenase 279 elyeelyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGY 340
                                       ++yee++++   +e+ +r+++  +v ++ + ++g++ l+++n+ sge e+ e+d vvlA G 
  gi|488599885|ref|YP_007906356.1| 432 RMYEEFFRRV--QEKGVRFVR-ARVADIIEVEDGNLLLNYENTLSGEYEEKEFDLVVLAVGM 490
                                       3444444332..355677776.568888888889*************************996 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001     0.056       1      33 [.     150     182 ..     150     184 .. 0.95
   2 ?   -1.4   0.0         2   1.1e+03     227     264 ..     449     492 ..     433     502 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EE CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtv 33 
                                       +aG+ aA   ++ G +V ++E r+ +GG+++t 
  gi|488599885|ref|YP_007906356.1| 150 IAGIEAALNIADSGIKVYLVEKRPTIGGHMATL 182
                                       89****************************995 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                       TSEEEEEEEE.ETTCEEEEETTSTEE.....EESEEEE-S-HHH CS
                     Amino_oxidase 227 lntrVkeikr.egdgvtvtledgevv.....eaDaVvvTvplgv 264
                                       +++rV +i   e++   +++e+  +      e+D Vv++v + +
  gi|488599885|ref|YP_007906356.1| 449 VRARVADIIEvEDGNLLLNYENTLSGeyeekEFDLVVLAVGMEA 492
                                       6788888888666668888886666666689********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 ?   13.8   0.0   4.9e-05     0.026      31      63 ..     143     175 ..     135     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrpar 63 
                                        lviGgG+aG++A+ + +  g kV+++++rp+ 
  gi|488599885|ref|YP_007906356.1| 143 ALVIGGGIAGIEAALNIADSGIKVYLVEKRPTI 175
                                       69***************************9976 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 ?    2.1   0.8      0.54   2.9e+02       1      17 [.     238     255 ..     238     281 .. 0.88
   2 ?    7.3   1.5     0.013         7       1      16 [.     286     301 ..     286     318 .. 0.83
   3 ?   13.4   2.5   0.00015     0.083       1      16 [.     571     586 ..     571     588 .. 0.95
   4 ?    8.4   4.5    0.0055         3       1      17 [.     600     616 ..     600     618 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.54
                           Fer4_13   1 VDrdtCiac.gaCvelaP 17 
                                       VD ++C +c + C +++P
  gi|488599885|ref|YP_007906356.1| 238 VDTSKCKGCiDDCSSVCP 255
                                       899999999788999998 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.013
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       +D + Ci+c +C +++
  gi|488599885|ref|YP_007906356.1| 286 IDWEHCIGCRLCEKAC 301
                                       7889**********99 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00015
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       VDrd+Ci+cg+C+ ++
  gi|488599885|ref|YP_007906356.1| 571 VDRDKCIGCGICRRVC 586
                                       9************999 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0055
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD ++C+ cg+Cv+++P
  gi|488599885|ref|YP_007906356.1| 600 VDSNSCVMCGICVSACP 616
                                       8***************9 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   7.1e-05     0.038       4      35 ..     143     174 ..     140     178 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                        l++G+G aG+ +al  +  G++v lvekr t
  gi|488599885|ref|YP_007906356.1| 143 ALVIGGGIAGIEAALNIADSGIKVYLVEKRPT 174
                                       69***************************975 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00047      0.26      36      85 ..      44      93 ..      10      95 .. 0.80
   2 ?   -2.4   0.0       8.6   4.7e+03      74      90 ..     134     151 ..     122     167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
                       B12-binding 36 anvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvv 85
                                       +  +e+i++ai++++ d +++Sa + + +e++ + v l+++i+p + v+
  gi|488599885|ref|YP_007906356.1| 44 SDSAQEEIINAIKEHNLDRIVVSACSPKLHEHTFRNVALRAGINPYMVVM 93
                                      34455*******************88888999999999999999977665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.6
                       B12-binding  74 l.lkrirprvkvvvGGah 90 
                                       +  k +++ + v+ GG++
  gi|488599885|ref|YP_007906356.1| 134 RvDKPVKKSALVIGGGIA 151
                                       247888888888888864 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4      0.21   1.1e+02      72      95 ..     233     257 ..     219     258 .. 0.82
   2 ?    6.3   0.2     0.031        17      76      93 ..     285     302 ..     276     305 .. 0.83
   3 ?    9.0   2.5    0.0046       2.5      72      93 ..     566     587 ..     544     590 .. 0.73
   4 ?    7.4   2.0     0.015         8      77      94 ..     600     617 ..     588     619 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.21
                           Fer4_22  72 efkekfgesgCvGC.gRCieacpvk 95 
                                       ++ + +++s+C GC   C+++cpv+
  gi|488599885|ref|YP_007906356.1| 233 KYPRYVDTSKCKGCiDDCSSVCPVE 257
                                       5566779999****668*****987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.031
                           Fer4_22  76 kfgesgCvGCgRCieacp 93 
                                       +++ ++C+GC  C++ac 
  gi|488599885|ref|YP_007906356.1| 285 SIDWEHCIGCRLCEKACE 302
                                       567789***********7 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0046
                           Fer4_22  72 efkekfgesgCvGCgRCieacp 93 
                                        + + +++ +C+GCg C ++c 
  gi|488599885|ref|YP_007906356.1| 566 PYFAFVDRDKCIGCGICRRVCR 587
                                       444455999************7 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.015
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       +++++Cv Cg C++acpv
  gi|488599885|ref|YP_007906356.1| 600 VDSNSCVMCGICVSACPV 617
                                       48899**********997 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2      0.01       5.4       3      34 ..     144     172 ..     142     189 .. 0.83
   2 ?    3.7   0.0      0.04        22     121     210 ..     394     491 ..     380     496 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                                       EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlvese 34 
                                       +++GGG+aG  aA  +a  +   ++v lve+ 
  gi|488599885|ref|YP_007906356.1| 144 LVIGGGIAGIEAALNIADSG---IKVYLVEKR 172
                                       69***************999...99****985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.04
                                       HHH-SCHHHHHTTB.-SB-TTS-B-S--EEEE-HHH....HHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEE CS
                    Trp_halogenase 121 dysleavaakakkf.sprekdglsalsyAyhldaal....yakfLrrvaearGvtrvegkvvevqldedgrveslrl 192
                                        y+ +   +++ k   + ++ +  +  y y +d +     y++f rr  +++Gv+ v+++v+++   edg+   l++
  gi|488599885|ref|YP_007906356.1| 394 RYCSRVCCMATLKNaFTIKERYPDSEIYVYYIDIRAfgrmYEEFFRR-VQEKGVRFVRARVADIIEVEDGNLL-LNY 468
                                       44443333333222023333334455688888876511115667766.5899***********9888888763.333 PP

                                       TT.....S-EEE-SEEEE-SGGG CS
                    Trp_halogenase 193 ed.....greveadlfiDcsGfr 210
                                       e+      +e e+dl++ + G++
  gi|488599885|ref|YP_007906356.1| 469 ENtlsgeYEEKEFDLVVLAVGME 491
                                       32333333456777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (781 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.90u 0.36s 00:00:01.26 Elapsed: 00:00:00.54
# Mc/sec: 4355.29
//
Query:       gi|488599886|ref|YP_007906357.1|  [L=385]
Description: phosphoserine phosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-22   79.7   0.0    5.1e-22   79.2   0.0    1.2  1  HAD              haloacid dehalogenase-like hydrolase
    9.1e-18   64.0   0.5      8e-13   48.2   0.2    2.5  2  ACT_6            ACT domain
    9.2e-18   65.3   3.1    4.3e-17   63.1   2.1    2.1  2  Hydrolase        haloacid dehalogenase-like hydrolase
    1.5e-15   56.6   5.8    1.5e-07   31.1   0.3    3.6  3  ACT              ACT domain
    2.9e-14   53.4   4.4    1.9e-10   40.9   3.7    3.1  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    2.3e-10   40.9   5.0    6.6e-06   26.6   0.5    3.0  3  ACT_4            ACT domain
    2.8e-09   36.7   0.1    2.7e-06   27.0   0.0    2.2  2  Put_Phosphatase  Putative Phosphatase
    4.9e-09   36.5   5.7    3.3e-06   27.3   0.5    2.8  3  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0018   18.0   0.1       0.29   10.9   0.1    3.0  3  ACT_7            ACT domain
  ------ inclusion threshold ------
      0.015   14.9   0.1       0.04   13.5   0.0    1.7  2  AA_kinase        Amino acid kinase family
      0.027   14.0   0.2        1.1    8.8   0.0    2.2  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 !   79.2   0.0   3.1e-25   5.1e-22       1     183 [.     173     336 ..     173     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 3.1e-25
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       ++fD+D T++d + +++l++ ++++      +++++ + +a+    ++ld +++ +   +ll+gl+ e l++  +++
  gi|488599886|ref|YP_007906357.1| 173 IVFDMDSTIVDAEIIDELAK-VAGV-----EEEVKRLTAKAM---EGELDFKSALKERVKLLKGLPvEVLEKIYNEI 240
                                       79**********77777777.4444.....456666666666...566666777788999******66666666666 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrge 152
                                                l+ ga+el++  ++ G+ v+vvSgg+++++ +l +elg d+  ++ele ++ rltg+  l g ++   
  gi|488599886|ref|YP_007906357.1| 241 K--------LTDGAKELIKSLKESGYVVAVVSGGFSYFTDRLKEELGLDYAFGNELEIENgRLTGR--LKGRIIDAV 307
                                       6........779******************************************************..********* PP

                               HAD 153 gkvaalrewlaaegegidleevvayGDspsD 183
                                       +k++ ++e   a++egi+ e++va+GD+ +D
  gi|488599886|ref|YP_007906357.1| 308 EKARIIEE--IAKKEGIAKENIVAVGDGAND 336
                                       ********..999999**************9 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.2   4.9e-16     8e-13       2      75 ..       3      78 ..       2      79 .. 0.95
   2 !   13.7   0.0   2.8e-05     0.046       4      47 ..      93     136 ..      90     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 4.9e-16
                             ACT_6  2 illitvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp..edalarlekaLlflakelgltvef 75
                                      ++ i+v+G dr G+++ +++vlae++vni+Dieq+v+ g ++  l  +++    +l +l ++L +  +e g++v++
  gi|488599886|ref|YP_007906357.1|  3 LIAISVYGLDRKGIVKNISGVLAENNVNIVDIEQSVLQGVFTMFLIADVSrcRIDLDELITQLKESGREVGVNVDV 78
                                      5679**********************************************8778*******************997 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.8e-05
                             ACT_6   4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgll 47 
                                       ++tv+G+d+ G++ +++s   e g+ni   ++    +  ++  +
  gi|488599886|ref|YP_007906357.1|  93 IVTVLGEDKVGIVHRISSFFYEMGINIERTNLTARDKLIAIDFV 136
                                       89************************987776655555555555 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.29   4.7e+02     106     139 ..      41      74 ..      17     108 .. 0.83
   2 !   63.1   2.1   2.6e-20   4.3e-17       2     210 .]     171     344 ..     170     344 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 106 ralavftiadplkvkpeaaeavasLkaagievvl 139
                                        +  +f iad  + + ++ e++ +Lk+ g ev++
  gi|488599886|ref|YP_007906357.1|  41 GVFTMFLIADVSRCRIDLDELITQLKESGREVGV 74 
                                       4667888889999999999*******99999887 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 2.6e-20
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78 
                                       +++vfD+d T+++ e     +i+++                     a+  ++++++++ ++     ++++g+ ++  
  gi|488599886|ref|YP_007906357.1| 171 RLIVFDMDSTIVDAE-----IIDEL---------------------AKVAGVEEEVKRLTA-----KAMEGELDFKS 216
                                       68*************.....*****.....................9**************.....*********** PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                       al               + r   l+   +  + +i +++k+ ++a+e+++sLk+ g+ v++++g+++ + +r+ ++l
  gi|488599886|ref|YP_007906357.1| 217 AL---------------KERVKLLKGLPVEVLEKIYNEIKLTDGAKELIKSLKESGYVVAVVSGGFSYFTDRLKEEL 278
                                       **...............88888887778888889999**************************************** PP

                                       T.GGGESEEEEHHCES..........STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       x.xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 G.ddyfdaviasdiet..........vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       G d +f +++++++             a  + ++ ++++++ ++ +e++++VGDg+nD  ++++Ag
  gi|488599886|ref|YP_007906357.1| 279 GlDYAFGNELEIENGRltgrlkgriiDAVEKARIIEEIAKKEGIAKENIVAVGDGANDKIMIENAG 344
                                       *88888888888888876655444433333888888888888899******************998 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.3   8.9e-11   1.5e-07       3      64 ..       6      67 ..       4      70 .. 0.90
   2 !   25.1   0.1   6.7e-09   1.1e-05       1      60 [.      92     149 ..      92     153 .. 0.82
   3 ?    1.4   0.1      0.17   2.8e+02      41      66 ..     169     194 ..     160     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 8.9e-11
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64
                                      ++v+  Dr+G+   ++g+la++++Ni+ ieq+     + ++ +  +  +  dl+e++ +lk+
  gi|488599886|ref|YP_007906357.1|  6 ISVYGLDRKGIVKNISGVLAENNVNIVDIEQSVLQGVFTMFLIADVSRCRIDLDELITQLKE 67
                                      88999*****************************9988888888888888888888888875 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 6.7e-09
                                       EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHH CS
                               ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevle 60 
                                       +++ v+ +D++G+ +r+++ + ++giNi++ + +  +      +++v+  d+e++++ ++
  gi|488599886|ref|YP_007906357.1|  92 YIVTVLGEDKVGIVHRISSFFYEMGINIERTNLTARDK--LIAIDFVVDLDDEGAKKKIK 149
                                       67899*************************99999987..67777777777766665554 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.17
                                       CEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  41 agivfvvivvdeedleevlealkkle 66 
                                        ++ +v++  ++ +++e++++l k++
  gi|488599886|ref|YP_007906357.1| 169 SKRLIVFDMDSTIVDAEIIDELAKVA 194
                                       578999999*************9986 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.33   5.3e+02       1      12 [.     173     184 ..     173     212 .. 0.85
   2 !    9.4   0.0    0.0005      0.81      15      72 ..     241     302 ..     236     308 .. 0.79
   3 !   40.9   3.7   1.2e-13   1.9e-10     186     255 .]     307     375 ..     303     375 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.33
                                       EEEEIIIIIS-T CS
                       Hydrolase_3   1 ialDlDGTLlns 12 
                                       i++D+D T+++ 
  gi|488599886|ref|YP_007906357.1| 173 IVFDMDSTIVDA 184
                                       89*******985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0005
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC....SEEEEGGGTEEECTTTE CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgld....lpvialNGaliddekgk 72 
                                       k+++ +ke ik lke g+ v++ +G   +++ ++ eelgld    + +   NG l+   kg+
  gi|488599886|ref|YP_007906357.1| 241 KLTDGAKELIKSLKESGYVVAVVSGGFSYFTDRLKEELGLDyafgNELEIENGRLTGRLKGR 302
                                       678999***********************************444433333888877555555 PP

  == domain 3  score: 40.9 bits;  conditional E-value: 1.2e-13
                                       -SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHHH CS
                       Hydrolase_3 186 vsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVakal 255
                                       v K+  ++++ak+ +i +e+++a+GDg ND  M+e aglg+A  na++ +k++Ad  + + n  G+a +l
  gi|488599886|ref|YP_007906357.1| 307 VEKARIIEEIAKKEGIAKENIVAVGDGANDKIMIENAGLGIAF-NAKKALKEVADGSISKENLIGIASVL 375
                                       89****************************************7.9***************9999999886 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.5   4.1e-09   6.6e-06       8      70 ..       5      66 ..       3      69 .. 0.89
   2 !   15.2   0.1   1.5e-05     0.025      10      58 ..      95     141 ..      91     153 .. 0.91
   3 ?   -3.1   0.0       7.7   1.3e+04      64      77 ..     185     198 ..     184     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.1e-09
                             ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdve.hLsrviakLr 70
                                       ++v++ drkg++++i+ v++e+++niv+++ +    +g++++ +   V+  + +L+++i++L+
  gi|488599886|ref|YP_007906357.1|  5 AISVYGLDRKGIVKNISGVLAENNVNIVDIEQSVL--QGVFTMFLIADVSRCRiDLDELITQLK 66
                                      699*******************************5..58******9999875438999999987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                             ACT_4  10 eveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkd 58 
                                       +v +ed+ g++ +i++ + e+++ni+  n+++  +d+l  i++ v + d
  gi|488599886|ref|YP_007906357.1|  95 TVLGEDKVGIVHRISSFFYEMGINIERTNLTA--RDKLIAIDFVVDLDD 141
                                       6899****************************..589*****9999877 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 7.7
                             ACT_4  64 rviakLraipgVis 77 
                                       ++i+ L ++ gV++
  gi|488599886|ref|YP_007906357.1| 185 EIIDELAKVAGVEE 198
                                       68999999999964 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.6e-09   2.7e-06       2     116 ..     172     284 ..     171     292 .. 0.89
   2 !    7.5   0.0    0.0014       2.3     151     182 ..     309     337 ..     302     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.6e-09
                   Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkgl..wnelmdrvlkelheqgvseadikkvlrsiplspgl 76 
                                       l+vfD D ti+d +  + + + ++ +e+ ++l ++  +g   +++ +++ +k l+  g   + ++k++++i l+ g 
  gi|488599886|ref|YP_007906357.1| 172 LIVFDMDSTIVDAEIIDELAKVAGVEEEVKRLTAKAMEGEldFKSALKERVKLLK--GLPVEVLEKIYNEIKLTDGA 246
                                       89******************************99887664338899999999996..56667899************ PP

                   Put_Phosphatase  77 velikslakkkleldliiiSDaNsffieeileaagledlF 116
                                        eliksl  k++++ + ++S   s+f + + e +gl   F
  gi|488599886|ref|YP_007906357.1| 247 KELIKSL--KESGYVVAVVSGGFSYFTDRLKEELGLDYAF 284
                                       *******..688****************999998888777 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0014
                   Put_Phosphatase 151 KgkvleelvaeqaregveyerliYvGDganDl 182
                                       K +++ee+ ++   eg++ e ++ vGDganD 
  gi|488599886|ref|YP_007906357.1| 309 KARIIEEIAKK---EGIAKENIVAVGDGANDK 337
                                       78899999888...89**************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 ?   -3.9   0.0       7.9   1.3e+04      84     100 ..      58      74 ..      56      75 .. 0.77
   2 !   27.3   0.5     2e-09   3.3e-06       1     122 [.     173     284 ..     173     287 .. 0.75
   3 !   10.9   0.2   0.00022      0.36     138     173 ..     310     345 ..     299     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.9
                             HAD_2  84 vkelLeeLkeagyklgi 100
                                       + el+ +Lke g ++g+
  gi|488599886|ref|YP_007906357.1|  58 LDELITQLKESGREVGV 74 
                                       67888899888888776 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2e-09
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkke 77 
                                       i+FD+D T++d e     ++ el++  g++e  +   +k ++ +l +  + l+e+    ++++ l  ++ e+ ++ e
  gi|488599886|ref|YP_007906357.1| 173 IVFDMDSTIVDAE-----IIDELAKVAGVEEEVKRLTAKAMEGEL-DFKSALKER---VKLLKGLPVEVLEKIYN-E 239
                                       89*********64.....566666666776444444455555555.222233333...23788888888888888.9 PP

                             HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyF 122
                                       +k+ dg+kel+++Lke gy +++v+ + +  +++  e+lg++  F
  gi|488599886|ref|YP_007906357.1| 240 IKLTDGAKELIKSLKESGYVVAVVSGGFSYFTDRLKEELGLDYAF 284
                                       ***************************999999999999998777 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00022
                             HAD_2 138 peviekaleklklkkeeviyvGDsptDieaakkagi 173
                                       +++ie++ +k ++ ke+++ vGD  +D +   +ag+
  gi|488599886|ref|YP_007906357.1| 310 ARIIEEIAKKEGIAKENIVAVGDGANDKIMIENAGL 345
                                       689***************************999997 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00018      0.29      16      39 ..      11      32 ..       2      37 .. 0.80
   2 ?    3.4   0.0      0.04        66       8      39 ..      93     120 ..      87     131 .. 0.79
   3 ?   -2.2   0.0       2.3   3.7e+03      25      47 ..     247     272 ..     243     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                      ---SS--HHHHHHHHHHTTT---E CS
                             ACT_7 16 lpfdvtGivaklaspLaeagIsif 39
                                      l  d  Giv+ ++++Lae++++i 
  gi|488599886|ref|YP_007906357.1| 11 L--DRKGIVKNISGVLAENNVNIV 32
                                      3..889****************96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.04
                                       EEEE-S-.---SS--HHHHHHHHHHTTT---E CS
                             ACT_7   8 klsvvgsglpfdvtGivaklaspLaeagIsif 39 
                                        ++v g+    d +Giv +++s   e gI+i 
  gi|488599886|ref|YP_007906357.1|  93 IVTVLGE----DKVGIVHRISSFFYEMGINIE 120
                                       5555566....99*****************95 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.3
                                       HHHHHHHHTTT---EEEE...-SS-E CS
                             ACT_7  25 aklaspLaeagIsifqiS...tyrtd 47 
                                       ++l++ L e g  + ++S   +y+td
  gi|488599886|ref|YP_007906357.1| 247 KELIKSLKESGYVVAVVSggfSYFTD 272
                                       67888888888888888888888887 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         2   3.2e+03     185     192 ..     174     181 ..     101     201 .. 0.60
   2 ?   13.5   0.0   2.5e-05      0.04      25      82 ..     248     309 ..     237     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                                       CESSTTTT CS
                         AA_kinase 185 Vydadpkk 192
                                       V+d d  +
  gi|488599886|ref|YP_007906357.1| 174 VFDMDSTI 181
                                       33444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC........E..HHHHHHHHHHHH CS
                         AA_kinase  25 eqiaalkesgnklvvVhGg.gsftdgllalksglssgelaa....glrstleeagevatrdal 82 
                                       e i+ lkesg+ ++vV+Gg + ftd+l ++  gl+  + ++      r+t   +g ++  ++ 
  gi|488599886|ref|YP_007906357.1| 248 ELIKSLKESGYVVAVVSGGfSYFTDRLKEE-LGLDYAFGNEleieNGRLTGRLKGRIIDAVEK 309
                                       568999999*********************.****9999988888444444444444444333 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.036        58       2      29 ..     170     195 ..     169     215 .. 0.83
   2 ?    8.8   0.0   0.00065       1.1     166     212 ..     309     354 ..     304     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.036
                                       SEEEEE-TBTTTB.S-HHHHHHHHHHHH CS
                              S6PP   2 klllvsdLDntlvdgdnealarlnelle 29 
                                       k+l+v d+D+t+v  d+e +++l ++  
  gi|488599886|ref|YP_007906357.1| 170 KRLIVFDMDSTIV--DAEIIDELAKVAG 195
                                       689**********..8888888887765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00065
                                       HHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HH CS
                              S6PP 166 kgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqee 212
                                       k++ ++ +akk ++  e+i+ +Gd  nD+ ++++  lg+   na+++
  gi|488599886|ref|YP_007906357.1| 309 KARIIEEIAKKEGIAKENIVAVGDGANDKIMIENAGLGIAF-NAKKA 354
                                       6666777889999*******************999999875.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.35s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2223.79
//
Query:       gi|488599887|ref|YP_007906358.1|  [L=175]
Description: Transcription factor E (TFE) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-28   98.2   3.9    2.2e-28   98.2   3.9    1.6  2  TFIIE_alpha     TFIIE alpha subunit
     0.0028   17.7   1.3      0.033   14.3   0.1    2.4  2  Sigma70_r3      Sigma-70 region 3
  ------ inclusion threshold ------
      0.019   14.8   0.2      0.058   13.3   0.0    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.022   14.3   0.0      0.036   13.6   0.0    1.4  1  MazG_C          MazG C-terminal domain
      0.068   12.8   0.0       0.17   11.6   0.0    1.6  1  GntR            Bacterial regulatory proteins, gntR family
        0.1   12.3   1.2       0.31   10.8   0.9    2.0  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.11   12.6   0.0       0.23   11.6   0.0    1.6  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.11   12.5   0.4       0.22   11.5   0.4    1.5  1  Fer2_3          2Fe-2S iron-sulfur cluster binding domain
        2.7    7.9   5.2         31    4.5   0.3    3.3  3  Rad50_zn_hook   Rad50 zinc hook motif


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 !   98.2   3.9   1.1e-31   2.2e-28       1     104 [.       7     109 ..       7     110 .. 0.98
   2 ?   -2.2   0.1       1.9   3.8e+03      42      44 ..     159     161 ..     146     173 .. 0.43

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.1e-31
                                       HHHHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEE CS
                       TFIIE_alpha   1 ellkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrin 77 
                                       el++e++ +++g e+ lv+  L  + e+t+e++++el+i++ne+rk+L+ Lye+++++y+r+rdee++w++yyw+in
  gi|488599887|ref|YP_007906358.1|   7 ELIAELIERVAG-EVGLVVYTLRPQREFTDEEISQELGIEINEVRKALFSLYEIGIAEYRRKRDEETGWMEYYWKIN 82 
                                       79**********.9*************************************************************** PP

                                       CCCHCCCHHHHHHHHHHHHHHHHCCCT CS
                       TFIIE_alpha  78 yeklvdvvkrkleevvkkLeeklekee 104
                                       y++  d+v r+l ++ +kLe kle e+
  gi|488599887|ref|YP_007906358.1|  83 YDRERDIVLRELLKTKRKLEAKLEMED 109
                                       ************************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                                       HHH CS
                       TFIIE_alpha  42 nel 44 
                                       +++
  gi|488599887|ref|YP_007906358.1| 159 EKI 161
                                       222 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.7e-05     0.033      18      41 ..      30      53 ..      27      73 .. 0.90
   2 ?    1.7   0.2      0.14   2.8e+02       3      18 ..      91     106 ..      90     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                      SSXXXHHHHHHHHTXXHHHHHHHH CS
                        Sigma70_r3 18 grePtpeEiAeeLglseekVrevl 41
                                      +re t+eEi +eLg+++++Vr++l
  gi|488599887|ref|YP_007906358.1| 30 QREFTDEEISQELGIEINEVRKAL 53
                                      58889****************998 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHS CS
                        Sigma70_r3   3 lnkikraqreLeqelg 18 
                                       l+++ +++r+Le +l+
  gi|488599887|ref|YP_007906358.1|  91 LRELLKTKRKLEAKLE 106
                                       78999********996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.9e-05     0.058      21      58 ..      31      68 ..      23      83 .. 0.86
   2 ?   -2.1   0.0       1.9   3.8e+03      24      40 ..      97     113 ..      90     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       + t +ei++elg++ + v ++L sL + G+ e +++r
  gi|488599887|ref|YP_007906358.1| 31 REFTDEEISQELGIEINEVRKALFSLYEIGIAEYRRKR 68
                                      67899**************************9988776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                       HHCHHCCCTTSSCHCHH CS
                              TrmB  24 tadeiaeelgvprskvY 40 
                                       t +++  +l+ + s vY
  gi|488599887|ref|YP_007906358.1|  97 TKRKLEAKLEMEDSAVY 113
                                       66777778888888888 PP

>> MazG_C  MazG C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.8e-05     0.036      77     123 ..      90     135 ..      88     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                            MazG_C  77 vlRaLlkrKRksdpkvdeaeDggRaivieEgisalvfseakelelfe 123
                                       vlR+Llk+KRk ++k+ e eD++   +   g +++ ++ a e++++ 
  gi|488599887|ref|YP_007906358.1|  90 VLRELLKTKRKLEAKL-EMEDSAVYYICINGCVKVKYEAAMEMNFMC 135
                                       89**********9998.6899999999999999999****9998875 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.17      19      59 ..      28      67 ..      22      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                                      -TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 19 rpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      rp     + +e+++e+g+  + vR+AL  L + g++e r++
  gi|488599887|ref|YP_007906358.1| 28 RPQREF-TDEEISQELGIEINEVRKALFSLYEIGIAEYRRK 67
                                      555556.779*************************998876 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 ?   10.8   0.9   0.00016      0.31      32      52 ..     118     140 ..     108     142 .. 0.89
   2 ?   -1.7   0.0       1.3   2.6e+03       2      10 ..     161     169 ..     161     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                    zinc_ribbon_10  32 nGlap..keeleevkyrCpkCga 52 
                                       nG+++   e++ e+++ Cp Cga
  gi|488599887|ref|YP_007906358.1| 118 NGCVKvkYEAAMEMNFMCPRCGA 140
                                       9***9867778899*******97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                    zinc_ribbon_10   2 fDrvldvLv 10 
                                       +D+++++L+
  gi|488599887|ref|YP_007906358.1| 161 IDKMISYLM 169
                                       59*****98 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 ?   11.6   0.0   0.00011      0.23      11      27 ..     127     143 ..      97     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                          zf-Mss51  11 apkhvdfeCpdCGipty 27 
                                       a  +++f Cp+CG p  
  gi|488599887|ref|YP_007906358.1| 127 AAMEMNFMCPRCGAPLD 143
                                       66789*********975 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   0.4   0.00011      0.22       4      58 ..      61     117 ..      58     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                            Fer2_3   4 vkRfdprrdrgkqkvqey.eveae.eedtvldaLlkikeevdptlafrasCregiCG 58 
                                       +  ++++rd+++ +++ y +++++ e+d vl+ Llk k++++ +l  + s    iC 
  gi|488599887|ref|YP_007906358.1|  61 IAEYRRKRDEETGWMEYYwKINYDrERDIVLRELLKTKRKLEAKLEMEDSAVYYICI 117
                                       667888899999999988689999899*******************99999999994 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       2.6   5.2e+03      31      39 ..       5      14 ..       2      16 .. 0.52
   2 ?    4.0   0.1     0.022        44      26      42 ..      30      47 ..      30      54 .. 0.83
   3 ?    4.5   0.3     0.015        31      22      42 ..     135     159 ..     130     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                                      HHH.HHHHHH CS
                     Rad50_zn_hook 31 eeh.rseLik 39
                                      +++  +eLi+
  gi|488599887|ref|YP_007906358.1|  5 SDElIAELIE 14
                                      5555555554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.022
                                      --EE-HHH.HHHHHHHHH CS
                     Rad50_zn_hook 26 gReldeeh.rseLikelq 42
                                      +Re+++e+  +eL  e++
  gi|488599887|ref|YP_007906358.1| 30 QREFTDEEiSQELGIEIN 47
                                      79******9999977765 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.015
                                       -TTT--EE-...HHH.HHHHHHHHH CS
                     Rad50_zn_hook  22 CPlCgReld...eeh.rseLikelq 42 
                                       CP Cg +ld   +   +++L++e++
  gi|488599887|ref|YP_007906358.1| 135 CPRCGAPLDyldSTVaKEKLMEEIE 159
                                       *******973323335777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1026.73
//
Query:       gi|488599888|ref|YP_007906359.1|  [L=420]
Description: hypothetical protein Asulf_00334 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-12   47.2   0.6    2.3e-12   47.2   0.6    2.6  3  Toprim_4  Toprim domain
    1.5e-06   28.5   0.0    3.6e-06   27.3   0.0    1.6  1  Toprim_2  Toprim-like
      0.007   16.6   0.2      0.007   16.6   0.2    3.0  3  Toprim    Toprim domain
  ------ inclusion threshold ------
       0.12   11.3   7.1      0.081   11.9   4.0    1.9  2  DUF3818   Domain of unknown function in PX-proteins (DUF3818)
       0.95    9.8   8.0       0.16   12.3   0.9    3.3  3  Mnd1      Mnd1 HTH domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   4.3e+03      25      49 ..      86     111 ..      82     125 .. 0.64
   2 !   47.2   0.6   6.5e-16   2.3e-12       2      76 ..     175     258 ..     174     274 .. 0.85
   3 ?   -3.1   0.0       3.3   1.2e+04      11      38 ..     360     387 ..     358     397 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                          Toprim_4  25 avlggalspldgirpeklkt.enlve 49 
                                       a+l  al++ + ++p   k+  +++e
  gi|488599888|ref|YP_007906359.1|  86 AILAAALETIERVGPCTAKIkIKKIE 111
                                       66778888888888877777434333 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 6.5e-16
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGe 68 
                                       +ii+VEg+aDvl+l k+gi+nv+av g+++ p+  i+++k+kt +++++    ++ ++ke++++ + D+     eG+
  gi|488599888|ref|YP_007906359.1| 175 AIIVVEGRADVLNLLKCGIRNVIAVEGTNV-PKTIIELSKKKTvTAFLDgdrgGDLILKELLQVAEIDYvakapEGK 250
                                       79****************************.************999999****9**************977777776 PP

                          Toprim_4  69 ataerlae 76 
                                        + +   +
  gi|488599888|ref|YP_007906359.1| 251 GVEDLTQK 258
                                       66655555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.3
                          Toprim_4  11 Dvlaleka.giknvvavlggalspldgir 38 
                                       D+++  k+  ik+   v +g + ++  i 
  gi|488599888|ref|YP_007906359.1| 360 DLVKTLKTnNIKGDTIVFDGVI-TQRVID 387
                                       7777778888888888888877.776665 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     1e-09   3.6e-06       1      84 [.     177     250 ..     177     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1e-09
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvreki 77 
                                       +v+Eg  D+l l++ gi+   nv+a+ Gt + ++ + +l+++  k+v   lD D+ G+   k+l ++++     + +
  gi|488599888|ref|YP_007906359.1| 177 IVVEGRADVLNLLKCGIR---NVIAVEGT-NVPKTIIELSKK--KTVTAFLDGDRGGDLILKELLQVAEI----DYV 243
                                       69***************8...********.555555566666..689999**********9999998852....345 PP

                          Toprim_2  78 relpegk 84 
                                       ++ pegk
  gi|488599888|ref|YP_007906359.1| 244 AKAPEGK 250
                                       5566555 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3      0.43   1.5e+03      38      65 ..     128     155 ..      23     157 .. 0.61
   2 !   16.6   0.2   1.9e-06     0.007       2      92 ..     176     244 ..     175     255 .. 0.86
   3 !    5.9   0.6    0.0041        15      64      92 ..     215     244 ..     212     316 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.43
                                       TTEEEEEECTTTHHHHHHHHHHHHHHSE CS
                            Toprim  38 efkpvyeeiedkkkvlkalkelakrade 65 
                                        +k  +ee e + +++++l ++a ra+e
  gi|488599888|ref|YP_007906359.1| 128 MLKSLFEEPEIESEKIGELVRQAARAEE 155
                                       2222223555555555555555555555 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.9e-06
                                       EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHH CS
                            Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGea 78 
                                       +++vEg +d+ ++ k    g  +v+a+ G+ +  +                      ++++ + +   +D+Dr G  
  gi|488599888|ref|YP_007906359.1| 176 IIVVEGRADVLNLLKC---GIRNVIAVEGTNVPKTI--------------------IELSKKKTVTAFLDGDRGGDL 229
                                       89**************...9*********9998877....................556677889999********* PP

                                       HHHHHHHHHT.HHHT CS
                            Toprim  79 iawellevlk.elle 92 
                                       i +ell+v++ +++ 
  gi|488599888|ref|YP_007906359.1| 230 ILKELLQVAEiDYVA 244
                                       *******99865554 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0041
                                       SEEEEECSSSHHHHHHHHHHHHHHT.HHHT CS
                            Toprim  64 deiilatDpDreGeaiawellevlk.elle 92 
                                       + +   +D+Dr G  i +ell+v++ +++ 
  gi|488599888|ref|YP_007906359.1| 215 KTVTAFLDGDRGGDLILKELLQVAEiDYVA 244
                                       4566679**************999865554 PP

>> DUF3818  Domain of unknown function in PX-proteins (DUF3818)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0     0.099   3.5e+02     207     236 ..     109     138 ..      79     158 .. 0.79
   2 ?   11.9   4.0   2.3e-05     0.081     144     238 ..     258     354 ..     228     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.099
                           DUF3818 207 lfedlkellklylrerDkellikllqepel 236
                                        +ed++   +  + er ke+l++l +epe+
  gi|488599888|ref|YP_007906359.1| 109 KIEDVRATKRKKIVERAKEMLKSLFEEPEI 138
                                       456666666777788889999999999887 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.3e-05
                           DUF3818 144 qeeireeseeekl.dllvvilrseelpklske..qleeviesykaykeakkeeksasekeenedaelfedlkellkl 217
                                       +e +++  ++  + ++ ++ +r +++++l++e  +++e++e  +   ea+++ek+++ +ee+e+ + f d kel++ 
  gi|488599888|ref|YP_007906359.1| 258 KEIVKALRNKVPVeQIHLIKMRDSKSKRLEREkdEVKEIKEIRETR-EAEEKEKAEEAEEEKEEGKKFFDPKELFRK 333
                                       4444444444445466667788889999998877899998886666.555666666777778888889********* PP

                           DUF3818 218 ylrerDkellikllqepelse 238
                                         re + +l+  +l++++l +
  gi|488599888|ref|YP_007906359.1| 334 HKREVEGKLIARILENDTLVK 354
                                       ****************99975 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.9   4.5e-05      0.16      20      52 ..     114     145 ..     102     147 .. 0.81
   2 ?   -1.0   0.0      0.64   2.3e+03      21      40 ..     246     265 ..     241     272 .. 0.77
   3 ?   -1.0   0.2      0.62   2.2e+03      18      39 ..     344     365 ..     319     370 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                              Mnd1  20 lapkekgivsqsVkdvlqsLvdDglveveKiGs 52 
                                       +a+k k+iv+   k++l+sL ++  +e+eKiG 
  gi|488599888|ref|YP_007906359.1| 114 RATKRKKIVER-AKEMLKSLFEEPEIESEKIGE 145
                                       46678887765.6*******************6 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.64
                              Mnd1  21 apkekgivsqsVkdvlqsLv 40 
                                       ap  kg+   + k+++++L 
  gi|488599888|ref|YP_007906359.1| 246 APEGKGVEDLTQKEIVKALR 265
                                       66678888888899999885 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.62
                              Mnd1  18 eklapkekgivsqsVkdvlqsL 39 
                                        ++++  + +++  V+d+++ L
  gi|488599888|ref|YP_007906359.1| 344 ARILENDTLVKEIPVRDLVKTL 365
                                       3334444445555566666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2294  (0.127949); expected 358.6 (0.02)
Passed bias filter:                      915  (0.0510346); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
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: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.52
# Mc/sec: 2448.67
//
Query:       gi|488599889|ref|YP_007906360.1|  [L=336]
Description: putative permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-32  111.7  42.2    4.1e-32  111.7  42.2    1.6  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 !  111.7  42.2   2.3e-36   4.1e-32       2     236 .]      56     325 ..      54     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 2.3e-36
                              TauE   2 llagllaGfvagllGiGggliavPlLlll..lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliG 76 
                                       l++  ++G++a l+G+Ggg+i++Pl+l +  ++  ++ +t l+++++++l++a  +++rg  ++rll++ +++ +  
  gi|488599889|ref|YP_007906360.1|  56 LVVSTVIGMIAVLAGVGGGVIFTPLMLGFtpIDSLIVRGTGLFVAMTGALVAARPFLKRGLANIRLLYFSAVPYATF 132
                                       678899******************99887455777788******************************999999999 PP

                              TauE  77 allGallllllpsel.......lkllfgvlllllallmllrkkr.........................srakgrer 121
                                       a++Gall+ ++++++       ++l +g+l++l+a l+l+  +r                         s ++ +++
  gi|488599889|ref|YP_007906360.1| 133 AVIGALLAVYIKQTMgqtgeayVRLGLGILVVLIASLFLFAGNRieypevrqvdsftrrvglamayweeSLGRVVQY 209
                                       9999999999997755566666****************99777779*******999999999998877733334455 PP

                              TauE 122 rptaillvliggl.vGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllll 197
                                       + t+ +l+l+ ++ vGl+sGl+G G+G  +vp+l l++  plk+a+a+s +li +   a+++ y+++g + + ++++
  gi|488599889|ref|YP_007906360.1| 210 EVTRSWLGLVLFAgVGLVSGLFGLGAGWAMVPVLNLVMMAPLKVAAASSKVLIGIGDTAAIWPYIMQGTIFPLFAVP 286
                                       55555566666667*************************************************************** PP

                              TauE 198 llpgallGallGarlarrlsertlrrlfallllvlgvkl 236
                                        ++g +lG+++Ga+++ ++++  +r +++++++++g++l
  gi|488599889|ref|YP_007906360.1| 287 CMIGLILGTMIGAKIMLKVKAGFIRYIIIVIMFLSGARL 325
                                       ************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2430.67
//
Query:       gi|488599890|ref|YP_007906361.1|  [L=146]
Description: hypothetical protein Asulf_00336 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-06   26.4   2.9    1.5e-05   25.0   2.9    1.6  1  DUF1634        Protein of unknown function (DUF1634)
  ------ inclusion threshold ------
      0.099   12.5   9.0      0.054   13.4   2.3    2.0  2  7TMR-DISM_7TM  7TM diverse intracellular signalling
        8.7    6.0   8.4         24    4.6   8.4    1.6  1  Tetraspanin    Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   2.9   2.4e-09   1.5e-05       6     101 ..      25     138 ..      21     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.4e-09
                           DUF1634   6 riGvllsaavvllGlilllvkhgs.............se.....senseltslseilegllelk.glaiiqlGllvL 63 
                                        + vl+  ++ l+G++++l+++++             +e      e+    ++++  + l++l+ g +i +lG+ + 
  gi|488599890|ref|YP_007906361.1|  25 YWVVLIGTIISLIGVMMILTTDSNyidsncllsglwgKEkpseiWEKCAGGHPEGH-WYLSRLStGDGIAMLGIALS 100
                                       5889*******************666666666655541133322222222223333.344444448899******** PP

                           DUF1634  64 iatPvlrVvlsliaFlkekdilyviitliVLliLllsl 101
                                        +  v+ V +s +a l++k+il+ i++l+  +iL+ s+
  gi|488599890|ref|YP_007906361.1| 101 CLAAVIGVWASSFAMLRDKEILFFIFALVTAIILTASA 138
                                       ***************************99999999885 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 ?    3.3   0.6     0.011        64     152     180 ..      25      53 ..      14      60 .. 0.62
   2 ?   13.4   2.3     9e-06     0.054       4      52 ..      94     142 ..      92     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.011
                     7TMR-DISM_7TM 152 aryfliawlllligvlidilsllgllpsn 180
                                        +  li+ ++ ligv++ + +  ++++sn
  gi|488599890|ref|YP_007906361.1|  25 YWVVLIGTIISLIGVMMILTTDSNYIDSN 53 
                                       45566777777777777554444466555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9e-06
                     7TMR-DISM_7TM   4 lqglllGvllalalynlflffslrdksylyYalyllsfllyllslngll 52 
                                       ++g+ l +l+a++    + f +lrdk+ l++++ l++ +++++s +g++
  gi|488599890|ref|YP_007906361.1|  94 MLGIALSCLAAVIGVWASSFAMLRDKEILFFIFALVTAIILTASATGII 142
                                       5799999*************************************99986 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   8.4    0.0039        24       3      95 ..      25     139 ..      23     145 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0039
                                       XXXXXXXXXXXXXXXXXXXX.............XXXXXX............XXX.....................XX CS
                                       xxxxxxxxxxxxxxxxxxxx.............xxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin   3 yllfffnllfwligivllav.............Gvwlrl............khaeaalacllsesaedpailailli 54 
                                       y ++++  ++ lig++++               G+w +             +  e      + +  +  + +a+l i
  gi|488599890|ref|YP_007906361.1|  25 YWVVLIGTIISLIGVMMILTtdsnyidsncllsGLWGKEkpseiwekcaggH-PEGH---WYLSRLSTGDGIAMLGI 97 
                                       6677777788888888887777777777777776666664444333333321.1111...11122333444455566 PP

                                       XXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  55 vvGvllfllgflG.cigalkenkcllltfsllllvlfllela 95 
                                       ++++l +++g+    +++l+++ +l ++f+l+  +++ +  +
  gi|488599890|ref|YP_007906361.1|  98 ALSCLAAVIGVWAsSFAMLRDKEILFFIFALVTAIILTASAT 139
                                       666666666665557778888888888888888777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); 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:                         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 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 979.60
//
Query:       gi|488599891|ref|YP_007906362.1|  [L=149]
Description: Lactoylglutathione lyase-related lyase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   46.7   0.0    4.5e-12   46.2   0.0    1.2  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    9.8e-11   42.0   0.0    1.4e-10   41.4   0.0    1.3  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.4e-08   34.3   0.0      4e-08   33.6   0.0    1.3  1  Glyoxalase_3  Glyoxalase-like domain
    9.4e-05   22.6   0.0    0.00014   22.1   0.0    1.3  1  Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-term
  ------ inclusion threshold ------
      0.011   14.7   0.0      0.014   14.4   0.0    1.1  1  Phytase       Phytase
      0.022   15.5   0.0      0.029   15.2   0.0    1.2  1  Glyoxalase_6  Glyoxalase-like domain
      0.059   13.3   0.1       0.12   12.2   0.1    1.7  1  DUF4252       Domain of unknown function (DUF4252)


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   1.8e-15   4.5e-12       1     102 [.       9     109 ..       9     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.8e-15
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT....-THHHTS-EEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp....eflaehgeglhhla 73 
                                       d++ ++V+D e+a+++fs+llG+++ ++ +++ ++++ ++   g     +eL  p +++    +f++++gegl  l 
  gi|488599891|ref|YP_007906362.1|   9 DHVVVAVKDAEKAMRFFSELLGIEFDEIGEERNWKFKSYMSPEG-----LELLVPTSEDsetaKFIEKRGEGLFALS 80 
                                       69**************************9888777777666555.....5666666655555699999********* PP

                                       EEES-HHHHHHHHCTTTEEEEEEEE-GGG CS
                      Glyoxalase_4  74 ywvddldaavarleeqGfevvqkgvraga 102
                                       + v+d +++ +++ee G++++ k  r+g 
  gi|488599891|ref|YP_007906362.1|  81 FKVSDAEKIAKKAEEMGIRIIGKIEREGF 109
                                       *******************9998777776 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 !   41.4   0.0   5.6e-14   1.4e-10       1     126 [.       7     124 ..       7     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.6e-14
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       +idhv+++v+d+ek+++F+ + LG +  +  +    +  +++    + +g   lv  + +s  ak+    e+ ++++
  gi|488599891|ref|YP_007906362.1|   7 KIDHVVVAVKDAEKAMRFFSELLGIEFDEIGE----ERNWKFKSYMSPEGLELLVPTSEDSETAKFI---EKRGEGL 76 
                                       69***********************9988888....5555555555555555566666666666666...34789** PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGill 126
                                         + ++v d +k  ++++e g+++ ++++r++f+ ++ +  +D +Gi +
  gi|488599891|ref|YP_007906362.1|  77 FALSFKVSDAEKIAKKAEEMGIRIIGKIEREGFKEIFLH-PKDCFGIQI 124
                                       ************************************966.999999976 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.6e-11     4e-08       1     101 [.       8      99 ..       8     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.6e-11
                      Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdgYlEllavdpeapaperprlfgldrlakgeg 77 
                                       +DHvv+av+d e+a++ f + lG+++++ ge   +  + ++ +     lEll +  e  +    + f  +   +geg
  gi|488599891|ref|YP_007906362.1|   8 IDHVVVAVKDAEKAMRFFSELLGIEFDEIGEERNWKFKSYMSPE---GLELLVPTSEDSE---TAKFIEK---RGEG 75 
                                       7*********************************9999877664...49***96444443...2345433...59** PP

                      Glyoxalase_3  78 lhtlalrtddidataarlraaGvd 101
                                       l +l ++++d+++ a+++++ G+ 
  gi|488599891|ref|YP_007906362.1|  76 LFALSFKVSDAEKIAKKAEEMGIR 99 
                                       *******************99975 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 !   22.1   0.0   5.3e-08   0.00014      13      97 ..      11      99 ..       4     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.3e-08
                      Glyoxalase_5 13 vefaapeaealeelfek.lG..ftavarhrskdvtlyrq.GginfilneepdsaaakfarehGpsacalafrvkdakka 87
                                      v  a ++ae+  ++f++ lG  f+++ + r+ + + y    g+++++ + +ds++akf ++ G +  al+f+v da+k+
  gi|488599891|ref|YP_007906362.1| 11 VVVAVKDAEKAMRFFSElLGieFDEIGEERNWKFKSYMSpEGLELLVPTSEDSETAKFIEKRGEGLFALSFKVSDAEKI 89
                                      556666666666666542444489999999999999976368************************************* PP

                      Glyoxalase_5 88 yeralekGak 97
                                       ++a e+G +
  gi|488599891|ref|YP_007906362.1| 90 AKKAEEMGIR 99
                                      ***9999976 PP

>> Phytase  Phytase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.5e-06     0.014     260     315 ..      47     102 ..      43     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-06
                           Phytase 260 yyaedgegyliassqgdnsyavydregkneyvadfeiadgeeidgtsdtdgidvlg 315
                                       y +++g   l+ +s+ +++    +++g++ +  +f+++d+e+i   ++  gi ++g
  gi|488599891|ref|YP_007906362.1|  47 YMSPEGLELLVPTSEDSETAKFIEKRGEGLFALSFKVSDAEKIAKKAEEMGIRIIG 102
                                       889999999*******99999*********************************99 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.1e-05     0.029       2      82 ..      11      99 ..      10     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                      Glyoxalase_6  2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.........paknrvHldlavedlda 71
                                      vv++++d++++++F++++lg e ++   + ++++  +    ++  ll+ + ++         +++  + l ++v+d+++
  gi|488599891|ref|YP_007906362.1| 11 VVVAVKDAEKAMRFFSELLGIEFDEIG-EERNWKFKSYMSPEGLELLVPTSEDsetakfiekRGEGLFALSFKVSDAEK 88
                                      899*******************99988.44555555555556666666666667777776555556799999****999 PP

                      Glyoxalase_6 72 evarlvalGAr 82
                                       +++++++G r
  gi|488599891|ref|YP_007906362.1| 89 IAKKAEEMGIR 99
                                      99999999965 PP

>> DUF4252  Domain of unknown function (DUF4252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.8e-05      0.12      78     123 ..      32      75 ..       8     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                           DUF4252  78 ttenkadaeklkkevkkilkknkyeeLmrvkdkgekvkiyvkekkd 123
                                        ++  ++ e+   ++k++++ +++e L+ +++++e++k+  k++++
  gi|488599891|ref|YP_007906362.1|  32 EFD--EIGEERNWKFKSYMSPEGLELLVPTSEDSETAKFIEKRGEG 75 
                                       555..78888999**************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        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 0.30s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1037.38
//
Query:       gi|488599892|ref|YP_007906363.1|  [L=125]
Description: SSU ribosomal protein S8E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-32  110.9   5.8    5.7e-32  110.8   5.8    1.0  1  Ribosomal_S8e  Ribosomal protein S8e
  ------ inclusion threshold ------
      0.029   14.7   0.1      0.039   14.3   0.1    1.2  1  DUF4467        Domain of unknown function with cystatin-like 


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 !  110.8   5.8   6.4e-36   5.7e-32       4     137 .]       2     124 ..       1     124 [. 0.98

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 6.4e-36
                                       BXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEE CS
                     Ribosomal_S8e   4 srdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlg 80 
                                        +++++ r+ tG   ++ rkkrk+e+gr++ +t +g++++k+ r+rgG++k +++r k anv+ p e++++++++++
  gi|488599892|ref|YP_007906363.1|   2 VWQGRSRRTYTGKLIRPARKKRKYEMGRPQVETLIGERKIKKERCRGGNIKIKLVRDKFANVYVPAEGKVVRAEVTN 78 
                                       5899************************************************************************* PP

                                       EECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  81 VkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       V++n ++ +y+r++v+tKgaii++++++           A+vt+rP q+G++na+l+
  gi|488599892|ref|YP_007906363.1|  79 VVENRAHVHYARKNVITKGAIIQTSLGK-----------AKVTNRPSQEGVINAILI 124
                                       ****************************...........****************96 PP

>> DUF4467  Domain of unknown function with cystatin-like fold (DUF4467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.4e-06     0.039      13      71 ..      38      98 ..      31     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-06
                           DUF4467 13 ekkqqklakkgndvevd.ikkedanvyVyedgKlivlay.kllknreevtyvaYeikdkkv 71
                                      e+k +k   +g +++++ +  + anvyV  +gK++  +  ++++nr++v+y   ++  k +
  gi|488599892|ref|YP_007906363.1| 38 ERKIKKERCRGGNIKIKlVRDKFANVYVPAEGKVVRAEVtNVVENRAHVHYARKNVITKGA 98
                                      66777777788999***566677*************997257899******8777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 740.92
//
Query:       gi|488599893|ref|YP_007906364.1|  [L=375]
Description: ATP-utilizing enzymes of ATP-grasp superfamily (probably carboligases) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.3e-61  205.4   0.0    7.1e-61  205.0   0.0    1.2  1  DUF1297     Domain of unknown function (DUF1297)
    3.2e-43  146.6   0.0    5.1e-43  145.9   0.0    1.3  1  DUF1246     Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
       0.17   11.5   1.9       0.45   10.2   1.9    1.8  1  Nup54_57_C  NUP57/Nup54 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.0   0.0   1.2e-64   7.1e-61       1     188 []     179     375 .]     179     375 .] 0.98

  Alignments for each domain:
  == domain 1  score: 205.0 bits;  conditional E-value: 1.2e-64
                                       HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTT...TEEEEEEEEEEEEEECCCHCCS-HHHHHCC CS
                           DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplk...eevellgidrRyesnldglvrlpakeqlel 74 
                                       ++++++eel+++g+i+ee lkka+ieeyv+Ga+fn+n+++++lk   ++++++g+++R+++nl+g+++lpa++ql++
  gi|488599893|ref|YP_007906364.1| 179 DYYRQAEELIKQGVITEEGLKKARIEEYVLGARFNANFHCYALKdvfGDFDFVGFSDRRQVNLQGFLNLPARDQLKI 255
                                       89*****************************************98999***************************** PP

                                       T----EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-...TTS-EEEEEEESSB-GGGGG CS
                           DUF1297  75 evepeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvt...kdlelvvfdvsaRivggtnv 148
                                       +v ++++++G+++v++REs++++v+e++ekf+++++k++ppG+iG+F+Lq++++   ++le++vfdvs+R++g++++
  gi|488599893|ref|YP_007906364.1| 256 NVPVKNEEIGHYGVTMRESKQQMVYEYAEKFIRTCEKEYPPGLIGLFGLQGAIAydnDRLEFFVFDVSPRVPGDPAI 332
                                       ****************************************************9877799****************** PP

                                       GTT--CCHHHTTSS---HHHHHH.......HHHHHHHHCT-GGGCEE CS
                           DUF1297 149 ymegspyskllfgeplsmGrria.......lEikeaiekdrleeivt 188
                                           +p+s ++++ ++++++ri+       lE+ +a e +rl+e+vt
  gi|488599893|ref|YP_007906364.1| 333 ----GPTSPEMRNLSIKHKKRIEdpldltmLELISARELGRLKEVVT 375
                                       ....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 !  145.9   0.0   8.5e-47   5.1e-43       1     122 []      20     146 ..      20     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.9 bits;  conditional E-value: 8.5e-47
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT..TT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf..kvidevivldkfkdilkeevqeklreenailvPhgsf 75 
                                       +++++SHsa ++  +Ak+ g+rt++v++kgr++lY++f  +++devivld+fkd+l++evqekl+e+n+i++P++sf
  gi|488599893|ref|YP_007906364.1|  20 VGIFGSHSAKETGISAKSFGLRTVVVVQKGRDRLYTDFnrHLYDEVIVLDSFKDLLNREVQEKLVEMNTIFIPNRSF 96 
                                       6899**********************************99999********************************** PP

                                       HHHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--BE CS
                           DUF1246  76 veYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkki 122
                                       ++Yvg++ ie e++vpi+Gnr++lr+Eer+ +k +y  L+kAg+r+Pk++
  gi|488599893|ref|YP_007906364.1|  97 AVYVGYDGIEsEFEVPIYGNRYMLRAEERNFEKGQYylLDKAGLRYPKEF 146
                                       *******************************9999999*********986 PP

>> Nup54_57_C  NUP57/Nup54 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9   7.5e-05      0.45       2      12 ..       6      16 ..       5      17 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.5e-05
                        Nup54_57_C  2 aKaKKILeDYe 12
                                      +K KKI+eDY+
  gi|488599893|ref|YP_007906364.1|  6 EKIKKIVEDYD 16
                                      69********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2448.33
//
Query:       gi|488599894|ref|YP_007906365.1|  [L=490]
Description: (R)-citramalate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  258.5   1.6    1.7e-76  257.3   1.6    1.6  1  HMGL-like   HMGL-like
    5.1e-36  123.5   2.6    1.2e-35  122.3   2.6    1.7  1  LeuA_dimer  LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
      0.013   15.5   0.0         11    6.1   0.0    3.6  3  DUF4974     Domain of unknown function (DUF4974)
      0.045   13.7   0.2        0.1   12.5   0.2    1.6  1  DUF1308     Protein of unknown function (DUF1308)


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 !  257.3   1.6   3.8e-80   1.7e-76       2     264 .]       4     262 ..       3     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 257.3 bits;  conditional E-value: 3.8e-80
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       v+++dttLRDGeq+++++l+ve+kl ia aLd++gvd+iE+g + ase+df+++++i +a+ +a+i++ +r +++di
  gi|488599894|ref|YP_007906365.1|   4 VRVFDTTLRDGEQTPGVSLTVEQKLIIASALDKLGVDVIEAGTAIASEGDFKAIKEISNAGLNAEICSFCRIKKEDI 80 
                                       789************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHH.SSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkakl.kkdreevakkaeeavkaarslgkdvelsledasrtdleflaevvea 154
                                       +a ++    a+a+++ ++ + s++h+k+k+  k re+v+++++ a+++a+++g  ve+++edasr+dlef++e+  +
  gi|488599894|ref|YP_007906365.1|  81 DASAD----AEADSIFMVAPSSDIHIKSKFpDKGREDVIEMSVSAIEYAKERGLIVEFGAEDASRADLEFIVELFRN 153
                                       *****....*********************5588******************************************* PP

                                       HHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSB CS
                         HMGL-like 155 aeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGera 231
                                       a++a a+r+  aDtvGvltP++a  ++++l ++ +  v++++HcH+d+GlA+ nt+ A++aGa++  +tvnG+Gera
  gi|488599894|ref|YP_007906365.1| 154 AVSAKADRLTYADTVGVLTPEKAESIMKRLTSEFN--VPIAIHCHDDFGLATINTVYAIKAGASEFHATVNGIGERA 228
                                       ***********************************..**************************************** PP

                                       BB-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 232 Gnaaleelvaalealg.vdtgldlqklrsiaalv 264
                                       Gnaalee+v+ale     +t +  ++++++++lv
  gi|488599894|ref|YP_007906365.1| 229 GNAALEEIVMALEFHYgFKTSIIKENIYETSKLV 262
                                       *************764499999999999999887 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   2.6   2.7e-39   1.2e-35       2     132 ..     358     489 ..     357     490 .] 0.97

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 2.7e-39
                                       XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T CS
                        LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..d 75 
                                       vtd+d++++++++l+ ++ +++kle+l+++sg + ++ta+vkl++ +g+e  ++a+G GpvdA++nA++ka+++  d
  gi|488599894|ref|YP_007906365.1| 358 VTDADVKTIIETVLQIKQeKKVKLEDLSIVSGMHIMPTASVKLRI-NGQEIIEAATGLGPVDAAINAVKKAVSEfaD 433
                                       9**************9888**************************.9****************************** PP

                                       -EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  76 ikLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                       ikL +Y+v+ait+gtda+++v V+l+ +++++v+++G+++di++AS++Al+++ln+l
  gi|488599894|ref|YP_007906365.1| 434 IKLVSYHVDAITGGTDALVDVIVQLS-RGDQIVTARGARTDIIMASVEALLEGLNML 489
                                       **************************.77777***********************87 PP

>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.018        82      10      27 ..     177     194 ..     170     200 .. 0.86
   2 ?    6.1   0.0    0.0025        11       6      31 ..     230     255 ..     229     261 .. 0.86
   3 ?    1.2   0.0     0.083   3.7e+02       7      17 ..     323     333 ..     321     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHT--EEE- CS
                           DUF4974  10 eeilkkLerwYnveivie 27 
                                       e+i+k+L   +nv i i+
  gi|488599894|ref|YP_007906365.1| 177 ESIMKRLTSEFNVPIAIH 194
                                       89***********99886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0025
                                       EEEHHHHHHHHHHHHT--EEE-TTS- CS
                           DUF4974   6 nesLeeilkkLerwYnveivieneel 31 
                                       n+ Leei+  Le +Y+++ +i +e++
  gi|488599894|ref|YP_007906365.1| 230 NAALEEIVMALEFHYGFKTSIIKENI 255
                                       789**************999877665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.083
                                       EEHHHHHHHHH CS
                           DUF4974   7 esLeeilkkLe 17 
                                       +s+eei+kkL+
  gi|488599894|ref|YP_007906365.1| 323 ASIEEIMKKLG 333
                                       799*****996 PP

>> DUF1308  Protein of unknown function (DUF1308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.3e-05       0.1      50     116 ..     310     386 ..     276     401 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                           DUF1308  50 kgkkLivcetAve.dfqeilstvgGpkEkeraeeLlkrievvpDkaseraekev.........lklsgkikerskvi 116
                                       ++++L++ + A + +++ei++ +g + +k++++e+l r++ + Dk ++ ++++v         +k  +k+k   + i
  gi|488599894|ref|YP_007906365.1| 310 RKRQLVLGKHAGRaSIEEIMKKLGYKADKNQMKEILVRVKELGDKGKRVTDADVktiietvlqIKQEKKVKLEDLSI 386
                                       4678999998865279****************************999988887777866666666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3018.81
//
Query:       gi|488599895|ref|YP_007906366.1|  [L=551]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-116  388.2  14.0     6e-116  388.0  14.0    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.0  14.0  3.4e-120    6e-116       1     564 []       7     541 ..       7     541 .. 0.94

  Alignments for each domain:
  == domain 1  score: 388.0 bits;  conditional E-value: 3.4e-120
                           DUF2070   1 leklskyifrlPswkvsllliillalligllaflssk...lfgillfglpalvaflltlpvlrilggrltykrslfl 74 
                                       +ek+++++f++P+ +vs+l+ i++++++++l+ ++sk   +++++++gl++++++l+ +++l+i+   ++++r +fl
  gi|488599895|ref|YP_007906366.1|   7 IEKFYSKLFTIPRKRVSVLIGIITIVFASFLNGTVSKsffAQRYFFIGLSLIISLLIASKLLKIA---FNSRRVFFL 80 
                                       589*********************************9***************************9...********* PP

                           DUF2070  75 alltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly..f 149
                                       al+++++v i++ +ai++ + +     + ++++ ++++   +l+l+++s+++++ka+l++++++l+++++ +++   
  gi|488599895|ref|YP_007906366.1|  81 ALFILIFVEIFDSIAIHILHNF-----NLIIMAPSAMATGLTLILFFTSETEEFKASLLSTTILLSIYPIDYAFsfE 152
                                       *******************766.....9999999999999*********************************9989 PP

                           DUF2070 150 spesfllllllslifalavylfivvvdrplkrnlgvsaldllsaFlahileg.skelEeffeeigeeadvpvkvlsf 225
                                       +p++f  ++++++i + +++lfi+++dr++ r   +++ +ll+ F+ ++l+   + +E+ +e+i+e+++  vk+l++
  gi|488599895|ref|YP_007906366.1| 153 APHRFTGYVAATVIGVSLALLFIKFIDRNYGR---FNSKRLLRNFILFWLTSdPSFFERELERISETKEGFVKCLKI 226
                                       9*****************************99...9****************99999******************** PP

                           DUF2070 226 rredgekallvvPniHPGPlgeiGGsnLpkilaerldelvlvlHgtatHdfNlvserevekiveavkealeeleyss 302
                                            ++++lv++++HPGP+++iGG+ L+++l ++   + ++lH+  +Hd N++++r+ve+iv+++k+  + +  s 
  gi|488599895|ref|YP_007906366.1| 227 -----NDVHLVTTSFHPGPIRNIGGALLVEKLLDE---NRIYLHSLVKHDSNPSTSRDVEEIVRKAKNLSSFI--SL 293
                                       .....***********************9666444...58****************************99775..58 PP

                           DUF2070 303 kaskpvrvesgdvkllgqrfgdslllvitrapegiDDiplsvglsimaeakaegfedvllVDaHNsfseeagevlpg 379
                                       k+ kpv+ve +++kl++++f++ l+l++   +++iDDip s+         ++ f+++++VD+HN++s+  + +   
  gi|488599895|ref|YP_007906366.1| 294 KCFKPVSVEGERFKLMAFPFDK-LTLIFISGKKAIDDIPESINR-----FAEKIFGECIVVDCHNCHSQGYEMS--- 361
                                       9*********************.66666677***********32.....233369***************9998... PP

                           DUF2070 380 sedaeeliraaekalekleaaeeselkvgvarsetpkltpeeglGdlgiqvlvlevdgqktayvliDgNNmepglre 456
                                       s d+ e+++++e + ek++ +e ++l++  a+++++  +        ++++l+l++dg++++++++DgNN++++++ 
  gi|488599895|ref|YP_007906366.1| 362 SGDIIEILELMEALKEKIDFREVNRLRYSLASARIDGKSC------ERVSMLILDYDGERFVLLMLDGNNINCEFKS 432
                                       **********************************997444......6****************************** PP

                           DUF2070 457 eirealke.vdlevevmTTDtHvvngvsl..gynpvGekv.skdelielvlelvekAiadlepvevgyatervevkv 529
                                       e+++ + + +  + ++++TD+H+++gvs+  gy+pvG++v +++ +i+ +++   + ++d    evgy++++v+v+v
  gi|488599895|ref|YP_007906366.1| 433 ELENFFLKsGL-QPVIFSTDNHSKTGVSPkiGYMPVGSDVaERKAIIDFIMRNLGRELKD--VGEVGYSHDTVKVRV 506
                                       *******8666.***************************945888999999888888888..4599*********** PP

                           DUF2070 530 fgedrfeelvstvnsvvsvakilaaallllaills 564
                                       +ged+f+ + +++ +++++a+++++ ++l+ +++s
  gi|488599895|ref|YP_007906366.1| 507 MGEDFFKAVEKMFVDLGEKAIYIFISIVLIQFFTS 541
                                       *******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3291.72
//
Query:       gi|488599896|ref|YP_007906367.1|  [L=98]
Description: hypothetical protein Asulf_00342 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 651.20
//
Query:       gi|488599897|ref|YP_007906368.1|  [L=184]
Description: KH domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-14   53.9   9.7    5.3e-08   32.6   1.8    2.3  2  KH_1      KH domain
    6.4e-08   32.3  10.5    0.00041   20.1   1.2    2.4  2  KH_2      KH domain
     0.0043   16.9   5.5        1.5    8.8   0.1    2.9  3  KH_4      KH domain
  ------ inclusion threshold ------
      0.074   13.7   0.0       0.17   12.5   0.0    1.6  2  MgtE_N    MgtE intracellular N domain
        1.3    9.2   6.5          4    7.6   1.0    2.6  3  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 !   32.6   1.8   1.5e-11   5.3e-08       2      52 ..       6      49 ..       5      64 .. 0.79
   2 !   25.9   1.2   1.8e-09   6.3e-06       9      65 ..     100     148 ..      92     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.5e-11
                                      EEEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE CS
                              KH_1  2 lrilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG 52
                                      ++i vP s vg i+Gk G++ keI+e+tg+ + v k       +  +t++ 
  gi|488599897|ref|YP_007906368.1|  6 TEIRVPESRVGVIVGKDGETKKEIEEKTGCEMIVRK-------DGAITLIC 49
                                      789****************************99763.......23466555 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.8e-09
                                       GHHHHHHTGGGHHHHHHHHHH.T-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                              KH_1   9 slvgriIGkgGsnIkeIreet.gakIkvpksedegsderevtisGspeavekAkelie 65 
                                       + +griIGk G++ k I+e t  ++  +  +       + v i+G+ e+v  A+e+i+
  gi|488599897|ref|YP_007906368.1| 100 RIMGRIIGKDGKMKKTIEE-TlEVNLSIR-D-------KSVAIIGDVENVGVAREAIM 148
                                       569****************.88*****76.3.......359**************997 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.2   1.1e-07   0.00041      25      63 ..       4      42 ..       2      91 .. 0.86
   2 !   17.0   2.4   1.1e-06     0.004      36      68 ..     102     133 ..      98     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-07
                                      CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHT CS
                              KH_2 25 nrviiviresqpgivIGkgGsnikkigkelrkdiekleg 63
                                      ++++i + es+ g+++Gk G++ k+i+++ + ++ + ++
  gi|488599897|ref|YP_007906368.1|  4 HQTEIRVPESRVGVIVGKDGETKKEIEEKTGCEMIVRKD 42
                                      789999***********************9988855444 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.1e-06
                                       HHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                              KH_2  36 pgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                                       +g++IGk G++ k+i+++l+ ++  +++k V +
  gi|488599897|ref|YP_007906368.1| 102 MGRIIGKDGKMKKTIEETLEVNLS-IRDKSVAI 133
                                       89*********************5.99999984 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00041       1.5      29      50 ..       4      25 ..       2      27 .. 0.90
   2 !    8.7   1.9   0.00043       1.5      39      51 ..     101     113 ..      82     134 .. 0.86
   3 ?   -1.3   0.0      0.57   2.1e+03      15      31 ..     117     133 ..     112     142 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00041
                              KH_4 29 veielnvegedlGrvIGkrGrt 50
                                      ++ e++v ++ +G+++Gk+G+t
  gi|488599897|ref|YP_007906368.1|  4 HQTEIRVPESRVGVIVGKDGET 25
                                      677999**************98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00043
                              KH_4  39 dlGrvIGkrGrtl 51 
                                        +Gr+IGk+G++ 
  gi|488599897|ref|YP_007906368.1| 101 IMGRIIGKDGKMK 113
                                       59*********85 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.57
                              KH_4  15 peevevteeeeeeevei 31 
                                       +e++ev++++ +++v i
  gi|488599897|ref|YP_007906368.1| 117 EETLEVNLSIRDKSVAI 133
                                       45666666665555544 PP

>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.7e-05      0.17      42      85 ..      62     105 ..      55     121 .. 0.86
   2 ?   -3.0   0.0       3.1   1.1e+04      24      40 ..     150     166 ..     143     178 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                                       CCHHHHCS-HHHHHHHHCCS-HHHHHHHHCCCHHHHHHHHHHCS CS
                            MgtE_N  42 qeeliealsdeelaelleeldsDdaadlleelpeekveellsal 85 
                                        + + + +s++++ +ll++  + +++d+ e +pe+ v++++ ++
  gi|488599897|ref|YP_007906368.1|  62 IKAIANGFSPSTAFKLLNDFVTLEIIDISEYVPENAVKRIMGRI 105
                                       57788999********************************9765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                                       HS-HHHHHHHHCTS-CC CS
                            MgtE_N  24 llpkeeaaevleelded 40 
                                       l++  +++ v++ ++ +
  gi|488599897|ref|YP_007906368.1| 150 LIDGSTHSTVMKFMERR 166
                                       44444444444444443 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.011        40      18      36 ..      14      32 ..       4      44 .. 0.85
   2 ?   -3.3   0.0       2.7   9.8e+03      50      61 ..      60      71 ..      57      74 .. 0.61
   3 ?    7.6   1.0    0.0011         4      19      51 ..     102     140 ..      86     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.011
                              KH_5 18 pvGaivgkkGsrikavsse 36
                                       vG ivgk G+  k+++++
  gi|488599897|ref|YP_007906368.1| 14 RVGVIVGKDGETKKEIEEK 32
                                      49**********9999987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.7
                              KH_5 50 DlaefianalsP 61
                                      ++ + ian +sP
  gi|488599897|ref|YP_007906368.1| 60 NIIKAIANGFSP 71
                                      455566666666 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0011
                              KH_5  19 vGaivgkkGsrikavsseLk......gekidvvewseDl 51 
                                       +G i+gk G+  k++++ L+      ++ + ++  +e++
  gi|488599897|ref|YP_007906368.1| 102 MGRIIGKDGKMKKTIEETLEvnlsirDKSVAIIGDVENV 140
                                       69*****************99999999999998888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.35s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 1004.71
//
Query:       gi|488599898|ref|YP_007906369.1|  [L=269]
Description: Serine/threonine protein kinase involved in cell cycle control [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-60  202.3   0.5    7.2e-60  201.8   0.1    1.4  2  RIO1            RIO1 family
    3.8e-05   23.7   0.1     0.0018   18.2   0.0    2.2  2  APH             Phosphotransferase enzyme family
    9.5e-05   21.8   0.8    0.00066   19.1   0.0    2.3  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0073   15.7   0.1      0.011   15.2   0.1    1.4  1  Pkinase         Protein kinase domain
  ------ inclusion threshold ------
      0.045   12.5   0.1      0.073   11.8   0.1    1.2  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.5   5.3e+03     177     183 ..      18      24 ..       7      46 .. 0.49
   2 !  201.8   0.1     2e-63   7.2e-60       1     181 [.      66     251 ..      66     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.5
                                       TTC---- CS
                              RIO1 177 rkgvekv 183
                                       +  +++ 
  gi|488599898|ref|YP_007906369.1|  18 KLRIKER 24 
                                       3333322 PP

  == domain 2  score: 201.8 bits;  conditional E-value: 2e-63
                                       EEEEEEE.TTTE..EEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S-- CS
                              RIO1   1 nVyhavs.edgk..evaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPk 74 
                                       nV++a    dg+   +a+Kiy+++t+eF+k++ y  g+krf+++  k++++ ++ +waekEfrnL++++++gv+vP+
  gi|488599898|ref|YP_007906369.1|  66 NVFYADGlVDGEemPLAVKIYRIETSEFHKMEDYLFGDKRFDMK--KISKKTIIYIWAEKEFRNLQKAYQEGVNVPR 140
                                       5777776634443489**************************88..9****************************** PP

                                       EEEEETTEEEEE--EETTEEGGBHHHCG.-...HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE- CS
                              RIO1  75 pielkrhvlvmefigedgvaapklkdve.e...eeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviI 147
                                       p+++ +++l+mef+ged+++ p l d++ +     + ++l+ee+le++++l+  a+lvHaDLSeyN+l++++k+++I
  gi|488599898|ref|YP_007906369.1| 141 PVHYLKNILLMEFLGEDEIPSPSLFDLRkNladFVNPKDLLEEILENVERLVVSAELVHADLSEYNILLHNGKPYFI 217
                                       **************************995575445889*************************************** PP

                                       -GTTEEETTSTTHHHHHHHHHHHHHHHHHTTC-- CS
                              RIO1 148 DvsQaveldhpnalefLerDveniikfFrrkgve 181
                                       D++Qav ldhpn+ +fLerD++ni++fF++ g +
  gi|488599898|ref|YP_007906369.1| 218 DMGQAVLLDHPNSISFLERDLKNISRFFEKFGLK 251
                                       ******************************9987 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.015        52      38      60 ..     122     144 ..     120     175 .. 0.79
   2 !   18.2   0.0   5.1e-07    0.0018     145     197 ..     177     223 ..     152     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHTT-B--B-CTT CS
                               APH  38 rrevallrlLakagvpvPevlag 60 
                                       ++e++ l+   + gv vP+++++
  gi|488599898|ref|YP_007906369.1| 122 EKEFRNLQKAYQEGVNVPRPVHY 144
                                       78999****************95 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 5.1e-07
                                       HHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                               APH 145 leeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                         +l e++l+ +++l+    ++ l+H Dl+  N+l++  +g+  ++iD + a+
  gi|488599898|ref|YP_007906369.1| 177 PKDLLEEILENVERLVV---SAELVHADLSEYNILLH--NGKP-YFIDMGQAV 223
                                       45677779999999999...7****************..7776.8***99887 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2       1.6   5.6e+03     180     199 ..       6      25 ..       5      28 .. 0.77
   2 !   19.1   0.0   1.8e-07   0.00066      58     191 ..     121     246 ..     107     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                               Kdo 180 ekdLarLkrsflkieltead 199
                                       +k+L++++r++ k  ++e+d
  gi|488599898|ref|YP_007906369.1|   6 DKELKNIERYLDKLRIKERD 25 
                                       57888889988888888887 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.8e-07
                               Kdo  58 avrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwae..laeelkrallkavgrlia 132
                                       a +Efr+l++ +++gv+vp+pv +  +   +e     l e+  +  +L dl ++ a+   ++ l +++l++v rl+ 
  gi|488599898|ref|YP_007906369.1| 121 AEKEFRNLQKAYQEGVNVPRPVHYLKNILLME----FLGEDEIPSPSLFDLRKNLADfvNPKDLLEEILENVERLVV 193
                                       679*******************9864433222....23344445555666555555554567888889999998886 PP

                               Kdo 133 klhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwr..ekdLarLkrsfl 191
                                          +a++ Hadl   nill++++      ++iD+ +a l   ++  +  e+dL+++ r f+
  gi|488599898|ref|YP_007906369.1| 194 ---SAELVHADLSEYNILLHNGK-----PYFIDMGQAVLLDHPNSISflERDLKNISRFFE 246
                                       ...79****************97.....999999999888776654333788888888776 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     3e-06     0.011      75     153 ..     149     230 ..      93     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-06
                                       EEEE--TTEB.....HHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEEEE-SGTTS CS
                           Pkinase  75 lvleyvegge.....ladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgelKitDFGla 145
                                       l++e++ ++e     l+dl +     +  + k+++++ile +e l  s++++H Dl   NiL++ +g+   +D G a
  gi|488599898|ref|YP_007906369.1| 149 LLMEFLGEDEipspsLFDLRK--NLADFVNPKDLLEEILENVERLVvSAELVHADLSEYNILLH-NGKPYFIDMGQA 222
                                       567777666655444555443..34455577999*********9987999**************.***********9 PP

                                       EESSSSCS CS
                           Pkinase 146 kelesssk 153
                                         l++ ++
  gi|488599898|ref|YP_007906369.1| 223 VLLDHPNS 230
                                       99887765 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     2e-05     0.073     298     361 ..     170     224 ..     165     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                    Pkinase_fungal 298 piekaespkellealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlake 361
                                        + ++ +pk+lle + +     ++L+  a+++H D Se+Nil+       + k   iD+  a+ 
  gi|488599898|ref|YP_007906369.1| 170 NLADFVNPKDLLEEILEN---VERLVVSAELVHADLSEYNILLH------NGKPYFIDMGQAVL 224
                                       566677777777665554...578999****************9......44445555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1653.55
//
Query:       gi|488599899|ref|YP_007906370.1|  [L=78]
Description: translation initiation factor 1A (aeIF-1A) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    2.9e-25   87.8   0.4    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 !   87.8   0.4   1.6e-29   2.9e-25       3      64 .]       1      61 [.       1      61 [. 0.97

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.6e-29
                                      EEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  3 vigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      + ++V  +lg ++++V+++ +g+e+la+ipgk+R+kiwi++Gd+V++ ++p+++++++Iv+r
  gi|488599899|ref|YP_007906370.1|  1 MFAIVDSMLGAGHIKVRCE-DGEERLARIPGKMRKKIWIREGDIVIIVPWPFQKSRADIVWR 61
                                      5799**************7.6***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 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:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 583.04
//
Query:       gi|488599900|ref|YP_007906371.1|  [L=322]
Description: tyrosyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-58  196.3   0.0      8e-58  196.1   0.0    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
      0.001   18.1   0.0       0.27   10.1   0.0    2.2  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 !  196.1   0.0   8.9e-62     8e-58       4     292 ..      31     312 ..      28     313 .. 0.93

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 8.9e-62
                                       S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTC CS
                      tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgl 80 
                                       ++lr+y+G +P+g++HlG+++ ++kl++lq+ag+++++l+aD+hA+++++   +  ++r+ +e+   a    +a gl
  gi|488599900|ref|YP_007906371.1|  31 KKLRAYVGYEPSGEIHLGHVMTVNKLMDLQNAGIDIVVLLADVHAYLNEKG--DFDEIREIAEYNRRA---FIALGL 102
                                       789**********************************************99..899999999999999...****** PP

                                       HTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEE CS
                      tRNA-synt_1b  81 dpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgG 157
                                       + +k+e+vl+s+ + + +++ ++ +++++++l+r  +  + ++r +e++   ++++ Ypl+qa+Di++l++dl +gG
  gi|488599900|ref|YP_007906371.1| 103 EESKVEFVLGSDFQLERDYILDVLKMARITTLKRARRSMDEVSRRKEDP--MVSQMVYPLMQALDIAHLRVDLAVGG 177
                                       ***********************************99888778888855..8************************* PP

                                       GGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..S CS
                      tRNA-synt_1b 158 sDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..e 232
                                        DQ+++  l+r+ ++r+++      p +l +p+l gldGe KmS+S+gn +I   d++e+v+ ki+ka++  ++  +
  gi|488599900|ref|YP_007906371.1| 178 IDQRKIHMLARENLPRLGYP----SPICLHTPILLGLDGE-KMSSSKGN-YISVRDSEEDVRRKIRKAFCPEKQieN 248
                                       *****************997....****************.********.***********************9965 PP

                                       HHHHHHHHHTHHH....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 233 vekllklktelsn....elierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                       +      ++ +++     +ier e ++g  ++ ++eel +++ ++++h++dlk   a+ ln++l
  gi|488599900|ref|YP_007906371.1| 249 NPVIQIAQYHIFPrfekVVIERDERFGGDVEYLSFEELRKDYMEGKLHPMDLKMSIANYLNKIL 312
                                       554444445555555549**********999******************************998 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0   0.00055         5      23      45 ..      31      53 ..      10      89 .. 0.80
   2 !   10.1   0.0     3e-05      0.27     262     298 ..     195     231 ..     170     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00055
                      tRNA-synt_1f 23 devvvesGispSGliHiGnlrev 45
                                      ++     G+ pSG iH+G +  v
  gi|488599900|ref|YP_007906371.1| 31 KKLRAYVGYEPSGEIHLGHVMTV 53
                                      4566678***********97655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 3e-05
                      tRNA-synt_1f 262 ggeaPekvvYelillkggekmssSkGnvltledwlev 298
                                       g++ P+ +   ++l   gekmssSkGn+++++d  e 
  gi|488599900|ref|YP_007906371.1| 195 GYPSPICLHTPILLGLDGEKMSSSKGNYISVRDSEED 231
                                       5556665555555555677************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2205.39
//
Query:       gi|488599901|ref|YP_007906372.1|  [L=421]
Description: Cytosine deaminase-related metal-dependent hydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-76  256.8   0.1    3.9e-76  256.6   0.1    1.0  1  Amidohydro_1  Amidohydrolase family
    2.1e-19   70.4   0.0    2.6e-15   56.9   0.0    2.1  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.6   0.1   4.3e-80   3.9e-76       1     343 [.      49     392 ..      49     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 256.6 bits;  conditional E-value: 4.3e-80
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       +vlPGl +aH+Hl +sl+rg     +l++wl          + p ++++++  gi++++k Gtt + d ++    ++
  gi|488599901|ref|YP_007906372.1|  49 FVLPGLFNAHTHLAMSLFRGFaedmPLLEWLktkiwkverlLEPKDVYWGSMLGIAEMIKTGTTCFSDLYI----HM 121
                                       79****************999**************************************************....9* PP

                                       HHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHH CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealke 140
                                       + +++a+ee   g+r+++++++ drgs+e  k++ +  ++    +i   +++ +k+ ++ph+++++s e l+++ + 
  gi|488599901|ref|YP_007906372.1| 122 DEVARACEES--GMRAVLCYGMADRGSEERAKEELKIGEK----FIERWNGEKIKAVFGPHAPYTCSLEFLSQIRER 192
                                       *********9..************9776655555444433....34444777788999******************* PP

                                       HHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEH CS
                      Amidohydro_1 141 akkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvah 217
                                       a++ ++ ++iH++etk+eve+ ++a     +   ++e ++++g+l+e  +++ahg++l ++e+ +l++r  +++vah
  gi|488599901|ref|YP_007906372.1| 193 ADELNVGIHIHVSETKEEVENFIKANS---KP--PVEKLDEIGFLKE-DVVIAHGIWLNDKEIDILAKR--KVSVAH 261
                                       *************************99...55..*************.*********************..****** PP

                                       HHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHH CS
                      Amidohydro_1 218 cpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingA 294
                                        p sn++l+sg++++ +++++Gv+v lgtDgaas+n+ nl+ee++l  +lq+ +l++  ++ l++ +al+ma+ ng 
  gi|488599901|ref|YP_007906372.1| 262 NPVSNLKLASGIARVVDMVKAGVNVCLGTDGAASNNTYNLFEEIKLTSLLQKIKLMK--ADALKARDALDMACKNGY 336
                                       ********************************************************6..889*************** PP

                                       HHTT-TTTSSSS-TTSB--EEEECC.........CTCGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 295 kalglddkvGsievGkdADlvvvdl.........dilaafvglkkdgnvkkvivkGkl 343
                                       +a+g+  + G+i++Gk AD++++d          ++  ++v+++  ++v+++iv+Gk+
  gi|488599901|ref|YP_007906372.1| 337 RAYGI--DGGEIKEGKLADIIILDSkrlnfipayNPVYSIVYSTTGCEVTHTIVDGKI 392
                                       *****..8*****************876555544449999****************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   1.4e-05      0.12       3      23 ..      43      63 ..      41      97 .. 0.87
   2 !   56.9   0.0   2.9e-19   2.6e-15     225     472 ..     145     393 ..     104     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                      Amidohydro_3  3 iDakGrlvlPGFvDsHtHlag 23
                                      i a+G +vlPG+  +HtHla 
  gi|488599901|ref|YP_007906372.1| 43 IKARGSFVLPGLFNAHTHLAM 63
                                      779***************764 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 2.9e-19
                      Amidohydro_3 225 gseeltigavklfad......gvlgsrtalltepyftgwpdfedealaelvaaadergldvaihaigdaavd.dvld 294
                                       gsee  ++ +k++++      g+    ++ ++ py      ++ e l ++ ++ade  + ++ih+ +++    ++++
  gi|488599901|ref|YP_007906372.1| 145 GSEERAKEELKIGEKfierwnGEKIKAVFGPHAPYT-----CSLEFLSQIRERADELNVGIHIHVSETKEEVeNFIK 216
                                       556666677777777666666777777888888888.....6666699999**************99998888**** PP

                      Amidohydro_3 295 afeaa.....aekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellna 366
                                       a  +       e   ++  + ++h+ ++++++i+ +a+  v  +  pv+n            + a+g+++v  + +a
  gi|488599901|ref|YP_007906372.1| 217 ANSKPpveklDEIGFLKEDVVIAHGIWLNDKEIDILAKRKVSVAHNPVSNL-----------KLASGIARVVDMVKA 282
                                       *9888855532222333333*******************************...........899************ PP

                      Amidohydro_3 367 gvkvalgsD..apvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadAD 441
                                       gv+v+lg+D  a  ++++ + +i  +  +++    ++      l  ++al++  +++ +a+g +   G +++G+ AD
  gi|488599901|ref|YP_007906372.1| 283 GVNVCLGTDgaASNNTYNLFEEIKLTSLLQKI---KL-MKADALKARDALDMACKNGYRAYGIDG--GEIKEGKLAD 353
                                       ***********9*******************7...44.46669**********************..********** PP

                      Amidohydro_3 442 lvvldadpldvdppelaear.........vrltvvdGrvv 472
                                       +++ld ++l + p+ +             v +t+vdG+++
  gi|488599901|ref|YP_007906372.1| 354 IIILDSKRLNFIPAYNPVYSivysttgceVTHTIVDGKIL 393
                                       ************9954444488****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2845.61
//
Query:       gi|488599902|ref|YP_007906373.1|  [L=141]
Description: hypothetical protein Asulf_00351 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       285  (0.015896); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 849.81
//
Query:       gi|488599903|ref|YP_007906374.1|  [L=279]
Description: hypothetical protein Asulf_00352 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   47.7   0.0    1.6e-07   31.2   0.0    2.2  2  PQQ_2     PQQ-like domain
    6.6e-10   39.2   0.0        1.3    9.6   0.0    5.8  5  PQQ_3     PQQ-like domain
    1.6e-09   37.2   4.9     0.0077   16.1   0.0    6.4  8  PQQ       PQQ enzyme repeat
     0.0084   15.5   0.1      0.014   14.8   0.1    1.3  1  CPSF_A    CPSF A subunit region
  ------ inclusion threshold ------
      0.019   15.0   0.0       0.46   10.6   0.0    3.0  4  Vault_4   Major Vault Protein repeat domain
       0.15   11.8   0.2       0.99    9.1   0.1    2.2  2  SUKH_5    SMI1-KNR4 cell-wall
        3.5    7.3   5.7         19    4.9   0.1    4.3  5  Kelch_1   Kelch motif


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   6.1e-11   1.6e-07      16     129 ..       4     123 ..       2     135 .. 0.76
   2 !   21.4   0.0     6e-08   0.00015       2     134 ..      79     247 ..      78     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 6.1e-11
                             PQQ_2  16 lWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvva......... 83 
                                       lW+     + +++v+  + ++++l+    g  l++l+++tGk++W+++ + ++  +p+ +   + + a         
  gi|488599903|ref|YP_007906374.1|   4 LWSY----RPDSEVENVSFDEDYLVFS-SGSSLYCLNTNTGKIIWKKRMTTTFYRDPFSDVSITALDAkgpmiaagt 75 
                                       5666....3588899999999999996.999*************************655555553333333333334 PP

                             PQQ_2  84 ..sdgqlialdaedGkrlWstqqrseepaelrssaspava.gdtvvvge 129
                                          dg ++ +  ++Gk+lW+ q ++  ++  r+ +  av+ gd++v+++
  gi|488599903|ref|YP_007906374.1|  76 nfMDGKIYLFT-KTGKLLWEHQFATIASLGWRPEDVTAVGiGDNFVAVG 123
                                       66677777788.********55555588888888888888988888876 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 6e-08
                             PQQ_2   2 egvvsaldaatGaelWrvdlar............................................p.lgggvsrav 33 
                                       +g ++ + + tG++lW+   a+                                            +  +g v ra 
  gi|488599903|ref|YP_007906374.1|  79 DGKIYLFTK-TGKLLWEHQFATiaslgwrpedvtavgigdnfvavgtefigeyiyvytfkrermfqKrVDGTV-RAI 153
                                       678888886.9*******6655555666667777777777777777766666666666655555542355555.999 PP

                             PQQ_2  34 lsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepa 110
                                        +++ l+v ++  +l+ ++  +G+++++ t++++ v++   +e  +   +s+++++ ++  +Gk+lW+   + e ++
  gi|488599903|ref|YP_007906374.1| 154 AANRCLAV-GTDKKLYVFE-LDGRERFSITAQVTDVKI---TETGI-ITSSGNRVYMFS-SNGKELWHKNFDCEIKQ 223
                                       55555555.5889999998.99********99985555...55555.566899*****9.9*******777777555 PP

                             PQQ_2 111 elrssaspavagdtvvvgessgkl 134
                                         +  +  a+ag++vvv+ ++g++
  gi|488599903|ref|YP_007906374.1| 224 LYCNGRVYAIAGKRVVVMSENGDV 247
                                       57999999999******9999987 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00056       1.4       4      40 .]       4      38 ..       2      38 .. 0.87
   2 ?    4.1   0.0     0.028        71       1      34 [.      39      83 ..      39      87 .. 0.79
   3 !    9.6   0.0   0.00052       1.3       1      38 [.      89     155 ..      89     173 .. 0.81
   4 ?    3.0   0.0     0.062   1.6e+02      21      35 ..     199     232 ..     182     236 .. 0.60
   5 !    7.7   0.0     0.002       5.1       1      33 [.     209     247 ..     209     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00056
                             PQQ_3  4 lWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40
                                      lWs++ +++v   + +d++++++++g  +ly+l+++t
  gi|488599903|ref|YP_007906374.1|  4 LWSYRPDSEV-ENVSFDEDYLVFSSG-SSLYCLNTNT 38
                                      8999888888.569***********9.******9987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                             PQQ_3  1 GevlWsvqlpgpvnssp.......avd..gglvyvgtg..dGtly 34
                                      G+++W+++     ++ p       a+d  g  + +gt   dG++y
  gi|488599903|ref|YP_007906374.1| 39 GKIIWKKRMTTTFYRDPfsdvsitALDakGPMIAAGTNfmDGKIY 83
                                      899999988887778888888877666668888888889999998 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00052
                             PQQ_3   1 GevlWsvqlpgpvnssp..........avdgglvyvgtg.....................dGtlyAlDa 38 
                                       G++lW++q+   + +s+           ++++ v vgt+                     dGt++A+ a
  gi|488599903|ref|YP_007906374.1|  89 GKLLWEHQFAT-I-ASLgwrpedvtavGIGDNFVAVGTEfigeyiyvytfkrermfqkrvDGTVRAIAA 155
                                       99*****7663.2.3444444666633667999999999999999999999999999999999999987 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.062
                             PQQ_3  21 gglvyvgtg...................dGtlyA 35 
                                       g++vy+ ++                   +G++yA
  gi|488599903|ref|YP_007906374.1| 199 GNRVYMFSSngkelwhknfdceikqlycNGRVYA 232
                                       5556665554444444444444444444555555 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.002
                             PQQ_3   1 GevlWsvqlpgpvnssp.......avdgglvyvgtgdGtl 33 
                                       G++lW ++++ ++  ++       a++g +v+v +++G +
  gi|488599903|ref|YP_007906374.1| 209 GKELWHKNFDCEI-KQLycngrvyAIAGKRVVVMSENGDV 247
                                       99*****888877.56777777789***********9987 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.26   6.8e+02      23      32 ..       4      13 ..       2      17 .. 0.84
   2 !   16.1   0.0     3e-06    0.0077       5      27 ..      23      46 ..      22      56 .. 0.83
   3 ?   -2.3   0.0       2.1   5.3e+03      12      18 ..      61      67 ..      60      67 .. 0.84
   4 !    8.2   0.0   0.00099       2.5       9      26 ..      79      95 ..      71      97 .. 0.89
   5 ?   -2.3   0.0       2.1   5.3e+03       6      15 ..     144     153 ..     140     153 .. 0.74
   6 !    6.3   0.0    0.0038       9.9       4      26 ..     194     215 ..     192     216 .. 0.86
   7 ?   -0.1   0.1      0.41     1e+03       8      15 ..     226     233 ..     224     233 .. 0.86
   8 ?   -1.0   0.0      0.76     2e+03      18      34 ..     243     259 ..     237     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.26
                                      EEEEESSSCG CS
                               PQQ 23 lWrfktggpv 32
                                      lW+++++++v
  gi|488599903|ref|YP_007906374.1|  4 LWSYRPDSEV 13
                                      8*****9987 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3e-06
                                      EE.ETTSEEEEEETTTCCEEEEEE CS
                               PQQ  5 lg.sadGylyAlDadTGkvlWrfk 27
                                      l  s +  ly l+ +TGk++W+++
  gi|488599903|ref|YP_007906374.1| 23 LVfSSGSSLYCLNTNTGKIIWKKR 46
                                      56667778*************987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.1
                                      EEEEETT CS
                               PQQ 12 lyAlDad 18
                                      + AlDa+
  gi|488599903|ref|YP_007906374.1| 61 ITALDAK 67
                                      89***96 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.00099
                                      TSEEEEEETTTCCEEEEE CS
                               PQQ  9 dGylyAlDadTGkvlWrf 26
                                      dG++y +  +TGk+lW++
  gi|488599903|ref|YP_007906374.1| 79 DGKIYLFT-KTGKLLWEH 95
                                      89999999.*******97 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 2.1
                                       EETTSEEEEE CS
                               PQQ   6 gsadGylyAl 15 
                                          dG+++A+
  gi|488599903|ref|YP_007906374.1| 144 KRVDGTVRAI 153
                                       5679999996 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.0038
                                       EEEETTSEEEEEETTTCCEEEEE CS
                               PQQ   4 ylgsadGylyAlDadTGkvlWrf 26 
                                       +++s ++++y +  ++Gk+lW++
  gi|488599903|ref|YP_007906374.1| 194 IITSSGNRVYMFS-SNGKELWHK 215
                                       5778899999999.*******86 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.41
                                       TTSEEEEE CS
                               PQQ   8 adGylyAl 15 
                                       ++G++yA+
  gi|488599903|ref|YP_007906374.1| 226 CNGRVYAI 233
                                       59*****7 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 0.76
                                       TTCCEEEEEESSSCGSS CS
                               PQQ  18 dTGkvlWrfktggpvls 34 
                                       ++G+vl  +++++++++
  gi|488599903|ref|YP_007906374.1| 243 ENGDVLKDVELESDPVG 259
                                       799***99999999887 PP

>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   5.4e-06     0.014      44     137 ..     108     192 ..      96     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.4e-06
                                       B--EEEEEEE---SSS--E...EEEEEEEEEE-SS--EEEEEEEEEEEES----EEEETTEEEEE-SSEEEEEEE-T CS
                            CPSF_A  44 kellvVGtafnlgedpaars..GrilvfeiievpetnrkLklvhkeevkgavtalaefqGrllvgvgqkvrvydlge 118
                                       +++ +VG++ n+     +++   +i+v++++         + +++++v+g+v+a+a  +  l+vg  +k++v++l+ 
  gi|488599903|ref|YP_007906374.1| 108 EDVTAVGIGDNFVAVG-TEFigEYIYVYTFKR--------ERMFQKRVDGTVRAIAA-NRCLAVGTDKKLYVFELDG 174
                                       6788899998888877.4445779******99........689************86.668**************** PP

                                       TS-EEEEEEEE-SS-EEEE CS
                            CPSF_A 119 dktLlrkafldtqlyvvsl 137
                                       ++ +  +a+  t++++++ 
  gi|488599903|ref|YP_007906374.1| 175 RERFSITAQV-TDVKITET 192
                                       **99999998.88877663 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 ?   -1.1   0.0      0.79     2e+03      13      41 ..      34      47 ..      26      51 .. 0.56
   2 ?   -0.9   0.0      0.68   1.7e+03      25      40 ..      80      96 ..      75     100 .. 0.76
   3 ?   -3.2   0.0       3.6   9.3e+03      33      48 ..     138     153 ..     131     157 .. 0.69
   4 ?   10.6   0.0   0.00018      0.46      15      50 ..     190     226 ..     185     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.79
                           Vault_4 13 RdiktGkvrvviGetYmlteeEelWeKeL 41
                                       +++tGk+               +W+K++
  gi|488599903|ref|YP_007906374.1| 34 LNTNTGKI---------------IWKKRM 47
                                      44444443...............466655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.68
                           Vault_4 25 GetYmlteeEe.lWeKe 40
                                      G+ Y+ t+  + lWe +
  gi|488599903|ref|YP_007906374.1| 80 GKIYLFTKTGKlLWEHQ 96
                                      88999999877359876 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.6
                           Vault_4  33 eEelWeKeLpedVeeL 48 
                                        E + +K++  +V ++
  gi|488599903|ref|YP_007906374.1| 138 RERMFQKRVDGTVRAI 153
                                       5777888877777665 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00018
                           Vault_4  15 iktGkvrvviGetYmltee.EelWeKeLpedVeeLla 50 
                                       ++tG +++     Ym   +  elW K++  ++++L  
  gi|488599903|ref|YP_007906374.1| 190 TETGIITSSGNRVYMFSSNgKELWHKNFDCEIKQLYC 226
                                       78999999999*****987479******999999865 PP

>> SUKH_5  SMI1-KNR4 cell-wall
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00038      0.99      84     117 ..      17      45 ..       5      59 .. 0.78
   2 ?   -0.3   0.0      0.31   7.9e+02      57     104 ..     134     182 ..     125     212 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00038
                                       ---TTEEEEEE-SSEEEEEECCC-BB--EEEEET CS
                            SUKH_5  84 glpknlivieedgegvyCldtnegkegeVvsWsh 117
                                        + ++++v++  g+++yCl+tn+gk    ++W++
  gi|488599903|ref|YP_007906374.1|  17 SFDEDYLVFS-SGSSLYCLNTNTGK----IIWKK 45 
                                       5667899999.9*********9999....88883 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                                       -S-.-......SSS-HHHHHHHHHHH..S---TTEEEEEE-SSEEEEEEC CS
                            SUKH_5  57 lgiadpkshtyeslpevveetreyrk..yglpknlivieedgegvyCldt 104
                                       ++++++++++   +  +v+     r    g  k+l+v+e dg   + +  
  gi|488599903|ref|YP_007906374.1| 134 YTFKRERMFQK-RVDGTVRAIAANRClaVGTDKKLYVFELDGRERFSITA 182
                                       55555555555.33333333222222237888999999999888777765 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         1   2.6e+03      27      38 ..      29      40 ..      27      40 .. 0.85
   2 ?    0.2   0.0      0.23   5.9e+02       6      17 ..      74      85 ..      72      85 .. 0.80
   3 ?    0.2   0.4      0.23   5.9e+02       6      16 ..     123     133 ..     119     134 .. 0.83
   4 ?   -0.8   0.0      0.45   1.1e+03       4      17 ..     157     170 ..     154     170 .. 0.82
   5 ?    4.9   0.1    0.0075        19      10      30 ..     226     252 ..     224     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                                      EEEEEEETTTTE CS
                           Kelch_1 27 ssvevyDpetnt 38
                                      ss++++++ t++
  gi|488599903|ref|YP_007906374.1| 29 SSLYCLNTNTGK 40
                                      799999999875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.23
                                      EEEEETTEEEEE CS
                           Kelch_1  6 gavvvggkiYvi 17
                                      g   ++gkiY +
  gi|488599903|ref|YP_007906374.1| 74 GTNFMDGKIYLF 85
                                      66789*****75 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.23
                                       EEEEETTEEEE CS
                           Kelch_1   6 gavvvggkiYv 16 
                                       g   +g++iYv
  gi|488599903|ref|YP_007906374.1| 123 GTEFIGEYIYV 133
                                       77889*****9 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.45
                                       SEEEEEETTEEEEE CS
                           Kelch_1   4 gagavvvggkiYvi 17 
                                       ++ av  + k+Yv+
  gi|488599903|ref|YP_007906374.1| 157 RCLAVGTDKKLYVF 170
                                       67899999****97 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.0075
                                       ETTEEEEEEEBCS......SSBEEEEE CS
                           Kelch_1  10 vggkiYviGGsdg......gnalssve 30 
                                       ++g++Y+i G +       g  l++ve
  gi|488599903|ref|YP_007906374.1| 226 CNGRVYAIAGKRVvvmsenGDVLKDVE 252
                                       79********99988888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); 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:                         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 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1868.52
//
Query:       gi|488599904|ref|YP_007906375.1|  [L=488]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-45  153.5  25.6    3.6e-33  114.8  18.3    2.3  2  Cons_hypoth698  Conserved hypothetical protein 698


Domain annotation for each model (and alignments):
>> Cons_hypoth698  Conserved hypothetical protein 698
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8  18.3     2e-37   3.6e-33       6     202 ..     108     303 ..     103     311 .. 0.90
   2 !   43.3   0.7   1.2e-15   2.1e-11     184     302 ..     315     455 ..     305     457 .. 0.84

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 2e-37
                    Cons_hypoth698   6 llliavlalllakve.llfaklsalllAillGillgnflklqeqlkaGvafskkklLrlgivllGfrltlsdiakvG 81 
                                       + + +vl  + +  e +++ +l+a+l+A+l+G+l++n++kl++ ++aG  +  ++ +++giv+lG++l ++ i+  G
  gi|488599904|ref|YP_007906375.1| 108 VYIASVLIAVFSANEtAHHYNLEAPLFALLVGLLISNTIKLPKWMDAGFRV--EYYIKTGIVMLGATLPFTLILYAG 182
                                       4444444333333344799*****************************665..67********************** PP

                    Cons_hypoth698  82 lkgvlldiivlistfllvlllgakllkldkklalLvaaGssiCGasAilavepvikareeevalaiavivllgtvam 158
                                         +++  +i  +stfl++ ++g+k+l++d++ a++++aG ++CG+sA +a++ +++a++e+va+ i ++++  ++++
  gi|488599904|ref|YP_007906375.1| 183 PVAFIQATIIAVSTFLTIYFVGTKVLGMDRRFASVLGAGGAVCGVSASIAMAAAVRAKKEHVAMGITTVIVWAIIMI 259
                                       ***************************************************************************** PP

                    Cons_hypoth698 159 llyPalatllsltdeefgvfaGasvhevaqVvaagelvseeaak 202
                                       ++ P++ ++l l++  +g+++G+s    a   aa+++++++ a+
  gi|488599904|ref|YP_007906375.1| 260 FAIPLISKALVLHPGVAGAWVGTSEFADAAGFAAAAAYGSMFAN 303
                                       ************************98888888888888887665 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 1.2e-15
                    Cons_hypoth698 184 hevaqVvaagelvseeaakiAv....ivKlt.Rvlllapvvlllslllakreeesetkea...kit....iPwFvlg 248
                                       + vaqV+a +++v+ +  +iAv    ++K++ R +++++  ++++++ + r e +et ++   k      +P+Fvlg
  gi|488599904|ref|YP_007906375.1| 315 KTVAQVIAEAKAVGVDIDDIAVrtftLMKVIgRDIWIGLWAFVMAIIATTRWEVEETGTKpsaK-EiwwrFPKFVLG 390
                                       5799999999999999999775433378864599****99999998887777766666654442.14688******* PP

                    Cons_hypoth698 249 Flvvallntlvllp...........selvsalktlstlllvmalaAlglktdlkalkkaglkpll 302
                                       F +++l+ ++++             + lv  +kt+ t+ +++++  +gl+t +++l  ag+kp +
  gi|488599904|ref|YP_007906375.1| 391 FFAASLFISILTAGvplseylqhmkPLLVGPIKTMRTWTFIFTFFSIGLTTRFRELTAAGSKPWI 455
                                       **********999899999999998999999*******************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3075.73
//
Query:       gi|488599905|ref|YP_007906376.1|  [L=738]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  179.5   0.0      1e-16   60.9   0.0    3.7  3  PAS            PAS fold
    4.2e-49  165.1   4.6    9.3e-17   61.2   0.1    4.0  3  PAS_9          PAS domain
    2.7e-43  146.7   0.0    4.8e-13   49.3   0.0    3.6  3  PAS_4          PAS fold
    1.9e-37  127.4   0.0    3.1e-13   49.8   0.0    3.6  3  PAS_3          PAS fold
    8.9e-24   83.8   0.2    8.9e-24   83.8   0.2    2.5  3  DUF835         Protein of unknown function (DUF835)
    3.2e-22   78.1   0.0    7.1e-07   29.1   0.0    3.7  3  PAS_8          PAS domain
    5.3e-12   45.8   0.0    1.4e-05   25.0   0.0    2.9  3  MEKHLA         MEKHLA domain
    1.5e-09   38.4   0.1     0.0022   18.6   0.0    3.7  3  PAS_10         PAS domain
    3.9e-09   36.8   0.0    1.6e-08   34.8   0.0    2.0  2  HAMP           HAMP domain
      1e-08   35.3   0.0    9.7e-06   25.7   0.0    3.7  3  PAS_7          PAS fold
     0.0026   18.2   0.9     0.0059   17.1   0.1    2.1  1  HTH_27         Winged helix DNA-binding domain
     0.0052   16.4   0.1      0.013   15.1   0.1    1.7  1  GntR           Bacterial regulatory proteins, gntR family
     0.0061   16.7   0.0        2.3    8.4   0.0    3.2  3  PAS_11         PAS domain
      0.008   16.1   0.3      0.058   13.4   0.0    2.7  1  HTH_45         Winged helix-turn-helix
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.03   14.4   0.0    1.6  1  HTH_20         Helix-turn-helix domain
      0.021   14.6   0.0      0.058   13.2   0.0    1.8  1  LexA_DNA_bind  LexA DNA binding domain
      0.029   13.3   0.9      0.044   12.7   0.2    1.6  2  LMBR1          LMBR1-like membrane protein
      0.049   13.2   0.0       0.14   11.7   0.0    1.9  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.06   13.3   0.0       0.13   12.2   0.0    1.5  1  MarR_2         MarR family
      0.075   12.8   0.0       0.22   11.3   0.0    1.8  1  HTH_DeoR       DeoR-like helix-turn-helix domain
      0.076   13.0   0.0       0.23   11.5   0.0    1.8  1  HTH_36         Helix-turn-helix domain
      0.083   13.0   3.2          4    7.6   0.9    2.4  2  DUF3585        Bivalent Mical/EHBP Rab binding domain
        0.1   12.8   1.5       0.68   10.1   0.2    2.4  2  PHM7_cyt       Cytosolic domain of 10TM putative phosphate tr
       0.11   12.6   0.3        2.4    8.4   0.1    2.9  2  PI_PP_I        Phosphoinositide phosphatase insertion domain
       0.22   11.5   5.0        1.6    8.7   1.3    2.4  2  Sec2p          GDP/GTP exchange factor Sec2p
       0.49   11.1   2.5         30    5.4   0.5    2.4  2  FliD_N         Flagellar hook-associated protein 2 N-terminus


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 !   54.2   0.0   1.9e-17   1.3e-14       2     113 .]     114     225 ..     113     225 .. 0.90
   2 !   60.1   0.0   2.6e-19   1.8e-16       4     113 .]     239     347 ..     236     347 .. 0.97
   3 !   60.9   0.0   1.5e-19     1e-16       3     113 .]     381     490 ..     379     490 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.9e-17
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r+++e+  d +f vDe+ + +y +++ +++lG+++eev+gk+ +d+++e+++ + +e++e   +++ ++++ e  
  gi|488599905|ref|YP_007906376.1| 114 KYRSLIEDVNDWVFEVDENFVYTYSSPKVRDILGYEPEEVVGKKPFDFMPEDERKKAVEEFEVIKRDKIPFCGLENV 190
                                       699************************************************98767777777777777777777777 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       f ++dg+ + le++ +p++d++g+++g+ gv rdi
  gi|488599905|ref|YP_007906376.1| 191 FMRKDGSHVILETCGRPFFDEKGNLRGYRGVSRDI 225
                                       766***************************99998 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 2.6e-19
                                       HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEE CS
                               PAS   4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfk 80 
                                        +i +++ d+i+ +D d ri+ +N+ ae ++G++++ev+gk+l  l++ee  +  +  +++++ +g  + ++ ++++
  gi|488599905|ref|YP_007906376.1| 239 ASITDHTVDAIVSLDLDSRIVSWNKGAEMMFGYKESEVIGKPLATLMPEENWDSCRVNFKKAIFEGYARDIETVRIT 315
                                       67888999******************************************999************************ PP

                                       CTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  81 lrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + dgr i ++++ ++++d  ge+ gf+ ++rdi
  gi|488599905|ref|YP_007906376.1| 316 K-DGRRILVDQTLTTIYDSNGEHMGFVAIMRDI 347
                                       *.******************************8 PP

  == domain 3  score: 60.9 bits;  conditional E-value: 1.5e-19
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       l +ile++ d+i  v+ dg+i+ +N++ae+l+G++ +e+lg +   l++ e      + l q ++ g +  ++e+++
  gi|488599905|ref|YP_007906376.1| 381 LANILENSNDAIYSVNLDGVITSWNKTAEKLFGWTKKEALGMPADVLLPDEIK-NETSFLIQKIKKGVRYISYETRR 456
                                       789**************************************998877765544.699999999999999******99 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++dg++i +++++sp++d++g++ gf ++ rdi
  gi|488599905|ref|YP_007906376.1| 457 LTKDGEIIDVDLTVSPILDEEGKPAGFSVITRDI 490
                                       99******************************98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   7.6e-19   5.2e-16       3     104 .]     125     227 ..     123     227 .. 0.90
   2 !   61.2   0.1   1.3e-19   9.3e-17       2     104 .]     247     349 ..     246     349 .. 0.91
   3 !   44.7   0.0   1.8e-14   1.2e-11       2     103 ..     390     491 ..     389     491 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 7.6e-19
                             PAS_9   3 gilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetf 76 
                                        ++ +++++ +  y +++++++lGy peev+gk+ +d++ +++e+++ ++++   +r+  +++  e+v++rk+g+ +
  gi|488599905|ref|YP_007906376.1| 125 WVFEVDENF-VYtYSSPKVRDILGYEPEEVVGKKPFDFM-PEDERKKAVEEFEVIKRDkiPFCGLENVFMRKDGSHV 199
                                       567788999.666**************************.77777777777777777799***************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                         + + +p++d++g+l+g+ +++rDit+
  gi|488599905|ref|YP_007906376.1| 200 ILETCGRPFFDEKGNLRGYRGVSRDITA 227
                                       **************************95 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 1.3e-19
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+i+  + d ri+++N++a+ ++Gy++ ev+gk++ +l+  ++ ++ + ++++a+ +g   +r+ e+v i+k+g+++
  gi|488599905|ref|YP_007906376.1| 247 DAIVSLDLDSRIVSWNKGAEMMFGYKESEVIGKPLATLMpeENWDSCRVNFKKAIFEGY--ARDIETVRITKDGRRI 321
                                       67887789*******************************99777777777777777777..8*************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       +v+ t+++++d++ge +g+++i+rDit+
  gi|488599905|ref|YP_007906376.1| 322 LVDQTLTTIYDSNGEHMGFVAIMRDITK 349
                                       **************************95 PP

  == domain 3  score: 44.7 bits;  conditional E-value: 1.8e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetf 76 
                                       d+i  +n dg i+++N++a++l+G +++e lg + + l+  ++e +++ + +++ ++k     ++e+   +k+ge +
  gi|488599905|ref|YP_007906376.1| 390 DAIYSVNLDGVITSWNKTAEKLFGWTKKEALGMPADVLL--PDEIKNETSFLIQKIKKgvRYISYETRRLTKDGEII 464
                                       6677789***666**************************..5555555555555555566699************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDit 103
                                        v+lt+sp+ d++g+  g+ vi rDi+
  gi|488599905|ref|YP_007906376.1| 465 DVDLTVSPILDEEGKPAGFSVITRDIS 491
                                       **************************7 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   1.8e-14   1.2e-11       2     109 ..     120     229 ..     119     230 .. 0.89
   2 !   48.4   0.0   1.4e-15   9.5e-13       2     110 .]     243     352 ..     242     352 .. 0.97
   3 !   49.3   0.0   6.9e-16   4.8e-13       1     106 [.     385     491 ..     385     493 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.8e-14
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pg 76 
                                       + ++d+++ +d++++++y ++  ++++g++pee++Gk++++++pe+ +    +  +   + + p   le +    +g
  gi|488599905|ref|YP_007906376.1| 120 EDVNDWVFEVDENFVYTYSSPKVRDILGYEPEEVVGKKPFDFMPEDERKKAVEEFEVIKRDKIPFCGLENVFMrkDG 196
                                       5689*****************************************988888888877777766666665444479** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +++++e+  +P++de+G  +g+ ++srDiT+r+
  gi|488599905|ref|YP_007906376.1| 197 SHVILETCGRPFFDEKGNLRGYRGVSRDITARK 229
                                       *******************************97 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 1.4e-15
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pge 77 
                                       d++ da++ ld d+r++ +N+ a+ +fg+   e++Gk+la l+pee  +  + + ++++ ++ + + ++++ + +g+
  gi|488599905|ref|YP_007906376.1| 243 DHTVDAIVSLDLDSRIVSWNKGAEMMFGYKESEVIGKPLATLMPEENWDSCRVNFKKAIFEGYARDIETVRITkDGR 319
                                       8999******************999***********************************************9**** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       +  ++ +l+ + d++Ge +g+++i+rDiT r++
  gi|488599905|ref|YP_007906376.1| 320 RILVDQTLTTIYDSNGEHMGFVAIMRDITKRKE 352
                                       ******************************985 PP

  == domain 3  score: 49.3 bits;  conditional E-value: 6.9e-16
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       l++++da++ ++ dg+++ +N++a++lfg++ +e+lG++   llp+e + + +  +++  +g + i+ ++ +l+ +g
  gi|488599905|ref|YP_007906376.1| 385 LENSNDAIYSVNLDGVITSWNKTAEKLFGWTKKEALGMPADVLLPDEIKNETSFLIQKIKKGVRYISYETRRLTkDG 461
                                       79************************************************************9999999988889** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiT 106
                                       e   ++l+++P++de+G++ g+ vi+rDi+
  gi|488599905|ref|YP_007906376.1| 462 EIIDVDLTVSPILDEEGKPAGFSVITRDIS 491
                                       ****************************96 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   4.4e-16   3.1e-13       2      88 ..     136     221 ..     135     222 .. 0.93
   2 !   36.0   0.0   9.1e-12   6.2e-09       2      88 ..     259     343 ..     258     344 .. 0.96
   3 !   37.5   0.0   3.2e-12   2.2e-09       2      86 ..     402     484 ..     401     487 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 4.4e-16
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.py.egeyRirrkdGeyrwveararvir 76 
                                       +y s++v++ilGy+pee+ gk  +  d++  ++r+++ e+++ ++k+++ p+   e  ++rkdG+++ +e+++r+++
  gi|488599905|ref|YP_007906376.1| 136 TYSSPKVRDILGYEPEEVVGK--KPFDFMPEDERKKAVEEFE-VIKRDKiPFcGLENVFMRKDGSHVILETCGRPFF 209
                                       6889*****************..******************8.66666669999*********************** PP

                             PAS_3  77 dengkpvrvigv 88 
                                       de+g+   + gv
  gi|488599905|ref|YP_007906376.1| 210 DEKGNLRGYRGV 221
                                       *****9999887 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 9.1e-12
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +++++  e ++Gy ++e++gk   ++ l+  e  + +r ++++a+ +g + ++e  +++kdG  + v+ + + i+d+
  gi|488599905|ref|YP_007906376.1| 259 VSWNKGAEMMFGYKESEVIGK--PLATLMPEENWDSCRVNFKKAIFEGYARDIETVRITKDGRRILVDQTLTTIYDS 333
                                       89*******************..9999999999******************************************** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       ng+   ++++
  gi|488599905|ref|YP_007906376.1| 334 NGEHMGFVAI 343
                                       ***9998876 PP

  == domain 3  score: 37.5 bits;  conditional E-value: 3.2e-12
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepy.egeyRirrkdGeyrwveararvird 77 
                                       ++++++ e+++G+++ e lg     +d++ p+++++  + l + +kkg +y + e R+++kdGe++ v+ ++++i d
  gi|488599905|ref|YP_007906376.1| 402 TSWNKTAEKLFGWTKKEALGM---PADVLLPDEIKNETSFLIQKIKKGVRYiSYETRRLTKDGEIIDVDLTVSPILD 475
                                       68*******************...99***********************887************************* PP

                             PAS_3  78 engkpvrvi 86 
                                       e+gkp  + 
  gi|488599905|ref|YP_007906376.1| 476 EEGKPAGFS 484
                                       *****9876 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       5.9   4.1e+03      92     108 ..      92     108 ..      86     113 .. 0.84
   2 ?   -3.1   0.0       8.6   5.9e+03      86     112 ..     370     396 ..     368     405 .. 0.76
   3 !   83.8   0.2   1.3e-26   8.9e-24       6     135 ..     523     646 ..     518     647 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.9
                            DUF835  92 ngFesvlkflltlkDav 108
                                       + F+ ++++l++ kD++
  gi|488599905|ref|YP_007906376.1|  92 KAFNYMVDVLTKQKDML 108
                                       679999999****9997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.6
                            DUF835  86 eyLvlengFesvlkflltlkDavllkn 112
                                       e+L  +++ e  + +l++ +Da+++ n
  gi|488599905|ref|YP_007906376.1| 370 ELLKSQKELEYLANILENSNDAIYSVN 396
                                       566667777888888888888888765 PP

  == domain 3  score: 83.8 bits;  conditional E-value: 1.3e-26
                            DUF835   6 ekakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekgvvli 82 
                                       + a e+++dlvk+g+++ +itR+ p++++  v  +n++ +wl++++++nt sP+ ++++++ti +  ++++   vl+
  gi|488599905|ref|YP_007906376.1| 523 DLALEVFNDLVKCGYSGTIITRKLPDELK--V-ENNSTHFWLSEKKGKNTLSPD-ISEIEATIMNLPNWNN--AVLL 593
                                       66789**********************87..5.667789**************5.88**************..7*** PP

                            DUF835  83 DgleyLvlengFesvlkflltlkDavl.lkngtlilvidkealeekelalLkre 135
                                       + l+y++l+ngF+++++f++ lk a++ lk+g+++l++d+++l+e++++lL++e
  gi|488599905|ref|YP_007906376.1| 594 E-LDYIILKNGFDETFRFIQRLKEAFYlLKKGIVLLTLDPDILDERQIKLLRKE 646
                                       9.**********************986267**********************98 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-05     0.012       2      59 ..     114     168 ..     113     178 .. 0.79
   2 !   28.8   0.0   1.3e-09   8.7e-07       1      55 [.     236     291 ..     236     305 .. 0.88
   3 !   29.1   0.0     1e-09   7.1e-07       1      52 [.     379     431 ..     379     447 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellgqllpvlrplleda 59 
                                       ++r+l+e ++d ++ vd +    ++  ++  ++lGy+    +e++g+ + +++p+ e+ 
  gi|488599905|ref|YP_007906376.1| 114 KYRSLIEDVNDWVFEVDeNF-VYTYSSPKVRDILGYE---PEEVVGKKPFDFMPEDERK 168
                                       7****************444.5999***********9...5577777777777777744 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.3e-09
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       ++l ++ ++  d+i+ +dl+ riv +N+ a++++Gy+  +++g++l +l+p+ +  
  gi|488599905|ref|YP_007906376.1| 236 AYLASITDHTVDAIVSLDLDSRIVSWNKGAEMMFGYKeSEVIGKPLATLMPEENWD 291
                                       58999*************999********************999999888887655 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 1e-09
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvl 52 
                                       e+l +++e+s+d+i  v+l++ i+ +N++a++l+G++ ++ +g++ ++llp+ 
  gi|488599905|ref|YP_007906376.1| 379 EYLANILENSNDAIYSVNLDGVITSWNKTAEKLFGWTkKEALGMPADVLLPDE 431
                                       7999**************7788*********************9999666654 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.9     4e+03      48     115 ..     132     200 ..     126     204 .. 0.73
   2 !   25.0   0.0     2e-08   1.4e-05      38     139 ..     247     345 ..     218     349 .. 0.83
   3 !   17.4   0.0   4.6e-06    0.0031      10     140 ..     360     489 ..     352     492 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.9
                            MEKHLA  48 dpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgf.venysGvrisstGrrfs 115
                                       + v++y+  +  d+l ++ ee++  +    + ++e+++  +++e ++++ +  +  + v + ++G ++ 
  gi|488599905|ref|YP_007906376.1| 132 NFVYTYSSPKVRDILGYEPEEVVGKKPFDFMPEDERKKAVEEFEVIKRDKIpFCGLENVFMRKDGSHVI 200
                                       568899999999999999999998877777777887777888888887765356666666666666665 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 2e-08
                            MEKHLA  38 favlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgfvenysGvrisstGrrf 114
                                       +a++s +l+     +  N+ a  ++ ++ +e++  p+   + +e+ ++ +  ++k+  +g++++ + vri+++Grr+
  gi|488599905|ref|YP_007906376.1| 247 DAIVSLDLD--SRIVSWNKGAEMMFGYKESEVIGKPLATLMPEENWDSCRVNFKKAIFEGYARDIETVRITKDGRRI 321
                                       566666654..44445599999********************9999998999************************* PP

                            MEKHLA 115 sienavvWkvldeegkahGqAamfs 139
                                        +++++  +++d++g+++G  a+++
  gi|488599905|ref|YP_007906376.1| 322 LVDQTL-TTIYDSNGEHMGFVAIMR 345
                                       **9865.59********99888776 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 4.6e-06
                            MEKHLA  10 SYrrltg..keLlessesaeelakaLfeapfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeeke 84 
                                        Yr+l +  +eLl+s+++ e la+ L + ++a+ s +l  d v +  N++a +l+  t +e   +p +  + +e k+
  gi|488599905|ref|YP_007906376.1| 360 AYRQLEEktQELLKSQKELEYLANILENSNDAIYSVNL--DGVITSWNKTAEKLFGWTKKEALGMPADVLLPDEIKN 434
                                       5666543116899999999**************99986..6999****************************77799 PP

                            MEKHLA  85 eRealLekvaeqgfvenysGvrisstGrrfsienavvWkvldeegkahGqAamfsn 140
                                       e + l++k+++      y+  r++++G  + ++  +v  +ldeegk+ G  ++ ++
  gi|488599905|ref|YP_007906376.1| 435 ETSFLIQKIKKGVRYISYETRRLTKDGEIIDVD-LTVSPILDEEGKPAGFSVITRD 489
                                       96666677766666779**********999986.67889*******9999887765 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.1   7.5e+02      16     106 .]     130     226 ..     125     226 .. 0.67
   2 !   18.6   0.0   3.2e-06    0.0022      11     106 .]     248     348 ..     238     348 .. 0.80
   3 !   14.2   0.0   7.3e-05      0.05       1     105 [.     381     490 ..     381     491 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.1
                            PAS_10  16 DdnlqirrFtpaakklfklipad.vGrpladihpkkavknveeviealrtgek...devevvvpkngkwvlvry..l 86 
                                       D+n   ++ +p+ + ++ + p++ vG +  d+ p+++ k++ e +e +++ +      ++v + k+g +v++++  +
  gi|488599905|ref|YP_007906376.1| 130 DENFVYTYSSPKVRDILGYEPEEvVGKKPFDFMPEDERKKAVEEFEVIKRDKIpfcGLENVFMRKDGSHVILETcgR 206
                                       55555555566666666666544268888899888666666555666666665455667777888888877665448 PP

                            PAS_10  87 pyrdedgeiaGvvetfvDit 106
                                       p+ de+g+ +G   +  Dit
  gi|488599905|ref|YP_007906376.1| 207 PFFDEKGNLRGYRGVSRDIT 226
                                       99999999999888877775 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.2e-06
                            PAS_10  11 eltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknveeviealrtg.ek.devevvvpkngkwvlv. 83 
                                       +++ lD + +i  +++ a+++f +++++ +G pla++ p+++ ++ +  +++ + +    d ++v ++k+g+ +lv 
  gi|488599905|ref|YP_007906376.1| 248 AIVSLDLDSRIVSWNKGAEMMFGYKESEvIGKPLATLMPEENWDSCRVNFKKAIFEgYArDIETVRITKDGRRILVd 324
                                       6899********************987626**********9999998776655544144255556668999886652 PP

                            PAS_10  84 .rylpyrdedgeiaGvvetfvDit 106
                                        +   ++d +ge  G v ++ Dit
  gi|488599905|ref|YP_007906376.1| 325 qTLTTIYDSNGEHMGFVAIMRDIT 348
                                       27899******************7 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 7.3e-05
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklip.advGrpladihpkkavknveeviealrtgek..devevvv 74 
                                       l n+L++ + ++  ++ +  i+ ++++a+klf  ++ + +G p + + p+++++++  +i+++++g +   +++   
  gi|488599905|ref|YP_007906376.1| 381 LANILENSNDAIYSVNLDGVITSWNKTAEKLFGWTKkEALGMPADVLLPDEIKNETSFLIQKIKKGVRyiSYETRRL 457
                                       67999999999*********************98761579**************************99655566666 PP

                            PAS_10  75 pkngkw..vlvrylpyrdedgeiaGvvetfvDi 105
                                       +k+g++  v ++++p+ de+g+ aG  ++  Di
  gi|488599905|ref|YP_007906376.1| 458 TKDGEIidVDLTVSPILDEEGKPAGFSVITRDI 490
                                       8****94455689*******************9 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   2.3e-11   1.6e-08       1      51 [.      52     101 ..      52     103 .. 0.94
   2 ?   -1.5   0.0       4.8   3.3e+03       2      28 ..     439     471 ..     438     479 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.3e-11
                                       HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHHHHH CS
                              HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMldrL 51 
                                       ++a++i+ PL+rL+   ++i +G+  + ++v+++DE+ +La+afN M+d L
  gi|488599905|ref|YP_007906376.1|  52 FVAGSITEPLERLRNGFENIMRGESAY-IEVNTGDELEDLAKAFNYMVDVL 101
                                       799*********************777.*******************9976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.8
                                       HHHTTHHHHHHHHHHHHHHT.TT.....BTSST CS
                              HAMP   2 larrilrPLrrLaraarria.aG.....dldtr 28 
                                       l+  i + +r ++  +rr+  +G     dl+++
  gi|488599905|ref|YP_007906376.1| 439 LIQKIKKGVRYISYETRRLTkDGeiidvDLTVS 471
                                       667788889999999999995578887777766 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.1   1.4e+03      79     115 .]     192     233 ..     165     233 .. 0.68
   2 !   25.7   0.0   1.4e-08   9.7e-06       3     115 .]     244     355 ..     242     355 .. 0.78
   3 ?    4.7   0.0     0.046        32       1      45 [.     385     428 ..     385     498 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                             PAS_7  79 ererpdgrvievrgnpl.pdgGfVtty....tDiTerrraee 115
                                        r+  ++ ++e  g+p  +++G +  y     DiT+r+ aee
  gi|488599905|ref|YP_007906376.1| 192 MRKDGSHVILETCGRPFfDEKGNLRGYrgvsRDITARKHAEE 233
                                       555556666666666654334444444222269999999986 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.4e-08
                             PAS_7   3 nmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellryn.aergefg.agdveaeverrlaaaragkphs 77 
                                       +  ++i+ +D d r+v wN+    ++++ e+ v +g+pl++l+     +   ++ ++++ + ++r ++ +r  k   
  gi|488599905|ref|YP_007906376.1| 244 HTVDAIVSLDLDSRIVSWNKGAEMMFGYKESEV-IGKPLATLMPEEnWDSCRVNfKKAIFEGYARDIETVRITKDG- 318
                                       56678999*************************.********9544244444444466666667777777764443. PP

                             PAS_7  78 fererpdgrvievrgnplpdgGfVttytDiTerrraee 115
                                         r   d +   +  +  ++ GfV++  DiT+r++aee
  gi|488599905|ref|YP_007906376.1| 319 -RRILVDQTLTTIYDSNGEHMGFVAIMRDITKRKEAEE 355
                                       .55566777888888888999***************96 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.046
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleell 45 
                                       len +++i  ++ d+ ++ wN+   +l++++++ +  g+p + ll
  gi|488599905|ref|YP_007906376.1| 385 LENSNDAIYSVNLDGVITSWNKTAEKLFGWTKKEA-LGMPADVLL 428
                                       788999999999******************99988.888877665 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   8.6e-06    0.0059      17      68 .]     676     724 ..     666     724 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.6e-06
                            HTH_27  17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +r   +d++ + n+   ++ + ++ L+ekGL+   +  +d+r k v++T+kG
  gi|488599905|ref|YP_007906376.1| 676 ERPPVRDIMAKFNIARNTAKKRIRYLEEKGLL---KVLRDGRIKVVEVTEKG 724
                                       566679999999**999***************...55689***********9 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     2e-05     0.013      25      62 ..     678     715 ..     671     717 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                                       --HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR  25 PsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62 
                                       P++r+++a+f++ r+t  + +r Le++gl+ + + + +
  gi|488599905|ref|YP_007906376.1| 678 PPVRDIMAKFNIARNTAKKRIRYLEEKGLLKVLRDGRI 715
                                       8*****************************99876665 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.071        49      28      60 ..     146     178 ..     141     215 .. 0.77
   2 !    8.4   0.0    0.0033       2.3       6     108 ..     250     348 ..     246     353 .. 0.80
   3 ?   -1.0   0.0       2.8   1.9e+03       5      19 ..     454     468 ..     451     473 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.071
                            PAS_11  28 lglekeelvgrsiydLchpqdlstlkshlrevi 60 
                                       lg+e ee+vg+  +d++ +++++++ + ++ + 
  gi|488599905|ref|YP_007906376.1| 146 LGYEPEEVVGKKPFDFMPEDERKKAVEEFEVIK 178
                                       79*****************99999998887665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0033
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvk 82 
                                       + ld+d +I+s ++    a++  g++++e++g+ + +L+ ++   + +  +++ i +  +  + ++R++  +++ + 
  gi|488599905|ref|YP_007906376.1| 250 VSLDLDSRIVSWNK---GAEMMFGYKESEVIGKPLATLMPEENWDSCRVNFKKAIFEGYARDIETVRITK-DGRRIL 322
                                       679***********...********************************999999666666777888876.777777 PP

                            PAS_11  83 vktksklfknqksneqdfimathtll 108
                                       v  ++   ++++ +   f+ ++  + 
  gi|488599905|ref|YP_007906376.1| 323 VDQTLTTIYDSNGEHMGFVAIMRDIT 348
                                       77777776666666666666665555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.8
                            PAS_11   5 ttrldidgkIisvDt 19 
                                       t rl+ dg Ii+vD 
  gi|488599905|ref|YP_007906376.1| 454 TRRLTKDGEIIDVDL 468
                                       558899*******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 !   13.4   0.0   8.4e-05     0.058      24      66 ..     682     728 ..     675     734 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.4e-05
                            HTH_45  24 kimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlell 66 
                                        im k n+  ++++k + +L ekgl+    + + +  ++TekG+e+ 
  gi|488599905|ref|YP_007906376.1| 682 DIMAKFNIARNTAKKRIRYLEEKGLLkvlrDGRIKVVEVTEKGKEFF 728
                                       59***********************8767555888999******986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.4e-05      0.03      22      61 .]     675     714 ..     662     714 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-05
                                       CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  22 aegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       +e   + ++++ + +++nt+ +++r Lee gL++v r gr
  gi|488599905|ref|YP_007906376.1| 675 GERPPVRDIMAKFNIARNTAKKRIRYLEEKGLLKVLRDGR 714
                                       555667799**************************99987 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 ?   13.2   0.0   8.5e-05     0.058      23      58 ..     675     709 ..     662     714 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-05
                                       SS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind  23 gypPsireiaralglkSpsaveehLkaLerKGyier 58 
                                       g  P +r+i+ +++++  ++++++ + Le KG++++
  gi|488599905|ref|YP_007906376.1| 675 GERPPVRDIMAKFNIA-RNTAKKRIRYLEEKGLLKV 709
                                       55699**********9.9**************9975 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.6   1.8e+03     492     507 ..      37      52 ..       8     128 .. 0.68
   2 ?   12.7   0.2   6.4e-05     0.044     181     240 ..     338     395 ..     337     465 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.6
                             LMBR1 492 iyypifilllvvatlf 507
                                       +yy+ ++++++ +++f
  gi|488599905|ref|YP_007906376.1|  37 VYYSYMFIIILGISFF 52 
                                       3333333333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.4e-05
                             LMBR1 181 yGlvelPrslwreiksdldeelkklyfeaaklntekeeaereledllkevkk.lrksises 240
                                       +G+v++ r++ +  +++ +eelk++y ++++ ++e+ ++++ele +l ++ + +++ i + 
  gi|488599905|ref|YP_007906376.1| 338 MGFVAIMRDITK--RKEAEEELKRAYRQLEEKTQELLKSQKELE-YLANILEnSNDAIYSV 395
                                       6*********99..******************************.5555544044444333 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.14      20      48 .]     680     708 ..     676     708 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                            HTH_24  20 qreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                        r++  + ++ ++t ++r++ Lee+Gl+k
  gi|488599905|ref|YP_007906376.1| 680 VRDIMAKFNIARNTAKKRIRYLEEKGLLK 708
                                       799***********************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.13      18      59 ..     674     712 ..     661     715 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                       TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                            MarR_2  18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59 
                                        g++  v+++ +++++ + ++ ++++ L+++GL+   +   D
  gi|488599905|ref|YP_007906376.1| 674 VGERPPVRDIMAKFNIARNTAKKRIRYLEEKGLLKVLR---D 712
                                       444569***************************97654...4 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   0.00032      0.22      17      45 ..     680     708 ..     679     717 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                          HTH_DeoR  17 veelvellgvSeaTiRRDLneLeeqgllt 45 
                                       v ++++ ++++ +T+ + +++Lee+gll+
  gi|488599905|ref|YP_007906376.1| 680 VRDIMAKFNIARNTAKKRIRYLEEKGLLK 708
                                       679************************86 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.23      26      55 .]     678     707 ..     667     707 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                            HTH_36  26 psqetlakrlglsknTvsraikeLeqlGyi 55 
                                       p ++++++++++ +nT+ + i+ Le++G++
  gi|488599905|ref|YP_007906376.1| 678 PPVRDIMAKFNIARNTAKKRIRYLEEKGLL 707
                                       6789************************97 PP

>> DUF3585  Bivalent Mical/EHBP Rab binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.036        24      53     100 ..      69     116 ..      57     126 .. 0.90
   2 ?    7.6   0.9    0.0058         4      32      68 ..     348     384 ..     338     396 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.036
                           DUF3585  53 nelvrreseLmilareqeLedeqadleqelrelmakeekeKteedker 100
                                       ++++r es ++ +    eLed  +  ++ + +l+++++  K++edk r
  gi|488599905|ref|YP_007906376.1|  69 ENIMRGESAYIEVNTGDELEDLAKAFNYMVDVLTKQKDMLKKSEDKYR 116
                                       57899999999999*******************************976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0058
                           DUF3585  32 esgeeeeeellqewfeLvneknelvrreseLmilare 68 
                                       ++++e eeel + + +L ++ +el++ ++eL +la+ 
  gi|488599905|ref|YP_007906376.1| 348 TKRKEAEEELKRAYRQLEEKTQELLKSQKELEYLANI 384
                                       467999***************************9875 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       0.6   4.1e+02      17      71 ..      62     117 ..      56     190 .. 0.80
   2 ?   10.1   0.2   0.00099      0.68      33      73 ..     339     379 ..     310     466 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.6
                          PHM7_cyt  17 eklkeffeelypgkv.vesvqivrdvkkldklveerekavrkleaalskykkngkk 71 
                                       e+l++ fe++  g+  + +v+   ++ +l k  +   +++ k + +l+k++ + ++
  gi|488599905|ref|YP_007906376.1|  62 ERLRNGFENIMRGESaYIEVNTGDELEDLAKAFNYMVDVLTKQKDMLKKSEDKYRS 117
                                       78899999976544446789999999999999999999999988888888766555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00099
                          PHM7_cyt  33 esvqivrdvkkldklveerekavrkleaalskykkngkklp 73 
                                         v i rd++k ++  ee ++a+r+le+ +++++k +k+l+
  gi|488599905|ref|YP_007906376.1| 339 GFVAIMRDITKRKEAEEELKRAYRQLEEKTQELLKSQKELE 379
                                       3389*******************************998765 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.97   6.7e+02      52      82 ..     345     375 ..     336     409 .. 0.78
   2 ?    8.4   0.1    0.0034       2.4      34      70 ..     554     590 ..     535     599 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.97
                                       HHHHHHHCT-SS--HHHHTS-HHHHHHHHHH CS
                           PI_PP_I  52 edLnkiannktplPsWfnelskaqqellrvl 82 
                                        d++k ++ ++ l + +++l+++ qell+  
  gi|488599905|ref|YP_007906376.1| 345 RDITKRKEAEEELKRAYRQLEEKTQELLKSQ 375
                                       5666667777788888888888888888754 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHT CS
                           PI_PP_I  34 nqfllkWeeikktslsLeedLnkiannktplPsWfne 70 
                                       n+ +  W + kk   +L+ d+++i++   +lP+W n+
  gi|488599905|ref|YP_007906376.1| 554 NNSTHFWLSEKKGKNTLSPDISEIEATIMNLPNWNNA 590
                                       555778999999999*******************886 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.092        64      21      63 ..      85     123 ..      74     132 .. 0.86
   2 ?    8.7   1.3    0.0023       1.6      43      85 ..     348     390 ..     338     393 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHC CS
                             Sec2p  21 kEledLtasLFeeANkmVaaarkekealekkneklkeqLkeke 63 
                                        EledL+++     N mV    k+k+ l+k ++k ++ +++ +
  gi|488599905|ref|YP_007906376.1|  85 DELEDLAKAF----NYMVDVLTKQKDMLKKSEDKYRSLIEDVN 123
                                       6999999885....9******************9999998866 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXX CS
                             Sec2p  43 kekealekkneklkeqLkeketlleslqeqLkeLkevlekmee 85 
                                        +++++e++ ++ ++qL+ek + l ++q++L+ L ++le+ ++
  gi|488599905|ref|YP_007906376.1| 348 TKRKEAEEELKRAYRQLEEKTQELLKSQKELEYLANILENSND 390
                                       56788999999*************************9998765 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 ?    5.2   0.1      0.05        35       5      46 ..      83     124 ..      80     133 .. 0.89
   2 ?    5.4   0.5     0.044        30      22      75 ..     346     395 ..     341     409 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHH CS
                            FliD_N   5 tdslvkqlmkaerakldkleqkktklewkqsayrelnsklsn 46 
                                       t + +++l ka ++ +d l+++k  l++  ++yr+l  ++++
  gi|488599905|ref|YP_007906376.1|  83 TGDELEDLAKAFNYMVDVLTKQKDMLKKSEDKYRSLIEDVND 124
                                       55567889999999**********************999875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.044
                                       XXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXXGGGGGXEEEEECSTTTEEE CS
                            FliD_N  22 kleqkktklewkqsayrelnsklsnlksalsalsksstfsakkatssdesvvta 75 
                                        ++++k+  e+ + ayr+l+ k ++l ++ ++l    ++ a+  + s++++ ++
  gi|488599905|ref|YP_007906376.1| 346 DITKRKEAEEELKRAYRQLEEKTQELLKSQKEL----EYLANILENSNDAIYSV 395
                                       588999999999999****99999999955555....44444445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1528  (0.0852251); expected 358.6 (0.02)
Passed bias filter:                      982  (0.0547716); expected 358.6 (0.02)
Passed Vit filter:                       158  (0.00881254); 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: 0.96u 0.35s 00:00:01.31 Elapsed: 00:00:00.54
# Mc/sec: 4143.52
//
Query:       gi|488599906|ref|YP_007906377.1|  [L=319]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  188.6  21.1    1.5e-55  188.2  21.1    1.1  1  Cons_hypoth698  Conserved hypothetical protein 698
  ------ inclusion threshold ------
      0.077   12.7   0.0       0.16   11.7   0.0    1.5  1  PUF             Pumilio-family RNA binding repeat
        3.8    7.1   5.5        2.8    7.5   1.7    2.4  2  SLATT_6         SMODS and SLOG-associating 2TM effector domai


Domain annotation for each model (and alignments):
>> Cons_hypoth698  Conserved hypothetical protein 698
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.2  21.1   2.5e-59   1.5e-55       4     304 .]      15     300 ..      12     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 188.2 bits;  conditional E-value: 2.5e-59
                    Cons_hypoth698   4 llllliavlalllakvellfaklsalllAillGillgnflklqeqlkaGvafskkklLrlgivllGfrltlsdiakv 80 
                                       +++ + +++++++++   + ++l al+lA+++Gi +g fl+ ++ ++   + s    L lgivl+G+++ + +  ++
  gi|488599906|ref|YP_007906377.1|  15 MMITIPGIVSYFVSS---FYPALDALFLALIFGITIGSFLNSSK-IRYLAEESLAVTLPLGIVLYGAKIKIPYPSDF 87 
                                       455566778888887...78*****************9888766.55556666679********************* PP

                    Cons_hypoth698  81 GlkgvlldiivlistfllvlllgakllkldkklalLvaaGssiCGasAilavepvikareeevalaiavivllgtva 157
                                          +v++ +i     ++++++l+ak +++++kl+lL+a+G++iCG+sAi +v++++k+r+ee+++ai vi+++g+++
  gi|488599906|ref|YP_007906377.1|  88 PT-QVIVLTIFSTLLMGTAVFLFAKTFRVSEKLSLLLACGTAICGVSAITIVSSIVKPRKEEFSAAIIVITVVGLTG 163
                                       99.56666666667789999999****************************************************** PP

                    Cons_hypoth698 158 mllyPalatllsltdeefgvfaGasvhevaqVvaagelvseeaakiAvivKltRvlllapvvlllslllakreeese 234
                                       ++lyP+l+  l+l++e ++++ Ga++h+++ V +a+  +++ + +  + vK +R++l+  ++ll+s++ a++     
  gi|488599906|ref|YP_007906377.1| 164 AILYPFLGYHLGLSPECYAILSGATLHQTSLVEIASLPFGNYVMQEGLAVKGIRIALISVATLLISFIYAEN----- 235
                                       ********************************************99999999**************776643..... PP

                    Cons_hypoth698 235 tkeakitiPwFvlgFlvvallntlvllpselvsalktlstlllvmalaAlglktdlkalkkaglkpllla 304
                                           ++++Pw+v++Fl+va l+++vl p e+v +++ lst+++ ++la +gl +++++++++ l pl++a
  gi|488599906|ref|YP_007906377.1| 236 ----RFYVPWYVVAFLIVAFLSSFVLTP-EIVRVIEPLSTIAFSITLASIGLSVNIRDIQRVHLSPLIAA 300
                                       ....79*******************998.*************************************9975 PP

>> PUF  Pumilio-family RNA binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.7e-05      0.16       4      20 ..     192     208 ..     191     209 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                                       GGHHHHHTSTTHHHHHH CS
                               PUF   4 gnlvqLstdqyGnyvvQ 20 
                                       ++lv++++ ++Gnyv+Q
  gi|488599906|ref|YP_007906377.1| 192 TSLVEIASLPFGNYVMQ 208
                                       679*************9 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.7   0.00047       2.8      27      73 ..     112     162 ..     104     166 .. 0.86
   2 ?   -0.2   0.1      0.11   6.6e+02      37      83 ..     194     237 ..     187     240 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00047
                           SLATT_6  27 tydiveKlpglislislavGilalv.ieels...tkllsalliiigiialy 73 
                                       t+ + eKl+ l++  + + G+ a++ + ++    +++ sa++i+i +++l+
  gi|488599906|ref|YP_007906377.1| 112 TFRVSEKLSLLLACGTAICGVSAITiVSSIVkprKEEFSAAIIVITVVGLT 162
                                       899********************9954445457799************996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.11
                           SLATT_6  37 lislislavGilalvieelstkllsalliiigiialyisayekdkek 83 
                                       l+ + sl +G + +  e+l+ k + ++l  i++++l+is+  ++++ 
  gi|488599906|ref|YP_007906377.1| 194 LVEIASLPFGNYVM-QEGLAVKGIRIAL--ISVATLLISFIYAENRF 237
                                       66777888887755.5777777776665..57788888887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2084.83
//
Query:       gi|488599907|ref|YP_007906378.1|  [L=110]
Description: hypothetical protein Asulf_00356 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-36  125.7  12.0    1.3e-36  125.6  12.0    1.0  1  AF0941-like  AF0941-like
     0.0023   18.4   1.6      0.003   18.0   1.6    1.2  1  RBFA         Ribosome-binding factor A


Domain annotation for each model (and alignments):
>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6  12.0   1.5e-40   1.3e-36       1     113 []       1     109 [.       1     109 [. 0.99

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 1.5e-40
                                       SB---HHHHHHHHHHT...TSS-GGGHHHHT-HHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHTHH CS
                       AF0941-like   1 MaykntyleklgellkkeviddiekvldelldkeeieelfrsdvedvleklkagdieeeeakknlklLkvyvvsqLd 77 
                                       M+y+n+yl++l+e+l    +++++k++d+l+++++ie++f++dv++v+ek+++++i+e +akknl+lLkv+vv+qL+
  gi|488599907|ref|YP_007906378.1|   1 MEYINSYLDRLREFL----VNKDQKMADQLISEAKIEKMFIDDVKNVYEKYRKNEIAEVDAKKNLDLLKVFVVTQLN 73 
                                       9**************....9********************************************************* PP

                                       HHHHHHHHHHHCTT-----HHHHHHHHHHHHHHCT- CS
                       AF0941-like  78 ehykrvlelledkekkiekevvdeIveaieraeeei 113
                                       +++k+v+e++++++++i++evv++Ive+ie+a e+i
  gi|488599907|ref|YP_007906378.1|  74 NKRKDVMESVGKQPEDIDGEVVKRIVEFIEDAIERI 109
                                       ********************************9975 PP

>> RBFA  Ribosome-binding factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.6   3.3e-07     0.003      11      79 ..      30      98 ..      18     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.3e-07
                                      HHHHHHHHHCT-HCCT.GHHCEEEEEEESTTSSEEEEEEE.ESS-HHHHHHHHHHHHHTHHHHHHHHHHHC CS
                              RBFA 11 relseilqeelkdprl.gklvtiteVkvsrDlskakVyvs.vlgseeekeevlkaLkkaagflrrelakrl 79
                                       ++++++ +++k+     +  +i eV+ +++l   kV+v   l+  +++++v++ + k+ + +  e+ kr+
  gi|488599907|ref|YP_007906378.1| 30 AKIEKMFIDDVKNVYEkYRKNEIAEVDAKKNLDLLKVFVVtQLN--NKRKDVMESVGKQPEDIDGEVVKRI 98
                                      458888877777443322389*****************551444..5899*****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1322  (0.0737353); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 717.02
//
Query:       gi|488599908|ref|YP_007906379.1|  [L=234]
Description: ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-31  107.5   0.0    1.4e-30  106.6   0.0    1.4  1  ABC_tran         ABC transporter
    2.4e-08   34.1   0.0    0.00049   20.0   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0007   19.9   0.6     0.0029   17.9   0.6    2.0  1  AAA_22           AAA domain
     0.0018   18.7   0.0     0.0074   16.7   0.0    1.9  1  AAA              ATPase family associated with various cellul
      0.002   18.1   0.1     0.0045   16.9   0.1    1.5  1  NACHT            NACHT domain
     0.0023   18.5   0.0     0.0039   17.7   0.0    1.4  1  AAA_23           AAA domain
     0.0026   17.7   0.0     0.0052   16.7   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
     0.0032   17.9   0.1     0.0048   17.3   0.1    1.4  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.017   15.7   0.0      0.084   13.4   0.0    1.9  2  AAA_18           AAA domain
      0.019   14.3   0.4        2.7    7.3   0.0    3.0  4  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.027   14.5   0.1       0.12   12.4   0.0    1.9  2  AAA_5            AAA domain (dynein-related subfamily)
      0.029   14.3   0.1      0.045   13.7   0.1    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.033   13.8   0.1      0.061   13.0   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.033   14.4   0.0      0.091   13.0   0.0    1.8  2  AAA_28           AAA domain
      0.036   13.2   0.1      0.059   12.5   0.1    1.3  1  NB-ARC           NB-ARC domain
      0.039   13.4   0.1       0.57    9.6   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.043   13.5   0.0        0.1   12.4   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
      0.052   13.2   0.2       0.26   11.0   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
       0.07   12.8   0.1       0.13   12.0   0.0    1.5  1  AAA_24           AAA domain
      0.086   12.3   0.0       0.62    9.5   0.0    2.0  2  PhoH             PhoH-like protein
        0.1   11.4   0.0       0.16   10.7   0.0    1.2  1  DLIC             Dynein light intermediate chain (DLIC)
       0.11   12.2   0.2       0.24   11.1   0.2    1.5  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.15   12.4   0.0        0.3   11.4   0.0    1.5  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
       0.18   11.7   0.0       0.32   10.9   0.0    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
        0.2   12.1   0.2        0.7   10.3   0.0    1.9  2  RNA_helicase     RNA helicase
       0.23   11.1   0.0       0.35   10.5   0.0    1.3  1  AAA_15           AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0     2e-33   1.4e-30       2     137 .]      17     150 ..      16     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 2e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++ +k +eg+ v i+Ge+G+GK+tLl+++agl++  eG+i+++g+       e+ r++ig+++q+++l p  t+ e
  gi|488599908|ref|YP_007906379.1|  17 DRIRFKAEEGSFVCILGESGCGKTTLLRIIAGLES-FEGTIKYRGR-------EIDREKIGFVFQDDRLIPWRTALE 85 
                                       7899*****************************98.6****77755.......5566******************** PP

                                       H..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n          e+ e++ kal+ +glk+ +     + p++LSgG++qr+ +aral+ +p++ll+DEp+a
  gi|488599908|ref|YP_007906379.1|  86 NvtfplelrgiEDAERALKALEMVGLKGYES----YYPKHLSGGMRQRIGIARALVINPEILLMDEPFA 150
                                       ******9977766666777777777777443....456*****************************85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.1e-07   0.00049       1      61 [.      28      94 ..      28     102 .. 0.89
   2 !   12.1   0.0   0.00019      0.13     236     299 ..     121     182 ..     112     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.1e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl......drdvegltdelsggggirkipslldlydpeipfefe 61
                                      + ++ G  g+GK++LL+++ +l ++      ++  +++  +   +++ r ip++  l + + p e++
  gi|488599908|ref|YP_007906379.1| 28 FVCILGESGCGKTTLLRIIAGLESFegtikyRGREIDREKIGFVFQDDRLIPWRTALENVTFPLELR 94
                                      5789*******************99999999999999999999999999999999998888888776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00019
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHSp 299
                                       +lS G+++ ++++ al   +    +ll DEp ++L+    ++   ell++  +n++ ++++THS 
  gi|488599908|ref|YP_007906379.1| 121 HLSGGMRQRIGIARALVINP---EILLMDEPFASLDELTRAKMQmELLRIWMENRVTILFVTHSI 182
                                       79999999999999999988...9************9333333257777777789********95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.6   4.2e-06    0.0029       4     117 ..      25     170 ..      22     186 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralgl 66 
                                       + +++++ GesG+GKTtllr ++     e  +++              ++++++         +++ l+++   l+l
  gi|488599908|ref|YP_007906379.1|  25 EGSFVCILGESGCGKTTLLRIIAGLESFEGTIKYrgreidrekigfvfQDDRLI--------PWRTALENVTFPLEL 93 
                                       67899***************9887765555554477775554444444333333........333333333333333 PP

                            AAA_22  67 elka.................erlsseellealeqalrarav....ielliiDEaqh.lr...s.eealeeLrslln 117
                                       ++ +                 e    ++l   ++q +  +++    +e+l+ DE    l+   + + ++e Lr++++
  gi|488599908|ref|YP_007906379.1|  94 RGIEdaeralkalemvglkgyESYYPKHLSGGMRQRIGIARAlvinPEILLMDEPFAsLDeltRaKMQMELLRIWME 170
                                       33333333333333344445545555555544444444444455677777777733335544323444555555554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05    0.0074       1      70 [.      29     155 ..      29     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                                       EEEESSTTSSHHHHHHHHHHHHTHE.EEEEETTTCS.SS...................................... CS
                               AAA   1 vllyGppGtGKTllakavakelgve.fleisgsell.sk...................................... 37 
                                       v++ G  G+GKT+l + +a   ++e  ++  g e+  +k                                      
  gi|488599908|ref|YP_007906379.1|  29 VCILGESGCGKTTLLRIIAGLESFEgTIKYRGREIDrEKigfvfqddrlipwrtalenvtfplelrgiedaeralka 105
                                       6899***************9865543355555555522255555555666666666666666666666666666666 PP

                                       ............STTHHHHHHHHHHHHHHHTS.TSEEEEEET....GGGH CS
                               AAA  38 ............yvgesekkirelfkeakeka.kpsilfiDE....idal 70 
                                                   y ++ +  +r+ +  a++   +p il++DE    +d+l
  gi|488599908|ref|YP_007906379.1| 106 lemvglkgyesyYPKHLSGGMRQRIGIARALViNPEILLMDEpfasLDEL 155
                                       66666667666688888888888888888777889999999843334444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   6.5e-06    0.0045       2      21 ..      28      47 ..      27      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.5e-06
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                       v++ Ge+G+GKTtLl+ +a
  gi|488599908|ref|YP_007906379.1| 28 FVCILGESGCGKTTLLRIIA 47
                                      589*************9886 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   5.6e-06    0.0039      15      40 ..      19      47 ..       6      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.6e-06
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAik 40
                                      i F   +  +++I G+ G+GKTT+l+ i 
  gi|488599908|ref|YP_007906379.1| 19 IRFkaeEGSFVCILGESGCGKTTLLRIIA 47
                                      56677666789**************9885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.5e-06    0.0052      85     121 ..      11      48 ..       2      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.5e-06
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       + k+ +++++ + ++ ++++++G+SG GK+tL+  +++
  gi|488599908|ref|YP_007906379.1|  11 NGKKVIDRIRFKAEEgSFVCILGESGCGKTTLLRIIAG 48 
                                       456788999999988899***************99887 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   0.1     7e-06    0.0048      22      45 ..      24      47 ..      14     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrell 45
                                       +++ v + GesG+GK++l+r ++
  gi|488599908|ref|YP_007906379.1| 24 EEGSFVCILGESGCGKTTLLRIIA 47
                                      455899**************9776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.084       1      41 [.      29      81 ..      29     111 .. 0.79
   2 ?    0.1   0.0       1.6   1.1e+03      37      87 ..     142     184 ..     121     220 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf............gvnlrdvakenglllev 41
                                      +++ G +G+GKttl + ++ ++ f             +++++v+++++l  ++
  gi|488599908|ref|YP_007906379.1| 29 VCILGESGCGKTTLLRIIAGLESFegtikyrgreidREKIGFVFQDDRLIPWR 81
                                      79****************98877788888888888877777777777776555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.6
                            AAA_18  37 lllevdpealdeskrldedkldklldaleenssaleegknlvidghlaele 87 
                                       +ll+++p+  +  +  + +++++ll++++en+         ++   ++  e
  gi|488599908|ref|YP_007906379.1| 142 ILLMDEPF-ASLDELTRAKMQMELLRIWMENRV-------TILFVTHSIEE 184
                                       55555555.222233345566788888888753.......33333333333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.054        37      25      45 ..      29      49 ..      11      52 .. 0.84
   2 ?   -1.4   0.0       1.9   1.3e+03     101     135 ..      62      96 ..      51     110 .. 0.78
   3 ?   -1.3   0.0       1.7   1.2e+03     179     196 ..     116     133 ..     107     141 .. 0.83
   4 ?    7.3   0.0    0.0039       2.7     111     187 ..     151     230 ..     121     234 .] 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.054
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsl 45
                                      + ++G +G+GKt l + +++l
  gi|488599908|ref|YP_007906379.1| 29 VCILGESGCGKTTLLRIIAGL 49
                                      6789*********99888765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                      Mg_chelatase 101 eislahnGvLfLDElpefkrkvlevLRePledgev 135
                                       ei + + G +f D+     r++le +  Ple + +
  gi|488599908|ref|YP_007906379.1|  62 EIDREKIGFVFQDDRLIPWRTALENVTFPLELRGI 96 
                                       77888889999998888889999999999997766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.7
                      Mg_chelatase 179 erYlsklsgplldRidlq 196
                                       + Y ++lsg +  Ri + 
  gi|488599908|ref|YP_007906379.1| 116 SYYPKHLSGGMRQRIGIA 133
                                       468899********9886 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0039
                      Mg_chelatase 111 fLDElpefkrkvlevLRePledge..vtisrakakvefparfqlvaamNpcpc.gk.lkdkekectcsekeierYls 183
                                        LDEl+  k   +e LR  +e++   + ++ + +++ f a+  +v++  p++  g+ + d ++  +++ ++ ++Y++
  gi|488599908|ref|YP_007906379.1| 151 SLDELTRAKM-QMELLRIWMENRVtiLFVTHSIEEAVFLADKVVVLSRKPSRVaGEvFIDLKRPRNRTDQRFNEYRK 226
                                       5888887654.58********9752134677778899**************96255245666667778888899998 PP

                      Mg_chelatase 184 klsg 187
                                        l +
  gi|488599908|ref|YP_007906379.1| 227 ELMR 230
                                       8865 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 ?   12.4   0.0   0.00017      0.12       2      22 ..      29      49 ..      28      68 .. 0.87
   2 ?   -0.6   0.0       1.7   1.2e+03      69      96 ..     150     175 ..     116     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                      EEEE--SSSSHHHHHHHGGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaaa 22
                                      v+++G++G+gK++l + +a +
  gi|488599908|ref|YP_007906379.1| 29 VCILGESGCGKTTLLRIIAGL 49
                                      89*************999865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                       EEEESGGG--HHHHHHHHHHHHSSEEE. CS
                             AAA_5  69 lvlDEveraesevlnsLlslleerrlll 96 
                                       + lDE++r   +++++Ll++  e+r+ +
  gi|488599908|ref|YP_007906379.1| 150 ASLDELTR--AKMQMELLRIWMENRVTI 175
                                       45777774..456677777766666554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.6e-05     0.045       8      42 ..      16      48 ..      10      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
                          ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeiie 42
                                      +++++  +e+   +++ i G  g+GKt+Ll+ i+ 
  gi|488599908|ref|YP_007906379.1| 16 IDRIRFKAEE--GSFVCILGESGCGKTTLLRIIAG 48
                                      5666666666..7899**************97764 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.8e-05     0.061       1      35 [.      12      47 ..      12      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-05
                                      SSHHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  1 GirvlDal.fpivqGqrtlipgafgvGktvisqsls 35
                                      G +v+D + f   +G  ++i+g++g+Gkt++++ ++
  gi|488599908|ref|YP_007906379.1| 12 GKKVIDRIrFKAEEGSFVCILGESGCGKTTLLRIIA 47
                                      66888876478889*****************98876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013     0.091       2      22 ..      29      49 ..      28     104 .. 0.74
   2 ?   -1.8   0.0       4.8   3.3e+03     134     162 ..     157     184 ..     145     192 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                            AAA_28  2 ivitGgestGKTtlleaLaar 22
                                      ++i+G +++GKTtll+ +a  
  gi|488599908|ref|YP_007906379.1| 29 VCILGESGCGKTTLLRIIAGL 49
                                      89**************99943 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.8
                            AAA_28 134 reaiderlrealrelgipviivpsgdvee 162
                                       r++++  l+ ++ e ++ ++ v + ++ee
  gi|488599908|ref|YP_007906379.1| 157 RAKMQMELLRIWMENRVTILFV-THSIEE 184
                                       5555555555555555555555.555544 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   8.5e-05     0.059       7      40 ..      14      46 ..       9      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                                      HHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC  7 kviekLlekdelqslvvalvGmgGvGKttlakqi 40
                                      kvi++   k e +  +v + G  G+GKttl++ i
  gi|488599908|ref|YP_007906379.1| 14 KVIDRIRFKAEEG-SFVCILGESGCGKTTLLRII 46
                                      6777776666666.699*************9866 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 ?    9.6   0.0   0.00082      0.57       5      43 ..       2      45 ..       1      64 [. 0.79
   2 ?    2.0   0.0      0.18   1.2e+02     135     184 ..     120     166 ..      84     203 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00082
                                      EEEESETTEECEEEEEET.....TSSEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  5 leienFksyagktvilpf.....sksftaivGpNGSGKsnlldA 43
                                      le++  ks++gk+vi ++     + sf +i+G+ G+GK+ ll  
  gi|488599908|ref|YP_007906379.1|  2 LEVDVSKSFNGKKVIDRIrfkaeEGSFVCILGESGCGKTTLLRI 45
                                      567778999999988654222224589************99865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.18
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH.HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv.aellk 184
                                       + LSgG ++ + +a  + i+   p  + l+De  a LDe  ++k+  ell+
  gi|488599908|ref|YP_007906379.1| 120 KHLSGGMRQRIGIARALVIN---P-EILLMDEPFASLDELTRAKMqMELLR 166
                                       56777777766666554443...3.36678888888888776665134555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015       0.1      19      39 ..      23      43 ..       9      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                            AAA_29 19 idlkg.atlltGpsGsGKSTll 39
                                       + +g ++ + G+sG GK+Tll
  gi|488599908|ref|YP_007906379.1| 23 AE-EGsFVCILGESGCGKTTLL 43
                                      33.346999************8 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037      0.26       8      42 ..      12      46 ..       6      57 .. 0.85
   2 ?   -0.3   0.0       1.1   7.5e+02      99     123 ..     152     174 ..     140     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                                      HHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat  8 lkelleqikkvaktdlsvlitGesGtGKellarai 42
                                       k+++++i+  a+  + v i+GesG+GK++l r i
  gi|488599908|ref|YP_007906379.1| 12 GKKVIDRIRFKAEEGSFVCILGESGCGKTTLLRII 46
                                      578899999999999**************998876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                       EETGGGS-HHHHHHHHHHHHHSEEE CS
                   Sigma54_activat  99 LDeigelplelQekLlrvlqegeve 123
                                       LDe+++  +++Q +Llr+  e++v+
  gi|488599908|ref|YP_007906379.1| 152 LDELTR--AKMQMELLRIWMENRVT 174
                                       666665..57899999998777766 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   0.00019      0.13       5      35 ..      29      70 ..      26     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                            AAA_24  5 iliyGpsgiGKTtlakel..........gpkplfidtek.Gl 35
                                      ++i G+sg GKTtl++ +          +++   id ek G+
  gi|488599908|ref|YP_007906379.1| 29 VCILGESGCGKTTLLRIIaglesfegtiKYRGREIDREKiGF 70
                                      79************9988777777777777777777777666 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0009      0.62       6      42 ..       9      50 ..       6      72 .. 0.77
   2 ?    0.6   0.0      0.48   3.3e+02     130     152 ..     154     176 ..     129     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0009
                                      SHHHHHHHHHHH....H-SEEEEE--TTSSTTHH.HHHHHHH CS
                              PhoH  6 tkeQkeylealk....kndivfaiGpaGtGKtyl.avalave 42
                                      + + k++++ ++    + ++v+++G++G+GKt l  + +++e
  gi|488599908|ref|YP_007906379.1|  9 SFNGKKVIDRIRfkaeEGSFVCILGESGCGKTTLlRIIAGLE 50
                                      66778888888875444559***********86515555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.48
                                       G--HHHHHHHHTTB-TT-EEEEE CS
                              PhoH 130 nttkeqmkmfltRlGenskvvvt 152
                                       ++t+++m+m l R+  + +v ++
  gi|488599908|ref|YP_007906379.1| 154 ELTRAKMQMELLRIWMENRVTIL 176
                                       58999999999999888887664 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.16      17      51 ..      18      52 ..      12      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                              DLIC 17 rsssklPsgksvlvlGedgsGkttliaklqGveee 51
                                      r + k   g  v +lGe+g+Gkttl+  + G+e  
  gi|488599908|ref|YP_007906379.1| 18 RIRFKAEEGSFVCILGESGCGKTTLLRIIAGLESF 52
                                      566677778889*************9988888753 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00035      0.24       4      25 ..      29      50 ..      27      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                         PduV-EutP  4 illiGkvgsGKttLtqalkgee 25
                                      + ++G++g+GKttL + + g e
  gi|488599908|ref|YP_007906379.1| 29 VCILGESGCGKTTLLRIIAGLE 50
                                      6789***********9998854 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 ?   11.4   0.0   0.00043       0.3      52      84 ..     128     160 ..     120     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                           SbcCD_C  52 alyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                       + ++ a++   +++++++DE F++lDe ++a++
  gi|488599908|ref|YP_007906379.1| 128 QRIGIARALVINPEILLMDEPFASLDELTRAKM 160
                                       55555544566799*************988876 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00046      0.32       2      23 ..      29      49 ..      28      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                              MobB  2 lgivgksgsGKTtLleklipel 23
                                      ++i g sg+GKTtLl  +i+ l
  gi|488599908|ref|YP_007906379.1| 29 VCILGESGCGKTTLLR-IIAGL 49
                                      799***********95.55555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     0.001       0.7       1      19 [.      29      47 ..      29      61 .. 0.86
   2 ?   -1.5   0.0       4.6   3.2e+03      50      83 ..     140     174 ..     137     196 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                      RNA_helicase  1 iwlyGpsgeGKStlakeLa 19
                                      +++ G+sg+GK+tl + +a
  gi|488599908|ref|YP_007906379.1| 29 VCILGESGCGKTTLLRIIA 47
                                      6899**********98754 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.6
                      RNA_helicase  50 qevvvidDfgqvkdee.npsdlaelirlvsstpyp 83 
                                       +e++++d+  ++ de    ++ +el+r+   + ++
  gi|488599908|ref|YP_007906379.1| 140 PEILLMDEPFASLDELtRAKMQMELLRIWMENRVT 174
                                       56777888777777776666666666665444333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0005      0.35      22      48 ..      22      51 ..      14     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                            AAA_15 22 see...ltvliGkNnsGKSsilealdlFln 48
                                      + e   + ++ G+ ++GK+++l+++  + +
  gi|488599908|ref|YP_007906379.1| 22 KAEegsFVCILGESGCGKTTLLRIIAGLES 51
                                      44455699****************965554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 1318.02
//
Query:       gi|488599909|ref|YP_007906380.1|  [L=251]
Description: ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-20   72.5  10.7    3.5e-20   72.5  10.7    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.26   11.2   4.7        1.4    8.9   0.5    2.4  3  PTP_tm        Transmembrane domain of protein tyrosine phosph


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 ?   -1.7   1.3      0.23     2e+03      26      30 ..      21      25 ..       5      71 .. 0.48
   2 !   72.5  10.7   3.9e-24   3.5e-20       1     173 [.      72     241 ..      72     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.23
                      BPD_transp_1 26 vllsl 30
                                      ++ ++
  gi|488599909|ref|YP_007906380.1| 21 AGVMV 25
                                      22222 PP

  == domain 2  score: 72.5 bits;  conditional E-value: 3.9e-24
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       +i+lGi+++   n+ +d++l++++++++ +P++++++l + +f    ++ + +    i++++++a+++ +l +r++ 
  gi|488599909|ref|YP_007906380.1|  72 AIPLGIVMG--WNRGIDEFLSTFTEIFRPIPPLAWIPLSYILF---ASFSNPVQTaQIFIVFVGAFFPCLLSVREFA 143
                                       69*******..***********************999988544...4444455553799****************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw.pGlgtllleailgydyse 152
                                       rs +++l+e a+a  as+ +i++k+v+P+++p +++g+++ +g  +   v++e+l+++ +Glg++++  ++    +e
  gi|488599909|ref|YP_007906380.1| 144 RSTDRNLIEMAKAFNASDSEILKKIVIPSSIPGMLSGIRIGLGVGWMTIVAAEMLATSgSGLGYFIMVMYEVGGRTE 220
                                       ******************************************************9865156*****99998776666 PP

                      BPD_transp_1 153 isnggvlalviavlllnlvad 173
                                        +  g+la++i+  l+++++ 
  gi|488599909|ref|YP_007906380.1| 221 EILSGMLAIGIIGYLMSTLVV 241
                                       665888888888888887764 PP

>> PTP_tm  Transmembrane domain of protein tyrosine phosphatase, receptor type J
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.5   0.00015       1.4     137     168 ..     108     139 ..      92     144 .. 0.94
   2 ?    4.0   0.0    0.0049        44     128     174 ..     147     195 ..     140     198 .. 0.84
   3 ?   -3.3   0.1      0.86   7.7e+03     158     181 ..     228     251 .]     225     251 .] 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00015
                            PTP_tm 137 syvsfspyseavllPqdPgviaGavlGcilga 168
                                       sy+ f+++s+ v   q   v +Ga + c+l++
  gi|488599909|ref|YP_007906380.1| 108 SYILFASFSNPVQTAQIFIVFVGAFFPCLLSV 139
                                       9****************************986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0049
                            PTP_tm 128 ekgliegeesy.vsfspyseavllPqd.PgviaGavlGcilgalvivav 174
                                       +++lie ++++  s s++ +++++P   Pg+++G  +G  +g + iva 
  gi|488599909|ref|YP_007906380.1| 147 DRNLIEMAKAFnASDSEILKKIVIPSSiPGMLSGIRIGLGVGWMTIVAA 195
                                       5678888887736889999******8669*****************995 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.86
                            PTP_tm 158 aGavlGcilgalvivavgGfifwr 181
                                       a  ++G +++ lv+   +  + wr
  gi|488599909|ref|YP_007906380.1| 228 AIGIIGYLMSTLVVRVESKLLRWR 251
                                       556899999999988777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1503.41
//
Query:       gi|488599910|ref|YP_007906381.1|  [L=325]
Description: hypothetical protein Asulf_00359 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   90.6   0.1    1.1e-14   54.8   0.0    2.2  2  NMT1_2          NMT1-like family
    3.4e-08   33.7   0.7      1e-07   32.1   0.3    1.9  3  NMT1            NMT1/THI5 like
    0.00015   21.5   0.1    0.00026   20.6   0.1    1.4  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.061   12.6   0.2         12    5.1   0.0    3.1  3  DUF3834         Protein of unknown function (DUF3834)


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 !   54.8   0.0   2.5e-18   1.1e-14     151     251 ..      18     111 ..       9     113 .. 0.90
   2 !   34.0   0.0   5.3e-12   2.4e-08       5     150 ..     194     322 ..     190     325 .] 0.84

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.5e-18
                            NMT1_2 151 eadvklvvvpppqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntaral 227
                                       ++ + +v + pp+mv+++k ++idg+++ eP+ ++    + G  +lts e+w +hP++v++ + d+   n  +++a+
  gi|488599910|ref|YP_007906381.1|  18 QNAIYVVRLSPPDMVEQFKLKQIDGYVAWEPFVSKG--AKYGKVLLTSHEIWSNHPCCVVA-SGDI---NESALNAV 88 
                                       56788999************************6664..577889**************975.6777...7789**** PP

                            NMT1_2 228 vkalleAtkwldakkenraeaakl 251
                                       v a+++At +++ ++enr+++++ 
  gi|488599910|ref|YP_007906381.1|  89 VWAHIKATSFIK-NPENREKVVEY 111
                                       ************.*******9985 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 5.3e-12
                            NMT1_2   5 keqlklGfial.tdaaplvvakekglfakeGltvelekqaswaelrdkllagelDaahvltpapllidlGiggakad 80 
                                       +e++++G+    ++   l +a ++g+ ++ Gl  el++ +++ +++d++  +e+D+a+   +ap  +++     +++
  gi|488599910|ref|YP_007906381.1| 194 SEHIRIGYLTAdLHQLALYIAVKEGYLDQTGLRYELKQYKNGVAVMDAFRVNEIDVAYL-GGAPATLKRIN--DNTK 267
                                       678999997652667778***************************************98.78887777765..899* PP

                            NMT1_2  81 mkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldp 150
                                       ++++a  n +G ai++++          ++++dl       k+ kia++  g  +d+llr   +++Gl++
  gi|488599910|ref|YP_007906381.1| 268 IRIVAGANNEGSAIVVQD--------YINSVEDL-------KGRKIAIPGYGTVQDFLLRIVAEEHGLKV 322
                                       ****************84........67777777.......56778888888888888888888888875 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.46   2.1e+03     119     175 ..      18      68 ..      14     103 .. 0.61
   2 ?   -3.5   0.0       1.9   8.4e+03      96     129 ..     157     189 ..     155     194 .. 0.72
   3 !   32.1   0.3   2.3e-11     1e-07       6     117 ..     210     320 ..     206     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.46
                                       GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE-GGGTT--- CS
                              NMT1 119 psdvtlvnvggtslakalltgkvDaaiggyenwegvelesegkelrifaladlgvpd 175
                                        +++ +v+ +  ++++++  +++D     y +we +   s+g ++  + l+ +++  
  gi|488599910|ref|YP_007906381.1|  18 QNAIYVVRLSPPDMVEQFKLKQIDG----YVAWEPFV--SKGAKYGKVLLTSHEIWS 68 
                                       5666777777778888888888884....44666666..555555555555555544 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                                       EEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.T CS
                              NMT1  96 igyvgspfekallkallakdggdpsdvtlvnvgg 129
                                       + + g ++e+ +++ +l+kd   ++++++v++++
  gi|488599910|ref|YP_007906381.1| 157 VNTIGFENEDEFFSNFLRKDVY-EEAMKMVEMNQ 189
                                       5567778888888888888866.77788877754 PP

  == domain 3  score: 32.1 bits;  conditional E-value: 2.3e-11
                                       HHHHHHHTTHHHHTTEEEEEE--SSTTHHHHHHHCTS-SEE.EE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEEC CS
                              NMT1   6 glyvAkekGYFkeeGldVeivepadpsdatelvasgkadfg.vsyqesllaarakglpvvsvaallqeplsglivlk 81 
                                        ly+A + GY  + Gl  e++++++   ++++   ++ d++ +   + +l +   + +++ va  ++e  s+++v++
  gi|488599910|ref|YP_007906381.1| 210 ALYIAVKEGYLDQTGLRYELKQYKNGVAVMDAFRVNEIDVAyLGGAPATLKRINDNTKIRIVAGANNEG-SAIVVQD 285
                                       79**************************************83566777778888999999999988555.4444444 PP

                                       CC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT- CS
                              NMT1  82 dsgikspkDLkGkrigyvg.spfekallkallakdgg 117
                                          i+s++DLkG++i+++g + +++ ll+ + +++g+
  gi|488599910|ref|YP_007906381.1| 286 --YINSVEDLKGRKIAIPGyGTVQDFLLRIVAEEHGL 320
                                       ..5****************555566666666666665 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 !   20.6   0.1   5.9e-08   0.00026      26     111 ..     222     301 ..     214     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.9e-08
                                       HHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEETTSS--SHHH CS
                    Phosphonate-bd  26 elGvevelvvatdyaavvealragqvDiaflgplayvqardqagveplatrvrsdGsasyrsviivradsdiqsled 102
                                       ++G + el+ +++  av+ a+r +++D+a+lg+ ++   r +++++   +     G++   s+i+v++   i+s+ed
  gi|488599910|ref|YP_007906381.1| 222 QTGLRYELKQYKNGVAVMDAFRVNEIDVAYLGGAPATLKRINDNTKIRIVA----GANNEGSAIVVQD--YINSVED 292
                                       689999999999**************************9999997655444....558999*****98..5****** PP

                                       HGG-EEEE- CS
                    Phosphonate-bd 103 Lkgktiafv 111
                                       Lkg++ia++
  gi|488599910|ref|YP_007906381.1| 293 LKGRKIAIP 301
                                       *******86 PP

>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.021        92     102     199 ..      27     131 ..       6     133 .. 0.65
   2 ?    1.3   0.0     0.037   1.7e+02      87     133 ..     219     265 ..     214     288 .. 0.82
   3 ?    5.1   0.0    0.0026        12      54      94 ..     281     321 ..     267     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.021
                           DUF3834 102 dpeevlkllnegevdsavva.selkkgeaf.edllkklgvyvpGsCgaavken.eee....fidaYeeGIelik..e 169
                                        p ++++  + +++d  v     ++kg  +   ll+++++     C + + ++ +e+    ++ a  +   +ik  e
  gi|488599910|ref|YP_007906381.1|  27 SPPDMVEQFKLKQIDGYVAWePFVSKGAKYgKVLLTSHEIWSNHPCCVVASGDiNESalnaVVWAHIKATSFIKnpE 103
                                       57789999999999999988567899999966678899988766666655555344411114445555556665223 PP

                           DUF3834 170 dpeeaaeyiaskLpikidkefiknilknae 199
                                       + e++ ey ++   + +++++++n lkn +
  gi|488599910|ref|YP_007906381.1| 104 NREKVVEYASEF--TGLERDVVENALKNIK 131
                                       445555555554..5567777777777766 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.037
                           DUF3834  87 lldlkkikaevvyaddpeevlkllnegevdsavvaselkkgeafedl 133
                                       +ld ++++ e+  + +   v+++   +e+d a ++++ ++ ++++d 
  gi|488599910|ref|YP_007906381.1| 219 YLDQTGLRYELKQYKNGVAVMDAFRVNEIDVAYLGGAPATLKRINDN 265
                                       78999999999999999999999999999999999776666666665 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0026
                           DUF3834  54 vvikkllviipkigkekIavwrkGsaaDvllrilldlkkik 94 
                                       +v+++ +  + +++ +kIa+   G++ D+llri+++ +++k
  gi|488599910|ref|YP_007906381.1| 281 IVVQDYINSVEDLKGRKIAIPGYGTVQDFLLRIVAEEHGLK 321
                                       5666666666677788******************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2157.19
//
Query:       gi|488599911|ref|YP_007906382.1|  [L=159]
Description: putative transcriptional regulator with an HTH domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-09   36.2   0.0    8.1e-09   35.4   0.0    1.4  1  HTH_3     Helix-turn-helix
    0.00018   21.9   0.0    0.00034   21.0   0.0    1.4  1  HTH_26    Cro/C1-type HTH DNA-binding domain
     0.0043   16.7   0.8      0.012   15.1   0.3    1.8  1  PrpR_N    Propionate catabolism activator
     0.0074   16.6   0.0      0.013   15.9   0.0    1.4  1  HTH_31    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   14.7   0.0       0.09   12.5   0.0    2.2  2  HTH_psq   helix-turn-helix, Psq domain
       0.12   12.5   0.0       0.27   11.3   0.0    1.7  1  HTH_19    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 !   35.4   0.0   2.7e-12   8.1e-09       7      53 ..      26      72 ..      20      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 2.7e-12
                                      HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53
                                      + g++++ ++e +Gv++ t+++i +Ger+P+ +tl k+++a++ + +
  gi|488599911|ref|YP_007906382.1| 26 ESGMDLKHFSEICGVPYPTLYKIVRGERKPTATTLRKILRAFKRDEE 72
                                      67999999**********************************98876 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.1e-07   0.00034       2      51 ..      20      68 ..      19      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                      L +++++ g+  + +++ +g+  +tl+++v g+ + ++++tL ki +a++
  gi|488599911|ref|YP_007906382.1| 20 LERVIHESGMDLKHFSEICGVPYPTLYKIVRGE-RKPTATTLRKILRAFK 68
                                      8899*****************************.8************985 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   4.2e-06     0.012      12      65 ..     101     153 ..      94     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-06
                            PrpR_N  12 gdleeavelakeleaegvdviiSrGgtaellrkhvsvPVveikvsgyDilralk 65 
                                        ++eea+  a ++e+eg+++ii +    + ++k v+vPV  +++++  +++a++
  gi|488599911|ref|YP_007906382.1| 101 NNFEEAIVNAVRAEKEGARAIIVAPILSSTIEKIVDVPVFTMRPKY-SLIKAVE 153
                                       48*************************************9999864.4555555 PP

>> HTH_31  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     0.013       3      58 ..      17      71 ..      15      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.3e-06
                            HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldp 58
                                       ++L +   ++G+ +++  e +gv   tl ++ +G+r  p+  +l++++ra+  d+
  gi|488599911|ref|YP_007906382.1| 17 SRELERVIHESGMDLKHFSEICGVPYPTLYKIVRGER-KPTATTLRKILRAFKRDE 71
                                      56666666788999999********************.6************98765 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 ?   12.5   0.0     3e-05      0.09       2      39 ..      13      51 ..      12      55 .. 0.86
   2 ?   -2.2   0.1       1.2   3.7e+03       2      11 ..     104     113 ..     102     117 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                           HTH_psq  2 pealaaAleavv..nGkmSirkAArkYgiPrsTLwrrkrg 39
                                      +ea+++ le v+  +G m + + + + g+P++TL++ +rg
  gi|488599911|ref|YP_007906382.1| 13 DEAFSRELERVIheSG-MDLKHFSEICGVPYPTLYKIVRG 51
                                      5788888999996666.9999999999***********98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                           HTH_psq   2 pealaaAlea 11 
                                       +ea+  A++a
  gi|488599911|ref|YP_007906382.1| 104 EEAIVNAVRA 113
                                       4555555554 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.9e-05      0.27       6      58 ..      22      73 ..      18      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.9e-05
                            HTH_19  6 eaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidley 58
                                      +++ e g+ ++  +e +g+    +++i  g++ +p+a +l+ki++a++ d+e 
  gi|488599911|ref|YP_007906382.1| 22 RVIHESGMDLKHFSEICGVPYPTLYKIVRGER-KPTATTLRKILRAFKRDEEF 73
                                      556666777777778888877789********.**************999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 880.85
//
Query:       gi|488599912|ref|YP_007906383.1|  [L=261]
Description: putative dioxygenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-79  264.7   0.6    8.2e-79  264.5   0.6    1.0  1  Memo           Memo-like protein
     0.0048   16.0   0.0     0.0078   15.3   0.0    1.3  1  LigB           Catalytic LigB subunit of aromatic ring-openin
  ------ inclusion threshold ------
      0.035   13.5   0.0       0.07   12.5   0.0    1.5  1  TniB           Bacterial TniB protein
      0.047   13.7   0.0      0.077   13.0   0.0    1.3  1  DNA_primase_S  DNA primase small subunit


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 !  264.5   0.6   1.8e-82   8.2e-79       3     271 .]       5     258 ..       3     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 264.5 bits;  conditional E-value: 1.8e-82
                              Memo   3 avAGsfYpedeeelkkqleeflekntgkkeiarviisPHagyvysgevaakayaelesskvervvilGpsHtilgsk 79 
                                        vAG+fYp+d e+lk+q+ e++ kn  +     + +sPHagy+ysg+va+++++ l +   e+ vi+Gp+Ht++gs+
  gi|488599912|ref|YP_007906383.1|   5 VVAGLFYPSDSESLKAQIAEYTSKNPDDSV--IACVSPHAGYMYSGRVAGRVHSLLPDV--ETYVIIGPNHTGYGSP 77 
                                       59*****************99888888763..44455******************9875..9*************** PP

                              Memo  80 vsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqseeta 156
                                       ++v+  +e+eTPlG ++vD e+v+++ +  +i+d+de+a+++EHS+Evq+pfL++l+k+  fkivPi+v++q+ eta
  gi|488599912|ref|YP_007906383.1|  78 IAVSV-DEWETPLGVVEVDVEFVKAMPH--RIIDIDEIAHREEHSIEVQVPFLQYLHKD--FKIVPICVGMQDDETA 149
                                       ****9.*********************9..6****************************..**************** PP

                              Memo 157 kevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGekpi 231
                                        e+++ +  + ++    ++vi+SsD++Hy      p+e +++  D+evika+ee++ +++  ++ + ++++cG+++i
  gi|488599912|ref|YP_007906383.1| 150 YEIAQEIIAAKEKLGreVVVIASSDMHHYL-----PDERCRRL-DEEVIKAIEEMDVRKYFSTICRLQASVCGYGVI 220
                                       *******9999998888999**********.....********.********************************* PP

                              Memo 232 avilkalkklgakkakllkYaqssdvtsdtdsvVsyaslv 271
                                       av+++ +++ + +ka+l++Ya+s++v+ +++ vV+ya++v
  gi|488599912|ref|YP_007906383.1| 221 AVAMNFARHYN-AKANLVAYATSGEVA-NRSNVVGYAGIV 258
                                       ***********.9**************.9********975 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-06    0.0078     137     204 ..     134     199 ..     121     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
                              LigB 137 ikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakadaqtlllneefd 204
                                       +k+  +++ +++ ++e  y++ + +  a e+l ++v++++s ++ H+l++++    d ++ ++ ee+d
  gi|488599912|ref|YP_007906383.1| 134 FKI--VPICVGMQDDETAYEIAQEIIAAKEKLGREVVVIASSDMHHYLPDERCRRLDEEVIKAIEEMD 199
                                       443..44446789*************************************998766665555555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05      0.07     112     165 ..      96     146 ..      82     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                              TniB 112 lrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteea 165
                                       +++ +++  r++ iDEi + ++ s    +  + +l++L+ ++ki  ++vG ++ 
  gi|488599912|ref|YP_007906383.1|  96 VEFVKAMPHRIIDIDEIAHREEHS---IEVQVPFLQYLHKDFKIVPICVGMQDD 146
                                       68899999***********99555...556678899**************9975 PP

>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05     0.077      25      76 ..     151     197 ..     142     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHHH CS
                     DNA_primase_S  25 svavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaivn 76 
                                       + a++++  + +e +g++++++  s    +H++ +d+++r+l++e ++ai +
  gi|488599912|ref|YP_007906383.1| 151 EIAQEII--AAKEKLGREVVVIASSD---MHHYLPDERCRRLDEEVIKAIEE 197
                                       5677777..5679***9966666666...9******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.37s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1416.30
//
Query:       gi|488599913|ref|YP_007906384.1|  [L=320]
Description: putative H4MPT-linked C1 transfer pathway protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   62.3   0.0    8.1e-08   31.9   0.0    2.1  2  Hydantoinase_A  Hydantoinase/oxoprolinase
  ------ inclusion threshold ------
      0.081   11.5   0.0       0.16   10.5   0.0    1.5  1  MutL            MutL protein


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     9e-11     8e-07       4     100 ..      54     142 ..      51     159 .. 0.81
   2 !   31.9   0.0   9.1e-12   8.1e-08     162     264 ..     185     287 ..     178     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9e-11
                    Hydantoinase_A   4 tavvnAylspilreylesveksle.krgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagek 79 
                                        +v++A+ls+ +r+++e++e +    r++  ++++++ +G+l +       p  + +S++ a+  ++++     +++
  gi|488599913|ref|YP_007906384.1|  54 GVVITAELSDAFRSKAEGIEIISGiCRDVFDEVYFLDVNGNLKKEI---DDPELFSASNWVASTLFLKK-----TYD 122
                                       689***************9865431345559*********997654...445679***********999.....677 PP

                    Hydantoinase_A  80 kvItfDmGGTstDvslikdge 100
                                       + +++D+G+T+tD+++ k  e
  gi|488599913|ref|YP_007906384.1| 123 NFLFVDIGSTTTDLIPAK-EE 142
                                       79*************988.44 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 9.1e-12
                    Hydantoinase_A 162 eltvTDanlvLGrlqpedfls.gpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrklsverg 237
                                       + +++D+ lv+G ++++d++  +pdg++k+ +e+++r      + l +  +++  ++     e+m ++v++   er 
  gi|488599913|ref|YP_007906384.1| 185 FSITADIFLVCGDIKEKDYTVeTPDGRGKSLHECMQRISRVFCADLDEVGKDFIRNFAASCREKMISEVKEA-IERH 260
                                       6789**********************************9666666666655555555566666666666665.5566 PP

                    Hydantoinase_A 238 ldpkeltlvvfGGaGaqhaaalaeelg 264
                                       + +  l  ++  G G++++ ++ e+l+
  gi|488599913|ref|YP_007906384.1| 261 VSRYSLDRIIACGIGEFLIREAFERLD 287
                                       888888888999999999888877665 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   1.8e-05      0.16     236     265 ..     115     140 ..      80     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.8e-05
                              MutL 236 ellaeeeekglgdllvvDvGGaTTdvhsva 265
                                        +l++    +++++l vD+G++TTd++ + 
  gi|488599913|ref|YP_007906384.1| 115 LFLKK----TYDNFLFVDIGSTTTDLIPAK 140
                                       44555....688*************98873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1745.34
//
Query:       gi|488599914|ref|YP_007906385.1|  [L=205]
Description: putative archaeal kinase related to aspartokinase, uridylate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   43.1   0.4    1.3e-07   31.5   0.0    2.2  2  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 !    9.6   0.1   3.6e-05      0.65       2      63 ..       1      56 [.       1      88 [. 0.76
   2 !   31.5   0.0   7.3e-12   1.3e-07     148     207 ..     104     156 ..      93     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 3.6e-05
                                      EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC CS
                         AA_kinase  2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgela 63
                                      ++VvKlGGs+  + ++  l + +  + +   +g+ + +++Ggg  +d   +   +++++ ++
  gi|488599914|ref|YP_007906385.1|  1 MIVVKLGGSVKNNWKT--LTDTLISVWRV--KGESILIITGGGELADIVRKM--NVDDENSH 56
                                      59*******9998888..77776666666..799999999997766655554..77776665 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 7.3e-12
                                       EEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHC CS
                         AA_kinase 148 gldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdea 207
                                         d+  +++ ++sD ia ++A +l+A+k+i +tdVdG+y +         l++ei+++e+
  gi|488599914|ref|YP_007906385.1| 104 SKDPLPHSWSVTSDSIAIWVAGELNAEKMIKITDVDGIYRDG-------ILINEIRAEEL 156
                                       55666778999****************************653.......67777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.39s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1114.97
//
Query:       gi|488599915|ref|YP_007906386.1|  [L=53]
Description: putative Zn-ribbon RNA-binding protein with a function in translation [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   34.8  11.4    1.8e-08   34.2   4.8    2.2  2  DUF1610          Domain of unknown function (DUF1610)
    0.00022   21.2  12.5       0.36   10.9   0.7    3.9  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
     0.0036   17.7   9.0     0.0041   17.5   9.0    1.1  1  Rhodanese_C      Rhodanase C-terminal
     0.0045   17.0   4.3       0.65   10.1   5.4    2.2  1  zf-MYND          MYND finger
  ------ inclusion threshold ------
       0.01   15.8  10.5       0.34   11.0  10.5    2.3  1  DZR              Double zinc ribbon
      0.015   15.3   8.0      0.022   14.8   8.0    1.2  1  Zn_Tnp_IS91      Transposase zinc-binding domain
      0.029   14.8  10.2        0.1   13.1  10.2    1.8  1  zf-CHY           CHY zinc finger
       0.03   14.6  12.6       0.23   11.8   3.6    2.3  2  C1_2             C1 domain
      0.037   14.0   8.6       0.18   11.8   8.6    1.9  1  zinc-ribbons_6   zinc-ribbons
      0.084   12.8   9.2        2.3    8.2   5.4    2.2  2  C1_1             Phorbol esters/diacylglycerol binding domain
      0.098   12.7   3.2        8.2    6.6   0.1    2.9  3  DUF2752          Protein of unknown function (DUF2752)
       0.12   12.0  13.2        1.7    8.3   0.2    3.3  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.16   12.0   9.0       0.86    9.6   0.4    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.18   12.2   6.1       0.33   11.3   1.6    2.5  2  zf-UBP           Zn-finger in ubiquitin-hydrolases and other 
       0.27   11.2  17.0        2.3    8.2   0.2    3.8  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.28   11.2  11.1       0.39   10.7   5.0    2.3  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
       0.31   11.0   9.3        6.8    6.7   7.4    2.3  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.66    9.7  17.3       0.98    9.2   0.6    3.9  4  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.69    9.4  16.8       0.91    9.0   0.3    3.6  3  zf-ribbon_3      zinc-ribbon domain
       0.72    7.6   5.2       0.74    7.6   5.2    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
        1.7    8.3  15.3       0.95    9.1   0.3    3.7  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
        1.9    8.3  20.5        3.8    7.4   6.3    3.8  4  zinc_ribbon_2    zinc-ribbon domain
        1.9    7.2   4.3        2.1    7.1   4.3    1.0  1  NMDAR2_C         N-methyl D-aspartate receptor 2B3 C-terminus
          2    8.7   7.4        2.2    8.5   7.4    1.1  1  FYVE_2           FYVE-type zinc finger
        2.2    9.3  13.3         23    6.2   0.4    4.0  4  zf-C2H2_4        C2H2-type zinc finger
        2.3    8.2  15.6         15    5.6   0.1    3.9  3  zinc_ribbon_4    zinc-ribbon domain
        2.3    8.1  23.6         15    5.5   9.3    3.6  2  zf-HIT           HIT zinc finger
        2.6    7.7  13.7        1.8    8.2   5.7    2.9  3  RecR             RecR protein
        3.3    7.9  12.5         11    6.2   1.3    2.6  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        4.7    6.6   8.6        4.9    6.5   8.6    1.0  1  NMD3             NMD3 family
        4.7    7.1  11.5       0.72    9.7   0.4    3.0  3  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
        5.3    7.7  20.4        4.3    7.9   0.8    4.0  3  zf-H2C2_2        Zinc-finger double domain
        7.4    6.8  18.3         17    5.6   2.7    3.5  2  Zn-ribbon_8      Zinc ribbon domain
        8.6    6.3  17.8         13    5.8   0.2    4.0  4  TFIIS_C          Transcription factor S-II (TFIIS)


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 !   34.2   4.8   3.5e-11   1.8e-08       1      22 [.       6      26 ..       6      28 .. 0.98
   2 ?    4.8   0.5     0.051        27      18      23 ..      44      49 ..      42      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.5e-11
                           DUF1610  1 CtSCGaelaprEravvFpCPNC 22
                                      C+SCG  l++ + +v+FpCPNC
  gi|488599915|ref|YP_007906386.1|  6 CISCGENLIGMN-YVKFPCPNC 26
                                      ************.********* PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.051
                           DUF1610 18 pCPNCG 23
                                       CP CG
  gi|488599915|ref|YP_007906386.1| 44 KCPSCG 49
                                      599999 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.3    0.0042       2.2       2      11 ..       4      13 ..       4      14 .. 0.87
   2 !   10.9   0.7   0.00068      0.36       4      13 ..      23      32 ..      21      33 .. 0.95
   3 ?    0.6   0.2       1.2   6.1e+02       3       8 ..      32      37 ..      32      39 .. 0.76
   4 !    8.3   0.1    0.0046       2.4       3       8 ..      44      49 ..      42      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0042
                            zf-ACC  2 tKCpsCgeml 11
                                      +KC sCge l
  gi|488599915|ref|YP_007906386.1|  4 HKCISCGENL 13
                                      5******976 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00068
                            zf-ACC  4 CpsCgemlyk 13
                                      Cp C+e++y+
  gi|488599915|ref|YP_007906386.1| 23 CPNCNESIYR 32
                                      *********8 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.2
                            zf-ACC  3 KCpsCg 8 
                                      +C +C 
  gi|488599915|ref|YP_007906386.1| 32 RCKRCR 37
                                      599996 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0046
                            zf-ACC  3 KCpsCg 8 
                                      KCpsCg
  gi|488599915|ref|YP_007906386.1| 44 KCPSCG 49
                                      9****8 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   9.0   7.7e-06    0.0041      18      63 ..       3      48 ..       1      49 [. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.7e-06
                       Rhodanese_C 18 vgkCieCgkpvdelrkrnCanedCnelvlvCeeCaeklkgv.cseeC 63
                                      v kCi Cg++   +++++  +++Cne +  C++C++ ++ + c  +C
  gi|488599915|ref|YP_007906386.1|  3 VHKCISCGENLIGMNYVKFPCPNCNESIYRCKRCRKLANLYkCP-SC 48
                                      679********999988888889************998887554.77 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   5.4    0.0012      0.65       1      30 [.       6      40 ..       6      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                                      -TTT--.....B-SC.E-TTTS-SEESSHHHHHHC CS
                           zf-MYND  1 CavCgk....aealk.kCagCksvfYCskeCqrad 30
                                      C +Cg+     +  k +C++C+   Y +k C++ +
  gi|488599915|ref|YP_007906386.1|  6 CISCGEnligMNYVKfPCPNCNESIYRCKRCRKLA 40
                                      88999999984555559****99999999999865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  10.5   0.00065      0.34       1      49 []       6      49 ..       2      52 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                               DZR  1 CpqCgee...lppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                      C +Cge+   ++  +  C++C++++      +rC +C + +++    Cp+CG
  gi|488599915|ref|YP_007906386.1|  6 CISCGENligMNYVKFPCPNCNESI------YRCKRCRKLANLY--KCPSCG 49
                                      6666666444333344566666666......6777777776666..599998 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 ?   14.8   8.0   4.1e-05     0.022      23      64 ..       2      49 ..       1      51 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-05
                       Zn_Tnp_IS91 23 avekilrCrtaalGfarye..CeeCghekivyfsCksrh....CpsCq 64
                                      +v+k ++C+++  G++ ++  C++C+++ + + +C++ +    CpsC+
  gi|488599915|ref|YP_007906386.1|  2 EVHKCISCGENLIGMNYVKfpCPNCNESIYRCKRCRKLAnlykCPSCG 49
                                      699********9998877666**************98543456****7 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  10.2   0.00019       0.1      19      74 ..       3      50 ..       1      51 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00019
                            zf-CHY 19 lyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCkl 74
                                      +++C +C e     +l  ++  ++ c +C++   +   Ck+C+k ++ y+Cp C +
  gi|488599915|ref|YP_007906386.1|  3 VHKCISCGE-----NLIGMNYVKFPCPNCNE---SIYRCKRCRKLANLYKCPSCGF 50
                                      678888888.....67778888898999998...5999****************75 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.0    0.0048       2.5      19      39 ..       4      27 ..       2      31 .. 0.76
   2 ?   11.8   3.6   0.00044      0.23      17      41 ..      29      51 ..      27      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0048
                              C1_2 19 fnCsaCgrk...idgff...YsCseCd 39
                                      ++C  Cg++   +   +   + C+ C+
  gi|488599915|ref|YP_007906386.1|  4 HKCISCGENligM---NyvkFPCPNCN 27
                                      68*******7544...335599*99*8 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00044
                              C1_2 17 esfnCsaCgrkidgffYsCseCdfs 41
                                      + ++C+ C++    + Y+C+ C f+
  gi|488599915|ref|YP_007906386.1| 29 SIYRCKRCRKLA--NLYKCPSCGFV 51
                                      6789******94..67******995 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   8.6   0.00035      0.18       2      48 ..       5      48 ..       2      51 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                                      --SSS-S--E.E-SSEEE-TTT--EEEEEEE-SSS-S---EEEETTEE CS
                    zinc-ribbons_6  2 kCpeCqqele.krgeqyhCeaCqedlkkealCpeCeqelevlkaCgav 48
                                      kC +C ++l   +  ++ C +C+e++     C +C++ l  l +C + 
  gi|488599915|ref|YP_007906386.1|  5 KCISCGENLIgMNYVKFPCPNCNESIY---RCKRCRK-LANLYKCPSC 48
                                      577777777766667777777776443...3444432.3333333332 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 ?    8.2   5.4    0.0044       2.3      12      38 ..       4      30 ..       1      39 [. 0.83
   2 ?    6.4   1.9     0.016       8.3      13      36 ..      32      50 ..      27      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0044
                                      -B-TTT-SB--SSSS-EEEETTT--EE CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCkllv 38
                                      ++C  Cge l g +++ + C +C++++
  gi|488599915|ref|YP_007906386.1|  4 HKCISCGENLIGMNYVKFPCPNCNESI 30
                                      79********99999999999999876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.016
                                      B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1 13 fCkhCgeflwgkekqglkCswCkl 36
                                      +Ck C+++        +kC  C++
  gi|488599915|ref|YP_007906386.1| 32 RCKRCRKLA-----NLYKCPSCGF 50
                                      799999999.....9999999987 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.5     8e+02      10      15 ..       5      10 ..       4      11 .. 0.88
   2 ?    5.3   0.1     0.039        21       7      14 ..      19      26 ..      16      28 .. 0.83
   3 ?    6.6   0.1     0.016       8.2       9      16 ..      43      50 ..      37      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.5
                           DUF2752 10 pCPGCG 15
                                      +C  CG
  gi|488599915|ref|YP_007906386.1|  5 KCISCG 10
                                      7****9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.039
                           DUF2752  7 tGipCPGC 14
                                        +pCP C
  gi|488599915|ref|YP_007906386.1| 19 VKFPCPNC 26
                                      689***** PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.016
                           DUF2752  9 ipCPGCGl 16
                                      ++CP CG 
  gi|488599915|ref|YP_007906386.1| 43 YKCPSCGF 50
                                      68*****6 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0033       1.7       4      14 ..       1      11 [.       1      15 [. 0.90
   2 ?    3.4   2.3      0.11        59       5      12 ..      29      36 ..      24      41 .. 0.86
   3 ?    7.9   0.2    0.0045       2.4       5      13 ..      41      49 ..      37      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0033
                                      T-EEE-TTT-- CS
                   Desulfoferrod_N  4 levYkCevCGn 14
                                      +ev kC  CG+
  gi|488599915|ref|YP_007906386.1|  1 MEVHKCISCGE 11
                                      69********6 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                                      -EEE-TTT CS
                   Desulfoferrod_N  5 evYkCevC 12
                                       +Y+C+ C
  gi|488599915|ref|YP_007906386.1| 29 SIYRCKRC 36
                                      69****99 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0045
                                      -EEE-TTT- CS
                   Desulfoferrod_N  5 evYkCevCG 13
                                      + YkC  CG
  gi|488599915|ref|YP_007906386.1| 41 NLYKCPSCG 49
                                      68******* PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4    0.0016      0.86      72      94 ..       5      28 ..       2      31 .. 0.81
   2 ?    7.4   2.7    0.0082       4.3      70      93 ..      30      49 ..      27      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                                      EETTTS-EEECHHH.HHS-TTTSS CS
                              HypA 72 rCreCgkefeleek.alrCpkCgs 94
                                      +C +Cg++    ++ ++ Cp+C++
  gi|488599915|ref|YP_007906386.1|  5 KCISCGENLIGMNYvKFPCPNCNE 28
                                      8*****99995555589*****97 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0082
                                      EEEETTTS-EEECHHHHHS-TTTS CS
                              HypA 70 kvrCreCgkefeleekalrCpkCg 93
                                       +rC++C+k  +l     +Cp+Cg
  gi|488599915|ref|YP_007906386.1| 30 IYRCKRCRKLANLY----KCPSCG 49
                                      579*****777754....8****8 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 ?    2.9   0.2      0.27   1.4e+02      10      20 ..       2      12 ..       1      20 [. 0.78
   2 ?   11.3   1.6   0.00063      0.33       1      21 [.      33      52 ..      22      53 .] 0.94

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.27
                                      SEEEETTT--E CS
                            zf-UBP 10 nlWlCLkCghv 20
                                      +++ C++Cg  
  gi|488599915|ref|YP_007906386.1|  2 EVHKCISCGEN 12
                                      57899999975 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00063
                                      -TTTH--.SSEEEETTT--EE CS
                            zf-UBP  1 CseCnsenknlWlCLkCghvg 21
                                      C+ C++   nl+ C +Cg+vg
  gi|488599915|ref|YP_007906386.1| 33 CKRCRKL-ANLYKCPSCGFVG 52
                                      9999977.9**********97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.14        73       5      12 ..       4      11 ..       3      15 .. 0.77
   2 ?    2.4   8.7      0.28   1.5e+02      24      31 ..      29      37 ..      21      40 .. 0.80
   3 ?    8.2   0.2    0.0044       2.3       5      11 ..      43      49 ..      42      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
                    Zn_ribbon_SprT  5 YrCtgCgr 12
                                      ++C +Cg+
  gi|488599915|ref|YP_007906386.1|  4 HKCISCGE 11
                                      78999996 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.28
                    Zn_ribbon_SprT 24 n.YrCrrCk 31
                                      + YrC+rC+
  gi|488599915|ref|YP_007906386.1| 29 SiYRCKRCR 37
                                      26******8 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0044
                    Zn_ribbon_SprT  5 YrCtgCg 11
                                      Y+C++Cg
  gi|488599915|ref|YP_007906386.1| 43 YKCPSCG 49
                                      ******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 ?   10.7   5.0   0.00074      0.39      19      49 ..       5      35 ..       2      40 .. 0.86
   2 ?    3.7   2.0      0.12        63      28      41 ..      36      49 ..      32      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00074
                          zf-C2HC5 19 nClnCGkiiCakeglskpCsfCgspllssee 49
                                       C++CG  +  ++ ++ pC+ C+++++  + 
  gi|488599915|ref|YP_007906386.1|  5 KCISCGENLIGMNYVKFPCPNCNESIYRCKR 35
                                      7***********************9987665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                          zf-C2HC5 28 CakeglskpCsfCg 41
                                      C k +   +C++Cg
  gi|488599915|ref|YP_007906386.1| 36 CRKLANLYKCPSCG 49
                                      66666668999997 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.8     0.029        15      30      56 ..       5      30 ..       3      41 .. 0.90
   2 ?    6.7   7.4     0.013       6.8      31      55 ..      23      51 ..      23      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.029
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                      +C  Cg+++    +  +f CpnC+ ++
  gi|488599915|ref|YP_007906386.1|  5 KCISCGENLIG-MNYVKFPCPNCNESI 30
                                      799*******9.99*********9875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.013
                    OrfB_Zn_ribbon 31 CseCgsknke....alsgrtfkCpnCgfe 55
                                      C++C +  ++    ++  +++kCp+Cgf+
  gi|488599915|ref|YP_007906386.1| 23 CPNCNESIYRckrcRKLANLYKCPSCGFV 51
                                      999998888888899999*********96 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.44   2.3e+02      46      52 ..       5      11 ..       3      13 .. 0.83
   2 ?    9.2   0.6    0.0019      0.98      41      52 ..      17      28 ..      15      30 .. 0.86
   3 ?    4.7   0.5     0.047        25      43      53 ..      29      39 ..      27      40 .. 0.81
   4 ?    2.5   5.0      0.24   1.3e+02      45      52 ..      43      50 ..      33      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.44
                    zinc_ribbon_10 46 rCpkCga 52
                                      +C +Cg+
  gi|488599915|ref|YP_007906386.1|  5 KCISCGE 11
                                      7****97 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                    zinc_ribbon_10 41 eevkyrCpkCga 52
                                      ++vk+ Cp+C++
  gi|488599915|ref|YP_007906386.1| 17 NYVKFPCPNCNE 28
                                      689*******98 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.047
                    zinc_ribbon_10 43 vkyrCpkCgal 53
                                        yrC  C+ l
  gi|488599915|ref|YP_007906386.1| 29 SIYRCKRCRKL 39
                                      57******976 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.24
                    zinc_ribbon_10 45 yrCpkCga 52
                                      y+Cp+Cg+
  gi|488599915|ref|YP_007906386.1| 43 YKCPSCGF 50
                                      89999996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.069        36      19      25 ..       6      12 ..       2      15 .. 0.59
   2 ?    7.7   1.2    0.0044       2.3       4      10 ..      22      28 ..      19      32 .. 0.79
   3 ?    9.0   0.3    0.0017      0.91       4       9 ..      44      49 ..      41      51 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.069
                       zf-ribbon_3 19 CpyCGtk 25
                                      C +CG+ 
  gi|488599915|ref|YP_007906386.1|  6 CISCGEN 12
                                      5555554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0044
                       zf-ribbon_3  4 rCPnCGa 10
                                       CPnC++
  gi|488599915|ref|YP_007906386.1| 22 PCPNCNE 28
                                      7****98 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0017
                       zf-ribbon_3  4 rCPnCG 9 
                                      +CP+CG
  gi|488599915|ref|YP_007906386.1| 44 KCPSCG 49
                                      566666 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 ?    7.6   5.2    0.0014      0.74     618     662 ..       3      49 ..       1      52 [. 0.59

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                          PolC_DP2 618 rrkCkkCgketl.....earCeeCgekteeklvCkkceeeveeekcekce 662
                                        +kC +Cg++ +     ++ C++C+e++   ++Ck+c++ ++  kc+ c+
  gi|488599915|ref|YP_007906386.1|   3 VHKCISCGENLIgmnyvKFPCPNCNESI---YRCKRCRKLANLYKCPSCG 49 
                                       5678888765431111144566665544...5588888887777788775 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.6   8.2e+02       4      11 ..       5      12 ..       2      14 .. 0.75
   2 ?    9.1   0.3    0.0018      0.95       3      12 ..      21      30 ..      19      31 .. 0.89
   3 ?    4.1   1.3     0.065        34       3      10 ..      31      38 ..      29      39 .. 0.87
   4 ?    4.8   0.1     0.042        22       2       9 ..      42      49 ..      41      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.6
                            zf_UBZ  4 lCerCgke 11
                                       C  Cg++
  gi|488599915|ref|YP_007906386.1|  5 KCISCGEN 12
                                      68889986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                            zf_UBZ  3 ylCerCgkei 12
                                      ++C+ C+++i
  gi|488599915|ref|YP_007906386.1| 21 FPCPNCNESI 30
                                      99******98 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.065
                            zf_UBZ  3 ylCerCgk 10
                                      y C+rC k
  gi|488599915|ref|YP_007906386.1| 31 YRCKRCRK 38
                                      89****87 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.042
                            zf_UBZ  2 tylCerCg 9 
                                       y C+ Cg
  gi|488599915|ref|YP_007906386.1| 42 LYKCPSCG 49
                                      69*****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 ?    5.7   0.2     0.024        13      16      23 .]       6      13 ..       2      14 .. 0.66
   2 ?    7.4   6.3    0.0072       3.8       1      20 [.       5      27 ..       5      30 .. 0.87
   3 ?    1.3   0.4      0.59   3.1e+02       1       6 [.      32      37 ..      32      39 .. 0.75
   4 ?    7.0   0.9    0.0093       4.9       1       6 [.      44      49 ..      44      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.024
                     zinc_ribbon_2 16 CpyCGtpl 23
                                      C  CG++l
  gi|488599915|ref|YP_007906386.1|  6 CISCGENL 13
                                      66676654 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0072
                     zinc_ribbon_2  1 fCpnCGael.q.dnakF.CpyCG 20
                                      +C +CG+ l   + +kF Cp+C 
  gi|488599915|ref|YP_007906386.1|  5 KCISCGENLiGmNYVKFpCPNCN 27
                                      799******8679*********5 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.59
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +C++C 
  gi|488599915|ref|YP_007906386.1| 32 RCKRCR 37
                                      699995 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0093
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +Cp+CG
  gi|488599915|ref|YP_007906386.1| 44 KCPSCG 49
                                      799998 PP

>> NMDAR2_C  N-methyl D-aspartate receptor 2B3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.3     0.004       2.1     386     422 ..       5      44 ..       1      46 [. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.004
                                       XXXXXXXXXXXX.XXXXXXX...XXX.XXXXXXXXXXXXX CS
                          NMDAR2_C 386 hCRsClsklsaygagsssvr...spykrCdaCkklgnLYd 422
                                       +C sC  +l ++   ++       ++ rC  C+kl+nLY 
  gi|488599915|ref|YP_007906386.1|   5 KCISCGENLIGMNYVKFPCPncnESIYRCKRCRKLANLYK 44 
                                       588998877555444443223336666************6 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.4    0.0042       2.2      53     100 ..       2      48 ..       1      51 [. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0042
                            FYVE_2  53 gethCilCleefkllvnskrqCldCklnv..CkkCsvenkkekvwlCkiC 100
                                       ++++Ci C e++  +   k  C +C+  +  Ck+C    k  + + C  C
  gi|488599915|ref|YP_007906386.1|   2 EVHKCISCGENLIGMNYVKFPCPNCNESIyrCKRCR---KLANLYKCPSC 48 
                                       6799********999999*******97652266665...55667777776 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.48   2.5e+02       1       9 [.       4      12 ..       4      18 .. 0.85
   2 ?    4.6   0.3      0.14        72       1       8 [.      21      28 ..      21      30 .. 0.86
   3 ?    3.5   0.2      0.32   1.7e+02       1       8 [.      31      38 ..      31      41 .. 0.85
   4 ?    6.2   0.4     0.043        23       1      10 [.      43      50 ..      43      53 .] 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.48
                         zf-C2H2_4  1 fkCpiCgks 9 
                                      +kC  Cg++
  gi|488599915|ref|YP_007906386.1|  4 HKCISCGEN 12
                                      69****986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.14
                         zf-C2H2_4  1 fkCpiCgk 8 
                                      f+Cp C++
  gi|488599915|ref|YP_007906386.1| 21 FPCPNCNE 28
                                      89****87 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.32
                         zf-C2H2_4  1 fkCpiCgk 8 
                                      ++C+ C+k
  gi|488599915|ref|YP_007906386.1| 31 YRCKRCRK 38
                                      89****65 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.043
                         zf-C2H2_4  1 fkCpiCgksF 10
                                      +kCp C   F
  gi|488599915|ref|YP_007906386.1| 43 YKCPSC--GF 50
                                      8*****..55 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.2     0.033        17      19      34 ..      14      29 ..       5      31 .. 0.70
   2 ?    3.1   2.2      0.17        89      27      33 ..      32      38 ..      28      39 .. 0.80
   3 ?    5.6   0.1     0.028        15       4      10 ..      44      50 ..      42      52 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.033
                     zinc_ribbon_4 19 lpakgvkvrCskCghv 34
                                      +  + vk  C++C+++
  gi|488599915|ref|YP_007906386.1| 14 IGMNYVKFPCPNCNES 29
                                      5556667777777765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.17
                     zinc_ribbon_4 27 rCskCgh 33
                                      rC++C++
  gi|488599915|ref|YP_007906386.1| 32 RCKRCRK 38
                                      8888875 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.028
                     zinc_ribbon_4  4 tCpsCka 10
                                       CpsC++
  gi|488599915|ref|YP_007906386.1| 44 KCPSCGF 50
                                      4777765 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2  15.6       3.6   1.9e+03       8      20 ..      23      37 ..       3      40 .. 0.86
   2 ?    5.5   9.3     0.029        15       5      20 ..      33      49 ..      32      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.6
                                      T-S..B-SEE-TTT- CS
                            zf-HIT  8 Cgf..pakYkCpkCn 20
                                      C++  ++ Y+C +C+
  gi|488599915|ref|YP_007906386.1| 23 CPNcnESIYRCKRCR 37
                                      888889999999997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.029
                                      -TTT-S.B-SEE-TTT- CS
                            zf-HIT  5 CgvCgf.pakYkCpkCn 20
                                      C  C +    YkCp C+
  gi|488599915|ref|YP_007906386.1| 33 CKRCRKlANLYKCPSCG 49
                                      999***9999******7 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2       0.1        53      15      23 ..       2      10 ..       1      13 [. 0.89
   2 ?    1.1   0.5      0.56     3e+02      18      23 ..      22      27 ..      16      28 .. 0.81
   3 ?    8.2   5.7    0.0034       1.8      13      34 ..      27      48 ..      25      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                                      H-EE-TTT- CS
                              RecR 15 kvrhCsrCg 23
                                      +v+ C  Cg
  gi|488599915|ref|YP_007906386.1|  2 EVHKCISCG 10
                                      69******8 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.56
                                      E-TTT- CS
                              RecR 18 hCsrCg 23
                                      +C++C+
  gi|488599915|ref|YP_007906386.1| 22 PCPNCN 27
                                      588886 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0034
                                      HHH-EE-TTT--EESSSS-CCC CS
                              RecR 13 kekvrhCsrCgnlteedlCaIC 34
                                       e++ +C+rC+ l+    C+ C
  gi|488599915|ref|YP_007906386.1| 27 NESIYRCKRCRKLANLYKCPSC 48
                                      68899***************99 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   5.7     0.049        26      11      30 ..      15      34 ..       5      38 .. 0.77
   2 ?    6.2   1.3     0.021        11      16      24 ..      42      50 ..      35      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.049
                          zf-Mss51 11 apkhvdfeCpdCGiptycse 30
                                        + v+f Cp+C  ++y ++
  gi|488599915|ref|YP_007906386.1| 15 GMNYVKFPCPNCNESIYRCK 34
                                      56789*******99999887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.021
                          zf-Mss51 16 dfeCpdCGi 24
                                       ++Cp CG+
  gi|488599915|ref|YP_007906386.1| 42 LYKCPSCGF 50
                                      59******8 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.6    0.0093       4.9       1      43 [.       6      50 ..       6      53 .] 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0093
                              NMD3  1 CcrCGkei..eeling...lCedCllkevditegiekievevCkeCgr 43
                                      C+ CG++       n     C++C  + ++  ++ + +++  C++Cg 
  gi|488599915|ref|YP_007906386.1|  6 CISCGENLigM---NYvkfPCPNCNESIYRCKRCRKLANLYKCPSCGF 50
                                      *******9442...434569****9999999999888*********96 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 ?    9.7   0.4    0.0014      0.72       2      23 ..       5      26 ..       5      28 .. 0.95
   2 ?    3.0   0.9      0.18        94      18      26 ..      31      39 ..      27      40 .. 0.77
   3 ?    1.2   0.2      0.61   3.2e+02      20      23 ..      45      48 ..      42      52 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                                      B-SSS--B--SS-S---B-TTT CS
                        HscB_4_cys  2 rCWnCGgpgapgrgdefFCpqC 23
                                      +C +CG+ + +++  +f Cp C
  gi|488599915|ref|YP_007906386.1|  5 KCISCGENLIGMNYVKFPCPNC 26
                                      5999****************** PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.18
                                      -B-TTT--B CS
                        HscB_4_cys 18 fFCpqCRAL 26
                                      + C +CR L
  gi|488599915|ref|YP_007906386.1| 31 YRCKRCRKL 39
                                      56*****66 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.61
                                      -TTT CS
                        HscB_4_cys 20 CpqC 23
                                      Cp C
  gi|488599915|ref|YP_007906386.1| 45 CPSC 48
                                      5555 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   5.9      0.81   4.3e+02      14      21 ..      20      27 ..       2      29 .. 0.68
   2 ?    6.4   0.4     0.024        13      12      22 ..      28      38 ..      27      41 .. 0.88
   3 ?    7.9   0.8    0.0082       4.3      14      22 ..      42      50 ..      40      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.81
                         zf-H2C2_2 14 pyeCplCd 21
                                      ++ Cp C+
  gi|488599915|ref|YP_007906386.1| 20 KFPCPNCN 27
                                      58999998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                         zf-H2C2_2 12 ekpyeCplCdk 22
                                      e++y C+ C+k
  gi|488599915|ref|YP_007906386.1| 28 ESIYRCKRCRK 38
                                      899******99 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0082
                         zf-H2C2_2 14 pyeCplCdk 22
                                       y+Cp+C+ 
  gi|488599915|ref|YP_007906386.1| 42 LYKCPSCGF 50
                                      69*****86 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.7     0.032        17       7      34 ..       5      28 ..       2      30 .. 0.71
   2 ?    2.8   7.8      0.24   1.3e+02       6      33 ..      31      49 ..      30      50 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.032
                       Zn-ribbon_8  7 rCeeCghefevlqsis.dapltaCPeCgs 34
                                      +C +Cg   e l  ++    + +CP+C++
  gi|488599915|ref|YP_007906386.1|  5 KCISCG---ENLIGMNyV--KFPCPNCNE 28
                                      688999...777777732..344***985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCg 33
                                      YrC++C     +l+      l +CP+Cg
  gi|488599915|ref|YP_007906386.1| 31 YRCKRCR----KLAN-----LYKCPSCG 49
                                      9999999....4432.....55599998 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.063        33      29      36 ..       4      11 ..       2      13 .. 0.71
   2 ?    3.7   1.1      0.11        57       1       8 [.      21      28 ..      21      30 .. 0.80
   3 ?    3.7   0.8      0.11        57      28      36 ..      30      38 ..      28      39 .. 0.81
   4 ?    5.8   0.2     0.024        13      29      35 ..      43      49 ..      40      51 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.063
                           TFIIS_C 29 ykCtkCgh 36
                                      +kC++Cg+
  gi|488599915|ref|YP_007906386.1|  4 HKCISCGE 11
                                      57777775 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                           TFIIS_C  1 akCpkCgs 8 
                                      ++Cp+C++
  gi|488599915|ref|YP_007906386.1| 21 FPCPNCNE 28
                                      68999986 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.11
                           TFIIS_C 28 fykCtkCgh 36
                                      +y+C+ C +
  gi|488599915|ref|YP_007906386.1| 30 IYRCKRCRK 38
                                      699999975 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.024
                           TFIIS_C 29 ykCtkCg 35
                                      ykC +Cg
  gi|488599915|ref|YP_007906386.1| 43 YKCPSCG 49
                                      7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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):              34  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 308.59
//
Query:       gi|488599916|ref|YP_007906387.1|  [L=88]
Description: translation elongation factor 1B (aEF-1B) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-20   70.8   4.3    9.1e-20   70.6   4.3    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
      0.038   14.4   3.0      0.056   13.8   3.0    1.4  1  NBD94     Nucleotide-Binding Domain 94 of RH


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 !   70.6   4.3     1e-23   9.1e-20       2      88 ..       6      86 ..       5      88 .] 0.96

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1e-23
                                      EEEEEEESSS---HHHHHHHHHH.HS-TSEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SE CS
                           EF1_GNE  2 vvlevkPeddetdleelekkvksikleglvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVq 80
                                      + ++v+P+d+++dle++  ++++ik e++ + +  k++piafGlk+L +++v++d+    de  e+i++ieg     V+
  gi|488599916|ref|YP_007906387.1|  6 MKIKVMPADVNVDLEKIYSEIEKIKSEKISLRD-KKIQPIAFGLKALLLMAVMPDEGSIGDEFVEAIKKIEG-----VE 78
                                      679*****************************6.**************************************.....** PP

                                      EEEEEEEE CS
                           EF1_GNE 81 sveivsfn 88
                                      svei+s++
  gi|488599916|ref|YP_007906387.1| 79 SVEIESVE 86
                                      ******97 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.0   6.3e-06     0.056      16      52 ..      14      52 ..       2      87 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.3e-06
                             NBD94 16 kiyeniekllnEleeiekektsl..eevknielsYgrsL 52
                                      ++  ++ek+++E+e+i+ ek+sl  ++++ i    + +L
  gi|488599916|ref|YP_007906387.1| 14 DVNVDLEKIYSEIEKIKSEKISLrdKKIQPIAFGLKALL 52
                                      577789****************93335666666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 527.29
//
Query:       gi|488599917|ref|YP_007906388.1|  [L=289]
Description: Conserved secreted protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-15   57.8   0.0    8.8e-11   42.2   0.0    2.3  2  LEA_2      Late embryogenesis abundant protein
  ------ inclusion threshold ------
       0.07   13.2   2.8       0.56   10.2   0.2    2.3  2  DNMT1-RFD  Cytosine specific DNA methyltransferase replicatio


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   9.8e-15   8.8e-11       2     100 ..      48     141 ..      47     144 .. 0.93
   2 !   13.2   0.0   1.1e-05     0.098      12      81 ..     198     263 ..     194     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 9.8e-15
                                       EEEEESSSS-EEEEEEEEEEEESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEEE CS
                             LEA_2   2 lrvrNPNsfgvrydgleldlsyngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleytl 78 
                                       ++v+NPN+++++++++e +++ n  +++ ++s  +  ++a+ ++t+e++ +++++++++++ +++  ++g++ +  +
  gi|488599917|ref|YP_007906388.1|  48 IKVYNPNPVPIPLKDVETKIYMNSIEMG-HGSALKSEIAANTESTIELSTKIDNSKIPEWWVSHI--KNGEKSTMLF 121
                                       89**************************.************************************..8999999999 PP

                                       EEEEE.EEETTTSCEEEEEEEE CS
                             LEA_2  79 rgrlkvlgkpilgsvtvpvkvs 100
                                       +g l  ++++ ++ +++p+k +
  gi|488599917|ref|YP_007906388.1| 122 EGDL--VFDLKVTEFKYPIKLT 141
                                       9999..4567779999999875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.1e-05
                                       EEEEEEEEEEEESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEEEEEE CS
                             LEA_2  12 vrydgleldlsyngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleytlrgr 81 
                                       v +++++++++ ng +++  + ++ + q+ +g+t +e+  ++++++l +++ ++l  ++g+++e++l ++
  gi|488599917|ref|YP_007906388.1| 198 VMLEKISYTIEMNGIKVG--EGESNILQEVGGKTKVEFITKIDNNKLTEWWISHL--KNGERTEVRLNAK 263
                                       55789*************..55566888888999999999***************..5666666666554 PP

>> DNMT1-RFD  Cytosine specific DNA methyltransferase replication foci domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   6.3e-05      0.56       7      85 ..      43     119 ..      38     125 .. 0.76
   2 ?    3.0   0.2     0.011        95      51      85 ..     224     258 ..     179     263 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.3e-05
                                       EEEEEEEEEETTSBB--STTSTTTTT--EEEEEEEEETT...----SSTT.SEEEEE....ES-ECEEEEEECSSSS CS
                         DNMT1-RFD   7 rkltdfelydkdgelvslevleieknadifisgvvkdids..edeekkkekgiedkglqiklgpIkeWtisgvdege 81 
                                       + +t+  +y+ + ++++l   ++e   +i+++++ +  +s   +e + ++++  + + +i  ++I eW++s  ++ge
  gi|488599917|ref|YP_007906388.1|  43 EVITNIKVYNPNPVPIPLK--DVE--TKIYMNSIEMGHGSalKSEIAANTESTIELSTKIDNSKIPEWWVSHIKNGE 115
                                       5789999999999999998..555..78999999888887774444444445666666899999**********998 PP

                                       BEEE CS
                         DNMT1-RFD  82 kali 85 
                                       k  +
  gi|488599917|ref|YP_007906388.1| 116 KSTM 119
                                       7655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.011
                                       SSTT.SEEEEE....ES-ECEEEEEECSSSSBEEE CS
                         DNMT1-RFD  51 kkkekgiedkglqiklgpIkeWtisgvdegekali 85 
                                       + ++k   +   +i  ++  eW+is  ++ge+  +
  gi|488599917|ref|YP_007906388.1| 224 EVGGKTKVEFITKIDNNKLTEWWISHLKNGERTEV 258
                                       3334333344447788889******9999986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1726.74
//
Query:       gi|488599918|ref|YP_007906389.1|  [L=429]
Description: DNA repair exonuclease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-16   60.2   0.4    6.8e-16   59.4   0.4    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    2.3e-10   40.9   0.0    2.4e-09   37.6   0.0    2.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.032   14.2   0.1      0.094   12.7   0.1    1.8  1  Rrp44_S1       S1 domain


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.4   1.1e-19   6.8e-16       2     203 ..       3     206 ..       2     207 .. 0.61

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.1e-19
                                       EEEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.......HHHHHHHHHHHHHHHH CS
                       Metallophos   2 rilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrg.......dlekellellaalvky 63 
                                       ++++++D+H+        +++    +++l++++ + +e k+d++++ GDl++          l+      ++++++ 
  gi|488599918|ref|YP_007906389.1|   3 KFAHLADVHVgnrqygsyERQMDFAQAFLNAIKFCVSE-KVDFIIISGDLFHKKseidpltLLQ------VKKVLEI 72 
                                       99*********666644444444444444444444666.**************98555544333......3333333 PP

                                       ....TSEEEEEC-TTS......CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETH CS
                       Metallophos  64 ....pipvylllGNHe......gfee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellv 129
                                            ipv+++ GNH+      +++  ++l   + l + ++ + +   v ++    ++++   + + ++G       
  gi|488599918|ref|YP_007906389.1|  73 pkkaEIPVIAVEGNHDstyfreNYTWlDYLAGSDLLINLKPSFDDGLVVEEWDGEGAYIDL--DGVRIYGM------ 141
                                       555559**********543333222222222222222223333333444444444444444..55555655...... PP

                                       HHHHHHHHHHSCHHHHCCHHHHHH.HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHH.HHHTTESEEEEESSSS CS
                       Metallophos 130 sldklgslnleleapepgdewlkd.lekrekadwvivlgHsplyrgsgylfgdealedl.lkkygvdlvisGHtHv 203
                                                     +   + +l +  +k ++  ++i+++H++++ +  + +g     +l   +++vd++  GH+H+
  gi|488599918|ref|YP_007906389.1| 142 ----------KYYGSLT-ERILDEyAKKIKRSGFTIFVSHIGVEGYVKNMYGCIGSSKLhRLRGRVDYIALGHVHK 206
                                       ..........2222222.5666667778999*************5555555555555777899************7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   4.1e-13   2.4e-09       2     149 ..       3     223 ..       2     241 .. 0.66

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 4.1e-13
                     Metallophos_2   2 klaiiSDlH..........snldaleavlealk...evgvdaiihaGDl....eeeepevleellela........p 53 
                                       k+a+++D+H          +++d  +a+l+a+k   +++vd ii +GDl     e++p +l ++++++        p
  gi|488599918|ref|YP_007906389.1|   3 KFAHLADVHvgnrqygsyeRQMDFAQAFLNAIKfcvSEKVDFIIISGDLfhkkSEIDPLTLLQVKKVLeipkkaeiP 79 
                                       89*************9999777777777777662226799********887555555545555555556668888** PP

                     Metallophos_2  54 vlaVrGNnD...........................................eevveedvlreaaelgtdl...... 81 
                                       v+aV GN+D                                           +                 l      
  gi|488599918|ref|YP_007906389.1|  80 VIAVEGNHDstyfrenytwldylagsdllinlkpsfddglvveewdgegayiD-----------------Ldgvriy 139
                                       *********66666666666666666666655555555555554444433331.................0333333 PP

                     Metallophos_2  82 ..............peeaelelagekvlliHgdpl.........gvkdalaellkeaeegsdvvvcGHtHvpeveke 135
                                                     + +++++  g+++++ H              ++ +l++l+ +    +d++++GH H++ ve++
  gi|488599918|ref|YP_007906389.1| 140 gmkyygslterildEYAKKIKRSGFTIFVSHIGVEgyvknmygcIGSSKLHRLRGR----VDYIALGHVHKAFVEDD 212
                                       33333443333332233444447777888888755877766665555666666655....77*************** PP

                     Metallophos_2 136 ggvlvvnPGsvgep 149
                                           + nPGs++  
  gi|488599918|ref|YP_007906389.1| 213 ---FIFNPGSLEIC 223
                                       ...899****9865 PP

>> Rrp44_S1  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.6e-05     0.094       6      29 ..     155     178 ..     151     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                       EEEEEESSEEEEEETTTTEEEEEE CS
                          Rrp44_S1   6 yvikvfsNGvvvlvprfGiEglir 29 
                                       y  k+ + G+ ++v++ G+Eg ++
  gi|488599918|ref|YP_007906389.1| 155 YAKKIKRSGFTIFVSHIGVEGYVK 178
                                       7789*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2606.44
//
Query:       gi|488599919|ref|YP_007906390.1|  [L=884]
Description: ATPase involved in DNA repair [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-13   49.9  23.6    3.8e-13   49.9  23.6    4.1  2  AAA_15        AAA ATPase domain
    9.8e-12   44.8  50.9    8.6e-11   41.7  50.9    2.4  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.8e-08   35.1 152.8    3.7e-08   34.1  64.2    7.3  4  AAA_23        AAA domain
    3.8e-08   33.5  11.3    3.2e-06   27.2   0.2    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00013   21.7   0.0    0.00023   20.8   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00013   20.8  94.9      0.017   13.8  28.7    5.0  5  AAA_13        AAA domain
    0.00021   21.5   0.1     0.0015   18.7   0.0    2.3  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
    0.00076   19.4   7.6    0.00076   19.4   7.6   10.6 12  Prefoldin_2   Prefoldin subunit
     0.0012   18.4   0.0     0.0012   18.4   0.0    5.7  9  AAA_27        AAA domain
     0.0015   18.9   7.8     0.0015   18.9   7.8    7.0  1  Uso1_p115_C   Uso1 / p115 like vesicle tethering protein, C t
     0.0046   17.2   1.1        4.1    7.7   0.0    3.2  2  PP-binding_2  Acyl-carrier
     0.0047   17.4  25.9       0.01   16.4   0.0    6.0  1  ABC_tran      ABC transporter
  ------ inclusion threshold ------
      0.018   15.7   4.0      0.018   15.7   4.0    8.4  7  Occludin_ELL  Occludin homology domain
      0.034   14.2  32.0          3    7.9   1.3    6.9  7  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
      0.063   12.6  50.9      0.061   12.7   0.4    4.3  3  DUF4407       Domain of unknown function (DUF4407)
       0.23   11.5  75.6        1.2    9.2   2.7    7.8  8  DUF1664       Protein of unknown function (DUF1664)
       0.27   10.1 115.1       0.31    9.9  28.6    5.5  4  Spc7          Spc7 kinetochore protein
       0.33   11.4  51.8        4.5    7.8   0.0    9.0  5  NPV_P10       Nucleopolyhedrovirus P10 protein
       0.33   10.2  76.0       0.73    9.1  10.4    6.5  6  DUF3450       Protein of unknown function (DUF3450)
       0.56   10.5 119.5        0.3   11.4  14.9    8.4  9  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
       0.97    9.7   0.0       0.97    9.7   0.0    4.0  5  AAA_22        AAA domain
        2.2    7.8  69.4        4.6    6.7  16.5    4.4  4  Exonuc_VII_L  Exonuclease VII, large subunit
          3    7.1 121.8       0.96    8.8   5.7    6.8  6  GAS           Growth-arrest specific micro-tubule binding
        3.1    5.2  90.4       0.22    9.0  21.6    4.2  4  DUF3584       Protein of unknown function (DUF3584)
        9.5    6.2  48.6          2    8.4   3.2    7.0  7  LOH1CR12      Tumour suppressor protein


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 !   49.9  23.6   5.2e-16   3.8e-13       1     265 [.       1     359 [.       1     369 [. 0.56
   2 !   12.2  10.0   0.00015      0.11     119     367 ..     614     863 ..     597     864 .. 0.70

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 5.2e-16
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn...............kkvikiek 62 
                                       M I+++ ++N +s++   i++se l+ +iG+N++GK++ilea+ + l  +  ++               + ++ ++ 
  gi|488599919|ref|YP_007906390.1|   1 M-IREVVLENIKSYEFERIEFSEGLNAIIGENGAGKTTILEAIGFALFDSIAYKisdflrrgakkglvrVRFTSLDG 76 
                                       7.9****************************************875555644445799***********88899999 PP

                            AAA_15  63 edleifeniseskdikIdvef........................................................ 83 
                                        d+e+ ++i es + +  ++                                                         
  gi|488599919|ref|YP_007906390.1|  77 RDYEVVRKITESGTSEYYINDleagrvaegkdvlefiklafgidgdqktffenaigvlqgkmtsqflespsvrnrif 153
                                       999999999999988877777889999999999999999999999999999999999999999999******99999 PP

                            AAA_15  84 .............................aekekakeyektlks.kekkkadlllkkkesdlkktikdkklklkkne 130
                                                                        ++k+ ++++k+ + k + + +lkk++ +++++ik+kk+ lk+ +
  gi|488599919|ref|YP_007906390.1| 154 spiigvesykkayersreyenflsdkihdG---EKKI-ISLKKDvELKSSVEQDLKKLKAKKDSLIKKKKIILKELN 226
                                       999888876655554444444433321110...1111.111111011111122222222222233333333332222 PP

                            AAA_15 131 lsdekisvekkks.....kkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisa 202
                                         ++k++   + +      k+  + k++kl +eke+l++ k+                 el+++l+ + ++ +l  +
  gi|488599919|ref|YP_007906390.1| 227 ALKKKHDELSEIKdkiddLKQKISRKQDKLSSEKEDLSKLKQ-----------------ELSKILEIEKKTKELEAS 286
                                       222222221111112122222222222222233333333333.................444444444455555555 PP

                            AAA_15 203 kRnvsd.....edsekkssllgklkekileealqekl....eeelteklkeiqeklkeidkklaeelk.....kilk 265
                                        R++ d     e+ + ++  l+k++++++e +++ +     + +++++lkei+ek keid++     +     ++l 
  gi|488599919|ref|YP_007906390.1| 287 YREYLDlenrlEELDAEERDLSKKLDELSEVSVEIEKlktqISSTKKALKEIEEKEKEIDGIK----EdarreEVLL 359
                                       555555543334444444444444555544443322212222222333333333333333332....2333344444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00015
                            AAA_15 119 ikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaii 195
                                       +k    +      +d+  s+  + +kk+  k++ ++le  ++ lk +  +++  +k lee++++ee     ++s+++
  gi|488599919|ref|YP_007906390.1| 614 LKILRPA------YDSYLSLAPQIKKKDELKNRISELEGGINRLKQEIVSMEVQLKSLEEKFNSEE-----FESLSQ 679
                                       4443333......24445555555677777788888888888888888888888888999999999.....99**** PP

                            AAA_15 196 klllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk........... 261
                                       k+l i++++   + + +  s++++kl +++ e + +ek          +++++ + ++ kl+   +           
  gi|488599919|ref|YP_007906390.1| 680 KMLEIMSEKGKVEGEIKGVSESIEKLESSLAELKEREKE-------YLRLKDEMDRLKRKLEFIRAlreifnlavpe 749
                                       *********999999999999999999999996554444.......3333333333333332222233222244555 PP

                            AAA_15 262 ..........kilkkkidkik.kfnykgkkneeieik...ddeelplnknGsGvqrllllillileaekkdekeekn 324
                                                 +i + +++++  + n  +++ e   ik    + e+++++++ G q +  +++ ++ +       ++ 
  gi|488599919|ref|YP_007906390.1| 750 itkayvsavsEIANRFFCELMdDYNWEIEWTEDFGIKaryRGREISFAQMSGGEQMCAAIAIRLALMTVL----SNM 822
                                       5566666666777777777776777788888887777*********************************....*** PP

                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnkt..QviitTHSph 367
                                       ++ +++EP  +      k l+ +l ++    k+  Q+++ TH + 
  gi|488599919|ref|YP_007906390.1| 823 KVAFFDEPTQNMDEVRRKNLAIQLSKI----KGfrQIFVITHDDT 863
                                       ********7665444444444444444....33559999999875 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 !   41.7  50.9   1.2e-13   8.6e-11       1     219 [.       1     881 [.       1     882 [. 0.97

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.2e-13
                                       EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkka 77 
                                       +++++++en ksy  +   ++fs++++ai+G+NG+GK+ +l+Ai F L + s     + k+sd + +      +kk+
  gi|488599919|ref|YP_007906390.1|   1 MIREVVLENIKSY--EFERIEFSEGLNAIIGENGAGKTTILEAIGFALFD-SI----AYKISDFLRR-----GAKKG 65 
                                       6899*********..78999****************************94.44....6899999997.....88999 PP

                                       EEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.................. RF
                             SMC_N  78 eveitfdnedkklkiekeevsisrrvkrkgeseykingkevtk.kevsellesagiske.................. 135
                                        v + f+  d +      ++++ r++ ++g+sey+in+ e+ + +e +++le  ++                     
  gi|488599919|ref|YP_007906390.1|  66 LVRVRFTSLDGR------DYEVVRKITESGTSEYYINDLEAGRvAEGKDVLEFIKLAFGidgdqktffenaigvlqg 136
                                       999*99999998......89****************987665447777777766666556677************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|488599919|ref|YP_007906390.1| 137 kmtsqflespsvrnrifspiigvesykkayersreyenflsdkihdgekkiislkkdvelkssveqdlkklkakkds 213
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|488599919|ref|YP_007906390.1| 214 likkkkiilkelnalkkkhdelseikdkiddlkqkisrkqdklssekedlsklkqelskileiekktkeleasyrey 290
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|488599919|ref|YP_007906390.1| 291 ldlenrleeldaeerdlskkldelsevsveieklktqisstkkalkeieekekeidgikedarreevllkeisaiel 367
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|488599919|ref|YP_007906390.1| 368 lsverdqlkkrlrditkdieqksikleelkrreekfreamekleklsnieekyekllklsvrlsedrksiienikav 444
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|488599919|ref|YP_007906390.1| 445 ktnlcpildekcdrihqkiddlerklrvveerleevdkkmnaakkavevknrlesaisklkaelkqkeeieneikek 521
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|488599919|ref|YP_007906390.1| 522 iktrneiesrtkeidskleqkeniiqefervkgslerlkileseigkksdlieelknlenrlehlnsiakdlepsks 598
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|488599919|ref|YP_007906390.1| 599 kytsvkeeiekiakrlkilrpaydsylslapqikkkdelknriselegginrlkqeivsmevqlksleekfnseefe 675
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|488599919|ref|YP_007906390.1| 676 slsqkmleimsekgkvegeikgvsesieklesslaelkerekeylrlkdemdrlkrklefiralreifnlavpeitk 752
                                       ***************************************************************************** PP

                                       .............................................CS-HHHHHHHHHHHHHHHHC.CS--SEEEECT CS
                                       .............................................xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 136 .............................................lLSgGektLvalaLlfAiqk.vkpaplyllDe 166
                                                                                    ++SgGe+  +a+a+++A+    +   + ++De
  gi|488599919|ref|YP_007906390.1| 753 ayvsavseianrffcelmddynweiewtedfgikaryrgreisfaQMSGGEQMCAAIAIRLALMTvLSNMKVAFFDE 829
                                       **************************************************************655157888999*** PP

                                       TTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 167 idaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkvengvs 219
                                         +++De ++k++a  l + +   Q++vi++++++ e +++ +++ k eng+s
  gi|488599919|ref|YP_007906390.1| 830 PTQNMDEVRRKNLAIQLSKIKGFRQIFVITHDDTFEEMVENAIKIVK-ENGIS 881
                                       *********************9**********9999999*****999.77765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1  64.2   5.1e-11   3.7e-08       2     167 ..       5     316 ..       4     387 .. 0.61
   2 ?   -2.5  18.7       8.8   6.3e+03     146     197 ..     370     425 ..     348     427 .. 0.78
   3 ?   -1.7  23.6       4.7   3.4e+03     114     200 .]     443     540 ..     425     550 .. 0.57
   4 ?    2.4  11.7      0.26   1.9e+02     144     199 ..     547     614 ..     540     615 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5.1e-11
                            AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprl.srksgrgfeksdveiese......... 68 
                                       + +en++s++ + i+Fs gl++I+G+NGaGKTTil+Ai +aL+   +   s+  +rg++k+ v++ +          
  gi|488599919|ref|YP_007906390.1|   5 VVLENIKSYEFERIEFSEGLNAIIGENGAGKTTILEAIGFALFDSIAYKiSDFLRRGAKKGLVRVRFTsldgrdyev 81 
                                       679*****************************************884431444477777777776666666455555 PP

                            AAA_23  69 .........................gkvkayveltfenkdgry.................................. 86 
                                                                ++v ++++l f                                         
  gi|488599919|ref|YP_007906390.1|  82 vrkitesgtseyyindleagrvaegKDVLEFIKLAF------Gidgdqktffenaigvlqgkmtsqflespsvrnri 152
                                       555555555555555555555555555555566665......04444579999999999**********99999999 PP

                            AAA_23  87 ............................................trsiererelskkkgkttkkaklellei.dele 118
                                                                                   + s+e++ ++ k k+++  k+k+ +l++ ++l+
  gi|488599919|ref|YP_007906390.1| 153 fspiigvesykkayersreyenflsdkihdgekkiislkkdvelKSSVEQDLKKLKAKKDSLIKKKKIILKElNALK 229
                                       99999999999999888888888888888888888888887777677777666666666666555555555555555 PP

                            AAA_23 119 qfisellgskki..ilnlilflgqer.........feefelkdkke............................... 153
                                       ++ +el ++k++   l++ +  +q++         +        k+                               
  gi|488599919|ref|YP_007906390.1| 230 KKHDELSEIKDKidDLKQKISRKQDKlssekedlsK-------LKQelskileiekktkeleasyreyldlenrlee 299
                                       555554443333233333333333333322222220.......2222222222333333355555544444443333 PP

                            AAA_23 154 ...rleelekeleeled 167
                                          + ++l+k+l+el++
  gi|488599919|ref|YP_007906390.1| 300 ldaEERDLSKKLDELSE 316
                                       33322222222222222 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.8
                            AAA_23 146 felkdkkerleelekeleeledekkllekl....eqekekekeleeleeeleeilk 197
                                        e+ + k+rl++++k++e+++ + ++l+++     ++ ek ++l+++ee+ e++lk
  gi|488599919|ref|YP_007906390.1| 370 VERDQLKKRLRDITKDIEQKSIKLEELKRReekfREAMEKLEKLSNIEEKYEKLLK 425
                                       34467789*************99999999977776888899999999999998876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.7
                            AAA_23 114 i.........deleqfisellgskkiilnlilf.lgqerfeefelkdkke...rleelekeleeledekkllekleq 177
                                                 de++++i ++++  ++ l+++   l + ++++++ k+  e   rle+++ +l+ + ++k+++e+++ 
  gi|488599919|ref|YP_007906390.1| 443 AvktnlcpilDEKCDRIHQKIDDLERKLRVVEErLEEVDKKMNAAKKAVEvknRLESAISKLKAELKQKEEIENEI- 518
                                       1222333345778888888888888888776541444445555555554455566666666666666666666543. PP

                            AAA_23 178 ekekekeleeleeeleeilkele 200
                                        kek k+ +e+e++ +ei+++le
  gi|488599919|ref|YP_007906390.1| 519 -KEKIKTRNEIESRTKEIDSKLE 540
                                       .5566666666666666666664 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.26
                            AAA_23 144 eefel.kdkkerleelekeleeledekkllekleqekekek...........eleeleeeleeilkel 199
                                       +efe+ k  +erl+ le e+ +++d +++l++le+++e  +           +++ ++ee+e+i k l
  gi|488599919|ref|YP_007906390.1| 547 QEFERvKGSLERLKILESEIGKKSDLIEELKNLENRLEHLNsiakdlepsksKYTSVKEEIEKIAKRL 614
                                       44455577888**********************88888888888888888889999999999998876 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 !   27.2   0.2   4.5e-09   3.2e-06       1      56 [.      24      78 ..      24     135 .. 0.73
   2 ?   -3.2   6.7       8.2   5.8e+03      99     211 ..     208     323 ..     171     344 .. 0.61
   3 ?   -1.9   1.4       3.1   2.2e+03     142     142 ..     372     372 ..     293     448 .. 0.49
   4 !   18.2   6.2   2.5e-06    0.0018     124     299 ..     580     862 ..     492     865 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.5e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpei 56
                                      ln++iG Ng+GK+++L+a+ ++ + d+ +    d+l++g + + ++ ++++ d + 
  gi|488599919|ref|YP_007906390.1| 24 LNAIIGENGAGKTTILEAIGFALF-DSIAYKISDFLRRGAKKGLVRVRFTSLDGRD 78
                                      79*******************988.7777777777777666666666666555554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.2
                            AAA_21  99 lldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke...rigllnif 172
                                         +k+sl++ ++ + ++ ++ + + ++ +  + ++++ +++ ++  ++++s++++l +l+++l k    ++ + ++ 
  gi|488599919|ref|YP_007906390.1| 208 KAKKDSLIKKKKIILKELNALKKKHDELSEIKDKIDDLKQKISRKQDKLSSEKEDLSKLKQELSKIleiEKKTKELE 284
                                       44556666666666666666666666666666666666666666666666666666666666666666655555555 PP

                            AAA_21 173 adyfgfakekrllqrlvrslklveielsdlgegeelias 211
                                       a+y  + ++ ++l++l  + ++   +l+ l e++++i++
  gi|488599919|ref|YP_007906390.1| 285 ASYREYLDLENRLEELDAEERDLSKKLDELSEVSVEIEK 323
                                       555555555555555555555555555555555555444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.1
                            AAA_21 142 k 142
                                       +
  gi|488599919|ref|YP_007906390.1| 372 R 372
                                       1 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 2.5e-06
                            AAA_21 124 vfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveiels 200
                                       +++l +l+ +  + + +++ +t+++++++++++ l  lr+++ ++l+++    +++++k+++++l++++++   e+ 
  gi|488599919|ref|YP_007906390.1| 580 ENRLEHLNSIAKDLEPSKSKYTSVKEEIEKIAKRLKILRPAYDSYLSLAPQIKKKDELKNRISELEGGINRLKQEIV 656
                                       34445555555555666777788888888888888888888999999999999999999999999999999999999 PP

                            AAA_21 201 dlgegeeliasvderlrer.......................................................... 219
                                        ++++ ++ ++ ++ + ++                                                          
  gi|488599919|ref|YP_007906390.1| 657 SMEVQLKSLEEKFNSEEFEslsqkmleimsekgkvegeikgvsesieklesslaelkerekeylrlkdemdrlkrkl 733
                                       999999999999988888899999999999999999999999999999999999999999999************** PP

                            AAA_21 220 ................................................gvvflengdgqelparelSdGtkrllall 248
                                                                                       ++ +  + +g+e++++++S G + ++a++
  gi|488599919|ref|YP_007906390.1| 734 efiralreifnlavpeitkayvsavseianrffcelmddynweiewteDFGIKARYRGREISFAQMSGGEQMCAAIA 810
                                       *************************************************************************8444 PP

                            AAA_21 249 tallralkkg..sllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                         l+     +  ++ ++DEp  +++  + + l+  l k++  +  Q+++ TH+ 
  gi|488599919|ref|YP_007906390.1| 811 IRLALMTVLSnmKVAFFDEPTQNMDEVRRKNLAIQLsKIK--GFRQIFVITHDD 862
                                       4333333333459********************5551555..37********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 !   20.8   0.0   3.2e-07   0.00023       5      46 ..       6      46 ..       2      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.2e-07
                            AAA_29  5 qlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                       l N  +++ ++ie++ +g   ++G++G+GK+T+l Ai + L
  gi|488599919|ref|YP_007906390.1|  6 VLENIKSYEFERIEFS-EGLNAIIGENGAGKTTILEAIGFAL 46
                                      56677788889999*9.779*****************97766 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0015       1.1      16      36 ..      22      42 ..       9      53 .. 0.81
   2 !   13.8  28.7   2.4e-05     0.017     294     475 ..     165     351 ..     158     358 .. 0.87
   3 ?    3.6  31.0     0.028        20     285     455 ..     372     548 ..     366     552 .. 0.68
   4 !    7.3  13.5    0.0022       1.6     281     457 ..     552     720 ..     547     737 .. 0.62
   5 ?    3.4   0.0     0.034        25     557     583 ..     848     874 ..     815     882 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                            AAA_13 16 kriNliYGwNGaGKTtLSrll 36
                                      +  N i G NGaGKTt+ +++
  gi|488599919|ref|YP_007906390.1| 22 EGLNAIIGENGAGKTTILEAI 42
                                      457*************97665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.4e-05
                            AAA_13 294 kveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksve.lesvkakiesikk 369
                                        +e+++ e+ + l + +++ ++++++ ++  elk+  e+  ++Lk+ ++ l +K+k + k+++ l++  +++++ik+
  gi|488599919|ref|YP_007906390.1| 165 AYERSR-EYENFLSDKIHDGEKKIISLKKDVELKSSVEQDLKKLKAKKDSLIKKKKIILKELNaLKKKHDELSEIKD 240
                                       455554.5666688888887778888888889999999999*********************9679999999***** PP

                            AAA_13 370 lvaeineliakhNekvanleeekeeakkklelhl.veeleseldeykkkykklekaieklekelkeeeaelkklee. 444
                                       +++++++ i++   k ++ +e+ +++k++l + l +e+ ++el++  ++y +le+ +e+l++e ++ +++l +l e 
  gi|488599919|ref|YP_007906390.1| 241 KIDDLKQKISRKQDKLSSEKEDLSKLKQELSKILeIEKKTKELEASYREYLDLENRLEELDAEERDLSKKLDELSEv 317
                                       ******************************997669999999999999*************9999999988887763 PP

                            AAA_13 445 ..eikeLekqlrdekpaaeeinkeLkaf.Glgel 475
                                         ei+ L++q+++ k+a +ei+++ k++ G++e+
  gi|488599919|ref|YP_007906390.1| 318 svEIEKLKTQISSTKKALKEIEEKEKEIdGIKED 351
                                       336********************99999998876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.028
                            AAA_13 285 qerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvk 361
                                        ++L+k++ ++ +++++ + kl+++  ++++ +++ e+ e+l+ ++e+  e+L +l+ +l++ rk + ++++  +++
  gi|488599919|ref|YP_007906390.1| 372 RDQLKKRLRDITKDIEQKSIKLEELKRREEKFREAMEKLEKLS-NIEEKYEKLLKLSVRLSEDRKSIIENIKAVKTN 447
                                       5789999999999999888899888887766555555555554.566666777778888999999999977653332 PP

                            AAA_13 362 aki........esikklvaeineliakhNekvanleeekeeakkklelhl.veeleseldeykkkykklekaiekle 429
                                         +        ++i ++++++++  +   e+ ++++++ ++akk++e    +e++ s+l++  k+++++e++i++  
  gi|488599919|ref|YP_007906390.1| 448 --LcpildekcDRIHQKIDDLERKLRVVEERLEEVDKKMNAAKKAVEVKNrLESAISKLKAELKQKEEIENEIKEKI 522
                                       ..21134444479*********************************9743245555555555566666666666666 PP

                            AAA_13 430 kelkeeeaelkkleeeikeLekqlrd 455
                                       k  +e+e+++k+++ + +++e+ +++
  gi|488599919|ref|YP_007906390.1| 523 KTRNEIESRTKEIDSKLEQKENIIQE 548
                                       66666666666666666666655544 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0022
                            AAA_13 281 feekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvel 357
                                       ++ + erL+ l +++ +k+  l+e+lk++ ++ +  +  ++d e  k++   ++e+++++ ++l+  r    + ++l
  gi|488599919|ref|YP_007906390.1| 552 VKGSLERLKILESEIGKKS-DLIEELKNLENRLEHLNSIAKDLEPSKSKYTSVKEEIEKIAKRLKILRPAYDSYLSL 627
                                       5666777777777777775.588888888887656666778888888888888888888888886666554454555 PP

                            AAA_13 358 esvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelke 434
                                           +k +++k+ ++e++  i++  + + ++e + +++++k+   + e+l        +k+ ++  +  k+e e+k 
  gi|488599919|ref|YP_007906390.1| 628 APQIKKKDELKNRISELEGGINRLKQEIVSMEVQLKSLEEKFNSEEFESLS-------QKMLEIMSEKGKVEGEIKG 697
                                       555555556666666666666666666666666666666666665555555.......5555555555555555555 PP

                            AAA_13 435 eeaelkkleeeikeLekqlrdek 457
                                        ++ ++kle   +eL+++ ++  
  gi|488599919|ref|YP_007906390.1| 698 VSESIEKLESSLAELKEREKEYL 720
                                       55555555555555555555444 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.034
                            AAA_13 557 kkkkakQlfiLTHnleffkevkkntkr 583
                                       k k ++Q+f+ TH  +f   v++++k 
  gi|488599919|ref|YP_007906390.1| 848 KIKGFRQIFVITHDDTFEEMVENAIKI 874
                                       4478**********9999999988874 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 ?   -0.8   0.1       2.7   1.9e+03       5      34 ..     286     315 ..     284     316 .. 0.87
   2 !   18.7   0.0   2.1e-06    0.0015      28      84 ..     794     842 ..     772     847 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.7
                           SbcCD_C   5 dyRnylsfevevrdedgkekelsrssgtlS 34 
                                        yR+yl++e + ++ d +e++ls++  +lS
  gi|488599919|ref|YP_007906390.1| 286 SYREYLDLENRLEELDAEERDLSKKLDELS 315
                                       69*******999988888888999999888 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.1e-06
                           SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                        s++++SGGe+ + a++a+ +al  ++s+       +++ f+DE  +++De ++++l
  gi|488599919|ref|YP_007906390.1| 794 ISFAQMSGGEQ-MCAAIAIRLALMTVLSN-------MKVAFFDEPTQNMDEVRRKNL 842
                                       57899******.****************9.......79*************998865 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   8.8       1.2   8.4e+02      62     101 ..     195     234 ..     186     237 .. 0.89
   2 ?    2.9   8.4      0.15   1.1e+02      64     103 ..     235     274 ..     231     277 .. 0.89
   3 ?    1.0   4.0      0.58   4.1e+02      12      45 ..     271     304 ..     265     308 .. 0.83
   4 !    7.6   3.7     0.005       3.6       5      42 ..     288     325 ..     281     327 .. 0.92
   5 ?    2.5  21.6       0.2   1.4e+02       2      97 ..     309     412 ..     308     416 .. 0.79
   6 ?   -0.6   0.3       1.8   1.3e+03      65      99 ..     414     448 ..     409     449 .. 0.70
   7 !    8.6   1.8    0.0025       1.8      62     102 ..     447     487 ..     441     492 .. 0.78
   8 ?   -0.0   6.9       1.2   8.4e+02      62      93 ..     492     523 ..     486     528 .. 0.61
   9 ?    4.2   3.8     0.056        40       2      41 ..     520     559 ..     519     561 .. 0.89
  10 !   19.4   7.6   1.1e-06   0.00076       2     100 ..     571     670 ..     570     673 .. 0.93
  11 ?    4.5   0.3     0.047        33       5      40 ..     672     707 ..     670     711 .. 0.88
  12 ?    1.6   1.6      0.36   2.6e+02      69      99 ..     703     733 ..     698     738 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekeleelkeelqk 101
                                       e+k+ +e+++++l+++ ++l k+++ + kel+ lk+++ +
  gi|488599919|ref|YP_007906390.1| 195 ELKSSVEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDE 234
                                       789999*****************************99876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                       Prefoldin_2  64 keeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                                       ++e ++++++l+++i++ +++l++ +++l++lk+el k l
  gi|488599919|ref|YP_007906390.1| 235 LSEIKDKIDDLKQKISRKQDKLSSEKEDLSKLKQELSKIL 274
                                       678999*****************************99865 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT- CS
                       Prefoldin_2  12 qqlqqlaqqikqletqlkelelvleelelldedt 45 
                                       +++ +++++ k+le+  +e  + ++ le+ld ++
  gi|488599919|ref|YP_007906390.1| 271 SKILEIEKKTKELEASYREYLDLENRLEELDAEE 304
                                       5677899999999999999999999999999885 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.005
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                       Prefoldin_2   5 nkfqqlqqqlqqlaqqikqletqlkelelvleelelld 42 
                                        ++ +l+++l++l+++ ++l ++l+el +v+ e+e+l+
  gi|488599919|ref|YP_007906390.1| 288 REYLDLENRLEELDAEERDLSKKLDELSEVSVEIEKLK 325
                                       57899******************************996 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT....--EEEEETTE.EEEE-HHHHHHHHHHHHHH CS
                       Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelellded....tkvyklvGdv.lvkqdkeevkeeLeerket 73 
                                       +++ ++++   ++++l++qi + ++ lke+e+ ++e++ ++ed    +   k +  + l++++++++k++L +  ++
  gi|488599919|ref|YP_007906390.1| 309 KKLDELSEVSVEIEKLKTQISSTKKALKEIEEKEKEIDGIKEDarreEVLLKEISAIeLLSVERDQLKKRLRDITKD 385
                                       577888899999*******************************8887778889998878888888888888765555 PP

                                       HHH...HHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  74 lek...eiktlekqleklekeleelke 97 
                                       +e+   ++++l++++ek ++ +e+l++
  gi|488599919|ref|YP_007906390.1| 386 IEQksiKLEELKRREEKFREAMEKLEK 412
                                       554111567777777777777777765 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeel 99 
                                       ++ ee+ e+l k + +l++  +++ ++++ +k++l
  gi|488599919|ref|YP_007906390.1| 414 SNIEEKYEKLLKLSVRLSEDRKSIIENIKAVKTNL 448
                                       46677777777777777777777777777777765 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                       Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                       ++ + L+e+ +++ ++i+ le++l+ +e++lee+ ++ +++
  gi|488599919|ref|YP_007906390.1| 447 NLCPILDEKCDRIHQKIDDLERKLRVVEERLEEVDKKMNAA 487
                                       56677888888899999999999999999999888887765 PP

  == domain 8  score: -0.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekele 93 
                                       evk++Le  + +l++e+k+ e+ + +++++++
  gi|488599919|ref|YP_007906390.1| 492 EVKNRLESAISKLKAELKQKEEIENEIKEKIK 523
                                       45566666666666666666666666655554 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                       Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelell 41 
                                       e+i+  ++++++ ++++++++q+e+ ++e e v+  le l
  gi|488599919|ref|YP_007906390.1| 520 EKIKTRNEIESRTKEIDSKLEQKENIIQEFERVKGSLERL 559
                                       6788889999999********************9999987 PP

  == domain 10  score: 19.4 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEE.EETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyk.lvGdvlvkqdkeevkeeLeerketleke 77 
                                       +li+++++l+++l+ l +  k+le  +++  +v+ee+e++++  k+ +      l + ++ + k+eL++r+ +le  
  gi|488599919|ref|YP_007906390.1| 571 DLIEELKNLENRLEHLNSIAKDLEPSKSKYTSVKEEIEKIAKRLKILRpAYDSYLSLAPQIKKKDELKNRISELEGG 647
                                       6899***************************************888883566777888******************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelq 100
                                       i++l++++ ++e +l+ l+e+ +
  gi|488599919|ref|YP_007906390.1| 648 INRLKQEIVSMEVQLKSLEEKFN 670
                                       *******************9976 PP

  == domain 11  score: 4.5 bits;  conditional E-value: 0.047
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   5 nkfqqlqqqlqqlaqqikqletqlkelelvleelel 40 
                                       ++f+ l q++ ++++++ ++e ++k + + +e le+
  gi|488599919|ref|YP_007906390.1| 672 EEFESLSQKMLEIMSEKGKVEGEIKGVSESIEKLES 707
                                       689999****************99999999999886 PP

  == domain 12  score: 1.6 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  69 erketlekeiktlekqleklekeleelkeel 99 
                                       e++e+  +e+k+ ek++ +l+ e++ lk +l
  gi|488599919|ref|YP_007906390.1| 703 EKLESSLAELKEREKEYLRLKDEMDRLKRKL 733
                                       3445555555555666666666666666655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.7e-06    0.0012      18      91 ..      17      88 ..       2     123 .. 0.82
   2 ?    0.2   0.4      0.66   4.7e+02     157     195 ..     199     237 ..     196     248 .. 0.83
   3 ?   -1.6   0.3       2.4   1.7e+03     157     199 ..     248     289 ..     245     296 .. 0.73
   4 ?   -1.3   1.1       1.9   1.4e+03     162     197 ..     297     335 ..     262     362 .. 0.55
   5 ?   -0.6   0.2       1.1   8.2e+02     147     199 ..     357     409 ..     347     419 .. 0.70
   6 ?   -1.4   0.1         2   1.4e+03     165     201 ..     452     488 ..     441     495 .. 0.84
   7 ?   -2.9   1.2       5.9   4.2e+03     165     195 ..     477     506 ..     457     527 .. 0.46
   8 ?   -2.2   1.3       3.6   2.6e+03     168     195 ..     503     530 ..     472     556 .. 0.47
   9 ?   -1.2   0.2       1.8   1.3e+03     136     179 ..     683     726 ..     635     742 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkdnfl.hdakkLrigavleeadgeelefaRrkgrk 91
                                      +++fs   ++l  i+G N AGK+t+l+Ai   lf   + +  +fl   akk  ++ ++++ dg+  e++R+ +++
  gi|488599919|ref|YP_007906390.1| 17 RIEFS---EGLNAIIGENGAGKTTILEAIGFALFDSIAYKISDFLrRGAKKGLVRVRFTSLDGRDYEVVRKITES 88
                                      45555...89********************999976666666666155777788999999999999999986655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.66
                            AAA_27 157 slrevleaLeaeadelfkprkskkrainealeeleeakk 195
                                       s+++ l++L+a++d+l k++k   +++n+ +++++e+++
  gi|488599919|ref|YP_007906390.1| 199 SVEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDELSE 237
                                       67888999**********999999999999998888765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.4
                            AAA_27 157 slrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       ++++ +++L++e+++l k +++ + +i e +++ +e+++++re
  gi|488599919|ref|YP_007906390.1| 248 KISRKQDKLSSEKEDLSKLKQELS-KILEIEKKTKELEASYRE 289
                                       566777788888888877777777.777777777777777665 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.9
                            AAA_27 162 leaLeaeadelfkprkskk...rainealeeleeakkel 197
                                       le+L+ae ++l k+  + +    +i + +++++++kk+l
  gi|488599919|ref|YP_007906390.1| 297 LEELDAEERDLSKKLDELSevsVEIEKLKTQISSTKKAL 335
                                       444444444444443333211122333333333333333 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.1
                            AAA_27 147 lLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       +L++  ++++ l+  +++L+++ +++ k+ ++k+ ++ e +++ e+ ++++++
  gi|488599919|ref|YP_007906390.1| 357 VLLKEISAIELLSVERDQLKKRLRDITKDIEQKSIKLEELKRREEKFREAMEK 409
                                       66666777777778888888888888887777776666666666665555544 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 2
                            AAA_27 165 Leaeadelfkprkskkrainealeeleeakkelreaq 201
                                       L+++ d+++++    +r+++  +e+lee++k++++a+
  gi|488599919|ref|YP_007906390.1| 452 LDEKCDRIHQKIDDLERKLRVVEERLEEVDKKMNAAK 488
                                       7889999999999999999999999999999998875 PP

  == domain 7  score: -2.9 bits;  conditional E-value: 5.9
                            AAA_27 165 Leaeadelfkprkskkrainealeeleeakk 195
                                       Le+  +++ + +k+ +   n+ +++++++k+
  gi|488599919|ref|YP_007906390.1| 477 LEEVDKKMNAAKKAVE-VKNRLESAISKLKA 506
                                       2222222222222222.22222222222222 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 3.6
                            AAA_27 168 eadelfkprkskkrainealeeleeakk 195
                                       + ++  k++++ +++i+e+ ++ +e ++
  gi|488599919|ref|YP_007906390.1| 503 KLKAELKQKEEIENEIKEKIKTRNEIES 530
                                       1111112222222233333333333333 PP

  == domain 9  score: -1.2 bits;  conditional E-value: 1.8
                            AAA_27 136 alleaegelgqlLfeasaGlaslrevleaLeaeadelfkprksk 179
                                       ++++++g++   +   s ++++l++ l++L+++ +e+ + + + 
  gi|488599919|ref|YP_007906390.1| 683 EIMSEKGKVEGEIKGVSESIEKLESSLAELKEREKEYLRLKDEM 726
                                       45555555555555555566666666666666655555444444 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 !   18.9   7.8   2.1e-06    0.0015       4      83 ..     642     727 ..     632     729 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-06
                       Uso1_p115_C   4 seleseaaslkdeneklkaelqslskalesleqk...eakkaaesqakeleaenkklekeleklraelkeekekeke 77 
                                       sele   + lk+e  +++ +l+sl+++ +s+e +   ++  ++ s++ ++e e+k +++ +ekl++ l+e ke+eke
  gi|488599919|ref|YP_007906390.1| 642 SELEGGINRLKQEIVSMEVQLKSLEEKFNSEEFEslsQKMLEIMSEKGKVEGEIKGVSESIEKLESSLAELKEREKE 718
                                       67888888999999999999999999999999888999999**********************************98 PP

                       Uso1_p115_C  78 k...qkEld 83 
                                           ++E+d
  gi|488599919|ref|YP_007906390.1| 719 YlrlKDEMD 727
                                       888888887 PP

>> PP-binding_2  Acyl-carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.013       9.6      31      64 ..     389     422 ..     373     441 .. 0.86
   2 !    7.7   0.0    0.0057       4.1      33      82 ..     707     763 ..     681     771 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.013
                      PP-binding_2  31 psskleelrtredrlwdgldtvefvedveelfdv 64 
                                        s kleel+ re+++ ++++ +e + ++ee ++ 
  gi|488599919|ref|YP_007906390.1| 389 KSIKLEELKRREEKFREAMEKLEKLSNIEEKYEK 422
                                       478**************************98875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0057
                      PP-binding_2  33 skleelrtred...rlwdgld....tvefvedveelfdvivsdevadnfetlqeiad 82 
                                       s l el+ re+   rl d +d     +ef+  + e+f++ v++ +     ++ eia+
  gi|488599919|ref|YP_007906390.1| 707 SSLAELKEREKeylRLKDEMDrlkrKLEFIRALREIFNLAVPEITKAYVSAVSEIAN 763
                                       5677888777545578888883333469******************999*****997 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   1.4e-05      0.01      14      31 ..      25      42 ..      18      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-05
                                      EEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkll 31
                                       ai+GenGaGK+t+l+++
  gi|488599919|ref|YP_007906390.1| 25 NAIIGENGAGKTTILEAI 42
                                      58*************998 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   4.0   2.5e-05     0.018      15      71 ..     281     337 ..     274     366 .. 0.83
   2 ?    3.7   3.7      0.14     1e+02      26      72 ..     374     419 ..     367     442 .. 0.67
   3 ?    0.2  10.6       1.8   1.3e+03      21      79 ..     460     522 ..     452     551 .. 0.61
   4 ?    1.3   4.5      0.78   5.6e+02      30      85 ..     503     559 ..     496     567 .. 0.63
   5 ?    6.3   2.1     0.022        16      27      97 ..     572     642 ..     568     655 .. 0.78
   6 ?    2.8   1.5      0.27   1.9e+02      23      88 ..     599     668 ..     596     673 .. 0.59
   7 ?   12.1   3.6   0.00036      0.25      29      95 ..     672     739 ..     663     744 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                      Occludin_ELL  15 aeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk 71 
                                       +e ++ Y+eY +l+++lee+ ++ ++L+++l+el+e s e++k++ +i ++ k lk+
  gi|488599919|ref|YP_007906390.1| 281 KELEASYREYLDLENRLEELDAEERDLSKKLDELSEVSVEIEKLKTQISSTKKALKE 337
                                       678899*****************************************9876555544 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.14
                      Occludin_ELL  26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkd 72 
                                       +l+++l++++k++++ + +l+elk++++++++++e+ l+++++++++
  gi|488599919|ref|YP_007906390.1| 374 QLKKRLRDITKDIEQKSIKLEELKRREEKFREAMEK-LEKLSNIEEK 419
                                       566777777777777777777777777777777777.6666666443 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.8
                      Occludin_ELL  21 YkeYkelhaeleevskkfseLerelkelkegsk...eykkieeeilqeykklkk.dpeyqekk 79 
                                       +++  +l+++l+ v+++++e++++++++k+  +   + +++++++  e+k++++ ++e +ek 
  gi|488599919|ref|YP_007906390.1| 460 HQKIDDLERKLRVVEERLEEVDKKMNAAKKAVEvknRLESAISKLKAELKQKEEiENEIKEKI 522
                                       566677888888888888888888888887777555555555666666666665444444432 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.78
                      Occludin_ELL  30 eleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyL 85 
                                       +l++  k+ +e+e+e+ke  ++++e++++++ei ++++++++  +e+ + k  +e L
  gi|488599919|ref|YP_007906390.1| 503 KLKAELKQKEEIENEIKEKIKTRNEIESRTKEIDSKLEQKENiIQEFERVKGSLERL 559
                                       344444455566677777777777777777777777777777666666666555555 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.022
                      Occludin_ELL  27 lhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKklik 97 
                                       l +el+++++++++L++  k+l++++++y++++eei +  k+lk   p+y +      ++k+k + +K++i+
  gi|488599919|ref|YP_007906390.1| 572 LIEELKNLENRLEHLNSIAKDLEPSKSKYTSVKEEIEKIAKRLKIlRPAYDSYLSLAPQIKKK-DELKNRIS 642
                                       678999999999999999999999999999999998777777776777777666666666655.45555555 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.27
                      Occludin_ELL  23 eYkelhaeleevskkfseLe...relkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkek 88 
                                       +Y ++++e+e+++k+++ L+   +   +l+++ k+ ++++++i +    +++ ++e  +++ +++ L+ek
  gi|488599919|ref|YP_007906390.1| 599 KYTSVKEEIEKIAKRLKILRpayDSYLSLAPQIKKKDELKNRISELEGGINRlKQEIVSMEVQLKSLEEK 668
                                       6888888888888888888855533444455555555555554333333444556666666666666665 PP

  == domain 7  score: 12.1 bits;  conditional E-value: 0.00036
                      Occludin_ELL  29 aeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKkl 95 
                                       +e+e++s+k+ e+ +e  + + + k +++ +e++ +++++lk+ ++ey++ k +++ Lk+kL+ i++l
  gi|488599919|ref|YP_007906390.1| 672 EEFESLSQKMLEIMSEKGKVEGEIKGVSESIEKLESSLAELKErEKEYLRLKDEMDRLKRKLEFIRAL 739
                                       5667777777777777777777777888888888999999988899*****************99875 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 ?    0.4   7.1      0.87   6.2e+02      53     109 ..     262     336 ..     195     346 .. 0.62
   2 ?    4.6   1.0     0.043        31      36      93 ..     368     444 ..     356     454 .. 0.63
   3 ?    7.9   1.3    0.0042         3      33      87 ..     463     518 ..     433     525 .. 0.56
   4 ?    5.1   0.6      0.03        22      24      90 ..     527     596 ..     523     618 .. 0.45
   5 ?    6.9   0.6    0.0084         6      24     126 ..     578     680 ..     569     687 .. 0.57
   6 ?    6.6   0.1     0.011       7.6      36     104 ..     637     712 ..     626     717 .. 0.49
   7 ?    1.5   0.0      0.39   2.8e+02      40      77 ..     688     734 ..     672     763 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.87
                      Baculo_PEP_C  53 dlksllaeldt...................rldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLn 109
                                       dl++l +el++                   +l++ l++L++    l+++l  eL  +  ++  L +++  ++++L+
  gi|488599919|ref|YP_007906390.1| 262 DLSKLKQELSKileiekktkeleasyreylDLENRLEELDAEERDLSKKL-DELSEVSVEIEKLKTQISSTKKALK 336
                                       22222222222333333445444466667777777777777777777665.4677777777777777777777766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.043
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldt...................rldtlltnLtdalnalqdtlrneLtnlnsi 93 
                                       l+   d+++++L ++++d+++ + +l++                   ++++  ++L +   +l+++ ++ ++n++++
  gi|488599919|ref|YP_007906390.1| 368 LSVERDQLKKRLRDITKDIEQKSIKLEElkrreekfreamekleklsNIEEKYEKLLKLSVRLSEDRKSIIENIKAV 444
                                       56677889999999999999988888777777774554444444455555555555555555555555555555554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0042
                      Baculo_PEP_C  33 laqlatlldaietqLnalsedlkslla..eldtrldtlltnLtdalnalqdtlrneL 87 
                                       + +l++ l  +e++L++++++++++ +  e+++rl++++++L++ l++ +++++ne+
  gi|488599919|ref|YP_007906390.1| 463 IDDLERKLRVVEERLEEVDKKMNAAKKavEVKNRLESAISKLKAELKQ-KEEIENEI 518
                                       245666666666666666666665543113444666666666666655.24555554 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.03
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalqdtlrneLtnl 90 
                                        i + + +i ++l++  + i++ ++ ++ +l++l   l++      +l + l+nL++ l +l+ ++ ++L+  
  gi|488599919|ref|YP_007906390.1| 527 EIESRTKEIDSKLEQKENIIQE-FERVKGSLERLKI-LESeigkksDLIEELKNLENRLEHLN-SIAKDLEPS 596
                                       4555555666666655554443.6666666655322.33322322233333333333333333.444444444 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0084
                      Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsiltnLl 98 
                                        + + +  + + +a++l+  +++ ++++e++++  + l + l  + +   +   +++  d+l+n++  l+  ++ L 
  gi|488599919|ref|YP_007906390.1| 578 NLENRLEHL-NSIAKDLEPSKSKYTSVKEEIEKIAKRL-KILRPAYDSYLSLAPQIKkkDELKNRISELEGGINRLK 652
                                       333333333.4444444444444444444444422222.22333333333333344488999999999999999999 PP

                      Baculo_PEP_C  99 ssvtNinstLnnllqalnnldlgalsqe 126
                                        ++  ++  L++l +  n+ + ++lsq+
  gi|488599919|ref|YP_007906390.1| 653 QEIVSMEVQLKSLEEKFNSEEFESLSQK 680
                                       9999999999999888777777776665 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.011
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldt........rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssv 101
                                       l++ + ++e+ +n l++++ s+  +l++        ++++l++++ +          +++ e++++   +  L ss+
  gi|488599919|ref|YP_007906390.1| 637 LKNRISELEGGINRLKQEIVSMEVQLKSleekfnseEFESLSQKMLEI----MsekGKVEGEIKGVSESIEKLESSL 709
                                       333333333333333333333222222233321112344444443333....3334678888888888888888887 PP

                      Baculo_PEP_C 102 tNi 104
                                       + +
  gi|488599919|ref|YP_007906390.1| 710 AEL 712
                                       765 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.39
                      Baculo_PEP_C  40 ldaietqLnalsedlksllaeldt.........rldtlltnLtdaln 77 
                                       + ++e++++ +se++++l ++l++         rl++ +++L+++l 
  gi|488599919|ref|YP_007906390.1| 688 KGKVEGEIKGVSESIEKLESSLAElkerekeylRLKDEMDRLKRKLE 734
                                       45566666666666666655555555466667777777777776655 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7  27.2       8.4     6e+03     130     229 ..     217     355 ..     151     426 .. 0.73
   2 ?    5.4  14.7     0.014        10     119     251 ..     433     563 ..     388     574 .. 0.71
   3 ?   12.7   0.4   8.5e-05     0.061     130     226 ..     628     733 ..     559     744 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.4
                           DUF4407 130 a....................ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaak 186
                                       +                     ++++++l+++i++ q ++++ +++l++l++e+ k l+ +k+t+    +    ++ 
  gi|488599919|ref|YP_007906390.1| 217 KkkiilkelnalkkkhdelseIKDKIDDLKQKISRKQDKLSSEKEDLSKLKQELSKILEIEKKTK--ELEASYREYL 291
                                       13333333344444334445588999999999999999999999999999999999999866444..5666667777 PP

                           DUF4407 187 ekkaqldaaqaelaelkakld.....................atarlaalraelaeleaerake 229
                                         ++ l++++ae  +l++kld                     a ++++++++e++++++++++e
  gi|488599919|ref|YP_007906390.1| 292 DLENRLEELDAEERDLSKKLDelsevsveieklktqisstkkALKEIEEKEKEIDGIKEDARRE 355
                                       7788888888888888888766666444444433333344444444444444444444433333 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                           DUF4407 119 eakelkeqlaaa.......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakek 188
                                       + k++ e+++a        l+++ +++ ++i++l+++++  e+rl++  +++++  +       + +++ + a  + 
  gi|488599919|ref|YP_007906390.1| 433 DRKSIIENIKAVktnlcpiLDEKCDRIHQKIDDLERKLRVVEERLEEVDKKMNAAKK-----AVEVKNRLESAISKL 504
                                       333333333333555777788888888888888888888888877776666664433.....334466777888888 PP

                           DUF4407 189 kaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarleald 251
                                       ka+l+++++  +e+k+k++ + +++++ +e+++  ++++++++++++     +G l+rl++l+
  gi|488599919|ref|YP_007906390.1| 505 KAELKQKEEIENEIKEKIKTRNEIESRTKEIDSKLEQKENIIQEFER----VKGSLERLKILE 563
                                       99999999999999999999999999999999999999999999997....678899999976 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 8.5e-05
                           DUF4407 130 a........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.........gtgttgvaGkgpaakekk 189
                                       a        l+++++ele  i++l++ei + e +l+ l++++++e +                  +   + + k   
  gi|488599919|ref|YP_007906390.1| 628 ApqikkkdeLKNRISELEGGINRLKQEIVSMEVQLKSLEEKFNSEEFESLsqkmleimsE-----KGKVEGEIKGVS 699
                                       0444444559999**********************************8775444433211.....112223333344 PP

                           DUF4407 190 aqldaaqaelaelkakldatarlaalraelaeleaer 226
                                       + +++++  laelk++   +++  +l++e+++l++++
  gi|488599919|ref|YP_007906390.1| 700 ESIEKLESSLAELKER---EKEYLRLKDEMDRLKRKL 733
                                       4444444444444444...444444444444444443 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  11.4     0.041        29      40     122 ..     197     278 ..     191     287 .. 0.71
   2 ?    4.5   4.2     0.047        34      50     100 ..     293     346 ..     290     354 .. 0.64
   3 ?    6.4   7.0     0.012       8.9      23     123 ..     359     462 ..     355     476 .. 0.59
   4 ?    8.5  11.6    0.0027         2      41     115 ..     475     551 ..     464     560 .. 0.70
   5 ?    5.9   0.3     0.017        12      59     104 ..     567     615 ..     550     631 .. 0.63
   6 ?    9.2   2.7    0.0016       1.2      43     123 ..     586     668 ..     577     676 .. 0.83
   7 ?    4.1   0.4     0.062        45      83     122 ..     675     714 ..     670     717 .. 0.79
   8 ?    1.8   0.1      0.32   2.3e+02      46      89 ..     698     747 ..     695     761 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.041
                           DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       ++ ve+  k+l+  ++sl + k+ + ++++ + kk de +ei+ +i++  ++++++ ++++++ e ++++ ++l sk
  gi|488599919|ref|YP_007906390.1| 197 KSSVEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDELSEIKDKIDDLKQKISRKQDKLSSEKEDLSKLKQEL-SK 272
                                       5555666677888889**********************999998887665566555555555555555555555.34 PP

                           DUF1664 117 leriee 122
                                       + +ie+
  gi|488599919|ref|YP_007906390.1| 273 ILEIEK 278
                                       444444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.047
                           DUF1664  50 leqvseslaatkrhLssridrvdk...kldeqkeiskeikeevtevredlseig 100
                                       le+  e+l a  r+Ls+++d++ +   ++++ k  ++++k+ ++e++e+ +ei+
  gi|488599919|ref|YP_007906390.1| 293 LENRLEELDAEERDLSKKLDELSEvsvEIEKLKTQISSTKKALKEIEEKEKEID 346
                                       666677777777888877775443222667777777777777777777666664 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.012
                           DUF1664  23 wkGwklsdlmfvTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevt...evredl 96 
                                        k ++  +l+ v +  l++ + +++k++eq s +l++ kr+ +++  +  +kl++ ++i ++ ++ ++   +++ed 
  gi|488599919|ref|YP_007906390.1| 359 LKEISAIELLSVERDQLKKRLRDITKDIEQKSIKLEELKRR-EEKFREAMEKLEKLSNIEEKYEKLLKlsvRLSEDR 434
                                       57788889999*********************888887775.33333444444444444444333332111345555 PP

                           DUF1664  97 seigedvesvkeave.glesklerieek 123
                                       ++i e++++vk+  +  l++k +ri +k
  gi|488599919|ref|YP_007906390.1| 435 KSIIENIKAVKTNLCpILDEKCDRIHQK 462
                                       5555555555543331455555555443 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0027
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevt...evredlseigedvesvkeavegle 114
                                       + +e+v k+++  ++++ ++k++L+s i ++ ++l++ +ei +eike+++   e+++ ++ei++++e+ +++++++e
  gi|488599919|ref|YP_007906390.1| 475 ERLEEVDKKMNAAKKAV-EVKNRLESAISKLKAELKQKEEIENEIKEKIKtrnEIESRTKEIDSKLEQKENIIQEFE 550
                                       34455555555555444.45778999999999999999999999999995333688889999999988888888877 PP

                           DUF1664 115 s 115
                                        
  gi|488599919|ref|YP_007906390.1| 551 R 551
                                       5 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.017
                           DUF1664  59 atkrhLssridrvdkkldeqkeiskei...keevtevredlseigedve 104
                                         k +L +++++++++l++ + i+k++   k++ t+v+e++++i + ++
  gi|488599919|ref|YP_007906390.1| 567 GKKSDLIEELKNLENRLEHLNSIAKDLepsKSKYTSVKEEIEKIAKRLK 615
                                       4577777777777777777766666542223455555555555555444 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.0016
                           DUF1664  43 vesvskqleqvseslaatkrh...Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       ++s++k+le  +++ +++k++   +++r++ +    d+   ++ +ik++ +e+++ +se++  ++ +k+ + ++e +
  gi|488599919|ref|YP_007906390.1| 586 LNSIAKDLEPSKSKYTSVKEEiekIAKRLKILRPAYDSYLSLAPQIKKK-DELKNRISELEGGINRLKQEIVSMEVQ 661
                                       6789999998887777777651116789999999999999999999988.899999999999999999999999999 PP

                           DUF1664 117 lerieek 123
                                       l+++eek
  gi|488599919|ref|YP_007906390.1| 662 LKSLEEK 668
                                       9999986 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.062
                           DUF1664  83 keikeevtevredlseigedvesvkeavegleskleriee 122
                                       +++++++ e+ ++  +++ +++ v+e +e+les+l++++e
  gi|488599919|ref|YP_007906390.1| 675 ESLSQKMLEIMSEKGKVEGEIKGVSESIEKLESSLAELKE 714
                                       5567778888888888999999999999999999988875 PP

  == domain 8  score: 1.8 bits;  conditional E-value: 0.32
                           DUF1664  46 vskqleqvseslaatkr......hLssridrvdkkldeqkeiskeikeev 89 
                                       vs+++e++ +sla+ k+      +L++++dr+ +kl+   ++ +  +  v
  gi|488599919|ref|YP_007906390.1| 698 VSESIEKLESSLAELKErekeylRLKDEMDRLKRKLEFIRALREIFNLAV 747
                                       66666666666666655222222366677777777766666555555544 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  28.6   0.00043      0.31     139     255 ..     195     316 ..     180     318 .. 0.85
   2 ?    1.3  29.1      0.17   1.2e+02     144     262 ..     293     419 ..     292     451 .. 0.75
   3 ?    3.5  25.5     0.038        27     150     271 ..     429     552 ..     415     567 .. 0.49
   4 ?    8.0  19.4    0.0016       1.1     142     281 ..     570     715 ..     560     735 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00043
                              Spc7 139 gLkegleenlegleedkelLekqeeeldellpeleeeka...eleeeleklqe...aaeelesidkeeLeelreela 209
                                       +Lk+++e+ l++l++ k+ L k+++ + + l++l+++++   e+++++++l++   ++++  s++ke+L +l++el+
  gi|488599919|ref|YP_007906390.1| 195 ELKSSVEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDelsEIKDKIDDLKQkisRKQDKLSSEKEDLSKLKQELS 271
                                       799*********************************99944455678888888655455555589999999999999 PP

                              Spc7 210 elkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                                       ++  eie+k kel+   ++  +le+++eel+++ ++l +++ e  +
  gi|488599919|ref|YP_007906390.1| 272 KI-LEIEKKTKELEASYREYLDLENRLEELDAEERDLSKKLDELSE 316
                                       88.6899999999999999999999999999999999999888765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqe...aaeeles.....idkeeLeelreelaelk 212
                                       le++le+l+++++ L+k+ +el+e+  e+e+ k++++++ + l+e   +++e++        +e L +  ++++ l+
  gi|488599919|ref|YP_007906390.1| 293 LENRLEELDAEERDLSKKLDELSEVSVEIEKLKTQISSTKKALKEieeKEKEIDGikedaRREEVLLKEISAIELLS 369
                                       8999*********************9999999998888777777733344444443322211233444445667777 PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckg 262
                                       +e +++kk+l + ++++e+++ k+eelk + ++++e++++ e++ + +++
  gi|488599919|ref|YP_007906390.1| 370 VERDQLKKRLRDITKDIEQKSIKLEELKRREEKFREAMEKLEKLSNIEEK 419
                                       88889999999999999999999999999999998888888887766554 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.038
                              Spc7 150 gleedkelLekqeeel.dellpeleeekaeleeeleklqe....aaeelesidkeeLeelreel......aelkaei 215
                                        l ed++ + ++ + + ++l p l+e+ +++++++++l++     +e le++dk +++++++++      +++ +++
  gi|488599919|ref|YP_007906390.1| 429 RLSEDRKSIIENIKAVkTNLCPILDEKCDRIHQKIDDLERklrvVEERLEEVDK-KMNAAKKAVevknrlESAISKL 504
                                       566777766666666646777888888888888888888855543334444443.3444443330000003333333 PP

                              Spc7 216 eekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrl 271
                                       ++  k+ +e +++++e+ ++ +e++++ +e+ ++++++e++++e         +r+
  gi|488599919|ref|YP_007906390.1| 505 KAELKQKEEIENEIKEKIKTRNEIESRTKEIDSKLEQKENIIQEF--------ERV 552
                                       333333333333333333333344444444444444444444443........333 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0016
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqe...aaeeles..idkeeLeelreelaelka 213
                                       + l e+l++le+  e+L++  + l+  + ++++ k+e+e+ +++l+    a+++  s   + ++  el+++++el+ 
  gi|488599919|ref|YP_007906390.1| 570 SDLIEELKNLENRLEHLNSIAKDLEPSKSKYTSVKEEIEKIAKRLKIlrpAYDSYLSlaPQIKKKDELKNRISELEG 646
                                       44555555555555555555555555555554444444444444444222333333333223445678999999999 PP

                              Spc7 214 eieekkkelaelqeqleeleeki..eelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleel 281
                                        i+++k+e+ +++ ql++leek+  ee ++  +++ e ++e+ +v  e kg+ses +++l++++ +l+e 
  gi|488599919|ref|YP_007906390.1| 647 GINRLKQEIVSMEVQLKSLEEKFnsEEFESLSQKMLEIMSEKGKVEGEIKGVSES-IEKLESSLAELKER 715
                                       9999999999999999999998632577888888888888888888888888875.88888888888764 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   9.5      0.34   2.4e+02       6      64 ..     221     276 ..     176     283 .. 0.72
   2 ?    6.6   2.6     0.015        11      22      62 ..     306     346 ..     288     367 .. 0.65
   3 ?    1.5   1.0      0.59   4.2e+02       8      58 ..     381     410 ..     355     444 .. 0.50
   4 ?    1.0   0.1      0.87   6.2e+02      13      36 ..     648     671 ..     626     692 .. 0.59
   5 ?    7.8   0.0    0.0062       4.5      12      57 ..     694     746 ..     689     763 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.34
                           NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                        l  +++ k+  d ++ +++++dd++++   ++  ++kL +  + L +l++++++I +i
  gi|488599919|ref|YP_007906390.1| 221 ILKELNALKKKHDELSEIKDKIDDLKQK---ISRKQDKLSSEKEDLSKLKQELSKILEI 276
                                       2333333444444444444555555544...4445678888888888888877777665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                           NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                        l++++d+++e + ++++l++++ +  ++L+e+e+k ++I+
  gi|488599919|ref|YP_007906390.1| 306 DLSKKLDELSEVSVEIEKLKTQISSTKKALKEIEEKEKEID 346
                                       45556666666666666666666666666666666555554 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.59
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                        I +di++ + k++ l+ + ++ +e +++                     +
  gi|488599919|ref|YP_007906390.1| 381 DITKDIEQKSIKLEELKRREEKFREAMEK---------------------L 410
                                       23333333333333333222222222222.....................2 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.87
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpd 36 
                                       i+ +++ + +++ q+++++e+++ 
  gi|488599919|ref|YP_007906390.1| 648 INRLKQEIVSMEVQLKSLEEKFNS 671
                                       455555555555555555554443 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0062
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet.......k 57 
                                       +ik v++ ++ l++++++++e  ++   l++++d++  +L+ + +       +
  gi|488599919|ref|YP_007906390.1| 694 EIKGVSESIEKLESSLAELKEREKEYLRLKDEMDRLKRKLEFIRAlreifnlA 746
                                       7999*********************************9998776544444442 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  10.4     0.001      0.73      24     103 ..     196     275 ..     188     277 .. 0.92
   2 ?    5.2   7.9     0.015        11      29      96 ..     280     350 ..     274     366 .. 0.60
   3 ?    2.5   5.6       0.1        75      60     104 ..     365     409 ..     339     412 .. 0.58
   4 ?    5.8  14.5      0.01       7.2      34     156 ..     385     507 ..     373     515 .. 0.81
   5 ?    5.3   7.1     0.015        11      19     101 ..     512     596 ..     499     607 .. 0.81
   6 ?    5.0   6.7     0.018        13      37     138 ..     632     729 ..     628     745 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                           DUF3450  24 eaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvp 100
                                        +++  +  ++  +k+d+l ++k+ +l+e++alk++ ++l+  +++ ++l ++  ++ ++l  ++e+++++++el+ 
  gi|488599919|ref|YP_007906390.1| 196 LKSSVEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDELSEIKDKIDDLKQKISRKQDKLSSEKEDLSKLKQELSK 272
                                       5566778889999**************************************************************99 PP

                           DUF3450 101 lle 103
                                       +le
  gi|488599919|ref|YP_007906390.1| 273 ILE 275
                                       885 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                           DUF3450  29 vaaaaqsqkkidklddekqellaeyralkeelesl...evyneqlerlvasqeqeiasleeqieeieeier 96 
                                       +++ ++s +++ +l++  +el ae r+l+++l++l   +v+ e+l+ +++s ++ ++++ee+ +ei+ i++
  gi|488599919|ref|YP_007906390.1| 280 TKELEASYREYLDLENRLEELDAEERDLSKKLDELsevSVEIEKLKTQISSTKKALKEIEEKEKEIDGIKE 350
                                       44444455555555555555555555555444433111567777777777777777777777777777665 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.1
                           DUF3450  60 leslevyneqlerlvasqeqeiasleeqieeieeierelvpllek 104
                                       +e l+v+++ql++ +++  ++i++   ++ee+++ e++    +ek
  gi|488599919|ref|YP_007906390.1| 365 IELLSVERDQLKKRLRDITKDIEQKSIKLEELKRREEKFREAMEK 409
                                       445555555555555555555555555555555555555555554 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.01
                           DUF3450  34 qsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLe 110
                                       ++++k  kl++ k   ++++r++ e+le+l+  +e++e+l++   +  ++ +  ie+i++++++l p+l++  dr++
  gi|488599919|ref|YP_007906390.1| 385 DIEQKSIKLEELK-RREEKFREAMEKLEKLSNIEEKYEKLLKLSVRLSEDRKSIIENIKAVKTNLCPILDEKCDRIH 460
                                       5555555555444.46889********************************************************** PP

                           DUF3450 111 qfveldlPflleeRqarlakLkelmdrad..vslaekyrrvleayqiE 156
                                       q +  dl  +l   ++rl++ ++ m+ a+  v+++ +++  +  ++ E
  gi|488599919|ref|YP_007906390.1| 461 QKI-DDLERKLRVVEERLEEVDKKMNAAKkaVEVKNRLESAISKLKAE 507
                                       **9.59*******************98862255566666666655555 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.015
                           DUF3450  19 dqalkeaekavaaaaqsqkkidkld...dekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       +++++e ++ ++++ +++++ +++d   ++k+++ +e++++k  le+l++ +++  +   ++ +e+++le+++e ++
  gi|488599919|ref|YP_007906390.1| 512 EEIENEIKEKIKTRNEIESRTKEIDsklEQKENIIQEFERVKGSLERLKILESEIGKKS-DLIEELKNLENRLEHLN 587
                                       566677777777777766555555433389************************99976.57789************ PP

                           DUF3450  93 eierelvpl 101
                                        i+++l+p 
  gi|488599919|ref|YP_007906390.1| 588 SIAKDLEPS 596
                                       ******996 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.018
                           DUF3450  37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfv 113
                                       kk+d+l++  +el+  +++lk+e+ s+ev+ + le+  +s  +e++sl +++ ei   + +++  ++ + +++e++ 
  gi|488599919|ref|YP_007906390.1| 632 KKKDELKNRISELEGGINRLKQEIVSMEVQLKSLEEKFNS--EEFESLSQKMLEIMSEKGKVEGEIKGVSESIEKLE 706
                                       7899999999************************999887..68999999999999999999999999999999987 PP

                           DUF3450 114 eldlPflleeRqarlakLkelmdra 138
                                        +     l+eR++++ +Lk+ mdr 
  gi|488599919|ref|YP_007906390.1| 707 SSLAE--LKEREKEYLRLKDEMDRL 729
                                       77764..568999999999999985 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 ?    7.6  19.2     0.006       4.3      25     105 ..     191     271 ..     175     274 .. 0.91
   2 ?   11.4  14.9   0.00041       0.3      23      94 ..     275     346 ..     265     355 .. 0.91
   3 ?    1.4  10.4       0.5   3.6e+02      40     100 ..     367     423 ..     349     432 .. 0.57
   4 ?    8.6  11.7     0.003       2.2      12      98 ..     394     485 ..     392     487 .. 0.80
   5 ?    2.2  21.7      0.29   2.1e+02       3     100 ..     433     535 ..     433     544 .. 0.78
   6 ?   -2.2  21.4       6.6   4.7e+03      13      96 ..     486     569 ..     482     581 .. 0.82
   7 ?    1.9  15.2      0.36   2.6e+02      13     104 ..     517     614 ..     516     617 .. 0.82
   8 ?    5.6   1.9     0.025        18      58      98 ..     630     670 ..     626     672 .. 0.85
   9 ?    7.7   5.9    0.0056         4      25     107 ..     668     750 ..     663     751 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.006
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  25 kadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       k+dv+   ++++  ++l+++ ++l ++++ + ke   +kkk+++ +e+++++++lk+++++++++l+  +++l kl 
  gi|488599919|ref|YP_007906390.1| 191 KKDVELKSSVEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDELSEIKDKIDDLKQKISRKQDKLSSEKEDLSKLK 267
                                       567788889999*************************************************************9998 PP

                                       CTS- CS
                      Seryl_tRNA_N 102 laiP 105
                                       +++ 
  gi|488599919|ref|YP_007906390.1| 268 QELS 271
                                       7775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00041
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkele 94 
                                       e +++ +el + +++   l+++leel ae   lsk+  ++++   ++e+l+ ++++ k+ lk++e+++ke++
  gi|488599919|ref|YP_007906390.1| 275 EIEKKTKELEASYREYLDLENRLEELDAEERDLSKKLDELSEVSVEIEKLKTQISSTKKALKEIEEKEKEID 346
                                       667888999999**********************************************************98 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  40 elqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                        l ve ++l+++   ++k I++++ k e+ ++  ++ +e  e+l++l    +++e++ ekl
  gi|488599919|ref|YP_007906390.1| 367 LLSVERDQLKKRLRDITKDIEQKSIKLEELKRREEKFREAMEKLEKL----SNIEEKYEKL 423
                                       45677788888888888888888776544333333333333333333....3333333333 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.003
                                       HHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.....S-TCCCCCCCHHHHHHH CS
                      Seryl_tRNA_N  12 eavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.....edaeeliaevkelkeel 83 
                                       e++k++ +k +e+ +++++l  ++ek ++l +    l + r+++ ++I+  k +      e+ +++ +++++l  +l
  gi|488599919|ref|YP_007906390.1| 394 EELKRREEKFREAMEKLEKLSNIEEKYEKLLKLSVRLSEDRKSIIENIKAVKTNLcpildEKCDRIHQKIDDLERKL 470
                                       66677776666999**************************************9977777677777777777777777 PP

                                       HHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  84 kaleaelkeleaele 98 
                                         +e++l+e++++++
  gi|488599919|ref|YP_007906390.1| 471 RVVEERLEEVDKKMN 485
                                       777777777777665 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.29
                                       -HHHHHH-HHHHHHHHCCCT..CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCC.. CS
                      Seryl_tRNA_N   3 DiklirenpeavkeklkkRg..edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliae.. 75 
                                       D k i en++avk +l      + +   +++ +l++k r ++ +lee+ ++ N++ k+++ + + +  +++l+ae  
  gi|488599919|ref|YP_007906390.1| 433 DRKSIIENIKAVKTNLCPILdeKCDRIHQKIDDLERKLRVVEERLEEVDKKMNAAKKAVEVKNRLESAISKLKAElk 509
                                       78999999999999985433226677888999999999999999999999999999999999998866666655511 PP

                                       .CHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  76 .vkelkeelkaleaelkeleaelekl 100
                                         +e+ +e+k++ ++ +e+e++ +++
  gi|488599919|ref|YP_007906390.1| 510 qKEEIENEIKEKIKTRNEIESRTKEI 535
                                       15678899999999999988877765 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 6.6
                                       HHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  13 avkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleae 89 
                                       a k++++ +++ ++ + +l +  ++++e+++e+ e  + rNe+    +++  k e++e +i+e + +k  l++l+  
  gi|488599919|ref|YP_007906390.1| 486 AAKKAVEVKNRLESAISKLKAELKQKEEIENEIKEKIKTRNEIESRTKEIDSKLEQKENIIQEFERVKGSLERLKIL 562
                                       678889999999******************************98888887777788888888888888888888887 PP

                                       HHHHHHH CS
                      Seryl_tRNA_N  90 lkeleae 96 
                                       ++e+ ++
  gi|488599919|ref|YP_007906390.1| 563 ESEIGKK 569
                                       7777665 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.36
                                       HHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHHH CS
                      Seryl_tRNA_N  13 avkeklkkRgedkadvdelleldekrrelqveleelq...aerNelskeIgkakkkk...edaeeliaevkelkeel 83 
                                       ++kek+k+R+e ++  +e+ +  e+++++++e+e ++   ++ + l  eIgk+++     ++ e  ++  +++ ++l
  gi|488599919|ref|YP_007906390.1| 517 EIKEKIKTRNEIESRTKEIDSKLEQKENIIQEFERVKgslERLKILESEIGKKSDLIeelKNLENRLEHLNSIAKDL 593
                                       69********************************9984445678889999999987644566666666777777777 PP

                                       HHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  84 kaleaelkeleaeleklllai 104
                                       +  + + + +++e+ek++ ++
  gi|488599919|ref|YP_007906390.1| 594 EPSKSKYTSVKEEIEKIAKRL 614
                                       777889999999999998775 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.025
                                       HCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  58 eIgkakkkkedaeeliaevkelkeelkaleaelkeleaele 98 
                                       +I+k+ + k+ ++el   ++ lk+e+  +e +lk le++++
  gi|488599919|ref|YP_007906390.1| 630 QIKKKDELKNRISELEGGINRLKQEIVSMEVQLKSLEEKFN 670
                                       78888888899999999999999999999999999999986 PP

  == domain 9  score: 7.7 bits;  conditional E-value: 0.0056
                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  25 kadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                       k + +e+ +l +k+ e+++e  ++  e + +s++I+k+  + ++ +e  +e   lk+e+++l+ +l+ ++a  e + 
  gi|488599919|ref|YP_007906390.1| 668 KFNSEEFESLSQKMLEIMSEKGKVEGEIKGVSESIEKLESSLAELKEREKEYLRLKDEMDRLKRKLEFIRALREIFN 744
                                       45778999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       CTS--- CS
                      Seryl_tRNA_N 102 laiPNi 107
                                       la+P i
  gi|488599919|ref|YP_007906390.1| 745 LAVPEI 750
                                       999877 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    0.0014      0.97       4      25 ..      21      42 ..      17      93 .. 0.76
   2 ?   -2.7   0.2         9   6.5e+03      46      66 ..     224     244 ..     186     276 .. 0.48
   3 ?   -1.9   0.3       5.2   3.8e+03      57      60 ..     379     382 ..     286     438 .. 0.53
   4 ?   -2.6   0.7       8.7   6.2e+03      80     114 ..     533     561 ..     473     594 .. 0.58
   5 ?    2.8   0.1      0.18   1.3e+02      96     118 ..     722     745 ..     658     765 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                            AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                      ++g+ +++Ge G+GKTt l+ +
  gi|488599919|ref|YP_007906390.1| 21 SEGLNAIIGENGAGKTTILEAI 42
                                      678889************9975 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9
                            AAA_22  46 tlpsstsskdllrellralgl 66 
                                       +l+++++  d l+e+  ++++
  gi|488599919|ref|YP_007906390.1| 224 ELNALKKKHDELSEIKDKIDD 244
                                       333333333333333333333 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.2
                            AAA_22  57 lrel 60 
                                       lr++
  gi|488599919|ref|YP_007906390.1| 379 LRDI 382
                                       2222 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 8.7
                            AAA_22  80 ealeqalraravielliiDEaqhlrseealeeLrs 114
                                       + +   l+++      ii E++++  +  le L++
  gi|488599919|ref|YP_007906390.1| 533 KEIDSKLEQKEN----IIQEFERV--KGSLERLKI 561
                                       333333333333....55555555..333333333 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.18
                            AAA_22  96 iiDEaqhlr.seealeeLrsllnl 118
                                       + DE+++l  + e ++ Lr+++nl
  gi|488599919|ref|YP_007906390.1| 722 LKDEMDRLKrKLEFIRALREIFNL 745
                                       55******6559999999999996 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 ?    5.7  18.8     0.013       9.2     142     258 ..     193     316 ..     185     336 .. 0.71
   2 ?    0.6  14.6      0.48   3.4e+02     134     215 ..     364     446 ..     307     485 .. 0.39
   3 ?    6.7  16.5    0.0065       4.6     133     261 ..     485     619 ..     429     626 .. 0.53
   4 ?    4.4   9.4     0.032        23     143     256 ..     570     726 ..     566     750 .. 0.36

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                      Exonuc_VII_L 142 kaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelk 218
                                         el++++e+  ++l+ + ++l+++kk  l++l+ +lk++++ l++ ++++d+l+++++r  + +l++++e+l++lk
  gi|488599919|ref|YP_007906390.1| 193 DVELKSSVEQDLKKLKAKKDSLIKKKKIILKELN-ALKKKHDELSEIKDKIDDLKQKISR-KQDKLSSEKEDLSKLK 267
                                       5678888999999999999999999999999885.8888999999999999999999999.8889999999999999 PP

                      Exonuc_VII_L 219 erl.k........ekleekkerlkklkerlelleekkerleeleeklea 258
                                       ++l k        ++le+  +++ +l++rle+l++++++l++  ++l+ 
  gi|488599919|ref|YP_007906390.1| 268 QELsKileiekktKELEASYREYLDLENRLEELDAEERDLSKKLDELSE 316
                                       9996584444333223333333344555555555555554444444443 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.48
                      Exonuc_VII_L 134 aAelvvpdkaeleeqleelerrlekaikr..lleekkqrleklasrlkspeellerkrqrldeleerleralkkqlk 208
                                       a el++ ++++l+++l+++++ +e++  +   l++++++++++ ++l+ + + +e+k ++l +l+ rl++  k+ ++
  gi|488599919|ref|YP_007906390.1| 364 AIELLSVERDQLKKRLRDITKDIEQKSIKleELKRREEKFREAMEKLE-KLSNIEEKYEKLLKLSVRLSEDRKSIIE 439
                                       333333333333333333333333333210012222222222222221.1223333333333333333333333333 PP

                      Exonuc_VII_L 209 kkrerle 215
                                       + ++  +
  gi|488599919|ref|YP_007906390.1| 440 NIKAVKT 446
                                       2222222 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0065
                      Exonuc_VII_L 133 aaAelvvpdkaeleeqleelerrlek..aikrlleekkqrleklasrlkspeellerkrqrlde...leerlera.. 202
                                       +aA+++v++k++le+ +++l+++l++  +i++ ++ek +  ++++sr k+ +++le+k++ ++e   ++ +ler   
  gi|488599919|ref|YP_007906390.1| 485 NAAKKAVEVKNRLESAISKLKAELKQkeEIENEIKEKIKTRNEIESRTKEIDSKLEQKENIIQEferVKGSLERLki 561
                                       35666666666666666666665554334555555555555555555554444444444433330002222222111 PP

                      Exonuc_VII_L 203 lkkqlkkkrerleelkerlkekleekkerlkklkerle....lleekkerleeleeklealsp 261
                                       l++++ kk+  +eelk +l+++le+ ++  k+l    e    + ++ ke++e+++++l+ l p
  gi|488599919|ref|YP_007906390.1| 562 LESEIGKKSDLIEELK-NLENRLEHLNSIAKDL----EpsksKYTSVKEEIEKIAKRLKILRP 619
                                       3333444444444444.2222222222222222....23333566666666666666666655 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.032
                      Exonuc_VII_L 143 aeleeqleelerrlek..aikrll.........................................eekkqrleklas 176
                                       ++l e+l++le+rle+  +i++ l                                         +e k+r+++l+ 
  gi|488599919|ref|YP_007906390.1| 570 SDLIEELKNLENRLEHlnSIAKDLepskskytsvkeeiekiakrlkilrpaydsylslapqikkkDELKNRISELEG 646
                                       55666677777766652233333322222221111111111111112222222222222222222222223333333 PP

                      Exonuc_VII_L 177 rlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleekkerlkklkerlelleekkerleele 253
                                        +++ ++ + + + +l++lee+++++  ++l++k  ++ + k +++ +++  +e+++kl+++l++l+e+++++ +l+
  gi|488599919|ref|YP_007906390.1| 647 GINRLKQEIVSMEVQLKSLEEKFNSEEFESLSQKMLEIMSEKGKVEGEIKGVSESIEKLESSLAELKEREKEYLRLK 723
                                       33333333333333333333333333333333333333333333322222222333444444443444444333333 PP

                      Exonuc_VII_L 254 ekl 256
                                       +++
  gi|488599919|ref|YP_007906390.1| 724 DEM 726
                                       333 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3  26.5      0.51   3.7e+02      11     129 ..     170     287 ..     159     291 .. 0.77
   2 ?    8.6  27.8    0.0016       1.1      32     162 ..     280     411 ..     275     412 .. 0.85
   3 ?   -2.5  27.2       3.9   2.8e+03      25     167 ..     410     548 ..     408     555 .. 0.79
   4 ?    7.9   6.6    0.0024       1.7      55     118 ..     568     631 ..     550     640 .. 0.83
   5 ?    4.8  11.5     0.022        16      28     121 ..     573     668 ..     571     687 .. 0.44
   6 ?    8.8   5.7    0.0013      0.96      33      95 ..     672     734 ..     670     742 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.51
                               GAS  11 neiknYYnditrnNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqsl 87 
                                       +e++n+ +d +++  ++I slK+++e +       e++l+++++++ +l ++ k   +e++ L+k+  + ++ k ++
  gi|488599919|ref|YP_007906390.1| 170 REYENFLSDKIHDGEKKIISLKKDVELKSS----VEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDELSEIKDKI 242
                                       677777888888888899999999976554....5566777888899999999999999999999999999999999 PP

                               GAS  88 knlkarlkelekelkdlkwehevleqrfekv...ekerdelykkf 129
                                       + lk+++++ +++l++ k++   l+q+++k+   ek+ +el++++
  gi|488599919|ref|YP_007906390.1| 243 DDLKQKISRKQDKLSSEKEDLSKLKQELSKIleiEKKTKELEASY 287
                                       999999999999999999999999999887522255666666555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
                               GAS  32 KeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkweh 108
                                        +e+e   ++    e++l+e+ +e ++l+++L ++ e   e +k   + ++ k++lk+++++ ke +   +d + e 
  gi|488599919|ref|YP_007906390.1| 280 TKELEASYREYLDLENRLEELDAEERDLSKKLDELSEVSVEIEKLKTQISSTKKALKEIEEKEKEIDGIKEDARREE 356
                                       56788888888899****************************************************99999999887 PP

                               GAS 109 evleq..rfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkke 162
                                         l++   +e ++ erd+l+k+ ++  +++ qk+  k   L+++ ++ +e++Ek e
  gi|488599919|ref|YP_007906390.1| 357 VLLKEisAIELLSVERDQLKKRLRDITKDIEQKS-IKLEELKRREEKFREAMEKLE 411
                                       66665223455666*******************7.556667888888888888765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.9
                               GAS  25 LelIkslKeeieelkkkeernekelseisqenkrlkepLkk.aeeeveeLrkqlknyekdkqslknlkarlkeleke 100
                                       Le+  +  e+ e+l k   r + + + i ++ k  k +L   ++e++++ ++++ + e+   +l+ +++rl+e++k+
  gi|488599919|ref|YP_007906390.1| 410 LEKLSNIEEKYEKLLKLSVRLSEDRKSIIENIKAVKTNLCPiLDEKCDRIHQKIDDLER---KLRVVEERLEEVDKK 483
                                       66667777777777777777777777777777777777764256777888888888887...899999999999999 PP

                               GAS 101 lkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqlee 167
                                       +++ k   ev++   ++++k + el++k e   +e+++k++ +n + e + k+++ +lE+ke  ++e
  gi|488599919|ref|YP_007906390.1| 484 MNAAKKAVEVKNRLESAISKLKAELKQKEE-IENEIKEKIKTRNEI-ESRTKEIDSKLEQKENIIQE 548
                                       999999999999988899999999888765.579999999999975.99999999999999988887 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0024
                               GAS  55 enkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekv 118
                                       ++++l e+Lk++e+ +e+L+  +k+ e  k++++++k+++++  k lk l+  +++      ++
  gi|488599919|ref|YP_007906390.1| 568 KKSDLIEELKNLENRLEHLNSIAKDLEPSKSKYTSVKEEIEKIAKRLKILRPAYDSYLSLAPQI 631
                                       567899******************************************9998888766555555 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.022
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyek...dkqslknlkarlkelekel 101
                                       I++lK+ +e+  +  ++  k+l+  +++  + ke+++k  + ++ Lr +   y +   + ++ ++lk+r++ele  +
  gi|488599919|ref|YP_007906390.1| 573 IEELKN-LENRLEHLNSIAKDLEPSKSKYTSVKEEIEKIAKRLKILRPAYDSYLSlapQIKKKDELKNRISELEGGI 648
                                       333332.2333333334444444445555555555555555555555544444331112333344444444444444 PP

                               GAS 102 kdlkwehevleqrfekveke 121
                                       ++lk+e  ++e +++++e++
  gi|488599919|ref|YP_007906390.1| 649 NRLKQEIVSMEVQLKSLEEK 668
                                       44444444444444444443 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.0013
                               GAS  33 eeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlk 95 
                                       ee e l +k  +   e  +++ e k  +e ++k+e  ++eL+++ k+y + k ++++lk++l+
  gi|488599919|ref|YP_007906390.1| 672 EEFESLSQKMLEIMSEKGKVEGEIKGVSESIEKLESSLAELKEREKEYLRLKDEMDRLKRKLE 734
                                       6778888888888899999999*************************************9986 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.04        29      20      35 ..      25      40 ..      16      43 .. 0.80
   2 ?   -2.1  45.0      0.68   4.9e+02     239     486 ..     179     422 ..     170     447 .. 0.48
   3 ?    9.0  21.6   0.00031      0.22     351     499 ..     454     605 ..     451     613 .. 0.77
   4 ?    8.7  12.6   0.00038      0.27     245     408 ..     574     738 ..     556     764 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.04
                           DUF3584 20 tnieGtNaaGKTtLlr 35
                                        i G N+aGKTt+l 
  gi|488599919|ref|YP_007906390.1| 25 NAIIGENGAGKTTILE 40
                                      4689*********986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.68
                           DUF3584 239 aiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkq..qlrtledelkeaidelnqe 313
                                       +i+  +++i  l++++e   s+e+ L+ lk++  + +++ +  ++e ++ k++  +  +++ + d+lk++i++ + +
  gi|488599919|ref|YP_007906390.1| 179 KIHDGEKKIISLKKDVELKSSVEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDElsEIKDKIDDLKQKISRKQDK 255
                                       56677788899999999999999999988887777776666666666666555543114444556666666666666 PP

                           DUF3584 314 lsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkike 390
                                       ls +k++l++ ++el ++ e +kk ++  +e    +   l++  +el + e++l   +++  +v  + +++k +i++
  gi|488599919|ref|YP_007906390.1| 256 LSSEKEDLSKLKQELSKILEIEKKTKE--LEASYREYLDLENRLEELDAEERDLSKKLDELSEVSVEIEKLKTQISS 330
                                       666666666666666665555544332..332222333333333344444444444444444444444445444444 PP

                           DUF3584 391 ele..eeleklkerleaireekdrlkaaieealeale..sqlrkqleaqkeelneeekelesrlselklrldsatat 463
                                        ++  +e+e+ +++ + i+e + r  ++  ++ +a+e  s  r+ql++  +++       ++ ++++  +l++ +  
  gi|488599919|ref|YP_007906390.1| 331 TKKalKEIEEKEKEIDGIKEDARR-EEVLLKEISAIEllSVERDQLKKRLRDI-------TKDIEQKSIKLEELKRR 399
                                       332113344444444444444443.3333444444431122222222222333.......23333333333333333 PP

                           DUF3584 464 eEeleqieeadealekaqeelek 486
                                       eE+  +  e+ e+l++ +e++ek
  gi|488599919|ref|YP_007906390.1| 400 EEKFREAMEKLEKLSNIEEKYEK 422
                                       33333333333333333333333 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00031
                           DUF3584 351 dqlpsirseleeleeeldaltekhqdvqekydrrkqk..ikeeleeeleklkerleaireekdrl...kaaieeale 422
                                       ++ + i +++ +le++l+ ++e+ ++v++k+++ k++  +k++le +++klk++l+ ++ee ++    k + +++ e
  gi|488599919|ref|YP_007906390.1| 454 EKCDRIHQKIDDLERKLRVVEERLEEVDKKMNAAKKAveVKNRLESAISKLKAELK-QKEEIENEikeKIKTRNEIE 529
                                       677899999***********************988762257888999999999854.44444444334333344444 PP

                           DUF3584 423 alesqlrkqleaqkeelneeekelesrlselklrldsatateEeleqieeadealekaqeelekaeaevealqaeee 499
                                          ++  ++l +qke++ +e ++++ +l++lk +  + + ++++ e++++ +++le+ ++ ++  e ++++ ++ +e
  gi|488599919|ref|YP_007906390.1| 530 SRTKEIDSKL-EQKENIIQEFERVKGSLERLKILESEIGKKSDLIEELKNLENRLEHLNSIAKDLEPSKSKYTSVKE 605
                                       4444444333.367888889999**********************************99999988888887766555 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00038
                           DUF3584 245 peieklqeefeqleslelrLsllkgel...kadeerlaekqeevqeakaelkqq..lrtledelkeaidelnqelsa 316
                                       +e+++l+++ e+l+s+ + L   k ++   k+++e++a++++    a  ++ +   + +++delk++i+el++ ++ 
  gi|488599919|ref|YP_007906390.1| 574 EELKNLENRLEHLNSIAKDLEPSKSKYtsvKEEIEKIAKRLKILRPAYDSYLSLapQIKKKDELKNRISELEGGINR 650
                                       45667777777777777777777666511134444444444444444444433211456677777777777777777 PP

                           DUF3584 317 akaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkike..e 391
                                       +k+++  +e +l  lee   k++ ++ e+l++++    +i se  ++e e++++ e+++++++ + ++k   ke  +
  gi|488599919|ref|YP_007906390.1| 651 LKQEIVSMEVQLKSLEE---KFNSEEFESLSQKML---EIMSEKGKVEGEIKGVSESIEKLESSLAELKEREKEylR 721
                                       77777777777776664...788999999988764...678888999999999999999999999888776665336 PP

                           DUF3584 392 leeeleklkerleaire 408
                                       l++e+ +lk +le ir 
  gi|488599919|ref|YP_007906390.1| 722 LKDEMDRLKRKLEFIRA 738
                                       77888888888877775 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   5.3     0.034        24      47     113 ..     200     266 ..     195     280 .. 0.85
   2 ?    0.6   1.6      0.75   5.4e+02      61     119 ..     293     351 ..     275     361 .. 0.72
   3 ?    8.4   3.2    0.0028         2      48     115 ..     369     436 ..     362     445 .. 0.86
   4 ?    1.5   0.5       0.4   2.8e+02      49     115 ..     432     496 ..     421     501 .. 0.63
   5 ?   -0.2   6.9       1.3   9.1e+02      55     123 ..     491     559 ..     454     565 .. 0.77
   6 ?    6.0   0.2     0.016        12      35     112 ..     582     660 ..     569     673 .. 0.71
   7 ?    6.9   0.1    0.0084         6      46     108 ..     683     748 ..     668     754 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.034
                          LOH1CR12  47 vAadqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtl 113
                                       v  d +kl ++  ++ +k + +l+el++ +k++++  e   k+ +l++++sr q+ l    + l +l
  gi|488599919|ref|YP_007906390.1| 200 VEQDLKKLKAKKDSLIKKKKIILKELNALKKKHDELSEIKDKIDDLKQKISRKQDKLSSEKEDLSKL 266
                                       6677788999999999999999********************************9998766655555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.75
                          LOH1CR12  61 vdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlnelLde 119
                                       +++++++l ae r+  k+ ++  e   ++++l+ q+s+ ++ l++i +   +++ + ++
  gi|488599919|ref|YP_007906390.1| 293 LENRLEELDAEERDLSKKLDELSEVSVEIEKLKTQISSTKKALKEIEEKEKEIDGIKED 351
                                       56677777777788888888888888888888888888888888776655555555444 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0028
                          LOH1CR12  48 AadqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlne 115
                                         + ++l +r +++ ++i++   +l e +++ +++ ea++k+++ls++  + +++l+  v l E   +
  gi|488599919|ref|YP_007906390.1| 369 SVERDQLKKRLRDITKDIEQKSIKLEELKRREEKFREAMEKLEKLSNIEEKYEKLLKLSVRLSEDRKS 436
                                       6788999*************99999999***************9999999999999888887776555 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.4
                          LOH1CR12  49 adqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlne 115
                                        d + ++e+ik v++++  +l e  ++   +++  +   k++++++ l  +++ ++   + +E  n 
  gi|488599919|ref|YP_007906390.1| 432 EDRKSIIENIKAVKTNLCPILDEKCDR--IHQKIDDLERKLRVVEERLEEVDKKMNAAKKAVEVKNR 496
                                       566777777777777777777765554..34444444456666666666666666666666655544 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.3
                          LOH1CR12  55 verikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlnelLdedeRL 123
                                       ve    ++  i++l ael++k++  ++  e+++  ne+++  + i++ le++ +++ ++  +  + eRL
  gi|488599919|ref|YP_007906390.1| 491 VEVKNRLESAISKLKAELKQKEEIENEIKEKIKTRNEIESRTKEIDSKLEQKENIIQEFERVKGSLERL 559
                                       333345777888888899999999999999999999***99999*999999776666666655555555 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.016
                          LOH1CR12  35 RlqeHlavcAkavAadqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiile...divp 108
                                       Rl eHl+  Ak     + k +  +ke  +ki + l+ lr   + y s a +++k  el++ +s ++  ++   + + 
  gi|488599919|ref|YP_007906390.1| 582 RL-EHLNSIAKDLEPSKSKYTS-VKEEIEKIAKRLKILRPAYDSYLSLAPQIKKKDELKNRISELEGGINrlkQEIV 656
                                       54.6888888877777777654.444445677777777777777777889999999***999998865432226777 PP

                          LOH1CR12 109 llEt 112
                                       ++E 
  gi|488599919|ref|YP_007906390.1| 657 SMEV 660
                                       7774 PP

  == domain 7  score: 6.9 bits;  conditional E-value: 0.0084
                          LOH1CR12  46 avAadqaklverikevdakiitl...laelrekqkqyasyaealskvnelsdqlsriqiiledivp 108
                                       ++ +++ k+  +ik v+++i++l   lael+e++k+y    +++ ++++  + ++ ++ i++  vp
  gi|488599919|ref|YP_007906390.1| 683 EIMSEKGKVEGEIKGVSESIEKLessLAELKEREKEYLRLKDEMDRLKRKLEFIRALREIFNLAVP 748
                                       57789999999******9998773347777777777777777777777766677777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (884 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3182  (0.177478); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                       258  (0.0143901); expected 17.9 (0.001)
Passed Fwd filter:                       164  (0.00914719); 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: 4.07u 0.37s 00:00:04.44 Elapsed: 00:00:00.88
# Mc/sec: 3033.21
//
Query:       gi|488599920|ref|YP_007906391.1|  [L=291]
Description: hypothetical protein Asulf_00369 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-19   68.0   0.5    1.6e-18   67.3   0.5    1.4  1  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.5     9e-23   1.6e-18       2     242 .]      55     264 ..      54     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 9e-23
                                       EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCC CS
                              NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekg 78 
                                       rv++vDGS+     + g+++ ++++a+   ++++ e+  +   +   s     + + +l +  lElk    +lee +
  gi|488599920|ref|YP_007906391.1|  55 RVVGVDGSQLRYLKEFGVPFGAVQVAKLILIHGKGEYRVDYRTKWVES-----DKSLDLERFELELK---TMLEELE 123
                                       79*************************999999999998887777777.....**************...******* PP

                                       SCEEEEECSHHCCCHHHHHHHHHHHHHHHHHHHHHHTT-...TTCEEEEESS-SCTCCHCCC......S--HHHHCC CS
                              NurA  79 edllllDGsligslvefdelheeleyeeylyslsrllea...glnlvgvaKsfrskellnllletlligesisDial 152
                                        d+l++DGs++ s+    +++  + + +y++ +s+ le+   ++ +vg + +++sk+l++             D  +
  gi|488599920|ref|YP_007906391.1| 124 SDILFFDGSFSVSFA---NQYRKDIRDRYFQLISEFLEKsknRAFVVGFIDRSYSKDLFRPY-----------DSFI 186
                                       ***************...******************************************88...........**** PP

                                       HHCCHCH---STTS-HHHHTT-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHH.C..CHHHHHHHHHH..TTB- CS
                              NurA 153 lgallrkpgytspllkilrekpllrealidkeiyfaYvrlegggsilrleipaevs.t..akdedvlsllasqrlsi 226
                                       l+ +lr+  yt+p++             +  +++f Y+++  g s++r+e+p +   +       v+ +++    s 
  gi|488599920|ref|YP_007906391.1| 187 LKNYLRNFEYTEPMPC-----------TELNDVFFSYLKI--GNSVVRVEFPKWMAgMhdVFMRYVVAECL--LGST 248
                                       ***************4...........334459*******..************77666566677888888..99** PP

                                       SSSBCCHHHHHHHHCC CS
                              NurA 227 sGYprpLalAhelaki 242
                                       + Yp+ L++Ah +a+i
  gi|488599920|ref|YP_007906391.1| 249 RQYPYVLERAHMYAVI 264
                                       **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 00:00:00.43
# Mc/sec: 2034.85
//
Query:       gi|488599921|ref|YP_007906392.1|  [L=156]
Description: hypothetical protein Asulf_00370 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1144.60
//
Query:       gi|488599922|ref|YP_007906393.1|  [L=520]
Description: putative ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-42  143.7   1.6    1.4e-41  143.1   1.6    1.3  1  DUF87            Helicase HerA, central domain
      1e-05   24.7   0.1    7.4e-05   21.8   0.1    2.1  1  AAA_10           AAA-like domain
    0.00015   21.8   0.0       0.01   15.8   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
    0.00019   20.5   0.0       0.51    9.2   0.0    2.1  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    0.00076   18.2   0.0     0.0022   16.7   0.0    1.7  2  DUF853           Bacterial protein of unknown function (DUF85
     0.0011   17.8   0.0     0.0023   16.8   0.0    1.4  2  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
     0.0017   18.6   0.3        1.5    9.1   0.3    3.1  1  AAA_22           AAA domain
     0.0029   17.4   0.0       0.17   11.7   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.053   13.2   0.0    1.8  2  Zot              Zonular occludens toxin (Zot)
       0.03   14.8   0.5       0.85   10.0   0.1    2.5  2  AAA              ATPase family associated with various cellul
      0.051   13.2   0.2         16    5.1   0.1    2.7  2  SWI2_SNF2        SWI2/SNF2 ATPase
      0.061   12.2   0.3       0.11   11.3   0.1    1.4  2  DUF2791          P-loop Domain of unknown function (DUF2791)


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 !  143.1   1.6   9.3e-45   1.4e-41       1     227 []     133     345 ..     133     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.1 bits;  conditional E-value: 9.3e-45
                             DUF87   1 ieiGrll.sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkal....... 68 
                                       i+iG+ll  +++vp+ l  +++v++H++il+sTGsGKS++++vL+eell+  ++a++lilDpHGEY++++       
  gi|488599922|ref|YP_007906393.1| 133 IHIGYLLnRDDDVPAVLETSSIVSEHMCILASTGSGKSYLAGVLVEELLKpHNSASVLILDPHGEYHTLKeieglde 209
                                       79*****77778**************************************99999********************** PP

                             DUF87  69 ..ekllsekvkvitpspsakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepv 143
                                          +++s +vk+++++      e+ki++++l+++ell++l+     ++++ +++l++++++++     +k++s++++
  gi|488599922|ref|YP_007906393.1| 210 frDEGYSARVKILEKD------EIKIRLSELEYDELLNILPN----LTDKMEAILNSVYRELE----GTKFTSNDLI 272
                                       **9************9......9*******************....999***********886....9********* PP

                             DUF87 144 eklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvv 220
                                         ++   +        +++ ++++l++++++ +++ + +    +d+i+  l+++ ++g  t+i++s + +l+qql++
  gi|488599922|ref|YP_007906393.1| 273 DAIQRRAE-------DERDVTARALSWRIRRYIENVEII----DDYIHISLKDILRPGMATVIQMSDMGDLDQQLLT 338
                                       *9999888.......9999******************99....99999999999*********************** PP

                             DUF87 221 svilrri 227
                                       svil+ri
  gi|488599922|ref|YP_007906393.1| 339 SVILKRI 345
                                       *****97 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1     5e-08   7.4e-05      21     295 ..     156     419 ..     148     449 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5e-08
                            AAA_10  21 asasliiGdlGnGKSvlakllvlyisllg..gkaliiDpkkerekfketlpeiakkinvvtLdseeenegvLdPlvl 95 
                                       + ++ i+ ++G GKS+la +lv  ++       +li+Dp  e    ++tl+ei        Ld e + eg    + +
  gi|488599922|ref|YP_007906393.1| 156 SEHMCILASTGSGKSYLAGVLVEELLKPHnsASVLILDPHGE----YHTLKEIE------GLD-EFRDEGYSARVKI 221
                                       678999****************987754445889********....78888833......355.667778888999* PP

                            AAA_10  96 lkeekeaeslaedilelllgvkkkesekkaalseaveavlegkqrgllavieelrkedekvareiarhlesvvkksl 172
                                       l++ +++++l e   + ll++ ++ ++k +a+ ++v + leg +  + ++i+ ++++ e      ar l   ++  +
  gi|488599922|ref|YP_007906393.1| 222 LEKDEIKIRLSELEYDELLNILPNLTDKMEAILNSVYRELEGTKFTSNDLIDAIQRRAEDERDVTARALSWRIRRYI 298
                                       **999*****9999999*************************************99888877778999988999999 PP

                            AAA_10 173 aklvfsdgsveeaislekkvtvlevedLdLPdkderlerlteekllsvavlfvi.aafarefass.dkkefkv.vif 246
                                        ++ + d+ +  +isl+  +      ++    +   +++l+++ l sv +  ++ a +  e + s +k e  v vi+
  gi|488599922|ref|YP_007906393.1| 299 ENVEIIDDYI--HISLKDIL---R-PGMATVIQMSDMGDLDQQLLTSVILKRILnARINAEKGLSgEKIEYPVfVIV 369
                                       9999999975..46755432...2.2333333444557776666666655555413454455555144444442678 PP

                            AAA_10 247 DEawiftssa.eGkkllkelvRiGRsynaavylvtqsadDvlkeelknni 295
                                        Ea  f+s + +  ++lk ++  GR++   v l++q ++ ++ + l++ +
  gi|488599922|ref|YP_007906393.1| 370 EEAHRFASRDsKSFEVLKTILSEGRKFGVGVCLISQRPSKIDSDILSQCM 419
                                       99999998762566899999999****99999999999988877665555 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 !   15.8   0.0     7e-06      0.01      24      64 ..     156     196 ..     111     282 .. 0.81
   2 ?    3.8   0.0     0.033        50     129     151 ..     360     384 ..     322     399 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7e-06
                                       TSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk 64 
                                        ++++i + TG+GK+++a  l+e+llk ++   +l+l p  
  gi|488599922|ref|YP_007906393.1| 156 SEHMCILASTGSGKSYLAGVLVEELLKPHNSASVLILDPHG 196
                                       5799***********************99988999887654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.033
                                       HTTT-S...EEEEETGGGTTS...TTTH CS
                            ResIII 129 lrdrfd...viiiDEaHrlgak..kswr 151
                                       +    +   ++i+ EaHr+++   ks++
  gi|488599922|ref|YP_007906393.1| 360 KI---EypvFVIVEEAHRFASRdsKSFE 384
                                       23...25559*********997433444 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 !    9.2   0.0   0.00035      0.52      14      55 ..     155     198 ..     144     201 .. 0.84
   2 !    9.2   0.0   0.00034      0.51     167     310 ..     286     427 ..     243     456 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00035
                     TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairarg..draivlDltGaf 55 
                                         +h+ i+ +tGsGK+  +  l++++ +      +++lD++G++
  gi|488599922|ref|YP_007906393.1| 155 VSEHMCILASTGSGKSYLAGVLVEELLKPHnsASVLILDPHGEY 198
                                       578*********************998866336789******98 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00034
                     TrwB_AAD_bind 167 taasiratlatnlevlelLaekgerFSireWleeedesgwlflts..kaeqrallrpllsawldlaikallslpesr 241
                                       ta  +   + +++e +e++++  +  S+++ l+ +    ++ ++   + +q+ l+  +l  +l+  i+a + l+ ++
  gi|488599922|ref|YP_007906393.1| 286 TARALSWRIRRYIENVEIIDDYIH-ISLKDILRPGM-ATVIQMSDmgDLDQQLLTSVILKRILNARINAEKGLSGEK 360
                                       555566666667777777666666.67777666664.4444444311334555566667777777777777777655 PP

                     TrwB_AAD_bind 242 err.lWfflDElpaL.....grleelksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvs 310
                                        +  +++++ E +       +  e lk++l egRkfG+ v l  q  +++           ils + t++i+r+ 
  gi|488599922|ref|YP_007906393.1| 361 IEYpVFVIVEEAHRFasrdsKSFEVLKTILSEGRKFGVGVCLISQRPSKIDS--------DILSQCMTQIIMRIV 427
                                       4433888888877662222245788***********************9963........455555555555532 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   1.8e+03      17      60 ..     152     197 ..     139     215 .. 0.72
   2 !   16.7   0.0   1.5e-06    0.0022     258     362 ..     365     461 ..     357     471 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                            DUF853  17 lklanrhGliaGatGtGktvtLqvlaeslse..aGvpvfladvkGd 60 
                                        +++  h  i  +tG Gk     vl e+l +     +v++ d  G+
  gi|488599922|ref|YP_007906393.1| 152 SSIVSEHMCILASTGSGKSYLAGVLVEELLKphNSASVLILDPHGE 197
                                       5667889999999****99998999888754224556666666665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.5e-06
                            DUF853 258 klvfffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavka 334
                                        +v+  +eah +    +k++ e +  ++   r  GvGv +++q P+ +  ++L+q  +  q  +r   p+dq  ++ 
  gi|488599922|ref|YP_007906393.1| 365 VFVI-VEEAHRFASRDSKSF-EVLKTILSEGRKFGVGVCLISQRPSKIDSDILSQCMT--QIIMRIVNPADQDNIRD 437
                                       5544.578887766666665.7788888888999*********************876..5589************* PP

                            DUF853 335 aadtfranpefdveeaiteLgvGealvs 362
                                       +++++ +    d+ + +  L  G+alv+
  gi|488599922|ref|YP_007906393.1| 438 SVESIGK----DLISELPGLTKGQALVA 461
                                       **99866....56677777777777775 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 !   16.8   0.0   1.6e-06    0.0023      12      84 ..     110     200 ..     105     204 .. 0.88
   2 ?   -4.0   0.0       3.1   4.6e+03     319     343 ..     384     408 ..     383     412 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-06
                   T4SS-DNA_transf  12 gllkrektikgevltkdkk...alyaggllntdGdf...........ehvlvvAptrsgKg..vgvviPnllkwkq. 71 
                                        +l +e++i + +++k+ +   ++  g lln+d d            eh+ + A t+sgK+  +gv +  llk  + 
  gi|488599922|ref|YP_007906393.1| 110 VYLAEEEVISETLFKKKLGevgSIHIGYLLNRDDDVpavletssivsEHMCILASTGSGKSylAGVLVEELLKPHNs 186
                                       478889999999999988788888899999999888************************9777********98776 PP

                   T4SS-DNA_transf  72 .siVvlDpkgElae 84 
                                        s+ +lDp gE + 
  gi|488599922|ref|YP_007906393.1| 187 aSVLILDPHGEYHT 200
                                       79*********876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.1
                   T4SS-DNA_transf 319 eileealatiagYgirltlIiQsis 343
                                       e l++ l  ++++g+ + lI Q  s
  gi|488599922|ref|YP_007906393.1| 384 EVLKTILSEGRKFGVGVCLISQRPS 408
                                       7789999999**********99765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.3     0.001       1.5      74     127 ..     338     402 ..     156     428 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                            AAA_22  74 sseellealeqalrarav........ielliiDEaqhlr..seealeeLrsllnl.srkgvqliL 127
                                       +s  l + l+  ++a +         ++++i++Ea+++     + +e L+++l   +++gv + L
  gi|488599922|ref|YP_007906393.1| 338 TSVILKRILNARINAEKGlsgekieyPVFVIVEEAHRFAsrDSKSFEVLKTILSEgRKFGVGVCL 402
                                       33333344444444443355555566677777788877654255555555544433455555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00011      0.17      14     112 ..     156     254 ..     145     300 .. 0.70
   2 ?    3.6   0.0     0.035        52     119     139 ..     361     381 ..     293     397 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       TCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHH.HHHHHHHHHTTT.STSEEEEEETTSSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                              DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLae.qtlnnlkkfkky.idlrvlliiggvaar 88 
                                        +++++ a TGsGK+  + + v + +   k  +   +li+ P  e    + ++ l +f ++ ++ rv+ i+++++ +
  gi|488599922|ref|YP_007906393.1| 156 SEHMCILASTGSGKSYLAGVLVEELL---KPHNSASVLILDPHGEYHTlKEIEGLDEFRDEgYSARVK-ILEKDEIK 228
                                       46899************999998777...7899999****9998853212333333443332334443.66777777 PP

                                       HHHHHHHTT..CSEEEEEHHHHHHHH CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxx RF
                              DEAD  89 dqlskldng..vdivvgtpgrlddll 112
                                         ls+l+ +  ++i+   ++++  +l
  gi|488599922|ref|YP_007906393.1| 229 IRLSELEYDelLNILPNLTDKMEAIL 254
                                       77777753334666655555555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.035
                                       CTTEEEEEEETHHHHHHTTTH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldqgfs 139
                                       ++   f+++ Ea+r+ + + +
  gi|488599922|ref|YP_007906393.1| 361 IEYPVFVIVEEAHRFASRDSK 381
                                       445567*********998544 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.5e-05     0.053      82     135 ..     365     415 ..     326     425 .. 0.86
   2 ?   -3.0   0.0       3.2   4.8e+03      22      78 ..     435     494 ..     430     497 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.5e-05
                               Zot  82 allviDEcqeifpvrakegrkdpevi.naftehRhlgwDivlltqdiskihkevr 135
                                        ++++ E++++ +  +k      ev+   + e R++g  ++l+ q +ski++++ 
  gi|488599922|ref|YP_007906393.1| 365 VFVIVEEAHRFASRDSKS----FEVLkTILSEGRKFGVGVCLISQRPSKIDSDIL 415
                                       599*******87777774....6788799**********************9985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.2
                               Zot  22 llpalke.gRkiitnidGlrlerieqvlgekvstarlirid...npegaetlkefakwati 78 
                                       +++ + + g+ +i ++ Gl++ ++    g + +t+ lir        g    +++++w+++
  gi|488599922|ref|YP_007906393.1| 435 IRDSVESiGKDLISELPGLTKGQALV-AGVALNTPVLIRARkrlTSHGGASKNAPEIWRRY 494
                                       55555546888899999998666543.5777788888887655544555555666666665 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 ?    2.6   0.1      0.11   1.7e+02       2      23 ..     160     186 ..     159     302 .. 0.65
   2 ?   10.0   0.1   0.00057      0.85      58     128 ..     363     422 ..     328     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                       EEESSTTSSHHHHHHHHHHHH.....T CS
                               AAA   2 llyGppGtGKTllakavakel.....g 23 
                                       ++    G GK++la  +++el     +
  gi|488599922|ref|YP_007906393.1| 160 CILASTGSGKSYLAGVLVEELlkphnS 186
                                       66677899*****99999997544431 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00057
                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrki 128
                                        p+ ++++E++++a+++        ++  ++L t l++ +k    v v+++++rp+k+d+ +l + +  +i
  gi|488599922|ref|YP_007906393.1| 363 YPVFVIVEEAHRFASRD--------SKSFEVLKTILSEGRKF--GVGVCLISQRPSKIDSDIL-SQCMTQI 422
                                       5899*********9888........77799999999999996..599****************.6665554 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.011        17      23      54 ..     161     191 ..     147     196 .. 0.78
   2 ?    5.1   0.1     0.011        16     112     146 ..     355     391 ..     313     405 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.011
                         SWI2_SNF2  23 iWHtqGSGKsltmvflakklleeelknpkvvv 54 
                                       i   +GSGKs+   +l+++ll+   +++ v++
  gi|488599922|ref|YP_007906393.1| 161 ILASTGSGKSYLAGVLVEELLK-PHNSASVLI 191
                                       55689***************99.444555544 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.011
                         SWI2_SNF2 112 klevlsereniivlvDEaHRsqyg..elakklrkalp 146
                                        l+  + +  ++v+v EaHR  +   +  + l+++l 
  gi|488599922|ref|YP_007906393.1| 355 GLSGEKIEYPVFVIVEEAHRFASRdsKSFEVLKTILS 391
                                       3344444456999999999965541244455555555 PP

>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.7     4e+03      59      71 ..     166     178 ..     161     182 .. 0.82
   2 ?   11.3   0.1   7.4e-05      0.11     324     410 ..     224     316 ..     202     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.7
                           DUF2791  59 GsGKtFllqllre 71 
                                       GsGK++l+ +l e
  gi|488599922|ref|YP_007906393.1| 166 GSGKSYLAGVLVE 178
                                       9******988766 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.4e-05
                           DUF2791 324 lrapvirLkplteeellvlleklrdiyaegyeeev...lvsdeelkafleevtgrlgakvgvtpRev...irdfvdv 394
                                         +  irL++l+++ell +l +l+d  ++  ++ +   + ++ + +++++++++r  ++ +vt R +   ir +++ 
  gi|488599922|ref|YP_007906393.1| 224 KDEIKIRLSELEYDELLNILPNLTDKMEAILNSVYrelEGTKFTSNDLIDAIQRRAEDERDVTARALswrIRRYIEN 300
                                       55678*******************99999866666623344455678******************966669****** PP

                           DUF2791 395 Ldileqnpdldpeell 410
                                        +i++++ +++++++l
  gi|488599922|ref|YP_007906393.1| 301 VEIIDDYIHISLKDIL 316
                                       *****99998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 3232.18
//
Query:       gi|488599923|ref|YP_007906394.1|  [L=375]
Description: ABC-type transport system, involved in lipoprotein release, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-25   89.7   0.1    3.1e-25   89.7   0.1    2.0  3  MacB_PCD   MacB-like periplasmic core domain
    4.9e-13   49.4   5.8    4.9e-13   49.4   5.8    3.3  4  FtsX       FtsX-like permease family
     0.0081   15.0   7.5      0.021   13.7   6.2    2.2  2  LptF_LptG  Lipopolysaccharide export system permease LptF/Lpt
  ------ inclusion threshold ------
        8.1    6.4   6.5         40    4.2   2.1    2.6  2  PetG       Cytochrome B6-F complex subunit 5


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.1     7e-29   3.1e-25       1     194 [.      17     216 ..      17     217 .. 0.77
   2 ?   -4.2   1.6       3.9   1.8e+04       2      21 ..     248     268 ..     247     282 .. 0.65
   3 ?   -4.7   2.9         4   1.8e+04       5      32 ..     305     332 ..     302     356 .. 0.78

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 7e-29
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk..gsgeslsdpdvealrrevp.veavapvv. 73 
                                       s+l+++Gi+iGv+a+ +i+++gegl+ svl++++d +n v++tp++  g+   ++ + v+ ++ ++   e+v+p+  
  gi|488599923|ref|YP_007906394.1|  17 SVLAIIGIVIGVMAIASIGIFGEGLKLSVLKNFQDVANEVIITPSYthGYTK-IDRDSVKKIE-KLTfLESVTPIKm 91 
                                       79************************************99999986432222.2223343332.467899****855 PP

                          MacB_PCD  74 ...tvrgggsgeeevtvvg.vdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl..kpft 143
                                          +v + ++  +++t++g +  d  ++f+ +  +G+          ++++v+g+ lae+l  +vG ++ +  + f+
  gi|488599923|ref|YP_007906394.1|  92 ksgVVQYKNK-KTYTTIYGmGRKDIEEMFKAE--KGSI-------KLSGSCVVGNYLAEKLNlRVGVKLSIegEVFR 158
                                       6654445543.334678886556676777662..3532.......25678**********8899*********99** PP

                          MacB_PCD 144 VvGvledppgsgsalg.ddavylp.......lttlqrrsitvrlkdgadleaaaaelek 194
                                       V+G+le++ g+ ++++ ++a++++       +++ ++++++vr+++ +++e+++++++k
  gi|488599923|ref|YP_007906394.1| 159 VSGILEEE-GARFDINpNNAIFISekdfenlFNEKDYSMVIVRVEKIENIEELKDAVDK 216
                                       *****776.76666668999****888444444447899*****************987 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 3.9
                          MacB_PCD   2 lltvLGiaiGvaaviaiv.sl 21 
                                       ll++ Gi + va v+++  +l
  gi|488599923|ref|YP_007906394.1| 248 LLAIAGISLLVAGVSILNiML 268
                                       577777777777776665444 PP

  == domain 3  score: -4.7 bits;  conditional E-value: 4
                          MacB_PCD   5 vLGiaiGvaaviaivslgeglqasvlsq 32 
                                       + +++ G+ ++ a +++ +g++ +v+  
  gi|488599923|ref|YP_007906394.1| 305 IGSVIGGILSIFAGFLIEAGMLHTVEYL 332
                                       5667778999999999999998888764 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.075   3.4e+02      28      44 ..      19      34 ..      11      67 .. 0.59
   2 ?   -3.1   0.0       2.5   1.1e+04      36      54 ..     131     149 ..     126     180 .. 0.72
   3 ?    1.2   0.3      0.12   5.2e+02      24      86 ..     247     264 ..     213     273 .. 0.58
   4 !   49.4   5.8   1.1e-16   4.9e-13       2      96 .]     276     368 ..     275     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.075
                              FtsX 28 itlvalviGlglgllaa 44
                                      ++++++viG + +++ +
  gi|488599923|ref|YP_007906394.1| 19 LAIIGIVIG-VMAIASI 34
                                      455555555.2222222 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                              FtsX  36 Glglgllaaqllsdvllss 54 
                                       ++++g+ +a+ l+  ++  
  gi|488599923|ref|YP_007906394.1| 131 SCVVGNYLAEKLNLRVGVK 149
                                       3888888888777666554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.12
                              FtsX  24 eillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagll 86 
                                        +l+i+ ++l+++                                              +++l
  gi|488599923|ref|YP_007906394.1| 247 FLLAIAGISLLVA---------------------------------------------GVSIL 264
                                       2222222222222.............................................11222 PP

  == domain 4  score: 49.4 bits;  conditional E-value: 1.1e-16
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                       reig++ra+G+++ ++++++l+e+l+++++++viG +l+++a  l+ +++l  v    l +   +++++ +i+++++
  gi|488599923|ref|YP_007906394.1| 276 REIGVMRAVGASRQTIMRVFLYEALILGAIGSVIGGILSIFAGFLIEAGMLHTV--EYLFVPSTFFAIAKGIFFGMI 350
                                       9************************************************99997..466666666777888999*** PP

                              FtsX  79 lallagllsiskilkkep 96 
                                       +a+++g+++++k+++ ep
  gi|488599923|ref|YP_007906394.1| 351 TAVISGFYPAWKASNLEP 368
                                       **************9997 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 ?    1.8   0.3     0.019        84     170     291 ..     106     252 ..      57     262 .. 0.63
   2 !   13.7   6.2   4.7e-06     0.021      42     112 ..     241     309 ..     225     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.019
                         LptF_LptG 170 tiydltegkgltsiitAksgvlvksad.......elqlrLfngeiyevgddek..kysretferyridinldpadls 237
                                       tiy   ++k+++++++A++g+++ s +        ++l L+ g    + ++    +  + + e  r+din ++a + 
  gi|488599923|ref|YP_007906394.1| 106 TIYGM-GRKDIEEMFKAEKGSIKLSGScvvgnylAEKLNLRVGVKLSIEGE-VfrVSGILEEEGARFDINPNNAIFI 180
                                       44554.778888888888888887777866555555555555555544333.1463334444444444444444444 PP

                         LptF_LptG 238 teeesp................delslselkekikalrsegle.vrryr.aelhkrlalplaclvfaliaap 291
                                       +e+  +                +  ++ elk + ++l +++   vr ++  ++  r++ ++  + ++l+a++
  gi|488599923|ref|YP_007906394.1| 181 SEKDFEnlfnekdysmvivrveKIENIEELKDAVDKLINSRETkVRVFEmKTIIERITEAFNQINLFLLAIA 252
                                       433332334443444444444422245777777777766666657778877888888888888888888875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.7e-06
                         LptF_LptG  42 gdllelilynlpyilelalPlavLlavlltfgrLaedsEltalrsaGislgrllrpililalllsvlsfll 112
                                       +  + l+l++++ i  l++ +++L   ++ +++  +++E+ ++r+ G s+  ++r +l  al+l ++  ++
  gi|488599923|ref|YP_007906394.1| 241 FNQINLFLLAIAGISLLVAGVSIL--NIMLISTIERTREIGVMRAVGASRQTIMRVFLYEALILGAIGSVI 309
                                       556678888888888888888888..5999***************************99999888765555 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 ?    4.2   2.1     0.009        40       7      22 ..      22      37 ..      19      39 .. 0.92
   2 ?    3.5   0.1     0.015        65       6      27 ..     342     362 ..     340     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.009
                              PetG  7 lGiVLGLvpVTlaGLF 22
                                      +GiV+G +++  +G F
  gi|488599923|ref|YP_007906394.1| 22 IGIVIGVMAIASIGIF 37
                                      7*************99 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.015
                              PetG   6 LlGiVLGLvpVTlaGLFvaAYl 27 
                                         Gi  G+++  + G F+ A++
  gi|488599923|ref|YP_007906394.1| 342 AKGIFFGMITAVISG-FYPAWK 362
                                       57************9.788885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1255  (0.0699983); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2184.70
//
Query:       gi|488599924|ref|YP_007906395.1|  [L=222]
Description: ABC-type antimicrobial peptide transport system, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-36  124.0   0.0    7.8e-36  123.6   0.0    1.2  1  ABC_tran        ABC transporter
    5.5e-11   42.8   0.1    1.2e-06   28.6   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    3.1e-09   36.6   0.3    2.8e-08   33.4   0.3    2.0  1  SMC_N           RecF/RecN/SMC N terminal domain
    1.3e-05   24.8   0.0    2.6e-05   23.9   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
    7.3e-05   23.1   0.2     0.0054   17.0   0.0    2.1  2  AAA_22          AAA domain
    0.00015   21.7   0.2    0.00035   20.5   0.1    1.6  2  RsgA_GTPase     RsgA GTPase
     0.0005   19.7   0.0    0.00088   18.9   0.0    1.4  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
    0.00084   19.1   0.0       0.18   11.5   0.0    2.2  2  IstB_IS21       IstB-like ATP binding protein
      0.002   18.6   0.1     0.0028   18.0   0.1    1.6  1  AAA_16          AAA ATPase domain
      0.008   16.1   0.6       0.85    9.5   0.1    2.2  2  NTPase_1        NTPase
     0.0081   16.2   0.8      0.037   14.1   0.8    2.3  1  MMR_HSR1        50S ribosome-binding GTPase
     0.0091   16.5   0.5      0.026   15.0   0.1    1.8  2  AAA_23          AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.022   14.5   0.0    1.6  2  AAA_24          AAA domain
      0.029   13.6   0.3       0.27   10.4   0.1    2.0  2  NB-ARC          NB-ARC domain
       0.03   13.9   0.0      0.075   12.6   0.0    1.7  2  AAA_25          AAA domain
       0.03   13.4   0.3       0.08   12.0   0.1    1.7  2  T2SSE           Type II/IV secretion system protein
      0.032   14.1   0.2       0.11   12.4   0.1    1.9  2  ATPase_2        ATPase domain predominantly from Archaea
       0.04   13.6   0.3          3    7.5   0.1    2.1  2  AAA_15          AAA ATPase domain
      0.059   12.2   0.1        1.9    7.2   0.1    2.0  2  ABC_ATPase      Predicted ATPase of the ABC class
      0.064   13.4   0.2        0.2   11.8   0.2    1.9  1  AAA_33          AAA domain
      0.068   12.9   0.1       0.31   10.7   0.0    1.8  2  AAA_30          AAA domain
      0.078   13.5   0.2       0.26   11.8   0.1    1.9  2  AAA_18          AAA domain
      0.079   13.2   0.2       0.49   10.6   0.1    2.1  2  AAA_28          AAA domain
      0.081   12.8   0.0       0.13   12.2   0.0    1.5  1  Rad17           Rad17 P-loop domain
      0.092   13.0   0.0        1.4    9.2   0.0    2.2  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
       0.17   11.6   0.1       0.29   10.8   0.1    1.4  1  Cytidylate_kin  Cytidylate kinase
       0.19   10.9   0.1        0.2   10.8   0.1    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 !  123.6   0.0   1.2e-38   7.8e-36       1     136 [.      23     171 ..      23     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 1.2e-38
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ vs+++k+ge +ai+G++G+GKStLl+++  l kpt+G++ ++g +++     + ++  r  +g+++q+ +l p+
  gi|488599924|ref|YP_007906395.1|  23 LNGVSMEVKRGEFIAIMGPSGSGKSTLLNMIGCLDKPTKGKVIINGVETSGldddTLTRLRRDTVGFVFQQYNLIPT 99 
                                       789******************************************9999988885556667789************* PP

                                       SBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       lt+ en           ++e+ +ka + l+l++l++  +k++p+++SgGq+qrva+aral+++p++ll+DEpt
  gi|488599924|ref|YP_007906395.1| 100 LTAIENvelpmifkgiSKREREKKAFELLNLVGLEK-EAKRKPNEMSGGQQQRVAIARALANNPEILLCDEPT 171
                                       **99999********966666777777777777444.446788*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   0.00016      0.11       1      26 [.      35      57 ..      35      99 .. 0.74
   2 !   28.6   0.0   1.7e-09   1.2e-06     230     301 ..     137     205 ..     106     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarld 26
                                      + ++ Gp gsGKS+LL  + +l   d
  gi|488599924|ref|YP_007906395.1| 35 FIAIMGPSGSGKSTLLNMIGCL---D 57
                                      57899***********999988...3 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.7e-09
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                        ++ ++e+S G+++  a++ al+  +    +ll DEp  +L+ k  ++++++l+el+++g+ +i++TH+p++
  gi|488599924|ref|YP_007906395.1| 137 AKRKPNEMSGGQQQRVAIARALANNP---EILLCDEPTGNLDTKSGEKIMQILSELNERGVTLIIVTHDPSI 205
                                       45678999******989999999888...9***********************999999***********98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.3   4.3e-11   2.8e-08      24     212 ..      33     216 ..      15     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 4.3e-11
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--....BTTCSSTTEEEEEEEEEETTEESSSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk....skekasvkkaeveitfdnedkklkiekee 96 
                                        +f ai+Gp GSGKs ll+ i  +L + ++ k+  + ++          ++  ++ + +v  +f++ +   ++ +  
  gi|488599924|ref|YP_007906395.1|  33 GEFIAIMGPSGSGKSTLLNMI-GCLDKPTKGKVIINGVE----TsgldDDTLTRLRRDTVGFVFQQYNLI-PTLTAI 103
                                       3699****************9.67775544343333333....123336788999999999999998887.666666 PP

                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                        +++  ++ kg s+ + ++k  +  ++  l ++a+ +++++SgG+++ va+a  +A    +p  + l De   +LD 
  gi|488599924|ref|YP_007906395.1| 104 ENVELPMIFKGISKREREKKAFELLNLVGLEKEAKRKPNEMSGGQQQRVAIARALAN---NP-EILLCDEPTGNLDT 176
                                       678888888999999999999999999999999999999***********9988773...34.47789********* PP

                                       HHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                       k  +k+ ++l e +++ + +i+++++  + e a+k+v++ 
  gi|488599924|ref|YP_007906395.1| 177 KSGEKIMQILSELNERgVTLIIVTHDPSIAEYANKTVRIL 216
                                       ************9998799*****************9985 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.8e-08   2.6e-05      12      42 ..      23      53 ..      20      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.8e-08
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAi 42
                                      ++g ++e+++ +++ ++GpsGsGKSTll  i
  gi|488599924|ref|YP_007906395.1| 23 LNGVSMEVKRGEFIAIMGPSGSGKSTLLNMI 53
                                      677899999777***************9655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.1e-06    0.0054       4      25 ..      32      53 ..      28      90 .. 0.88
   2 ?    4.3   0.0     0.069        46      59     130 ..     126     201 ..     113     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.1e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                      +  +++++G+sG+GK+tll+++
  gi|488599924|ref|YP_007906395.1| 32 RGEFIAIMGPSGSGKSTLLNMI 53
                                      6789**************9976 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.069
                            AAA_22  59 ellralglelkaerlsseellealeqalrarav...ielliiDEaqh.lr..seealeeLrsllnlsrkgvqliLvG 129
                                       ell+ +gle++a+r+ +e    + ++ + ara    +e+l+ DE    l+  s e + ++ s ln  + gv+li+v 
  gi|488599924|ref|YP_007906395.1| 126 ELLNLVGLEKEAKRKPNEMSGGQQQRVAIARALannPEILLCDEPTGnLDtkSGEKIMQILSELN--ERGVTLIIVT 200
                                       68888999999966666666666666655555579999******887798765555555545557..8888888775 PP

                            AAA_22 130 t 130
                                       +
  gi|488599924|ref|YP_007906395.1| 201 H 201
                                       5 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   5.3e-07   0.00035      78     119 ..      11      53 ..       3      71 .. 0.78
   2 ?   -2.8   0.0       7.9   5.3e+03      35      51 ..     182     198 ..     173     212 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.3e-07
                                       EEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                       +++++  ++  +l+ ++ ++k  ++++++G+SG GKStL+n++
  gi|488599924|ref|YP_007906395.1|  11 KIYKIGGEEVYALNGVSMEVKRgEFIAIMGPSGSGKSTLLNMI 53 
                                       5555555666666667767766699****************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.9
                                       HHHHHHHHHHTT-EEEE CS
                       RsgA_GTPase  35 ldrfLvlaeekgiepvi 51 
                                       + ++L +++e+g++++i
  gi|488599924|ref|YP_007906395.1| 182 IMQILSELNERGVTLII 198
                                       33444444444444444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.3e-06   0.00088       3      48 ..      36      81 ..      34      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                      EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHC CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellre 48
                                      + + G+ GsGK+tLln +    +  k  vi+N + + ++D + l++
  gi|488599924|ref|YP_007906395.1| 36 IAIMGPSGSGKSTLLNMIGCLDKPTKGKVIINGVETSGLDDDTLTR 81
                                      6799**************999999************9**9998854 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   0.00028      0.18      32      68 ..      17      54 ..       1      65 [. 0.75
   2 ?    5.7   0.0     0.017        11     104     155 ..     157     209 ..     142     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                         IstB_IS21 32 krkvkeLatlsf.iekkenivllGpsGvGKshlaialg 68
                                       ++v +L + s  +++ e i+++GpsG GKs l   +g
  gi|488599924|ref|YP_007906395.1| 17 GEEVYALNGVSMeVKRGEFIAIMGPSGSGKSTLLNMIG 54
                                      556667766665489999*************9977666 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                         IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfeviekryerrs..iiitsnlpfaewd 155
                                       +   ++++l+ D+  + +ld ++ e++++++++  er    ii+t + ++ae+ 
  gi|488599924|ref|YP_007906395.1| 157 ALANNPEILLCDEP-TGNLDTKSGEKIMQILSELNERGVtlIIVTHDPSIAEYA 209
                                       33445678888875.6789*****************976225678888888875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   4.3e-06    0.0028      11      44 ..      22      53 ..      17     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                            AAA_16 11 qLlsalervrsgrpelvllsGesGvGKsslvrel 44
                                      +L+ +   v++g  e + + G+sG+GKs+l++++
  gi|488599924|ref|YP_007906395.1| 22 ALNGVSMEVKRG--EFIAIMGPSGSGKSTLLNMI 53
                                      555555556666..79***************876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0013      0.85       2      36 ..      36      72 ..      35      89 .. 0.75
   2 ?    5.2   0.1     0.027        18      88     140 ..     153     208 ..     117     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                                      EEEE--TTSSHHHHHHHH..HHHH...GGGEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkv..lellkssgvkvgGfyte 36
                                      ++i Gp+G+GK+Tl++ +  l++  +  v ++G+ t+
  gi|488599924|ref|YP_007906395.1| 36 IAIMGPSGSGKSTLLNMIgcLDKPTKGKVIINGVETS 72
                                      6899***********9982234444556777777776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.027
                                       HHHHHH.HHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHH CS
                          NTPase_1  88 alrkal.seadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrkdlal 140
                                       a+ +al +++++++ DE  G++  ks + + ++   L+ +++ +++v h ++  + 
  gi|488599924|ref|YP_007906395.1| 153 AIARALaNNPEILLCDEpTGNLDTKSGEKIMQILSELNeRGVTLIIVTHDPSIAEY 208
                                       34444448999******88******9888888777777799999999999973333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.8   5.6e-05     0.037       2      19 ..      36      53 ..      35     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-05
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      +ai+G + +GKStL+n +
  gi|488599924|ref|YP_007906395.1| 36 IAIMGPSGSGKSTLLNMI 53
                                      89**************88 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.9e-05     0.026      21      39 ..      35      53 ..      21      56 .. 0.88
   2 ?   -0.5   0.1       2.2   1.4e+03     109     109 ..     128     128 ..      58     192 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-05
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                      + +I Gp G+GK+T+l+ i
  gi|488599924|ref|YP_007906395.1| 35 FIAIMGPSGSGKSTLLNMI 53
                                      578*************987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.2
                            AAA_23 109 l 109
                                       l
  gi|488599924|ref|YP_007906395.1| 128 L 128
                                       1 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   3.3e-05     0.022       5      33 ..      36      71 ..      32     128 .. 0.74
   2 ?   -3.1   0.0       8.1   5.4e+03     108     130 ..     179     201 ..     173     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                            AAA_24  5 iliyGpsgiGKTtlakel.......gpkplfidtek 33
                                      i+i+Gpsg+GK+tl++++       + k+++  +e 
  gi|488599924|ref|YP_007906395.1| 36 IAIMGPSGSGKSTLLNMIgcldkptKGKVIINGVET 71
                                      89**************99888877666666666666 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.1
                            AAA_24 108 aeefrrllkklqelrknvifiah 130
                                       +e+++++l  l+e + + i++ h
  gi|488599924|ref|YP_007906395.1| 179 GEKIMQILSELNERGVTLIIVTH 201
                                       56677777777777778888777 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    0.0004      0.27      21      40 ..      34      53 ..      20      64 .. 0.85
   2 ?    1.4   0.0      0.22   1.5e+02      65     148 ..     121     210 ..      76     217 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       ++a++G  G+GK+tl++ i
  gi|488599924|ref|YP_007906395.1| 34 EFIAIMGPSGSGKSTLLNMI 53
                                      499*************9876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                                       HHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEEEE...-SHHHH.....HHHH.CHTTSEE CS
                            NB-ARC  65 seeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlDDV...weeedwdkigvvlpa.renrlrv 134
                                       +++ +e +l+ ++l+++   + +e          + r+L +   +l+ D      +++  +ki++ l++ +e+++  
  gi|488599924|ref|YP_007906395.1| 121 EKKAFE-LLNLVGLEKEAKRKPNEMSGgqqQRVAIARALANNPEILLCDEPtgnLDTKSGEKIMQILSElNERGVTL 196
                                       444444.3333333333333333322243355566666666666666665411133444556666555424555666 PP

                                       EEEESBCCCCCCS- CS
                            NB-ARC 135 llTTRdeevanavs 148
                                       ++ T d ++a++++
  gi|488599924|ref|YP_007906395.1| 197 IIVTHDPSIAEYAN 210
                                       66666666666655 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   0.00011     0.075      31      50 ..      31      50 ..      23      91 .. 0.90
   2 ?   -2.2   0.0       3.9   2.6e+03     128     186 ..     180     199 ..     147     201 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            AAA_25 31 pagelallaGapgtGKttla 50
                                       +ge+++++G++g+GK+tl+
  gi|488599924|ref|YP_007906395.1| 31 KRGEFIAIMGPSGSGKSTLL 50
                                      68****************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllv 186
                                       +++ ++  +++e  gv l++                                      v
  gi|488599924|ref|YP_007906395.1| 180 EKIMQILSELNE-RGVTLII--------------------------------------V 199
                                       344444455555.4455555......................................4 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.08     125     149 ..      29      53 ..      11      88 .. 0.84
   2 ?   -0.7   0.0      0.86   5.7e+02      94     155 ..     116     188 ..      90     213 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                             T2SSE 125 avrerglilvsGgTgsGKttllyal 149
                                        v++   i + G+ gsGK+tll+++
  gi|488599924|ref|YP_007906395.1|  29 EVKRGEFIAIMGPSGSGKSTLLNMI 53 
                                       566777899*************975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.86
                             T2SSE  94 viRkksakeltlddlgaeealk..........ekiaevlrkavrerglilv.sGgTgsGKttllyallkeink 155
                                       + R++++k+++l +l+  e+ +          ++++ ++++a++++  il+   +Tg   t +   +++++ +
  gi|488599924|ref|YP_007906395.1| 116 SKREREKKAFELLNLVGLEKEAkrkpnemsggQQQRVAIARALANNPEILLcDEPTGNLDTKSGEKIMQILSE 188
                                       4466666666666655555444455777777655555555555555544441346665555554433333333 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00017      0.11      17      40 ..      30      53 ..      18     141 .. 0.72
   2 ?   -0.0   0.1         1   6.9e+02      97     123 ..     173     199 ..     110     208 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkei 40
                                       ++ e++ i Gp gsGK++Ll+ i
  gi|488599924|ref|YP_007906395.1| 30 VKRGEFIAIMGPSGSGKSTLLNMI 53
                                      55678999*************865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1
                          ATPase_2  97 eksklvfkaielllekikkkgkkiiii 123
                                       +  ++  ++i ++l +++++g  +ii+
  gi|488599924|ref|YP_007906395.1| 173 NLDTKSGEKIMQILSELNERGVTLIIV 199
                                       344445677888889999999887766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0045         3      24      46 ..      33      56 ..      22      77 .. 0.80
   2 ?    4.4   0.0     0.038        25     321     369 .]     159     206 ..      99     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0045
                            AAA_15 24 e.ltvliGkNnsGKSsilealdlF 46
                                        +  + G+ +sGKS++l+++  +
  gi|488599924|ref|YP_007906395.1| 33 GeFIAIMGPSGSGKSTLLNMIGCL 56
                                      44899**************99655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.038
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                        +++ ill +EP  +L ++  + +++ l el + +   +ii TH p i+
  gi|488599924|ref|YP_007906395.1| 159 ANNPEILLCDEPTGNLDTKSGEKIMQILSELNERGV-TLIIVTHDPSIA 206
                                       345678999*********************999997.9********985 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 ?    7.2   0.1    0.0028       1.9     240     264 ..      28      53 ..      22      57 .. 0.90
   2 ?    3.0   0.0     0.053        35     322     378 ..     143     199 ..     134     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0028
                                       EEE-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAl 264
                                       m +++G  ++I+G+   GKsTLL+ +
  gi|488599924|ref|YP_007906395.1|  28 MEVKRGeFIAIMGPSGSGKSTLLNMI 53 
                                       8899999999*************976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.053
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHH CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvd 378
                                       + SG   q ++i++al ++ ++lL DE t         + mq l + +++++t ++ 
  gi|488599924|ref|YP_007906395.1| 143 EMSGGQQQRVAIARALANNPEILLCDEPTGNLDTKSGEKIMQILSELNERGVTLIIV 199
                                       569999*********************987766666677777777777777766665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2    0.0003       0.2       3      19 ..      37      53 ..      35     214 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                            AAA_33  3 llvGlpGsGKstlaerl 19
                                       + G++GsGKstl+  +
  gi|488599924|ref|YP_007906395.1| 37 AIMGPSGSGKSTLLNMI 53
                                      578**********9865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00047      0.31      19      50 ..      34      65 ..      27      80 .. 0.83
   2 ?   -0.3   0.0       1.1   7.5e+02      86     114 ..     159     188 ..     120     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       + ++ Gp G+GK+t+l+ +  + +  +g+vi
  gi|488599924|ref|YP_007906395.1| 34 EFIAIMGPSGSGKSTLLNMIGCLDKPTKGKVI 65
                                      47789*************99887777766666 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                            AAA_30  86 lepgtllivDE.agmvdtkqlaallkaaek 114
                                        ++ ++l+ DE +g +dtk+ +++++++++
  gi|488599924|ref|YP_007906395.1| 159 ANNPEILLCDEpTGNLDTKSGEKIMQILSE 188
                                       333378888886677788777766665544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0004      0.26       1      16 [.      36      51 ..      36      97 .. 0.91
   2 ?   -1.0   0.0       3.7   2.5e+03      44      82 ..     171     201 ..     134     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                            AAA_18  1 IlltGtpGvGKttlak 16
                                      I+++G++G+GK+tl +
  gi|488599924|ref|YP_007906395.1| 36 IAIMGPSGSGKSTLLN 51
                                      89***********976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.7
                            AAA_18  44 ealdeskrldedkldklldaleenssaleegknlvidgh 82 
                                               ld++  +k++++l e +   e g +l+i  h
  gi|488599924|ref|YP_007906395.1| 171 T-----GNLDTKSGEKIMQILSELN---ERGVTLIIVTH 201
                                       3.....3334444444444444443...35555555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00074      0.49       2      18 ..      36      52 ..      35      67 .. 0.90
   2 ?   -0.2   0.0       1.6   1.1e+03      65      80 ..     154     169 ..     129     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00074
                            AAA_28  2 ivitGgestGKTtllea 18
                                      i+i+G++++GK+tll+ 
  gi|488599924|ref|YP_007906395.1| 36 IAIMGPSGSGKSTLLNM 52
                                      89************986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                            AAA_28  65 eeeaaaaankvlfcDr 80 
                                        + a a+++++l+cD 
  gi|488599924|ref|YP_007906395.1| 154 IARALANNPEILLCDE 169
                                       1224458999999995 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002      0.13      34      67 ..      22      55 ..       9     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                             Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                      +l+  ++e ++ + + i GPsG gkst ++++  
  gi|488599924|ref|YP_007906395.1| 22 ALNGVSMEVKRGEFIAIMGPSGSGKSTLLNMIGC 55
                                      577778888888899************9988754 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0021       1.4      23      88 ..     134     186 ..     116     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                           SbcCD_C  23 ekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       eke +r+ +++SGG++q    +a+a     ++ +      ++++++ DE  ++lD +s ++++++l
  gi|488599924|ref|YP_007906395.1| 134 EKEAKRKPNEMSGGQQQR---VAIA----RALAN------NPEILLCDEPTGNLDTKSGEKIMQIL 186
                                       566788888999999943...3333....33333......47889999999999999999999887 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00044      0.29       1      18 [.      36      53 ..      36      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00044
                                      EEEE-STTSSHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaral 18
                                      iai GP+gsGKs++  ++
  gi|488599924|ref|YP_007906395.1| 36 IAIMGPSGSGKSTLLNMI 53
                                      89***********97665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0003       0.2      26      50 ..      36      60 ..      24     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                      EEEEESTTSSHHHHHHHHHHHCS-- CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkg 50
                                      + ++G s+SGKsT+l+ + +l k++
  gi|488599924|ref|YP_007906395.1| 36 IAIMGPSGSGKSTLLNMIGCLDKPT 60
                                      7799**************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1398.97
//
Query:       gi|488599925|ref|YP_007906396.1|  [L=450]
Description: hypothetical protein Asulf_00374 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.023   14.9   0.0       0.31   11.3   0.0    2.5  2  ASH              Abnormal spindle-like microcephaly-assoc'd, 
       0.31   11.1   4.8        2.1    8.4   0.7    2.8  3  CarbopepD_reg_2  CarboxypepD_reg-like domain


Domain annotation for each model (and alignments):
>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.068   6.1e+02      60      97 ..      77     113 ..      48     114 .. 0.82
   2 ?   11.3   0.0   3.5e-05      0.31      19      95 ..     228     304 ..     213     307 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.068
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               ASH  60 levqpgesvtltvtwtPteegavrevLqflvndvlkhq 97 
                                        e++ g+s+ l +t + +++g+ +  +++++n  +k+q
  gi|488599925|ref|YP_007906396.1|  77 GEISRGSSYELPITIKAKKAGTYKVEMTIVGNT-TKKQ 113
                                       68889999999999999****999999999995.4444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.5e-05
                                       ---EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX CS
                               ASH  19 vkvGssaerlLtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvtwtPteega..vrevLqflvndv 93 
                                        ++G  +  +L+++N  e+++  +v ++   +  +   ++   ++p+++  lt  ++P+++g+  +++ ++f ++  
  gi|488599925|ref|YP_007906396.1| 228 LAIGDVTPITLKLTNLREDTIYRIVATAT--SDSYREVKELAILEPKQTAILTYRFSPSKAGEneITFSITFDDDLG 302
                                       56777777778888887777333333333..2222222333889*****************9866888888877765 PP

                                       XX CS
                               ASH  94 lk 95 
                                       ++
  gi|488599925|ref|YP_007906396.1| 303 NS 304
                                       55 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.7   0.00023       2.1      37      86 ..      90     138 ..      89     139 .. 0.86
   2 ?    3.2   0.1    0.0095        86      30      70 ..     172     215 ..     167     227 .. 0.74
   3 ?   -2.4   0.0      0.57   5.1e+03      36      53 ..     279     296 ..     278     325 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00023
                   CarbopepD_reg_2  37 elknlpagkytLvvsyvGyktqekkvtvskektldvnillkeealeleev 86 
                                       ++k+++ag+y++ ++ vG +t+++  +v    +   +i lk+++++l+ev
  gi|488599925|ref|YP_007906396.1|  90 TIKAKKAGTYKVEMTIVGNTTKKQIFNVVVLDKY-PSIILKKTKIMLNEV 138
                                       68999****************9999998755444.479999999****99 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0095
                   CarbopepD_reg_2  30 TdenGnFelknlpagkytLvvsyvG...yktqekkvtvskektl 70 
                                       +  +G+F++ +++a+  ++++s++    y++  ++v+v+ ++++
  gi|488599925|ref|YP_007906396.1| 172 STIDGSFKFLAKEAKPLKFRISFYNgrnYHEIVQTVNVDYKESK 215
                                       5579******************9742337777777777655554 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.57
                   CarbopepD_reg_2  36 FelknlpagkytLvvsyv 53 
                                       ++++  +ag+ ++++s  
  gi|488599925|ref|YP_007906396.1| 279 YRFSPSKAGENEITFSIT 296
                                       777777888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2867.68
//
Query:       gi|488599926|ref|YP_007906397.1|  [L=136]
Description: hypothetical protein Asulf_00375 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-14   51.3   0.1    1.7e-13   50.3   0.1    1.6  1  Methyltranf_PUA  RNA-binding PUA-like domain of methyltransfe
     0.0021   18.1   0.0     0.0039   17.2   0.0    1.5  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 !   50.3   0.1   1.9e-17   1.7e-13       1      49 [.      86     135 ..      86     136 .] 0.94

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.9e-17
                   Methyltranf_PUA   1 alrYlkGetielep.dlkkGwvlVcydgyplGwgKlvggrlKNkyPkglR 49 
                                       alr+++Ge ie+++ d  +G+v+++y+ y +G+gKl++g+++N++Pk++R
  gi|488599926|ref|YP_007906397.1|  86 ALRWMRGEAIEINQtDVSEGYVILKYGSYFIGCGKLRNGKIINFVPKDRR 135
                                       89***********976677*****************************99 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 !   17.2   0.0   4.4e-07    0.0039       3      52 ..      79     126 ..      78     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.4e-07
                          TruB-C_2   3 veLseesakrflqGQrvklaaglpaeglVRvydeegrFlGvGeitddgvl 52 
                                       ve++ee a r++ G ++++++++ +eg V +   +  F+G G+ + +g++
  gi|488599926|ref|YP_007906397.1|  79 VEVDEEKALRWMRGEAIEINQTDVSEGYVILK-YGSYFIGCGKLR-NGKI 126
                                       99*************************99885.8999******99.7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 899.40
//
Query:       gi|488599927|ref|YP_007906398.1|  [L=312]
Description: tRNA (cytosine-48,49-C(5)-) methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  183.7   0.0    4.5e-54  183.1   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.4e-19   70.4   0.0    2.7e-19   69.4   0.0    1.5  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    1.8e-06   28.2   0.0      3e-06   27.4   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
      4e-06   26.7   0.1    8.9e-06   25.6   0.1    1.6  1  Met_10           Met-10+ like-protein
    0.00011   22.8   0.1      0.034   14.9   0.1    3.1  2  Methyltransf_25  Methyltransferase domain
    0.00023   21.0   0.0    0.00038   20.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0097   15.3   0.1      0.017   14.5   0.1    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.031   14.0   0.0    1.6  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.062   12.9   0.1       0.13   11.9   0.1    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.14   11.8   0.0       0.22   11.1   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95


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 !  183.1   0.0   2.5e-57   4.5e-54       2     199 ..     105     308 ..     104     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 183.1 bits;  conditional E-value: 2.5e-57
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                       ++L+ +++ ++lD++a+PGgKTt ia  m+n+g+++A+d++ +R++ +++n+++ gvtn+iv+ +D+r + ++    
  gi|488599927|ref|YP_007906398.1| 105 VVLDVRQGMMVLDMAASPGGKTTQIASYMENTGCIIANDVKFSRVNILISNIQKCGVTNAIVTMMDGRAFGRFEN-- 179
                                       58999999**************************************************************87766.. PP

                                       .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLk 155
                                       +fDr+LlDaPCs  g+ir++ +     k++d+++l++lqk+l+ +a + lk+gGvlvYsTC++ +eEne+vi+++Lk
  gi|488599927|ref|YP_007906398.1| 180 TFDRVLLDAPCSNVGMIRKNFKYLKIWKQRDVIALSRLQKQLIRSAYKALKEGGVLVYSTCTLDPEENEAVIDSLLK 256
                                       6*******************8877777889**********************************************9 PP

                                       H-.TTEEEESSBSTTSTTSSECEEC..........TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 156 kr.edvelvetelsepkglklgeea..........gtlrllPhtenkdgffiakl 199
                                       ++ + ve ++++++ ++  +                 lr+ P+ ++++gff+ak+
  gi|488599927|ref|YP_007906398.1| 257 TTsARVEKIDLPVKRTRCFRE---FdgvefddsvkHCLRIHPQDNDTEGFFVAKI 308
                                       872345555555443222221...12334455556789***************96 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   1.5e-22   2.7e-19       2      90 .]      10     101 ..       9     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.5e-22
                                       -HHHHHHHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH.-SS--B-TT-TTEEES---.......TT CS
                   Methyltr_RsmF_N   2 PeeFiekmkellgeeaeaflaaleeprkkglRvNtlKisveeleklse.efelepvpwceeGfyleeeerp....gk 73 
                                       + eF e+++  l ++ ++f++++ +p +k++RvNtlK++v+ + +  + +f+le+vpwc+eGf++e e +     +k
  gi|488599927|ref|YP_007906398.1|  10 NPEFFERYS--LIDSSDEFIDYMLKPLRKSIRVNTLKADVDVVVNNLKrNFRLERVPWCREGFFVEGEIEGemeiTK 84 
                                       567777776..457899**********************9987665555****************9986555566** PP

                                       SHHHHTTS-EE--TTTH CS
                   Methyltr_RsmF_N  74 hplheaGlyYiQEpSam 90 
                                       +++h+ Gl+++QE+S+m
  gi|488599927|ref|YP_007906398.1|  85 TMEHQLGLIFSQEASSM 101
                                       ****************9 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.7e-09     3e-06      20     147 ..     110     253 ..      80     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.7e-09
                                       -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHH.......SSEE CS
                              FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealse.......rkvd 89 
                                       ++g+ v+D +a+PGg +  ++  ++++g ++a D++     ++v+++  +i++  + ++i +++++       + +d
  gi|488599927|ref|YP_007906398.1| 110 RQGMMVLDMAASPGGKTTQIASYMENTGCIIANDVKF----SRVNILISNIQKCGVTNAIVTMMDGrafgrfeNTFD 182
                                       47788***************9**999999*****987....89*****************998888999999999** PP

                                       EEEE--S.-SS-CHHHHHHHHH..........CCCCHHHHCCHCCCCECCCEEEECCCH..CCCHHHHHHH CS
                              FtsJ  90 lvvsDga.pdvsgvhdldeylq..........sqLllaalelalkllkpggtfvlkifr..geeteallkq 147
                                        v+ D   ++v  +++  +yl+          s+L ++ ++ a k lk+gg++v  +++   ee ea++  
  gi|488599927|ref|YP_007906398.1| 183 RVLLDAPcSNVGMIRKNFKYLKiwkqrdvialSRLQKQLIRSAYKALKEGGVLVYSTCTldPEENEAVIDS 253
                                       *****6437888889999999999999999999*********************99988754444466665 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1     5e-09   8.9e-06      95     189 ..     106     204 ..      91     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5e-09
                                       HTT--TT-EEEETT-TTTCCHHHCCHHT.TSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-E CS
                            Met_10  95 aklveegevVvdvfAGiGpfaipiakys.kakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqla 169
                                       +  v++g +V+d+ A  G  +  ia y  +   ++a+d+  + v+ l +ni+   v + + + ++Dgr + r e+++
  gi|488599927|ref|YP_007906398.1| 106 VLDVRQGMMVLDMAASPGGKTTQIASYMeNTGCIIANDVKFSRVNILISNIQKCGVTNAI-VTMMDGRAFGRfENTF 181
                                       556899****************99999725678***************************.889********9**** PP

                                       EEEEE--TTTGGGGHHH...HHH CS
                            Met_10 170 drvvmnlpksaieFldk...vla 189
                                       drv++++p s +  + k    l+
  gi|488599927|ref|YP_007906398.1| 182 DRVLLDAPCSNVGMIRKnfkYLK 204
                                       *9999999988888887333334 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.051        91      14      56 ..       8      48 ..       4      60 .. 0.80
   2 !   14.9   0.1   1.9e-05     0.034       1      70 [.     115     186 ..     115     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.051
                                      HHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCC CS
                   Methyltransf_25 14 alakrlgkakvtgvDiseemleaareraeeeglnvefvqgdae 56
                                      +l  ++  +++  +D s+e+++++ + +++ +++v+ +++d++
  gi|488599927|ref|YP_007906398.1|  8 KLNPEF-FERYSLIDSSDEFIDYMLKPLRK-SIRVNTLKADVD 48
                                      566666.589999***********999965.589999999985 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.9e-05
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       vLd+++ +G  t ++a  + + + +++ D+  + +++  +++++ g+ n+ +  +d +++   +++fD v++
  gi|488599927|ref|YP_007906398.1| 115 VLDMAASPGGKTTQIASYMeNTGCIIANDVKFSRVNILISNIQKCGVtNAIVTMMDGRAFGRFENTFDRVLL 186
                                       9*****************9769**********************9999999*********99999*****98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.1e-07   0.00038       3     113 ..     111     241 ..     109     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.1e-07
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +g+ vlD ++  G +t ++a+ +   + ++  D +   ++   +n qk g++n+ +   d  ++   +e ++fD +l
  gi|488599927|ref|YP_007906398.1| 111 QGMMVLDMAASPGGKTTQIASYMENTGCIIANDVKFSRVNILISNIQKCGVTNAIVTMMDGRAFGR-FE-NTFDRVL 185
                                       7899*****************9999999************************98888888888665.66.99***** PP

                   Methyltransf_31  80 sn......................evlnaladpdkileeiervlkpggilliedpr 113
                                        +                      +v+++   +++ ++++ ++lk+gg+l+ +++ 
  gi|488599927|ref|YP_007906398.1| 186 LDapcsnvgmirknfkylkiwkqrDVIALSRLQKQLIRSAYKALKEGGVLVYSTCT 241
                                       **8888888888888888888888888***************************99 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   9.3e-06     0.017      45     168 ..     109     228 ..     102     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.3e-06
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvt 121
                                       v++g  vlD+a+  g  + ++++ ++++g ++  D++ + +++    +++ g++n    + ++ ++   +++fD v 
  gi|488599927|ref|YP_007906398.1| 109 VRQGMMVLDMAASPGGKTTQIASYMENTGCIIANDVKFSRVNILISNIQKCGVTNAIVTMMDGRAFGRFENTFDRVL 185
                                       7899**************************************************9999999**************** PP

                                       EES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHH CS
                   Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayel 168
                                       +     nv      +++ ++ lk   +  v+ +s+ + +l++ ay++
  gi|488599927|ref|YP_007906398.1| 186 LDAPCSNVG----MIRKNFKYLKIWKQRDVIALSRLQKQLIRSAYKA 228
                                       999999987....566778899999999****************987 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05     0.031      69     152 ..     107     190 ..      83     196 .. 0.89
   2 ?   -2.3   0.0       1.7     3e+03     155     170 ..     221     236 ..     210     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                       TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEE CS
                              PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYda 145
                                       l++++g+ vL++ +  G +t  +a +++++g +++ +   + v+    n++k +++n iv++ DGr     +  +d+
  gi|488599927|ref|YP_007906398.1| 107 LDVRQGMMVLDMAASPGGKTTQIASYMENTGCIIANDVKFSRVNILISNIQKCGVTNAIVTMMDGRAFGRFENTFDR 183
                                       7799*************************************************************987677777888 PP

                                       EEESSBB CS
                              PCMT 146 ihvgaaa 152
                                       +++ a  
  gi|488599927|ref|YP_007906398.1| 184 VLLDAPC 190
                                       8777655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                       --HHHHHTEEEEEEEE CS
                              PCMT 155 iPealidQLkeGGrlv 170
                                       + ++  + LkeGG lv
  gi|488599927|ref|YP_007906398.1| 221 LIRSAYKALKEGGVLV 236
                                       4555567799999888 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.1e-05      0.13       3      60 ..     114     175 ..     112     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.1e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfek...viaieinleklacaqhNaevYgvsdki.tlvlgdvfe 60 
                                       ++lD+ +  GG++ q+a + e+   +ia +++ +++++   N +  gv + i t++ g  f 
  gi|488599927|ref|YP_007906398.1| 114 MVLDMAASPGGKTTQIASYMENtgcIIANDVKFSRVNILISNIQKCGVTNAIvTMMDGRAFG 175
                                       699***************97652226778999****************87761555666555 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.22      45     148 ..     115     212 ..     104     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       EEETT-TTSHHHHHHHHTT-SEEEEEES-HH..HHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE CS
                     Cons_hypoth95  45 vLDlfaGsGalglEAlSRgakkavlvekdke..avkilkenleelkleeetaelkedaleallklakkkeefdivfl 119
                                       vLD+ a  G+     +S   +   ++ +d +   v+il  n++++++++  a++ + + +a+ +    ++ fd v l
  gi|488599927|ref|YP_007906398.1| 115 VLDMAASPGGKTTQIASYMENTGCIIANDVKfsRVNILISNIQKCGVTN--AIVTMMDGRAFGRF---ENTFDRVLL 186
                                       5555555555555555555555555555554115779*********998..66666666777666...456****** PP

                                       --SSSTTCH.HHHHHHHHHTT-EEEEEEE CS
                     Cons_hypoth95 120 DPPyakellieevlelleekkllkenalv 148
                                       D P  ++ +i++ +++l+   + k++ ++
  gi|488599927|ref|YP_007906398.1| 187 DAPCSNVGMIRKNFKYLK---IWKQRDVI 212
                                       **************9998...44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2018.05
//
Query:       gi|488599928|ref|YP_007906399.1|  [L=236]
Description: dihydroorotate oxidase B, electron transfer subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-13   47.9   4.1    1.4e-12   47.2   4.1    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    9.4e-07   29.5   0.0    3.2e-05   24.5   0.0    2.2  1  NAD_binding_1    Oxidoreductase NAD-binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   4.1   1.6e-16   1.4e-12       1      41 [.     198     231 ..     198     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.6e-16
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e++M+CG+G+C+ Cv+k          rvC++GPvF ++e+
  gi|488599928|ref|YP_007906399.1| 198 ESYMKCGIGVCGTCVLKD-------GSRVCVEGPVFSGEEL 231
                                       89****************.......47************98 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 !   24.5   0.0   3.6e-09   3.2e-05       1     104 [.      93     177 ..      93     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.6e-09
                                       EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSH CS
                     NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrv 77 
                                       ++agG G aP++ + + + +      +v++++G +t++dl+ ++++e+++ +             +e+g+eg +g+v
  gi|488599928|ref|YP_007906399.1|  93 LVAGGIGSAPLYYLHDYLKN---LGAEVHVIFGGKTSADLIWKDRFESVELS-------------TEDGSEGYEGTV 153
                                       79*********976666555...579***************99999999333.............344667899*** PP

                                       HHHHHHHHHHHSSTTEEEEEECSHHHH CS
                     NAD_binding_1  78 qdalleellslkkeethvyvCGppgMi 104
                                        d ++ + l+   + + +y+CGp+gM 
  gi|488599928|ref|YP_007906399.1| 154 IDLMRGKDLE---GFDKIYICGPEGML 177
                                       *999666555...899**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1726.94
//
Query:       gi|488599929|ref|YP_007906400.1|  [L=294]
Description: dihydroorotate oxidase B, catalytic subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-57  192.7   0.0    9.4e-57  192.5   0.0    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    2.2e-08   33.9   0.3    4.5e-08   32.9   0.3    1.5  1  NMO           Nitronate monooxygenase
    3.7e-08   32.8   0.0    4.7e-07   29.2   0.0    2.0  1  Dus           Dihydrouridine synthase (Dus)
    1.1e-06   28.3   0.1    2.1e-06   27.4   0.1    1.6  1  His_biosynth  Histidine biosynthesis protein
    0.00032   19.8   0.2    0.00085   18.4   0.0    1.6  2  IMPDH         IMP dehydrogenase / GMP reductase domain
    0.00079   18.6   0.2     0.0056   15.8   0.2    1.9  1  FMN_dh        FMN-dependent dehydrogenase
     0.0056   15.9   0.1     0.0092   15.1   0.1    1.2  1  Glu_synthase  Conserved region in glutamate synthase
     0.0066   15.9   0.1       0.05   13.0   0.0    2.1  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
  ------ inclusion threshold ------
       0.14   11.3   0.0        2.4    7.3   0.0    2.1  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
       0.15   11.2   0.4       0.22   10.6   0.0    1.6  2  DUF561        Protein of unknown function (DUF561)


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 !  192.5   0.0   5.3e-60   9.4e-57       1     292 [.       1     274 [.       1     276 [. 0.92

  Alignments for each domain:
  == domain 1  score: 192.5 bits;  conditional E-value: 5.3e-60
                                       GG-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-H CS
                            DHO_dh   1 slatkvlglkfknpiglAaGfdkegeeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGl 77 
                                       +l++++  l+++np++lA+G+ +  ++ l+ l   +ga+  +sv+ +++eG  +P v++++++  +lN++Gl ++G+
  gi|488599929|ref|YP_007906400.1|   1 MLEVQISSLTLQNPLILASGILGSYSSSLNRLSEHAGALVAKSVGIEEREGYRNPVVVNTPHG--LLNAVGLSSPGA 75 
                                       799************************************************************..************ PP

                                       HHHHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCCTS.CCCGCHHHHHHHH CS
                            DHO_dh  78 davlekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSsPntpgl.rdlqekeelkail 153
                                       ++ + +l++ r        +  ++s   ++    d++ve++r ++ +ad++elN+S+P+++gl  ++++++el  ++
  gi|488599929|ref|YP_007906400.1|  76 EKFALELENYRGD------AKLIVSLFASN---PDEFVEIARYFD-MADAFELNLSCPHVKGLgLTVGNDPELVGDI 142
                                       ****999998866......33455555555...699****99985.8**************863699********** PP

                                       HHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHH CS
                            DHO_dh 154 lkvvkevskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdia 230
                                       ++ +k+ ++ p+++K++     +  +++a+ + e ++dg++++Nt ++++aid+ s+k++  n  GG sG+a+k++a
  gi|488599929|ref|YP_007906400.1| 143 VRRLKKETSRPIFAKISA---FSSYIEVAKSAEEAGVDGVVAINT-LKGMAIDIGSKKPILSNVSGGYSGEAVKPVA 215
                                       *****************9...566788889999999999999996.78899************************** PP

                                       HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHH CS
                            DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkele 292
                                       +kv+++ly++l+  ipiI++GG +s +D++e + aGAs+vq+++a+ f  + i+  +k+ l+
  gi|488599929|ref|YP_007906400.1| 216 MKVVWDLYEELD--IPIIASGGATSWKDVVEFMLAGASAVQIGSAF-FYSYRIFYSLKESLK 274
                                       ************..********************************.778899999888887 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.3   2.5e-11   4.5e-08     167     226 ..     203     260 ..     144     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.5e-11
                               NMO 167 aGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                       +GG+ G  +v +   +++v    + +diP+iA GG    ++v   + +GAs+vqig++f 
  gi|488599929|ref|YP_007906400.1| 203 SGGYSG-EAV-KPVAMKVVWDLYEELDIPIIASGGATSWKDVVEFMLAGASAVQIGSAFF 260
                                       688888.222.3467889999999999********************************7 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.6e-10   4.7e-07      47     231 ..      82     275 ..      73     294 .] 0.79

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.6e-10
                                       -GGGGGTSCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS CS
                               Dus  47 lseeeeetplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkavei 123
                                       l++ + + +l+v l++s+p++ +e A+  +   ad+ +lN+ CP  k    g G +  ++p+lv +iv+ ++k ++ 
  gi|488599929|ref|YP_007906400.1|  82 LENYRGDAKLIVSLFASNPDEFVEIARYFDM--ADAFELNLSCPHVK----GLGLTVGNDPELVGDIVRRLKKETSR 152
                                       555566689******************9987..***********876....66777779****************** PP

                                       -EEEEEESESSTTTC.HHHHHHHHHHCT-SEE....EEESS..............ECCCTT-C....G--CHHHHHH CS
                               Dus 124 PvtvkirigiddeeenalelakiveaaGaqal....tvHgR..............traqnyeg....tadweaIkev 178
                                       P+ +ki+ +        +e+ak +e+aG++ +    t+ g               +   +y+g    ++  + + ++
  gi|488599929|ref|YP_007906400.1| 153 PIFAKISAFSS-----YIEVAKSAEEAGVDGVvainTLKGMaidigskkpilsnvS--GGYSGeavkPVAMKVVWDL 222
                                       ******99977.....5677778888877655211345555*****9999997442..44554446789999***** PP

                                       HHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHH CS
                               Dus 179 kqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stavkt 231
                                        +++ ip+ia G+ ++++d+ + +   Ga +v ig +  +   +f + ++ +k 
  gi|488599929|ref|YP_007906400.1| 223 YEELDIPIIASGGATSWKDVVEFMLA-GASAVQIGSAFFYSYRIFYSlKESLKA 275
                                       ************************99.********9988888888764444443 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.1e-09   2.1e-06     181     225 ..     217     261 ..     135     264 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.1e-09
                                       HHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHT CS
                      His_biosynth 181 eltkelaeavkipviasGGvgsledlkelksegvdavivgsalye 225
                                       +++ +l e+++ip+iasGG++s +d+ e   +g++av +gsa+++
  gi|488599929|ref|YP_007906400.1| 217 KVVWDLYEELDIPIIASGGATSWKDVVEFMLAGASAVQIGSAFFY 261
                                       56678899***********************************86 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.7   1.3e+03      96     127 ..     155     187 ..     139     194 .. 0.73
   2 !   18.4   0.0   4.7e-07   0.00085     195     239 ..     215     259 ..     207     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.7
                                       EEEE-SSTTHHHHHHHHHHTT-S.EEEEE-STS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             IMPDH  96 gaavgvkedalervkalveagvd.vlvvdsahg 127
                                        a +++ ++++e +k   eagvd v+++++ +g
  gi|488599929|ref|YP_007906400.1| 155 FAKISAFSSYIEVAKSAEEAGVDgVVAINTLKG 187
                                       466777788888888888888885566776665 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.7e-07
                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                       A+  v +  ++ ++p+ia GG ++ +d+v  + aGa+av +Gs +
  gi|488599929|ref|YP_007906400.1| 215 AMKVVWDLYEELDIPIIASGGATSWKDVVEFMLAGASAVQIGSAF 259
                                       566677888999******************************987 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   3.1e-06    0.0056     233     306 ..     189     262 ..     126     266 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                                       HHHTTESEEEE--GGGTSSTT-..--HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHH CS
                            FMN_dh 233 aveaGvdgivvSNHGGRqldga..patidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyg 306
                                       a+++G +  ++SN  G     a  p +++v  ++ e++  +i+++++gG ++ +Dv+  +  GA+av +G +f y 
  gi|488599929|ref|YP_007906400.1| 189 AIDIGSKKPILSNVSGGYSGEAvkPVAMKVVWDLYEEL--DIPIIASGGATSWKDVVEFMLAGASAVQIGSAFFYS 262
                                       44444444444444333322220144455555555555..5********************************997 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 !   15.1   0.1   5.2e-06    0.0092     190     306 ..     139     259 ..     133     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.2e-06
                                       HHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-S.EEEEE...-TT---SSEEHHHHHHB---HHHHHHHH CS
                      Glu_synthase 190 laqliedLkevnkeakvsvKlvaeagvetiaagvakanad.iilid...GleGGTGAspkssikhaGlPlelalaev 262
                                       + + ++ Lk+ + + +++ K+ a + +  +a  + +a++d +++i+   G+    G  +  + + +G     a+  v
  gi|488599929|ref|YP_007906400.1| 139 VGDIVRRLKKET-SRPIFAKISAFSSYIEVAKSAEEAGVDgVVAINtlkGMAIDIGSKKPILSNVSGGYSGEAVKPV 214
                                       567899999988.99**********99999999******94445651115555789999999999988877777665 PP

                                       .HHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHH CS
                      Glu_synthase 263 .dqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaa 306
                                         +++ +      + +ia+Gg  + +dvv  ++ GA av+ig+a 
  gi|488599929|ref|YP_007906400.1| 215 aMKVVWDLYEELDIPIIASGGATSWKDVVEFMLAGASAVQIGSAF 259
                                       156666666677899***************************986 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.24   4.4e+02     124     147 ..     136     161 ..     130     194 .. 0.58
   2 !   13.0   0.0   2.8e-05      0.05     127     167 ..     215     255 ..     209     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.24
                                       SGGGHHHHCTSTTS...EEEE..ESS CS
                      G3P_antiterm 124 Pglvpkvikeikkelkipiia..GGL 147
                                       P lv ++++++kke++ pi+a  + +
  gi|488599929|ref|YP_007906400.1| 136 PELVGDIVRRLKKETSRPIFAkiSAF 161
                                       66677777788888877777644223 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.8e-05
                                       GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                       ++kv+ ++ +el+ipiia+G  ++ +dv e + aGa+av  
  gi|488599929|ref|YP_007906400.1| 215 AMKVVWDLYEELDIPIIASGGATSWKDVVEFMLAGASAVQI 255
                                       4688899999****************************976 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 ?    7.3   0.0    0.0013       2.4     122     183 ..     205     266 ..      99     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0013
                                       TSSTTS-.SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHH CS
                              NanE 122 GytkeeekaepDfalvkalsea.glkviaeGrintPekakkaieiGvdavvvGsaitrleeia 183
                                       Gy +e+ k    +++v +l e+ ++ +ia G   + +   + +  G+ av +Gsa     +i 
  gi|488599929|ref|YP_007906400.1| 205 GYSGEAVK-PVAMKVVWDLYEElDIPIIASGGATSWKDVVEFMLAGASAVQIGSAFFYSYRIF 266
                                       44444443.334666777765438899999999999999999999999999999986666665 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         3   5.4e+03     186     197 ..      12      23 ..       7      44 .. 0.66
   2 ?   10.6   0.0   0.00013      0.22     153     216 ..     187     258 ..     143     278 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                            DUF561 186 slPvicasGlsd 197
                                       + P+i asG+  
  gi|488599929|ref|YP_007906400.1|  12 QNPLILASGILG 23 
                                       568888888754 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00013
                            DUF561 153 Gkitsiskakkvndlieksls.......tlastyeiskkvslPvicasGlsdvtvplals.lgasGiGigsa 216
                                       G + +i  +k +  ++    s       ++  ++ + +++++P+i++ G ++    + +  +gas + igsa
  gi|488599929|ref|YP_007906400.1| 187 GMAIDIGSKKPILSNVSGGYSgeavkpvAMKVVWDLYEELDIPIIASGGATSWKDVVEFMlAGASAVQIGSA 258
                                       4444454555555555444434445556788899999**************999888875269******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 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:                        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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1708.99
//
Query:       gi|488599930|ref|YP_007906401.1|  [L=114]
Description: hypothetical protein Asulf_00379 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.4   0.0       0.01   16.2   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 !   16.2   0.0   5.8e-07      0.01      56     131 ..      20      91 ..       5      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.8e-07
                                       TGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  56 epllypdfvellerlaklavpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevl 131
                                        pl+++df e+++ +  +   g+ + ++tng+l+  e+ +   +l  + +++++l++++ e + k+ +  ++fe  +
  gi|488599930|ref|YP_007906401.1|  20 KPLYRKDFFEIAKFAEDC---GLVVNLTTNGFLV-NEISKNYSKLSmFSQINISLDSISREGYTKIREY-DGFENAM 91 
                                       699999999999999998...*************.**************************66666643.6666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 740.11
//
Query:       gi|488599931|ref|YP_007906402.1|  [L=99]
Description: hypothetical protein Asulf_00380 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 657.03
//
Query:       gi|488599932|ref|YP_007906403.1|  [L=413]
Description: Protoporphyrinogen oxidase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   97.3   0.0    1.7e-27   96.8   0.0    1.2  1  Amino_oxidase   Flavin containing amine oxidoreductase
    6.1e-07   29.6   0.1    1.5e-06   28.4   0.1    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00085   19.0   0.0     0.0012   18.5   0.0    1.3  1  DAO             FAD dependent oxidoreductase
     0.0034   16.6   0.2      0.018   14.3   0.1    2.0  2  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.023   14.0   0.1      0.035   13.4   0.1    1.2  1  FAD_binding_3   FAD binding domain
      0.068   12.4   0.0       0.18   11.0   0.0    1.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
       0.11   12.5   0.0        2.5    8.1   0.0    2.2  2  NAD_binding_9   FAD-NAD(P)-binding
       0.14   12.1   0.0       0.24   11.3   0.0    1.3  1  YfdX            YfdX protein
       0.15   12.6   0.0       0.42   11.2   0.0    1.8  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.19   11.0   0.0       0.35   10.1   0.0    1.3  1  DNA_processg_A  DNA recombination-mediator protein A


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   9.6e-31   1.7e-27       1     451 [.      10     406 ..      10     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 9.6e-31
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEET..TEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCCGC CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsd..GylielGamwftgagnpllellkelgledslslpdpgap 75 
                                       l+GL++Ar L +   dV v+E+++  GG +++++ +  Gy+ie   + +++++ +l el+++l l+ +l+++     
  gi|488599932|ref|YP_007906403.1|  10 LTGLTCARLLGEY-ADVKVFESESA-GGLLSSYYNSerGYWIEKFYHHCFRNDEHLIELIRDLRLSGKLVWRIAR-- 82 
                                       69*****977655.9******9875.*******************************************988866.. PP

                                       EEEEETTEECCTTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHH CS
                     Amino_oxidase  76 krvlskggrefpgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepg 152
                                        + +      ++g++ p++ ++e+l          ++l++k+rl++  l+    +++++    ++  + e  r+e+g
  gi|488599932|ref|YP_007906403.1|  83 -TGVA-----VDGRIYPLNTPFEILRY------PYMRLMDKVRLARFTLR----AKKRNFIDFDDVGVVEGIRDELG 143
                                       .3333.....377777***********......9****************....78888888888888888999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHHHHTTTTEEEETSE CS
                     Amino_oxidase 153 dvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpealaeelrgldirlnt 229
                                       d e+++ +++p l +k++ +   + + +  l+a++++ ++++++g++ + l  +gG++ql+e+lae   g+di +++
  gi|488599932|ref|YP_007906403.1| 144 D-ELLNDFFLPLLKSKFGENYERVSYAW--LLARVSIRSNRRYSGEELGYL--KGGFQQLVERLAE---GVDIAFSK 212
                                       9.******************99999999..****************99966..89***********...*******7 PP

                                       EEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSHHHHHHHHHSEEEEEEEEEEEESSGGSGCST CS
                     Amino_oxidase 230 rVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPplpdekaeairnlgfgsvnkvilefdrkfwedna 306
                                           i++ g++ +v    ge  ++DaVv T+pl++l       +l   +a+ + + ++ s++ + +  ++   ed  
  gi|488599932|ref|YP_007906403.1| 213 --AAIAKAGEKFAV---MGE--RFDAVVYTAPLPALD-----REL--RRAAGLPETKYQSSVCALIGAEEGITED-- 273
                                       ..589**9999999...566..6**************.....667..899999999***************9222.. PP

                                       SECE.CECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHHHHHH.HTGTSSTCS CS
                     Amino_oxidase 307 lgqg.vlvseltttlgeafissdfpsrappgkglvllvyvggdaaneleslsdeelvqavlrdLrkl.fgeevpepk 381
                                            + +  +++  g     ++f + ++ g +++ l+  +  ++++  ++s++ l +  +++L+++  g       
  gi|488599932|ref|YP_007906403.1| 274 ---IyWINLKNPSIFGAIIEHTNFMDFEDYGEHVIYLASYSTPEGQL-FNTSNDKLEKLYMKELERFgIG------- 339
                                       ...12455555555555555555999999999998888888666555.799**************99666....... PP

                                       EEEEEECCTETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE.SGGGCTTTTTS.HHHHHHHHHHHHHHH CS
                     Amino_oxidase 382 atlvtrWhtdplargsysyvsvgpghedydplakpegdprlffAGehtsreypgt.vegAilSGlraAari 451
                                            +W   +++++ +s + +  g ++    +++  ++++++AG    ++yp + ++g i+SG+++A  +
  gi|488599932|ref|YP_007906403.1| 340 -SESINW--IRVFKARFSGPIYEKGYLRKITDYRT-RVKGFYVAGMTSRHNYPERsMNGSIRSGIEVAKVV 406
                                       .77779*..59999*********************.********************************987 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   8.1e-10   1.5e-06       1      68 []       5      70 ..       5      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 8.1e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE..TTCEECTS---EEETTHHHHCHHHHCCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev..pgvrvdygahifhgsgyypnvrrllrel 68
                                      ++GaGl+Gl++A+lL ++ +dv ++e+  + GG ++sy +   g++++   h  +   +++++ +l+r+l
  gi|488599932|ref|YP_007906403.1|  5 VIGAGLTGLTCARLLGEY-ADVKVFESE-SAGGLLSSYYNseRGYWIEKFYHHCFR--NDEHLIELIRDL 70
                                      8****************9.9******96.777877777553567888876665555..358888888765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.5e-07    0.0012       1      41 [.       2      43 ..       2     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.5e-07
                                      EEEEECTSHHHHHHHHHHHHTT.EEEEESSSSTT.SSGGGSSE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekgdiag.sgaSgrns 41
                                      +v++iG+G +Gl++A+ L +   V ++e++  ag   +S  ns
  gi|488599932|ref|YP_007906403.1|  2 RVAVIGAGLTGLTCARLLGEYAdVKVFESE-SAGgLLSSYYNS 43
                                      59****************77657*******.555145555554 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1     1e-05     0.018      20      45 ..       3      28 ..       1      37 [. 0.83
   2 ?   -0.3   0.0      0.29   5.3e+02     208     224 ..     369     385 ..     359     395 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                                      EEEE--SHHHHHHHHHHHHCTTS-EE CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkva 45
                                      v+++GaG +GLt+a+ l++  d+kv 
  gi|488599932|ref|YP_007906403.1|  3 VAVIGAGLTGLTCARLLGEYADVKVF 28
                                      89******************998874 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.29
                                       ECEEETTEEE-THHHHH CS
                              Thi4 208 trevvpnlyvaGmevae 224
                                        r  v+++yvaGm +  
  gi|488599932|ref|YP_007906403.1| 369 YRTRVKGFYVAGMTSRH 385
                                       57789********9865 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     2e-05     0.035       3      31 ..       2      29 ..       1      34 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlve 31
                                       V+++GaG++Gl+ a+lL e+  +v + e
  gi|488599932|ref|YP_007906403.1|  2 RVAVIGAGLTGLTCARLLGEY-ADVKVFE 29
                                      69******************9.7777766 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001      0.18       2      28 ..       2      27 ..       1      52 [. 0.63
   2 ?   -3.6   0.0       2.9   5.2e+03     163     198 ..     299     338 ..     295     339 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                                      SEEEE--SHHHHHHHHHHHHHTS-EEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtl 28
                                      +v+viG+G  Gl++a+ l++  a+v +
  gi|488599932|ref|YP_007906403.1|  2 RVAVIGAGLTGLTCARLLGE-YADVKV 27
                                      55666666666666665555.233333 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.9
                                       HHT-EEEEEESSSSSS....TTS-HHHHHHHHHHHHHTTE CS
                                       xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 163 klgkevtlveardrll....raldkelsaaleealekeGv 198
                                       ++g++v ++   +++     ++ +++l++ ++++le+ G+
  gi|488599932|ref|YP_007906403.1| 299 DYGEHVIYLASYSTPEgqlfNTSNDKLEKLYMKELERFGI 338
                                       6666666666655554444577889999999999999887 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 ?    8.1   0.0    0.0014       2.5       1      40 [.       4      36 ..       4      50 .. 0.76
   2 ?    1.9   0.0      0.11     2e+02      99     126 ..     190     217 ..     180     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0014
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                      a++GaG +Gl++++ L + a      ++++f+ +++g g 
  gi|488599932|ref|YP_007906403.1|  4 AVIGAGLTGLTCARLLGEYA------DVKVFESESAG-GL 36
                                      89********9987777775......99999999987.44 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                     NAD_binding_9  99 Ylrdlfeellarlpegvtvevhraevvd 126
                                       Yl+  f++l++rl egv++ + +a + +
  gi|488599932|ref|YP_007906403.1| 190 YLKGGFQQLVERLAEGVDIAFSKAAIAK 217
                                       99999***************99987765 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.24      83     145 ..     211     272 ..     199     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       HTT-HHHHHHHHHHTT-EEEEEEEEEEHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHT-EE CS
                              YfdX  83 kkgdtqaArelLkllgseidittallPLatypaavkkAaelleegkyyeAkeaLkealntlvf 145
                                        k   ++A e+ +++g+  d +++ +PL + +  + +Aa l e  ky+    aL  a++++ +
  gi|488599932|ref|YP_007906403.1| 211 SKAAIAKAGEKFAVMGERFDAVVYTAPLPALDRELRRAAGLPE-TKYQSSVCALIGAEEGITE 272
                                       566778999*****************************99876.***************9976 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   0.0   0.00023      0.42       1      31 [.       2      31 ..       2      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                      +v+v+G+G++gl +A  l e++ +V+v+e +
  gi|488599932|ref|YP_007906403.1|  2 RVAVIGAGLTGLTCARLLGEYA-DVKVFESE 31
                                      79****************9999.77777654 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 ?   10.1   0.0   0.00019      0.35      79     109 ..     202     232 ..     192     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                    DNA_processg_A  79 lAlGiDaaahraaleaggktvavlgtgldki 109
                                       lA G+D a  +aa+++ g+ +av+g+ +d +
  gi|488599932|ref|YP_007906403.1| 202 LAEGVDIAFSKAAIAKAGEKFAVMGERFDAV 232
                                       8*************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2679.67
//
Query:       gi|488599933|ref|YP_007906404.1|  [L=387]
Description: glutamate N-acetyltransferase/amino-acid acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-131  438.2   2.9   2.3e-131  438.0   2.9    1.0  1  ArgJ      ArgJ family


Domain annotation for each model (and alignments):
>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.0   2.9  1.3e-135  2.3e-131       7     376 .]      20     387 .]      14     387 .] 0.95

  Alignments for each domain:
  == domain 1  score: 438.0 bits;  conditional E-value: 1.3e-135
                                       XSSS..SXXEEEEEEEEEEEEEEEEEXXSSXXHHHHHHHHHHH.HHSEEEEEEEEEEXXXSXHHHHHHHHHHHHHHH CS
                              ArgJ   7 agikkkkkdlalivseepasaaavfTknkvkAapvkvsrevlkkkkgaravvvnsgnANavtgeqGledaeemaeav 83 
                                        g+k+ k+ l ++ +  + ++a+vfT+n++kAapv v++e++k++  +++++vnsgnANa+tge+G+++a++mae++
  gi|488599933|ref|YP_007906404.1|  20 YGVKEGKNGLGIVKC--RGRVAGVFTENRIKAAPVMVTSEHIKNGW-VEGIIVNSGNANAYTGEEGIKNAKRMAELL 93 
                                       589988999999998..6789*********************8654.****************************** PP

                                       HHHHTSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X......HHHHHHHXSSXSSXXEEEEEEEETEEEEEEE CS
                              ArgJ  84 aealgikeeevlvasTGviGerlpmekieagieklvekle......eeaaeAimTTDtvpKlaavevelgkevtiag 154
                                       ae++g+++e+v+v+sTGviG++l+me ie+++++++++l+      ee+a++imTTD +pK++av++   +++ +ag
  gi|488599933|ref|YP_007906404.1|  94 AEKIGCDAEKVAVCSTGVIGRQLDMEWIEKKVDEVYSRLSasrksaEEFAKSIMTTDRYPKEFAVKF---GDCIVAG 167
                                       *************************************9977888889********************...69***** PP

                                       EEEXSSSXXXXEE--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TTTT.STTHHHHHH CS
                              ArgJ 155 iaKGaGmihPnmaTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaaeeeeedleefee 231
                                       +aKGaGmi+PnmaTmLafi+t+a+v+   l ++l  avd+sFn ++vDgdtSTnDtvll+++ ++   e d e+f+ 
  gi|488599933|ref|YP_007906404.1| 168 VAKGAGMIAPNMATMLAFIFTNAKVE--NLYDCLGYAVDRSFNVMTVDGDTSTNDTVLLISTDEV---EVDEETFKL 239
                                       ************************97..699*********************************9...6899***** PP

                                       HHHHHHHHHHHHHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHHHHHHHHSSS---T CS
                              ArgJ 232 altevlqeLakqivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRilaavGyagaeldp 308
                                       al+ev+ +Lak+ivrDGEGatk++ev+V+gaks+e+A ++aksva+s LvKtA+fG D+nwGRi+aa+Gyag+++++
  gi|488599933|ref|YP_007906404.1| 240 ALKEVCFNLAKMIVRDGEGATKVFEVHVHGAKSDEDAFNLAKSVASSLLVKTAVFGCDPNWGRIIAALGYAGVDISE 316
                                       ****************************************************************************9 PP

                                       TS-EE....TT...EEEEETTEE----HHHHHHHH.H-SSEEEEEE--SSSEEEEEEEE---HHHHHHHTT-XX CS
                              ArgJ 309 ekvsv..llge...vkvlekgepeevdeerakeil.keeeveievdlgegeeeatvwtcDLsyeYvkiNadYrt 376
                                       + + +  +  +   + +l++g++ + +e++a+e + k+++++i v+l+ g++   + +cDL+y+Yvk+Na+Y+t
  gi|488599933|ref|YP_007906404.1| 317 DITLIfeN--DdesIALLDEGKQ-TGRESEAEEFMrKNDDFRIAVRLKLGDGYGYAIGCDLTYDYVKLNAEYTT 387
                                       98888551..24459******86.47999******8899*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2713.74
//
Query:       gi|488599934|ref|YP_007906405.1|  [L=180]
Description: hypothetical protein Asulf_00385 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1280.70
//
Query:       gi|488599935|ref|YP_007906406.1|  [L=322]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-30  106.8   0.0    1.8e-30  106.3   0.0    1.2  1  ABC_tran         ABC transporter
    1.6e-18   67.0   0.2    2.6e-18   66.3   0.2    1.4  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    8.3e-09   35.7   0.8    4.1e-06   26.8   0.3    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.4e-06   27.9   0.1    8.9e-05   22.8   0.1    2.2  1  AAA_22           AAA domain
    7.4e-06   25.5   0.0    2.2e-05   24.0   0.0    1.7  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0014   18.4   0.0     0.0033   17.2   0.0    1.7  1  PRK              Phosphoribulokinase / Uridine kinase family
     0.0087   15.5   0.0       0.36   10.2   0.0    2.2  2  TniB             Bacterial TniB protein
     0.0092   16.4   0.1      0.012   16.0   0.1    1.3  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.096   13.1   0.0    1.9  1  AAA              ATPase family associated with various cellul
      0.024   14.3   0.0      0.024   14.3   0.0    1.1  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.091   12.8   0.2       0.27   11.2   0.1    1.7  2  AAA_5            AAA domain (dynein-related subfamily)
      0.096   12.9   0.0       0.81   10.0   0.0    2.1  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
       0.13   12.4   0.0       0.23   11.6   0.0    1.4  1  tRNA_lig_kinase  tRNA ligase kinase domain
       0.19   11.3   0.3         17    4.9   0.1    2.2  2  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   1.4e-33   1.8e-30       2     137 .]      33     183 ..      32     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 1.4e-33
                                       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+ +++++l +pt G+il++gkd+ +   ++++++r++ ++++q+  ++l+p+
  gi|488599935|ref|YP_007906406.1|  33 DGVSFEILRGETFGLVGESGCGKTTVGRTILRLIEPTDGQILFEGKDIMKfskKDINRFRRKAQIMFQDpySSLNPR 109
                                       78**********************************************99999****************999***** PP

                                       SBHHHH..........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx..........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        tv +           e d+    + ++l+++g   l+++++++ p+++SgGq+qr+a+ar+l  kp++++lDEpt+
  gi|488599935|ref|YP_007906406.1| 110 QTVFQIvmepvrhhgiEVDDPeafVIDLLERVG---LNESHLYRYPHEFSGGQRQRIAMARILSLKPEFVVLDEPTS 183
                                       ***999999999998844444223555555555...555999999******************************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 !   66.3   0.2     2e-21   2.6e-18       2      65 .]     235     301 ..     234     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 2e-21
                         oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekd...klekikgeapslerldeGCpFapRCpfaleeC 65 
                                       E g+s+ +f+eplHPYTkaL +++p +d+  +   +  k+ ge+ps+ + +eGC+F+pRC++a+++C
  gi|488599935|ref|YP_007906406.1| 235 EVGNSESIFEEPLHPYTKALFSAIPIPDPDIEkkkERIKVIGEPPSPINPPEGCRFNPRCQYAKDIC 301
                                       899**********************9999888767788889*************************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 !    7.9   0.0    0.0019       2.4       3      48 ..      46      74 ..      45      95 .. 0.68
   2 !   26.8   0.3   3.2e-09   4.1e-06     165     302 ..      93     218 ..      74     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0019
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsl 48
                                      +l+G  g+GK+++ +++  l                  ++++   l
  gi|488599935|ref|YP_007906406.1| 46 GLVGESGCGKTTVGRTILRLI-----------------EPTDGQIL 74
                                      69***************8884.................44444444 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 3.2e-09
                            AAA_21 165 rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGt 241
                                       r+++  +++ y   +++++ +q  + +++  +ie++d ++++ +  ++  +          n++   + ++e+S G+
  gi|488599935|ref|YP_007906406.1|  93 RKAQIMFQDPYSSLNPRQTVFQIVMEPVRHHGIEVDDPEAFVIDLLERVGL----------NESHLYRYPHEFSGGQ 159
                                       666777778899999999********************9999999887776..........88899999******** PP

                            AAA_21 242 krllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       ++ +a++ +l   +    ++++DEp + L+ ++++ +l  lk+ ++  +   ++ +H+  ++
  gi|488599935|ref|YP_007906406.1| 160 RQRIAMARILSLKP---EFVVLDEPTSALDVSVQANILNTLKDIQDeYKLTYLFISHDLAIV 218
                                       ***77777777655...9***********************88877799999*****99876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1     7e-08   8.9e-05      10     128 ..      47     211 ..      42     220 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7e-08
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee....................................erpevvfvtlpss 50 
                                       ++GesG+GKTt+ r++l+  +      +                                    +            
  gi|488599935|ref|YP_007906406.1|  47 LVGESGCGKTTVGRTILRLIEPT----DgqilfegkdimkfskkdinrfrrkaqimfqdpysslN------------ 107
                                       79****************98543....23455888888888888887654333333333333331............ PP

                            AAA_22  51 tsskdllrellralglelka..................erlsseellealeqalrarav...........ielliiD 98 
                                             ++ +++++ ++  +                   +l++++l+++ ++ +  ++            +e++++D
  gi|488599935|ref|YP_007906406.1| 108 -----PRQTVFQIVMEPVRHhgievddpeafvidllerVGLNESHLYRYPHEFSGGQRQriamarilslkPEFVVLD 179
                                       .....3344444444444445555666666666666665566666666666666666666667777788999***** PP

                            AAA_22  99 Eaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       E    l+   ++++l++L+++++  +++++ +++
  gi|488599935|ref|YP_007906406.1| 180 EPTSaLDvsvQANILNTLKDIQD--EYKLTYLFI 211
                                       *99989885559*********99..988887765 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   1.7e-08   2.2e-05      29     213 ..      47     229 ..      30     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.7e-08
                                       EEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  29 ivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                       +vG+ G+GK+ +   il ++  ++ + l   + +d+++ sk+  +  + + +i+f+++ ++l+ +++ ++i  + +r
  gi|488599935|ref|YP_007906406.1|  47 LVGESGCGKTTVGRTILRLIEPTDGQIL-F-EGKDIMKFSKKDINRFRRKAQIMFQDPYSSLNPRQTVFQIVMEPVR 121
                                       7899999999999999777776665333.3.3455555555555555566677788888887777777777777777 PP

                                       TSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 106 kgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                       +    +++++ e+    v +lle++g++++       ++SgG+++ +a+a +++++   p  +++lDe  +aLD + 
  gi|488599935|ref|YP_007906406.1| 122 HHG--IEVDDPEA---FVIDLLERVGLNEShlyryphEFSGGQRQRIAMARILSLK---P-EFVVLDEPTSALDVSV 189
                                       666..56666554...4667777777777777777779************998875...4.49************** PP

                                       HHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 176 vkkvaellkekskn..aQfivislreemlekadklvgvtk 213
                                        +++ + lk  +++    ++ is++  +++ +++ +gv+ 
  gi|488599935|ref|YP_007906406.1| 190 QANILNTLKDIQDEykLTYLFISHDLAIVKYMSHRIGVMY 229
                                       *********666553378999******9999999999875 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.6e-06    0.0033       3      80 ..      46     122 ..      44     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.6e-06
                               PRK   3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyevlk 79 
                                       g+ g+SG+Gkttv r++  +++ +  +    eg+ ++++ + + +   ++++  ++  +s l+p+   f+ + e ++
  gi|488599935|ref|YP_007906406.1|  46 GLVGESGCGKTTVGRTILRLIEPTDGQ-ILFEGKDIMKFSKKDINRFRRKAQIMFQDPYSSLNPRQTVFQIVMEPVR 121
                                       889******************944444.6669999999999888888888888999999999999999988877776 PP

                               PRK  80 e 80 
                                       +
  gi|488599935|ref|YP_007906406.1| 122 H 122
                                       5 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.044        57      38      57 ..      45      64 ..      38      75 .. 0.78
   2 !   10.2   0.0   0.00028      0.36     106     157 ..     159     208 ..     127     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.044
                              TniB 38 lllvGdsnnGKtmivekFar 57
                                        lvG+s +GKt++ +   r
  gi|488599935|ref|YP_007906406.1| 45 FGLVGESGCGKTTVGRTILR 64
                                      569**********9776665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00028
                              TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipi 157
                                       + ++ +++ + +lk++ +++DE  ++l   ++ q ++ln+lk +++e+k++ 
  gi|488599935|ref|YP_007906406.1| 159 QRQRIAMARILSLKPEFVVLDEPTSAL--DVSVQANILNTLKDIQDEYKLTY 208
                                       55666777788999*************..777899************99875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   9.4e-06     0.012      28      56 ..      46      74 ..      38     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.4e-06
                            AAA_16 28 llsGesGvGKsslvrellralekdggifl 56
                                       l+GesG+GK+++ r++lr +e ++g  l
  gi|488599935|ref|YP_007906406.1| 46 GLVGESGCGKTTVGRTILRLIEPTDGQIL 74
                                      589***************99999865553 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   7.5e-05     0.096       3      74 ..      47     188 ..      45     225 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-05
                                       EESSTTSSHHHHHHHHHHHH..........T...HEEEEEETTTCSSS............................. CS
                               AAA   3 lyGppGtGKTllakavakel..........g...vefleisgsellsk............................. 37 
                                       l+G  G+GKT++ + + + +          g   ++f + +  +++ k                             
  gi|488599935|ref|YP_007906406.1|  47 LVGESGCGKTTVGRTILRLIeptdgqilfeGkdiMKFSKKDINRFRRKaqimfqdpysslnprqtvfqivmepvrhh 123
                                       89****************98444432223212223344444444443366777777777777777777777777777 PP

                                       ...........................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA  38 ...........................yvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                                                  y  e +   r+ ++ a+  + kp  +++DE  +    +
  gi|488599935|ref|YP_007906406.1| 124 gievddpeafvidllervglneshlyrYPHEFSGGQRQRIAMARILSlKPEFVVLDEPTSALDVS 188
                                       77777777777777777777777777777777777777777777777777777788776666665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05     0.024       4      41 ..      31      69 ..      29     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                      HHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS CS
                                      xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  4 vlDal.fpivqGqrtlipgafgvGktvisqslskqsnsd 41
                                      ++D + f i +G++ +++g++g+Gkt++ +++++  + +
  gi|488599935|ref|YP_007906406.1| 31 AVDGVsFEILRGETFGLVGESGCGKTTVGRTILRLIEPT 69
                                      566543889********************9999876555 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 ?   11.2   0.1   0.00021      0.27       4      23 ..      47      66 ..      45      78 .. 0.88
   2 ?   -2.3   0.0       3.2   4.1e+03      65      89 ..     172     197 ..     158     203 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      LvG++G+gK+++ + +++++
  gi|488599935|ref|YP_007906406.1| 47 LVGESGCGKTTVGRTILRLI 66
                                      9****************998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                       G-SEEEEESGGG--.HHHHHHHHHHH CS
                             AAA_5  65 egeilvlDEverae.sevlnsLlsll 89 
                                       ++e +vlDE + a   +v++  l+ l
  gi|488599935|ref|YP_007906406.1| 172 KPEFVVLDEPTSALdVSVQANILNTL 197
                                       67788888877776555555444444 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 ?   10.0   0.0   0.00063      0.81      25      89 ..     147     198 ..     128     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00063
                           SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +l+r   + SGG++q         a+a  +s       ++++v+LDE  s lD   +a++l++l+
  gi|488599935|ref|YP_007906406.1| 147 HLYRYPHEFSGGQRQR-------IAMARILSL------KPEFVVLDEPTSALDVSVQANILNTLK 198
                                       5666666666666643.......345555566......589******************999987 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.23       9      77 ..      52     116 ..      47     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                       TSSHHHHHHHHHHH-TT.SEEEEGGGS-TT-SS-HHHHHHHTTSSTT--EEEEES---SHHHHHHHHHHH CS
                   tRNA_lig_kinase   9 GCGkttvaltlenlfge.WghvqnDnitgkdkkklvkealellkkdeskvvlvDrnnhqkreRkqlfeei 77 
                                       GCGkttv +t+ +l     g++     +gkd  k+ k+ ++ + + + ++++ D   +  + R+++f+ +
  gi|488599935|ref|YP_007906406.1|  52 GCGKTTVGRTILRLIEPtDGQIL---FEGKDIMKFSKKDINRF-RRKAQIMFQDPY-SSLNPRQTVFQIV 116
                                       9**********999873233333...37889999999999999.777777777754.5567788887765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.013        17      32      49 ..      41      58 ..      35      63 .. 0.88
   2 ?    4.4   0.0      0.02        25     142     188 ..     172     213 ..     116     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                            AAA_25 32 agelallaGapgtGKttl 49
                                      +ge+  l+G +g+GKtt+
  gi|488599935|ref|YP_007906406.1| 41 RGETFGLVGESGCGKTTV 58
                                      788888**********97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.02
                            AAA_25 142 gvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                       ++++vv+D  ++al+ + +     + +++ l++i+++++ + l++ H
  gi|488599935|ref|YP_007906406.1| 172 KPEFVVLDEPTSALDVSVQ-----ANILNTLKDIQDEYKLTYLFISH 213
                                       4899999999999999888.....5699****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2112.44
//
Query:       gi|488599936|ref|YP_007906407.1|  [L=326]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-23   82.2   0.0    6.5e-23   81.8   0.0    1.2  1  ABC_tran         ABC transporter
      3e-20   72.5   0.0      6e-20   71.5   0.0    1.6  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    2.7e-07   30.7   0.0    1.4e-05   25.0   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00062   20.0   0.2     0.0041   17.4   0.2    2.0  1  AAA_22           AAA domain
     0.0025   17.6   0.0      0.069   12.9   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
     0.0043   16.5   0.1      0.054   12.9   0.1    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.006   17.0   0.2       0.11   12.9   0.0    2.6  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.012   15.8   0.1      0.032   14.3   0.0    1.6  2  DUF87            Helicase HerA, central domain
      0.013   15.9   0.0       0.02   15.3   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.018   14.6   0.1        4.3    6.9   0.0    2.2  2  AAA_25           AAA domain
      0.039   14.0   0.0      0.067   13.2   0.0    1.3  1  AAA_5            AAA domain (dynein-related subfamily)
        0.1   12.3   0.0        1.3    8.7   0.0    2.0  2  AAA_30           AAA domain
       0.12   12.0   0.1       0.37   10.5   0.0    1.7  2  Sigma54_activat  Sigma-54 interaction domain
       0.16   12.4   0.0        0.3   11.5   0.0    1.4  1  RNA_helicase     RNA helicase
       0.19   11.4   0.0        5.9    6.5   0.0    2.1  2  AAA_15           AAA ATPase domain
       0.21   10.5   0.0       0.35    9.7   0.0    1.4  1  AAA_10           AAA-like domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   5.8e-26   6.5e-23       2     136 ..      26     188 ..      25     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 5.8e-26
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE............EETTCEGGG......B-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxx......xxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGei............lldgkdlke......qeleslrke 60 
                                       ++vs++++ ge+ a+vGe+G+GKS  +++l++l +   G+i            ++d            + +++  +e
  gi|488599936|ref|YP_007906407.1|  26 EKVSFDVYMGETFALVGETGCGKSVTARALTQLIE-SPGRIvggevyytsdkgRVD-----LlklseeEIRKIRGSE 96 
                                       689******************************98.56777566666665555444.....13333357888999** PP

                                       EEEE-SS..--S-TTSBHHHH............HHHTC......HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHH CS
                                       xxxxxxx..xxxxxxxxxxxx............xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  61 igvlpqe..pqlfpeltvren............esdee......iekalsklglkelkdtvvksspssLSgGqkqrv 117
                                       i++++q+  ++l+p +t++ +            +          + ++l+++ +++ ++++v++ p+++SgG+kqr 
  gi|488599936|ref|YP_007906407.1|  97 IAYIFQDpqSSLDPLYTIGYQisealyvhkrveN---LkdgikkAVEILRTVLMPD-PEKRVSNYPHEMSGGMKQRA 169
                                       *******888899****99999999988666552...0344344666666776666.88888899************ PP

                                       HHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 118 alarallkkpkllllDEpt 136
                                        +   + ++pkll++DEpt
  gi|488599936|ref|YP_007906407.1| 170 TIGIGISNNPKLLIADEPT 188
                                       ******************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   5.3e-23     6e-20       1      65 []     240     304 ..     240     304 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 5.3e-23
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE g++ ++f++plHPYT++Llr+vp +  + ++le+i+g++psl + +eGC+F+pRCp a+++C
  gi|488599936|ref|YP_007906407.1| 240 VELGDVYAIFKKPLHPYTQGLLRAVPNPLVKIERLETIPGTVPSLINPPEGCRFSPRCPLASSIC 304
                                       8***************************************************************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 ?    3.9   0.0     0.036        40       3      23 ..      39      59 ..      38     108 .. 0.80
   2 !   25.0   0.0   1.3e-08   1.4e-05     234     302 ..     158     224 ..      72     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.036
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      +l+G  g+GKS   +al  l 
  gi|488599936|ref|YP_007906407.1| 39 ALVGETGCGKSVTARALTQLI 59
                                      79***************9884 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.3e-08
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                       ++e+S G+k+  a + + ++ ++  +ll+ DEp + L+  +++ +l+l+ + ++r ga vil TH+  ++
  gi|488599936|ref|YP_007906407.1| 158 PHEMSGGMKQR-ATIGIGISNNP--KLLIADEPTTALDVTVQTQILDLIkDMKERYGATVILITHDMGVV 224
                                       6788*******.77777777776..79**********************555555**********98776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   3.6e-06    0.0041       9     128 ..      39     217 ..      35     223 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdllrellralglelka............ 70 
                                       +++Ge+G+GK++++r l++  +        +p+ +   +v+ +s++++ dll+   +++   + +            
  gi|488599936|ref|YP_007906407.1|  39 ALVGETGCGKSVTARALTQLIE--------SPGRIvggEVYYTSDKGRVDLLKLSEEEIRKIRGSeiayifqdpqss 107
                                       79*****************986........44444466666666665555555444444433333444455544444 PP

                            AAA_22  71 ..........................................erlsseellealeqalrarav........iellii 97 
                                                                                 ++++ + + + +   +++ra+        ++lli 
  gi|488599936|ref|YP_007906407.1| 108 ldplytigyqisealyvhkrvenlkdgikkaveilrtvlmpdPEKRVSNYPHEMSGGMKQRATigigisnnPKLLIA 184
                                       66666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                            AAA_22  98 DEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       DE    l+   + ++l  ++++ +  r+g ++iL+
  gi|488599936|ref|YP_007906407.1| 185 DEPTTaLDvtvQTQILDLIKDMKE--RYGATVILI 217
                                       666665655444555555566666..666666665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   6.2e-05     0.069      33      95 ..      20      87 ..       2      97 .. 0.70
   2 ?    2.5   0.0     0.095   1.1e+02     108     149 ..     178     221 ..     164     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
                         IstB_IS21 33 rkvkeLatlsf.iekkenivllGpsGvGKshlaialgveavr....aglsvlfvrvedLveelkrarr 95
                                       +vk++ + sf +   e ++l+G +G GKs  a al +         g +v++++ +  v  lk+ ++
  gi|488599936|ref|YP_007906407.1| 20 GIVKAIEKVSFdVYMGETFALVGETGCGKSVTARALTQLIESpgriVGGEVYYTSDKGRVDLLKLSEE 87
                                      56777777777677899*******************87543311124556777777666666666655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.095
                         IstB_IS21 108 kvdllilDdlgllpld...qaeaellfeviekryerrsiiitsnl 149
                                       +++lli D+  +  ld   q +  +l + +++ry+ + i+it ++
  gi|488599936|ref|YP_007906407.1| 178 NPKLLIADEPTT-ALDvtvQTQILDLIKDMKERYGATVILITHDM 221
                                       568999999543.44400144445555556789999999999876 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   0.1   4.8e-05     0.054     135     213 ..     150     235 ..      21     241 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-05
                                       T.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                             SMC_N 135 e.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislree 200
                                                 ++SgG k+ + + + +     +   l + De   aLD +  +++ +l+k  +++  a +i i+++ +
  gi|488599936|ref|YP_007906407.1| 150 PekrvsnyphEMSGGMKQRATIGIGI----SNNPKLLIADEPTTALDVTVQTQILDLIKDMKERygATVILITHDMG 222
                                       13444444448888888887777653....334458899********************777765599********* PP

                                       HCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxx RF
                             SMC_N 201 mlekadklvgvtk 213
                                       +++ +   vgv+ 
  gi|488599936|ref|YP_007906407.1| 223 VVAGMADRVGVMY 235
                                       ****999999986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0    0.0001      0.11       3      37 ..      40      91 ..      38     188 .. 0.66
   2 ?    1.4   0.0      0.35     4e+02      83     113 ..     193     222 ..     176     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                      EESSTTSSHHHHHHHHHHHHTHE..................EEEEETTTCSSS CS
                               AAA  3 lyGppGtGKTllakavakelgve..................fleisgsellsk 37
                                      l+G  G+GK+ +a+a+ + ++++                  +l++s  e++ k
  gi|488599936|ref|YP_007906407.1| 40 LVGETGCGKSVTARALTQLIESPgrivggevyytsdkgrvdLLKLSEEEIR-K 91
                                      89****************985443333333333333333335555555555.3 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHTTTSSSTEEEEEEESSGG CS
                               AAA  83 ervvnqLlteldgvkkkeskvivigatnrpd 113
                                        +v+ q+l  ++++k++ +  +vi++t+++ 
  gi|488599936|ref|YP_007906407.1| 193 VTVQTQILDLIKDMKERYG-ATVILITHDMG 222
                                       5799999******999866.89999998875 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.8e-05     0.032      14      47 ..      28      59 ..      21      66 .. 0.82
   2 ?   -1.7   0.0       2.3   2.6e+03     161     199 ..     192     209 ..      89     225 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                             DUF87 14 vyldlnklvtrHlAilgsTGsGKSntvavLleel 47
                                      v++d+  +  + +A +g+TG GKS t++ L + +
  gi|488599936|ref|YP_007906407.1| 28 VSFDV--YMGETFALVGETGCGKSVTARALTQLI 59
                                      55566..55788*****************98755 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                             DUF87 161 knqaiarlldkledllrkggsfsnsstdliallleklek 199
                                       +                      + +t++++l+ +++e+
  gi|488599936|ref|YP_007906407.1| 192 D---------------------VTVQTQILDLIKDMKER 209
                                       2.....................23333344444333333 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   1.8e-05      0.02      25      76 ..      36      85 ..      22     148 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysalaqal 76
                                      e   l+Ge G+GKs  +r+l + +e        ++++++ k +          l+++ 
  gi|488599936|ref|YP_007906407.1| 36 ETFALVGETGCGKSVTARALTQLIESPgrivggEVYYTSDKGRVD--------LLKLS 85
                                      56789****************877777656553355555555555........33333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.011        12      32      50 ..      34      52 ..      23      59 .. 0.87
   2 ?    6.9   0.0    0.0038       4.3     165     188 ..     195     219 ..     181     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                            AAA_25 32 agelallaGapgtGKttla 50
                                      +ge+ +l+G +g+GK++ a
  gi|488599936|ref|YP_007906407.1| 34 MGETFALVGETGCGKSVTA 52
                                      68999***********977 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0038
                            AAA_25 165 v.galvealeriarrtgaavllvhH 188
                                       v +++++ ++++++r+ga+v+l+ H
  gi|488599936|ref|YP_007906407.1| 195 VqTQILDLIKDMKERYGATVILITH 219
                                       358999999***************9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.9e-05     0.067       3      38 ..      39      74 ..      37      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
                                      EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--H CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnreveyvqltrdtte 38
                                       LvG++G+gKs  a+ l ++++++  +v +  ++t+
  gi|488599936|ref|YP_007906407.1| 39 ALVGETGCGKSVTARALTQLIESPGRIVGGEVYYTS 74
                                      59*******************999888877766665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0012       1.3      21      49 ..      38      66 ..      31     107 .. 0.84
   2 ?    1.7   0.0      0.16   1.8e+02      32      67 ..     197     232 ..     118     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrv 49
                                       +l+G  G GK+ + +al++++e+ g+ v
  gi|488599936|ref|YP_007906407.1| 38 FALVGETGCGKSVTARALTQLIESPGRIV 66
                                      6799*******************988322 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.16
                            AAA_30  32 ttalkalreaweaaggrviglAptgkaAkvLaeelg 67 
                                       t +l  ++++ e+ g +vi++++   + + +a+ +g
  gi|488599936|ref|YP_007906407.1| 197 TQILDLIKDMKERYGATVILITHDMGVVAGMADRVG 232
                                       555556666666666666666666666666655555 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   0.00033      0.37      18      45 ..      31      58 ..      17      66 .. 0.74
   2 ?   -1.9   0.0       2.1   2.4e+03     103     128 ..     189     213 ..     174     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                                      HCTSSS-EEEECSTTSSHHHHHHHHHHH CS
                   Sigma54_activat 18 vaktdlsvlitGesGtGKellaraihea 45
                                       + +  +  ++Ge+G+GK++ ara+ + 
  gi|488599936|ref|YP_007906407.1| 31 DVYMGETFALVGETGCGKSVTARALTQL 58
                                      44555677899*************9885 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                                       GGS-HHHHHHHHHHHHHSEEESBTSS CS
                   Sigma54_activat 103 gelplelQekLlrvlqegevervGss 128
                                       + l++++Q+++l ++++ + er G++
  gi|488599936|ref|YP_007906407.1| 189 TALDVTVQTQILDLIKDMK-ERYGAT 213
                                       4678889999998887644.555655 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   0.00026       0.3       3      35 ..      40      71 ..      38      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvy 35
                                      l+G++g+GKS++a+ L++ +++    +  ++vy
  gi|488599936|ref|YP_007906407.1| 40 LVGETGCGKSVTARALTQLIESPG-RIVGGEVY 71
                                      79*************888777444.44445555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0052       5.9      18      48 ..      31      60 ..      23     140 .. 0.78
   2 ?    3.1   0.0     0.056        63     319     365 ..     174     220 ..     164     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0052
                            AAA_15 18 eidlseeltvliGkNnsGKSsilealdlFln 48
                                      ++ + e +  l+G+ ++GKS  ++al  +++
  gi|488599936|ref|YP_007906407.1| 31 DVYMGE-TFALVGETGCGKSVTARALTQLIE 60
                                      445555.889***************987776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.056
                            AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++++++++l+ +EP + L    q+++ +l+k++ +     vi+ TH 
  gi|488599936|ref|YP_007906407.1| 174 GISNNPKLLIADEPTTALDVTVQTQILDLIKDMKERYGATVILITHD 220
                                       678999*******************************99*******7 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00031      0.35      22      59 ..      36      77 ..      19     153 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00031
                            AAA_10 22 sasliiGdlGnGKSvlakllvlyisllg....gkaliiDpkk 59
                                         +++G++G GKSv+a+ l   i   g    g + +   k 
  gi|488599936|ref|YP_007906407.1| 36 ETFALVGETGCGKSVTARALTQLIESPGrivgGEVYYTSDKG 77
                                      55699*************999887544333325555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.64u 0.40s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 1763.81
//
Query:       gi|488599937|ref|YP_007906408.1|  [L=378]
Description: ABC-type dipeptide/oligopeptide/nickel transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-30  105.8  14.3    1.4e-29  103.2   9.4    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne
    1.3e-07   31.4   0.5    1.3e-07   31.4   0.5    3.1  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 !    5.2   0.1    0.0018        16      12      54 ..      17      88 ..      14     145 .. 0.85
   2 !  103.2   9.4   1.5e-33   1.4e-29       1     185 []     149     364 ..     145     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0018
                      BPD_transp_1 12 rnkkldkllrpliivllslPsfv.............................laillvlvfvilsilghlil 54
                                      ++++ld++++ +i+v+ s+ s+v                             ++++lv +fv+l+i+g +  
  gi|488599937|ref|YP_007906408.1| 17 QRSILDRISDLFIEVVVSIISLVrkdwreknrsriaewklmfyalnrsppgiIGLFLVTMFVLLGIFGPYLA 88
                                      678999999999999999999999999999999999999999999999999999999999988888775544 PP

  == domain 2  score: 103.2 bits;  conditional E-value: 1.5e-33
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........................vilsilgh 51 
                                       gi+lG++a+ ++++k+d++++++++++l++P+++lai + +v+                             + lg 
  gi|488599937|ref|YP_007906408.1| 149 GIILGLVAG-YFGGKVDEIIMRITDMFLAFPPLILAIAFAAVLperitglidsspllqqillwlfaldtREAGNLGR 224
                                       677888888.****************************99999**************************888889** PP

                      BPD_transp_1  52 lilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavll 128
                                       l   +i+++++ +++y+r++r + l +++  +ve a+a G+s  +i+ +++lPn++ pi+  + l fg+++   + l
  gi|488599937|ref|YP_007906408.1| 225 LLAVMIAMAVVWWPGYARITRGSTLTEREVLYVESAKAIGLSSTTIMARHILPNIIGPILVYITLDFGSVVLTEAGL 301
                                       ***************************************************************************** PP

                      BPD_transp_1 129 eflgswpGlgtllleailgydyseis..........nggvlalviavlllnlvadilqrlldprvrk 185
                                       +flg    lg +   a +g+ +  +s          +++ l++++ vl  nl+ d l ++ldp++r+
  gi|488599937|ref|YP_007906408.1| 302 SFLG----LGATPPIADWGRIVYDGSqffpkawwliVFPGLIVLLDVLGWNLLGDSLRDVLDPKLRR 364
                                       ****....************9999999*****99999999999999999***************985 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 !   31.4   0.5   1.5e-11   1.3e-07       3      51 .]      54     108 ..      53     108 .. 0.87
   2 ?   -8.2   8.9         2   1.8e+04      19      30 ..     134     145 ..     130     205 .. 0.65
   3 ?   -3.3   0.1         1   9.4e+03      23      31 ..     226     234 ..     225     239 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.5e-11
                            OppC_N   3 wqdawrrFkrNklAvvglvilllllliaifaPliaPydp.qdli.qn....llpP 51 
                                       w+ +++ + r +  ++gl+++  ++l+ if+P++aPy++  ++i  n    l pP
  gi|488599937|ref|YP_007906408.1|  54 WKLMFYALNRSPPGIIGLFLVTMFVLLGIFGPYLAPYKYnYFPIfENgrtyLSPP 108
                                       99************************************98666544566656666 PP

  == domain 2  score: -8.2 bits;  conditional E-value: 2
                            OppC_N  19 glvillllllia 30 
                                       +lvi ++++l+ 
  gi|488599937|ref|YP_007906408.1| 134 SLVISIIVILLG 145
                                       556555555552 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1
                            OppC_N  23 lllllliai 31 
                                       l++++++a+
  gi|488599937|ref|YP_007906408.1| 226 LAVMIAMAV 234
                                       667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:01.06
# Mc/sec: 1082.96
//
Query:       gi|488599938|ref|YP_007906409.1|  [L=333]
Description: ABC-type dipeptide/oligopeptide/nickel transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-37  128.5  15.5    2.3e-37  128.5  15.5    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.4      0.13   2.2e+03      55      67 ..      17      29 ..       6      41 .. 0.49
   2 !  128.5  15.5   1.3e-41   2.3e-37       1     185 []     116     333 .]     116     333 .] 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.13
                      BPD_transp_1 55 pviillllsaapy 67
                                      p ii ++l  +++
  gi|488599938|ref|YP_007906409.1| 17 PTIIGITLIVFAI 29
                                      2222222222222 PP

  == domain 2  score: 128.5 bits;  conditional E-value: 1.3e-41
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       gi+lG+++al+r + +d ++r++  ++ s+P+f+l+ +l+++f                                  
  gi|488599938|ref|YP_007906409.1| 116 GIPLGLISALKRDSAIDTFVRIFALIGVSTPVFWLGYILIYIFfvnfriinlagvppspevaithvpvidallngdf 192
                                       89*************************************************************************** PP

                      BPD_transp_1  44 .vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafg 119
                                         + + +   +lp+++l++++a+ ++r++r+++l+++  d++e+ +a+G+++   +++++++n+l pi+t l+l+fg
  gi|488599938|ref|YP_007906409.1| 193 eLFRQHVARFWLPGFVLGFMGAGVVARFVRNSFLEAMGGDYIEFLKAKGVPKLG-IYRHAMKNSLVPIMTVLGLQFG 268
                                       ******************************************************.666******************* PP

                      BPD_transp_1 120 gllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                       gll ga ++e++++ pG+g+  + +i   d+++i  ++++++++++++ nl++di+++++dprvr+
  gi|488599938|ref|YP_007906409.1| 269 GLLSGAPITETVFGLPGIGLYAIFSIRTLDFPAIV-AVTFVFALVYVIANLIVDIFYAVVDPRVRY 333
                                       ***********************************.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2268.88
//
Query:       gi|488599939|ref|YP_007906410.1|  [L=699]
Description: ABC-type dipeptide transport system, periplasmic component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-62  209.9  13.2    1.3e-61  208.6  13.2    1.6  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 !  208.6  13.2   7.5e-66   1.3e-61       1     373 [.     244     688 ..     244     691 .. 0.87

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 7.5e-66
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B....-TTSS.B-SHHHHHHHHHHHHTGGGHCTTHHHHHC......... CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvk....FsDGt.pltAeDvvfsferlldpdtasgyasllee......... 63 
                                       +v p+LA + w  ++Dg+++ f +R gv     + D t p+ A Dv+fsf r+ + +++ +++ ++++         
  gi|488599939|ref|YP_007906410.1| 244 KVSPDLAVA-WAHNADGTEWYFVIRGGVVaydpWNDKTyPIDATDVAFSFWRVHRIGHSVSWMLDFTDlnksiamte 319
                                       689******.7****************965555888857*************************9997777888887 PP

                                       ............................TCTEEEEEEEETTEEEEEESSETTTTTTHCHHHHHHHGC.......... CS
                         SBP_bac_5  64 ............................dqdikkveavddytvrftlkkpnalfltllaavpasiak.......... 102
                                                                     +  +       + +++l++p+a+ l +++++  si            
  gi|488599939|ref|YP_007906410.1| 320 defkevlakggiyaeyegksgevksmdeLLKMFGYSGSTAGVYKLVLPQPYAPILGVITDPFLSILPmeyllgdkye 396
                                       777777777777777777777777666644445555555555555556666666666666666555599******** PP

                                       ..................CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTST..........TTSCSS CS
                         SBP_bac_5 103 ..................kaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYw..........gggkpk 151
                                                         ++  ked++     +kpv tGPY ++e++ +++iv + np+Yw          +g k+k
  gi|488599939|ref|YP_007906410.1| 397 ealaasqngkdpsvwnayVSEGKEDATHQLMHQKPVCTGPYYIAEYEENSYIVAKMNPYYWgkslwdemysDGTKAK 473
                                       ***************999999999999999*********************************************** PP

                                       SSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHH.....HHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHH CS
                         SBP_bac_5 152 ldriefkvipdsdaraaalqsGeiddvaepppsdieql.....keakglkvlyespgggvtylafNtkkppfddkrv 223
                                        + +++ + +d+ +r++ +q+G +d+v+  pp+ i+ +     +  +++    +  ++++ty +fNt+k+pf++++v
  gi|488599939|ref|YP_007906410.1| 474 HETVIWIINNDAVSRINLFQTGTVDFVV-APPERIDDVkgltfQGFNSVV-QTDLLEPTITYGVFNTYKEPFNNPKV 548
                                       *********9999999999*****7776.566666666243433333333.47777********************* PP

                                       HHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEE CS
                         SBP_bac_5 224 RqAlsyAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklklt 300
                                       RqAl+yA+++++i+++v+ g  ++ ++++p ++pg+ e+  ++y +++++kAkkl++e G++ ++++        + 
  gi|488599939|ref|YP_007906410.1| 549 RQALAYAVPYDQIIEQVYSGNLERNYAAIPIGWPGYTEYGIEKY-EFNMAKAKKLIEESGIDPSKYT--------IE 616
                                       ************************************99988876.79*****************995........** PP

                                       EEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTT CS
                         SBP_bac_5 301 lllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsss 373
                                       +++++g++a+++i +l+q+++ ++G+k +v +++w  +yl++ + g++d +  gw +dy d+dn + p+++++
  gi|488599939|ref|YP_007906410.1| 617 ITYNAGNSAREKISALLQNTWSQLGFKCTVSSLEW-PVYLSKGEHGQYDYYTIGWVPDYLDTDNWVGPLYYGA 688
                                       ***********************************.*****************************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (699 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 4212.32
//
Query:       gi|488599940|ref|YP_007906411.1|  [L=82]
Description: hypothetical protein Asulf_00391 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   13.2   0.1      0.036   13.1   0.1    1.0  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     2e-06     0.036     293     352 ..      10      64 ..       2      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-06
                                       HHT----HHHHHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..- CS
                            AFOR_C 293 vtGidvteeellkaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvlede 352
                                       + G +++++el + Ge+iy  +  + + +G+++++ +  +r++e +      +gk++ ++
  gi|488599940|ref|YP_007906411.1|  10 ILGTHIKPDELKRKGEKIYREKLKLKVDMGFDKSKLKPQKRVFEVET----FRGKLD-ER 64 
                                       6899***************************************5333....344442.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 526.70
//
Query:       gi|488599941|ref|YP_007906412.1|  [L=40]
Description: hypothetical protein Asulf_00392 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       151  (0.00842211); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 244.95
//
Query:       gi|488599942|ref|YP_007906413.1|  [L=407]
Description: hypothetical protein Asulf_00393 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   26.3   0.2    1.6e-05   25.1   0.2    1.6  1  DHH       DHH family
  ------ inclusion threshold ------
      0.053   13.8   0.0        0.1   12.8   0.0    1.5  1  DUF1433   Protein of unknown function (DUF1433)
        0.1   12.4   0.3       0.39   10.5   0.1    2.1  2  DUF1953   Domain of unknown function (DUF1953)


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 !   25.1   0.2   2.6e-09   1.6e-05       8      73 ..      31     127 ..      27     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.6e-09
                                       CSSSHHHHHHHHHHHH.................................CECS--TCGGCGCCHHCCCSEEEEEEE- CS
                                       xxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   8 knpDtDsigSaialan.................................llvDhneksqavegeakeeaedviiiDH 51 
                                        + D+D+i+S+  l++                                 +  D    + ++++++++   +viiiDH
  gi|488599942|ref|YP_007906413.1|  31 YHNDADGICSSAILSRvceyfglkteliciekvnpdiieiihadrdgiiIYTDLAGLAAEAIDRINAGRGKVIIIDH 107
                                       578*******7777775888888888888888888877777777777777*************************** PP

                                       S---SS---SS--EEEE-SSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  52 Hrlgeefetlapilflnepvgs 73 
                                       H  + e+e    +++ln++++ 
  gi|488599942|ref|YP_007906413.1| 108 HPAK-EIESD-SVFVLNPELSG 127
                                       ***8.66666.67777777664 PP

>> DUF1433  Protein of unknown function (DUF1433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.7e-05       0.1       6      61 ..     261     318 ..     256     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                           DUF1433   6 eeRielylkynvkeiksvtFtel..kesPmgvavieGYindnkeldFvAsisteenfe 61 
                                        e++  +lk n+k+ k v++ ++    sPmgv+v+  +    k++ Fv + ++   f+
  gi|488599942|ref|YP_007906413.1| 261 FEKMVEFLKTNLKQEKHVQWFHIgdSFSPMGVKVVGEFCELIKDMTFVDDSKYLIGFQ 318
                                       577889************9866521679*******************99887766666 PP

>> DUF1953  Domain of unknown function (DUF1953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   6.6e-05      0.39      14      45 ..     185     216 ..     179     227 .. 0.88
   2 ?   -2.8   0.0      0.95   5.7e+03      34      47 ..     293     306 ..     291     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.6e-05
                                       EEETTTEEEEEESSSS-EEEEEEEEEEETTTT CS
                           DUF1953  14 fmrGdkvlvivktlnrdydieidGeytdvitd 45 
                                        mr  +v +++  +   y i+  Gey+dv+++
  gi|488599942|ref|YP_007906413.1| 185 AMRMKQVKIMIDGMKERYYIDFFGEYADVVAE 216
                                       69999************************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.95
                                       EEEEEEEETTTTEE CS
                           DUF1953  34 eidGeytdvitdet 47 
                                       ++ Ge+ ++i d t
  gi|488599942|ref|YP_007906413.1| 293 KVVGEFCELIKDMT 306
                                       67799999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2567.99
//
Query:       gi|488599943|ref|YP_007906414.1|  [L=180]
Description: hypothetical protein Asulf_00394 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0064   16.4   1.7      0.017   15.0   0.1    2.3  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   9.5e-07     0.017       1      34 [.       7      40 ..       7      42 .. 0.96
   2 ?   -0.5   0.2     0.074   1.3e+03       9      20 ..      79      90 ..      73      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.5e-07
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlr 34
                                      r+si +d  +++ L+ +++++++S+Se++R  +r
  gi|488599943|ref|YP_007906414.1|  7 RLSIAVDNYTYKVLEDIVKKEQKSMSEVVRNSIR 40
                                      89****************************8887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.074
                                      HHHHHHHHHHHH CS
                             RHH_1  9 ellerLdelarr 20
                                       +le +de++++
  gi|488599943|ref|YP_007906414.1| 79 AILEIIDEKKKE 90
                                      57899**99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1152.31
//
Query:       gi|488599944|ref|YP_007906415.1|  [L=100]
Description: hypothetical protein Asulf_00395 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 742.94
//
Query:       gi|488599945|ref|YP_007906416.1|  [L=61]
Description: hypothetical protein Asulf_00396 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 409.99
//
Query:       gi|488599946|ref|YP_007906417.1|  [L=158]
Description: hypothetical protein Asulf_00397 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-38  129.2   0.8    4.6e-38  129.2   0.1    1.4  2  DUF22     Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.1   2.6e-42   4.6e-38       2     106 .]       4     111 ..       3     111 .. 0.98
   2 ?   -3.3   0.1       0.4   7.1e+03      43      57 ..     113     128 ..     112     131 .. 0.65

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 2.6e-42
                             DUF22   2 vkivyrkd...geivrekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalg 75 
                                       v+ivy++d   g+++++k++vep+g+++s++a+w++li++ed+ev++++v++i++++i++pen iv+pl imrhalg
  gi|488599946|ref|YP_007906417.1|   4 VEIVYWDDrinGSLKSDKINVEPYGFQLSPIAEWRILISAEDKEVEESKVCAIDVEPIDVPENAIVSPLPIMRHALG 80 
                                       89******9988***************************************************************** PP

                             DUF22  76 tvldvvekgkpkkveeereiteavflpvedG 106
                                       ++ldv+  gk kkvee+++it+a+flpv++G
  gi|488599946|ref|YP_007906417.1|  81 VLLDVYVPGKLKKVEESKKITQAIFLPVMSG 111
                                       ****************************998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.4
                             DUF22  43 vkkGev.kkikikeie 57 
                                       ++kGe+  +i+i+ ++
  gi|488599946|ref|YP_007906417.1| 113 IRKGELiGVINIRYVK 128
                                       7788762467777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1094.56
//
Query:       gi|488599947|ref|YP_007906418.1|  [L=43]
Description: hypothetical protein Asulf_00398 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 306.61
//
Query:       gi|488599948|ref|YP_007906419.1|  [L=160]
Description: hypothetical protein Asulf_00399 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-31  106.5   5.5    7.2e-31  106.0   0.9    2.0  2  DUF22     Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.9     4e-35   7.2e-31       1     106 []       2     107 ..       2     107 .. 0.99
   2 !    3.0   0.3    0.0045        81      74     100 ..     117     143 ..     115     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 4e-35
                             DUF22   1 evkivyrkdgeivrekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtv 77 
                                       ev+i yrkd+e+v ek++ve++gy++ +va++  ++Adedvevk+++vk+ik++e+++ +n+ ++ l+ +rhalgt+
  gi|488599948|ref|YP_007906419.1|   2 EVTISYRKDSEVVYEKANVEEAGYFLGPVAYFVNIVADEDVEVKANRVKVIKVQEFKISGNERLTLLDRYRHALGTL 78 
                                       689************************************************************************** PP

                             DUF22  78 ldvvekgkpkkveeereiteavflpvedG 106
                                       + vve+gkp++++  ++++++vf+p++dG
  gi|488599948|ref|YP_007906419.1|  79 VAVVEDGKPERIDVPSRVKYVVFYPIADG 107
                                       ****************************9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0045
                             DUF22  74 lgtvldvvekgkpkkveeereiteavf 100
                                       +g+v  v ++ k   ve+ re+++a+ 
  gi|488599948|ref|YP_007906419.1| 117 VGVVTTVKKEAKEAIVEKLREVDKAIS 143
                                       68999999999*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1280.55
//
Query:       gi|488599949|ref|YP_007906420.1|  [L=475]
Description: putative permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-34  118.9  28.7    2.6e-34  118.9  28.7    2.0  2  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.22   10.3   0.0       0.35    9.7   0.0    1.2  1  Imm65     Immunity protein 65


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 !  118.9  28.7   2.9e-38   2.6e-34       1     235 [.      27     296 ..      27     297 .. 0.91
   2 ?   -4.1   3.4       1.1   9.6e+03      74      74 ..     380     380 ..     315     434 .. 0.52

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 2.9e-38
                              TauE   1 lllagllaGfvagllGiGggliavPlLll.llppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliG 76 
                                       ll++g+++G+++g++G Gg+++++P ++  ++p ++ava+++++ ++ +++ga++  + g++d++l++l+++++++G
  gi|488599949|ref|YP_007906420.1|  27 LLALGFFGGMLSGFIGSGGAFVLTPGMMSiGVPGPIAVASNMCHKFPKAMIGAWRRKKVGHLDVKLAILMAFSAILG 103
                                       5799*************************669***********************9999****************** PP

                              TauE  77 allGallllllpsel........lkllfgvlllllallmll...rkkr.......................srak.. 117
                                       +++G+ + +++ ++l        ++++f ++l  +a+l+++   ++k+                          k  
  gi|488599949|ref|YP_007906420.1| 104 VQVGIQVQKYILEQLgptgtnlyVTIAFLIVLPSVAALLIRdvfKAKKygiedtepefakklekkfrippmI--Kfd 178
                                       *******9999999777888888999999999889998877432555599**99999999888777655553..055 PP

                              TauE 118 grerrptaillvligglvGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyal.agavdwp 193
                                        + r+++++l++++g+++G+l++ + +G Gf++vp ++++ g +  +a +t l +++v++ +g+++ a+ +gavd++
  gi|488599949|ref|YP_007906420.1| 179 VAGRTQSLWLTIPLGFATGFLAATIAVG-GFIGVPSMIYVIGASSAVASGTELGIAFVMGSTGTFTWAYlLGAVDFR 254
                                       7889999999****999**********9.9************************************85569****** PP

                              TauE 194 llllllpgallGallGarlarrlsertlrrlfallllvlgvk 235
                                       l  l+l+++l+G+++Ga  ++++ + ++++++a+++l++ v+
  gi|488599949|ref|YP_007906420.1| 255 LTTLILATSLIGVQIGAVGTTYVRQYYIKLAMAVVMLLVTVS 296
                                       **************************************9885 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.1
                              TauE  74 l 74 
                                       +
  gi|488599949|ref|YP_007906420.1| 380 I 380
                                       1 PP

>> Imm65  Immunity protein 65
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   3.9e-05      0.35     120     176 ..     384     449 ..     370     465 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.9e-05
                             Imm65 120 pnyyrlfeypelwsyfsgdipqekt....a....lmgltshdiivpssyipdlfel.eidslknyv 176
                                        nyy lf  p+ w yf  +ip+  t    a    ++ l+ +  iv  s+  ++++l +i +lk+ v
  gi|488599949|ref|YP_007906420.1| 384 INYYFLFRDPNAWPYFITQIPHMGTfgaiAytlgVIALAIYWSIVHGSFAHNFLDLiNITALKDEV 449
                                       49*******************987633221211133444455577777777776653677777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3283.89
//
Query:       gi|488599950|ref|YP_007906421.1|  [L=73]
Description: hypothetical protein Asulf_00401 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00054   21.0   0.0    0.00071   20.6   0.0    1.2  1  DUF5320   Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.9e-08   0.00071      36      99 .]       7      70 ..       1      70 [. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.9e-08
                           DUF5320 36 gfGr...grggrglgrgfgrrrraggarlaaaetaeaskeeekelLeeqaeaLeeeleaikkrlkel 99
                                      g+ +     g+ g+ rg  r + + ++r+     ++ + +++ ++Le+ ++ Le ele+i++r++el
  gi|488599950|ref|YP_007906421.1|  7 GWRWwykATGKPGWMRGDYRCFGYLRYRGL---RYQDEFRDDLDVLERIKRNLELELEDIRRRIDEL 70
                                      444444444455555554444444555555...78899**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 509.65
//
Query:       gi|488599951|ref|YP_007906422.1|  [L=115]
Description: hypothetical protein Asulf_00402 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   86.5   0.1    1.4e-24   86.3   0.1    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.1   7.6e-29   1.4e-24       2      94 ..      13     100 ..      12     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 7.6e-29
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEE CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagiev 78 
                                       ++ v++hFG+a++F+iy++e++ev+++ n      +++ gg g++++l+ +++vdvvi+g++G +a+a +++ gi+v
  gi|488599951|ref|YP_007906422.1|  13 DDYVCDHFGKAETFTIYDTESKEVEVIRNT-----SEHFGGFGRPPELIRAKNVDVVICGGMGAKAIALFKSYGIKV 84 
                                       688***************************.....888899************************************ PP

                                       EES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  79 ykgaggtveealkevl 94 
                                       ++ga+g+v++a++++l
  gi|488599951|ref|YP_007906422.1|  85 FMGASGKVKDAIDQFL 100
                                       ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 808.43
//
Query:       gi|488599952|ref|YP_007906423.1|  [L=141]
Description: hypothetical protein Asulf_00403 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-20   73.6   0.1    1.7e-20   73.1   0.1    1.2  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.1   9.6e-25   1.7e-20       2      94 ..      13     107 ..      12     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 9.6e-25
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEE..E.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTS CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenr..veeaadaegggggklaqllaeegvdvvivgkiGpralakleaagi 76 
                                       ++ v + FGr++ F+i++ +++ ++i  ++   ++a+++++g+g++++ql+ + gv+++++gkiGp+a++ l++ag+
  gi|488599952|ref|YP_007906423.1|  13 EDNVTPQFGRTEKFTIVDFDKEMKEIKAVEvvDNKAKSQPSGAGIAASQLIIDLGVEILLTGKIGPKAMKVLKSAGV 89 
                                       789*****************8866655555557789999************************************** PP

                                       EEEES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co  77 evykgaggtveealkevl 94 
                                       +vy ++g +v+ a++++ 
  gi|488599952|ref|YP_007906423.1|  90 KVYNAEGMNVKYAVDAFT 107
                                       *************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 886.64
//
Query:       gi|488599953|ref|YP_007906424.1|  [L=97]
Description: hypothetical protein Asulf_00404 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   10.3   0.1       0.24   10.2   0.1    1.1  1  Fe-ADH    Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   1.3e-05      0.24     288     339 ..      29      79 ..      12      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 1.3e-05
                                       .....HHHHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT.-HH CS
                            Fe-ADH 288 aaperlaqlaralggesdeeaaeeliealrellkelglptsLselgvde.edl 339
                                       +a++r+++l+r l +e d++++e+++e l e+lk+ ++  +L+++g+d  +++
  gi|488599953|ref|YP_007906424.1|  29 EAKKRYEELVRDLLKE-DNTEKEKELELLVEFLKKANFS-RLRKMGFDGnKEV 79 
                                       44799*******9666.89999*****************.9*****9983455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1366  (0.0761894); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 589.86
//
Query:       gi|488599954|ref|YP_007906425.1|  [L=262]
Description: MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-19   70.6   0.0    1.5e-19   70.3   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    6.5e-12   45.4   0.6    1.6e-05   24.5   0.0    3.2  2  ParA         NUBPL iron-transfer P-loop NTPase
    7.1e-09   35.1  16.2    3.6e-05   23.4   2.1    2.4  2  Fer4         4Fe-4S binding domain
    1.2e-08   35.1   0.2     0.0012   18.8   0.0    2.2  2  AAA_31       AAA domain
      1e-06   29.6   6.1     0.0012   19.8   0.3    2.4  2  Fer4_16      4Fe-4S double cluster binding domain
    2.8e-05   24.6  11.1    0.00029   21.4  11.8    2.2  2  Fer4_7       4Fe-4S dicluster domain
    4.3e-05   23.6  10.2    0.00013   22.0  10.4    1.7  1  Fer4_9       4Fe-4S dicluster domain
    0.00012   21.9   0.1    0.00096   19.0   0.0    2.0  2  AAA_26       AAA domain
      0.005   16.9  17.2       0.27   11.4   7.1    2.5  2  Fer4_2       4Fe-4S binding domain
     0.0069   15.6   0.7      0.018   14.2   0.4    1.7  2  ArsA_ATPase  Anion-transporting ATPase
     0.0081   16.7  12.4       0.24   11.9   1.2    2.4  2  Fer4_17      4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   15.8  13.8       0.24   11.6   1.5    2.4  3  Fer4_21      4Fe-4S dicluster domain
       0.02   14.9   2.7       0.02   14.9   2.7    2.6  2  Fer4_6       4Fe-4S binding domain
      0.026   15.0  15.2        0.7   10.5   6.4    2.6  2  Fer4_4       4Fe-4S binding domain
      0.029   15.2   5.5        2.3    9.1   0.4    2.2  2  Fer4_22      4Fe-4S dicluster domain
      0.034   14.3  15.8        0.1   12.7   1.4    2.2  3  Fer4_10      4Fe-4S dicluster domain
       0.05   14.6  17.2       0.31   12.1   4.7    2.5  2  Fer4_3       4Fe-4S binding domain
      0.062   12.5   0.0       0.08   12.2   0.0    1.1  1  DUF2075      Uncharacterized conserved protein (DUF2075)
        0.2   12.2  15.2       0.74   10.3   2.3    2.4  3  Fer4_8       4Fe-4S dicluster domain
       0.98   10.0  11.2        1.1    9.8   0.5    2.5  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
        4.9    8.0   8.4        3.7    8.4   0.2    2.4  2  Fer4_15      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.7e-22   1.5e-19       1     128 []       3     247 ..       3     247 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.7e-22
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ia+as+kGG+GKTt+++nLa+      + V l+D+D++ +n++ ++ + n++e+                       
  gi|488599954|ref|YP_007906425.1|   3 IAVASGKGGTGKTTVSVNLAF-----FNSVDLFDLDVEEPNDH-IFIKGNKKENlvfrkvpevndccngcgvcrdvc 73 
                                       89*******************.....5569*************.7777777777789******************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|488599954|ref|YP_007906425.1|  74 qfsaiyvidraypipelchscgacsylcpekaikevdyqtgkvvtvegdikltygeltvgeaspvflikhvkqlmgk 150
                                       ***************************************************************************** PP

                                       ....................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHH CS
                                       ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllke 95 
                                                                           dlk  ++++++l           gv++n+++ +  +   ++
  gi|488599954|ref|YP_007906425.1| 151 naiidsppgttcpmvesvidsdyvilvaeptpfslhDLKIAVNVVSDLNLD-------FGVLINKYGLP--FDGVEK 218
                                       *********************************999999999999999988.......9********99..776666 PP

                                       HHHHHHHHCTS-EEEEEE--CCHCCCCHHTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  96 aleelkqrygvpvlgviprdeavaeapargepv 128
                                        ++ +    g++++g+ip++ ++a+ +++g+++
  gi|488599954|ref|YP_007906425.1| 219 YCKSE----GIEIIGKIPFSAEIAKKYSKGKLI 247
                                       66665....********************9865 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 !   24.5   0.0   1.8e-08   1.6e-05       6      43 ..       3      35 ..       1      57 [. 0.81
   2 !   14.5   0.3   2.2e-05     0.018     116     223 ..     153     245 ..     140     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.8e-08
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiy 43
                                      iav+SgKGG GK+tv+vnlA+       +v l+D+D+ 
  gi|488599954|ref|YP_007906425.1|  3 IAVASGKGGTGKTTVSVNLAFF-----NSVDLFDLDVE 35
                                      99******************85.....45666666665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.2e-05
                              ParA 116 iiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkg 192
                                       iiD PPGt+     v + ++ + +++V+ p   +l+d k a++++++++++  Gv+ N  g+           f  +
  gi|488599954|ref|YP_007906425.1| 153 IIDSPPGTTCPM--VESVIDSDYVILVAEPTPFSLHDLKIAVNVVSDLNLDF-GVLINKYGLP----------F--D 214
                                       8*******8553..445568999**************************996.6665544433..........3..6 PP

                              ParA 193 ggeklaeelgvpllgeipldpeireasdegk 223
                                       g+ek++++ g++++g+ip++ ei+++  +gk
  gi|488599954|ref|YP_007906425.1| 215 GVEKYCKSEGIEIIGKIPFSAEIAKKYSKGK 245
                                       8999999999999999999999999998887 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   6.6   4.1e-06    0.0035       5      24 .]      60      79 ..      56      79 .. 0.91
   2 !   23.4   2.1   4.2e-08   3.6e-05       3      24 .]      86     107 ..      84     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.1e-06
                                      TTTSSS-THHHHHSTTTEEE CS
                              Fer4  5 eekCigCGaCvevCPvgAIt 24
                                       + C gCG C +vC + AI+
  gi|488599954|ref|YP_007906425.1| 60 NDCCNGCGVCRDVCQFSAIY 79
                                      589***************96 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 4.2e-08
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                        ++e+C  CGaC   CP  AI+
  gi|488599954|ref|YP_007906425.1|  86 PIPELCHSCGACSYLCPEKAIK 107
                                       689*****************96 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-06    0.0012       4      24 ..       3      23 ..       1      36 [. 0.92
   2 !   14.6   0.1   2.8e-05     0.024     121     167 ..     152     198 ..      99     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                            AAA_31  4 IaianqKGGvGKTTtsvnlaa 24
                                      Ia+a  KGG GKTT svnla 
  gi|488599954|ref|YP_007906425.1|  3 IAVASGKGGTGKTTVSVNLAF 23
                                      9******************96 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.8e-05
                            AAA_31 121 iiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktieev 167
                                        iiD pP   + ++ +++ sd+vi + ++++++l+ l+  ++ ++++
  gi|488599954|ref|YP_007906425.1| 152 AIIDSPPGTTCPMVESVIDSDYVILVAEPTPFSLHDLKIAVNVVSDL 198
                                       59*********************************999988888765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   1.3   0.00034      0.29      52      66 ..      61      75 ..      33      80 .. 0.67
   2 !   19.8   0.3   1.4e-06    0.0012       2      22 ..      91     111 ..      90     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00034
                           Fer4_16 52 eaitgCdiCqdvCPa 66
                                        + gC++C dvC +
  gi|488599954|ref|YP_007906425.1| 61 DCCNGCGVCRDVCQF 75
                                      445777777777765 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.4e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C++Cg+C   CP++aike  +
  gi|488599954|ref|YP_007906425.1|  91 CHSCGACSYLCPEKAIKEVDY 111
                                       *****************9843 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  11.8   3.3e-07   0.00029       1      52 []      62     105 ..      62     105 .. 0.92
   2 !   14.2   1.9     6e-05     0.052       2      22 ..      91     111 ..      90     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.3e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C gCg C ++C  +ai++ ++        ++  pe C +CgaC   CP +a
  gi|488599954|ref|YP_007906425.1|  62 CCNGCGVCRDVCQFSAIYVIDR--------AYPIPELCHSCGACSYLCPEKA 105
                                       5******************776........67899**************876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6e-05
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       C  CgaC   Cp kai+  ++
  gi|488599954|ref|YP_007906425.1|  91 CHSCGACSYLCPEKAIKEVDY 111
                                       999**********99986655 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0  10.4   1.5e-07   0.00013       2      51 .]      63     106 ..      62     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.5e-07
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       C+gCg C ++C++ ++   + ++ +         C++CgaC   Cp++ai
  gi|488599954|ref|YP_007906425.1|  63 CNGCGVCRDVCQFSAIYVIDRAYPIPE------LCHSCGACSYLCPEKAI 106
                                       ***************966666666553......5*************987 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.67   5.7e+02       3      22 ..       3      22 ..       2      25 .. 0.84
   2 !   19.0   0.0   1.1e-06   0.00096     131     194 ..     174     237 ..     171     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.67
                            AAA_26  3 ifvtgtdtgvGKTvvslgLv 22
                                      i v++   g GKT+vs  L+
  gi|488599954|ref|YP_007906425.1|  3 IAVASGKGGTGKTTVSVNLA 22
                                      678888899*******8875 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.1e-06
                            AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNkvrnp.envetlekksgipvlGvvPylpdl 194
                                       vilVa ++  ++ +l ++++++ + n+  +Gv +Nk   p + ve+++k+ gi+++G +P ++++
  gi|488599954|ref|YP_007906425.1| 174 VILVAEPTPFSLHDLKIAVNVVSDLNLD-FGVLINKYGLPfDGVEKYCKSEGIEIIGKIPFSAEI 237
                                       9*********************995554.8******988899******************99876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   7.1   0.00031      0.27       8      20 ..      61      73 ..      55      75 .. 0.86
   2 !   10.6   2.5   0.00058       0.5       7      22 .]      88     103 ..      82     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                            Fer4_2  8 drCigCgaCvsaC 20
                                      d C+gCg C+++C
  gi|488599954|ref|YP_007906425.1| 61 DCCNGCGVCRDVC 73
                                      77*********** PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       ++ C +CgaC   CP+
  gi|488599954|ref|YP_007906425.1|  88 PELCHSCGACSYLCPE 103
                                       789*9*****999**5 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.4   2.1e-05     0.018       1      23 [.       1      23 [.       1      28 [. 0.89
   2 ?   -1.5   0.0       1.3   1.1e+03     202     248 ..     169     213 ..     162     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                      -EEEEEEESTTSSHHHHHHHHHH CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatav 23
                                      +++ + +GKGG GKttvs  +a 
  gi|488599954|ref|YP_007906425.1|  1 MRIAVASGKGGTGKTTVSVNLAF 23
                                      788899************99885 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                       TSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE.E-TT CS
                       ArsA_ATPase 202 tdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNk.llpe 248
                                       +d ++  ++lV  p   sl++ + a++ ++ ++++   v++Nk  lp 
  gi|488599954|ref|YP_007906425.1| 169 IDSDY--VILVAEPTPFSLHDLKIAVNVVSDLNLDFG-VLINKyGLPF 213
                                       56665..888999999999999999999999999875.5667745664 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   1.2   0.00029      0.24       2      20 ..      63      81 ..      62      89 .. 0.80
   2 !   10.4   3.4   0.00085      0.73      44      58 ..      89     103 ..      81     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                           Fer4_17  2 CiqCgyClpeCpsyeaydn 20
                                      C++Cg C+++C + ++y  
  gi|488599954|ref|YP_007906425.1| 63 CNGCGVCRDVCQFSAIYVI 81
                                      ***********99877655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00085
                           Fer4_17  44 slCieCgeCerkCPq 58 
                                       +lC++Cg C++ CP+
  gi|488599954|ref|YP_007906425.1|  89 ELCHSCGACSYLCPE 103
                                       79************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 ?    8.9   5.1    0.0019       1.6      33      52 ..      55      74 ..      36      80 .. 0.72
   2 ?    8.8  14.9    0.0021       1.8       6      58 ..      61     107 ..      58     109 .. 0.84
   3 ?   11.6   1.5   0.00028      0.24       6      36 ..      89     119 ..      84     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0019
                           Fer4_21 33 vlkvvedeCvGCnlCssvCP 52
                                      +++ v+d C GC +C +vC 
  gi|488599954|ref|YP_007906425.1| 55 KVPEVNDCCNGCGVCRDVCQ 74
                                      446689*************6 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0021
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       d C gCg C  +C+     ai + ++++   + + C  C  Cs  CP e++i+
  gi|488599954|ref|YP_007906425.1|  61 DCCNGCGVCRDVCQ---FSAIYVIDRAY--PIPELCHSCGACSYLCP-EKAIK 107
                                       67999*********...67887765555..6899*************.78875 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00028
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkv 36 
                                       + C +Cg C   C++++++ +++++ +v++v
  gi|488599954|ref|YP_007906425.1|  89 ELCHSCGACSYLCPEKAIKEVDYQTGKVVTV 119
                                       5677777777777777777777666666655 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   7.0     0.071        61       7      24 .]      61      78 ..      59      78 .. 0.88
   2 ?   14.9   2.7   2.4e-05      0.02       6      24 .]      88     106 ..      87     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.071
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                      d C+gCg C +vC + ai
  gi|488599954|ref|YP_007906425.1| 61 DCCNGCGVCRDVCQFSAI 78
                                      78***********88776 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.4e-05
                            Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                       p++C +Cg+C   CPe+ai
  gi|488599954|ref|YP_007906425.1|  88 PELCHSCGACSYLCPEKAI 106
                                       89***************98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   6.4   0.00082       0.7       4      15 ..      63      74 ..      55      76 .. 0.91
   2 ?    9.0   1.5    0.0027       2.3       1      16 [.      88     103 ..      88     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00082
                            Fer4_4  4 CigCgsCvaaCP 15
                                      C+gCg+C+++C 
  gi|488599954|ref|YP_007906425.1| 63 CNGCGVCRDVCQ 74
                                      9**********5 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0027
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +e C  Cg+C + CP 
  gi|488599954|ref|YP_007906425.1|  88 PELCHSCGACSYLCPE 103
                                       588***********94 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4    0.0027       2.3      79      93 ..      60      74 ..      26      77 .. 0.82
   2 ?    8.4   0.7    0.0044       3.8       2      14 ..      91     103 ..      90     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0027
                           Fer4_22 79 esgCvGCgRCieacp 93
                                      +  C GCg C ++c+
  gi|488599954|ref|YP_007906425.1| 60 NDCCNGCGVCRDVCQ 74
                                      56799*********7 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0044
                           Fer4_22   2 ClsCgaCtlvCpt 14 
                                       C sCgaC+++Cp 
  gi|488599954|ref|YP_007906425.1|  91 CHSCGACSYLCPE 103
                                       999********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 ?   12.3  15.2   0.00016      0.14       6      56 .]      60     102 ..      55     102 .. 0.90
   2 ?   12.7   1.4   0.00012       0.1       6      25 ..      88     107 ..      83     125 .. 0.71
   3 ?   -2.9   0.0       9.3     8e+03      18      21 ..     161     164 ..     160     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        d+C +Cg C+++C        +  ++  +++    +e C+ cgaC   CP
  gi|488599954|ref|YP_007906425.1|  60 NDCCNGCGVCRDVC--------QFSAIYVIDRAYPIPELCHSCGACSYLCP 102
                                       589***********........46899999999999**************9 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                           Fer4_10   6 ddtCirCgkCvkaCPadlts 25 
                                       ++ C  Cg+C   CP ++ +
  gi|488599954|ref|YP_007906425.1|  88 PELCHSCGACSYLCPEKAIK 107
                                       67899999999999995522 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.3
                           Fer4_10  18 aCPa 21 
                                        CP+
  gi|488599954|ref|YP_007906425.1| 161 TCPM 164
                                       6998 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.6    0.0076       6.5       1      13 [.      63      75 ..      63      77 .. 0.89
   2 ?   12.1   4.7   0.00036      0.31       1      15 []      91     105 ..      91     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0076
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+gCg C +vC  
  gi|488599954|ref|YP_007906425.1| 63 CNGCGVCRDVCQF 75
                                      ***********76 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00036
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ CgaC   CP++A
  gi|488599954|ref|YP_007906425.1|  91 CHSCGACSYLCPEKA 105
                                       999*********998 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.4e-05      0.08       3      49 ..       3      55 ..       1      61 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.4e-05
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael......eddeeertavylsvNhplvlvlre 49
                                      + + +G+ GtGKt v +nl++         d ee + ++++ +N++++lv r+
  gi|488599954|ref|YP_007906425.1|  3 IAVASGKGGTGKTTVSVNLAFFNsvdlfdLDVEEPNDHIFIKGNKKENLVFRK 55
                                      67889************998777679998899999************999886 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.5     0.014        12       4      16 ..      62      74 ..      35      77 .. 0.70
   2 ?    6.7   5.2     0.011       9.8       4      17 ..      62      75 ..      59      87 .. 0.80
   3 ?   10.3   2.3   0.00087      0.74      49      64 ..      89     104 ..      80     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                            Fer4_8  4 kCieCgaCqsaCp 16
                                       C++Cg C++ C 
  gi|488599954|ref|YP_007906425.1| 62 CCNGCGVCRDVCQ 74
                                      3666666666664 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                            Fer4_8  4 kCieCgaCqsaCpv 17
                                       C++Cg C++ C +
  gi|488599954|ref|YP_007906425.1| 62 CCNGCGVCRDVCQF 75
                                      59999999999964 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00087
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       + C++cgaC+  Cp++
  gi|488599954|ref|YP_007906425.1|  89 ELCHSCGACSYLCPEK 104
                                       6899999999999986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.6       0.1        85       1      16 [.      59      73 ..      59      83 .. 0.91
   2 ?    9.8   0.5    0.0013       1.1       4      18 ..      89     103 ..      88     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      V+ d C +cg+C++++
  gi|488599954|ref|YP_007906425.1| 59 VN-DCCNGCGVCRDVC 73
                                      67.99*********99 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0013
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       + C +cgaC  l+P+
  gi|488599954|ref|YP_007906425.1|  89 ELCHSCGACSYLCPE 103
                                       56************8 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   3.3      0.41   3.5e+02       6      18 ..      61      73 ..      60      84 .. 0.85
   2 ?    8.4   0.2    0.0043       3.7       6      27 ..      89     111 ..      88     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.41
                           Fer4_15  6 daCigcglCvaea 18
                                      d C gcg+C +++
  gi|488599954|ref|YP_007906425.1| 61 DCCNGCGVCRDVC 73
                                      67*******9998 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0043
                           Fer4_15   6 daCigcglCvaeape.vfelded 27 
                                       ++C +cg+C  ++pe  +++ ++
  gi|488599954|ref|YP_007906425.1|  89 ELCHSCGACSYLCPEkAIKEVDY 111
                                       68***********7515555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1475.96
//
Query:       gi|488599955|ref|YP_007906426.1|  [L=296]
Description: MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-18   66.5   0.0    2.9e-18   66.2   0.0    1.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.6e-12   46.7  14.1    1.3e-06   28.0   0.5    2.9  2  Fer4             4Fe-4S binding domain
    5.7e-11   42.0  10.3    3.2e-05   23.8   2.5    3.0  2  Fer4_6           4Fe-4S binding domain
    2.1e-10   40.5   0.0    9.3e-05   22.0   0.0    2.8  2  ParA             NUBPL iron-transfer P-loop NTPase
    4.1e-10   40.1   6.1    0.00012   22.5   0.2    2.6  2  Fer4_7           4Fe-4S dicluster domain
    8.2e-09   36.3   3.0    0.00018   22.3   0.2    2.6  2  Fer4_16          4Fe-4S double cluster binding domain
    1.6e-08   34.5  15.9    3.1e-07   30.4   8.1    2.1  2  Fer4_21          4Fe-4S dicluster domain
    2.4e-08   33.9   3.3    0.00047   20.2   0.1    2.7  2  Fer4_10          4Fe-4S dicluster domain
    4.6e-08   33.2   0.1    0.00077   19.4   0.0    2.3  2  AAA_31           AAA domain
    2.1e-07   30.6  11.4    0.00058   19.8   3.1    2.6  2  Fer4_2           4Fe-4S binding domain
    3.1e-06   27.5   2.0      0.021   15.3   0.2    2.6  2  Fer4_8           4Fe-4S dicluster domain
    2.1e-05   24.6  11.2    0.00056   20.0  11.5    2.5  3  Fer4_9           4Fe-4S dicluster domain
    2.3e-05   24.8   3.1       0.13   12.8   0.2    2.6  2  Fer4_17          4Fe-4S dicluster domain
    0.00088   20.0   3.4        0.2   12.4   0.1    2.8  2  Fer4_15          4Fe-4S single cluster domain
     0.0014   18.5   0.1       0.23   11.4   0.0    2.3  2  RsgA_GTPase      RsgA GTPase
     0.0034   17.8  19.0     0.0039   17.6   1.8    3.1  2  Fer4_4           4Fe-4S binding domain
     0.0041   17.6   8.4       0.47   11.0   1.3    2.6  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
       0.03   13.5   2.4        0.1   11.7   0.6    2.3  2  ArsA_ATPase      Anion-transporting ATPase
       0.03   13.8   0.3      0.066   12.7   0.0    1.7  2  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.064   11.9   0.0      0.096   11.3   0.0    1.2  1  AAA_13           AAA domain
      0.098   10.6   0.0       0.14   10.1   0.0    1.2  1  Herpes_Helicase  Helicase
        0.1   12.5   0.2         14    5.6   0.0    2.3  2  Phage_30_8       Phage GP30.8 protein
       0.12   12.5   0.0        1.6    8.8   0.0    2.6  2  AAA_33           AAA domain
       0.14   10.8   0.0        0.2   10.3   0.0    1.2  1  PEPCK_ATP        Phosphoenolpyruvate carboxykinase
       0.16   11.6   0.2       0.56    9.9   0.0    1.9  3  AAA_30           AAA domain
       0.33   12.0  18.9       0.57   11.2   2.9    2.9  2  Fer4_3           4Fe-4S binding domain
        3.1    7.7  11.2          4    7.3   1.3    2.3  2  zf-C2H2_11       zinc-finger C2H2-type
        4.4    8.2  12.0        2.6    8.9   2.2    2.6  2  Fer4_22          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   4.5e-21   2.9e-18       1     126 [.      17     273 ..      17     276 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 4.5e-21
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       iai+s+kGG+GKTt++a ++ +        +  D+D++a+nl+il   e+ + +                       
  gi|488599955|ref|YP_007906426.1|  17 IAIISGKGGTGKTTFSALIHSIEGC-----VIADCDVDAPNLHILLNPEILEVEeyyaskkarilqdkcsscglcye 88 
                                       89***************99997776.....9************95555555555666669***************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|488599955|ref|YP_007906426.1|  89 vcrfnaifdnpytvndkrcegcgfcysacpekaivmetvktgeiyksktryghfvhallkageentgrlvtevrqra 165
                                       ***************************************************************************** PP

                                       ..............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEES CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ..............................................dlkrllellealgkkkalllkiagvvlnrvd 85 
                                                                                     dlkr+l l+ ++g k       a+v +n++d
  gi|488599955|ref|YP_007906426.1| 166 kkiaedmnfefvivdappgvgcpvmasltdvdvaiviseptlsglnDLKRILDLCDHFGVK-------AFVTVNKYD 235
                                       ***********************************************************99.......********* PP

                                       S...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  86 geneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                        +++ +l + +++e     +v++lg+ip+d++++e +++ +
  gi|488599955|ref|YP_007906426.1| 236 LNESMALKIRDYCESR---EVEFLGFIPFDKDLIEQVSNLK 273
                                       **98888888888887...****************999865 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.5     2e-09   1.3e-06       3      23 ..      75      95 ..      73      96 .. 0.91
   2 !   26.6   2.8   5.5e-09   3.5e-06       2      23 ..     101     122 ..     100     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2e-09
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      i ++kC  CG+C+evC ++AI
  gi|488599955|ref|YP_007906426.1| 75 ILQDKCSSCGLCYEVCRFNAI 95
                                      678*****************9 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 5.5e-09
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       +++  +C gCG C+++CP  AI
  gi|488599955|ref|YP_007906426.1| 101 TVNDKRCEGCGFCYSACPEKAI 122
                                       7999*****************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   1.1   2.3e-07   0.00015       2      24 .]      73      95 ..      72      95 .. 0.91
   2 !   23.8   2.5   5.1e-08   3.2e-05       3      24 .]     101     122 ..     101     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.3e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      ++i +dkC +Cg C+ vC ++ai
  gi|488599955|ref|YP_007906426.1| 73 ARILQDKCSSCGLCYEVCRFNAI 95
                                      67889**************9998 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 5.1e-08
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       ++++ +C gCg C+++CPe+ai
  gi|488599955|ref|YP_007906426.1| 101 TVNDKRCEGCGFCYSACPEKAI 122
                                       68999***************98 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.4e-05     0.015       5      47 ..      16      53 ..      14      79 .. 0.70
   2 !   22.0   0.0   1.5e-07   9.3e-05     111     233 ..     173     283 ..     155     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                              ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsi 47
                                       ia++SgKGG GK+t+++ +      +     + D D+  p++
  gi|488599955|ref|YP_007906426.1| 16 QIAIISGKGGTGKTTFSALIH-----SIEGCVIADCDVDAPNL 53
                                      69*************996542.....22333455555555555 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.5e-07
                              ParA 111 elDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekte 187
                                       + +++i+D PPG g   ++ +   +++ a++++ p    l+d k+ ++++++  vk +  v+               
  gi|488599955|ref|YP_007906426.1| 173 NFEFVIVDAPPGVGCPVMASLT--DVDVAIVISEPTLSGLNDLKRILDLCDHFGVKAFVTVNKYDLNESM------- 240
                                       4679**********98776555..55789*************************9988777654433222....... PP

                              ParA 188 ifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepese 233
                                            + ++++e+ +v++lg ip+d+++ e++ + k  +  +  ++
  gi|488599955|ref|YP_007906426.1| 241 ---ALKIRDYCESREVEFLGFIPFDKDLIEQVSNLKYPFDGTAAEK 283
                                       ...2467889999999999999999999999888775554444444 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.3   1.5e-06   0.00099      12      52 .]      46      94 ..      39      94 .. 0.64
   2 !   22.5   0.2   1.9e-07   0.00012       1      22 [.     106     127 ..     106     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-06
                            Fer4_7 12 Cpvkaield........eeenekgtekveidpekClgCgaCvavCPtga 52
                                      C v+a +l+        e+e+    +k++i ++kC++Cg C +vC ++a
  gi|488599955|ref|YP_007906426.1| 46 CDVDAPNLHillnpeilEVEEYYASKKARILQDKCSSCGLCYEVCRFNA 94
                                      5555555552222222223333355899*****************9987 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.9e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                       rC gCg+C +aCp kai ++ +
  gi|488599955|ref|YP_007906426.1| 106 RCEGCGFCYSACPEKAIVMETV 127
                                       7****************99865 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   0.00012     0.079       1      17 [.      79      95 ..      58     105 .. 0.68
   2 !   22.3   0.2   2.9e-07   0.00018       1      33 [.     106     135 ..     106     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                           Fer4_16  1 rCgtCgkCaevCPtnai 17
                                      +C +Cg C evC  nai
  gi|488599955|ref|YP_007906426.1| 79 KCSSCGLCYEVCRFNAI 95
                                      36666666666666665 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 2.9e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy 33 
                                       rC +Cg C ++CP++ai +++ k+    e  ++
  gi|488599955|ref|YP_007906426.1| 106 RCEGCGFCYSACPEKAIVMETVKT---GEIYKS 135
                                       6*****************994444...333333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.9   1.2e-05    0.0078      32      52 ..      71      91 ..      63      97 .. 0.72
   2 !   30.4   8.1   4.8e-10   3.1e-07       1      59 []      73     124 ..      73     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                           Fer4_21 32 tvlkvvedeCvGCnlCssvCP 52
                                      +++++++d+C  C lC++vC 
  gi|488599955|ref|YP_007906426.1| 71 KKARILQDKCSSCGLCYEVCR 91
                                      566777888888888888885 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 4.8e-10
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                       Ari +dkC +Cg+C+ +C+    +ai    ++ ++v +++C GC  C+s CP e++i m
  gi|488599955|ref|YP_007906426.1|  73 ARILQDKCSSCGLCYEVCR---FNAIF---DNPYTVNDKRCEGCGFCYSACP-EKAIVM 124
                                       8999***************...78886...456789****************.788876 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.6    0.0001     0.067      36      55 ..      71      90 ..      58      93 .. 0.68
   2 !   20.2   0.1   7.4e-07   0.00047       4      24 ..     102     128 ..     100     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                           Fer4_10 36 eavrkkvekCtgcgaCveaC 55
                                      ++ r+  +kC  cg C+e+C
  gi|488599955|ref|YP_007906426.1| 71 KKARILQDKCSSCGLCYEVC 90
                                      55555666666666666666 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 7.4e-07
                           Fer4_10   4 idddtCirCgkCvkaCPadl......t 24 
                                       ++d++C +Cg C +aCP ++      +
  gi|488599955|ref|YP_007906426.1| 102 VNDKRCEGCGFCYSACPEKAivmetvK 128
                                       6899**************766643330 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2    0.0003      0.19       2      20 ..      15      33 ..      14      46 .. 0.90
   2 !   19.4   0.0   1.2e-06   0.00077      72     165 ..     121     221 ..     102     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                            AAA_31  2 kvIaianqKGGvGKTTtsv 20
                                      k Iai+  KGG GKTT s 
  gi|488599955|ref|YP_007906426.1| 15 KQIAIISGKGGTGKTTFSA 33
                                      78**************986 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.2e-06
                            AAA_31  72 aiiktkvenldlipssidLaeaeielvelekk.....eeilkellekvkde..YDyiiiDcpPsLglltenaLvasd 141
                                       ai+ ++v++ ++  s++   ++   l+++ ++      + +++  +k+ ++  + ++i+D+pP +g+ ++ +L+  d
  gi|488599955|ref|YP_007906426.1| 121 AIVMETVKTGEIYKSKTRYGHFVHALLKAGEEntgrlVTEVRQRAKKIAEDmnFEFVIVDAPPGVGCPVMASLTDVD 197
                                       55555566666777777777766667666666444332224555566655444************************ PP

                            AAA_31 142 sviipvqaeayaleGleqllktie 165
                                         i++ +++   l+ l+++l+  +
  gi|488599955|ref|YP_007906426.1| 198 VAIVISEPTLSGLNDLKRILDLCD 221
                                       ********8888888887776655 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.3   2.5e-05     0.016       5      20 ..      75      90 ..      71      92 .. 0.88
   2 !   19.8   3.1     9e-07   0.00058       3      22 .]     100     119 ..      98     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                            Fer4_2  5 vdtdrCigCgaCvsaC 20
                                      +  d+C +Cg C+ +C
  gi|488599955|ref|YP_007906426.1| 75 ILQDKCSSCGLCYEVC 90
                                      6689************ PP

  == domain 2  score: 19.8 bits;  conditional E-value: 9e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       + v+  rC gCg C+saCP+
  gi|488599955|ref|YP_007906426.1| 100 YTVNDKRCEGCGFCYSACPE 119
                                       778999*************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 !   11.6   0.1   0.00045      0.29       3      16 ..      78      91 ..      54     101 .. 0.74
   2 !   15.3   0.2   3.3e-05     0.021       3      17 ..     105     132 ..     103     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      +kC  Cg+C + C 
  gi|488599955|ref|YP_007906426.1| 78 DKCSSCGLCYEVCR 91
                                      45666666666664 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.3e-05
                            Fer4_8   3 ekCieCgaCqsaCp.............v 17 
                                       ++C +Cg+C saCp             +
  gi|488599955|ref|YP_007906426.1| 105 KRCEGCGFCYSACPekaivmetvktgeI 132
                                       58***********988875554444442 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   2.1   9.9e-05     0.063      25      51 .]      72      95 ..      40      95 .. 0.72
   2 !   20.0  11.5   8.7e-07   0.00056       1      51 []      79     122 ..      79     122 .. 0.84
   3 !   13.8   2.5   7.7e-05     0.049       1      24 [.     106     129 ..     106     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.9e-05
                            Fer4_9 25 karlraase....eaCigCgaCveaCpkgai 51
                                      k       +    ++C +Cg C+e+C  +ai
  gi|488599955|ref|YP_007906426.1| 72 K-------ArilqDKCSSCGLCYEVCRFNAI 95
                                      2.......0333458***********98776 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 8.7e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC +Cg C e+C ++++ +   +  ++       +C gCg C+ aCp++ai
  gi|488599955|ref|YP_007906426.1|  79 KCSSCGLCYEVCRFNAIFDNPYTVNDK-------RCEGCGFCYSACPEKAI 122
                                       7**************996655444444.......4*************987 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 7.7e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaer 24 
                                       +C gCg C +aCp +++v++ +++
  gi|488599955|ref|YP_007906426.1| 106 RCEGCGFCYSACPEKAIVMETVKT 129
                                       588888888888888888777665 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   0.3   0.00039      0.25       1      17 [.      79      95 ..      60     104 .. 0.72
   2 !   12.8   0.2    0.0002      0.13       1      17 [.     106     122 ..     106     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00039
                           Fer4_17  1 rCiqCgyClpeCpsyea 17
                                      +C++Cg C ++C ++++
  gi|488599955|ref|YP_007906426.1| 79 KCSSCGLCYEVCRFNAI 95
                                      46666666666666555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0002
                           Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                       rC +Cg+C  +Cp  ++
  gi|488599955|ref|YP_007906426.1| 106 RCEGCGFCYSACPEKAI 122
                                       6999*****99997554 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.9     0.015       9.3       5      18 ..      77      90 ..      74      98 .. 0.85
   2 !   12.4   0.1   0.00031       0.2       3      20 ..     102     119 ..     101     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                           Fer4_15  5 rdaCigcglCvaea 18
                                      +d+C +cglC++++
  gi|488599955|ref|YP_007906426.1| 77 QDKCSSCGLCYEVC 90
                                      79**********99 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00031
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       v+ ++C+gcg C+ ++pe
  gi|488599955|ref|YP_007906426.1| 102 VNDKRCEGCGFCYSACPE 119
                                       7889************85 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.032        20      99     120 ..      15      36 ..       7      49 .. 0.78
   2 !   11.4   0.0   0.00035      0.23      15      64 ..     195     243 ..     159     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.032
                                       TSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinall 120
                                       ++++++ G+ G GK+t+   ++
  gi|488599955|ref|YP_007906426.1|  15 KQIAIISGKGGTGKTTFSALIH 36 
                                       5889999999999999765554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00035
                                       S--EEEEEEESTTTT--.HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH.H CS
                       RsgA_GTPase  15 Nvdqllivvslkepels.lnlldrfLvlaeekgiepvivlnKiDlleeee.e 64 
                                        vd +++   ++ep+ls ln l+r+L l+ + g++  + +nK Dl e++  +
  gi|488599955|ref|YP_007906426.1| 195 DVDVAIV---ISEPTLSgLNDLKRILDLCDHFGVKAFVTVNKYDLNESMAlK 243
                                       4444444...44555553799************************9998832 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   3.8    0.0017       1.1       1      16 [.      77      92 ..      77      93 .. 0.91
   2 !   17.6   1.8   6.2e-06    0.0039       2      16 ..     105     119 ..     104     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      q++C  Cg C+ +C +
  gi|488599955|ref|YP_007906426.1| 77 QDKCSSCGLCYEVCRF 92
                                      79************76 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.2e-06
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       +rC gCg C++aCP 
  gi|488599955|ref|YP_007906426.1| 105 KRCEGCGFCYSACPE 119
                                       69************4 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.9    0.0015      0.95       3      16 ..      77      90 ..      75      97 .. 0.91
   2 !   11.0   1.3   0.00073      0.47       1      18 [.     102     119 ..     102     120 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                           Fer4_13  3 rdtCiacgaCvela 16
                                      +d+C++cg+C+e++
  gi|488599955|ref|YP_007906426.1| 77 QDKCSSCGLCYEVC 90
                                      589**********9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00073
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       V+ ++C +cg C++++P+
  gi|488599955|ref|YP_007906426.1| 102 VNDKRCEGCGFCYSACPE 119
                                       7779*************8 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   0.00016       0.1       3      19 ..      17      33 ..      15      38 .. 0.87
   2 ?    0.7   0.0      0.38   2.4e+02     116     134 ..     165     183 ..     158     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                      EEEEEESTTSSHHHHHH CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsa 19
                                      + +++GKGG GKtt sa
  gi|488599955|ref|YP_007906426.1| 17 IAIISGKGGTGKTTFSA 33
                                      6689************8 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.38
                                       HHHHHHCSSSSEEEEESBS CS
                       ArsA_ATPase 116 llkyvkeeeydvvvlDtaP 134
                                        +k  ++++++ v++D +P
  gi|488599955|ref|YP_007906426.1| 165 AKKIAEDMNFEFVIVDAPP 183
                                       56778899********998 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.6   2.3e+03       8      23 ..      20      35 ..      16      43 .. 0.75
   2 ?   12.7   0.0    0.0001     0.066      66     142 ..     170     244 ..     126     282 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.6
                                      EEESTTSSHHHHHHHH CS
                          GTP_EFTU  8 iighvDhGKtTLtdrL 23
                                      i g   +GKtT++  +
  gi|488599955|ref|YP_007906426.1| 20 ISGKGGTGKTTFSALI 35
                                      56777899*9998755 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                                       TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHH CS
                          GTP_EFTU  66 etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkei 142
                                       e  ++++ ++D+P  v     v ++l  +D+a+++ + +    +  +++l l+   gv+ +v +NK D  ++   +i
  gi|488599955|ref|YP_007906426.1| 170 EDMNFEFVIVDAPPGV--GCPVMASLTDVDVAIVISEPTLSGLNDLKRILDLCDHFGVKAFVTVNKYDLNESMALKI 244
                                       5556666777776555..356899***************99999************************985554444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015     0.096      14      40 ..      13      39 ..       2      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                            AAA_13 14 dfkriNliYGwNGaGKTtLSrllrsle 40
                                      + k+i +i G+ G+GKTt+S l+ s+e
  gi|488599955|ref|YP_007906426.1| 13 EPKQIAIISGKGGTGKTTFSALIHSIE 39
                                      4789999****************9986 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00021      0.14      51     103 ..      11      58 ..       1      69 [. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                   Herpes_Helicase  51 eeselslPFsaylitGtAGaGkstsiqalaenldClitgatvvAaqnlsakLk 103
                                       +      P ++ +i+G  G+Gk+t  +al ++++  + +   v a nl+  L+
  gi|488599955|ref|YP_007906426.1|  11 NS----EPKQIAIISGKGGTGKTTF-SALIHSIEGCVIADCDVDAPNLHILLN 58 
                                       33....488999**********986.666666665555678999****99998 PP

>> Phage_30_8  Phage GP30.8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.046        30      54     110 ..     122     174 ..     101     181 .. 0.68
   2 ?    5.6   0.0     0.022        14      49      78 ..     218     247 ..     192     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.046
                        Phage_30_8  54 ievenfftgeiyrlnsvvvgkirskty..edeelgesedvvwyetarnraesliekikk 110
                                       i +e   tgeiy+  +  +g          +e++g         + r+ra+++ e +  
  gi|488599955|ref|YP_007906426.1| 122 IVMETVKTGEIYKSKTR-YGHFVHALLkaGEENTGR-----LVTEVRQRAKKIAEDMNF 174
                                       6788899*****98765.676633332002334444.....667999***999999875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                        Phage_30_8  49 dftytievenfftgeiyrlnsvvvgkirsk 78 
                                       d++ +  v+ f t + y+ln  +  kir  
  gi|488599955|ref|YP_007906426.1| 218 DLCDHFGVKAFVTVNKYDLNESMALKIRDY 247
                                       8999********************999754 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0026       1.6       3      31 ..      19      47 ..      17     139 .. 0.64
   2 ?    0.2   0.0       1.2   7.5e+02      84     103 ..     161     180 ..     144     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllssd 31
                                      ++ G  G+GK+t++  ++  +g+v+ + d
  gi|488599955|ref|YP_007906426.1| 19 IISGKGGTGKTTFSALIHSIEGCVIADCD 47
                                      678999*********99988885553333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                            AAA_33  84 erarflklarrlgvpvrivv 103
                                        r+r  k+a+++++++ iv+
  gi|488599955|ref|YP_007906426.1| 161 VRQRAKKIAEDMNFEFVIVD 180
                                       57899999999998888875 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00031       0.2     202     281 ..       9      98 ..       4     108 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                       EEEE-T.TS-EEEEEE-TTSSHHHHH...-BTTB-EEESSE......EEE-SS-EEES-SEEEEE-TT--TTTSHH. CS
                         PEPCK_ATP 202 sanvgekkgdvalfFGLSGtGKTtLs...adperkligdDe......hgwsdegvfniegGcYaKtidLskekepe. 268
                                       san + k  ++a+  G  GtGKTt+s      e  +i+d +      h++ +  + ++e+ +  K  ++ ++k  + 
  gi|488599955|ref|YP_007906426.1|   9 SANSEPK--QIAIISGKGGTGKTTFSaliHSIEGCVIADCDvdapnlHILLNPEILEVEEYYASKKARILQDKCSSc 83 
                                       7777743..6****************444455666777643222333556666666666655555555555544432 PP

                                       ..HHHHHSTT-EEES CS
                         PEPCK_ATP 269 ..iynairfgavlEN 281
                                          y+ +rf+a+++N
  gi|488599955|ref|YP_007906426.1|  84 glCYEVCRFNAIFDN 98 
                                       224666666666666 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   0.00088      0.56      14      37 ..      11      34 ..       7      39 .. 0.82
   2 ?   -2.4   0.0         5   3.2e+03     135     163 ..     141     169 ..     138     175 .. 0.69
   3 ?   -1.9   0.0       3.7   2.4e+03      30      30 ..     186     186 ..     147     229 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00088
                            AAA_30 14 ltsgdrvavltGpAGtGKttalka 37
                                       ++++++a++ G  GtGKtt  + 
  gi|488599955|ref|YP_007906426.1| 11 NSEPKQIAIISGKGGTGKTTFSAL 34
                                      567899**************8665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                            AAA_30 135 gvlrdlveaagigtaeLtevvRqkeseer 163
                                       + ++ l++a + +t +L + vRq+ ++++
  gi|488599955|ref|YP_007906426.1| 141 HFVHALLKAGEENTGRLVTEVRQRAKKIA 169
                                       55666667677778888888888766554 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.7
                            AAA_30  30 G 30 
                                       G
  gi|488599955|ref|YP_007906426.1| 186 G 186
                                       2 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   2.9   0.00089      0.57       1      15 []      80      94 ..      80      94 .. 0.94
   2 ?    9.5   4.3    0.0033       2.1       1      15 []     107     121 ..     107     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00089
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C  Cg+C evC+ +A
  gi|488599955|ref|YP_007906426.1| 80 CSSCGLCYEVCRFNA 94
                                      889*********998 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0033
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg C  +CP++A
  gi|488599955|ref|YP_007906426.1| 107 CEGCGFCYSACPEKA 121
                                       99**********998 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.3    0.0062         4       6      14 ..      79      87 ..      78      88 .. 0.94
   2 ?    5.1   2.9     0.031        20       6      15 ..     106     115 ..     103     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0062
                        zf-C2H2_11  6 qCleCGlcf 14
                                      +C  CGlc+
  gi|488599955|ref|YP_007906426.1| 79 KCSSCGLCY 87
                                      7*******9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.031
                        zf-C2H2_11   6 qCleCGlcft 15 
                                       +C  CG c++
  gi|488599955|ref|YP_007906426.1| 106 RCEGCGFCYS 115
                                       8********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 ?    4.1   2.3      0.13        82      75      93 ..      73      91 ..      63      95 .. 0.73
   2 ?    8.9   2.2    0.0041       2.6      76      95 ..     101     120 ..      91     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                           Fer4_22 75 ekfgesgCvGCgRCieacp 93
                                      +++ + +C  Cg C e+c 
  gi|488599955|ref|YP_007906426.1| 73 ARILQDKCSSCGLCYEVCR 91
                                      4556778888888888886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0041
                           Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                       +++ + C GCg C +acp+k
  gi|488599955|ref|YP_007906426.1| 101 TVNDKRCEGCGFCYSACPEK 120
                                       467899***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 1959.06
//
Query:       gi|488599956|ref|YP_007906427.1|  [L=560]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  104.0   0.0    7.9e-13   48.5   0.0    4.8  4  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    1.6e-14   53.9   0.4    1.9e-08   34.4   0.0    5.0  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
      2e-11   44.1   0.4     0.0034   17.6   0.0    5.3  6  FixG_C           IG-like fold at C-terminal of FixG, putative
    2.8e-08   33.7   3.2    2.7e-05   24.1   0.7    4.3  5  CarbopepD_reg_2  CarboxypepD_reg-like domain
    1.6e-07   31.1   3.5     0.0011   18.8   0.2    3.8  3  PEGA             PEGA domain
      5e-06   26.9   0.0         27    5.3   0.0    5.7  5  MG2              MG2 domain
    1.3e-05   25.8   0.6        1.2    9.8   0.0    5.4  4  fn3_5            Fn3-like domain
    0.00013   22.1   3.4       0.27   11.5   0.1    5.6  5  CARDB            CARDB
    0.00029   21.1   0.0      0.092   13.1   0.0    3.6  4  DUF11            Domain of unknown function DUF11
    0.00089   19.5   3.4      0.032   14.5   0.1    3.9  4  Invasin_D3       Invasin, domain 3
     0.0014   19.0   2.7     0.0034   17.8   0.4    2.9  3  DUF3869          Domain of unknown function (DUF3869)
     0.0015   18.8   0.0        1.9    8.9   0.0    3.6  3  Transglut_N      Transglutaminase family
     0.0019   18.5   0.1       0.56   10.5   0.0    3.7  4  Alpha_adaptinC2  Adaptin C-terminal domain
     0.0019   18.0   1.8        2.1    8.2   0.1    3.3  2  fn3_3            Polysaccharide lyase family 4, domain II
     0.0078   16.3   1.8         12    5.9   0.0    5.2  5  DUF916           Bacterial protein of unknown function (DUF91
  ------ inclusion threshold ------
      0.013   16.1   0.2      0.071   13.7   0.2    2.4  1  YtkA             YtkA-like
       0.02   14.8   0.1         13    5.5   0.0    4.1  4  DUF4832          Domain of unknown function (DUF4832)
      0.021   14.8   0.1        3.5    7.7   0.0    2.9  2  Big_1            Bacterial Ig-like domain (group 1)
      0.037   13.9   0.2       0.18   11.7   0.1    2.3  2  DoxA             TQO small subunit DoxA
      0.055   13.6   0.1         30    4.9   0.0    3.7  4  fn3_6            Fibronectin type-III domain
      0.057   13.5   0.0       0.25   11.4   0.0    2.1  1  7TMR-DISMED2     7TMR-DISM extracellular 2
       0.14   12.3   0.2        1.4    9.1   0.0    2.7  2  MG4              Macroglobulin domain MG4
       0.17   12.0   0.0       0.73   10.0   0.0    2.1  1  DUF2012          Protein of unknown function (DUF2012)
       0.18   11.7   2.1        6.7    6.7   0.1    3.7  3  FlgD_ig          FlgD Ig-like domain
       0.19   12.1   0.2         15    6.1   0.0    3.3  3  DUF5060          Domain of unknown function (DUF5060)
       0.42   10.5   9.8        4.6    7.2   0.8    4.8  4  DUF1533          Protein of unknown function (DUF1533)


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 !   21.6   0.0   2.8e-07   0.00019       2      76 ..      32     108 ..      31     110 .. 0.87
   2 !   15.5   0.0   2.3e-05     0.016       1      73 [.     136     210 ..     136     212 .. 0.91
   3 !   12.2   0.0   0.00025      0.17      40      76 ..     368     406 ..     363     408 .. 0.88
   4 !   48.5   0.0   1.2e-15   7.9e-13       2      77 ..     440     515 ..     439     516 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.8e-07
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWt....vvevspasaaslapGetveatvkVtppagaaaGdyevta 74 
                                        pG+tvt++lt+ ndg+ ++++  ls  +P+G +    v  v+++++ sl p  + +++++V +p++   G y++ +
  gi|488599956|ref|YP_007906427.1|  32 IPGQTVTFDLTIRNDGE-STRDYMLSYNAPSGFNgrflVNGVEVKEI-SLSPYSSITVQFEVDVPDDLNEGIYNIWV 106
                                       59*************97.57999***********7665555555555.7*************************988 PP

                       NPCBM_assoc  75 ka 76 
                                       +a
  gi|488599956|ref|YP_007906427.1| 107 SA 108
                                       76 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.3e-05
                       NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa...slapGetveatvkVtppagaaaGdyevt 73 
                                       ve+G++v++ l v n  + a   v ls ++Pe W+ + + +++      l p et +  ++V + ++a+ G+y v+
  gi|488599956|ref|YP_007906427.1| 136 VEAGDEVSFPLNVENRLN-AYYPVDLSCKVPEKWECRFFYGDNQVykiVLGPKETRTIYFRVESDSSADVGEYAVK 210
                                       578999999999999875.5778************99999998888899************************996 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00025
                       NPCBM_assoc  40 spasaa..slapGetveatvkVtppagaaaGdyevtaka 76 
                                       sp+s++   ++ Ge+  + ++V +p++a+ G+y++t+ +
  gi|488599956|ref|YP_007906427.1| 368 SPESISevFIKGGESKDVYLEVIVPPRAKVGTYNLTVHV 406
                                       788888656899************************987 PP

  == domain 4  score: 48.5 bits;  conditional E-value: 1.2e-15
                       NPCBM_assoc   2 epGetvtltltvtndg.taaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                       epG++v+++  + n+g +a +tn+++s+++PeGW+ v+v+p s ++l++G+ +  +++ ++p+++++++y++++k++
  gi|488599956|ref|YP_007906427.1| 440 EPGAEVKYQGLLRNTGiGADITNIEISVDAPEGWK-VNVDPSSSPALKAGDFLPINIQAKIPPNTIPSEYKLKLKIK 515
                                       79*********************************.*************************************9987 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.11        73      21      52 ..      43      79 ..      20     148 .. 0.73
   2 !   34.4   0.0   2.8e-11   1.9e-08       5      74 ..     238     299 ..     236     307 .. 0.92
   3 ?   -2.0   0.0       6.8   4.7e+03      37      55 ..     344     352 ..     334     359 .. 0.62
   4 !    8.8   0.0    0.0029         2      47      77 ..     397     426 ..     390     436 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
                   CarboxypepD_reg 21 vtnadtg.....tvastttdadGafrlrglppgtysv 52
                                      ++n++++      ++++ ++ +G+f ++g++  ++s+
  gi|488599956|ref|YP_007906427.1| 43 IRNDGEStrdymLSYNAPSGFNGRFLVNGVEVKEISL 79
                                      4444443333334788999999999999888876665 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 2.8e-11
                   CarboxypepD_reg   5 rVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqt 74 
                                       +V d++g+p+++a+V +       + +  t  dG+  ++ +p g+y+v++s++Gy   ++ +v++ ag++
  gi|488599956|ref|YP_007906427.1| 238 KVSDKDGKPVTNAEVKIN------NETFYTSGDGSALIE-VPDGSYKVKISKDGYYDKEV-DVEIKAGKE 299
                                       69****************......799***********8.*******************9.6***99986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.8
                   CarboxypepD_reg  37 dGafrlrglppgtysvtvs 55 
                                       d          gty++ vs
  gi|488599956|ref|YP_007906427.1| 344 D----------GTYTLSVS 352
                                       2..........55555554 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0029
                   CarboxypepD_reg  47 pgtysvtvsapGyatatreevtltagqtttl 77 
                                        gty++tv  +Gy +at+ ++tl+ +++ ++
  gi|488599956|ref|YP_007906427.1| 397 VGTYNLTVHVEGYCSATK-NLTLNLKGEYRV 426
                                       4****************6.8**998877766 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00072       0.5      35      90 ..      39      98 ..      38     130 .. 0.76
   2 ?   -0.4   0.0       1.9   1.3e+03      50      84 ..     115     149 ..     110     160 .. 0.74
   3 ?    2.2   0.0      0.28     2e+02      67     102 ..     180     225 ..     143     259 .. 0.75
   4 ?   -0.2   0.0       1.6   1.1e+03      65      89 ..     274     298 ..     236     325 .. 0.56
   5 !   17.6   0.0   4.9e-06    0.0034      35     102 ..     333     407 ..     304     421 .. 0.83
   6 ?    5.9   0.0     0.021        15      47     109 ..     461     526 ..     444     536 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00072
                                      EEEEEEE-SSS-EEEEEEEES-S....S-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG- CS
                            FixG_C 35 YtlkilNktekprrytlsveglp....glelagraekeitvapgekrkvpvfvrvpaeal 90
                                      + l+i+N  e++r y+ls +        + ++g++ kei++ p ++ +v + v vp +  
  gi|488599956|ref|YP_007906427.1| 39 FDLTIRNDGESTRDYMLSYNAPSgfngRFLVNGVEVKEISLSPYSSITVQFEVDVPDDLN 98
                                      789*****************7554544444467788*******************99882 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                                       EEEEES.-SS-EE.E.S--EEEE-TT-EEEEEEEEE CS
                            FixG_C  50 tlsveg.lpglelagraekeitvapgekrkvpvfvr 84 
                                       ++++ + ++ l++ + + + i+v++g ++++p+ v+
  gi|488599956|ref|YP_007906427.1| 115 EINIVNvEKPLRI-TSSITGIKVEAGDEVSFPLNVE 149
                                       5555553347778.5567899999999999999886 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.28
                                       -EEEE-TT-EEEEEEEEEE-GGG..........-SSSEEEEEEEEE CS
                            FixG_C  67 keitvapgekrkvpvfvrvpaea..........lkkkstpitfkvt 102
                                        +i + p+e+r+++++v+ +++a          l k+s+++++++t
  gi|488599956|ref|YP_007906427.1| 180 YKIVLGPKETRTIYFRVESDSSAdvgeyavkpiLGKQSITLNIEIT 225
                                       4678899999999999999888866666655543355556666665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.6
                                       S--EEEE-TT-EEEEEEEEEE-GGG CS
                            FixG_C  65 aekeitvapgekrkvpvfvrvpaea 89 
                                       ++ ++++ +++  ++ v v+++a++
  gi|488599956|ref|YP_007906427.1| 274 GSYKVKISKDGYYDKEVDVEIKAGK 298
                                       3344444444444444444443333 PP

  == domain 5  score: 17.6 bits;  conditional E-value: 4.9e-06
                                       EEEEEEE-SSS-EEEEEEEES-S...S-EE......E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE CS
                            FixG_C  35 YtlkilNktekprrytlsveglp...glel.....agraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt 102
                                       ++lki N    + +ytlsv+glp    +++     + ++ +e+ ++ ge+++v++ v vp+ a k ++ ++t++v+
  gi|488599956|ref|YP_007906427.1| 333 FRLKIENIGYADGTYTLSVSGLPenfYARFkesadSPESISEVFIKGGESKDVYLEVIVPPRA-KVGTYNLTVHVE 407
                                       89*******************986664444555432366899*******************99.556669999997 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.021
                                       EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEE.EEEEEEE..EGGGTEE CS
                            FixG_C  47 rrytlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkst.pitfkvt..dddeket 109
                                        ++++sv+  +g +++ +++++ ++++g  + + +  ++p++ ++++ + ++++k +  ++ e+++
  gi|488599956|ref|YP_007906427.1| 461 TNIEISVDAPEGWKVNVDPSSSPALKAGDFLPINIQAKIPPNTIPSEYKlKLKIKSDqlEETEEIK 526
                                       45899999989999988999***********************88766666666664332322222 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 ?   -1.8   0.0       4.5   3.1e+03      30      51 ..      61      80 ..      56     104 .. 0.64
   2 ?   -2.0   0.0       5.3   3.6e+03      41      63 ..      97     119 ..      88     132 .. 0.69
   3 !   24.1   0.7   3.9e-08   2.7e-05       4      80 ..     238     310 ..     238     317 .. 0.87
   4 ?   -0.5   0.0       1.8   1.3e+03      46      66 ..     333     353 ..     324     376 .. 0.67
   5 ?    5.6   0.0     0.024        16      42      70 ..     396     424 ..     393     431 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.5
                   CarbopepD_reg_2 30 TdenGnFelknlpagkytLvvs 51
                                      +  nG+F ++ ++ ++     s
  gi|488599956|ref|YP_007906427.1| 61 SGFNGRFLVNGVEVKEI--SLS 80
                                      56789999988877764..334 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.3
                   CarbopepD_reg_2  41 lpagkytLvvsyvGyktqekkvt 63 
                                       l++g y + vs+ G +  e+++ 
  gi|488599956|ref|YP_007906427.1|  97 LNEGIYNIWVSAGGQERLEINIV 119
                                       56677777788777777776654 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 3.9e-08
                   CarbopepD_reg_2   4 tVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkeea 80 
                                       +V+dk+ ++p+  a V +++ +   +T  +G+  + ++p+g y++++s  Gy  +e+ v+++ +k+++ ++ll+++a
  gi|488599956|ref|YP_007906427.1| 238 KVSDKD-GKPVTNAEVKINNET--FYTSGDGSALI-EVPDGSYKVKISKDGYYDKEVDVEIKAGKEIEKSVLLEKKA 310
                                       588886.58*******997766..57888899888.5*******************************999998876 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.8
                   CarbopepD_reg_2  46 ytLvvsyvGyktqekkvtvsk 66 
                                       ++L+++ +Gy   + +++vs+
  gi|488599956|ref|YP_007906427.1| 333 FRLKIENIGYADGTYTLSVSG 353
                                       567777777777766666654 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.024
                   CarbopepD_reg_2  42 pagkytLvvsyvGyktqekkvtvskektl 70 
                                       + g+y L+v + Gy +++k++t++ + + 
  gi|488599956|ref|YP_007906427.1| 396 KVGTYNLTVHVEGYCSATKNLTLNLKGEY 424
                                       789******************99855555 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.8   6.7e+03      50      66 ..     132     148 ..     125     151 .. 0.69
   2 !   18.8   0.2   1.6e-06    0.0011      23      69 ..     263     309 ..     247     310 .. 0.80
   3 !   10.7   0.1   0.00054      0.38      32      62 ..     396     426 ..     393     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.8
                              PEGA  50 ktvtvtagetvklnltL 66 
                                       + ++v+ag++v++ l+ 
  gi|488599956|ref|YP_007906427.1| 132 TGIKVEAGDEVSFPLNV 148
                                       45777888877776665 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.6e-06
                              PEGA  23 GkTPvtlsleaGnyslrvekeGYedlektvtvtagetvklnltLekt 69 
                                       G     ++++ G+y+++++k+GY d e +v+++ag++++ ++ Lek+
  gi|488599956|ref|YP_007906427.1| 263 GDGSALIEVPDGSYKVKISKDGYYDKEVDVEIKAGKEIEKSVLLEKK 309
                                       55666788*****************************9999888875 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00054
                              PEGA  32 eaGnyslrvekeGYedlektvtvtagetvkl 62 
                                       + G+y l+v  eGY  ++k  t++ + ++++
  gi|488599956|ref|YP_007906427.1| 396 KVGTYNLTVHVEGYCSATKNLTLNLKGEYRV 426
                                       68*********************96555555 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.039        27      13      84 ..      33     110 ..      32     118 .. 0.73
   2 ?    0.5   0.0       1.2   8.5e+02      45      79 ..     176     210 ..     174     217 .. 0.91
   3 ?    5.1   0.0     0.044        31      36      86 ..     235     286 ..     220     295 .. 0.80
   4 ?    2.3   0.0      0.34   2.4e+02      63      82 ..     387     406 ..     370     427 .. 0.79
   5 ?    4.8   0.0     0.057        39      13      85 ..     441     517 ..     438     534 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.039
                                       TT-EEEEEEEEES.....TTCSB---EEEEEEEE.-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEEC CS
                               MG2  13 PgetVslkallrd.....etlqglaklplkltir.dpdgkevkelplatdetggaesefalpeaaklGeysvelsad 83 
                                       Pg+tV +   +r+     +++    ++p  ++ r   +g evke +l   ++ ++++e+++p++   G y++ +sa 
  gi|488599956|ref|YP_007906427.1|  33 PGQTVTFDLTIRNdgestRDYMLSYNAPSGFNGRfLVNGVEVKEISLSPYSSITVQFEVDVPDDLNEGIYNIWVSAG 109
                                       677777777777766655555555556665555413578899999999999999*****************999444 PP

                                       S CS
                               MG2  84 s 84 
                                       +
  gi|488599956|ref|YP_007906427.1| 110 G 110
                                       3 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                                       SSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEE CS
                               MG2  45 gkevkelplatdetggaesefalpeaaklGeysve 79 
                                       +++v++  l  +et ++ ++++  ++a  Gey v+
  gi|488599956|ref|YP_007906427.1| 176 DNQVYKIVLGPKETRTIYFRVESDSSADVGEYAVK 210
                                       7899999999999999****************986 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.044
                                       EEEEEE-TTSSEEEEEEEEE-CTTE.EEEEEE--TT--SEEEEEEEEECSTT CS
                               MG2  36 lkltirdpdgkevkelplatdetgg.aesefalpeaaklGeysvelsadsae 86 
                                       l l+++d dgk v + +++ +++ +  +++     + + G+y+v++s+d+  
  gi|488599956|ref|YP_007906427.1| 235 LILKVSDKDGKPVTNAEVKINNETFyTSGDGSALIEVPDGSYKVKISKDGYY 286
                                       56899************955555553899*****************665544 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.34
                                       EEEE--TT--SEEEEEEEEE CS
                               MG2  63 sefalpeaaklGeysvelsa 82 
                                        e+ +p  ak G+y+++++ 
  gi|488599956|ref|YP_007906427.1| 387 LEVIVPPRAKVGTYNLTVHV 406
                                       6777999*********9943 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.057
                                       TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEE...EE-CTTE..EEEEEE--TT--SEEEEEEEEECS CS
                               MG2  13 PgetVslkallrdetlqglaklplkltirdpdgkevkelpl...atdetgg..aesefalpeaaklGeysvelsads 84 
                                       Pg +V++++llr+ t+ g+  +++++++  p+g +v+  p    a ++  +  ++ + ++p ++   ey+++l+ +s
  gi|488599956|ref|YP_007906427.1| 441 PGAEVKYQGLLRN-TGIGADITNIEISVDAPEGWKVNVDPSsspALKAGDFlpINIQAKIPPNTIPSEYKLKLKIKS 516
                                       9999******986.55566667899********99999999665344444466888889999999999999984333 PP

                                       T CS
                               MG2  85 a 85 
                                       +
  gi|488599956|ref|YP_007906427.1| 517 D 517
                                       3 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0018       1.2       3      88 ..      29      99 ..      27     112 .. 0.74
   2 ?    0.6   0.0       1.3   8.6e+02      65      88 ..     181     204 ..     174     210 .. 0.83
   3 ?   -0.7   0.1       3.2   2.2e+03      74      95 ..     288     314 ..     213     317 .. 0.67
   4 ?    4.8   0.0     0.064        44      10      88 ..     331     397 ..     325     426 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                             fn3_5  3 Lkei.gdkfsftltlkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtl 80
                                      ++ i g++ +f+lt++N ++ ++ y +s n      a   +g +     +      ++++e +++ + + ss tv++ +
  gi|488599956|ref|YP_007906427.1| 29 INAIpGQTVTFDLTIRNDGESTRDYMLSYN------A--PSGFNG---RF-----LVNGVEVKEISLSPYSSITVQFEV 91
                                      566777778888888888888888888877......2..223322...22.....278899999999999999999999 PP

                             fn3_5 81 dlpsdakk 88
                                      d+p+d+++
  gi|488599956|ref|YP_007906427.1| 92 DVPDDLNE 99
                                      99999887 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.3
                             fn3_5  65 kvtvpAnssktvtvtldlpsdakk 88 
                                       k+++++++++t+ + +  +s+a++
  gi|488599956|ref|YP_007906427.1| 181 KIVLGPKETRTIYFRVESDSSADV 204
                                       899************999888877 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.2
                             fn3_5  74 ktvtvtldlpsdakk.....kngyfve 95 
                                       k+v+v + ++++++k     k+ yfve
  gi|488599956|ref|YP_007906427.1| 288 KEVDVEIKAGKEIEKsvlleKKAYFVE 314
                                       566777777666666666666666665 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.064
                             fn3_5  10 fsftltlkNtsnkaltykvsandvlTdladkeegklilkaaspeikeaaltfetskvtvpAnssktvtvtldlpsda 86 
                                         f+l+++N++  + ty++s +  l +  +++ ++  + ++           + s+v ++ ++sk+v + + +p  a
  gi|488599956|ref|YP_007906427.1| 331 PMFRLKIENIGYADGTYTLSVS-GLPENFYARFKESADSPE-----------SISEVFIKGGESKDVYLEVIVPPRA 395
                                       5689999999999999999999.444444333333332332...........3455555555555555555555555 PP

                             fn3_5  87 kk 88 
                                       k+
  gi|488599956|ref|YP_007906427.1| 396 KV 397
                                       54 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00039      0.27       4      84 ..      17     108 ..      15     115 .. 0.72
   2 ?   -0.9   0.0       2.8     2e+03       4      30 ..     125     151 ..     123     157 .. 0.88
   3 ?    1.1   0.1      0.66   4.6e+02      49      84 ..     201     239 ..     178     259 .. 0.69
   4 ?    2.3   0.0      0.29     2e+02      56      85 ..     376     407 ..     313     413 .. 0.60
   5 ?    1.3   0.0       0.6   4.1e+02      25      87 ..     449     517 ..     439     525 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                                       EEE....EEEC-SEEETTSEEEEEEEEEE-SSS.........-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEE CS
                             CARDB   4 Ltv...tntlnpseafvgeentitvtvkNqGta.........asgatkvalyldgelvgtvtvpsLaagesttvsft 68 
                                       Ltv   +++++  +a +g+++t+ +t++N G+          a   ++ ++ ++g +v+++   sL++ +s+tv+f 
  gi|488599956|ref|YP_007906427.1|  17 LTVgslQTSIKSINAIPGQTVTFDLTIRNDGEStrdymlsynAPSGFNGRFLVNGVEVKEI---SLSPYSSITVQFE 90 
                                       566666778888999****************972222222213346788888888887755...5688888888888 PP

                                       EE-S..-S-CEEEEEEEE CS
                             CARDB  69 wtte..ategevtltvvv 84 
                                       + ++  ++eg + + v++
  gi|488599956|ref|YP_007906427.1|  91 VDVPddLNEGIYNIWVSA 108
                                       777667888888877665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                                       EEE.EEEC-SEEETTSEEEEEEEEEE- CS
                             CARDB   4 LtvtntlnpseafvgeentitvtvkNq 30 
                                       L +t++++  ++++g+e+++ ++v+N 
  gi|488599956|ref|YP_007906427.1| 125 LRITSSITGIKVEAGDEVSFPLNVENR 151
                                       678889999999*************96 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.66
                                       E...EEEEESEE-CTEEEEEEEEEE-S-S-CEEE.EEEEE CS
                             CARDB  49 v...gtvtvpsLaagesttvsftwtteategevt.ltvvv 84 
                                           g+  v+++  ++s+t ++ +t + ++ge   l+++v
  gi|488599956|ref|YP_007906427.1| 201 SadvGEYAVKPILGKQSITLNIEITKT-HKGENGvLILKV 239
                                       223488889999999999999999988.555544355544 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.29
                                       EE-CTEEEEEEEEEE-S..-S-CEEEEEEEES CS
                             CARDB  56 sLaagesttvsftwtte..ategevtltvvvD 85 
                                        ++ ges++v + + ++  a+ g++ ltv+v+
  gi|488599956|ref|YP_007906427.1| 376 FIKGGESKDVYLEVIVPprAKVGTYNLTVHVE 407
                                       45667776666555555457788888888776 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.6
                                       EEEEE-SSS-.EEEEEEEEEETTEEEEEEEE.....SEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT CS
                             CARDB  25 vtvkNqGtaa.sgatkvalyldgelvgtvtv.....psLaagesttvsftwtte..ategevtltvvvDpd 87 
                                         ++N+G +a    t++++ +d  +  +v+v     p+L+ag+   ++++ +++  + ++e++l++++ +d
  gi|488599956|ref|YP_007906427.1| 449 GLLRNTGIGAdI--TNIEISVDAPEGWKVNVdpsssPALKAGDFLPINIQAKIPpnTIPSEYKLKLKIKSD 517
                                       447888877633..444444444443344447777799999999888888888865677888899988765 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00013     0.092       9      85 ..      30     100 ..      21     105 .. 0.75
   2 ?    3.1   0.0      0.16   1.1e+02       9      30 ..     135     156 ..     126     238 .. 0.71
   3 ?   -2.3   0.0       8.2   5.7e+03      77      86 ..     390     399 ..     362     420 .. 0.61
   4 ?   -1.8   0.0       5.6   3.9e+03      12      28 ..     441     457 ..     439     502 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv..gsLeagesatlsftvrvtrtaa 83 
                                       ++ pG+tvt+ lt +N g +++ ++ ++   P+g+++     +     ++  v   sL + +s t++f+v v+   +
  gi|488599956|ref|YP_007906427.1|  30 NAIPGQTVTFDLTIRNDGESTR-DYMLSYNAPSGFNGRFLVNG-----VE--VkeISLSPYSSITVQFEVDVPDDLN 98 
                                       788*******************.99999999999985444444.....22..2335788888888888888877766 PP

                             DUF11  84 sg 85 
                                       +g
  gi|488599956|ref|YP_007906427.1|  99 EG 100
                                       55 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.16
                             DUF11   9 evrpGdtvtytltvtNtgpasa 30 
                                       +v +Gd+v++ l v N+ +a  
  gi|488599956|ref|YP_007906427.1| 135 KVEAGDEVSFPLNVENRLNAYY 156
                                       7899************988754 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.2
                             DUF11  77 rvtrtaasga 86 
                                       +v+++a+ g+
  gi|488599956|ref|YP_007906427.1| 390 IVPPRAKVGT 399
                                       4444444332 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.6
                             DUF11  12 pGdtvtytltvtNtgpa 28 
                                       pG++v+y   ++Ntg  
  gi|488599956|ref|YP_007906427.1| 441 PGAEVKYQGLLRNTGIG 457
                                       78888888888888744 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.3   1.6e+03      34      49 ..      30      47 ..      20      54 .. 0.76
   2 ?   -2.0   0.0       6.9   4.8e+03      38      75 ..      84     115 ..      71     138 .. 0.64
   3 !   14.5   0.1   4.7e-05     0.032      23      68 ..     234     282 ..     217     306 .. 0.82
   4 ?    2.3   0.0      0.32   2.2e+02      69      93 ..     395     418 ..     379     421 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.3
                        Invasin_D3 34 npvsgltvtfstt..sag 49
                                      n++ g+tvtf  t  ++g
  gi|488599956|ref|YP_007906427.1| 30 NAIPGQTVTFDLTirNDG 47
                                      779999999998755444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.9
                        Invasin_D3  38 gltvtfsttsagtlsavtdngdGtytatLtattagtat 75 
                                         tv+f  +       ++d ++G+y   ++a   + + 
  gi|488599956|ref|YP_007906427.1|  84 SITVQFEVD------VPDDLNEGIYNIWVSAGGQERLE 115
                                       444444444......23466678887777765555554 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 4.7e-05
                        Invasin_D3  23 tltvtlkDangnpvsgltvtfstt...sagtlsavtdngdGtytatLta 68 
                                       +l +++ D++g+pv++++v+++ +    +g  sa+ +  dG y+++++ 
  gi|488599956|ref|YP_007906427.1| 234 VLILKVSDKDGKPVTNAEVKINNEtfyTSGDGSALIEVPDGSYKVKISK 282
                                       6889******************66677788889999*******999865 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.32
                        Invasin_D3  69 ttagtatitptvnGvaiaatatvtl 93 
                                       +++gt+++t++v+G   +at+++tl
  gi|488599956|ref|YP_007906427.1| 395 AKVGTYNLTVHVEG-YCSATKNLTL 418
                                       579***********.5577777766 PP

>> DUF3869  Domain of unknown function (DUF3869)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.9   2.7e+03      45      45 ..      44      44 ..      21     123 .. 0.57
   2 ?   -1.7   0.0       5.5   3.8e+03       8      19 ..     112     123 ..      70     149 .. 0.62
   3 !   17.8   0.4   4.9e-06    0.0034      25      85 ..     234     298 ..     216     314 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.9
                                      C CS
                           DUF3869 45 s 45
                                       
  gi|488599956|ref|YP_007906427.1| 44 R 44
                                      3 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.5
                                       XXXXXXXX---- CS
                           DUF3869   8 edldatvtlaeA 19 
                                       e l++++  +e 
  gi|488599956|ref|YP_007906427.1| 112 ERLEINIVNVEK 123
                                       333333333333 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 4.9e-06
                                       EEE..EETTTTEE-CGCCEECCCCCSSEEEECCS......CT-EEEEEEECTETTEEEEEEEE--B- CS
                           DUF3869  25 gtvldieattgtdvtdkatistssgtatfkggae......laakavkisatGYegiktatVsvaalk 85 
                                       + +l++ +++g+ vt +a+++ ++ t+  +g+        +++++vkis++GY++ + + V+++a k
  gi|488599956|ref|YP_007906427.1| 234 VLILKVSDKDGKPVT-NAEVKINNETFYTSGDGSalievpDGSYKVKISKDGYYDKE-VDVEIKAGK 298
                                       56889999*******.5555544433333332222344559****************.888887654 PP

>> Transglut_N  Transglutaminase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.4   9.4e+02      81     113 ..     177     209 ..     135     211 .. 0.76
   2 !    8.9   0.0    0.0027       1.9      92     117 ..     380     406 ..     347     407 .. 0.76
   3 ?    4.6   0.0     0.057        39      79     118 .]     468     515 ..     453     515 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                       Transglut_N  81 eskWsaeveessgnsltvsitspanaivgrykl 113
                                       ++ +++++  ++++++ + + s ++a vg+y +
  gi|488599956|ref|YP_007906427.1| 177 NQVYKIVLGPKETRTIYFRVESDSSADVGEYAV 209
                                       4455555664556799999999999*9*99986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0027
                       Transglut_N  92 sg.nsltvsitspanaivgryklsvet 117
                                        + + + +++ +p+ a vg y+l+v++
  gi|488599956|ref|YP_007906427.1| 380 GEsKDVYLEVIVPPRAKVGTYNLTVHV 406
                                       3337899******************98 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.057
                       Transglut_N  79 edeskWsaeveessg.n.......sltvsitspanaivgryklsvetk 118
                                       +++++W+++v+ ss+          ++++ ++p+n+i ++ykl++++k
  gi|488599956|ref|YP_007906427.1| 468 DAPEGWKVNVDPSSSpAlkagdflPINIQAKIPPNTIPSEYKLKLKIK 515
                                       46889999999655432456776677777889************9975 PP

>> Alpha_adaptinC2  Adaptin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.41   2.8e+02      54      84 ..      21      48 ..      14      61 .. 0.77
   2 ?   -1.5   0.0       4.5   3.1e+03      48      81 ..     120     150 ..      78     165 .. 0.56
   3 ?    0.3   0.0       1.2   8.5e+02       7      52 ..     214     259 ..     211     262 .. 0.79
   4 !   10.5   0.0   0.00081      0.56      33      91 ..     452     514 ..     435     528 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.41
                                      EEEEEEES-S-B-TTCEEEEEEEEEEESCTT CS
                   Alpha_adaptinC2 54 klqlqppsstvlppnpggqitqvllienpsk 84
                                       lq +  s + +p   g+++t +l+i n ++
  gi|488599956|ref|YP_007906427.1| 21 SLQTSIKSINAIP---GQTVTFDLTIRNDGE 48
                                      5777888888888...9*********98433 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.5
                                       EEBTTCEEEEEEES-S-B-TTCEEEEEEEEEEES CS
                   Alpha_adaptinC2  48 avpkslklqlqppsstvlppnpggqitqvllien 81 
                                       +v k+l+++ +     v++   g++++  l++en
  gi|488599956|ref|YP_007906427.1| 120 NVEKPLRITSSITGIKVEA---GDEVSFPLNVEN 150
                                       4444444443333333333...566666666665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.2
                                       EETTEEEEEEEEETTSTTEEEEEEEEEE-SSS-EEEEEEEEEEBTT CS
                   Alpha_adaptinC2   7 ekddlqIgfkfekperpgqiritlsftNkssqpisnfsfqaavpks 52 
                                        k+++ + ++++k+ +++++++ l+ + k  +p++n   ++++  +
  gi|488599956|ref|YP_007906427.1| 214 GKQSITLNIEITKTHKGENGVLILKVSDKDGKPVTNAEVKINNETF 259
                                       5788888888898888888999999999999999988888777665 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00081
                                       EE-S.SS-EEEEEEEEEEBTTCEEEEEEES-S-B-TTCEEEEEEEEEE..ES.CTTS-EEEEE CS
                   Alpha_adaptinC2  33 tNks.sqpisnfsfqaavpkslklqlqppsstvlppnpggqitqvlli..en.pskkplrmrl 91 
                                        N+   ++i+n+ ++++ p+++k+++ p ss  l +    +i+ + +i  ++ ps+ +l++++
  gi|488599956|ref|YP_007906427.1| 452 RNTGiGADITNIEISVDAPEGWKVNVDPSSSPALKAGDFLPINIQAKIppNTiPSEYKLKLKI 514
                                       56666889**************************98666666666666322233333333333 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 !    8.2   0.1     0.003       2.1      41      73 ..     270     300 ..     246     302 .. 0.84
   2 !    7.6   0.0    0.0048       3.3      40      63 ..     393     414 ..     391     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.003
                             fn3_3  41 nVkpGtYrltvYadglfgdykqdsvtVtagktt 73 
                                        V  G+Y++ + +dg+  +    +v+++agk++
  gi|488599956|ref|YP_007906427.1| 270 EVPDGSYKVKISKDGYYDKE--VDVEIKAGKEI 300
                                       5899*************777..********987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0048
                             fn3_3  40 pnVkpGtYrltvYadglfgdykqd 63 
                                       p+ k GtY+ltv ++g+  ++  +
  gi|488599956|ref|YP_007906427.1| 393 PRAKVGTYNLTVHVEGYCSAT--K 414
                                       56689***********99888..3 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 ?    0.6   0.0      0.82   5.7e+02      22      49 ..      30      57 ..      28      66 .. 0.83
   2 ?    5.9   0.0     0.018        12      84     111 ..      73     101 ..      66     110 .. 0.90
   3 ?   -0.9   0.0       2.4   1.7e+03      86     103 ..     181     198 ..     175     208 .. 0.57
   4 ?   -0.4   1.4       1.7   1.2e+03      41     101 ..     216     304 ..     213     317 .. 0.62
   5 ?    1.6   0.0      0.41   2.8e+02      76     111 ..     361     399 ..     346     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.82
                            DUF916 22 kvkpgqeqelevkikNssdkeitveitv 49
                                      ++ pgq+ ++ ++i+N+ +++  + ++ 
  gi|488599956|ref|YP_007906427.1| 30 NAIPGQTVTFDLTIRNDGESTRDYMLSY 57
                                      5669************999987777665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
                            DUF916  84 p.keitlpakesktvklkikmPkeefdGv 111
                                       + kei+l + +s tv++++++P++  +G+
  gi|488599956|ref|YP_007906427.1|  73 EvKEISLSPYSSITVQFEVDVPDDLNEGI 101
                                       4599********************99997 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.4
                            DUF916  86 eitlpakesktvklkikm 103
                                       +i l +ke++t+ + ++ 
  gi|488599956|ref|YP_007906427.1| 181 KIVLGPKETRTIYFRVES 198
                                       455556666666555543 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.7
                            DUF916  41 keitveitvntAvTndnGvidYskskek............................kdkslkvslselvkipkeitl 89 
                                       ++it++i++++    +nGv+  + s+++                            +d s kv++s+    +ke+ +
  gi|488599956|ref|YP_007906427.1| 216 QSITLNIEITKTHKGENGVLILKVSDKDgkpvtnaevkinnetfytsgdgsalievPDGSYKVKISKDGYYDKEVDV 292
                                       66777777777777777777777555555566666666666666666666666666666666666666666666666 PP

                            DUF916  90 pakesktvklki 101
                                       + k  k+++ ++
  gi|488599956|ref|YP_007906427.1| 293 EIKAGKEIEKSV 304
                                       666655555554 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.41
                            DUF916  76 slselvkip...keitlpakesktvklkikmPkeefdGv 111
                                       +++e ++ p   +e+ ++ +esk+v l++ +P  +  G+
  gi|488599956|ref|YP_007906427.1| 361 RFKESADSPesiSEVFIKGGESKDVYLEVIVPPRAKVGT 399
                                       5667777666678999***************99887776 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2    0.0001     0.071       4      45 ..     217     257 ..     214     293 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
                              YtkA   4 sddlevelvspeepkagentivv.t.vtqggkpVedadvkvefw 45 
                                       s +l++e++++    +gen + + +  +++gkpV++a+vk++ +
  gi|488599956|ref|YP_007906427.1| 217 SITLNIEITKT---HKGENGVLIlKvSDKDGKPVTNAEVKINNE 257
                                       55666666655...78999765534589***********99755 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.019        13     120     196 ..      33     107 ..      21     116 .. 0.70
   2 ?   -1.4   0.0       2.5   1.7e+03     161     203 ..     205     245 ..     179     257 .. 0.59
   3 ?    0.9   0.0       0.5   3.4e+02     125     197 ..     332     406 ..     316     415 .. 0.64
   4 ?    2.0   0.0      0.24   1.6e+02     126     202 ..     447     519 ..     435     529 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                           DUF4832 120 aggtlsleltlkNeGfAalynerkvelvlrdeegeekyklk..ldadprkwlpgttttitiklklpselakGkykvy 194
                                       +g+t++++lt++N+G ++    r+  l +   +g   + l+  +++   ++ p ++ t++ ++++p++l++G y+++
  gi|488599956|ref|YP_007906427.1|  33 PGQTVTFDLTIRNDGEST----RDYMLSYNAPSGFNGRFLVngVEVKEISLSPYSSITVQFEVDVPDDLNEGIYNIW 105
                                       677788888888888654....6666666666665543344234444556677888888888************998 PP

                           DUF4832 195 Ln 196
                                       ++
  gi|488599956|ref|YP_007906427.1| 106 VS 107
                                       75 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                           DUF4832 161 ldadprkwlpgttttitiklklpselakGkykvyLnlpdpseg 203
                                        ++ ++ +l++++  it+++++ ++ + ++  ++L+++d++ +
  gi|488599956|ref|YP_007906427.1| 205 GEYAVKPILGKQS--ITLNIEITKTHKGENGVLILKVSDKDGK 245
                                       4555555555553..4444555555555577888999998876 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.5
                           DUF4832 125 sleltlkNeGfAalynerkvelvlrdeegeekyklk..ldadprkwlpgttttitiklklpselakGkykvyLnl 197
                                        ++l+++N G+A      +v+ + ++   + k++    ++++   +++g+++++ +++ +p   + G+y++ +++
  gi|488599956|ref|YP_007906427.1| 332 MFRLKIENIGYADGTYTLSVSGLPENFYARFKESADspESISEVFIKGGESKDVYLEVIVPPRAKVGTYNLTVHV 406
                                       577888888888766655555444443333332222113333333455777777788888888888888887776 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.24
                           DUF4832 126 leltlkNeGfAalynerkvelvlrdeegeekyklkldadprk...wlpgttttitiklklpselakGkykvyLnlpd 199
                                       ++  l+N+G +a + +  +e+ +   eg +     +++dp++   ++ g+   i+i++k+p ++   +yk+ L++++
  gi|488599956|ref|YP_007906427.1| 447 YQGLLRNTGIGADITN--IEISVDAPEGWK-----VNVDPSSspaLKAGDFLPINIQAKIPPNTIPSEYKLKLKIKS 516
                                       5555666666655543..444444444433.....4555554111444666669999****8888999***999987 PP

                           DUF4832 200 pse 202
                                        + 
  gi|488599956|ref|YP_007906427.1| 517 DQL 519
                                       764 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 ?    3.7   0.0     0.087        60      19      31 ..      30      42 ..      27      52 .. 0.85
   2 ?    7.7   0.0    0.0051       3.5       9      29 ..     235     255 ..     231     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.087
                             Big_1 19 npvagatVtfsvs 31
                                      n+++g+tVtf  +
  gi|488599956|ref|YP_007906427.1| 30 NAIPGQTVTFDLT 42
                                      99********876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0051
                             Big_1   9 ltatvkDangnpvagatVtfs 29 
                                       l   v D++g+pv +a+V+++
  gi|488599956|ref|YP_007906427.1| 235 LILKVSDKDGKPVTNAEVKIN 255
                                       56789*************876 PP

>> DoxA  TQO small subunit DoxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.5   2.4e+03      28      54 ..     111     137 ..     101     155 .. 0.74
   2 ?   11.7   0.1   0.00026      0.18      12      51 ..     216     252 ..     208     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.5
                              DoxA  28 ngtLvleitrveGpdvYgafvikiell 54 
                                       ++ L ++i+ ve p    +++++i++ 
  gi|488599956|ref|YP_007906427.1| 111 QERLEINIVNVEKPLRITSSITGIKVE 137
                                       567888888888888888888888775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00026
                              DoxA  12 kskkpkleitgaklaengtLvleitrveGpdvYgafviki 51 
                                       +s + ++eit+++  eng L+l++ + +G  v  a   ++
  gi|488599956|ref|YP_007906427.1| 216 QSITLNIEITKTHKGENGVLILKVSDKDGKPVTNA---EV 252
                                       7999*************************988444...33 PP

>> fn3_6  Fibronectin type-III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.092        63      16      59 ..      34      77 ..      23     119 .. 0.72
   2 ?   -2.2   0.0       6.8   4.7e+03      34      71 ..     275     317 ..     269     325 .. 0.60
   3 ?   -1.6   0.0       4.7   3.2e+03      21      41 ..     333     353 ..     314     364 .. 0.81
   4 ?    4.9   0.0     0.044        30      31      53 ..     459     481 ..     440     542 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.092
                             fn3_6 16 kgtvtvtRtvtnVgsseatYkakveapegvkvtVePseLefsek 59
                                       +tvt+  t++n g+s+  Y  + +ap+g++ +   +  e++e 
  gi|488599956|ref|YP_007906427.1| 34 GQTVTFDLTIRNDGESTRDYMLSYNAPSGFNGRFLVNGVEVKEI 77
                                      689999*********************99986655544444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.8
                             fn3_6  34 tYkakveap....egvkvtVeP.seLefsekgekksftvtvta 71 
                                       +Yk+k+++     ++v+v+++  +e+e s   ekk++ v++++
  gi|488599956|ref|YP_007906427.1| 275 SYKVKISKDgyydKEVDVEIKAgKEIEKSVLLEKKAYFVEISV 317
                                       6777777543333666666665345555555666666666655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.7
                             fn3_6  21 vtRtvtnVgsseatYkakvea 41 
                                       ++ ++ n+g ++ tY+ +v+ 
  gi|488599956|ref|YP_007906427.1| 333 FRLKIENIGYADGTYTLSVSG 353
                                       556789999999999999974 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.044
                             fn3_6  31 seatYkakveapegvkvtVePse 53 
                                         ++ +++v+apeg kv+V Ps+
  gi|488599956|ref|YP_007906427.1| 459 DITNIEISVDAPEGWKVNVDPSS 481
                                       45666889*************64 PP

>> 7TMR-DISMED2  7TMR-DISM extracellular 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00036      0.25      94     126 ..     171     203 ..     145     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                                       -SS-TTEEEEEE--SSS-E.EEEEEEEESS-EE CS
                      7TMR-DISMED2  94 Rpvahrnfvfplplppgetvtvylrvksegsll 126
                                       R ++  n+v+++ l+p et+t+y+rv+s++s+ 
  gi|488599956|ref|YP_007906427.1| 171 RFFYGDNQVYKIVLGPKETRTIYFRVESDSSAD 203
                                       45666789999******************9975 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.9     2e+03      20      70 ..      72     124 ..      69     134 .. 0.52
   2 ?    9.1   0.0    0.0021       1.4      20      64 ..     237     282 ..     234     302 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.9
                               MG4  20 VlvkdpdgspaknvpVkiealk....seteekeslttdedGtakfsintpedaks 70 
                                       V+vk+   sp + ++V+ e+ +       e   ++  ++ G  ++ in+ +  k 
  gi|488599956|ref|YP_007906427.1|  72 VEVKEISLSPYSSITVQFEV-DvpddL-NEGIYNIWVSAGGQERLEINIVNVEKP 124
                                       56666666777777777766.322210.122223334455555555555555555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                               MG4  20 VlvkdpdgspaknvpVkiea...lkseteekeslttdedGtakfsint 64 
                                       ++v+d+dg+p+ n  Vki+    +   + ++++l +  dG  k+ i  
  gi|488599956|ref|YP_007906427.1| 237 LKVSDKDGKPVTNAEVKINNetfY--TSGDGSALIEVPDGSYKVKISK 282
                                       58*****************93321..3455556666666666665555 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0011      0.73       9      68 ..     249     302 ..     241     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                           DUF2012   9 ntrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkgkaka 68 
                                       n++v +++++      ++  DGs ++ ++p+gsY +++ + +y  +++ V++k  ++ ++
  gi|488599956|ref|YP_007906427.1| 249 NAEVKINNETF-----YTSGDGS-ALIEVPDGSYKVKISKDGYYDKEVDVEIKAGKEIEK 302
                                       55666655555.....7888999.5668*************************4443333 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.81   5.6e+02      33      76 ..      70     109 ..      68     112 .. 0.81
   2 ?    6.7   0.1    0.0097       6.7      26      75 ..     236     282 ..     214     284 .. 0.88
   3 ?    0.5   0.0       0.8   5.5e+02      65      74 ..     343     352 ..     339     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.81
                                       S--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEEEEEE CS
                           FlgD_ig  33 sGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvkvtat 76 
                                       +G +V+ i+l + s+ +v+f+ d   +d   l +G Y++ v+a 
  gi|488599956|ref|YP_007906427.1|  70 NGVEVKEISLSPYSSITVQFEVD-VPDD---LNEGIYNIWVSAG 109
                                       68889999999999999999999.4444...7899999999885 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0097
                                       EEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEEEEE CS
                           FlgD_ig  26 tvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvkvta 75 
                                        +++ D+ G+ V + +++  ++   +f   G +++   ++dG+Y+vk++ 
  gi|488599956|ref|YP_007906427.1| 236 ILKVSDKDGKPVTNAEVKINNE---TFYTSGDGSALIEVPDGSYKVKISK 282
                                       5789999999999999999999...999999999999**********986 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.8
                                       -SEEEEEEEE CS
                           FlgD_ig  65 adGaYtvkvt 74 
                                       adG+Yt++v+
  gi|488599956|ref|YP_007906427.1| 343 ADGTYTLSVS 352
                                       89******98 PP

>> DUF5060  Domain of unknown function (DUF5060)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.021        15      31      69 ..     160     198 ..     141     199 .. 0.78
   2 ?   -0.9   0.0       3.2   2.2e+03      39      55 ..     254     280 ..     245     290 .. 0.66
   3 ?    1.6   0.0      0.53   3.7e+02      38      57 ..     403     430 ..     395     432 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                                       EEET.TEEEEEE-EE-STTEEEEEE---S-EEEEEEEEE CS
                           DUF5060  31 FtspsgksltvpGFYdGdgayrvrFaPdeeGeWtYktss 69 
                                       ++++  ++++ + FY  +++y++   P+e+ +  ++++s
  gi|488599956|ref|YP_007906427.1| 160 LSCKVPEKWECRFFYGDNQVYKIVLGPKETRTIYFRVES 198
                                       4444457788899999999***********999999987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.2
                                       EEEE-EE...-ST.......TEEEEEE CS
                           DUF5060  39 ltvpGFY...dGd.......gayrvrF 55 
                                       ++ + FY   dG+       g+y+v+ 
  gi|488599956|ref|YP_007906427.1| 254 INNETFYtsgDGSalievpdGSYKVKI 280
                                       566778884444455555555587765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.53
                                       EEEEE-EE-ST........TEEEEEE-- CS
                           DUF5060  38 sltvpGFYdGd........gayrvrFaP 57 
                                       ++ v+G++           g+yrv F P
  gi|488599956|ref|YP_007906427.1| 403 TVHVEGYCSATknltlnlkGEYRVYFEP 430
                                       688999994443455555588*****98 PP

>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.8    0.0066       4.6      41      59 ..     273     291 ..     250     292 .. 0.91
   2 ?   -0.7   0.0         2   1.4e+03      45      58 ..     334     347 ..     332     349 .. 0.82
   3 ?    5.0   0.0     0.033        23      40      57 ..     396     413 ..     395     416 .. 0.86
   4 ?   -1.0   0.0       2.3   1.6e+03      26      44 ..     507     525 ..     498     532 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0066
                           DUF1533  41 aGentIvIkakGYeDvtit 59 
                                       +G+++++I+ +GY D+++ 
  gi|488599956|ref|YP_007906427.1| 273 DGSYKVKISKDGYYDKEVD 291
                                       79*************9985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                           DUF1533  45 tIvIkakGYeDvti 58 
                                       +++I + GY+D t 
  gi|488599956|ref|YP_007906427.1| 334 RLKIENIGYADGTY 347
                                       5899******9775 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.033
                           DUF1533  40 kaGentIvIkakGYeDvt 57 
                                       k+G+++++++  GY  +t
  gi|488599956|ref|YP_007906427.1| 396 KVGTYNLTVHVEGYCSAT 413
                                       89************7665 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.3
                           DUF1533  26 ssigkLklkasvfnkaGen 44 
                                       +++ kLk+k++ +++  e 
  gi|488599956|ref|YP_007906427.1| 507 EYKLKLKIKSDQLEETEEI 525
                                       5666799999999665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 3322.73
//
Query:       gi|488599957|ref|YP_007906428.1|  [L=305]
Description: ABC-type transport system involved in multi-copper enzyme maturation, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  150.6  10.6    1.4e-42  146.0  10.6    2.0  1  ABC2_membrane_2  ABC-2 family transporter protein
    6.1e-06   26.3  15.9    6.1e-06   26.3  15.9    2.5  2  ABC2_membrane_4  ABC-2 family transporter protein
    0.00062   19.4  27.7    0.00069   19.2  22.0    2.8  2  ABC2_membrane_5  ABC-2 family transporter protein
     0.0041   16.9   2.3       0.15   11.9   0.0    2.9  3  SurA_N_3         SurA N-terminal domain
     0.0073   16.4   0.0      0.012   15.7   0.0    1.2  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
  ------ inclusion threshold ------
      0.062   13.7   0.0       0.78   10.2   0.0    2.2  2  DUF4094          Domain of unknown function (DUF4094)


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.0  10.6   4.6e-46   1.4e-42       2     287 ..       5     303 ..       4     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 4.6e-46
                   ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvs 78 
                                       ++akkEf d+++s+rfl + ++++l+  +  +l+ +g++  +   ++ e   +   +                    
  gi|488599957|ref|YP_007906428.1|   5 TVAKKEFVDHITSKRFLMFLAIILLL-TVFSFLQGIGDYRAT-RISVMEFFGFS--GT------------------- 58 
                                       79************************.777777777766554.45666666662..22................... PP

                   ABC2_membrane_2  79 timavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgiv 155
                                         ++ ++ ++++++g+d+i++E+e g+lk lLs+Pv+Rd+i++gK++g l++   i + ++  ++++l+i+l+ g  
  gi|488599957|ref|YP_007906428.1|  59 IGLSSFGSLLGLAMGFDLISKEREGGSLKTLLSHPVYRDQIINGKALGALMA---ITLVVFLNTVIGLGIVLIKGFT 132
                                       28899*********************************************99...777777777999********** PP

                   ABC2_membrane_2 156 laledllllvvasvlllllv.vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp..... 226
                                       ++++d++ +v +++l+++++ +f++++ll S+++++s +++  a+++f+vl++++p +++ v++   gp +      
  gi|488599957|ref|YP_007906428.1| 133 PTIDDMIAIVKFALLTIAYIfTFFSISLLTSTTSKNSGSSLVKAIAIFIVLSFVIPFIGSIVSNYIVGPPPDvythe 209
                                       *******************9*****************************************99999998888999** PP

                   ABC2_membrane_2 227 .................................qeindflsllsptsayntllneilagsdlnalgstatnllilll 270
                                                                        + i+ +++++sp+++y+ l++ i+++  + ++   ++n++ +++
  gi|488599957|ref|YP_007906428.1| 210 vpirvgddkakyeeiqrkmeererilneyykkkRAISELFEIFSPGMNYMKLISKISESNMFFESEDVTKNFVGFVV 286
                                       ************************************************************9999************* PP

                   ABC2_membrane_2 271 llavllvlgyvlFkrkD 287
                                       l++v++ l+y +F r +
  gi|488599957|ref|YP_007906428.1| 287 LPVVMFTLSYIRFLRSE 303
                                       **************986 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 !   26.3  15.9     2e-09   6.1e-06      14     177 ..      20     185 ..      10     187 .. 0.64
   2 ?    0.3   0.2       0.2   5.9e+02      30      66 ..     256     293 ..     234     302 .. 0.52

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2e-09
                   ABC2_membrane_4  14 ivwllvlaallvpllallyfnllgktgldpaefysls.vfgftlllllplilgi.iasylifrEeqndtlknLltiP 88 
                                       ++++l +++ll ++  l  +   ++t ++  ef+ +s ++g  l   +  +lg+ ++  li++E++++ lk Ll  P
  gi|488599957|ref|YP_007906428.1|  20 FLMFLAIILLLTVFSFLQGIGDYRATRISVMEFFGFSgTIG--LS-SFGSLLGLaMGFDLISKEREGGSLKTLLSHP 93 
                                       33333333333333334444555667777777777763333..33.3444555526788****************** PP

                   ABC2_membrane_4  89 vsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvf..favlpiialvllkk 163
                                       v r +++ +K +  l+ + l++++ ++i + + l+ gf+++  + ++ ++k  l++++++f  f ++ +   ++ ++
  gi|488599957|ref|YP_007906428.1|  94 VYRDQIINGKALGALMAITLVVFLNTVIGLGIVLIKGFTPTI-DDMIAIVKFALLTIAYIFtfFSISLLTSTTSKNS 169
                                       ********************************9****99874.4444445544444444440044443333333333 PP

                   ABC2_membrane_4 164 sy..vlpliltlvyti 177
                                       ++  v ++++ +v+++
  gi|488599957|ref|YP_007906428.1| 170 GSslVKAIAIFIVLSF 185
                                       3322556666666666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
                   ABC2_membrane_4  30 llyfnllgktgldpaefysls.vfgftlllllplilgi 66 
                                       + y++l++k + ++  f s + + +f  +++lp+++  
  gi|488599957|ref|YP_007906428.1| 256 MNYMKLISKISESNMFFESEDvTKNFVGFVVLPVVMFT 293
                                       44555555555444444443312335556677766643 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 !   19.2  22.0   2.3e-07   0.00069      36     165 ..      57     191 ..       8     205 .. 0.70
   2 ?    0.6   0.3      0.12   3.5e+02     171     199 ..     269     297 ..     238     301 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.3e-07
                   ABC2_membrane_5  36 vllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn.v 111
                                       +++ +s +  ++   + + ++s+++  ++ k ll+ Pv r +i++ K l++l+ i++++++ +++++ +vlikg   
  gi|488599957|ref|YP_007906428.1|  57 GTIGLSSFGSLLGLAMGFDLISKEREGGSLKTLLSHPVYRDQIINGKALGALMAITLVVFLNTVIGLGIVLIKGFtP 133
                                       3444555555566666779************************************************99***99985 PP

                   ABC2_membrane_5 112 tise...vllsiliglvialiflaivlPlyfkfgvekgri.vliiiifgiifllvaif 165
                                       ti++   +++++l+ ++++++f++i+l      +++ + +  +i+i++++ f+++ i 
  gi|488599957|ref|YP_007906428.1| 134 TIDDmiaIVKFALLTIAYIFTFFSISLLTSTTSKNSGSSLvKAIAIFIVLSFVIPFIG 191
                                       5555111445555555555666666666666666655555423333333444333222 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                   ABC2_membrane_5 171 elslidlsnyilliillviillliivSyf 199
                                        +++++   +  +++++v+ ++++ +Sy+
  gi|488599957|ref|YP_007906428.1| 269 NMFFESEDVTKNFVGFVVLPVVMFTLSYI 297
                                       23333333334455666666777888876 PP

>> SurA_N_3  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.023        68      11      35 ..      19      44 ..      10      50 .. 0.65
   2 ?   -0.4   0.2      0.28   8.5e+02      13      38 ..     141     166 ..     134     175 .. 0.75
   3 !   11.9   0.0     5e-05      0.15       7      68 ..     167     238 ..     162     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.023
                          SurA_N_3 11 swiakillgliilaFvl.wGvgsyls 35
                                       +++ + ++l++ +F +  G+g+y+ 
  gi|488599957|ref|YP_007906428.1| 19 RFLMFLAIILLLTVFSFlQGIGDYRA 44
                                      3444455555555577669**99975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.28
                          SurA_N_3  13 iakillgliilaFvlwGvgsylsgsg 38 
                                       i+k+ l++i+  F+++ ++ + s ++
  gi|488599957|ref|YP_007906428.1| 141 IVKFALLTIAYIFTFFSISLLTSTTS 166
                                       77888888888899999987666555 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 5e-05
                          SurA_N_3   7 knakswiakillgliilaFv..l..wGvgsylsgsgns......vakVngekIsraefqqayrrqleqlrqq 68 
                                       kn+ s ++k++ + i+l+Fv  +    v++y  g + +       ++V+++k +++e+q+++++  + l++ 
  gi|488599957|ref|YP_007906428.1| 167 KNSGSSLVKAIAIFIVLSFVipFigSIVSNYIVGPPPDvythevPIRVGDDKAKYEEIQRKMEERERILNEY 238
                                       566667889999999999985531133555666666225677878*****************9977766654 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 !   15.7   0.0     4e-06     0.012      59     119 ..     220     282 ..     218     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4e-06
                             Mod_r  59 lrselqekleelkelekefeekeqeldellqkfspdallarLqtavaeaee..eSealaeefl 119
                                       + +e+q k+ee +++ +e+ +k++  +el++ fsp  ++++L  +++e++   eSe++ ++f+
  gi|488599957|ref|YP_007906428.1| 220 KYEEIQRKMEERERILNEYYKKKRAISELFEIFSPGMNYMKLISKISESNMffESEDVTKNFV 282
                                       6689**********************************************8779999999997 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.26   7.9e+02       5      17 ..      27      39 ..      25      40 .. 0.88
   2 ?   10.2   0.0   0.00026      0.78       5      72 ..     177     259 ..     174     270 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.26
                           DUF4094  5 vllLcvasflagl 17
                                      +llL v+sfl g+
  gi|488599957|ref|YP_007906428.1| 27 ILLLTVFSFLQGI 39
                                      79*******9886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00026
                           DUF4094   5 vllLcvasf...lagllftnRlwtvpsdiirqs.k...eelklvsedcds.kdaesrskdilgevskthkaiqtL.. 71 
                                       ++++ v sf   ++g +++n +   p+d+  ++      +    + ++++ +++ ++ + il+e+ k++ ai+ L  
  gi|488599957|ref|YP_007906428.1| 177 IAIFIVLSFvipFIGSIVSNYIVGPPPDVYTHEvPirvGDD---KAKYEEiQRKMEERERILNEYYKKKRAISELfe 250
                                       55555555522267999999987555455555432223222...2333335444444569*************9966 PP

                           DUF4094  72 ........d 72 
                                                
  gi|488599957|ref|YP_007906428.1| 251 ifspgmnyM 259
                                       666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1380  (0.0769703); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 1867.47
//
Query:       gi|488599958|ref|YP_007906429.1|  [L=298]
Description: ABC-type multidrug transport system, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-29  103.6   0.0    1.8e-29  103.0   0.0    1.3  1  ABC_tran      ABC transporter
    1.2e-13   51.5   0.2      3e-09   37.1   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.8e-05   23.3   3.6    0.00014   22.4   3.6    1.8  1  AAA_23        AAA domain
    0.00014   22.3   0.0      0.001   19.5   0.0    2.2  1  AAA           ATPase family associated with various cellular 
     0.0016   18.2   0.5     0.0035   17.1   0.1    1.6  1  AAA_15        AAA ATPase domain
     0.0022   17.6   0.0     0.0069   16.0   0.0    1.7  2  SRP54         SRP54-type protein, GTPase domain
      0.008   16.5   0.0      0.083   13.3   0.0    2.4  2  RNA_helicase  RNA helicase
  ------ inclusion threshold ------
      0.022   14.7   0.0       0.04   13.8   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
      0.029   14.1   0.0      0.052   13.3   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
      0.067   12.6   0.1        4.8    6.5   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.072   13.0   0.0       0.15   12.0   0.0    1.5  1  Rad17         Rad17 P-loop domain
       0.12   11.8   0.0       0.21   11.0   0.0    1.3  1  PhoH          PhoH-like protein
       0.15   11.7   0.0       0.39   10.3   0.0    1.6  2  AAA_27        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   1.3e-32   1.8e-29       1     137 []      18     162 ..      18     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 1.3e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+n++l++  +e+ +++G+nGaGK+t +++l+g+l+pt+G++++ g d+ + +  +++k  g+lp+   + +++t+r
  gi|488599958|ref|YP_007906429.1|  18 LDNLNLEIDDNEVFGFLGPNGAGKTTTINILMGMLQPTSGRVEISGIDVVR-NPFEVKKICGYLPERVGFYDNMTAR 93 
                                       79*************************************************.566678999**************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +n             e+ +ei+++l+ +gl + +d++v     ++S+G+kqr+ +a+all++p++++lDEpt+
  gi|488599958|ref|YP_007906429.1|  94 QNllyfsefykipknEALKEIDDLLELVGLADSADKKV----GEFSKGMKQRLGMANALLNDPEVIFLDEPTS 162
                                       ***********988888888999999999999999999....*****************************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 !   12.3   0.3     8e-05      0.11       2      24 ..      31      53 ..      30      76 .. 0.75
   2 !   37.1   0.0   2.2e-12     3e-09     158     297 ..      83     191 ..      68     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       ++ GpNg+GK++ + +l ++ +
  gi|488599958|ref|YP_007906429.1| 31 FGFLGPNGAGKTTTINILMGMLQ 53
                                      5789*************966654 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 2.2e-12
                            AAA_21 158 ldglrke.rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelp 233
                                         g++++ + +++ +  ++f++ ++++ l++  + l lv++ +s+ +++                            
  gi|488599958|ref|YP_007906429.1|  83 RVGFYDNmTARQNLLYFSEFYKIPKNEALKEIDDLLELVGLADSADKKV---------------------------- 131
                                       5555555556666666666666666666666666666666666666644............................ PP

                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                         e+S G+k+ l+++ all ++    ++++DEp +gL+Pk  + + +++k ++++g  +++++H
  gi|488599958|ref|YP_007906429.1| 132 -GEFSKGMKQRLGMANALLNDP---EVIFLDEPTSGLDPKGSADFRKIIKMKKKEGKTIFFSSH 191
                                       .578****************99...9************************************** PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   3.6     1e-07   0.00014       7      68 ..      12      76 ..       3     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1e-07
                            AAA_23  7 frsf...rdqeidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese 68
                                      f++f   ++ +++  ++ ++ + GpNGaGKTT ++ +  +L    ++    sg + +++ +e+++ 
  gi|488599958|ref|YP_007906429.1| 12 FGKFkalDNLNLEIdDNEVFGFLGPNGAGKTTTINILMGMLQPT-SGRVEISGIDVVRNPFEVKKI 76
                                      555644477777778889*****************999999875.455566788888888887665 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 !   19.5   0.0   7.3e-07     0.001       3      66 ..      33     159 ..      31     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.3e-07
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       + Gp G GKT++++ ++  l+  +  +eisg +++ +                                        
  gi|488599958|ref|YP_007906429.1|  33 FLGPNGAGKTTTINILMGMLQptSGRVEISGIDVVRNpfevkkicgylpervgfydnmtarqnllyfsefykipkne 109
                                       68******************754567999999999556999999999999999999999999999999999999999 PP

                                       ....................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 ....................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                            vge +k +++ +  a +   +p ++f+DE
  gi|488599958|ref|YP_007906429.1| 110 alkeiddllelvgladsadkKVGEFSKGMKQRLGMANALLnDPEVIFLDE 159
                                       9999999999999999999999999999999999998888999******9 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.6e-06    0.0035      11      50 ..      15      55 ..      13     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-06
                            AAA_15 11 FRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      F++l++  ++++++ +  + G+N++GK++ +++l  +l+ +
  gi|488599958|ref|YP_007906429.1| 15 FKALDNLNLEIDDNeVFGFLGPNGAGKTTTINILMGMLQPT 55
                                      9**********9998999****************9999976 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   0.0     5e-06    0.0069       3      41 ..      30      68 ..      28      70 .. 0.92
   2 ?   -1.5   0.0       1.2   1.6e+03      68     109 ..     235     277 ..     176     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                      v+ ++G++GaGKTtt+  L  +l+    +v +   D+ R
  gi|488599958|ref|YP_007906429.1| 30 VFGFLGPNGAGKTTTINILMGMLQPTSGRVEISGIDVVR 68
                                      56689*******************************999 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHTT.SSEEEEEE--SSTTHHHHHHHHHHHH CS
                             SRP54  68 paavakeavekakeek.idvvlvDTaGrlqndkelmeelkkik 109
                                       p   ++e + + k+e+    ++ D   r ++ k+l+ee   ik
  gi|488599958|ref|YP_007906429.1| 235 PDPSIFEDFGEVKAENdRFWIISDRDCRTEISKKLFEEGYLIK 277
                                       3334444444444443134577788888888888887755555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     6e-05     0.083       3      74 ..      33     121 ..      31     132 .. 0.74
   2 ?   -0.0   0.0      0.83   1.2e+03      84     100 ..     176     192 ..     171     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkkl.............klkkkdsvysrnpeddfwdgYt.gqevvvidDfgqvkdee 65 
                                       + Gp+g GK+t+++ L+  l+ ++              ++ k+ + + + +  f+d+ t +q+ + + +f++++++e
  gi|488599958|ref|YP_007906429.1|  33 FLGPNGAGKTTTINILMGMLQPTSgrveisgidvvrnPFEVKKICGYLPERVGFYDNMTaRQNLLYFSEFYKIPKNE 109
                                       67******************977788888888888865555444445888888998888888888899999988664 PP

                      RNA_helicase  66 ..nps.dlaeli 74 
                                         ++  dl el+
  gi|488599958|ref|YP_007906429.1| 110 alKEIdDLLELV 121
                                       233334444444 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.83
                      RNA_helicase  84 lnmasleekgtlftSkv 100
                                       ++m++ e k ++f+S +
  gi|488599958|ref|YP_007906429.1| 176 IKMKKKEGKTIFFSSHI 192
                                       67999999977777765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.9e-05      0.04      88     127 ..      16      56 ..       6      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       ++l++l+ +++d ++  ++G+ G+GK+t in l++ l+   
  gi|488599958|ref|YP_007906429.1|  16 KALDNLNLEIDDnEVFGFLGPNGAGKTTTINILMGMLQPTS 56 
                                       56788888888879999****************99876555 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   3.8e-05     0.052      13      50 ..      19      56 ..      13      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      d+  +eid ++++ + Gp+G+GK+T +  ++ +L p++
  gi|488599958|ref|YP_007906429.1| 19 DNLNLEIDDNEVFGFLGPNGAGKTTTINILMGMLQPTS 56
                                      55667888778999***********9988877777765 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 ?    6.5   0.1    0.0035       4.8       9      42 ..      14      46 ..       7      60 .. 0.72
   2 ?    4.0   0.0     0.022        30     161     212 ..     154     206 ..      96     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0035
                                      SETTEECEEEEEETTSSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  9 nFksyagktvilpfsksftaivGpNGSGKsnlld 42
                                      +Fk + + + +++ ++ +   +GpNG+GK+  ++
  gi|488599958|ref|YP_007906429.1| 14 KFKALDNLNLEIDDNE-VFGFLGPNGAGKTTTIN 46
                                      6888865555555444.44568*******98776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.022
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                       + +lDe  + LD k  + + +++k k+k+   ++  s+    ++++ ++vg+ 
  gi|488599958|ref|YP_007906429.1| 154 VIFLDEPTSGLDPKGSADFRKIIKMKKKEgKTIFFSSHILSEVKEVCEVVGII 206
                                       5679********************88888344555666666666666666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.15      34     102 ..      17      86 ..       7     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                             Rad17  34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelgik.lrewlnpvslkepdnqksdfkgltekesrf 102
                                       +l+   Le   +++    GP G gk+t++++L   l +   r  + ++ +   +++++ + g +     f
  gi|488599958|ref|YP_007906429.1|  17 ALDNLNLEIDDNEVFGFLGPNGAGKTTTINILMGMLQPTsGRVEISGIDVVRNPFEVKKICGYLPERVGF 86 
                                       677788888888999999**************98887641456677777777777777766666665556 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.21      16      71 ..      25      83 ..      13     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                      HHH-SEEEEE--TTSSTT.HHHHHHHHHHHHTTS-S..EEEEEE-S--TT----SS--- CS
                              PhoH 16 lkkndivfaiGpaGtGKt.ylavalavealkkkkvk..riiltrpaveageelGflpgd 71
                                      +++n++   +Gp G+GKt  + + +++ + ++++v+   i ++r+ +e+++  G+lp  
  gi|488599958|ref|YP_007906429.1| 25 IDDNEVFGFLGPNGAGKTtTINILMGMLQPTSGRVEisGIDVVRNPFEVKKICGYLPER 83
                                      56899999*********7368999**999888766544999**********99999975 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00028      0.39       9      46 ..      10      48 ..       2      56 .. 0.82
   2 ?   -3.1   0.0       3.5   4.9e+03     136     163 ..     174     201 ..     173     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                            AAA_27  9 eryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAi 46
                                      + +Gkf+   +l+++ +++++   +GpN AGK+t+++ +
  gi|488599958|ref|YP_007906429.1| 10 KIFGKFKALdNLNLEIDDNEVFGFLGPNGAGKTTTINIL 48
                                      569999874389999999999999**********98755 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.5
                            AAA_27 136 alleaegelgqlLfeasaGlaslrevle 163
                                       ++++ + + g+++f +s  l++++ev e
  gi|488599958|ref|YP_007906429.1| 174 KIIKMKKKEGKTIFFSSHILSEVKEVCE 201
                                       6888999999999999988888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2062.36
//
Query:       gi|488599959|ref|YP_007906430.1|  [L=333]
Description: Phosphate/sulfate permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.4e-101  338.7  30.0   1.2e-100  336.9  30.0    1.7  1  PHO4             Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.9  30.0  6.4e-105  1.2e-100       1     336 [.      20     321 ..      20     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 336.9 bits;  conditional E-value: 6.4e-105
                              PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwl 77 
                                       iGanD+an++ats gs+altlrq++i+a+i+ef+Ga+l+G++V++t++kgiv +e  dp+++++g+l+a+l+a++w 
  gi|488599959|ref|YP_007906430.1|  20 IGANDAANSMATSYGSGALTLRQIIIIAGILEFSGAFLFGSRVTKTVGKGIVPIEHLDPTIVTIGALSAILSAGLWI 96 
                                       7**************************************************************************** PP

                              PHO4  78 llatvlglPvStthslvGaliGaalaa.....eggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkek 149
                                       ++at+++lPvSt+hs+vGa++G+++aa        e++kw+ l ki+lswv+sPl g+++a+++f l++ +il    
  gi|488599959|ref|YP_007906430.1|  97 TIATYYHLPVSTSHSIVGAMLGFGFAAvaedlIPLESIKWGVLYKIALSWVVSPLTGALLAFIIFSLIRIFILS--- 170
                                       ***************************8765433599**********************************883... PP

                              PHO4 150 lknalralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiyka 226
                                                                    + d +++e +f++lqv++a++v+fahG+nDvana+Gp+ a++      
  gi|488599959|ref|YP_007906430.1| 171 -----------------------------NMDVDKVEGVFRYLQVLTACYVAFAHGSNDVANAVGPISATF-GF--- 214
                                       .............................356789999*****************************5544.32... PP

                              PHO4 227 skevplwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvG 303
                                        +e+p w+l+lggl+ia+G++++G+rvi+tvG++it+ ltp+rGf+ae+a+a+tvl as++g+P+StTh+lvg+v+G
  gi|488599959|ref|YP_007906430.1| 215 -SETPSWILALGGLGIAIGVATWGYRVIETVGKRITE-LTPTRGFSAEFATATTVLSASYFGMPISTTHTLVGSVLG 289
                                       .389********************************5.*************************************** PP

                              PHO4 304 vGlakkresavnwklvrnivlaWvlTlpvsall 336
                                       vG+a  + ++v+ ++v++i+ +WvlT+p++a+l
  gi|488599959|ref|YP_007906430.1| 290 VGFAG-GLASVDISVVKRIIYSWVLTIPAAATL 321
                                       *****.79**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2453.56
//
Query:       gi|488599960|ref|YP_007906431.1|  [L=226]
Description: TIGR00153 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  164.0  10.5    3.3e-48  163.8  10.5    1.0  1  PhoU_div      Protein of unknown function DUF47
     0.0078   15.9   2.5     0.0078   15.9   2.5    1.7  2  SHE3          SWI5-dependent HO expression protein 3
  ------ inclusion threshold ------
      0.028   14.0   3.9       0.06   13.0   3.9    1.4  1  DUF4795       Domain of unknown function (DUF4795)
      0.037   14.2   0.6      0.073   13.2   0.2    1.7  2  Herpes_BLRF2  Herpesvirus BLRF2 protein
      0.094   12.9   3.2      0.079   13.1   1.0    1.9  2  DUF3585       Bivalent Mical/EHBP Rab binding domain
       0.14   12.6   1.4       0.83   10.1   1.4    2.2  1  ZapB          Cell division protein ZapB
        2.3    8.6   6.3        1.9    8.8   1.3    2.6  2  DUF1947       Domain of unknown function (DUF1947)
        4.4    7.2   7.2       0.33   10.8   0.5    2.4  3  DUF919        Nucleopolyhedrovirus protein of unknown functio
        6.9    7.2   8.9        1.2    9.6   0.2    3.1  3  FlaC_arch     Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8  10.5   1.7e-51   3.3e-48       3     213 ..       9     224 ..       7     225 .. 0.96

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 1.7e-51
                          PhoU_div   3 flfgsspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRed 79 
                                        +fg+sp+k + +h+e ++ +++ l ++++a++ gd+ +ve++  ei+ lE+eAD++k e+r +++k+l lPvdR+d
  gi|488599960|ref|YP_007906431.1|   9 DVFGYSPFKTIHKHSEYCVVAIDHLLDQFEAFVMGDMASVEKIEMEIDTLEHEADKLKAEVRTHVTKSLRLPVDRQD 85 
                                       59*************************************************************************** PP

                          PhoU_div  80 llelveslDeildvlediamlvtlrkv.efpeelkdeflallkktveaiealaevieeleklletalskk......d 149
                                       ll ++  +Dei+++ e++ ++ t + v +++++++ ++++ll k+ e++ +++e+i+ +   ++ +lskk      +
  gi|488599960|ref|YP_007906431.1|  86 LLTFLAFQDEIINYTEHVCHMFTYKIVeNMDKDVEKKLRNLLYKLNEIVCLYEEMIDDMLEWIARSLSKKeiggilE 162
                                       *******************99988765269**************************************99******* PP

                          PhoU_div 150 iveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisiill 213
                                       +v +ie+ E+e+D++q+ l+kklf+ +  + +l+++ll +i+ +l+++++  ++++d ++ ++l
  gi|488599960|ref|YP_007906431.1| 163 KVDKIEKTEHECDKVQIALHKKLFNSD--MEFLDIILLRNIVIHLGEIANSTARASDSLRTMVL 224
                                       *************************43..69*****************************9986 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 !   15.9   2.5   3.9e-06    0.0078      99     222 ..      19     147 ..      14     152 .. 0.82
   2 ?    4.6   2.1     0.012        23     158     217 ..     109     169 ..      91     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-06
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX......XXXXX CS
                              SHE3  99 ssaseteleeelerlkvqYdalvdsqkeYkehYqqeieeLkesleklklenekqleelqerissndk.....didtk 170
                                        +++++ +   +++l  q++a v + +   e+ + ei++L+++ +klk e + ++++  +  ++ +      +++ +
  gi|488599960|ref|YP_007906431.1|  19 IHKHSEYCVVAIDHLLDQFEAFVMGDMASVEKIEMEIDTLEHEADKLKAEVRTHVTKSLRLPVDRQDlltflAFQDE 95 
                                       56777788888999999**********************************99998888776665531223357899 PP

                                       XXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 171 ldsynnkkknl..esieeeknkkllkkleslaseldleswlelykelkeliley 222
                                       + +y++ + ++   +i e+ +k ++kkl +l+ +  l++ + ly+e+ + +le+
  gi|488599960|ref|YP_007906431.1|  96 IINYTEHVCHMftYKIVENMDKDVEKKLRNLLYK--LNEIVCLYEEMIDDMLEW 147
                                       99*****9999444688999999****9999865..679999999998888775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.012
                                       XXXXXX.X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 158 erissn.dkdidtkldsynnkkknlesieeeknkkllkkleslaseldleswlelykelke 217
                                        +i++n dkd+++kl ++  k +++  ++ee    +l+ + +++s+ ++   le+  + ++
  gi|488599960|ref|YP_007906431.1| 109 YKIVENmDKDVEKKLRNLLYKLNEIVCLYEEMIDDMLEWIARSLSKKEIGGILEKVDKIEK 169
                                       4455443899********9999999999999999999999999999999888888776665 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.9     3e-05      0.06      38     125 ..      49     155 ..      42     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                           DUF4795  38 edkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq.................fDeakkeLekml 97 
                                       e+ e ++++l+ ++++l+ +   +++v++ l++++d+++L t    ++                 ++++ k+ ek+l
  gi|488599960|ref|YP_007906431.1|  49 EKIEMEIDTLEHEADKLKAE--VRTHVTKSLRLPVDRQDLLTFLAFQDeiinytehvchmftykiVENMDKDVEKKL 123
                                       45566777777777777655..578*****************998887899************************** PP

                           DUF4795  98 eellekle....eqeealkkaldtLqeelkek 125
                                       + ll kl+      ee+++ +l+ + ++l +k
  gi|488599960|ref|YP_007906431.1| 124 RNLLYKLNeivcLYEEMIDDMLEWIARSLSKK 155
                                       ******99777777777777777777444443 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.6e-05     0.073       2      70 ..      46     121 ..      45     149 .. 0.80
   2 ?   -1.5   0.0       1.3   2.6e+03      45      68 ..     145     168 ..     121     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                      Herpes_BLRF2   2 ltvEdlaaelakLkvENkaLkkklkssvs.......pkdeeLTaaekeavltstvgrlsskaakkieervrkevlk 70 
                                       ++vE+++ e+  L+ E  +Lk +++ +v        +++  LT  + +  + + ++++ +  + ki e ++k+v+k
  gi|488599960|ref|YP_007906431.1|  46 ASVEKIEMEIDTLEHEADKLKAEVRTHVTkslrlpvDRQDLLTFLAFQDEIINYTEHVCHMFTYKIVENMDKDVEK 121
                                       589*************************999***887778899776666666666666666666666666666654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                      Herpes_BLRF2  45 ltstvgrlsskaakkieervrkev 68 
                                       l  +   ls+k    i e+v+k+ 
  gi|488599960|ref|YP_007906431.1| 145 LEWIARSLSKKEIGGILEKVDKIE 168
                                       444445566666666666666654 PP

>> DUF3585  Bivalent Mical/EHBP Rab binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.0     4e-05     0.079       4      87 ..      47     128 ..      45     134 .. 0.89
   2 ?   -1.1   0.0      0.94   1.9e+03       6      26 ..     165     185 ..     154     218 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                           DUF3585   4 eleeieeeqreleergvelEkaLRgeaeesgeeeeeellqewfeLvneknelvrreseLmilareqeLedeqadleq 80 
                                        +e+ie e ++le+++ +l  + R++ +  ++ + +   q++++ +  ++e++ ++++  ++   + +e+  +d+e+
  gi|488599960|ref|YP_007906431.1|  47 SVEKIEMEIDTLEHEADKLKAEVRTHVT--KSLRLPVDRQDLLTFLAFQDEIINYTEHVCHMFTYKIVENMDKDVEK 121
                                       5799********************6663..45556666799************************************ PP

                           DUF3585  81 elrelma 87 
                                       +lr+l+ 
  gi|488599960|ref|YP_007906431.1| 122 KLRNLLY 128
                                       ***9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.94
                           DUF3585   6 eeieeeqreleergvelEkaL 26 
                                       ++ie++  e ++   +l k+L
  gi|488599960|ref|YP_007906431.1| 165 DKIEKTEHECDKVQIALHKKL 185
                                       444444444444444444444 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.4   0.00041      0.83       6      71 .]      34     132 ..      32     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00041
                              ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlk.............................. 52 
                                       L+q E+ +      +++  mei+ L++e  +lk e r    +    +                              
  gi|488599960|ref|YP_007906431.1|  34 LDQFEAFVMGDMASVEKIEMEIDTLEHEADKLKAEVRTHVTKSL--Rlpvdrqdlltflafqdeiinytehvchmft 108
                                       6667777777777899999**************98877653333..3336666666677777777777777777778 PP

                              ZapB  53 .....eereawqerlkkLLgklee 71 
                                            +  + ++++l++LL kl+e
  gi|488599960|ref|YP_007906431.1| 109 ykiveNMDKDVEKKLRNLLYKLNE 132
                                       888778888999999999999987 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.21   4.2e+02      32      54 ..     118     139 ..     107     143 .. 0.77
   2 ?    8.8   1.3   0.00097       1.9       5      38 ..     152     184 ..     151     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.21
                                       EEEE-SS-EEEEETTEEEEEESS CS
                           DUF1947  32 EieeekkeklYlingvpilfeee 54 
                                       ++e++ +  lY  n++ +l+e e
  gi|488599960|ref|YP_007906431.1| 118 DVEKKLRNLLYKLNEIVCLYE-E 139
                                       6888889999*******9993.3 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00097
                                       --HHHHHHHHHHHHTTT---TT--..-EEEE-SS CS
                           DUF1947   5 LSkKeakeileklkekyisislesdkiEieeekk 38 
                                       LSkKe+  ilek+++   + + e dk+ i+ +kk
  gi|488599960|ref|YP_007906431.1| 152 LSKKEIGGILEKVDKIE-KTEHECDKVQIALHKK 184
                                       9****************.***********99986 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2         1   2.1e+03      32      47 ..      47      62 ..      45      68 .. 0.76
   2 ?   -2.3   0.1         2     4e+03       4      10 ..     124     130 ..     114     134 .. 0.45
   3 ?   10.8   0.5   0.00017      0.33      28      58 ..     162     196 ..     161     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
                            DUF919 32 kitKnpkElqdlekkl 47
                                      +++K + E+  le++ 
  gi|488599960|ref|YP_007906431.1| 47 SVEKIEMEIDTLEHEA 62
                                      6889999999999865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                            DUF919   4 qsLrqqL 10 
                                       ++L  +L
  gi|488599960|ref|YP_007906431.1| 124 RNLLYKL 130
                                       2333333 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00017
                            DUF919  28 ErlkkitKnpkElqd....lekklnklRqeFLnfg 58 
                                       E++ ki+K ++E  +    l+kkl+++ +eFL+ +
  gi|488599960|ref|YP_007906431.1| 162 EKVDKIEKTEHECDKvqiaLHKKLFNSDMEFLDII 196
                                       9***********9863333789**********976 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0006       1.2       8      31 ..      47      70 ..      46      77 .. 0.91
   2 ?    0.7   0.8      0.36   7.1e+02      24      45 ..     117     138 ..     108     146 .. 0.56
   3 ?   -0.1   0.1      0.63   1.2e+03      20      36 ..     154     170 ..     148     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0006
                         FlaC_arch  8 klsklsteletvkkeneelsksve 31
                                       ++k+++e++t++ e ++l+ +v 
  gi|488599960|ref|YP_007906431.1| 47 SVEKIEMEIDTLEHEADKLKAEVR 70
                                      589****************99985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.36
                         FlaC_arch  24 eelsksveelkenVkdllsLYE 45 
                                       ++++k++ +l  + ++++ LYE
  gi|488599960|ref|YP_007906431.1| 117 KDVEKKLRNLLYKLNEIVCLYE 138
                                       3344444444444456666665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.63
                         FlaC_arch  20 kkeneelsksveelken 36 
                                       kke+  + ++v++++++
  gi|488599960|ref|YP_007906431.1| 154 KKEIGGILEKVDKIEKT 170
                                       66777777888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1380.63
//
Query:       gi|488599961|ref|YP_007906432.1|  [L=411]
Description: isocitrate dehydrogenase (NADP) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-110  367.8   0.0   7.5e-110  367.3   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 !  367.3   0.0  4.2e-114  7.5e-110       2     348 .]      30     404 ..      29     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 367.3 bits;  conditional E-value: 4.2e-114
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkeke 78 
                                       i+ +egdgiG++vv+aa+ vl++a++ +g+e+++ +v++G+ a++ +g+ lp++t++ai+e +v+l+g+++tp++++
  gi|488599961|ref|YP_007906432.1|  30 IPYFEGDGIGKDVVPAAIMVLDEAAKLYGKEISWFKVYAGEDAYRLYGKYLPDDTINAIREFRVALKGPLTTPVGGG 106
                                       7899************************************************************************* PP

                                       SSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET............ CS
                            Iso_dh  79 vrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg............ 143
                                        r+ n  +++r++ldl+an+rp+ ++   +v+sp+++  +e+vd+vi+Re+t+++Y+g e  + +            
  gi|488599961|ref|YP_007906432.1| 107 FRSLN--VTIRQMLDLYANVRPIYYL--NGVPSPIRH--PEKVDMVIFRENTEDVYSGVEWPRGSegalkvikflad 177
                                       *****..9******************..8*******8..9********************9999999********** PP

                                       ....TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC......... CS
                            Iso_dh 144 ....sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee......... 206
                                           +   e++++++k++se +++r++r+a+++A+++++++vtlv+K+n++k +e ++r++ +eva+e         
  gi|488599961|ref|YP_007906432.1| 178 elgvN-IREDSGIGIKPISEFATKRLVRMAIQYAIDNNRESVTLVHKGNIMKYTEgAFRDWGYEVAREefgdvtite 253
                                       *9854.6999******************************************************************* PP

                                       ..........TTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEE CS
                            Iso_dh 207 ..........eypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifE 273
                                                 + ++i ++++++D++ +q++++ +++dV++++Nl+GD++SD+aaa+vG+lG++p++++g +++++fE
  gi|488599961|ref|YP_007906432.1| 254 telwenyggeAKGKIVIKDRIADNMFQQILTRTDEYDVLAMPNLNGDYMSDAAAAMVGGLGIAPGSNIG-DGIGVFE 329
                                       *********88899*******************************************************.79***** PP

                                       ESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS.TCCCHHHHHHHHH CS
                            Iso_dh 274 avHGsapdiagkdkaNpiavilSaalmLryslgleeaAdkiekAvekvleagivTkDlagea.akevstsefgdav 348
                                       ++HGsap++ag++k+Np+a il  alm +y lg++ea+++i+kAvek++++givT+D+ +    + v t+ef  +v
  gi|488599961|ref|YP_007906432.1| 330 PIHGSAPKYAGQNKVNPTAEILTGALMFEY-LGWKEASEMIKKAVEKTIQSGIVTYDIHRHIgGNLVGTREFAAEV 404
                                       ******************************.****************************9987999*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2231.48
//
Query:       gi|488599962|ref|YP_007906433.1|  [L=258]
Description: TIGR00268 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-12   44.7   0.2    1.5e-08   34.0   0.0    2.1  2  NAD_synthase   NAD synthase
    1.3e-08   34.6   0.0    1.4e-06   28.0   0.0    2.3  2  QueC           Queuosine biosynthesis protein QueC
      2e-05   23.5   0.2       0.14   10.9   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
    6.4e-05   22.8   0.0     0.0001   22.1   0.0    1.3  1  Asn_synthase   Asparagine synthase
     0.0017   18.1   0.2      0.041   13.6   0.0    2.3  2  ATP_bind_3     PP-loop family
     0.0049   16.5   0.0          2    7.9   0.0    2.3  2  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
       0.04   14.0   0.0       0.41   10.7   0.0    2.1  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
      0.088   12.8   0.1          2    8.4   0.0    2.3  2  FlpD           Methyl-viologen-reducing hydrogenase, delta su
      0.091   13.1   0.2        1.1    9.6   0.0    2.3  2  Radical_SAM    Radical SAM superfamily
       0.15   11.9   0.3       0.25   11.2   0.3    1.3  1  DUF4032        Domain of unknown function (DUF4032)
       0.15   11.7   0.0       0.34   10.6   0.0    1.6  1  Choline_kin_N  Choline kinase N terminus


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 !   34.0   0.0   9.4e-12   1.5e-08       8      83 ..       9      81 ..       4      90 .. 0.87
   2 !    8.7   0.0   0.00051      0.83     148     177 ..     140     167 ..     135     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 9.4e-12
                                      HHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                      NAD_synthase  8 flkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                                       ++e++++ + k+vv   SGG DS+lva++++++  +e  +a+ + ++  +e+++e a++lae+lg++   +++++
  gi|488599962|ref|YP_007906433.1|  9 KIREEIASLEGKKVV-AFSGGADSTLVAYICKMV--DEDSVAVTIKGEAIPEREIEYAKMLAEKLGLNHRILELSQ 81
                                      678888888888866.69*************987..588999**************************99888765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00051
                                       BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                       + p+++ +K +v+eLak+l  P+   +kpP
  gi|488599962|ref|YP_007906433.1| 140 ISPLKNYTKEQVRELAKQLKLPN--WDKPP 167
                                       89*******************97..45555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   8.5e-10   1.4e-06       2      65 ..      21      83 ..      20      88 .. 0.95
   2 ?    4.5   0.0     0.013        22     150     176 ..     135     161 ..     111     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 8.5e-10
                                      EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGG CS
                              QueC  2 avvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllk 65
                                       vv +SGG DSt v+++ k   +   a+t++ +   ++e+e+ak +a++lg+ +h+il+l+ lk
  gi|488599962|ref|YP_007906433.1| 21 KVVAFSGGADSTLVAYICKMVDEDSVAVTIKGEAIPEREIEYAKMLAEKLGL-NHRILELSQLK 83
                                      699****************************9999*****************.******99876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                                       S--EEE-TTTT--HHHHHHHHHHTTHH CS
                              QueC 150 kkieieaPlidlsKaeivklgkelgvp 176
                                       k++ +  Pl + +K+++ +l+k+l++p
  gi|488599962|ref|YP_007906433.1| 135 KDLGVISPLKNYTKEQVRELAKQLKLP 161
                                       5678999*****************976 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00012      0.19       4      71 ..      22      80 ..      20      82 .. 0.84
   2 !   10.9   0.0   8.8e-05      0.14     164     192 ..     139     167 ..     132     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfe 71
                                      vva+SgG DS+++a++ k    + ++v++k  +           e+++++a++ aeklg+++++++++
  gi|488599962|ref|YP_007906433.1| 22 VVAFSGGADSTLVAYICKMVDEDSVAVTIKGEA---------IPEREIEYAKMLAEKLGLNHRILELS 80
                                      79*****************99999999987543.........45678899999999999999888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.8e-05
                     tRNA_Me_trans 164 llfPlgeltKeevrkiAkeaglavaekkd 192
                                       ++ Pl ++tKe+vr++Ak+ +l++ +k+ 
  gi|488599962|ref|YP_007906433.1| 139 VISPLKNYTKEQVRELAKQLKLPNWDKPP 167
                                       567********************998874 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.4e-08    0.0001      23      81 ..      24      81 ..      20     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.4e-08
                      Asn_synthase 23 lLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlte 81
                                       +SGG DS+l+a++ +   + +  +++i+ e+    e++yak +ae+lg++h+ l+l++
  gi|488599962|ref|YP_007906433.1| 24 AFSGGADSTLVAYICKMVDE-DSVAVTIKGEAIPEREIEYAKMLAEKLGLNHRILELSQ 81
                                      58**************9987.88899999988999******************999886 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.5e-05     0.041       2      66 ..      21      79 ..      20      94 .. 0.72
   2 ?    2.1   0.0     0.089   1.4e+02     135     162 ..     134     161 ..     120     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                                      EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE- CS
                        ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekv 66
                                       +vA+SgG+DS++  ++ +   +    + va+++  +  +  ++e e+ k l++kl+++++i ++
  gi|488599962|ref|YP_007906433.1| 21 KVVAFSGGADSTLVAYICKMVDE----DSVAVTIKGE--AIPEREIEYAKMLAEKLGLNHRILEL 79
                                      58************999999876....4556655444..34456667777777777777776665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.089
                                       ETTCCEE-CCCT--HHHHHHHHHHTT-- CS
                        ATP_bind_3 135 iasirlvRPlLkvskeeleeylkekkik 162
                                       i++  ++ Pl +++ke+++e++k+ k++
  gi|488599962|ref|YP_007906433.1| 134 IKDLGVISPLKNYTKEQVRELAKQLKLP 161
                                       45667899***************98875 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0034       5.6       3      61 ..      18      75 ..      16     108 .. 0.84
   2 !    7.9   0.0    0.0012         2     132     191 ..     131     192 ..     122     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0034
                              ThiI  3 qgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqt 61
                                      +gk ++  SgG DS   ay+        v+v++k     +e++ie  ++lae+l  ++ 
  gi|488599962|ref|YP_007906433.1| 18 EGKKVVAFSGGADSTLVAYICKMVDEDSVAVTIK-GEAIPEREIEYAKMLAEKLGLNHR 75
                                      57888899***********998888889999997.566788999999999999987765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0012
                              ThiI 132 isavvnllilrPLigldKeeiiklAkeigtyeisiekedkCsv..la.khPttkakleeveka 191
                                       i+a  +l +++PL  + Ke++ +lAk++   +    +   C++  +  +h  tk  l+++e+a
  gi|488599962|ref|YP_007906433.1| 131 IKAIKDLGVISPLKNYTKEQVRELAKQLKLPNWDKPPA-SCTAtrVQfNHQITKDLLSRIERA 192
                                       56777999*******************98776655444.333311335566666666666555 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.41       3      59 ..      22      78 ..      20     163 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                      EEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE CS
                       PAPS_reduct  3 vvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvye 59
                                      vv++sgG+ds+ +  ++  ++++   v ++ +   +  ie+ + l+e++gl+  + e
  gi|488599962|ref|YP_007906433.1| 22 VVAFSGGADSTLVAYICKMVDEDSVAVTIKGEAIPEREIEYAKMLAEKLGLNHRILE 78
                                      89********9888888888888889999999999999***********99944333 PP

>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0012         2      47     102 ..      24      84 ..      20      90 .. 0.88
   2 ?    1.9   0.0      0.13   2.2e+02      73     109 ..     184     220 ..     168     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                              FlpD  47 alekGadgVlvl.gChpgd....ChyvkGnekaerrveklkelleelgiepeRvrleevsa 102
                                       a++ Gad  lv+  C+  d       +kG+   er +e +k l e+lg++++ ++l+++++
  gi|488599962|ref|YP_007906433.1|  24 AFSGGADSTLVAyICKMVDedsvAVTIKGEAIPEREIEYAKMLAEKLGLNHRILELSQLKI 84 
                                       8999***99997459987777877888***********************99999999887 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                              FlpD  73 kaerrveklkelleelgiepeRvrleevsaaegekfa 109
                                          +r+e++++ l elg+   Rvr+++   ++  +++
  gi|488599962|ref|YP_007906433.1| 184 DLLSRIERAEDRLLELGFRVVRVRVYQTFNGDDVRLQ 220
                                       5567999999**************9998777766665 PP

>> 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       0.3   4.9e+02      31      58 ..       7      31 ..       1      75 [. 0.55
   2 ?    9.6   0.0   0.00069       1.1       4     111 ..      88     254 ..      87     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.3
                                      HHHHHHHHHHHHHHTTSEEEEEESSTGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 31 veeileevkelkaekgvkevilgggepl 58
                                      + +i ee+ +l    g+k+v ++gg  +
  gi|488599962|ref|YP_007906433.1|  7 IAKIREEIASL---EGKKVVAFSGGADS 31
                                      34455555555...25777777777333 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00069
                                       ESEESS--TTTSCCTT.................................HHHHHHHHHHHHHHHHHHHHHHH.HHTT CS
                                       xxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpet.................................vrregrgrslsveeileevkelk.aekg 46 
                                       ++  + rC +C                                       +   + ++ ++e++ e++k+lk  +++
  gi|488599962|ref|YP_007906433.1|  88 MQNPPERCYYCKKAMIyrtmvefpkakildgsnasdfsdyrpgikaikdLGVISPLKNYTKEQVRELAKQLKlPNWD 164
                                       5667889999988888888999999999999999999999999999999888899999999**********999999 PP

                                       SEEEEEESSTGGGSTTHHHHHHHHHHTC..........CCTEEEEEEECSSCHG...............HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxx...............xxxxxxxx RF
                       Radical_SAM  47 vkevilgggepllypdfvellerlakla..........vpgiritvetngtlpd...............eeklerll 98 
                                       +     +   + ++  ++++l+ ++++a          v  +r+  + ng  ++               +e++  l+
  gi|488599962|ref|YP_007906433.1| 165 KPPASCTATRVQFNHQITKDLLSRIERAedrllelgfrVVRVRVYQTFNGDDVRlqvaedevsrafeirKEIASILR 241
                                       999999999999999999999999999999999999996666666677777766777777777999999******** PP

                                       HTT-SEEEEEEBS CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM  99 elgvdrvslglea 111
                                       e g+ rv+l++e 
  gi|488599962|ref|YP_007906433.1| 242 EFGFSRVALDVEG 254
                                       **********997 PP

>> DUF4032  Domain of unknown function (DUF4032)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00015      0.25      11      53 ..     180     222 ..     173     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                           DUF4032  11 vfeaderyrieerirrlneLGFdveeleletdedgerlrlrpk 53 
                                       ++++d   rie+  +rl eLGF v  +++ ++ +g+++rl+++
  gi|488599962|ref|YP_007906433.1| 180 QITKDLLSRIERAEDRLLELGFRVVRVRVYQTFNGDDVRLQVA 222
                                       56777788999999**********************9998865 PP

>> Choline_kin_N  Choline kinase N terminus
   #    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      16      49 ..     115     170 ..     108     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                     Choline_kin_N  16 vLDnskpsdy......................FKeeilrLlhtLalkgWrdvplda 49 
                                       +LD+s  sd+                       Ke + +L++ L+l+ W + p+ +
  gi|488599962|ref|YP_007906433.1| 115 ILDGSNASDFsdyrpgikaikdlgvisplknyTKEQVRELAKQLKLPNWDKPPASC 170
                                       67777777777777777777777777777777899999*************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1819.90
//
Query:       gi|488599963|ref|YP_007906434.1|  [L=366]
Description: ATP-utilizing enzymes of ATP-grasp superfamily (probably carboligases) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-81  270.2   1.0    9.4e-81  269.8   1.0    1.1  1  DUF1297   Domain of unknown function (DUF1297)
    6.5e-44  148.8   0.0    1.1e-43  148.1   0.0    1.3  1  DUF1246   Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.8   1.0     1e-84   9.4e-81       1     187 [.     179     365 ..     179     366 .] 0.99

  Alignments for each domain:
  == domain 1  score: 269.8 bits;  conditional E-value: 1e-84
                                       HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-- CS
                           DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqleleve 77 
                                       +f +k+e++l++gliee+dlk++ i+ey+vGan++++yfysp+ ++vel+++drRyesn+dgl r+pa+ q+++e +
  gi|488599963|ref|YP_007906434.1| 179 DFLQKSEQMLKQGLIEEKDLKEVFIQEYIVGANVYFSYFYSPVFSRVELIAVDRRYESNVDGLGRIPAEIQMKMEFS 255
                                       7999************************************************************************* PP

                                       --EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--C CS
                           DUF1297  78 peyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegsp 154
                                       p+y+vvGn+pvvlREsll++v+++ge +ve++k++++pG++GpFcL++v+++++e++vf++saRiv+gtnv + +sp
  gi|488599963|ref|YP_007906434.1| 256 PTYTVVGNYPVVLRESLLSQVLRAGEAVVEVSKEIAYPGMVGPFCLEAVFNENAEMIVFEISARIVAGTNVGIPASP 332
                                       ***************************************************************************** PP

                                       CHHHTTSS---HHHHHHHHHHHHHHCT-GGGCE CS
                           DUF1297 155 yskllfgeplsmGrrialEikeaiekdrleeiv 187
                                       ys++lfge+++mG+ria+Eik a+e+d+lee++
  gi|488599963|ref|YP_007906434.1| 333 YSYILFGENMYMGKRIAREIKLALEQDMLEELI 365
                                       ******************************987 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.0   1.2e-47   1.1e-43       1     121 [.      25     147 ..      25     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 1.2e-47
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvidevivldkfkdilkeevqeklreenailvPhgsfve 77 
                                       iatl+SHsal+ilkgAk+egfrt+++c+++++ +Ye+f+v+de+i++d+++d+l++++q++++++n il+Phgsf++
  gi|488599963|ref|YP_007906434.1|  25 IATLGSHSALNILKGAKEEGFRTVCICREKERIIYESFGVADEIIEIDDYSDLLRKDLQREIADMNGILIPHGSFNA 101
                                       89*************************************************************************** PP

                                       HC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHH....HHHTT-BB--B CS
                           DUF1246  78 YvgiekieelkvpifGnrkllrwEerrekkrky....LekAgiriPkk 121
                                       Y+g  +  elk+pifGnr+l+ wE+ re+++++    L++Ag+r+P++
  gi|488599963|ref|YP_007906434.1| 102 YIGKLD--ELKLPIFGNRELMYWETVREMQDRWlnsaLSSAGLRTPRI 147
                                       ***766..*************************99999999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2130.66
//
Query:       gi|488599964|ref|YP_007906435.1|  [L=254]
Description: NCAIR mutase (PurE)-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-21   74.8   1.3    5.3e-21   74.8   1.3    1.8  2  AIRC      AIR carboxylase
  ------ inclusion threshold ------
      0.079   13.1   1.3        2.3    8.5   0.0    3.2  4  UPF0180   Uncharacterised protein family (UPF0180)


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 ?   -0.8   0.0      0.11   9.8e+02      37      63 ..      55      81 ..      42      85 .. 0.83
   2 !   74.8   1.3   5.9e-25   5.3e-21       1     131 [.     117     249 ..     117     254 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.11
                                      TTSHHHHHHHHHHCHTTTEEEEEEEEE CS
                              AIRC 37 hrtpeelleyaeeaeerglkviIagAG 63
                                       ++pee+++++++a ++   v+++ A 
  gi|488599964|ref|YP_007906435.1| 55 GKSPEEVVKIIKNALKHLKGVLVTRAS 81
                                      588999999999999998889888776 PP

  == domain 2  score: 74.8 bits;  conditional E-value: 5.9e-25
                                       EEEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHH CS
                              AIRC   1 kVgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvva 73 
                                       kV+ii + +sD++v+++a+++++ lg+     y++ v+  hr     ++ ++e++++ ++ +I++AG++ +Lp+vva
  gi|488599964|ref|YP_007906435.1| 117 KVAIISAGTSDIPVAEEAVKTCEFLGLevkkYYDAGVAGIHRL----IKPIKEINSDSVDSVIVVAGMEGALPSVVA 189
                                       69**********************9993333346666666665....55566666677889**************** PP

                                       HHSSS-EEEEEE-...-STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT- CS
                              AIRC  74 slttlPVigvPvk...skalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkd 131
                                       +l+++PVi+vP++     +l gl +l+S++q +s  +va v+i+++  A+++A  i  + +
  gi|488599964|ref|YP_007906435.1| 190 GLVDVPVIAVPTSigyGVSLGGLTALFSMLQSCS-SGVAVVNIDNGFGAGVFAYLISRTIR 249
                                       ************9443258*************98.478888899*********98866554 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00025       2.3      60      76 ..      51      67 ..      39      68 .. 0.89
   2 ?    1.7   0.0     0.033   2.9e+02      56      77 .]      74      95 ..      70      95 .. 0.85
   3 ?   -2.2   0.1      0.53   4.8e+03      32      44 ..     168     181 ..     160     198 .. 0.59
   4 ?   -2.8   0.0      0.83   7.4e+03      18      28 ..     223     233 ..     210     238 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00025
                           UPF0180 60 InAsgktaeeIlqevee 76
                                      I A+gk++ee+++ +++
  gi|488599964|ref|YP_007906435.1| 51 IYAEGKSPEEVVKIIKN 67
                                      88*************97 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.033
                           UPF0180 56 kapvInAsgktaeeIlqeveer 77
                                      +++v  As+  +eeI++e ++r
  gi|488599964|ref|YP_007906435.1| 74 GVLVTRASKEQIEEIKKEFRDR 95
                                      788999**********998765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.53
                           UPF0180  32 aqsvdaiVv.tGqd 44 
                                        +svd ++v  G++
  gi|488599964|ref|YP_007906435.1| 168 SDSVDSVIVvAGME 181
                                       55666544436665 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 0.83
                           UPF0180  18 ekGYeVvdlet 28 
                                       ++G  Vv++++
  gi|488599964|ref|YP_007906435.1| 223 SSGVAVVNIDN 233
                                       35666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      772  (0.0430587); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1474.09
//
Query:       gi|488599965|ref|YP_007906436.1|  [L=1080]
Description: carbamoyl-phosphate synthase large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-114  381.1   0.1    1.7e-73  246.6   0.1    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    6.2e-44  149.3   2.0    9.6e-44  148.6   0.6    2.1  2  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    1.2e-24   86.3   0.0    2.7e-23   81.9   0.1    3.2  3  MGS              MGS-like domain
    1.2e-15   57.7   0.2    6.8e-08   32.3   0.0    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    4.2e-15   55.7   0.1    1.4e-07   31.2   0.0    2.5  2  ATP-grasp        ATP-grasp domain
      4e-11   42.8   0.0    1.8e-06   27.8   0.0    2.7  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    3.9e-10   39.6   0.0    8.7e-06   25.5   0.0    2.9  3  RimK             RimK-like ATP-grasp domain
    4.2e-09   36.6   0.4    1.4e-05   25.2   0.0    2.7  2  ATP-grasp_3      ATP-grasp domain
    7.4e-09   35.6   0.1     0.0002   21.2   0.0    2.4  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
      4e-08   33.0   0.0     0.0015   18.0   0.0    2.6  2  ATP-grasp_5      ATP-grasp domain
    1.1e-07   31.5   1.2    0.00037   20.1   0.0    3.3  3  ATP-grasp_4      ATP-grasp domain
    3.4e-07   30.0   0.0     0.0013   18.3   0.0    2.8  2  ATP-grasp_2      ATP-grasp domain
     0.0026   18.2   0.2      0.056   13.9   0.0    3.2  2  CoA_binding_2    CoA binding domain
  ------ inclusion threshold ------
      0.014   14.9   0.1      0.027   14.0   0.1    1.4  1  Vps5             Vps5 C terminal like
      0.031   14.3   0.0         14    5.8   0.0    3.0  2  DUF4176          Domain of unknown function (DUF4176)
      0.034   14.2   0.0        5.5    7.1   0.0    3.1  3  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.035   13.7   0.5        5.6    6.5   0.1    3.6  3  PrpR_N           Propionate catabolism activator
       0.12   13.0   0.0       0.68   10.5   0.0    2.4  1  TIR_2            TIR domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.6   0.1   1.7e-76   1.7e-73       1     210 [.     128     334 ..     128     335 .. 0.99
   2 !  132.5   0.0   1.4e-41   1.4e-38       1     210 [.     675     876 ..     675     877 .. 0.96

  Alignments for each domain:
  == domain 1  score: 246.6 bits;  conditional E-value: 1.7e-76
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+e +k+ ++ki+ +v +s +a  ++++eal+ia+eigyPv+i++af+lGG+G+++a n+eel+++++++l++++  
  gi|488599965|ref|YP_007906436.1| 128 DRELFKKSMEKIGLEVPKSDTA--NSVDEALSIAEEIGYPVVIRPAFTLGGTGGGIAFNREELKDIAERGLEMSM-- 200
                                       9*******************99..**************************************************7.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                          +q+l+e+ + g+ke+E+ev+rD ++nv+++c++en++++  +t+++i+vAP+qtLtd e+q+lr +a+k++re+
  gi|488599965|ref|YP_007906436.1| 201 --INQILIEEGVIGWKEYELEVMRDLADNVVIICSIENFDPMgvHTGDSITVAPAQTLTDVEYQYLRDSAIKIIREI 275
                                       ..9************************************************************************** PP

                                       T-EEEE.EEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgag.tveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       gv+++g +++f+++p++++ + iE+N+R+s++sala+kaTG++++k+aak+a g++L+e
  gi|488599965|ref|YP_007906436.1| 276 GVETGGsNIQFAVNPDNGRVVAIEMNPRVSRSSALASKATGFPIAKIAAKLAIGYTLDE 334
                                       **98887**************************************************97 PP

  == domain 2  score: 132.5 bits;  conditional E-value: 1.4e-41
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+e+++++++++++p  p  +a   +leea +i+k+ig+Pv++++++ lGG+ m ++++e+ +++ v++a++ ++  
  gi|488599965|ref|YP_007906436.1| 675 DRERFSDLIERLGIPQPPNGIA--FSLEEAREIVKKIGFPVLVRPSYVLGGRAMVIVYDEQSFENYVAEAFDVSE-- 747
                                       9*****************9999..9*************************************************6.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                         +k vl++k+l+   e+Ev+ l D ++  i  + +e + +   + +++  v P   Lt+e+ ++++  + k++ ++
  gi|488599965|ref|YP_007906436.1| 748 --DKPVLIDKFLEDAIEVEVDALCDGEDVLI-GGIMEHVEEAgiHSGDSACVLPPISLTNEHIETIKDYTRKIALAL 821
                                       ..9**********************998655.577888888778********************************* PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       +v+g  +++++++    + yv+EvN+R s+  +  +kaTG++l+k+aak+ +g+kL+e
  gi|488599965|ref|YP_007906436.1| 822 NVIGLLNIQYAIKD---KVYVLEVNPRASRTVPFVSKATGIPLAKIAAKLMTGKKLRE 876
                                       ************95...99*************************************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 !  148.6   0.6   9.6e-47   9.6e-44       2     122 .]     425     549 ..     424     549 .. 0.97
   2 ?   -3.1   0.0       9.8   9.8e+03      62      89 ..    1052    1077 ..    1045    1078 .. 0.71

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 9.6e-47
                       CPSase_L_D3   2 elkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkk.....eldeellreakklGfsD 73 
                                       +l++p++ Rif+i  al +glsveei++ltkidpwF++k++++++le+elk+ +k     +l+++ l +ak+ GfsD
  gi|488599965|ref|YP_007906436.1| 425 RLASPHPSRIFYIRYALLKGLSVEEISRLTKIDPWFITKIKNILDLENELKELSKkytieDLPRKYLLKAKRFGFSD 501
                                       799*************************************************99999999999999*********** PP

                       CPSase_L_D3  74 kqiaelleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                        q+a + + ++e evr+ rk+lgi++vyk+vDtcAaeFea+tpY+YstY
  gi|488599965|ref|YP_007906436.1| 502 VQLAYIFK-TTEMEVRKRRKELGINAVYKMVDTCAAEFEAKTPYYYSTY 549
                                       ******76.78888**********************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.8
                       CPSase_L_D3   62 llreakklGfsDkqiaelleeeeeeevr 89  
                                        +++++k++Gf +  ++++ + e +ee+r
  gi|488599965|ref|YP_007906436.1| 1052 AIESIKRKGFEEVIVKSI-Q-EYHEEIR 1077
                                        678899999999888888.3.3444455 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.6   2.6e+03      51      72 ..      32      53 ..      12      68 .. 0.75
   2 ?   -0.9   0.0         2     2e+03       4      20 ..     650     666 ..     648     709 .. 0.70
   3 !   81.9   0.1   2.8e-26   2.7e-23       2      95 .]     956    1041 ..     955    1041 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.6
                                      HHHHHHHTTSCCEEEEE--THH CS
                               MGS 51 eildaikngeidlvintlypfk 72
                                      +  +a+k++++++v ++ +p +
  gi|488599965|ref|YP_007906436.1| 32 QACKALKEEGYEVVLVNSNPAT 53
                                      5667888888888888888766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                                       HHHHHHHHTTCEEEEEH CS
                               MGS   4 elakklkelgfellATg 20 
                                       ++ k+l+++g+++l T+
  gi|488599965|ref|YP_007906436.1| 650 NITKNLEKAGVRILGTS 666
                                       67889999999999997 PP

  == domain 3  score: 81.9 bits;  conditional E-value: 2.8e-26
                                        HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHH CS
                               MGS    2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatva 76  
                                        ++e+a+klke+gf++lAT+GTa +l+++g++ +evv k++eg r++    + dai n +id++int+++++ ++ 
  gi|488599965|ref|YP_007906436.1|  956 ILEVARKLKEMGFRILATSGTATYLRDNGVD-AEVVLKVSEG-RPN----VIDAIINRKIDFIINTPSGKRGKT- 1023
                                        89*****************************.**********.***....***********************8. PP

                                        CHHHHHHHHHHHTTSHEES CS
                               MGS   77 kdgykirraaenidIplpt 95  
                                         +g+ irraa++++Ip++t
  gi|488599965|ref|YP_007906436.1| 1024 -EGFLIRRAAVDHNIPYIT 1041
                                        .8***************98 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.3e-08   4.3e-05      22     174 ..     149     302 ..     138     310 .. 0.82
   2 !   32.3   0.0   6.9e-11   6.8e-08      27     174 ..     701     844 ..     682     870 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.3e-08
                                       H-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSS CS
                   Dala_Dala_lig_C  22 eekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgnek 95 
                                        ++ +   ++ ee+gypv+++pa +    G   + ++eelk+  e+ +++   +++l+Ee++   +e e  v+ +  
  gi|488599965|ref|YP_007906436.1| 149 ANSVDEALSIAEEIGYPVVIRPAFTLGGTGGGIAFNREELKDIAERGLEMSmiNQILIEEGViGWKEYELEVMRD-- 223
                                       44446677899************887778888899**********988765339******99899*********3.. PP

                                       CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT-.-SEEEEEEEE.ETTTEEEEE CS
                   Dala_Dala_lig_C  96 levsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldl.rGlaRvDffl.teegeivln 170
                                          +  + i+ + + +d    +++d++++    +l++ +++ +++ a+k+ + +++ +G + + f +  ++g++v  
  gi|488599965|ref|YP_007906436.1| 224 --LADNVVIICSIENFDPMGVHTGDSITVAPAQTLTDVEYQYLRDSAIKIIREIGVeTGGSNIQFAVnPDNGRVVAI 298
                                       ..44444566666778888888889999988888999999**************9845999******6667889999 PP

                                       EEES CS
                   Dala_Dala_lig_C 171 EvNt 174
                                       E+N+
  gi|488599965|ref|YP_007906436.1| 299 EMNP 302
                                       9996 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 6.9e-11
                                       HHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT..T-SCEEEEE--.ESEEEEEEEEE.TSSCEEE CS
                   Dala_Dala_lig_C  27 llekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk..ydekvlvEeai.egreievavlg.neklevs 99 
                                         +++++++g+pv+V+p+       +  v  e+ ++++++eaf    d+ vl+++++ ++ e+ev  l   e++ + 
  gi|488599965|ref|YP_007906436.1| 701 EAREIVKKIGFPVLVRPSYVLGGRAMVIVYDEQSFENYVAEAFDvsEDKPVLIDKFLeDAIEVEVDALCdGEDVLIG 777
                                       46799*************9877788999**************96226899*******99******6665177899** PP

                                       EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 100 evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                        + e+v + g+       s+d+a +  p++l++e  e+i+++  k+  al++ Gl  + + ++  +++++ EvN+
  gi|488599965|ref|YP_007906436.1| 778 GIMEHVEEAGIH------SGDSACVLPPISLTNEHIETIKDYTRKIALALNVIGLLNIQYAIK--DKVYVLEVNP 844
                                       *******99986......679999*******************************99998887..99*******7 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.1e-07   0.00011       2     160 ..     137     304 ..     136     313 .. 0.85
   2 !   31.2   0.0   1.4e-10   1.4e-07       2     160 ..     684     846 ..     683     849 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       ek gl+vp+  +++s +e+ ++aee+g+pvv++ +     G G  +  ++e+l++++e        +++++Ee v  
  gi|488599965|ref|YP_007906436.1| 137 EKIGLEVPKSDTANSVDEALSIAEEIGYPVVIR-PAFTLGGTGGGIAFNREELKDIAERGlemsMINQILIEEGVIG 212
                                       6899*****************************.9999999999999999999999987767667788999999998 PP

                                       SEEEEEEEEEETTC-EEE--EEEEEEETTEEE...EEEECEE-SCH.HHHHHHHHHHHHHHHHTS.SEEEEEEEEEE CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvqedgilr...lsvapaevsek.aqkkaeeiakkiveeLgg.vGvfavElFvl 146
                                        kE  + v+r+   +++++  +e+    g+     + vapa+  ++ + +  ++ a ki++e+g+  G   + + v 
  gi|488599965|ref|YP_007906436.1| 213 WKEYELEVMRDLADNVVIICSIENFDPMGVHTgdsITVAPAQTLTDvEYQYLRDSAIKIIREIGVeTGGSNIQFAVN 289
                                       899999999****************99999853337899999877735677899999*****997568888988888 PP

                                       .TTCTEEEEEEESS- CS
                         ATP-grasp 147 .edgellvnElapRp 160
                                        ++g++++ E+ pR+
  gi|488599965|ref|YP_007906436.1| 290 pDNGRVVAIEMNPRV 304
                                       444559999999998 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.4e-10
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       e+lg+p p+  ++ s ee++e+++++g+pv+v+ +     G+   +v +e++ e+ ++++    ++++v++ +f + 
  gi|488599965|ref|YP_007906436.1| 684 ERLGIPQPPNGIAFSLEEAREIVKKIGFPVLVR-PSYVLGGRAMVIVYDEQSFENYVAEAfdvsEDKPVLIDKFLED 759
                                       67899999999999*******************.99999**************999999889999**********99 PP

                                       SEEEEEEEEEETTC-EEE--EEEEEEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvle 147
                                         E+ v +  + e  + +  ++e+v+e gi       ++ p ++++++ ++++++++ki+ +L+++G++ +   ++ 
  gi|488599965|ref|YP_007906436.1| 760 AIEVEVDALCDGED-VLIGGIMEHVEEAGIHsgdsACVLPPISLTNEHIETIKDYTRKIALALNVIGLLNIQYAIK- 834
                                       99998877765554.677777888887666422116788899*****************************99888. PP

                                       TCTEEEEEEESS- CS
                         ATP-grasp 148 dgellvnElapRp 160
                                        ++++v E+ pR 
  gi|488599965|ref|YP_007906436.1| 835 -DKVYVLEVNPRA 846
                                       .78********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 !   12.1   0.0   0.00012      0.12      49     118 ..     264     337 ..     253     349 .. 0.78
   2 !   27.8   0.0   1.8e-09   1.8e-06      41     116 ..     794     877 ..     747     892 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                      ATPgrasp_Ter  49 lielaerlaeefgld.glvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteevee 118
                                       l + a ++++e+g++ g  n+Q+  + d+   + +E+NpR+s      s ++G  ++++a+kl+ g   +e+++
  gi|488599965|ref|YP_007906436.1| 264 LRDSAIKIIREIGVEtGGSNIQFAVNPDNgrVVAIEMNPRVSRSSAlASKATGFPIAKIAAKLAIGYTLDEIPN 337
                                       5577899999999973679****98877666888*******96555156777*************986555554 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.8e-09
                      ATPgrasp_Ter  41 q........elekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalkll 108
                                                + e+ e + ++++++a ++++ gl n+Q+   +d+ ++LE+NpRas ++  +s ++G+ l+++a+kl+
  gi|488599965|ref|YP_007906436.1| 794 AcvlppislTNEHIETIKDYTRKIALALNVIGLLNIQYAI-KDKVYVLEVNPRASRTVPfVSKATGIPLAKIAAKLM 869
                                       1555555444466678889999***************965.67899************8357778************ PP

                      ATPgrasp_Ter 109 lgleteev 116
                                       +g++  e 
  gi|488599965|ref|YP_007906436.1| 870 TGKKLREL 877
                                       **854443 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         4   3.9e+03     141     172 ..      23      56 ..      18      64 .. 0.67
   2 !   10.7   0.0    0.0003       0.3       9      84 ..     134     208 ..     126     217 .. 0.89
   3 !   25.5   0.0   8.7e-09   8.7e-06       1     182 [.     673     863 ..     673     869 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                                       HCT-SEEEEEEEE..ETTEEEEEEEESS--SHHH CS
                              RimK 141 amelvvaGvDllr..akrgllvlEvnsspgleki 172
                                       a e ++ G    +  +++g+ v+ vns+p + + 
  gi|488599965|ref|YP_007906436.1|  23 AAEFDYSGSQACKalKEEGYEVVLVNSNPATIMT 56 
                                       555555555544311467899999*****98765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0003
                                       HHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.GGG--EEEEE--S CS
                              RimK   9 klLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.lkeailvqeyiee 84 
                                       k + k +++vp++  a++ ++a ++ e+i  + Pvv++  ++  G +  +a ++++lk++ e  l+ +++ q  iee
  gi|488599965|ref|YP_007906436.1| 134 KSMEKIGLEVPKSDTANSVDEALSIAEEI--GYPVVIRPAFTLGGTGGGIAFNREELKDIAERgLEMSMINQILIEE 208
                                       556677899********************..6****************************98679999999988876 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 8.7e-09
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.....G CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.....l 72 
                                       a+d+ +   l+ + +i+ p   +a + e+a+++++ki  +fPv+v+ ++   G  +v+  +eq+ ++ +        
  gi|488599965|ref|YP_007906436.1| 673 AEDRERFSDLIERLGIPQPPNGIAFSLEEAREIVKKI--GFPVLVRPSYVLGGRAMVIVYDEQSFENYVAEafdvsE 747
                                       5677788899999************************..6************************9987644488666 PP

                                       GG--EEEEE--SS-SEEEEEEEETTEE.EEEEEEE--SSS----TTTT-EE...EE----HHHHHHHHHHHHHCT-S CS
                              RimK  73 keailvqeyieeaenediRvlvvddev.vaalrrvskeGdFRsnlhrGgva...eklqlseeekelAikaakamelv 145
                                       ++ +l+ +++e a + ++  l  +++v ++++    +e    + +h G  a    +++l++e  e     ++ ++l 
  gi|488599965|ref|YP_007906436.1| 748 DKPVLIDKFLEDAIEVEVDALCDGEDVlIGGIMEHVEE----AGIHSGDSAcvlPPISLTNEHIETIKDYTRKIALA 820
                                       6778******************9999846888888788....7788886551116899***9999988899988777 PP

                                       EEEEEEEE....ETTEEEEEEEE..SS--SHHHHHHHT--HHH CS
                              RimK 146 vaGvDllr....akrgllvlEvn..sspglekiektlgidiak 182
                                       +  + ll+     k+ ++vlEvn  +s  +  ++k +gi +ak
  gi|488599965|ref|YP_007906436.1| 821 LNVIGLLNiqyaIKDKVYVLEVNprASRTVPFVSKATGIPLAK 863
                                       6666665422225899*******66677788899999998875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0013       1.3       2     158 ..     127     304 ..     126     307 .. 0.63
   2 !   25.2   0.0   1.4e-08   1.4e-05       5     158 ..     677     846 ..     673     849 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                                       TSHHHHHHHHTTT.S---.........-EESS--.......SSSEEEEESS-------B--SS--TTE......... CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP.....tkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve.. 64 
                                       +d   + k +++ g++vP     +     +++e+        +++v+ p+   gg++  ++ ++ee++ + e     
  gi|488599965|ref|YP_007906436.1| 127 EDRELFKKSMEKIGLEVPksdtaN-----SVDEAlsiaeeiGYPVVIRPAFTLGGTGGGIAFNREELKDIAERGLem 198
                                       56667788899999****655431.....3333344455569*********99999988888887776544433356 PP

                                       ......EEEE---S.EEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEE...EES----H...HHHHHHHHHHHH CS
                       ATP-grasp_3  65 ......lvqefieG.kplSvsllsdgekvlvlavnrqliekaekefvyaGn...vtpietel...keevvelaeevv 128
                                             l+ e + G k++ ++++ d  +++v+ ++ +  +      v +G    v+p++t      + +++ a +++
  gi|488599965|ref|YP_007906436.1| 199 sminqiLIEEGVIGwKEYELEVMRDLADNVVIICSIENFDPM---GVHTGDsitVAPAQTLTdveYQYLRDSAIKII 272
                                       665666444433334899999999999999998887777653...55555411145555544222455667777777 PP

                                       TTST.T--EEEEEEEEESS...SEEEEEEESS- CS
                       ATP-grasp_3 129 ekle.glaGyvGvDlvlkd..eepyviEvNPRl 158
                                       +++  ++ G   + + ++   +  + iE NPR+
  gi|488599965|ref|YP_007906436.1| 273 REIGvET-GGSNIQFAVNPdnGRVVAIEMNPRV 304
                                       7775344.4444777666444566679999997 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE...............EE CS
                       ATP-grasp_3   5 lktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........lv 66 
                                        ++ + +++ g++ P        +   e +++   ++ v p++  gg ++++v ++++ e+ ++e          l+
  gi|488599965|ref|YP_007906436.1| 677 ERFSDLIERLGIPQPpngiafsLEEAREIVKKIGFPVLVRPSYVLGGRAMVIVYDEQSFENYVAEAFdvsedkpvLI 753
                                       55666778888888887754422222333344477899******************9999877776689999***** PP

                                       EE---.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES-..---HHHHHHHHHHHHHTTST...T--EE CS
                       ATP-grasp_3  67 qefie.GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpi..etelkeevvelaeevvekle...glaGy 137
                                        +f+e   ++ v++l+dge+vl+  + + + e      + +G ++ +  + +l++e +e++++ ++k+    ++ G+
  gi|488599965|ref|YP_007906436.1| 754 DKFLEdAIEVEVDALCDGEDVLIGGIMEHVEEA----GIHSGDSACVlpPISLTNEHIETIKDYTRKIAlalNVIGL 826
                                       ****9468*************999998887776....55555544331134678888888888888877667999** PP

                                       EEEEEEESS.SEEEEEEESS- CS
                       ATP-grasp_3 138 vGvDlvlkdeepyviEvNPRl 158
                                       + +   +kd + yv+EvNPR 
  gi|488599965|ref|YP_007906436.1| 827 LNIQYAIKD-KVYVLEVNPRA 846
                                       *********.**********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 !   12.0   0.1   0.00013      0.13       4     114 ..     130     237 ..     127     283 .. 0.76
   2 !   21.2   0.0     2e-07    0.0002       8     106 ..     681     775 ..     675     819 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCC CS
                            GARS_A   4 sfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeag 80 
                                       +  k+ ++k+g++ ++ ++ ++++ea ++ ee + ++ V++++   +g g  +a ++ee  ++++  le     +  
  gi|488599965|ref|YP_007906436.1| 130 ELFKKSMEKIGLEVPKSDTANSVDEALSIAEEIGYPV-VIRPAFTLGGTGGGIAFNREELKDIAERGLEM----SMI 201
                                       556899*******************************.*****999*************98888888873....456 PP

                                       SSEEEEE---S.EEEEEEEEEC.TTEEEE---BEEE CS
                            GARS_A  81 ekvviEelleG.eEvsllalvd.gktvkplplaqdh 114
                                       ++++iEe + G +E  l ++ d  ++v+ + +  ++
  gi|488599965|ref|YP_007906436.1| 202 NQILIEEGVIGwKEYELEVMRDlADNVVIICSIENF 237
                                       89*****99885677777777733444445555554 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2e-07
                                       HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEE CS
                            GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvv 84 
                                       dl+++ gip +      + eea+e++++ ++++  v+++ + +g+ ++++ +e+   ++v+e ++     +  + v+
  gi|488599965|ref|YP_007906436.1| 681 DLIERLGIPQPPNGIAFSLEEAREIVKKIGFPV-LVRPSYVLGGRAMVIVYDEQSFENYVAEAFD----VSEDKPVL 752
                                       79999******9999999***************.99****************************8....44689*** PP

                                       EEE---.SEEEEEEEEECTTEEE CS
                            GARS_A  85 iEelle.GeEvsllalvdgktvk 106
                                       i+++le  +Ev + al+dg++v 
  gi|488599965|ref|YP_007906436.1| 753 IDKFLEdAIEVEVDALCDGEDVL 775
                                       *****8368***********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 !   18.0   0.0   1.5e-06    0.0015      18      52 ..     135     169 ..     120     173 .. 0.90
   2 !   12.0   0.0    0.0001       0.1      16      51 ..     680     715 ..     674     718 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                       ATP-grasp_5  18 lleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                                        +e +g++v+++  a+s++ea+++aeeigypvv++
  gi|488599965|ref|YP_007906436.1| 135 SMEKIGLEVPKSDTANSVDEALSIAEEIGYPVVIR 169
                                       4789*****************************96 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0001
                       ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                        +l+e +gip ++  +a s eea e++++ig+pv +
  gi|488599965|ref|YP_007906436.1| 680 SDLIERLGIPQPPNGIAFSLEEAREIVKKIGFPVLV 715
                                       6799*****************************976 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.7e-07   0.00037       2     151 ..     163     303 ..     162     309 .. 0.83
   2 ?   -1.4   0.0       1.6   1.6e+03      73     102 ..     591     621 ..     577     630 .. 0.77
   3 !    8.2   0.1    0.0017       1.7      48     151 ..     744     845 ..     709     849 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.7e-07
                       ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieG.eEfavdayfdeeGe 77 
                                        +Pvvi+P+   +  G  ++ n+ee+k+  ++            + +++  +++l+Ee + G +E+ +++  d   +
  gi|488599965|ref|YP_007906436.1| 163 GYPVVIRPAFTLGGTGGGIAFNREELKDIAERGL----------EMSMI--NQILIEEGVIGwKEYELEVMRDLADN 227
                                       7999999999999999999999999988333332..........33444..6899998766659**********999 PP

                       ATP-grasp_4  78 pvilnilkkefaseedvsdrlyvtsakvieetleal.eellkevnallglknfpvHiElrvs.edgkiipiEvnpl 151
                                        vi+  ++    +  ++ d + v +a+ +++ +++   +   ++ +++g++ + + i + v+ ++g+++ iE+np+
  gi|488599965|ref|YP_007906436.1| 228 VVIICSIENFDPMGVHTGDSITVAPAQTLTDVEYQYlRDSAIKIIREIGVETGGSNIQFAVNpDNGRVVAIEMNPR 303
                                       9999888999999999*********998888776654999999******************93456*********6 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                       ATP-grasp_4  73 deeGepvilnilkkefasee.dvsdrlyvts 102
                                       +e+G+++i+   + e+ s++ d+sdrly+ +
  gi|488599965|ref|YP_007906436.1| 591 KEDGYETIMVNCNPETVSTDyDTSDRLYFEP 621
                                       57888888766666666555169****9876 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0017
                       ATP-grasp_4  48 evveeesflvEeyieGe.EfavdayfdeeGepvilnilkkefaseedvsdrlyvt.sakvieetlealeellkevna 122
                                       +v e++ +l+ +++e   E+ vda+ d e   +i  i+++      +  d   v+ + ++++e++e++++++++++ 
  gi|488599965|ref|YP_007906436.1| 744 DVSEDKPVLIDKFLEDAiEVEVDALCDGE-DVLIGGIMEHVEEAGIHSGDSACVLpPISLTNEHIETIKDYTRKIAL 819
                                       3456677888888875339*******544.45566899998888777777776661679****************98 PP

                       ATP-grasp_4 123 llglknfpvHiElrvsedgkiipiEvnpl 151
                                       +l++  + + i   +++  k++++Evnp+
  gi|488599965|ref|YP_007906436.1| 820 ALNVI-GLLNIQYAIKD--KVYVLEVNPR 845
                                       87764.56677777766..5888999997 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-06    0.0013       9     125 ..     134     233 ..     130     237 .. 0.84
   2 !    8.4   0.0    0.0014       1.4       9      53 ..     681     724 ..     678     745 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                                       HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TTS CS
                       ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkqt 85 
                                       + ++k g++vp++  a+s +ea ++a+++g  + v++     GG G  gG+ +  + ee+k++a++ l ++++    
  gi|488599965|ref|YP_007906436.1| 134 KSMEKIGLEVPKSDTANSVDEALSIAEEIGYPV-VIRPAFTLGGTG--GGIAF--NREELKDIAERGLEMSMI---- 201
                                       66899**************************99.*********876..99876..689********9999888.... PP

                                       -TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEE CS
                       ATP-grasp_2  86 gkeGkkvekvlveealdikkElYlsivlDraskkvvviaS 125
                                              +++l+ee +   kE+ l ++ D a  +vv+i+S
  gi|488599965|ref|YP_007906436.1| 202 -------NQILIEEGVIGWKEYELEVMRDLAD-NVVIICS 233
                                       .......8888888888888888877777654.4555655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0014
                                       HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTC CS
                       ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGR 53 
                                       +++++ g++ p + +a+s eea+e++kk+g  +  v+     GGR
  gi|488599965|ref|YP_007906436.1| 681 DLIERLGIPQPPNGIAFSLEEAREIVKKIGFPV-LVRPSYVLGGR 724
                                       68999**************************99.66666667887 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.6e-05     0.056       5      89 ..      19     117 ..      18     168 .. 0.83
   2 ?   -0.4   0.0       1.6   1.6e+03      64     107 ..     620     664 ..     589     675 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                                       EET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T.....T--EEEE-S-HHHHGGGHHHHHHH-- CS
                     CoA_binding_2   5 VvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslae.dpepvdlvdvftppeatpeivkealalga 80 
                                       ++G  ++ +  g ++ + l+e+g++vv Vn +  +i   ++ a+ +  +p + d v  ++ +e+  +i+  ++ + a
  gi|488599965|ref|YP_007906436.1|  19 IIGQAAEFDYSGSQACKALKEEGYEVVLVNSNPATIMTDPEMADKTYiEPITADFVAKIIEREVPDAILPTLGGQTA 95 
                                       567777777789999***********************99888888756999********************99999 PP

                                       SEEEE-TT.............- CS
                     CoA_binding_2  81 kavwlqpg.............s 89 
                                         v +q+g              
  gi|488599965|ref|YP_007906436.1|  96 LNVAVQLGelgvldrygieliG 117
                                       9999999966666666666553 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                                       -HHHHGGGHHHHHHH--SEEEE-TT---H.HHHHHHHHTT-EEE. CS
                     CoA_binding_2  64 ppeatpeivkealalgakavwlqpgsede.eaaelaeeagirvvg 107
                                        p + +++++  + +ga+++++q g + +  + + +e+ag+r++g
  gi|488599965|ref|YP_007906436.1| 620 EPITFEDVLNIYENEGAEGIIVQFGGQTPlNITKNLEKAGVRILG 664
                                       445555666666777888888887744432677777777777775 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.8e-05     0.027      16      54 ..     450     488 ..     441     499 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                              Vps5  16 stkfeEqDewFedkkqeldslesqLkkLykaiellvsqr 54 
                                       +++++  D+wF++k +++ +le++Lk+L+k   + +  r
  gi|488599965|ref|YP_007906436.1| 450 ISRLTKIDPWFITKIKNILDLENELKELSKKYTIEDLPR 488
                                       5677889**********************9776655555 PP

>> DUF4176  Domain of unknown function (DUF4176)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.025        25      14      37 ..       7      30 ..       4      41 .. 0.91
   2 ?    5.8   0.0     0.014        14      12      37 ..     558     583 ..     555     588 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                           DUF4176 14 tkkvmiigrrqieeeekkiydYvg 37
                                       +k+m+ig  +i  ++ + +dY+g
  gi|488599965|ref|YP_007906436.1|  7 LRKIMVIGSGPIIIGQAAEFDYSG 30
                                      579*************9*****99 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                           DUF4176  12 ggtkkvmiigrrqieeeekkiydYvg 37 
                                        ++kk+mi+g  +++ +++  +dY+ 
  gi|488599965|ref|YP_007906436.1| 558 SNKKKIMILGSGPNRIGQGIEFDYTC 583
                                       679*********************86 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.11     1e+02      20      69 ..      34     142 ..      32     167 .. 0.78
   2 ?    7.1   0.0    0.0055       5.5      21      74 ..     588     699 ..     582     714 .. 0.85
   3 ?   -2.5   0.0       4.9   4.9e+03      76     121 ..    1008    1052 ..     923    1058 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                                       HHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                              CbiA  20 aralarrglrVllvDaDpqannlaileglendiep.......................................... 54 
                                       ++al+++g++V+lv   p + ++   + ++ +iep                                          
  gi|488599965|ref|YP_007906436.1|  34 CKALKEEGYEVVLVNSNPATIMTDPEMADKTYIEPitadfvakiierevpdailptlggqtalnvavqlgelgvldr 110
                                       789****************9999989999999999999999999999999999999999999999999999999999 PP

                                       .................CCHCCCHHHHHHCHC CS
                                       .................xxxxxxxxxxxxxxx RF
                              CbiA  55 .................dlkrllellealgkk 69 
                                                        d++ +++++e++g +
  gi|488599965|ref|YP_007906436.1| 111 ygieligaklsaikkaeDRELFKKSMEKIGLE 142
                                       95555555555555555555555555554444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0055
                                       HHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
                              CbiA  21 ralarrglrVllvDaDpqannlaileglendiep........................................... 54 
                                       ++l+++g+++++v + p++ ++ +   ++ + ep                                           
  gi|488599965|ref|YP_007906436.1| 588 FSLKEDGYETIMVNCNPETVSTDYDTSDRLYFEPitfedvlniyenegaegiivqfggqtplnitknlekagvrilg 664
                                       689999************99999866666666668888889999999999*************************** PP

                                       ..........CCHCCCHHHHHHCHCHHHH...... CS
                                       ..........xxxxxxxxxxxxxxxxxxx.....x RF
                              CbiA  55 ..........dlkrllellealgkkkall.....l 74 
                                                 d++r++ l+e+lg++++++     l
  gi|488599965|ref|YP_007906436.1| 665 tspdsidiaeDRERFSDLIERLGIPQPPNgiafsL 699
                                       *************************9988766554 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.9
                                        EEEEEEEEESS...-TTCHHHHHHHHHHC..TS-EEEEEE--CCHCCC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                              CbiA   76 iagvvlnrvdgeneetllkealeelkqry..gvpvlgviprdeavaea 121 
                                         + +++n + g+    + + +l ++  +   ++p +  i+  +av++a
  gi|488599965|ref|YP_007906436.1| 1008 KIDFIINTPSGK--RGKTEGFLIRRA-AVdhNIPYITTISGAKAVVRA 1052
                                        344455555554..222233333222.112355555555555555555 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   1.2e+03     129     150 ..      33      54 ..      29      62 .. 0.66
   2 ?    6.5   0.1    0.0057       5.6       5      51 ..     944     990 ..     940     995 .. 0.84
   3 ?    2.4   0.0       0.1     1e+02     127     155 ..    1026    1054 ..    1025    1058 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                            PrpR_N 129 vadlAekaGlksvlltsgkesv 150
                                       ++++ ++ G+++vl+ s ++++
  gi|488599965|ref|YP_007906436.1|  33 ACKALKEEGYEVVLVNSNPATI 54 
                                       4555666666666666665555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0057
                            PrpR_N   5 ldievvegdleeavelakeleaegvdviiSrGgtaellrkhv.svPVv 51 
                                       + i+v+e+d  + +e+a++l+++g++++ +  gta++lr++  +  Vv
  gi|488599965|ref|YP_007906436.1| 944 VFISVKEADRAKILEVARKLKEMGFRILATS-GTATYLRDNGvDAEVV 990
                                       56899*********************87665.6999999986577776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.1
                            PrpR_N  127 gvvadlAekaGlksvlltsgkesvrqAie 155 
                                         ++ ++A   +++++   sg+++v +Aie
  gi|488599965|ref|YP_007906436.1| 1026 FLIRRAAVDHNIPYITTISGAKAVVRAIE 1054
                                        577899999*******************8 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00069      0.68       1      28 [.     944     971 ..     944     984 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00069
                             TIR_2   1 VFiSyssedkewaeklaeaLeaagirvw 28 
                                       VFiS  ++d++ + ++a++L++ g+r++
  gi|488599965|ref|YP_007906436.1| 944 VFISVKEADRAKILEVARKLKEMGFRIL 971
                                       9************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1080 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.93u 0.32s 00:00:01.25 Elapsed: 00:00:00.51
# Mc/sec: 6327.01
//
Query:       gi|488599966|ref|YP_007906437.1|  [L=362]
Description: carbamoyl-phosphate synthase small subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-53  178.3   0.0    1.2e-52  177.1   0.0    1.6  2  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    1.7e-48  164.9   0.0    2.5e-48  164.4   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
    6.8e-07   29.3   0.1    0.00016   21.5   0.1    2.3  1  Peptidase_C26    Peptidase C26
  ------ inclusion threshold ------
      0.072   13.4   0.0       0.13   12.5   0.0    1.3  1  AlkA_N           AlkA N-terminal domain


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.1   0.0   2.7e-56   1.2e-52       2     128 .]       7     134 ..       6     134 .. 0.98
   2 ?   -2.4   0.0      0.88   3.9e+03      66     102 ..     149     185 ..     136     192 .. 0.67

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 2.7e-56
                   CPSase_sm_chain   2 avLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglv 77 
                                        +L+LedGt++eG++fg ++ + GE+vfnT+mtGY e+ltDpsYagqil++typliGnyGv eed+es+ ikv+g+v
  gi|488599966|ref|YP_007906437.1|   7 GALALEDGTFIEGYGFGaEGYVEGELVFNTSMTGYVEALTDPSYAGQILMMTYPLIGNYGVCEEDFESDGIKVEGFV 83 
                                       579**************77999******************************************************* PP

                   CPSase_sm_chain  78 vrelseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgvi 128
                                       +rel++ psnwr+++sL+++lke++ipg++gvDTRaLt+k r  gamk+v+
  gi|488599966|ref|YP_007906437.1|  84 IRELCRVPSNWRCRKSLDDFLKEYSIPGLEGVDTRALTRKTRVYGAMKAVL 134
                                       ************************************************985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.88
                   CPSase_sm_chain  66 vesekikvaglvvrelseepsnwraeesLsewlkeek 102
                                       ve+ +i+   lv r +++ep++++a+ +L+ +l + +
  gi|488599966|ref|YP_007906437.1| 149 VEQPSITEVDLVDRVCVKEPKRIEADGKLEVVLVDCG 185
                                       4445555555666666778888888888887776655 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.4   0.0   5.5e-52   2.5e-48       1     189 [.     180     357 ..     180     358 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 5.5e-52
                                       EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEE CS
                            GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLG 76 
                                       +l+D++  ++++++++lv++g++++vvp++++ae+i+  + npdg+++s+Gpg+p  v+ +ie+i+++++ + P+ G
  gi|488599966|ref|YP_007906437.1| 180 VLVDCG--IKNSIIRQLVKRGINLTVVPYNYPAEKIK--ELNPDGVFISNGPGDPMrVKPTIETIRKLAG-EFPMAG 251
                                       589***..****************************5..79*****************************.****** PP

                                       ETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEE CS
                            GATase  77 ICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddee 153
                                       ICLG+Ql+a+++g+k+ k k ++h+g++++++d      y++++++i +++H+++v++k+l  +glevt  + +d +
  gi|488599966|ref|YP_007906437.1| 252 ICLGNQLVALALGAKTFKLK-FGHRGANQPVKD------YETGRVFISSQNHGFAVDEKSLDGTGLEVTQLNLNDMT 321
                                       ********************.************......9************************************* PP

                                       EEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 154 lmeiiekknpfvgvQFHPEststpegpellfnflik 189
                                       ++++++k++p++ vQ+HPE+ ++p+++ ++f+++++
  gi|488599966|ref|YP_007906437.1| 322 VEGMRHKEYPLITVQYHPEAGPGPHDTYFFFDNFHR 357
                                       ********************************9975 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   3.7e-08   0.00016      87     216 .]     229     340 ..     198     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.7e-08
                     Peptidase_C26  87 dpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashav.kvekgsllael 162
                                       dp R + ++  ir+ l+ ++P+ giC+G ql++ alG ++++ ++       hr ++     + v + e+g+++ + 
  gi|488599966|ref|YP_007906437.1| 229 DPMRVKPTIETIRK-LAGEFPMAGICLGNQLVALALGAKTFK-LK-----FGHRGAN-----QPVkDYETGRVFISS 293
                                       55566666666654.5678*****************998875.44.....2454444.....444135667776666 PP

                     Peptidase_C26 163 lgseeievnslHhqaike...laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                        +         H +a++e    +++l+v+     D ++E ++++e  ++++ vQ+HPE
  gi|488599966|ref|YP_007906437.1| 294 QN---------HGFAVDEkslDGTGLEVTQLNLnDMTVEGMRHKE--YPLITVQYHPE 340
                                       55.........99999997756799****99988********999..78********9 PP

>> AlkA_N  AlkA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05      0.13      13      71 ..      98     157 ..      86     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                            AlkA_N  13 aallaFlaaraiegvEavdedsygRtlrldga.kGvvevrhepeksalkvrlslsdlral 71 
                                       + l +Fl++  i+g+E vd+ +++R+ r+ ga k+v++v   +++++lk  +++ +++++
  gi|488599966|ref|YP_007906437.1|  98 KSLDDFLKEYSIPGLEGVDTRALTRKTRVYGAmKAVLAVGDYDKDQMLKRAVEQPSITEV 157
                                       46889*****************9998887765499**99999999999988887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2320.99
//
Query:       gi|488599967|ref|YP_007906438.1|  [L=337]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-29  102.7   0.0    7.2e-29  101.1   0.0    1.7  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0     4e-33   7.2e-29      17     240 ..      19     267 ..       2     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 4e-33
                                       TEEEEEEESEEEECCC.TEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE........................ CS
                       SAICAR_synt  17 dklllvakDrisAfdv.vlkeeipgKGkvltqlsafwfeklek..ipnhliksld...pe................. 70 
                                          ++ ++Dr s+fd+  ++++i+gKG+ l+ +sa++fe le+  i++h++  ld   ++                 
  gi|488599967|ref|YP_007906438.1|  19 GVGVFTFSDRYSVFDYgEMPDKIDGKGASLCLISAYFFERLEEegIETHYLGLLDgekVKrideiekpvnemkvklf 95 
                                       556899*********6489***********************668*****988886552244444333333444444 PP

                                       ....-SSSEEEEE-EEEESE......................EEEEEEE-.-HHH.........HH....HH..T-- CS
                       SAICAR_synt  71 ...qlegrsmlvkklkmlpv......................EvvvRgyl.tGsl.wkeykks.gkvcgirlpeglk 119
                                          +                                      Ev+ R+ l  Gs  ++  +++  k+ ++ l+e   
  gi|488599967|ref|YP_007906438.1|  96 rviK---------------PhknngydysafkeglknyliplEVIYRNKLpEGSSvFRRLERGeLKLEDLGLKEKPV 157
                                       4440...............25555555555555555555555******98557653777777667888888888889 PP

                                       TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HTT-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETT CS
                       SAICAR_synt 120 egeklpepiftpstKaeegehDeniseeevvealgteeeaeeieelalavyekaaelaaergiilvDtKlEFGldee 196
                                        g kl++pi+++stK e+   D  +s +e+ e+ g  e++e++ +l++++++++++ + e gi   D K+EF +de 
  gi|488599967|ref|YP_007906438.1| 158 PGMKLERPIIDFSTKLEDE--DRYLSVQEAKEISGLGENLEKLIDLTMKINDIITRRMVEIGIENEDGKVEFAVDE- 231
                                       99***************94..9*********9999999*************************************6. PP

                                       TTEEEEES--.STTTEEEEETTT.....GGGB-STHHHHTT-ST CS
                       SAICAR_synt 197 dgelvLaDevltpDssRfwdaetyeegkeqeslDKqfvRdwlee 240
                                       +g++vL+D v tpD +Rf             +l K+++R++ ++
  gi|488599967|ref|YP_007906438.1| 232 KGSIVLVDAVGTPDECRFSYDGF--------ELSKEILRRHYRK 267
                                       9*****************76443........4666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2267.97
//
Query:       gi|488599968|ref|YP_007906439.1|  [L=339]
Description: hypothetical protein Asulf_00419 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   45.2   0.0    1.2e-11   44.4   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
      7e-11   42.0   0.0    1.2e-10   41.2   0.0    1.3  1  Dimerisation2    Dimerisation domain
    0.00013   22.6   0.0    0.00021   21.9   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0032   18.2   0.0     0.0065   17.2   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
       0.03   13.9   0.0      0.051   13.1   0.0    1.3  1  MTS              Methyltransferase small domain
       0.03   14.1   0.0      0.052   13.3   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
      0.068   13.8   0.0       0.14   12.9   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      0.095   12.1   0.0       0.15   11.4   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
        0.1   12.4   0.2        0.6    9.9   0.0    2.2  2  rve_3            Integrase core 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 !   44.4   0.0   5.8e-15   1.2e-11      53     127 ..     160     235 ..     139     265 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 5.8e-15
                                       HHHHSS-.GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS-----TTEEEEES-TTTS---- CS
                    Methyltransf_2  53 kvleafd.leglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsageeervefvgGdffkdslPe 127
                                       k++ + + +++ ++l+D+GGG G    a + +  ++k+ vfDlp+Vve+ k+++   +++rv+++ G+ff d+l e
  gi|488599968|ref|YP_007906439.1| 160 KLISSLNfFRKARKLLDLGGGHGLYSIAFTMLNENLKAYVFDLPDVVEETKKYIRKYNARRVDVIPGNFFTDELGE 235
                                       567777779999***********************************************************99974 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   6.1e-14   1.2e-10       3      87 ..      23     100 ..      21     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 6.1e-14
                     Dimerisation2   3 lellnGFlaSkaLftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntel 79 
                                        ++lnGF+      +A++ g+Fd+Lke  p++++e+ ++ g++ k +  +l+ +v LgLL+++     ++ Y n+e+
  gi|488599968|ref|YP_007906439.1|  23 EDILNGFRKFFLFKSAVDVGIFDMLKE--PKTLHEIESKTGFNNKILFLFLENLVKLGLLRKD-----GDRYVNSEM 92 
                                       68999***999999***********99..9*******************************54.....357****** PP

                     Dimerisation2  80 astyLvss 87 
                                       a+++L+ s
  gi|488599968|ref|YP_007906439.1|  93 ADKFLTDS 100
                                       *****975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.1e-07   0.00021       2      97 .]     175     265 ..     174     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-07
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       LdlG G+G +++a+    ++ k + +D+ ++ +e++++ +++ ++ +v+++ g++ + ++  + +D+v+ss+     
  gi|488599968|ref|YP_007906439.1| 175 LDLGGGHGLYSIAFTMLNENLKAYVFDL-PDVVEETKKYIRKYNArRVDVIPGNFFTDELG-EDYDIVFSSY----N 245
                                       9************9988668*******9.789999***9*998889*********776655.48******74....4 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +  ++++++ +i+r+Lk+gG
  gi|488599968|ref|YP_007906439.1| 246 PGGKRAELIPKIWRCLKNGG 265
                                       778899*************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.3e-06    0.0065       1      98 [.     175     266 ..     175     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.3e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+G G ++ a+   +++++ ++ D+   +   +k+ ++k   +n+ +v++   + + ++ g+ +D+v++s    
  gi|488599968|ref|YP_007906439.1| 175 LDLGGGHGLYSIAFTMLNENLKAYVFDLPDVVE-ETKKYIRK---YNARRVDVIPGNFFTDELGEDYDIVFSSYNPG 247
                                       8**************************955554.55555555...5578999999999999999******9986555 PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                          +++e++ +i ++Lk+gG+
  gi|488599968|ref|YP_007906439.1| 248 G--KRAELIPKIWRCLKNGGI 266
                                       4..777888888888888885 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-05     0.051      24     103 ..     162     242 ..     153     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                       HHHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-E CS
                               MTS  24 letlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkf 98 
                                       ++ l+   +++k+lDlG G G+ ++a+   +++++  ++d     +e +k+ +++ +++ v+v+  + + +   +++
  gi|488599968|ref|YP_007906439.1| 162 ISSLNFFrKARKLLDLGGGHGLYSIAFTMLNENLKAYVFDLPD-VVEETKKYIRKYNARrVDVIPGNFFTDELGEDY 237
                                       555554447889***************************9865.566666666665555599999999988888999 PP

                                       EEEEE CS
                               MTS  99 dlivs 103
                                       d++ s
  gi|488599968|ref|YP_007906439.1| 238 DIVFS 242
                                       99875 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.6e-05     0.052      46      92 ..     170     216 ..     151     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                   Methyltransf_16  46 sklsvlELGsGtGlvGlavaellpeakviltDleellellkknieln 92 
                                       + ++ l+LG G Gl  +a+  l +++k ++ Dl++++e  kk i   
  gi|488599968|ref|YP_007906439.1| 170 KARKLLDLGGGHGLYSIAFTMLNENLKAYVFDLPDVVEETKKYIRKY 216
                                       56789*********************************999999874 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-05      0.14       1      95 [.     175     268 ..     175     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                                       EEET-TTSHHHHHHH..HTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaeala..krgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+G G G+++ a++  +   + + +Dl + +++  k+ +++ +  +v+++ +++ +  + +  +D+v+ss      
  gi|488599968|ref|YP_007906439.1| 175 LDLGGGHGLYSIAFTmlNENLKAYVFDL-PDVVEETKKYIRKYNArRVDVIPGNFFTDELGE-DYDIVFSSYNPG-- 247
                                       8*************96544489999996.6667777777777666789********867766.9******97433.. PP

                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                        ++++++ +i+R+Lk+gG+ +
  gi|488599968|ref|YP_007906439.1| 248 GKRAELIPKIWRCLKNGGIYI 268
                                       569***************976 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.5e-05      0.15     158     256 ..     167     267 ..     153     270 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadvi 230
                                       + ++ +++lD+G G G+ +ia  +L+ + k++  D+ +v v+ +k+ +++ + ++ ++v ++++ ++    e +d++
  gi|488599968|ref|YP_007906439.1| 167 FFRKARKLLDLGGGHGLYSIAFTMLNENlKAYVFDLPDV-VEETKKYIRKYNARR-VDV-IPGNFFTdelGEDYDIV 240
                                       4678899******************87548899999887.566666555444433.223.33443322233678888 PP

                              PrmA 231 vaNIL.aevlielaedikklvkeggll 256
                                       ++         el+++i++++k+gg+ 
  gi|488599968|ref|YP_007906439.1| 241 FSSYNpGGKRAELIPKIWRCLKNGGIY 267
                                       876541345567777777777777766 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.68   1.4e+03      23      52 ..      89     118 ..      88     121 .. 0.84
   2 ?    9.9   0.0    0.0003       0.6      25      57 ..     189     220 ..     184     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.68
                             rve_3  23 ngtlrdellneelfrslaearekleawred 52 
                                       n  + d++l+ +++++l  +r ++e+ + +
  gi|488599968|ref|YP_007906439.1|  89 NSEMADKFLTDSPYSQLYYVRNAMESSLIW 118
                                       78899********99999999998887766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0003
                             rve_3  25 tlrdellneelfrslaearekleawredYNteR 57 
                                       t+ +e l+++ f +l+++ e +++++++YN +R
  gi|488599968|ref|YP_007906439.1| 189 TMLNENLKAYVF-DLPDVVEETKKYIRKYNARR 220
                                       788888999999.*****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2052.68
//
Query:       gi|488599969|ref|YP_007906440.1|  [L=117]
Description: hypothetical protein Asulf_00420 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   37.4   0.1    7.5e-09   36.2   0.0    1.6  2  ABC_tran  ABC transporter
    1.4e-05   25.1   0.1    1.7e-05   24.8   0.1    1.2  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.014   14.9   0.4      0.017   14.5   0.4    1.2  1  TniB      Bacterial TniB protein
      0.038   14.2   0.2       0.23   11.7   0.1    2.2  2  SbcCD_C   Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   1.7e-12   7.5e-09     109     137 .]       1      29 [.       1      29 [. 0.98
   2 ?   -1.5   0.0      0.72   3.2e+03      38      45 ..      75      82 ..      38     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.7e-12
                                       S-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 109 LSgGqkqrvalarallkkpkllllDEpta 137
                                       +SgG+ q+v++aral+++pk+lllDEpt+
  gi|488599969|ref|YP_007906440.1|   1 MSGGELQKVVIARALAQEPKILLLDEPTN 29 
                                       7***************************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.72
                                      SEEEEEET CS
                                      xxxxxxxx RF
                          ABC_tran 38 teGeilld 45
                                      ++G+i  +
  gi|488599969|ref|YP_007906440.1| 75 KNGRIVAN 82
                                      34444333 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   3.8e-09   1.7e-05     251     301 ..      12      63 ..       1      65 [. 0.78

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.8e-09
                            AAA_21 251 llralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                         ++++++++ll+DEp n+L+ k + +l+++l ++++++++  ilt H+  l
  gi|488599969|ref|YP_007906440.1|  12 ARALAQEPKILLLDEPTNNLDLKNQIELMDILrRIAEERKISAILTMHDLNL 63 
                                       344455559***********************77777789999999998776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   3.8e-06     0.017     107     160 ..       6      57 ..       2      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-06
                              TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       l++ v++   + ++++L++DE  n l    ++q e++ +l+++ +e ki+ +l 
  gi|488599969|ref|YP_007906440.1|   6 LQKVVIARALAQEPKILLLDEPTNNL--DLKNQIELMDILRRIAEERKISAILT 57 
                                       56666666677899**********99..899*******************9986 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   5.2e-05      0.23      62      89 ..      17      44 ..       1      45 [. 0.86
   2 ?   -3.4   0.0       2.7   1.2e+04       7      22 ..      94     109 ..      92     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                           SbcCD_C 62 palrlvfLDEAFsklDeesiatllelle 89
                                      + +++++LDE  ++lD +++ +l+++l+
  gi|488599969|ref|YP_007906440.1| 17 QEPKILLLDEPTNNLDLKNQIELMDILR 44
                                      5689*********************997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.7
                           SbcCD_C   7 Rnylsfevevrdedgk 22 
                                       R+ + ++v+v ++dgk
  gi|488599969|ref|YP_007906440.1|  94 RQVYGISVSVFEKDGK 109
                                       6777778888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 770.04
//
Query:       gi|488599970|ref|YP_007906441.1|  [L=228]
Description: Formylmethanofuran dehydrogenase subunit E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  121.2   0.0    3.6e-35  120.9   0.0    1.1  1  FmdE            FmdE, Molybdenum formylmethanofuran dehydroge
    6.7e-07   29.1   0.3    1.5e-06   28.1   0.3    1.5  1  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
  ------ inclusion threshold ------
      0.035   14.0   1.4      0.045   13.7   0.1    1.8  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.8    8.8   6.6       0.11   12.7   1.4    1.6  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


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 !  120.9   0.0     8e-39   3.6e-35       1     130 [.      17     160 ..      17     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 8e-39
                                       HHSS--CHHHHHHHHHHHHHHCC....-TT....SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEE CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeeg....deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltf 73 
                                       fHGH+Cp+lvlG++++ +al++lg++++e     +ee+ aive+++C++D++q++tgct+G+++li+ d gk+a+t+
  gi|488599970|ref|YP_007906441.1|  17 FHGHICPFLVLGIKASVIALNKLGIDRAEYkesvGEEILAIVECNNCFADGVQIATGCTFGNNSLIYADIGKNAVTV 93 
                                       9************************98777999******************************************** PP

                                       EETTT-EEEEEEE-..........CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHH CS
                              FmdE  74 kkrktgkavrlklk..........eelpelreklakgkakeekeeeeleeeleeaikkilnapeeel 130
                                       +kr++ k++r++++          +++ el+++++ +++ +eke ee+++++e++++++   pee++
  gi|488599970|ref|YP_007906441.1|  94 VKRGEWKGIRVYVDaenirskyfpKDVLELFDRVIVRREGDEKELEEFRQLWEDIGRELAGVPEEDF 160
                                       ***************************************9999*****************9999975 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 !   28.1   0.3   3.3e-10   1.5e-06       1      30 [.     174     206 ..     174     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.3e-10
                      zf-dskA_traR   1 giygs..CeeCGEpIpeaR.lralPgarlCveC 30 
                                       +i+ s  C++CGE ++e + ++ ++g+++C++C
  gi|488599970|ref|YP_007906441.1| 174 PIFNSlrCSVCGELVMETKtRKDRDGKVFCLAC 206
                                       6888999************55556********* PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.9   8.3e+03      30      34 ..      59      63 ..      58      69 .. 0.61
   2 ?   13.7   0.1   9.9e-06     0.045      13      57 ..     163     211 ..     161     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                    OrfB_Zn_ribbon 30 tCseC 34
                                      +C++C
  gi|488599970|ref|YP_007906441.1| 59 ECNNC 63
                                      45555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.9e-06
                    OrfB_Zn_ribbon  13 keyGikveevnpayTSktCseCgsknke....alsgrtfkCpnCgfead 57 
                                       ke  +k +e  p + S +Cs+Cg+ + e    ++ + ++ C +C  + +
  gi|488599970|ref|YP_007906441.1| 163 KEVNVKPIERAPIFNSLRCSVCGELVMEtktrKDRDGKVFCLACLDHVH 211
                                       566788899999************9988887778888899999976655 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 ?   -4.0   0.3         4   1.8e+04      18      21 ..      60      63 ..      59      65 .. 0.74
   2 ?   12.7   1.4   2.5e-05      0.11      17      39 ..     180     206 ..     178     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4
                     Auto_anti-p27 18 CpvC 21
                                      C +C
  gi|488599970|ref|YP_007906441.1| 60 CNNC 63
                                      8888 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.5e-05
                     Auto_anti-p27  17 tCpvCgvPLmrdr....kggkvyCvaC 39 
                                        C+vCg   m+++     +gkv+C aC
  gi|488599970|ref|YP_007906441.1| 180 RCSVCGELVMETKtrkdRDGKVFCLAC 206
                                       5************997758******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1551.66
//
Query:       gi|488599971|ref|YP_007906442.1|  [L=376]
Description: formylmethanofuran dehydrogenase, subunit F [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-56  186.1  92.5    2.1e-08   33.6   1.1   10.5 10  Fer4         4Fe-4S binding domain
    1.8e-40  137.3  77.0    1.4e-10   41.6   6.0    7.0  9  Fer4_7       4Fe-4S dicluster domain
    2.1e-34  117.4  75.7    3.3e-08   33.6   5.7    7.0  7  Fer4_9       4Fe-4S dicluster domain
    4.7e-34  117.1  78.2    1.4e-07   32.3   4.1    9.2  9  Fer4_16      4Fe-4S double cluster binding domain
    1.3e-31  106.7  96.1    0.00019   21.3   4.4   10.9 11  Fer4_2       4Fe-4S binding domain
    1.2e-30  105.3  86.4    1.7e-07   31.3  12.8    8.5 10  Fer4_21      4Fe-4S dicluster domain
    2.7e-30  103.2 104.6    1.2e-05   25.1   4.6   10.6 11  Fer4_6       4Fe-4S binding domain
    8.2e-29   99.5  86.7    4.3e-06   26.7  11.3    7.9 10  Fer4_10      4Fe-4S dicluster domain
      3e-15   56.5  85.3     0.0004   20.9   6.6    8.9  8  Fer4_17      4Fe-4S dicluster domain
      1e-14   54.7  89.7    0.00082   19.8   9.7    8.6  8  Fer4_8       4Fe-4S dicluster domain
    3.5e-13   48.9 100.5     0.0093   16.4   2.8   11.1 11  Fer4_4       4Fe-4S binding domain
    6.7e-08   33.0  92.8        0.1   13.1   1.5   10.8 11  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
    7.9e-06   26.5 119.7      0.069   14.1   3.3   10.8 11  Fer4_3       4Fe-4S binding domain
     0.0049   17.6  81.1      0.088   13.6   2.2   10.8 10  Fer4_15      4Fe-4S single cluster domain
  ------ inclusion threshold ------
        0.7   10.1  80.5        1.1    9.4   1.9    9.6 10  Fer4_18      4Fe-4S dicluster domain
        1.6    8.4   5.5        7.2    6.3   0.2    2.9  2  Redoxin      Redoxin
        3.6    8.1   8.2         11    6.5   0.0    4.5  5  Neprosin_AP  Neprosin activation peptide


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.6     2e-08   2.1e-05       5      24 .]      19      38 ..      15      38 .. 0.89
   2 !   21.1   2.3   1.8e-07   0.00018       6      23 ..      52      69 ..      51      70 .. 0.94
   3 !   33.6   1.1     2e-11   2.1e-08       2      24 .]      94     116 ..      93     116 .. 0.94
   4 !   23.5   2.5   3.3e-08   3.4e-05       6      24 .]     135     153 ..     131     153 .. 0.91
   5 !   27.1   5.4   2.2e-09   2.4e-06       1      24 []     158     181 ..     158     181 .. 0.94
   6 !   29.4   4.9   4.4e-10   4.7e-07       1      24 []     199     222 ..     199     222 .. 0.95
   7 !   10.8   0.5   0.00033      0.35      11      24 .]     243     256 ..     241     256 .. 0.92
   8 !   27.2   2.9   2.2e-09   2.3e-06       2      24 .]     265     287 ..     264     287 .. 0.93
   9 !   14.1   2.4     3e-05     0.032       5      19 ..     317     331 ..     313     332 .. 0.91
  10 !   27.6   3.4   1.6e-09   1.7e-06       1      24 []     347     370 ..     347     370 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2e-08
                                      TTTSSS-THHHHHSTTTEEE CS
                              Fer4  5 eekCigCGaCvevCPvgAIt 24
                                       e+C gC +C +vCP +AI+
  gi|488599971|ref|YP_007906442.1| 19 GELCRGCQICTSVCPRNAIS 38
                                      599***************96 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.8e-07
                                      TTSSS-THHHHHSTTTEE CS
                              Fer4  6 ekCigCGaCvevCPvgAI 23
                                      + C  CG+C + CP+gA+
  gi|488599971|ref|YP_007906442.1| 52 DNCNLCGTCSDFCPYGAL 69
                                      78***************7 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 2e-11
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        +d +kC++CG+C++ CP++AI+
  gi|488599971|ref|YP_007906442.1|  94 SVDDSKCTYCGLCMQNCPHDAIS 116
                                       69*******************96 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 3.3e-08
                                       TTSSS-THHHHHSTTTEEE CS
                              Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                       + Ci+C +Cv+ CP+ AI+
  gi|488599971|ref|YP_007906442.1| 135 DGCINCRLCVMFCPTKAIS 153
                                       77***************96 PP

  == domain 5  score: 27.1 bits;  conditional E-value: 2.2e-09
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       ++i+e++Ci+C +C  vCP ++I+
  gi|488599971|ref|YP_007906442.1| 158 PEINEDRCIYCEICSAVCPKDVIS 181
                                       58*******************995 PP

  == domain 6  score: 29.4 bits;  conditional E-value: 4.4e-10
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       v++de++C  CG+C+evCP +AI+
  gi|488599971|ref|YP_007906442.1| 199 VEVDESRCATCGICAEVCPENAIR 222
                                       689********************6 PP

  == domain 7  score: 10.8 bits;  conditional E-value: 0.00033
                                       -THHHHHSTTTEEE CS
                              Fer4  11 CGaCvevCPvgAIt 24 
                                       C +C e+CP+ AI+
  gi|488599971|ref|YP_007906442.1| 243 CSICKEICPNLAIQ 256
                                       9***********95 PP

  == domain 8  score: 27.2 bits;  conditional E-value: 2.2e-09
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       vi  ++C +CG C++ CP gAI+
  gi|488599971|ref|YP_007906442.1| 265 VIFLDRCNFCGVCENSCPAGAIE 287
                                       6889******************6 PP

  == domain 9  score: 14.1 bits;  conditional E-value: 3e-05
                                       TTTSSS-THHHHHST CS
                              Fer4   5 eekCigCGaCvevCP 19 
                                        + C gCG+C + CP
  gi|488599971|ref|YP_007906442.1| 317 NDNCFGCGICSSLCP 331
                                       699***********9 PP

  == domain 10  score: 27.6 bits;  conditional E-value: 1.6e-09
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       vv+d + C++CG C + CP gAIt
  gi|488599971|ref|YP_007906442.1| 347 VVVDSSACTACGVCSSNCPAGAIT 370
                                       69*********************7 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.9e-06     0.002       2      21 ..      22      41 ..       9      52 .. 0.87
   2 !   41.6   6.0   1.3e-13   1.4e-10       2      52 .]      54     114 ..      53     114 .. 0.83
   3 !   34.4   9.9   2.3e-11   2.4e-08       2      52 .]     137     179 ..     136     179 .. 0.95
   4 !   26.1  19.3   9.2e-09   9.8e-06       1      52 []     164     220 ..     164     220 .. 0.82
   5 !   22.4  11.4   1.3e-07   0.00014       1      50 [.     205     252 ..     205     254 .. 0.87
   6 !   24.1   9.4   3.8e-08     4e-05       4      52 .]     242     285 ..     237     285 .. 0.88
   7 !   28.6   9.0   1.5e-09   1.6e-06       1      49 [.     270     331 ..     270     333 .. 0.79
   8 !   26.4  10.0   7.2e-09   7.6e-06       2      52 .]     320     368 ..     319     368 .. 0.90
   9 !   15.6   4.1   1.8e-05     0.018       1      22 [.     353     374 ..     353     375 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                            Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                      C gC+ C+++Cp +ai++  
  gi|488599971|ref|YP_007906442.1| 22 CRGCQICTSVCPRNAISVFR 41
                                      99999999999999998764 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 1.3e-13
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek...........gtekveidpekClgCgaCvavCPtga 52 
                                       C  Cg C + Cp++a+ ++ +  +k           ++ekv +d +kC++Cg C++ CP++a
  gi|488599971|ref|YP_007906442.1|  54 CNLCGTCSDFCPYGALAVKRD-GKKgifteilkkelEFEKVSVDDSKCTYCGLCMQNCPHDA 114
                                       *****************9876.44435555555555669********************987 PP

  == domain 3  score: 34.4 bits;  conditional E-value: 2.3e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       Ci+C+ Cv  Cp+kai++ ++        +ei++++C++C+ C avCP+++
  gi|488599971|ref|YP_007906442.1| 137 CINCRLCVMFCPTKAISVSDR--------PEINEDRCIYCEICSAVCPKDV 179
                                       ******************887........79*****************985 PP

  == domain 4  score: 26.1 bits;  conditional E-value: 9.2e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaield......eeenekgtekveidpekClgCgaCvavCPtga 52 
                                       rCi C+ C a+Cp ++i+++      ++ ++    +ve+d+++C +Cg C++vCP +a
  gi|488599971|ref|YP_007906442.1| 164 RCIYCEICSAVCPKDVISVHcdscrlQA-SNVLEGRVEVDESRCATCGICAEVCPENA 220
                                       8*****************9955543322.2223389*******************987 PP

  == domain 5  score: 22.4 bits;  conditional E-value: 1.3e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClg..CgaCvavCPt 50 
                                       rC  Cg C+++Cp +ai+++   + ++    ++++ekC+g  C  C + CP 
  gi|488599971|ref|YP_007906442.1| 205 RCATCGICAEVCPENAIRVNRLFKGRQ----HFKAEKCYGldCSICKEICPN 252
                                       7*******************9975555....8999***7644999******6 PP

  == domain 6  score: 24.1 bits;  conditional E-value: 3.8e-08
                            Fer4_7   4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                        C  C + Cp+ ai++++       ek +i  ++C +Cg+C++ CP+ga
  gi|488599971|ref|YP_007906442.1| 242 DCSICKEICPNLAIQYRYT-----PEKEVIFLDRCNFCGVCENSCPAGA 285
                                       6***************997.....3456899****************97 PP

  == domain 7  score: 28.6 bits;  conditional E-value: 1.5e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.............gtekveidpekClgCgaCvavCP 49 
                                       rC  Cg C++ Cp++aie++ e +++              +++v  + ++C gCg C + CP
  gi|488599971|ref|YP_007906442.1| 270 RCNFCGVCENSCPAGAIEIERELSDDvnlleihlngkkvNKKSVIAVNDNCFGCGICSSLCP 331
                                       7******************97655555555555554443336667789*************9 PP

  == domain 8  score: 26.4 bits;  conditional E-value: 7.2e-09
                            Fer4_7   2 CigCgaCvaaCp..vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C gCg C + Cp   + +++d +      + v++d++ C+ Cg+C + CP+ga
  gi|488599971|ref|YP_007906442.1| 320 CFGCGICSSLCPliKGGLTIDLA----HGKAVVVDSSACTACGVCSSNCPAGA 368
                                       ************99999999877....346799******************97 PP

  == domain 9  score: 15.6 bits;  conditional E-value: 1.8e-05
                            Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                       +C+ Cg C ++Cp++ai+++e+
  gi|488599971|ref|YP_007906442.1| 353 ACTACGVCSSNCPAGAITIREV 374
                                       5****************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 !   17.7   1.2   2.9e-06    0.0031      33      51 .]      14      37 ..       2      37 .. 0.72
   2 !   33.6   5.7   3.1e-11   3.3e-08       1      51 []      53     115 ..      53     115 .. 0.84
   3 !   29.9  10.5   4.3e-10   4.5e-07       2      51 .]     137     180 ..     136     180 .. 0.96
   4 !   13.5   7.0   5.8e-05     0.061      32      51 .]     202     221 ..     182     221 .. 0.65
   5 !   26.2   5.7   6.1e-09   6.4e-06       2      51 .]     238     286 ..     224     289 .. 0.92
   6 !   11.7   0.8   0.00022      0.23      24      47 ..     310     331 ..     300     335 .. 0.67
   7 !   24.6   7.7   1.9e-08     2e-05       1      51 []     319     369 ..     319     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-06
                            Fer4_9 33 e.....eaCigCgaCveaCpkgai 51
                                      e     e C gC+ C+ +Cp++ai
  gi|488599971|ref|YP_007906442.1| 14 ElyfsgELCRGCQICTSVCPRNAI 37
                                      14444579*************987 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 3.1e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase............eaCigCgaCveaCpkgai 51 
                                       +C+ Cg+C + Cp+g+   ++ ++k   ++  +            ++C+ Cg C++ Cp++ai
  gi|488599971|ref|YP_007906442.1|  53 NCNLCGTCSDFCPYGALAVKRDGKKGIFTEILKkelefekvsvddSKCTYCGLCMQNCPHDAI 115
                                       6**************996666665555544433599************************997 PP

  == domain 3  score: 29.9 bits;  conditional E-value: 4.3e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       C++C+ Cv  Cp+++++ ++ +++++       +Ci C+ C ++Cpk++i
  gi|488599971|ref|YP_007906442.1| 137 CINCRLCVMFCPTKAISVSDRPEINED------RCIYCEICSAVCPKDVI 180
                                       **************************7......6*************976 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 5.8e-05
                            Fer4_9  32 seeaCigCgaCveaCpkgai 51 
                                       +e++C +Cg C+e+Cp++ai
  gi|488599971|ref|YP_007906442.1| 202 DESRCATCGICAEVCPENAI 221
                                       2258*************987 PP

  == domain 5  score: 26.2 bits;  conditional E-value: 6.1e-09
                            Fer4_9   2 Ctg..CgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       C+g  C  C e Cp+ +++++  ++k  +  +   +C +Cg C++ Cp gai
  gi|488599971|ref|YP_007906442.1| 238 CYGldCSICKEICPNLAIQYRYTPEKEVIFLD---RCNFCGVCENSCPAGAI 286
                                       66666********************9998764...8*************987 PP

  == domain 6  score: 11.7 bits;  conditional E-value: 0.00022
                            Fer4_9  24 rkarlraaseeaCigCgaCveaCp 47 
                                       +k  +     ++C+gCg C   Cp
  gi|488599971|ref|YP_007906442.1| 310 KKSVIAVN--DNCFGCGICSSLCP 331
                                       33333332..47999999999999 PP

  == domain 7  score: 24.6 bits;  conditional E-value: 1.9e-08
                            Fer4_9   1 kCtgCgaCveaCp..agvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C gCg C + Cp  +g  + d a++ka +   s  aC+ Cg C   Cp gai
  gi|488599971|ref|YP_007906442.1| 319 NCFGCGICSSLCPliKGGLTIDLAHGKAVVVDSS--ACTACGVCSSNCPAGAI 369
                                       6***********6446777888888888887776..5*************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 !   18.8   0.7   2.3e-06    0.0024       2      19 ..      22      39 ..      21      46 .. 0.90
   2 !   14.7   0.2   4.1e-05     0.043       1      22 [.      53      74 ..      53      96 .. 0.83
   3 !   21.2   0.8   3.8e-07    0.0004       1      27 [.      99     123 ..      99     132 .. 0.84
   4 !   23.4   2.3   8.2e-08   8.6e-05       2      31 ..     137     166 ..     136     167 .. 0.95
   5 !    8.9   6.4    0.0027       2.8       1      20 [.     164     183 ..     164     198 .. 0.85
   6 !   15.4  12.7   2.6e-05     0.027       1      65 [.     205     251 ..     205     253 .. 0.75
   7 !    7.3   2.3    0.0088       9.3       4      20 ..     242     258 ..     237     266 .. 0.76
   8 !   32.3   4.1   1.4e-10   1.4e-07       1      65 [.     270     331 ..     270     332 .. 0.75
   9 !   13.3   3.8   0.00012      0.12       2      20 ..     354     372 ..     353     376 .] 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-06
                           Fer4_16  2 CgtCgkCaevCPtnaike 19
                                      C +C+ C++vCP nai+ 
  gi|488599971|ref|YP_007906442.1| 22 CRGCQICTSVCPRNAISV 39
                                      ****************85 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.1e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                                      +C  Cg C + CP +a+  k++
  gi|488599971|ref|YP_007906442.1| 53 NCNLCGTCSDFCPYGALAVKRD 74
                                      59**************998844 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 3.8e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiea 27 
                                       +C+ Cg C++ CP++ai+ k  +++++
  gi|488599971|ref|YP_007906442.1|  99 KCTYCGLCMQNCPHDAISVK--RKLNI 123
                                       5*****************99..55554 PP

  == domain 4  score: 23.4 bits;  conditional E-value: 8.2e-08
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieareci 31 
                                       C++C+ C++ CPt+ai+   ++ei+ ++ci
  gi|488599971|ref|YP_007906442.1| 137 CINCRLCVMFCPTKAISVSDRPEINEDRCI 166
                                       *******************9******9997 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0027
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       rC+ C+ C  vCP ++i+  
  gi|488599971|ref|YP_007906442.1| 164 RCIYCEICSAVCPKDVISVH 183
                                       69************999865 PP

  == domain 6  score: 15.4 bits;  conditional E-value: 2.6e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       rC tCg CaevCP+nai+ +  + ++ r+            + ++ekc+       C iC+++CP
  gi|488599971|ref|YP_007906442.1| 205 RCATCGICAEVCPENAIRVN--RLFKGRQ------------HFKAEKCY----GLDCSICKEICP 251
                                       6*****************99..4444444............44557777....667888888887 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.0088
                           Fer4_16   4 tCgkCaevCPtnaikek 20 
                                       +C  C e+CP  ai+ +
  gi|488599971|ref|YP_007906442.1| 242 DCSICKEICPNLAIQYR 258
                                       59999999999998866 PP

  == domain 8  score: 32.3 bits;  conditional E-value: 1.4e-10
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeieare.cisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       rC  Cg C ++CP++ai+ +  +e+  +    + + ++kk  +++  + +   +++gC+iC   CP
  gi|488599971|ref|YP_007906442.1| 270 RCNFCGVCENSCPAGAIEIE--RELSDDVnLLEIHLNGKKVNKKSVIAVN--DNCFGCGICSSLCP 331
                                       699***************99..4443333033446777776666666665..89************ PP

  == domain 9  score: 13.3 bits;  conditional E-value: 0.00012
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C+ Cg C + CP++ai+ +
  gi|488599971|ref|YP_007906442.1| 354 CTACGVCSSNCPAGAITIR 372
                                       ****************865 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.5   2.4e-06    0.0026       8      21 ..      20      33 ..      14      34 .. 0.88
   2 !   14.6   2.8   2.4e-05     0.025       8      22 .]      52      66 ..      48      66 .. 0.92
   3 !   17.8   1.7   2.4e-06    0.0025       2      22 .]      92     112 ..      91     112 .. 0.91
   4 !   16.8   1.6   4.8e-06    0.0051       7      22 .]     134     149 ..     130     149 .. 0.90
   5 !   19.0   3.5     1e-06    0.0011       2      21 ..     157     176 ..     156     177 .. 0.94
   6 ?   -0.8   0.2         2   2.1e+03      12      17 ..     183     188 ..     182     190 .. 0.57
   7 !   19.8   3.5   5.6e-07   0.00059       2      22 .]     198     218 ..     197     218 .. 0.93
   8 !    9.0   0.8    0.0015       1.5       3      22 .]     231     252 ..     229     252 .. 0.88
   9 !   12.5   1.8   0.00012      0.12       7      22 .]     268     283 ..     263     283 .. 0.89
  10 !   15.0   1.7   1.9e-05      0.02       6      21 ..     316     331 ..     311     332 .. 0.83
  11 !   21.3   4.4   1.8e-07   0.00019       3      22 .]     347     366 ..     345     366 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                            Fer4_2  8 drCigCgaCvsaCP 21
                                      + C gC +C+s+CP
  gi|488599971|ref|YP_007906442.1| 20 ELCRGCQICTSVCP 33
                                      78************ PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.4e-05
                            Fer4_2  8 drCigCgaCvsaCPa 22
                                      d+C+ Cg+C + CP+
  gi|488599971|ref|YP_007906442.1| 52 DNCNLCGTCSDFCPY 66
                                      79************5 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2.4e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       +v vd  +C+ Cg C ++CP+
  gi|488599971|ref|YP_007906442.1|  92 KVSVDDSKCTYCGLCMQNCPH 112
                                       6789999*************7 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 4.8e-06
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       +d Ci+C+ Cv  CP+
  gi|488599971|ref|YP_007906442.1| 134 RDGCINCRLCVMFCPT 149
                                       678************7 PP

  == domain 5  score: 19.0 bits;  conditional E-value: 1e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++++++drCi C++C  +CP
  gi|488599971|ref|YP_007906442.1| 157 RPEINEDRCIYCEICSAVCP 176
                                       689****************9 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2
                            Fer4_2  12 gCgaCv 17 
                                       +C +C+
  gi|488599971|ref|YP_007906442.1| 183 HCDSCR 188
                                       455553 PP

  == domain 7  score: 19.8 bits;  conditional E-value: 5.6e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       +v+vd+ rC  Cg+C  +CP+
  gi|488599971|ref|YP_007906442.1| 198 RVEVDESRCATCGICAEVCPE 218
                                       689*****************5 PP

  == domain 8  score: 9.0 bits;  conditional E-value: 0.0015
                            Fer4_2   3 vvvdtdrCig..CgaCvsaCPa 22 
                                        ++ +++C g  C++C   CP+
  gi|488599971|ref|YP_007906442.1| 231 QHFKAEKCYGldCSICKEICPN 252
                                       68999***9889****999**5 PP

  == domain 9  score: 12.5 bits;  conditional E-value: 0.00012
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                        drC+ Cg C ++CPa
  gi|488599971|ref|YP_007906442.1| 268 LDRCNFCGVCENSCPA 283
                                       589************8 PP

  == domain 10  score: 15.0 bits;  conditional E-value: 1.9e-05
                            Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                       + d+C gCg+C s CP
  gi|488599971|ref|YP_007906442.1| 316 VNDNCFGCGICSSLCP 331
                                       4588***********9 PP

  == domain 11  score: 21.3 bits;  conditional E-value: 1.8e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       vvvd+ +C++Cg C s+CPa
  gi|488599971|ref|YP_007906442.1| 347 VVVDSSACTACGVCSSNCPA 366
                                       89*****************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   6.2e-07   0.00066      33      58 ..      14      38 ..       3      39 .. 0.78
   2 !    7.9   1.7    0.0032       3.3      37      55 ..      50      67 ..      40      71 .. 0.81
   3 !   17.9  10.6   2.3e-06    0.0025       6      58 ..      52     116 ..      48     117 .. 0.79
   4 !   29.4  11.6   6.3e-10   6.6e-07       3      58 ..      95     153 ..      93     154 .. 0.83
   5 !   31.3  12.8   1.6e-10   1.7e-07       5      58 ..     134     181 ..     129     182 .. 0.88
   6 !   24.2  17.7   2.6e-08   2.8e-05       2      58 ..     159     222 ..     158     223 .. 0.74
   7 !   21.5  11.1   1.8e-07   0.00018       3      52 ..     201     251 ..     199     257 .. 0.78
   8 !   11.8   9.4   0.00019       0.2       5      58 ..     235     287 ..     232     288 .. 0.78
   9 !   19.5   1.6   7.3e-07   0.00077      30      53 ..     309     332 ..     296     338 .. 0.80
  10 !   17.7   2.5   2.7e-06    0.0028      26      58 ..     339     370 ..     335     371 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.2e-07
                           Fer4_21 33 vlkvvedeCvGCnlCssvCPvedcie 58
                                       l    + C GC++C+svCP  ++i+
  gi|488599971|ref|YP_007906442.1| 14 ELYFSGELCRGCQICTSVCP-RNAIS 38
                                      45566799************.69886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0032
                           Fer4_21 37 vedeCvGCnlCssvCPved 55
                                      v d+C  C  Cs+ CP  +
  gi|488599971|ref|YP_007906442.1| 50 VGDNCNLCGTCSDFCPY-G 67
                                      6799************5.5 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 2.3e-06
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvl..............kvvedeCvGCnlCssvCPvedcie 58 
                                       d+C  Cg C   C+  +  a++ d+k+ +               v +++C+ C lC++ CP +d+i+
  gi|488599971|ref|YP_007906442.1|  52 DNCNLCGTCSDFCPY-GALAVKRDGKKGIfteilkkelefekvSVDDSKCTYCGLCMQNCP-HDAIS 116
                                       7999**********5.66788878777545556666666775577899*************.69997 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 6.3e-10
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvl......kv.vedeCvGCnlCssvCPvedcie 58 
                                       +d++kC  Cg+C++ C+   h+ai+++ k  +      k+ + d C+ C lC+  CP+ ++i+
  gi|488599971|ref|YP_007906442.1|  95 VDDSKCTYCGLCMQNCP---HDAISVKRKLNIgkirggKIeIRDGCINCRLCVMFCPT-KAIS 153
                                       899**************...9***9888865555566655369**************7.7775 PP

  == domain 5  score: 31.3 bits;  conditional E-value: 1.6e-10
                           Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +d Ci+C +C++ C+   ++ai+++++   ++ ed+C+ C++Cs+vCP +d+i+
  gi|488599971|ref|YP_007906442.1| 134 RDGCINCRLCVMFCP---TKAISVSDR--PEINEDRCIYCEICSAVCP-KDVIS 181
                                       478************...699*99754..4689***************.79886 PP

  == domain 6  score: 24.2 bits;  conditional E-value: 2.6e-08
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai.......eidaktvl....kvvedeCvGCnlCssvCPvedcie 58 
                                        i+ed+Ci C+ C  +C++   + i       +++a++vl    +v e++C  C +C++vCP e++i+
  gi|488599971|ref|YP_007906442.1| 159 EINEDRCIYCEICSAVCPK---DVIsvhcdscRLQASNVLegrvEVDESRCATCGICAEVCP-ENAIR 222
                                       69****************6...5553333344333333224444999***************.79997 PP

  == domain 7  score: 21.5 bits;  conditional E-value: 1.8e-07
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvG..CnlCssvCP 52 
                                       +de++C  Cg C+ +C+++++   ++  k + +  +++C G  C +C ++CP
  gi|488599971|ref|YP_007906442.1| 201 VDESRCATCGICAEVCPENAIRVNRLF-KGRQHFKAEKCYGldCSICKEICP 251
                                       89***************9666555433.444567889998888********* PP

  == domain 8  score: 11.8 bits;  conditional E-value: 0.00019
                           Fer4_21   5 edkC..igCgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPvedcie 58 
                                        +kC  ++C  C   C++    ai++      +v+  d+C  C +C + CP  ++ie
  gi|488599971|ref|YP_007906442.1| 235 AEKCygLDCSICKEICPN---LAIQYRYTPEKEVIfLDRCNFCGVCENSCPA-GAIE 287
                                       56775568*********7...6776665555556548**************5.9997 PP

  == domain 9  score: 19.5 bits;  conditional E-value: 7.3e-07
                           Fer4_21  30 aktvlkvvedeCvGCnlCssvCPv 53 
                                       +k+ +  v+d+C GC +Css CP+
  gi|488599971|ref|YP_007906442.1| 309 NKKSVIAVNDNCFGCGICSSLCPL 332
                                       444555679**************7 PP

  == domain 10  score: 17.7 bits;  conditional E-value: 2.7e-06
                           Fer4_21  26 ieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       i++++ + + v ++ C++C +Css CP  ++i+
  gi|488599971|ref|YP_007906442.1| 339 IDLAHGKAVVVDSSACTACGVCSSNCPA-GAIT 370
                                       55666677788899*************5.9997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.5   2.9e-05      0.03       7      24 .]      20      37 ..      16      37 .. 0.92
   2 !   16.3   2.2   7.2e-06    0.0076       7      24 .]      52      69 ..      52      69 .. 0.96
   3 !   22.3   2.1   9.3e-08   9.8e-05       1      24 []      92     115 ..      92     115 .. 0.96
   4 !   15.2   3.1   1.6e-05     0.017       9      24 .]     137     152 ..     133     152 .. 0.92
   5 !   17.3   5.5   3.4e-06    0.0036       2      24 .]     158     180 ..     157     180 .. 0.94
   6 ?   -2.3   0.4       5.5   5.8e+03       9      13 ..     184     188 ..     183     189 .. 0.82
   7 !   25.1   4.6   1.2e-08   1.2e-05       2      24 .]     199     221 ..     198     221 .. 0.97
   8 !    8.1   1.5    0.0028         3       3      21 ..     232     252 ..     232     255 .. 0.79
   9 !   15.3   2.6   1.4e-05     0.015       4      24 .]     266     286 ..     265     286 .. 0.90
  10 ?    5.6   2.0     0.017        18       6      20 ..     317     331 ..     313     335 .. 0.91
  11 !   23.9   4.1   2.8e-08   2.9e-05       2      24 .]     347     369 ..     346     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                      ++C gC  C++vCP +ai
  gi|488599971|ref|YP_007906442.1| 20 ELCRGCQICTSVCPRNAI 37
                                      79************9998 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.2e-06
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                      d+C+ Cg C + CP+ga+
  gi|488599971|ref|YP_007906442.1| 52 DNCNLCGTCSDFCPYGAL 69
                                      79**************97 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 9.3e-08
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +v +d++kC+ Cg C+ +CP++ai
  gi|488599971|ref|YP_007906442.1|  92 KVSVDDSKCTYCGLCMQNCPHDAI 115
                                       689*******************98 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 1.6e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci C+ Cv+ CP++ai
  gi|488599971|ref|YP_007906442.1| 137 CINCRLCVMFCPTKAI 152
                                       **************98 PP

  == domain 5  score: 17.3 bits;  conditional E-value: 3.4e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       +ei++d+Ci C+ C +vCP ++i
  gi|488599971|ref|YP_007906442.1| 158 PEINEDRCIYCEICSAVCPKDVI 180
                                       89*****************9886 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 5.5
                            Fer4_6   9 CigCg 13 
                                       C++C+
  gi|488599971|ref|YP_007906442.1| 184 CDSCR 188
                                       99997 PP

  == domain 7  score: 25.1 bits;  conditional E-value: 1.2e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       ve+d+++C  Cg C+ vCPe+ai
  gi|488599971|ref|YP_007906442.1| 199 VEVDESRCATCGICAEVCPENAI 221
                                       89********************8 PP

  == domain 8  score: 8.1 bits;  conditional E-value: 0.0028
                            Fer4_6   3 eidpdkCi..gCgdCvrvCPe 21 
                                       +++++kC   +C  C  +CP 
  gi|488599971|ref|YP_007906442.1| 232 HFKAEKCYglDCSICKEICPN 252
                                       58899996448*********5 PP

  == domain 9  score: 15.3 bits;  conditional E-value: 1.4e-05
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       i  d+C+ Cg C++ CP+gai
  gi|488599971|ref|YP_007906442.1| 266 IFLDRCNFCGVCENSCPAGAI 286
                                       56699***************8 PP

  == domain 10  score: 5.6 bits;  conditional E-value: 0.017
                            Fer4_6   6 pdkCigCgdCvrvCP 20 
                                        d+C gCg C + CP
  gi|488599971|ref|YP_007906442.1| 317 NDNCFGCGICSSLCP 331
                                       58999*********9 PP

  == domain 11  score: 23.9 bits;  conditional E-value: 2.8e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       v++d ++C+ Cg C ++CP+gai
  gi|488599971|ref|YP_007906442.1| 347 VVVDSSACTACGVCSSNCPAGAI 369
                                       89********************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 !   21.0  10.5   2.5e-07   0.00026       7      56 .]      20      65 ..      15      65 .. 0.94
   2 !   13.4   1.9   5.8e-05     0.061       7      23 ..      52      68 ..      47      85 .. 0.75
   3 !   26.7  11.3   4.1e-09   4.3e-06       2      56 .]      93     148 ..      92     148 .. 0.89
   4 !   21.9  12.9   1.3e-07   0.00014       6      56 .]     134     176 ..     130     176 .. 0.95
   5 !   21.9  17.9   1.4e-07   0.00014       3      56 .]     159     217 ..     157     217 .. 0.95
   6 !   20.9  11.2   2.6e-07   0.00028       2      56 .]     199     251 ..     198     251 .. 0.95
   7 !   17.7  10.9   2.7e-06    0.0028       5      56 .]     234     282 ..     230     282 .. 0.92
   8 !   17.9   9.8   2.4e-06    0.0025       4      56 .]     266     331 ..     263     331 .. 0.77
   9 !   24.5   9.4     2e-08   2.2e-05       3      56 .]     314     365 ..     312     365 .. 0.82
  10 !   16.0   3.0   9.4e-06    0.0099       2      22 ..     347     367 ..     346     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                           Fer4_10  7 dtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + C +C+ C+++CP     +  + ++++++   ++ ++C  cg C + CP
  gi|488599971|ref|YP_007906442.1| 20 ELCRGCQICTSVCPR----NAISVFRDDGGFTAEVGDNCNLCGTCSDFCP 65
                                      78*************....9999**************************9 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.8e-05
                           Fer4_10  7 dtCirCgkCvkaCPadl 23
                                      d C  Cg+C ++CP+ +
  gi|488599971|ref|YP_007906442.1| 52 DNCNLCGTCSDFCPYGA 68
                                      78************955 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 4.1e-09
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                       v +dd++C+ Cg C++ CP d+ sv+ k  + ++   ++   + C++c  Cv  CP
  gi|488599971|ref|YP_007906442.1|  93 VSVDDSKCTYCGLCMQNCPHDAISVKRKLNIGKIRGGKIeIRDGCINCRLCVMFCP 148
                                       789*******************8888888888888888867899***********9 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 1.3e-07
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d Ci+C+ Cv +CP+        +++s +++ +++ ++C+ c+ C ++CP
  gi|488599971|ref|YP_007906442.1| 134 RDGCINCRLCVMFCPT--------KAISVSDRPEINEDRCIYCEICSAVCP 176
                                       689*************........**************************9 PP

  == domain 5  score: 21.9 bits;  conditional E-value: 1.4e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +i++d+Ci C+ C ++CP d+     +s + ++ +  e++v+++ ++C +cg C+e+CP
  gi|488599971|ref|YP_007906442.1| 159 EINEDRCIYCEICSAVCPKDVisvhcDSCRLQASNVLEGRVEVDESRCATCGICAEVCP 217
                                       799*****************9***999999999999999999****************9 PP

  == domain 6  score: 20.9 bits;  conditional E-value: 2.6e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                       v++d+++C  Cg C ++CP     +  +  +  +++++ k ekC g  c  C e+CP
  gi|488599971|ref|YP_007906442.1| 199 VEVDESRCATCGICAEVCPE----NAIRVNRLFKGRQHFKAEKCYGldCSICKEICP 251
                                       6789****************....9999999*************99889*******9 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 2.7e-06
                           Fer4_10   5 dddtC..irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +++C  + C  C++ CP       a++++   e++ + +++C +cg C  +CP
  gi|488599971|ref|YP_007906442.1| 234 KAEKCygLDCSICKEICPN-----LAIQYRYTPEKEVIFLDRCNFCGVCENSCP 282
                                       568896679**********.....9999999**********************9 PP

  == domain 8  score: 17.9 bits;  conditional E-value: 2.4e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadl.............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       i  d+C  Cg C ++CPa +              +   +g++ +++ v  + ++C gcg C + CP
  gi|488599971|ref|YP_007906442.1| 266 IFLDRCNFCGVCENSCPAGAieierelsddvnlLEIHLNGKKVNKKSVIAVNDNCFGCGICSSLCP 331
                                       6679**************99********88887333344444444444445689***********9 PP

  == domain 9  score: 24.5 bits;  conditional E-value: 2e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +   d C +Cg C + CP    + g +     ++av +++++Ct+cg C + CP
  gi|488599971|ref|YP_007906442.1| 314 IAVNDNCFGCGICSSLCPL--IKGGLTIDLAHGKAVVVDSSACTACGVCSSNCP 365
                                       556799*************..555555556666667779**************9 PP

  == domain 10  score: 16.0 bits;  conditional E-value: 9.4e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPad 22 
                                       vv+d++ C+ Cg C + CPa 
  gi|488599971|ref|YP_007906442.1| 347 VVVDSSACTACGVCSSNCPAG 367
                                       7899****************3 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3  11.1    0.0016       1.6       2      59 ..      22      67 ..      21      69 .. 0.82
   2 !   19.0   9.7   1.5e-06    0.0016       1      59 [.      53     113 ..      53     115 .. 0.83
   3 !   13.8  12.6   6.2e-05     0.065       1      58 [.      99     149 ..      99     152 .. 0.76
   4 !   10.4   2.5   0.00072      0.76      44      60 ..     163     179 ..     150     180 .. 0.82
   5 !    8.7  17.4    0.0024       2.5       1      59 [.     164     219 ..     164     221 .. 0.73
   6 !    7.0  22.6    0.0079       8.3       1      59 [.     205     284 ..     205     285 .. 0.68
   7 !   20.9   6.6   3.8e-07    0.0004       1      57 [.     270     331 ..     270     332 .. 0.66
   8 !   12.4   1.0   0.00016      0.17      44      59 ..     352     367 ..     343     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      C++C+ C+ +Cp++++  ++ +    a            e+ ++C+ Cg C+  CP+g
  gi|488599971|ref|YP_007906442.1| 22 CRGCQICTSVCPRNAISVFRDDGGFTA------------EVGDNCNLCGTCSDFCPYG 67
                                      **************9977755544433............56789************97 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.5e-06
                           Fer4_17   1 rCiqCgyClpeCpsyea..ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       +C+ Cg C + Cp+++    ++ +k +  ++  ++le ++ +   s+C+ Cg+C + CP++
  gi|488599971|ref|YP_007906442.1|  53 NCNLCGTCSDFCPYGALavKRDGKKGIFTEILKKELEFEKVSVDDSKCTYCGLCMQNCPHD 113
                                       6*************88754666788899998777777666667889*************97 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 6.2e-05
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       +C+ Cg C+++Cp  ++  +      r++++g++++  k e  + Ci+C++C++ CP 
  gi|488599971|ref|YP_007906442.1|  99 KCTYCGLCMQNCPHDAISVK------RKLNIGKIRGG-KIEIRDGCINCRLCVMFCPT 149
                                       6************9877443......55555555552.2245699************7 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00072
                           Fer4_17  44 slCieCgeCerkCPqgl 60 
                                       ++Ci C+ C+++CP+++
  gi|488599971|ref|YP_007906442.1| 163 DRCIYCEICSAVCPKDV 179
                                       78999999999999886 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0024
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       rCi C+ C ++Cp   +   + ++ + +a++  le+   e   s+C++Cg C+++CP++
  gi|488599971|ref|YP_007906442.1| 164 RCIYCEICSAVCPKDVISVHC-DSCRLQASN-VLEGR-VEVDESRCATCGICAEVCPEN 219
                                       7************98875554.445555444.34442.234669*************97 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0079
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraakl...................glleeaeke....ekaslCieCgeCer 54 
                                       rC+ Cg C+++Cp ++++ n+  k ++ +k+                    + +++          ++C+ Cg Ce 
  gi|488599971|ref|YP_007906442.1| 205 RCATCGICAEVCPENAIRVNRLFKGRQHFKAekcygldcsickeicpnlaIQYRYT--PekevIFLDRCNFCGVCEN 279
                                       7*************999777666666666655556666666665555543122223..13323578*********** PP

                           Fer4_17  55 kCPqg 59 
                                       +CP+g
  gi|488599971|ref|YP_007906442.1| 280 SCPAG 284
                                       ***86 PP

  == domain 7  score: 20.9 bits;  conditional E-value: 3.8e-07
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydnepkkllraaklgllee.aeke...ekaslCieCgeCerkCP 57 
                                       rC+ Cg C+++Cp +++ ++ e    ++ ++++l+++ ++k+    + ++C +Cg C++ CP
  gi|488599971|ref|YP_007906442.1| 270 RCNFCGVCENSCPAGAIeIERELSDDVNLLEIHLNGKkVNKKsviAVNDNCFGCGICSSLCP 331
                                       7************98885333333333333333333303344355688*************9 PP

  == domain 8  score: 12.4 bits;  conditional E-value: 0.00016
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       s C+ Cg C++ CP+g
  gi|488599971|ref|YP_007906442.1| 352 SACTACGVCSSNCPAG 367
                                       5788888888888875 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   3.2    0.0025       2.6      49      64 ..      20      35 ..       3      36 .. 0.83
   2 !   12.3   1.2   0.00017      0.18      45      64 ..      48      67 ..      36      68 .. 0.76
   3 !   19.8   9.7   7.8e-07   0.00082       3      64 ..      98     150 ..      96     151 .. 0.69
   4 !   14.3  15.0   3.9e-05     0.041       3      64 ..     163     219 ..     161     220 .. 0.79
   5 ?    2.4  12.5      0.21   2.2e+02      48      64 ..     268     284 ..     234     285 .. 0.56
   6 !   15.2  10.4   2.1e-05     0.022       2      62 ..     268     331 ..     267     332 .. 0.63
   7 !   14.5  12.5   3.5e-05     0.037       3      64 ..     318     367 ..     316     368 .. 0.77
   8 !   11.0   4.4   0.00041      0.44       3      17 ..     352     366 ..     350     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0025
                            Fer4_8 49 wsCttcgaCtevCpvg 64
                                      + C +c+ Ct+vCp +
  gi|488599971|ref|YP_007906442.1| 20 ELCRGCQICTSVCPRN 35
                                      68************86 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                            Fer4_8 45 eealwsCttcgaCtevCpvg 64
                                      +e  ++C+ cg C++ Cp g
  gi|488599971|ref|YP_007906442.1| 48 AEVGDNCNLCGTCSDFCPYG 67
                                      56678899999999999975 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 7.8e-07
                            Fer4_8   3 ekCieCgaCqsaCp..vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       +kC+ Cg+C+++Cp  +++ ++   + + rg+++e              + C +c+ C+  Cp++
  gi|488599971|ref|YP_007906442.1|  98 SKCTYCGLCMQNCPhdAISVKRkLNIGKIRGGKIE---I---------RDGCINCRLCVMFCPTK 150
                                       69************553333332344444444344...2.........257************97 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 3.9e-05
                            Fer4_8   3 ekCieCgaCqsaCp..vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ++Ci C+ C + Cp  v++      +l+a +  ++  +e ++        +C tcg C+evCp++
  gi|488599971|ref|YP_007906442.1| 163 DRCIYCEICSAVCPkdVISVHCdSCRLQASNVLEG-RVEVDE-------SRCATCGICAEVCPEN 219
                                       58***********9995555553666777777677.666666.......89************97 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.21
                            Fer4_8  48 lwsCttcgaCtevCpvg 64 
                                       l++C+ cg C++ Cp g
  gi|488599971|ref|YP_007906442.1| 268 LDRCNFCGVCENSCPAG 284
                                       66777777777777765 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 2.1e-05
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae......dvqeeqvlee..eealwsCttcgaCtevCp 62 
                                       l++C+ Cg C+++Cp+   + ++ l+   +  e      +v +     +      ++C +cg C++ Cp
  gi|488599971|ref|YP_007906442.1| 268 LDRCNFCGVCENSCPAGAIEIERELSDDVNLLEihlngkKVNK-----KsvIAVNDNCFGCGICSSLCP 331
                                       579************6555544333333333333333321222.....12245689************9 PP

  == domain 7  score: 14.5 bits;  conditional E-value: 3.5e-05
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ++C +Cg C s Cp+++        a g+a   v+++          +Ct+cg C+++Cp g
  gi|488599971|ref|YP_007906442.1| 318 DNCFGCGICSSLCPLIKGGLTI-DLAHGKA-V-VVDS---------SACTACGVCSSNCPAG 367
                                       69************99998544.5555552.2.3333.........47************86 PP

  == domain 8  score: 11.0 bits;  conditional E-value: 0.00041
                            Fer4_8   3 ekCieCgaCqsaCpv 17 
                                       ++C+ Cg C s+Cp+
  gi|488599971|ref|YP_007906442.1| 352 SACTACGVCSSNCPA 366
                                       688888888888886 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   2.2   0.00011      0.12       2      16 ..      20      34 ..      19      41 .. 0.91
   2 !   14.6   2.8   3.3e-05     0.035       2      17 .]      52      67 ..      51      67 .. 0.94
   3 ?    4.9   2.0     0.041        44       3      15 ..      99     111 ..      97     119 .. 0.91
   4 !   15.8   2.9   1.3e-05     0.014       2      16 ..     135     149 ..     134     150 .. 0.89
   5 ?    4.5   4.2     0.058        61       2      16 ..     163     177 ..     162     178 .. 0.92
   6 ?    2.3   0.3      0.29     3e+02       5      11 ..     182     188 ..     182     190 .. 0.86
   7 !    8.1   2.7    0.0041       4.3       2      16 ..     204     218 ..     203     224 .. 0.91
   8 ?    4.7   1.3     0.051        54       2      15 ..     236     251 ..     235     259 .. 0.88
   9 !   16.4   2.8   8.8e-06    0.0093       2      17 .]     269     284 ..     268     285 .. 0.91
  10 !   12.6   0.9   0.00015      0.15       2      15 ..     318     331 ..     317     338 .. 0.93
  11 !    9.5   4.3    0.0015       1.6       2      16 ..     352     366 ..     351     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C gC  C+++CP 
  gi|488599971|ref|YP_007906442.1| 20 ELCRGCQICTSVCPR 34
                                      67************6 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.3e-05
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C+ Cg C ++CP+g
  gi|488599971|ref|YP_007906442.1| 52 DNCNLCGTCSDFCPYG 67
                                      79************86 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.041
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       +C+ Cg C+  CP
  gi|488599971|ref|YP_007906442.1|  99 KCTYCGLCMQNCP 111
                                       8***********9 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 1.3e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + Ci+C+ Cv +CP+
  gi|488599971|ref|YP_007906442.1| 135 DGCINCRLCVMFCPT 149
                                       56************8 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.058
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       +rCi C  C a+CP 
  gi|488599971|ref|YP_007906442.1| 163 DRCIYCEICSAVCPK 177
                                       8*************5 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.29
                            Fer4_4   5 igCgsCv 11 
                                       ++C+sC+
  gi|488599971|ref|YP_007906442.1| 182 VHCDSCR 188
                                       69****7 PP

  == domain 7  score: 8.1 bits;  conditional E-value: 0.0041
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       +rC  Cg C  +CP 
  gi|488599971|ref|YP_007906442.1| 204 SRCATCGICAEVCPE 218
                                       59************5 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.051
                            Fer4_4   2 erC..igCgsCvaaCP 15 
                                       e+C  ++C  C  +CP
  gi|488599971|ref|YP_007906442.1| 236 EKCygLDCSICKEICP 251
                                       789889*********9 PP

  == domain 9  score: 16.4 bits;  conditional E-value: 8.8e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       +rC+ Cg+C+++CP g
  gi|488599971|ref|YP_007906442.1| 269 DRCNFCGVCENSCPAG 284
                                       9*************75 PP

  == domain 10  score: 12.6 bits;  conditional E-value: 0.00015
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       ++C+gCg C + CP
  gi|488599971|ref|YP_007906442.1| 318 DNCFGCGICSSLCP 331
                                       89***********9 PP

  == domain 11  score: 9.5 bits;  conditional E-value: 0.0015
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C+ Cg+C + CP 
  gi|488599971|ref|YP_007906442.1| 352 SACTACGVCSSNCPA 366
                                       57************7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.5    0.0073       7.7       4      18 ..      20      34 ..      19      46 .. 0.89
   2 ?    5.7   1.3     0.021        22       4      17 ..      52      65 ..      50      67 .. 0.92
   3 !    9.1   2.5    0.0017       1.8       1      18 [.      95     112 ..      95     113 .. 0.94
   4 !   13.1   1.5   9.7e-05       0.1       3      17 ..     134     148 ..     131     150 .. 0.91
   5 !   10.4   4.2   0.00072      0.76       1      18 [.     160     177 ..     160     178 .. 0.94
   6 ?   -1.3   0.0       3.3   3.4e+03       8      20 ..     183     195 ..     182     198 .. 0.81
   7 !   11.7   4.7   0.00027      0.28       1      18 [.     201     218 ..     201     219 .. 0.96
   8 ?    4.5   1.4     0.049        52       8      19 ..     242     253 ..     235     269 .. 0.72
   9 ?    2.0   2.9       0.3   3.2e+02       4      17 ..     269     282 ..     266     284 .. 0.91
  10 !   11.5   1.3   0.00031      0.33       1      17 [.     316     331 ..     316     333 .. 0.92
  11 !   10.8   3.8   0.00053      0.56       1      17 [.     349     365 ..     349     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0073
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      + C +c++C +++P 
  gi|488599971|ref|YP_007906442.1| 20 ELCRGCQICTSVCPR 34
                                      56************6 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.021
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d+C  cg+C +++P
  gi|488599971|ref|YP_007906442.1| 52 DNCNLCGTCSDFCP 65
                                      89***********9 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0017
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD ++C+ cg+C + +P+
  gi|488599971|ref|YP_007906442.1|  95 VDDSKCTYCGLCMQNCPH 112
                                       899**************5 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 9.7e-05
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                       rd Ci+c +Cv+++P
  gi|488599971|ref|YP_007906442.1| 134 RDGCINCRLCVMFCP 148
                                       799************ PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00072
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +++d+Ci c++C +++P+
  gi|488599971|ref|YP_007906442.1| 160 INEDRCIYCEICSAVCPK 177
                                       799**************6 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 3.3
                           Fer4_13   8 acgaCvelaPdvF 20 
                                        c++C+  a +v 
  gi|488599971|ref|YP_007906442.1| 183 HCDSCRLQASNVL 195
                                       69***99998876 PP

  == domain 7  score: 11.7 bits;  conditional E-value: 0.00027
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD+++C  cg+C+e++P+
  gi|488599971|ref|YP_007906442.1| 201 VDESRCATCGICAEVCPE 218
                                       9****************8 PP

  == domain 8  score: 4.5 bits;  conditional E-value: 0.049
                           Fer4_13   8 acgaCvelaPdv 19 
                                       +c +C e++P++
  gi|488599971|ref|YP_007906442.1| 242 DCSICKEICPNL 253
                                       8*********96 PP

  == domain 9  score: 2.0 bits;  conditional E-value: 0.3
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                       d+C  cg+C + +P
  gi|488599971|ref|YP_007906442.1| 269 DRCNFCGVCENSCP 282
                                       79***********9 PP

  == domain 10  score: 11.5 bits;  conditional E-value: 0.00031
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       V+ d+C +cg+C +l+P
  gi|488599971|ref|YP_007906442.1| 316 VN-DNCFGCGICSSLCP 331
                                       67.9************* PP

  == domain 11  score: 10.8 bits;  conditional E-value: 0.00053
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD + C+acg+C + +P
  gi|488599971|ref|YP_007906442.1| 349 VDSSACTACGVCSSNCP 365
                                       89*************** PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   4.7    0.0021       2.2       1      15 []      22      36 ..      22      36 .. 0.96
   2 !   14.1   3.3   6.6e-05     0.069       1      15 []      54      68 ..      54      68 .. 0.98
   3 !   13.2   5.0   0.00013      0.14       1      15 []     100     114 ..     100     114 .. 0.96
   4 !   12.8   3.7   0.00018      0.19       1      15 []     137     151 ..     137     151 .. 0.98
   5 !    8.9   3.3     0.003       3.2       1      14 [.     165     178 ..     165     179 .. 0.94
   6 ?   -1.1   0.3       4.8     5e+03       3       7 ..     183     187 ..     182     190 .. 0.70
   7 !    7.9   6.0    0.0063       6.7       1      15 []     206     220 ..     206     220 .. 0.92
   8 ?    2.3   1.8      0.39   4.1e+02       4      13 ..     243     252 ..     238     254 .. 0.76
   9 !    9.1   6.0    0.0025       2.7       1      15 []     271     285 ..     271     285 .. 0.97
  10 ?    6.8   2.2     0.014        15       1      12 [.     320     331 ..     320     336 .. 0.88
  11 ?    3.3   7.2      0.19     2e+02       1      15 []     354     368 ..     354     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0021
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gC+ C  vCP +A
  gi|488599971|ref|YP_007906442.1| 22 CRGCQICTSVCPRNA 36
                                      99**99*******98 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.6e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cg+C + CP+gA
  gi|488599971|ref|YP_007906442.1| 54 CNLCGTCSDFCPYGA 68
                                      **************9 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00013
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct Cg+C++ CP +A
  gi|488599971|ref|YP_007906442.1| 100 CTYCGLCMQNCPHDA 114
                                       ************998 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00018
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C++C++Cv  CP++A
  gi|488599971|ref|YP_007906442.1| 137 CINCRLCVMFCPTKA 151
                                       *************98 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.003
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ C+ C  vCP++
  gi|488599971|ref|YP_007906442.1| 165 CIYCEICSAVCPKD 178
                                       9***********97 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 4.8
                            Fer4_3   3 gCgaC 7  
                                       +C  C
  gi|488599971|ref|YP_007906442.1| 183 HCDSC 187
                                       78777 PP

  == domain 7  score: 7.9 bits;  conditional E-value: 0.0063
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  Cg C evCP++A
  gi|488599971|ref|YP_007906442.1| 206 CATCGICAEVCPENA 220
                                       778**********98 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.39
                            Fer4_3   4 CgaCvevCPv 13 
                                       C+ C e CP+
  gi|488599971|ref|YP_007906442.1| 243 CSICKEICPN 252
                                       999******7 PP

  == domain 9  score: 9.1 bits;  conditional E-value: 0.0025
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ Cg C+++CP gA
  gi|488599971|ref|YP_007906442.1| 271 CNFCGVCENSCPAGA 285
                                       ************998 PP

  == domain 10  score: 6.8 bits;  conditional E-value: 0.014
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C gCg C   CP
  gi|488599971|ref|YP_007906442.1| 320 CFGCGICSSLCP 331
                                       99********** PP

  == domain 11  score: 3.3 bits;  conditional E-value: 0.19
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct Cg C   CP gA
  gi|488599971|ref|YP_007906442.1| 354 CTACGVCSSNCPAGA 368
                                       9***********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 ?    5.9   0.4     0.021        22       6      20 ..      20      34 ..      16      50 .. 0.77
   2 ?    4.2   0.3     0.069        73       6      19 ..      52      65 ..      51      89 .. 0.75
   3 !   12.0   1.5   0.00026      0.27       1      19 [.      93     111 ..      93     117 .. 0.94
   4 ?    3.2   3.2      0.14   1.5e+02       5      20 ..     134     149 ..     130     152 .. 0.88
   5 ?    6.3   4.0     0.015        16       3      20 ..     160     177 ..     159     192 .. 0.90
   6 !   13.6   2.2   8.3e-05     0.088       1      20 [.     199     218 ..     199     224 .. 0.94
   7 ?   -2.6   0.5       9.2   9.7e+03      58      64 ..     249     255 ..     241     256 .. 0.65
   8 ?    0.3   4.8       1.1   1.2e+03       6      20 ..     269     283 ..     266     297 .. 0.80
   9 ?    6.1   0.4     0.018        19       6      19 ..     318     331 ..     315     343 .. 0.88
  10 !   12.1   1.5   0.00024      0.26       1      19 [.     347     365 ..     347     371 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                           Fer4_15  6 daCigcglCvaeape 20
                                      ++C gc  C  ++p+
  gi|488599971|ref|YP_007906442.1| 20 ELCRGCQICTSVCPR 34
                                      78********99974 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.069
                           Fer4_15  6 daCigcglCvaeap 19
                                      d+C  cg C + +p
  gi|488599971|ref|YP_007906442.1| 52 DNCNLCGTCSDFCP 65
                                      89*********997 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00026
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V vD ++C+ cglC++++p
  gi|488599971|ref|YP_007906442.1|  93 VSVDDSKCTYCGLCMQNCP 111
                                       89****************8 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.14
                           Fer4_15   5 rdaCigcglCvaeape 20 
                                       rd Ci c lCv  +p+
  gi|488599971|ref|YP_007906442.1| 134 RDGCINCRLCVMFCPT 149
                                       89**********9985 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.015
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       +++d+Ci c+ C a++p+
  gi|488599971|ref|YP_007906442.1| 160 INEDRCIYCEICSAVCPK 177
                                       899*************86 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 8.3e-05
                           Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                       V+vD+++C  cg C++++pe
  gi|488599971|ref|YP_007906442.1| 199 VEVDESRCATCGICAEVCPE 218
                                       89****************97 PP

  == domain 7  score: -2.6 bits;  conditional E-value: 9.2
                           Fer4_15  58 aCPvdAI 64 
                                        CP  AI
  gi|488599971|ref|YP_007906442.1| 249 ICPNLAI 255
                                       4777776 PP

  == domain 8  score: 0.3 bits;  conditional E-value: 1.1
                           Fer4_15   6 daCigcglCvaeape 20 
                                       d+C  cg+C   +p 
  gi|488599971|ref|YP_007906442.1| 269 DRCNFCGVCENSCPA 283
                                       799999999888874 PP

  == domain 9  score: 6.1 bits;  conditional E-value: 0.018
                           Fer4_15   6 daCigcglCvaeap 19 
                                       d+C gcg C  ++p
  gi|488599971|ref|YP_007906442.1| 318 DNCFGCGICSSLCP 331
                                       89***********8 PP

  == domain 10  score: 12.1 bits;  conditional E-value: 0.00024
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       VvvD +aC+ cg+C  ++p
  gi|488599971|ref|YP_007906442.1| 347 VVVDSSACTACGVCSSNCP 365
                                       89***************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 ?    1.0   8.1      0.45   4.7e+02      60      95 ..      21      64 ..       3      66 .. 0.65
   2 ?    4.1   0.6     0.047        50      58      74 ..      51      67 ..      34      83 .. 0.80
   3 ?    9.3   1.1    0.0012       1.3      53      84 ..      92     124 ..      70     133 .. 0.71
   4 ?    9.4   1.9    0.0011       1.1      59      74 ..     135     150 ..     125     157 .. 0.83
   5 ?    5.8   5.8     0.014        15      55      75 ..     159     179 ..     150     190 .. 0.78
   6 ?    5.7   5.0     0.016        17      48      74 ..     193     219 ..     181     225 .. 0.81
   7 ?   -2.0   7.8       3.7   3.9e+03      56      86 ..     235     266 ..     219     283 .. 0.60
   8 ?    2.5   0.7      0.15   1.6e+02      59      77 ..     269     288 ..     253     296 .. 0.80
   9 ?    6.3   0.6    0.0099        10      52      73 ..     311     332 ..     297     351 .. 0.70
  10 ?    6.4   2.0    0.0096        10      57      79 ..     350     373 ..     342     375 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.45
                           Fer4_18 60 dcidcescvkvcPtg.idi.rk..Glqle....ciscllcidac 95
                                       c  c+ c +vcP + i + r+  G+  e    c  c+ c d c
  gi|488599971|ref|YP_007906442.1| 21 LCRGCQICTSVCPRNaISVfRDdgGFTAEvgdnCNLCGTCSDFC 64
                                      4999*********7535543443345443223388888888888 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.047
                           Fer4_18 58 agdcidcescvkvcPtg 74
                                        +c  c++c + cP g
  gi|488599971|ref|YP_007906442.1| 51 GDNCNLCGTCSDFCPYG 67
                                      467999*********87 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0012
                           Fer4_18  53 rkekgagdcidcescvkvcPtg.idirkGlqle 84 
                                       + + ++++c+ c+ c++ cP + i ++  l + 
  gi|488599971|ref|YP_007906442.1|  92 KVSVDDSKCTYCGLCMQNCPHDaISVKRKLNIG 124
                                       34567789************7437777666665 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0011
                           Fer4_18  59 gdcidcescvkvcPtg 74 
                                         ci+c+ cv  cPt+
  gi|488599971|ref|YP_007906442.1| 135 DGCINCRLCVMFCPTK 150
                                       579**********996 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.014
                           Fer4_18  55 ekgagdcidcescvkvcPtgi 75 
                                       e ++  ci ce c +vcP ++
  gi|488599971|ref|YP_007906442.1| 159 EINEDRCIYCEICSAVCPKDV 179
                                       456778************875 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.016
                           Fer4_18  48 kekeerkekgagdcidcescvkvcPtg 74 
                                       +  e r e +++ c +c+ c +vcP +
  gi|488599971|ref|YP_007906442.1| 193 NVLEGRVEVDESRCATCGICAEVCPEN 219
                                       5566677888999************75 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 3.7
                           Fer4_18  56 kgagdcidcescvkvcPt.gidirkGlqleci 86 
                                       +++   +dc+ c ++cP   i  r     e i
  gi|488599971|ref|YP_007906442.1| 235 AEKCYGLDCSICKEICPNlAIQYRYTPEKEVI 266
                                       33444589********9536777765444433 PP

  == domain 8  score: 2.5 bits;  conditional E-value: 0.15
                           Fer4_18  59 gdcidcescvkvcPtg.idi 77 
                                         c  c++c + cP g i+i
  gi|488599971|ref|YP_007906442.1| 269 DRCNFCGVCENSCPAGaIEI 288
                                       56999*********974565 PP

  == domain 9  score: 6.3 bits;  conditional E-value: 0.0099
                           Fer4_18  52 erkekgagdcidcescvkvcPt 73 
                                       +   + + +c  c+ c ++cP 
  gi|488599971|ref|YP_007906442.1| 311 KSVIAVNDNCFGCGICSSLCPL 332
                                       333455678************6 PP

  == domain 10  score: 6.4 bits;  conditional E-value: 0.0096
                           Fer4_18  57 gagdcidcescvkvcPtg.idirk 79 
                                       +++ c++c++c + cP g i ir+
  gi|488599971|ref|YP_007906442.1| 350 DSSACTACGVCSSNCPAGaITIRE 373
                                       5678************97577875 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.034        36      29      50 ..     262     285 ..     254     318 .. 0.80
   2 ?    6.3   0.2    0.0068       7.2      22      49 ..     340     365 ..     331     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.034
                                       SEEEEEEESTTT-HHHHHTHH..H CS
                           Redoxin  29 kkvvvnfvpgafcPtCsaehp..y 50 
                                        k v++  +++fc++C ++ p  +
  gi|488599971|ref|YP_007906442.1| 262 EKEVIFLDRCNFCGVCENSCPagA 285
                                       45599999*********9988652 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0068
                                       EHHHHTTSEEEEEEESTTT-HHHHHTHH CS
                           Redoxin  22 slsefkgkkvvvnfvpgafcPtCsaehp 49 
                                       +l+   gk vvv + +++ c++Cs + p
  gi|488599971|ref|YP_007906442.1| 340 DLAH--GKAVVVDSSACTACGVCSSNCP 365
                                       4544..9*****************9876 PP

>> Neprosin_AP  Neprosin activation peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.6   1.7e+03      67      83 ..      64      80 ..      58      99 .. 0.81
   2 ?    0.3   0.0      0.93   9.8e+02      66      77 ..     109     120 ..     105     130 .. 0.89
   3 ?   -1.6   0.1       3.5   3.7e+03      66      77 ..     215     226 ..     211     230 .. 0.85
   4 ?    6.5   0.0     0.011        11      65      84 ..     279     298 ..     250     320 .. 0.81
   5 ?    0.9   0.8      0.57     6e+02      65      78 ..     362     375 ..     354     376 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.6
                       Neprosin_AP 67 CPegTvpirRtteedll 83
                                      CP g  +++R  ++ + 
  gi|488599971|ref|YP_007906442.1| 64 CPYGALAVKRDGKKGIF 80
                                      **********9888765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.93
                       Neprosin_AP  66 kCPegTvpirRt 77 
                                       +CP++ + ++R 
  gi|488599971|ref|YP_007906442.1| 109 NCPHDAISVKRK 120
                                       7*********96 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.5
                       Neprosin_AP  66 kCPegTvpirRt 77 
                                        CPe+ + + R 
  gi|488599971|ref|YP_007906442.1| 215 VCPENAIRVNRL 226
                                       6*******9996 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.011
                       Neprosin_AP  65 ekCPegTvpirRtteedllr 84 
                                       ++CP g + i R  ++d+  
  gi|488599971|ref|YP_007906442.1| 279 NSCPAGAIEIERELSDDVNL 298
                                       58***************865 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.57
                       Neprosin_AP  65 ekCPegTvpirRtt 78 
                                       ++CP g + ir ++
  gi|488599971|ref|YP_007906442.1| 362 SNCPAGAITIREVK 375
                                       48*********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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):              17  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 2432.64
//
Query:       gi|488599972|ref|YP_007906443.1|  [L=217]
Description: reduced coenzyme F420:NADP oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   73.4   0.2    4.4e-20   72.1   0.1    1.7  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00013   22.4   0.0    0.00025   21.5   0.0    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0017   18.5   0.0     0.0031   17.7   0.0    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.002   18.0   0.1     0.0037   17.2   0.1    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0027   17.8   0.0     0.0047   17.0   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0053   16.2   0.2       0.01   15.3   0.2    1.4  1  adh_short        short chain dehydrogenase
     0.0093   16.0   0.0      0.015   15.3   0.0    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
  ------ inclusion threshold ------
      0.011   15.4   0.1       0.16   11.6   0.0    2.1  2  ApbA             Ketopantoate reductase PanE/ApbA
      0.053   13.8   0.3       0.12   12.6   0.1    1.8  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.074   12.9   0.2       0.14   12.0   0.2    1.6  1  LpxI_N           LpxI N-terminal domain
       0.11   12.0   0.1       0.28   10.8   0.1    1.7  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
       0.16   11.4   0.1       0.23   10.9   0.1    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family


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 !   72.1   0.1     3e-23   4.4e-20       1      97 []       2     102 ..       2     102 .. 0.98
   2 ?   -1.5   0.0       2.6   3.9e+03      33      33 ..     139     139 ..     117     174 .. 0.46

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 3e-23
                                       EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........vkvtavdneeaaeeadvvvla 68 
                                       ki++i G+G++g++la +l+ +g   ++++++ sr  eka+  aee++        ++v + +ne+aaee+++ ++a
  gi|488599972|ref|YP_007906443.1|   2 KIALIgGTGHLGRGLAIRLAMNG---YDVIIG-SRGLEKAKRVAEEYNsvlhkissARVRGLANEDAAEECEIAIFA 74 
                                       79*********************...****88.******************************************** PP

                                       S-HHHHHHHHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  69 vkpedveevlselakdalkgklvisvlag 97 
                                       ++++++ +++++l + +lkgk+vis l++
  gi|488599972|ref|YP_007906443.1|  75 IPWRHAFSTAEKL-RGKLKGKIVISPLVP 102
                                       *************.***********9875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                                       E CS
                     F420_oxidored  33 s 33 
                                       +
  gi|488599972|ref|YP_007906443.1| 139 N 139
                                       2 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 !   21.5   0.0   1.6e-07   0.00025       1      94 [.       2      97 ..       2     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.GGTTTECEBEEE.GGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.aleegkdlkved.vdeeelkevdivflalpag 77
                                      k+a++G+tG  G+ l+ +L+ + +   v + s+  ++ k++ae ++  l +++  +v+  ++e++ +e++i+++a p  
  gi|488599972|ref|YP_007906443.1|  2 KIALIGGTGHLGRGLAIRLAMNGY--DVIIGSRGLEKAKRVAEEYNsVLHKISSARVRGlANEDAAEECEIAIFAIPWR 78
                                      79*************888877553..3334566667889998888878899999999998888888************* PP

                                      HHHHHHHHH..HHTTSEEE CS
                    Semialdhyde_dh 78 vskelapkl..aeagvkvi 94
                                       + + a+kl    +g +vi
  gi|488599972|ref|YP_007906443.1| 79 HAFSTAEKLrgKLKGKIVI 97
                                      *****99994444566666 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.1e-06    0.0031       1      65 [.       2      77 ..       2      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                                      EEEEE.--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...........EEE-SSHHHHHHHCSEEEE-SSS CS
                     NAD_binding_2  1 kigfi.GlGvMGsnmalnllkagykvavynrtkekveelvaeg...........akaaesieelvasldvvitmvka 65
                                      ki++i G+G +G+ +a +l+ +gy+v++  r  ek++++++e            +++++  e++++++++ i+ ++ 
  gi|488599972|ref|YP_007906443.1|  2 KIALIgGTGHLGRGLAIRLAMNGYDVIIGSRGLEKAKRVAEEYnsvlhkissarVRGLA-NEDAAEECEIAIFAIPW 77
                                      57888469********************************9986677666664333333.35677777777777765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.5e-06    0.0037       2      53 ..       3      55 ..       2      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.5e-06
                                      EEEE--.SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTT CS
                           3HCDH_N  2 vaviGa.GtmGagiaavfasagleVvlvdiseealekalekieksleklvekg 53
                                      +a iG  G +G+g+a  +a +g++V +  +  e++++++e+ ++ l+k  +++
  gi|488599972|ref|YP_007906443.1|  3 IALIGGtGHLGRGLAIRLAMNGYDVIIGSRGLEKAKRVAEEYNSVLHKISSAR 55
                                      6777655***********************99999999999999777765433 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.2e-06    0.0047      15      84 ..       4      76 ..       1     100 [. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.2e-06
                                      EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E..T-EEEEGCGH..HHHHHT-SEEEE-SS CS
                      Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge..eiealkleel..kellaeadvvisata 84
                                      +l+ G+G +++ +a  L+ +g++ v++  R le+ak++aee++++  +i+  ++  l  +++ +e+++ i a+ 
  gi|488599972|ref|YP_007906443.1|  4 ALIGGTGHLGRGLAIRLAMNGYD-VIIGSRGLEKAKRVAEEYNSVlhKISSARVRGLanEDAAEECEIAIFAIP 76
                                      455589****************9.******************87711233333333311345556666666655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   6.7e-06      0.01       3      47 ..       3      47 ..       2      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.7e-06
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee 47
                                      +  +G+++ +Gr +a +la +G++v++ +r  ek+++va+e ++ 
  gi|488599972|ref|YP_007906443.1|  3 IALIGGTGHLGRGLAIRLAMNGYDVIIGSRGLEKAKRVAEEYNSV 47
                                      456799999*******************************99875 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05     0.015       1     101 [.       2      98 ..       2     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                                       -EEEE-.-SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE- CS
                    NAD_Gly3P_dh_N   1 kiavlG.aGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlv 76 
                                       kia++G +G  G  lA+ la ng +v + +r  e ++++ ee + v  L +i  ++ ++     ++a+++++i +++
  gi|488599972|ref|YP_007906443.1|   2 KIALIGgTGHLGRGLAIRLAMNGYDVIIGSRGLEKAKRVAEEYNSV--LHKI-SSARVRGL-ANEDAAEECEIAIFA 74 
                                       68888627***********************999999998765544..5543.34455544.4578889999***** PP

                                       --HHHHHHHHHHHCCC--TT-EEEE CS
                    NAD_Gly3P_dh_N  77 vPsqalrevlkklkgllkkkailvs 101
                                       +P  +  ++++kl g+lk k i++s
  gi|488599972|ref|YP_007906443.1|  75 IPWRHAFSTAEKLRGKLKGK-IVIS 98 
                                       ***************99654.4444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.16       2      96 ..       5      95 ..       4     101 .. 0.72
   2 ?    1.6   0.0      0.13     2e+02      83     103 ..     119     139 ..     114     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGG CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKay 79
                                      +i G+G +G+ la +La +g+dv++  r+  +++++ ++  ++  +  +  +r++  ++++    +e++++ i++++  
  gi|488599972|ref|YP_007906443.1|  5 LIGGTGHLGRGLAIRLAMNGYDVIIGSRGLeKAKRVAEEYNSVLHKISS--ARVRGLANED---AAEECEIAIFAIPWR 78
                                      588*************************998888855554444333333..3444444444...558888888888888 PP

                                      GHHHHHHHHGGGECTCE CS
                              ApbA 80 qteealeeikplldpnt 96
                                      ++ + +e+++  l+ + 
  gi|488599972|ref|YP_007906443.1| 79 HAFSTAEKLRGKLKGKI 95
                                      88888888888887764 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                                       HHHHHHGGGECTCEEEEEESS CS
                              ApbA  83 ealeeikplldpntvvlllqN 103
                                       +a+++++++l++ tv++ + N
  gi|488599972|ref|YP_007906443.1| 119 SAAQKLASILKDSTVICAFNN 139
                                       78999************9998 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.2e-05      0.12       1      49 [.       3      49 ..       3      72 .. 0.82
   2 ?   -3.5   0.0       7.6   1.1e+04      69      87 ..      92     111 ..      84     112 .. 0.74
   3 ?   -3.5   0.0       7.6   1.1e+04      19      41 ..     150     170 ..     146     176 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.2e-05
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCE CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrf 49
                                      + +iG+ G  G+++a  la ++ +  ++++ +r +ek++++a++ ++v +
  gi|488599972|ref|YP_007906443.1|  3 IALIGGtGHLGRGLAIRLAMNG-Y--DVIIGSRGLEKAKRVAEEYNSVLH 49
                                      5689999*************98.5..7**************998755433 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.6
                                       TSSEEEE-SSGG.GHHHHHH CS
                   Sacchrp_dh_NADP  69 egdlvvnlsppi.ssldvlk 87 
                                       +g++v++ ++p+  + dv++
  gi|488599972|ref|YP_007906443.1|  92 KGKIVISPLVPMeKDGDVMR 111
                                       45788888888866777776 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 7.6
                                       CTCCT-GEEEEEESSHHHHHHHH CS
                   Sacchrp_dh_NADP  19 rhfdvdaeitvadrskekleala 41 
                                        +fd+   ++v++ +++  ++++
  gi|488599972|ref|YP_007906443.1| 150 SKFDW--SVAVCGDDDDAKKKVI 170
                                       45555..7777777777766665 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   9.6e-05      0.14       1      64 [.       2      66 ..       2      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.6e-05
                            LpxI_N  1 kigliAGsGrlPllvaeaakaagrevvvvalegeadeelekivd.evaevsvgqlgklikaLkre 64
                                      ki+li G G+l   +a ++  +g++v++ +   e  ++++++ +   +++s +++  l +    e
  gi|488599972|ref|YP_007906443.1|  2 KIALIGGTGHLGRGLAIRLAMNGYDVIIGSRGLEKAKRVAEEYNsVLHKISSARVRGLANEDAAE 66
                                      79************************998877666666666555477888888888777665555 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 ?   10.8   0.1   0.00019      0.28       6      55 ..       2      52 ..       1      97 [. 0.78
   2 ?   -2.4   0.0       2.1   3.1e+03      13      29 ..     118     134 ..     111     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                      -EEEE.S-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHH CS
                              IlvN  6 kiavi.GyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltva 55
                                      kia+i G G  G+  a  l  +g dv++g r  +k  + A+e +   ++++
  gi|488599972|ref|YP_007906443.1|  2 KIALIgGTGHLGRGLAIRLAMNGYDVIIGSRGLEKAKRVAEEYNSVLHKIS 52
                                      78988358**********************999988888877665444443 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.1
                                       SHHHHHHHHHHHHTT-- CS
                              IlvN  13 GsqGhaqalnlrdsgld 29 
                                       Gs ++  a  l+ds + 
  gi|488599972|ref|YP_007906443.1| 118 GSAAQKLASILKDSTVI 134
                                       77777888888888764 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00016      0.23       2      40 ..       4      42 ..       3      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHC CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarl 40
                                       ++G+tG +G+ l+ +l+ +gy+vi  +r  ++ ++ ++
  gi|488599972|ref|YP_007906443.1|  4 ALIGGTGHLGRGLAIRLAMNGYDVIIGSRGLEKAKRVAE 42
                                      679********************9888887555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1565.20
//
Query:       gi|488599973|ref|YP_007906444.1|  [L=458]
Description: Malic enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-32  112.2   0.0    4.6e-30  104.8   0.0    2.4  1  malic     Malic enzyme, N-terminal domain
    8.5e-21   74.4   0.3    1.3e-18   67.2   0.3    2.2  1  Malic_M   Malic enzyme, NAD binding domain


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.0   5.1e-34   4.6e-30       3     182 .]      29     160 ..      27     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 5.1e-34
                                       TECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBT CS
                             malic   3 knetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriL 79 
                                       k+e++++  +++    +++++YtP+v+++c e++e+++k++ +y+++ ++                v++vtdg+r+L
  gi|488599973|ref|YP_007906444.1|  29 KIEIVPKCAIRDL--GDFSVWYTPGVAKPCLEIAEDPEKVY-DYTNKWNT----------------VAIVTDGTRVL 86 
                                       6677777777777..899***********************.********................*********** PP

                                       TTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHHH CS
                             malic  80 GlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveavk 155
                                       GlGd+G  a++++m+GK+ L++ l+g+d   ++p+vld +                           + d+f+e+vk
  gi|488599973|ref|YP_007906444.1|  87 GLGDIGpKAALPVMEGKALLFKYLGGVD---AIPIVLDEK---------------------------DPDRFIEVVK 133
                                       ****************************...*********...........................99******** PP

                                       HHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 156 elfppkaliqfEDfkaknafeileryr 182
                                       ++ p++++i++ED++++++f+il+r+r
  gi|488599973|ref|YP_007906444.1| 134 AISPTFGGINLEDISKPKCFYILDRLR 160
                                       *************************97 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.3   1.5e-22   1.3e-18       2     251 ..     173     398 ..     172     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.5e-22
                                       HHHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S-- CS
                           Malic_M   2 qgTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekl 78 
                                       qgTa+ +la+ l+alk+ gkklse  i v+G G+a +  + +    l+k+G+      kki++vD+kG+l+ +r+++
  gi|488599973|ref|YP_007906444.1| 173 QGTATATLAATLGALKVVGKKLSEVYISVIGVGAANVAAVRL----LIKAGAD----PKKIFIVDSKGILHPNRKDI 241
                                       9**********************************9865555....5556644....589***************** PP

                                       -..TTTGGGS.BS--SS--S....SHHHHHHHH--SEEEE-SS.SSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSS CS
                           Malic_M  79 e..eekkpfa.kkkeelkeakdkltLeevvkkvkptvliGlsg.vagafteeivremaksterPiilplSNPtskaE 151
                                       e  + k p+  +   e++    +  ++e+++    +vli +s   +g++++e v++m +     i++   NP  +  
  gi|488599973|ref|YP_007906444.1| 242 EagKDKDPYKwRYCLETNGEGREGGMAEAIEG--TDVLIAASKpGPGVIRKEWVEKMND---DAIVFLEANPIPE-- 311
                                       6324566776234456666668899*****97..68****9972579********9975...67********975.. PP

                                       S-HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HH CS
                           Malic_M 152 ataedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvsee 228
                                         + ++ +   g+ +v +G          +   ++Q NN+++fP++  gv+ +ra++itdem  +aa+al  +++++
  gi|488599973|ref|YP_007906444.1| 312 MWPWEAKE--AGARIVGTG----------RSDFPNQVNNSLVFPAVFRGVLEVRARTITDEMAIEAAKALVAYAERK 376
                                       56666554..577788887..........56679******************************************* PP

                                       HHHTT-SS--GGGHHHHHHHHHH CS
                           Malic_M 229 elkegsllPelseirevslkvav 251
                                        l+e+ + P++se  +v  +va+
  gi|488599973|ref|YP_007906444.1| 377 GLSEDYVIPKMSEP-DVFPEVAT 398
                                       **********9973.33334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3271.97
//
Query:       gi|488599974|ref|YP_007906445.1|  [L=184]
Description: hypothetical protein Asulf_00425 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-07   28.8   0.1    1.3e-06   28.1   0.1    1.4  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.11   12.4   0.8       0.27   11.2   0.8    1.6  1  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   1.5e-10   1.3e-06       1      37 [.       7      43 ..       7      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.5e-10
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                      rvs+ ld+++ e L+ l+r+ + ++Se+IR+A+  y 
  gi|488599974|ref|YP_007906445.1|  7 RVSVALDKKTEEMLNILVRKKNTTVSEIIRRAINTYF 43
                                      9********************************9985 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8     3e-05      0.27       3      41 ..       6      44 ..       4      44 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                             RHH_3  3 trttvsidpelaekLkaLSekTrIprSklldeAiellLe 41
                                      tr++v++d++  e+L+ L +k    +S++++ Ai  ++e
  gi|488599974|ref|YP_007906445.1|  6 TRVSVALDKKTEEMLNILVRKKNTTVSEIIRRAINTYFE 44
                                      79********************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1128.22
//
Query:       gi|488599975|ref|YP_007906446.1|  [L=197]
Description: imidazole glycerol phosphate synthase subunit hisH [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-23   83.1   0.0    2.3e-23   83.0   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.3e-09   38.2   0.0    4.3e-09   36.5   0.0    1.7  1  SNO            SNO glutamine amidotransferase family
    9.4e-06   25.5   0.2    8.1e-05   22.5   0.1    2.3  2  Peptidase_C26  Peptidase C26
     0.0048   16.0   0.0       0.01   14.9   0.0    1.6  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
      0.062   12.9   0.0      0.083   12.5   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 !   83.0   0.0   6.4e-27   2.3e-23       2     187 ..       4     192 ..       3     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 6.4e-27
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikearenkiPiLG 76 
                                       ++D++ ++ +++++al  +g+k+++ + d   +e    lkn  gi++ +G+g++   +e+  e+ +++ + ++P+LG
  gi|488599975|ref|YP_007906446.1|   4 IVDYGVGNLKSIKKALEMVGAKTKITR-D---LED---LKNSSGIVL-PGVGAVRpaMEKLKELKEFIKSTDVPVLG 72 
                                       79***********************99.3...455...456788776.5677666647777777778888******* PP

                                       ETHHHHHHHHHTTT..EEE...............EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGC CS
                            GATase  77 ICLGmQllaiefgr..kvv...............kekekehhggtmrlgddetallyglknevierhrHryevnpke 136
                                       ICLGmQl a  + +  +v+                 k  +h+g+++    ++++ll+g ++    ++ H+y ++   
  gi|488599975|ref|YP_007906446.1|  73 ICLGMQLFATLSYEggEVEclniipgvvrkfqddVGK-IPHMGWNQIEIVKDNELLHGIESGTFFYFVHSYFLET-- 146
                                       ******9876543335454555557777899995555.9******98888899*********************7.. PP

                                       HHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 137 lepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                         ++ ++ t ++  + +++ ++ k+n ++gvQFHPE++    g +ll+nf+
  gi|488599975|ref|YP_007906446.1| 147 --EKSFILTETD-YGISFASAVSKDN-YYGVQFHPEKSGD-DGIKLLENFY 192
                                       ..6778887777.6779999999999.*********8655.5588888885 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.2e-12   4.3e-09       6     186 ..      10     195 ..       9     197 .] 0.79

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.2e-12
                                       SSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHC CS
                               SNO   6 GaveehveaikkclaenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlills 82 
                                       G+++   +a++ ++a++k  ++ edl++  ++++PG    a++  +e+ +   +l+ef+k ++ +vlG C G+ l++
  gi|488599975|ref|YP_007906446.1|  10 GNLKSIKKALEMVGAKTKITRDLEDLKNSSGIVLPGV--GAVRPAMEKLK---ELKEFIKSTDVPVLGICLGMQLFA 81 
                                       56666778999999**********************5..57888899887...9*******************8887 PP

                                       C.EETTBSS-SS--CCEEEET..TTT-SCCGEEEEEEEETTTC...SEE.EEEESS--EEEEE-.TTTCEEEEECT. CS
                               SNO  83 k.elenelvktlellkvkvkr..nafGrqvdsfekeldfknli...ekf.tavfiraPvieeilddeavkvlyeld. 151
                                           e+ +v+ l+++  +v++  +  G+  +   +++++ + +   + +  ++f    v    l+ e+  +l+e+d 
  gi|488599975|ref|YP_007906446.1|  82 TlSYEGGEVECLNIIPGVVRKfqDDVGKIPHMGWNQIEIVKDNellHGIeSGTFFYF-VHSYFLETEKSFILTETDy 157
                                       5144555********999986336799998888888887544413333315677764.557789999*********8 PP

                                       T.EEEEEE.ETTEEEESS-GGGS.TTHCHHHHHHHHHH CS
                               SNO 152 g.eivvak.qkkilatsfhPela.eddirvhdyfveev 186
                                       g +  +a  ++++ ++ fhPe + +d+i++ + f + +
  gi|488599975|ref|YP_007906446.1| 158 GiSFASAVsKDNYYGVQFHPEKSgDDGIKLLENFYRIC 195
                                       76666666466**********98356789998887765 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.4   1.4e+03      56      76 ..      35      55 ..      24      66 .. 0.81
   2 !   22.5   0.1   2.2e-08   8.1e-05     102     216 .]      64     178 ..      53     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.4
                     Peptidase_C26 56 ldkldgllltGgqdvePslyg 76
                                      l++  g++l+G   v+P++ +
  gi|488599975|ref|YP_007906446.1| 35 LKNSSGIVLPGVGAVRPAMEK 55
                                      5677899****9999998765 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.2e-08
                     Peptidase_C26 102 lergvPilgiCrGlqllnva.lGGtlyqdieeqsgltdhreheq....saashavkvekgsllaellgseeievnsl 173
                                        + +vP+lgiC+G+ql++   + G  ++ ++ ++g+++  +++          +++++k+  l + ++ + +    +
  gi|488599975|ref|YP_007906446.1|  64 KSTDVPVLGICLGMQLFATLsYEGGEVECLNIIPGVVRKFQDDVgkipHMGWNQIEIVKDNELLHGIE-SGTFFYFV 139
                                       4679************9864244555566777788887777773345567788999999988888777.55556677 PP

                     Peptidase_C26 174 HhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       H+  ++  ++++  +   +D  i + ++ +++  ++gvQ+HPE
  gi|488599975|ref|YP_007906446.1| 140 HSYFLE-TEKSFILT--ETDYGISFASAVSKD-NYYGVQFHPE 178
                                       887765.45666554..557777777777755.89*******9 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 !   14.9   0.0   2.9e-06      0.01      79     108 ..      56      85 ..       4     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
                          GATase_5  79 realekflnredtlaLGiCnGfqlLvklgl 108
                                        ++l++f++++d  +LGiC G+ql++ l +
  gi|488599975|ref|YP_007906446.1|  56 LKELKEFIKSTDVPVLGICLGMQLFATLSY 85 
                                       5799*********************99875 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.3e-05     0.083      33      90 ..      31      82 ..       3     110 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                          GATase_3 33 kdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGe 90
                                        e+l ++   ++lpG   ++ +++ l+e  l+e ik+   +++pvlgiC G+q++ +
  gi|488599975|ref|YP_007906446.1| 31 DLEDL-KNSSGIVLPGVGAVRPAMEKLKE--LKEFIKS---TDVPVLGICLGMQLFAT 82
                                      33445.44788888888888777666655..6666666...79***********9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 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:                        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: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1147.16
//
Query:       gi|488599976|ref|YP_007906447.1|  [L=241]
Description: RNA methyltransferase, TrmH family, group 1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-30  104.5   0.0    9.1e-30  103.7   0.0    1.3  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0   5.1e-34   9.1e-30       4     142 .]       5     153 ..       3     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 5.1e-34
                                       EEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEE CS
                    SpoU_methylase   4 vvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalv 79 
                                       v lve+++p+N+G +aR++k+fg+++lvl +  ++   ++e + +a++a++vle + +v++le++l+e   + + ++
  gi|488599976|ref|YP_007906447.1|   5 VCLVELKTPENIGFVARVMKNFGFKNLVLYN--CN--VSDESYITASHAKDVLEnALIVENLEDYLSEKSLV-VGTT 76 
                                       89***************************88..54..58999999***********************9999.5554 PP

                                       EEST..T-SEGCCS..HHH...........TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS
                    SpoU_methylase  80 atsl..kgkslsei..dlk...........ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141
                                       ++++  +++ l++     +            ++ ++fG+Ed Gl ne+++l+d lv++p+s+e++ +Nv++Ava+ll
  gi|488599976|ref|YP_007906447.1|  77 GITTlsDETYLRKPvfY-PdelsehlkgkaPSISILFGREDYGLYNEEIKLCDVLVSVPTSPEYPVMNVSHAVAVLL 152
                                       44443244444433330.234445577888999*******************************************9 PP

                                       H CS
                    SpoU_methylase 142 y 142
                                       y
  gi|488599976|ref|YP_007906447.1| 153 Y 153
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 1815.70
//
Query:       gi|488599977|ref|YP_007906448.1|  [L=336]
Description: putative permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-56  191.9  42.1    1.9e-56  191.6  42.1    1.0  1  AI-2E_transport  AI-2E family transporter
  ------ inclusion threshold ------
        0.2   11.6   0.2        0.4   10.6   0.2    1.4  1  GA-like          GA-like domain


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 !  191.6  42.1   2.1e-60   1.9e-56       3     326 ..      15     334 ..      12     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 191.6 bits;  conditional E-value: 2.1e-60
                   AI-2E_transport   3 lilvllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaql 79 
                                       l++ +++ l ++++f+s+ll  +l+++ ++y+++p++k+L  +++++ ++ l+ +l++lv + +l+++ + + i q+
  gi|488599977|ref|YP_007906448.1|  15 LFIGIVATLSLMVYFFSPLLDGILMGVAFSYVAKPIKKKL-DTKMNKNVSSLIATLIILVPVSILLFYGIFQGIMQA 90 
                                       566677778888888888**********************.77888888888888888888888888888899**** PP

                   AI-2E_transport  80 tqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssi.lnsllsllasllglilslvlvllllf 155
                                       ++++++ + ++d++ +il++    l e +  i+++++ + +ils i ++i  +s+++l+ ++++++++++++++++f
  gi|488599977|ref|YP_007906448.1|  91 ANIITHQKEFQDQIIDILKDSG--LSEYY--IKQIESFIPNILSFISKNIlQMSAIDLTFKIISFVMNFFISMVVCF 163
                                       *******************988..44444..68*****************556789********************* PP

                   AI-2E_transport 156 fllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglan 232
                                       + l+dg+++ ++ l+++p+++r+++ ++++e+++++ g++ g++ va++ig++++ ++l++++py  ll+ l++la+
  gi|488599977|ref|YP_007906448.1| 164 YALADGDTFIKKSLRIIPDEYRTKFGNFIEEVDNVFLGLWFGNFAVAVLIGIASIPFFLAFNIPYTALLSGLIFLAA 240
                                       ***************************************************************************** PP

                   AI-2E_transport 233 liPyiGavivlipiaiialltggikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGl 309
                                       liP++  ++vlip+ i+++l    +++++++++++++ ++ + il+P+l++ + ++hpl+ills+++gg+++G+ G+
  gi|488599977|ref|YP_007906448.1| 241 LIPVFAEWMVLIPVTIYIALQSVHAAIWFIVLGAIFLYILPELILRPYLLSYTSRIHPLIILLSFIGGGMVAGVTGF 317
                                       ***************************************************************************** PP

                   AI-2E_transport 310 ilavpltavikaileay 326
                                       +la++++++++ai++ y
  gi|488599977|ref|YP_007906448.1| 318 FLAPMIAGLVTAIYNIY 334
                                       *************9987 PP

>> GA-like  GA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   4.5e-05       0.4       9      35 ..      98     123 ..      96     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.5e-05
                           GA-like   9 keAKeaAkaeLkaaGitsdfyiekIdk 35 
                                       ke +++ ++ Lk+ G  s++yi++I++
  gi|488599977|ref|YP_007906448.1|  98 KEFQDQIIDILKDSGL-SEYYIKQIES 123
                                       6778999*********.********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1404  (0.0783089); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 2285.45
//
Query:       gi|488599978|ref|YP_007906449.1|  [L=250]
Description: phosphate ABC transporter ATP-binding protein, PhoT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-33  113.7   0.0    1.1e-32  113.4   0.0    1.1  1  ABC_tran      ABC transporter
    1.7e-15   57.7   0.0    3.8e-09   36.8   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.7e-09   36.8   0.0    7.1e-09   35.4   0.0    1.6  1  SMC_N         RecF/RecN/SMC N terminal domain
    5.2e-08   33.0   0.0     0.0065   16.2   0.0    2.1  2  AAA_15        AAA ATPase domain
    1.5e-05   25.6   0.0    2.4e-05   24.9   0.0    1.4  1  AAA_23        AAA domain
    0.00018   21.2   0.0    0.00034   20.3   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0003   20.8   0.0    0.00057   19.9   0.0    1.4  1  Rad17         Rad17 P-loop domain
    0.00031   21.0   0.0    0.00091   19.5   0.0    2.0  1  AAA_22        AAA domain
     0.0005   20.0   0.0     0.0012   18.7   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
    0.00058   20.3   0.0     0.0023   18.3   0.0    1.9  1  AAA_16        AAA ATPase domain
     0.0031   18.1   0.1     0.0053   17.3   0.1    1.7  1  AAA_18        AAA domain
     0.0032   17.9   0.0      0.034   14.6   0.0    2.2  1  AAA           ATPase family associated with various cellular 
     0.0042   16.9   0.0     0.0074   16.0   0.0    1.5  1  PRK           Phosphoribulokinase / Uridine kinase family
     0.0049   16.6   0.0     0.0098   15.6   0.0    1.5  1  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.047   13.4   0.0    1.7  2  AAA_30        AAA domain
      0.014   15.0   0.1      0.078   12.5   0.1    2.3  1  AAA_25        AAA domain
      0.018   15.2   0.0      0.025   14.8   0.0    1.5  1  AAA_33        AAA domain
      0.018   15.0   0.0      0.044   13.7   0.0    1.6  2  NACHT         NACHT domain
       0.02   14.8   0.2      0.051   13.5   0.1    2.0  1  ATPase_2      ATPase domain predominantly from Archaea
      0.031   13.1   0.0      0.047   12.5   0.0    1.2  1  PPV_E1_C      Papillomavirus helicase
      0.049   12.4   0.0       0.46    9.2   0.0    2.0  2  ABC_ATPase    Predicted ATPase of the ABC class
       0.05   14.0   0.0       0.13   12.6   0.0    1.8  1  RNA_helicase  RNA helicase
      0.053   13.1   0.0        0.1   12.2   0.0    1.3  1  AAA_27        AAA domain
      0.059   12.3   0.0        0.1   11.5   0.0    1.4  1  AAA_PrkA      PrkA AAA domain
      0.062   13.5   0.0       0.12   12.6   0.0    1.5  1  AAA_28        AAA domain
      0.067   12.3   0.0      0.073   12.2   0.0    1.1  1  G-alpha       G-protein alpha subunit
      0.072   13.2   0.0       0.18   11.9   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
      0.098   12.7   0.0       0.31   11.0   0.0    1.9  1  AAA_5         AAA domain (dynein-related subfamily)
        0.1   12.6   0.0       0.18   11.9   0.0    1.8  1  AAA_14        AAA domain
       0.13   12.0   0.0       0.28   10.9   0.0    1.5  1  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.14   11.3   0.0       0.77    8.9   0.0    1.8  2  NB-ARC        NB-ARC domain
       0.14   11.5   0.0       0.42    9.9   0.0    1.7  2  ATPase        KaiC


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.0     2e-35   1.1e-32       2     137 .]      20     175 ..      19     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 2e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqepqlfpe 73 
                                       k+++lk+ e ++ ai+G++G+GKSt+l++l +ll+       +G+i+l gk++ e +  ++rk+ig+++q+ + fp+
  gi|488599978|ref|YP_007906449.1|  20 KEINLKIPEKRVFAIMGPSGCGKSTFLRALNRLLELnesarVKGDIRLYGKSIFEMNPVEVRKRIGMVFQQVNPFPH 96 
                                       799*****************************99987888899********************************** PP

                                       SBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       l+v +n               e  e+++ al+k  l +  +++++  ++sLSgGq+qr+++aral+ kp+++l+DEp
  gi|488599978|ref|YP_007906449.1|  97 LSVFDNvaiglrlnrvlkskkEIMERVKWALKKSALWDEVKDRLEAPATSLSGGQQQRLCIARALALKPEVILMDEP 173
                                       ****************9777777777******************9999***************************** PP

                                       TT CS
                                       xx RF
                          ABC_tran 136 ta 137
                                       ta
  gi|488599978|ref|YP_007906449.1| 174 TA 175
                                       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 !   19.3   0.0   1.5e-06   0.00082       2      54 ..      32      77 ..      31     119 .. 0.84
   2 !   36.8   0.0   6.7e-12   3.8e-09     222     300 ..     132     206 ..      91     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydp 54
                                       ++ Gp g+GKS++L+al  l         l+ +++ +g+ir + +++++ +p
  gi|488599978|ref|YP_007906449.1| 32 FAIMGPSGCGKSTFLRALNRLL-------ELNESARVKGDIRLYGKSIFEMNP 77
                                      6899****************95.......678888888888888877776655 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 6.7e-12
                            AAA_21 222 vflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        + e +d+ e pa++lS G+++ l+++ al+  +    ++l DEp ++L+P +++++ +l+ el+r +  ++++THS
  gi|488599978|ref|YP_007906449.1| 132 LWDEVKDRLEAPATSLSGGQQQRLCIARALALKP---EVILMDEPTANLDPVATEKIEDLIYELKR-DYTIVIVTHS 204
                                       5667899****************99999998877...9**************************99.********** PP

                            AAA_21 299 pl 300
                                       p+
  gi|488599978|ref|YP_007906449.1| 205 PS 206
                                       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 !   35.4   0.0   1.3e-11   7.1e-09      23     207 ..      28     213 ..       7     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.3e-11
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHC..CCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrsek..lsdlihkskekasvkkaeveitfdnedkk.lkiekee 96 
                                       +k++ ai+Gp G+GKs +l A+  +L  +++  ++ +   + + i+  + ++   + ++ ++f++ +        ++
  gi|488599978|ref|YP_007906449.1|  28 EKRVFAIMGPSGCGKSTFLRALNRLLELNESARVKGDIrlYGKSIF--EMNPVEVRKRIGMVFQQVNPFpHLSVFDN 102
                                       577899*********************9888777765411345555..4788888889*****99998842333456 PP

                                       EEEEEEEETTSEEEEEETTE...EE-HHHHHHHHHC.TT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTT CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingk...evtkkevselles.agiskelLSgGektLvalaLlfAiqkvkpaplyllDeida 169
                                       v i  r+ r  +s+ +i ++     +k+ + + +++  +   ++LSgG+++ + +a  +A++   p+ + l+De  a
  gi|488599978|ref|YP_007906449.1| 103 VAIGLRLNRVLKSKKEIMERvkwALKKSALWDEVKDrLEAPATSLSGGQQQRLCIARALALK---PE-VILMDEPTA 175
                                       66666666666666555333111223333333333212334569*******99999998875...55.679****** PP

                                       TS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 170 aLDeknvkkvaellkeksknaQfivislreemlekadk 207
                                       +LD   ++k+ +l+ e + +  +++++++  + ++++ 
  gi|488599978|ref|YP_007906449.1| 176 NLDPVATEKIEDLIYELKRDYTIVIVTHSPSQAARVSD 213
                                       ****************************9988776654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05    0.0065      16      54 ..      21      60 ..      16     122 .. 0.73
   2 !   15.0   0.0   2.7e-05     0.015     284     366 ..     134     205 ..      97     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn 54
                                      ++ +++ e+ +  + G+ ++GKS++l+al+ +l+ +e+  
  gi|488599978|ref|YP_007906449.1| 21 EINLKIPEKrVFAIMGPSGCGKSTFLRALNRLLELNESAR 60
                                      5445554557999********************9886554 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.7e-05
                            AAA_15 284 ieikddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360
                                       +e+kd  e p++  + G+q+ l ++  ++ + +         ++l++EP a+L p a + + +l++el +d    ++
  gi|488599978|ref|YP_007906449.1| 134 DEVKDRLEAPATSLSGGQQQRLCIARALALKPE---------VILMDEPTANLDPVATEKIEDLIYELKRDYT--IV 199
                                       344499999999999999999999877766555.........5*****************************6..** PP

                            AAA_15 361 itTHSp 366
                                       i THSp
  gi|488599978|ref|YP_007906449.1| 200 IVTHSP 205
                                       *****9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.3e-08   2.4e-05      13      52 ..      20      63 ..       4     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.3e-08
                            AAA_23 13 qeidF...skgltlItGpNGaGKTTildAiklaL.ygetprlsr 52
                                      +ei++   +k +++I Gp G+GK+T+l+A+   L  +e++r ++
  gi|488599978|ref|YP_007906449.1| 20 KEINLkipEKRVFAIMGPSGCGKSTFLRALNRLLeLNESARVKG 63
                                      568889999*********************98885555555544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     6e-07   0.00034      17      47 ..      24      54 ..      16      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                      ++i +k ++ ++GpsG GKST+l A++ lL 
  gi|488599978|ref|YP_007906449.1| 24 LKIPEKRVFAIMGPSGCGKSTFLRALNRLLE 54
                                      567666799*****************99985 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     1e-06   0.00057      40      70 ..      24      54 ..      15      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-06
                             Rad17 40 LesrkkriLLisGPsGCgkstvvkvLskelg 70
                                      L+  +kr+  i GPsGCgkst ++ L + l 
  gi|488599978|ref|YP_007906449.1| 24 LKIPEKRVFAIMGPSGCGKSTFLRALNRLLE 54
                                      5566789******************998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.6e-06   0.00091       5      37 ..      29      61 ..      26     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee 37
                                      +++ +++G+sG+GK+t lr l + l+  ++a+ 
  gi|488599978|ref|YP_007906449.1| 29 KRVFAIMGPSGCGKSTFLRALNRLLELNESARV 61
                                      67899******************9976665554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.2e-06    0.0012      86     123 ..      15      53 ..       2      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                       +++ ++e++ ++ + ++ +++G+SG GKSt++ al+  l
  gi|488599978|ref|YP_007906449.1|  15 SSHVIKEINLKIPEkRVFAIMGPSGCGKSTFLRALNRLL 53 
                                       556788888888776999**************9998654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.1e-06    0.0023      23      61 ..      28      66 ..      18     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.1e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgkcd 61
                                      + ++  + G+sG+GKs+ +r+l r le ++   ++g+ +
  gi|488599978|ref|YP_007906449.1| 28 EKRVFAIMGPSGCGKSTFLRALNRLLELNESARVKGDIR 66
                                      457889*****************9777664333333333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   9.5e-06    0.0053       3      25 ..      34      62 ..      33     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.5e-06
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf......g 25
                                      ++G++G+GK+t+ ++L+++l++       
  gi|488599978|ref|YP_007906449.1| 34 IMGPSGCGKSTFLRALNRLLELnesarvK 62
                                      89**************9998555553330 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 !   14.6   0.0   6.1e-05     0.034       3      54 ..      34      92 ..      32     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.1e-05
                                      EESSTTSSHHHHHHHHHHHHTHE.......EEEEETTTCSSSSTTHHHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgve.......fleisgsellskyvgesekkirelfkeak 54
                                      ++Gp G+GK+++ +a+ + l+ +        +++ g++++++   e  k+i ++f+++ 
  gi|488599978|ref|YP_007906449.1| 34 IMGPSGCGKSTFLRALNRLLELNesarvkgDIRLYGKSIFEMNPVEVRKRIGMVFQQVN 92
                                      68***************998533333344436666666666666666677777777653 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-05    0.0074       1      36 [.      31      64 ..      31     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegd 36
                                      v ++ g+SG+Gk+t+ r+l+ +++ ++   a ++gd
  gi|488599978|ref|YP_007906449.1| 31 VFAIMGPSGCGKSTFLRALNRLLELNES--ARVKGD 64
                                      5689*****************9994443..344333 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   1.7e-05    0.0098       2      30 ..      29      56 ..      28      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                            AAA_24  2 klkiliyGpsgiGKTtlakelgpkplfid 30
                                      k+ ++i+Gpsg GK+t+++ l ++ l ++
  gi|488599978|ref|YP_007906449.1| 29 KRVFAIMGPSGCGKSTFLRAL-NRLLELN 56
                                      67899****************.9998875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.3e-05     0.047      18      45 ..      29      56 ..      23      68 .. 0.85
   2 ?   -0.9   0.0         2   1.1e+03      90     129 ..     166     209 ..     113     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.3e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                      +rv ++ Gp G GK+t l+al++++e +
  gi|488599978|ref|YP_007906449.1| 29 KRVFAIMGPSGCGKSTFLRALNRLLELN 56
                                      67999****************9999865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                            AAA_30  90 tllivDEagmv....dtkqlaallkaaekagakvilvGDerQla 129
                                       ++++ DE        +t+++++l+ +++++ + vi+   + Q a
  gi|488599978|ref|YP_007906449.1| 166 EVILMDEPTANldpvATEKIEDLIYELKRDYTIVIVTHSPSQAA 209
                                       55556664443333366666666666666445555544455544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00014     0.078      30      52 ..      26      48 ..      17     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                            AAA_25 30 lpagelallaGapgtGKttlald 52
                                      +p++ + +++G++g+GK+t++  
  gi|488599978|ref|YP_007906449.1| 26 IPEKRVFAIMGPSGCGKSTFLRA 48
                                      899****************9855 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.4e-05     0.025       2      33 ..      32      80 ..      31     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.4e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg...avllssdt..............l 33
                                      + + G++G+GKst+++ l + l      ++  d+              +
  gi|488599978|ref|YP_007906449.1| 32 FAIMGPSGCGKSTFLRALNRLLElneSARVKGDIrlygksifemnpveV 80
                                      5678************985544444577777777666666666666651 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.8e-05     0.044       1      26 [.      30      55 ..      30      68 .. 0.84
   2 ?   -2.3   0.0       6.5   3.7e+03     109     136 ..     185     212 ..     170     245 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-05
                                      SCEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalawae 26
                                      r+ ++ G++G+GK+t+l+ l +++  
  gi|488599978|ref|YP_007906449.1| 30 RVFAIMGPSGCGKSTFLRALNRLLEL 55
                                      67899*************99888765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.5
                                       HHHHHCTTTTT--EEEEEEECCCHHHHC CS
                             NACHT 109 Lselirkkllpeasllltvrpralrdle 136
                                       +++li +     + +++t +p++  ++ 
  gi|488599978|ref|YP_007906449.1| 185 IEDLIYELKRDYTIVIVTHSPSQAARVS 212
                                       4445544333345555555555554444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.1e-05     0.051      20      49 ..      29      57 ..      17     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-05
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdk 49
                                      +++  i Gp g+GK+++l+ +   l ++++
  gi|488599978|ref|YP_007906449.1| 29 KRVFAIMGPSGCGKSTFLRALNRLL-ELNE 57
                                      67889*************9765444.4443 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.4e-05     0.047     253     287 ..      20      54 ..      14      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                          PPV_E1_C 253 kefLkgvPkknclvllGppntGkslfamslikfLk 287
                                       ke   ++P k ++ ++Gp+  Gks+f  +l+++L+
  gi|488599978|ref|YP_007906449.1|  20 KEINLKIPEKRVFAIMGPSGCGKSTFLRALNRLLE 54 
                                       6666689*************************996 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 ?    9.2   0.0   0.00082      0.46     240     266 ..      24      51 ..       8      64 .. 0.90
   2 ?    0.9   0.0      0.27   1.5e+02     324     351 ..     148     175 ..     137     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00082
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlek 266
                                       + ip++ v++I+G+   GKsT L+Al++
  gi|488599978|ref|YP_007906449.1|  24 LKIPEKrVFAIMGPSGCGKSTFLRALNR 51 
                                       5688888******************985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts 351
                                       SG   q   i++al ++ +++L+DE t+
  gi|488599978|ref|YP_007906449.1| 148 SGGQQQRLCIARALALKPEVILMDEPTA 175
                                       899999999****************876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00024      0.13       3      23 ..      34      54 ..      32      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00024
                      RNA_helicase  3 lyGpsgeGKStlakeLakall 23
                                      + Gpsg+GKSt+ + L + l+
  gi|488599978|ref|YP_007906449.1| 34 IMGPSGCGKSTFLRALNRLLE 54
                                      79************9766554 PP

>> AAA_27  AAA 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      19      50 ..      22      53 ..      18      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      ++++  e+++  i+Gp   GKst lrA+++ll
  gi|488599978|ref|YP_007906449.1| 22 INLKIPEKRVFAIMGPSGCGKSTFLRALNRLL 53
                                      566666899999*****************997 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018       0.1      87     115 ..      28      56 ..       6      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                          AAA_PrkA  87 rkqilyllGPvggGksslverlkklleaa 115
                                       +k+++ ++GP g Gks++  +l +lle +
  gi|488599978|ref|YP_007906449.1|  28 EKRVFAIMGPSGCGKSTFLRALNRLLELN 56 
                                       699***********************976 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   0.00022      0.12       2      21 ..      32      51 ..      31      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      ++i+G++++GK+t l+aL++
  gi|488599978|ref|YP_007906449.1| 32 FAIMGPSGCGKSTFLRALNR 51
                                      68****************85 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013     0.073      25     120 ..      31     165 ..      13     235 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                       EEEEEESTTSSHHHHHHHHHHHCS--....--HHHHHCCHHHHHH.HHHHHHHHHHHHHHHT..T.......HHHC- CS
                           G-alpha  25 kllllGqseSGKsTilkqlkllykkg....fseeelatwraviql.nivrsiktilealesl..eselsesfelqel 94 
                                        + ++G s++GKsT+l+ l +l + +    ++  +++ + + i++ n v+ +++ +  + ++    ++ + f++ ++
  gi|488599978|ref|YP_007906449.1|  31 VFAIMGPSGCGKSTFLRALNRLLELNesarVKG-DIRLYGKSIFEmNPVE-VRKRIGMVFQQvnPFPHLSVFDNVAI 105
                                       46789**************97663331222222.2344444444413332.33333333332112344445577777 PP

                                       SS-SCCCS-HCHHHH............................................H CS
                           G-alpha  95 kerldplkkveasliaklssateee..................................q 120
                                         rl++++k++++++++ ++a +++                                   
  gi|488599978|ref|YP_007906449.1| 106 GLRLNRVLKSKKEIMERVKWALKKSalwdevkdrleapatslsggqqqrlciaralalkP 165
                                       777777777777777777777777766666666666655555555555555555555440 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00032      0.18       2      21 ..      32      51 ..      31      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      +ai+G +  GKSt+++al +
  gi|488599978|ref|YP_007906449.1| 32 FAIMGPSGCGKSTFLRALNR 51
                                      59***************964 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00055      0.31       4      25 ..      34      57 ..      31      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                                      EE--SSSSHHHHHHHGGGGB..S- CS
                             AAA_5  4 LvGppGtgKselaerlaaal..nr 25
                                      + Gp+G+gKs++ + l ++l  n 
  gi|488599978|ref|YP_007906449.1| 34 IMGPSGCGKSTFLRALNRLLelNE 57
                                      68****************996655 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   0.00031      0.18       2      27 ..      29      53 ..      28     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikell 27
                                      +++ +i+G+  +GK+t+l+ l + ll
  gi|488599978|ref|YP_007906449.1| 29 KRVFAIMGPSGCGKSTFLRALNR-LL 53
                                      68999************998853.33 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 ?   10.9   0.0   0.00051      0.28       1      23 [.      34      56 ..      34      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelr 23
                                      ++Gp G GK+tf +al+ +lel+
  gi|488599978|ref|YP_007906449.1| 34 IMGPSGCGKSTFLRALNRLLELN 56
                                      79***************999987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0014      0.77      18      42 ..      27      51 ..      14      66 .. 0.81
   2 ?    0.4   0.0      0.55   3.1e+02      65     110 ..     116     171 ..      82     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                                      SCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlakqiln 42
                                      +++ v a++G  G+GK+t ++  ++
  gi|488599978|ref|YP_007906449.1| 27 PEKRVFAIMGPSGCGKSTFLRALNR 51
                                      455699************9987665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.55
                                       HHHHHHXXHHHHHCCCTTSSSS-STTS...........HHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  65 seeiletilkeLslseddleekeeves...........lkrklvrlLltkrfllvlD 110
                                       ++ei+e++   L++s + ++e +++ +               + r+L  k  ++++D
  gi|488599978|ref|YP_007906449.1| 116 KKEIMERVKWALKKS-ALWDEVKDRLEapatslsggqqQRLCIARALALKPEVILMD 171
                                       567888888888666.77777777766677777777444445567788888888877 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00075      0.42      16      35 ..      26      45 ..      19      49 .. 0.91
   2 ?   -2.4   0.0       4.2   2.4e+03     142     169 ..     183     209 ..     175     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00075
                            ATPase 16 ipegrvvlitGepGtGKtif 35
                                      ipe+rv  i+G +G+GK++f
  gi|488599978|ref|YP_007906449.1| 26 IPEKRVFAIMGPSGCGKSTF 45
                                      8*****************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                            ATPase 142 eilrqlvrvlkklgvTailvseksssee 169
                                       e +  l+++lk    T ++v+  +s++ 
  gi|488599978|ref|YP_007906449.1| 183 EKIEDLIYELKRD-YTIVIVTHSPSQAA 209
                                       6677778887654.45555555566554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 1438.19
//
Query:       gi|488599979|ref|YP_007906450.1|  [L=290]
Description: phosphate ABC transporter membrane protein 2, PhoT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-16   58.6  15.3    6.3e-16   58.6  15.3    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 ?   -0.7   1.0     0.056     1e+03     152     179 ..      22      48 ..       6      55 .. 0.47
   2 !   58.6  15.3   3.5e-20   6.3e-16       1     172 [.      96     279 ..      92     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.056
                      BPD_transp_1 152 eisnggvlalviavlllnlvadilqrll 179
                                       e + +++ ++v+  ++++ ++ i++ ++
  gi|488599979|ref|YP_007906450.1|  22 EKI-FLISIAVFTAAAIIPLFHIIYSVI 48 
                                       333.444444444444444444444444 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 3.5e-20
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirraal 76 
                                       +il+Gi++a ++n++l +l  +l +++l +P++++++++  v+vi    g +++l+++++l++ ++pyv + +++al
  gi|488599979|ref|YP_007906450.1|  96 AILAGIYSAEYPNSILGRLTKTLLQIMLEFPTILVGVFVMQVVVI--PMGsYSALAGAFALAIVMMPYVAISTEEAL 170
                                       578999999*************************99986654333..455477888999999999************ PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..........lgtllle 143
                                       +++p  ++ea   lG+sr+++++++++++a   i+tg+++ ++ + g+++ l+f ++++           +      
  gi|488599979|ref|YP_007906450.1| 171 KEIPFTYREAGFSLGLSRFKVVFHILMKMARKGILTGVLIGMAKVAGETAPLLFSAGGSSriyfagldkpV------ 241
                                       ********************************************************555466655544443...... PP

                      BPD_transp_1 144 ailgydyseis................nggvlalviavlllnlva 172
                                               +i                 ++  +alv++++ l +++
  gi|488599979|ref|YP_007906450.1| 242 -------GAIPlliynliqqpyenyhqIAWGAALVLMLIFLGIFI 279
                                       .......33334444444455555778444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1916.84
//
Query:       gi|488599980|ref|YP_007906451.1|  [L=300]
Description: phosphate ABC transporter membrane protein 1, PhoT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-09   37.4  32.7    4.1e-09   36.5  28.2    2.6  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        7.1    5.6  13.7         51    2.7  13.7    2.2  1  PHO4          Phosphate transporter 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 ?   -0.7   5.3      0.11     1e+03      27      70 ..      15      89 ..       2     104 .. 0.59
   2 !   36.5  28.2   4.5e-13   4.1e-09      10     183 ..      91     297 ..      58     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.11
                      BPD_transp_1 27 llslPsfvlaillvlvf..................................vilsilghlilpviillllsaapyvrl 70
                                      ++++    +++l v+++                                  +i ++l+++il+vi+ l ls+ + v++
  gi|488599980|ref|YP_007906451.1| 15 IFGIF---VLMLSVYIInsvevfhrqglsiyttnqwvasedpekerygvlsAIYGSLYTSILAVIFSLPLSISFAVFV 89
                                      33333...3333343445667778888888888888888888888866555555555555555555555555554444 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 4.5e-13
                      BPD_transp_1  10 lnrnkkldkllrpliivllslPsfv...laillvlvf...................vilsilghlilpviillllsa 64 
                                        +   +l+++l ++ +++ ++P+++   ++ +++  f                   ++    g++ l++ ill ++ 
  gi|488599980|ref|YP_007906451.1|  91 DYAPERLKEWLIIMNDIMAGMPTVIygiWGAFILIPFlrdfimyplyrllsfiplfSFEPLSGYSYLSAGILLGIMV 167
                                       566678899999999999999999977744444444467778888899999999988888999************** PP

                      BPD_transp_1  65 apyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtll 141
                                       +p++  i+r+a r +p  ++eaa  lGa+r +   k++l  ++p i++g+ilafg+++g++v+++++ +++ ++   
  gi|488599980|ref|YP_007906451.1| 168 TPFASSIIREAYRMVPFTYREAAFSLGATRYE-ATKILLGYIKPAIVAGIILAFGRAIGETVAVSLVVGNT-FNIHP 242
                                       ********************************.999********************************666.55555 PP

                      BPD_transp_1 142 leailgydyseis.............nggvlalviavlllnlvadilqrlldprv 183
                                         +  gy +s+ +               +++ ++++++l+ l+++il  +  +r 
  gi|488599980|ref|YP_007906451.1| 243 SLFAPGYTISSLIanqfgnafiyrymTSALFSAGLSLFLIGLAVNILGMYMLKRW 297
                                       555555555544466666677888888999*****************98888776 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  13.7    0.0057        51      22     175 ..      11     177 ..       8     291 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0057
                              PHO4  22 rqAvilaaifeflGavllGaeVaetirkgiv..dvelf......dpselmlgmlaallgaavwlllatvlglPvStt 90 
                                        +A+i+  ++ +l ++++  +V  + r+g+    +         dp++  +g+l+a+ g+    +la++++lP S +
  gi|488599980|ref|YP_007906451.1|  11 FTAIIFGIFVLMLSVYII-NSVEVFHRQGLSiyTT--NqwvaseDPEKERYGVLSAIYGSLYTSILAVIFSLPLSIS 84 
                                       567777777777777776.7788888888863322..1446778888888**************************9 PP

                              PHO4  91 hslvGaliGaalaaeggeavkw............kklvkivlswvlsPllggiiaallfllvkrlilvkeklknalr 155
                                       +++     +           +w            + +  i  + +l P+l  +i + l+ l+ ++ l++        
  gi|488599980|ref|YP_007906451.1|  85 FAVFVIDYAPERL------KEWliimndimagmpTVIYGIWGAFILIPFLRDFIMYPLYRLLSFIPLFS-------- 147
                                       9986433333333......24422223343333334555566666666666666666666666654444........ PP

                              PHO4 156 alpvl..............vlvtiailalsilfk 175
                                           +              + ++++ +a si+++
  gi|488599980|ref|YP_007906451.1| 148 ----FeplsgysylsagilLGIMVTPFASSIIRE 177
                                       ....022222222222211334444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1949.10
//
Query:       gi|488599981|ref|YP_007906452.1|  [L=362]
Description: phosphate ABC transporter substrate-binding protein, PhoT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-59  199.9   0.1      8e-59  199.6   0.1    1.0  1  PBP_like_2  PBP superfamily domain
    4.8e-17   62.9   0.3    6.3e-17   62.5   0.3    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
      1e-06   28.0   0.0    1.6e-05   24.1   0.0    2.2  1  PBP_like    PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.6   0.1   1.3e-62     8e-59       7     281 ..      39     333 ..      33     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 1.3e-62
                        PBP_like_2   7 tsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaang.a 82 
                                        +  +i g+G+t+p+p ++k++d ++++    +++y+++GSg+g+++++ng vdfa sd pl+es     w   + +
  gi|488599981|ref|YP_007906452.1|  39 EV--TIIGSGATFPQPQIEKWIDSYKNV----RIEYTGKGSGGGQNDFKNGLVDFACSDPPLKES----LWRELEsK 105
                                       33..599**************9666555....899******************************....68888889 PP

                        PBP_like_2  83 ggliqvpvaigaialvvnkd..nplnlsreaLakIfsgkItnWnd........vlglpadgpIkvvhrsdgsgttfl 149
                                       g++ q+p+ +ga+++v+n +  ++l+l+ +++a+If g+I  W+d         ++lp  + I vvhrsd+sgtt +
  gi|488599981|ref|YP_007906452.1| 106 GQPLQFPIIVGAVVVVHNIPgvDELKLTGDVVADIFMGRIEYWDDerivslnpSANLP-HERIIVVHRSDSSGTTSV 181
                                       9*****************99799999***********************999877777.999*************** PP

                        PBP_like_2 150 fstalaeq.................gpwtasgigasgsegvasav.snngaigyvsvaywlavkgysladvtngagk 208
                                       f+++l+                    + t +gig +g+ gv++a+ +n + igy+++ay + + ++++++++n+agk
  gi|488599981|ref|YP_007906452.1| 182 FTEYLSLSsddwaekvgsgktvewpVDETGRGIGGKGNQGVVTAIkNNRYSIGYTELAYVYKE-NLKTVALKNKAGK 257
                                       ******99*9999999999998877666689999**********9666*************99.************* PP

                        PBP_like_2 209 fvlptaataasalkvakias....nplawslqpveeniadgayPlsrftyiivyqpyayh.gnnaalakaFldylls 280
                                       fv+++++t++sa++ ++++     +  +++l  + ++ ++++yP+++f+++i+ + y    ++++ ++k+F++++l+
  gi|488599981|ref|YP_007906452.1| 258 FVTASEETIKSAVSRVSYSIpsvrEGYKENLRAMLNADGEKSYPIVAFSHMIIWDSY--IdKAKERAIKDFVKWILT 332
                                       ***************9997799**8899999*9**9999****************55..55788***********98 PP

                        PBP_like_2 281 d 281
                                       d
  gi|488599981|ref|YP_007906452.1| 333 D 333
                                       7 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 !   62.5   0.3     1e-20   6.3e-17       6     314 ..      45     336 ..      41     337 .. 0.76

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1e-20
                                       HHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE....CGGHHHHHHHT....TSBECC CS
                         SBP_bac_1   6 egaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav....dndwiarlaka....glllpl 74 
                                       +ga+++++ ++++   ++++ +e++  gsg++++    ++ +G  + D +++      + +++l ++    ++++ +
  gi|488599981|ref|YP_007906452.1|  45 SGATFPQPQIEKWIDSYKNVRIEYTGKGSGGGQN----DFKNGL-V-DFACSdpplKESLWRELESKgqplQFPIIV 115
                                       5899********8677899***************....666666.5.666665555667777888887777777888 PP

                                       HHHHHHTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTC CS
                         SBP_bac_1  75 dpyvkaylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkk 151
                                       +++v+  ++pgv+  ++kl+++v+++i+ +             i              + Wd+  ++  ++ ++ + 
  gi|488599981|ref|YP_007906452.1| 116 GAVVVVHNIPGVD--ELKLTGDVVADIFMG------------RI--------------EYWDDERIVSLNPSANLPH 164
                                       8888888888877..9***********994............33..............4****************** PP

                                       T.HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT......................HHCSHHHHS..HHHHHHHH CS
                         SBP_bac_1 152 p.iggarggsasgtayyfalalakslggkvfdkdgg......................gldnpegvt..aatylvkl 203
                                       + i+++++++ sgt+++f+++l++s++ +++ +++g                      g+++ +  +  +++y + +
  gi|488599981|ref|YP_007906452.1| 165 ErIIVVHRSDSSGTTSVFTEYLSLSSD-DWA-EKVGsgktvewpvdetgrgiggkgnqGVVTAIKNNrySIGYTELA 239
                                       ***************************.444.444459***************555554444444445555555555 PP

                                       HHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTT CS
                         SBP_bac_1 204 yavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggk 280
                                       y +++   +lk +   nk g +++a  e+ + a+  v+ + +      ++ +    ++ ++++e  +++        
  gi|488599981|ref|YP_007906452.1| 240 YVYKE---NLKTVALKNKAGKFVTASEETIKSAVSRVSYSIP---SVREGYKENLRAMLNADGEKSYPI-------- 302
                                       54444...6666666677777777777777777766665553...333555555555555555556666........ PP

                                       SEEEEEEEEEEBTTCSTHHH....HHHHHHHHTSHHHH CS
                         SBP_bac_1 281 pgilgayglaipkgsknpea....AkkFldfllspeaq 314
                                           +a  ++i ++s   +a    +k+F++++l+++++
  gi|488599981|ref|YP_007906452.1| 303 ----VAFSHMIIWDSYIDKAkeraIKDFVKWILTDGQK 336
                                       ....*************9999999***********997 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.7e-09   1.6e-05       9     185 ..      62     280 ..      55     282 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.7e-09
                                       TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCC.....EEEEEEEEEEEE-CC-HCHCCCCHCCHH CS
                          PBP_like   9 pgvrvavanvGsggGlkalrageadiagshlldketeeynapal.....rkaldgievvlvnlarreqglvvakgnp 80 
                                       ++vr+++++ GsggG + +++g +d a s+ + ke+   +++          ++g+ vv+v++     +l +  +  
  gi|488599981|ref|YP_007906452.1|  62 KNVRIEYTGKGSGGGQNDFKNGLVDFACSDPPLKESLWRELESKgqplqFPIIVGA-VVVVHNIPGVDELKLTGD-- 135
                                       689*****************************888766555544222222234453.444444433333333333.. PP

                                       HS...................--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT.................. CS
                          PBP_like  81 kk...................itnwkdladaplrlvnRetGSGtrdlfdellkkegisk.................. 120
                                                            ++  + l+ +++ +v R  +SGt  +f+e l+                        
  gi|488599981|ref|YP_007906452.1| 136 -VvadifmgrieywdderivsLNPSANLPHERIIVVHRSDSSGTTSVFTEYLSLS---Sddwaekvgsgktvewpvd 208
                                       .13345555666666666666777788899**********************663...3234555666666666643 PP

                                       E-SSTTSEEESSHHHHHCCHCCETTCCECCC.........GG-HCCCCCCECTTCE-EEEEEEEECTCCCSHHH CS
                          PBP_like 121 ssikgyaqearshlavaaaVaagradvgvgi.........eavaeelkgldfvplaeerydlvvrkealddpev 185
                                       +  +g +   + ++ v +a++++r  +g++          ++va + k ++fv  +ee    +v++  +  p v
  gi|488599981|ref|YP_007906452.1| 209 E--TGRGIGGKGNQGVVTAIKNNRYSIGYTElayvykenlKTVALKNKAGKFVTASEETIKSAVSRVSYSIPSV 280
                                       1..2223344566666************8665666666667777777788888888888777777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2496.71
//
Query:       gi|488599982|ref|YP_007906453.1|  [L=319]
Description: Phosphate uptake regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   46.6   0.9    3.6e-12   46.6   0.9    2.9  4  PhoU            PhoU domain
    4.7e-06   26.4   0.0    1.1e-05   25.2   0.0    1.6  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.075   11.7   0.8       0.11   11.2   0.8    1.1  1  Peptidase_S46   Peptidase S46
      0.098   12.8   0.1       0.19   11.8   0.0    1.4  1  ApoLp-III       Apolipophorin-III precursor (apoLp-III)


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 ?   -2.6   0.1       1.8     8e+03      47      47 ..      77      77 ..      56     114 .. 0.58
   2 ?   -3.4   0.0       3.1   1.4e+04      25      47 ..      99     121 ..      84     127 .. 0.59
   3 !   46.6   0.9     8e-16   3.6e-12       1      88 [.     135     224 ..     135     225 .. 0.88
   4 !    6.9   4.0    0.0019       8.5       3      87 ..     237     312 ..     235     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                                      H CS
                              PhoU 47 s 47
                                      +
  gi|488599982|ref|YP_007906453.1| 77 Y 77
                                      2 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  25 elarevierddeidrlekeiers 47 
                                        +a e++   + +++l  ei+ +
  gi|488599982|ref|YP_007906453.1|  99 SIASEILIGVEIMEDLGSEIQIE 121
                                       44555555555556666666555 PP

  == domain 3  score: 46.6 bits;  conditional E-value: 8e-16
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriar 73 
                                       ++r+ +i++++++d + a+e+ d+ ++  +i+r++e d+l+++  r  l+++ +++ l e    d +  ++++ ++r
  gi|488599982|ref|YP_007906453.1| 135 IDRITKICQSIFSDFCLAFENFDKYICTTIIARENETDKLHFLALRL-LKLAENYSDLKEkfqlDGK-TMEYRTVVR 209
                                       578899*****************7777*****************999.8888898988886755333.488999*** PP

                                       HHHHHHHHHHHHHHH CS
                              PhoU  74 dlERigDhavniaer 88 
                                        lERi+Dh++ iae+
  gi|488599982|ref|YP_007906453.1| 210 ALERIADHSAIIAES 224
                                       *************97 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERig 79 
                                       ++a+ ++e +++a+ +l ++d ela+e +++  +  + ek  ++++l +          +re+l +  i  +  Ri 
  gi|488599982|ref|YP_007906453.1| 237 EIANFARETVQMAIFSLHREDAELAEETLSMVSKYMEKEKSYYEKILDME---------VREALLMKTILDSFFRIL 304
                                       678999**********************9999999988888888855433.........555555555666666666 PP

                                       HHHHHHHH CS
                              PhoU  80 Dhavniae 87 
                                        ++++iae
  gi|488599982|ref|YP_007906453.1| 305 NYSADIAE 312
                                       66666666 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 !   25.2   0.0   2.5e-09   1.1e-05       5      44 ..      13      52 ..      10      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-09
                                      TEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHS CS
                    MazE_antitoxin  5 nsgavriPkevrfelgireGdevelevdgdkiilrplksl 44
                                      +s+ +++Pk++  ++g+++Gd v + v +++i+++p+++ 
  gi|488599982|ref|YP_007906453.1| 13 SSYLITLPKDWIVSNGLKAGDQVFMDVGSERIVIYPKEAV 52
                                      8999********************************9875 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   2.4e-05      0.11     329     442 ..     185     294 ..     173     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHHCT-H.HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHHHH....HH- CS
                     Peptidase_S46 329 qaeeaalrawlkkdpekkekygkalselealvkekrklaersalleeaessgsellslarklvrlaeerekpdaere 405
                                       +++  +l+++ + d++   +y +++ +le++ ++++ +ae+  ll++   +  e++++ar++v++a       +  +
  gi|488599982|ref|YP_007906453.1| 185 AENYSDLKEKFQLDGKT-MEYRTVVRALERIADHSAIIAESLLLLKKPVPEMCEIANFARETVQMAIFSL---HRED 257
                                       56677899999999986.8******************************************999998777...5777 PP

                                       HHHHHHHHHHHHHHCHHHHCS--HHHHHHHHHHHHHH CS
                     Peptidase_S46 406 eeyqeralealekeleridkdldaevdkavlaallke 442
                                       +e  e++l++++k +e++++ +++ +d +v +all +
  gi|488599982|ref|YP_007906453.1| 258 AELAEETLSMVSKYMEKEKSYYEKILDMEVREALLMK 294
                                       899999************8888888999999988865 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.2e-05      0.19      64     133 ..     218     287 ..     204     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.2e-05
                         ApoLp-III  64 kkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqeakeklakaikqayddav 133
                                        + i+e    l++  Pe+ + a+  +e+vQ +++sl  e ++lae+  + +++  ek +   ++++d  v
  gi|488599982|ref|YP_007906453.1| 218 SAIIAESLLLLKKPVPEMCEIANFARETVQMAIFSLHREDAELAEETLSMVSKYMEKEKSYYEKILDMEV 287
                                       55666777779999*******************************9988888888888888888887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2094.73
//
Query:       gi|488599983|ref|YP_007906454.1|  [L=232]
Description: putative phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   59.9   0.0    2.7e-16   59.5   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0061   16.6   0.7       0.01   15.9   0.7    1.3  1  DUF5360       Family of unknown function (DUF5360)
     0.0084   15.6   0.0      0.011   15.2   0.0    1.3  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 !   59.5   0.0   4.6e-20   2.7e-16      13     123 ..      18     127 ..       9     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 4.6e-20
                                       EEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE..........EE----TT CS
                      Pribosyltran  13 davarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes..rlledpag 87 
                                         ++r a++  e+ +++p ++v+ argG+  +  l d L+  l+++ + k ++ +++ a+ g +++    + ++++g
  gi|488599983|ref|YP_007906454.1|  18 ILCRRVAEQVKED-GFEPEIIVALARGGWFAGRVLCDLLD--LDDLTSLKIEHYVGTAAKSGEVKIKypLPDGSVEG 91 
                                       4566777777777.*************************9..5555555555555555555555544559******* PP

                                       SEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEE CS
                      Pribosyltran  88 kkVliVDDildtGgTllaalelLkekgpeevriavl 123
                                       k+VliVDDi dtGg+l+ a e++ ++++ e+++a+l
  gi|488599983|ref|YP_007906454.1|  92 KRVLIVDDIADTGGSLKTAKEHVMSQNAGEIKTATL 127
                                       **********************************98 PP

>> DUF5360  Family of unknown function (DUF5360)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.7   1.7e-06      0.01      20      74 ..     126     180 ..     122     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                           DUF5360  20 fleliPkellfkdyenellvaWnwsflPldilisitgllslyltkrkkalwkala 74 
                                       +l+l+ +++   dy  e +  W w  +P + +  +t ++s  ++k+kk +w+++ 
  gi|488599983|ref|YP_007906454.1| 126 TLQLLYTSKFIPDYFGEYMEEWAWVIFPWNFIEDMTDIISRLMRKEKKDFWTEWD 180
                                       678888899999***************************************9885 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-06     0.011      70     166 ..      36     136 ..       9     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                           UPRTase  70 alVpilRaGegmeealrellpearvghlglqreeet...lepveyynkLPkki.aertvlllDpviaTGgsaaaaiq 142
                                       ++V++ R+G    + l +ll    +  l+++    t      v +   LP+   + ++vl++D +  TGgs+ +a +
  gi|488599983|ref|YP_007906454.1|  36 IIVALARGGWFAGRVLCDLLDLDDLTSLKIEHYVGTaakSGEVKIKYPLPDGSvEGKRVLIVDDIADTGGSLKTAKE 112
                                       56777777777777777776666666666655443311122344445699988899********************* PP

                           UPRTase 143 lLkergvgeekIlvlsvlaseegv 166
                                       ++ ++++ge k   l++l  ++ +
  gi|488599983|ref|YP_007906454.1| 113 HVMSQNAGEIKTATLQLLYTSKFI 136
                                       ********9999999998877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1690.56
//
Query:       gi|488599984|ref|YP_007906455.1|  [L=282]
Description: methylthioadenosine phosphorylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-46  157.5   0.0    3.5e-46  157.3   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3   0.0     2e-50   3.5e-46       2     233 ..       5     240 ..       4     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 2e-50
                                       EEEEESSH....HHHHHHHHHEEEEEEEEEE.TTEEEEEEEE.TTEEEEEEE--....SSHHHHHHHHHHHHHHHC- CS
                         PNP_UDP_1   2 iaiivgsp....gevellaespleetpfgregrgfkfvtGtl.kgkpvvivstG....iGkpnaavvaeirllkefg 69 
                                       i+ii+g++      +e+++e    +tpfg++  + ++++G+  ++k+ ++ ++G     +++n+ ++a+i ++k +g
  gi|488599984|ref|YP_007906455.1|   5 IGIIGGTGvydqSAFENIKEI-SVDTPFGKP--SSEIILGEFeGKKVAFLPRHGkghvFSPTNVPYRANIYAMKKLG 78 
                                       9**********9999999999.*********..*********5555559********88****************** PP

                                       -SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE. CS
                         PNP_UDP_1  70 vkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr. 145
                                       v +i++i ++G+l++++++ D+v+pd++++ +  + ++++++  + +++++ + ++++  +l++e a++l+ kvh+ 
  gi|488599984|ref|YP_007906455.1|  79 VHTILSIAAVGSLKEEIEPLDIVVPDQIYDRTKHRISTFFEDI-VVHIGFANP-FCKRTSRLICETARKLNFKVHEg 153
                                       ***************************9996666666666665.899999998.*********************** PP

                                       EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHH CS
                         PNP_UDP_1 146 GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaa 222
                                       G++++ +g++++t+ae++ +r lg d+++M++ ++a lAre++i++a+i++v+d ++ + + e ++++v e +++++
  gi|488599984|ref|YP_007906455.1| 154 GTYVCIEGPQFSTKAESQVYRALGFDIIGMTALPEAKLAREAEICYATIATVTD-YDVWKESEVDVATVLEYMAKNE 229
                                       ******************************************************.888******************* PP

                                       HHHHHHHHHHH CS
                         PNP_UDP_1 223 knaaalllall 233
                                       +++++ll++++
  gi|488599984|ref|YP_007906455.1| 230 EKVKTLLREII 240
                                       ********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1649.68
//
Query:       gi|488599985|ref|YP_007906456.1|  [L=431]
Description: hypothetical protein Asulf_00436 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-82  269.6   2.2    7.7e-29   99.5   0.1    3.2  3  DUF22     Domain of unknown function DUF22


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.1   1.3e-30   2.3e-26       2     106 .]       3     106 ..       2     106 .. 0.95
   2 !   99.5   0.1   4.3e-33   7.7e-29       2     106 .]     147     249 ..     146     249 .. 0.98
   3 !   77.1   0.0   4.1e-26   7.3e-22      14     106 .]     299     390 ..     287     390 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1.3e-30
                             DUF22   2 vkivyrkdgeivrekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtvl 78 
                                       v+i   +++ i+re  e++pfg+++s++ +w +l+Ade+v+v+k+e+  ikik+i+lp+nt+++++ ++rh ++tvl
  gi|488599985|ref|YP_007906456.1|   3 VNIPILTKDGIFREAREFTPFGFKMSEYVRWGFLVADERVKVSKNELFLIKIKPIKLPKNTMISSIGVVRHPVVTVL 79 
                                       5666667789******************************************************************* PP

                             DUF22  79 dvvekgkpkkveeereiteavflpvedG 106
                                       dv  ++k ++ + e+ei+ea++++ +dG
  gi|488599985|ref|YP_007906456.1|  80 DVKGDHKDES-KGESEIREALVIASDDG 106
                                       ****999999.***************99 PP

  == domain 2  score: 99.5 bits;  conditional E-value: 4.3e-33
                             DUF22   2 vkivyrkdgeivrekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtvl 78 
                                       ++i++r+d+ei++ ++  +++gy+rs+++++e+li++e++++k+Gev++++ik++e+p+nti+vp  ++++  g+v+
  gi|488599985|ref|YP_007906456.1| 147 FTIKTRTDSEIKSFQTIKSTHGYWRSNYGYIEYLISNESKKIKQGEVVEVEIKQVEMPSNTIAVPNGLISNIDGCVI 223
                                       7899************************************************************************* PP

                             DUF22  79 dvvekgkpkkveeereiteavflpvedG 106
                                       d++  g+ + +ee+r++++++f+pv+dG
  gi|488599985|ref|YP_007906456.1| 224 DLI--GSFRGIEEDRVLSKVLFIPVADG 249
                                       ***..5*********************9 PP

  == domain 3  score: 77.1 bits;  conditional E-value: 4.1e-26
                             DUF22  14 rekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtvldvvekgkpkkve 90 
                                       ++   + p+ y+r+++++w +++Ade+v vkkG+++++ki+++ lpe +i++p+++m++ +gt+l v++  +   + 
  gi|488599985|ref|YP_007906456.1| 299 KKMKYFPPVFYKRKNTGRWGIIVADERVYVKKGKPVIVKIRDFILPERSIITPMYLMKNDMGTLLGVIQ-PGIADIH 374
                                       4555567899**********************************************************9.778899* PP

                             DUF22  91 eereiteavflpvedG 106
                                       +e+ it+avflp+ dG
  gi|488599985|ref|YP_007906456.1| 375 SEKYITHAVFLPLIDG 390
                                       ************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2691.98
//
Query:       gi|488599986|ref|YP_007906457.1|  [L=181]
Description: hypothetical protein Asulf_00437 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-09   35.0   2.2    1.1e-08   34.7   0.2    2.2  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.2   6.1e-13   1.1e-08       1      37 [.      12      48 ..      12      49 .. 0.98
   2 ?   -1.9   0.1      0.21   3.7e+03      10      19 ..      81      90 ..      80      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 6.1e-13
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                      r+s+ +dee+   L+el+++++r+ Se+IR+A+ +y+
  gi|488599986|ref|YP_007906457.1| 12 RLSVAIDEETNGILEELVEKENRTASEIIRQAITQYY 48
                                      89*********************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.21
                                      HHHHHHHHHH CS
                             RHH_1 10 llerLdelar 19
                                      +l++L+e+a 
  gi|488599986|ref|YP_007906457.1| 81 MLDELNEKAS 90
                                      7888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1179.48
//
Query:       gi|488599987|ref|YP_007906458.1|  [L=232]
Description: phosphoglycerol geranylgeranyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-83  278.5   1.6    3.9e-83  278.3   1.6    1.0  1  PcrB         PcrB family
    0.00092   19.2   0.2      0.018   15.1   0.0    2.2  2  B12-binding  B12 binding domain
     0.0011   18.5   0.1      0.022   14.2   0.0    2.1  2  BtpA         BtpA family
     0.0049   15.7   0.0        2.1    7.1   0.0    2.6  3  Trp_syntA    Tryptophan synthase alpha chain
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.51   10.1   0.0    1.8  2  DisA-linker  DisA bacterial checkpoint controller linker regi


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 !  278.3   1.6   1.1e-86   3.9e-83       2     221 ..       5     230 ..       4     232 .] 0.98

  Alignments for each domain:
  == domain 1  score: 278.3 bits;  conditional E-value: 1.1e-86
                                       HGGGTSEEEEE-TTSS-CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEE CS
                              PcrB   2 dileerhltklDPeeenpdEiveiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvryaDal 78 
                                       ++ ++rh+tklDP++en dEi+++v+esgtDavm++G+++vtld++ rl+  ++ ++lPiv+eps++++vv++ D+l
  gi|488599987|ref|YP_007906458.1|   5 EWKKWRHITKLDPDRENSDEIIKAVAESGTDAVMVSGTEGVTLDKAKRLFDAIKDYNLPIVVEPSDPQNVVYEGDYL 81 
                                       799************************************************************************** PP

                                       EEEEETTBSSTTTTTH.......HHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-B-TTHHHHHHHHHHH CS
                              PcrB  79 FvmsllnsanadWivg.......ahalglkkvkklieseeilaegYlvvePdskvaavteakvdlnkediaayalla 148
                                       Fv+++lns++++Wi+g       +h + l+++kkl     +++egY+v++Pds+va+vt   +dl  e++a+ya+++
  gi|488599987|ref|YP_007906458.1|  82 FVPTVLNSQDSEWITGkhakwvsMHFNELERFKKLL--DRAIIEGYIVLNPDSAVAKVTRSICDLSAEEVASYAIVG 156
                                       ************************************..99************************************* PP

                                       HHHTT-SEEEEE-TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHH.HCHHHH CS
                              PcrB 149 akllglrliYlEasGaledveevialkkklekarlivGGGirsaEkAkevveaADvivvGnvveekd.erkida 221
                                       +++++l++iY+E+sG+++++  v++ + +leka l++GGGi+s+EkA e++++AD+i+vGnv++ek+ +r +++
  gi|488599987|ref|YP_007906458.1| 157 ERIYNLPIIYIEYSGTYGNPAVVKKASEVLEKAVLVYGGGIDSREKAMEMLNYADIIIVGNVIYEKGiDRYLET 230
                                       ******************************************************************97766665 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     5e-06     0.018      34      85 ..      15      65 ..       7      66 .. 0.88
   2 ?    1.7   0.1     0.071   2.6e+02      71     111 ..     178     216 ..     172     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-06
                       B12-binding 34 lganven.edivaairaekpdvvglSalltsqleavkelvellkrirprvkvv 85
                                      l+ + en ++i++a+++   d+v++S + + +l+++k+l +++k ++   ++v
  gi|488599987|ref|YP_007906458.1| 15 LDPDRENsDEIIKAVAESGTDAVMVSGTEGVTLDKAKRLFDAIKDYNL--PIV 65
                                      67788888************************************9954..555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.071
                       B12-binding  71 lvellkrirprvkvvvGGahpsldpeetleak.lgiddvvvg 111
                                       +v+ + ++ +++ +v GG +     e  +e   +++d+++vg
  gi|488599987|ref|YP_007906458.1| 178 VVKKASEVLEKAVLVYGGGI--DSREKAME-MlNYADIIIVG 216
                                       56667777788888888877..34444344.34888998888 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.027        97      36     181 ..      27      42 ..      11      74 .. 0.65
   2 !   14.2   0.0   6.2e-06     0.022     128     234 ..     108     223 ..     103     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.027
                              BtpA  36 kaleegGvDavilenygdaPflkevdpetvaamtvivkevksdvsiplGvnvLrndavaalaiAkavgakFiRvnvl 112
                                       ka++e+G Dav++                                                                
  gi|488599987|ref|YP_007906458.1|  27 KAVAESGTDAVMV---------------------------------------------------------------- 39 
                                       4455555555555................................................................ PP

                              BtpA 113 tgvalsdeGilegkaaellrykkllesrvkiladvavkhavplverdlesavkdtvergladavilsGk 181
                                                                                                         sG 
  gi|488599987|ref|YP_007906458.1|  40 ------------------------------------------------------------------SGT 42 
                                       ..................................................................554 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.2e-06
                              BtpA 128 aellrykkllesr.vkiladvavkhavplverdlesavkdtver.....gladav.ilsGkatGgevdleelklake 197
                                       +el r+kkll++  ++ ++ ++++ av  v+r++++   + v         +  + i+    +G+  + + +k+a e
  gi|488599987|ref|YP_007906458.1| 108 NELERFKKLLDRAiIEGYIVLNPDSAVAKVTRSICDLSAEEVASyaivgERIYNLpIIYIEYSGTYGNPAVVKKASE 184
                                       688999999998878999999999999999999999887776663332223333337888999************** PP

                              BtpA 198 tvk.vkvlvgsGvs.eenlekllsiadGvivgtsikkdG 234
                                       +++  + + g G++  e + ++l++ad +ivg +i  +G
  gi|488599987|ref|YP_007906458.1| 185 VLEkAVLVYGGGIDsREKAMEMLNYADIIIVGNVIYEKG 223
                                       ***44555578886267899*************998887 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0015       5.2      16      41 ..      12      37 ..       9      65 .. 0.94
   2 ?   -2.7   0.0      0.57     2e+03     104     209 ..     110     129 ..      94     144 .. 0.54
   3 !    7.1   0.0   0.00059       2.1     201     229 ..     191     219 ..     175     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0015
                                      EETTSS-HHHHHHHHHHHHHCT-SSE CS
                         Trp_syntA 16 vtagdpdleqsleilkalekagadvi 41
                                      +t  dpd e+s ei+ka++++g+d++
  gi|488599987|ref|YP_007906458.1| 12 ITKLDPDRENSDEIIKAVAESGTDAV 37
                                      8889********************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.57
                                       HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTS CS
                         Trp_syntA 104 eerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveqaegfvYvvsraGvTgaen 180
                                        erf + l  a ++g iv                                                           
  gi|488599987|ref|YP_007906458.1| 110 LERFKKLLDRAIIEGYIV----------------------------------------------------------- 127
                                       344555555555555554........................................................... PP

                                       SB-TTHHHHHHHHHHCTSS-EEEESSS-S CS
                         Trp_syntA 181 avaaevdelverlkkltavPvavGFGist 209
                                                                   +
  gi|488599987|ref|YP_007906458.1| 128 ---------------------------LN 129
                                       ...........................33 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00059
                                       EEEESSS-SHHHHHHHHTT-SEEEE-HHH CS
                         Trp_syntA 201 vavGFGistkeqvkqvakvadGvivGSal 229
                                       +  G Gi ++e++ ++ + ad +ivG  +
  gi|488599987|ref|YP_007906458.1| 191 LVYGGGIDSREKAMEMLNYADIIIVGNVI 219
                                       34699*********************887 PP

>> DisA-linker  DisA bacterial checkpoint controller linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         1   3.7e+03      61      77 ..      23      39 ..      19      61 .. 0.65
   2 ?   10.1   0.0   0.00014      0.51      71     129 ..      97     155 ..      95     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
                                      HHHHHHHHHTGGGGHHH CS
                       DisA-linker 61 eeiekyiveLGteGrli 77
                                      +ei k + e Gt++ ++
  gi|488599987|ref|YP_007906458.1| 23 DEIIKAVAESGTDAVMV 39
                                      57777777777776555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
                                       GGGGHHHHHHHHHHHTTHHHHHHHHHHHHSSS--HHHHHHHHHHH...HTTS---HHHH CS
                       DisA-linker  71 GteGrlislqleeLlanveeeeellikDYlkeekeeeaeeileelkelsseelldlski 129
                                       G++++ +s+ ++eL +  +   +++i+ Y+  + ++ ++++ +++ +ls+ee+ +   +
  gi|488599987|ref|YP_007906458.1|  97 GKHAKWVSMHFNELERFKKLLDRAIIEGYIVLNPDSAVAKVTRSICDLSAEEVASYAIV 155
                                       8999***************************999******************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1511.69
//
Query:       gi|488599988|ref|YP_007906459.1|  [L=283]
Description: geranylgeranylglycerol-phosphate geranylgeranyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-39  133.5  13.5    9.9e-39  133.1  13.5    1.2  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1  13.5   5.5e-43   9.9e-39       3     246 ..      21     263 ..      19     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 5.5e-43
                              UbiA   3 ipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllil 79 
                                       + +++g+++ a+ s+++ ++++ +l++++++a+a alNdyfD+e D  ++r  +RPlv+G++s+k+ali++i+l+ +
  gi|488599988|ref|YP_007906459.1|  21 FGVVIGMVVVARLSFNPMHMFFGVLTAIFLQASAFALNDYFDYEVDLANKR-IDRPLVRGELSRKTALILSIILFPI 96 
                                       568899******************************************888.89*********************** PP

                              UbiA  80 gllllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfllt 156
                                       g++++ +l+n+++++l+l++ +l+++Y  + lK +++ g++ +g++++ p+++g ++++ ++ l +++l+l+ fl  
  gi|488599988|ref|YP_007906459.1|  97 GIFFA-YLINLQAFILALIISILGLLYD-FKLKEFGVAGNIYIGFTMCAPFIFGGVIAG-DIGLVTAVLSLMAFLSG 170
                                       *****.**********************.9***************************85.5688888888888**** PP

                              UbiA 157 waialandlrdregDrkagiktlpvvlGrkaaril.lalllavllla..llllllalllllylllalllaalallra 230
                                       +a  +++ ++d+egD  + +kt + + G  +a ++ +al+l+ ++++  ++l+    +l l +l+ +l+  ++l++ 
  gi|488599988|ref|YP_007906459.1| 171 VAREIMKGIEDVEGDSLRDVKTVARTKGIDVAGRIsAALFLISVVISpiPFLFINEFFLDLKYLIPVLFTDIILIKI 247
                                       **********************************8655555555555887777777777787777777777777766 PP

                              UbiA 231 arlvrrrdakkaakff 246
                                       a+++ r  ++++ +++
  gi|488599988|ref|YP_007906459.1| 248 AHNLLRGARREDISKY 263
                                       6666655555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1742.04
//
Query:       gi|488599989|ref|YP_007906460.1|  [L=180]
Description: Uncharacterized protein containing a ferredoxin domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  106.7   0.3    6.9e-31  106.1   0.3    1.3  1  DUF2148   Uncharacterized protein containing a ferredoxin dom
  ------ inclusion threshold ------
       0.22   11.2   3.6       0.25   11.1   2.2    1.8  2  FeS       Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.3   7.7e-35   6.9e-31       2      68 .]     114     179 ..     113     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 7.7e-35
                           DUF2148   2 gplCafkaiDlGiAlgsavkvaadlrvDnRvmysvGaaAkslgllkeasvvlgiplsvsgKsifFDR 68 
                                       gp+Ca+k+iDlGiAlgs++k a++++vDnR+my++G+aA++lg+ k a++v+gipl  +gK++fFDR
  gi|488599989|ref|YP_007906460.1| 114 GPMCAYKLIDLGIALGSVAKLASIMGVDNRIMYRIGTAARKLGYAK-ADIVMGIPLTSAGKNPFFDR 179
                                       9*********************************************.*******************9 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.82   7.4e+03      18      25 ..      50      57 ..      49      61 .. 0.77
   2 ?   11.1   2.2   2.7e-05      0.25       3      17 ..      88     101 ..      88     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.82
                               FeS 18 Aealvege 25
                                      Ae++ve +
  gi|488599989|ref|YP_007906460.1| 50 AEKMVEMK 57
                                      89999865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.7e-05
                               FeS   3 gtNCgaCGypgCmaf 17 
                                       g+NCgaCG  +C+++
  gi|488599989|ref|YP_007906460.1|  88 GLNCGACGL-TCDEM 101
                                       79******9.99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1144.82
//
Query:       gi|488599990|ref|YP_007906461.1|  [L=318]
Description: ribosomal RNA methyltransferase NOP2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-60  202.5   0.0    6.8e-60  202.1   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    6.8e-08   32.9   0.0    1.7e-07   31.6   0.0    1.7  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    8.7e-05   22.7   0.0    0.00012   22.3   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
      0.002   17.9   0.1     0.0085   15.9   0.1    2.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0053   16.6   0.0     0.0094   15.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.018   14.8   0.0    1.3  1  Met_10           Met-10+ like-protein
       0.11   12.0   0.2       0.48    9.9   0.1    2.1  3  Methyltransf_4   Putative methyltransferase
       0.11   12.4   0.0       0.21   11.4   0.0    1.4  1  DAO_C            C-terminal domain of alpha-glycerophosphate 


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 !  202.1   0.0     3e-63   6.8e-60       2     199 ..     114     315 ..     113     316 .. 0.93

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 3e-63
                                       HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC. CS
                   Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgge 78 
                                       l+L+p++ + ++D +++PGgKTt+ia+lm+nkg+++A++++keR+ ++++n++r+gv nt +++aD +ki   ++g+
  gi|488599990|ref|YP_007906461.1| 114 LALEPEKTDVVIDFASSPGGKTTFIAQLMENKGVILAIEVQKERIPALKDNIHRMGVMNTVIVNADSTKI--HSAGI 188
                                       689*******************************************************************..56668 PP

                                       .EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHH CS
                   Methyltr_RsmB-F  79 lfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLk 155
                                       + DriLlDaPC+g g+i++dp  k +r ekdia ++ lq  ll +ai++l++gGvlvYsTCs+++eEne v+ ++L 
  gi|488599990|ref|YP_007906461.1| 189 KADRILLDAPCTGEGIIHKDPTRKHSRGEKDIAFCSGLQFSLLISAIKTLRRGGVLVYSTCSMTPEENEIVVSKVLD 265
                                       8*************************************************************************997 PP

                                       H...-TTEEEESSBSTTSTTSSECEEC...TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 156 k...redvelvetelsepkglklgeea...gtlrllPhtenkdgffiakl 199
                                           r + +l+++++ +   +  g+     +++rl+Ph+++  gff+ak+
  gi|488599990|ref|YP_007906461.1| 266 YfdgRVELRLETIPYGDKALIMDGVRDelkNARRLYPHKHQCSGFFVAKI 315
                                       52226688899999888777776666577789****************97 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   7.8e-11   1.7e-07       7      89 ..      26     109 ..      21     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7.8e-11
                                       HHHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH....-SS--B-TT-TTEEES---...TTSHHHHT CS
                   Methyltr_RsmF_N   7 ekmkellgeeaeaflaaleeprkkglRvNtlKisveeleklse....efelepvpwceeGfyleeeerpgkhplhea 79 
                                       +++ +++g+ea ++++a+e+ + k +R+NtlKi+++el +  e      e ++v++c +  +l+e  + g +p++ +
  gi|488599990|ref|YP_007906461.1|  26 RRWINFFGDEAVEIIEAMEKVP-KYIRINTLKIEENELIERLEkrgfILEKTEVDYCYK--VLKEAYSIGATPEYLM 99 
                                       5677899***********9875.55********99998665555854456667777765..7899999********* PP

                                       TS-EE--TTT CS
                   Methyltr_RsmF_N  80 GlyYiQEpSa 89 
                                       G+yY+ + S+
  gi|488599990|ref|YP_007906461.1| 100 GYYYVMDKSS 109
                                       *****99987 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.2e-08   0.00012      21     144 ..     120     258 ..      62     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.2e-08
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......HHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEE CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......aplpgvttiqgditdpetiekikealserkvdlv 91 
                                       +++ v+D +++PGg + +++q +++kg+++a+ +q+       +++ ++ ++++ i + +  +    +  + k+d +
  gi|488599990|ref|YP_007906461.1| 120 KTDVVIDFASSPGGKTTFIAQLMENKGVILAIEVQKEripalkDNIHRMGVMNTVIVNADSTK---IHSAGIKADRI 193
                                       3466*******************99*********99854433322233333333333332222...2223468**** PP

                                       EE--S-SS-CHHHHHHHHH...........CCCCHHHHCCHCCCCECCCEEEECCCH.CCCHHHH CS
                              FtsJ  92 vsDgapdvsgvhdldeylq...........sqLllaalelalkllkpggtfvlkifr.geeteal 144
                                       + D     +g+ ++d +++           s L  + l  a+k+l++gg++v  ++   +e +++
  gi|488599990|ref|YP_007906461.1| 194 LLDAPCTGEGIIHKDPTRKhsrgekdiafcSGLQFSLLISAIKTLRRGGVLVYSTCSmTPEENEI 258
                                       ***987778888888888889999999998899999999999**********8887743333343 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.8e-06    0.0085      72     137 ..     119     184 ..      57     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.8e-06
                                       -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTT CS
                              PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGy 137
                                       +k + v++  s  G +t  +a+l+++kg +++ie +ke + + k n+++ +++n ++v +D +k +
  gi|488599990|ref|YP_007906461.1| 119 EKTDVVIDFASSPGGKTTFIAQLMENKGVILAIEVQKERIPALKDNIHRMGVMNTVIVNADSTKIH 184
                                       4567799999**************************************************988755 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.2e-06    0.0094       2     115 ..     119     252 ..     118     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-06
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDl 77 
                                       +k+ +v+D ++  G +t  +a+++  k+ +  i+ ++e i   + n  + g+ n     +d +++ ++ ++    D 
  gi|488599990|ref|YP_007906461.1| 119 EKTDVVIDFASSPGGKTTFIAQLMENKGVILAIEVQKERIPALKDNIHRMGVMNTVIVNADSTKIHSAgIK---ADR 192
                                       67889****************99989999************************************987666...9** PP

                   Methyltransf_31  78 ilsnevl..naladpdkile....................eiervlkpggilliedprll 115
                                       il ++++    + ++d + +                    ++++ l+ gg+l+ +++++ 
  gi|488599990|ref|YP_007906461.1| 193 ILLDAPCtgEGIIHKDPTRKhsrgekdiafcsglqfslliSAIKTLRRGGVLVYSTCSMT 252
                                       ****88888444444444444444555555566667888899**************9933 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   8.2e-06     0.018      99     186 ..     119     207 ..     113     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.2e-06
                                       -TT-EEEETT-TTTCCHHHCCHHT.TSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EEEEE CS
                            Met_10  99 eegevVvdvfAGiGpfaipiakys.kakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqladrvv 173
                                       e+ +vV+d     G  +  ia++  ++  +lai+++ e +  lk+ni++  v ++v  +++D+ ++     +adr++
  gi|488599990|ref|YP_007906461.1| 119 EKTDVVIDFASSPGGKTTFIAQLMeNKGVILAIEVQKERIPALKDNIHRMGVMNTV-IVNADSTKIHSaGIKADRIL 194
                                       5667888877776666666666541556789*************************.89*******997789***** PP

                                       E--TTTGGGGHHH CS
                            Met_10 174 mnlpksaieFldk 186
                                       +++p + +  ++k
  gi|488599990|ref|YP_007906461.1| 195 LDAPCTGEGIIHK 207
                                       **99888877776 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.53   1.2e+03     102     118 ..      61      77 ..      36      91 .. 0.61
   2 ?    9.9   0.1   0.00022      0.48       6      63 ..     125     183 ..     120     194 .. 0.76
   3 ?   -3.1   0.0       2.1   4.8e+03      99     117 ..     230     248 ..     226     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.53
                                       HHHHHEEEEEEEEEEES CS
                    Methyltransf_4 102 elarvLkkgGvlelaTD 118
                                       el ++L+k+G++  +T 
  gi|488599990|ref|YP_007906461.1|  61 ELIERLEKRGFILEKTE 77 
                                       45556666666666665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                                       EEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
                    Methyltransf_4   6 leiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63 
                                       ++  +  G+ +  +A+ ++ +  +l+iE++++++ ++ ++i++ ++ N  i++ d +k+
  gi|488599990|ref|YP_007906461.1| 125 IDFASSPGGKTTFIAQlMENKGVILAIEVQKERIPALKDNIHRMGVMNTVIVNADSTKI 183
                                       5555555555555565234556789*****************************98765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.1
                                       HHHHHHHHEEEEEEEEEEE CS
                    Methyltransf_4  99 llkelarvLkkgGvlelaT 117
                                       ll  + ++L+ gGvl+  T
  gi|488599990|ref|YP_007906461.1| 230 LLISAIKTLRRGGVLVYST 248
                                       556677899****998877 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.4e-05      0.21      18      58 ..      10      61 ..       4      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.4e-05
                                      ..TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH.............. CS
                             DAO_C 18 laaelaqeygldeevaehLaerYGsraeevlelakedekp...........e 58
                                      l+++la++yg+de  ++++++ +G++a e++e  ++  k            e
  gi|488599990|ref|YP_007906461.1| 10 LSRKLAEKYGYDEFIVRRWINFFGDEAVEIIEAMEKVPKYirintlkieenE 61
                                      7899**************************9665554433555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1937.63
//
Query:       gi|488599991|ref|YP_007906462.1|  [L=185]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-12   45.2   0.0      1e-11   44.6   0.0    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    3.6e-08   33.2   2.3    2.1e-07   30.7   0.4    2.4  2  TrmB            Sugar-specific transcriptional regulator TrmB
    9.4e-08   31.5   0.0    2.4e-07   30.2   0.0    1.8  1  HTH_24          Winged helix-turn-helix DNA-binding
    9.8e-08   31.8   0.0    2.3e-07   30.6   0.0    1.6  1  MarR            MarR family
    2.3e-07   30.6   0.0    4.9e-07   29.5   0.0    1.6  1  MarR_2          MarR family
    2.5e-06   27.2   0.0    4.4e-06   26.5   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    3.5e-05   23.8   0.0      7e-05   22.8   0.0    1.4  1  HTH_20          Helix-turn-helix domain
    0.00069   19.8   0.2     0.0014   18.8   0.2    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0011   18.7   0.0     0.0026   17.5   0.0    1.7  1  HTH_23          Homeodomain-like domain
     0.0037   17.2   0.4      0.033   14.1   0.0    2.6  3  HTH_11          HTH domain
     0.0077   16.0   0.1       0.59   10.0   0.0    3.1  2  HTH_10          HTH DNA binding domain
  ------ inclusion threshold ------
      0.013   15.5   0.3      0.028   14.5   0.3    1.5  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.015   15.5   0.1      0.026   14.7   0.1    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.022   14.9   0.1       0.05   13.7   0.1    1.5  1  FUR             Ferric uptake regulator family
      0.023   14.5   0.0      0.041   13.7   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.023   15.2   0.1      0.081   13.4   0.0    1.9  2  HTH_27          Winged helix DNA-binding domain
       0.06   12.4   1.8      0.073   12.1   1.7    1.4  1  VAR1            Mitochondrial ribosomal protein (VAR1)
      0.067   13.0   0.0       0.19   11.5   0.0    1.8  2  TetR_N          Bacterial regulatory proteins, tetR family
      0.068   13.5   0.3        0.2   12.0   0.0    1.9  2  Rrf2            Transcriptional regulator
      0.089   12.6   0.0       0.18   11.5   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
        0.1   13.2   0.3       0.26   11.9   0.1    1.9  1  Mga             Mga helix-turn-helix domain
        0.1   13.3   0.2        1.1   10.0   0.0    2.3  3  RPA_C           Replication protein A C terminal
       0.16   12.0   0.0       0.88    9.6   0.0    2.0  2  HTH_Crp_2       Crp-like 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 !   44.6   0.0   1.3e-14     1e-11      11      74 ..      95     157 ..      84     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.3e-14
                                       THHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  11 eqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       ++ +e+ e++ ++p Vv +y++ Gd dy+++ ++ + e+l r+++  +a+++gv+rt+t  vl+
  gi|488599991|ref|YP_007906462.1|  95 ATGKEIGEKISAIPGVVAVYYILGDIDYIVISKALNREDLKRIIDS-IANIEGVERTSTQYVLN 157
                                       5668999***************************************.*************9996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.4   2.7e-10   2.1e-07       3      55 ..      17      69 ..      14      73 .. 0.95
   2 ?    1.6   0.1      0.34   2.6e+02      26      45 ..     139     158 ..     128     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.7e-10
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      k++L+    k+  ++ ++g+ +++ i++elgvp+s+vY   ++Led Gl++++
  gi|488599991|ref|YP_007906462.1| 17 KVDLTPLQLKILYKISEHGEVNMEVISKELGVPKSTVYYNYKKLEDSGLIRKI 69
                                      899***********************************************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.34
                                       CHHCCCTTSSCHCHHHHHHH CS
                              TrmB  26 deiaeelgvprskvYevLrs 45 
                                       d ia++ gv+r++ + vL+ 
  gi|488599991|ref|YP_007906462.1| 139 DSIANIEGVERTSTQYVLNV 158
                                       789999*********99985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   3.1e-10   2.4e-07       3      48 .]      22      67 ..      20      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.1e-10
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       +++kIL  + +++  ++  ++++lg+++stv +  k+Le++GlI+
  gi|488599991|ref|YP_007906462.1| 22 PLQLKILYKISEHGEVNMEVISKELGVPKSTVYYNYKKLEDSGLIR 67
                                      6799*****************************************7 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     3e-10   2.3e-07       1      49 [.      20      68 ..      20      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3e-10
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      lt+ q++iL++++e+g+ ++  + k lgv kstv    ++Le+ Gli++
  gi|488599991|ref|YP_007906462.1| 20 LTPLQLKILYKISEHGEVNMEVISKELGVPKSTVYYNYKKLEDSGLIRK 68
                                      899********************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   6.3e-10   4.9e-07       2      54 ..      19      69 ..      18      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.3e-10
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +ltp q+ +L+ +  +++  +++  + ++lg++ks+v +  k+L++ GL+++ 
  gi|488599991|ref|YP_007906462.1| 19 DLTPLQLKILYKISEHGE--VNMEVISKELGVPKSTVYYNYKKLEDSGLIRKI 69
                                      79****************..******************************986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   5.6e-09   4.4e-06       2      47 .]      22      68 ..      21      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.6e-09
                                      HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      p +lkIL+  +e ge     +++elg+++stv +  kkL+++GL++k
  gi|488599991|ref|YP_007906462.1| 22 PLQLKILYKISEhGEVNMEVISKELGVPKSTVYYNYKKLEDSGLIRK 68
                                      789******************************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0     9e-08     7e-05      10      55 ..      22      67 ..      19      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9e-08
                                      HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      P +++il  +++ +++  + + ++l+++k+t++y+ ++Le+ gL++
  gi|488599991|ref|YP_007906462.1| 22 PLQLKILYKISEHGEVNMEVISKELGVPKSTVYYNYKKLEDSGLIR 67
                                      8899999999999999****************************98 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   1.8e-06    0.0014      10      52 ..      25      66 ..      23      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                                      HHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 10 LetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      L+ +Y++s e++ v    ++++L+v +s+V    kkLe+ G++
  gi|488599991|ref|YP_007906462.1| 25 LKILYKIS-EHGEVNMEVISKELGVPKSTVYYNYKKLEDSGLI 66
                                      8999****.89999***************************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.3e-06    0.0026      17      46 ..      36      65 ..      24      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                        + + I++eLgv+++Tvy   k+ + +Gl
  gi|488599991|ref|YP_007906462.1| 36 EVNMEVISKELGVPKSTVYYNYKKLEDSGL 65
                                      567889*************77777766887 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   4.3e-05     0.033       2      43 ..      24      64 ..      23      75 .. 0.88
   2 ?   -0.5   0.0       1.6   1.2e+03      16      25 ..      95     104 ..      80     110 .. 0.77
   3 ?   -1.5   0.1       3.2   2.5e+03      33      49 ..     131     147 ..     125     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      +l+il  + +++g ++ e +++eL+v ++tv+   k+Le++g
  gi|488599991|ref|YP_007906462.1| 24 QLKILYKI-SEHGEVNMEVISKELGVPKSTVYYNYKKLEDSG 64
                                      6899999*.77777*************************999 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                            HTH_11  16 isgeeLAeeL 25 
                                        +g+e+ e++
  gi|488599991|ref|YP_007906462.1|  95 ATGKEIGEKI 104
                                       6888888886 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.2
                            HTH_11  33 rrdIkaLeelgvpIese 49 
                                       r d+k++ ++ + Ie++
  gi|488599991|ref|YP_007906462.1| 131 REDLKRIIDSIANIEGV 147
                                       56888888888899886 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00075      0.59      23      44 ..      36      57 ..      20      63 .. 0.80
   2 ?    1.9   0.0      0.25     2e+02      26      47 ..     138     159 ..     134     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00075
                            HTH_10 23 rvtlkeLAkelGIskstlsehL 44
                                      +v+++ ++kelG+ kst+++  
  gi|488599991|ref|YP_007906462.1| 36 EVNMEVISKELGVPKSTVYYNY 57
                                      68999*************9865 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.25
                            HTH_10  26 lkeLAkelGIskstlsehLrka 47 
                                       ++++A++ G+ ++++++ L+ +
  gi|488599991|ref|YP_007906462.1| 138 IDSIANIEGVERTSTQYVLNVI 159
                                       5789**************9865 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   3.6e-05     0.028       3      54 ..      17      68 ..      15      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                           DUF2250  3 eleedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLler 54
                                      ++  ++l+lk+l+ + + +      i+kel +p++ v   +kkLe+ GL+ +
  gi|488599991|ref|YP_007906462.1| 17 KVDLTPLQLKILYKISEHGEVNMEVISKELGVPKSTVYYNYKKLEDSGLIRK 68
                                      67788999*******999999999**************************87 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.4e-05     0.026      16      53 ..      33      71 ..      21      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                    B-block_TFIIIC 16 ysGitqsdLa.keskqdprslfyrlksLekkgLIvkqsi 53
                                      ++G+  ++++ ke++  ++ ++y  k+Le++gLI k+ +
  gi|488599991|ref|YP_007906462.1| 33 EHGEVNMEVIsKELGVPKSTVYYNYKKLEDSGLIRKIMV 71
                                      46888888887************************9877 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.5e-05      0.05      18      64 ..      29      72 ..      23      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                                      HHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET CS
                               FUR 18 ekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefe 64
                                      +k  eh    ev +e+ +++  +  +TVY + k le++gl++++ ++
  gi|488599991|ref|YP_007906462.1| 29 YKISEH---GEVNMEVISKELGVPKSTVYYNYKKLEDSGLIRKIMVD 72
                                      555555...58999****************************99876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.2e-05     0.041      13      50 ..      32      68 ..      25      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-05
                                      CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +e+++ ++   +++++g+pkStv+   + L+  G++++
  gi|488599991|ref|YP_007906462.1| 32 SEHGE-VNMEVISKELGVPKSTVYYNYKKLEDSGLIRK 68
                                      55555.68888**************9999999999985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0    0.0001     0.081       1      49 [.      20      67 ..      20      70 .. 0.95
   2 ?   -1.5   0.0       4.6   3.6e+03      30      30 ..     147     147 ..     124     167 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                            HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                      lt++q  +L  i  +++++  + +++ l v +s++ y+ kkL+  GL+ 
  gi|488599991|ref|YP_007906462.1| 20 LTPLQLKILYKIS-EHGEVNMEVISKELGVPKSTVYYNYKKLEDSGLIR 67
                                      7999999******.*********************************94 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.6
                            HTH_27  30 v 30 
                                       v
  gi|488599991|ref|YP_007906462.1| 147 V 147
                                       2 PP

>> VAR1  Mitochondrial ribosomal protein (VAR1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.7   9.4e-05     0.073     145     210 ..       9      80 ..       2     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.4e-05
                              VAR1 145 nilsyyynkkvtiepiklkyly.......lnsdilskslslkdsnkynnglslkylkllnnklPklndklisk 210
                                       ni+  + +kkv + p++lk ly       +n +++sk l + +s  y n  +l+ + l+ +++  lnd+l+  
  gi|488599991|ref|YP_007906462.1|   9 NII-NHVKKKVDLTPLQLKILYkisehgeVNMEVISKELGVPKSTVYYNYKKLEDSGLIRKIMVDLNDELLGL 80 
                                       554.3579***********99955555545889************************************9865 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 ?   11.5   0.0   0.00025      0.19      17      38 ..      37      58 ..      34      62 .. 0.89
   2 ?   -3.0   0.0       8.3   6.5e+03       9      25 ..      87     103 ..      80     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                      --HHHHHHHHTSSHHHHHHHTS CS
                            TetR_N 17 ttvreIAkrAGvskgalYryFp 38
                                      + ++ I k++Gv k+++Y+ ++
  gi|488599991|ref|YP_007906462.1| 37 VNMEVISKELGVPKSTVYYNYK 58
                                      78999*************9875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.3
                                       HHHHHTTT--HHHHHHH CS
                            TetR_N   9 faerGydattvreIAkr 25 
                                       f +  y+++t +eI ++
  gi|488599991|ref|YP_007906462.1|  87 FVRGKYAGATGKEIGEK 103
                                       55555778888888775 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025       0.2      11      56 ..      25      67 ..      13      70 .. 0.80
   2 ?   -1.9   0.0       5.7   4.5e+03      28      44 ..     141     157 ..     123     162 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      l++l+ ++++     v++e i+++ ++++s +    +kL+ +gl++
  gi|488599991|ref|YP_007906462.1| 25 LKILYKISEHG---EVNMEVISKELGVPKSTVYYNYKKLEDSGLIR 67
                                      44455555544...59****************************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.7
                                       HHHHHHHHTS-HHHHHH CS
                              Rrf2  28 seeiaerqnispsylek 44 
                                       +++i     +s +y+  
  gi|488599991|ref|YP_007906462.1| 141 IANIEGVERTSTQYVLN 157
                                       33333344444455444 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 ?   11.5   0.0   0.00024      0.18       4      47 ..      26      69 ..      24      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      +il  + ++g ++ e ++ +lgv + T+    ++Le +gl++++
  gi|488599991|ref|YP_007906462.1| 26 KILYKISEHGEVNMEVISKELGVPKSTVYYNYKKLEDSGLIRKI 69
                                      79999***********************************9986 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00033      0.26       5      55 ..       7      61 ..       3      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                                      THHHHHHHHHH....SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                               Mga  5 leellqellke....slkyqllkflfeeeevsieelaqelyiSestlkrkikeln 55
                                      ++++++++ k+     l++++l  + e+ ev++e +++el + +st++   k+l+
  gi|488599991|ref|YP_007906462.1|  7 FKNIINHVKKKvdltPLQLKILYKISEHGEVNMEVISKELGVPKSTVYYNYKKLE 61
                                      56666665555666667889999999**********************9999986 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 ?   10.0   0.0    0.0014       1.1      65      97 ..      33      66 ..       8      68 .. 0.87
   2 ?   -2.0   0.0       7.3   5.7e+03      74      93 ..     124     143 ..     120     147 .. 0.71
   3 ?    0.3   0.0       1.4   1.1e+03      49      60 ..     150     161 ..     132     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                                      TTT.EEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 65 eeG.vhvdeiaqklrlsvndvkqavdeLsneGii 97
                                      e+G v++++i+++l++++++v    ++L++ G+i
  gi|488599991|ref|YP_007906462.1| 33 EHGeVNMEVISKELGVPKSTVYYNYKKLEDSGLI 66
                                      45559***************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.3
                                       HHHSTSXHHHHHHHHHHHHH CS
                             RPA_C  74 aqklrlsvndvkqavdeLsn 93 
                                         +  l+ +d+k+++d+ +n
  gi|488599991|ref|YP_007906462.1| 124 VISKALNREDLKRIIDSIAN 143
                                       44445688999999998776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHH CS
                             RPA_C  49 alaqqvlnlikq 60 
                                         +q vln+ik+
  gi|488599991|ref|YP_007906462.1| 150 TSTQYVLNVIKE 161
                                       457899***998 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 ?    9.6   0.0    0.0011      0.88      22      53 ..      37      68 ..      25      78 .. 0.88
   2 ?   -0.5   0.0       1.6   1.2e+03      26      47 ..     140     161 ..     128     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisr 53
                                      +++e ++  lG+  +tv    ++L++ gli++
  gi|488599991|ref|YP_007906462.1| 37 VNMEVISKELGVPKSTVYYNYKKLEDSGLIRK 68
                                      67899*************************94 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                                       HHHHHTTSSHHHHHHHHHHHHH CS
                         HTH_Crp_2  26 elAsmlGltretvsrilseLkr 47 
                                        +A++ G+ r ++  +l+  k+
  gi|488599991|ref|YP_007906462.1| 140 SIANIEGVERTSTQYVLNVIKE 161
                                       5888889999998888876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1146.16
//
Query:       gi|488599992|ref|YP_007906463.1|  [L=326]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-87  292.9   0.2    3.5e-87  292.5   0.2    1.1  1  DUF1616   Protein of unknown function (DUF1616)
  ------ inclusion threshold ------
          1    9.7   4.6        1.3    9.4   0.6    2.4  2  DUF4395   Domain of unknown function (DUF4395)


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 !  292.5   0.2   3.9e-91   3.5e-87       2     280 ..      13     289 ..      12     300 .. 0.93

  Alignments for each domain:
  == domain 1  score: 292.5 bits;  conditional E-value: 3.9e-91
                           DUF1616   2 lvlalllllailvpvlnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtp 78 
                                       l+ +++++l++++  +++++lR v+glp++Lf+PGY li+ LFPek+d+d ieR+aLSfglSiai+pligl+ln+tp
  gi|488599992|ref|YP_007906463.1|  13 LLSSFSIILILIIYLFPDSFLRKVIGLPFILFFPGYSLITFLFPEKKDLDSIERVALSFGLSIAITPLIGLALNYTP 89 
                                       566788999999999************************************************************** PP

                           DUF1616  79 wgirlepilvslslftlllalvAivrRsrlpeeerfsvplralieslkeeleeksesrldkalnvlLvvsivlavaa 155
                                        girl+pil+sl+ f + ++l++i+rRs   ++   ++++        ++l +++ srld++l+v+L+++i++++aa
  gi|488599992|ref|YP_007906463.1|  90 FGIRLTPILLSLATFNITFSLLSIYRRSIARDPFIPRIDF--------SSLGWEEMSRLDRILTVILLIAIITSIAA 158
                                       ***************************9998888888862........33444466789****************** PP

                           DUF1616 156 lgyavvaPkegekfTelyllgedgdelvaenypteltagesqevivgieNhEheevnYtvvvllqev........td 224
                                       l+y++v+Pk+gekfTe+y+lge+g   +a++ypt+l +g++ ++i+gi NhE+++vnYtv+++l +          +
  gi|488599992|ref|YP_007906463.1| 159 LIYIIVTPKQGEKFTEFYILGEKG---KAADYPTKLRVGQNATIIIGIANHEYRTVNYTVEIWLVNAayynnttlIH 232
                                       ************************...**************************************99****999999 PP

                           DUF1616 225 eeevevlerteldrrevtladnet..weqelevepeatgenlrleflLYkdevpeept 280
                                       ++++ +  + +l+ ++++++ n+t  we++++++++++g + +++flL+kd +p  p+
  gi|488599992|ref|YP_007906463.1| 233 HMYFFDRFNVTLNHTNINIEGNWTpqWEKKYTFSISKAG-KYKMWFLLFKDVAPPLPS 289
                                       9999999*****************************999.9**********6654443 PP

>> DUF4395  Domain of unknown function (DUF4395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6   0.00014       1.3      27     117 ..      22     109 ..      10     110 .. 0.68
   2 ?    1.3   0.2     0.045     4e+02      12      32 ..     143     163 ..     135     167 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                           DUF4395  27 wllallavvfalralagprlsplgllarrlvaprlgpkpeledaapkrFAqliGlvfllvalvlfllgapvlglvlt 103
                                       +l++ l+ + +lr ++g  + +++  ++++ +  +  + + +    +r A   Gl ++++ l++++l+++++g+ lt
  gi|488599992|ref|YP_007906463.1|  22 ILIIYLFPDSFLRKVIGLPFILFFPGYSLI-T--FLFPEKKDLDSIERVALSFGLSIAITPLIGLALNYTPFGIRLT 95 
                                       444444444455555554333333333333.2..334555555667899**************************** PP

                           DUF4395 104 alllvaafleaafg 117
                                        +ll +a+++ +f 
  gi|488599992|ref|YP_007906463.1|  96 PILLSLATFNITFS 109
                                       **********9985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.045
                           DUF4395  12 lvvvllvlalltgapwllall 32 
                                       +++v+l++a++t+ ++l++++
  gi|488599992|ref|YP_007906463.1| 143 ILTVILLIAIITSIAALIYII 163
                                       455566666666655555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2176.11
//
Query:       gi|488599993|ref|YP_007906464.1|  [L=173]
Description: Carbonic anhydrase/acetyltransferase, isoleucine patch superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.1e-17   60.1  18.3      1e-06   28.2   0.1    4.2  4  Hexapep     Bacterial transferase hexapeptide (six repeats)
    6.1e-08   32.3  16.0    6.7e-05   22.5   4.7    4.1  4  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.043   12.7   0.1      0.099   11.6   0.1    1.7  1  Fucokinase  L-fucokinase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   1.7e-10     1e-06       2      36 .]      12      46 ..      11      46 .. 0.95
   2 !    5.0   0.1    0.0037        22       2      16 ..      51      65 ..      50      66 .. 0.77
   3 !   21.6   3.4     2e-08   0.00012       2      29 ..      73      99 ..      72     102 .. 0.95
   4 !   21.3   5.0   2.6e-08   0.00016       1      36 []      89     124 ..      89     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.7e-10
                                      EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                      ++I ++v+I  +a+i+g+V+IG+ + ++ ++v++g
  gi|488599993|ref|YP_007906464.1| 12 PIIKDGVFIAENATIAGDVEIGRESSVWYNAVLRG 46
                                      589*****************************986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0037
                                      EEEETTEEE-TTEEE CS
                           Hexapep  2 tvIGsnvlIgpfavi 16
                                      +v+G+++ I  +av+
  gi|488599993|ref|YP_007906464.1| 51 IVVGEKTNIQDNAVV 65
                                      578888888888887 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 2e-08
                                      EEEETTEEE-TTEEEETTEEE-TTEEEE CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIg 29
                                      t IG+ v+Ig+ avi ++++I ++v+Ig
  gi|488599993|ref|YP_007906464.1| 73 TEIGDRVTIGHSAVI-HGCIIESDVVIG 99
                                      89*************.***********8 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 2.6e-08
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +++I+s+v+Ig ++ i++++kI +n++++ag+v++g
  gi|488599993|ref|YP_007906464.1|  89 GCIIESDVVIGLNSAILNGAKISENSIVAAGAVVTG 124
                                       699*******************************97 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.1    0.0048        29       6      26 ..      16      38 ..      13      44 .. 0.80
   2 ?    1.6   0.1     0.039   2.3e+02      17      26 ..      54      65 ..      51      66 .. 0.77
   3 !   15.4   1.3   1.9e-06     0.011       1      26 [.      72      98 ..      72      98 .. 0.96
   4 !   22.5   4.7   1.1e-08   6.7e-05       3      33 ..      91     123 ..      89     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0048
                                      TT-EE-TT-EE.S.EEE-TT-EE CS
                         Hexapep_2  6 dnCliGanagi.G.vslGdncvv 26
                                      d ++i  na+i G v++G+++ v
  gi|488599993|ref|YP_007906464.1| 16 DGVFIAENATIaGdVEIGRESSV 38
                                      7889999***9955****98865 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.039
                                      S..EEE-TT-EE CS
                         Hexapep_2 17 G..vslGdncvv 26
                                      G  +++ dn+vv
  gi|488599993|ref|YP_007906464.1| 54 GekTNIQDNAVV 65
                                      5558999***98 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.9e-06
                                      .EEE-TT-EE-TT-EE.SEEE-TT-EE CS
                         Hexapep_2  1 pviIGdnCliGanagi.GvslGdncvv 26
                                      p+ IGd++ iG +a+i G +++ ++v+
  gi|488599993|ref|YP_007906464.1| 72 PTEIGDRVTIGHSAVIhGCIIESDVVI 98
                                      789**********************98 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 1.1e-08
                                       EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                       iI+ +++iG n+ i  G ++ +n++v+aG v+t
  gi|488599993|ref|YP_007906464.1|  91 IIESDVVIGLNSAIlnGAKISENSIVAAGAVVT 123
                                       8**********9999*****************9 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.7e-05     0.099     281     373 ..      75     160 ..       6     171 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                        Fucokinase 281 lessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilqtlslklskekeyvtvvfGieDdlkss 357
                                       +  +v++g ++vi  + ++++v ig ns + +          ++ +++i+   +++++k+     +++Gi  ++ ++
  gi|488599993|ref|YP_007906464.1|  75 IGDRVTIGHSAVIHGCIIESDVVIGLNSAILN--------GAKISENSIVAAGAVVTGKKYPPNSLLMGIPAKVVRE 143
                                       34455555555555555555555555543321........3334455555555555555444455566666666665 PP

                        Fucokinase 358 ve.aekltflgkplkkf 373
                                       v+ +e ++++ +++k++
  gi|488599993|ref|YP_007906464.1| 144 VTeDEVKSLIERSWKEY 160
                                       55455555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.99
# Mc/sec: 525.88
//
Query:       gi|488599994|ref|YP_007906465.1|  [L=211]
Description: putative ICC-like phosphoesterase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-06   26.3   0.1      9e-06   26.0   0.1    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    5.9e-05   23.7   5.8     0.0001   22.9   5.8    1.5  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1     1e-09     9e-06       4     102 ..      20     140 ..      18     181 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1e-09
                     Metallophos_2   4 aiiSDlH.....snldaleavlealkevgvdaiihaGDl......eeeepevleellela........pvlaVrGNn 61 
                                       ++++DlH       ++ +e++++a+++   d +i++GD+        +e++ +e+l++ +         ++ V+GN+
  gi|488599994|ref|YP_007906465.1|  20 IVLADLHlglvhFDRKVIENAVRAAEGY--DGVILLGDVkhdiglRLRELKEVENLKDNLlnlgidegNIVLVKGNH 94 
                                       7999***955554455555556665555..********652212222333444444444478889999********* PP

                     Metallophos_2  62 D...eev..veedvlreaaelgtdlpeeaelelagekvlliHgdpl 102
                                       D   +ev   e  +  + +++ + + +  e  l+ +++ + H +p 
  gi|488599994|ref|YP_007906465.1|  95 DggiDEVikTEGFFISKDTGFFHGHRKPPEEVLESRNIVFAHIHPA 140
                                       *888444455666677777777777444444445788999999975 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   5.8   1.1e-08    0.0001       4      79 ..      20     117 ..      18     201 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-08
                                       EEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH.......TSEEEEEC-T CS
                       Metallophos   4 lvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky.......pipvylllGN 73 
                                       +v++DlHl l + +   +++++   ++ e+ d v+l+GD+ ++ +l  + l+ ++ l ++         +++l++GN
  gi|488599994|ref|YP_007906465.1|  20 IVLADLHLGLVHFDRKVIENAV---RAAEGYDGVILLGDVKHDIGLRLRELKEVENLKDNllnlgidEGNIVLVKGN 93 
                                       6899999544444444455555...6668**************9555555555555555555556667889****** PP

                                       TS..................CHHH CS
                       Metallophos  74 He..................gfee 79 
                                       H+                  gf +
  gi|488599994|ref|YP_007906465.1|  94 HDggideviktegffiskdtGFFH 117
                                       **7766665555333333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1462.89
//
Query:       gi|488599995|ref|YP_007906466.1|  [L=124]
Description: hypothetical protein Asulf_00446 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-20   71.4   0.1    7.1e-20   70.6   0.1    1.5  1  ACT_7       ACT domain
    3.8e-06   26.6   0.2    1.3e-05   24.9   0.2    1.9  1  ACT         ACT domain
  ------ inclusion threshold ------
      0.016   15.3   0.1       0.06   13.5   0.0    1.8  2  DUF2007     Putative prokaryotic signal transducing protein
       0.11   12.2   0.0       0.19   11.5   0.0    1.4  1  MaAIMP_sms  Putative methionine and alanine importer, small s


Domain annotation for each model (and alignments):
>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.1   1.6e-23   7.1e-20       2      64 ..      54     115 ..      53     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.6e-23
                                       EEEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   2 sedgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiStyrtdyiLVpeedlekAveaLh 64 
                                       +e++++ ++++   lpfdv+G++ak++++ a+++Isif+iS+y td+iL++e+dl++A+++L+
  gi|488599995|ref|YP_007906466.1|  54 AERDFRLITFDLI-LPFDVVGFIAKISTAMADENISIFVISSYSTDSILIREKDLDRALRVLK 115
                                       79999********.***********************************************96 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   2.8e-09   1.3e-05       7      54 ..      67     106 ..      61     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.8e-09
                                       EE.SSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHH CS
                               ACT   7 vp.DrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeed 54 
                                       +p D++G +a++++a+ad +i+i  i+++s++          i++ e+d
  gi|488599995|ref|YP_007906466.1|  67 LPfDVVGFIAKISTAMADENISIFVISSYSTDS---------ILIREKD 106
                                       5669***************************65.........4444444 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.36   1.6e+03      19      55 ..       4      45 ..       1      48 [. 0.54
   2 ?   13.5   0.0   1.3e-05      0.06      24      64 ..      77     115 ..      76     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.36
                           DUF2007 19 lLeeagIeavvkdeftssileGalgelp.....vrilVaeed 55
                                      +L +    +v +d+ +s  l G  +++      + +  +e+ 
  gi|488599995|ref|YP_007906466.1|  4 ILYKDKFAVVKADRIDSVNLDGEFFAIIrdrgeITVVLRESE 45
                                      555566667777887666677664322235544444445555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.3e-05
                           DUF2007  24 gIeavvkdeftssileGa.lgelp.vrilVaeedleeAreile 64 
                                        I + ++de+    ++ + ++ ++   il++e+dl++A ++l+
  gi|488599995|ref|YP_007906466.1|  77 KISTAMADEN----ISIFvISSYStDSILIREKDLDRALRVLK 115
                                       6888899999....7777434444689**************98 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 ?   11.5   0.0   4.1e-05      0.19      31      56 ..      83     109 ..      71     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                        MaAIMP_sms  31 PDeksGilGtspyAtDdvLie.qEler 56 
                                        De+  i+  s y tD++Li  ++l+r
  gi|488599995|ref|YP_007906466.1|  83 ADENISIFVISSYSTDSILIReKDLDR 109
                                       5999****************6145555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 780.45
//
Query:       gi|488599996|ref|YP_007906467.1|  [L=620]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-72  244.1   0.1    2.3e-72  243.7   0.1    1.2  1  GatB_N     GatB/GatE catalytic domain
    4.6e-16   59.0   1.5      1e-15   57.9   0.1    2.1  2  GatB_Yqey  GatB domain
    2.1e-14   53.5   0.0    4.8e-14   52.4   0.0    1.6  1  GAD        GAD domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.7   0.1   3.9e-76   2.3e-72       2     272 ..      11     439 ..      10     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 243.7 bits;  conditional E-value: 3.9e-76
                                       EEEEEEEEEB--SB-SSSSSBSSSSCE.............STTSS--TTTTTS........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxx........................ RF
                            GatB_N   2 viGlEiHaqlktksKlFssasteeege.............epnsevsevdlal........................ 41 
                                       ++G+EiH+ql+t++KlF++++t + ++             +++se++e d a+                        
  gi|488599996|ref|YP_007906467.1|  11 KVGIEIHQQLDTERKLFCNCPTFH-RDvedsnfeffrylrAKKSEMGEEDRAAkeevlrskkfiykfydttclvead 86 
                                       89*******************763.2223445667777745777888888887***********************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+++ai++a++ln+++ +e++++RK+++++++++g+Q+t+    +a +G+l++ +k++++++++
  gi|488599996|ref|YP_007906467.1|  87 eeP---PTeINREALKIAIQVAKMLNMDVVDEIHVMRKIVIDGSNTTGFQRTA---LVALNGHLDIgDKRIGVSTLC 157
                                       998...999********************************************...677*******999******** PP

                                       EEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 115 lEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvr 191
                                       +Ee+a+++v+e + +++++l+R+G+pLiEi t+pd+++p+ea+++++kl+++lr++g++++++  G++R+DvN+S++
  gi|488599996|ref|YP_007906467.1| 158 VEEEACRKVEEGEGYVVYSLDRLGIPLIEIGTDPDITNPDEAMETARKLGMILRSTGKVKRGL--GTIRQDVNISIK 232
                                       **********9999*************************************************..************ PP

                                       TSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                            GatB_N 192 eeekgeeegtrvEiKnlnslksiekaieyeierqiell....................................... 229
                                       +       g+rvEiK++++l+ ++k++eye+ rqi+ll                                       
  gi|488599996|ref|YP_007906467.1| 233 D-------GARVEIKGVQELDILAKIVEYEVIRQINLLkirdelksrnaevvhevydvrevfkdtkskilrkagfig 302
                                       4.......49******************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|488599996|ref|YP_007906467.1| 303 aivlrkfagivgreiqpnrrlgtefsdiaktfglggifhtdelpaygiskeeveklreylnageedavilaggsrdr 379
                                       ***************************************************************************** PP

                                       ....................-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHHH CS
                                       ....................xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 ....................qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseeli 272
                                                           +eTrk++ed g+t++lR+ + +a   r++pe+d+  ++++eel+
  gi|488599996|ref|YP_007906467.1| 380 vikalericeraeaclhgipEETRKANED-GTTSYLRPLPgSA---RMYPETDVSSVVVDEELL 439
                                       *****************************.**********555...***************987 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.17     1e+03      78     120 ..     255     295 ..     240     311 .. 0.82
   2 !   57.9   0.1   1.7e-19     1e-15       1     148 []     474     614 ..     474     614 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                                       HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTST CS
                         GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekal 120
                                       e+i++ +L +i+d  el++  +ev+ e  ++ e +k+ k k l
  gi|488599996|ref|YP_007906467.1| 255 EVIRQINLLKIRD--ELKSRNAEVVHEVYDVREVFKDTKSKIL 295
                                       6788889999988..9999999999999888888888888766 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 1.7e-19
                                       HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXH CS
                         GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gksp 76 
                                       d+fee+ k+   a+ +++ +l+ + +el+k g ++++  l+  +++  l+l+++gkI+k+ + evl+ ++ + + s 
  gi|488599996|ref|YP_007906467.1| 474 DVFEEYSKHL--APALVARVLHLTPSELKKDGFDVSR--LERMHFVVTLDLLKDGKIAKEGVYEVLKIFCSNpSASE 546
                                       6899999998..88888999*****************..9********************************9**** PP

                                       HHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  77 eeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       eeiie  g +    e+ le+++   i e+    + ++++  +a+k l+G vMk+ +Gk+d+k++ + lk k+
  gi|488599996|ref|YP_007906467.1| 547 EEIIEMVGGTEDL-EKDLESFISSLITEK---SDFIRERGINAFKPLMGLVMKEFRGKIDGKVIADKLKAKI 614
                                       *****99744433.478999999999999...888999******************************9986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   8.1e-18   4.8e-14       5      95 .]     295     384 ..     292     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 8.1e-18
                                       HHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTEE CS
                               GAD   5 lksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegDi 80 
                                       l + g + a+++++ +a+++++ei++ +++++e+++ ++++ +++g ++t++++++ +++eev+kl+e ++a e+D+
  gi|488599996|ref|YP_007906467.1| 295 LRKAGFIGAIVLRK-FAGIVGREIQPNRRLGTEFSDIAKTF-GLGGIFHTDELPAYgISKEEVEKLREYLNAGEEDA 369
                                       667899********.8*************************.*********************************** PP

                                       EEEEEEEHHHHHHHH CS
                               GAD  81 llfvAdkkktvnkal 95 
                                       ++++ + ++ v kal
  gi|488599996|ref|YP_007906467.1| 370 VILAGGSRDRVIKAL 384
                                       **********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4009.44
//
Query:       gi|488599997|ref|YP_007906468.1|  [L=286]
Description: hypothetical protein Asulf_00448 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   0.5      0.049   13.3   0.5    1.4  1  Med4      Vitamin-D-receptor interacting Mediator subunit 4
       0.15   12.4   0.0       0.29   11.4   0.0    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> 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 ?   13.3   0.5   5.5e-06     0.049      10      70 ..     180     237 ..     177     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-06
                              Med4  10 addelskslkeleehqknearilqLraeveslDekikeivksLkeyekeLkavpdqenskl 70 
                                       +  +++++++e+   + n a+il+L+++ve+lD    ++++sL+ +++ L +v++++++k 
  gi|488599997|ref|YP_007906468.1| 180 VSSRIEAMVDEMVDIYTNVADILNLDERVEELDM---DTATSLMAMYSLLVRVLEEAKEKK 237
                                       5678999**************************7...67899************8888775 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.3e-05      0.29       8      55 ..     209     258 ..     207     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                                       CSSSHHHHHHHHHHHHCECS--TCGGCG..CCHHCCCSEEEEEEE-S--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                               DHH   8 knpDtDsigSaialanllvDhneksqav..egeakeeaedviiiDHHrlg 55 
                                       ++ D+D ++S +a++ llv + e+++++  ++++++e++++++ D H l 
  gi|488599997|ref|YP_007906468.1| 209 EELDMDTATSLMAMYSLLVRVLEEAKEKksIEKFISENMEMEVEDMHILV 258
                                       688***************999888776511456999*********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1978.71
//
Query:       gi|488599998|ref|YP_007906469.1|  [L=254]
Description: ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-24   85.8  13.4      3e-24   85.8  13.4    1.7  1  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0025   17.2   0.5     0.0055   16.1   0.5    1.5  1  DUF4407       Domain of unknown function (DUF4407)
  ------ inclusion threshold ------
       0.95    9.6   9.3       0.12   12.4   0.7    3.2  3  DUF4229       Protein of unknown function (DUF4229)


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 !   85.8  13.4   5.1e-28     3e-24       8     183 ..      85     250 ..      78     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 5.1e-28
                      BPD_transp_1   8 aa.lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdl 83 
                                       ++ + ++   d++++p+i++l+ +P++vl++l++        +g +  + i+l+++ +++ +++++r+  r++++ +
  gi|488599998|ref|YP_007906469.1|  85 LGlMCFKDSADRIISPFIFLLYPIPHIVLLPLII------LLFGIGDASKIFLIAMILFFQILVTTRDSARNISEYY 155
                                       3444458899************************......99*********************************** PP

                      BPD_transp_1  84 veaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvla 160
                                       +   + lGas+w ++r+vv+P++lp i+t +++++g ++   +++e +++ +Glg+++++a +  dy      +++a
  gi|488599998|ref|YP_007906469.1| 156 ILSLKSLGASDWDVYRHVVFPASLPRILTAMRISVGTAIAVLFFAESFATTTGLGYVIMDAWSRADYK-----SLYA 227
                                       ********************************************************************.....788* PP

                      BPD_transp_1 161 lviavlllnlvadilqrlldprv 183
                                       ++i+++ll ++++i+ +++++r+
  gi|488599998|ref|YP_007906469.1| 228 GIISMALLGFSMYIVLEIIEKRL 250
                                       *********************97 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   9.2e-07    0.0055      55     110 ..      28      96 ..      19     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.2e-07
                           DUF4407  55 llIfnlDRfivssi.............kkrakkrrelalalpRlllAvligvvisepleLkiFekeIda 110
                                       + + +l  +ivss               k  +  +++a+ l+R++ ++++++ is pl L  F+++ d+
  gi|488599998|ref|YP_007906469.1|  28 ITVWSLTSYIVSSPalpqpfevviyflIKLPELSKHVAVSLFRVVYSIILALSISIPLGLMCFKDSADR 96 
                                       56777888888888888888888888888899999*****************************99776 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   2.1e-05      0.12      17      56 ..      50      96 ..      47      98 .. 0.78
   2 ?   -0.8   0.2      0.28   1.7e+03      17      36 ..     117     134 ..     110     149 .. 0.50
   3 ?    1.2   0.1     0.068   4.1e+02       9      45 ..     197     234 ..     184     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                           DUF4229 17 villvarliglp.......vpllvaallAlvvalplSmvllkklRdr 56
                                      vi+++ +l +l+       ++++++++lAl ++ pl+++ +k   dr
  gi|488599998|ref|YP_007906469.1| 50 VIYFLIKLPELSkhvavslFRVVYSIILALSISIPLGLMCFKDSADR 96
                                      5566655555556666779**********************976555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.28
                           DUF4229  17 villvarliglpvpllvaal 36 
                                       +ill++  ig +++++++a+
  gi|488599998|ref|YP_007906469.1| 117 IILLFG--IGDASKIFLIAM 134
                                       444444..333333333332 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.068
                           DUF4229   9 aLfvvltavillvarliglp.vpllvaallAlvvalpl 45 
                                       + f+ ++a   +++++i  + ++  +  l A +++++l
  gi|488599998|ref|YP_007906469.1| 197 LFFAESFATTTGLGYVIMDAwSRADYKSLYAGIISMAL 234
                                       45666777777777776666777777778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1511.62
//
Query:       gi|488599999|ref|YP_007906470.1|  [L=245]
Description: ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-35  120.6   0.0    4.1e-34  118.0   0.0    1.9  2  ABC_tran     ABC transporter
    1.1e-08   35.3   2.6    0.00051   20.0   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.4e-05   23.4   0.0      0.099   12.1   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00043   20.7   0.2     0.0066   16.9   0.2    2.2  1  AAA          ATPase family associated with various cellular a
    0.00079   19.4   0.1     0.0037   17.2   0.0    1.9  2  Rad17        Rad17 P-loop domain
    0.00084   19.6   0.1     0.0026   18.0   0.1    1.7  1  AAA_22       AAA domain
     0.0011   18.7   0.1     0.0022   17.7   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0011   18.9   0.4     0.0054   16.6   0.1    2.0  2  RsgA_GTPase  RsgA GTPase
     0.0041   17.5   0.1     0.0055   17.1   0.1    1.4  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.037   14.2   0.0    1.6  1  AAA_33       AAA domain
      0.026   14.5   0.3      0.053   13.4   0.1    1.6  2  ATPase_2     ATPase domain predominantly from Archaea
      0.033   13.0   0.0          1    8.1   0.0    2.0  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.042   12.6   0.2       0.11   11.2   0.1    1.6  2  Adeno_IVa2   Adenovirus IVa2 protein
      0.052   13.1   0.0        0.3   10.6   0.0    2.0  2  AAA_25       AAA domain
      0.056   13.2   0.1       0.22   11.3   0.0    2.0  3  IstB_IS21    IstB-like ATP binding protein
      0.062   13.8   0.3       0.11   13.0   0.3    1.4  1  AAA_23       AAA domain
       0.11   12.1   0.5       0.37   10.4   0.1    1.7  2  AAA_15       AAA ATPase domain
       0.14   12.4   0.1       0.37   11.1   0.1    1.7  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 !  118.0   0.0   4.1e-37   4.1e-34       2     136 ..      19     157 ..      18     158 .. 0.97
   2 ?    0.5   0.0      0.81     8e+02      29      79 ..     170     217 ..     167     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 4.1e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + +s+++++ge+  i+G++G+GKStLl +++gll+pt Ge+l+dgk +++     +rk ++ + q+  lfp +tvre
  gi|488599999|ref|YP_007906470.1|  19 ESISFEVEKGEICSIIGPSGCGKSTLLLIFSGLLEPTGGEVLIDGKIVNS-----VRKDVALILQDYGLFPWKTVRE 90 
                                       679*****************************************998887.....********************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e d++++ +++klgl++++++      ++LSgG++qrva aral+ kp++ll+DEp+
  gi|488599999|ref|YP_007906470.1|  91 NiaiglkiqkypkdEIDNRVKFLIRKLGLEGFENSYP----KHLSGGMRQRVAFARALAMKPSILLMDEPF 157
                                       ************9999999**************9998....*****************************7 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.81
                                       HHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  29 kllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                       + l++  + t+ +ill  ++++e     l k+i vl++ p   +++ v+++
  gi|488599999|ref|YP_007906470.1| 170 NFLIKIWQETSATILLVTHNIEE--AVLLGKKIVVLTERPGRVKRI-VKNE 217
                                       56777888888899888888888..999999999999998877777.5444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4     1e-05      0.01       4      24 ..      33      53 ..      30     127 .. 0.86
   2 !   20.0   0.1   5.1e-07   0.00051     235     298 ..     128     189 ..     100     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                            AAA_21  4 liGpNgsGKSnLLdaldllar 24
                                      +iGp g+GKS+LL ++++l  
  gi|488599999|ref|YP_007906470.1| 33 IIGPSGCGKSTLLLIFSGLLE 53
                                      9****************9963 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.1e-07
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                        +lS G+++  a++ al+  +   s+ll DEp ++L+    +rl  +l k+ +++ a ++l+TH+
  gi|488599999|ref|YP_007906470.1| 128 KHLSGGMRQRVAFARALAMKP---SILLMDEPFSSLDALSRERLQNFLiKIWQETSATILLVTHN 189
                                       478*****9999999999877...**************8888888888633333557*******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 !    9.5   0.2    0.0006       0.6       2      41 ..       7      45 ..       6      49 .. 0.77
   2 !   12.1   0.0   9.9e-05     0.099     110     199 ..      58     190 ..      47     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0006
                                      EEEEEEESETTEECEEEEEETTS.SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpfsk.sftaivGpNGSGKsnll 41
                                      ++++  +++k +  ++++ +++k ++ +i+Gp G+GKs ll
  gi|488599999|ref|YP_007906470.1|  7 ISKIYENGVKAI--ESISFEVEKgEICSIIGPSGCGKSTLL 45
                                      567777788888..57777776624889**********985 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.9e-05
                                       EEEETTEEE-H..HHHHHHHHCTT-STT...........................................CS-HHH CS
                                       xxxxxxxxxxx..xxxxxxxxxxxxxxx...........................................xxxxxx RF
                             SMC_N 110 eykingkevtk..kevsellesagiske...........................................lLSgGe 141
                                       e+ i+gk v++  k+v+ +l++ g+ +                                             LSgG 
  gi|488599999|ref|YP_007906470.1|  58 EVLIDGKIVNSvrKDVALILQDYGLFPWktvreniaiglkiqkypkdeidnrvkflirklglegfensypkHLSGGM 134
                                       567777777665678888888888877777888888888888888888888888888888888888888889***** PP

                                       HHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH..HCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                             SMC_N 142 ktLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke..ksknaQfivislre 199
                                       ++ va a  +A++     ++ l+De  + LD+  ++++ ++l +  ++++a ++ ++++ 
  gi|488599999|ref|YP_007906470.1| 135 RQRVAFARALAMK----PSILLMDEPFSSLDALSRERLQNFLIKiwQETSATILLVTHNI 190
                                       **99998888764....4689*****************9987641134446677777764 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   6.6e-06    0.0066       3     107 ..      33     186 ..      31     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-06
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       ++Gp G+GK++l       l+ +                                                      
  gi|488599999|ref|YP_007906470.1|  33 IIGPSGCGKSTLLLIFSGLLEPTggevlidgkivnsvrkdvalilqdyglfpwktvreniaiglkiqkypkdeidnr 109
                                       68999****99999999998433333334444444445555555555555555555555555555555555555555 PP

                                       ....EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET....GGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  26 ....fleisgsellskyvgesekkirelfkeakeka.kpsilfiDE....idalaksrsgseseeeervvnqLltel 93 
                                           + ++ +  + ++y ++ +  +r+ ++ a++ a kpsil++DE    +dal +          er++n L++ +
  gi|488599999|ref|YP_007906470.1| 110 vkflIRKLGLEGFENSYPKHLSGGMRQRVAFARALAmKPSILLMDEpfssLDALSR----------ERLQNFLIKIW 176
                                       5553333444444466*9*9999999999999999999********5555555554..........55888888888 PP

                                       HHTTTSSSTEEEEE CS
                               AAA  94 dgvkkkeskvivig 107
                                       ++ +      i+++
  gi|488599999|ref|YP_007906470.1| 177 QETSAT----ILLV 186
                                       887772....3333 PP

>> Rad17  Rad17 P-loop 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      33      68 ..      16      51 ..       4      62 .. 0.83
   2 ?   -0.4   0.0      0.92   9.2e+02     132     173 ..     147     188 ..      97     194 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLske 68
                                      +++++ + e +k +i  i GPsGCgkst + + s  
  gi|488599999|ref|YP_007906470.1| 16 KAIESISFEVEKGEICSIIGPSGCGKSTLLLIFSGL 51
                                      46777888999999***************9998865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.92
                             Rad17 132 dkklilvedlP.nkfyrds.dalrevirkylrssealplilvit 173
                                       + +++l+++ P +     s ++l++ + k  + + a +++lv  
  gi|488599999|ref|YP_007906470.1| 147 KPSILLMDE-PfSSLDALSrERLQNFLIKIWQETSA-TILLVTH 188
                                       444555554.43555554448888887777666666.4555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.6e-06    0.0026       4     129 ..      27     187 ..      24     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.............erpevvfvtlpsstsskdllrellralgle 67 
                                       +  i+ ++G+sG+GK+tll  +   l+    ++              +++  +  +  ++  +k+++++++  l+ +
  gi|488599999|ref|YP_007906470.1|  27 KGEICSIIGPSGCGKSTLLLIFSGLLE----PTGgevlidgkivnsvRKDVALILQDYGLFPWKTVRENIAIGLKIQ 99 
                                       567899**************9999994....2335688999999986555555666666668888888888888887 PP

                            AAA_22  68 lka.......................erlsseellealeqalrarav.ielliiDEaqh.lr..s.eealeeLrsll 116
                                       +                         +++ ++  +++    +ra a+ +++l+ DE    l+  s e++ ++L +++
  gi|488599999|ref|YP_007906470.1| 100 KYPkdeidnrvkflirklglegfensYPKHLSGGMRQRVAFARALAMkPSILLMDEPFSsLDalSrERLQNFLIKIW 176
                                       77788888888888888888888677555555555555555555555789999999555466665377777778888 PP

                            AAA_22 117 nlsrkgvqliLvG 129
                                          +++ +++Lv 
  gi|488599999|ref|YP_007906470.1| 177 Q--ETSATILLVT 187
                                       8..8888887764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.2e-06    0.0022      17      39 ..      23      45 ..      12      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.2e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                      +e++  g ++ ++GpsG GKSTll
  gi|488599999|ref|YP_007906470.1| 23 FEVEK-GeICSIIGPSGCGKSTLL 45
                                      45553.4699*************8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.5e-06    0.0054      87     117 ..      15      46 ..       4      61 .. 0.82
   2 ?   -0.3   0.0      0.86   8.5e+02      29      54 ..     162     187 ..     157     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-06
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHH CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLin 117
                                        +++e+++ ++++ +++ ++G+SG GKStL+ 
  gi|488599999|ref|YP_007906470.1|  15 VKAIESISFEVEKgEICSIIGPSGCGKSTLLL 46 
                                       46789999999888****************85 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.86
                                       T--HHHHHHHHHHHHHTT-EEEEEEE CS
                       RsgA_GTPase  29 elslnlldrfLvlaeekgiepvivln 54 
                                        ls ++l+ fL+ ++++    +++++
  gi|488599999|ref|YP_007906470.1| 162 ALSRERLQNFLIKIWQETSATILLVT 187
                                       688999*******9999887777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.5e-06    0.0055      21      62 ..      27      67 ..      13     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-06
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdq 62
                                      +g  e++ ++G+sG+GKs+l+  +   le +gg + + gk + 
  gi|488599999|ref|YP_007906470.1| 27 KG--EICSIIGPSGCGKSTLLLIFSGLLEPTGGEVlIDGKIVN 67
                                      34..89***************7777666666655546666555 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   3.7e-05     0.037       4     111 ..      33     195 ..      30     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                            AAA_33   4 lvGlpGsGKstla...erllkklgavllssdt............................................. 32 
                                       ++G++G+GKstl+    +ll+++g+++l   +                                             
  gi|488599999|ref|YP_007906470.1|  33 IIGPSGCGKSTLLlifSGLLEPTGGEVLIDGKivnsvrkdvalilqdyglfpwktvreniaiglkiqkypkdeidnr 109
                                       69*********974447899999955544444367777777888888888888888888888877777777777777 PP

                            AAA_33  33 ...lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil.datnls......rrerarflklarrlgvpv 99 
                                          l+r+l  ++ +  +++++++  ++q++ ++ar al+ + +++l d ++ s      +r +  ++k++++ ++ +
  gi|488599999|ref|YP_007906470.1| 110 vkfLIRKLGLEGFE-NSYPKHLSGGMRQRV-AFAR-ALAMKPSILLmDEPFSSldalsrERLQNFLIKIWQETSATI 183
                                       66655555444444.458899999999999.8886.56666664444999888776642344467789999999999 PP

                            AAA_33 100 rivvvetdeetl 111
                                       ++v+ +  e++l
  gi|488599999|ref|YP_007906470.1| 184 LLVTHNIEEAVL 195
                                       999999888876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.4e-05     0.053       8      39 ..      15      47 ..      12      61 .. 0.79
   2 ?   -2.9   0.0       5.2   5.2e+03     197     197 ..     168     168 ..     135     202 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-05
                          ATPase_2  8 lkeleei.lerepneiyfiYGpegsGKtaLlke 39
                                      +k +e+i  e e+ ei  i Gp g+GK++Ll  
  gi|488599999|ref|YP_007906470.1| 15 VKAIESIsFEVEKGEICSIIGPSGCGKSTLLLI 47
                                      55666653577889****************975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.2
                          ATPase_2 197 a 197
                                        
  gi|488599999|ref|YP_007906470.1| 168 L 168
                                       1 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 ?    2.8   0.0     0.041        40     242     261 ..      25      45 ..      17      50 .. 0.90
   2 ?    8.1   0.0     0.001         1     324     377 ..     131     184 ..     120     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.041
                                       E-SS.EEEEEE-TTSSHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLL 261
                                       + kG +  I+G+   GKsTLL
  gi|488599999|ref|YP_007906470.1|  25 VEKGeICSIIGPSGCGKSTLL 45 
                                       678889**************9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.001
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HH CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplv 377
                                       SG + q ++ ++al ++ ++lL+DE  s    + r ++ + l++ ++e+  +++
  gi|488599999|ref|YP_007906470.1| 131 SGGMRQRVAFARALAMKPSILLMDEPFSSLDALSRERLQNFLIKIWQETSATIL 184
                                       9*****************************************999999866665 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.11      88     121 ..      29      60 ..       3      69 .. 0.77
   2 ?   -1.6   0.0      0.91     9e+02     232     250 ..     177     195 ..     135     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                        Adeno_IVa2  88 viGviyGPtGsGksqllrnlissklisPiPetvi 121
                                        i  i GP G+Gks ll  li s l++P+   v+
  gi|488599999|ref|YP_007906470.1|  29 EICSIIGPSGCGKSTLL--LIFSGLLEPTGGEVL 60 
                                       466788**********9..99999**99976665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.91
                        Adeno_IVa2 232 kctgfsvlvvlhnlnPrsd 250
                                       + t+ ++l+v hn++    
  gi|488599999|ref|YP_007906470.1| 177 QETSATILLVTHNIEEAVL 195
                                       4567788899999876655 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   0.00031       0.3      31      51 ..      26      46 ..      21      53 .. 0.91
   2 ?   -0.5   0.0      0.79   7.9e+02     169     188 ..     169     188 ..     157     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                            AAA_25 31 pagelallaGapgtGKttlal 51
                                       +ge++ ++G++g+GK+tl+l
  gi|488599999|ref|YP_007906470.1| 26 EKGEICSIIGPSGCGKSTLLL 46
                                      68999**************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.79
                            AAA_25 169 vealeriarrtgaavllvhH 188
                                        + l +i ++t a++llv H
  gi|488599999|ref|YP_007906470.1| 169 QNFLIKIWQETSATILLVTH 188
                                       55566778899*******99 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.22      32      63 ..      12      44 ..       2      51 .. 0.83
   2 ?   -2.6   0.0         4   3.9e+03     106     123 ..      69      86 ..      63      96 .. 0.71
   3 ?   -2.4   0.0       3.4   3.4e+03      22      50 ..     155     183 ..     135     190 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                         IstB_IS21 32 krkvkeLatlsf.iekkenivllGpsGvGKshl 63
                                      ++ vk++ + sf +ek e + ++GpsG GKs l
  gi|488599999|ref|YP_007906470.1| 12 ENGVKAIESISFeVEKGEICSIIGPSGCGKSTL 44
                                      66788999999988999999**********987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4
                         IstB_IS21 106 llkvdllilDdlgllpld 123
                                       + k   lil d+gl p +
  gi|488599999|ref|YP_007906470.1|  69 VRKDVALILQDYGLFPWK 86 
                                       444456999999998765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.4
                         IstB_IS21  22 idfraarsldkrkvkeLatlsfiekkeni 50 
                                         f++   l+++++++     + e+++ i
  gi|488599999|ref|YP_007906470.1| 155 EPFSSLDALSRERLQNFLIKIWQETSATI 183
                                       33333333444444444444444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   0.00011      0.11      12      36 ..      20      45 ..       4      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            AAA_23 12 dqeidF...skgltlItGpNGaGKTTil 36
                                         i F   +  +  I+Gp G+GK+T+l
  gi|488599999|ref|YP_007906470.1| 20 S--ISFeveKGEICSIIGPSGCGKSTLL 45
                                      3..445554446889***********98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00037      0.37      13      48 ..      17      53 ..       7      78 .. 0.77
   2 ?   -0.8   0.0      0.96   9.5e+02     315     365 ..     146     189 ..      85     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                            AAA_15 13 slkdveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      ++++++ ++++  +  +iG+ ++GKS++l ++  +l+
  gi|488599999|ref|YP_007906470.1| 17 AIESISFEVEKGeICSIIGPSGCGKSTLLLIFSGLLE 53
                                      5555444444446999*************99987776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.96
                            AAA_15 315 ekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +k       + ill++EP  +L     + l + l+++ ++++  +++ TH+
  gi|488599999|ref|YP_007906470.1| 146 MK-------PSILLMDEPFSSLDALSRERLQNFLIKIWQETSATILLVTHN 189
                                       33.......478888888888888888888888888888888888888886 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00037      0.37      62      88 ..     146     172 ..     124     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllell 88 
                                        +++++++DE Fs+lD+ s+++l ++l
  gi|488599999|ref|YP_007906470.1| 146 MKPSILLMDEPFSSLDALSRERLQNFL 172
                                       46899*************999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1663.85
//
Query:       gi|488600000|ref|YP_007906471.1|  [L=304]
Description: ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-19   68.8   1.5    7.4e-19   67.8   1.5    1.5  1  Lipoprotein_9   NLPA lipoprotein
    9.5e-16   58.4   0.1    1.3e-15   57.9   0.1    1.1  1  NMT1            NMT1/THI5 like
    1.9e-12   47.4   0.0    1.9e-10   40.9   0.0    2.1  1  NMT1_2          NMT1-like family
    1.9e-07   30.7   0.3    4.6e-07   29.5   0.3    1.7  1  SBP_bac_3       Bacterial extracellular solute-binding protei
      0.003   17.2   0.0     0.0076   15.9   0.0    1.7  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.038   14.4   0.2         10    6.6   0.0    2.5  2  DUF836          Glutaredoxin-like domain (DUF836)
      0.042   14.2   0.2      0.087   13.2   0.2    1.5  1  Minor_capsid_3  Minor capsid protein from bacteriophage


Domain annotation for each model (and alignments):
>> Lipoprotein_9  NLPA lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   1.5   2.9e-22   7.4e-19       1     232 [.      29     248 ..      29     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 2.9e-22
                                       EEEEEETTTHHHHHH..HHHHHHHTTTEEEEEEEESSSSHHHHHHHTTSSSEEEEEEHHHHHHHHHHTT-.EEEEEE CS
                     Lipoprotein_9   1 lkvGvlsgpeaevle..kvkkllkkkgldleiveFtdyvqpNkaladgeiDanaFQhlpyLeqfnkekgkklvavgn 75 
                                       lk+G+l+++++ ++   + +k+++k gld+e+v+F ++ +++ a ++ +iD  ++++l ++  +n   ++k+v+++ 
  gi|488600000|ref|YP_007906471.1|  29 LKIGILPIEDSLPIVvaDEEKIFEKYGLDVEVVTFQSALERDSAFTSASIDGMITDPLDVILLKNSGVDVKIVSLCL 105
                                       79*********9999778889999999************************************************** PP

                                       EEE---EEE-......SS-SSGGG--TT-EEEEESSHHHHHHHHHHHHHTTSSEE-TT-CTT--GGGEEE-TT--EE CS
                     Lipoprotein_9  76 thvepiglYS......kkykslselkeGatiavpndpsnegRaLllLekagLikLkdgkgllatvkdIteNpknLki 146
                                       ++++  g+++       ++++ ++l +G+++a++ +++ e   +++L +  + k++        +k+I  ++++L  
  gi|488600000|ref|YP_007906471.1| 106 GKTPSEGVFAvlaspnSQIEKPEDL-AGKQVAISKNTIIEFVTDMMLRDIPIEKIE--------IKKIPLRMQALLD 173
                                       **********999555555555555.6**********************9888888........************* PP

                                       EEE-GGGHHHHGGTSSEEEE-HHHH.HHTT--HHHH-SEE-SSTSSG-EEEEEETTCTTSHHHHHHHHHHTSHHHHH CS
                     Lipoprotein_9 147 keleaaqlpralddvdaavintnya.lkagldpkkdalfeedkdspyvniivvrekdkddeavkklveayqseevkk 222
                                       ++++aa+lp+ l+         ++a +k+++ + +da f +   s  +++iv++  d d ++vk++++ay  e+v++
  gi|488600000|ref|YP_007906471.1| 174 NKVDAAVLPEPLA---------SFAeSKGAKRTISDADFDK---SISQTVIVMKG-DVDTDTVKRFLKAYD-EAVEQ 236
                                       *************.........6774555555556666655...88999999998.***************.99999 PP

                                       HHHHH..TTTSS CS
                     Lipoprotein_9 223 aiekk..ykgav 232
                                       ++++   y+ ++
  gi|488600000|ref|YP_007906471.1| 237 INSNPskYRSKF 248
                                       998764355555 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.1   5.1e-19   1.3e-15       4     214 ..      39     242 ..      37     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 5.1e-19
                                       GHHHHHHHHTTHHHHTTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--....EE CS
                              NMT1   4 haglyvAkekGYFkeeGldVeivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqepl....sg 76 
                                         +++vA e   F++ GldVe+v  +   +   +  s   d  ++++ ++++ + +g++v+ v   l +++    ++
  gi|488600000|ref|YP_007906471.1|  39 SLPIVVADEEKIFEKYGLDVEVVTFQSALERDSAFTSASIDGMITDPLDVILLKNSGVDVKIVSLCLGKTPsegvFA 115
                                       679**********************************************************8876665544111167 PP

                                       EEEECCC--SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHH CS
                              NMT1  77 livlkdsgikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenweg 153
                                       +++  +s+i++p+DL+Gk++++++  + + + + +l+   +++ +++ ++   ++   all++kvDaa+   e +  
  gi|488600000|ref|YP_007906471.1| 116 VLASPNSQIEKPEDLAGKQVAISKNTIIEFVTDMMLRDIPIEKIEIKKIPL-RMQ---ALLDNKVDAAV-LPEPLAS 187
                                       88899999*********************************8888888888.444...8*********9.4444332 PP

                                       HHHHHTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHH CS
                              NMT1 154 velesegkelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPe 214
                                         +es+g + r+++ ad++   + ++v++ +   +++  ++vk+Fl+A+ +++e +  +P 
  gi|488600000|ref|YP_007906471.1| 188 -FAESKGAK-RTISDADFDK-SISQTVIVMK-GDVDT--DTVKRFLKAYDEAVEQINSNPS 242
                                       .34566665.5566677774.5566555555.55666..8****************99997 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   7.5e-14   1.9e-10       3     240 ..      24     239 ..      23     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 7.5e-14
                            NMT1_2   3 pekeqlklGfialtdaaplvvakekglfakeGltvelekqaswaelrdkllagelDaahv.ltpapllidlGiggak 78 
                                       +ek++lk+G  ++ d  p+vva e+++f+k+Gl+ve+++++s+ e   ++ + ++D+ +     ++ll + G+   k
  gi|488600000|ref|YP_007906471.1|  24 QEKKTLKIGILPIEDSLPIVVADEEKIFEKYGLDVEVVTFQSALERDSAFTSASIDGMITdPLDVILLKNSGV-DVK 99 
                                       699*******************************************************998888899999999.444 PP

                            NMT1_2  79 admkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldpeadvk 155
                                            l +  ++G + +l+        s+ ++ +dl++k+       +a+ ++    ++ + + L  +++     ++
  gi|488600000|ref|YP_007906471.1| 100 IVSLCLGKTPSEGVFAVLASP-----NSQIEKPEDLAGKQ-------VAI-SKNTIIEFVTDMML--RDI----PIE 157
                                       444444456666666666543.....35666666664444.......445.44445566677777..344....345 PP

                            NMT1_2 156 lvvvpp.pqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntaralvkal 231
                                        + ++  p  +++l   ++d+++ +eP  + a+ +g+    +++++  k    +v++++ d+     +t+++++ka 
  gi|488600000|ref|YP_007906471.1| 158 KIEIKKiPLRMQALLDNKVDAAVLPEPLASFAESKGA-KRTISDADFDKSISQTVIVMKGDV---DTDTVKRFLKAY 230
                                       5555555667788888999999999999999999998.566666666666678888888888...446888888888 PP

                            NMT1_2 232 leAtkwlda 240
                                        eA + ++ 
  gi|488600000|ref|YP_007906471.1| 231 DEAVEQINS 239
                                       888887776 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.3   1.8e-10   4.6e-07      90     193 ..     115     216 ..      47     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.8e-10
                                       EEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC..TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  90 lvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk..gaeivefdtleealqaLkngrvdavvadspvla 164
                                       +v ++     s+i++++dL+gk+v++++++  e +++  + +   +e +e + ++  +qaL +++vda+v  +p + 
  gi|488600000|ref|YP_007906471.1| 115 AVLAS---PNSQIEKPEDLAGKQVAISKNTIIE-FVTDMMLRdiPIEKIEIKKIPLRMQALLDNKVDAAVLPEPLAS 187
                                       44422...236899999**************99.99998888554555689***********************999 PP

                                       HHHHHCCGCCEEEEECGGCECEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 165 ylvkknpdkkvvlveeplsseeyaiavrk 193
                                        +  k ++ ++  ++ + s ++ +i+++ 
  gi|488600000|ref|YP_007906471.1| 188 FAESKGAKRTISDADFDKSISQTVIVMKG 216
                                       98888877777775555555555554443 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 !   15.9   0.0     3e-06    0.0076      25     164 ..      52     182 ..      47     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                                       HHHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEETT..SS--S CS
                    Phosphonate-bd  25 eelGvevelvvatdyaavvealragqvDiaflgplayvqardqagveplatrvrsdGsasyrsviivrad..sdiqs 99 
                                       e+ G +ve+v++++  +   a+ + ++D   ++pl ++ +++ +gv++  ++    G++  ++v++v a+  s+i++
  gi|488600000|ref|YP_007906471.1|  52 EKYGLDVEVVTFQSALERDSAFTSASIDGMITDPLDVILLKN-SGVDVKIVSLC-LGKTPSEGVFAVLASpnSQIEK 126
                                       56799***********************************96.78888888886.8888888888777762267*** PP

                                       HHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEE CS
                    Phosphonate-bd 100 ledLkgktiafvspsStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavs 164
                                        edL+gk++a+  ++      v  ++L   +++++e+       ++ +  ++a+l++++daa+++
  gi|488600000|ref|YP_007906471.1| 127 PEDLAGKQVAISKNTIIE--FVTDMML---RDIPIEKI----EIKKIPLRMQALLDNKVDAAVLP 182
                                       **********98777555..5555556...35555432....33444555666666677766654 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.004        10      36      58 ..      44      66 ..      17      88 .. 0.73
   2 ?    5.3   0.1      0.01        27      29      67 ..     211     251 ..     192     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.004
                                      TTT-CCCHCCCCTTTTEEEECTT CS
                            DUF836 36 IakdeeleakYgleipvlalegv 58
                                      +a++e+ ++kYgl+++v+ ++  
  gi|488600000|ref|YP_007906471.1| 44 VADEEKIFEKYGLDVEVVTFQSA 66
                                      3355669*************983 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                                       EEEEEEETTT-CC..CHCCCCTTTTEEEECTTCGGB.TCCE CS
                            DUF836  29 leleviDIakdee..leakYgleipvlalegvkktssllee 67 
                                       + + + D+++d +  + ++Y++ ++++  ++ k+ s+++e+
  gi|488600000|ref|YP_007906471.1| 211 VIVMKGDVDTDTVkrFLKAYDEAVEQINSNPSKYRSKFIEI 251
                                       66778899988888899**************8777776655 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 ?   13.2   0.2   3.4e-05     0.087      14     107 ..     159     256 ..     149     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                    Minor_capsid_3  14 ignldlklritalkekdesivvlalpgss......nkkeymDGtkevelnyeiaakskdeqkasqvleelselldel 84 
                                       i+   ++lr++al +++ +++vl+ p +s       k++  D + +++++ ++++ + d +  ++v   l+++ +++
  gi|488600000|ref|YP_007906471.1| 159 IEIKKIPLRMQALLDNKVDAAVLPEPLASfaeskgAKRTISDADFDKSISQTVIVMKGDVD-TDTVKRFLKAYDEAV 234
                                       4444456699999998888888887755422222256788899999999888877777555.677777888888888 PP

                    Minor_capsid_3  85 eielpslngsYtfesleitskPf 107
                                       e +++s++++Y+ + +ei+ +P+
  gi|488600000|ref|YP_007906471.1| 235 E-QINSNPSKYRSKFIEIARVPQ 256
                                       8.899*************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1893.90
//
Query:       gi|488600001|ref|YP_007906472.1|  [L=80]
Description: hypothetical protein Asulf_00452 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   26.8   1.0    6.2e-06   26.5   1.0    1.2  1  GTP_EFTU_D2      Elongation factor Tu domain 2
  ------ inclusion threshold ------
      0.028   14.4   0.9      0.074   13.1   0.3    2.0  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.039   13.5   0.1      0.052   13.1   0.1    1.2  1  MS_channel       Mechanosensitive ion channel


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 !   26.5   1.0     1e-09   6.2e-06      12      59 ..      24      68 ..      16      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1e-09
                                      EEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEE CS
                       GTP_EFTU_D2 12 tlkkGdevrilgndtskkeivtrissletfhededeavaganaGviva 59
                                      +lk+Gd+++i gn+t+ +     + s+e +h+++d a +g+ +G++v+
  gi|488600001|ref|YP_007906472.1| 24 KLKVGDRIKIKGNTTDFE---QIVESIEINHKKVDSALPGDLVGIKVK 68
                                      69********88999888...*************************98 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.2e-05     0.074      28      73 ..       5      54 ..       2      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                      EEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTS..SEEEEEEEE CS
                   tRNA_anti-codon 28 griqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpgg..elelkveei 73
                                      gr++ ++ +   +a  l ++lk+Gd ++++G  + +++    +e++++++
  gi|488600001|ref|YP_007906472.1|  5 GRVTHYFSKagVAAVVLTKKLKVGDRIKIKGNTTDFEQIveSIEINHKKV 54
                                      7777777777777778899**************99965555688888776 PP

>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.7e-06     0.052      55      82 ..      19      50 ..      14      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-06
                                      HHTT-SS-TT-EEESS....SEEEEEEEE-SS CS
                        MS_channel 55 llfekpfkiGDlveig....dieGtVediglr 82
                                      ++++k++k+GD+++i+    d+e +Ve+i++ 
  gi|488600001|ref|YP_007906472.1| 19 VVLTKKLKVGDRIKIKgnttDFEQIVESIEIN 50
                                      5789************9999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 538.46
//
Query:       gi|488600002|ref|YP_007906473.1|  [L=374]
Description: hypothetical protein Asulf_00453 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-05   22.2   5.5      0.037   13.4   0.2    2.4  2  TraF_2           F plasmid transfer operon, TraF, protein
    0.00092   19.0   8.1       0.32   10.8   3.4    3.1  3  Lectin_N         Hepatic lectin, N-terminal domain
     0.0018   18.4   4.0      0.013   15.7   0.3    3.5  3  WXG100           Proteins of 100 residues with WXG
     0.0023   18.6  17.6      0.017   15.9   3.5    3.7  4  DUF2203          Uncharacterized conserved protein (DUF2203)
     0.0025   17.5  13.2       0.17   11.6   1.0    2.5  2  Med4             Vitamin-D-receptor interacting Mediator subu
     0.0032   17.7   9.5     0.0032   17.7   9.5    3.6  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0041   16.0   7.7     0.0041   16.0   7.7    2.6  3  Spc7             Spc7 kinetochore protein
     0.0052   16.6   0.8      0.012   15.4   0.8    1.6  1  FAM209           FAM209 family
     0.0076   16.8  20.1      0.036   14.6   2.5    3.4  3  FlgN             FlgN protein
  ------ inclusion threshold ------
      0.011   16.1   7.9      0.011   16.1   7.9    3.1  2  CCDC-167         Coiled-coil domain-containing protein 167
      0.018   15.0   3.2      0.018   15.0   3.2    3.6  3  FlxA             FlxA-like protein
      0.029   14.7   4.6      0.029   14.7   4.6    3.0  2  Lzipper-MIP1     Leucine-zipper of ternary complex factor MIP
      0.031   14.5   9.8      0.032   14.5   1.1    2.9  2  FliJ             Flagellar FliJ protein
      0.045   13.5   0.4      0.045   13.5   0.4    2.4  3  DUF4239          Protein of unknown function (DUF4239)
      0.053   13.6   4.9       0.51   10.5   0.3    3.4  3  Trans_reg_C      Transcriptional regulatory protein, C termin
      0.074   13.1  21.5       0.19   11.8   6.9    3.7  3  DUF1664          Protein of unknown function (DUF1664)
       0.11   12.7   0.3       0.11   12.7   0.3    3.9  3  Uds1             Up-regulated During Septation
       0.15   12.5  14.9        8.6    6.9   0.8    4.7  4  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.16   11.8   1.1         12    5.8   0.0    3.0  2  DUF3772          Protein of unknown function (DUF3772)
       0.19   11.7  12.4        1.7    8.7   1.9    4.1  4  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.31   11.1  14.5       0.18   11.9   1.3    4.7  3  TolA_bind_tri    TolA binding protein trimerisation
       0.42   10.7  29.1        7.3    6.7   9.1    4.2  2  BRE1             BRE1 E3 ubiquitin ligase
       0.46    9.7  16.4       0.13   11.6   7.4    2.6  2  JMY              Junction-mediating and -regulatory protein
       0.71   10.1  23.7       0.21   11.8   4.4    4.5  3  Spc24            Spc24 subunit of Ndc80
       0.74    9.9  21.9      0.049   13.7   5.5    4.2  4  Med9             RNA polymerase II transcription mediator com
       0.76    9.2  15.6        1.8    8.1   5.3    2.5  2  Allexi_40kDa     Allexivirus 40kDa protein
        1.1    9.9  10.0         11    6.6   0.8    3.8  3  MerR-DNA-bind    MerR, DNA binding
        1.1    8.7   7.0       0.63    9.5   2.9    2.1  2  Pro_dh           Proline dehydrogenase
        1.1    9.1   9.3        3.9    7.3   0.1    4.9  5  DASH_Dam1        DASH complex subunit Dam1
        1.5    8.6  26.3      0.035   13.9   9.0    2.9  3  DUF724           Protein of unknown function (DUF724)
        1.6    9.2  18.7      0.071   13.6   6.3    3.6  3  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
        2.1    8.2  17.7        2.3    8.0   2.9    2.9  2  Nsp1_C           Nsp1-like C-terminal region
        2.3    7.4  20.3       0.13   11.4   5.6    2.8  3  TMPIT            TMPIT-like protein
        2.7    7.1  14.4        5.4    6.2   1.3    2.3  2  ISG65-75         Invariant surface glycoprotein
        2.9    8.6  14.8          8    7.2   0.9    4.4  4  SlyX             SlyX
          3    8.1  12.2         13    6.1   0.5    4.1  3  DUF948           Bacterial protein of unknown function (DUF94
        3.1    8.2  25.5          2    8.9   1.1    5.0  4  YgaB             YgaB-like protein
        3.3    7.8  11.8       0.72    9.9   3.0    2.6  2  MCU              Mitochondrial calcium uniporter
        3.4    8.0  14.9      0.041   14.1   4.8    2.9  2  DUF2683          Protein of unknown function (DUF2683)
        3.5    8.1  37.9    1.7e+02    2.5  18.3    3.2  1  AAA_23           AAA domain
        3.7    7.9  19.6       0.37   11.1   1.9    5.1  5  Rx_N             Rx N-terminal domain
        4.4    7.8  32.7        0.1   13.2  10.6    3.3  3  APG6_N           Apg6 coiled-coil region
        4.7    6.9  15.3       0.22   11.2   3.0    3.3  3  DUF4972          Domain of unknown function (DUF4972)
        4.9    6.4  19.9      0.068   12.5   2.1    3.0  3  CorA             CorA-like Mg2+ transporter protein
        5.3    6.4  15.2        4.6    6.6   6.7    2.9  2  FliD_C           Flagellar hook-associated protein 2 C-termin
        5.6    7.3  21.9        3.6    7.9   8.5    3.5  3  OmpH             Outer membrane protein (OmpH-like)
        6.8    6.7  34.7      0.046   13.7   6.4    5.3  5  Prefoldin_2      Prefoldin subunit
        7.1    6.6   9.1         16    5.4   0.0    3.7  4  MtrG             Tetrahydromethanopterin S-methyltransferase,
        8.6    6.9  27.5        2.2    8.7   1.1    5.0  4  Snapin_Pallidin  Snapin/Pallidin


Domain annotation for each model (and alignments):
>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2    0.0001     0.037      15      78 ..     144     218 ..     135     231 .. 0.81
   2 !   10.5   1.3   0.00076      0.28      29      81 ..     282     353 ..     267     367 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                            TraF_2  15 eddvglllplsvgvevgdvdnlvDkiDdlsdildgleaavnaasad...........etq.vdeaaddlnalLedl 78 
                                        +d + ll++++  ++++ + l+D+iD+l ++l+++e++++++s+            e + + ++++++++ Le +
  gi|488600002|ref|YP_007906473.1| 144 RNDSRYLLSINMLEKITQFERLIDEIDRLREKLNEIERIEKNESEIdvaelerlyskE-KeLMDKVNQIESKLEYI 218
                                       5678889999999*********************999999998877888887776543.24777777777777765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00076
                            TraF_2  29 evgdvdnlvDkiDdlsdildgleaavnaasad..................etq.vdeaaddlnalLedlggd 81 
                                       +v+d d++++++D+l+ +l ++++ +++++                    +++  ++++++l+++L++++++
  gi|488600002|ref|YP_007906473.1| 282 MVSDADKMIEEVDNLKRELTDVQSRIKNLKSImaskssntidkevrslrkQIEeKENELKKLKTELSEMAKK 353
                                       578999999999966666665555555544444444333666656655443335566666666666666665 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.7   1.4e+03      60      78 ..      19      37 ..       9      63 .. 0.64
   2 !    8.8   0.1    0.0035       1.3      52      97 ..     171     216 ..     165     220 .. 0.94
   3 !   10.8   3.4   0.00087      0.32      49     116 ..     285     353 ..     275     361 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.7
                          Lectin_N 60 Lketfsnfssstlaeiqal 78
                                      Lke+++n+  + + ei+  
  gi|488600002|ref|YP_007906473.1| 19 LKEALKNIKRDQEIEIERF 37
                                      7778888877777777653 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0035
                          Lectin_N  52 qLqreLetLketfsnfssstlaeiqalssqggslsekvtsleakle 97 
                                       +L++ L+ ++   +n s+   ae++ l s+ ++l +kv+ +e+kle
  gi|488600002|ref|YP_007906473.1| 171 RLREKLNEIERIEKNESEIDVAELERLYSKEKELMDKVNQIESKLE 216
                                       79999999999999******************************98 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00087
                          Lectin_N  49 qnsqLqreLetLketfsnfssstlaeiqalssq.ggslsekvtsleaklekkqqdlkadhselllhvkq 116
                                          ++ +e+  Lk +++++ s+++   + ++s+  + ++++v+sl+ ++e+k+++lk+ ++el    k+
  gi|488600002|ref|YP_007906473.1| 285 DADKMIEEVDNLKRELTDVQSRIKNLKSIMASKsSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKK 353
                                       45678889999999999998877654444445536778999*************999888777655554 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 ?    0.4   0.0       2.1   7.5e+02      52      70 ..     161     179 ..     155     183 .. 0.57
   2 ?    0.1   0.0       2.6   9.4e+02      17      37 ..     198     218 ..     192     220 .. 0.73
   3 !   15.7   0.3   3.5e-05     0.013      13      85 ..     286     358 ..     281     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHHHHHHH CS
                            WXG100  52 efeewkqaaqklvdaLeei 70 
                                       +fe++  ++++l ++L+ei
  gi|488600002|ref|YP_007906473.1| 161 QFERLIDEIDRLREKLNEI 179
                                       3444555555555555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHHHHHC CS
                            WXG100  17 qkqaeeledelqrlkaevdal 37 
                                        ++++el+d +++++++++++
  gi|488600002|ref|YP_007906473.1| 198 YSKEKELMDKVNQIESKLEYI 218
                                       566788888888888888775 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  13 aarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                       a ++ ++ ++l+ el+++++ +++l+s    +++++ ++e   +++++++  ++L+++  +l + a+++ da+
  gi|488600002|ref|YP_007906473.1| 286 ADKMIEEVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDAE 358
                                       778888999***********************************************************99987 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       1.6     6e+02      24      74 ..      11      61 ..       4      85 .. 0.72
   2 ?   -0.9   0.0       7.1   2.6e+03       9      29 ..     127     147 ..      91     161 .. 0.71
   3 ?    7.0   3.6     0.025       9.1      12      77 ..     159     223 ..     122     241 .. 0.84
   4 !   15.9   3.5   4.5e-05     0.017       6      84 ..     284     362 ..     281     371 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.6
                           DUF2203 24 alrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGv 74
                                      + r  + el+e+l+++k+++e + ++  +++++ l++ +++++ e+e++ +
  gi|488600002|ref|YP_007906473.1| 11 RERLTIPELKEALKNIKRDQEIEIERFINSRISDLRDAVSDFILELESFPI 61
                                      555556677777777777766666777888888888888888888877655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 7.1
                           DUF2203   9 nalLpllkelleelralrkel 29 
                                       n+ + +++e+++++ alr++ 
  gi|488600002|ref|YP_007906473.1| 127 NNAIKRITEIIKQYEALRNDS 147
                                       445555555555555555554 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.025
                           DUF2203  12 LpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevk 77 
                                       +++ ++l++e+ +lr++l+e+ e++e++++e +  e ++l ++++el+++++++ +++e +  ++k
  gi|488600002|ref|YP_007906473.1| 159 ITQFERLIDEIDRLREKLNEI-ERIEKNESEIDVAELERLYSKEKELMDKVNQIESKLEYILGVIK 223
                                       456678888888999998885.68888888888888899999999999999999888887655555 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 4.5e-05
                           DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleag 82 
                                        +A +++ ++++l +el ++++++++l++ ++++++++  +e ++l++++ee e+e+++l +e++e+  ++ d+e  
  gi|488600002|ref|YP_007906473.1| 284 SDADKMIEEVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDAEVE 360
                                       57888899999999999999999999888888888887777788888888888888888888888888777777766 PP

                           DUF2203  83 lv 84 
                                       lv
  gi|488600002|ref|YP_007906473.1| 361 LV 362
                                       55 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 !   11.6   1.0   0.00046      0.17       4      68 ..     162     224 ..     159     270 .. 0.85
   2 !   10.5   5.1   0.00094      0.35       6      60 ..     299     355 ..     294     369 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                              Med4   4 aekLlaaddelskslkeleehqknearilqLraeveslDekikeivksLkeyekeLkavpdqens 68 
                                       +e L++  d+l+++l+e+e+ +kne +i+   ae e l  k ke++ +++++e++L+  + + ++
  gi|488600002|ref|YP_007906473.1| 162 FERLIDEIDRLREKLNEIERIEKNESEIDV--AELERLYSKEKELMDKVNQIESKLEYILGVIKK 224
                                       68999999********************95..8999999***************99987755555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00094
                              Med4   6 kLlaaddelsk..slkeleehqknearilqLraeveslDekikeivksLkeyekeLk 60 
                                       +L++++ ++++  s+   +  + + +++++Lr+++e++++++k++ ++L e+ k+L 
  gi|488600002|ref|YP_007906473.1| 299 ELTDVQSRIKNlkSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLY 355
                                       6777777777422566667778899****************************9986 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 ?   -0.4   0.1       3.8   1.4e+03      61      82 ..       8      29 ..       4      53 .. 0.65
   2 ?    4.5   8.3      0.11        41      29     101 ..     153     219 ..     127     224 .. 0.59
   3 !   17.7   9.5   8.7e-06    0.0032      30     104 ..     278     354 ..     258     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.8
                                      CCCCTTS-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N 61 kakkkkedaeeliaevkelkee 82
                                      k+k++   + el++  k++k +
  gi|488600002|ref|YP_007906473.1|  8 KKKRERLTIPELKEALKNIKRD 29
                                      4444445555555555555554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                         +le  ++ ++l+ e++ l+++ Ne+ +    + k+  + e  +ae + l  + k+l ++++++e++le +l
  gi|488600002|ref|YP_007906473.1| 153 INMLEKITQFERLIDEIDRLREKLNEIER----IEKN--ESEIDVAELERLYSKEKELMDKVNQIESKLEYIL 219
                                       46677777888888888888888887643....3332..3344466666666666666666666666666555 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 8.7e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkk..edaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       + l++ +   +++ e+++l++e   ++  I+++k     +  + + +ev++l ++++++e+elk+l++el +++ ++
  gi|488600002|ref|YP_007906473.1| 278 KNLSMVSDADKMIEEVDNLKRELTDVQSRIKNLKSIMasKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKL 354
                                       556667777899999*************99999998887899999*************************9998876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.1   2.2e+03     271     284 ..      19      32 ..       7      57 .. 0.49
   2 !    7.5   5.5    0.0045       1.6     145     223 ..     137     216 ..     122     233 .. 0.64
   3 !   16.0   7.7   1.1e-05    0.0041     170     239 ..     287     357 ..     260     365 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.1
                              Spc7 271 lkeevkaleeltgw 284
                                       lke +k++++  ++
  gi|488600002|ref|YP_007906473.1|  19 LKEALKNIKRDQEI 32 
                                       22222222222222 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0045
                              Spc7 145 eenlegleedkelLekqeeeldel..lpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekk 219
                                        +++e+l++d++ L +  + l+++   ++l  e ++l+e+l+++++ +++ ++id +eLe l ++ +el+ ++++ +
  gi|488600002|ref|YP_007906473.1| 137 IKQYEALRNDSRYLLSI-NMLEKItqFERLIDEIDRLREKLNEIERIEKNESEIDVAELERLYSKEKELMDKVNQIE 212
                                       44555555555555433.22222211356666777777777777777777777888888888777777777777776 PP

                              Spc7 220 kela 223
                                        +l+
  gi|488600002|ref|YP_007906473.1| 213 SKLE 216
                                       6654 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.1e-05
                              Spc7 170 peleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                                       +++ ee ++l++el++ q++ ++l+si  +++ +++ +e+++l ++ieek++el++l+++l e ++k+ ++
  gi|488600002|ref|YP_007906473.1| 287 DKMIEEVDNLKRELTDVQSRIKNLKSIMaSKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDA 357
                                       34455666677777777776666666554555566666666666666666666666666666666665544 PP

>> FAM209  FAM209 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   3.3e-05     0.012      76     126 ..     272     322 ..     254     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-05
                            FAM209  76 frsplkKkqkaspskdyafntltqlemdLvkfvskvrnLKlamatgsnlrl 126
                                        r ++ K+ +   + d +++ + +l+ +L    s+++nLK +ma+ s+  +
  gi|488600002|ref|YP_007906473.1| 272 QRDLILKNLSMVSDADKMIEEVDNLKRELTDVQSRIKNLKSIMASKSSNTI 322
                                       456677899999999*****************************9977655 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.2     0.068        25      24      97 ..     107     180 ..      91     184 .. 0.64
   2 !   14.6   2.5   9.9e-05     0.036       2      71 ..     160     225 ..     155     254 .. 0.89
   3 ?    6.0   6.9     0.043        16       1      69 [.     289     358 ..     282     371 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHTT...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHHHH CS
                              FlgN  24 lleeEteaLkag...dieaLeelleekqellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqelk 97 
                                        +++ +++L a    ++e+L++ +++++e++++ e+l ++ + ll+   l+ + +  ++l+   e ++l+e+ +e++
  gi|488600002|ref|YP_007906473.1| 107 AIAKNFRLLFAVkppELEGLNNAIKRITEIIKQYEALRNDSRYLLSINMLE-KITQFERLID--EIDRLREKLNEIE 180
                                       556666666666444677777777788888888888888877777655555.3445555554..5555555555554 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.9e-05
                                       ..HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                              FlgN   2 elleeLielleeelelleeLlelleeEteaLkagdieaLeelleekqellekleqleqkrakllaelgls 71 
                                       +++e+Li+ +++++e l+e++++ + E e+    d+++Le+l  +++el++k++q+e k++ +l  ++++
  gi|488600002|ref|YP_007906473.1| 160 TQFERLIDEIDRLREKLNEIERIEKNESEI----DVAELERLYSKEKELMDKVNQIESKLEYILGVIKKP 225
                                       678999*********************998....***************************999888876 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.043
                                       ....HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              FlgN   1 M.elleeLielleeelelleeLlelleeEteaLkagdieaLeelleekqellekleqleqkrakllaelg 69 
                                       M e++++L++ l++ +  +++L+++ + +    +++++++L + +eek+  l+kl+++  ++ak l +++
  gi|488600002|ref|YP_007906473.1| 289 MiEEVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDAE 358
                                       5678999*************************************************99999998886665 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   7.9      0.59   2.2e+02       5      59 ..     161     216 ..     157     224 .. 0.83
   2 ?   16.1   7.9   2.9e-05     0.011       3      64 ..     283     346 ..     281     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.59
                          CCDC-167   5 eIdkleeklascrerLeaver.rlrkeelseeeResleeEeaslkeqleenekeLk 59 
                                       + ++l +++ ++re+L+++er + ++ e+   e e+l+  e++l+ ++++ e++L+
  gi|488600002|ref|YP_007906473.1| 161 QFERLIDEIDRLREKLNEIERiEKNESEIDVAELERLYSKEKELMDKVNQIESKLE 216
                                       667888899999999999998345566888888999999999********999997 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.9e-05
                          CCDC-167   3 aseIdkleeklascrerLeaverrlrkee..lseeeResleeEeaslkeqleenekeLksLrke 64 
                                       +s+ dk+ e++ +++++L +v +r+++ +  + ++  + + +E +sl++q+ee+e+eLk+L+ e
  gi|488600002|ref|YP_007906473.1| 283 VSDADKMIEEVDNLKRELTDVQSRIKNLKsiMASKSSNTIDKEVRSLRKQIEEKENELKKLKTE 346
                                       677889999999***********999655226677788899********************988 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   2.2       1.2   4.4e+02      18      65 ..     161     215 ..     154     218 .. 0.67
   2 ?    0.7   0.1       1.4   5.2e+02      15      37 ..     289     311 ..     278     315 .. 0.64
   3 ?   15.0   3.2   4.9e-05     0.018       6      44 ..     313     352 ..     309     358 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.2
                              FlxA  18 qiasLqkQiknlqkqLkelses.deltkeekk......kqqqliqaQIqqlqaQI 65 
                                       q ++L  +i++l ++L+e+    +++++ +         +++++  +++q+++ +
  gi|488600002|ref|YP_007906473.1| 161 QFERLIDEIDRLREKLNEIERIeKNESEIDVAelerlySKEKELMDKVNQIESKL 215
                                       6778888899999999998876422222222234455688888888888888766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.4
                              FlxA  15 sasqiasLqkQiknlqkqLkels 37 
                                       + +++ +L+++++++q  +k+l+
  gi|488600002|ref|YP_007906473.1| 289 MIEEVDNLKRELTDVQSRIKNLK 311
                                       44556666777777777776665 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 4.9e-05
                              FlxA   6 asssssssgsasqiasLqkQiknlqkqLkelses.deltk 44 
                                         +s+ss++++++++sL+kQi++ +++Lk+l+++ +e+ k
  gi|488600002|ref|YP_007906473.1| 313 IMASKSSNTIDKEVRSLRKQIEEKENELKKLKTElSEMAK 352
                                       56899***************************99777765 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   2.9       4.7   1.7e+03      13      64 ..     130     183 ..     123     201 .. 0.57
   2 ?   14.7   4.6   7.8e-05     0.029      11      83 ..     291     356 ..     284     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 4.7
                      Lzipper-MIP1  13 veqLqerLqeeeklrraLekalssssdgsllslstllp..kkakellkeiallE 64 
                                       +++  e  ++ e+lr   +  ls +   ++ + + l++  +  +e l ei+ +E
  gi|488600002|ref|YP_007906473.1| 130 IKRITEIIKQYEALRNDSRYLLSINMLEKITQFERLIDeiDRLREKLNEIERIE 183
                                       555555555555555555555544444445555555553346666666666655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.8e-05
                      Lzipper-MIP1  11 qeveqLqerLqeeeklrraLekalssssdgsllslstllpkkakellkeiallEeevvkLEqkllsLyrklfq 83 
                                       +ev +L+++L + ++  + L++ ++ s      ++s+ ++k+++ l+k i+  E+e  kL+ +l+++  kl++
  gi|488600002|ref|YP_007906473.1| 291 EEVDNLKRELTDVQSRIKNLKSIMA-S------KSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYD 356
                                       799*********9999999999993.3......346669******************************9986 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.0      0.13        48       7      69 ..     155     216 ..     151     224 .. 0.85
   2 ?   14.5   1.1   8.6e-05     0.032      16      88 ..     288     360 ..     281     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                              FliJ   7 Laeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqela 69 
                                       + e  +++++   ++++l++ ++e +   ++e+  +++ael  + +  + l ++++q++++l+
  gi|488600002|ref|YP_007906473.1| 155 MLEKITQFERLIDEIDRLREKLNEIERIEKNES-EIDVAELERLYSKEKELMDKVNQIESKLE 216
                                       556778899999999*********988888887.99999999999999999999999888776 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.6e-05
                              FliJ  16 qaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqe 88 
                                       ++ e++++l++++ + q+++++  + ++     ++ +  ++l+++i++ ++el++++ ++++  +++  a+ e
  gi|488600002|ref|YP_007906473.1| 288 KMIEEVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDAEVE 360
                                       667899*****************99999999999**************************9999999888766 PP

>> DUF4239  Protein of unknown function (DUF4239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   0.00012     0.045      41     112 ..     108     178 ..      97     207 .. 0.81
   2 ?   -0.1   1.3       1.8   6.5e+02      77     111 ..     268     305 ..     191     336 .. 0.47
   3 ?    0.3   1.5       1.4     5e+02      67     123 ..     294     350 ..     262     361 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                           DUF4239  41 vtrnlislftselerkeakaliadyvktivseerslvrasrgelslkasseltkLldllaevkgdassesaa 112
                                       + +n+  lf  ++ + e+ + +++ +  i+++   l ++sr  ls+ + +++t+++ l++e+++ + + +  
  gi|488600002|ref|YP_007906473.1| 108 IAKNFRLLFAVKPPELEGLNNAIKRITEIIKQYEALRNDSRYLLSINMLEKITQFERLIDEIDRLREKLN-E 178
                                       5677777887777788999*******************************************99887773.3 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                           DUF4239  77 vrasrgelslk...asseltkLldllaevkgdassesa 111
                                       v++s+ +l lk   + s+ +k+ + ++++k++  + + 
  gi|488600002|ref|YP_007906473.1| 268 VKDSQRDLILKnlsMVSDADKMIEEVDNLKRELTDVQS 305
                                       22232223222222333333333333333333333322 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                           DUF4239  67 ktivseerslvrasrgelslkasseltkLldllaevkgdassesaaveellseiaql 123
                                       + + +e   +    ++  s++as+  +++ + +  +++++ ++++  ++l  e+ ++
  gi|488600002|ref|YP_007906473.1| 294 DNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEM 350
                                       333222222332235566777777777777777777777777777766666665554 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 ?   -0.2   0.0       2.9     1e+03      34      59 ..      26      51 ..      16      55 .. 0.78
   2 ?    2.6   0.1       0.4   1.5e+02      50      61 ..     169     180 ..     160     191 .. 0.80
   3 ?   10.5   0.3    0.0014      0.51      39      68 ..     315     344 ..     292     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.9
                                      HTTTTSTSHTHHHHHHHHHHHHHHHT CS
                       Trans_reg_C 34 vwgededvddrtvdvhisrLRkkLed 59
                                      + +++e   +r +++ is LR+ ++d
  gi|488600002|ref|YP_007906473.1| 26 IKRDQEIEIERFINSRISDLRDAVSD 51
                                      555555566889999******99876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.4
                                       HHHHHHHHHTTT CS
                       Trans_reg_C  50 isrLRkkLedde 61 
                                       i rLR+kL++ e
  gi|488600002|ref|YP_007906473.1| 169 IDRLREKLNEIE 180
                                       89*******964 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0014
                                       STSHTHHHHHHHHHHHHHHHTTTTSSSSEE CS
                       Trans_reg_C  39 edvddrtvdvhisrLRkkLeddekkprlIe 68 
                                          +++t+d  ++ LRk +e++e++ + ++
  gi|488600002|ref|YP_007906473.1| 315 ASKSSNTIDKEVRSLRKQIEEKENELKKLK 344
                                       5679*****************765555555 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       1.6   5.7e+02      74     105 ..      27      58 ..       9      74 .. 0.76
   2 ?    6.4   4.0     0.024       8.9      62     118 ..     163     220 ..     123     224 .. 0.79
   3 ?   11.8   6.9   0.00052      0.19      48     120 ..     284     357 ..     258     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.6
                           DUF1664  74 kldeqkeiskeikeevtevredlseigedves 105
                                       k d+ +ei + i++ ++++r+ +s++  ++es
  gi|488600002|ref|YP_007906473.1|  27 KRDQEIEIERFINSRISDLRDAVSDFILELES 58 
                                       45677888888999999999988888777665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                           DUF1664  62 rhLssridrvdkkldeqkeiskei.keevtevredlseigedvesvkeavegleskle 118
                                       ++L ++idr+ +kl+e ++i k+  + +v+e+++  s+ +e +++v+++ ++le  l 
  gi|488600002|ref|YP_007906473.1| 163 ERLIDEIDRLREKLNEIERIEKNEsEIDVAELERLYSKEKELMDKVNQIESKLEYILG 220
                                       579999**********999987651558888888888888888888888777776655 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00052
                           DUF1664  48 kqleqvseslaatkrhLs...sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       ++ +++ e++ + kr+L+   sri+++ + +   ++ s+ i++ev ++r++++e +++++++k+  +++++kl + 
  gi|488600002|ref|YP_007906473.1| 284 SDADKMIEEVDNLKRELTdvqSRIKNLKSIMA--SKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDA 357
                                       45577888999999998633367777776664..456889********************************9865 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.3       4.6   1.7e+03      79      79 ..     182     182 ..     122     220 .. 0.54
   2 ?   12.7   0.3   0.00029      0.11      20      45 ..     290     315 ..     288     319 .. 0.88
   3 ?    5.2   3.6     0.062        23      81     119 ..     316     354 ..     311     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.6
                              Uds1  79 s 79 
                                        
  gi|488600002|ref|YP_007906473.1| 182 I 182
                                       1 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00029
                              Uds1  20 leeVeelkkelkaLeerlealrkkLa 45 
                                       +eeV++lk+el+ +++r+++l+  +a
  gi|488600002|ref|YP_007906473.1| 290 IEEVDNLKRELTDVQSRIKNLKSIMA 315
                                       69******************998765 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.062
                              Uds1  81 reslakaeeelaeserkvdelaselekleeraaevrrrL 119
                                       ++s+++ ++e+ ++ ++++e ++el+kl++++ e+ ++L
  gi|488600002|ref|YP_007906473.1| 316 SKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKL 354
                                       568899999***********************9999998 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.9   6.8e+02      50      66 ..     122     138 ..     117     146 .. 0.80
   2 ?    6.3   1.2     0.036        13      15      66 ..     164     216 ..     151     225 .. 0.68
   3 ?    6.9   0.8     0.024       8.6      35      66 ..     284     315 ..     265     322 .. 0.78
   4 ?    4.2   0.3      0.17        61      18      63 ..     324     352 ..     317     365 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.9
                           NPV_P10  50 qLaeletkvenIqdiLn 66 
                                       +L+ l+++++ I++i  
  gi|488600002|ref|YP_007906473.1| 122 ELEGLNNAIKRITEIIK 138
                                       57889999999999876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.036
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvteln.ekLdaqsaqLaeletkvenIqdiLn 66 
                                        + d +d l +++++++   ++ +e+  ++L+++  + +el +kv++I++ L 
  gi|488600002|ref|YP_007906473.1| 164 RLIDEIDRLREKLNEIERIEKNESEIDvAELERLYSKEKELMDKVNQIESKLE 216
                                       44456666666666666666665666426788888888888889999998775 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.024
                           NPV_P10  35 pdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                        d +++ e++d++  +L+++++ ++n ++i+ 
  gi|488600002|ref|YP_007906473.1| 284 SDADKMIEEVDNLKRELTDVQSRIKNLKSIMA 315
                                       45567778889999999999999999999876 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.17
                           NPV_P10  18 dkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                       + V                   l +++++  ++L++l+t++++  +
  gi|488600002|ref|YP_007906473.1| 324 KEVR-----------------SLRKQIEEKENELKKLKTELSEMAK 352
                                       4444.................4444444444444444444444333 PP

>> DUF3772  Protein of unknown function (DUF3772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.19        68      10      23 ..     161     174 ..     157     177 .. 0.84
   2 ?    5.8   0.0     0.032        12       7      25 ..     282     300 ..     279     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
                           DUF3772  10 rAdqLsdqIsklRR 23 
                                       + ++L+d+I++lR 
  gi|488600002|ref|YP_007906473.1| 161 QFERLIDEIDRLRE 174
                                       6689********95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                           DUF3772   7 lkvrAdqLsdqIsklRRer 25 
                                       ++++Ad +++++++l Re+
  gi|488600002|ref|YP_007906473.1| 282 MVSDADKMIEEVDNLKREL 300
                                       5789*************97 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 ?   -0.3   0.0       2.8     1e+03      19      49 ..      20      51 ..      14      80 .. 0.47
   2 ?    5.4   1.1     0.048        17      21      84 ..     155     216 ..     122     227 .. 0.69
   3 ?    7.1   0.3     0.014       5.1      78     100 ..     289     313 ..     247     320 .. 0.58
   4 ?    8.7   1.9    0.0046       1.7      40      98 ..     293     351 ..     287     368 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.8
                      Baculo_PEP_C 19 tnvLnair.lqnvqilaqlatlldaietqLna 49
                                       ++L+ i+  q+++i   +++ + ++   +++
  gi|488600002|ref|YP_007906473.1| 20 KEALKNIKrDQEIEIERFINSRISDLRDAVSD 51
                                      33343332123333333333333333333222 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.048
                      Baculo_PEP_C  21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt....rldtlltnLtdalnalqdtlr 84 
                                       +L+ i    +q    l   +d + ++Ln+++  +++  +e+d     rl +  ++L d++n+++ +l+
  gi|488600002|ref|YP_007906473.1| 155 MLEKI----TQF-ERLIDEIDRLREKLNEIER-IEKNESEIDVaeleRLYSKEKELMDKVNQIESKLE 216
                                       34444....222.3334444555556666543.66656666557677888899999999999987665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.014
                      Baculo_PEP_C  78 alq..dtlrneLtnlnsiltnLlss 100
                                        ++  d+l+ eLt ++s + nL s 
  gi|488600002|ref|YP_007906473.1| 289 MIEevDNLKRELTDVQSRIKNLKSI 313
                                       2223345566666666666666554 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0046
                      Baculo_PEP_C  40 ldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLl 98 
                                       +d+++++L+++++++k+l + ++   +++++++++ + +l    ++ +neL+ l+++l++++
  gi|488600002|ref|YP_007906473.1| 293 VDNLKRELTDVQSRIKNLKSIMA---SKSSNTIDKEVRSLRkqiEEKENELKKLKTELSEMA 351
                                       66677777777777776544333...344555555555555334444566666666666555 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   3.4       1.6   5.8e+02      20      44 ..     155     179 ..     126     216 .. 0.78
   2 ?    1.5   0.1       0.9   3.3e+02      38      55 ..     290     307 ..     268     319 .. 0.55
   3 ?   11.9   1.3   0.00049      0.18      28      58 ..     320     350 ..     302     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.6
                     TolA_bind_tri  20 llelqqqlealqqelreLRGqiEel 44 
                                       +le  +q e+l  e+++LR ++ e 
  gi|488600002|ref|YP_007906473.1| 155 MLEKITQFERLIDEIDRLREKLNEI 179
                                       5555678888888888888766554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.9
                     TolA_bind_tri  38 RGqiEelqyqleqleerQ 55 
                                         +++ l+ +l +++ r 
  gi|488600002|ref|YP_007906473.1| 290 IEEVDNLKRELTDVQSRI 307
                                       333333333333333333 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00049
                     TolA_bind_tri  28 ealqqelreLRGqiEelqyqleqleerQrdl 58 
                                       ++  +e+r+LR qiEe +++l++l++   ++
  gi|488600002|ref|YP_007906473.1| 320 NTIDKEVRSLRKQIEEKENELKKLKTELSEM 350
                                       56789******************99877665 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   9.1      0.02       7.3      32      86 ..     161     216 ..     122     224 .. 0.83
   2 ?    5.8  11.7      0.04        15      10      69 ..     284     348 ..     278     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.02
                              BRE1  32 kklrleaekakadqkyfaamr.skdalenelkkLnkllsKsselieqLkelekefv 86 
                                       +  rl  e+++ ++k  +++r +k+  e+++  L +l+sK++el+++ +++e+++ 
  gi|488600002|ref|YP_007906473.1| 161 QFERLIDEIDRLREKLNEIERiEKNESEIDVAELERLYSKEKELMDKVNQIESKLE 216
                                       4569999**************77999**************************9875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.04
                              BRE1  10 kafeelseqlskkvkeltileekklrleaekaka.....dqkyfaamrskdalenelkkLnklls 69 
                                          +++ e++++++ elt+ +++++ l++ +a       d++  +++++++  enelkkL++ ls
  gi|488600002|ref|YP_007906473.1| 284 SDADKMIEEVDNLKRELTDVQSRIKNLKSIMASKssntiDKEVRSLRKQIEEKENELKKLKTELS 348
                                       55677888999999999999999998877555443334478889999999999999999998876 PP

>> JMY  Junction-mediating and -regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.6      0.15        56     103     152 ..     164     215 ..     132     220 .. 0.75
   2 ?   11.6   7.4   0.00035      0.13     256     342 ..     253     339 ..     248     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.15
                               JMY 103 gleeelqrakeelrevlekhkkad..kmveLlkvYeeedeayqeLvtaatel 152
                                       +l +e++r +e+l+e+ +  k+ +   + eL ++Y++e e + + +++ ++l
  gi|488600002|ref|YP_007906473.1| 164 RLIDEIDRLREKLNEIERIEKNESeiDVAELERLYSKEKELMDKVNQIESKL 215
                                       46688899999999986655555511578999******99999988887765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00035
                               JMY 256 llaketLqllrakelclkqkraeikeemesleekekavaevdeLeiqyyelqLelyevqleiLkeeellltaqLdsl 332
                                       l +k +  +++ +   ++ +r+ i +++  +++ +k ++evd+L+ ++ ++q  + + +  +  +    + +++ sl
  gi|488600002|ref|YP_007906473.1| 253 LASKTSTAIMKGEVRVKDSQRDLILKNLSMVSDADKMIEEVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSL 329
                                       5567777889999999999*****************************************999************** PP

                               JMY 333 rrqikekqde 342
                                       r+qi+ek++e
  gi|488600002|ref|YP_007906473.1| 330 RKQIEEKENE 339
                                       *******987 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   5.1      0.71   2.6e+02      20      48 ..     162     189 ..     146     231 .. 0.63
   2 ?    3.8   0.5      0.18        65      12      41 ..     285     314 ..     268     323 .. 0.54
   3 ?   11.8   4.4   0.00057      0.21       8      56 ..     321     369 ..     313     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.71
                             Spc24  20 lesleselaelkeeleeleeeseekeser 48 
                                        e+l  e ++l+e+l+e+e+ +++ ese+
  gi|488600002|ref|YP_007906473.1| 162 FERLIDEIDRLREKLNEIERIEKN-ESEI 189
                                       556666666677777777666666.2222 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.18
                             Spc24  12 elsdleselesleselaelkeeleeleees 41 
                                       +++++ +e+++l+ el++ ++++++l++  
  gi|488600002|ref|YP_007906473.1| 285 DADKMIEEVDNLKRELTDVQSRIKNLKSIM 314
                                       444444455555555555555555554443 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00057
                             Spc24   8 riakelsdleselesleselaelkeeleeleeeseekeservedetllk 56 
                                       +i ke+++l +++e+ e+el++lk+el e+ ++  + e e+v d+++ k
  gi|488600002|ref|YP_007906473.1| 321 TIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDAEVELVFDAKADK 369
                                       6788999999999999999999999999988888776666655666555 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.18        66       3      42 ..      16      49 ..      15      52 .. 0.76
   2 ?   -0.1   0.0       2.7     1e+03      58      77 ..     122     141 ..     120     144 .. 0.88
   3 ?   -1.4   4.1       7.2   2.6e+03      31      54 ..     165     188 ..     130     219 .. 0.60
   4 ?   13.7   5.5   0.00013     0.049      26      78 ..     291     345 ..     274     351 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.18
                              Med9  3 lPliydilksiekdpnlsskdletktgelrhkLkkareli 42
                                      +P++ ++lk+i++d++++++ +      ++ +++  r ++
  gi|488600002|ref|YP_007906473.1| 16 IPELKEALKNIKRDQEIEIERF------INSRISDLRDAV 49
                                      899************8888877......666666666555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.7
                              Med9  58 eieeleeqlakKrelLkkyk 77 
                                       e+e l++ +++  e +k+y 
  gi|488600002|ref|YP_007906473.1| 122 ELEGLNNAIKRITEIIKQYE 141
                                       78999999999999999997 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 7.2
                              Med9  31 lrhkLkkarelirelpgidrsvee 54 
                                       l + +++ re ++e++ i+++  e
  gi|488600002|ref|YP_007906473.1| 165 LIDEIDRLREKLNEIERIEKNESE 188
                                       555677777777777777766444 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 0.00013
                              Med9  26 tktgelrhkLkkarelirelpg..idrsveeqeaeieeleeqlakKrelLkkykn 78 
                                        ++++l+  L  + + i++l+    ++s  + ++e+++l++q++ K++ Lkk+k 
  gi|488600002|ref|YP_007906473.1| 291 EEVDNLKRELTDVQSRIKNLKSimASKSSNTIDKEVRSLRKQIEEKENELKKLKT 345
                                       4555566666666666666666444577777888888888888888888888875 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.7    0.0094       3.5      68     128 ..     150     216 ..     106     236 .. 0.55
   2 ?    8.1   5.3    0.0048       1.8      62     141 ..     274     354 ..     269     363 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0094
                      Allexi_40kDa  68 lnpvsllsqttlLselrdalrtltklldklksvekklelsaet......asdskllkklesietsle 128
                                       l ++++l + t++ +l d++ +l+++l++++++ek+ ++           ++++l++k++ ie +le
  gi|488600002|ref|YP_007906473.1| 150 LLSINMLEKITQFERLIDEIDRLREKLNEIERIEKNESEIDVAelerlySKEKELMDKVNQIESKLE 216
                                       3445555577777777777777777777777766654332222000000233344444444444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0048
                      Allexi_40kDa  62 dsiinklnpvslls.qttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldel 137
                                       d i+++l  vs    +  ++ +l+ +l+ +++ +++lks++ +++ ++ +++ ++l k++e  e++l++l+++l e+
  gi|488600002|ref|YP_007906473.1| 274 DLILKNLSMVSDADkMIEEVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEM 350
                                       66777777775544244556677777777777777777777766666666666777788888888888888888888 PP

                      Allexi_40kDa 138 ssse 141
                                       +++ 
  gi|488600002|ref|YP_007906473.1| 351 AKKL 354
                                       7765 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.8      0.03        11      41      64 ..     155     178 ..     129     179 .. 0.76
   2 ?    1.0   0.1       1.7   6.3e+02      34      56 ..     290     311 ..     280     317 .. 0.58
   3 ?    5.7   0.5      0.06        22      45      64 ..     330     349 ..     316     350 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  41 larklaeleeriaeLqalraeLaa 64 
                                         +k+ + e+ i+e+++lr+ L++
  gi|488600002|ref|YP_007906473.1| 155 MLEKITQFERLIDEIDRLREKLNE 178
                                       5689*****************987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  34 cqdvrallarklaeleeriaeLq 56 
                                        ++v+  l+r l +++ ri+ L+
  gi|488600002|ref|YP_007906473.1| 290 IEEVD-NLKRELTDVQSRIKNLK 311
                                       33444.45566666666666665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.06
                                       HHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  45 laeleeriaeLqalraeLaa 64 
                                       ++++ee+ +eL++l++eL +
  gi|488600002|ref|YP_007906473.1| 330 RKQIEEKENELKKLKTELSE 349
                                       789***************86 PP

>> Pro_dh  Proline dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.1   4.1e+02       3      52 ..     138     187 ..     123     216 .. 0.55
   2 ?    9.5   2.9    0.0017      0.63      25     102 ..     281     365 ..     254     371 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHT.TEEEEEEES-SS--SHHHHHHHHHHHHHHHHHHHHHHCCS- CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh   3 ktieklkkr.gvrlsldllgeavlteedadryleayleaiksiekaskalk 52 
                                       k+ e+l+++  + ls+++l++ ++ e+ +d+ +++++e +++ie+ +k+++
  gi|488600002|ref|YP_007906473.1| 138 KQYEALRNDsRYLLSINMLEKITQFERLIDE-IDRLREKLNEIERIEKNES 187
                                       4455566554666777777664444433333.3444444444444443222 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0017
                                       -SHHHHHHHHHHHHHHHHHHHHHHCCS-TTCC-S.EEE-GGG.......T.T-SGGGHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.......x.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Pro_dh  25 lteedadryleayleaiksiekaskalkvleapg.vsvklsa.......p.rletaeeeevmeelverlrtlakeak 92 
                                          +dad+++e++ ++ +++ +++++ k  + ++ ++ k s        + r + +e+e+ +++l+ +l+++ak+ +
  gi|488600002|ref|YP_007906473.1| 281 SMVSDADKMIEEVDNLKRELTDVQSRIK--NLKSiMASKSSNtidkevrSlRKQIEEKENELKKLKTELSEMAKKLY 355
                                       4456777777777777777777666333..3333577777777776654258888888889**************** PP

                                       HTT-EEEE-- CS
                                       xxxxxxxxxx RF
                            Pro_dh  93 elgvrlliDa 102
                                       +++v+l++Da
  gi|488600002|ref|YP_007906473.1| 356 DAEVELVFDA 365
                                       *********9 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.91   3.3e+02       3      36 ..      40      75 ..      38      78 .. 0.73
   2 ?    7.3   0.1     0.011       3.9       4      28 ..     161     185 ..     159     189 .. 0.92
   3 ?   -1.2   0.0       4.8   1.8e+03       6      20 ..     202     216 ..     197     223 .. 0.81
   4 ?    1.5   0.1      0.74   2.7e+02       4      26 ..     292     314 ..     289     319 .. 0.78
   5 ?   -0.6   0.1       3.2   1.2e+03       9      22 ..     337     350 ..     322     356 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.91
                         DASH_Dam1  3 pafaeLaDsletLdknled..LqqihesLsdfNeSF 36
                                       ++++L D+++++   le   ++ +h +L+++ ++F
  gi|488600002|ref|YP_007906473.1| 40 SRISDLRDAVSDFILELESfpIEFLHPKLQGVAKNF 75
                                      578999999999988887633577777777776666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
                         DASH_Dam1   4 afaeLaDsletLdknledLqqihes 28 
                                       +f++L D+++ L+++l+++++i+++
  gi|488600002|ref|YP_007906473.1| 161 QFERLIDEIDRLREKLNEIERIEKN 185
                                       8********************9986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.8
                         DASH_Dam1   6 aeLaDsletLdknle 20 
                                       +eL D++++++++le
  gi|488600002|ref|YP_007906473.1| 202 KELMDKVNQIESKLE 216
                                       688899998888876 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.74
                         DASH_Dam1   4 afaeLaDsletLdknledLqqih 26 
                                       +  +L+ +l+++++++++L++i 
  gi|488600002|ref|YP_007906473.1| 292 EVDNLKRELTDVQSRIKNLKSIM 314
                                       56678889999999999998885 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 3.2
                         DASH_Dam1   9 aDsletLdknledL 22 
                                       + +l++L++ l+++
  gi|488600002|ref|YP_007906473.1| 337 ENELKKLKTELSEM 350
                                       33333333333333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       6.9   2.5e+03     110     143 ..      25      57 ..       7      63 .. 0.57
   2 ?    3.8   4.7      0.12        44      93     184 ..     129     218 ..     122     220 .. 0.76
   3 ?   13.9   9.0   9.5e-05     0.035      72     146 ..     288     361 ..     265     369 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.9
                            DUF724 110 erkklekkieeeesekrkleeeidelekkilele 143
                                       ++k+ +++ie e+  ++++++  d ++  ilele
  gi|488600002|ref|YP_007906473.1|  25 NIKR-DQEIEIERFINSRISDLRDAVSDFILELE 57 
                                       2222.44555555555556666666666666655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                            DUF724  93 rlnkLlslkdeqtklleerkk.lekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseae 168
                                        ++++ ++ ++++ l++ ++  l  ++ e+ ++ ++l +eid l +k  e+er +   k++ e + +e+ rl s+++
  gi|488600002|ref|YP_007906473.1| 129 AIKRITEIIKQYEALRNDSRYlLSINMLEKITQFERLIDEIDRLREKLNEIERIE---KNESEIDVAELERLYSKEK 202
                                       5666666666666665554441566788888888888888888888888888888...589999999********** PP

                            DUF724 169 kleeeledveqeFeav 184
                                       +l ++++++e++ e +
  gi|488600002|ref|YP_007906473.1| 203 ELMDKVNQIESKLEYI 218
                                       ******9999988765 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 9.5e-05
                            DUF724  72 slkeslaeLekhGFdVkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerql 146
                                       +++e++ +L+++  dV++  + l+ +++ k++   + +e + l k+iee+e+e +kl++e++e+ kk  + e +l
  gi|488600002|ref|YP_007906473.1| 288 KMIEEVDNLKRELTDVQSRIKNLKSIMASKSSN-TIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDAEVEL 361
                                       444445555555555555555555555555443.46667777777777777777777777777777776666554 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.7      0.63   2.3e+02      31      75 ..     133     173 ..     122     175 .. 0.81
   2 ?    0.2   0.9       2.9   1.1e+03      22      61 ..     167     205 ..     161     219 .. 0.45
   3 ?   13.6   6.3   0.00019     0.071      22      75 ..     291     344 ..     286     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.63
                       Cep57_MT_bd  31 lqelaaqynaldpslgkrkRkdLaeeleelvkrlEaKadqIykLy 75 
                                        +e  +qy+al     + +R  L  ++ e + + E+  d I +L+
  gi|488600002|ref|YP_007906473.1| 133 ITEIIKQYEALR----NDSRYLLSINMLEKITQFERLIDEIDRLR 173
                                       455566666665....999**********************9997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.9
                       Cep57_MT_bd  22 dEfehlklelqelaaqynaldpslgkrkRkdLaeeleelv 61 
                                       dE++ l+ +l e + ++++ ++ ++ ++ + L ++ +el+
  gi|488600002|ref|YP_007906473.1| 167 DEIDRLREKLNEIE-RIEKNESEIDVAELERLYSKEKELM 205
                                       44444444444432.3444444444444444443333333 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00019
                       Cep57_MT_bd  22 dEfehlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEaKadqIykLy 75 
                                       +E++ lk el+++++++++l + + +++ +++ +e++ l k++E+K++  +kL+
  gi|488600002|ref|YP_007906473.1| 291 EEVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLK 344
                                       89*************************************************997 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 ?    8.0   2.9    0.0063       2.3      53     108 ..     166     222 ..     122     227 .. 0.82
   2 ?    7.8   3.8    0.0075       2.7      45     111 ..     293     357 ..     276     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0063
                            Nsp1_C  53 vengekIskLysevleaeqeqnkid.qeLeyiesqqdeLeslLdnyEkeleellskl 108
                                       ++  +++++  +e++++e+++++id  eLe + s+ +eL + ++++E++le +l+ +
  gi|488600002|ref|YP_007906473.1| 166 IDEIDRLREKLNEIERIEKNESEIDvAELERLYSKEKELMDKVNQIESKLEYILGVI 222
                                       444455555556778889999****669**********************9988655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0075
                            Nsp1_C  45 vneWDrvLvengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsklesq 111
                                       v +  r L +  ++I++L+   + a +++n id+e   + +q +e e+ L+++ +el+e+ +kl+ +
  gi|488600002|ref|YP_007906473.1| 293 VDNLKRELTDVQSRIKNLK--SIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDA 357
                                       5555566777777888876..578999*********************************9988765 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3       2.7     1e+03      38     125 ..       8      95 ..       4     116 .. 0.53
   2 ?    5.7   1.5      0.02       7.2       4     115 ..     123     237 ..     121     242 .. 0.64
   3 ?   11.4   5.6   0.00037      0.13      14      93 ..     268     352 ..     256     373 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.7
                             TMPIT  38 eikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllpkknglylklvlGnvn...vsllnk 111
                                       + k+++  + elk++lk++k+++   e e+ + +++++++ +  +++    l +    +l+  l  v    v  ++k
  gi|488600002|ref|YP_007906473.1|   8 KKKRERLTIPELKEALKNIKRDQ---EIEIERFINSRISDLRDAVSDFILELESFPIEFLHPKLQGVAknfVATMKK 81 
                                       45555666667777777777663...333334444555555555554444444444444443333221112455555 PP

                             TMPIT 112 qdkfkyKdeYekFk 125
                                       q  fk Kd+ e F 
  gi|488600002|ref|YP_007906473.1|  82 QWVFKDKDNTEYFN 95 
                                       55666666666665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                             TMPIT   4 weelekefkeleetakeykqkleelsklqs.kcskei...kkqkkrlkelksslkklkksvkeeeeeeveelkeelk 76 
                                       +e l++ +k++ e  k+y++  ++   l s ++ ++i   ++   ++ +l+++l+++++  k+e+e  v+el++  +
  gi|488600002|ref|YP_007906473.1| 123 LEGLNNAIKRITEIIKQYEALRNDSRYLLSiNMLEKItqfERLIDEIDRLREKLNEIERIEKNESEIDVAELERLYS 199
                                       56778888888888888888888776665423444440004444566677788888888777888888888888888 PP

                             TMPIT  77 erkkvlkevesllpkknglylklvlGnvnvsllnkqdkf 115
                                       ++k+ +++v+++  +k  + l ++  ++++ + ++  ++
  gi|488600002|ref|YP_007906473.1| 200 KEKELMDKVNQI-ESKLEYILGVIKKPIKLYAHSTGRRV 237
                                       888888877776.55555566665555555555555555 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00037
                             TMPIT  14 leetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk....eeeeeeveelkeelkerkkvlkeve 86 
                                       ++++++ ++ k  ++ +  +k+ +e+++ k++l++++s++k+lk+ +     +  ++ev++l+++++e+++ lk+++
  gi|488600002|ref|YP_007906473.1| 268 VKDSQRDLILKNLSMVSDADKMIEEVDNLKRELTDVQSRIKNLKSIMAskssNTIDKEVRSLRKQIEEKENELKKLK 344
                                       55666666666666677777788888888888888888888877765433333334455556666666666666555 PP

                             TMPIT  87 sllpkk.n 93 
                                         l +  +
  gi|488600002|ref|YP_007906473.1| 345 TELSEMaK 352
                                       55544333 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.3     0.015       5.4      55     127 ..     151     223 ..     129     233 .. 0.80
   2 ?    6.0   5.8     0.017       6.3      57     127 ..     287     355 ..     278     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                          ISG65-75  55 llketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekae 127
                                       l  ++ +k+++ e  ++++d+ +ekl+++ + +k++++++ ++ e+l++  +e  +k+++ ++k +  l +++
  gi|488600002|ref|YP_007906473.1| 151 LSINMLEKITQFERLIDEIDRLREKLNEIERIEKNESEIDVAELERLYSKEKELMDKVNQIESKLEYILGVIK 223
                                       445788999999999*****************99999999999999988888888888888887776665555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                          ISG65-75  57 ketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekae 127
                                       +++ +++++++ ++  v+ + ++l+s++++  + +++ +++++ l+k++ee +++ kk +++  + ++k  
  gi|488600002|ref|YP_007906473.1| 287 DKMIEEVDNLKRELTDVQSRIKNLKSIMAS--KSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLY 355
                                       567788889999999999999999999998..57888889999***************9999999888765 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4      0.14        50      30      55 ..     159     184 ..     150     194 .. 0.78
   2 ?   -1.2   0.0       8.8   3.2e+03      33      51 ..     194     212 ..     189     217 .. 0.53
   3 ?    4.2   0.1      0.19        69      32      56 ..     292     316 ..     285     322 .. 0.80
   4 ?    7.2   0.9     0.022         8      17      51 ..     324     358 ..     317     368 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  30 qqqidrlqrqlrllaerlkeleessg 55 
                                         q +rl  ++++l+e+l+e+e  ++
  gi|488600002|ref|YP_007906473.1| 159 ITQFERLIDEIDRLREKLNEIERIEK 184
                                       56889999999999999999987755 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 8.8
                                       HHHHHHHHHHHHHT-XXXX CS
                              SlyX  33 idrlqrqlrllaerlkele 51 
                                       ++rl  + ++l+++++++e
  gi|488600002|ref|YP_007906473.1| 194 LERLYSKEKELMDKVNQIE 212
                                       4444444455555554444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHT-XXXXXXXXX CS
                              SlyX  32 qidrlqrqlrllaerlkeleessga 56 
                                       ++d l+r+l  ++ r+k+l++ +++
  gi|488600002|ref|YP_007906473.1| 292 EVDNLKRELTDVQSRIKNLKSIMAS 316
                                       7899999999999999999887654 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                              SlyX  17 dtieeLndvvaeqqqqidrlqrqlrllaerlkele 51 
                                       + + +L +++ e + ++++l+++l ++a++l ++e
  gi|488600002|ref|YP_007906473.1| 324 KEVRSLRKQIEEKENELKKLKTELSEMAKKLYDAE 358
                                       44455555555566666666666666666654444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5      0.15        56      40      65 ..     160     184 ..     103     224 .. 0.50
   2 ?    3.4   0.5      0.24        89      55      88 ..     278     311 ..     249     316 .. 0.64
   3 ?    6.1   0.5     0.035        13      23      58 ..     321     356 ..     312     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.15
                            DUF948  40 kqvdpilkevedllakvnelledvne 65 
                                        q + +++e+++l +k ne  e +++
  gi|488600002|ref|YP_007906473.1| 160 TQFERLIDEIDRLREKLNE-IERIEK 184
                                       5555555555555555555.333333 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.24
                            DUF948  55 kvnelledvneklekvdplteavadlgesvseln 88 
                                       k   +++d  + +e+vd+l  ++ d+   +++l+
  gi|488600002|ref|YP_007906473.1| 278 KNLSMVSDADKMIEEVDNLKRELTDVQSRIKNLK 311
                                       4445666666666666666666666666666664 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.035
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvne 58 
                                        + k +++++++iee e++++++ +e+ ++ +k  +
  gi|488600002|ref|YP_007906473.1| 321 TIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYD 356
                                       578899999999999999999999999999998765 PP

>> YgaB  YgaB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.4       3.7   1.3e+03      48      73 ..      15      40 ..       8      43 .. 0.83
   2 ?    8.9   1.1    0.0053         2      35      62 ..     155     182 ..     151     190 .. 0.86
   3 ?    3.6   0.0      0.23        85       2      26 ..     194     218 ..     193     233 .. 0.84
   4 ?    6.0   6.1     0.043        16       8      61 ..     292     345 ..     281     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.7
                              YgaB 48 eikrkkkeLkeiqkvFekQteevirs 73
                                       i ++k+ Lk+i++  e  +e  i+s
  gi|488600002|ref|YP_007906473.1| 15 TIPELKEALKNIKRDQEIEIERFINS 40
                                      57889999999999888888888887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0053
                              YgaB  35 klekeaklesiqeeikrkkkeLkeiqkv 62 
                                        lek +++e + +ei+r++++L+ei+++
  gi|488600002|ref|YP_007906473.1| 155 MLEKITQFERLIDEIDRLREKLNEIERI 182
                                       67899********************987 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.23
                              YgaB   2 FerLVseQmktmdkLLflQselerC 26 
                                        erL s+  ++mdk+ ++ s+le  
  gi|488600002|ref|YP_007906473.1| 194 LERLYSKEKELMDKVNQIESKLEYI 218
                                       689999999***********99965 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.043
                              YgaB   8 eQmktmdkLLflQselerCqeiekeLlklekeaklesiqeeikrkkkeLkeiqk 61 
                                       e  ++  +L ++Qs +   + i +   +   + +++s++++i++k +eLk++++
  gi|488600002|ref|YP_007906473.1| 292 EVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKT 345
                                       555555678889999999999999999999999999999999999999998875 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.5       0.4   1.5e+02      46      78 ..     144     184 ..      87     237 .. 0.58
   2 ?    9.9   3.0     0.002      0.72      26      83 ..     279     353 ..     248     363 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.4
                                       S.........SSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHH CS
                               MCU  46 l.........nveeeqlkkereleekleelreelepleekke 78 
                                                 n+  e+  + ++l +++++lre+l+++e+ ++
  gi|488600002|ref|YP_007906473.1| 144 RndsryllsiNML-EKITQFERLIDEIDRLREKLNEIERIEK 184
                                       1444444444333.2333333444455555555555444222 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.002
                                       X...............XXXXXXXXXXXXXXXXX-SS..SSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCC CS
                               MCU  26 e...............eeakvllrvkqlvkalesal..nveeeqlkkereleekleelreelepleekkeeidek 83 
                                       +               + +++l++v++ +k+l+s++  + ++   k++r+l++++ee ++el++l+++ +e+++k
  gi|488600002|ref|YP_007906473.1| 279 NlsmvsdadkmieevdNLKRELTDVQSRIKNLKSIMasKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKK 353
                                       2444455555555565557899*************9765555566777888888888888888877755555443 PP

>> DUF2683  Protein of unknown function (DUF2683)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.8   0.00011     0.041      11      74 ..     129     197 ..     125     201 .. 0.87
   2 ?   -1.0   0.3       5.8   2.1e+03      27      41 ..     317     331 ..     281     352 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00011
                           DUF2683  11 esnriieivKakydlkdksa...Aidll..ieqyaeyllEaElkPefvekirnimKgeepidigdiedl 74 
                                         +ri ei+K    l+++s     i++l  i+q++  + E +   e +++i  i K+e  id+++ e l
  gi|488600002|ref|YP_007906473.1| 129 AIKRITEIIKQYEALRNDSRyllSINMLekITQFERLIDEIDRLREKLNEIERIEKNESEIDVAELERL 197
                                       569*******999******644489998889*********98888999***************999876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.8
                           DUF2683  27 dksaAidllieqyae 41 
                                       + s  id+ +    +
  gi|488600002|ref|YP_007906473.1| 317 KSSNTIDKEVRSLRK 331
                                       333444444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  18.3      0.48   1.7e+02     100     195 ..      25     179 ..       2     223 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.48
                            AAA_23 100 kgkttkkaklellei......deleqfisellgskkiilnlilflgqer............feefelkdkke..... 153
                                       + k+ ++ + e          ++l++ +s+ +    +++++ +++++ +            ++ f++kd  e     
  gi|488600002|ref|YP_007906473.1|  25 NIKRDQEIEIE---RfinsriSDLRDAVSDFILEL-ESFPIEFLHPKLQgvaknfvatmkkQWVFKDKDNTEyfnsv 97 
                                       22222222111...122234477777777654443.45777777777778888888888887888887777788888 PP

                            AAA_23 154 ........................rleelekeleeledekkllekl.........eqekekek.......eleelee 190
                                                               +le l+++++ +++++k+ e+l         ++ +ek         e++ l+e
  gi|488600002|ref|YP_007906473.1|  98 sksterlviaiaknfrllfavkppELEGLNNAIKRITEIIKQYEALrndsryllsINMLEKITqferlidEIDRLRE 174
                                       88999999999999999999999988888888888888888777777777777774444444422233334444444 PP

                            AAA_23 191 eleei 195
                                       +l+ei
  gi|488600002|ref|YP_007906473.1| 175 KLNEI 179
                                       44433 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       8.7   3.2e+03      52      68 ..      36      52 ..      13      83 .. 0.64
   2 ?   -0.8   0.0       5.2   1.9e+03       2      47 ..      97     143 ..      96     150 .. 0.78
   3 ?   -0.3   4.4       3.7   1.3e+03      17      41 ..     198     222 ..     129     228 .. 0.70
   4 ?    2.0   0.1      0.69   2.5e+02      22      42 ..     288     308 ..     273     314 .. 0.77
   5 ?   11.1   1.9     0.001      0.37       6      45 ..     307     358 ..     303     370 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 8.7
                              Rx_N 52 eavkeWlkelrdlayda 68
                                        ++  +++lrd++ d 
  gi|488600002|ref|YP_007906473.1| 36 RFINSRISDLRDAVSDF 52
                                      44555666777766654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 5.2
                              Rx_N   2 vsallqkLadllaeeakllkgvk.eeleklkdeLesiqavLedaeer 47 
                                       vs   ++L   +a++++ll  vk  ele l +  ++i  ++++ e  
  gi|488600002|ref|YP_007906473.1|  97 VSKSTERLVIAIAKNFRLLFAVKpPELEGLNNAIKRITEIIKQYEAL 143
                                       56677788888888888888888668999999999999999988874 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.7
                              Rx_N  17 akllkgvkeeleklkdeLesiqavL 41 
                                       +++ k++ +++++++++Le i +v+
  gi|488600002|ref|YP_007906473.1| 198 YSKEKELMDKVNQIESKLEYILGVI 222
                                       3556666666666666666666665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.69
                              Rx_N  22 gvkeeleklkdeLesiqavLe 42 
                                       ++ ee+++lk+eL  +q+ ++
  gi|488600002|ref|YP_007906473.1| 288 KMIEEVDNLKRELTDVQSRIK 308
                                       555889999999999987655 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.001
                              Rx_N   6 lqkLadllaeea............kllkgvkeeleklkdeLesiqavLedae 45 
                                       +++L +++a++             k++++ ++el+klk+eL+ +   L dae
  gi|488600002|ref|YP_007906473.1| 307 IKNLKSIMASKSsntidkevrslrKQIEEKENELKKLKTELSEMAKKLYDAE 358
                                       566666666666666676669888888999999*****************99 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       9.9   3.6e+03      30      95 ..      21      31 ..       6      60 .. 0.43
   2 ?    3.4   9.1      0.28     1e+02      16      77 ..     160     215 ..     122     223 .. 0.64
   3 ?   13.2  10.6   0.00027       0.1      13      91 ..     288     361 ..     274     364 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 9.9
                            APG6_N 30 eflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleale 95
                                      e lk++k++                                                        e
  gi|488600002|ref|YP_007906473.1| 21 EALKNIKRD-------------------------------------------------------QE 31
                                      222222222.......................................................22 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.28
                            APG6_N  16 kqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkeleker 77 
                                       +q+e++ +e+d ++e l+++++ +k+      e e    ele+l ++e+el+ + +++e++ 
  gi|488600002|ref|YP_007906473.1| 160 TQFERLIDEIDRLREKLNEIERIEKN------ESEIDVAELERLYSKEKELMDKVNQIESKL 215
                                       34555555555555555555555322......334445566666666666666666666554 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00027
                            APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaalee 89 
                                       ++ ++++++++e  + ++  k+lk+         ++ + +++e++ l+k+ ee+++eLk+l++e +e++++l ++e 
  gi|488600002|ref|YP_007906473.1| 288 KMIEEVDNLKRELTDVQSRIKNLKSIM-----ASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKLYDAEV 359
                                       334444444444444444444444442.....345678999999999999999999999999999999999999998 PP

                            APG6_N  90 el 91 
                                       el
  gi|488600002|ref|YP_007906473.1| 360 EL 361
                                       85 PP

>> DUF4972  Domain of unknown function (DUF4972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       5.7   2.1e+03      84     110 ..      16      42 ..      13      53 .. 0.64
   2 ?   11.2   3.0   0.00059      0.22      46     117 ..     130     205 ..     121     211 .. 0.80
   3 ?    2.3   0.3      0.34   1.2e+02      37      62 ..     321     346 ..     312     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.7
                           DUF4972  84 ivklkesiakikegnkaeaeeeadrli 110
                                       i +lke++++ik  ++ e e   +  i
  gi|488600002|ref|YP_007906473.1|  16 IPELKEALKNIKRDQEIEIERFINSRI 42 
                                       677888888888887776655555444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00059
                           DUF4972  46 ieqleelinkltdLrdesqyGekkgmYPeesr.aiLedaivklkesiakikegnkaea...eeeadrlikeakkai 117
                                       i++++e i++ ++Lr++s+y    +m  +  + + L d+i++l+e +++i+  +k e+     e +rl  + k+ +
  gi|488600002|ref|YP_007906473.1| 130 IKRITEIIKQYEALRNDSRYLLSINMLEKITQfERLIDEIDRLREKLNEIERIEKNESeidVAELERLYSKEKELM 205
                                       89***********************998755537899**************9999999332345555555555555 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.34
                           DUF4972  37 veevkteiyieqleelinkltdLrde 62 
                                       + + ++   ++q+ee+ n+l++L+ e
  gi|488600002|ref|YP_007906473.1| 321 TIDKEVRSLRKQIEEKENELKKLKTE 346
                                       5566788999************9976 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.1   0.00019     0.068      65     162 ..     101     206 ..      87     247 .. 0.66
   2 ?    5.1   1.2     0.034        12     194     229 ..     286     321 ..     266     329 .. 0.81
   3 ?    0.6   0.5      0.79   2.9e+02     123     159 ..     322     360 ..     318     367 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                              CorA  65 eeeevplsillgdnflitvrreplealdevikrlk.....deggkpkspgellyrlldeiv..drlfellekleeel 134
                                        e+ v ++i+ + ++l+ v   +le l+++ikr++      e  + +s + l +  l++i+  +rl+++++ l e+l
  gi|488600002|ref|YP_007906473.1| 101 TERLV-IAIAKNFRLLFAVKPPELEGLNNAIKRITeiikqYEALRNDSRYLLSINMLEKITqfERLIDEIDRLREKL 176
                                       33344.777777788999*****************999953334444555555555555432256666666666666 PP

                              CorA 135 deledel..edstkkeilrelaqlrrrlvk 162
                                       +e+e+    e++++  +l++l+  +++l  
  gi|488600002|ref|YP_007906473.1| 177 NEIERIEknESEIDVAELERLYSKEKELMD 206
                                       666654456666666666666666666554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.034
                              CorA 194 lrdlldelerllemlealrerleslqdtyssllser 229
                                        + +++e+++l ++l+ +++r+ +l+++++s +s+ 
  gi|488600002|ref|YP_007906473.1| 286 ADKMIEEVDNLKRELTDVQSRIKNLKSIMASKSSNT 321
                                       46899999***********************99986 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.79
                              CorA 123 lfellekleeeldeledel..edstkkeilrelaqlrrr 159
                                       ++++++ l ++++e e+el   + +  e++++l++ + +
  gi|488600002|ref|YP_007906473.1| 322 IDKEVRSLRKQIEEKENELkkLKTELSEMAKKLYDAEVE 360
                                       556666677777777777765555556666666666555 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.4      0.11        41     174     222 ..     130     178 ..     123     216 .. 0.85
   2 ?    6.6   6.7     0.012       4.6     172     238 ..     288     354 ..     228     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHH CS
                            FliD_C 174 atrlenllksyvkssngtlqtasknltkqikdldkkiedldkrletlee 222
                                       ++r+++++k+y + +n++   +s n+ ++i+++++ i+++d+  e+l+e
  gi|488600002|ref|YP_007906473.1| 130 IKRITEIIKQYEALRNDSRYLLSINMLEKITQFERLIDEIDRLREKLNE 178
                                       79999*******9999999999999999999999999999887776653 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                                       SHHHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH CS
                            FliD_C 172 glatrlenllksyvkssngtlqtasknltkqikdldkkiedldkrletleerlkkqfaalekavskl 238
                                        ++++++nl +++++ ++ + + +s +  k  +++dk++ +l k++e++e++lkk  ++l ++++kl
  gi|488600002|ref|YP_007906473.1| 288 KMIEEVDNLKRELTDVQSRIKNLKSIMASKSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKL 354
                                       4556666666666666666666666666677777777777777777777777777777777776664 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       4.9   1.8e+03      15      44 ..      17      47 ..       7     111 .. 0.62
   2 ?    6.5   1.5     0.026       9.7      33     112 ..     160     216 ..     121     235 .. 0.43
   3 ?    7.9   8.5    0.0098       3.6      19      56 ..     317     354 ..     266     371 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.9
                                      HHHHHHHHHHHHHHH.HHHHHHHHHHHHHHH CS
                              OmpH 15 pegkaaqeqlekkfk.klqaeleakekelqk 44
                                      pe k+a ++++++++ +++  ++++  +l++
  gi|488600002|ref|YP_007906473.1| 17 PELKEALKNIKRDQEiEIERFINSRISDLRD 47
                                      4444444444444433444444433333333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHH CS
                              OmpH  33 aeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqe....llkpildkinkaikev 105
                                       +++e++ +e+++l+e+l++                             + ++k++ e    +l++++ k ++ +++v
  gi|488600002|ref|YP_007906473.1| 160 TQFERLIDEIDRLREKLNEI----------------------------ERIEKNESEidvaELERLYSKEKELMDKV 208
                                       23333333333333333211............................22222222232223333333333333333 PP

                                       HH.HTT-S CS
                              OmpH 106 ak.ekgyd 112
                                       ++ e ++ 
  gi|488600002|ref|YP_007906473.1| 209 NQiESKLE 216
                                       33333333 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0098
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS CS
                              OmpH  19 aaqeqlekkfkklqaeleakekelqklqeelqkkakkl 56 
                                       +  + ++k+ ++l++++e+ke+el+kl++el + akkl
  gi|488600002|ref|YP_007906473.1| 317 KSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAKKL 354
                                       22233444444444444444444444444443333332 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       7.1   2.6e+03      62      72 ..      18      28 ..       5      48 .. 0.58
   2 ?    2.8   1.1       0.3   1.1e+02       3      26 ..     158     181 ..     154     195 .. 0.61
   3 ?    3.9   0.9      0.14        50       5      31 ..     192     218 ..     188     230 .. 0.67
   4 ?    4.5   0.5     0.088        32      72      97 ..     287     312 ..     248     318 .. 0.76
   5 ?   13.7   6.4   0.00013     0.046      69     104 ..     317     352 ..     314     354 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.1
                                      HHHHHHHHHHH CS
                       Prefoldin_2 62 evkeeLeerke 72
                                      e+ke L++ k 
  gi|488600002|ref|YP_007906473.1| 18 ELKEALKNIKR 28
                                      33333333333 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   3 linkfqqlqqqlqqlaqqikqlet 26 
                                       +i +f++l ++++ l ++++++e+
  gi|488600002|ref|YP_007906473.1| 158 KITQFERLIDEIDRLREKLNEIER 181
                                       556666666666666666655554 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   5 nkfqqlqqqlqqlaqqikqletqlkel 31 
                                       +++++l ++ ++l+ +++q+e +l+ +
  gi|488600002|ref|YP_007906473.1| 192 AELERLYSKEKELMDKVNQIESKLEYI 218
                                       556666666666666666666666655 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  72 etlekeiktlekqleklekeleelke 97 
                                       +++ +e+++l+++l++++ ++++lk+
  gi|488600002|ref|YP_007906473.1| 287 DKMIEEVDNLKRELTDVQSRIKNLKS 312
                                       45556777777777777777777775 PP

  == domain 5  score: 13.7 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  69 erketlekeiktlekqleklekeleelkeelqkklq 104
                                       ++ +t++ke+++l kq+e++e+el++lk+el ++ +
  gi|488600002|ref|YP_007906473.1| 317 KSSNTIDKEVRSLRKQIEEKENELKKLKTELSEMAK 352
                                       56789**************************99976 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.9      0.13        48      10      33 ..     167     189 ..     165     193 .. 0.87
   2 ?    5.4   0.0     0.043        16      13      33 ..     202     222 ..     198     237 .. 0.85
   3 ?   -0.5   0.1       3.1   1.1e+03      11      38 ..     292     319 ..     283     329 .. 0.75
   4 ?   -2.0   0.1       9.4   3.4e+03      10      26 ..     338     354 ..     331     362 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                              MtrG  10 ddfnevkkrLdeieekvefvnsEi 33 
                                       d+++++ ++L+eie ++e  +sEi
  gi|488600002|ref|YP_007906473.1| 167 DEIDRLREKLNEIE-RIEKNESEI 189
                                       78999********7.799999997 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.043
                              MtrG  13 nevkkrLdeieekvefvnsEi 33 
                                       +e++++ ++ie k+e++ + i
  gi|488600002|ref|YP_007906473.1| 202 KELMDKVNQIESKLEYILGVI 222
                                       6899************98866 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3.1
                              MtrG  11 dfnevkkrLdeieekvefvnsEiaqriG 38 
                                       + +++k+ L +++ ++ + +s +a +  
  gi|488600002|ref|YP_007906473.1| 292 EVDNLKRELTDVQSRIKNLKSIMASKSS 319
                                       6677788899999999988887776655 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 9.4
                              MtrG  10 ddfnevkkrLdeieekv 26 
                                       ++ +++k  L e+ +k+
  gi|488600002|ref|YP_007906473.1| 338 NELKKLKTELSEMAKKL 354
                                       56777777777777776 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       3.3   1.2e+03      36      56 ..      16      32 ..      13      51 .. 0.67
   2 ?    7.1   4.0      0.02       7.5      30      85 ..     163     214 ..     154     219 .. 0.65
   3 ?    8.7   1.1    0.0061       2.2      48      83 ..     278     311 ..     260     317 .. 0.73
   4 ?    4.0   2.0      0.18        65      11      43 ..     322     354 ..     312     370 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 3.3
                   Snapin_Pallidin 36 ldrlnekLkeleeaqeaevlp 56
                                      + +l+e+Lk+++++qe     
  gi|488600002|ref|YP_007906473.1| 16 IPELKEALKNIKRDQE----I 32
                                      6677888888888887....3 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.02
                   Snapin_Pallidin  30 eeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkR 85 
                                       e L +++drl+ekL+e+e+++++e+  d+    + L ++  + ++l +++++++ +
  gi|488600002|ref|YP_007906473.1| 163 ERLIDEIDRLREKLNEIERIEKNESEIDV----AELERLYSKEKELMDKVNQIESK 214
                                       5799******************4444443....44444333333334444444433 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0061
                   Snapin_Pallidin  48 eaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83 
                                       ++ +  +++d+++ ++ + n+k++++ +++r+++lk
  gi|488600002|ref|YP_007906473.1| 278 KNLS--MVSDADKMIEEVDNLKRELTDVQSRIKNLK 311
                                       4444..778888888888888888888888888877 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.18
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekL 43 
                                       +  +++ l+++++e +++ ++L+ +l+++++kL
  gi|488600002|ref|YP_007906473.1| 322 IDKEVRSLRKQIEEKENELKKLKTELSEMAKKL 354
                                       444444444444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2711  (0.151208); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        98  (0.005466); 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: 1.18u 0.35s 00:00:01.52 Elapsed: 00:00:00.54
# Mc/sec: 2087.95
//
Query:       gi|488600003|ref|YP_007906474.1|  [L=217]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-56  188.8   0.2    1.1e-55  188.6   0.2    1.0  1  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.6   0.2   6.2e-60   1.1e-55      25     219 ..      22     210 ..       5     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 6.2e-60
                            DUF166  25 slivavvevpeeldefiedpeelLpe...lkeaDiviaytlhpDlllelaekakekkvkalivpaeapkaglrkelk 98 
                                       ++ v+v+++pe+l+e+ie+p+e+L+      eaD++++y  hpD++lel++k++    k++i +  a+  g + +lk
  gi|488600003|ref|YP_007906474.1|  22 FFDVVVFKIPEDLPELIENPSEYLNLpeeFLEADMFVSYAGHPDINLELLKKLS---NKLVIFSGGAKA-GSYVQLK 94 
                                       23599******************97655799*********************99...788999999888.9****** PP

                            DUF166  99 ekleelgievavpkpfCsleeegkpkideFleefGkPelevevkdgkikkVeVlrsapCGstwyvakklkGkeveea 175
                                       ++ e+ gi+v++++++C+  e  +++ +eF+++fGkPe+ev+++++++++VeV+rsa+CG+t++va+k+kG +v+ea
  gi|488600003|ref|YP_007906474.1|  95 KEGEKRGIKVVWEEICCATPEIDDKRYREFFKHFGKPEVEVKLEGDRVAEVEVKRSAFCGATYFVAEKIKGLDVNEA 171
                                       ***************************************************************************** PP

                            DUF166 176 eekageahqsYpClAsmerdfelketklhkAgyihkeavekAlk 219
                                       ++kag  +q +pC A ++      e+++hkA+++hk+avekA++
  gi|488600003|ref|YP_007906474.1| 172 PSKAGYYTQIFPCYATRG-----IEGGIHKAARVHKRAVEKAIQ 210
                                       ******************.....89*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1316.87
//
Query:       gi|488600004|ref|YP_007906475.1|  [L=183]
Description: HemK-related putative methylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   30.2   0.0    1.8e-06   27.6   0.0    1.9  2  MTS              Methyltransferase small domain
    5.7e-05   22.6   0.0    8.8e-05   22.0   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00019   22.1   0.0    0.00046   20.8   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    0.00025   20.9   0.0    0.00051   19.9   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
    0.00063   20.3   0.0     0.0017   19.0   0.0    1.7  2  Methyltransf_11  Methyltransferase domain
    0.00095   19.9   0.0      0.011   16.5   0.0    2.2  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.041   13.8   0.0      0.068   13.1   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.045   13.5   0.0       0.13   12.0   0.0    1.7  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.082   12.8   0.1       0.15   12.0   0.1    1.4  1  UPF0146          Uncharacterised protein family (UPF0146)
       0.12   11.5   0.0       0.16   11.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.12   12.2   0.0       0.16   11.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain


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 !   27.6   0.0   1.1e-09   1.8e-06      20     111 ..      14      98 ..      10     106 .. 0.83
   2 ?    0.2   0.0       0.3   4.9e+02     112     138 ..     115     141 ..     111     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.1e-09
                                       HHHHHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST CS
                               MTS  20 sklLletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve 94 
                                       ++lLle+  ke  +++ vl +G+G G+++ +++++++   +++ d++ +A+++a++        +++v  d+l  ++
  gi|488600004|ref|YP_007906475.1|  14 TELLLEAALKEvkKDDIVLEVGTGSGYVAKNVKDRCKF--LVASDISPYAVRVAHNQ------GLNAVRGDLLTCFK 82 
                                       788998765554555569****************9998..9***********98743......256789*******9 PP

                                       TS-EEEEEE---STTTC CS
                               MTS  95 ekkfdlivsNPPfhagk 111
                                        kkf li+ NPP+ +  
  gi|488600004|ref|YP_007906475.1|  83 -KKFTLILFNPPYVELD 98 
                                       .***********98755 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.3
                                       HCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                               MTS 112 atelavaeeliaeAkeaLkegGeLliV 138
                                       ++  +v+++++ +  +aL +gG+ ++ 
  gi|488600004|ref|YP_007906475.1| 115 EKGVDVMRRFLSQLDDALVDGGRAVMT 141
                                       447889999999999****99997765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   5.4e-08   8.8e-05     148     213 ..      14      77 ..      12      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.4e-08
                              PrmA 148 TklclealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakl 213
                                       T+l lea  k vk+++ vl vGtGSG  a   +k   k  va Di + Av+va +N  lN v+  l
  gi|488600004|ref|YP_007906475.1|  14 TELLLEAALKEVKKDDIVLEVGTGSGYVAK-NVKDRCKFLVASDISPYAVRVA-HNQGLNAVRGDL 77 
                                       788888888999**************9885.56778999*************9.699999998755 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.8e-07   0.00046       1      41 [.      31      69 ..      31     102 .. 0.85
   2 ?   -2.0   0.0       3.6   5.9e+03      84      96 ..     123     135 ..     106     171 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.8e-07
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHH CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarera 41
                                      vL++G+G+G +++++ +r+  + +++ Dis+ +++ a+++ 
  gi|488600004|ref|YP_007906475.1| 31 VLEVGTGSGYVAKNVKDRC--KFLVASDISPYAVRVAHNQG 69
                                      9*****************9..9***************9876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                                       HHHHHHHHHEEEE CS
                   Methyltransf_25  84 kalkeiarvLkpg 96 
                                       ++l+++ ++L +g
  gi|488600004|ref|YP_007906475.1| 123 RFLSQLDDALVDG 135
                                       3333333333333 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.1e-07   0.00051      13      62 ..      18      72 ..       9     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.1e-07
                   Methyltransf_23 13 lerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....k 62
                                      le +l++ +++  vL++G+G+G++++  +++ + +++ D+sp av  a       
  gi|488600004|ref|YP_007906475.1| 18 LEAALKEVKKDDIVLEVGTGSGYVAKNVKDRCKFLVASDISPYAVRVAHnqglnA 72
                                      344455568999****************99988999*******999875433331 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     1e-06    0.0017       1      39 [.      32      70 ..      32      91 .. 0.86
   2 ?   -2.5   0.0       5.1   8.4e+03      75      95 ..     119     139 ..     107     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCC CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekas 39
                                      L+vG+G+G++a+ +++r++ +v+ D+s++++++a++++ 
  gi|488600004|ref|YP_007906475.1| 32 LEVGTGSGYVAKNVKDRCKFLVASDISPYAVRVAHNQGL 70
                                      89*****************************99976654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.1
                                       CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                       + ++++l+++   L  gG+ v
  gi|488600004|ref|YP_007906475.1| 119 DVMRRFLSQLDDALVDGGRAV 139
                                       455677777777777777765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.8e-06     0.011       1      48 [.      32      78 ..      32     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.8e-06
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsai.edakeklakrennnn 48
                                      Le+G+G+G +++ + ++   + ++++Disp a+ +++ + l++ +++  
  gi|488600004|ref|YP_007906475.1| 32 LEVGTGSGYVAKNVKDR--CKFLVASDISPYAVrVAHNQGLNAVRGDLL 78
                                      8*************999..88888*********4444444444444443 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.2e-05     0.068       5      57 ..      18      68 ..      15      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-05
                   Methyltransf_18  5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekaken 57
                                      L+a  + v+k+++v+ +Gt  gy++  +   +++k  +asDi++ +++ a+++
  gi|488600004|ref|YP_007906475.1| 18 LEAALKEVKKDDIVLEVGTGSGYVAKNVK--DRCKFLVASDISPYAVRVAHNQ 68
                                      7888999*****************99985..899*********9999988765 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 ?   12.0   0.0   7.9e-05      0.13      70      88 ..      24      42 ..      13      63 .. 0.84
   2 ?   -1.5   0.0       1.1   1.8e+03     161     187 ..     130     157 ..     118     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                                      T--TT-EEEEES-TTSHHH CS
                              PCMT 70 elkkgarvLevGsGsGylt 88
                                      e+kk + vLevG+GsGy +
  gi|488600004|ref|YP_007906475.1| 24 EVKKDDIVLEVGTGSGYVA 42
                                      4889999**********87 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                       HTEEEEEEEEEEESB.SSSEEEEEEEEE CS
                              PCMT 161 dQLkeGGrlvvPvge.eeeQvlklvdkk 187
                                       d L +GGr v+   + ++  v + +dk+
  gi|488600004|ref|YP_007906475.1| 130 DALVDGGRAVMTFSSyNTPDVYEILDKS 157
                                       5567899988877765555555555655 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   9.1e-05      0.15      13      61 ..      27      78 ..      15      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                                      -SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S........STTEE---SS CS
                           UPF0146 13 argkvvEvGiGrkldvaealakrgvdlvatDikek..kak..egvrivrDDvt 61
                                      +   v EvG G   +va++++ r   lva Di +   ++   +g+++vr D+ 
  gi|488600004|ref|YP_007906475.1| 27 KDDIVLEVGTGS-GYVAKNVKDRCKFLVASDISPYavRVAhnQGLNAVRGDLL 78
                                      344689*****7.69********989*******98563333588999999985 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001      0.16      27      57 ..      24      54 ..      10      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                                      -GGTTSEEEEES-TTTCCHHHHHCC-SEEEE CS
                            RrnaAD 27 nleekltvleigpGkGilTeeLakrakqvvv 57
                                      ++++++ vle+g+G G   +++ +r+k +v+
  gi|488600004|ref|YP_007906475.1| 24 EVKKDDIVLEVGTGSGYVAKNVKDRCKFLVA 54
                                      56799*********************99887 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    0.0001      0.16       3      46 ..      27      67 ..      25     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                   Methyltransf_31  3 kglrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielAre 46
                                      k+  vl++G+G+G+ +++  ++     + +v  Dis+ a+++A +
  gi|488600004|ref|YP_007906475.1| 27 KDDIVLEVGTGSGYVAKNVKDRC----KfLVASDISPYAVRVAHN 67
                                      67789**********99999764....4399***********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1094.89
//
Query:       gi|488600005|ref|YP_007906476.1|  [L=256]
Description: dimethyladenosine transferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-49  168.9   0.0    1.2e-49  168.8   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    1.4e-09   38.5   0.0    3.3e-09   37.3   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    3.6e-06   27.5   0.0    8.1e-06   26.4   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.2e-05   25.2   0.0    1.7e-05   24.6   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      4e-05   23.5   0.0    6.5e-05   22.8   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00024   21.0   0.0    0.00038   20.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00025   21.8   0.0    0.00052   20.7   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
     0.0022   17.6   0.0     0.0033   17.0   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0052   16.4   0.0      0.011   15.4   0.0    1.5  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.019   15.0   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.018   14.8   0.0       0.97    9.1   0.0    2.2  2  UPF0020          Putative RNA methylase family UPF0020
      0.038   13.3   0.0      0.067   12.5   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.064   12.5   0.0       0.13   11.6   0.0    1.5  2  CMAS             Mycolic acid cyclopropane synthetase
      0.069   12.6   0.0       0.11   12.0   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
       0.15   12.3   0.0       0.55   10.5   0.0    1.9  2  TrkA_N           TrkA-N 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 !  168.8   0.0     1e-52   1.2e-49       6     238 ..       5     226 ..       1     251 [. 0.94

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 1e-52
                                       XGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...TCCCEE CS
                            RrnaAD   6 ksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls...kdeklk 79 
                                       ks  q+ l++k+++ +I++ ++l+e+ tvle+g G+G+lTe L+  + +v  +E+d r++  l+ k+     ++k  
  gi|488600005|ref|YP_007906476.1|   5 KSRDQHLLVSKSILYRIIQLSELKEDETVLEVGCGTGNLTELLLRNSGKVIGIEKDARFVRYLRSKFYdeiREGKFR 81 
                                       56679**************************************************************99999***** PP

                                       EE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SH CS
                            RrnaAD  80 vvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsr 156
                                       ++h D+l  ++p +           ++++n+Py ist+l ++lle s+f    +++  q+efa+rl+ar g+k+++r
  gi|488600005|ref|YP_007906476.1|  82 LIHGDALRINFPRFD----------KFISNIPYSISTPLTFKLLE-SKF--DLAIITYQQEFAERLTAREGEKSYGR 145
                                       *************77..........89*****************6.777..789999******************** PP

                                       HHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHH CS
                            RrnaAD 157 lsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpgge 233
                                       +sv+++a++ vk++ kv++++f+P pkvdsa+v+l++k+e +++kd+++++ ++r  +  krk   ++lk+ l++  
  gi|488600005|ref|YP_007906476.1| 146 ISVAVKAYCRVKILFKVPRTAFRPIPKVDSAVVKLIPKPE-IEVKDVDVFNDLLRTSFSMKRKLFGKVLKEWLKKYD 221
                                       ****************************************.5**********************9999999888877 PP

                                       HHHCT CS
                            RrnaAD 234 lqals 238
                                       +++++
  gi|488600005|ref|YP_007906476.1| 222 AESVI 226
                                       76665 PP

>> Methyltransf_25  Methyltransferase 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   3.3e-09       1      71 [.      33     101 ..      33     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.7e-12
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvss 71 
                                       vL++GcGtG+lt+ l+++   +kv+g++ +++++++ r+++ +e +   ++++++gda +++f+   fD  +s+
  gi|488600005|ref|YP_007906476.1|  33 VLEVGCGTGNLTELLLRNS--GKVIGIEKDARFVRYLRSKFYDE-IregKFRLIHGDALRINFPR--FDKFISN 101
                                       9***************995..9*******************773.33569*************96..9999885 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   6.8e-09   8.1e-06       1      65 [.      34      98 ..      34     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.8e-09
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEE CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlv 65
                                      L+vGcGtG l+e l ++ ++v+g++ +++++++ ++k  +e    k++++++da +++f+   fD  
  gi|488600005|ref|YP_007906476.1| 34 LEVGCGTGNLTELLLRNSGKVIGIEKDARFVRYLRSKFYDEIRegKFRLIHGDALRINFPR--FDKF 98
                                      89*************999*****************9999998899999*********9997..6655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.4e-08   1.7e-05       2      81 ..      28     101 ..      27     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.4e-08
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDl 77 
                                       +++ +vl++GCGtG+lt  l +     ++v+Gi+ +++ +++ r++  +   +  +++ +gd+  ++  +   +fD 
  gi|488600005|ref|YP_007906476.1|  28 KEDETVLEVGCGTGNLTELLLR---NSGKVIGIEKDARFVRYLRSKFYDEIREgKFRLIHGDALRIN--FP--RFDK 97 
                                       67889**************994...4789*************9997766655577888889999988..77..4888 PP

                   Methyltransf_31  78 ilsn 81 
                                        +sn
  gi|488600005|ref|YP_007906476.1|  98 FISN 101
                                       8887 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 !   22.8   0.0   5.4e-08   6.5e-05      64     116 ..      20      69 ..       8      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.4e-08
                                       HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH CS
                              PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakr 116
                                       ++++l elk+ + vLevG+G+G lt +   l++++g+v++ie+ +++v+  + 
  gi|488600005|ref|YP_007906476.1|  20 RIIQLSELKEDETVLEVGCGTGNLTEL---LLRNSGKVIGIEKDARFVRYLRS 69 
                                       6789999****************9976...5789*********9988876555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.1e-07   0.00038      16      60 ..      24      67 ..       9     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.1e-07
                   Methyltransf_23 16 llpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveia 60
                                      l++ l+++  vL++GcGtG+l+e+l +n  +v+g++ + + v  +
  gi|488600005|ref|YP_007906476.1| 24 LSE-LKEDETVLEVGCGTGNLTELLLRNSGKVIGIEKDARFVRYL 67
                                      443.89999****************99999999999886544444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.3e-07   0.00052       1      71 [.      34     123 ..      34     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.3e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg............. 64 
                                       Le+GcGtG+l++ ll++    +++g++ +++++   + k+ +++++    ++l + d+l    +             
  gi|488600005|ref|YP_007906476.1|  34 LEVGCGTGNLTELLLRN--SGKVIGIEKDARFVRYLRSKFYDEIREGK--FRLIHGDALRINFPrfdkfisnipysi 106
                                       8****************..**************777777766665443..333333322222222456666666666 PP

                   Methyltransf_12  65 ..........ssfDlvv 71 
                                                 s+fDl +
  gi|488600005|ref|YP_007906476.1| 107 stpltfklleSKFDLAI 123
                                       66666666666666665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.8e-06    0.0033      25     109 ..      25     106 ..      15     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.8e-06
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EE CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfd 99 
                                       + l++  +++vl +GcG+G l+  l+++s +  v  +++dar ++  +  + ++  e   ++++ d+l      +fd
  gi|488600005|ref|YP_007906476.1|  25 SELKE--DETVLEVGCGTGNLTELLLRNSGK--VIGIEKDARFVRYLRSKFYDEIREgkFRLIHGDALRINF-PRFD 96 
                                       44444..667****************99988..99***************9998777668899999998777.89** PP

                                       EEEE---STT CS
                               MTS 100 livsNPPfha 109
                                         +sN P+  
  gi|488600005|ref|YP_007906476.1|  97 KFISNIPYSI 106
                                       *****99865 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.1e-06     0.011      11      49 ..      27      64 ..      18      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.1e-06
                              MetW 11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegv 49
                                      +k+  +vl++GcG G+l ell   +  +  G+e+d++ v
  gi|488600005|ref|YP_007906476.1| 27 LKEDETVLEVGCGTGNLTELLLR-NSGKVIGIEKDARFV 64
                                      678889*************9865.45577899*999876 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.6e-05     0.019      21      64 ..      25      64 ..      13      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                   Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelv 64
                                      ++ ++++tv++vG+G g L+  l      ++ kv+gi+  ++ v
  gi|488600005|ref|YP_007906476.1| 25 SELKEDETVLEVGCGTGNLTELLLR----NSGKVIGIEKDARFV 64
                                      4557899****************99....599******988766 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.043        51      16      42 ..      17      43 ..      12      45 .. 0.87
   2 ?    9.1   0.0   0.00081      0.97      75     135 ..      50     108 ..      44     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.043
                                      HHHHHHHHTT--TTS-EEETT-TTSHH CS
                           UPF0020 16 LAaalvrlagwkpgepllDPmCGsGti 42
                                      + + +++l+++k++e+ l+  CG+G +
  gi|488600005|ref|YP_007906476.1| 17 ILYRIIQLSELKEDETVLEVGCGTGNL 43
                                      557789*******************76 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00081
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-------- CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerl 135
                                       +  k++g+++d+r v+  r++      +++  +   da  ++     +d  ++n PY +++
  gi|488600005|ref|YP_007906476.1|  50 NSGKVIGIEKDARFVRYLRSKFYDEIREGKFRLIHGDALRIN--FPRFDKFISNIPYSIST 108
                                       55679**********************************999..4459*********9876 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-05     0.067      39     114 ..      21      94 ..       6     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
                                       HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS- CS
                   Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfed 114
                                       +++l+  k+ ++vl+v +Gtg+l+  l+   +++gkv++++ ++  ++  + k  +e    + ++++++a +++f  
  gi|488600005|ref|YP_007906476.1|  21 IIQLSELKEDETVLEVGCGTGNLTELLL---RNSGKVIGIEKDARFVRYLRSKFYDEIREgKFRLIHGDALRINFPR 94 
                                       67788889999************98775...6899*************99999998887779999999999999876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.13      54      91 ..      21      57 ..       4      94 .. 0.86
   2 ?   -3.0   0.0         3   3.6e+03     228     255 ..     215     232 ..     175     234 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                      HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEE CS
                              CMAS 54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvgl 91
                                      i++  elk+ +t+L++GcG G+l+    ++   kv+g+
  gi|488600005|ref|YP_007906476.1| 21 IIQLSELKEDETVLEVGCGTGNLTELLLRN-SGKVIGI 57
                                      5666789****************9988888.7788887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3
                                       HHHHHHHHTHHHHHHHSHHHHHHHHHHH CS
                              CMAS 228 aWaealqenkdeaialvseevarmyelY 255
                                       +W          +++   e+v++ +e Y
  gi|488600005|ref|YP_007906476.1| 215 EW----------LKKYDAESVIDEFEEY 232
                                       22..........2222334455555555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.1e-05      0.11       3      62 ..      31      89 ..      29     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                                      EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC.TTSSEEEEES-CCC CS
                    Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal.elkNlrilrgdalk 62
                                       +vle+GcG G+++  l  +  + +++GiE+  + v+++ +k  ++ +   +r+++gdal+
  gi|488600005|ref|YP_007906476.1| 31 ETVLEVGCGTGNLTELLLRN--SGKVIGIEKDARFVRYLRSKFYDEiREGKFRLIHGDALR 89
                                      579********987665444..4579**************998877677788899998865 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00046      0.55      12      43 ..      42      73 ..      36      92 .. 0.71
   2 ?   -2.3   0.0       4.3   5.1e+03      20      40 ..     118     137 ..     110     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00046
                                      HHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE CS
                            TrkA_N 12 slaeeLse.ggkdvvvidkdeerveelreegle 43
                                      +l+e L + +g +v++i+kd + v+ lr ++++
  gi|488600005|ref|YP_007906476.1| 42 NLTELLLRnSG-KVIGIEKDARFVRYLRSKFYD 73
                                      57778888455.6**************999965 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                                       TTEEEEEEESSHHHHHHHHHT CS
                            TrkA_N  20 ggkdvvvidkdeerveelree 40 
                                       +  d  +i  ++e +e+l+++
  gi|488600005|ref|YP_007906476.1| 118 KF-DLAIITYQQEFAERLTAR 137
                                       33.577778888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1731.45
//
Query:       gi|488600006|ref|YP_007906477.1|  [L=211]
Description: putative RNA-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-74  249.0   2.4    3.2e-74  248.8   2.4    1.0  1  DUF655    Protein of unknown function (DUF655)
    5.7e-06   26.5   0.0    3.1e-05   24.1   0.0    2.0  2  HHH_6     Helix-hairpin-helix motif
    7.1e-05   23.0   0.0    0.00037   20.7   0.0    2.0  2  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 !  248.8   2.4   5.3e-78   3.2e-74       1     180 [.      31     210 ..      31     211 .] 0.99

  Alignments for each domain:
  == domain 1  score: 248.8 bits;  conditional E-value: 5.3e-78
                                       X--EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGG CS
                            DUF655   1 leeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyed 77 
                                       +e++a+++D++p+G+p+dk+ +h+++p++q +ge+++tLle++++k++  l++d+v igkg++d ++kikr+++yed
  gi|488600006|ref|YP_007906477.1|  31 MEDYAYIIDFMPYGHPEDKRPIHKREPLAQIVGEKSFTLLEVSIKKDKSPLVMDRVFIGKGERDIVNKIKRRLRYED 107
                                       699************************************************************************** PP

                                       S-HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT- CS
                            DUF655  78 LtdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkgl 154
                                       Lt +a++eLp+v+e ivke+E+rfv+ffn+aepit++lH+LelLpgvgkk++++i++eR++++F+ F+d+++rvkgl
  gi|488600006|ref|YP_007906477.1| 108 LTTAAKSELPYVIEYIVKEHEQRFVDFFNKAEPITTKLHQLELLPGVGKKTMWAIIDERKKQPFKDFKDLAERVKGL 184
                                       ***************************************************************************** PP

                                       --HHHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 155 kdpaeilverileEiedktekYylFv 180
                                       ++p++++ +ri++Ei+++++kY++F+
  gi|488600006|ref|YP_007906477.1| 185 QHPEKLITNRIIYEIKNPKTKYKIFT 210
                                       *************************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 ?   -0.1   0.0       0.2   1.2e+03      40      72 ..     120     149 ..     117     152 .. 0.56
   2 !   24.1   0.0   5.2e-09   3.1e-05      30      66 ..     149     184 ..     145     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                             HHH_6  40 aerivaeRekegpfksledlarrvds..lnkrqle 72 
                                       +e iv+e e  + f    d+++++++   + +qle
  gi|488600006|ref|YP_007906477.1| 120 IEYIVKEHE--QRFV---DFFNKAEPitTKLHQLE 149
                                       778888776..4555...55555554224555555 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 5.2e-09
                             HHH_6  30 aaikglgeaaaerivaeRekegpfksledlarrvdsl 66 
                                       + + g+g++++ +i++eR+ ++pfk+++dla+rv+ l
  gi|488600006|ref|YP_007906477.1| 149 ELLPGVGKKTMWAIIDERK-KQPFKDFKDLAERVKGL 184
                                       55679*************9.8*************953 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.31   1.9e+03       7      19 ..     107     119 ..     107     143 .. 0.76
   2 !   20.7   0.0   6.2e-08   0.00037      10      52 ..     142     184 ..     140     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.31
                             HHH_3   7 diNtAsaeeLqkl 19 
                                       d+ tA ++eL ++
  gi|488600006|ref|YP_007906477.1| 107 DLTTAAKSELPYV 119
                                       7889999999985 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 6.2e-08
                             HHH_3  10 tAsaeeLqklpGlgpklAknIvayReknGpfksreeLl.kvkgl 52 
                                       t ++ +L+ lpG+g+k+  +I++ R k++pfk++++L  +vkgl
  gi|488600006|ref|YP_007906477.1| 142 TTKLHQLELLPGVGKKTMWAIIDER-KKQPFKDFKDLAeRVKGL 184
                                       567889*******************.666********9779988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1374.36
//
Query:       gi|488600007|ref|YP_007906478.1|  [L=423]
Description: Amino acid transporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  148.8  48.3    2.7e-43  148.4  48.3    1.2  1  AA_permease_2   Amino acid permease
    2.7e-26   92.2  48.0    7.4e-26   90.8  48.0    1.6  1  AA_permease     Amino acid permease
    2.6e-05   23.2  25.4    2.6e-05   23.2  25.4    2.3  2  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4  48.3   4.5e-47   2.7e-43       2     377 ..      10     378 ..       9     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 4.5e-47
                     AA_permease_2   2 sllsafalvigsvigsgifvkn.laas.ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkv 76 
                                       sl++a+++ ig+++gsg+++ + +aa+ +g+a+++ +++++l+  ++ +l++  l+s++p+ gGi+ ++k+afgk+ 
  gi|488600007|ref|YP_007906478.1|  10 SLFQAVGIFIGVILGSGVLILPsMAANvAGAASLIAWVVMTLLA-VPIALTFGYLASKFPSAGGISEFSKQAFGKRT 85 
                                       89****************99998555548888777777766666.79999***9*999***************8887 PP

                     AA_permease_2  77 a........flsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqn 145
                                                 +++++++    ++ +++l  +asyl ++lg d+ g    ++ +ai+ l++ +lin+rg++ +++iq+
  gi|488600007|ref|YP_007906478.1|  86 VgsitldaeMITGFLFLAVVPIGPPIVLLTGASYLGSILGLDFPG----VVALAILMLLTMFLINLRGVRFTGNIQT 158
                                       779999998999999888888888999999************976....7899************************ PP

                     AA_permease_2 146 ilgilkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvp 220
                                       +++i  + ++l++++++++ +v+++            f      + ++++ ++w+++G+e++++ see k+  +d+p
  gi|488600007|ref|YP_007906478.1| 159 MITISIV-ILLLFVVLTAFHLVNPDNLK---------FELDIYPIGRAMALIFWCYVGWEAVTHLSEEFKNpeRDFP 225
                                       ***9999.8************9776554.........334455589**********************777669*** PP

                     AA_permease_2 221 kaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssr 297
                                       + i ++l++v+++yllv+++++g  + +     ++  s++++  + +g   ++ +v++++++ ++ ++n +v++ sr
  gi|488600007|ref|YP_007906478.1| 226 LSILMALGVVGIMYLLVSFVVVGTHTYGDSL--RGMTSLVEIANRSLG-INGKLFVALIGFMTCFASANVYVASPSR 299
                                       *****************99999998876665..453334555555544.5889999999999*************** PP

                     AA_permease_2 298 vlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrk 374
                                       +l+al+r g+lP++f + n++++p +a+i +a   ++ l++++l  s ++ +ll +s+  +i  yl+ +i+++il  
  gi|488600007|ref|YP_007906478.1| 300 LLYALSRSGYLPEVFGNLNRKHAPQNALIAVAASMVFTLIAMYLF-SISVETLLLLSNSIFITLYLIGSIAGIILLE 375
                                       *******************999*********99975444444444.5677888888888888888887777777765 PP

                     AA_permease_2 375 krp 377
                                       kr 
  gi|488600007|ref|YP_007906478.1| 376 KRV 378
                                       522 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8  48.0   1.2e-29   7.4e-26       5     422 ..      17     400 ..      10     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.2e-29
                       AA_permease   5 ialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                       i +g + G g+++  + +++ aG  + l+a++++++  + ++l++g++a+++p++gg++ ++++  g++  ++i l 
  gi|488600007|ref|YP_007906478.1|  17 IFIGVILGSGVLILPSMAANVAGA-ASLIAWVVMTLLAVPIALTFGYLASKFPSAGGISEFSKQAFGKRTVGSITLD 92 
                                       445666666666655555555555.778****************************************999999999 PP

                       AA_permease  82 ......ylfswitvl..ale.ltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiia 149
                                             +lf+ ++ +  ++  lt+as+l +++    d p   + ++++l+ +++inl gv++ g +++++++  i++
  gi|488600007|ref|YP_007906478.1|  93 aemitgFLFLAVVPIgpPIVlLTGASYLGSIL--GLDFPGVVALAILMLLTMFLINLRGVRFTGNIQTMITI-SIVI 166
                                       97777755555555422333144444444444..77777666778888888888999999999998887554.4445 PP

                       AA_permease 150 iiafiivg.iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEv 225
                                       ++ f++++ ++l+  ++  k+                   +        ++ +  +++ ++  + G e+v+ +++E 
  gi|488600007|ref|YP_007906478.1| 167 LLLFVVLTaFHLVNPDN-LKF-----------------ELD--------IYPIGRAMALIFWCYVGWEAVTHLSEEF 217
                                       55666666243333333.333.................344........888889********************** PP

                       AA_permease 226 kdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaals 302
                                       k+Pe++ P +il+++  ++i+Y+l++++++ +  + d           s+++i+ +++g+++ + +++++ +++++ 
  gi|488600007|ref|YP_007906478.1| 218 KNPERDFPLSILMALGVVGIMYLLVSFVVVGTHTYGDSLRGM-----TSLVEIANRSLGING-KLFVALIGFMTCFA 288
                                       *************************99999888888733322.....489**********98.78899999****** PP

                       AA_permease 303 sansslysasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaligliv 379
                                       san +++s sR+ly+l+++g++P v++++++++ P +a++++++  ++ l++++l ++  +v + ll ++ + + + 
  gi|488600007|ref|YP_007906478.1| 289 SANVYVASPSRLLYALSRSGYLPEVFGNLNRKHAPQNALIAVAASMVFTLIAMYLFSI--SVETLLLLSNSIFITLY 363
                                       ******************************************9999999999999999..88888887777777776 PP

                       AA_permease 380 wlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaal 422
                                       ++ +i+ ++ + k   ++ +    ++f ++++ l+++   ++ 
  gi|488600007|ref|YP_007906478.1| 364 LIGSIAGIILLEKR--VYPM----ISFVICFATLLFVGESVIY 400
                                       67777766644333..5555....6666666666554333332 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  25.4   4.3e-09   2.6e-05       2     256 ..       9     273 ..       8     347 .. 0.74
   2 ?   -6.4  10.3         3   1.8e+04     101     159 ..     336     395 ..     325     421 .. 0.50

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.3e-09
                    Spore_permease   2 istkqlfvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpe.ktliellkkilg.kw 76 
                                       +s +q++ + + ++lG+g+l+lp ++a+ a++ + i+ ++  ++++ ++l++ +l +kfp+   + e++k+ +g + 
  gi|488600007|ref|YP_007906478.1|   9 VSLFQAVGIFIGVILGSGVLILPSMAANVAGAASLIAWVVMTLLAVPIALTFGYLASKFPSaGGISEFSKQAFGkRT 85 
                                       7899*********************99999777777777777777777777777777777626799********667 PP

                    Spore_permease  77 LGsl.lsilfilyFlllaafelRefseliq......vflledtplwiiilllllvilYlv.vkGieslareflfiiv 145
                                       +Gs+ l    i+ Fl+la++ +   + l++       +l  d p ++ +++l+l++++l+   G++       +i++
  gi|488600007|ref|YP_007906478.1|  86 VGSItLDAEMITGFLFLAVVPIGPPIVLLTgasylgSILGLDFPGVVALAILMLLTMFLInLRGVRFTGNIQTMITI 162
                                       8874389999********98777666666511111145556788888888888888877736899999988899999 PP

                    Spore_permease 146 illiilllillfslklaeiknlrPvlgngikpvlkslkttslsflgveillllvpflkdkkk.vkkaallgvlistl 221
                                        ++i ll+++l  + l++++nl+  ++  i p+ +++  +   ++g e ++ l +  k++++ +   +l++++++++
  gi|488600007|ref|YP_007906478.1| 163 SIVILLLFVVLTAFHLVNPDNLK--FELDIYPIGRAMALIFWCYVGWEAVTHLSEEFKNPERdFPLSILMALGVVGI 237
                                       9*********************9..9**********************9999998888877616678899******* PP

                    Spore_permease 222 lyllttlivilvlsveqlkkatwptlsll.kvievp 256
                                       +yll+ ++v+++ +   + + +  +++++ +++ ++
  gi|488600007|ref|YP_007906478.1| 238 MYLLVSFVVVGTHTYGDSLRGMTSLVEIAnRSLGIN 273
                                       **********99888777777777777653455555 PP

  == domain 2  score: -6.4 bits;  conditional E-value: 3
                    Spore_permease 101 seliqvflle.dtplwiiilllllvilYlvvkGieslar.eflfiivilliilllillfsl 159
                                         li ++l+   + + +++   ++++lYl+  +i  ++  e  ++ +i ++i +++llf+ 
  gi|488600007|ref|YP_007906478.1| 336 FTLIAMYLFSiSVETLLLLSNSIFITLYLIG-SIAGIILlEKRVYPMISFVICFATLLFVG 395
                                       3445555554233444444444555555543.33333333344445555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1241  (0.0692175); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3025.88
//
Query:       gi|488600008|ref|YP_007906479.1|  [L=145]
Description: hypothetical protein Asulf_00459 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   27.7   1.1    3.8e-06   27.4   1.1    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 !   27.4   1.1   2.1e-10   3.8e-06      50     119 ..      53     122 ..      18     125 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.1e-10
                                       HCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                               PIN  50 skrekaaelvellll.lsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                       sk+  +++++++++l   + + + +d++i+++a+e+ +   l+p Dal++A+A+++ +  + t De  ++v
  gi|488600008|ref|YP_007906479.1|  53 SKIPDEERRRKVEILaSISKEKVIVDDNIVKRALELEKIG-LKPVDALHVACAEKSADVMLTTDDEIVKKV 122
                                       33444455555555533333444479************97.*****************8774555545555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 991.50
//
Query:       gi|488600009|ref|YP_007906480.1|  [L=72]
Description: hypothetical protein Asulf_00460 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 435.94
//
Query:       gi|488600010|ref|YP_007906481.1|  [L=388]
Description: GTP-binding conserved hypothetical protein TIGR00650 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-34  118.4   0.1    3.9e-34  117.6   0.1    1.4  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    2.9e-21   75.7   0.0    1.7e-20   73.2   0.0    2.2  2  MMR_HSR1       50S ribosome-binding GTPase
    1.5e-13   50.6   0.1    2.9e-13   49.6   0.1    1.5  1  TGS            TGS domain
      9e-08   31.8   0.4    8.4e-07   28.6   0.0    2.5  3  FeoB_N         Ferrous iron transport protein B
    1.1e-05   25.6   1.1    0.00084   19.5   0.3    2.9  2  YchF-GTPase_C  Protein of unknown function (DUF933)
     0.0051   16.4   0.1        1.3    8.5   0.1    3.0  3  GTP_EFTU       Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.1   1.3e-37   3.9e-34       2     112 .]     218     319 ..     217     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 1.3e-37
                        MMR_HSR1_C   2 lNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekir 78 
                                       +NKaD+ a++e i++lk+ ++    v+p+sA++ElaLr+a+k+g+i+Y pgd+dfei ++    l+ekqkkaLe +r
  gi|488600010|ref|YP_007906481.1| 218 ANKADK-APEELINRLKNLEE---IVIPTSAEIELALRTASKNGYIRYYPGDMDFEIIKE----LNEKQKKALEIMR 286
                                       8*****.************99...8********************************999....************* PP

                        MMR_HSR1_C  79 dlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       + +lk+ ++TGVqe+ln++vf+lld+ivVYPVed
  gi|488600010|ref|YP_007906481.1| 287 S-FLKKNNGTGVQECLNRIVFDLLDYIVVYPVED 319
                                       *.******************************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 !   73.2   0.0   5.7e-24   1.7e-20       1      87 [.       3     114 ..       3     147 .. 0.78
   2 ?   -1.0   0.1       0.6   1.8e+03      65      90 ..     343     368 ..     305     385 .. 0.52

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 5.7e-24
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEET....................TEEEEEEECGGCS CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklk....................gkeielvDtpGli 57 
                                       e++i+G+pN+GKSt++++ t + ++++++p+tT+++n g  +++                      +i+l+D++Gl+
  gi|488600010|ref|YP_007906481.1|   3 EIGIAGKPNAGKSTFFKSATMADVEIANYPFTTIEPNVGVAHVRvdcvcrelnldcgncfegrrYIPIKLIDVAGLV 79 
                                       699************************************8774433444444444444444432355********99 PP

                                       SHHHHHHHHHHHHHHHHC.TSEEEEEEETT....T CS
                          MMR_HSR1  58 egaseekglgkaflalee.adlillvvdas....e 87 
                                        +a++++glg++fl++ + ++ i++vvdas     
  gi|488600010|ref|YP_007906481.1|  80 PEAHKGRGLGNEFLDNLRqSEGIIHVVDASgstdA 114
                                       99*************88879********9843330 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHCT.SEEEEEEETTTTCS CS
                          MMR_HSR1  65 glgkaflaleea.dlillvvdaseekl 90 
                                         + a+l + +  + +++ +da+++ +
  gi|488600010|ref|YP_007906481.1| 343 ARELAYLIHTDIgKNFIHAIDAKKK-M 368
                                       3444455456644778888887632.2 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.1   9.9e-17   2.9e-13       3      59 ..     329     385 ..     324     386 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 9.9e-17
                                       EEETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS   3 vytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       +++Pd+++  +++g+t++++Ay Ih++++k+fi+A+  +  +rv  d++L+++dv++Iv
  gi|488600010|ref|YP_007906481.1| 329 NVLPDAML--VKKGTTARELAYLIHTDIGKNFIHAIDAKkkMRVADDYELKHNDVIKIV 385
                                       57888888..*****************************999****************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 !   28.6   0.0   2.8e-10   8.4e-07       2      43 ..       3      44 ..       2      51 .. 0.91
   2 ?   -3.5   0.0       2.1   6.4e+03      78      89 ..      98     109 ..      91     110 .. 0.80
   3 ?    0.0   0.1      0.18   5.5e+02      95     124 ..     201     230 ..     196     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.8e-10
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklk 43
                                      ++ ++G+pn+Gk+t+f + t a+ +++N+p +t+e + g  +
  gi|488600010|ref|YP_007906481.1|  3 EIGIAGKPNAGKSTFFKSATMADVEIANYPFTTIEPNVGVAH 44
                                      6889*******************************9998876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
                                       SSSEEEEEEEGG CS
                            FeoB_N  78 epdvvvnvvdat 89 
                                       + + +++vvda+
  gi|488600010|ref|YP_007906481.1|  98 QSEGIIHVVDAS 109
                                       567899999996 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.18
                                       HHHHHHHHHTTSSEEEEEETHHHHHHTTEE CS
                            FeoB_N  95 LyLtlqllelgvpvvlalnmideaekkgie 124
                                       +++  +l   ++++++  n+ d+a ++ i+
  gi|488600010|ref|YP_007906481.1| 201 MTFAFELRKKRMRMIISANKADKAPEELIN 230
                                       5677888999999*********99887664 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 ?    3.4   0.0     0.029        85      55      83 ..     176     205 ..     153     206 .. 0.76
   2 !   19.5   0.3   2.8e-07   0.00084      16      42 ..     336     362 ..     323     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.029
                     YchF-GTPase_C  55 eaaakeagklrlegkdy.vvqdgDiilfkf 83 
                                        ++++ +  l++ gk++  + d+Di++f f
  gi|488600010|ref|YP_007906481.1| 176 FKEIQVKEALKVIGKEVwHFSDEDIMTFAF 205
                                       56777778888889986379********87 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.8e-07
                     YchF-GTPase_C  16 tikkgttapqaAgviHsDfekgFirae 42 
                                        +kkgtta + A  iH+D+ k+Fi+a 
  gi|488600010|ref|YP_007906481.1| 336 LVKKGTTARELAYLIHTDIGKNFIHAI 362
                                       689*********************994 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     0.013        40       4      23 ..       2      21 ..       1      32 [. 0.81
   2 ?   -0.2   0.0      0.21   6.3e+02      86     106 ..      91     111 ..      86     120 .. 0.78
   3 !    8.5   0.1   0.00043       1.3     115     154 ..     204     268 ..     197     320 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.013
                                      EEEEEEESTTSSHHHHHHHH CS
                          GTP_EFTU  4 rnigiighvDhGKtTLtdrL 23
                                      + igi+g  ++GK+T+  + 
  gi|488600010|ref|YP_007906481.1|  2 IEIGIAGKPNAGKSTFFKSA 21
                                      679************98765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.21
                                       HHHHHHHT-SEEEEEEETTTB CS
                          GTP_EFTU  86 evirglrvlDgavlvvdaveG 106
                                       e    lr+ +g + vvda+  
  gi|488600010|ref|YP_007906481.1|  91 EFLDNLRQSEGIIHVVDASGS 111
                                       556679999********9854 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00043
                                       HHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH.........................H CS
                          GTP_EFTU 115 lrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk.........................e 154
                                       +  ++k+++++i+  NK+D++ +el +  +++++ +  +                          
  gi|488600010|ref|YP_007906481.1| 204 AFELRKKRMRMIISANKADKAPEELINRLKNLEEIVIPTsaeielalrtaskngyiryypgdmdF 268
                                       55678999*************66666655555544422234445556666666666666655553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2348.78
//
Query:       gi|488600011|ref|YP_007906482.1|  [L=99]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-11   44.4   1.4    1.8e-09   37.7   0.6    2.0  2  DUF2095       Uncharacterized protein conserved in archaea (D
  ------ inclusion threshold ------
      0.011   16.2   0.5       0.02   15.4   0.3    1.6  2  HTH_40        Helix-turn-helix domain
      0.016   15.1   1.7      0.019   14.8   0.5    1.7  2  TFIIE_alpha   TFIIE alpha subunit
      0.046   13.7   0.1      0.079   13.0   0.1    1.5  1  DUF2680       Protein of unknown function (DUF2680)
      0.099   12.7   0.0       0.11   12.6   0.0    1.2  1  FANCM-MHF_bd  FANCM to MHF binding domain
        0.2   11.9   3.0       0.33   11.2   3.0    1.6  1  TMF_TATA_bd   TATA element modulatory factor 1 TATA binding


Domain annotation for each model (and alignments):
>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0041        12      15      35 ..       4      24 ..       2      34 .. 0.84
   2 !   37.7   0.6     6e-13   1.8e-09      66     127 ..      36      95 ..      29      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0041
                           DUF2095 15 ydleefkrrfpalareleeer 35
                                       d e+fk+ fp l+ el   +
  gi|488600011|ref|YP_007906482.1|  4 IDNEKFKKMFPKLSDELSSSE 24
                                      5889************98665 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 6e-13
                           DUF2095  66 ptiidflrrcetdeealeiinwmeergeithemakelrvvlvkkgvra.fgpkkewgwyerhg 127
                                       pti+d + rce deea+eii+++ + gei +e a el+  +  k +r  fg +k  g yer g
  gi|488600011|ref|YP_007906482.1|  36 PTIMDHIERCENDEEAMEIIDFFLKIGEIKEEDAEELKNNI--KELRDlFGTRK-RGDYERRG 95 
                                       9************************************9765..55665166655.69999988 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   3.5e+03      65      81 ..       5      21 ..       2      25 .. 0.75
   2 ?   15.4   0.3   6.6e-06      0.02      22      65 ..      31      80 ..      15      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                            HTH_40 65 gseklkpikealpeevs 81
                                      ++ek+k+++ +l +e+s
  gi|488600011|ref|YP_007906482.1|  5 DNEKFKKMFPKLSDELS 21
                                      56789999999988877 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 6.6e-06
                            HTH_40 22 rglkesTIegHLaelieegeeidlerl......vseeeekeIeeaiekvg 65
                                      r+ k  TI++H+ ++ +++e +++ ++      ++ee+++e+++ i++++
  gi|488600011|ref|YP_007906482.1| 31 RKRKLPTIMDHIERCENDEEAMEIIDFflkigeIKEEDAEELKNNIKELR 80
                                      888999*************9999988877777779999999999999854 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.73   2.2e+03      87     104 ..       7      24 ..       2      25 .. 0.69
   2 ?   14.8   0.5   6.5e-06     0.019      10      47 ..      46      82 ..      37      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHHHHCCCT CS
                       TFIIE_alpha  87 rkleevvkkLeeklekee 104
                                       +k +++  kL ++l+ +e
  gi|488600011|ref|YP_007906482.1|   7 EKFKKMFPKLSDELSSSE 24 
                                       577778888888877665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.5e-06
                                      CS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHH CS
                       TFIIE_alpha 10 fygeeavlvldvLlekgevteedlakelkidlnelrkl 47
                                      + +eea++++d  l+ ge++eed a+elk +++elr l
  gi|488600011|ref|YP_007906482.1| 46 ENDEEAMEIIDFFLKIGEIKEED-AEELKNNIKELRDL 82
                                      45699******************.799*********87 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.7e-05     0.079      22      46 ..      53      77 ..      38      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                           DUF2680 22 qivdKyVeaGllTkeqgekikkniD 46
                                      +i+d + + G++ +e++e+ k+ni 
  gi|488600011|ref|YP_007906482.1| 53 EIIDFFLKIGEIKEEDAEELKNNIK 77
                                      79999******************95 PP

>> FANCM-MHF_bd  FANCM to MHF binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.7e-05      0.11      54      96 ..      17      60 ..       1      79 [. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                      FANCM-MHF_bd 54 sreLSLsew..rvWQnkplPthlvdHSdrckhFievmelielmre 96
                                      s eLS se   ++  +++lPt  +dH +rc++  e me+i+   +
  gi|488600011|ref|YP_007906482.1| 17 SDELSSSESvgSLVRKRKLPTI-MDHIERCENDEEAMEIIDFFLK 60
                                      5566665542256678999996.6****************97544 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.0   0.00011      0.33      84     108 ..      59      83 ..       5      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                       TMF_TATA_bd  84 LellGeksEeveELraDvaDlKemy 108
                                       L++   k+E  eEL++ +++l++++
  gi|488600011|ref|YP_007906482.1|  59 LKIGEIKEEDAEELKNNIKELRDLF 83 
                                       4444449999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 611.34
//
Query:       gi|488600012|ref|YP_007906483.1|  [L=294]
Description: putative acyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   35.0   9.4    0.00045   20.5   2.0    3.5  2  Bactofilin  Polymer-forming cytoskeletal
    0.00053   19.6  11.9        1.5    8.6   0.2    4.9  5  Hexapep     Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.0     5e-08   0.00045       3      92 ..      12     106 ..      10     110 .. 0.74
   2 !   16.1   0.9   1.2e-06      0.01      16      93 ..     175     251 ..     154     270 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5e-08
                        Bactofilin   3 igegtkikG.elevegdlri.dGkveGdieakgklvvgeggkvegnikaeevvva..GtvkGnveaeekvelkktak 75 
                                       i ++t+++  ++ ve+d  + +G+  G    ++k++vge++++eg+i+ eev+++   ++ G+v++++   + + a+
  gi|488600012|ref|YP_007906483.1|  12 IPPNTRFEErNIVVENDAIVgAGSKLGYGIIGKKIIVGERASIEGSIQGEEVRIDswCSIGGDVYCNGDAYIGEFAS 88 
                                       5566666664566665555534533333233568********************9555688**************** PP

                        Bactofilin  76 veGdika.ksleieegav 92 
                                       ++G++++ + lei ++++
  gi|488600012|ref|YP_007906483.1|  89 IDGKLTVfGDLEIGRNVR 106
                                       ****99878888776665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-06
                        Bactofilin  16 egdlridG.kveGdieakgklvvgeggkvegnikaeevvva.GtvkGnveaeekvelkktakveGdikaksleieeg 90 
                                        +dl  +  ++ G+i+ak +++  ++ ++ g+i+a+++v++  +v+G ve + ++ l ++++v G +k +++ +ee 
  gi|488600012|ref|YP_007906483.1| 175 GTDLIAESsRILGNIKAK-NVKA-DRCEIFGSIRAKDIVLSsCRVHGAVEGK-RIYLINETEVYGYVKGDKVYMEEK 248
                                       344444444666777665.5554.5666777777766555535577777776.777777777777777777777776 PP

                        Bactofilin  91 avf 93 
                                       +++
  gi|488600012|ref|YP_007906483.1| 249 CRI 251
                                       655 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1   0.00024       2.1      13      30 ..      22      39 ..      11      40 .. 0.72
   2 ?    1.7   0.3     0.026   2.3e+02      16      30 ..      42      56 ..      41      57 .. 0.85
   3 !    7.5   0.1    0.0004       3.6       5      34 ..      60      89 ..      60      91 .. 0.86
   4 !    8.6   0.2   0.00017       1.5       2      30 ..      81     109 ..      80     110 .. 0.76
   5 ?   -2.8   0.0      0.68   6.1e+03       4      12 ..     245     253 ..     243     263 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00024
                                      TEEEETTEEE-TTEEEET CS
                           Hexapep 13 faviggnVkIGdnvkIga 30
                                      + v+ +++++G ++k+g 
  gi|488600012|ref|YP_007906483.1| 22 NIVVENDAIVGAGSKLGY 39
                                      556777777777777765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.026
                                      EETTEEE-TTEEEET CS
                           Hexapep 16 iggnVkIGdnvkIga 30
                                      ig  +++G+++ I+ 
  gi|488600012|ref|YP_007906483.1| 42 IGKKIIVGERASIEG 56
                                      888999999999985 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0004
                                      ETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  5 GsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                                      G+ v I++++ igg+V    +++Ig+++ i
  gi|488600012|ref|YP_007906483.1| 60 GEEVRIDSWCSIGGDVYCNGDAYIGEFASI 89
                                      8899************98888888888877 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.00017
                                       EEEETTEEE-T.TEEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgp.faviggnVkIGdnvkIga 30 
                                       + IG+ + I+   +v+ g+ +IG+nv+Ig 
  gi|488600012|ref|YP_007906483.1|  81 AYIGEFASIDGkLTVF-GDLEIGRNVRIGK 109
                                       5677777777745556.9999*******95 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 0.68
                                       EETTEEE-T CS
                           Hexapep   4 IGsnvlIgp 12 
                                        ++++ I+ 
  gi|488600012|ref|YP_007906483.1| 245 MEEKCRIDE 253
                                       578888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2109.62
//
Query:       gi|488600013|ref|YP_007906484.1|  [L=412]
Description: phosphoglycerate mutase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-57  193.2   0.1    4.7e-57  192.6   0.1    1.3  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
    4.3e-44  150.7   0.3    4.9e-44  150.5   0.3    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    0.00029   20.6   0.1      0.036   13.7   0.0    2.2  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
     0.0067   15.4   0.1      0.011   14.8   0.1    1.2  1  Alk_phosphatase  Alkaline phosphatase


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.6   0.1     1e-60   4.7e-57       1     170 []      37     211 ..      37     211 .. 0.97

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 1e-60
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC......TTCEE CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdee....dgiii 73 
                                       Ak G+ G++dt+++g++pgSd+A+l++lGy+p+++y+GRGp+EA+g G+elk+gdvafR+n+ tv+ e    d++++
  gi|488600013|ref|YP_007906484.1|  37 AKIGINGIMDTIAPGVRPGSDTAHLALLGYNPHECYSGRGPIEAAGSGIELKEGDVAFRANFGTVEGEgsifDKVVV 113
                                       789**************************************************************99999999**** PP

                                       ETTGGG-.-TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE....--S-B--S--..SSTTS------BS.SG CS
                      PhosphMutase  74 drragristeeakeLikalneel..eegvevkfypgveyrhllvl....lsdkitdtdpphdkegkeikellplkse 144
                                       drragri  +e++eL+kaln+    e gv+v ++ g+++r+++v+    lsd++tdtdp  +k g ++k +++l +e
  gi|488600013|ref|YP_007906484.1| 114 DRRAGRI--DETDELVKALNKIDlsEFGVKVMVRRGTGHRAAVVFrgegLSDRVTDTDP--KKIGSKVKMCKAL-DE 185
                                       *******..99**********9895499*******************************..************8.68 PP

                                       GGHHHHHHHHHHHHHHHHHHHHSHHH CS
                      PhosphMutase 145 eaketaellnelieksqeiLedhpvN 170
                                       +a++ta+++n+++e++++iLe+hpvN
  gi|488600013|ref|YP_007906484.1| 186 NAEKTARIINKFMEEAHRILENHPVN 211
                                       9************************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.5   0.3   1.1e-47   4.9e-44       1     244 [.       4     399 ..       4     403 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 1.1e-47
                                       -EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                     Metalloenzyme   1 kkvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel.......... 67 
                                       kk++ +v+DG++++  d+   +  A+tP+ld ++k        +++g++ +++ + +++s+++Hl+l          
  gi|488600013|ref|YP_007906484.1|   4 KKILFIVIDGISDRLIDNKTPLDSARTPNLDYFAKI-------GINGIMDTIAPGVRPGSDTAHLALlgynphecys 73 
                                       68999*************999*************99.......99******************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|488600013|ref|YP_007906484.1|  74 grgpieaagsgielkegdvafranfgtvegegsifdkvvvdrragridetdelvkalnkidlsefgvkvmvrrgtgh 150
                                       ***************************************************************************** PP

                                       ..............................................................HHHHTT-----EEEE CS
                                       ..............................................................xxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ..............................................................lrisetvkfahvtff 82 
                                                                                                      r +++  +++ +++
  gi|488600013|ref|YP_007906484.1| 151 raavvfrgeglsdrvtdtdpkkigskvkmckaldenaektariinkfmeeahrilenhpvnlEREKNGLLKGNAILL 227
                                       **************************************************************999************ PP

                                       EEEE-S---SSHHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  83 wnggrsgyfnpleereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvni 139
                                       ++gg+ ++++++eer++++ + ++ + l                    +++++ ++++++al+a+  +++d+v+v+i
  gi|488600013|ref|YP_007906484.1| 228 RGGGMVKKVESFEERFGLKLAFIAGTTLikgigkiigadvlevegvtgNKHTNLKNKFNAALEAL--NTHDFVLVHI 302
                                       *****************************************************************..669******* PP

                                       -HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 140 knaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkgl 216
                                       k +D++GH+gd+e++ + ie++D+ ++ +l +++ ++ +lv+tADH+++ ++++        Ht++pVP+++v++g+
  gi|488600013|ref|YP_007906484.1| 303 KATDELGHDGDFEGKKSFIEKIDQEIA-VLRELDFTEICLVITADHSTPINVKD--------HTADPVPVIVVHEGV 370
                                       **************************9.8999**********************........*************** PP

                                       ---S--S.SHHHHTT-TTEEEEGGGHHHH CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 217 apdkvke.gakfrekggLanvaatllnll 244
                                       ++d+v + ++ ++ +ggL+++++  l ++
  gi|488600013|ref|YP_007906484.1| 371 RTDEVDRfSELVAYRGGLCRIRGIDLFNI 399
                                       *******8888888*******99877665 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0031        14       2      42 ..       7      50 ..       6      56 .. 0.87
   2 !   13.7   0.0     8e-06     0.036     157     237 ..     281     352 ..     116     391 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0031
                                      EEEEETT-BTTHHHHHG.S...TSHHHHHHHHHSEEESEEE-SSS CS
                      Phosphodiest  2 lvislDGlradlldrla.e...llpnlaaLakegvsapnlrpvfP 42
                                      l+i++DG + +l+d+       ++pnl+++ak g+++  +++++P
  gi|488600013|ref|YP_007906484.1|  7 LFIVIDGISDRLIDNKTpLdsaRTPNLDYFAKIGINGI-MDTIAP 50
                                      78*******9999995443789***************9.999988 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8e-06
                                       HHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                      Phosphodiest 157 ldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHG 233
                                       l++ f   ++ ++l + d++lv++ +tD  gH    d +  +  ++++D+ i+ L+e ld +    e  +++++DH 
  gi|488600013|ref|YP_007906484.1| 281 LKNKFN--AALEALNTHDFVLVHIKATDELGHDG--DFEGKKSFIEKIDQEIAVLRE-LDFT----EICLVITADHS 348
                                       444442..333444999***************76..444456899*******98876.6666....5779******8 PP

                                       -EEE CS
                      Phosphodiest 234 madv 237
                                          +
  gi|488600013|ref|YP_007906484.1| 349 TPIN 352
                                       6544 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.4e-06     0.011     228     336 ..     276     377 ..     266     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-06
                                       CTCCE--HHHHHHHHHHHHTTSTT-EEEEEEETCHHHHHHTTTHHHH..HHHHHHHHHHHHHHHHHCHHCTTEEEEE CS
                   Alk_phosphatase 228 deatdPsLkemtevAiklLsknekGFFLlVEGsrIDhaaHendavga..lsEvvefdeAvkaalefakkeketlvvv 302
                                       +++t  +Lk+  ++A+++L+  +   F lV     D+ +H++d  g+    E ++ + Av + l+f++      +v 
  gi|488600013|ref|YP_007906484.1| 276 NKHT--NLKNKFNAALEALNTHD---FVLVHIKATDELGHDGDFEGKksFIEKIDQEIAVLRELDFTE----ICLVI 343
                                       5555..899**********9887...8999************98776115566666667777777777....78889 PP

                                       EESSEESEEEESTTSTT..TTSEECCEETTTSSE CS
                   Alk_phosphatase 303 TaDHshvfsfggyttrgesvlglepllaadkkpv 336
                                       TaDHs+ +++  +t+ +  v+  ++ + +d+ + 
  gi|488600013|ref|YP_007906484.1| 344 TADHSTPINVKDHTADPVPVIVVHEGVRTDEVDR 377
                                       *******999999999888777777776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2626.13
//
Query:       gi|488600014|ref|YP_007906485.1|  [L=180]
Description: putative domain HDIG [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-16   59.9   0.7    4.3e-16   59.3   0.7    1.3  1  HD               HD domain
     0.0028   17.2   0.0        1.8    8.0   0.0    2.2  2  HDOD             HDOD domain
  ------ inclusion threshold ------
       0.03   14.7   0.3        0.2   12.0   0.0    2.0  2  Phage_int_SAM_5  Phage integrase SAM-like domain
        0.1   12.8   0.0       0.21   11.8   0.0    1.5  1  Rhomboid_N       Cytoplasmic N-terminal domain of rhomboid se
          2    8.4  12.4       0.74    9.8   3.2    2.8  3  Nore1-SARAH      Novel Ras effector 1 C-terminal SARAH (Sav/R


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 !   59.3   0.7   1.2e-19   4.3e-16       1     121 [.      31     140 ..      31     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.2e-19
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgl 76 
                                       +l+H++ V+  a r+a+++++ +e r l+ ++a lHD+G  +++             ++H++ gaeilr+ + ++  
  gi|488600014|ref|YP_007906485.1|  31 VLNHTFTVLDSALRIANRMKLsDEQRKLIIAGAMLHDVGRSLSHG------------MDHAVLGAEILRKDGFDD-- 93 
                                       589***************************************664............89****************.. PP

                                       HHHHHHHHHHTTCCHHHHHHHHH.....HHHCCTSCHHHHHHHHHHHHHH CS
                                HD  77 dledvaklirehheswegkkrpr.....glaerqlslearivklaDrlaa 121
                                           ++k++++h +   ++k+ +     ++++ + +le+++v+laD+l a
  gi|488600014|ref|YP_007906485.1|  94 ---RIIKIVERHIGAGLTAKEAKkfglpERDYIPETLEEKLVALADNLVA 140
                                       ...**************99999446677*******************966 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00049       1.8      94     132 ..      30      70 ..      16      74 .. 0.81
   2 !    7.4   0.0   0.00076       2.7     165     193 ..      74     102 ..      70     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHHHHHHHHHHHTT-S-H..HHHHHHHHTTTHHH CS
                              HDOD  94 klwehslavAlvarelaeelgledp..eeaflaGLLhdiGk 132
                                       ++ +h+++v   a ++a++++l+d+  + +  +++Lhd+G+
  gi|488600014|ref|YP_007906485.1|  30 DVLNHTFTVLDSALRIANRMKLSDEqrKLIIAGAMLHDVGR 70 
                                       56788999999999******99995445555667******7 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00076
                                       HSS-HHHHHHHHHHHTT--HHHHHHHHHT CS
                              HDOD 165 lgtdhaevGaallekWnlPeelveaiayh 193
                                        g+dha +Ga++l+k  +++ ++++++ h
  gi|488600014|ref|YP_007906485.1|  74 HGMDHAVLGAEILRKDGFDDRIIKIVERH 102
                                       689***********************998 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 ?   12.0   0.0   5.6e-05       0.2      49      92 ..      13      55 ..       2      58 .. 0.89
   2 ?    0.5   0.1      0.22   7.8e+02       9      36 ..     153     179 ..     147     180 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                                      HHHHHHHHHHHHTS---HHHHHHHHHHHHHHHHHHHHTTS--S- CS
                   Phage_int_SAM_5 49 efleeFedYLkkkkglsentiskyfkklkavlnkAikegilkkn 92
                                      e++++  +YL k+kg+s+   ++ f+ l  +l+ A + ++ +++
  gi|488600014|ref|YP_007906485.1| 13 ELIKALSEYL-KEKGVSNDVLNHTFTVLDSALRIANRMKLSDEQ 55
                                      7899******.9***********************999987765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                                       HTHHHHTTS-HHHHHHHHHHHHHTTTS- CS
                   Phage_int_SAM_5   9 yiekkkkkgskgtlrnykstlkhlkkFl 36 
                                       +i++k +  +k  l ++ ++l+ +++F 
  gi|488600014|ref|YP_007906485.1| 153 HIKQKFRD-EKEVLDRHLALLNEFEEFV 179
                                       33333333.4677888888888888886 PP

>> Rhomboid_N  Cytoplasmic N-terminal domain of rhomboid serine protease
   #    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       2      35 ..       4      37 ..       3      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                        Rhomboid_N  2 ilLlslenpraaqafidYlrsqgiklelrseeeg 35
                                      i++l+le+ ++++a+ +Yl+++g+++++ +++  
  gi|488600014|ref|YP_007906485.1|  4 IEILELEEDELIKALSEYLKEKGVSNDVLNHTFT 37
                                      57899**********************9888655 PP

>> Nore1-SARAH  Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.1     0.036   1.3e+02      11      25 ..       4      18 ..       4      21 .. 0.87
   2 ?   -3.3   0.0       2.5   8.8e+03       4      13 ..      36      45 ..      35      47 .. 0.81
   3 ?    9.8   3.2   0.00021      0.74      12      40 .]     143     169 ..     143     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.036
                       Nore1-SARAH 11 LriLeeEEeeeiqqi 25
                                      ++iLe EE+e i+++
  gi|488600014|ref|YP_007906485.1|  4 IEILELEEDELIKAL 18
                                      68********99876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                       Nore1-SARAH  4 lPELqnFLri 13
                                      +++L++ Lri
  gi|488600014|ref|YP_007906485.1| 36 FTVLDSALRI 45
                                      6799999987 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00021
                       Nore1-SARAH  12 riLeeEEeeeiqqikrkYtalrqklqqaL 40 
                                       riL +EE  +i+ ik+k++ +++ l ++L
  gi|488600014|ref|YP_007906485.1| 143 RILRKEE--YIRHIKQKFRDEKEVLDRHL 169
                                       6777876..****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1151.59
//
Query:       gi|488600015|ref|YP_007906486.1|  [L=331]
Description: methylenetetrahydromethanopterin reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-69  235.2   0.0    1.4e-69  234.9   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.031   14.2   0.1    1.6  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


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 !  234.9   0.0   1.6e-73   1.4e-69      24     314 .]      15     305 ..       6     305 .. 0.94

  Alignments for each domain:
  == domain 1  score: 234.9 bits;  conditional E-value: 1.6e-73
                    Bac_luciferase  24 ylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGR 100
                                       +l  ++++aE+ +fd+vw+++h+++    ++ +++l+ la  T++i+lg +vt++y  +Pav+A ++at++++s+GR
  gi|488600015|ref|YP_007906486.1|  15 ELEYYVKLAEDNKFDFVWITDHYNN----RNVYSMLTILALKTNTIKLGPGVTNPYHISPAVTASAIATINEISNGR 87 
                                       667789******************9....************************************************ PP

                    Bac_luciferase 101 fglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspa 177
                                       ++lg+g+g   v ++r G+d+ ++++r+rE+ve++r+l +g++v+++Ge f+ +ga+   + g+  iP+y++a +p+
  gi|488600015|ref|YP_007906486.1|  88 AVLGIGAGDK-VTFERIGIDWVKPLKRMREAVEIIRALHAGKPVKYDGEIFKFNGARMDFKAGS--IPIYIGAQGPK 161
                                       *******976.566999**********************99999********988888888843..7********** PP

                    Bac_luciferase 178 glelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...raliagld.. 249
                                       +l+laa+ +dg+l++ ++p++ + + e+++ag ++ag++++++++++ ++ +v++++++Ar  a    a+i  +   
  gi|488600015|ref|YP_007906486.1| 162 MLQLAAELGDGVLINASHPKDFEVAKENIDAGLSKAGKSRDAFDTVAYASMSVDKDRDKARNAAkivVAFIVAGSpe 238
                                       ****************************************************************888666644447* PP

                    Bac_luciferase 250 ..fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvde 314
                                         f ++  ++ + ++ +++   ++++++w g+ +av+de+++++ + Gtp++v+er+ ++ +agv++
  gi|488600015|ref|YP_007906486.1| 239 viFERHGIAAEDVQKVRDALNAAFTKGDWPGVSKAVTDEMIDTFSISGTPDDVIERINELSKAGVTQ 305
                                       ****************************************************************985 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.5e-06     0.031      19      45 ..      90     115 ..      87     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-06
                                       CCEECTCEEEEEECTTCCCCCCCHHSX CS
                    MazE_antitoxin  19 lgireGdevelevdgdkiilrplkslp 45 
                                       lgi +Gd+v++e+ g +++++plk+++
  gi|488600015|ref|YP_007906486.1|  90 LGIGAGDKVTFERIG-IDWVKPLKRMR 115
                                       7*************9.********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2220.38
//
Query:       gi|488600016|ref|YP_007906487.1|  [L=472]
Description: TIGR03663 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   31.9  15.4    1.4e-07   31.9  15.4    2.9  2  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9  15.4   7.6e-12   1.4e-07       2     130 ..      52     181 ..      51     223 .. 0.79
   2 ?   -2.9   5.5      0.39     7e+03      77     113 ..     296     330 ..     256     364 .. 0.53

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 7.6e-12
                             PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdapl 78 
                                       h P+ ++ +a ++++fg+s++  rlv+++++++++l+ ++  r + g   a++ ++++ +++ ++++s+ +++d + 
  gi|488600016|ref|YP_007906487.1|  52 HGPFLYFSTASIFMIFGDSNFTSRLVPVIFSIIGALVSMKFRRWIGG--GAYILTFFMIFSTSILYYSRYLRNDMIV 126
                                       8999************************************9888866..899999999999999*****9******* PP

                             PMT_2  79 vllwalalylllrale....knklkyw.llagvlfGlgflsKytaallliaall.yll 130
                                       ++  +l++y ++r+le    k k  ++ +la +++++++ sK ++ ++l+ +l  +++
  gi|488600016|ref|YP_007906487.1| 127 LPSFLLIIYSYFRYLEvdglK-K-DAFaYLAVLFATIMLCSKENSYIYLF-ILTsFIF 181
                                       ****************65422.2.23447777777788889999888888.5544333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.39
                             PMT_2  77 plvllwalalylllraleknklkywllagvlfGlgfl 113
                                       ++ + w+ +++ +++ l ++ +  wll+ +++ l+f+
  gi|488600016|ref|YP_007906487.1| 296 LFSAYWVVTTLTIYQILSHKVP--WLLVHLVAPLAFF 330
                                       2333444444444444444432..4444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3156.30
//
Query:       gi|488600017|ref|YP_007906488.1|  [L=766]
Description: Protein related to penicillin acylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-205  684.1   0.0   3.5e-205  683.9   0.0    1.0  1  Penicil_amidase  Penicillin amidase


Domain annotation for each model (and alignments):
>> Penicil_amidase  Penicillin amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.9   0.0    2e-209  3.5e-205       2     666 ..      67     765 ..      66     766 .] 0.91

  Alignments for each domain:
  == domain 1  score: 683.9 bits;  conditional E-value: 2e-209
                                       EEEEEEGGGEEEEE-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH-TBHHHHHHHHHHHT-HHHHHHHHH CS
                   Penicil_amidase   2 VeirrDewgvphIyAkneedlffaqGyvhAqdrlwqmellrrtarGrlaelfGpealesDrllrtlglrraaeaela 78 
                                       ++i++De+gvphIyAkne+ l++a+Gyv+A+drl+qm+l rr+++G+l+e+fG++ ++sD+++ +l++++aa+a+++
  gi|488600017|ref|YP_007906488.1|  67 AKITYDEYGVPHIYAKNEKALYYAVGYVQAKDRLFQMDLHRRLMKGTLSEVFGESLVDSDIFHIKLDFYGAAKATWE 143
                                       68**************************************************************************8 PP

                                       TS.....HHHHHHHHHHHHHHHHH-..-ST-HH.HHHH---....S.........SS-.XXXXXX.....XXX.XXX CS
                   Penicil_amidase  79 alldpetralleaYaaGvNaylaelkakalPlefallgykpepWtpvdslavakvmaldlagnleeelararalaak 155
                                       +  ++   +l+eaY +GvNay+++ +   lPlef+ll+y+pepW+p+d++++ k ++++l+gn+  +l ra  +a+k
  gi|488600017|ref|YP_007906488.1| 144 EINKTPFGDLIEAYCDGVNAYMTS-N---LPLEFRLLNYRPEPWKPEDVFLIDKEISWELTGNFW-DLKRAL-IAEK 214
                                       8855455***************74.4...9******************************99998.899987.7776 PP

                                       XXXXX......................................X-EEEEE-TTTBTTSS-EEEEE-EEESSGGG--E CS
                   Penicil_amidase 156 lgdekvaelfpp...............................gSNnwvvsgerTasGkpllanDPHlglsapslwy 201
                                       l+++   el+p+                               gSNnwv+sg++Ta+Gkp+lanDPHl+l++p +wy
  gi|488600017|ref|YP_007906488.1| 215 LPSAL--ELYPEylnhtspiirtnlvdkelldwlkpfekkgdvGSNNWVISGKYTANGKPILANDPHLSLTVPPVWY 289
                                       66544..456644445566777778888888888889999999********************************** PP

                                       EEEEEETTEEEEEEE-TT-S.SSEEEESSEEEEEEE-SS-SEEEEEEEEETTEEEEEEETTEEEE-EEEEEEEEEE- CS
                   Penicil_amidase 202 qahlqapgldviGaslpGlPgvliGhnediAWglTnagadvqdlyaeklnpddptrylydgkwepmetrtetikvkg 278
                                       ++h+++ +++v+G+++pG+P+++iG n+++AWg+Tn+gadv+d+y + ++    ++yly+g+w+++e ++++++vk 
  gi|488600017|ref|YP_007906488.1| 290 EMHIKTDEINVRGVTFPGIPVIIIGMNDHVAWGVTNVGADVIDFYYYVTKG---DKYLYKGEWKNFEIEEKKMRVKT 363
                                       *********************************************997663...4699******************9 PP

                                       TT...EEEEEEEEETTEEEE-......TB--EEEEG-TTHHHHHHHHHT--SHHHHHHHHHHH---SEEEEEEETT- CS
                   Penicil_amidase 279 gdd..svtltvreTrhGPvvsd.gkavalrwtalepgdrsldallalnrarnvaefraalkdlaapaqnvvyADreG 352
                                       +++  ++t+ v++T hGPv+++ gk++a++wt+    ++++ a++++n+arn+++f + lk++++paqn+vy D++G
  gi|488600017|ref|YP_007906488.1| 364 ANGyeERTVLVKKTVHGPVIEKnGKEFAIAWTGFAA-TNEFYAIYKYNHARNMSDFIEGLKYFDVPAQNLVYIDADG 439
                                       99988889999**********96666*****99985.5*************************************** PP

                                       -EEEE--S--B---...TT--EEETT-GGGS--...........TB--GGGS-EEEE..SSEEEESSS----S.... CS
                   Penicil_amidase 353 nigyqaagrvPvrpaaddgllpvpGsdsayeWt...........gyipfeelPqvvnPargyivtaNnrvlpddypa 418
                                       ni+y+ ag++P+r+  + g+++++Gs ++ eW+           g+ipfee+P+++n   +y++taN+rv+ d y++
  gi|488600017|ref|YP_007906488.1| 440 NIMYYPAGKFPIRD--T-GNIIFNGSAGEGEWKgfkpygkstweGFIPFEEIPHLIN--PDYVATANQRVVFD-YQY 510
                                       **************..5.**************88***********************..66********9998.999 PP

                                       .......--T-HHHHHHHHHH..S.S...-B-HHHHHHHHHT-BBTHHHHHHHHH........-..GGGHHHHHHHH CS
                   Penicil_amidase 419 alg..sdwappyRarrirelLeek.aagkkvtledmaalqtdtrsllaerllpll.al....eaaeaeaaaaldlLr 487
                                       +lg  +++a+pyR+ ri+e+++++ +agkk+++e ++++q+dt+s +ae l++++ +l    +   ++a+  +d L 
  gi|488600017|ref|YP_007906488.1| 511 YLGdsGYFADPYRGMRIYEMIDDAvKAGKKIDMEYVMKMQRDTYSKPAEFLIKQIkELkpkfS---EKAKMYADELM 584
                                       9985455**********************************************9985454432...2234479**** PP

                                       H-.SB-STT-THHHHHHHHHHHHTT..............................---TTSTTT-SE.SHH.HHHHH CS
                   Penicil_amidase 488 aWdgrmdadsaaaalfaawlaalvralfedelg.........rlaealeklledasfwwddptttpk.trdelllaa 554
                                       +Wd+rmd++s++a++fa wl+++++++f de+          + +  + + l+d+s+w+dd +t +  ++++++++a
  gi|488600017|ref|YP_007906488.1| 585 NWDYRMDKNSRQALIFAIWLKHYINETFGDEFYsagldsdyyP-KLWVLQNLDDNSKWFDDIRTSKVeNKADIMARA 660
                                       ********************************9***9976643.223333333559*********99*9******** PP

                                       HHHHHHHHHHST-T-B.....HHHHEEEE.E............EE---B-GGG.........EEEEEEE-EEEEEE- CS
                   Penicil_amidase 555 laealaeleaaglgadpakwrwgklhrlelrhplg...fnrg.lpvgGgeetvnatsysarafrvtrgpsyrmvvdl 627
                                       +++a++e+e++ +        +g+++rl+++hp++   +n+  lp++G+e+tv + + +   + ++ g+s+rmvv++
  gi|488600017|ref|YP_007906488.1| 661 MDKAVEEIEKNNYRV------YGDYNRLKMNHPFNldfLNYPnLPMNGSEYTVFNFRVND--KPFQVGSSWRMVVSF 729
                                       **********97533......************99***9**************9777765..67788********99 PP

                                       -T.S.EEEEETT-S-S-TTSTTSSHHHHHHHTT--EEE- CS
                   Penicil_amidase 628 adrdkaravlpgGqsgnpgsphyaDqlelwaegeylplp 666
                                       +   ka++v+pgG+sgn +s++y+Dqle+w +gey++++
  gi|488600017|ref|YP_007906488.1| 730 D---KAYCVIPGGNSGNYFSKNYDDQLEMWVNGEYKEMV 765
                                       8...7*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 4713.95
//
Query:       gi|488600018|ref|YP_007906489.1|  [L=95]
Description: hypothetical protein Asulf_00469 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.3    7.6   8.4          2    8.9   3.6    2.0  2  DUF4231   Protein of unknown function (DUF4231)


Domain annotation for each model (and alignments):
>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.6   0.00011         2      15      70 ..      13      69 ..       7      73 .. 0.85
   2 ?    1.3   0.2     0.026   4.7e+02      23      36 ..      74      87 ..      70      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00011
                           DUF4231 15 rrfrllrlitivlgallpilvs.sklgagvsvlkiltallsalvailaaleeffryk 70
                                      +++++  + +i++g +  i+ s +k  a++ ++ i+++++ ++   + +le+ff ++
  gi|488600018|ref|YP_007906489.1| 13 AITYFHWIGLIIGGLICGIFGStKKAFASAIAFSIIVSVAFIVKMSMISLEKFFAMG 69
                                      577888899*************87788888888899999988888899999999875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.026
                           DUF4231 23 itivlgallpilvs 36
                                      ++ ++++llp+l+s
  gi|488600018|ref|YP_007906489.1| 74 LSFIIAFLLPLLSS 87
                                      56788999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 702.48
//
Query:       gi|488600019|ref|YP_007906490.1|  [L=548]
Description: dihydroxyacid dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-210  700.5   1.3   1.4e-210  700.3   1.3    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  700.3   1.3  7.9e-215  1.4e-210       1     517 []      31     544 ..      31     544 .. 0.98

  Alignments for each domain:
  == domain 1  score: 700.3 bits;  conditional E-value: 7.9e-215
                          ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmlea 77 
                                       kp+ig+an+y+ +vp+h+ l+++++avkeg+ +aggvp+ef +ig++Dgiamg++gm++ LpsReliads+e+m+ea
  gi|488600019|ref|YP_007906490.1|  31 KPFIGVANAYNTIVPGHMSLDKITQAVKEGIYAAGGVPFEFGVIGICDGIAMGHDGMKFALPSRELIADSIEAMVEA 107
                                       8**************************************************************************** PP

                          ILVD_EDD  78 qllDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaa 152
                                       +++D+lv++++CDKi+Pg+lma++rlniPa++v+gGpm++++ +  ++++s++fea+g+++ gkiseeel+ +e+ +
  gi|488600019|ref|YP_007906490.1| 108 HRFDGLVVVGSCDKIIPGMLMAVLRLNIPAVVVTGGPMNPERIDgrNVTISTAFEAAGMYKGGKISEEELKLYEDFC 184
                                       ****************************************77545599***************************** PP

                          ILVD_EDD 153 cpgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvl 229
                                       +p +GsC+g++TAntm++++e+lG+slp++a+ p  s+++ ++a+++gkr+velv+++++pr+ +t+++feNAi+++
  gi|488600019|ref|YP_007906490.1| 185 APYCGSCQGLYTANTMQIMTETLGMSLPYCATSPCGSSRKLRIAKQSGKRVVELVKQEINPREYVTEKSFENAITMD 261
                                       ***************************************************************************** PP

                          ILVD_EDD 230 lalGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvl 306
                                       + +GGStN+vlHl+AiA+eag++l ld fde++rk+p+++ + P+++y++ dl++ GGvp+++k+ + +  l ++ +
  gi|488600019|ref|YP_007906490.1| 262 MLIGGSTNTVLHLPAIAKEAGIKLPLDLFDEIGRKTPHIVAIDPASNYTIADLDESGGVPMLIKKAK-E--LFNNEM 335
                                       ****************************************************************988.3..77899* PP

                          ILVD_EDD 307 tvtgktlaenleeaevkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeavea 383
                                       tv+g ++ + +e+a ++  ++ir+l++p++++gg+a+LkGnLa++Gav+K +av+e++++feg+A++f+se+ a++a
  gi|488600019|ref|YP_007906490.1| 336 TVSGMKIYDIAEKAISRGGNIIRDLSNPIHEQGGIAILKGNLAEKGAVIKSAAVSEDMMVFEGNAKCFNSEQLALKA 412
                                       ***********99**************************************************************** PP

                          ILVD_EDD 384 ilkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialv 460
                                       il+g+i++gdvvviry GPkG+pGmpEml pt+a+ g+g  k+valitDGRfSGa++g++ighvsPEA++gG ialv
  gi|488600019|ref|YP_007906490.1| 413 ILNGEIEEGDVVVIRYMGPKGAPGMPEMLLPTAAISGMGY-KRVALITDGRFSGATRGPCIGHVSPEAMVGGSIALV 488
                                       ***************************************9.************************************ PP

                          ILVD_EDD 461 edGDiieidiekrtlelevseeelaaRraawkp.ekkvktrgllakyaklvssaseGA 517
                                       edGD+i i+i++r++el+vse+ela+Rr++wkp e   + +g+lakyaklv sa+eGA
  gi|488600019|ref|YP_007906490.1| 489 EDGDRILINIPERKIELKVSEDELADRREKWKPpE--RELKGYLAKYAKLVGSADEGA 544
                                       *********************************44..4449****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 3499.73
//
Query:       gi|488600020|ref|YP_007906491.1|  [L=234]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   74.1   0.1    2.1e-20   72.4   0.0    2.0  2  TrmB             Sugar-specific transcriptional regulator Trm
    6.5e-05   22.7   0.0    0.00012   21.8   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
      0.001   18.6   0.0     0.0032   17.0   0.0    1.9  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0024   17.7   0.0     0.0042   16.9   0.0    1.4  1  MarR_2           MarR family
     0.0066   16.4   0.0      0.012   15.5   0.0    1.4  1  MarR             MarR family
      0.007   16.7   0.0      0.042   14.2   0.0    2.1  2  Rrf2             Transcriptional regulator
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.043   14.2   0.0    2.0  3  Penicillinase_R  Penicillinase repressor
      0.014   15.3   0.1       0.32   10.9   0.0    2.7  3  DUF2498          Protein of unknown function (DUF2498)
       0.06   13.4   0.0       0.15   12.2   0.0    1.6  1  HTH_7            Helix-turn-helix domain of resolvase
       0.14   12.3   0.0       0.32   11.1   0.0    1.7  1  HTH_28           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0   1.1e-23   2.1e-20       1      66 [.       7      71 ..       7      73 .. 0.96
   2 ?   -1.9   0.0       1.8   3.2e+03      35      46 ..     103     117 ..      98     133 .. 0.56

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.1e-23
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                      L+++G+s+yEa++ +aLl++g+++a+ei+ ++g+pr++vY+v+ sL++kG+Ve   g+p++++a++
  gi|488600020|ref|YP_007906491.1|  7 LKAFGFSDYEARALTALLSQGEMSAKEISLISGIPRTSVYDVMDSLVSKGFVEAY-GKPRKFKALQ 71
                                      899**************************************************98.9*****9975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                       SCHCHHH...HHHHH CS
                              TrmB  35 prskvYe...vLrsL 46 
                                       ++ +vY+   vL++L
  gi|488600020|ref|YP_007906491.1| 103 EEVRVYRgdlVLEKL 117
                                       445555433334444 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   6.8e-08   0.00012      14      49 ..      25      59 ..      17      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.8e-08
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      ++ +e++ +e++  +g+p+++v+  + +Lv  G+ve
  gi|488600020|ref|YP_007906491.1| 25 SQ-GEMSAKEISLISGIPRTSVYDVMDSLVSKGFVE 59
                                      44.459*****************************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 !   17.0   0.0   1.8e-06    0.0032       9      48 .]      20      59 ..      13      59 .. 0.94
   2 ?   -2.9   0.0         3   5.4e+03      39      48 .]      68      77 ..      67      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                            HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      L +L  ++ +s +e++  +g++++ v   ++ L+++G+++
  gi|488600020|ref|YP_007906491.1| 20 LTALLSQGEMSAKEISLISGIPRTSVYDVMDSLVSKGFVE 59
                                      88999********************************996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                            HTH_24 39 krLeeeGlIk 48
                                      k L+++++Ik
  gi|488600020|ref|YP_007906491.1| 68 KALQSDEIIK 77
                                      7899999997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.3e-06    0.0042       2      52 ..      11      59 ..      10      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      g++  +ar+L aL   ++  ++++e+    g+++ +v  + + Lv++G+ve
  gi|488600020|ref|YP_007906491.1| 11 GFSDYEARALTALLSQGE--MSAKEISLISGIPRTSVYDVMDSLVSKGFVE 59
                                      5666699**********9..******************************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.6e-06     0.012       5      50 ..      16      61 ..      12      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.6e-06
                                      HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      + ++L+ l +qg++s +e+   +g+ +++v  v d L+ kG++e +
  gi|488600020|ref|YP_007906491.1| 16 EARALTALLSQGEMSAKEISLISGIPRTSVYDVMDSLVSKGFVEAY 61
                                      668999*************************************965 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.4e-05     0.042       7      57 ..      13      60 ..       7      62 .. 0.90
   2 ?   -0.4   0.0      0.84   1.5e+03      28      54 ..      76     102 ..      69     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2  7 teyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ++y  +al+ L ++ e   +s++ei+   +i+++ +  ++  L  +g+v++
  gi|488600020|ref|YP_007906491.1| 13 SDYEARALTALLSQGE---MSAKEISLISGIPRTSVYDVMDSLVSKGFVEA 60
                                      5788888888888777...99****************************96 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.84
                                       HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                              Rrf2  28 seeiaerqnispsylekilakLrkagl 54 
                                       ++ i+er+n   ++++k l k + a++
  gi|488600020|ref|YP_007906491.1|  76 IKIISERVNQDLEFIKKELPKFESAKI 102
                                       678999999999999999888877765 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.4e-05     0.043       2      67 ..      13      72 ..      12      97 .. 0.85
   2 ?   -3.2   0.0       5.8     1e+04      23      43 ..     113     133 ..     111     143 .. 0.72
   3 ?   -3.2   0.0       6.1   1.1e+04      69      84 ..     208     223 ..     202     231 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                      --S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE---- CS
                   Penicillinase_R  2 gelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvs 67
                                      ++ Ea  + +l ++ge+++ke+      +    +++V  ++  Lv Kg+++++ + r+f   +l+s
  gi|488600020|ref|YP_007906491.1| 13 SDYEARALTALLSQGEMSAKEISLISGIP----RTSVYDVMDSLVSKGFVEAYGKPRKF--KALQS 72
                                      78999999*************97665555....9****************999877776..56655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.8
                                       HHHT--GGG---HHHHHHHHH CS
                   Penicillinase_R  23 vveeleeekelaysTVktllr 43 
                                       v e+l+e +e a++++  +l+
  gi|488600020|ref|YP_007906491.1| 113 VLEKLKEFTESAKESIYGMLS 133
                                       566777777777777777776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.1
                                       XXXXXXXXXXXXXXXX CS
                   Penicillinase_R  69 eeavasavkqlldklf 84 
                                       + ++a ++k++l+ l+
  gi|488600020|ref|YP_007906491.1| 208 SPVIAMFAKEMLNPLL 223
                                       4444444444444433 PP

>> DUF2498  Protein of unknown function (DUF2498)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.7   1.3e+03      23      44 ..      35      56 ..      21      70 .. 0.78
   2 ?    0.0   0.0      0.45     8e+02      37      50 ..     103     116 ..      92     138 .. 0.77
   3 ?   10.9   0.0   0.00018      0.32      15      48 ..     171     202 ..     160     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.7
                           DUF2498 23 dyleGmeatdveqkedvLvFkG 44
                                        ++G+  t+v +  d Lv kG
  gi|488600020|ref|YP_007906491.1| 35 SLISGIPRTSVYDVMDSLVSKG 56
                                      5689999999999999999998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.45
                           DUF2498  37 edvLvFkGeyflde 50 
                                       e+v v++G++ l++
  gi|488600020|ref|YP_007906491.1| 103 EEVRVYRGDLVLEK 116
                                       68999***999986 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00018
                           DUF2498  15 nklikehedyleGmeatdveqkedvLvFkGeyfl 48 
                                        +l++eh+dy +Gm + d  + + + +FkGe  l
  gi|488600020|ref|YP_007906491.1| 171 KELMEEHKDYCNGMLVFD--DIKTIFMFKGENVL 202
                                       5799**********9854..567899***99766 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.2e-05      0.15      15      39 ..      21      46 ..      14      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                                      GSSTTTT.--STTTSSSS---SSSS- CS
                             HTH_7 15 vkLleeG.isiskIAkevnisRsTvY 39
                                       +Ll++G +s+++I  +++i R++vY
  gi|488600020|ref|YP_007906491.1| 21 TALLSQGeMSAKEISLISGIPRTSVY 46
                                      579*********************** PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.32       4      39 ..      18      55 ..      17      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                            HTH_28  4 eiiklla.aGh.svreaArelgisrrtvyrWikryeeg 39
                                      +++ +l+ +G+ s++e++ + gi r++vy+ +  + + 
  gi|488600020|ref|YP_007906491.1| 18 RALTALLsQGEmSAKEISLISGIPRTSVYDVMDSLVSK 55
                                      788888856779*****************998765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1527.32
//
Query:       gi|488600021|ref|YP_007906492.1|  [L=622]
Description: hypothetical protein Asulf_00472 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-14   52.7   0.0      0.024   14.9   0.0    5.9  5  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
    2.5e-08   34.1   1.3      0.043   14.1   0.1    4.8  6  CARDB        CARDB
    1.4e-06   27.7   0.0     0.0021   17.2   0.0    2.2  2  PHTB1_C      PTHB1 C-terminus
  ------ inclusion threshold ------
      0.036   14.3   2.5       0.96    9.7   0.2    3.5  3  CBM_4_9      Carbohydrate binding domain
       0.09   12.8   0.7          1    9.4   0.1    2.9  3  DUF2393      Protein of unknown function (DUF2393)
       0.94    9.5   7.1         50    4.0   0.0    5.1  8  DUF1573      Protein of unknown function (DUF1573)


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 !    8.6   0.0   0.00071       2.1      36      78 ..      97     139 ..      82     140 .. 0.93
   2 !    9.4   0.0   0.00043       1.3       4      47 ..     234     277 ..     232     282 .. 0.87
   3 !    7.3   0.0    0.0019       5.8      45      77 ..     325     356 ..     314     358 .. 0.84
   4 ?    4.7   0.0     0.012        37       9      78 ..     399     465 ..     394     466 .. 0.76
   5 !   14.9   0.0     8e-06     0.024       2      78 ..     498     573 ..     497     574 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00071
                       NPCBM_assoc  36 vvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                       vve+ p+++++l+p   +  +  +++ +g+++G+y++++k+++
  gi|488600021|ref|YP_007906492.1|  97 VVETPPQKIPALKPMTPLNLQYLLKVDEGIKPGEYNLKLKVTF 139
                                       79999***********************************987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00043
                       NPCBM_assoc   4 GetvtltltvtndgtaaatnvslslslPeGWtvvevspasaasl 47 
                                       G + ++++ v n+g+++a+n +l l++P+G + ++ s +s++s 
  gi|488600021|ref|YP_007906492.1| 234 GGKGKIEIKVRNSGEKTARNAYLVLEAPSGFEPSALSMTSMSSM 277
                                       5678899***********************99888888877765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0019
                       NPCBM_assoc  45 aslapGetveatvkVtppagaaaGdyevtakar 77 
                                        +l+p+et+eat+ ++++ +   G y+++++a 
  gi|488600021|ref|YP_007906492.1| 325 GELKPNETTEATFYIKINVKDG-GRYPLKVRAV 356
                                       38***************98865.9****99986 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.012
                       NPCBM_assoc   9 ltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                       l++t+t + + +  +v +s+  P     v +s   +  ++ G++ +a +k++++ + ++  y+v++ +++
  gi|488600021|ref|YP_007906492.1| 399 LRVTFTTSANLSDASVLISANPPLS---VLSSEYYIGNIEKGKEYTAIFKLKASGESKPVRYPVKLYIKY 465
                                       5666666666666666666666653...44677778899**************************99887 PP

  == domain 5  score: 14.9 bits;  conditional E-value: 8e-06
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa.slapGetveatvkVtppagaaaGdyevtakar 77 
                                       ++G ++ +t+ ++n+g+  +++ + +++  +  t  +++ +s+  +l+p+e+ e+ +k+++ ++a +  y + ++++
  gi|488600021|ref|YP_007906492.1| 498 QAGTEKVVTFKIVNTGDFEIKDANARITIVDPFT--STDDTSFIgDLKPNESKEVRFKIKVDSDATPKIYALNLEVK 572
                                       7899999999******999999999999988888..555555555**********************99***99998 PP

                       NPCBM_assoc  78 l 78 
                                       +
  gi|488600021|ref|YP_007906492.1| 573 Y 573
                                       7 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.6   7.8e+03      52      84 ..     103     137 ..      94     138 .. 0.79
   2 ?    4.0   0.0      0.02        60       8      38 ..     224     254 ..     218     262 .. 0.79
   3 !    8.5   0.0   0.00078       2.3      53      94 ..     323     368 ..     314     369 .. 0.80
   4 ?    1.7   0.0       0.1     3e+02       7      79 ..     426     456 ..     386     479 .. 0.64
   5 ?    4.6   0.0     0.013        38       2      68 ..     420     508 ..     419     510 .. 0.81
   6 !   14.1   0.1   1.4e-05     0.043      13      84 ..     495     571 ..     484     577 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.6
                                       EEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEE CS
                             CARDB  52 vtvpsLaagesttvsftwtte..ategevtltvvv 84 
                                       +++p+L++ +  + ++  +++  +++ge+ l+++v
  gi|488600021|ref|YP_007906492.1| 103 QKIPALKPMTPLNLQYLLKVDegIKPGEYNLKLKV 137
                                       56788888888888888888888899999988876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.02
                                       EEEC-SEEETTSEEEEEEEEEE-SSS-EEEE CS
                             CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgat 38 
                                       ++++ +++  g + +i+++v+N+G++++++ 
  gi|488600021|ref|YP_007906492.1| 224 VEVKGEDLIGGGKGKIEIKVRNSGEKTARNA 254
                                       5666667777778899***********9986 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00078
                                       EESEE-CTEEEEEEEEEE-S.-S-CEEEEEE...EESTT-SS--SS CS
                             CARDB  53 tvpsLaagesttvsftwtte.ategevtltv...vvDpdnevaEsn 94 
                                        v +L+++e+t+ +f ++++    g + l+v   +vD++++v+E++
  gi|488600021|ref|YP_007906492.1| 323 FVGELKPNETTEATFYIKINvKDGGRYPLKVravYVDANGDVKETE 368
                                       5889****************6666777787522279********85 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.1
                                       .EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE CS
                             CARDB   7 tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevt 79 
                                       +                                          ++ ++ +++ g+++t  f+ +++ +++ v 
  gi|488600021|ref|YP_007906492.1| 426 S------------------------------------------SEYYIGNIEKGKEYTAIFKLKASGESKPVR 456
                                       3..........................................556667777777777777666663333332 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.013
                                       --EEE..EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE......EEEEE................. CS
                             CARDB   2 pDLtv.tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv......gtvtv................. 54 
                                       p L v ++++  ++ ++g+e+t  +++k +G+ +     v+ly+           ++  v                 
  gi|488600021|ref|YP_007906492.1| 420 PPLSVlSSEYYIGNIEKGKEYTAIFKLKASGESKPVRYPVKLYIKYRALneyaetDE--Vsvgvkvnpklsfevlgt 494
                                       557777888889999999999999999999999999999999999888777774444..444888899999999999 PP

                                       SEE-CTEEEEEEEE CS
                             CARDB  55 psLaagesttvsft 68 
                                       ps++ag+++ v+f+
  gi|488600021|ref|YP_007906492.1| 495 PSIQAGTEKVVTFK 508
                                       99999999999987 PP

  == domain 6  score: 14.1 bits;  conditional E-value: 1.4e-05
                                       SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEE CS
                             CARDB  13 seafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..ategevtltvvv 84 
                                        +  +g+e  +t+++ N+G+ + ++ ++++++ +  +   +t+ +  L+++es++v+f+++++  at++ ++l++ v
  gi|488600021|ref|YP_007906492.1| 495 PSIQAGTEKVVTFKIVNTGDFEIKDANARITIVDPFTstdDTSFIGDLKPNESKEVRFKIKVDsdATPKIYALNLEV 571
                                       5677899999********************999988878888899*****************998888888898876 PP

>> PHTB1_C  PTHB1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     7e-07    0.0021       2      70 ..     399     467 ..     398     482 .. 0.92
   2 !    8.3   0.0   0.00036       1.1       4      69 ..     509     574 ..     506     586 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7e-07
                           PHTB1_C   2 vkvtlkssttlenvqlsvqvdkplaaskstfviesldesasteliisvflkgslipaslevevvasYts 70 
                                       ++vt+++s++l++ ++++++++pl +  s++ i +++++++ ++i++   +g++ p    v+ ++ Y+ 
  gi|488600021|ref|YP_007906492.1| 399 LRVTFTTSANLSDASVLISANPPLSVLSSEYYIGNIEKGKEYTAIFKLKASGESKPVRYPVKLYIKYRA 467
                                       5799************************************************************99984 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00036
                           PHTB1_C   4 vtlkssttlenvqlsvqvdkplaaskstfviesldesasteliisvflkgslipaslevevvasYt 69 
                                       +  +   ++++ +  + + +p++ +++t +i +l++++s+e+++++ +  +++p     +  + Y+
  gi|488600021|ref|YP_007906492.1| 509 IVNTGDFEIKDANARITIVDPFTSTDDTSFIGDLKPNESKEVRFKIKVDSDATPKIYALNLEVKYK 574
                                       5566778999999***********************************888888877777777776 PP

>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.36   1.1e+03      56     122 ..     340     408 ..     321     422 .. 0.61
   2 ?    9.7   0.2   0.00032      0.96      57     101 ..     432     480 ..     427     514 .. 0.68
   3 ?    1.2   0.0      0.13     4e+02      78     119 ..     547     583 ..     537     593 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                                       ECCS-TT-EEEEEEEEEESSTS.....EEEEEEEEEESSTTSCTCEEEEEEEEEES.TSEEEEEEEEE-SSCS CS
                           CBM_4_9  56 tirlekgktYtvsfwvkassgk.....srtikvkigdtdadganydevadekvelk.gewktlegtFtipkst 122
                                       +i+++ g +Y +++ + ++ ++     ++ + + i  +++   + +e++d k ++  +   +l  tFt++  +
  gi|488600021|ref|YP_007906492.1| 340 KINVKDGGRYPLKVRAVYVDANgdvkeTEAVPFGIDVQAS---PVIEIKDVKSNIYvNAKGELRVTFTTS-AN 408
                                       4566666666666666666555555555556666666655...566666554444446666666666666.44 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00032
                                       CCS-TT-EEEEEEEEEESSTS...EEEEEEEEEESSTTS.CTCEEEEEE CS
                           CBM_4_9  57 irlekgktYtvsfwvkassgk...srtikvkigdtdadg.anydevade 101
                                        ++ekgk+Yt  f+ kas ++      +k+ i++++ ++ a++dev  +
  gi|488600021|ref|YP_007906492.1| 432 GNIEKGKEYTAIFKLKASGESkpvRYPVKLYIKYRALNEyAETDEVSVG 480
                                       579**************99999665555555555555444555555444 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.13
                                       EEEEEEEEEESSTTSCTCEEEEEEEEEESTSEEEEEEEEE-S CS
                           CBM_4_9  78 srtikvkigdtdadganydevadekvelkgewktlegtFtip 119
                                       s+++++ki+ +++  +++++    + +l+ ++k+leg+++++
  gi|488600021|ref|YP_007906492.1| 547 SKEVRFKIKVDSDA-TPKIY----ALNLEVKYKDLEGEWVTS 583
                                       46666666666662.22222....234556666777776666 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   4.3e+03      65      82 ..     239     256 ..     238     260 .. 0.79
   2 ?   -0.4   0.0      0.36   1.1e+03      61      78 ..     335     352 ..     326     394 .. 0.81
   3 ?    9.4   0.1   0.00034         1      60     116 ..     500     556 ..     491     571 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                           DUF2393  65 vdgtitNeGkftikeCkl 82 
                                       ++++++N G++t ++ +l
  gi|488600021|ref|YP_007906492.1| 239 IEIKVRNSGEKTARNAYL 256
                                       678999999999887766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.36
                           DUF2393  61 eafvvdgtitNeGkftik 78 
                                        +f+++++++  G++++k
  gi|488600021|ref|YP_007906492.1| 335 ATFYIKINVKDGGRYPLK 352
                                       57999*****99999876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00034
                           DUF2393  60 teafvvdgtitNeGkftikeCkleiklvnkshnkkskellkklkplvsksevikedl 116
                                        +  vv+++i N+G+f+ik    +i++v++   +  + ++  lkp +sk+  +k ++
  gi|488600021|ref|YP_007906492.1| 500 GTEKVVTFKIVNTGDFEIKDANARITIVDPFTSTDDTSFIGDLKPNESKEVRFKIKV 556
                                       566799***********************9999955555555555555555555444 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.5     1e+04      53      67 ..     125     140 ..     123     148 .. 0.75
   2 ?   -3.4   0.4       3.5     1e+04       5      28 ..     162     185 ..     159     188 .. 0.51
   3 ?   -0.9   0.0      0.58   1.7e+03      47      73 ..     224     250 ..     203     272 .. 0.69
   4 ?   -3.4   0.0       3.4     1e+04      13      26 ..     327     340 ..     320     366 .. 0.59
   5 ?   -0.2   0.0      0.34     1e+03      51      77 ..     388     412 ..     381     421 .. 0.71
   6 ?    4.0   0.0     0.017        51       5      31 ..     426     452 ..     422     457 .. 0.87
   7 ?    4.0   0.0     0.017        50      12      33 ..     496     517 ..     488     529 .. 0.84
   8 ?   -2.2   0.0       1.4   4.3e+03      10      33 ..     539     562 ..     530     569 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.5
                           DUF1573  53 piapGe.sgkikvtfn 67 
                                        i+pGe + k+kvtf+
  gi|488600021|ref|YP_007906492.1| 125 GIKPGEyNLKLKVTFE 140
                                       5788874579999997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.5
                           DUF1573   5 ettidfgkieegekvtatFeftNt 28 
                                       +t  d  +i +++++ ++ ++tNt
  gi|488600021|ref|YP_007906492.1| 162 NTMTDEYSIVTKNPTDTNVTLTNT 185
                                       444444455555555555555555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.58
                           DUF1573  47 peypkepiapGesgkikvtfnakgrpg 73 
                                       +e++ e +  G +gki+++  ++g++ 
  gi|488600021|ref|YP_007906492.1| 224 VEVKGEDLIGGGKGKIEIKVRNSGEKT 250
                                       555556666677777777777666443 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 3.4
                           DUF1573  13 ieegekvtatFeft 26 
                                       ++ +e+++atF ++
  gi|488600021|ref|YP_007906492.1| 327 LKPNETTEATFYIK 340
                                       55555555555443 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.34
                           DUF1573  51 kepiapGesgkikvtfnakgrpgefnk 77 
                                       k+ i  + +g+++vtf++++  +  + 
  gi|488600021|ref|YP_007906492.1| 388 KSNIYVNAKGELRVTFTTSA--NLSDA 412
                                       66778889999999999987..33344 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.017
                           DUF1573   5 ettidfgkieegekvtatFeftNtgka 31 
                                       ++++ +g+ie+g++ ta F+++  g++
  gi|488600021|ref|YP_007906492.1| 426 SSEYYIGNIEKGKEYTAIFKLKASGES 452
                                       68899****************999976 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.017
                           DUF1573  12 kieegekvtatFeftNtgkapl 33 
                                       +i++g+++ +tF++ Ntg+ ++
  gi|488600021|ref|YP_007906492.1| 496 SIQAGTEKVVTFKIVNTGDFEI 517
                                       588999************9764 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 1.4
                           DUF1573  10 fgkieegekvtatFeftNtgkapl 33 
                                       +g+++ +e+++++F+++ +++a+ 
  gi|488600021|ref|YP_007906492.1| 539 IGDLKPNESKEVRFKIKVDSDATP 562
                                       678888888888888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4419.65
//
Query:       gi|488600022|ref|YP_007906493.1|  [L=750]
Description: The (Largely Archaeal Putative) Hydrophobe/Amphiphile Efflux-3 (HAE3) Family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-61  207.7  18.4    2.9e-33  115.2   2.3    2.2  2  MMPL            MMPL family
    1.6e-14   53.0  33.8    3.8e-10   38.5   6.9    3.8  3  Patched         Patched family
    5.7e-12   45.7  16.3    1.8e-07   31.2   0.4    3.2  3  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    1.4e-05   24.6   5.1    1.4e-05   24.6   5.1    2.5  2  SecD_SecF       Protein export membrane protein
  ------ inclusion threshold ------
      0.018   15.2   0.9      0.018   15.2   0.9    3.4  3  PIG-F           GPI biosynthesis protein family Pig-F
      0.023   15.1   1.1       0.18   12.2   0.1    2.8  2  DUF1689         Protein of unknown function (DUF1689)
      0.025   14.9   4.0      0.086   13.2   4.0    1.9  1  Herpes_UL20     Herpesvirus egress protein UL20


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 !  115.2   2.3   1.1e-36   2.9e-33       3     308 ..      48     364 ..      46     392 .. 0.82
   2 !   98.0   8.4     2e-31     5e-28     126     302 ..     559     729 ..     526     740 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 1.1e-36
                              MMPL   3 spadaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdf......... 70 
                                         +d+ + k+ ++ +++f    ++++i ++v+  gde +   +  +++ +l ++l+  +++ g +s++         
  gi|488600022|ref|YP_007906493.1|  48 FNKDNVVYKQYELYQKDFGT--GTQNIFIIVK--GDEVVST-DVYRYMLDLQRSLEYIDGVSGTLSPAsiiveivgy 119
                                       56777778888888888877..5567777777..5555555.88888888888888888888888888777777777 PP

                              MMPL  71 ........lsdpdvaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrd 139
                                               ++ ++  a  +++ ++ + + v l+   ++++++e  ++++++ve  +p++gl+vevtG +a++  +++
  gi|488600022|ref|YP_007906493.1| 120 lppdeaqlMQLTERYARDLAPEKTMTLIFVHLAT-NDKEKQNEISKEVERVVETSHPPAGLRVEVTGIPALNVQIQE 195
                                       7777666633344445556899999999999994.566666678899****************************** PP

                              MMPL 140 asdrdlklievvtlvvilviLlivyrSlv....aallplltvvvsllaalglvlilalllglelstfvlgllvvlli 212
                                         +++ +++ +v+ v+ ++iL++++  +v    +al+pl+  vvs+ + +gl      +lg+ ls  + g +  +li
  gi|488600022|ref|YP_007906493.1| 196 EIKKSFGVTMAVSTVLMVLILFLTFSGVVrrkyTALMPLMISVVSVQTVYGL----MPILGIPLSEHTNG-ALPMLI 267
                                       ************************9888755557888888888888888887....789999**999877.556789 PP

                              MMPL 213 avGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvl 289
                                       + ++ Y   L  Ry ee+++g+d++e++   +++tg ++++a +t +i ++++++  +p++aq+G+ ++lG++++  
  gi|488600022|ref|YP_007906493.1| 268 GLAIEYGAQLQNRYEEERKEGRDKDESIVISITRTGVAIVMALITTVIGFMSMLAPGIPSMAQFGIIASLGLIMAYI 344
                                       99*************************************************************************** PP

                              MMPL 290 ivlTllPAllvllGraa.la 308
                                        +lT+lPA+l l+ r +  +
  gi|488600022|ref|YP_007906493.1| 345 FTLTFLPAILKLIDREKtEV 364
                                       ************99984333 PP

  == domain 2  score: 98.0 bits;  conditional E-value: 2e-31
                              MMPL 126 evtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstf 202
                                       +vtG+++++a++ ++  +  +++++++ ++i+++Ll+vyrS+  a++pl+ + + +++  ++++     l  + +t+
  gi|488600022|ref|YP_007906493.1| 559 YVTGSPVIYAEMGNIMINGQTTMTLTAYALIVILLLVVYRSIRKAVVPLIAITTVIGVMNTIMY-----LTGTKHTM 630
                                       9***************************************************999999998833.....33345667 PP

                              MMPL 203 vlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGva 279
                                       +   l  ++++ G+D+ + ++ Ry ee++  +   e+v r++ +tgk++t ++lt+a+ + +L+++++p+++++G+ 
  gi|488600022|ref|YP_007906493.1| 631 ISIALNSITLGLGIDFSIHVLERYFEERQSYSPI-ESVRRTIERTGKAITTSALTMAGGFGSLMFSSFPIMQSFGFI 706
                                       77777889**********************9999.8***************************************** PP

                              MMPL 280 ialGvlvdvlivlTllPAllvll 302
                                       + +++++++  +lT++PA+l+++
  gi|488600022|ref|YP_007906493.1| 707 ALIAIVFSLISALTVVPAFLMVT 729
                                       ******************99874 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.016        42     430     536 ..       2     105 ..       1     137 [. 0.77
   2 !   38.5   6.9   1.5e-13   3.8e-10     169     391 ..     155     365 ..     128     479 .. 0.79
   3 !   19.4  14.2   8.9e-08   0.00023     661     809 ..     579     729 ..     565     731 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.016
                           Patched 430 skffreiyapfllnksvrlvvlllfvvylaiaiyGcvnikegLepkklvledsplvevlkliekeiwkeglqvevvv 506
                                       ++ f+e++a f+++k + +v+++ +++ l+       n+k +   + ++ +d+ + + ++l +k +    +++ ++v
  gi|488600022|ref|YP_007906493.1|   2 FQEFLENVARFVARKPGLVVSVVSLLIILSAISA--QNVKLTSGTESMFNKDNVVYKQYELYQKDFGTGTQNIFIIV 76 
                                       567999***********99999988876655444..455555556789*************9999888888888888 PP

                           Patched 507 nNppdltikesrdrleelveefentpyalg 536
                                       +   ++   + + ++  l  ++e +  + g
  gi|488600022|ref|YP_007906493.1|  77 KG-DEVVSTDVYRYMLDLQRSLEYIDGVSG 105
                                       64.556666677777777777777776666 PP

  == domain 2  score: 38.5 bits;  conditional E-value: 1.5e-13
                           Patched 169 deeeveelskeyerelekllkdkyasehievsilhsqiledelqrnaktllpflvvtiaiLlvfs.iivsvvlssda 244
                                       d+e++    +e ++e+e+ ++ +  +  + v ++    l+  +q+    ++  + vt+a+ +v   +i ++++s   
  gi|488600022|ref|YP_007906493.1| 155 DKEKQ----NEISKEVERVVETSHPPAGLRVEVTGIPALNVQIQEE---IKKSFGVTMAVSTVLMvLILFLTFSG-- 222
                                       33333....4445555555555666665666666655555555543...34445555555444330344456666.. PP

                           Patched 245 lkidwvrskpilailgvlspvlAivsslGlllwlGfrfnsi.vtvtPFLv.LaiGvDdmflmvaawkrteaklsvkk 319
                                            v+ + + a++ ++ +v+++ +  Gl+ +lG++  +  +   P L+ Lai    + l++   ++ +  +++ +
  gi|488600022|ref|YP_007906493.1| 223 -----VVRRKYTALMPLMISVVSVQTVYGLMPILGIPLSEHtNGALPMLIgLAIEY-GAQLQNRYEEERKEGRDKDE 293
                                       .....6667799************************98776156889998777754.45677777777777788*** PP

                           Patched 320 rigealseagvaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaakaeaegr 391
                                        i   +  +gvai++  +T v+ F       +p ++ F i++++ +++++i+++tf+ a+l ++ +  +e r
  gi|488600022|ref|YP_007906493.1| 294 SIVISITRTGVAIVMALITTVIGFMSMLAPGIPSMAQFGIIASLGLIMAYIFTLTFLPAILKLIDREKTEVR 365
                                       ************************9999999*******************************9987766654 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 8.9e-08
                           Patched 661 qnivlallcmfvvallfipelitvlvitlsivsidigvi.GflslWgvdLDpismitiimsiGfsvdlsaHiayafv 736
                                       ++++l+   ++v+ ll ++ +i  +v+ l  +++ igv+  ++ l g +   is++   +  G  +d+s H+  +++
  gi|488600022|ref|YP_007906493.1| 579 TTMTLTAYALIVILLLVVYRSIRKAVVPLIAITTVIGVMnTIMYLTGTKHTMISIALNSITLGLGIDFSIHVLERYF 655
                                       5788899999*******************99999***9945899*******9*9999999***************** PP

                           Patched 737 rsekd.dakeRvvealealgwPvvqgalSTilgvlvLlfvdsymvqvFfktvvLvvvigllHgLlilPillslf 809
                                       +++++ ++ e v++++e  g  +  +al    g  +L+f    ++q F    ++ +v++l+ +L ++P +l++ 
  gi|488600022|ref|YP_007906493.1| 656 EERQSySPIESVRRTIERTGKAITTSALTMAGGFGSLMFSSFPIMQSFGFIALIAIVFSLISALTVVPAFLMVT 729
                                       ****99**********************99999**************************************975 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 ?   -2.9   0.0       2.2   5.5e+03      50      59 ..      68      77 ..      66      86 .. 0.81
   2 !   31.2   0.4   6.9e-11   1.8e-07       9     140 ..     230     361 ..     222     370 .. 0.88
   3 !   20.5   6.1   1.3e-07   0.00033      13     143 ..     607     737 ..     599     746 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                                      CHHCCHHCHH CS
                    Sterol-sensing 50 gvdnifvlvk 59
                                      g+ nif++vk
  gi|488600022|ref|YP_007906493.1| 68 GTQNIFIIVK 77
                                      899*****98 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 6.9e-11
                                       HHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCC CS
                    Sterol-sensing   9 glagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgps 84 
                                       +l+ ++i ++sv   +gl+ +lg++l+  +   lP l+    ++    l + +++  ++ ++ +e i   ++++g++
  gi|488600022|ref|YP_007906493.1| 230 ALMPLMISVVSVQTVYGLMPILGIPLSEHTNGALPMLI-GLAIEYGAQLQNRYEEERKEGRDkDESIVISITRTGVA 305
                                       6677889999*************************886.66667777889999988777666599************ PP

                                       CHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH CS
                    Sterol-sensing  85 illtsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirre 140
                                       i++ ++t ++ ++  ++  +p + +F + a +++++ +++ +tf  a+L l  r +
  gi|488600022|ref|YP_007906493.1| 306 IVMALITTVIGFMSMLAPGIPSMAQFGIIASLGLIMAYIFTLTFLPAILKLIDREK 361
                                       *************88899*******************************9977766 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 1.3e-07
                                       HHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHHCC CS
                    Sterol-sensing  13 viivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrsldeseriaealgevgpsillts 89 
                                       +i +++ + +  +++++ g + t+i++  l  + l  g+d +  +++ + +  +s +  e + ++++++g +i+ ++
  gi|488600022|ref|YP_007906493.1| 607 LIAITTVIGVMNTIMYLTGTKHTMISI-ALNSITLGLGIDFSIHVLERYFEERQSYSPIESVRRTIERTGKAITTSA 682
                                       556666677777899999*******99.9999*********99999999999999999******************* PP

                                       CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH.HCT CS
                    Sterol-sensing  90 ltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirre.ese 143
                                       lt +  +   +++++p +q+F + a +a++++ +  +t+  a+L + ++ +  s+
  gi|488600022|ref|YP_007906493.1| 683 LTMAGGFGSLMFSSFPIMQSFGFIALIAIVFSLISALTVVPAFLMVTEKIKvGSN 737
                                       ********777*********************************99999874554 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   5.1   5.4e-09   1.4e-05      25     183 ..     193     354 ..     176     360 .. 0.80
   2 ?   -0.1  14.9       0.2   5.1e+02      23     184 ..     568     727 ..     560     731 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.4e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT.....-HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTS CS
                         SecD_SecF  25 vskelaekavlallialvliliyvalrF.....ewrvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGY 96 
                                       + +e++++  + +++++vl+++ ++l F     +++ al  ++  v  v ++ g++ +lgi+++ +t +al ++iG 
  gi|488600022|ref|YP_007906493.1| 193 IQEEIKKSFGVTMAVSTVLMVLILFLTFsgvvrRKYTALMPLMISVVSVQTVYGLMPILGIPLSEHTNGALPMLIGL 269
                                       45566666666666666666666666663333355667777777777888999************************ PP

                                       SSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTT CS
                         SecD_SecF  97 SvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgty 173
                                        ++    + +r +e++++   ++ +e i  s++ t +  +++ +tt++  +++l  g  s+++f ++  +Gli+  +
  gi|488600022|ref|YP_007906493.1| 270 AIEYGAQLQNRYEEERKE--GRDKDESIVISITRTGVAIVMALITTVIGFMSMLAPGIPSMAQFGIIASLGLIMAYI 344
                                       **************9555..6777899999******************************************99877 PP

                                       THHHHHHHHH CS
                         SecD_SecF 174 ssifiaspll 183
                                        ++ +  ++l
  gi|488600022|ref|YP_007906493.1| 345 FTLTFLPAIL 354
                                       7766655555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSS CS
                         SecD_SecF  23 psvskelaekavlallialvliliyvalrFew.rvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSv 98 
                                       +++++ +++      l+a +li+i + + ++  r a+  +ia+   + ++ +++ l+g + ++ ++a     +G  +
  gi|488600022|ref|YP_007906493.1| 568 AEMGNIMINGQTTMTLTAYALIVILLLVVYRSiRKAVVPLIAITTVIGVMNTIMYLTGTKHTMISIALNSITLGLGI 644
                                       678888888888889999999999999999853889999***999999************9999987666779**** PP

                                       HHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHH.HHHHHHTTTTHHHHHHHHHHTSTTTTT CS
                         SecD_SecF  99 ndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvv.allllggdslkdfalallvGlivgtys 174
                                       + ++ v +r  e++++    +  e + + ++ t + +i+ts+ t+   + +l++    ++++f ++ l+++++  +s
  gi|488600022|ref|YP_007906493.1| 645 DFSIHVLERYFEERQS---YSPIESVRRTIERTGK-AITTSALTMAGGFgSLMFSSFPIMQSFGFIALIAIVFSLIS 717
                                       ********99998555...5556677788888754.888888777766515666666*******************9 PP

                                       HHHHHHHHHH CS
                         SecD_SecF 175 sifiasplll 184
                                       ++ +  ++l+
  gi|488600022|ref|YP_007906493.1| 718 ALTVVPAFLM 727
                                       9887776665 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 ?   15.2   0.9     7e-06     0.018       3     102 ..     209     344 ..     207     354 .. 0.78
   2 ?    3.4   0.7      0.03        76      37      84 ..     341     405 ..     327     416 .. 0.64
   3 ?   -0.1   1.9      0.34   8.8e+02      26      45 ..     584     656 ..     562     747 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7e-06
                             PIG-F   3 palllallalrfsalvadpvstLlsslivlallqvlyvvlcl.................................ek 46 
                                       ++l++ +l+l+fs +v+ ++++L+  +i ++ +q++y ++ +                                 e+
  gi|488600022|ref|YP_007906493.1| 209 TVLMVLILFLTFSGVVRRKYTALMPLMISVVSVQTVYGLMPIlgiplsehtngalpmliglaieygaqlqnryeeER 285
                                       6788899999****************************99999********************99999988776447 PP

                             PIG-F  47 kkkkskkskivlallsllltll...latlllaillvlfGApllthlleTlllalhlsll 102
                                       k+ ++k ++iv +++++ ++++   ++t++ ++ ++  G p + ++   + l l ++ +
  gi|488600022|ref|YP_007906493.1| 286 KEGRDKDESIVISITRTGVAIVmalITTVIGFMSMLAPGIPSMAQFGIIASLGLIMAYI 344
                                       77788888888888887665552335666667777777777766666666666666544 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.03
                             PIG-F  37 vlyvvlcl..............ekkkk......kskkskivlallsllltlllatlllaillvlfGAp 84 
                                       ++y+++ +              e          k + ++ ++++ sl+ t  ++ l++a+++v+fG  
  gi|488600022|ref|YP_007906493.1| 341 MAYIFTLTflpailklidrektE---VravekeKGILERSLAMISSLTATRPVGILVFAFAIVVFGLY 405
                                       33333333344444555544330...13333335677788889999999999*************955 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.34
                             PIG-F  26 lsslivlallqvlyvvlcl.....................................................e 45 
                                       +  +++++ll v+y  ++                                                      e
  gi|488600022|ref|YP_007906493.1| 584 TAYALIVILLLVVYRSIRKavvpliaittvigvmntimyltgtkhtmisialnsitlglgidfsihvleryfE 656
                                       3444444444444444444444444444444444444444444455555555555555555555555554442 PP

>> DUF1689  Protein of unknown function (DUF1689)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.55   1.4e+03      66      91 ..     369     420 ..     330     438 .. 0.70
   2 ?   12.2   0.1   7.2e-05      0.18      16      88 ..     537     632 ..     524     663 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.55
                           DUF1689  66 r..........................sfllGlvalvvssqlaakyaykkkl 91 
                                       +                          +f++ +++l++ss++  +++y+k +
  gi|488600022|ref|YP_007906493.1| 369 KekgilerslamissltatrpvgilvfAFAIVVFGLYASSYIQLETNYNKYV 420
                                       2446666666666666666677777778999999999999999999999876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.2e-05
                           DUF1689  16 aeDRleLakklqsiaraqllggwlgfsavflaptayrryktgaikgvkvpr.......................... 66 
                                       + +R      ++si r   ++gw+g+  v ++p++y  + +  i+g  + +                          
  gi|488600022|ref|YP_007906493.1| 537 EYER-----LYESIKRDVQYFGWSGGYYVTGSPVIYAEMGNIMINGQTTMTltayalivilllvvyrsirkavvpli 608
                                       4444.....49****************************88888886555578888888888888888888887777 PP

                           DUF1689  67 ..sfllGlvalvvssqlaakyayk 88 
                                         + ++G++++++  + + +++ +
  gi|488600022|ref|YP_007906493.1| 609 aiTTVIGVMNTIMYLTGTKHTMIS 632
                                       777777777777766655555555 PP

>> Herpes_UL20  Herpesvirus egress protein UL20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.0   3.4e-05     0.086      48     115 ..     568     632 ..     559     653 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                       Herpes_UL20  48 ltgrlllvagllaltvlyyvtlllellvvYvNiksDllPlstyqklllgalvilggillvalayetlf 115
                                       ++   +++ g +++t + y  +++ llvvY+ i++  +Pl + + ++    v+ + ++l ++ + +++
  gi|488600022|ref|YP_007906493.1| 568 AEMGNIMINGQTTMTLTAYALIVILLLVVYRSIRKAVVPLIAITTVIG---VMNTIMYLTGTKHTMIS 632
                                       455678999999999999999999******************776654...55555666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1241  (0.0692175); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.93u 0.34s 00:00:01.27 Elapsed: 00:00:00.54
# Mc/sec: 4207.50
//
Query:       gi|488600023|ref|YP_007906494.1|  [L=448]
Description: hypothetical protein Asulf_00474 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.034   14.1   0.0    1.8  2  FIST      FIST N domain
      0.058   13.3   0.9       0.14   12.0   0.1    2.0  2  Takusan   Takusan


Domain annotation for each model (and alignments):
>> FIST  FIST N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.8e-06     0.034       1     138 [.      37     234 ..      37     281 .. 0.59
   2 ?   -0.2   0.0     0.098   8.8e+02     118     138 ..     213     234 ..     178     383 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-06
                              FIST   1 dlvlvfas.aeasdleallealrealpgapliGcstageiasegleledgvvalalasa...........da..... 60 
                                       d++l+f++    +d+ +  e  ++ +p+a+++Gc+ +g + + ++  + g+va+   ++           da     
  gi|488600023|ref|YP_007906494.1|  37 DFILLFFTkGTMNDYLRYNEIFKKNFPDAQMLGCVIEGYMVE-EEVWTIGLVAMLANFDgkvqvfwesgnDArvvse 112
                                       688999887778899999999******************963.3335555555555555888888877662244222 PP

                              FIST  61 .ageelak......al...........................pkl...............lllla.dglssneeel 87 
                                        +g+++ +      a+                           +                       + +   ++e+
  gi|488600023|ref|YP_007906494.1| 113 rVGRKIGDkwdvvlAMfpafyfpsklrfleaflkdriqyvsyrN-KgtkeekeeilrnisrY---YrENFIYPVDEV 185
                                       34444444554433114333444333333333333333333230.02333333333332221...224444556677 PP

                              FIST  88 legldealaspdvpivGGlagdgtlafktyvlf.nggvledgvvvvllsges 138
                                       legl    ++ +  i+G +     ++++++v++ n + +  g++v  ++g+ 
  gi|488600023|ref|YP_007906494.1| 186 LEGLG---RHCNAKIIGMNLMPIEAQPNMPVILaNYRDIGRGLAVMCFKGKV 234
                                       77777...33377778775555545556677777777777777777777765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.098
                              FIST 118 vlf.nggvledgvvvvllsges 138
                                       v++ n + +  g++v  ++g+ 
  gi|488600023|ref|YP_007906494.1| 213 VILaNYRDIGRGLAVMCFKGKV 234
                                       4443444444444444444432 PP

>> Takusan  Takusan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.6e-05      0.14      13      60 ..      13      58 ..       7      63 .. 0.87
   2 ?   -2.2   0.1      0.43   3.9e+03      13      28 ..     157     172 ..     153     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                           Takusan 13 eqakkklEeLkleLrkitreRdELrdiLalytegslndrpsvrlnpey 60
                                      ++ +   EeL+ e+ ki++   E   iL ++t+g++nd  + r n  +
  gi|488600023|ref|YP_007906494.1| 13 NEYQHAREELIEEINKIKKSGFEVDFILLFFTKGTMND--YLRYNEIF 58
                                      5667788*******************************..88888655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.43
                           Takusan  13 eqakkklEeLkleLrk 28 
                                       + +k+++Ee+++ +  
  gi|488600023|ref|YP_007906494.1| 157 KGTKEEKEEILRNISR 172
                                       5578999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2987.22
//
Query:       gi|488600024|ref|YP_007906495.1|  [L=290]
Description: hypothetical protein Asulf_00475 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   59.7  13.6    3.8e-16   59.1  13.6    1.2  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.011   16.0   2.0      0.011   16.0   2.0    2.9  2  YwiC      YwiC-like 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 !   59.1  13.6   4.3e-20   3.8e-16       9     237 ..      27     258 ..      19     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 4.3e-20
                              UbiA   9 lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilglllla 85 
                                       + +a  g   +  l+ ++l+t+ + aa+n++N++ D+e+D +    +n  + s +  ++ +li+++vl+  ++l+  
  gi|488600024|ref|YP_007906495.1|  27 FIFALSGNREIGDLINTILFTFPFFAAVNLFNHVNDIEEDLL--AGKNN-IFSDKKIRNLGLIIVLVLYSSSILFY- 99 
                                       556667777888999***************************..77788.88777777999999999999999998. PP

                              UbiA  86 lllnpltallgllalllyvvYt.......g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfl 154
                                       + +    ++  +++l++ ++Y+          rlK + +   ++  ++ ++++l  w++v+ +   +  ++a+ +f+
  gi|488600024|ref|YP_007906495.1| 100 FSIKSEYIIYPIITLIFTWLYSdkivfgrYiKRLKEHYITEVLTYTVTAVTFALSIWFIVSDFNVRAYCAVAVVLFI 176
                                       ***********************999998677*******99999999999**********99988899999999999 PP

                              UbiA 155 ltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraa 231
                                         w+++l  dl+d+ +D+ ag++t++v++ +++ +  ++++l++l+l+++l+ + + l+ +++l+++++ ++  + +
  gi|488600024|ref|YP_007906495.1| 177 NLWTVFLK-DLKDVSSDKLAGLYTMAVKFSPETLYTASTVILIALYLSIFLFSMNNILPRPAILVSFVGFFPATVLI 252
                                       99999997.*********************99999999999999999988888888888888888888877777777 PP

                              UbiA 232 rlvrrr 237
                                       +lv+++
  gi|488600024|ref|YP_007906495.1| 253 KLVKSE 258
                                       777665 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   2.0   1.3e-06     0.011      38     113 ..     119     194 ..     105     206 .. 0.82
   2 ?    2.6   0.8     0.017   1.5e+02      29      78 ..     235     288 ..     198     290 .] 0.62

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                              YwiC  38 gYlaffplllllkarrrarylkplliYgavallllllalllqpa.llwwallflplvavavyeakrkreRsllndla 113
                                       +Y  +  ++ ++k r +++y   +l+Y++ a+ ++l ++++     + ++ ++++++ ++++ ++ k+ + + +d +
  gi|488600024|ref|YP_007906495.1| 119 LYSDKIVFGRYIK-RLKEHYITEVLTYTVTAVTFALSIWFIVSDfNVRAYCAVAVVLFINLWTVFLKDLKDVSSDKL 194
                                       5666666777777.599*******************9999988867888899999999**********999999854 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.017
                              YwiC  29 llllvawlvgYlaffplllllka....rrrarylkplliYgavallllllalll 78 
                                        ++ ++ +vg++  + l  l+k+    +  ++y + +    +++l++l+++++l
  gi|488600024|ref|YP_007906495.1| 235 RPAILVSFVGFFPATVLIKLVKSewdfASVHKYIRIIPQINILSLVFLTVIIAL 288
                                       344444555555555555555556665577777777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1876.36
//
Query:       gi|488600025|ref|YP_007906496.1|  [L=193]
Description: hypothetical protein Asulf_00476 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-29   99.7   0.5    7.6e-29   99.7   0.5    1.6  2  DUF502    Protein of unknown function (DUF502)


Domain annotation for each model (and alignments):
>> DUF502  Protein of unknown function (DUF502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5      0.18   3.3e+03       4      29 ..      11      36 ..       8      38 .. 0.68
   2 !   99.7   0.5   4.2e-33   7.6e-29       1     106 []      54     159 ..      54     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.18
                            DUF502  4 lllillvGllasnligrkllklgerl 29
                                        l+++v + a+ +++ +++k++e +
  gi|488600025|ref|YP_007906496.1| 11 TGLLIFVPISATLFLIFWVFKYIEDF 36
                                      55666777777778888888887766 PP

  == domain 2  score: 99.7 bits;  conditional E-value: 4.2e-33
                            DUF502   1 lvvlllillvGllasnligrkllklgerllkriPlvksiYsalkqvvetfsseekksfrevvlveyprkglwalgFv 77 
                                       lvv+l i+l Gll + ++g+++l++ e  ++riP++++iY  +k+ +++++ +e+++++ vvl+eyprkg+++lgF 
  gi|488600025|ref|YP_007906496.1|  54 LVVVLTIFLFGLLGRFTLGNRILGYAETQVRRIPIIRTIYVGVKEATKAILVSEAERLKGVVLIEYPRKGVYTLGFT 130
                                       6899***********************************************99************************ PP

                            DUF502  78 tget.egelatkgeedlvaVfvPtspnpts 106
                                       tg+  e+ ++ k++++l++VfvPtspnpts
  gi|488600025|ref|YP_007906496.1| 131 TGSViEDAIE-KTGKKLINVFVPTSPNPTS 159
                                       ****888886.5999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1366.01
//
Query:       gi|488600026|ref|YP_007906497.1|  [L=397]
Description: acetyl-CoA acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  181.5   0.0    4.5e-53  180.3   0.0    1.6  2  Thiolase_N     Thiolase, N-terminal domain
    8.8e-48  161.0   0.7    1.9e-47  160.0   0.3    1.8  2  Thiolase_C     Thiolase, C-terminal domain
  ------ inclusion threshold ------
      0.026   14.1   2.3      0.026   14.1   2.3    2.3  3  ketoacyl-synt  Beta-ketoacyl synthase, N-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 !  180.3   0.0   7.5e-57   4.5e-53       1     259 [.       4     266 ..       4     267 .. 0.90
   2 ?   -1.7   0.0      0.25   1.5e+03      30      95 ..     327     393 ..     299     397 .] 0.55

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 7.5e-57
                                       EEEEEEEEE--EET......TSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHT CS
                        Thiolase_N   1 vvivsaartpigkf......ggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqn.iarqaalka 70 
                                       v+iv+ +rtp+ ++      + ++++++ +eL++++l +++ekag+++e v+ +++G+     e+++   r ++l a
  gi|488600026|ref|YP_007906497.1|   4 VYIVDYVRTPFSRSrpkkpeKDVFHKIRGDELAKIVLDRIVEKAGISKEIVERIVMGCAFGVWENWAyGGRGISLLA 80 
                                       79*********875222222578999999*********************************99999899******* PP

                                       TS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTE CS
                        Thiolase_N  71 gipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgla 147
                                       + p e++++  +++c+S++++  +a  +i+ag +dv++agG E+m+++p+ ++ + +   + + + ++d   ++   
  gi|488600026|ref|YP_007906497.1|  81 EYPVETATMITDMQCGSSIASAQTASLEIMAGVCDVAIAGGYEHMTRVPMGMENQHI---SPNFRLIQDERYKK--Y 152
                                       **************************************************9985444...33333333333333..4 PP

                                       ETTTTSEHHHHHHHHHHH.HT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSE.EEE-S-TTS-TT-- CS
                        Thiolase_N 148 dafneehmGltaenlakk.ykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgk.ktvdkdeairsevt 222
                                       ++  +  mGltae+l ++  +i++e++de+ ++sh+ a ++ k+g F+ ei P++ ++ +g+  +v++d+ ir ++t
  gi|488600026|ref|YP_007906497.1| 153 EMNIGFVMGLTAERLFQEaKNITKEDLDEWGLRSHRLAYESLKSGYFRGEITPISAEQADGSvIVVESDQSIRGDTT 229
                                       455789********9765168*****************************************99************* PP

                                       HHHHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 223 aekLaklkpaFkkeGtvtAgnasqisDGaaavllmse 259
                                       +e++++l p+F  +G +tAgn+s+++ Ga+a+llms+
  gi|488600026|ref|YP_007906497.1| 230 LEQISNLPPVFMPNGVITAGNSSPLNAGASALLLMSA 266
                                       ***********************************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.25
                                       HHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSCHHHHHH.HHTTS-TTSEEEEEEHGGGHHHHHHHHH CS
                        Thiolase_N  30 alkallekagvdpeevdevivGnvlqa.gegqniarqaa.lkagipeevpavtvnkvcsSglkavala 95 
                                       +   ++++ g++pe v+ v+ G ++ +   g++ ar +  l+  + e+ +   v  +c+ g +++a++
  gi|488600026|ref|YP_007906497.1| 327 VTLYAVHELGIEPERVN-VHGGAIAIGhPLGATGARLIGtLARTLREKEADYGVATACIGGGQGIAMV 393
                                       34445555566666664.44444444445666666655413334555555566777777777777665 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         1     6e+03      29      51 ..      41      63 ..      38      65 .. 0.76
   2 !  160.0   0.3   3.1e-51   1.9e-47       2     123 .]     275     396 ..     274     396 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                                      HHHHHHHT--GGGESEEEE--SB CS
                        Thiolase_C 29 kkvlkkagltvedidlfEinEAF 51
                                       ++++kag++ e ++ + +  AF
  gi|488600026|ref|YP_007906497.1| 41 DRIVEKAGISKEIVERIVMGCAF 63
                                      67899999999888877766666 PP

  == domain 2  score: 160.0 bits;  conditional E-value: 3.1e-51
                                       --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH CS
                        Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaial 78 
                                       +plaki+++ ++gv+p+ +g gP++a+kk+++ka l+++did++EinEAFa ++L+++++l++++e+vNv+GGaia+
  gi|488600026|ref|YP_007906497.1| 275 EPLAKIKAFGYSGVHPAVMGKGPVPASKKAVEKANLKLSDIDYWEINEAFAIVTLYAVHELGIEPERVNVHGGAIAI 351
                                       79*************************************************************************** PP

                                       -B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                        Thiolase_C  79 GHPlGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                       GHPlGa+GaR++ tl+++l+++++ +gva++Cigggqg+a+vie+
  gi|488600026|ref|YP_007906497.1| 352 GHPLGATGARLIGTLARTLREKEADYGVATACIGGGQGIAMVIER 396
                                       *******************************************96 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 ?   -2.7   0.0      0.59   3.5e+03      95     125 ..      39      70 ..      34      87 .. 0.72
   2 ?   14.1   2.3   4.3e-06     0.026     168     206 ..      88     126 ..      81     136 .. 0.87
   3 ?   -1.3   0.1      0.22   1.3e+03     176     200 ..     357     381 ..     341     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.59
                                       HHHHHHHHHTS-HHTCTTGGEEEEEEESST.H CS
                     ketoacyl-synt  95 aawealedagltpeeldgsrvgvfiGvgag.d 125
                                       + ++ +e+ag+++e ++   +g+  Gv  +  
  gi|488600026|ref|YP_007906497.1|  39 VLDRIVEKAGISKEIVERIVMGCAFGVWENwA 70 
                                       66778899999997767666999999887754 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.3e-06
                                       EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                     ketoacyl-synt 168 svtvdtACsSslvavhaavqslrsgeadvalaGGvelll 206
                                       ++ +d  C Ss +  + a  ++++g +dva+aGG e ++
  gi|488600026|ref|YP_007906497.1|  88 TMITDMQCGSSIASAQTASLEIMAGVCDVAIAGGYEHMT 126
                                       5677888****99999999***************99765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.22
                                       GHH.HHHHHHHHHHHHTTS-SEEEEE CS
                     ketoacyl-synt 176 sSs.lvavhaavqslrsgeadvalaG 200
                                       +++   ++ +a + lr++ead+ +a 
  gi|488600026|ref|YP_007906497.1| 357 ATGaRLIGTLA-RTLREKEADYGVAT 381
                                       66645566677.99999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3018.11
//
Query:       gi|488600027|ref|YP_007906498.1|  [L=200]
Description: HTH DNA binding domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   73.4   0.6    1.6e-20   72.6   0.2    1.7  2  HTH_10     HTH DNA binding domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.029   14.3   0.0    1.6  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.032   14.3   0.0       0.08   13.0   0.0    1.6  1  HTH_3      Helix-turn-helix
      0.045   13.9   0.0       0.17   12.1   0.0    1.9  2  PilN       Fimbrial assembly protein (PilN)
      0.051   13.5   0.0      0.091   12.7   0.0    1.4  1  MarR_2     MarR family
      0.098   12.6   0.0       0.22   11.5   0.0    1.5  1  MarR       MarR family
       0.12   12.1   0.0       0.26   11.1   0.0    1.5  1  HTH_psq    helix-turn-helix, Psq domain
       0.17   11.5   0.0       0.24   11.1   0.0    1.2  1  DUF3394    Domain of unknown function (DUF3394)


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 ?   -3.1   0.0       3.2   7.2e+03      25      32 ..      18      25 ..      17      28 .. 0.78
   2 !   72.6   0.2   7.3e-24   1.6e-20       1      53 []     143     195 ..     143     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.2
                            HTH_10 25 tlkeLAke 32
                                      tlke++ke
  gi|488600027|ref|YP_007906498.1| 18 TLKEISKE 25
                                      78899987 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 7.3e-24
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       +T ++ evl++A+++GYFdyP++++l+eLA  +GI++stlse+Lr+a++k++e
  gi|488600027|ref|YP_007906498.1| 143 ITYREEEVLRIALQKGYFDYPKKIKLEELASYFGIAPSTLSEILRRAQKKVLE 195
                                       589***********************************************985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.029      22      48 ..     166     192 ..     148     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHT CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkre 48 
                                       +  eelAs+ G+ ++t+s il++ +++
  gi|488600027|ref|YP_007906498.1| 166 IKLEELASYFGIAPSTLSEILRRAQKK 192
                                       6679******************98775 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.6e-05      0.08       8      31 ..     164     187 ..     162     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-05
                                       TTHHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3   8 lglsqeeLAeklGvsrstisriEn 31 
                                       +++ +eeLA + G+ +st+s i +
  gi|488600027|ref|YP_007906498.1| 164 KKIKLEELASYFGIAPSTLSEILR 187
                                       68999****************987 PP

>> PilN  Fimbrial assembly protein (PilN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.4e-05      0.17       6      42 ..       6      44 ..       4      51 .. 0.86
   2 ?   -2.5   0.0       2.5   5.7e+03      29      43 ..      63      77 ..      63      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.4e-05
                              PilN  6 LsravPkgvwltsisqegn..qltitGsAvsndeVaefm 42
                                      +   +P+++ l+++++  +  +l+i+G + s++++  ++
  gi|488600027|ref|YP_007906498.1|  6 IKTKLPENCALSTLKEISKevTLKIEGLTISKNRIKGLV 44
                                      67789**********776656999**********98876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.5
                              PilN 29 tGsAvsndeVaefmr 43
                                      +G Avs++e   ++r
  gi|488600027|ref|YP_007906498.1| 63 DGLAVSQKEAKVLIR 77
                                      588999988887776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.1e-05     0.091      23      48 ..     167     192 ..     150     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                                       EHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  23 tvgelarrlglsksavsrilkrLvaa 48 
                                          ela ++g+ +s++s il+r++++
  gi|488600027|ref|YP_007906498.1| 167 KLEELASYFGIAPSTLSEILRRAQKK 192
                                       5679*******************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.9e-05      0.22      18      40 ..     166     188 ..     161     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.9e-05
                                       EEHHHHHHHHTS-HHHHHHHHHH CS
                              MarR  18 lsvseLakklgvskstvtrvldr 40 
                                       +++ eLa+ +g+ +st++++l+r
  gi|488600027|ref|YP_007906498.1| 166 IKLEELASYFGIAPSTLSEILRR 188
                                       7889*****************98 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 ?   11.1   0.0   0.00012      0.26      21      40 ..     170     189 ..     165     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                           HTH_psq  21 kAArkYgiPrsTLwrrkrgk 40 
                                       ++A+++gi+ sTL++ +r+ 
  gi|488600027|ref|YP_007906498.1| 170 ELASYFGIAPSTLSEILRRA 189
                                       78*************99985 PP

>> DUF3394  Domain of unknown function (DUF3394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.24      74     128 ..      23      79 ..       6     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                           DUF3394  74 gselrlkvegenlegeeiektvalplgeeatgeerLeaa..Gltlleedgkvlvdev 128
                                       ++e++lk+eg +++ ++i+  v+l+  + ++  e L ++  Gl + +++ kvl+ e 
  gi|488600027|ref|YP_007906498.1|  23 SKEVTLKIEGLTISKNRIKGLVNLKATKVGEILENLPSFcdGLAVSQKEAKVLIREH 79 
                                       789*********************************87779************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1345.10
//
Query:       gi|488600028|ref|YP_007906499.1|  [L=354]
Description: putative ATPase (AAA+ superfamily) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-36  123.3   0.0    1.6e-35  122.4   0.0    1.4  1  AAA              ATPase family associated with various cellul
    1.6e-07   31.6   0.0    3.4e-07   30.6   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
    3.2e-06   26.6   0.0    7.2e-06   25.4   0.0    1.5  2  TIP49            TIP49 P-loop domain
    1.1e-05   25.1   0.0    2.9e-05   23.8   0.0    1.7  1  AAA_lid_3        AAA+ lid domain
    1.3e-05   25.7   0.1     0.0024   18.3   0.0    2.3  2  AAA_16           AAA ATPase domain
    1.3e-05   25.0   0.0    4.4e-05   23.3   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.8e-05   22.4   0.0    0.00018   20.8   0.0    1.7  2  DUF815           Protein of unknown function (DUF815)
     0.0011   19.2   0.0     0.0017   18.5   0.0    1.4  1  AAA_33           AAA domain
     0.0019   18.5   0.3      0.069   13.4   0.0    2.5  2  AAA_22           AAA domain
      0.002   18.0   0.4     0.0061   16.4   0.4    1.7  1  Bac_DnaA         Bacterial dnaA  protein
     0.0048   17.0   0.0      0.019   15.1   0.0    1.9  2  Torsin           Torsin
     0.0074   16.0   0.0      0.013   15.3   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.013   15.5   0.1       0.05   13.6   0.0    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
      0.013   15.2   0.0      0.031   14.0   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
      0.021   14.2   0.1      0.053   12.9   0.1    1.7  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.025   14.1   0.2      0.062   12.8   0.0    1.6  2  AAA_7            P-loop containing dynein motor region
      0.036   14.0   0.2       0.33   10.9   0.0    2.2  2  NACHT            NACHT domain
       0.04   13.9   0.0      0.075   13.0   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.043   14.4   0.0      0.086   13.4   0.0    1.6  1  AAA_18           AAA domain
       0.07   13.0   0.0       0.15   11.9   0.0    1.5  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.092   12.1   0.1       0.28   10.6   0.0    1.8  2  TniB             Bacterial TniB protein
      0.097   13.1   0.0       0.19   12.1   0.0    1.6  1  RNA_helicase     RNA helicase
       0.12   12.2   0.0       0.22   11.4   0.0    1.4  1  RsgA_GTPase      RsgA GTPase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   0.0     2e-38   1.6e-35       1     131 [.     140     268 ..     140     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 2e-38
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       vl++G  GtGKT++aka+a+e++v+fl+i+ ++l+ ++vg+s+++i+el ++a++ a p+i+f+DE+da+a +r  +
  gi|488600028|ref|YP_007906499.1| 140 VLFHGYSGTGKTMMAKALANEAKVPFLSIKSTKLIGEHVGDSARRIHELYDRARNLA-PCIVFLDEFDAIALDRnYQ 215
                                       79******************************************************9.****************888 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                       + +++ ++vvn Llteldg +++e+ ++ i+atnr++++d  +  +Rf+++i ++
  gi|488600028|ref|YP_007906499.1| 216 DLRGDVSEVVNSLLTELDGIQSNEG-ICTIAATNRIEMIDYSIK-SRFEEEIMFD 268
                                       9999******************866.******************.******9886 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   4.3e-10   3.4e-07       5     105 ..     139     234 ..     136     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.3e-10
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                       ++l+ g +g+Gkt++akala+  +v    ++  +  ++l+     eh+ ++    ++ y +a +    iv+lDE d 
  gi|488600028|ref|YP_007906499.1| 139 NVLFHGYSGTGKTMMAKALANEAKV----PFLSIKSTKLIG----EHVGDSARRIHELYDRARNLApcIVFLDEFDA 207
                                       799********************98....************....*******************9999********* PP

                                       ----...---------HHHHHHHHHHHH- CS
                             AAA_2  80 ihpk...essgadvSregVqrdLLqileg 105
                                       i+     +  + dvS  +V++ LL  l+g
  gi|488600028|ref|YP_007906499.1| 208 IALDrnyQDLRGDVS--EVVNSLLTELDG 234
                                       **9877888888998..899999998887 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   9.2e-09   7.2e-06      23      89 ..     106     174 ..      90     189 .. 0.85
   2 ?   -2.8   0.0       3.7   2.9e+03     312     327 ..     235     250 ..     194     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9.2e-09
                                       XXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  23 eeglvGqkkareaagvivelike....kklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevy 89 
                                        + +vG ++a++ + +i+e +k+    +k a + vL+ G sgtGkt +a a+++e   +vpf +++++++ 
  gi|488600028|ref|YP_007906499.1| 106 LDDVVGHEEAKKKVRIILEYLKNpekfGKWAPKNVLFHGYSGTGKTMMAKALANEA--KVPFLSIKSTKLI 174
                                       4689*****************9844445778899*******************995..7******998876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                                       XXXXXXXXXXXXXXXX CS
                             TIP49 312 latnrgiakirGtdii 327
                                       + +n gi++i  t+ i
  gi|488600028|ref|YP_007906499.1| 235 IQSNEGICTIAATNRI 250
                                       5678888888888765 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.7e-08   2.9e-05       3      44 ..     293     335 ..     291     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.7e-08
                         AAA_lid_3   3 dlkeLAerTeGySGADlaa.lcreAallAlrrgikeitmedfe 44 
                                       +l+ +A+ TeG+SG Dl++ +++ A ++A+ +g + i++ d++
  gi|488600028|ref|YP_007906499.1| 293 NLEIVASNTEGFSGRDLVEkVIKPALHRAIADGKDYIETNDLI 335
                                       677799***********777*******************9985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.1e-06    0.0024      24      57 ..     134     167 ..     116     178 .. 0.73
   2 ?    5.3   0.1     0.029        23     115     146 ..     177     209 ..     165     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.1e-06
                            AAA_16  24 p...elvllsGesGvGKsslvrellralekdggiflr 57 
                                            +vl++G+sG+GK+ ++++l+++++     fl+
  gi|488600028|ref|YP_007906499.1| 134 KwapKNVLFHGYSGTGKTMMAKALANEAKVP---FLS 167
                                       455599*******************977644...555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.029
                            AAA_16 115 easrllellkrllallsrderplvlvlDdlq..w 146
                                       +  + ++ + +l +++++   p +++lD+++   
  gi|488600028|ref|YP_007906499.1| 177 HVGDSARRIHELYDRARN-LAPCIVFLDEFDaiA 209
                                       555666777888899999.556*********443 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 !   23.3   0.0   5.7e-08   4.4e-05       2      82 ..     102     188 ..     101     226 .. 0.76
   2 ?   -1.5   0.0       2.4   1.8e+03     135     154 ..     243     262 ..     235     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.7e-08
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkree....aldhvllyGpPGlGkttlakiiakelgvkl.kitsgPvl.eka 72 
                                       r  +l++ +g e+ k+k++i++e  k+ e+    a   vl++G  G Gkt +ak +a+e +v +  i s+  + e+ 
  gi|488600028|ref|YP_007906499.1| 102 RDVTLDDVVGHEEAKKKVRIILEYLKNPEKfgkwAPKNVLFHGYSGTGKTMMAKALANEAKVPFlSIKSTKLIgEHV 178
                                       7789*****************99877765433337899***********************9861445555554556 PP

                            RuvB_N  73 gdlaalltnl 82 
                                       gd a  + +l
  gi|488600028|ref|YP_007906499.1| 179 GDSARRIHEL 188
                                       6666655555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                            RuvB_N 135 lvgattragllssPlrdrfg 154
                                        ++at r  ++   +++rf 
  gi|488600028|ref|YP_007906499.1| 243 TIAATNRIEMIDYSIKSRFE 262
                                       68999999999999999996 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.3e-07   0.00018      20     129 ..      99     218 ..      84     264 .. 0.73
   2 ?   -1.0   0.0      0.98   7.7e+02     181     219 ..     256     293 ..     238     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.3e-07
                            DUF815  20 eevdevklddLvgidkqkeal......venteqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlieve 88 
                                       e v+ v+ldd+vg ++ k+++      ++n e+f + +p +nvL+ G  GtGK  + kal ne++     ++  ++ 
  gi|488600028|ref|YP_007906499.1|  99 EIVRDVTLDDVVGHEEAKKKVriileyLKNPEKFGKWAP-KNVLFHGYSGTGKTMMAKALANEAKVPFlsIKSTKLI 174
                                       5577899********999987333343588888876655.89*********************99988342224444 PP

                            DUF815  89 kedlkelpklvellrerp...erfilfvDDLsFeeeeeeyksLk 129
                                        e++ +  + +++l +r+     +i+f+D     + +++y+ L+
  gi|488600028|ref|YP_007906499.1| 175 GEHVGDSARRIHELYDRArnlAPCIVFLDEFDAIALDRNYQDLR 218
                                       55555544444444443311145899999888778888887776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.98
                            DUF815 181 sLsdRFGlwlgFykldqeeYleiveklakklglelekee 219
                                       s+  RF   + F  ++ +e lei++k  k++ l+++  +
  gi|488600028|ref|YP_007906499.1| 256 SIKSRFEEEIMFDLPSFNERLEILRKNFKDFPLKVKA-N 293
                                       7778999999999999999999999999888877764.4 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.2e-06    0.0017       2      47 ..     140     190 ..     140     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt...d 47 
                                       vl++G +G+GK+  a+ l+++ +  +  + s +l+  ++g+  +++    d
  gi|488600028|ref|YP_007906499.1| 140 VLFHGYSGTGKTMMAKALANEAKvpFLSIKSTKLIGEHVGDSARRIHelyD 190
                                       79*****************99998788889999999998866555542231 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   8.9e-05     0.069       8      40 ..     140     163 ..     136     175 .. 0.82
   2 ?    2.5   0.1       0.2   1.6e+02      75     112 ..     181     217 ..     169     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.9e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                       ++ +G sGtGKT+ ++ l++++         ++
  gi|488600028|ref|YP_007906499.1| 140 VLFHGYSGTGKTMMAKALANEA---------KV 163
                                       6789****************98.........44 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.2
                            AAA_22  75 seellealeqalraravielliiDEaqhlrs.eealeeL 112
                                       s + ++ l++ +r+ a   ++ +DE++ +   ++++++L
  gi|488600028|ref|YP_007906499.1| 181 SARRIHELYDRARNLAP-CIVFLDEFDAI-AlDRNYQDL 217
                                       45556777777888888.*********98.444444444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   7.8e-06    0.0061      36     199 ..     139     302 ..     105     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.8e-06
                                       -EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHH..HHHHHT..T-HHHHHHHHTT-SEEEEE.-GG CS
                          Bac_DnaA  36 PlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnel..vkalrd..kkaeefkeklrkvDvLliD.Diq 107
                                        ++++g +G Gkt + ka++ne++  + + + + l +e+   ++  ++ l d  ++++    +l + D++ +D + q
  gi|488600028|ref|YP_007906499.1| 139 NVLFHGYSGTGKTMMAKALANEAKVPFLSIKSTKLIGEHVGDSArrIHELYDraRNLAPCIVFLDEFDAIALDrNYQ 215
                                       3899*************************999999999875443114455442234445556677888888874466 PP

                                       GGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT- CS
                          Bac_DnaA 108 flagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaekl 184
                                       +l g  ++ e +  ++++l + + +  +++  + +++e ++  ++srfe  ++ d+  p ++ rl+il+k+ +   l
  gi|488600028|ref|YP_007906499.1| 216 DLRG--DVSEVVNSLLTELDGIQSNEGICTIAATNRIEMIDYSIKSRFEEEIMFDL--PSFNERLEILRKNFKDFPL 288
                                       6665..456777777777766666666777778899**************999887..78899**********9999 PP

                                       ---TTHHHHHHHH-- CS
                          Bac_DnaA 185 evpeevlefiaervt 199
                                       +v+ + le +a++ +
  gi|488600028|ref|YP_007906499.1| 289 KVKAN-LEIVASNTE 302
                                       98877.455665544 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-05     0.019      35      76 ..     116     160 ..      89     170 .. 0.77
   2 ?   -1.7   0.0       3.8     3e+03      42      69 ..     302     329 ..     282     339 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHT-S.S-SS..-EEEEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  35 klvvksvkaylene.kpkk..pLvlsfhGwtGtGknfvaeiiaen 76 
                                       k  v+ +  yl+n+ k  k  p  + fhG++GtGk  +a+ +a++
  gi|488600028|ref|YP_007906499.1| 116 KKKVRIILEYLKNPeKFGKwaPKNVLFHGYSGTGKTMMAKALANE 160
                                       44567888888888444444478899***************9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.8
                                       HHHHT-SS-SS-EEEEEEE-TTSSHHHH CS
                            Torsin  42 kaylenekpkkpLvlsfhGwtGtGknfv 69 
                                       +++  ++ ++k +  ++h     Gk+++
  gi|488600028|ref|YP_007906499.1| 302 EGFSGRDLVEKVIKPALHRAIADGKDYI 329
                                       4555555556666666666666666666 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05     0.013      48      72 ..     138     162 ..     100     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveav 72 
                                       +n+++ G sG+GK+ +a al+ ea 
  gi|488600028|ref|YP_007906499.1| 138 KNVLFHGYSGTGKTMMAKALANEAK 162
                                       79******************99884 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.5e-05      0.05       1      77 [.     139     208 ..     139     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vl  G +GtgK+++a+ la   + +++ +  t+      l+g+     g+ +++  +l++ ar   ++i++lDE++
  gi|488600028|ref|YP_007906499.1| 139 NVLFHGYSGTGKTMMAKALANEAKVPFLSIKSTK------LIGEHV---GDSARRIHELYDRARnlAPCIVFLDEFD 206
                                       68999***************99999999776665......888877...7777888999999999999999999998 PP

                                       G- CS
                             AAA_5  76 ra 77 
                                        +
  gi|488600028|ref|YP_007906499.1| 207 AI 208
                                       65 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     4e-05     0.031      22      54 ..     137     166 ..     108     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-05
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfv 54 
                                       + +vl +G sGtGK+++a+a+ ++ k    pf+
  gi|488600028|ref|YP_007906499.1| 137 PKNVLFHGYSGTGKTMMAKALANEAK---VPFL 166
                                       479*****************977544...4555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.8e-05     0.053      23      43 ..     138     158 ..     105     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                      Mg_chelatase  23 HnlllvGppGsGKtmlakrlp 43 
                                        n+l+ G +G+GKtm+ak+l+
  gi|488600028|ref|YP_007906499.1| 138 KNVLFHGYSGTGKTMMAKALA 158
                                       69****************986 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     8e-05     0.062      34      58 ..     138     162 ..     135     173 .. 0.86
   2 ?   -3.1   0.0       6.2   4.9e+03     102     115 ..     198     211 ..     188     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       k+vl+ G +GtGKt+++k l ++ +
  gi|488600028|ref|YP_007906499.1| 138 KNVLFHGYSGTGKTMMAKALANEAK 162
                                       89****************9988765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.2
                             AAA_7 102 lvvFvDDlnmpake 115
                                       ++vF+D+++  a +
  gi|488600028|ref|YP_007906499.1| 198 CIVFLDEFDAIALD 211
                                       99****99887766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00042      0.33       3      26 ..     140     163 ..     138     174 .. 0.88
   2 ?    0.8   0.0       0.5   3.9e+02      85     163 ..     200     283 ..     169     285 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                                       EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                       v+ +G +G GKT++++ la +++ 
  gi|488600028|ref|YP_007906499.1| 140 VLFHGYSGTGKTMMAKALANEAKV 163
                                       7899***************99875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.5
                                       EEEE-STT-SS-TCH..........HHHHHCT.TTTT--EEEEEEECCCHHH.....HCTTSSCE..EEEE--TCCH CS
                             NACHT  85 lilDglDelvtdlgq.kekqpvrtlLselirk.kllpeasllltvrpralrd.....leeqleeaivlevegfsesr 154
                                         lD +D ++ d +  + +  v ++ ++l+++   ++++  + t+  +++ +     +++ +ee+i++ +++f+e  
  gi|488600028|ref|YP_007906499.1| 200 VFLDEFDAIALDRNYqDLRGDVSEVVNSLLTElDGIQSNEGICTIAATNRIEmidysIKSRFEEEIMFDLPSFNE-- 274
                                       556777776655444444555555555555541123334444444444443344577899999999999999976.. PP

                                       HHHHHHHCT CS
                             NACHT 155 rkqlvrkyf 163
                                       r +++rk f
  gi|488600028|ref|YP_007906499.1| 275 RLEILRKNF 283
                                       456666665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.6e-05     0.075      13      50 ..     131     170 ..     113     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.6e-05
                                       HHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..---- CS
                              TsaE  13 klakalgdvilLeGdLGaGKTtlvrglakalgve..evkS 50 
                                       k++k + + +l++G  G+GKT+++++la++ +v   ++kS
  gi|488600028|ref|YP_007906499.1| 131 KFGKWAPKNVLFHGYSGTGKTMMAKALANEAKVPflSIKS 170
                                       3444345679********************9997777877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.086       1      39 [.     140     189 ..     140     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...........gvnlrdvakenglll 39 
                                       +l  G++G+GKt +ak+L+++ ++           g++++d a+  + l+
  gi|488600028|ref|YP_007906499.1| 140 VLFHGYSGTGKTMMAKALANEAKVpflsikstkliGEHVGDSARRIHELY 189
                                       5678**************99977788877888888777766666544444 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.15       4      37 ..     140     173 ..     138     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDaf 37 
                                       +l +G s +GK+ +a+al + ++ p+l +++ ++
  gi|488600028|ref|YP_007906499.1| 140 VLFHGYSGTGKTMMAKALANEAKVPFLSIKSTKL 173
                                       899************************9987665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00036      0.28       7      58 ..     106     160 ..     101     171 .. 0.81
   2 ?   -1.9   0.0       2.5   1.9e+03     162     181 ..     243     263 ..     182     268 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                              TniB   7 adrwigyprakeilerLeeLleypk...rkrmpnlllvGdsnnGKtmivekFarl 58 
                                        d+ +g+++ak+ ++ + e l++p+   +  ++n+l++G s +GKtm+++  a++
  gi|488600028|ref|YP_007906499.1| 106 LDDVVGHEEAKKKVRIILEYLKNPEkfgKWAPKNVLFHGYSGTGKTMMAKALANE 160
                                       577899999999999988888888744345679***************9987765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                              TniB 162 teealralr.tDpqlasRFep 181
                                       t +a++ ++  D  ++sRFe+
  gi|488600028|ref|YP_007906499.1| 243 TIAATNRIEmIDYSIKSRFEE 263
                                       444444443146667777766 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   0.00025      0.19       1      30 [.     140     169 ..     140     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkk 30 
                                       ++++G sg+GK+++ak La++    + ++k
  gi|488600028|ref|YP_007906499.1| 140 VLFHGYSGTGKTMMAKALANEAKVPFLSIK 169
                                       679****************99876654444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00028      0.22      98     141 ..     136     179 ..     114     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S------------- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTT 141
                                       + k +++ G SG GK+ + +al++e+++   ++++++  G h  
  gi|488600028|ref|YP_007906499.1| 136 APKNVLFHGYSGTGKTMMAKALANEAKVPFLSIKSTKLIGEHVG 179
                                       567889**********************9999999999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2136.15
//
Query:       gi|488600029|ref|YP_007906500.1|  [L=182]
Description: 2-5 RNA ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  110.9   0.2    3.1e-18   65.7   0.0    2.0  2  LigT_PEase       LigT like Phosphoesterase
    1.4e-13   51.1   0.0    1.6e-13   50.8   0.0    1.2  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    1.1e-11   45.0   0.1    1.3e-11   44.8   0.1    1.2  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
     0.0095   15.4   0.0      0.011   15.2   0.0    1.1  1  HVSL             Uncharacterised conserved protein
  ------ inclusion threshold ------
      0.065   13.6   0.1       0.13   12.7   0.1    1.4  1  Tli4_N           Tle cognate immunity protein 4 N-terminal do


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 !   65.7   0.0   8.8e-22   3.1e-18       1      87 []       7      88 ..       7      88 .. 0.96
   2 !   43.7   0.0   6.7e-15   2.4e-11       9      87 .]      95     173 ..      89     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 8.8e-22
                                      EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEE CS
                        LigT_PEase  1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfps 79
                                      ++++e+++ee++rl + +    +  g+k v+++n+HiTL+flgev+e+k++++ e+l+ei   +e+fel ++g+g fp+
  gi|488600029|ref|YP_007906500.1|  7 VDLSENVREEVYRLTRSFT---PFNGVKTVEKENLHITLKFLGEVKESKLNKITEKLGEI--DFEKFELSFRGIGFFPN 80
                                      68899**************...999***********************************..5669************* PP

                                      CCSCCEEE CS
                        LigT_PEase 80 rlrprviy 87
                                        r rvi+
  gi|488600029|ref|YP_007906500.1| 81 ISRMRVIW 88
                                      *******9 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 6.7e-15
                                       HHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCC CS
                        LigT_PEase   9 eelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrl.rpr 84 
                                        +++ la+e+e++la+l++k + +f+ H T+a+++  ++++  ++l+ l++ + + e  ++ v++++l +s+l +++
  gi|488600029|ref|YP_007906500.1|  95 SKINILAEEVEKRLAELKFKRENRFKAHATIARIKRLNPSDKTRILNLLEGYEDR-EFGDMVVEKFVLKKSTLtPKG 170
                                       478889********************************88888888888887644.2337***************** PP

                                       EEE CS
                        LigT_PEase  85 viy 87 
                                       +iy
  gi|488600029|ref|YP_007906500.1| 171 PIY 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 !   50.8   0.0   4.6e-17   1.6e-13      14     123 ..      26     140 ..       7     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 4.6e-17
                   2_5_RNA_ligase2  14 rslydkayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks.vvylsvsdsealqal 87 
                                         ++ k +++  +HitL+++++ +e+   +++e l ++  ++e+fe+++ g+g+F+      v+++ v+d+++++ l
  gi|488600029|ref|YP_007906500.1|  26 PFNGVKTVEKENLHITLKFLGEVKESKlNKITEKLGEI--DFEKFELSFRGIGFFPNiSRMrVIWVGVKDDSKINIL 100
                                       566778899***************99889999999999..8*****************5555*************** PP

                   2_5_RNA_ligase2  88 raallealpeagdkedsgeftPHlTiaqsadstsa.....a 123
                                        +++++ l+e + k++  +f+ H+Tia+ ++ +++      
  gi|488600029|ref|YP_007906500.1| 101 AEEVEKRLAELKFKRE-NRFKAHATIARIKRLNPSdktriL 140
                                       *************997.**********99998888554442 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.1   3.5e-15   1.3e-11      38     192 ..      33     167 ..       4     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 3.5e-15
                                       --TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE.....TTTEEEEEE--SHHHHHH CS
                         AKAP7_NLS  38 ikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfnddpakarVlYakveeesneekL 114
                                       +++e+lH+Tl  l   +++++++ +e L e+        d ++++l+++G+++f  + ++ rV++++v+++   +k+
  gi|488600029|ref|YP_007906500.1|  33 VEKENLHITLKFLGEVKESKLNKITEKLGEI--------DFEKFELSFRGIGFF-PNISRMRVIWVGVKDD---SKI 97 
                                       799*********9988888888888877777........3389***********.79999*********65...59* PP

                                       HHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT-EEEEEE--EEEEEESSS CS
                         AKAP7_NLS 115 qeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkdfefgeekineihLsqles 191
                                       + la+ + k++  a+l+ +++++ +k HaT++ +++ +   + +     + ++l+ ++d efg+  ++++ L + + 
  gi|488600029|ref|YP_007906500.1|  98 NILAEEVEKRL--AELKFKRENR-FKAHATIARIKRLNPSDKTR-----ILNLLEGYEDREFGDMVVEKFVLKKSTL 166
                                       ***********..6777777777.99*******99877666544.....588*****************99987665 PP

                                       - CS
                         AKAP7_NLS 192 d 192
                                       +
  gi|488600029|ref|YP_007906500.1| 167 T 167
                                       5 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.2e-06     0.011      67     185 ..      15     126 ..       4     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
                              HVSL  67 ekl.eeevklhslltsdlgaplplHiSLSrplvlrthqkdsfldslkkelkssakrrFevsfsglkwvsndektRsF 142
                                       e++   + +++++   +  ++++lHi+L     +  + k+s l++++++l +   ++Fe+sf+g+ +++n  + R+ 
  gi|488600029|ref|YP_007906500.1|  15 EEVyRLTRSFTPFNGVKTVEKENLHITL----KFLGEVKESKLNKITEKLGEIDFEKFELSFRGIGFFPNISRMRVI 87 
                                       4443445566666667778888999987....5667899999999*****999999*******************87 PP

                              HVSL 143 lvlrvkspendeLkklleavnkvleefglpplykdeaFHiSia 185
                                       +v  v  +++++++ l e+v+k l+e + +      + H  ia
  gi|488600029|ref|YP_007906500.1|  88 WVG-V--KDDSKINILAEEVEKRLAELKFKREN-RFKAHATIA 126
                                       776.5..45579*********999997766533.344466666 PP

>> Tli4_N  Tle cognate immunity protein 4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.5e-05      0.13      42     104 ..     101     165 ..      84     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                            Tli4_N  42 rqriakreqeLkaekrikekdepllkkavslpdn.kgrifirnesvsk.edaareleayvydngv 104
                                        ++++kr +eLk ++++  k+++++ ++ +l+++ k+ri++  e+ ++ e   +++e +v+++++
  gi|488600029|ref|YP_007906500.1| 101 AEEVEKRLAELKFKRENRFKAHATIARIKRLNPSdKTRILNLLEGYEDrEFGDMVVEKFVLKKST 165
                                       689*************99***********************999999878888999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 997.51
//
Query:       gi|488600030|ref|YP_007906501.1|  [L=448]
Description: tRNA adenylyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  137.1   0.0    4.5e-40  136.4   0.0    1.4  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    4.7e-12   46.0   0.1    1.7e-11   44.2   0.1    2.0  1  NTP_transf_2     Nucleotidyltransferase domain


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 !  136.4   0.0     5e-44   4.5e-40       1     112 [.     155     264 ..     155     265 .. 0.96

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 5e-44
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEET CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDP 77 
                                       ++vr+lK flk+ g+YG+e++v+GfsGYl+Ell+++ygsf+e++++a +w+++++i++  +e    + ++ l+v+DP
  gi|488600030|ref|YP_007906501.1| 155 NDVRILKGFLKANGIYGAEYQVRGFSGYLCELLIIHYGSFKELVKRAINWRRGLKIEVGGNEG--FERNHVLFVVDP 229
                                       79******************************************************9777776..66689******* PP

                                       TEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
                   tRNA_NucTransf2  78 vDpkRNvaaalsleklaefilaareflkkpseeff 112
                                       vD+kRNv+a+lsl+++a+f++ +r+f ++p++eff
  gi|488600030|ref|YP_007906501.1| 230 VDSKRNVSANLSLDNFAKFVEICRDFYSSPKIEFF 264
                                       **********************************9 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   1.9e-15   1.7e-11      12      94 ..      46     141 ..      33     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.9e-15
                                       TTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH............HHHEHHHHHHHHCCCEEECTTEEEEEEC CS
                      NTP_transf_2  12 epvakvvlfGSyarGtalkg.SDiDllvvlpeevsre............kkeegleklaeiikfleellglevdlvt 75 
                                       +p  +    GS+ r+t+lkg  ++Dl++++pe++s+               +  + ++a +++ +  ++g+evd+v+
  gi|488600030|ref|YP_007906501.1|  46 YPELEYRFLGSFPRNTWLKGnLELDLFILFPENFSEKdlerigleigkrLLDSWEARYASHPYIHGTVMGVEVDVVP 122
                                       457778889************************9988***********966677899******************** PP

                                       EEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  76 rekledpllvksileerpl 94 
                                       ++kl++ +++ks+++++p+
  gi|488600030|ref|YP_007906501.1| 123 CYKLKSAEKIKSAVDRTPF 141
                                       ***************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 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:                        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 0.30s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2537.94
//
Query:       gi|488600031|ref|YP_007906502.1|  [L=219]
Description: hypothetical protein Asulf_00482 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0049   16.2   0.2      0.028   13.8   0.2    1.9  2  Phytochelatin_C  Domain of unknown function (DUF1984)


Domain annotation for each model (and alignments):
>> Phytochelatin_C  Domain of unknown function (DUF1984)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.025   4.6e+02     147     187 ..      21      58 ..       7      67 .. 0.73
   2 !   13.8   0.2   1.5e-06     0.028      38      69 ..     158     189 ..     153     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.025
                   Phytochelatin_C 147 lccretcvkclkadddkeitvvsgtvvsdGneqgvdvlvPl 187
                                       lc  e c+++ + d++ +++vv ++ vs G  +  +v+vP 
  gi|488600031|ref|YP_007906502.1|  21 LC--ERCLRTERYDGNVAAMVVDASFVSIGL-NYFNVIVPA 58 
                                       33..456677777999999999999998774.456777775 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-06
                   Phytochelatin_C  38 dvekvlsvvlkslPskleefikWvaEvRrqed 69 
                                        v+kv++ ++ s+P k  efikWv ++ ++ +
  gi|488600031|ref|YP_007906502.1| 158 IVRKVFTEIFGSVPKKDIEFIKWVEDISKKTE 189
                                       589***********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1435.16
//
Query:       gi|488600032|ref|YP_007906503.1|  [L=437]
Description: phenylacetate-CoA ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-29   99.8   1.1    1.7e-28   98.7   1.1    1.6  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    1.6e-20   73.1   0.0    5.7e-19   68.0   0.0    2.0  1  AMP-binding      AMP-binding enzyme
    5.4e-05   22.4   0.0      0.026   13.6   0.0    2.2  2  LuxE             Acyl-protein synthetase, LuxE
      6e-05   22.1   0.0    0.00065   18.7   0.0    2.1  2  GH3              GH3 auxin-responsive promoter
  ------ inclusion threshold ------
        0.1   11.4   0.0       0.15   10.8   0.0    1.1  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
       0.15   11.6   0.0       0.37   10.4   0.0    1.6  1  DmpG_comm        DmpG-like communication domain


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 !   98.7   1.1   5.8e-32   1.7e-28       1      96 []     338     434 ..     338     434 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 5.8e-32
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvel 76 
                                       G+nvfPsqie+vl++i+ev++++q+ +tr+g+lDe++v+vE+ +  f+ el++ +++++k++++l ++l+++++vel
  gi|488600032|ref|YP_007906503.1| 338 GINVFPSQIEDVLMRIPEVGDHFQVLITRNGSLDEITVRVEMVDeVFTGELSDFQRIQQKVQRELYKELNLRTNVEL 414
                                       99****************************************99557789*************************** PP

                                       E-TT-S---------EEE-S CS
                   AMP-binding_C_2  77 vepgtlprsegKakrviDkR 96 
                                       ve+gt++r + K+krviD R
  gi|488600032|ref|YP_007906503.1| 415 VEKGTIERFKLKSKRVIDMR 434
                                       ******************98 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   1.9e-22   5.7e-19     155     423 .]      81     337 ..      40     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.9e-22
                                       S-BTTSEEEEEEE--SSSS-EEEEEEHHHH...HHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHT CS
                       AMP-binding 155 elkpddlayiiYTSGTTGkPKGVmlshrnl...vanvaslkletr.fklkeddvvlsilplahifglilelllalls 227
                                       ++++++++ i  +SGT GkPK V ++ + l   +++va +    +  +++++dv+  ++++ + +g   + ++a   
  gi|488600032|ref|YP_007906503.1|  81 AVDKKEIIRIHTSSGTSGKPKVVGYTRDDLenwINMVARCL---YmVGIRDHDVFQNMVSYTFFTGGLGFHYAAERI 154
                                       5788999999****************977644366666652...33557789******9999999987888888888 PP

                                       T-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHH CS
                       AMP-binding 228 GatvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlss.lrlvllggeplspellrf 302
                                       Ga +v+++++ ++++   ++++ +++ tvi+++P+ + ++ e ++              lr+  +g+ep s ++ ++
  gi|488600032|ref|YP_007906503.1| 155 GA-MVVPSGTGQTEK--QIQYMFDFGTTVIHATPSYAMHIKEvAEGMG----IDPREIgLRIGCFGAEPWSDNTRKR 224
                                       88.677777777553..3689999****************66443333....2234445***999************ PP

                                       HHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SE CS
                       AMP-binding 303 fralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvrgpgvmkg 377
                                       +++ +  + +++YGl+E+ g  + +++ee+      +G  ++  +  ++i+D+et+epv dge+Gel++        
  gi|488600032|ref|YP_007906503.1| 225 LEDAYDIKAYDSYGLSEMNGPGVAFECEEQ------YGLHIWadHYFIEIIDPETLEPVSDGEKGELVLT------- 288
                                       *****99*************9984554444......56555334999********************985....... PP

                                       BTT-HHHHHHHEEETCCEEEEEEEEEEETTS..........EEEEEEECCCEEEET CS
                       AMP-binding 378 YlkkpeataeafdsegrwlrTGDlgrldedG..........yleivgRkkdliklr 423
                                             +t++a+      +rTGD+ ++ ++G            +i+gR++d++++r
  gi|488600032|ref|YP_007906503.1| 289 -----PLTKQALP-LI-RYRTGDITYILDEGkcscgrthprIHRILGRSDDMVVIR 337
                                       .....36777773.23.69*******98899999999999668999*****99985 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0     0.001         3      80     156 ..      77     151 ..      14     166 .. 0.68
   2 !   13.6   0.0   8.8e-06     0.026     268     360 ..     235     332 ..     224     345 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.001
                              LuxE  80 tkllsvsedeikaklqssatsGlkstvlldklsierllravarvmkevlspkdrqielvdldPdrfnatnlgakiva 156
                                         l +v+++ei    +ss+tsG +  v   +  +e  ++ var +  v+   d+++   ++    f +  lg++++a
  gi|488600032|ref|YP_007906503.1|  77 FGLFAVDKKEIIRIHTSSGTSGKPKVVGYTRDDLENWINMVARCLYMVG-IRDHDVF-QNMVSYTFFTGGLGFHYAA 151
                                       358899999**********************************997665.5666653.4555555556666666665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.8e-06
                              LuxE 268 diygfteqvelntpdfkdelkrkrvysdviir...deetlkvvgdGkvGlleyvdalstsyPafvvltddlG.viee 340
                                       d yg++e  +   ++  +e    ++ +d +     d+etl++v+dG  G l     + ++ P     t d+  +++e
  gi|488600032|ref|YP_007906503.1| 235 DSYGLSEMNGPGVAFECEEQYGLHIWADHYFIeiiDPETLEPVSDGEKGELVLTPLTKQALPLIRYRTGDITyILDE 311
                                       55666655555555433444445666655433356****************999999999**99999*99975899* PP

                              LuxE 341 slcegqkaGklv.kvlrrvkk 360
                                        +c ++++  ++ ++l+r + 
  gi|488600032|ref|YP_007906503.1| 312 GKCSCGRTHPRIhRILGRSDD 332
                                       ******998776369999875 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.2e-07   0.00065      74     116 ..      85     129 ..      52     198 .. 0.78
   2 ?    1.3   0.0     0.039   1.2e+02     353     418 ..     276     351 ..     261     425 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-07
                                       SS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHHHHH...H CS
                               GH3  74 epiklfalsSGTtsgksKliPvteeslkelallvlallaall...s 116
                                       ++i+++ +sSGT+ gk+K++ +t++ l+++ ++v++ l+ +    +
  gi|488600032|ref|YP_007906503.1|  85 KEIIRIHTSSGTS-GKPKVVGYTRDDLENWINMVARCLYMVGirdH 129
                                       7899*********.***************99998888877765541 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.039
                                       CS-TTSEEEEEEE....STTS-SSEEECEEEEEEE.....EETTEEEE.EEEECCTEEE-SSSS-CCHHHHHHHHH CS
                               GH3 353 evevGkeYelvvT....tfaGLyRYrigDvvrvtg.....fynkaPrl.eFvgRknvvlsidgeklteeelqkave 418
                                        v  G++ elv+T    ++  L RYr+gD+  + +        + Pr+ +++gR++ ++ i+g  +  +++++++ 
  gi|488600032|ref|YP_007906503.1| 276 PVSDGEKGELVLTpltkQALPLIRYRTGDITYILDegkcsCGRTHPRIhRILGRSDDMVVIRGINVFPSQIEDVLM 351
                                       56666666666664433345699******98875411111334556442466666666666666666666666665 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     5e-05      0.15     187     245 ..     351     410 ..     341     420 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5e-05
                                       HH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--.SHHHHHHHHHHHHHHHHHHHHHHS CS
                   AdoMet_Synthase 187 kklpevGeDiKvmglRekkkielTvavalvdrlvk.dleeYlevkeeikeeveelakklt 245
                                        ++pevG+  +v+ +R+++  e+Tv v +vd++ + +l+++ ++++++++e+ + ++  t
  gi|488600032|ref|YP_007906503.1| 351 MRIPEVGDHFQVLITRNGSLDEITVRVEMVDEVFTgELSDFQRIQQKVQRELYKELNLRT 410
                                       579****************************9765278999999999*999988776554 PP

>> DmpG_comm  DmpG-like communication domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00012      0.37      18      42 ..     186     210 ..     185     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                         DmpG_comm  18 sFllhaeraaerygvdardilvelG 42 
                                       s+  h++++ae  g+d+r+i +++G
  gi|488600032|ref|YP_007906503.1| 186 SYAMHIKEVAEGMGIDPREIGLRIG 210
                                       899*****************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2628.28
//
Query:       gi|488600033|ref|YP_007906504.1|  [L=524]
Description: hypothetical protein Asulf_00484 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-07   29.7   0.3     0.0061   16.8   0.0    3.7  3  CARDB        CARDB
    0.00013   22.1   1.0      0.046   13.9   0.1    3.0  3  FixG_C       IG-like fold at C-terminal of FixG, putative oxi
    0.00036   20.7   0.0        2.7    8.3   0.0    4.5  4  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
      0.025   15.1   0.0       0.97   10.0   0.0    3.0  3  DUF4981      Domain of unknown function(DUF4981)


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 !    5.8   0.0    0.0036        16      34      86 ..      75     130 ..      45     133 .. 0.81
   2 !   16.8   0.0   1.4e-06    0.0061      13      84 ..     180     252 ..     172     256 .. 0.86
   3 ?    2.6   0.0     0.036   1.6e+02       2      83 ..     391     473 ..     390     484 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0036
                                       -EEEEEEEEEETTEEE..EEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEEEEST CS
                             CARDB  34 asgatkvalyldgelv..gtvtvpsLaagesttvsftwtte.ategevtltvvvDp 86 
                                       ++++ +++l  d+ +   + v +p L a+++  vsf++ ++   +ge+tlt+ v  
  gi|488600033|ref|YP_007906504.1|  75 NAYNLTLELESDEIKIltERVRIPVLPANSQQVVSFQISVPnNLSGEHTLTLRVNY 130
                                       66777777777777667788899***************9998899*****999875 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.4e-06
                                       SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEE CS
                             CARDB  13 seafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtteategevtltvvv 84 
                                       s++++ e+ +i ++++N G  ++++++v+l   g +v   g+v+vp L +++ t v+f ++++  ege  +++ +
  gi|488600033|ref|YP_007906504.1| 180 STLYASEQDRIALQLANVGLSDARNVEVTLE--GIEViqpGKVIVPHLGPSSITVVEFDVVAPEREGELNVKARI 252
                                       678999999************9999887765..4444458***********************999999998877 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.036
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S... CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte... 72 
                                       pD++v   ln   ++   en ++++v N G   ++++  +l  +   +    ++++++L+ +e +++sf + ++   
  gi|488600033|ref|YP_007906504.1| 391 PDFIV---LNKPIVYH-GENIVKLEVMNVGGY-AKNVHFKLNPSPGIKlkmPEAYIAELKRDERANISFRVDVDddv 462
                                       56666...33333444.445588888888754.44444444444333344777888888888888888887777665 PP

                                       -S-CEEEEEEE CS
                             CARDB  73 ategevtltvv 83 
                                       ++ +e+ + ++
  gi|488600033|ref|YP_007906504.1| 463 IAGNEYRIDIT 473
                                       44455545444 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0045        20      41     102 ..      71     129 ..      69     144 .. 0.73
   2 ?   -2.6   0.0       1.4   6.3e+03      46      78 ..     202     232 ..     191     254 .. 0.51
   3 !   13.9   0.1     1e-05     0.046      32     115 ..     405     487 ..     382     491 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0045
                                       E-SSS-EEEEEEEES-SS-EE.E.S--EEE.E-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE CS
                            FixG_C  41 Nktekprrytlsveglpglelagraekeit.vapgekrkvpvfvrvpaealkkkstpitfkvt 102
                                       N++ ++ ++tl++e+ +++++ ++ +  i  +++++++ v + ++vp +   ++++++t++v+
  gi|488600033|ref|YP_007906504.1|  71 NMSLNAYNLTLELES-DEIKILTE-RVRIPvLPANSQQVVSFQISVPNNL--SGEHTLTLRVN 129
                                       777788888888885.69999443.3444406777777788999999998..88888888885 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                       -EEEEEEEES-SS-EE.E.S--EEEE-TT-EEE CS
                            FixG_C  46 prrytlsveglpglelagraekeitvapgekrk 78 
                                       +r++++++eg + ++  g +    ++ p + + 
  gi|488600033|ref|YP_007906504.1| 202 ARNVEVTLEGIEVIQP-G-KVIVPHLGPSSITV 232
                                       4447777775443333.1.12233344444444 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 1e-05
                                       EEEEEEEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEEEGGGTE CS
                            FixG_C  32 eNsYtlkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvtdddeke 108
                                       eN   l+++N    +++++++++  pg++l+ +++   +++ +e  ++ ++v v+ + ++  +  i ++ +  +++e
  gi|488600033|ref|YP_007906504.1| 405 ENIVKLEVMNVGGYAKNVHFKLNPSPGIKLKMPEAYIAELKRDERANISFRVDVDDDVIAGNEYRIDITYK-AENTE 480
                                       79999******************999****77888899*******************98865556666664.23344 PP

                                       EEEEEEE CS
                            FixG_C 109 tverksr 115
                                        +e +++
  gi|488600033|ref|YP_007906504.1| 481 GEEISDS 487
                                       4444455 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0006       2.7      42      78 ..      95     130 ..      91     131 .. 0.91
   2 ?   -0.0   0.0      0.24   1.1e+03       9      29 ..     190     210 ..     184     255 .. 0.53
   3 ?    2.6   0.0     0.036   1.6e+02       2      35 ..     292     325 ..     291     368 .. 0.75
   4 ?    3.1   0.0     0.025   1.1e+02      11      74 ..     410     472 ..     405     477 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0006
                       NPCBM_assoc  42 asaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                        +++ l+++ ++ + +++++p++   G++++t+++++
  gi|488600033|ref|YP_007906504.1|  95 VRIPVLPANSQQVVSFQISVPNNLS-GEHTLTLRVNY 130
                                       67899******************99.9******9987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.24
                       NPCBM_assoc   9 ltltvtndgtaaatnvslsls 29 
                                       + l ++n g + a+nv+++l+
  gi|488600033|ref|YP_007906504.1| 190 IALQLANVGLSDARNVEVTLE 210
                                       556666666666666666664 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.036
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWt 35 
                                       e+Ge+  ++l v n+   ++++++l +s P+G  
  gi|488600033|ref|YP_007906504.1| 292 ERGESGVIDLFVMNNYLYPIKGLELVISEPDGID 325
                                       789999*************************955 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.025
                       NPCBM_assoc  11 ltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd.yevta 74 
                                       l+v n g+  a+nv ++l   +G +  ++  a +a+l+ +e++   ++V + ++ +aG  y++ +
  gi|488600033|ref|YP_007906504.1| 410 LEVMNVGGY-AKNVHFKLNPSPGIK-LKMPEAYIAELKRDERANISFRVDVDDDVIAGNeYRIDI 472
                                       555555554.456777777767777.677778899**********************98677655 PP

>> DUF4981  Domain of unknown function(DUF4981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00022      0.97      10      64 ..      72     128 ..      69     134 .. 0.84
   2 ?    1.0   0.0      0.14   6.1e+02      19      65 ..     205     251 ..     194     274 .. 0.71
   3 ?   -1.9   0.0       1.1   4.8e+03      36      59 ..     459     485 ..     440     507 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                                       --GGGEEEEEEEEETTEEEEEEEEEE-.--TT-EEEEE--S.---TSS.EEEEEEEE CS
                           DUF4981  10 tdlsdldlswellkdGkvvasgelelp.vaPgesatvtlpetkeaees.eyfltvsf 64 
                                       ++l+ ++l+ el+ d  ++ ++++ +p +++ ++++v+++ + +++ s e +lt+++
  gi|488600033|ref|YP_007906504.1|  72 MSLNAYNLTLELESDEIKILTERVRIPvLPANSQQVVSFQISVPNNLSgEHTLTLRV 128
                                       6899************999999*****777788888999888777666899999887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                                       EEEEETT.EEEEEEEEEE-.--TT-EEEEE--S.---TSSEEEEEEEEE CS
                           DUF4981  19 wellkdG.kvvasgelelp.vaPgesatvtlpetkeaeeseyfltvsfr 65 
                                       +e++ +G +v++ g++ +p + P + ++v+++  +++ e+e  l+v++r
  gi|488600033|ref|YP_007906504.1| 205 VEVTLEGiEVIQPGKVIVPhLGPSSITVVEFDVVAPEREGE--LNVKAR 251
                                       45666676889999999999999999999998888877665..444333 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
                                       -..--TT-EEEEE--S.---TSS.EEE CS
                           DUF4981  36 p..vaPgesatvtlpetkeaees.eyf 59 
                                       +  v +g + ++++ +++e++e+ e+ 
  gi|488600033|ref|YP_007906504.1| 459 DddVIAGNEYRIDITYKAENTEGeEIS 485
                                       334556666666666666655554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3783.53
//
Query:       gi|488600034|ref|YP_007906505.1|  [L=288]
Description: ABC-type multidrug transport system, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-30  104.6   0.0    1.2e-29  103.6   0.0    1.5  1  ABC_tran      ABC transporter
    4.4e-15   56.3   0.5    4.8e-08   33.2   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.4e-05   23.9   0.0       0.12   11.8   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00097   19.7   0.0     0.0019   18.7   0.0    1.6  1  AAA_23        AAA domain
    0.00099   18.9   0.0          1    9.0   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0011   19.6   0.0     0.0024   18.5   0.0    1.6  1  DUF4162       Domain of unknown function (DUF4162)
      0.006   17.0   0.0      0.013   15.9   0.0    1.8  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.032   14.5   0.0    1.8  1  AAA_22        AAA domain
      0.014   15.1   0.1      0.029   14.1   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.029   14.0   0.0      0.049   13.2   0.0    1.3  1  AAA_27        AAA domain
      0.064   13.2   0.0       0.13   12.2   0.0    1.6  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
       0.08   12.7   0.1       0.23   11.1   0.1    1.8  2  AAA_30        AAA domain
      0.081   13.3   0.0       0.11   12.9   0.0    1.6  1  AAA_16        AAA ATPase domain
        0.1   12.5   0.0       0.16   11.9   0.0    1.3  1  Rad17         Rad17 P-loop domain
       0.11   11.7   0.2        4.5    6.5   0.0    2.8  3  Zeta_toxin    Zeta toxin
       0.16   12.0   0.0       0.33   11.0   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.24   11.7   0.4       0.44   10.9   0.3    1.7  1  AAA_19        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.0   1.1e-32   1.2e-29       2     137 .]      20     149 ..      19     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.1e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       k+ slk+++ge+++++G+nGaGK+t ++++ g+++  eG+i            ++   +ig++pq++ l  +ltv+e
  gi|488600034|ref|YP_007906505.1|  20 KDFSLKVRRGEILGLLGPNGAGKTTTIRAIFGMVS-YEGKI------------RINAGSIGWMPQNSPLYLNLTVEE 83 
                                       899*******************************8.7****............55589******************* PP

                                       H...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n           +++++ie++l+ ++l +++++ v    ++LSgG+kqr +la+a++ +p+ll+lDEpta
  gi|488600034|ref|YP_007906505.1|  84 NmrfftslhgirNAEQRIEELLRLVNLYDFRKRLV----RNLSGGMKQRAMLACAMIHDPDLLILDEPTA 149
                                       ************9**********************....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   1.6e-07   0.00017       3      52 ..      33      76 ..      31      84 .. 0.88
   2 !   33.2   0.0   4.6e-11   4.8e-08     228     297 ..     112     178 ..      77     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldly 52
                                      +l GpNg+GK++ ++a+      +++v  ++ ++ + g+i+++p  ++ly
  gi|488600034|ref|YP_007906505.1| 33 GLLGPNGAGKTTTIRAI------FGMVSYEGKIRINAGSIGWMPQNSPLY 76
                                      799**************......888999999999999999999887776 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 4.6e-11
                            AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       d +++ +r+lS G+k+     +a++  +++ +ll++DEp +g +P l ++++e ++el+++g  +++tTH
  gi|488600034|ref|YP_007906505.1| 112 DFRKRLVRNLSGGMKQR--AMLACAMIHDP-DLLILDEPTAGVDPPLRKTFWEHFEELNAEGKTILVTTH 178
                                       3445556899******9..44445555555.*************************************** 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 !   10.2   0.1   0.00036      0.38      28      49 ..      33      53 ..      15      66 .. 0.79
   2 !   11.8   0.0   0.00012      0.12     113     212 ..      91     193 ..      67     199 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00036
                                      EEEESTTSSHHHHHHHHHHHCT CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnlldAilFvLG 49
                                       ++GpNG+GK+  + Ai F + 
  gi|488600034|ref|YP_007906505.1| 33 GLLGPNGAGKTTTIRAI-FGMV 53
                                      689**************.6554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                                       ETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 113 ingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                       + g +  ++ ++ell+ ++++        +LSgG k+ ++la      +++   l +lDe  a  D   +k + e +
  gi|488600034|ref|YP_007906505.1|  91 LHGIRNAEQRIEELLRLVNLYDFrkrlvrNLSGGMKQRAMLA----CAMIHDPDLLILDEPTAGVDPPLRKTFWEHF 163
                                       444455555555555555555434445559****77655543....3355667799********************* PP

                                       HHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 184 kekskn.aQfivislreemlekadklvgvt 212
                                       +e + +   ++v+++  +  e++d++v ++
  gi|488600034|ref|YP_007906505.1| 164 EELNAEgKTILVTTHYMDEAENCDRIVLMR 193
                                       *99988466778888888788777776554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.8e-06    0.0019      20      40 ..      30      50 ..       4     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.8e-06
                            AAA_23 20 gltlItGpNGaGKTTildAik 40
                                       +  + GpNGaGKTT ++Ai 
  gi|488600034|ref|YP_007906505.1| 30 EILGLLGPNGAGKTTTIRAIF 50
                                      466789**************7 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00099         1      15      46 ..      20      52 ..      10     116 .. 0.76
   2 !    8.2   0.0    0.0016       1.7     322     364 ..     137     178 ..     118     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00099
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlF 46
                                      kd+++++    +  l G+N++GK++ ++a+  +
  gi|488600034|ref|YP_007906505.1| 20 KDFSLKVRRGeILGLLGPNGAGKTTTIRAIFGM 52
                                      6666666655577799*************9444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0016
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        ++++l+++EP a   p + k +++ + el  ++k  +++tTH
  gi|488600034|ref|YP_007906505.1| 137 HDPDLLILDEPTAGVDPPLRKTFWEHFEELNAEGK-TILVTTH 178
                                       5789******************************9.9****** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.3e-06    0.0024       1      81 []     201     286 ..     201     286 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-06
                                       E-HHHHHTTS.-SSEEEEE.-------..--...-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE- CS
                           DUF4162   1 GtleeiKrsy.gknrieve.adaeelleepg...veeveeeggelelkled.eeaanellkal.tsgveirsFeeee 70 
                                       G++e++Kr   g+++++++ +d   ++++ +    e+v  + + + +k    +   +++ + l + gve++++e ++
  gi|488600034|ref|YP_007906505.1| 201 GSPEDVKRWAlGGEIVRIRvDDRQRAFRLLSsadYEVVV-D-DWVAVKTAMaSPEVPRIVDLLkAGGVEVKEVETVK 275
                                       999****97779*******75544445443312133333.3.3466666644789********77************ PP

                                       --HHHHHHHHH CS
                           DUF4162  71 PsLndIFiekv 81 
                                       ++L++ F+++v
  gi|488600034|ref|YP_007906505.1| 276 ATLEEAFLRLV 286
                                       ********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 !   15.9   0.0   1.2e-05     0.013       3      35 ..      34      67 ..      32     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                                      EESSTTSSHHHHHHHHHHHHTHEE.EEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgvef.leisgsell 35
                                      l Gp G GKT++++a+   ++ e  ++i++ ++ 
  gi|488600034|ref|YP_007906505.1| 34 LLGPNGAGKTTTIRAIFGMVSYEGkIRINAGSIG 67
                                      89*****************986644777777765 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   3.1e-05     0.032       6     102 ..      30     149 ..      26     184 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsst............sskdllrel 60 
                                        il + G+ G+GKTt++r ++     e k++           +  + ++ +l++++            + ++  +el
  gi|488600034|ref|YP_007906505.1|  30 EILGLLGPNGAGKTTTIRAIFGMVSYEGKIRInagsigwmpqN--SPLYLNLTVEEnmrfftslhgirNAEQRIEEL 104
                                       677789****************986655555599999999641..33344444444112221111112444445555 PP

                            AAA_22  61 lralglelkaerlsseell.ealeqalrarav...ielliiDEaqh 102
                                       lr ++l   +     + l   + ++a+ a+a+   + lli+DE   
  gi|488600034|ref|YP_007906505.1| 105 LRLVNLYDFR-KRLVRNLSgGMKQRAMLACAMihdPDLLILDEPTA 149
                                       5555544444.44444444477788888888899999999999555 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   2.8e-05     0.029      17      56 ..      24      63 ..      13      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpakkvrfNk 56
                                      +++++ ++  l Gp+G+GK+T + Ai  +   + k+r N+
  gi|488600034|ref|YP_007906505.1| 24 LKVRRGEILGLLGPNGAGKTTTIRAIFGMVSYEGKIRINA 63
                                      45554448889************99988777777788876 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.6e-05     0.049      10      47 ..      12      50 ..       4      55 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                            AAA_27 10 ryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAis 47
                                      r+G f   + ++++  + ++  ++GpN AGK+t++rAi 
  gi|488600034|ref|YP_007906505.1| 12 RFGDFLAvKDFSLKVRRGEILGLLGPNGAGKTTTIRAIF 50
                                      788874313455555577777789*************95 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 ?   12.2   0.0   0.00012      0.13       2      13 ..     197     208 ..     196     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                      BCA_ABC_TP_C   2 vIAeGtPaEvrn 13 
                                       +IAeG+P++v++
  gi|488600034|ref|YP_007906505.1| 197 KIAEGSPEDVKR 208
                                       9*********85 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00022      0.23      20      46 ..      31      57 ..      22      69 .. 0.81
   2 ?   -2.8   0.0         4   4.2e+03      81      96 ..     126     146 ..      91     152 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                            AAA_30 20 vavltGpAGtGKttalkalreaweaag 46
                                      +  l Gp G+GKtt+++a+  ++  +g
  gi|488600034|ref|YP_007906505.1| 31 ILGLLGPNGAGKTTTIRAIFGMVSYEG 57
                                      66789*************988877765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                            AAA_30  81 k.....grarlepgtllivDE 96 
                                       k     + a +++ +lli DE
  gi|488600034|ref|YP_007906505.1| 126 KqramlACAMIHDPDLLILDE 146
                                       134444334455667777777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011      0.11      20      51 ..      27      56 ..      18     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd 51
                                      r+g  e++ l G+ G GK++ +r+++  ++ +
  gi|488600034|ref|YP_007906505.1| 27 RRG--EILGLLGPNGAGKTTTIRAIFGMVSYE 56
                                      444..8999***************99644444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.16      38      78 ..      22      62 ..      16      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                             Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewln 78
                                       +L+ r+ +iL + GP G gk+t+++ +    +++ +  +n
  gi|488600034|ref|YP_007906505.1| 22 FSLKVRRGEILGLLGPNGAGKTTTIRAIFGMVSYEGKIRIN 62
                                      567788888****************9887766666655555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0042       4.5      22      51 ..      35      63 ..      20      66 .. 0.82
   2 ?    0.9   0.0      0.23   2.4e+02     147     192 ..     182     228 ..     175     234 .. 0.79
   3 ?    0.2   0.0      0.37   3.9e+02     100     125 ..     245     269 ..     224     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0042
                        Zeta_toxin 22 gGqpGAGKselaellkdelerqgnvvrldp 51
                                       G  GAGK+++++++   + ++++ +r+++
  gi|488600034|ref|YP_007906505.1| 35 LGPNGAGKTTTIRAIFGMV-SYEGKIRINA 63
                                      5889**********98887.5888888875 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
                        Zeta_toxin 147 evae.gRlvpkeehdeafeglresvealeeekqldrvkikdrdgktv 192
                                       e+++  R+v  ++  ++ eg +e v++ +    ++r+++ dr++  +
  gi|488600034|ref|YP_007906505.1| 182 EAENcDRIVLMRNGTKIAEGSPEDVKRWALGGEIVRIRVDDRQRAFR 228
                                       43443599999999999999999999999999999999999988555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.37
                        Zeta_toxin 100 vegtlrspdvvkklaealkkaGYeve 125
                                       v ++++sp+v++ +++ lk+ G ev+
  gi|488600034|ref|YP_007906505.1| 245 VKTAMASPEVPR-IVDLLKAGGVEVK 269
                                       4599*******9.9999999998874 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   0.00031      0.33      18      46 ..      21      56 ..       5      63 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                                      H.......TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 18 l.......gdvilLeGdLGaGKTtlvrglakalgve 46
                                              g+++ L G+ GaGKTt +r++   + +e
  gi|488600034|ref|YP_007906505.1| 21 DfslkvrrGEILGLLGPNGAGKTTTIRAIFGMVSYE 56
                                      2333334477899***************98777665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00041      0.44      10      40 ..      29      59 ..      23     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggv 40
                                       ++l ++++ G GKT+++++i  ++  +g++
  gi|488600034|ref|YP_007906505.1| 29 GEILGLLGPNGAGKTTTIRAIFGMVSYEGKI 59
                                      5678899*************99888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1589.21
//
Query:       gi|488600035|ref|YP_007906506.1|  [L=106]
Description: hypothetical protein Asulf_00490 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-09   36.6   5.2    3.6e-09   36.1   5.2    1.2  1  SHOCT          Short C-terminal domain
  ------ inclusion threshold ------
      0.011   14.8   4.6      0.013   14.6   4.6    1.1  1  Acyl_transf_3  Acyltransferase family
      0.015   15.3   0.0       0.02   15.0   0.0    1.1  1  DUF1707        Domain of unknown function (DUF1707)
      0.082   12.8   0.0       0.12   12.2   0.0    1.2  1  VbhA           Antitoxin VbhA
      0.084   12.8   0.1      0.084   12.8   0.1    1.9  2  DUF4083        Domain of unknown function (DUF4083)
      0.087   12.8   0.1       0.11   12.5   0.1    1.3  1  GvpG           Gas vesicle protein G
        0.1   12.5   0.4       0.11   12.4   0.4    1.1  1  Wzy_C_2        Virulence factor membrane-bound polymerase, C-
       0.12   12.3   7.6       0.19   11.8   7.6    1.3  1  DUF997         Protein of unknown function (DUF997)
        0.4   10.1   2.0       0.47    9.8   2.0    1.1  1  DUF2417        Region of unknown function (DUF2417)
        0.6   10.6   4.4        1.1    9.6   4.4    1.5  1  DUF805         Protein of unknown function (DUF805)
        3.9    7.9   6.0         98    3.4   6.0    2.1  1  FtsH_ext       FtsH Extracellular


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 !   36.1   5.2   2.2e-12   3.6e-09       5      27 ..      82     104 ..      82     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.2e-12
                             SHOCT   5 kLkeLyarGeIteEEFeakKakL 27 
                                       +Lke+yarGeI+eEEF ++K++L
  gi|488600035|ref|YP_007906506.1|  82 ILKERYARGEISEEEFKRMKEEL 104
                                       7*********************9 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   4.6   8.2e-06     0.013     180     242 ..       6      67 ..       2      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.2e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 180 elfgpatsvgllplpsvlallfflfGalladaddrdrnlsrglkislllsllllalillalfg 242
                                       + fg+++++++ +   ++ ++f+++G+l+++   +++ +   + i+++l +++l++ l+++  
  gi|488600035|ref|YP_007906506.1|   6 HQFGYPFGFFYGFNIFWW-IIFLAIGYLVYQDANKRGMNGPLWFILVILPMVGLIFLLIYIVI 67 
                                       445555555555544444.***********999999999999999999999999999988765 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.2e-05      0.02       5      31 ..      73      99 ..      71     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                           DUF1707  5 dadReravelLrealaeGrLtldEfde 31
                                       ++R++ + +L+e +a+G ++ +Ef +
  gi|488600035|ref|YP_007906506.1| 73 KSERDEPMYILKERYARGEISEEEFKR 99
                                      689**********************86 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.4e-05      0.12      28      42 ..      85      99 ..      83     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                              VbhA 28 eayvrGeIdadElvr 42
                                      e+y+rGeI+ +E +r
  gi|488600035|ref|YP_007906506.1| 85 ERYARGEISEEEFKR 99
                                      8***********987 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.7      0.81   1.3e+03       1      12 [.      19      30 ..      17      35 .. 0.62
   2 ?   12.8   0.1   5.1e-05     0.084       6      34 ..      47      75 ..      44      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.81
                           DUF4083  1 nlgdliyliivi 12
                                      n++ +i+ +++ 
  gi|488600035|ref|YP_007906506.1| 19 NIFWWIIFLAIG 30
                                      566666666664 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.1e-05
                           DUF4083  6 iyliivivLilllvfsftlfiRrvvsrsa 34
                                       + ++++ +++l++  ++++iR ++ +s 
  gi|488600035|ref|YP_007906506.1| 47 WFILVILPMVGLIFLLIYIVIRETSGKSE 75
                                      57888999999999999999999999975 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     7e-05      0.11      40      61 ..      83     104 ..      50     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                              GvpG  40 LqqeLdaGeIdeeeFdrrEeel 61 
                                       L+ +  +GeI+eeeF r  eel
  gi|488600035|ref|YP_007906506.1|  83 LKERYARGEISEEEFKRMKEEL 104
                                       788899***********99987 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   6.7e-05      0.11      21      70 ..      15      63 ..       5      89 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-05
                           Wzy_C_2 21 wYsp..fllaaflvlglldsksrsrrlrlrpklvlrvvalvlallglallls 70
                                       Y++  f +++fl++g+l   + +++ +  + + l++  ++l+++gl +ll 
  gi|488600035|ref|YP_007906506.1| 15 FYGFniFWWIIFLAIGYLVY-QDANKRG--MNGPLWFILVILPMVGLIFLLI 63
                                      45534499*******66666.2222222..4555666666666666555543 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   7.6   0.00012      0.19      14      64 ..      17      68 ..       8      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                            DUF997 14 llyflwwllf...aYglgskeveeyyilglPlWfflscillpilfivlvillvk 64
                                       ++++ww++f   +Y++ ++   +   ++ PlWf+l ++ ++ l+++l++++++
  gi|488600035|ref|YP_007906506.1| 17 GFNIFWWIIFlaiGYLVYQDA--NKRGMNGPLWFILVILPMVGLIFLLIYIVIR 68
                                      567888887644479999444..6678888********9999999999999987 PP

>> DUF2417  Region of unknown function (DUF2417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.0   0.00029      0.47      49     100 ..      14      66 ..       5      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00029
                           DUF2417  49 illlinliwlvllLisdFvslpglnnrg.sgFndlalillslianllnllffg 100
                                       ++  +n+ w++++L   +      n+rg +g   ++l++l ++ +++ l+ + 
  gi|488600035|ref|YP_007906506.1|  14 FFYGFNIFWWIIFLAIGYLVYQDANKRGmNGPLWFILVILPMVGLIFLLIYIV 66 
                                       57779**************888899987589****************999865 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.4    0.0007       1.1      46      98 ..      17      73 ..       4      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0007
                            DUF805 46 vlallllvpslavtvRRlHDtgrsgw....llllllvplialllllvllllpgtpge 98
                                       + ++ +++ la+      D ++ g+    +++l+++p+++l++ll+ ++++ t+g+
  gi|488600035|ref|YP_007906506.1| 17 GFNIFWWIIFLAIGYLVYQDANKRGMngplWFILVILPMVGLIFLLIYIVIRETSGK 73
                                      4556666666777777789999999999999999999***99999999988877765 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   6.0      0.06        98       2      20 ..      20      38 ..      19     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.06
                          FtsH_ext  2 llwlllallllllllslfg 20
                                      ++w++++l++++l+++ ++
  gi|488600035|ref|YP_007906506.1| 20 IFWWIIFLAIGYLVYQDAN 38
                                      89**********9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 679.86
//
Query:       gi|488600036|ref|YP_007906507.1|  [L=91]
Description: hypothetical protein Asulf_00491 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 664.90
//
Query:       gi|488600037|ref|YP_007906508.1|  [L=327]
Description: small GTP-binding protein domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-34  117.2   0.0    1.4e-33  116.1   0.0    1.5  1  NOG1_N         NOG1 N-terminal helical domain
    1.6e-21   75.8   0.1    3.6e-21   74.7   0.1    1.6  1  NOG1           Nucleolar GTP-binding protein 1 (NOG1)
    4.2e-20   71.9   0.0    7.5e-20   71.1   0.0    1.4  1  MMR_HSR1       50S ribosome-binding GTPase
      9e-11   41.5   0.0    1.8e-10   40.5   0.0    1.5  1  FeoB_N         Ferrous iron transport protein B
    0.00019   20.8   0.0    0.00029   20.2   0.0    1.3  1  AIG1           AIG1 family
    0.00058   19.8   0.8     0.0047   16.9   0.1    2.5  2  RsgA_GTPase    RsgA GTPase
     0.0027   17.2   0.0     0.0059   16.1   0.0    1.6  1  SRPRB          Signal recognition particle receptor beta subu
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.052   13.2   0.0    2.2  2  Ras            Ras family
      0.032   14.3   0.5        2.4    8.2   0.0    2.3  2  Dynamin_N      Dynamin family
      0.037   12.6   0.0      0.075   11.6   0.0    1.4  2  EspG           EspG protein
       0.12   12.1   0.0        3.7    7.2   0.0    2.4  2  Guanylate_kin  Guanylate kinase
       0.12   12.8   0.0       0.35   11.2   0.0    1.8  2  AAA_16         AAA ATPase domain
       0.14   12.4   0.0       0.61   10.3   0.0    2.1  1  Roc            Ras of Complex, Roc, domain of DAPkinase
       0.16   11.7   0.0         13    5.5   0.0    2.3  2  ATP_bind_1     Conserved hypothetical ATP binding protein


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 !  116.1   0.0   1.1e-36   1.4e-33       2     158 ..      23     167 ..      22     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 1.1e-36
                            NOG1_N   2 ekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrell 78 
                                       +k+ptv+t+eelidka+rra++   + kk+ ++i+        k+ t+sn+++d +  i+ + P+ ++l+ Fyrel+
  gi|488600037|ref|YP_007906508.1|  23 RKLPTVLTAEELIDKAFRRASKVVGRNKKE-RAIN--------KLSTLSNVFKDYFDRIISAHPSYNNLPDFYRELV 90 
                                       69*********************9999775.5665........669******************************* PP

                            NOG1_N  79 dvlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrk 155
                                       d+lv++ +l+ksL++++wa ++i+k+ ++ ++++k +++++    + ++ +gr+as++++++++l+fL+ +++k+r+
  gi|488600037|ref|YP_007906508.1|  91 DILVGIGNLRKSLGALSWADTTIQKVINKGIREIKGGKNPD---IVLKSTYGRIASIVEQIGDSLEFLNSAKQKMRE 164
                                       ***************************************88...999****************************** PP

                            NOG1_N 156 Lpa 158
                                       +p+
  gi|488600037|ref|YP_007906508.1| 165 IPT 167
                                       *97 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 !   74.7   0.1   2.8e-24   3.6e-21       1      58 []     238     294 ..     238     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 2.8e-24
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       +IE++Ai++Lk+la++++F++Dp+e+cg+++e+Q sLleeik +f+ +p+i v++K+D
  gi|488600037|ref|YP_007906508.1| 238 KIERKAILSLKYLANCIVFVIDPTETCGFEVEKQQSLLEEIKREFR-VPIIAVYSKAD 294
                                       5*********************************************.*********99 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   5.9e-23   7.5e-20       2     114 .]     174     292 ..     173     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 5.9e-23
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee. 75 
                                       v+++G+pNvGKS+L++a++  + +v+++p+tT++i  g+ k++g  ++++DtpGl++   ++++k ++ka+l+l+  
  gi|488600037|ref|YP_007906508.1| 174 VVVAGYPNVGKSSLVSAISTVQPEVASYPFTTKKIFVGKGKIDGVTFQIIDTPGLLDrpIQKRNKIERKAILSLKYl 250
                                       89****************************************************98644445555788889988888 PP

                                       TSEEEEEEETTTT....CSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  76 adlillvvdasee....klkpldeeleelleeakkplilvlnk 114
                                       a+ i++v+d + e    +++++++ lee+++e + p+i v++k
  gi|488600037|ref|YP_007906508.1| 251 ANCIVFVIDPT-EtcgfEVEKQQSLLEEIKREFRVPIIAVYSK 292
                                       9********66.3355567778788888888888888888766 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   1.4e-13   1.8e-10       2      90 ..     173     262 ..     172     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.4e-13
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       tv+++G pnvGk++l+ a++ ++ +v+ +p +t +   gk k++g +++i+D PG  +  ++ + +k+ r+ +l+ +
  gi|488600037|ref|YP_007906508.1| 173 TVVVAGYPNVGKSSLVSAISTVQPEVASYPFTTKKIFVGKGKIDGVTFQIIDTPGLLD-RPIQKRNKIERKAILSLK 248
                                       689****************************************************987.789999999999999666 PP

                                       ..SSEEEEEEEGGG CS
                            FeoB_N  79 ..pdvvvnvvdatn 90 
                                         ++++v v+d t+
  gi|488600037|ref|YP_007906508.1| 249 ylANCIVFVIDPTE 262
                                       33699999999774 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.3e-07   0.00029       2     115 ..     173     286 ..     172     324 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.3e-07
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTC.CHHCHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsv.sadkiskeivrcl 77 
                                       t+v+ G   +GkS+ + +i   +  e  +s    tkk    +++ dg + ++iDTPgl+d    + +ki+++ + +l
  gi|488600037|ref|YP_007906508.1| 173 TVVVAGYPNVGKSSLVSAISTVQP-EV-ASYPFTTKKIFVGKGKIDGVTFQIIDTPGLLDRPIqKRNKIERKAILSL 247
                                       789999999999999988832222.22.234567888889999*****************98625777888877788 PP

                                       HHCTT-ESEEEEEEETTB-S.HHHHHHHHHHHHHHCGGG CS
                              AIG1  78 llseegihalllvlslgrft.eedekalktlkelFGeki 115
                                       ++ ++ i +++  +++  f+ e+ +++l+++k+ F   i
  gi|488600037|ref|YP_007906508.1| 248 KYLANCIVFVIDPTETCGFEvEKQQSLLEEIKREFRVPI 286
                                       888886666666677765551445667788888876554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   3.6e-06    0.0047      65     121 ..     138     193 ..     128     231 .. 0.82
   2 ?   -0.2   0.0      0.65   8.3e+02       4      66 ..     241     301 ..     233     322 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  65 leelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallp 121
                                       + ++++ +e++g ++ ++++  k++++e+ +l ++ t+v++G   vGKS+L+ a+  
  gi|488600037|ref|YP_007906508.1| 138 YGRIASIVEQIGDSLEFLNSA-KQKMREIPTLSDEPTVVVAGYPNVGKSSLVSAIST 193
                                       6678899999*9999999877.899******9999*****************99876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.65
                                       -S-EETTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHT.T-EEEEEEE-GGG--HHHHHH CS
                       RsgA_GTPase   4 RknelvrpkvaNvdqllivvslkepelslnlldrfLvlaeek.giepvivlnKiDlleeeeele 66 
                                       Rk  l+ +  aN+  ++++  +++  ++++  + +L +++++ +++++ v +K+Dl + ++  +
  gi|488600037|ref|YP_007906508.1| 241 RKAILSLKYLANC-IVFVIDPTETCGFEVEKQQSLLEEIKREfRVPIIAVYSKADLHDFRD--K 301
                                       4444444446665.34445555556666666666666665542566777889999988766..3 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 !   16.1   0.0   4.6e-06    0.0059       2      86 ..     170     261 ..     169     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                       ---EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG.......GGTT-SEEEETT-....GCCSHHHHHHH CS
                             SRPRB   2 skpavllvGlsdsGKTslftrLttdsvkktvtSqessaalkv....ksekgskltliDfPGh....eklrqkllekl 70 
                                        +p+v+++G  + GK sl   ++t +  + v+S  + +++k+     + +g ++++iD PG      + r+k+  k 
  gi|488600037|ref|YP_007906508.1| 170 DEPTVVVAGYPNVGKSSLVSAISTVQ--PEVASY-PFTTKKIfvgkGKIDGVTFQIIDTPGLldrpIQKRNKIERKA 243
                                       579*****************998764..334443.2222232233246799**********6222234577777766 PP

                                       HHHGG..EEEEEEEEETT CS
                             SRPRB  71 kakss..lkglvfvvDSt 86 
                                       + + +  +  +vfv+D t
  gi|488600037|ref|YP_007906508.1| 244 ILSLKylANCIVFVIDPT 261
                                       65555457889****977 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.6   4.6e+03      81      99 ..      73      91 ..      71      95 .. 0.83
   2 ?   13.2   0.0     4e-05     0.052       2     120 ..     174     299 ..     173     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                                      TTBHHHHHTHHHHHHHHHH CS
                               Ras 81 itsresfenvkkwveeikr 99
                                      i+ + s++n+ ++++e+ +
  gi|488600037|ref|YP_007906508.1| 73 ISAHPSYNNLPDFYRELVD 91
                                      5678899**9999999876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4e-05
                                       EEEEESTTSSHHHHHHHHHHSSCSSSCTT.TSSEEEEEEEEEETTEEEEEEEEEETT......SGGGHHHHHHHHTT CS
                               Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyes.TigvdfytkeievdgkevkleiwDTAG......qeefkslrelyyrd 71 
                                       +v+ G  +vGK+sl+    + + +  + + T     ++ + ++d   v+++i DT G      q + k  r++ ++ 
  gi|488600037|ref|YP_007906508.1| 174 VVVAGYPNVGKSSLVSAISTVQPEVASYPfTT-KKIFVGKGKID--GVTFQIIDTPGlldrpiQKRNKIERKAILSL 247
                                       7999***********98876655443333033.44444444444..589********77776655554444444332 PP

                                       ...ESEEEEEEETTBHHHHH..THHHHHHHHHHHSTTTSEEEEEEETTTGGGG- CS
                               Ras  72 ...aegillvyditsresfe..nvkkwveeikrvaeenvpivLvGnKvDleekr 120
                                          a++i+ v d t++  fe  + ++++eeikr  +  vpi+ v  K+Dl++ r
  gi|488600037|ref|YP_007906508.1| 248 kylANCIVFVIDPTETCGFEveKQQSLLEEIKREFR--VPIIAVYSKADLHDFR 299
                                       222678888888888888862245599999999999..9***********9843 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.023        30       1      24 [.     174     197 ..     174     216 .. 0.75
   2 ?    8.2   0.0    0.0019       2.4     100     157 ..     217     281 ..     201     293 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.023
                                       EEEEEBTTTTHHHHHHHHHTS--S CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedil 24 
                                       ++v G  + GKSS++ a+   +  
  gi|488600037|ref|YP_007906508.1| 174 VVVAGYPNVGKSSLVSAISTVQPE 197
                                       7899999**********9887743 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                                       S-SEEEEE---B-SSSGTTS.....HHHHHHH.STTEEEEEEEETTS.-CCC-CHHHHHHHHSTT CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdq.....elvkeyi.kkadiilavtsanh.dlsnsealflarevdpk 157
                                         +  ++D+PGl +++ ++      + + ++    ++i++++ + ++  +   +++ l +e++ +
  gi|488600037|ref|YP_007906508.1| 217 GVTFQIIDTPGLLDRPIQKRnkierKAILSLKyLANCIVFVIDPTETcGFEVEKQQSLLEEIKRE 281
                                       55678*******99887777667774444444234555555555554233333555555555555 PP

>> EspG  EspG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.9e-05     0.075     147     239 ..      23     122 ..      12     137 .. 0.79
   2 ?   -3.3   0.0       1.9   2.5e+03     117     150 ..     266     299 ..     252     304 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                                       --SSSHHHHHHHHHHHTTS-EEE--B-TTT-TT-SSSTTTTHHHHHHHHTTSSEEEETTE.EE-HHH......HHHH CS
                              EspG 147 eelkdaksmrellefasklstsiiPnddktdplsgdtpfnsvfaDtyRglgnsklslngv.eipaea......qalL 216
                                        +l +  +++el++ a + ++ ++  ++k   + + + ++ vf+D +  + +++ s n++ +  +e+      +  L
  gi|488600037|ref|YP_007906508.1|  23 RKLPTVLTAEELIDKAFRRASKVVGRNKKERAINKLSTLSNVFKDYFDRIISAHPSYNNLpDFYRELvdilvgIGNL 99 
                                       567788999**************************************999777777777644555551111114467 PP

                                       HHHCT-SSSTSS--HHHHHH-S- CS
                              EspG 217 inelGlkdtisspkenvidnGis 239
                                       ++ lG     +   ++vi++Gi 
  gi|488600037|ref|YP_007906508.1| 100 RKSLGALSWADTTIQKVINKGIR 122
                                       78888888888888888888885 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                                       E---TTT-TGGGSS-EE--SC-EEEE--TT--SS CS
                              EspG 117 lesneqnrLLksLPiqlhlpyikvhtalveeelk 150
                                        e ++q+ LL+ +  ++ +p i v+      +++
  gi|488600037|ref|YP_007906508.1| 266 FEVEKQQSLLEEIKREFRVPIIAVYSKADLHDFR 299
                                       5778999999999999999999888766666655 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.081     1e+02     127     165 ..      38      75 ..      31      94 .. 0.78
   2 ?    7.2   0.0    0.0029       3.7       4      73 ..     173     243 ..     170     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.081
                                       HHHHHHTTSSSSHHHHHHHHHHHHHHHHGGGCSSEEEEE CS
                     Guanylate_kin 127 elqrrlksrgkeqeeklakrlaaaekelqeyefdvvivn 165
                                       + +r  k  g++++e   ++l+++ + ++ y fd +i  
  gi|488600037|ref|YP_007906508.1|  38 AFRRASKVVGRNKKERAINKLSTLSNVFKDY-FDRIISA 75 
                                       5567778899999999***************.****974 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0029
                                       EEEEESTTTSSHHHHHHHHHHHSTTTEEE--EEESS---TTS-TTTSEEE-.-HHHHHHHHHTTTEEEEEE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfgvsvshtTrdprkgevdGkdYyFv.skeemekdiskneflEaae 73 
                                       +vv+ g   +Gkssl +a+ + +pe  +++ +       kg +dG  +  + +   + + i+k++ +E+  
  gi|488600037|ref|YP_007906508.1| 173 TVVVAGYPNVGKSSLVSAISTVQPEVASYPFTTKKIFVGKGKIDGVTFQIIdTPGLLDRPIQKRNKIERKA 243
                                       799999999***************998887655555568999*********7778889999***9999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.35      23      46 ..     170     193 ..     155     231 .. 0.83
   2 ?   -2.8   0.0       5.7   7.3e+03      40      71 ..     274     306 ..     272     319 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                            AAA_16  23 rpelvllsGesGvGKsslvrellr 46 
                                       +++ v++ G++ vGKsslv ++ +
  gi|488600037|ref|YP_007906508.1| 170 DEPTVVVAGYPNVGKSSLVSAIST 193
                                       45899**************99874 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.7
                            AAA_16  40 lvrellralekdggiflrgkcdql..esaipysa 71 
                                       l++e++r+++   +i+++ k+d +  + + +ysa
  gi|488600037|ref|YP_007906508.1| 274 LLEEIKREFRVP-IIAVYSKADLHdfRDKPAYSA 306
                                       666666666666.667777777775455555555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00048      0.61       2     119 ..     174     294 ..     173     295 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-S......GGCTTTT CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaG......qerfrsl 72 
                                       vv+ G  +vGK+sl++ + +  ++    +  ++ f+tk++  +     + k++ v+++i Dt G      q+r +  
  gi|488600037|ref|YP_007906508.1| 174 VVVAGYPNVGKSSLVSAIST--VQ---PEVASYPFTTKKIF-VG----KGKIDGVTFQIIDTPGlldrpiQKRNKIE 240
                                       7899***********99883..43...34566778888774.22....34677899999999995544433333322 PP

                                       -HHHH...CTSCEEEEEEE.GHHH....HCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  73 hplyl...reaalailvyd.srss....enlkeWlkelkkvagkspvilvgnkiD 119
                                       ++  l     a+++++v+d +++     e+ ++ l+e+k++  + p+i v +k+D
  gi|488600037|ref|YP_007906508.1| 241 RKAILslkYLANCIVFVIDpTETCgfevEKQQSLLEEIKREF-RVPIIAVYSKAD 294
                                       222221113455566666642221212234445555555443.456666666666 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.031        39       1      22 [.     176     197 ..     176     204 .. 0.88
   2 ?    5.5   0.0      0.01        13      94     174 ..     221     301 ..     210     323 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.031
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilel 22 
                                       v+G + +GK+++v+a+s + ++
  gi|488600037|ref|YP_007906508.1| 176 VAGYPNVGKSSLVSAISTVQPE 197
                                       89**************998776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.01
                        ATP_bind_1  94 llfDtPGQie..lfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDl 168
                                        ++DtPG +   + +  +  +k + +L+   a ++v+++D++      +  ++  +   +  + ++P + v++k+Dl
  gi|488600037|ref|YP_007906508.1| 221 QIIDTPGLLDrpIQKRNKIERKAILSLK-YLANCIVFVIDPTETCG-FEVEKQQSLLEEIKREFRVPIIAVYSKADL 295
                                       5777777543224444455556666777.58999999999765433.222222223445888899************ PP

                        ATP_bind_1 169 lkekle 174
                                        + +++
  gi|488600037|ref|YP_007906508.1| 296 HDFRDK 301
                                       774444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 1820.28
//
Query:       gi|488600038|ref|YP_007906509.1|  [L=448]
Description: Adenylosuccinate lyase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-51  174.0   0.2    1.1e-50  172.9   0.0    1.6  2  Lyase_1   Lyase
    1.5e-18   67.1   0.4    3.7e-18   65.8   0.4    1.7  1  ADSL_C    Adenylosuccinate lyase C-terminus
    3.3e-05   24.0   4.8    3.7e-05   23.8   2.7    2.2  2  ASL_C     Adenylosuccinate 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 !  172.9   0.0   1.8e-54   1.1e-50      80     312 .]      74     297 ..      38     297 .. 0.90
   2 ?   -2.0   0.1      0.31   1.8e+03      49      75 ..     348     373 ..     312     419 .. 0.54

  Alignments for each domain:
  == domain 1  score: 172.9 bits;  conditional E-value: 1.8e-54
                                       HHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEE CS
                           Lyase_1  80 gtavnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiG 156
                                       ++++ + l + i ++     +++++vh+g++snD+++Ta + +l++al ++L+ ++++L + l  ka+e+k vv +G
  gi|488600038|ref|YP_007906509.1|  74 KHDIMA-LVKAITSK--LDEDTARWVHFGATSNDIIDTATATQLRDAL-KVLECKIRRLLKLLIHKAEEYKGVVCLG 146
                                       333333.44444433..44699**************************.88************************** PP

                                       EETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEES CS
                           Lyase_1 157 rThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvka 232
                                       rTh+q+A P+t g  ++ +a ++ r+++rlke+++rl+v++++g++++ + ++ +  e +++v++ l+   +   k 
  gi|488600038|ref|YP_007906509.1| 147 RTHGQPALPTTYGFRFALWASEVARHYQRLKEIRERLIVGQMSGAVGTQASFGEKGmEIEKRVMELLN---L---KP 217
                                       ********************************************998888888887688888888888...5...66 PP

                                       SSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHH CS
                           Lyase_1 233 pnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagr 309
                                       + +  ++ +rD + e+l  l++l t L k+a   r+l+  e+g+v + + +++ GSS+MP+K+NP+++E++ g a+ 
  gi|488600038|ref|YP_007906509.1| 218 AVISSQIIPRDIYCEYLEFLANLSTTLEKIATNFRILQRAEVGEVMERFGKKQVGSSTMPHKRNPIDSENICGLARV 294
                                       77777999********************************************************************9 PP

                                       HHH CS
                           Lyase_1 310 vvG 312
                                       v G
  gi|488600038|ref|YP_007906509.1| 295 VRG 297
                                       988 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHCHCHHCGGHHHBSS CS
                           Lyase_1  49 eaaaiikaldevleegklddqfvlkvi 75 
                                        ++ai + l++  + ++l +++ ++  
  gi|488600038|ref|YP_007906509.1| 348 DMEAIKRNLEQQKQ-LNLSEAVMIELT 373
                                       33333333333333.333333444433 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.4   6.2e-22   3.7e-18       2      71 ..     362     437 ..     361     439 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 6.2e-22
                                       GGGHHHHHHHHHH.TH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHH.C.HHCHHHHHT-GGGCCTTHHHHHH CS
                            ADSL_C   2 lifservllaLvk.glgReeAyelVqeaamkawee...llelLaadpevk.k.seeeldalfdpayylgsadeivd 71 
                                       l +se+v+++L+k g+gR+ A+e+ +e amka e+   l+e+L+ ++evk + s +el++l++ ++ylg a + v+
  gi|488600038|ref|YP_007906509.1| 362 LNLSEAVMIELTKrGVGRQSAHEILRESAMKAYERklsLFEALKDNEEVKkYiSSDELKELLKAENYLGTAKKRVE 437
                                       568*********66*******************99***************55*999**************998776 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.81   4.8e+03      92     112 ..      44      64 ..      25      88 .. 0.57
   2 !   23.8   2.7   6.2e-09   3.7e-05       5     109 ..     312     422 ..     309     429 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.81
                                       HHHCS-S-HHHHHHHHC--CC CS
                             ASL_C  92 fieslevseeakeeLkaltpa 112
                                       f      s+++k+++  +tp+
  gi|488600038|ref|YP_007906509.1|  44 FGYFSMNSKDVKKRMLMVTPD 64 
                                       333333344445555444443 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 6.2e-09
                                       --TCHHHHHTTCHHHHHHHH.HHHHHHHHHHCCEEE-HHHHHHHHHT-GGG.GHHHHHHHHHHT..T-TTHHHHHHH CS
                             ASL_C   5 RDLtdStvlRnlgvalahsl.ialksllkglsklevneealaedLdenwev.laEaiqtvlrre..giekpYeklke 77 
                                       RDLt+S+  R + v  +  +   l++++k ++ l++++ea++++L+++ ++ l+Ea+ + l +   g ++++e l+e
  gi|488600038|ref|YP_007906509.1| 312 RDLTNSSAERITLVESSVLVdHILTKMIKVVESLSLDMEAIKRNLEQQKQLnLSEAVMIELTKRgvGRQSAHEILRE 388
                                       **********9888877665235789*********************988779*****9998662256899999999 PP

                                       HHTTS---HHHHHHHHHCS.-S-HHHH.HHHHC- CS
                             ASL_C  78 ltrgkkitkeslkefiesl.evseeak.eeLkal 109
                                          ++  +k sl e ++++ ev++ ++ +eLk+l
  gi|488600038|ref|YP_007906509.1| 389 SAMKAYERKLSLFEALKDNeEVKKYISsDELKEL 422
                                       9988877776766666665257776542677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2734.01
//
Query:       gi|488600039|ref|YP_007906510.1|  [L=140]
Description: hypothetical protein Asulf_00494 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 944.24
//
Query:       gi|488600040|ref|YP_007906511.1|  [L=93]
Description: Molybdopterin converting factor, small subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-07   29.4   0.3    3.1e-06   27.7   0.3    1.8  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.063   13.1   0.1        6.5    6.7   0.0    2.3  2  Ub-Mut7C  Mut7-C ubiquitin


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.3   3.5e-10   3.1e-06       3      77 .]       7      93 .]       5      93 .] 0.80

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.5e-10
                                      ETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG............TTTTEEEEETTEEEGCCTTTSB--TTCEEE CS
                              ThiS  3 lfaelrelageeelelaegstvaelleaLgerypela............lerrvavavNgeivprlwldtelkdgDeva 69
                                      lfa+lre+   ++l+++ +  +++ + + +   +e++             ++   + vNg+++++     +lkdgD +a
  gi|488600040|ref|YP_007906511.1|  7 LFATLREKYRVKKLDVEFEGDLHDFFVSASRILGEEFlndvysnfeeriFRDDRLITVNGRNLKDIKGIPQLKDGDLIA 85
                                      788888888866777777777777777777777766677888888788877888999********6667889******* PP

                                      EEESTTC- CS
                              ThiS 70 ilppVaGG 77
                                      ++ppVaGG
  gi|488600040|ref|YP_007906511.1| 86 VFPPVAGG 93
                                      *******9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0043        38       3      21 ..      19      37 ..      17      45 .. 0.87
   2 ?    6.7   0.0   0.00073       6.5      51      75 ..      61      88 ..      60      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0043
                          Ub-Mut7C  3 titfrfyaeLndflprarr 21
                                      +++++f   L+df+ +a r
  gi|488600040|ref|YP_007906511.1| 19 KLDVEFEGDLHDFFVSASR 37
                                      6789**********99988 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00073
                          Ub-Mut7C 51 lilvnGesvg.fshi..ledGdrvavyp 75
                                      li+vnG++ + ++ i  l+dGd++av p
  gi|488600040|ref|YP_007906511.1| 61 LITVNGRNLKdIKGIpqLKDGDLIAVFP 88
                                      7999999864255551157*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 733.42
//
Query:       gi|488600041|ref|YP_007906512.1|  [L=477]
Description: Mg-chelatase subunit ChlI [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   44.2   0.1    6.1e-08   32.8   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    2.2e-08   34.0   0.0    2.2e-05   24.2   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      4e-08   32.9   0.0     0.0049   16.3   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.5e-06   26.3   0.0    0.00014   21.1   0.0    2.3  2  MCM              MCM P-loop domain
    9.6e-06   25.5   0.0    0.00035   20.4   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
     0.0011   19.1   0.0      0.062   13.4   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
     0.0021   18.5   0.1      0.018   15.5   0.1    2.3  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.021   14.0   0.3      0.077   12.2   0.1    2.0  2  TIP49            TIP49 P-loop domain
        0.1   12.6   0.1       0.24   11.4   0.1    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.17   11.8   0.5       0.66    9.9   0.0    2.4  3  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1   0.00073       1.3       1      30 [.      82     111 ..      82     115 .. 0.86
   2 !   32.8   0.0   3.4e-11   6.1e-08      24     138 .]     144     259 ..     129     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00073
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyv 30 
                                       ++l +G +G gK++++++++++l  +++ +
  gi|488600041|ref|YP_007906512.1|  82 NILFKGMKGFGKTTFSKSISKLLPERILAI 111
                                       5799*******************8777655 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 3.4e-11
                                       S--EEEEE--TT--HHHHH--B--.................--------G-SEEEEESGGG--HHHHHHHHHHHHSS CS
                             AAA_5  24 nreveyvqltrdtteedlkgrreik........ngttslvdsplvraaregeilvlDEveraesevlnsLlslleer 92 
                                       +r+++ +++   +t+++l+g+++i+        ++ ++++++ + +a  +  i+++DE+  ++s+++  L+ lleer
  gi|488600041|ref|YP_007906512.1| 144 GRKWVRILGDPMMTTRQLIGGISIQklregydiDSPEVFSPGRILKA--NRGIAYVDELGAIPSAMQTLLHELLEER 218
                                       8899999999**************99987777777777777777744..557************************* PP

                                       EEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  93 rllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ++ ++eg+     + d     + +ia++np++ r+ ++++++l++R+
  gi|488600041|ref|YP_007906512.1| 219 QVTTPEGDII-PMRID-----TLFIASTNPANyRGTADIKEPLLDRM 259
                                       ***8887754.44443.....8************************7 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0019       3.5      13      45 ..      71     103 ..      65     113 .. 0.87
   2 !   24.2   0.0   1.2e-08   2.2e-05      86     162 ..     184     259 ..     180     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0019
                                       HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
                   Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKellaraihea 45 
                                       e++k++  + +++l +G +G GK++++++i + 
  gi|488600041|ref|YP_007906512.1|  71 EMVKNALLSGSNILFKGMKGFGKTTFSKSISKL 103
                                       6788999999*****************999765 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.2e-08
                                       EHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEE.SBTSSSEEE--EEEEEEESS-HHHHHHTTSS-HHHHHH CS
                   Sigma54_activat  86 kGlfekadgGtlfLDeigelplelQekLlrvlqegeve.rvGsskeikvdvriiaatnedleeaveegkfredLyyr 161
                                        G++ ka+ G+ ++De+g +p ++Q+ L ++l+e++v+ + G+  ++++d+ +ia+tn    +   +  ++e L+ r
  gi|488600041|ref|YP_007906512.1| 184 PGRILKANRGIAYVDELGAIPSAMQTLLHELLEERQVTtPEGDIIPMRIDTLFIASTNPA--NYRGTADIKEPLLDR 258
                                       5999******************************99862789999***********9954..333344466666666 PP

                                       H CS
                   Sigma54_activat 162 l 162
                                       +
  gi|488600041|ref|YP_007906512.1| 259 M 259
                                       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 !   16.3   0.0   2.7e-06    0.0049       3      48 ..      61     106 ..      59     111 .. 0.95
   2 !   13.9   0.0   1.4e-05     0.026      97     159 ..     182     243 ..     176     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.7e-06
                      Mg_chelatase   3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpp 48 
                                        +++G++  k+ ++ a   g n+l+ G  G GKt   k +++llp+
  gi|488600041|ref|YP_007906512.1|  61 PEIVGKDMEKEMVKNALLSGSNILFKGMKGFGKTTFSKSISKLLPE 106
                                       689******************************************7 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.4e-05
                      Mg_chelatase  97 pkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                         pG i +a++G+ ++DEl  + + +   L e le+++vt       +    ++ ++a++Np+
  gi|488600041|ref|YP_007906512.1| 182 FSPGRILKANRGIAYVDELGAIPSAMQTLLHELLEERQVTTPEG-DIIPMRIDTLFIASTNPA 243
                                       57*************************************97544.445666677777777776 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.033        59      49      85 ..      72     108 ..      35     115 .. 0.79
   2 !   21.1   0.0   7.7e-08   0.00014     111     178 ..     181     245 ..     170     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.033
                                       SSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEE CS
                               MCM  49 edktklrgdinvllvgdpgtaKsqlLkyveklaprav 85 
                                         k+ l +  n+l+ g  g +K+++ k+++kl+p+ +
  gi|488600041|ref|YP_007906512.1|  72 MVKNALLSGSNILFKGMKGFGKTTFSKSISKLLPERI 108
                                       3345677888999999999999999999999999866 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 7.7e-08
                                       EEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSC CS
                               MCM 111 vleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagry 178
                                       v+  G ++ a++G++++De+  + ++ ++ lhE +E+ ++++  + i + ++  t ++a++np++  y
  gi|488600041|ref|YP_007906512.1| 181 VFSPGRILKANRGIAYVDELGAIPSAMQTLLHELLEERQVTTPEGDI-IPMRIDTLFIASTNPAN--Y 245
                                       567899**************************************996.568899999*****986..3 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 ?    2.5   0.0     0.068   1.2e+02       2      24 ..      83     105 ..      82     113 .. 0.86
   2 !   20.4   0.0     2e-07   0.00035      65     129 ..     194     259 ..     147     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.068
                             AAA_3   2 vllegvPGlaktllvkalakald 24 
                                       +l++g+ G +kt++ k+++k l 
  gi|488600041|ref|YP_007906512.1|  83 ILFKGMKGFGKTTFSKSISKLLP 105
                                       7999**************99885 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2e-07
                             AAA_3  65 llladeinrappktqsalleameerqvtv.egethklpepflvlatqnPieqeGtyplpeaqldrf 129
                                       +  +de+   p+ +q+ l e +eerqvt+ eg+  ++    l +a  nP +++Gt  + e  ldr+
  gi|488600041|ref|YP_007906512.1| 194 IAYVDELGAIPSAMQTLLHELLEERQVTTpEGDIIPMRIDTLFIASTNPANYRGTADIKEPLLDRM 259
                                       66789**********************9746788999999999*********************95 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.044        79       4      28 ..      81     105 ..      78     139 .. 0.88
   2 !   13.4   0.0   3.5e-05     0.062      56     130 ..     179     243 ..     166     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.044
                                       --EEEE--TTSSHHHHHHHHHHHTT CS
                             AAA_2   4 isilllgptgvGktelakalaellf 28 
                                       ++il+ g +g Gkt  +k++++ll 
  gi|488600041|ref|YP_007906512.1|  81 SNILFKGMKGFGKTTFSKSISKLLP 105
                                       79*************9999999875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.5e-05
                                       HHHHTTT-HHHHTTSEEEEETGGG-------------HHHHHHHHHHHH--EE-------EE-T.T-EEEEEE--T CS
                             AAA_2  56 ligappgyvgaeegGivllDEidKihpkessgadvSregVqrdLLqileggtltdkqgrkvdtk.nilfImtgafg 130
                                        ++ +pg + ++++Gi ++DE+  i +             q++L  +le+ ++t+ +g+ +  + ++lfI++++ +
  gi|488600041|ref|YP_007906512.1| 179 PEVFSPGRILKANRGIAYVDELGAIPS-----------AMQTLLHELLEERQVTTPEGDIIPMRiDTLFIASTNPA 243
                                       5666899999*****************...........********************88888768*******955 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 !   15.5   0.1   9.9e-06     0.018       1     127 [.      83     262 ..      83     266 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.9e-06
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS........................................ CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk........................................ 37 
                                       +l+ G +G GKT++ k++ k l  ++l i+g ++ ++                                        
  gi|488600041|ref|YP_007906512.1|  83 ILFKGMKGFGKTTFSKSISKLLPERILAIKGCKIHDDparpvcfsckkkvledneveltwvgrkwvrilgdpmmttr 159
                                       6999*******************************778999999999999999999999999999996666555555 PP

                                       ..STTHHHHHHHHHHHHHHHTS................TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                               AAA  38 ..yvgesekkirelfkeakeka................kpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                                         + g s +k+re                         +  i  +DE+ a+ ++         ++++ +Ll+e +  
  gi|488600041|ref|YP_007906512.1| 160 qlIGGISIQKLREG-------YdidspevfspgrilkaNRGIAYVDELGAIPSAM--------QTLLHELLEERQVT 221
                                       55333333333333.......0333333455556665555888999999984444........44444444444444 PP

                                       TTS......SSTEEEEEEESS.....GGGSTHHHHSTTSSEE CS
                               AAA  97 kkk......eskvivigatnr.....pdkldpallrgRfdrk 127
                                       + +      + ++++i+ tn        +++++ll +R++++
  gi|488600041|ref|YP_007906512.1| 222 TPEgdiipmRIDTLFIASTNPanyrgTADIKEPLL-DRMEEI 262
                                       44488888855578888888766667778888888.888776 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.3e-05     0.077      41      78 ..      71     108 ..      66     118 .. 0.89
   2 ?   -2.5   0.0       1.3   2.3e+03      93     109 ..     444     460 ..     442     470 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  41 elikekklaGravLlaGpsgtGktalaiaiskelgedv 78 
                                       e++k+  l+G  +L++G +g Gkt  + +isk l e +
  gi|488600041|ref|YP_007906512.1|  71 EMVKNALLSGSNILFKGMKGFGKTTFSKSISKLLPERI 108
                                       8*******************************998765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                                       XXXXXXXXXXXXXXXXX CS
                             TIP49  93 vkktevltqalrksigv 109
                                       v+ te++++ lr+  g+
  gi|488600041|ref|YP_007906512.1| 444 VSTTEIILESLRRCTGI 460
                                       6789*********9987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00013      0.24      15      43 ..      73     104 ..      62     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                       HHCH...TEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  15 akal...gdvilLeGdLGaGKTtlvrglakal 43 
                                        k++   g+ il++G  G GKTt+++++ k l
  gi|488600041|ref|YP_007906512.1|  73 VKNAllsGSNILFKGMKGFGKTTFSKSISKLL 104
                                       2222355777****************998765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00037      0.66       2      47 ..      83     126 ..      82     218 .. 0.82
   2 ?   -2.3   0.0         2   3.6e+03      48      70 ..     299     321 ..     291     345 .. 0.69
   3 ?   -3.5   0.0       4.7   8.4e+03     117     147 ..     379     410 ..     374     421 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigF 47 
                                       ++  G+ G GKtT+ k +++ll ++ + ++G     + +  r ++F
  gi|488600041|ref|YP_007906512.1|  83 ILFKGMKGFGKTTFSKSISKLLPERILAIKGCKI--HDDPARPVCF 126
                                       66679********************999999544..3444555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                                       EEEET.T--EEEEEETT---SSE CS
                          NTPase_1  48 kivdlasgeegiLarveakrepr 70 
                                       +iv +a ++eg ++r e + ++r
  gi|488600041|ref|YP_007906512.1| 299 RIVRIARKKEGKFSRIEVEPSCR 321
                                       68888888888888888555555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.7
                                       HHHHHHT.TTSEEEEE--SS--SHHHHHHHT- CS
                          NTPase_1 117 aveevLk.sekpvlavihrrkdlalveeirer 147
                                        vee+L+ +   v   i++++ +++v+e++e 
  gi|488600041|ref|YP_007906512.1| 379 LVEEALNkTAIEVYSKIPKENFNDFVKELSEI 410
                                       45556653334444455555555666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2801.75
//
Query:       gi|488600042|ref|YP_007906513.1|  [L=402]
Description: hypothetical protein Asulf_00497 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   35.4   0.1    1.7e-07   31.8   0.1    2.3  1  VWA_2     von Willebrand factor type A domain
    1.6e-06   27.7   0.1    5.6e-06   25.9   0.1    2.0  2  VWA_CoxE  VWA domain containing CoxE-like protein
    2.1e-06   28.1   0.0     0.0001   22.6   0.0    2.3  1  VWA       von Willebrand factor type A domain
     0.0015   17.7   1.0     0.0028   16.8   0.1    1.9  2  DUF444    Protein of unknown function (DUF444)
  ------ inclusion threshold ------
       0.03   13.8   0.1      0.045   13.2   0.1    1.2  1  GbpC      Glucan-binding protein C
       0.25   11.0   2.7       0.22   11.2   0.8    1.9  2  DUF1699   Protein of unknown function (DUF1699)


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 !   31.8   0.1   5.7e-11   1.7e-07       2     107 .]     237     328 ..     236     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 5.7e-11
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdav...eallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakggg 75 
                                       v+++D+S Smr++     ++  a + +   +++++++++  + +v+f+++++ +     ++++il+    l ++ g 
  gi|488600042|ref|YP_007906513.1| 237 VMLIDVSDSMRGK-----KFVGAIESAiglRKVIERRAEKELRVVSFNHDVREV-----NRGEILS----LYPH-GR 298
                                       89**********9.....55555443313388888999*************965.....6777776....9996.** PP

                             VWA_2  76 tnlaaaLqlarkalkkrrkgekrvivlitDge 107
                                       t+++ aL++ar+++++   + + vi+litDge
  gi|488600042|ref|YP_007906513.1| 299 TDIGLALRKAREIVERS--NSSGVIFLITDGE 328
                                       ***************66..6**********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 ?   -3.3   0.0       1.6   4.8e+03      22      39 ..      38      55 ..      21      59 .. 0.81
   2 !   25.9   0.1   1.9e-09   5.6e-06      31     164 ..     209     331 ..     201     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.6
                          VWA_CoxE 22 rrrgrriDlrrtlranlr 39
                                      +r+++++D+r  +r+ ++
  gi|488600042|ref|YP_007906513.1| 38 SRKKGEVDVRDYIREHMK 55
                                      678899999999999887 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.9e-09
                          VWA_CoxE  31 rrtlranlrhggelvelvrrkprerkprelvllvDvSgSmaaysaiflallhAllqqlprtevfaFdtrlvdlTral 107
                                         t  +n   g ++ ++v r p++r++   v+l+DvS Sm    +++ a+  A+  +    +    + r+v+  +++
  gi|488600042|ref|YP_007906513.1| 209 HETFVRN--KGFRFKDIVARAPKHREKIVYVMLIDVSDSMRG-KKFVGAIESAIGLRKVIERRAEKELRVVSFNHDV 282
                                       5555444..56678899999**********************.77777777777655554444556889******** PP

                          VWA_CoxE 108 rerDpaeaLarvsaavedlgGgTrigaalaeflelvtrpaLsrravvvlvsDglerg 164
                                       re  + e L          +G T+ig al++++e v+r+   +  v+ l++Dg+ + 
  gi|488600042|ref|YP_007906513.1| 283 REVNRGEILSLYP------HGRTDIGLALRKAREIVERSN--SSGVIFLITDGEPTS 331
                                       *999999999888......******************888..88999*****97654 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 !   22.6   0.0   3.5e-08    0.0001       3     119 ..     237     336 ..     237     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.5e-08
                                       EEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC CS
                               VWA   3 vfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgggtt 79 
                                       v ++D+S+sm++++f  + e ++ l + +e  +    + +v+f+++v+++   n+     e+     +l   ++g t
  gi|488600042|ref|YP_007906513.1| 237 VMLIDVSDSMRGKKFVGAIESAIGLRKVIE-RRAEKELRVVSFNHDVREV---NR----GEI----LSL--YPHGRT 299
                                       679*******************99988888.666677***********99...43....334....344..677788 PP

                                       -HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS...H CS
                               VWA  80 ntgkalkyaleklfkssagaRenakkviilltdGksndg...d 119
                                       ++g al +a+e + ++s++     + vi l+tdG+++++    
  gi|488600042|ref|YP_007906513.1| 300 DIGLALRKARE-IVERSNS-----SGVIFLITDGEPTSSynpH 336
                                       8********99.6666666.....69**********9944341 PP

>> DUF444  Protein of unknown function (DUF444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.68     2e+03     106     127 ..     105     125 ..      73     143 .. 0.53
   2 !   16.8   0.1   9.4e-07    0.0028     225     327 ..     212     314 ..     204     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.68
                            DUF444 106 egedefefelsreEfldllfed 127
                                       eg+   e els+ E+ld l e+
  gi|488600042|ref|YP_007906513.1| 105 EGR-IDESELSPTELLDHLKEE 125
                                       222.223455555555555555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 9.4e-07
                            DUF444 225 fidelDlRYrrve.kepkpesnaVmfclmDvSGSMdetkkdlakrfFilLylFLkrkYekvevvFirHtteAkeVde 300
                                       f+++   R++ ++ + pk +++ V ++l DvS SM+ +k   a    i L   ++r+ ek e+  ++ +++ +eV++
  gi|488600042|ref|YP_007906513.1| 212 FVRNKGFRFKDIVaRAPKHREKIVYVMLIDVSDSMRGKKFVGAIESAIGLRKVIERRAEK-ELRVVSFNHDVREVNR 287
                                       777778899987626789999****************999999999*********99765.888888888999**** PP

                            DUF444 301 eeFFysresGGTvvSsalelmkeiiee 327
                                        e       G T +  al++++ei+e+
  gi|488600042|ref|YP_007906513.1| 288 GEILSLYPHGRTDIGLALRKAREIVER 314
                                       *************************95 PP

>> GbpC  Glucan-binding protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.5e-05     0.045       4      74 ..      15      87 ..      13     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                      HHHGGHHHH..S--EE-S-.-TT-EEEEES---EE-HHHHHHHTTS-HHHHT-GGG--GGGEE.S--S-TTS- CS
                              GbpC  4 KnedGyveeplaqaLvfds.EPnAklsletdnqaltkseakakadekilqvtgldvldasdle.snkvkskee 74
                                      K+e+G+++e la++Lv+   +P  +   e d + + ++++k++ ++ i++ ++++++   + +  +k++  +e
  gi|488600042|ref|YP_007906513.1| 15 KKEEGRISETLAKELVYSLfNPYSRKKGEVDVRDYIREHMKENLSDSIDEFNEINTFGFLNTNwIEKMDRMDE 87
                                      9*****************999*999999999999**************8866666555544433333333333 PP

>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   7.2e-05      0.22      52     128 ..      54     130 ..      49     132 .. 0.90
   2 ?   -2.4   0.0       1.1   3.4e+03       3      19 ..     273     289 ..     272     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-05
                           DUF1699  52 ykktlsksakmfleiqgiellegdvwghrkdineyyevseevierikelkseglseeeiaeklsketklspdlikfl 128
                                        k++ls s++ f ei+   +l+ + + + + ++ey +  e+  e+ik+ ++eg  +e+  +  +   +l++++i+ l
  gi|488600042|ref|YP_007906513.1|  54 MKENLSDSIDEFNEINTFGFLNTNWIEKMDRMDEYRKAREKAWEQIKRDINEGRIDESELSPTELLDHLKEEIIEDL 130
                                       5789**************************************************99998888888888888888755 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                           DUF1699   3 irvvsskeeietlnene 19 
                                       +rvvs  ++++++n+ e
  gi|488600042|ref|YP_007906513.1| 273 LRVVSFNHDVREVNRGE 289
                                       79*********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2454.24
//
Query:       gi|488600043|ref|YP_007906514.1|  [L=403]
Description: acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-36  124.6   0.0    5.5e-36  124.2   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    3.3e-16   59.2   0.0    1.8e-15   56.8   0.0    2.0  2  M20_dimer      Peptidase dimerisation domain
     0.0025   17.5   0.0     0.0038   16.9   0.0    1.2  1  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
       0.28   11.0   0.8        5.7    6.9   0.0    2.3  2  RCC1_2         Regulator of chromosome condensation (RCC1) re


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 !  124.2   0.0   1.2e-39   5.5e-36       3     203 ..      87     397 ..      85     399 .. 0.92

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 1.2e-39
                                       EEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.TH CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                     Peptidase_M20   3 gsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gG 77 
                                        sH+DvVpe+++  w+t pf++ +edGk+yGrG+ d+  +++a l a +a+ + g++p +t+ l+f++dEE+g+  G
  gi|488600043|ref|YP_007906514.1|  87 VSHMDVVPEGDERLWNTpPFRAVVEDGKIYGRGSEDNGQSLVASLIAGKAILELGLTPYYTLGLAFVADEETGSkYG 163
                                       69******999999*********************************************************9888** PP

                                       HHHHHH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE...................................... CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                     Peptidase_M20  78 akalle.gleerekvdavfelhieepgileagklaigvv...................................... 115
                                       +++l++ g++  ek d    +++ ++g ++ g   i +                                       
  gi|488600043|ref|YP_007906514.1| 164 IQELIKrGVF--EKDDL---IVVPDGGTPK-GD-MIEIAeksvvwfkfsvfgkqthasmpekglnanrmamefllgi 233
                                       ******7776..47777...4599999999.44.3333367999********************************* PP

                                       ...........................................................................EE CS
                                       ...........................................................................xx RF
                     Peptidase_M20 116 ...........................................................................kv 117
                                                                                                                  ++
  gi|488600043|ref|YP_007906514.1| 234 dralrdkysktnpifqppvstfeptkreanvdnvntipgldvsymdcrilpeynvdeviefvnrmkegfekekgcRI 310
                                       **************************************************************************889 PP

                                       EEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSGGCTTSTTTEEEH CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 118 evelleggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgsglaHspnEyvdl 191
                                       eve ++++ +++++ +s++v++l++a+e++ g ++ ++ +g g+t  +ff  ag +t+++   +  +aH+pnEy+++
  gi|488600043|ref|YP_007906514.1| 311 EVEVVQREFSPPTDeNSEVVRVLSRAIESVRGIRPGVYGMG-GNTCGAFFrkAGFQTAVWSTVD-NTAHQPNEYCRI 385
                                       999999999999999**************99*777777777.8999999987788999886666.8*********** PP

                                       HHHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                     Peptidase_M20 192 edlekgikvlar 203
                                       ++l++ +kv+a 
  gi|488600043|ref|YP_007906514.1| 386 DNLVEDAKVFAY 397
                                       *********986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.26   1.2e+03      26      38 ..      13      25 ..      10      75 .. 0.72
   2 !   56.8   0.0     4e-19   1.8e-15       1      97 [.     194     295 ..     194     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.26
                                      TB-HHHHHHHHHH CS
                         M20_dimer 26 gaNAieklarlla 38
                                       ++Aie+l+++++
  gi|488600043|ref|YP_007906514.1| 13 RDSAIEILSKIIE 25
                                      5789999999884 PP

  == domain 2  score: 56.8 bits;  conditional E-value: 4e-19
                                       SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.........TCCTCCCCCEECCE-C.CCCEE CS
                         M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia....eerslprttlnvtgiegGs.aknvi 72 
                                       i++k ++++k +v gk+ H+++p++g NA+++++++l  +    +d+     + +++p +t+++t  e+   + n+i
  gi|488600043|ref|YP_007906514.1| 194 IAEKSVVWFKFSVFGKQTHASMPEKGLNANRMAMEFLLGIDRALRDKYsktnPIFQPPVSTFEPTKREANVdNVNTI 270
                                       5899**********************************9999999988999999***************99****** PP

                                       SSEEEEEEEEEHHHHHHHHHHHHHH CS
                         M20_dimer  73 pdeaeakidiRllpgedpeevleei 97 
                                       p+    ++d+R+lp+ +++ev+e +
  gi|488600043|ref|YP_007906514.1| 271 PGLDVSYMDCRILPEYNVDEVIEFV 295
                                       *********************9866 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.4e-07    0.0038       1      82 [.      71     168 ..      71     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.4e-07
                                       EEEEEESTTCESEEEEEEEE--B-TTT...............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSE CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg...............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkr 61 
                                       N++a+++g++ ++++ + +H+D v++g               +g+    G  Dn+ + +a L   +++ + g +p +
  gi|488600043|ref|YP_007906514.1|  71 NILARIRGEQ-KRTIWIVSHMDVVPEGderlwntppfravveDGKiYGRGSEDNGQSLVASLIAGKAILELGLTPYY 146
                                       99********.9**************9*****99999888876666668********9999999999999999**** PP

                                       EEEEEEESSCSG.SSHHHHHHH CS
                     Peptidase_M28  62 gvrflffdaEEa.gllGSkafa 82 
                                       ++ ++f+  EE  + +G + ++
  gi|488600043|ref|YP_007906514.1| 147 TLGLAFVADEETgSKYGIQELI 168
                                       ***********95566666655 PP

>> RCC1_2  Regulator of chromosome condensation (RCC1) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0013       5.7      13      30 .]     108     125 ..     108     125 .. 0.95
   2 ?    2.4   0.2     0.033   1.5e+02      20      29 ..     347     356 ..     341     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0013
                            RCC1_2  13 aLtedGeVlcWGsNsdGQ 30 
                                       a++edG++++ Gs+++GQ
  gi|488600043|ref|YP_007906514.1| 108 AVVEDGKIYGRGSEDNGQ 125
                                       679**************9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.033
                            RCC1_2  20 VlcWGsNsdG 29 
                                       V++ G N++G
  gi|488600043|ref|YP_007906514.1| 347 VYGMGGNTCG 356
                                       9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2705.53
//
Query:       gi|488600044|ref|YP_007906515.1|  [L=153]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   18.1   0.1     0.0052   16.9   0.0    1.7  1  DUF2250   Uncharacterized protein conserved in archaea (DUF22
     0.0023   17.7   0.0     0.0038   17.0   0.0    1.4  1  DUF4364   Domain of unknown function (DUF4364)
     0.0068   16.4   0.0      0.025   14.6   0.0    1.9  2  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.056   13.8   0.1       0.12   12.7   0.0    1.6  2  Rrf2      Transcriptional regulator


Domain annotation for each model (and alignments):
>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-06    0.0052       8      70 ..      14      79 ..       8      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                           DUF2250  8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve...gktikrteaklKkk 70
                                      e +lk+l+  +k +  Y++ i+ke+  p ++++++l + ee  L+e       +++k+t+  +K +
  gi|488600044|ref|YP_007906515.1| 14 EIMLKILEAEEKGEEAYPLGISKEVGSPYSYISKVLSEFEENALIESEFkgrVRVVKFTRDGRKIA 79
                                      679******************************************975412246778877766655 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.4e-07    0.0038      33      75 ..      42      84 ..      34     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.4e-07
                           DUF4364 33 YfdlqqalseLvesglieeeekenktlykiTekGketlelfen 75
                                      Y +++++lse +e+ lie+e k    + k T +G++++elf+ 
  gi|488600044|ref|YP_007906515.1| 42 YSYISKVLSEFEENALIESEFKGRVRVVKFTRDGRKIAELFKR 84
                                      999*****************99******************974 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.5e-06     0.025       5      74 ..      13      87 ..      11      90 .. 0.84
   2 ?   -2.8   0.0       1.4   6.4e+03       2      15 ..      96     109 ..      96     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                            HTH_45  5 leIiadILeais.egeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkelee 74
                                      +eI++ ILea +  +ea +  i +++   y+ ++k L+   e+ li    k +    + T  G+++ e +k+l+ 
  gi|488600044|ref|YP_007906515.1| 13 VEIMLKILEAEEkGEEAYPLGISKEVGSPYSYISKVLSEFEENALIesefKGRVRVVKFTRDGRKIAELFKRLRA 87
                                      79*******998344677899*************************7644444555678**********999875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                            HTH_45   2 RskleIiadILeai 15 
                                       R kl+++ ++L++ 
  gi|488600044|ref|YP_007906515.1|  96 RKKLSVLEEVLNQA 109
                                       77888888888866 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-05      0.12      14      58 ..      16      61 ..       8      79 .. 0.80
   2 ?   -3.5   0.0         3   1.4e+04      30      45 ..     126     141 ..     124     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                                      HHHH.HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 14 llyL.akeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      +l + ++ee++e +    i+++++ + sy++k+l++ +++ l++s+
  gi|488600044|ref|YP_007906515.1| 16 MLKIlEAEEKGEEAYPLGISKEVGSPYSYISKVLSEFEENALIESE 61
                                      444325555555577778**************************95 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3
                                       HHHHHHTS-HHHHHHH CS
                              Rrf2  30 eiaerqnispsyleki 45 
                                       ei +rq   ++ leki
  gi|488600044|ref|YP_007906515.1| 126 EILKRQTSDKEALEKI 141
                                       6777888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 976.82
//
Query:       gi|488600045|ref|YP_007906516.1|  [L=304]
Description: Geranylgeranyl pyrophosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-46  158.7   0.1    1.7e-46  158.4   0.1    1.2  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
       0.06   13.5   0.3       0.55   10.4   0.0    2.5  3  TIP49_C          TIP49 AAA-lid domain


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 !  158.4   0.1   1.9e-50   1.7e-46       3     197 ..      27     211 ..      25     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 1.9e-50
                                       HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTC CS
                   polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvG 79 
                                        +++al+y+++agGKr+Rp++vll+ ++++    ++++++++a  vel+h+asL hDDi+D   +RR+  + h +++
  gi|488600045|ref|YP_007906516.1|  27 KIKKALKYIISAGGKRTRPIIVLLSGKMCG---GDYNDVLNAAISVELIHTASLAHDDIIDRGVMRRNVRTLHIEYD 100
                                       6899**************************...4689**************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCH CS
                   polyprenyl_synt  80 nklAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfa 156
                                        ++Ai++gd l ++++el++ +  ++ e+++ f+ v   + eG+lld++++ ++++s   +++y + ++ KTa+lfa
  gi|488600045|ref|YP_007906516.1| 101 LPVAILVGDWLISKSVELTSIY--GE-EIVKEFASVGRMMSEGELLDVYST-REEFS---EKDYFKCIESKTASLFA 170
                                       *********************9..77.*********************655.67777...***************** PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   polyprenyl_synt 157 lpvalaallagasdeelealkdiglelGlaFQiqDDylDlf 197
                                       ++++ a+ +   +++++e+l ++g++lG+a+Q++DD++ + 
  gi|488600045|ref|YP_007906516.1| 171 YSAKNACRIVSDDEKAAEELFKYGRNLGMAYQLVDDLIEYL 211
                                       *********99888999*******************99886 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.34   3.1e+03       9      25 ..       6      22 ..       5      36 .. 0.78
   2 ?   -1.3   0.0      0.28   2.5e+03      14      32 ..     183     201 ..     166     219 .. 0.66
   3 ?   10.4   0.0   6.1e-05      0.55      14      50 ..     254     290 ..     251     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                           TIP49_C  9 EgvkldeeAldlLakig 25
                                      E+ k+ + Al+ L++ +
  gi|488600045|ref|YP_007906516.1|  6 EEFKIINRALNELVENS 22
                                      67788899999999865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.28
                           TIP49_C  14 deeAldlLakigtetSLRY 32 
                                       de+A + L k g + ++ Y
  gi|488600045|ref|YP_007906516.1| 183 DEKAAEELFKYGRNLGMAY 201
                                       4566666666666655555 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 6.1e-05
                           TIP49_C  14 deeAldlLakigtetSLRYaiqLltpasilakkrkkk 50 
                                       +e+Ald++ +  ++  LRY i+ +t  +i + ++k+k
  gi|488600045|ref|YP_007906516.1| 254 SEKALDYFDHSEEREKLRYMINYMTRNQIRSYIEKNK 290
                                       689**************************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1821.45
//
Query:       gi|488600046|ref|YP_007906517.1|  [L=509]
Description: hypothetical protein Asulf_00501 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   83.6   7.7    2.1e-23   82.9   3.8    2.5  2  Peptidase_M50   Peptidase family M50
    1.3e-11   44.6   0.2    9.3e-06   25.9   0.0    2.6  2  PDZ_2           PDZ domain
    2.7e-11   43.1   0.0    5.2e-06   26.2   0.0    2.3  2  PDZ_6           PDZ domain
    0.00028   21.2   0.2      0.059   13.7   0.0    2.8  3  PDZ             PDZ domain
    0.00083   19.1   0.3    0.00083   19.1   0.3    2.2  3  Peptidase_M50B  Peptidase M50B-like
     0.0024   17.9   0.0        1.5    8.9   0.0    2.5  2  PDZ_1           PDZ-like domain
  ------ inclusion threshold ------
      0.033   14.2   0.1         11    6.1   0.0    2.4  2  Tricorn_PDZ     Tricorn protease PDZ domain
       0.44    9.4  13.8      0.069   12.1   8.7    2.1  2  MFS_1           Major Facilitator Superfamily


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 ?   -2.5   0.1       1.1   2.4e+03      90     107 ..      72      89 ..      57     105 .. 0.79
   2 !   82.9   3.8   9.5e-27   2.1e-23       3     249 ..     123     490 ..     121     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                                       XXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  90 ivlAGplanfilailvfv 107
                                        v+AG ++ f+l il+ +
  gi|488600046|ref|YP_007906517.1|  72 AVFAGMIFMFVLIILMDI 89 
                                       578999999999888654 PP

  == domain 2  score: 82.9 bits;  conditional E-value: 9.5e-27
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                       ++ l++ +vvHE+ H+++ + +gvkv++++i +                al+p+GG+ + ++ +  +          
  gi|488600046|ref|YP_007906517.1| 123 VIGLLVTLVVHEFSHAILCRVEGVKVKAMGIIL----------------ALVPIGGFAEPDEGQLMS---------- 173
                                       799*************************99998................***********9999443.......... PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX................................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................ RF
                     Peptidase_M50  80 lkkspwqrllivlAGplanfilailvfvv................................................ 108
                                       ++ + +qr++i+ AG + nfi+ai++f +                                                
  gi|488600046|ref|YP_007906517.1| 174 QSVKRIQRIRIFSAGVISNFIVAIFAFSLffylinflsptvsvigvyedsplyglvekdsiitkingvevktpedmd 250
                                       577889*********************999*******************************************9999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|488600046|ref|YP_007906517.1| 251 kvlkseiltieiekngvvkeikvenlagprivylldgypaknaglkegmiiysingertysinsffnamkktkpeqv 327
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ...............-EEECE...CTTTSCEE-SEEEC-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                                       ...............xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                     Peptidase_M50 109 ...............pkkske...seeekrgviGvspkpvkkegllealkegvektlkvvvltvkalgklitg.kls 166
                                                           +     + + g++Gvs +  + +g+  a ++ + + lk++  ++++ ++l+   +++
  gi|488600046|ref|YP_007906517.1| 328 vevvlysdgkfitkeV----KltkHPNYDSGFLGVSVEE-QISGMRIAYSSLLLDWLKSIPDMLSSPKGLFILvSMP 399
                                       9999988888865431....2344667788999999988.7777777777777777777777777666666653333 PP

                                       XX..XXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xx..xxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 167 lk..tlggpisiaqlaseaaeagls......sflqllalisvnLgilNLlPipvLDGghllfalleairrkplserk 235
                                       l+   +g   s++ l +  +e + +      ++l+++ +i++ +g++N lP  +LDGg+++ ++++++  ++   r+
  gi|488600046|ref|YP_007906517.1| 400 LNfrGFGEETSFYFLPQGFWEDKGEtifyllNTLYWIGWINFYVGLFNCLPAIPLDGGRVFHETMTMLLSRKYGDRA 476
                                       3322566666666555333333222555677********************************************** PP

                                       XXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxx RF
                     Peptidase_M50 236 eevanlvglallll 249
                                       e++ + +g +l +l
  gi|488600046|ref|YP_007906517.1| 477 EKISMNTGKVLAIL 490
                                       *****999998876 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   4.6e-06      0.01      15      58 ..     213     255 ..     206     274 .. 0.83
   2 !   25.9   0.0   4.2e-09   9.3e-06      15      82 .]     278     345 ..     268     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHT CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllk 58 
                                        v+v+ V+e++P  +  ++++ +i+k++g++vk+ ed+++ l +
  gi|488600046|ref|YP_007906517.1| 213 TVSVIGVYEDSPLYGL-VEKDSIITKINGVEVKTPEDMDKVLKS 255
                                       688999******7666.*********************998864 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 4.2e-09
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevkl 82 
                                       g  +v   +g Pa++aglk g +i++++g +  s  ++ +++ k+kp + V++ ++ dgk  t evkl
  gi|488600046|ref|YP_007906517.1| 278 GPRIVYLLDGYPAKNAGLKEGMIIYSINGERTYSINSFFNAMKKTKPEQVVEVVLYSDGKFITKEVKL 345
                                       67788888999*************************************************99999987 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   8.6e-06     0.019       2      54 ..     216     262 ..     215     264 .. 0.89
   2 !   26.2   0.0   2.3e-09   5.2e-06       6      54 ..     285     331 ..     280     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.6e-06
                             PDZ_6   2 VtaVdpgsPAdrAG.lrvGDiilsvNGqpveglsladvaallrgsagesvvlvv 54 
                                       V  V+++sP +  G ++   ii+++NG++v  ++++d    l+    e++++++
  gi|488600046|ref|YP_007906517.1| 216 VIGVYEDSPLY--GlVEKDSIITKINGVEV--KTPEDMDKVLK---SEILTIEI 262
                                       66899999999..9999*************..**********9...77777776 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 2.3e-09
                             PDZ_6   6 dpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesvvlvv 54 
                                         g PA +AGl+ G ii s+NG+ +  +s++ + ++++   +e+vv vv
  gi|488600046|ref|YP_007906517.1| 285 LDGYPAKNAGLKEGMIIYSINGERT--YSINSFFNAMKKTKPEQVVEVV 331
                                       5799*********************..***********77777777665 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.021        47      44      68 ..     229     253 ..     211     263 .. 0.80
   2 !   13.7   0.0   2.6e-05     0.059      29      79 ..     280     330 ..     260     332 .. 0.79
   3 ?   -2.3   0.0       2.7   6.1e+03       5      21 ..     348     365 ..     344     370 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.021
                                       SSTTEEEEEETTEETTTSHHHHHHH CS
                               PDZ  44 lkvGDkIlsvNgvdvenvsheeavq 68 
                                       ++++ +I+++Ngv v++ +++++v+
  gi|488600046|ref|YP_007906517.1| 229 VEKDSIITKINGVEVKTPEDMDKVL 253
                                       6778899********9999998886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.6e-05
                                       EEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEE CS
                               PDZ  29 fvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtL 79 
                                        +  +l g +a+ +glk+G +I s+Ng+ + +++   ++ + +++ ++v +
  gi|488600046|ref|YP_007906517.1| 280 RIVYLLDGYPAKNAGLKEGMIIYSINGERTYSINSFFNAMKKTKPEQVVEV 330
                                       566678898999999*************99999877777777777666655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.7
                                       ETS.TTSESSEEEEEETT CS
                               PDZ   5 eke.grgglGfslkggsd 21 
                                       +++   g+lG+s++++ +
  gi|488600046|ref|YP_007906517.1| 348 HPNyDSGFLGVSVEEQIS 365
                                       555578999999998765 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       3.7   8.4e+03     101     110 ..      10      19 ..       4      27 .. 0.45
   2 ?   -3.8   0.6       3.6   8.1e+03     182     194 ..      72      84 ..      64      91 .. 0.49
   3 !   19.1   0.3   3.7e-07   0.00083      16      89 ..     120     204 ..     109     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.7
                    Peptidase_M50B 101 vllllvllll 110
                                       v +++v++++
  gi|488600046|ref|YP_007906517.1|  10 VGIFIVYWVV 19 
                                       3333333322 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.6
                    Peptidase_M50B 182 allwvvlwllvsl 194
                                       a++ ++++++v +
  gi|488600046|ref|YP_007906517.1|  72 AVFAGMIFMFVLI 84 
                                       3333333333322 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 3.7e-07
                    Peptidase_M50B  16 llrpfkllvv.ffHElGHalaalLtGgrvkgielhsd..........esGvtvtrgpgglgqiltllaGYlgpallG 81 
                                        + ++ llv+ ++HE++Ha+ + + G +vk++ +              +G  ++++ +++++i + +aG +   ++ 
  gi|488600046|ref|YP_007906517.1| 120 EWGVIGLLVTlVVHEFSHAILCRVEGVKVKAMGIILAlvpiggfaepDEGQLMSQSVKRIQRIRIFSAGVISNFIVA 196
                                       5666666555168******************9999999999****999********888999*******87666666 PP

                    Peptidase_M50B  82 lllillsa 89 
                                       ++++ l +
  gi|488600046|ref|YP_007906517.1| 197 IFAFSLFF 204
                                       55555544 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0047        10      48      73 ..     229     254 ..     213     256 .. 0.86
   2 !    8.9   0.0   0.00065       1.5      47      75 ..     294     322 ..     280     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0047
                             PDZ_1  48 ekkgviitsinnqptpnLdefievvk 73 
                                       ++k+ iit+in++++++ +++ +v+k
  gi|488600046|ref|YP_007906517.1| 229 VEKDSIITKINGVEVKTPEDMDKVLK 254
                                       6899*************999999987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00065
                             PDZ_1  47 kekkgviitsinnqptpnLdefievvkki 75 
                                       + k g+ii+sin++ t + + f +++kk 
  gi|488600046|ref|YP_007906517.1| 294 GLKEGMIIYSINGERTYSINSFFNAMKKT 322
                                       4799***********************86 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0047        11      41      66 ..     230     255 ..     220     273 .. 0.84
   2 ?    5.6   0.0    0.0071        16      35      76 ..     292     332 ..     287     344 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0047
                                       .TT-EEEEETTEE-BTTB-HHHHHHT CS
                       Tricorn_PDZ  41 reGdlilavdgepvskekgiaelLvg 66 
                                       ++ ++i++++g++v++ ++++++L +
  gi|488600046|ref|YP_007906517.1| 230 EKDSIITKINGVEVKTPEDMDKVLKS 255
                                       56679*****************9975 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0071
                                       GGS---.TT-EEEEETTEE-BTTB-HHHHHHTTTT.SEEEEEE CS
                       Tricorn_PDZ  35 epGvnvreGdlilavdgepvskekgiaelLvgkag.keveLtv 76 
                                       + G++  eG +i++++ge++ + +++ +++  ++  + ve+ +
  gi|488600046|ref|YP_007906517.1| 292 NAGLK--EGMIIYSINGERTYSINSFFNAMKKTKPeQVVEVVL 332
                                       56666..************998888877777665414555554 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   8.7   3.1e-05     0.069     145     314 ..      65     211 ..      63     228 .. 0.65
   2 ?   -1.2   0.2      0.34   7.6e+02     262     294 ..     467     498 ..     408     506 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                             MFS_1 145 asslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfff 221
                                        +++g +avf  + ++++l +++ ++l++ +pp+++  +pk  +  +g   ++p         + w  +i+ll++  
  gi|488600046|ref|YP_007906517.1|  65 FANAGIPAVFAGMIFMFVLIILMDIVLFTNPPPPSEITNPKNILLIPGVNDWIP---------FEW-GVIGLLVT-- 129
                                       45899*********************************9988874444445555.........335.55555555.. PP

                             MFS_1 222 gfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavts 298
                                        +   +++  l    v g + +  +g++lal+ ++g ++ +  g+l+    +r++++ ++++++++ +++a++a++ 
  gi|488600046|ref|YP_007906517.1| 130 LVVHEFSHAIL--CRVEGVK-VKAMGIILALVPIGG-FAEPDEGQLMSQSVKRIQRIRIFSAGVISNFIVAIFAFS- 201
                                       23334555555..7777777.777777777777777.555666666655555566666666666666666666666. PP

                             MFS_1 299 savllllvlvliGfgl 314
                                             l+++li f +
  gi|488600046|ref|YP_007906517.1| 202 ------LFFYLINFLS 211
                                       ......3333333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.34
                             MFS_1 262 llagrlsdrlgrrrrlllallllllaalglall 294
                                       ll+ ++ dr   ++ ++ + +l++l++++++l 
  gi|488600046|ref|YP_007906517.1| 467 LLSRKYGDRA-EKISMNTGKVLAILVFASIILS 498
                                       3333444442.2344444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3195.63
//
Query:       gi|488600047|ref|YP_007906518.1|  [L=102]
Description: Uncharacterized protein involved in tolerance to divalent cations [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  126.7   0.8    2.7e-37  126.6   0.8    1.0  1  CutA1     CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
      0.078   13.0   0.0       0.12   12.5   0.0    1.3  1  DEP       Domain found in Dishevelled, Egl-10, and Pleckstrin


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 !  126.6   0.8     3e-41   2.7e-37       2      98 ..       4      99 ..       3     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 3e-41
                                      EEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EE CS
                             CutA1  2 lvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpei 80
                                      +++vta++eeea+k+a+ l+e++l+ACvn+++ i+S+Y W+gkie++ Ev++++kt++ek++e+ +++k++h+yevp+i
  gi|488600047|ref|YP_007906518.1|  4 FIYVTAKDEEEAEKIATVLLEKRLVACVNMFN-IKSMYIWEGKIEKSPEVVMILKTKAEKFKEIRDEIKRIHSYEVPCI 81
                                      69******************************.********************************************** PP

                                      EEEEESEEEHHHHHHHHH CS
                             CutA1 81 ialpieagseaYlkWiee 98
                                      +a++ie+g +++l+Wi+e
  gi|488600047|ref|YP_007906518.1| 82 CAISIEDGLREFLSWIDE 99
                                      ****************97 PP

>> DEP  Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.3e-05      0.12      27      56 ..       3      32 ..       1      40 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                                      HHHHTSSSSHHHHHHHHHHHHHCTSCECSS CS
                               DEP 27 LldnldiedreeAvalgqlLldqgliehve 56
                                      L  +++++d eeA++++  Ll+++l+ +v+
  gi|488600047|ref|YP_007906518.1|  3 LFIYVTAKDEEEAEKIATVLLEKRLVACVN 32
                                      56678899******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); 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: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 622.34
//
Query:       gi|488600048|ref|YP_007906519.1|  [L=235]
Description: putative nucleotidyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-06   25.8   0.3    2.2e-05   24.7   0.3    2.0  1  NTP_transf_2    Nucleotidyltransferase domain
    0.00068   19.7   0.8     0.0019   18.2   0.2    2.1  2  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.075   13.0   0.0        0.2   11.7   0.0    1.7  1  AsnC_trans_reg  Lrp/AsnC ligand binding 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 !   24.7   0.3   3.7e-09   2.2e-05      16      48 ..      44      80 ..      28     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.7e-09
                                      EEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH....H CS
                      NTP_transf_2 16 kvvlfGSyarGtalkgSDiDllvvlpeevsre....k 48
                                         ++GS+arG+ +  SDiD++v l+ +++      +
  gi|488600048|ref|YP_007906519.1| 44 PSGVYGSVARGDVNVSSDIDIFVNLRLPSYLIellvE 80
                                      55699*********************99775444440 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   3.3e-07    0.0019      18      39 ..      47      68 ..      29      81 .. 0.83
   2 ?   -2.3   0.0      0.79   4.7e+03      64      90 ..     167     192 ..     155     195 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.3e-07
                                      EEEEEE-S------EEEEEEEE CS
                           Polbeta 18 lFGSrakgkareeSDiDlavll 39
                                      ++GS+a+g+ + +SDiD++v l
  gi|488600048|ref|YP_007906519.1| 47 VYGSVARGDVNVSSDIDIFVNL 68
                                      8******************976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.79
                                       EEEEETTTS-HHHHHHHHHS-EEEES- CS
                           Polbeta  64 vDlvdlneapplllyeilkegkllysk 90 
                                       +D ++l++    +   i++e k ++++
  gi|488600048|ref|YP_007906519.1| 167 IDEIELSKI-VGVSLDIIRERKRVLER 192
                                       444444444.56666777777777666 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.3e-05       0.2      18      67 ..     181     230 ..     168     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                                       HHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEE CS
                    AsnC_trans_reg  18 ealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvart 67 
                                       + ++e + V+e  r tG    +l   v+d e++e  l++  +++p v+++
  gi|488600048|ref|YP_007906519.1| 181 DIIRERKRVLERRRETGRTGVFLNQLVPDHESFESYLEQIASKNPAVRKV 230
                                       6689999********************************9999**99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1534.87
//
Query:       gi|488600049|ref|YP_007906520.1|  [L=338]
Description: putative conserved protein related to pyruvate formate-lyase activating enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-11   43.4   0.2    1.4e-09   38.5   0.1    2.6  1  Radical_SAM  Radical SAM superfamily
    9.7e-09   35.4   0.1    4.5e-08   33.3   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain
    8.6e-08   32.5   0.0    1.8e-07   31.5   0.0    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 !   38.5   0.1   2.4e-13   1.4e-09       6     108 ..      36     135 ..      32     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.4e-13
                                       EESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                        C + C +C+++e      v      +++s+e+i++e++ ++    +++  ++ggepl+  +   ++++  k+   +
  gi|488600049|ref|YP_007906520.1|  36 ECVHSCYYCPISEErkgkdVMFANEREVKSLEDIEKEIELMS----AEGAGITGGEPLAKQKRLLEVLKFLKE--FD 106
                                       6****************************************9....*************99999999999999..7* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslg 108
                                       ++i++ t+ +   ++ +e+++++  d + ++
  gi|488600049|ref|YP_007906520.1| 107 MHIHIYTSIPAG-WRTIEKIADYT-DEIRFH 135
                                       ***********9.*********99.444433 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   7.5e-12   4.5e-08       2      89 ..      32     115 ..      31     135 .. 0.75
   2 ?   -0.9   0.0       0.3   1.8e+03      65      88 ..     277     305 ..     242     320 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 7.5e-12
                           Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilk..dlkkseikiqglvltGGePLhyenkkellklvkrlke 76 
                                       f+ ++ C +sC  C  +e  ++     +++e +++ l+  +++ + ++++g  +tGGePL  +++k ll+++k lke
  gi|488600049|ref|YP_007906520.1|  32 FL-TGECVHSCYYCPISE-ERKGKDVMFANEREVKSLEdiEKEIELMSAEGAGITGGEPL--AKQKRLLEVLKFLKE 104
                                       66.99**********666.3444455566666666666334445677889999*******..89*********9988 PP

                           Fer4_14  77 eypekkiwletng 89 
                                           ++i+++t+ 
  gi|488600049|ref|YP_007906520.1| 105 FD--MHIHIYTSI 115
                                       77..999999985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.3
                           Fer4_14  65 kellklvkrlkeey...pe..kkiwletn 88 
                                       ++ ++++ ++ eey    +  ++i+ et 
  gi|488600049|ref|YP_007906520.1| 277 QKAIDFLTMVSEEYvriSDieVEIRTETA 305
                                       45566777777777433222255555554 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0     3e-11   1.8e-07       4      91 ..      25     112 ..      22     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3e-11
                           Fer4_12   4 eGvrlslf.vsgCnlsCkgCfnketwsfk...sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelv 76 
                                       +G+ l+lf ++ C +sC +C   e ++ k     +e + + le i ++++  s eg  ++GGEPl+  +++ lle++
  gi|488600049|ref|YP_007906520.1|  25 DGGKLVLFlTGECVHSCYYCPISEERKGKdvmFANEREVKSLEDIEKEIELMSAEGAGITGGEPLA--KQKRLLEVL 99 
                                       678888985777********7555444442225555567788888888888999************..999999999 PP

                           Fer4_12  77 kevkeekpekdiwly 91 
                                       k +ke  ++  i +y
  gi|488600049|ref|YP_007906520.1| 100 KFLKEFDMH--IHIY 112
                                       988887763..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2046.56
//
Query:       gi|488600050|ref|YP_007906521.1|  [L=127]
Description: hypothetical protein Asulf_00505 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   96.8   2.6    9.9e-28   96.2   2.6    1.3  1  DUF2551        Protein of unknown function (DUF2551)
    0.00078   19.1   0.2     0.0017   18.0   0.2    1.6  1  Arg_repressor  Arginine repressor, DNA binding domain
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.021   14.1   0.0    1.2  1  DUF1611        Domain of unknown function (DUF1611_C) P-loop 
       0.16   12.2   2.4       0.51   10.6   1.0    2.4  2  SRP54_N        SRP54-type protein, helical bundle domain


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   2.6   2.2e-31   9.9e-28       1      83 []      31     111 ..      31     111 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 2.2e-31
                           DUF2551   1 LkkylerDksGiRrevLklfleakkltveeiyeklkek.fdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLk 76 
                                       L+kyl+rDk+ +R+++L+++l++kk+t++eiye+lk++ +d++++gv++mvGli++rlGI+k+   + g+kn+Y+Lk
  gi|488600050|ref|YP_007906521.1|  31 LRKYLDRDKKKVRSALLRILLSGKKYTTDEIYEELKASgVDIKMRGVSAMVGLISARLGIVKM---ELGNKNRYYLK 104
                                       89*************************************************************...9********** PP

                           DUF2551  77 eeyadlv 83 
                                       +ey dlv
  gi|488600050|ref|YP_007906521.1| 105 KEYYDLV 111
                                       *****98 PP

>> Arg_repressor  Arginine repressor, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   3.9e-07    0.0017       3      63 ..      40     103 ..      38     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-07
                                       HHHHHHHHHHHHHHS---SHHHHHHHHHTTT----HHHHHHHH....HHHT-EEEETTSTSEEEE CS
                     Arg_repressor   3 keerqklikkiikeekissQkelvelLkeeGidvtQatvSRdL....kelglvkvraengeyvYv 63 
                                       k+ r +l++ +++ +k  + +e+ e+Lk+ G+d+    vS ++      lg+vk++  n++ +Y 
  gi|488600050|ref|YP_007906521.1|  40 KKVRSALLRILLSGKK-YTTDEIYEELKASGVDIKMRGVSAMVglisARLGIVKMELGNKNRYYL 103
                                       5666666666666666.5669*********************855555899*****888887774 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.6e-06     0.021      24      61 ..      52      90 ..      50      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                           DUF1611 24 vGKrttaleleealeerGlkaafvaTgqtgili.agegv 61
                                       GK++t+ e++e+l+++G+++++++   +  li a+ g+
  gi|488600050|ref|YP_007906521.1| 52 SGKKYTTDEIYEELKASGVDIKMRGVSAMVGLIsARLGI 90
                                      6***********************998887777566666 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 ?   10.6   1.0   0.00011      0.51      36      61 ..      16      51 ..      15      65 .. 0.69
   2 ?   -1.8   0.0      0.85   3.8e+03      19      35 ..     104     120 ..      93     123 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                      HTT--HHHHHHHHHHHHHHHHCTTS...........S CS
                           SRP54_N 36 eaDVgvkvvkklienvkkkavgekk...........l 61
                                      +aDV+ kv+k++  +++k  + ++k           l
  gi|488600050|ref|YP_007906521.1| 16 SADVNPKVTKEIEVRLRK-YLDRDKkkvrsallrilL 51
                                      59**************99.777666444444444443 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.85
                                       HHHHHHHHHHHHHHHHH CS
                           SRP54_N  19 deedleealkeleeaLl 35 
                                       ++e ++ + + lee ++
  gi|488600050|ref|YP_007906521.1| 104 KKEYYDLVRRILEEYMI 120
                                       55666665566666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 906.85
//
Query:       gi|488600051|ref|YP_007906522.1|  [L=261]
Description: Undecaprenyl pyrophosphate synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-76  255.4   0.1    5.1e-76  255.1   0.1    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.097   12.8   0.1       0.25   11.5   0.1    1.7  2  bPH_5         Bacterial PH domain
       0.12   12.5   0.1       0.52   10.5   0.0    2.0  2  TAFH          NHR1 homology to TAF


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 !  255.1   0.1   8.5e-80   5.1e-76       1     221 [.      32     252 ..      32     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 255.1 bits;  conditional E-value: 8.5e-80
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellke 74 
                                       imDGNrR+A++rg +++++Gh  G ++ +e+l++c el +k +t YafSteNf+R++ee ++++el+k   ++l+++
  gi|488600051|ref|YP_007906522.1|  32 IMDGNRRYARSRG-MPVKMGHYFGSKKAEEVLNWCWELRIKNLTAYAFSTENFRRDNEEKKNIFELMKrelRRLVED 107
                                       9************.77888************************************************9555445544 PP

                                       HHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GG CS
                      Prenyltransf  75 elkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.ee 150
                                          +++k++vrvr+iG+++llpe++ e +e++e++tkk ++ + ln+a++Yg+r+ei++a++++++++++ k + ++
  gi|488600051|ref|YP_007906522.1| 108 P--RIHKNKVRVRIIGRRDLLPESLIEVVEEVERRTKKYKN-FFLNLAIAYGGRQEILDAIKNILRNVKDGKIDlDD 181
                                       4..9*********************************6655.**********************9999877777677 PP

                                       HSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHH CS
                      Prenyltransf 151 ideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrer 221
                                       ide+ +e+hlyt+   p++DlliRt+Ge+RlSnFl wq+a+   yf+d +WP+f+k dll+a++++q+ ++
  gi|488600051|ref|YP_007906522.1| 182 IDENLIEQHLYTNCGNPKVDLLIRTGGEQRLSNFLPWQSAKGVAYFCDIYWPEFRKIDLLRAIRTWQNLKE 252
                                       89*********96559**********************99999************************9665 PP

>> bPH_5  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   6.7e+03      78      88 ..      71      82 ..      38      85 .. 0.66
   2 ?   11.5   0.1   4.1e-05      0.25       5      58 ..     110     163 ..     107     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                             bPH_5 78 kd.kiygisPed 88
                                      k+ + y++s e+
  gi|488600051|ref|YP_007906522.1| 71 KNlTAYAFSTEN 82
                                      333445555555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.1e-05
                             bPH_5   5 ldeeglvIrwifgkeeIplseIeavrvsegvikgvrlfgtskpgyalGrfkikd 58 
                                       + ++++++r i++++  p s Ie v+++e ++k+ + f+++    + Gr +i d
  gi|488600051|ref|YP_007906522.1| 110 IHKNKVRVRIIGRRDLLPESLIEVVEEVERRTKKYKNFFLNLAIAYGGRQEILD 163
                                       78999*****************************************9*999765 PP

>> TAFH  NHR1 homology to TAF
   #    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      19      50 ..      57      89 ..      52     106 .. 0.68
   2 ?   10.5   0.0   8.6e-05      0.52       2      50 ..     141     188 ..     140     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.39
                              TAFH 19 qspevaenvkeL.vqelldgkiepeeftsklqe 50
                                      +++ev +   eL +++l   +++ e+f++  +e
  gi|488600051|ref|YP_007906522.1| 57 KAEEVLNWCWELrIKNLTAYAFSTENFRRDNEE 89
                                      555555555555577777888888888766555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.6e-05
                              TAFH   2 vkKcknFLatLiklagkqspevaenvkeLvqelldgkiepeeftsklqe 50 
                                        kK knF+ +L  +a    +e+ +++k++ +++ dgki+ ++  ++l e
  gi|488600051|ref|YP_007906522.1| 141 TKKYKNFFLNLA-IAYGGRQEILDAIKNILRNVKDGKIDLDDIDENLIE 188
                                       59******9995.7788889**********************9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); 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 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1747.40
//
Query:       gi|488600052|ref|YP_007906523.1|  [L=407]
Description: peptide chain release factor subunit 1 (aeRF-1) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-46  156.1   0.0      1e-45  155.3   0.0    1.4  1  eRF1_2          eRF1 domain 2
    3.7e-36  124.0   0.4    8.1e-36  122.9   0.4    1.6  1  eRF1_3          eRF1 domain 3
    1.1e-15   57.8   0.0    1.7e-15   57.1   0.0    1.4  1  eRF1_1          eRF1 domain 1
    1.4e-14   54.6   0.0    3.2e-14   53.4   0.0    1.6  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    4.1e-14   53.0   0.0    1.2e-13   51.4   0.0    1.8  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
  ------ inclusion threshold ------
      0.051   14.1   0.0       0.17   12.4   0.0    1.9  2  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
        0.1   12.4   0.1       0.75    9.6   0.0    2.3  2  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
       0.18   11.9   2.0         20    5.4   0.3    2.8  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3   0.0   4.6e-49     1e-45       2     133 .]     138     268 ..     137     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 4.6e-49
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +gliv+d++eA igll+g+r+evl+  +++vP+Kh++Ggqs+ rfeRlre +++ef+kkv+++a++a+l  + ++l 
  gi|488600052|ref|YP_007906523.1| 138 YGLIVIDRREAAIGLLRGKRIEVLNYASSMVPGKHRQGGQSSVRFERLREIAIHEFYKKVGDKATEALL-PHLENLV 213
                                       8******************************************************************88.58***** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                       g++++gp+++keef+++++l++el+k++i l+dvsy++esgl e++eka+++l++
  gi|488600052|ref|YP_007906523.1| 214 GVLIGGPSPTKEEFYEGEYLHHELQKRIIGLFDVSYTDESGLYELVEKAQDKLQE 268
                                       ****************************************************986 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.4   3.6e-39   8.1e-36       1     112 [.     271     403 ..     271     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 3.6e-39
                                       HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS................... CS
                            eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv................... 58 
                                       li+ekkl+++fl+e+akd g+++YG+eev+k+le+gAv+ LL+se+l+++r+++k++v                   
  gi|488600052|ref|YP_007906523.1| 271 LIREKKLISRFLHEIAKD-GLVAYGEEEVRKYLEIGAVDILLLSEDLRYDRVKYKCPVcgkeeivtlrqgmekipkc 346
                                       589***************.********************************99*99999****************** PP

                                       -HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  59 ketgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                       +e+g+++e+ve   ++ el+e +e++ga+ve+is+eseeG++l++afgGi+aiLR+k
  gi|488600052|ref|YP_007906523.1| 347 EEDGVTMEEVEredVVLELTELAESMGARVEFISTESEEGAMLMNAFGGIGAILRFK 403
                                       ********************************************************8 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   7.8e-19   1.7e-15       6     128 ..      15     131 ..      10     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 7.8e-19
                                       E..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT... CS
                            eRF1_1   6 r..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd... 77 
                                       +  +++++g++++tL++++d+ + ++ n ++++ s++a++++k +r         ++v   L+   ++++++k+   
  gi|488600052|ref|YP_007906523.1|  15 EleKMKGRGTELITLYIPPDKNIADVANQLRSELSQAANIKSKQTR---------TSVMAGLEAILQRLKYYKKppe 82 
                                       445899*************************************999.........8******************999 PP

                                       SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  78 agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                       +g++ +sG +  + +   +++ +t  +e+++p+ ++k++ ++sf+le+Lk++
  gi|488600052|ref|YP_007906523.1|  83 HGMVILSGNIDLGGG---KQKQITEIIEPPEPVPLYKYHcDSSFYLEPLKDM 131
                                       9**************...9*******************99**********98 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 !   53.4   0.0   1.4e-17   3.2e-14       2     136 ..     124     263 ..     124     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.4e-17
                    baeRF_family10   2 ylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAe 78 
                                       yl+pL + l+e + yg++++dr++a++   ++ ++e    +++ vpg++++gg+ s  rf+r +e  +++++k+v++
  gi|488600052|ref|YP_007906523.1| 124 YLEPLKDMLKEKKVYGLIVIDRREAAIGLLRGKRIEVLNYASSMVPGKHRQGGQ-SSVRFERLREIAIHEFYKKVGD 199
                                       799***************************************************.********************** PP

                    baeRF_family10  79 llaklleerg..verlvlgGdeeetaalld..rlpkalrarvvgtlplpvda..saaaVlekae 136
                                        ++++l ++   +  +++gG+   ++++ +   l+ +l++r++g ++++ ++     +++eka 
  gi|488600052|ref|YP_007906523.1| 200 KATEALLPHLenLVGVLIGGPSPTKEEFYEgeYLHHELQKRIIGLFDVSYTDesGLYELVEKAQ 263
                                       ********98889999*****999999985337************9999855455566666665 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   5.5e-17   1.2e-13       4     125 ..     140     263 ..     137     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 5.5e-17
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...v 77 
                                       +++++rr + a+g+++g++++  +  ++ v g++++GG+S  Rf+R re  + + +++v ++a + l ++ ++   v
  gi|488600052|ref|YP_007906523.1| 140 LIVIDRREA-AIGLLRGKRIEVLNYASSMVPGKHRQGGQSSVRFERLREIAIHEFYKKVGDKATEALLPHLENlvgV 215
                                       477889998.*********************************************************999999999* PP

                           acVLRF1  78 vlgGdrslvaevledarlaplatlare..elldvpdprravLedavrrar 125
                                       ++gG+  + +e+ e + l   ++l+++   l+dv   +++ L + v++a+
  gi|488600052|ref|YP_007906523.1| 216 LIGGPSPTKEEFYEGEYL--HHELQKRiiGLFDVSYTDESGLYELVEKAQ 263
                                       **************9663..345555555677777777887777777765 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 ?   -3.2   0.0       5.2   1.2e+04      83      97 ..     129     143 ..     127     151 .. 0.55
   2 ?   12.4   0.0   7.8e-05      0.17      45     130 ..     166     253 ..     162     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.2
                    baeRF_family12  83 kkrakegkferlvlv 97 
                                       k+++ke+k+  l+++
  gi|488600052|ref|YP_007906523.1| 129 KDMLKEKKVYGLIVI 143
                                       555555555555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.8e-05
                    baeRF_family12  45 sdrpGrsssggagrsameetdfkeqeeerFakeladeLkkrakeg..kferlvlvappetlgelrkh..lhkevkkr 117
                                       s+ pG++++gg++  ++  +  +e + ++F+k++ d+  ++++ +  +   + + +p +t +e+ +   lh e++kr
  gi|488600052|ref|YP_007906523.1| 166 SMVPGKHRQGGQS--SVRFERLREIAIHEFYKKVGDKATEALLPHleNLVGVLIGGPSPTKEEFYEGeyLHHELQKR 240
                                       5668888888877..445445555599************99876522555566889********97555******** PP

                    baeRF_family12 118 lvgeiaknltkhp 130
                                       + g ++  +t+++
  gi|488600052|ref|YP_007906523.1| 241 IIGLFDVSYTDES 253
                                       *********9987 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 ?   -0.4   0.0      0.42   9.4e+02      11      42 ..      57      93 ..      43     117 .. 0.77
   2 ?    9.6   0.0   0.00034      0.75      11      48 ..     286     323 ..     278     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.42
                                      HHHTE.EEESHHHHHHHHHTT....TESEEEEETTSS CS
                    Ribosomal_L7Ae 11 kkagk.lvlGlkevtkalerg....eaklvilAedve 42
                                      k++++ ++ Gl+ +++ l+      e  +vil+ +++
  gi|488600052|ref|YP_007906523.1| 57 KQTRTsVMAGLEAILQRLKYYkkppEHGMVILSGNID 93
                                      3334448888888888887554456888999999986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00034
                                       HHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHH CS
                    Ribosomal_L7Ae  11 kkagklvlGlkevtkalergeaklvilAedvepeekkk 48 
                                       +k g +++G +ev k le g + + +l+ed + ++ k 
  gi|488600052|ref|YP_007906523.1| 286 AKDGLVAYGEEEVRKYLEIGAVDILLLSEDLRYDRVKY 323
                                       567779************************98777654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.011        25       2      19 ..     113     129 ..     113     137 .. 0.72
   2 ?    5.4   0.3    0.0089        20       6      14 ..     323     331 ..     318     355 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                       Zn-ribbon_8   2 PiYeYrCeeCghefevlq 19 
                                       P+Y Y+C++     e+l 
  gi|488600052|ref|YP_007906523.1| 113 PLYKYHCDS-SFYLEPLK 129
                                       9******98.44555555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0089
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       Y+C  Cg+e
  gi|488600052|ref|YP_007906523.1| 323 YKCPVCGKE 331
                                       777777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2521.87
//
Query:       gi|488600053|ref|YP_007906524.1|  [L=559]
Description: arginyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-34  120.0   0.2    1.4e-34  119.6   0.2    1.2  1  tRNA-synt_1d     tRNA synthetases class I (R)
    1.2e-33  115.8   0.3    2.2e-32  111.7   0.1    2.9  2  DALR_1           DALR anticodon binding domain
    2.2e-13   50.6   0.5    9.5e-13   48.6   0.1    2.3  2  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    7.1e-09   35.1   0.0    0.00083   18.4   0.0    2.4  2  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0002   20.3   0.3      0.043   12.6   0.1    3.1  3  tRNA-synt_1g     tRNA synthetases class I (M)
      0.005   16.2   0.8      0.021   14.2   0.0    2.3  3  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0091   14.3   0.1      0.017   13.4   0.1    1.5  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
       0.29   11.9   2.2        5.9    7.6   0.5    3.0  2  DUF2203          Uncharacterized conserved protein (DUF2203)


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 !  119.6   0.2   6.5e-38   1.4e-34       2     337 ..      91     417 ..      90     429 .. 0.87

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 6.5e-38
                                       HHHHHCCTTTT.---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHH CS
                      tRNA-synt_1d   2 vssiLvqkrklqkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLia 78 
                                       v++iL +++ +   ++e+ +v+++++s n   ++h+Gh+r  iiGd+++r++  +G++v+   ++ D G+q  l + 
  gi|488600053|ref|YP_007906524.1|  91 VNTILDEDEDY-GSMTEQGEVLIEHTSANPDGPLHIGHIRNSIIGDTLARIFRKAGFNVTTQYYMNDMGRQVALAVL 166
                                       67889999998.78999***********************************************************9 PP

                                       HHHHHTTTTTTS-----SCCCHHHHHHHHCC....CSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1d  79 ylekkqdekllqeqelqdLeafykeakkdyd....eeeifaerarnyvvkLqsgdedirklwkllvditrtelqkly 151
                                       ++++ +      e++   + + y e+++ ++    e e ++ +a  ++   + g e+  + ++++v+ + t   ++ 
  gi|488600053|ref|YP_007906524.1| 167 GVRRFGLSD---EKPDHAVAKAYIEINRLMEdnpeEKEKIQAEADRIMLDYELGKEYAVEEFRRVVETALTGIMETL 240
                                       999987554...566677777788887765411115566******************9999999************* PP

                                       HHCT---EC.--CC..CCCCCHHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHH CS
                      tRNA-synt_1d 152 drldvtlie.rGes..lykeslneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaaker 225
                                        +l++   e   es  + +  +++++k++++ gl   +dGa  ++l+  g +  vvv++++G++ly t+D+a   + 
  gi|488600053|ref|YP_007906524.1| 241 SNLNIEHDEvVWESefIRNGYVDKVLKKIEELGLLL-KDGAWFIDLQSKGYEKNVVVRRENGTTLYITRDLAY--HA 314
                                       *****998885555548999*************985.79********************************86..56 PP

                                       HHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHH CS
                      tRNA-synt_1d 226 keelkadkvlyvidsrqslhlqqiflilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealera 302
                                        +++++++ + ++ s  +l  +q+  il+ +g +p   ++   +f  +    + +++trkG+ +  +dl+    + a
  gi|488600053|ref|YP_007906524.1| 315 WKNENFERFINILGSDHKLIGKQLSDILQLLGLKPP--EIVFFEFVSL---PEGSMSTRKGKFISADDLIRRVYNEA 386
                                       78999***************************9664..4444555444...6779********************** PP

                                       HHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCCCC CS
                      tRNA-synt_1d 303 lqlikeknkdkvlqadelekvaeavgvgaikyaDl 337
                                        +l+k++n       +e++++a +v+vga+++  +
  gi|488600053|ref|YP_007906524.1| 387 YSLLKDRNFS----EEEKKEIARSVAVGALRFDFV 417
                                       **99888866....99*************998655 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.26   5.9e+02     100     117 ..     334     351 ..     331     353 .. 0.85
   2 !  111.7   0.1   9.7e-36   2.2e-32       1     119 []     443     559 .]     443     559 .] 0.97

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHTT----S CS
                            DALR_1 100 vrqvLangLdlLGieape 117
                                       + + L++ L+lLG+++pe
  gi|488600053|ref|YP_007906524.1| 334 IGKQLSDILQLLGLKPPE 351
                                       5678999*********98 PP

  == domain 2  score: 111.7 bits;  conditional E-value: 9.7e-36
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       +qy+haR++si+rka e+g  + e    +  + ee++L+ +l +f  v+e++++el+p++ a+yl ++a  f++fY+
  gi|488600053|ref|YP_007906524.1| 443 IQYSHARACSIMRKAVEKGMPDLEISGEI-CTMEERKLILTLSKFTTVIERILRELRPNVFADYLMDVAIRFNDFYT 518
                                       7******************9998888887.999******************************************** PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                        ++vlke++e++ ++RLa+v+a+r vL+ngL+lLGi+a+ekm
  gi|488600053|ref|YP_007906524.1| 519 THPVLKESSEVR-MHRLAIVDATRIVLKNGLELLGIDALEKM 559
                                       **********99.****************************9 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   4.2e-16   9.5e-13       5      84 ..       7      81 ..       3      82 .. 0.78
   2 ?   -2.1   0.1       2.7   6.2e+03      14      37 ..     189     214 ..     179     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 4.2e-16
                                      HHHHHHHHHHHSS-HHHHGGG-E.-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT.E CS
                   Arg_tRNA_synt_N  5 eaiaealkkaagadleeeeivie.kpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagpGF 80
                                      + +++al+++   +      ++    ++++++D+++ va++lak+  ++P+eiAeei+e+l ++ +  i +ve++  G+
  gi|488600053|ref|YP_007906524.1|  7 KDVEKALESVL--GY-----SVSnFVRESEHADLSCTVAFKLAKERERKPNEIAEEIVEELVDEISeyIGSVEAVN-GY 77
                                      45555555552..22.....333134789********************************9995556******88.9* PP

                                      EEEE CS
                   Arg_tRNA_synt_N 81 iNff 84
                                      iNf 
  gi|488600053|ref|YP_007906524.1| 78 INFN 81
                                      **95 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                                       HH..SS-HHHHGGG-E-.SSGGG-SE CS
                   Arg_tRNA_synt_N  14 aa..gadleeeeiviekpknpkfGDy 37 
                                       +    +d+ ee+++i++ ++  + Dy
  gi|488600053|ref|YP_007906524.1| 189 INrlMEDNPEEKEKIQAEADRIMLDY 214
                                       22555567777888888888888888 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 !   14.1   0.0   7.1e-06     0.016      20      71 ..     103     157 ..      86     161 .. 0.81
   2 !   18.4   0.0   3.7e-07   0.00083     239     310 ..     326     393 ..     310     440 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-06
                      tRNA-synt_1f  20 a..ekdevvve.sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                       +  e++ev++e + + p G++HiG +r+ + +d +ar +rk g +v + ++++dm
  gi|488600053|ref|YP_007906524.1| 103 SmtEQGEVLIEhTSANPDGPLHIGHIRNSIIGDTLARIFRKAGFNVTTQYYMNDM 157
                                       3336778877648899******************************999999998 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.7e-07
                      tRNA-synt_1f 239 paGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilr 310
                                         G Dh       ++ s+i ++lg ++Pe v +e+++l +g  ms  kG++++ +d+++ + +e  ++l  r
  gi|488600053|ref|YP_007906524.1| 326 ILGSDHKL---IGKQLSDILQLLGLKPPEIVFFEFVSLPEG-SMSTRKGKFISADDLIRRVYNEAYSLLKDR 393
                                       56888888...4567899**********************9.9**************998888877776555 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   1.9e-05     0.043      10      40 ..     119     149 ..     110     165 .. 0.84
   2 !    4.2   0.0    0.0065        14     311     353 ..     348     388 ..     309     410 .. 0.81
   3 ?   -2.0   0.0       0.5   1.1e+03     191     229 ..     435     469 ..     425     497 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                                       -SS---HHHHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevl 40 
                                       ++g+lH+Gh+++ i++D +aR  r+ g +v+
  gi|488600053|ref|YP_007906524.1| 119 PDGPLHIGHIRNSIIGDTLARIFRKAGFNVT 149
                                       6799***********************9986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0065
                                       --S-EEEE--EEE--------------HHHHHHHH-HHHHHHH CS
                      tRNA-synt_1g 311 lpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYy 353
                                       +p ++v  e++ + ++ +S+ +g ++ a++++ r+  ++  Y 
  gi|488600053|ref|YP_007906524.1| 348 KPPEIVFFEFVSLPEGSMSTRKGKFISADDLIRRVYNEA--YS 388
                                       46678889************************9977775..44 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.5
                                       GHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ES CS
                      tRNA-synt_1g 191 fekklkewieeeekeleenvkkivkewlkegLkdlaisr 229
                                       fe++  ++i+      + ++ +i+++ +++g+ dl is 
  gi|488600053|ref|YP_007906524.1| 435 FERQTASYIQY----SHARACSIMRKAVEKGMPDLEISG 469
                                       56666666633....346777777777888888887774 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 ?   -1.1   0.0      0.41   9.3e+02     101     145 ..      57     107 ..      22     121 .. 0.67
   2 !   14.2   0.0   9.2e-06     0.021      23      96 ..     123     249 ..     117     292 .. 0.75
   3 ?   -3.4   0.0       2.2   4.9e+03     136     179 ..     384     427 ..     369     437 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.41
                                       GGGGHHHHHHHHHHH......HHTTSEEE-TTS-EEE-GGG-TTTTTTTT- CS
                      tRNA-synt_1e 101 vsekvdeiielvekl......iekgyaYavsdgdvyfdvskkeeYgklskq 145
                                       v e vdei e++  +      i+ + +Y+  ++ v     ++e+Yg++ +q
  gi|488600053|ref|YP_007906524.1|  57 VEELVDEISEYIGSVeavngyINFNASYEFLEDAVNTILDEDEDYGSMTEQ 107
                                       444555555554443110111555556777668888778888888888776 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.2e-06
                                       -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-............................ CS
                      tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks............................ 71 
                                        h+Gh R+ ++ D l+ri++++g++v+    + D+  ++ +      ++                            
  gi|488600053|ref|YP_007906524.1| 123 LHIGHIRNSIIGDTLARIFRKAGFNVTTQYYMNDMGRQVALAVLGVRRFglsdekpdhavakayieinrlmednpee 199
                                       7*************************988888888877777666666666667777777777777777777777777 PP

                                       .........................HHHHHHHHHHHHHHHHHHTT----S CS
                      tRNA-synt_1e  72 .........................vkelaekfieefkkdleaLnvlkpt 96 
                                                                +++++e+  +  ++ l++Ln+ + +
  gi|488600053|ref|YP_007906524.1| 200 kekiqaeadrimldyelgkeyaveeFRRVVETALTGIMETLSNLNIEHDE 249
                                       77777777777777777777777776666777777777777777766654 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.2
                                       -TTTTTTTT--HHHHHHT----S--S-SSTT-EEEEEE--TTS- CS
                      tRNA-synt_1e 136 keeYgklskqnleelelgaegevseekkdkkDfaLWkaskegep 179
                                       +e Y+ l+ +n +e e+++  +  +    + Df+    +k+   
  gi|488600053|ref|YP_007906524.1| 384 NEAYSLLKDRNFSEEEKKEIARSVAVGALRFDFVRVSPEKPMTF 427
                                       56677777777776666666666666666666665555555555 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   7.4e-06     0.017      32      73 ..     117     158 ..      98     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-06
                       tRNA-synt_1  32 PyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaG 73 
                                        +  G lHiGh+ ++++ d++ r+ r  G++v+ +  +   G
  gi|488600053|ref|YP_007906524.1| 117 ANPDGPLHIGHIRNSIIGDTLARIFRKAGFNVTTQYYMNDMG 158
                                       57789**************************99887666666 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.13   2.8e+02      41      82 ..      43      76 ..       6      89 .. 0.57
   2 ?    7.6   0.5    0.0026       5.9      61      95 ..     261     294 ..     180     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
                           DUF2203 41 aeaekseaaeleaeleeleaeieelveeieelGvevkdleag 82
                                      +e+e++  + +e+ +eel +ei+e++  +e++         g
  gi|488600053|ref|YP_007906524.1| 43 KERERKPNEIAEEIVEELVDEISEYIGSVEAVN--------G 76
                                      222333355555555666666666665555543........4 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0026
                           DUF2203  61 eieelveeieelGvevkdleaglvDFpakldgeev 95 
                                        +++++++ieelG  +kd  a+ +D  +k  +++v
  gi|488600053|ref|YP_007906524.1| 261 YVDKVLKKIEELGLLLKDG-AWFIDLQSKGYEKNV 294
                                       578999************9.6*****999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 3548.38
//
Query:       gi|488600054|ref|YP_007906525.1|  [L=547]
Description: methylmalonyl-CoA mutase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-243  808.7   0.4   2.1e-243  808.6   0.4    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
      0.028   13.9   0.0      0.068   12.7   0.0    1.6  1  Flu_M1         Influenza Matrix protein (M1)
       0.11   12.9   3.4       0.26   11.8   3.4    1.6  1  KGK            KGK domain


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.6   0.4  3.4e-247  2.1e-243       1     513 []      26     539 ..      26     539 .. 0.99

  Alignments for each domain:
  == domain 1  score: 808.6 bits;  conditional E-value: 3.4e-247
                     MM_CoA_mutase   1 kTaegievkplYtaedleek.klgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtgls 76 
                                       kTa+g+ev+++Yt+ed++ + + + s+PG +PftRGv++tmyrgr Wt+rqyagf+taeetn+ryk+lLe+Gqtgls
  gi|488600054|ref|YP_007906525.1|  26 KTASGFEVDRVYTPEDVTIDyEEELSFPGAYPFTRGVYPTMYRGRLWTMRQYAGFGTAEETNKRYKYLLEQGQTGLS 102
                                       69***************444456778*************************************************** PP

                     MM_CoA_mutase  77 vafdlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdlek 153
                                       vafdlpt++gyDsdhp+a+gevGk+Gvaid++edm++l+dgi+ld+vs+smtin++++++l+my+a+ae+qgv++++
  gi|488600054|ref|YP_007906525.1| 103 VAFDLPTQIGYDSDHPMAAGEVGKVGVAIDTIEDMQILFDGIPLDRVSTSMTINSTCAQVLSMYIAIAESQGVSRAQ 179
                                       ***************************************************************************** PP

                     MM_CoA_mutase 154 lsgtiqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvr 230
                                       l+gt+qnD+Lke++argtyi+ppe s++l++dii ++akevpk+n+is+sgyh++eaGat+vqE+AftladG++Yv+
  gi|488600054|ref|YP_007906525.1| 180 LRGTVQNDMLKEYIARGTYIFPPEASIKLATDIIMFCAKEVPKWNSISISGYHMEEAGATPVQEVAFTLADGITYVE 256
                                       ***************************************************************************** PP

                     MM_CoA_mutase 231 alleaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvN 307
                                       +++e+G++vdefaprlsFffa+g++  ee+Ak+RAaRrlWa+i+k++fgak+++s++lr+h+qT+g++ltaq+p++N
  gi|488600054|ref|YP_007906525.1| 257 KVIERGMKVDEFAPRLSFFFAAGNNLLEEVAKFRAARRLWAKIMKDRFGAKDKRSMMLRFHTQTAGCTLTAQQPENN 333
                                       ***************************************************************************** PP

                     MM_CoA_mutase 308 ilRttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekaw 384
                                       i+R+t++alaAvlggtqslhtnsfDeal+lPte+++riA++tq+i+aeEsgva+vvDPlgGSyy+E+LTd+++e+a+
  gi|488600054|ref|YP_007906525.1| 334 IIRVTIQALAAVLGGTQSLHTNSFDEALSLPTEKAVRIALRTQQIIAEESGVADVVDPLGGSYYLEWLTDKIEEEAM 410
                                       ***************************************************************************** PP

                     MM_CoA_mutase 385 klfqeieeaGGmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlea 461
                                       k++++i+e+GGm+kaie+G++q+ei++sa+++qk+i+s++ ++vGvNk+ + eee +le+l+ide++ ++q+erl++
  gi|488600054|ref|YP_007906525.1| 411 KYIEKIDEMGGMIKAIEQGFPQREIQKSAYEKQKKIDSGEITVVGVNKY-QIEEEIQLEILRIDENMVRKQIERLKR 486
                                       *************************************************.5666899******************** PP

                     MM_CoA_mutase 462 lraerdeaavkaaLaalgeaarse.nllaraveaaralatlGeisdaleevfg 513
                                       +r++rd+++v++aL++l++ a+s+ nl++ ++e+++a+atlGei+d+l+evfg
  gi|488600054|ref|YP_007906525.1| 487 FRDSRDKSKVESALDKLRRSAESGdNLMPPILECVKAKATLGEITDVLREVFG 539
                                       **********************889**************************98 PP

>> Flu_M1  Influenza Matrix protein (M1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05     0.068       3      61 ..     248     306 ..     246     313 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHTTS-SSHHHHHHHHHHHHHHCT-S--HHHHHHHHHT-SSS-HHHHHHHHH CS
                            Flu_M1   3 lteviayllsliedGelkaelaekledvfaGketdlevllewlktkrilsdltkallGa 61 
                                       l++ i+y+  +ie G    e+a +l  +fa  +  le + ++  ++r+ +++ k  +Ga
  gi|488600054|ref|YP_007906525.1| 248 LADGITYVEKVIERGMKVDEFAPRLSFFFAAGNNLLEEVAKFRAARRLWAKIMKDRFGA 306
                                       6899********************************************99999987776 PP

>> KGK  KGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.4   4.3e-05      0.26      23     115 ..     419     506 ..     400     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.3e-05
                               KGK  23 isklkealeklfknkklkkeleeelkeqksaeikietkseekwfkeGidceiLkigskgWqkGklkikvsleFipde 99 
                                       ++ +++a+e+ f +++++k+ +e++k+  s+ei++    ++ +++e i+ eiL i+ +  +k   +    l+   d 
  gi|488600054|ref|YP_007906525.1| 419 MGGMIKAIEQGFPQREIQKSAYEKQKKIDSGEITVV-GVNKYQIEEEIQLEILRIDENMVRKQIER----LKRFRDS 490
                                       556789999************************996.89*****************9998884333....5556788 PP

                               KGK 100 peikepespLddlRre 115
                                        ++++ es Ld lRr+
  gi|488600054|ref|YP_007906525.1| 491 RDKSKVESALDKLRRS 506
                                       888999*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3578.13
//
Query:       gi|488600055|ref|YP_007906526.1|  [L=139]
Description: hypothetical protein Asulf_00510 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   68.5   4.3    3.3e-19   68.5   4.3    2.2  2  Biotin_lipoyl    Biotin-requiring enzyme
      6e-13   48.4   0.9    4.2e-08   32.9   0.1    3.1  3  Biotin_lipoyl_2  Biotin-lipoyl like
    4.4e-06   27.3   1.3     0.0027   18.4   0.1    3.0  3  HlyD_3           HlyD family secretion protein
    9.6e-05   22.5   0.6    0.00022   21.4   0.6    1.8  1  Peptidase_M23    Peptidase family M23
    0.00033   20.4   5.0        0.1   12.3   2.6    3.0  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
    0.00033   19.9   2.1      0.084   12.1   0.1    2.6  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0026   17.7   5.3      0.068   13.1   0.1    3.4  4  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0049   16.7   2.0     0.0049   16.7   2.0    2.2  2  GCV_H            Glycine cleavage H-protein
      0.005   17.6   2.9       0.37   11.6   0.3    2.1  2  PCB_OB           Penicillin-binding protein OB-like domain
     0.0071   16.4   1.5        2.2    8.4   0.0    2.5  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
  ------ inclusion threshold ------
       0.02   14.9   5.6       0.59   10.1   0.1    2.4  2  DUF2118          Uncharacterized protein conserved in archaea
       0.02   15.4   2.1        1.7    9.2   0.1    2.9  3  DUF2190          Uncharacterized conserved protein (DUF2190)


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.6      0.81   1.2e+03      20      20 ..      58      58 ..      22      70 .. 0.56
   2 !   68.5   4.3   2.2e-22   3.3e-19       3      73 .]      73     138 ..      71     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.81
                                      S CS
                     Biotin_lipoyl 20 l 20
                                       
  gi|488600055|ref|YP_007906526.1| 58 R 58
                                      2 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 2.2e-22
                                       EEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   3 iksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                       +k+ m+G++++     vl+++G+++++g+ ++++eamKme+ i+apk+G++++i vkeGd v++gd++a i
  gi|488600055|ref|YP_007906526.1|  73 VKVSMAGVITK-----VLKNEGEEIEEGEDILILEAMKMENAISAPKSGKITKITVKEGDRVSAGDVVAYI 138
                                       77888888888.....****************************************************987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.56   8.4e+02       7      20 ..      26      39 ..      21      42 .. 0.85
   2 !   14.2   0.0   1.9e-05     0.028       4      42 ..      72     110 ..      64     111 .. 0.92
   3 !   32.9   0.1   2.8e-11   4.2e-08       5      33 ..     110     138 ..     108     139 .] 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.56
                   Biotin_lipoyl_2  7 apvsGrVaqlnVkd 20
                                       +vsG+ a++ V++
  gi|488600055|ref|YP_007906526.1| 26 VSVSGKTATIKVEE 39
                                      68999999999986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.9e-05
                   Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqlal 42 
                                       +++ + +G++++++  +G ++++G  +++l+  + ++a+
  gi|488600055|ref|YP_007906526.1|  72 PVKVSMAGVITKVLKNEGEEIEEGEDILILEAMKMENAI 110
                                       678888**************************9999997 PP

  == domain 3  score: 32.9 bits;  conditional E-value: 2.8e-11
                   Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                       I+ap sG+++++ Vk+G+rV aGdv a +
  gi|488600055|ref|YP_007906526.1| 110 ISAPKSGKITKITVKEGDRVSAGDVVAYI 138
                                       9************************9987 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.56   8.3e+02      68      91 ..      11      40 ..       1      65 [. 0.57
   2 ?    6.0   0.0     0.013        19       2      28 ..      73      99 ..      72     106 .. 0.89
   3 !   18.4   0.1   1.8e-06    0.0027       2      30 ..     110     138 ..     109     139 .] 0.95

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.56
                            HlyD_3 68 tlkgkierisp.....tvdaktgaykv.ev 91
                                      +++ ++e+i p     +v  kt ++kv ev
  gi|488600055|ref|YP_007906526.1| 11 KYDVEVEEIEPnvfsvSVSGKTATIKVeEV 40
                                      556666666663332222224444444334 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                            HlyD_3  2 lrApvdGvvvelnveegevvqagdell 28
                                      ++++ +Gv++++  +ege +++g+ +l
  gi|488600055|ref|YP_007906526.1| 73 VKVSMAGVITKVLKNEGEEIEEGEDIL 99
                                      678999******************987 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.8e-06
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                       + Ap +G+++++ v+eg+ v+agd+++ i
  gi|488600055|ref|YP_007906526.1| 110 ISAPKSGKITKITVKEGDRVSAGDVVAYI 138
                                       78*************************98 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.6   1.4e-07   0.00022       4      72 ..      61     138 ..      58     139 .] 0.71

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                                       SSEEEEETTT-EEEESSSEEEEEEEEET....TTEEEEEEEECTCEEEEEEE.....ESEESS-TTEEE-TTCEEEE CS
                     Peptidase_M23   4 kGidiaapkgtpVlAaadGtVvfagkke....gyGnvviidhgdgystlyah.....lskisvkegqkVkaGqvIGt 71 
                                       k+ +++a +gtpV+  ++G+++++ k+e    + G+ ++i  + +++  +       + ki+vkeg++V+aG+v+++
  gi|488600055|ref|YP_007906526.1|  61 KAEKVEAGEGTPVKVSMAGVITKVLKNEgeeiEEGEDILILEAMKMENAISApksgkITKITVKEGDRVSAGDVVAY 137
                                       67789999*************88877555666445555555544444444331222378888*************98 PP

                                       E CS
                     Peptidase_M23  72 v 72 
                                       +
  gi|488600055|ref|YP_007906526.1| 138 I 138
                                       7 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   2.6   6.9e-05       0.1      12     110 ..      14     108 ..       3     115 .. 0.75
   2 !    6.4   0.0    0.0048       7.2      81     101 ..     116     136 ..     111     139 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                                       EEGGGSSSHHHHT-TTSEEEEEEE-SSEEEES--EEEEE--SSSSEEEEESSSS-EEEEE-SSSTTTTTTTTEEES- CS
                        PTS_EIIA_1  12 vpleevpDevfaekmlGdGvaiepsegkvvapvdGkvekvfptkHaigiktddgvevlihiGidtvklkgegFellv 88 
                                       v++ee++ +vf+  + G+ ++i+ +e  +  pv+ kvekv   +     +++++ve        +v++ g   ++l 
  gi|488600055|ref|YP_007906526.1|  14 VEVEEIEPNVFSVSVSGKTATIKVEEVSFAKPVEEKVEKVERVERV---EKAEKVEAG-EGTPVKVSMAGVITKVLK 86 
                                       57899*********************9********99999874433...333333311.111125788899999999 PP

                                       ---SEE-SEEEEEEE-HHHHGG CS
                        PTS_EIIA_1  89 kegdkVkagdklvevdleaikk 110
                                       +eg+++++g+ ++ ++  ++++
  gi|488600055|ref|YP_007906526.1|  87 NEGEEIEEGEDILILEAMKMEN 108
                                       9999999999998887777766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0048
                                       TTTEEES----SEE-SEEEEE CS
                        PTS_EIIA_1  81 gegFellvkegdkVkagdklv 101
                                       g+  ++ vkegd+V+agd ++
  gi|488600055|ref|YP_007906526.1| 116 GKITKITVKEGDRVSAGDVVA 136
                                       777899************986 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 !    7.5   0.1    0.0014       2.1      22      59 ..      73     109 ..      64     111 .. 0.83
   2 !   12.1   0.1   5.6e-05     0.084     109     139 ..     108     138 ..     102     139 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23  22 vsarveGwveklyvnatgdkVkkGqpLaelyspelvaa 59 
                                       v+ +++G ++k+  n +g+++++G+ ++ l++ ++ +a
  gi|488600055|ref|YP_007906526.1|  73 VKVSMAGVITKVLKN-EGEEIEEGEDILILEAMKMENA 109
                                       778899999999999.9999999999999988877665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 109 vtvkapisGvVteknvreGqyvqpgdtlfti 139
                                         ++ap sG +t+ +v eG++v++gd+++ i
  gi|488600055|ref|YP_007906526.1| 108 NAISAPKSGKITKITVKEGDRVSAGDVVAYI 138
                                       5688999999999999999999999988766 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 ?    0.6   0.1      0.36   5.4e+02      69      87 ..      23      42 ..       8      55 .. 0.70
   2 !    5.9   0.1    0.0081        12      46      90 ..      53      94 ..      41     101 .. 0.66
   3 !   13.1   0.1   4.6e-05     0.068      38      81 ..      78     122 ..      71     123 .. 0.86
   4 !    9.1   0.2   0.00083       1.2      38      59 ..     115     136 ..     103     139 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.36
                            RnfC_N 69 vha.svsGtVkaiekrlvah 87
                                      v++ svsG+  +i+  +v+ 
  gi|488600055|ref|YP_007906526.1| 23 VFSvSVSGKTATIKVEEVSF 42
                                      55448999988887665554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0081
                            RnfC_N 46 vkvgdkVlkGqkiaeaegfvsapvhasvsGtVkaiekrlvahgsg 90
                                      v+  ++V+k +k+ + eg+   pv  s++G ++++ k +  + ++
  gi|488600055|ref|YP_007906526.1| 53 VERVERVEKAEKVEAGEGT---PVKVSMAGVITKVLKNEGEEIEE 94
                                      4445566666666666665...99*******99998776665555 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 4.6e-05
                            RnfC_N  38 iGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81 
                                       +G  +k+l ++g+++++G+ i   e+  +  ++ a+ sG++++i+
  gi|488600055|ref|YP_007906526.1|  78 AGVITKVLKNEGEEIEEGEDILILEAmKMENAISAPKSGKITKIT 122
                                       6888999************9887776556999**********995 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00083
                            RnfC_N  38 iGapakplvkvgdkVlkGqkia 59 
                                        G+ +k+ vk+gd+V  G+++a
  gi|488600055|ref|YP_007906526.1| 115 SGKITKITVKEGDRVSAGDVVA 136
                                       5888999***********9998 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.0      0.33   4.9e+02      39      55 ..      44      60 ..      10      76 .. 0.54
   2 !   16.7   2.0   3.3e-06    0.0049      27      74 ..      75     121 ..      58     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.33
                                      --TT-EE-TT-EEEEEE CS
                             GCV_H 39 pevgtkvkkgeslaavE 55
                                      ++v +kv+k e +  vE
  gi|488600055|ref|YP_007906526.1| 44 KPVEEKVEKVERVERVE 60
                                      22333333333333333 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.3e-06
                                       HHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                             GCV_H  27 qeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                                        +++g ++   l+++g+++++ge++ ++E+ K+   + ap sG+++++
  gi|488600055|ref|YP_007906526.1|  75 VSMAGVITK-VLKNEGEEIEEGEDILILEAMKMENAISAPKSGKITKI 121
                                       555665555.59*********************************987 PP

>> PCB_OB  Penicillin-binding protein OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.3   0.00025      0.37      39      85 ..      16      61 ..       6      75 .. 0.83
   2 !    6.9   0.5    0.0067        10      35      93 ..      77     135 ..      57     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                                      EEEEETTEEEEEETTS-EEEEEGGGGTTTGCCTTTS-B---CCCHCC CS
                            PCB_OB 39 Vlsvseksarvglrdgetgtipleglkwarkvlsdkkqgkapksasd 85
                                      V +++++ ++v + +g+t+ti++e++++a++v ++ ++ ++++++++
  gi|488600055|ref|YP_007906526.1| 16 VEEIEPNVFSVSV-SGKTATIKVEEVSFAKPVEEKVEKVERVERVEK 61
                                      7788999999999.9****************9877777777666554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0067
                                       EEEEEEEEETTEEEEEETTS-EEEEEGGGGTTTGCCTTTS-B---CCCHCCC--TTEEE CS
                            PCB_OB  35 rpAvVlsvseksarvglrdgetgtipleglkwarkvlsdkkqgkapksasdvlkpGdvv 93 
                                        ++v+++v +++ +   ++++   +++ +++ a  + +++k  k   +  d++++Gdvv
  gi|488600055|ref|YP_007906526.1|  77 MAGVITKVLKNEGEEIEEGEDILILEAMKMENAISAPKSGKITKITVKEGDRVSAGDVV 135
                                       46888999888888766677888888889999999877777777778899********9 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.3    0.0045       6.7      39      69 ..      75     103 ..      47     107 .. 0.76
   2 !    8.4   0.0    0.0014       2.2      49      67 ..     120     138 ..     106     139 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0045
                                       HHHHHTTTEEEESS-TT-EEETTEEEEEEEE CS
                         QRPTase_N  39 vfellpglevellvkDGervekgdvlleieG 69 
                                       v   + g+ +++l+++Ge++e+g+ +l +e+
  gi|488600055|ref|YP_007906526.1|  75 VSM-A-GVITKVLKNEGEEIEEGEDILILEA 103
                                       433.4.78899***************99876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0014
                                       EESS-TT-EEETTEEEEEE CS
                         QRPTase_N  49 ellvkDGervekgdvllei 67 
                                       ++ vk+G+rv++gdv++ i
  gi|488600055|ref|YP_007906526.1| 120 KITVKEGDRVSAGDVVAYI 138
                                       6899************987 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 ?    7.0   2.6    0.0034       5.1      56     130 ..      46     118 ..       8     122 .. 0.80
   2 ?   10.1   0.1   0.00039      0.59      90     112 ..     116     138 ..     109     139 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0034
                           DUF2118  56 leekvtrdviivlpderklillkkGdklklipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvV 130
                                       +eekv +   ++ +++ + +   +G+ +k + ++gv   +  ++G+++eeg+ +  + + k e   + ap+ g++
  gi|488600055|ref|YP_007906526.1|  46 VEEKVEKVERVERVEKAEKVEAGEGTPVK-VSMAGVITKVLKNEGEEIEEGEDILILEAMKME-NAISAPKSGKI 118
                                       56666666667777777777778888886.8999*******************9999999988.56777777776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00039
                           DUF2118  90 gvkvtlivdvGdrveegdtlaav 112
                                       g    ++v++Gdrv  gd++a++
  gi|488600055|ref|YP_007906526.1| 116 GKITKITVKEGDRVSAGDVVAYI 138
                                       5566789**************98 PP

>> DUF2190  Uncharacterized conserved protein (DUF2190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.19   2.9e+02      28      53 ..      19      46 ..       5      68 .. 0.68
   2 ?    9.2   0.1    0.0011       1.7      37      66 ..      66      99 ..      59     112 .. 0.84
   3 ?    2.9   0.1     0.099   1.5e+02       3      24 ..     115     136 ..     113     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.19
                           DUF2190 28 l..kvlGVAatdaaaGetvtvaveGvf....v 53
                                      +  +v+ V +    +G+t+t++ve v     v
  gi|488600055|ref|YP_007906526.1| 19 IepNVFSVSV----SGKTATIKVEEVSfakpV 46
                                      4556777775....999999999998777441 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                           DUF2190 37 daaaGetvtvaveGvf....veaaaaiavGdkVy 66
                                      +a +G +v+v ++Gv+    ++ +++i++G+ + 
  gi|488600055|ref|YP_007906526.1| 66 EAGEGTPVKVSMAGVItkvlKNEGEEIEEGEDIL 99
                                      6778999999*****9***999******998765 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.099
                           DUF2190   3 dgksldvtvaaaaaitagqvvv 24 
                                        gk+ ++tv+++  ++ag+vv+
  gi|488600055|ref|YP_007906526.1| 115 SGKITKITVKEGDRVSAGDVVA 136
                                       5778888999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); 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:                        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 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 984.55
//
Query:       gi|488600056|ref|YP_007906527.1|  [L=40]
Description: hypothetical protein Asulf_00511 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 256.93
//
Query:       gi|488600057|ref|YP_007906528.1|  [L=518]
Description: methylmalonyl-CoA decarboxylase alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-201  668.6   0.1     6e-201  668.4   0.1    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    2.8e-05   23.7   0.1     0.0001   21.9   0.0    1.8  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.4   0.1  6.7e-205    6e-201       1     494 []      29     516 ..      29     516 .. 0.99

  Alignments for each domain:
  == domain 1  score: 668.4 bits;  conditional E-value: 6.7e-205
                                       SSCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSG CS
                    Carboxyl_trans   1 kehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgp 76 
                                       k+h+ Gkltareri++lld+gsF e++ ++++r t++g+ k  lp+dgvvtg+G+++Gr v+v+aqd+tv+ggslg+
  gi|488600057|ref|YP_007906528.1|  29 KQHELGKLTARERIEILLDKGSFNEINPFVEKRNTDFGLdKVYLPGDGVVTGYGTIDGRPVAVFAQDFTVMGGSLGE 105
                                       699************************************9889********************************** PP

                                       GGCEEECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHH CS
                    Carboxyl_trans  77 akgekllkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpal 153
                                       ++g k+ ++++ a+k g p+ig+ndsgGa  riqegv++l+g+G+if++n++asg+Ipqis+++g+caGg++Y+pa+
  gi|488600057|ref|YP_007906528.1| 106 MHGYKIAYIMDFAMKMGIPIIGLNDSGGA--RIQEGVDALKGYGDIFYRNTLASGVIPQISVIMGPCAGGAVYSPAI 180
                                       *****************************..********************************************** PP

                                       TSEEEEETT.EEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSG CS
                    Carboxyl_trans 154 gdrvimvee.tskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnn 229
                                       gd++im+++ + ++f+tGp vik+v+g ee+t +elgG+++h+ ksG++h++aedd +al+l+rkl+sylP    nn
  gi|488600057|ref|YP_007906528.1| 181 GDFIIMTKNkSCYMFITGPGVIKTVTG-EEITPQELGGWEAHAVKSGNCHIVAEDDVHALQLVRKLISYLP---LNN 253
                                       *********999***************.*******************************************...999 PP

                                       GSS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE-- CS
                    Carboxyl_trans 230 resaPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnet 303
                                        +++P+++t d+p r    +++i+P++++kpyDvr+vi+++vd+geF+Ei+++yA++  vGfAr++G++vG+vAn++
  gi|488600057|ref|YP_007906528.1| 254 LDDPPVIQTGDDPARTtprIYDIIPEDPQKPYDVRDVIREVVDNGEFFEIHANYAPNATVGFARMDGRSVGIVANNP 330
                                       99*************999888******************************************************** PP

                                       SEEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEE CS
                    Carboxyl_trans 304 rveaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkay 380
                                       + +aG  l+ +s++K arf+r+cda+n+P+++++dv+G+l+G +qeyggi++hGak+++a++ea+vP +t+ilrkay
  gi|488600057|ref|YP_007906528.1| 331 KFFAG-TLDVNSSDKIARFVRFCDAFNIPIITFMDVPGYLPGVDQEYGGIIRHGAKILYAYSEATVPLVTIILRKAY 406
                                       *****.*********************************************************************** PP

                                       HHHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Carboxyl_trans 381 GGayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaarg 457
                                       GGay++m+sk++gad+v+a pta+iaV+gpega+ei+frke++ ++    ++++++ +k++ey+e ++npy+aa+rg
  gi|488600057|ref|YP_007906528.1| 407 GGAYIAMGSKHLGADIVYAYPTAEIAVMGPEGAAEIVFRKEIKSSD----NPEETKLQKIAEYRERFANPYRAASRG 479
                                       *******************************************999....99************************* PP

                                       HHHTTSSHHHHHHTTSSSEEEHGGGHHHHHHHHHHHH CS
                    Carboxyl_trans 458 faDavidpsetraklvialelewkkarklparkrrni 494
                                       ++D+vidp+ tr k++ al++  +k++klp++k++ni
  gi|488600057|ref|YP_007906528.1| 480 YIDDVIDPKFTRSKIISALRIIDTKREKLPPKKHGNI 516
                                       ***********************************97 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.14   1.2e+03      19      81 ..      77     139 ..      71     179 .. 0.67
   2 !   21.9   0.0   1.1e-08    0.0001      64     151 ..     356     443 ..     304     453 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.14
                                       EEEEEETTEEEEEEEE---TT...SS-B-HHHHHHHHHHHHHHHTSSS--EEEEEEEE--B--SHH CS
                              MdcE  19 vldgsltlesvrfvaVigdan...kgevGvdealaLaaaVleaieraekrpilvlvDvasQrlgrr 81 
                                       v++g  t  ++r+vaV ++     +g +G  +++++a   + a+  +   pi+ l D+ + r+  +
  gi|488600057|ref|YP_007906528.1|  77 VVTGYGTI-DGRPVAVFAQDFtvmGGSLGEMHGYKIAYIMDFAM--KMGIPIIGLNDSGGARIQEG 139
                                       55555554.77888887765456688888888888888777776..56677777777777666544 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.1e-08
                                       --EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET- CS
                              MdcE  64 krpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahg...lqanrlialpgv 137
                                       + pi+  +Dv++   g  +E  Gi    a +  a+  A +   p+++++  ka  Ga++a+g   l a+ + a p +
  gi|488600057|ref|YP_007906528.1| 356 NIPIITFMDVPGYLPGVDQEYGGIIRHGAKILYAYSEATV---PLVTIILRKAYGGAYIAMGskhLGADIVYAYPTA 429
                                       579*********************9999999999988875...*****************99665679********* PP

                                       EEESS-HHHHHHHH CS
                              MdcE 138 qvavmdkasaArvT 151
                                       ++avm+   aA + 
  gi|488600057|ref|YP_007906528.1| 430 EIAVMGPEGAAEIV 443
                                       *********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3274.59
//
Query:       gi|488600058|ref|YP_007906529.1|  [L=129]
Description: methylmalonyl-CoA epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-25   87.2   0.0    9.6e-25   87.0   0.0    1.0  1  Glyoxalase_4     Glyoxalase/Bleomycin resistance protein/Diox
    5.4e-16   59.0   0.0      6e-16   58.8   0.0    1.0  1  Glyoxalase       Glyoxalase/Bleomycin resistance protein/Diox
    6.8e-12   45.8   0.0    7.6e-12   45.7   0.0    1.1  1  Glyoxalase_3     Glyoxalase-like domain
    0.00024   21.3   0.0     0.0003   21.0   0.0    1.1  1  Glyoxalase_5     Hydroxyphenylpyruvate dioxygenase, HPPD, N-t
     0.0072   15.6   0.0      0.066   12.4   0.0    1.9  2  DUF1338          Domain of unknown function (DUF1338)
  ------ inclusion threshold ------
      0.028   14.3   0.4       0.33   10.8   0.1    2.2  2  PASTA            PASTA domain
      0.063   13.2   0.0       0.11   12.4   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      0.071   13.9   0.0       0.28   12.0   0.0    1.8  1  Glyoxalase_6     Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   4.3e-28   9.6e-25       1     109 []       4     113 ..       4     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 4.3e-28
                                       EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT....-THHHTS-EEEEEE CS
                      Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp....eflaehgeglhhla 73 
                                       d+igi+V++l++av+ +++ lG+++  + ++e+q+v++a++ +g++  +ieL e+ + +    +f++++geg+hh+a
  gi|488600058|ref|YP_007906529.1|   4 DHIGIAVKNLDEAVELYKK-LGFEVKGIEEVEEQKVKVAMLPVGES--KIELLEATSPEsaiaKFIEKRGEGIHHIA 77 
                                       6*****************9.************************95..9*****99999677788888********* PP

                                       EEES-HHHHHHHHCTTTEEEEEEEE-GGGTT-EEEE CS
                      Glyoxalase_4  74 ywvddldaavarleeqGfevvqkgvragaagrrfay 109
                                       + v+d+++a+++++++G++++++++r ga+g ++a+
  gi|488600058|ref|YP_007906529.1|  78 INVEDIERALEKVKAEGLTLIDEKPRIGAGGKKVAF 113
                                       **********************************98 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 !   58.8   0.0   2.7e-19     6e-16       1     128 []       2     126 ..       2     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.7e-19
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEE CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhv 77 
                                       +idh+ ++v++l+++++ Y+k LGf++   ++   e+++++ a + +g+ +iel+ + +p++a +++  ie+ ++++
  gi|488600058|ref|YP_007906529.1|   2 KIDHIGIAVKNLDEAVELYKK-LGFEVKGIEE--VEEQKVKVAMLPVGESKIELLEATSPESAIAKF--IEKRGEGI 73 
                                       69*******************.******9999..9********************************..66679*** PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEE..EEEETTSEEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysf..yfrDpdGillei 128
                                       ++ia +ved+++al+++k++g+   +e  r + g+   +  + +  +G+lle+
  gi|488600058|ref|YP_007906529.1|  74 HHIAINVEDIERALEKVKAEGLTLIDEKPRIGAGGKKVAfvHPKSTKGVLLEF 126
                                       **********************9999999988777665534666777777776 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   3.4e-15   7.6e-12       1     115 [.       3     112 ..       3     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.4e-15
                      Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdgYlElla.vdpeapaperprlfgldrlakge 76 
                                       +DH+++av++l+ea++ + ++lGf+v    e ++   + a+++ g++ +Ell+   pe + +     f     ++ge
  gi|488600058|ref|YP_007906529.1|   3 IDHIGIAVKNLDEAVELY-KKLGFEVKGIEEVEEQKVKVAMLPVGESKIELLEaTSPESAIA----KFIE---KRGE 71 
                                       7***************88.9********9999999999999999********8457777753....3433...369* PP

                      Glyoxalase_3  77 glhtlalrtddidataarlraaGvd..eagrrvrpdggdlr 115
                                       g+h++a++++di+++ ++++a+G++  ++  r+   g++++
  gi|488600058|ref|YP_007906529.1|  72 GIHHIAINVEDIERALEKVKAEGLTliDEKPRIGAGGKKVA 112
                                       ***********************998744444444444444 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 !   21.0   0.0   1.3e-07    0.0003      22     103 ..      15     102 ..       2     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                      Glyoxalase_5  22 aleelfeklGft.....avarhrskdvtl.yrqGginfilneepdsaaakfarehGpsacalafrvkdakkayeral 92 
                                       +  el++klGf+     +v + + k   l     +i+++  + p+sa+akf ++ G ++  +a+ v+d ++a+e++ 
  gi|488600058|ref|YP_007906529.1|  15 EAVELYKKLGFEvkgieEVEEQKVKVAMLpVGESKIELLEATSPESAIAKFIEKRGEGIHHIAINVEDIERALEKVK 91 
                                       455677777775221114555554433332345679****************************************9 PP

                      Glyoxalase_5  93 ekGakpveket 103
                                       ++G + +++++
  gi|488600058|ref|YP_007906529.1|  92 AEGLTLIDEKP 102
                                       99988777665 PP

>> DUF1338  Domain of unknown function (DUF1338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.044        99     207     235 ..       2      30 ..       1      43 [. 0.80
   2 !   12.4   0.0   2.9e-05     0.066     182     235 ..      44     100 ..      25     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.044
                           DUF1338 207 aiNHlTprvldidalqafleergiklkde 235
                                        i H+ ++v+++d++ +  ++ g+++k  
  gi|488600058|ref|YP_007906529.1|   2 KIDHIGIAVKNLDEAVELYKKLGFEVKGI 30 
                                       589********************999943 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.9e-05
                           DUF1338 182 pvakadyelLaaesey..aAwvl.vngyaiNHlTprvldidalqafleergiklkde 235
                                       pv +++ elL+a+s+   +A  +  +g  i H+++ v+di+++ ++++++g++l de
  gi|488600058|ref|YP_007906529.1|  44 PVGESKIELLEATSPEsaIAKFIeKRGEGIHHIAINVEDIERALEKVKAEGLTLIDE 100
                                       56777777888777651134444499**************************99864 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00015      0.33       9      32 ..      11      34 ..       7      41 .. 0.84
   2 ?    1.3   0.0      0.14   3.1e+02      10      45 ..      82     116 ..      78     123 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                      SBHHHHHHHHHHTT--CCCEEEEC CS
                             PASTA  9 msvdeAkatLkalGlkiktveets 32
                                      +++deA+++ k+lG+ +k++ee+ 
  gi|488600058|ref|YP_007906529.1| 11 KNLDEAVELYKKLGFEVKGIEEVE 34
                                      689************999999844 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                                       BHHHHHHHHHHTT--CCCEEEECTCCGTTB.EEEECS CS
                             PASTA  10 svdeAkatLkalGlkiktveetsddvpeGt.VisQsP 45 
                                       +++ A +  ka Gl  + + e++   + G+ V+ + P
  gi|488600058|ref|YP_007906529.1|  82 DIERALEKVKAEGL--TLIDEKPRIGAGGKkVAFVHP 116
                                       45666777777888..455555555555555555555 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     5e-05      0.11      89     118 ..       8      37 ..       1      43 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-05
                   Acetyltransf_10  89 ltvnaspyavpfYeklGFkavgeeqeenGi 118
                                       + v+  ++av++Y+klGF++ g e++e+  
  gi|488600058|ref|YP_007906529.1|   8 IAVKNLDEAVELYKKLGFEVKGIEEVEEQK 37 
                                       56777789************9777766554 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.28       6      89 ..      10     103 ..       5     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                      Glyoxalase_6   6 aadpaalaaFwaaalgweveree..aaledpegvgpaaedaatllfqrvpe.........paknrvHldlavedlda 71 
                                       +++ +++++ +++ lg+ev+  e  ++++ + ++ p +e++  ll  + pe         +++   H+ ++ved+++
  gi|488600058|ref|YP_007906529.1|  10 VKNLDEAVELYKK-LGFEVKGIEevEEQKVKVAMLPVGESKIELLEATSPEsaiakfiekRGEGIHHIAINVEDIER 85 
                                       5666666666665.4555555553322334445666777888888888888999999877666679*********** PP

                      Glyoxalase_6  72 evarlvalGArvlreprd 89 
                                       + +++ a G + ++e+  
  gi|488600058|ref|YP_007906529.1|  86 ALEKVKAEGLTLIDEKPR 103
                                       *******99998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 821.08
//
Query:       gi|488600059|ref|YP_007906530.1|  [L=163]
Description: methylmalonyl-CoA mutase C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-20   71.1   0.1    9.7e-20   70.8   0.1    1.1  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.013   15.8   0.0    1.3  1  Radical_SAM  Radical SAM superfamily


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 !   70.8   0.1   1.1e-23   9.7e-20       1     116 [.      29     144 ..      29     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 1.1e-23
                       B12-binding   1 ikvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel... 74 
                                       i+vl+a+ g d h++G++v+a+al dagfeV++ g+  ++ +i++ + +e++dv+glS+l++++le    ++e+   
  gi|488600059|ref|YP_007906530.1|  29 IRVLVAKPGLDGHDRGAKVVARALMDAGFEVIYSGIRRTPSEIAETALQEDVDVIGLSILSGAHLELSPMIIEElrk 105
                                       589*****************************************************************999999874 PP

                       B12-binding  75 ..lkrirprvkvvvGGahpsldpeetleaklgiddvvvgegeda 116
                                         l + +++v +++GG++p  d +  l++ lg +  ++g g+ +
  gi|488600059|ref|YP_007906530.1| 106 rgL-EPNKDVVLLIGGIIPKEDVDK-LKE-LG-FSGIFGPGT-P 144
                                       432.33579****************.555.**.888***998.4 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   1.5e-06     0.013      28     103 ..      65     136 ..      39     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  28 slsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvd 103
                                        +++ ei+e + +  ++  ++  il+g +  l p ++e+l+++  +  p+  +++ + g+ p +e +++l+elg+ 
  gi|488600059|ref|YP_007906530.1|  65 RRTPSEIAETALQEDVDV-IGLSILSGAHLELSPMIIEELRKRGLE--PNKDVVLLIGGIIP-KEDVDKLKELGFS 136
                                       688999999996665666.9999999*******************9..9*************.**********954 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:                      416  (0.0232026); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 974.74
//
Query:       gi|488600060|ref|YP_007906531.1|  [L=263]
Description: hypothetical protein Asulf_00515 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.6    7.1  15.5       0.48    9.6  10.8    1.8  2  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 ?   -0.4   0.1     0.028   5.1e+02     158     168 ..      26      36 ..      10     109 .. 0.50
   2 ?    9.6  10.8   2.7e-05      0.48       6     111 ..     128     247 ..     123     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.028
                                       xxxxxxxxxxx RF
                            CitMHS 158 lvgllplvllf 168
                                       l++l +l++++
  gi|488600060|ref|YP_007906531.1|  26 LIFLGYLIIAY 36 
                                       33333333333 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 2.7e-05
                                       xxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   6 leklrldvvallvlvll...........vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggk 71 
                                       ++++ +d+  +l+l++l           +  + ea+  i+ +ii+lll    ++ +  ++G+fd +a+  + l +++
  gi|488600060|ref|YP_007906531.1| 128 MKVIKIDLLGILILIALsspsfilyylnFPILGEAYMSISMTIIFLLLTFSKFAIVDRDAGVFDAVARGSAFLLRNS 204
                                       56688888888888887777776665554445558888888888888888888888899*********999999998 PP

                                       xx.xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                            CitMHS  72 rd.llvllvlltallsafvsndgv...vlimipivlslakrlkk 111
                                        + +l++++ ++  + +++++ +v   + + +p+v++l++ +++
  gi|488600060|ref|YP_007906531.1| 205 FTvILAFFAWFVISF-PIITLSAVfppLFLALPLVITLFHTMMG 247
                                       774444444444444.5555555599999999999999987444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1935.86
//
Query:       gi|488600061|ref|YP_007906532.1|  [L=229]
Description: Uroporphyrinogen-III synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-39  133.8   0.0    6.5e-39  133.6   0.0    1.0  1  HEM4         Uroporphyrinogen-III synthase HemD
     0.0077   16.3   0.1      0.034   14.2   0.0    1.9  2  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.028   14.1   0.2      0.068   12.8   0.1    1.7  1  SPECT1       Plasmodium host cell traversal SPECT1
       0.03   15.0   0.1       0.34   11.7   0.1    2.5  3  PTS_IIB      PTS system, Lactose/Cellobiose specific IIB subu
      0.044   13.2   0.0      0.076   12.4   0.0    1.5  1  SBP_bac_3    Bacterial extracellular solute-binding proteins,


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.0   1.8e-42   6.5e-39       2     231 ..       9     224 ..       8     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 1.8e-42
                                       HHHHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEE CS
                              HEM4   2 elaealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaa 78 
                                       e+ + le++G+e + +P+++ie       ++  +     ++yd++i+tS++  ++++e+         +l + +++a
  gi|488600061|ref|YP_007906532.1|   9 ETRKILEENGFEIISAPFLKIEE------VEVDIS----ESYDYVIVTSQTSARIVVERYP-------ELLKGRIIA 68 
                                       67788******************......777774....5***************999998.......88899**** PP

                                       SSHHHHHHHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEE.EE- CS
                              HEM4  79 vGpaTaraLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYet.vpa 154
                                       +G++Ta ++e  g++++ +ps +++++ L ee++++l+gkrv ++r++ +++ l +      ++vde++vY+    +
  gi|488600061|ref|YP_007906532.1|  69 IGRKTASVFEGMGVENVETPS-KFDSKTLYEEFHQKLRGKRVAIVRSNMGDPVLLKLK--EFCDVDEIVVYRIeFEH 142
                                       *****************9**9.********************************9866..5799*********5444 PP

                                       HHHHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH......HHHCTSEEEEESHHHHHHHHHTT---SEEETS- CS
                              HEM4 155 eeepeelkealkagevdavvftSpstvrnllellkdeg......delkevkvaaiGptTaealkklglkvdvvaeep 225
                                        +++ e+ +++ +ge++a+vf S  +vr++++l+++        + lk+++v+aiGp T+ +l+++g+ + v++ee+
  gi|488600061|ref|YP_007906532.1| 143 GDKQREFLRRVAEGEAEAIVFSSRMMVRSFFSLAEKLDlvddvkNALKKMRVVAIGPPTKSELERYGVDA-VMPEEY 218
                                       5588999999*9***********************999********************************.****** PP

                                       -HHHHH CS
                              HEM4 226 taeglv 231
                                       t eg v
  gi|488600061|ref|YP_007906532.1| 219 TFEGVV 224
                                       ***988 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.34   1.2e+03      24      76 ..      14      63 ..      11      75 .. 0.58
   2 !   14.2   0.0   9.5e-06     0.034      40     118 ..     142     221 ..     118     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.34
                       B12-binding 24 lrdagfeVqllganven.edivaairaekpdvvglSalltsqleavkelvellk 76
                                      l+++gfe++     + + e+++  i  e +d v +++  ts    v+++ ellk
  gi|488600061|ref|YP_007906532.1| 14 LEENGFEIISA--PFLKiEEVEVDIS-ESYDYVIVTS-QTSARIVVERYPELLK 63
                                      66666666322..2222244444443.4477777777.6777777776666655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.5e-06
                       B12-binding  40 n....edivaairaekpdvvglSal.ltsqleav...kelvellkrirprvkvvvGGahpsldpeetleaklgiddv 108
                                       +     ++++++++ +++++++S++ +  ++       +lv+ +k + ++++vv+ G++ +  + e      g+d  
  gi|488600061|ref|YP_007906532.1| 142 HgdkqREFLRRVAEGEAEAIVFSSRmMVRSFFSLaekLDLVDDVKNALKKMRVVAIGPP-TKSELE---R-YGVDA- 212
                                       4445589****************99434444444333666666**************86.444433...3.79666. PP

                       B12-binding 109 vvgegedale 118
                                        v   e+++e
  gi|488600061|ref|YP_007906532.1| 213 -VMPEEYTFE 221
                                       .556666666 PP

>> SPECT1  Plasmodium host cell traversal SPECT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.9e-05     0.068      83     126 ..     114     155 ..      71     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                            SPECT1  83 kkvcdlilkkvkklvelskinkyriilkfGkgdrkkeildkvkn 126
                                         + d +l k+k+  ++++i  yri   f +gd+++e l +v +
  gi|488600061|ref|YP_007906532.1| 114 SNMGDPVLLKLKEFCDVDEIVVYRIE--FEHGDKQREFLRRVAE 155
                                       4699********************96..5556677788887765 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   9.4e-05      0.34      20      59 ..      10      51 ..       7      86 .. 0.82
   2 ?   -3.2   0.0       4.2   1.5e+04      61      75 ..     123     135 ..     118     147 .. 0.57
   3 ?    0.5   0.0      0.28     1e+03      41      64 ..     185     207 ..     164     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.4e-05
                                      HHHHHHHCTEEEEETTEE...GGGHHHHHHT-SEEEEEESSGG CS
                           PTS_IIB 20 lekaakelgieaegeagv...eleaeeiaddaDlvllapqvrv 59
                                       +k+++e+g+e++++      e+e++  ++ +D+v+++ q+  
  gi|488600061|ref|YP_007906532.1| 10 TRKILEENGFEIISAPFLkieEVEVDISES-YDYVIVTSQTSA 51
                                      589*********999999986666766666.*********984 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                                       THHHHTTSEEEEECT CS
                           PTS_IIB  61 dlarfagkpvavini 75 
                                       +l++f++  v+ i +
  gi|488600061|ref|YP_007906532.1| 123 KLKEFCD--VDEIVV 135
                                       5677777..333332 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.28
                                       HHHHHHT-SEEEEEESSGGCTHHH CS
                           PTS_IIB  41 aeeiaddaDlvllapqvrvkdlar 64 
                                       +++  +++ +v ++p ++  +l+r
  gi|488600061|ref|YP_007906532.1| 185 VKNALKKMRVVAIGPPTKS-ELER 207
                                       4555556777777777773.5554 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.1e-05     0.076      83     165 ..      47     170 ..      31     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                                       EEEEEEEEEEETT...................................SHGTCCHSSCGCGTTSEEEEETTSHHHHH CS
                                       xxxxxxxxxxxxx...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  83 fsagqvllvrkkd...................................askissiksladLkgkkvgvqagstaeel 124
                                        +++ +++v++                                     ++  +++   ++L gk+v+++++   +  
  gi|488600061|ref|YP_007906532.1|  47 SQTSARIVVER-YpellkgriiaigrktasvfegmgvenvetpskfdsKTLYEEFH--QKLRGKRVAIVRSNMGDPV 120
                                       55555555553.13466666666666666666666666666655554444445555..69*************9999 PP

                                       HHHHHHC..........TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHH CS
                                       xxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 125 lkeelkk..........gaeivefdtleealqaLkngrvdavvadspvlay 165
                                       l + lk+           +e  + d ++e l+++++g+++a+v++s ++  
  gi|488600061|ref|YP_007906532.1| 121 LLK-LKEfcdvdeivvyRIEFEHGDKQREFLRRVAEGEAEAIVFSSRMMVR 170
                                       887.44567788777666777889*******************99877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1666.60
//
Query:       gi|488600062|ref|YP_007906533.1|  [L=747]
Description: phosphoenolpyruvate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-114  381.6   0.8   6.4e-114  380.6   0.8    1.4  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    1.1e-87  293.9   1.1    1.6e-87  293.4   1.1    1.3  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    2.6e-28   97.5   2.5      1e-27   95.7   2.5    2.1  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
       0.02   15.0   0.3        7.8    6.7   0.0    3.0  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
      0.031   13.1   0.1      0.079   11.8   0.1    1.6  2  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
      0.078   12.8   0.0       0.61   10.0   0.0    2.5  2  Tap-RNA_bind     Tap, RNA-binding
      0.091   13.0   0.5        2.7    8.3   0.2    2.7  2  NUMOD3           NUMOD3 motif (2 copies)


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.6   0.8  2.5e-117  6.4e-114       2     317 ..      15     320 ..      14     327 .. 0.97

  Alignments for each domain:
  == domain 1  score: 380.6 bits;  conditional E-value: 2.5e-117
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelP 78 
                                       +lvGGKganL+el + ++ipvP+gf++ ++++r+f+e +g++eki+++l+ +dv+d+d+l+k+s++ir+l+ s+++P
  gi|488600062|ref|YP_007906533.1|  15 PLVGGKGANLGELFR-NEIPVPNGFVVDSKTYRHFIEVTGIKEKIEKMLEGIDVEDTDALTKTSQDIRKLVESTPIP 90 
                                       69***********55.9************************************************************ PP

                            PPDK_N  79 eeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYr 155
                                       ee+ e+i++ay++l+++ g++ + vaVRSSataEDlp asfaGqqdt+Lnv+  ++++e ++++++Sl+++rAi+Yr
  gi|488600062|ref|YP_007906533.1|  91 EEVAEEIMNAYRKLCEEEGEK-VYVAVRSSATAEDLPGASFAGQQDTFLNVD-GDSLVEYVRKCWSSLYTPRAIYYR 165
                                       ****************99987.*****************************7.688********************* PP

                            PPDK_N 156 kekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilek 232
                                        +kg++he+v++avvvqkmvns+  +sGV+f+ +p tG k e +i+a++GlGea+V+G+vtpd+++ ++++rki++ 
  gi|488600062|ref|YP_007906533.1| 166 VQKGFRHEDVSIAVVVQKMVNSE--KSGVMFTSHPVTG-KLETIIEAVFGLGEAIVSGMVTPDTYIFDREKRKIVDI 239
                                       ***********************..*************.************************************** PP

                            PPDK_N 233 kigekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpe 309
                                       k+gek+i+i+ ++ +  t+++e++e+++++ +Lsdee+ +L e+++ ie+hy++p+d+E+ai+  +gk+y++Q+Rp 
  gi|488600062|ref|YP_007906533.1| 240 KVGEKNIMITKKDGK--TVKIELDEKKAKERVLSDEEIIRLVELGEIIEDHYENPQDVEWAIE--KGKIYIVQSRPV 312
                                       **********99987..67********************************************..************ PP

                            PPDK_N 310 trtsekke 317
                                       t+ ++  +
  gi|488600062|ref|YP_007906533.1| 313 TTIQAGRV 320
                                       *9887665 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 !  293.4   1.1   6.2e-91   1.6e-87       5     292 ..     439     735 ..     435     737 .. 0.91

  Alignments for each domain:
  == domain 1  score: 293.4 bits;  conditional E-value: 6.2e-91
                                       TSCCCCCCCHCC.CXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCC..HHHHHH.........HHHHHH CS
                   PEP-utilizers_C   5 gklktllavtkd.gkkikvlaNidtpedaekalengaeGiGLlRtEflfmaree..lpteee.........qaeayk 69 
                                       +k ++++av ++  ++++v +N++ p++ae+a+++ga+G+GL+R+E++ +   +  +++++e         +++  k
  gi|488600062|ref|YP_007906533.1| 439 KKEEKVMAVETPiLTATEVKVNVSIPDAAERAAATGADGVGLFRIEHMVLGLGKhpMQYIKEgkvdeyieeLYKGMK 515
                                       444444444333146778888*****************************99664344455599************* PP

                                       HHHHHTTTSEEEEEXXXSSCC..GGSGGCHHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCC..CCEEEEEE CS
                   PEP-utilizers_C  70 kvleamngrpvvvRtlDiggd..kelpelkeepeevNPmlGfRgirlglsepelfetqlrAllrasa..agkleiml 142
                                       +v+ea++++pv++RtlD+++d  + ++ +++ep e+NPmlGfRgir+ l e e f++++rA+++     ++++ iml
  gi|488600062|ref|YP_007906533.1| 516 RVVEAFYPKPVWIRTLDAPTDefRAMEGGEDEPIEANPMLGFRGIRRDLLETEHFRAEMRAIKKLIDegFTNIGIML 592
                                       *********************88889**************************************9985667****** PP

                                       SSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTT.SSEEEEXHHHHHHHHHTXXCC CS
                   PEP-utilizers_C 143 PmvasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklake.vdFfSiGtNDLtQytlavdRd 218
                                       P++++vee+++ak++i e+   l        +k+++GiM+E+p+aal++++l+ke +dF+S+GtNDLtQyt+avdR+
  gi|488600062|ref|YP_007906533.1| 593 PLITNVEEVRKAKQLIIEEGIPL--------NKIEFGIMVETPAAALIIEDLVKEgIDFVSFGTNDLTQYTIAVDRN 661
                                       ****************9994443........479********************99********************* PP

                                       CHCHHHHSXTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCT CS
                   PEP-utilizers_C 219 neevaklydplepavlrlikevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqv 292
                                       ne+va+l+d+++pav +li++vik+++e+g+k++iCG+++++p++ve lv lG+d++S++ ++v a+r+++ ++
  gi|488600062|ref|YP_007906533.1| 662 NENVAYLFDETHPAVMKLIEMVIKVCREHGVKTSICGQAGSYPHVVEKLVLLGIDSVSANQDAVKAVRETVYRA 735
                                       ********************************************************************999776 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 !   95.7   2.5   3.9e-31     1e-27       1      73 []     355     427 ..     355     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 3.9e-31
                                       G--S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   1 kleegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       k++eg++Lv+++t+p++++++++a++ivt++GGmt+HaAiv+relg+PaVvg+++at++lk+g ++tvDg++G
  gi|488600062|ref|YP_007906533.1| 355 KIQEGDVLVTSMTTPDMVPAMKRASAIVTDEGGMTCHAAIVSRELGVPAVVGTKNATKVLKDGMIVTVDGEKG 427
                                       5899*******************************************************************99 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0031       7.8      37      73 ..      70     108 ..      37     124 .. 0.88
   2 ?    5.1   0.1    0.0096        25       2      16 ..     332     352 ..     331     385 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHHHHHH.T-HH.HHHHHHHHHHHHT-H CS
                   PEP-utilisers_N  37 eeAlekvreelealaeka.lgee.eaaifeahlmlleDp 73 
                                       ++Al+k+ +++++l e++   ee +++i++a++ l e +
  gi|488600062|ref|YP_007906533.1|  70 TDALTKTSQDIRKLVESTpIPEEvAEEIMNAYRKLCEEE 108
                                       58*****************66664567******998865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0096
                                       -EEEE-SEEEEEEE......- CS
                   PEP-utilisers_N   2 GiaaspGiaiGkav......e 16 
                                       G++aspGia G +       e
  gi|488600062|ref|YP_007906533.1| 332 GLGASPGIATGVVKiigderE 352
                                       99*********9987665331 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 ?   -3.8   0.0       1.7   4.4e+03     178     195 ..     186     203 ..     176     219 .. 0.69
   2 ?   11.8   0.1   3.1e-05     0.079     235     319 ..     352     439 ..     337     454 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.7
                                       --SS-EEEEE---HHHHT CS
                       Epimerase_2 178 lkekkyvlvtlHrrened 195
                                        +ek+ v++t H+++   
  gi|488600062|ref|YP_007906533.1| 186 NSEKSGVMFTSHPVTGKL 203
                                       357888999999998766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.1e-05
                                       HHHH-.TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHH....CT--EEESSSS-S-THHHHTTSEEE.-TT- CS
                       Epimerase_2 235 eleel.envtlieplgyldflsllknaklvltdSgGiqeEaps....lgvpvvnlReeteRpegveagtnvl.vgtd 305
                                       e++++ e   l++++ + d++ ++k+a +++td gG+   a++    lgvp+v+    t+  + v +   ++ v+ +
  gi|488600062|ref|YP_007906533.1| 352 EISKIqEGDVLVTSMTTPDMVPAMKRASAIVTDEGGMTCHAAIvsreLGVPAVVG---TKNATKVLKDGMIVtVDGE 425
                                       455564566899*************************999988677789999998...5555555555555448888 PP

                                       HHHHHHHHHHHCT- CS
                       Epimerase_2 306 keeIvaaleklled 319
                                       k  ++a + k  e+
  gi|488600062|ref|YP_007906533.1| 426 KGLVYAGAVKKEEK 439
                                       88888877666644 PP

>> Tap-RNA_bind  Tap, RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.2     3e+03      34      70 ..      35      71 ..      32      76 .. 0.83
   2 ?   10.0   0.0   0.00024      0.61      52      80 ..      92     120 ..      90     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                      Tap-RNA_bind 34 pvefhyeknkavFfVedastAsaLkkvsrkItdedge 70
                                      p  f +++++ + f+e + + ++++k+ + I  ed +
  gi|488600062|ref|YP_007906533.1| 35 PNGFVVDSKTYRHFIEVTGIKEKIEKMLEGIDVEDTD 71
                                      5568899999999999999999999999988888765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00024
                      Tap-RNA_bind  52 stAsaLkkvsrkItdedgekisilvrpsa 80 
                                       ++A++++++ rk ++e+gek+ + vr+sa
  gi|488600062|ref|YP_007906533.1|  92 EVAEEIMNAYRKLCEEEGEKVYVAVRSSA 120
                                       79************************996 PP

>> NUMOD3  NUMOD3 motif (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.12     3e+02      10      26 ..     182     202 ..     181     204 .. 0.88
   2 ?    8.3   0.2     0.001       2.7       9      27 ..     233     255 ..     230     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                            NUMOD3  10 aKmsealk.G...ennpfyGK 26 
                                       +Km+++ k G    ++p++GK
  gi|488600062|ref|YP_007906533.1| 182 QKMVNSEKsGvmfTSHPVTGK 202
                                       89****9996666*******9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.001
                            NUMOD3   9 KaKmsealkGennpfy....GKk 27 
                                       K+K+++++ Ge+n++     GK+
  gi|488600062|ref|YP_007906533.1| 233 KRKIVDIKVGEKNIMItkkdGKT 255
                                       9**************97777876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (747 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.52
# Mc/sec: 4335.42
//
Query:       gi|488600063|ref|YP_007906534.1|  [L=325]
Description: diphthamide biosynthesis enzyme Dph2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-73  246.8   0.0    3.8e-73  246.6   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
  ------ inclusion threshold ------
      0.027   14.1   0.0        2.9    7.5   0.0    2.5  3  DUF1847          Protein of unknown function (DUF1847)


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.6   0.0   4.2e-77   3.8e-73       1     302 [.      30     320 ..      30     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 246.6 bits;  conditional E-value: 4.2e-77
                   Diphthamide_syn   1 fPegllpdsaeiadileefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvdrlpvlYvfveieldve 77 
                                       +P+gl+  ++eiadi+e+ g ev+i+g +++GaC++d   +++  +d+lvH++h+++ +     v+Y ++  e+d++
  gi|488600063|ref|YP_007906534.1|  30 LPDGLKFRAKEIADIFESRGYEVIISGSHSFGACDLDLSLLDE--VDVLVHFAHTPIYE--LDMVIYAPYYYEYDFD 102
                                       6*****************************************9..9************9..569************* PP

                   Diphthamide_syn  78 hlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeevdaily 154
                                       ++ + lk++   +kkivl++t+qya+++ee+k+ lee+g+ev  ++ +++ + +g+vlgc++ +l+       ai+y
  gi|488600063|ref|YP_007906534.1| 103 RIYDILKETG--EKKIVLAGTAQYAWKFEELKRFLEERGFEVS-INPAKRVKFRGQVLGCSYGALR----AEGAIVY 172
                                       *******999..899*********************99**999.55566****************7....4579*** PP

                   Diphthamide_syn 155 igdgrfhllslmlsnpklpvyrydpyskklt.eesydakkllrrRyaaiekakd..akkvGiivgtlgvqgrlelve 228
                                       igdg fh+ ++ + + + +vy+++p s++l+   + +++ +l+ Ry ai+ka++   + vGiiv ++ +q+r++l++
  gi|488600063|ref|YP_007906534.1| 173 IGDGLFHAFGAGVYTGR-RVYAINPLSGELRvIGEREINDFLKARYLAISKAMEriDEGVGIIVTSKIGQKRIALAR 248
                                       ***************77.9***********9777889****************977788****************** PP

                   Diphthamide_syn 229 rlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalgerewteey 302
                                       +lkk++++a+  s +++ + ++p+kLanf ++ ++V++aCpr+s+dd +++++P++tp+E+e++lg r+w+ +y
  gi|488600063|ref|YP_007906534.1| 249 KLKKMADNANVASKILFFDDISPEKLANF-NFGVYVNTACPRISYDDIRRYDRPIITPQEFEIVLGLRKWE-DY 320
                                       *****************************.****************************************5.44 PP

>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00032       2.9      46      85 ..      14      53 ..       6      74 .. 0.89
   2 ?    3.7   0.0    0.0047        42      45      86 ..     103     144 ..      88     165 .. 0.82
   3 ?   -2.7   0.0      0.46   4.1e+03      49      76 ..     235     263 ..     217     269 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00032
                           DUF1847 46 iiefakrmgykkiGiafCvglleeakalakileakgfevv 85
                                      i e  kr ++ ++G+    gl+  ak++a+i+e++g+ev+
  gi|488600063|ref|YP_007906534.1| 14 IFEELKRRNALRVGLQLPDGLKFRAKEIADIFESRGYEVI 53
                                      56667899999***************************96 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0047
                           DUF1847  45 eiiefakrmgykkiGiafCvglleeakalakileakgfevvs 86 
                                        i +  k++g kki +a     +   ++l+++le++gfev  
  gi|488600063|ref|YP_007906534.1| 103 RIYDILKETGEKKIVLAGTAQYAWKFEELKRFLEERGFEVSI 144
                                       56667789999********9*******************975 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.46
                           DUF1847  49 fakrmgykkiGiafCv.glleeakalaki 76 
                                        + ++g k+i +a  +  ++++a++ +ki
  gi|488600063|ref|YP_007906534.1| 235 VTSKIGQKRIALARKLkKMADNANVASKI 263
                                       45677888887776541344555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2175.75
//
Query:       gi|488600064|ref|YP_007906535.1|  [L=334]
Description: Ca2+/Na+ antiporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-22   77.7  37.4      6e-12   45.8  15.2    2.0  2  Na_Ca_ex        Sodium/calcium exchanger protein
  ------ inclusion threshold ------
        0.1   11.0   2.4        0.2   10.0   2.4    1.4  1  SID-1_RNA_chan  dsRNA-gated channel SID-1


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 !   38.0  14.2   1.7e-13   1.5e-09       9     150 ..      17     164 ..      11     165 .. 0.83
   2 !   45.8  15.2   6.7e-16     6e-12       4     150 ..     193     330 ..     191     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.7e-13
                                       HHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHH.TTT...HHHHHHHHHHHHHHHHHT CS
                          Na_Ca_ex   9 slllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaal.tge...vdlaignvlGsnifnlll 81 
                                        ++++ ++a ++v+++e++++ +++ gs++G +l +l++slpE+i+ ++a+  +g      +++g+v+G  ++   l
  gi|488600064|ref|YP_007906535.1|  17 EIFVVFIAALLFVNAIEYLGSLFELGGSFVGAILSPLFTSLPEMIVFLVAIFfSGVesgEAIGVGTVFGQPFMASSL 93 
                                       4677778999999********9*************************99999544456799*********9988766 PP

                                       HHHH...HHHHHH..BTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  82 viGl...ialigs..lkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                         Gl   ++l+g     +d + l++d +l + +a++++++ l+l+ p+f      +l g++++l+Y+ y++ ++
  gi|488600064|ref|YP_007906535.1|  94 SYGLvgiSVLLGYhlKRRDDLVLEVDRELVIPYAVVSIAFPLTLV-PAF--LGFHKLFGILFFLIYVSYIFTMY 164
                                       655511155555565577777899999888999999999999966.998..*******************9876 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 6.7e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex   4 vlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnll 80 
                                       + +i s++l++ +++ lvss++e+++ l+is+  l+l+++++++ +pE++s++i   +g  +l+i++++G  i+  +
  gi|488600064|ref|YP_007906535.1| 193 IQLISSVILLYYGSHGLVSSVDEVSRMLNISPLGLALIIIPAATAIPETASALIWSFRGRDSLSIASLIGEKILYST 269
                                       67899************************************************************************ PP

                                       THHHHHHHHHHBTTSSCECCHHH.HHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  81 lviGlialigslkvdseslkldl.gllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                       +  ++ +l++s       ++ld+  +++++   +++l+ll ++++  + r+ ++  +v ++++++y vl +
  gi|488600064|ref|YP_007906535.1| 270 FYPAMGLLLTS-------WTLDVhAYMSVIGTTAISLILL-YFVA--KQRVPWWGLIVGFVFFIVYSVLIF 330
                                       *9999999955.......4788866666666666555554.5444..5******************99865 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 ?   10.0   2.4   2.2e-05       0.2     363     546 ..     100     312 ..      88     314 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.2e-05
                    SID-1_RNA_chan 363 vlcmlklyqkRhpdinasaysafal.lavvillgvigvlegknkfwilfsiihllatlllslqiyymgrwkl....d 434
                                       ++ +l  + kR++d+  ++  ++++  avv++++ ++++     f  lf i+ +l++++  + +y  g+ +     +
  gi|488600064|ref|YP_007906535.1| 100 ISVLLGYHLKRRDDLVLEVDRELVIpYAVVSIAFPLTLVPAFLGFHKLFGILFFLIYVSYIFTMYKNGMGETlesaE 176
                                       55667778899999998888887764678888888888875555555555555555555555555545443322335 PP

                    SID-1_RNA_chan 435 vgilrrile.................vlkkeviqqcsrply...........ksrm........vllvlgnlvnvsl 475
                                          ++r++                                y            srm        +l+++ ++ ++  
  gi|488600064|ref|YP_007906535.1| 177 EPYACRVIPnqkaggiiqlissvillY-------------YgshglvssvdeVSRMlnisplglALIIIPAATAIPE 240
                                       556666666556666655555554321.............1222222222224566777777778888888888888 PP

                    SID-1_RNA_chan 476 avlglvlkpkdfasylLaifivnlllYlvfYiimKlr.sserilllalllivltlvvwavalyfffqkessW 546
                                       ++  l+ + +   s  +a +i++ +lY +fY  m l  +s ++ + a + ++ t+ +  + lyf ++++  W
  gi|488600064|ref|YP_007906535.1| 241 TASALIWSFRGRDSLSIASLIGEKILYSTFYPAMGLLlTSWTLDVHAYMSVIGTTAISLILLYFVAKQRVPW 312
                                       88888888877778888899**************99857889999*********************999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2327.14
//
Query:       gi|488600065|ref|YP_007906536.1|  [L=417]
Description: 3-isopropylmalate dehydratase, large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-98  330.8   0.1    1.7e-96  324.0   0.1    2.2  1  Aconitase  Aconitase family (aconitate hydratase)
    0.00011   21.0   0.0    0.00016   20.6   0.0    1.1  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 !  324.0   0.1  1.9e-100   1.7e-96       2     461 .]      10     408 ..       9     408 .. 0.92

  Alignments for each domain:
  == domain 1  score: 324.0 bits;  conditional E-value: 1.9e-100
                         Aconitase   2 kiwdahlvee..eg...iayv.pdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeal 72 
                                       ki++++  ++   g   i     d+++lqd t++ a+ +++++ +++r  + t   +dh+ p+              
  gi|488600065|ref|YP_007906536.1|  10 KIFSEKSGSDvrAGdivI--AeIDQIALQDGTAPLAIRQVKEMSKEIRGSEITHFFVDHASPSP------------- 71 
                                       565544332222333223..256****************************************9............. PP

                         Aconitase  73 eknledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgie 149
                                           ++e+++     +f++++a+++ +++ ppg+GI+Hq+++E  ++ pg + vg DSHT+++gg+G++ +G G+++
  gi|488600065|ref|YP_007906536.1|  72 ----RKELSN---DQKFIRNFAEEHSMDFNPPGEGIIHQIMVER-YVKPGDLAVGADSHTCTYGGIGAFSTGMGSTD 140
                                       ....344444...458999*************************.******************************** PP

                         Aconitase 150 aeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaE 226
                                       ++ ++l ++ ++++p+v +++++Gk ++gv akDl+l++ig l+++g++ k++Ef G+ ++++++e+r+Ti+NMa+E
  gi|488600065|ref|YP_007906536.1| 141 VAVAILLRKNWFRVPEVFRFNISGKFEKGVFAKDLILKIIGDLGVDGATYKAMEFDGD-IHNIEVEGRLTISNMAVE 216
                                       *********************************************************6.9***************** PP

                         Aconitase 227 vGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpl 303
                                       +GA++g+fp de t +YL+  gr+++       +      e++ad++aey+k++  +ls+lep+++ p++++++ ++
  gi|488600065|ref|YP_007906536.1| 217 CGAKAGIFPSDELTKQYLAELGRADDF------K------EIKADANAEYEKEFYYELSDLEPMISKPHNVDNTAEV 281
                                       *******************99994443......2......467899*****************************99 PP

                         Aconitase 304 selvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsv 380
                                        ++v                           + +++d+++ig CTN++++d+r +a++l+     g+kv+++++++v
  gi|488600065|ref|YP_007906536.1| 282 -SEV---------------------------EGTEIDQVFIGTCTNGRISDLRVVAKILK-----GRKVSKKIRLIV 325
                                       .333...........................344699***********************.....************ PP

                         Aconitase 381 aPGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLaSPelvv 455
                                        P+S+++  ++ +eGll+++ +aG  v+ +gC++C+g  ++ l++ge+++s+ NRNF+gR+g p++  yL SP+ ++
  gi|488600065|ref|YP_007906536.1| 326 GPASRRIYLKAMEEGLLKTIVEAGGVVLPPGCGPCVGiHQGILADGEVCLSTQNRNFKGRMGnPEGFIYLSSPATAA 402
                                       *************************************************************6488888********* PP

                         Aconitase 456 aaAlaG 461
                                       a+A++G
  gi|488600065|ref|YP_007906536.1| 403 ASAIKG 408
                                       ****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 !   20.6   0.0   1.7e-08   0.00016     277     357 ..     276     357 ..     242     373 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-08
                            DUF521 277 eevleelskakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvk 351
                                       +++ e +s+ + +++d v++G c    +++lr +a++lkg+k+++k++l+v  +sr ++ +a ++gl++++ +aG+ 
  gi|488600065|ref|YP_007906536.1| 276 DNTAE-VSEVEGTEIDQVFIGtCTNGRISDLRVVAKILKGRKVSKKIRLIVGpASRRIYLKAMEEGLLKTIVEAGGV 351
                                       44444.55778889******9788899***********************9648999******************** PP

                            DUF521 352 vlsdtC 357
                                       vl   C
  gi|488600065|ref|YP_007906536.1| 352 VLPPGC 357
                                       *99888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2874.45
//
Query:       gi|488600066|ref|YP_007906537.1|  [L=1516]
Description: hypothetical protein Asulf_00521 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-62  208.4  17.3    2.8e-34  117.6   5.5    3.7  3  DUF2341      Domain of unknown function (DUF2341)
    6.6e-46  154.0  28.4    2.2e-16   59.4   3.9    5.1  4  PKD          PKD domain
    2.7e-17   62.9  12.6    7.1e-17   61.5   5.7    4.4  3  CARDB        CARDB
    7.6e-09   36.4   0.4    7.6e-09   36.4   0.4    4.5  6  Pilin_N      Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.019   14.7   5.4         10    6.0   0.1    4.4  4  PKD_3        PKD-like domain
        7.9    6.7  24.0        4.8    7.4   1.0    4.8  4  DUF5011      Domain of unknown function (DUF5011)


Domain annotation for each model (and alignments):
>> DUF2341  Domain of unknown function (DUF2341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1         5   1.5e+04      31      68 ..     154     193 ..     149     197 .. 0.48
   2 !  117.6   5.5   9.3e-38   2.8e-34       1      83 [.     392     474 ..     392     475 .. 0.98
   3 !   97.2   0.9   2.1e-31   6.2e-28       1      74 [.     797     870 ..     797     875 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5
                           DUF2341  31 iWvkvpsipangnktikiy..ygnptatstsngdatfelF 68 
                                       i +kv++ + + n++i iy  + n + ++ ++  ++ +++
  gi|488600066|ref|YP_007906537.1| 154 ISLKVSNANPEVNEEITIYadVMNVGSEDINESFTVRFYY 193
                                       5667766665555555555004444444443333333334 PP

  == domain 2  score: 117.6 bits;  conditional E-value: 9.3e-38
                           DUF2341   1 dgsdiRfvdsdgtt.LpywieswdantekaliWvkvpsipangnktikiyygnptatstsngdatfelFDdfsgtel 76 
                                       dgsdiRf++sdg+t L+ywieswd+++++a+iWvkv +ipa+++kti++yygn++ats+sngd+tf +FDdf+gt+l
  gi|488600066|ref|YP_007906537.1| 392 DGSDIRFTESDGSTfLNYWIESWDPSNQTATIWVKV-NIPASTSKTIYMYYGNSSATSMSNGDSTFVFFDDFEGTSL 467
                                       79**********************************.8*************************************** PP

                           DUF2341  77 dttkWtv 83 
                                       +ttkW +
  gi|488600066|ref|YP_007906537.1| 468 NTTKWAT 474
                                       *****75 PP

  == domain 3  score: 97.2 bits;  conditional E-value: 2.1e-31
                           DUF2341   1 dgsdiRfvdsdgtt.LpywieswdantekaliWvkvpsipangnktikiyygnptatstsngdatfelFDdfsgt 74 
                                       dgsdiRf++sdg+t L+ywieswd+++++a+iWvkv +ipa+++kti++yygn++ats+sn+++t++l+++f+++
  gi|488600066|ref|YP_007906537.1| 797 DGSDIRFTESDGSTfLNYWIESWDPSNQTATIWVKV-NIPASTSKTIYMYYGNSSATSMSNPEKTMFLYENFESD 870
                                       79**********************************.8**********************************985 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.45   1.4e+03      45      59 ..     215     229 ..     204     235 .. 0.80
   2 !   46.9   1.6   6.1e-16   1.8e-12       8      70 ..     273     336 ..     266     337 .. 0.86
   3 !   59.4   3.9   7.5e-20   2.2e-16       5      68 ..     671     738 ..     664     741 .. 0.92
   4 !   59.4   3.9   7.5e-20   2.2e-16       5      68 ..    1084    1151 ..    1077    1154 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.45
                                       EEEEEE-SSEEEEEE CS
                               PKD  45 tvthtYlspGeYeVt 59 
                                       ++++t++s+G+++++
  gi|488600066|ref|YP_007906537.1| 215 SFSYTPTSTGQHVIK 229
                                       699*********986 PP

  == domain 2  score: 46.9 bits;  conditional E-value: 6.1e-16
                                       -BSSEEEEEEEES....-.SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                               PKD   8 lvpgatvaftaav...pd.ganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                       + +g  ++f+a++   pd ++++ y Wdfgd   + + ++  +th+Y+spG+Y Vt+t+ +++g ++
  gi|488600066|ref|YP_007906537.1| 273 PLVGDIITFNASSsydPDgDKITDYIWDFGD---GDTATGVVTTHSYSSPGTYDVTLTVYDERGGVN 336
                                       55677799*****99966255677*******...******************************987 PP

  == domain 3  score: 59.4 bits;  conditional E-value: 7.5e-20
                                       -S--BSSEEEEEEEES......-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                               PKD   5 ptvlvpgatvaftaav.....pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgs 68 
                                       p+ + ++++++f+a++     p g++++y+Wdfgd ++v ++++pt+thtY+s+ +Y Vt+t+++++g+
  gi|488600066|ref|YP_007906537.1| 671 PSTPQVNEEITFNASSstpsePGGSITNYHWDFGD-GNVIDTTSPTITHTYSSANTYSVTLTVTDSLGR 738
                                       67899***********9966666************.******************************997 PP

  == domain 4  score: 59.4 bits;  conditional E-value: 7.5e-20
                                        -S--BSSEEEEEEEES......-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                               PKD    5 ptvlvpgatvaftaav.....pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgs 68  
                                        p+ + ++++++f+a++     p g++++y+Wdfgd ++v ++++pt+thtY+s+ +Y Vt+t+++++g+
  gi|488600066|ref|YP_007906537.1| 1084 PSTPQVNEEITFNASSstpsePGGSITNYHWDFGD-GNVIDTTSPTITHTYSSANTYSVTLTVTDSLGR 1151
                                        67899***********9966666************.******************************997 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   5.7   2.4e-20   7.1e-17       2     101 ..     150     249 ..     148     250 .. 0.98
   2 ?   -3.2   0.0       3.4     1e+04      37      51 ..    1001    1015 ..     999    1023 .. 0.79
   3 ?    1.9   0.2     0.089   2.6e+02      63      94 ..    1288    1319 ..    1281    1321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 2.4e-20
                                       --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CE CS
                             CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelvgtvtvpsLaagesttvsftwtteatege 77 
                                        DLt++ +++ ++++v+ee+ti++ v N G+++  ++++v++y d  +  + ++++L +++ + +sf++t++ ++g+
  gi|488600066|ref|YP_007906537.1| 150 KDLTISLKVSNANPEVNEEITIYADVMNVGSEDiNESFTVRFYYDSIEIYNEIINGLTSQSVEHISFSYTPT-STGQ 225
                                       5********************************9*************************************9.**** PP

                                       EEEEEEESTT-SS--SSCCCSEEE CS
                             CARDB  78 vtltvvvDpdnevaEsnEtNNelt 101
                                       + ++ vvD+d+ + E nE+NN+ +
  gi|488600066|ref|YP_007906537.1| 226 HVIKGVVDADGAIVEDNENNNVSS 249
                                       *********************987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.4
                                        EEEEEEEETTEEEEE CS
                             CARDB   37 atkvalyldgelvgt 51  
                                        + ++++yldg++v++
  gi|488600066|ref|YP_007906537.1| 1001 KANTRIYLDGSEVAS 1015
                                        67999*****99954 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.089
                                        EEEEEEEE-S-S-CEEEEEEEESTT-SS--SS CS
                             CARDB   63 ttvsftwtteategevtltvvvDpdnevaEsn 94  
                                        t++ +++ t+ t++e+ +++++D++n+v   n
  gi|488600066|ref|YP_007906537.1| 1288 TNIYISDSTIDTSSEYNMKISIDATNYVFANN 1319
                                        67778899988999999**********96655 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.4   2.6e-12   7.6e-09       1      75 [.      12      79 ..      12      85 .. 0.82
   2 ?   -2.7   0.0       4.1   1.2e+04      47      67 ..     389     406 ..     359     411 .. 0.58
   3 ?   -2.5   0.1       3.4     1e+04      36      77 ..     672     719 ..     668     724 .. 0.64
   4 ?   -2.7   0.0       3.8   1.1e+04      47      67 ..     794     811 ..     762     816 .. 0.57
   5 ?   -2.6   0.1       3.8   1.1e+04      36      77 ..    1085    1132 ..    1083    1137 .. 0.62
   6 ?   -1.5   0.2       1.7   5.2e+03      26      76 ..    1371    1423 ..    1364    1432 .. 0.42

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.6e-12
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgknavslehkgGdsidtkdlkiv 75
                                      +AVS+ i +iLm+aitv +++via+++ ++    ++ p+ + +++ ++ +++    +++ h gG+ ++ +d+ i 
  gi|488600066|ref|YP_007906537.1| 12 RAVSELISIILMIAITVGAFSVIAVSIYSF---LQTPPSKHADFQAEKIGDE----LVIYHTGGEELSGDDIIIF 79
                                      69****************************...3444554444455666665....*************999875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.1
                           Pilin_N  47 dssastgkna....vslehkgGdsi 67 
                                        +       +    + +++++G ++
  gi|488600066|ref|YP_007906537.1| 389 AN-------SdgsdIRFTESDGSTF 406
                                       11.......1233489999988876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.4
                           Pilin_N  36 kapqasievkidssastgkna......vslehkgGdsidtkdlkivln 77 
                                       ++pq++ e++ ++s+st ++             +G++idt + +i+ +
  gi|488600066|ref|YP_007906537.1| 672 STPQVNEEITFNASSSTPSEPggsitnYHWDFGDGNVIDTTSPTITHT 719
                                       578888777777776665444556333444456788888888777754 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 3.8
                           Pilin_N  47 dssastgkna....vslehkgGdsi 67 
                                        +       +    + +++++G ++
  gi|488600066|ref|YP_007906537.1| 794 AN-------SdgsdIRFTESDGSTF 811
                                       11.......1233388888888776 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 3.8
                           Pilin_N   36 kapqasievkidssastgkna......vslehkgGdsidtkdlkivln 77  
                                        ++pq++ e++ ++s+st ++             +G++idt + +i+ +
  gi|488600066|ref|YP_007906537.1| 1085 STPQVNEEITFNASSSTPSEPggsitnYHWDFGDGNVIDTTSPTITHT 1132
                                        578888777777666665444556333444456788888888777754 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 1.7
                           Pilin_N   26 fvlgl.asneekapqasievkidssastgkna...vslehkgGdsidtkdlkivl 76  
                                         v+ + a+++ +a  ++i+ +  ++++ +        l+  gG+  ++ ++ i++
  gi|488600066|ref|YP_007906537.1| 1371 GVVTInAGTQLTASDIKIDNTKAYNKKVE--IyssGDLNITGGEIRSKGNVLIQT 1423
                                        55555444555555555533322222221..122333333444444444444443 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.054   1.6e+02      35      66 ..     297     328 ..     288     330 .. 0.85
   2 ?   -2.3   0.0       1.3   3.9e+03      43      65 ..     600     622 ..     563     624 .. 0.60
   3 ?    6.0   0.1    0.0033        10      34      67 ..     698     733 ..     677     734 .. 0.88
   4 ?    6.0   0.1    0.0033        10      34      67 ..    1111    1146 ..    1090    1147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.054
                             PKD_3  35 faWtieGkivsteptytfteeelgsyevtlev 66 
                                       + W   +    t  + t + ++ g+y+vtl+v
  gi|488600066|ref|YP_007906537.1| 297 YIWDFGDGDTATGVVTTHSYSSPGTYDVTLTV 328
                                       78888888888999999999**********98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                             PKD_3  43 ivsteptytfteeelgsyevtle 65 
                                       + s  p+++++ ++  ++++ + 
  gi|488600066|ref|YP_007906537.1| 600 ENSAKPSLEYSGSTFSTFYLGIA 622
                                       44666777777777777777665 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0033
                             PKD_3  34 afaWtie.Gkiv.steptytfteeelgsyevtleve 67 
                                       ++ W    G+++  t pt+t t +++ +y vtl+v+
  gi|488600066|ref|YP_007906537.1| 698 NYHWDFGdGNVIdTTSPTITHTYSSANTYSVTLTVT 733
                                       6999998678663679*****************996 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0033
                             PKD_3   34 afaWtie.Gkiv.steptytfteeelgsyevtleve 67  
                                        ++ W    G+++  t pt+t t +++ +y vtl+v+
  gi|488600066|ref|YP_007906537.1| 1111 NYHWDFGdGNVIdTTSPTITHTYSSANTYSVTLTVT 1146
                                        6999998678663679*****************996 PP

>> DUF5011  Domain of unknown function (DUF5011)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.6    0.0087        26       9      66 ..     279     339 ..     275     344 .. 0.67
   2 ?    7.4   1.0    0.0016       4.8      44      71 .]     721     748 ..     705     748 .. 0.92
   3 ?    7.4   1.0    0.0016       4.8      44      71 .]    1134    1161 ..    1118    1161 .. 0.92
   4 ?   -3.9   0.3       5.4   1.6e+04      10      37 ..    1374    1400 ..    1370    1410 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0087
                                       EEEETT-------EEEEET.....TEE-GGG-EEES---TTS-EEEEEEEEEE-TTSEEEEEE CS
                           DUF5011   9 itievgetYkepGatatdd.....dgditskvkvtgsVdtskvGtYtitYtvtdssgneatvt 66 
                                       it +  ++Y+  G + td      dgd  + v +t+s  +s +GtY +t tv d++g  ++ t
  gi|488600066|ref|YP_007906537.1| 279 ITFNASSSYDPDGDKITDYiwdfgDGDTATGVVTTHS--YSSPGTYDVTLTVYDERGGVNSTT 339
                                       6777788888888888876221223444444444443..689*************99665554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                                       TS-EEEEEEEEEE-TTSEEEEEEEEEEE CS
                           DUF5011  44 skvGtYtitYtvtdssgneatvtRtVkV 71 
                                       s + tY++t tvtds g + +vt +V+V
  gi|488600066|ref|YP_007906537.1| 721 SSANTYSVTLTVTDSLGRQDSVTKQVEV 748
                                       56679*********************98 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0016
                                        TS-EEEEEEEEEE-TTSEEEEEEEEEEE CS
                           DUF5011   44 skvGtYtitYtvtdssgneatvtRtVkV 71  
                                        s + tY++t tvtds g + +vt +V+V
  gi|488600066|ref|YP_007906537.1| 1134 SSANTYSVTLTVTDSLGRQDSVTKQVEV 1161
                                        56679*********************98 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 5.4
                                        EEETT-------EEEEETTEE-GGG-EE CS
                           DUF5011   10 tievgetYkepGatatdddgditskvkv 37  
                                        ti+ g++ + ++++  d+ +  ++kv++
  gi|488600066|ref|YP_007906537.1| 1374 TINAGTQLTASDIKI-DNTKAYNKKVEI 1400
                                        555555555555443.344445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.80u 0.27s 00:00:01.07 Elapsed: 00:00:00.45
# Mc/sec: 10166.56
//
Query:       gi|488600067|ref|YP_007906538.1|  [L=190]
Description: hypothetical protein Asulf_00522 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0041   17.2   0.7     0.0085   16.2   0.7    1.6  1  DiS_P_DiS      Bacterial Peptidase A24 N-terminal domain
  ------ inclusion threshold ------
      0.024   14.7   1.1        3.7    7.7   0.1    2.2  2  UPF0547        Uncharacterised protein family UPF0547
      0.049   13.9   0.5         21    5.4   0.0    3.1  4  zf-LITAF-like  LITAF-like zinc ribbon domain
      0.069   13.2   0.0       0.14   12.2   0.0    1.4  1  DZR            Double zinc ribbon
       0.11   12.4   2.0       0.81    9.7   0.1    2.4  2  zinc_ribbon_4  zinc-ribbon domain
       0.29   10.6   0.1       0.29   10.6   0.1    2.2  2  zf-ribbon_3    zinc-ribbon domain
       0.34   10.7   2.8          8    6.3   0.2    2.4  2  zinc_ribbon_5  zinc-ribbon domain
        1.3    8.5   3.3         17    4.9   0.3    2.9  3  Mu-like_Com    Mu-like prophage protein Com
        1.6    8.5   8.1        3.6    7.4   1.2    2.4  2  Rubredoxin_2   Rubredoxin metal binding domain
        1.8    8.8   6.1         17    5.7   0.6    2.9  4  zf-RING_7      C4-type zinc ribbon domain
        2.4    8.0   6.8       0.74    9.6   0.5    2.2  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.7   5.2e-06    0.0085      29      65 ..       4      43 ..       1      62 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-06
                         DiS_P_DiS 29 rCpkCghklkwleliPvlSylllrg...rCraCkakislr 65
                                      rCp+Cg++l w+  i  +Sy   +g   +C +C++ i+++
  gi|488600067|ref|YP_007906538.1|  4 RCPNCGTRLPWWWRIAEISYRRSGGyynKCPSCRRWIKVK 43
                                      8********************9998777999999988875 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.008        13       3      10 ..       5      12 ..       3      14 .. 0.58
   2 ?    7.7   0.1    0.0023       3.7       2      14 ..      32      44 ..      31      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.008
                           UPF0547  3 CPeCeakv 10
                                      CP C + +
  gi|488600067|ref|YP_007906538.1|  5 CPNCGTRL 12
                                      66665555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                           UPF0547  2 vCPeCeakvPvaa 14
                                      +CP C++ ++v a
  gi|488600067|ref|YP_007906538.1| 32 KCPSCRRWIKVKA 44
                                      7******999866 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.017        28      56      66 ..       2      12 ..       1      15 [. 0.74
   2 ?    5.4   0.0     0.013        21      58      68 ..      32      42 ..      27      67 .. 0.74
   3 ?   -3.1   0.0         6   9.7e+03      27      38 ..      94     105 ..      91     110 .. 0.57
   4 ?   -1.4   0.0       1.7   2.8e+03      17      39 ..     122     144 ..     117     158 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                     zf-LITAF-like 56 ehyCpnCgall 66
                                      e +CpnCg++l
  gi|488600067|ref|YP_007906538.1|  2 ELRCPNCGTRL 12
                                      56789998876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                     zf-LITAF-like 58 yCpnCgallgt 68
                                      +Cp+C++++++
  gi|488600067|ref|YP_007906538.1| 32 KCPSCRRWIKV 42
                                      56777666654 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6
                     zf-LITAF-like  27 twllalllclfg 38 
                                        +l+a+++++  
  gi|488600067|ref|YP_007906538.1|  94 VYLAAFMIVFSV 105
                                       455555554443 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.7
                     zf-LITAF-like  17 Tsveyksgkltwllalllclfgc 39 
                                        s+e+k  +l + lall  ++ +
  gi|488600067|ref|YP_007906538.1| 122 PSIEKKRLSLKFALALLTPMLVL 144
                                       56777777777766644433333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.7e-05      0.14      15      40 ..       5      42 ..       2      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
                               DZR 15 CseCgtklkavaa............edrCpsCgekvdp 40
                                      C++Cgt+l+   +             ++CpsC + ++ 
  gi|488600067|ref|YP_007906538.1|  5 CPNCGTRLPWWWRiaeisyrrsggyYNKCPSCRRWIKV 42
                                      *******97555588899999***999*****987665 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0005      0.81       1      11 [.       1      11 [.       1      12 [. 0.76
   2 ?    1.7   0.2      0.15   2.4e+02      27      32 ..      32      37 ..      29      41 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                     zinc_ribbon_4  1 MkitCpsCkak 11
                                      M  +Cp+C+++
  gi|488600067|ref|YP_007906538.1|  1 MELRCPNCGTR 11
                                      78888888875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                     zinc_ribbon_4 27 rCskCg 32
                                      +C+ C+
  gi|488600067|ref|YP_007906538.1| 32 KCPSCR 37
                                      466665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00018      0.29       4      10 ..       4      10 ..       1      13 [. 0.64
   2 ?    1.1   2.0      0.17   2.8e+02       4       8 ..      32      36 ..      30      36 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                       zf-ribbon_3  4 rCPnCGa 10
                                      rCPnCG+
  gi|488600067|ref|YP_007906538.1|  4 RCPNCGT 10
                                      7777776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.17
                       zf-ribbon_3  4 rCPnC 8 
                                      +CP+C
  gi|488600067|ref|YP_007906538.1| 32 KCPSC 36
                                      45555 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0049         8       2      11 ..       2      11 ..       1      12 [. 0.83
   2 ?    4.2   0.3     0.022        36       4      25 ..      32      52 ..      31      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0049
                     zinc_ribbon_5  2 iirCpdCdtk 11
                                        rCp+C+t 
  gi|488600067|ref|YP_007906538.1|  2 ELRCPNCGTR 11
                                      579*****95 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.022
                     zinc_ribbon_5  4 rCpdCdtkFklvdsklKksgkk 25
                                      +Cp C+   k+  +  K + k+
  gi|488600067|ref|YP_007906538.1| 32 KCPSCRRWIKVKAEH-KRLEKR 52
                                      7*****999999887.777766 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 ?    4.9   0.3     0.011        17      24      32 ..       2      10 ..       1      12 [. 0.84
   2 ?    2.5   0.1     0.061     1e+02      26      44 ..      32      50 ..      29      56 .. 0.79
   3 ?   -0.4   0.0      0.49   7.9e+02      12      25 ..     160     173 ..     157     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                       Mu-like_Com 24 tiKCPRCGt 32
                                      +++CP CGt
  gi|488600067|ref|YP_007906538.1|  2 ELRCPNCGT 10
                                      579*****9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.061
                       Mu-like_Com 26 KCPRCGtLnHlkaesldae 44
                                      KCP C     +kae    e
  gi|488600067|ref|YP_007906538.1| 32 KCPSCRRWIKVKAEHKRLE 50
                                      9****99999999877666 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.49
                       Mu-like_Com  12 RLLaKaeAlDelti 25 
                                       RLLa   A+D l i
  gi|488600067|ref|YP_007906538.1| 160 RLLAMVAAVDILSI 173
                                       9*********7766 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.9     0.015        24      16      21 ..       4       9 ..       4      17 .. 0.62
   2 ?    7.4   1.2    0.0022       3.6      16      23 ..      32      39 ..      25      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                      Rubredoxin_2 16 rCpsCg 21
                                      rCp+Cg
  gi|488600067|ref|YP_007906538.1|  4 RCPNCG 9 
                                      566665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0022
                      Rubredoxin_2 16 rCpsCgsW 23
                                      +CpsC+ W
  gi|488600067|ref|YP_007906538.1| 32 KCPSCRRW 39
                                      9******* 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 ?    5.7   0.6      0.01        17      25      30 ..       4       9 ..       2      10 .. 0.88
   2 ?    5.2   0.1     0.015        25      25      32 ..      32      39 ..      19      40 .. 0.90
   3 ?   -3.0   0.0       5.5     9e+03       7      13 ..      87      93 ..      87      94 .. 0.85
   4 ?   -3.1   0.0       5.7   9.4e+03      11      20 ..     104     113 ..      99     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                                      E-TTT- CS
                         zf-RING_7 25 tCpeCG 30
                                      +Cp+CG
  gi|488600067|ref|YP_007906538.1|  4 RCPNCG 9 
                                      9****9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                                      E-TTT--E CS
                         zf-RING_7 25 tCpeCGRI 32
                                      +Cp+C R+
  gi|488600067|ref|YP_007906538.1| 32 KCPSCRRW 39
                                      6******7 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.5
                                      -B--CCH CS
                         zf-RING_7  7 melppqv 13
                                      me++p++
  gi|488600067|ref|YP_007906538.1| 87 MEINPEL 93
                                      99***97 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5.7
                                       CCHHHHHCCS CS
                         zf-RING_7  11 pqvlselrag 20 
                                       +  +s+l+++
  gi|488600067|ref|YP_007906538.1| 104 SVIWSDLKRA 113
                                       5578999987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5   0.00045      0.74       2       9 ..       5      12 ..       4      13 .. 0.63
   2 ?    1.5   1.0      0.17   2.7e+02       1       5 [.      32      36 ..      31      38 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00045
                     zinc_ribbon_2  2 CpnCGael 9 
                                      CpnCG+ l
  gi|488600067|ref|YP_007906538.1|  5 CPNCGTRL 12
                                      77777655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                     zinc_ribbon_2  1 fCpnC 5 
                                      +Cp+C
  gi|488600067|ref|YP_007906538.1| 32 KCPSC 36
                                      68888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1101.72
//
Query:       gi|488600068|ref|YP_007906539.1|  [L=479]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-104  348.7   0.0     3e-104  348.2   0.0    1.1  1  GatB_N     GatB/GatE catalytic domain
      3e-45  153.7   0.1    5.2e-45  153.0   0.1    1.4  1  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
      0.021   14.5   0.0       0.16   11.7   0.0    2.2  2  SH3_2      Variant SH3 domain
      0.021   15.1   0.4       0.04   14.2   0.4    1.4  1  zf-Di19    Drought induced 19 protein (Di19), zinc-binding


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.2   0.0  6.7e-108    3e-104       1     267 [.       8     283 ..       8     288 .. 0.97

  Alignments for each domain:
  == domain 1  score: 348.2 bits;  conditional E-value: 6.7e-108
                                       EEEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEE CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N   1 lviGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRK 76 
                                       +viGlE+H+ql++ ++KlF+s+st+ +++epn++v++v+l+lPG++Pv+nkeav+ a+k+alaln+e+++ + fdRK
  gi|488600068|ref|YP_007906539.1|   8 VVIGLEVHVQLNKlNTKLFCSCSTSYHEDEPNTHVCPVCLGLPGAMPVINKEAVKFAVKTALALNAEVQPFTVFDRK 84 
                                       69*********998*********8888899*********************************************** PP

                                       E-TCTTCTTSEEEEESSS.SEEEEEEEE.....TEEEEEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                            GatB_N  77 nyfypdlpkgyQitqkeeplakeGslel.....ekkvrierihlEeDaaksvh....eekeeslvdlnRaGvpLiEi 144
                                       nyfypdlpkg+Qi+q+++pla +G++++     ekk+ ++rih+EeD +k  +    +++++sl+d+nR+G+pL+Ei
  gi|488600068|ref|YP_007906539.1|  85 NYFYPDLPKGFQISQYDNPLALGGYVTIetdsgEKKITLKRIHMEEDPGKLSYkgsiTTAKYSLIDYNRSGMPLLEI 161
                                       ***************************999*9999****************9988875777**************** PP

                                       EE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 145 vtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieye 221
                                       vtep ++sp+ear++++klr +l++l+v dg++ eG++R+D+N+S++        g rvEiKn++s+k +e+a++ye
  gi|488600068|ref|YP_007906539.1| 162 VTEPVMHSPKEAREFLNKLRIILEYLDVFDGSL-EGAMRVDANISLKG-------GGRVEIKNISSFKGVERALTYE 230
                                       *********************************.7************4.......48******************** PP

                                       HHHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE- CS
                                       xxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 222 ierqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlpplei 267
                                       i+rq +ll       +eTr+fde+++ tvslR+kee++dYryfpepdl+p+  
  gi|488600068|ref|YP_007906539.1| 231 ITRQKNLLrrgrkveRETRHFDEANNITVSLRTKEEEQDYRYFPEPDLVPIYT 283
                                       **************************************************975 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   0.1   1.2e-48   5.2e-45       1     148 []     327     475 ..     327     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 1.2e-48
                                       HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTC..SSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXX CS
                         GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleiee..lkltpeqlaellkliaegkIskkiakevleelleegks 75 
                                       d+feev+++  d+k+aa+w+++ l geln++++++     +++p ++++++++++++kI++k+a e++++ l++g++
  gi|488600068|ref|YP_007906539.1| 327 DYFEEVASKV-DSKKAARWIVDVLRGELNYRDKDFRYayERFPPGDMVRVIEYLENEKITDKSAVEIIRTKLDHGGD 402
                                       89*******7.***********************9986679************************************ PP

                                       HHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  76 peeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       ++ ii+ek+L++i +eee+ +l+ ++++enpkavedy sgk++a++flvGqvMk+tkG+adp++  +++k+++
  gi|488600068|ref|YP_007906539.1| 403 VDGIIQEKNLFAIDEEEEILNLCRKAVEENPKAVEDYLSGKKNAINFLVGQVMKATKGRADPAECFQIIKKII 475
                                       **********************************************************************986 PP

>> SH3_2  Variant SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.22   9.7e+02      21      39 ..     370     394 ..     366     412 .. 0.57
   2 ?   11.7   0.0   3.5e-05      0.16       3      32 ..     434     461 ..     434     469 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.22
                                       TEEEEEE........EEEECTTEEE CS
                             SH3_2  21 Gdvikvls......lgskdsdgwwe 39 
                                       Gd ++v++      + +k+  + ++
  gi|488600068|ref|YP_007906539.1| 370 GDMVRVIEylenekITDKSAVEIIR 394
                                       9999999876444444444444444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.5e-05
                                       EESS-B-SCGCCB--B-TTEEEEEE..EEE CS
                             SH3_2   3 raiedyvgedkseLsfkkGdvikvlslgsk 32 
                                       +a+edy + +k+ ++f +G+v k++  +++
  gi|488600068|ref|YP_007906539.1| 434 KAVEDYLSGKKNAINFLVGQVMKAT--KGR 461
                                       79**********************9..444 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   8.9e-06      0.04      12      38 ..      21      47 ..      17      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.9e-06
                           zf-Di19 12 ltvkeLveHvedeHrveskevvCPvCa 38
                                      l++k +++  ++ H +e + +vCPvC 
  gi|488600068|ref|YP_007906539.1| 21 LNTKLFCSCSTSYHEDEPNTHVCPVCL 47
                                      6678888889999*************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2720.77
//
Query:       gi|488600069|ref|YP_007906540.1|  [L=670]
Description: DNA topoisomerase I [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-129  432.4   1.7   2.6e-129  431.8   1.7    1.2  1  Topoisom_bac    DNA topoisomerase
    6.9e-17   61.6   0.4      2e-16   60.1   0.4    1.8  1  Toprim          Toprim domain
    1.3e-13   50.4   3.1    1.3e-13   50.4   3.1    2.4  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
      0.036   14.5   0.0       0.12   12.8   0.0    2.0  1  Toprim_4        Toprim domain
       0.11   13.3   1.2         11    6.8   0.0    3.4  3  CsgA            Minor curli fiber component A
       0.67   10.2   3.5       0.48   10.7   0.4    2.4  3  DUF2283         Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.8   1.7  8.8e-133  2.6e-129       2     412 ..     152     550 ..     151     551 .. 0.94

  Alignments for each domain:
  == domain 1  score: 431.8 bits;  conditional E-value: 8.8e-133
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76 
                                       +++nl+++ae+R+++D+++G+ l+rl++++  +  k++ls+GRVq+ptL+liveRe+ei+nF+p++ywe+ a++ k+
  gi|488600069|ref|YP_007906540.1| 152 VDFNLAKSAEIRQKIDLIWGAVLTRLISLSSGRlgKDFLSVGRVQSPTLRLIVEREEEIKNFKPKKYWEIFASFRKG 228
                                       689**************************5444569*************************************9888 PP

                      Topoisom_bac  77 kkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqk 153
                                       ++ +   + k+++r++dke+ae++++k+ + + +v+s+ekke+ ++pp+pf+tt++++eas+   +s +k++++a++
  gi|488600069|ref|YP_007906540.1| 229 EEVF---QCKHEKRFEDKEQAEKAFAKVGD-KGVVVSFEKKERAEKPPTPFNTTEFLREASKF--MSVNKAMMVAES 299
                                       8888...699******************55.6******************************9..************ PP

                      Topoisom_bac 154 LYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklk 230
                                       LY + g+i+YpRTd+t+++++ +l+ai+e+l++    e+++ ae +l+++k ++++++k+ ++H++I+Pt  ++k++
  gi|488600069|ref|YP_007906540.1| 300 LYMS-GYISYPRTDNTVYPKTINLRAIVEKLTQG---EFKKEAEFVLSQEKLRATRGKKESKDHPPIHPT-AVAKKD 371
                                       ***7.****************77*********96...678888888887776667888888*********.556569 PP

                      Topoisom_bac 231 elsddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegee 307
                                       els+de+ +Yel+vrrfla+l++da++  ++ k+++++e f+++g++++e+G++k+y ++k+ee +  +p+l+ege 
  gi|488600069|ref|YP_007906540.1| 372 ELSKDEWVIYELVVRRFLATLSPDAIWVVRRGKIDSSGEIFRFNGRKLIEEGWRKIYIYSKAEEVP--VPDLQEGEV 446
                                       *********************************************************999999886..********* PP

                      Topoisom_bac 308 vkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.k 383
                                       +++ + +leek+Tkpp+ry+ +sLik+mek g+Gt++Tr+eii+kl++r+Yv  +   l+p+e G+a++++l+k  +
  gi|488600069|ref|YP_007906540.1| 447 LDIVSKKLEEKETKPPNRYSSGSLIKEMEKLGLGTKSTRHEIINKLYSRKYVYGNP--LRPSEIGMAVINALKKEaE 521
                                       ****************************************************9966..**************5555* PP

                      Topoisom_bac 384 dlvspelTaeleekLdeIaegkadakevl 412
                                       ++++p++T++lee++ +Iaegk++ + v+
  gi|488600069|ref|YP_007906540.1| 522 TITQPDMTSKLEEDMYAIAEGKLSDEYVV 550
                                       ***********************999887 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.4   6.5e-20     2e-16       2     102 ..       6     136 ..       5     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 6.5e-20
                                       EEEESSHHHHHHHHHTHT...............STEEEEEEESSSSEEEHS.....TTEEEEE.........ECTTT CS
                            Toprim   2 lvivEgpsdaktiakalg...............sgfqavtaslGhildlet.....efkpvye.........eiedk 49 
                                       l+i E+++ a+ i+++l                 +++ v+ ++Ghi++l++     ++++v           ++ ++
  gi|488600069|ref|YP_007906540.1|   6 LIITEKDNTARRISSILFknvkkvrkkginvyqADNTYVIGLKGHIVQLDFpeeynNWSKVPLksllradiiKKVTE 82 
                                       8***************999**************999***************76666444444488887887677888 PP

                                       HHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESS CS
                            Toprim  50 kkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefse 102
                                       k+ +++lk++ak+ d++ +atD DreGe i+ e+le +++ ++n ++ rv+ s 
  gi|488600069|ref|YP_007906540.1|  83 KNLVEVLKSIAKEIDRVTIATDYDREGELIGVEALEIIRNENPNvRFDRVRYSA 136
                                       889999*********************************888888888888776 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 !   50.4   3.1   4.5e-17   1.3e-13       1      38 [.     583     622 ..     583     623 .. 0.95
   2 ?    0.2   0.1      0.22   6.6e+02      24      38 ..     654     665 ..     637     668 .. 0.71

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 4.5e-17
                                       -EE-SSS--EEEEEE-SSS..EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   1 vekCPkCggdLvlkrgkkG..kFvGCsnYPeCkftkklkk 38 
                                       v+kCPkC  dLv++++k    +F+GCs YP+C+ft +l++
  gi|488600069|ref|YP_007906540.1| 583 VGKCPKCSRDLVIRKKKGDsrRFIGCSGYPDCNFTLPLPQ 622
                                       58****************9******************997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.22
                                       ESST.T----EEB-G CS
                    zf-C4_Topoisom  24 CsnYPeCkftkklkk 38 
                                       C   P C++ ++ +k
  gi|488600069|ref|YP_007906540.1| 654 C---PYCNYLEWQEK 665
                                       4...55777777666 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-05      0.12      30      76 ..      71     118 ..      57     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                          Toprim_4  30 alspldgirpeklktenlve....aekkvkevilaldgDaeGeataerlae 76 
                                        l  +d i+  k  ++nlve      k++++v++a+d D eGe    +++e
  gi|488600069|ref|YP_007906540.1|  71 LL-RADIIK--KVTEKNLVEvlksIAKEIDRVTIATDYDREGELIGVEALE 118
                                       44.666666..777788999988888899*************987766666 PP

>> CsgA  Minor curli fiber component A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.7   1.4e+04      45      75 ..      81     111 ..      74     114 .. 0.50
   2 ?    6.8   0.0    0.0038        11      22      43 ..     322     343 ..     308     349 .. 0.86
   3 ?    3.3   0.1     0.045   1.4e+02       2      23 ..     551     571 ..     517     583 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.7
                              CsgA  45 seeEiefLnkiLeeeikyakeeqdekRakqL 75 
                                       +e+    + k + +ei+  +   d+ R  +L
  gi|488600069|ref|YP_007906540.1|  81 TEKNLVEVLKSIAKEIDRVTIATDYDREGEL 111
                                       4444333333345566666666666665555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0038
                              CsgA  22 gkeiykkleekeykseeefvkd 43 
                                        + i++kl+++e+k+e efv +
  gi|488600069|ref|YP_007906540.1| 322 LRAIVEKLTQGEFKKEAEFVLS 343
                                       5789***************954 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.045
                              CsgA   2 dqtLaYLrEvlsnyteesevgk 23 
                                       ++++++L E+lsn  ++++ +k
  gi|488600069|ref|YP_007906540.1| 551 EESIRFLDEILSNL-DRESLSK 571
                                       45566666666664.5555555 PP

>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00016      0.48      26      46 ..      96     117 ..      85     119 .. 0.81
   2 ?   -2.3   0.0       1.8   5.4e+03      24      44 ..     244     263 ..     236     267 .. 0.52
   3 ?   -3.1   0.1       3.2   9.6e+03      12      25 ..     428     443 ..     427     449 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                           DUF2283  26 vdd.diilDfDedGrlvGIEiL 46 
                                       +d   i  D+D++G+l+G+E L
  gi|488600069|ref|YP_007906540.1|  96 IDRvTIATDYDREGELIGVEAL 117
                                       55546779************76 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                           DUF2283  24 eevdddiilDfDedGrlvGIE 44 
                                       e+ ++  +  + ++G +v++E
  gi|488600069|ref|YP_007906540.1| 244 EQ-AEKAFAKVGDKGVVVSFE 263
                                       44.444445555555555554 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.2
                           DUF2283  12 YIyl..segpveesee 25 
                                       YIy   +e pv++ +e
  gi|488600069|ref|YP_007906540.1| 428 YIYSkaEEVPVPDLQE 443
                                       7887444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); 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: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 4089.66
//
Query:       gi|488600070|ref|YP_007906541.1|  [L=257]
Description: hypothetical protein Asulf_00525 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  197.3   0.0    3.6e-58  197.2   0.0    1.0  1  ATP_bind_1    Conserved hypothetical ATP binding protein
     0.0032   17.8   0.0     0.0092   16.3   0.0    1.8  1  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.044   13.2   0.0    1.3  1  PhoH          PhoH-like protein
      0.043   13.8   0.1        0.3   11.1   0.0    2.1  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.043   13.6   0.0        1.4    8.7   0.0    2.8  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.095   12.8   0.0       0.12   12.4   0.0    1.2  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
       0.14   12.7   0.0       0.48   11.0   0.0    1.9  2  AAA_18        AAA domain
       0.17   12.3   0.0        1.6    9.2   0.0    2.2  2  RNA_helicase  RNA helicase
       0.21   11.8   0.0       0.33   11.2   0.0    1.3  1  AAA_28        AAA domain
       0.27   11.4   0.0       0.41   10.8   0.0    1.3  1  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2   0.0     2e-61   3.6e-58       1     239 [.       8     246 ..       8     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 2e-61
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflre 77 
                                       ++G+aGsGKt++++a++++l+ ++ +  +vNLDP+ae+lpY+++vdir+++tledvm ++g+gpnga +++++++++
  gi|488600070|ref|YP_007906541.1|   8 FIGTAGSGKTYLTKAFADWLDFKNLENIIVNLDPGAENLPYSPEVDIRDYFTLEDVMLNYGVGPNGAQIISADLIST 84 
                                       59*************************************************************************** PP

                        ATP_bind_1  78 sldwldeeleke.eddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsaml 153
                                       ++ ++++e+ ++ +  y+l+DtPGQ+elft+++s   +++ L  + + v+vyL+D+ ++++p+ f+s l++a+s ++
  gi|488600070|ref|YP_007906541.1|  85 KIGDIKDEI-DYfDVPYVLIDTPGQMELFTLRQSSNLLIDFLG-RDRSVMVYLFDPVVAKTPSGFLSLLFMASSSVF 159
                                       **99*****.77588***************************9.79******************************* PP

                        ATP_bind_1 154 rlelPhvvvlnkfDllkek.lekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesie 229
                                       +l+lP++ vl k D+l+++  e+ +e+  d+e+l   l  e +  k+   ++  +l + +l   ++p+s+ + +++e
  gi|488600070|ref|YP_007906541.1| 160 KLKLPQIQVLAKSDILEDYeVERIVEWSDDPETLFDDLGREVSNIKNISGELFYMLRDLGLFRTLIPVSAMDSTGME 236
                                       *****************9999************999999999*********************************** PP

                        ATP_bind_1 230 dllslideal 239
                                       d+++ i+e++
  gi|488600070|ref|YP_007906541.1| 237 DVYDGIQEIF 246
                                       ******9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.2e-06    0.0092       7      31 ..       5      29 ..       3      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqlde 31
                                      +++ +G +G+GKT+l + ++++ld 
  gi|488600070|ref|YP_007906541.1|  5 LIYFIGTAGSGKTYLTKAFADWLDF 29
                                      6899******************973 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.044      21      53 ..       5      36 ..       2      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                      EEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEE CS
                              PhoH 21 ivfaiGpaGtGKtylavalavealkkkkvkrii 53
                                      ++  iG aG+GKtyl+ a a + l  k++++ii
  gi|488600070|ref|YP_007906541.1|  5 LIYFIGTAGSGKTYLTKAFA-DWLDFKNLENII 36
                                      57789***********9987.556666666666 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016       0.3      21      46 ..       5      30 ..       1      35 [. 0.85
   2 ?    0.1   0.0      0.43   7.6e+02      88     106 ..     174     193 ..     158     209 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                      EEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 21 vilLeGdLGaGKTtlvrglakalgve 46
                                      +i++ G  G+GKT l++++a  l+++
  gi|488600070|ref|YP_007906541.1|  5 LIYFIGTAGSGKTYLTKAFADWLDFK 30
                                      6999***************9988765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.43
                                       CCS.TSCEEEEETGGGGCCC CS
                              TsaE  88 yle.eeavvlvEWpekleel 106
                                       +le +e   +vEW++  e+l
  gi|488600070|ref|YP_007906541.1| 174 ILEdYEVERIVEWSDDPETL 193
                                       44323345699**9985544 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00078       1.4       4      23 ..       6      25 ..       3      36 .. 0.87
   2 ?    1.2   0.0      0.16   2.9e+02      39      47 ..     101     109 ..      91     186 .. 0.67
   3 ?   -0.7   0.0      0.59   1.1e+03     115     142 ..     215     243 ..     200     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00078
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      i +iG+ gsGKt Lt+a+ +
  gi|488600070|ref|YP_007906541.1|  6 IYFIGTAGSGKTYLTKAFAD 25
                                      789*************9865 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.16
                         PduV-EutP  39 eviDtPGey 47 
                                        +iDtPG+ 
  gi|488600070|ref|YP_007906541.1| 101 VLIDTPGQM 109
                                       579999974 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.59
                         PduV-EutP 115 LksaGa.ekifevsavekegieellkyle 142
                                       L+  G  ++++ vsa++++g+e++ + ++
  gi|488600070|ref|YP_007906541.1| 215 LRDLGLfRTLIPVSAMDSTGMEDVYDGIQ 243
                                       5555641456899********99987665 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 ?   12.4   0.0   6.8e-05      0.12       6      55 ..      10      88 ..       5     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                                      SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.............................. CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                              CbiA  6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.............................. 54
                                      ++ G+GKT l+ ++a  l  ++l+ + v +Dp a+nl   +  e di+                               
  gi|488600070|ref|YP_007906541.1| 10 GTAGSGKTYLTKAFADWLDFKNLENIIVNLDPGAENLP--YSPEVDIRDyftledvmlnygvgpngaqiisadlistki 86
                                      678**********************************9..555555555556666666677777766666444444444 PP

                                      .C CS
                                      .x RF
                              CbiA 55 .d 55
                                       d
  gi|488600070|ref|YP_007906541.1| 87 gD 88
                                      40 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.48       1      35 [.       6      61 ..       6     125 .. 0.80
   2 ?   -0.9   0.0       1.3   2.3e+03      25      49 ..     172     197 ..     156     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvaken 35
                                      I   Gt+G+GKt l+k+ ++ l f                      v +rd+++ +
  gi|488600070|ref|YP_007906541.1|  6 IYFIGTAGSGKTYLTKAFADWLDFknleniivnldpgaenlpyspEVDIRDYFTLE 61
                                      6678*************987765555555566666666666666655555555554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                            AAA_18  25 gvnlrdvakenglllevdpe.aldes 49 
                                       +++l d+  e+  ++++dpe  +d+ 
  gi|488600070|ref|YP_007906541.1| 172 SDILEDYEVERIVEWSDDPEtLFDDL 197
                                       46777888888888888887544443 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00088       1.6       1      22 [.       6      27 ..       6      52 .. 0.85
   2 ?    0.3   0.0       0.5   8.9e+02      49      73 ..     188     214 ..     165     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00088
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakal 22
                                      i++ G +g GK++l+k +a+ l
  gi|488600070|ref|YP_007906541.1|  6 IYFIGTAGSGKTYLTKAFADWL 27
                                      79***************87655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.5
                      RNA_helicase  49 gqevvvidDfgqvkdee.nps.dlael 73 
                                       + + +++dD+g+ +++  n s +l+ +
  gi|488600070|ref|YP_007906541.1| 188 DDPETLFDDLGREVSNIkNISgELFYM 214
                                       566788999999998866766666655 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   0.00019      0.33       2      21 ..       6      25 ..       5      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      i+++G+ ++GKT l++a+a+
  gi|488600070|ref|YP_007906541.1|  6 IYFIGTAGSGKTYLTKAFAD 25
                                      99***************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   0.0   0.00023      0.41       1      20 [.       5      24 ..       5      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      l++++G +GsGK++l +  +
  gi|488600070|ref|YP_007906541.1|  5 LIYFIGTAGSGKTYLTKAFA 24
                                      79*************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1646.83
//
Query:       gi|488600071|ref|YP_007906542.1|  [L=453]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-18   64.3   0.0    1.7e-17   63.1   0.0    1.7  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 !   63.1   0.0   9.5e-22   1.7e-17       1      67 [.     316     379 ..     316     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 9.5e-22
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       frkl+ +l+yk ++ G++v+ v p+ TS +C+ Cg  + +  ++++f+Cp  g++ ++D nA++Nil
  gi|488600071|ref|YP_007906542.1| 316 FRKLQLFLKYKLEWLGVPVKFVPPEDTSRRCPLCGVLGIR--HKKLFTCP-NGHKGHADRNASVNIL 379
                                       89**************************************..********.8**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2628.90
//
Query:       gi|488600072|ref|YP_007906543.1|  [L=637]
Description: putative RNA-binding protein-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-82  275.6  16.2    9.2e-82  275.2  16.2    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
    2.3e-22   79.7   0.0    6.3e-22   78.3   0.0    1.8  1  NFACT-R_1      NFACT protein RNA binding domain
      3e-05   24.4   0.0      3e-05   24.4   0.0    3.1  4  Ribosomal_S13  Ribosomal protein S13/S18
    9.8e-05   22.5   0.5    0.00045   20.4   0.0    2.3  2  NFACT-R_2      NFACT protein RNA binding domain
    0.00031   20.7   0.0    0.00085   19.3   0.0    1.8  1  H2TH           Formamidopyrimidine-DNA glycosylase H2TH domai
  ------ inclusion threshold ------
      0.047   14.1   0.6       0.22   12.0   0.6    2.1  1  Ago_N_1        Fungal Argonaute N-terminal domain
      0.088   12.8   0.2       0.17   11.9   0.2    1.5  1  PTS_2-RNA      RNA 2'-phosphotransferase, Tpt1 / KptA family
       0.12   12.5   9.2       0.34   11.0   2.7    2.7  2  Mod_r          Modifier of rudimentary (Mod(r)) protein
       0.53   10.6   6.4         38    4.7   6.4    2.6  1  Lzipper-MIP1   Leucine-zipper of ternary complex factor MIP1
       0.73    9.9   4.6        8.5    6.5   0.3    3.3  4  Chalcone_3     Chalcone isomerase-like
        3.6    7.7  18.1       0.78    9.8  11.7    2.6  2  DHR10          Designed helical repeat protein 10 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 !  275.2  16.2   5.7e-85   9.2e-82       2     420 ..       6     423 ..       5     439 .. 0.95

  Alignments for each domain:
  == domain 1  score: 275.2 bits;  conditional E-value: 5.7e-85
                                       HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEEETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHH CS
                              FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlranrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRk 78 
                                       +++++a+++EL+  +++gridkiy   +de+++++r+ + +  L ++a   ++rihlt+ p++ p  p++F+mlLRk
  gi|488600072|ref|YP_007906543.1|   6 AVDIKAIISELKV-IEDGRIDKIYHNPPDEIRIRIRKPGSKFELIIEA---GKRIHLTKFPRQAPRIPSSFAMLLRK 78 
                                       689**********.***********************9***9******...************************** PP

                                       HHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTT CS
                              FbpA  79 yLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpg 155
                                       +L+g+ri +i q++fdRiv  ++e+       e++ Li+Ei+ + +N+iL de+ kIi ++k   ++         g
  gi|488600072|ref|YP_007906543.1|  79 HLEGGRIRRIYQHDFDRIVFVEVERE------EKKVLIAEIFKK-GNVILADENWKIIMPLKPFFKS---------G 139
                                       *************************9......9999********.*******999*********444.........* PP

                                       XBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............H CS
                              FbpA 156 ekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerly 232
                                       e+Y lP +  + +P+e+++ e+++ l    +k++vkaL++++  +++ +aee++ rag++k++ a+el++e+ +r+ 
  gi|488600072|ref|YP_007906543.1| 140 ETYRLPKP--QKSPFELKK-EDLDVL---GDKEIVKALATSL-SVGGIYAEEICLRAGINKKKLASELNDEEKDRIV 209
                                       ********..889999999.776666...799**********.********************************** PP

                                       HHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHH.HHHHHHHHHH CS
                              FbpA 233 ealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrve.qkrsdlekrv 308
                                        a++e++ ++ +e+f+p++++ke +  +f +++l+  +++ek++fds+++a+de+Y++k  +++ + +++++  +r+
  gi|488600072|ref|YP_007906543.1| 210 RAVEEIFLPIANESFKPHILIKEGEYADFLPIELRIFDDYEKKYFDSFNDAVDEFYSRKIVEEAEKrEEENKELQRL 286
                                       ***********************9999999999*9999*********************99999994566666788* PP

                                       HHHHHHHHHHHHHHHHHHHCCGGH.....HHHHCCHH-----------------------..--............. CS
                              FbpA 309 eneleklekklkklekelekaeka.....enyrligelltaylyaikkgmsevelenyyde.ge............. 366
                                       +++le + +  +++e+e+++ +k+     e+y +i+ +l ++++a+ +++s++e++++ ++ ++             
  gi|488600072|ref|YP_007906543.1| 287 RKRLEDQLSAKERFEREMDELRKKgdfiyEQYTKIEKILDVFRKAR-EKKSWDEIKEIVKKdKKlrelvkdinsaen 362
                                       *******************************************999.667**********96559************ PP

                                       .......---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 367 .......evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeeleylesveaal 420
                                              + tI L  +k+ ++ A+ y+ k+kK++++ e+v ++i +tk+ +e++++ + ++
  gi|488600072|ref|YP_007906543.1| 363 rvsvrldGYTIDLYLDKTLPQIADIYYSKAKKIRQKYEGVLKAIDNTKAAMEKIKNEKRFV 423
                                       ******999*********************************************9987665 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   3.8e-25   6.3e-22       2     109 .]     438     546 ..     437     546 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 3.8e-25
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia. 77 
                                       ++wF++s+g+lvi+G++++ nee++++y+e++d++fh  + +++ ++l+  +g+  +  e++leeaa + + +S+  
  gi|488600072|ref|YP_007906543.1| 438 FRWFITSEGFLVIGGRNAKMNEEIVSRYMEKNDLFFHTQVPGAPATILK--NGQ--SAGEKSLEEAAIFSATYSSLw 510
                                       99***********************************************..777..89******************* PP

                         NFACT-R_1  78 gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       ++ + s +v+yv++++++++a+    l++Gs+ ++g
  gi|488600072|ref|YP_007906543.1| 511 REGKYSGEVYYVRPEQVKRSAKageyLARGSFYIEG 546
                                       88888****************9999******99976 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.8e-08     3e-05       5      85 ..     159     239 ..     157     251 .. 0.85
   2 ?   -1.4   1.1       1.8   2.9e+03      40      93 ..     272     323 ..     263     343 .. 0.62
   3 ?   -1.7   0.2       2.1   3.5e+03      38      84 ..     305     352 ..     300     368 .. 0.51
   4 ?   -2.0   0.1       2.7   4.3e+03      19      78 ..     383     443 ..     376     467 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-08
                     Ribosomal_S13   5 tdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwinrqkdikdGkd 81 
                                        d+ g+k+++ al++   +G  +a++i+ +a+++++k ++el++ee ++i+  ve+     +++ +     ik+G++
  gi|488600072|ref|YP_007906543.1| 159 LDVLGDKEIVKALATSLSVGGIYAEEICLRAGINKKKLASELNDEEKDRIVRAVEEIFLPIANESFKPHILIKEGEY 235
                                       6899**************************************************99777666666666666666666 PP

                     Ribosomal_S13  82 shvv 85 
                                          +
  gi|488600072|ref|YP_007906543.1| 236 ADFL 239
                                       6555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                     Ribosomal_S13  40 dkrigelteeeiekieeivenkaqykipnwinrqkdikdGkdshvvendlrrkl 93 
                                       ++  +e +++e++++++++e   q  +++ ++r  d    k ++  e+  + ++
  gi|488600072|ref|YP_007906543.1| 272 EAEKREEENKELQRLRKRLED--QLSAKERFEREMDELRKKGDFIYEQYTKIEK 323
                                       455566677888888888888..5555666666666555555555444444444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.1
                     Ribosomal_S13  38 dedkrigelteeeiekieeivenkaqykipnwinrqkd.ikdGkdshv 84 
                                       de  + g++  e+  kie+i++ +++ + ++  +  k+ +k+ k+  +
  gi|488600072|ref|YP_007906543.1| 305 DELRKKGDFIYEQYTKIEKILDVFRKAREKKSWDEIKEiVKKDKKLRE 352
                                       555555666666666666666655555444433333330333333344 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.7
                     Ribosomal_S13  19 aikGiGrrkakiilkka.dvdedkrigelteeeiekieeivenkaqykipnwinrqkdikd 78 
                                       +i  i + kak+i +k  +v + +   + + e+i++ +  v   +  +  +w++r + +++
  gi|488600072|ref|YP_007906543.1| 383 QIADIYYSKAKKIRQKYeGVLKAIDNTKAAMEKIKNEKRFVTSIRVSRKREWYERFRWFIT 443
                                       5666666667777666414555555555555666666666666666666666666555555 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4       4.5   7.3e+03      17      31 ..     276     289 ..     274     297 .. 0.78
   2 !   20.4   0.0   2.7e-07   0.00045       2      74 ..     439     514 ..     439     535 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.5
                         NFACT-R_2  17 eeeEnkflkgllkkd 31 
                                        eeEnk+l++l +k+
  gi|488600072|ref|YP_007906543.1| 276 REEENKELQRL-RKR 289
                                       68999999999.554 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.7e-07
                         NFACT-R_2   2 RhfrlsekaklIvgReeeEnkflkgll..kkdfvslrakshkGplvli.dg.elseedlelaarivarYskgkeeee 74 
                                       R f +se++ +I gR+++ n+++ + +  k+d++ ++++   +p +++ +g ++ e+ le aa + a Ys+  +e +
  gi|488600072|ref|YP_007906543.1| 439 RWFITSEGFLVIGGRNAKMNEEIVSRYmeKNDLF-FHTQVPGAPATILkNGqSAGEKSLEEAAIFSATYSSLWREGK 514
                                       88999*************9999865444555555.7777777788999557355599*************9655544 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.2e-07   0.00085      39      78 ..     177     216 ..     155     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.2e-07
                                       --HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHH CS
                              H2TH  39 lGNiyadEvLfrakihPerlakslskeelellhqeikevl 78 
                                       +G iya+E+  ra+i+ ++la++l++ee +++++++ e++
  gi|488600072|ref|YP_007906543.1| 177 VGGIYAEEICLRAGINKKKLASELNDEEKDRIVRAVEEIF 216
                                       89*********************************99985 PP

>> Ago_N_1  Fungal Argonaute N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00014      0.22       8      68 ..     297     359 ..     292     374 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                       SHHHHH-TT----HHHHHHHHHHHHHHHHS..TTTS----CCHHHHHHHH-HHHHCCCTT-EE CS
                           Ago_N_1   8 dpkfkenekeqytlldWilecykqaeaark..aktkgkpsakdlnlfveknkdikdllkGlkv 68 
                                       + +f+ + +e     d+i e y ++e+  +   k ++k s +++  +v+k+k++++l+k +  
  gi|488600072|ref|YP_007906543.1| 297 KERFEREMDELRKKGDFIYEQYTKIEKILDvfRKAREKKSWDEIKEIVKKDKKLRELVKDINS 359
                                       5677777777777789**********888877789999*********************8765 PP

>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00011      0.17      30     100 ..     318     421 ..     307     495 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                         PTS_2-RNA  30 yvkvedlLelpklkslkvtleeikevVesndKqRFelv.el.................................eel 72 
                                       y k+e++L+  +  + k +++eike+V++++K R   v ++                                 ++ 
  gi|488600072|ref|YP_007906543.1| 318 YTKIEKILDVFRKAREKKSWDEIKEIVKKDKKLREL-VkDInsaenrvsvrldgytidlyldktlpqiadiyysKAK 393
                                       899999**9777777789***********9999955.5366899999999999999999999999999999985337 PP

                         PTS_2-RNA  73 liranqghsikkvesselllepiesaee 100
                                        ir +    +k+++++++ +e+i++++ 
  gi|488600072|ref|YP_007906543.1| 394 KIRQKYEGVLKAIDNTKAAMEKIKNEKR 421
                                       8888887777888888888888877764 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 ?   11.0   2.7   0.00021      0.34      40      93 ..     267     320 ..     248     331 .. 0.89
   2 ?    4.5   0.5     0.021        35       2      28 ..     334     360 ..     333     422 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                             Mod_r  40 aeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfsp 93 
                                        ++++ aek  ++++el+ lr++l+++l+  ++ e+e++e+ ++ d +++++++
  gi|488600072|ref|YP_007906543.1| 267 RKIVEEAEKREEENKELQRLRKRLEDQLSAKERFEREMDELRKKGDFIYEQYTK 320
                                       5678899999999*********************************99999975 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.021
                             Mod_r   2 klSkeeLqelledeeklealvktlpev 28 
                                       k+S +e++e++++++kl++lvk++++ 
  gi|488600072|ref|YP_007906543.1| 334 KKSWDEIKEIVKKDKKLRELVKDINSA 360
                                       8999*****************977653 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   6.4     0.023        38       3      67 ..     273     364 ..     271     380 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.023
                      Lzipper-MIP1   3 sekrssLeqeveqLqerLqeeeklrraLekal...........ssssdgsllslstllpk................. 51 
                                        ekr + ++e ++L++rL+++ + ++  e+ +           +     +  ++++ l+                  
  gi|488600072|ref|YP_007906543.1| 273 AEKREEENKELQRLRKRLEDQLSAKERFEREMdelrkkgdfiyE-----QYTKIEKILDVfrkarekkswdeikeiv 344
                                       678888899**********************9865444333220.....2222333233122333343333333333 PP

                      Lzipper-MIP1  52 ....kakellkeiallEeev 67 
                                           k +el k+i  +E+ v
  gi|488600072|ref|YP_007906543.1| 345 kkdkKLRELVKDINSAENRV 364
                                       33445555555555555555 PP

>> Chalcone_3  Chalcone isomerase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       0.7   1.1e+03      85     120 ..     278     320 ..     255     342 .. 0.49
   2 ?   -0.2   0.2      0.57   9.3e+02      59     106 ..     308     356 ..     287     367 .. 0.73
   3 ?    6.5   0.3    0.0052       8.5      24      77 ..     359     411 ..     352     438 .. 0.73
   4 ?    2.6   0.0     0.078   1.3e+02     100     144 ..     458     504 ..     443     510 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.7
                        Chalcone_3  85 ntaeelaelkari.......ekfkalfakevkkgdvitldylp 120
                                       ++++el++l++r+       e+f++ +++  kkgd i  +y++
  gi|488600072|ref|YP_007906543.1| 278 EENKELQRLRKRLedqlsakERFEREMDELRKKGDFIYEQYTK 320
                                       2233344444444111122234444444445555555444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.57
                        Chalcone_3  59 airleilsrd.vsseklkkaleegfekntaeelaelkariekfkalfak 106
                                       +++ ++++++  + ek+ + ++++ ek++ +e++e+ ++ +k+++l+++
  gi|488600072|ref|YP_007906543.1| 308 RKKGDFIYEQyTKIEKILDVFRKAREKKSWDEIKEIVKKDKKLRELVKD 356
                                       4555666655467789999999999999999999988888888887764 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0052
                        Chalcone_3  24 GaGlRskfffkvYvagLYlpekssdaeailaaeekairleilsrdvsseklkka 77 
                                        a  R  + ++ Y++ LYl ++  + ++i+ ++ k+ir ++    +++ + +ka
  gi|488600072|ref|YP_007906543.1| 359 SAENRVSVRLDGYTIDLYLDKTLPQIADIYYSKAKKIRQKYE-GVLKAIDNTKA 411
                                       5566888999********************998776665543.22333333333 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.078
                        Chalcone_3 100 fkalfakevkkgdvitldylpgkgvvvvvngkqlg..tiegedfakA 144
                                        ++++++ ++k+d +  + +pg   ++++ng+  g  ++e+++++ A
  gi|488600072|ref|YP_007906543.1| 458 NEEIVSRYMEKNDLFFHTQVPGAPATILKNGQSAGekSLEEAAIFSA 504
                                       45688889***********************9975346777666655 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  11.7   0.00048      0.78      44     109 ..     268     333 ..     266     342 .. 0.89
   2 ?    0.6   0.1      0.34   5.6e+02      47      74 ..     394     421 ..     389     427 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00048
                             DHR10  44 eieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaak 109
                                       +i +e +k ee++k+l++lr++le++   ++  er+ + l+++ +   e++++ ++  +  r+a +
  gi|488600072|ref|YP_007906543.1| 268 KIVEEAEKREEENKELQRLRKRLEDQLSAKERFEREMDELRKKGDFIYEQYTKIEKILDVFRKARE 333
                                       5789************************************************99987766666555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                             DHR10  47 aelakleeakkklkelrdaleekeielr 74 
                                       +  +k+e + k ++++++a+e+ ++e+r
  gi|488600072|ref|YP_007906543.1| 394 KIRQKYEGVLKAIDNTKAAMEKIKNEKR 421
                                       5567777777777888888877777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2020  (0.112667); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.88u 0.36s 00:00:01.24 Elapsed: 00:00:00.57
# Mc/sec: 3382.14
//
Query:       gi|488600073|ref|YP_007906544.1|  [L=497]
Description: hypothetical protein Asulf_00530 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-22   79.4   0.7    6.6e-17   61.7   0.0    3.6  4  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.5e-16   60.7   6.3    6.9e-06   25.9   0.0    3.5  3  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    1.7e-05   23.6   0.0    0.00079   18.1   0.0    2.2  2  MutL            MutL protein
    2.3e-05   24.7   2.5       0.28   11.6   0.0    3.4  3  FtsA            Cell division protein FtsA
    0.00063   19.1   0.1      0.021   14.1   0.0    2.5  3  StbA            StbA protein
     0.0028   17.2   0.1       0.84    9.1   0.0    2.7  3  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
     0.0031   15.8   0.4        1.2    7.2   0.2    2.2  2  HSP70           Hsp70 protein
     0.0041   16.0   1.6       0.34    9.7   0.0    2.9  3  MreB_Mbl        MreB/Mbl protein
     0.0082   15.6   0.2       0.43   10.0   0.0    2.3  2  Ppx-GppA        Ppx/GppA phosphatase family


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   3.4e-05     0.068      81     103 ..       2      24 ..       1      51 [. 0.83
   2 ?   -1.9   0.0      0.77   1.5e+03     213     251 ..     122     158 ..      92     159 .. 0.69
   3 !   61.7   0.0   3.3e-20   6.6e-17       1     170 [.     164     314 ..     164     359 .. 0.82
   4 ?    1.0   0.0       0.1   2.1e+02     254     288 ..     368     401 ..     338     403 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                    Hydantoinase_A  81 vItfDmGGTstDvslikdgevev 103
                                        I++D+GGT tD++ ikd+e+++
  gi|488600073|ref|YP_007906544.1|   2 FIGIDVGGTNTDIAIIKDNEIKT 24 
                                       599***************99864 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.77
                    Hydantoinase_A 213 vAegilsvavenmanavrklsvergldpkeltlvvfGGa 251
                                       ++ ++ sv +  + n++ ++  ++  d++  +l  +GG+
  gi|488600073|ref|YP_007906544.1| 122 ISSKF-SVRNASIENKIFEI-ARKYCDERSIALSHYGGG 158
                                       44443.78899999999999.555578888999999885 PP

  == domain 3  score: 61.7 bits;  conditional E-value: 3.3e-20
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       r +ta++nA +   + e  + +++ +       ++++ ++dGg+++ + a ++p e+  S Paa +vga     l++
  gi|488600073|ref|YP_007906544.1| 164 RINTAIINAKIIKTVYELTDTIKSLVG------DFFYYKGDGGIIPYQIALRNPSELYNSSPAAVAVGAYF---LTK 231
                                       667888888777666666666666554......59*********************************999...888 PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpa 154
                                       e+k++++D+GGT+tD  li+dg ++++ + e  g k+ ++ +d  ++  gG+s +   e+g  +++p   g    p 
  gi|488600073|ref|YP_007906544.1| 232 ERKALVIDIGGTTTDFVLIEDGLPKIVENIEFFGRKTLIRCVDSFSIPFGGDSAV---ENG--KLKPGRIGK---P- 299
                                       8899***************************************************...433..455554443...4. PP

                    Hydantoinase_A 155 cyrkGgteltvTDanl 170
                                         + Gg++ t+TDa +
  gi|488600073|ref|YP_007906544.1| 300 -IAFGGENFTLTDALN 314
                                       .356889999999976 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.1
                    Hydantoinase_A 254 qhaaalaeelgvkkvivppyagvlsalGmalAdvr 288
                                        +a+++ ++  v +vivp ++++++a+G+a+++++
  gi|488600073|ref|YP_007906544.1| 368 YLAKRISRASKV-SVIVPDHSESVNAVGVAVSRIS 401
                                       555555555444.57788888*********99875 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 !   25.9   0.0   3.4e-09   6.9e-06       2      75 ..       3      65 ..       2      77 .. 0.71
   2 !   24.0   0.3   1.3e-08   2.6e-05     119     177 ..      89     144 ..      77     145 .. 0.90
   3 !   12.3   0.2   5.3e-05       0.1       2      18 ..     236     252 ..     235     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.4e-09
                        Hydant_A_N  2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerk 75
                                      igIDvGGT+TD+ +++++  e++++K++ + +  + ++r++ +e +e+        + + ++T + +N ll r 
  gi|488600073|ref|YP_007906544.1|  3 IGIDVGGTNTDIAIIKDN--EIKTIKIPNE-EGFEGAFRRIPAEDIEK--------SRIAVSTSLPLNLLLSRS 65
                                      8***************65..7*******99.55555555554444433........445566666666666665 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.3e-08
                        Hydant_A_N 119 vderveadgevlkpldeeevrealkalkaagvesiavvllhSylnpehElrvaeiarei 177
                                       v++ v+++g+v++++de e++e+lk+     ++ ia+++ +S++n++ E ++ eiar++
  gi|488600073|ref|YP_007906544.1|  89 VRGFVNHRGDVVEDIDEREIEEILKSSE---YDNIAISSKFSVRNASIENKIFEIARKY 144
                                       56778999***************98765...789***********************97 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 5.3e-05
                        Hydant_A_N   2 igIDvGGTfTDavalde 18 
                                       + ID+GGT TD+v++++
  gi|488600073|ref|YP_007906544.1| 236 LVIDIGGTTTDFVLIED 252
                                       57************985 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.013        26     250     274 ..       3      25 ..       1      35 [. 0.74
   2 !   18.1   0.0   3.9e-07   0.00079     226     273 ..     217     259 ..     209     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.013
                              MutL 250 lvvDvGGaTTdvhsvaegspekekv 274
                                       +++DvGG+ Td+  +  +++e++++
  gi|488600073|ref|YP_007906544.1|   3 IGIDVGGTNTDIAII--KDNEIKTI 25 
                                       789*********999..44444444 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.9e-07
                              MutL 226 pTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekek 273
                                        +PaAv  ++ +l +e  +   ++lv+D+GG+TTd   + +g p++ +
  gi|488600073|ref|YP_007906544.1| 217 SSPAAVAVGAYFLTKE--R---KALVIDIGGTTTDFVLIEDGLPKIVE 259
                                       68*************3..3...47*************99988887655 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00014      0.28       1      28 [.       3      27 ..       3      67 .. 0.81
   2 !   11.1   0.1   0.00021      0.42       2      28 ..     237     263 ..     236     284 .. 0.84
   3 ?   -0.7   0.1      0.93   1.9e+03      43      52 ..     351     360 ..     310     424 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                      EEEEE-SSSEEEEEEETTEEEEEEEES- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedgalvhlrvigv 28
                                      +++D+G++ td+a+++d++++    i++
  gi|488600073|ref|YP_007906544.1|  3 IGIDVGGTNTDIAIIKDNEIKT---IKI 27
                                      58***************86555...444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00021
                                       EEEE-SSSEEEEEEETTEEEEEEEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA   2 lvDiGagktdvavaedgalvhlrvigv 28 
                                       ++DiG+++td++++edg ++ ++ i +
  gi|488600073|ref|YP_007906544.1| 237 VIDIGGTTTDFVLIEDGLPKIVENIEF 263
                                       8***************98777776665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.93
                                       --HHHHHHHH CS
                                       xxxxxxxxxx RF
                              FtsA  43 taveeAerik 52 
                                       +   eAeri 
  gi|488600073|ref|YP_007906544.1| 351 IESMEAERII 360
                                       2333455554 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.047        93       3      25 ..       3      25 ..       1      43 [. 0.66
   2 !   14.1   0.0     1e-05     0.021     144     187 ..     213     257 ..     204     266 .. 0.84
   3 ?   -3.8   0.0       2.9   5.8e+03     215     247 ..     350     382 ..     338     397 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.047
                              StbA  3 ivvDDGstnikLawledgevktl 25
                                      i +D G tn  +a + d+e+kt 
  gi|488600073|ref|YP_007906544.1|  3 IGIDVGGTNTDIAIIKDNEIKTI 25
                                      55666666666666666666655 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1e-05
                              StbA 144 vlPeslPagfealke.ldeleslLiiDlGGttLDvakvrgklegi 187
                                        l +s Pa++ + +  l +  + L+iD+GGtt D   ++  l +i
  gi|488600073|ref|YP_007906544.1| 213 ELYNSSPAAVAVGAYfLTKERKALVIDIGGTTTDFVLIEDGLPKI 257
                                       567899******9998999999************99998877766 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.9
                              StbA 215 rtssfladeliknrkdeeyLkrrindedkresv 247
                                          s+ a+++i       yL +ri+ + k++ +
  gi|488600073|ref|YP_007906544.1| 350 SIESMEAERIILTGYLSRYLAKRISRASKVSVI 382
                                       445556666666666666777777666666555 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00042      0.84       1      36 [.       3      37 ..       3     141 .. 0.87
   2 !    5.1   0.0    0.0067        13       3      17 ..     238     252 ..     213     268 .. 0.85
   3 ?   -1.4   0.0      0.68   1.3e+03     200     262 ..     338     394 ..     309     397 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00042
                                      EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvr 36
                                      +GiD+G+T t  ++++++ e+ +  i n + +e++ 
  gi|488600073|ref|YP_007906544.1|  3 IGIDVGGTNTDIAIIKDN-EIKTIKIPNEEGFEGAF 37
                                      7**************999.77777787776666554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0067
                                       EEE-SSEEEEEEEET CS
                       BcrAD_BadFG   3 iDgGsTttkavlmde 17 
                                       iD+G+Ttt +vl+++
  gi|488600073|ref|YP_007906544.1| 238 IDIGGTTTDFVLIED 252
                                       888999998888876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.68
                                       HHHHHHHHHHHHTT---SS..EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHH CS
                       BcrAD_BadFG 200 raialrvialisrsggvtde.vtltGGvakneaavkelrklvkenygevkininpdsiytgalG 262
                                       rai + v+ ++++++  + e ++ltG +++       l k + ++  +v++ ++ +s+   a+G
  gi|488600073|ref|YP_007906544.1| 338 RAIDSFVEMIAKSIESMEAErIILTGYLSRY------LAKRI-SRASKVSVIVPDHSESVNAVG 394
                                       5666666666666666655557777766666......33333.344455555555555555555 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2   0.00061       1.2       2      29 ..       3      32 ..       2      36 .. 0.86
   2 !    6.7   0.0   0.00089       1.8     172     204 ..     219     251 ..     205     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00061
                                      EEEEEXSSEEEEEEEETTEEEEEX..XTTS CS
                             HSP70  2 iGiDLGttnsvvavmeggkievia..neeg 29
                                      iGiD+G tn+ +a++++++i++i+  neeg
  gi|488600073|ref|YP_007906544.1|  3 IGIDVGGTNTDIAIIKDNEIKTIKipNEEG 32
                                      9********************985336666 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00089
                                       HHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEE CS
                             HSP70 172 AaalaYGldkkdkernvlvyDlGggtfdvSile 204
                                        aa+a G +   ker+ lv+D+Gg t+d  ++e
  gi|488600073|ref|YP_007906544.1| 219 PAAVAVGAYFLTKERKALVIDIGGTTTDFVLIE 251
                                       467888888888889*************87764 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.011        21     150     169 ..       5      24 ..       2      30 .. 0.86
   2 !    9.7   0.0   0.00017      0.34     129     163 ..     218     251 ..     213     265 .. 0.80
   3 ?   -0.9   0.0      0.29   5.7e+02      71     313 ..     354     393 ..     340     403 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                                       EEE-SS-EEEEEEETTEEEE CS
                          MreB_Mbl 150 vdiGggttevavislggivt 169
                                       +d+Gg  t++a+i  ++i t
  gi|488600073|ref|YP_007906544.1|   5 IDVGGTNTDIAIIKDNEIKT 24 
                                       8************9888865 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00017
                                       HHHHHHHHTT--TTSSS-EEEEEE-SS-EEEEEEE CS
                          MreB_Mbl 129 eplaAAiGaglpveepsgnmvvdiGggttevavis 163
                                        p a A+Ga    +e +  +v+diGg tt+ ++i 
  gi|488600073|ref|YP_007906544.1| 218 SPAAVAVGAYFLTKE-RKALVIDIGGTTTDFVLIE 251
                                       577889999886655.5579**********99885 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-E CS
                          MreB_Mbl  71 levaeellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgn 147
                                       +e+   +l  ++++   k++ + ++v + vP ++++v+                                       
  gi|488600073|ref|YP_007906544.1| 354 MEAERIILTGYLSRYLAKRISRASKVSVIVPDHSESVN--------------------------------------- 391
                                       55555555555555555555555555555555555554....................................... PP

                                       EEEEE-SS-EEEEEEETTEEEEEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHHEEEEEE CS
                          MreB_Mbl 148 mvvdiGggttevavislggivtsksvrvaGdeldeaiikyirkkynlliGertaekikieigsavkeeeeekmeikG 224
                                                                                                                    
  gi|488600073|ref|YP_007906544.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       EETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-E CS
                          MreB_Mbl 225 rdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllseetglpv 301
                                                                                                                    
  gi|488600073|ref|YP_007906544.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       EE-SSTTTHHHH CS
                          MreB_Mbl 302 kvaedpltcvak 313
                                                 a 
  gi|488600073|ref|YP_007906544.1| 392 ----------AV 393
                                       ..........43 PP

>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.024        48     115     136 ..       3      24 ..       1      26 [. 0.88
   2 !   10.0   0.0   0.00022      0.43     107     136 ..     227     257 ..     218     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.024
                                       EEEEEETTEEEEEEEETTEEEE CS
                          Ppx-GppA 115 lviDiGGGStElvlgeekevsk 136
                                       + iD+GG  t++++++++e++ 
  gi|488600073|ref|YP_007906544.1|   3 IGIDVGGTNTDIAIIKDNEIKT 24 
                                       779*************999875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00022
                                       HT.---SSEEEEEEETTEEEEEEEETTEEEE CS
                          Ppx-GppA 107 sl.lekgrglviDiGGGStElvlgeekevsk 136
                                        +  ++ + lviDiGG  t+ vl+e+  ++ 
  gi|488600073|ref|YP_007906544.1| 227 YFlTKERKALVIDIGGTTTDFVLIEDGLPKI 257
                                       444678889***************9976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 2832.43
//
Query:       gi|488600074|ref|YP_007906545.1|  [L=157]
Description: transcriptional regulator, XRE family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   46.3   3.6    3.4e-12   46.2   2.7    1.5  2  HTH_3     Helix-turn-helix
    2.1e-07   31.2   0.0    3.5e-07   30.5   0.0    1.3  1  HTH_31    Helix-turn-helix domain
    2.7e-07   30.5   2.8    5.3e-07   29.6   2.8    1.4  1  HTH_19    Helix-turn-helix domain
     0.0016   18.3   2.4     0.0021   17.9   1.8    1.6  1  HTH_25    Helix-turn-helix domain
     0.0075   15.7   0.8     0.0099   15.3   0.8    1.1  1  TMEM156   TMEM156 protein 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 ?   -3.2   0.0       2.6   9.4e+03      10      17 ..      42      49 ..      41      50 .. 0.73
   2 !   46.2   2.7   9.3e-16   3.4e-12       1      54 [.      75     128 ..      75     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.6
                                      HHHHHHHH CS
                             HTH_3 10 lsqeeLAe 17
                                      +sq+++ +
  gi|488600074|ref|YP_007906545.1| 42 ISQKDVKK 49
                                      68888866 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 9.3e-16
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                       +k+ R+++g+sqe LA+k+  + s i++iEn e  P  e+++kl++ ++++l+e
  gi|488600074|ref|YP_007906545.1|  75 IKREREKRGWSQEVLAKKIQEKESLIRKIENAEITPETEVIEKLERLFNIKLRE 128
                                       89************************************************9987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   9.8e-11   3.5e-07       8      56 ..      77     124 ..      75     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 9.8e-11
                            HTH_31   8 alReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                       + Re++G+sqe +A+ ++  es ++++E+++++ p  +v+e+l r+++ 
  gi|488600074|ref|YP_007906545.1|  77 REREKRGWSQEVLAKKIQEKESLIRKIENAEIT-PETEVIEKLERLFNI 124
                                       67******************************6.**********99876 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   2.8   1.5e-10   5.3e-07       4      56 ..      75     126 ..      74     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.5e-10
                            HTH_19   4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidl 56 
                                       +k+ Re++g++qe la++++   s i++iEn ++ +p+ e++ k+ ++++i l
  gi|488600074|ref|YP_007906545.1|  75 IKREREKRGWSQEVLAKKIQEKESLIRKIENAEI-TPETEVIEKLERLFNIKL 126
                                       7888******************************.*********999999975 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.8   5.9e-07    0.0021       3      35 ..      76     108 ..      74     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.9e-07
                                       HHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                            HTH_25   3 raaRearglsleevaketkIrkdylealEeddf 35 
                                       +++Re+rg+s e +ak+++ ++++++++E+ ++
  gi|488600074|ref|YP_007906545.1|  76 KREREKRGWSQEVLAKKIQEKESLIRKIENAEI 108
                                       899**************************9875 PP

>> TMEM156  TMEM156 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.8   2.8e-06    0.0099      54     162 ..      22     127 ..      18     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-06
                           TMEM156  54 selklcssclvceskgnvdfisQeqtsKvlimkgSvevkaedfispckyfNftvapavdeveeynttcllkthtrks 130
                                       se+++c +c    s++ v+ isQ   +Kv+++k+S   k e    + + +N+ + +  ++ + ++     k++ ++s
  gi|488600074|ref|YP_007906545.1|  22 SEVNVCKRCKSLGSEKPVERISQKDVKKVFLRKKSPRKKIEFEEELLENYNLIIKREREKRGWSQEVLAKKIQEKES 98 
                                       78999***********************************99999***********999999999999999999999 PP

                           TMEM156 131 avveeeaakekslnhtCrimeslnnCinisLq 162
                                        +++ e a+   +     ++e+l+   ni L+
  gi|488600074|ref|YP_007906545.1|  99 LIRKIENAE---ITPETEVIEKLERLFNIKLR 127
                                       999988887...33445677777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1462  (0.0815439); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 994.03
//
Query:       gi|488600075|ref|YP_007906546.1|  [L=401]
Description: hypothetical protein Asulf_00532 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0095   15.5   0.0      0.033   13.7   0.0    1.8  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0     0.086   1.5e+03      98     139 ..       5      43 ..       2      61 .. 0.75
   2 !   13.7   0.0   1.9e-06     0.033       3      76 ..      95     165 ..      93     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.086
                   Methyltransf_15  98 lkplkleqllkeslklskniilfLPrnsdlnqlaaltaevle 139
                                       +kp  +e++ +e+   +k+i   LP++  +++++++   +l 
  gi|488600075|ref|YP_007906546.1|   5 IKPTDFEKIDREVRFAQKKISEGLPKERIIRKIRRT---ILS 43 
                                       788888888889889999999999999999999877...344 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.9e-06
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe..llaklklekikvdlvf 76 
                                        i D+ +G G + i fa+++ + +++e ++++  +a+ N  + gv+  +    gd ++  +++ +k+ ++  +++f
  gi|488600075|ref|YP_007906546.1|  95 AIADISCGVGAQLIFFAKKG-RAMGVELDRKRAILAKLNLIAMGVDGLVV--AGDALSdeVISIVKSFEA--EVIF 165
                                       688***************99.99**********************99875..555554334444444444..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2495.05
//
Query:       gi|488600076|ref|YP_007906547.1|  [L=556]
Description: glutamyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-73  246.8   0.0    3.7e-73  246.2   0.0    1.3  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    3.4e-22   79.1   0.5    2.2e-21   76.5   0.0    2.5  2  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 !  246.2   0.0   4.2e-77   3.7e-73       2     313 ..      94     400 ..      93     401 .. 0.96

  Alignments for each domain:
  == domain 1  score: 246.2 bits;  conditional E-value: 4.2e-77
                                       -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSC..CC--HHHHHHHHHHHHHTT---SSEEEEGGG CS
                      tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdp..erekeeaeesiledlkwlgikwdekptyqsd 76 
                                       V+ RfaP+P+G + +G+a+ +++n  +A+ ++G++ilR++DTdp  +r   ea e  led +wlg+++ ++  y+s+
  gi|488600076|ref|YP_007906547.1|  94 VVMRFAPNPNGPPTLGSARGMIVNGEYARMYDGRLILRFDDTDPrtKRPMVEAYEWYLEDFEWLGYEP-DETLYASK 169
                                       899****************************************84456778999**************.5699**** PP

                                       GHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTT CS
                      tRNA-synt_1c  77 rfdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkidee 153
                                       r  ++++y+++Li+  kAY c+c+ ee +++r +    ++++r  + e+ ++++ e+m  g+++++++v+R+k d++
  gi|488600076|ref|YP_007906547.1| 170 RIPIYYDYIKKLIEMEKAYACFCSREEFKKHRDS--GTECPHRGLPAEDTMDVW-EKMLAGEYREGEVVIRIKTDMQ 243
                                       ********************************99..99999*************.9********************* PP

                                       SS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-E CS
                      tRNA-synt_1c 154 ss.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevpp 229
                                       ++  ++rD v+ ri +e+   h+l+++ + +yPt df  +i D+l +ith++r+++ +d+++++  +++++g+e p 
  gi|488600076|ref|YP_007906547.1| 244 HKdPAIRDWVAFRIIYEE---HPLTGDEYFVYPTLDFESAIEDHLNGITHIIRGKDLIDSERRQKYIYRYFGWEYPM 317
                                       999***************...*****************************************************999 PP

                                       EEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHH CS
                      tRNA-synt_1c 230 fiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnreskslea 306
                                         h   +   e  klS   ++  ++e ++++wdd+++++l++l r+G++pe+++++f + ++++++ +++++k+l a
  gi|488600076|ref|YP_007906547.1| 318 TKHWGRVKIHEFGKLSTSSIKKAIEEGKFTGWDDPKLPTLRALKRRGFSPEAIKKFFISLGVSEND-VSVSMKNLYA 393
                                       9998888888999****************************************************9.*****99999 PP

                                       HHHHHHH CS
                      tRNA-synt_1c 307 fdrkkLe 313
                                        +rk ++
  gi|488600076|ref|YP_007906547.1| 394 ENRKIID 400
                                       9988765 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 ?   -1.2   0.1      0.18   1.6e+03     119     161 ..      51      93 ..      13      95 .. 0.66
   2 !   76.5   0.0   2.5e-25   2.2e-21       1     173 [.     403     542 ..     403     543 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.18
                    tRNA-synt_1c_C 119 evrlYdrLfkeee.dedfllnpdslkvleeglaepalanlkkgd 161
                                        ++++d+L +e++ +  + +++++++  ++ +a p l++++kg 
  gi|488600076|ref|YP_007906547.1|  51 VIKEFDSLPEEKKlELFEQYKEEKKER-KKEIALPPLQSAEKGR 93 
                                       466778887666655533344444433.5556666666666665 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 2.5e-25
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveev 77 
                                       A+Ry++V++pv ++i++l+     e++vpl pk    g rk++ ++++yi+ +D++r+ +ge +rLk+++n++v + 
  gi|488600076|ref|YP_007906547.1| 403 ANRYFFVENPVLIEIKGLE--FDGEVDVPLSPK---GGVRKLKGESRVYISSSDFNRFGDGEIFRLKDFCNVRVVSK 474
                                       89**************887..456999999999...8*************************************665 PP

                    tRNA-synt_1c_C  78 ekdesgevtelkleydgesleearkkkgiihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepal 154
                                                el +e+ + +l++ +k k+ii+Wv++++av++                ++l  + +    +g ae ++
  gi|488600076|ref|YP_007906547.1| 475 --------EELIFEFADFELKNVKKGKNIIQWVPESQAVDC----------------EVLGLERN---YTGKAEINA 524
                                       ........24556666666766678888*************................89888887...579*****9 PP

                    tRNA-synt_1c_C 155 anlkkgdivQfeRiGyfrv 173
                                        n  +g++vQfeR+ ++r+
  gi|488600076|ref|YP_007906547.1| 525 VN-DVGKVVQFERFAFCRI 542
                                       99.9************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3605.24
//
Query:       gi|488600077|ref|YP_007906548.1|  [L=323]
Description: farnesyl-diphosphate synthase /geranylgeranyl-diphosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-66  223.4   0.0      3e-66  223.1   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 !  223.1   0.0   1.6e-70     3e-66       4     255 ..      33     274 ..      30     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: 223.1 bits;  conditional E-value: 1.6e-70
                                       HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCH CS
                   polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGn 80 
                                       l+ a+++l++agGKrlRp+l l ++eal+  + +++k +  a+++e++h+++L+hDDimD++e+RRG +++h+ +G+
  gi|488600077|ref|YP_007906548.1|  33 LYVATRHLFKAGGKRLRPVLSLVVSEALN--R-DYRKILPSAVAIETIHNFTLIHDDIMDQDEMRRGVKTVHNMWGE 106
                                       566889***********************..4.789***************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH..STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHH CS
                   polyprenyl_synt  81 klAindgdfllarafellaklf..eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTayl 154
                                       ++Ai++gd l++ af+l++ +   +++ ++ ++++++v+++++eGq+ld++ e+++++s   +eey e+v++KT++l
  gi|488600077|ref|YP_007906548.1| 107 PVAILAGDTLFSEAFYLMTFCDvdKENlIRGVRTLADVCVKICEGQYLDMSFEEREKVS---EEEYIEMVTKKTSVL 180
                                       *******************888877778**********************999999999...*************** PP

                                       CHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHH CS
                   polyprenyl_synt 155 falpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeq 231
                                       +a+++al a+l g ++e++++l d+g + G+ FQi+DD+lDl+g  +++gK+ ++Di egk t++++ka+e     q
  gi|488600077|ref|YP_007906548.1| 181 IAASCALPAILFGEDEEVIQSLWDFGIYSGIGFQIHDDVLDLVGR-DKTGKDWASDILEGKKTIITIKAFE-----Q 251
                                       *************99999*************************98.566**********************.....3 PP

                                       HHHHHHHTTSSHHHHHHHHHHHHH CS
                   polyprenyl_synt 232 rkvlkeilgkkaekeedvkealel 255
                                         +l ei+gk +++ e+++ a+++
  gi|488600077|ref|YP_007906548.1| 252 G-RLPEIFGKGKASTEEIEDAVKI 274
                                       3.7***************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2022.56
//
Query:       gi|488600078|ref|YP_007906549.1|  [L=364]
Description: isopentenyl-diphosphate delta-isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   76.7   0.8    6.8e-15   54.9   0.7    2.2  2  FMN_dh        FMN-dependent dehydrogenase
    0.00094   18.4   0.6     0.0016   17.7   0.1    1.7  2  Glu_synthase  Conserved region in glutamate synthase
     0.0026   16.8   9.9        1.5    7.7   7.9    3.3  2  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
       0.02   14.3   1.9      0.023   14.1   0.1    1.9  2  NMO           Nitronate monooxygenase
       0.14   11.3   2.4        0.3   10.2   0.1    2.3  2  DHO_dh        Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     1e-07   0.00038      27     101 ..      26     101 ..       4     114 .. 0.82
   2 !   54.9   0.7   1.9e-18   6.8e-15     204     343 ..     173     331 ..     128     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-07
                                       HHGGGGEEE---SSSS-SS-B..--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS-H CS
                            FMN_dh  27 raaferirlrprvlrdvskvd..lsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstvastsl 101
                                        + +e++ l ++ l +   +d  +++++lG kls+P+lia++       +d +++la a +++gi ++++++ ++++
  gi|488600078|ref|YP_007906549.1|  26 YTGLEDVMLLHNSLPELDLADiiTEVRFLGSKLSAPLLIASMTGGHPDTKDINRNLAMAVEETGIGMGVGSQ-RAAI 101
                                       5667777888888876655542278899**************99999999******************9987.4444 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 1.9e-18
                                       -HHHHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG..................TSSTT---HHH CS
                            FMN_dh 204 twddikwlreqtklplvvKGv...ltaedakraveaGvdgivvSNHGG..................Rqldgapatid 259
                                        ++ i+++ ++ k+p++vK+    ++ + a+++ ++Gv+++ v   GG                    +d+    i 
  gi|488600078|ref|YP_007906549.1| 173 GYSAIENVVKEIKVPVIVKETgggISNRVARKLRNCGVEAVDVGGAGGtswtavefyrtkddigkrIAIDFWDWGIP 249
                                       56789**************888889***********************99999999988888887546777777777 PP

                                       CHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-S CS
                            FMN_dh 260 vLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvk 336
                                       +  +i e ++  ++v++ gG r+G Dv+k +alGA++  ++ pfl++ a+   + v + ++ + + l+ +m l+G +
  gi|488600078|ref|YP_007906549.1| 250 TSFSIIECAE-ILPVIATGGLRSGLDVAKCIALGAEIGSSALPFLHA-AMRSSDEVVKEINYFIKGLKVAMFLTGSR 324
                                       7788877775.89*******************************999.778888899999***************** PP

                                       BHHHHHC CS
                            FMN_dh 337 svaeldr 343
                                       +v++l++
  gi|488600078|ref|YP_007906549.1| 325 RVKDLRD 331
                                       ****976 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.3   4.7e+03      64     100 ..      58      95 ..      49      97 .. 0.68
   2 !   17.7   0.1   4.4e-07    0.0016     273     299 ..     259     285 ..     169     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.3
                                       HHTTEE---B-TTTS.-HHHHHHHHHHHHHHT-B-EET CS
                      Glu_synthase  64 ikkriltsamSyGal.seeahealakamnrlgtksntG 100
                                       ++ ++l++ m  G    ++ +  la+a+++ g+ +  G
  gi|488600078|ref|YP_007906549.1|  58 LSAPLLIASMTGGHPdTKDINRNLAMAVEETGIGMGVG 95 
                                       55666666666665413445667888888888877666 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4.4e-07
                                       GG-EEEEESS--SHHHHHHHHHHT-SE CS
                      Glu_synthase 273 drvsliadGglktgadvvkalalGAda 299
                                       + + +ia+Ggl++g dv+k++alGA+ 
  gi|488600078|ref|YP_007906549.1| 259 EILPVIATGGLRSGLDVAKCIALGAEI 285
                                       556789*******************95 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   7.9   0.00042       1.5     134     231 ..     179     284 ..      78     287 .. 0.75
   2 !    6.2   0.0    0.0012       4.3     293     327 ..     297     331 ..     293     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00042
                                       HHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHH....HHHCS...........B---HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx...........xxxxxxxx RF
                             IMPDH 134 eavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCtt....rvvag...........vGvpqltA 195
                                       ++vkeik  v  v+  +G + +   a++L ++g++av vG   G   t     r+               G+p   +
  gi|488600078|ref|YP_007906549.1| 179 NVVKEIKVPV-IVKETGGGISN-RVARKLRNCGVEAVDVGGAGGTSWTAvefyRTKDDigkriaidfwdWGIPTSFS 253
                                       4455555444.35555666654.467888888888888884444333322222222220011111111146666666 PP

                                       HHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 196 vaevaeaakkagvpviaDGGikysgdivkAlaaGad 231
                                       ++e+ae+      pvia GG+++  d++k +a+Ga+
  gi|488600078|ref|YP_007906549.1| 254 IIECAEI-----LPVIATGGLRSGLDVAKCIALGAE 284
                                       7776665.....69*********************8 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0012
                                       EE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 293 vpykgsvkevveqlvgglrsgmgylGaktieelke 327
                                       +  + +v + ++++++gl+ +m  +G++ +++l++
  gi|488600078|ref|YP_007906549.1| 297 MRSSDEVVKEINYFIKGLKVAMFLTGSRRVKDLRD 331
                                       5667789999***********************86 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      0.48   1.7e+03     185     222 ..     177     216 ..     158     218 .. 0.62
   2 ?   14.1   0.1   6.4e-06     0.023     193     222 ..     259     289 ..     247     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.48
                               NMO 185 vpqvldavdiPviA..aGGiidrrgvaaaLalGAsgvqig 222
                                       +++v++ +++Pvi   +GG i +r        G ++v +g
  gi|488600078|ref|YP_007906549.1| 177 IENVVKEIKVPVIVkeTGGGISNRVARKLRNCGVEAVDVG 216
                                       5667777788888544555444443333334566666665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.4e-06
                               NMO 193 d.iPviAaGGiidrrgvaaaLalGAsgvqig 222
                                       + +PviA+GG+  + +va  +alGA+    +
  gi|488600078|ref|YP_007906549.1| 259 EiLPVIATGGLRSGLDVAKCIALGAEIGSSA 289
                                       358**********************865555 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.14   5.1e+02     240     271 ..     125     154 ..     118     185 .. 0.85
   2 ?   10.2   0.1   8.5e-05       0.3     244     292 ..     260     308 ..     253     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.14
                                       HTTT.S-EEEESS--SHHHHHHHHHHTECEEE CS
                            DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvq 271
                                       ++   ip I   G+e +e a+e+i a A ++ 
  gi|488600078|ref|YP_007906549.1| 125 NIG--IPQIIKHGVEYAEKAVEMIDADALAIH 154
                                       444..88888889***********99987765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 8.5e-05
                                       .S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHH CS
                            DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkele 292
                                        +p+I++GG+ sg D+   i  GA +      +  + + + +++ ke++
  gi|488600078|ref|YP_007906549.1| 260 ILPVIATGGLRSGLDVAKCIALGAEIGSSALPFLHAAMRSSDEVVKEIN 308
                                       58*********************98765555555566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2414.96
//
Query:       gi|488600079|ref|YP_007906550.1|  [L=264]
Description: putative archaeal kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  114.8   0.2    5.2e-33  114.6   0.2    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 !  114.6   0.2   2.9e-37   5.2e-33       2     241 .]       6     241 ..       5     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 2.9e-37
                                       EEEEEE-TTCCCCTCC........HHHHHHHHHHHHH.HHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E. CS
                         AA_kinase   2 rvVvKlGGssltdkee........aslrrlaeqiaal.kesgnklvvVhGggsftdgllalksglssgelaaglrst 69 
                                       ++++K+GGs++tdk++        ++++r+ ++i+++ +e+ +k+++VhG+gsf++ ++++ ++l+++++       
  gi|488600079|ref|YP_007906550.1|   6 IIILKIGGSIITDKSKgsfekakfDVIERISREISQFlMENRKKIILVHGAGSFGHPHVEK-YNLKEKKEL------ 75 
                                       79**********99999********************666669******************.999999998...... PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESE CS
                         AA_kinase  70 leeagevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgf 146
                                          +g + t+ a+  l+++++++ll++g++a g+++  +   +++          +++++ + ++l ++++pv++g+
  gi|488600079|ref|YP_007906550.1|  76 ---RGVLTTHFACKRLNSIVCDKLLENGVHALGIHPLTSFFLDEKL---------NINIDLFLDMLTEDIIPVTHGD 140
                                       ...89*******************************9999887777.........********************** PP

                                       EEEETTTE.EEEE-HHHHHHHHHHHCTS..SEEEEEESSSSC.ESSTTTTCCTTCECCEEEHHHCHH.........C CS
                         AA_kinase 147 igldeege.lgrgssDtiaallAealgA..dkliiltdVdGV.ydadpkkvpdarllpeisvdeaee.........s 210
                                         ++++ + + ++s+D i+++l  +l+    ++ ++tdVdGV yd  +++v   + ++  +++e+++         +
  gi|488600079|ref|YP_007906550.1| 141 MIYNRKRKfFEVLSGDSIISALMGELSDrkLRVGLATDVDGViYD--GRVV---KEINADNFEEVLSaidksamdaE 212
                                       ********999*******99999999983456789*******664..4566...5666666666666********** PP

                                       SSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 211 aselatgGmkvkhpaalaaarrggipvvItn 241
                                        + ++tgGmk k+ a ++ ++++  +v+I+n
  gi|488600079|ref|YP_007906550.1| 213 RKSDVTGGMKGKIGALFRSIHGS--EVRIFN 241
                                       *****************999887..666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1744.64
//
Query:       gi|488600080|ref|YP_007906551.1|  [L=296]
Description: mevalonate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   58.8   0.1      9e-16   57.9   0.1    1.5  1  GHMP_kinases_N   GHMP kinases N terminal domain
    4.4e-14   52.6   0.1      1e-13   51.4   0.1    1.7  1  GHMP_kinases_C   GHMP kinases C terminal
  ------ inclusion threshold ------
      0.053   13.1   0.0      0.098   12.2   0.0    1.5  1  GalKase_gal_bdg  Galactokinase galactose-binding signature
      0.093   12.7   0.0        0.2   11.7   0.0    1.5  1  HTH_11           HTH 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 !   57.9   0.1     2e-19     9e-16       1      66 []      78     145 ..      78     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2e-19
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       di+iks iP+++GLGSS+A++va+++Al a ++  l  ee +++a   e  +q g gsg D + s+yGg
  gi|488600080|ref|YP_007906551.1|  78 DIEIKSQIPPASGLGSSSAVTVAVLKALDAEFEAALtnEEiYEMARMVELDVQ-GIGSGTDPFLSTYGG 145
                                       79******************************877865448************.**************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 !   51.4   0.1   2.3e-17     1e-13       1      82 [.     205     283 ..     205     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.3e-17
                    GHMP_kinases_C   1 llealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                       +++ale++d++ + +l + +q   l+  +g++ +e++e++ +l+elG ++ak++GaGgG+++++l+ +kd+  ++ +
  gi|488600080|ref|YP_007906551.1| 205 AIPALENRDYDKIFDLFRINQC--LLKAIGVSRREIDEMIAKLEELG-ISAKITGAGGGGCIIGLG-EKDALTKATE 277
                                       689*******************..899********************.******************.8888777777 PP

                    GHMP_kinases_C  78 al.ree 82 
                                        + +++
  gi|488600080|ref|YP_007906551.1| 278 IFgNAF 283
                                       665555 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 ?   12.2   0.0   2.2e-05     0.098      13      48 ..       2      37 ..       1      38 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                      EEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEEE CS
                   GalKase_gal_bdg 13 vasAPGRvnLiGEHtDYngGfVlpmAieqdiyiavs 48
                                      +asAPG + L GEH      + + +Ai++++ + vs
  gi|488600080|ref|YP_007906551.1|  2 IASAPGKLFLFGEHAVVYKKKAIVTAINLRCFAKVS 37
                                      89************9999999999999999887666 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.4e-05       0.2      23      51 ..     229     259 ..     225     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.4e-05
                            HTH_11  23 eeLnvSrrtvrrdIkaLeelg..vpIesepg 51 
                                       + ++vSrr +   I++Leelg  ++I++  g
  gi|488600080|ref|YP_007906551.1| 229 KAIGVSRREIDEMIAKLEELGisAKITGAGG 259
                                       789******************9999998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2147.14
//
Query:       gi|488600081|ref|YP_007906552.1|  [L=119]
Description: hypothetical protein Asulf_00538 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-44  150.8   0.1    1.5e-44  150.6   0.1    1.0  1  Cyclophil_like   Cyclophilin-like
    3.9e-06   26.8   0.0    4.2e-06   26.7   0.0    1.1  1  Cyclophil_like2  Cyclophilin-like family


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 !  150.6   0.1   1.7e-48   1.5e-44       5     117 ..       3     115 ..       1     117 [. 0.97

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 1.7e-48
                                       EEETTEEEEEEEETTHHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEESS-- CS
                    Cyclophil_like   5 idiesseveveLddtetaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclffGkt 81 
                                       ++++ ++ e+eL  t+ta+ ik++lPi++ vn+Wg+EiYf+t++++++e+n+kevve+gd+ayw+pGka+c+ffGkt
  gi|488600081|ref|YP_007906552.1|   3 VRVGDIVREIELLPTKTAEIIKNSLPIRGIVNRWGDEIYFHTDIEVSEEDNSKEVVELGDVAYWIPGKAICIFFGKT 79 
                                       567888999******************************************************************** PP

                                       TT-TTSB--SSSEEEEEEEEC-GGGGGG--TTEEEE CS
                    Cyclophil_like  82 PisddeirpaspvnviGrivedlellkkvkdgekvr 117
                                       Pisdd+irpas+vnv+G+++++le lk++ dge+++
  gi|488600081|ref|YP_007906552.1|  80 PISDDKIRPASAVNVFGKVKGSLEELKSIMDGEEIE 115
                                       *********************************997 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   4.7e-10   4.2e-06       2      85 ..       4      83 ..       3     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.7e-10
                   Cyclophil_like2  2 tiggqtftatLednaaaralleklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfe 80
                                      ++g+ + +++L  +++a+ + + lP+   +++ +  E +++ + +++ +d  +++ ++ Gd+ay+ p++ +++f++++ 
  gi|488600081|ref|YP_007906552.1|  4 RVGDIVREIELLPTKTAEIIKNSLPIRGIVNRWG-DEIYFHTDIEVSEEDN-SKEVVELGDVAYWIPGKAICIFFGKTP 80
                                      578888899******************9999998.9*******9****999.8888999*****************995 PP

                   Cyclophil_like2 81 esysy 85
                                      +  s+
  gi|488600081|ref|YP_007906552.1| 81 I--SD 83
                                      5..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 769.97
//
Query:       gi|488600082|ref|YP_007906553.1|  [L=142]
Description: ACT domain-containing protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-19   67.1   0.3    9.6e-09   34.9   0.0    2.1  2  ACT         ACT domain
    2.3e-08   33.7   0.1      0.009   15.8   0.0    2.5  2  ACT_7       ACT domain
    1.4e-07   32.0   0.3      0.012   16.2   0.0    2.2  2  ACT_4       ACT domain
     0.0018   18.5   0.0       0.59   10.3   0.0    2.3  2  Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygena
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.16   11.3   0.0    1.4  1  CbiK        Cobalt chelatase (CbiK)


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 !   30.6   0.0   5.9e-11   2.1e-07       3      56 ..      10      60 ..       8      66 .. 0.77
   2 !   34.9   0.0   2.7e-12   9.6e-09       2      65 ..      75     136 ..      75     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5.9e-11
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHH CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedle 56
                                      ++v+v+++PG L+ v+  l ++giNi+  ++++ +d   gi+  ++v d++ + 
  gi|488600082|ref|YP_007906553.1| 10 VSVFVENKPGRLSSVTEKLFNAGINIRAFTIAEAGD--FGII-RMVVDDTDKAY 60
                                      89*********************************9..4444.44444444333 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 2.7e-12
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                       vl v+v+D+PG L  ++ al+d+giNi+ +  ++s+    +  ++  v d +++ e+le+  +l
  gi|488600082|ref|YP_007906553.1|  75 VLGVEVKDEPGGLYNIAKALGDAGINIEYVYAFTSGG--DRALIILRVDDINRAIEILEKEGAL 136
                                       5889*********************************..8999999999999999999886665 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.2e-06     0.011      19      64 ..      16      64 ..       3      65 .. 0.79
   2 !   15.8   0.0   2.5e-06     0.009      19      64 ..      82     131 ..      74     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-06
                                      SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEE..GGGHHHHHHHHH CS
                             ACT_7 19 dvtGivaklaspLaeagIsifqiS.tyrtdyiLVp..eedlekAveaLh 64
                                      + +G++++++++L +agI+i +++  +  d+ +++   +d +kA+++L+
  gi|488600082|ref|YP_007906553.1| 16 NKPGRLSSVTEKLFNAGINIRAFTiAEAGDFGIIRmvVDDTDKAYDTLK 64
                                      589*****************99999888888888744588888888886 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.5e-06
                                       SS--HHHHHHHHHHTTT---EEEE-SS-E....EEEEEGGGHHHHHHHHH CS
                             ACT_7  19 dvtGivaklaspLaeagIsifqiStyrtd....yiLVpeedlekAveaLh 64 
                                       d +G +  +a++L +agI+i ++  ++++     i+ + +d+ +A+e+L+
  gi|488600082|ref|YP_007906553.1|  82 DEPGGLYNIAKALGDAGINIEYVYAFTSGgdraLIILRVDDINRAIEILE 131
                                       67899999*************9986665434447888***********98 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.4e-05     0.049       8      54 ..       9      53 ..       2      59 .. 0.85
   2 !   16.2   0.0   3.3e-06     0.012       9      48 ..      76     114 ..      64     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                             ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitv 54
                                      +++v +e+++g L+++t+ + ++++ni++ ++ +  +  +  i++ v
  gi|488600082|ref|YP_007906553.1|  9 QVSVFVENKPGRLSSVTEKLFNAGINIRAFTIAE--AGDFGIIRMVV 53
                                      6899***************************999..45577777655 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.3e-06
                             ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkdgla 48 
                                       l ve++d++g L +i++++ ++++ni+ v a t   d  a
  gi|488600082|ref|YP_007906553.1|  76 LGVEVKDEPGGLYNIAKALGDAGINIEYVYAFTSGGD-RA 114
                                       5699************************999885433.33 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00017      0.59      74     102 ..      43      71 ..       7     103 .. 0.72
   2 !    6.9   0.0    0.0019       6.9      73     103 ..     109     139 ..      72     142 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                                       SEEEEEEEEEHCHHHHHHHHHHHTTGEEE CS
                        Glyoxalase  74 vhhvafialdvedvgkaldrlkeagvkvv 102
                                          ++ i   v+d +ka+d lk+ag+ v+
  gi|488600082|ref|YP_007906553.1|  43 AGDFGIIRMVVDDTDKAYDTLKKAGFTVS 71 
                                       55677888889**************6654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0019
                                       TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEE CS
                        Glyoxalase  73 tvhhvafialdvedvgkaldrlkeagvkvva 103
                                       ++   a+i l v+d+ +a+++l+++g  + +
  gi|488600082|ref|YP_007906553.1| 109 SGGDRALIILRVDDINRAIEILEKEGALFKE 139
                                       56677999*****************987765 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.4e-05      0.16     177     238 ..      12      72 ..       1     105 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                                       EETTSSS-.HHHHHHHHHHHT--EEEEEE-SS.S--HHHHCCCCSSSTTSHHHHHHHTT--EEE CS
                              CbiK 177 gtvegyPe.veevieelkkkgikevkliPlml.vAGdHaknDmasdeedswkealeaaGikvei 238
                                       + ve +P+ +++v e+l ++gi   +++ + +  AGd     m  d++d+   +l++aG++v+ 
  gi|488600082|ref|YP_007906553.1|  12 VFVENKPGrLSSVTEKLFNAGI---NIRAFTIaEAGDFGIIRMVVDDTDKAYDTLKKAGFTVSL 72 
                                       4567777437777777777765...566665416***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 875.92
//
Query:       gi|488600083|ref|YP_007906554.1|  [L=223]
Description: ribose-5-phosphate isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-60  203.2   0.1    2.7e-60  202.9   0.1    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    1.4e-07   31.6   0.2    5.4e-05   23.2   0.0    2.1  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.082   12.0   0.0       0.13   11.4   0.0    1.3  1  Sugar-bind      Putative sugar-binding domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.9   0.1   4.6e-64   2.7e-60       2     173 .]      48     217 ..      47     217 .. 0.97

  Alignments for each domain:
  == domain 1  score: 202.9 bits;  conditional E-value: 4.6e-64
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       gvp+S+q+++la e+gi++++l + ee+dl++DGaD+vde+ln+iKG+GgallrEKiva+aa+++i+i+d++K+v+ 
  gi|488600083|ref|YP_007906554.1|  48 GVPSSYQSHMLAVENGITVTDLIQFEELDLCVDGADQVDENLNCIKGKGGALLREKIVAQAAEEVIIIVDSRKIVDV 124
                                       7**************************************************************************** PP

                                       TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEE CS
                    Rib_5-P_isom_A  79 lgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVve 155
                                       l+   vPveV pfa+ +  +e++kl gg+++lRe+++k g ++Tdngn+ilDv+f ++iedpe le +++ i+GV e
  gi|488600083|ref|YP_007906554.1| 125 LD-ERVPVEVFPFAYGNAVKEIKKL-GGEAVLRESDRKLGACITDNGNFILDVDF-GRIEDPEGLECRINCIAGVFE 198
                                       *7.89******************75.*********99******************.6788***************** PP

                                       ESEE-S.--SEEEEEETTC CS
                    Rib_5-P_isom_A 156 tGlFlg.ladkvlvgkedg 173
                                       +G+F + l d+v+vg++dg
  gi|488600083|ref|YP_007906554.1| 199 NGIFPRrLIDRVIVGTKDG 217
                                       *****87*********997 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     9e-09   5.4e-05       5      41 ..       2      38 ..       1      66 [. 0.92
   2 !    7.1   0.0    0.0008       4.8      92     139 ..      74     121 ..      39     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 9e-09
                             DeoRC  5 eKrrIAkaAaeliedgdtifldaGtTtlelaraLaek 41
                                      eK++ Ak+Aa+liedg++i +++G+T++ + ++L ++
  gi|488600083|ref|YP_007906554.1|  2 EKANSAKEAARLIEDGMVIGIGSGSTVEIFLNELGKR 38
                                      79999***********************999999775 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0008
                             DeoRC  92 nvdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKf 139
                                       ++d+++ ga+ +d++ ++++ +      ++ +++aa++vi+++Ds K+
  gi|488600083|ref|YP_007906554.1|  74 ELDLCVDGADQVDENLNCIKGKGGALLREKIVAQAAEEVIIIVDSRKI 121
                                       57777777888887777777777777778899999************8 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.1e-05      0.13      45      74 ..       9      39 ..       4      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.1e-05
                                      HHHHH--TTEEEEE-SSHHHHHHHHHTHH.C CS
                        Sugar-bind 45 llesllkdgdvvgvgwGrtlsavaealtp.k 74
                                         +l++dg+v+g+g+G t++ ++++l +  
  gi|488600083|ref|YP_007906554.1|  9 EAARLIEDGMVIGIGSGSTVEIFLNELGKrI 39
                                      56799***************99999887644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1379.09
//
Query:       gi|488600084|ref|YP_007906555.1|  [L=81]
Description: hypothetical protein Asulf_00541 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.3   0.1    1.9e-06   27.9   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 !   27.9   0.1     1e-10   1.9e-06      45      93 .]       5      51 ..       1      51 [. 0.94

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1e-10
                                      HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-EEEES-SHH CS
                           Polbeta 45 leeelelaaelediklgkkvDlvdlneapplllyeilkegkllyskdee 93
                                      l++el+l+ae+e++  +  vD+ +ln+ap+ ++y+ +k g+ll sk+ee
  gi|488600084|ref|YP_007906555.1|  5 LDYELKLSAEIEKA-VRLPVDVRVLNSAPLSFKYKTIK-GELLTSKNEE 51
                                      5789**********.99*********************.********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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 0.30s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 488.25
//
Query:       gi|488600085|ref|YP_007906556.1|  [L=141]
Description: hypothetical protein Asulf_00542 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-30  104.7   1.0    3.4e-30  104.3   1.0    1.1  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 !  104.3   1.0   1.9e-34   3.4e-30       2     118 ..      17     134 ..      15     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 1.9e-34
                                       HHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHHH CS
                             DUF86   2 kealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdy..ifeilaekgviaeepe 76 
                                       k+ l +l+ ++ el+ e+fls+   +da+++ l v++Eaai +++h++ +  ++ p++y  +f il ++g+i+++ +
  gi|488600085|ref|YP_007906556.1|  17 KQLLGELRNIV-ELGLEKFLSNSYLRDAAKYKLIVAIEAAISVCNHIVVRVVKEIPSSYsdCFIILGKHGIISQYLA 92 
                                       66778888998.9**************************************************************** PP

                                       HHHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHH CS
                             DUF86  77 epwrkmiglRNrLvHgYlgidpeivwsiikenlpdleefles 118
                                       e+++ m+++RN+ vH Y+++d+++v++i ++++ dleef+e+
  gi|488600085|ref|YP_007906556.1|  93 EKLAYMAKFRNMFVHIYWKVDDRKVYEIMRKDISDLEEFIEE 134
                                       ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1037.90
//
Query:       gi|488600086|ref|YP_007906557.1|  [L=99]
Description: hypothetical protein Asulf_00543 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-11   42.3   0.2    6.5e-11   42.1   0.2    1.1  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.2   3.6e-15   6.5e-11      11      84 ..      22      94 ..      13      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.6e-15
                                      HHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHHHH CS
                               CMD 11 reallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaaae 84
                                       ea+++ eg++++k++ L+a++v a+ g ++ v++ + +A+e+G+t+ee+ae+l++a   +g  a+   ++a++
  gi|488600086|ref|YP_007906557.1| 22 EEAAFS-EGSIPLKYKYLMAMVVDAVEGAVEGVKVLAVRAMENGATKEEVAEALRVAYYIGGAGAVYTSANALR 94
                                      567787.99*****************************************************999988888876 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:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 608.54
//
Query:       gi|488600087|ref|YP_007906558.1|  [L=235]
Description: phosphate ABC transporter ATP-binding protein, PhoT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-34  119.6   0.0    1.9e-34  119.1   0.0    1.2  1  ABC_tran     ABC transporter
      6e-09   36.1   0.0     0.0029   17.5   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    8.9e-06   26.0   0.0    1.9e-05   25.0   0.0    1.5  1  AAA_22       AAA domain
      4e-05   23.2   0.3    0.00028   20.4   0.3    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00059   19.7   0.0       0.12   12.1   0.0    2.2  2  AAA_15       AAA ATPase domain
     0.0025   17.5   0.0     0.0053   16.5   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0033   17.3   0.0     0.0064   16.4   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0038   17.6   0.0     0.0049   17.3   0.0    1.4  1  AAA_16       AAA ATPase domain
     0.0074   15.0   0.2       0.18   10.4   0.0    2.1  2  AAA_13       AAA domain
  ------ inclusion threshold ------
      0.011   16.0   0.1       0.43   10.8   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.011   15.9   0.1      0.082   13.2   0.1    2.0  2  AAA_28       AAA domain
      0.013   15.4   1.2       0.16   11.9   1.2    2.1  1  ATPase_2     ATPase domain predominantly from Archaea
      0.022   15.3   0.1      0.058   13.9   0.1    1.7  1  AAA_18       AAA domain
      0.023   15.2   0.3      0.042   14.3   0.3    1.4  1  AAA_23       AAA domain
       0.03   14.2   0.1       0.14   12.1   0.0    2.0  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.032   14.1   0.1      0.073   13.0   0.0    1.6  2  NACHT        NACHT domain
      0.052   13.3   0.0        1.4    8.6   0.0    2.3  2  PRK          Phosphoribulokinase / Uridine kinase family
      0.059   13.1   0.1       0.27   10.9   0.0    2.0  3  AAA_30       AAA domain
      0.069   13.2   0.0       0.14   12.2   0.0    1.4  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
      0.078   11.8   0.3        2.1    7.1   0.3    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.094   12.6   0.0       0.16   11.9   0.0    1.3  1  Rad17        Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.0   2.2e-37   1.9e-34       1     137 []      18     158 ..      18     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.2e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++++lk++ege++ai+G++GaGK+tLl++la l++p eG+  ++g++ ++    ++r +i +++q+p +f+++ v+
  gi|488600087|ref|YP_007906558.1|  18 LNKINLKIREGEILAIIGNSGAGKTTLLRILAMLERPSEGKYYYRGEEAND----RVRGKITMVFQKPVMFNTS-VY 89 
                                       789**********************************************99....*****************99.99 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +n             e de+++kal+ +gl++ + +++    + LSgG++qrva+ara++ +p++l+lDEpta
  gi|488600087|ref|YP_007906558.1|  90 NNvayglklrgyskkEVDERVAKALNMMGLDGYARHNA----KRLSGGEQQRVAIARAIVIEPEMLVLDEPTA 158
                                       999********998888888999999999999888888....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.4e-06    0.0029       2      24 ..      31      53 ..      30      85 .. 0.82
   2 !   16.9   0.0   5.1e-06    0.0044     238     299 ..     131     189 ..     102     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.4e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       ++iG  g+GK++LL++l +l r
  gi|488600087|ref|YP_007906558.1| 31 LAIIGNSGAGKTTLLRILAMLER 53
                                      58****************99944 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.1e-06
                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       S G ++  a++ a+   +     l++DEp ++L+P+ +  + +++k+ + +g+ v+l+TH+ 
  gi|488600087|ref|YP_007906558.1| 131 SGGEQQRVAIARAIVIEP---EMLVLDEPTANLDPSNVVIIEKIIKDIACKGVTVVLATHNL 189
                                       555555556666666666...99************99999999998888899********96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.2e-08   1.9e-05       4     127 ..      27     184 ..      24     192 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.2e-08
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsstsskdllrellralglel 68 
                                       +  il+++G sG+GKTtllr l++     ++  +            +++ ++ ++ p+    ++++++++  l+l++
  gi|488600087|ref|YP_007906558.1|  27 EGEILAIIGNSGAGKTTLLRILAMLER-PSEG-KyyyrgeeandrvRGKITMVFQKPVMF-NTSVYNNVAYGLKLRG 100
                                       6789*****************999862.2222.258999998886644444444444444.7777777777777777 PP

                            AAA_22  69 ka....................erlsseell.ealeqalrarav...ielliiDEaqh.lr.s.eealeeLrsllnl 118
                                        +                    +r++ ++l     ++ + ara    +e+l++DE    l+ s   ++e++  + ++
  gi|488600087|ref|YP_007906558.1| 101 YSkkevdervakalnmmgldgyARHNAKRLSgGEQQRVAIARAIviePEMLVLDEPTAnLDpSnVVIIEKI--IKDI 175
                                       7777888888888888888888899999999544444444444489999*****97666754234444444..3333 PP

                            AAA_22 119 srkgvqliL 127
                                       + kgv+++L
  gi|488600087|ref|YP_007906558.1| 176 ACKGVTVVL 184
                                       456666655 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 !   20.4   0.3   3.3e-07   0.00028      25     189 ..      29     178 ..      14     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.3e-07
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       ++ ai+G+ G+GK+ ll  +  +L        r ++ +      +e +   +++++++f+++      ++   ++  
  gi|488600087|ref|YP_007906558.1|  29 EILAIIGNSGAGKTTLLRIL-AMLE-------RPSEGKYYYRG-EEANDRVRGKITMVFQKPVMF--NTSVYNNVAY 94 
                                       46789999999999998866.2333.......44455555554.777888889999999988776..3333355666 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                        +k  g s+ +++++ ++  +++ l   a+ + + LSgGe++ va+a  + i   +p+ + +lDe  a+LD +nv +
  gi|488600087|ref|YP_007906558.1|  95 GLKLRGYSKKEVDERVAKALNMMGLDGYARHNAKRLSGGEQQRVAIARAIVI---EPE-MLVLDEPTANLDPSNVVI 167
                                       777778888889999999999999999999999*********9999977555...444.789*************** PP

                                       HHHHHHHHCTT CS
                                       xxxxxxxxxxx RF
                             SMC_N 179 vaellkekskn 189
                                       + +++k    +
  gi|488600087|ref|YP_007906558.1| 168 IEKIIKDIACK 178
                                       *****987633 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00014      0.12      17      55 ..      21      73 ..      12     132 .. 0.68
   2 ?    5.7   0.0     0.012        10     323     366 ..     147     189 ..     128     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn..............k 55
                                      + +++ e  +  +iG  ++GK+++l++l  +   +e  +              k
  gi|488600087|ref|YP_007906558.1| 21 INLKIREGeILAIIGNSGAGKTTLLRILAMLERPSEG-KyyyrgeeandrvrgK 73
                                      33444444799*****************777666632.2244555555555553 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                       ++  l+++EP a+L p++  ++ k +k++a+++   v++ TH+ 
  gi|488600087|ref|YP_007906558.1| 147 EPEMLVLDEPTANLDPSNVVIIEKIIKDIACKGV-TVVLATHNL 189
                                       56789****************************7.9******85 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.2e-06    0.0053      17      39 ..      23      45 ..      17      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      ++i++ ++  ++G+sG+GK+Tll
  gi|488600087|ref|YP_007906558.1| 23 LKIREGEILAIIGNSGAGKTTLL 45
                                      567655599*************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.5e-06    0.0064      90     120 ..      18      49 ..       8      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.5e-06
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinall 120
                                       l++++ ++++ ++ +++G+SG+GK+tL+  l+
  gi|488600087|ref|YP_007906558.1|  18 LNKINLKIREgEILAIIGNSGAGKTTLLRILA 49 
                                       566777777779****************9886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.7e-06    0.0049      22      51 ..      26      54 ..      14     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.7e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                       ++e++ ++G+sG GK++l+r l+  le+ 
  gi|488600087|ref|YP_007906558.1| 26 REGEILAIIGNSGAGKTTLLRILA-MLERP 54
                                      34599***************9887.55555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00021      0.18      21      67 ..      33      90 ..      10     113 .. 0.75
   2 ?    2.8   0.0     0.043        37     525     579 ..     146     197 ..     120     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsi...........eitngeeldirVfN 67
                                      i G  GaGKTtL r+l+ le+ +  + +  g+             +++   +++ V+N
  gi|488600087|ref|YP_007906558.1| 33 IIGNSGAGKTTLLRILAMLERPSEGKYYYRGEEandrvrgkitmVFQKPVMFNTSVYN 90
                                      77999**************998877766665543444444444333333455555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.043
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                                        + ++ v+D P   LD   + i+   ik+ +    k   + + THnl   k + +
  gi|488600087|ref|YP_007906558.1| 146 IEPEMLVLDEPTANLDPSNVVIIEKIIKDIA---CKGVTVVLATHNLFQAKRLAD 197
                                       37899************************99...67778999****977666665 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 ?   10.8   0.1    0.0005      0.43       5      80 ..      97     164 ..      94     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                           SbcCD_C   5 dyRnylsfevevrded.....gkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFskl 76 
                                       + R y++ ev++r ++     g ++  ++++++lSGGe+q +   a+a     ++         +++++LDE  ++l
  gi|488600087|ref|YP_007906558.1|  97 KLRGYSKKEVDERVAKalnmmGLDGYARHNAKRLSGGEQQRV---AIA----RAIVI------EPEMLVLDEPTANL 160
                                       5677777788888433466667777789999********643...333....22323......35678888888888 PP

                           SbcCD_C  77 Dees 80 
                                       D+ +
  gi|488600087|ref|YP_007906558.1| 161 DPSN 164
                                       7765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.6e-05     0.082       3      22 ..      32      53 ..      30      75 .. 0.75
   2 ?    0.7   0.0      0.66   5.6e+02      74     104 ..      80     110 ..      65     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.6e-05
                            AAA_28  3 vitGgestGKTtlleaLa..ar 22
                                      +i+G +++GKTtll+ La  +r
  gi|488600087|ref|YP_007906558.1| 32 AIIGNSGAGKTTLLRILAmlER 53
                                      79***************95533 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.66
                            AAA_28  74 kvlfcDrglldtlaYarayggeaeaeleaaa 104
                                       k +++ +++ +++aY   + g  ++e+++ +
  gi|488600087|ref|YP_007906558.1|  80 KPVMFNTSVYNNVAYGLKLRGYSKKEVDERV 110
                                       5688999999999999888887777887733 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.2   0.00018      0.16       7      61 ..      17      67 ..      14     215 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                          ATPase_2  7 elkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialrees 61
                                      +l++++  +++   ei+ i G  g GKt+Ll+ ++   +  ++   yy+  +e +
  gi|488600087|ref|YP_007906558.1| 17 ALNKINLKIRE--GEILAIIGNSGAGKTTLLRILAMLERP-SE-GKYYYRGEEAN 67
                                      67777777777..79****************977665543.33.44555444433 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.8e-05     0.058       3     113 ..      33     198 ..      31     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf................................gvnlrdvakenglllevdpe.al 46 
                                       + G +G+GKttl + L+ ++                                    +++ va+   l+ +  +e + 
  gi|488600087|ref|YP_007906558.1|  33 IIGNSGAGKTTLLRILAMLE-RpsegkyyyrgeeandrvrgkitmvfqkpvmfnTSVYNNVAYGLKLRGYSKKEvDE 108
                                       899*************6553.22355567887777777777777777777777766666666666666666666333 PP

                            AAA_18  47 deskrldedkldklldaleenss................aleegknlvidghlaeleseaakdikk........... 96 
                                       +  k l+++ ld   + +    +                   e++ lv+d   a+l + + ++i k           
  gi|488600087|ref|YP_007906558.1| 109 RVAKALNMMGLDGYARHN----AkrlsggeqqrvaiaraIVIEPEMLVLDEPTANLDPSNVVIIEKiikdiackgvt 181
                                       344444443332222222....2344467777777777755556666666666666666666666666666666666 PP

                            AAA_18  97 vvLtaspeelleRlekR 113
                                       vvL +++   ++Rl++R
  gi|488600087|ref|YP_007906558.1| 182 VVLATHNLFQAKRLADR 198
                                       77777777777777777 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3     5e-05     0.042      16      39 ..      22      48 ..      12      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-05
                            AAA_23 16 dF...skgltlItGpNGaGKTTildAi 39
                                      ++   +  + +I+G+ GaGKTT+l+ +
  gi|488600087|ref|YP_007906558.1| 22 NLkirEGEILAIIGNSGAGKTTLLRIL 48
                                      55555556889*************876 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.14       1      19 [.      30      48 ..      30      55 .. 0.85
   2 ?   -0.6   0.0       1.3   1.1e+03      81      97 ..     153     169 ..     122     193 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                              MobB  1 vlgivgksgsGKTtLlekl 19
                                      +l+i+g+sg+GKTtLl  l
  gi|488600087|ref|YP_007906558.1| 30 ILAIIGNSGAGKTTLLRIL 48
                                      799************9754 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                              MobB  81 leellarlsevDlvlvE 97 
                                       l+e +a l++  +v++E
  gi|488600087|ref|YP_007906558.1| 153 LDEPTANLDPSNVVIIE 169
                                       55555555555555554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.6e-05     0.073       2      22 ..      30      50 ..      29      58 .. 0.88
   2 ?   -3.1   0.0       7.7   6.6e+03     104     128 ..     163     187 ..     152     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-05
                                      CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                      ++++ G +G GKTtLl+ la+
  gi|488600087|ref|YP_007906558.1| 30 ILAIIGNSGAGKTTLLRILAM 50
                                      5789*************9987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.7
                                       .....HHHHHCTTTTT--EEEEEEE CS
                             NACHT 104 pvrtlLselirkkllpeasllltvr 128
                                       +  + ++++i+   +++++++l+++
  gi|488600087|ref|YP_007906558.1| 163 SNVVIIEKIIKDIACKGVTVVLATH 187
                                       4456778888888888888888775 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0016       1.4       1      19 [.      30      48 ..      30      65 .. 0.87
   2 ?    2.2   0.0      0.15   1.3e+02     140     167 ..     163     190 ..     158     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                               PRK  1 vIgvagsSGaGkttvarkl 19
                                      ++++ g+SGaGktt+ r l
  gi|488600087|ref|YP_007906558.1| 30 ILAIIGNSGAGKTTLLRIL 48
                                      679***********98866 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                               PRK 140 idlelarklqRDiaeRGrsleavldsil 167
                                       +++ ++ k+++Dia +G ++   +++++
  gi|488600087|ref|YP_007906558.1| 163 SNVVIIEKIIKDIACKGVTVVLATHNLF 190
                                       5899*************99877666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00032      0.27      19      41 ..      29      51 ..      21      71 .. 0.84
   2 ?   -1.5   0.0         2   1.7e+03      81      96 ..     134     155 ..     105     188 .. 0.54
   3 ?   -1.6   0.0       2.2   1.9e+03      40      67 ..     173     200 ..     165     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                            AAA_30 19 rvavltGpAGtGKttalkalrea 41
                                       + ++ G  G+GKtt+l+ l+ +
  gi|488600087|ref|YP_007906558.1| 29 EILAIIGNSGAGKTTLLRILAML 51
                                      47899************998755 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                            AAA_30  81 k......grarlepgtllivDE 96 
                                       +      +ra + + ++l+ DE
  gi|488600087|ref|YP_007906558.1| 134 EqqrvaiARAIVIEPEMLVLDE 155
                                       1344444223333335555555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.2
                            AAA_30  40 eaweaaggrviglAptgkaAkvLaeelg 67 
                                       + ++ +g +v++++++  +Ak+La+ + 
  gi|488600087|ref|YP_007906558.1| 173 KDIACKGVTVVLATHNLFQAKRLADRTA 200
                                       5555678899999999999999988765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.14      18      40 ..      21      49 ..       3      53 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                      H......TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 18 l......gdvilLeGdLGaGKTtlvrgla 40
                                      +      g+++++ G+ GaGKTtl r la
  gi|488600087|ref|YP_007906558.1| 21 InlkireGEILAIIGNSGAGKTTLLRILA 49
                                      1333344778***************9886 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 ?    7.1   0.3    0.0024       2.1     241     264 ..      24      48 ..      20      50 .. 0.90
   2 ?    2.6   0.0     0.056        48     324     351 ..     131     158 ..     120     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0024
                                       EE-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAl 264
                                        i++G + +I+G    GK+TLL+ l
  gi|488600087|ref|YP_007906558.1|  24 KIREGeILAIIGNSGAGKTTLLRIL 48 
                                       699999****************976 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.056
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts 351
                                       SG   q ++i++a+ ++ ++l++DE t+
  gi|488600087|ref|YP_007906558.1| 131 SGGEQQRVAIARAIVIEPEMLVLDEPTA 158
                                       99999********************887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.16      38      67 ..      21      50 ..      10      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                             Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                        L+ r+ +iL i G sG gk+t +++L+ 
  gi|488600087|ref|YP_007906558.1| 21 INLKIREGEILAIIGNSGAGKTTLLRILAM 50
                                      556777788*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 1670.85
//
Query:       gi|488600088|ref|YP_007906559.1|  [L=237]
Description: ABC-type tungstate transport system, periplasmic component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   43.6  18.7    3.3e-11   43.3  18.7    1.1  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3  18.7   1.8e-15   3.3e-11       2     183 ..      47     236 ..      46     237 .] 0.85

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.8e-15
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilghlilpviillllsaapyvrlirr 73 
                                       +++Gi+++ +++++++++l ++++ ll++P++vl+++l+l++       + +l ++ +++ +   l ++p+++ +++
  gi|488600088|ref|YP_007906559.1|  47 FPIGIMLG-MHSFTGKNILKGFFNSLLGIPTVVLGLILYLMLvpfgpLGFLKLIYTEMGISFGQSLLITPIMISFIA 122
                                       69******.********************************9*****77779999********************** PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG....lgtllleail 146
                                       + +++++ + +e+ar+lGa++++     v+  +++ ++  +i +f +++ +  ++ ++g++        ++++ ++ 
  gi|488600088|ref|YP_007906559.1| 123 SSIEAVEGEIRELARTLGAGEIEASI-AVMSESISGVLLAVIASFNRAIAELGIAIMIGGNIFvkgsALNTRVLTTA 198
                                       ***********************666.77888999999999******************543255553344445555 PP

                      BPD_transp_1 147 gydyseis.nggvlalviavlllnlvadilqrlldprv 183
                                       +++y++   + +++al+i++l +++++  +  l++ r+
  gi|488600088|ref|YP_007906559.1| 199 MQMYTARGeIDMAIALGIILLSIVFAVSTISNLIQSRL 236
                                       55555444877888888888888888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1611.36
//
Query:       gi|488600089|ref|YP_007906560.1|  [L=337]
Description: ABC-type tungstate transport system, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   79.1   0.1    5.8e-22   78.7   0.1    1.1  1  PBP_like_2  PBP superfamily domain
    2.2e-08   34.1   0.0    8.2e-08   32.3   0.0    1.8  1  SBP_bac_11  Bacterial extracellular solute-binding protein
     0.0006   19.7   0.3        1.9    8.2   0.0    3.1  3  SBP_bac_8   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.014   15.4   0.2        5.8    6.8   0.0    2.8  3  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 !   78.7   0.1   1.3e-25   5.8e-22       6     282 .]      36     269 ..      29     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.3e-25
                        PBP_like_2   6 atsvgeifgaGsttpa.palrk.lada.fekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwa 78 
                                       +  v  ++++++t+++ ++l++ ++ + f++a +g+++   ++G+ga+i++  ng++d+++++++ +e e++ +g++
  gi|488600089|ref|YP_007906560.1|  36 EERV--LTISTTTSLYdTGLLEdAIAPaFKDA-TGIELHFIPKGTGAAIQDAMNGAADAIIVHARSKEIEFMeNGYG 109
                                       3333..66666666542555551655577777.8******************************************* PP

                        PBP_like_2  79 angaggliqvpvaigaialvvnkdnpln....lsreaLakIfs.gkItnWndvlglpadgpIkvvhrsdgsgttflf 150
                                        n+        +a++ +++v+++++p++       eaL+kI+  g+            +g+   v+r dgsg     
  gi|488600089|ref|YP_007906560.1| 110 VNR------KIIAYNFFVIVGPENDPAGikglSPVEALKKIVEeGR------------KGNAIWVSRDDGSG----- 163
                                       ***......***************999999*8889******88554............**************..... PP

                        PBP_like_2 151 stalaeqgpwtasgigasgsegvasav....snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkv 223
                                        t+++e ++w+++g      +++++ +    ++ g++ ++++ +    ++y+l+d      +++l++    +     
  gi|488600089|ref|YP_007906560.1| 164 -TNTKEIALWEKAGYN---YSEIKKESwfrnTGTGMGKTLNYCNNV--RAYTLSD-----MGTYLKY----RM---- 221
                                       .***********9998...55556664455588********99555..8******.....7899999....22.... PP

                        PBP_like_2 224 akiasnplawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsde 282
                                               ++++++ +   +d+   l + + iiv++p++   +++++a++ +++l+s+e
  gi|488600089|ref|YP_007906560.1| 222 --------DGLIDLAV--LVDKGEELINIYAIIVVNPEKF-NKDFDGAMELVKWLTSRE 269
                                       ........34555444..5589999***********9865.566************976 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 !   32.3   0.0   1.8e-11   8.2e-08      14     228 ..      56     278 ..      40     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.8e-11
                                       HHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEEEEESTT-T CS
                        SBP_bac_11  14 relaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplviavpkgnp 90 
                                       +++a+aF+ +tg+++++  +g g++++   +ga+  +++ a s+ +e + ++g+++  +++ +a++  vi+ p++ p
  gi|488600089|ref|YP_007906560.1|  56 DAIAPAFKDATGIELHFIPKGTGAAIQDAMNGAADAIIVHARSKEIEFM-ENGYGV--NRKIIAYNFFVIVGPENDP 129
                                       479*****************************65555556667777777.79****..******************* PP

                                       T---SHHHHHHS......S--...EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHHHHHTTT CS
                        SBP_bac_11  91 kkikgwadLlkp......glk...lavadPttspsGlaalalleaagaqellkalekkvvklgessrqlltaveage 158
                                       ++ikg+  + +       g k   + v+    s++ +  +al+e+ag +++  + e++ ++ g++ + +l++ ++ +
  gi|488600089|ref|YP_007906560.1| 130 AGIKGLSPVEALkkiveeGRKgnaIWVSRDDGSGTNTKEIALWEKAGYNYSEIKKESWFRNTGTGMGKTLNYCNNVR 206
                                       *99977665553334554443433667766555555577799*****98888899999**999999******77766 PP

                                       -SEEEEEHHHHH..HSTT.SS.EEEE--TTT--...EEEEEEEE-T...T--HHHHHHHHHTTSHHHHHHHHHTT CS
                        SBP_bac_11 159 adagivyeseakaaengd.kl.eavylpeglnldpldypaavlkka...akreaAraFlafLrspeaqailrkyG 228
                                       a  +    + +k++  g  +l ++v   e+l      y+++v++ +   ++   A +++++L+s+e+q+++ +yG
  gi|488600089|ref|YP_007906560.1| 207 AYTLSDMGTYLKYRMDGLiDLaVLVDKGEELI---NIYAIIVVNPEkfnKDFDGAMELVKWLTSREGQKTIGEYG 278
                                       66666666666665333323303334444444...377888887553336669*********************9 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 ?    2.5   0.0     0.023     1e+02       2      31 ..      58      87 ..      57      96 .. 0.74
   2 !    5.4   0.1    0.0031        14     107     172 ..     127     209 ..     103     236 .. 0.74
   3 !    8.2   0.0   0.00043       1.9     226     257 ..     244     276 ..     225     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.023
                                      HHHHHHHH-TEEEEEEE--SSSHHHHHHHH CS
                         SBP_bac_8  2 lakefekktgvkvnvvtaasndleqklkaa 31
                                      +a +f+++tg+++ +++ +++ ++q + + 
  gi|488600089|ref|YP_007906560.1| 58 IAPAFKDATGIELHFIPKGTGAAIQDAMNG 87
                                      7889**************776655554443 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0031
                                       S.---BHHHH..HHHHHHH.....HHH-SE..GG---G..GGGGGTHHETTEE---H.........HHH.HHHHHHH CS
                         SBP_bac_8 107 aedpktwdel..laaakkl.....kgkfgl..pdpasg..wlqaallakdgksldddg.......gkdglkealell 165
                                       + dp+++++l  ++a+kk+     kg++++   d++sg  + ++al+ k+g+++++ +       +  g  ++l++ 
  gi|488600089|ref|YP_007906560.1| 127 N-DPAGIKGLspVEALKKIveegrKGNAIWvsRDDGSGtnTKEIALWEKAGYNYSEIKkeswfrnTGTGMGKTLNYC 202
                                       4.8888888877777888888888888899543555443388******99999999865666544444448888888 PP

                                       HHHHHTT CS
                         SBP_bac_8 166 kklkdng 172
                                       ++ +++ 
  gi|488600089|ref|YP_007906560.1| 203 NNVRAYT 209
                                       8888775 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00043
                                       EEEBTTS-HHHH.HHHHHHHHHTTSHHHHHHHH CS
                         SBP_bac_8 226 lavpknaknedl.aAldFlkwltspenqaalae 257
                                       ++v+  + n+d  +A++++kwlts e+q+   e
  gi|488600089|ref|YP_007906560.1| 244 IVVNPEKFNKDFdGAMELVKWLTSREGQKTIGE 276
                                       56666666777779**************97655 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 ?    6.8   0.0    0.0013       5.8       9      57 ..      53      94 ..      45     113 .. 0.77
   2 ?   -1.3   0.0      0.37   1.7e+03     139     165 ..     138     165 ..     136     192 .. 0.72
   3 ?    5.5   0.0    0.0031        14     284     315 .]     238     272 ..     208     272 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0013
                                      HHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE CS
                         SBP_bac_1  9 alqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav 57
                                       l+ ++a af+   +gi+  +++ g+g+ +q    + ++G++  D i+v
  gi|488600089|ref|YP_007906560.1| 53 LLEDAIAPAFKD-ATGIELHFIPKGTGAAIQ----DAMNGAA--DAIIV 94
                                      677788899955.9*****************....******4..54444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.37
                                       HHHHHHHHHHCTCT.HCCHCCEEHHHHH CS
                         SBP_bac_1 139 veaakklkekgkkp.iggarggsasgta 165
                                       vea+kk++e g+k+  +++ + ++sgt+
  gi|488600089|ref|YP_007906560.1| 138 VEALKKIVEEGRKGnAIWVSRDDGSGTN 165
                                       7899999999999965555555555554 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0031
                                       EEEEEEEEBTTCS.THHH..HHHHHHHHTSHHHHH CS
                         SBP_bac_1 284 lgayglaipkgsk.npea..AkkFldfllspeaqa 315
                                       ++ y +++++  k n++   A +++++l+s e+q+
  gi|488600089|ref|YP_007906560.1| 238 INIYAIIVVNPEKfNKDFdgAMELVKWLTSREGQK 272
                                       66666555555552455588************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2303.17
//
Query:       gi|488600090|ref|YP_007906561.1|  [L=362]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-118  396.5  14.6   1.3e-118  396.3  14.6    1.0  1  DUF373           Domain of unknown function (DUF373)
  ------ inclusion threshold ------
      0.021   15.0   1.2      0.021   15.0   1.2    2.3  2  Phage_holin_3_3  LydA holin phage, holin superfamily III
       0.15   11.3   0.2       0.23   10.7   0.2    1.2  1  DUF1442          Protein of unknown function (DUF1442)
       0.95    9.8  14.1         11    6.4   1.8    4.3  4  DUF4134          Domain of unknown function (DUF4134)


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 !  396.3  14.6    3e-122  1.3e-118       2     335 .]       4     347 ..       3     347 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.3 bits;  conditional E-value: 3e-122
                            DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvg 78 
                                        ++l++DrD+Dlgrkag+++ ++Gre++l+aa+kla  dPeDSD+N++fgaik+ydeL++ gedvev+++tGd +vg
  gi|488600090|ref|YP_007906561.1|   4 KVILAIDRDNDLGRKAGIEGVIIGREDNLNAAIKLAENDPEDSDINTIFGAIKIYDELRNAGEDVEVVTITGDISVG 80 
                                       58*************************************************************************** PP

                            DUF373  79 veadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrk 155
                                       v +d+kiae+ld + sk++++s+ivV+DG+eDe+vlp+i+sr+k+dsvkr++Vkqs++iE t+y+l+k+l+dp++ k
  gi|488600090|ref|YP_007906561.1|  81 VVSDSKIAEHLDYIASKIKPESVIVVTDGSEDEFVLPLISSRFKIDSVKRIIVKQSKTIEGTVYMLRKVLSDPKVVK 157
                                       ***************************************************************************** PP

                            DUF373 156 tiLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvalllll 232
                                        +++p+G++l+iy++++++++p++a++ +++l+G+y++lr+++ld  +e+++++lk++l egri+fvty+++++l+ 
  gi|488600090|ref|YP_007906561.1| 158 NFFTPIGVTLIIYSIFVIADYPQYAIGGMIFLIGVYMILRAYELDIGIETFFSNLKTALLEGRISFVTYIISAILFT 234
                                       ***************************************************************************** PP

                            DUF373 233 igiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglv 309
                                       ig+i+g++++++++ ++vs+gl+ l+++fiyg++++++++++ +slgk++d+++  e+k+  ++l++ fl++++gl 
  gi|488600090|ref|YP_007906561.1| 235 IGVIEGFYTFWKLTLQPVSPGLIALATSFIYGVIWYFTAGGISISLGKMLDAVI--ERKSYVKYLTISFLIVSAGLA 309
                                       ******************************************************..446889*************** PP

                            DUF373 310 lygasaylls............lsilalslvvgivval 335
                                       l+g s y+ls            ++++als+++ i++a+
  gi|488600090|ref|YP_007906561.1| 310 LWGGSVYILSnyenfsmgseeaIRTFALSIFGSIFIAV 347
                                       ********99************9***********9985 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 ?   -2.0   0.0      0.87   3.9e+03      41      67 ..     165     191 ..     141     209 .. 0.63
   2 ?   15.0   1.2   4.6e-06     0.021       4      47 ..     306     351 ..     303     357 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.87
                   Phage_holin_3_3  41 vGllvfllceelglsqlltlaiaglsG 67 
                                       v l+ + +   ++ +q++ ++++ l+G
  gi|488600090|ref|YP_007906561.1| 165 VTLIIYSIFVIADYPQYAIGGMIFLIG 191
                                       444555555555555555555555555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.6e-06
                   Phage_holin_3_3   4 ivlAllGGlvsylmrakk.g.rrrfsikellleivvSgfvGllvfl 47 
                                       ++lAl+GG v  l + ++ +  +++ i+ ++l+i+ S+f+++++++
  gi|488600090|ref|YP_007906561.1| 306 AGLALWGGSVYILSNYENfSmGSEEAIRTFALSIFGSIFIAVIGMA 351
                                       689************9996369*********************986 PP

>> DUF1442  Protein of unknown function (DUF1442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   5.2e-05      0.23      96     183 ..      81     169 ..      59     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.2e-05
                           DUF1442  96 elpevivaeevektmeklqGvdflvv.dskrkefvanalrla.klskrGavlvcknalrrsisgfkwkkvlrdrrvv 170
                                        +++  +ae+++ +  k++    +vv d  + efv   +    k+ +   ++v ++  +   + + ++kvl+d +vv
  gi|488600090|ref|YP_007906561.1|  81 VVSDSKIAEHLDYIASKIKPESVIVVtDGSEDEFVLPLISSRfKIDSVKRIIVKQS-KTIEGTVYMLRKVLSDPKVV 156
                                       55666778888888888887776665488999999655543314455555555555.444667899*********** PP

                           DUF1442 171 rsvtlpvggGlei 183
                                       +  + p+g  l i
  gi|488600090|ref|YP_007906561.1| 157 KNFFTPIGVTLII 169
                                       *******988866 PP

>> DUF4134  Domain of unknown function (DUF4134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.017        75      50      69 ..      50      69 ..      47      78 .. 0.83
   2 ?    4.0   0.1     0.014        63      76      92 ..     183     199 ..     180     199 .. 0.91
   3 ?    1.6   0.2     0.077   3.4e+02      31      60 ..     217     246 ..     204     253 .. 0.71
   4 ?    6.4   1.8    0.0025        11      32      87 ..     291     350 ..     257     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.017
                           DUF4134 50 glvgalkvYikwnsgdqdvk 69
                                       + ga+k+Y  + +  +dv+
  gi|488600090|ref|YP_007906561.1| 50 TIFGAIKIYDELRNAGEDVE 69
                                      799*********99999986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.014
                           DUF4134  76 fgaciflvvaatvlkaf 92 
                                       +g++ifl+ + ++l+a+
  gi|488600090|ref|YP_007906561.1| 183 IGGMIFLIGVYMILRAY 199
                                       79************997 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.077
                           DUF4134  31 vasyfdpvtkliyaiaavvglvgalkvYik 60 
                                       +++ +  vt++i ai   +g++ ++  + k
  gi|488600090|ref|YP_007906561.1| 217 LEGRISFVTYIISAILFTIGVIEGFYTFWK 246
                                       555666777777777777777777776666 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0025
                           DUF4134  32 asyfdpvtkliyaiaavvglvga....lkvYikwnsgdqdvkksiaawfgaciflvvaat 87 
                                       +sy++++t   +++ a ++l g+    l+ Y ++++g ++  ++ a  +++ if++v+++
  gi|488600090|ref|YP_007906561.1| 291 KSYVKYLTISFLIVSAGLALWGGsvyiLSNYENFSMGSEEAIRTFALSIFGSIFIAVIGM 350
                                       78999999999999999999887444456699*****99999999999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2304.42
//
Query:       gi|488600091|ref|YP_007906562.1|  [L=126]
Description: hypothetical protein Asulf_00548 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-18   65.7   0.0    4.6e-18   65.5   0.0    1.1  1  CbiX            CbiX
  ------ inclusion threshold ------
      0.081   12.0   0.0      0.098   11.7   0.0    1.1  1  Ferrochelatase  Ferrochelatase
       0.13   12.6   0.0       0.23   11.8   0.0    1.4  1  PFOR_II         Pyruvate:ferredoxin oxidoreductase core domai


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 !   65.5   0.0   7.6e-22   4.6e-18       1     105 [.      10     117 ..      10     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 7.6e-22
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCE.CCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHC CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgflelee.psleealrelaeqgvkrivvvPlflfaGvhvkeDIpeel 76 
                                       HGS++p+++e +ek+ ++++++g f++v+++f+  ++ ps +ea+r++   + + ++vvPlf++ G hv+eD+pe+l
  gi|488600091|ref|YP_007906562.1|  10 HGSQLPHYREVMEKHRDRIEKSGVFDEVRIAFAARNRkPSPDEAIRSM---QSEVVYVVPLFISYGLHVTEDLPEIL 83 
                                       *********************************999879999999887...99**********************99 PP

                                       T......--SSSS-TTEEEEE---CCCSCCHHHHH CS
                              CbiX  77 e......eaeeahpkdveieytepLGthplvaevl 105
                                       +        e ++ ++ +++++ep+G++  v+ ++
  gi|488600091|ref|YP_007906562.1|  84 NfpkgigVKEGEF-EGKKVIICEPIGEDIFVTYAI 117
                                       9666553333344.599***********9998877 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.6e-05     0.098      71     127 ..      17      72 ..       6      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHHH-..--EEEEEEESSSSSBHHHHHHHHHCTT-SEEEEEES-SS-- CS
                    Ferrochelatase  71 trkqaealekelaerg..idvkvylamrywePsiedaleelkadgvervvvlplyPqys 127
                                        r+  e+ +++++++g  ++v++++a r+ +Ps ++a++ +++   e v+v+pl+  y+
  gi|488600091|ref|YP_007906562.1|  17 YREVMEKHRDRIEKSGvfDEVRIAFAARNRKPSPDEAIRSMQS---EVVYVVPLFISYG 72 
                                       4556666677777777889***********************6...5677888776665 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   3.9e-05      0.23       4      63 ..       6      70 ..       4      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                                      EEEE-STHHHHHHHHHHHHHHTT--EEEE.EES--B......S--HHHHHHHSTT-SEEEEEE-S-- CS
                           PFOR_II  4 vivamGsvagtaksavdelReegikvGll.rlrtlr......PFPeeelkellkkvkkvvvldrnis 63
                                      viv++Gs     +++++++R++ +k G++  +r+ +      P P e+++++    + v v+ + is
  gi|488600091|ref|YP_007906562.1|  6 VIVGHGSQLPHYREVMEKHRDRIEKSGVFdEVRIAFaarnrkPSPDEAIRSMQ--SEVVYVVPLFIS 70
                                      9**************************97423333233344499999999986..555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 864.17
//
Query:       gi|488600092|ref|YP_007906563.1|  [L=186]
Description: Precorrin-6B methylase 1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   82.8   0.0    4.3e-23   82.4   0.0    1.2  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.0   2.4e-27   4.3e-23       1     207 [.       1     168 [.       1     174 [. 0.77

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 2.4e-27
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       +l++VG G+  +++lT rA +++++a+vv+g++ +al+ ++++++           + +++ +  e+  + ++e+ +
  gi|488600092|ref|YP_007906563.1|   1 MLTVVGSGI-CRDHLTDRAKKIIERAEVVYGSK-KALDNVREFIKG----------KFKVMKGFSEAEYSEIVEESK 65 
                                       699******.56*********************.******999854..........345566666655556666665 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                       + k+Vv++++GDP+v+g g + +            ev PG+ss+q a a+lg++l++  ++ +++    ++ + re+
  gi|488600092|ref|YP_007906563.1|  66 R-KNVVVVSTGDPMVAGLGTKFH-----------AEVEPGISSVQVALAKLGVDLCDVVVMNAHS----KEVNLREI 126
                                       5.47**************99998...........5788***************************....55678888 PP

                      TP_methylase 155 eallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrg 207
                                        ++l+ ++++++l ++r       ++k+   + +++v++ e++++ +erv++g
  gi|488600092|ref|YP_007906563.1| 127 MHFLK-FRSVLILANRR------FDIKKL--G-ELKVVLLENMCM-NERVREG 168
                                       88898.67777776666......334444..3.336666666666.5566555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1204.06
//
Query:       gi|488600093|ref|YP_007906564.1|  [L=284]
Description: hypothetical protein Asulf_00550 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-37  128.7   0.1    2.6e-37  128.5   0.1    1.1  1  CbiD      CbiD
  ------ inclusion threshold ------
      0.053   13.2   0.6       0.26   10.9   0.3    2.1  2  OpcA      Outer membrane protein OpcA


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 !  128.5   0.1   2.9e-41   2.6e-37       2     212 ..      37     228 ..      36     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 2.9e-41
                              CbiD   2 rsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee.aavikdaGddp.DvTngaeivae 76 
                                       r+G+Tt ++A++A++aA+  l+++ +  +ve+ +p+g+kl+++   +++++ +  + +k +Gd+  DvTng+eiva+
  gi|488600093|ref|YP_007906564.1|  37 RRGITTATTACCAMNAAIKSLFDN-SDCSVEVLTPAGIKLRLK---AKAKD-GvGVAEKFSGDHEfDVTNGIEIVAR 108
                                       89*******************865.5679************99...44433.34999******755*********** PP

                              CbiD  77 veeeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleeakegvevtisvpeGeelAkkTlNprlGiv 153
                                       v+e+  i+ G+G+G   k+      g++A+++ + ++i+en++ ++++++ +  v i +p+Ge++AkkT N++lGi+
  gi|488600093|ref|YP_007906564.1| 109 VTEKRGIRFGKGIGE--KN------GKKAVSRSAMAQIKENFSYYTKKYGFSGGVLIEIPDGEKIAKKTKNAELGIE 177
                                       **9899********8..43......7***********************99999*********************** PP

                              CbiD 154 gGiSiLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpe 212
                                       gGiSiLG tG vep+ +e +  +i    ++  a++++++ ++tG+++ ++a kk  +pe
  gi|488600093|ref|YP_007906564.1| 178 GGISILGSTGFVEPWCDELVETKI----EI--AKRYRRISITTGRRAWHYALKK--FPE 228
                                       ***************988765544....33..4567899999999999999884..444 PP

>> OpcA  Outer membrane protein OpcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   2.9e-05      0.26      78     130 ..      95     147 ..      74     151 .. 0.88
   2 ?   -0.5   0.0     0.091   8.1e+02     138     165 ..     182     209 ..     175     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.9e-05
                              OpcA  78 nrvdvyaGytytqslsealklrvGaGlGyekskdavkiekntlssereafylk 130
                                       ++ dv  G      + e+ ++r G G+G +++k av+ ++ +   e  ++y+k
  gi|488600093|ref|YP_007906564.1|  95 HEFDVTNGIEIVARVTEKRGIRFGKGIGEKNGKKAVSRSAMAQIKENFSYYTK 147
                                       56899999999999**************************99999999***99 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.091
                              OpcA 138 qlGsGWyinPWaevkvdldarlkenatv 165
                                        lGs  +++PW++  v+ +  + +++  
  gi|488600093|ref|YP_007906564.1| 182 ILGSTGFVEPWCDELVETKIEIAKRYRR 209
                                       6999999****86555555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2016.07
//
Query:       gi|488600094|ref|YP_007906565.1|  [L=195]
Description: Precorrin isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  153.5   0.7    1.2e-44  152.3   0.7    1.5  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 !  152.3   0.7   6.7e-49   1.2e-44       2     195 ..      15     189 ..      14     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 6.7e-49
                                       HHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHH CS
                              CbiC   2 IeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkr 78 
                                       I+++S +i ++ +     ++ + e++rR++ at+d+++++++rf+ +a e+g+ea+ +g++i++Dv+m+kaG++ k 
  gi|488600094|ref|YP_007906565.1|  15 IARKSAEIARKLIPG---DDLKSEILRRCVIATGDPSVKDIIRFK-GAPEKGVEAIWEGCEIIVDVNMIKAGLRAKS 87 
                                       899999999999974...58999*********************7.789************************7665 PP

                                       HHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE---- CS
                              CbiC  79 leklgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvG 155
                                        ++        ++ ++     +++  tr + +++k++++ +g+++ iGn+P+A ++++e+   +kv+pa+++++PvG
  gi|488600094|ref|YP_007906565.1|  88 ISA--------MEFAD-----SKSTDTRVVSGFKKLHSRIDGCLLGIGNSPSAAMHICEIA--EKVRPAFIVATPVG 149
                                       554........33332.....34688*********************************85..5689********** PP

                                       SCCHHHHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHH CS
                              CbiC 156 FvgaaesKealaesevpyitveGrkGGsavAaaivnaLle 195
                                       Fv+aaesKe+++e+++p+it+ G++GGs+++aai+n L++
  gi|488600094|ref|YP_007906565.1| 150 FVNAAESKEMIRELDIPSITTVGTRGGSTICAAIINCLID 189
                                       ************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1389.57
//
Query:       gi|488600095|ref|YP_007906566.1|  [L=250]
Description: precorrin-3 methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-35  121.5   0.0    5.3e-35  121.3   0.0    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 !  121.3   0.0   2.9e-39   5.3e-35       1     211 [.       6     210 ..       6     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 2.9e-39
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal..aea 75 
                                       kly+VG+GpG+++llT++Al+alk+++ +lg +  + +++ dl+           k+k++ e ++   +e++  a +
  gi|488600095|ref|YP_007906566.1|   6 KLYVVGIGPGSTDLLTIKALNALKDSEYILGHK-TYIKRIYDLV-----------KDKKVIESGMGREVERVrmAVK 70 
                                       79*******************************.7777776766...........4577777775444444448777 PP

                      TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakee 150
                                       l++  +V l+++GDP++yg+   ++e +++++ +++ve iPGv++ +aa + lg  ++ ++ v s++  l +++k+e
  gi|488600095|ref|YP_007906566.1|  71 LAEESRVSLISGGDPSIYGILPLVIEYVSRNNIDVDVEAIPGVTASCAASSLLGSAISGDHAVISLSdlLIPWKKIE 147
                                       777789************************999999*********************************999***** PP

                      TP_methylase 151 ereleallangdtlvllkapr.k.....laelaelLkealyddttpvavveragtedervvrgtlee 211
                                       +r+l+al    d++v++++p+ +     l +++e+++e+ ++ +  + +v++a +e+e v   +++e
  gi|488600095|ref|YP_007906566.1| 148 KRLLHALKG--DFVVVIYNPSsRrrksnLIRAMEIIREH-RG-DAMIGIVKNAYREGEMVLFKRVSE 210
                                       ****99987..**********746889999999******.55.459************988666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1675.55
//
Query:       gi|488600096|ref|YP_007906567.1|  [L=233]
Description: Cobalamin biosynthesis protein CbiG [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   88.8   0.0    3.3e-25   87.9   0.0    1.5  1  CbiG_N    Cobalamin synthesis G N-terminal
    1.3e-24   87.0   0.3      2e-24   86.4   0.3    1.3  1  CbiG_C    Cobalamin synthesis G C-terminus
  ------ inclusion threshold ------
      0.065   13.2   0.3       0.21   11.6   0.1    1.8  2  DUF4974   Domain of unknown function (DUF4974)
      0.065   12.7   0.0        7.7    5.9   0.0    2.4  2  CbiJ      Precorrin-6x reductase CbiJ/CobK
      0.081   12.3   0.0       0.51    9.7   0.0    2.0  2  PALP      Pyridoxal-phosphate dependent enzyme
       0.11   12.5   0.5       0.69   10.0   0.1    2.2  3  ROS_MUCR  ROS/MUCR transcriptional regulator protein


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   1.1e-28   3.3e-25       5      81 ..      39     113 ..      35     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 1.1e-28
                                       HHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX CS
                            CbiG_N   5 elfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtat 81 
                                       e +++yd++v+ + +GivvR i+p+lk+K+tDpaVvv+d+   ++i++l+Gh +g+ne+A+ + +++g++++iTta 
  gi|488600096|ref|YP_007906567.1|  39 EDLTDYDCVVAYMPSGIVVRGICPYLKSKWTDPAVVVLDKPLMHAIPVLGGH-HGGNEIAKYL-ETFGMKAIITTAM 113
                                       56789***********************************************.**********.999********96 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.3   6.7e-28     2e-24       1     116 []     119     232 ..     119     232 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 6.7e-28
                                       EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT- CS
                            CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnps 77 
                                       l vG+G+r+ ++a+ei  ai+++l+e + ++e+v+ l+ti+ K+    +le+a++l+ p+ +++++eL++++v   +
  gi|488600096|ref|YP_007906567.1| 119 LSVGVGFRKSVKADEIILAIRNTLKEINAEMEDVRVLSTIEDKKGS-VILEVADELKKPIIFVKRDELNSMDV---Q 191
                                       579****************************************987.799**********************9...8 PP

                                       CHHHCCCSSS-HHHHHHHHHC...EECSCEEEETTEEEEEE CS
                            CbiG_C  78 efvkkevGvpsVaEaaAllaa..arllvpKqakggvTvAia 116
                                       e+ +k +Gv++VaEa+A+  +  ++ll+pK+ +ggvTvAia
  gi|488600096|ref|YP_007906567.1| 192 ETKAKIIGVKNVAEACAIYSSssGELLLPKRVYGGVTVAIA 232
                                       888999************875447****************8 PP

>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     7e-05      0.21       6      28 ..      12      34 ..       6      44 .. 0.83
   2 ?   -2.0   0.0       1.2   3.7e+03      40      63 ..     125     149 ..     118     155 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7e-05
                                      EEEHHHHHHHHHHHHT--EEE-T CS
                           DUF4974  6 nesLeeilkkLerwYnveivien 28
                                       e L+ei + Le++Y+v+ vi +
  gi|488600096|ref|YP_007906567.1| 12 AEKLKEIKRFLEKKYDVDTVIYK 34
                                      489**************998865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                                       ES-.-.HHHHHHHHHHH.H--EEEE CS
                           DUF4974  40 fsrnesleevLelLekt.ggikyki 63 
                                       f+++ + +e++ ++++t   i+ ++
  gi|488600096|ref|YP_007906567.1| 125 FRKSVKADEIILAIRNTlKEINAEM 149
                                       6666777777777777734465555 PP

>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0026       7.7       2      34 ..      84     116 ..      83     137 .. 0.90
   2 ?    4.4   0.0    0.0074        22      83     116 ..     167     208 ..     163     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0026
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEE---SS CS
                              CbiJ   2 ililgGTsearelaeaLaeagievvvsvateyg 34 
                                       i +lgG   ++e+a+ L+  g+++++++a e  
  gi|488600096|ref|YP_007906567.1|  84 IPVLGGHHGGNEIAKYLETFGMKAIITTAMEFS 116
                                       669*************************98866 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0074
                                       HHHHHHHT-EEEEE-------........EEEEESSHHHHH. CS
                              CbiJ  83 aeackelgipylrleRpswea........kiievdsleeaae 116
                                        e+++el+ p++ ++R++ ++        kii v++++ea+ 
  gi|488600096|ref|YP_007906567.1| 167 LEVADELKKPIIFVKRDELNSmdvqetkaKIIGVKNVAEACA 208
                                       578889999999999999888999999999999999999884 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00017      0.51     150     191 ..      37      77 ..      30     100 .. 0.86
   2 ?   -0.8   0.0      0.28   8.3e+02      16      32 ..     169     186 ..     163     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00017
                                       HHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEE CS
                              PALP 150 ileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigve 191
                                       ++e+l ++ d+vv+ + +G  + Gi+ +lk++++d+ v++ +
  gi|488600096|ref|YP_007906567.1|  37 VWEDL-TDYDCVVAYMPSGIVVRGICPYLKSKWTDPAVVVLD 77 
                                       57889.69****************************999875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.28
                                       TCCCCCCE.EEEEEGGGS CS
                              PALP  16 lskelgvp.lflKlEsln 32 
                                       +++el+ p +f+K++ ln
  gi|488600096|ref|YP_007906567.1| 169 VADELKKPiIFVKRDELN 186
                                       6789999999****9998 PP

>> ROS_MUCR  ROS/MUCR transcriptional regulator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00023      0.69      67      97 ..       5      36 ..       2      49 .. 0.84
   2 ?   -0.6   0.0      0.44   1.3e+03      56      68 ..     123     135 ..      93     149 .. 0.70
   3 ?   -0.2   0.0      0.33   9.9e+02      18      37 ..     128     147 ..     123     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                          ROS_MUCR 67 iicle.dGkklksLkrhLasahgltpeeYrak 97
                                      ++c+e d +klk +kr+L+++++++   Y++ 
  gi|488600096|ref|YP_007906567.1|  5 LLCFErDAEKLKEIKRFLEKKYDVDTVIYKKH 36
                                      6788758899*****************99975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.44
                          ROS_MUCR  56 vpikksvtpdaii 68 
                                       v  +ksv+ d+ii
  gi|488600096|ref|YP_007906567.1| 123 VGFRKSVKADEII 135
                                       4556666666665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.33
                          ROS_MUCR  18 kveaeelpslikevhaalka 37 
                                       +v+a+e+   i+++ + ++a
  gi|488600096|ref|YP_007906567.1| 128 SVKADEIILAIRNTLKEINA 147
                                       55666665555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1415.78
//
Query:       gi|488600097|ref|YP_007906568.1|  [L=243]
Description: precorrin-4 C11-methyltransferase /cobalt-factor II C20-methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  143.9   0.0    7.3e-42  143.7   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    1.9e-06   28.4   0.0    4.2e-06   27.3   0.0    1.5  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.7   0.0   8.1e-46   7.3e-42       1     212 [.       4     203 ..       4     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 8.1e-46
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsr.aleilldllaeeleleapmgkekepleeayeeiaealaeal 76 
                                       k+y++G GpGdpellTv+A ++lk+ad++++++s    e+l ++          +g++ ++ + + eei++++ +al
  gi|488600097|ref|YP_007906568.1|   4 KVYFIGFGPGDPELLTVKAFNLLKKADLIIYPGSIiEEESLSQF----------KGEKISSYGLTLEEIVDIIEKAL 70 
                                       79*******************************55555555444..........45566899999************ PP

                      TP_methylase  77 ragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeere 153
                                       ++gk Vv++ sGDP++yg+ +e +++l+   +gi+veviPGvss+ a  a+lgi+lt g   +++l+p+  + ee+ 
  gi|488600097|ref|YP_007906568.1|  71 NEGKLVVRVQSGDPSIYGAIAEQINELKS--RGIDVEVIPGVSSVFASSASLGIELTAGCNGVAILRPKGRTLEEDY 145
                                       *****************************..9*************************99999999988889999999 PP

                      TP_methylase 154 leallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       le++++ + t+v+l ++ k+++++e   + ++  + p+avv +a++ede  + ++l+ +
  gi|488600097|ref|YP_007906568.1| 146 LEEVAKLPLTIVILLGVAKIDYIVEKVGKIRGF-DEPCAVVYHASREDEIKIISSLRNI 203
                                       ***************************999555.55*************9988988765 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   4.6e-10   4.2e-06      27     150 ..      55     220 ..      46     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.6e-10
                                       HHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.................CCTEEEEEEECS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxx RF
                       Radical_SAM  27 rslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.................vpgiritvetng 86 
                                       + l++eei+++++++  + g+ +v + +g+p+ y  ++e + +l+ +                  + gi++t  +ng
  gi|488600097|ref|YP_007906568.1|  55 YGLTLEEIVDIIEKA-LNEGKLVVRVQSGDPSIYGAIAEQINELKSRGidvevipgvssvfassaSLGIELTAGCNG 130
                                       6689***********.8*****************99999999999999999**9999999999999*********** PP

                                       SCHG........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH...................HHHHHHHH CS
                                       xxxx........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxx RF
                       Radical_SAM  87 tlpd........eeklerllelg.vdrvslgleaaddekvlklmnrghtf...................eevleale 135
                                       + +         e++le+ ++l+ + ++ lg+  +d+  v k  +   +f                   + + +  e
  gi|488600097|ref|YP_007906568.1| 131 VAILrpkgrtleEDYLEEVAKLPlTIVILLGVAKIDYI-VEKVGK-IRGFdepcavvyhasredeikiiSSLRNIAE 205
                                       **99*********************************9.666664.3344335667777777777777788888888 PP

                                       HHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 136 klreagikrvvdriv 150
                                         r++gi+r+ ++i+
  gi|488600097|ref|YP_007906568.1| 206 DVRKLGIRRTATIII 220
                                       888888887666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1515.12
//
Query:       gi|488600098|ref|YP_007906569.1|  [L=215]
Description: hypothetical protein Asulf_00555 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1464.08
//
Query:       gi|488600099|ref|YP_007906570.1|  [L=75]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-13   48.3   0.4    7.9e-13   48.2   0.4    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    8.5e-05   22.9   0.3    0.00012   22.5   0.3    1.1  1  HMA             Heavy-metal-associated domain
    0.00029   20.8   0.2    0.00035   20.6   0.2    1.1  1  NapD            NapD protein
     0.0023   17.2   0.2     0.0024   17.2   0.2    1.1  1  Pox_P35         Poxvirus P35 protein
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.012   15.6   0.1    1.2  1  GYD             GYD domain
      0.016   15.5   0.1      0.019   15.2   0.1    1.1  1  RNA_binding     RNA binding


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.4   2.6e-16   7.9e-13       1      74 [.       6      75 .]       6      75 .] 0.96

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 2.6e-16
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74
                                      +l+++e g+    e++ +al ++  V+e++ v G yd+++k+ ++d++ l++++++ +++  g+++t t+iv +
  gi|488600099|ref|YP_007906570.1|  6 ILINTEIGD---EEKVYDALMNMNGVMEVHIVYGVYDIVVKAQAEDTDTLRKIVEN-IRKKAGLRSTLTLIVTK 75
                                      689999999...9****************************************999.**************975 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3     4e-08   0.00012      14      59 ..      16      62 ..      15      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4e-08
                               HMA 14 akvekvLselpgVesvkvdlatktvtVegdaes.tklrkiieaieka 59
                                       kv ++L +++gV +v + ++    +V+ +ae+ ++lrki+e i+k+
  gi|488600099|ref|YP_007906570.1| 16 EKVYDALMNMNGVMEVHIVYGVYDIVVKAQAEDtDTLRKIVENIRKK 62
                                      68999****************************************95 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   1.2e-07   0.00035       6      63 ..       6      64 ..       4      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                              NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpg 63
                                      +++++  ++ ++v +al ++ gv Evh + +   +Vv  +ae++d+l +++e+i++  g
  gi|488600099|ref|YP_007906570.1|  6 ILINTEIGDEEKVYDALMNMNGVmEVHIVYGVYDIVVKAQAEDTDTLRKIVENIRKKAG 64
                                      68999****************977******************************98776 PP

>> Pox_P35  Poxvirus P35 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2     8e-07    0.0024     163     215 ..      21      73 ..       4      75 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8e-07
                           Pox_P35 163 tllnqekkeelysytGgyDvsLsAYiirvsaakklieeiikekGlssslsfEi 215
                                       +l+n++   e++   G yD+ + A     ++++k++e+i k+ Gl+s+l++ +
  gi|488600099|ref|YP_007906570.1|  21 ALMNMNGVMEVHIVYGVYDIVVKAQAEDTDTLRKIVENIRKKAGLRSTLTLIV 73 
                                       445666778888899*********************************98765 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   3.9e-06     0.012      23      79 ..      16      70 ..       7      75 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.9e-06
                               GYD 23 eeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetl 79
                                      e++ +al  ++ g + +++++ G yD+vv   a+D +t  ++   ++++  +r++++
  gi|488600099|ref|YP_007906570.1| 16 EKVYDAL-MNMNGVM-EVHIVYGVYDIVVKAQAEDTDTLRKIVENIRKKAGLRSTLT 70
                                      5566666.6666655.89*************************99999988888554 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   6.3e-06     0.019      13      68 ..      14      63 ..       4      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.3e-06
                                      -HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHH CS
                       RNA_binding 13 deekVlealsnllpeeeveieeeeaeGhygnpitileaelekkka.kkvlkkllell 68
                                      deekV +al n+        e+  + G y+   ++++a+ e+ +  +k++++++++ 
  gi|488600099|ref|YP_007906570.1| 14 DEEKVYDALMNMNGVM----EVHIVYGVYD---IVVKAQAEDTDTlRKIVENIRKKA 63
                                      9***********9966....4666777777...999999999666666666655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 549.72
//
Query:       gi|488600100|ref|YP_007906571.1|  [L=309]
Description: GTP cyclohydrolase MptA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-76  257.9   1.8    1.1e-76  257.7   1.8    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
     0.0046   17.5   0.4      0.014   16.0   0.4    1.8  1  FolB      Dihydroneopterin aldolase
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.34   10.7   0.0    1.9  2  Leo1      Leo1-like protein


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 !  257.7   1.8   1.9e-80   1.1e-76       1     259 []       2     290 ..       2     290 .. 0.95

  Alignments for each domain:
  == domain 1  score: 257.7 bits;  conditional E-value: 1.9e-80
                                       .XXXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHHHS-SSEEG... CS
                            GCHY-1   1 lpDvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevleeaeeelee... 74 
                                       lpDvq  +++++i l+rVG +gvk++v+v++++k+++ l++++d+fvdLp+++kG+++SR++e+++e  e+l+    
  gi|488600100|ref|YP_007906571.1|   2 LPDVQLLEPDVPIGLSRVGATGVKKLVQVERDGKRPIILISNFDVFVDLPSTRKGVNLSRNFEAVDEVIENLTAtpv 78 
                                       79****************************************************************77777776666 PP

                                       GGHHH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEEEEE- CS
                            GCHY-1  75 kslee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaelerkeevkltvgvevpvttlC 147
                                       k++ee    ++++llek+eya++aev++ +e++++k++pv++++++e ++++++a + ++ + ++ vgvev+++t C
  gi|488600100|ref|YP_007906571.1|  79 KTVEEltikMADALLEKHEYATKAEVKMVSELILRKRTPVTHQKTQEVVKIFCDAVKWKDGNQRILVGVEVTGITSC 155
                                       666668889**********************************************9988558*************** PP

                                       HHHHHHS........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S--- CS
                            GCHY-1 148 PCskeisrell....................eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellK 204
                                       PC++e++++++                    ++++HnQR+++++k+e+ ++  + +i++lie+++ss+s e+ye+lK
  gi|488600100|ref|YP_007906571.1| 156 PCAQELVKAKYaevlknsfsddeiskimqiiPFPSHNQRGRARIKMEV-KDGFSPSIDELIEVARSSMSYEIYEILK 231
                                       *******98889***********************************5.68999*********************** PP

                                       HHHHHHHHHHHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                            GCHY-1 205 ReDEkavtekayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                       ReDE av+e+ ++np+FvED vR +a++      ve+f           ++eneESiH+Hn+vA
  gi|488600100|ref|YP_007906571.1| 232 REDELAVVENVHKNPRFVEDSVRIMAKKT-----VEKFvnapddilvIFRQENEESIHQHNVVA 290
                                       ****************************9.....777777789999999*************98 PP

>> FolB  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   2.3e-06     0.014      33      93 ..      48     106 ..      28     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-06
                                       E-CHHHHHHTTGGGSS-HHHHHHHHHHHHHSSEES-HHHHHHHHHHHHHCHST.ESEEEEEE CS
                              FolB  33 ldlskaaesddledtvdYaelakavkelvesssfkllEalaeriaealleefp.vekvevrv 93 
                                       +dl   ++ + ++ + +++++ + +++l ++ ++k++E l  + a+alle+++ ++k+ev++
  gi|488600100|ref|YP_007906571.1|  48 VDL--PSTRKGVNLSRNFEAVDEVIENLTAT-PVKTVEELTIKMADALLEKHEyATKAEVKM 106
                                       333..34444466677888888888877767.*****************9888877777443 PP

>> Leo1  Leo1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.16   9.8e+02     109     151 ..      64     106 ..      58     125 .. 0.70
   2 ?   10.7   0.0   5.7e-05      0.34      65     128 ..     131     194 ..      86     295 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.16
                              Leo1 109 eaqgvitekltfrPasleseahrrltravakrhkkkakktkli 151
                                       ea+ ++ e+lt +P ++ +e   +++ a+ ++h+  +k++ ++
  gi|488600100|ref|YP_007906571.1|  64 EAVDEVIENLTATPVKTVEELTIKMADALLEKHEYATKAEVKM 106
                                       6667778888889987777777777777777766553444333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.7e-05
                              Leo1  65 ArivrWsDGSlsLqlGsevfdvtrkaladsntyLvvsheaeevleaq...gvitekltfrPa.slese 128
                                          v+W+DG   + +G ev  +t+ + a++        + +evl+      +i++ +++ P  s +++
  gi|488600100|ref|YP_007906571.1| 131 CDAVKWKDGNQRILVGVEVTGITSCPCAQELVKA----KYAEVLKNSfsdDEISKIMQIIPFpSHNQR 194
                                       5679*******************99994443332....333344332222556666666665444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2290.49
//
Query:       gi|488600101|ref|YP_007906572.1|  [L=481]
Description: hypothetical protein Asulf_00558 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   77.2   1.2    1.2e-14   54.3   0.0    2.3  2  PLDc_2    PLD-like domain
    4.5e-05   23.4   0.4      0.081   13.1   0.0    2.6  2  PLDc      Phospholipase D Active site motif
  ------ inclusion threshold ------
      0.031   14.6   1.4       0.32   11.4   0.7    2.3  2  bPH_3     Bacterial PH 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 !   21.5   0.2   2.8e-08   0.00017       8     131 ..     168     275 ..     165     277 .. 0.68
   2 !   54.3   0.0     2e-18   1.2e-14       2     133 .]     320     452 ..     319     452 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.8e-08
                            PLDc_2   8 Akksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetll.gslH 83 
                                       A++s+ +a+y++       d+++++ +++ ++ +lld+   ++ +     l e++ +  ++  +v++ ++++ + +H
  gi|488600101|ref|YP_007906572.1| 168 ANYSVVLASYIL------HDDFHDMVDENINLTLLLDA---NPVGG--IPLDEMEVV--RKADQVYFLKSQSyKNFH 231
                                       566666666666......45567788888888888888...22222..234444444..22234555553234779* PP

                            PLDc_2  84 aKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFer 131
                                        K++++d+k viv++ N+ +     n+ ++++++++++ak+l+e  ++
  gi|488600101|ref|YP_007906572.1| 232 YKFAVVDDKRVIVTTENWKTT----NRGFLIEFKSEKIAKRLKELVDN 275
                                       ******************975....56778889999999998888776 PP

  == domain 2  score: 54.3 bits;  conditional E-value: 2e-18
                            PLDc_2   2 iqliksAkksidiatyyf....vsdreildallkaakrgvkvrilldskkddaga.vdeaslkelkellleagvevr 73 
                                        ++i+++++++ i ++y+      d+++ld l+   ++g k+rillds   +++a ++ +    l+++ ++  +e +
  gi|488600101|ref|YP_007906572.1| 320 FDMIAESREELLIEVPYMdltwFGDDYLLDLLKSSCENGAKIRILLDS---KHSAeRNLKLIEFLNHF-RNCDLEAK 392
                                       67899*************8887777778999999**************...44440444444445555.77777777 PP

                            PLDc_2  74 vfe.tllgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFerlw 133
                                       +++ + ++slH K++  dg+ v ++S+N+++ gl+ln+E+++ i++k + + l+++F  +w
  gi|488600101|ref|YP_007906572.1| 393 MIKlKGFDSLHGKMLYADGRCV-ITSANFNEYGLKLNREIAILIDNKSACNFLRNQFYDDW 452
                                       765323389*********9765.67*******************************99998 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1   0.00064       3.8       6      24 ..     231     249 ..     229     250 .. 0.91
   2 !   13.1   0.0   1.4e-05     0.081       3      25 ..     400     421 ..     398     422 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00064
                                       ---EEEETTTEEEEE---S CS
                              PLDc   6 HqKivivDdrvafvGgaNL 24 
                                       H K+ +vDd++++v++ N+
  gi|488600101|ref|YP_007906572.1| 231 HYKFAVVDDKRVIVTTENW 249
                                       88************99776 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.4e-05
                                       BEE---EEEETTTEEEEE---SS CS
                              PLDc   3 gthHqKivivDdrvafvGgaNLc 25 
                                        ++H K++  D+r +++++aN++
  gi|488600101|ref|YP_007906572.1| 400 DSLHGKMLYADGR-CVITSANFN 421
                                       689**********.*******98 PP

>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.077   4.6e+02       4      73 ..      98     170 ..      96     188 .. 0.54
   2 ?   11.4   0.7   5.3e-05      0.32       3      72 ..     215     282 ..     213     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.077
                             bPH_3   4 dEkilyltkgqinak..ldkpglivvTnkRiifldpkmfggkdfeeipYksIksvdlkkgl.......lgakitlet 71 
                                       +E+i+ ++ + + +     ++g+i   ++ +++++++       +++ Y + +s++   +        + +k++++ 
  gi|488600101|ref|YP_007906572.1|  98 GEEIYLYCNNTLADTfsYGRNGMIPYCDRDVVYYRSD------GWDFRYLNWTSFEPVSDTvsariviFPNKFKIKA 168
                                       5677777766666556667777777777777777776......4444444444444444440111133555555555 PP

                             bPH_3  72 sg 73 
                                       + 
  gi|488600101|ref|YP_007906572.1| 169 NY 170
                                       44 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.3e-05
                             bPH_3   3 kdEkilyltkgqinakldkpglivvTnkRiifldpkmfggkdfeeipYksIksvdlkkgllgakitlets 72 
                                       k +++++l +++++    +++++vv +kR+i++++   + ++   i++ks k ++  k+l+++ i+  ts
  gi|488600101|ref|YP_007906572.1| 215 KADQVYFLKSQSYK--NFHYKFAVVDDKRVIVTTENWKTTNRGFLIEFKSEKIAKRLKELVDNDIKYATS 282
                                       67899999999999..89*****************98888888888888877777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3128.40
//
Query:       gi|488600102|ref|YP_007906573.1|  [L=434]
Description: glutamyl-tRNA reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  152.0   0.7    1.8e-44  151.1   0.3    1.7  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    3.2e-37  127.5   0.0    6.5e-37  126.5   0.0    1.5  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    5.5e-15   55.6   0.1    1.3e-14   54.4   0.1    1.6  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    3.4e-09   37.2   0.1    1.2e-08   35.4   0.1    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.9e-06   28.2   0.1    3.7e-06   27.2   0.1    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      6e-05   23.2   0.1    0.00015   21.9   0.1    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    0.00018   20.9   0.1    0.00036   19.9   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00018   21.7   0.1    0.00044   20.5   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00044   20.6   0.1     0.0012   19.3   0.1    1.7  1  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
       0.01   14.8   0.1      0.018   14.0   0.1    1.3  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
      0.018   14.7   0.0      0.035   13.7   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.038   13.9   0.1      0.098   12.5   0.1    1.7  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.056   12.7   0.2       0.11   11.8   0.2    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
       0.12   13.3   0.0       0.28   12.0   0.0    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


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 !  151.1   0.3   1.4e-47   1.8e-44       1     137 [.     161     294 ..     161     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 1.4e-47
                                       HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-S CS
                      Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaead 77 
                                       ela++ l+sl+++k+lliGaGem++lva+ +++k++  v++aNRt+e+a+ela++++g+   a++++ l++++ ++d
  gi|488600102|ref|YP_007906573.1| 161 ELAEDVLGSLDGRKILLIGAGEMGTLVANSIANKNACTVLIANRTYEKAEELAKKIGGV---AVRFDMLESCMTDCD 234
                                       79*********************************************************...*************** PP

                                       EEEE-SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHH CS
                      Shikimate_DH  78 vvisataseepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLke 137
                                       v+isat+++++il+k+ ve+++++r++ +l+vDia+PRdve++v+++ +v+lyt+DdL+ 
  gi|488600102|ref|YP_007906573.1| 235 VIISATSAPHYILRKDTVERVMRNRDRGILIVDIALPRDVEEDVKQIPGVELYTIDDLRI 294
                                       **********************************************************85 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 !  126.5   0.0   5.1e-40   6.5e-37       3     145 ..       8     145 ..       6     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 5.1e-40
                           GlutR_N   3 inhktapvelreklafseeelkellkel.eekvkeaviLsTCNRtEiylsaeeeeeaseellellaevs.leelk.e 76 
                                       i+hk+ap++++ek++ ++   k +++ l +++++e+++L TCNR+E+yl+ ++       ++++l e+s + e++ +
  gi|488600102|ref|YP_007906573.1|   8 ISHKKAPIDVLEKIWQKDL-RKVIVDMLsRKEISECAFLMTCNRVELYLVGNN-------TMDVLREFSsKFEIDeS 76 
                                       89***********998633.34445555555999**************75543.......45566555323344457 PP

                           GlutR_N  77 klyvlegeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrte 145
                                       ++++++++ a+ Hl+rV+sGL+S+++GEdqIlgQv+e y+ +k+ g +g +L+ +f+kai+++++vr+ 
  gi|488600102|ref|YP_007906573.1|  77 YVEYKKDDSAIMHLMRVCSGLESMMVGEDQILGQVREYYHICKDLGGIGGYLDLVFKKAINTGRKVRNL 145
                                       9999***************************************************************85 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 !   54.4   0.1   9.9e-18   1.3e-14       2      96 ..     310     409 ..     309     409 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 9.9e-18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S......--------TTHHHHHHHHHHHHHH CS
                       GlutR_dimer   2 AeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla....ldgedreelekltrslvnkllhept 74 
                                       Ae+iI ee+ ++++ +k+++++ +I+ ++++ae+i+++e+ ++ +kl+    +d+     le +++slv+k+l+ pt
  gi|488600102|ref|YP_007906573.1| 310 AEKIIHEEFINLKNAIKEKKANHAISLMYSSAERIKRDEIIELYNKLSakygVDETVLPILEGFVNSLVKKYLRLPT 386
                                       9***********************************************999888888888***************** PP

                                       HHHHSS-TTTT.HHHHHHHHH.. CS
                       GlutR_dimer  75 arLkeaedeee.ellealrrlFn 96 
                                        rL+ea+++++ e++e ++ lF+
  gi|488600102|ref|YP_007906573.1| 387 MRLREAARNGKpEIIEYVEYLFG 409
                                       ******888889**********6 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.1   9.4e-12   1.2e-08       1      95 [.     174     269 ..     174     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.4e-12
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE-S-HHHH.. CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.vkvtavdneeaaeeadvvvlavkpedv.. 74 
                                       ki +iGaG+mg  +a+ +++++  +  +++a +r+ ekaeela+++g v v     e +++++dv++ a    ++  
  gi|488600102|ref|YP_007906573.1| 174 KILLIGAGEMGTLVANSIANKN--ACTVLIA-NRTYEKAEELAKKIGgVAVRFDMLESCMTDCDVIISATSAPHYil 247
                                       6789***************999..8999988.**************955555555666777********99999855 PP

                                       .HHHHHHCGHHHHTTSEEEEES CS
                     F420_oxidored  75 .eevlselakdalkgklvisvl 95 
                                        +++++ ++++ ++g l+++++
  gi|488600102|ref|YP_007906573.1| 248 rKDTVERVMRNRDRGILIVDIA 269
                                       56999999************98 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 !   27.2   0.1   2.9e-09   3.7e-06       2      89 ..     175     268 ..     174     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.9e-09
                                       EEEE--SHHHHHHHHHHH.HTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHHHH..HHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnll.kagykvavynrtkekveelvaeg...akaaesieelvasldvvitmvkagkav..dev 72 
                                       i +iG G+MG+  a+ ++ k+ ++v + nrt ek+eel+++    a+ ++ +e++++++dv+i   +a + +  +++
  gi|488600102|ref|YP_007906573.1| 175 ILLIGAGEMGTLVANSIAnKNACTVLIANRTYEKAEELAKKIggvAVRFDMLESCMTDCDVIISATSAPHYIlrKDT 251
                                       779**************636779*****************9557899999*************99888877644678 PP

                                       HHSHCCC--TT-EEEE- CS
                     NAD_binding_2  73 iegllealkkgdilidg 89 
                                       +e+++++ ++g +++d 
  gi|488600102|ref|YP_007906573.1| 252 VERVMRNRDRGILIVDI 268
                                       88888888888888885 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.2e-07   0.00015       2      76 ..     174     241 ..     173     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB.SSHHHHHHH-SEEEE-S- CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt.ddleevlekadvliDFTt 76 
                                       k++++Ga G mG+ v++ + +++ +++  a  + e   +     e l ++  gvav  d le++++++dv+i  T+
  gi|488600102|ref|YP_007906573.1| 174 KILLIGA-GEMGTLVANSIANKNACTVLIANRTYE---K----AEELAKKIGGVAVRfDMLESCMTDCDVIISATS 241
                                       899***9.*************99999988866655...2....23333445578887799************9996 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 !   19.9   0.1   2.8e-07   0.00036      33      99 ..     169     240 ..     143     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.8e-07
                                       -GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH....CHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlk.afgmkviaydrskkkee....eeeelgvelvsleellaesDivslhl 99 
                                       +l g+++ +iG+G++G+ va+ ++ +  + v++ +r+ +k e    +   + v+++ le  + ++D+++ ++
  gi|488600102|ref|YP_007906573.1| 169 SLDGRKILLIGAGEMGTLVANSIAnKNACTVLIANRTYEKAEelakKIGGVAVRFDMLESCMTDCDVIISAT 240
                                       699*****************977748888***9999988877554333344569999**********98765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   3.4e-07   0.00044       1      50 [.     175     222 ..     175     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.4e-07
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEE CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfe 50 
                                       +l+iGaG +G  va  +a+++    ++ +a r+ ek+e+la+k+ gv + 
  gi|488600102|ref|YP_007906573.1| 175 ILLIGAGEMGTLVANSIANKNAC--TVLIANRTYEKAEELAKKIGGVAVR 222
                                       89*******************99..9**************9988776554 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1     9e-07    0.0012       5      72 ..     170     243 ..     166     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9e-07
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk......laeeelekdlegadlviaatddr 72 
                                       l+g+k+l++G+Ge+++  ++++++++a  +++a+++ e++eel k      ++ + le+ +++ d++i at+ +
  gi|488600102|ref|YP_007906573.1| 170 LDGRKILLIGAGEMGTLVANSIANKNACTVLIANRTYEKAEELAKkiggvaVRFDMLESCMTDCDVIISATSAP 243
                                       89*********************************888888766654444244555699999********9876 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 ?   14.0   0.1   1.4e-05     0.018     124     214 ..     167     253 ..     156     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                       HS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE- CS
                   OCD_Mu_crystall 124 LarkdasvlaiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtv 200
                                       L + d + + +iGaG +  + ++ + +  +  +v i +r+ e+ae +a+++ +  ++v+  +  e    ++d+++ +
  gi|488600102|ref|YP_007906573.1| 167 LGSLDGRKILLIGAGEMGTLVANSIANK-NACTVLIANRTYEKAEELAKKIGG--VAVR-FDMLESCMTDCDVIISA 239
                                       6677889999********9999988665.556899****************95..6666.46678899********* PP

                                       ---SS-SB-GGGS- CS
                   OCD_Mu_crystall 201 Taakapilkaewvk 214
                                       T a + il ++ v+
  gi|488600102|ref|YP_007906573.1| 240 TSAPHYILRKDTVE 253
                                       ********999987 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.8e-05     0.035       1      38 [.     175     214 ..     175     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                                       EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHH CS
                              ApbA   1 iailGaGaiGsllaakLak.agadvtlilrsr.rlealkk 38 
                                       i+ +GaG +G+l+a ++a+ ++++v + +r+  ++e+l k
  gi|488600102|ref|YP_007906573.1| 175 ILLIGAGEMGTLVANSIANkNACTVLIANRTYeKAEELAK 214
                                       789**************99777788888887777777544 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 ?   12.5   0.1   7.6e-05     0.098       2      44 ..     175     218 ..     174     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-05
                                       EEEE--SCCHHHHHHHHHHT.T-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasa.gleVvlvdiseealekalekiek 44 
                                       +  iGaG mG+ +a+ +a++  ++V + +++ e++e+ ++ki  
  gi|488600102|ref|YP_007906573.1| 175 ILLIGAGEMGTLVANSIANKnACTVLIANRTYEKAEELAKKIGG 218
                                       667****************9567888888999999998888865 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   8.5e-05      0.11      29     129 ..     173     270 ..     160     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.5e-05
                                       -EEEEESTSHHHHH.HHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTS CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlq.AiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGk 104
                                        k+l iG+G  G+  A ++a++   +V + +   +++e+l +   k +  ++   + l++ + ++dv+i++   p  
  gi|488600102|ref|YP_007906573.1| 173 RKILLIGAGEMGTLvANSIANKNACTVLIANRTYEKAEELAK---K-IGGVAVRFDMLESCMTDCDVIISATSAPHY 245
                                       589******999761556777777788888777777777665...4.444577788999***********9766655 PP

                                       S---SC-HHHHHTS-TTEEEEETTG CS
                       AlaDh_PNT_C 105 kaPkLvteemvksMkpgsVivDvAi 129
                                          k   e+++++   g  ivD+A 
  gi|488600102|ref|YP_007906573.1| 246 ILRKDTVERVMRNRDRGILIVDIAL 270
                                       5544444445555567999999997 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 ?   12.0   0.0   0.00022      0.28       2      72 ..     174     242 ..     173     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTTESEEEE-S-G CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladpeidavivatpn 72 
                                       ++++iGaG +g+  ++++ ++  ++  v + ++  e+ae++a++ g     ++ le  ++  ++d++i at +
  gi|488600102|ref|YP_007906573.1| 174 KILLIGAGEMGTLVANSIANK--NACTVLIANRTYEKAEELAKKIGGVavRFDMLESCMT--DCDVIISATSA 242
                                       799************988888..77778899************99877577888999888..88887766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 2379.53
//
Query:       gi|488600103|ref|YP_007906574.1|  [L=314]
Description: porphobilinogen synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-143  477.8   0.2   1.7e-143  477.6   0.2    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase
  ------ inclusion threshold ------
       0.16   12.7   1.1          2    9.2   0.1    2.6  3  PTS_IIB   PTS system, Lactose/Cellobiose specific IIB subunit


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 !  477.6   0.2  1.8e-147  1.7e-143       4     316 ..       1     312 [.       1     313 [. 0.99

  Alignments for each domain:
  == domain 1  score: 477.6 bits;  conditional E-value: 1.8e-147
                                       GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS CS
                              ALAD   4 lrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpee 80 
                                       +rrlrk++ lr++++e rls+++li+p+fv+e+ +e+ ei+smp ++r+++d +v+eve++++ g+ka++lFg+p+ 
  gi|488600103|ref|YP_007906574.1|   1 MRRLRKKK-LRQILKEVRLSKDNLIVPIFVDENLKEPYEIPSMPSYFRYPIDGVVDEVERCMEIGLKAFILFGLPSY 76 
                                       58888766.9******************************************************************* PP

                                       -BSS-GGGGSTTSHHHHHHHHHHHH-TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT-SE CS
                              ALAD  81 kdeegsealnedglvqrairaikeevpelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGadi 157
                                       kde+gs+a+++dg++q+a+ra+ +e+++ ++itDvclceytshGhcg++e  e++nd tlel+a++a+s+aeaGadi
  gi|488600103|ref|YP_007906574.1|  77 KDEKGSSAYDRDGVIQKALRAVSKEFDDAILITDVCLCEYTSHGHCGVVEGMEILNDPTLELIAETALSHAEAGADI 153
                                       ***************************************************************************** PP

                                       EEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHH CS
                              ALAD 158 vapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldl 234
                                       vapS+mmDg+v+aire+Ld +gf++++i+sYsaKyaS+fY PFr+aa+s  +fgdrk+Yqmd++ns+ea+re+eld+
  gi|488600103|ref|YP_007906574.1| 154 VAPSGMMDGMVKAIREKLDGNGFQDIPIMSYSAKYASSFYSPFREAADSGFAFGDRKSYQMDIHNSDEAMREIELDI 230
                                       ***************************************************************************** PP

                                       HTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTH CS
                              ALAD 235 eeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltYfa 311
                                        eGADivmvKPalaylDiir++k++f++p+aay+vSGEYam+k+a + gwld k++++E l++ikRAGadli+tY+a
  gi|488600103|ref|YP_007906574.1| 231 MEGADIVMVKPALAYLDIIRRAKDTFNIPLAAYNVSGEYAMVKSAEKLGWLDGKAIAYEILTAIKRAGADLIITYHA 307
                                       ***************************************************************************** PP

                                       HHHHH CS
                              ALAD 312 kevak 316
                                       ke+a+
  gi|488600103|ref|YP_007906574.1| 308 KEIAD 312
                                       **996 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.4   1.3e+04      15      25 ..     163     172 ..     145     186 .. 0.57
   2 ?    9.2   0.1   0.00022         2      29      76 ..     214     266 ..     205     278 .. 0.67
   3 ?    1.9   0.1     0.041   3.7e+02      19      55 ..     270     306 ..     268     313 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHH CS
                           PTS_IIB  15 maaeklekaak 25 
                                       m+ +++++ ++
  gi|488600103|ref|YP_007906574.1| 163 MV-KAIREKLD 172
                                       22.44444444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00022
                                       EEEEETTEE.GGGHHHHHHT-SEEEEEESSGG.CTHHHHTT...SEEEEECTT CS
                           PTS_IIB  29 ieaegeagv.eleaeeiaddaDlvllapqvrv.kdlarfag...kpvavinik 76 
                                       ++++ + ++ +    +i++ aD+v++ p +++ + + r+++   +p+a +n++
  gi|488600103|ref|YP_007906574.1| 214 MDIHNSDEAmREIELDIMEGADIVMVKPALAYlDIIRRAKDtfnIPLAAYNVS 266
                                       66777777774445566777************776666666655665555554 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.041
                                       HHHHHHHHCT.EEEEETTEEGGGHHHHHHT-SEEEEEE CS
                           PTS_IIB  19 klekaakelg.ieaegeagveleaeeiaddaDlvllap 55 
                                       ++ k a++lg ++ +  a   l+a + a  aDl+++ +
  gi|488600103|ref|YP_007906574.1| 270 AMVKSAEKLGwLDGKAIAYEILTAIKRAG-ADLIITYH 306
                                       67899999998777666666566666666.****9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1853.59
//
Query:       gi|488600104|ref|YP_007906575.1|  [L=419]
Description: glutamate-1-semialdehyde 2,1-aminomutase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-64  215.5   0.0    1.2e-63  215.2   0.0    1.1  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
      0.094   11.9   0.0       0.19   10.9   0.0    1.6  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.2   0.0   1.3e-67   1.2e-63      10     342 ..      34     347 ..      26     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 215.2 bits;  conditional E-value: 1.3e-67
                                       CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                       Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                       ++  + a+G++++dvdg++y+D   ++ +++lGhahP v +a++ q++k ++   +    e  ++  + + kl p  
  gi|488600104|ref|YP_007906575.1|  34 PFYTKYAKGSRIVDVDGNEYIDCCMAYGPLILGHAHPVVREAIERQLEKGWLYGTP---VELEIEYGKLIKKLYPS- 106
                                       4667779*******************************************999944...45555555555666777. PP

                                       .SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TT CS
                       Aminotran_3  87 ldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkyp 163
                                       ++++ ++nsGseA+++A++lar        t k+ki++++g+fHG   + l  +gs  +  t   p++++v+    +
  gi|488600104|ref|YP_007906575.1| 107 IEMLRFVNSGSEATMSAIRLARG------FTGKKKIVKVEGSFHGAHDAVLVKAGS--GATTHGVPNSAGVPEEFVA 175
                                       999********************......***************************..6666666667777776666 PP

                                       BGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT.. CS
                       Aminotran_3 164 deevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf.. 238
                                        + ++++n+      +e+l +l  +k+++va +i+Epi g+   + +++++l+++r++++++dvlli+DE+ tGf  
  gi|488600104|ref|YP_007906575.1| 176 NTLQVPYND------AEALADLL-EKNEDVACLILEPIMGNSSLILPEEDYLKEVRKITAENDVLLIFDEIITGFrv 245
                                       689999999......77788877.7899***********************************************77 PP

                                       TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTT CS
                       Aminotran_3 239 GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeek 312
                                       +  G   A e +g++pD++tl+K  +gGlp   + +++e+m+ ++p +   +++Tf+Gnpl   +  a+++ + e++
  gi|488600104|ref|YP_007906575.1| 246 SIGG---AQELYGIKPDITTLGKIAGGGLPCGIFGGRKEIMESISPVGpvyQAGTFSGNPLTLTAGYATVRFLMENE 319
                                       7778...9*************************************999999************************** PP

                                       HHHHHHHHHHHHHHHHHHHCTT-TTEEEEE CS
                       Aminotran_3 313 llenaqelgaalkegLeelqkkyevikevR 342
                                       + +  ++l + + e+ ++++k +  ++++ 
  gi|488600104|ref|YP_007906575.1| 320 VYNYLKKLTEDIAERVRDAAKVD--VGHIA 347
                                       *****************999876..44444 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 ?   10.9   0.0   2.1e-05      0.19     130     221 ..     183     265 ..     163     412 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.1e-05
                                       E-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHG CS
                     Aminotran_1_2 130 ldlealeealkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatra 205
                                       +d+eal ++l+++ e+     ++++e +  ++  ++++e+ l+++ +++ ++ +ll++De+  gf     +a++ + 
  gi|488600104|ref|YP_007906575.1| 183 NDAEALADLLEKN-EDV---ACLILEPIMGNSSLILPEEDyLKEVRKITAENDVLLIFDEIITGFRVSIGGAQE-LY 254
                                       7999****99993.444...57777777777777776665389999**************98888665434444.55 PP

                                       GSTTSTTEEEEEESSS CS
                     Aminotran_1_2 206 nveeepnllivgslsK 221
                                       ++++++      +l+K
  gi|488600104|ref|YP_007906575.1| 255 GIKPDIT-----TLGK 265
                                       5555544.....5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2895.78
//
Query:       gi|488600105|ref|YP_007906576.1|  [L=293]
Description: hydroxymethylbilane synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-70  235.0   0.1    6.8e-70  234.7   0.1    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    1.8e-08   34.6   0.2    4.6e-08   33.3   0.2    1.7  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
  ------ inclusion threshold ------
      0.042   13.8   0.1       0.21   11.6   0.0    2.2  3  SLATT_fungal     SMODS and SLOG-associating 2TM effector doma


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 !  234.7   0.1   1.1e-73   6.8e-70       2     201 ..       6     205 ..       5     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.7 bits;  conditional E-value: 1.1e-73
                    Porphobil_deam   2 rigtRkSkLAlaqaelvaeaLkeeeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlp 78 
                                        +gtR+SkLAlaq++ v+e+L+++ evei +iktkGD  +dkpL+ ++g+g+F+++++eaL++ eid+aVhSlKD+p
  gi|488600105|ref|YP_007906576.1|   6 VVGTRGSKLALAQTNKVVERLRDQYEVEIRIIKTKGDIMKDKPLYAFKGSGAFVRAIDEALANSEIDIAVHSLKDVP 82 
                                       79*******************88888*************************************************** PP

                    Porphobil_deam  79 telpeglelaavlkredprDvlvvks..sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldege 153
                                       +e  eg+++ a+l+re+p D+++ k+  +lee++ gav+gTsSlRR+aql++ r+dl +k++RGn+dtRlrkl  + 
  gi|488600105|ref|YP_007906576.1|  83 VERVEGTVISAYLERESPYDAFISKDgsRLEEMEYGAVIGTSSLRRAAQLRRFREDLVIKNIRGNLDTRLRKLG-DG 158
                                       ***********************755779********************************************7.56 PP

                    Porphobil_deam 154 ydaiiLAaAGLkRlgleerisevlspeellpavgQGalavevrkedee 201
                                       yd+ii+A+AGL Rl+l+ + ++ l++e+++p++ QG++av +r+++e+
  gi|488600105|ref|YP_007906576.1| 159 YDGIIVAEAGLIRLSLDIDYQR-LDSESFIPSANQGIIAVATREGEES 205
                                       ***************8887787.*********************9876 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 !   33.3   0.2   7.6e-12   4.6e-08       2      57 ..     217     269 ..     216     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 7.6e-12
                                       HHHHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE CS
                   Porphobil_deamC   2 levlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakg 57 
                                       l ++aER++lk L+ GC vP G  ae ++ + +k ++ +l++dg++  v +++ + 
  gi|488600105|ref|YP_007906576.1| 217 LSAIAEREVLKVLGIGCTVPAGILAETDGSS-MKVTCEILEPDGKE--VLKMSEEF 269
                                       5689**********************77666.************87..76666555 PP

>> SLATT_fungal  SMODS and SLOG-associating 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.52   3.1e+03     102     115 ..      18      31 ..       7      34 .. 0.70
   2 ?   -3.9   0.0       2.1   1.3e+04      75      88 ..     125     138 ..     123     144 .. 0.78
   3 ?   11.6   0.0   3.5e-05      0.21      35      96 ..     215     273 ..     213     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.52
                      SLATT_fungal 102 dvreeieelrrrye 115
                                       ++++ +e+lr++ye
  gi|488600105|ref|YP_007906576.1|  18 QTNKVVERLRDQYE 31 
                                       34477888888887 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.1
                      SLATT_fungal  75 srkrrkdlekvire 88 
                                       s +r+++l++++++
  gi|488600105|ref|YP_007906576.1| 125 SLRRAAQLRRFRED 138
                                       56788889988876 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 3.5e-05
                      SLATT_fungal  35 taLgalssgrtqvaitvLGalnTviAglLArlrgsgePersrkrrkdlekvireieafelda 96 
                                       t L+a+++++   +  vLG+  Tv Ag+LA   gs +    +  + d ++v++  e+f +d 
  gi|488600105|ref|YP_007906576.1| 215 TMLSAIAERE---VLKVLGIGCTVPAGILAETDGSSMKVTCEILEPDGKEVLKMSEEFSFDG 273
                                       7899997666...999*******************999888888888888888888888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); 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:                         3  (0.000167327); expected 0.2 (1e-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: 2030.65
//
Query:       gi|488600106|ref|YP_007906577.1|  [L=270]
Description: uroporphyrinogen-III C-methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-56  189.1   0.3    1.1e-55  188.9   0.3    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
     0.0031   17.9   1.2      0.027   14.9   1.1    2.6  1  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.015   15.5   0.3        0.8    9.9   0.1    2.3  2  ApbA_C        Ketopantoate reductase PanE/ApbA C terminal


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 !  188.9   0.3   1.9e-59   1.1e-55       2     212 ..       8     221 ..       7     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: 188.9 bits;  conditional E-value: 1.9e-59
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealra 78 
                                       +yl+G+GpGdpellT++Alr++++adv l dd +  + +++l+++e++ + + gk++ ++ ++++ei+e l +++ +
  gi|488600106|ref|YP_007906577.1|   8 VYLIGAGPGDPELLTLKALRLIREADVALIDD-LIGDEIKELVRRECKEVIDVGKRAGRHKKTQDEINELLYRYASE 83 
                                       8*******************************.*999999***99999999999999******************** PP

                      TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl......lpglake 149
                                       gk+V+++++GDP+v+g+g+e++e+l++  +gi+v+v+PG+ss+ aa+  +gipl++++ + +v+      +++ + +
  gi|488600106|ref|YP_007906577.1|  84 GKKVARIKGGDPFVFGRGGEEAEFLAE--RGIRVKVVPGISSAIAAPPLAGIPLNHRRFSPAVVimtgreRESREGK 158
                                       ***************************..9******************************99999****97777888 PP

                      TP_methylase 150 eereleallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       e+  ++al++ + t+v+l+++++l++ ++ L+e+ +d++tpva++e+a++e++rvv+g+l+ +
  gi|488600106|ref|YP_007906577.1| 159 ERITWDALAKINATIVILMGVSNLERNVRKLIEHGKDPETPVAIIENATMENQRVVEGKLKNI 221
                                       99999999999***********************667788********************976 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.1   4.4e-06     0.027      25     141 ..      64     210 ..      39     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC........................CCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxx RF
                       Radical_SAM  25 rgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla........................vpg 77 
                                         + ++++ei e++ ++ a+ g+k+  + gg+p++  +  e++e la++                         ++ 
  gi|488600106|ref|YP_007906577.1|  64 GRHKKTQDEINELLYRY-ASEGKKVARIKGGDPFVFGRGGEEAEFLAERGirvkvvpgissaiaapplagiplnHRR 139
                                       567899***********.899*************************9998888896666666666666666666555 PP

                                       EEEEEEECSSCHG.......HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxx.......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd.......eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreag 141
                                       ++ +v++  ++ +       +  +++l++ + + ++ +g+  +    v+kl++ g+++e  ++ +e+++  +
  gi|488600106|ref|YP_007906577.1| 140 FSPAVVIMTGREResregkeRITWDALAKINaTIVILMGVSNLERN-VRKLIEHGKDPETPVAIIENATMEN 210
                                       5555555555544888888755556666666677888888888888.8888887788866666666665544 PP

>> 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 ?    9.9   0.1   0.00013       0.8      34      73 ..      43      83 ..      25      92 .. 0.81
   2 ?    3.8   0.0     0.011        63      97     121 ..     218     242 ..     169     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                            ApbA_C 34 pelralvrallkEalavaeaegve.lseerleeaveavlek 73
                                       e+++lvr+ +kE+++v +++g +  ++++++e + +++ +
  gi|488600106|ref|YP_007906577.1| 43 DEIKELVRRECKEVIDVGKRAGRHkKTQDEINELLYRYASE 83
                                      679*******************7767777788877776655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                            ApbA_C  97 nGavvklAeklgvetPvnellyell 121
                                       + +++++A+k gv++P++  + +++
  gi|488600106|ref|YP_007906577.1| 218 LKNIAEIARKKGVKAPAIIIIGDVV 242
                                       6789999999999999987776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1874.83
//
Query:       gi|488600107|ref|YP_007906578.1|  [L=182]
Description: GTP:adenosylcobinamide-phosphate guanylyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-18   67.2   0.0    2.4e-18   67.0   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
    0.00078   19.4   0.0     0.0016   18.4   0.0    1.5  1  CTP_transf_3  Cytidylyltransferase
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.038   13.7   0.0    1.3  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 !   67.0   0.0     4e-22   2.4e-18       2     114 ..       5     113 ..       4     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 4e-22
                                       EEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHH CS
                      NTP_transf_3   2 viLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplasl 76 
                                       viLAGG+SsRmg++Ka l++ggk+l+ervlda+ + + ++ +v+  +  +e ++ +++ +++ ++ +  gkg ++ +
  gi|488600107|ref|YP_007906578.1|   5 VILAGGKSSRMGREKAVLKVGGKRLIERVLDAVLDTS-SDCLVALSRntPETERFCKQNEIPHIRTP--GKGYVEDV 78 
                                       8**********************************95.566665433259999*************7..9******* PP

                                       HHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHH CS
                      NTP_transf_3  77 aaalraaadadavlvlacDmPlltpelverllaaaaas 114
                                          l++     a++ ++cD+P+++++ ++++ +a+ ++
  gi|488600107|ref|YP_007906578.1|  79 VWILKEY---GAFISISCDIPFIRKDDIKAIERAFSED 113
                                       ****987...8******************998888654 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.7e-07    0.0016       3      68 ..       5      71 ..       3     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.7e-07
                                      EEEE-SSSSSS.TTGGGSEETTEEHHHHHHHHHHHTTTTSE.EEEEES-HHHHHHHHHTTSEEEE--T CS
                      CTP_transf_3  3 IipARsgSkRl.pgKnlldlggkpliayvleaalkskafek.vivaTDseeiknvakefgasvlvtrs 68
                                      +i+A  +S+R+  +K+ l+ ggk+li++vl+a+l+    ++ v ++    e++ ++k+  +  ++t++
  gi|488600107|ref|YP_007906578.1|  5 VILAGGKSSRMgREKAVLKVGGKRLIERVLDAVLDTSS-DClVALSRNTPETERFCKQNEIPHIRTPG 71
                                      58899999999679*********************655.66799999999******998766666555 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   6.3e-06     0.038       2      54 ..       3      51 ..       2      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-06
                                      EEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GG CS
                              IspD  2 vvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvsed 54
                                        vi A G+ +Rm+  ++K+ l++ g+ l+e+ +da+l+ +  +  +v++s++
  gi|488600107|ref|YP_007906578.1|  3 LKVILAGGKSSRMG--REKAVLKVGGKRLIERVLDAVLDTS--SDCLVALSRN 51
                                      569999*****995..679*******************954..3444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1045.57
//
Query:       gi|488600108|ref|YP_007906579.1|  [L=231]
Description: cobalamin 5-phosphate synthase/cobalamin synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-38  131.6  10.1    4.8e-38  131.4  10.1    1.0  1  CobS             Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4  10.1   2.7e-42   4.8e-38       2     203 ..       5     220 ..       4     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 2.7e-42
                              CobS   2 lsflTrlPvp....elaralaffPlvGlllGlllllallllllllllaallavaalvlltgglHlDGlaDtaDglgs 74 
                                       +sf+Tr+Pv+    + ++ +a++Pl+Gl+++++  +a++l++   ++ ++l+++ l+l+ g++H+DGlaD++Dgl++
  gi|488600108|ref|YP_007906579.1|   5 ISFFTRIPVNgdiyKARQEIALLPLIGLITAFI--PAAILYAN-IPFKSFLSLLSLYLIIGIIHIDGLADFFDGLAT 78 
                                       79*******876645577***************..46666654.46677787777789*****************99 PP

                              CobS  75 grdrerrleImkDsrvGafGvlalvlvlllkvaalaala...lllapvlsRlaallaiallpyaeeglgalfaeaqk 148
                                       ++  +r++++mk  +vG+ Gvl++vl++++++ al a++   +++a+v s++++ll+++  + + +g+g++fae  +
  gi|488600108|ref|YP_007906579.1|  79 KGGAQRKIRAMKGVEVGTAGVLSIVLIIAVQLQALEAIPfmgVFAAEVNSKMSMLLMLSNRDFM-DGMGKFFAEGLS 154
                                       99********************************977778898999***********9999966.8*******9544 PP

                              CobS 149 k..lv...llal..avlllllall.......laallvalllrrlarrklggvtGDvlGavieltellvl 203
                                       +  lv   +  +  av+++l + +        +a+++ ++++  +r+++gg++GD++Ga+ e+t++l l
  gi|488600108|ref|YP_007906579.1| 155 RsrLVlssI--IymAVIVFLSM-IdrvyllsTLAMITPYIVAGESRKNFGGINGDCVGACAEITRALSL 220
                                       445333332..12222222112.2333444444444555677788888*****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1329.17
//
Query:       gi|488600109|ref|YP_007906580.1|  [L=286]
Description: adenosylcobinamide-phosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-78  261.8   0.0    7.9e-78  261.4   0.0    1.1  1  CobD_Cbib  CobD/Cbib protein
  ------ inclusion threshold ------
      0.035   14.5   0.4        0.1   13.0   0.4    1.9  1  DUF4199    Protein of unknown function (DUF4199)
      0.039   13.3   0.5      0.077   12.4   0.5    1.5  1  ThrE       Putative threonine/serine exporter


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 !  261.4   0.0   1.3e-81   7.9e-78       1     275 [.       8     266 ..       8     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 261.4 bits;  conditional E-value: 1.3e-81
                         CobD_Cbib   1 lllAlllDlllgdprrllhPvvligklisalekrl.rkakkerlaGvllalllvllallvallllllalaallglvl 76 
                                       lllAl++Dl++g+p++++hP v++gk+i+++++++ r+ k + +aG+++ ++++++a+l++ +  ll   + lgl+l
  gi|488600109|ref|YP_007906580.1|   8 LLLALAIDLAVGEPPEIIHPTVWFGKIIGFFDRIWeRRGKIDFFAGMAFSVFVIAFAFLLSRIPDLLD--P-LGLIL 81 
                                       689******************************99546778999*********999999888887743..2.3679* PP

                         CobD_Cbib  77 ealllkltlalrsLleevrkvakalkgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyfll 153
                                       +a+llk+t+++rsL+e+vr+ a +   d++  Re +++iV+R++++l+++e+++A +Es+aEN++D+v++Plfy+ll
  gi|488600109|ref|YP_007906580.1|  82 SAYLLKTTFSIRSLEEHVRNTAVE---DISLQREMTAKIVSRNVENLERHELCSASIESLAENMVDAVISPLFYYLL 155
                                       ******************976544...9************************************************* PP

                         CobD_Cbib 154 lglpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllalaaalriarrdarkhpSpNsgwpe 230
                                       +glpga++y+a+nT+D+m+GYk+ery++fG++ A+lDD+ln+iPARl++++++  +  +++  ++++    N    +
  gi|488600109|ref|YP_007906580.1| 156 FGLPGAMVYRAINTMDAMIGYKDERYHHFGKFVAKLDDMLNFIPARLAVIFFIPFNPKKVWNYYRKARYKIND-KAI 231
                                       ****************************************************998777888888888888996.679 PP

                         CobD_Cbib 231 aalAgalgvrLggpnvY.lgkleekptlgdkkrpleaedieralrl 275
                                       a++ ++lgv+L++++vY ++   +         ++e+edi ra+r+
  gi|488600109|ref|YP_007906580.1| 232 AMMSAVLGVKLEKKGVYsFE--GR---------DPEVEDILRAIRV 266
                                       *****************544..22.........2356677777765 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   1.7e-05       0.1      61     167 ..      45     165 ..       5     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                           DUF4199  61 gGfisfgqafgfgflislvagllsavfq......yiyfnfi.dpdfienyiaeilekleeakeesaeeenaemseee 130
                                        G+i f  ++ f ++++++a lls +        +i+ +++   +f  + ++e   +++         e +++++e+
  gi|488600109|ref|YP_007906580.1|  45 RGKIDFFAGMAFSVFVIAFAFLLSRIPDlldplgLILSAYLlKTTFSIRSLEEHVRNTA--------VEDISLQREM 113
                                       689***********************998888888888877788888777777776655........4556666666 PP

                           DUF4199 131 ikeale....sls..........pi.ivalqsflgnliiGlilsliiAlilk 167
                                       +++ ++     l+          ++  +++  +++ l+++l+++l+ A + +
  gi|488600109|ref|YP_007906580.1| 114 TAKIVSrnveNLErhelcsasieSLaENMVDAVISPLFYYLLFGLPGAMVYR 165
                                       6553333222333444555545544255********************9876 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   1.3e-05     0.077     112     179 ..       4      71 ..       1      86 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                              ThrE 112 vlaaglaaaafallfggdwidflvaflagllggllrlllakrglnsfvleavaaflasllallavslg 179
                                       +l a l+a a+ l +g  +  +  ++  g ++g++ ++ ++rg ++f++ ++ ++++ ++a+l+ ++ 
  gi|488600109|ref|YP_007906580.1|   4 MLLALLLALAIDLAVGEPPEIIHPTVWFGKIIGFFDRIWERRGKIDFFAGMAFSVFVIAFAFLLSRIP 71 
                                       677888899999999999999999*************************************9999973 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1742.51
//
Query:       gi|488600110|ref|YP_007906581.1|  [L=480]
Description: Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   74.6   0.0    4.4e-20   72.7   0.0    2.0  3  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.19   3.3e+03     127     152 ..      83     106 ..      56     123 .. 0.74
   2 !   72.7   0.0   2.5e-24   4.4e-20       2     166 ..     183     340 ..     182     341 .. 0.92
   3 ?   -3.5   0.0      0.64   1.1e+04     121     139 ..     370     387 ..     343     394 .. 0.42

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivgl 152
                                        e+v +a e+l+++g+      i g+
  gi|488600110|ref|YP_007906581.1|  83 EEDVFKAYEILKKSGFS--GLKIAGG 106
                                       58899999999999988..4444444 PP

  == domain 2  score: 72.7 bits;  conditional E-value: 2.5e-24
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +++rgC ++C+fC++++    + + r ++ e +le +++++ +  v+ v l    p+++p+f e+++ la       
  gi|488600110|ref|YP_007906581.1| 183 EIGRGCVRNCRFCIVRR---IYFPCRWRDAELLLEVAEKNR-KF-VDKVALIAPSPSDHPEFREIVFGLADM----- 249
                                       689*************8...7*******************7.55.************************996..... PP

                                       EEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEE CS
                                       xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivg 151
                                        ++v+ + ++ d   ee++  l+  g+ ++++  ea++++  ++ +n+g ++e+++++  ++ e+gi++   +++vg
  gi|488600110|ref|YP_007906581.1| 250 GFSVSPSSIRADkidEEIIGVLKASGLRTLTIAPEAGSER-LREALNKGIGYEDIIRTSGLAGEYGIEKiKLYFMVG 325
                                       555555555555567*************************.****************************99****** PP

                                       BTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleellel 166
                                       lpGe +e+l+e+++l
  gi|488600110|ref|YP_007906581.1| 326 LPGERKEDLDEIVNL 340
                                       ***********9987 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.64
                                       HTCTSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 121 mnrghtfeevlealeklre 139
                                          g+ +e ++e ++ l+e
  gi|488600110|ref|YP_007906581.1| 370 S-FGGKLEFRKEDIRELKE 387
                                       2.33333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 3016.04
//
Query:       gi|488600111|ref|YP_007906582.1|  [L=291]
Description: hypothetical protein Asulf_00568 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-27   94.5   0.8      1e-26   94.2   0.8    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
      2e-07   30.7   0.0    2.9e-07   30.2   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.8   1.2e-30     1e-26      44     197 .]      56     211 ..      21     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 1.2e-30
                                       GEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH.......TTCHCGCCEEEEETTT CS
                       Lactamase_B  44 dvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll.......lagvsadkpdvdeeel 113
                                        +d++++TH HlDH Gg+g+l + +d++v++++++ ++l+++e+   as + l        ++++++ + +++ e++
  gi|488600111|ref|YP_007906582.1|  56 GLDYIFITHIHLDHGGGVGHLLKNFDAKVVCHPKAVKHLTNPEKLWKASEQALGevarvygKPEPVDEGAIIPAEDG 132
                                       68******************************************7777777666*********************** PP

                                       EECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCH CS
                       Lactamase_B 114 dgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglka 190
                                       +++++g    +v+++pgh+++h++++++++k+lf GD    +++gr+ +     ++++p   + +++sl+k + l++
  gi|488600111|ref|YP_007906582.1| 133 QEFDLGSDVIKVIHTPGHSPHHISFYLRERKILFPGDSAGFHSEGRLLP-----TAPPPFMFDLAIESLDKQISLDY 204
                                       *************************************************.....9999999**************** PP

                                       SEEEESS CS
                       Lactamase_B 191 evlvpgH 197
                                       e+++++H
  gi|488600111|ref|YP_007906582.1| 205 EYIAYSH 211
                                       ******9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   3.2e-11   2.9e-07      28     153 ..      54     179 ..      34     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.2e-11
                                       ..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHHHCHTT...............TTEEEE CS
                     Lactamase_B_2  28 lppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvylaleee...............pavnvh 88 
                                       +  +d +++th H DH  g+ +l + +    ++++++++  ++l++  +     e+               ++ ++ 
  gi|488600111|ref|YP_007906582.1|  54 MGGLDYIFITHIHLDHGGGVGHLLKnFD---AKVVCHPKAVKHLTNPEKLWKASEQalgevarvygkpepvDEGAII 127
                                       5689*********************554...579**********999776666666999999999988888788888 PP

                                       EE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHH CS
                     Lactamase_B_2  89 eldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeiger 153
                                       + + g++f+lg+ ++ i+++  ++ s+          +++ ++  ++++++ gD++ ++ e + +
  gi|488600111|ref|YP_007906582.1| 128 PAEDGQEFDLGS-DV-IKVIHTPGHSPH--------HISFYLR--ERKILFPGDSAGFHSEGR-L 179
                                       889*******95.65.999999*****9........9999999..8**********9997733.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1987.20
//
Query:       gi|488600112|ref|YP_007906583.1|  [L=474]
Description: phenylalanyl-tRNA synthetase, alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-93  311.1   0.0    6.7e-93  310.7   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    8.2e-08   31.9   0.0    4.1e-06   26.4   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0029   16.7   0.3      0.051   12.7   0.0    2.6  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.051   13.6   0.0        0.1   12.7   0.0    1.4  1  YqeY             Yqey-like 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 !  310.7   0.0   1.5e-96   6.7e-93       1     244 [.     198     466 ..     198     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 310.7 bits;  conditional E-value: 1.5e-96
                                       C.-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-. CS
                      tRNA-synt_2d   1 kidvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka. 76 
                                       k+dv +p+k i ++k hp++k++ e+++ifle+gf+e++g+ v+s+f+nfdaL++pqdhpaRdmqdtFyl+  e+  
  gi|488600112|ref|YP_007906583.1| 198 KYDVRIPSKTIFTAKYHPYEKIVAECRKIFLEMGFTEIKGSFVQSSFWNFDALFQPQDHPARDMQDTFYLDAYEDLd 274
                                       69********************************************************************8888879 PP

                                       .............................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SE CS
                      tRNA-synt_2d  77 .............................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlae 123
                                                                    +++kl+LRthtta++i++l  +++pp+k ++i+rv+Rr+++Dathl+e
  gi|488600112|ref|YP_007906583.1| 275 ddfvekvkrthidgwktgstgwggdwsldTARKLVLRTHTTAITIHYLaMNPEPPVKAFCIDRVYRRESIDATHLPE 351
                                       *****************************999****************9999************************* PP

                                       EEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHH CS
                      tRNA-synt_2d 124 FhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevl 200
                                       F q+eg+++d++v +++l+g+l+e++ k+ g+e +vrfrp yfp+tePs+e +vy+  ++ +w+El+gaG++r+ev+
  gi|488600112|ref|YP_007906583.1| 352 FDQLEGVLLDKDVGFRHLLGLLREFFLKM-GFE-DVRFRPGYFPYTEPSVEPEVYV--DGLGWVELGGAGVFRKEVT 424
                                       *****************************.***.**********************..******************* PP

                                       HHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 201 eavgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       e++gi  + +++a+GlG+ Rlaml++g++D+R+l+++dl +lr+
  gi|488600112|ref|YP_007906583.1| 425 EPLGI--KGKVLAWGLGMGRLAMLRLGMKDLRKLYQPDLGWLRE 466
                                       *****..**********************************997 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.011        50       5      39 ..     203     237 ..     200     261 .. 0.78
   2 !   26.4   0.0   9.1e-10   4.1e-06      92     209 ..     325     435 ..     307     439 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.011
                   tRNA_synthFbeta   5 lPkapttegelnkeqklrrklrdllagaGlnEvit 39 
                                       +P+ ++  ++ ++ +k+  ++r++  ++G++E+  
  gi|488600112|ref|YP_007906583.1| 203 IPSKTIFTAKYHPYEKIVAECRKIFLEMGFTEIKG 237
                                       677777777799********************964 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 9.1e-10
                   tRNA_synthFbeta  92 rgnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepa 167
                                       + ++ v++F i +v++ +  + +   e  +l +vl  k+           v+f +l g++++++ ++g+e+v+f+p 
  gi|488600112|ref|YP_007906583.1| 325 NPEPPVKAFCIDRVYRREsIDATHLPEFDQLEGVLLDKD-----------VGFRHLLGLLREFFLKMGFEDVRFRPG 390
                                       5667799***********87778899*************...........*************************** PP

                   tRNA_synthFbeta 168 ehpalhpgrsAeikvdgk...evGvlGelhpevleafdlkqrvyv 209
                                         p+ +p    e++vdg    e+G +G + +ev e +++k++v +
  gi|488600112|ref|YP_007906583.1| 391 YFPYTEPSVEPEVYVDGLgwvELGGAGVFRKEVTEPLGIKGKVLA 435
                                       ***************996666*******************99876 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.069   3.1e+02      27      48 ..     218     239 ..     206     266 .. 0.88
   2 !   12.7   0.0   1.1e-05     0.051      93     119 ..     331     356 ..     329     363 .. 0.94
   3 ?   -1.1   0.0      0.18   7.9e+02     287     307 ..     436     456 ..     435     458 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.069
                                       HHHHHHHHHHHHTT-EE----S CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  27 tvtkavrkyleengfieietPi 48 
                                       ++++  rk++ e gf+ei+  +
  gi|488600112|ref|YP_007906583.1| 218 KIVAECRKIFLEMGFTEIKGSF 239
                                       789999************8655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.1e-05
                                       EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                       + f+i r++R E++++++ + EF q+e
  gi|488600112|ref|YP_007906583.1| 331 KAFCIDRVYRRESIDATHLP-EFDQLE 356
                                       68******************.****98 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.18
                                       EEEEHHHHHHHHCT-SSGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                       +glG+ Rl ml lg+++ r++
  gi|488600112|ref|YP_007906583.1| 436 WGLGMGRLAMLRLGMKDLRKL 456
                                       69999***********99986 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05       0.1      84     135 ..      66     119 ..      65     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                       GGGS-----HHHHHHHHHHHHHHTT--..BGGGHHHHHHHHHHHHTTTS-HHHH CS
                              YqeY  84 eeYlPeqlseeeiealvkeaiaevgae..smkdmGkvmkalkpkvkGkaDgkkv 135
                                       e+Yl e l ee++ +l+k+ +++++++  +mkd+G  ++ l++k  +k++gkk+
  gi|488600112|ref|YP_007906583.1|  66 EKYLSEGLPEERLYSLIKQGVDSIDQAkkEMKDFGIAIGWLRKKGIAKIEGKKI 119
                                       68*********************9654349*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3273.39
//
Query:       gi|488600113|ref|YP_007906584.1|  [L=547]
Description: phenylalanyl-tRNA synthetase beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  151.7   0.0    3.5e-44  150.8   0.0    1.5  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.1e-20   73.7   0.8    8.8e-16   58.0   0.1    3.2  4  B5               tRNA synthetase B5 domain
    6.2e-14   52.0   0.0    1.2e-13   51.1   0.0    1.6  1  B3_4             B3/4 domain
    0.00028   21.0   0.0      0.042   14.1   0.0    2.9  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
  ------ inclusion threshold ------
      0.072   12.6   0.1       0.35   10.3   0.0    2.0  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.1   7.4e+03     141     161 ..      50      70 ..      38      87 .. 0.77
   2 !  150.8   0.0   9.6e-48   3.5e-44       3     214 .]     344     537 ..     342     537 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.1
                   tRNA_synthFbeta 141 vdfydlkgivealleslgiek 161
                                        d y + g+++al + +gie+
  gi|488600113|ref|YP_007906584.1|  50 PDLYSVEGVARALRGFFGIET 70 
                                       689999999999999999933 PP

  == domain 2  score: 150.8 bits;  conditional E-value: 9.6e-48
                   tRNA_synthFbeta   3 stlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldkll..eddderkavelanPlsedqsvlRts 77 
                                       +  Pk++t +   +k++++r+ +r++++g+G++Evit+++ se +  +++    ++ +  v +++Pl+e++ ++R+s
  gi|488600113|ref|YP_007906584.1| 344 PEYPKTSTIGN-THKWNDVRDMVREIMIGLGFTEVITFTLRSERVQYDYMgrTAKPWEVYVPVEHPLTEEHRIIRSS 419
                                       56899999999.88*********************************999966669999****************** PP

                   tRNA_synthFbeta  78 LlpglLevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgiveall 154
                                       +lp+l+evl+ N ++ ++  r+FE g+v+ ++      +++  la+++t+++           ++f ++  +v+a++
  gi|488600113|ref|YP_007906584.1| 420 ILPSLIEVLSLNKHHIMP-QRIFEAGDVVVAR------KNRLSLAGAITHSK-----------ANFSEIRSVVQAVM 478
                                       ******************.*************......9*************...........************** PP

                   tRNA_synthFbeta 155 eslgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                        +l +  +e e++++ a+  grsA+i+vdgk +G++Ge++pevle+f++ ++v++fE+dl
  gi|488600113|ref|YP_007906584.1| 479 HELDL-GWEAEESDDRAFIEGRSASIVVDGKSIGCFGEINPEVLEKFQITNPVVGFEIDL 537
                                       *****.9999************************************************98 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   3.5e-05      0.12       2      52 ..       5      53 ..       4      60 .. 0.89
   2 ?   -3.6   0.0         4   1.4e+04      11      45 ..     227     260 ..     225     264 .. 0.69
   3 !   58.0   0.1   2.5e-19   8.8e-16       3      67 .]     276     339 ..     274     339 .. 0.95
   4 ?   -2.6   0.0         2   7.3e+03      21      45 ..     365     404 ..     362     405 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                                      EEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  2 slrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDle 52
                                      +l  ++++kl+G  +++e+i + L  lgc+++  ++d l+V+  + R+Dl 
  gi|488600113|ref|YP_007906584.1|  5 TLYWDELEKLVG--VDRERILEKLPMLGCDIERVEEDHLDVEFFPNRPDLY 53
                                      66778999****..689*************************9999***95 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4
                                       HHTS---HHHHHHHHHHTT-E.EESSTTCEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  11 llGidlseeeiikiLkrlgceriekdkdlllVtvP 45 
                                       ++G d + ++  ki +++ ++r   + ++++V  P
  gi|488600113|ref|YP_007906584.1| 227 VTGFDENVDKALKIISAMFYDR-GGEIETVEVVYP 260
                                       5677777788888888887765.555566666655 PP

  == domain 3  score: 58.0 bits;  conditional E-value: 2.5e-19
                                       EEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   3 lrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       ++ +++ +llG ++++ee++  L+++ + +   ++++++V+vP +R D+ + +D+iE++a+ yGY
  gi|488600113|ref|YP_007906584.1| 276 VERDEVVSLLGFEINDEEVVAALEKMRFGV-RLGEKGFHVEVPCYRADIMHTWDIIEDIAIGYGY 339
                                       6789999**********************8.888899***************************9 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2
                                       HHHHHHHTT-E................EESSTTCEEEE-- CS
                                       xxxxxxxxxxx...............xxxxxxxxxxxxxx RF
                                B5  21 iikiLkrlgce...............riekdkdlllVtvP 45 
                                       + +i+  lg++               +   +++ ++V vP
  gi|488600113|ref|YP_007906584.1| 365 VREIMIGLGFTevitftlrservqydYMGRTAKPWEVYVP 404
                                       4556666666655555555555555544556666777776 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   3.4e-17   1.2e-13       3     142 ..      95     241 ..      93     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 3.4e-17
                                       SEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TTE CS
                              B3_4   3 pryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiqgdivvrlakege 74 
                                       pr +++++r++k   +                + +v  i++ ++  +g+     +++++Dl+ki+ +++ r  k+++
  gi|488600113|ref|YP_007906584.1|  95 PRIVGCIVRNLKMSDEV---------------VRSVMQIQEDLHWTIGRnrrkmAIGVHDLSKIEFPLTYRAVKSDF 156
                                       66666666666655555...............8899999************************************** PP

                                       EEEBTTS-.EEEE-T...................TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HH CS
                              B3_4  75 klvtldgk.erelde...................edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpv 130
                                       ++v+ld + + +++e                   ++++i+d+++   s +++++ e+++v+e+T + f+ +++fd+ 
  gi|488600113|ref|YP_007906584.1| 157 SFVPLDFDeTMTVKEilekhpkgiqfrfilegkdSYPMIVDATGSAiSFPPIINAEKTRVTEKTMDLFIDVTGFDE- 232
                                       *****86625555779**************************99666****************************9. PP

                                       HHHHHHHHTT-- CS
                              B3_4 131 sirktarrlglr 142
                                          +  ++l++ 
  gi|488600113|ref|YP_007906584.1| 233 ---NVDKALKII 241
                                       ...444444443 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.2e-05     0.042      50      81 ..      35      66 ..       1      68 [. 0.89
   2 ?    3.7   0.0     0.021        74      28      74 ..     282     330 ..     268     337 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                         PhetRS_B1 50 kseeviykidipAnryDLLcleglaralkvFl 81
                                      + ee  + ++   nr+DL ++eg+aral+ F 
  gi|488600113|ref|YP_007906584.1| 35 RVEEDHLDVEFFPNRPDLYSVEGVARALRGFF 66
                                      567888999999****************9986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.021
                         PhetRS_B1  28 lfefGlElDeiveeee..kkkadkkseeviykidipAnryDLLclegla 74 
                                       +  +G E+ + +  ++  k + + +  e+ +++++p  r D++ +  + 
  gi|488600113|ref|YP_007906584.1| 282 VSLLGFEINDEEVVAAleKMRFGVRLGEKGFHVEVPCYRADIMHTWDII 330
                                       5556777755443333325567778888999999999999998776665 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 ?   10.3   0.0   9.7e-05      0.35       9     110 ..     348     446 ..     339     481 .. 0.86
   2 ?   -1.1   0.0      0.31   1.1e+03     189     212 ..     510     533 ..     509     538 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.7e-05
                                       SCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-S CS
                      tRNA-synt_2d   9 krieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRt 85 
                                       k  + g++h  ++v++ ++ei++ lgf+ev    + se    d +       a+ ++   ++++p +  ee++++R+
  gi|488600113|ref|YP_007906584.1| 348 KTSTIGNTHKWNDVRDMVREIMIGLGFTEVITFTLRSERVQYDYMG----RTAKPWEVYVPVEHPLT--EEHRIIRS 418
                                       5567899****************************99999999985....57888888889988888..889999*9 PP

                                       STHHHHHHHH...TTS-SSEEEEEEEEE CS
                      tRNA-synt_2d  86 httavqirtl...ekkkppikiisigrv 110
                                          +  i +l   +++ +p++i+  g v
  gi|488600113|ref|YP_007906584.1| 419 SILPSLIEVLslnKHHIMPQRIFEAGDV 446
                                       9999999999876666699999988865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.31
                                       EEEEEEE-HHHHHHTT-.TTSEEE CS
                      tRNA-synt_2d 189 llgaGmvrpevleavgideevsgf 212
                                       ++ +G ++pevle++ i + v gf
  gi|488600113|ref|YP_007906584.1| 510 IGCFGEINPEVLEKFQITNPVVGF 533
                                       5678999**********6555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3771.20
//
Query:       gi|488600114|ref|YP_007906585.1|  [L=376]
Description: TIGR01213 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-13   49.5   0.2    1.3e-12   48.0   0.2    1.7  1  THUMP          THUMP domain
  ------ inclusion threshold ------
        6.3    7.2   9.7        9.1    6.7   0.5    2.6  2  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 !   48.0   0.2   1.4e-16   1.3e-12      40     142 ..       6     124 ..       3     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.4e-16
                                       HHHHHHTSTTECEEEEE..EEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS..............SSH CS
                             THUMP  40 lkealekargiqrvipv..cevceadledileaakeivkkkfeeeketFaVrvkrrgkhf..............eft 100
                                       ++e++ +++g  rv+ +  c  c   l ++ e+a+ i ++ +  e  tF ++++++g+                 + 
  gi|488600114|ref|YP_007906585.1|   6 VCEKCRRLTGFGRVVEPenCLYCSGILWKLDELAERIHSDLIDYEYSTFLIGCRVEGSLKaieeyfielgmdekNVL 82 
                                       56777777788888877799999******************999888***********99***************** PP

                                       HHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEE CS
                             THUMP 101 sreinrevGkaivektglkVdlenPdivvrveiikdkayisi 142
                                       ++ei+re+G+++ e++g++Vd+e+Pd++++  + +d++  +i
  gi|488600114|ref|YP_007906585.1|  83 KNEIKRELGRIFSERYGKRVDFEKPDVTIIFNPERDELSYQI 124
                                       *********************************999876555 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5     0.001       9.1      42      65 ..       8      30 ..       1      31 [. 0.77
   2 ?    3.9   3.1    0.0078        70       1      24 [.     147     162 ..     135     194 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.001
                     DnaJ_CXXCXGXG 42 stCpeCeGtGkvikekdkCkkCkG 65
                                      ++C++  G G+v+ e ++C  C+G
  gi|488600114|ref|YP_007906585.1|  8 EKCRRLTGFGRVV-EPENCLYCSG 30
                                      5788888****99.5569****98 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0078
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsG 24 
                                       C +C+G+g        C++C+ +G
  gi|488600114|ref|YP_007906585.1| 147 CGRCRGKG--------CEECNFTG 162
                                       66666666........66666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2727.29
//
Query:       gi|488600115|ref|YP_007906586.1|  [L=94]
Description: LSU ribosomal protein L21E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  102.5   1.4      1e-29  102.4   1.4    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   1.4   5.6e-34     1e-29       3      97 ..       4      93 ..       2      94 .] 0.98

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 5.6e-34
                                      -S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEET CS
                    Ribosomal_L21e  3 nskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvg 81
                                      +s+g+r ++ ++++k++r+kg +++ ++l+e++ G++V+i+i+p+v+kgmph+r++G+tg+v  ++ r+++++v++++g
  gi|488600115|ref|YP_007906586.1|  4 KSHGFRFKSGRKLRKRVREKG-IRIRKVLQEFEIGQRVNIDIEPAVHKGMPHPRFQGRTGEV--IGIRGKCYLVRVRDG 79
                                      79******************9.79**************************************..*************** PP

                                      TE..EEEEEE-GGGEE CS
                    Ribosomal_L21e 82 gkileKriivriehlk 97
                                      g    K++ivr+ehlk
  gi|488600115|ref|YP_007906586.1| 80 GM--YKTLIVRPEHLK 93
                                      **..***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 00:00:00.42
# Mc/sec: 669.37
//
Query:       gi|488600116|ref|YP_007906587.1|  [L=116]
Description: DNA-directed RNA polymerase, subunit F [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-09   36.1   1.2    1.1e-08   35.4   1.2    1.3  1  RNA_pol_Rpb4  RNA polymerase Rpb4
     0.0097   15.7   0.2      0.011   15.5   0.2    1.1  1  DUF1678       Protein of unknown function (DUF1678)
  ------ inclusion threshold ------
      0.027   14.3   0.3      0.038   13.8   0.2    1.3  1  HeLo          Prion-inhibition and propagation


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 !   35.4   1.2   1.9e-12   1.1e-08       6     122 ..      16     115 ..       6     116 .] 0.84

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.9e-12
                                       HHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.S.THH CS
                      RNA_pol_Rpb4   6 Evllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfe.L.tka 80 
                                       E++++++                 +i++k++ k +l  +++++l+ l+  fs+l   +k++elv++l+  + +  k 
  gi|488600116|ref|YP_007906587.1|  16 EAREIME-----------------NIAKKRQEKAELLFETRRALKNLRS-FSKLP-VDKAKELVNELEGLSfIsRKD 73 
                                       4444443.................2556677788999999********9.*****.9***********888752666 PP

                                       HHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHHH CS
                      RNA_pol_Rpb4  81 EklqlvnlkPesavelktlieeleerfedeqleeiLdelkev 122
                                        ++++ +++P+  +e++t++++++  ++ eq++eiLd++  +
  gi|488600116|ref|YP_007906587.1|  74 LAVKIADIMPRIPDEVRTIFAKERFTLTPEQIKEILDTVDRY 115
                                       6789***********************************988 PP

>> DUF1678  Protein of unknown function (DUF1678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.9e-06     0.011      79     153 ..      24      93 ..       3     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-06
                           DUF1678  79 vsldrkevlklaralrralrsvlktllteleelvkkkvrrvlarllalefdarrlgspgirdvleelpdrledil 153
                                       ++++r+e+ +l  + rral++     l+  ++l+ +k++  +  l  l+f +r+    +i d++  +pd ++ i+
  gi|488600116|ref|YP_007906587.1|  24 IAKKRQEKAELLFETRRALKN-----LRSFSKLPVDKAKELVNELEGLSFISRKDLAVKIADIMPRIPDEVRTIF 93 
                                       344455555555555554433.....7889******************************************987 PP

>> HeLo  Prion-inhibition and propagation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   6.4e-06     0.038     127     188 ..      17      78 ..       8      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-06
                                       HH.HHHHHHHHHS----S-----EEE-SHHHHHHH.HHHHHHHHHHHHHTTT-H..HHHHHHH CS
                              HeLo 127 lkrlmrkaakkrqkrtslpkrlrWaivdkkkfeel.vkdlkelvdsLeeLlpasqqqrvqrlv 188
                                        +++m+++akkrq++++l   +r a+    +f++l v++ kelv++Le L   s ++ ++  +
  gi|488600116|ref|YP_007906587.1|  17 AREIMENIAKKRQEKAELLFETRRALKNLRSFSKLpVDKAKELVNELEGLSFIS-RKDLAVKI 78 
                                       3447999***************************99************998777.45555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 895.12
//
Query:       gi|488600117|ref|YP_007906588.1|  [L=338]
Description: Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase-related flavin-dependent oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  205.5   0.0    1.5e-60  205.2   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 !  205.2   0.0   8.6e-65   1.5e-60      26     314 .]      17     308 ..       7     308 .. 0.92

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 8.6e-65
                    Bac_luciferase  26 velaraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsg 98 
                                       ++ a+ a++ Gfd+v++++h+ g g +     +aftll++la  T++++lgt+v+ + +rhPavlAq a+tL++ s 
  gi|488600117|ref|YP_007906588.1|  17 IKSAVFADRNGFDSVFTPDHLVGIGIKnwssYEAFTLLGVLAKLTTKVKLGTCVSDVIRRHPAVLAQFAVTLHDFSS 93 
                                       6789*****************997777************************************************** PP

                    Bac_luciferase  99 GRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaas 175
                                       GR++lglg+g+ ++    +G+d +     l+E v+++r+l++ e+ +f+G+ff v++a++ pr     +P+++a+ s
  gi|488600117|ref|YP_007906588.1|  94 GRAVLGLGAGEGMNL-VPYGMDNSYLASKLEEGVRIVRGLMENEKLTFKGRFFEVDNAFIMPRR---KVPIWIAGNS 166
                                       ***************.*************************88999******************...69******** PP

                    Bac_luciferase 176 paglelaarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...raliagl 248
                                       p+++e++a++adg++++     + + e+++r+r  a+++gr   +i+ g+   v+v+++ e A +++   ++l+ ++
  gi|488600117|ref|YP_007906588.1| 167 PRTMEITAKYADGWIPTAgMGAKRYGEHLRRIRNLAEKFGR---RIEAGVFGYVVVDNDYESAVRRIelpAKLL-SI 239
                                       ******************9**********************...***********************9976666.44 PP

                    Bac_luciferase 249 d...fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvde 314
                                       +   +++   e+ +  + +++ ++e + ++  + a+ ++ + v+   + Gtpe+v+e+l+++++ag+++
  gi|488600117|ref|YP_007906588.1| 240 MspaRKQFLKEEIDVPDLLSFTFDEDTVKKALEIASKIDFDEVKHRFIFGTPEDVIEKLDEFRKAGAEH 308
                                       45774444444444444557999999999999999999999*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2037.09
//
Query:       gi|488600118|ref|YP_007906589.1|  [L=120]
Description: hypothetical protein Asulf_00575 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-08   34.5   2.9    1.6e-08   34.0   1.4    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    1.2e-07   31.6   0.9    1.7e-07   31.1   0.2    1.6  2  MarR            MarR family
    0.00021   21.1   0.1    0.00067   19.5   0.0    1.8  2  MarR_2          MarR family
      0.001   19.2   0.0      0.001   19.2   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0015   18.3   0.3     0.0028   17.5   0.1    1.6  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0076   16.1   1.9     0.0095   15.8   0.2    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.013   15.5   0.1       0.27   11.3   0.0    2.1  2  HTH_20          Helix-turn-helix domain
      0.023   14.6   1.0      0.023   14.6   1.0    1.7  2  TFIIE_alpha     TFIIE alpha subunit
      0.028   14.9   0.0      0.034   14.7   0.0    1.1  1  Peptidase_S66C  LD-carboxypeptidase C-terminal domain
      0.065   13.2   0.2       0.14   12.2   0.2    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.096   12.8   1.4        0.2   11.8   1.4    1.5  1  ENT             ENT domain
       0.11   12.7   0.0       0.22   11.8   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


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 !   34.0   1.4   1.1e-11   1.6e-08       7      48 .]       6      47 ..       1      47 [. 0.95
   2 ?   -0.6   0.0      0.66   9.8e+02      17      26 ..      75      84 ..      71      89 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.1e-11
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +I+++L+k+++i q++L ++l + +s ++r l++Le+e +I+
  gi|488600118|ref|YP_007906589.1|  6 EIIQILEKKGSILQKDLWKELKIDSSKCSRILRKLEKEDIIR 47
                                      6****************************************7 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.66
                            HTH_24 17 risqreLAer 26
                                       +s +e+ er
  gi|488600118|ref|YP_007906589.1| 75 ELSLQEIMER 84
                                      5566666555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.2   1.1e-10   1.7e-07       8      50 ..       7      49 ..       3      55 .. 0.93
   2 ?   -2.1   0.0       2.6   3.9e+03      16      27 ..      74      85 ..      71      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.1e-10
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      i+ il+ +g++ +++L+k l++++s  +r+l++Lek++ i+R 
  gi|488600118|ref|YP_007906589.1|  7 IIQILEKKGSILQKDLWKELKIDSSKCSRILRKLEKEDIIRRV 49
                                      8899**************************************6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                                      TTEEHHHHHHHH CS
                              MarR 16 gplsvseLakkl 27
                                      ++ls++e+ +++
  gi|488600118|ref|YP_007906589.1| 74 EELSLQEIMERM 85
                                      678899998887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.5e-07   0.00067      22      55 ..      17      50 ..       7      55 .. 0.87
   2 ?   -1.1   0.0       1.2   1.8e+03      13      31 ..      67      85 ..      66      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.5e-07
                                      EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      + +++l ++l+++ s  sril++L++   ++r++
  gi|488600118|ref|YP_007906589.1| 17 ILQKDLWKELKIDSSKCSRILRKLEKEDIIRRVE 50
                                      6799***************************985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                      HHHCTTTSEEEHHHHHHHH CS
                            MarR_2 13 aLgrrpgrdltvgelarrl 31
                                      ++  + +++l+ +e+ +r+
  gi|488600118|ref|YP_007906589.1| 67 EIEEEKEEELSLQEIMERM 85
                                      5666667789999999986 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 !   19.2   0.0   6.7e-07     0.001      19      55 ..      17      55 ..      12     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.7e-07
                    B-block_TFIIIC 19 itqsdLakeskqdprslfyrlksLekkgLIvkqsii..d 55
                                      i+q+dL+ke+k+d+++   +l++Lek   I +++++   
  gi|488600118|ref|YP_007906589.1| 17 ILQKDLWKELKIDSSKCSRILRKLEKEDIIRRVEVVvdG 55
                                      78******************************9996551 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.9e-06    0.0028      19      63 ..      13      60 ..       6      64 .. 0.80
   2 ?   -3.2   0.0       5.6   8.3e+03      24      31 ..      77      84 ..      72      87 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST...TTEEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr...pklYr 63
                                      k+g+   +++ +el+++ sk+ ++Lr+Le+ ++++r++      k ++
  gi|488600118|ref|YP_007906589.1| 13 KKGSILQKDLWKELKIDSSKCSRILRKLEKEDIIRRVEVVvdgVKTFK 60
                                      66666778999************************9986545555555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.6
                                      HHCHHCCC CS
                              TrmB 24 tadeiaee 31
                                      + +ei e+
  gi|488600118|ref|YP_007906589.1| 77 SLQEIMER 84
                                      44444444 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   6.4e-06    0.0095       3      46 ..       3      47 ..       2      48 .. 0.94
   2 ?   -1.1   0.1       1.2   1.8e+03      13      25 ..      73      85 ..      71      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.4e-06
                                      HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      tR +I+++L++ g+    +l +el++  s+ S+ L+kL+++++++
  gi|488600118|ref|YP_007906589.1|  3 TRDEIIQILEKkGSILQKDLWKELKIDSSKCSRILRKLEKEDIIR 47
                                      7889*******999999*************************996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                      TSSEEHHHHHHHH CS
                             HTH_5 13 egelcvcelaeel 25
                                      e+el+  e++e +
  gi|488600118|ref|YP_007906589.1| 73 EEELSLQEIMERM 85
                                      5889999999975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.27      28      58 ..      20      50 ..       2      52 .. 0.78
   2 ?    2.3   0.0      0.12   1.8e+02      22      35 ..      73      87 ..      66      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                      HHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 28 selaerldlskntlsyHLrvLeeagLvevvr 58
                                      ++l ++l ++ + +s+ Lr+Le+ +++++v+
  gi|488600118|ref|YP_007906589.1| 20 KDLWKELKIDSSKCSRILRKLEKEDIIRRVE 50
                                      566678999*******************986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                                      CTTB-HHHHHHHH.T CS
                            HTH_20 22 aegltaselaerl.d 35
                                      +e+l++ e++er+ d
  gi|488600118|ref|YP_007906589.1| 73 EEELSLQEIMERMeD 87
                                      7999*******9954 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.0   1.5e-05     0.023      17      58 ..       6      47 ..       2      62 .. 0.88
   2 ?   -1.5   0.1       1.6   2.3e+03      26      35 ..      69      78 ..      46      86 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      +++++L +kg +   dl kelkid  +  ++L +L ++ ++ 
  gi|488600118|ref|YP_007906589.1|  6 EIIQILEKKGSILQKDLWKELKIDSSKCSRILRKLEKEDIIR 47
                                      799********************************9988875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                      TSEBHHHHHH CS
                       TFIIE_alpha 26 gevteedlak 35
                                       e +ee+l+ 
  gi|488600118|ref|YP_007906589.1| 69 EEEKEEELSL 78
                                      3344455444 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.3e-05     0.034      27     111 ..      14     103 ..       2     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                                       ..EEEEEE--TT...HHHHHHHHHHHHCTSTTGGG--EEEEEE--.......G...CC...---HHHHHHHHHT-GG CS
                    Peptidase_S66C  27 kgkILflEdvse...spyridrmLtqlkeagvldkvkGivlGrftkp.....eekeeeeekeeykealeevlaeile 95 
                                       kg+IL  +  +e   + +++ r+L++l++  ++ +v+ +v G ++ +        +e ee++e++  l+e+++++ +
  gi|488600118|ref|YP_007906589.1|  14 KGSILQKDLWKElkiDSSKCSRILRKLEKEDIIRRVEVVVDG-VKTFkiipaG--AEIEEEKEEELSLQEIMERMED 87 
                                       44444444444466788999**********************.4444556431..3333446667889999988888 PP

                                       GTTS-EEEEESESSSB CS
                    Peptidase_S66C  96 dlkiPvlynldiGHts 111
                                        +++P +y+++i  ++
  gi|488600118|ref|YP_007906589.1|  88 LTGLPPCYGCKITDCE 103
                                       888******9987655 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 ?   12.2   0.2   9.3e-05      0.14      34      54 ..      29      49 ..      16      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.3e-05
                                      SHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 34 tretvsrilseLkreglisrg 54
                                        + +sril++L++e +i+r 
  gi|488600118|ref|YP_007906589.1| 29 DSSKCSRILRKLEKEDIIRRV 49
                                      56789*************963 PP

>> ENT  ENT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.4   0.00013       0.2      27      67 ..      12      53 ..       4      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                               ENT 27 eekkkll.teLrkeLsIsterHraelrrvksDerlktireti 67
                                      e+k ++l ++L keL+I++ +  ++lr+ ++++ +++++ ++
  gi|488600118|ref|YP_007906589.1| 12 EKKGSILqKDLWKELKIDSSKCSRILRKLEKEDIIRRVEVVV 53
                                      5666666358**************************998766 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.22      15      50 ..       9      44 ..       6      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      HHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                    Fe_dep_repress 15 tlseekkvvktkdlaerLnvspssVsemlkkLekdG 50
                                      ++ e+k+ + +kdl ++L++  s  s  l+kLek+ 
  gi|488600118|ref|YP_007906589.1|  9 QILEKKGSILQKDLWKELKIDSSKCSRILRKLEKED 44
                                      678999***************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 727.95
//
Query:       gi|488600119|ref|YP_007906590.1|  [L=73]
Description: Small nuclear ribonucleoprotein, LSM family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-20   71.3   1.8    4.4e-20   71.2   1.8    1.0  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.026   14.7   0.1       0.03   14.5   0.1    1.1  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   1.8   4.9e-24   4.4e-20       3      67 .]       7      71 ..       5      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 4.9e-24
                                      HHHTTTSEEEEEETTS.EEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  3 lkklinkkvtvelkng.relrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                      +k li+k + ve+k++   l+G+L+++D++mNl+L++++e+++d+ ++r+lg +++RGnn++li++
  gi|488600119|ref|YP_007906590.1|  7 VKTLIGKMIKVEMKGEeSDLVGILESVDDYMNLHLSNAVEYKNDE-KVRNLGHIVLRGNNVILIQP 71
                                      6899***********7599**************************.*****************986 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.3e-06      0.03       8      57 ..       7      52 ..       5      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                                      HHTTTTSEEEEEETTS-E.EEEEEEEE-T..T--EEEEEEEETTS...... CS
                            SM-ATX  8 ltslvGkevevtvknGev.yeGifstvslekdfsvvLkmarkvkkanskss 57
                                      +++l+Gk ++v++k  e    Gi+ +v+    +++ L +a + k+   +++
  gi|488600119|ref|YP_007906590.1|  7 VKTLIGKMIKVEMKGEESdLVGILESVDD--YMNLHLSNAVEYKN---DEK 52
                                      789***********98877**********..***********999...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.47
# Mc/sec: 467.67
//
Query:       gi|488600120|ref|YP_007906591.1|  [L=301]
Description: Nucleoside-diphosphate-sugar epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-51  173.7   0.0    5.1e-51  173.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.4e-50  172.5   0.2    1.6e-49  169.1   0.2    2.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.9e-15   56.6   0.0    2.9e-15   56.0   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    3.2e-15   56.0   0.0    4.6e-15   55.5   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    4.2e-15   55.6   0.1    7.6e-13   48.2   0.1    2.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      1e-11   44.5   0.0    1.4e-07   31.0   0.0    2.6  2  NAD_binding_4    Male sterility protein
    4.3e-06   26.3   0.2      0.001   18.6   0.0    2.6  2  adh_short        short chain dehydrogenase
    7.1e-05   22.8   0.0    0.00013   21.9   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
     0.0096   16.2   0.1       0.02   15.2   0.1    1.5  1  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.038   13.9   0.0       0.13   12.2   0.0    1.8  2  KR               KR domain
      0.044   13.3   0.0       0.11   12.1   0.0    1.7  2  NmrA             NmrA-like family
      0.077   12.9   0.0       0.23   11.3   0.0    1.7  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


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 !  173.5   0.0   3.4e-54   5.1e-51       1     241 []       3     227 ..       3     227 .. 0.96

  Alignments for each domain:
  == domain 1  score: 173.5 bits;  conditional E-value: 3.4e-54
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +lVtG++GfiGs++v++l + gy+v+++d+lss++++ +++ +e++++dl  +     +  e ++d+v h+Aa  +v
  gi|488600120|ref|YP_007906591.1|   3 ALVTGGAGFIGSHVVDRLVDMGYDVVVIDNLSSGKKEYLNDSAEFIHADLSRE-----V-PEIKVDEVWHIAANPDV 73 
                                       59***************************************99******9953.....3.4459************* PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       +  se+pa+++++n+  t nlle++rk g +r++f s+s+vYG+ + +p+ e+    p+ p s Y+a+Kla e l++
  gi|488600120|ref|YP_007906591.1|  74 RIGSESPAEIYDNNILATFNLLEMMRKVGNDRIIFTSTSTVYGEAEVIPTPEDY---PTVPISIYGASKLACEALIT 147
                                       *******************************************99999*99999...99****************** PP

                                       HHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvda 231
                                       +y +++g++  i r  n++G r    ++++vi  +i k++++++e+ +lg+g++   ++y++D++ a+ + l+    
  gi|488600120|ref|YP_007906591.1| 148 SYCHTFGMKSWIYRFANVIGRR----SNHGVIYDFIMKLKKNRNELEILGNGEQNKSYIYIDDCISAMFWGLKS--- 217
                                       **********************....***************999******************************... PP

                                       -STTEEEEES CS
                         Epimerase 232 gdkgeiyniG 241
                                       +++ +i+niG
  gi|488600120|ref|YP_007906591.1| 218 DEAVNIFNIG 227
                                       56678****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 !  169.1   0.2   1.1e-52   1.6e-49       1     331 [.       4     291 ..       4     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 1.1e-52
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+++++L++ gy+v++i+++ss       e l         ++ +++++Dl+        + e+++d
  gi|488600120|ref|YP_007906591.1|   4 LVTGGAGFIGSHVVDRLVDMGYDVVVIDNLSSGK----KEYLN--------DSAEFIHADLSR------EVPEIKVD 62 
                                       9**************************9998863....34443........345799999875......589***** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       ev + AA   V+   e+P++ +++n+l+t++LLe++r++g +   r++++Sts+vYG+++ +p  E+ p+ P s Y+
  gi|488600120|ref|YP_007906591.1|  63 EVWHIAANPDVRIGSESPAEIYDNNILATFNLLEMMRKVGND---RIIFTSTSTVYGEAEVIPTPEDYPTVPISIYG 136
                                       ***************************************965...9******************************* PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       a+Kl+++ ++++y +++g+   + ++ n  + r  ++     i +++++ +++++e  +lGn+++ +++ +++D ++
  gi|488600120|ref|YP_007906591.1| 137 ASKLACEALITSYCHTFGMKSWIYRFANVIGRRS-NH---GVIYDFIMKLKKNRNELEILGNGEQNKSYIYIDDCIS 209
                                       ****************************999884.44...56************99999****************** PP

                                       HHHHHHHCSS-.--EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 232 amwlmlqqdkp.edyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       am   l++d++ + ++i++ ++  v++++e+  +e+g +  +                  v +  ++  +g+v  +l
  gi|488600120|ref|YP_007906591.1| 210 AMFWGLKSDEAvNIFNIGSDDQIMVKKIAEIVSEEMGLSPRF------------------VFTGGRRGWKGDVPIML 268
                                       *999999887636799999999****9999999999986544..................233334555799***** PP

                                       B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvre 331
                                         ++k+k +LgW pk+s ee vr+
  gi|488600120|ref|YP_007906591.1| 269 LSNEKLK-KLGWMPKYSSEEAVRK 291
                                       ******9.9***********9986 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 !   56.0   0.0   1.9e-18   2.9e-15       1     221 [.       4     207 ..       4     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.9e-18
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G+++v +Lv+++   +v v+D   s ++  e  +   + +i++D+  +  + e   +vd v h+a+  
  gi|488600120|ref|YP_007906591.1|   4 LVTGGAGFIGSHVVDRLVDMG--YDVVVIDNLSSGKK--EYLNDSAE-FIHADLSRE--VPEI--KVDEVWHIAANP 71 
                                       69*******************..59999998777776..44443333.899999754..3332..57889******* PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                       dv+    +  ei++ n+  T n+le+ +k g  ++++tS+  v g+     e++   E   y++++ ++y  sK   
  gi|488600120|ref|YP_007906591.1|  72 DVRIgSESPAEIYDNNILATFNLLEMMRKVGNDRIIFTSTSTVYGE----AEVIPTPE--DYPTVPISIYGASKLAC 142
                                       *984499999***********************************9....55554555..68999************ PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNv 221
                                       E+l+ +           +     R a + G +++  ++  ++ +l+k++++l  +g+ e+ ++++Y +  
  gi|488600120|ref|YP_007906591.1| 143 EALITSYCH---TF--GMKSWIYRFANVIGRRSNhgVIYDFIMKLKKNRNELEILGNGEQNKSYIYIDDC 207
                                       ****99888...33..478888999*****99873357899*************************9865 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   3.1e-18   4.6e-15       1     176 [.       1     192 [.       1     252 [. 0.84

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.1e-18
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHHHHHHHHHHH--SEEEE------HHHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre..........eldltdaeavaellkeakpdvvvnaAAytavDka 67 
                                       mk lvtG+ G +Gs+++++l   g++v+ +++           ++++   + + + + e+k d v + AA  +v   
  gi|488600120|ref|YP_007906591.1|   1 MKALVTGGAGFIGSHVVDRLVDMGYDVVVIDNLssgkkeylndSAEFI-HADLSREVPEIKVDEVWHIAANPDVRIG 76 
                                       899**************************9765677766544333333.34567778999***************** PP

                                       HHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S.. CS
                     RmlD_sub_bind  68 EseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk.. 141
                                        + +++ y  n  a+ +l e+ ++vg   +i+ St  V+  ++  p  ed +t P+++YG++Kla E  + ++++  
  gi|488600120|ref|YP_007906591.1|  77 SESPAEIYDNNILATFNLLEMMRKVGNdRIIFTSTSTVYGEAEVIPTPEDYPTVPISIYGASKLACEALITSYCHtf 153
                                       *************************97479*********999999***************************66533 PP

                                       ..SEEEEEE-SEESSSSS-..HHHHHHHHHHH-SEEEEE CS
                     RmlD_sub_bind 142 ..kalivRtswvygekgkn..fvktmlrlakereelkvv 176
                                         k +i R++ v g++ +       +++l k+r+el++ 
  gi|488600120|ref|YP_007906591.1| 154 gmKSWIYRFANVIGRRSNHgvIYDFIMKLKKNRNELEIL 192
                                       3389**********9665511446789999****99986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.1   5.1e-16   7.6e-13       2     269 ..       4     261 ..       3     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 5.1e-16
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                       lvtG++G iGs++v++++++    +++ + +  k   ++++          ++           ++ l++ + e+kv
  gi|488600120|ref|YP_007906591.1|   4 LVTGGAGFIGSHVVDRLVDMGYDVVVIDNLSSGKKEYLNDSA---------EFI----------HADLSREVPEIKV 61 
                                       89*****************99988877555544444444332.........223..........455677778899* PP

                                       SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE..............GGGSS--SHHHHH CS
                   Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt..............DKAvnPtnvmGat 141
                                       d v+h AA   V +  e p+e  ++N+l+t n++e+  + g +++++ St              D    P++++Ga+
  gi|488600120|ref|YP_007906591.1|  62 DEVWHIAANPDVRIGSESPAEIYDNNILATFNLLEMMRKVGNDRIIFTSTstvygeaeviptpeDYPTVPISIYGAS 138
                                       *************************************************955555555555555566789******* PP

                                       HHHHHHHHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTT.SSEEE.S-TT-EEEEE-HHHHHHHHH CS
                   Polysacc_synt_2 142 KrlaekllqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeg.gpvtv.TdpemtRyfmtieeavqLvl 214
                                       K+++e l++++ ++     +k  + Rf NV+g  S+  vi  F  ++k++ +++ +  + e  + ++ i++ ++ ++
  gi|488600120|ref|YP_007906591.1| 139 KLACEALITSYCHTF---GMKSWIYRFANVIGrrSNHGVIYDFIMKLKKNrNELEIlGNGEQNKSYIYIDDCISAMF 212
                                       *********999988...7899999******966677899999999988878998735678999999********** PP

                                       HHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE----TT-- CS
                   Polysacc_synt_2 215 qalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlRpGEk 269
                                         l+  +  +if     +++ ++++a+ + e +gl+++        +tG R G k
  gi|488600120|ref|YP_007906591.1| 213 WGLKSDEAVNIFNIGSDDQIMVKKIAEIVSEEMGLSPR------FVFTGGRRGWK 261
                                       **999999999999999999999999999998888665......58888888876 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00012      0.18       1      23 [.       5      27 ..       5      42 .. 0.86
   2 !   31.0   0.0   9.4e-11   1.4e-07      87     216 ..      60     176 ..      48     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                      EE-TTSHHHHHHHHHHHHHS-.T CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpev 23
                                      +TG+ GF+G++++ +L++   +v
  gi|488600120|ref|YP_007906591.1|  5 VTGGAGFIGSHVVDRLVDMGYDV 27
                                      7****************988765 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 9.4e-11
                                       H--EEEE--SS..-S.S.TTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......H CS
                     NAD_binding_4  87 evdviihsaAt..vnfd.epykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeek 160
                                       +vd ++h+aA+  v++  e+  e+++ N+++t ++le+ +k+ +   +++ ST++v+ge e  +             
  gi|488600120|ref|YP_007906591.1|  60 KVDEVWHIAANpdVRIGsESPAEIYDNNILATFNLLEMMRKVGND-RIIFTSTSTVYGEAE-VI------------- 121
                                       79********8334444246678*******************999.***************.33............. PP

                                       HH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST--- CS
                     NAD_binding_4 161 ldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwin 216
                                          + ++  +     Y  sK + E l+ ++ +  g++  i+R  +++g +s  G+i 
  gi|488600120|ref|YP_007906591.1| 122 --PTPEDYPTVPISIYGASKLACEALITSYCHTFGMKSWIYRFANVIGrRSNHGVIY 176
                                       ..3445555566679********************************9666667664 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   6.9e-07     0.001       3      59 ..       3      53 ..       1      61 [. 0.79
   2 !    5.0   0.1    0.0098        15     142     165 ..     128     151 ..      77     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.9e-07
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvt 59
                                      +lvtG+++ IG  ++++l+ +G++vvv+d+ ++  +e      +  ++a +i++D++
  gi|488600120|ref|YP_007906591.1|  3 ALVTGGAGFIGSHVVDRLVDMGYDVVVIDNLSSGKKEY----LN--DSAEFIHADLS 53
                                      8**************************99887755333....32..24666666665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0098
                                       B-TTBHHHHHHHHHHHHHHHHHHH CS
                         adh_short 142 pvagvaaYsAsKaavagltrslak 165
                                       p    + Y+AsK a ++l+ s  +
  gi|488600120|ref|YP_007906591.1| 128 PTVPISIYGASKLACEALITSYCH 151
                                       4455789*********99998776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   8.9e-08   0.00013       1     106 [.       7     119 ..       7     151 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.9e-08
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH.HHHCTTTCEEEE--TT-......CCHHHHHHTT-SEEEES--- CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekla.eleaeeglevvegdvtd......vedlaealkgadaVvsalgg 70 
                                       G+ G +G+++v++l++  g++v+ ++ n ++ + e+  ++ +e +++d++       v+++ +  ++ d+ + + ++
  gi|488600120|ref|YP_007906591.1|   7 GGAGFIGSHVVDRLVDM-GYDVV-VIDNLSSGKkEYL-NDSAEFIHADLSRevpeikVDEVWHIAANPDVRIGSESP 80 
                                       99***************.5**86.5677555541443.799********9522222234444444444443333333 PP

                                       TCC..HHHH..HHHHHHHHHHCT--EEEEEEETTTTSGCG CS
                    NAD_binding_10  71 ggk..deeg..aknivdaakeagvkRfvlvsaigvgdevp 106
                                         +  d+++  + n+++ +++ g  R+++ s+  v+ e++
  gi|488600120|ref|YP_007906591.1|  81 A-EiyDNNIlaTFNLLEMMRKVGNDRIIFTSTSTVYGEAE 119
                                       3.145666699************************97643 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.3e-05      0.02       5      52 ..       8      55 ..       4      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                      S-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSH CS
                            TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatde 52
                                      G+G +G++++++L + g+ dvvvid+  +  +e+ ++ +e++++d ++e
  gi|488600120|ref|YP_007906591.1|  8 GAGFIGSHVVDRLVDmGY-DVVVIDNLSSGKKEYLNDSAEFIHADLSRE 55
                                      89*************888.7*************************9875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.5e-05      0.13       4      30 ..       4      30 ..       2      67 .. 0.77
   2 ?   -1.5   0.0       1.4     2e+03     117     143 ..      92     117 ..      77     122 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-05
                                      EEETTTSHHHHHHHHHHHHHHS-EEEE CS
                                KR  4 litGGlGgLGlelarwlaekgarhlvl 30
                                      l+tGG+G +G ++++ l++ g   +v+
  gi|488600120|ref|YP_007906591.1|  4 LVTGGAGFIGSHVVDRLVDMGYDVVVI 30
                                      9********************988886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                       HHHHHHTTTS--SEEEEEEEHHHHH-- CS
                                KR 117 wnLhelledesldffvlfSSiagllgs 143
                                        nL e++++   d  ++f+S ++++g+
  gi|488600120|ref|YP_007906591.1|  92 FNLLEMMRKVGNDR-IIFTSTSTVYGE 117
                                       45555555433333.345555555554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.1e-05      0.11       2      53 ..       4      53 ..       3     111 .. 0.82
   2 ?   -2.3   0.0       1.8   2.7e+03     157     226 ..     179     246 ..     173     252 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.1e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdld 53
                                      lv+G++G +G++vv+ l++ g++v ++  d  s   k+  +  +e++++dl 
  gi|488600120|ref|YP_007906591.1|  4 LVTGGAGFIGSHVVDRLVDMGYDVVVI--DNLSSGKKEYLNDSAEFIHADLS 53
                                      79*********************9653..45555555555666888888875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                                       BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHT CS
                              NmrA 157 vgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkig 226
                                       +++++++++ +++lg+g+ +  ++   +D  +++   lk  +++++  i  + + + +++i+e+ ++++g
  gi|488600120|ref|YP_007906591.1| 179 IMKLKKNRNELEILGNGEQNKSYI-YIDDCISAMFWGLKSDEAVNIFNI-GSDDQIMVKKIAEIVSEEMG 246
                                       566666777777777777666666.666666666666666666666555.35666667777777777776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.23       6      56 ..       8      62 ..       4      84 .. 0.88
   2 ?   -2.1   0.0         2     3e+03     101     116 ..      98     113 ..      90     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                      --SCCHHHHHHHHHHTT-EEEEE-S....-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                           3HCDH_N  6 GaGtmGagiaavfasagleVvlvdi....seealekalekieksleklvekgklk 56
                                      GaG +G+ +   ++  g++Vv++d     ++e l++++e i++ l++ v + k++
  gi|488600120|ref|YP_007906591.1|  8 GAGFIGSHVVDRLVDMGYDVVVIDNlssgKKEYLNDSAEFIHADLSREVPEIKVD 62
                                      9***********************9988889999999999999999988777766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                                       HCCS-TTSEEEE--SS CS
                           3HCDH_N 101 ekiakpdailasnTSs 116
                                        + + +d i+ ++TS+
  gi|488600120|ref|YP_007906591.1|  98 MRKVGNDRIIFTSTST 113
                                       4456778899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 1678.24
//
Query:       gi|488600121|ref|YP_007906592.1|  [L=182]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-39  131.7  12.6    5.9e-21   74.6   4.4    2.1  2  UPF0016   Uncharacterized protein family UPF0016
    7.7e-06   25.7  10.9     0.0039   16.9   2.7    2.4  2  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.06   12.9   7.4      0.089   12.4   3.0    2.1  2  DUF998    Protein of unknown function (DUF998)
      0.063   13.5   1.9       0.11   12.6   0.8    2.2  1  MHYT      Bacterial signalling protein N terminal repeat
        1.4    8.3  10.6       0.17   11.3   3.6    2.1  2  LysE      LysE type translocator
        2.7    8.3  13.3        1.1    9.5   2.9    3.4  3  DUF3784   Domain of unknown function (DUF3784)
        5.8    7.4  11.8    2.1e+02    2.5  11.8    2.9  1  DUF202    Domain of unknown function (DUF202)


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 !   62.5   1.1   1.3e-20   3.4e-17       4      75 .]       9      81 ..       6      81 .. 0.96
   2 !   74.6   4.4   2.3e-24   5.9e-21       1      75 []     102     176 ..     102     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.3e-20
                           UPF0016  4 flliflaElGDkTqlaaalLaary.kplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75
                                      f++i+laElGDkTql  +lL++++ k l+ f+Ga+ +++++++ ++llGs++++ +pe+++++++ ++F+l G
  gi|488600121|ref|YP_007906592.1|  9 FITIALAELGDKTQLSLLLLSTKTkKRLQLFFGAMTGFLIVDGSAILLGSWISEIVPEDYLKIFSSAVFILAG 81
                                      99**********************88889*****************************************977 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 2.3e-24
                           UPF0016   1 laaflliflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75 
                                       l+af+lif++E+GDkTq+a al+a+ry+ l Vf+ ++lAla+ ++l+++lG+ +++rl+++ + +va+v+F+++G
  gi|488600121|ref|YP_007906592.1| 102 LSAFILIFATEWGDKTQIASALFATRYDLLFVFFSVMLALAVLSILAIYLGELISERLDRKKVSRVAGVVFIVIG 176
                                       589************************9999******************************************98 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.9   1.6e-05     0.042      75     113 ..      52      90 ..      30     114 .. 0.70
   2 !   16.9   2.7   1.5e-06    0.0039     187     235 ..     130     178 ..     116     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                              TauE  75 iGallGallllllpsellkllfgvlllllallmllrkkr 113
                                        ++llG++++  +p+++lk++ +++ +l+++++l + + 
  gi|488600121|ref|YP_007906592.1|  52 SAILLGSWISEIVPEDYLKIFSSAVFILAGIFVLKSGED 90 
                                       46799*****************99999999999865443 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.5e-06
                              TauE 187 agavdwpllllllpgallGallGarlarrlsertlrrlfallllvlgvk 235
                                       +  v ++++l+l++ ++l ++lG  ++ rl+++++ r+ +++ +v+gv+
  gi|488600121|ref|YP_007906592.1| 130 LLFVFFSVMLALAVLSILAIYLGELISERLDRKKVSRVAGVVFIVIGVS 178
                                       445556677789***********************************97 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.025        65      41      84 ..      42      85 ..      23      93 .. 0.78
   2 ?   12.4   3.0   3.5e-05     0.089      24      86 ..     116     182 .]     100     182 .] 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.025
                            DUF998 41 lfnaglvllgllvlalavgllraargragragrlllavaglglv 84
                                      ++++ l++ g ++l+++++   +++  ++ ++++++++ag++++
  gi|488600121|ref|YP_007906592.1| 42 AMTGFLIVDGSAILLGSWISEIVPEDYLKIFSSAVFILAGIFVL 85
                                      46777777777778877766555888888888888888888876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.5e-05
                            DUF998  24 lrhaiSeLgaeggpggwlfnaglvllgllvla..lavgllra..argragragrlllavaglglvla 86 
                                        ++  S L a++ +  ++f   +++l++l+++  ++  l+++   r++++r+++++++v g++++l+
  gi|488600121|ref|YP_007906592.1| 116 KTQIASALFATRYDLLFVFFSVMLALAVLSILaiYLGELISErlDRKKVSRVAGVVFIVIGVSFALV 182
                                       57889999997777777888888888888887543333444489*******************9875 PP

>> MHYT  Bacterial signalling protein N terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   4.4e-05      0.11      19      54 ..     124     162 ..     104     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                              MHYT  19 gpigydpaltalSlliaivas.vlAlal..avrrrdtrl 54 
                                       ++++yd+++++ S+ +a+++  +lA++l  ++++r  r+
  gi|488600121|ref|YP_007906592.1| 124 FATRYDLLFVFFSVMLALAVLsILAIYLgeLISERLDRK 162
                                       4799*********777766655*****988555555554 PP

>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.6      0.07   1.8e+02     131     190 ..      30      85 ..      23      88 .. 0.81
   2 ?   11.3   3.6   6.7e-05      0.17     136     191 ..     130     181 ..      95     182 .] 0.52

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.07
                              LysE 131 ygdagrlilaaglvvasliwfsllaflaarlsrrlsskkvlriinvvvgvlligfavkll 190
                                       +++ +rl l++g++ + li     ++l++++s+ + +     +++++ ++++i+ ++++l
  gi|488600121|ref|YP_007906592.1|  30 TKTKKRLQLFFGAMTGFLIVDGSAILLGSWISEIVPED----YLKIFSSAVFILAGIFVL 85 
                                       56678888999999999999999999999999998888....677888888888888776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.7e-05
                              LysE 136 rlilaaglvvasliwfsllaflaarlsrrlsskkvlriinvvvgvlligfavklll 191
                                       +l+ ++++++a  +  +l + l++++s+rl +k     ++ v+gv++i+++v ++l
  gi|488600121|ref|YP_007906592.1| 130 LLFVFFSVMLALAVLSILAIYLGELISERLDRK----KVSRVAGVVFIVIGVSFAL 181
                                       222223333333333333334455555555555....5779***********9985 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.6      0.07   1.8e+02      55      88 ..      52      85 ..      32      91 .. 0.50
   2 ?   -1.3   2.5      0.97   2.5e+03      73      85 ..     135     147 ..     101     155 .. 0.55
   3 ?    9.5   2.9   0.00043       1.1      35      59 ..     157     181 ..     130     182 .] 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.07
                           DUF3784 55 ilflllgllsaiesealliialiviiiiviyliv 88
                                       ++ll + +s i  e +l i+  +++i++ ++++
  gi|488600121|ref|YP_007906592.1| 52 SAILLGSWISEIVPEDYLKIFSSAVFILAGIFVL 85
                                      4444444444444444444444433333333333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.97
                           DUF3784  73 iialiviiiiviy 85 
                                        ++++++ +++i+
  gi|488600121|ref|YP_007906592.1| 135 FSVMLALAVLSIL 147
                                       2222233333333 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00043
                           DUF3784  35 ekydekklsrfmgivllligilfll 59 
                                       e+ d kk+sr +g+v+++ig+ f+l
  gi|488600121|ref|YP_007906592.1| 157 ERLDRKKVSRVAGVVFIVIGVSFAL 181
                                       789*****************87776 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  11.8     0.081   2.1e+02      15      56 ..     136     181 ..      10     182 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.081
                            DUF202  15 Rtslalialglallrffl....tgepsalgkilglilivlgiltll 56 
                                       +++lal++l+++ + +      + +++++++++g+++iv+g+ ++l
  gi|488600121|ref|YP_007906592.1| 136 SVMLALAVLSILAIYLGEliseRLDRKKVSRVAGVVFIVIGVSFAL 181
                                       455666666666665433777788888899************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1026.02
//
Query:       gi|488600122|ref|YP_007906593.1|  [L=218]
Description: putative phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-11   42.2   1.7    7.8e-10   38.5   1.7    2.1  1  Pribosyltran   Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.025   14.4   0.0      0.048   13.5   0.0    1.4  1  DUF2154        Cell wall-active antibiotics response 4TMS Yvq
      0.073   12.5   0.0        0.1   12.0   0.0    1.2  1  UPRTase        Uracil phosphoribosyltransferase
       0.16   10.6   0.0        0.2   10.3   0.0    1.1  1  PhoPQ_related  PhoPQ-activated pathogenicity-related protein


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   1.7   1.8e-13   7.8e-10      18     145 ..      24     185 ..      13     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.8e-13
                                       TTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE....................... CS
                      Pribosyltran  18 laaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes............... 79 
                                       ++a+ + +     dvv++i+ gGvp+a ++a+  + pl ++ ++k   + ++ea   + ++s               
  gi|488600122|ref|YP_007906593.1|  24 KLASFIPD----FDVVIAIPAGGVPIAVEVARVKKMPLRVLPVSKILLPYTTEAG--FGAISmfgdveinerlasgl 94 
                                       33333334....6*********************999998888888888888885..44555668899999999999 PP

                                       .........................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                      Pribosyltran  80 .........................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpatee 131
                                                                + l+    ++  iVDD+l++G T++ a+++ k+ +  e+ ++v+ +  + + 
  gi|488600122|ref|YP_007906593.1|  95 deetirlqiektkekierrlkiipeKFLKYESANSAAIVDDGLASGFTMITAIKAAKRFYR-EIYVVVPTASTSAVD 170
                                       99999999999*********999988888888999********************999998.59999999******* PP

                                       HHHHH-TTS...... CS
                      Pribosyltran 132 evdknakrvfsls.p 145
                                        v+k+++ vf l+  
  gi|488600122|ref|YP_007906593.1| 171 LVEKKCDGVFVLNlR 185
                                       ****99999977754 PP

>> DUF2154  Cell wall-active antibiotics response 4TMS YvqF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.048      52     104 ..      64     117 ..      60     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                           DUF2154  52 kilVPedvevsveasvifGdvkvldekeagllneslkleseeyeea.ekkvkii 104
                                       kil+P+ +e    a ++fGdv++ ++  +gl  e++ l+ e+++e  e+++kii
  gi|488600122|ref|YP_007906593.1|  64 KILLPYTTEAGFGAISMFGDVEINERLASGLDEETIRLQIEKTKEKiERRLKII 117
                                       89*************************************99887777*****98 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.3e-05       0.1      99     178 ..     101     181 ..      88     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                           UPRTase  99 lqreeetlepveyynkLPkki....aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlae 171
                                       lq e+++ + +  ++ +P+k+    +++++ ++D  +a+G ++++ai+  k+  +  ++I v+   as+++v+ + +
  gi|488600122|ref|YP_007906593.1| 101 LQIEKTKEKIERRLKIIPEKFlkyeSANSAAIVDDGLASGFTMITAIKAAKR--F-YREIYVVVPTASTSAVDLVEK 174
                                       44444444444555667777776667888********************999..5.578999999999999999998 PP

                           UPRTase 172 efpkvkv 178
                                       +  +v v
  gi|488600122|ref|YP_007906593.1| 175 KCDGVFV 181
                                       8887755 PP

>> PhoPQ_related  PhoPQ-activated pathogenicity-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.5e-05       0.2      72     164 ..      82     176 ..      63     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.5e-05
                     PhoPQ_related  72 ggsnenvkkkskesesetlaeiaretkavvaelsdvPnqpltfeddgkarkEDdlvAytwrkfle..eekdetlpll 146
                                       g+++ n++ +s   e+ +  +i ++ +++   l+ +P ++l++e  ++a   Dd +A  ++       +k+     +
  gi|488600122|ref|YP_007906593.1|  82 GDVEINERLASGLDEETIRLQIEKTKEKIERRLKIIPEKFLKYESANSAAIVDDGLASGFTMITAikAAKRFYREIY 158
                                       5555555555555666677788899999999**************************99998877635555666788 PP

                     PhoPQ_related 147 lpmtkaavraMdlvqefl 164
                                       ++  +a ++a dlv++  
  gi|488600122|ref|YP_007906593.1| 159 VVVPTASTSAVDLVEKKC 176
                                       88889999*****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1379.40
//
Query:       gi|488600123|ref|YP_007906594.1|  [L=127]
Description: hypothetical protein Asulf_00581 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   32.5   0.0    1.5e-07   32.0   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    0.00059   20.5   0.0    0.00095   19.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    0.00086   19.1   0.0    0.00086   19.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0014   19.3   0.0     0.0022   18.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
     0.0066   16.3   0.0     0.0066   16.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.029   13.7   0.0      0.038   13.3   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.14   12.3   0.0       0.19   11.9   0.0    1.2  1  Flavodoxin_NdrI  NrdI Flavodoxin like


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 !   32.0   0.0   5.8e-11   1.5e-07      49      96 .]       5      52 ..       1      52 [. 0.94

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.8e-11
                                      TEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11 49 vadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllvi 96
                                      +ad + l f+++ fD v++  +l++ e+pek++ke++R Lk++G+lv+
  gi|488600123|ref|YP_007906594.1|  5 KADGRYLSFKNDVFDYVYIIPTLCFAEEPEKIIKEARRALKKNGKLVL 52
                                      789999***************************************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.7e-07   0.00095      50      97 .]       3      48 ..       1      48 [. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.7e-07
                                      EEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25 50 fvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97
                                      + ++d + l+f+++ fD+v+++ +l++ +  + ek++ke++r+Lk++G
  gi|488600123|ref|YP_007906594.1|  3 LSKADGRYLSFKNDVFDYVYIIPTLCFAE--EPEKIIKEARRALKKNG 48
                                      5689999**************87788765..567************99 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.4e-07   0.00086      70     119 ..      13      62 ..       1     117 [. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.4e-07
                   Methyltransf_31  70 ledekfDlilsnevlnaladpdkileeiervlkpggilliedprllaelp 119
                                       ++ + fD++    +l+   +p+ki++e+ r+lk++g l++  +   +el 
  gi|488600123|ref|YP_007906594.1|  13 FKNDVFDYVYIIPTLCFAEEPEKIIKEARRALKKNGKLVLGIITSDSELG 62 
                                       66789*********************************987777444444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.6e-07    0.0022      65      99 .]      16      50 ..       2      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.6e-07
                   Methyltransf_12 65 ssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99
                                      + fD+v+++ +l+  ++++++++++r++Lk++G+l
  gi|488600123|ref|YP_007906594.1| 16 DVFDYVYIIPTLCFAEEPEKIIKEARRALKKNGKL 50
                                      68*******************************97 PP

>> Methyltransf_23  Methyltransferase 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    0.0066      78     124 ..      13      59 ..       4     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                   Methyltransf_23  78 epqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl 124
                                       ++++ fd+++ + +l+  + p++ ++ +++ lk +G l+l  +++++
  gi|488600123|ref|YP_007906594.1|  13 FKNDVFDYVYIIPTLCFAEEPEKIIKEARRALKKNGKLVLGIITSDS 59 
                                       67899**********************************98887765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.038     104     151 ..       5      52 ..       1      65 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                       E--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran 104 qanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                       +a++  L f++d fD+v +   l    + +k +kea+r lk  G+lv 
  gi|488600123|ref|YP_007906594.1|   5 KADGRYLSFKNDVFDYVYIIPTLCFAEEPEKIIKEARRALKKNGKLVL 52 
                                       688999*************************************99874 PP

>> Flavodoxin_NdrI  NrdI Flavodoxin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.5e-05      0.19      38      92 ..      19      70 ..       9      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                                      -EEEEEE--TTSSSSTSS-HHHHHHHTSHHHHHCEEEEEEEE-GGGGGGTTHHHH CS
                   Flavodoxin_NdrI 38 pyvlivptygegeekkavpkqvieflnkeknrkllrGviasGnrnfgeqyalaak 92
                                      +yv i+pt    ee +++ k+ ++ l+  kn kl++G+i+s + + g++y+  +k
  gi|488600123|ref|YP_007906594.1| 19 DYVYIIPTLCFAEEPEKIIKEARRALK--KNGKLVLGIITS-DSELGKEYIEKGK 70
                                      7************9999*******999..9*********99.5678888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 781.10
//
Query:       gi|488600124|ref|YP_007906595.1|  [L=297]
Description: hypothetical protein Asulf_00582 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1994.38
//
Query:       gi|488600125|ref|YP_007906596.1|  [L=288]
Description: hypothetical protein Asulf_00583 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-14   52.7   0.1    1.5e-13   51.5   0.1    1.7  2  Radical_SAM     Radical SAM superfamily
  ------ inclusion threshold ------
      0.036   14.1   0.1      0.075   13.1   0.1    1.5  1  OTT_1508_deam   OTT_1508-like deaminase
      0.077   13.3   0.6       0.32   11.3   0.5    1.9  2  Ribosomal_L32p  Ribosomal L32p protein family


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 !   51.5   0.1   2.5e-17   1.5e-13       3     153 ..      21     173 ..      19     189 .. 0.81
   2 ?   -1.2   0.0      0.38   2.3e+03      51      66 ..     203     218 ..     173     273 .. 0.50

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.5e-17
                                       EESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC..C CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                       Radical_SAM   3 vtrgCnlr.CsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla..v 75 
                                        t gC+++ C+fC  ++    ++r r++++ee++e +   k + g v+ ++l  g+ l+ p  ++lle l       
  gi|488600125|ref|YP_007906596.1|  21 ATIGCSHNaCTFCGMYK----GKRFRIRDIEEVKEDILMSKDYYGsVRRIFLADGNALAMP-TEDLLEILNFAYtvY 92 
                                       678*************5....9***************999977788*************66.778888888887884 PP

                                       CTEEEEEEECSSCHG.....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEE CS
                                       xxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpd.....eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvd 147
                                       p+++ +    g++ d     +e l++l e g+  ++lg+e++dde  l+ +++g + +e +ea  k+ ++gi  +v+
  gi|488600125|ref|YP_007906596.1|  93 PELERVSAYAGPK-DlleksDEELRLLYENGLKLLYLGVETGDDE-LLREIRKGVNADEMVEAGLKAVRNGITLSVT 167
                                       4444444444444.24678**************************.**************************97344 PP

                                       EEEEBT CS
                                       xxxxxx RF
                       Radical_SAM 148 rivglp 153
                                       +++gl 
  gi|488600125|ref|YP_007906596.1| 168 VLIGLG 173
                                       433333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.38
                                       EEESSTGGGSTTHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM  51 ilgggepllypdfvel 66 
                                       +l+ g+pl+ + +  l
  gi|488600125|ref|YP_007906596.1| 203 MLVPGTPLYKKAKMGL 218
                                       4445555554333222 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 ?   13.1   0.1   1.3e-05     0.075      22      38 ..      20      36 ..       7      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                     OTT_1508_deam 22 pryIgcSKpaCylCely 38
                                        +IgcS  aC +C +y
  gi|488600125|ref|YP_007906596.1| 20 QATIGCSHNACTFCGMY 36
                                      469***********998 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   5.4e-05      0.32      38      52 ..      26      40 ..      22      42 .. 0.90
   2 ?   -1.6   0.0      0.57   3.4e+03      26      42 ..     234     250 ..     230     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                                      TTC-BTTTTBSSSBX CS
                    Ribosomal_L32p 38 pHrvcpscGyYkgre 52
                                      +H +c+ cG+Ykg+ 
  gi|488600125|ref|YP_007906596.1| 26 SHNACTFCGMYKGKR 40
                                      8************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.57
                                       EEEETTTCCEECTTC-B CS
                    Ribosomal_L32p  26 lvecpncgelklpHrvc 42 
                                       l e+ nc+ + ++ ++ 
  gi|488600125|ref|YP_007906596.1| 234 LIEDINCKTVFRSNHAS 250
                                       57899***999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2136.08
//
Query:       gi|488600126|ref|YP_007906597.1|  [L=534]
Description: hypothetical protein Asulf_00584 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   42.1   0.2    1.7e-08   34.0   0.1    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 !    6.0   0.0   0.00032       5.7      63     154 ..     116     235 ..      95     243 .. 0.69
   2 !   34.0   0.1   9.3e-13   1.7e-08     192     295 ..     290     396 ..     283     406 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00032
                                       HHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETT..S---GGGGS-----...................... CS
                      Glu_synthase  63 kikkriltsamSyGalseeahealakamnrlgtksntGE..GGedeerlktakdv...................... 115
                                       ++k +i+++a     ++++    la+++  +g+    GE   G+d++    +  v                      
  gi|488600126|ref|YP_007906597.1| 116 RVKVPIAMGAYGSTDIARKYWDGLAVGAALAGAILIVGEnvCGVDPASEFSNGRVvrspemerrvklfkefwdgkyg 192
                                       55555666655555567777777777777777777777744366665444444445777777777777777777777 PP

                                       ...SEEEE-TT-TT--HHHHHH-S..EEEEE---TTSTTS--EE CS
                      Glu_synthase 116 ...aikQvasgrFGvteeyLnnak..aleikiaQGakpgeGgql 154
                                            + +   r Gv+e+++++ +   +e k +QGak+  Gg++
  gi|488600126|ref|YP_007906597.1| 193 diaVQTNIEDQRIGVDEYVISKLEvnIVERKWGQGAKAI-GGEI 235
                                       75333567889*********9865116999*******97.8876 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 9.3e-13
                                       HHHHHHHHH-TTSEEEEEEE-STTHHHHHHH..HHHTT-SEEEEE-TT---SSEEHHHHHHB---HHH...HHHHHH CS
                      Glu_synthase 192 qliedLkevnkeakvsvKlvaeagvetiaag..vakanadiilidGleGGTGAspkssikhaGlPlel...alaevd 263
                                       + +e+L+e++  + v++K +a +++++  +   +++a++d i+ dG  GGTG sp  ++++ G+P++     + ++ 
  gi|488600126|ref|YP_007906597.1| 290 EDVEKLREMG-AKVVTIKTGAYRPADVAWTMkvASEAKVDYITFDGAGGGTGMSPVPMMNEMGVPTIYlesLILKAA 365
                                       6799*****9.889********999976554437899****************************864221466666 PP

                                       HHHHHTT-GGG-EEEEESS--SHHHHHHHHHH CS
                      Glu_synthase 264 qtlkeeglrdrvsliadGglktgadvvkalal 295
                                       + l+e+g +   ++ ++G +   ++++ka+a+
  gi|488600126|ref|YP_007906597.1| 366 RILREHG-KYVPDISMAGAFINETQIFKAIAM 396
                                       6666655.455589999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3420.00
//
Query:       gi|488600127|ref|YP_007906598.1|  [L=560]
Description: Aldehyde:ferredoxin oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.2e-103  347.1   0.0   1.5e-103  346.8   0.0    1.1  1  AFOR_C          Aldehyde ferredoxin oxidoreductase, domains 2
    2.3e-74  249.5   0.2    4.6e-74  248.6   0.2    1.5  1  AFOR_N          Aldehyde ferredoxin oxidoreductase, N-termina
  ------ inclusion threshold ------
      0.071   12.9   0.0       0.17   11.6   0.0    1.6  1  Thrombin_light  Thrombin light chain


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.8   0.0  2.5e-107  1.5e-103      18     365 ..     223     559 ..     208     560 .] 0.92

  Alignments for each domain:
  == domain 1  score: 346.8 bits;  conditional E-value: 2.5e-107
                                       HHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE......ETEE-- CS
                            AFOR_C  18 aelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevkveegkkvkvegp 94 
                                       +++++yGT ++ n++ne+g+lptk++++g+fe+ eki++ea+++ y+ k  +C++C ++Cg+  k   g+ v+vegp
  gi|488600127|ref|YP_007906598.1| 223 EGMKRYGTLGIANLTNEAGVLPTKYWERGSFEELEKINAEAFDR-YTEKSTACYGCAVSCGKIRKA--GD-VEVEGP 295
                                       389*****************************************.*****99***********994..33.559*** PP

                                       -HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-THHHHHHHHH CS
                            AFOR_C  95 eyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdaeallellek 171
                                       eyetl+a+G+ + ++d e+i+++n+lcd++G+DtisaGn++af+m ++e+G +++       ++fgd +a+lell+k
  gi|488600127|ref|YP_007906598.1| 296 EYETLYAFGPLCYNSDAESIFRANDLCDRYGMDTISAGNVVAFYMACSERGEVDE------RVDFGDSNAILELLKK 366
                                       *****************************************************99......78************** PP

                                       HHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-THHHH..S---TT CS
                            AFOR_C 172 iAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlrayliale..ekvdpl 246
                                       iA r++igd+lAeG+k ++e++g    a+hvkGle+p ydprg+++malaY ts rGacH+r+ ++ ++   +vd++
  gi|488600127|ref|YP_007906598.1| 367 IAFRQDIGDILAEGSKIASERMGVSVEAVHVKGLEPPGYDPRGLYSMALAYVTSHRGACHMRSCAYRPNltGAVDRF 443
                                       **************************************************************77777777799**** PP

                                       --HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHT- CS
                            AFOR_C 247 etegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynleRlfnlreGl 323
                                       + +++aelvk+ +d+ ++vds+++C+f       + ++++a+l++ vtG +v+ e+l kaGe i+nl+R fnlreG+
  gi|488600127|ref|YP_007906598.1| 444 SVDKQAELVKDLEDFYCVVDSFVFCRFLCLPVIGMYWQDIARLYEIVTGNSVSVEDLKKAGESIWNLTREFNLREGV 520
                                       *****************************656678899*************************************98 PP

                                       -HHHS---HHHHHS---SSTTTT---...-HHHHHHHHHHHHT CS
                            AFOR_C 324 trkddtlperlleeplkegpakgkvl.edeleemldeyYelrG 365
                                          d +lp  ++  p k  + +  v+ ++++++m+++y  lrG
  gi|488600127|ref|YP_007906598.1| 521 V--DENLPSTFF-RPVKHYDRE-LVVrKEDFDRMVEKYRSLRG 559
                                       5..99*******.788666555.4443555*********9999 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.6   0.2   7.7e-78   4.6e-74       2     197 ..       2     195 ..       1     196 [. 0.98

  Alignments for each domain:
  == domain 1  score: 248.6 bits;  conditional E-value: 7.7e-78
                                       EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE- CS
                            AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaks 78 
                                       +i+r++Ls+g+i+v ++p + ++ y+Gg+g+a+kll+  + p+vdp++p+n ++f++Gp++g++++g++r+++v+ks
  gi|488600127|ref|YP_007906598.1|   2 NIARINLSKGTITVSKIPSD-LKPYIGGKGIATKLLFG-ILPKVDPFHPDNAIIFGIGPVNGIRLSGASRVTAVFKS 76 
                                       699***************65.68***************.6699********************************** PP

                                       TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTSEEEEE CS
                            AFOR_N  79 PltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgdkvavi 155
                                       Plt ++ges++Gg++++e+k+aG+d++ i+Gka+kpvy+++ed ++ei+da++lwg+d yet+e l++e+g ++++i
  gi|488600127|ref|YP_007906598.1|  77 PLTFGYGESQCGGYLAYEMKKAGIDFLYITGKARKPVYISVEDRNIEIKDASHLWGKDSYETEEILEKEEGGEILSI 153
                                       ***************************************************************************** PP

                                       -HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 156 GpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                       G+aGenlvrfA+i++ +gr++grgG GavmgsK lkaivv+g
  gi|488600127|ref|YP_007906598.1| 154 GQAGENLVRFACINHRKGRQFGRGGAGAVMGSKMLKAIVVKG 195
                                       *************999************************99 PP

>> Thrombin_light  Thrombin light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.9e-05      0.17       7      22 ..      73      88 ..      68      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                                      XTSTHHHHSSSGTTTT CS
                    Thrombin_light  7 tFFnpktFGeGEadCG 22
                                      +F +p tFG GE++CG
  gi|488600127|ref|YP_007906598.1| 73 VFKSPLTFGYGESQCG 88
                                      577899*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3613.11
//
Query:       gi|488600128|ref|YP_007906599.1|  [L=33]
Description: hypothetical protein Asulf_00586 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        81  (0.00451782); expected 358.6 (0.02)
Passed bias filter:                       76  (0.00423894); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 221.36
//
Query:       gi|488600129|ref|YP_007906600.1|  [L=58]
Description: hypothetical protein Asulf_00587 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.1   0.0     0.0034   16.1   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.9e-07    0.0034     283     321 ..      15      51 ..       1      58 [] 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-07
                                       -TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                       Aminotran_3 283 apgshgsTfgGnplacavalavleiieeekllenaqelg 321
                                       + g+ g+T gGnpl  a+al+++e+++++  l+na ++g
  gi|488600129|ref|YP_007906600.1|  15 HIGGVGGTCGGNPLVYAAALESIEVVKDS--LDNAIKVG 51 
                                       56889*********************985..55555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 369.49
//
Query:       gi|488600130|ref|YP_007906601.1|  [L=102]
Description: hypothetical protein Asulf_00588 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.0   0.0    2.1e-07   30.8   0.0    1.1  1  Arginase  Arginase family
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.13   11.5   0.0    1.0  1  TIMELESS  Timeless protein


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.3e-11   2.1e-07     232     278 ..       9      53 ..       7      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.3e-11
                                       HHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHHH CS
                          Arginase 232 rellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrell 278
                                       +e++++l +l++ l++vgaD+vE+ P+ d ++ +t++l+a++vrel+
  gi|488600130|ref|YP_007906601.1|   9 KEFFEVLTKLSK-LKVVGADLVEICPSCDYSD-MTSLLGAKIVRELI 53 
                                       79999*****88.*****************66.************64 PP

>> TIMELESS  Timeless protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.4e-05      0.13      26      71 ..      10      69 ..       1      91 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.4e-05
                          TIMELESS 26 nrrdvaralaeakilqndLipiLiqweek.......kkk........lalaclrLlvaLTw 71
                                      +  +v+  l++ k++  dL++i  +++ +         k        ++l++l+Ll++L +
  gi|488600130|ref|YP_007906601.1| 10 EFFEVLTKLSKLKVVGADLVEICPSCDYSdmtsllgA-KivrelivgVFLNILELLTFLSI 69
                                      5578999****************99777665666651.156667888999999*9999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 763.15
//
Query:       gi|488600131|ref|YP_007906602.1|  [L=380]
Description: phosphoglycerate mutase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-46  156.7   0.0    1.5e-45  155.2   0.0    1.7  2  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    4.3e-39  134.4   0.0    4.8e-39  134.2   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
     0.0025   17.4   0.0      0.044   13.4   0.0    2.1  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
  ------ inclusion threshold ------
      0.059   13.4   0.0        0.1   12.6   0.0    1.3  1  DUF1743        Domain of unknown function (DUF1743)
       0.16   11.7   0.3        1.1    9.0   0.0    2.1  2  YfmQ           Uncharacterised protein from bacillus cereus g


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 !  155.2   0.0   4.1e-49   1.5e-45       1     167 [.      37     194 ..      37     197 .. 0.96
   2 ?   -1.6   0.0      0.58   2.1e+03      53      88 ..     287     320 ..     278     339 .. 0.83

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 4.1e-49
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTG CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrra 77 
                                       Ak+G++G+++t+p+g++pgSd+Anl+ilG+d +kyytGRGp+EAl+ ++    gd++fRcnlv v+  d+++id+++
  gi|488600131|ref|YP_007906602.1|  37 AKEGACGITKTIPDGFEPGSDIANLTILGVDVRKYYTGRGPIEALARDI---FGDMVFRCNLVYVK--DDTMIDYSG 108
                                       89***********************************************...8************5..89******* PP

                                       GG-.-TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE.--S-B--S--..SSTTS------BS.SGGGHHHHH CS
                      PhosphMutase  78 gristeeakeLikalneel..eegvevkfypgveyrhllvl.lsdkitdtdpphdkegkeikellplkseeaketae 151
                                        r++++ea ++ik+ln++   +    ++f++g +yr+l+++ + ++ ++t+pphd++gk+i++++p k    ++ a+
  gi|488600131|ref|YP_007906602.1| 109 RRVDDHEALRIIKHLNKNRelD---FIEFHAGRSYRNLMTVnGIKEEVKTTPPHDIQGKRIDPYMP-K---GGKLAK 178
                                       ******************9766...8****************88889*******************.5...59**** PP

                                       HHHHHHHHHHHHHHHS CS
                      PhosphMutase 152 llnelieksqeiLedh 167
                                       +l +++e+s+ +L+d 
  gi|488600131|ref|YP_007906602.1| 179 ILADIMEWSKAVLSDL 194
                                       *************986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.58
                                       TT-EEEEEEEEEEC..TTCEEETTGGG-.-TTHHHH CS
                      PhosphMutase  53 pgdvafRcnlvtvdeedgiiidrragristeeakeL 88 
                                       +gdv  ++  +t+   d++i+ +  ++i+ ee++ +
  gi|488600131|ref|YP_007906602.1| 287 EGDVEKKVEAITLY--DEKIVGYILDHIDHEETRIM 320
                                       78888899999995..67888999999998888765 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.0   1.3e-42   4.8e-39       1     240 [.       1     371 [.       1     380 [] 0.95

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 1.3e-42
                                       -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                     Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel....... 67 
                                       +k++l++ DG+++++ +el+    ++vA+tP+++ L+ke       +a+g+ +++p++ +++s++++l++       
  gi|488600131|ref|YP_007906602.1|   1 MKYLLLIPDGMADWEVKELGKktpLEVADTPNINYLAKE-------GACGITKTIPDGFEPGSDIANLTIlgvdvrk 70 
                                       5889*************9999999***************.......9****************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|488600131|ref|YP_007906602.1|  71 yytgrgpiealardifgdmvfrcnlvyvkddtmidysgrrvddhealriikhlnknreldfiefhagrsyrnlmtvn 147
                                       ***************************************************************************** PP

                                       .........................................HHHHTT-----EEEEEEEE-S---SSHHHHHT--EE CS
                                       .........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 .........................................lrisetvkfahvtffwnggrsgyfnpleereeipsd 103
                                                                                  +s     ++++++w+gg++++f++l++r++  + 
  gi|488600131|ref|YP_007906602.1| 148 gikeevkttpphdiqgkridpympkggklakiladimewskAVLSDLDVGPNMVWLWGGGEMPSFPKLKDRIGKTGV 224
                                       ***************************************973356666778************************** PP

                                       EE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHH CS
                                       xxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 104 tvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaaiea 160
                                       ++ ++dl                    + +++++ +a++a++ ++ +  d+vv++++  D++GH+gd+e++++ai  
  gi|488600131|ref|YP_007906602.1| 225 MISEVDLligigkglgmeavevegatgYIDTNYKGLAKSAIRSLKRE--DFVVLHTEGIDEIGHEGDVEKKVEAITL 299
                                       ********************************************555..**************************** PP

                                       HHH.HHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT----S--S.SHHHHTT-TTEE CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                     Metalloenzyme 161 aDe.avkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvke.gakfrekggLan 235
                                       +De +v+ ild+i+++++ +++++DH+++ ++++        Ht+e VP+li+g +  +d+v++ ++k ++kg  + 
  gi|488600131|ref|YP_007906602.1| 300 YDEkIVGYILDHIDHEETRIMLLPDHPTPVRLKT--------HTAEEVPFLIYGWR--RDDVRNfTEKKCRKGFYGF 366
                                       **9889****************************........************96..5678888899999888887 PP

                                       EEGGG CS
                                       xxxxx RF
                     Metalloenzyme 236 vaatl 240
                                       v++  
  gi|488600131|ref|YP_007906602.1| 367 VEGLD 371
                                       77654 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.034   1.2e+02       3      35 ..       5      44 ..       3      50 .. 0.68
   2 !   13.4   0.0   1.2e-05     0.044     157     232 ..     253     325 ..     185     328 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.034
                                      EEEETT-B....TTHHHHHG.S..TSHHHHHHHHHSEEES CS
                      Phosphodiest  3 vislDGlr....adlldrla.e..llpnlaaLakegvsap 35
                                      +++ DG+      +l ++   e  ++pn+++Lakeg  + 
  gi|488600131|ref|YP_007906602.1|  5 LLIPDGMAdwevKELGKKTPlEvaDTPNINYLAKEGACGI 44
                                      6666666665554445555545669***********9876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.2e-05
                                       HHCHTHSHHHHHCT....SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEE CS
                      Phosphodiest 157 ldaafakvvlekel....ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilv 229
                                       +d++ +   l+k+     ++ d+++++ e++D +gH+ G  +++ve+   +  k +g++l+ +d +    et i+l+
  gi|488600131|ref|YP_007906602.1| 253 IDTNYKG--LAKSAirslKREDFVVLHTEGIDEIGHE-GDVEKKVEAITLYDEKIVGYILDHIDHE----ETRIMLL 322
                                       5555543..3333346679*****************5.566888998888888999********99....******* PP

                                       ES- CS
                      Phosphodiest 230 SDH 232
                                        DH
  gi|488600131|ref|YP_007906602.1| 323 PDH 325
                                       **9 PP

>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.9e-05       0.1      37      86 ..     291     353 ..     282     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                                       -EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSS.............EEEEEEES-HHH CS
                           DUF1743  37 evdeesvieadektypetfdnvDlshklvvlvPhtpdp.............vlfGirgedpea 86 
                                       e + e +  +dek + +  d +D+++++++l P+ p+p             +++G r +d+ +
  gi|488600131|ref|YP_007906602.1| 291 EKKVEAITLYDEKIVGYILDHIDHEETRIMLLPDHPTPvrlkthtaeevpfLIYGWRRDDVRN 353
                                       556677888999999***********************9999999999888888888887755 PP

>> YfmQ  Uncharacterised protein from bacillus cereus group
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00031       1.1      41      71 ..      99     129 ..      88     149 .. 0.85
   2 ?    0.1   0.1      0.18   6.4e+02      77     111 ..     312     345 ..     285     360 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00031
                              YfmQ  41 eenvtitlegknlegeekskviqefneaifl 71 
                                       ++++ i + g++++++e+ ++i+++n+   l
  gi|488600131|ref|YP_007906602.1|  99 KDDTMIDYSGRRVDDHEALRIIKHLNKNREL 129
                                       68999********************987544 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                              YfmQ  77 yPgdeelflepeeggtPlvietkkGkkdvklfvys 111
                                         ++e + +   + +tP+ ++t+   ++v + +y 
  gi|488600131|ref|YP_007906602.1| 312 IDHEETRIMLLPDHPTPVRLKTHT-AEEVPFLIYG 345
                                       345555555555566666666554.3456666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2678.76
//
Query:       gi|488600132|ref|YP_007906603.1|  [L=271]
Description: Sugar phosphate isomerase/epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-09   35.6   0.0    8.6e-09   35.1   0.0    1.3  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.012   15.9   1.1       0.19   12.1   0.5    2.3  2  Imm41         Immunity protein 41


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 !   35.1   0.0   9.6e-13   8.6e-09       3     210 .]      19     219 ..      17     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 9.6e-13
                                       HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSE..EEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHH CS
                      AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglr..iaslslftrfgypdederear.reesvdalkrai 76 
                                       + ++ Gf ++E+ ++ +  + ++++ + +e+ ++  +++l   i++  + t+f +          r++s ++l+++i
  gi|488600132|ref|YP_007906603.1|  19 FTSRQGFSHIEILMDHP--WYHHEKLNYAEILELKGSYDLDvlIHASATATNFISISS-----QmRAASYRELEKTI 88 
                                       56777888888866543..333334566777777666666611566666666666544.....346666******** PP

                                       HHHHHHTBSEEEEEBCC.........GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHH CS
                      AP_endonuc_2  77 elaaaLGapllvlhpGt.........agagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeel 144
                                        +a++   +l+++h+G          + +  ++  e +++ l   + + +++ +     lalE++ + +  ++ + +
  gi|488600132|ref|YP_007906603.1|  89 SFAYKTESELITFHIGWnpglitaggFVYKKEWYSEHNYRVLTGEMLKFLRKID--SSILALENTIEIDYAMR-SAI 162
                                       ************************997677777777888888888888888876..679**********9999.*** PP

                                       HHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 145 arlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                       + ll+++d   + +++D+gH++       +++ ++ dr++ +H++D++g      d h+p+g+G++
  gi|488600132|ref|YP_007906603.1| 163 EVLLEKTD---LSLTFDIGHWNVK--SSHQIFIENFDRVRNIHLHDNNG----DYDSHLPLGKGNV 219
                                       ********...***********98..777888888899***********....***********85 PP

>> Imm41  Immunity protein 41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.033   2.9e+02      37      65 ..      70      97 ..      64     106 .. 0.73
   2 ?   12.1   0.5   2.1e-05      0.19      18      97 ..     116     197 ..     110     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.033
                             Imm41 37 ieilkkykdkdlkrelvkgisytykrile 65
                                      i i ++ +     rel k+is++yk+  e
  gi|488600132|ref|YP_007906603.1| 70 ISISSQMR-AASYRELEKTISFAYKTESE 97
                                      66666666.55679**********98544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.1e-05
                             Imm41  18 lleessfndeeyWklenalieilkkykdkdlkrelvkgisytykrilelllvhfaksdlfei..sdipdrfiafyER 92 
                                       ++ +  + +++y  l  ++++ l+k  + +l  e ++ i y+ +  +e+ll + + s +f+i   +++   + f+E 
  gi|488600132|ref|YP_007906603.1| 116 VYKKEWYSEHNYRVLTGEMLKFLRKIDSSILALENTIEIDYAMRSAIEVLLEKTDLSLTFDIghWNVKSSHQIFIEN 192
                                       5666678899999999999*******************************************774555557788888 PP

                             Imm41  93 lkyil 97 
                                       ++ + 
  gi|488600132|ref|YP_007906603.1| 193 FDRVR 197
                                       87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1806.56
//
Query:       gi|488600133|ref|YP_007906604.1|  [L=290]
Description: N-acetylglutamate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  159.6   3.3    1.1e-46  159.4   3.3    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 !  159.4   3.3   6.2e-51   1.1e-46       2     241 .]      21     267 ..      20     267 .. 0.98

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 6.2e-51
                                       EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHH CS
                         AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevat 78 
                                       r V+KlGG+++ ++    +++ +++i  l   g+k++v+hGgg+ + + +++  gl++++++ glr+t+ e++e+++
  gi|488600133|ref|YP_007906604.1|  21 RMVIKLGGHAMVNEAV--MEKTIRDILLLYFVGIKPIVIHGGGPEISEKMEK-FGLKPKFID-GLRVTDRETLEIVE 93 
                                       78************99..**********************************.*********.************** PP

                                       HHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE................HHHTTTCEEECCHHHHHHHTT-EE CS
                         AA_kinase  79 rdalaslgerlvaallaaglpavglsaaaldateagr..............degsdgnvesvdaeaieelleagvvp 141
                                       +++ +++++++v+ ++++g +avg+sa++ +++ a++              d g +g+ e ++ + +e l++++++p
  gi|488600133|ref|YP_007906604.1|  94 MVLDGKINSKIVSTFIKHGGKAVGISAKDGLLVVARKktvkkkvgdeeielDLGFVGESEVINPDILEVLVNNKFIP 170
                                       ********************************999999*************************************** PP

                                       EEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTT CS
                         AA_kinase 142 vltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatg 217
                                       v+++++ +d eg + ++++D++a ++A a++A+kli ltdV+G++ ++++ +    l+++i+v+e+ee  +++ ++g
  gi|488600133|ref|YP_007906604.1| 171 VISPIA-ADKEGNVFNLNADVVAGHIAGAVKAKKLIMLTDVPGLLRDPNDRN---SLISTIRVSELEEmLKENKIKG 243
                                       ****76.******99******************************9999888...**************99999*** PP

                                       HHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 218 GmkvkhpaalaaarrggipvvItn 241
                                       Gm++k+++ + a+++g+ +++I++
  gi|488600133|ref|YP_007906604.1| 244 GMIPKVESVIYAVKNGVEKAHIID 267
                                       **********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2032.22
//
Query:       gi|488600134|ref|YP_007906605.1|  [L=100]
Description: hypothetical protein Asulf_00592 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 715.63
//
Query:       gi|488600135|ref|YP_007906606.1|  [L=158]
Description: hypothetical protein Asulf_00593 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-13   49.6   0.0    6.1e-13   49.2   0.0    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00012   21.6   0.0    0.00014   21.4   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.016   15.1   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.079   12.9   0.0      0.094   12.7   0.0    1.2  1  Mur_ligase_M   Mur ligase middle 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 !   49.2   0.0   1.4e-16   6.1e-13       9     148 ..      19     157 ..      13     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.4e-16
                                       EEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                       Lactamase_B   9 yliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                       y+++ +++v+++ + +s +a+r+      l+  + ++d+vi++H+H+DH+Gg++ l    dv+++a++++a+   +e
  gi|488600135|ref|YP_007906606.1|  19 YYVVKGEEVVIFESDLSCSAERL------LEELDVEPDYVIVSHGHFDHVGGVAILEVYLDVKIAAHPAVAELAGKE 89 
                                       56668999999999999999998......5899999***************************************** PP

                                       HHHHHHHHCCHH.....TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEE CS
                       Lactamase_B  86 eaddaasrkgll.....lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlft 148
                                        +  + +++ ++     ++ + +d   v  + + +++g +++l+++ +p h+ ++++v+ + ++ +f+
  gi|488600135|ref|YP_007906606.1|  90 KVINSCGADDAElcrnyYKKEGVDELNVSVDLEVTERGQVGELEIMETPSHSKDCISVYPRRENAVFC 157
                                       **8877777777*****888888888888888899999999******************999999985 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 !   21.4   0.0   3.1e-08   0.00014      30      69 ..      48      85 ..      34     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.1e-08
                                      SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHH CS
                     Lactamase_B_2 30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlav 69
                                      + d V+++h+H+DH+ g+  l    + ++++ a++ v++ 
  gi|488600135|ref|YP_007906606.1| 48 EPDYVIVSHGHFDHVGGVAILEV--YLDVKIAAHPAVAEL 85
                                      679************99888877..234788888888774 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.6e-06     0.016      30      75 ..      42      87 ..      13     157 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.6e-06
                     Lactamase_B_3 30 yeppaeeaDlvlisqaledHahletlkqlaenvkvleegeslevgg 75
                                      +e+  +e+D v++s+++ dH    ++ +++ +vk+ ++++ +e++g
  gi|488600135|ref|YP_007906606.1| 42 LEELDVEPDYVIVSHGHFDHVGGVAILEVYLDVKIAAHPAVAELAG 87
                                      4445599**************9999999955555555544433322 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05     0.094      47     139 ..      23     119 ..       6     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                       TT-SEEEEE--HCHHHCTTTCCH.CBESEEEE---TSTTHHHHSSHHHHHHHHHHHHHTSETTC..EEEEE...TTS CS
                      Mur_ligase_M  47 keaeyavlEvsshglgekrlegl.lkpdvavitnispdHldfhgtlenyaeaKaelferlkeeg..iavin...add 117
                                       k+ e++++E   +  +e+ le+l ++pd++++     dH++    le y++ K   +  + e +    vin   add
  gi|488600135|ref|YP_007906606.1|  23 KGEEVVIFESDLSCSAERLLEELdVEPDYVIVSHGHFDHVGGVAILEVYLDVKIAAHPAVAELAgkEKVINscgADD 99 
                                       599**********9999***********************************9987755554333456666554555 PP

                                       C...CHHHHHCTCCTCEEEEES CS
                      Mur_ligase_M 118 pyakelikklkkakvkvvtfgl 139
                                          + +++  kk++v+ + ++ 
  gi|488600135|ref|YP_007906606.1| 100 A--ELCRNYYKKEGVDELNVSV 119
                                       5..6666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1057.49
//
Query:       gi|488600136|ref|YP_007906607.1|  [L=246]
Description: MIP family channel protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-49  169.3  17.8    1.2e-49  169.1  17.8    1.0  1  MIP       Major intrinsic protein


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 !  169.1  17.8   6.6e-54   1.2e-49       6     227 .]       3     240 ..       1     240 [. 0.90

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 6.6e-54
                                       HHHHHHHHHHHHHHHHHHHHHH.HHHCCCSSCSSSSTTSS............HHHHHHHHHHHHHHHHHHHHHHHCH CS
                               MIP   6 kflravlAEflatlllvfigvg.salnvkkkvsslaslvs............vtleavalafglalavlvylaagiS 69 
                                       +++r+ lAE ++t++lvf+g g +a+++   ++s a++++            ++++a+ laf++a+++++y++++iS
  gi|488600136|ref|YP_007906607.1|   3 DLVRRSLAELVGTFILVFFGPGaAAITL--MIASGAAKPNdfnigigvlgglGDWLAIGLAFAFAITAAIYAVGKIS 77 
                                       568999****************544444..44444444445566677779999************************ PP

                                       T-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHHHHHHHHHHHHHC.HHHHHHTTTTSSSSSTTSSHHHHHHHHHHHH CS
                               MIP  70 GaHlNPavTlallvarkisllrailYivaQllGaivaaallkllt.kglesraglfanslkpglsagqalvvEiilt 145
                                       G H+NPavT+al+ +++++   ++ Yi aQl+Ga ++++   ++  + +++  gl+a+++ pg+s gqa+ +Eii t
  gi|488600136|ref|YP_007906607.1|  78 GCHINPAVTIALWATKRFPTNEVLPYILAQLVGAALGSLAFAAVAgMDAVTIGGLGATAPFPGISYGQAMLAEIIGT 154
                                       **************************************988877624557899999********************* PP

                                       HHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHHHHTH......STTTTHHHHHH CS
                               MIP 146 fvLvlvvfaltddkrkvslgelaplaigllvaliilvgipltGaamNpArslgpavvlnk......fedhwvylvGP 216
                                       f+L++v+++++ d r+ +  ++a+l igl+va ii+  ++++G ++NpAr +gp +          ++++ +y++GP
  gi|488600136|ref|YP_007906607.1| 155 FLLMFVIMGIAVDSRAPQ--QFAGLIIGLTVAGIIITIGNISGSSLNPARTFGPYLGDFLlgginlWSFFPIYVIGP 229
                                       ***************999..99********************************997776778999*********** PP

                                       HHHHHHHHHHH CS
                               MIP 217 liGailgalvY 227
                                       ++Ga+l+a++Y
  gi|488600136|ref|YP_007906607.1| 230 IVGAVLAAFLY 240
                                       *********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); 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:                         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: 00:00:00.44
# Mc/sec: 1688.05
//
Query:       gi|488600137|ref|YP_007906608.1|  [L=33]
Description: hypothetical protein Asulf_00595 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   35.4   1.4    7.9e-09   35.4   1.4    1.0  1  DUF2180   Uncharacterized protein conserved in archaea (DUF21


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 !   35.4   1.4   4.4e-13   7.9e-09       1      31 [.       1      29 [.       1      33 [] 0.86

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 4.4e-13
                           DUF2180  1 mkCYeCakegkdtdavaiCivCGkGvCkdHl 31
                                      mkCY C+++gk+tda  i ivCG+G  k+ +
  gi|488600137|ref|YP_007906608.1|  1 MKCYICKEQGKNTDA--IYIVCGMGDSKNRV 29
                                      9*************7..679*****777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.31s 00:00:00.68 Elapsed: 00:00:00.48
# Mc/sec: 208.16
//
Query:       gi|488600138|ref|YP_007906609.1|  [L=499]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-280  930.3   0.8   2.5e-280  930.1   0.8    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 !  930.1   0.8  1.4e-284  2.5e-280       1     498 []       2     499 .]       2     499 .] 1.00

  Alignments for each domain:
  == domain 1  score: 930.1 bits;  conditional E-value: 1.4e-284
                           DUF2193   1 kelyekmidealaaqkadvevikkkrgkefkiedakayvdavkkmkaaegqskevidLhkesvkahyeilksltdtv 77 
                                       ke++ekm++ea+aaq+adv+++k+krg ef i+d kayv+a++kmka+++qsk+v++Lh++sv+ah+eilkslt+tv
  gi|488600138|ref|YP_007906609.1|   2 KEVFEKMVEEAMAAQWADVKTVKEKRGGEFVIDDVKAYVEAANKMKAVGNQSKAVFRLHVDSVNAHFEILKSLTKTV 78 
                                       589************************************************************************** PP

                           DUF2193  78 rPeddpfvehyqtPaileiLyeeDeefrksvekfieaieksealigkeavrrygGfyGptcvvDfalipGstsnvvn 154
                                       rPeddpfvehyqtPaileiLy+eDe+frks+e+fieai+ksealig+e vrrygGfyGptcvvDfal+pGstsnvvn
  gi|488600138|ref|YP_007906609.1|  79 RPEDDPFVEHYQTPAILEILYDEDESFRKSMEAFIEAIGKSEALIGLECVRRYGGFYGPTCVVDFALVPGSTSNVVN 155
                                       ***************************************************************************** PP

                           DUF2193 155 kilkkvdipeehkkaiLaaksWglntsygiGdefakaieegktlaeavekevealksiyeePveaqaklmdeaglks 231
                                       +ilk++dipe+hk+aiLaaksWg+ntsygiG++fa++ie+g+tl+eav+keve+l++iy++P e qaklmde g++s
  gi|488600138|ref|YP_007906609.1| 156 RILKTLDIPEHHKQAILAAKSWGMNTSYGIGEVFANEIEKGATLNEAVKKEVEMLQFIYDQPTEGQAKLMDELGHTS 232
                                       ***************************************************************************** PP

                           DUF2193 232 fdvrkymeeykkkmepvvkaalddgvhyanivtvPaycvGDiahhisqstynmckddvvlaiieavtevlestlrka 308
                                       fdvr+ym++y+k+me +vk+a+ddgvhy+nivtvPaycvGDiahhi+qst+nmckddv++a+ieavtev++stlr+a
  gi|488600138|ref|YP_007906609.1| 233 FDVREYMSRYRKRMEGAVKEAIDDGVHYGNIVTVPAYCVGDIAHHIAQSTFNMCKDDVIMAVIEAVTEVMDSTLRNA 309
                                       ***************************************************************************** PP

                           DUF2193 309 leklkseydvlslatgasaaavekileldgfnaemvvdlltkrfhnyvqlyptrgaaaeLhnvDflDliyrGeklld 385
                                       ++ +k+ey+ lslatgasa+a+e+ileldgf+a+m+vdlltkrfhnyvqlyptrg aaeLhn+Df+D+iyrG+k+ld
  gi|488600138|ref|YP_007906609.1| 310 IDGFKNEYQPLSLATGASAVATEYILELDGFTAPMIVDLLTKRFHNYVQLYPTRGGAAELHNHDFMDMIYRGWKYLD 386
                                       ***************************************************************************** PP

                           DUF2193 386 karrakagseeklvpkvkglevdlspieenevlmnpqryayPacaitvrfsalmrlaDyPClLtsepvtatlltnii 462
                                       karr k+gs +klvpkv+g++vdlspi+enevlmnpqryayP cai+vrfsalmrlaDyPClLtsepvtat++tn+i
  gi|488600138|ref|YP_007906609.1| 387 KARRNKNGSADKLVPKVGGFDVDLSPIHENEVLMNPQRYAYPGCAISVRFSALMRLADYPCLLTSEPVTATMVTNVI 463
                                       ***************************************************************************** PP

                           DUF2193 463 alekekaaaParvCknCasaslidarheyCqwkeav 498
                                       al+ke++ aParvCk+Ca+a+lid+rh+yCqwkeav
  gi|488600138|ref|YP_007906609.1| 464 ALHKETPGAPARVCKDCATAALIDVRHDYCQWKEAV 499
                                       **********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3172.13
//
Query:       gi|488600139|ref|YP_007906610.1|  [L=220]
Description: putative DNA binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   65.3   0.0    7.7e-18   64.0   0.0    1.7  2  HTH_10        HTH DNA binding domain
    2.7e-07   30.6   0.1    0.00011   22.2   0.1    2.6  2  SpoIIID       Stage III sporulation protein D
      0.001   18.9   0.0     0.0026   17.5   0.0    1.7  1  HTH_IclR      IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.017   15.3   0.0    1.3  1  HTH_Tnp_1_2   Helix-turn-helix of insertion element transposa
       0.02   14.7   0.0       0.06   13.2   0.0    1.8  1  MarR_2        MarR family
      0.022   14.3   0.2       0.05   13.1   0.0    1.8  2  Sigma70_r4    Sigma-70, region 4
      0.022   15.2   1.8      0.037   14.5   0.5    2.1  3  HTH_40        Helix-turn-helix domain
      0.025   14.2   0.1      0.054   13.2   0.0    1.6  1  Sigma70_r4_2  Sigma-70, region 4
      0.044   13.8   0.1        0.1   12.7   0.1    1.6  1  RhoGEF67_u2   Unstructured region two on RhoGEF 6 and 7
      0.071   12.7   0.0       0.25   10.9   0.0    1.9  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.077   12.8   0.0       0.27   11.1   0.0    2.0  1  HTH_23        Homeodomain-like domain
      0.078   13.6   0.0       0.22   12.1   0.0    1.8  1  DUF134        Protein of unknown function  DUF134
      0.093   12.3   0.0       0.14   11.7   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
       0.12   12.4   0.0       0.32   11.1   0.0    1.7  1  HTH_20        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 ?   -2.9   0.0       4.9   6.2e+03       6      14 ..     120     128 ..     119     129 .. 0.80
   2 !   64.0   0.0     6e-21   7.7e-18       1      53 []     151     203 ..     151     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.9
                            HTH_10   6 levlklAye 14 
                                       l++lk+Ay+
  gi|488600139|ref|YP_007906610.1| 120 LTMLKQAYD 128
                                       678999997 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 6e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT  q++v+k+A emGYF   R++t+k++A+++GI+kst+++hL +a+ k++e
  gi|488600139|ref|YP_007906610.1| 151 LTRSQMRVVKTACEMGYFSPKRKATIKDIADAMGIAKSTAHKHLHEAICKIVE 203
                                       89************************************************985 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0      0.01        13      35      61 ..     121     147 ..      84     150 .. 0.87
   2 !   22.2   0.1     9e-08   0.00011       6      56 ..     160     210 ..     155     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                           SpoIIID  35 tvhkDvterLkkinkklakqvkevLek 61 
                                       t+ k   +rLkki ++  ++vk++++ 
  gi|488600139|ref|YP_007906610.1| 121 TMLKQAYDRLKKIGNWRVEEVKKIMDS 147
                                       77788899****************986 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 9e-08
                           SpoIIID   6 eRvleiakyiveskatvRkaakvfgvskstvhkDvterLkkinkklakqvk 56 
                                       + + e++++  ++kat++++a ++g++kst hk + e + ki ++  ++ k
  gi|488600139|ref|YP_007906610.1| 160 KTACEMGYFSPKRKATIKDIADAMGIAKSTAHKHLHEAICKIVEHYVESGK 210
                                       5677888888999************************99999777666555 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     2e-06    0.0026      11      40 ..     167     195 ..     165     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                                       T-CTTBSS-BHHHHHHHHTS-HHHHHHHHH CS
                          HTH_IclR  11 alaeapqeltlselArrtglpkStvhRlLq 40 
                                       +++  + + t++++A++ g++kSt+h +L+
  gi|488600139|ref|YP_007906610.1| 167 YFSPKRKA-TIKDIADAMGIAKSTAHKHLH 195
                                       56666665.9****************9997 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 ?   15.3   0.0   1.3e-05     0.017       3      49 ..     147     196 ..     141     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                       HHHHHS-HHHHHHHHHHHHHHH....--S-HHHHHHHHTS-HHHHHHHHH- CS
                       HTH_Tnp_1_2   3 kkldeLtakQkkaaellvendy....ekltldeiaeevgvsrsTlykWkkk 49 
                                       +k + Lt  Q+++++   e  y     k t+++ia+ +g+++sT +k +++
  gi|488600139|ref|YP_007906610.1| 147 SK-PLLTRSQMRVVKTACEMGYfspkRKATIKDIADAMGIAKSTAHKHLHE 196
                                       34.459*******************999******************98865 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   4.7e-05      0.06      17      44 ..     169     196 ..     161     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                                       TTTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  17 rpgrdltvgelarrlglsksavsrilkr 44 
                                       +p r+ t++++a+++g+ ks+++++l +
  gi|488600139|ref|YP_007906610.1| 169 SPKRKATIKDIADAMGIAKSTAHKHLHE 196
                                       577789*****************99876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       6.1   7.8e+03      42      50 .]     124     132 ..     123     132 .. 0.83
   2 ?   13.1   0.0   3.9e-05      0.05      18      47 ..     171     200 ..     151     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.1
                                       HHHHHHHHH CS
                        Sigma70_r4  42 krAlrkLRk 50 
                                       k+A ++L+k
  gi|488600139|ref|YP_007906610.1| 124 KQAYDRLKK 132
                                       799999996 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.9e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                        ++ T ++I++ +gi +++++ ++++A+ k
  gi|488600139|ref|YP_007906610.1| 171 KRKATIKDIADAMGIAKSTAHKHLHEAICK 200
                                       5789***********************865 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.4   6.9e+03      59      74 ..      57      72 ..      27      86 .. 0.61
   2 ?   -2.2   0.0       4.8   6.1e+03      53      57 ..     140     144 ..     120     169 .. 0.52
   3 ?   14.5   0.5   2.9e-05     0.037      11      58 ..     172     216 ..     159     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.4
                            HTH_40 59 eaiekvgseklkpike 74
                                      ++ie+++s ++ +i e
  gi|488600139|ref|YP_007906610.1| 57 DIIENHKSTRFLQILE 72
                                      3444444444333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.8
                            HTH_40  53 eekeI 57 
                                       e k+I
  gi|488600139|ref|YP_007906610.1| 140 EVKKI 144
                                       22233 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.9e-05
                            HTH_40  11 eglsieeIAkerglkesTIegHLaelieegeeidlerlvse.eeekeIe 58 
                                        + +i++IA+  g+++sT  +HL e+i +      e++v++ ++ + Ie
  gi|488600139|ref|YP_007906610.1| 172 RKATIKDIADAMGIAKSTAHKHLHEAICKIV----EHYVESgKKLEDIE 216
                                       6789**********************98853....66665546666665 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.2e-05     0.054      28      50 ..     175     197 ..     174     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                       -HHHHHHHHT--HHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRA 50 
                                       ++k+IA  +gi  +t  ++l+ A
  gi|488600139|ref|YP_007906610.1| 175 TIKDIADAMGIAKSTAHKHLHEA 197
                                       68*******************88 PP

>> RhoGEF67_u2  Unstructured region two on RhoGEF 6 and 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.8e-05       0.1      52     101 ..     160     209 ..     148     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.8e-05
                       RhoGEF67_u2  52 kspktvkkflpkrkterkpsdeefalrkstaaleedaqilkvieayctga 101
                                       k+  ++  f pkrk+  k+  + + + ksta       i k++e y  + 
  gi|488600139|ref|YP_007906610.1| 160 KTACEMGYFSPKRKATIKDIADAMGIAKSTAHKHLHEAICKIVEHYVESG 209
                                       666778899*************************999*********9875 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   0.00019      0.25      18      38 ..     174     194 ..     171     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                            HTH_24  18 isqreLAerlglSpstvnrrl 38 
                                        +++++A++ g+ +st +++l
  gi|488600139|ref|YP_007906610.1| 174 ATIKDIADAMGIAKSTAHKHL 194
                                       79*****************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00021      0.27      17      36 ..     173     192 ..     157     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                            HTH_23  17 GlsvreIAreLgvsrrTvyr 36 
                                       ++++++IA+++g+ ++T  +
  gi|488600139|ref|YP_007906610.1| 173 KATIKDIADAMGIAKSTAHK 192
                                       789**************876 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.22      51      84 ..     174     207 ..     157     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                            DUF134  51 lkqeeaaklmGiskatlwrlltearkkiakalve 84 
                                        + ++ a+ mGi+k+t ++ l ea  ki +  ve
  gi|488600139|ref|YP_007906610.1| 174 ATIKDIADAMGIAKSTAHKHLHEAICKIVEHYVE 207
                                       578999**********************998776 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.14     112     174 ..     128     190 ..     117     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTT CS
                      Peripla_BP_2 112 deaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigdlldalgieniaa 174
                                       d+ +k+ ++  +++ +++++ + ++++ + v+ +a e gy+ ++++  i+d++da+gi+  +a
  gi|488600139|ref|YP_007906610.1| 128 DRLKKIGNWRVEEVKKIMDSKPLLTRSQMRVVKTACEMGYFSPKRKATIKDIADAMGIAKSTA 190
                                       777777777778888888888888*********************************987655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.32      21      46 ..     170     195 ..     150     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                       TCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  21 raegltaselaerldlskntlsyHLr 46 
                                       +++ +t +++a++++++k+t+++HL+
  gi|488600139|ref|YP_007906610.1| 170 PKRKATIKDIADAMGIAKSTAHKHLH 195
                                       567899******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.57
# Mc/sec: 1160.56
//
Query:       gi|488600140|ref|YP_007906611.1|  [L=329]
Description: Galactose-1-phosphate uridylyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.092   13.5   0.0       0.18   12.6   0.0    1.4  1  HIT       HIT domain


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 ?   12.6   0.0   9.9e-06      0.18      11      90 ..      85     163 ..      80     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-06
                                       E-SSEEEEE-SS-SSSSEEEEEESS.TGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSS CS
                               HIT  11 eddlvlafldidpkapghlLvipkk.hlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsva 86 
                                       + +++++f +i p ++  + +   + h+ +++++++e + + + ++k+v ++l++   +  + + +n  + ag s++
  gi|488600140|ref|YP_007906611.1|  85 KRNEAVLFSNIVPYSRYSFVIRLTEaHYLDISEFKKEHFEDAFYLIKEVLSKLGD--GKYYISIGMNYLKPAGSSIM 159
                                       56788899999999988777755556****************************9..778999************** PP

                                       S-EE CS
                               HIT  87 hlHi 90 
                                       h Hi
  gi|488600140|ref|YP_007906611.1| 160 HPHI 163
                                       ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1982.84
//
Query:       gi|488600141|ref|YP_007906612.1|  [L=333]
Description: Pyruvate-formate lyase-activating enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-23   83.2   0.1    8.9e-23   81.5   0.1    1.7  2  Radical_SAM     Radical SAM superfamily
    0.00031   20.1   6.2       0.12   11.8   0.2    3.4  3  zf-ribbon_3     zinc-ribbon domain
     0.0031   17.2  11.4       0.28   11.0   0.5    3.5  3  zinc_ribbon_2   zinc-ribbon domain
     0.0065   16.7   0.5     0.0065   16.7   0.5    2.6  2  IBR             IBR domain, a half RING-finger domain
     0.0094   16.0   0.4     0.0094   16.0   0.4    2.9  3  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.037   13.3   0.0    1.4  1  CcmH            Cytochrome C biogenesis protein
      0.022   13.5   0.1      0.022   13.5   0.1    1.5  2  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.026   14.6   4.2        5.4    7.2   0.1    4.2  4  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.027   14.4   0.1      0.027   14.4   0.1    3.7  4  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.054   13.3   6.0        2.5    7.9   0.0    3.7  4  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.23   10.5   0.0       0.33   10.0   0.0    1.1  1  Citrate_synt    Citrate synthase, C-terminal domain
       0.58   10.2  14.9        4.1    7.4   0.4    4.0  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.61    9.7   4.5         61    3.2   0.2    3.4  3  TF_Zn_Ribbon    TFIIB zinc-binding
        2.3    8.3   6.9         14    5.7   0.2    3.5  3  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        2.7    8.1   7.8        2.7    8.1   0.0    3.6  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        3.9    7.6  11.6        4.3    7.5   0.0    3.4  3  UPF0547         Uncharacterised protein family UPF0547


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 !   81.5   0.1     8e-26   8.9e-23       6     165 ..      81     231 ..      79     233 .. 0.94
   2 ?   -1.9   0.0       3.3   3.7e+03     122     144 ..     259     281 ..     240     291 .. 0.67

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 8e-26
                                       EESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                        Cn+rC++C+++e      ++++ r+ls+e++le +   k    ++++ ++  ep  + +f+ +  +l+k+  +g+ 
  gi|488600141|ref|YP_007906612.1|  81 SCNFRCPHCQNYEIafsDLTYPYLRELSPEDVLEMALTRK----ADGIAWTYNEPAIWHEFALDSSELVKR--EGLF 151
                                       5****************9******************9998....***************************..8*** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                       +++++ng++  +e ++ +    +d v+++++a+++  + k++  +  fe+vle++ +l e+ i  v  +++++pGen
  gi|488600141|ref|YP_007906612.1| 152 VVYVSNGYMS-RESIDQFEG-ILDAVNVDVKAFNEN-FYKKL-CKARFERVLECVAYLVEKKIF-VELTYLIIPGEN 223
                                       *********8.*********.77*************.66666.3599*****************.************ PP

                                       HHHHHHHHH CS
                                       xxxxxxxxx RF
                       Radical_SAM 157 deeleelle 165
                                       d e +el +
  gi|488600141|ref|YP_007906612.1| 224 DNE-DELKR 231
                                       *99.77765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                                       TCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 122 nrghtfeevlealeklreagikr 144
                                       ++  +++ + +a +++++ag++ 
  gi|488600141|ref|YP_007906612.1| 259 KPATSIQTLERAYRIAKDAGLEY 281
                                       44566777777888888888774 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.057        64       4       8 ..      85      89 ..      83      98 .. 0.75
   2 !    7.0   0.1    0.0036         4       3      11 ..     295     304 ..     293     308 .. 0.71
   3 !   11.8   0.2   0.00011      0.12      13      25 ..     316     328 ..     313     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.057
                       zf-ribbon_3  4 rCPnC 8 
                                      rCP+C
  gi|488600141|ref|YP_007906612.1| 85 RCPHC 89
                                      56666 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0036
                       zf-ribbon_3   3 vrCPnCGa.p 11 
                                       ++CP+CG  +
  gi|488600141|ref|YP_007906612.1| 295 TYCPRCGYpV 304
                                       6899999744 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00011
                       zf-ribbon_3  13 ssddnvCpyCGtk 25 
                                       + dd++Cp+CG++
  gi|488600141|ref|YP_007906612.1| 316 DLDDSKCPKCGYE 328
                                       669********96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.1      0.17   1.9e+02       1       6 [.      85      90 ..      84      91 .. 0.78
   2 !   11.0   0.5   0.00025      0.28      13      23 .]     294     304 ..     293     304 .. 0.84
   3 !    9.6   0.1   0.00066      0.74      10      22 ..     316     328 ..     313     329 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.17
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +Cp+C 
  gi|488600141|ref|YP_007906612.1| 85 RCPHCQ 90
                                      699996 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00025
                     zinc_ribbon_2  13 akFCpyCGtpl 23 
                                       +++Cp+CG+p+
  gi|488600141|ref|YP_007906612.1| 294 STYCPRCGYPV 304
                                       789****9985 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00066
                     zinc_ribbon_2  10 qdnakFCpyCGtp 22 
                                       + ++  Cp+CG++
  gi|488600141|ref|YP_007906612.1| 316 DLDDSKCPKCGYE 328
                                       5556667777765 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 ?   -0.2   5.5       1.1   1.2e+03      11      45 ..       7      90 ..       2      96 .. 0.71
   2 !   16.7   0.5   5.8e-06    0.0065      18      47 ..     294     328 ..     287     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                               IBR 11 slesdpnlkwCprpdCeaiiekseg....cks............................................... 38
                                       ++++++++ C    C + ++ ++g    c                                                 
  gi|488600141|ref|YP_007906612.1|  7 LYKKEEKWVTCL--TCMHRCRIKDGewgrCRVrknedgilrvynygqtsaialdpiekkplhnfkpaskvlsfgsvscn 83
                                      456788999**9..9*999999988655422255566777777777777777777777777777777777777776666 PP

                               IBR 39 vtCskCg 45
                                       +C++C+
  gi|488600141|ref|YP_007906612.1| 84 FRCPHCQ 90
                                      6677775 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.8e-06
                               IBR  18 lkwCprpdCeaiiekseg...cks.....vtCskCgfe 47 
                                        ++Cp   C++++ + +g   + +     ++C+kCg+e
  gi|488600141|ref|YP_007906612.1| 294 STYCP--RCGYPVIQRQGfyiE-KidlddSKCPKCGYE 328
                                       68***..9*****999998861.23555599*****98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.4       1.9   2.1e+03      30      38 ..      16      24 ..       8      41 .. 0.68
   2 ?    1.5   0.1      0.28   3.1e+02      30      35 ..      85      90 ..      50      95 .. 0.81
   3 !   16.0   0.4   8.4e-06    0.0094      11      37 ..     293     328 ..     289     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                               DZR 30 rCpsCgekv 38
                                      +C  C + +
  gi|488600141|ref|YP_007906612.1| 16 TCLTCMHRC 24
                                      455554444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.28
                               DZR 30 rCpsCg 35
                                      rCp+C+
  gi|488600141|ref|YP_007906612.1| 85 RCPHCQ 90
                                      566665 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 8.4e-06
                               DZR  11 darfCseCgtklkavaa.........edrCpsCgek 37 
                                       ++ +C++Cg ++ + +            +Cp+Cg++
  gi|488600141|ref|YP_007906612.1| 293 ESTYCPRCGYPVIQRQGfyiekidldDSKCPKCGYE 328
                                       6789*******9966669*******999*****986 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.3e-05     0.037      15      50 ..      63      98 ..      51     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                                      GGGS--SSHHHHHHHHHHHHHEE-TTSSS-BTTT-- CS
                              CcmH 15 eedeelkdpaqeararalseeLRClvCqnqsiadSn 50
                                      ++ +++k +++  ++ ++s ++RC+ Cqn +ia S+
  gi|488600141|ref|YP_007906612.1| 63 KPLHNFKPASKVLSFGSVSCNFRCPHCQNYEIAFSD 98
                                      5666777777788889999*************9987 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       3.1   3.4e+03     520     529 ..      84      93 ..      78     104 .. 0.79
   2 ?   13.5   0.1     2e-05     0.022     476     529 ..     257     329 ..     254     333 .] 0.77

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.1
                                       SB-TTT--BE CS
                              NRDD 520 ekCpkCgsee 529
                                       ++Cp+C++ e
  gi|488600141|ref|YP_007906612.1|  84 FRCPHCQNYE 93 
                                       67****9654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2e-05
                                       BSS--SSHHHHHHHHHHHHHTT--EEEE......E--EEEETT.--..EESS.............SB-TTT--BE CS
                              NRDD 476 ldeekknpealeklvkiakktgigYfsi......npkidvCnecgy..kgei.............ekCpkCgsee 529
                                       ld++ +++++le+  +iak++g+ Y+ +        ++++C++cgy     +              kCpkCg e+
  gi|488600141|ref|YP_007906612.1| 257 LDKPATSIQTLERAYRIAKDAGLEYVYLgnvwghKYESTYCPRCGYpvI--QrqgfyiekidlddSKCPKCGYEQ 329
                                       678889999999999*******9997652112115689********652..4457889*******89*****766 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 ?    1.2   0.1      0.35     4e+02      15      22 ..      82      89 ..      60      96 .. 0.85
   2 ?    1.5   0.0      0.29   3.3e+02      21      32 ..     240     251 ..     239     254 .. 0.89
   3 ?    7.2   0.1    0.0048       5.4      17      27 ..     295     305 ..     285     313 .. 0.83
   4 ?    2.1   0.1      0.19   2.1e+02      18      24 ..     321     327 ..     315     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.35
                          zf-Mss51 15 vdfeCpdC 22
                                       +f Cp+C
  gi|488600141|ref|YP_007906612.1| 82 CNFRCPHC 89
                                      57888887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.29
                          zf-Mss51  21 dCGiptycseeh 32 
                                       d Gip++ s+ h
  gi|488600141|ref|YP_007906612.1| 240 DAGIPVHFSRFH 251
                                       78*******977 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0048
                          zf-Mss51  17 feCpdCGipty 27 
                                         Cp+CG+p+ 
  gi|488600141|ref|YP_007906612.1| 295 TYCPRCGYPVI 305
                                       57*******95 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.19
                          zf-Mss51  18 eCpdCGi 24 
                                       +Cp+CG+
  gi|488600141|ref|YP_007906612.1| 321 KCPKCGY 327
                                       8*****7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.3       2.6   2.9e+03      30      49 ..      16      34 ..       5      40 .. 0.69
   2 ?    0.3   0.4       0.6   6.8e+02      46      54 ..      83      91 ..      77      95 .. 0.82
   3 ?   -1.4   0.0       2.1   2.3e+03      13      29 ..     146     162 ..     140     164 .. 0.84
   4 ?   14.4   0.1   2.4e-05     0.027      24      56 ..     290     329 ..     271     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.6
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkC 49
                                      tC  C ++ +  ++g++ +C
  gi|488600141|ref|YP_007906612.1| 16 TCLTCMHRCRI-KDGEWGRC 34
                                      67777777766.55555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.6
                    OrfB_Zn_ribbon 46 tfkCpnCgf 54
                                      +f+Cp+C+ 
  gi|488600141|ref|YP_007906612.1| 83 NFRCPHCQN 91
                                      699**9986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.1
                    OrfB_Zn_ribbon  13 keyGikveevnpayTSk 29 
                                       k++G  v++v+  y S 
  gi|488600141|ref|YP_007906612.1| 146 KREGLFVVYVSNGYMSR 162
                                       7899*******999776 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 2.4e-05
                    OrfB_Zn_ribbon  24 payTSktCseCgsknke.......alsgrtfkCpnCgfea 56 
                                         y S+ C++Cg+ + +       + + +  kCp+Cg+e 
  gi|488600141|ref|YP_007906612.1| 290 HKYESTYCPRCGYPVIQrqgfyieKIDLDDSKCPKCGYEQ 329
                                       4689*********999999***999999*********986 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 ?   -0.6   0.1         1   1.2e+03       4       8 ..      86      90 ..      83      94 .. 0.79
   2 ?   -2.5   0.0       4.2   4.7e+03       9      19 ..     142     152 ..     141     156 .. 0.72
   3 ?    7.9   0.0    0.0023       2.5       3      16 ..     296     309 ..     294     311 .. 0.90
   4 ?    5.9   0.2      0.01        11       2       8 ..     320     326 ..     319     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1
                                      -SSS- CS
                    zf-C4_Topoisom  4 CPkCg 8 
                                      CP C 
  gi|488600141|ref|YP_007906612.1| 86 CPHCQ 90
                                      99996 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                                       -EEEEEE-SSS CS
                    zf-C4_Topoisom   9 gdLvlkrgkkG 19 
                                       ++Lv+++g + 
  gi|488600141|ref|YP_007906612.1| 142 SELVKREGLFV 152
                                       68999998665 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0023
                                       E-SSS--EEEEEE- CS
                    zf-C4_Topoisom   3 kCPkCggdLvlkrg 16 
                                        CP Cg ++++++g
  gi|488600141|ref|YP_007906612.1| 296 YCPRCGYPVIQRQG 309
                                       7***********98 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.01
                                       EE-SSS- CS
                    zf-C4_Topoisom   2 ekCPkCg 8  
                                        kCPkCg
  gi|488600141|ref|YP_007906612.1| 320 SKCPKCG 326
                                       69****9 PP

>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00029      0.33      31     102 ..     204     271 ..     201     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00029
                                       HHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHC.TTS--HHHHHHHHCSSTTS-HHHHHHHHHHHHHHHS CS
                      Citrate_synt  31 eLaeekssfeevaylLltgelPtkeelkefkeelae.arklpekvlealealpkdahpmavlraavsalsadd 102
                                        L+ ek+ f e +yl++ ge  +++elk+f+e + e ++ +p ++     +++ d ++++  ++++++l+ ++
  gi|488600141|ref|YP_007906612.1| 204 YLV-EKKIFVELTYLIIPGENDNEDELKRFSEWVYElDAGIPVHF----SRFHPDFQILDKPATSIQTLERAY 271
                                       689.7999************************9999777888777....555555556666666666666555 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 ?    7.4   0.4    0.0037       4.1      19      28 ..      84      93 ..      78      99 .. 0.82
   2 ?    7.1   0.1    0.0049       5.5      14      26 ..     287     302 ..     282     311 .. 0.81
   3 ?    4.6   0.0     0.028        31      20      27 ..     321     328 ..     317     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                     Zn_Tnp_IS1595 19 fvCPhCgsrk 28
                                      f+CPhC++ +
  gi|488600141|ref|YP_007906612.1| 84 FRCPHCQNYE 93
                                      89****9865 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0049
                     Zn_Tnp_IS1595  14 rWpng...fvCPhCgs 26 
                                       +W+++     CP+Cg+
  gi|488600141|ref|YP_007906612.1| 287 VWGHKyesTYCPRCGY 302
                                       8999999656*****6 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.028
                     Zn_Tnp_IS1595  20 vCPhCgsr 27 
                                        CP+Cg++
  gi|488600141|ref|YP_007906612.1| 321 KCPKCGYE 328
                                       6*****87 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.067        75       1      11 [.      84      94 ..      84     103 .. 0.82
   2 ?    3.1   0.0     0.059        66      20      27 ..     295     302 ..     290     308 .. 0.78
   3 ?    3.2   0.2     0.054        61       2       8 ..     321     327 ..     320     333 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.067
                                      EEETTTTCEEC CS
                      TF_Zn_Ribbon  1 ykCPnCgstnl 11
                                      ++CP C ++++
  gi|488600141|ref|YP_007906612.1| 84 FRCPHCQNYEI 94
                                      68****99876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.059
                                       EEESSSSB CS
                      TF_Zn_Ribbon  20 lvCtdCGl 27 
                                       ++C++CG+
  gi|488600141|ref|YP_007906612.1| 295 TYCPRCGY 302
                                       57888885 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.054
                                       EETTTTC CS
                      TF_Zn_Ribbon   2 kCPnCgs 8  
                                       kCP+Cg 
  gi|488600141|ref|YP_007906612.1| 321 KCPKCGY 327
                                       7999985 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.077        87      18      26 ..      82      90 ..      73      95 .. 0.79
   2 ?    1.0   0.1      0.39   4.4e+02      15      27 ..     290     302 ..     280     302 .. 0.59
   3 ?    5.7   0.2     0.013        14       3       9 ..     320     326 ..     316     330 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.077
                    PhnA_Zn_Ribbon 18 allvCpeCa 26
                                      +++ Cp+C 
  gi|488600141|ref|YP_007906612.1| 82 CNFRCPHCQ 90
                                      566688885 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.39
                    PhnA_Zn_Ribbon  15 edgallvCpeCah 27 
                                       +  +   Cp C++
  gi|488600141|ref|YP_007906612.1| 290 HKYESTYCPRCGY 302
                                       5555556999985 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.013
                    PhnA_Zn_Ribbon   3 pkCplCa 9  
                                       +kCp+C+
  gi|488600141|ref|YP_007906612.1| 320 SKCPKCG 326
                                       7888886 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 ?   -1.7   1.0       2.7     3e+03       1       5 [.      85      89 ..      85      91 .. 0.77
   2 ?    8.1   0.0    0.0024       2.7       2      14 ..     297     309 ..     296     316 .. 0.87
   3 ?    2.4   0.4      0.15   1.7e+02       1       6 [.     321     326 ..     321     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.7
                    DNA_ligase_ZBD  1 hCPvC 5 
                                      +CP C
  gi|488600141|ref|YP_007906612.1| 85 RCPHC 89
                                      59999 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0024
                    DNA_ligase_ZBD   2 CPvCGsavvReeg 14 
                                       CP CG +v++ +g
  gi|488600141|ref|YP_007906612.1| 297 CPRCGYPVIQRQG 309
                                       *********8776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.15
                    DNA_ligase_ZBD   1 hCPvCG 6  
                                       +CP CG
  gi|488600141|ref|YP_007906612.1| 321 KCPKCG 326
                                       6****9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.3      0.18     2e+02      16      21 ..      85      90 ..      79      91 .. 0.75
   2 ?    2.6   1.4      0.13   1.4e+02      17      22 ..     297     302 ..     294     303 .. 0.86
   3 ?    7.5   0.0    0.0039       4.3      16      23 ..     321     328 ..     313     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                           UPF0547 16 fCphCG 21
                                      +CphC+
  gi|488600141|ref|YP_007906612.1| 85 RCPHCQ 90
                                      489996 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                           UPF0547  17 CphCGy 22 
                                       Cp CGy
  gi|488600141|ref|YP_007906612.1| 297 CPRCGY 302
                                       999998 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0039
                           UPF0547  16 fCphCGyv 23 
                                       +Cp CGy+
  gi|488600141|ref|YP_007906612.1| 321 KCPKCGYE 328
                                       8******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2008.00
//
Query:       gi|488600142|ref|YP_007906613.1|  [L=272]
Description: Tetrahydromethanopterin S-methyltransferase, subunit H [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-65  219.2   0.3    8.5e-65  218.8   0.3    1.0  1  MtrH      Tetrahydromethanopterin S-methyltransferase MtrH su
  ------ inclusion threshold ------
       0.12   11.6   0.0       0.14   11.3   0.0    1.2  1  DUF763    Protein of unknown function (DUF763)


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 !  218.8   0.3   9.5e-69   8.5e-65      20     286 ..       7     257 ..       2     268 .. 0.92

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 9.5e-69
                              MtrH  20 yPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGeteeaivkyidfvadvtdaPlli 96 
                                          vl+g+ify++h+ived  kGifd+++ae+li+ qee++dk     l++vv e +eaivky+dfvad td P+++
  gi|488600142|ref|YP_007906613.1|   7 DRIVLIGSIFYSRHRIVEDPVKGIFDENKAEQLINLQEEMEDKFNITGLLDVVSEGKEAIVKYMDFVADRTDKPFIL 83 
                                       5679************************************************************************* PP

                              MtrH  97 dstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmdptvegklkileegegtaek 173
                                       d    e+++a+ kya+evGl dr+iynsin+    +ei+alke+ ve+ai+++++p  +t   +l +l+      ek
  gi|488600142|ref|YP_007906613.1|  84 DGY-LEARIAGLKYASEVGLVDRIIYNSINTMNTADEIKALKEASVESAIIFCYDPAYTTPFRRLILLT------EK 153
                                       *75.69**********************************************************99986......58 PP

                              MtrH 174 gllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdwlrefkkkekekaaeyevad 250
                                       gll+ ae+ Gi++ l+dv+ t++ s +g  + + l +k+ + +P G g  nv     +l +f k+e +++++ ++  
  gi|488600142|ref|YP_007906613.1| 154 GLLKRAEDIGIKNLLVDVVPTDIKS-LGEVIETLLLIKTTYNYPAGCGPANVS---YYLSDFLKEEIDTTTIVSS-- 224
                                       9**********************99.*************************97...4899****99998883333.. PP

                              MtrH 251 vganlvqvilgsdfvlyGPienakkvfPavamvdil 286
                                          +     l sdf++yGPie a+ +f + ++v+ +
  gi|488600142|ref|YP_007906613.1| 225 ---VNAVSHLFSDFLFYGPIERAEIAFGSAYIVEEV 257
                                       ...333345789*****************9999865 PP

>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.6e-05      0.14     174     231 ..      19      77 ..      15     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.6e-05
                            DUF763 174 lesfveephsgiagekkeeevlnlvskesee.arkaildlvkekpekllkelkelkall 231
                                        +++ve+p +gi  e+k e+ +nl+++  ++ + + +ld+v+e++e ++k++  +++ +
  gi|488600142|ref|YP_007906613.1|  19 RHRIVEDPVKGIFDENKAEQLINLQEEMEDKfNITGLLDVVSEGKEAIVKYMDFVADRT 77 
                                       56799*******************9987766266889************9998776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 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:                        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 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1894.62
//
Query:       gi|488600143|ref|YP_007906614.1|  [L=482]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-199  662.5   5.0   4.8e-199  661.9   5.0    1.2  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 !  661.9   5.0  2.7e-203  4.8e-199       3     496 ..       1     478 [.       1     480 [. 0.99

  Alignments for each domain:
  == domain 1  score: 661.9 bits;  conditional E-value: 2.7e-203
                           DUF2193   3 lyekmidealaaqkadvevikkkrgkefkiedakayvdavkkmkaaegqskevidLhkesvkahyeilksltdtvrP 79 
                                       ++ek+idea++aqk++v++i+++r+++fk+e+a+++v++v++mk++egqs+e+++L+++sv +hye+l sltd+++P
  gi|488600143|ref|YP_007906614.1|   1 MIEKVIDEAISAQKEIVNAIDRYRFSDFKLEHARDFVKSVERMKVSEGQSDEAFQLYRKSVLVHYEALVSLTDSITP 77 
                                       589************************************************************************** PP

                           DUF2193  80 eddpfvehyqtPaileiLyeeDeefrksvekfieaieksealigkeavrrygGfyGptcvvDfalipGstsnvvnki 156
                                        +++f+e++qtP++l+iLye D++fr+sv +f+++++++++++++ea+r+++GfyG+t+++Dfa+ipGst+++++ki
  gi|488600143|ref|YP_007906614.1|  78 FESAFLEWMQTPSTLQILYELDPSFRESVIEFAKMVDECDDILSLEAMRIVNGFYGVTSAKDFAAIPGSTYCIMAKI 154
                                       ***************************************************************************** PP

                           DUF2193 157 lkkvdipeehkkaiLaaksWglntsygiGdefakaieegktlaeavekevealksiyeePveaqaklmdeaglksfd 233
                                        ++++i+++hkkaiL+a+sWgl tsy++G+ef ++++e+k+++ a+e+e++ +ks++ ePv++qa++m+++g++sf+
  gi|488600143|ref|YP_007906614.1| 155 AERTSIDKNHKKAILSANSWGL-TSYIFGNEFLRSFKEKKDFKLALEREKDLMKSMLLEPVKTQAEIMEQFGFRSFR 230
                                       **********************.****************************************************** PP

                           DUF2193 234 vrkymeeykkkmepvvkaalddgvhyanivtvPaycvGDiahhisqstynmckddvvlaiieavtevlestlrkale 310
                                       +++y+++y+++++pvv++a+d+ vh+aniv++P++ vGDi+hhi++++y++c+d+++++++++++++l+s+l ka+e
  gi|488600143|ref|YP_007906614.1| 231 PSDYFTKYMQNFRPVVEQAIDS-VHLANIVMLPTH-VGDIGHHIGWQYYYICRDEINMELLRVHLNLLQSNLIKAYE 305
                                       *********************9.************.***************************************** PP

                           DUF2193 311 k..lkseydvlslatgasaaavekileldgfnaemvvdlltkrfhnyvqlyp.trgaaaeLhnvDflDliyrGekll 384
                                       +  +ks++dv+s+at++sa++++k+le++gf+a+m+v+l+t+rf+ny+q+++ +r++++eLh++DflD+i+rGe+l 
  gi|488600143|ref|YP_007906614.1| 306 NgvIKSVFDVTSTATAISALYLYKLLEDEGFTADMIVRLFTERFYNYIQRKQfERNVVNELHINDFLDFIHRGERLS 382
                                       *99*************************************************9************************ PP

                           DUF2193 385 dkarrakagseeklvpkvkglevdlspieenevlmnpqryayPacaitvrfsalmrlaDyPClLtsepvtatlltni 461
                                       +++r++                ++++++++++vl++p+ ya+P+cait++f+alm++aD+PClL++epv+++ l+n+
  gi|488600143|ref|YP_007906614.1| 383 RDKRMSF---------------IEWDALNSSKVLNSPELYAFPFCAITTKFAALMKFADMPCLLAPEPVSIISLVNA 444
                                       9999666...............99***************************************************** PP

                           DUF2193 462 ialekekaaaParvCknCasaslidarheyCqwke 496
                                       +al++e + + +++Ck Ca+asl+++++ +C++++
  gi|488600143|ref|YP_007906614.1| 445 VALNPEVDLV-SKFCKGCATASLQPNKCLHCMLNQ 478
                                       ********99.9*******************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3208.24
//
Query:       gi|488600144|ref|YP_007906615.1|  [L=87]
Description: hypothetical protein Asulf_00602 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.078   13.0   0.0       0.13   12.3   0.0    1.4  1  MraZ      MraZ protein, putative antitoxin-like


Domain annotation for each model (and alignments):
>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.2e-06      0.13      23      51 ..      56      84 ..      47      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-06
                                      HHHTTSCSEEEEEECCSEEEEEEHHHHHH CS
                              MraZ 23 reeaklekevvviGvsncLeiwpraeWek 51
                                       + a++e + ++++v++cLe++ +a +e+
  gi|488600144|ref|YP_007906615.1| 56 ANNASEEDVTMIKAVKSCLELFTMASFER 84
                                      5789999999***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 518.30
//
Query:       gi|488600145|ref|YP_007906616.1|  [L=175]
Description: hypothetical protein Asulf_00603 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   35.4   0.3    1.3e-08   34.5   0.3    1.5  1  RHH_1         Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.033   14.9   1.5      0.033   14.9   1.5    2.1  2  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.3   1.4e-12   1.3e-08       1      38 [.       4      41 ..       4      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.4e-12
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                      r+si++d++++++L+ l+r+r+++ SelIR+++ + +e
  gi|488600145|ref|YP_007906616.1|  4 RLSISIDDSTKKKLETLKRKREKNTSELIRDLIDFGYE 41
                                      89*******************************98776 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.5   3.7e-06     0.033       3      33 ..       7      39 ..       6      72 .. 0.76
   2 ?   -1.8   0.1      0.61   5.5e+03      57      66 ..     110     119 ..     103     128 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-06
                      VAPB_antitox  3 IsIsdevYekLkklKr.egeSFsdvIerLle.k 33
                                      IsI+d++++kL+ lKr  ++  s++I+ L++  
  gi|488600145|ref|YP_007906616.1|  7 ISIDDSTKKKLETLKRkREKNTSELIRDLIDfG 39
                                      9***********9999657789*******9863 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.61
                      VAPB_antitox  57 iekaskelrk 66 
                                       iek+++ ++k
  gi|488600145|ref|YP_007906616.1| 110 IEKILRYVEK 119
                                       3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1226.40
//
Query:       gi|488600146|ref|YP_007906617.1|  [L=659]
Description: acetyl-coenzyme A synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  334.0   0.0    1.3e-99  333.7   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      1e-32  112.9   1.2      2e-32  112.0   1.2    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    1.5e-12   47.2   2.9    3.9e-12   45.9   2.9    1.8  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.7   0.0  2.1e-103   1.3e-99       2     422 ..      98     531 ..      97     532 .. 0.90

  Alignments for each domain:
  == domain 1  score: 333.7 bits;  conditional E-value: 2.1e-103
                                       HHHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEE CS
                       AMP-binding   2 eeqaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvv 75 
                                       ++qa+ +++k a+++    g+ ++lTY++l+++vnr+A++L+ lG++kgdrV i+lp+ pe+ +a+la++k+Ga+++
  gi|488600146|ref|YP_007906617.1|  98 DKQAKLRKNKLAYIWegePGDIRKLTYHDLYREVNRFANALKDLGIRKGDRVTIWLPMIPELPIAMLACAKIGAIHS 174
                                       7899999**********9999******************************************************** PP

                                       EEETTS-HHHHHHHHHHHTESEEE......E..TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCC CS
                       AMP-binding  76 plnptltaeelayiledseakvli......a..tvdsel.leklleaaakleavklvivldadellkeeelkeeees 143
                                       ++ +++++++l   ++d+eak+li      +  +   ++  ++++++ ++  + + viv+d+ +++   ++  +  +
  gi|488600146|ref|YP_007906617.1| 175 VVFSGFSEKALLDRIQDAEAKLLItadgfyRggK--VIElKSRADQILDQ-TTIENVIVYDRTNINPPMKEGRDHWW 248
                                       ************************9988763432..45545666666664.689999*******9999888888888 PP

                                       SCTT.S-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHH CS
                       AMP-binding 144 eeka.ekpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifgli 218
                                       +++   +++e+e  +++d+++i+YTSGTTGkPKGV++ h +++v ++++l+    f++kedd +++ +++ +i+g++
  gi|488600146|ref|YP_007906617.1| 249 QDVLgSRKCETEIMDANDTLFILYTSGTTGKPKGVIHAHgGYAVGTASTLH--FIFDIKEDDIWWCSADIGWITGHS 323
                                       877653788999***************************556666666653..3388899***************** PP

                                       HHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS- CS
                       AMP-binding 219 lelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggep 294
                                       + ++++l+ Gat v++++ ++ ++p++++e ie+++vtv++++P++++++++ g+++   +++dls lrl+ ++gep
  gi|488600146|ref|YP_007906617.1| 324 YIVYAPLILGATSVMYEGAPThPTPARWWEIIERYGVTVFYTAPTAIRMFMRLGEKY--PQNHDLSTLRLLGTVGEP 398
                                       *********************788****************************77776..4578************** PP

                                       EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEE CS
                       AMP-binding 295 lspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGell 368
                                       ++pe++ ++++  g+   ++++++++TEt++ ++  pl+    k+gs+ kp+pg+++ + D+e++ + +++  G l+
  gi|488600146|ref|YP_007906617.1| 399 INPEAWVWYYKYIGNeqcQIMDTWWQTETGMQMI-SPLPITPLKPGSATKPFPGIDADVFDPEGNSLHGRNAGGYLV 474
                                       **************9******************8.6667777799******************7777778888**** PP

                                       EEET..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 369 vrgp..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                       +++p   + +g ++ +e+   +++s  ++ + TGD +r+d +Gy++i gR++d++++
  gi|488600146|ref|YP_007906617.1| 475 IKKPwpAMLRGLWRAEERYINTYWSAyPNIYFTGDAARVDSEGYFWIQGRLDDVLNV 531
                                       ****667*****************84657*************************987 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   1.2   3.3e-36     2e-32       1      76 []     540     618 ..     540     618 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 3.3e-36
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsalvshpaV+eaaVvG+p+evkGea+vafVvlk+g  + e+l ++Lk+hv+ke+g++a+p++++fv++lpktrs
  gi|488600146|ref|YP_007906617.1| 540 EVESALVSHPAVSEAAVVGKPHEVKGEAIVAFVVLKSGiePsEQLIDDLKQHVAKEIGKIARPDEIYFVPDLPKTRS 616
                                       8***********************************99753355********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|488600146|ref|YP_007906617.1| 617 GK 618
                                       *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 !   45.9   2.9   6.5e-16   3.9e-12       6      53 ..      47      94 ..      42      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 6.5e-16
                                      HHHHH-HHHHHHHHHCC..S--SB--S-SECSTTTCT-EESTT-EE-HHH CS
                            ACAS_N  6 keSiedpeaFWaeqake..ldWekpfdkvldgskgpfikWFeGGklNicy 53
                                      ++  ++ e+FW+e+a+e  ++W++p+++vl++ ++p++kWF ++k Ni +
  gi|488600146|ref|YP_007906617.1| 47 RK-AQNIEWFWSEMAREvsIEWYEPYTQVLEW-NPPYAKWFINAKYNIVH 94
                                      44.4899*********999*************.9*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 4037.92
//
Query:       gi|488600147|ref|YP_007906618.1|  [L=84]
Description: putative solute:sodium symporter small subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-17   61.4   4.9      9e-17   61.2   4.9    1.0  1  DUF4212   Domain of unknown function (DUF4212)
     0.0023   17.7   3.0     0.0031   17.3   3.0    1.2  1  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
      0.072   11.8   0.5      0.085   11.6   0.5    1.0  1  DUF2207   Predicted membrane protein (DUF2207)
       0.12   12.5   0.4       0.16   12.1   0.4    1.1  1  GWT1      GWT1
        5.3    7.2  10.8       0.57   10.2   2.1    2.1  2  DUF2798   Protein of unknown function (DUF2798)


Domain annotation for each model (and alignments):
>> DUF4212  Domain of unknown function (DUF4212)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   4.9   2.5e-20     9e-17       2      75 ..       9      80 ..       8      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 2.5e-20
                           DUF4212  2 kaYwrenlrlililLviWfvvsfglgillaeelntirtflgfplgFwfaaqgsilvfvvlifvYalrmdrlDek 75
                                      ++Yw++ +++++i++++W + +++ +++ +e + +i  f g+p++++ aa  +i++ ++lif+Ya++mdr D++
  gi|488600147|ref|YP_007906618.1|  9 ERYWKRLKKITIIWMLAWTFPAIL-LHIPVEFMRRI-YFNGIPMHWFNAAFLAIVIGIALIFLYAYVMDRTDRE 80
                                      79**********************.77888999999.6**********************************98 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.0   8.7e-07    0.0031      78     133 ..      14      76 ..       7      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.7e-07
                              PAP2  78 krkkig....lvllalillllavlvalsRlylg...vHflsDvlaGlliGialaalayrlvqk 133
                                       + kki+    l +++  +ll + +  + R+y++   +H++++ + +++iGial++l+ +++++
  gi|488600147|ref|YP_007906618.1|  14 RLKKITiiwmLAWTFPAILLHIPVEFMRRIYFNgipMHWFNAAFLAIVIGIALIFLYAYVMDR 76 
                                       3333345667777777777777777888888876779*******************9998765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   2.4e-05     0.085     382     436 ..      11      76 ..       2      81 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                           DUF2207 382 klsalglgliilglilillallllvll..............lvfllilllillliaiivlllfsrllgr 436
                                       ++  l  + ii++l++++ a+ll +++              ++ +++l++++++++i+++++    ++r
  gi|488600147|ref|YP_007906618.1|  11 YWKRLKKITIIWMLAWTFPAILLHIPVefmrriyfngipmhWFNAAFLAIVIGIALIFLYAYV---MDR 76 
                                       344555566666666666666666666677888889988766666666666666665555554...444 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   4.4e-05      0.16      46     106 ..       8      68 ..       2      81 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                              GWT1  46 esketlkllikllllsilllllllllelyvefvSRrlaNlpYvlwvvalnltllllfllie 106
                                       +++++ +l +  +++++++++ ++ll++ vef+ R+ +N   + w  a  l++++ + li 
  gi|488600147|ref|YP_007906618.1|   8 SERYWKRLKKITIIWMLAWTFPAILLHIPVEFMRRIYFNGIPMHWFNAAFLAIVIGIALIF 68 
                                       5677888888889999999999999999999976666665555554444444443333332 PP

>> DUF2798  Protein of unknown function (DUF2798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   2.0     0.056     2e+02      34      51 ..      22      37 ..      15      46 .. 0.69
   2 ?   10.2   2.1   0.00016      0.57      26      54 ..      48      76 ..      39      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.056
                           DUF2798 34 wllAwpvAfpivllvaPl 51
                                      w+lAw+  fp++ll +P+
  gi|488600147|ref|YP_007906618.1| 22 WMLAWT--FPAILLHIPV 37
                                      888887..5666655554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                           DUF2798 26 flsaWlkawllAwpvAfpivllvaPlvrk 54
                                         +W++a +lA ++ + +++l+a+++ +
  gi|488600147|ref|YP_007906618.1| 48 IPMHWFNAAFLAIVIGIALIFLYAYVMDR 76
                                      5689********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 565.60
//
Query:       gi|488600148|ref|YP_007906619.1|  [L=584]
Description: putative sodium:solute symporter, VC_2705 subfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  156.4  31.5      9e-33  113.7  20.3    2.8  3  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   2.4      0.42   7.6e+03     349     387 ..      13      48 ..       6      57 .. 0.51
   2 !  113.7  20.3     5e-37     9e-33       1     252 [.      59     322 ..      59     347 .. 0.86
   3 !   56.8   3.3   9.3e-20   1.7e-15     283     406 .]     385     513 ..     374     513 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 0.42
                               SSF 349 vvislaillavqeeqkgvlklvelafaglasavlavill 387
                                        +i  ai++ v    +   ++ ++a+a+++s ++ vi+ 
  gi|488600148|ref|YP_007906619.1|  13 LMIYFAIVAGVALTGN---TFTASAIAVFGSLFIYVIVA 48 
                                       3344444444444444...44555666666666666654 PP

  == domain 2  score: 113.7 bits;  conditional E-value: 5e-37
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylsk 77 
                                       +++agrs++++++g s+a++ +s+asfv +aGa+a  G++ + + +g +l++ ++ +++a+  r+++ +T+p++++ 
  gi|488600148|ref|YP_007906619.1|  59 FYVAGRSIGSLPIGSSIASNWMSGASFVSMAGAIAVLGYDSMPYIIGWTLGYCIAAFMIAPFIRKSNTYTVPEFVET 135
                                       8**************************************************************************** PP

                               SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlm 154
                                       R  + +i ++++++ l++v +++l ++lv+ +++i   lG+   ++ +l+ a+++l+  +GG ++vv++++ q  ++
  gi|488600148|ref|YP_007906619.1| 136 RASNWSIARVIAVVMLFIVSFTYLVAQLVATGVIIGRFLGMPAVVGAFLGSAIVILFAGTGGWRSVVWVQVTQYWIL 212
                                       ***************************************************************************** PP

                               SSF 155 lvgalilliivllevG........gleslveklkeaapkv.vdllt...pdslkllrdpltalslwlglvlGvaglp 219
                                       + +  i  + + + +G        g+  l+++l + +     + +t    +++      ++ +   + l+lG++glp
  gi|488600148|ref|YP_007906619.1| 213 ITAYWIAFLTAAYIAGifkpwphfGYGDLLNQLEANEIAHgLNAFTepfTKAFGGGTGQINWIFSAICLMLGTVGLP 289
                                       **9998887777766655555555666666655444333333333333333344445566666677899******** PP

                               SSF 220 hilvRflaakdakailkgvlkltivlilvligm 252
                                       h+l  f+ + ++++++ gv  ++++++l+++ +
  gi|488600148|ref|YP_007906619.1| 290 HVLSQFYLVRNVRTARYGVGWGLTFIALLYLTA 322
                                       **************************9999875 PP

  == domain 3  score: 56.8 bits;  conditional E-value: 9.3e-20
                               SSF 283 eLvvkllpnllaGlllav.mlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislailla 358
                                        +    + +++++ ++a+  lAa +st ++ll++     t+D+Yk+++  +  +e+++++v+r++++v+++++ l+ 
  gi|488600148|ref|YP_007906619.1| 385 GMPDMFGLPWFFATIVAIgGLAAALSTANGLLMVMTVGATRDIYKRFINPN-VSERREIWVGRVMLVVLAVISGLAG 460
                                       55555566777777788746*******************************.99*****************998886 PP

                               SSF 359 vqeeq....kg.vlklvelafaglasavlavillalfwkrvneqGAlagliiG 406
                                       + + q    +  v+ lv  af  +++ +++vi+l++fwk +n++G  ag+++G
  gi|488600148|ref|YP_007906619.1| 461 ARALQdptfSKyVALLVGWAFVFATASFTPVIILGIFWKGLNRYGIVAGMVAG 513
                                       6554411123369999999*******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4173.83
//
Query:       gi|488600149|ref|YP_007906620.1|  [L=449]
Description: putative signal-transduction protein containing cAMP-binding and CBS domains [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   76.6   5.7    1.2e-12   48.1   0.2    3.5  3  CBS       CBS domain
    9.2e-21   74.1   0.0    1.9e-20   73.1   0.0    1.5  1  DUF294_C  Putative nucleotidyltransferase substrate binding d
    8.8e-12   45.0   0.0      2e-11   43.8   0.0    1.6  1  DUF294    Putative nucleotidyltransferase DUF294
  ------ inclusion threshold ------
      0.043   14.2   0.0         12    6.3   0.0    3.0  3  DUF3269   Protein of unknown function (DUF3269)
       0.11   12.4   0.9        3.4    7.7   0.3    2.6  2  SpoV      Stage V sporulation protein family


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.2   3.3e-16   1.2e-12       1      56 [.       6      60 ..       6      61 .. 0.93
   2 !   29.1   0.2   2.8e-10     1e-06       1      52 [.      69     121 ..      69     124 .. 0.88
   3 ?   -0.5   0.1      0.49   1.8e+03      17      38 ..     421     445 ..     419     449 .] 0.77

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3.3e-16
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      V+d+ ++++v v+p+t l++++++m +++vs++ VV +++k++Givt++Dl r+++
  gi|488600149|ref|YP_007906620.1|  6 VRDFIRKKLVHVTPETKLRDCAKIMYKENVSSV-VVLKNNKPLGIVTDSDLRRLIA 60
                                      89***********************9999****.6548999************997 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 2.8e-10
                                       HHHH..SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   1 Vgdi..mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       Vg++  m + +v v+ d++++eal +m e+g+ +  V+ ++g + G++t  D++
  gi|488600149|ref|YP_007906620.1|  69 VGSFirMKKGLVAVDADDDVHEALSRMLEHGIKHTVVL-DNGLPSGVITIGDIA 121
                                       667668999**********************9999455.699777*******97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.49
                                       BHHHHHHHHHHHT...SSEEEE.EET CS
                               CBS  17 tleealelmrekg...vsrlPV.Vde 38 
                                       +l e+ ++m+e++   v+r+ V V e
  gi|488600149|ref|YP_007906620.1| 421 SLPEIERKMVENAmkiVRRFQVyV-E 445
                                       688999999988888899998866.3 PP

>> DUF294_C  Putative nucleotidyltransferase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0   5.3e-24   1.9e-20       6     145 .]     324     448 ..     321     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 5.3e-24
                          DUF294_C   6 rlarnalrfkpplglfgrlvtersgehkgelDLKkagifplvdlvRllALeagieatnTleRlkalaeagvlsaela 82 
                                       +l++n+l++kp+++lfg+   e        +D+K +gi+p+   vR+lA+ +gi + nT  R++ la++g + ++la
  gi|488600149|ref|YP_007906620.1| 324 FLVANSLMYKPAITLFGQAAKE--------FDIKARGIAPVEYPVRALAVVNGIYEVNTELRIRSLADNGIIPRDLA 392
                                       6788888888888888885544........*********************************************** PP

                          DUF294_C  83 edlleayefllrlrlrhqleaieageepdnyvdpeeLsklerdlLkealkvvkrlqellklrf 145
                                        +l+ ay++ll ++++ q e         n+v +++L++ er+  ++a+k+v+r+q  +++++
  gi|488600149|ref|YP_007906620.1| 393 HELIMAYNILLAQKIKVQNEG-------RNEVLLSSLPEIERKMVENAMKIVRRFQVYVERNY 448
                                       ***************988764.......489*************************9998876 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   5.6e-15     2e-11      31     137 ..     180     287 ..     160     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 5.6e-15
                            DUF294  31 llrrlielaeeelgkppvpfallvmGSeGReEqtlktDqDnalvled....eeeeaareyfaelaervneaLaalGy 103
                                       +++ +++++++ lg  p+++ + v+GS GR+Eq l tD D+  +++      +e  ++  ++e+ e + + ++++G+
  gi|488600149|ref|YP_007906620.1| 180 VTDTAVRVLADLLGV-PENIVYAVTGSWGRREQYLLTDRDTISIYRLdgegVDELIDEMVYREFIEDLEDCMDEVGF 255
                                       444444444444443.6899999**********************9977655555667788999************* PP

                            DUF294 104 plCpggimasnpewrkslseWkeqfrkwirepep 137
                                       p+Cp+g+  +n  +  s +  ++ + k++++pe+
  gi|488600149|ref|YP_007906620.1| 256 PPCPHGYTSRN--YSYSFEDMQKVILKCCKNPEE 287
                                       ********986..788899999999999988875 PP

>> DUF3269  Protein of unknown function (DUF3269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0033        12      15      52 ..      24      58 ..      12      66 .. 0.82
   2 ?    4.2   0.0     0.016        57      27      49 ..     197     219 ..     192     230 .. 0.89
   3 ?   -2.4   0.0       1.8   6.3e+03      49      66 ..     321     338 ..     310     348 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0033
                           DUF3269 15 edikvikykdnvnevysltgahfsdekkimtdrdlkrf 52
                                       d   i yk+nv  v  l          i+td+dl+r+
  gi|488600149|ref|YP_007906620.1| 24 RDCAKIMYKENVSSVVVLKNN---KPLGIVTDSDLRRL 58
                                      5777899******99999765...45689******996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.016
                           DUF3269  27 nevysltgahfsdekkimtdrdl 49 
                                       n vy++tg+    e+ ++tdrd 
  gi|488600149|ref|YP_007906620.1| 197 NIVYAVTGSWGRREQYLLTDRDT 219
                                       779******************95 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                           DUF3269  49 lkrfkgahgllyeqelgl 66 
                                         rf  a  l+y+  + l
  gi|488600149|ref|YP_007906620.1| 321 KNRFLVANSLMYKPAITL 338
                                       358999999999876654 PP

>> SpoV  Stage V sporulation protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3   0.00095       3.4       3      11 ..     130     138 ..     130     138 .. 0.90
   2 ?    2.2   0.0      0.05   1.8e+02      16      24 ..     144     152 ..     144     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00095
                              SpoV   3 FYTIKLPkF 11 
                                       +YTIKL+++
  gi|488600149|ref|YP_007906620.1| 130 YYTIKLRRA 138
                                       6******96 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.05
                              SpoV  16 VraiLgsFk 24 
                                       Vr iL+sFk
  gi|488600149|ref|YP_007906620.1| 144 VREILESFK 152
                                       9*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.30s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2598.80
//
Query:       gi|488600150|ref|YP_007906621.1|  [L=518]
Description: hypothetical protein Asulf_00608 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-23   81.2  10.3    2.5e-11   43.9   1.7    3.3  3  CBS           CBS domain
      1e-08   35.1   0.0    2.7e-08   33.7   0.0    1.8  2  cNMP_binding  Cyclic nucleotide-binding domain
  ------ inclusion threshold ------
       0.26   11.0   0.5        1.3    8.7   0.2    2.2  2  Prolactin_RP  Prolactin-releasing peptide


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   1.7   4.1e-15   2.5e-11       4      56 ..     148     199 ..     142     200 .. 0.90
   2 !   41.6   0.4   2.1e-14   1.3e-10       1      55 [.     208     261 ..     208     263 .. 0.96
   3 ?   -3.7   0.0       2.8   1.7e+04      16      27 ..     309     320 ..     308     322 .. 0.71

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4.1e-15
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       i ++++v+++ +++l+ a++lmr ++vs++ VV  d+k+vGivt +Dl+r+l 
  gi|488600150|ref|YP_007906621.1| 148 IIRKKPVVCRAEDSLRHAVKLMRANDVSSVVVV-RDEKPVGIVTHSDLVRVLD 199
                                       6899******************7777****778.6888************996 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 2.1e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       Vgd+m+++v  ++ ++++ +a  ++++k++++l VV edg++vG+++ +D+l+ +
  gi|488600150|ref|YP_007906621.1| 208 VGDVMSSPVEAIDSESPVMDAYLKFVSKAINHLAVV-EDGRVVGVISSKDILSRM 261
                                       89**********************************.9**************976 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.8
                                       SBHHHHHHHHHH CS
                               CBS  16 ttleealelmre 27 
                                        t++ +++lm++
  gi|488600150|ref|YP_007906621.1| 309 ITISSIADLMVR 320
                                       578888888865 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   4.6e-12   2.7e-08       4      89 .]      34     110 ..      31     110 .. 0.90
   2 ?   -3.5   0.0       1.9   1.1e+04      19      30 ..     239     250 ..     236     259 .. 0.56

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 4.6e-12
                                       E-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHH CS
                      cNMP_binding   4 fkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprd 80 
                                       +k+g +if++G++ ++ly+v++G+v ++    dg+  +++++++ +++G     + ++ +  ++A++++ +++++ +
  gi|488600150|ref|YP_007906621.1|  34 YKPGKIIFKKGKKLKKLYFVREGKVGIF----DGDD-LIEIVNEDEMIGI----DYSNPAFAARAIEETICFEIELE 101
                                       9**************************5....7766.9**********97....55668999*************** PP

                                       HHHHHHHH- CS
                      cNMP_binding  81 dflellqqd 89 
                                       +++ l++++
  gi|488600150|ref|YP_007906621.1| 102 KVNFLFKRN 110
                                       999998875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                                       EEEEEEES-EEE CS
                      cNMP_binding  19 slyivlsGevrv 30 
                                       +l +v+ G+v  
  gi|488600150|ref|YP_007906621.1| 239 HLAVVEDGRVVG 250
                                       555666666543 PP

>> Prolactin_RP  Prolactin-releasing peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.24   1.4e+03      27      38 ..     335     346 ..     334     351 .. 0.80
   2 ?    8.7   0.2   0.00021       1.3      29      42 ..     487     500 ..     477     503 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.24
                      Prolactin_RP  27 vGRFGkRraalg 38 
                                       +G +G+R + + 
  gi|488600150|ref|YP_007906621.1| 335 IGDYGRREILFP 346
                                       899****98765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00021
                      Prolactin_RP  29 RFGkRraalgdvvk 42 
                                       RFG+Rr +++dvv+
  gi|488600150|ref|YP_007906621.1| 487 RFGRRREKIDDVVR 500
                                       9**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3140.91
//
Query:       gi|488600151|ref|YP_007906622.1|  [L=204]
Description: exonuclease, DNA polymerase III, epsilon subunit family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-26   92.4   0.0    5.3e-26   92.1   0.0    1.1  1  RNase_T         Exonuclease
    1.9e-07   31.2   0.0    6.4e-07   29.5   0.0    1.8  1  DUF5051         3' exoribonuclease, RNase T-like
    0.00053   20.0   0.0     0.0021   18.1   0.0    1.9  1  RNase_H_2       RNase_H superfamily
     0.0099   15.6   0.2        3.1    7.5   0.0    2.9  2  DNA_pol_A_exo1  3'-5' exonuclease
  ------ inclusion threshold ------
      0.075   12.2   0.1        6.3    5.9   0.0    2.7  3  CAF1            CAF1 family ribonuclease


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.0   1.5e-29   5.3e-26       2     165 .]      18     178 ..      17     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 1.5e-29
                                       EEEEEESSSTTCTTS-EEEEEEEEEETTCCEEEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHH CS
                           RNase_T   2 viDlEttgldakekdeiieiaaisidggeneigetfhfyvkptelakltdecteftgitqemldeapsfkevleefk 78 
                                       v+DlEttgl++ +kdeii+ia i ++g +    +  + ++  ++++k + +++ f+gi + +l +ap f++v  e+ 
  gi|488600151|ref|YP_007906622.1|  18 VLDLETTGLNP-KKDEIIAIAMIPMKGLKI---QAKDCFYSLVKSDKFNYKSITFHGICPGDLHNAPRFEDVTGEIL 90 
                                       89*********.8***************95...445566666666667***************************** PP

                                       HHHHHHTCCCETTTCEEEESSHHHHHHHHHHHHHHHHHCSEHCECHHHHHHHHHC......HHHHHHHHHTTCHSSS CS
                           RNase_T  79 ellrklallvahnaafdvgflraadkrilkkevpkrnqfldtlildkatlkelar......tsldklaeklgleedg 149
                                       + l+ +++lv++ + fd+ fl++a++++  ++++  + ++d ++l   +l + ++        ld++++++ ++  g
  gi|488600151|ref|YP_007906622.1|  91 DRLE-GRILVGYATLFDIDFLKRAFRKL-RIKMS-FERYVDVAELEAGIL-RKKGmavsyrLDLDAIMKTYSISIKG 163
                                       ****.9*********************9.88899.888999999844444.333347888899************** PP

                                       STSSHHHHHHHHHHHH CS
                           RNase_T 150 raHrAldDaeataklf 165
                                       r H+Al+Da ata++f
  gi|488600151|ref|YP_007906622.1| 164 R-HNALSDAYATARIF 178
                                       9.***********998 PP

>> DUF5051  3' exoribonuclease, RNase T-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.8e-10   6.4e-07       2     163 ..      16     179 ..      15     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.8e-10
                           DUF5051   2 klmiDiEtlgne.etaelvsIGaVffpetG.......eFyaeidlesdeeagidaetieWWlkqskearaellkdtq 70 
                                       ++++D+Et+g + ++ e+++I+++  p  G        Fy+ ++ ++ + ++            s        +d  
  gi|488600151|ref|YP_007906622.1|  16 YAVLDLETTGLNpKKDEIIAIAMI--PMKGlkiqakdCFYSLVKSDKFN-YK------------SITFHGICPGDLH 77 
                                       5789******999999********..888888888899*****996664.22............3334444446668 PP

                           DUF5051  71 eakslkdalqaleeFlekslkvwangasfDlviLraafell.ipwkywndrdvrtlvala....pelekgeekkrei 142
                                       +a+ ++d+  ++ + le    ++++   fD+  L+ af+ l i++++ ++ dv  l a+          +   ++++
  gi|488600151|ref|YP_007906622.1|  78 NAPRFEDVTGEILDRLE-GRILVGYATLFDIDFLKRAFRKLrIKMSFERYVDVAELEAGIlrkkG----M-AVSYRL 148
                                       9***************5.889******************95588999999999999998854331....3.233333 PP

                           DUF5051 143 pfe..........gvkHnALaDAkhqakavs 163
                                         +          + +HnAL DA + a++++
  gi|488600151|ref|YP_007906622.1| 149 DLDaimktysisiKGRHNALSDAYATARIFQ 179
                                       3333344577778889***********9987 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.9e-07    0.0021       2     102 ..      18     142 ..      17     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.9e-07
                         RNase_H_2   2 ffDiEttGlspkknliyliGvldvdekeiek...ltqllaeepeeekail.............elf......lelle 56 
                                        +D+EttGl+pkk+ i+ i+++ +++ +i+    ++ l+++++   k+i              + f        +  
  gi|488600151|ref|YP_007906622.1|  18 VLDLETTGLNPKKDEIIAIAMIPMKGLKIQAkdcFYSLVKSDKFNYKSITfhgicpgdlhnapR-FedvtgeILDRL 93 
                                       59**********************998887778999****999999999966666666655551.145443333334 PP

                         RNase_H_2  57 kkkalvtfngksFDvpflkrlfkkykldeeefrhiDLlk....elrkkkl 102
                                       + + lv +  + FD++flkr f+k +++    r +D+ +    +lrkk++
  gi|488600151|ref|YP_007906622.1|  94 EGRILVGYA-TLFDIDFLKRAFRKLRIKMSFERYVDVAEleagILRKKGM 142
                                       447899998.899*********8888888444788876533334455555 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 !    7.5   0.0   0.00086       3.1      11      46 ..       5      38 ..       2      50 .. 0.87
   2 !    4.2   0.0    0.0089        32      79     120 ..      97     149 ..      82     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00086
                                      HHHHHHHTTSSEEEEEEEEE-SSSTTSSEEEEEEEE CS
                    DNA_pol_A_exo1 11 eelieelknlkvvavDtEttsldlisatlvliliql 46
                                      e l +el+++++  +D Ett+l++  +++++i i++
  gi|488600151|ref|YP_007906622.1|  5 EVLSSELEEAEYAVLDLETTGLNP--KKDEIIAIAM 38
                                      567899******************..9999998875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0089
                                       EEEESSHHHHHHHHHHH.....HTS--SSEEEH.HHHHHHTTHSTT.....SS CS
                    DNA_pol_A_exo1  79 tkvghnakfDlevlard.....fgielenlfdt.mlaayvldyers.....hs 120
                                       + vg +  fD+++l+r      +++  e+++d+ +l a +l ++        +
  gi|488600151|ref|YP_007906622.1|  97 ILVGYATLFDIDFLKRAfrklrIKMSFERYVDVaELEAGILRKKGMavsyrLD 149
                                       56788888888888888777666777777777777776666555433444444 PP

>> CAF1  CAF1 family ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0018       6.3      13      36 ..       7      28 ..       4      40 .. 0.80
   2 ?    0.1   0.0       0.1   3.7e+02     198     225 ..      85     114 ..      57     118 .. 0.78
   3 ?    2.6   0.0     0.017        62     302     319 .]     161     178 ..     110     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0018
                                      HHHHHHH-SEEEEEEEES-SS--- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                              CAF1 13 ilkaikeasFvAiDlEftGlsege 36
                                      + ++++ea++  +DlE tGl+   
  gi|488600151|ref|YP_007906622.1|  7 LSSELEEAEYAVLDLETTGLN--P 28
                                      56789***************2..2 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.1
                                       HHHHHHHC..--EEEESSTHHHHHHHHHHH CS
                                       xxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                              CAF1 198 vfealvks..rkpiVgHNgllDllflyqtf 225
                                       v  +++ +   +++Vg+  l+D+ fl ++f
  gi|488600151|ref|YP_007906622.1|  85 VTGEILDRleGRILVGYATLFDIDFLKRAF 114
                                       5555554433689**********9998887 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.017
                                       ------HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                              CAF1 302 eesaHeAGyDafmTGlvf 319
                                        ++ H+A  Da+ T+ +f
  gi|488600151|ref|YP_007906622.1| 161 IKGRHNALSDAYATARIF 178
                                       3459***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1258.91
//
Query:       gi|488600152|ref|YP_007906623.1|  [L=232]
Description: siroheme synthase, N-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-20   72.4   0.1      6e-20   71.6   0.1    1.4  1  NAD_binding_7    Putative NAD(P)-binding
    0.00011   22.5   0.5    0.00018   21.7   0.2    1.5  1  TrkA_N           TrkA-N domain
     0.0012   18.2   0.0     0.0022   17.4   0.0    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0012   18.5   0.3     0.0021   17.7   0.3    1.5  1  PrkA             PrkA serine protein kinase C-terminal domain
     0.0074   15.7   0.0      0.016   14.5   0.0    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0096   15.2   0.5      0.089   12.0   0.1    2.1  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.025   14.6   0.1    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.016   15.1   0.4      0.027   14.3   0.1    1.6  2  NAD_binding_10   NAD(P)H-binding
      0.024   14.5   0.2      0.068   13.1   0.2    1.8  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.032   13.8   0.2      0.051   13.1   0.2    1.3  1  NmrA             NmrA-like family
      0.033   13.6   0.0      0.058   12.9   0.0    1.4  1  Sirohm_synth_M   Sirohaem biosynthesis protein central
      0.038   13.4   0.1       0.05   13.1   0.1    1.3  1  adh_short        short chain dehydrogenase
       0.04   13.5   0.1      0.079   12.5   0.1    1.5  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.042   14.4   0.1      0.097   13.3   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.072   12.1   0.1       0.13   11.2   0.1    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      0.075   13.3   0.1       0.16   12.2   0.1    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.13   12.4   0.3        2.1    8.5   0.1    2.1  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.23   10.8   2.0       0.98    8.7   0.4    2.1  2  ThiF             ThiF family


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 !   71.6   0.1     6e-23     6e-20       1     103 [.       5     118 ..       5     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 6e-23
                     NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele........elvklaeee.....lekdlegadl 64 
                                       l++++++k+vl++GgG v++++++k+++aga+v+v++ ++++el+        el+k++        lek le+a +
  gi|488600152|ref|YP_007906623.1|   5 LYIEMSDKNVLIIGGGGVGTSRAKKFISAGANVKVLSLDFSDELKslekenklELIKAS--AydsniLEKLLEWANI 79 
                                       7899***********************************64444455555444444433..1223335899****** PP

                     NAD_binding_7  65 viaatddrelneriaeaakarrilvnvadkpelcdfifp 103
                                       v +at+d  +n+ + + a++++ ++n a+++ ++++++p
  gi|488600152|ref|YP_007906623.1|  80 VTVATEDLGVNDVVKKIARNKKCFLNFANDSRETEVVVP 118
                                       **************************************9 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   1.9e-07   0.00018       1      85 [.      14      99 ..      14     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-07
                                      EEEES-SHHHHHHHHHHHHTT..EEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLsegg..kdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddean 76
                                      ++iiG G vG+s a+++ ++g   +v+  d + + +++l++e+ le ++++a d ++Le++ +e a++v +at+d  +n
  gi|488600152|ref|YP_007906623.1| 14 VLIIGGGGVGTSRAKKFISAGanVKVLSLDFS-DELKSLEKENkLELIKASAYDSNILEKL-LEWANIVTVATEDLGVN 90
                                      68*****************5534235555554.67888887777***************98.9***********99999 PP

                                      HHHHHHHHH CS
                            TrkA_N 77 ilavllake 85
                                       ++ ++a++
  gi|488600152|ref|YP_007906623.1| 91 DVVKKIARN 99
                                      999888885 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 !   17.4   0.0   2.2e-06    0.0022      29      96 ..      12      81 ..       6      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESS.HHHHHHHHH.TTTCECEEHCHHHHHHHHHHHH-SEEE CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvr.parleqles.lgakfvevlksqeellaeavkeadvvi 96
                                       +vl+iGgG +G++ ++   + ga+V+vl ++ ++ l+ le+  + + +++ + +++ l++ ++ a++v 
  gi|488600152|ref|YP_007906623.1| 12 KNVLIIGGGGVGTSRAKKFISAGANVKVLSLDfSDELKSLEKeNKLELIKASAYDSNILEKLLEWANIVT 81
                                      58************************99987733566777776888888888888899999988888874 PP

>> PrkA  PrkA serine protein kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   2.1e-06    0.0021      30      81 ..     131     177 ..     104     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                              PrkA  30 ereGmsGispRyvikilsealssseakeekcinpldvlealeeglkehevis 81 
                                       ++eG+sG+ +R v++ + e+l     k++++i+ l+ +++l++ +k + +++
  gi|488600152|ref|YP_007906623.1| 131 TTEGKSGVVARMVRDSILEMLK----KDDEIISLLKAMDYLKRYMKSE-KVP 177
                                       37******************95....459*****************95.444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.7e-05     0.016      32      98 ..       7      83 ..       2      90 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                      S-GTTSEEEEES-SHHHHHHHHHHHHTT-..EEEEESSSHHHHH........CHHHHTCEECSHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C 32 kelsgktvGiiGlGrIGqavakrlkafgm..kviaydrskkkee........eeeelgvelvsleellaesDivslh 98
                                       e+s+k v iiG G +G++ ak++ + g+  kv+  d s + ++          ++  ++   le+ll+++ iv+++
  gi|488600152|ref|YP_007906623.1|  7 IEMSDKNVLIIGGGGVGTSRAKKFISAGAnvKVLSLDFSDELKSlekenkleLIKASAYDSNILEKLLEWANIVTVA 83
                                      6899******************9986666226666665554322332232322233333445688888888888876 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 !   12.0   0.1   8.9e-05     0.089     161     224 ..       8      76 ..       3     136 .. 0.65
   2 ?    1.2   0.0      0.17   1.7e+02      74     103 ..     154     183 ..     136     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-05
                       Pyr_redox_3 161 kyagqkvvViGgknSavDaAlelvrkgaeVtvvtrg..seiekeesdpsysl...kpdienrleelvke 224
                                       ++++++v++iGg+  +   A +++++ga+V+v+  +  +e+++ e++ + +l   +++  n le+l++ 
  gi|488600152|ref|YP_007906623.1|   8 EMSDKNVLIIGGGGVGTSRAKKFISAGANVKVLSLDfsDELKSLEKENKLELikaSAYDSNILEKLLEW 76 
                                       6899****************************9765113334333333332211145555666665554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
                       Pyr_redox_3  74 keeklsrkealeYlrevaksfelpiklfee 103
                                       ++e +s  +a++Yl++++ks+++p+ l  +
  gi|488600152|ref|YP_007906623.1| 154 DDEIISLLKAMDYLKRYMKSEKVPVDLRMK 183
                                       56667778899*************998766 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.5e-05     0.025       9      84 ..       8      85 ..       4     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                      ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH.HHHHHHHHHHT.ET-..EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtl.erakelaeelkgeei..ealkleelkellaeadvvisata 84
                                      ++++k+vl+iG G +++  ak+++++g++ v v+  ++ +  k+l +e k e i  +a + + l++ll+ a++v +at 
  gi|488600152|ref|YP_007906623.1|  8 EMSDKNVLIIGGGGVGTSRAKKFISAGAN-VKVLSLDFsDELKSLEKENKLELIkaSAYDSNILEKLLEWANIVTVATE 85
                                      5799***********************99.8888776524567777766555440045555669999999999999986 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 ?   14.3   0.1   2.7e-05     0.027       3      72 ..      19      88 ..      18     117 .. 0.85
   2 ?   -2.0   0.0       2.8   2.7e+03     114     114 ..     191     191 ..     130     220 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                      TSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealkgadaVvsalgggg 72
                                       G+vG   +k+ +++g  +v++l  + +++l++le+e++le++++++ d++ l++ l+ a++V +a+   g
  gi|488600152|ref|YP_007906623.1| 19 GGGVGTSRAKKFISAG-ANVKVLSLDfSDELKSLEKENKLELIKASAYDSNILEKLLEWANIVTVATEDLG 88
                                      599************5.999999888799************************************995433 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                       H CS
                    NAD_binding_10 114 k 114
                                       +
  gi|488600152|ref|YP_007906623.1| 191 D 191
                                       1 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   6.8e-05     0.068       2      43 ..      14      56 ..      13     102 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-.HHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis.eealekalekie 43
                                      v +iG G +G++ a+ f+sag +V+++  + ++ l++ +++ +
  gi|488600152|ref|YP_007906623.1| 14 VLIIGGGGVGTSRAKKFISAGANVKVLSLDfSDELKSLEKENK 56
                                      889**********************998851333333333333 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   5.1e-05     0.051       1      73 [.      14      85 ..      14     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                      +l+iG+ G  G s ++ +++ag +v++l  d + el    ke+  el+k++++d ++l+++l+ ++ v ++t+
  gi|488600152|ref|YP_007906623.1| 14 VLIIGGGG-VGTSRAKKFISAGANVKVLSLDFSDELKSLEKENKLELIKASAYDSNILEKLLEWANIVTVATE 85
                                      68888855.8*********************98776666678899**********************999987 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.8e-05     0.058       7      26 ..     129     148 ..     126     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.8e-05
                    Sirohm_synth_M   7 aiSTnGksPrLAaliRreie 26 
                                       a++T Gks + A+++R+ i 
  gi|488600152|ref|YP_007906623.1| 129 AVTTEGKSGVVARMVRDSIL 148
                                       8****************985 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   0.1     5e-05      0.05       1      68 [.      12      80 ..      12     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESC.HHHHHHHHHHHHHTTSEEEEEE-TTT.SHHHHHHHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrs.eekleevakelkeegakalaiqvDvt.dreevealv 68
                                      k vl++G++ G+G   ak+++++Ga+v v++   +++l+ + ke k e  ka a+  ++  +  e+ ++v
  gi|488600152|ref|YP_007906623.1| 12 KNVLIIGGG-GVGTSRAKKFISAGANVKVLSLDfSDELKSLEKENKLELIKASAYDSNILeKLLEWANIV 80
                                      789****98.*****************9955441455655555544444444444444433444455555 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.9e-05     0.079       2      83 ..       9      98 ..       8     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                                      HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-.........HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HH CS
                              IlvN  2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregs.........ksvkkAkeegfevltvaeavkkadvvmiliPDe 71
                                      +++k++ +iG G  G ++a+++  +g +v v   + s         ++++  k+++++   ++++ ++a++v++ + D 
  gi|488600152|ref|YP_007906623.1|  9 MSDKNVLIIGGGGVGTSRAKKFISAGANVKVLSLDFSdelkslekeNKLELIKASAYDSNILEKLLEWANIVTVATEDL 87
                                      689**************************885544332343333334555667778888888999999***99999999 PP

                                      HHHHHHHHHTGG CS
                              IlvN 72 lqkevyeeeiep 83
                                        ++v+ ++i+ 
  gi|488600152|ref|YP_007906623.1| 88 GVNDVV-KKIAR 98
                                      999999.55655 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 ?   13.3   0.1   9.7e-05     0.097       2      81 ..      14      96 ..      13     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.7e-05
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...-EEECECH...HHHHHH-SEEEE-S-HHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...vkvtavdn...eeaaeeadvvvlavkpedv 74
                                      + iiG+G +g + a+++++ag    ++ v +    +++++l++e +   +k++a d    e+++e a++v +a     v
  gi|488600152|ref|YP_007906623.1| 14 VLIIGGGGVGTSRAKKFISAG---ANVKVLSLDFSDELKSLEKENKlelIKASAYDSnilEKLLEWANIVTVATEDLGV 89
                                      569******************...8888776666777888877766556444433321225666677777777777777 PP

                                      HHHHHHC CS
                     F420_oxidored 75 eevlsel 81
                                       +v++++
  gi|488600152|ref|YP_007906623.1| 90 NDVVKKI 96
                                      7777777 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 ?   11.2   0.1   0.00013      0.13       2      86 ..      16      99 ..      15     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                         3Beta_HSD  2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihla...slv 77
                                      ++Gg+G +G +  k++++++   +v+vl l++s+el++ l+k n  ++i++   d + le+ le +++v +     +++
  gi|488600152|ref|YP_007906623.1| 16 IIGGGG-VGTSRAKKFISAGA--NVKVLSLDFSDELKS-LEKENKLELIKASAYDSNILEKLLEWANIVTVATedlGVN 90
                                      788877.9************5..899999999999955.4455555599999999999999999998876643233677 PP

                         3Beta_HSD 78 dvagklted 86
                                      dv +k+ ++
  gi|488600152|ref|YP_007906623.1| 91 DVVKKIARN 99
                                      777766655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016      0.16       1     101 [.      14     108 ..      14     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       vliiG+G+vG + a++    +    ++   d+s+e   + ++  ++ ++e i+  a +    L++ll+ + +v  ++
  gi|488600152|ref|YP_007906623.1|  14 VLIIGGGGVGTSRAKKFISAGAN-VKVLSLDFSDEL--KSLE--KENKLELIKASAYDSNI-LEKLLEWANIVTVAT 84 
                                       89**********99987666654.288888888888..6666..56667777777777775.899***9**999999 PP

                                       SGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCietgvhyvdtsi 101
                                        +   +dv+k  ++++  +++ ++
  gi|488600152|ref|YP_007906623.1|  85 EDLGVNDVVKKIARNKKCFLNFAN 108
                                       999999999999999999999887 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 ?    8.5   0.1    0.0021       2.1       3      79 ..      15      99 ..      13     117 .. 0.82
   2 ?    2.1   0.0      0.19   1.9e+02      51      88 ..     137     179 ..     111     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                                      EEE--SHHHHHHHHHHHHTT-EEEEE-SSHH.HHHHHHHTT....EEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHH CS
                     NAD_binding_2  3 gfiGlGvMGsnmalnllkagykvavynrtke.kveelvaeg....akaaesieelvasl...dvvitmvkagkavdevi 73
                                       +iG G  G++ a+++++ag +v v  ++ + ++++l +e+    +ka +  ++++++l     ++t+ +++  v++v+
  gi|488600152|ref|YP_007906623.1| 15 LIIGGGGVGTSRAKKFISAGANVKVLSLDFSdELKSLEKENklelIKASAYDSNILEKLlewANIVTVATEDLGVNDVV 93
                                      589************************8865055555555599987777777788888888889999999999999999 PP

                                      HSHCCC CS
                     NAD_binding_2 74 egllea 79
                                      ++++++
  gi|488600152|ref|YP_007906623.1| 94 KKIARN 99
                                      998765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.19
                                       HHHHHC..SEEEE-SSSHHHHHHHHHS...HCCC--TT-EEEE CS
                     NAD_binding_2  51 elvasl..dvvitmvkagkavdevieg...llealkkgdilid 88 
                                        +va++  d ++ m+k+++++ ++++    l++++k++++ +d
  gi|488600152|ref|YP_007906623.1| 137 GVVARMvrDSILEMLKKDDEIISLLKAmdyLKRYMKSEKVPVD 179
                                       4555556899999999999999999999999999999998887 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4   0.00098      0.98      17      43 ..      10      36 ..       4      47 .. 0.84
   2 ?    1.3   0.0      0.18   1.8e+02      82     135 ..      49     102 ..      44     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00098
                                      HTSEEEEE--SHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 17 rdskvllvGaGglGsellknLalsGvg 43
                                      +d+ vl++G Gg+G   +k ++ +G  
  gi|488600152|ref|YP_007906623.1| 10 SDKNVLIIGGGGVGTSRAKKFISAGAN 36
                                      6899*******************9965 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.18
                                       HHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  82 qeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgi 135
                                       +++  + ++e ++++  d+++le+lle +++V  a+  + +   v++++++k+ 
  gi|488600152|ref|YP_007906623.1|  49 KSLEKENKLELIKASAYDSNILEKLLEWANIVTVATEDLGVNDVVKKIARNKKC 102
                                       5556666667777777777789999999*********99999999999887763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); 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:                        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: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1248.98
//
Query:       gi|488600153|ref|YP_007906624.1|  [L=318]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-32  109.8   0.0    3.7e-16   59.0   0.0    2.5  2  AsnC_trans_reg2  AsnC-like ligand binding domain
  ------ inclusion threshold ------
       0.13   12.9   0.1        1.2    9.8   0.0    2.2  2  FtsX_ECD         FtsX extracellular domain
       0.15   12.1   0.7         18    5.5   0.1    3.4  3  HTH_19           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 !   48.4   0.0   1.3e-16   7.9e-13       4      82 .]      68     142 ..      65     142 .. 0.90
   2 !   59.0   0.0   6.2e-20   3.7e-16       1      81 [.     229     312 ..     229     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.3e-16
                   AsnC_trans_reg2   4 fkanalvawkvpeerveevaevvaelpevtHcYeRe.wpynlyfmvharseeeveevlaeiaaatgledyevLpstr 79 
                                       ++    v + ++ +rv+eva+++++++   H+Y+R+  +yn++f++  r+ +++++ ++ei +a+g+ dy  Lps+r
  gi|488600153|ref|YP_007906624.1|  68 YA----VLVGAKADRVDEVAAIINSFKP-KHNYLRDcEEYNIWFTIKSRDIDALRAKVEEIVKAAGIADYVFLPSKR 139
                                       55....44455689************87.7*****856*************************************** PP

                   AsnC_trans_reg2  80 efK 82 
                                        +K
  gi|488600153|ref|YP_007906624.1| 140 VYK 142
                                       **9 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 6.2e-20
                   AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledye 73 
                                       k+Gf++n++  +++ e+  + + + v e+pe+tH +eR    +w+y lyfmvha s++++ee+ ++ a+  g+e+++
  gi|488600153|ref|YP_007906624.1| 229 KIGFRENGMNLIRT-EKPKKVALKLVREFPEITHLVERvpdeKWNYPLYFMVHAVSRSSIEEIKSKAAEMPGVEEIR 304
                                       79***********7.55666677899************99877********************************** PP

                   AsnC_trans_reg2  74 vLpstref 81 
                                       +L+s+r++
  gi|488600153|ref|YP_007906624.1| 305 TLYSIRDL 312
                                       ****9986 PP

>> FtsX_ECD  FtsX extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.17     1e+03      70      93 ..     106     129 ..      76     142 .. 0.60
   2 ?    9.8   0.0    0.0002       1.2      43      96 .]     251     303 ..     234     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.17
                          FtsX_ECD  70 fevklkdpekleevaeelkklpgV 93 
                                       f++k +d + l++ +ee+ k +g+
  gi|488600153|ref|YP_007906624.1| 106 FTIKSRDIDALRAKVEEIVKAAGI 129
                                       444555555555555555555554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                          FtsX_ECD  43 efkeqlgednsellegltedeNpLpdsfevklkdpekleevaeelkklpgVeeV 96 
                                       ++ +++  +   l+e + +++   p  f v++ + +++ee++++ +++pgVee+
  gi|488600153|ref|YP_007906624.1| 251 KLVREFP-EITHLVERVPDEKWNYPLYFMVHAVSRSSIEEIKSKAAEMPGVEEI 303
                                       5556666.3677788877777778889*************************96 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.048   2.9e+02      48      65 .]      27      44 ..      19      44 .. 0.89
   2 ?    0.7   0.0     0.091   5.5e+02      20      35 ..     169     184 ..     156     211 .. 0.65
   3 ?    5.5   0.1     0.003        18      24      58 ..     282     316 ..     281     317 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.048
                            HTH_19 48 iaealgidleyllqgede 65
                                      i+e+ g+dl+y l +++e
  gi|488600153|ref|YP_007906624.1| 27 ISEFTGLDLDYVLRKTKE 44
                                      899**********99875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.091
                            HTH_19  20 erlgisrskisaiEng 35 
                                       e+lg+++  ++a+E +
  gi|488600153|ref|YP_007906624.1| 169 EELGVDPELLRALERE 184
                                       4777777777777743 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.003
                            HTH_19  24 isrskisaiEngkkdvpsaelllkiaealgidley 58 
                                       +srs+i +i +   ++p+ e+++ ++ + +++++y
  gi|488600153|ref|YP_007906624.1| 282 VSRSSIEEIKSKAAEMPGVEEIRTLYSIRDLNPNY 316
                                       68**********99************999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1765.26
//
Query:       gi|488600154|ref|YP_007906625.1|  [L=181]
Description: RecB family exonuclease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   33.5   0.0      5e-08   33.2   0.0    1.1  1  Cas_Cas4        Domain of unknown function DUF83
  ------ inclusion threshold ------
      0.022   15.1   0.1      0.037   14.4   0.1    1.4  1  PDDEXK_3        PD-(D/E)XK nuclease superfamily
      0.062   13.2   1.9       0.35   10.8   1.9    1.9  1  PDDEXK_1        PD-(D/E)XK nuclease superfamily
      0.068   12.8   0.2      0.093   12.4   0.2    1.1  1  Lipoprotein_22  Uncharacterised lipoprotein family


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.1e-11     5e-08      34     161 ..      38     175 ..       6     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.1e-11
                          Cas_Cas4  34 Gkllheesyerek.......kevelse...sikiDv..vekekeklvvvEvKkskkk...eeaaklQllyYlllLek 95 
                                       G+ + +++ +++        + +el++    +k D+  ++k++++ +vvEvKk +++   + ++ +Ql  Y   L++
  gi|488600154|ref|YP_007906625.1|  38 GEKIAKDYLKKDYwifptrkRFIELDDfkiVGKADFkvLSKDEKRFEVVEVKKVREIvtpRVEWIAQLNLY---LKM 111
                                       44444433333224444443666665566656666521669999************944444556677655...899 PP

                          Cas_Cas4  96 kgveikeGvleypkekkree..velteelreelekaikeieeiissekppkvkkkkiCkkCayaelCl 161
                                       +g+e+  G l  +  +  ee  v++++ l e+    ++e++e+is+  +p++     C  C+y+ lC+
  gi|488600154|ref|YP_007906625.1| 112 EGIER--GLLLQVGDNIIEErvVHFNDGLYERSIGFYSEVHEYISRGIVPPK--TGNCMGCSYERLCI 175
                                       **986..5777777776666679***********************988875..567**********7 PP

>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   8.2e-06     0.037      64     113 ..      72     129 ..      52     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.2e-06
                          PDDEXK_3  64 Dllv.....eekvivElKaveelke...eheaqllnYlkltklklGlliNFnkkklke 113
                                       D+ v     ++  +vE+K v+e+ +   e  aql  Ylk+ +++ Gll+  + + ++e
  gi|488600154|ref|YP_007906625.1|  72 DFKVlskdeKRFEVVEVKKVREIVTprvEWIAQLNLYLKMEGIERGLLLQVGDNIIEE 129
                                       55555555444459********9872324579*****************998866655 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 ?   10.8   1.9   7.7e-05      0.35     124     254 ..      60     174 ..      16     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.7e-05
                          PDDEXK_1 124 gg.ekvrLkGriDr.vd.dkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrl 197
                                           +++++G+ D  v  ++e+++++++ K  ++   ++   +++   Ql lYl +   +          + l+l++
  gi|488600154|ref|YP_007906625.1|  60 IElDDFKIVGKADFkVLsKDEKRFEVVEVKKVREI-VTP---RVEWIAQLNLYLKMEGIE----------RGLLLQV 122
                                       3334688*******87756666********76633.444...467777*****9987666..........3355666 PP

                          PDDEXK_1 198 eepkvkdeevvkkmalteeel.eallqeleelaeeilagefparpskkCeyCpyksvC 254
                                            +d+ + +++++  + l e+    ++e+ e i +g +p++ + +C  C+y ++C
  gi|488600154|ref|YP_007906625.1| 123 -----GDNIIEERVVHFNDGLyERSIGFYSEVHEYISRGIVPPKTG-NCMGCSYERLC 174
                                       .....34444444444446666777777777777788888888888.58888888888 PP

>> Lipoprotein_22  Uncharacterised lipoprotein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   2.1e-05     0.093      88     148 ..      29      93 ..      22     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                                       S--S-EEETTEEEE..E.--SEEETTS-...-S-SEEEEE-HHHHCT--S-EEEEEEEEESS--T CS
                    Lipoprotein_22  88 eevkqielegkevkvky.egnvviGesr...ayakkivivdDaaynklkaeektlavlkfkkdpk 148
                                       ++ k+i   g+++  +y +++++i  +r      +++ iv +a+++ l+++ek   v+++kk  +
  gi|488600154|ref|YP_007906625.1|  29 SKIKEIGNLGEKIAKDYlKKDYWIFPTRkrfIELDDFKIVGKADFKVLSKDEKRFEVVEVKKVRE 93 
                                       566777667899999999*******9996554589**************************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1066.27
//
Query:       gi|488600155|ref|YP_007906626.1|  [L=1151]
Description: DNA polymerase II large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1318.3   0.4          0 1314.7   0.0    1.9  2  PolC_DP2        DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.021   14.9  15.7        1.2    9.3   9.4    2.9  2  DZR             Double zinc ribbon
      0.046   13.7  12.2        0.5   10.4   7.3    2.4  2  zinc-ribbons_6  zinc-ribbons
       0.97    9.5  12.8       0.94    9.5   3.7    3.5  3  YhfH            YhfH-like protein
          2    8.5  15.0       0.72   10.0   7.9    2.6  2  DUF1272         Protein of unknown function (DUF1272)
          3    8.4   9.1         44    4.7   0.1    2.6  2  zf-CHY          CHY 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 ! 1314.7   0.0         0         0       1     864 []      30     901 ..      30     901 .. 0.98
   2 ?    1.7   0.1     0.015        44     587     673 ..    1033    1126 ..    1023    1149 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1314.7 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirele.kelsreevalkiakei 76 
                                       +Y++ l k++eeay++ae+arskgldp+++vEip+Ak++a+Rvekl+gi+ +a+ri ele + l+re++++kia+ei
  gi|488600155|ref|YP_007906626.1|  30 DYHSLLLKKVEEAYHVAETARSKGLDPERRVEIPVAKNMAERVEKLIGIP-IAKRIEELEeSGLEREKICFKIAEEI 105
                                       5999*********************************************9.********956789************ PP

                          PolC_DP2  77 aegkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaD 153
                                       ++g++g+++  e+a+d a+r a+a+ltegvvaAP+eGia+v +++n dg+++lk+yyaGPiRsaGGtaq++svLv+D
  gi|488600155|ref|YP_007906626.1| 106 IKGEFGKFD-VERALDLAIRSAVAILTEGVVAAPIEGIARVGVGNNYDGSKFLKIYYAGPIRSAGGTAQVISVLVGD 181
                                       *******97.899**************************************************************** PP

                          PolC_DP2 154 yvrkklgldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnr 230
                                       yvr+ +gl+ry p+eeei Ry+eEi lY++va+lqy psdeeirliv+n+pv+idGe+ted+evsg+r+lervetnr
  gi|488600155|ref|YP_007906626.1| 182 YVRRIAGLNRYIPTEEEILRYIEEIPLYKKVANLQYLPSDEEIRLIVSNCPVCIDGEPTEDAEVSGHRNLERVETNR 258
                                       ***************************************************************************** PP

                          PolC_DP2 231 vRGGmllvlaeGialkakKikkkvkklklegWewleelika.ekeekkeeeeekkevkpkekylrdliaGRpvlshp 306
                                       vRGGm+lv+aeGialka+K+kk+v++lkl+gWewl++li++ +k+e+k++++ek+e+kpk+kyl+d++aGRpv+shp
  gi|488600155|ref|YP_007906626.1| 259 VRGGMALVIAEGIALKAPKLKKMVDELKLTGWEWLDKLINKeSKKEEKKDSNEKEEIKPKDKYLSDIVAGRPVFSHP 335
                                       ***************************************9944556667777789********************** PP

                          PolC_DP2 307 srkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddve 383
                                       srkGGfRLrYGR+rn+g+at+gi+Patm+++ +f+a+Gtq+k+erPgKa +vvpv++i+gPtv+lknGdvv+i++++
  gi|488600155|ref|YP_007906626.1| 336 SRKGGFRLRYGRARNSGFATVGINPATMKITGDFIAIGTQMKIERPGKAGGVVPVSTIDGPTVRLKNGDVVKINTIK 412
                                       ***************************************************************************** PP

                          PolC_DP2 384 ealeikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaeekpsaeealelseeldvpLhP 460
                                       +a+ +k++++ ild+GeiL++yG+flennhpL+pasy++eww++e+++  +   + ++++++ea++l++e++vpLhP
  gi|488600155|ref|YP_007906626.1| 413 QAEMYKDRIDAILDIGEILINYGDFLENNHPLLPASYCYEWWREEVKNILHG--DFRNIDEDEAIKLCDEYGVPLHP 487
                                       *********************************************9955544..4579******************* PP

                          PolC_DP2 461 kytylwhdisveelekLaeavaekkkl....eeeklvleleeevkeiLekllvehkvkeekivieealallkslgld 533
                                       ++tylwhdi+ +el +L+++v+ek+k+     ++ l+++l++++k+iLek+l+ehkv+++ iv+e++++++++lgld
  gi|488600155|ref|YP_007906626.1| 488 DHTYLWHDIDLDELIQLRDYVSEKGKIegkyGKSCLIFPLNRDIKTILEKILIEHKVRDGFIVLEKWKVFARCLGLD 564
                                       *************************9999987899****************************************** PP

                          PolC_DP2 534 leeekleke.eekdalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkeaak.k 608
                                        + +k+++  +ekd+le ++ lsgl+vr+kap+rigaRmGRPeK+keR+m+p++h+Lfp+g++gg++r++k+a++ +
  gi|488600155|ref|YP_007906626.1| 565 GSLKKIRDVdREKDVLENIRYLSGLDVRAKAPARIGARMGRPEKAKERRMSPPPHMLFPLGQSGGNTRDLKNAINyM 641
                                       **99998876778**************************************************************63 PP

                          PolC_DP2 609 ......kgeieveiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkell 679
                                             kgeiev++  + C++Cgket++++Ce Cg   ++ ++C++c++  +ee+c++c+ ea+  ++kki+++el+
  gi|488600155|ref|YP_007906626.1| 642 ksynsaKGEIEVDLPVKICERCGKETIWSMCE-CGGFAHQAYYCPRCDRVLKEERCPRCGGEANGFRRKKINVRELY 717
                                       799999**************************.******************************************** PP

                          PolC_DP2 680 ekaleklgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklr 756
                                       ekale+lgere  ++ +kgv glt+k+k++E++eKgilRakh+v+vfkdgt+RyDmtdlplthf+p+eig+s+ekl+
  gi|488600155|ref|YP_007906626.1| 718 EKALENLGERE-VKSAIKGVIGLTNKNKVCERIEKGILRAKHGVFVFKDGTIRYDMTDLPLTHFKPSEIGISIEKLK 793
                                       *********76.8899************************************************************* PP

                          PolC_DP2 757 elGYteDieGkplesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPH 833
                                       elGY+ D++Gkpl++edqivelk+qDi+l++da+ey+l+v++f+D+lL+k+yg+e+fYn+ek edLiG+lviglaPH
  gi|488600155|ref|YP_007906626.1| 794 ELGYSYDYRGKPLTDEDQIVELKPQDIILAKDAGEYMLRVSQFIDELLVKFYGMEPFYNAEKLEDLIGHLVIGLAPH 870
                                       ***************************************************************************** PP

                          PolC_DP2 834 tsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                       tsagvlgRiiGf+++ +gyahPyfHaakRRn
  gi|488600155|ref|YP_007906626.1| 871 TSAGVLGRIIGFADVLAGYAHPYFHAAKRRN 901
                                       ******************************9 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.015
                          PolC_DP2  587 hvLfpigeaggkrrsvkeaak.k.kgei.eveiarrkCkkCgke....tlearCeeCgekteeklvCkkceeeve 654 
                                        + Lf+++e++ ++r +++    +  g++   + ++ +C kC+++     l+ +C +Cg ++  +++ +++++  e
  gi|488600155|ref|YP_007906626.1| 1033 EKLFAVDEHDVAERVITTHFLpDlIGNLrAFSKQEFRCVKCNTKyrrvPLKGKCYKCGGNIILTVHESSIKKYLE 1107
                                        67999999999999999887742544443666777788888775222257789******9999888777777555 PP

                          PolC_DP2  655 eekcekcekeakavkkkki 673 
                                         +k    + ++++++k+++
  gi|488600155|ref|YP_007906626.1| 1108 LSKFLSEKYNVSNYTKQRL 1126
                                        4443333333333333333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   9.4   0.00039       1.2       1      37 [.     660     702 ..     660     705 .. 0.91
   2 ?    7.9   0.4     0.001         3      11      37 ..    1066    1092 ..    1061    1097 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00039
                               DZR   1 CpqCgee..........lppdarfCseCgtklkavaaedrCpsCgek 37 
                                       C +Cg+e            ++a +C++C   lk    e+rCp+Cg +
  gi|488600155|ref|YP_007906626.1| 660 CERCGKEtiwsmcecggFAHQAYYCPRCDRVLK----EERCPRCGGE 702
                                       9999999999999999999**************....9******965 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.001
                               DZR   11 darfCseCgtklkavaaedrCpsCgek 37  
                                        +   C +C+tk ++v+ + +C +Cg  
  gi|488600155|ref|YP_007906626.1| 1066 QEFRCVKCNTKYRRVPLKGKCYKCGGN 1092
                                        5567*********9999*******966 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.3   0.00017       0.5       2      38 ..     659     702 ..     658     708 .. 0.88
   2 ?    5.5   0.2    0.0058        17      14      36 ..    1065    1090 ..    1055    1100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                       --SSS-S--EE-S........SEEE-TTT--EEEEEEE-SSS-S- CS
                    zinc-ribbons_6   2 kCpeCqqelekrg........eqyhCeaCqedlkkealCpeCeqe 38 
                                       +C++C +e+ ++         + y C  C++ l ke  Cp+C+ e
  gi|488600155|ref|YP_007906626.1| 659 ICERCGKETIWSMcecggfahQAYYCPRCDRVL-KEERCPRCGGE 702
                                       6**********999***************9866.5679****976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0058
                                        SSEEE-TTT--EEEEEEE...-SSS- CS
                    zinc-ribbons_6   14 geqyhCeaCqedlkkeal...CpeCe 36  
                                        +++++C +C++++++++l   C +C+
  gi|488600155|ref|YP_007906626.1| 1065 KQEFRCVKCNTKYRRVPLkgkCYKCG 1090
                                        57899999999777765422277776 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.7   0.00031      0.94      10      29 ..     654     674 ..     647     687 .. 0.89
   2 ?   -1.0   0.2      0.61   1.8e+03      15      21 ..     695     701 ..     689     704 .. 0.76
   3 ?    4.2   0.1     0.014        42       8      23 ..    1077    1093 ..    1075    1100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00031
                              YhfH  10 nLPkKkCteCGke.ieEqaec 29 
                                        LP K C  CGke i  ++ec
  gi|488600155|ref|YP_007906626.1| 654 DLPVKICERCGKEtIWSMCEC 674
                                       69**********99******9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.61
                              YhfH  15 kCteCGk 21 
                                        C+ CG 
  gi|488600155|ref|YP_007906626.1| 695 RCPRCGG 701
                                       7****96 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.014
                              YhfH    8 frnLPkK.kCteCGkei 23  
                                        +r+ P K kC +CG +i
  gi|488600155|ref|YP_007906626.1| 1077 YRRVPLKgKCYKCGGNI 1093
                                        899999989*****986 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.9   0.00024      0.72       7      50 ..     659     702 ..     656     707 .. 0.92
   2 ?    1.9   0.6     0.081   2.4e+02      32      52 ..    1070    1094 ..    1065    1096 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                           DUF1272   7 nCecCdkdlppdseearicsyEctFCaeCaeevlenvCPncgGe 50 
                                        Ce+C k+   +  e    ++   +C +C   + e++CP cgGe
  gi|488600155|ref|YP_007906626.1| 659 ICERCGKETIWSMCECGGFAHQAYYCPRCDRVLKEERCPRCGGE 702
                                       5******999999999999**********8888799*******9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.081
                           DUF1272   32 CaeCaeev....lenvCPncgGelv 52  
                                        C++C ++     l++ C  cgG+++
  gi|488600155|ref|YP_007906626.1| 1070 CVKCNTKYrrvpLKGKCYKCGGNII 1094
                                        55554443222589********975 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   5.3     0.016        48      43      73 ..     659     688 ..     646     702 .. 0.78
   2 ?    4.7   0.1     0.015        44      35      62 ..    1061    1091 ..    1050    1111 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                            zf-CHY  43 lcllCeteqekavlCkkCkk.efaeyfCpiCk 73 
                                       +c +C +e ++ ++C+ C+    ++y+Cp C+
  gi|488600155|ref|YP_007906626.1| 659 ICERCGKE-TIWSMCE-CGGfAHQAYYCPRCD 688
                                       58888875.6677777.544488999999997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.015
                            zf-CHY   35 erlevkevlcllCeteqekavl...CkkCkk 62  
                                        + ++++e+ c++C+t+ + + l   C kC+ 
  gi|488600155|ref|YP_007906626.1| 1061 RAFSKQEFRCVKCNTKYRRVPLkgkCYKCGG 1091
                                        5677888999999988754443223888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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):               6  [number of targets reported over threshold]
# CPU time: 0.89u 0.33s 00:00:01.22 Elapsed: 00:00:00.53
# Mc/sec: 6512.99
//
Query:       gi|488600156|ref|YP_007906627.1|  [L=208]
Description: Zn-dependent hydrolase, including glyoxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   76.3   0.3    2.6e-19   70.0   0.3    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0042   17.0   0.0      0.011   15.6   0.0    1.7  2  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.015   14.8   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.3   4.3e-23   2.6e-19       4     197 .]      17     181 ..      15     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 4.3e-23
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       d++n+y+i  d+ +++iD+G+  +++ ++ ++   ++++ dvd v++THlH DH+  +  + ++  +  +   +  +
  gi|488600156|ref|YP_007906627.1|  17 DSSNTYII-RDEVTFIIDPGCYKSFTNLFGLMNNDRIPLSDVDVVFNTHLHKDHCESNSMFLRKGAILAFNIND--R 90 
                                       679*****.6****************************************************999776665554..4 PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SHH CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.age 156
                                       + ++e +                   d d      +  g ++l+++++pgh++g+ ++++ + + l++GD+++ +g 
  gi|488600156|ref|YP_007906627.1|  91 VIRNEKP-------------------DLDVSKIKHYSTGKLDLEFIHTPGHTPGSTCIYINEFDALISGDLVFeNGL 148
                                       4444444...................46999******************************************4444 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        gr+        ++++s +++ ++sl+k+ +l +e+++pgH
  gi|488600156|ref|YP_007906627.1| 149 PGRT--------DLHGSNNRDMIKSLEKIHDLSPELILPGH 181
                                       4444........46*************************** PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.9e-06     0.011       5      57 ..      16      77 ..      14     145 .. 0.64
   2 ?   -1.5   0.0      0.33     2e+03     148     163 .]     166     181 ..     155     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                     Lactamase_B_3  5 lghnsflletagarilvDPf........ka.nlgyeppaeeaDlvlisqaledHahletlkq 57
                                      ++++   +  ++++ ++DP+        ++   + ++p  ++D+v  ++ ++dH++ + +  
  gi|488600156|ref|YP_007906627.1| 16 MDSSNTYIIRDEVTFIIDPGcyksftnlFGlMNNDRIPLSDVDVVFNTHLHKDHCESNSMFL 77
                                      5666666777889999****9988877733455677888****************9987544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.33
                     Lactamase_B_3 148 lelakrLkpklvlPmh 163
                                       le ++ L+p+l+lP h
  gi|488600156|ref|YP_007906627.1| 166 LEKIHDLSPELILPGH 181
                                       6778999******966 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.6e-06     0.015       5      53 ..      32      80 ..      29     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-06
                                      ES--TT.....HHHHHTCGGS--SSS--..SEEEEE-SS--HHHH.GGGGCCCCC CS
                     Lactamase_B_2  5 iDagpd.....lrqqalralqPvelrdelppidaVllthaHyDHl.aglltlrel 53
                                      iD+g       l++ ++        r  l+++d+V+ th H DH+  + ++lr++
  gi|488600156|ref|YP_007906627.1| 32 IDPGCYksftnLFGLMNND------RIPLSDVDVVFNTHLHKDHCeSNSMFLRKG 80
                                      5665554433333332222......344779**************8788888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.54
# Mc/sec: 1165.36
//
Query:       gi|488600157|ref|YP_007906628.1|  [L=250]
Description: putative metal-dependent hydrolases with the TIM-barrel fold [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   57.5   0.0    2.4e-15   56.6   0.0    1.5  1  TatD_DNase    TatD related DNase
     0.0062   15.9   0.0      0.012   15.0   0.0    1.6  1  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.021   14.6   0.0       0.28   10.9   0.0    2.2  1  Amidohydro_2  Amidohydrolase
      0.036   13.5   0.0       0.47    9.8   0.0    2.1  2  PTE           Phosphotriesterase family


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   5.4e-19   2.4e-15       2     254 ..       5     248 ..       4     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.4e-19
                                       EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG.............GGHHHHHHHHTT..TTTEEEEE---GG CS
                        TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtss.............kdskavlelakk.ypnkvyavlGiHPn 64 
                                       D+H+H +        +++l +++e+g+ +v ++   +              + ++ + +  k + +++y+++GiHP 
  gi|488600157|ref|YP_007906628.1|   5 DTHTHSEG-----RSAGELVEMAEKGIVKVNTCAFYPvkplygetmidlfRKLEEFEPYRGKkAGIDIYPAIGIHPR 76 
                                       66666655.....24555555555666666544444455566655555444444555444445999*********** PP

                                       GGGCC.CCHHHHHHHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HH..... CS
                        TatD_DNase  65 evdeasedlleelkelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaee..... 136
                                        + e+ e++  ++  +  +++ ++  iGeiGL          e  +ev+++ql++Ak+++ p +iH+ ++ +     
  gi|488600157|ref|YP_007906628.1|  77 CIPENWEKVKGKILGY--LENARI--IGEIGLET------ANELEREVLKAQLEVAKKFDIPCIIHTPRSNKtevtr 143
                                       ***9888888888777..777777..*******9......457899**********************944444455 PP

                                       HHHHHHHHCG.GCCSEEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEEC CS
                        TatD_DNase 137 dlleilkeaa.eakakvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpk 212
                                       ++l++l+++  +++++v+ H    s e++ ++l ++y+ +l+    + n+k++ e+v++   +r+++ +D  +++  
  gi|488600157|ref|YP_007906628.1| 144 TVLDVLEKVSfPEELAVIDHV---SPETVGEVL-KRYHAGLTVEEGKLNEKQVLEIVESYGAERVMLNSDNGFGSA- 215
                                       9*********88888******...999999999.88999999988899999*******************655554. PP

                                       CCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 213 pyrgkrnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                               +   +y   k  e   ++ e+l ++++eNak++f
  gi|488600157|ref|YP_007906628.1| 216 --------DYLSTYKTVKFLEC-RISKEDLTKTAYENAKKFF 248
                                       ........23333333333332.4567777777777777777 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.6e-06     0.012      81     176 ..      60     158 ..       2     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-06
                                       EESSEGGS.....GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE CS
                      Amidohydro_1  81 ggkvsldr.....gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHa 152
                                       g+k  +d        + + ++++ek+k  +   +   ++ ++  +++ + a ++++e lk+ l++akk d+p  iH+
  gi|488600157|ref|YP_007906628.1|  60 GKKAGIDIypaigIHPRCIPENWEKVKGKI---LGYLENARIIGEIGLETANELEREVLKAQLEVAKKFDIPCIIHT 133
                                       444444446666667788999999998886...66667777779********************************* PP

                                       .TSSCHHHHHHHHHHTTTEEEETTT CS
                      Amidohydro_1 153 .letkgevedaeaafgetiehgthl 176
                                         ++k ev  ++ +  e++ ++  l
  gi|488600157|ref|YP_007906628.1| 134 pRSNKTEVTRTVLDVLEKVSFPEEL 158
                                       9888888877666666444443333 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.3e-05      0.28     230     290 ..     189     249 ..     104     250 .] 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHHHHH-GGGEEEE--..BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHHCT CS
                      Amidohydro_2 230 ppalarlieavgpdrilfGsD..yPhptleaepealalldlvallsdeerekilggNAarlyg 290
                                        + + +++e +g++r++  sD  +   ++  ++++++ l+     s+e++ k +++NA ++++
  gi|488600157|ref|YP_007906628.1| 189 EKQVLEIVESYGAERVMLNSDngFGSADYLSTYKTVKFLECRI--SKEDLTKTAYENAKKFFR 249
                                       5567789999***********7766677788888888888766..****************98 PP

>> PTE  Phosphotriesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00011      0.47     124     171 ..      96     142 ..      89     194 .. 0.80
   2 ?    1.4   0.0     0.038   1.7e+02     251     297 ..     201     248 ..     181     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                                       EEEEEEEE-CTBS-HHHHHHHHHHHHHHHHH---EEEEEGCCTTCHHH CS
                               PTE 124 aGiikeigtsgkltpseekvleavaqahkqtGaPisihtsaslragle 171
                                       a ii+eig ++   ++e+ vl+a  +  k+   P +iht +s ++ + 
  gi|488600157|ref|YP_007906628.1|  96 ARIIGEIGLETA-NELEREVLKAQLEVAKKFDIPCIIHTPRSNKTEVT 142
                                       67999**99864.799***********************999876554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.038
                                       EECCCSCCCCCHH.TTHHHHTHHHHHHHTT--HHHHHHHHTHHHHHHH CS
                               PTE 251 kfralkkelvgya.ydllltdviPklkqrGlteeqldkiLvenPkqil 297
                                         r+++++ +g++  d+l t    k++   +++e+l k   en k+++
  gi|488600157|ref|YP_007906628.1| 201 AERVMLNSDNGFGsADYLSTYKTVKFLECRISKEDLTKTAYENAKKFF 248
                                       457888999999879999999999999999****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1454.60
//
Query:       gi|488600158|ref|YP_007906629.1|  [L=94]
Description: hypothetical protein Asulf_00617 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-28   98.9   0.5    1.6e-28   98.8   0.5    1.0  1  DUF424    Protein of unknown function (DUF424)
  ------ inclusion threshold ------
       0.15   11.6   0.1       0.15   11.6   0.1    1.1  1  DUF1974   Domain of unknown function (DUF1974)


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 !   98.8   0.5   1.8e-32   1.6e-28       1      92 []       4      94 .]       4      94 .] 0.98

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 1.8e-32
                                      EEETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-E CS
                            DUF424  1 yrtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVl 79
                                      yr++ + +lvavcd++++g+t++    ++++se+fyg+e ++eee+ k+L++atiaNi ge+av+la++aG++d+++Vl
  gi|488600158|ref|YP_007906629.1|  4 YRVQRE-VLVAVCDSSIVGNTYRSDGFKIEISEEFYGKEEVGEEEVRKALKSATIANISGEKAVKLAIEAGIIDEENVL 81
                                      789999.************************************************************************ PP

                                      EETTEEEEEEEE- CS
                            DUF424 80 vidgvphaqigkl 92
                                      ++++  haq++ l
  gi|488600158|ref|YP_007906629.1| 82 RVGDCWHAQMVVL 94
                                      **********975 PP

>> DUF1974  Domain of unknown function (DUF1974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.7e-05      0.15     229     269 ..      44      84 ..      30      94 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                           DUF1974 229 lekklkkaikkgklkklkleelleealekgviteeeaelle 269
                                        e+ ++ka k+ ++++ + e+ ++ a+e+g+i+ee++ ++ 
  gi|488600158|ref|YP_007906629.1|  44 GEEEVRKALKSATIANISGEKAVKLAIEAGIIDEENVLRVG 84 
                                       5789******************************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 614.43
//
Query:       gi|488600159|ref|YP_007906630.1|  [L=135]
Description: translation initiation factor 2 subunit beta (aeIF-2b) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-39  132.8   0.3    6.1e-39  132.5   0.3    1.0  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.055   13.1   0.0      0.059   13.0   0.0    1.1  1  DUF2334          Uncharacterized protein conserved in bacteri
        0.1   12.7   0.2       0.93    9.6   0.0    2.1  2  Ribosomal_L18A   Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18
       0.16   12.3   0.0       0.24   11.6   0.0    1.4  1  Poly_export      Polysaccharide biosynthesis/export protein
       0.17   12.3   1.7       0.49   10.8   0.2    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   0.3   1.7e-42   6.1e-39       7     117 .]      21     129 ..      16     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 1.7e-42
                                       SSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHH CS
                      eIF-5_eIF-2B   7 kkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldky 83 
                                       ++er+++p+++v++eg+ +t+i+Nf++i+k Lnr++eh++kyl+k lgt+g + e+gr+il+gkf+++++++ l++y
  gi|488600159|ref|YP_007906630.1|  21 RRERFEIPEVNVQREGN-RTIIKNFSQIVKVLNRSEEHFFKYLVKSLGTAGFL-ESGRVILQGKFTREEIQDELNSY 95 
                                       578**************.***********************************.9********************** PP

                                       HHHHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                      eIF-5_eIF-2B  84 ieeyVlCkeCkspetelekeerllvlkCkaCgak 117
                                       ++eyV+CkeC+ p+te++keer+l+l+C aCgak
  gi|488600159|ref|YP_007906630.1|  96 VKEYVICKECQAPDTEFVKEERVLFLRCLACGAK 129
                                       ********************************85 PP

>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.6e-05     0.059     100     166 ..       4      68 ..       1     101 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                           DUF2334 100 akeriekGieilkklgikpkgFeaPhyaaseetykalkkyfsiiyerykeykgqkegltyipenlgy 166
                                        +e +ek+ +++ ++ i+ + Fe P+  +++e+++ + k+fs i++ ++ ++  ++ ++y+ ++lg 
  gi|488600159|ref|YP_007906630.1|   4 YEELLEKAYAEMPEEVIRRERFEIPEVNVQREGNRTIIKNFSQIVKVLNRSE--EHFFKYLVKSLGT 68 
                                       67899****************************************8877666..8999999988876 PP

>> 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 ?    9.6   0.0   0.00026      0.93      45      92 ..      20      67 ..       4      75 .. 0.85
   2 ?    1.0   0.0      0.12   4.2e+02      56      75 ..      86     105 ..      77     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00026
                                      ..................................TEEEEEEEEEEESS CS
                    Ribosomal_L18A 45 vkkanGeilavkkieekkptkvknygiwlrydsrsgthnfykeyrdlt 92
                                      ++++  ei +v+  +e ++t +kn++ ++++  rs+ h f   +++l 
  gi|488600159|ref|YP_007906630.1| 20 IRRERFEIPEVNVQREGNRTIIKNFSQIVKVLNRSEEHFFKYLVKSLG 67
                                      57777899999999**********************998877776665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                                       .................... CS
                    Ribosomal_L18A  56 kkieekkptkvknygiwlry 75 
                                       ++i+++ +  vk y+i    
  gi|488600159|ref|YP_007906630.1|  86 EEIQDELNSYVKEYVICKEC 105
                                       56777777777777776543 PP

>> Poly_export  Polysaccharide biosynthesis/export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.7e-05      0.24      26      72 ..      42     100 ..       9     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-05
                       Poly_export  26 s...........ssqalqgylVdpdGtIslPllGkikvaGl.tveelreeieeklskyl 72 
                                       +           s++ + +ylV++ Gt  +   G++ ++G+ t+ee+++e+ + +++y+
  gi|488600159|ref|YP_007906630.1|  42 KnfsqivkvlnrSEEHFFKYLVKSLGTAGFLESGRVILQGKfTREEIQDELNSYVKEYV 100
                                       0555555666676788999*********************88999*****999887764 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 ?   10.8   0.2   0.00014      0.49      27      44 ..      93     115 ..      57     120 .. 0.74
   2 ?    1.9   0.1     0.082     3e+02      28      37 ..     120     129 ..     110     135 .] 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                   Lar_restr_allev  27 q.....cvyCadCgastpwfkia 44 
                                             +v+C++C a  ++f  +
  gi|488600159|ref|YP_007906630.1|  93 NsyvkeYVICKECQAPDTEFVKE 115
                                       033445*********65555554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.082
                   Lar_restr_allev  28 cvyCadCgas 37 
                                       +  C  Cga 
  gi|488600159|ref|YP_007906630.1| 120 FLRCLACGAK 129
                                       688*****93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 889.24
//
Query:       gi|488600160|ref|YP_007906631.1|  [L=228]
Description: putative Zn-dependent hydrolases of the beta-lactamase fold protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-28   98.8   0.1    3.8e-28   98.4   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
      8e-27   94.1   0.1      1e-26   93.7   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.2e-12   46.2   0.8    6.7e-12   45.8   0.8    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.084   13.0   0.1       0.15   12.2   0.1    1.3  1  Tox-PL-2       Papain fold toxin 2


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.1   8.4e-32   3.8e-28       1     163 []       2     190 ..       2     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 8.4e-32
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfka...nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee....... 67 
                                       +++wlgh++f le + +++++DPf     ++ ++++++ aDl+++++++ dH   +   +  ++ +vl         
  gi|488600160|ref|YP_007906631.1|   2 KIRWLGHAAFELEAK-KKVIIDPFLTgnpSAPVKAENVVADLIVVTHGHGDHLGDAVEIAKRNDCPVLCIhelsryl 77 
                                       699*********976.78899***6555588899999***************8655433323334443333377777 PP

                     Lactamase_B_3  68 ............geslevggleiravatshdavggser.....genngflleqdgltiyhlGhlahelsseelkelg 127
                                                   g++++v+g++++ v++ h a +++ +     g  +g ++e+dg ++yh G+++  l+++ + el 
  gi|488600160|ref|YP_007906631.1|  78 skkgveavgmniGGTARVKGVSVTMVQALHSADVEEGEeiistGDACGVIVEMDGKRVYHAGDTDVFLDMQLIGELH 154
                                       778888888888999***************776555222466588******************************** PP

                     Lactamase_B_3 128 rvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                       ++Dv+l+P+g+ +t+g + a+++++++kpk+ +Pmh
  gi|488600160|ref|YP_007906631.1| 155 KPDVMLVPIGDWYTMGIKGAVKALELVKPKYAIPMH 190
                                       ***********************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.1   2.3e-30     1e-26       3     201 .]      19     191 ..      17     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 2.3e-30
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       ++iD+++      ++   Pv++ +     d++++th+H DHl ++  ++++   + p+++  +++++l+++      
  gi|488600160|ref|YP_007906631.1|  19 VIIDPFLT---G-NPSA-PVKAEN--VVADLIVVTHGHGDHLGDAVEIAKRN--DCPVLCIHELSRYLSKK------ 80 
                                       67777777...2.4554.665444..599*********************43..499************99...... PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C...TCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHH CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgr...rldrnagdtlGlriegggkrvyyigDtgyip.eeige 152
                                           +v+++ +++g++ +++  g+++t+++a h++     ++   +gd++G+++e +gkrvy++gDt  +   ++  
  gi|488600160|ref|YP_007906631.1|  81 ----GVEAVGMNIGGTARVK--GVSVTMVQALHSADVeegEEIISTGDACGVIVEMDGKRVYHAGDTDVFLdMQLIG 151
                                       ....56799**********9..799************9988888999*********************988445667 PP

                                       HHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 153 rlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       +l+++d++l++i+         +++++ +++av+a++ +++k ++++H+
  gi|488600160|ref|YP_007906631.1| 152 ELHKPDVMLVPIG---------DWYTMGIKGAVKALELVKPKYAIPMHY 191
                                       9999*********.........679***********************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 !   45.8   0.8   1.5e-15   6.7e-12      15     163 ..      16     156 ..      10     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.5e-15
                                       TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHH CS
                       Lactamase_B  15 ggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaa 91 
                                       ++ ++iD+ +++  +        ++ +    d +++TH+H DH G++ +++++ d+pv + +e  ++l + +++   
  gi|488600160|ref|YP_007906631.1|  16 KKKVIIDPFLTGNPSAP------VKAENVVADLIVVTHGHGDHLGDAVEIAKRNDCPVLCIHELSRYLSKKGVEAVG 86 
                                       67889999999999998......5788888899****************************************9999 PP

                                       HHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.... CS
                       Lactamase_B  92 srkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl...t 163
                                       +       g++a+ ++v     +  +  +++ +   + +  +++++ve++g++v  +GD+    +  +i++   +
  gi|488600160|ref|YP_007906631.1|  87 MNI-----GGTARVKGVSVTMVQALHSADVEEGEEIISTGDACGVIVEMDGKRVYHAGDTDVFLDMQLIGElhkP 156
                                       996.....69**************************************************887777776665552 PP

>> Tox-PL-2  Papain fold toxin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.4e-05      0.15      10      80 ..      57     133 ..      50     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                          Tox-PL-2  10 vkrfklleC.veCAaalekyLkeqgisGkrlklktksaedaasf.....ilserlekqaaisenGrHegveveidgl 80 
                                       v+  k  +C v C ++l++yL ++g++   +++  +++ +  s      + s  +e+ + i ++G   gv ve+dg+
  gi|488600160|ref|YP_007906631.1|  57 VEIAKRNDCpVLCIHELSRYLSKKGVEAVGMNIGGTARVKGVSVtmvqaLHSADVEEGEEIISTGDACGVIVEMDGK 133
                                       555566677568**************9888887655554433330000034444455555999************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1718.04
//
Query:       gi|488600161|ref|YP_007906632.1|  [L=85]
Description: hypothetical protein Asulf_00620 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 583.12
//
Query:       gi|488600162|ref|YP_007906633.1|  [L=190]
Description: hypothetical protein Asulf_00621 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-11   43.2   0.0      6e-11   42.5   0.0    1.3  1  DUF429          Protein of unknown function (DUF429)
     0.0034   17.3   0.1       0.39   10.6   0.0    2.1  2  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> DUF429  Protein of unknown function (DUF429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   6.7e-15     6e-11       1     201 [.       8     167 ..       8     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.7e-15
                            DUF429   1 GvDlagcrtgwaavaledgrlrlvdveaeeivaalaallaaaeeaavvaiDaPiglperetggRaaDraarkllarr 77 
                                       G+D    + + ++v+led ++ + d      + +++++++ +  a   ++DaP++ p ++  +R++++++    +r 
  gi|488600162|ref|YP_007906633.1|   8 GID--VGKRASHYVLLED-NAVV-D------MGKFEDVVDLKIRANYAGVDAPLSFP-TSGSYRECEKELI---KR- 69 
                                       777..4445555555554.3444.1......34455555558888************.9***********5...77. PP

                            DUF429  78 gasvfpvparaalaagkglserafgllpklrevdelldarpelrgrvvEvhPeaafvalnggaplakkkktaegrae 154
                                       g++ fp++a+  +       ++  ++  k++   ++l+   e ++ v+Ev+P a    l + ap +kk+ t++ +  
  gi|488600162|ref|YP_007906633.1|  70 GIRLFPPNAN-FF-------RKITHIGMKIA---RFLR---ENGTEVFEVYPYATRKIL-NIAPELKKN-TKSNMRL 130
                                       **********.22.......24466777776...5554...66789********99999.677777776.4444444 PP

                            DUF429 155 Rrellara..iaellleseakkeklvaadDvlDAvacaltArraarGra 201
                                        +e l+++  +               +++D+lD+++ alt + + +Gr 
  gi|488600162|ref|YP_007906633.1| 131 IQEELRKYlnF------------DEFENHDLLDSAISALTVKLFLEGRG 167
                                       44444444342............467899***********999988886 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0024        21       1      18 [.       7      24 ..       7      41 .. 0.80
   2 !   10.6   0.0   4.4e-05      0.39      56     107 ..      85     136 ..      55     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0024
                    DEDD_Tnp_IS110  1 vGiDvakdkhdacvidae 18
                                      +GiDv+k+ ++ ++++++
  gi|488600162|ref|YP_007906633.1|  7 LGIDVGKRASHYVLLEDN 24
                                      5********999999643 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.4e-05
                    DEDD_Tnp_IS110  56 ghygallvaflleagitvvvvnplavkrlrklylrkaKtDakDAkvIAdllr 107
                                       +h+g  ++ fl+e+g +v+ v p+a++++ ++ +  +K+ +   ++I + lr
  gi|488600162|ref|YP_007906633.1|  85 THIGMKIARFLRENGTEVFEVYPYATRKILNIAPELKKNTKSNMRLIQEELR 136
                                       7899999***********************9999999998888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1229.49
//
Query:       gi|488600163|ref|YP_007906634.1|  [L=147]
Description: SSU ribosomal protein S13P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-41  140.2   1.8    5.5e-41  139.9   1.8    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18
     0.0033   17.5   0.1      0.017   15.2   0.0    2.1  2  HHH_2          Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.049   13.9   0.0       0.11   12.7   0.0    1.6  1  HHH_6          Helix-hairpin-helix motif
       0.06   12.1   0.0       0.06   12.1   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
       0.13   12.3   0.1       0.18   11.8   0.1    1.2  1  DUF1451        Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   1.8   1.5e-44   5.5e-41       1     127 [.       9     135 ..       9     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 1.5e-44
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwinrqkdik 77 
                                       Ri++tdidgkkkv++alt+ikGiG r ak i + +++d ++++gel++e ++++++ ve+ +++ +++++nr+kd  
  gi|488600163|ref|YP_007906634.1|   9 RIADTDIDGKKKVVFALTQIKGIGCRVAKSITNYLGIDPNAKLGELDDETVDRLKKFVEEDIEQMPDWMMNRRKDRY 85 
                                       99**********************************************************7777766667******* PP

                     Ribosomal_S13  78 dGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgR 127
                                       +G+d h++++d+++ +  die ++++++yrG+RH +G kvRGQrT++tgR
  gi|488600163|ref|YP_007906634.1|  86 SGRDLHLLSKDVDFARMVDIEMMMRMKCYRGIRHAKGKKVRGQRTRSTGR 135
                                       *************************************************9 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.6e-06     0.017      36      60 ..      24      48 ..       1      51 [. 0.82
   2 ?   -0.7   0.0      0.43   1.5e+03      25      42 ..      58      75 ..      57      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.6e-06
                             HHH_2 36 eLlevddiGeeiAqsivefFenekn 60
                                       L+++++iG ++A+si++++  + n
  gi|488600163|ref|YP_007906634.1| 24 ALTQIKGIGCRVAKSITNYLGIDPN 48
                                      79*****************976665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.43
                             HHH_2 25 sldaLkkasleeLlevdd 42
                                      ++d+Lkk  +e++ + +d
  gi|488600163|ref|YP_007906634.1| 58 TVDRLKKFVEEDIEQMPD 75
                                      7899***99999998765 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.1e-05      0.11      18      44 ..      15      40 ..       2      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                             HHH_6 18 veeedgairlGLaaikglgeaaaeriv 44
                                      ++  +++++++L++ikg+g ++a++i 
  gi|488600163|ref|YP_007906634.1| 15 ID-GKKKVVFALTQIKGIGCRVAKSIT 40
                                      33.4566*****************997 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 ?   12.1   0.0   1.7e-05      0.06     188     243 ..      20      74 ..       1     113 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                                       XXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX CS
                              FbpA 188 dlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqelleele 243
                                       ++v + +++++G++  +a+ +++ +g+d++ ++ el++e+++rl++ ++e +e++ 
  gi|488600163|ref|YP_007906634.1|  20 KVV-FALTQIKGIGCRVAKSITNYLGIDPNAKLGELDDETVDRLKKFVEEDIEQMP 74 
                                       333.4457789**********************************99998887765 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     5e-05      0.18      26      64 ..      49      85 ..      44     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5e-05
                           DUF1451 26 seaeeltkeelelvaeylkrDleeaarsleeskeeleew 64
                                      ++++el++e ++++++++++D+e++ + + +++++    
  gi|488600163|ref|YP_007906634.1| 49 AKLGELDDETVDRLKKFVEEDIEQMPDWMMNRRKD--RY 85
                                      5789**********************999988883..34 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1026.15
//
Query:       gi|488600164|ref|YP_007906635.1|  [L=183]
Description: SSU ribosomal protein S4P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   54.4   0.1    2.5e-14   52.7   0.1    1.9  1  S4            S4 domain
    4.7e-07   30.6   0.8    5.5e-05   24.0   0.4    2.2  2  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
  ------ inclusion threshold ------
      0.065   13.2   0.0       0.11   12.5   0.0    1.4  1  Lum_binding   Lumazine binding 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 !   52.7   0.1   4.2e-18   2.5e-14       1      46 [.     109     154 ..     109     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.2e-18
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                       rRL+++++++gla ++++ArqlI hG++ ++G +v+ p+  V+ ++
  gi|488600164|ref|YP_007906635.1| 109 RRLQTIVFKQGLANTIKQARQLITHGHIAIDGVRVTVPGRLVTKEE 154
                                       8*****************************************9876 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.4   9.3e-09   5.5e-05      27      80 ..       5      60 ..       2      90 .. 0.83
   2 !    5.1   0.0    0.0074        44       9      48 ..     107     170 ..     104     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 9.3e-09
                                      STTTTS.-----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHH CS
                      Ribosomal_S4 27 Gqhgkr.rkklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlq 80
                                        h ++  + + ++ k +l+++ + + +Ygl+ +++++r ++++r++r + +++Ll+
  gi|488600164|ref|YP_007906635.1|  5 KRHRRKyVTPPRPWDKvRLEKEVEYIIKYGLRnKRELWRSQNILRKYR-RVARELLA 60
                                      5555555666789***********************************.*****997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0074
                                       HHCHCTS-STSSS......................S-S-SSTTTTS..-----CHCHHHHHHHH CS
                      Ribosomal_S4   9 llRrvgfklflkg......................reyppGqhgkr..rkklseYgkqlrekqk 48 
                                       l+Rr+++ +f++g                      r + pG   ++  ++k+s Y++    k +
  gi|488600164|ref|YP_007906635.1| 107 LSRRLQTIVFKQGlantikqarqlithghiaidgvRVTVPGRLVTKeeETKISYYQNSPFAKRE 170
                                       689999999999999999999999999999***********774444599***99987666665 PP

>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05      0.11       2      50 ..      87     146 ..      86     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                       S--SEEEEEEEEE.EC.......GCTTEETEES........GGGGG..TTT-EEEETTEEEEEE CS
                       Lum_binding   2 GiVeevgtvesiekee.......kledltielp........elakylvekGdsiavnGvcLTVv 50 
                                       Gi ee +t+ +i + +       +l+++             + a++l+++G  ia++Gv  TV 
  gi|488600164|ref|YP_007906635.1|  87 GILEEGATIDDILNLTvdaflsrRLQTIV---FkqglantiKQARQLITHG-HIAIDGVRVTVP 146
                                       66666666666622223344433222222...13446677789999*****.***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1302.45
//
Query:       gi|488600165|ref|YP_007906636.1|  [L=131]
Description: SSU ribosomal protein S11P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-47  159.0   3.0    5.7e-47  158.7   3.0    1.1  1  Ribosomal_S11    Ribosomal protein S11
  ------ inclusion threshold ------
      0.066   13.6   0.0      0.093   13.1   0.0    1.2  1  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 
       0.13   13.1   0.0        0.2   12.5   0.0    1.4  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   3.0   9.6e-51   5.7e-47       1     110 []       9     127 ..       9     127 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 9.6e-51
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       G+ahi++s+nntiititd++G e++v+++Gg+ vkasr +  Py+a++aa +aaek+++kGi+ v++kv++      
  gi|488600165|ref|YP_007906636.1|   9 GIAHIFSSYNNTIITITDITGSETIVRISGGMIVKASRdEGNPYTAMQAAIRAAEKAMEKGIEGVHIKVRApggnkh 85 
                                       9*************************************99************************************* PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG++aa+ralaraGlkigriedvtPiPhdg+r+p+++r
  gi|488600165|ref|YP_007906636.1|  86 tnPGPGAQAAIRALARAGLKIGRIEDVTPIPHDGTRPPGGKR 127
                                       **************************************9987 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.093      29      89 ..      13      73 ..       7      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                      EEE-SS-EEEEEE-TTT--EEEEECS-SCCCTS-SSSCHHHHHHHHHHHHHHHCHHCHTC- CS
                    Ribosomal_L18p 29 vfrsnrhiyaQviddvkgktlasastlekelklkstknkeaakkvgeliAerakekgiekv 89
                                      +f s ++  + + d + ++t++ +s+       + ++n   a + +   Ae+a+ekgie v
  gi|488600165|ref|YP_007906636.1| 13 IFSSYNNTIITITDITGSETIVRISGGMIVKASRDEGNPYTAMQAAIRAAEKAMEKGIEGV 73
                                      77888999999**************966555578999*********************987 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.4e-05       0.2      43      80 ..      31      68 ..       9      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                      EEEEEECTTEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                   Ribosomal_S30AE 43 evtirlakgkviraeeesedlyaaidlavdklerqlrk 80
                                      e  +r+++g +++a+  + + y+a+ +a+ ++e+ ++k
  gi|488600165|ref|YP_007906636.1| 31 ETIVRISGGMIVKASRDEGNPYTAMQAAIRAAEKAMEK 68
                                      344445578889999999****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 873.79
//
Query:       gi|488600166|ref|YP_007906637.1|  [L=261]
Description: DNA-directed RNA polymerase, subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-29  102.3   0.3    9.9e-29  100.0   0.0    2.1  3  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    7.3e-11   41.4   0.0    1.6e-10   40.3   0.0    1.6  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    5.4e-07   29.7  22.4    4.7e-06   26.7  11.7    2.4  3  Fer4_9         4Fe-4S dicluster domain
    8.8e-07   28.5  15.8     0.0005   19.8   2.1    2.8  3  Fer4           4Fe-4S binding domain
    3.4e-05   24.7  11.2      0.022   15.7   1.0    3.1  3  Fer4_16        4Fe-4S double cluster binding domain
    5.4e-05   23.7  13.1     0.0063   17.1   0.5    2.9  3  Fer4_7         4Fe-4S dicluster domain
    0.00052   20.0  26.7     0.0021   18.0   3.5    3.3  3  Fer4_6         4Fe-4S binding domain
    0.00092   19.3  10.5    0.00092   19.3  10.5    2.2  2  Fer4_10        4Fe-4S dicluster domain
     0.0099   16.3  16.5      0.089   13.3   2.0    2.6  2  Fer4_8         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.058   13.9   2.4      0.058   13.9   2.4    3.2  3  Fer4_4         4Fe-4S binding domain
      0.062   13.8   4.7        4.4    7.9   0.7    2.5  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I


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 !  100.0   0.0     6e-32   9.9e-29       1     112 []      43     151 ..      43     151 .. 0.94
   2 ?   -1.4   0.4       1.9   3.1e+03      24      24 ..     190     190 ..     161     217 .. 0.52
   3 ?   -0.7   0.2       1.1   1.8e+03      34      54 ..     195     217 ..     184     254 .. 0.70

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 6e-32
                                       EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCE CS
                     RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadve 77 
                                       V ++ nts+l+DE++aHr+glip++++ +++  ++  ++v    eg+++++v+l+Ln++gp+ v++gd+ +ed+++ 
  gi|488600166|ref|YP_007906637.1|  43 VDFYLNTSYLYDEILAHRIGLIPIKTDLQRF--NFQDKCV-CGGEGCPNCQVSLRLNIEGPKVVYSGDFISEDPEIV 116
                                       67899********************888777..8888886.368********************************* PP

                                       ESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  78 ivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       +v ++i++++L kgq++ +ea ++ G+Gkeh+k++
  gi|488600166|ref|YP_007906637.1| 117 PVFDNIPVVELDKGQQIMIEAVARLGTGKEHVKWQ 151
                                       **********************************6 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                                       C CS
                     RNA_pol_A_bac  24 l 24 
                                       +
  gi|488600166|ref|YP_007906637.1| 190 G 190
                                       1 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                                       HHHCTT-..ETSSSSTTCSEEEE CS
                     RNA_pol_A_bac  34 lnlkelv..eeeeegeeeksvel 54 
                                       +n+ e+   +e+ + +ee+ +e+
  gi|488600166|ref|YP_007906637.1| 195 ENVLECSmcMECVNVCEENAIEI 217
                                       34444543346777777775544 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 !   40.3   0.0   9.8e-14   1.6e-10       8      68 ..      20     249 ..      15     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 9.8e-14
                                       xxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                         RNA_pol_L   8 dhtlgNaLRrillsevpgvaiea...................................................... 30 
                                       +++++N+LRr + s vp++a++                                                       
  gi|488600166|ref|YP_007906637.1|  20 STAFANSLRRAMKSLVPTLAVDYvdfylntsylydeilahriglipiktdlqrfnfqdkcvcggegcpncqvslrln 96 
                                       789********************************************999999999999999999999999999999 PP

                                       .......................................................xx.................... RF
                         RNA_pol_L  31 .......................................................pv.................... 32 
                                                                                              pv                    
  gi|488600166|ref|YP_007906637.1|  97 iegpkvvysgdfisedpeivpvfdnipvveldkgqqimieavarlgtgkehvkwqPVslcgyrivpeinitencklc 173
                                       99999999999999999999888888777666666666666666666666666661155555555555555555555 PP

                                       .................................xxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  33 .................................vkvn.........tdkdklilevetdgslkPeealkeAlkiLke 67 
                                                                        v  n         ++ +++ +  e +g+l+++ +l+eAlki+k+
  gi|488600166|ref|YP_007906637.1| 174 mecidacprnvfsvvegklsaenvlecsmcmecV--NvceenaieiKETNNFLFIAEGTGALPVRTVLEEALKIIKR 248
                                       5555656656666666655555555555555442..1557777888999***************************9 PP

                                       x RF
                         RNA_pol_L  68 k 68 
                                       k
  gi|488600166|ref|YP_007906637.1| 249 K 249
                                       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 ?   -0.8   0.4       1.1   1.8e+03      35      36 ..      85      86 ..      60      93 .. 0.59
   2 !   16.0   2.9   6.2e-06      0.01      33      49 ..     161     183 ..     129     185 .. 0.74
   3 !   26.7  11.7   2.9e-09   4.7e-06       1      51 []     169     215 ..     169     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                            Fer4_9 35 aC 36
                                       C
  gi|488600166|ref|YP_007906637.1| 85 GC 86
                                      12 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.2e-06
                            Fer4_9  33 e......eaCigCgaCveaCpkg 49 
                                              e+C  C++C++aCp++
  gi|488600166|ref|YP_007906637.1| 161 VpeinitENCKLCMECIDACPRN 183
                                       044444568************98 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 2.9e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C  C +C++aCp +v++  +++  a++      +C +C++Cv++C+++ai
  gi|488600166|ref|YP_007906637.1| 169 NCKLCMECIDACPRNVFSVVEGKLSAENVL----ECSMCMECVNVCEENAI 215
                                       59**********************999987....5************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   0.1       6.2     1e+04       6       9 ..      77      80 ..      76      80 .. 0.76
   2 !   19.8   2.1   3.1e-07    0.0005       5      22 ..     167     184 ..     164     186 .. 0.90
   3 !   16.5   2.9   3.4e-06    0.0055       7      24 .]     199     216 ..     196     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.2
                                      TTSS CS
                              Fer4  6 ekCi 9 
                                      +kC+
  gi|488600166|ref|YP_007906637.1| 77 DKCV 80
                                      8997 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3.1e-07
                                       TTTSSS-THHHHHSTTTE CS
                              Fer4   5 eekCigCGaCvevCPvgA 22 
                                       +e C  C++C+++CP ++
  gi|488600166|ref|YP_007906637.1| 167 TENCKLCMECIDACPRNV 184
                                       799************997 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 3.4e-06
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                        C  C++Cv+vC  +AI+
  gi|488600166|ref|YP_007906637.1| 199 ECSMCMECVNVCEENAIE 216
                                       6****************6 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2       1.1   1.8e+03      49      61 ..      74      90 ..      54      92 .. 0.72
   2 !   15.7   1.0   1.4e-05     0.022       1      20 [.     169     188 ..     169     197 .. 0.83
   3 !   14.8   0.3   2.5e-05     0.041       2      22 ..     200     220 ..     199     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                           Fer4_16 49 kkqeai....tgCdiCq 61
                                      + q ++     gC +Cq
  gi|488600166|ref|YP_007906637.1| 74 NFQDKCvcggEGCPNCQ 90
                                      44444555778999998 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C+ C +C+++CP n+++  
  gi|488600166|ref|YP_007906637.1| 169 NCKLCMECIDACPRNVFSVV 188
                                       6**************98765 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.5e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C  C +C++vC +nai+ k+ 
  gi|488600166|ref|YP_007906637.1| 200 CSMCMECVNVCEENAIEIKET 220
                                       9***************98854 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.1       2.6   4.2e+03      36      45 ..      77      90 ..      68      92 .. 0.66
   2 !   15.0   0.4   1.7e-05     0.028      36      52 .]     168     184 ..     129     194 .. 0.78
   3 !   17.1   0.5   3.9e-06    0.0063       2      23 ..     200     221 ..     199     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                            Fer4_7 36 ekCl....gCgaCv 45
                                      +kC+    gC +C+
  gi|488600166|ref|YP_007906637.1| 77 DKCVcggeGCPNCQ 90
                                      55554444566665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.7e-05
                            Fer4_7  36 ekClgCgaCvavCPtga 52 
                                       e+C  C +C+++CP ++
  gi|488600166|ref|YP_007906637.1| 168 ENCKLCMECIDACPRNV 184
                                       56666666666666653 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 3.9e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeee 23 
                                       C  C  Cv++C  +aie++e +
  gi|488600166|ref|YP_007906637.1| 200 CSMCMECVNVCEENAIEIKETN 221
                                       99****************9875 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   2.4       1.6   2.6e+03       6      15 ..      76      89 ..      72      91 .. 0.78
   2 !   18.0   3.5   1.3e-06    0.0021       2      23 ..     162     184 ..     161     185 .. 0.85
   3 !   14.5   5.2   1.7e-05     0.027       9      24 .]     200     215 ..     200     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                            Fer4_6  6 pdkCi....gCgdC 15
                                      +dkC+    gC +C
  gi|488600166|ref|YP_007906637.1| 76 QDKCVcggeGCPNC 89
                                      899*9998888666 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.3e-06
                            Fer4_6   2 veid.pdkCigCgdCvrvCPega 23 
                                       +ei+  ++C  C++C+++CP ++
  gi|488600166|ref|YP_007906637.1| 162 PEINiTENCKLCMECIDACPRNV 184
                                       6777789*************776 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1.7e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C  C++Cv+vC e+ai
  gi|488600166|ref|YP_007906637.1| 200 CSMCMECVNVCEENAI 215
                                       99*************8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   2.3       4.1   6.8e+03       9      16 ..      81      90 ..      74      92 .. 0.58
   2 !   19.3  10.5   5.7e-07   0.00092       6      55 ..     167     210 ..     163     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.1
                           Fer4_10  9 C..irCgkCv 16
                                      C   +C +C+
  gi|488600166|ref|YP_007906637.1| 81 CggEGCPNCQ 90
                                      3434677776 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 5.7e-07
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaC 55 
                                       ++ C  C +C +aCP        + +   e++ +  +v +C +c +Cv +C
  gi|488600166|ref|YP_007906637.1| 167 TENCKLCMECIDACPR-------NVFSVVEGKLSAeNVLECSMCMECVNVC 210
                                       578*************.......77777777777669************** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   6.9    0.0022       3.5      44      65 .]     151     184 ..      77     184 .. 0.70
   2 !   13.3   2.0   5.5e-05     0.089      45      64 ..     194     213 ..     186     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                            Fer4_8  44 e............eealwsCttcgaCtevCpvgi 65 
                                       +             ++ ++C  c++C ++Cp ++
  gi|488600166|ref|YP_007906637.1| 151 QpvslcgyrivpeINITENCKLCMECIDACPRNV 184
                                       144556666666678999*************986 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.5e-05
                            Fer4_8  45 eealwsCttcgaCtevCpvg 64 
                                       +e++ +C++c++C++vC ++
  gi|488600166|ref|YP_007906637.1| 194 AENVLECSMCMECVNVCEEN 213
                                       67899************986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   4.2       1.7   2.7e+03       1      10 [.      76      89 ..      76      92 .. 0.87
   2 ?   13.9   2.4   3.6e-05     0.058       2      16 ..     168     182 ..     167     186 .. 0.91
   3 ?   10.9   1.1   0.00032      0.53       4      15 ..     200     211 ..     195     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                            Fer4_4  1 qerCi....gCgsC 10
                                      q++C+    gC+ C
  gi|488600166|ref|YP_007906637.1| 76 QDKCVcggeGCPNC 89
                                      799*99999**999 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.6e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C  C+ C++aCP 
  gi|488600166|ref|YP_007906637.1| 168 ENCKLCMECIDACPR 182
                                       89************6 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00032
                            Fer4_4   4 CigCgsCvaaCP 15 
                                       C  C+ Cv++C+
  gi|488600166|ref|YP_007906637.1| 200 CSMCMECVNVCE 211
                                       999********8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.7    0.0027       4.4       4      20 ..     168     185 ..     164     194 .. 0.79
   2 ?    7.2   0.2    0.0046       7.6       5      18 ..     199     212 ..     196     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0027
                           Fer4_13   4 dtCiacgaCvelaP.dvF 20 
                                       ++C  c+ C +++P +vF
  gi|488600166|ref|YP_007906637.1| 168 ENCKLCMECIDACPrNVF 185
                                       89************4456 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0046
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                       +C+ c+ Cv+++ +
  gi|488600166|ref|YP_007906637.1| 199 ECSMCMECVNVCEE 212
                                       7***********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); 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: 00:00:00.40
# Mc/sec: 1979.60
//
Query:       gi|488600167|ref|YP_007906638.1|  [L=415]
Description: Kef-type K+ transport systems, membrane component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-60  205.2  41.2    1.7e-60  204.8  41.2    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.8  41.2   9.5e-65   1.7e-60       2     379 ..      16     396 ..      14     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 204.8 bits;  conditional E-value: 9.5e-65
                                       HHHHHHHHHHHH.HHHHTTSXHHHHHHHHHHHHTTTTTS...............HHHCHCCHHHHCHHCCHHHHCTC CS
                    Na_H_Exchanger   2 vllillallvgl.larrlklpeivgliiaGlllGpsglg..l.ieps.......eedlevlselglilllFlaGlel 67 
                                       ++li+ a ++g  + +r+k+p ++g+++aG+++Gp+ lg  + i+p          d+++++++ +illlF aGle+
  gi|488600167|ref|YP_007906638.1|  16 IILIS-AKIFGEiVENRFKQPAVLGELLAGMVIGPFALGpyIgIHPVpgaplpiPPDVDMIANISVILLLFVAGLET 91 
                                       34444.555555269************************8755777799999999********************** PP

                                       GCCTGCCTHHHHHHHHHHHHHHHHHHHHHHHH.HHT.XTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCC CS
                    Na_H_Exchanger  68 dlrelrknlksilllallgvlitvvliGlllyllli.lgiplleallfgailsatdpvvvlailkeegrvperlgtl 143
                                       d++++++ +  + l++  g++++++l G+l+  l+   +  ++++l+ ga+l+at++++++++l ++g++ +  g++
  gi|488600167|ref|YP_007906638.1|  92 DIEKFLRFGLISGLVGAMGIVLPFFL-GFLAIELFYdAPNKFAAGLFTGAALTATSVGITARVLNDLGKLTTPEGST 167
                                       **************************.**999875557789************************************ PP

                                       HHHHHHHHHHHCCCCCHHHHHHTX..XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHH CS
                    Na_H_Exchanger 144 llgesvlnDavavvllavllalak..eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevll 218
                                       +lg++v++D++++++la+++a+ +  +ea  ++++++ ++i++v+ +g+++lgl +    ++i+ ++ + + +++ +
  gi|488600167|ref|YP_007906638.1| 168 ILGAAVIDDVLGILVLAIVVAITGveGEAMSTFEIAKTIVIAVVFWIGVIFLGLKFVDQISRILSMF-KMPGSQLTV 243
                                       ***********************99988888888888888888888888888887776666666665.9******** PP

                                       HHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHH CS
                    Na_H_Exchanger 219 vlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlil 295
                                       ++++ l++++la+l+++  i+ga +aGl+ls ++++  l+e++ ++   +++p+fFv +G+ +d+k +   ++  +l
  gi|488600167|ref|YP_007906638.1| 244 AIAFGLMISYLASLVKLAPIIGAYAAGLALSASAHRDFLAERMIPIY-EFLVPIFFVAMGMLVDVKRI---PEIALL 316
                                       *******************************9999999*********.9***************9999...899999 PP

                                       HHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHH CS
                    Na_H_Exchanger 296 vllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqG 372
                                        ++i+v+ ++g++ + ++++++ g++ + a  ig+g+++rg+v l++a  g + g+++++ y++++v+ ++t+    
  gi|488600167|ref|YP_007906638.1| 317 GVVIIVFAIIGKFFGCYVAAYFGGFNKHGASRIGIGMVPRGEVGLIVAYYGLKYGVIDEHIYTIAVVMSFVTTM--- 390
                                       999999999****************************************************************9... PP

                                       HHHHHHH CS
                    Na_H_Exchanger 373 lslkpll 379
                                        +++pll
  gi|488600167|ref|YP_007906638.1| 391 -ITPPLL 396
                                       .344443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); 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:                         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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2502.37
//
Query:       gi|488600168|ref|YP_007906639.1|  [L=101]
Description: hypothetical protein Asulf_00627 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-14   52.4   4.0    5.1e-14   52.1   4.0    1.1  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   4.0   2.8e-18   5.1e-14       5      75 ..       4      75 ..       1      79 [. 0.93

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 2.8e-18
                                      CS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.......-EEEEEGG.CEECCCTEEEETTS CS
                               PRC  5 rasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi..gekevliPfdlavkigkdriivdap 75
                                      ++s l G++Vyt++G+++GkV+Dvvid +   + +l + + ++  i  +   v+iP++  vk+++d+i+++ +
  gi|488600168|ref|YP_007906639.1|  4 EISTLFGLKVYTDEGRYVGKVNDVVIDVEHRVIKGLAIVDYNKSLIesKAPGVIIPYR-FVKSVNDIILIKDI 75
                                      689**************************************99655************.***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1384  (0.0771934); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 645.92
//
Query:       gi|488600169|ref|YP_007906640.1|  [L=125]
Description: LSU ribosomal protein L18AE [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   54.6   0.1      1e-14   54.4   0.1    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    9.7e-11   42.5   0.2    1.6e-10   41.8   0.2    1.4  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.077   12.8   0.2       0.11   12.3   0.2    1.2  1  TIR             TIR 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 !   54.4   0.1   1.7e-18     1e-14      13     138 ..       6     124 ..       1     125 [] 0.84

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.7e-18
                     Ribosomal_L18  13 krkapksenvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDv 89 
                                       kr a k++   ++l+  l ++ a + +sk  + v   L + r++++ + ls++ +++++    +++a+v g+v+   
  gi|488600169|ref|YP_007906640.1|   6 KRMARKTNPNLIRLIEDLLEHSA-KNESKLWREVAEHLAKPRRKQAEVNLSKIQRYLRD----GEVAIVPGKVLGSG 77 
                                       45555555555666666766655.468999999************************95....69*********997 PP

                     Ribosomal_L18  90 rllevPklsvaALrftetararilkaGGeiltlDqLalraPtGkntvLl 138
                                        + +   l+vaAL f+e+ar++i+ aGGe++++++L   +P+G+++ +l
  gi|488600169|ref|YP_007906640.1|  78 EIDK--PLKVAALAFSEKARSKIVSAGGECMSIEDLMKVNPKGSKVRIL 124
                                       7654..39***********************************998665 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 !   41.8   0.2   2.7e-14   1.6e-10      55     127 ..      32     106 ..       3     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.7e-14
                                       HHHHHTTTTGTTS------EEEGGGTTTTSSS......SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  55 kdLdelideerleladeaeeidleelaeaglikk..kdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       ++L++ ++e   +   +++e++l+++  ++ ++      v  Kvlg+ge+ k+lkv a +fS+kA++kI +aGG+++
  gi|488600169|ref|YP_007906640.1|  32 SKLWREVAEHLAKPRRKQAEVNLSKI--QRYLRDgeVAIVpgKVLGSGEIDKPLKVAALAFSEKARSKIVSAGGECM 106
                                       566655555554433688999**999..44444457444457*********************************96 PP

>> TIR  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.8e-05      0.11     127     162 ..      14      49 ..       2      62 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                                       TTHHHHHHHHHHSTTTTCCHHHHHHCCCCSHHHHCH CS
                               TIR 127 ekvlkWrealteksvkdeskfikkirkaikseklkk 162
                                        + ++  e+l e+s k+esk+++++++++ + ++k+
  gi|488600169|ref|YP_007906640.1|  14 PNLIRLIEDLLEHSAKNESKLWREVAEHLAKPRRKQ 49 
                                       466666788999*****************4433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 837.88
//
Query:       gi|488600170|ref|YP_007906641.1|  [L=155]
Description: LSU ribosomal protein L13P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   51.4   0.2    1.2e-11   45.0   0.2    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 !   45.0   0.2   6.6e-16   1.2e-11       2     114 ..      15     113 ..      14     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 6.6e-16
                                       EEEEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHH CS
                     Ribosomal_L13   2 WyviDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtake 78 
                                       + viDAe++vlgrl+s iak+L              G+ +vv+na+k ++tg++    + +   +y +g ke     
  gi|488600170|ref|YP_007906641.1|  15 FTVIDAENHVLGRLSSIIAKRLL------------NGEKIVVVNADKAVITGERSMV-FNRYREKYERGSKEKGP-- 76 
                                       679*****************996............5888*************97654.44445678899888654.. PP

                                       HHCCSHHHHHHHHHHCCS-.SSHHHHHHGCTEEEESS CS
                     Ribosomal_L13  79 llekkpeeilekaVkgmLp.knklgrrrlkrLkvyag 114
                                          ++pe+i++++V+gmLp k + gr+ +++Lkv+ g
  gi|488600170|ref|YP_007906641.1|  77 YYPRHPERIFKRTVRGMLPwKSRRGREAYRNLKVFIG 113
                                       6789***************7788999999******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 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:                        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: 00:00:00.42
# Mc/sec: 1102.28
//
Query:       gi|488600171|ref|YP_007906642.1|  [L=132]
Description: SSU ribosomal protein S9P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-33  115.3   1.1    2.5e-33  115.2   1.1    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16
     0.0041   17.7   0.7     0.0069   17.0   0.7    1.4  1  SnAC          Snf2-ATP coupling, chromatin remodelling comple


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   1.1   2.8e-37   2.5e-33       1     121 []       8     132 .]       8     132 .] 0.93

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 2.8e-37
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiar 76 
                                       G+rK++vAr++i++gkg++++n+ ++e  ++ e+ar+ ++epl ++++l + +d+ v+++gGG++gqaeA+r++iar
  gi|488600171|ref|YP_007906642.1|   8 GKRKSAVARATIRPGKGRVRINKIPIEL-ITPEMARNIIMEPLIMAKELANkVDIDVNTNGGGFMGQAEAARTAIAR 83 
                                       8***************************.666**************998855************************* PP

                                       HHHHHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  77 aLvalekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       aLv+++    +eL+      +++ll++D R++E+kK   ++ARk+ q s+R
  gi|488600171|ref|YP_007906642.1|  84 ALVEWSG--DEELRkvyleyDRTLLVNDIRRKEPKKQMGRGARKRRQTSYR 132
                                       *****88..466775556688****************************99 PP

>> SnAC  Snf2-ATP coupling, chromatin remodelling complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.7   7.6e-07    0.0069      28      68 ..      91     132 .]      70     132 .] 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.6e-07
                                       ----------.-------HHHHHHHHHHHH-XXXXXXXXXXX CS
                              SnAC  28 eseLPefyek.dgveekkeekeeldeqlygrgkRaRkevsYe 68 
                                       ++eL ++y + d     ++ + ++ ++++grg+R+R+++sY+
  gi|488600171|ref|YP_007906642.1|  91 DEELRKVYLEyDRTLLVNDIRRKEPKKQMGRGARKRRQTSYR 132
                                       789999**99433334455555667899*************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 789.79
//
Query:       gi|488600172|ref|YP_007906643.1|  [L=87]
Description: DNA-directed RNA polymerase, subunit K [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-13   49.1   0.1    5.2e-13   48.7   0.1    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1   2.9e-17   5.2e-13       8      49 .]      24      69 ..      23      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 2.9e-17
                                      -HHHHHHHHHHHHHHH....HT........SS-SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  8 trYelvriaakRArQieegesl........etqkpvviAlrEiaegkipi 49
                                      tr+e++ri+++RA+Qi     +        ++++p++iA +E + g ipi
  gi|488600172|ref|YP_007906643.1| 24 TRFEKARIIGARALQI----AMgapvlidtDKTDPLDIAREEFERGAIPI 69
                                      9***************....5555555764478***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 684.28
//
Query:       gi|488600173|ref|YP_007906644.1|  [L=402]
Description: enolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-73  245.8   1.9    7.6e-73  245.3   1.9    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    1.4e-29  103.0   0.3      6e-29  100.9   0.1    2.2  2  Enolase_N  Enolase, N-terminal domain
      5e-12   45.9   0.0    9.4e-12   45.0   0.0    1.4  1  MR_MLE_C   Enolase C-terminal domain-like
    0.00086   18.5   0.2      0.002   17.3   0.1    1.5  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.3   1.9   1.7e-76   7.6e-73       3     283 ..     127     393 ..     125     399 .. 0.94

  Alignments for each domain:
  == domain 1  score: 245.3 bits;  conditional E-value: 1.7e-76
                                       EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSH CS
                         Enolase_C   3 vlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsn 79 
                                        lP P+ nvi GG ha ++ ++qef+++Pvga+ f  a    + v++k+k+ +++++    ++ GdeG +a +++ +
  gi|488600173|ref|YP_007906644.1| 127 ELPYPLGNVIGGGAHAKGSTSIQEFLVIPVGAKDFFTAQYANTMVHKKIKEEMNARG--IFSAKGDEGAWAAQIS-D 200
                                       59******************************************************9..88899*********96.6 PP

                                       HHHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEE CS
                         Enolase_C  80 kealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsi 154
                                       + a+++i++ai+    ++  +v +++dva++e++  + ++y  + k        klt+e+   ++ el++ky ++ i
  gi|488600173|ref|YP_007906644.1| 201 EMAFEIIKAAIDGVRDETgiEVRMGIDVAATELW--DGERYVYSDK--------KLTTEEQIAYMAELSDKYDLLYI 267
                                       78*********9887776689999**********..4568876655........588888889************** PP

                                       ES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EE CS
                         Enolase_C 155 edpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygv 231
                                       edpl e+d+e++++lt+ ++    + Gdd++vtn kr++++ie ++an++l+k nqiG+lt+++ avkl+ke+gy +
  gi|488600173|ref|YP_007906644.1| 268 EDPLHENDFEGFAELTKAVN--CMVCGDDIFVTNIKRIQKGIEMGSANTVLIKPNQIGTLTDTFRAVKLSKENGYDI 342
                                       ********************..999**************************************************** PP

                                       EEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGC CS
                         Enolase_C 232 vvshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelge 283
                                       vvshrsGeted tia+l+v+ +a  iktG +   er+ak+n+l+rie+e+ +
  gi|488600173|ref|YP_007906644.1| 343 VVSHRSGETEDETIAHLSVAFNATLIKTGVV-GGERIAKLNELIRIEDEMNK 393
                                       *****************************86.58***************976 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.1   1.3e-32     6e-29       1     131 []       3     120 ..       3     120 .. 0.95
   2 ?   -3.9   0.0       3.3   1.5e+04      45      61 ..     230     246 ..     228     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.3e-32
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I+++  r ++dSrGn Tve+ev  + +  +ra++p+GaStg++ea+ ++D              +++v+ek+++al+
  gi|488600173|ref|YP_007906644.1|   3 IEDLIYRIVFDSRGNRTVECEVFSD-EFSARAIAPAGASTGTEEAI-VKDV-----------SFIDEVQEKVSRALV 66 
                                       7888999*****************6.6789****************.7775...........6899*********** PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       g++v+dq e+D++l e+Dgten s++G+N ++  SlAvak a++ ++ ply yl
  gi|488600173|ref|YP_007906644.1|  67 GISVFDQVEVDETLREIDGTENFSNIGGNFAITASLAVAKLASAISGFPLYAYL 120
                                       *****************************************************7 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.3
                                       -B----SSTTSGGGT-- CS
                         Enolase_N  45 alelrDgdkkrylgkgv 61 
                                       a el Dg++  y +k +
  gi|488600173|ref|YP_007906644.1| 230 ATELWDGERYVYSDKKL 246
                                       78999998888888765 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 !   45.0   0.0   2.1e-15   9.4e-12      32     172 ..     209     364 ..     172     389 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.1e-15
                                       HHHHHHHHHHTTTSTSEEEEE-TTT..S............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHH CS
                          MR_MLE_C  32 ervravreavgpgddvdlmvDanqa..w............dlatAirvarelee.ldllwlEEPvppeddleglael 93 
                                       + +  vr+++  g +v++ +D+ +   w            ++++ i ++ el + +dll++E+P++  +d eg ael
  gi|488600173|ref|YP_007906644.1| 209 AAIDGVRDET--GIEVRMGIDVAATelWdgeryvysdkklTTEEQIAYMAELSDkYDLLYIEDPLHE-NDFEGFAEL 282
                                       5677899999..778899999777766688888999999999**********888***********9.88******* PP

                                       HHHH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS.CS.SHHHHHHH CS
                          MR_MLE_C  94 rara.sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs.gs.gglglaas 166
                                       + +a ++ ++++    + ++++++ +e g +  v ++++++g +t + + ++l +++g+++++ +  + +  +++a+
  gi|488600173|ref|YP_007906644.1| 283 T-KAvNCMVCGDDIFVTnIKRIQKGIEMGSANTVLIKPNQIGTLTDTFRAVKLSKENGYDIVVSHrSGeTEDETIAH 358
                                       *.8889******987766******************************************77666233257777777 PP

                                       HHHHHT CS
                          MR_MLE_C 167 lhlaaa 172
                                       l++a  
  gi|488600173|ref|YP_007906644.1| 359 LSVAFN 364
                                       777544 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 !   17.3   0.1   4.6e-07     0.002      95     226 ..     254     371 ..     239     392 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.6e-07
                            MAAL_C  95 ylakleeaaapyk.lliegPldagskeeqierlaelreklkekgikvelvaDe.Wcntledirefvdaeaadlvqik 169
                                       y+a+l+     y+ l+ie+Pl ++    + e +ael+++++       +  D+ +  +++ i++ ++ ++a+ v ik
  gi|488600173|ref|YP_007906644.1| 254 YMAELS---DKYDlLYIEDPLHEN----DFEGFAELTKAVNCM-----VCGDDiFVTNIKRIQKGIEMGSANTVLIK 318
                                       444443...344414678887644....455666666655444.....444332678899***************** PP

                            MAAL_C 170 tPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhvalatrpaqlLakPG 226
                                          +G++++t  av  +ke+g  + +   + et+   ++++h+++a++++  L k G
  gi|488600173|ref|YP_007906644.1| 319 PNQIGTLTDTFRAVKLSKENGYDIVVSHRSGETED--ETIAHLSVAFNAT--LIKTG 371
                                       ******************************99986..6788999998875..55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 2605.90
//
Query:       gi|488600174|ref|YP_007906645.1|  [L=209]
Description: SSU ribosomal protein S2P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-28   97.5   0.1    1.3e-15   57.2   0.6    2.1  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
      0.012   15.2   0.6      0.021   14.4   0.6    1.3  1  Peripla_BP_4  Periplasmic binding protein domain
      0.076   13.1   0.0       0.13   12.4   0.0    1.4  1  BRCT_3        BRCA1 C Terminus (BRCT) domain


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.5e-13   9.2e-10       2      95 ..      27     117 ..      26     122 .. 0.94
   2 !   57.2   0.6   2.3e-19   1.3e-15     147     212 ..     124     189 ..     119     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.5e-13
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L+agvh+G q +    +mk++Iy++r +g +++d+++  + +r a+k+++++  +  +il v+ ++  ++  +  ak
  gi|488600174|ref|YP_007906645.1|  27 LSAGVHIGTQIK--SGDMKRFIYKVRpDGLYVLDIRQLDERIRVAAKFLSKF--DPPRILVVSARQYGQKPARMFAK 99 
                                       79******8888..789********9779*********************97..6789******************* PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTN 95 
                                        +++ +++ r+++GtLTN
  gi|488600174|ref|YP_007906645.1| 100 IVGADVITGRFVPGTLTN 117
                                       ****************** PP

  == domain 2  score: 57.2 bits;  conditional E-value: 2.3e-19
                      Ribosomal_S2 147 klPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladai 212
                                       + Pd+vvv+dp  ++ avkEa+ +gipv+a++D+n + ++vd +Ip N++  +++ l++ +la+ +
  gi|488600174|ref|YP_007906645.1| 124 REPDVVVVTDPAIDSQAVKEATDVGIPVVALCDSNNQAENVDLVIPTNNKGRKALALVYLLLAREM 189
                                       67*********************************************************9999876 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 ?   14.4   0.6   3.5e-06     0.021      58     105 ..     128     173 ..     124     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-06
                                       EEEE--SSHHHHH.HHHHHHHHTT-EEEE.ESTTGCTTT-CEEEEEC-HH CS
                      Peripla_BP_4  58 giivapvdstala.palkkakaaGIpVva.fdsddapsgerlayvgfdne 105
                                       +++v+  d+ a+  +a+k+a++ GIpVva  ds  +++++++ ++ ++n+
  gi|488600174|ref|YP_007906645.1| 128 VVVVT--DP-AIDsQAVKEATDVGIPVVAlCDSN-NQAENVDLVIPTNNK 173
                                       44443..65.5555**************956777.888888888888886 PP

>> BRCT_3  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.1e-05      0.13      49      74 ..     128     153 ..      75     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                            BRCT_3  49 dvvvtdsscpeevlkkaeqlkipvvS 74 
                                        vvvtd+ + ++++k+a+ ++ipvv+
  gi|488600174|ref|YP_007906645.1| 128 VVVVTDPAIDSQAVKEATDVGIPVVA 153
                                       3669*********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1460.10
//
Query:       gi|488600175|ref|YP_007906646.1|  [L=222]
Description: putative DNA binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-20   72.0   0.2    1.7e-19   69.3   0.1    2.1  2  HTH_10    HTH DNA binding 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 ?    0.1   0.0     0.039     7e+02      31      48 ..     125     142 ..     119     144 .. 0.86
   2 !   69.3   0.1   9.7e-24   1.7e-19       1      52 [.     166     217 ..     166     218 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.039
                            HTH_10  31 kelGIskstlsehLrkae 48 
                                       + l Is +t+ e ++++e
  gi|488600175|ref|YP_007906646.1| 125 ENLEISSNTYVEKVKEIE 142
                                       6799******99998876 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 9.7e-24
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+ ql++lk+Ay  GY+++PR+++l eLAk  GIsk++++++Lr ae+k+i
  gi|488600175|ref|YP_007906646.1| 166 LTEIQLKTLKQAYSGGYYEVPRKCSLFELAKLNGISKNAFLKRLRGAEKKII 217
                                       9**************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1454.69
//
Query:       gi|488600176|ref|YP_007906647.1|  [L=314]
Description: hypothetical protein Asulf_00636 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-99  332.8  15.8    4.5e-99  332.6  15.8    1.0  1  Lactate_perm  L-lactate permease
  ------ inclusion threshold ------
        5.7    7.1  10.2       0.84    9.7   0.6    2.9  3  DUF1634       Protein of unknown function (DUF1634)


Domain annotation for each model (and alignments):
>> Lactate_perm  L-lactate permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.6  15.8    5e-103   4.5e-99       2     274 ..       3     297 ..       2     312 .. 0.97

  Alignments for each domain:
  == domain 1  score: 332.6 bits;  conditional E-value: 5e-103
                      Lactate_perm   2 salvalvPIlllllalavlklkgykaallslavsviiallvykmpvekvlaavlkgalsgllpialviiaavflykl 78 
                                       +al+a++PIll+l+++a ++++++ka++++++v+viia  ++kmp ++++aa++kg+l+ +  i+lv+++av+ly++
  gi|488600176|ref|YP_007906647.1|   3 EALIAATPILLVLVLMAGFRMSAMKAMPIGWLVTVIIAYAYWKMPLQWIAAATVKGTLV-AISILLVVFGAVYLYYD 78 
                                       79*********************************************************.779************** PP

                      Lactate_perm  79 svksgafeiirksilsispdrriqvlligfafgaflEGaaGfGtpvAIsaalLvglGfkPlyaaglcLIantapvaf 155
                                       ++ sga+++i++ ++s+s drriq+  i+f++++f+EGaaGfGtp AI+++lLvg+Gf+P++aa+l+LI++++pv+f
  gi|488600176|ref|YP_007906647.1|  79 ARLSGATRAITRGMMSLSRDRRIQAG-IAFLLVTFFEGAAGFGTPGAIVGPLLVGIGFPPAIAAPLVLIFDSSPVSF 154
                                       **************************.************************************************** PP

                      Lactate_perm 156 GavGiPitagagatkls......................aleisslvgiilvlislliplllvilldg.vkdiketf 209
                                       GavGiP+++g+ga+ +s                      ++++++l+gi++++++l+ + +lvi+++g ++d+k+++
  gi|488600176|ref|YP_007906647.1| 155 GAVGIPVWGGLGASLDSpvveqvlsqygitlqqflykdvTFWTATLHGIMAIFVPLMGATFLVIWSGGkLSDVKDAV 231
                                       ****************9************************************************************ PP

                      Lactate_perm 210 pavlvsglsfaiaqflisnvlGpelpsilgalvslvilalflka.fqpkeifrfagkeeskeksel 274
                                       p++l++glsfai+++l++++ Gpe+ps++g++++l+i+a+ lka f pk++++f +k + +e++ +
  gi|488600176|ref|YP_007906647.1| 232 PSLLLAGLSFAIPYWLLARFFGPEFPSLVGGIIGLAIYAALLKAgFAPKTTWDFPKKMDVGEEHVK 297
                                       *********************************************************998887655 PP

>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.0     0.017   1.5e+02      62      82 ..       5      25 ..       3      44 .. 0.73
   2 ?    9.7   0.6   9.4e-05      0.84       8      66 ..      60     111 ..      54     113 .. 0.88
   3 ?   -2.6   0.0      0.64   5.7e+03      10      27 ..     203     220 ..     197     234 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.017
                           DUF1634 62 vLiatPvlrVvlsliaFlkek 82
                                      ++ atP+l V++ +  F +  
  gi|488600176|ref|YP_007906647.1|  5 LIAATPILLVLVLMAGFRMSA 25
                                      5789**********9998765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9.4e-05
                           DUF1634   8 GvllsaavvllGlilllvkhgssesenseltslseilegllelkglaiiqlGllvLiat 66 
                                        v++s+++v++G + l++  +            ++i +g+++l+    iq G+  L++t
  gi|488600176|ref|YP_007906647.1|  60 LVAISILLVVFGAVYLYYDARL-------SGATRAITRGMMSLSRDRRIQAGIAFLLVT 111
                                       5899*********999999983.......356788999*****************9987 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.64
                           DUF1634  10 llsaavvllGlilllvkh 27 
                                       +++++v l+G ++l++ +
  gi|488600176|ref|YP_007906647.1| 203 IMAIFVPLMGATFLVIWS 220
                                       466777777776665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2349.53
//
Query:       gi|488600177|ref|YP_007906648.1|  [L=242]
Description: hypothetical protein Asulf_00637 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  238.4  24.6    2.5e-70  237.7  24.6    1.3  1  Lactate_perm  L-lactate permease
  ------ inclusion threshold ------
        1.9    8.4   0.0        1.9    8.4   0.0    4.0  4  Flp_Fap       Flp/Fap pilin component


Domain annotation for each model (and alignments):
>> Lactate_perm  L-lactate permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.7  24.6   2.8e-74   2.5e-70     280     521 ..       2     232 ..       1     233 [. 0.97

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 2.8e-74
                      Lactate_perm 280 lkAlsPfvllvavivltsipllkalfeeggllatkllsleleelsklilkikpiveeatalevvfkfkllsspgtii 356
                                       l+A++P+vll+a + lt+  l++++ +    ++t+           l++ i +i++    ++++++fkll++pgti+
  gi|488600177|ref|YP_007906648.1|   2 LEAMVPYVLLTAGLLLTR--LVPSIKA----FSTS----------FLTIPIGNILS----TSLSHTFKLLYNPGTIF 58 
                                       79****************..8898888....5555..........46888999999....999************** PP

                      Lactate_perm 357 llaavlsiavlklsskdalkvlketlkelklpilaiilvlalanlmnvsG........lsktlalalae.tGsaftl 424
                                       ++a+++s+++++ls+++++++lk+t+k+++++++a+i++++l+++m++sG        ++k++a +la  tG+ +++
  gi|488600177|ref|YP_007906648.1|  59 IIAVLVSNVIFRLSPNHTKNALKTTAKGVAPAAIALIFAVSLSQIMMNSGhneagmdsMLKVMAESLAMaTGKGYIF 135
                                       ***************************************************************************** PP

                      Lactate_perm 425 fspllGalGvfltGSdtvsNllFgslQletaeqiglsevlllaantvGgvvgkmispqsiaiacaavglvgkEsdll 501
                                       +++++G+lG++++GS+tvsN+lFg +Q+e+a  +gl++++++a+++vGg+vg+mi++++++++c+++g++g E++++
  gi|488600177|ref|YP_007906648.1| 136 LAVFVGILGAYMAGSNTVSNILFGGFQFEIAGFVGLPKTIVVALQNVGGAVGNMICVHNVVAVCTTCGILGSEGEVI 212
                                       ***************************************************************************** PP

                      Lactate_perm 502 rktviysliyliivgvvall 521
                                       rk++ +s +y+iiv+vva++
  gi|488600177|ref|YP_007906648.1| 213 RKNLLPSALYAIIVSVVAAI 232
                                       *****************998 PP

>> Flp_Fap  Flp/Fap pilin component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00021       1.9      15      38 ..      59      83 ..      59      91 .. 0.90
   2 ?   -1.2   0.1      0.21   1.9e+03      21      29 ..      91      99 ..      86     106 .. 0.74
   3 ?   -0.2   0.2       0.1   9.3e+02      23      37 ..     174     188 ..     165     190 .. 0.77
   4 ?    0.1   5.8     0.084   7.5e+02      13      28 ..     222     237 ..     222     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00021
                           Flp_Fap 15 LIaaliAvvii.ayvttlgtaLktk 38
                                      +Ia+l++ vi+ +  + +++aLkt 
  gi|488600177|ref|YP_007906648.1| 59 IIAVLVSNVIFrLSPNHTKNALKTT 83
                                      6**********************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                           Flp_Fap 21 Avviiayvt 29
                                      A+++i++v+
  gi|488600177|ref|YP_007906648.1| 91 AIALIFAVS 99
                                      788888776 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.1
                           Flp_Fap  23 viiayvttlgtaLkt 37 
                                       +i+ +++++g+a+ +
  gi|488600177|ref|YP_007906648.1| 174 TIVVALQNVGGAVGN 188
                                       588999999999876 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.084
                           Flp_Fap  13 YgLIaaliAvviiayv 28 
                                       Y++I+ ++A ++++++
  gi|488600177|ref|YP_007906648.1| 222 YAIIVSVVAAIVVFAL 237
                                       9************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1794.90
//
Query:       gi|488600178|ref|YP_007906649.1|  [L=311]
Description: L-lactate dehydrogenase (FMN-dependent)-related alpha-hydroxy acid dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  198.8   0.0    5.9e-41  140.6   0.0    2.0  2  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.013   14.5   0.0      0.049   12.6   0.0    1.8  2  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.036   13.2   0.0      0.062   12.4   0.0    1.3  1  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0     4e-19   2.4e-15       8     149 ..      20     157 ..      11     166 .. 0.92
   2 !  140.6   0.0   9.9e-45   5.9e-41     201     346 ..     171     309 ..     159     310 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 4e-19
                                       HHHHHHH--STTSHHHHHHHHGGGGEEE---SSSS-SS-B--EEETTEEESSSEEE--B.STGGGTSTTHHHHHHHH CS
                            FMN_dh   8 kafayvaggagdevtlrenraaferirlrprvlrdvskvdlsttllGqklslPvliaPv.glaklahpdgelalara 83 
                                          + ++gg++++ t+ +nr+ +++i +++rv+ d++  +ls ++lG+k+s+Pv+ aP+ gl k ++++    + ++
  gi|488600178|ref|YP_007906649.1|  20 VNLSILEGGTERGLTILRNREVLDSIGIKMRVIGDIEP-SLSSKFLGRKISMPVMPAPLsGLVKSVDARCFHRIIKE 95 
                                       456789******************************98.9******************99***************** PP

                                       HHHHTS-EEEETT-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS- CS
                            FMN_dh  84 aakagipfvlstvastsleevaaaaegplwfqlyvpkdrelteellkraeaagykalvltvDtpvl 149
                                         +ag++ +++   +  +e   +    p+++ + ++kdr+++ + ++rae++++ a+ +++D +  
  gi|488600178|ref|YP_007906649.1|  96 SWDAGVVPWIGYPIQDDVESFEQ----PFVWIIKPMKDRDKIYQEIERAEKSKALAVGIDIDSAAG 157
                                       *************9999999966....9*******************************9999876 PP

  == domain 2  score: 140.6 bits;  conditional E-value: 9.9e-45
                                       TC--HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEE CS
                            FMN_dh 201 psltwddikwlreqtklplvvKGvltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvD 277
                                       ++l+ ++++ + ++tklp++vKGvl+++d   a     d++v+SNHGGR +d+a++++++L ++ + v+      vD
  gi|488600178|ref|YP_007906649.1| 171 KALSKKELEDIASTTKLPFIVKGVLSEKDYYDASSFS-DAVVISNHGGRVIDSAVSPLEILANVEKVVE----TGVD 242
                                       678899*****************************98.***********************99988775....89** PP

                                       SS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHCGGE CS
                            FMN_dh 278 gGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvaeldrsll 346
                                       +G+r GsDvlkAlal Ad+vl+GRp++y+la   e+G++++le++ +el+r m l+G+k+v e++r+++
  gi|488600178|ref|YP_007906649.1| 243 SGFRYGSDVLKALALNADFVLIGRPVVYALAF--ENGLKEILEVIGEELKRIMVLTGFKEVGEINREAV 309
                                       *****************************997..9******************************9976 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.1e-06     0.049     208     237 ..     237     266 ..     217     290 .. 0.85
   2 ?   -1.5   0.0      0.16   9.8e+02     296     329 ..     275     308 ..     268     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-06
                                       -EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 208 vpviaDGGikysgdivkAlaaGadavmlGs 237
                                       v+   D G +y  d+ kAla+ ad+v++G+
  gi|488600178|ref|YP_007906649.1| 237 VETGVDSGFRYGSDVLKALALNADFVLIGR 266
                                       566679***********************7 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.16
                                       -B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 296 kgsvkevveqlvgglrsgmgylGaktieelkeka 329
                                       +  +ke++e + ++l+  m  +G k++ e++++a
  gi|488600178|ref|YP_007906649.1| 275 ENGLKEILEVIGEELKRIMVLTGFKEVGEINREA 308
                                       5668999999999*************99998765 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 ?   12.4   0.0     1e-05     0.062     271     309 ..     233     271 ..     219     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1e-05
                                       -GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHHH CS
                      Glu_synthase 271 lrdrvsliadGglktgadvvkalalGAdavgigtaalia 309
                                       + + v+  +d g++ g dv+kalal Ad+v ig+  + a
  gi|488600178|ref|YP_007906649.1| 233 VEKVVETGVDSGFRYGSDVLKALALNADFVLIGRPVVYA 271
                                       55667888999**********************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2163.84
//
Query:       gi|488600179|ref|YP_007906650.1|  [L=463]
Description: FAD/FMN-containing dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  221.3   0.9      2e-65  220.9   0.4    1.4  2  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    4.1e-45  152.9   0.1    7.5e-45  152.1   0.1    1.5  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
      0.053   13.1   0.0       0.19   11.4   0.0    1.8  2  Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (
       0.17   12.2   1.3         11    6.3   0.0    2.7  3  RNA_binding    RNA binding


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 ?   -3.6   0.0       1.5   6.7e+03       7      31 ..      38      62 ..      36      63 .. 0.79
   2 !  220.9   0.4   4.5e-69     2e-65       3     250 .]     213     462 ..     211     462 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.5
                                      EEEEEESSHHHHHHHHHHHHHHT-- CS
                     FAD-oxidase_C  7 valvafpsfeaavkavreiaqagii 31
                                       a+v+ ++ e+++k v  ++++gi+
  gi|488600179|ref|YP_007906650.1| 38 IAVVFPENTEQVAKIVKFCYENGIK 62
                                      6777888999999999999998875 PP

  == domain 2  score: 220.9 bits;  conditional E-value: 4.5e-69
                                       SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHH CS
                     FAD-oxidase_C   3 earavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeee 79 
                                       e+ ++a+++f++ e+a++av+ei++++i pa +e+ d++ +++++++ ++     d+e+ +l++++e+++ e+ e+ 
  gi|488600179|ref|YP_007906650.1| 213 ENMVYAAAFFETAEKAMAAVAEIRKRRILPAVMEFFDEDVVRMGREMVDV-----DGEGNMLIIGVECNH-EASERI 283
                                       7889**********************************************.....***************.666666 PP

                                       HHHHHHHTTT-EEEEE..........E..TGGGGGGGGHH....HHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHH CS
                     FAD-oxidase_C  80 lealveaileatgaadvlvaqdeaeae..alwkaRkaalp....ylrdallkagvavlseDtsvPvsrladlvrdik 150
                                       ++ ++ +il+  + + v va+d++eae  +l  +R+a++p    + ++ ++ +++ vl+eD +vPvs+l+++++++k
  gi|488600179|ref|YP_007906650.1| 284 AS-TLNEILSRDASK-VIVAKDAREAEekNLMGLRRAFYPlaikLGSEEFKTSSTLVLIEDFAVPVSKLPEAINAVK 358
                                       66.888888887777.5*****9999999***********7766667778899************************ PP

                                       HHHHHHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT---------------....----- CS
                     FAD-oxidase_C 151 alldkyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkka....ylere 223
                                       ++ +kyg++v + gH+gdgn+h++i++ ++d+++ ++aek++ ev+++a++lgG++s+EHG+G +kk     ++++ 
  gi|488600179|ref|YP_007906650.1| 359 EIGKKYGFTVLTGGHVGDGNIHPMIWTSPEDKDMLDKAEKFYIEVMEVALKLGGTVSAEHGIGEMKKLglemEMKYR 435
                                       *******************************************************************99999***** PP

                                       ---THHHHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 224 kgeeglalmrriKaalDPkgiLNPgkv 250
                                       ++e++l++mr+iK+++DPk+iLNPgkv
  gi|488600179|ref|YP_007906650.1| 436 NSEKALEIMREIKKVFDPKNILNPGKV 462
                                       **************************8 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.1   0.1   1.7e-48   7.5e-45       3     138 ..      39     174 ..      37     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.1 bits;  conditional E-value: 1.7e-48
                                       EEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHH CS
                     FAD_binding_4   3 avvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlve 79 
                                       avv+pe++e+va++++++ e+g+++ ++G+ + l+g+++  +g+v+++s++n+i+ei+ ++g+a+v++Gv+l +l+e
  gi|488600179|ref|YP_007906650.1|  39 AVVFPENTEQVAKIVKFCYENGIKIYPQGSSTELSGSSTPHRGIVISFSKMNSIEEINITDGYAVVQPGVRLVELEE 115
                                       8**************************************9************************************* PP

                                       HHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  80 alaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       +l+++g++++++pgs+ ++tvGGai t+agG++  kyG+++d+vlgle+vl++Ge++++
  gi|488600179|ref|YP_007906650.1| 116 ELNKHGYMFPVDPGSLRSATVGGAINTGAGGMRGAKYGTMVDWVLGLEAVLPTGEIINI 174
                                       ********************************************************987 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.55   2.5e+03      33      66 ..      33      66 ..      30      73 .. 0.82
   2 ?   11.4   0.0   4.2e-05      0.19      56     116 ..     392     452 ..     387     454 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.55
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B 33 slgpsikefldkriekiqeelnqsrnlkeealke 66
                                      ++g++i+  + +  e++ ++ +  +++ ++++ +
  gi|488600179|ref|YP_007906650.1| 33 KVGEAIAVVFPENTEQVAKIVKFCYENGIKIYPQ 66
                                      7888999999999999999999999988888765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B  56 srnlkeealkerieqekklqslveltkslfevskeqvaleaeaferelqaklareikkkld 116
                                       + ++ e+ + e++e   kl  +v+  + + e++k+ +++e +++++e + +++reikk+ d
  gi|488600179|ref|YP_007906650.1| 392 MLDKAEKFYIEVMEVALKLGGTVSAEHGIGEMKKLGLEMEMKYRNSEKALEIMREIKKVFD 452
                                       567778888999999999999*************************************976 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0025        11       8      48 ..      25      64 ..      20      76 .. 0.85
   2 ?    4.1   0.1     0.012        55      15      88 ..     238     311 ..     229     316 .. 0.74
   3 ?   -3.4   0.1       2.6   1.2e+04       9      26 ..     435     452 ..     428     457 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0025
                                      E-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEE CS
                       RNA_binding  8 vhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitil 48
                                      +ha +   kV ea++ ++pe+ +e   + ++ +y+n i+i+
  gi|488600179|ref|YP_007906650.1| 25 LHAKDAIGKVGEAIAVVFPEN-TEQVAKIVKFCYENGIKIY 64
                                      68888999***********88.5778888999999999987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                                       HHHHHHHHTTSTTS..E---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHHHCCHCCB-TTS CS
                       RNA_binding  15 ekVlealsnllpee..eveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeikeLlkeleervdekg 88 
                                        ++l a+ ++++e+  ++  e  ++ G  + +++i+ +e++++  ++++++l e l++++ k++  +  +  +ek+
  gi|488600179|ref|YP_007906650.1| 238 RRILPAVMEFFDEDvvRMGREMVDVDG--EGNMLIIGVECNHEASERIASTLNEILSRDASKVIVAKDAREAEEKN 311
                                       688899999999886522224555555..557999999999988899*****999999998777665555555554 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.6
                                       -TTC-HHHHHHHHHTTST CS
                       RNA_binding   9 haTEdeekVlealsnllp 26 
                                       + +E+  ++++ ++++++
  gi|488600179|ref|YP_007906650.1| 435 RNSEKALEIMREIKKVFD 452
                                       334444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3062.10
//
Query:       gi|488600180|ref|YP_007906651.1|  [L=101]
Description: hypothetical protein Asulf_00640 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-10   40.9  14.1    9.2e-10   38.9   4.8    1.4  2  Fer4_17        4Fe-4S dicluster domain
    1.4e-09   38.2   2.3    2.1e-09   37.7   2.3    1.3  1  Fer4_8         4Fe-4S dicluster domain
    5.5e-07   29.6   6.3      3e-06   27.3   6.8    1.8  2  Fer4_9         4Fe-4S dicluster domain
    9.8e-07   28.3  14.4    0.00017   21.2   1.4    2.2  2  Fer4           4Fe-4S binding domain
    3.4e-06   27.6   9.9    1.2e-05   25.8  10.0    1.8  1  Fer4_7         4Fe-4S dicluster domain
    5.6e-06   26.5  11.8     0.0023   18.3   1.2    2.2  2  Fer4_4         4Fe-4S binding domain
    6.1e-06   26.0   3.7     0.0095   15.7   0.1    2.1  2  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
      7e-06   26.1  10.0     0.0014   18.7  11.9    2.1  2  Fer4_10        4Fe-4S dicluster domain
    0.00024   22.0   8.3    0.00063   20.6   8.5    1.6  2  Fer4_16        4Fe-4S double cluster binding domain
    0.00046   20.4   4.4       0.02   15.1   0.4    2.1  2  Fer4_18        4Fe-4S dicluster domain
     0.0019   18.3   3.1        0.8    9.9   0.2    2.2  2  Fer4_21        4Fe-4S dicluster domain
     0.0026   17.8  13.5      0.062   13.4   1.5    2.2  2  Fer4_6         4Fe-4S binding domain
      0.004   17.2  13.4       0.27   11.4   4.0    2.3  2  Fer4_2         4Fe-4S binding domain
  ------ inclusion threshold ------
      0.045   14.6   9.9       0.23   12.3   0.6    2.1  2  Fer4_22        4Fe-4S dicluster domain
       0.12   13.2   3.7       0.58   10.9   0.3    2.2  2  Fer4_15        4Fe-4S single cluster domain
       0.23   12.5  16.3        2.5    9.2   3.8    2.2  2  Fer4_3         4Fe-4S binding domain
       0.33   10.7   8.9       0.42   10.4   0.9    2.2  2  A2L_zn_ribbon  A2L zinc ribbon domain
        2.1    9.0  11.5        1.6    9.3   1.7    2.1  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.8   9.5e-05     0.095      42      59 ..       8      25 ..       6      27 .. 0.85
   2 !   38.9   4.8   9.2e-13   9.2e-10       1      61 []      11      76 ..      11      76 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-05
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                      ++s+C+ Cg Ce++CP  
  gi|488600180|ref|YP_007906651.1|  8 EISRCSFCGFCEAACPTR 25
                                      689999999999999975 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 9.2e-13
                           Fer4_17  1 rCiqCgyClpeCps.yeaydne.pkkllraakl...glleeaekeekaslCieCgeCerkCPqgld 61
                                      rC+ Cg+C+++Cp+ +++ +n+ p+  ++ + +   ++l+++e  + + +C+eCg C+ +CP+g+d
  gi|488600180|ref|YP_007906651.1| 11 RCSFCGFCEAACPTrFMIKRNYtPRGRINTIIFalkNRLTTIESVNGIFSCLECGACKPYCPAGID 76
                                      7************635555553244444444446666777777789*****************997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   2.3   2.1e-12   2.1e-09       2      65 .]       9      75 ..       8      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.1e-12
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                      +++C  Cg+C++aCp+     k+++++rg+ +      +  +    e+ ++++sC++cgaC+  Cp gi
  gi|488600180|ref|YP_007906651.1|  9 ISRCSFCGFCEAACPTRFMI-KRNYTPRGRINTiifalK-NRLTTIESVNGIFSCLECGACKPYCPAGI 75
                                      689************54444.677888998888777641.22223333899***************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 !   13.8   1.9   5.1e-05     0.051      34      49 ..      10      25 ..       3      27 .. 0.79
   2 !   27.3   6.8     3e-09     3e-06       1      49 [.      11      74 ..      11      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-05
                            Fer4_9 34 eaCigCgaCveaCpkg 49
                                      ++C +Cg C++aCp+ 
  gi|488600180|ref|YP_007906651.1| 10 SRCSFCGFCEAACPTR 25
                                      4799999999999986 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase...............eaCigCgaCveaCpkg 49
                                      +C  Cg C++aCp+  +++++ +   r++                    +C++CgaC   Cp g
  gi|488600180|ref|YP_007906651.1| 11 RCSFCGFCEAACPTRFMIKRNYTPRGRINTIIFalknrlttiesvngiFSCLECGACKPYCPAG 74
                                      5*************999888877777775544478999**********99************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.4   1.8e-07   0.00017       6      21 ..      10      25 ..       9      27 .. 0.91
   2 !   12.2   5.6   0.00013      0.13       8      21 ..      61      74 ..      60      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.8e-07
                                      TTSSS-THHHHHSTTT CS
                              Fer4  6 ekCigCGaCvevCPvg 21
                                      ++C +CG C+ +CP+ 
  gi|488600180|ref|YP_007906651.1| 10 SRCSFCGFCEAACPTR 25
                                      69************95 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                      SSS-THHHHHSTTT CS
                              Fer4  8 CigCGaCvevCPvg 21
                                      C  CGaC   CP g
  gi|488600180|ref|YP_007906651.1| 61 CLECGACKPYCPAG 74
                                      99**********98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8  10.0   1.2e-08   1.2e-05       1      52 []      11      75 ..      11      75 .. 0.62

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.2e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt.ekv.............eidpekClgCgaCvavCPtga 52
                                      rC  Cg+C+aaCp++ +  ++++ ++g+  ++             +    +Cl CgaC   CP+g+
  gi|488600180|ref|YP_007906651.1| 11 RCSFCGFCEAACPTRFMIKRNYT-PRGRiNTIifalknrlttiesVNGIFSCLECGACKPYCPAGI 75
                                      7************8876655442.332221113333333332221223568************996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   3.5   9.9e-05     0.098       3      17 .]      11      25 ..       9      26 .. 0.89
   2 !   18.3   1.2   2.3e-06    0.0023       3      17 .]      60      74 ..      54      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.9e-05
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      rC  Cg C+aaCP++
  gi|488600180|ref|YP_007906651.1| 11 RCSFCGFCEAACPTR 25
                                      8999*********85 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.3e-06
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C++Cg+C  +CP g
  gi|488600180|ref|YP_007906651.1| 60 SCLECGACKPYCPAG 74
                                      6************75 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 !   11.7   0.6   0.00017      0.17      18      43 ..       6      29 ..       2      35 .. 0.88
   2 !   15.7   0.1   9.6e-06    0.0095      19      50 ..      56      85 ..      37      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                      HHHHTT----TT-HHHHCSTT---HH CS
                           Fer4_20 18 leeAsRClqCkkapcvkgCPveidip 43
                                      l+e sRC  C    c+++CP++  i+
  gi|488600180|ref|YP_007906651.1|  6 LREISRCSFC--GFCEAACPTRFMIK 29
                                      6899******..89*******99987 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 9.6e-06
                                      HHHTT----TT-HHHHCSTT---HHHHHHHHH CS
                           Fer4_20 19 eeAsRClqCkkapcvkgCPveidipefikkia 50
                                      +    Cl+C    c+  CP+ idip+ i++ +
  gi|488600180|ref|YP_007906651.1| 56 NGIFSCLEC--GACKPYCPAGIDIPRVIREFR 85
                                      55557****..78**************99865 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  11.9   1.5e-06    0.0014       6      56 .]       9      72 ..       4      72 .. 0.83
   2 !   15.4   1.9   1.5e-05     0.015       8      23 ..      60      75 ..      53      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                           Fer4_10  6 ddtCirCgkCvkaCPadl.............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       ++C  Cg C +aCP+ +             t   a + +    +   ++ +C +cgaC   CP
  gi|488600180|ref|YP_007906651.1|  9 ISRCSFCGFCEAACPTRFmikrnytprgrinTIIFALKNRLTTIESVNGIFSCLECGACKPYCP 72
                                      579*************99***********995555555555555556669*************9 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.5e-05
                           Fer4_10  8 tCirCgkCvkaCPadl 23
                                      +C++Cg+C+  CPa +
  gi|488600180|ref|YP_007906651.1| 60 SCLECGACKPYCPAGI 75
                                      7*************66 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 !   20.6   8.5   6.3e-07   0.00063       1      66 [.      11      73 ..      11      74 .. 0.81
   2 !    9.3   3.2    0.0022       2.2       2      15 ..      61      74 ..      60      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.3e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                      rC  Cg C  +CPt+ + ++   ++ +r  i++     k+  +++e+ +    +  C++C+  CPa
  gi|488600180|ref|YP_007906651.1| 11 RCSFCGFCEAACPTRFMIKR---NYTPRGRINTIIFALKNRLTTIESVNGIFSCLECGACKPYCPA 73
                                      6999***********99888...677777777766666666666666666889************8 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0022
                           Fer4_16  2 CgtCgkCaevCPtn 15
                                      C +Cg+C   CP++
  gi|488600180|ref|YP_007906651.1| 61 CLECGACKPYCPAG 74
                                      99999999999986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.3    0.0052       5.2      58      78 ..       9      29 ..       4      39 .. 0.86
   2 !   15.1   0.4     2e-05      0.02      54      78 ..      54      78 ..      35      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0052
                           Fer4_18 58 agdcidcescvkvcPtgidir 78
                                       + c  c++c + cPt   i+
  gi|488600180|ref|YP_007906651.1|  9 ISRCSFCGFCEAACPTRFMIK 29
                                      56799***********98886 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2e-05
                           Fer4_18 54 kekgagdcidcescvkvcPtgidir 78
                                      + +g   c++c++c   cP gidi 
  gi|488600180|ref|YP_007906651.1| 54 SVNGIFSCLECGACKPYCPAGIDIP 78
                                      4567779****************95 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.3    0.0011       1.1      39      55 ..      10      26 ..       4      30 .. 0.76
   2 !    9.9   0.2    0.0008       0.8       7      19 ..      60      72 ..      38      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                           Fer4_21 39 deCvGCnlCssvCPved 55
                                      ++C  C  C + CP+  
  gi|488600180|ref|YP_007906651.1| 10 SRCSFCGFCEAACPTRF 26
                                      46888999999999755 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0008
                           Fer4_21  7 kCigCgkCliaCe 19
                                      +C++Cg C   C+
  gi|488600180|ref|YP_007906651.1| 60 SCLECGACKPYCP 72
                                      4666666666666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   1.5   6.2e-05     0.062       7      21 ..      10      24 ..       8      28 .. 0.86
   2 !    9.5   4.7     0.001         1       8      23 ..      60      75 ..      60      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                            Fer4_6  7 dkCigCgdCvrvCPe 21
                                      ++C  Cg C+++CP+
  gi|488600180|ref|YP_007906651.1| 10 SRCSFCGFCEAACPT 24
                                      57888*********8 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.001
                            Fer4_6  8 kCigCgdCvrvCPega 23
                                      +C+ Cg+C   CP+g+
  gi|488600180|ref|YP_007906651.1| 60 SCLECGACKPYCPAGI 75
                                      6************985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   1.9   0.00033      0.33       9      22 .]      11      24 ..       5      24 .. 0.88
   2 !   11.4   4.0   0.00027      0.27       9      22 .]      60      73 ..      59      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                            Fer4_2  9 rCigCgaCvsaCPa 22
                                      rC  Cg C  aCP+
  gi|488600180|ref|YP_007906651.1| 11 RCSFCGFCEAACPT 24
                                      7888*********7 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00027
                            Fer4_2  9 rCigCgaCvsaCPa 22
                                      +C++CgaC   CPa
  gi|488600180|ref|YP_007906651.1| 60 SCLECGACKPYCPA 73
                                      5************8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.7    0.0087       8.6       1      17 [.      11      27 ..      11      41 .. 0.84
   2 ?   12.3   0.6   0.00023      0.23      68      96 .]      47      75 ..      29      75 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0087
                           Fer4_22  1 rClsCgaCtlvCptCsC 17
                                      rC  Cg C ++Cpt + 
  gi|488600180|ref|YP_007906651.1| 11 RCSFCGFCEAACPTRFM 27
                                      7999*********9765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                           Fer4_22 68 hklsefkekfgesgCvGCgRCieacpvki 96
                                      ++l+++++  g  +C  Cg C+  cp++i
  gi|488600180|ref|YP_007906651.1| 47 NRLTTIESVNGIFSCLECGACKPYCPAGI 75
                                      55666666777888888888888888765 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00058      0.58       6      25 ..      10      29 ..       8      40 .. 0.89
   2 ?    3.6   0.3      0.12   1.1e+02       8      22 ..      61      75 ..      59      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00058
                           Fer4_15  6 daCigcglCvaeapevfeld 25
                                      ++C  cg C a++p++f ++
  gi|488600180|ref|YP_007906651.1| 10 SRCSFCGFCEAACPTRFMIK 29
                                      69***************986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                           Fer4_15  8 CigcglCvaeapevf 22
                                      C  cg+C   +p  +
  gi|488600180|ref|YP_007906651.1| 61 CLECGACKPYCPAGI 75
                                      999********8655 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.8    0.0025       2.5       1      13 [.      12      24 ..      12      25 .. 0.93
   2 ?    9.1   4.6    0.0028       2.8       1      14 [.      61      74 ..      61      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C  Cg C+ +CP+
  gi|488600180|ref|YP_007906651.1| 12 CSFCGFCEAACPT 24
                                      999*********7 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0028
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ CgaC   CP g
  gi|488600180|ref|YP_007906651.1| 61 CLECGACKPYCPAG 74
                                      9***********77 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.6     0.026        26      24      31 ..      12      19 ..       8      21 .. 0.86
   2 ?   10.4   0.9   0.00043      0.42      20      33 .]      57      70 ..      54      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.026
                     A2L_zn_ribbon 24 CieCgasf 31
                                      C +Cg+++
  gi|488600180|ref|YP_007906651.1| 12 CSFCGFCE 19
                                      99999997 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00043
                     A2L_zn_ribbon 20 gylvCieCgasfpy 33
                                      g+ +C eCga+ py
  gi|488600180|ref|YP_007906651.1| 57 GIFSCLECGACKPY 70
                                      6789********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 ?    9.3   1.7    0.0016       1.6       4      23 ..      10      29 ..       8      34 .. 0.86
   2 ?    4.8   2.5     0.041        40       5      17 ..      60      72 ..      59      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                           Fer4_13  4 dtCiacgaCvelaPdvFeed 23
                                      ++C+ cg C +++P  F ++
  gi|488600180|ref|YP_007906651.1| 10 SRCSFCGFCEAACPTRFMIK 29
                                      58*************99776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.041
                           Fer4_13  5 tCiacgaCvelaP 17
                                      +C +cgaC   +P
  gi|488600180|ref|YP_007906651.1| 60 SCLECGACKPYCP 72
                                      6***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 604.46
//
Query:       gi|488600181|ref|YP_007906652.1|  [L=309]
Description: hypothetical protein Asulf_00641 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   47.4   0.0    5.3e-09   36.2   0.0    2.2  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 !    9.3   0.0   7.2e-05       1.3      17      79 ..     104     167 ..      94     173 .. 0.80
   2 !   36.2   0.0     3e-13   5.3e-09       1      85 []     205     287 ..     205     287 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7.2e-05
                               CCG  17 vrkalkkllealgveleelekesCCGagggrsgkee.laealakrnvetaeetgadaivtacpg 79 
                                         + +  ll+ +g+++++  +  C      +   ++  +e+ ak  +e++e++g+++ivt +p+
  gi|488600181|ref|YP_007906652.1| 104 ILRGIYSLLNDAGIDVYYRPELDCYSGILLYDFGDDeGFEEHAKFVAENLEKAGVKKIVTVDPH 167
                                       5555668899999999999888887777777666666999*********************998 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 3e-13
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaiv 74 
                                       v+++d+C+++r+   ++++rk+l+ + +++ +++    +  sCCG ++   + + +++++ak ++e++ +     iv
  gi|488600181|ref|YP_007906652.1| 205 VVIHDPCYYGRYLeiSEKPRKLLESI-GVEYANIRNSgNLTSCCGGPIEALSPK-ISRDVAKLRLEELGN---GRIV 276
                                       789***********999999999999.********************9976666.9*******9988877...58** PP

                               CCG  75 tacpgCllqlk 85 
                                       t cp C ++l+
  gi|488600181|ref|YP_007906652.1| 277 TMCPVCMANLR 287
                                       ******99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2324.27
//
Query:       gi|488600182|ref|YP_007906653.1|  [L=122]
Description: hypothetical protein Asulf_00642 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   32.8   0.2    1.3e-06   28.3   0.1    2.2  2  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 !    2.7   0.0    0.0052        93       1      21 [.       1      21 [.       1      30 [. 0.85
   2 !   28.3   0.1   7.3e-11   1.3e-06      85     188 ..      29     120 ..      22     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0052
                           LUD_dom  1 leefienleangaevyyakta 21
                                      +e++ie+l++n +ev++ ++ 
  gi|488600182|ref|YP_007906653.1|  1 MEKLIEALKRNSVEVIISEDP 21
                                      689************998875 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 7.3e-11
                           LUD_dom  85 advgitganfaiAetGtlvlvdnegnrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfi 161
                                       ++v+++ a  a  +tG ++ v  e+       l  +h+++v++  i+pd  +a   + +     ++       v   
  gi|488600182|ref|YP_007906653.1|  29 SNVFVCEAASAAEDTGIIFFVGFEKRKN--AALAAHHVAIVKKADIMPDTISAYLHAAK-----KG-----DIVFAS 93 
                                       5788899998888888888887777663..45788**************9999988888.....56.....445555 PP

                           LUD_dom 162 sgpsrtadielvlvygvhgpkrihvil 188
                                       s+ s+tadie +lv g+hgpk+++vil
  gi|488600182|ref|YP_007906653.1|  94 SSASKTADIEGKLVWGMHGPKKLTVIL 120
                                       888***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 831.03
//
Query:       gi|488600183|ref|YP_007906654.1|  [L=363]
Description: putative conserved protein containing a ferredoxin-like domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-29  103.6   0.3    1.9e-29  102.8   0.3    1.4  1  LUD_dom     LUD domain
    1.3e-07   32.0   3.3    2.7e-07   30.9   3.3    1.6  1  Fer4_8      4Fe-4S dicluster domain
    3.2e-06   27.1   2.8      0.013   15.6   0.1    2.4  2  Fer4_10     4Fe-4S dicluster domain
    0.00073   20.0   7.2      0.003   18.1   7.3    2.0  2  Fer4_17     4Fe-4S dicluster domain
     0.0022   18.5   3.1      0.075   13.6   0.1    2.3  2  Fer4_7      4Fe-4S dicluster domain
     0.0062   16.6   5.9        0.1   12.7   0.5    2.4  2  Fer4_6      4Fe-4S binding domain
     0.0066   16.6   5.4       0.19   11.9   0.2    2.4  2  Fer4_21     4Fe-4S dicluster domain
     0.0088   16.9   4.5      0.035   14.9   0.1    2.5  2  Fer4_22     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   15.9   8.2        0.1   12.8   8.9    2.1  2  Fer4_9      4Fe-4S dicluster domain
      0.018   15.0   0.2       0.69    9.9   0.0    2.4  2  UBA_6       UBA-like domain
      0.026   14.3   0.8      0.026   14.3   0.8    2.4  2  Fer4_20     Dihydroprymidine dehydrogenase domain II, 4Fe-4S 
      0.028   14.2   1.5      0.028   14.2   1.5    2.4  2  Fer4        4Fe-4S binding domain
      0.031   14.4   2.0      0.031   14.4   2.0    2.4  2  Fer4_2      4Fe-4S binding domain
      0.044   14.0   3.0        0.6   10.3   0.3    2.4  2  Fer4_18     4Fe-4S dicluster domain
      0.058   13.7   0.4        0.2   12.0   0.1    2.0  2  Mur_ligase  Mur ligase family, catalytic domain
       0.09   12.6   0.0        4.2    7.2   0.0    2.5  2  NAGLU_N     Alpha-N-acetylglucosaminidase (NAGLU) N-terminal 
       0.26   10.6   0.1       0.39   10.0   0.1    1.2  1  UbiA        UbiA prenyltransferase family
        1.4    9.9  11.8         52    4.9  11.9    2.8  1  Fer4_16     4Fe-4S double cluster binding domain
          9    7.1  12.3       0.25   12.0   0.8    2.3  2  Fer4_4      4Fe-4S binding 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 !  102.8   0.3     2e-32   1.9e-29       1     139 [.      59     238 ..      59     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 2e-32
                           LUD_dom   1 leefienleangaevyyaktaeealelilellkeksv.....................vseggstdlgeigl..... 51 
                                       +++++++le  ga+vy+a++ae+a++++ e++ ++++                     + e+++tdlge+++     
  gi|488600183|ref|YP_007906654.1|  59 IDKAAKALEDAGATVYFAENAEKARKIAGEIVGSGKIvvkaksmvseeihlreylqqlGNEVWETDLGELIIqland 135
                                       6899************************************************************************* PP

                           LUD_dom  52 ......apalhsgreevldlfeekl.........treareelrekfltadvgitganfaiAetGtlvlvdnegnrra 113
                                             +palh  +++v++++++ +         ++  r  +rekf +advgi+g+n+   e+  ++l++negn r+
  gi|488600183|ref|YP_007906654.1| 136 kpmhivIPALHYSEQQVAEILKKIGiegrnaeemAKGVRVFMREKFKNADVGISGCNAFSVENARVFLIENEGNIRL 212
                                       **********************************9**********************9999**************** PP

                           LUD_dom 114 ltflpkvhivvvginkivpdledavk 139
                                        t+lpk++i+++ i+ki+pd   a+k
  gi|488600183|ref|YP_007906654.1| 213 STSLPKTYIALISIDKILPDDILALK 238
                                       *******************9666665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   3.3   2.9e-10   2.7e-07       3      63 ..     284     345 ..     282     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.9e-10
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvlee..eealwsCttcgaCtevCpv 63 
                                        +C++Cg+Cq +Cp+++ ++  +  + +g+ ++ + ++  + e  e+a+ sC  c +C+ vCp+
  gi|488600183|ref|YP_007906654.1| 284 LSCVRCGRCQLECPIFQLSGnIWGGSVYGGPMG-MGWSAITGEmtENAFLSC-LCSKCKHVCPM 345
                                       68******************77***********.666666555757777777.6*********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 !   15.6   0.1   1.4e-05     0.013       6      21 ..     283     298 ..     280     321 .. 0.82
   2 !   11.2   0.4   0.00032       0.3      11      23 ..     335     347 ..     327     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                           Fer4_10   6 ddtCirCgkCvkaCPa 21 
                                       + +C+rCg+C+  CP 
  gi|488600183|ref|YP_007906654.1| 283 QLSCVRCGRCQLECPI 298
                                       568************8 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00032
                           Fer4_10  11 rCgkCvkaCPadl 23 
                                        C kC+ +CP+++
  gi|488600183|ref|YP_007906654.1| 335 LCSKCKHVCPMYI 347
                                       5**********55 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   3.0    0.0047       4.4      45      57 ..     285     297 ..     276     298 .. 0.90
   2 !   18.1   7.3   3.2e-06     0.003       2      61 .]     286     348 ..     285     348 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0047
                           Fer4_17  45 lCieCgeCerkCP 57 
                                       +C+ Cg+C+ +CP
  gi|488600183|ref|YP_007906654.1| 285 SCVRCGRCQLECP 297
                                       7***********9 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.2e-06
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraakl....glleeaekeekaslCieCgeCerkCPqgld 61 
                                       C +Cg C  eCp ++  +n     ++   +    + ++++++e+++ +C  C +C+++CP+ +d
  gi|488600183|ref|YP_007906654.1| 286 CVRCGRCQLECPIFQLSGNIWGGSVYGGPMgmgwSAITGEMTENAFLSC-LCSKCKHVCPMYID 348
                                       ****************888433333333332233555565565666666.6*********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 !   13.6   0.1     8e-05     0.075      33      49 ..     281     297 ..     252     304 .. 0.77
   2 ?    4.9   0.4     0.042        39      41      49 ..     336     344 ..     311     347 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8e-05
                            Fer4_7  33 idpekClgCgaCvavCP 49 
                                       +++ +C+ Cg+C+ +CP
  gi|488600183|ref|YP_007906654.1| 281 VEQLSCVRCGRCQLECP 297
                                       34668999999999999 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.042
                            Fer4_7  41 CgaCvavCP 49 
                                       C +C  vCP
  gi|488600183|ref|YP_007906654.1| 336 CSKCKHVCP 344
                                       566666666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.5   0.00011       0.1       8      20 ..     285     297 ..     280     303 .. 0.87
   2 ?    6.1   0.6     0.013        13      12      22 ..     336     346 ..     335     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                       +C+ Cg+C   CP
  gi|488600183|ref|YP_007906654.1| 285 SCVRCGRCQLECP 297
                                       7************ PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                            Fer4_6  12 CgdCvrvCPeg 22 
                                       C +C  vCP++
  gi|488600183|ref|YP_007906654.1| 336 CSKCKHVCPMY 346
                                       *********85 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2    0.0002      0.19      36      53 ..     281     298 ..     262     302 .. 0.60
   2 ?    6.3   1.0     0.012        11      44      53 ..     336     345 ..     323     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                           Fer4_21  36 vvedeCvGCnlCssvCPv 53 
                                       v + +Cv C  C   CP+
  gi|488600183|ref|YP_007906654.1| 281 VEQLSCVRCGRCQLECPI 298
                                       224467777777777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                           Fer4_21  44 CnlCssvCPv 53 
                                       C  C +vCP+
  gi|488600183|ref|YP_007906654.1| 336 CSKCKHVCPM 345
                                       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 !   14.9   0.1   3.8e-05     0.035      55      93 ..     259     297 ..     249     299 .. 0.83
   2 ?    2.0   1.5      0.42     4e+02       5      13 ..     336     344 ..     327     347 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-05
                           Fer4_22  55 rkekkerlrqrllhklsefkekfgesgCvGCgRCieacp 93 
                                       r+ +++ ++  +++  ++ +e +++ +Cv CgRC+  cp
  gi|488600183|ref|YP_007906654.1| 259 RPVAGQEMHAIFIDNGRSSTEFVEQLSCVRCGRCQLECP 297
                                       556677778888888888888899**************8 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.42
                           Fer4_22   5 CgaCtlvCp 13 
                                       C++C+ vCp
  gi|488600183|ref|YP_007906654.1| 336 CSKCKHVCP 344
                                       777777776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.5    0.0011         1      35      47 ..     285     297 ..     263     301 .. 0.70
   2 ?   12.8   8.9   0.00011       0.1       2      48 ..     286     345 ..     285     349 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                            Fer4_9  35 aCigCgaCveaCp 47 
                                       +C+ Cg+C   Cp
  gi|488600183|ref|YP_007906654.1| 285 SCVRCGRCQLECP 297
                                       5777777777776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                            Fer4_9   2 CtgCgaCveaC................pagvvvedaaerkarlraase..............eaCigCgaCveaCpk 48 
                                       C++Cg+C+  C                                   ++               +C+ C +C ++Cp 
  gi|488600183|ref|YP_007906654.1| 286 CVRCGRCQLECpifqlsgniwggsvygG----------------PMGMgwsaitgemtenafLSCL-CSKCKHVCPM 345
                                       ***********66666444444444331................33333344555666666678**.*********7 PP

>> UBA_6  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.15   1.4e+02      19      39 ..     110     129 ..     105     130 .. 0.78
   2 ?    9.9   0.0   0.00073      0.69      13      28 ..     147     162 ..     144     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                             UBA_6  19 qavLekLGpeadedkvLsELI 39 
                                       +  L++LG e+ e + L+ELI
  gi|488600183|ref|YP_007906654.1| 110 REYLQQLGNEVWETD-LGELI 129
                                       6679******95544.89998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00073
                             UBA_6  13 YseeqvqavLekLGpe 28 
                                       Yse+qv  +L+k+G e
  gi|488600183|ref|YP_007906654.1| 147 YSEQQVAEILKKIGIE 162
                                       **************86 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 ?    0.6   0.4      0.49   4.6e+02      22      38 ..     284     298 ..     270     302 .. 0.77
   2 ?   14.3   0.8   2.8e-05     0.026      25      50 ..     332     357 ..     323     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.49
                                       TT----TT-HHHHCSTT CS
                           Fer4_20  22 sRClqCkkapcvkgCPv 38 
                                         C++C    c+ +CP+
  gi|488600183|ref|YP_007906654.1| 284 LSCVRC--GRCQLECPI 298
                                       569999..679999997 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.8e-05
                                       ---TT-HHHHCSTT---HHHHHHHHH CS
                           Fer4_20  25 lqCkkapcvkgCPveidipefikkia 50 
                                       l+C  ++c++ CP+ idipe i+ki+
  gi|488600183|ref|YP_007906654.1| 332 LSCLCSKCKHVCPMYIDIPEIIRKIR 357
                                       678889*****************997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.5     3e-05     0.028       7      19 ..     285     297 ..     280     299 .. 0.89
   2 ?    1.6   3.2      0.28   2.7e+02      11      20 ..     336     345 ..     334     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                       TSSS-THHHHHST CS
                              Fer4   7 kCigCGaCvevCP 19 
                                        C++CG+C   CP
  gi|488600183|ref|YP_007906654.1| 285 SCVRCGRCQLECP 297
                                       7************ PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.28
                                       -THHHHHSTT CS
                              Fer4  11 CGaCvevCPv 20 
                                       C +C  vCP 
  gi|488600183|ref|YP_007906654.1| 336 CSKCKHVCPM 345
                                       9********5 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.0   3.3e-05     0.031       5      21 ..     281     297 ..     279     297 .. 0.89
   2 ?    2.6   3.5      0.18   1.7e+02      13      21 ..     336     344 ..     332     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       v+  +C++Cg C+  CP
  gi|488600183|ref|YP_007906654.1| 281 VEQLSCVRCGRCQLECP 297
                                       67789***********9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                            Fer4_2  13 CgaCvsaCP 21 
                                       C++C ++CP
  gi|488600183|ref|YP_007906654.1| 336 CSKCKHVCP 344
                                       99******* PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.077        73      57      72 ..     282     297 ..     259     301 .. 0.71
   2 ?   10.3   0.3   0.00063       0.6      60      79 ..     333     351 ..     319     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.077
                           Fer4_18  57 gagdcidcescvkvcP 72 
                                       ++  c+ c+ c   cP
  gi|488600183|ref|YP_007906654.1| 282 EQLSCVRCGRCQLECP 297
                                       5556777777777777 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00063
                           Fer4_18  60 dcidcescvkvcPtgidirk 79 
                                        c  c++c +vcP+ idi +
  gi|488600183|ref|YP_007906654.1| 333 SC-LCSKCKHVCPMYIDIPE 351
                                       44.5*************965 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00021       0.2      32      85 ..      63     118 ..      48     121 .. 0.86
   2 ?   -1.5   0.0       3.4   3.2e+03      38      51 ..     171     184 ..     159     228 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                                       SHCHHHTT-EEEES-HGGGG..EE-TS-TTCHHHHHHHHTTEEEEEHHHHHHHHHH CS
                        Mur_ligase  32 ieslialGaaavvghdaani..vvssiskdnpeleaakepgipvesraeaLaelaa 85 
                                       ++ l+++Ga++++++ a+    ++++i  + + +++ak  + + ++++e L++l +
  gi|488600183|ref|YP_007906654.1|  63 AKALEDAGATVYFAENAEKArkIAGEIVGSGKIVVKAKSMVSEEIHLREYLQQLGN 118
                                       455*************99889988887778999999*****************976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.4
                                       TT-EEEES-HGGGG CS
                        Mur_ligase  38 lGaaavvghdaani 51 
                                       +G+++++ ++ +n 
  gi|488600183|ref|YP_007906654.1| 171 KGVRVFMREKFKNA 184
                                       55555555544433 PP

>> NAGLU_N  Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.098        93      38      62 ..      92     116 ..      40     123 .. 0.79
   2 ?    7.2   0.0    0.0045       4.2      39      61 ..     157     179 ..     134     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.098
                                       SS-EEEEESSHHHHHHHHHHHHHHH CS
                           NAGLU_N  38 ggkilIrGnsgvalasGlnwYLkyy 62 
                                       +gki+++++s v+    l+ YL++ 
  gi|488600183|ref|YP_007906654.1|  92 SGKIVVKAKSMVSEEIHLREYLQQL 116
                                       36***********999999999876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0045
                                       S-EEEEESSHHHHHHHHHHHHHH CS
                           NAGLU_N  39 gkilIrGnsgvalasGlnwYLky 61 
                                       +ki I+G ++ ++a+G++ ++++
  gi|488600183|ref|YP_007906654.1| 157 KKIGIEGRNAEEMAKGVRVFMRE 179
                                       59****************99986 PP

>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00041      0.39     117     148 ..     302     333 ..     299     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                              UbiA 117 lgtvvggiafglppllgwaavtgslsllalll 148
                                        g+++gg ++g p  +gw a+tg+++  a+l 
  gi|488600183|ref|YP_007906654.1| 302 SGNIWGGSVYGGPMGMGWSAITGEMTENAFLS 333
                                       689*********************97777665 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  11.9     0.055        52       2      66 ..     286     345 ..     285     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.055
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeai..tgCdiCqdvCPa 66 
                                       C++Cg+C   CP   ++++      +     y  ++  +++  + +++ ++a     C +C+ vCP+
  gi|488600183|ref|YP_007906654.1| 286 CVRCGRCQLECPIFQLSGN------IWGGSVYGGPMGMGWSAITGEMT-ENAFlsCLCSKCKHVCPM 345
                                       ****************999......33344566777777777777766.33333588*********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 ?   12.0   0.8   0.00026      0.25       3      15 ..     285     297 ..     283     312 .. 0.90
   2 ?   -0.7   4.8       2.9   2.7e+03       7      16 ..     336     345 ..     334     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       +C++Cg+C   CP
  gi|488600183|ref|YP_007906654.1| 285 SCVRCGRCQLECP 297
                                       7***********9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                            Fer4_4   7 CgsCvaaCPq 16 
                                       C +C  +CP+
  gi|488600183|ref|YP_007906654.1| 336 CSKCKHVCPM 345
                                       999******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); 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):              19  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2446.34
//
Query:       gi|488600184|ref|YP_007906655.1|  [L=160]
Description: hypothetical protein Asulf_00644 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   11.0   0.1       0.36   11.0   0.1    2.8  3  Tantalus  Drosophila Tantalus-like


Domain annotation for each model (and alignments):
>> Tantalus  Drosophila Tantalus-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.14   2.4e+03      36      54 ..      25      43 ..      17      47 .. 0.65
   2 ?   -1.5   2.6      0.15   2.7e+03       9      23 ..      75     107 ..      62     110 .. 0.55
   3 ?   11.0   0.1     2e-05      0.36       7      31 ..     128     157 ..     122     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.14
                          Tantalus 36 krLETIFEePsdenaaivk 54
                                      k+ ET+   ++d+n ++ +
  gi|488600184|ref|YP_007906655.1| 25 KNSETVAQGKNDKNDSQIL 43
                                      3468888888888877655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.15
                          Tantalus   9 pvrkkkkel..................siEeiY 23 
                                       p+++ k+ +                   +EeiY
  gi|488600184|ref|YP_007906655.1|  75 PKKIDKETEeivvkaykinldpvnlekKMEEIY 107
                                       333222222345555555555555555666666 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 2e-05
                          Tantalus   7 pkpvrkkkkel.....siEeiYtnknlkkf 31 
                                        k vr+++ +      s+++iY n++lk +
  gi|488600184|ref|YP_007906655.1| 128 SKRVRIQRWRNsidlcSCKNIYYNRQLKAY 157
                                       5677766655577889************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1465  (0.0817112); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1143.20
//
Query:       gi|488600185|ref|YP_007906656.1|  [L=227]
Description: indole-3-glycerol phosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  163.9   1.6    4.2e-48  163.7   1.6    1.0  1  IGPS       Indole-3-glycerol phosphate synthase
     0.0092   15.5   0.0      0.019   14.4   0.0    1.5  1  PcrB       PcrB family
  ------ inclusion threshold ------
      0.022   14.5   1.2      0.036   13.8   0.7    1.5  2  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
      0.048   13.0   0.8       0.12   11.7   0.7    1.7  1  NMO        Nitronate monooxygenase
      0.081   11.7   0.1        0.1   11.4   0.1    1.1  1  DUF2254    Predicted membrane protein (DUF2254)


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 !  163.7   1.6   1.2e-51   4.2e-48      47     253 ..      16     223 ..       2     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 1.2e-51
                                       S-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHHH-SS-EEEES---SHHH CS
                              IGPS  47 klaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrqavslpvlrKdFiideyq 123
                                          +iaE+K  SP +g +  + ++ +i ++ye+a A  iS +t  + F+G++e+L+ + ++ +lpvlrKdFi+++ +
  gi|488600185|ref|YP_007906656.1|  16 VNPVIAEIKTYSPIHGDLVRNRNVIDILRAYENANAVGISYITARE-FKGDFENLKLICKETELPVLRKDFILSKEE 91 
                                       4579***************************************876.9***************************** PP

                                       HHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE...-CH CS
                              IGPS 124 ieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlev...dln 197
                                       ie++  + a aiLLi+++l +++ +e+++ a++ +le+LvEvh++e+++++ +++a+iiG+NnR++ +le    d+ 
  gi|488600185|ref|YP_007906656.1|  92 IERTASAEASAILLIARLLGHKT-AEFVDLAHESDLEALVEVHSAEDIQIVEESKAEIIGINNRDIMKLEKddgDVS 167
                                       ********************998.89****************************************99997222688 PP

                                       HHHHHCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                              IGPS 198 tteeLaklvpkd.vllvaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                        te+L+ l+  + +++v+ SGi+t ed+++  +  ++a+L+G++lm ++d e ++r+
  gi|488600185|ref|YP_007906656.1| 168 VTERLSGLISVKgRIVVSASGIRTLEDLKRALKC-ADAVLIGTALMMADDPESKLRS 223
                                       99********555******************999.***************9999876 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.3e-06     0.019     179     224 ..     179     226 ..     145     227 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-06
                                       SSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHH..HCHHHHHHH CS
                              PcrB 179 ekarlivGGGirsaEkAkevveaADvivvGnvveekd..erkidaile 224
                                       ++ +++   Gir  E+ k+ ++ AD++++G+++   d  e+k+++++e
  gi|488600185|ref|YP_007906656.1| 179 KGRIVVSASGIRTLEDLKRALKCADAVLIGTALMMADdpESKLRSFVE 226
                                       556677789**********************98654445999999987 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.5   1.8e+03      89     120 ..      88     120 ..      86     129 .. 0.66
   2 ?   13.8   0.7     1e-05     0.036      76     158 ..     121     211 ..     109     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.5
                                       SHHHHHHHHHHT-SEEEEES.--HHHHHHHHHH CS
                         QRPTase_C  89 sleeleevleaeadiimLDn.fsveelkkavee 120
                                       s+ee+e+ ++aea+ i+L   +  ++++++v++
  gi|488600185|ref|YP_007906656.1|  88 SKEEIERTASAEASAILLIArLLGHKTAEFVDL 120
                                       678999999999988887430344666666665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1e-05
                                       HHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES-.........-HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHH CS
                         QRPTase_C  76 avdkevkievevesleeleevleaeadiimLDnf.........sveelkkaveelkeknkrvlievSGgvtlenvee 143
                                       a++  ++  vev+s e+++ v e +a+ii + n              +++ +  l + ++r+++++SG  tle+++ 
  gi|488600185|ref|YP_007906656.1| 121 AHESDLEALVEVHSAEDIQIVEESKAEIIGINNRdimklekddGDVSVTERLSGLISVKGRIVVSASGIRTLEDLKR 197
                                       555667789**********************998555555443123444555555677778**************99 PP

                                       HHCTT-SEEEECHHC CS
                         QRPTase_C 144 yaksgvdvisvgalt 158
                                         k   d++ +g++ 
  gi|488600185|ref|YP_007906656.1| 198 ALKCA-DAVLIGTAL 211
                                       98888.888888765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   3.5e-05      0.12     119     232 ..     108     218 ..      53     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                               NMO 119 fgfglpteevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgd.kglfaLvpqvldavd. 193
                                         +g +t e v+  +e+++ +++ + s++++++ve++ a ++ ++  +       ++ ++  g +++ ++    ++ 
  gi|488600185|ref|YP_007906656.1| 108 RLLGHKTAEFVDLAHESDLEALVEVHSAEDIQIVEESKAEIIGINNRDI------MKLEKdDGDVSVTERLSGLISv 178
                                       4468888899999999999999999999999999999998875554432......3333335555666655555553 PP

                               NMO 194 ..iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesd 232
                                           v+ a Gi + ++++ aL   A +v igt+++++++ +
  gi|488600185|ref|YP_007906656.1| 179 kgRIVVSASGIRTLEDLKRALKC-ADAVLIGTALMMADDPE 218
                                       3334999**************86.************99865 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.8e-05       0.1     181     279 ..     126     226 ..      88     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                           DUF2254 181 akdeeeseeeeatpiraersGylqaidveaLvklaeehdlvielevrpGdfvvkgeplakvwgee..ddeelaeklr 255
                                        +   e +++e  +i++e++  +  i+ ++++kl ++ + v   e+  G   vkg+ +++++g +  +d + a k++
  gi|488600185|ref|YP_007906656.1| 126 LEALVEVHSAEDIQIVEESKAEIIGINNRDIMKLEKDDGDVSVTERLSGLISVKGRIVVSASGIRtlEDLKRALKCA 202
                                       34455667788889999****************8777777777777789999999999999988899888899999* PP

                           DUF2254 256 eafligrertfeqDpefglrqLvE 279
                                       +a+lig+   + +Dpe  lr  vE
  gi|488600185|ref|YP_007906656.1| 203 DAVLIGTALMMADDPESKLRSFVE 226
                                       ********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1593.50
//
Query:       gi|488600186|ref|YP_007906657.1|  [L=324]
Description: anthranilate phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-73  247.7   0.0    1.8e-73  247.3   0.0    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    7.1e-10   38.6   0.2    3.7e-09   36.3   0.1    2.1  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.3   0.0     2e-77   1.8e-73       3     247 ..      66     304 ..      65     308 .. 0.96

  Alignments for each domain:
  == domain 1  score: 247.3 bits;  conditional E-value: 2e-77
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       ++ D++gTGGdg+nt+N+St++ai+++ +  +vakhgn s++sksGsaD+L alg+n  l+pee+++++e+++++fl
  gi|488600186|ref|YP_007906657.1|  66 EVCDTCGTGGDGSNTINVSTTSAIILS-CYKRVAKHGNTSITSKSGSADLLKALGINYWLSPEEAKECIEKTNFTFL 141
                                       578*********************997.6689********************************************* PP

                                       EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHH CS
                   Glycos_transf_3  80 fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevs 156
                                       fap yh+a+k v+pvr+elgirTvfn+LGPL npa++++ql+gv s++l+  +ae+l+ lgve a+vvhg+G de++
  gi|488600186|ref|YP_007906657.1| 142 FAPLYHPALKRVMPVRKELGIRTVFNVLGPLANPANPEHQLIGVSSEHLVDVVAEALMFLGVE-AVVVHGNGIDEAN 217
                                       ************************************************************997.6799********* PP

                                       HHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSS CS
                   Glycos_transf_3 157 llakttvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagka 233
                                       +  ++ +a +  ++i+++ ++pedfgl+  +   + g  ++e+a+ + +vl+gk  +++r+ +++n + al   g +
  gi|488600186|ref|YP_007906657.1| 218 PRKESVIAVV-SEDIEKFRIKPEDFGLTPVKIIPCSG--AEESADRIFRVLSGKGFREDRNFIVINSALALFSTG-I 290
                                       *999888777.577*********************99..9*******************************9999.9 PP

                                       SSHHHHHHHHHHHH CS
                   Glycos_transf_3 234 dslkegvakaeevi 247
                                       d+ +e ++ ae+v+
  gi|488600186|ref|YP_007906657.1| 291 DDFHECRELAESVL 304
                                       **********9987 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 !   36.3   0.1   4.2e-13   3.7e-09       7      63 .]       5      59 ..       1      59 [. 0.92
   2 ?   -0.7   0.0      0.15   1.3e+03      12      23 ..     123     134 ..     113     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.2e-13
                                      HHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N  7 lrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                      l+++++L+ + ++++++++++   +++ i+A L+Al +kG + eE+a++a+Amr+++
  gi|488600186|ref|YP_007906657.1|  5 LVEKKKLDFDSAYNLFTEMFN--ESEIRISAYLSALQTKGYSGEELAGFAKAMRDKA 59
                                      678899999***********9..689****************************986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.15
                                       ---HHHHHHHHH CS
                   Glycos_trans_3N  12 eLtaeeirfaih 23 
                                        L++ee++++i+
  gi|488600186|ref|YP_007906657.1| 123 WLSPEEAKECIE 134
                                       599*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2065.33
//
Query:       gi|488600187|ref|YP_007906658.1|  [L=433]
Description: anthranilate synthase, component I [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-86  289.3   0.0    7.6e-86  287.9   0.0    1.6  2  Chorismate_bind  chorismate binding enzyme
    9.3e-17   61.6   0.4    1.9e-15   57.3   0.1    2.7  3  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.18   1.6e+03      56      80 ..      24      55 ..       6      62 .. 0.66
   2 !  287.9   0.0   8.4e-90   7.6e-86       2     258 .]     167     418 ..     166     418 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.18
                                      EEEEEETT.......EEEEEEESSEEEEEETT CS
                   Chorismate_bind 56 sflleled.......sellgaSPElllkvegg 80
                                       f+le  d       ++ +++ PE +++++++
  gi|488600187|ref|YP_007906658.1| 24 PFILESADknelkarHTYISSNPEYIVQINKS 55
                                      4444333344555556789********99965 PP

  == domain 2  score: 287.9 bits;  conditional E-value: 8.4e-90
                                       HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEE CS
                   Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkve 78 
                                       r+d+ e+v ++k++i agd +++vlsr++ +   ++++p+++yr+l++ np+py+fl+e+e + + gaSPE++ +v 
  gi|488600187|ref|YP_007906658.1| 167 RDDFVEMVYRAKDYILAGDAFQIVLSREYAVD--TELTPFEFYRNLKRINPSPYMFLFEFE-KAIAGASPETMASVI 240
                                       799*****************************..89************************6.77************* PP

                                       TTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEE CS
                   Chorismate_bind  79 ggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhl 155
                                       g+  ++++piaGT++rgk+ eede l ++l++deKe+aEh m++dl+rnd++kv+++gsv+v+++++v +ys+v+h+
  gi|488600187|ref|YP_007906658.1| 241 GN-IVKINPIAGTIKRGKDGEEDEILIKKLMSDEKEIAEHIMLLDLARNDVRKVSRSGSVSVSRYMEVVKYSHVIHI 316
                                       77.************************************************************************** PP

                                       EEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETT CS
                   Chorismate_bind 156 vstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdk 232
                                        s++ g l+++++++d++++ fP+g++tGaPk rameii+elE ++R vY+G+vgy++++g a++a++IR+a+++ k
  gi|488600187|ref|YP_007906658.1| 317 ESEVCGVLEDGKTAFDAMESAFPAGTLTGAPKIRAMEIIRELERSQRVVYGGCVGYFSSNGWADMAIAIRMAEFDGK 393
                                       ****************************************************************************9 PP

                                       EEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 233 elrlgaGaGIvadSdpeaEyeEtlaK 258
                                        +r++aGaGIv dS pe+Ey Et+ K
  gi|488600187|ref|YP_007906658.1| 394 -CRVRAGAGIVSDSVPENEYYETERK 418
                                       .**********************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 !   57.3   0.1   2.1e-19   1.9e-15       3     141 ..       9     131 ..       7     132 .. 0.90
   2 ?   -2.8   0.0      0.72   6.4e+03       3      22 ..     201     223 ..     199     223 .. 0.79
   3 ?    1.5   0.0     0.036   3.2e+02      88      99 ..     363     374 ..     275     377 .. 0.79

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.1e-19
                     Anth_synt_I_N   3 ltplsvylklaeeehkflLeSaeneggegrySfigldpflelkskngevevegpegeeleeeepldalrellerfrs 79 
                                       ++p ++y  l++++++f+LeSa++++ ++r  +i  +p   ++++++ +++++  ++ ++ ++p++al++l++ +  
  gi|488600187|ref|YP_007906658.1|   9 VEPEKLYCVLRDDSYPFILESADKNELKARHTYISSNPEYIVQINKSGMKINR--KRVSKVSNPFKALKNLINGCVG 83 
                                       68999******************77777*************************..99999999*************6 PP

                     Anth_synt_I_N  80 aedseptelpfvgGlvGylgYDlvreieklpksakddlnlpdarlilydtlivfDhkerrly 141
                                        e+       fvgGlvGy+ Y +v ++ +       dl    a + +y +++v+D+  r+ly
  gi|488600187|ref|YP_007906658.1|  84 GER-------FVGGLVGYIPYQAVYNYID------GDL-SEPAVFGFYPHVFVYDNFARTLY 131
                                       654.......*************998843......233.44589***************998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.72
                     Anth_synt_I_N   3 ltplsvylklaeee...hkflLe 22 
                                       ltp + y+ l+  +   + fl+e
  gi|488600187|ref|YP_007906658.1| 201 LTPFEFYRNLKRINpspYMFLFE 223
                                       79999999999887777777776 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.036
                     Anth_synt_I_N  88 lpfvgGlvGylg 99 
                                         ++gG vGy++
  gi|488600187|ref|YP_007906658.1| 363 RVVYGGCVGYFS 374
                                       3489******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2717.26
//
Query:       gi|488600188|ref|YP_007906659.1|  [L=189]
Description: anthranilate synthase, component II [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-43  147.1   0.0    5.7e-43  146.9   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    8.7e-14   51.8   0.0    1.4e-12   47.8   0.0    2.0  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 !  146.9   0.0   6.4e-47   5.7e-43       1     180 [.       3     174 ..       3     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 6.4e-47
                                       EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEE CS
                            GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLG 76 
                                       +liDn ds+++nl+++   ++ +v vv +  +  e   ++++pdgi++s+Gpgsp+ +e   ++++ ++e ++PiLG
  gi|488600188|ref|YP_007906659.1|   3 VLIDNRDSFVWNLAEYTSLFD-RVRVVDNGIKLYEL--KKMDPDGIIISPGPGSPErREDIGNCAEIVIEMDVPILG 76 
                                       58***************9999.9*******999999..479***************66666677888899******* PP

                                       ETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEE CS
                            GATase  77 ICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddee 153
                                       ICLG+Q++a++fg+ v + k  + hg+++ + +d++ ++++ +n++   ++H+++v++   +p+g+e++a + d+ +
  gi|488600188|ref|YP_007906659.1|  77 ICLGHQIIAHAFGGLVGRIK--PVHGKKSLIMHDGKTIFSDVQNPIFGGRYHSLAVKK---VPKGFEISAITCDG-T 147
                                       *****************988..9***********************************...***********887.9 PP

                                       EEEEEEETTTEEEESSBTTSTTSTTHH CS
                            GATase 154 lmeiiekknpfvgvQFHPEststpegp 180
                                       +m+i+ k++p+ g+QFHPEs++t+ + 
  gi|488600188|ref|YP_007906659.1| 148 IMGIRCKNRPIEGLQFHPESVLTEFER 174
                                       **********************98754 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   1.6e-16   1.4e-12     100     216 .]      66     166 ..      49     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.6e-16
                     Peptidase_C26 100 aalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhq 176
                                        ++e +vPilgiC+G+q+++ a+GG l+ +i+             ++ ++++ ++ g+ + + ++ + i    +H+ 
  gi|488600188|ref|YP_007906659.1|  66 IVIEMDVPILGICLGHQIIAHAFGG-LVGRIKP------------VHGKKSLIMHDGKTIFSDVQ-NPIFGGRYHSL 128
                                       57899*******************9.6778884............22344555555555555555.5777799**** PP

                     Peptidase_C26 177 aikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       a+k++ ++++++A++ Dg+i  i+ +++  ++ g+Q+HPE
  gi|488600188|ref|YP_007906659.1| 129 AVKKVPKGFEISAITCDGTIMGIRCKNR--PIEGLQFHPE 166
                                       ***************************4..6********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1337.88
//
Query:       gi|488600189|ref|YP_007906660.1|  [L=220]
Description: phosphoribosylanthranilate isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-31  108.9   0.0    3.1e-31  108.7   0.0    1.1  1  PRAI             N-(5'phosphoribosyl)anthranilate (PRA) isome
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.19   11.1   0.0    1.3  1  BtpA             BtpA family
       0.14   12.3   0.0       0.17   12.0   0.0    1.3  1  Cob_adeno_trans  Cobalamin adenosyltransferase


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 !  108.7   0.0   5.2e-35   3.1e-31       1     192 [.       3     200 ..       3     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 5.2e-35
                                       TCE----SHHHHHHHHHHTSSEEEEE--TTBTTB--HHHHHHHCCCS--EEEEEESSS-HHHHHHHHHHCTECEEEE CS
                              PRAI   1 akicgltrasdvkaavkagadelglifaesskrevseeqaqellekvpaklVGVfvNqpieevlriaqelgldvvQL 77 
                                       +kicg+++a ++   v++ ad++g+i +++s+r++s e+a el+  +    V V   ++ e   +i+++l+ +++Q+
  gi|488600189|ref|YP_007906660.1|   3 VKICGIRSAGELD-LVEKYADFTGVIVKSQSRRCISLEKAGELIDISSI-PVFVVSTASFEVWNEIIRKLNPEFIQI 77 
                                       6899999999876.6788888**********************998876.799999999999*************** PP

                                       -CGG.-HHHHHHHHHHS-TTSEEEEEEE-S........SS--S-SSTT-SEEEEESSS-SSSXXXXGGGGTTSXX.. CS
                              PRAI  78 HGdedeqeyeellktelpvikalkvaesvd........evkearradhvdllllDsgaGGtGelldwsliskllks. 145
                                       H + +++ ++e+ + +l ++k +kv+ sv          vk+++ +++ dl+llDsg+G +G+  d+ +  ++ +  
  gi|488600189|ref|YP_007906660.1|  78 HSEMPAEFVQEFRDMGLFIMKVFKVPLSVLdyiqfseeLVKKIESFPA-DLILLDSGNG-SGKMHDLRVSREICRRv 152
                                       ***999999*****************9985555552233444444555.*******999.*********99999889 PP

                                       .TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHH CS
                              PRAI 146 .lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfv 192
                                        +k++LAGGL+p+Nv  ++ + +++gvDvssGVE++G+kD+ +i++f+
  gi|488600189|ref|YP_007906660.1| 153 eRKIMLAGGLNPQNVGYVVSFVNPYGVDVSSGVERDGKKDKSLIQNFL 200
                                       9*********************************************97 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.2e-05      0.19     161     237 ..     113     192 ..      96     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.2e-05
                              BtpA 161 esavkdtvergladavil.sGkatGgevdleelklaketvkvkvlvgsGvseenlekllsiad..GvivgtsikkdG 234
                                       ++ + + +e  +ad ++l sG  +G+  dl   + + + v+ k++   G + +n+  ++s+ +  Gv v++ + +dG
  gi|488600189|ref|YP_007906660.1| 113 SEELVKKIESFPADLILLdSGNGSGKMHDLRVSREICRRVERKIMLAGGLNPQNVGYVVSFVNpyGVDVSSGVERDG 189
                                       55566678888999888879****************************************99877999********* PP

                              BtpA 235 kia 237
                                       k  
  gi|488600189|ref|YP_007906660.1| 190 KKD 192
                                       965 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.8e-05      0.17      89     137 ..     111     159 ..      30     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHHS--EESEEES-S..SHHHHHHHHHHHHHHHHHHHHHHH CS
                   Cob_adeno_trans  89 eelekeideleaelpplksfilpgg..spaaaalhvaRtvcRraERavvel 137
                                       +  e+ ++++e+ +p  +  +l +g  s  +  l v R +cRr+ER+++ +
  gi|488600189|ref|YP_007906660.1| 111 QFSEELVKKIES-FP-ADLILLDSGngSGKMHDLRVSREICRRVERKIMLA 159
                                       455555555554.22.22233333322556678999***********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1431.50
//
Query:       gi|488600190|ref|YP_007906661.1|  [L=384]
Description: tryptophan synthase, beta chain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  164.8   0.5    3.5e-48  164.5   0.5    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 !  164.5   0.5   1.9e-52   3.5e-48       3     294 .]      50     369 ..      48     369 .. 0.83

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 1.9e-52
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                       ++ +pTPl  +++ls+++g++++lK+E+l ++g++K++      + +k   +++ ++e+++G+hg+a+A+a++l++l
  gi|488600190|ref|YP_007906661.1|  50 YAGRPTPLYYAKNLSEKHGAKIYLKREDLLHGGAHKINNTIGQALLAKYMGKKRIIAETGAGQHGVATAMAGSLFKL 126
                                       5789**********************************99955555555549999999999**************** PP

                                       EEEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH...........STTCEE--TTTSHHHHHH CS
                              PALP  80 kvtivvpadas...pekvallrllGaevvevggdydeavaaaaelaae...........gegaylvsqfdnptvieg 142
                                       k +i++ a +    + +v +++llGaev+ v++++ + ++a++e++++           +++++  +++  pt++  
  gi|488600190|ref|YP_007906661.1| 127 KTEIYMGAEDVerqKTNVFRMKLLGAEVIPVNSGTRTLKDAINEALRDwvasfesthylIGSVVGPHPY--PTIVRD 201
                                       **********95555****************99999999999999999888887445544444444454..778888 PP

                                       .HHTHHHHHHHHTT....TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCC.S..S.SS..B. CS
                              PALP 143 .ygtiglEileqlg....gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarsl.ragrrvtvpvs 213
                                        ++ ig+E  eq+       pd+vv++vGgG+++ Gi +++ e   dv++igve+ g+   +++    g+   ++ +
  gi|488600190|ref|YP_007906661.1| 202 fQSVIGFETREQILkaegSLPDTVVACVGGGSNAIGIFHAFVE--DDVELIGVEAGGNGVNNSASlNSGDKGVLHGM 276
                                       8********966656666************************9..679*****998444333333333333333333 PP

                                       ...............SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHH CS
                              PALP 214 ...............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalk 275
                                                      ++ia gl+ + +++++  l d +  e+v vsde+al a ++l + egi++   sa+a+a + 
  gi|488600190|ref|YP_007906661.1| 277 lsyflqnedgqmkdtHSIAAGLDYPGVGPEHAYLRDTKRAEYVVVSDEDALNAFVELSKLEGIIPALESAHAIAHA- 352
                                       666777777777777****************9999*****************************************. PP

                                       HHHHHCCTTCEEEEEEE-B CS
                              PALP 276 lreagelkegdrvvviltg 294
                                         + +e ++g  +vv l+g
  gi|488600190|ref|YP_007906661.1| 353 -IKIAEERGG-IIVVNLSG 369
                                       .555555666.78888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2651.10
//
Query:       gi|488600191|ref|YP_007906662.1|  [L=251]
Description: tryptophan synthase, alpha chain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-81  272.5   0.1    2.5e-81  272.3   0.1    1.0  1  Trp_syntA       Tryptophan synthase alpha chain
    8.1e-07   28.7   0.1    3.3e-06   26.7   0.0    1.9  2  His_biosynth    Histidine biosynthesis protein
    0.00018   20.6   0.0    0.00025   20.2   0.0    1.1  1  FMN_dh          FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.028   13.8   0.0    1.6  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.02   14.4   0.2      0.051   13.0   0.0    1.7  2  BtpA            BtpA family
      0.047   13.7   0.0        2.9    8.0   0.0    2.3  2  PA              PA domain
      0.067   12.5   0.0        0.1   11.9   0.0    1.4  1  TMP-TENI        Thiamine monophosphate synthase
      0.072   12.4   0.0       0.31   10.3   0.0    1.8  2  ThiG            Thiazole biosynthesis protein ThiG


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 !  272.3   0.1   1.1e-84   2.5e-81       9     257 ..       4     249 ..       1     251 [] 0.96

  Alignments for each domain:
  == domain 1  score: 272.3 bits;  conditional E-value: 1.1e-84
                                       B-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHC CS
                         Trp_syntA   9 raafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkke 85 
                                       ++ +++++tagdp+ + +++ l a+ek +ad++ElG+pfsdP+adG vIq+an raL++ ++l++v+ +vee+r ++
  gi|488600191|ref|YP_007906662.1|   4 NKSIITFITAGDPSKKATINFLFAMEK-YADILELGIPFSDPVADGEVIQRANYRALKH-MRLQDVFYIVEEFR-EH 77 
                                       5789**********************9.*****************************86.9*************.99 PP

                                       SSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH CS
                         Trp_syntA  86 vevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveq 162
                                       ++ P++l+ty+n+v+++g e+f+ ++keagvdgliv+DlP++ea++l ++ +k+g+  vfl ap+ts++rlk + e 
  gi|488600191|ref|YP_007906662.1|  78 SDKPLILMTYYNPVFRMGLEKFVSRAKEAGVDGLIVVDLPVDEADDLIKVSRKYGIGNVFLSAPNTSESRLKAIDE- 153
                                       ************************************************************************9966. PP

                                       --S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHCTTT CS
                         Trp_syntA 163 aegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkieeeae 238
                                       ++ f+Y+vs  GvTg+++++++   e+++r+k++ + PvavGFG+s++++v+++  ++adGv++GSa+v+ ie+  e
  gi|488600191|ref|YP_007906662.1| 154 VSEFIYLVSTYGVTGERDKISKLAFESLSRIKRICNSPVAVGFGVSKEDHVRELFdAGADGVVMGSAIVRLIERYGE 230
                                       667***************************************************99********************* PP

                                       SHHHHHHHHHHHHHHHHHC CS
                         Trp_syntA 239 ekeqalekleelarelkea 257
                                       ++e  ++k  + ++++ke+
  gi|488600191|ref|YP_007906662.1| 231 DAEDLIAKKLKAISAVKEK 249
                                       ***9999999888877776 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.41   9.2e+02      37      51 ..     102     116 ..      95     134 .. 0.77
   2 !   26.7   0.0   1.5e-09   3.3e-06      62     110 ..     178     226 ..     152     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.41
                                       HHHHHT-SEEEEEEH CS
                      His_biosynth  37 ryeeegadelhvvDl 51 
                                       r +e+g+d l+vvDl
  gi|488600191|ref|YP_007906662.1| 102 RAKEAGVDGLIVVDL 116
                                       556888888888888 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.5e-09
                                       HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-TH CS
                      His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpe 110
                                        + +++i + ++ pv vG G+++ ++v+el++agad v++g+a v+  e
  gi|488600191|ref|YP_007906662.1| 178 FESLSRIKRICNSPVAVGFGVSKEDHVRELFDAGADGVVMGSAIVRLIE 226
                                       5678889999999******************************998665 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.1e-07   0.00025     101     243 ..      71     217 ..      47     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHTT-EEEEEE-C.SSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHHHHCT--BSTT-T.G.TTGGGS CS
                            FMN_dh 101 leevaaaaegplwfqlyvp.kdrelteellkraeaagykalvltvDtpvlgkRerdlrngfslppklklrnllqela 176
                                       +ee  +++++pl+   y +   r   e+++ ra++ag++ l++ vD pv+   ++dl + +s + +++ + +l++  
  gi|488600191|ref|YP_007906662.1|  71 VEEFREHSDKPLILMTYYNpVFRMGLEKFVSRAKEAGVDGLIV-VDLPVDE--ADDLIK-VSRKYGIG-NVFLSAPN 142
                                       56667766666665555442789999**************987.9****98..566665.67777766.44666666 PP

                                       TSGSCCTTH...........THHHHHHCCCHB.......-TC--HHHHHHHHHHHSSEEEEE.EE-SHHHHHHHHHT CS
                            FMN_dh 177 kpewaaeal.........kkasaaaefvgkql.......dpsltwddikwlreqtklplvvK.Gvltaedakravea 236
                                       + e + +a                    +++         ++l +++++++++ ++ p+ v  Gv +++ ++++ +a
  gi|488600191|ref|YP_007906662.1| 143 TSESRLKAIdevsefiylV---------STYGvtgerdkISKLAFESLSRIKRICNSPVAVGfGVSKEDHVRELFDA 210
                                       6666666663444333221.........221122222223678******************66************** PP

                                       TESEEEE CS
                            FMN_dh 237 Gvdgivv 243
                                       G+dg+v 
  gi|488600191|ref|YP_007906662.1| 211 GADGVVM 217
                                       *****96 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      0.31   6.9e+02      63     113 ..      61     115 ..      50     126 .. 0.66
   2 ?   13.8   0.0   1.3e-05     0.028      91     197 ..     118     221 ..      94     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.31
                                       EEESSSHHHCHHHHHHCT-S..EEEEE-S..T-TTHHHHHHHHHHTTSEEEEEE- CS
                    Ribul_P_3_epim  63 HLmveevdrivpefaeagas..iisvHaE..alehlkrtiqeikeaGakaglvln 113
                                       H+ +++v  iv+ef e+  +  i++  +       l++++++ keaG+   +v++
  gi|488600191|ref|YP_007906662.1|  61 HMRLQDVFYIVEEFREHSDKplILMTYYNpvFRMGLEKFVSRAKEAGVDGLIVVD 115
                                       6667777777777777765542344444433344567888888888888777764 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.3e-05
                                       -TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS-.---CCHHHHHHHHHHHHHHHT-- CS
                    Ribul_P_3_epim  91 lehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQ.kFipevlekikkvrklidekeld 166
                                       +++ + +i+  ++ G+       p+t  + l+ + e  +++ l s     g   k  +  +e ++++++++++    
  gi|488600191|ref|YP_007906662.1| 118 VDEADDLIKVSRKYGIGNVFLSAPNTSESRLKAIDEVSEFIYLVSTYGVTGERdKISKLAFESLSRIKRICNS---- 190
                                       6677788888899999888888999999999998888888888877644444414556679999999999998.... PP

                                       -EEEEESS--.TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 167 lkievDGGvk.ldnieqiaeagadvlVagsav 197
                                         + v  Gv+ +d ++++ +agad +V+gsa+
  gi|488600191|ref|YP_007906662.1| 191 -PVAVGFGVSkEDHVRELFDAGADGVVMGSAI 221
                                       .88999999615789****************8 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.57   1.3e+03      37      48 ..     102     113 ..      96     128 .. 0.80
   2 ?   13.0   0.0   2.3e-05     0.051     187     232 ..     176     223 ..     144     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.57
                              BtpA  37 aleegGvDavil 48 
                                         +e+GvD++i+
  gi|488600191|ref|YP_007906662.1| 102 RAKEAGVDGLIV 113
                                       56899****997 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.3e-05
                              BtpA 187 vdleelklaketvkvkvlvgsGvsee.nlekllsi.adGvivgtsikk 232
                                          e+l ++k++ + +v vg Gvs+e  +++l+++ adGv++g+ i +
  gi|488600191|ref|YP_007906662.1| 176 LAFESLSRIKRICNSPVAVGFGVSKEdHVRELFDAgADGVVMGSAIVR 223
                                       5678999****************97625888887659******98743 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0013       2.9      39      62 ..     100     123 ..      71     147 .. 0.76
   2 ?    3.8   0.0     0.026        59      36      54 ..     201     219 ..     152     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                                PA  39 arnAqaaGAagviivndgelgaat 62 
                                       +  A++aG  g+i+v+ + ++a++
  gi|488600191|ref|YP_007906662.1| 100 VSRAKEAGVDGLIVVDLPVDEADD 123
                                       678************776644444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.026
                                PA  36 aeKarnAqaaGAagviivn 54 
                                        + +r   +aGA gv++ +
  gi|488600191|ref|YP_007906662.1| 201 EDHVRELFDAGADGVVMGS 219
                                       667888899*******983 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   0.0   4.7e-05       0.1     109     181 .]     147     221 ..     100     221 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                          TMP-TENI 109 aeeaealgadYigvGpifpTdtKkda.eplgleglkelaealeiPvva.iGGitlenvaevleagadgvavvsai 181
                                        ++a ++   +i + + +  +   d+ + l  e l+++++ ++ Pv +  G  ++++v e+++agadgv + sai
  gi|488600191|ref|YP_007906662.1| 147 RLKAIDEVSEFIYLVSTYGVTGERDKiSKLAFESLSRIKRICNSPVAVgFGVSKEDHVRELFDAGADGVVMGSAI 221
                                       55555555566666666666666666688899999999999998875515556778999**********999998 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.38   8.5e+02     190     218 ..     100     129 ..      93     134 .. 0.77
   2 ?   10.3   0.0   0.00014      0.31     167     208 ..     181     222 ..     173     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.38
                                       HHHHHHTT-SEEE.ESHHHHTSSSHHHHHH CS
                              ThiG 190 aaqamelGadavl.lntavaeakdpvamAr 218
                                       +  a e G+d+++ ++  v ea+d +++ r
  gi|488600191|ref|YP_007906662.1| 100 VSRAKEAGVDGLIvVDLPVDEADDLIKVSR 129
                                       56788999*996516789999999998876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                                       HHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
                              ThiG 167 lkiiieeakvPvivDAGigspsdaaqamelGadavllntava 208
                                       l+ i + ++ Pv v  G+ +  ++ + ++ Gad+v++ +a+ 
  gi|488600191|ref|YP_007906662.1| 181 LSRIKRICNSPVAVGFGVSKEDHVRELFDAGADGVVMGSAIV 222
                                       5566666799******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1752.76
//
Query:       gi|488600192|ref|YP_007906663.1|  [L=221]
Description: RNA ligase partner, MJ_0950 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-90  300.9   0.0    4.1e-90  300.7   0.0    1.0  1  PIN_5     PINc domain ribonuclease


Domain annotation for each model (and alignments):
>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.7   0.0   2.3e-94   4.1e-90       1     206 []       4     214 ..       4     214 .. 0.97

  Alignments for each domain:
  == domain 1  score: 300.7 bits;  conditional E-value: 2.3e-94
                             PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyip.psvykElkeflkreeveeeviakldtwl 76 
                                       rfvlDT+altd+ +rek g e+++++++kll++ia+arlkl+iscyip p+vy+El +flkr++++e+viak+dtwl
  gi|488600192|ref|YP_007906663.1|   4 RFVLDTTALTDTGMREKEGFESICDSTNKLLTFIAKARLKLDISCYIPyPTVYNELLSFLKRYNCDEDVIAKMDTWL 80 
                                       8**************************************************************************** PP

                             PIN_5  77 vkkspdryevkipaeilyeyveevrerinkGlrvaEeavreaaeesekl...e.keeeeeevgelikklRekYreal 149
                                       vkk+p+ryevkipa+i+yeyv ++r++in+G ++aEe ++e+++ ++kl   + + + e+e+g+li+++Re+Yr +l
  gi|488600192|ref|YP_007906663.1|  81 VKKTPNRYEVKIPAAIFYEYVLTMRQKINQGKKLAEEYLWESSAITSKLigsKsSGDIEKEIGNLISRFRERYRVTL 157
                                       ********************************************99998765335669******************* PP

                             PIN_5 150 RkGilDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeylk 206
                                       R GilDs++D+dvllLAkEL+a+vvssD+Gi+kwaeklGlr+vea+kfp++l+eylk
  gi|488600192|ref|YP_007906663.1| 158 RGGILDSEPDIDVLLLAKELEAGVVSSDAGIRKWAEKLGLRYVEASKFPRMLREYLK 214
                                       *******************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1339.30
//
Query:       gi|488600193|ref|YP_007906664.1|  [L=413]
Description: histidyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-63  212.3   0.0    1.2e-62  212.0   0.0    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    1.5e-15   57.1   0.5    4.3e-15   55.6   0.5    1.8  1  HGTP_anticodon  Anticodon binding domain
    1.4e-12   47.9   0.0    3.4e-12   46.7   0.0    1.6  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.1e-05   24.7   2.3    0.00084   18.5   0.6    2.9  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)
     0.0046   16.5   0.0     0.0091   15.5   0.0    1.5  1  tRNA-synt_2d    tRNA synthetases class II core domain (F)


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 !  212.0   0.0   3.3e-66   1.2e-62       1     310 []       8     305 ..       8     305 .. 0.93

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 3.3e-66
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd+lp+ +e++++++r + +++e++GY+++++P++E+l+ ++ ++ge    +++ ++D+sgr l+lR+++T+ v 
  gi|488600193|ref|YP_007906664.1|   8 GTRDFLPDVMERRRSIERIMRETAERYGYREICTPTFEHLELFTIKSGEGIVeEIYAFKDKSGRDLALRPELTAPVM 84 
                                       78************************************************6549*********************** PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlg 152
                                       R++ +  +  +rp+R++Y+ +++r ++ + gr re+ Q+G+El+G+ +  adlEv+ l++++l+  +++ e++l +g
  gi|488600193|ref|YP_007906664.1|  85 RVVVNECSvMQRPMRFYYFSNCFRYENPQKGRYREFWQFGVELVGSGSYLADLEVIVLAYNILK-NLNI-EFELRIG 159
                                       ******999******************************************************7.9999.9****** PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHHHH CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalarkdlaelkelaaeaglkealrellkal.elygdaevleealealaaapal 228
                                       hvgl+r+l+++  lse++ +++++++++ +l+el++l        +++e+++ l  l+g++ev++ a++ +++    
  gi|488600193|ref|YP_007906664.1| 160 HVGLMRELFKD--LSEERYRKVMRLIDKNNLEELEKLQP------DYAEMVRELiALKGKREVIDLARRLVPEF--- 225
                                       **********7..66******************998875......567888888899**********9977766... PP

                                       HHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEET...T-SS-SEEEEEECTTTGGG.T---EEE CS
                     tRNA-synt_His 229 qaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayae...gvgqaiarGGrYdelgaaf.grarpAt 301
                                           ++le+l ++l+ l+   +++++D++ +rg++YytG+vF+a+a+   g++++i +GG Y  l + f g+  p+t
  gi|488600193|ref|YP_007906664.1| 226 --DFEHLERLSNALDLLG---IEYSIDFSIVRGLDYYTGIVFEAFAKrglGAQNQICGGGSY-RLTHLFgGEDIPST 296
                                       ..3699999999999986...*************************73225778********.9*****99****** PP

                                       EEEEEHHHH CS
                     tRNA-synt_His 302 Gfsldleal 310
                                       Gf++  +++
  gi|488600193|ref|YP_007906664.1| 297 GFAIGFDRI 305
                                       ***988875 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.5   1.2e-18   4.3e-15       9      93 ..     323     406 ..     317     407 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.2e-18
                                       SSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETT CS
                    HGTP_anticodon   9 ekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsld 85 
                                       + + ++  +a+ +ae Lr++g++v  d  +++++k+++ a+ ++  fa++vGe+e++ g+v v+d++t++qerv++d
  gi|488600193|ref|YP_007906664.1| 323 S-TPAMRVEAMLVAEMLRKEGLKVYADVMERNLRKQLSFANSINAEFAIIVGEDEYKAGEVVVKDLETGKQERVAID 398
                                       4.4567788999********************************************99******************* PP

                                       HHHHHHHH CS
                    HGTP_anticodon  86 elveklke 93 
                                       ++++++k 
  gi|488600193|ref|YP_007906664.1| 399 SIASEIKR 406
                                       ****9985 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 !   46.7   0.0   9.6e-16   3.4e-12       1     119 [.      63     263 ..      63     317 .. 0.69

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 9.6e-16
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld 77 
                                       Y ++d+ +r+++L+P+ ++++++++ +e     + P+++y+++ ++R+E++ ++G  R+reF q + + +++ +  +
  gi|488600193|ref|YP_007906664.1|  63 YAFKDKSGRDLALRPELTAPVMRVVVNE-CSVMQRPMRFYYFSNCFRYENP-QKG--RYREFWQFGVELVGSGS--Y 133
                                       89**************************.444556****************.***..**************999..5 PP

                                       HHHHHHHHHHHHHHHHTT.SCEEEEEE...GTTSC.......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx.......................................... RF
                      tRNA-synt_2b  78 dslrdlikaisriferlglefraiiel...msaks.......................................... 109
                                         + ++i ++++i+++l +ef   i+    m                                              
  gi|488600193|ref|YP_007906664.1| 134 LADLEVIVLAYNILKNLNIEFELRIGHvglM---Relfkdlseeryrkvmrlidknnleeleklqpdyaemvrelia 207
                                       566799*************995444442222...2233444445555555555555566666666666666666665 PP

                                       ..............................................BTTSEEEEEE CS
                                       ..............................................xxxxxxxxxx RF
                      tRNA-synt_2b 110 ..............................................adykdkkefe 119
                                                                                     +dy+   +fe
  gi|488600193|ref|YP_007906664.1| 208 lkgkrevidlarrlvpefdfehlerlsnaldllgieysidfsivrgLDYYTGIVFE 263
                                       55555555555555555555555555555555555555555555555555555555 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 !   18.5   0.6   2.3e-07   0.00084      20     147 ..      15     156 ..       7     200 .. 0.75
   2 !    3.7   0.0    0.0075        27     275     296 ..     286     307 ..     261     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT...TEEE................-E-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx................xxxxx RF
                       tRNA-synt_2  20 kvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrek..ekeff................aLtqs 78 
                                       +v++ r ++ +++r+  e+ g+ ei tP++ +       +lF++ks e   e e +                  ++ 
  gi|488600193|ref|YP_007906664.1|  15 DVMERRRSIERIMRETAERYGYREICTPTFEHL------ELFTIKSGEGivE-EIYafkdksgrdlalrpelTAPVM 84 
                                       67889999999999999999********99888......8888877776532.444456777775545553334455 PP

                                       SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEE....ET-SCHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  79 pqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaem....sfieeedimqvleelikslvkevle 147
                                            e  ++    r + ++++FR E+ ++ r   EF+q+ +e+    s++ + +++ ++ +++k+l  e+  
  gi|488600193|ref|YP_007906664.1|  85 RVVVNECSVMQRPMRFYYFSNCFRYENPQKGRYR-EFWQFGVELvgsgSYLADLEVIVLAYNILKNLNIEFEL 156
                                       555667777777889******************9.********999999999999999999999998887733 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0075
                                       HHHHCT--SEEEEEEEHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 275 ealeyGapphgGlglGldRlvm 296
                                       +++     p  G+++G+dR+  
  gi|488600193|ref|YP_007906664.1| 286 HLFGGEDIPSTGFAIGFDRIAE 307
                                       55555667999********875 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.5e-06    0.0091      65     161 ..      59     158 ..       5     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                                       TTSEBTCTSSS-ECESEEE-SSTHHHHHHHH....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT-- CS
                      tRNA-synt_2d  65 qdtFylkkpekaveekllLRthttavqirtl....ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvs 137
                                        +  y  k+++   ++l LR   ta  +r++    +  + p+++  + ++fR ++  + +  eF q    +v+++  
  gi|488600193|ref|YP_007906664.1|  59 VEEIYAFKDKS--GRDLALRPELTAPVMRVVvnecSVMQRPMRFYYFSNCFRYENPQKGRYREFWQFGVELVGSGSY 133
                                       44445545555..688*********999999877777889************************************* PP

                                       HHHHHHH..HHHHHHHHCTSTEEEEE CS
                      tRNA-synt_2d 138 ladlkgv..leellkklfgaevkvrf 161
                                       ladl ++  + ++lk+l + e+++r+
  gi|488600193|ref|YP_007906664.1| 134 LADLEVIvlAYNILKNL-NIEFELRI 158
                                       ***98651157788888.88888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); 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: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2502.14
//
Query:       gi|488600194|ref|YP_007906665.1|  [L=476]
Description: replication factor C large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-15   56.1   0.1    2.2e-14   54.0   0.0    2.1  2  AAA              ATPase family associated with various cellul
    1.3e-10   41.5   0.2    2.3e-09   37.4   0.2    2.7  1  Rad17            Rad17 P-loop domain
    2.8e-07   30.6   0.0    1.1e-06   28.7   0.0    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
    3.2e-06   27.5   0.0    1.4e-05   25.4   0.0    2.1  1  AAA_22           AAA domain
    3.2e-06   27.2   3.0    6.9e-05   22.9   0.0    2.9  3  AAA_14           AAA domain
    4.7e-06   26.5   0.0    1.3e-05   25.0   0.0    1.7  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    1.2e-05   25.1   0.0    2.9e-05   23.9   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.8e-05   25.0   0.0    5.4e-05   23.4   0.0    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
    2.8e-05   23.9   0.0    8.1e-05   22.4   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
    0.00052   20.4   0.0     0.0037   17.7   0.0    2.3  1  AAA_16           AAA ATPase domain
    0.00092   19.5   0.2     0.0043   17.4   0.1    2.2  1  AAA_assoc_2      AAA C-terminal domain
     0.0013   18.9   0.0      0.066   13.3   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0029   16.9   0.0     0.0091   15.2   0.0    1.8  2  TIP49            TIP49 P-loop domain
     0.0034   17.3   0.5       0.24   11.3   0.2    2.8  2  NACHT            NACHT domain
     0.0036   17.2   0.1       0.11   12.4   0.1    2.5  1  Bac_DnaA         Bacterial dnaA  protein
     0.0077   16.0   0.0      0.016   14.9   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
     0.0089   16.6   2.1      0.061   13.9   0.0    2.9  2  AAA_18           AAA domain
      0.009   15.5   0.0      0.015   14.8   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.012   15.9   0.6       0.35   11.2   0.1    2.9  2  AAA_19           AAA domain
      0.014   15.0   0.2      0.063   12.9   0.0    2.1  2  AAA_25           AAA domain
      0.014   15.4   0.9       0.28   11.2   0.0    2.8  3  ResIII           Type III restriction enzyme, res subunit
      0.034   13.8   0.0      0.072   12.8   0.0    1.5  1  AAA_24           AAA domain
      0.035   13.4   0.0       0.13   11.6   0.0    1.9  1  DnaB_C           DnaB-like helicase C terminal domain
      0.074   13.5   3.2          2    8.9   0.0    3.5  4  AAA_17           AAA domain
      0.078   13.4   0.0       0.82   10.1   0.0    2.6  1  RNA_helicase     RNA helicase
       0.11   13.0   0.4          1    9.9   0.0    2.4  3  ABC_tran         ABC transporter
       0.17   11.8   5.0       0.21   11.5   0.1    2.9  2  ATPase_2         ATPase domain predominantly from Archaea
       0.59    9.9   4.6       0.79    9.5   0.0    2.4  2  AAA_11           AAA domain
       0.73    9.9   3.4        1.6    8.7   3.4    1.5  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa


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 !   54.0   0.0   3.6e-17   2.2e-14       1     127 [.      39     161 ..      39     166 .. 0.80
   2 ?   -1.6   0.0       5.3   3.3e+03      16      35 ..     377     403 ..     345     448 .. 0.58

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.6e-17
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS..........STTHHHHHHHHHHHHHHHTSTSEEEEEETG CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk..........yvgesekkirelfkeakekakpsilfiDEi 67 
                                       +ll GppG+GKT+la a+a++ g e +e+++s+ ++            ++e+ ++  e++++ ++    +++++DE+
  gi|488600194|ref|YP_007906665.1|  39 LLLAGPPGVGKTSLALAIANTYGWEAVEMNASDQRNWeiitrivgegAFSETLSESGEFLRSSEKR--RKVIILDEV 113
                                       69*********************************6689988775555555555555555554444..4******** PP

                                       GGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                               AAA  68 dalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                       d+++k++       +     +L++ +++         +i+++n+   l+++l+ g ++ +
  gi|488600194|ref|YP_007906665.1| 114 DNIHKRE-------DAGGERALIRIIKKKPP----QPLILIANDLYALSKELR-GLCKLI 161
                                       ***9988.......77778999999998877....379999999999999999.777655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.3
                                       HHHHHHHT.......HEEEEEETTTCS CS
                               AAA  16 kavakelg.......vefleisgsell 35 
                                       ka+++ l+       + f+e++  +l 
  gi|488600194|ref|YP_007906665.1| 377 KALMERLDdercariSAFYEFDKEDLE 403
                                       444444322122222223333333333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.2   3.8e-12   2.3e-09       8      75 ..       2      66 ..       1     154 [. 0.69

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 3.8e-12
                             Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75
                                      lW+eky+P+++ ++   kk i+e+k+w ++   +s+ ++ LL++GP+G gk+     ++  +g +  e
  gi|488600194|ref|YP_007906665.1|  2 LWVEKYRPKTLSDVVAEKKVISEIKKWAET--FDSH-RKPLLLAGPPGVGKTSLALAIANTYGWEAVE 66
                                      6**************************766..5555.457999*********9888888888876555 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 !   28.7   0.0   1.7e-09   1.1e-06       1      79 [.      38     118 ..      38     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.7e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------.G-SEEEEESG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraar.egeilvlDEv 74 
                                       ++lL GppG+gK++la  +a  +++e ++++ +++ + e ++ r+  +   ++t  + +++ r+ + + ++++lDEv
  gi|488600194|ref|YP_007906665.1|  38 PLLLAGPPGVGKTSLALAIANTYGWEAVEMNASDQRNWE-IITRIVGEgaFSETLSESGEFLRSSEkRRKVIILDEV 113
                                       589*************************99998866655.55555533354445555555555554799******** PP

                                       GG--H CS
                             AAA_5  75 eraes 79 
                                       +++++
  gi|488600194|ref|YP_007906665.1| 114 DNIHK 118
                                       **996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.3e-08   1.4e-05       3     105 ..      34     119 ..      30     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.3e-08
                            AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseell 79 
                                       ++++ l++ G++G+GKT l+  +++++         + e v+++++ + +++ +     r++g+++ +   +++e  
  gi|488600194|ref|YP_007906665.1|  34 SHRKPLLLAGPPGVGKTSLALAIANTY---------GWEAVEMNASDQRNWEII----TRIVGEGAFS--ETLSE-S 94 
                                       578999*********************.........9************88776....7777776667..33333.3 PP

                            AAA_22  80 ealeqalraravielliiDEaqhlr.s 105
                                         + + +++r++  ++i+DE++++  +
  gi|488600194|ref|YP_007906665.1|  95 GEFLRSSEKRRK--VIILDEVDNIHkR 119
                                       456666666666..9********9542 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.1e-07   6.9e-05       2      81 ..      36     121 ..      35     168 .. 0.69
   2 ?   -1.1   0.0       2.9   1.8e+03      36      73 ..     219     259 ..     210     287 .. 0.70
   3 ?    2.7   1.0      0.19   1.2e+02      34      82 ..     393     438 ..     372     450 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderd..........kkladpekllelileklke...... 62 
                                       rk+l++ G+  vGKT l+  +++++     + +++n  d+r+                  + e +     e      
  gi|488600194|ref|YP_007906665.1|  36 RKPLLLAGPPGVGKTSLALAIANTYG---WEAVEMNASDQRNweiitrivgeG------AFSETLS----Esgeflr 99 
                                       7999******************9999...999*******99955444333220......2222222....1222333 PP

                            AAA_14  63 ...ekktylflDEiqevpewek 81 
                                          +++++++lDE+ ++ + e+
  gi|488600194|ref|YP_007906665.1| 100 sseKRRKVIILDEVDNIHKRED 121
                                       455799**********955443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                            AAA_14  36 inldderdkkladpe...kllelileklkeekktylflDEi 73 
                                       ++l+d   +k+++++   k+l++i++  ++     ++lDE 
  gi|488600194|ref|YP_007906665.1| 219 VKLEDLAIAKRTQETdvfKVLQMIFKTDNDAYSASMLLDET 259
                                       56667666665555423455555555533345556999996 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.19
                            AAA_14  34 lyinldderdkkladpekllelileklkeekktylflDEiqevpeweka 82 
                                        ++++d+e+++ l++ +   e i + +  e+k++ + DE   ++++e++
  gi|488600194|ref|YP_007906665.1| 393 AFYEFDKEDLEFLTNAK-KAERIIKII--EEKNLHMVDESNILDGFERF 438
                                       23344444443333332.344555544..47899999**9999999887 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 !   25.0   0.0   2.1e-08   1.3e-05      58     172 ..     105     212 ..     102     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.1e-08
                                       EEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHH CS
                    DNA_pol3_delta  58 krivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkw 134
                                       +++++l+   ++   + +++    +L +++++ p++ l ilia+ +l     l k+L    +++++ +l+   + k 
  gi|488600194|ref|YP_007906665.1| 105 RKVIILDEVDNI--HKREDAGGERALIRIIKKKPPQPL-ILIAN-DLY---ALSKELRGLCKLIQFRRLNVRSIAKV 174
                                       799999999999..7777999999********777765.55566.444...68899999999999************ PP

                                       HHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHH CS
                    DNA_pol3_delta 135 iqkraqelglkiekealelLlelvennlsaikqelekL 172
                                       ++++++ +g+k e+ +le+++++++++l+a+ + l+ +
  gi|488600194|ref|YP_007906665.1| 175 LKRICSIEGIKVEEGVLEEIAKNSGGDLRAAINDLQAV 212
                                       *********************************99865 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 !   23.9   0.0   4.7e-08   2.9e-05       2      59 ..       8      62 ..       7      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.7e-08
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgv 59
                                      rPk+l++ ++ +kv +++k   e+     ++   +ll+GpPG+Gkt+la  ia+  g 
  gi|488600194|ref|YP_007906665.1|  8 RPKTLSDVVAEKKVISEIKKWAETFD---SHRKPLLLAGPPGVGKTSLALAIANTYGW 62
                                      9**************99997666555...555567******************98765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   8.8e-08   5.4e-05       6      89 ..      39     121 ..      36     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.8e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...........E CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...........i 71 
                                       +ll+gp gvGkt la a+a++       + + ++as+        ++++r +g+  +     e+G           +
  gi|488600194|ref|YP_007906665.1|  39 LLLAGPPGVGKTSLALAIANTYGW----EAVEMNASDQRN----WEIITRIVGEGAFSETLSESGeflrssekrrkV 107
                                       5899******************96....666666666666....788****************************** PP

                                       EEEETGGG---------- CS
                             AAA_2  72 vllDEidKihpkessgad 89 
                                       + lDE+d ih++    +d
  gi|488600194|ref|YP_007906665.1| 108 IILDEVDNIHKR----ED 121
                                       ***********5....33 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.3e-07   8.1e-05      42     141 ..      31     139 ..      13     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-07
                         IstB_IS21  42 sfiekkenivllGpsGvGKshlaial....gveavragl..svlfvrvedLveelkrarrdgklaralkrllkv.dl 111
                                        f ++++ ++l Gp+GvGK+ la a+    g eav+ +   +  +  ++++v e +  ++  +  + l++  k  ++
  gi|488600194|ref|YP_007906665.1|  31 TFDSHRKPLLLAGPPGVGKTSLALAIantyGWEAVEMNAsdQRNWEIITRIVGEGAFSETLSESGEFLRSSEKRrKV 107
                                       566778899***************99333346899965511578999*****999998888888888877765549* PP

                         IstB_IS21 112 lilDdlgllpldqae..aellfeviekryerr 141
                                       +ilD++   +  +++  ++ l ++i+k+  + 
  gi|488600194|ref|YP_007906665.1| 108 IILDEVDNIHKREDAggERALIRIIKKKPPQP 139
                                       *****987666555422567889998876555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.9e-06    0.0037      21     127 ..      34     132 ..      20     150 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.9e-06
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                       s+r   +ll G++GvGK+sl+ ++++ +  + ++ +++  +++        +++ +  e+ + + l+e+ + +++  
  gi|488600194|ref|YP_007906665.1|  34 SHR-KPLLLAGPPGVGKTSLALAIANTYGWE-AVEMNASDQRN------WEIITRIVGEGAFSETLSESGEFLRSSE 102
                                       333.6799*************9999755544.33344444444......3333333355666655555333333333 PP

                            AAA_16  98 rekleealaavpelagaeasrllellkrll 127
                                       +++    l +v++++  e     ++l r++
  gi|488600194|ref|YP_007906665.1| 103 KRRKVIILDEVDNIHKREDAGGERALIRII 132
                                       333233333444444444455555555555 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 !   17.4   0.1   6.9e-06    0.0043       4      38 ..     183     217 ..     181     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.9e-06
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaae 38 
                                        +k+e+ +le +a+ ++GD R+a+n L++++e +e
  gi|488600194|ref|YP_007906665.1| 183 GIKVEEGVLEEIAKNSGGDLRAAINDLQAVCEGKE 217
                                       5899************************9998765 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 !   13.3   0.0   0.00011     0.066       2      46 ..      17      61 ..      16     120 .. 0.83
   2 ?    3.2   0.1      0.14        88      69     127 ..     138     193 ..     101     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                      ---HHHHHHHHHHHHHHT-SS-EEEEEETT--HHHHHHCC--TTS CS
                   Sigma54_activ_2  2 gasaaiqelkerLeqaaqsklpvfltGekGsgkelvArlLhknsg 46
                                      ++ ++i+e+k+  e   +   p++l+G++G gk++ A ++++  g
  gi|488600194|ref|YP_007906665.1| 17 AEKKVISEIKKWAETFDSHRKPLLLAGPPGVGKTSLALAIANTYG 61
                                      5667899******************************99998655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                                       TTSEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEEEEE-TTT..----HHHHHHHH CS
                   Sigma54_activ_2  69 kggtLylkdiadlskaeqkeLlellakaeksslrlVstsskdleqlleagafdekLlke 127
                                       ++ +L+ +d+  lsk+ + +L +l+++  + ++r ++  +k++ + +e  +++e  l+e
  gi|488600194|ref|YP_007906665.1| 138 QPLILIANDLYALSKE-LRGLCKLIQFR-RLNVRSIAKVLKRICS-IEGIKVEEGVLEE 193
                                       56789999*****986.679*******9.9******999999887.7777776666655 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05    0.0091      51      76 ..      37      62 ..      25      79 .. 0.82
   2 ?   -3.5   0.1       7.5   4.6e+03     111     150 ..     206     246 ..     184     252 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 51 ravLlaGpsgtGktalaiaiskelge 76
                                      + +LlaGp+g Gkt+la+ai++  g 
  gi|488600194|ref|YP_007906665.1| 37 KPLLLAGPPGVGKTSLALAIANTYGW 62
                                      679******************99883 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.5
                                       XXX-S-EEEE.EEEEEEE...-SSS-..TTS--EEEEEE-S CS
                             TIP49 111 ikeekevleG.evveleveeaenplskekkikevkitlkta 150
                                       i + + v eG e v+le     + ++++   k  ++++kt 
  gi|488600194|ref|YP_007906665.1| 206 INDLQAVCEGkEFVKLEDLAIAKRTQETDVFKVLQMIFKTD 246
                                       66667777775567777766666666666777777777775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00039      0.24       2     115 ..      38     134 ..      37     185 .. 0.60
   2 ?   -1.6   0.0       3.6   2.2e+03      86     102 ..     431     447 ..     406     455 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCC CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavlle 78 
                                       +++l G++G+GKT L+  +a +   +  + +a            s++ n   +++ ++ ++  ++  ++ +  ++ +
  gi|488600194|ref|YP_007906665.1|  38 PLLLAGPPGVGKTSLALAIANTYGWEAVEMNA------------SDQRNW-EIITRIVGEGAFSETLSESGEFLRSS 101
                                       57899***********9999876655544422............222222.45666666666555555555556666 PP

                                       SCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                             NACHT  79 lperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                        ++r ++ilD +D +++  ++      ++ L ++i+k
  gi|488600194|ref|YP_007906665.1| 102 EKRRKVIILDEVDNIHKREDA----GGERALIRIIKK 134
                                       777777777777777775544....333334344444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.6
                                       EEE-STT-SS-TCH... CS
                             NACHT  86 ilDglDelvtdlgqkek 102
                                       ilDg+++++++ ++ e+
  gi|488600194|ref|YP_007906665.1| 431 ILDGFERFERKKRETER 447
                                       99*****9998887333 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   0.00017      0.11      26     212 ..      28     209 ..      16     216 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                       HHHSTTT.S--EEEE-SSSSSHHHHHHHHHHH.....HHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT CS
                          Bac_DnaA  26 vaeapgkkynPlfiygevGlGktHLlkaigne.....vlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrk 97 
                                        ae+ +++  Pl++ g+ G+Gkt L  ai+n+     v+ na+++r   + +    + + +   +++ e ++ + ++
  gi|488600194|ref|YP_007906665.1|  28 WAETFDSHRKPLLLAGPPGVGKTSLALAIANTygweaVEMNASDQRNWEIITRIVGEGAFSETLSESGEFLRSSEKR 104
                                       4555667899*******************987111113344444444444443333333333334455556677777 PP

                                       -SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHH..HHHHSSEEEE--..---HHH CS
                          Bac_DnaA  98 vDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlr..srfeaGlvvdie..ppdlet 170
                                         v+++D++  ++++e+   e              + +   ++P+ l  + + l   s+  +Gl   i+  + +   
  gi|488600194|ref|YP_007906665.1| 105 RKVIILDEVDNIHKREDAGGERAL-----------IRIIKKKPPQPLILIANDLYalSKELRGLCKLIQfrRLNVRS 170
                                       888999999999888876554221...........222223333333333333321123334554444400444444 PP

                                       HHHHHHHHHHHTT----TTHHHHHHHH--S-HHHHHHHHHHH CS
                          Bac_DnaA 171 rlailkkkieaeklevpeevlefiaervtdnvRelegalnrl 212
                                        +++lk+  + e+++v e vle ia++      +l++a+n l
  gi|488600194|ref|YP_007906665.1| 171 IAKVLKRICSIEGIKVEEGVLEEIAKNSGG---DLRAAINDL 209
                                       456777777777777777777777765444...344555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-05     0.016       3     107 ..      17     118 ..      15     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                                       --SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSST CS
                   Sigma54_activat   3 gesealkelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFt 79 
                                       +e++ ++e+ + ++++ +++ ++l+ G  G+GK+ la ai ++      + v++n ++  +  + +++ G  +GaF+
  gi|488600194|ref|YP_007906665.1|  17 AEKKVISEIKKWAETFDSHRKPLLLAGPPGVGKTSLALAIANTYG---WEAVEMNASDQRNWEIITRIVG--EGAFS 88 
                                       55666677777777777888********************88766...4568999998877666677877..79999 PP

                                       TTSS-BEHHH.HHTT..TSEEEEETGGGS-H CS
                   Sigma54_activat  80 GAekekkGlf.ekad..gGtlfLDeigelpl 107
                                        + +e  G f ++++    ++ LDe+ ++  
  gi|488600194|ref|YP_007906665.1|  89 ETLSES-GEFlRSSEkrRKVIILDEVDNIHK 118
                                       988765.555144431146899999988865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   9.9e-05     0.061       2      21 ..      40      59 ..      39     142 .. 0.67
   2 ?    0.3   1.1       1.5   9.4e+02      26      82 ..     369     435 ..     348     460 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.9e-05
                            AAA_18  2 lltGtpGvGKttlakeLskr 21
                                      ll+G+pGvGKt+la ++++ 
  gi|488600194|ref|YP_007906665.1| 40 LLAGPPGVGKTSLALAIANT 59
                                      69************999776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.5
                            AAA_18  26 vnlrdvakenglllevdpe.....aldeskrldedkldklldaleenss......aleegknlvidgh 82 
                                        n ++++ +  ++  +d+      a+ e++++d ++l ++ +a + +        ++ +++n ++dg+
  gi|488600194|ref|YP_007906665.1| 369 HNEMFYLIKALMERLDDERcarisAFYEFDKEDLEFLTNAKKAERIIKIieeknlHMVDESN-ILDGF 435
                                       56667777777777777777777777777777777766666555544333334334444444.55555 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 !   14.8   0.0   2.4e-05     0.015      22      72 ..      25      72 ..      10     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                             AAA_7 22 ysyllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                      ++ + e++ +++kp+ll Gp G+GKt+++  + +++    +  + +n s q
  gi|488600194|ref|YP_007906665.1| 25 IKKWAETFDSHRKPLLLAGPPGVGKTSLALAIANTYG---WEAVEMNASDQ 72
                                      5667788899******************998888776...56666666555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00057      0.35       7      37 ..      33      63 ..      27     143 .. 0.91
   2 ?    0.0   0.1       1.6   9.8e+02      78     115 ..     395     433 ..     344     439 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00057
                            AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvel 37
                                      ++++k+ll+ ++pG GKT +  +i + + ++
  gi|488600194|ref|YP_007906665.1| 33 DSHRKPLLLAGPPGVGKTSLALAIANTYGWE 63
                                      67899*************9988887776655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.6
                            AAA_19  78 ldfddlltealelle....eaeeekklqeeellivDEfqdvd 115
                                        +fd++    le+l      ++  k ++e++l +vDE+  +d
  gi|488600194|ref|YP_007906665.1| 395 YEFDKED---LEFLTnakkAERIIKIIEEKNLHMVDESNILD 433
                                       4444444...55555443222333455444589999988776 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    0.0001     0.063      33      54 ..      36      57 ..       8      67 .. 0.81
   2 ?   -2.4   0.0         5   3.1e+03     127     155 ..     408     439 ..     376     451 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                            AAA_25 33 gelallaGapgtGKttlaldla 54
                                       +  llaG+pg+GKt lal +a
  gi|488600194|ref|YP_007906665.1| 36 RKPLLLAGPPGVGKTSLALAIA 57
                                      56789*************9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                            AAA_25 127 tadvdaleaaieevegvrlv....viDplsral 155
                                       + + +++++ iee +++++v    ++D + r+ 
  gi|488600194|ref|YP_007906665.1| 408 AKKAERIIKIIEE-KNLHMVdesnILDGFERFE 439
                                       3446777777777.6777776666666666665 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 ?   11.2   0.0   0.00045      0.28      12      48 ..      25      60 ..      17      67 .. 0.87
   2 ?    1.0   0.1      0.61   3.7e+02     123     147 ..      95     119 ..      66     142 .. 0.67
   3 ?   -1.3   0.2         3   1.9e+03      65      96 ..     430     458 ..     377     472 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                                      HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH CS
                            ResIII 12 ienlleklkskrdkrglikmaTGtGKTlvaaklierl 48
                                      i++++e+++  ++k +l++ + G+GKT +a++++  +
  gi|488600194|ref|YP_007906665.1| 25 IKKWAETFD-SHRKPLLLAGPPGVGKTSLALAIANTY 60
                                      778889998.99*******************998766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.61
                                       ....HHHTTT-SEEEEETGGGTTS. CS
                            ResIII 123 eeseellrdrfdviiiDEaHrlgak 147
                                        e  + +++r +vii DE+ ++++ 
  gi|488600194|ref|YP_007906665.1|  95 GEFLRSSEKRRKVIILDEVDNIHKR 119
                                       455667778888******8766665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3
                                       HHHHHHHHHGGGGTGG.....GEEEESSS-B-- CS
                            ResIII  65 slleqtleefkkflseayke.igkkvsgdkkka 96 
                                       +     l+ f++f  ++++    +k +gd++++
  gi|488600194|ref|YP_007906665.1| 430 N----ILDGFERFERKKRETeRAEKADGDTNRK 458
                                       2....2355555555555444555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012     0.072       5      77 ..      39     116 ..      35     124 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfi.dtekGlksldadkfpdie......swedfldevvel.aaeladyktlviDt 73 
                                       +l+ Gp+g+GKT+la+ +  ++     +e+  ++ d ++ + i+      ++ + l+e  e+ +  +++ k++++D 
  gi|488600194|ref|YP_007906665.1|  39 LLLAGPPGVGKTSLALAI-ANTYGWeAVEM--NASDQRNWEIITrivgegAFSETLSESGEFlRSSEKRRKVIILDE 112
                                       789**************9.44443313333..333333333333445555444444444443777788889999998 PP

                            AAA_24  74 idel 77 
                                       +d +
  gi|488600194|ref|YP_007906665.1| 113 VDNI 116
                                       8876 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.13      22      68 ..      39      82 ..      31     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                      EEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 22 iiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRll 68
                                      +++A+ p++Gkt+lal ia++        v +   +  + ++++R++
  gi|488600194|ref|YP_007906665.1| 39 LLLAGPPGVGKTSLALAIANTYGW---EAVEMNASDQRNWEIITRIV 82
                                      579****************98765...35667777777777777766 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0032         2       2      26 ..      43      67 ..      42      72 .. 0.90
   2 ?   -0.1   0.0       1.9   1.2e+03      25      68 ..      93     135 ..      77     157 .. 0.74
   3 ?   -2.4   0.0       9.4   5.8e+03      42      69 ..     360     387 ..     347     410 .. 0.69
   4 ?    1.9   0.5      0.45   2.8e+02      55      94 ..     412     450 ..     386     460 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0032
                                      E-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17  2 GgPGsGKgtqceklvekygfthlsa 26
                                      G+PG+GK+ ++  ++  yg + +++
  gi|488600194|ref|YP_007906665.1| 43 GPPGVGKTSLALAIANTYGWEAVEM 67
                                      9*****************9988765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                                       EHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHH CS
                            AAA_17  25 saGdllreeakrgglakardemrklpleekkelqkeaaekiaee 68 
                                       + G+ lr+  kr++     de+++  ++e+    + +++ i+++
  gi|488600194|ref|YP_007906665.1|  93 ESGEFLRSSEKRRKV-IILDEVDNIHKREDAGGERALIRIIKKK 135
                                       679999988888886.4778888888888776666666555554 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.4
                                       SHHHHCTSHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17  42 ardemrklpleekkelqkeaaekiaeea 69 
                                       + +  +k  ++e   l k ++e++ +e+
  gi|488600194|ref|YP_007906665.1| 360 HSHMSMKKAHNEMFYLIKALMERLDDER 387
                                       4444457777778888888888887765 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHH CS
                            AAA_17  55 kelqkeaaekiaeeakkkgvlvdghprikeqagfldglpk 94 
                                       +++ k+++ek  ++  ++  ++dg+ r+++++++ ++ +k
  gi|488600194|ref|YP_007906665.1| 412 ERIIKIIEEKNLHM-VDESNILDGFERFERKKRETERAEK 450
                                       34444444444444.456689*******999988776665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0013      0.82       2      81 ..      40     136 ..      39     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl..................klkkkdsvys.rnpeddfwdgYt.gqevvvidDf 58 
                                       +l Gp+g+GK++la  +a++   +                   +   ++ +    + + +f+ + + + +v++ d++
  gi|488600194|ref|YP_007906665.1|  40 LLAGPPGVGKTSLALAIANTYGWEAvemnasdqrnweiitrivG---EGAFSEtLSESGEFLRSSEkRRKVIILDEV 113
                                       689*************9988874445667777777777763321...233322345666777444447777777777 PP

                      RNA_helicase  59 gqvkdeenpsdlaelirlvsstp 81 
                                        +++++e+   +  lir+++ +p
  gi|488600194|ref|YP_007906665.1| 114 DNIHKREDAGGERALIRIIKKKP 136
                                       77776645557777777777666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0016         1      14      42 ..      39      67 ..      34      85 .. 0.80
   2 ?   -1.7   0.0       6.2   3.8e+03     121     135 ..      99     113 ..      80     115 .. 0.83
   3 ?   -1.3   0.1       4.6   2.8e+03      44      80 ..     397     440 ..     348     470 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0016
                                      EEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkpteGei 42
                                      + + G+ G GK++L+ ++a+ + +++ e+
  gi|488600194|ref|YP_007906665.1| 39 LLLAGPPGVGKTSLALAIANTYGWEAVEM 67
                                      5789*****************99977665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.2
                                       HHHHHTSSEEEEEST CS
                                       xxxxxxxxxxxxxxx RF
                          ABC_tran 121 rallkkpkllllDEp 135
                                       r+  k++k+++lDE 
  gi|488600194|ref|YP_007906665.1|  99 RSSEKRRKVIILDEV 113
                                       56668899*****96 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.6
                                       ETTCEGGG.B-HHHCCHCEEEE-SS.--S-TTSBHHHH.....H CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxx.....x RF
                          ABC_tran  44 ldgkdlke.qeleslrkeigvlpqe.pqlfpeltvren.....e 80 
                                       +d++dl+  ++ +++++ i++++++  ++ +e+++ +       
  gi|488600194|ref|YP_007906665.1| 397 FDKEDLEFlTNAKKAERIIKIIEEKnLHMVDESNILDGferfeR 440
                                       44555555445555555555555554344444433333555542 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 ?   11.5   0.1   0.00034      0.21       7      43 ..      21      59 ..      18     143 .. 0.84
   2 ?   -3.1   2.0       9.4   5.8e+03      78      78 ..     414     414 ..     342     474 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                          ATPase_2  7 elkeleeiler..epneiyfiYGpegsGKtaLlkeiien 43
                                       ++e+++++e+  + ++++++ Gp g+GKt+L   i++ 
  gi|488600194|ref|YP_007906665.1| 21 VISEIKKWAETfdSHRKPLLLAGPPGVGKTSLALAIANT 59
                                      58999999997447899***************9999886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.4
                          ATPase_2  78 l 78 
                                       +
  gi|488600194|ref|YP_007906665.1| 414 I 414
                                       1 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0013      0.79      13      41 ..      32      60 ..      22     254 .. 0.85
   2 ?    0.7   2.3      0.62   3.8e+02     121     194 ..     384     473 ..     337     475 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                            AAA_11 13 alseseitliqGPPGtgKTktivellsql 41
                                      + s+++  l+ GPPG gKT+  +++ +  
  gi|488600194|ref|YP_007906665.1| 32 FDSHRKPLLLAGPPGVGKTSLALAIANTY 60
                                      445566689***********999998876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.62
                            AAA_11 121 e..................kaqlakeiskeleklakelrafeeeeek........................eklkks 155
                                       +                  +                                                    + +  
  gi|488600194|ref|YP_007906665.1| 384 DdercarisafyefdkedlE--------------------------FltnakkaeriikiieeknlhmvdeSNILDG 434
                                       13334444444333333221..........................0222222222223333444445555666777 PP

                            AAA_11 156 kekskskleqerrklkkerkelskeleeaeesleeevld 194
                                       +e +++k+++++r+ k+  ++++k+++++ ++++e  ld
  gi|488600194|ref|YP_007906665.1| 435 FERFERKKRETERAEKADGDTNRKDVKTKGKKVKEMTLD 473
                                       777778888888888888888888888888887776665 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.4    0.0026       1.6      30     127 ..     362     455 ..     347     467 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0026
                                       EEE-STB-HHHHHHHHHHHHHT.T-EEEEEE-SCHHHHHHHHHH-S-THHHCHHHHHHTHHHHHHHHHCTTECEEE- CS
                       PAPS_reduct  30 fvdtghefpetiefvdeleery.glrlkvyepeeevaekinaekhgsslyeeaaeriaKveplkkaLekldedallt 105
                                       ++ +++ ++e+  ++++l er+ + r +  +       ++ +e+  + +  ++aeri+K+ + k+ L+ +de+ +l 
  gi|488600194|ref|YP_007906665.1| 362 HMSMKKAHNEMFYLIKALMERLdDERCARISA----FYEFDKEDLEFLTNAKKAERIIKIIEEKN-LHMVDESNILD 433
                                       77788899999999999999995222222222....23333333222222237899******999.*********** PP

                                       ---CCCTTTTTTSSSEEECTTT CS
                       PAPS_reduct 106 GaRrdesksraklpiveidedf 127
                                       G  r e k+r++++  + d d 
  gi|488600194|ref|YP_007906665.1| 434 GFERFERKKRETERAEKADGDT 455
                                       **************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 2889.67
//
Query:       gi|488600195|ref|YP_007906666.1|  [L=333]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-89  298.8  30.7    3.9e-89  298.5  30.7    1.1  1  Cons_hypoth698  Conserved hypothetical protein 698
     0.0057   16.0  17.9     0.0057   16.0  17.9    2.6  3  KdgT            2-keto-3-deoxygluconate permease
  ------ inclusion threshold ------
        7.7    6.5   8.0       0.43   10.5   1.1    2.3  2  ApoO            Apolipoprotein O


Domain annotation for each model (and alignments):
>> Cons_hypoth698  Conserved hypothetical protein 698
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.5  30.7   6.6e-93   3.9e-89       1     303 [.      13     313 ..      13     314 .. 0.98

  Alignments for each domain:
  == domain 1  score: 298.5 bits;  conditional E-value: 6.6e-93
                    Cons_hypoth698   1 pGLllllliavlalllakvellfaklsalllAillGillgnflklqeqlkaGvafskkklLrlgivllGfrltlsdi 77 
                                       pGL ++ ++av+a++la++  +  ++s+l+lAi++G++++n+++l+e +++G++fs k++Lr++i+llG++l++ +i
  gi|488600195|ref|YP_007906666.1|  13 PGLAFSSALAVVAIILAHIVNKYVAISPLILAIVVGMIFRNTVGLPEVFSQGMQFSLKRVLRIAIILLGLKLSIAEI 89 
                                       79****************999999***************************************************** PP

                    Cons_hypoth698  78 akvGlkgvlldiivlistfllvlllgakllkldkklalLvaaGssiCGasAilavepvikareeevalaiavivllg 154
                                       ++vG+kg++++++++  t+ + +++g k ++++++la+L++ G siCGasA +a++ vi+ar+ +va aia+++++g
  gi|488600195|ref|YP_007906666.1|  90 LQVGSKGLIVVVVSVTLTLAFSIWIG-KRFRISEELATLIGTGVSICGASAAIAIAGVINARDRNVAFAIATVTVFG 165
                                       **************************.************************************************** PP

                    Cons_hypoth698 155 tvamllyPalatllsltdeefgvfaGasvhevaqVvaagelvseeaakiAvivKltRvlllapvvlllslllakree 231
                                       tvam+lyP+la++++l+   +gv+aGas+hevaqVvaag++vs+e+++iA+ivKl+Rv+llapv ++l++ +a++++
  gi|488600195|ref|YP_007906666.1| 166 TVAMFLYPVLASVMGLSSTVYGVWAGASIHEVAQVVAAGYAVSDESGNIATIVKLSRVVLLAPVAVILGIAFARKSA 242
                                       *********************************************************************99999988 PP

                    Cons_hypoth698 232 esetkeakitiPwFvlgFlvvallntlvllpselvsalktlstlllvmalaAlglktdlkalkkaglkplll 303
                                        + +   +  +P+F++gF++++ +n++ ++p +++ +l ++++++l++a+aA+gl+t +++++++g+ p+ +
  gi|488600195|ref|YP_007906666.1| 243 GGFSFR-SVPVPYFIFGFIAMIFINSMAIIPDQITRMLIQIDNFMLAVAMAAMGLNTSFREMRETGITPFYV 313
                                       666666.999*********************************************************99876 PP

>> KdgT  2-keto-3-deoxygluconate permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  17.9   9.5e-07    0.0057     160     301 ..      34     178 ..       8     182 .. 0.71
   2 ?    1.9   5.5     0.019   1.1e+02     210     287 ..     144     221 ..     141     240 .. 0.78
   3 ?    1.7   4.8     0.022   1.3e+02     177     236 ..     268     327 ..     231     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.5e-07
                              KdgT 160 piqslvaviiPlivGiilGn...ldeelrkflkkgvkilipflafalGaginlktivkaglsGilLgvivvvvtgil 233
                                       ++ ++  +i+ ++vG+i+ n   l e + + ++ + k ++ +  + lG ++++++i+++g +G+++ v+ v +t  +
  gi|488600195|ref|YP_007906666.1|  34 KYVAISPLILAIVVGMIFRNtvgLPEVFSQGMQFSLKRVLRIAIILLGLKLSIAEILQVGSKGLIVVVVSVTLTLAF 110
                                       5566666788888888888833334444444444455678899999*************************999999 PP

                              KdgT 234 lylvdrlllkkk...gvagaAasstAgnavatPaavaaadpsfapvaasAtaqvaaavivtailvPlltal 301
                                        +++ + ++ ++   + +g+++s   g+++a+  a+a + ++    +a A a v++   v ++l P+l+++
  gi|488600195|ref|YP_007906666.1| 111 SIWIGKRFRISEelaTLIGTGVSI-CGASAAI--AIAGVINARDRNVAFAIATVTVFGTVAMFLYPVLASV 178
                                       887766665555355667777664.3444433..5666666666777888888888999999999999886 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.019
                              KdgT 210 ktivkaglsGilLgvivvvvtgillylvdrlllkkkgvagaAasstAgnavatPaavaaadpsfapvaasAtaqvaa 286
                                       + +++a    +  ++++v v g+++++++ +l    g +++  +  Ag+++   a v+aa  ++++   + +++v  
  gi|488600195|ref|YP_007906666.1| 144 AGVINARDRNVAFAIATVTVFGTVAMFLYPVLASVMGLSSTVYGVWAGASIHEVAQVVAAGYAVSDESGNIATIVKL 220
                                       5677778888999**************************************99888888876665444444444444 PP

                              KdgT 287 a 287
                                       +
  gi|488600195|ref|YP_007906666.1| 221 S 221
                                       4 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.022
                              KdgT 177 lGnldeelrkflkkgvkilipflafalGaginlktivkaglsGilLgvivvvvtgillyl 236
                                       ++ + +++ ++l +  ++++ + + a+G +++++++ ++g++   +g iv+++ +++ y+
  gi|488600195|ref|YP_007906666.1| 268 MAIIPDQITRMLIQIDNFMLAVAMAAMGLNTSFREMRETGITPFYVGFIVWIFIATISYA 327
                                       455667888899999999999999999999999999999999999999999988888776 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   7.2e-05      0.43      76     116 ..     141     180 ..     135     189 .. 0.84
   2 ?   -1.9   0.9       0.5     3e+03      75      93 ..     229     249 ..     222     265 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.2e-05
                              ApoO  76 agLaGsilarrrsilkRvlyPlalgglaaslfyPqtakntg 116
                                        ++aG+i ar r++ + +++ +++g+ +a  +yP+ a+++g
  gi|488600195|ref|YP_007906666.1| 141 IAIAGVINARDRNVAFAIATVTVFGT-VAMFLYPVLASVMG 180
                                       579*************9999999999.67789999988776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.5
                              ApoO  75 vagLaGsilar..rrsilkRv 93 
                                       va+++G  +ar   +++ +R 
  gi|488600195|ref|YP_007906666.1| 229 VAVILGIAFARksAGGFSFRS 249
                                       8999******94446666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1207  (0.0673211); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2065.74
//
Query:       gi|488600196|ref|YP_007906667.1|  [L=271]
Description: Universal stress protein UspA-related nucleotide-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  180.1   8.1    1.1e-25   90.8   4.8    3.2  2  Usp          Universal stress protein family
     0.0013   19.0   0.0       0.54   10.5   0.0    2.4  2  VWA          von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.016   15.3   0.1         17    5.5   0.1    3.2  3  B12-binding  B12 binding 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 !   90.8   4.8   1.8e-29   1.1e-25       4     141 .]      14     131 ..      12     131 .. 0.87
   2 !   81.2   0.1   1.7e-26   9.9e-23       3     141 .]     137     264 ..     136     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.8e-29
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       rI+Va+Dg+e+s+kA+++A+ela++ + +l+++ v+  + + + +       ee l++ ++              ++
  gi|488600196|ref|YP_007906667.1|  14 RIIVATDGTEASEKAVRFAVELARSLDYDLHAVSVVCNQLKRQKA-------EETLDYIKK-------------MHP 70 
                                       8**********************************9976543322.......222222222.............257 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        ++v v+eg+paeei+ +a+e++a+liVvGs ++s+l+rl++GSvse+v+rha+ +Vlv r
  gi|488600196|ref|YP_007906667.1|  71 RTHVAVKEGKPAEEIVSYAKEINANLIVVGSGDKSRLERLFIGSVSEKVVRHAKTSVLVAR 131
                                       8899*******************************************************76 PP

  == domain 2  score: 81.2 bits;  conditional E-value: 1.7e-26
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       kr+lV +Dgse+s +Al+w  +l ++   e+++lhv d+++++++  + ee ++ + +  +a++e         + g
  gi|488600196|ref|YP_007906667.1| 137 KRVLVTTDGSECSNRALRWVQKLKERIPFEVTVLHVMDTSDPAPSQLYLEELQRRRDCALGAARE---------IFG 204
                                       89************************99*********************************9885.........334 PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        + e v   g+  ++ + va + d+dl+V+Gs+grsg++ lllGSv+e+v+r +  ++lv r
  gi|488600196|ref|YP_007906667.1| 205 DSAEYVSMKGH--PVFVIVAISADYDLVVLGSHGRSGIDYLLLGSVAERVVRFSRTSTLVLR 264
                                       55555555555..55566677788***********************************987 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 !   10.5   0.0     9e-05      0.54     107     153 ..      15      67 ..      12      88 .. 0.78
   2 !    6.0   0.0    0.0021        13      86     137 ..     117     170 ..     104     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9e-05
                                       EEEEESS--CS.SHTHHHHHHHHGCTEEEEEEEE......SSSHHHHHHHHHSS CS
                               VWA 107 iilltdGksnd.gdpkeaaneakeqgikvfavGv......gnadekelLnkias 153
                                       ii+ tdG++ + + ++ a++ a++ +++++av v      ++  e++ L  i +
  gi|488600196|ref|YP_007906667.1|  15 IIVATDGTEASeKAVRFAVELARSLDYDLHAVSVvcnqlkRQKAEET-LDYIKK 67 
                                       8********8856*********************9988854444444.666644 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHGTSST.TSEEEEEEEESS--CSSHTHHHHHHHHGC.TEEEEEE CS
                               VWA  86 kyaleklfkssagaRe.nakkviilltdGksndgdpkeaaneakeq.gikvfav 137
                                       +++++++ +s   aR+   +k +++ tdG + ++  ++ ++++ke+   +v ++
  gi|488600196|ref|YP_007906667.1| 117 EKVVRHAKTSVLVARSsALPKRVLVTTDGSECSNRALRWVQKLKERiPFEVTVL 170
                                       4455544444444555599************77899999999998755555555 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0028        17      44      86 ..      33      76 ..      14      76 .. 0.85
   2 ?    2.0   0.0     0.033     2e+02      68      88 ..      82     102 ..      79     114 .. 0.81
   3 ?    3.7   0.0      0.01        60       2      36 ..     138     172 ..     137     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0028
                       B12-binding 44 vaairaekpdvvglSal.ltsqleavkelvellkrirprvkvvv 86
                                      v+ +r++++d+ ++S++  + + ++++e+++ +k+++pr++v+v
  gi|488600196|ref|YP_007906667.1| 33 VELARSLDYDLHAVSVVcNQLKRQKAEETLDYIKKMHPRTHVAV 76
                                      67889999999777766366789999*************99986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.033
                       B12-binding  68 vkelvellkrirprvkvvvGG 88 
                                       ++e+v  +k+i+++++vv  G
  gi|488600196|ref|YP_007906667.1|  82 AEEIVSYAKEINANLIVVGSG 102
                                       578888999999998888777 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.01
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllga 36 
                                       +vl++t g+++ +++l+++   +++  feV++l +
  gi|488600196|ref|YP_007906667.1| 138 RVLVTTDGSECSNRALRWVQKLKERIPFEVTVLHV 172
                                       799**********************9****99855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1721.72
//
Query:       gi|488600197|ref|YP_007906668.1|  [L=276]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-21   74.7   0.1    6.2e-21   74.1   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00014   21.1   0.0    0.00032   20.0   0.0    1.6  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0024   17.7   0.1     0.0053   16.6   0.1    1.6  1  MarR_2          MarR family
     0.0077   16.3   0.3      0.072   13.2   0.0    2.3  2  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.8   1.3      0.025   14.9   1.3    1.5  1  CLZ             C-terminal leucine zipper domain of cyclic nu
       0.07   13.9   0.6       0.19   12.5   0.6    1.7  1  PSK_trans_fac   Rv0623-like transcription factor
       0.12   12.4   0.0        0.5   10.4   0.0    2.0  2  PadR            Transcriptional regulator PadR-like 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 !   74.1   0.1   2.4e-24   6.2e-21       1      67 [.      16      82 ..      16      83 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 2.4e-24
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L+++GL+ yEa++Y +Ll+ g+ata  +a+ +gvp++++Y++L sLe+kG+++ ++ +pk+Y a+++
  gi|488600197|ref|YP_007906668.1| 16 LRDYGLTAYEARAYYVLLAAGEATAGAVAKLSGVPQQRIYDTLASLERKGFIQARHTNPKRYAALSV 82
                                      789************************************************************9875 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.2e-07   0.00032       2     136 ..     127     257 ..     126     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-07
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHH.HHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLe.elreeliaaaergvtVllliypdedleeldleevatevrvr 77 
                                       vwvv+++e++i ri e+I+sAe+ + ++++  l+    +  +++   +gv+ + l    e+    ++ +v  e+   
  gi|488600197|ref|YP_007906668.1| 127 VWVVEGEEAIIARILEMIRSAEKSVKLAGERPLFTlNCKGVFRKYLPEGVKLYALGKF-EKVCRDEIRSVGGEIHDV 202
                                       9******************************999834577888888999887655443.344444555666677777 PP

                                       ---S.EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEE CS
                    Regulator_TrmB  78 rsgapllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktsevik 136
                                       +s   +l+ivD +r +++     +d+   ++++ +++ +i+  + +F ++ W++ ++  
  gi|488600197|ref|YP_007906668.1| 203 ESYCHYLLIVDDSRLLIVYF---DDDGIPHGLYTENEGIIRPHVLFFDQI-WEMHSESV 257
                                       77778999999999999866...689999999988888888776666666.98876665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.1e-06    0.0053       2      56 ..      20      73 ..      19      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE.ES CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr.pg 56
                                      glt  +ar+ ++L ++++   t+g++a+  g++++++  +l+ L+++G+++ r ++
  gi|488600197|ref|YP_007906668.1| 20 GLTAYEARAYYVLLAAGE--ATAGAVAKLSGVPQQRIYDTLASLERKGFIQARhTN 73
                                      888899999999999999..9*****************************877555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   2.8e-05     0.072      21      55 ..      34      68 ..      30      73 .. 0.91
   2 ?    0.4   0.1      0.27     7e+02      29      50 ..      92     113 ..      81     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLve 55
                                       a+++ta+++a++ +++++ +++ L+ Le+ g++ 
  gi|488600197|ref|YP_007906668.1| 34 AAGEATAGAVAKLSGVPQQRIYDTLASLERKGFIQ 68
                                      7899****************************996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                                       HHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_20  29 elaerldlskntlsyHLrvLee 50 
                                       +l +++d + ++l  +++ Le+
  gi|488600197|ref|YP_007906668.1|  92 QLRAEFDAREQELKERIDDLEK 113
                                       6788889999999999998886 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.3     1e-05     0.025      42      71 .]      85     114 ..      81     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                               CLZ  42 aLqtrlarLlaeyessqrkLkqRitkLEkk 71 
                                       aL++r+++L ae+++ +++Lk+Ri +LEk+
  gi|488600197|ref|YP_007906668.1|  85 ALTNRIRQLRAEFDAREQELKERIDDLEKR 114
                                       699*************************96 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   7.3e-05      0.19      29      61 ..      82     117 ..      78     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.3e-05
                                       XXXXXXXXXXXXXXX...XX--HHHHHHHHHHHHHT CS
                     PSK_trans_fac  29 vrrAleerlerlrre...raepllerllallrraaa 61 
                                       vrrAl +r+++lr+e   r+++l+er+++l +ra  
  gi|488600197|ref|YP_007906668.1|  82 VRRALTNRIRQLRAEfdaREQELKERIDDLEKRAPK 117
                                       9*************9***************999876 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.8   4.5e+03      59      72 ..      26      39 ..      22      42 .. 0.81
   2 ?   10.4   0.0   0.00019       0.5      32      53 ..      52      73 ..      41      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                                      -EEEEEESHCCCHH CS
                              PadR 59 prkyYrlTdaGrre 72
                                      +r yY l +aG+++
  gi|488600197|ref|YP_007906668.1| 26 ARAYYVLLAAGEAT 39
                                      79999999999875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00019
                                      HHHHHHHHHHHHTTSEEEEEE- CS
                              PadR 32 GslYpaLkrLekeglvesewee 53
                                       ++Y++L++Le++g+++++ ++
  gi|488600197|ref|YP_007906668.1| 52 QRIYDTLASLERKGFIQARHTN 73
                                      589**************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1682.70
//
Query:       gi|488600198|ref|YP_007906669.1|  [L=213]
Description: Membrane-associated phospholipid phosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-22   79.3   1.5    3.1e-22   78.8   0.5    1.7  1  PAP2      PAP2 superfamily
    4.7e-10   39.5   2.9    2.6e-09   37.1   2.6    2.0  1  PAP2_3    PAP2 superfamily
  ------ inclusion threshold ------
       0.16   12.3   1.7       0.16   12.3   0.6    1.7  2  DUF1772   Domain of unknown function (DUF1772)
       0.24   12.0   0.1       0.24   12.0   0.1    2.4  3  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.5   6.9e-26   3.1e-22       4     129 ..      97     203 ..      94     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 6.9e-26
                              PAP2   4 alllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrk 80 
                                        +l++ a+  +++  lK++v rpRP+ + +e ++ ++ +            sfPSgHs  afala +l+   ++k+ 
  gi|488600198|ref|YP_007906669.1|  97 LILVVAAIGSIIVAPLKTIVHRPRPYLTLQEVIPLEKATG----------MSFPSGHSEKAFALASVLSNDNKTKK- 162
                                       4555666677777999********************9654..........6**************99986555555. PP

                              PAP2  81 kiglvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayr 129
                                               l+l+++a+ +a+sR+y+gvH++ Dv+aG ++G++++ ++ +
  gi|488600198|ref|YP_007906669.1| 163 --------LVLYAYATSIAFSRVYIGVHYPIDVVAGSILGWIVGKITLK 203
                                       ........55********************************9987765 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   2.6   5.7e-13   2.6e-09     124     187 ..     136     197 ..      75     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 5.7e-13
                            PAP2_3 124 laafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalva 187
                                        ++fPS H   a+ +a +l   ++++  ++++ +++  ++++ v+ g HY +Dv+aG +l++++
  gi|488600198|ref|YP_007906669.1| 136 GMSFPSGHSEKAFALASVLSNDNKTK--KLVLYAYATSIAFSRVYIGVHYPIDVVAGSILGWIV 197
                                       468***************88888888..********************************9986 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   3.6e-05      0.16      24      88 ..      63     120 ..      29     163 .. 0.71
   2 ?   -2.1   0.0         1   4.5e+03      55      71 ..     155     170 ..     146     182 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                           DUF1772  24 llkqwrrlfkrgkavfpplallsalafa.ylaaraasrgarllylaaaallllsivpyTllvmvPt 88 
                                       l++++ ++     ++   ++++++l+ a y+a     r+   l+l++aa+ ++ ++p+  +v +P 
  gi|488600198|ref|YP_007906669.1|  63 LNPVFVTIT----HLGS-AVAVVSLGIAlYIA---GYRREGVLILVVAAIGSIIVAPLKTIVHRPR 120
                                       444444444....4444.55555555554888...5555566666889999999***999999885 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                           DUF1772  55 araasrgarllylaaaa 71 
                                       +++ ++++  ly+  a 
  gi|488600198|ref|YP_007906669.1| 155 SNDNKTKKLVLYAY-AT 170
                                       23333333334422.22 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         1   4.7e+03      43      49 ..      10      16 ..       2      31 .. 0.58
   2 ?   -1.5   0.1      0.85   3.8e+03      32      45 ..      94     107 ..      67     111 .. 0.55
   3 ?   12.0   0.1   5.4e-05      0.24      26      66 ..     155     195 ..     139     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                            PAP2_C 43 glfliia 49
                                      ++++i++
  gi|488600198|ref|YP_007906669.1| 10 IILCIVI 16
                                      3333332 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.85
                            PAP2_C  32 lkvillllallglf 45 
                                         v++l++a++g++
  gi|488600198|ref|YP_007906669.1|  94 EGVLILVVAAIGSI 107
                                       34455555555544 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 5.4e-05
                            PAP2_C  26 pkklailkvillllallglfliiasrkHYtvDVllglyitt 66 
                                       ++  ++ k++l  +a ++ f+ ++   HY +DV+ g ++  
  gi|488600198|ref|YP_007906669.1| 155 SNDNKTKKLVLYAYATSIAFSRVYIGVHYPIDVVAGSILGW 195
                                       333334688999999********************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.68
# Mc/sec: 941.50
//
Query:       gi|488600199|ref|YP_007906670.1|  [L=218]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-39  135.4   6.2      2e-39  135.2   6.2    1.0  1  DUF599    Protein of unknown function, DUF599


Domain annotation for each model (and alignments):
>> DUF599  Protein of unknown function, DUF599
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.2   6.2   1.1e-43     2e-39       2     208 ..       9     211 ..       8     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 1.1e-43
                            DUF599   2 lvplflllwagYhlwllrrirrrplrtviginaaaRraWvrammderknrilavqtlrnlimastllAstaillisg 78 
                                       ++++fl+++agYh  +l   ++ p+++v ++++  R++ +++++ ++ + ++ vq lr++i  s l+As+++++i++
  gi|488600199|ref|YP_007906670.1|   9 ALIVFLICFAGYHGSYLILSKKYPKKVVKTYTNIFREKGIENVI-KKREPLVLVQQLRDAIYVSNLFASASLIFIGM 84 
                                       7899****************************************.99999999************************ PP

                            DUF599  79 laallsstdklsdllkslpvfgatsealfelKlllllliflvAFlkfvqsirlynhasfligavPe..deaeaeata 153
                                       l++ll + + l   ++sl++   t+  lfe+K+l+++++ +++F++fv s+r+y  +s l ++ Pe  +e+   ++ 
  gi|488600199|ref|YP_007906670.1|  85 LLNLLINLNTL---AESLKI---TDVGLFEFKILFIAALQAISFIFFVSSLRYYRMVSLLATTPPEtiREHLGIEAY 155
                                       ********965...558898...**************************************665559988888999* PP

                            DUF599 154 eyvarvlergslffnlGlRafyfalplllWifgPlllllasllvvavlyr.lDfvs 208
                                       +y+a++l+rg++f++lG R + +++ ll+W+++ +l+++ ++l+++++ + +Dfv 
  gi|488600199|ref|YP_007906670.1| 156 KYLAHLLNRGCSFYTLGSRGILYSILLLAWFVNEWLFMAIVVLTTVLFAKyRDFVR 211
                                       ***************************************99998888776588875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1219.16
//
Query:       gi|488600200|ref|YP_007906671.1|  [L=395]
Description: Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-76  258.1   0.0      2e-76  257.9   0.0    1.1  1  HGD-D     2-hydroxyglutaryl-CoA dehydratase, D-component
  ------ inclusion threshold ------
      0.034   14.2   0.1        3.3    7.9   0.0    2.4  2  AsiA      Anti-Sigma Factor A


Domain annotation for each model (and alignments):
>> 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 !  257.9   0.0   2.2e-80     2e-76       3     323 .]      37     395 .]      35     395 .] 0.92

  Alignments for each domain:
  == domain 1  score: 257.9 bits;  conditional E-value: 2.2e-80
                                       TS-HHHHHHTT-EE.........EE-.----GGGHHHHTTT.S-SSS-HHHHHHHHHHHT.........HH-SEEEE CS
                             HGD-D   3 yypeellaAaglvp.........iflargpsrepldlaeky.lpsfgCglardalgaale.........kpddlvva 60 
                                        +p e l+A+++ p         i  a++++ e+++lae+  +++++C++ar+++ga+++         kp +l+++
  gi|488600200|ref|YP_007906671.1|  37 GAPVEFLYAMDIYPaypenhsalI-GANKTAPEYCELAERNgYSQDLCSYARCDIGAVFAgtspigglpKPNFLFAC 112
                                       689*******************66.66************99***************9999***************** PP

                                       ES-SHHHHHHHHHHTTT..S-EEEE---.......HHHHHHHHHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHH CS
                             HGD-D  61 nttCdqvkkilenlaki..ipytvldiP.......eeavkyledelenliaaleeitgkrideesleaaikeanetr 128
                                       n++C++v k++e l++i  +p+++ld+P       e+ v+y+e++l +++++le+i+g+++de++++++++++ e  
  gi|488600200|ref|YP_007906671.1| 113 NNICNTVVKWYEVLGRIfkVPVFLLDVPfvrkelkESHVDYVESQLYDFVDFLEKISGREFDEKKFRKVLELSREGV 189
                                       *******************99******************************************************** PP

                                       HHHHHHHHHTTSSS-SS-HHHHH.HHHHHTT.S-HHHHHHHHHHHHHHHHHH.T.....S..TS-EEEEEES---TT CS
                             HGD-D 129 ellkelytllpqspapihgfdll.llakvvf.lgkeeatealeelleeleer.s....ks..eriRllltGipvell 196
                                       e +k++  + +++p+p++ fd++ ++a +v+  g+e+ +e++ e+ +eleer +     +  e++Rll+  ipv++ 
  gi|488600200|ref|YP_007906671.1| 190 ERYKDVLYMGRNKPSPLTCFDAFlNMAPIVClRGTEKPVEFYSEMKKELEERiKnevyAVddEKYRLLWDNIPVWYR 266
                                       *****9999999*******************66******************43343443257*************** PP

                                       --HHHHHHHHT.T-EEEEEESTTTHHHHS-....SSHHH.HHHHHHHHHT--TTS.S-HHHHHHHHHHHHHTT-SEE CS
                             HGD-D 197 aaklmkaleaglgavvvnndacypsrlvry....vgdvgqplealasgyykcpvs.pkerrlewirdlideykvdgv 268
                                       ++ l + +  +  ++v+ +++    ++       + +++++++++a+ y k++ +   ++++e i +lid y vdgv
  gi|488600200|ref|YP_007906671.1| 267 LKWLSEFFIRNNACMVADTYT---NAWTGFlsadSASKKDVMRSIAETYTKIYLNiGLDEMVETINRLIDLYDVDGV 340
                                       *********996666666666...55551134575566679*****66669999779******************** PP

                                       EEEEETT-HHHHHHHHHHHHHHHHTT--EEEEEE-S-STT...HHHHHHHHHHHHHH- CS
                             HGD-D 269 ifqtgggCrpasgyiglirralekegiPvlsletDqsdir...egqlktRVeaflEiL 323
                                       +++++++C+p+s+ +++i++ l    +P +++e+D++d+r   e+q+++R+eaflEiL
  gi|488600200|ref|YP_007906671.1| 341 VIHSNRSCKPYSFGQYEIKKML---DVPAVIIEADMTDPRafsEAQIESRLEAFLEIL 395
                                       **********************...5******************************97 PP

>> AsiA  Anti-Sigma Factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0067        60      24      60 ..     152     183 ..     144     200 .. 0.70
   2 ?    7.9   0.0   0.00037       3.3       3      56 ..     301     355 ..     299     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0067
                                       HHHTSHH.HHHHHHHHHT-.ESSSSE--HHHHHHHHHT CS
                              AsiA  24 eivenrk.lfvellneiGvrtteGkkltqnsfrkivar 60 
                                       + ve +   fv++l  i      G+++  + frk++ +
  gi|488600200|ref|YP_007906671.1| 152 DYVESQLyDFVDFLEKI-----SGREFDEKKFRKVL-E 183
                                       56666532577777765.....689********986.3 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00037
                                       HHHHHHHHH.HHHHHHHHTTTHHHHTSHHHHHHHHHHHT-.ESSSSE--HHHHHH CS
                              AsiA   3 tielvldii.avaslLvklsrdeivenrklfvellneiGvrtteGkkltqnsfrk 56 
                                       + ++++ i+ ++  + + ++ de+ve  + +++l +  Gv  +  +  +  sf +
  gi|488600200|ref|YP_007906671.1| 301 KKDVMRSIAeTYTKIYLNIGLDEMVETINRLIDLYDVDGVVIHSNRSCKPYSFGQ 355
                                       568889997689****************************99*999999988866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2947.42
//
Query:       gi|488600201|ref|YP_007906672.1|  [L=328]
Description: Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-41  142.3   0.1    3.4e-41  142.1   0.1    1.0  1  HGD-D           2-hydroxyglutaryl-CoA dehydratase, D-componen
  ------ inclusion threshold ------
      0.089   12.8   0.1        4.2    7.4   0.0    2.7  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
       0.14   12.6   0.1       0.22   11.9   0.1    1.3  1  Staphylokinase  Staphylokinase/Streptokinase family


Domain annotation for each model (and alignments):
>> 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 !  142.1   0.1   5.7e-45   3.4e-41       1     323 []       8     327 ..       8     327 .. 0.87

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 5.7e-45
                                       STTS-HHHHHHTT-EEEE-.----GGGHHHHTTTS-SSS-HHHHHHHHHHHT.HH-S.EEEEES-SHHHHHHHHHHT CS
                             HGD-D   1 qwyypeellaAaglvpiflargpsrepldlaekylpsfgCglardalgaale.kpdd.lvvanttCdqvkkilenla 75 
                                       ++++p e+++Aa+l+p+++   +++  +  a+++++s++C+ ++ +l+ +l+ ++d+ +vv++ +Cd+ +++ ++++
  gi|488600201|ref|YP_007906672.1|   8 CTFTPKEIIRAANLMPVRV--LANNTAVSTANAHIQSYCCSQVKVSLERMLRgEFDFhGVVFTRSCDSLMRLADIWE 82 
                                       899*************966..4566778888888******************9555438999999************ PP

                                       TT..S-EEEE---....HHHHHHHHHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHTTSSS-SS- CS
                             HGD-D  76 ki..ipytvldiP....eeavkyledelenliaaleeitgkrideesleaaikeanetrellkelytllpqspapih 146
                                       k   ++++ ++ P     +a+++l+ e+ ++++ + +  g++i+eesl+ ai+e+ e ++ l e+++  p       
  gi|488600201|ref|YP_007906672.1|  83 KNsdMKVYSIEFPtkidGRAKEFLKREFYDFKDEIGKW-GEEITEESLMDAIEEYLELERVLSEVFRTKPDY----- 153
                                       ***977***********9**********9999996665.88***********************99888663..... PP

                                       HHHHHHHHHHTT.S-HHHHHHHHHHHHHHHHHHT..STS-EEEEEES---TT--HHHHHHHHT.T-EEEEEESTTTH CS
                             HGD-D 147 gfdllllakvvf.lgkeeatealeelleeleersk.seriRllltGipvellaaklmkaleaglgavvvnndacyps 221
                                               ++v  +++e+  + +ee  + le   + ++r R+l+tG+ + ++  +++ ++e+  g + v +d+c++ 
  gi|488600201|ref|YP_007906672.1| 154 --------DLVLkAETEDPGKVIEEAKKRLES--EgDDRKRVLVTGSVCPFP--EIFAMFEDV-G-FAVEDDLCTGR 216
                                       ........234445666666666666666666..4349**************..*******88.3.69********* PP

                                       HHHS-.........SSHHH.HHHHHHHHHT...--TT.S.S-HHHHHHHHHHHHHTT-SEEEEEEETT-HHHHHHHH CS
                             HGD-D 222 rlvry.........vgdvgqplealasgyy...kcpv.s.pkerrlewirdlideykvdgvifqtgggCrpasgyig 284
                                       r++ +         +   +++++ las+y+   +cp+ s + +rr +++ + +    vd+v+f+ +++C+p++++++
  gi|488600201|ref|YP_007906672.1| 217 RFF-DfgakvelrgN-GMDDLIDFLASKYLekaPCPTkSyEGDRRFKYLLERC--RDVDAVVFLLLKFCEPHFFDYP 289
                                       ***.33677899854.4456***********8888888878************..99******************** PP

                                       HHHHHHHHTT--EEEEEE-S-STTHHHHHHHHHHHHHH- CS
                             HGD-D 285 lirralekegiPvlsletDqsdiregqlktRVeaflEiL 323
                                        +++ +e++g  +l le +   +  +ql+tRVeaf E+L
  gi|488600201|ref|YP_007906672.1| 290 QLKEKIEEMGKKTLLLEIEFPFS-VEQLRTRVEAFYEML 327
                                       ******************87665.9*************8 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.025   1.5e+02      33      54 ..      57      78 ..      54      89 .. 0.88
   2 ?    7.4   0.0   0.00071       4.2      14      47 ..     131     164 ..     121     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.025
                                      SSSSSEEEEEEESSHHHHHHHH CS
                    AsnC_trans_reg 33 tGdydyllkvvvrdlealerfl 54
                                       G++d++  v +r+ ++l r+ 
  gi|488600201|ref|YP_007906672.1| 57 RGEFDFHGVVFTRSCDSLMRLA 78
                                      6*****************9984 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00071
                                       HHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSH CS
                    AsnC_trans_reg  14 eefeealaelpeVvecyrvtGdydyllkvvvrdl 47 
                                       +++ee l+      e++r+  dyd++lk+ ++d 
  gi|488600201|ref|YP_007906672.1| 131 DAIEEYLELERVLSEVFRTKPDYDLVLKAETEDP 164
                                       444444444444569****************996 PP

>> Staphylokinase  Staphylokinase/Streptokinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.7e-05      0.22       7      55 ..      90     139 ..      83     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                    Staphylokinase   7 ftvnf.vdvdgkkeellsplavelaikngkigekltseeLlkaieeqLda 55 
                                       + ++f +++dg+ +e l+     ++++ gk ge +t e L +aiee L+ 
  gi|488600201|ref|YP_007906672.1|  90 YSIEFpTKIDGRAKEFLKREFYDFKDEIGKWGEEITEESLMDAIEEYLEL 139
                                       778887899*************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2038.64
//
Query:       gi|488600202|ref|YP_007906673.1|  [L=196]
Description: transcriptional regulator, XRE family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-23   81.8   0.9    1.5e-11   44.6   0.1    2.4  2  CBS             CBS domain
    5.4e-15   55.2   0.5    4.8e-14   52.2   0.3    2.2  2  HTH_3           Helix-turn-helix
    3.1e-08   33.9   0.0    5.1e-08   33.1   0.0    1.3  1  HTH_31          Helix-turn-helix domain
    4.2e-08   33.1   0.1      1e-07   31.9   0.1    1.7  1  HTH_19          Helix-turn-helix domain
    2.6e-06   27.6   0.1    1.4e-05   25.2   0.0    2.0  2  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
    6.5e-05   22.8   0.1    0.00024   21.0   0.0    2.1  2  HTH_37          Helix-turn-helix domain
     0.0019   18.0   0.0     0.0033   17.3   0.0    1.3  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.057   13.4   0.0    1.8  1  Pou             Pou domain - N-terminal to homeobox domain
      0.019   13.9   0.1       0.02   13.9   0.1    1.1  1  AAA_10          AAA-like domain
      0.035   13.9   0.1        9.5    6.1   0.1    2.3  2  HTH_38          Helix-turn-helix domain
      0.041   13.4   0.1        0.2   11.2   0.0    2.3  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.051   13.4   0.0       0.11   12.4   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.097   13.1   0.6       0.32   11.5   0.0    2.2  2  HTH_26          Cro/C1-type HTH DNA-binding 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 !   44.6   0.1   1.1e-14   1.5e-11       1      56 [.      65     119 ..      65     120 .. 0.95
   2 !   35.7   0.1   6.4e-12   8.8e-09       1      55 [.     131     182 ..     131     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.1e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       ++++m+++v++v+p+++l++++e m ekg+s++PV  e g+++G +t++ +l+ +l
  gi|488600202|ref|YP_007906673.1|  65 AKSVMNPNVMYVSPNQSLRKVIEVMLEKGISQMPVF-ELGRVLGTITESSILEIVL 119
                                       579*********************************.9**************9765 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 6.4e-12
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+d m ++++tv pd+ le + ++++ ++  +++VV e g++ Gi+t++D+++a+
  gi|488600202|ref|YP_007906673.1| 131 VKDCMESPLPTVQPDEKLEYICKMLI-HN-PAVLVV-EKGEVRGIITKHDIMKAI 182
                                       7899********************75.44.5999**.8***************98 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.3   3.5e-17   4.8e-14       1      49 [.       8      56 ..       8      59 .. 0.97
   2 ?    0.6   0.0      0.43     6e+02       4      26 ..      88     114 ..      85     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 3.5e-17
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                                      +k++Rk+lg++q++LAe++Gvs+  i+riE+G+  P l+ +kk+ ++L+
  gi|488600202|ref|YP_007906673.1|  8 IKRKRKKLGITQKKLAELVGVSQPLIARIESGDIDPKLSLVKKIFEVLD 56
                                      89********************************************997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                                       HHHHTTHHH...HHHHHHHT.SSHHHH CS
                             HTH_3   4 lRkqlglsq...eeLAeklG.vsrsti 26 
                                        ++++g+sq    eL ++lG ++ s+i
  gi|488600202|ref|YP_007906673.1|  88 VMLEKGISQmpvFELGRVLGtITESSI 114
                                       567889999777788888888888877 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   3.7e-11   5.1e-08       7      55 ..       9      56 ..       6      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.7e-11
                            HTH_31  7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                      ++ R++ G++q+ +Ae++gvs+  + r+E+G ++ p+++ + ++ ++l+
  gi|488600202|ref|YP_007906673.1|  9 KRKRKKLGITQKKLAELVGVSQPLIARIESGDID-PKLSLVKKIFEVLD 56
                                      6679999**************************7.********999987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   7.4e-11     1e-07       4      52 ..       8      55 ..       5      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 7.4e-11
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                      +k+ R++lg+tq++lae +g+s+  i+ iE+g + +p+ +l++ki e l
  gi|488600202|ref|YP_007906673.1|  8 IKRKRKKLGITQKKLAELVGVSQPLIARIESGDI-DPKLSLVKKIFEVL 55
                                      8999******************************.**********9987 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 !   25.2   0.0   9.8e-09   1.4e-05      72     121 ..       6      56 ..       1      59 [. 0.91
   2 ?    0.0   0.0      0.61   8.4e+02      62     130 ..      61     129 ..      58     130 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 9.8e-09
                    MqsA_antitoxin  72 afiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvk.llklld 121
                                       ++i+r rkkl+++q+++ae+ G+     +r e+G + p+l+lvk ++++ld
  gi|488600202|ref|YP_007906673.1|   6 EEIKRKRKKLGITQKKLAELVGVSQPLIARIESGDIDPKLSLVKkIFEVLD 56 
                                       7899**************************************963778887 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.61
                    MqsA_antitoxin  62 kkvnaelvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvkllk.lldrhPelleei 130
                                       kkvna++v    ++ v  +  l +  ++ ++  G+  +  +e G+v   ++   +l+ +l++ Pe  ee+
  gi|488600202|ref|YP_007906673.1|  61 KKVNAKSVMNPNVMYVSPNQSLRK-VIEVMLEKGISQMPVFELGRVLGTITESSILEiVLEKGPEGAEEM 129
                                       566666666666666666655543.345566778888888899998888777777763578889888887 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.8e-07   0.00024      22      57 ..       7      42 ..       3      69 .. 0.83
   2 ?   -2.4   0.0       3.6   4.9e+03       6      16 ..     122     132 ..     118     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--T CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrgkls 57
                                      +i+++++k++++q+++a+l g++qP + r++ g+++
  gi|488600202|ref|YP_007906673.1|  7 EIKRKRKKLGITQKKLAELVGVSQPLIARIESGDID 42
                                      79*****************************99987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                                       X--HHHHHHHH CS
                            HTH_37   6 geedaeelkaK 16 
                                       g+e aee+k K
  gi|488600202|ref|YP_007906673.1| 122 GPEGAEEMKVK 132
                                       89999999988 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.4e-06    0.0033       3      36 ..       9      42 ..       7      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                                      HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                                      +++R+++g++ +++a+   +++ ++ ++E++d+d
  gi|488600202|ref|YP_007906673.1|  9 KRKRKKLGITQKKLAELVGVSQPLIARIESGDID 42
                                      799****************************987 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.1e-05     0.057      11      52 ..       6      41 ..       2      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                               Pou 11 kefkqkRiklgltQadvglaLgklygkefSqttIcrFEkLdl 52
                                      +e k+kR klg+tQ+++++     +   +Sq  I r+E+ d+
  gi|488600202|ref|YP_007906673.1|  6 EEIKRKRKKLGITQKKLAEL----V--GVSQPLIARIESGDI 41
                                      689***********987654....3..479999999998766 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.4e-05      0.02     104     184 ..      46     125 ..       6     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                            AAA_10 104 slaedilelllgvkkkesekkaalseaveavlegkqrgllavieelrke..dekvareiarhlesvvkkslaklvfs 178
                                       sl ++i+e+l  ++ k+ + k +++  v  v  +++++l +vie + ++  ++  + e++r l  +++ s++++v++
  gi|488600202|ref|YP_007906673.1|  46 SLVKKIFEVLDSLEGKKVNAKSVMNPNVMYV--SPNQSLRKVIEVMLEKgiSQMPVFELGRVLGTITESSILEIVLE 120
                                       5667888888888888888888888877766..6889*********88866788899******************** PP

                            AAA_10 179 dgsvee 184
                                       +g  e+
  gi|488600202|ref|YP_007906673.1| 121 KGP-EG 125
                                       *96.44 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0069       9.5       9      39 ..       4      35 ..       3      36 .. 0.85
   2 ?    5.6   0.0    0.0096        13       9      31 ..      82     107 ..      79     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0069
                            HTH_38  9 eReeIerll.aeGlslreIArrLgrspsTIsR 39
                                      e eeI r + + G ++++ A ++g+s   I+R
  gi|488600202|ref|YP_007906673.1|  4 EIEEIKRKRkKLGITQKKLAELVGVSQPLIAR 35
                                      6788888873578*************999998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0096
                            HTH_38   9 eReeIerllaeGlslr...eIArrLg 31 
                                        R +Ie +l++G s+    e +r Lg
  gi|488600202|ref|YP_007906673.1|  82 LRKVIEVMLEKGISQMpvfELGRVLG 107
                                       699*********99976777777776 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 ?   11.2   0.0   0.00015       0.2      17      36 ..      16      35 ..      12      36 .. 0.90
   2 ?   -2.4   0.0       2.6   3.5e+03       4      15 ..     110     121 ..     108     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                            HTH_24 17 risqreLAerlglSpstvnr 36
                                      +i+q+ LAe +g+S++ + r
  gi|488600202|ref|YP_007906673.1| 16 GITQKKLAELVGVSQPLIAR 35
                                      7*************998876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                            HTH_24   4 tdrkILelLqkn 15 
                                       t+  ILe++ ++
  gi|488600202|ref|YP_007906673.1| 110 TESSILEIVLEK 121
                                       667899999886 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.8e-05      0.11       9      28 ..      17      36 ..       8      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                    YdaS_antitoxin  9 GgqkaLAealgvsqqaVsqW 28
                                       +qk+LAe++gvsq+ + + 
  gi|488600202|ref|YP_007906673.1| 17 ITQKKLAELVGVSQPLIARI 36
                                      58*************99876 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.32       6      50 ..      12      55 ..       7      57 .. 0.82
   2 ?   -2.1   0.0       3.9   5.3e+03      41      50 ..     146     155 ..     143     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                            HTH_26  6 madrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaL 50
                                       ++ git+++La+ +g+s++ ++r+ +g +  ++l+   ki ++L
  gi|488600202|ref|YP_007906673.1| 12 RKKLGITQKKLAELVGVSQPLIARIESGDI-DPKLSLVKKIFEVL 55
                                      56779***********************98.77777777776666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                            HTH_26  41 dtLdkiCdaL 50 
                                       + L+ iC+ L
  gi|488600202|ref|YP_007906673.1| 146 EKLEYICKML 155
                                       5688999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1256.89
//
Query:       gi|488600203|ref|YP_007906674.1|  [L=201]
Description: hypothetical protein Asulf_00663 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1349.64
//
Query:       gi|488600204|ref|YP_007906675.1|  [L=314]
Description: beta-ribofuranosylaminobenzene 5-phosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-06   27.8   1.0    5.5e-06   26.5   1.0    1.7  1  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0021   18.4   0.0     0.0054   17.1   0.0    1.7  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.0   6.1e-10   5.5e-06       2      66 .]      72     132 ..      71     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.1e-10
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHH.HHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleae.rlaqggngsggDvaasvyGg 66 
                                       ++i s+   + GLGS++  a+a++ A+ +l+gl+l     +l     l+++g +sg+ + a+ yGg
  gi|488600204|ref|YP_007906675.1|  72 LEILSTYRNHVGLGSGTQSALAVAEAFKKLYGLDL-----SLYELaSLVGRGGTSGIGIHAFKYGG 132
                                       6788999999**********************655.....444444666779************98 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 !   17.1   0.0   6.1e-07    0.0054       2      83 ..     213     288 ..     212     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.1e-07
                    GHMP_kinases_C   2 lealergdlellgellnlsqrs.elkavvgilppeleelleal.selGalgaklsGaGgGptvfalfkdkdeaeqva 76 
                                       l+ + ++dl++++e++ + qr   +    +++ +   +l+     ++  +++++s +  Gptv+a++  +++a+ v+
  gi|488600204|ref|YP_007906675.1| 213 LPSIVEKDLDSFAEGISRIQRIgFK----RVEIEQYGNLIWDVmGSVSGCAVGMSST--GPTVYAIT--DSNANSVK 281
                                       5778999999999999999997655....5555555555555536666678888888..*******9..99999**9 PP

                    GHMP_kinases_C  77 ralreef 83 
                                       r l ++f
  gi|488600204|ref|YP_007906675.1| 282 RDLISAF 288
                                       9997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1986.42
//
Query:       gi|488600205|ref|YP_007906676.1|  [L=219]
Description: CRISPR-associated protein Cas4 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-12   45.5   3.5    8.8e-10   38.9   0.4    2.1  2  Cas_Cas4  Domain of unknown function DUF83
    9.6e-05   22.4   0.1    9.6e-05   22.4   0.1    1.9  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.2   0.00042       3.8       2      20 ..       6      24 ..       5      31 .. 0.89
   2 !   38.9   0.4   9.8e-14   8.8e-10      54     161 ..      98     208 ..      78     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00042
                          Cas_Cas4  2 gtkiqyyliCkrklwlish 20
                                      ++++ +y++C+r +++i++
  gi|488600205|ref|YP_007906676.1|  6 VSEVTSYAYCPRYCYFIQR 24
                                      6899************986 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 9.8e-14
                          Cas_Cas4  54 sikiDvvekekeklvv..vEvKkskkkeeaa.klQllyYlllLe.kkgveikeGvleypkekkreevelteelreel 126
                                       ++++D + +++e l++  + +K  ++  + + ++ ++ +++lLe k   ++k+G+++y    + ++ve+++++r  +
  gi|488600205|ref|YP_007906676.1|  98 KGVVDEIVTKNEMLYPlsISYKAPERGVWFKdRVKITCFCILLEeKLKDKVKRGFVYYCRDGRLRDVEISRKDRMTV 174
                                       788888886777777666778888888887779***********99999**************************** PP

                          Cas_Cas4 127 ekaikeieeiissekppkvkkkkiCkkCayaelCl 161
                                        ++i+++ ++ ++  +p+ k++ +Ck C+++e Cl
  gi|488600205|ref|YP_007906676.1| 175 LRMIERVIRLRKN-FIPERKESGKCKFCSFRENCL 208
                                       *********9888.89******************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 ?   -0.0   0.5     0.074   6.6e+02       2      16 ..       4      18 ..       4      28 .. 0.78
   2 !   22.4   0.1   1.1e-08   9.6e-05     113     254 ..      80     207 ..      40     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.074
                          PDDEXK_1  2 lSvsrletfleCplr 16
                                      +Svs++  ++ Cp+ 
  gi|488600205|ref|YP_007906676.1|  4 VSVSEVTSYAYCPRY 18
                                      69**********974 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.1e-08
                          PDDEXK_1 113 gfrpvalelefggekvrLkGriDrvddkeg..elriiDyKtgsappkskelaelkeglQlllYllalaegeelkeeg 187
                                       ++ pv  e++ ++ek+rLkG +D + +k++  +   i yK      ++    + k+++  +  + +l+e+  lk++ 
  gi|488600205|ref|YP_007906676.1|  80 ELVPVDWEVSLTNEKFRLKGVVDEIVTKNEmlYPLSISYK-AP---ERGV--WFKDRVKITCFCILLEEK--LKDKV 148
                                       36788899888899************777779********.33...4555..889999************..55443 PP

                          PDDEXK_1 188 epagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskk.CeyCpyksvC 254
                                       +++ ++y+r         ++++ ++ +++++  +l+ +e++  ++++  +p r +   C++C++++ C
  gi|488600205|ref|YP_007906676.1| 149 KRGFVYYCR--------DGRLRDVEISRKDRMTVLRMIERV-IRLRKNFIPERKESGkCKFCSFRENC 207
                                       255555555........5899999999999*9999999998.5555555666555558********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1526.36
//
Query:       gi|488600206|ref|YP_007906677.1|  [L=112]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-47  159.1   0.0    3.4e-47  158.9   0.0    1.0  1  DUF555    Protein of unknown function (DUF555)
  ------ inclusion threshold ------
      0.043   14.1   0.1       0.14   12.5   0.0    1.8  2  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   0.0   3.8e-51   3.4e-47       1     101 []       2     102 ..       2     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 3.8e-51
                            DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpeldfveievgetecPkcgeelesalvvadtalvglllemkvf 77 
                                       +y v l++ wivr++ksv+dA++iA++eagkrlnp+ld+vei+vg+t+cP+c+ +++sa++va++alvgl++emkvf
  gi|488600206|ref|YP_007906677.1|   2 NYIVRLQGGWIVRKAKSVEDAMNIAVAEAGKRLNPDLDYVEIDVGDTACPACNVPFKSAFMVAGVALVGLIFEMKVF 78 
                                       79*************************************************************************** PP

                            DUF555  78 naeseEhaeriakseigkaledvP 101
                                       naes+Eha riak+eigk+l ++P
  gi|488600206|ref|YP_007906677.1|  79 NAESKEHAGRIAKYEIGKRLGRIP 102
                                       ***********************9 PP

>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.5e-05      0.14      13      38 ..      17      43 ..      14      48 .. 0.84
   2 ?   -1.6   0.0      0.36   3.2e+03      46      55 ..      85      94 ..      72      99 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                                      S-HHHHHHHHHHHHHHH-S.SEEEEEE CS
                           Dodecin 13 kSwedAiqnAiaeAsktlr.nirwveV 38
                                      kS+edA++ A+aeA k l+ +++ ve+
  gi|488600206|ref|YP_007906677.1| 17 KSVEDAMNIAVAEAGKRLNpDLDYVEI 43
                                      8***************99745666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.36
                                      CTTCCEEEEE CS
                           Dodecin 46 edgkiaeYqv 55
                                      + g+ia+Y +
  gi|488600206|ref|YP_007906677.1| 85 HAGRIAKYEI 94
                                      4588888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 733.59
//
Query:       gi|488600207|ref|YP_007906678.1|  [L=523]
Description: putative ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  137.3   0.0    1.6e-39  136.3   0.0    1.5  1  DUF87            Helicase HerA, central domain
    1.2e-08   34.0   0.0     0.0013   17.4   0.0    2.3  2  DUF853           Bacterial protein of unknown function (DUF85
    6.5e-07   29.4   2.2    1.2e-06   28.6   0.4    2.3  2  HAS-barrel       HAS barrel domain
    1.8e-05   23.9   0.0     0.0012   17.9   0.0    2.3  2  AAA_10           AAA-like domain
    0.00086   18.3   0.0      0.042   12.8   0.0    2.5  3  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0013   18.8   0.4      0.024   14.6   0.0    2.6  3  ResIII           Type III restriction enzyme, res subunit
     0.0017   17.3   0.0     0.0031   16.4   0.0    1.4  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
     0.0043   17.3   1.0        4.6    7.5   0.0    3.2  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.011   16.1   0.1       0.41   11.1   0.0    2.7  3  AAA              ATPase family associated with various cellul
      0.067   13.0   0.1       0.53   10.0   0.1    2.6  1  DEAD             DEAD/DEAH box helicase
          2    8.5   8.2        2.4    8.2   6.9    1.9  1  YqzE             YqzE-like protein


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.0   9.8e-43   1.6e-39       2     226 ..     121     338 ..     120     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 9.8e-43
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal.......... 68 
                                       ++G l+++++++v ld+n+lv++H++il++TGsGKS+t++v++eel+ ++g+++ i+DpHGEY++++          
  gi|488600207|ref|YP_007906678.1| 121 YLG-LIEDTDIRVNLDVNSLVQKHCCILAKTGSGKSYTAGVIIEELI-ERGVPLFIIDPHGEYASLKepnrdeeekm 195
                                       567.669****************************************.*********************99999999 PP

                             DUF87  69 ......ekllsekvkvitpspsa....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeeke 135
                                             +k++ +kv+v+ p++s+     d  l+++  +l+ ee+++l+++     +++q+++l++al+++k     +
  gi|488600207|ref|YP_007906678.1| 196 kiygisPKGYGNKVRVYVPPNSPfanrADGILRLDGLNLSAEEIIELAGI----TNTTQQALLYQALKNLK----GQ 264
                                       99999999999999999999888***************************....7788**********998....89 PP

                             DUF87 136 klssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvd 212
                                       ++++++++            e++++k++a+ +ll +le++l++g +   +st ++ ll     ++++  ++d+ g +
  gi|488600207|ref|YP_007906678.1| 265 EYTIEDIID-----------EVEQIKHSAKVALLGSLEKILESGLFG-RDSTPVDILL-----QKERAIVLDMRGTP 324
                                       9*****999...........5667889****************9999.5555555555.....66666777****** PP

                             DUF87 213 elaqqlvvsvilrr 226
                                        + q+l+vs ++ +
  gi|488600207|ref|YP_007906678.1| 325 PEHQDLIVSRVCAK 338
                                       **********9976 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 !   17.4   0.0   8.1e-07    0.0013      18      71 ..     138     191 ..     124     201 .. 0.84
   2 !   14.3   0.0   7.1e-06     0.012     282     362 ..     373     451 ..     346     516 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.1e-07
                            DUF853  18 klanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGevk 71 
                                       +l+ +h  i   tG Gk  t  v+ e+l e Gvp f+ d  G+ +++ ++ + +
  gi|488600207|ref|YP_007906678.1| 138 SLVQKHCCILAKTGSGKSYTAGVIIEELIERGVPLFIIDPHGEYASLKEPNRDE 191
                                       56889***************************************9999887654 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.1e-06
                            DUF853 282 eqvvrLirsk....GvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteL 354
                                        qv+r i s     G G+  ++q P+ + ++v++q  +  q  lr   p+d +a+k+ ++++ a    ++ + i+ L
  gi|488600207|ref|YP_007906678.1| 373 TQVLRTIASEgrkfGLGLLVISQRPARVDKNVISQCNT--QIILRVTNPNDLNAIKKGVEGLTA----EMVDEIKRL 443
                                       4788888665222379*******************876..568*****************9976....466777888 PP

                            DUF853 355 gvGealvs 362
                                         G alv 
  gi|488600207|ref|YP_007906678.1| 444 PPGTALVV 451
                                       88888875 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.4   7.4e-10   1.2e-06       1      76 [.       5      78 ..       5     114 .. 0.78
   2 ?   -1.1   0.1       1.3   2.2e+03      47      71 ..     482     504 ..     446     512 .. 0.59

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 7.4e-10
                        HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddeva 76
                                      +G+++g ++s+++ f+v ++k+vk  +y++++++ +++v  +v+d+ +  s+ ++ ++  +  + ++e + + +++
  gi|488600207|ref|YP_007906678.1|  5 VGRIYGNAGSTEFNFVVLEPKEVKRTDYIKVWNDSEGWVVAQVLDVIA--STDLKETDVLKGRDAEREIYIAKAYV 78
                                      79**********************************************..33333333333333333333333333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                        HAS-barrel  47 rrgnselsndlalvlsleeleeang 71 
                                       ++  +     +a+v+++++ +ea +
  gi|488600207|ref|YP_007906678.1| 482 EK--KKRTERTAKVRDVKDKKEAKK 504
                                       33..333444555555555555544 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.2e-07    0.0012      22     152 ..     142     278 ..     133     317 .. 0.69
   2 ?    3.5   0.0     0.016        27     229     323 ..     335     439 ..     330     451 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.2e-07
                            AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiakkinvvtLdse...eenegvLdPlvl 95 
                                        ++ i+ ++G GKS++a +++  +  +g  ++iiDp  e    ke  +   +k+++  ++++   ++ ++   P + 
  gi|488600207|ref|YP_007906678.1| 142 KHCCILAKTGSGKSYTAGVIIEELIERGVPLFIIDPHGEYASLKEPNRDEEEKMKIYGISPKgygNKVRVYVPPNSP 218
                                       6899***********************************98898888777788888888765444566677777776 PP

                            AAA_10  96 lkeekeaeslaedilel....llgvk.kkesekkaalseaveavlegkqrgllavieelrke 152
                                       +++      l  d l+l    + ++   +++ ++a+l +a +  l+g++  ++++i+e+++ 
  gi|488600207|ref|YP_007906678.1| 219 FANRA-DGILRLDGLNLsaeeIIELAgITNTTQQALLYQALK-NLKGQEYTIEDIIDEVEQI 278
                                       66553.333334444443333333332455555555555554.4567777788888887533 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.016
                            AAA_10 229 faref.assdkkef..kvvifDEawift.ssaeGkkllkelvR....iGRsynaavylvtqsadDvlkee...lknn 294
                                       ++ ++   ++++e+   ++++ Ea  f  +   Gk+++ +++R     GR++   ++ ++q +  v+k+     +++
  gi|488600207|ref|YP_007906678.1| 335 VCAKLfELRKREEVppGMIVIEEAHNFIpERGMGKAVSTQVLRtiasEGRKFGLGLLVISQRPARVDKNVisqCNTQ 411
                                       554441444444442246889999988625567999999999944445******************99982223334 PP

                            AAA_10 295 iglklaFretdkeeikkvLeflgldvede 323
                                       i l++  +++d ++ikk++e l ++  de
  gi|488600207|ref|YP_007906678.1| 412 IILRVT-NPNDLNAIKKGVEGLTAEMVDE 439
                                       444443.3467778888888777777655 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.6e-05     0.042      13      57 ..     139     183 ..     132     190 .. 0.92
   2 ?   -3.2   0.0       1.8   2.9e+03      42      54 ..     311     323 ..     308     324 .. 0.86
   3 ?    2.5   0.0     0.034        56     261     313 ..     376     420 ..     371     432 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                     TrwB_AAD_bind  13 retqhilivGttGsGKtqalekllrairargdraivlDltGafvs 57 
                                         ++h  i+  tGsGK+ ++  +++++ +rg    ++D++G++ s
  gi|488600207|ref|YP_007906678.1| 139 LVQKHCCILAKTGSGKSYTAGVIIEELIERGVPLFIIDPHGEYAS 183
                                       5789*************************************9975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                     TrwB_AAD_bind  42 rgdraivlDltGa 54 
                                       +++raivlD+ G+
  gi|488600207|ref|YP_007906678.1| 311 QKERAIVLDMRGT 323
                                       789*******995 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.034
                     TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdae 313
                                       l +++ egRkfG  + +  q  a++         ++++s +nt++ilrv++ +
  gi|488600207|ref|YP_007906678.1| 376 LRTIASEGRKFGLGLLVISQRPARVD--------KNVISQCNTQIILRVTNPN 420
                                       56677778888877766667776665........4789999999999988765 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 !   14.6   0.0   1.5e-05     0.024      23      51 ..     140     168 ..     116     182 .. 0.87
   2 ?    1.4   0.0      0.18   2.9e+02      96     147 ..     282     364 ..     244     390 .. 0.56
   3 ?   -3.6   0.6         6   9.8e+03      86      91 ..     499     504 ..     473     516 .. 0.40

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                       TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII  23 rdkrglikmaTGtGKTlvaaklierllkk 51 
                                        +k+ +i + TG+GK+++a  +ie+l + 
  gi|488600207|ref|YP_007906678.1| 140 VQKHCCILAKTGSGKSYTAGVIIEELIER 168
                                       4899**********************986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.18
                                       -.......................-SEEEEEHHHHHHTH.....................HHHTTT-S......EEE CS
                            ResIII  96 a................kekdstnkkilvttiqsldadseee.............eeeseellrdrfd......vii 137
                                       a                + +dst  +il+ ++ ++  d++ +              +  e  +           +i+
  gi|488600207|ref|YP_007906678.1| 282 AkvallgslekilesglFGRDSTPVDILLQKERAIVLDMRGTppehqdlivsrvcAKLFELRK----ReevppgMIV 354
                                       244455555555666666677777777777777777777666676666666553322222222....1234578999 PP

                                       EETGGGTTS. CS
                            ResIII 138 iDEaHrlgak 147
                                       i EaH++  +
  gi|488600207|ref|YP_007906678.1| 355 IEEAHNFIPE 364
                                       9999988764 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6
                                       EEEESS CS
                            ResIII  86 gkkvsg 91 
                                       +k+ ++
  gi|488600207|ref|YP_007906678.1| 499 KKEAKK 504
                                       111111 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 !   16.4   0.0   1.9e-06    0.0031      15     104 ..     103     204 ..      98     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                   T4SS-DNA_transf  15 krektikgevltkdkkalyaggllntdGdf.........ehvlvvAptrsgK..gvgvviPnllkwkqsiVvlDpkg 80 
                                       k+ek+++ +vl+ +k+++y g + +td            +h  + A t+sgK  ++gv+i  l+  +  + ++Dp g
  gi|488600207|ref|YP_007906678.1| 103 KAEKELIVDVLGLEKDGIYLGLIEDTDIRVnldvnslvqKHCCILAKTGSGKsyTAGVIIEELIERGVPLFIIDPHG 179
                                       567788888999999988888855555333666788889*************6669********************* PP

                   T4SS-DNA_transf  81 ElaeltskiRkkqgr.kVfvlePan 104
                                       E a l    R ++ + k++  +P+ 
  gi|488600207|ref|YP_007906678.1| 180 EYASLKEPNRDEEEKmKIYGISPKG 204
                                       ****999999999888999888875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.8     0.012        20       5      38 ..     141     193 ..     139     310 .. 0.53
   2 !    7.5   0.0    0.0028       4.6      75     128 ..     327     415 ..     298     421 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee........................e 38 
                                       ++++++ + +G+GK++++  + e+l e     +                        e
  gi|488600207|ref|YP_007906678.1| 141 QKHCCILAKTGSGKSYTAGVIIEELIE-----RgvplfiidphgeyaslkepnrdeeE 193
                                       678899999999999999888888733.....22333444544444444444444441 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                            AAA_22  75 seell.ealeqalrarav.....ielliiDEaqhlr...s......eealeeLrsl..................... 115
                                        ++l+ +++   l + ++     +++++i+Ea++++           ++l++   +                     
  gi|488600207|ref|YP_007906678.1| 327 HQDLIvSRVCAKLFELRKreevpPGMIVIEEAHNFIperGmgkavsTQVLRT---Iasegrkfglgllvisqrparv 400
                                       455555666666666666677899**********988651544333444444...3222344455555554444443 PP

                            AAA_22 116 lnl...srkgvqliLv 128
                                             s++++q+iL 
  gi|488600207|ref|YP_007906678.1| 401 D-KnviSQCNTQIILR 415
                                       1.13466666666665 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 ?    1.8   0.0      0.18     3e+02       4      30 ..     147     176 ..     144     196 .. 0.83
   2 ?   -2.1   0.0       2.9   4.8e+03      63      72 ..     271     280 ..     226     295 .. 0.61
   3 ?   11.1   0.0   0.00025      0.41      47     128 ..     337     412 ..     331     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.18
                                       ESSTTSSHHHHHHHHHHHH...THEEEEEE CS
                               AAA   4 yGppGtGKTllakavakel...gvefleis 30 
                                           G GK+++a  +++el   gv+++ i+
  gi|488600207|ref|YP_007906678.1| 147 LAKTGSGKSYTAGVIIEELierGVPLFIID 176
                                       5678**************876667777665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                                       EEETGGGHHH CS
                               AAA  63 fiDEidalak 72 
                                       +iDE++++  
  gi|488600207|ref|YP_007906678.1| 271 IIDEVEQIKH 280
                                       5677777644 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00025
                                       HHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHST CS
                               AAA  47 relfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrg 122
                                       ++lf+  k+++  p  ++i+E+++++++r     + ++ v  q l+ +  + +k + + ++++++rp ++d+ ++ +
  gi|488600207|ref|YP_007906678.1| 337 AKLFELRKREEvPPGMIVIEEAHNFIPER-----GMGKAVSTQVLRTIASEGRKFG-LGLLVISQRPARVDKNVI-S 406
                                       56777766666667***************.....8888899999999988888766.999*************99.8 PP

                                       TSSEEE CS
                               AAA 123 Rfdrki 128
                                        ++ +i
  gi|488600207|ref|YP_007906678.1| 407 QCNTQI 412
                                       888877 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00032      0.53      14      48 ..     141     250 ..     133     494 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00032
                                       TCEEEEEESTTSSHHHHHHHHHHHHHHHS.........TTSTS.................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxx.................................. RF
                              DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyet.........kgktg.................................. 47 
                                       ++++++ a+TGsGK+  + + + + + e+         +   g                                  
  gi|488600207|ref|YP_007906678.1| 141 QKHCCILAKTGSGKSYTAGVIIEELI-ERgvplfiidpH---Geyaslkepnrdeeekmkiygispkgygnkvrvyv 213
                                       6799***********99887666544.533555444431...03334444444555556666666666666666666 PP

                                       ....................................- CS
                                       ....................................x RF
                              DEAD  48 ....................................p 48 
                                                                            
  gi|488600207|ref|YP_007906678.1| 214 ppnspfanradgilrldglnlsaeeiielagitnttQ 250
                                       6666666666666666666666666666666666662 PP

>> YqzE  YqzE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.9    0.0015       2.4      18      44 ..     497     523 .]     487     523 .] 0.90

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                              YqzE  18 dtPkeeRkkkkeekkeekepfsyrwFG 44 
                                          ke +k+kk +kk+ ++ f+ r+FG
  gi|488600207|ref|YP_007906678.1| 497 KDKKEAKKEKKDSKKKSRKGFLRRMFG 523
                                       5669**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1627  (0.0907468); expected 358.6 (0.02)
Passed bias filter:                      969  (0.0540465); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.44
# Mc/sec: 3548.87
//
Query:       gi|488600208|ref|YP_007906679.1|  [L=464]
Description: radical SAM additional 4Fe4S-binding domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-24   87.5   0.0    2.3e-24   86.7   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    1.4e-08   35.1   0.0    3.7e-08   33.7   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain
    2.2e-06   28.1   2.5      7e-06   26.5   2.5    1.9  1  SPASM        Iron-sulfur cluster-binding domain
    1.6e-05   25.0   0.0    1.6e-05   25.0   0.0    2.3  3  Fer4_14      4Fe-4S single cluster domain
     0.0018   17.9   0.0     0.0028   17.2   0.0    1.2  1  HMGL-like    HMGL-like
  ------ inclusion threshold ------
      0.049   13.7   0.0       0.17   12.0   0.0    1.9  1  HTH_22       HTH 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 !   86.7   0.0   7.6e-28   2.3e-24       3     164 ..     123     273 ..     121     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 7.6e-28
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       +t+ CnlrC +C+ +     ++ g++l++ e le+v +l  e gv  + ++ggepl+ +df   +e++++l   g++
  gi|488600208|ref|YP_007906679.1| 123 FTKMCNLRCQHCYSN----AGKMGHELTLLEKLELVNQL-DEAGVVAISFSGGEPLMSSDFWLTAEHAKRL---GFH 191
                                       7999***********....59******************.7999**************************9...*** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGe 155
                                       ++v tngtl+de+++++l+   vd+v+++l++++++  ++ ++  ++ fe  +e ++++ +agi  + + ++     
  gi|488600208|ref|YP_007906679.1| 192 VSVATNGTLIDEDVAKKLKG-IVDYVEISLDSPNPK-AHDSFRgVKGAFEGAIERIKNCIKAGIQ-TGIATTAT-KK 264
                                       **********9999999999.66*************.8888888********************9.44443333.35 PP

                                       SHHHHHHHH CS
                                       xxxxxxxxx RF
                       Radical_SAM 156 ndeeleell 164
                                       n +e+ el+
  gi|488600208|ref|YP_007906679.1| 265 NLSEIPELV 273
                                       555555555 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   0.0   1.3e-11   3.7e-08      11     118 ..     123     223 ..     115     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.3e-11
                           Fer4_12  11 fvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekd 87 
                                       f++ Cnl+C+ C+       k g+e t   + e++++l++  +  ++++GGEPl+    +++   +++ k+ ++  +
  gi|488600208|ref|YP_007906679.1| 123 FTKMCNLRCQHCYS---NAGKMGHELTLLEKLELVNQLDEAGVVAISFSGGEPLM---SSDFWLTAEHAKRLGF-HV 192
                                       5899*********5...556778888877777899999999**************...7788888999999999.59 PP

                           Fer4_12  88 iwlytgytleelskkekeellkeidvlvdGk 118
                                        ++++g+ ++e  +k+ + +++++++ +d +
  gi|488600208|ref|YP_007906679.1| 193 SVATNGTLIDEDVAKKLKGIVDYVEISLDSP 223
                                       9************99**********999976 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   2.5   2.3e-09     7e-06       1      68 []     374     433 ..     374     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.3e-09
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefr.kskkfplielCrnCp 68 
                                       C a++ ++ I+++Gd++pC++       ++++Gn re s+ ++w+    ++++r +   ++ +  C++C+
  gi|488600208|ref|YP_007906679.1| 374 CGAGRLYCGIRPNGDITPCVFI------PIVVGNYRE-SFIKVWQENrVLEALRdR---DSTNYGCSKCE 433
                                       77888999***********555......7******98.******999566669942...33334588885 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 !   25.0   0.0   5.4e-09   1.6e-05       6     109 ..     125     217 ..     122     223 .. 0.67
   2 ?   -1.9   0.0       1.2   3.6e+03      63      87 ..     304     328 ..     292     345 .. 0.84
   3 ?   -7.9   5.0         6   1.8e+04       6      16 ..     430     442 ..     428     447 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 5.4e-09
                           Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                         Cnl C+ C+ ++ ++ +  +  ++ +l+++l   ++  +    ++++GGePL+    +++    ++ k+ +  ++
  gi|488600208|ref|YP_007906679.1| 125 KMCNLRCQHCYSNAGKMGHELTLLEKLELVNQL---DEAGV--VAISFSGGEPLMS---SDFWLTAEHAKRLG--FH 191
                                       67*********9885554444444444444455...44444..349********66...77776667666666..** PP

                           Fer4_14  83 iwletngtleielektpdlkekleals 109
                                       + + tngtl  + +++++lk +++ ++
  gi|488600208|ref|YP_007906679.1| 192 VSVATNGTLI-DEDVAKKLKGIVDYVE 217
                                       *******997.6565556655554444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                           Fer4_14  63 nkkellklvkrlkeeypekkiwlet 87 
                                       n++e+  l+k l +++p+k+i+l +
  gi|488600208|ref|YP_007906679.1| 304 NDTEIEWLLKFLYDSMPNKDIQLLS 328
                                       7888888999999999999999865 PP

  == domain 3  score: -7.9 bits;  conditional E-value: 6
                           Fer4_14   6 sgCnlsCk..gCd 16 
                                       s+C+  C   gC 
  gi|488600208|ref|YP_007906679.1| 430 SKCEYRCIcgGCR 442
                                       7899888655775 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   9.5e-07    0.0028      17     164 ..     142     285 ..     139     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.5e-07
                                       SS---HHHHHHHHHHHHHHT-SEE--..TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-S CS
                         HMGL-like  17 kaalsveeklaiakaLdeagvdeiEv..gfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagak 91 
                                       ++ l++ ekl+++++Ldeagv +i    g p +s d +   + +++ + + ++ +  ++ ++d+++  +      ++
  gi|488600208|ref|YP_007906679.1| 142 GHELTLLEKLELVNQLDEAGVVAISFsgGEPLMSSDFWLTAEHAKRLGFHVSVATNGTLIDEDVAKKLK----GIVD 214
                                       7899999******************9999*****99999999999999999999999999999999888....6667 PP

                                       EEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT-BTTTBS--HHHHHHHHHHHHHHT-SEEE CS
                         HMGL-like  92 rvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..velsledasrtdleflaevveaaeeaGatrin 164
                                        v++ +   +     k + ++  v+  +e a++++++  k    +  +++a++ +l ++ e+ve +ee+Ga+r+ 
  gi|488600208|ref|YP_007906679.1| 215 YVEISLDSPN----PKAHDSFRGVKGAFEGAIERIKNCIKAgiQTGIATTATKKNLSEIPELVELVEELGAYRLV 285
                                       7777666554....889999999*************999888556667899********************9875 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.6e-05      0.17       6      37 ..     131     162 ..     126     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                            HTH_22   6 ieevladlgkpverltkeekieivraLdekGi 37 
                                        ++++++ gk  ++lt  ek+e+v +Lde+G+
  gi|488600208|ref|YP_007906679.1| 131 CQHCYSNAGKMGHELTLLEKLELVNQLDEAGV 162
                                       68999**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2855.19
//
Query:       gi|488600209|ref|YP_007906680.1|  [L=254]
Description: diphthine synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-18   65.7   0.0    6.3e-18   65.5   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.092   12.2   0.0       0.15   11.4   0.0    1.4  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0     7e-22   6.3e-18       1     201 [.       1     201 [.       1     213 [. 0.76

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 7e-22
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvv....lgddsr..aleilldllaeeleleapmgkekepleea.yeeiae 70 
                                       +l+++G+G+ d+e++++++lr  +++d v    ++++     +++l +l+           ke+  l +   ee+++
  gi|488600209|ref|YP_007906680.1|   1 MLIFIGTGLWDAEDISLKGLRYARSSDEVylelYTSK-PniDTDSLSELIG----------KEVGLLSRSdLEENSR 66 
                                       79***************************55544444.3466666666664..........5556655554999999 PP

                      TP_methylase  71 alaealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpgla 147
                                        l+e++++  d+v+lv+GDP+v++t+ +l   ++a+++g+++ +i   s+l+a++  +g++++++g++ ++++p  +
  gi|488600209|ref|YP_007906680.1|  67 YLVEKAKER-DIVILVPGDPMVATTHTALR--VEAKKRGVKTVIIHSSSILSAVCGITGLHIYKFGKSATISYPYRE 140
                                       999999996.8******************7..77777***********************************55555 PP

                      TP_methylase 148 keeereleallan....gdtlvllkapr....klaelaelLkea.lyddttpvavveragted 201
                                       k +++ ++ + +n    ++tl++l +++    k+++++ lL +      ++  + ++rag e+
  gi|488600209|ref|YP_007906680.1| 141 KVSKTPVDVIESNrkinAHTLLFL-DLHpepmKIDKAISLLEQVgN-VSEYYGVGIARAGSEN 201
                                       556666666666666667888888.555445469999999987732.2233445556666665 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05      0.15     116     170 ..      69     124 ..      51     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                           UPRTase 116 Pkki.aertvlll..DpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                        +k  +++ v+l+  Dp++aT ++a  +    k+rgv++  I   s+l++ +g++ l+
  gi|488600209|ref|YP_007906680.1|  69 VEKAkERDIVILVpgDPMVATTHTALRV--EAKKRGVKTVIIHSSSILSAVCGITGLH 124
                                       445524555777688**********997..457889*****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1579.86
//
Query:       gi|488600210|ref|YP_007906681.1|  [L=354]
Description: small GTP-binding protein domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-33  115.0   0.2    3.2e-33  113.9   0.2    1.6  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
    6.1e-22   77.9   0.0    1.4e-21   76.7   0.0    1.6  1  MMR_HSR1       50S ribosome-binding GTPase
    4.7e-19   68.2   0.0    9.8e-19   67.2   0.0    1.6  1  TGS            TGS domain
    6.9e-15   54.9   0.3      3e-14   52.8   0.0    2.1  3  FeoB_N         Ferrous iron transport protein B
    1.9e-05   24.6   0.1     0.0069   16.3   0.0    2.6  2  RsgA_GTPase    RsgA GTPase
    2.2e-05   24.6   0.2      0.011   15.7   0.1    2.5  2  Dynamin_N      Dynamin family
    0.00011   21.6   0.1    0.00025   20.4   0.0    1.6  2  AIG1           AIG1 family
     0.0022   18.1   0.1      0.053   13.7   0.1    2.4  1  YchF-GTPase_C  Protein of unknown function (DUF933)
     0.0085   16.1   0.5      0.018   15.0   0.5    1.5  1  Sipho_Gp157    Siphovirus Gp157
  ------ inclusion threshold ------
      0.018   15.2   0.1        0.7   10.1   0.0    2.3  2  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.031   13.7   0.0      0.064   12.7   0.0    1.5  1  SRPRB          Signal recognition particle receptor beta subu
      0.064   12.8   0.2        4.1    6.9   0.0    3.0  3  GTP_EFTU       Elongation factor Tu GTP binding domain
       0.12   12.8   0.1       0.47   11.0   0.0    1.9  2  ABC_tran       ABC transporter
       0.16   12.4   0.2        0.4   11.0   0.1    1.6  1  AAA_16         AAA ATPase domain
       0.18   12.1   0.1       0.49   10.6   0.1    1.8  1  AAA_28         AAA domain
       0.21   11.2   0.5        6.4    6.3   0.1    2.7  3  cobW           CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.2   2.9e-36   3.2e-33       1     106 []     181     280 ..     181     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 2.9e-36
                      MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldela 77 
                                       +gG+kitstv+l+ +de+t+ ++l+ey+ihnaevliredvtvD++id+i  nrvYip+++v+NKiDl +  +l +  
  gi|488600210|ref|YP_007906681.1| 181 RGGLKITSTVPLS-IDEQTIYEVLREYRIHNAEVLIREDVTVDRFIDAILRNRVYIPAIVVVNKIDLYNPGNLPD-- 254
                                       69*********98.*******************************************************999975.. PP

                      MMR_HSR1_Xtn  78 repnsvviSaekelnldeLkekiweeLnL 106
                                          +++++Saek++nld L + i+e+L+L
  gi|488600210|ref|YP_007906681.1| 255 ---SVIPVSAEKKINLDLLAKSIYEKLDL 280
                                       ...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 !   76.7   0.0   1.2e-24   1.4e-21       2     109 ..      63     173 ..      62     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 1.2e-24
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.ad 77 
                                       v++vG p vGKS+L+naltg+k++++++ +tT++++ g ++++g +i+++D+pG++egas+++g g+++ +  + +d
  gi|488600210|ref|YP_007906681.1|  63 VVLVGFPSVGKSSLLNALTGAKSEIGAYDFTTLKPVPGMLEYNGAKIQIIDLPGIVEGASKGRGKGREIISAVRnSD 139
                                       89****************************************************99**********9999977669* PP

                                       EEEEEEETT.TTCSHHHHHHHHHHHHH.TTSEEE CS
                          MMR_HSR1  78 lillvvdas.eeklkpldeeleellee.akkpli 109
                                       l++++ d    e++k +++el +   + ++kp  
  gi|488600210|ref|YP_007906681.1| 140 LVVIIADPFnLESIKIIQRELYNGGIRlNQKPPE 173
                                       ******9556555777777776665445555554 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   8.8e-22   9.8e-19       1      59 [.     281     353 ..     281     354 .] 0.98

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 8.8e-22
                                       EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       ir+++ P+G + d      ++rg tv D+++k+h+++ ++f+yA+V G       qrvg+dhvLedgd+++I 
  gi|488600210|ref|YP_007906681.1| 281 IRIFLkPPGGKADlnepmiIKRGMTVGDVCKKLHKDMYRNFRYARVIGksakfkeQRVGIDHVLEDGDILTIY 353
                                       89*********************************************************************96 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 !   52.8   0.0   2.7e-17     3e-14       2      93 ..      62     152 ..      61     167 .. 0.89
   2 ?   -1.9   0.0       1.9   2.1e+03     104     117 ..     233     246 ..     188     252 .. 0.62
   3 ?   -1.7   0.0       1.6   1.8e+03     137     155 ..     255     273 ..     243     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.7e-17
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CT CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.ee 77 
                                       tv+lvG p vGk++l+naltgak+++g +  +t +   g l+++g +++i+DlPGi  ++  s+     r+++   +
  gi|488600210|ref|YP_007906681.1|  62 TVVLVGFPSVGKSSLLNALTGAKSEIGAYDFTTLKPVPGMLEYNGAKIQIIDLPGI--VEGASKGRGKGREIISaVR 136
                                       799****************************************************9..5788888888999998357 PP

                                       SSSEEEEEEEGGGHHH CS
                            FeoB_N  78 epdvvvnvvdatnler 93 
                                       + d+vv ++d  nle 
  gi|488600210|ref|YP_007906681.1| 137 NSDLVVIIADPFNLES 152
                                       7899******999986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                                       TTSSEEEEEETHHH CS
                            FeoB_N 104 lgvpvvlalnmide 117
                                       + +p ++++n+id 
  gi|488600210|ref|YP_007906681.1| 233 VYIPAIVVVNKIDL 246
                                       45778888888886 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.6
                                       -EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 137 pvvktsakkkegieellka 155
                                        v+++sa+kk +++ l k+
  gi|488600210|ref|YP_007906681.1| 255 SVIPVSAEKKINLDLLAKS 273
                                       6899999999999988776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.2e-06    0.0069      80     123 ..      42      84 ..      13      97 .. 0.71
   2 ?    5.8   0.0     0.011        12      34      63 ..     220     251 ..     213     287 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                                       EE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  80 llvsaktkegleelkellkdktsvlvGqSGvGKStLinallpel 123
                                        + +akt++   ++k+   d t+vlvG   vGKS+L+nal++ +
  gi|488600210|ref|YP_007906681.1|  42 EKQKAKTGRPSFSIKKD-GDATVVLVGFPSVGKSSLLNALTGAK 84 
                                       45555544444444444.34799*****************9963 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHTT-..EEEEEEE-GGG--HHH CS
                       RsgA_GTPase  34 lldrfLvlaeekgi..epvivlnKiDlleeee 63 
                                       ++drf+ ++ ++++  + ++v+nKiDl++  +
  gi|488600210|ref|YP_007906681.1| 220 TVDRFIDAILRNRVyiPAIVVVNKIDLYNPGN 251
                                       688998777777654499*********99876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     1e-05     0.011       1      22 [.      63      84 ..      63      98 .. 0.86
   2 !    6.3   0.0    0.0079       8.9     100     134 ..     106     143 ..     100     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                                      EEEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                      +++vG  S GKSS+lnaL+g++
  gi|488600210|ref|YP_007906681.1| 63 VVLVGFPSVGKSSLLNALTGAK 84
                                      799*****************87 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0079
                                       S-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEE CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdq...elvkeyikkadiila 134
                                         ++ ++DlPG+ + + +     + + ++++++d+++ 
  gi|488600210|ref|YP_007906681.1| 106 GAKIQIIDLPGIVEGASKGRgkgREIISAVRNSDLVVI 143
                                       57899********9988877777666666666666665 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.3   4.8e+03     180     205 ..       6      31 ..       3      38 .. 0.72
   2 !   20.4   0.0   2.3e-07   0.00025       2      78 ..      62     136 ..      61     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.3
                                       HHHHHHHHTTTT--B-HHHHHHHHCC CS
                              AIG1 180 lveaivkenggkpytnelyekikeea 205
                                       +++++++e ++ py + + ++i + +
  gi|488600210|ref|YP_007906681.1|   6 QIRQLEEEIKNTPYNKATEHHIGRLK 31 
                                       57788888888888888887776655 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.3e-07
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS--.-SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsv.tkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcl 77 
                                       t+vlvG   +GkS+  N++ g k   s++ a    t k+     + +g ki++iD Pg+++  ++     +ei+  +
  gi|488600210|ref|YP_007906681.1|  62 TVVLVGFPSVGKSSLLNALTGAK---SEIGAYDFtTLKPVPGMLEYNGAKIQIIDLPGIVEGASKGRGKGREIISAV 135
                                       89*******************97...666665550556667777*******************99999999999765 PP

                                       H CS
                              AIG1  78 l 78 
                                        
  gi|488600210|ref|YP_007906681.1| 136 R 136
                                       4 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 !   13.7   0.1   4.7e-05     0.053      17      47 ..     300     330 ..     295     354 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
                     YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraevikye 47 
                                       ik+g+t+ + +++ H+D+ ++F  a+vi  +
  gi|488600210|ref|YP_007906681.1| 300 IKRGMTVGDVCKKLHKDMYRNFRYARVIGKS 330
                                       89*************************9643 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.5   1.6e-05     0.018      53     110 ..       3      59 ..       1      67 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                       Sipho_Gp157  53 leaeaeaikeeekrLaerkkslenkaenLKeyleeameaaglkkiktplftlsirksp 110
                                       le ++ +++ee+k+ +  +k++e+++ +LK+ l++  e+a+++k kt + ++si+k  
  gi|488600210|ref|YP_007906681.1|   3 LEEQIRQLEEEIKN-TPYNKATEHHIGRLKAKLARLREEAEKQKAKTGRPSFSIKKDG 59 
                                       77788888888887.66799***********************************983 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00062       0.7       2      23 ..      63      84 ..      62      97 .. 0.88
   2 ?    2.8   0.0      0.12   1.3e+02      91     120 .]     217     246 ..     194     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00062
                                      EEEESSTTSSHHHHHHCHCT-C CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedk 23
                                      vvlvG  +vGK+sll+ ++  k
  gi|488600210|ref|YP_007906681.1| 63 VVLVGFPSVGKSSLLNALTGAK 84
                                      89**************998655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                                       HHHCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                               Roc  91 ssenlkeWlkelkkvagkspvilvgnkiDl 120
                                       ++ ++++ ++ + +++  +p+i+v+nkiDl
  gi|488600210|ref|YP_007906681.1| 217 EDVTVDRFIDAILRNRVYIPAIVVVNKIDL 246
                                       4556778888888889999*********95 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.7e-05     0.064       4      60 ..      61     118 ..      58     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                                       -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-G CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhe 60 
                                        +v+lvG    GK sl++ Lt  + +         + +  + + +g k+++iD+PG +
  gi|488600210|ref|YP_007906681.1|  61 ATVVLVGFPSVGKSSLLNALTGAKSEIGAYDFtTLKPVPGMLEYNGAKIQIIDLPGIV 118
                                       589******************886555444442334444445669***********65 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 ?   -0.9   0.0      0.87   9.8e+02       7      30 ..      64      87 ..      61      94 .. 0.77
   2 ?    2.1   0.0      0.11   1.2e+02      66      82 ..     103     119 ..      86     147 .. 0.75
   3 ?    6.9   0.0    0.0036       4.1     120     150 ..     232     278 ..     218     345 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.87
                                      EEEESTTSSHHHHHHHHHHHTTSS CS
                          GTP_EFTU  7 giighvDhGKtTLtdrLlyktgai 30
                                      +++g    GK++L+ +L+ ++++i
  gi|488600210|ref|YP_007906681.1| 64 VLVGFPSVGKSSLLNALTGAKSEI 87
                                      56666778*********9776665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                                       TCSSEEEEEEEESSSGG CS
                          GTP_EFTU  66 etkkylinliDtPGHvd 82 
                                       e++  +i++iD PG v+
  gi|488600210|ref|YP_007906681.1| 103 EYNGAKIQIIDLPGIVE 119
                                       58999*********775 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0036
                                       HTTTEEEEEEESCGST................HHHHHHHHHHHHHHH CS
                          GTP_EFTU 120 kegvpiivfiNKmDrl................kaelkeiveevkqkl 150
                                       ++ +p iv++NK+D                  k +l+ +++ +++kl
  gi|488600210|ref|YP_007906681.1| 232 RVYIPAIVVVNKIDLYnpgnlpdsvipvsaekKINLDLLAKSIYEKL 278
                                       455789********997666665555555554445555555555555 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   0.00042      0.47      11      36 ..      60      85 ..      50     117 .. 0.83
   2 ?   -1.6   0.0       3.3   3.7e+03      32      79 ..     157     202 ..     150     233 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                                      TSEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllk 36
                                      + +v++vG    GKS+Ll++l+g  +
  gi|488600210|ref|YP_007906681.1| 60 DATVVLVGFPSVGKSSLLNALTGAKS 85
                                      5789******************9865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                                       TTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  32 agllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                        ++l   +G i+l++k+ +   ++  r  +++ +  p   +e t++e 
  gi|488600210|ref|YP_007906681.1| 157 QREL--YNGGIRLNQKPPEVYVKKLERGGLKITSTVPLSIDEQTIYEV 202
                                       4444..467777777777766666666666666666666666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00036       0.4      25      45 ..      61      81 ..      44      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                            AAA_16 25 elvllsGesGvGKsslvrell 45
                                        v+l+G + vGKssl+++l 
  gi|488600210|ref|YP_007906681.1| 61 ATVVLVGFPSVGKSSLLNALT 81
                                      6899*************9986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00044      0.49       2      21 ..      63      82 ..      62      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      +v++G +s GK++ll+aL+ 
  gi|488600210|ref|YP_007906681.1| 63 VVLVGFPSVGKSSLLNALTG 82
                                      8*****************84 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 ?    6.3   0.1    0.0058       6.4       2      22 ..      62      82 ..      61      89 .. 0.84
   2 ?   -2.6   0.0       3.1   3.5e+03     115     147 ..     108     143 ..     105     147 .. 0.76
   3 ?    2.1   0.0      0.12   1.3e+02     133     155 ..     227     249 ..     179     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0058
                                      EEEEEESTTCCHHHHHHHHHC CS
                              cobW  2 vtvltGflGsGKTtLlnhlle 22
                                      ++vl+Gf+  GK++Lln+l+ 
  gi|488600210|ref|YP_007906681.1| 62 TVVLVGFPSVGKSSLLNALTG 82
                                      589**************9983 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                                       EEEEEETTTH....CCHCCHHHHHHHHHHTSSEEEE CS
                              cobW 115 vvavvDaknl...eaeeekieekaedqlaaadllvl 147
                                       ++ ++D   +    ++++ + +++ + +  +dl+v+
  gi|488600210|ref|YP_007906681.1| 108 KIQIIDLPGIvegASKGRGKGREIISAVRNSDLVVI 143
                                       567777766666667788888888899999999886 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.12
                                       HHHHHHHHTSSEEEEE-HHHHCH CS
                              cobW 133 ekaedqlaaadllvlnKtDllde 155
                                         +++ +    ++v+nK+Dl + 
  gi|488600210|ref|YP_007906681.1| 227 AILRNRVYIPAIVVVNKIDLYNP 249
                                       5566667777899******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2234.75
//
Query:       gi|488600211|ref|YP_007906682.1|  [L=86]
Description: small redox-active disulfide protein 1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   51.4   0.4    1.1e-13   51.1   0.4    1.1  1  Thioredoxin_3  Thioredoxin domain
    5.1e-09   36.2   0.1    7.5e-09   35.7   0.1    1.2  1  Glutaredoxin   Glutaredoxin
    1.9e-07   31.1   0.2    0.00034   20.5   0.0    2.0  2  DSBA           DSBA-like thioredoxin domain
    2.8e-06   27.4   0.1      3e-06   27.4   0.1    1.1  1  DUF1525        Protein of unknown function (DUF1525)
    2.5e-05   24.2   0.0    2.7e-05   24.1   0.0    1.1  1  Thioredoxin    Thioredoxin
    8.2e-05   23.0   0.1    0.00016   22.1   0.1    1.5  1  Thioredoxin_2  Thioredoxin-like domain
    0.00012   22.3   0.1      0.055   13.6   0.0    2.0  2  Thioredoxin_4  Thioredoxin
    0.00037   20.4   0.0    0.00041   20.2   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0027   17.8   0.0     0.0044   17.1   0.0    1.2  1  DUF1223        Protein of unknown function (DUF1223)
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.016   14.8   0.0    1.0  1  FAM83          FAM83 A-H
      0.024   15.0   0.0      0.024   15.0   0.0    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)


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 !   51.1   0.4   6.5e-17   1.1e-13       2      76 .]       3      81 ..       2      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 6.5e-17
                                      EEEEE.SSSSTTCHHHHHHHHHHCHCCT.CEC...EEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                     Thioredoxin_3  2 eikvl.gpgCakCpklekavkeaaaekg.ika...evekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                      +ik l +p+C++Cp ++ +v++ +++++ + a    v   + ++e  k+g++ vPal+i+++ v+ G vps  e+++++
  gi|488600211|ref|YP_007906682.1|  3 KIKLLtSPTCPYCPMAADVVRKFVEKNKdVVAieiPVNTDEGLKEAVKFGIRGVPALIINDQAVILG-VPSMGELQRVV 80
                                      677744889****************995465555466677889999*********************.*******9988 PP

                                      H CS
                     Thioredoxin_3 76 e 76
                                      e
  gi|488600211|ref|YP_007906682.1| 81 E 81
                                      5 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   4.6e-12   7.5e-09       1      59 [.       4      65 ..       4      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4.6e-12
                                      EEEEESTSSHHHHHHHHHH.....HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                      Glutaredoxin  1 vvlftkptCpyCkkakrlL.....kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59
                                      + l t+ptCpyC++a ++      k++ v   ei v+ de ++e++  + g+r vP + i+++ 
  gi|488600211|ref|YP_007906682.1|  4 IKLLTSPTCPYCPMAADVVrkfveKNKDVVAIEIPVNTDEGLKEAV--KFGIRGVPALIINDQA 65
                                      56889**************6655444448899*******9999999..55***********986 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00052      0.84       8      32 ..      10      35 ..       3      39 .. 0.82
   2 !   20.5   0.0   2.1e-07   0.00034     155     190 ..      43      78 ..      36      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00052
                                      TTBHHHHHHHHHHHHHHHHCCT.EEE CS
                              DSBA  8 vlCPyCylgkerleklaarspd.vkv 32
                                        CPyC +++++++k +++++d v +
  gi|488600211|ref|YP_007906682.1| 10 PTCPYCPMAADVVRKFVEKNKDvVAI 35
                                      57*****************9885555 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHH CS
                              DSBA 155 entaaaqslgvtGvPtvvvdgkrmvfGadrldtlad 190
                                       e  ++a++ g++GvP+ +++++ ++ G++++  l++
  gi|488600211|ref|YP_007906682.1|  43 EGLKEAVKFGIRGVPALIINDQAVILGVPSMGELQR 78 
                                       56689**************************99987 PP

>> DUF1525  Protein of unknown function (DUF1525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.8e-09     3e-06      49     112 ..      21      84 ..      13      86 .] 0.75

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.8e-09
                           DUF1525  49 lvrqrlnspdwaaleeqie.qayqgvadawqlgikkiPAVvvdrraVvYGeadvaaAlelyeker 112
                                       +vr+++++ +   +  +i  +  +g+ +a++ gi+ +PA +++++aV+ G++++ +  +++e+ r
  gi|488600211|ref|YP_007906682.1|  21 VVRKFVEKNK-DVVAIEIPvNTDEGLKEAVKFGIRGVPALIINDQAVILGVPSMGELQRVVEQMR 84 
                                       5555555555.4444444315679****************************9988777777665 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.7e-08   2.7e-05      26      80 ..       8      63 ..       4      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.7e-08
                                      E-TTSHHHHCHHHHHHHHHHHCTTTSEE.EEEETTTSHHHHHHTT-SSSSEEEEEE CS
                       Thioredoxin 26 yApwCghCkalaPeleklaeelkdkvkl.akvdvdenedlakkyevegiPtlklfk 80
                                      ++p C+ C + a ++ k+ e+ kd v + + v++de  + a k++++g+P+l++  
  gi|488600211|ref|YP_007906682.1|  8 TSPTCPYCPMAADVVRKFVEKNKDVVAIeIPVNTDEGLKEAVKFGIRGVPALIIND 63
                                      5899*******************855553579********************7654 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   9.6e-08   0.00016      11      98 ..       6      69 ..       2      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.6e-08
                     Thioredoxin_2 11 vftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfldg 89
                                      + t+p+CpyC    +++++            ++++ + +a++i  ++++           + a k+g+rg+P++++ d+
  gi|488600211|ref|YP_007906682.1|  6 LLTSPTCPYCPMAADVVRKF-----------VEKNKDVVAIEIPVNTDEG---------LKEAVKFGIRGVPALIINDQ 64
                                      5799********99999999...........7777788888888888886.........778****************9 PP

                     Thioredoxin_2 90 keivarlpG 98
                                           ++ G
  gi|488600211|ref|YP_007906682.1| 65 A----VILG 69
                                      9....4444 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0028       4.6      17      42 ..       4      29 ..       1      44 [. 0.79
   2 !   13.6   0.0   3.4e-05     0.055     130     165 ..      45      81 ..      39      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0028
                                      EEEEE-TT-HHHHHHHHHHHHHHHHH CS
                     Thioredoxin_4 17 vieyedlrCphCakfeeeveklleey 42
                                      + + ++ +Cp+C   +  v k++e+ 
  gi|488600211|ref|YP_007906682.1|  4 IKLLTSPTCPYCPMAADVVRKFVEKN 29
                                      666789*******9999999999985 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHT--SS-EEEETTEE.E-TT--HHHHHHHHT CS
                     Thioredoxin_4 130 skeakkagiestPtfiingek.veepqtyeelkalid 165
                                       +kea k gi ++P +iin++  + + +++ el+++++
  gi|488600211|ref|YP_007906682.1|  45 LKEAVKFGIRGVPALIINDQAvILGVPSMGELQRVVE 81 
                                       68999*************9996678999999999987 PP

>> TraF  F plasmid transfer operon 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   0.00041     136     202 ..       7      65 ..       4      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.5e-07
                              TraF 136 FyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpk 202
                                       + +++cpyc ++a+++++f +k + +v+a+ +  + +++l++       a ++g++ +Pal++ d+ 
  gi|488600211|ref|YP_007906682.1|   7 LTSPTCPYCPMAADVVRKFVEKNK-DVVAIEIPVNTDEGLKE-------AVKFGIRGVPALIINDQA 65 
                                       56899***************9976.89999999999988989.......89**********997765 PP

>> DUF1223  Protein of unknown function (DUF1223)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.7e-06    0.0044       3      38 ..       5      40 ..       4      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.7e-06
                                      EEEE-TT-TT-HHHHHHHHHH.HHHTSSEEEEEE-S CS
                           DUF1223  3 ELFtSqGCssCPpAdallselaaedkdvvaLalhVd 38
                                       L tS  C  CP A  +++++ +++kdvva+ ++V+
  gi|488600211|ref|YP_007906682.1|  5 KLLTSPTCPYCPMAADVVRKFVEKNKDVVAIEIPVN 40
                                      699*****************************9996 PP

>> FAM83  FAM83 A-H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   9.8e-06     0.016     112     178 ..       4      68 ..       1      84 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.8e-06
                             FAM83 112 vtvytqppkekaphikevvrkliqkaqkviavvmdvftDvdilkdlleaaskrkvpvyilLdeknlk 178
                                       ++++t p     p   +vvrk+++k + v+a+ + v tD   lk+ ++ +  r+vp  i+ d++ + 
  gi|488600211|ref|YP_007906682.1|   4 IKLLTSPTCPYCPMAADVVRKFVEKNKDVVAIEIPVNTDE-GLKEAVKFGI-RGVPALIINDQAVIL 68 
                                       6677777778888899***********************8.5788889988.669999999987665 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.5e-05     0.024       1      47 [.       3      52 ..       3      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                      -EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETT..T-CCCHC..CCC CS
                            DUF836  1 kltLyskpgChlCeqakekLkelkleegleleviDIa..kdeelea..kYg 47
                                      k+ L++ p C+ C  a ++++++ ++++ +++ i I   +de l++  k+g
  gi|488600211|ref|YP_007906682.1|  3 KIKLLTSPTCPYCPMAADVVRKFVEKNK-DVVAIEIPvnTDEGLKEavKFG 52
                                      6889*****************9766666.8999999854555577645555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 646.04
//
Query:       gi|488600212|ref|YP_007906683.1|  [L=108]
Description: thioredoxin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-28   99.2   0.1    1.3e-28   99.0   0.1    1.0  1  Thioredoxin    Thioredoxin
    1.6e-09   38.2   0.1    3.9e-09   36.9   0.1    1.6  1  Thioredoxin_2  Thioredoxin-like domain
    1.8e-07   31.4   0.0    1.5e-06   28.5   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    2.3e-05   24.2   0.1    4.7e-05   23.1   0.1    1.5  2  Redoxin        Redoxin
    7.1e-05   22.8   0.0      9e-05   22.5   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
    0.00017   21.3   0.0     0.0002   21.1   0.0    1.1  1  Thioredoxin_9  Thioredoxin
    0.00041   20.3   0.1    0.00098   19.0   0.1    1.6  2  AhpC-TSA       AhpC/TSA family
    0.00074   18.5   0.0    0.00084   18.4   0.0    1.1  1  Phosducin      Phosducin
    0.00081   19.2   0.0    0.00091   19.0   0.0    1.1  1  DIM1           Mitosis protein DIM1
    0.00093   18.6   0.0    0.00098   18.6   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
      0.003   17.5   0.0     0.0062   16.5   0.0    1.5  2  HyaE           Hydrogenase-1 expression protein HyaE
     0.0065   16.3   0.0     0.0082   16.0   0.0    1.2  1  TraF           F plasmid transfer operon protein
     0.0082   16.1   0.0      0.009   15.9   0.0    1.2  1  Thioredoxin_6  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.013   15.7   0.1       0.02   15.0   0.1    1.4  1  Thioredoxin_7  Thioredoxin-like


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 !   99.0   0.1     1e-31   1.3e-28       3     102 ..       2     100 ..       1     101 [. 0.96

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 1e-31
                                       EESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEE CS
                       Thioredoxin   3 lvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklf 79 
                                       ++l++enF +e++k kklv+v+F+A+wC +C++l+P lek+ +e+ +kv +akv++den+ la+++++ +iPt+++f
  gi|488600212|ref|YP_007906683.1|   2 KNLNEENFYDEIKK-KKLVVVDFWAEWCMPCRMLTPILEKVEKEYDGKVEFAKVNTDENPALASRFGIFSIPTVLMF 77 
                                       6799**********.************************************************************** PP

                                       ETTEEEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  80 kngkevkkyegarekeklaaflk 102
                                        +g+ v+ ++ga ++ ++++ ++
  gi|488600212|ref|YP_007906683.1|  78 YDGEIVNAFVGALPEGAVKHEIE 100
                                       *************9988888776 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1     3e-12   3.9e-09       3     103 ..      14      93 ..      12      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3e-12
                     Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvr 79 
                                       +++k v+v+f++++C  C+ l   l+++   ++      ++ +   +++++ ++++++           la ++g++
  gi|488600212|ref|YP_007906683.1|  14 KKKKLVVVDFWAEWCMPCRMLTPILEKV---EKE-----YDGK--VEFAKVNTDENPA-----------LASRFGIF 69 
                                       789******************9999998...556.....6666..8899999999997...........******** PP

                     Thioredoxin_2  80 gtPtiv.fldgkeivarlpGyvpae 103
                                       + Pt++ f+dg+ iv+  +G++p+ 
  gi|488600212|ref|YP_007906683.1|  70 SIPTVLmFYDGE-IVNAFVGALPEG 93 
                                       ****555*****.********9985 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.1e-09   1.5e-06       2      46 ..      17      59 ..      15      63 .. 0.95
   2 ?    3.4   0.0     0.078     1e+02      66      87 ..      54      75 ..      52      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-09
                                      SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS- CS
                     Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkk 46
                                      k+v++ f+a+wc pc+  tp l ++++++    kve+  v+ d++
  gi|488600212|ref|YP_007906683.1| 17 KLVVVDFWAEWCMPCRMLTPILEKVEKEYD--GKVEFAKVNTDEN 59
                                      89***************************9..9********9986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.078
                                      E-TT-HHHHTT-S--TT-SEEE CS
                     Thioredoxin_8 66 fddkkrnklkkkynvkaiPtlv 87
                                      ++ +++ +l++++++ +iPt++
  gi|488600212|ref|YP_007906683.1| 54 VNTDENPALASRFGIFSIPTVL 75
                                      56677889************86 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   3.7e-08   4.7e-05      26      93 ..      13      80 ..       2      90 .. 0.78
   2 ?    4.0   0.0     0.029        37      89     145 ..      54     101 ..      52     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.7e-08
                                      HTTSE.EEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.HHHHHHH.TT-TSEEEE-T CS
                           Redoxin 26 fkgkk.vvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.vkefwgk.eglkfpvlsDg 93
                                       k+kk vvv f++  +c +C+  +p lek++++  ++ v++  v++d+++  +++f g    +++++++Dg
  gi|488600212|ref|YP_007906683.1| 13 IKKKKlVVVDFWAE-WCMPCRMLTPILEKVEKE-YDGKVEFAKVNTDENPAlASRF-GIfSIPTVLMFYDG 80
                                      56677477789999.*****************9.7888***********9944444.44255566667775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.029
                                       EEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.STTSHHH CS
                           Redoxin  89 vlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet.eesnaea 145
                                       v +D++ a+++ +G+           +p++ ++  dg +v  +v++ pe+  ++++e+
  gi|488600212|ref|YP_007906683.1|  54 VNTDENPALASRFGIF---------SIPTVLMF-YDGEIVNAFVGALPEGaVKHEIEK 101
                                       5689999999999933.........78887777.5899******99997665555555 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     7e-08     9e-05      10      69 ..      28      94 ..      12     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7e-08
                                      STTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEE..ECTTCEE..EESS---CC CS
                     Thioredoxin_3 10 CakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPal..vidgkvv..vsGkvpsee 69
                                      C  C+ l+ +++++ +e + k+e+ kv   +++ + +++g+ s+P++  ++dg++v  ++G++p+++
  gi|488600212|ref|YP_007906683.1| 28 CMPCRMLTPILEKVEKEYDGKVEFAKVntDENPALaSRFGIFSIPTVlmFYDGEIVnaFVGALPEGA 94
                                      999***************999999999845667779**********9999***98655899999864 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.6e-07    0.0002      40     120 ..      15      93 ..       3     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                                       -S-EEEEEE--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEEE CS
                     Thioredoxin_9  40 ekklkilvltedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvwg 115
                                       +kkl ++ + ++wC  +++  P+l+k+  e+  ++e+  +  den+ l  ++   g  +iPt++++ ++  + +  g
  gi|488600212|ref|YP_007906683.1|  15 KKKLVVVDFWAEWCMPCRMLTPILEKVEkEYDGKVEFAKVNTDENPALASRF---GIFSIPTVLMFYDGEIVNAFVG 88 
                                       45556666889****************9567789******************...88*****998766544444466 PP

                                       SS-HH CS
                     Thioredoxin_9 116 erPae 120
                                        +P+ 
  gi|488600212|ref|YP_007906683.1|  89 ALPEG 93 
                                       66665 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   7.6e-07   0.00098      22      72 ..      12      61 ..       2      66 .. 0.84
   2 ?   -2.1   0.0       2.7   3.5e+03      27      35 ..      72      80 ..      68      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.6e-07
                                      HH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHH CS
                          AhpC-TSA 22 dy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspes 72
                                      ++ k+k vv+ f+++ wc +C+   p l+k+ +e++  +ve   v++d+  +
  gi|488600212|ref|YP_007906683.1| 12 EIkKKKLVVVDFWAE-WCMPCRMLTPILEKVEKEYD-GKVEFAKVNTDENPA 61
                                      554669*********.******************99.679999999987765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                                      EEEEEEEST CS
                          AhpC-TSA 27 pvvlffypk 35
                                      p+vl+fy +
  gi|488600212|ref|YP_007906683.1| 72 PTVLMFYDG 80
                                      689999986 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.6e-07   0.00084     134     216 ..       7      88 ..       3     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.6e-07
                                       HHHHHHHHSS-TT-EEEEEEE-TTSTTHHHHHHHHHHHHHH-T.TSEEEEEEHHHH--.TTSS-TTT-SEEEEEETT CS
                         Phosducin 134 eqfldtidkeqkitlivvhiyedgvkgtealnssliclaaeyp.tvkfckvkasviga.sdrfsrdvlpallvykag 208
                                       e+f d i+   k  l+vv  + +    +  l   l  +  ey   v f kv++    a ++rf    +p++l++  g
  gi|488600212|ref|YP_007906683.1|   7 ENFYDEIK---KKKLVVVDFWAEWCMPCRMLTPILEKVEKEYDgKVEFAKVNTDENPAlASRFGIFSIPTVLMFYDG 80 
                                       56666665...556999*************************648******998665549***************** PP

                                       EEEEEETT CS
                         Phosducin 209 ellsnfvr 216
                                       e+++ fv 
  gi|488600212|ref|YP_007906683.1|  81 EIVNAFVG 88 
                                       ******95 PP

>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.1e-07   0.00091      18      86 ..      14      82 ..       5     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.1e-07
                                      -SSSEEEEEEE-TT-HHHHHHHHHHHHHHHHTTTTEEEEEEETTT--TTSCCCTT-SSSEEEEEETTEE CS
                              DIM1 18 eeerlvviRFGrdedaeClklDelLakiaeklknfaviylvdidevpdfnkmyeledpvtilffyrnkh 86
                                      ++++lvv+ F  ++   C  l  +L+k+ ++    ++++ v++de p + + + + +  t+l+fy +  
  gi|488600212|ref|YP_007906683.1| 14 KKKKLVVVDFWAEWCMPCRMLTPILEKVEKEYDGKVEFAKVNTDENPALASRFGIFSIPTVLMFYDGEI 82
                                      579*****************************************************8888888888765 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 !   18.6   0.0   7.6e-07   0.00098      46     103 ..      28      78 ..      14     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.6e-07
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfp 103
                                       C +Cr + p +e+v k ++ +       + Fakv+ de++ + +++g+ s+P +l+f 
  gi|488600212|ref|YP_007906683.1|  28 CMPCRMLTPILEKVEKEYDGK-------VEFAKVNTDENPALASRFGIFSIPTVLMFY 78 
                                       999999999999999988877.......88*************************996 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.9e-06    0.0062      50      98 ..      38      85 ..      33      92 .. 0.84
   2 ?    2.1   0.0      0.14   1.9e+02      51      76 ..      80     104 ..      80     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.9e-06
                                      HHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEE CS
                              HyaE 50 lpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgv 98
                                      l  + k++    + a v+ ++++ ala+rfg++  P++l++ dge++ +
  gi|488600212|ref|YP_007906683.1| 38 LEKVEKEYDGKVEFAKVN-TDENPALASRFGIFSIPTVLMFYDGEIVNA 85
                                      566778888888888888.88899********************99876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                                       HHHHCT-TTS-EEEEEETHHHHHHHH CS
                              HyaE  51 pEllkaFpnalraavvadreqeeala 76 
                                       +E+++aF  al   +v+ +e e+al+
  gi|488600212|ref|YP_007906683.1|  80 GEIVNAFVGALPEGAVK-HEIEKALK 104
                                       599**************.99999987 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.4e-06    0.0082     131     201 ..      18      79 ..       2      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.4e-06
                              TraF 131 ygLlfFyrgkcpyceaqapilqafadkyglevra..VsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdp 201
                                          + F ++ c  c+++ pil++++++y  +v +  V++d++p   l++         r+g+ ++P+++++  
  gi|488600212|ref|YP_007906683.1|  18 LVVVDFWAEWCMPCRMLTPILEKVEKEYDGKVEFakVNTDENPA--LAS---------RFGIFSIPTVLMFYD 79 
                                       5666688999******************7666651166666666..999.........**********99875 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     7e-06     0.009      82     157 ..       4      76 ..       1      97 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7e-06
                                       -SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEE CS
                     Thioredoxin_6  82 ltpenaeelfeeglppllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivi 157
                                       l++en+ + ++++ +++++ f  +     + l  ++ekv+ke+ +k+ fa +++++++ + +++g+   ++P++ +
  gi|488600212|ref|YP_007906683.1|   4 LNEENFYDEIKKK-KLVVVDFWAEWCMPCRMLTPILEKVEKEYDGKVEFAKVNTDENPALASRFGIF--SIPTVLM 76 
                                       5677777766666.4477777776677777788899****************************997..7887776 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.6e-05      0.02      15      81 ..      14      77 ..       2      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                      HHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                     Thioredoxin_7 15 ergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafl 81
                                      +++k v v+f a+wc +C+ l   +++    k+ +++k+ + +v+ +e+ a   ++    +P+v+++
  gi|488600212|ref|YP_007906683.1| 14 KKKKLVVVDFWAEWCMPCRMLTPILEKV--EKE-YDGKVEFAKVNTDENPALASRFGIFSIPTVLMF 77
                                      68899999***********998777655..344.999999999999998885534433558888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 699.76
//
Query:       gi|488600213|ref|YP_007906684.1|  [L=127]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   58.1   0.2    8.4e-16   57.6   0.2    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0086   16.0   0.1      0.017   15.1   0.1    1.6  1  HTH_36         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.025   15.0   0.0    1.5  1  FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2


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 !   57.6   0.2   1.4e-19   8.4e-16       2      68 .]      18      91 ..      17      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.4e-19
                                      H.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE--HH CS
                              TrmB  2 q.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravdpe 68
                                      +  +G++e ++ v+++L+kl  a++d++++ lg+ +++vY++L++L+ +G+V+r k++      +++Y++vd+e
  gi|488600213|ref|YP_007906684.1| 18 EcLYGMNEADIIVFKTLVKLRGAKIDTLSKTLGRRENSVYKSLQKLMLAGIVTRDKKTindggyYYIYKPVDVE 91
                                      5569***********************************************************999*****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 !   15.1   0.1   2.9e-06     0.017       6      55 .]      26      69 ..      21      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-06
                            HTH_36  6 saklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                       +++++ +l ++     g  +  +tl+k lg  +n+v++ +++L+ +G++
  gi|488600213|ref|YP_007906684.1| 26 ADIIVFKTLVKLR----G--AKIDTLSKTLGRRENSVYKSLQKLMLAGIV 69
                                      5566666666666....2..457************************985 PP

>> FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   4.2e-06     0.025      26      62 ..      88     124 ..      83     127 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.2e-06
                     FAA_hydro_N_2  26 vdaseiaptlqaaLdnWdevepaLeelyeaLnagtak 62 
                                       vd++e+a+++ ++Ld+W +  +++ ++  aLn+++++
  gi|488600213|ref|YP_007906684.1|  88 VDVEELAKEMIKLLDDWYRRMREVIDEFVALNRSAKE 124
                                       89*****************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 767.41
//
Query:       gi|488600214|ref|YP_007906685.1|  [L=56]
Description: hypothetical protein Asulf_00674 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-12   44.6  14.6    1.3e-07   31.1   3.0    2.1  2  Fer4      4Fe-4S binding domain
    1.7e-11   43.7  13.5    1.4e-08   34.5   2.9    2.1  2  Fer4_6    4Fe-4S binding domain
    1.9e-09   38.0  13.0    5.9e-09   36.4  13.1    1.6  1  Fer4_7    4Fe-4S dicluster domain
    4.6e-09   36.3  11.1    5.8e-09   36.0  11.1    1.1  1  Fer4_9    4Fe-4S dicluster domain
    5.6e-09   36.0  25.7    4.4e-05   23.5   2.6    1.9  2  Fer4_10   4Fe-4S dicluster domain
    2.4e-06   27.3  14.0    8.2e-05   22.5   2.5    2.1  2  Fer4_2    4Fe-4S binding domain
    3.4e-06   27.6  16.9    0.00041   21.1   3.9    2.2  2  Fer4_3    4Fe-4S binding domain
      4e-06   26.8  11.8    6.7e-06   26.1  11.8    1.4  1  Fer4_21   4Fe-4S dicluster domain
    6.5e-06   27.0  10.6      0.013   16.4   1.6    2.0  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00012   22.6  11.9       0.05   14.1  11.9    2.0  1  Fer4_17   4Fe-4S dicluster domain
    0.00036   20.8  16.3     0.0086   16.5   3.1    2.1  2  Fer4_4    4Fe-4S binding domain
    0.00061   20.0  11.4     0.0022   18.2  11.4    1.6  1  Fer4_18   4Fe-4S dicluster domain
     0.0011   19.4  14.3      0.037   14.5   2.3    2.1  2  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.024   15.3   9.3       0.13   13.0   1.4    2.3  2  Fer4_15   4Fe-4S single cluster domain
       0.08   13.5   3.2       0.08   13.5   3.2    2.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        1.6    9.6  14.9          5    8.0   1.6    2.1  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   3.9   5.1e-07   0.00057       7      23 ..       6      22 ..       4      23 .. 0.94
   2 !   31.1   3.0   1.2e-10   1.3e-07       2      23 ..      31      52 ..      30      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.1e-07
                                      TSSS-THHHHHSTTTEE CS
                              Fer4  7 kCigCGaCvevCPvgAI 23
                                       C gCG+C  vC +gAI
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKTGAI 22
                                      5***************9 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.2e-10
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       id +kC  C  Cve+CP+gA+
  gi|488600214|ref|YP_007906685.1| 31 RIDHDKCLECYDCVEACPYGAL 52
                                      69*******************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 !   15.1   3.0   1.6e-05     0.018       8      24 .]       6      22 ..       5      22 .. 0.96
   2 !   34.5   2.9   1.2e-11   1.4e-08       1      24 []      29      52 ..      29      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                            Fer4_6  8 kCigCgdCvrvCPegai 24
                                      +C gCg C rvC +gai
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKTGAI 22
                                      6***************8 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 1.2e-11
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v++id dkC+ C+dCv +CP+ga+
  gi|488600214|ref|YP_007906685.1| 29 VARIDHDKCLECYDCVEACPYGAL 52
                                      689*******************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 !   36.4  13.1   5.3e-12   5.9e-09       2      52 .]       7      51 ..       6      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 5.3e-12
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C gCg C ++C+++ai  + +      + ++id++kCl C+ Cv++CP+ga
  gi|488600214|ref|YP_007906685.1|  7 CQGCGTCDRVCKTGAIIRNGA------KVARIDHDKCLECYDCVEACPYGA 51
                                      ****************99775......6789******************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 !   36.0  11.1   5.2e-12   5.8e-09       1      50 [.       6      51 ..       6      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.2e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      +C gCg+C ++C++g++++  a+  +  +     +C++C +CveaCp ga
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKTGAIIRNGAKVARIDHD----KCLECYDCVEACPYGA 51
                                      6****************9888777766654....7************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 !   23.3  15.3   4.6e-08   5.2e-05       8      56 .]       6      48 ..       1      48 [. 0.91
   2 !   23.5   2.6   3.9e-08   4.4e-05       3      21 ..      31      49 ..      29      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.6e-08
                           Fer4_10  8 tCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       C +Cg+C ++C      + +  ++++ ++ r++ +kC +c  CveaCP
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVC------KTGAIIRNGAKVARIDHDKCLECYDCVEACP 48
                                      6***********......578889999999999***************9 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.9e-08
                           Fer4_10  3 vidddtCirCgkCvkaCPa 21
                                      +id d+C++C +Cv+aCP+
  gi|488600214|ref|YP_007906685.1| 31 RIDHDKCLECYDCVEACPY 49
                                      79****************8 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.9    0.0004      0.45       9      22 .]       6      19 ..       2      19 .. 0.87
   2 !   22.5   2.5   7.3e-08   8.2e-05       4      22 .]      31      49 ..      28      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                            Fer4_2  9 rCigCgaCvsaCPa 22
                                      +C gCg+C  +C +
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKT 19
                                      7***********75 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 7.3e-08
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                       +d d+C++C  Cv aCP+
  gi|488600214|ref|YP_007906685.1| 31 RIDHDKCLECYDCVEACPY 49
                                      6899**************6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   5.2   0.00019      0.21       1      15 []       7      21 ..       7      21 .. 0.97
   2 !   21.1   3.9   3.6e-07   0.00041       1      15 []      37      51 ..      37      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg+C +vC +gA
  gi|488600214|ref|YP_007906685.1|  7 CQGCGTCDRVCKTGA 21
                                      *************98 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.6e-07
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C+ Cve+CP+gA
  gi|488600214|ref|YP_007906685.1| 37 CLECYDCVEACPYGA 51
                                      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 !   26.1  11.8     6e-09   6.7e-06       6      57 ..       5      53 ..       1      55 [. 0.88

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6e-09
                           Fer4_21  6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                       +C gCg C  +C+   + ai  ++++v+++ +d+C  C  C++ CP    i
  gi|488600214|ref|YP_007906685.1|  5 LNCQGCGTCDRVCK---TGAIIRNGAKVARIDHDKCLECYDCVEACPYGALI 53
                                      58************...5899999***********************75555 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   2.0   1.3e-05     0.014       1      24 [.       6      29 ..       6      36 .. 0.80
   2 !   16.4   1.6   1.2e-05     0.013       1      17 [.      36      52 ..      36      56 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkeke 24
                                      +C++Cg C  vC t+ai  + +k+
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKTGAIIRNGAKV 29
                                      6***************98875554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.2e-05
                           Fer4_16  1 rCgtCgkCaevCPtnai 17
                                      +C +C  C+e+CP +a+
  gi|488600214|ref|YP_007906685.1| 36 KCLECYDCVEACPYGAL 52
                                      5*************997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  11.9   4.5e-05      0.05       1      59 [.       6      50 ..       6      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-05
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      +C++Cg C ++C ++++++n  +k++r       +        ++C+eC  C+++CP+g
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKTGAIIRNG-AKVARI------D-------HDKCLECYDCVEACPYG 50
                                      6****************9983.333333......3.......378************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   5.4    0.0008       0.9       3      17 .]       6      20 ..       6      20 .. 0.91
   2 !   16.5   3.1   7.7e-06    0.0086       2      17 .]      35      50 ..      34      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0008
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C+gCg C ++C++g
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKTG 20
                                      6***********975 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.7e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C++C  Cv aCP+g
  gi|488600214|ref|YP_007906685.1| 35 DKCLECYDCVEACPYG 50
                                      89************86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2  11.4   1.9e-06    0.0022      60      95 ..       6      47 ..       2      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                           Fer4_18 60 dcidcescvkvcPtgidirkGlql......eciscllcidac 95
                                      +c  c++c +vc tg  ir+G ++      +c++c  c++ac
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKTGAIIRNGAKVaridhdKCLECYDCVEAC 47
                                      8********************9874445556999*******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 !   10.8   4.4   0.00046      0.52      48      64 ..       4      20 ..       2      21 .. 0.78
   2 !   14.5   2.3   3.3e-05     0.037      48      64 ..      34      50 ..      22      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                      + +C++cg C++vC++g
  gi|488600214|ref|YP_007906685.1|  4 VLNCQGCGTCDRVCKTG 20
                                      55799999999999875 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.3e-05
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                       ++C++c  C+e+Cp g
  gi|488600214|ref|YP_007906685.1| 34 HDKCLECYDCVEACPYG 50
                                      46788888888888865 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   1.3    0.0093        10       7      20 ..       6      19 ..       5      28 .. 0.87
   2 ?   13.0   1.4   0.00012      0.13       2      19 ..      31      48 ..      30      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0093
                           Fer4_15  7 aCigcglCvaeape 20
                                      +C+gcg C +++++
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKT 19
                                      6*******999974 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      ++D+d+C  c  Cv+++p
  gi|488600214|ref|YP_007906685.1| 31 RIDHDKCLECYDCVEACP 48
                                      59***************8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.8     0.035        39       5      16 ..       6      17 ..       5      19 .. 0.89
   2 ?   13.5   3.2   7.1e-05      0.08       1      17 [.      32      48 ..      32      49 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.035
                           Fer4_13  5 tCiacgaCvela 16
                                      +C +cg+C  ++
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVC 17
                                      6*******9998 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.1e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      +D d+C +c  Cve++P
  gi|488600214|ref|YP_007906685.1| 32 IDHDKCLECYDCVEACP 48
                                      89**************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 ?    7.5   5.8    0.0064       7.2      81      94 ..       6      19 ..       2      22 .. 0.76
   2 ?    8.0   1.6    0.0044         5      81      93 ..      36      48 ..      21      51 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0064
                           Fer4_22 81 gCvGCgRCieacpv 94
                                       C GCg C+++c++
  gi|488600214|ref|YP_007906685.1|  6 NCQGCGTCDRVCKT 19
                                      68888888888875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0044
                           Fer4_22 81 gCvGCgRCieacp 93
                                      +C  C  C+eacp
  gi|488600214|ref|YP_007906685.1| 36 KCLECYDCVEACP 48
                                      5555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 365.77
//
Query:       gi|488600215|ref|YP_007906686.1|  [L=214]
Description: hypothetical protein Asulf_00675 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1381.72
//
Query:       gi|488600216|ref|YP_007906687.1|  [L=286]
Description: putative archaeal coiled-coil protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0009   19.4  11.5     0.0009   19.4  11.5    4.7  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0016   18.2  34.2     0.0023   17.7  13.1    2.9  3  Laminin_I        Laminin Domain I
     0.0023   18.2   7.6       0.15   12.4   0.2    4.9  4  WXG100           Proteins of 100 residues with WXG
     0.0023   18.2   6.9     0.0023   18.2   6.9    4.6  3  HalX             HalX domain
     0.0028   17.7  31.7        0.6   10.2   3.3    4.2  4  DUF1664          Protein of unknown function (DUF1664)
     0.0037   17.1  25.9      0.018   15.0   4.9    3.9  4  Sec34            Sec34-like family
     0.0066   16.7  13.9       0.18   12.1   0.5    4.0  2  DUF948           Bacterial protein of unknown function (DUF94
  ------ inclusion threshold ------
      0.013   15.5  34.7      0.037   14.0   7.0    3.6  3  Laminin_II       Laminin Domain II
      0.029   13.9   0.0       0.07   12.6   0.0    1.8  1  UCH              Ubiquitin carboxyl-terminal hydrolase
      0.036   13.3  40.1      0.061   12.6   9.9    3.6  4  TMPIT            TMPIT-like protein
      0.045   13.6  12.1       0.29   10.9   2.2    3.4  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      0.077   12.9  13.2       0.05   13.5   2.5    3.5  3  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
      0.091   13.2  17.1         13    6.2   0.7    5.8  6  LPP              Lipoprotein leucine-zipper
      0.095   11.8  35.1       0.19   10.8  11.4    2.1  2  AIP3             Actin interacting protein 3
        0.1   13.0  45.4        1.2    9.5   3.4    3.9  4  CENP-H           Centromere protein H (CENP-H)
       0.12   12.9  32.2       0.27   11.8   4.2    4.4  3  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.16   12.4  50.1       0.67   10.4  22.5    2.5  2  Fez1             Fez1
        0.2   11.8  47.6       0.21   11.7   6.0    4.1  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.23   11.3  54.1       0.12   12.1  28.4    3.6  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.26   10.1  56.8      0.092   11.6  23.4    3.0  3  Spc7             Spc7 kinetochore protein
        0.3   11.4  37.4        1.8    8.9   7.5    4.8  4  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.32   11.8  39.4        5.4    7.8   8.5    4.2  4  Occludin_ELL     Occludin homology domain
       0.38   10.6  20.4       0.88    9.4   3.4    3.6  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.51   10.5  34.2        1.4    9.1  13.2    3.1  3  Fib_alpha        Fibrinogen alpha/beta chain family
       0.62    8.5   9.3          1    7.8   1.6    2.2  3  FUSC             Fusaric acid resistance protein family
       0.64    8.6  43.5       0.01   14.5  31.7    2.1  2  AAA_13           AAA domain
        0.7   10.3  72.1      0.037   14.4  27.0    3.6  3  DUF4200          Domain of unknown function (DUF4200)
        0.7    8.9  49.7      0.097   11.7  24.9    2.3  2  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.76    9.8  33.6       0.16   12.0   8.0    3.2  3  GldM_N           GldM N-terminal domain
        0.8    9.0  32.8        8.2    5.7  18.5    2.2  2  DUF4407          Domain of unknown function (DUF4407)
       0.83   10.0  54.7          2    8.8  20.5    4.1  2  OmpH             Outer membrane protein (OmpH-like)
       0.96   10.1  28.6        1.6    9.4  10.5    2.8  2  AATF-Che1        Apoptosis antagonizing transcription factor
          1    9.4  53.6       0.69   10.0   4.2    4.9  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        1.1    9.9  40.8        1.3    9.7   8.5    4.6  4  YabA             Initiation control protein YabA
        1.4    8.1  15.2       0.56    9.4   2.7    2.1  2  Dynein_C         Dynein heavy chain C-terminal domain
          2    6.5  56.4      0.075   11.2   4.9    3.6  3  HOOK             HOOK protein
        2.4    7.9  61.5        4.4    7.0  29.4    3.1  3  ERM              Ezrin/radixin/moesin family
        3.7    8.2  31.5        1.6    9.4   6.3    5.6  5  SlyX             SlyX
        3.7    7.9  54.2       0.96    9.8  13.0    4.4  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
          4    7.3  56.9       0.73    9.6   5.9    6.0  3  DivIC            Septum formation initiator
        4.1    7.1  10.8         19    4.9   0.1    4.2  3  TetR             Bacterial transcriptional repressor
        4.2    7.2  37.1        7.3    6.4   6.6    5.2  5  SKA2             Spindle and kinetochore-associated protein 2
          5    7.9  39.0          3    8.6   5.7    4.7  4  DUF2203          Uncharacterized conserved protein (DUF2203)
        5.4    5.9  40.0       0.27   10.1  14.8    3.2  3  IFT57            Intra-flagellar transport protein 57
        6.6    7.2  33.2       0.87   10.1  13.2    3.3  3  FlgN             FlgN protein
        6.7    7.1   6.7          5    7.6   0.2    3.1  3  Desmo_N          Viral Desmoplakin N-terminus
        8.2    4.7  53.0        1.1    7.6  29.3    2.2  2  MAD              Mitotic checkpoint protein


Domain annotation for each model (and alignments):
>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  10.4      0.04        15      32      82 ..       4      58 ..       2      63 .. 0.71
   2 !   19.4  11.5   2.4e-06    0.0009      26     104 ..      47     122 ..      33     125 .. 0.92
   3 ?    1.1  18.9       1.2   4.5e+02       7      99 ..     135     224 ..     123     246 .. 0.66
   4 ?    0.6  10.7       1.8   6.7e+02      15      85 ..     192     268 ..     188     278 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.04
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N 32 leldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkee 82
                                       +l e++++l++e++el ++r el+k+  +  +k         el+a+vke+ke+
  gi|488600216|ref|YP_007906687.1|  4 EKLMERKEQLEKEVQELTKKRDELNKAAREYADKRdelnSLVRELLAKVKEIKEK 58
                                      5788899999999999999999999999998887644444555555555555555 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       ++++++ e+ ekr e ++++ el++++N+l++eI k+ ++    ++l++++++ +  l+++e+e + le ++++++l
  gi|488600216|ref|YP_007906687.1|  47 ELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRE---LDKLRKSIDKGGRPLSEIEKEIRRLEFRQQTAVL 120
                                       6789999*******************************95...79***************************99999 PP

                                       TS CS
                      Seryl_tRNA_N 103 ai 104
                                       +i
  gi|488600216|ref|YP_007906687.1| 121 TI 122
                                       88 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.2
                                       HHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHH CS
                      Seryl_tRNA_N   7 irenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeel 83 
                                       + +++e+ k +l++ +e+k +++++ el ek re+ +e+ e+ +e  +  +e+ k  +   +++e + e++++ e +
  gi|488600216|ref|YP_007906687.1| 135 LKKELEERKYQLERHEEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQ---EIDEKRSEADKMHEMF 208
                                       5667777777777777888888888888888888888877777776666666666664...3455555555555555 PP

                                       HHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  84 kaleaelkeleaelek 99 
                                        + ++e + + +e+ k
  gi|488600216|ref|YP_007906687.1| 209 VNSKKEADRIHNEIIK 224
                                       5555555555544433 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.8
                                       HHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT......S-TCCCCCCCHHHHHHHHH CS
                      Seryl_tRNA_N  15 keklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk......edaeeliaevkelkeelka 85 
                                       +e  +kR e+++  + ++   ++  ++ +e+ + ++  + l k I+ +k+k+       ++eeli ++ke+ e +k+
  gi|488600216|ref|YP_007906687.1| 192 QEIDEKRSEADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQarsrvdREKEELIRKAKEIYEMFKR 268
                                       44556677777777777777777788888888888888888888888887765555555555555555555555554 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7  13.1     6e-06    0.0023     158     257 ..       4     106 ..       1     108 [. 0.85
   2 ?    6.8  11.3     0.013       4.9      17     110 ..     128     227 ..     117     245 .. 0.74
   3 ?    0.9   0.9      0.81   3.1e+02     177     206 ..     217     244 ..     210     272 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6e-06
                         Laminin_I 158 srvqtllqklqeenkaLkealrdsLa....eyeakLsDlrelleeAaaktrdanrlnlanqanlreiekkkeevsee 230
                                       ++  ++ ++l +e + L ++ rd+L+    ey +k + l +l++e  ak+++ ++   +n+++ +e+++kk+ +++e
  gi|488600216|ref|YP_007906687.1|   4 EKLMERKEQLEKEVQELTKK-RDELNkaarEYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNRE 79 
                                       55555556666666666555.6666533338********************************************** PP

                         Laminin_I 231 knqleetlktardsLdaanllLqeldd 257
                                         +l   l + r+s+d++ + L+e+++
  gi|488600216|ref|YP_007906687.1|  80 IDKLYRELDKLRKSIDKGGRPLSEIEK 106
                                       *************************97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                         Laminin_I  17 inanledltkeLqeklskesakks......kieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeL 87 
                                       + + +++l+keL+e+  + + +++      +i+ l++++ ++ qe+ e++++a +  a+  k+ +e+++  ++a ++
  gi|488600216|ref|YP_007906687.1| 128 LVERIAKLKKELEERKYQLERHEEfkrliaRIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKM 204
                                       55566777777777766666665322222267778888999999999999999999999999999999999999999 PP

                         Laminin_I  88 aekikkladnikeilekvatlne 110
                                        e  +++++++  i + + +  +
  gi|488600216|ref|YP_007906687.1| 205 HEMFVNSKKEADRIHNEIIKHRK 227
                                       99999999999988888766555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.81
                         Laminin_I 177 alrdsLaeyeakLsDlrelleeAaaktrda 206
                                        + +++ ++   L+Dl +++++ +ak   a
  gi|488600216|ref|YP_007906687.1| 217 RIHNEIIKHRKDLKDLDKVIKALKAKQ--A 244
                                       566777778888888887777654443..3 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 ?    7.1   0.3     0.016       6.2       7      37 ..      25      55 ..       3      65 .. 0.81
   2 !   12.4   0.2   0.00038      0.15       7      82 ..      25     102 ..      23     106 .. 0.85
   3 ?    4.2   0.4      0.13        51      14      36 ..     157     179 ..     148     225 .. 0.50
   4 ?   -0.3   0.0       3.4   1.3e+03      27      61 ..     229     260 ..     210     268 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.016
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100  7 eelrqaaarfqkqaeeledelqrlkaevdal 37
                                      +el +aa++++++++el +++++l a+v+++
  gi|488600216|ref|YP_007906687.1| 25 DELNKAAREYADKRDELNSLVRELLAKVKEI 55
                                      5778888888888888888888888888776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.GC.GCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdal.qs.gWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanaf 81 
                                       +el +aa++++++++el +++++l a+v+++ +  + + + a++ ++  + ++++++kl+++L+++++++++ ++ +
  gi|488600216|ref|YP_007906687.1|  25 DELNKAAREYADKRDELNSLVRELLAKVKEIkEKrDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSIDKGGRPL 101
                                       6899***************************5442444888889999999****************99999877665 PP

                                       H CS
                            WXG100  82 e 82 
                                       +
  gi|488600216|ref|YP_007906687.1| 102 S 102
                                       5 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  14 arfqkqaeeledelqrlkaevda 36 
                                       ar+++ +e++++++q+++  v++
  gi|488600216|ref|YP_007906687.1| 157 ARIKELKEKVREIHQEMMEFVEE 179
                                       44444444444444444444333 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHH CS
                            WXG100  27 lqrlkaevdalqsgWsGaaadafqaefeewkqaaq 61 
                                       l++l++ ++al+++   +a+++ + e ee+ ++a+
  gi|488600216|ref|YP_007906687.1| 229 LKDLDKVIKALKAK---QARSRVDREKEELIRKAK 260
                                       44444444444432...455555555555555555 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   2.3      0.82   3.1e+02      35      56 ..      15      36 ..       3      45 .. 0.50
   2 ?    1.4   5.9       1.1   4.1e+02       2      59 ..      38      95 ..      32     119 .. 0.75
   3 !   18.2   6.9     6e-06    0.0023      14      60 ..     127     175 ..     100     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.82
                              HalX 35 eeYqeLearleelraqldetld 56
                                       e qeL+   +el   + e +d
  gi|488600216|ref|YP_007906687.1| 15 KEVQELTKKRDELNKAAREYAD 36
                                      2444444444444444444444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.1
                              HalX  2 rseYdeelqelfaL..asKravLeaekseaeLadseeYqeLearleelraqldetldeld 59
                                      r+e+++ ++el a   ++K+   e +k + eL   +++  L ++++ l ++ld +  ++d
  gi|488600216|ref|YP_007906687.1| 38 RDELNSLVRELLAKvkEIKEKRDENNKKAKEL--KQKKNSLNREIDKLYRELDKLRKSID 95
                                      67777777777553112333344777777777..56888999999999999998888765 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 6e-06
                              HalX  14 aLasKravLeaeksea..eLadseeYqeLearleelraqldetldeldd 60 
                                       aL+++ a+L+ e+ e+  +L+ +ee+ +L ar+ el++++ e+ +e+ +
  gi|488600216|ref|YP_007906687.1| 127 ALVERIAKLKKELEERkyQLERHEEFKRLIARIKELKEKVREIHQEMME 175
                                       899**********996448************************999554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.8     0.012       4.6      55     121 ..       4      70 ..       1      72 [. 0.67
   2 !   10.2   3.3    0.0016       0.6      58     122 ..      42     106 ..      39     125 .. 0.62
   3 ?    7.3   5.2     0.012       4.5      53     106 ..     128     183 ..     113     197 .. 0.49
   4 !    8.7   8.3    0.0044       1.7      38     116 ..     161     242 ..     160     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       e+l + k++L+++++++ kk de +++++e +++ +e+++ ++e+  +v+++ke   + ++k ++++
  gi|488600216|ref|YP_007906687.1|   4 EKLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELK 70 
                                       5677777777777777777777777777777777777777777777777777776666666555554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0016
                           DUF1664  58 aatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       ++  r+L ++++++ +k de+++ +ke+k++ ++++++++++ ++++++++ + + +  l++ie+
  gi|488600216|ref|YP_007906687.1|  42 NSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSIDKGGRPLSEIEK 106
                                       44556666666666666666666666666666666666666666666666666555555555553 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.012
                           DUF1664  53 vseslaatkrhLssridrvdkk..ldeqkeiskeikeevtevredlseigedvesv 106
                                       + e +a+ k++L++r  +++++   +  ++ +ke+ke+v e+++++ e+ e+ ++ 
  gi|488600216|ref|YP_007906687.1| 128 LVERIAKLKKELEERKYQLERHeeFKRLIARIKELKEKVREIHQEMMEFVEEADKY 183
                                       33445555555555554444321123333444444445555554444444444443 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0044
                           DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkk...ldeqkeiskeikeevtevredlseigedvesvkeave 111
                                        l++ v ++ +++ ++ e+  +   ++++  +++d+k    d++ e+  + k+e +++++++ + ++d++ ++++++
  gi|488600216|ref|YP_007906687.1| 161 ELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKrseADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIK 237
                                       6899999*********************999999987322577888888999************************* PP

                           DUF1664 112 glesk 116
                                        l++k
  gi|488600216|ref|YP_007906687.1| 238 ALKAK 242
                                       *9988 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.1      0.11        41      22      60 ..       6      44 ..       2      48 .. 0.45
   2 !   11.2   3.1   0.00068      0.26       9      62 ..      42      95 ..      34     119 .. 0.82
   3 ?   -0.3   0.1       2.3   8.8e+02      72     101 ..     130     159 ..     101     162 .. 0.69
   4 !   15.0   4.9   4.6e-05     0.018       5      91 ..     162     250 ..     158     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                             Sec34 22 aleqLeeleekfksvsektsslheaceqlleeqkrleel 60
                                      ++e  e+le+++++ ++k  +l++a+ +  +++++l++l
  gi|488600216|ref|YP_007906687.1|  6 LMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSL 44
                                      333334444555555555555555555555555555444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00068
                             Sec34  9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelae 62
                                      ++ ++ell++++e++e+ +e ++k k+ ++k +sl+++ ++l++e ++l++  +
  gi|488600216|ref|YP_007906687.1| 42 NSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSID 95
                                      566789999999999999999999999999999999999999999888877655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.3
                             Sec34  72 eeldpitrkLnspgsslvksesFlemLkkl 101
                                       e + +++++L++ + +l ++e+F+ ++ ++
  gi|488600216|ref|YP_007906687.1| 130 ERIAKLKKELEERKYQLERHEEFKRLIARI 159
                                       445566667777777777777777777766 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 4.6e-05
                             Sec34   5 Leske.eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrk 80 
                                       L++k  e  +e++e ++ea +  +e+++ f++++ek s+ +++ e  ++++k+ +++++ei ++ k  ++ld++ + 
  gi|488600216|ref|YP_007906687.1| 162 LKEKVrEIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKA 238
                                       555540456789999************************************************************** PP

                             Sec34  81 Lnspgss.lvks 91 
                                       L+++++   v++
  gi|488600216|ref|YP_007906687.1| 239 LKAKQARsRVDR 250
                                       **9998866665 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   5.1     0.058        22      25      88 ..      14      77 ..       1     141 [. 0.69
   2 !   12.1   0.5   0.00047      0.18      23      76 ..     154     207 ..     149     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.058
                            DUF948 25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88
                                      +k ++e+++  +el+k ++++ ++ ++l + v+ell+ v+e  ek d+  +++++l ++ ++ln
  gi|488600216|ref|YP_007906687.1| 14 EKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLN 77
                                      4555555555555555555555555555555555555555555555555555555544444444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00047
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                       +l   ++e+++ ++e+ +++ + ++e+++  a++ ++ +++ ek  + d++ e 
  gi|488600216|ref|YP_007906687.1| 154 RLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEM 207
                                       556678899999999999999999999999999999999999998888887665 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   7.0   9.7e-05     0.037      26      86 ..       3      63 ..       1      64 [. 0.93
   2 ?    8.5   7.6    0.0048       1.8       7     103 ..      61     167 ..      59     169 .. 0.73
   3 ?    4.6   8.4     0.082        31       2      85 ..     163     246 ..     149     273 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.7e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.. CS
                        Laminin_II 26 lentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeass 86
                                      le++ e  ++++++v+e ++k +++nka r+  ++  +L+ l+ +Ll+k+ke+k+++++++
  gi|488600216|ref|YP_007906687.1|  3 LEKLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENN 63
                                      6778888899**********************************************99865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0048
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXX--TTT.TTGGGHHHHHH CS
                        Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdA..rrsvkkLeklap.qLldklkelkq 80 
                                       e n++ake +++++ l+ +++++  +l ++++s+++    +++  k ir    r++   L+   +  L++++ +lk+
  gi|488600216|ref|YP_007906687.1|  61 ENNKKAKELKQKKNSLNREIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRLefRQQTAVLTIDKErALVERIAKLKK 137
                                       67899999999999999999999999999999999998888888888875411455555555444158888888887 PP

                                       HHHH..........HHHHHHHHHHHHHHHH CS
                        Laminin_II  81 leeasss.......lsdniseikelIaqAR 103
                                         e+++         ++ i +ikel ++ R
  gi|488600216|ref|YP_007906687.1| 138 ELEERKYqlerheeFKRLIARIKELKEKVR 167
                                       777766565666678888888888876666 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.082
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       ke+++e+ + + e  e   + ++++ +t +++ e ++++++++e   +++k  +   +++ k  k + +L + +k l
  gi|488600216|ref|YP_007906687.1| 163 KEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKAL 239
                                       56666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                       HHHHHH. CS
                        Laminin_II  79 kqleeas 85 
                                       k ++  s
  gi|488600216|ref|YP_007906687.1| 240 KAKQARS 246
                                       6665553 PP

>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018      0.07      36     118 ..      53     193 ..      39     278 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                       CSSTCCCCC-...TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE--.............................HHH CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxx RF
                               UCH  36 kkesrnkkel..nesnplgkkgelakalkdlfkellkskskavsP.............................kkl 81 
                                       k+++++++e+  ++++ ++kk+ l +++ +l++el k  +k++                               ++l
  gi|488600216|ref|YP_007906687.1|  53 KEIKEKRDENnkKAKELKQKKNSLNREIDKLYRELDK-LRKSIDKggrplseiekeirrlefrqqtavltidkeRAL 128
                                       2222222222113333333333666666666666662.233333333446667777777888888888889999999 PP

                                       HHHHHHHSGGGT.SSSTCEHHHHHHHHHHHHHHHHCC...........................H CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...........................x RF
                               UCH  82 kktlsklaksfs.gykqqDaqEflaflLdqlhedlnr...........................e 118
                                       ++ ++kl+k+++    q   +E ++ l+++++e  ++                           e
  gi|488600216|ref|YP_007906687.1| 129 VERIAKLKKELEeRKYQLERHEEFKRLIARIKELKEKvreihqemmefveeadkyhaemtktfqE 193
                                       99999999999855557788888888888887777776667666666665555554433333330 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   9.9   0.00016     0.061       2      82 ..      15      94 ..       2     101 .. 0.85
   2 ?   11.2   9.2   0.00041      0.16       3      88 ..      58     152 ..      56     158 .. 0.88
   3 ?    9.2   7.6    0.0017      0.65       2      86 ..     150     233 ..     149     235 .. 0.86
   4 ?    8.5   8.9    0.0027         1       5      86 ..     185     270 ..     181     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                             TMPIT  2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80
                                      +e++el+k+ +el+++a+ey  k +el++l  ++  ++k+ k++  e +++ k+lk+++ ++ ++e+++l +el++ +k
  gi|488600216|ref|YP_007906687.1| 15 KEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKK-NSLNREIDKLYRELDKLRK 92
                                      78999999999999999999999999999999999999999999999999999999884.6777788888888888777 PP

                             TMPIT 81 vl 82
                                      ++
  gi|488600216|ref|YP_007906687.1| 93 SI 94
                                      66 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00041
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.........eeeeeevee 70 
                                       + +e +k++kel+++++++++++++l +  +k++k+i+k  + l+e+++++++l+ +++         +   e++++
  gi|488600216|ref|YP_007906687.1|  58 KRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRLEFRQQtavltidkeRALVERIAK 134
                                       56778899**********************************************99877788988655555678999 PP

                             TMPIT  71 lkeelkerkkvlkevesl 88 
                                       lk+el+erk +l++ e++
  gi|488600216|ref|YP_007906687.1| 135 LKKELEERKYQLERHEEF 152
                                       ***********9987765 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0017
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       ee+++l  ++kel+e+ +e++q++ e  +  +k   e++k  +++ e +s+ +k+++    ++++e++++++e+ + 
  gi|488600216|ref|YP_007906687.1| 150 EEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEMF-VNSKKEADRIHNEIIKH 225
                                       68889999999999999999999999999999999999999999999999999999886.58888999999999999 PP

                             TMPIT  79 kkvlkeve 86 
                                       +k lk+++
  gi|488600216|ref|YP_007906687.1| 226 RKDLKDLD 233
                                       99888875 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0027
                             TMPIT   5 eelekefkeleetakey...kqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelke 77 
                                       +e++k f+e+ e+ +e    ++   + +k  +++ +ei k++k+lk+l++ +k lk+++  ++ ++e eel ++ ke
  gi|488600216|ref|YP_007906687.1| 185 AEMTKTFQEIDEKRSEAdkmHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQArSRVDREKEELIRKAKE 261
                                       678888999988875550004455567888999***********************996534455566677777777 PP

                             TMPIT  78 rkkvlkeve 86 
                                       + +++k+ e
  gi|488600216|ref|YP_007906687.1| 262 IYEMFKRGE 270
                                       777776544 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.9     0.035        13     109     168 ..      10      69 ..       1      83 [. 0.61
   2 ?    4.9   0.2     0.055        21      76     133 ..      54     111 ..      48     140 .. 0.75
   3 ?   10.9   2.2   0.00077      0.29      86     159 ..     147     219 ..     132     232 .. 0.82
   4 ?    2.2   0.2      0.38   1.4e+02      74     121 ..     201     246 ..     200     268 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.035
                                       .HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 109 leetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveev 168
                                        e+ +++v+e +++ +e ++a +e +++ +e+++lv+e+ a ++e+ +  +e n+  +e+
  gi|488600216|ref|YP_007906687.1|  10 KEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKEL 69 
                                       455556666666666666666666666666666666666666666666666655555444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHH CS
                         MCPsignal  76 EVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkei 133
                                       E+++  ++  ++ake+++    +++ei++  + l++ r+ +++g    +e +++++++
  gi|488600216|ref|YP_007906687.1|  54 EIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRL 111
                                       6666667778888888888888888888888888888888888888777777777765 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00077
                                       HHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  86 qaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasie 159
                                       ++ +e ++li++i++  +++ e+ +e  + vee+ +  +e +++++ei e+ +e  d ++e+ + s++ +  i+
  gi|488600216|ref|YP_007906687.1| 147 ERHEEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEA-DKMHEMFVNSKKEADRIH 219
                                       5678999******99999999999************************9998885.667888888777776654 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHH CS
                         MCPsignal  74 AdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegse 121
                                       Ad  +++  +s++ a  i++ ii+  k+ +d  ++++  + +  ++ +
  gi|488600216|ref|YP_007906687.1| 201 ADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAK--QARS 246
                                       566777778899999999999999999888877777654433..2222 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.6     0.051        19      32      58 ..       3      29 ..       1      37 [. 0.89
   2 ?   13.5   2.5   0.00013      0.05      20      57 ..      54      91 ..      49      95 .. 0.95
   3 ?   -1.2   0.1       5.1   1.9e+03      40      49 ..     160     169 ..     128     186 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.051
                            GIT_CC 32 iqqLlkvNtslsdelrlLQskvqkLqa 58
                                      +++L++ +++l++e+++L +k ++L++
  gi|488600216|ref|YP_007906687.1|  3 LEKLMERKEQLEKEVQELTKKRDELNK 29
                                      5789****************9999986 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00013
                            GIT_CC 20 elKkalaaseakiqqLlkvNtslsdelrlLQskvqkLq 57
                                      e+K++    + k ++L++ ++sl++e+ +L ++++kL 
  gi|488600216|ref|YP_007906687.1| 54 EIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLR 91
                                      89**********************************97 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.1
                            GIT_CC  40 tslsdelrlL 49 
                                       ++l++++r++
  gi|488600216|ref|YP_007906687.1| 160 KELKEKVREI 169
                                       2333333333 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.05        19       3      26 ..      11      34 ..       9      38 .. 0.82
   2 ?    6.2   0.7     0.035        13       2      34 ..      38      70 ..      37      73 .. 0.87
   3 ?    4.0   0.1      0.17        66       5      30 ..      69      94 ..      65     110 .. 0.69
   4 ?    5.2   0.0     0.073        28      11      38 ..     154     181 ..     149     187 .. 0.79
   5 ?    0.4   0.2       2.3   8.7e+02      15      39 ..     193     217 ..     185     227 .. 0.79
   6 ?   -1.0   0.1       6.3   2.4e+03       8      27 ..     228     247 ..     225     257 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.05
                               LPP  3 deLssqVsqLkskvdqlssdvnsa 26
                                      ++L ++V++L +k d+l++ + + 
  gi|488600216|ref|YP_007906687.1| 11 EQLEKEVQELTKKRDELNKAAREY 34
                                      689999999999999999877655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.035
                               LPP  2 ldeLssqVsqLkskvdqlssdvnsakaaaqaak 34
                                       deL+s V +L +kv++++++ ++ ++ a++ k
  gi|488600216|ref|YP_007906687.1| 38 RDELNSLVRELLAKVKEIKEKRDENNKKAKELK 70
                                      599*****************9988888887766 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.17
                               LPP  5 LssqVsqLkskvdqlssdvnsakaaa 30
                                      L +  ++L++++d+l  +++++++ +
  gi|488600216|ref|YP_007906687.1| 69 LKQKKNSLNREIDKLYRELDKLRKSI 94
                                      55555677777777777777666554 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.073
                               LPP  11 qLkskvdqlssdvnsakaaaqaakeEAa 38 
                                       +L + +++l+++v ++++++++  eEA 
  gi|488600216|ref|YP_007906687.1| 154 RLIARIKELKEKVREIHQEMMEFVEEAD 181
                                       5677888888888888888888888885 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 2.3
                               LPP  15 kvdqlssdvnsakaaaqaakeEAaR 39 
                                       ++d+  s+++++++   + k+EA R
  gi|488600216|ref|YP_007906687.1| 193 EIDEKRSEADKMHEMFVNSKKEADR 217
                                       5666678889999999999999987 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 6.3
                               LPP   8 qVsqLkskvdqlssdvnsak 27 
                                       ++++L + +++l+++++ ++
  gi|488600216|ref|YP_007906687.1| 228 DLKDLDKVIKALKAKQARSR 247
                                       56666666777766544443 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  11.4   0.00051      0.19     125     215 ..       8      95 ..       2      97 .. 0.88
   2 ?    7.1  15.6    0.0067       2.5      65     203 ..     118     262 ..      99     274 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00051
                                       XX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHH CS
                              AIP3 125 lakkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvkeaslastkkssnrayiekgkkkLseesd 201
                                        +k++l+++++e+++ r +L+     y+++++e+++ + el +k+k++k  +    +++++ + +++ k++L++e d
  gi|488600216|ref|YP_007906687.1|   8 ERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIK--EK-RDENNKKAKELKQKKNSLNREID 81 
                                       4578999******************************************..44.556777778899*********** PP

                                       HHHHHHHHHHHHHH CS
                              AIP3 202 klvtkvddLqDlve 215
                                       kl +++d L   ++
  gi|488600216|ref|YP_007906687.1|  82 KLYRELDKLRKSID 95 
                                       *********98887 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0067
                                       XXXXXX.....XXXXXXXXXXXXXXXXXX..XXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX........ CS
                              AIP3  65 svLsLn.....iepldevkkhideslasl..skelkelkssiesqkaslqevserqeeaakekaseslakkelkaql 134
                                        vL++      +e + ++kk+++e   +l  ++e+k+l ++i++ k++ +e++++  e ++e+ +    ++e ++ +
  gi|488600216|ref|YP_007906687.1| 118 AVLTIDkeralVERIAKLKKELEERKYQLerHEEFKRLIARIKELKEKVREIHQEMMEFVEEADK---YHAEMTKTF 191
                                       45555544444446667777776666655334556666666666666666655555555544444...234677788 PP

                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXX.XXXXXXHHHHHHHHHHHHHHHHHHH CS
                              AIP3 135 kevqslrrdLavlrqlysefkseikeslselrekakkvk..easlastkkssnrayiekgkkkLseesdkl 203
                                       +e+ + r +   + ++  ++k+e + + +e+ ++ k++k  +  ++  k +++r+ +++ k++L ++++++
  gi|488600216|ref|YP_007906687.1| 192 QEIDEKRSEADKMHEMFVNSKKEADRIHNEIIKHRKDLKdlDKVIKALKAKQARSRVDREKEELIRKAKEI 262
                                       88888888888888888888888888888888888888855555667777888888888888887777665 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  15.1    0.0068       2.6       7      74 ..       5      72 ..       2      80 .. 0.76
   2 ?    9.5   3.4    0.0033       1.2       6      76 ..      78     147 ..      73     151 .. 0.76
   3 ?    7.0  10.5     0.019       7.3       7      91 ..     151     238 ..     146     251 .. 0.75
   4 ?    1.4   3.2       1.1   4.2e+02       7      50 ..     214     259 ..     210     278 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0068
                            CENP-H  7 qrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleae 74
                                      + +e  ++l+k  qel+++++el+++ +e  + + + ++l++ell + ke ++++++++++ ++l+++
  gi|488600216|ref|YP_007906687.1|  5 KLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQK 72
                                      55566678889999999999999999999999999999999999888888888885666666666554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0033
                            CENP-H   6 eqrdelssellklsqelrelqeeltevekenlrlkrknrelaael.lelakekesekeklkeelekleaelk 76 
                                       +++d+l  el kl +++ +  + l+e+eke++rl+ ++++ + ++  e a  ++    klk+ele+ + +l+
  gi|488600216|ref|YP_007906687.1|  78 REIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRLEFRQQTAVLTIdKERALVERI--AKLKKELEERKYQLE 147
                                       679******************************************3333333333..346666666555544 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.019
                            CENP-H   7 qrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksrq 80 
                                       +  +l+ ++++l++++re+++e++e  +e+ + +++  + ++e+ e+++e+++      + k+e +++++e+ k r+
  gi|488600216|ref|YP_007906687.1| 151 EFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHemfVNSKKEADRIHNEIIKHRK 227
                                       56788999999999999999999999999999999999999999666666655555895566666777766666666 PP

                            CENP-H  81 rwrvvknvasa 91 
                                         + + +v++a
  gi|488600216|ref|YP_007906687.1| 228 DLKDLDKVIKA 238
                                       66655555544 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 1.1
                            CENP-H   7 qrdelssellklsqelrelqeelt..evekenlrlkrknrelaael 50 
                                       + d++  e++k+ ++l++l + +   ++++ + r+ r+++el+++ 
  gi|488600216|ref|YP_007906687.1| 214 EADRIHNEIIKHRKDLKDLDKVIKalKAKQARSRVDREKEELIRKA 259
                                       4566666777777777777765551134445556666777766654 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   4.0       0.1        39       8      55 ..      11      57 ..       2      61 .. 0.43
   2 ?    0.1  16.3       3.2   1.2e+03      10      95 ..      41     166 ..      34     204 .. 0.64
   3 ?   11.8   4.2   0.00071      0.27       8      79 ..     178     251 ..     174     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.1
                      Syntaxin-6_N  8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiew 55
                                      e+ +k+++++++  ++ ++  ++   ++++el+++ +eL +++++i++
  gi|488600216|ref|YP_007906687.1| 11 EQLEKEVQELTKKRDELNKAAREYA-DKRDELNSLVRELLAKVKEIKE 57
                                      3333333333333333332222222.2355666666666666555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 3.2
                      Syntaxin-6_N  10 VqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetv...................... 64 
                                        ++ ++++ + +++ ++ +++++ ++ +el++ ++ L+++++++  +l+ L++++                      
  gi|488600216|ref|YP_007906687.1|  41 LNSLVRELLAKVKEIKEKRDENN-KKAKELKQKKNSLNREIDKLYRELDKLRKSIdkggrplseiekeirrlefrqq 116
                                       44444444444444444334433.469****************************7777777555555554444444 PP

                      Syntaxin-6_N  65 ..........rivek...........npskfkide.kelsrrrafveevreev 95 
                                                 +               +++k++++  +e +r  a ++e++e+v
  gi|488600216|ref|YP_007906687.1| 117 tavltidkerA---LveriaklkkelEERKYQLERhEEFKRLIARIKELKEKV 166
                                       44444444431...022233333333444555544234444445555555555 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00071
                      Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfkidek 79 
                                       ee  k   ++++++++  + ++++++  +   ++++  + +++++ + ++dl+dL+++++++++++++ ++d +
  gi|488600216|ref|YP_007906687.1| 178 EEADKYHAEMTKTFQEIDEKRSEADKmhEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSRVDRE 251
                                       566666677777888886555555553334556666777789999999**************999988777653 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  26.7     0.022       8.3      16     156 ..      10     150 ..       3     154 .. 0.77
   2 ?   10.4  22.5    0.0018      0.67      12     150 ..     132     268 ..     131     276 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.022
                              Fez1  16 KqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekl 92 
                                       K+QL    +e+t+k +e+ +   +  + r +l++  +e+    ++++ek +e+++  +el++kk+  +l re ++kl
  gi|488600216|ref|YP_007906687.1|  10 KEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKN--SLNRE-IDKL 83 
                                       88998888899999999999999999999999999999999999999999999999999988764..44444.8999 PP

                              Fez1  93 eeelkelreelselsleeeeaalesdeakaqrqe....aeeleelkreverlraeLkeerqkkeeqas 156
                                        +el +lr+++ +  +  +e ++e ++ + ++q+     ++ ++l +++++l++eL+e + + e++ +
  gi|488600216|ref|YP_007906687.1|  84 YRELDKLRKSIDKGGRPLSEIEKEIRRLEFRQQTavltIDKERALVERIAKLKKELEERKYQLERH-E 150
                                       999999999999988777777777766666655566655666677777888888888887777665.3 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0018
                              Fez1  12 islLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrek 88 
                                       i+ LK+ L + + ++ ++ +e   l a+++el++k++e  +e++e+ e++++ ++e+ +  +e+++k+sea+ ++e 
  gi|488600216|ref|YP_007906687.1| 132 IAKLKKELEERKYQL-ERHEEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEM 207
                                       788888888877665.6888999999999999999999999999999999999999999999999999999999999 PP

                              Fez1  89 vekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqk 150
                                         + ++e  ++++e+ ++ ++ ++  +  ++ ka+++ +++++++k+e+ r  +e+ e  ++
  gi|488600216|ref|YP_007906687.1| 208 FVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQA-RSRVDREKEELIRKAKEIYEMFKR 268
                                       9999999999988888766555555444444444333.345555555555555555544444 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 ?   11.7   6.0   0.00055      0.21      46      89 ..       3      46 ..       1      48 [. 0.93
   2 ?    7.1  12.8     0.014       5.3      15     108 ..      38     140 ..      36     145 .. 0.76
   3 ?    1.4   1.7      0.81   3.1e+02      30      75 ..     228     274 ..     214     283 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00055
                             Mod_r 46 aeknlslepeleelrselqekleelkelekefeekeqeldellq 89
                                      +ek ++++++le++ +el++k++el+++ +e+ +k  el++l++
  gi|488600216|ref|YP_007906687.1|  3 LEKLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVR 46
                                      6899***********************************99975 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                             Mod_r  15 eeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqeklee.......lkelekefeekeqe 83 
                                        + l++lv +l  +vk++ke+++e  ++ ++l +k+ sl+ e+++l  el + +++       l e+eke +++e +
  gi|488600216|ref|YP_007906687.1|  38 RDELNSLVRELlAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSidkggrpLSEIEKEIRRLEFR 114
                                       589******999*********************99999988666666666555555555555599999999999999 PP

                             Mod_r  84 ldellqkfspd.allarLqtavaeae 108
                                       +++++   +++ al +r  +  +e e
  gi|488600216|ref|YP_007906687.1| 115 QQTAVLTIDKErALVERIAKLKKELE 140
                                       99988666655355555555555555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.81
                             Mod_r  30 qlkeekeellaeneslaeknlsl.epeleelrselqekleelkelek 75 
                                       +lk+  + + a   + a++  ++ ++el  + +e+ e ++  ++le+
  gi|488600216|ref|YP_007906687.1| 228 DLKDLDKVIKALKAKQARSRVDReKEELIRKAKEIYEMFKRGEKLET 274
                                       33333333333344455555666555666666666666666665554 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  28.4   0.00032      0.12      32     165 ..       4     137 ..       2     147 .. 0.86
   2 ?   -2.5  22.8       9.9   3.8e+03      19     141 ..     134     251 ..     133     282 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                          KASH_CCD  32 etaeetnakLteeieeLkkklkstQqalqkaklleeEle....elkalvkeleEkrarlkaqnkqlekenqsLiaki 104
                                       e+  e  ++L  e++eL kk   + +a+ ++    +El+    el a vke++Ekr + + ++k+l++ ++sL+ +i
  gi|488600216|ref|YP_007906687.1|   4 EKLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNslvrELLAKVKEIKEKRDENNKKAKELKQKKNSLNREI 80 
                                       77779999***********9999888888777666666522227788899*************************** PP

                          KASH_CCD 105 esLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqieeLkl 165
                                       ++L  e+ kl+  +d+  + l e+ ke+  L  +  ++  l+ +ke++l+e+ ++    k 
  gi|488600216|ref|YP_007906687.1|  81 DKLYRELDKLRKSIDKGGRPLSEIEKEIRRLEFRQ-QTAVLTIDKERALVERIAKL---KK 137
                                       *******************************9988.899***********997664...44 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.9
                          KASH_CCD  19 kLaeenskLkkavetaeetnakLteeieeLkkklk.stQqalqkaklleeEleelkalvkeleEkrarlkaqnkqle 94 
                                       kL++e +  k ++e  ee  ++L++ i+eLk+k++ + Q  +++ +  ++  +e+ ++ +e++Ekr ++    +   
  gi|488600216|ref|YP_007906687.1| 134 KLKKELEERKYQLERHEEF-KRLIARIKELKEKVReIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEMFV 209
                                       6777777778888888776.689999999999987456777888888888888999998888888877765544332 PP

                          KASH_CCD  95 kenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlhe 141
                                         +    ++ + + +e+ik + +   l k +k L +++a  + +  e
  gi|488600216|ref|YP_007906687.1| 210 NSK----KEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSRVDR-E 251
                                       222....23344445555555555555555555555554444443.2 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  23.4   0.00024     0.092     142     254 ..       4     112 ..       2     125 .. 0.63
   2 ?    6.0  10.1     0.012       4.7     178     250 ..     103     180 ..     100     183 .. 0.65
   3 ?    0.8  24.8      0.49   1.9e+02     139     259 ..     134     259 ..     131     278 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieek 218
                                       e+l e+ e+le++ ++L+k+++el+++  e+  +++el++ +++l ++++e+++   e+ ++  +el++ k+ ++  
  gi|488600216|ref|YP_007906687.1|   4 EKLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDEN-NKKAKELKQKKNSLN-- 77 
                                       56777778888888888888888888888888888888888888877777766633332.333333444444444.. PP

                              Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                        +e+++l ++l++l+++i++     se+e+ei++ e
  gi|488600216|ref|YP_007906687.1|  78 -REIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRLE 112
                                       .56666666666666666666666666666666554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                              Spc7 178 eleeeleklqe.aaeelesidk.....eeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkselee 248
                                       e+e+e+++l+  +++ + +idk     e++++l++el+e k ++e + +e ++l ++++el+ek+ e+++++ e+ e
  gi|488600216|ref|YP_007906687.1| 103 EIEKEIRRLEFrQQTAVLTIDKeralvERIAKLKKELEERKYQLE-RHEEFKRLIARIKELKEKVREIHQEMMEFVE 178
                                       556666666542222333344311111568888888888888888.7788888888888888888888888888887 PP

                              Spc7 249 ei 250
                                       e 
  gi|488600216|ref|YP_007906687.1| 179 EA 180
                                       75 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.49
                              Spc7 139 gLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles....id..keeLeelreela 209
                                       +Lk++lee+  +le+ + + ++  + ++el+++++e ++e++e +e+  + ++e+++    id  + e  +++e ++
  gi|488600216|ref|YP_007906687.1| 134 KLKKELEERKYQLERHE-EFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKtfqeIDekRSEADKMHEMFV 209
                                       67788888888887644.34555555555555555555555555555555444444433335544566667777777 PP

                              Spc7 210 elkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                       + k+e ++  +e+ + +++l++l++ i++lk++ ++ + + +++e ++++
  gi|488600216|ref|YP_007906687.1| 210 NSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSRVDREKEELIRKA 259
                                       77777777777777777777777777777766655544444443333332 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.8     0.066        25      34      83 ..       8      54 ..       2      58 .. 0.55
   2 ?    8.9   7.5    0.0048       1.8      25      76 ..      41      96 ..      36     117 .. 0.67
   3 ?    4.1   5.3      0.15        57      34      79 ..     123     171 ..     102     184 .. 0.75
   4 ?    7.2   4.3     0.017       6.4      33      94 ..     181     242 ..     172     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.066
                           BLOC1_2 34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavse 83
                                      e+ ++l++++++l+kk ++ln+   + ++y ++ d+++  v+eL + v+e
  gi|488600216|ref|YP_007906687.1|  8 ERKEQLEKEVQELTKKRDELNK---AAREYADKRDELNSLVRELLAKVKE 54
                                      4445566666666666666666...5555555555555556666555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0048
                           BLOC1_2 25 LeklNeaasekykklkdvaaslekkleklnekyeelq....pylqqidqiekqvte 76
                                      L+ l ++  +k+k++k++ ++ +kk+++l++k+++l+    ++ +++d++ k++++
  gi|488600216|ref|YP_007906687.1| 41 LNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNreidKLYRELDKLRKSIDK 96
                                      66677777889999999999999999999998886550000444455555555554 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.15
                           BLOC1_2  34 ekykklkdvaaslekklekln...ekyeelqpylqqidqiekqvteLee 79 
                                        k  +l +++a+l+k+le+ +   e++ee++ ++ +i++++++v+e+ +
  gi|488600216|ref|YP_007906687.1| 123 DKERALVERIAKLKKELEERKyqlERHEEFKRLIARIKELKEKVREIHQ 171
                                       555667778888888888877444568899999**********998654 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.017
                           BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                        +  +++++  +++ +k ++ ++++e + + +++ d+i++++ +  +  + LD+ +k+L+ak
  gi|488600216|ref|YP_007906687.1| 181 DKYHAEMTKTFQEIDEKRSEADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAK 242
                                       444579*****************************************************988 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  10.4     0.033        13      26      96 ..      12      80 ..       4      82 .. 0.82
   2 ?    7.8   8.5     0.014       5.4      12      94 ..      75     171 ..      70     178 .. 0.61
   3 ?    7.2  10.6     0.022       8.3      19      88 ..     147     221 ..     132     226 .. 0.72
   4 ?    4.7   4.7      0.13        50       9      69 ..     200     262 ..     196     276 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.033
                      Occludin_ELL 26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKkli 96
                                      +l++e++e++kk  eL++  +e++++++e +++++e+l + k++k+  +  e+ k+ ++Lk+k + + + i
  gi|488600216|ref|YP_007906687.1| 12 QLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKE--KRDENNKKAKELKQKKNSLNREI 80
                                      6889999999999999999999999999999999999999999965..55566777788999988777776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.014
                      Occludin_ELL  12 rYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegsk..............eykkieeeilqeykklkkdpe 74 
                                       + ++e +k Y+e  +l +++++  + +se+e+e+++l+ +++              +++k+++e+ ++  +l++++e
  gi|488600216|ref|YP_007906687.1|  75 SLNREIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRLEFRQQtavltidkeralveRIAKLKKELEERKYQLERHEE 151
                                       55677788999999999999999999999998888888777776766653232333333333333333334444555 PP

                      Occludin_ELL  75 yqekkkrceyLkekLshiKk 94 
                                       +++  +r+++Lkek + i +
  gi|488600216|ref|YP_007906687.1| 152 FKRLIARIKELKEKVREIHQ 171
                                       55555555555555555555 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.022
                      Occludin_ELL  19 keYkeYkelhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkk.dpeyqekkkrceyLkek 88 
                                       + ++e+k+l a+++e+++k++e+++e+ e+ e+ +    e++k+ +ei ++ ++  k ++ + + kk+ + ++++
  gi|488600216|ref|YP_007906687.1| 147 ERHEEFKRLIARIKELKEKVREIHQEMMEFVEEADkyhaEMTKTFQEIDEKRSEADKmHEMFVNSKKEADRIHNE 221
                                       579999999999999999999999999888777773444555555555555555555567788888888888876 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.13
                      Occludin_ELL   9 qrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegsk..eykkieeeilqeykkl 69 
                                       ++++  ++F +  ke  ++h+e+ + +k++++L++ +k+lk ++   ++++ +ee++++ k++
  gi|488600216|ref|YP_007906687.1| 200 EADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQArsRVDREKEELIRKAKEI 262
                                       666677788888888899999999999999999988888877766654444444443333332 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   4.2     0.055        21     112     173 ..       4      65 ..       1      68 [. 0.88
   2 ?    6.5   3.3     0.018       6.9     112     171 ..      53     112 ..      36     118 .. 0.74
   3 ?    9.4   3.4    0.0023      0.88      98     172 ..     150     227 ..     128     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.055
                      Bacillus_HBL 112 eeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgk 173
                                       e++++ +++ ++ ++eL+k +++l+k  +++  + del+s +    +++++++++  + ++k
  gi|488600216|ref|YP_007906687.1|   4 EKLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKK 65 
                                       6789999**********************************999999999999887776665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                      Bacillus_HBL 112 eeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlq 171
                                       +ei ++  e ++++keLk+ k++l+ +  ++  ++d+l + +   +  +s++++ei +l+
  gi|488600216|ref|YP_007906687.1|  53 KEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRLE 112
                                       356777777888899999999999999999999999999999999999999999998876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0023
                      Bacillus_HBL  98 kdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdelts...ilagdsgvisqlqneiedlq 171
                                       ++ + l +++++L+e++ ++ +e+ + ++e  k++ +++k  ++ +++ +e+++   +  +++++ + + nei + +
  gi|488600216|ref|YP_007906687.1| 150 EEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKmheMFVNSKKEADRIHNEIIKHR 226
                                       55567889999*****************************9999999986666511155677777777777776655 PP

                      Bacillus_HBL 172 g 172
                                       +
  gi|488600216|ref|YP_007906687.1| 227 K 227
                                       5 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  13.2    0.0037       1.4      27     128 ..       7     111 ..       2     118 .. 0.59
   2 ?    1.2   0.2         1   3.8e+02      30      54 ..     125     149 ..     117     162 .. 0.62
   3 ?    7.6  10.0      0.01       3.9      35     117 ..     157     242 ..     141     254 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0037
                                       CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC CS
                         Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeik...dslrekqkskkdndnvikksskeleeeilrlketidaq 100
                                        + +++++k++++l+++ +e+++  +e  +   e++     l +k k+ k++    +k +kel+++ + l+++id+ 
  gi|488600216|ref|YP_007906687.1|   7 MERKEQLEKEVQELTKKRDELNKAAREYADKRDELNslvRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKL 83 
                                       44555666666666554444444333333333333300033333444444445556677778888888888888888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 101 esnirvLqnvlesneqkiqkLeqdidqk 128
                                        +++ +L++ +++  + ++++e++i  +
  gi|488600216|ref|YP_007906687.1|  84 YRELDKLRKSIDKGGRPLSEIEKEIRRL 111
                                       8888888888888888888888888766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1
                                       CCCCCHHHCCCCCCCCCCCCHHHHH CS
                         Fib_alpha  30 ekdvkkdlekleneleeisnstkea 54 
                                       e+ + ++++kl++elee + + +  
  gi|488600216|ref|YP_007906687.1| 125 ERALVERIAKLKKELEERKYQLERH 149
                                       5666778888888888766544333 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.01
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.............HHCCCHHHHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskel.............eeeilrlketid 98 
                                        ++++l+++++ei+++          +++ ++e+ k +++ +++++++ ++              ++e  r++++i+
  gi|488600216|ref|YP_007906687.1| 157 ARIKELKEKVREIHQE----------MMEFVEEADKYHAEMTKTFQEIDEKRseadkmhemfvnsKKEADRIHNEII 223
                                       3344444444444333..........333333333333333333333333320000000000111223346666666 PP

                                       CCHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqnvlesneqk 117
                                       ++ + ++ L +v+++++ k
  gi|488600216|ref|YP_007906687.1| 224 KHRKDLKDLDKVIKALKAK 242
                                       6666666666666665544 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.7     0.029        11     254     329 ..      18      95 ..       1     119 [. 0.50
   2 ?    7.8   1.6    0.0027         1     239     329 ..     105     202 ..      61     219 .. 0.61
   3 ?    7.6   1.8    0.0031       1.2     191     267 ..     126     224 ..     114     275 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.029
                              FUSC 254 pelaallaelaal..eaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaai 328
                                       +el +  +el ++  e a+  ++l   +++l a+++++++ +++ +  a +l +   +l +e   l+++l++l++ i
  gi|488600216|ref|YP_007906687.1|  18 QELTKKRDELNKAarEYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSI 94 
                                       22222223332223323334445555555555555555555555555666666666666666666666666655555 PP

                              FUSC 329 a 329
                                        
  gi|488600216|ref|YP_007906687.1|  95 D 95 
                                       4 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0027
                              FUSC 239 arllarlraeeaaavpe...laallaelaal....eaaaaaealeaalaalrarlralrraleadadtaalllarla 308
                                       +++ +rl  ++++av +    +al++++a+l    e+++ + + +++ ++l ar+++l++   +  +  ++++++++
  gi|488600216|ref|YP_007906687.1| 105 EKEIRRLEFRQQTAVLTidkERALVERIAKLkkelEERKYQLERHEEFKRLIARIKELKEKVREIHQEMMEFVEEAD 181
                                       33344444333333333333334444444445556556677777777777777777777777767777777777777 PP

                              FUSC 309 ellaelaqllaslraleaaia 329
                                          ae++ + +++++ ++++ 
  gi|488600216|ref|YP_007906687.1| 182 KYHAEMTKTFQEIDEKRSEAD 202
                                       777777777777777666655 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0031
                              FUSC 191 arlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaal. 266
                                       ++l+++i+ l + ++   y  +r     +  +rl +r+ +l   ++++++++ +  +e ++ ++e+ ++++e+++  
  gi|488600216|ref|YP_007906687.1| 126 RALVERIAKLKKELEERKYQLER----HEEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKr 198
                                       55666666666666666665555....66777888888888888888888888888888888888888888888877 PP

                              FUSC 267 .........................e 267
                                                                +
  gi|488600216|ref|YP_007906687.1| 199 seadkmhemfvnskkeadrihneiiK 224
                                       77774444444333333333322222 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5  31.7   2.7e-05      0.01     268     455 ..       8     203 ..       4     207 .. 0.83
   2 ?    2.4  20.3      0.12        47     282     412 ..     133     263 ..     125     276 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
                            AAA_13 268 erkaaLeahFddefeekqerLekliekveskkselleklkavsde....asensafeedkeelkaeaealeeqLkgl 340
                                       erk++Le+   +  ++k ++L+k++ +++ k++el   + ++ ++    ++++ + +++ +elk++++ l+ ++++l
  gi|488600216|ref|YP_007906687.1|   8 ERKEQLEKEVQE-LTKKRDELNKAAREYADKRDELNSLVRELLAKvkeiKEKRDENNKKAKELKQKKNSLNREIDKL 83 
                                       788999999876.89999**********9999887766666666544335555666667999*************** PP

                            AAA_13 341 qraleaKrkepfk.svelesvkakiesikklvaeineliakhN...ekvanleeekeeakkklelhl.veeleseld 412
                                       +r+l++ rk + k    l++++++i +++  ++++  +i k     e++a+l++e ee k +le+h+  ++l + ++
  gi|488600216|ref|YP_007906687.1|  84 YRELDKLRKSIDKgGRPLSEIEKEIRRLEFRQQTAVLTIDKERalvERIAKLKKELEERKYQLERHEeFKRLIARIK 160
                                       *************6667**********************98871114555556666666778999876799999999 PP

                            AAA_13 413 eykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                       e+k+k++++ +++ +  +e+++  ae+ k  +ei e++ +  +
  gi|488600216|ref|YP_007906687.1| 161 ELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADK 203
                                       ************************************9988765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                            AAA_13 282 eekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvel. 357
                                       ++ +++Le+++ ++e+++ e++  ++ + + +++ ++ +++  e+ +ea++  +++++  +++++Kr e  k  e+ 
  gi|488600216|ref|YP_007906687.1| 133 AKLKKELEERKYQLERHE-EFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEMf 208
                                       233333444444444433.2333333334445555556666666666666666666666666666666666655554 PP

                            AAA_13 358 esvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseld 412
                                        ++k+++++i +++ +  +  ++  + ++ l++++++ +++ e+ ++ +  +e+ 
  gi|488600216|ref|YP_007906687.1| 209 VNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSRVDREKEELIRKAKEIY 263
                                       5555555666666666666666666666666666666665555555444444444 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4  27.0   9.8e-05     0.037       8     101 ..       6      99 ..       3     112 .. 0.92
   2 ?    0.2  16.6       2.5   9.5e+02      60     111 ..     130     185 ..     100     193 .. 0.73
   3 ?    3.7  17.7      0.21        79       7      92 ..     186     272 ..     182     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.8e-05
                           DUF4200   8 mfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikk 84 
                                       ++e +e+le+  +e+ ++ ++l+++ +e+ +k+ el+  + ++   +ke+++kr + +kka+e +++k + ++ei k
  gi|488600216|ref|YP_007906687.1|   6 LMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDK 82 
                                       678889999******************************************************************** PP

                           DUF4200  85 lkaeietlkseieklee 101
                                       l  e+++l++ i+k  +
  gi|488600216|ref|YP_007906687.1|  83 LYRELDKLRKSIDKGGR 99 
                                       *********99998655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.5
                           DUF4200  60 kraralkkaeeerklkkekeaeikklkaeietlk....seiekleekleeykkYee 111
                                       +r+  lkk  eerk + e+ +e k+l a i++lk    + ++++ e +ee  kY +
  gi|488600216|ref|YP_007906687.1| 130 ERIAKLKKELEERKYQLERHEEFKRLIARIKELKekvrEIHQEMMEFVEEADKYHA 185
                                       67788899999999999999999999999999995444445566677777777765 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.21
                           DUF4200   7 emfevqealeakkeeiqrleealkqreeelekkeqel...eedllkfdkflkendakraralkkaeeerklkkekea 80 
                                       em ++ +++++k+ e  +++e + + ++e ++  +e+   ++dl  +dk +k  +ak+  a+ ++++e+++  +k++
  gi|488600216|ref|YP_007906687.1| 186 EMTKTFQEIDEKRSEADKMHEMFVNSKKEADRIHNEIikhRKDLKDLDKVIKALKAKQ--ARSRVDREKEELIRKAK 260
                                       8888999***************999999999988776444788999999999988876..66788888888888888 PP

                           DUF4200  81 eikklkaeietl 92 
                                       ei ++ +  e+l
  gi|488600216|ref|YP_007906687.1| 261 EIYEMFKRGEKL 272
                                       887776655555 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  24.9   0.00025     0.097      31     168 ..       3     135 ..       1     137 [. 0.90
   2 ?    0.8  21.1      0.56   2.1e+02      29     171 ..     130     265 ..     111     277 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                             Atg14  31 laklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakl 107
                                       l kl ++ke+l+k+++++ ++++   +l+++++  ++k +el sl+++l ++++e+k+k+++++k+ +e k+k  +l
  gi|488600216|ref|YP_007906687.1|   3 LEKLMERKEQLEKEVQELTKKRD---ELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSL 76 
                                       678999**********8888887...*************************************************** PP

                             Atg14 108 sdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslssktlesrsslcselakl 168
                                       ++++ k +++l++l++++ +   + ++++ ++i+r e   ++   +t+++ + l++ +akl
  gi|488600216|ref|YP_007906687.1|  77 NREIDKLYRELDKLRKSIDKG-GRPLSEIEKEIRRLEFR-QQTAVLTIDKERALVERIAKL 135
                                       *****************9876.56899999999999988.556677777788888888776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.56
                             Atg14  29 erlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkkla 105
                                       er+aklk+e e+ k ++e+ +           + k++ a+++elk +++++++++ e  +  ++  +e+ ++ +++ 
  gi|488600216|ref|YP_007906687.1| 130 ERIAKLKKELEERKYQLERHE-----------EFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEID 195
                                       445555555555444444444...........444466666666666666666666666666666666666666666 PP

                             Atg14 106 klsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslssktles.....rsslcselaklygl 171
                                       +++++  +++ ++   +++ + r +++i k+ +++k  ++++++l+ k + s     + +l++ + ++y++
  gi|488600216|ref|YP_007906687.1| 196 EKRSEA-DKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSrvdreKEELIRKAKEIYEM 265
                                       666664.3444434444444444455555566666655555555555555554444455566666666655 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.6      0.29   1.1e+02      23      68 ..      12      57 ..       2      58 .. 0.71
   2 ?   12.0   8.0   0.00042      0.16      27     115 ..      51     141 ..      38     153 .. 0.77
   3 ?    7.2  10.5     0.012       4.7      41     132 ..     158     240 ..     149     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.29
                            GldM_N 23 kNaalyasleakaeenpekakewlekAkevkkksdelynyiealKe 68
                                      + ++ +++l +k  e ++ a+e ++k +e++ +  el + ++++Ke
  gi|488600216|ref|YP_007906687.1| 12 QLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKE 57
                                      4455566777777777777777888888888888888888888886 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00042
                            GldM_N  27 lyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkdedvgeikakdnldaaselmlaeg.. 101
                                        ++++++k  en++kake+++k + ++++ d+ly  +++l++ i k      e ++ei++ +  ++++ l ++++  
  gi|488600216|ref|YP_007906687.1|  51 KVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRLEFRQQTAVLTIDKEra 127
                                       46889999999999999999999999999999999999999999777766666689999999888888888866645 PP

                            GldM_N 102 ksgkGkeLkkkine 115
                                         ++ ++Lkk+++e
  gi|488600216|ref|YP_007906687.1| 128 LVERIAKLKKELEE 141
                                       55566666666655 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.012
                            GldM_N  41 kakewlekAkevkkksdelynyiealKeeivkeaggkdedvgeikakdnldaaselmlaegksgkGkeLkkkineyr 117
                                       + ke++ek  e++++  e+++  ++  +e++k   + de+      +++ d++ e+++++  ++++  + ++i + r
  gi|488600216|ref|YP_007906687.1| 158 RIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEK------RSEADKMHEMFVNS--KKEADRIHNEIIKHR 226
                                       6788999999999999999999999999999999976555......8999********64..5************** PP

                            GldM_N 118 eellklvndlakdak 132
                                       ++l++l +   k  k
  gi|488600216|ref|YP_007906687.1| 227 KDLKDLDKV-IKALK 240
                                       ***999886.22222 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  18.5     0.021       8.2     129     235 ..      11     117 ..       2     150 .. 0.42
   2 ?    4.3  13.3     0.058        22     130     236 ..     135     253 ..     102     271 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                           DUF4407 129 aaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkak 205
                                       ++l++e++el++++++l+++ ++  +++d+l+  +++ l   k +  +++  + + ake k++ + +++e+++l ++
  gi|488600216|ref|YP_007906687.1|  11 EQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVK-EIKEKRDENNKKAKELKQKKNSLNREIDKLYRE 86 
                                       2244555555555555544444444444444444443333322.222224444555555555555555555555555 PP

                           DUF4407 206 ld...............atarlaalraelaeleaerakeraasqa 235
                                       ld                              e+e+++ + ++q+
  gi|488600216|ref|YP_007906687.1|  87 LDklrksidkggrplseI--------------EKEIRRLEFRQQT 117
                                       555222222544444341..............3333332222222 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.058
                           DUF4407 130 a............ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqlda 194
                                                      +e ++l a+i++l++++++ ++++ +  +ea+k ++ + +++ + +  k  +a++  ++   
  gi|488600216|ref|YP_007906687.1| 135 LkkeleerkyqleRHEEFKRLIARIKELKEKVREIHQEMMEFVEEADK-YHAEMTKTFQEIDEKRSEADKMHEMFVN 210
                                       011122223333345555555555555555555555554444433332.2222233323334444455554444445 PP

                           DUF4407 195 aqaelaelkakld.atarlaalraelaeleaerakeraasqaa 236
                                        ++e + +++++   +++l++l++ ++ l+a++a++r + +++
  gi|488600216|ref|YP_007906687.1| 211 SKKEADRIHNEIIkHRKDLKDLDKVIKALKAKQARSRVDREKE 253
                                       5555555554444777777777777777777777777776664 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  20.5    0.0052         2      30      99 ..       8      84 ..       2      92 .. 0.69
   2 ?    5.6  13.8     0.049        19       8      93 ..     167     258 ..     165     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0052
                                      HHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH.......HHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHH CS
                              OmpH 30 klqaeleakekelqklqeelqkkakklekeekeqe.......lqkkeqelqqkqqqka...qelqkkqqellkpildki 98
                                      +++++le++ +el+k+++el+k+a++   ++k+ e       l +k++e+++k+++++   +el++k++ l ++i dk+
  gi|488600216|ref|YP_007906687.1|  8 ERKEQLEKEVQELTKKRDELNKAARE--YADKRDElnslvreLLAKVKEIKEKRDENNkkaKELKQKKNSLNREI-DKL 83
                                      67888888888888888888877766..44444444446666999999999977777788888999999888863.443 PP

                                      H CS
                              OmpH 99 n 99
                                      +
  gi|488600216|ref|YP_007906687.1| 84 Y 84
                                      3 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.049
                                       HHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.........-HHHHHHHHHHHHHHHHHH CS
                              OmpH   8 qkileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e.......keekeqelqkkeqelqqkq 76 
                                        +i +e+ e+ +  +++ ++ +k  +e+++k+ e +k+ e + +++k++          +++ ++l+k  ++l++kq
  gi|488600216|ref|YP_007906687.1| 167 REIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEMFVNSKKEAdRihneiikHRKDLKDLDKVIKALKAKQ 243
                                       67889999999999999999999999999999999999999997776654377775543344444555555555533 PP

                                       HHHHHHHHHHHHHHHHH CS
                              OmpH  77 qqkaqelqkkqqellkp 93 
                                       ++    + ++++el+++
  gi|488600216|ref|YP_007906687.1| 244 AR--SRVDREKEELIRK 258
                                       33..3444444444442 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  10.5    0.0042       1.6      39     126 ..      11      95 ..       1      99 [. 0.57
   2 ?    5.7  10.2     0.058        22      34     116 ..     145     234 ..     124     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0042
                         AATF-Che1  39 etlkeflesseefeealeeaekalkkll...eslleLreelleqne.ikklaeskeeeekkkskrkrkkkkkeetsl 111
                                       e+l++ +   +e++++ +e+ ka+++     ++l +L  ell++ + ik+    k++e++kk+k+ ++kk++ ++++
  gi|488600216|ref|YP_007906687.1|  11 EQLEKEV---QELTKKRDELNKAAREYAdkrDELNSLVRELLAKVKeIKE----KRDENNKKAKELKQKKNSLNREI 80 
                                       2222222...2333333333333333335559999999999888887774....44344455555555556667788 PP

                         AATF-Che1 112 eelwkeleklekalk 126
                                       ++l++el+kl k+++
  gi|488600216|ref|YP_007906687.1|  81 DKLYRELDKLRKSID 95 
                                       889999999888775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.058
                         AATF-Che1  34 qLpqpetlkeflesseefeealeeaekalkklleslleLreelleqne.ikklaeskeeeekkkskrkrkkk..... 104
                                       qL ++e++k+++ + +e++e+++e+++++++++e+  +   e++++ + i + ++++++ +++  + k++ +     
  gi|488600216|ref|YP_007906687.1| 145 QLERHEEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQeIDEKRSEADKMHEMFVNSKKEADrihne 221
                                       8899999999999999***************************7777766654433333333322222222212222 PP

                         AATF-Che1 105 .kkeetsleelwk 116
                                         k+ ++l++l k
  gi|488600216|ref|YP_007906687.1| 222 iIKHRKDLKDLDK 234
                                       2222223333333 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 ?   10.0   4.2    0.0018      0.69      93     117 ..       5      29 ..       3      32 .. 0.91
   2 ?    7.9   9.0    0.0077       2.9      54     113 ..      36      95 ..      30      97 .. 0.79
   3 ?    3.3  15.4      0.22        82       3     114 ..     101     214 ..      99     218 .. 0.80
   4 ?    4.8   3.2     0.073        28      39      81 ..     212     254 ..     201     275 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0018
                        TPR_MLP1_2  93 sweeqkeelekelselekriedlne 117
                                       ++ e+ke+leke++el+k++++ln+
  gi|488600216|ref|YP_007906687.1|   5 KLMERKEQLEKEVQELTKKRDELNK 29 
                                       6679*******************97 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0077
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekrie 113
                                       +  +el++l  el    +ei+e ++e+++  +el+++++s++++ ++l +el++l+k i+
  gi|488600216|ref|YP_007906687.1|  36 DKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSID 95 
                                       556677777777777778888888888888889999999999999999999999888876 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.22
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqq.kYerelvkh.aedvkelqalreelnelkaeiaelk 77 
                                       l++ e+ei +l+ +++ a  ++ k +  +e  a++ ke ++ kY+ e  +  +  +  +++l+e++ e+ +e+ e+ 
  gi|488600216|ref|YP_007906687.1| 101 LSEIEKEIRRLEFRQQTAVLTIDKERALVERIAKLKKELEErKYQLERHEEfKRLIARIKELKEKVREIHQEMMEFV 177
                                       57788899999999999988888888888888888888764267666554425689999999999999999999999 PP

                        TPR_MLP1_2  78 aeaesakaeleeseesweeqkeelekelselekried 114
                                       +ea++ +ae+ +  ++++e+++e +k  + + +  ++
  gi|488600216|ref|YP_007906687.1| 178 EEADKYHAEMTKTFQEIDEKRSEADKMHEMFVNSKKE 214
                                       9999999999999999999999998888777766666 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.073
                        TPR_MLP1_2  39 keaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                       k+  ++ ++e++kh +d+k+l ++ + l+  +a+ +  +++ e
  gi|488600216|ref|YP_007906687.1| 212 KKEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSRVDREKEE 254
                                       5555667888899999999888888877555554444333333 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  12.6      0.09        34       4      73 ..       4      76 ..       1      78 [. 0.74
   2 ?    7.2  10.3     0.021         8       4      53 ..      46     107 ..      44     157 .. 0.81
   3 ?    9.7   8.5    0.0033       1.3       9      79 ..     151     221 ..     145     234 .. 0.69
   4 ?    1.2   0.8       1.5   5.6e+02       9      50 ..     221     264 ..     214     282 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.09
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...XXXXXXXXXXXXXXXXXXXXX CS
                              YabA  4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...eeeekkekekkkelsegkenL 73
                                      ++l+++ e+le++++el+++ +el+++  e  ++ +eL+   ++l  ++   +e+++++++k kel++ k++L
  gi|488600216|ref|YP_007906687.1|  4 EKLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVkeiKEKRDENNKKAKELKQKKNSL 76
                                      5689999999999999999999999999999999999977766666666555555555555666666666665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH............X CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl............e 53 
                                       +el++k++e++e+ +e +++ +elk++ ++l  e ++L  e +klr+ +            e
  gi|488600216|ref|YP_007906687.1|  46 RELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSIdkggrplseiekE 107
                                       7999*******************************************996666555544440 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlYee 79 
                                       ++++l  +++el+e+++e+++e+ e +ee ++ ++e +k  ++++e+++++++ ++   ++k++  r+++e
  gi|488600216|ref|YP_007906687.1| 151 EFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEMFVNSKKEADRIHNE 221
                                       56667777777777777777777777777777777777777777666666666666666666666666655 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHH CS
                              YabA   9 kleeleeqleelleeleelkeela..elleenaeLeleneklre 50 
                                       ++ +  ++l++l + +++lk++ a  ++  e +eL    +++ e
  gi|488600216|ref|YP_007906687.1| 221 EIIKHRKDLKDLDKVIKALKAKQArsRVDREKEELIRKAKEIYE 264
                                       44444444444444444444332200223333344333333333 PP

>> Dynein_C  Dynein heavy chain C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.8     0.045        17       6      93 ..      12     108 ..       2     116 .. 0.61
   2 ?    9.4   2.7    0.0015      0.56       7      96 ..     128     239 ..     122     249 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.045
                                       HHHHHHHHCCCTTT----..---..CCH--------------..----...............-HHHH...HHHHHH CS
                          Dynein_C   6 ellstllslqpressssg..sggssreekvlelaadileklpelfdlee.aekk....pteyeeplnt...vllqEl 72 
                                       +l +++++l +++++ ++  ++  ++ +++++l++++l+k+ e+ + ++ +++k     ++++++ln+    l +El
  gi|488600216|ref|YP_007906687.1|  12 QLEKEVQELTKKRDELNKaaREYADKRDELNSLVRELLAKVKEI-KEKRdENNKkakeLKQKKNSLNReidKLYREL 87 
                                       44445555555544222222333335679*************83.22212111123456778888888666677788 PP

                                       HHHHHHHHHHHHHHHHHHC-- CS
                          Dynein_C  73 erfnkLleeirrsLkelqkai 93 
                                       +++ k +++  r L+e++k i
  gi|488600216|ref|YP_007906687.1|  88 DKLRKSIDKGGRPLSEIEKEI 108
                                       887777777777777777766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                                       HHHHHHHCCCTTT----..---..CCH..............--------------......----............ CS
                          Dynein_C   7 llstllslqpressssg..sggssree..............kvlelaadileklpe....lfdleeaekk....... 56 
                                       l++++ +l+++ ++ +   +    r+e              kv+e+ ++++e + e    +    ++++k       
  gi|488600216|ref|YP_007906687.1| 128 LVERIAKLKKELEERKYqlE----RHEefkrliarikelkeKVREIHQEMMEFVEEadkyH----AEMTKtfqeide 196
                                       55666655555443222221....1111221222222111144444444444333322221....111113444455 PP

                                       ........-HHHHHHHHHHHHHHHHHHHHHHHHHHHHC----- CS
                          Dynein_C  57 ...pteyeeplntvllqElerfnkLleeirrsLkelqkaikGe 96 
                                          + ++   + +  ++E++r+++ + + r++Lk+l+k+ik +
  gi|488600216|ref|YP_007906687.1| 197 krsEADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKAL 239
                                       55678888899999**************************976 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.9    0.0002     0.075     262     297 ..       9      44 ..       4      46 .. 0.92
   2 ?    6.2   8.6    0.0064       2.4     366     416 ..      45      95 ..      42      97 .. 0.92
   3 ?    0.6  27.2      0.32   1.2e+02     463     594 ..     115     242 ..     100     281 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                              HOOK 262 kceelekevlelqqrneeltslaeEaqaLkDEvDvL 297
                                       + e+lekev+el ++ +el+++a E +  +DE+  L
  gi|488600216|ref|YP_007906687.1|   9 RKEQLEKEVQELTKKRDELNKAAREYADKRDELNSL 44 
                                       779*****************************9876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0064
                              HOOK 366 vqelhkklseeskkadklefelkkleeklealqkekerllaerdaLketne 416
                                       v+el +k++e ++k d  +  +k+l++k ++l++e ++l  e d L++ ++
  gi|488600216|ref|YP_007906687.1|  45 VRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRELDKLRKSID 95 
                                       789999999*9***********************************98876 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.32
                              HOOK 463 hENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkl 539
                                       +   +L + +e+   e++++l+++le+ + ++++ e+ +rl   ri+eL+++v e+++++ e   +a+     + ++
  gi|488600216|ref|YP_007906687.1| 115 QQTAVLTIDKERALVERIAKLKKELEERKYQLERHEEFKRLI-ARIKELKEKVREIHQEMMEFVEEADK---YHAEM 187
                                       444567788888888888888888888888888777666664.68888888888888887775555554...44555 PP

                              HOOK 540 eehleklkevqeelqkkkeqleelepklssnkqkieeleeaLkkkdedlkameer 594
                                       ++ ++++ e  +e  k +e++ + +++++   + i + ++ Lk  d+ +ka+ ++
  gi|488600216|ref|YP_007906687.1| 188 TKTFQEIDEKRSEADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAK 242
                                       5555555555555555555554444444444444444444444444444443332 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  22.1     0.029        11      44     126 ..       5      87 ..       1      96 [. 0.65
   2 ?    1.2   0.2      0.71   2.7e+02       4      43 ..      77     116 ..      75     120 .. 0.80
   3 ?    7.0  29.4     0.012       4.4       8     148 ..     126     252 ..     121     276 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.029
                               ERM  44 raeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeeleeareaee 120
                                       ++ e +e+Le++ +e++++ ++l+++a++ + ++++l+  +re  +++++++e++++ +++a++Lk++    +++  
  gi|488600216|ref|YP_007906687.1|   5 KLMERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREID 81 
                                       44566677777777777777777777777777777777777777777777777777777777777776666555555 PP

                               ERM 121 eakekl 126
                                       +  ++l
  gi|488600216|ref|YP_007906687.1|  82 KLYREL 87 
                                       444444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.71
                               ERM   4 erekreleerLkqlqeeaekaqeaLreseetaelLaekar 43 
                                        re ++l ++L +l++ ++k  + L+e e+++++L+ +++
  gi|488600216|ref|YP_007906687.1|  77 NREIDKLYRELDKLRKSIDKGGRPLSEIEKEIRRLEFRQQ 116
                                       5777888889999999999999999999999999986665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.012
                               ERM   8 releerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerkl 84 
                                       r l er+ +l++e e+++ +L++ ee  +l a          ++L++k +e+++e+ ++ e+a k ++e  k  +++
  gi|488600216|ref|YP_007906687.1| 126 RALVERIAKLKKELEERKYQLERHEEFKRLIA--------RIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEI 194
                                       56667777777777777777777776544444........3457888888888999999999999999999999999 PP

                               ERM  85 reaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpskseseenveesete 148
                                       +e+ +ea +++e   + ++ea+r ++e+++ r+++++   k+ +al++++ +     ++ + ++
  gi|488600216|ref|YP_007906687.1| 195 DEKRSEADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLD-KVIKALKAKQAR-----SRVDREK 252
                                       999999999999998889999999999999988886655.455555554222.....1111222 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.3    0.0041       1.6       3      57 ..       8      62 ..       6      68 .. 0.90
   2 ?    6.2   0.3     0.042        16      21      48 ..      68      95 ..      63     112 .. 0.75
   3 ?    0.2   1.1       3.1   1.2e+03      37      49 ..     129     141 ..     101     151 .. 0.46
   4 ?    1.5   4.4       1.2   4.6e+02      28      55 ..     147     174 ..     130     216 .. 0.81
   5 ?    3.4   0.3      0.32   1.2e+02      22      49 ..     218     245 ..     208     265 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0041
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXX CS
                              SlyX  3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgas 57
                                      er e+LE ++  + +  +eLn++  e +++ d+l   +r+l  ++ke++e+  ++
  gi|488600216|ref|YP_007906687.1|  8 ERKEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDEN 62
                                      78899*******************************************9987654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.042
                                      HHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                              SlyX 21 eLndvvaeqqqqidrlqrqlrllaerlk 48
                                      eL +     +++id+l r+l++l++ + 
  gi|488600216|ref|YP_007906687.1| 68 ELKQKKNSLNREIDKLYRELDKLRKSID 95
                                      5666666778999999999999988774 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3.1
                                       HHHHHHHHHT-XX CS
                              SlyX  37 qrqlrllaerlke 49 
                                        +++++l+++l+e
  gi|488600216|ref|YP_007906687.1| 129 VERIAKLKKELEE 141
                                       2222222222222 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  28 eqqqqidrlqrqlrllaerlkeleessg 55 
                                       e +++ +rl +++++l+e+++e+ ++++
  gi|488600216|ref|YP_007906687.1| 147 ERHEEFKRLIARIKELKEKVREIHQEMM 174
                                       4566777888888888888887777665 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHHHHHHHHHHHT-XX CS
                              SlyX  22 Lndvvaeqqqqidrlqrqlrllaerlke 49 
                                         +++++++++++ l + +++l+ + + 
  gi|488600216|ref|YP_007906687.1| 218 IHNEIIKHRKDLKDLDKVIKALKAKQAR 245
                                       5566777777777777777777766533 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 ?    9.8  13.0    0.0025      0.96       8      88 ..     178     280 ..     172     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0025
                       Uso1_p115_C   8 seaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekek...... 78 
                                       +ea ++  e +k+ +e++++++++ +++++  + +++++a+++ +e++k +k+l++l++ +k+ k k+  +      
  gi|488600216|ref|YP_007906687.1| 178 EEADKYHAEMTKTFQEIDEKRSEADKMHEM--FVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSrvdrek 252
                                       68899999999*******************..888888888888888888887777777777766666544666666 PP

                       Uso1_p115_C  79 ..................qkEldDLLll 88 
                                                         + E +DLLll
  gi|488600216|ref|YP_007906687.1| 253 eelirkakeiyemfkrgeKLETEDLLLL 280
                                       6666667799999999988899999986 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.9    0.0019      0.73      33      64 ..       3      33 ..       2      40 .. 0.92
   2 ?    6.8   8.8     0.015       5.6      17      52 ..      50      85 ..      39      97 .. 0.86
   3 ?    9.1   6.3    0.0029       1.1      14      73 ..     210     271 ..     207     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                                      HHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXX CS
                             DivIC 33 laklkaeneeLeaevkdLksdedyieerARse 64
                                      l+kl +++e+Le+ev++L++ +d + + AR e
  gi|488600216|ref|YP_007906687.1|  3 LEKLMERKEQLEKEVQELTKKRDELNKAAR-E 33
                                      68999*************************.4 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.015
                                      XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC 17 laykqlkqeiaalqaelaklkaeneeLeaevkdLks 52
                                       ++k++k+++++ +++ ++lk+++++L++e+++L  
  gi|488600216|ref|YP_007906687.1| 50 AKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYR 85
                                      57889999************************9965 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0029
                                       XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX..XXXXXXXXXXXXXXXXXXXXX CS
                             DivIC  14 kgllaykqlkqeiaalqaelaklkaeneeLeaevkdLks..dedyieerARselglvkpgEt 73 
                                       ++     ++++ei +  ++l+ l + +++L+a+ ++ +   +++ + ++A++ + + k gE+
  gi|488600216|ref|YP_007906687.1| 210 NSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSRVdrEKEELIRKAKEIYEMFKRGEK 271
                                       6666677899**************************977788999999************96 PP

>> TetR  Bacterial transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.066        25      44      67 ..       3      26 ..       2      58 .. 0.85
   2 ?    4.9   0.1      0.05        19      44      71 ..     152     179 ..     149     180 .. 0.87
   3 ?    2.0   0.8      0.39   1.5e+02       2      27 ..     183     208 ..     182     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.066
                                      HHHHHHC-HHHHHHHHHHHHHHHH CS
                              TetR 44 laellsrnpeLakryrqlleelqa 67
                                      l++l++r ++L+k++++l++++ +
  gi|488600216|ref|YP_007906687.1|  3 LEKLMERKEQLEKEVQELTKKRDE 26
                                      689***************998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.05
                                       HHHHHHC-HHHHHHHHHHHHHHHHHHHH CS
                              TetR  44 laellsrnpeLakryrqlleelqaqlre 71 
                                       +  l++r++eL++++r++++e++++++e
  gi|488600216|ref|YP_007906687.1| 152 FKRLIARIKELKEKVREIHQEMMEFVEE 179
                                       67899*****************999875 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.39
                                       HHHHHHHHT---SSS--SHHHHHHHH CS
                              TetR   2 yeeeleellkppedeslsledlwryl 27 
                                       y++e+++ ++ +++++ +++++++++
  gi|488600216|ref|YP_007906687.1| 183 YHAEMTKTFQEIDEKRSEADKMHEMF 208
                                       99999999999999998888887766 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 ?    5.2   2.8     0.048        18      48      77 ..       4      33 ..       2      44 .. 0.60
   2 ?    5.3   4.1     0.044        17      40      82 ..      45      90 ..      33     109 .. 0.73
   3 ?    5.0   1.6     0.053        20       6      62 ..      89     147 ..      85     154 .. 0.66
   4 ?    6.4   6.6     0.019       7.3      44      90 ..     149     195 ..     134     207 .. 0.59
   5 ?    2.9   1.7      0.24        91      44      98 ..     188     242 ..     184     257 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.048
                              SKA2 48 kkvkeelqaLkeqceellaekkelidkirt 77
                                      +k+ e+ ++L+++++el +++ el +++r 
  gi|488600216|ref|YP_007906687.1|  4 EKLMERKEQLEKEVQELTKKRDELNKAARE 33
                                      566666666666666666666666665554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.044
                              SKA2 40 pvkLlerlkkvkeelqaLkeqceellaekkel...idkirttlvan 82
                                      +++Ll+++k++ke+  + +++++el ++k  l   idk+ + l + 
  gi|488600216|ref|YP_007906687.1| 45 VRELLAKVKEIKEKRDENNKKAKELKQKKNSLnreIDKLYRELDKL 90
                                      578***********************99996511144444444444 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.053
                              SKA2   6 klealFqkaesdLdyvq...hrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqce 62 
                                       kl++  +k  + L  ++   +rLe++ q+++       + L+er++k+k+el++ k q+e
  gi|488600216|ref|YP_007906687.1|  89 KLRKSIDKGGRPLSEIEkeiRRLEFRQQTAVLTI-DKERALVERIAKLKKELEERKYQLE 147
                                       5555555555555555522246666655555554.57899***********998877776 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.019
                              SKA2  44 lerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLq 90 
                                       +e++k++ +++++Lke+++e+ +e  e ++++ +  +++++++q++ 
  gi|488600216|ref|YP_007906687.1| 149 HEEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEID 195
                                       34556666666666666666666666666666666666666666654 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.24
                              SKA2  44 lerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa.elppl 98 
                                        + ++++ e+ ++  + + e+  + k+ +d+i++ +++ r+ l++L + +  l+++
  gi|488600216|ref|YP_007906687.1| 188 TKTFQEIDEKRSEADKMH-EMFVNSKKEADRIHNEIIKHRKDLKDLDKVIkALKAK 242
                                       555666666666655544.4555555557999999999999999999888633333 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  13.0      0.42   1.6e+02       7      63 ..      40      95 ..       1     117 [. 0.56
   2 ?    6.3   5.4     0.039        15      15      71 ..     125     175 ..     112     182 .. 0.48
   3 ?    8.6   5.7    0.0078         3      10      82 ..     154     235 ..     150     241 .. 0.61
   4 ?    5.6   2.3     0.068        26      17      68 ..     217     268 ..     213     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.42
                           DUF2203  7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeie 63
                                      e n+l+ +l  +++e++++r+e +++++el+++k++ ++ e  +l +el++l+++i+
  gi|488600216|ref|YP_007906687.1| 40 ELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNR-EIDKLYRELDKLRKSID 95
                                      334444444444444444444444444444444444332.24444444444444444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.039
                           DUF2203  15 lkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeiee 71 
                                        + l+e++++l+kelee++ +le++++      +++l a+++el+++++e+ +e+ e
  gi|488600216|ref|YP_007906687.1| 125 ERALVERIAKLKKELEERKYQLERHEE------FKRLIARIKELKEKVREIHQEMME 175
                                       344444445555555544444444443......444555555555555555554443 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0078
                           DUF2203  10 alLpllkelleelralrkeleeleeeleeakaeaekse.........aaeleaeleeleaeieelveeieelGvevk 77 
                                       +l+ ++kel e++r+  +e+ e +ee ++ +ae++k+          a ++++ + + ++e++++ +ei ++  ++k
  gi|488600216|ref|YP_007906687.1| 154 RLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFqeidekrseADKMHEMFVNSKKEADRIHNEIIKHRKDLK 230
                                       55555555555555555555555554444444433222444444466777777778888888888888888888888 PP

                           DUF2203  78 dleag 82 
                                       dl+++
  gi|488600216|ref|YP_007906687.1| 231 DLDKV 235
                                       88865 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.068
                           DUF2203  17 elleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelvee 68 
                                       ++ +e+++ rk+l++l + +++ ka++++s   ++++el + ++ei e++++
  gi|488600216|ref|YP_007906687.1| 217 RIHNEIIKHRKDLKDLDKVIKALKAKQARSRVDREKEELIRKAKEIYEMFKR 268
                                       677899999*********9999999999888888888888888888888776 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  14.8   0.00072      0.27     237     344 ..      10     111 ..       2     122 .. 0.54
   2 ?    2.0  15.0      0.21        81     257     348 ..     128     222 ..     102     225 .. 0.78
   3 ?    0.3   3.9      0.69   2.6e+02     226     299 ..     194     269 ..     192     281 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00072
                             IFT57 237 eeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeisee 313
                                       +e+l++  ++l+k  ++++k+  +   +   lns ++ell++ +e +e+ +e ++k k+l+++ ++l+re +++  e
  gi|488600216|ref|YP_007906687.1|  10 KEQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREIDKLYRE 86 
                                       23333333445555555555555555555555555555555555555555555555555555555555555555555 PP

                             IFT57 314 lekvkqemeergssmtDgsplvkikkaltkl 344
                                       l+k+ + +++       g+pl +i k + +l
  gi|488600216|ref|YP_007906687.1|  87 LDKLRKSIDKG------GRPLSEIEKEIRRL 111
                                       55555555543......56666666666665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.21
                             IFT57 257 tlekiesrEkylnsqleel..lqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDg 331
                                        +e+i +  k l+++  +l   +e++ + ++++e+kek++++ ++++e  +e ++   e++k+ qe++e+ s++   
  gi|488600216|ref|YP_007906687.1| 128 LVERIAKLKKELEERKYQLerHEEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKM 204
                                       468999999999765443311567**********************************************9987665 PP

                             IFT57 332 .splvkikkaltklkkEi 348
                                        +  v+ kk  +++ +Ei
  gi|488600216|ref|YP_007906687.1| 205 hEMFVNSKKEADRIHNEI 222
                                       244578888888888888 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.69
                             IFT57 226 leqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqe..yreaqeelsevkekykqlseg 299
                                       +++ ++  +++ e + ++k++ +++h++i k  + ++  +k +     ++ +    re++e + ++ke y++ ++g
  gi|488600216|ref|YP_007906687.1| 194 IDEKRSEADKMHEMFVNSKKEADRIHNEIIKHRKDLKDLDKVIKALKAKQARSrvDREKEELIRKAKEIYEMFKRG 269
                                       5556666778888888999999999999999999999999988654333332222455555566666666666555 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  13.2    0.0023      0.87      40     111 ..       3      78 ..       2      94 .. 0.73
   2 ?    1.4  11.5       1.1   4.3e+02      45     103 ..     123     180 ..      67     200 .. 0.56
   3 ?    1.4  10.4       1.1   4.3e+02      46     104 ..     124     181 ..     121     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0023
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--.....SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHH.HHHH CS
                              FlgN  40 Leelleekqellekleqleqkrakllaelgls.....aeeatlsellakeedeelkelwqelkelleelkel.nelN 110
                                       Le+l+e+k++l +++++l +kr++l +++ +      + +  ++ella  + +e+ke+++e  + ++elk++ n+lN
  gi|488600216|ref|YP_007906687.1|   3 LEKLMERKEQLEKEVQELTKKRDELNKAAREYadkrdELNSLVRELLA--KVKEIKEKRDENNKKAKELKQKkNSLN 77 
                                       8999********************999999997444444444444444..777777777777777777766513444 PP

                                       H CS
                              FlgN 111 g 111
                                       +
  gi|488600216|ref|YP_007906687.1|  78 R 78 
                                       3 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHH CS
                              FlgN  45 eekqellekleqleqkrakllaelglsaeeatlsellak..eedeelkelwqelkelleel 103
                                       +++ +l+e++++l++++++   +l+     ++ ++l+a+  e +e+++e+ qe  e +ee+
  gi|488600216|ref|YP_007906687.1| 123 DKERALVERIAKLKKELEERKYQLERH---EEFKRLIARikELKEKVREIHQEMMEFVEEA 180
                                       334444444444444444444444333...3444444444444444444444444444443 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHHH CS
                              FlgN  46 ekqellekleqleqkrakllaelglsaeeatlsellak..eedeelkelwqelkelleelk 104
                                       ++ +l+e++++l++++++   +l+     ++ ++l+a+  e +e+++e+ qe  e +ee+ 
  gi|488600216|ref|YP_007906687.1| 124 KERALVERIAKLKKELEERKYQLERH---EEFKRLIARikELKEKVREIHQEMMEFVEEAD 181
                                       55556666666666665555555555...55555555555555555555555555555544 PP

>> Desmo_N  Viral Desmoplakin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       6.5   2.5e+03      30      72 ..      11      53 ..       5      68 .. 0.72
   2 ?    7.6   0.2     0.013         5      28      60 ..     158     190 ..     150     203 .. 0.85
   3 ?    1.7   0.1       0.9   3.4e+02      32      62 ..     225     255 ..     204     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 6.5
                           Desmo_N 30 edyeeklreihkvvlilkPslkknsaemdalpllimqflsdlk 72
                                      e+ e++++e+ k    l+ ++++ + + d l+ l+ ++l+++k
  gi|488600216|ref|YP_007906687.1| 11 EQLEKEVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVK 53
                                      6778888888888888888888888888888888888887654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.013
                           Desmo_N  28 tledyeeklreihkvvlilkPslkknsaemdal 60 
                                        +++  ek+reih+ ++ +   ++k  aem+  
  gi|488600216|ref|YP_007906687.1| 158 RIKELKEKVREIHQEMMEFVEEADKYHAEMTKT 190
                                       4567789**********************9965 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.9
                           Desmo_N  32 yeeklreihkvvlilkPslkknsaemdalpl 62 
                                       + + l+++ kv+ +lk    +  ++ + ++l
  gi|488600216|ref|YP_007906687.1| 225 HRKDLKDLDKVIKALKAKQARSRVDREKEEL 255
                                       5677889999999998877777777666554 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  29.3    0.0028       1.1      70     220 ..       8     153 ..       2     154 .. 0.77
   2 ?    1.1  19.1      0.25        95      47     141 ..     149     243 ..     143     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0028
                               MAD  70 alreqiEl.arlkkknlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllk 145
                                       + +eq+E+ ++ ++k+ ++lnk+++e  +k  e++ + ++l  +++e k++  +++ + +e ++++++l+++ d   
  gi|488600216|ref|YP_007906687.1|   8 ERKEQLEKeVQELTKKRDELNKAAREYADKRDELNSLVRELLAKVKEIKEKRDENNKKAKELKQKKNSLNREID--- 81 
                                       34555554145567888889999999999999999999999888888888888888888888888888877665... PP

                               MAD 146 kklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddslivknskselaripelekelerlreenkklnelk 220
                                       k + el++l+++ +k  + l+e e+ i+ Lef+   q+   l + + ++ ++ri++l+kele+ +++ ++ +e k
  gi|488600216|ref|YP_007906687.1|  82 KLYRELDKLRKSIDKGGRPLSEIEKEIRRLEFR---QQTAVLTIDKERALVERIAKLKKELEERKYQLERHEEFK 153
                                       456678888899999999999999999999997...445566777778888*************99998887765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.25
                               MAD  47 sdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekq 123
                                       ++  + l +rik+l+++  e ++++ e +E+a +++  ++++ ++  ek s+  +++e+  + k+e  + +++i k 
  gi|488600216|ref|YP_007906687.1| 149 HEEFKRLIARIKELKEKVREIHQEMMEFVEEADKYHAEMTKTFQEIDEKRSEADKMHEMFVNSKKEADRIHNEIIKH 225
                                       34455666777777777777777777777777777777777777788888888999999999999999999999999 PP

                               MAD 124 elelsekeseleelqerl 141
                                         +l+  ++ +++l+ ++
  gi|488600216|ref|YP_007906687.1| 226 RKDLKDLDKVIKALKAKQ 243
                                       888888777666665433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4004  (0.223325); expected 358.6 (0.02)
Passed bias filter:                      865  (0.0482459); expected 358.6 (0.02)
Passed Vit filter:                       309  (0.0172346); expected 17.9 (0.001)
Passed Fwd filter:                       208  (0.0116013); 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: 2.69u 0.41s 00:00:03.10 Elapsed: 00:00:00.71
# Mc/sec: 1215.37
//
Query:       gi|488600217|ref|YP_007906688.1|  [L=189]
Description: hypothetical protein Asulf_00677 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   49.8   0.3      2e-13   49.8   0.3    2.3  2  DUF1648   Protein of unknown function (DUF1648)
  ------ inclusion threshold ------
      0.047   13.7   0.7      0.047   13.7   0.7    2.6  3  DUF997    Protein of unknown function (DUF997)
       0.12   12.7   2.2       0.23   11.8   0.6    2.1  2  DUF4149   Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> DUF1648  Protein of unknown function (DUF1648)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.3   3.3e-17     2e-13       2      47 ..      30      74 ..      29      75 .. 0.94
   2 ?   -3.2   0.7       1.2     7e+03       6      13 ..     167     174 ..     163     178 .. 0.51

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 3.3e-17
                           DUF1648  2 llllplvvglllypkLPdqiPtHfnasGepDgygsKlfalfllPll 47
                                      ll+ ++v+g+ +y  LPd++PtHf+a+G p++yg K ++ ++lPl 
  gi|488600217|ref|YP_007906688.1| 30 LLITMWVLGIHAYLTLPDMVPTHFDAQGRPTSYGKK-EVYLILPLA 74
                                      78999999****************************.*******85 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                           DUF1648   6 plvvglll 13 
                                       p++v l++
  gi|488600217|ref|YP_007906688.1| 167 PFAVILIF 174
                                       55554443 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.12     7e+02       9      25 ..      26      42 ..      20      51 .. 0.54
   2 ?   -1.0   0.1      0.31   1.9e+03      21      44 ..      84     106 ..      65     108 .. 0.65
   3 ?   13.7   0.7   7.8e-06     0.047      14      70 ..     133     185 ..     121     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                            DUF997  9 tllltllyflwwllfaY 25
                                      +ll++l+++ +  + aY
  gi|488600217|ref|YP_007906688.1| 26 SLLMLLITMWVLGIHAY 42
                                      33333333333344555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.31
                            DUF997  21 llfaYglgskeveey.yilglPlWf 44 
                                       +++ Y +     ++y y+++lP+ f
  gi|488600217|ref|YP_007906688.1|  84 VITRYRFT--LINKYpYLINLPAFF 106
                                       44444444..334677888888766 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 7.8e-06
                            DUF997  14 llyflwwllfaYglgskeveeyyilglPlWfflscillpilfivlvillvkfvFkdi 70 
                                       + + +++ll+ +g+ ++         lP Wf l  +++p+ +i++  + ++++ ++i
  gi|488600217|ref|YP_007906688.1| 133 VTLSAYMLLLEWGIYEGA----LHGSLPSWFNLTAVITPFAVILIFLYYMRKLSREI 185
                                       444566666667776555....7778*************999999999988876665 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.23   1.4e+03      47      59 ..      24      36 ..      12      52 .. 0.60
   2 ?   11.8   0.6   3.9e-05      0.23      18      90 ..     102     179 ..      80     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.23
                           DUF4149 47 alsvlllltevav 59
                                      als+l+ll ++ v
  gi|488600217|ref|YP_007906688.1| 24 ALSLLMLLITMWV 36
                                      4444444444333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.9e-05
                           DUF4149  18 apvlfrsL...prhqfgelqsklFplyfglglalsvlllltevavg..seklaseellqlllllvvllltllnafyl 89 
                                        p  f+++   p +q g  +++ F ++  lg+ ls+++ll+e   +    + +   ++ l ++++ ++++l++ +y 
  gi|488600217|ref|YP_007906688.1| 102 LPAFFANIhriPSEQRGLWVNRYFDALLALGVTLSAYMLLLEWGIYegALHGSLPSWFNLTAVITPFAVILIFLYYM 178
                                       67788885555*******************************98884322233333444444444444555544444 PP

                           DUF4149  90 e 90 
                                        
  gi|488600217|ref|YP_007906688.1| 179 R 179
                                       3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1197.33
//
Query:       gi|488600218|ref|YP_007906689.1|  [L=869]
Description: valyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.1e-142  476.4   3.3   1.7e-141  472.5   3.3    2.2  1  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    6.1e-41  139.9   0.4    1.4e-40  138.8   0.4    1.6  1  Anticodon_1     Anticodon-binding domain of tRNA
    1.2e-22   80.2   0.4    3.4e-13   49.1   0.0    3.1  3  tRNA-synt_1g    tRNA synthetases class I (M)
    4.8e-07   29.4   0.0     0.0011   18.4   0.0    2.5  3  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    0.00021   20.3   0.1       0.26   10.2   0.0    2.5  2  tRNA-synt_1f    tRNA synthetases class I (K)
    0.00051   19.6   0.0     0.0011   18.5   0.0    1.6  1  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
     0.0011   18.9   0.7       0.23   11.5   0.1    3.2  3  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.014   15.1   1.1       0.91    9.3   0.1    2.6  2  Zn_Tnp_IS1      InsA N-terminal domain
      0.087   12.7   0.7       0.32   10.9   0.7    2.0  1  CAP18_C         LPS binding domain of CAP18 (C terminal)
      0.095   12.5   0.2       0.21   11.4   0.2    1.5  1  Secapin         Honey bee peptides
       0.23   11.6   5.5       0.22   11.7   0.4    2.9  2  Zn-ribbon_8     Zinc ribbon domain
        0.5    9.9   1.9         59    3.2   0.1    3.6  3  Mu-like_Com     Mu-like prophage protein Com
       0.83    9.8  10.4        9.8    6.3   0.3    4.4  4  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.85    9.1   9.3        2.9    7.4   0.1    4.1  4  zf-ribbon_3     zinc-ribbon domain
          1    8.7   3.2         18    4.7   0.1    3.5  3  zf-TFIIB        Transcription factor zinc-finger
        1.3    8.9   3.5         11    5.9   0.0    3.2  3  zinc_ribbon_5   zinc-ribbon domain
        3.8    7.5   5.3         14    5.7   0.0    3.5  4  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.5   3.3  1.6e-144  1.7e-141       1     599 [.      16     555 ..      16     558 .. 0.95

  Alignments for each domain:
  == domain 1  score: 472.5 bits;  conditional E-value: 1.6e-144
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       k+++ W+e+ ++      + +k+++i+  +PPy tGs HiG+ l+    d++ rykrm+G+ev +  GwD++Gl++e
  gi|488600218|ref|YP_007906689.1|  16 KWLNLWDESMYYFDW---NSRKPHYIIDTPPPYPTGSFHIGNTLNWCYIDFIARYKRMRGYEVMFPQGWDCHGLPTE 89 
                                       58999****999887...7889******************************************************* PP

                       tRNA-synt_1  78 akvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                        kve+k g++++    ++ r+ fr+ + e+ +  ++++r+++kr+G s+D+++ey+T+++e+ + ++  fvr++dkg
  gi|488600218|ref|YP_007906689.1|  90 VKVEEKHGISKN----DVPRDVFRKMCVEFTEGNIKKMRETMKRMGFSIDWSNEYITMYPEYFKKTQISFVRMYDKG 162
                                       ******999886....************************************************************* PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitke 231
                                       liyr+ ++v ++++++t+++ +E+eyk  k +l +++f+    e   +viaTT+Pe +++ +a+av+p+        
  gi|488600218|ref|YP_007906689.1| 163 LIYRAYHPVIHCPRCQTTIALAEIEYKSGKTMLNYIKFD----E--DVVIATTRPELIPACVALAVHPD-------- 225
                                       *************************************96....4..48*********************........ PP

                       tRNA-synt_1 232 klilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                                              der+k+++gkev+ p ++ k+++iad+ vd e+GtG+V i    d +D +  kk
  gi|488600218|ref|YP_007906689.1| 226 -----------------------DERYKNIVGKEVTVPTTEYKVRVIADEEVDPEFGTGIVMICTFGDRQDVKWWKK 279
                                       .......................9***************************************************** PP

                       tRNA-synt_1 309 ynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvk 385
                                       ++le+ +ild dg+l+e+a+ ++gl++ +ar+k++e+l+++g+ lk+e+i+h+v++c+r k+p++  a eqWfvr++
  gi|488600218|ref|YP_007906689.1| 280 HDLELRMILDRDGRLNEKAGRYQGLSIREARQKILEDLEKEGRVLKKEEIDHNVGTCWRCKTPVEIIAEEQWFVRIE 356
                                       ****************************************************************************9 PP

                       tRNA-synt_1 386 eladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeae 461
                                       +  d +l+  +k++++p+   +r   w+e ++ dW+iSRqr+  ++ip+++ k+ +e+ v   ++e+        + 
  gi|488600218|ref|YP_007906689.1| 357 H--DRILDGARKIKWIPEHMFSRLVGWVEGMEwDWVISRQRIFATPIPAWYCKKCGEILV--AKEEWLP-----VDP 424
                                       5..99************************9877***************************..3344444.....222 PP

                       tRNA-synt_1 462 kkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlills 538
                                       +k+  k       ++  e+  ++dvlD+W +S+ +p ++ g+p e     +k +p+ +  +G Diir W    il s
  gi|488600218|ref|YP_007906689.1| 425 TKDYPKIPCP--SCGSVEFVGEDDVLDTWMDSSITPLAITGWPYE-----HKEYPTHLRPQGHDIIRTWAFYTILRS 494
                                       2232222222..4577799*************************9.....4579*********************** PP

                       tRNA-synt_1 539 laltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdi 599
                                       lal ++ P+ e++++g+v+ e+GrKmSKslgN+i+p++vi+kygadalR + ++ ++g+d+
  gi|488600218|ref|YP_007906689.1| 495 LALADEIPWYEIVINGMVLGEDGRKMSKSLGNIISPEEVIEKYGADALRQWAASGSTGSDV 555
                                       *****************************************************99999987 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 !  138.8   0.4   1.3e-43   1.4e-40       1     149 [.     600     749 ..     600     753 .. 0.90

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 1.3e-43
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       drwils+ln++++++ +++++yrf++ ++a+  f w dl+d yle+vk+rlys s+e+k   a+++l++ +++l+r+
  gi|488600218|ref|YP_007906689.1| 600 DRWILSKLNRVIEKAINSMDSYRFDETLKAIRGFAWYDLADDYLEIVKSRLYSGSEEEK-VgAKYALYKTISALIRM 675
                                       9****************************************************999888.6699************* PP

                       Anticodon_1  77 laPfmPfitEelwqr...eeeel.gkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpssel 148
                                       laPf+Pf++Ee+w+           ++es++++++pe ++e+ ++++ ee  el+++i++ irkl+ + +++ +++l
  gi|488600218|ref|YP_007906689.1| 676 LAPFTPFLAEECWNIfckA---TeSGNESVHKQSYPEvEEEFIDDDA-EERGELMRRIISEIRKLKHDRNMALNAPL 748
                                       *************557631...22578*********97776667777.89************************996 PP

                       Anticodon_1 149 k 149
                                       k
  gi|488600218|ref|YP_007906689.1| 749 K 749
                                       6 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 !   49.1   0.0   3.3e-16   3.4e-13       2     136 ..      38     187 ..      37     195 .. 0.77
   2 ?   -1.2   0.0      0.64   6.7e+02     168     238 ..     335     402 ..     309     416 .. 0.64
   3 !   27.4   0.0   1.2e-09   1.3e-06     302     373 ..     494     564 ..     443     569 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3.3e-16
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH.TTS-....HH........H CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek.egvt....pe........e 65 
                                       ++ t+ pY++g+ H+G+ l+    D +aRykr+rg+ev+f  g D hG p+e+k e+ +g++    p+        e
  gi|488600218|ref|YP_007906689.1|  38 IIDTPPPYPTGSFHIGNTLNWCYIDFIARYKRMRGYEVMFPQGWDCHGLPTEVKVEEkHGISkndvPRdvfrkmcvE 114
                                       789999************************************************87526787222233111111112 PP

                                       HHHHHHHHHHHHHHH..TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                      tRNA-synt_1g  66 lvekvheeikelfkk..lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                       ++e + ++++e++k+  ++i +++ + t   e  + +q  f ++++kgliy+    ++ cp+++++++  ++e
  gi|488600218|ref|YP_007906689.1| 115 FTEGNIKKMRETMKRmgFSIDWSNEYITMYPEYFKKTQISFVRMYDKGLIYRAYHPVIHCPRCQTTIALAEIE 187
                                       233344567778887334556666667888899999999999*********************9988766665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.64
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       ++  +++  e+  +e++f ++++  +++ +   ++ k  +e++ + +  w++    d+ isr+  ++ p+P
  gi|488600218|ref|YP_007906689.1| 335 TCWRCKTPVEIIAEEQWFVRIEH--DRILDGA-RKIKWIPEHMFSRLVGWVEGMEWDWVISRQRIFATPIP 402
                                       46666666677777777777653..4444444.33334566677777788887777899999888888888 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 1.2e-09
                                       HHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1g 302 aillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfve 373
                                       ++ l+ e+   + v+    l  +g+K+SkS g+++ ++e++e++ ad+lR + aa++++ +D+ f+w+++v 
  gi|488600218|ref|YP_007906689.1| 494 SLALADEIPWYEIVINGMVLGEDGRKMSKSLGNIISPEEVIEKYGADALRQW-AASGSTGSDVIFTWKEVVS 564
                                       344445566666666666677899**************************87.5678899********9986 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0015       1.5      22      52 ..      49      79 ..      45     125 .. 0.94
   2 !   18.4   0.0     1e-06    0.0011     231     282 ..     496     548 ..     480     565 .. 0.79
   3 ?   -3.4   0.0       4.6   4.9e+03      83     126 ..     785     832 ..     758     843 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                                      --BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                      tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvq 52
                                        h+G++ +   +D ++r+ +++gY+v+f q
  gi|488600218|ref|YP_007906689.1| 49 SFHIGNTLNWCYIDFIARYKRMRGYEVMFPQ 79
                                      57**************************965 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1e-06
                                       HHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                      tRNA-synt_1e 231 aafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                       a+ d  ++ ++ +   +l  +g+kmsksL+n+i+ ++v++k+ + +lR   +s
  gi|488600218|ref|YP_007906689.1| 496 ALADeIPWYEIVINGMVLGEDGRKMSKSLGNIISPEEVIEKYGADALRQWAAS 548
                                       5555345555555444556789**************************87665 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.6
                                       HHHHHHHTT----SB--BGGGGHHHHHHH....HHHHHHTTSEEE-TT CS
                      tRNA-synt_1e  83 fkkdleaLnvlkptleprvsekvdeiiel....vekliekgyaYavsd 126
                                        k+   +  +  p+++ ++ e ++++  +    + kl+e+gy  +v+ 
  gi|488600218|ref|YP_007906689.1| 785 IKQLKPKYSIIGPKFRDKAKEIIKAVNSFgekeMRKLLEEGYEIEVNG 832
                                       444444555666666666666666666653323445666676666663 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 !    7.6   0.0    0.0015       1.6      33     145 ..      46     154 ..      28     204 .. 0.79
   2 !   10.2   0.0   0.00025      0.26     273     312 ..     511     550 ..     464     582 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0015
                      tRNA-synt_1f  33 pSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenlpekllekylgkpltsiPdp.kgk.hesy 107
                                       p G+ HiGn  +    d++ar  r rg ev +   +D       +p ++    +e+  g   +++P   + k + ++
  gi|488600218|ref|YP_007906689.1|  46 PTGSFHIGNTLNWCYIDFIARYKRMRGYEVMFPQGWDC----HGLPTEVK---VEEKHGISKNDVPRDvFRKmCVEF 115
                                       88999****************99999999888888874....34555554...5577799999***752444699** PP

                      tRNA-synt_1f 108 aehfnaelvesLdelgievefisat.elYksglydeaik 145
                                        e + ++++e+++++g+ +++ ++   +Y +   + +i 
  gi|488600218|ref|YP_007906689.1| 116 TEGNIKKMRETMKRMGFSIDWSNEYiTMYPEYFKKTQIS 154
                                       ********************9876526676666555555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                      tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlrflilrrk 312
                                       ++l + g+kms+S Gn++++e+++e +  + lr   ++  
  gi|488600218|ref|YP_007906689.1| 511 MVLGEDGRKMSKSLGNIISPEEVIEKYGADALRQWAASGS 550
                                       66778889*****************999999987766655 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 !   18.5   0.0     1e-06    0.0011      86     145 ..     234     293 ..     200     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1e-06
                     tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpede 145
                                       g +++ P t+ k+ +   + v  e+gtg vm +   d++D +++kk++l+++ ++  +++
  gi|488600218|ref|YP_007906689.1| 234 GKEVTVPTTEYKVRVIADEEVDPEFGTGIVMICTFGDRQDVKWWKKHDLELRMILDRDGR 293
                                       678999**********************************************99986553 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.21   2.2e+02      29      38 ..     172     181 ..     153     187 .. 0.75
   2 ?    1.3   0.0      0.33   3.4e+02      28      38 ..     333     343 ..     316     350 .. 0.65
   3 !   11.5   0.1   0.00022      0.23      12      36 ..     403     438 ..     397     443 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.21
                               DZR  29 drCpsCgekv 38 
                                       ++Cp+C++ +
  gi|488600218|ref|YP_007906689.1| 172 IHCPRCQTTI 181
                                       5677776654 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.33
                               DZR  28 edrCpsCgekv 38 
                                         +C++C+++v
  gi|488600218|ref|YP_007906689.1| 333 VGTCWRCKTPV 343
                                       34566665554 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00022
                               DZR  12 arfCseCgtklkavaa...........edrCpsCge 36 
                                       a +C++Cg+ l a ++           ++ CpsCg+
  gi|488600218|ref|YP_007906689.1| 403 AWYCKKCGEILVAKEEwlpvdptkdypKIPCPSCGS 438
                                       679********87777******************97 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00086      0.91       6      14 ..     172     180 ..     171     192 .. 0.91
   2 ?    3.7   0.1     0.047        50       6      15 ..     431     440 ..     430     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00086
                        Zn_Tnp_IS1   6 ihCPrCsst 14 
                                       ihCPrC+ t
  gi|488600218|ref|YP_007906689.1| 172 IHCPRCQTT 180
                                       9******86 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.047
                        Zn_Tnp_IS1   6 ihCPrCsstd 15 
                                       i CP+C s +
  gi|488600218|ref|YP_007906689.1| 431 IPCPSCGSVE 440
                                       88****9988 PP

>> CAP18_C  LPS binding domain of CAP18 (C terminal)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00031      0.32       3      17 ..     305     319 ..     303     322 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHHHHH CS
                           CAP18_C   3 lLrkggeKIgEKLkk 17 
                                       ++r++++KI E L+k
  gi|488600218|ref|YP_007906689.1| 305 SIREARQKILEDLEK 319
                                       69************9 PP

>> Secapin  Honey bee peptides
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2    0.0002      0.21      18      38 ..      34      54 ..      32      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                           Secapin 18 ePrYiidvPPrCPPGskfvkn 38
                                       P Yiid PP  P Gs  + n
  gi|488600218|ref|YP_007906689.1| 34 KPHYIIDTPPPYPTGSFHIGN 54
                                      69**************98877 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.36   3.8e+02      25      34 ..     170     179 ..     165     182 .. 0.75
   2 ?   11.7   0.4   0.00021      0.22       7      35 ..     405     440 ..     400     442 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.36
                       Zn-ribbon_8  25 pltaCPeCgs 34 
                                       p ++CP+C+ 
  gi|488600218|ref|YP_007906689.1| 170 PVIHCPRCQT 179
                                       4567**9976 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00021
                       Zn-ribbon_8   7 rCeeCghefe......vlqsisdapltaCPeCgs.e 35 
                                        C++Cg+         ++ + +d p+++CP+Cgs e
  gi|488600218|ref|YP_007906689.1| 405 YCKKCGEILVakeewlPVDPTKDYPKIPCPSCGSvE 440
                                       59****8877888888888888999999*****955 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 ?    3.2   0.1     0.056        59      25      32 ..     172     179 ..     167     185 .. 0.87
   2 ?    2.2   0.1      0.12   1.2e+02      24      35 ..     430     441 ..     406     446 .. 0.79
   3 ?    0.8   0.0      0.33   3.4e+02      33      44 ..     580     591 ..     579     599 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.056
                       Mu-like_Com  25 iKCPRCGt 32 
                                       i CPRC t
  gi|488600218|ref|YP_007906689.1| 172 IHCPRCQT 179
                                       99****88 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                       Mu-like_Com  24 tiKCPRCGtLnH 35 
                                       +i CP CG +  
  gi|488600218|ref|YP_007906689.1| 430 KIPCPSCGSVEF 441
                                       799*****9765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.33
                       Mu-like_Com  33 LnHlkaesldae 44 
                                       +nHlk+  +d+ 
  gi|488600218|ref|YP_007906689.1| 580 VNHLKGYKPDSK 591
                                       6******99996 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 ?    2.5   0.1      0.15   1.6e+02       3      13 ..     173     183 ..     172     187 .. 0.75
   2 ?    2.4   0.0      0.16   1.7e+02      10      26 .]     323     339 ..     321     339 .. 0.89
   3 ?    6.3   0.3    0.0093       9.8       3      15 ..     405     417 ..     404     417 .. 0.89
   4 ?    2.3   0.4      0.18   1.9e+02       4       9 ..     433     438 ..     431     439 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                            zf-ACC   3 KCpsCgemlyk 13 
                                        Cp+C +++  
  gi|488600218|ref|YP_007906689.1| 173 HCPRCQTTIAL 183
                                       5*****99865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                            zf-ACC  10 mlykkeLernlyVCPkC 26 
                                       +l k+e+++n  +C  C
  gi|488600218|ref|YP_007906689.1| 323 VLKKEEIDHNVGTCWRC 339
                                       799***********888 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0093
                            zf-ACC   3 KCpsCgemlykke 15 
                                        C +Cge+l +ke
  gi|488600218|ref|YP_007906689.1| 405 YCKKCGEILVAKE 417
                                       6********9997 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.18
                            zf-ACC   4 CpsCge 9  
                                       CpsCg+
  gi|488600218|ref|YP_007906689.1| 433 CPSCGS 438
                                       ****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 ?    1.8   0.2      0.16   1.7e+02       3       8 ..     172     177 ..     170     182 .. 0.67
   2 ?    1.6   0.1      0.19     2e+02       4      13 ..     335     344 ..     335     345 .. 0.84
   3 ?    0.9   0.1      0.32   3.4e+02       5      11 ..     406     413 ..     405     418 .. 0.62
   4 ?    7.4   0.1    0.0028       2.9       2      11 ..     430     439 ..     429     448 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                       zf-ribbon_3   3 vrCPnC 8  
                                       ++CP+C
  gi|488600218|ref|YP_007906689.1| 172 IHCPRC 177
                                       567776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.19
                       zf-ribbon_3   4 rCPnCGapls 13 
                                       +C++C++p++
  gi|488600218|ref|YP_007906689.1| 335 TCWRCKTPVE 344
                                       5*****9875 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.32
                       zf-ribbon_3   5 CPnCGa.p 11 
                                       C +CG+ +
  gi|488600218|ref|YP_007906689.1| 406 CKKCGEiL 413
                                       66677644 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0028
                       zf-ribbon_3   2 tvrCPnCGap 11 
                                       ++ CP+CG++
  gi|488600218|ref|YP_007906689.1| 430 KIPCPSCGSV 439
                                       688*****95 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.018        18       1       9 [.     173     181 ..     173     194 .. 0.75
   2 ?    1.2   0.0      0.23   2.4e+02      17      26 ..     401     410 ..     393     412 .. 0.85
   3 ?    0.4   0.1       0.4   4.2e+02       2       8 ..     433     440 ..     432     444 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.018
                          zf-TFIIB   1 kCPkCqdel 9  
                                       +CP+Cq++ 
  gi|488600218|ref|YP_007906689.1| 173 HCPRCQTTI 181
                                       7*****874 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.23
                          zf-TFIIB  17 veidyCpqCr 26 
                                       ++ +yC +C+
  gi|488600218|ref|YP_007906689.1| 401 IPAWYCKKCG 410
                                       899******7 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.4
                          zf-TFIIB   2 CPkCqd.e 8  
                                       CP+C++ e
  gi|488600218|ref|YP_007906689.1| 433 CPSCGSvE 440
                                       99998645 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.011        11       3      18 ..     172     187 ..     171     193 .. 0.79
   2 ?    0.6   0.1      0.45   4.8e+02      28      37 .]     406     415 ..     405     415 .. 0.89
   3 ?    0.8   0.1      0.39   4.1e+02       3      10 ..     431     438 ..     430     447 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.011
                     zinc_ribbon_5   3 irCpdCdtkFklvdsk 18 
                                       i Cp C+t+  l++ +
  gi|488600218|ref|YP_007906689.1| 172 IHCPRCQTTIALAEIE 187
                                       99*******9888766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.45
                     zinc_ribbon_5  28 CakCaevFda 37 
                                       C kC+e+ +a
  gi|488600218|ref|YP_007906689.1| 406 CKKCGEILVA 415
                                       99*****886 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.39
                     zinc_ribbon_5   3 irCpdCdt 10 
                                       i Cp C++
  gi|488600218|ref|YP_007906689.1| 431 IPCPSCGS 438
                                       77999998 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 ?    2.2   0.0      0.16   1.7e+02      26      34 ..     173     181 ..     133     185 .. 0.85
   2 ?    5.7   0.0     0.013        14      24      36 ..     403     415 ..     390     417 .. 0.69
   3 ?   -1.2   0.2       1.8   1.9e+03       7      11 ..     433     437 ..     433     441 .. 0.82
   4 ?   -2.6   0.1       5.2   5.5e+03      12      24 ..     469     481 ..     468     484 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.16
                    Zn_ribbon_SprT  26 rCrrCkgtL 34 
                                       +C+rC+ t+
  gi|488600218|ref|YP_007906689.1| 173 HCPRCQTTI 181
                                       466666655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                    Zn_ribbon_SprT  24 nYrCrrCkgtLrg 36 
                                       +++C++C++ L+ 
  gi|488600218|ref|YP_007906689.1| 403 AWYCKKCGEILVA 415
                                       49*****998875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.8
                    Zn_ribbon_SprT   7 CtgCg 11 
                                       C++Cg
  gi|488600218|ref|YP_007906689.1| 433 CPSCG 437
                                       9***9 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.2
                    Zn_ribbon_SprT  12 reythhlsirrhn 24 
                                       +ey+ hl+ + h 
  gi|488600218|ref|YP_007906689.1| 469 KEYPTHLRPQGHD 481
                                       58999*****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (869 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 5624.96
//
Query:       gi|488600219|ref|YP_007906690.1|  [L=245]
Description: 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-66  224.7   0.0    1.3e-66  224.4   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 !  224.4   0.0   7.5e-71   1.3e-66       2     215 ..      48     239 ..      47     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 224.4 bits;  conditional E-value: 7.5e-71
                                       EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--H CS
                     FAA_hydrolase   2 ivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsv 78 
                                        +c+g+ny++h++e g   +++pd     ep++f+k+ ++++g+gd i +P+ se++dyE+ELavv+ k++++v s 
  gi|488600219|ref|YP_007906690.1|  48 LICVGVNYRDHAEEFG---KDVPD-----EPIIFMKPDTAVIGDGDAIILPNMSERVDYEGELAVVLAKKCKNV-SY 115
                                       79************98...78999.....888******************************************.99 PP

                                       HHHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGG CS
                     FAA_hydrolase  79 eeAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkd 155
                                       ++A+d+i+Gyt +nDv+aRdlq+++    +w++gksfdtf+p+Gp +v+  +l dp++le+++ +ng +vq snt++
  gi|488600219|ref|YP_007906690.1| 116 DDAKDYILGYTCFNDVTARDLQMKDG---QWTRGKSFDTFAPLGPYVVS--NL-DPRNLEIKTYLNGRVVQASNTSN 186
                                       *************************9...******************76..67.5689******************* PP

                                       TTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEE CS
                     FAA_hydrolase 156 mifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrn 215
                                       m+f+ ++l++ +s+++tL++Gd+i+tGTpsgvg        l+dgD+vev+ieg+G lrn
  gi|488600219|ref|YP_007906690.1| 187 MVFDAFRLLEFVSSIMTLKRGDVIATGTPSGVG-------PLRDGDVVEVHIEGIGVLRN 239
                                       *******************************98.......5*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1866.39
//
Query:       gi|488600220|ref|YP_007906691.1|  [L=352]
Description: hypothetical protein Asulf_00680 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-36  124.5   1.2    4.8e-36  123.6   1.2    1.4  1  TPD       Protein of unknown function TPD sequence-motif


Domain annotation for each model (and alignments):
>> TPD  Protein of unknown function TPD sequence-motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   1.2   2.7e-40   4.8e-36       2     127 ..     105     229 ..     104     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 2.7e-40
                               TPD   2 dkrlakevkeaieedsvyspladairssvGeeyEellekllkekgiafkteedlrekgldktPDvkLevpvavegkv 78 
                                       d++l++e  ++i +d +ysp a + + ++G  +E++le++lk+++i+fkte+dlr k+++ktPD+ + + v + g+ 
  gi|488600220|ref|YP_007906691.1| 105 DEDLRRETWKSIFTDYIYSPFAIKNQYVRGDLGEKILEEWLKSRDIEFKTEKDLR-KEFSKTPDFYFPDGVNIAGEE 180
                                       899***************************************************9.689****************** PP

                               TPD  79 vnWiesKalfgdeeehkkylkkQlssYvnrfGpGlviYwfGyvdelese 127
                                       ++WiesKalfgd + h  y kkQ+s+Y + fG+G viYwfG v+e+++ 
  gi|488600220|ref|YP_007906691.1| 181 IRWIESKALFGDFRIHWVYWKKQFSKYLEMFGNGFVIYWFGRVKEIDKV 229
                                       *********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2431.58
//
Query:       gi|488600221|ref|YP_007906692.1|  [L=94]
Description: hypothetical protein Asulf_00681 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    1.9e-08   34.1   0.0    1.1  1  NMD3            NMD3 family
  ------ inclusion threshold ------
       0.07   13.2   0.1       0.14   12.2   0.0    1.5  1  LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
       0.13   12.2   0.0       0.16   11.8   0.0    1.3  1  UPF0728         Uncharacterised protein family UPF0728


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 !   34.1   0.0   3.2e-12   1.9e-08     177     242 ..      24      87 ..       4      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.2e-12
                              NMD3 177 dahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgkevyrltysvr 242
                                       +++ f  +i+++k G+D+yf++ ++Ark+++ lk+++  k+k s k ++  +k g+ +  ++ys+r
  gi|488600221|ref|YP_007906692.1|  24 ERKGFEFEIEKAKKGYDVYFSDVNDARKFISDLKRNYRFKIKMSTKYAGL-RK-GRVRVLFVYSLR 87 
                                       5788999*******************************************.66.898888888876 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.14      35      72 ..      17      54 ..       8      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                    LAGLIDADG_WhiA 35 eqlqkllnefeleakilerrkkyvvylKkaeqIvdlLk 72
                                       +lq +l++ ++e++i + +k+y vy+ ++++  ++ +
  gi|488600221|ref|YP_007906692.1| 17 TNLQRVLERKGFEFEIEKAKKGYDVYFSDVNDARKFIS 54
                                      689*************************9999887765 PP

>> UPF0728  Uncharacterised protein family UPF0728
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.6e-05      0.16      19      48 ..       8      37 ..       3      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                           UPF0728 19 vvkhrterleglqavlkkdGheveLekted 48
                                      +++ r   l++lq+vl+++G+e e+ek ++
  gi|488600221|ref|YP_007906692.1|  8 ILQLRNLPLTNLQRVLERKGFEFEIEKAKK 37
                                      67788889******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 653.66
//
Query:       gi|488600222|ref|YP_007906693.1|  [L=208]
Description: hypothetical protein Asulf_00682 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.8   0.0      0.025   14.4   0.0    1.2  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-06     0.025      14      96 ..      19      93 ..       8     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-06
                                      CCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHHCHCCT CS
                   Phage_integrase 14 aleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellskaleeae 92
                                      a+++  +  + ++++l+ +t +  +E+++++ kd++  +  ++v  r   g+k r+ pl +  + ll+++ +++    +
  gi|488600222|ref|YP_007906693.1| 19 ASRK--NEVEHCIVRLIISTLATPAEIAGITKKDIRRYRDFHTV--RLRSGRKVRVSPLDKRTYDLLTRISADK----S 89
                                      4444..5567899*******************************..66678888****************9998....3 PP

                                      TTSB CS
                   Phage_integrase 93 ksel 96
                                      +s+ 
  gi|488600222|ref|YP_007906693.1| 90 SSQQ 93
                                      3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1377.06
//
Query:       gi|488600223|ref|YP_007906694.1|  [L=422]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  183.5  32.8    6.2e-54  183.3  32.8    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 !  183.3  32.8   3.5e-58   6.2e-54       4     408 ..      26     410 ..      23     411 .. 0.92

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 3.5e-58
                              TctA   4 vllGvllGtliGllPGlhatlavalllpltf....gldpeaalilllgiyvgaifggsipaillgvPGtpssvatvl 76 
                                       +++G+llG+++GllPG+h +++ al++   f     ++pe +++++ + +++++f+++ p++++g+P ++++++++l
  gi|488600223|ref|YP_007906694.1|  26 LAVGILLGIVSGLLPGIHNNTFSALMISNIFilteFFEPEEIALIIFANSITHTFLDILPTVFIGAP-DEDTAVSIL 101
                                       689*************************999999888******************************.********* PP

                              TctA  77 dgyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailse......... 144
                                       +++ +++ Gr+ eA++++a++S+i+ ++s++++++    l +++lk  + e +a +l+ +v+++ilse         
  gi|488600223|ref|YP_007906694.1| 102 PAHAMLLDGRGFEAVSISAFSSLISYVLSIPVFFV----LLNLSLKGILMELTAPFLILVVILLILSEredrfagsl 174
                                       ******************99999999888887654....445779999***************************** PP

                              TctA 145 ...ksllkglialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskiplslkdlk 218
                                           ++  +l+++ll++++g++++++        f     + g  ++p++iG+F i+ l++s ++  +ip ++ +l 
  gi|488600223|ref|YP_007906694.1| 175 nrvLRMSEALAIILLSGVIGYIAFKYS-------FLFEVRAGGNIFIPMMIGFFSIPVLIQSRKT--SIPDQRIELA 242
                                       99999999****************776.......44456788999****************9964..5665677777 PP

                              TctA 219 kslptilrgsliGtivGilPgvGasiaaflayavakrlskkpekfgkgaiegvaapeaannaaaggaliplltlgip 295
                                        +   ++ g + G++v+++Pgv++ ia++++ +  +           +++e+++++++an+++a       +++g  
  gi|488600223|ref|YP_007906694.1| 243 IPGRRVFHGCAGGFLVSMFPGVSSGIASVISSFSNR-----------KEEEYITSVSSANTSNALLCYAIFFSMGFK 308
                                       55667***************************9965...........689*************************** PP

                              TctA 296 gsgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll.kipkelLlpiilvllv 371
                                       +sg++ +++ ++   +l         +   +  l++  +i +v+++++++ll+ +f+++l +++++ L+ + +v+lv
  gi|488600223|ref|YP_007906694.1| 309 RSGAVDAFSRIV--SDL---------DYGEIRNLILLGAIVVVIAFFVTILLGYIFSRVLrEVDTHNLSKLLIVFLV 374
                                       *****9999965..333.........4556677999999999****************9999*************** PP

                              TctA 372 igayalnnslfdvlvmlifgvlGlllrrlgvplaplv 408
                                       + +y ++++ +++l++++++++Gll  +lgv++++++
  gi|488600223|ref|YP_007906694.1| 375 AYTYFMTGT-YGILFLITSTIVGLLAAKLGVRRINCM 410
                                       *********.************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); 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:                         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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2519.43
//
Query:       gi|488600224|ref|YP_007906695.1|  [L=107]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-07   28.9   0.5    2.6e-06   27.4   0.2    1.9  3  HTH_3           Helix-turn-helix
    0.00013   21.9   0.7     0.0016   18.4   0.7    2.0  1  HTH_19          Helix-turn-helix domain
    0.00016   21.4   0.0    0.00029   20.5   0.0    1.4  1  HTH_23          Homeodomain-like domain
    0.00018   21.0   0.4    0.00092   18.7   0.0    2.3  3  HTH_24          Winged helix-turn-helix DNA-binding
    0.00067   20.0   0.0     0.0011   19.2   0.0    1.4  1  HTH_31          Helix-turn-helix domain
    0.00093   19.1   0.1     0.0016   18.3   0.1    1.3  1  HTH_1           Bacterial regulatory helix-turn-helix protein
     0.0011   18.8   0.0      0.002   17.9   0.0    1.4  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.002   18.0   0.2     0.0095   15.9   0.0    1.9  2  HTH_37          Helix-turn-helix domain
     0.0096   15.8   0.0      0.024   14.5   0.0    1.8  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.022   14.4   0.1    1.5  1  HTH_50          Helix-turn-helix domain
      0.018   14.8   0.1      0.063   13.1   0.1    2.0  1  LacI            Bacterial regulatory proteins, lacI family
      0.021   13.8   0.1      0.023   13.7   0.1    1.1  1  TnsD            Tn7-like transposition protein D
      0.022   14.4   0.1      0.047   13.4   0.1    1.6  1  Sigma70_r4_2    Sigma-70, region 4
       0.03   14.2   0.6       0.14   12.0   0.0    2.2  3  HTH_5           Bacterial regulatory protein, arsR family
      0.041   14.0   0.0       0.11   12.7   0.0    1.6  2  HTH_28          Helix-turn-helix domain
      0.087   13.1   0.1       0.18   12.1   0.0    1.6  1  KORA            TrfB plasmid transcriptional repressor
      0.087   12.9   0.1       0.13   12.3   0.1    1.3  1  Cro             Cro
       0.14   12.0   0.0        0.2   11.5   0.0    1.3  1  DAO_C           C-terminal domain of alpha-glycerophosphate o
       0.16   11.7   0.1        1.3    8.8   0.0    1.8  2  DUF2520         Domain of unknown function (DUF2520)


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 !   27.4   0.2   2.7e-09   2.6e-06       2      37 ..      23      58 ..      23      65 .. 0.90
   2 ?   -1.1   0.0       2.2   2.1e+03      25      35 ..      59      69 ..      56      72 .. 0.80
   3 ?   -2.8   0.0       7.2   6.8e+03      28      39 ..      79      90 ..      76      91 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.7e-09
                                      HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSB CS
                             HTH_3  2 kelRkqlglsqeeLAeklGvsrstisriEnGernPs 37
                                      kel +  gl ++++A++lG+++s++s++++ +r  +
  gi|488600224|ref|YP_007906695.1| 23 KELIENYGLKRKDVAKLLGLTQSAVSQYMSSKRGLT 58
                                      788999************************988665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                                      HHHHHHTTSSC CS
                             HTH_3 25 tisriEnGern 35
                                       i++iE+ er+
  gi|488600224|ref|YP_007906695.1| 59 GIQMIERSERA 69
                                      58999999884 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.2
                                      HHHTTSSCSBHH CS
                             HTH_3 28 riEnGernPsle 39
                                      ++++Ge +++ e
  gi|488600224|ref|YP_007906695.1| 79 KLIKGEFSIDDE 90
                                      677888887765 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   1.7e-06    0.0016       5      62 ..      23      83 ..      21     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                            HTH_19  5 keaReelgltqeelaerlgisrskisaiEngkkdvpsaell...lkiaealgidleyllqg 62
                                      ke++e++gl+ +++a+ lg ++s  s++ + k+  +++ ++    +++e  +  +e l++g
  gi|488600224|ref|YP_007906695.1| 23 KELIENYGLKRKDVAKLLGLTQSAVSQYMSSKRGLTGIQMIersERASEVINELIEKLIKG 83
                                      89***************************99998888777766677777777777777766 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.1e-07   0.00029       6      48 ..      17      59 ..      15      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.1e-07
                            HTH_23  6 eRlrillllae..GlsvreIAreLgvsrrTvyrwlkryreeGleg 48
                                       R++i++ l e  Gl ++++A++Lg +++ v+++ +   + Gl g
  gi|488600224|ref|YP_007906695.1| 17 LRAKIAKELIEnyGLKRKDVAKLLGLTQSAVSQYMSS--KRGLTG 59
                                      69*******************************9887..666665 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 ?   -1.8   0.0       2.5   2.3e+03      29      39 ..       1      11 [.       1      12 [. 0.85
   2 !   18.7   0.0   9.8e-07   0.00092      10      39 ..      23      52 ..      17      54 .. 0.92
   3 ?   -1.3   0.0       1.7   1.6e+03      34      41 ..      73      80 ..      57      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.5
                            HTH_24 29 lSpstvnrrlk 39
                                      +S++++   +k
  gi|488600224|ref|YP_007906695.1|  1 MSKPPCMVIVK 11
                                      699***99998 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 9.8e-07
                            HTH_24 10 elLqknprisqreLAerlglSpstvnrrlk 39
                                      ++L +n ++  +++A+ lgl++s+v++++ 
  gi|488600224|ref|YP_007906695.1| 23 KELIENYGLKRKDVAKLLGLTQSAVSQYMS 52
                                      79**************************95 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.7
                            HTH_24 34 vnrrlkrL 41
                                      +n+ +++L
  gi|488600224|ref|YP_007906695.1| 73 INELIEKL 80
                                      44455555 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06    0.0011      13      50 ..      21      66 ..      14      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                            HTH_31 13 a........GLsqeevAerlgvsestlsrlEqGrrgrpspavleal 50
                                               GL++++vA++lg+++s +s++++ +rg+   + +e+ 
  gi|488600224|ref|YP_007906695.1| 21 IakelienyGLKRKDVAKLLGLTQSAVSQYMSSKRGLTGIQMIERS 66
                                      345555666***********************99997777777765 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.7e-06    0.0016      19      51 ..      36      68 ..      34      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                                      HHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSS CS
                             HTH_1 19 AAeeLglsqpavsrqikrLEeelgvpLfeRtgr 51
                                       A+ Lgl+q+avs+ +++ + + g + +eR+ r
  gi|488600224|ref|YP_007906695.1| 36 VAKLLGLTQSAVSQYMSSKRGLTGIQMIERSER 68
                                      59****************************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 !   17.9   0.0   2.2e-06     0.002       3      29 ..      23      50 ..      22      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                                      HHHHHHHSSHHH.HHHHHTS-HHHHHHH CS
                           P22_Cro  3 kdvikhFGgvek.vAkalgvtksAVsqW 29
                                      k++i+ +G ++k vAk+lg t+sAVsq 
  gi|488600224|ref|YP_007906695.1| 23 KELIENYGLKRKdVAKLLGLTQSAVSQY 50
                                      7899999988766**************7 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-05    0.0095      24      52 ..      23      51 ..      16      57 .. 0.88
   2 ?   -0.3   0.0       1.1     1e+03      15      29 ..      64      79 ..      57      84 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                      HHHHHHCT--HHHHHHHHT--HHHHHHHH CS
                            HTH_37 24 aeliekrelsqseaaqllgiaqPkvsrll 52
                                      +elie  +l+ +++a+llg +q+ vs+ +
  gi|488600224|ref|YP_007906695.1| 23 KELIENYGLKRKDVAKLLGLTQSAVSQYM 51
                                      589***********************976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                      HHHHHHHH.HHHHHHH CS
                            HTH_37 15 aKaqlala.iaeliek 29
                                       +++ a++ i+eliek
  gi|488600224|ref|YP_007906695.1| 64 ERSERASEvINELIEK 79
                                      5666677777788776 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   2.6e-05     0.024      11      35 ..      33      58 ..      23      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                    YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlkgkkq.v 35
                                      +k +A++lg +q+aVsq ++ k++  
  gi|488600224|ref|YP_007906695.1| 33 RKDVAKLLGLTQSAVSQYMSSKRGlT 58
                                      6789***************9888753 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.3e-05     0.022      13      41 ..      19      48 ..      10      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                            HTH_50 13 relikkayekYpStRk.lAkrLGvShtaia 41
                                      +++ k+++e+Y+  Rk +Ak LG++++a+ 
  gi|488600224|ref|YP_007906695.1| 19 AKIAKELIENYGLKRKdVAKLLGLTQSAVS 48
                                      67778999*******99***********96 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.7e-05     0.063       3      24 ..      34      55 ..      33      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                                      HHHHHHCTS-HHHHHHHCTTSS CS
                              LacI  3 kDVArlAGVSkaTVSrvLnnke 24
                                      kDVA+l G + ++VS+++++k+
  gi|488600224|ref|YP_007906695.1| 34 KDVAKLLGLTQSAVSQYMSSKR 55
                                      8*****************9983 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.5e-05     0.023     191     238 ..      22      69 ..       8      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                              TnsD 191 lkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesre 238
                                       +keL+e+ gl+ k++Ak lg++ + V +y +++ +l+  +  ++++r 
  gi|488600224|ref|YP_007906695.1|  22 AKELIENYGLKRKDVAKLLGLTQSAVSQYMSSKRGLTGIQMIERSERA 69 
                                       799****************************99998865555555444 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 ?   13.4   0.1     5e-05     0.047      20      48 ..      24      52 ..      18      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5e-05
                                      HHHHTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 20 llryleglsykEIAellgisegtVksrls 48
                                      +l++  gl+ k++A+llg++ ++V +++s
  gi|488600224|ref|YP_007906695.1| 24 ELIENYGLKRKDVAKLLGLTQSAVSQYMS 52
                                      578889******************99975 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.14       4      36 ..      18      51 ..      16      53 .. 0.79
   2 ?   -2.8   0.0       6.3     6e+03      18      24 ..      73      79 ..      66      84 .. 0.53
   3 ?   -0.3   0.0       1.1     1e+03      18      25 ..      94     101 ..      85     107 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                      HHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHH CS
                             HTH_5  4 RlkILklLaege.lcvcelaeelglsqstvShHL 36
                                      R kI k L e+  l+  + a+ lgl+qs+vS++ 
  gi|488600224|ref|YP_007906695.1| 18 RAKIAKELIENYgLKRKDVAKLLGLTQSAVSQYM 51
                                      5666667777555778899************985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.3
                                      HHHHHHH CS
                             HTH_5 18 vcelaee 24
                                      + el e+
  gi|488600224|ref|YP_007906695.1| 73 INELIEK 79
                                      3444443 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.1
                                       HHHHHHHH CS
                             HTH_5  18 vcelaeel 25 
                                       +c ++e+l
  gi|488600224|ref|YP_007906695.1|  94 ICRICEIL 101
                                       56666665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011      0.11       2      31 ..      18      49 ..      17      53 .. 0.89
   2 ?   -2.2   0.0       4.9   4.6e+03       6      20 ..      77      96 ..      75     101 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                            HTH_28  2 RleiikllaaGh..svreaArelgisrrtvyr 31
                                      R++i k+l++     ++++A++lg++++ v++
  gi|488600224|ref|YP_007906695.1| 18 RAKIAKELIENYglKRKDVAKLLGLTQSAVSQ 49
                                      9********976569999***********987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.9
                            HTH_28  6 ikllaaGh.svre....aAr 20
                                      i+ l++G+ s+++    ++r
  gi|488600224|ref|YP_007906695.1| 77 IEKLIKGEfSIDDevdyICR 96
                                      66677888887765555555 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.18      31      51 ..      30      50 ..      10      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                              KORA 31 gkkqadvatelgltkqavsqa 51
                                      g k++dva+ lglt+ avsq 
  gi|488600224|ref|YP_007906695.1| 30 GLKRKDVAKLLGLTQSAVSQY 50
                                      569****************96 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014      0.13      16      44 ..      34      62 ..      19      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                      HHHHHHHTS-HHHHHHHHHCT-EEEEEEE CS
                               Cro 16 aktAkdlgvkqsaIsKAlkakRnIylivd 44
                                      + +Ak lg +qsa+s  +  kR +  i+ 
  gi|488600224|ref|YP_007906695.1| 34 KDVAKLLGLTQSAVSQYMSSKRGLTGIQM 62
                                      458***************99997665555 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022       0.2      28      79 ..      17      96 ..       7     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                      --HHHHHHHHHHHGGGHHHHHHHHHHTH...............................HHHHHTTS-HHHHHHHHHHH CS
                             DAO_C 28 ldeevaehLaerYGsraeevlelakedekp............................elaerlspelpyieaevvYav 78
                                      l ++ a++L+e+YG + ++v++l   +++                             el e+l + +  i  ev Y +
  gi|488600224|ref|YP_007906695.1| 17 LRAKIAKELIENYGLKRKDVAKLLGLTQSAvsqymsskrgltgiqmierserasevinELIEKLIKGEFSIDDEVDYIC 95
                                      77899****************9888877667777777777777777777777777777777777777777777777766 PP

                                      H CS
                             DAO_C 79 r 79
                                      r
  gi|488600224|ref|YP_007906695.1| 96 R 96
                                      5 PP

>> DUF2520  Domain of unknown function (DUF2520)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0014       1.3      41      95 ..       7      59 ..       6      60 .. 0.81
   2 ?    0.9   0.0      0.39   3.7e+02       4      30 ..      62      88 ..      60      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                      HHHHHCCHHHH.HHHHHHHHHCTT-S-..HHHHHHHHHHHHHHHHHHS-HHHH--S CS
                           DUF2520 41 avlasNflvtl.valaaellreagldekdaakallpLleatlenalkagpkaalTG 95
                                      +v++ N l +l +++a+el+++ gl++kd ak+l+ L + +++++++++    lTG
  gi|488600224|ref|YP_007906695.1|  7 MVIVKNILPALrAKIAKELIENYGLKRKDVAKLLG-LTQSAVSQYMSSKR--GLTG 59
                                      688889998883458***********888888776.99999999888774..7887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                                      EEEESCCCHHHHHHHHHCCSS-EEE-- CS
                           DUF2520  4 aiegdeealaiaeelaeelggevvvid 30
                                      +ie +e+a ++++el+e+l +  + id
  gi|488600224|ref|YP_007906695.1| 62 MIERSERASEVINELIEKLIKGEFSID 88
                                      689999999999999999877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 618.22
//
Query:       gi|488600225|ref|YP_007906696.1|  [L=258]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  236.2   3.2    1.8e-70  236.0   3.2    1.1  1  DUF2202         Uncharacterized protein domain (DUF2202)
  ------ inclusion threshold ------
       0.01   16.0   7.5      0.014   15.5   7.5    1.1  1  Keratin_2_head  Keratin type II head
      0.026   14.9   0.0      0.067   13.6   0.0    1.7  2  Rubrerythrin    Rubrerythrin


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 !  236.0   3.2     3e-74   1.8e-70       1     161 [.      99     257 ..      99     258 .] 0.98

  Alignments for each domain:
  == domain 1  score: 236.0 bits;  conditional E-value: 3e-74
                           DUF2202   1 ekdsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnk 77 
                                       e+d+++ymreeeklarDvYl lYd+w+lqif+nia+seq h+dav  l++kY+l+dp+k+   G f++++lqelY++
  gi|488600225|ref|YP_007906696.1|  99 EIDGIMYMREEEKLARDVYLALYDKWGLQIFSNIARSEQMHMDAVLALIKKYNLTDPAKDV--GEFTNPHLQELYDN 173
                                       7899*****************************************************9865..************** PP

                           DUF2202  78 LvekgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYepqyiseee 154
                                       Lve+gsks +daLkvga+ie++di+Dl+ +l ++dn+di+ vY+nl++Gs+nhlR+f++ l+++g +Yepq ise+e
  gi|488600225|ref|YP_007906696.1| 174 LVEQGSKSEVDALKVGALIEEVDIKDLKDWLAKNDNEDIELVYDNLMRGSENHLRAFTSVLKNYGVTYEPQVISEDE 250
                                       ***************************************************************************** PP

                           DUF2202 155 fdeivss 161
                                       ++ei+++
  gi|488600225|ref|YP_007906696.1| 251 YQEIINA 257
                                       *****98 PP

>> Keratin_2_head  Keratin type II head
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   7.5   2.4e-06     0.014      89     127 ..      45      81 ..      10      92 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                    Keratin_2_head  89 gGvglgfgagggvGggfGgggglvGgggfGgggfGggGf 127
                                       +G+g g+g+g gvG g G+g+  +G++g+G g++G +G 
  gi|488600225|ref|YP_007906696.1|  45 TGMGNGIGVGHGVGQGQGAGQ--HGNSGMGNGNMGSMGS 81 
                                       455555655666666666666..8999999999996554 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.067      10      83 ..     110     174 ..     106     234 .. 0.68
   2 ?   -0.7   0.0      0.29   1.7e+03      25      62 ..     206     244 ..     198     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHH CS
                      Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttak 83 
                                       E  ar +Y +l++k         ++F  +A+ E+ H + +  l++k++++      ++v e++ +  ++l  + 
  gi|488600225|ref|YP_007906696.1| 110 EKLARDVYLALYDKWG------LQIFSNIARSEQMHMDAVLALIKKYNLTDP---AKDVGEFTNPHLQELYDNL 174
                                       7788999999999999......67**********************887765...6777777776666644443 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.29
                                       HTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.. CS
                      Rubrerythrin  25 kegypqiaelFeelAeeEreHakilnklleklepele.l 62 
                                       k+ +++i+ ++  l +  + H + +  +l+++  ++e  
  gi|488600225|ref|YP_007906696.1| 206 KNDNEDIELVYDNLMRGSENHLRAFTSVLKNYGVTYEpQ 244
                                       466788888888888888999999999999988888833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1522.39
//
Query:       gi|488600226|ref|YP_007906697.1|  [L=259]
Description: dihydrodipicolinate reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-40  135.6   0.0    1.1e-39  135.2   0.0    1.2  1  DapB_C          Dihydrodipicolinate reductase, C-terminus
    4.5e-31  107.5   0.8    8.1e-31  106.7   0.8    1.4  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.023   15.1   0.3      0.083   13.3   0.2    1.9  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.064   13.9   1.5       0.13   12.9   1.5    1.5  1  CoA_binding     CoA binding domain


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 !  135.2   0.0   2.5e-43   1.1e-39       1     121 []     122     257 ..     122     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 2.5e-43
                                       HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH.....................-S-ETTCC CS
                            DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia.......egke..........arkkkeig 60 
                                       Gvn++ k++e a+ +l++ yd+ei+E+Hh+ K+D+PSGTAl+ ++ i+          +          + + +eig
  gi|488600226|ref|YP_007906697.1| 122 GVNIFWKILEFATPYLSS-YDIEIVEIHHRFKKDSPSGTALKAGRLIKdilekkgI--KrelkfersglSPRGEEIG 195
                                       9***************99.*****************************88866551..1556676667756668*** PP

                                       CEEEETTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCT.SSEESHHHHH CS
                            DapB_C  61 ihsvRgggvvgehevlfagegevieikhealsreiFaeGallaaewlakkk.kglysmedvL 121
                                       i  +Rgg+vvgeh+v++ g+ge+iei+h+alsr+ Fa+Ga++aa+w+++ + +g+y+m+dvL
  gi|488600226|ref|YP_007906697.1| 196 IFGIRGGDVVGEHTVFYFGNGERIEITHRALSRQAFASGAIQAAKWISRVEkPGIYTMDDVL 257
                                       **********************************************86554499*******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 !  106.7   0.8   1.8e-34   8.1e-31       1     124 []       2     119 ..       2     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 1.8e-34
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-H CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtp 77 
                                       i++a++G +GrmGk +v    ++++l+lv+a+d ++   +g+dage++g+gk+gv ++d+++e+   advliDFT+ 
  gi|488600226|ref|YP_007906697.1|   2 ISIAIAGSAGRMGKLLVANTVSDPELKLVQAFDVQR---VGEDAGEVAGVGKTGVIISDNIDELN--ADVLIDFTVA 73 
                                       689*******************************99...9**********************997..5********* PP

                                       HHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTTSEEEE-S-- CS
                            DapB_N  78 eavlenlklalekgvklViGTTGlseeelaeleelakkigvviapNf 124
                                       +++ +n+k a ekgvklV+GTTG++ee+ +e+e+   ++++vi+pNf
  gi|488600226|ref|YP_007906697.1|  74 DSSIKNIKKACEKGVKLVVGTTGFDEEQWHEIES-VISVPAVISPNF 119
                                       **********************************.567********8 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.8e-05     0.083       2      94 ..       4      91 ..       3     117 .. 0.87
   2 ?   -1.7   0.0      0.84   3.8e+03      17      57 ..     143     183 ..     134     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                      EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvsk 80
                                      +ai G  G +G+ l+    ++pe++lv ++  +r  G+   e+++   +++ + ++d +++el ++d+++  + a+ s 
  gi|488600226|ref|YP_007906697.1|  4 IAIAGSAGRMGKLLVANTVSDPELKLVQAFDVQR-VGEDAGEVAG--VGKTGVIISD-NIDEL-NADVLIDFTVADSSI 77
                                      89********************************.********88..5566666666.77777.99*****9******* PP

                                      HHHHHHHHTTSEEE CS
                    Semialdhyde_dh 81 elapklaeagvkvi 94
                                      +  +k+ e+gvk++
  gi|488600226|ref|YP_007906697.1| 78 KNIKKACEKGVKLV 91
                                      ***********876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.84
                                       HHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEE CS
                    Semialdhyde_dh  17 rlLeehpevelvvllsssrsaGkklaeavkaleegkdlkve 57 
                                       +++e h  ++    ++++ +aG+ +++  ++   +++lk+e
  gi|488600226|ref|YP_007906697.1| 143 EIVEIHHRFKKDSPSGTALKAGRLIKDILEKKGIKRELKFE 183
                                       55666777888888888888888888888877777777766 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.5     3e-05      0.13       5      91 ..       3      92 ..       1      96 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                                      EEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEET........TEEEESCHHHHHHHCTTTEEEEES-HHH CS
                       CoA_binding  5 kviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevl........glpvyksvdeleektevdvavitvPaes 74
                                      ++++ G  g+ +++l  ++ ++ + +++++f+v+    g++ +        g+ + +++del ++    v + ++ a+s
  gi|488600226|ref|YP_007906697.1|  3 SIAIAGSAGRMGKLLvANTVSDPELKLVQAFDVQRV--GEDAGevagvgktGVIISDNIDELNAD----VLIDFTVADS 75
                                      7999999999999999*****************965..444444445888899999999999888....7777777899 PP

                                      HHHHHHHHHHTT-SEEE CS
                       CoA_binding 75 aqeavdelveagikgiv 91
                                        + ++++ e+g+k++v
  gi|488600226|ref|YP_007906697.1| 76 SIKNIKKACEKGVKLVV 92
                                      99999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1597.21
//
Query:       gi|488600227|ref|YP_007906698.1|  [L=289]
Description: dihydrodipicolinate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-93  313.1   0.0    1.2e-93  313.0   0.0    1.0  1  DHDPS          Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.23   11.1   0.0    1.5  2  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro


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 !  313.0   0.0   1.4e-97   1.2e-93       2     288 ..       4     285 ..       3     286 .. 0.98

  Alignments for each domain:
  == domain 1  score: 313.0 bits;  conditional E-value: 1.4e-97
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                       f+g+i+al+tpf+ed  +d++ ++++ e+ ++k vd++v aGttGE+atls ee++++v+++ e+   ++pvi+g+G
  gi|488600227|ref|YP_007906698.1|   4 FKGVIPALITPFKEDLSVDFKGIDRNLEY-LEKHVDAVVPAGTTGEAATLSYEEHIEVVRYVCEV--SKVPVIGGAG 77 
                                       89**************************9.5999****************************998..58******** PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTST CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaele 155
                                       snst+ea+ ++k+ e+aGad+++ vtPYYnkp++ gly h+ka   + + p+i+Ynvpsrtg +l+p++vkrLae+e
  gi|488600227|ref|YP_007906698.1|  78 SNSTREALYIGKEVEKAGADAAMFVTPYYNKPNPDGLYLHYKALSDELSIPIIVYNVPSRTGINLTPDVVKRLAEIE 154
                                       *********************************************9999**************************** PP

                                       TEEEEEE-SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHH CS
                             DHDPS 156 nivgvKeavgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaael 232
                                       n++++Kea+g+l+++ +i+++  ++++++sGdd l+l++l lG++Gvisv++n+a+++m++++++  eGd+  a+el
  gi|488600227|ref|YP_007906698.1| 155 NVAAIKEASGNLKQISDIIRT-VPEITVLSGDDFLTLPVLCLGGTGVISVAANVAPHLMKEMYNKFVEGDMTAAREL 230
                                       ******************999.789**************************************************** PP

                                       HHHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
                             DHDPS 233 nekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                                       +++l pl+++lf  +n+i+vk al+l+Gl +++  r Pl++l+ee+ e+l+a+lk 
  gi|488600227|ref|YP_007906698.1| 231 HHRLTPLFNALFIDTNPIPVKKALNLMGLAAGK-PRLPLVELNEEKTEKLKAVLKS 285
                                       *********************************.******************9985 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 ?   11.1   0.0   2.6e-05      0.23      99     155 ..      22      77 ..       6      92 .. 0.80
   2 ?   -3.5   0.0      0.75   6.7e+03      76      92 ..     153     169 ..     145     192 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.6e-05
                                       TSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHH CS
                     ELFV_dehydrog  99 kaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAk 155
                                       +++ i+ + e le +vd +vP++t  e    + ++ i+  v++v+E++ +p+   A 
  gi|488600227|ref|YP_007906698.1|  22 DFKGIDRNLEYLEKHVDAVVPAGTTGEAATLSYEEHIE-VVRYVCEVSKVPVIGGAG 77 
                                       45666666677889********************9999.9********999877665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.75
                                       HHHHHHHHHCSSSSTTH CS
                     ELFV_dehydrog  76 ieellelkeerksvkey 92 
                                       ie+++++ke+ +++k++
  gi|488600227|ref|YP_007906698.1| 153 IENVAAIKEASGNLKQI 169
                                       44444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 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:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2006.72
//
Query:       gi|488600228|ref|YP_007906699.1|  [L=65]
Description: SSU ribosomal protein S17E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-12   46.4   0.1    3.9e-12   46.2   0.1    1.0  1  Ribosomal_S17e  Ribosomal S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.1   2.2e-16   3.9e-12       1      60 [.       1      60 [.       1      63 [. 0.96

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2.2e-16
                                      XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHH CS
                    Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkr 60
                                      mg v+   +K  a +++++y   +t+ F++nkk++ e a i+sk +rn++aGy+t+ ++r
  gi|488600228|ref|YP_007906699.1|  1 MGTVKPAYIKVIALELLKRYPDMFTESFEENKKLVAEYADIKSKTVRNRVAGYITRRVRR 60
                                      8999999************************************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 342.21
//
Query:       gi|488600229|ref|YP_007906700.1|  [L=119]
Description: proteasome Rpn11 subunit JAMM motif , Metallo peptidase, MEROPS family M67B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   49.6   0.0    3.7e-13   49.3   0.0    1.1  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
       0.06   13.3   0.0       0.11   12.4   0.0    1.5  1  RadC      RadC-like JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   4.1e-17   3.7e-13       3     117 ..       6     105 ..       4     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 4.1e-17
                          Prok-JAB   3 svlsalvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpg 79 
                                       ++l+ ++a a++ hp+E ++l++g++ + ee i+ p +           +++++a ++ ++   g++++g +HSHp 
  gi|488600229|ref|YP_007906700.1|   6 ELLELMLAVAKENHPNEIVALITGRKGIGEELIFLPFE-----------SGETMAIIHTDMLPLGMKILGSFHSHPR 71 
                                       678999********************99********65...........566666666699**************** PP

                          Prok-JAB  80 gsarPSetDrrdaaalarvkalliivgdkaeelrawrl 117
                                       +  +PS++D++++++++  k+++i++    +++++wr+
  gi|488600229|ref|YP_007906700.1|  72 PILEPSQADLSMFSRIG--KFHIIVAYP--YDKKSWRC 105
                                       ****************9..777777764..67778885 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.11      70      93 ..      66      89 ..      47      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                      EEE-TTS--S--HHHHHHHHHHHH CS
                              RadC 70 aHnhPsgdlepSeeDieltkrlke 93
                                      +H hP   lepS++D+++  r+ +
  gi|488600229|ref|YP_007906700.1| 66 FHSHPRPILEPSQADLSMFSRIGK 89
                                      7*****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 665.03
//
Query:       gi|488600230|ref|YP_007906701.1|  [L=183]
Description: TATA binding protein of transcription factor TFIID [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-63  208.8   0.1    2.5e-30  104.3   0.1    2.0  2  TBP         Transcription factor TFIID (or TATA-binding prote
    2.5e-08   33.9   0.0     0.0014   18.7   0.0    2.2  2  DUF3378     Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.097   13.0   0.0        5.6    7.3   0.0    2.2  2  T4bSS_IcmS  Type IVb secretion, IcmS, effector-recruitment


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 !  104.3   0.1   4.2e-34   2.5e-30       1      84 [.       5      86 ..       5      87 .. 0.97
   2 !  102.9   0.0   1.1e-33   6.8e-30       2      83 ..      97     178 ..      96     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 4.2e-34
                                      EEEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHH CS
                               TBP  1 dfkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkia 79
                                      ++ki+Nvvas+++g ++dL+k+a++   ++aeY+p++fpglv+r ++pk++aliF+sGkvv+tG ks+e++++a+++++
  gi|488600230|ref|YP_007906701.1|  5 KIKIENVVASTQIGENIDLNKIAREI--KDAEYKPKQFPGLVLRTKDPKAAALIFRSGKVVCTGSKSVEDANRAVRQVV 81
                                      589********************998..*************************************************** PP

                                      HHHHH CS
                               TBP 80 pilkk 84
                                      +i++k
  gi|488600230|ref|YP_007906701.1| 82 KIISK 86
                                      ***98 PP

  == domain 2  score: 102.9 bits;  conditional E-value: 1.1e-33
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       +k+qN+vasa+lg++l+L+++a  +  +n+eYepe+fpglvyrl++p+v++liF sGk+v+tG k +e++r a++ki
  gi|488600230|ref|YP_007906701.1|  97 VKVQNIVASADLGVDLNLNAIAIGLGLENIEYEPEQFPGLVYRLNKPRVVVLIFGSGKMVVTGGKGPEDARLAVEKI 173
                                       89********************99779************************************************** PP

                                       HHHHH CS
                               TBP  79 apilk 83 
                                       a+ l+
  gi|488600230|ref|YP_007906701.1| 174 ADELS 178
                                       *9886 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.4e-07    0.0014      10      61 ..      22      74 ..      18      79 .. 0.88
   2 !   13.1   0.0   1.3e-05     0.076      24      58 ..     130     164 ..     125     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-07
                           DUF3378 10 tikkmkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61
                                      +++k+  + k+   + k+ p+ v + k++++   +++SgKV+  G++  ++A+
  gi|488600230|ref|YP_007906701.1| 22 DLNKIAREIKDAeYKPKQFPGLVLRTKDPKAAALIFRSGKVVCTGSKSVEDAN 74
                                      57888888888757899****************************99888886 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaea 58 
                                        ++ p+ v++  k+ +++ ++ SgK ++ G +  +
  gi|488600230|ref|YP_007906701.1| 130 PEQFPGLVYRLNKPRVVVLIFGSGKMVVTGGKGPE 164
                                       5789***********************99976555 PP

>> T4bSS_IcmS  Type IVb secretion, IcmS, effector-recruitment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00094       5.6       9      61 ..      12      64 ..       4      82 .. 0.80
   2 ?    3.8   0.0     0.012        73      12      62 ..     106     158 ..      96     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00094
                        T4bSS_IcmS  9 ilaeeadddfdddasaisaeeveedtglleqliraadqlaSlaLffglkatve 61
                                      + + +++++ d++  a   ++ e    + ++l+ ++++ + +aL f+ ++ v 
  gi|488600230|ref|YP_007906701.1| 12 VASTQIGENIDLNKIAREIKDAEYKPKQFPGLVLRTKDPKAAALIFRSGKVVC 64
                                      556678889998888888888889999*******************9987664 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.012
                        T4bSS_IcmS  12 eeadddfdddasai..saeeveedtglleqliraadqlaSlaLffglkatvek 62 
                                       ++++ d +++a ai    e++e + ++ ++l+ + ++   + L fg ++ v+ 
  gi|488600230|ref|YP_007906701.1| 106 ADLGVDLNLNAIAIglGLENIEYEPEQFPGLVYRLNKPRVVVLIFGSGKMVVT 158
                                       4556666666666522579***************************9998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1079.39
//
Query:       gi|488600231|ref|YP_007906702.1|  [L=202]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-38  130.1  12.6    8.7e-38  129.8  12.6    1.1  1  DUF1405   Protein of unknown function (DUF1405)


Domain annotation for each model (and alignments):
>> DUF1405  Protein of unknown function (DUF1405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8  12.6   4.8e-42   8.7e-38       1     156 [.      32     190 ..      32     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 4.8e-42
                           DUF1405   1 gtvyGyiyYgkqlaetplllwpfvpDSPtAtlffalallllllgrelellealAfvtlikyGlWtvvvlllvllkgg 77 
                                       g+vyGy+yY++ql+++p ++w++++D+P A+lf+a+a++l+l+gr+++ +++++   l+kyGlWt+ vl+++ +   
  gi|488600231|ref|YP_007906702.1|  32 GAVYGYYYYRYQLMASPEYFWILITDCPNASLFIAVAVTLILIGRKSDDFSFFSSANLFKYGLWTMSVLIYHKAY-- 106
                                       89*******************************************************************999732.. PP

                           DUF1405  78 leelm...........LilsHlamavealllaril.rfsvkalavalawlllndvvDYvlgvlpelhetleeeleli 142
                                           +           ++++H+ ++ve+++l++++ ++s+k l+++++w++lnd+ DY+l+++p+++e+    +el+
  gi|488600231|ref|YP_007906702.1| 107 ----FfsggryilysfIFVTHFLLFVESFWLISLAeNVSRKGLMLTVLWMVLNDFSDYILNTHPYIPESG---IELV 176
                                       ....223333345666*****************99789**************************999555...**** PP

                           DUF1405 143 aafavvltvlslll 156
                                       aa++v+l+ +s+ll
  gi|488600231|ref|YP_007906702.1| 177 AAYTVILSAVSILL 190
                                       ***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); 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:                         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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1237.37
//
Query:       gi|488600232|ref|YP_007906703.1|  [L=180]
Description: hypothetical protein Asulf_00692 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   50.7   8.1    3.3e-10   39.5   1.9    2.6  2  Hexapep_2  Hexapeptide repeat of succinyl-transferase
    5.5e-13   48.1  12.3      3e-10   39.4   2.3    3.3  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
  ------ inclusion threshold ------
      0.033   13.2   0.1        1.7    7.7   0.0    2.1  2  MMM1       Maintenance of mitochondrial morphology protein 1


Domain annotation for each model (and alignments):
>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.5   4.7e-06     0.028       2      33 ..      58      95 ..      57      96 .. 0.88
   2 !   39.5   1.9   5.6e-14   3.3e-10       2      28 ..     109     137 ..     108     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-06
                                      EEE-TT-EE-TT-E..E..S..EEE-TT-EE-TT-EE- CS
                         Hexapep_2  2 viIGdnCliGanag..i..G..vslGdncvvgaGvvit 33
                                      v+ G+n+ +G  ++  i  +  +++G+n+++g + vi 
  gi|488600232|ref|YP_007906703.1| 58 VKLGNNVSFGLESTldIffPelIEIGNNSIIGFNTVIL 95
                                      889***********66677689*************997 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 5.6e-14
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvga 28 
                                       v+IG+n+ iGan++i  Gv++Gdn++++a
  gi|488600232|ref|YP_007906703.1| 109 VRIGKNVTIGANCTIlpGVEIGDNSIISA 137
                                       99*************************98 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.021   1.3e+02      19      28 ..      57      66 ..      55      67 .. 0.72
   2 !   11.7   0.5   2.7e-05      0.16      21      34 ..      81      94 ..      80      96 .. 0.88
   3 !   39.4   2.3     5e-14     3e-10       2      35 ..     109     142 ..     108     143 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.021
                                      TEEE-TTEEE CS
                           Hexapep 19 nVkIGdnvkI 28
                                      +Vk+G+nv  
  gi|488600232|ref|YP_007906703.1| 57 GVKLGNNVSF 66
                                      6788888765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.7e-05
                                      EE-TTEEEETTEEE CS
                           Hexapep 21 kIGdnvkIgagvvi 34
                                      +IG+n++Ig ++vi
  gi|488600232|ref|YP_007906703.1| 81 EIGNNSIIGFNTVI 94
                                      79**********99 PP

  == domain 3  score: 39.4 bits;  conditional E-value: 5e-14
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       ++IG+nv+Ig++++i+++V+IGdn++I a++ ++
  gi|488600232|ref|YP_007906703.1| 109 VRIGKNVTIGANCTILPGVEIGDNSIISAHSLVN 142
                                       68****************************9986 PP

>> MMM1  Maintenance of mitochondrial morphology protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0047        28     160     206 ..      34      78 ..      28      84 .. 0.82
   2 ?    7.7   0.0   0.00028       1.7     145     169 ..     100     124 ..      83     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0047
                                       --EEEEEEE.EE-TTTTSS-EEEEEEEEEEEEEEEEEEEEEEESSSS CS
                              MMM1 160 fPifsncriikeskesekkrLeakidvdlsDtltlgietkLllnyPk 206
                                       + i++ cri+   + s k  L  +i v l +++++g+e +L + +P 
  gi|488600232|ref|YP_007906703.1|  34 YIIIAICRILP--SLSLKCWLLRRIGVKLGNNVSFGLESTLDIFFPE 78 
                                       66888899955..3445788999******************999997 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00028
                                       TEEEEEEEEEE--S---EEEEEEE. CS
                              MMM1 145 yldkikvteidlGedfPifsncrii 169
                                        +d+++v e+ +G++  i +nc i+
  gi|488600232|ref|YP_007906703.1| 100 LIDELRVGEVRIGKNVTIGANCTIL 124
                                       48*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1129.79
//
Query:       gi|488600233|ref|YP_007906704.1|  [L=304]
Description: RNAse Z [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   70.1   0.0    1.7e-08   34.2   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    6.9e-12   45.8   0.0      5e-11   43.0   0.0    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
    9.4e-09   34.8   0.0    1.8e-08   33.9   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.26   11.2   0.0    1.8  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 !   34.2   0.0   3.8e-12   1.7e-08       2     130 ..      32     147 ..      31     156 .. 0.80
   2 !   33.9   0.0   4.6e-12   2.1e-08     132     201 .]     198     267 ..     182     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.8e-12
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEE.HHHHHHCCT CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyap.kgvlavlea 72 
                                        +L+D+g ++  q++ a      +  +++++ +++th H DH+ag+  l e      r++kl+++ p +  l++l +
  gi|488600233|ref|YP_007906704.1|  32 KVLFDCGEGTQRQMMIA------KTGFRRLNNIFITHLHTDHFAGIFGLIEtlslnDRKDKLTIHSPnAIFLRKLFE 102
                                       59*******76664433......5689*************************9965444449999663777999999 PP

                                       TCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEE CS
                     Lactamase_B_2  73 nfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlri 130
                                        f y++ e e  ++v++++ +  fe++  g+++ a+   h  +          +G+++
  gi|488600233|ref|YP_007906704.1| 103 MFGYNNIEYE--IEVKDVKDNSVFEFD--GFRVVAFRTDHIVES---------YGYAF 147
                                       9999999998..**************8..777888877775554.........55554 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 4.6e-12
                                       CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliHi 201
                                       ++g+++ y+gDt  ++  + e  ++adll++d+ +++d +  + +  H+t +e +e+a ++++k l+l+Hi
  gi|488600233|ref|YP_007906704.1| 198 RPGRKIIYSGDTRPCETTL-EISRNADLLIHDASFTSDLMEWAiETKHSTAKECAEIASKANVKMLILTHI 267
                                       689*************775.599************999664449**************************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 !   43.0   0.0   1.1e-14     5e-11       4     120 ..      19     130 ..      17     154 .. 0.83
   2 ?    0.3   0.0      0.13     6e+02     141     163 ..     199     223 ..     185     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.1e-14
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       ++ +s+li  +g+ +L+D+G +t+++++      ++ + +++  +++THlH+DH++g  gl+e+   + ++ +++ +
  gi|488600233|ref|YP_007906704.1|  19 RNPSSILINYNGEKVLFDCGEGTQRQMMI-----AKTGFRRLNNIFITHLHTDHFAGIFGLIETLSLNDRKDKLTIH 90 
                                       56799***********************9.....89999************************************99 PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTE CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggr 120
                                       +++   + + ++++g   +++ +  +dv+++   +++g+r
  gi|488600233|ref|YP_007906704.1|  91 SPNAIFLRKLFEMFGYNNIEYEIEVKDVKDNSVFEFDGFR 130
                                       9999999888888887755555555555555555554444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                                       TTCCEEEECTTTSSHHCCCCCC... CS
                       Lactamase_B 141 gggkvlftGDallagetgridl..t 163
                                       +g+k++++GD+ + + t++i++   
  gi|488600233|ref|YP_007906704.1| 199 PGRKIIYSGDTRPCETTLEISRnaD 223
                                       6788999999987666666666332 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   4.1e-12   1.8e-08       4      62 ..      13      69 ..      11      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.1e-12
                     Lactamase_B_4  4 ttptsDtsgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssig 62
                                      t p++D + +++l+++  ++ lf ++gEgtQR ++  k+ + +l++iF+t+ +  ++ +
  gi|488600233|ref|YP_007906704.1| 13 TIPSVDRNPSSILINYNGEKVLF-DCGEGTQRQMMIAKTGFRRLNNIFITHLH-TDHFA 69
                                      5689999999*************.***************************99.55555 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 ?   11.2   0.0   5.8e-05      0.26       8      86 ..      22     148 ..      19     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.8e-05
                     Lactamase_B_3   8 nsflletagarilvDPfka.nlgyeppa....eeaDlvlisqaledHah..letlkql................... 58 
                                       +s+l++ +g ++l D +++ + ++ + a    ++ + + i++ ++dH++     ++ l                   
  gi|488600233|ref|YP_007906704.1|  22 SSILINYNGEKVLFDCGEGtQRQMMI-AktgfRRLNNIFITHLHTDHFAgiFGLIETLslndrkdkltihspnaifl 97 
                                       899************99874333333.3578899*************973223333448888888888888888888 PP

                     Lactamase_B_3  59 ..............aenvkvleegeslevggleiravatsh.........d 86 
                                                     + +vk +++ + +e++g+++ a++t+h          
  gi|488600233|ref|YP_007906704.1|  98 rklfemfgynnieyEIEVKDVKDNSVFEFDGFRVVAFRTDHivesygyafI 148
                                       888888888777776677777778889999999999999985555555440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2196.49
//
Query:       gi|488600234|ref|YP_007906705.1|  [L=106]
Description: SSU ribosomal protein S10P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-26   91.3   0.0    3.8e-26   91.2   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.017   15.9   0.0       0.04   14.7   0.0    1.6  2  PriA_C         Primosomal protein N C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.0   4.2e-30   3.8e-26       1      97 [.       9     102 ..       9     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 4.2e-30
                                       EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HH CS
                     Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatke 76 
                                       rirl++ ++++L++++++i+++a ++g++++gpvplPtkr+ v+v+k p ++ +++ +++e+r+hkRlidi  a+++
  gi|488600234|ref|YP_007906705.1|   9 RIRLSGLNPSDLDRICNQIKEIAGKTGVEISGPVPLPTKRLVVPVRKAPDGEgSETYDHWEMRIHKRLIDI-AADER 84 
                                       8**********************************************************************.5**** PP

                                       HHHHHS-...S---SS-EEEE CS
                     Ribosomal_S10  77 tidtllkllqlnlpegVsvev 97 
                                        ++++++   +++p+ V++e+
  gi|488600234|ref|YP_007906705.1|  85 ALRQIMR---IQVPKDVNIEI 102
                                       *******...*********97 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.5e-06      0.04       6      51 ..       8      49 ..       5      54 .. 0.91
   2 ?   -1.7   0.0      0.62   5.5e+03      66      74 ..      83      91 ..      69     102 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-06
                            PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiaki 51
                                      a+ir+sg + + + + +++++e+  +    ++vei gp+p p +++
  gi|488600234|ref|YP_007906705.1|  8 ARIRLSGLNPSDLDRICNQIKEIAGK----TGVEISGPVPLPTKRL 49
                                      89*******************99888....6799********9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.62
                            PriA_C 66 rkalqkllk 74
                                      ++al+++++
  gi|488600234|ref|YP_007906705.1| 83 ERALRQIMR 91
                                      334444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 749.84
//
Query:       gi|488600235|ref|YP_007906706.1|  [L=423]
Description: translation elongation factor 1A (EF-1A/EF-Tu) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-61  207.6   0.1    1.8e-61  207.1   0.1    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.3e-38  131.7   0.5    5.1e-38  129.8   0.1    2.1  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.3e-16   60.7   0.6    5.2e-16   58.8   0.6    2.1  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    2.1e-09   37.5   0.0    5.5e-08   32.9   0.0    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
    7.6e-06   25.4   0.2    1.4e-05   24.6   0.2    1.3  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    3.6e-05   23.6   1.0    9.9e-05   22.2   1.0    1.7  1  GTP_EFTU_D4  Elongation factor Tu domain 4
     0.0002   20.9   0.4      0.038   13.5   0.6    2.9  2  FeoB_N       Ferrous iron transport protein B
    0.00033   20.8   0.1       0.44   10.6   0.0    2.8  3  Dynamin_N    Dynamin family
     0.0016   18.7   0.1       0.28   11.4   0.1    2.3  2  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0019   17.8   0.4     0.0076   15.9   0.3    1.9  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.017   15.1   0.9        2.6    7.9   0.4    2.4  2  RsgA_GTPase  RsgA GTPase
      0.025   14.0   0.1       0.24   10.8   0.1    2.2  1  SRPRB        Signal recognition particle receptor beta subuni
      0.039   13.4   0.6        1.1    8.7   0.4    2.6  2  Arf          ADP-ribosylation factor family
      0.058   13.0   0.2       0.26   10.9   0.2    2.0  2  Ras          Ras family
      0.067   12.3   0.1        9.4    5.3   0.0    2.2  2  G-alpha      G-protein alpha subunit


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 !  207.1   0.1   1.5e-64   1.8e-61       1     182 [.       5     193 ..       5     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 207.1 bits;  conditional E-value: 1.5e-64
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST............HCHSHHHHHHTSCSSCEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv............lDtlkeErergiTiksaais 62 
                                       k+++ni++ighvDhGK+TL++rLly++g+i ++  ++   e  ++            +D+lkeErergiTi++a+ +
  gi|488600235|ref|YP_007906706.1|   5 KEHINIAMIGHVDHGKSTLIGRLLYEAGEIPEHIIEKyrkE--AQekgkatfefawvMDRLKEERERGITIDVAHRK 79 
                                       689****************************9888886431..225678899************************* PP

                                       EETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST... CS
                          GTP_EFTU  63 leketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl... 135
                                       +e  t+ky i+++D+PGH+dF+k++i+g++++D a+lvvda++Gv++qt+e++ l +++g++ +iv+iNKmD++   
  gi|488600235|ref|YP_007906706.1|  80 FE--TDKYYITIVDCPGHRDFIKNMITGASQADAAILVVDANDGVQAQTKEHVFLSRTLGINqLIVAINKMDKVnyd 154
                                       **..************************************************************************9 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH CS
                          GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk 182
                                       +++++e++e+v+ kl      ++ +g+k + evp++++Sa++g++v 
  gi|488600235|ref|YP_007906706.1| 155 QKRFEEVKEQVS-KL------IRMVGYKPD-EVPMIPTSAYNGDNVL 193
                                       9**********9.78......8999***96.*************986 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.8   2.1e+03      28      56 ..     128     155 ..     103     192 .. 0.63
   2 !  129.8   0.1   4.3e-41   5.1e-38       3     110 ..     313     418 ..     311     420 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.8
                                       EEEEESSS-EEEEEEEEEEECCSSTTSB- CS
                       GTP_EFTU_D3  28 rpvlyirtadvtgkvveLlskldkktekv 56 
                                       + v+  rt  ++  +v++ +k+dk + ++
  gi|488600235|ref|YP_007906706.1| 128 EHVFLSRTLGINQLIVAI-NKMDKVNYDQ 155
                                       567778888888777777.6666554333 PP

  == domain 2  score: 129.8 bits;  conditional E-value: 4.3e-41
                                       EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCE CS
                       GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikp 79 
                                       + +++f+Aq+++l++  +t+it gY+pv +++ta+v++++veL++k+d++t++++e+ p+++k+Gd++iv++e+++p
  gi|488600235|ref|YP_007906706.1| 313 TVVKDFTAQIVVLQH--PTAITVGYTPVVHAHTAQVACRFVELQKKIDPRTGQAKEEYPQYLKTGDAAIVKLEPTRP 387
                                       6789***********..************************************************************ PP

                                       EEE--TTTHCCCCEEEEECTTCEEEEEEEEE CS
                       GTP_EFTU_D3  80 ialekgseypqlGrFaiReggrTvaaGvvte 110
                                       +++ek++e+p+lGrFaiR++g+TvaaG+v +
  gi|488600235|ref|YP_007906706.1| 388 MVIEKVKEIPPLGRFAIRDMGQTVAAGMVLD 418
                                       ****************************986 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 !   58.8   0.6   4.3e-19   5.2e-16       1      73 [.     239     305 ..     239     306 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.3e-19
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       Gtv  grv++G+lk+Gd+v + +   + k   ++++s+e++he+  +a++g+n+G++v+++  ++ i++Gd+ 
  gi|488600235|ref|YP_007906706.1| 239 GTVPVGRVETGILKVGDKVIFQPG--GSK---GEVKSIEMHHEPIPQAEPGDNIGFNVRGVSKNE-IRRGDVC 305
                                       99*******************664..346...9********************************.*****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   4.6e-11   5.5e-08       1     113 [.       9     146 ..       9     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.6e-11
                                       EEEEEESTTSSHHHHHHHHH.................T..............STEEESSSTTSSSSEEEEEEEETTE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinalt.................g..............ekaivsdkpgtTrdinegrvklkgk 46 
                                       ++a +G+   GKStLi +l+                                ++ + +++ g T+d+ ++++++++ 
  gi|488600235|ref|YP_007906706.1|   9 NIAMIGHVDHGKSTLIGRLLyeageipehiiekyrkeAqekgkatfefawvmDRLKEERERGITIDVAHRKFETDKY 85 
                                       589****************977776666666666555055566666666655689999999***********99999 PP

                                       EEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSE.EEEEEE CS
                          MMR_HSR1  47 eielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkp.lilvln 113
                                        i++vD+pG  +    +  +++ +    +ad+++lvvda+ ++++++ +e   l +  +++ li+++n
  gi|488600235|ref|YP_007906706.1|  86 YITIVDCPG--H----RDFIKNMITGASQADAAILVVDAN-DGVQAQTKEHVFLSRTLGINqLIVAIN 146
                                       9********..4....23466666667789********88.557666555444433322221444555 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 !   24.6   0.2   1.2e-08   1.4e-05      29     161 ..      67     188 ..      58     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-08
                         Gtr1_RagA  29 lrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesre.leedletlkeilea 104
                                       ++ g+tidv + ++  +++ ++ ++Dc+G ++f++++++       ++ ++ i V+D++  + ++ + ++ +  l++
  gi|488600235|ref|YP_007906706.1|  67 RERGITIDVAHRKF-ETDKYYITIVDCPGHRDFIKNMITG-----ASQADAAILVVDAN--DgVQAQ-TKEHVFLSR 134
                                       56689*********.58999****************8654.....4677999*******..413333.333444555 PP

                         Gtr1_RagA 105 lrqyspeakvfvlihKmDliqedereeifeerkeeireeiekleke..eiqffaTSiwd 161
                                          ++   ++ v i+KmD+++ d  ++ fee ke++++ i+ ++ +  e+ +  TS ++
  gi|488600235|ref|YP_007906706.1| 135 TLGIN---QLIVAINKMDKVNYD--QKRFEEVKEQVSKLIRMVGYKpdEVPMIPTSAYN 188
                                       55555...57899*******655..5679999999999999777666699999999997 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 !   22.2   1.0   8.3e-08   9.9e-05      21      83 ..     243     303 ..     227     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.3e-08
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT- CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegd 83 
                                       vG +v +G++k+g k+i + G + Ge+++i+ +++ + +a+ G++++  ++g     +i  gd
  gi|488600235|ref|YP_007906706.1| 243 VG-RVETGILKVGDKVIFQPGGSKGEVKSIEMHHEPIPQAEPGDNIGFNVRGVS-KNEIRRGD 303
                                       88.9*********************************************99965.56666666 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.038        45       1      21 [.       8      28 ..       8      55 .. 0.85
   2 !   13.5   0.6   3.2e-05     0.038      32     127 ..      70     160 ..      68     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.038
                                      EEEEEEESTTSSHHHHHHHHH CS
                            FeoB_N  1 itvalvGnpnvGkttlfnalt 21
                                      i++a++G  + Gk+tl+ +l 
  gi|488600235|ref|YP_007906706.1|  8 INIAMIGHVDHGKSTLIGRLL 28
                                      579**************9885 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.2e-05
                                       TSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGGG....HHHHHHHHHHHHHT CS
                            FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvvvnvvdatn....lernLyLtlqllel 104
                                       G+t++ ++ k++++++ ++ivD PG  ++          + +   +++d+ + vvda+       ++ +++ + l +
  gi|488600235|ref|YP_007906706.1|  70 GITIDVAHRKFETDKYYITIVDCPGHRDFI--------KNMITGASQADAAILVVDANDgvqaQTKEHVFLSRTLGI 138
                                       99***********************86553........333333667777777887754211122333344444444 PP

                                       TSSEEEEEETHHHHHHTTEEE-H CS
                            FeoB_N 105 gvpvvlalnmideaekkgieidl 127
                                         ++++a+n++d+++ ++ + ++
  gi|488600235|ref|YP_007906706.1| 139 -NQLIVAINKMDKVNYDQKRFEE 160
                                       .57899******99877666543 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0033         4       1      21 [.      10      30 ..      10      39 .. 0.90
   2 !   10.6   0.0   0.00037      0.44      66     152 ..      57     134 ..      29     148 .. 0.62
   3 ?   -2.4   0.0       3.7   4.5e+03      60      78 ..     345     363 ..     314     390 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0033
                                      EEEEEBTTTTHHHHHHHHHTS CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlge 21
                                      ia +G++ +GKS+++  Ll e
  gi|488600235|ref|YP_007906706.1| 10 IAMIGHVDHGKSTLIGRLLYE 30
                                      899************999865 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00037
                                       HHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS.. CS
                         Dynamin_N  66 sevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanh.. 140
                                         v + +++e+e+         ++ + +++++ ++  +t+vD PG  +  k+   +++  + +ad+ ++v++an   
  gi|488600235|ref|YP_007906706.1|  57 AWVMDRLKEERERGI-------TIDVAHRKFETDKYYITIVDCPGHRDFIKN---MITG-ASQADAAILVVDANDgv 122
                                       333333333333322.......3366788999999**********9996654...4554.57788888888888732 PP

                                       -CCC-CHHHHHH CS
                         Dynamin_N 141 dlsnsealflar 152
                                       ++ ++e  fl+r
  gi|488600235|ref|YP_007906706.1| 123 QAQTKEHVFLSR 134
                                       344445556655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.7
                                       -EB--CHHHHHHHHHHHHH CS
                         Dynamin_N  60 kkledfsevreeieketek 78 
                                       +    f e++++i+ +t +
  gi|488600235|ref|YP_007906706.1| 345 QVACRFVELQKKIDPRTGQ 363
                                       3333333333333333333 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 ?    4.9   0.0     0.024        29       2      22 ..      10      30 ..       9      40 .. 0.88
   2 !   11.4   0.1   0.00024      0.28       9     120 .]      48     150 ..      46     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.024
                                      EEEESSTTSSHHHHHHCHCT- CS
                               Roc  2 vvlvGdsgvGKtsllkrfved 22
                                      + ++G    GK++l+ r++ +
  gi|488600235|ref|YP_007906706.1| 10 IAMIGHVDHGKSTLIGRLLYE 30
                                      789**************9875 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00024
                                       TSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEE CS
                               Roc   9 gvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalail 85 
                                       + GK ++   +v d+ +e+++  i +d+++++++      +    +k+ + i D  G+ +f + +    ++a++ail
  gi|488600235|ref|YP_007906706.1|  48 EKGKATFEFAWVMDRLKEERERGITIDVAHRKFE------T----DKYYITIVDCPGHRDFIKNMITGASQADAAIL 114
                                       679999999*******************998862......2....357899************99999********* PP

                                       EEEGHHH.HCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                               Roc  86 vydsrss.enlkeWlkelkkvagkspvilvgnkiDl 120
                                       v+d+++  +   +    l++  g +++i+ +nk+D+
  gi|488600235|ref|YP_007906706.1| 115 VVDANDGvQAQTKEHVFLSRTLGINQLIVAINKMDK 150
                                       ***7764255556666778888899999999*9995 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 ?   -1.3   0.0       1.2   1.4e+03       7      23 ..      14      30 ..      10      41 .. 0.77
   2 !   15.9   0.3   6.3e-06    0.0076     103     169 ..     100     168 ..      87     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                                      ESTTCCHHHHHHHHHCT CS
                              cobW  7 GflGsGKTtLlnhllen 23
                                      G +  GK+tL+ +ll +
  gi|488600235|ref|YP_007906706.1| 14 GHVDHGKSTLIGRLLYE 30
                                      66677******999944 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.3e-06
                                       SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEE.EE-HHHHCHC...HHHHHHHHHHH CS
                              cobW 103 eeelksdltldavvavvDaknleaeeekieekaedqlaaadllv.lnKtDlldee.allekleerlrql 169
                                       ++ ++ + ++da + vvDa+   ++++k++  + + l    l+v +nK+D ++++ +  e+++e++++l
  gi|488600235|ref|YP_007906706.1| 100 KNMITGASQADAAILVVDANDGVQAQTKEHVFLSRTLGINQLIVaINKMDKVNYDqKRFEEVKEQVSKL 168
                                       5667788999**********99999****************99879********956666666666554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.016        20     102     123 ..      10      31 ..       2      98 .. 0.74
   2 ?    7.9   0.4    0.0022       2.6      13      75 ..     106     168 ..      95     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                                       EEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                       ++++G+   GKStLi +ll e+
  gi|488600235|ref|YP_007906706.1|  10 IAMIGHVDHGKSTLIGRLLYEA 31 
                                       57899999*********99874 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0022
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH.HHHHHHHHHHHT CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee.eleelkeeleal 75 
                                       ++  d +++vv ++ + ++ ++ + + +l  + gi ++++++nK+D ++ ++ ++ee+ke++++l
  gi|488600235|ref|YP_007906706.1| 106 ASQADAAILVVDAN-DGVQAQTKEHV-FLSRTLGInQLIVAINKMDKVNYDQkRFEEVKEQVSKL 168
                                       67788889998888.56665555554.55566666478889*******98886555555555443 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 ?   10.8   0.1    0.0002      0.24      41      86 ..      77     119 ..       5     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                       TTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETT CS
                             SRPRB  41 lkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDSt 86 
                                       ++  ++++  +t++D PGh  + +++++     s++ + + vvD+ 
  gi|488600235|ref|YP_007906706.1|  77 HRKFETDKYYITIVDCPGHRDFIKNMITG---ASQADAAILVVDAN 119
                                       34346778889**********99999988...77889999999975 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.12   1.5e+02      11      36 ..       4      29 ..       1      37 [. 0.84
   2 ?    8.7   0.4   0.00094       1.1      34     163 ..      63     191 ..      47     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                                      .TTEEEEEEEESTTSSHHHHHHHHHH CS
                               Arf 11 kkkelrilllGLDnaGKtTilkklkl 36
                                      +k ++ i ++G    GK+T++ +l  
  gi|488600235|ref|YP_007906706.1|  4 EKEHINIAMIGHVDHGKSTLIGRLLY 29
                                      578899***************99865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00094
                                       HHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEETT-CTTHHHHHHHHHHHCTS CS
                               Arf  34 lkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektdavifvvDsadreRleeakeeLkallee 110
                                       lk+e+      Ti    ++ e+ ++ +t+ D  G++   +   +  ++ da i vvD++d    ++ +    +++ +
  gi|488600235|ref|YP_007906706.1|  63 LKEERE--RGITIDVAHRKFETDKYYITIVDCPGHRDFIKNMITGASQADAAILVVDANDGVQAQTKE----HVFLS 133
                                       333333..44588889999999999**********99999999999************9986544332....34455 PP

                                       GCCTTSEEEEEEE-TTSTTSS-H..HHHHHHTT.GGGSS..SSSSEEEEEEBTTTTBT CS
                               Arf 111 eelkevallvlaNKqDlpealse..eelrellg.leelk..gkrkleiqkcsavkgeg 163
                                       ++l   +l+v  NK+D  +  ++  ee++e+++ l ++   +  ++ ++ +sa +g++
  gi|488600235|ref|YP_007906706.1| 134 RTLGINQLIVAINKMDKVNYDQKrfEEVKEQVSkLIRMVgyKPDEVPMIPTSAYNGDN 191
                                       678888899999****876543311455554321222222223444455566666655 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0         1   1.2e+03       2      19 ..      10      27 ..       9      38 .. 0.85
   2 ?   10.9   0.2   0.00022      0.26      10     128 ..      49     162 ..      46     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1
                                      EEEEESTTSSHHHHHHHH CS
                               Ras  2 lvlvGdsavGKtslllrf 19
                                      + ++G    GK++l+ r 
  gi|488600235|ref|YP_007906706.1| 10 IAMIGHVDHGKSTLIGRL 27
                                      6799**********9775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                                       SSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHH CS
                               Ras  10 vGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsres 86 
                                        GK+++ + +v d+ kee e  i +d   +++e+d  ++ ++i D  G  +f +   +  ++a++++lv d ++   
  gi|488600235|ref|YP_007906706.1|  49 KGKATFEFAWVMDRLKEERERGITIDVAHRKFETD--KYYITIVDCPGHRDFIKNMITGASQADAAILVVDANDGV- 122
                                       59*********************999999988877..567789*********99999999********97765544. PP

                                       HHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHH CS
                               Ras  87 fenvkkwveeikrvaeenvpivLvGnKvDleekravsteege 128
                                        +  +k +  ++r+     ++++  nK+D  +  + ++ee++
  gi|488600235|ref|YP_007906706.1| 123 -QAQTKEHVFLSRTLGI-NQLIVAINKMDKVNYDQKRFEEVK 162
                                       .3333334445555552.345555588887774444444433 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.009        11      19      41 ..       3      25 ..       1      49 [. 0.79
   2 ?    5.3   0.0    0.0079       9.4     186     234 ..      70     117 ..      40     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.009
                                      XE..EEEEEEEESTTSSHHHHHH CS
                           G-alpha 19 kkkrevkllllGqseSGKsTilk 41
                                      k+k+++++ ++G+ + GKsT++ 
  gi|488600235|ref|YP_007906706.1|  3 KEKEHINIAMIGHVDHGKSTLIG 25
                                      44689***************975 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0079
                                       ----SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEE CS
                           G-alpha 186 lktvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvs 234
                                         t+ + + kfe d k+ ++ivd+ G+r+  k+ ++  +++da i +v 
  gi|488600235|ref|YP_007906706.1|  70 GITIDVAHRKFETD-KYYITIVDCPGHRDFIKNMITGASQADAAILVVD 117
                                       45999********9.*************999998888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2968.27
//
Query:       gi|488600236|ref|YP_007906707.1|  [L=728]
Description: translation elongation factor 2 (EF-2/EF-G) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-67  224.8   0.1    1.2e-66  224.0   0.1    1.4  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.1e-30  105.0   0.1    5.5e-30  103.6   0.1    1.8  1  EFG_IV       Elongation factor G, domain IV
    1.1e-25   89.5   1.2    2.3e-25   88.5   0.4    2.0  2  EFG_II       Elongation Factor G, domain II
    5.7e-25   87.2   0.2    2.5e-24   85.1   0.1    2.2  2  EFG_C        Elongation factor G C-terminus
      1e-15   57.9   0.2    3.2e-15   56.3   0.2    2.0  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00013   22.0   0.0    0.00043   20.3   0.0    1.9  2  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.053   13.1   0.0    1.5  1  Ras          Ras family
      0.078   12.4   0.1       0.18   11.2   0.1    1.6  1  TniB         Bacterial TniB protein


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.0   0.1   5.3e-70   1.2e-66       2     193 ..      20     256 ..      19     257 .. 0.92

  Alignments for each domain:
  == domain 1  score: 224.0 bits;  conditional E-value: 5.3e-70
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliD 76 
                                       +irn+gi++h+DhGKtTL+d+Ll+ +g+is+  e a+ + +lD+ ++E+ergiTi++a++s+ +  ++++ylinliD
  gi|488600236|ref|YP_007906707.1|  20 KIRNMGIVAHIDHGKTTLSDNLLAGAGMISE--ELAGRQLYLDFDEQEQERGITINAANVSMVHnyKGEEYLINLID 94 
                                       89*****************************..889999************************4469********** PP

                                       ESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  77 tPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                       tPGHvdF  +v+r++r++Dga++vvdaveGv+pqte+vlr+al+e+v++++f+NK+Drl++el+ ++ee++++l ++
  gi|488600236|ref|YP_007906707.1|  95 TPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQALRENVKPVLFVNKVDRLIKELELSPEEMQKRLIDV 171
                                       **************************************************************************777 PP

                                       HHHHHHHHHTTT...........TTEEEEEEBTTTTBTHH..................................HHH CS
                          GTP_EFTU 154 eeklekygekge...........kevpvvfgSalkgegvk..................................tll 185
                                        ++++k     +           ++ +v+fgSal +++v+                                   +l
  gi|488600236|ref|YP_007906707.1| 172 INEVNKLIKAMKperydewrldvTKGSVAFGSALYKWAVSvpamketgigfkevteyikegkvnelskksplhtVVL 248
                                       555555544444778888899999999**********99988999999999999999999999999****999779* PP

                                       HHHHHHSH CS
                          GTP_EFTU 186 ealvellp 193
                                       +++v++lp
  gi|488600236|ref|YP_007906707.1| 249 DMVVRHLP 256
                                       *****998 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.1   2.5e-33   5.5e-30       2     121 .]     506     617 ..     505     617 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 2.5e-33
                                       CCESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TT CS
                            EFG_IV   2 qVayrEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGpl 78 
                                       +V ++    +++ker+++l +  g ++++a  i e ++     gn+f d tkg+q+++e++e++ +Gf+ea++ Gpl
  gi|488600236|ref|YP_007906707.1| 506 KVDMK----MDKKERRRILEE-LGLTKEEAAGIQEYYE-----GNIFTDVTKGIQYLNETMELILEGFREAMRAGPL 572
                                       67777....899956655555.9***************.....9********************************* PP

                                       TS--EESEEEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC- CS
                            EFG_IV  79 agepvtdvkvtLldgslhe..vdsseaafkpaarralkeallkAs 121
                                       a+epv++vkv+L+d++lhe  v++++a+++pa+r a+ +a+l+A+
  gi|488600236|ref|YP_007906707.1| 573 AREPVMGVKVKLVDCKLHEdaVHRGPAQVIPAVRSAIFAAILQAQ 617
                                       ******************************************996 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.4     1e-28   2.3e-25       1      74 [.     386     459 ..     386     460 .. 0.97
   2 ?   -2.2   0.0         2   4.5e+03      37      51 ..     549     563 ..     542     566 .. 0.77

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1e-28
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       ++ePv+++aie+k+ +d  kl ++L+ +++EDptl+v+ +eeT+e +lsGmGelHle++ve+++r+ ++ev ++
  gi|488600236|ref|YP_007906707.1| 386 VSEPVVTMAIEAKNPRDLPKLIEVLRAIAKEDPTLQVTLNEETGEHLLSGMGELHLEVTVEKIRRDKNLEVVTS 459
                                       689*******************************************************************9875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                            EFG_II  37 verdeeTketilsGm 51 
                                       +++ +eT e+il+G 
  gi|488600236|ref|YP_007906707.1| 549 IQYLNETMELILEGF 563
                                       66678********96 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 ?   -3.2   0.0       4.1   9.1e+03      14      38 ..     161     185 ..     160     192 .. 0.75
   2 !   85.1   0.1   1.1e-27   2.5e-24       2      85 ..     620     702 ..     619     705 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.1
                                       ECCCCCCHHHHHHHCT-EEEEEEEE CS
                             EFG_C  14 peeyvgkvisdlssrrGeiedmeqd 38 
                                       pee++++ i+ +++ +  i+ m+++
  gi|488600236|ref|YP_007906707.1| 161 PEEMQKRLIDVINEVNKLIKAMKPE 185
                                       8899999999888877777777665 PP

  == domain 2  score: 85.1 bits;  conditional E-value: 1.1e-27
                                       EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEE CS
                             EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgY 78 
                                       llEP++kv i+vp++++g v  +++ rrG+i +m+++ +++v++ a++P++e++gfa ++rs+T+G++++s+e+sg+
  gi|488600236|ref|YP_007906707.1| 620 LLEPYQKVFISVPQDMLGSVSREIQGRRGQIMEMKTE-GDMVTVVAKAPVKEMFGFAGDIRSATAGKAIWSTELSGF 695
                                       8************************************.*************************************** PP

                                       EE--HHH CS
                             EFG_C  79 eevpgdk 85 
                                       eevp+ +
  gi|488600236|ref|YP_007906707.1| 696 EEVPQGM 702
                                       ***9865 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.2   1.4e-18   3.2e-15       1      73 [.     305     371 ..     305     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.4e-18
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G++a gr++sGt+k G+e+ +  +d + k    ri+ +  f+++++ +v++ +aG+iva++gl+da ++G+t 
  gi|488600236|ref|YP_007906707.1| 305 GEIAVGRLFSGTIKSGMELFV--VDRKAK---NRIQNVGLFMGPKRVDVPEIPAGNIVAVVGLKDA-VAGSTC 371
                                       89*******************..999888...*********************************8.****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 !   20.3   0.0   1.9e-07   0.00043       3     113 ..      25     148 ..      23     149 .. 0.59
   2 ?   -3.7   0.0       5.5   1.2e+04      65      86 ..     308     329 ..     278     338 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.9e-07
                                       EEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE..ETT..EEEEEEECGGCSSH CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk..lkg..keielvDtpGlieg 59 
                                       +iv +   GK+tL   l+                 +  + +++ g T++     +   +kg    i+l+DtpG ++ 
  gi|488600236|ref|YP_007906707.1|  25 GIVAHIDHGKTTLSDNLLAgagmiseelagrqlylDFDEQEQERGITINAANVSMVhnYKGeeYLINLIDTPGHVD- 100
                                       566667789999998888444455555554443333446677777777774444432422212559*******665. PP

                                       HHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHH.HHHTTSEEEEEEE CS
                          MMR_HSR1  60 aseekglgkaflaleeadlillvvdaseeklkpldeeleel.leeakkplilvln 113
                                          + ++++a+   + +d +++vvda  e++ p+ e++ +  l+e+ kp +l +n
  gi|488600236|ref|YP_007906707.1| 101 --FGGDVTRAM---RAVDGAIVVVDAV-EGVMPQTETVLRQaLRENVKP-VLFVN 148
                                       ..222344444...458********99.667777766655504555566.45455 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHCTSEEEEEEETT CS
                          MMR_HSR1  65 glgkaflaleeadlillvvdas 86 
                                        +g+ f   +++ + l+vvd +
  gi|488600236|ref|YP_007906707.1| 308 AVGRLFSGTIKSGMELFVVDRK 329
                                       6677777778888888999833 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.4e-05     0.053      25     116 ..      65     152 ..      56     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                                       SSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHH.HH CS
                               Ras  25 keeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeik.rv 100
                                       ++e   Ti +++ +   +++g+e+ +++ DT G  +f    +  +r ++g+++v d  +      v   +e +  + 
  gi|488600236|ref|YP_007906707.1|  65 EQERGITINAANVSMVHNYKGEEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVE-----GVMPQTETVLrQA 136
                                       4556679999999999**************************************88654.....4443333333033 PP

                                       STTTSEEEEEEETTTG CS
                               Ras 101 aeenvpivLvGnKvDl 116
                                        +env+ vL  nKvD 
  gi|488600236|ref|YP_007906707.1| 137 LRENVKPVLFVNKVDR 152
                                       4478888999999994 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   7.8e-05      0.18      14      53 ..       2      39 ..       1      51 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.8e-05
                              TniB 14 prakeilerLeeLleypkrkrmpnlllvGdsnnGKtmive 53
                                      +rak+++++++eL+ +p++ r  n+ +v + + GKt++ +
  gi|488600236|ref|YP_007906707.1|  2 ARAKKMIDKIQELMYKPEKIR--NMGIVAHIDHGKTTLSD 39
                                      689***************999..**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.49
# Mc/sec: 4474.65
//
Query:       gi|488600237|ref|YP_007906708.1|  [L=194]
Description: SSU ribosomal protein S7P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-40  135.8   3.4    1.1e-39  135.5   3.4    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
       0.12   12.7   0.6       0.28   11.5   0.6    1.6  1  FAM25         FAM25 family


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 !  135.5   3.4   1.2e-43   1.1e-39      17     149 .]      53     194 .]      40     194 .] 0.94

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 1.2e-43
                                       STTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEE CS
                      Ribosomal_S7  17 kynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpv 89 
                                       k +  +ve+link+m+    +Gkk lA++iv++a++iie+ktkk+pl+vl++Al n+ Pr+e+ ++++GG++++ +v
  gi|488600237|ref|YP_007906708.1|  53 KRKVFIVERLINKVMRkeknTGKKILAYNIVKSAFEIIEKKTKKNPLQVLVDALINAGPREEIVRLKYGGIAVPKSV 129
                                       556679*************9********************************************************* PP

                                       EE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  90 evrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       + ++ Rr ++Alr+i+e+a   ++++++s++ +La+E+i+Aa+++  + av k+ee++r+A+++r
  gi|488600237|ref|YP_007906708.1| 130 DTSSLRRLDIALRNIAEGArkaSFKSKRSIEACLADEIISAANNDskSFAVAKKEEIERVAKSAR 194
                                       *******************7777788999***************98899*************987 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   3.1e-05      0.28       3      41 ..      57      96 ..      55     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.1e-05
                             FAM25  3 haveevvkevveHaKeaGEKAia.dalKkAqesgekvvKe 41
                                       +ve  ++ v+   K++G K +a + +K A e  ek+ K 
  gi|488600237|ref|YP_007906708.1| 57 FIVERLINKVMRKEKNTGKKILAyNIVKSAFEIIEKKTKK 96
                                      579*******************97899******9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1370.82
//
Query:       gi|488600238|ref|YP_007906709.1|  [L=142]
Description: SSU ribosomal protein S12P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-47  159.2   0.3    3.1e-47  158.9   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 !  158.9   0.3   1.7e-51   3.1e-47       1     113 [.      27     140 ..      27     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 1.7e-51
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r+ lr++ ksd+legap++rG+vlek++vea++Pns +Rk+vrv+Likngk++ af+pg+g++nf+dEhdev+v+ i
  gi|488600238|ref|YP_007906709.1|  27 RRVLRLNVKSDPLEGAPMARGIVLEKLGVEARQPNSGIRKAVRVQLIKNGKQISAFTPGDGSINFIDEHDEVVVEKI 103
                                       6788999********************************************************************99 PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                       +++ g++++D+pG+rykv+kv++vslk+l+k++kekp
  gi|488600238|ref|YP_007906709.1| 104 GGRmGRSMGDIPGIRYKVIKVNNVSLKELWKGRKEKP 140
                                       9888*******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1051.33
//
Query:       gi|488600239|ref|YP_007906710.1|  [L=139]
Description: NusA family KH domain protein, archaeal [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   69.2  11.5    1.1e-13   50.7   2.8    2.1  2  KH_2      KH domain
    3.6e-13   49.4   2.9    3.6e-13   49.4   2.9    2.5  3  KH_5      NusA-like KH domain
    9.8e-09   35.0   3.3    2.6e-06   27.2   0.3    2.3  2  KH_4      KH domain
    5.8e-05   22.8  11.2      0.011   15.6   1.3    2.4  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 !   50.7   2.8   2.5e-17   1.1e-13       6      66 ..      15      85 ..      13      95 .. 0.86
   2 !   22.4   3.9   1.8e-08   8.1e-05       8      56 ..      89     129 ..      83     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 2.5e-17
                                      HHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC............E CS
                              KH_2  6 laveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk............V 66
                                      l++++++a v+++ +++  ++v++v++++ +g +IGkgG ni++ ++ ++k+ie++e+++            +
  gi|488600239|ref|YP_007906710.1| 15 LFESLTGASVKDCLVQE--DKVVFVVKKGDMGTAIGKGGINIERTREIIGKKIEVVEYSDdpvefivnifkpI 85
                                      899************55..****************************************99988876655552 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.8e-08
                                       HHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHH CS
                              KH_2   8 veikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrk 56 
                                       v+i++++ +k         +ii +    +g+vIGkgG+ni+k ++ +++
  gi|488600239|ref|YP_007906710.1|  89 VKIQEKDDKK--------IAIINVNPQLKGLVIGKGGKNINKAKELAKR 129
                                       4444444444........45699*********************99976 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   2.9   8.1e-17   3.6e-13       2      65 ..      31      88 ..      30      91 .. 0.95
   2 ?    1.7   0.2      0.06   2.7e+02      37      55 ..      94     112 ..      86     113 .. 0.74
   3 ?    3.1   1.3     0.022     1e+02       6      32 ..      98     122 ..      93     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 8.1e-17
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevl 65
                                      +++++++Vk+++     +G+++gk+G +i+   + + g+ki+vve+s+D++efi n+++P +++
  gi|488600239|ref|YP_007906710.1| 31 EDKVVFVVKKGD-----MGTAIGKGGINIERTREII-GKKIEVVEYSDDPVEFIVNIFKPINIT 88
                                      6899********.....**************99999.***********************9985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.06
                              KH_5  37 LkgekidvvewseDlaefi 55 
                                        +++ki +++ ++ l+ ++
  gi|488600239|ref|YP_007906710.1|  94 KDDKKIAIINVNPQLKGLV 112
                                       3599*****9999888776 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.022
                              KH_5   6 kvaVkshnpnvdpvGaivgkkGsrika 32 
                                       k+a+ + np++   G ++gk+G++i++
  gi|488600239|ref|YP_007906710.1|  98 KIAIINVNPQL--KGLVIGKGGKNINK 122
                                       45555555443..68899999999987 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2   0.00036       1.6      27      51 ..      30      54 ..      14      64 .. 0.82
   2 !   27.2   0.3   5.8e-10   2.6e-06       8      52 ..      78     121 ..      73     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00036
                              KH_4 27 eeveielnvegedlGrvIGkrGrtl 51
                                      +e+++   v++ d+G  IGk G ++
  gi|488600239|ref|YP_007906710.1| 30 QEDKVVFVVKKGDMGTAIGKGGINI 54
                                      4567777788************776 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 5.8e-10
                              KH_4   8 lkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtld 52 
                                       + +++ +p +++v+++e+++++   +nv+++ +G+vIGk G++++
  gi|488600239|ref|YP_007906710.1|  78 IVNIF-KPINITVKIQEKDDKKIAIINVNPQLKGLVIGKGGKNIN 121
                                       33445.577999999999************************997 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   3.8   5.4e-05      0.24       3      41 ..      35      74 ..      33     102 .. 0.82
   2 !   15.6   1.3   2.4e-06     0.011       4      24 ..     102     122 ..      99     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT. CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sede 41
                                      ++ v++  +g  IGkgG nI + re  g kI v++ s+d+
  gi|488600239|ref|YP_007906710.1| 35 VFVVKKGDMGTAIGKGGINIERTREIIGKKIEVVEySDDP 74
                                      57899999*****************88*******777665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.4e-06
                                       EEEGGGHHHHHHTGGGHHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIke 24 
                                       i v+ +l g++IGkgG+nI++
  gi|488600239|ref|YP_007906710.1| 102 INVNPQLKGLVIGKGGKNINK 122
                                       7899999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 912.25
//
Query:       gi|488600240|ref|YP_007906711.1|  [L=95]
Description: LSU ribosomal protein L30E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   70.5   0.1    8.2e-20   70.4   0.1    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
     0.0024   17.7   0.0     0.0028   17.4   0.0    1.0  1  Hydrolase_3     haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.017   15.2   0.0    1.2  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
      0.018   15.2   0.0      0.019   15.1   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
      0.029   14.4   0.0      0.037   14.1   0.0    1.1  1  BRCT_3          BRCA1 C Terminus (BRCT) domain
      0.073   12.9   0.0      0.074   12.9   0.0    1.1  1  Asp_Glu_race    Asp/Glu/Hydantoin racemase
      0.098   12.6   0.1       0.12   12.3   0.1    1.3  1  BRCA-2_OB1      BRCA2, oligonucleotide/oligosaccharide-bindin
       0.13   12.5   0.0       0.14   12.4   0.0    1.0  1  Hydrolase       haloacid dehalogenase-like hydrolase


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 !   70.4   0.1   3.6e-23   8.2e-20       3      94 ..       5      92 ..       3      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 3.6e-23
                                      HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECS CS
                    Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvs 81
                                      + ++l+ a+++gk+ lG k+++kal++g aklvi+A+++++e  +k l+++  e++v  +++++  +LG+ +gk++ vs
  gi|488600240|ref|YP_007906711.1|  5 VDKALRRALNTGKVYLGSKRTIKALKKGDAKLVIMANNCPEEIAEK-LKQF--EIPVITYNGTN-IDLGATCGKPFSVS 79
                                      6799******************************************.6555..999*9******.************** PP

                                      EEEEEESTTTHHH CS
                    Ribosomal_L7Ae 82 alaikdegdskdl 94
                                       lai+++g+s++l
  gi|488600240|ref|YP_007906711.1| 80 MLAIIEPGESEIL 92
                                      **********997 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06    0.0028       3      67 ..       3      67 ..       2      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                      EEIIIIIS-..TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEE CS
                       Hydrolase_3  3 lDlDGTLln..sdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGalid 67
                                      +D+D  L +  +++k+   +k++ik lk+ + k+vi   + ++++ + l++++   pvi++NG+ id
  gi|488600240|ref|YP_007906711.1|  3 IDVDKALRRalNTGKVYLGSKRTIKALKKGDAKLVIMANNCPEEIAEKLKQFE--IPVITYNGTNID 67
                                      57777775544777888999******************************888..78********93 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   7.8e-06     0.017      11      58 ..      14      58 ..       3      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.8e-06
                                      ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT--- CS
                       Hydrolase_6 11 rgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvdi 58
                                      + +k++ g++++++al++   ++v++ Nn    +ee+a+kl+++++++
  gi|488600240|ref|YP_007906711.1| 14 NTGKVYLGSKRTIKALKKGDAKLVIMANNC---PEEIAEKLKQFEIPV 58
                                      5688999*********************98...678999999988875 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   8.3e-06     0.019      77     118 ..      15      56 ..       4      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.3e-06
                             HAD_2  77 evkpydgvkelLeeLkeagyklgivTsksreaveekleqlgi 118
                                       + k+y g k +++ Lk+ + kl i+ ++  e++ ekl+q++i
  gi|488600240|ref|YP_007906711.1|  15 TGKVYLGSKRTIKALKKGDAKLVIMANNCPEEIAEKLKQFEI 56 
                                       468999**********************************97 PP

>> BRCT_3  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.7e-05     0.037      40      74 ..      26      60 ..       8      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                            BRCT_3 40 aeeislgkldvvvtdsscpeevlkkaeqlkipvvS 74
                                       + ++ g  ++v+  ++cpee+ +k +q +ipv++
  gi|488600240|ref|YP_007906711.1| 26 IKALKKGDAKLVIMANNCPEEIAEKLKQFEIPVIT 60
                                      34467788899**********************97 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.3e-05     0.074      52      96 ..      15      59 ..       2      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                                      ..THH.HHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEE CS
                      Asp_Glu_race 52 ddpvl.klleaakkLekagadaiviaCnTahavadelqkkikiPvl 96
                                      + +v+   ++ +k+L+k +a+++++a n +   a++l+++  iPv+
  gi|488600240|ref|YP_007906711.1| 15 TGKVYlGSKRTIKALKKGDAKLVIMANNCPEEIAEKLKQF-EIPVI 59
                                      3446668899********************9999999966.99998 PP

>> BRCA-2_OB1  BRCA2, oligonucleotide/oligosaccharide-binding, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.5e-05      0.12      55      85 ..       1      31 [.       1      70 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                                      EEE---HHHHHHHHTT-S-TT-EEEES--EE CS
                        BRCA-2_OB1 55 ikavlDaalsrllkrgkikvGqKlvvagael 85
                                      +k+ +D+al+r+l++gk++ G+K  +  ++ 
  gi|488600240|ref|YP_007906711.1|  1 MKIDVDKALRRALNTGKVYLGSKRTIKALKK 31
                                      5789*******************99988865 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.4e-05      0.14     114     174 ..      13      75 ..       4      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-05
                                       HHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..GGGESEEEEHHCES..STTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx..xxxx RF
                         Hydrolase 114 adplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..ddyfdaviasdiet..vakp 174
                                        ++ kv+ + + ++++Lk+   ++v++ ++ pe   + ++q+     +++++      +  ++kp
  gi|488600240|ref|YP_007906711.1|  13 LNTGKVYLGSKRTIKALKKGDAKLVIMANNCPEEIAEKLKQFEipVITYNGTNIDL--GatCGKP 75 
                                       56778*************99*********************994322223333333..2336666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 607.24
//
Query:       gi|488600241|ref|YP_007906712.1|  [L=378]
Description: DNA-directed RNA polymerase, subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  196.4   7.2    1.3e-57  195.3   7.2    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5


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 !  195.3   7.2   7.2e-62   1.3e-57      66     265 ..      48     321 ..      12     323 .. 0.92

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 7.2e-62
                                       SB--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  66 glvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekak 142
                                       +lvepGea Gi+aaQSiGePgTQ+t++TFH+aGva+  vtlG+prl ei++v kn +++++t++l de+ak+++ka+
  gi|488600241|ref|YP_007906712.1|  48 NLVEPGEAAGIVAAQSIGEPGTQMTMRTFHYAGVAEIDVTLGLPRLIEIMDVRKNPSTPMMTIRLKDEYAKNRDKAR 124
                                       38*************************************************************************** PP

                                       HHHHHHSE..................................................................... CS
                                       xxxxxxxx..................................................................... RF
                    RNA_pol_Rpb1_5 143 kvkkaiek..................................................................... 150
                                       +v+++ie                                                                      
  gi|488600241|ref|YP_007906712.1| 125 EVANRIEAtyvtdiaeiltdivnmriiikpdthamerkqltleeikkkleknlkveveeeegnlviqikepsyktlm 201
                                       *******9********************************************************************* PP

                                       ............CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHH CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ............gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgieaar 215
                                                   gik+i+r++++     ke+ +e+vl teg nl++v+k+++ vd++++++n+i ei+e+lgieaar
  gi|488600241|ref|YP_007906712.1| 202 ntfdklkktvlvGIKEIRRVIIR-----KED-DEYVLYTEGSNLKKVMKIKG-VDFTRTTTNNIYEIYEVLGIEAAR 271
                                       *9998888888888888888888.....333.6789****************.************************ PP

                                       HHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 216 kallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                       +a+++e ++++++qg++v+drH++l++d mt  ge+ +v+r+G+  ++ s
  gi|488600241|ref|YP_007906712.1| 272 NAVINEAKSTLEEQGLEVDDRHIMLVADAMTSDGELRQVGRHGVAGEKRS 321
                                       *******************************************9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1349  (0.0752412); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2394.62
//
Query:       gi|488600242|ref|YP_007906713.1|  [L=876]
Description: DNA-directed RNA polymerase, subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-100  335.8   0.0   4.9e-100  334.9   0.0    1.5  2  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    1.2e-67  227.3   0.0    1.8e-67  226.7   0.0    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
      2e-37  128.6   0.0    3.6e-37  127.7   0.0    1.5  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    9.6e-32  109.1   0.2    2.7e-31  107.7   0.2    1.8  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    1.3e-26   93.7   0.0    2.7e-26   92.6   0.0    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.028   14.3   0.1       0.09   12.7   0.1    1.8  2  TraB            TraB family
       0.11   12.4   7.8        1.6    8.7   0.0    3.4  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.57   10.5   3.6        0.3   11.4   0.3    2.2  2  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
       0.95   10.2   9.6        4.2    8.2   0.1    3.1  3  WAK_assoc       Wall-associated receptor kinase C-terminal


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.9   0.0  2.5e-103  4.9e-100       2     312 .]       4     308 ..       3     308 .. 0.92
   2 ?   -3.9   0.1       3.4   6.7e+03     134     187 ..     555     619 ..     537     628 .. 0.62

  Alignments for each domain:
  == domain 1  score: 334.9 bits;  conditional E-value: 2.5e-103
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k+i++i+f+++sp+eir++Sv+++ ++et++++  +P e Gl+D+rlg+id  l+C+tCg k  eC+ghfGh+eLa+
  gi|488600242|ref|YP_007906713.1|   4 KRIDSIRFEVLSPQEIRRMSVTKIISSETYDDDG-FPIEAGLMDPRLGVIDPGLRCKTCGGKAGECPGHFGHVELAA 79 
                                       89******************************95.****************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TTSH.....HHHHHHCS.SSCCCCHHHHHHHHCCS-BE-SSSSB-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldeekkkll.sklkkrekl.eelkkrlkaieelckkinlcekCgavqpkle 153
                                       Pv+h+g+ kli k+l ++c+ec+++ll ++k++ + +++++r+ l +++++ +k++ ++ k  ++c +C a q  ++
  gi|488600242|ref|YP_007906713.1|  80 PVIHVGYAKLIAKLLASTCRECGRVLLPDSKRDKFiEEIERRKSLnQDYEDVVKEVFRITKAAKKCPHCHADQFDIK 156
                                       ***************************88876555045555555425678999****************97776665 PP

                                       EETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 154 eegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrs 230
                                        ++ ++    + +     + l++++v++ l+ri+d+d+ v g++++  rPew++ltvlPVpP+++RPs+ l++g+rs
  gi|488600242|ref|YP_007906713.1| 157 FDKPTFFY--EGD-----HRLTPKDVRERLERIPDSDLPVFGMNPKAVRPEWMVLTVLPVPPVTVRPSIILETGQRS 226
                                       55554443..333.....3488******************************************************* PP

                                       BECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 231 edDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGr 307
                                       edDlt+kl+dii++N+r+ +++++gap+li+e+ +elLQ+hv+t++dne+sg++pa+++s+rplk++ qrLk KeGr
  gi|488600242|ref|YP_007906713.1| 227 EDDLTHKLVDIIRINQRFIENKDAGAPQLILEDLWELLQYHVTTYLDNEVSGIPPARHRSGRPLKTIAQRLKEKEGR 303
                                       ***************************************************************************** PP

                                       CCCCT CS
                                       xxxxx RF
                    RNA_pol_Rpb1_1 308 fRgnL 312
                                       fRg+L
  gi|488600242|ref|YP_007906713.1| 304 FRGSL 308
                                       ***98 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.4
                                       HHHCCS-BE-..SSSSB-EEEEEETTEEEEEESSSST.........SCEEEE-HHHHHHHHHCST CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 134 elckkinlce..kCgavqpkleeegeklkaalkkske.........eekeklsaekvkkllkrie 187
                                       e+c+    c+  +C+  +  + ++ge +k ++++++          e  +k  +e+++k +++++
  gi|488600242|ref|YP_007906713.1| 555 EICQGCAECKgeDCEHDAYVIIKKGELIKGTIDEKSVgafkgiiidEIMRKYGPEETRKFIDNMT 619
                                       45555555544466666666667777777777666656666666555556666666666655555 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 !  226.7   0.0   8.9e-71   1.8e-67       1     165 [.     310     473 ..     310     474 .. 0.97

  Alignments for each domain:
  == domain 1  score: 226.7 bits;  conditional E-value: 8.9e-71
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrv++saR+vispdpnl++ evgvPis+a+ ltvp  vte ni++ r+++   ++++P a+yv+r+dg++ ++   
  gi|488600242|ref|YP_007906713.1| 310 GKRVNFSARTVISPDPNLSIMEVGVPISIAQELTVPIFVTEKNIDEAREYIL--RKEHPKANYVIRSDGRRIRVLDL 384
                                       9*************************************************99..789*************9998888 PP

                                       -S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SS CS
                    RNA_pol_Rpb1_2  78 kr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqs 153
                                       ++ ++a++le g+iver++kdgd+vl+NRqPsLh++simah+v+vl++kt+rln +v+ +yNaDFDGDemnlh+pqs
  gi|488600242|ref|YP_007906713.1| 385 NAeEIAERLEPGWIVERQLKDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTFRLNPAVCPPYNADFDGDEMNLHVPQS 461
                                       7768************************************************************************* PP

                                       HHHHHHHHHCSB CS
                    RNA_pol_Rpb1_2 154 eearaEaeelll 165
                                        ea+aEa+ l+ 
  gi|488600242|ref|YP_007906713.1| 462 LEAQAEAKVLMA 473
                                       **********97 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 !  127.7   0.0   1.8e-40   3.6e-37       1     156 [.     477     637 ..     477     638 .. 0.90

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 1.8e-40
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSE..BEEHHHHHHCCC CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpke..lwtgkqtfsril 75 
                                       +ilsp+ g P+ig ++D+++G+yllT+ +  +++ee++ l ++ ++           i  pke   wtgkq+fs+il
  gi|488600242|ref|YP_007906713.1| 477 HILSPRFGGPIIGGIHDHISGLYLLTRGEKKFTKEEVIYLTRRLDVG---------EIPEPKEdgYWTGKQIFSMIL 544
                                       7*******************************************443.........3445544559*********** PP

                                       HCCCCEEEE...SSSS............STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_3  76 pneinyerk...neek............dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldsl 137
                                       p++i +e k      +            d +v+ik+gelikG+id+k vg + +g +i++++++yg++et++f+d++
  gi|488600242|ref|YP_007906713.1| 545 PKDISLEYKaeiC--QgcaeckgedcehDAYVIIKKGELIKGTIDEKSVG-AFKGIIIDEIMRKYGPEETRKFIDNM 618
                                       **88888876440..2455577788888**********************.999*********************** PP

                                       HHHHHHHHHHHCEB-TGGG CS
                    RNA_pol_Rpb1_3 138 qrlgfkyllqsgftigigD 156
                                       ++l ++ ++++gf++gi+D
  gi|488600242|ref|YP_007906713.1| 619 TQLSIRAIMNAGFSFGISD 637
                                       *****************99 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.2   1.4e-34   2.7e-31       1     108 []     663     771 ..     663     771 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 1.4e-34
                                       HHHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEE CS
                    RNA_pol_Rpb1_4   1 ieeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqn 77 
                                       ie++++ g+le++pg+s ee++e+ki++ l +ardkag+iask+l  +Ns +iM+ sGa+Gs++n++q+a+c+Gqq+
  gi|488600242|ref|YP_007906713.1| 663 IEQYKQ-GNLEPMPGRSIEETLEMKIMQELGRARDKAGNIASKYLGMDNSAVIMAVSGARGSMLNLTQMAACIGQQS 738
                                       567777.99*************************************66***************************** PP

                                       BTTBSS--S..STSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  78 vegkripkg..fsgrtlphfkkidespesrGFv 108
                                       v+g+ri++g  +++rtl hfk+ d + ++rGFv
  gi|488600242|ref|YP_007906713.1| 739 VRGERIKRGytYTNRTLSHFKPGDLGSRARGFV 771
                                       *********99*********************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 !   92.6   0.0   1.4e-29   2.7e-26       1      66 [.     778     844 ..     778     870 .. 0.89

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 1.4e-29
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-.EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsgge.ivqflygedg 66 
                                       GL++ efffh+ ggReGL+DtAv+T++sGYlqRrl++al+d+ v+yd+tv++++ + ivqf+ygedg
  gi|488600242|ref|YP_007906713.1| 778 GLNPIEFFFHAVGGREGLVDTAVRTSQSGYLQRRLINALQDLKVDYDGTVKEQTSNvIVQFKYGEDG 844
                                       9*************************************************988765278*******8 PP

>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.6   7.1e+03      75     110 ..     170     207 ..     168     212 .. 0.72
   2 ?   12.7   0.1   4.5e-05      0.09     158     219 ..     635     697 ..     621     721 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.6
                              TraB  75 llseelyarlqkalakrglpla..aldkmkP.wllalll 110
                                       l +++ ++rl+++ ++  lp+   + + ++P w++  +l
  gi|488600242|ref|YP_007906713.1| 170 LTPKDVRERLERIPDS-DLPVFgmNPKAVRPeWMVLTVL 207
                                       5677788888888888.777752255699**99998776 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.5e-05
                              TraB 158 lpdeeqlealeetldele.eakdlleelveaykegdleal..eleaeaeeefpelkevlldeRnr 219
                                       ++dee  e+  ++++e   ea+++++el+e+yk+g+le +  +  + +e+   +++++l + R++
  gi|488600242|ref|YP_007906713.1| 635 ISDEEIPEEAVAQIREVLdEAEKKVDELIEQYKQGNLEPMpgR--SIEETLEMKIMQELGRARDK 697
                                       555555555555665544477889****************653..34455557889999999987 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 ?   -1.0   1.0      0.88   1.7e+03      12      18 ..      56      62 ..      54      63 .. 0.84
   2 ?    8.7   0.0    0.0008       1.6       8      23 ..      92     107 ..      90     110 .. 0.92
   3 ?    6.3   0.2    0.0045         9      27      37 .]     144     154 ..     141     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.88
                           DUF35_N 12 qrCpdCG 18
                                       rC+ CG
  gi|488600242|ref|YP_007906713.1| 56 LRCKTCG 62
                                      69****9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0008
                           DUF35_N   8 rLvgqrCpdCGtvqfP 23 
                                       +L+++ C+ CG+v  P
  gi|488600242|ref|YP_007906713.1|  92 KLLASTCRECGRVLLP 107
                                       699**********988 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0045
                           DUF35_N  27 vCphCgsddle 37 
                                        CphC++d+++
  gi|488600242|ref|YP_007906713.1| 144 KCPHCHADQFD 154
                                       6*******986 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00015       0.3      42      90 .]      92     149 ..      84     149 .. 0.78
   2 ?   -2.4   0.2         3     6e+03      42      52 ..     551     561 ..     542     564 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                       TCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EE.........EEETTTT CS
                              Rpr2  42 svkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlv.........vtClaCg 90 
                                       ++  ++C++Cg vl+p ++ +  +e+ +++k+ ++  +dv++          +C +C+
  gi|488600242|ref|YP_007906713.1|  92 KLLASTCRECGRVLLPDSKRDKFIEEIERRKSLNQDYEDVVKevfritkaaKKCPHCH 149
                                       556789*******************999999988888855444444445558898885 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                                       TCCCTB-TTT- CS
                              Rpr2  42 svkrtvCkkCg 52 
                                       ++k ++C+ C 
  gi|488600242|ref|YP_007906713.1| 551 EYKAEICQGCA 561
                                       56899999996 PP

>> WAK_assoc  Wall-associated receptor kinase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.6       4.3   8.6e+03      77      88 ..      57      68 ..      54      72 .. 0.91
   2 ?    7.2   0.1    0.0041       8.3      33      83 ..      97     150 ..      81     153 .. 0.70
   3 ?    8.2   0.1    0.0021       4.2      56      90 ..     537     570 ..     521     574 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.3
                         WAK_assoc 77 eCseCeksgGrC 88
                                       C++C  + G+C
  gi|488600242|ref|YP_007906713.1| 57 RCKTCGGKAGEC 68
                                      6*********** PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0041
                         WAK_assoc  33 eCeksvkvpvsesalkeleee.....eskegleevLkkgFelewkeksseCseCek 83 
                                       +C++  +v    s+ +++ ee     + ++++e+v+k+ F ++    +++C +C +
  gi|488600242|ref|YP_007906713.1|  97 TCRECGRVLLPDSKRDKFIEEierrkSLNQDYEDVVKEVFRITKA--AKKCPHCHA 150
                                       35555555444444444444444567899*************988..89*****87 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0021
                         WAK_assoc  56 kegleevLkkgFelewkeksseCseCeksgGr.Cgy 90 
                                       k+ ++ +L k+ +le+k  ++ C+ C + +G+ C +
  gi|488600242|ref|YP_007906713.1| 537 KQIFSMILPKDISLEYK--AEICQGCAECKGEdCEH 570
                                       6678899**********..899******99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.83u 0.33s 00:00:01.15 Elapsed: 00:00:00.52
# Mc/sec: 5074.64
//
Query:       gi|488600243|ref|YP_007906714.1|  [L=603]
Description: DNA-directed RNA polymerase, subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-130  435.7   0.0     2e-130  435.4   0.0    1.1  1  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
    6.2e-33  113.1   0.1    2.4e-32  111.2   0.1    1.9  2  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
    2.6e-24   85.3   1.0    5.8e-24   84.2   1.0    1.6  1  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4
    5.3e-09   36.5   5.0    1.6e-08   35.0   5.0    1.8  1  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.046   14.0   2.6       0.17   12.1   1.3    2.6  3  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
      0.086   13.4   3.3       0.18   12.3   3.3    1.5  1  Zn_ribbon_recom  Recombinase zinc beta 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 !  435.4   0.0  6.7e-134    2e-130       3     390 .]     136     506 ..     134     506 .. 0.95

  Alignments for each domain:
  == domain 1  score: 435.4 bits;  conditional E-value: 6.7e-134
                                       HT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEE CS
                    RNA_pol_Rpb2_6   3 klapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGq 79 
                                         +p++eh+ spr+++ aam kq+lgi   n + r +++ +ll+++q P+v+t  + + ++        ++e ++Gq
  gi|488600243|ref|YP_007906714.1| 136 GSIPYPEHNASPRNTMGAAMIKQSLGIPYSNLHWRADTRGHLLHYPQIPIVRTD-TQSEIK--------FDERPAGQ 203
                                       679***************************************************.555555........9******* PP

                                       EEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTSB CS
                    RNA_pol_Rpb2_6  80 navVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedGi 151
                                       n+vVAv+syeGYniEDa+i+n+++++r++ +s+++++ye+e  ++++g+e+ ++ +  +     + ea+++LdedG+
  gi|488600243|ref|YP_007906714.1| 204 NFVVAVISYEGYNIEDALIFNKASIERGLGRSHFFRTYETEEMRYPGGQEDKFEIPGADisgfrGAEAYAHLDEDGL 280
                                       *************************************************887776666699999************* PP

                                       --SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--E CS
                    RNA_pol_Rpb2_6 152 vrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnk 228
                                       v +++ev ++d+l+gk+  ++ ++ +e ++l    g + ++ ++ts++++s+e+g+Vd+v +        ++++++k
  gi|488600243|ref|YP_007906714.1| 281 VFPETEVGPDDVLIGKT--SPPRFLEEPTEL----GISPQKRRETSITMRSNEKGIVDRVFL-------AQSESGSK 344
                                       ****************8..888998666555....333344679******************.......788999** PP

                                       EEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSS CS
                    RNA_pol_Rpb2_6 229 lvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaaleg 305
                                       l+kv+v++ R +++GDKfasrhGqKGv++li+p+eDmPf+e+Giv+D+++NP+++PSRmt+g++lE++ gk+++leg
  gi|488600243|ref|YP_007906714.1| 345 LAKVRVRDLRIPELGDKFASRHGQKGVIGLIVPEEDMPFTESGIVPDMIINPHAIPSRMTVGHVLEMIGGKVGSLEG 421
                                       ***************************************************************************** PP

                                       S--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT- CS
                    RNA_pol_Rpb2_6 306 kkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltq 382
                                       ++vdat+F g+ke++++ +L++ g++++ kev+ydG+tG+k+ a+ifvGviYy+kL+h+++ KihaRs+Gp+++lt+
  gi|488600243|ref|YP_007906714.1| 422 RRVDATIFYGEKEKDLRAALKKYGFTHTCKEVMYDGITGKKFTADIFVGVIYYQKLYHMASSKIHARSRGPVQVLTR 498
                                       ***************************************************************************** PP

                                       -B-SCGGG CS
                    RNA_pol_Rpb2_6 383 QPlgGkaq 390
                                       QP++G+a+
  gi|488600243|ref|YP_007906714.1| 499 QPTEGRAR 506
                                       ******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 ?   -1.5   0.0       1.1   3.4e+03       6      27 ..     431     455 ..     429     463 .. 0.78
   2 !  111.2   0.1     8e-36   2.4e-32       1      85 [.     508     598 ..     508     600 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                                       EHHHHH...HHHHHTBHHHHHHHHT CS
                    RNA_pol_Rpb2_7   6 GEMErd...aliayGaaalLkerlt 27 
                                       GE E+d   al+ yG  ++ ke++ 
  gi|488600243|ref|YP_007906714.1| 431 GEKEKDlraALKKYGFTHTCKEVMY 455
                                       6777654447999999999999876 PP

  == domain 2  score: 111.2 bits;  conditional E-value: 8e-36
                                       BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHH CS
                    RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklL 71 
                                       GGlrfGEMErd+li++Gaa lLk+rl+++SD+vev+vcg+c+++a+++      +C +++++++i+kve+++afklL
  gi|488600243|ref|YP_007906714.1| 508 GGLRFGEMERDVLIGHGAAILLKDRLLEESDKVEVYVCGNCGHVATYDyrkrsaYCYVCDDDSNIHKVEMSYAFKLL 584
                                       9*********************************************99***************************** PP

                                       HHHHHHTTBEEEEE CS
                    RNA_pol_Rpb2_7  72 lqeLqslgialkll 85 
                                       l+eL+s++ia++l+
  gi|488600243|ref|YP_007906714.1| 585 LDELKSMMIAPRLV 598
                                       ***********987 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 !   84.2   1.0   1.9e-27   5.8e-24       1      61 [.       5      65 ..       5      66 .. 0.99

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 1.9e-27
                                      EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE- CS
                    RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiV 61
                                      V+vNG l+G+++d+kkl+e++R+lRR+gkis++v++v++ + +ev+i+tD+GR++RPli+V
  gi|488600243|ref|YP_007906714.1|  5 VYVNGALIGFHEDGKKLAEHIRRLRRAGKISTQVNVVYYADSNEVRINTDAGRARRPLIVV 65
                                      9***********************************************************9 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   5.0   5.4e-12   1.6e-08       1      58 []      87     127 ..      87     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 5.4e-12
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                       ++dL++ gv+EylDaeEEe+a+Ia+ +e+l+ +                 +TH+E++P
  gi|488600243|ref|YP_007906714.1|  87 FEDLVSIGVIEYLDAEEEENAYIAVNEEELTPE-----------------HTHLELDP 127
                                       89****************************776.................56666666 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.3   5.8e-05      0.17      12      36 ..      96     120 ..      90     127 .. 0.87
   2 ?   -1.8   0.0       1.3   3.9e+03      26      38 ..     269     281 ..     265     287 .. 0.78
   3 ?   -3.4   0.0       4.2   1.2e+04      38      55 ..     480     497 ..     478     499 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
                                       EEEEEHHHHTTSEEE-SSS-BETTS CS
                   RNA_pol_Rpb2_45  12 vvYLtAdeEekyviAqAnapldeeg 36 
                                       ++YL A+eEe+ +iA  +++l  e 
  gi|488600243|ref|YP_007906714.1|  96 IEYLDAEEEENAYIAVNEEELTPEH 120
                                       89*************9999998765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                       E-SSS-BETTSCB CS
                   RNA_pol_Rpb2_45  26 AqAnapldeegrf 38 
                                       A+A a+lde+g +
  gi|488600243|ref|YP_007906714.1| 269 AEAYAHLDEDGLV 281
                                       8999******954 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.2
                                       BSSSEEEEECSSCEEEEE CS
                   RNA_pol_Rpb2_45  38 fveerVlaRrkgevelve 55 
                                       +++ +++aR +g v++ +
  gi|488600243|ref|YP_007906714.1| 480 MASSKIHARSRGPVQVLT 497
                                       567899999999887766 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   3.3   6.1e-05      0.18       7      30 ..     544     567 ..     541     578 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-05
                   Zn_ribbon_recom   7 rCgeCGspmtrrkrkgkrhyYrCs 30 
                                       +Cg+CG+  t+ +rk++ ++Y+C 
  gi|488600243|ref|YP_007906714.1| 544 VCGNCGHVATYDYRKRSAYCYVCD 567
                                       8*************9999*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3779.75
//
Query:       gi|488600244|ref|YP_007906715.1|  [L=509]
Description: DNA-directed RNA polymerase, subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-43  146.8   0.0    1.7e-41  142.0   0.0    2.0  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    3.2e-32  111.7   0.1    5.4e-32  111.0   0.1    1.3  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
      8e-28   96.4   0.0    1.4e-27   95.6   0.0    1.4  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.0   0.0   2.9e-45   1.7e-41       2     202 ..      17     400 ..      16     401 .. 0.93

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 2.9e-45
                                       TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYs 78 
                                       Lv+ q+dSFn f+e+ l+++i+e+  ie++ +        ++k+++i+++kP+++e+d+se  ++P+ arlrnltY 
  gi|488600244|ref|YP_007906715.1|  17 LVKHQIDSFNRFIEEGLQRVIDEQRIIELDIPD------TYVKLGKIWVDKPIIREADGSEPPLVPSTARLRNLTYA 87 
                                       99******************************7......59************************************ PP

                                       EEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSST................TS.HHHHHHTTS.TTS..S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  79 aplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvls................easeeelvelkEcpldqGG 139
                                       a++ + +++v+   d+++e +ee v iG +P+M++s++c+l+                 + ee+l+ l+E+ ld+GG
  gi|488600244|ref|YP_007906715.1|  88 AKIQL-ITQVI---DEGRELDEEVVTIGMMPIMVKSEKCNLHpdnidealeklrypilSTYEEKLTLLGEDTLDPGG 160
                                       *9876.44444...599**********************9963322222221111111234788999********** PP

                                       SEEETTCEEEEXEEEE............................................................. CS
                                       xxxxxxxxxxxxxxxx............................................................. RF
                    RNA_pol_Rpb2_1 140 yFiinGtekvivaqek............................................................. 155
                                       yFiinG+e+ ++ +e+                                                             
  gi|488600244|ref|YP_007906715.1| 161 YFIINGSERALMTLEDlapnkillekeerygesieiakvfsqrsgyralvvverskgdilevsfpqlpktipfvtmm 237
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|488600244|ref|YP_007906715.1| 238 ralgvetdqeivtmvsedpeimkfllenledaevetqeqaieligkkvapgqskeykinranqvidqyflphlgttp 314
                                       ***************************************************************************** PP

                                       .......................................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHH CS
                                       .......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 .......................................laGeLlaslfrvllkklerdvkerlqksleklddlmlq 193
                                                                              laG+L++++frv++ +l +dvk +l++   +++ l+++
  gi|488600244|ref|YP_007906715.1| 315 esrrakafflarmaeavlelalglrreddkdhyankrlkLAGDLMEEIFRVAFLRLIKDVKYQLERAKVRGRPLKMS 391
                                       ***************************************************************************** PP

                                       HHSCSHHHH CS
                                       xxxxxxxxx RF
                    RNA_pol_Rpb2_1 194 llvnakpit 202
                                        +v+++ +t
  gi|488600244|ref|YP_007906715.1| 392 TAVRSDVLT 400
                                       ****98776 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.1     9e-36   5.4e-32       3     190 .]     180     353 ..     171     353 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 9e-36
                                       SCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSS CS
                    RNA_pol_Rpb2_2   3 ngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericyds 77 
                                       n+i+ eke++  +   +a+v s ++ +r++v++++++g++l ++ ++  + ip+v +++Alg+ +d+eI+  ++   
  gi|488600244|ref|YP_007906715.1| 180 NKILLEKEERYGESieIAKVFSQRSGYRALVVVERSKGDILEVSFPQLPKTIPFVTMMRALGVETDQEIVTMVS--- 253
                                       55555555544333588999****************************************************99... PP

                                       TTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH CS
                    RNA_pol_Rpb2_2  78 edsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenk 154
                                       ed+++++ lle+le ++e+ tqe+a++ igk+va ++++e ++ +a +++         + + l+ hlg+  +  ++
  gi|488600244|ref|YP_007906715.1| 254 EDPEIMKFLLENLE-DAEVETQEQAIELIGKKVAPGQSKEYKINRANQVI---------DQYFLP-HLGTTPE--SR 317
                                       68888876666665.56788***************************996.........899999.*****99..55 PP

                                       ..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 155 rlkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                       r+ka++++ m++++l+l+lg r +DD+Dh++nkR++
  gi|488600244|ref|YP_007906715.1| 318 RAKAFFLARMAEAVLELALGLRREDDKDHYANKRLK 353
                                       58********************************96 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.0   2.4e-31   1.4e-27       1      68 []     421     485 ..     421     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 2.4e-31
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                       q++dr n+ls +shlrrv s+   ls+++ ++e+Rdlhp++wGriCp+eTPEG+ncGlvk++a++a+v
  gi|488600244|ref|YP_007906715.1| 421 QLIDRHNYLSIISHLRRVISP---LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQYAEV 485
                                       789******************...******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3181.49
//
Query:       gi|488600245|ref|YP_007906716.1|  [L=77]
Description: DNA-directed RNA polymerase, subunit H [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  103.8   0.7    3.6e-30  103.6   0.7    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
      0.056   13.6   0.0      0.072   13.2   0.0    1.3  1  Ribosomal_S17   Ribosomal protein S17


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.7     4e-34   3.6e-30       3      73 .]       6      76 ..       4      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 4e-34
                                      -TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  3 itkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      +++H lvPkhevls+ee++++lk l+i++eqLPki+ +Dp+a+++g+k Gd+v++ r+s+tag++++YRlV
  gi|488600245|ref|YP_007906716.1|  6 LQDHILVPKHEVLSKEEAEKILKILNIEKEQLPKIKVTDPIAQEIGAKVGDIVRVERESPTAGKSIAYRLV 76
                                      689*******************************************************************9 PP

>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     8e-06     0.072      34      65 ..      39      74 ..      14      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-06
                                      EEEEE-TTTS...--TT-EEEEEEECECS.SSEEEE CS
                     Ribosomal_S17 34 kylahdenns...vkvGDiVrieecrPlS.ktkrfv 65
                                      k+++ d+  +   +kvGDiVr+e  +P + k++ ++
  gi|488600245|ref|YP_007906716.1| 39 KIKVTDPIAQeigAKVGDIVRVERESPTAgKSIAYR 74
                                      8899999888889**********9998763555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 452.52
//
Query:       gi|488600246|ref|YP_007906717.1|  [L=134]
Description: hypothetical protein Asulf_00707 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00036   20.2   5.0      0.018   14.8   1.9    3.2  3  Hexapep     Bacterial transferase hexapeptide (six repeats)
     0.0021   18.3   2.3      0.014   15.6   1.6    2.0  2  Bactofilin  Polymer-forming cytoskeletal
  ------ inclusion threshold ------
       0.19   12.1   0.0       0.31   11.4   0.0    1.2  1  ARL17       ADP-ribosylation factor-like protein 17


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 !   14.8   1.9   2.9e-06     0.018       3      30 ..      15      42 ..      14      43 .. 0.93
   2 ?    3.1   0.0     0.014        83       2      14 ..      59      71 ..      58      75 .. 0.69
   3 ?    1.0   0.0     0.065   3.9e+02      14      22 ..      97     105 ..      89     106 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-06
                                      EEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep  3 vIGsnvlIgpfaviggnVkIGdnvkIga 30
                                      v+ ++++I+++ ++ g V++G n++I+ 
  gi|488600246|ref|YP_007906717.1| 15 VVRKDAFIDKNIKVDGKVIVGANSIIWG 42
                                      7889**********************85 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.014
                                      EEEETTEEE-TTE CS
                           Hexapep  2 tvIGsnvlIgpfa 14
                                      +v+ ++++Ig+++
  gi|488600246|ref|YP_007906717.1| 59 SVTCEKAVIGANT 71
                                      6777777777775 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.065
                                       EEEETTEEE CS
                           Hexapep  14 aviggnVkI 22 
                                       a++++n++I
  gi|488600246|ref|YP_007906717.1|  97 AIVMENCEI 105
                                       666777766 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.6   2.4e-06     0.014      22      89 ..      19      85 ..       9      90 .. 0.78
   2 ?    3.7   0.1     0.013        75       2      44 ..      66     106 ..      65     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                        Bactofilin 22 dGkveGdieakgklvvgeggkvegnikaeevvvaGt..vkGnveaeekvelkktakveGdikaksleiee 89
                                      d+ ++ +i+ +gk++vg ++ + g+i+++e++v G+  +  +v++e k  + ++++ + di+++++ i++
  gi|488600246|ref|YP_007906717.1| 19 DAFIDKNIKVDGKVIVGANSIIWGKIECRELIV-GKssFLNSVTCE-KAVIGANTEFK-DITSDEIIIQN 85
                                      6678899***********************999.663466899999.77777777765.66666666665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.013
                        Bactofilin   2 ligegtkikGelevegdlridGkveGdieakgklvvgeggkve 44 
                                       +ig++t++k    +++++ i+ + +Gd  +++k +v e+ ++e
  gi|488600246|ref|YP_007906717.1|  66 VIGANTEFKDI--TSDEIIIQNRCKGDYVKARKAIVMENCEIE 106
                                       57777777764..667788888888888777788888877775 PP

>> ARL17  ADP-ribosylation factor-like protein 17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.1e-05      0.31      27      59 ..      33      65 ..      26      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.1e-05
                             ARL17 27 ilPhqsPawGPwGckdlssgfPsfltssilwks 59
                                      i+  +s  wG   c++l  g  sfl s +  k+
  gi|488600246|ref|YP_007906717.1| 33 IVGANSIIWGKIECRELIVGKSSFLNSVTCEKA 65
                                      66678899******************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 970.40
//
Query:       gi|488600247|ref|YP_007906718.1|  [L=171]
Description: Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   98.0   0.0    5.8e-28   96.8   0.0    1.6  2  TGT_C2      Patch-forming domain C2 of tRNA-guanine transglyc
    2.8e-19   68.9   2.7    4.1e-19   68.3   2.7    1.3  1  PUA         PUA domain
    8.3e-06   26.0   0.8    5.2e-05   23.4   0.4    2.3  3  UPF0113     UPF0113 PUA domain
     0.0014   18.4   0.2     0.0031   17.3   0.2    1.6  1  PUA_3       PUA-like domain
  ------ inclusion threshold ------
      0.024   14.9   0.0      0.055   13.8   0.0    1.6  1  Phage_CI_C  Bacteriophage CI repressor C-terminal domain
       0.13   12.3   0.0        0.2   11.7   0.0    1.2  1  Ehbp        Energy-converting hydrogenase B subunit P (EhbP)


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 !   96.8   0.0     2e-31   5.8e-28       2      71 .]      19      89 ..      18      89 .. 0.98
   2 ?   -2.3   0.0       1.7     5e+03      41      54 ..     124     137 ..     112     142 .. 0.61

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 2e-31
                            TGT_C2  2 rlraiadYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                      ++r +adYqFG+gag+ Lfp+ +++ +s +tgrirq+ ++g r+atl+a+ g+++Ls+eGa+r+++ +++P
  gi|488600247|ref|YP_007906718.1| 19 KIRWMADYQFGRGAGKVLFPDTCKFIVSpKTGRIRQITDKGIRIATLKASSGWFSLSIEGAKRIKDFFEYP 89
                                      89*******************************************************************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                            TGT_C2  41 gerlatlraqdgrl 54 
                                       g+ ++ + ++d++l
  gi|488600247|ref|YP_007906718.1| 124 GDEVVVVDEDDNLL 137
                                       44455555555555 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   2.7   1.4e-22   4.1e-19       2      72 ..      92     162 ..      91     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.4e-22
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                       rvvv +++ ++++ g++++a+ vv+v++++++gd+V++vded++l+a G+a + ++e++ +++g++v++++
  gi|488600247|ref|YP_007906718.1|  92 RVVVTNEVSEFIADGKNVFAKHVVDVDENLRAGDEVVVVDEDDNLLATGKAVLCASEMMLFNRGIAVNVRA 162
                                       8*******************************************************************997 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   4.5e+03      56      71 ..      43      59 ..      31      60 .. 0.65
   2 ?    2.2   0.0     0.073   2.2e+02      32      49 ..      89     106 ..      77     107 .. 0.72
   3 !   23.4   0.4   1.7e-08   5.2e-05      14      51 ..     105     142 ..      92     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                           UPF0113 56 k.aspgkivvknlaDiG 71
                                         sp+   +++++D+G
  gi|488600247|ref|YP_007906718.1| 43 FiVSPKTGRIRQITDKG 59
                                      44677777888888888 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.073
                           UPF0113  32 enqvvvVlnengeplGiG 49 
                                        +++vvV ne  e+++ G
  gi|488600247|ref|YP_007906718.1|  89 PRNRVVVTNEVSEFIADG 106
                                       4699******99999766 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1.7e-08
                           UPF0113  14 YGrdvlkesilkitesvkenqvvvVlnengeplGiGki 51 
                                        G++v+ ++++ ++e+++ ++ vvV++e++++l+ Gk+
  gi|488600247|ref|YP_007906718.1| 105 DGKNVFAKHVVDVDENLRAGDEVVVVDEDDNLLATGKA 142
                                       59**********************************98 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   1.1e-06    0.0031      18      49 ..     109     140 ..      93     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                             PUA_3  18 vfsneiasvegeledGdvVdvfsekgkflGtG 49 
                                       vf++ + +v+++l++Gd V v++e+++ l+tG
  gi|488600247|ref|YP_007906718.1| 109 VFAKHVVDVDENLRAGDEVVVVDEDDNLLATG 140
                                       9******************************9 PP

>> Phage_CI_C  Bacteriophage CI repressor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-05     0.055      52      87 ..      67     102 ..      55     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                        Phage_CI_C  52 vsdGkwLvdieGrlsirelariPvkklrvsgdevsf 87 
                                       +s G + + ieG++ i++ +  P +++ v+++ ++f
  gi|488600247|ref|YP_007906718.1|  67 ASSGWFSLSIEGAKRIKDFFEYPRNRVVVTNEVSEF 102
                                       57788999**********************998888 PP

>> Ehbp  Energy-converting hydrogenase B subunit P (EhbP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.6e-05       0.2      17      67 ..      87     139 ..      70     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.6e-05
                              Ehbp  17 efpyrnvivvnktdepikievPvfdeeWieehrkL..gLevvPveeeddflsl 67 
                                       e+p   v+v+n+ +e i     vf ++ ++  ++L  g evv v+e+d+ l  
  gi|488600247|ref|YP_007906718.1|  87 EYPRNRVVVTNEVSEFIADGKNVFAKHVVDVDENLraGDEVVVVDEDDNLLAT 139
                                       778889********************9998887775589**********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1118.62
//
Query:       gi|488600248|ref|YP_007906719.1|  [L=342]
Description: translation factor SUA5 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-56  189.5   0.2    7.3e-56  188.5   0.0    1.6  2  Sua5_yciO_yrdC  Telomere recombination
    1.2e-33  116.6   0.0    1.8e-33  116.0   0.0    1.3  1  SUA5            Putative GTP-binding controlling metal-bindin
  ------ inclusion threshold ------
       0.17   12.2   0.5        7.7    6.9   0.2    2.4  2  DUF5097         Domain of unknown function (DUF5097)


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 !  188.5   0.0   1.2e-59   7.3e-56       1     179 []      24     199 ..      24     199 .. 0.98
   2 ?   -2.4   0.0      0.48   2.9e+03     134     161 ..     253     280 ..     245     296 .. 0.58

  Alignments for each domain:
  == domain 1  score: 188.5 bits;  conditional E-value: 1.2e-59
                                       HHHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSS CS
                    Sua5_yciO_yrdC   1 ealrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGp 77 
                                       e++++Gg+va+ptetvYgL+++a +++av  ++++K+rp+d+pl+v+v + ++++++ae  +++ a kl++rf+PGp
  gi|488600248|ref|YP_007906719.1|  24 EIIKNGGLVAFPTETVYGLGANALDRKAVLGIYKAKERPADNPLIVHVCNKDMIEDIAE--LNDVAEKLIKRFFPGP 98 
                                       689*******************************************************8..**************** PP

                                       CEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS CS
                    Sua5_yciO_yrdC  78 itlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildg 154
                                       +t+++k+ ke +p+ev++gl+tv++r+Pd+++a++L+e  + p+ a+Sanl g+ps+t+ae+v e+l +++d+ildg
  gi|488600248|ref|YP_007906719.1|  99 LTVVVKK-KECIPQEVTAGLDTVAIRMPDNKVALKLIELSEVPISAPSANLAGKPSPTKAEHVIEDLYGRIDAILDG 174
                                       ******6.555****************************************************************** PP

                                       ---SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 155 geiavgvdstVvdltegkpkilRrG 179
                                       g++++g +stVvd t  ++++lR+G
  gi|488600248|ref|YP_007906719.1| 175 GPTNIGLESTVVDTTVYPVELLRPG 199
                                       ***************999*****98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.48
                                       -SSHHHHHHHC-TTSECB-SS---SSS- CS
                    Sua5_yciO_yrdC 134 itdaeeveeelgeivdlildggeiavgv 161
                                       i++a ++ ++ ++++ l+++  e  + +
  gi|488600248|ref|YP_007906719.1| 253 IKTAGQLIDKSNKKIGLVVSDSEPYKDI 280
                                       4455555555555555555555444444 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.0     3e-37   1.8e-33       2     133 ..     202     335 ..     201     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 3e-37
                                       -HHHHHHHS-.--.....-------------S-SSEEEEE--GGGHHHH.......HHHHHTTS-EEEEEEGGGTGG CS
                              SUA5   2 tleeleevld.avek.keekpraPGmkyrHYaPkapvvlveaeeeeeaake..ekleekkksgkkvgvlatseskea 74 
                                       ++eele+v+d +  + +e  pr+PGmkyrHYaP+a+++++ ++ e+  +k+   + +  +ks+kk+g++ ++ s++ 
  gi|488600248|ref|YP_007906719.1| 202 SVEELEKVVDiKIPElDEGIPRSPGMKYRHYAPSAELIVIYGKREDVVSKIikTAGQLIDKSNKKIGLVVSD-SEPY 277
                                       78******975333358999**********************9999988888888888999********954.4444 PP

                                       TSEEEEE...E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHT CS
                              SUA5  75 assvlsl.slgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAA 133
                                       ++  +++ ++g  +++ee+arnLF+aLrelD++g+dli++egv+e+glglAvmnRL+kA+
  gi|488600248|ref|YP_007906719.1| 278 KDIDVEIvEIG--RSVEEVARNLFSALRELDRRGIDLIIAEGVEEKGLGLAVMNRLKKAS 335
                                       44444442346..9*********************************************8 PP

>> DUF5097  Domain of unknown function (DUF5097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.02   1.2e+02      12      82 ..      69     138 ..      66     142 .. 0.68
   2 ?    6.9   0.2    0.0013       7.7      41      87 ..     245     291 ..     238     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.02
                           DUF5097  12 vkyflknstkdlkelsasivkilsskFlin.EkvfikkkekyGrivnlvkkeytvvihndngskkeevklqe 82 
                                       v+  +k++ +d+ el  ++ + l ++F+    +v++kkke++ + v    +  ++ +  dn+   + ++l+e
  gi|488600248|ref|YP_007906719.1|  69 VHVCNKDMIEDIAELN-DVAEKLIKRFFPGpLTVVVKKKECIPQEVTAGLDTVAIRM-PDNKVALKLIELSE 138
                                       5555666667777765.5566666666665168999999999888888888777777.56666666666665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0013
                           DUF5097  41 nEkvfikkkekyGrivnlvkkeytvvihndngskkeevklqeltRke 87 
                                       +E+v+ k  ++ G++++  +k+  +v+ + ++ k  +v+  e+ R  
  gi|488600248|ref|YP_007906719.1| 245 REDVVSKIIKTAGQLIDKSNKKIGLVVSDSEPYKDIDVEIVEIGRSV 291
                                       699999999******************99999***********9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2233.42
//
Query:       gi|488600249|ref|YP_007906720.1|  [L=277]
Description: hypothetical protein Asulf_00710 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-31  107.8   0.0    1.6e-30  106.9   0.0    1.5  1  Amidohydro_2  Amidohydrolase


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 !  106.9   0.0   9.2e-35   1.6e-30      61     290 ..      60     275 ..       4     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 9.2e-35
                                       HHHHHHHHHHHHHHHHHHHHCTTCBECEEECTS.SHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH..HHH CS
                      Amidohydro_2  61 ivaalcrgannrvlaeaakrpdrfvggaavvpl.dpedaaaeleraveelgfkGvrlnphvggddllgdrld..rpi 134
                                        + +l+ +a  +v++ + ++ dr+ +++ + p+ d +da++ le++  +lg+ G++l+p ++  +++++ l+     
  gi|488600249|ref|YP_007906720.1|  60 HTNGLGMEAVYSVIDYCREHRDRLYPFGSIYPHmDRKDAIEHLEKQY-DLGIAGIKLHPVHQYFYPNDYSLEslTAS 135
                                       3334444444459999*********9999875516899*********.***************************** PP

                                       HHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCE CS
                      Amidohydro_2 135 fealeelglpvdihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyv 211
                                       +e ++++ lp+ +htG     +   p++++ + +p  l++va +fP+l+i+++HgG+p  + r+a  +l+r+ nv++
  gi|488600249|ref|YP_007906720.1| 136 YEFAVDHELPILFHTG-----TSILPGARVKYGNPINLDDVALDFPELRIIMSHGGRP-IWMREAFFILRRHGNVWF 206
                                       **************99.....889**********************************.****************** PP

                                       EECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHH CS
                      Amidohydro_2 212 klsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarl 288
                                       ++sg+        +p+     +   +e+v +++ ++GsD+P p  +   e l l+  ++ l+   ++ki+++N ++l
  gi|488600249|ref|YP_007906720.1| 207 DISGI--------PPKKLMTEYFPRFELV-AEKSIYGSDFPSPGVKGIKENLELFLSLD-LDNSMKKKIAYHNFRKL 273
                                       ****4........5555555555556666.7**************88877777666655.6**************** PP

                                       CT CS
                      Amidohydro_2 289 yg 290
                                       y+
  gi|488600249|ref|YP_007906720.1| 274 YR 275
                                       *8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1874.78
//
Query:       gi|488600250|ref|YP_007906721.1|  [L=242]
Description: Lysophospholipase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   56.2   0.0    7.9e-10   38.4   0.1    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    6.5e-15   55.5   0.1    1.5e-08   34.6   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    2.1e-08   35.1   0.0    3.1e-07   31.2   0.0    1.9  2  Abhydrolase_6  Alpha/beta hydrolase family
    1.1e-05   25.3   0.0    1.7e-05   24.6   0.0    1.3  1  FSH1           Serine hydrolase (FSH1)
    1.3e-05   25.2   0.3       0.11   12.3   0.0    3.2  3  Abhydrolase_2  Phospholipase/Carboxylesterase
      2e-05   24.5   0.0    2.8e-05   23.9   0.0    1.3  1  PGAP1          PGAP1-like protein
    0.00092   18.0   0.0     0.0013   17.5   0.0    1.1  1  PhoPQ_related  PhoPQ-activated pathogenicity-related protein
      0.001   18.7   0.2          1    8.9   0.3    2.6  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
     0.0023   17.5   0.0       0.91    9.0   0.0    2.2  2  DLH            Dienelactone hydrolase family
     0.0027   17.5   0.0     0.0068   16.2   0.0    1.7  2  Abhydrolase_5  Alpha/beta hydrolase family
     0.0048   16.4   0.0     0.0074   15.8   0.0    1.3  1  Peptidase_S9   Prolyl oligopeptidase family
     0.0053   16.7   0.0     0.0095   15.9   0.0    1.4  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
     0.0093   14.7   0.1      0.014   14.1   0.1    1.2  1  Ndr            Ndr family
  ------ inclusion threshold ------
      0.018   15.0   0.0       0.04   13.8   0.0    1.5  2  DUF829         Eukaryotic protein of unknown function (DUF829
      0.043   13.1   0.1       0.72    9.1   0.0    2.3  2  LIP            Secretory lipase
      0.046   13.0   0.0      0.057   12.7   0.0    1.2  1  DUF915         Alpha/beta hydrolase of unknown function (DUF9
      0.054   13.4   0.0       0.14   12.0   0.0    1.7  1  UPF0227        Uncharacterised protein family (UPF0227)
      0.058   12.9   0.0       0.11   12.1   0.0    1.5  1  DUF2974        Protein of unknown function (DUF2974)
       0.06   12.8   0.2      0.099   12.1   0.2    1.5  1  DUF676         Putative serine esterase (DUF676)
       0.12   12.0   0.0       0.21   11.2   0.0    1.3  1  Abhydrolase_8  Alpha/beta hydrolase


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 !   38.4   0.1   8.8e-13   7.9e-10       5     108 ..      18     115 ..      15     145 .. 0.86
   2 !   16.2   0.0   5.2e-06    0.0047     189     228 ..     169     208 ..     119     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 8.8e-13
                       Hydrolase_4   5 avvvlvHGlaehsgr.....yaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpel 76 
                                        vvv++HGl   sg      y+++a+++a  G + +++D  G G s+g       ++ +v+Dl ++v+++k      
  gi|488600250|ref|YP_007906721.1|  18 DVVVFCHGLPYESGSvtqkgYDDIAKDFAYSGLNSVIFDFSGTGLSKGDFK----IENWVEDLLSIVHEFK------ 84 
                                       69*******988875444459*************************88887....999********98887...... PP

                       Hydrolase_4  77 plfllGhSmGGliallyllrypdkvaglilsa 108
                                        + l+G SmGG++a+ y+  ++d+++ l+l++
  gi|488600250|ref|YP_007906721.1|  85 SVSLVGFSMGGVVAT-YVSANSDNIKNLVLVG 115
                                       899********9876.66666667******98 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.2e-06
                       Hydrolase_4 189 kitlPllllhGeaDkvvdpeasrelyerlgskdktlklyp 228
                                       +++ P l++hG++D+++++e+ ++ly++++  +  l++ +
  gi|488600250|ref|YP_007906721.1| 169 EVRCPKLIVHGTSDQIIPYEDGERLYAEAKEPKYFLRVVN 208
                                       5669*************************98777666655 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.1   1.7e-11   1.5e-08       2     119 ..      19     127 ..      18     136 .. 0.75
   2 !   19.0   0.0   9.5e-07   0.00086     198     251 ..     161     212 ..     134     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.7e-11
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       v+v++hGlp +s++  ++   +++ak +f + +l++  +++S +++++   d+ + +  +dl  i+  ++  ++ lv
  gi|488600250|ref|YP_007906721.1|  19 VVVFCHGLPYESGSVTQK-GYDDIAK-DFAYSGLNSVIFDFSGTGLSK--GDFKIENWVEDLLSIVHEFK--SVSLV 89 
                                       8*********99985554.4448888.777777777777777777777..78887777777777765554..4556* PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrq 119
                                       G+SmGG +a+++ a   +++k+lvl+g   p+ +   ++++
  gi|488600250|ref|YP_007906721.1|  90 GFSMGGVVATYVSAN-SDNIKNLVLVGV--PCCAETVTDEM 127
                                       ******999988886.899********9..77666555555 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 9.5e-07
                                       HHHHHHHHCTHHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETCSSS CS
                     Abhydrolase_1 198 aklllrlrelknvlaptlvisgtsDplvpp.kaledlaqllpkkrlvvisdagHl 251
                                        +  +++    +v +p l+++gtsD+++p+ +  + +a++   k+ ++++++ H+
  gi|488600250|ref|YP_007906721.1| 161 YQPVNWI---GEVRCPKLIVHGTSDQIIPYeDGERLYAEAKEPKYFLRVVNGSHF 212
                                       3444444...45******************7777777777555799999999998 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   3.5e-10   3.1e-07       1      90 [.      20     109 ..      20     134 .. 0.69
   2 ?    1.2   0.0      0.51   4.6e+02     170     208 ..     171     212 ..     148     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.5e-10
                                       EEEE--GC.....G.C..HHHHHHHHCCT.CEEEEE--TTSTS-..GGCS--HHHCHHHHHHHCCTT..TTSEEEEE CS
                     Abhydrolase_6   1 vlllHGagssassW.l..vapLaallaag.vhvlapDlpGhGrs..dpppldledladlaalldelaagggpvvlvG 71 
                                       v+++HG+++ ++s  +  ++ +a+ +a      +++D+ G+G s  d +  ++  ++dl+ +++e+    + v lvG
  gi|488600250|ref|YP_007906721.1|  20 VVFCHGLPYESGSVtQkgYDDIAKDFAYSgLNSVIFDFSGTGLSkgDFKIENW--VEDLLSIVHEF----KSVSLVG 90 
                                       8*****99775555323445553333333444457******833236666777..9**********....9****** PP

                                       ETCHHHHHHHHHHCC..EE CS
                     Abhydrolase_6  72 HSlGGalalaaaplalvvg 90 
                                        S+GG++a+ + +  ++++
  gi|488600250|ref|YP_007906721.1|  91 FSMGGVVATYVSANSDNIK 109
                                       ********99444443333 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.51
                                       TTGCEEE.CTT-CHHH.....HCHHCCCHSTTEEETCE...SSS- CS
                     Abhydrolase_6 170 pvpllvl.ggeDplvp.....rllerllaqagarlpvvlpgaGHl 208
                                       ++p l++ g++D+++p     rl++++   +++ l   + +++H+
  gi|488600250|ref|YP_007906721.1| 171 RCPKLIVhGTSDQIIPyedgeRLYAEAKE-PKYFL--RVVNGSHF 212
                                       444477758****8884444444444444.44444..35566666 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.9e-08   1.7e-05     103     202 ..      85     213 ..      61     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.9e-08
                              FSH1 103 fdGiiGFSqGaalaallaslleellkea....................shpslkfail....vsGfkleepk....y 151
                                        + ++GFS G+++a+++ ++ ++ ++                      +h +lk ++     + +fk++ ++    y
  gi|488600250|ref|YP_007906721.1|  85 SVSLVGFSMGGVVATYVSANSDNIKNLVlvgvpccaetvtdemlveifEHNKLKGVLRglkdFESFKARIKRdldlY 161
                                       4679*******************998767777777777777777777766666655532222445555544455555 PP

                              FSH1 152 eeyyeedkiqtptLhvlGelDtvvdeerseaLaeafknsskvl.kHpggHfv 202
                                       ++     ++++p L v+G++D++++ e  e+L+   k+ + +l   +g Hf+
  gi|488600250|ref|YP_007906721.1| 162 QPVNWIGEVRCPKLIVHGTSDQIIPYEDGERLYAEAKEPKYFLrVVNGSHFL 213
                                       554444556**************************99975554146788886 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.11     1e+02      14      23 ..      17      26 ..      14      48 .. 0.80
   2 !   12.3   0.0   0.00012      0.11      86     126 ..      65     105 ..      49     123 .. 0.80
   3 !    6.8   0.0    0.0058       5.2     155     181 ..     170     196 ..     158     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                      -EEEEEE--T CS
                     Abhydrolase_2 14 qavviflHGl 23
                                      + vv+f+HGl
  gi|488600250|ref|YP_007906721.1| 17 EDVVVFCHGL 26
                                      579******9 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT- CS
                     Abhydrolase_2  86 saekleelidaelkkgipssriiigGFSqGaalalylaltl 126
                                        + k+e+ ++  l+   + + + ++GFS+G+++a+y +  +
  gi|488600250|ref|YP_007906721.1|  65 GDFKIENWVEDLLSIVHEFKSVSLVGFSMGGVVATYVSANS 105
                                       555677777777777788899***************87665 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0058
                                       GG-EEEEEEETT-SSS-HHHHHHHHHH CS
                     Abhydrolase_2 155 kklpilqiHgeeDpvvplalgkaakev 181
                                       +  p l +Hg+ D+++p+  g++++  
  gi|488600250|ref|YP_007906721.1| 170 VRCPKLIVHGTSDQIIPYEDGERLYAE 196
                                       55788899***********99998754 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.1e-08   2.8e-05      62     146 ..      59     134 ..      18     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.1e-08
                             PGAP1  62 GrtlldqaeylndaIkyIlslysssekeptsviliGHSmGGivaraaltlknyikqsvntiltlasPhalpplsfdk 138
                                       G+ l++    +++ ++ +ls+     +e +sv l+G SmGG+va    t+ +   +++++++ ++ P  +  + +d+
  gi|488600250|ref|YP_007906721.1|  59 GTGLSKGDFKIENWVEDLLSIV----HEFKSVSLVGFSMGGVVA----TYVSANSDNIKNLVLVGVPCCAETV-TDE 126
                                       5555555555666667777777....8899**************....444445799**********999988.788 PP

                             PGAP1 139 dilklyer 146
                                        +++++e+
  gi|488600250|ref|YP_007906721.1| 127 MLVEIFEH 134
                                       99998875 PP

>> PhoPQ_related  PhoPQ-activated pathogenicity-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.4e-06    0.0013     248     315 ..     158     226 ..     142     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                     PhoPQ_related 248 lkivDplsYlerltipkyiinasgDdffvpdstkfyfekLkgekalrivPnssHglsn.kevveslvaf 315
                                       l++  p++++ +++ pk+i+ ++ D+    ++ +  + + k++k+   v n sH l++ +ev+ ++ ++
  gi|488600250|ref|YP_007906721.1| 158 LDLYQPVNWIGEVRCPKLIVHGTSDQIIPYEDGERLYAEAKEPKYFLRVVNGSHFLRRhREVMGKIKEW 226
                                       67899***************************************998888*******999999988765 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 !    8.9   0.3    0.0012         1      47      84 ..      39      74 ..      19     117 .. 0.76
   2 !    7.0   0.0    0.0042       3.8     224     267 ..     167     211 ..     132     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                                      HGGGHHHHHTT-EEEEEE-TTSTTS-S---TTTTTHHH CS
                     Peptidase_S15 47 elqdkvfvarGYavVvqdvrGtggSeGeftvgdsdeae 84
                                      +  +k f+ +G  +V+ d  Gtg S+G+f+++  + +e
  gi|488600250|ref|YP_007906721.1| 39 DDIAKDFAYSGLNSVIFDFSGTGLSKGDFKIE--NWVE 74
                                      233445************************95..3333 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0042
                                       HCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-EEEEECECT CS
                     Peptidase_S15 224 adkvkapvllvgGwnDwnvk.ngaiklyealkapgvklilgpwtH 267
                                       + +v++p l+v+G  D++   +   +ly ++k+p+  l + +++H
  gi|488600250|ref|YP_007906721.1| 167 IGEVRCPKLIVHGTSDQIIPyEDGERLYAEAKEPKYFLRVVNGSH 211
                                       4789*************9999999**********98888888888 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0     0.001      0.91      97     124 ..      83     110 ..      60     115 .. 0.81
   2 !    6.4   0.0    0.0066       5.9     135     172 ..     162     199 ..     155     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                               DLH  97 tkkvgvvGfCmGGalalllaaevpevda 124
                                        k v +vGf mGG +a +++a+ + ++ 
  gi|488600250|ref|YP_007906721.1|  83 FKSVSLVGFSMGGVVATYVSANSDNIKN 110
                                       47899***************99987775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0066
                               DLH 135 keleeaakikapilalfgeeDefipadevekleealka 172
                                       ++++ + ++ +p l+++g+ D++ip ++ e+l  + k+
  gi|488600250|ref|YP_007906721.1| 162 QPVNWIGEVRCPKLIVHGTSDQIIPYEDGERLYAEAKE 199
                                       677788899******************99998877655 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.6e-06    0.0068       5      88 ..      28     115 ..      26     149 .. 0.81
   2 ?   -3.1   0.0       6.5   5.8e+03     101     119 ..     172     190 ..     167     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.6e-06
                     Abhydrolase_5   5 YpGakveaesYaelaeklaksGyevvlvklP.lnla..vlg.knkaeeiikeapklekfvvgGhslGGvvasrfaae 77 
                                       Y+   v ++ Y  +a++ a sG + v+  +   +l+   +  +n +e++++   + +   + G s+GGvva+ ++a+
  gi|488600250|ref|YP_007906721.1|  28 YESGSVTQKGYDDIAKDFAYSGLNSVIFDFSgTGLSkgDFKiENWVEDLLSIVHEFKSVSLVGFSMGGVVATYVSAN 104
                                       666788899999999999999999999887523444113332566788888888889999**************999 PP

                     Abhydrolase_5  78 eekiegvvfla 88 
                                        ++i+ +v+++
  gi|488600250|ref|YP_007906721.1| 105 SDNIKNLVLVG 115
                                       9*****99876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.5
                     Abhydrolase_5 101 kkvlsivgteDgvlnvksl 119
                                        + l + gt+D+++++++ 
  gi|488600250|ref|YP_007906721.1| 172 CPKLIVHGTSDQIIPYEDG 190
                                       5678889999999988765 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.3e-06    0.0074      66     175 ..      86     200 ..      74     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.3e-06
                                       EEEEEETHHHHHHHHHHHH-GGG-SEEEEESE---CCCHHCSTTS.THH.HCCCC--TTTCHHHHHHHHH..H-CGG CS
                      Peptidase_S9  66 laitGgSyGGyltgaalnqrpdlFkaavaevpvvdvlrydsdtdl.lte.eymewgnpeeneegykelsp..yspld 138
                                       + + G S GG+++  + ++ +++   ++ +vp+   + +d      +++ +  +     ++ e +k++ +  ++ ++
  gi|488600250|ref|YP_007906721.1|  86 VSLVGFSMGGVVATYVSANSDNIKNLVLVGVPCCAETVTDEMLVEiFEHnKLKGVLRGLKDFESFKARIKrdLDLYQ 162
                                       67889999999999999989999999999999876665555533358888888888888888888776542234444 PP

                                       G--....---EEEEEEETT-SSS-THHHHHHHHHHH--S-S CS
                      Peptidase_S9 139 nvk....aypplLlihGlaDdrvppaealklvaaLqkkgkn 175
                                        v+    + +p L++hG+ D+ +p++ +++l+a+ ++   +
  gi|488600250|ref|YP_007906721.1| 163 PVNwigeVRCPKLIVHGTSDQIIPYEDGERLYAEAKE---P 200
                                       4446679*************************98775...3 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 !   15.9   0.0   1.1e-05    0.0095      22     130 ..      84     186 ..      68     202 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                       SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB.--SSEEEETTE..EE----B-GGG-EE-TTS-EE-TT-B- CS
                            BAAT_C  22 dkigllGiSkGgelalllasflkkisavvlingsav.vvegklvykdeskvlpelklsmeklkvnknglldivdvla 97 
                                       + + l+G S Gg +a ++++ +++i+++vl+  ++   + + ++        + +++  +klk    gl d+    a
  gi|488600250|ref|YP_007906721.1|  84 KSVSLVGFSMGGVVATYVSANSDNIKNLVLVGVPCCaETVTDEMLV------EIFEH--NKLKGVLRGLKDFESFKA 152
                                       4799*************************98554440443333333......33333..333444455555555555 PP

                                       -TTTGGGCCCB--.GGG--SEEEEEEETT-SSS- CS
                            BAAT_C  98 llkeklaekalip.vekakgpillvvgedDknwp 130
                                        +k +l+  + ++ +++ ++p l+v g+ D+++p
  gi|488600250|ref|YP_007906721.1| 153 RIKRDLDLYQPVNwIGEVRCPKLIVHGTSDQIIP 186
                                       5555555444444157889999999999999887 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.6e-05     0.014      83     146 ..      70     130 ..      63     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                       HHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S---HHHHHHHH CS
                               Ndr  83 ddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaagwvewakeK 146
                                       ++  ++ll++++ fk  s++g+ +g    ++a +  ++++ ++ lvL+ + ++a+ +++ +   
  gi|488600250|ref|YP_007906721.1|  70 ENWVEDLLSIVHEFKSVSLVGFSMG---GVVATYVSANSDNIKNLVLVGVPCCAETVTDEMLVE 130
                                       6677999999999987777777655...3889999**********************9976554 PP

>> DUF829  Eukaryotic protein of unknown function (DUF829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         3   2.7e+03      73      86 ..      90     103 ..      78     113 .. 0.77
   2 ?   13.8   0.0   4.5e-05      0.04     140     214 ..     125     206 ..      97     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3
                            DUF829  73 vfsngGpllylall 86 
                                        fs+gG++++  ++
  gi|488600250|ref|YP_007906721.1|  90 GFSMGGVVATYVSA 103
                                       69999999877665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.5e-05
                            DUF829 140 rsllalalaltllvelilglesvasrsrkalndlatkplr.......cpqlylySkaDeviswrdveshaeeaeqrg 209
                                        ++l+ ++++ +l  ++ gl++ +s  ++  +dl + ++        cp+l +  ++D++i+++d e++ +ea++ +
  gi|488600250|ref|YP_007906721.1| 125 DEMLVEIFEHNKLKGVLRGLKDFESFKARIKRDLDLYQPVnwigevrCPKLIVHGTSDQIIPYEDGERLYAEAKEPK 201
                                       56666666677777777777777777777766666666666666677****************************88 PP

                            DUF829 210 vkvta 214
                                       ++ + 
  gi|488600250|ref|YP_007906721.1| 202 YFLRV 206
                                       87665 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.16   1.4e+02      68      90 ..      81     103 ..      72     158 .. 0.72
   2 ?    9.1   0.0    0.0008      0.72     216     239 ..     172     195 ..     168     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.16
                               LIP  68 ksdakvalwGYSgGslAsawAae 90 
                                       ++   v l G+S G++ +++ ++
  gi|488600250|ref|YP_007906721.1|  81 HEFKSVSLVGFSMGGVVATYVSA 103
                                       45567899999988876555443 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0008
                               LIP 216 iPvlvyhgvidelipikdakklak 239
                                        P l++hg++d++ip++d ++l+ 
  gi|488600250|ref|YP_007906721.1| 172 CPKLIVHGTSDQIIPYEDGERLYA 195
                                       6889****************9986 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 ?   12.7   0.0   6.3e-05     0.057      99     135 ..      80     110 ..      40     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-05
                            DUF915  99 kYnikkfnavGhSmGglaltsYleeyaddkslPqlkk 135
                                         ++k + +vG+SmGg+ +t+  ++  + k       
  gi|488600250|ref|YP_007906721.1|  80 VHEFKSVSLVGFSMGGVVATYVSANSDNIK------N 110
                                       4689************98876544444433......3 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.14      47     160 ..      74     197 ..      67     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                           UPF0227  47 keleklvaelgddnillvGssLGGyyatrlgerfg.lrqvllnPalkplenlagklgeeavqstqetyvleeyhiie 122
                                       + l ++v+e +  ++ lvG s+GG +at++++  + +++ +l       e++++ +  e  ++ + ++vl   ++ e
  gi|488600250|ref|YP_007906721.1|  74 EDLLSIVHEFK--SVSLVGFSMGGVVATYVSANSDnIKNLVLVGVPCCAETVTDEMLVEIFEHNKLKGVLRGLKDFE 148
                                       55566666666..589**************98764266666655556677777777777777777788888777777 PP

                           UPF0227 123 lkalelsr...........lkrperilvllskqDevldyrravaefraa 160
                                       +    ++r            + + + l+++++ D +++y+     +++a
  gi|488600250|ref|YP_007906721.1| 149 SFKARIKRdldlyqpvnwiGEVRCPKLIVHGTSDQIIPYEDGERLYAEA 197
                                       7777777777777788876566677788888888888886665555554 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.11      78     110 ..      79     109 ..      70     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                           DUF2974  78 ileesegkiylgGhSkGGnlAvyaamnaeddlq 110
                                       i++e++  + l+G+S GG +A+y+++n +d+++
  gi|488600250|ref|YP_007906721.1|  79 IVHEFKS-VSLVGFSMGGVVATYVSAN-SDNIK 109
                                       5555555.9*****************9.55555 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00011     0.099      54      98 ..      60     103 ..      17     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                            DUF676  54 kgidvlgerlaeevlevvkkkkdknkkiSfvghSlGgliaraaia 98 
                                        g+     ++ ++v + +   ++  k +S+vg+S+Gg++a+++ a
  gi|488600250|ref|YP_007906721.1|  60 TGLSKGDFKIENWVEDLLSIVHEF-KSVSLVGFSMGGVVATYVSA 103
                                       555555556667777777777776.689************99755 PP

>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.21      92     146 ..      67     120 ..      60     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                     Abhydrolase_8  92 aeLnallrdlratsvpgqhlallgHSYGSlvaslAlddaaseVsdvvlyGSPGle 146
                                        +++ +++dl ++    + ++l+g S G +va+    + + ++++ vl+G P   
  gi|488600250|ref|YP_007906721.1|  67 FKIENWVEDLLSIVHEFKSVSLVGFSMGGVVATYVSAN-SDNIKNLVLVGVPCCA 120
                                       5778888999998888999*************998888.99**********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 1540.99
//
Query:       gi|488600251|ref|YP_007906722.1|  [L=216]
Description: Adenylate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-66  221.5   0.1    6.1e-66  221.2   0.1    1.1  1  ADK              Adenylate kinase
    1.5e-34  119.4   1.9    1.6e-34  119.2   0.3    1.7  2  AAA_17           AAA domain
    3.9e-19   68.3   3.9    7.4e-19   67.4   3.9    1.5  1  ADK_lid          Adenylate kinase, active site lid
    3.8e-08   33.9   1.7     0.0053   17.1   0.1    2.6  3  Hydin_ADK        Hydin Adenylate kinase-like domain
    6.1e-07   29.7   0.0    1.6e-06   28.4   0.0    1.6  2  AAA_33           AAA domain
    1.2e-05   25.0   0.4       0.13   11.9   0.0    3.0  3  Thymidylate_kin  Thymidylate kinase
    5.2e-05   23.8   0.1    0.00013   22.5   0.0    1.7  2  AAA_18           AAA domain
     0.0041   16.8   0.1        3.7    7.2   0.0    2.6  3  CoaE             Dephospho-CoA kinase
     0.0083   15.6   1.8      0.021   14.3   1.8    1.7  1  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.027   14.7   0.1      0.082   13.1   0.0    1.8  2  AAA_28           AAA domain
      0.098   12.0   0.0       0.14   11.5   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
        0.1   11.4   0.1       0.14   11.0   0.1    1.1  1  VSP              Giardia variant-specific surface protein
       0.11   12.5   0.7       0.26   11.2   0.7    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.11   12.9   1.1        7.1    7.1   0.2    2.5  2  zf-IS66          zinc-finger binding domain of transposase IS
       0.55   10.3   4.2       0.69   10.0   0.4    2.4  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain


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 !  221.2   0.1   5.1e-69   6.1e-66       1     150 [.       5     190 ..       5     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.2 bits;  conditional E-value: 5.1e-69
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgf 77 
                                       llGaPgaGKGtqae++v kyg++++stGd+lR++v++gtelGk+ake+md+gelvpdevv+++vke+++++d++kgf
  gi|488600251|ref|YP_007906722.1|   5 LLGAPGAGKGTQAERIVAKYGIPQISTGDMLREAVAKGTELGKKAKEYMDRGELVPDEVVIGIVKERIAQPDCEKGF 81 
                                       79*************************************************************************** PP

                                       EEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                               ADK  78 llDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg................................ 122
                                       +lDGfPRt++qaeal+++lee+++k+d+v++++vpe+ +++R+++                                
  gi|488600251|ref|YP_007906722.1|  82 ILDGFPRTINQAEALDKMLEEMGKKIDAVINVSVPEDEIIKRIVNrrtcknckavyhliynppkeegkcdkcggely 158
                                       ***************************************************************************** PP

                                       ....GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 ....DneetvkkRletykkqtkplidyykkkg 150
                                           D+eetvk+Rl++yk+qt+pli+yy+kkg
  gi|488600251|ref|YP_007906722.1| 159 qrddDKEETVKERLKVYKSQTEPLIEYYSKKG 190
                                       *****************************987 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.3   1.3e-37   1.6e-34       1     124 [.       6     129 ..       6     135 .. 0.95
   2 ?   -1.3   0.1       2.2   2.7e+03     128     136 .]     161     169 ..     156     181 .. 0.60

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 1.3e-37
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       lG PG+GKgtq+e++v kyg++ +s+Gd+lre +++g +l +ka+++m++++l++++ +  +++e+ia+ +++kg++
  gi|488600251|ref|YP_007906722.1|   6 LGAPGAGKGTQAERIVAKYGIPQISTGDMLREAVAKGtELgKKAKEYMDRGELVPDEVVIGIVKERIAQPDCEKGFI 82 
                                       7******************************87777747779999******************************** PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTT CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrt 124
                                       +dg+pr+ +qa++ld++ +e+ +++  da+i ++++++ei++r  ++rt
  gi|488600251|ref|YP_007906722.1|  83 LDGFPRTINQAEALDKMLEEMGKKI--DAVINVSVPEDEIIKRIVNRRT 129
                                       ************************9..*******************987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                                       TS-SHHHHH CS
                            AAA_17 128 dddneesik 136
                                       ddd ee++k
  gi|488600251|ref|YP_007906722.1| 161 DDDKEETVK 169
                                       555554443 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 !   67.4   3.9   6.2e-22   7.4e-19       1      36 []     127     162 ..     127     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 6.2e-22
                                       EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                       Rr+C++C+++Yh+++npPk+eg+CDkCG++L+qR+D
  gi|488600251|ref|YP_007906722.1| 127 RRTCKNCKAVYHLIYNPPKEEGKCDKCGGELYQRDD 162
                                       9**********************************9 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05     0.015       2      51 ..       3      51 ..       2      56 .. 0.91
   2 !   17.1   0.1   4.4e-06    0.0053     170     197 ..      58      85 ..      53      86 .. 0.95
   3 ?   -2.5   0.0       4.5   5.4e+03     169     189 ..     113     133 ..     101     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgnssaGlrAre 51
                                      +i+ GaP +GK + a  +  kY++  ++  +++ eA+++g ++ G +A+e
  gi|488600251|ref|YP_007906722.1|  3 LILLGAPGAGKGTQAERIVAKYGIPQISTGDMLREAVAKG-TELGKKAKE 51
                                      6889*********************************987.567888887 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.4e-06
                         Hydin_ADK 170 vLPedllveIlsERlqlndCyrGvvfDg 197
                                       + P+++++ I+ ER+   dC +G ++Dg
  gi|488600251|ref|YP_007906722.1|  58 LVPDEVVIGIVKERIAQPDCEKGFILDG 85 
                                       57*************************9 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.5
                         Hydin_ADK 169 cvLPedllveIlsERlqlndC 189
                                       +  Ped +++ +  R  +++C
  gi|488600251|ref|YP_007906722.1| 113 VSVPEDEIIKRIVNRRTCKNC 133
                                       556888777777777788888 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.3e-09   1.6e-06       3     119 ..       4     128 ..       3     136 .. 0.76
   2 ?   -1.9   0.0       2.8   3.3e+03     126     140 ..     165     179 ..     152     206 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.3e-09
                            AAA_33   3 llvGlpGsGKstlaerllkklgavllssdtlrr.rlfg..tdqqsktdytrvldr.....lyqilnelarkalsagr 71 
                                       +l G+pG+GK t aer+++k g   +s+ +++r ++++  +  ++ ++y +  +      +++i++e+++     ++
  gi|488600251|ref|YP_007906722.1|   4 ILLGAPGAGKGTQAERIVAKYGIPQISTGDMLReAVAKgtELGKKAKEYMDRGELvpdevVIGIVKERIA-QPDCEK 79 
                                       789*******************666666555552666688445555555654444322356667777774.356679 PP

                            AAA_33  72 nvildatnlsrrerarflklarrlgvpv.rivvvetdeetlkeRlakRa 119
                                       ++ild   ++ ++ ++++k+++++g ++ +++ v+++e+++ +R+  R 
  gi|488600251|ref|YP_007906722.1|  80 GFILDGFPRTINQAEALDKMLEEMGKKIdAVINVSVPEDEIIKRIVNRR 128
                                       9****999999**************99835577*************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                            AAA_33 126 sevpeealdrqkarf 140
                                        e  +e l+ +k++ 
  gi|488600251|ref|YP_007906722.1| 165 EETVKERLKVYKSQT 179
                                       233333333333333 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00011      0.13       3      62 ..       7      68 ..       7      75 .. 0.77
   2 ?    1.7   0.0      0.15   1.8e+02     105     140 ..      94     129 ..      80     140 .. 0.76
   3 !    8.2   0.0    0.0015       1.8     138     185 .]     161     208 ..     154     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHH CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelllkeeeleeqteallfa 62
                                      G  GaGK tqae +++++    i+   +++    +gte+G+k++e++  + el +  +++ ++
  gi|488600251|ref|YP_007906722.1|  7 GAPGAGKGTQAERIVAKYGIPQIStgdMLREAVAKGTELGKKAKEYMD-RGELVPDEVVIGIV 68
                                      5569*************97766666567888889************98.66666655555555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                                       HHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS CS
                   Thymidylate_kin 105 dlvlslnedvllkPdltflldvdpevalkRlakrde 140
                                       +++ ++ e+++ k d+++ ++v++++ +kR+  r++
  gi|488600251|ref|YP_007906722.1|  94 EALDKMLEEMGKKIDAVINVSVPEDEIIKRIVNRRT 129
                                       455566666655889999999999999999999987 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0015
                                       TSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 138 rdeldeeeeeqldflrkvrerylelakederiliidasksieevheeI 185
                                        d ++e+++e+l+++++ +e + e + +++ ++ +d +ksi+ev ++I
  gi|488600251|ref|YP_007906722.1| 161 DDDKEETVKERLKVYKSQTEPLIEYYSKKGLVYNVDGTKSIDEVFKQI 208
                                       334689********************99999*************9998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.1e-07   0.00013       2     117 ..       4     131 ..       3     148 .. 0.80
   2 ?   -2.1   0.0       4.3   5.2e+03      25      47 ..     179     199 ..     161     214 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssalee 73 
                                       +l G+pG+GK t a+++  + g+     g+ lr+ ++++  l    +e  d+ + + +++   ++ +++e ++  + 
  gi|488600251|ref|YP_007906722.1|   4 ILLGAPGAGKGTQAERIVAKYGIpqistGDMLREAVAKGTELGKKAKEYMDRGELVPDEV---VIGIVKERIAQPDC 77 
                                       799**************9998889999999999999986666666666555555555555...44444444443345 PP

                            AAA_18  74 gknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRgyee 117
                                       +k  ++dg++    +++a d+            + + ++++e ++R+ +R++ +
  gi|488600251|ref|YP_007906722.1|  78 EKGFILDGFPRTINQAEALDKMLeemgkkidavINVSVPEDEIIKRIVNRRTCK 131
                                       778899999999999999988889999999999*****************9765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                            AAA_18  25 gvnlrdvakenglllevdpeald 47 
                                        + l+++ +++gl++ vd    +
  gi|488600251|ref|YP_007906722.1| 179 TEPLIEYYSKKGLVYNVDGT--K 199
                                       44556666666666666655..3 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0043       5.2       6      47 ..       6      48 ..       2      61 .. 0.85
   2 !    7.2   0.0    0.0031       3.7     117     147 ..     102     132 ..      98     148 .. 0.86
   3 ?   -2.2   0.0       2.3   2.7e+03     141     162 ..     159     180 ..     157     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
                                      EESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHH CS
                              CoaE  6 tGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkk 47
                                       G  ++GK t a+++ + +g+p + +  + r++v++g+e  kk
  gi|488600251|ref|YP_007906722.1|  6 LGAPGAGKGTQAERIVAkYGIPQISTGDMLREAVAKGTELGKK 48
                                      57789*******998877********99********9987665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0031
                                       TGGGGSSEEEEEE--HHHHHHHHHHCCTSTH CS
                              CoaE 117 qlekliervlvvdvelelqveRlvardgvse 147
                                       ++ k+i+ v+ v+v++++ ++R+v+r+  ++
  gi|488600251|ref|YP_007906722.1| 102 EMGKKIDAVINVSVPEDEIIKRIVNRRTCKN 132
                                       577899********************97765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.3
                                       HCCTSTHHHHHHHHHHS--HHH CS
                              CoaE 141 ardgvseeevkaiiaaQlseee 162
                                       +rd+ +ee vk++++   s+ e
  gi|488600251|ref|YP_007906722.1| 159 QRDDDKEETVKERLKVYKSQTE 180
                                       6788888888888776555544 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.8   1.8e-05     0.021       2      26 ..     129     154 ..     128     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                                       EETTTTCEE.CHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDpergelvCtdCG 26 
                                       +C+nC+  + l+++p   e  C +CG
  gi|488600251|ref|YP_007906722.1| 129 TCKNCKAVYhLIYNPPKEEGKCDKCG 154
                                       8******999***************6 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.9e-05     0.082       3      51 ..       4      55 ..       2      90 .. 0.75
   2 ?   -1.9   0.0       2.8   3.4e+03     121     139 ..     157     176 ..     133     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-05
                            AAA_28  3 vitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwved 51
                                      +++G++++GK t +e++ a+ g+p +   ++ re + ++++ g++a ++ ++
  gi|488600251|ref|YP_007906722.1|  4 ILLGAPGAGKGTQAERIVAKyGIPQIstGDMLREAVAKGTELGKKAKEYMDR 55
                                      799*************99877**987789*******9999998876665443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                            AAA_28 121 i.dddgeRredleereaide 139
                                       + ++d+  +e+++er ++++
  gi|488600251|ref|YP_007906722.1| 157 LyQRDDDKEETVKERLKVYK 176
                                       44777788888888888775 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.14      24      62 ..       2      42 ..       1      60 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsl..lpplseeealevakias 62
                                      nl+l+G+pG+GK   a+r+ +   +p++s+ ++l  a  + 
  gi|488600251|ref|YP_007906722.1|  2 NLILLGAPGAGKGTQAERIVAKygIPQISTGDMLREAVAKG 42
                                      89****************97532278888888887665554 PP

>> VSP  Giardia variant-specific surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00011      0.14      71     143 ..     125     200 ..      95     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                               VSP  71 dnkkickectvanckt...cedkgqlkacddGfyksgdac.spcdesvktcsagtasdcteclaGkvlkygndgtkg 143
                                        n+++ck+c++  ++    ++++g+++ c   +y+  d+  ++++e  k  ++ t     e  + k l y  dgtk 
  gi|488600251|ref|YP_007906722.1| 125 VNRRTCKNCKAVYHLIynpPKEEGKCDKCGGELYQRDDDKeETVKERLKVYKSQTE-PLIEYYSKKGLVYNVDGTKS 200
                                       5899******999864222789************9876651567777777777665.57889999999999999996 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 ?   11.2   0.7   0.00022      0.26      29      59 ..     128     161 ..     119     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                    OrfB_Zn_ribbon  29 ktCseCgsknke..alsgrtfkCpnCgfe.adrD 59 
                                        tC +C ++     ++ +++ kC++Cg e ++rD
  gi|488600251|ref|YP_007906722.1| 128 RTCKNCKAVYHLiyNPPKEEGKCDKCGGElYQRD 161
                                       478888877777778*************989998 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 ?    4.1   0.0     0.053        64      31      46 .]     119     134 ..      97     134 .. 0.75
   2 ?    7.1   0.2    0.0059       7.1       2      23 ..     148     172 ..     147     179 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.053
                           zf-IS66  31 rViehirpkyaCpcCe 46 
                                       ++i+ i  +++C++C+
  gi|488600251|ref|YP_007906722.1| 119 EIIKRIVNRRTCKNCK 134
                                       78999999*******5 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0059
                           zf-IS66   2 rtCpcCGg.l...lkpigedrvreel 23 
                                        +C++CGg l    +  +e+ v e+l
  gi|488600251|ref|YP_007906722.1| 148 GKCDKCGGeLyqrDDDKEET-VKERL 172
                                       68******556643333333.55665 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 ?    0.9   0.3      0.43   5.1e+02       3       8 ..     129     134 ..     126     137 .. 0.60
   2 ?   10.0   0.4   0.00058      0.69       3      15 ..     149     161 ..     149     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                            zf-ACC   3 KCpsCg 8  
                                        C  C+
  gi|488600251|ref|YP_007906722.1| 129 TCKNCK 134
                                       366665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00058
                            zf-ACC   3 KCpsCgemlykke 15 
                                       KC++Cg  ly+++
  gi|488600251|ref|YP_007906722.1| 149 KCDKCGGELYQRD 161
                                       9*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1315.04
//
Query:       gi|488600252|ref|YP_007906723.1|  [L=85]
Description: Uncharacterized protein, involved in the regulation of septum location [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.0    5.4e-31  106.6   0.0    1.0  1  SpoVG     SpoVG


Domain annotation for each model (and alignments):
>> SpoVG  SpoVG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0     3e-35   5.4e-31       2      82 .]       3      83 ..       2      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 3e-35
                             SpoVG  2 eitevrikkvesegrlkAfasvtlddsfvirdikiiegkkglfvamPsrktkdgeykdiahpinsearekleeavleaY 80
                                      eitevri+k ++eg +kA+a+v ld++fv++++ki+eg++gl v mPsr+tk+g+++di+hp n++arek+ +avleaY
  gi|488600252|ref|YP_007906723.1|  3 EITEVRIYKPKQEGTVKAYATVSLDNEFVVKGLKILEGENGLWVGMPSRRTKEGTFQDIFHPANKDAREKIVNAVLEAY 81
                                      8****************************************************************************** PP

                             SpoVG 81 ee 82
                                      +e
  gi|488600252|ref|YP_007906723.1| 82 RE 83
                                      85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 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:                        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 0.32s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 518.04
//
Query:       gi|488600253|ref|YP_007906724.1|  [L=109]
Description: hypothetical protein Asulf_00714 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-17   61.3   0.2    8.8e-17   60.6   0.2    1.3  1  Cupin_2       Cupin domain
    5.8e-06   26.3   0.0    6.9e-06   26.0   0.0    1.1  1  AraC_binding  AraC-like ligand binding domain
    1.9e-05   24.3   0.0    2.5e-05   23.9   0.0    1.2  1  Cupin_1       Cupin
    0.00088   19.0   0.0     0.0011   18.7   0.0    1.2  1  DMSP_lyase    Dimethlysulfonioproprionate lyase
     0.0028   17.8   0.5     0.0061   16.7   0.4    1.6  1  ARD           ARD/ARD' family
     0.0098   15.7   0.0      0.016   15.0   0.0    1.3  1  EutQ          Ethanolamine utilisation protein EutQ
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.016   15.4   0.0    1.2  1  CENP-C_C      Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.2   3.4e-20   8.8e-17       4      70 ..      37     102 ..      35     103 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 3.4e-20
                                       EEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   4 elppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       el+p +++++ +H+ge e+++VleG++e +v++  +++eaGd++  p++ pH+++N gd  a+++ +
  gi|488600253|ref|YP_007906724.1|  37 ELDPKAETEEYTHEGE-EVRIVLEGKIECKVGNIHYTMEAGDVIWHPSNIPHKMKNIGDRKAVYITI 102
                                       6899999*********.**********************************************9987 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 !   26.0   0.0   2.7e-09   6.9e-06      14      79 ..      42     107 ..      32     109 .] 0.90

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.7e-09
                                       -SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE--- CS
                      AraC_binding  14 hsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfege 79 
                                        ++++ +h+  ++ +v+eG+  +++++ +y +++Gd+++ p + pH +   ++    y +++ +++
  gi|488600253|ref|YP_007906724.1|  42 AETEEYTHEGEEVRIVLEGKIECKVGNIHYTMEAGDVIWHPSNIPHKMKNIGDRKAVYITIGTPPT 107
                                       56677799********************************************99999999888876 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   9.6e-09   2.5e-05      31     111 ..      29     101 ..      21     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9.6e-09
                                       STEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSE CS
                           Cupin_1  31 lgisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepa 107
                                       ++i++ +  l p++  +  +h   +e+ +vl+G+      +      ++h ++++Gdv++ P++++h ++n+gd +a
  gi|488600253|ref|YP_007906724.1|  29 SNIVVIKSELDPKAETEEYTH-EGEEVRIVLEGKIE----CK---VGNIHYTMEAGDVIWHPSNIPHKMKNIGDRKA 97 
                                       556666666666666666677.88999999999999....33...458999**********************9999 PP

                                       EEEE CS
                           Cupin_1 108 vaiv 111
                                       v i 
  gi|488600253|ref|YP_007906724.1|  98 VYIT 101
                                       8776 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.2e-07    0.0011     109     155 ..      45      90 ..      23      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.2e-07
                        DMSP_lyase 109 PdHhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikhamr 155
                                        +  h+ ee+ +vl g +e + g+ ++  +++G+vi+++++i+h+m+
  gi|488600253|ref|YP_007906724.1|  45 EEYTHEGEEVRIVLEGKIECKVGNIHY-TMEAGDVIWHPSNIPHKMK 90 
                                       56789*******************985.6899**************8 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   2.4e-06    0.0061      85     135 ..      44      89 ..      24     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.4e-06
                               ARD  85 feEhlhedeeirliveGtgyFdvrskdeawirvlvekGDLivlPagiyhrF 135
                                        eE +he ee+r+++eG+    v   + ++    +e+GD i  P +i h  
  gi|488600253|ref|YP_007906724.1|  44 TEEYTHEGEEVRIVLEGKIECKV--GNIHY---TMEAGDVIWHPSNIPHKM 89 
                                       499**************865544..34455...5***************75 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   6.3e-06     0.016      88     145 ..      44     101 ..      36     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.3e-06
                              EutQ  88 tfdwtlnydeidyvieGrldvlidGrkvvaeaGdviliPkgskiefsvtdeakflyva 145
                                       t ++t + +e+ +v+eG+++  +   + + eaGdvi  P +   ++   ++ k +y++
  gi|488600253|ref|YP_007906724.1|  44 TEEYTHEGEEVRIVLEGKIECKVGNIHYTMEAGDVIWHPSNIPHKMKNIGDRKAVYIT 101
                                       667888999******************************9988888888888888876 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 ?   15.4   0.0   6.4e-06     0.016      35      80 ..      53      98 ..      21     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.4e-06
                                      EEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS-EE CS
                          CENP-C_C 35 lvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnkeak 80
                                       v  V++G++e++v + ++++  g+v   P+    +++N+++++a+
  gi|488600253|ref|YP_007906724.1| 53 EVRIVLEGKIECKVGNIHYTMEAGDVIWHPSNIPHKMKNIGDRKAV 98
                                      56679***********************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 804.54
//
Query:       gi|488600254|ref|YP_007906725.1|  [L=475]
Description: pyruvate carboxylase subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-59  198.8   0.3    1.8e-58  197.6   0.2    1.6  2  PYC_OADA   Conserved carboxylase domain
    3.4e-48  164.5   0.0    4.4e-48  164.1   0.0    1.1  1  HMGL-like  HMGL-like
  ------ inclusion threshold ------
       0.17   11.0   0.0       0.27   10.3   0.0    1.2  1  TGT        Queuine tRNA-ribosyltransferase


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 ?   -2.6   0.0      0.64   3.8e+03     140     159 ..      82     102 ..      57     144 .. 0.55
   2 !  197.6   0.2     3e-62   1.8e-58       1     196 [.     291     470 ..     291     472 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.64
                                       SHHHHHHHHHSHHHHHH.HHH CS
                          PYC_OADA 140 teedvlsyalypkvaek.flk 159
                                         ++v+ y  yp+++ + f+ 
  gi|488600254|ref|YP_007906725.1|  82 RGQNVVGYRHYPDDIVEkFVL 102
                                       447777788887765431433 PP

  == domain 2  score: 197.6 bits;  conditional E-value: 3e-62
                                       HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TT CS
                          PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegry 77 
                                       V++++iPGG+++n+ +q+keq++ldk++evlke+++v+++lG++++VTP+S++vg +Av+nvl         +e ry
  gi|488600254|ref|YP_007906725.1| 291 VLVYQIPGGMFSNMINQLKEQNALDKLPEVLKEVPKVREDLGYPPLVTPTSQIVGVQAVVNVLV--------GE-RY 358
                                       789*************************************************************........86.** PP

                                       SS--HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHH CS
                          PYC_OADA  78 kdipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleeka..kteedvlsyalypk 152
                                       k ++++++dl++G++G++p++++e+++kk+l +e+pi++rpad+lep ++ek +kelee     t+e+vl+yal+p+
  gi|488600254|ref|YP_007906725.1| 359 KVVTKETKDLVRGMYGRTPAPIKEDIIKKILGDEKPIDCRPADLLEP-EFEKRKKELEEMGipATDENVLLYALFPQ 434
                                       ***********************************************.***********87555************* PP

                                       HHHHHHHHHHHHHHHH..CTTTS......-SEEEEEETTEEEE. CS
                          PYC_OADA 153 vaekflkfreeygdvsvlptkvffeglkvgeeveveveggkyli 196
                                       ++ kflk     g++   +++ f +  kv+ ++eve++g+ky++
  gi|488600254|ref|YP_007906725.1| 435 TGLKFLK-----GEI---EEEPFPSTGKVEGKFEVEIDGSKYNV 470
                                       ******9.....333...3455666678999**********985 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.1   0.0   7.3e-52   4.4e-48       2     263 ..       3     268 ..       2     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 7.3e-52
                                       -EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B.... CS
                         HMGL-like   2 vkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkkar... 66 
                                       v ivd tLRDG+q+l ++++++ + l+i+++ de g++++Ev          +++ ed++e++r+i k vk+ar   
  gi|488600254|ref|YP_007906725.1|   3 VDIVDLTLRDGHQSLlATRMRTRDILPIVEKFDESGISVLEVwggatfdsAHRFLNEDPWERLREIRKRVKNARism 79 
                                       89************99******************************99999999*******************7777 PP

                                       .......--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT CS
                         HMGL-like  67 ......ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..vel 135
                                             +++++++ ++ ++++v +  ++g + +++f+a ++              +++ e a+k a++   +  +++
  gi|488600254|ref|YP_007906725.1|  80 llrgqnVVGYRHYPDDIVEKFVLKTAENGLDFFRIFDALND--------------VRNLETAIKTAKRTSSHvqATI 142
                                       777888***********************************..............9**************9966678 PP

                                       -BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHH CS
                         HMGL-like 136 sledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaA 212
                                        ++ ++ +++e+ +e++++++   +++i i+D+ G+l+P++a+el++a+k++v   ++++vH H + G+A +++l+ 
  gi|488600254|ref|YP_007906725.1| 143 CYTISPVHTIEKYIEIAKELAVFEPDSICIKDMAGLLSPKVAYELVKAIKKEVG--IKINVHSHYTSGMASMALLKS 217
                                       8999**************************************************..********************* PP

                                       HHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHH CS
                         HMGL-like 213 veaGadrvdgtvnGlGeraGnaaleelvaalealgvdtgldlqklrsiaal 263
                                       veaGad vd++++ l+ ++ ++++e +v+ale +g++tg+dl+ l++i+++
  gi|488600254|ref|YP_007906725.1| 218 VEAGADMVDTCMSPLSMGTSHPPTESMVYALEEMGYKTGVDLEVLMEIRDY 268
                                       ************************************************986 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.6e-05      0.27     148     250 ..     124     229 ..     119     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHHHHHHHSE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-SSSSSSHHHHHHHHHHHHGGGS-TTS- CS
                               TGT 148 verTlrwldrcleahqa.lfgivqGglyedlreesaeelakrdfdgyaigGlsvgeekeellevveavtellpedkp 223
                                       +e+ ++ ++r   + qa ++  + +    +   e a+ela ++ d ++i  +++  + +  +e+v+a+++++  +  
  gi|488600254|ref|YP_007906725.1| 124 LETAIKTAKRTSSHVQAtICYTISPVHTIEKYIEIAKELAVFEPDSICIKDMAGLLSPKVAYELVKAIKKEVGIKIN 200
                                       66777778888766688899999999999999999*****99999********9999999*********99966554 PP

                                       EE..ETTB-SHHHHHHHHHTT--EEEESH CS
                               TGT 224 ry..lmGvgtPedlleavalGvDmfdcvy 250
                                       ++         + ll++v++G+Dm+d+ +
  gi|488600254|ref|YP_007906725.1| 201 VHshYTSGMASMALLKSVEAGADMVDTCM 229
                                       442155566899**************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2917.75
//
Query:       gi|488600255|ref|YP_007906726.1|  [L=295]
Description: putative permease, DMT superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-56  188.5  47.2    3.9e-29  101.6  19.5    2.0  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3  19.7     8e-31   1.4e-26       4     136 ..      14     144 ..      11     145 .. 0.96
   2 !  101.6  19.5   2.2e-33   3.9e-29       2     135 ..     158     292 ..     157     294 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 8e-31
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       +l +l+ +l+wa +fv++ki lr++ p+ l+f+rf++a+ +ll++  ++++ +  l+ kd+  +l+l++ g++l + 
  gi|488600255|ref|YP_007906726.1|  14 VLALLITMLIWAGSFVFIKISLREIGPFNLAFYRFILASPALLLVVYFRKKFQ-LLDAKDIPKILVLAITGVTLLYA 89 
                                       67899*************************************99999999999.9********************** PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++f al +t+a+n s++++ +++f++i+s  +lge++t+++ +gi+l+++Gv+li+
  gi|488600255|ref|YP_007906726.1|  90 VQFVALVYTTATNSSILINSSVIFIAIMSL-FLGERFTKLKAFGICLSFIGVVLIV 144
                                       ***************************875.55*********************97 PP

  == domain 2  score: 101.6 bits;  conditional E-value: 2.2e-33
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvl 77 
                                       +g++l++   ++waiy++l k ll+k++p  lt++ f +++ill+++a++++ ++   +s + w++ll+l+ll++v+
  gi|488600255|ref|YP_007906726.1| 158 IGDMLIIFDGFLWAIYTILGKSLLEKYNPEVLTAYAFALGSILLVPFAVYEGFSNpITFSTTVWISLLYLALLCSVF 234
                                       799****************************************************99******************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       a++++++al+ ++a++++++++++P ft+i+++++lge+l+ +++lg +l ++G++l+
  gi|488600255|ref|YP_007906726.1| 235 AYVMWYSALTAMDATRVAVFVYIVPFFTAIMAFFVLGERLGAFTVLGGILTIAGLYLT 292
                                       *******************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1889.56
//
Query:       gi|488600256|ref|YP_007906727.1|  [L=218]
Description: thiamine-phosphate diphosphorylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-61  205.9   0.2    3.6e-61  205.7   0.2    1.1  1  TMP-TENI      Thiamine monophosphate synthase
    0.00011   21.8   0.0    0.00015   21.2   0.0    1.2  1  NMO           Nitronate monooxygenase
    0.00016   21.1   0.1    0.00022   20.6   0.1    1.2  1  ThiG          Thiazole biosynthesis protein ThiG
     0.0034   16.9   0.0     0.0048   16.4   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein
     0.0037   16.5   0.5     0.0091   15.2   0.3    1.7  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.029   14.7   0.2      0.054   13.8   0.2    1.3  1  TraC          TraC-like protein
      0.036   13.5   0.2      0.065   12.7   0.2    1.4  1  BtpA          BtpA family
       0.08   12.0   0.2       0.17   11.0   0.0    1.6  2  Dus           Dihydrouridine synthase (Dus)


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 !  205.7   0.2   1.6e-64   3.6e-61       1     181 []       9     189 ..       9     189 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.7 bits;  conditional E-value: 1.6e-64
                          TMP-TENI   1 lylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgv 77 
                                       ly++td +++     ++v+e alk+gv+++qlRek l are++  a++l++l+ +y++ +i+ndr+d+a+ v+adg+
  gi|488600256|ref|YP_007906727.1|   9 LYFITDGRSH---GHERVAEMALKAGVKTIQLREKRLPAREIYGIAKRLRRLTYDYEALFIVNDRFDIAISVEADGI 82 
                                       79****7777...789999********************************************************** PP

                          TMP-TENI  78 Hlgqddlpvaearellg...pdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkda.eplgleglkelaeale 150
                                       H+gq+dlp++ +r l++   p++i+G+S+ +l+ea+eae + adY+gvGp+fpT+tK+da e++g++glk++++a++
  gi|488600256|ref|YP_007906727.1|  83 HVGQEDLPAKAIRSLIDekfPGMILGVSARDLSEALEAE-KYADYLGVGPVFPTSTKEDArEVIGIDGLKKVCSAVK 158
                                       ****************9333469***************9.789********************************** PP

                          TMP-TENI 151 iPvvaiGGitlenvaevleagadgvavvsai 181
                                       +PvvaiGGi+++nv evl+ag+ gvav+sai
  gi|488600256|ref|YP_007906727.1| 159 VPVVAIGGINHSNVSEVLKAGCTGVAVISAI 189
                                       ******************************8 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.9e-08   0.00015     185     231 ..     150     194 ..     131     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.9e-08
                               NMO 185 vpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkes 231
                                       +++v +av++Pv+A GGi+ + +v  +L +G  gv++ ++  + +e+
  gi|488600256|ref|YP_007906727.1| 150 LKKVCSAVKVPVVAIGGIN-HSNVSEVLKAGCTGVAVISAI-AFSEN 194
                                       57899************97.689*************98884.33444 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   9.8e-08   0.00022     164     221 ..     147     203 ..      90     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.8e-08
                                       HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHH CS
                              ThiG 164 kealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafk 221
                                          lk +++ +kvPv+   Gi   s++ ++++ G+++v + +a+a +++p + A+ + 
  gi|488600256|ref|YP_007906727.1| 147 IDGLKKVCSAVKVPVVAIGGIN-HSNVSEVLKAGCTGVAVISAIAFSENPEKSAEELL 203
                                       566899999*******999997.589************************99998765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.2e-06    0.0048     178     224 ..     145     190 ..      88     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.2e-06
                                       --HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHH CS
                      His_biosynth 178 pdleltkelaeavkipviasGGvgsledlkelksegvdavivgsaly 224
                                       + ++ +k++++avk+pv+a GG+ + + + e+ ++g+ +v v sa+ 
  gi|488600256|ref|YP_007906727.1| 145 IGIDGLKKVCSAVKVPVVAIGGI-NHSNVSEVLKAGCTGVAVISAIA 190
                                       667789999*************9.55679999999998887766664 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.72   1.6e+03     201     215 ..      72      86 ..      66      99 .. 0.84
   2 !   15.2   0.3   4.1e-06    0.0091     180     227 ..     152     199 ..     143     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.72
                            DUF561 201 plalslgasGiGigs 215
                                       ++a+s+ a Gi +g+
  gi|488600256|ref|YP_007906727.1|  72 DIAISVEADGIHVGQ 86 
                                       799999****99986 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.1e-06
                            DUF561 180 eiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndeeemv 227
                                       ++ ++v++Pv++  G++++ v+  l++g  G+ + sa+   ++ e+  
  gi|488600256|ref|YP_007906727.1| 152 KVCSAVKVPVVAIGGINHSNVSEVLKAGCTGVAVISAIAFSENPEKSA 199
                                       68899********************************98766655444 PP

>> TraC  TraC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.4e-05     0.054      27      61 ..      21      56 ..      16      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                              TraC 27 eRigRiAlkaGLgeieieeeeld.aifeeiaaRFRk 61
                                      eR++ +AlkaG+  i++ e+ l  + +  ia+R R+
  gi|488600256|ref|YP_007906727.1| 21 ERVAEMALKAGVKTIQLREKRLPaREIYGIAKRLRR 56
                                      9*********************626799******97 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.9e-05     0.065     189     230 ..     147     189 ..     137     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                              BtpA 189 leelklaketvkvkvlvgsGvseenlekllsi.adGvivgtsi 230
                                       ++ lk++  +vkv+v++  G+++ n++++l++ + Gv v + i
  gi|488600256|ref|YP_007906727.1| 147 IDGLKKVCSAVKVPVVAIGGINHSNVSEVLKAgCTGVAVISAI 189
                                       7889**************************9768999887766 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.56   1.3e+03     136     182 ..      16      71 ..       6      82 .. 0.56
   2 ?   11.0   0.0   7.5e-05      0.17     170     236 ..     145     212 ..     135     218 .] 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.56
                                       TTC.HHHHHHHHHHCT-SEEEEESS.........ECCCTT-CG--CHHHHHHHHH- CS
                               Dus 136 eeenalelakiveaaGaqaltvHgR.........traqnyegtadweaIkevkqav 182
                                        ++ + ++a+++ +aG++ + +             +++ ++ t d+ea   v +++
  gi|488600256|ref|YP_007906727.1|  16 RSHGHERVAEMALKAGVKTIQLREKrlpareiygIAKRLRRLTYDYEALFIVNDRF 71 
                                       55667778888888888877653223333355444444444455555555555555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.5e-05
                                       --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEE..EESCHHCCSTTHHHH.HHHHHHSC--- CS
                               Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaileetGadgv..migrgalgnPwlfae.stavktgeaep 236
                                       + ++  k+v+ av++pv+a G+I + ++++++l+  G+ gv  + + +  +nP  +ae    + +++++p
  gi|488600256|ref|YP_007906727.1| 145 IGIDGLKKVCSAVKVPVVAIGGINH-SNVSEVLKA-GCTGVavISAIAFSENPEKSAEeLLNLIENSNKP 212
                                       5677889****************87.678888888.8887621556677788888887544444445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1359.70
//
Query:       gi|488600257|ref|YP_007906728.1|  [L=216]
Description: putative phosphoesterase, related to the Icc protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   67.3   0.0    3.8e-18   66.2   0.0    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.4e-14   54.3   0.0    3.5e-14   53.8   0.0    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    2.1e-09   37.1   0.0    1.4e-06   27.8   0.0    2.6  3  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   6.3e-22   3.8e-18       1     151 [.       1     192 [.       1     200 [. 0.71

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 6.3e-22
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl...eeeepevleellela..pvlaVrGNnD.......... 62 
                                       M+++i+SD+Hs++d l+++le    v+vd  + +GDl    +e+  v+ e+l+    + + V+GN+D          
  gi|488600257|ref|YP_007906728.1|   1 MRVLILSDIHSRFDVLKRILES---VDVDCCFICGDLsdfRAEDVFVISEILSEVglKCYCVHGNCDpeeaidyieq 74 
                                       9*********999999999998...555********965444444555555555579**********9998888865 PP

                     Metallophos_2  63 .............eevveedvlreaaelgtdl.............peeaelel.........agekvlliHgdpl.. 102
                                                    e               t +              e+ + e+         +++++l+ H  p+  
  gi|488600257|ref|YP_007906728.1|  75 sgminlhckslpfE-------------NYTLHgvggsnytpfltpSEYSNEEMwsfvenfiyGERNILISHCPPKgi 138
                                       44444444333331.............333336666666666664133333333445666657777******98899 PP

                     Metallophos_2 103 ......gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprd 151
                                             g +++ +  ++  +e+ d+++cGH+H+++   ++g+lv+nPGsv  +++
  gi|488600257|ref|YP_007906728.1| 139 ldmtysGINAGCEVIRSI-MEKFDYIFCGHIHEAKGMYKNGTLVLNPGSVISGSF 192
                                       999985555555544444.55666*************************988754 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   5.9e-18   3.5e-14       1     203 [.       1     170 [.       1     171 [. 0.84

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 5.9e-18
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TTSC CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllGNHeg 76 
                                       +r+l+++D+H      ++d l+++l+ +    ++d  +++GDl d    + +++   l++++    ++y+++GN++ 
  gi|488600257|ref|YP_007906728.1|   1 MRVLILSDIH-----SRFDVLKRILESV----DVDCCFICGDLSDFRAEDVFVISEiLSEVGL---KCYCVHGNCD- 64 
                                       89********.....**********999....99*************8888888886888888...9*********. PP

                                       HHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH CS
                       Metallophos  77 feeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkd 153
                                            ++  +y++  ++++ ++      lp           ++lhG            +  ++ ++++ +++e+++ 
  gi|488600257|ref|YP_007906728.1|  65 ----PEEAIDYIEQSGMINLHC----KSLPFEN--------YTLHGV--------GGSNYTPFLTPSEYSNEEMWSF 117
                                       ....666666666668888888....7788877........555554........2345556666666666999999 PP

                                       HHHHTTCSEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 154 lekrekadwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGHtHv 203
                                        e++  ++  i+++H p+      ++sg   g e+++ + +k++  ++++GH+H+
  gi|488600257|ref|YP_007906728.1| 118 VENFIYGERNILISHCPPKgildmTYSGINAGCEVIRSIMEKFD--YIFCGHIHE 170
                                       999****************9999999999999999999988886..********7 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0   0.00091       5.5       7      48 ..       2      40 ..       1      48 [. 0.87
   2 ?   -1.0   0.0      0.15   8.9e+02      83     101 ..      47      65 ..      40      75 .. 0.83
   3 !   27.8   0.0   2.4e-10   1.4e-06     174     257 .]     125     207 ..     111     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00091
                                      EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHH CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvkaeak 48
                                      +vl +sd++ ++++l+r++e +   d+D   + Gdl   +a+
  gi|488600257|ref|YP_007906728.1|  2 RVLILSDIHSRFDVLKRILESV---DVDCCFICGDLSDFRAE 40
                                      89*************9998876...79999999*99776665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.15
                                       HHHHTT-SEEEEE--TTS- CS
                     Metallophos_3  83 relgeldvpafvvPGkrDa 101
                                       ++l e++++ ++v G+ D 
  gi|488600257|ref|YP_007906728.1|  47 EILSEVGLKCYCVHGNCDP 65 
                                       67999***********994 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 2.4e-10
                                       -EEEEEESS--S-SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--BGGGTEEEEEETTT CS
                     Metallophos_3 174 rrkvlllatpPigelvadkglkekgsevvaelvktlnPevvvvghavkeh.eelgktlvvnPGaleeGdfavvdlee 249
                                       +r +l+ + pP g l++     ++g ev+  ++ ++  + +++gh + ++    + tlv nPG++  G fav d++ 
  gi|488600257|ref|YP_007906728.1| 125 ERNILISHCPPKGILDMTYSGINAGCEVIRSIMEKF--DYIFCGHIHEAKgMYKNGTLVLNPGSVISGSFAVWDMNS 199
                                       799*************66665899999999999876..589*******995555679*******************9 PP

                                       TEEEEEE- CS
                     Metallophos_3 250 kkveleqv 257
                                       +  el++v
  gi|488600257|ref|YP_007906728.1| 200 NSFELKNV 207
                                       99988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1418.31
//
Query:       gi|488600258|ref|YP_007906729.1|  [L=408]
Description: putative exonuclease of the beta-lactamase fold involved in RNA processing [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-15   55.7   0.4    1.3e-13   50.7   0.0    2.4  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.7e-12   47.6   0.0    3.3e-12   46.7   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    9.5e-06   25.7   0.6    3.4e-05   23.9   0.5    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
    4.5e-05   23.1   0.0    8.9e-05   22.1   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.027   1.2e+02      26      40 ..      39      53 ..      38      59 .. 0.88
   2 !   50.7   0.0   2.8e-17   1.3e-13       2      62 .]     338     399 ..     337     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.027
                             RMMBL 26 irklkprnvilvHGe 40
                                      i+++ p+ vi+ HG+
  gi|488600258|ref|YP_007906729.1| 39 INGIAPKSVIISHGH 53
                                      7899**********8 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 2.8e-17
                             RMMBL   2 ipvkarieeidfSgHadknellelirklkprn...vilvHGeeeatsalarllkeeegidvfiP 62 
                                       +++k+ +e++dfS+Ha+ ++l+e++r+   +    v+ vHGe   t+++a+++++e gid+f+P
  gi|488600258|ref|YP_007906729.1| 338 VKLKMGVEQYDFSAHAGDSQLKEFVRLSADKGveiVFTVHGEN--TEDFANWIRDEIGIDAFAP 399
                                       789****************************************..9*******9999*****98 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   7.3e-16   3.3e-12       2     107 ..     219     322 ..     218     324 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 7.3e-16
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG...........E-SHH....HHHH..HHHS-SSEE CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae...........veakslewmeskkeelnsskgpkv 67 
                                       qe+l++L+++  +          yld+ +++++ ++ ++y++           ++++    +e+ k+  +  ++p+v
  gi|488600258|ref|YP_007906729.1| 219 QEVLMILDKYGIS---------PYLDG-MGKEVSRIIERYPSyirnakklrraIKNAI--TVERGKR-EKILEEPSV 282
                                       7888888888744.........39999.999999999999889888877766533333..2222222.234679*** PP

                                       EEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHH CS
                         Beta-Casp  68 ilassgmlegGrsrellkklledprntvilvgyqaegTlg 107
                                       ++++ gml+gG++  ++ +l +d ++ +il+gyq+egT g
  gi|488600258|ref|YP_007906729.1| 283 VVTTAGMLNGGPALFYISRLYNDDKSKIILTGYQVEGTNG 322
                                       **************************************98 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.5   7.7e-09   3.4e-05      40     162 ..      39     163 ..      13     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 7.7e-09
                                       SGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH...TTCHCGCCEEEEETTT CS
                       Lactamase_B  40 lkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll...lagvsadkpdvdeeel 113
                                       +++  ++ vi++H+HlDH+G ++ l+   + +    +  + +++        +  + +     +  + +  +++  +
  gi|488600258|ref|YP_007906729.1|  39 INGIAPKSVIISHGHLDHVGVAPNLMYYNPDVFMTPPTREISHILLKDSMNIMDNPPYgkrEFIQFESSITEVDYND 115
                                       66777899********************9999999888888888888877777766668888888888999999999 PP

                                       EECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 114 dgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                       +++++g++ +    g+ +g+ +++++ ++ ++l+tGD  l+  ++++  
  gi|488600258|ref|YP_007906729.1| 116 PFEVDGWEITFLNAGHIPGSASIHLSRDI-NILYTGDIKLEDTRLLVKA 163
                                       99999999999999999999999998877.6999999988777666655 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 !   22.1   0.0     2e-08   8.9e-05      32     174 ..      45     187 ..      24     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-08
                                       EEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH...HCCTTCGHHHCHTT........TTEEEEEE-TTSEEE CS
                     Lactamase_B_2  32 daVllthaHyDHlaglltlrelrpkklplyapkgvla...vleanfvylaleee........pavnvheldwgesfe 97 
                                       + V+++h+H DH+  ++ l    p   +++ ++ +++   +l + +  ++++++        ++ +++e+d +++fe
  gi|488600258|ref|YP_007906729.1|  45 KSVIISHGHLDHVGVAPNLMYYNP---DVFMTPPTREishILLKDSMNIMDNPPygkrefiqFESSITEVDYNDPFE 118
                                       45***********88888888666...46666666554445555555566666678888889999************ PP

                                       ECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S-SSTT CS
                     Lactamase_B_2  98 lgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip....eeigerlggadllllditayedd 170
                                       ++  g eit+  a h  g          ++  +   + +++y+gD +  +     +++  +   d+l+++ t++  +
  gi|488600258|ref|YP_007906729.1| 119 VD--GWEITFLNAGHIPGS---------ASIHLS-RDINILYTGDIKLEDtrllVKADMDFPETDILIVESTYFGTE 183
                                       *8..789****99998888.........777777.8889******99766333322345677799999999998887 PP

                                       HHHH CS
                     Lactamase_B_2 171 emir 174
                                        ++r
  gi|488600258|ref|YP_007906729.1| 184 HPER 187
                                       7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2809.25
//
Query:       gi|488600259|ref|YP_007906730.1|  [L=258]
Description: tRNA(1-methyladenosine) methyltransferase-related methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-14   54.0   0.0    2.7e-14   53.4   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    3.7e-13   49.5   0.1    4.9e-13   49.1   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
    1.1e-08   35.1   0.0    1.4e-08   34.7   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.3e-07   30.5   0.0    7.1e-07   29.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      1e-06   28.4   0.0    3.8e-06   26.6   0.0    1.8  1  MTS              Methyltransferase small domain
      3e-06   26.5   0.0    4.1e-06   26.1   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    4.7e-06   27.6   0.0    8.5e-05   23.5   0.0    2.1  2  Methyltransf_24  Methyltransferase domain
    2.1e-05   25.1   0.0    3.8e-05   24.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    0.00019   20.9   0.0    0.00026   20.5   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00089   18.9   0.0     0.0057   16.3   0.0    1.9  2  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.022   14.7   0.0    1.5  2  Methyltransf_18  Methyltransferase domain
      0.056   13.3   0.0       0.12   12.2   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
      0.062   12.5   0.2      0.092   11.9   0.2    1.2  1  Methyltransf_3   O-methyltransferase
       0.11   13.3   0.1       0.25   12.1   0.1    1.6  1  Methyltransf_12  Methyltransferase domain
       0.13   11.7   0.0       0.27   10.7   0.0    1.5  2  Methyltransf_4   Putative methyltransferase
       0.13   11.5   0.0       0.19   11.0   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   2.4e-17   2.7e-14      27     181 ..      87     236 ..      82     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.4e-17
                             GCD14  27 aDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvck 103
                                       +Di  ii    l+p s +++ GtGsg ls ++a      G + t+e  ++ a+ ar++f+  +l++ ++  + D+  
  gi|488600259|ref|YP_007906730.1|  87 KDIGAIIAFTGLRPDSAILDCGTGSGVLSAYLAYF-CRDGFVVTVEKRKDFAKIARKNFELAGLKN-IHQIVGDIF- 160
                                       79****************************99975.568***********************9975.666678886. PP

                             GCD14 104 eGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrtyevr 180
                                        G+ + ++ k D + LD+   ++ ip+a + l k++g l  + P i+  + +  a+ + +f++ie++e+    ye +
  gi|488600259|ref|YP_007906730.1| 161 -GLADSIKIKFDLIVLDMKDDDKFIPKARELL-KNSGYLVVYNPYIDATRDAYFAMLNNNFQDIESFEIVKIDYEHK 235
                                       .77889999***********************.8999*********************************9999987 PP

                             GCD14 181 k 181
                                       +
  gi|488600259|ref|YP_007906730.1| 236 R 236
                                       6 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.1   4.4e-16   4.9e-13       4     114 ..     101     207 ..      98     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.4e-16
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       +  +lD+G+G+G l+  la   + ++ vv ++  ++  + Ar+n +  gl+n++  +gdi+ l  +++  kfDli+ 
  gi|488600259|ref|YP_007906730.1| 101 DSAILDCGTGSGVLSAYLA-YFCRDGFVVTVEKRKDFAKIARKNFELAGLKNIHQIVGDIFGLADSIK-IKFDLIVL 175
                                       6689***************.99****************************************775566.79*****9 PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedpr...l 114
                                            +++d dk++ ++ ++lk+ g+l++ +p    +
  gi|488600259|ref|YP_007906730.1| 176 -----DMKDDDKFIPKARELLKNSGYLVVYNPYidaT 207
                                       .....5***********************99983332 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 !   34.7   0.0   1.3e-11   1.4e-08      60     132 ..      87     158 ..      62     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.3e-11
                                       HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  60 hmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       + +++++ +  l++ + +L+ G+GsG l+a la + ++ + vv++e+ k++++ a++n +  +l+n++ +vgD
  gi|488600259|ref|YP_007906730.1|  87 KDIGAIIAFTGLRPDSAILDCGTGSGVLSAYLAYFCRDGF-VVTVEKRKDFAKIARKNFELAGLKNIHQIVGD 158
                                       55667788889*********************98776655.*******************************9 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   6.4e-10   7.1e-07       1      97 []     104     195 ..     104     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 6.4e-10
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS.STTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpf.edgsfDlvvssgalh 75 
                                       +Ld+G+G+G l+++la  + ++ v+ v+  +++ ++ar+++e +gl n++ ++gd+  l    + +fDl+v+  +  
  gi|488600259|ref|YP_007906730.1| 104 ILDCGTGSGVLSAYLAYFCRDGFVVTVEKRKDFAKIARKNFELAGLkNIHQIVGDIFGLADsIKIKFDLIVLD-M-- 177
                                       8***************98889*********************9*************999862555******93.2.. PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                         +  d +k++ +++++Lk+ G
  gi|488600259|ref|YP_007906730.1| 178 --K--DDDKFIPKARELLKNSG 195
                                       ..3..44589999999999877 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   3.4e-09   3.8e-06      32     155 ..     101     221 ..      87     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.4e-09
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STT..TTSTTS-EEEEEE-- CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvl..eeveekkfdlivsNP 105
                                       +  +lD G+G Gvl+a la ++ +  v+ v++ +   ++a++n+e  +l+ ++ +  d++  ++  + kfdliv   
  gi|488600259|ref|YP_007906730.1| 101 DSAILDCGTGSGVLSAYLAYFCRDGFVVTVEKRKDFAKIARKNFELAGLKnIHQIVGDIFglADSIKIKFDLIVLD- 176
                                       4569***********************************************99999997522444469******74. PP

                                       -STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH.....HHHHHS- CS
                               MTS 106 PfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyesl.....leelfgn 155
                                        +++         +++i +A+e Lk++G L+ V+n  +++ +      l++ f++
  gi|488600259|ref|YP_007906730.1| 177 -MKD--------DDKFIPKARELLKNSGYLV-VYNPYIDATRDayfamLNNNFQD 221
                                       .222........3579999999999999875.56655544333233336666665 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   3.7e-09   4.1e-06      19      83 ..      89     157 ..      84     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.7e-09
                                       HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S CS
                            RrnaAD  19 ineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhq 83 
                                       i  I+  + l+++  +l+ g+G G+l++ La  +    vv +E+++++ak+ +k+++    +++  +  
  gi|488600259|ref|YP_007906730.1|  89 IGAIIAFTGLRPDSAILDCGTGSGVLSAYLAYFCrdGFVVTVEKRKDFAKIARKNFElaGLKNIHQIVG 157
                                       5678888999************************6556999*************999655556655555 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   7.5e-08   8.5e-05       2     103 ..     106     199 ..     105     202 .. 0.86
   2 ?    2.5   0.0      0.26     3e+02      66      92 ..     220     247 ..     186     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.5e-08
                   Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDllf 74 
                                        +G+ sGv +++l++ +r+     +v+v++ +   ++a++ar+    agl+ ++++i++d + ++ s +  ++Dl++
  gi|488600259|ref|YP_007906730.1| 106 DCGTGSGVLSAYLAYFCRDGF---VVTVEKRK---DFAKIARKnfelAGLK-NIHQIVGDIFGLADSIK-IKFDLIV 174
                                       79************8877754...8*******...9999999998855555.59999************.99***** PP

                   Methyltransf_24  75 iDgghaaeavledleallprlapggvvlf 103
                                       +D+     +  ++++ ++++l++ g++++
  gi|488600259|ref|YP_007906730.1| 175 LDMK----DDDKFIPKARELLKNSGYLVV 199
                                       **87....677779999999999998875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.26
                   Methyltransf_24  66 a.agsiDllfiDgghaaeavledleall 92 
                                       +  +s+ ++ iD +h+ + +++  ++++
  gi|488600259|ref|YP_007906730.1| 220 QdIESFEIVKIDYEHKRAGTRPSTRVWH 247
                                       2447899***********9999988886 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   3.4e-08   3.8e-05       1      96 []     105     199 ..     105     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.4e-08
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT.SS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaekl.pfednsfDlvvssevlhh 73 
                                       Ld+G+G+G l+++la  +  + vv+v+  k + k+a+++ + +gl ++  +v+d+  l    + +fDl+v+ +    
  gi|488600259|ref|YP_007906730.1| 105 LDCGTGSGVLSAYLAYFCrdGFVVTVEKRKDFAKIARKNFELAGLkNIHQIVGDIFGLaDSIKIKFDLIVLDM---- 177
                                       8**************777889***********************99888899999975444445999998874.... PP

                                       -CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllvi 96 
                                        +d +k++ +++ +Lk+ G+lv+
  gi|488600259|ref|YP_007906730.1| 178 -KDDDKFIPKARELLKNSGYLVV 199
                                       .99*****************986 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.4e-07   0.00026     160     258 ..      99     199 ..      93     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-07
                              PrmA 160 kegeevlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelNkveaklev....alseellkeekadviv 231
                                       ++++ +lD GtGSG+L+   a +  +  vv v   +   k+a++N+el ++++  ++    +  ++ +k  k+d+iv
  gi|488600259|ref|YP_007906730.1|  99 RPDSAILDCGTGSGVLSAYLAYFCRDgFVVTVEKRKDFAKIARKNFELAGLKNIHQIvgdiFGLADSIK-IKFDLIV 174
                                       67889************9877776552799999999999************997766233223566667.99***** PP

                              PrmA 232 aNILaevlielaedikklvkeggllil 258
                                         +  +   ++++++ +l+k++g+l++
  gi|488600259|ref|YP_007906730.1| 175 LDMKDD--DKFIPKARELLKNSGYLVV 199
                                       987666..7899999999999999875 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.1e-06    0.0057      43     120 ..     102     176 ..      92     199 .. 0.81
   2 ?    0.4   0.0       0.4   4.4e+02      23      42 ..     202     221 ..     185     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-06
                                       -EEEETT-TTSHHH..HHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  43 arvLDlfaGsGalg..lEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       + +LD+  GsG+l+  l   +R+   +v vek k  +ki ++n e  +l++ +++++ d +  +++    k +fd++
  gi|488600259|ref|YP_007906730.1| 102 SAILDCGTGSGVLSayLAYFCRD-GFVVTVEKRKDFAKIARKNFELAGLKN-IHQIVGDIFGLADSI---KIKFDLI 173
                                       568********998334567999.99**********************997.9********999888...789**** PP

                                       EE- CS
                     Cons_hypoth95 118 flD 120
                                        lD
  gi|488600259|ref|YP_007906730.1| 174 VLD 176
                                       *99 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.4
                                       SSSHHHHHHHHHHHCCCHCC CS
                     Cons_hypoth95  23 PttdrvrealFnilaaeieg 42 
                                       P  d  r+a F +l++++++
  gi|488600259|ref|YP_007906730.1| 202 PYIDATRDAYFAMLNNNFQD 221
                                       88999*********998665 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     2e-05     0.022      13      73 ..      99     158 ..      91     176 .. 0.84
   2 ?   -2.6   0.0       4.1   4.6e+03     123     149 ..     186     212 ..     181     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                   Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73 
                                       +++s ++D+Gt  g+l++yl+   +   v+ ++ ++   + a++n e agl+ +i+ +++d
  gi|488600259|ref|YP_007906730.1|  99 RPDSAILDCGTGSGVLSAYLAYFCRDGFVVTVEKRKDFAKIARKNFELAGLK-NIHQIVGD 158
                                       56789*********************************************96.57777776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                   Methyltransf_18 123 elRkylvengfkiedEelvkeegkiYe 149
                                       + R+ l ++g+ ++ + ++   +  Y 
  gi|488600259|ref|YP_007906730.1| 186 KARELLKNSGYLVVYNPYIDATRDAYF 212
                                       679999999999998888888777775 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.12      13      89 ..      93     176 ..      84     226 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                   Methyltransf_23  13 lerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.........kakkaqkdqfdeqeaae 78 
                                       +++++  lr+++ +Ld G+G+G l+ +l+++     v+ v+ +    +ia+         +                
  gi|488600259|ref|YP_007906730.1|  93 IAFTG--LRPDSAILDCGTGSGVLSAYLAYFCRdgFVVTVEKRKDFAKIARknfelaglkN---------------- 151
                                       55555..89999**************99877332234444444433333334444433333................ PP

                   Methyltransf_23  79 pqg................kfdlIvlr 89 
                                                          kfdlIvl 
  gi|488600259|ref|YP_007906730.1| 152 --IhqivgdifgladsikiKFDLIVLD 176
                                       ..0334444444555555688888764 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   8.2e-05     0.092      61     156 ..     112     200 ..     102     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.2e-05
                                       HHHHHHTT.S-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEEE-S-GGGH CS
                    Methyltransf_3  61 slLatala.lPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpefDfifvDaDkssy 136
                                        +L+  la +  DG ++++++ ++ ++ia+k ++ ag++  i+ i+gd     + +     + +fD+i +D   +  
  gi|488600259|ref|YP_007906730.1| 112 GVLSAYLAyFCRDGFVVTVEKRKDFAKIARKNFELAGLK-NIHQIVGDIFGLADSI-----KIKFDLIVLDMKDD-- 180
                                       455555542578*************************95.69999**988766554.....3569***9997544.. PP

                                       HHHHHHHHHTEEEEEEEEEE CS
                    Methyltransf_3 137 vnyyeklleLvkvGgliaiD 156
                                        ++  k+ eL+k  g +++ 
  gi|488600259|ref|YP_007906730.1| 181 DKFIPKARELLKNSGYLVVY 200
                                       47888888888876655544 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00023      0.25       1      98 [.     105     196 ..     105     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+ G+G+G l+++l+   +d  ++ v+  +++ + a++ +   + +n +++  +   l+d+ +  +fDl+v+     
  gi|488600259|ref|YP_007906730.1| 105 LDCGTGSGVLSAYLAYFCRDGFVVTVEKRKDFAKIARKNFELAGLKNIHQIVGDIFGLADSIKI-KFDLIVL----D 176
                                       899***********9999*********************************9999999888877.9999975....2 PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                        +kd ++++ ++r+lLk+ G+
  gi|488600259|ref|YP_007906730.1| 177 -MKDDDKFIPKARELLKNSGY 196
                                       .36667777777777776665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.27       4      60 ..     103     159 ..     100     170 .. 0.92
   2 ?   -3.0   0.0       3.8   4.2e+03      99     130 ..     183     214 ..     181     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                        +l+ G+G+G +   lA    d  ++ +E+r++  + + k+ e  +lkN++ + gd 
  gi|488600259|ref|YP_007906730.1| 103 AILDCGTGSGVLSAYLAYFCRDGFVVTVEKRKDFAKIARKNFELAGLKNIHQIVGDI 159
                                       689*************************************************99997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.8
                                       HHHHHHHHEEEEEEEEEEESHHHHHHHHHHHH CS
                    Methyltransf_4  99 llkelarvLkkgGvlelaTDveeyaeemlkvl 130
                                       ++ ++ + Lk++G+l++     + ++++   +
  gi|488600259|ref|YP_007906730.1| 183 FIPKARELLKNSGYLVVYNPYIDATRDAYFAM 214
                                       56666777788887776554444444444444 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.19      48     147 ..     101     200 ..      86     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                       CC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.....TTTTT-EEEE CS
                              GidB  48 krdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee.....kqeeekydvv 119
                                       +  +++D G+G G+ +  La ++ +  ++ +e   k+  F + + ++++l+ ++ +++ + +        + k+d++
  gi|488600259|ref|YP_007906730.1| 101 DS-AILDCGTGSGVLSAYLAYFCRDGFVVTVE---KRKDFAKIARKNFELAGLKNIHQIVGDifglaDSIKIKFDLI 173
                                       33.59*******************99977665...88899999999999999999999999988898888999**99 PP

                                       EEC-SSSHHHHHHHHCCCEEEEEEEEEE CS
                              GidB 120 tsRAlaslnelteillkllkegglilal 147
                                       +   +   ++++  +++llk+ g+++++
  gi|488600259|ref|YP_007906730.1| 174 VL-DMKDDDKFIPKARELLKNSGYLVVY 200
                                       98.5888889999999999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1499.95
//
Query:       gi|488600260|ref|YP_007906731.1|  [L=109]
Description: Nascent polypeptide associated complex NAC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-14   54.2   2.7    3.2e-14   52.6   2.6    1.7  2  NAC         NAC domain
     0.0065   16.3   0.1       0.01   15.6   0.1    1.3  1  UBA_4       UBA-like domain
  ------ inclusion threshold ------
      0.015   15.4   1.4      0.019   15.0   1.4    1.2  1  DUF3867     Protein of unknown function (DUF3867)
      0.015   15.0   0.6      0.027   14.1   0.1    1.5  1  Diacid_rec  Putative sugar diacid recognition
      0.016   15.2   4.6       0.13   12.3   2.4    2.3  2  UPF0154     Uncharacterised protein family (UPF0154)
      0.026   14.5   1.3      0.044   13.8   1.3    1.7  1  HOIP-UBA    HOIP UBA domain pair
      0.027   14.6   0.5      0.027   14.6   0.5    1.8  2  DUF1296     Protein of unknown function (DUF1296)
      0.041   13.8   0.2      0.041   13.8   0.2    1.8  2  DUF2015     Fungal protein of unknown function (DUF2015)
      0.095   12.6   1.7       0.19   11.7   0.2    2.1  2  UBA         UBA/TS-N domain
       0.19   11.8   2.8       0.48   10.6   0.3    2.2  2  AAA_lid_10  AAA lid domain
       0.36   11.0   3.2        0.6   10.3   0.2    2.0  2  SAM_KSR1    SAM like domain present in kinase suppressor RAS 
          4    7.9   9.0         14    6.2   1.2    2.8  2  DUF4258     Domain of unknown function (DUF4258)


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   2.6   2.2e-17   3.2e-14       1      55 [.       6      62 ..       6      63 .. 0.96
   2 ?   -1.0   0.0       1.2   1.8e+03      26      40 ..      72      85 ..      66      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.2e-17
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeae 55
                                      +k+++k++k++g+  +ei ++eeV+i++ + ++++f+nP+V    ++g +t++++G++e
  gi|488600260|ref|YP_007906731.1|  6 PKQMKKMMKQMGIdmEEI-EAEEVIIKTRG-EEMIFKNPSVIkiSAKGIETFQISGNYE 62
                                      79************9***.8*******999.***********999999*********98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                               NAC 26 ksdgkvlvfdnPkVq 40
                                       +d   l+ +++ V 
  gi|488600260|ref|YP_007906731.1| 72 EDD-IKLIMEQANVS 85
                                      444.88888888886 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     7e-06      0.01      11      33 ..      82     104 ..      73     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7e-06
                             UBA_4  11 TGadeekArqlLeannWdLerAi 33 
                                       ++++ee Ar+ Le +n+dL  A+
  gi|488600260|ref|YP_007906731.1|  82 ANVSEEDARKALEECNGDLAEAL 104
                                       5789***************9986 PP

>> DUF3867  Protein of unknown function (DUF3867)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.4   1.3e-05     0.019      74     153 ..       5      86 ..       3     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                           DUF3867  74 deeelekqlkslgidlkslnknveyesirks.lsfqekykekikeksvieykikndkndlk..illeeenvilisek 147
                                       ++++++k +k++gid+++++ +  + + r + + f++    ki+ k + +++i+ +   ++    ++e+++ li e+
  gi|488600260|ref|YP_007906731.1|   5 NPKQMKKMMKQMGIDMEEIEAEEVIIKTRGEeMIFKNPSVIKISAKGIETFQISGNYERIErrAEISEDDIKLIMEQ 81 
                                       678999*********99999985543333324788888888888888888888887777753367788888777654 PP

                           DUF3867 148 kidlsD 153
                                         ++s+
  gi|488600260|ref|YP_007906731.1|  82 -ANVSE 86 
                                       .34444 PP

>> Diacid_rec  Putative sugar diacid recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.8e-05     0.027      77     123 ..      45      91 ..      42      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                        Diacid_rec  77 ivfngevvGviGitGepeevrpyaelvkktaellleeaelkeqlqrr 123
                                       i++  + + ++ i+G++e++++ ae+ +  ++l++e+a+++e+  r+
  gi|488600260|ref|YP_007906731.1|  45 IKISAKGIETFQISGNYERIERRAEISEDDIKLIMEQANVSEEDARK 91 
                                       777788888999****************************9998776 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.4   8.9e-05      0.13      29      43 ..       3      17 ..       2      24 .. 0.92
   2 ?    2.7   0.0     0.084   1.3e+02      28      41 ..      68      81 ..      61      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.9e-05
                           UPF0154 29 pinekmirammkqmG 43
                                      p n k++++mmkqmG
  gi|488600260|ref|YP_007906731.1|  3 PTNPKQMKKMMKQMG 17
                                      789************ PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.084
                           UPF0154 28 Ppinekmirammkq 41
                                        i+e+ i+ +m+q
  gi|488600260|ref|YP_007906731.1| 68 AEISEDDIKLIMEQ 81
                                      56888888888888 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.3   2.9e-05     0.044     104     137 ..      75     108 ..       4     109 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                          HOIP-UBA 104 vkelaslgffdreevveaLrqsgGdvegAlveLq 137
                                       +k ++++ ++++e++ +aL++ +Gd+ +Al+ Lq
  gi|488600260|ref|YP_007906731.1|  75 IKLIMEQANVSEEDARKALEECNGDLAEALMRLQ 108
                                       6778888889999999999999999999998887 PP

>> DUF1296  Protein of unknown function (DUF1296)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.2   3.3e+03       3      12 ..       7      16 ..       6      30 .. 0.58
   2 ?   14.6   0.5   1.8e-05     0.027      10      42 ..      76     107 ..      69     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                           DUF1296  3 asvrkviqsi 12
                                      ++++k+ +++
  gi|488600260|ref|YP_007906731.1|  7 KQMKKMMKQM 16
                                      5555555443 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.8e-05
                           DUF1296  10 qsikEivgkhsdeeIyamLkecnmDpneavqkL 42 
                                       + i E ++  s+e+  ++L+ecn D  ea  +L
  gi|488600260|ref|YP_007906731.1|  76 KLIMEQAN-VSEEDARKALEECNGDLAEALMRL 107
                                       44666666.9*******************9998 PP

>> DUF2015  Fungal protein of unknown function (DUF2015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.85   1.3e+03      73      87 ..       8      22 ..       4      37 .. 0.72
   2 ?   13.8   0.2   2.7e-05     0.041      49      94 ..      53      95 ..      47     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.85
                           DUF2015 73 eikkimkkrrvkFde 87
                                      ++kk+mk+ +++ +e
  gi|488600260|ref|YP_007906731.1|  8 QMKKMMKQMGIDMEE 22
                                      567777777766654 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.7e-05
                           DUF2015 49 snFdlseNiesgdsRaGLdeaakeeikkimkkrrvkFdeARliyte 94
                                      ++F++s+N e+ ++Ra +   + ++ik im++ +v+ ++AR+   e
  gi|488600260|ref|YP_007906731.1| 53 ETFQISGNYERIERRAEI---SEDDIKLIMEQANVSEEDARKALEE 95
                                      68*************965...5679****************98765 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.53   7.9e+02       9      26 ..      13      32 ..      11      37 .. 0.73
   2 ?   11.7   0.2   0.00013      0.19      15      33 ..      85     103 ..      70     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.53
                                      HHHTT..S-HHHHHHHHHHT CS
                               UBA  9 LveMG..FdreevveALrat 26
                                      +++MG  +++ e++e    t
  gi|488600260|ref|YP_007906731.1| 13 MKQMGidMEEIEAEEVIIKT 32
                                      78899888888888866655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00013
                                       -HHHHHHHHHHTTTSHHHH CS
                               UBA  15 dreevveALratgnNeErA 33 
                                       ++e++++AL+ +++++  A
  gi|488600260|ref|YP_007906731.1|  85 SEEDARKALEECNGDLAEA 103
                                       699************9888 PP

>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.21   3.1e+02      35      57 ..       6      28 ..       2      40 .. 0.84
   2 ?   10.6   0.3   0.00032      0.48      42      72 ..      67      97 ..      39     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.21
                                      ----------------HHHHHHH CS
                        AAA_lid_10 35 Penvkkvrlkisddaieiasrkv 57
                                      P+++kk+  ++  d+ ei + +v
  gi|488600260|ref|YP_007906731.1|  6 PKQMKKMMKQMGIDMEEIEAEEV 28
                                      89999999999999999888776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00032
                                      ---------HHHHHHHHHHT.-TTTTHHHHHH CS
                        AAA_lid_10 42 rlkisddaieiasrkvAsvs.gdarrAlkiCk 72
                                      r +is+d i+++  + A+vs +dar+Al  C+
  gi|488600260|ref|YP_007906731.1| 67 RAEISEDDIKLIMEQ-ANVSeEDARKALEECN 97
                                      6689********876.8888359*****9996 PP

>> SAM_KSR1  SAM like domain present in kinase suppressor RAS 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.21   3.1e+02      97     118 ..       2      23 ..       1      33 [. 0.75
   2 ?   10.3   0.2    0.0004       0.6      75     123 ..      44      94 ..      40      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.21
                          SAM_KSR1  97 Lkmseeelkqllsevqaeeeel 118
                                       L  + +++k+++++++ + ee+
  gi|488600260|ref|YP_007906731.1|   2 LPTNPKQMKKMMKQMGIDMEEI 23 
                                       6677899999999977766654 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0004
                          SAM_KSR1  75 vvglsqetlea..ilnkklsleelLkmseeelkqllsevqaeeeelrRlla 123
                                       v+ +s++ +e+  i+++   +e   ++se+++k ++++ +++ee+ r+ l+
  gi|488600260|ref|YP_007906731.1|  44 VIKISAKGIETfqISGNYERIERRAEISEDDIKLIMEQANVSEEDARKALE 94 
                                       777888877753378889999************************998665 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.3     0.015        22       5      21 ..       9      25 ..       7      58 .. 0.80
   2 ?    6.2   1.2    0.0093        14       7      33 ..      62      89 ..      61     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                           DUF4258  5 ArermaeRgIseediee 21
                                      ++++m++ gI+ e+ie 
  gi|488600260|ref|YP_007906731.1|  9 MKKMMKQMGIDMEEIEA 25
                                      6899***********85 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0093
                           DUF4258  7 ermaeRg.IseedieevlenGeiieeys 33
                                      er ++R  Ise+di+ ++e   + ee+ 
  gi|488600260|ref|YP_007906731.1| 62 ERIERRAeISEDDIKLIMEQANVSEEDA 89
                                      5677776789999988888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 708.15
//
Query:       gi|488600261|ref|YP_007906732.1|  [L=389]
Description: Myo-inositol-1-phosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-44  152.0   0.0    4.9e-42  144.4   0.0    2.0  2  NAD_binding_5   Myo-inositol-1-phosphate synthase
    1.9e-26   92.4   0.0    4.6e-26   91.2   0.0    1.7  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> 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 !    5.4   0.4    0.0011        10       1      28 [.       1      28 [.       1      35 [. 0.87
   2 !  144.4   0.0   5.5e-46   4.9e-42      72     317 ..      42     381 ..      33     386 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0011
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5  1 lGvllvGlgGnngtTlvagvlankkgls 28
                                      ++++++G++G ++tT++ g   ++kg +
  gi|488600261|ref|YP_007906732.1|  1 MKIWVIGAYGIVSTTAMVGAKNIEKGFQ 28
                                      579****************998888776 PP

  == domain 2  score: 144.4 bits;  conditional E-value: 5.5e-46
                                       xxxxxxxxxxxxxxx.xxxxxxxxxx....xxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                     NAD_binding_5  72 lvnpndlvfgGwDis.slnlaeamer....akvldkdlqeqlkpeleki.kplksvydk.dfiaanqeeradnvlkg 141
                                       l+++n + fgG++i+ ++n+++a+ +    ++++d +l+e++k+eleki ++  ++ ++ + ++++ e ++ +    
  gi|488600261|ref|YP_007906732.1|  42 LMEINKFEFGGHEIRiKKNAYDAILEhwnlNRHFDFSLIENVKDELEKIeAKTGTALNCgSGLKELGEIKTLEDEG- 117
                                       678999********7478999998887999*******************655556666669999999988888864. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                     NAD_binding_5 142 kskleqleqirkdireFkkknkldkvivlwtanTEryievipgvndtlenllkaikeneee.ispstiyavAaileg 217
                                        + +e+++ + +d++eF +    d+++v++ a+TE   +++++ + tl+ +++ai+en++e is+s+iya+ a++ g
  gi|488600261|ref|YP_007906732.1| 118 YTLREIVDMVTSDMKEFAD----DETVVINIASTEPLQKYSEEYHGTLDGFERAIDENRTEhISASMIYAYSALKLG 190
                                       56****************9....89**********************************999*************** PP

                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                     NAD_binding_5 218 vpyingsPqntl.vpglvelAekkgvfiaGdDfKt.......................................... 251
                                        py+n++P+ +  +p+l elA k+++++aG+D Kt                                          
  gi|488600261|ref|YP_007906732.1| 191 LPYANFTPSIGSnLPALKELAMKTKTPHAGNDGKTgetlvkttlapmfayrnlrvlgwmgynilgdydgkvlshkdn 267
                                       ***************************************************************************** PP

                                       ...............................................................xxxxxxxxxxxxxx RF
                     NAD_binding_5 252 ...............................................................lLAaPlilDLvllv 265
                                                                                                      ++AaPlilDL++++
  gi|488600261|ref|YP_007906732.1| 268 keskviskdsvlekilgespysiteieyfpslvdnktafdfihfegflgtkmkmyfiwdaidaIVAAPLILDLARFL 344
                                       ***************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_5 266 eLaqrvevkkekkkefkklesvlsllsyflKaPlvskgtkvvnalfkQraal 317
                                        +a+r + +           +v++ l++f+K+P++ + ++     +kQ+++l
  gi|488600261|ref|YP_007906732.1| 345 LFAKRKGQH-----------GVIKELGFFFKSPMEIDVVN----THKQFEEL 381
                                       *****9999...........**************994444....45555555 PP

>> 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 !   91.2   0.0   5.2e-30   4.6e-26       1     108 [.     226     329 ..     226     330 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 5.2e-30
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEEEE-GG CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvikYvpy 77 
                                       G+T++k++La++++ r+l+v  ++ +NilG+ Dgk+ls++++++sK isK sv+++i++++++    +   i+Y+p+
  gi|488600261|ref|YP_007906732.1| 226 GETLVKTTLAPMFAYRNLRVLGWMGYNILGDYDGKVLSHKDNKESKVISKDSVLEKILGESPY----SITEIEYFPS 298
                                       99*********************************************************9876....469******* PP

                                       GTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH CS
                    Inos-1-P_synth  78 lgDsKvaldeieseiflggkntielkleceD 108
                                       l D+K+a+d i++e+flg+k+++ + +++ D
  gi|488600261|ref|YP_007906732.1| 299 LVDNKTAFDFIHFEGFLGTKMKMYFIWDAID 329
                                       ************************9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2279.53
//
Query:       gi|488600262|ref|YP_007906733.1|  [L=233]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-09   37.4   0.1    4.7e-09   36.2   0.1    1.7  1  HTH_3         Helix-turn-helix
    8.3e-06   25.7   0.1    2.2e-05   24.4   0.1    1.7  1  HTH_19        Helix-turn-helix domain
    0.00024   21.4   0.0    0.00043   20.6   0.0    1.4  1  HTH_31        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.041   13.5   0.0    1.9  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.034   14.4   0.2       0.14   12.5   0.2    2.0  1  FRD2          Bacteriophage FRD2 protein
      0.059   12.8   0.2          5    6.5   0.0    2.1  2  Rad9          Rad9
       0.12   12.1   0.0       0.41   10.4   0.0    1.8  2  Sigma70_r4_2  Sigma-70, region 4
       0.14   11.9   0.0       0.44   10.4   0.0    1.9  1  HTH_38        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.1   2.1e-12   4.7e-09       1      48 [.      25      73 ..      25      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.1e-12
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                      +k++R+    sq+e++ek+Gvs+s is++E++ + +P +  + k+  aL
  gi|488600262|ref|YP_007906733.1| 25 IKKWRNIFEVSQKEISEKIGVSPSVISDYESDrRKSPGIAFIRKIISAL 73
                                      7999999999***********************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 !   24.4   0.1   9.8e-09   2.2e-05       1      48 [.      22      69 ..      22      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9.8e-09
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllki 48
                                      G+ +k+ R  +  +q+e++e++g+s+s is +E+++++ p++  ++ki
  gi|488600262|ref|YP_007906733.1| 22 GKTIKKWRNIFEVSQKEISEKIGVSPSVISDYESDRRKSPGIAFIRKI 69
                                      77899******************************999***9888887 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.9e-07   0.00043       9      54 ..      28      73 ..      22      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                            HTH_31  9 lReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                      +R+   +sq+e  e +gvs+s +s++E+ rr  p  a+++++  al
  gi|488600262|ref|YP_007906733.1| 28 WRNIFEVSQKEISEKIGVSPSVISDYESDRRKSPGIAFIRKIISAL 73
                                      5555678********************************9998876 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   1.8e-05     0.041      18      36 ..      34      52 ..      33      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                            HTH_24 18 isqreLAerlglSpstvnr 36
                                       sq+e++e++g+Sps ++ 
  gi|488600262|ref|YP_007906733.1| 34 VSQKEISEKIGVSPSVISD 52
                                      69*************9886 PP

>> FRD2  Bacteriophage FRD2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   6.2e-05      0.14      67      99 ..     197     229 ..     191     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                              FRD2  67 eedevkdkvsgvtkihcivdennvdeiiellrk 99 
                                       + de+  k+s v ki  iv e+ v+++i+ lr+
  gi|488600262|ref|YP_007906733.1| 197 NVDEIALKISEVEKIPLIVSEKSVEDMIKSLRR 229
                                       5699*************************9997 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0022         5     135     186 ..      22      79 ..       4     118 .. 0.80
   2 ?    4.7   0.0    0.0079        18      45      96 ..     164     215 ..     138     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0022
                              Rad9 135 srvLsdllehfsssleeitielakervllksyeeeekdn......kkalstelsidee 186
                                        ++++++ + f+ s++ei+ +++    +++ ye + +++      +k +s+ +sid+e
  gi|488600262|ref|YP_007906733.1|  22 GKTIKKWRNIFEVSQKEISEKIGVSPSVISDYESDRRKSpgiafiRKIISALISIDKE 79 
                                       599*********************************9999999888999999999986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0079
                              Rad9  45 fFdkyekevseqirckil.vKsvlsvfrslsakektvekvkisi.dekksrliv 96 
                                       +F k ++  s+ + ++++  K+ l v+++l    ++v++++++i + +k  liv
  gi|488600262|ref|YP_007906733.1| 164 IFTKVSSGRSPMVAVRVSaFKPALIVLHGLK--AENVDEIALKIsEVEKIPLIV 215
                                       56666777888889998637*******9888..899********6556655555 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 ?   10.4   0.0   0.00018      0.41      23      41 ..      30      48 ..      28      50 .. 0.88
   2 ?   -3.3   0.0       3.5   7.7e+03      22      34 ..     191     203 ..     187     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                                      HTS---HHHHHHHHT--HH CS
                      Sigma70_r4_2 23 yleglsykEIAellgiseg 41
                                       +++ s+kEI+e++g+s++
  gi|488600262|ref|YP_007906733.1| 30 NIFEVSQKEISEKIGVSPS 48
                                      57899************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.5
                                       HHTS---HHHHHH CS
                      Sigma70_r4_2  22 ryleglsykEIAe 34 
                                       + l+    +EIA 
  gi|488600262|ref|YP_007906733.1| 191 HGLKAENVDEIAL 203
                                       4444445567764 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0002      0.44      13      38 ..      25      51 ..      23      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                            HTH_38 13 Ierlla.eGlslreIArrLgrspsTIs 38
                                      I ++++    s++eI  ++g+sps Is
  gi|488600262|ref|YP_007906733.1| 25 IKKWRNiFEVSQKEISEKIGVSPSVIS 51
                                      6666663348****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1453.83
//
Query:       gi|488600263|ref|YP_007906734.1|  [L=347]
Description: hydroxymethylglutaryl-CoA synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   41.6   0.0    4.4e-10   39.6   0.0    2.1  3  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    0.00031   20.2   0.1     0.0005   19.5   0.1    1.2  1  Thiolase_N      Thiolase, N-terminal domain
    0.00097   18.9   1.8     0.0037   17.1   0.1    2.4  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
     0.0016   18.1   0.3      0.013   15.1   0.1    2.0  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
     0.0025   17.7   0.1     0.0046   16.8   0.1    1.4  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.5   5.5e+03      58      71 ..      61      74 ..      38      78 .. 0.78
   2 ?   -3.3   0.0       2.9   1.1e+04      66      85 ..      88     107 ..      87     109 .. 0.78
   3 !   39.6   0.0   1.2e-13   4.4e-10       1      88 [.     220     307 ..     220     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                                      HHHHHTTSS-TT-E CS
                     ACP_syn_III_C 58 deaveegklkpgdl 71
                                       eave+gk++p + 
  gi|488600263|ref|YP_007906734.1| 61 REAVERGKINPKKI 74
                                      57888999988765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                                       S-TT-EEEEEEEETTTEEEE CS
                     ACP_syn_III_C  66 lkpgdlvllvgfGaGltwga 85 
                                       +kp  +++ +++G G  + a
  gi|488600263|ref|YP_007906734.1|  88 VKPTATIVGSAIGCGNFFHA 107
                                       57888999999999976655 PP

  == domain 3  score: 39.6 bits;  conditional E-value: 1.2e-13
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEE CS
                     ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllv 75 
                                       +e++g++p+d+ + v+h  n ++   + + lg+++e++ + l  +++Gnt + s++l ++  ++    k+gd++llv
  gi|488600263|ref|YP_007906734.1| 220 MERNGYRPSDFAYAVFHMPNGKFPVRASRMLGFSREQTEQGLvvRRVGNTYSGSSLLGFSAVLD--VAKAGDKILLV 294
                                       689*********************************66554434********************..99********* PP

                                       EEETTTEEEEEEE CS
                     ACP_syn_III_C  76 gfGaGltwgaall 88 
                                       +fG G    a ++
  gi|488600263|ref|YP_007906734.1| 295 SFGSGAGSDAFIV 307
                                       *****98888777 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.4e-07    0.0005      25     113 ..      54     142 ..      41     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHT CS
                        Thiolase_N  25 eLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaa 101
                                        ++ e +++++e+ +++p+++  ++vG   +    +  a  +  ++g  +  +a   + +c  g +++ +++ ++++
  gi|488600263|ref|YP_007906734.1|  54 TISVECAREAVERGKINPKKIGAIFVGSESHPYVVKPTATIVGSAIGCGNFFHAADFEFACKAGTAGIQTCMAMVKS 130
                                       56778899************************99999**************************************** PP

                                       TSHSEEEEEEEE CS
                        Thiolase_N 102 geadvvvagGvE 113
                                       g ++  +a+G+ 
  gi|488600263|ref|YP_007906734.1| 131 GMIEYGLAIGAD 142
                                       **********86 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     1e-06    0.0037       2      37 ..     109     144 ..     108     180 .. 0.83
   2 ?    0.3   0.2      0.18   6.4e+02      37      62 ..     278     308 ..     277     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                                       EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEG CS
                       ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetl 37 
                                       D++ aC++ ++++++  a+++sg++++ L iga+t 
  gi|488600263|ref|YP_007906734.1| 109 DFEFACKAGTAGIQTCMAMVKSGMIEYGLAIGADTS 144
                                       8899******************************94 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                                       GGGCS-TT...THHHHTTB-EEEE..EEEEE CS
                       ACP_syn_III  37 lskilDwk...drstavlfGDGAg..Avvle 62 
                                       +s +lD +   d+   v fG GAg  A++++
  gi|488600263|ref|YP_007906734.1| 278 FSAVLDVAkagDKILLVSFGSGAGsdAFIVN 308
                                       5777887644468888999999984456665 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 ?    0.7   0.0     0.088   3.2e+02      67      82 ..     227     242 ..     205     252 .. 0.71
   2 !   15.1   0.1   3.7e-06     0.013     142     206 ..     255     314 ..     245     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.088
                                       GGG-SEEEE--SSHHH CS
                    HMG_CoA_synt_C  67 lddfdyvifhsPfckl 82 
                                         df y +fh P  k+
  gi|488600263|ref|YP_007906734.1| 227 PSDFAYAVFHMPNGKF 242
                                       46899*******9986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.7e-06
                                       HHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--S CS
                    HMG_CoA_synt_C 142 kkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvs 206
                                       +++++ l v ++vGn Y  s    + ++l    +   ag +i+l s+GsG  +  f ++v++  +
  gi|488600263|ref|YP_007906734.1| 255 EQTEQGL-VVRRVGNTYSGSSLLGFSAVL----DVAKAGDKILLVSFGSGAGSDAFIVNVTDAIE 314
                                       4555555.5589*****************....3344799*******************998765 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 !   16.8   0.1   1.3e-06    0.0046       5     170 ..       4     166 ..       2     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                    HMG_CoA_synt_N   5 vgilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevg 81 
                                        gi++   y+p   ++  e+ +  g    +   glg  + +  +  ed  ++s+   ++ +er k++ ++ig + vg
  gi|488600263|ref|YP_007906734.1|   4 TGIVSYGTYIPKFRIKVEEIARIWGEVPENIKAGLGVQQKSVPDIDEDTATISVECAREAVERGKINPKKIGAIFVG 80 
                                       59999999************9998888888999******************************************** PP

                    HMG_CoA_synt_N  82 tetiidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgnarp 158
                                       +e+     k   +++   ++  gn      d   ac  gta +  ++  ++s + +  y l +  d +  + g++  
  gi|488600263|ref|YP_007906734.1|  81 SESHPYVVKPTATIVGSAIGC-GNF-FHAADFEFACKAGTAGIQTCMAMVKSGMIE--YGLAIGADTSQSAPGDPLE 153
                                       **9888888887777776665.664.68899999*******999999999998875..6677777777777777643 PP

                    HMG_CoA_synt_N 159 .tggagavallig 170
                                        +  ag  a++ig
  gi|488600263|ref|YP_007906734.1| 154 ySASAGGSAFIIG 166
                                       1456677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 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:                        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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2686.23
//
Query:       gi|488600264|ref|YP_007906735.1|  [L=387]
Description: Acetyl-CoA acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-22   79.6   0.1    3.3e-22   79.1   0.1    1.2  1  Thiolase_N       Thiolase, N-terminal domain
    8.9e-10   38.3   0.3    5.8e-09   35.7   0.2    2.3  2  Thiolase_C       Thiolase, C-terminal domain
      8e-05   22.6   0.7      0.025   14.6   0.1    3.2  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
     0.0059   16.2   4.6       0.23   11.0   2.4    2.5  2  ketoacyl-synt    Beta-ketoacyl synthase, N-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 !   79.1   0.1   7.3e-26   3.3e-22       1     259 [.       4     225 ..       4     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 7.3e-26
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-T. CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipe. 74 
                                       v+iv+   +++g+    l d   +++  +a++++l++ag++ +e++ ++vGn+  +   +q  i+  +a  +g++e 
  gi|488600264|ref|YP_007906735.1|   4 VAIVGVGQSEFGE----LWDRGFRDIVLKAGSEALDDAGLEGKEIEAIYVGNMSGGrYLEQEhISALIADYSGLAEl 76 
                                       6788888888888....9999999******************************99877777688888889999753 PP

                                       TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGS.SSSEEEEEHHHHHHTEETT CS
                        Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglk.lgdekakdllipdgladaf 150
                                        +pa++v+ + +Sg  a+ +a  ++a+g  dvv+a G+E+ +++   +++d++s++   + e  ++ +ip       
  gi|488600264|ref|YP_007906735.1|  77 GIPATRVEAADASGGLALRQAFLAVASGVHDVVMAAGAEKVTDVGSEMTADIMSSTAdREWEGFVGATIPA------ 147
                                       79***********************************************9999776515556789999999...... PP

                                       TTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHH CS
                        Thiolase_N 151 neehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLa 227
                                            ++ a++  +ky+ + e+++ + vk+h+++a ++ka+ +++ei              + ++ ++s+ +ae+L+
  gi|488600264|ref|YP_007906735.1| 148 ---LYAIMARKHFEKYGTTEEDLALVSVKNHRNGALNPKAQ-YRREI--------------KVEDVLNSPKVAEPLK 206
                                       ...99************************************.*****..............799************* PP

                                       TS-BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 228 klkpaFkkeGtvtAgnasqisDGaaavllmse 259
                                        l             ++ ++sDGa av+l+se
  gi|488600264|ref|YP_007906735.1| 207 LL-------------DCAPLSDGACAVILASE 225
                                       **.............***************98 PP

>> Thiolase_C  Thiolase, 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      27      46 ..      29      48 ..      27      63 .. 0.83
   2 !   35.7   0.2   1.3e-12   5.8e-09      25     118 ..     263     379 ..     238     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.23
                                      HHHHHHHHHT--GGGESEEE CS
                        Thiolase_C 27 aikkvlkkagltvedidlfE 46
                                      a +++l++agl+ ++i+++ 
  gi|488600264|ref|YP_007906735.1| 29 AGSEALDDAGLEGKEIEAIY 48
                                      66789*********999875 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 1.3e-12
                                       HHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TT CS
                        Thiolase_C  25 ayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlG 83 
                                         a++k+   a ++ +did++E+++ F+   +++ ++l++++                    vN  GG  a GH +G
  gi|488600264|ref|YP_007906735.1| 263 RVASEKAYRMARVEPRDIDVVEVHDSFTIAEIMAYEDLGFAEkgkgaeliregvtslegsLPVNTGGGLKACGHAVG 339
                                       4688999999***********************************************99888*************** PP

                                       THHHHHHHHHHHHHHHCTTSEEEE.....EEEETTTEEEE CS
                        Thiolase_C  84 asGaRivvtllselkkeggklgva.....alCigggqgva 118
                                       a+G R+++ ++ +l+ e gk  v      +l igg  ++a
  gi|488600264|ref|YP_007906735.1| 340 ATGIRQAIEITLQLRGEAGKRQVEcerglSLNIGGTGATA 379
                                       **************99988877642222245555555555 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 ?   -1.9   0.0      0.71   3.2e+03      31      47 ..      31      47 ..      27      53 .. 0.84
   2 !   14.6   0.1   5.6e-06     0.025      24      53 ..     260     289 ..     238     296 .. 0.83
   3 !    4.6   0.1    0.0069        31      87     109 ..     334     356 ..     320     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.71
                                      HHHHHHHT--GGGEEEE CS
                   Ketoacyl-synt_C 31 ekalaeagvdpedvdyv 47
                                       +al++ag++ ++++ +
  gi|488600264|ref|YP_007906735.1| 31 SEALDDAGLEGKEIEAI 47
                                      6899*******999987 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.6e-06
                                       HHHHHHHHHHHHHHT--GGGEEEEE-SS-S CS
                   Ketoacyl-synt_C  24 eaqaraiekalaeagvdpedvdyveahgtg 53 
                                       +a + a eka+++a+v+p+d+d+ve h++ 
  gi|488600264|ref|YP_007906735.1| 260 RAVRVASEKAYRMARVEPRDIDVVEVHDSF 289
                                       45566799*******************975 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0069
                                       H-B-GGGHHHHHHHHHHHHHHHT CS
                   Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkhg 109
                                        GH+ +A G+ ++i + l+l+ +
  gi|488600264|ref|YP_007906735.1| 334 CGHAVGATGIRQAIEITLQLRGE 356
                                       7*****************99865 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 !    5.2   0.0    0.0031        14      91     132 ..      25      66 ..      20      76 .. 0.83
   2 !   11.0   2.4   5.2e-05      0.23     167     206 ..      79     118 ..      60     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHH CS
                     ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgagdyaalaal 132
                                       ++l+a  eal dagl+ +e++   vg++ G  + ++++++al
  gi|488600264|ref|YP_007906735.1|  25 IVLKAGSEALDDAGLEGKEIEAIYVGNMSGGRYLEQEHISAL 66 
                                       67999***************9988999999888777665554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.2e-05
                                       SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                     ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvelll 206
                                       p+  v++A++S+  a+ +a  ++ sg  dv+ a G+e  +
  gi|488600264|ref|YP_007906735.1|  79 PATRVEAADASGGLALRQAFLAVASGVHDVVMAAGAEKVT 118
                                       8899********************************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2692.08
//
Query:       gi|488600265|ref|YP_007906736.1|  [L=132]
Description: putative nucleic-acid-binding protein containing a Zn-ribbon [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-19   67.6   0.0    9.1e-19   67.2   0.0    1.2  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
      3e-07   30.2   0.8    5.8e-07   29.3   0.8    1.5  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0054   16.7   0.4     0.0084   16.1   0.4    1.3  1  DZR             Double zinc ribbon
     0.0083   16.0   1.2      0.014   15.2   1.2    1.3  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.033   14.9   0.7      0.054   14.2   0.7    1.3  1  zinc_ribbon_15  zinc-ribbon family
      0.068   12.9   3.0       0.36   10.6   0.2    2.3  2  zf-CCHC_4       Zinc knuckle
       0.38   10.5   6.0        1.1    9.1   6.0    1.8  1  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   3.6e-22   9.1e-19       2      65 .]      46     108 ..      45     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 3.6e-22
                                       EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                       +++s +G++ s+tvvh ap++++  +Py+v+++eLd+gv +++++v +dp+ev+iGmrV+  fr
  gi|488600265|ref|YP_007906736.1|  46 QTFSSKGRILSYTVVHDAPDEYKLAKPYIVALIELDDGVVLTSQVV-CDPQEVHIGMRVKKAFR 108
                                       67899**********************************9999999.677889******98886 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 !   29.3   0.8   2.3e-10   5.8e-07       3      33 ..       9      39 ..       7      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.3e-10
                           DUF35_N  3 aaaegrLvgqrCpdCGtvqfPPravCphCgs 33
                                         ++ +vg+ C +CG+ ++PPr++Cp C++
  gi|488600265|ref|YP_007906736.1|  9 IKYRYDIVGTVCENCGSKFYPPRNFCPICRR 39
                                      677999*********************9975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   3.3e-06    0.0084      29      48 ..      18      37 ..       7      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                               DZR 29 drCpsCgekvdpearfCpeC 48
                                      ++C +Cg+k  p  +fCp C
  gi|488600265|ref|YP_007906736.1| 18 TVCENCGSKFYPPRNFCPIC 37
                                      67999999988888999988 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.2   5.5e-06     0.014      25      46 ..      19      40 ..      17      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-06
                                      E-HHHHHHHHHTT-B-TTT--B CS
                        zf-C3HC4_3 25 lCeeCaekllkrkkkCpiCrrp 46
                                      +Ce+C +k+   ++ CpiCrr+
  gi|488600265|ref|YP_007906736.1| 19 VCENCGSKFYPPRNFCPICRRK 40
                                      8********99*********97 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   2.1e-05     0.054      59      85 ..      11      37 ..       4      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                    zinc_ribbon_15 59 kkessekkeCknCgkeveeefkyCpkC 85
                                       + ++  ++C+nCg++  +  ++Cp C
  gi|488600265|ref|YP_007906736.1| 11 YRYDIVGTVCENCGSKFYPPRNFCPIC 37
                                      455556899****************** PP

>> zf-CCHC_4  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00014      0.36      20      38 ..       6      24 ..       3      25 .. 0.93
   2 ?    2.3   0.2     0.054   1.4e+02      31      40 ..      31      40 ..      31      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                         zf-CCHC_4 20 eatiefkYErLrsfCyiCg 38
                                      +++i+ +Y  ++++C++Cg
  gi|488600265|ref|YP_007906736.1|  6 WRKIKYRYDIVGTVCENCG 24
                                      899***************9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.054
                         zf-CCHC_4 31 rsfCyiCgvl 40
                                      r+fC iC++ 
  gi|488600265|ref|YP_007906736.1| 31 RNFCPICRRK 40
                                      68*****985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.0   0.00043       1.1       2      22 ..      20      40 ..      19      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C nCG +  +  +FCp C+ +
  gi|488600265|ref|YP_007906736.1| 20 CENCGSKFYPPRNFCPICRRK 40
                                      ******************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 907.10
//
Query:       gi|488600266|ref|YP_007906737.1|  [L=195]
Description: putative phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-24   84.7   0.1    6.2e-24   84.3   0.1    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
      9e-07   28.5   0.1    1.3e-06   28.0   0.1    1.1  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.1   6.9e-28   6.2e-24       9     157 ..      10     152 ..       5     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 6.9e-28
                                       --EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE---- CS
                      Pribosyltran   9 paildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledp 85 
                                         i++ + +l  +i e+  ++pdv+v+iargG+++a il d L+v+  y  k  + + ++++    ++    l  d+
  gi|488600266|ref|YP_007906737.1|  10 NDIYRSCIDLGVKIAES--FSPDVIVAIARGGWVPARILCDVLDVRELYSIKAVHWGRVATKNEARIVQK--LNVDL 82 
                                       55666777888888888..9************************99666666666666666666666654..99*** PP

                                       TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS......EEEEEEE-SEE- CS
                      Pribosyltran  86 agkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfsls.pdnfvavvgfeld 157
                                        gkkVliVDD+ dtG T+l a e++ke ++eevriav+  k+++++++d++a     ++   ++v +++++ d
  gi|488600266|ref|YP_007906737.1|  83 TGKKVLIVDDVTDTGETVLLAKEHIKELNAEEVRIAVVDHKRTSKFQPDFYAN---LNEeWMWIVYPWSCYED 152
                                       ************************************************99998...34446788888888766 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.4e-10   1.3e-06      70     157 ..      31     120 ..      20     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.4e-10
                           UPRTase  70 alVpilRaGegmeealrellpearvghlglqr..eeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlL 144
                                       ++V+i R+G   ++ l ++l   +++ ++     + +t++   +++kL  +++ ++vl++D v  TG+++  a +++
  gi|488600266|ref|YP_007906737.1|  31 VIVAIARGGWVPARILCDVLDVRELYSIKAVHwgRVATKNEARIVQKLNVDLTGKKVLIVDDVTDTGETVLLAKEHI 107
                                       689*******999999999887777777665533567889999********************************** PP

                           UPRTase 145 kergvgeekIlvl 157
                                       ke +++e +I v+
  gi|488600266|ref|YP_007906737.1| 108 KELNAEEVRIAVV 120
                                       *****99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1191.45
//
Query:       gi|488600267|ref|YP_007906738.1|  [L=421]
Description: hypothetical protein Asulf_00731 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  103.5   0.2    1.7e-14   53.4   0.0    2.9  3  TrkA_C         TrkA-C domain
    3.7e-18   65.8  15.0    8.3e-13   48.6   3.1    2.7  3  PhoU           PhoU domain
  ------ inclusion threshold ------
      0.043   13.6   2.4        3.7    7.3   0.2    2.4  2  Ribosomal_S7e  Ribosomal protein S7e


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   2.8e-18   1.7e-14       2      67 ..     135     202 ..     134     205 .. 0.92
   2 ?   -1.4   0.0      0.36   2.2e+03      34      48 ..     205     219 ..     200     221 .. 0.86
   3 !   47.0   0.0   2.8e-16   1.7e-12       1      67 [.     337     405 ..     337     407 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.8e-18
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       v  +v+++s +++ktl+e++l +r g +v+ai+R+ +++++p+ dt++ +GDvl+  g+ s+   ++e
  gi|488600267|ref|YP_007906738.1| 135 VKAVVSENSEIANKTLGEVRLHTRtGMRVIAIKREfDWIFNPDRDTKILKGDVLFARGDISGKPYFYE 202
                                       6679******************************************************9987666666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                                       -T-EEES--TT-B-- CS
                            TrkA_C  34 RggeliipsgdtvLe 48 
                                        g++++ip +dt+Le
  gi|488600267|ref|YP_007906738.1| 205 TGERIEIPVEDTELE 219
                                       578999*******97 PP

  == domain 3  score: 47.0 bits;  conditional E-value: 2.8e-16
                                       CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                       lv+++v+ ++ l+Gktl+++++++r g  ++ai rR+ ++  p   t+Le+GD ++  g++++++ lr+
  gi|488600267|ref|YP_007906738.1| 337 LVMFEVGDNCELDGKTLGDARVETRtGMHIMAIkRRNRWISRPKAGTKLESGDMIIAKGTREGMDLLRK 405
                                       6899*****************************5566****************************9997 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   2.5     8e-09   4.8e-05       2      86 ..      29     109 ..      28     112 .. 0.85
   2 ?   -3.1   0.0       1.8   1.1e+04      15      30 ..     134     149 ..     125     152 .. 0.77
   3 !   48.6   3.1   1.4e-16   8.3e-13       1      89 []     230     316 ..     230     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8e-09
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeierslleal.akrqplaedlrellsllriardlER 77 
                                       + +++++e  +d+a++a+  + +++a+ev+++++ + +l ++i  +++++l a+r   +e  + +++ll+ia     
  gi|488600267|ref|YP_007906738.1|  29 KNIKDTSEIVVDLAYSAILFDSEDIAEEVLDLENVLSDLLNQI--RIVTILsARRV--DE-AESVSTLLKIAGAAQK 100
                                       5678899999*******877778****************9999..88999945444..44.678999********** PP

                                       HHHHHHHHH CS
                              PhoU  78 igDhavnia 86 
                                       ig  a +ia
  gi|488600267|ref|YP_007906738.1| 101 IGSAAGDIA 109
                                       ********9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
                                       HHHHHHCT-HHHHHHH CS
                              PhoU  15 alealeekdtelarev 30 
                                       +++a+++++ e+a++ 
  gi|488600267|ref|YP_007906738.1| 134 VVKAVVSENSEIANKT 149
                                       6788888888888765 PP

  == domain 3  score: 48.6 bits;  conditional E-value: 1.4e-16
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       l +m++++e ++d+++++l  +++++a+ev  +++++d+l +e++  +l+  +k      +lr+l+++l++a+  E 
  gi|488600267|ref|YP_007906738.1| 230 LIEMKDLSELAVDLSYSSLIYENEDIANEVFYLEEKVDNLKFELKHWVLKSSKKVGDD--KLRDLIAILELATASEY 304
                                       679******************************************9988888774443..59*************** PP

                                       HHHHHHHHHHHH CS
                              PhoU  78 igDhavniaerv 89 
                                       i+D a++iae+v
  gi|488600267|ref|YP_007906738.1| 305 IADSAREIAEIV 316
                                       **********86 PP

>> Ribosomal_S7e  Ribosomal protein S7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2   0.00061       3.7      15      48 ..      51      84 ..      48      94 .. 0.89
   2 ?    5.9   0.2    0.0017        10      15      56 ..     253     294 ..     246     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00061
                                      HHHHHHHHHHHHHTSSCHHHHTT--ECEEEEEEE CS
                     Ribosomal_S7e 15 eqvaqalldleanssdlkaelrelqissakevev 48
                                      e++a+++ldle+  sdl +++r ++i sa+ v+ 
  gi|488600267|ref|YP_007906738.1| 51 EDIAEEVLDLENVLSDLLNQIRIVTILSARRVDE 84
                                      679***************************9985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHTSSCHHHHTT--ECEEEEEEETSSCEEEE CS
                     Ribosomal_S7e  15 eqvaqalldleanssdlkaelrelqissakevevkkkkkaiv 56 
                                       e++a++++ le++ ++lk el++  ++s k+v   k +  i 
  gi|488600267|ref|YP_007906738.1| 253 EDIANEVFYLEEKVDNLKFELKHWVLKSSKKVGDDKLRDLIA 294
                                       789*************************99886555455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2947.52
//
Query:       gi|488600268|ref|YP_007906739.1|  [L=292]
Description: hypothetical protein Asulf_00732 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   68.2   0.0    1.6e-18   67.5   0.0    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00055   19.5   0.0    0.00087   18.9   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.063   12.7   0.0    1.8  2  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 !   67.5   0.0   2.6e-22   1.6e-18       3     197 .]      14     203 ..      12     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.6e-22
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                       p pvn+ +i++ g+++LiDtG+++e +r     ++     ++++ +++TH+H+DH+Gg+ ++ ++ d+ v+a ++e 
  gi|488600268|ref|YP_007906739.1|  14 PNPVNIGVIVDSGKAFLIDTGLDEEVGRRI--FKLMSNHKLKISGIFNTHSHADHFGGNSYILKKVDARVYATSIES 88 
                                       679*************************97..7999999************************************** PP

                                       HCCHCHHHHHHHHHCCHH...TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS CS
                       Lactamase_B  80 palfmeeaddaasrkgll...lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall 153
                                            +++++ + +  ++   l    ++++    +   + + + + l+  ++ + gh++ + ++g ++vlf+ D ++
  gi|488600268|ref|YP_007906739.1|  89 GIIQSPYLEPLYLFSAHPvreLTVKFIMAKPSRVDHIVSHEIEFENLKLDVISLKGHSPNQAGIGVDGVLFCADSVF 165
                                       ***********9999999999777777777777777777778888888889999*********************** PP

                                       SHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 154 agetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       ++  ++  +       +   d e++ +sl+ l++++ + ++p+H
  gi|488600268|ref|YP_007906739.1| 166 SERVIKKYK------IPLFMDIESQKESLKFLENSNFDCYIPAH 203
                                       999999999......99999999999999999999999999999 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 !   18.9   0.0   1.5e-07   0.00087       3      82 ..      29     106 ..      27     179 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-07
                                       EEES--TT......HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE...HHHHHHC CS
                     Lactamase_B_2   3 iLiDagpd......lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyap...kgvlavl 70 
                                       +LiD+g+d      +++  ++        +   +i +++ th+H+DH+ g   + +  +  +++ya+    g+++  
  gi|488600268|ref|YP_007906739.1|  29 FLIDTGLDeevgrrIFKL-MS------NHK--LKISGIFNTHSHADHFGGNSYILKKVD--ARVYATsieSGIIQSP 94 
                                       799*****6543332222.22......223..49**************99988888443..5688774445555533 PP

                                       CTTCGHHHCHTT CS
                     Lactamase_B_2  71 eanfvylaleee 82 
                                         +  yl++ ++
  gi|488600268|ref|YP_007906739.1|  95 YLEPLYLFSAHP 106
                                       333334444444 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   1.1e-05     0.063       6      72 ..      26      84 ..      21      87 .. 0.84
   2 ?   -2.6   0.0      0.51     3e+03      63      94 ..      95     126 ..      90     140 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                     Lactamase_B_6  6 nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyat 72
                                      +  +L+D G de+ v  ++++k ++++  +++ i  +h+ ++h G+ +++++k+       ++vyat
  gi|488600268|ref|YP_007906739.1| 26 GKAFLIDTGLDEE-VG-RRIFKLMSNHKLKISGIFNTHSHADHFGGNSYILKKVD------ARVYAT 84
                                      4579*******97.54.68***************************999888764......566666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.51
                     Lactamase_B_6  63 lllnipvyatlpvvkLGrvslldlyaskgllg 94 
                                       +l  ++ ++ +pv +L   +++ +    +++ 
  gi|488600268|ref|YP_007906739.1|  95 YLEPLYLFSAHPVRELTVKFIMAKPSRVDHIV 126
                                       55667788999999998777765555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2083.13
//
Query:       gi|488600269|ref|YP_007906740.1|  [L=236]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  302.2   0.0    2.8e-90  302.0   0.0    1.0  1  4HFCP_synth  4-HFC-P synthase
     0.0018   18.1   0.0      0.026   14.3   0.0    2.2  2  QRPTase_C    Quinolinate phosphoribosyl transferase, C-termin
  ------ inclusion threshold ------
      0.075   13.0   0.0       0.22   11.5   0.0    1.7  2  Imm51        Immunity protein 51


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 !  302.0   0.0   4.6e-94   2.8e-90       1     227 [.       4     230 ..       4     231 .. 0.99

  Alignments for each domain:
  == domain 1  score: 302.0 bits;  conditional E-value: 4.6e-94
                                       EEE--SSHHHHHHHHHHT-SEEEE--GGG-TT----HHHHHHHHHHS-TT.SEEEEEEEEE-S-HHHHHHHHHHHHH CS
                       4HFCP_synth   1 LLvSvrnleEaelalaggadiiDvKnPaeGsLGalfpevireivevvpgs.vpvSaaiGdlpekpgtvslaalgaaa 76 
                                       +LvS+++++Ea ++l+ggadiiDvKnP+eGsLGa+fp+vi+ei e+v+++ +++Sa++Gdl++kpgt+slaalgaa+
  gi|488600269|ref|YP_007906740.1|   4 VLVSPMSIDEAYECLKGGADIIDVKNPKEGSLGANFPWVIKEIGEIVKKEgKELSATTGDLDFKPGTASLAALGAAV 80 
                                       59*********************************************9999************************** PP

                                       TT-SEEEEEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT---GGGHHHHHHHHT-SEEEEE-SS- CS
                       4HFCP_synth  77 agvdyvKvGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervasvsplellelaaeagaagvmlDTadK 153
                                       ag+dy+KvGl+g+k++e+a+e lk+v+++vk+ d++kkvv ++yaD++r++++sp++l+e+ + a+++g+m+DTa+K
  gi|488600269|ref|YP_007906740.1|  81 AGADYIKVGLYGVKNKEQAYEILKNVTRSVKDFDADKKVVGAAYADFHRINAISPFDLPEAGQMAEVDGIMIDTAIK 157
                                       ***************************************************************************** PP

                                       SS--HHHHS-HHHHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESGGGBTTSSTTSSB-HHHHHHH CS
                       4HFCP_synth 154 dgkslldflseeelaefveeareaglltaLAGslkledlpaLkklkpdilGvRgavCeegdRngkidaelvekl 227
                                       dg +l+d+l+e++l+efve+are+g+++aLAGs+++e+lp+Lkk++pdi+GvR++vC e+ R++ki++elve+l
  gi|488600269|ref|YP_007906740.1| 158 DGLTLFDHLKEPQLQEFVETARENGMFCALAGSINWEHLPVLKKISPDIIGVRTIVC-ESGRQSKIKSELVERL 230
                                       *********************************************************.777**********987 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.041   2.5e+02      83     113 ..       4      34 ..       1      64 [. 0.77
   2 !   14.3   0.0   4.3e-06     0.026      27     158 ..      68     213 ..      66     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.041
                                       EEEEESSHHHHHHHHHHT-SEEEEES--HHH CS
                         QRPTase_C  83 ievevesleeleevleaeadiimLDnfsvee 113
                                       + v   s +e+ e l+ +adii + n++   
  gi|488600269|ref|YP_007906740.1|   4 VLVSPMSIDEAYECLKGGADIIDVKNPKEGS 34 
                                       667777899999**********999996543 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.3e-06
                                       TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHH...HHTTTSE..EEEEESSHHHHHHHHH CS
                         QRPTase_C  27 PglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvre...avdkevk..ievevesleeleevle 98 
                                       Pg++ l+   + ++G+d  ++gL+ +   k+    +++++++ vk +++   +v+ + +    +++ s  +l e+ +
  gi|488600269|ref|YP_007906740.1|  68 PGTASLAALGAAVAGADYIKVGLYGV-KNKEQAYEILKNVTRSVKDFDAdkkVVGAAYAdfHRINAISPFDLPEAGQ 143
                                       89999999999999999999999975.45777788888888888887641113344433556677666666666644 PP

                                       .HT-SEEEEES-...........-HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHC CS
                         QRPTase_C  99 .aeadiimLDnf...........sveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalt 158
                                        ae+d+im+D+            +  +l+++ve  +++++ +    +G+++ e +  ++k+  d+i+v +++
  gi|488600269|ref|YP_007906740.1| 144 mAEVDGIMIDTAikdgltlfdhlKEPQLQEFVE--TARENGMFCALAGSINWEHLPVLKKISPDIIGVRTIV 213
                                       488*********9*****999988899******..45566688999***************99999997775 PP

>> Imm51  Immunity protein 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   6.7e+03      73      89 ..      97     113 ..      87     120 .. 0.54
   2 ?   11.5   0.0   3.6e-05      0.22      52      84 ..     167     201 ..     161     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                             Imm51  73 sedkealkelaellkel 89 
                                       ++  e lk ++  +k++
  gi|488600269|ref|YP_007906740.1|  97 EQAYEILKNVTRSVKDF 113
                                       33445555555555555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.6e-05
                             Imm51  52 kapelleklefDpEagmFvay..sedkealkelae 84 
                                       k+p+l+e +e+  E+gmF+a   s ++e l  l++
  gi|488600269|ref|YP_007906740.1| 167 KEPQLQEFVETARENGMFCALagSINWEHLPVLKK 201
                                       78******************998999998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1434.92
//
Query:       gi|488600270|ref|YP_007906741.1|  [L=227]
Description: hisA/hisF family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   85.5   0.6    5.8e-24   84.8   0.6    1.3  1  His_biosynth  Histidine biosynthesis protein
     0.0017   17.7   0.1      0.004   16.5   0.0    1.7  2  ThiG          Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.013   14.6   0.5      0.083   11.9   0.1    2.0  2  FMN_dh        FMN-dependent dehydrogenase
      0.038   13.1   0.0      0.054   12.6   0.0    1.2  1  Dus           Dihydrouridine synthase (Dus)
      0.061   12.7   0.0       0.19   11.1   0.0    1.8  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.13   11.6   0.0       0.18   11.1   0.0    1.2  1  TMP-TENI      Thiamine monophosphate synthase


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 !   84.8   0.6   1.9e-27   5.8e-24       2     228 ..       3     217 ..       2     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 1.9e-27
                                       EEEEEEEETTEEEEECTTCSTCEEEETTSHHH.....HHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S CS
                      His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpve.....lakryeeegadelhvvDldaakegreanldlveeiaeevf 73 
                                       +++++D+k+G vVr vkGdr++++ +  +++       ++ +++ + + l+++Dl+ ++ g + nl+++ee+ ++  
  gi|488600270|ref|YP_007906741.1|   3 LYFVMDIKNGIVVRGVKGDRESYKPVDLESLVvkssiPVQVFDAVKPKHLYIADLNRIM-GMGDNLKIIEELGKK-- 76 
                                       6899****************8777665554443455557899*************9886.***************.. PP

                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHH CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldav 150
                                       +++  + G +s e   e+  ag    ++g+++++ +  ++e+ e     ++vv++D+ +   v  +g  ee    + 
  gi|488600270|ref|YP_007906741.1|  77 AEIIADCGFKSPE---EVHGAGFTP-VLGSETFDLK-RLEEIKE----REVVVSLDIMDS-FVDASGSFEE----ID 139
                                       9************...666777765.5899988754.5555555....69*********9.9999999999....99 PP

                                       HHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTS CS
                      His_biosynth 151 elakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyege 227
                                       e +k l++  ++ +++  i r+Gt s  d +l+ ++    + pv a+GG+++l+d+ ++k+ g d+v+v++a ++g+
  gi|488600270|ref|YP_007906741.1| 140 EAVKFLNSFRLKGLIVLTIRRVGTSSSLDWDLIGKILGISDNPVFAGGGIRDLQDVMKAKDIGLDGVLVATAVHNGK 216
                                       ****************************************************************************9 PP

                                       S CS
                      His_biosynth 228 l 228
                                       +
  gi|488600270|ref|YP_007906741.1| 217 I 217
                                       8 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.95   2.8e+03     167     190 ..      67      91 ..      61      95 .. 0.68
   2 !   16.5   0.0   1.4e-06     0.004     170     215 ..     175     220 ..     155     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.95
                                       HHHHHHH-.SS-BEEES---SHHHH CS
                              ThiG 167 lkiiieea.kvPvivDAGigspsda 190
                                       lkii e   k  +i D G  sp+++
  gi|488600270|ref|YP_007906741.1|  67 LKIIEELGkKAEIIADCGFKSPEEV 91 
                                       5555554456778888888888776 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.4e-06
                                       HHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 170 iieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       i+   + Pv    Gi+  +d+++a ++G+d+vl++tav + k p +
  gi|488600270|ref|YP_007906741.1| 175 ILGISDNPVFAGGGIRDLQDVMKAKDIGLDGVLVATAVHNGKIPLE 220
                                       555567899999**************************99887765 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.059   1.8e+02     263     286 ..      68      91 ..      62      95 .. 0.86
   2 ?   11.9   0.1   2.8e-05     0.083     271     303 ..     180     212 ..     114     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.059
                                       HHHHHH..SS-EEEESS--SHHHH CS
                            FMN_dh 263 eiveavggrievlvDgGirrGsDv 286
                                       +i e++g+++e+++D+G+++ + v
  gi|488600270|ref|YP_007906741.1|  68 KIIEELGKKAEIIADCGFKSPEEV 91 
                                       6889999**********9987776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.8e-05
                                       SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 271 rievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       + +v++ gGir  +Dv+kA  +G d+vl++ ++
  gi|488600270|ref|YP_007906741.1| 180 DNPVFAGGGIRDLQDVMKAKDIGLDGVLVATAV 212
                                       457888888888888888888888888887666 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    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     165     215 ..     162     211 ..     135     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                       TT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCH CS
                               Dus 165 nyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrg 215
                                       + +  +dw+ I ++      pv+a G+I+d++d+ ++ +  G dgv+++ +
  gi|488600270|ref|YP_007906741.1| 162 GTSSSLDWDLIGKILGISDNPVFAGGGIRDLQDVMKAKDI-GLDGVLVATA 211
                                       556689********99888****************99887.******9976 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.51   1.5e+03      58      76 ..     137     154 ..     108     168 .. 0.73
   2 ?   11.1   0.0   6.4e-05      0.19     130     167 ..     171     208 ..     166     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.51
                                       SSHHHHHHHHH.TT-SEEE CS
                      G3P_antiterm  58 kdeaaveflkkeikvdGii 76 
                                       + ++av+fl++ ++ +G+i
  gi|488600270|ref|YP_007906741.1| 137 EIDEAVKFLNS-FRLKGLI 154
                                       45678888877.8888877 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.4e-05
                                       HHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 130 vikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                       +i +i   ++ p++aGG i++ +dv++a + G ++v +
  gi|488600270|ref|YP_007906741.1| 171 LIGKILGISDNPVFAGGGIRDLQDVMKAKDIGLDGVLV 208
                                       56777788899*********************999865 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.1e-05      0.18     125     180 ..     154     211 ..     132     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.1e-05
                          TMP-TENI 125 ifpTdtKkda.eplgleglkelaealeiPvvaiGGi.tlenvaevleagadgvavvsa 180
                                       i  T  + +  + l+++++ ++   +  Pv+a GGi +l++v ++ + g+dgv v +a
  gi|488600270|ref|YP_007906741.1| 154 IVLTIRRVGTsSSLDWDLIGKILGISDNPVFAGGGIrDLQDVMKAKDIGLDGVLVATA 211
                                       5555555566678999********************44799************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 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:                        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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1698.72
//
Query:       gi|488600271|ref|YP_007906742.1|  [L=276]
Description: ribose-phosphate pyrophosphokinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   78.8   0.5    1.1e-18   67.3   0.0    2.5  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    8.9e-18   64.3   1.1    1.6e-17   63.5   1.1    1.4  1  Pribosyltran    Phosphoribosyl transferase domain
    3.3e-10   40.3   1.6    5.4e-10   39.6   1.6    1.4  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    2.2e-06   27.3   0.4    3.6e-06   26.6   0.4    1.3  1  UPRTase         Uracil phosphoribosyltransferase
     0.0059   16.1   0.1     0.0093   15.5   0.1    1.3  1  PRTase_2        Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   3.1e-22   1.1e-18       1     113 [.       1     104 [.       1     106 [. 0.91
   2 !    9.7   0.1   0.00022       0.8      21      90 ..     166     237 ..     109     260 .. 0.71

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 3.1e-22
                    Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrra 77 
                                       +ki++g +s+ L++kia+ l+ e+++a+ +rf+dgE +v+ e+s    d +++qs++++  d+l+ l+lm++a++  
  gi|488600271|ref|YP_007906742.1|   1 MKILSGPASPFLGKKIADVLKAEIAQAEFKRFPDGELYVRAESS----D-VVVQSICSN--DDLVYLILMLSAIE-- 68 
                                       89**************************************9876....5.579****87..*************7.. PP

                    Pribosyltran_N  78 sakritaViPylgysrqdrk.ksrepisaklvaklLe 113
                                         ++ +aViPy+gy+rqdrk +  e++s + +a++ e
  gi|488600271|ref|YP_007906742.1|  69 -NSEKIAVIPYFGYARQDRKfQDGEAVSIREIARIVE 104
                                       .334469*************999*********99877 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00022
                    Pribosyltran_N  21 gvelgkakvsrfadgEikveiee.svrgkdvfiiqslskpvndnlmelllmidal..rrasakritaViPylg 90 
                                       ++     + +r +  E++++ ++ +v g+dv+i+ ++ +    +++e ++++  +  +  sa  + aV+  ++
  gi|488600271|ref|YP_007906742.1| 166 NCDYDYLEKRRISATEVEISPKNiDVEGRDVVIVDDIIST-GGTIVEATRILRNMgaKSVSAVCVHAVMSNFA 237
                                       5555556778889999999998889************987.89999*99999876224555666677777776 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   1.1   4.5e-21   1.6e-17      26     129 ..     140     235 ..     117     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 4.5e-21
                                       --GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHH CS
                      Pribosyltran  26 yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgT 102
                                       y+ k +v + +++g++ ++k  a + ++ ++y++k++ ++   e  +        + +d++g+ V+iVDDi++tGgT
  gi|488600271|ref|YP_007906742.1| 140 YRDKDVVMISPDKGSLERVKVSAEAANCDYDYLEKRRISATEVEISP--------KNIDVEGRDVVIVDDIISTGGT 208
                                       7889******************************9999988888887........899******************* PP

                                       HHHHHHHHHCC-BSEEEEEEEEE-HHH CS
                      Pribosyltran 103 llaalelLkekgpeevriavlvdkpat 129
                                       + +a+++L++ g+++v ++++++ ++ 
  gi|488600271|ref|YP_007906742.1| 209 IVEATRILRNMGAKSVSAVCVHAVMSN 235
                                       *********************976554 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   1.6   1.5e-13   5.4e-10      80     153 ..     190     263 ..     175     276 .] 0.92

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.5e-13
                                       --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHHT CS
                    Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqklr 153
                                       dv+Gr  +ivdd+i    ++v+a+++l++ Ga  + +++ h ++s+ a ++l ++ ++ev+ t+ti + + ++ 
  gi|488600271|ref|YP_007906742.1| 190 DVEGRDVVIVDDIISTGGTIVEATRILRNMGAKSVSAVCVHAVMSNFALNKLYSAGVKEVIATDTIERIVSRIS 263
                                       9*****************************************************************98776655 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.4   9.9e-10   3.6e-06     116     184 ..     186     256 ..     171     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9.9e-10
                           UPRTase 116 Pkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkvvtaavD 184
                                       Pk+i  + r v+++D +i+TGg++++a ++L++ g+++ + +++  ++s+ ++++l ++  k  + t +++
  gi|488600271|ref|YP_007906742.1| 186 PKNIdvEGRDVVIVDDIISTGGTIVEATRILRNMGAKSVSAVCVHAVMSNFALNKLYSAGVKEVIATDTIE 256
                                       6666658899**************************9999999999****999999887766666666665 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.6e-06    0.0093     120     150 ..     192     222 ..     176     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-06
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr 150
                                       + + +v+vDD istG t+++  r l++   +
  gi|488600271|ref|YP_007906742.1| 192 EGRDVVIVDDIISTGGTIVEATRILRNMGAK 222
                                       5689****************99999877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1736.26
//
Query:       gi|488600272|ref|YP_007906743.1|  [L=193]
Description: imidazoleglycerol-phosphate dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-52  175.1   0.3    1.3e-51  174.7   0.3    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 !  174.7   0.3   7.2e-56   1.3e-51       1     143 [.      33     173 ..      33     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 7.2e-56
                                       ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEE CS
                              IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaeval 77 
                                       T i+f+ hmL+++a+h++++l ++++gd+evd+Hhtved++i++G+a+++algdkrgi+Rfg+a++pmDe+++ + +
  gi|488600272|ref|YP_007906743.1|  33 TPIPFFTHMLETFARHAEIKLVLSAEGDVEVDEHHTVEDTAIVIGSAIEKALGDKRGIERFGDAIVPMDESVTLCGI 109
                                       89*************************************************************************** PP

                                       E--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHH CS
                              IGPD  78 dlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafara 143
                                       d+sgr ++ +++e++  +i+++++e++ +ffe+l++++gi++ ++++ g+n hh++e++fKafa +
  gi|488600272|ref|YP_007906743.1| 110 DISGRGVFRFDGEID-GEINNFKAENFLHFFETLSRESGINIYLNTR-GRNLHHMMESAFKAFALS 173
                                       ***********9998.669**************************88.***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 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:                        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 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1248.81
//
Query:       gi|488600273|ref|YP_007906744.1|  [L=241]
Description: 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino) imidazole-4-carboxamide isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-63  213.3   2.8    3.5e-63  213.1   2.8    1.0  1  His_biosynth    Histidine biosynthesis protein
     0.0002   20.6   0.1      0.062   12.5   0.0    2.4  2  IGPS            Indole-3-glycerol phosphate synthase
    0.00047   19.7   3.3       0.12   11.8   0.0    2.5  3  PcrB            PcrB family
     0.0015   17.7   0.1       0.78    8.8   0.0    2.1  2  Dus             Dihydrouridine synthase (Dus)
     0.0025   17.2   0.5          2    7.8   0.1    2.3  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
     0.0054   15.6   0.3       0.04   12.8   0.0    1.9  2  Trp_syntA       Tryptophan synthase alpha chain
      0.007   15.8   0.6      0.027   13.9   0.6    1.8  1  NMO             Nitronate monooxygenase


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 !  213.1   2.8   1.4e-66   3.5e-63       2     228 ..       7     230 ..       6     231 .. 0.99

  Alignments for each domain:
  == domain 1  score: 213.1 bits;  conditional E-value: 1.4e-66
                                       EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEE CS
                      His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqv 78 
                                       +ipa+DlkdG+v rlv+Gd ++ ++  ++p+++a+++  +ga+ lh++Dld+a+eg  ++   ++ei+++++++vqv
  gi|488600273|ref|YP_007906744.1|   7 VIPAIDLKDGRVTRLVQGDFSRITVQIDNPLDVARNWIMQGAKCLHIIDLDGAFEGALRHEREIREILSAFDVEVQV 83 
                                       8**************************************************************************** PP

                                       ESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHH CS
                      His_biosynth  79 GGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakk 155
                                       GGGIr+   +e+ll+a +d+vi+gt a+++p+ +ke+a   +s +i++a+D++++ kvaikgw+e+t+l+a++++  
  gi|488600273|ref|YP_007906744.1|  84 GGGIRDPGVIESLLDADVDRVILGTLALTEPDAVKEIAASNPS-RIMIAVDSKED-KVAIKGWTEKTSLSALDVIGM 158
                                       ***************************************9888.***********.********************* PP

                                       HHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                      His_biosynth 156 leelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                       +e++ + ++l+t+id +G  +G+d + + ++ +a + +v ++GG++s+ed++ ++++g+++vi+gsaly+g+l
  gi|488600273|ref|YP_007906744.1| 159 FEDVDV-SFLYTNIDVEGLIKGIDRKKLTNVLKASEKSVYVAGGISSIEDIAFIRDSGAEGVIIGSALYTGKL 230
                                       ****99.79*************************************************************997 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0026       6.6      69     137 ..      35     106 ..      27     147 .. 0.64
   2 !   12.5   0.0   2.4e-05     0.062     200     243 ..     183     227 ..     177     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0026
                                       -HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHHH-S...S-EEEES---SHHHHHHHHHCT-SEEEE CS
                              IGPS  69 dpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrqavs...lpvlrKdFiideyqieearalgadaiLL 137
                                       +p ++A+++   gA+++ ++     F+G+l + re+r+++s   + v     i d+  ie    +  d ++L
  gi|488600273|ref|YP_007906744.1|  35 NPLDVARNWIMQGAKCLHIIDLDGAFEGALRHEREIREILSafdVEVQVGGGIRDPGVIESLLDADVDRVIL 106
                                       6789999999999******999999***99988887776541115555566666666666444444444444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.4e-05
                                       HHHCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC CS
                              IGPS 200 eeLaklvpkd.vllvaeSGiktredveklkeegvnafLvGeslmr 243
                                       ++L+++++++   +    Gi++ ed+  ++++g++++++G++l  
  gi|488600273|ref|YP_007906744.1| 183 KKLTNVLKASeKSVYVAGGISSIEDIAFIRDSGAEGVIIGSALYT 227
                                       577777774434555568************************975 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   4.7e-05      0.12     152     223 ..      49     121 ..      22     124 .. 0.71
   2 ?    0.9   0.1       0.1   2.5e+02      23      85 ..     128     190 ..     113     195 .. 0.83
   3 !    7.7   0.7   0.00087       2.2     176     215 ..     189     229 ..     162     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                                       TT-SEEEEE-..TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHHHH CS
                              PcrB 152 lglrliYlEa..sGaledveevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekderkidail 223
                                         l +i l+    Gal +  e+ ++     + ++ vGGGir++   +  + a  D ++ G++   ++ +++++i+
  gi|488600273|ref|YP_007906744.1|  49 KCLHIIDLDGafEGALRHEREIREILSAF-DVEVQVGGGIRDPGVIESLLDAdVDRVILGTLALTEP-DAVKEIA 121
                                       45556666543567777777777777666.46789****************999*******988887.6677776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
                                       HHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEEEEEEETT CS
                              PcrB  23 veiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvryaDalFvmslln 85 
                                       + i+++s  D v i G ++ t   ++ ++   + +++  +    +veg+ +++D   +  +l 
  gi|488600273|ref|YP_007906744.1| 128 IMIAVDSKEDKVAIKGWTEKTSLSALDVIGMFEDVDVSFLYTNIDVEGLIKGIDRKKLTNVLK 190
                                       4566799999****9999999889999999999999999999999999999999877777765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00087
                                       HHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                              PcrB 176 kklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                        k +++ ++v GGi s E+ + +    A+ +++G +++  +
  gi|488600273|ref|YP_007906744.1| 189 LKASEKSVYVAGGISSIEDIAFIRDSgAEGVIIGSALYTGK 229
                                       345677899**********99999889**********9766 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0003      0.78     173     231 ..      68     125 ..      59     147 .. 0.86
   2 !    7.0   0.0     0.001       2.6     180     217 ..     190     226 ..     177     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0003
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHHHH CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestavkt 231
                                       ++I+e+  a+ + v + G+I+d+  ++  l+   +d v+ g  al +P  ++e +a++ 
  gi|488600273|ref|YP_007906744.1|  68 REIREILSAFDVEVQVGGGIRDPGVIESLLDA-DVDRVILGTLALTEPDAVKEIAASNP 125
                                       5899**************************99.9***************9997555544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.001
                                       HH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                               Dus 180 qavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                       +a + +v + G+I ++ed+  i +  Ga+gv+ig + +
  gi|488600273|ref|YP_007906744.1| 190 KASEKSVYVAGGISSIEDIAFIRDS-GAEGVIIGSALY 226
                                       5555689999*********887766.********8876 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 !    7.7   0.0    0.0008       2.1     153     195 ..      67     108 ..      58     111 .. 0.82
   2 !    7.8   0.1   0.00078         2     164     198 .]     191     226 ..     173     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0008
                                       HHHHHHHHHHHT---EEEEESS--TT.TCHHHHHHT--EEEESH CS
                    Ribul_P_3_epim 153 ikkvrklidekeldlkievDGGvkld.nieqiaeagadvlVags 195
                                        +++r+++++  +d++++v GG+++   ie + +a++d ++ g+
  gi|488600273|ref|YP_007906744.1|  67 EREIREILSA--FDVEVQVGGGIRDPgVIESLLDADVDRVILGT 108
                                       5778888887..9**********97626899********99996 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00078
                                       T---EEEEESS--.TTTCHHHHHHT--EEEESHHHH CS
                    Ribul_P_3_epim 164 eldlkievDGGvk.ldnieqiaeagadvlVagsavf 198
                                         +  ++v GG++  + i+ i + ga+ +++gsa++
  gi|488600273|ref|YP_007906744.1| 191 ASEKSVYVAGGISsIEDIAFIRDSGAEGVIIGSALY 226
                                       356789******73599*****************97 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     0.071   1.8e+02     189     231 ..      69     112 ..      61     139 .. 0.77
   2 !   12.8   0.0   1.6e-05      0.04     190     229 ..     185     225 ..     178     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.071
                                       HHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHH CS
                         Trp_syntA 189 lverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvk 231
                                        ++++ ++ +v v vG Gi+++  ++++  +  d vi G   ++
  gi|488600273|ref|YP_007906744.1|  69 EIREILSAFDVEVQVGGGIRDPGVIESLLdADVDRVILGTLALT 112
                                       57777777889999999999999999999888899999976554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.6e-05
                                       HHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHH CS
                         Trp_syntA 190 verlkkltavPvavGFGistkeqvkqva.kvadGvivGSal 229
                                       + ++ k++++ v v  Gis+ e+++ +  ++a+Gvi+GSal
  gi|488600273|ref|YP_007906744.1| 185 LTNVLKASEKSVYVAGGISSIEDIAFIRdSGAEGVIIGSAL 225
                                       5667778889999999************9**********98 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.6   1.1e-05     0.027     185     226 ..     185     226 ..      63     240 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                               NMO 185 vpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                       + +vl+a +  v  aGGi   +++a +   GA+gv ig+++ 
  gi|488600273|ref|YP_007906744.1| 185 LTNVLKASEKSVYVAGGISSIEDIAFIRDSGAEGVIIGSALY 226
                                       45688888889999*************************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1460.20
//
Query:       gi|488600274|ref|YP_007906745.1|  [L=411]
Description: Proteasome-activating nucleotidase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-46  156.7   0.4      1e-45  155.4   0.0    1.8  1  AAA              ATPase family associated with various cellul
    2.9e-14   52.6   0.7    7.4e-14   51.3   0.7    1.7  1  AAA_lid_3        AAA+ lid domain
    2.1e-12   46.8   0.2    4.4e-12   45.8   0.2    1.6  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    6.3e-09   36.2   0.1      2e-08   34.5   0.0    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.6e-06   27.6   0.0    4.5e-06   26.2   0.0    1.7  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    1.8e-06   28.4   1.7    0.00032   21.1   0.0    2.9  2  AAA_16           AAA ATPase domain
    1.2e-05   25.6   0.6     0.0025   18.1   0.1    2.5  2  AAA_22           AAA domain
      2e-05   24.6   0.1    0.00025   21.0   0.1    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
    2.4e-05   24.1   0.0    7.3e-05   22.6   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00016   20.9   0.0    0.00029   20.1   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
    0.00021   21.6   0.0    0.00043   20.6   0.0    1.5  1  RNA_helicase     RNA helicase
    0.00055   20.2   0.0     0.0012   19.1   0.0    1.6  1  AAA_28           AAA domain
     0.0012   19.1   2.2     0.0035   17.5   2.2    1.8  1  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
     0.0019   18.0   0.0     0.0063   16.3   0.0    1.9  1  IstB_IS21        IstB-like ATP binding protein
     0.0024   18.1   0.0     0.0069   16.6   0.0    1.8  1  AAA_33           AAA domain
     0.0029   16.9   0.0     0.0059   15.8   0.0    1.5  1  TIP49            TIP49 P-loop domain
     0.0036   17.9   0.6      0.014   16.0   0.0    2.3  2  AAA_18           AAA domain
      0.004   16.9   0.3       0.03   14.0   0.0    2.5  3  AAA_24           AAA domain
      0.008   15.6   0.0      0.017   14.5   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.026   14.1   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
      0.014   15.3   0.2      0.053   13.4   0.0    2.1  1  NTPase_1         NTPase
      0.016   15.0   0.0      0.037   13.9   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
      0.016   15.4   1.3       0.04   14.2   1.3    1.6  1  THOC7            Tho complex subunit 7
      0.017   15.2   0.0      0.042   13.9   0.0    1.7  1  AAA_14           AAA domain
      0.019   14.3   0.2       0.15   11.4   0.2    2.4  1  ATPase           KaiC
      0.028   14.2   3.0      0.085   12.7   3.0    1.8  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.031   14.1   0.1       0.37   10.5   0.0    2.2  2  AAA_11           AAA domain
      0.037   13.7   0.0       0.11   12.2   0.0    1.8  1  Sigma54_activat  Sigma-54 interaction domain
      0.042   12.5   0.5        3.6    6.1   0.0    2.4  2  AAA_13           AAA domain
      0.046   12.9   0.0       0.13   11.4   0.0    1.8  1  NB-ARC           NB-ARC domain
       0.05   12.7   0.0        0.1   11.7   0.0    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.05   13.5   0.2       0.59   10.0   0.0    2.2  2  NACHT            NACHT domain
      0.052   13.6   0.0      0.095   12.7   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.057   13.1   0.0       0.11   12.2   0.0    1.5  1  AAA_30           AAA domain
      0.058   13.0   0.8       0.72    9.4   0.2    2.5  2  AAA_25           AAA domain
       0.06   12.8   0.1       0.17   11.3   0.1    1.7  1  PhoH             PhoH-like protein
      0.078   12.9   3.2       0.18   11.7   0.1    2.8  2  ATPase_2         ATPase domain predominantly from Archaea
      0.081   12.2   0.6       0.19   11.0   0.0    1.9  2  Zeta_toxin       Zeta toxin
       0.13   12.8   0.0        0.4   11.2   0.0    2.0  1  ABC_tran         ABC transporter
       0.24   11.9   3.5       0.65   10.5   3.5    1.7  1  APG6_N           Apg6 coiled-coil region
       0.25   10.7   9.0       0.33   10.3   5.2    2.1  2  DUF2353          Uncharacterized coiled-coil protein (DUF2353
       0.29   11.4   5.8        2.5    8.4   5.8    2.5  1  HALZ             Homeobox associated leucine zipper
       0.36   10.2   2.7       0.77    9.2   2.7    1.5  1  DUF4349          Domain of unknown function (DUF4349)
       0.96    9.8   6.8        2.2    8.6   6.8    1.6  1  Troponin         Troponin


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 !  155.4   0.0   2.5e-48     1e-45       1     132 []     191     324 ..     191     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 2.5e-48
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vllyGppGtGKTllakava++++++f+++ gse+++ky+ge+++ +re+f+ akeka psi+fiDE+da+a +r   
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQTKATFIRVVGSEFVQKYIGEGARLVREVFQLAKEKA-PSIIFIDELDAIAARRtss 266
                                       79******************************************************9.****************986 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                       ++s ++e +r++ qLl+e+dg++++ ++v ++gatnr+d ldpa+lr gRfdr+ie++l
  gi|488600274|ref|YP_007906745.1| 267 DTSGDREVQRTLMQLLSEMDGFDNR-GDVKIVGATNRIDILDPAILRpGRFDRIIEVPL 324
                                       666888999***************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 !   51.3   0.7   1.8e-16   7.4e-14       1      45 []     346     390 ..     346     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.8e-16
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                       dvd+ eLAe+TeG SGAD++a+  eA++ A+r   + ++ edf++
  gi|488600274|ref|YP_007906745.1| 346 DVDFRELAEMTEGASGADIKAIATEAGMFAIRNEKTIVSREDFIK 390
                                       9******************************************75 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 !   45.8   0.2   1.1e-14   4.4e-12       1      57 []      78     133 ..      78     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.1e-14
                                       EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                       V+ +s+vl+d ++++Vk+s++ ++vv+ +  +++e+L+pg++V+++++t +i  +LP
  gi|488600274|ref|YP_007906745.1|  78 VGVISDVLED-GKVVVKSSTGPKFVVHTSQNINPEDLKPGARVSMNQQTLAIISVLP 133
                                       7889******.*********************************************9 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0     5e-11     2e-08       6     105 ..     191     284 ..     187     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5e-11
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    ++ir+  se+ +    + + +     ++  + a+e+   i+++DE+d i
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQTKA----TFIRVVGSEFVQ----KYIGEGARLVREVFQLAKEKApsIIFIDELDAI 259
                                       6889****************9985....************....88888888899999999999899********** PP

                                       ------------.HHHHHHHHHHHH- CS
                             AAA_2  81 hpkessgadvSr.egVqrdLLqileg 105
                                       ++ +++++d S+  +Vqr L+q+l +
  gi|488600274|ref|YP_007906745.1| 260 AA-RRTSSDTSGdREVQRTLMQLLSE 284
                                       **.777777776269********976 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.1e-08   4.5e-06       3      58 ..      79     135 ..      77     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.1e-08
                     Prot_ATP_OB_N   3 GtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEa.lvvVealgye 58 
                                       G++  v ++++ +  ++ g +++V  s ++++e+L+pG++V +n++ l+++ +l+++
  gi|488600274|ref|YP_007906745.1|  79 GVISDVLEDGKVVVKSSTGPKFVVHTSQNINPEDLKPGARVSMNQQtLAIISVLPPP 135
                                       666677767777778999**************************8736777777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   7.8e-07   0.00032      19      56 ..     183     217 ..     162     228 .. 0.78
   2 ?    5.2   0.1     0.062        25     122     149 ..     235     261 ..     231     291 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.8e-07
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggifl 56 
                                       v    p  vll+G++G+GK+ l+++++++ +++   f+
  gi|488600274|ref|YP_007906745.1| 183 VGIEPPKGVLLYGPPGTGKTLLAKAVANQTKAT---FI 217
                                       55555699*******************876655...43 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.062
                            AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                       l+++ ++l+++ + p ++++D+l+ + +
  gi|488600274|ref|YP_007906745.1| 235 LVREVFQLAKE-KAPSIIFIDELDAIAA 261
                                       55666688888.778*********4443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     6e-06    0.0025       8      42 ..     191     216 ..     186     229 .. 0.84
   2 ?    6.2   0.2     0.029        12      59     125 ..     219     296 ..     212     305 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpev 42 
                                       ++++G++GtGKT+l++ +++q          ++++
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQT---------KATF 216
                                       689*****************98.........4444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.029
                            AAA_22  59 ellralglelkaerlsseellealeqalraravielliiDEaqhlr....s..........eealeeLrsllnl.sr 120
                                        + +++ ++  +   +  +l++ + q ++++a  +++ iDE + +     s           ++++ L+++  + +r
  gi|488600274|ref|YP_007906745.1| 219 VVGSEFVQKYIG---EGARLVREVFQLAKEKAP-SIIFIDELDAIAarrtSsdtsgdrevqRTLMQLLSEMDGFdNR 291
                                       555555555555...677899999999999999.**********987765145667755543333333333333446 PP

                            AAA_22 121 kgvql 125
                                        +v++
  gi|488600274|ref|YP_007906745.1| 292 GDVKI 296
                                       66665 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 ?   -0.8   0.0       3.5   1.4e+03      25      49 ..      97     122 ..      88     131 .. 0.81
   2 !   21.0   0.1   6.2e-07   0.00025       1      77 [.     190     259 ..     190     312 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.5
                                       --EEEEE--TT--HHHHH--B--... CS
                             AAA_5  25 reveyvqltrdtteedlkgrreik.n 49 
                                        + ++v  ++++++edlk + +++ n
  gi|488600274|ref|YP_007906745.1|  97 GPKFVVHTSQNINPEDLKPGARVSmN 122
                                       57899999**********99998743 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 6.2e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ la+ +a  +++++  v ++++ ++    g r         v  ++   a+   ++i+++DE++
  gi|488600274|ref|YP_007906745.1| 190 GVLLYGPPGTGKTLLAKAVANQTKATFIRVVGSEFVQKYIGEGARL--------VREVFQ-LAKekAPSIIFIDELD 257
                                       59************************99999988554433333333........333333.3332467788888877 PP

                                       G- CS
                             AAA_5  76 ra 77 
                                        +
  gi|488600274|ref|YP_007906745.1| 258 AI 259
                                       65 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.8e-07   7.3e-05      34      96 ..     189     259 ..     182     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.8e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvk.lkitsgPvleka.gdlaal...ltnl...eekdvlfideihrl 96 
                                         vllyGpPG Gkt lak +a++ +++ +++  +  ++k  g+ a l   + +l   ++  ++fide+  +
  gi|488600274|ref|YP_007906745.1| 189 KGVLLYGPPGTGKTLLAKAVANQTKATfIRVVGSEFVQKYiGEGARLvreVFQLakeKAPSIIFIDELDAI 259
                                       569********************998725666666666642444444111334421134579999998765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     7e-07   0.00029      52     116 ..     187     256 ..     145     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7e-07
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                       p + vLL+G  GtGK  l ka+ n+++++ +r++  e  ++ + e  +lv+++    +++   i+f+D L
  gi|488600274|ref|YP_007906745.1| 187 PPKGVLLYGPPGTGKTLLAKAVANQTKATFIRVVgsEFVQKYIGEGARLVREVFqlaKEKAPSIIFIDEL 256
                                       6678******************************77777889999888887654122777889*****98 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.1e-06   0.00043       1      69 [.     191     250 ..     191     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.1e-06
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenpsd 69 
                                       ++lyGp+g+GK++lak            ++++ +++r + ++f+++Y g+ + ++ ++ q  +e+ ps+
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKA---------VANQTKATFIRVVGSEFVQKYIGEGARLVREVFQLAKEKAPSI 250
                                       689**************.........3466788899***********************9998876664 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.1e-06    0.0012       2      43 ..     191     237 ..     190     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.1e-06
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakge 43 
                                       + + G+++tGKT l++a a++     ++vv  E++ +++ e+++  +
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQtkatFIRVVgSEFVQKYIGEGARLVR 237
                                       6799***************6666668999999999999988875544 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.2   8.6e-06    0.0035       6      66 ..      11      71 ..       7      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.6e-06
                       TMF_TATA_bd  6 sagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkel 66
                                       ++++v l e+l  ++++lE E+  lk+ ++rle e++ ++ e ++  +e+ +l+++ ++l
  gi|488600274|ref|YP_007906745.1| 11 IKEKNVDLSEYLIDRLKQLEEEYVRLKNLYKRLEDEKRFVETERIRYEREVRRLRSEIERL 71
                                      567899******************************************9999999887765 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   1.5e-05    0.0063      46      73 ..     187     214 ..     175     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                         IstB_IS21  46 kkenivllGpsGvGKshlaialgveavr 73 
                                         ++++l Gp+G+GK+ la a++ ++ +
  gi|488600274|ref|YP_007906745.1| 187 PPKGVLLYGPPGTGKTLLAKAVANQTKA 214
                                       56789****************9988655 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   1.7e-05    0.0069       2      28 ..     191     219 ..     191     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avll 28 
                                       vll G+pG+GK+ la+ ++++++  ++++
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQTKatFIRV 219
                                       7899***************9999554444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-05    0.0059      51      91 ..     189     227 ..     157     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                                       ++vLl Gp+gtGkt la a++++   +  f+ ++gse+ + 
  gi|488600274|ref|YP_007906745.1| 189 KGVLLYGPPGTGKTLLAKAVANQT--KATFIRVVGSEFVQK 227
                                       89*******************975..689*******98655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       7.2   2.9e+03     104     114 ..      37      47 ..      16      92 .. 0.66
   2 !   16.0   0.0   3.4e-05     0.014       1      45 [.     191     259 ..     191     307 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 7.2
                            AAA_18 104 eelleRlekRg 114
                                       + l++Rle+ +
  gi|488600274|ref|YP_007906745.1|  37 KNLYKRLEDEK 47 
                                       34555555433 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.4e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe...a 45 
                                       +ll G+pG+GKt lak++++ ++                      ++++ ++ake+ +++ + +e    
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQTKAtfirvvgsefvqkyigegarlVREVFQLAKEKAPSIIFIDEldaI 259
                                       799***************999744478888766666666666666666666666665555555555551 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       8.1   3.3e+03      32      63 ..       5      33 ..       4      51 .. 0.58
   2 !   14.0   0.0   7.4e-05      0.03       5      24 ..     191     212 ..     188     263 .. 0.80
   3 ?   -0.7   0.0       2.4     1e+03      29      61 ..     367     400 ..     355     409 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.1
                            AAA_24 32 ekGlksldadkfpdieswedfldevvelaael 63
                                      e+G+ks++ ++++     e ++d +++l++e+
  gi|488600274|ref|YP_007906745.1|  5 EGGTKSIKEKNVDLS---EYLIDRLKQLEEEY 33
                                      567777777776644...33344444443333 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.4e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gp 24 
                                       +l+yGp+g+GKT lak    + 
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVanQT 212
                                       89*************9986544 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.4
                            AAA_24  29 idtekGlksldadkfpdieswedfldevvel...aa 61 
                                       i te+G+ ++ + k  +i s edf+++++++   ++
  gi|488600274|ref|YP_007906745.1| 367 IATEAGMFAIRNEK--TIVSREDFIKAIEKImkkDK 400
                                       77999998888888..67899999999999844333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.2e-05     0.017      25      43 ..     191     209 ..     182     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVA 209
                                       89*************9875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.3e-05     0.026      33      60 ..     188     215 ..     178     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-05
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldke 60 
                                        k vll+Gp GtGKt+++k + ++ + +
  gi|488600274|ref|YP_007906745.1| 188 PKGVLLYGPPGTGKTLLAKAVANQTKAT 215
                                       5789****************99988833 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00013     0.053       2      58 ..     191     248 ..     190     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T--EE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasgeeg 58 
                                       v++ GppG+GKt l k v+++ k   ++v G   ++++  +g r   ++ +la+++  
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQTKATFIRVVGSeFVQKYIGEGARLVREVFQLAKEKAP 248
                                       6788*************************9973578888999***9***999887765 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 ?   13.9   0.0     9e-05     0.037       2      30 ..     191     219 ..     190     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktll+ka+a++ +++f r+
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQTKATFIRV 219
                                       7999**********************998 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.3   9.9e-05      0.04      35      96 ..      12      73 ..       6      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.9e-05
                             THOC7 35 eeeleqlkedllldfaafelsierlqllakanerereryeaekeeieseieavreeieelka 96
                                      +e++  l e l  ++ ++e +  rl++l k  e e++ +e+e+ + e+e   +r+eie+l++
  gi|488600274|ref|YP_007906745.1| 12 KEKNVDLSEYLIDRLKQLEEEYVRLKNLYKRLEDEKRFVETERIRYEREVRRLRSEIERLRS 73
                                      6777888999999***********************************************95 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0    0.0001     0.042       5      77 ..     191     272 ..     188     324 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0001
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT l+k ++++       ++ +   +  +k + + ++l +++++++ke+  +++f+DE   +     
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQTK---ATFIRVVGSEFVQKYIGEGARLVREVFQLAKEKAPSIIFIDELDAIaarrt 264
                                       7899*************997777...666666665555555555556888888887777899******988855555 PP

                            AAA_14  77 .......p 77 
                                              +
  gi|488600274|ref|YP_007906745.1| 265 ssdtsgdR 272
                                       55554443 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00036      0.15      14      38 ..     183     207 ..     161     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                            ATPase  14 gGipegrvvlitGepGtGKtifalq 38 
                                        Gi   + vl++G pGtGKt++a+ 
  gi|488600274|ref|YP_007906745.1| 183 VGIEPPKGVLLYGPPGTGKTLLAKA 207
                                       578888899*************975 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.0   0.00021     0.085      60     108 ..      24      72 ..      10      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                          KASH_CCD  60 qkaklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLq 108
                                        + k leeE   lk+l k+le++++ +++++ + e+e   L+++ie L 
  gi|488600274|ref|YP_007906745.1|  24 DRLKQLEEEYVRLKNLYKRLEDEKRFVETERIRYEREVRRLRSEIERLR 72 
                                       67899*****************************************995 PP

>> AAA_11  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   2.7e+02     133     186 ..      15      73 ..       2      92 .. 0.62
   2 ?   10.5   0.0    0.0009      0.37      19      41 ..     190     212 ..     163     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.66
                            AAA_11 133 leklakelrafeeeeek.....eklkkskekskskleqerrklkkerkelskeleeaee 186
                                       + +l++ l ++ ++ e+     ++l k  e++k+  e+er   ++e+++l++e+e+ ++
  gi|488600274|ref|YP_007906745.1|  15 NVDLSEYLIDRLKQLEEeyvrlKNLYKRLEDEKRFVETERIRYEREVRRLRSEIERLRS 73 
                                       33333333333333333455556666777777778888888888888888888877664 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0009
                            AAA_11  19 itliqGPPGtgKTktivellsql 41 
                                        +l+ GPPGtgKT    ++ +q 
  gi|488600274|ref|YP_007906745.1| 190 GVLLYGPPGTGKTLLAKAVANQT 212
                                       4799*********8877777776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00028      0.11      23      48 ..     189     214 ..     178     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                                       S-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskr 48 
                                         vl+ G  GtGK+lla+a+ +++k 
  gi|488600274|ref|YP_007906745.1| 189 KGVLLYGPPGTGKTLLAKAVANQTKA 214
                                       579****************9887653 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.035        14     408     454 ..      23      69 ..       5      85 .. 0.58
   2 ?    6.1   0.0    0.0088       3.6      20     106 ..     192     261 ..     189     304 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.035
                            AAA_13 408 eseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlr 454
                                        + l++++++y +l++  + le+e++  e+e   +e e++ L+ +++
  gi|488600274|ref|YP_007906745.1|  23 IDRLKQLEEEYVRLKNLYKRLEDEKRFVETERIRYEREVRRLRSEIE 69 
                                       33444555555555555555666666666666666666666655554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0088
                            AAA_13  20 liYGwNGaGKTtLSrllrslelgetepkfangsieitngeeldirVfNrdFveenls.eqgelkpvftLGeesiekq 95 
                                       l+YG  G+GKT L+++ +++++      f              irV  ++Fv++ +  ++  ++ vf L++e++   
  gi|488600274|ref|YP_007906745.1| 192 LLYGPPGTGKTLLAKAVANQTK----ATF--------------IRVVGSEFVQKYIGeGARLVREVFQLAKEKAPSI 250
                                       68**************999743....223..............5666666666666622233666666666666666 PP

                            AAA_13  96 ekieklkkeik 106
                                         i++l+   +
  gi|488600274|ref|YP_007906745.1| 251 IFIDELDAIAA 261
                                       66666555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.13      22      46 ..     190     214 ..     173     303 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                       EEEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksde 46 
                                        v l+G +G GKt lak + n+ + 
  gi|488600274|ref|YP_007906745.1| 190 GVLLYGPPGTGKTLLAKAVANQTKA 214
                                       5889***************999443 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00025       0.1     117     138 ..     191     212 ..     186     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                       v++yGp+ tGkt la+a a+ +
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQT 212
                                       89****************9976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0014      0.59       3      24 ..     191     212 ..     189     225 .. 0.90
   2 ?    1.2   0.0      0.75   3.1e+02      66     115 ..     233     284 ..     222     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++G GKT L++ +a + 
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQT 212
                                       799*************999875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.75
                                       -SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCT CS
                             NACHT  66 aapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirk 115
                                       a+ v+ev+++  e + ++ +i D lD +++       ++ ++v++ L +l+++
  gi|488600274|ref|YP_007906745.1| 233 ARLVREVFQLAKEKAPSIIFI-DELDAIAARRTSsdtSGDREVQRTLMQLLSE 284
                                       567888888888888888775.8888888766666778888888888888865 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00023     0.095      20      48 ..     189     219 ..     160     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..-- CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..ev 48 
                                       + +lL+G+ G+GKT l++++a++ + +  +v
  gi|488600274|ref|YP_007906745.1| 189 KGVLLYGPPGTGKTLLAKAVANQTKATfiRV 219
                                       349*******************998875543 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   0.00027      0.11      21      51 ..     191     221 ..     178     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrvig 51 
                                       ++l Gp+GtGKt + ka+++  +a   rv+g
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQTKATFIRVVG 221
                                       6889**************9999988777776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2    0.0018      0.72      36      53 ..     191     208 ..     185     216 .. 0.88
   2 ?    1.1   0.0      0.64   2.6e+02     129     165 ..     235     270 ..     215     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll+G+pgtGKt la  +
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAV 208
                                       69***********99665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralggdensnsdv 165
                                        v+++ + ++e + +  + iD l+++ +    s++  
  gi|488600274|ref|YP_007906745.1| 235 LVREVFQLAKE-KAPSIIFIDELDAIAARRTSSDTSG 270
                                       46777888888.77***********888844444433 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00043      0.17      22      42 ..     191     211 ..     184     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt+la a+a +
  gi|488600274|ref|YP_007906745.1| 191 VLLYGPPGTGKTLLAKAVANQ 211
                                       6789***********999865 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 ?   11.7   0.1   0.00045      0.18      18      51 ..     186     219 ..     178     304 .. 0.75
   2 ?   -1.7   0.0       5.6   2.3e+03       3      19 ..     384     400 ..     316     404 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00045
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyv 51 
                                       ep + +++YGp g GKt L k ++++ +    +v
  gi|488600274|ref|YP_007906745.1| 186 EPPKGVLLYGPPGTGKTLLAKAVANQTKATFIRV 219
                                       56666899***********999999986543333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.6
                          ATPase_2   3 dRekelkeleeilerep 19 
                                        Re  +k +e+i+++++
  gi|488600274|ref|YP_007906745.1| 384 SREDFIKAIEKIMKKDK 400
                                       35555555555555544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       5.9   2.4e+03     141     183 ..      40      81 ..      31      95 .. 0.66
   2 ?   11.0   0.0   0.00045      0.19      14      52 ..     186     222 ..     177     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.9
                        Zeta_toxin 141 ldRyeeevaegRlvpkeeh..deafeglresvealeeekqldrvk 183
                                       ++R e e    R+v+ e++  ++ +++lr+++e+l +  +++ v+
  gi|488600274|ref|YP_007906745.1|  40 YKRLEDE---KRFVETERIryEREVRRLRSEIERLRSPPLIVGVI 81 
                                       4455555...68888876422677888888888888777666655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00045
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpD 52 
                                       e Pk +ll G pG GK+ la+++++++  +  ++r+ + 
  gi|488600274|ref|YP_007906745.1| 186 EPPKGVLLYGPPGTGKTLLAKAVANQT--KATFIRVVGS 222
                                       67999********************98..7777777665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00098       0.4       7      38 ..     184     215 ..     181     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00098
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpt 38 
                                        +++ + v + G+ G+GK+ L+k++a+++k t
  gi|488600274|ref|YP_007906745.1| 184 GIEPPKGVLLYGPPGTGKTLLAKAVANQTKAT 215
                                       577778899*****************998865 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.5    0.0016      0.65      50     100 ..      20      70 ..       5      73 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0016
                            APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                                       e l ++l++le+e  +l +  k+le+e++ +e e+  +e+e ++l  e er
  gi|488600274|ref|YP_007906745.1|  20 EYLIDRLKQLEEEYVRLKNLYKRLEDEKRFVETERIRYEREVRRLRSEIER 70 
                                       445556777777777777777777777777777777777777777666554 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.2   0.00081      0.33     121     178 ..      12      69 ..       1      73 [. 0.85
   2 ?    1.8   0.1       0.3   1.2e+02     116     145 ..     372     402 ..     327     406 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00081
                           DUF2353 121 rhssaeereelvkqlEklkekiqqlerdlkavldekeelvterdaykeKaerLnqeLn 178
                                       ++++ +  e l+ +l +l+e +  l+  +k + dek+ ++ter  y + ++rL  e+ 
  gi|488600274|ref|YP_007906745.1|  12 KEKNVDLSEYLIDRLKQLEEEYVRLKNLYKRLEDEKRFVETERIRYEREVRRLRSEIE 69 
                                       4445677899*******************************************99986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                           DUF2353 116 dlletrhss.aeereelvkqlEklkekiqql 145
                                       +++  r+++   +re+++k++Ek+ +k ++l
  gi|488600274|ref|YP_007906745.1| 372 GMFAIRNEKtIVSREDFIKAIEKIMKKDKKL 402
                                       4444333333789*************99887 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.8    0.0062       2.5       1      40 [.      27      66 ..      27      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0062
                              HALZ  1 KQLErDYdvLKasYdaLksdydsLkkenekLkaelqeLke 40
                                      KQLE +Y  LK  Y  L  +   ++ e+ + + e+++L++
  gi|488600274|ref|YP_007906745.1| 27 KQLEEEYVRLKNLYKRLEDEKRFVETERIRYEREVRRLRS 66
                                      9****************98888888888777777777775 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.7    0.0019      0.77      75     137 ..       9      73 ..       2      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                           DUF4349  75 tsrstsaeDVTeqyvDleaRlkaleasedrllallekak.....svedlleiereLsevqaeiesleg 137
                                       +s +++  D++e ++D   Rlk+le++  rl++l+++ +        + ++ ere+ + ++eie+l++
  gi|488600274|ref|YP_007906745.1|   9 KSIKEKNVDLSEYLID---RLKQLEEEYVRLKNLYKRLEdekrfVETERIRYEREVRRLRSEIERLRS 73 
                                       5666777788888888...8888899888888888885523343345778999************985 PP

>> Troponin  Troponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.8    0.0054       2.2      23      85 ..      14      72 ..       4      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0054
                                      XXXXXXXXXXXXXXXXX.XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Troponin 23 keeerlrvLkerieplkeldglseeqlqelckklheridkleeekydieekvakkdkeieelk 85
                                      k  +  ++L +r ++l+ ++      l++l+k+l +  + +e e+ + e++v++ + eie l+
  gi|488600274|ref|YP_007906745.1| 14 KNVDLSEYLIDRLKQLE-EEY---VRLKNLYKRLEDEKRFVETERIRYEREVRRLRSEIERLR 72
                                      45555566767777777.444...79**********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      919  (0.0512577); expected 358.6 (0.02)
Passed Vit filter:                       179  (0.00998383); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.87u 0.37s 00:00:01.24 Elapsed: 00:00:00.57
# Mc/sec: 2171.68
//
Query:       gi|488600275|ref|YP_007906746.1|  [L=67]
Description: archaeal histone [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   69.6   3.1    2.2e-19   69.5   3.1    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    1.1e-10   42.0   0.5    1.2e-10   41.9   0.5    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    4.4e-07   30.2   0.1    4.7e-07   30.1   0.1    1.1  1  CENP-S         CENP-S protein
    7.6e-07   29.2   0.3    8.1e-07   29.1   0.3    1.0  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    6.2e-05   23.1   0.1    6.9e-05   22.9   0.1    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
     0.0002   21.8   0.3    0.00021   21.7   0.3    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
    0.00046   20.1   0.0    0.00048   20.1   0.0    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
    0.00053   20.1   1.0    0.00059   20.0   1.0    1.0  1  DUF1931        Domain of unknown function (DUF1931)
    0.00071   19.7   1.5    0.00072   19.7   1.5    1.1  1  TAF            TATA box binding protein associated factor (TA
     0.0042   17.1   0.0     0.0046   16.9   0.0    1.1  1  Bromo_TP       Bromodomain associated
  ------ inclusion threshold ------
       0.16   12.2   2.2         12    6.2   0.1    2.2  2  PCP_red        Proto-chlorophyllide reductase 57 kD subunit


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   3.1   1.4e-22   2.2e-19       1      65 []       2      65 ..       2      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.4e-22
                                      XXXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                     CBFD_NFYB_HMF  1 aeLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                      aeLP+a+v+++++++ +a++++ dA   + e++e  ++e++++A+e++k+++rKt+kae+iklA+
  gi|488600275|ref|YP_007906746.1|  2 AELPAAPVERLIRNA-GAKRVSADAVAKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKLAL 65
                                      69*************.***********************************************97 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.5   7.2e-14   1.2e-10      62     129 ..       4      66 ..       1      67 [] 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 7.2e-14
                                       SXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                           Histone  62 iqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                        +++p++R++r+        +r+sa+av  + e+lE+  +e+ + A  +akha R+T+ ++Di+lA++
  gi|488600275|ref|YP_007906746.1|   4 LPAAPVERLIRNAGA-----KRVSADAVAKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKLALK 66 
                                       578999999998876.....**********************************************97 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   2.9e-10   4.7e-07      23      71 ..      18      66 ..       7      67 .] 0.89

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.9e-10
                            CENP-S 23 eveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71
                                        +++ +++a ++e+  +++ +++k     akHA+R+t++++D++L ++
  gi|488600275|ref|YP_007906746.1| 18 AKRVSADAVAKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKLALK 66
                                      456999****************************************876 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 !   29.1   0.3     5e-10   8.1e-07       8      75 ..       4      66 ..       1      67 [] 0.89

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5e-10
                          CENP-T_C  8 lPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                      lPaa v +l +++       ++++++a++++++++++    +++     akHagRKt++++D+ l +k
  gi|488600275|ref|YP_007906746.1|  4 LPAAPVERLIRNA-----GAKRVSADAVAKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKLALK 66
                                      7888888888777.....5569*****************************************98877 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 !   22.9   0.1   4.2e-08   6.9e-05      11      68 ..       9      66 ..       4      67 .] 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.2e-08
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiq 68
                                      ++ ++++ g + ++ + v +++++     +++ + A  +a+ha++k+v+++d++lA++
  gi|488600275|ref|YP_007906746.1|  9 VERLIRNAGAKRVSADAVAKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKLALK 66
                                      7889999*************************************************86 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   1.3e-07   0.00021      24      63 ..      27      66 ..       9      67 .] 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH CS
                       TFIID_20kDa 24 dlLleiaddFvesvtkfacklakhRksdklevrDiqlhle 63
                                        ++ei +d  ++++k+a+++akh   +++ + Di+l l+
  gi|488600275|ref|YP_007906746.1| 27 AKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKLALK 66
                                      4589*********************************998 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     3e-07   0.00048      24      65 ..      25      66 ..       7      67 .] 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                                      HHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXX CS
                       TFIID-18kDa 24 tvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliR 65
                                      +v  + +++++  +e+ ++a++vak+ g++ ++ ED++ +++
  gi|488600275|ref|YP_007906746.1| 25 AVAKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKLALK 66
                                      444555799999*************************98875 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.0   3.6e-07   0.00059       2      55 ..      10      63 ..       9      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.6e-07
                                      HHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-- CS
                           DUF1931  2 erlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPi 55
                                      erl+r+a    v  + ++++ +++e+k  ++  +a e Ak  gr++++ +D+ +
  gi|488600275|ref|YP_007906746.1| 10 ERLIRNAGAKRVSADAVAKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKL 63
                                      89*************************************************976 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 !   19.7   1.5   4.4e-07   0.00072      12      66 .]      12      66 ..       1      66 [. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.4e-07
                                      HHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                               TAF 12 iAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                      +    G + +s++a a + e +e +  ei ++a+   +h+ R++  ++D+  AL+
  gi|488600275|ref|YP_007906746.1| 12 LIRNAGAKRVSADAVAKMVEILEDKATEISKKAVEVAKHAGRKTVKAEDIKLALK 66
                                      555678889999*****************************************98 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.8e-06    0.0046      26      69 ..      27      66 ..       8      67 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.8e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHH CS
                          Bromo_TP 26 esaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLq 69
                                      + ++E L + a    +e++++a + a hagR +++ +D+ l+L+
  gi|488600275|ref|YP_007906746.1| 27 AKMVEILEDKA----TEISKKAVEVAKHAGRKTVKAEDIKLALK 66
                                      34555555555....**************************997 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 ?    6.2   0.1    0.0072        12      24      42 ..       9      27 ..       7      29 .. 0.89
   2 ?    5.9   0.4    0.0094        15      21      42 ..      41      62 ..      38      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0072
                                      HHHHHHHHT-SEE-HHHHH CS
                           PCP_red 24 aEklArerGleeVtvevve 42
                                      +E+l r++G ++V+++ v 
  gi|488600275|ref|YP_007906746.1|  9 VERLIRNAGAKRVSADAVA 27
                                      89*************9885 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0094
                                      HHHHHHHHHHHT-SEE-HHHHH CS
                           PCP_red 21 RraaEklArerGleeVtvevve 42
                                       ++a + A+ +G+++V +e ++
  gi|488600275|ref|YP_007906746.1| 41 SKKAVEVAKHAGRKTVKAEDIK 62
                                      5788899************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); 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:                        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 0.33s 00:00:00.84 Elapsed: 00:00:01.38
# Mc/sec: 146.57
//
Query:       gi|488600276|ref|YP_007906747.1|  [L=116]
Description: hypothetical protein Asulf_00741 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   60.3   5.8      2e-16   60.3   5.8    1.9  2  DUF4405       Domain of unknown function (DUF4405)
  ------ inclusion threshold ------
       0.14   12.3   4.4       0.13   12.5   0.8    2.1  2  SdpI          SdpI/YhfL protein family
        1.1    8.8   8.2       0.27   10.8   4.2    1.9  2  Ni_hydr_CYTB  Prokaryotic cytochrome b561


Domain annotation for each model (and alignments):
>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   5.8   3.3e-20     2e-16       1      66 []       9      75 ..       9      75 .. 0.98
   2 ?    1.0   0.2      0.11   6.4e+02       8      21 ..      96     109 ..      91     115 .. 0.58

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.3e-20
                           DUF4405  1 iidlllllsflvlaiSGillsfavlpsgrgaywa...flglskhqwrdiHeilgllflilvvlHlglhw 66
                                      iid+lll   +++ i+G+ ++ a  psgr+a+++   flgl+k++++d+H+++g++++++ v+Hl l+w
  gi|488600276|ref|YP_007906747.1|  9 IIDVLLLTGLIIMGITGLGMYLA--PSGRVAREThwtFLGLDKSTLGDVHTYFGFVMVAIGVIHLTLNW 75
                                      79*******************99..******************************************** PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                           DUF4405   8 lsflvlaiSGills 21 
                                       ++ l+l+i G+  +
  gi|488600276|ref|YP_007906747.1|  96 VLTLMLVIAGVFVY 109
                                       44445555555544 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.071   4.2e+02      33      44 ..      13      24 ..       4      47 .. 0.62
   2 ?   12.5   0.8   2.1e-05      0.13      26      61 ..      56     106 ..      53     110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.071
                              SdpI 33 wiiaGlilllla 44
                                      ++++Gli++ ++
  gi|488600276|ref|YP_007906747.1| 13 LLLTGLIIMGIT 24
                                      455555555444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                              SdpI  26 hrfagklwiiaGlilllla.................lgavvlvllvlvlllvi 61 
                                       h ++g +++++G+i+l l+                 +  + +vl ++++++ +
  gi|488600276|ref|YP_007906747.1|  56 HTYFGFVMVAIGVIHLTLNwkpltsllknlknsgsdM--AKVVLTLMLVIAGV 106
                                       99**************9999***********877442..22333333333222 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.2   4.6e-05      0.27     106     163 ..      12      72 ..       3      77 .. 0.76
   2 ?    2.4   3.4     0.017     1e+02      42      64 ..      52      74 ..      37     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHHHHHHHHHHT......HHHHHHHH...HTS-THHHHHHH.HHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB 106 lllyvllvvliltGlllsf......aatagfplllddkggaqlarelHellaaallafvvlHia 163
                                       +ll++ l+++ +tGl ++       a ++ + +    +  ++ ++ +H +++++++a  v+H+ 
  gi|488600276|ref|YP_007906747.1|  12 VLLLTGLIIMGITGLGMYLapsgrvARETHWTF---LGLDKSTLGDVHTYFGFVMVAIGVIHLT 72 
                                       6889999**********9877665533333333...5556778999999999999999999986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.017
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB 42 aralHklaGlvllalllfrllwl 64
                                      + ++H ++G+v++a+ ++ l + 
  gi|488600276|ref|YP_007906747.1| 52 LGDVHTYFGFVMVAIGVIHLTLN 74
                                      45678888888887775555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 744.87
//
Query:       gi|488600277|ref|YP_007906748.1|  [L=81]
Description: hypothetical protein Asulf_00742 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.53
# Mc/sec: 456.62
//
Query:       gi|488600278|ref|YP_007906749.1|  [L=269]
Description: translation initiation factor 2 subunit alpha (aeIF-2a) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   75.7   0.3    6.5e-21   74.6   0.2    1.7  2  EIF_2_alpha      Eukaryotic translation initiation factor 2 a
    1.3e-15   57.4   0.3    3.6e-15   56.1   0.3    1.8  1  S1               S1 RNA binding domain
  ------ inclusion threshold ------
      0.051   14.4   1.6       0.16   12.7   1.6    1.9  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
       0.21   11.8   3.0        3.5    7.9   0.1    2.9  3  PurS             Phosphoribosylformylglycinamidine (FGAM) syn


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.7   7.8e+03      72      84 ..      59      71 ..      48      89 .. 0.73
   2 !   74.6   0.2   1.4e-24   6.5e-21       4     116 .]     131     238 ..     129     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                                      HHHHHHHHHHHST CS
                       EIF_2_alpha 72 veaIkeaLkagee 84
                                      ++ I++  k+g++
  gi|488600278|ref|YP_007906749.1| 59 IKDIRDHVKKGQK 71
                                      7777777777666 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 1.4e-24
                                       CTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHH CS
                       EIF_2_alpha   4 evgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaL 79 
                                       evg kl ++y+++y +F ++  ++++++ ++   e++++a+ ei+k+++kp+kv+ir+ ++l++ ++dG+e+Ik+aL
  gi|488600278|ref|YP_007906749.1| 131 EVGKKLLKEYDTIYGVFeDVFYEGHKAILDI-AGEKLAKAIEEIAKENIKPHKVEIRGIFQLKSNAPDGIERIKSAL 206
                                       6899*************99999999977775.579****************************************** PP

                                       HHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  80 kageeasneeeveeeeevkikliapPeYvltvetldk 116
                                        + ++ s      + +++ki ++++P+Y++ ve++d+
  gi|488600278|ref|YP_007906749.1| 207 LEINNLS-----LDGVNIKIDYVGAPKYRIIVESEDY 238
                                       *555544.....456*******************997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.3     8e-19   3.6e-15       2      75 .]      17      91 ..      16      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 8e-19
                                      STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      p kge+v G+Vt+v ++GafV l+  ++ eg+v++se++    ++d+ +++k+G++v  kvl+++ +r+ i+lsik
  gi|488600278|ref|YP_007906749.1| 17 PSKGEIVIGTVTRVLDFGAFVSLDeyENREGLVHISEVAPG-WIKDIRDHVKKGQKVVCKVLDTNPKRGHIDLSIK 91
                                      88*************************************99.9*******************************97 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.6   3.7e-05      0.16      40      81 ..     215     259 ..     152     261 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                                       EEEEEEEEEC...TTEEEEEEEEESSHHHHHHHHHHHHHHHHHHC CS
                   Ribosomal_S30AE  40 kkvevtirla...kgkviraeeesedlyaaidlavdklerqlrky 81 
                                         v+++i+++   k ++i ++e  ++ ++a+++avdk+ ++++k 
  gi|488600278|ref|YP_007906749.1| 215 DGVNIKIDYVgapKYRIIVESEDYKTAEKALKKAVDKVLKKIKKL 259
                                       458999999866555666666778*******************95 PP

>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.85   3.8e+03      41      59 ..      86     104 ..      84     108 .. 0.83
   2 ?    7.9   0.1   0.00078       3.5      10      49 ..     156     197 ..     150     211 .. 0.87
   3 ?    3.1   0.1     0.024   1.1e+02      41      65 ..     229     253 ..     209     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.85
                                       EEEEEE-SSHHHHHHHHHH CS
                              PurS  41 ieleleaedeeeaeeevee 59 
                                       i+l++++ +e++ +e+v++
  gi|488600278|ref|YP_007906749.1|  86 IDLSIKDVNERQRREKVQQ 104
                                       7899999999999999987 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00078
                                       TTS--HHHHHHHHHHHHTTHTTEE..EEEEEEEEEEEEE-SS CS
                              PurS  10 kgvlDpqGkavkkalkslgyeeve..dvrvgkyieleleaed 49 
                                       k +lD  G+ ++ka++++  e+++  +v +  +++l+ +a d
  gi|488600278|ref|YP_007906749.1| 156 KAILDIAGEKLAKAIEEIAKENIKphKVEIRGIFQLKSNAPD 197
                                       78****************999999889999999999988876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.024
                                       EEEEEE-SSHHHHHHHHHHHHHHTT CS
                              PurS  41 ieleleaedeeeaeeeveemceklL 65 
                                       +++ +e+ed ++ae+ ++++ +k+L
  gi|488600278|ref|YP_007906749.1| 229 YRIIVESEDYKTAEKALKKAVDKVL 253
                                       68899***************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1093  (0.0609627); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); 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):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1744.48
//
Query:       gi|488600279|ref|YP_007906750.1|  [L=259]
Description: TIGR00162 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-51  175.5   0.1    1.7e-51  175.2   0.1    1.0  1  PAC2      PAC2 family
  ------ inclusion threshold ------
       0.12   12.7   0.1       0.32   11.4   0.0    1.7  2  DUF5099   Domain of unknown function (DUF5099)


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 !  175.2   0.1   1.9e-55   1.7e-51       2     210 ..      24     236 ..      23     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 1.9e-55
                                       EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEETTT...SEEEEEEE CS
                              PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyakdsg..srdllvlqg 74 
                                       i+G+pgiG+Vg+l++d+L+ +l+aek  ei+s y +p     p+v+vee+   +++++++y+++++    dl++l+g
  gi|488600279|ref|YP_007906750.1|  24 IEGLPGIGHVGKLVADHLVKELKAEKAVEIYSHY-FP-----PQVMVEEDgtIKMPKNEVYVHKANdvAPDLVILVG 94 
                                       9*********************************.**.....********7777777888999444479******** PP

                                       E-HSCHHH...HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH......CT..-C CS
                              PAC2  75 repilqye...efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele......es..ey 140
                                         +++ +e   e+++a +d+a+++gvk++++Lgg++ g++     ++p  v gaa+d++l+eel+      e+  ++
  gi|488600279|ref|YP_007906750.1|  95 DFQSISNEghfELVNAYIDIAKKFGVKRIFTLGGYGIGKLV----EEP-YVLGAANDPKLIEELSqydiqfEKgePG 166
                                       555555555555************************99996....688.89*************64655542288** PP

                                       EEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHH CS
                              PAC2 141 ggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqle 210
                                       ggi+g++gl+l+ a+ +gi++++l++ +++y++dPk+a+a+le+l k+l+++v++e Lee+a+e+e+ ++
  gi|488600279|ref|YP_007906750.1| 167 GGIIGASGLILGVAQLEGIESACLMGVTSGYMVDPKSAKAVLEVLMKMLKIDVSVEALEERAREMERIIA 236
                                       ******************************************************************9886 PP

>> DUF5099  Domain of unknown function (DUF5099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.6e-05      0.32      15      87 ..      37     117 ..      30     127 .. 0.76
   2 ?   -2.5   0.0      0.78     7e+03       8      27 ..     234     253 ..     230     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                           DUF5099  15 vskeeikklkkkygik........ivkligekkdkvlikeeidfenksvlpdlvilcndklvFklksplllykaEil 83 
                                       v ++++k+lk ++ ++         v++ ++ + k++ +e    + ++v pdlvil+ d      +  + l++a i 
  gi|488600279|ref|YP_007906750.1|  37 VADHLVKELKAEKAVEiyshyfppQVMVEEDGTIKMPKNEVYVHKANDVAPDLVILVGDFQSISNEGHFELVNAYID 113
                                       556677778877777777888876777777777777776666669*************9999999999999999887 PP

                           DUF5099  84 fkrk 87 
                                       + +k
  gi|488600279|ref|YP_007906750.1| 114 IAKK 117
                                       7766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.78
                           DUF5099   8 iinkysevskeeikklkkky 27 
                                       ii ++ e+++++i++ k+ +
  gi|488600279|ref|YP_007906750.1| 234 IIAHIREMQETTIQQWKSDE 253
                                       78888899999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      814  (0.0454013); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1633.65
//
Query:       gi|488600280|ref|YP_007906751.1|  [L=240]
Description: hypothetical protein Asulf_00745 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.3    2.2e-30  106.4   0.3    1.0  1  DUF72         Protein of unknown function DUF72
  ------ inclusion threshold ------
      0.027   13.9   0.0      0.037   13.5   0.0    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.3   2.4e-34   2.2e-30      12     217 ..      14     235 ..      10     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 2.4e-34
                                       HHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-...TT-EEEEE--CCCCCS..............G..-.SCHHHH CS
                             DUF72  12 eyYarhfntVEinstFYalpspetvakwaaqtp...edFrFavKapraithe.........r....n..e.daeeal 69 
                                       + Y++ f++VE++ tFY +p+ +++++w+++t     dF+F++Ka++ ith          +    n  + +  e++
  gi|488600280|ref|YP_007906751.1|  14 NKYFSFFDVVEVQKTFYDFPRIDSIKRWREKTDsinRDFEFIIKANQLITHPpssptykksKlkpkNsgFfRMVEEV 90 
                                       78*****************************985557**************54445554441445423533445555 PP

                                       HHHHHH.CHHHC.T-EEEEEEE--TT--S.HHHHHHHHHHTTTS-....S.EEEE--BGGGH.....HHHHHHHHTT CS
                             DUF72  70 erflesalepLg.eklgpllfQlppsfkfdeenlerLeaflaalp....l.lavEvRhrswf.....ellellrehg 135
                                       ++ l++++e     ++  +lfQ ppsfk++ en+e++e+f++a++      + +E+R   w      + le l +  
  gi|488600280|ref|YP_007906751.1|  91 TEALKKTVEIADiLRCDKILFQTPPSFKHSSENIENMERFFTAMKnygkFrIILELRG--WKeaeilDALERLSSFS 165
                                       555555344442246666***********988********99888888955******8..86654444555555566 PP

                                       -EEEEE--SSC----.----SSTEEEEEE--S....HHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCH CS
                             DUF72 136 vavvldepkkpklpl.edvttadfvyvRlhgr....eeryayrYseeelaewaerikawaaegrevyvffnndaegq 207
                                        ++++d       p+      ++f y+Rlhgr    +  y+y+Ys+ el  + + +k+        yv+fnn++   
  gi|488600280|ref|YP_007906751.1| 166 PVHCVD-------PFrSRQLSGEFQYFRLHGRyesnRIIYSYKYSNSELSSLKKLVKK-------GYVMFNNKY--- 225
                                       668889.......342334448***********9963689********9988888866.......59****966... PP

                                       HHHHHHHHHH CS
                             DUF72 208 aplnaraLae 217
                                       + ++a++++e
  gi|488600280|ref|YP_007906751.1| 226 MLEDAMRFKE 235
                                       5777777765 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 ?   13.5   0.0   4.1e-06     0.037      65     147 ..      87     161 ..      35     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-06
                                       HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHH...HHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSS CS
                      AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGtagagpkgsee...eawerlaeslneladyaekegvklalEtlagsgve 138
                                        ee  +alk+++e+a  L ++ + +++     ++ ++     e+ er+  +++  +++      +++lE   ++++e
  gi|488600280|ref|YP_007906751.1|  87 VEEVTEALKKTVEIADILRCDKILFQTP----PSFKHSSeniENMERFFTAMKNYGKF------RIILELRGWKEAE 153
                                       56779*********************66....33333330135666666655555555......9999999999966 PP

                                       STCHHHHHH CS
                      AP_endonuc_2 139 lgdeelarl 147
                                        + + l+rl
  gi|488600280|ref|YP_007906751.1| 154 IL-DALERL 161
                                       65.554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1538.46
//
Query:       gi|488600281|ref|YP_007906752.1|  [L=188]
Description: hypothetical protein Asulf_00746 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  181.9   0.0    8.4e-54  181.8   0.0    1.0  1  DUF99     Protein of unknown function DUF99
     0.0064   16.8   0.0      0.011   16.1   0.0    1.4  1  DUF4062   Domain of unknown function (DUF4062)


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 !  181.8   0.0   9.4e-58   8.4e-54       2     182 ..       3     180 ..       2     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.8 bits;  conditional E-value: 9.4e-58
                                       GSEEEEEEEEE..........-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-.TTTTEEEEEES CS
                             DUF99   2 eirvlGiddsfferkk.....kdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrl.eredirvvlld 72 
                                       ++r++G+ddsf  + +     k++k+v+vG+v +++ +++g+++ r++vdG+D+t+++i++vkr+ ++ ++++++l+
  gi|488600281|ref|YP_007906752.1|   3 NWRFVGFDDSFRIS-StvsdlKGEKAVIVGCV-TSGFYPEGFMVDRIEVDGDDSTDKMIRMVKRSkFHVQLKCIFLS 77 
                                       79*********653.2366669**********.6777**************************************** PP

                                       SSEETTTEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEES CS
                             DUF99  73 GitiagFNvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravG 149
                                       G+t++gFN++D++r++eetg+ v++v+r++pd++++++aL     + e+R+ liek+ +++ +v +    l+++ +G
  gi|488600281|ref|YP_007906752.1|  78 GLTFGGFNIADISRIAEETGIAVVVVMRKKPDFSSIKHALC--SANLEDRWLLIEKA-GEVFNVGE----LFIQKAG 147
                                       *****************************************..568899********.99999988....******* PP

                                       S-HHHHHHHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 150 ieleeaaklvrkltlegriPEPlRvAhliAsal 182
                                       ++leea+k +r  +++ +iPEPlR+Ah++Asa+
  gi|488600281|ref|YP_007906752.1| 148 CTLEEAKKFIRLSVKDAKIPEPLRLAHMVASAI 180
                                       *******************************98 PP

>> DUF4062  Domain of unknown function (DUF4062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.2e-06     0.011       4      57 ..      15      69 ..      14      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-06
                           DUF4062  4 iSStfrdlkeeRealieallelglep..vgmeefaardqsqlelcleevdecdifi 57
                                      iSSt++dlk e + +++ ++  g+ p  +++ + + + +++ + +++ v+++++ +
  gi|488600281|ref|YP_007906752.1| 15 ISSTVSDLKGEKAVIVGCVT-SGFYPegFMVDRIEVDGDDSTDKMIRMVKRSKFHV 69
                                      9******************9.9999987777789999999999999******9544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.56
# Mc/sec: 1016.98
//
Query:       gi|488600282|ref|YP_007906753.1|  [L=88]
Description: DNA-directed RNA polymerase, subunit L [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   78.5   0.1    2.8e-22   78.3   0.1    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
     0.0026   17.1   0.0     0.0032   16.9   0.0    1.2  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.1   3.2e-26   2.8e-22       2      73 ..      13      83 ..      12      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 3.2e-26
                                      EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdele 73
                                      ++++i+gEDhTL+nlL+h ll+++sV +a+Y+ipHPl+++ +l + t+ +++p+ ++k+  ++++++cde+ 
  gi|488600282|ref|YP_007906753.1| 13 IRLKIKGEDHTLLNLLQHNLLEDESVVIAKYDIPHPLIDEAELIVRTN-GEDPIAVIKRVNERIIAECDEIL 83
                                      6799*******************************************7.6*******************985 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 !   16.9   0.0   3.6e-07    0.0032       3      58 ..      16      68 ..      14      82 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.6e-07
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  3 llrgvdhtlgNaLRrillsevpgvaiea.....................pvvkvntdkdklilevetdgslkPeeal 58
                                       ++g+dhtl N L   ll e ++v i++                     p                         ++
  gi|488600282|ref|YP_007906753.1| 16 KIKGEDHTLLNLLQHNLL-EDESVVIAKydiphplideaelivrtngedP-----------------------IAVI 68
                                      699***************.********99998855555555554444443.......................3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.55
# Mc/sec: 483.40
//
Query:       gi|488600283|ref|YP_007906754.1|  [L=183]
Description: putative RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-11   43.5   0.0    3.4e-11   42.7   0.0    1.4  1  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
    6.2e-07   30.0   0.1    1.1e-06   29.2   0.1    1.6  1  EXOSC1          Exosome component EXOSC1/CSL4
     0.0013   18.6   0.6     0.0023   17.8   0.6    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
     0.0042   17.1   0.1     0.0078   16.2   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0077   16.1   1.1      0.019   14.9   1.1    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.019   15.0   0.0    1.4  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.019   13.6   0.5      0.072   11.7   0.1    1.8  2  FapA            Flagellar Assembly Protein A
       0.03   14.4   0.4      0.051   13.6   0.4    1.3  1  DZR             Double zinc ribbon
      0.039   13.6   0.1      0.051   13.2   0.1    1.2  1  TackOD1         Thaumarchaeal output domain 1
      0.066   12.9   2.9        0.2   11.4   2.9    1.8  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.094   12.7   4.5        2.4    8.2   0.1    2.5  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.095   12.8   0.2       0.18   12.0   0.2    1.4  1  DUF2318         Predicted membrane protein (DUF2318)
       0.11   12.4   4.7       0.48   10.4   0.3    2.4  2  zinc_ribbon_4   zinc-ribbon domain
       0.13   12.3   1.0       0.79    9.8   0.0    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.16   11.8   1.0       0.28   11.0   1.0    1.3  1  zf-RING_4       RING/Ubox like zinc-binding domain
       0.37   10.4   2.7       0.74    9.4   0.1    2.6  3  TF_Zn_Ribbon    TFIIB zinc-binding
       0.43   10.8   2.6        2.8    8.2   3.0    2.1  2  zf-RING_7       C4-type zinc ribbon domain
       0.59    9.9   3.7       0.78    9.5   2.1    2.0  2  A2L_zn_ribbon   A2L zinc ribbon domain
        1.3    8.5   7.4        0.6    9.6   3.8    2.2  3  zf-ribbon_3     zinc-ribbon domain
        3.6    7.4   9.9       0.38   10.5   4.7    2.1  1  zinc_ribbon_2   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 !   42.7   0.0   3.8e-14   3.4e-11       1      36 [.       5      40 ..       5      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 3.8e-14
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtve 36
                                      +V PG+ l+ +eef+ G+G+Y+++g++yAsvaG + 
  gi|488600283|ref|YP_007906754.1|  5 FVFPGDKLGIAEEFICGEGVYEEDGELYASVAGKLV 40
                                      79*******************************876 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   1.2e-09   1.1e-06       1      58 [.      54     119 ..      54     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.2e-09
                                       -S-T..T-EEEEEEEEEESSEEEEEEEEECTB.....SBCCCEEECCCTTSS--STS.TTSSCCHC CS
                            EXOSC1   1 lPke..gdvVLarvtrlrkkqalveilsvege.....nnvlsdsgvgangegavkei.eaggglds 58 
                                       +P++  gd +L+rv+++r+++al+e++ + g      + +++ +++++ ++ + k+i  a+ + d 
  gi|488600283|ref|YP_007906754.1|  54 IPNIerGDTILGRVVDVRNSIALIELSRKSGFdrdlmHTGIAALHISNIQNEYLKDInSAVKYMDV 119
                                       5766669*********************9988888989999****************999999887 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   2.6e-06    0.0023       4      34 ..     143     173 ..     141     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                       Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgtpyHraC 34 
                                       + +C+ C++el ++  +  Cp+Cg +  r+ 
  gi|488600283|ref|YP_007906754.1| 143 KAICSECRHELLKDGKVLKCPNCGNVERRKI 173
                                       689*********************9887765 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 !   16.2   0.1   8.7e-06    0.0078      38      96 ..     101     169 ..      90     176 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.7e-06
                                       T--HHHHHHHHHHHHCC.TTTT-EEE..........EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  38 gvepeaLefafellaegtvlegaeLe..........ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       ++++e+L+ + ++++  +v++  +++           +   vk+ C+eC++e  ++ k l+Cp+Cg+ +
  gi|488600283|ref|YP_007906754.1| 101 NIQNEYLKDINSAVKYMDVVKARVIDpkllklstkeSDMGVVKAICSECRHELLKDGKVLKCPNCGNVE 169
                                       555556555555555333333322223333333333445568999********9887789******865 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.1   2.1e-05     0.019      30      58 ..     145     171 ..     144     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadr 58 
                                        CseC +++ +  +g+++kCpnCg +  r
  gi|488600283|ref|YP_007906754.1| 145 ICSECRHELLK--DGKVLKCPNCGNVERR 171
                                       6**********..***********98777 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 ?   15.0   0.0   2.1e-05     0.019      30      72 ..     134     174 ..     101     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                       Zn_Tnp_IS91  30 CrtaalGfaryeCeeCghekivyfsCksrhCpsCqkkateewl 72 
                                        +++++G+ +  C+eC+he  +    k   Cp+C++ ++++ +
  gi|488600283|ref|YP_007906754.1| 134 TKESDMGVVKAICSECRHE--LLKDGKVLKCPNCGNVERRKIA 174
                                       56789***********985..678899999*******999876 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     8e-05     0.072     145     189 ..      16      56 ..      10      61 .. 0.85
   2 ?    0.7   0.1      0.18   1.6e+02     298     386 ..      61     156 ..      52     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8e-05
                              FapA 145 vplkagkgtevseedgnkliAaidGrpvvkkngisVdpvleikgd 189
                                        ++ +g+g++   ed  +l+A+++G++vvk++ ++V++v +i  +
  gi|488600283|ref|YP_007906754.1|  16 EEFICGEGVYE--ED-GELYASVAGKLVVKDRVLRVESVNKIP-N 56 
                                       67999*****8..56.5677******************99987.5 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                              FapA 298 gkivggnikalkevkakklGselgtkteiev.gldepelkeklkeleeeleeleeeleklkkk......ikklpklk 367
                                        +i g  + + +++ + +l  ++g   ++   g+  +++ + ++e  +++++  ++++ +k++      +k+  k++
  gi|488600283|ref|YP_007906754.1|  61 DTILGRVVDVRNSIALIELSRKSGFDRDLMHtGIAALHISNIQNEYLKDINSAVKYMDVVKARvidpklLKLSTKES 137
                                       56777778888888888888888888888888888555555559999999999999999999977777555555555 PP

                              FapA 368 aekqlesekkeqlkkllet 386
                                         + +++ ++e+ ++ll++
  gi|488600283|ref|YP_007906754.1| 138 DMGVVKAICSECRHELLKD 156
                                       5666666666666666655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   5.7e-05     0.051      13      36 ..     144     167 ..     138     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-05
                               DZR  13 rfCseCgtklkavaaedrCpsCge 36 
                                         CseC+++l +  +  +Cp+Cg 
  gi|488600283|ref|YP_007906754.1| 144 AICSECRHELLKDGKVLKCPNCGN 167
                                       57*******99999999*****97 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.7e-05     0.051      85     115 ..     141     171 ..      93     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-05
                           TackOD1  85 nvrevCpkCkSidieeqelihhftCgnvgpe 115
                                        v+ +C++C+   ++  +++++ +Cgnv+  
  gi|488600283|ref|YP_007906754.1| 141 VVKAICSECRHELLKDGKVLKCPNCGNVERR 171
                                       57889**********************9865 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.9   0.00022       0.2       2      24 ..     145     166 ..     145     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                       B-SSS--B----SSS----SSS- CS
                    DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCG 24 
                                       iC eC +e  lk g +++C +CG
  gi|488600283|ref|YP_007906754.1| 145 ICSECRHEL-LKDGKVLKCPNCG 166
                                       8****9986.9***********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 ?    5.3   1.3     0.022        19      21      28 ..     145     152 ..     144     154 .. 0.94
   2 ?    8.2   0.1    0.0027       2.4      15      27 ..     155     167 ..     153     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                    PhnA_Zn_Ribbon  21 vCpeCahE 28 
                                       +C+eC hE
  gi|488600283|ref|YP_007906754.1| 145 ICSECRHE 152
                                       9******9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
                    PhnA_Zn_Ribbon  15 edgallvCpeCah 27 
                                        dg +l Cp+C++
  gi|488600283|ref|YP_007906754.1| 155 KDGKVLKCPNCGN 167
                                       7999*******85 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2    0.0002      0.18      16      60 ..     125     168 ..     111     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                           DUF2318  16 kevrflvvkksdgklrvaldaCevCekkgYvqegeelvCknCgvr 60 
                                        + ++l + ++++ + v+  +C+ C+++   ++g+ l C nCg++
  gi|488600283|ref|YP_007906754.1| 125 IDPKLLKLSTKESDMGVVKAICSECRHE-LLKDGKVLKCPNCGNV 168
                                       45678888999999***********875.6799*********985 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.5     0.076        68      24      33 ..     142     151 ..     137     153 .. 0.83
   2 ?   10.4   0.3   0.00053      0.48      21      34 ..     155     168 ..     152     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.076
                     zinc_ribbon_4  24 vkvrCskCgh 33 
                                       vk+ Cs C+h
  gi|488600283|ref|YP_007906754.1| 142 VKAICSECRH 151
                                       6899****99 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00053
                     zinc_ribbon_4  21 akgvkvrCskCghv 34 
                                       ++g+ ++C++Cg+v
  gi|488600283|ref|YP_007906754.1| 155 KDGKVLKCPNCGNV 168
                                       68999*******97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4      0.57   5.1e+02      40      45 ..     146     151 ..     142     152 .. 0.83
   2 ?    9.8   0.0   0.00088      0.79      19      38 ..     160     182 ..     153     183 .] 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.57
                     Zn_Tnp_IS1595  40 CkeCrk 45 
                                       C+eCr+
  gi|488600283|ref|YP_007906754.1| 146 CSECRH 151
                                       999998 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00088
                     Zn_Tnp_IS1595  19 fvCPhCgsrkayrikt...rglf 38 
                                         CP+Cg+ + ++i++    g++
  gi|488600283|ref|YP_007906754.1| 160 LKCPNCGNVERRKIASdygSGKW 182
                                       46******999999876666665 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   0.00032      0.28      24      43 ..     145     165 ..     144     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                         zf-RING_4  24 iClfCyhrilee.eegrCPaC 43 
                                       iC  C h++l++ +  +CP+C
  gi|488600283|ref|YP_007906754.1| 145 ICSECRHELLKDgKVLKCPNC 165
                                       9*********9735789**** PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.1   3.6e+03      19      23 ..      17      21 ..      15      22 .. 0.75
   2 ?   -0.4   0.1       0.9   8.1e+02      21      25 ..     145     149 ..     143     158 .. 0.67
   3 ?    9.4   0.1   0.00083      0.74       2      10 ..     161     169 ..     160     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.1
                                      CEEES CS
                      TF_Zn_Ribbon 19 elvCt 23
                                      e++C+
  gi|488600283|ref|YP_007906754.1| 17 EFICG 21
                                      89997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.9
                                       EESSS CS
                      TF_Zn_Ribbon  21 vCtdC 25 
                                       +C++C
  gi|488600283|ref|YP_007906754.1| 145 ICSEC 149
                                       67776 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00083
                                       EETTTTCEE CS
                      TF_Zn_Ribbon   2 kCPnCgstn 10 
                                       kCPnCg+ +
  gi|488600283|ref|YP_007906754.1| 161 KCPNCGNVE 169
                                       899999954 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       2.3     2e+03      23      29 ..     142     149 ..     125     151 .. 0.70
   2 ?    8.2   3.0    0.0032       2.8      16      30 ..     152     166 ..     141     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.3
                                       -.EE-TTT CS
                         zf-RING_7  23 v.vtCpeC 29 
                                       v + C eC
  gi|488600283|ref|YP_007906754.1| 142 VkAICSEC 149
                                       45789999 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0032
                                       HHCCSTB-EE-TTT- CS
                         zf-RING_7  16 elragdevvtCpeCG 30 
                                       el + ++v +Cp+CG
  gi|488600283|ref|YP_007906754.1| 152 ELLKDGKVLKCPNCG 166
                                       5566789*******9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.6   3.3e+03      11      22 ..      21      31 ..      20      32 .. 0.80
   2 ?    9.5   2.1   0.00087      0.78       5      31 ..     145     169 ..     143     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.6
                     A2L_zn_ribbon 11 gngilnseqgyl 22
                                      g+g++  e+g+l
  gi|488600283|ref|YP_007906754.1| 21 GEGVY-EEDGEL 31
                                      68888.999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00087
                     A2L_zn_ribbon   5 vCsvCggngilnseqgylvCieCgasf 31 
                                       +Cs C+++ +  ++   l C++Cg+++
  gi|488600283|ref|YP_007906754.1| 145 ICSECRHELL--KDGKVLKCPNCGNVE 169
                                       7******965..69999*******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 ?   -3.5   0.1       9.2   8.2e+03       8      10 ..      20      22 ..      19      24 .. 0.59
   2 ?    9.6   3.8   0.00067       0.6       4      24 ..     145     167 ..     142     168 .. 0.79
   3 ?    9.3   1.0   0.00081      0.73       4      11 ..     161     168 ..     158     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.2
                       zf-ribbon_3  8 CGa 10
                                      CG+
  gi|488600283|ref|YP_007906754.1| 20 CGE 22
                                      664 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00067
                       zf-ribbon_3   4 rCPnCGa.plssd.dnvCpyCGt 24 
                                        C++C + +l+++ + +Cp+CG 
  gi|488600283|ref|YP_007906754.1| 145 ICSECRHeLLKDGkVLKCPNCGN 167
                                       79999999999883458999997 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00081
                       zf-ribbon_3   4 rCPnCGap 11 
                                       +CPnCG++
  gi|488600283|ref|YP_007906754.1| 161 KCPNCGNV 168
                                       68888876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.7   0.00043      0.38       2      20 ..     146     166 ..     145     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00043
                     zinc_ribbon_2   2 CpnCGael.qdnakF.CpyCG 20 
                                       C++C +el +d+ +  Cp+CG
  gi|488600283|ref|YP_007906754.1| 146 CSECRHELlKDGKVLkCPNCG 166
                                       ********77988888****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1108.69
//
Query:       gi|488600284|ref|YP_007906755.1|  [L=76]
Description: hypothetical protein Asulf_00749 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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      0.002   18.3   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 !   18.3   0.0   1.1e-07     0.002       2      62 ..       6      75 ..       5      76 .] 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-07
                                      EEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHH..........ESEEEEESSCSSSEHHHHH CS
                      Response_reg  2 livdDdplvrellrqlleeegyeevaeaedgkealellkeek..........vdlillDinmpgmdGlell 62
                                      ++v+Dd+  + l+++  +  g    ++++d +ea+++l +e+          +d+ill+++mp+ +G+e+l
  gi|488600284|ref|YP_007906755.1|  6 MLVEDDENDIFLIESSEKVGGG-LLTVTRDRDEAIQYLSREEryanrerfpiPDMILLNLKMPRKSGFEVL 75
                                      5677777777777777663333.57889999999999965555777888999*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 566.22
//
Query:       gi|488600285|ref|YP_007906756.1|  [L=729]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-38  129.9   3.4      1e-14   54.6   0.0    4.8  4  PAS_9         PAS domain
    1.8e-37  128.0   0.0      1e-11   45.1   0.0    3.3  3  PAS_4         PAS fold
    3.9e-27   94.4   0.0    1.1e-13   51.3   0.0    2.5  2  PAS_3         PAS fold
    4.3e-26   91.1   0.0    9.3e-12   45.0   0.0    3.5  3  PAS           PAS fold
    9.9e-19   66.9   0.0    8.1e-08   32.1   0.0    3.7  3  PAS_8         PAS domain
    6.2e-17   61.8   0.2    3.2e-16   59.5   0.2    2.3  1  Response_reg  Response regulator receiver domain
      2e-06   27.9   0.0     0.0053   16.9   0.0    3.2  3  PAS_11        PAS domain
    3.9e-06   27.2   0.0    1.7e-05   25.2   0.0    2.0  2  GAF_2         GAF domain
    1.9e-05   24.6   0.0    9.4e-05   22.4   0.0    2.3  1  HisKA         His Kinase A (phospho-acceptor) domain
    0.00091   19.1   0.0     0.0023   17.9   0.0    1.6  1  MEKHLA        MEKHLA domain
  ------ inclusion threshold ------
      0.011   15.5   1.6        3.2    7.6   0.3    2.8  2  dNK           Deoxynucleoside kinase
      0.022   15.1   0.0      0.052   13.9   0.0    1.6  1  GAF_3         GAF domain
      0.036   14.3   0.2       0.11   12.7   0.2    1.7  1  DUF5618       Domain of unknown function (DUF5618)
      0.063   12.9   7.1       0.45   10.1   0.2    3.0  4  PAS_12        UPF0242 C-terminal PAS-like domain
       0.11   12.8   0.2       0.11   12.8   0.2    2.3  3  Uso1_p115_C   Uso1 / p115 like vesicle tethering protein, C t
       0.14   11.8   0.0       0.29   10.7   0.0    1.4  1  NAPRTase      Nicotinate phosphoribosyltransferase (NAPRTase)


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0     9e-18     1e-14       5     104 .]     153     251 ..     149     251 .. 0.86
   2 !   53.4   0.3   2.2e-17   2.5e-14       3     103 ..     276     376 ..     274     377 .. 0.91
   3 !   17.4   0.0   3.6e-06     0.004       2     104 .]     401     493 ..     400     493 .. 0.77
   4 ?    1.1   0.0      0.42   4.7e+02      53      97 ..     569     616 ..     542     619 .. 0.71

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 9e-18
                             PAS_9   5 lidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                        + +pdg+ ++aN+  l+ +Gy++e +   s++d++  ++ ++a ++l++++ +g+  e ++e+ + +++g+++wv+
  gi|488600285|ref|YP_007906756.1| 153 YLLTPDGTFIDANKLTLNTFGYTKESLGKLSFKDIIadEHLEKALNDLQEIVSSGK--EISQEYLCKTRDGKQIWVE 227
                                       3456********************************66666666666666666666..******************* PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       ++  p+++ +g++v+i +i rD+t+
  gi|488600285|ref|YP_007906756.1| 228 IRSHPIFE-NGKIVAIQGIARDVTD 251
                                       ******96.68999999******96 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 2.2e-17
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk..kerevevvlirkngetfw 77 
                                        i+i+n  g+ + +N++++++lGys+ee++gk++++++ +++ ane ++++ ++ r+  + +  e++   k+g+++ 
  gi|488600285|ref|YP_007906756.1| 276 LIVITNLRGEFIEVNKTFEKVLGYSKEEIIGKNYREFL-PEECANEIFKEYNRAFRSgkNIYGIELEVFAKDGKKIV 351
                                       68999*********************************.77777777777777777788****************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDit 103
                                        + +++ +k+ +g++v++ + +rDit
  gi|488600285|ref|YP_007906756.1| 352 LEGNVRMIKE-NGKIVAFHGNFRDIT 376
                                       ********85.68899999******9 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.6e-06
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                         i+i +++g  l  N+a++  +   + + +gks+ ++f + + a++r++ + ++ +    e  + +  +nge+f  
  gi|488600285|ref|YP_007906756.1| 401 SHIAILDENGVFLELNPAMKSSI---KLDAVGKSLYEIF-PRDVAKKRMDYLKKMFE--TNEIIIFEDSRNGEYFR- 470
                                       5688989***666*******998...6889*********.55555555555555555..66666666667776666. PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                          ++p+  +++++++  +i++D+te
  gi|488600285|ref|YP_007906756.1| 471 -NFLVPLELKGKRYCL--LISKDLTE 493
                                       .7779**999999999..*******8 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.42
                             PAS_9  53 aleqgrk......kerevevvlirkngetfwvlltaspvkdddgelvgiiv 97 
                                       +l++++k      + +++e  +   +g  f   + ++p+k dd + +g+i 
  gi|488600285|ref|YP_007906756.1| 569 MLKALQKdgfivqNIKDREENCPFYDGDAFS--CIVFPMKVDD-TTKGFIT 616
                                       4555554455666777888888888888888..9999998764.5555555 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   8.9e-15     1e-11       1     110 []     145     254 ..     145     254 .. 0.96
   2 !   42.4   0.0   5.9e-14   6.6e-11       1     110 []     270     380 ..     270     380 .. 0.97
   3 !   36.9   0.0     3e-12   3.4e-09       1     108 [.     396     494 ..     396     496 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 8.9e-15
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       +++ +d+l+ l pdg++++aN+     fg++ e+l   ++ ++  +e+ +   ++l++ +++++ i+++   ++ +g
  gi|488600285|ref|YP_007906756.1| 145 WNNANDMLYLLTPDGTFIDANKLTLNTFGYTKESLGKLSFKDIIADEHLEKALNDLQEIVSSGKEISQEYLCKTrDG 221
                                       68999**********************************************************999999988889** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       ++ ++e+r +P++ e+G+++++ +i+rD+T+r+r
  gi|488600285|ref|YP_007906756.1| 222 KQIWVEIRSHPIF-ENGKIVAIQGIARDVTDRKR 254
                                       ************9.6*****************97 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 5.9e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..p 75 
                                       ++++ d++++ +  g ++ +N+++++++g++ ee++Gk ++e+lpee+a ++   ++r+ ++++ i+  e  ++  +
  gi|488600285|ref|YP_007906756.1| 270 FENSLDLIVITNLRGEFIEVNKTFEKVLGYSKEEIIGKNYREFLPEECANEIFKEYNRAFRSGKNIYGIELEVFakD 346
                                       78999*****************************************************************999999* PP

                             PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                       g+  ++e +++ + +e+G+++++ + +rDiT r+r
  gi|488600285|ref|YP_007906756.1| 347 GKKIVLEGNVRMI-KENGKIVAFHGNFRDITPRKR 380
                                       ************9.68***************9986 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 3e-12
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++ +p  +a+ld++g++l +N+a+ + ++    +++Gk+l+e++p ++a   +++l+++ e++e i+f++    ++ 
  gi|488600285|ref|YP_007906756.1| 396 FELSPSHIAILDENGVFLELNPAMKSSIK---LDAVGKSLYEIFPRDVAKKRMDYLKKMFETNEIIIFED----SRN 465
                                       6789999****************888444...4579**********************************....888 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTer 108
                                       ++++  +l+Pl + +G+ + +l+is D+Te+
  gi|488600285|ref|YP_007906756.1| 466 GEYFRNFLVPL-ELKGK-RYCLLISKDLTEL 494
                                       8**********.79***.***********97 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   9.4e-17   1.1e-13       2      89 .]     162     246 ..     161     246 .. 0.96
   2 !   40.6   0.0     2e-13   2.3e-10       2      87 ..     287     370 ..     286     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 9.4e-17
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       i +++   +++Gy++e+l +   s++d++  e +e++ ++lqe++++g+++++ey ++++dG+ +wve r  +i  e
  gi|488600285|ref|YP_007906756.1| 162 IDANKLTLNTFGYTKESLGKL--SFKDIIADEHLEKALNDLQEIVSSGKEISQEYLCKTRDGKQIWVEIRSHPI-FE 235
                                       677888899************..***************************************************.** PP

                             PAS_3  79 ngkpvrvigva 89 
                                       ngk+v ++g+a
  gi|488600285|ref|YP_007906756.1| 236 NGKIVAIQGIA 246
                                       *********96 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 2e-13
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       i v++++e++lGys+ee++gk  ++++++  e  +++++++++a+++g+  y +e  ++ kdG+ + +e  +r i  
  gi|488600285|ref|YP_007906756.1| 287 IEVNKTFEKVLGYSKEEIIGK--NYREFLPEECANEIFKEYNRAFRSGKnIYGIELEVFAKDGKKIVLEGNVRMI-K 360
                                       899******************..************************99899***********************.* PP

                             PAS_3  78 engkpvrvig 87 
                                       engk+v + g
  gi|488600285|ref|YP_007906756.1| 361 ENGKIVAFHG 370
                                       *****99987 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.3e-09   1.5e-06       2     113 .]     140     249 ..     139     249 .. 0.86
   2 !   45.0   0.0   8.3e-15   9.3e-12       2     113 .]     265     375 ..     264     375 .. 0.82
   3 !   14.0   0.0   3.3e-05     0.037       2      76 ..     391     461 ..     390     487 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesragei 77 
                                       +++++ +++ d+  ++  dg ++ +N+ +   +G++  e lgk  + +i+ +++  +    l++  ++g+e +++  
  gi|488600285|ref|YP_007906756.1| 140 KYSELWNNANDMLYLLTPDGTFIDANKLTLNTFGYTK-ESLGKLSFKDIIADEHLeKALNDLQEIVSSGKEISQEYL 215
                                       57888999***************************85.678999999999888877777777777777777777777 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + ++ dg+ i++e+r +p+++ g+ i  + g++rd+
  gi|488600285|ref|YP_007906756.1| 216 CKTR-DGKQIWVEIRSHPIFENGK-IVAIQGIARDV 249
                                       7777.*****************76.55*******97 PP

  == domain 2  score: 45.0 bits;  conditional E-value: 8.3e-15
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECC.CCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesra.gei 77 
                                       ++r ++e++ d i++++ +g++++vN+++e+ lG+s ee++gk++ ++++ee     +e+++++ ++ +++++ + i
  gi|488600285|ref|YP_007906756.1| 265 KYRDLFENSLDLIVITNLRGEFIEVNKTFEKVLGYSKEEIIGKNYREFLPEEC---ANEIFKEYNRAFRSGKNiYGI 338
                                       68999**********************************************97...555555555555554431344 PP

                                       EEEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        +++  +dg++i le +++ + + g+ i  f g +rdi
  gi|488600285|ref|YP_007906756.1| 339 ELEVfaKDGKKIVLEGNVRMIKENGK-IVAFHGNFRDI 375
                                       4444669**********999988865.66999999998 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCC CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrage 76 
                                       ++r i+e +p+ i ++De+g++l+ N+a+ +   l   +++gksl+ +i++ d a+ +  +++ + +++e  ++e
  gi|488600285|ref|YP_007906756.1| 391 KFRKIFELSPSHIAILDENGVFLELNPAMKSSIKL---DAVGKSLY-EIFPRDVAKKRMDYLKKMFETNEIIIFE 461
                                       7899*************************987766...56788888.5555555555555555555555555555 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.6e-06    0.0085       2      51 ..     140     190 ..     139     207 .. 0.78
   2 !   32.1   0.0   7.2e-11   8.1e-08       2      53 ..     265     317 ..     264     331 .. 0.79
   3 !   14.3   0.0   2.7e-05      0.03       1      31 [.     390     420 ..     390     450 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.6e-06
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg.qllpv 51 
                                       ++  l+++++d + ++  +g+ ++d+N+ +l  +Gy+++++g+l   +++ +
  gi|488600285|ref|YP_007906756.1| 140 KYSELWNNANDMLYLLTpDGT-FIDANKLTLNTFGYTKESLGKLSFkDIIAD 190
                                       78999***********96666.***************999998873344444 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 7.2e-11
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlr 53 
                                       ++r lfe+s d i++++ +g+ +++vN+++++ lGys ++++g+  +++lp+  
  gi|488600285|ref|YP_007906756.1| 265 KYRDLFENSLDLIVITNlRGE-FIEVNKTFEKVLGYSkEEIIGKNYREFLPEEC 317
                                       8****************7777.*************9977777666555555444 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.7e-05
                             PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaal 31 
                                       e++r +fe sp  ia++d +g  +++ N+a+ 
  gi|488600285|ref|YP_007906756.1| 390 EKFRKIFELSPSHIAILDeNGV-FLELNPAMK 420
                                       79****************6666.*******86 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.2   2.9e-19   3.2e-16       1     101 [.       3     103 ..       3     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.9e-19
                                       EEEESSSHHHHHHHHHHHH.H.TTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                      Response_reg   1 vlivdDdplvrellrqlle.e.egyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpvi 75 
                                       v+++d++p+ + l+++ l+ e +++ ev e  d ke+l+ l+ee +d++++D ++   +G+++lk+ire++p  pvi
  gi|488600285|ref|YP_007906756.1|   3 VMLIDNNPDDIILTTRELKkEfDDV-EVLEILDEKEFLNALEEE-FDVVITDYQLKWGTGIDILKKIREKHPFWPVI 77 
                                       789***************9533677.8999***********998.******************************** PP

                                       EEESSTSHHHHHHHHHCTESEEEESS CS
                      Response_reg  76 iltahseeedavealkagaddflsKp 101
                                       ++t +s+ee+a++a+kag dd++ K 
  gi|488600285|ref|YP_007906756.1|  78 MFTETSNEEVAIKAMKAGLDDYVLKS 103
                                       *************************7 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.8e-06    0.0053       8      90 ..     155     233 ..     149     246 .. 0.87
   2 !    6.9   0.0    0.0059       6.6       6      63 ..     278     331 ..     274     380 .. 0.81
   3 ?   -1.3   0.0       2.1   2.3e+03      23      63 ..     416     455 ..     403     459 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-06
                            PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvk 84 
                                       l++dg +i+ ++ +L+   + g++ke+l ++s++d++  ++l+++ + l+e++ s+g+  s+ y  +++++k ++v 
  gi|488600285|ref|YP_007906756.1| 155 LTPDGTFIDANKLTLN---TFGYTKESLGKLSFKDIIADEHLEKALNDLQEIV-SSGKEISQEYLCKTRDGKQIWVE 227
                                       5678888888883333...5699999***************************.**********************9 PP

                            PAS_11  85 tksklf 90 
                                        +s+  
  gi|488600285|ref|YP_007906756.1| 228 IRSHPI 233
                                       999865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0059
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissn 63 
                                       ++  + g +i+v++     + +lg++kee++g+ + +++ +++  ++ + +   + ++
  gi|488600285|ref|YP_007906756.1| 278 VITNLRGEFIEVNK---TFEKVLGYSKEEIIGKNYREFLPEECANEIFKEYNRAF-RS 331
                                       56678899999*99...99999*******************99888777777666.44 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.1
                            PAS_11  23 rasfslglekeelvgrsiydLchpqdlstlkshlrevissn 63 
                                       +  ++ +++  + vg+s+y+++  +  ++ ++ l++++++n
  gi|488600285|ref|YP_007906756.1| 416 NPAMKSSIKL-DAVGKSLYEIFPRDVAKKRMDYLKKMFETN 455
                                       4466666666.78999****999999999999999998554 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.1   2.3e+03      34     110 ..     167     245 ..     145     260 .. 0.61
   2 !   25.2   0.0   1.5e-08   1.7e-05       3     137 ..     516     642 ..     514     643 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                                       EEEEEEEES-TTSTT-S-B--.-TTHHHHHHHHTS-EEES-.GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEE CS
                             GAF_2  34 lrlaawgeaeeefgaaldrpl.geglvgealrtgrpvilnd.leedpdkkglpaghaglrsflavPlisegrvvGvl 108
                                       l+l ++g++ e++g    +++ ++  +++al + ++++ +    + ++ +  + g+  +  + + P++++g++v++ 
  gi|488600285|ref|YP_007906756.1| 167 LTLNTFGYTKESLGKLSFKDIiADEHLEKALNDLQEIVSSGkEISQEYLCKTRDGKQIWVEIRSHPIFENGKIVAIQ 243
                                       55556666666666555554444443466666666666555544455666666677777777788999999999987 PP

                                       EE CS
                             GAF_2 109 nl 110
                                       ++
  gi|488600285|ref|YP_007906756.1| 244 GI 245
                                       76 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-.EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG- CS
                             GAF_2   3 dleelldlvldelvel.gaalgyillvdddgg.lrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleed 77 
                                       d++ ll++++++l +l     ++++ ++  ++ +++ a+ ++   + +++  ++ +g + +al++   +i++++++ 
  gi|488600285|ref|YP_007906756.1| 516 DITLLLRRACEYLSTLeEYYSVWVGTLE--KNiVKTIAYDGEKTPHPGEF--DV-QGCMLKALQK-DGFIVQNIKDR 586
                                       6677999********9558888999999..55244557777777777777..66.4434499999.89********7 PP

                                       S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  78 pdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                       +  ++    + +  s++++P+  ++ + G++++ ++k    + e++elL++la+++a+ai
  gi|488600285|ref|YP_007906756.1| 587 EENCPFY--DGDAFSCIVFPMKVDDTTKGFITI-HSKIL-PNGEEIELLSTLANDLAFAI 642
                                       7777776..777779******99889******9.67776.49*****************9 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   8.3e-08   9.4e-05       6      66 ..     665     717 ..     647     718 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.3e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   6 lagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       +a +  ++r+PLs+i+g+ae+     k   + ke  e i ++++ +++lv++l d +++e+
  gi|488600285|ref|YP_007906756.1| 665 FAILVDQIRNPLSVISGTAEM-----K--VKNKEIAELILKQVEAINDLVKRL-DDGWLES 717
                                       5778899**************.....2..788********************8.7777665 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     2e-06    0.0023      23     117 ..     134     227 ..     124     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                            MEKHLA  23 sesaeelakaLfeapfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgfv 99 
                                        e++e++  +L++  + +l + l +d  f+ aN+  l+ + +t e l +l+ + ++ +e+ e+  ++L+++  +g  
  gi|488600285|ref|YP_007906756.1| 134 LEKSEKKYSELWNNANDML-YLLTPDGTFIDANKLTLNTFGYTKESLGKLSFKDIIADEHLEKALNDLQEIVSSGKE 209
                                       4567888999999777766.56789******************************9988866668************ PP

                            MEKHLA 100 enysGvrisstGrrfsie 117
                                         ++ ++ +++G+++++e
  gi|488600285|ref|YP_007906756.1| 210 ISQEYLCKTRDGKQIWVE 227
                                       ***************987 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0028       3.2     102     194 ..      85     178 ..      61     188 .. 0.77
   2 ?    5.9   0.0    0.0092        10     153     181 ..     525     553 ..     505     561 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0028
                                       -HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS..... CS
                               dNK 102 seeelkiykelldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnev..... 173
                                       +e+++k +k+ ld ++  l++p+++i L + +++    i+k+++e+e +i ++ lek ++ky+e  ++ n +     
  gi|488600285|ref|YP_007906756.1|  85 EEVAIKAMKAGLDDYV--LKSPKHFIRLSVAVKV---AIEKKKKEKELEIYRRELEKSEKKYSELWNNANDMlyllt 156
                                       5667777777777777..5667888888887665...5899*********************998888555555555 PP

                                       -.EEEEETSS.-TTTHCCHHHH CS
                               dNK 174 p.vlvidveeldlvaeeekred 194
                                       p  ++id+++l l ++   +e+
  gi|488600285|ref|YP_007906756.1| 157 PdGTFIDANKLTLNTFGYTKES 178
                                       6689999999998887766665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0092
                                       HHHHHHHHHHHHHHHTSGGCS-EEEEETS CS
                               dNK 153 ldYlekLhekyeewlkklnevpvlvidve 181
                                        +Yl +L+e+y+ w+ +l++  v +i ++
  gi|488600285|ref|YP_007906756.1| 525 CEYLSTLEEYYSVWVGTLEKNIVKTIAYD 553
                                       69**************9998877666555 PP

>> GAF_3  GAF 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     0.052      20     127 ..     533     642 ..     520     644 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                             GAF_3  20 evgalllldedgnklqvaagwdgkpalse.sldedsalarralssgevvsepsfaeedglpd..raa...lavPLva 90 
                                       e++++++ + ++n +  ++++dg++ ++  ++d + ++ +++++ +++++ +  ++e+++p   + a   ++ P+++
  gi|488600285|ref|YP_007906756.1| 533 EYYSVWVGTLEKNIV-KTIAYDGEKTPHPgEFDVQGCMLKALQK-DGFIVQNIKDREENCPFydGDAfscIVFPMKV 607
                                       566777777665555.5555789999988899999998888866.6688777777788887544444566778**** PP

                             GAF_3  91 grqviGvlalastkprafdaedlelleslArqiatai 127
                                        +++ G++ ++s+     + e+ ell++lA+ +a ai
  gi|488600285|ref|YP_007906756.1| 608 DDTTKGFITIHSKIL--PNGEEIELLSTLANDLAFAI 642
                                       99**********752..267***************99 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   9.5e-05      0.11      57      94 ..     117     154 ..     110     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-05
                                       S...SS-.--HHHHHHHHHCC-HHHHHHHHHHHHHHII CS
                           DUF5618  57 glekkkrpksvetYkealkkldkkllkefnsaydvLhl 94 
                                        +ekkk++k++e Y+ +l+k++kk  +  n+a+d+L l
  gi|488600285|ref|YP_007906756.1| 117 AIEKKKKEKELEIYRRELEKSEKKYSELWNNANDMLYL 154
                                       456788899**************************976 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 ?   -3.6   0.0         7   7.9e+03      89     115 ..      44      70 ..      40      89 .. 0.77
   2 ?    5.8   0.1    0.0089       9.9      71     133 ..     163     228 ..     143     238 .. 0.83
   3 ?   10.1   0.2    0.0004      0.45      54     139 ..     271     360 ..     264     365 .. 0.79
   4 ?   -2.8   0.1         4   4.5e+03     114     132 ..     680     698 ..     635     703 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7
                            PAS_12  89 qdfseivqegleeWkralaklssktes 115
                                       ++f  ++++   +W ++++ l++  e+
  gi|488600285|ref|YP_007906756.1|  44 EEFDVVITDYQLKWGTGIDILKKIREK 70 
                                       566677777788999999888877766 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0089
                            PAS_12  71 faNaqirallGwssdkflq.dfseivq.egleeWkralakl.sskteskirlvlKtKagqevllnc 133
                                        aN+ + +  G+ ++ + + +f++i+  e le+  ++l+++ ss +e + + + Kt+ g+++ +++
  gi|488600285|ref|YP_007906756.1| 163 DANKLTLNTFGYTKESLGKlSFKDIIAdEHLEKALNDLQEIvSSGKEISQEYLCKTRDGKQIWVEI 228
                                       589999999********76589**99626789999999876266799999***********98765 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0004
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflqdf......seivqegleeWkralaklsskteskirlvlKtK 124
                                       En+  ++v ++     + +N+ ++++lG+s+++++ +       +e+ +e ++e++ra    s k+   i+l++ +K
  gi|488600285|ref|YP_007906756.1| 271 ENSLDLIVITNLRGEFIEVNKTFEKVLGYSKEEIIGKNyreflpEECANEIFKEYNRAF--RSGKNIYGIELEVFAK 345
                                       5666677777777888899**************98543222244578888899999998..5677778899999999 PP

                            PAS_12 125 agqevllncllgiip 139
                                        g+++ l+  + +i 
  gi|488600285|ref|YP_007906756.1| 346 DGKKIVLEGNVRMIK 360
                                       999999999998885 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 4
                            PAS_12 114 eskirlvlKtKagqevlln 132
                                          +++++K+K+ +e+ l+
  gi|488600285|ref|YP_007906756.1| 680 SGTAEMKVKNKEIAELILK 698
                                       4467788888888877765 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 ?   12.8   0.2    0.0001      0.11      48      90 ..     114     156 ..      88     159 .. 0.91
   2 ?   -3.1   0.1       8.7   9.8e+03      55      69 ..     379     393 ..     377     395 .. 0.67
   3 ?   -2.7   0.2       6.5   7.3e+03      43      85 ..     651     695 ..     629     706 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                       Uso1_p115_C  48 keleaenkklekeleklraelkeekekekekqkEldDLLlllg 90 
                                        ++  e+kk ekele  r el+++++k++e  +  +D+L ll+
  gi|488600285|ref|YP_007906756.1| 114 VKVAIEKKKKEKELEIYRRELEKSEKKYSELWNNANDMLYLLT 156
                                       5667799**********************99**********97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.7
                       Uso1_p115_C  55 kklekeleklraelk 69 
                                       k+le+el++ +++ +
  gi|488600285|ref|YP_007906756.1| 379 KRLENELKDSEEKFR 393
                                       677777777777665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.5
                       Uso1_p115_C  43 aesqakeleaenkklekeleklraelkeekekekek..qkEldDL 85 
                                        +   +++e++++k    ++++r  l+    +++ k  +kE+ +L
  gi|488600285|ref|YP_007906756.1| 651 KKRAFRQIEDNIEKFAILVDQIRNPLSVISGTAEMKvkNKEIAEL 695
                                       333345555555666666666666666666666544556665555 PP

>> NAPRTase  Nicotinate phosphoribosyltransferase (NAPRTase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026      0.29      50      93 ..     114     157 ..      95     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                                       -HHHHHHHHHHHHHHCHHHHHCCHHHHHHHHHHHHHCCHIIEEE CS
                          NAPRTase  50 etsahealgkeqelsafrnnlkqfqkdaldlwvaiekgnlgiaL 93 
                                         +a+e   ke+el+ +r++l++++k+  +lw+++++   + + 
  gi|488600285|ref|YP_007906756.1| 114 VKVAIEKKKKEKELEIYRRELEKSEKKYSELWNNANDMLYLLTP 157
                                       56899******************************975545444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (729 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 4274.89
//
Query:       gi|488600286|ref|YP_007906757.1|  [L=67]
Description: archaeal histone [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-21   76.5   1.1    1.6e-21   76.4   1.1    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    5.8e-09   36.4   0.4    6.4e-09   36.3   0.4    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    2.1e-06   27.8   0.1    2.4e-06   27.6   0.1    1.0  1  CENP-T_C       Centromere kinetochore component CENP-T histon
      4e-05   23.9   0.1      5e-05   23.6   0.1    1.1  1  CENP-S         CENP-S protein
    4.7e-05   23.4   0.0    5.6e-05   23.2   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    0.00013   22.1   0.7    0.00015   21.9   0.7    1.1  1  TAF            TATA box binding protein associated factor (TA
     0.0013   18.7   0.0     0.0014   18.6   0.0    1.0  1  Bromo_TP       Bromodomain associated
  ------ inclusion threshold ------
      0.024   15.1   0.1      0.028   14.9   0.1    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
       0.07   13.2   0.0      0.075   13.1   0.0    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu


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 !   76.4   1.1   7.8e-25   1.6e-21       1      64 [.       1      63 [.       1      64 [. 0.99

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 7.8e-25
                                      XXXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                     CBFD_NFYB_HMF  1 aeLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                                      +eLP+a+v++I++++ +a ++++dAk+ +ae++ee++  +a++A++++++++rKt+kae+ik+A
  gi|488600286|ref|YP_007906757.1|  1 MELPLAPVERIIRNA-GASRVSEDAKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKMA 63
                                      79*************.**********************************************98 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.4   3.2e-12   6.4e-09      65     129 ..       6      65 ..       1      66 [. 0.92

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 3.2e-12
                                       HHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                           Histone  65 lpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                       +p++R++r+         r+s +a  al+ealE +   ++  A  la ha R+T+ ++Di++A++
  gi|488600286|ref|YP_007906757.1|   6 APVERIIRNAGA-----SRVSEDAKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKMAAK 65 
                                       788888888776.....9*********************************************86 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 !   27.6   0.1   1.2e-09   2.4e-06      14      72 ..       9      62 ..       2      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.2e-09
                          CENP-T_C 14 kklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvil 72
                                       ++ ++     +   +++++a kal +a++++   v++     a HagRKt++++D+ +
  gi|488600286|ref|YP_007906757.1|  9 ERIIRN-----AGASRVSEDAKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKM 62
                                      444444.....46679****************************************987 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   2.5e-08     5e-05      25      71 ..      19      65 ..       6      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.5e-08
                            CENP-S 25 eatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71
                                      ++++++ +al+e   + + ++a+     a HA+R+t++++D+++ a+
  gi|488600286|ref|YP_007906757.1| 19 RVSEDAKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKMAAK 65
                                      4777777888888888888899999999****************987 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 !   23.2   0.0   2.8e-08   5.6e-05      11      67 ..       8      64 ..       4      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.8e-08
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAi 67
                                      ++ i+++ g + ++e+  + L +    y  +v + A  la+ha++k+v+++d+++A 
  gi|488600286|ref|YP_007906757.1|  8 VERIIRNAGASRVSEDAKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKMAA 64
                                      678999*************************************************96 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 !   21.9   0.7   7.5e-08   0.00015      10      64 ..       9      63 ..       2      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.5e-08
                                      HHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHH CS
                               TAF 10 kviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsA 64
                                      + i    G + +s++a ++Lae +e+    ++++a+    h+ R++  ++D+ +A
  gi|488600286|ref|YP_007906757.1|  9 ERIIRNAGASRVSEDAKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKMA 63
                                      55666779999******************************************99 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   6.9e-07    0.0014      14      70 ..      10      66 ..       3      67 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.9e-07
                                      HHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHH CS
                          Bromo_TP 14 qileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLqe 70
                                       i ++aG +++ e a  +L e +++Y + ++++a   a hagR +++ +D+ ++ +e
  gi|488600286|ref|YP_007906757.1| 10 RIIRNAGASRVSEDAKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKMAAKE 66
                                      57888999999999999**********************************987665 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.4e-05     0.028      15      61 ..      17      63 ..       8      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                      S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHH CS
                       TFIID_20kDa 15 etkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlh 61
                                       +++ ed +  L+e  +++   v  +a+ la h   +++ + Di++ 
  gi|488600286|ref|YP_007906757.1| 17 ASRVSEDAKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKMA 63
                                      567899**************************************986 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.8e-05     0.075      24      63 ..      24      63 ..      10      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                      HHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXX CS
                       TFIID-18kDa 24 tvqlledlvrgyliellqqaakvaklrgsrkitlEDllfl 63
                                      + + l + +++y   +  +a+++a + g++ ++ ED++ +
  gi|488600286|ref|YP_007906757.1| 24 AKKALAEALEEYALTVARKAVDLATHAGRKTVKAEDIKMA 63
                                      5567888899***************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 462.94
//
Query:       gi|488600287|ref|YP_007906758.1|  [L=297]
Description: formylmethanofuran-tetrahydromethanopterin formyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  217.4   1.8    1.3e-64  216.8   1.8    1.3  1  FTR_C     FTR, proximal lobe
    1.6e-63  212.9   0.0    2.8e-63  212.1   0.0    1.4  1  FTR       Formylmethanofuran-tetrahydromethanopterin formyltr
  ------ inclusion threshold ------
       0.03   14.3   0.0      0.065   13.2   0.0    1.5  1  GPAT_N    Glycerol-3-phosphate acyltransferase N-terminal


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 !  216.8   1.8   2.1e-68   1.3e-64       1     149 []     147     296 ..     147     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 216.8 bits;  conditional E-value: 2.1e-68
                                       EEEEEES-EEEEEEEEEEEEEEEESSHHHHHHHHHHHHHHHHTSTTEE--SGGGEESS-EEES-.S-TT-SEEE-GG CS
                             FTR_C   1 geflieeklgvvkgvaGgnllilaedqeaaleaaeaaveaikkvegvitpFpGgivrsgSKvgs.kykflkastNea 76 
                                       g+f++e+++g+v+gvaGgn++i+ae+q + l+aa+aav+ai++vegvitpFpGgiv+sgSKvg+ kykflka+tNe+
  gi|488600287|ref|YP_007906758.1| 147 GDFIVENDIGYVDGVAGGNFFIFAETQPSGLAAAKAAVQAIEDVEGVITPFPGGIVASGSKVGAnKYKFLKATTNEK 223
                                       8***************************************************************9************ PP

                                       G-TTSTT....----TT--EEEEEEEEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS-SEEEEGGGG CS
                             FTR_C  77 fcptlkekveeselpedveavlEiVidgldeeavaeamkagieaavkvegvlkisAgNygGkLGkykfkLkel 149
                                       f+p++++++e++++pe+v+av+E+Vi+g++ +av+ea+k+gi aa+k++gv+ki+AgNygGkLG++ ++L+el
  gi|488600287|ref|YP_007906758.1| 224 FAPSIRDQIEDTQIPENVKAVYELVINGISIDAVKEATKVGILAATKIPGVVKITAGNYGGKLGQHLINLHEL 296
                                       ***********************************************************************97 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.1   0.0   4.7e-67   2.8e-63       1     142 []       1     144 [.       1     144 [. 0.98

  Alignments for each domain:
  == domain 1  score: 212.1 bits;  conditional E-value: 4.7e-67
                                       -EETTEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-EEEESEEB-GGGSTTSS-EEEEEEE CS
                               FTR   1 leingveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaEagiervlspeetpDgRpGvailif 77 
                                       +++ngveiedtfaEaF ikv+rv+iTa + +wak aateatgf+tsvi+c+aEagie+   p+etpDgRpG++i+i+
  gi|488600287|ref|YP_007906758.1|   1 MKVNGVEIEDTFAEAFGIKVARVLITAYDYDWAKVAATEATGFGTSVIMCPAEAGIEKKALPSETPDGRPGYYIQIC 77 
                                       89*************************************************************************** PP

                                       ESSHHHHHHHHHHHHHHHTTTSTT-EEEE--..GG-SEEHHHHHHGGGTT--EEEEETTEEEEEEEE CS
                               FTR  78 aaskkklekqlleRigqcvLtapttavfngl..aeekiklgkklrffgDgyeiekelggrkvwriPv 142
                                       ++skk le+qll+RigqcvLtaptta+fngl  ae+k+++g kl+ff+Dgye+e e+ggrk+w++P+
  gi|488600287|ref|YP_007906758.1|  78 HMSKKGLEEQLLARIGQCVLTAPTTAAFNGLpdAENKFDIGFKLKFFADGYEKELEVGGRKCWAVPM 144
                                       *******************************7666*******************************6 PP

>> GPAT_N  Glycerol-3-phosphate acyltransferase N-terminal
   #    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       3      35 ..     214     246 ..     212     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                            GPAT_N   3 kfldarseeellsvirkeveagkLpanvaagme 35 
                                       kfl+a+++e++   ir ++e+ ++p+nv a +e
  gi|488600287|ref|YP_007906758.1| 214 KFLKATTNEKFAPSIRDQIEDTQIPENVKAVYE 246
                                       79**************************99876 PP



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:                      301  (0.0167884); 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 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1993.81
//
Query:       gi|488600288|ref|YP_007906759.1|  [L=280]
Description: Universal stress protein UspA-related nucleotide-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-35  120.7   0.0    1.2e-20   74.4   0.0    3.1  2  Usp       Universal stress protein family
      0.007   16.3   0.0       0.43   10.5   0.0    2.9  2  ETF       Electron transfer flavoprotein domain
  ------ inclusion threshold ------
      0.026   15.3   0.0        2.6    8.9   0.0    2.3  2  GARS_N    Phosphoribosylglycinamide synthetase, N 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 !   74.4   0.0   2.1e-24   1.2e-20       2     141 .]       5     146 ..       5     146 .. 0.88
   2 !   36.9   0.0   7.6e-13   4.6e-09       3     139 ..     167     277 ..     166     279 .. 0.81

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 2.1e-24
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       + +Il+++D+s++s+k +e + e+a     e++llh+   +++  + + ++  e+ e+ +e+ae+e+++++   e++
  gi|488600288|ref|YP_007906759.1|   5 FNKILIPTDFSDYSRKTIECGREFADLGAEEIVLLHIGLYDPFILSLARMSVDEYVEKIKEKAENELKELAGIVEEK 81 
                                       579************************999******99888888888888888888888888888888866666666 PP

                                       TCEEEEE..EEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevv..veegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       g kv+++   +  dpaeei+++ eee++dli++Gs+g+++l+  l+G +se+v+r +++pVl+++
  gi|488600288|ref|YP_007906759.1|  82 GLKVRTIflATYTDPAEEIVRISEEEGVDLILIGSKGHGWLKAKLIGGTSESVARLSKVPVLITK 146
                                       6666655115789*************************************************986 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 7.6e-13
                                       SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTT CS
                               Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeagg 79 
                                       +r+l  +D+ e s+kAl+   e+ +   ++++l+hv++ r+ ++  ++ +e ++                    +g+
  gi|488600288|ref|YP_007906759.1| 167 DRVLFTFDKPEISEKALKILEEFSRV--GKVFLVHVVEKRNESEIEEEIREYGDFF------------------DGI 223
                                       58888999999999999888888777..5699999998887666555555554444..................456 PP

                                       CEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  80 vkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       ++ e +v++g+p  eil +a+e + +liVvG++     ++  lG v++++lrh+++p ++
  gi|488600288|ref|YP_007906759.1| 224 ANAEWKVLWGNPVNEILNYARETKSSLIVVGKKE----RK--LGKVADSLLRHSEIPIMI 277
                                       66799*****************************....44..899************998 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   7.1e-05      0.43      12     138 ..      13     168 ..       3     177 .. 0.79
   2 ?    0.2   0.0       0.1     6e+02      22      57 ..     180     217 ..     175     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.1e-05
                                       CE-HHHHHHHHHHHHHHHHHT.--EEEEEEES.........................S-CHHHHHHCT-SEEEEEE- CS
                               ETF  12 klnpvdlealeaArrlkekag.gevtavvvGp.....................peaeealrealaamGadkvilvdd 66 
                                        ++++++ ++e +r++++ +g +e++++ +G                      ++ae+ l+e la    +k + v +
  gi|488600288|ref|YP_007906759.1|  13 DFSDYSRKTIECGREFAD-LGaEEIVLLHIGLydpfilslarmsvdeyvekikEKAENELKE-LAGIVEEKGLKVRT 87 
                                       678999999999999999.5559999999999889999999999988888764445555554.44488899999999 PP

                                       GGGSS--CCHHHHHHHHHHHHC--SEEEEESSCCH.......HHHHHHHHHHCT-EEEEEESEEEEETCC....EEE CS
                               ETF  67 palagydaeatakalaalikkedpdlvlagataig.......kqvaprlAalLgvplitdvteleveggk....ltv 132
                                         la+y+    a+ ++ + ++e++dl+l+g++  g       + +   +A l +vp++    ++e+++g+    lt+
  gi|488600288|ref|YP_007906759.1|  88 IFLATYTD--PAEEIVRISEEEGVDLILIGSKGHGwlkakliGGTSESVARLSKVPVLITKFQVEEKDGEkycrLTF 162
                                       99998743..5899999999999999999999998899977777778899999999987777777744446999999 PP

                                       EEECCC CS
                               ETF 133 tRpieg 138
                                       +R ++ 
  gi|488600288|ref|YP_007906759.1| 163 ERLLDR 168
                                       998765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                                       HHHHHHHHH.HT.--EEEEEEES....S-CHHHHHHCT CS
                               ETF  22 eaArrlkek.ag.gevtavvvGppeaeealrealaamG 57 
                                       e+A+++ e+    g+v +v v +++ e+ ++e+++++G
  gi|488600288|ref|YP_007906759.1| 180 EKALKILEEfSRvGKVFLVHVVEKRNESEIEEEIREYG 217
                                       8999999999445**********999999999999887 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.012        73      28      59 ..      74     116 ..      57     138 .. 0.74
   2 ?    8.9   0.0   0.00043       2.6      37      79 ..     228     275 ..     180     278 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                                       EEEEE--CGG...........TTHHHHHHHHHHCTESEEEE-S CS
                            GARS_N  28 vyvapgNagt...........edlealvefakeekidlvvvGp 59 
                                       +  + + +g            + +e++v++ +ee++dl+++G 
  gi|488600288|ref|YP_007906759.1|  74 LAGIVEEKGLkvrtiflatytDPAEEIVRISEEEGVDLILIGS 116
                                       55555555555555555555333468***************97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00043
                                       G.....TTHHHHHHHHHHCTESEEEE-SHHHHHTTHHHHHHHHHT-EE CS
                            GARS_N  37 t.....edlealvefakeekidlvvvGpeapLvaGvadaleeekgikv 79 
                                             + +++++++a+e+k +l+vvG  +     vad l ++++i++
  gi|488600288|ref|YP_007906759.1| 228 WkvlwgNPVNEILNYARETKSSLIVVGKKERKLGKVADSLLRHSEIPI 275
                                       144444334589****************99999999999976667776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1704.44
//
Query:       gi|488600289|ref|YP_007906760.1|  [L=60]
Description: hypothetical protein Asulf_00754 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-06   25.5   0.0    9.6e-06   25.5   0.0    1.1  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    3.7e-05   23.2   0.1    8.3e-05   22.1   0.0    1.6  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00072   19.4   0.0    0.00085   19.2   0.0    1.1  1  MarR_2          MarR family
      0.001   19.6   0.0     0.0012   19.4   0.0    1.1  1  Phage_rep_O     Bacteriophage replication protein O
     0.0014   19.0   0.0     0.0016   18.8   0.0    1.1  1  Rrf2            Transcriptional regulator
     0.0055   16.6   0.0     0.0068   16.3   0.0    1.1  1  MarR            MarR family
     0.0074   15.9   0.0     0.0086   15.7   0.0    1.0  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.012   15.8   0.0    1.1  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.011   15.6   0.0      0.013   15.3   0.0    1.1  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.013   15.2   0.0      0.016   15.0   0.0    1.1  1  HTH_IclR        IclR helix-turn-helix domain
       0.02   14.7   1.0      0.034   14.0   0.2    1.9  2  IF2_N           Translation initiation factor IF-2, N-termina
      0.023   14.6   0.0      0.024   14.6   0.0    1.1  1  HTH_11          HTH domain
      0.027   14.5   0.0      0.048   13.7   0.0    1.4  1  PPR_3           Pentatricopeptide repeat domain
      0.037   14.0   0.1       0.14   12.2   0.0    1.8  2  DUF3783         Domain of unknown function (DUF3783)
      0.041   14.5   0.0      0.047   14.3   0.0    1.1  1  RPA_C           Replication protein A C terminal
       0.06   13.2   0.0      0.071   13.0   0.0    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
       0.12   11.9   0.0       0.17   11.5   0.0    1.2  1  HTH_47          winged helix-turn-helix
       0.13   11.8   0.0       0.15   11.7   0.0    1.1  1  SMC_ScpB        Segregation and condensation complex subunit 


Domain annotation for each model (and alignments):
>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   9.6e-09   9.6e-06      21      52 ..      18      49 ..       2      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 9.6e-09
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                      pl   e+A m+G+    vs+i++eLk+eg++ 
  gi|488600289|ref|YP_007906760.1| 18 PLRPGEIAKMIGMDSKEVSKIIGELKKEGIVI 49
                                      78888*************************75 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.3e-08   8.3e-05       1      47 [.       1      48 [.       1      49 [. 0.90
   2 ?   -0.8   0.0       1.2   1.2e+03      29      40 ..      49      60 .]      49      60 .] 0.87

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.3e-08
                            HTH_24  1 ldetdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +d+++ +++e+ +k +  +   e+A+++g+ +  v++ + +L++eG++
  gi|488600289|ref|YP_007906760.1|  1 MDDKKQAVIEAFKKsEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIV 48
                                      788899999999995555999**************************8 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                            HTH_24 29 lSpstvnrrlkr 40
                                      +Sp  + + lk+
  gi|488600289|ref|YP_007906760.1| 49 ISPKRCYYSLKE 60
                                      89999*999985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.5e-07   0.00085      17      51 ..      15      48 ..       5      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.5e-07
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      ++ + l++ge+a+  g++   vs+i+ +L + G v
  gi|488600289|ref|YP_007906760.1| 15 SEKP-LRPGEIAKMIGMDSKEVSKIIGELKKEGIV 48
                                      4444.9***************************98 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.2e-06    0.0012      42      83 ..      11      52 ..       5      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                       Phage_rep_O 42 gfkkksdwisnsqlveltgisrtkvskalkeLirekviikeg 83
                                       fkk +++++ +++++++g+++++vsk + eL +e+++i  +
  gi|488600289|ref|YP_007906760.1| 11 AFKKSEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIVISPK 52
                                      59***********************************99765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.6e-06    0.0016      20      57 ..      13      50 ..       6      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +++e+p++  eia++ ++  + ++ki+ +L+k+g+v s
  gi|488600289|ref|YP_007906760.1| 13 KKSEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIVIS 50
                                      456678999***************************87 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.8e-06    0.0068      15      49 ..      16      50 ..      14      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.8e-06
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      + pl+  e+ak++g+++  v++++ +L k+G + +
  gi|488600289|ref|YP_007906760.1| 16 EKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIVIS 50
                                      679999*************************9965 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.6e-06    0.0086      11      55 ..       6      50 ..       3      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.6e-06
                      HrcA_DNA-bdg 11 qaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLveg 55
                                      qa+ie ++k++++++  eiA++++ ++  v  ++  Lk  g+v +
  gi|488600289|ref|YP_007906760.1|  6 QAVIEAFKKSEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIVIS 50
                                      689***********************************9999876 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   1.2e-05     0.012      17      54 ..      13      50 ..       4      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                                      HHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 17 seekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                      ++++k+ ++ ++a+ ++     Vs+ + +L+k+G v+ 
  gi|488600289|ref|YP_007906760.1| 13 KKSEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIVIS 50
                                      4589999***************************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 ?   15.3   0.0   1.3e-05     0.013      20      56 ..      16      52 ..      12      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      ++p++  eia+++g +   v +++ +L++ G+V   k
  gi|488600289|ref|YP_007906760.1| 16 EKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIVISPK 52
                                      6789999*************************97655 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 ?   15.0   0.0   1.6e-05     0.016       7      48 ..       7      48 ..       3      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      a+++a+ +   +l+  e+A+ +g+    v+ ++  L ++G+v
  gi|488600289|ref|YP_007906760.1|  7 AVIEAFKKSEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIV 48
                                      799**********************99999999999999987 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 ?   -1.8   0.0       2.9   2.9e+03      43      52 ..       4      13 ..       2      15 .. 0.57
   2 ?   14.0   0.2   3.4e-05     0.034       2      22 ..      17      37 ..      16      51 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.9
                             IF2_N 43 taeliaeefg 52
                                       ++++ e+f+
  gi|488600289|ref|YP_007906760.1|  4 KKQAVIEAFK 13
                                      5566666665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.4e-05
                             IF2_N  2 skirVyeLAkeLgvkskevik 22
                                      + +r  e+Ak +g++skev k
  gi|488600289|ref|YP_007906760.1| 17 KPLRPGEIAKMIGMDSKEVSK 37
                                      567889********9999744 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.4e-05     0.024       2      47 ..       5      50 ..       4      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIe 47
                                      +++++e ++++++p+   e+A+ +++  + v + I +L++ g+ I 
  gi|488600289|ref|YP_007906760.1|  5 KQAVIEAFKKSEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIVIS 50
                                      5788999***********************************6664 PP

>> PPR_3  Pentatricopeptide repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.9e-05     0.048      30      54 ..      31      57 ..      25      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-05
                             PPR_3 30 nkklalevlermkkkgi..kPtvvtyN 54
                                      + k ++++++++kk+gi  +P +++y+
  gi|488600289|ref|YP_007906760.1| 31 DSKEVSKIIGELKKEGIviSPKRCYYS 57
                                      78999***********5449******7 PP

>> DUF3783  Domain of unknown function (DUF3783)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.72   7.1e+02      15      26 ..       7      18 ..       2      28 .. 0.74
   2 ?   12.2   0.0   0.00014      0.14       5      26 ..      27      48 ..      23      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.72
                           DUF3783 15 klldalkkaglp 26
                                      ++++a+kk   p
  gi|488600289|ref|YP_007906760.1|  7 AVIEAFKKSEKP 18
                                      789999998776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                           DUF3783  5 fsgfsseeldklldalkkaglp 26
                                      + g++s+e+ k++ +lkk+g+ 
  gi|488600289|ref|YP_007906760.1| 27 MIGMDSKEVSKIIGELKKEGIV 48
                                      559****************996 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 ?   14.3   0.0   4.7e-05     0.047      50      97 ..       4      48 ..       1      51 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-05
                                      HHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 50 laqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                       +q v++++k+   se+ +   eia+ ++++ ++v +++ eL +eGi+
  gi|488600289|ref|YP_007906760.1|  4 KKQAVIEAFKK---SEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIV 48
                                      67778888887...78888899************************98 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.1e-05     0.071      12      46 ..      15      49 ..       2      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                                      TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 12 aegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +e++l  +e+a+++g+    vS     L+++G+V 
  gi|488600289|ref|YP_007906760.1| 15 SEKPLRPGEIAKMIGMDSKEVSKIIGELKKEGIVI 49
                                      3599*****************************97 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.17      51      76 ..      23      48 ..      22      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                      HHHHHHT--HHHHHHHHHHHHHTT-E CS
                            HTH_47 51 diAeriglpfdrvaaiaraLaeagll 76
                                      +iA+ ig++ ++v +i+ +L+++g++
  gi|488600289|ref|YP_007906760.1| 23 EIAKMIGMDSKEVSKIIGELKKEGIV 48
                                      79*********************997 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.15      10      40 ..      15      45 ..       7      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                          SMC_ScpB 10 ageplsleeLakilelskeeveealeeLkee 40
                                      +++pl+  e+ak+++++++ev++++ eLk+e
  gi|488600289|ref|YP_007906760.1| 15 SEKPLRPGEIAKMIGMDSKEVSKIIGELKKE 45
                                      5689************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 453.38
//
Query:       gi|488600290|ref|YP_007906761.1|  [L=376]
Description: Arabinose efflux permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.3e-46  157.8  64.0    1.6e-31  109.5  28.1    2.0  2  MFS_1       Major Facilitator Superfamily
    2.1e-08   33.5  18.8    2.1e-08   33.5  18.8    2.7  3  Sugar_tr    Sugar (and other) transporter
      5e-06   25.1   3.9      5e-06   25.1   3.9    4.0  4  OATP        Organic Anion Transporter Polypeptide (OATP) fami
    1.2e-05   24.4  14.0    1.2e-05   24.4  14.0    2.3  2  MFS_1_like  MFS_1 like family
     0.0002   20.5  29.8        6.9    5.5  29.8    2.9  1  PUCC        PUCC protein
  ------ inclusion threshold ------
      0.087   12.6   8.6      0.077   12.8   1.2    2.7  2  IncD        Inclusion membrane protein D


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 !  109.5  28.1   5.3e-35   1.6e-31       1     180 [.       9     187 ..       9     205 .. 0.92
   2 !   53.7  28.7   5.1e-18   1.5e-14       2     169 ..     204     370 ..     203     375 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 5.3e-35
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       l++++f ++l+ +i+ p+lp ++ae+lg+++  ig ++++++l  av+++++G lsd  Grr ++l+gll+f + ++
  gi|488600290|ref|YP_007906761.1|   9 LFISVFSVMLGLGIVVPLLP-YYAESLGATGLWIGAIFSGFSLSRAVFMPLIGKLSDSRGRRFFILTGLLIFTILSF 84 
                                       799*****************.******************************************************77 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       + ++a+s++ l ++r++ G+++++++p+++a+iad++pk + g+++g ++a++ +G+ +gpl+gg++ + +g +avf
  gi|488600290|ref|YP_007906761.1|  85 IYIYANSVYSLTAVRIVHGIASAMVIPVALAYIADLSPKGREGMYMGTFMASMFFGMGFGPLVGGVIRDMYGMEAVF 161
                                       7777666669******************************************************************* PP

                             MFS_1 155 yilaivsllafvlfllllpeepperk 180
                                       + +a++s+++f++ ll+lpe++ + +
  gi|488600290|ref|YP_007906761.1| 162 ISMAVLSFISFLICLLFLPESRGKYR 187
                                       ************86677766665544 PP

  == domain 2  score: 53.7 bits;  conditional E-value: 5.1e-18
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       l+  +++a+a ++++++lp  l+    +  ++ g+l+++  +++a+++  +Gr++d++    ++ +g ++ a+++l+
  gi|488600290|ref|YP_007906761.1| 204 LFFRAMNAFANGVFMVFLP-VLGYLISLPSTQTGMLISTSIFTTAILQRRFGRFADNHNKAVLISAGSAIIAFCFLF 279
                                       5667899************.9*************************************5555999999999999333 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       + f  s+  ll++ ++ G+g+++++p+++al++    +  +g a+g +++++s+G+i +p+++g ++++ g   vf+
  gi|488600290|ref|YP_007906761.1| 280 IPFLKSFESLLLASLIIGIGGALSMPSAMALVTIAGREIGQGTAMGAFNTAMSIGMITAPMIAGGIMDAMGIYHVFL 356
                                       335366559************************99999*************************************** PP

                             MFS_1 156 ilaivsllafvlfl 169
                                       + + ++++++  fl
  gi|488600290|ref|YP_007906761.1| 357 VSGTICFISIPAFL 370
                                       *********76433 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5  18.8   6.9e-12   2.1e-08      18     194 ..      10     182 ..       4     191 .. 0.82
   2 !   11.6   5.6   3.1e-05     0.093      46      95 ..     128     177 ..     125     225 .. 0.84
   3 ?    0.4  14.4     0.079   2.4e+02      71     189 ..     255     373 ..     230     376 .] 0.71

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 6.9e-12
                                       CGGGTHHHHHHHHTSTT--SH.HHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  18 vigafltllkfaknfglsksk.sskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlq 93 
                                       +i++f+ +l+      l  ++ +s  ++ +++g+i+s f++ +++   ++g+l+d  GR+  +l++ ++f i +++ 
  gi|488600290|ref|YP_007906761.1|  10 FISVFSVMLGLGIVVPLLPYYaESLGATGLWIGAIFSGFSLSRAVFMPLIGKLSDSRGRRFFILTGLLIFTILSFIY 86 
                                       55555555555554444443303344477899********************************************* PP

                                       H-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHH CS
                          Sugar_tr  94 aaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgw 170
                                       + a+   sv+ l++ R++ Gi+  ++  ++  yi+ ++pk   g+ ++ +  ++ fG+ ++  +g ++ ++ +   +
  gi|488600290|ref|YP_007906761.1|  87 IYAN---SVYSLTAVRIVHGIASAMVIPVALAYIADLSPKGREGMYMGTFMASMFFGMGFGPLVGGVIRDMYG---M 157
                                       ****...*************************************************************77666...4 PP

                                       HHHHHCCHHHH.HHHHHHGGGS--- CS
                          Sugar_tr 171 rillglqlvpa.llllilllflPES 194
                                          + + +v++ + +li+llflPES
  gi|488600290|ref|YP_007906761.1| 158 EAVFISMAVLSfISFLICLLFLPES 182
                                       4444444444414478999****** PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.1e-05
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH- CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaa 95 
                                       +++g +++++++G  +G l++g + d++G   +++ +avl++i+ +++ +
  gi|488600290|ref|YP_007906761.1| 128 MYMGTFMASMFFGMGFGPLVGGVIRDMYGMEAVFISMAVLSFISFLICLL 177
                                       689*****************************************998865 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.079
                                       HHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCH.HHHHHHHHHH CS
                          Sugar_tr  71 drfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklR.galvslyqla 146
                                        + ++ +  + +++ + i a++  +++  +s+e l+++ +++Gig G+ s+ + m +  iA  ++  g+ ++ +++a
  gi|488600290|ref|YP_007906761.1| 255 RFADNHNKAVLISAGSAIIAFCFLFIPFLKSFESLLLASLIIGIG-GALSMPSAMALVTIAGREIGqGTAMGAFNTA 330
                                       33333334444444555555555555555***************9.999************999988********** PP

                                       HHHHHHHHHHHHHHHHTSS-TTHHHHHH..HCCHHHHHHHHHHGG CS
                          Sugar_tr 147 itfGilvaaifglglnktsnadgwrill..glqlvpallllilll 189
                                       +++G++ a ++  g+ +  +   ++++l  g  +++++  ++l++
  gi|488600290|ref|YP_007906761.1| 331 MSIGMITAPMIAGGIMDAMG--IYHVFLvsGTICFISIPAFLLMM 373
                                       ***********999977777..46666511344555555555555 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 ?   -1.0   1.1      0.13     4e+02      38      87 ..      41      90 ..       5      98 .. 0.78
   2 !   25.1   3.9   1.7e-09     5e-06     134     195 ..      94     155 ..      87     168 .. 0.92
   3 !    7.1   2.2   0.00048       1.4       6      81 ..     203     278 ..     199     287 .. 0.91
   4 ?    0.1   2.5     0.063   1.9e+02     466     524 ..     291     349 ..     284     355 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.13
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 38 sgliassneignillilfvsYfggrghrPrwigigallmalgslllalPh 87
                                      +g i s++ ++ ++++ +++ + +++ r  +i +g+l++++ s++++  +
  gi|488600290|ref|YP_007906761.1| 41 IGAIFSGFSLSRAVFMPLIGKLSDSRGRRFFILTGLLIFTILSFIYIYAN 90
                                      57888888888888888888888888888888888888888888877655 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.7e-09
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkly 195
                                        + +  +++Gi+++++++++++Yi D + k +  +y+g+++a  ++G+ +G l+G+++  +y
  gi|488600290|ref|YP_007906761.1|  94 SLTAVRIVHGIASAMVIPVALAYIADLSPKGREGMYMGTFMASMFFGMGFGPLVGGVIRDMY 155
                                       5667789**************************************************99998 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00048
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP   6 lsllglvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsl 81 
                                       + ++  ++a+++g+f + +  +    +lps+++g++ s++  ++++l    + f+++ +++ +i +g+ ++a++ l
  gi|488600290|ref|YP_007906761.1| 203 ILFFRAMNAFANGVFMVFLPVLGYLISLPSTQTGMLISTSIFTTAILQRRFGRFADNHNKAVLISAGSAIIAFCFL 278
                                       66778889999************************************************************98655 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.063
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 466 llflvsflgalgrvpallvilRcV.kkedksfalGlqlllirllgliPgPiifGaiiDst 524
                                       l +l++ +g   ++p+ ++++ +   +     a+G   + +++ g+i +P+i G i+D +
  gi|488600290|ref|YP_007906761.1| 291 LASLIIGIGGALSMPSAMALVTIAgREIGQGTAMGAFNTAMSI-GMITAPMIAGGIMDAM 349
                                       4555555666666666665533330223455677777777777.9999999999999975 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4  14.0   3.9e-09   1.2e-05     231     383 ..      10     161 ..       3     163 .. 0.89
   2 ?    2.0  16.5     0.025        75     184     384 ..     159     356 ..     155     357 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.9e-09
                        MFS_1_like 231 llvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrflly 307
                                       ++ ++ +    gi+   l  Y ++lga++  +G++     ++  ++  +  kl +  G ++ ++++ll++++  ++y
  gi|488600290|ref|YP_007906761.1|  10 FISVFSVMLGLGIVVPLLPYYAESLGATGLWIGAIFSGFSLSRAVFMPLIGKLSDSRGRRFFILTGLLIFTILSFIY 86 
                                       4444444445677777788888******************************************************* PP

                        MFS_1_like 308 aiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                        + +++  +  + + hgi+ +++  +a  y++++ pk+ e+ ++g + + +f +G ++G l+GG++ d+++   +F
  gi|488600290|ref|YP_007906761.1|  87 IYANSVYSLTAVRIVHGIASAMVIPVALAYIADLSPKGREGMYMGTFMASMF-FGMGFGPLVGGVIRDMYGMEAVF 161
                                       9********************************************8865443.67789********9*99998888 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.025
                        MFS_1_like 184 yvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlfl..YLkelgas 258
                                       +v++++ v+s++++li+  +  es  k ++   +l+  lkn+ + ++l++ ++  +++g++  Fl +  YL     +
  gi|488600290|ref|YP_007906761.1| 159 AVFISMAVLSFISFLICLLFLPESRGKYRQ--ASLKGALKNKVMRAILFFRAMNAFANGVFMVFLPVlgYL--ISLP 231
                                       5788999999999999999999***99995..8899****************************7653488..8889 PP

                        MFS_1_like 259 ntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaav 335
                                       +t  G+l+    + + +l     +  +     +l+ ++  ++++ fl + +++++  +l++ ++ gi  +l   +a+
  gi|488600290|ref|YP_007906761.1| 232 STQTGMLISTSIFTTAILQRRFGRFADNHNKAVLISAGSAIIAFCFLFIPFLKSFESLLLASLIIGIGGALSMPSAM 308
                                       99999999999999999999999999*************************************************** PP

                        MFS_1_like 336 eyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                         v ++  +  ++t +g ++++ +++G     +i+G + d  +  ++F 
  gi|488600290|ref|YP_007906761.1| 309 ALVTIAGREIGQGTAMGAFNTA-MSIGMITAPMIAGGIMDAMGIYHVFL 356
                                       ****87778889*******998.89***999999999999999988886 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5  29.8    0.0023       6.9      18     366 ..      43     352 ..      36     373 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0023
                              PUCC  18 avlialpllvapfraliGfrSDtkralGwkRvpyiwlGslalalglaiaplalivlsgkgeaeaaatwaglilaava 94 
                                       a+   + l  a+f +liG+ SD+ +     R ++i +G l+++++++i   a  v s+                +++
  gi|488600290|ref|YP_007906761.1|  43 AIFSGFSLSRAVFMPLIGKLSDSRG-----RRFFILTGLLIFTILSFIYIYANSVYSL----------------TAV 98 
                                       555567778899***********99.....889***********88887665544444................556 PP

                              PUCC  95 fllvGlgvslsqTallALladlaeeeerpkvvgllyvmlligivvsaivvgallkdytearLirvvqgvalitlvln 171
                                        ++ G++  ++  + lA +adl+ + +     g     + +g+ ++ +v g++ + y  +     ++  ++i++++ 
  gi|488600290|ref|YP_007906761.1|  99 RIVHGIASAMVIPVALAYIADLSPKGREGMYMGTFMASMFFGMGFGPLVGGVIRDMYGMEAVFISMAVLSFISFLIC 175
                                       67889999999***********************9999**********99999999887777766666666666665 PP

                              PUCC 172 vlalWkievkskkkkeekeeeepslleawlklvaekqalaflaflllgtlaffmqdviLEpYgGevlgLtvgeTTkL 248
                                       +l l +    + ++++ k + ++++  a+l ++a +  +  +++++l +l             G  ++L+ ++T  L
  gi|488600290|ref|YP_007906761.1| 176 LLFLPESRG-KYRQASLKGALKNKVMRAILFFRAMNAFANGVFMVFLPVL-------------GYLISLPSTQTGML 238
                                       554433322.2222334555555555555555555555555555555555.............56788999999888 PP

                              PUCC 249 talfalGtlvGlllaglvlsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlm 325
                                        ++  + t +      +  +r +++++ a+l  ++ ++ ++  +++ +l++   l+++ l++G+++ l   +a++l+
  gi|488600290|ref|YP_007906761.1| 239 ISTSIFTTAI----LQRRFGRFADNHNKAVLISAGSAIIAFCFLFIPFLKSFESLLLASLIIGIGGALSMPSAMALV 311
                                       7776555544....44445555556666666555555555555667888888888899999***9998888888765 PP

                              PUCC 326 ldlaaee.raglalGaWGaaQaiaaglavllggalrdllkal 366
                                        ++a++e  +g+a+Ga   a +i    a +++g++ d + + 
  gi|488600290|ref|YP_007906761.1| 312 -TIAGREiGQGTAMGAFNTAMSIGMITAPMIAGGIMDAMGIY 352
                                       .6666662589*************************998765 PP

>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.2   2.6e-05     0.077      30      95 ..      94     159 ..      79     169 .. 0.80
   2 ?    3.1   1.1     0.026        76      47      81 ..     268     302 ..     259     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                              IncD  30 slptakrlv.avavatilavallvvagllfsgvlcspvsvlaaslffgvgafllggalvggvlttea 95 
                                       sl ta r+v  +a a ++ val  +a l   g     +  + as+ffg+g   l g ++  +   ea
  gi|488600290|ref|YP_007906761.1|  94 SL-TAVRIVhGIASAMVIPVALAYIADLSPKGREGMYMGTFMASMFFGMGFGPLVGGVIRDMYGMEA 159
                                       34.6666663699*************************************75555555555555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.026
                              IncD  47 avallvvagllfsgvlcspvsvlaaslffgvgafl 81 
                                       a + ++   +lf   l s  s+l asl++g+g  l
  gi|488600290|ref|YP_007906761.1| 268 AGSAIIAFCFLFIPFLKSFESLLLASLIIGIGGAL 302
                                       44555666789999*****************8655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.41
# Mc/sec: 2734.27
//
Query:       gi|488600291|ref|YP_007906762.1|  [L=382]
Description: Arabinose efflux permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-56  190.5  58.1    6.4e-29  101.0  23.5    2.0  2  MFS_1       Major Facilitator Superfamily
    2.4e-11   43.2  35.9    3.9e-05   22.7  10.3    3.3  3  Sugar_tr    Sugar (and other) transporter
    6.3e-08   31.5  14.8    0.00018   20.1   3.9    2.1  2  MFS_3       Transmembrane secretion effector
    7.3e-05   21.5  38.7    0.00012   20.8  14.9    2.8  3  MFS_2       MFS/sugar transport protein
    0.00054   18.9  30.9     0.0026   16.7  30.9    2.2  1  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0  23.5   1.8e-32   6.4e-29       1     176 [.      11     185 ..      11     201 .. 0.91
   2 !   95.5  26.8   8.4e-31     3e-27       6     173 ..     207     370 ..     200     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.8e-32
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.l 76 
                                       l++a+f+ +la si++p++ + ++  lg+++  +g + +++al+++++++++G ++drfG  r+ l+g+ lf+++ l
  gi|488600291|ref|YP_007906762.1|  11 LYFAGFVGYLAGSIVFPIIAP-YSMKLGANAFWAGVISGGFALVTSLTMVLFGMIADRFGKYRTSLIGFSLFIVApL 86 
                                       5799****************5.556999***********************************************66 PP

                             MFS_1  77 llllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWra 152
                                       ++++  s  +  ll++r+l Gl++++++pa++al+ d++ + ++g a+g++++++ lG+++gp +gg++a+ +g r 
  gi|488600291|ref|YP_007906762.1|  87 FYIV--SRNYiELLLARFLHGLAMAIFVPAINALVIDLSEEGRKGEALGWIATFTMLGYAFGPSIGGYVAEVFGVRE 161
                                       6666..777779***************************************************************** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeep 176
                                       vf+ + iv++++fv fll+ ++e+
  gi|488600291|ref|YP_007906762.1| 162 VFISCSIVAVIGFVPFLLFRVDER 185
                                       ************994444444443 PP

  == domain 2  score: 95.5 bits;  conditional E-value: 8.4e-31
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                       f+++++++++++   +++   lg++   ig+l+t+ +l +a+  +p+G lsd +Gr +v+++gl++ a+g ++l++ 
  gi|488600291|ref|YP_007906762.1| 207 FFATFGSAVISIYSIPLYLPRLGYDYRDIGFLVTFLFLSSALVRVPAGKLSDSIGRLPVIVFGLVIEAIG-IFLFL- 281
                                       667777777666665566799*************************************************.55555. PP

                             MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                       s+++ +++++ +l+Glg+g+++pag al++d++++e++g+a+g  s++ +l++ lgp++ g++++ +g++ vf++ +
  gi|488600291|ref|YP_007906762.1| 282 SQSFyAIALGTFLTGLGMGFANPAGFALLSDLVSPEHQGFAMGASSTSLQLAVFLGPAIMGYVTETYGFSFVFILSG 358
                                       66666************************************************************************ PP

                             MFS_1 159 ivsllafvlfllllp 173
                                        +++l++v   ++l+
  gi|488600291|ref|YP_007906762.1| 359 MFTALSAV---VYLV 370
                                       ******99...3433 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   7.1   2.2e-07   0.00078      42     121 ..      37     113 ..      10     126 .. 0.82
   2 !   14.5   2.3   3.4e-06     0.012      47      91 ..     131     175 ..     121     181 .. 0.91
   3 !   22.7  10.3   1.1e-08   3.9e-05      47     191 ..     234     371 ..     192     381 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.2e-07
                                       HH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHH CS
                          Sugar_tr  42 eessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGl 118
                                        + + + g+i + f ++  ++ +++g+++drfG+  + li+  lf+++ +  +++    ++  l+++R+l G+++ +
  gi|488600291|ref|YP_007906762.1|  37 GANAFWAGVISGGFALVTSLTMVLFGMIADRFGKYRTSLIGFSLFIVAPLFYIVSR---NYIELLLARFLHGLAMAI 110
                                       34567999************************************************...9**************988 PP

                                       HHH CS
                          Sugar_tr 119 asv 121
                                       +  
  gi|488600291|ref|YP_007906762.1| 111 FVP 113
                                       765 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.4e-06
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigav 91 
                                        +g+i+ ++++G ++G  ++g+++++fG + +++ +++++vig v
  gi|488600291|ref|YP_007906762.1| 131 ALGWIATFTMLGYAFGPSIGGYVAEVFGVREVFISCSIVAVIGFV 175
                                       589***************************************965 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                       ++g++v ++++ +++  + ag+l+d +GR ++++++ v+  ig++l   ++   s++++++g +l+G+g+G+a+   
  gi|488600291|ref|YP_007906762.1| 234 DIGFLVTFLFLSSALVRVPAGKLSDSIGRLPVIVFGLVIEAIGIFLFL-SQ---SFYAIALGTFLTGLGMGFANPAG 306
                                       6789999999999999999************************99865.55...5********************** PP

                                       HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                          Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllfl 191
                                         ++s +  +++ g+ ++   +++++  +++  ++  + +t +   + + + l+ +++ l +++ l+l
  gi|488600291|ref|YP_007906762.1| 307 FALLSDLVSPEHQGFAMGASSTSLQLAVFLGPAIMGYVTETYG---FSFVFILSGMFTALSAVVYLVL 371
                                       ******************************9655544444444...6788888888885555555544 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.2     4e-07    0.0014      57     178 ..      53     169 ..      37     187 .. 0.85
   2 !   20.1   3.9     5e-08   0.00018      60     184 ..     248     367 ..     241     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-07
                             MFS_3  57 PifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvk 133
                                        + l  +l G +aD f + +  l++ +l +++ ++ +v+        + ll   +l g+ +a+  Pa +A v +l +
  gi|488600291|ref|YP_007906762.1|  53 VTSLTMVLFGMIADRFGKYRTSLIGFSLFIVAPLFYIVSRN-----YIELLLARFLHGLAMAIFVPAINALVIDLSE 124
                                       555667889************99999999998877766543.....35678889*********************** PP

                             MFS_3 134 rrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnals 178
                                            +A    +    +  + GP +gG +  ++G   +f   ++ 
  gi|488600291|ref|YP_007906762.1| 125 EGRKGEALGWIATFTMLGYAFGPSIGGYVAEVFGVREVFISCSIV 169
                                       ********999999999******************9999765443 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5e-08
                             MFS_3  60 llsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrd 136
                                       l+ ++aG l+D++ r  v++ + ++ a++  l  + +++      ++   t+l+g+G+ + +Pa  A +++lv+ ++
  gi|488600291|ref|YP_007906762.1| 248 LVRVPAGKLSDSIGRLPVIVFGLVIEAIGIFLFLSQSFY------AIALGTFLTGLGMGFANPAGFALLSDLVSPEH 318
                                       77899**********999999999888876555554444......445569************************** PP

                             MFS_3 137 vpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnal.sylaliv 184
                                          A+  +s  + +a   GPA+ G +  + G  ++f +  + + l  +v
  gi|488600291|ref|YP_007906762.1| 319 QGFAMGASSTSLQLAVFLGPAIMGYVTETYGFSFVFILSGMfTALSAVV 367
                                       ************************************8764313444333 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8  14.9   3.3e-08   0.00012     236     387 ..      18     160 ..       9     180 .. 0.82
   2 !    6.9   2.3   0.00055         2     257     330 ..     128     216 ..     125     227 .. 0.79
   3 !    4.6  16.7    0.0027       9.5     226     396 ..     199     351 ..     195     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-08
                             MFS_2 236 aalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqp 311
                                        +la+ + + + + y  + lg n+++a v+++ + + + l+++l+  +a r+gk++t l+g++l iv   l++++  
  gi|488600291|ref|YP_007906762.1|  18 GYLAGSIVFPIIAPYSMK-LGaNAFWAGVISGGFALVTSLTMVLFGMIADRFGKYRTSLIGFSLFIVAP-LFYIV-S 91 
                                       555555555555555544.45599********999****************************999876.56777.8 PP

                             MFS_2 312 snlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsafgyr 387
                                       +n++ +l++ ++ g++   +a++++++ a v+D +e    + r+g++ +  ++++ l+ ++g ++ g++ + fg r
  gi|488600291|ref|YP_007906762.1|  92 RNYIELLLARFLHGLA---MAIFVPAINALVIDLSE----EGRKGEALGWIATFTMLGYAFGPSIGGYVAEVFGVR 160
                                       ****************...66666677777777777....5679*****************************984 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00055
                             MFS_2 257 ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll...............qpsnlllfl 318
                                       +g+a  +++++++++ + g  +  ++a  +g + +++++++++++++v +ll+               +++ + +++
  gi|488600291|ref|YP_007906762.1| 128 KGEALGWIATFTMLGYAFGPSIGGYVAEVFGVREVFISCSIVAVIGFVPFLLFrvderrgsfgfefdlDKKAMFAAM 204
                                       67888899999999999999999*************************99999999999999999998666666666 PP

                             MFS_2 319 vllviagfgvgv 330
                                       v +++++ ++++
  gi|488600291|ref|YP_007906762.1| 205 VPFFATFGSAVI 216
                                       655554433333 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0027
                             MFS_2 226 flillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltiv 301
                                       ++  +++ ++a+++ +v    ++  +   lg +++++ ++ +++++s++l+ + + +l   +g+  ++++g+++ ++
  gi|488600291|ref|YP_007906762.1| 199 AMFAAMVPFFATFGSAVISIYSIPLYLPRLGyDYRDIGFLVTFLFLSSALVRVPAGKLSDSIGRLPVIVFGLVIEAI 275
                                       45555555666666666655555555556777**************************************9999887 PP

                             MFS_2 302 llvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsg 378
                                       +   +l+l  ++ ++  + ++++g+g+g+a+ +  ++l+d+v           +g+++++ s+  +la+ +g +++g
  gi|488600291|ref|YP_007906762.1| 276 GI--FLFL-SQSFYAIALGTFLTGLGMGFANPAGFALLSDLVSPEH-------QGFAMGASSTSLQLAVFLGPAIMG 342
                                       75..5566.78*******************************8765.......99*********************9 PP

                             MFS_2 379 llLsafgyrakasvqspq 396
                                       ++ +++g+         +
  gi|488600291|ref|YP_007906762.1| 343 YVTETYGF---------S 351
                                       99999998.........3 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 !   16.7  30.9   7.3e-07    0.0026       9     384 ..      16     355 ..       5     356 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.3e-07
                        MFS_1_like   9 FfffaalgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkk.vvilslllsavlflsllf 84 
                                       F+ + a + ++P +  y  + g +a   g+i+    l++ l   ++g++aDrfgk+ + ++ +sl++ a lf     
  gi|488600291|ref|YP_007906762.1|  16 FVGYLAGSIVFPIIAPYSMKLGANAFWAGVISGGFALVTSLTMVLFGMIADRFGKYRTsLIGFSLFIVAPLFY---- 88 
                                       56677889999********************************************887477777777777777.... PP

                        MFS_1_like  85 ippskerqeesklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkelgedrkd..yGrqrlfGsvGya 159
                                       i+                     + +++ l+l ++l  + +a  ++ ++a+++   +e rk    G +  f  +Gya
  gi|488600291|ref|YP_007906762.1|  89 IV---------------------SRNYIELLLARFLHGLAMAIFVPAINALVIDLSEEGRKGeaLGWIATFTMLGYA 144
                                       33.....................699**************************9988666654459999999999999 PP

                        MFS_1_like 160 ifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvali 236
                                           i G++ + + v     + +++ + ++ vi ++ +l +  +e   + +             ++++++  +v ++
  gi|488600291|ref|YP_007906762.1| 145 FGPSIGGYVAEVFGV-----REVFISCSIVAVIGFVPFLLFRVDERRGSFGFEF--------DLDKKAMFAAMVPFF 208
                                       999999999888888.....459******************9999988888773........345788888888999 PP

                        MFS_1_like 237 lgmswgiienF.lflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiien 312
                                         + +++i  + + lYL  lg+    +G lv++  +++  + + a kl + +G   +++++l++ ++  +l  + ++
  gi|488600291|ref|YP_007906762.1| 209 ATFGSAVISIYsIPLYLPRLGYDYRDIGFLVTFLFLSSALVRVPAGKLSDSIGRLPVIVFGLVIEAIGIFLF-LSQS 284
                                       99999999999778**************************************************99987775.3378 PP

                        MFS_1_like 313 awlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       +  + +  +L g+ +g    a+    s++++++++++ +g  s+++  l  +lG  i G++ ++++  f+F 
  gi|488600291|ref|YP_007906762.1| 285 FYAIALGTFLTGLGMGFANPAGFALLSDLVSPEHQGFAMGA-SSTSLQLAVFLGPAIMGYVTETYGFSFVFI 355
                                       88888999********************************6.566799*************99999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2348.76
//
Query:       gi|488600292|ref|YP_007906763.1|  [L=135]
Description: Small primase-like proteins (Toprim domain) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-06   26.3   0.4    1.5e-05   25.4   0.1    1.7  2  Toprim_4  Toprim domain
    0.00035   20.8   0.4      0.058   13.6   0.4    2.4  1  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.3   1.2e+04      43      57 ..       4      18 ..       2      23 .. 0.59
   2 !   25.4   0.1   1.6e-09   1.5e-05       2      86 ..      26      97 ..      25      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                          Toprim_4 43 ktenlveaekkvkev 57
                                       +e+lve ++++ke+
  gi|488600292|ref|YP_007906763.1|  4 SYEELVEIREIIKEI 18
                                      455666666666666 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.6e-09
                          Toprim_4  2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaellle 80
                                      ++iiVEg+ D  al ++gi++ v +    +s+ ++i  ++ ++          + vil++d D++G++  ++l+++l+ 
  gi|488600292|ref|YP_007906763.1| 26 AVIIVEGRSDEKALKEMGIHGEVRFAS--ISSDAEIV-DSVRS----------RFVILLTDWDYRGNKIEKELSRKLEL 91
                                      79*********************9877..77777777.57777..........89********************8887 PP

                          Toprim_4 81 egvkvt 86
                                      +g+ v 
  gi|488600292|ref|YP_007906763.1| 92 NGIAVD 97
                                      788776 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.4   6.4e-06     0.058      61      88 ..      63      90 ..      26     108 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-06
                                      HHHSEEEEECSSSHHHHHHHHHHHHHHT CS
                            Toprim 61 kradeiilatDpDreGeaiawellevlk 88
                                       r   +il+tD D  G +i +el   l+
  gi|488600292|ref|YP_007906763.1| 63 VRSRFVILLTDWDYRGNKIEKELSRKLE 90
                                      234579****************997666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 830.95
//
Query:       gi|488600293|ref|YP_007906764.1|  [L=105]
Description: TIGR00251 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-20   70.7   1.2    1.1e-19   70.3   1.2    1.2  1  DUF167    Uncharacterised ACR, YggU family COG1872
    2.9e-05   23.9   0.1    3.5e-05   23.7   0.1    1.1  1  SAVED     SMODS-associated and fused to various effectors sen
  ------ inclusion threshold ------
      0.034   14.1   0.3       0.06   13.3   0.3    1.4  1  DUF4974   Domain of unknown function (DUF4974)


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   1.2   1.8e-23   1.1e-19       2      76 ..      14      84 ..      13      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.8e-23
                                      EEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                            DUF167  2 vilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                      +il++ v+ +akk++i+ ++++e+r+a++vr+++p++d+kAN+++i+ + k++gv   +vei++Geks++Kv+r+
  gi|488600293|ref|YP_007906764.1| 14 TILSISVSANAKKTRIP-HAYNEWRKAIEVRIKSPARDNKANREIISEMEKIFGV---EVEILKGEKSSNKVIRV 84
                                      589**************.9999********************************5...7***************9 PP

>> SAVED  SMODS-associated and fused to various effectors sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   5.9e-09   3.5e-05      74     148 ..       8      85 ..       2      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.9e-09
                             SAVED  74 igkgaevalalslsadidderlkellgdnlpiieitlpnpgndairspedlealakavrdalrelkaeh...gvkri 147
                                       +++g++++l++s+sa+++++r++++ +++++ ie+++++p +d+ +++e ++++ k +   ++ lk e+   +v r+
  gi|488600293|ref|YP_007906764.1|   8 KKDGDRTILSISVSANAKKTRIPHAYNEWRKAIEVRIKSPARDNKANREIISEMEKIFGVEVEILKGEKssnKVIRV 84 
                                       4556699***************************************************9999999998863444444 PP

                             SAVED 148 H 148
                                       H
  gi|488600293|ref|YP_007906764.1|  85 H 85 
                                       4 PP

>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3     1e-05      0.06      10      51 ..      55      96 ..      50      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                      HHHHHHHHHHHT--EEE-T.TS----EEEEEES-.-.HHHHHH CS
                           DUF4974 10 eeilkkLerwYnveivien.eelknyrftgtfsrnesleevLe 51
                                      +ei+ ++e+ ++ve++i + e+ +n+ +++ +  ++ + e+L+
  gi|488600293|ref|YP_007906764.1| 55 REIISEMEKIFGVEVEILKgEKSSNKVIRVHL-SYDRVVEILK 96
                                      79***************974668888899999.5567777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 642.01
//
Query:       gi|488600294|ref|YP_007906765.1|  [L=173]
Description: Nitroreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-37  128.7   0.3    8.6e-21   74.7   0.1    2.0  2  Nitroreductase  Nitroreductase family
      1e-14   54.6   0.0    9.8e-13   48.2   0.0    3.0  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 !   54.9   0.0   1.2e-18   1.1e-14       2      62 ..       9      69 ..       8      72 .. 0.95
   2 !   74.7   0.1   9.6e-25   8.6e-21      83     170 .]      66     151 ..      65     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.2e-18
                                      HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHH CS
                    Nitroreductase  2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelll 62
                                       +R SiRkF++e+vp++ l +il+a+  aPsagnlq  +f+vv+d++ + ++a+a+l+++ 
  gi|488600294|ref|YP_007906765.1|  9 FNRVSIRKFRKEKVPDDILLEILKAGNSAPSAGNLQARDFIVVRDEKMKVEIAKASLNQMF 69
                                      689******************************************************9996 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 9.6e-25
                                       HHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S.. CS
                    Nitroreductase  83 aqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpde 159
                                       +q ++a+apv+iv+ a++++s r ++er+  ya +da aa++n+l+aAtalGlg++++g+f e+   +  llg+pd+
  gi|488600294|ref|YP_007906765.1|  66 NQMFIAEAPVVIVVCANYPRSMRVYGERGKFYAEQDATAAVENMLIAATALGLGCVWVGAFHEEL--ISSLLGIPDH 140
                                       577899***********************************************************..********** PP

                                       SEEEEEEEEE- CS
                    Nitroreductase 160 eeivvliavGy 170
                                        ++v++i++Gy
  gi|488600294|ref|YP_007906765.1| 141 ARPVAIIPIGY 151
                                       **********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   1.1e-16   9.8e-13       3     152 ..       5     171 ..       3     173 .] 0.76

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.1e-16
                                       HHHHHH--B---B--S---HHHHHHHHH-----S...S----...-EE.E..............-SSSSEEEE---- CS
                    TM1586_NiRdase   3 yeaiekRhsvRkYkdealeeelleelkeaieeinkesglelq...lvidenkafkskvakl.gkfkgvpnyialvge 75 
                                       ++ i++R+s+Rk+++e++++++l e+ +a ++  ++ +l+ +   +v de+ + +++ a+l ++f   + ++++v+ 
  gi|488600294|ref|YP_007906765.1|   5 LDVIFNRVSIRKFRKEKVPDDILLEILKAGNSAPSAGNLQARdfiVVRDEKMKVEIAKASLnQMFIAEAPVVIVVCA 81 
                                       689**************************999998887776522144455544444444332355555555555555 PP

                                       SSHHHHHHHH....HHHHH........HHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS----. CS
                    TM1586_NiRdase  76 kkedleekaG....Yygeq........lvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktklve 139
                                       +  ++++ +G    +y eq        +++ +talGlg  Wvg+ +++  ++ + +++  + v++I +Gy+++k  +
  gi|488600294|ref|YP_007906765.1|  82 NYPRSMRVYGergkFYAEQdataavenMLIAATALGLGCVWVGAFHEElISSLLGIPDHARPVAIIPIGYPDEKPEK 158
                                       6677777777666766554333333339***************99999866779*********************** PP

                                       -----HHHHBSS- CS
                    TM1586_NiRdase 140 akrkpleelcevk 152
                                       ++r p++el++ +
  gi|488600294|ref|YP_007906765.1| 159 RRRYPIQELTHWE 171
                                       *********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1156.89
//
Query:       gi|488600295|ref|YP_007906766.1|  [L=526]
Description: D-3-phosphoglycerate dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-66  221.7   0.0    8.7e-66  220.7   0.0    1.6  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.7e-39  133.9   0.1    4.4e-39  133.2   0.1    1.3  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    2.6e-12   46.3   0.4    1.2e-11   44.2   0.0    2.3  2  ACT             ACT domain
    2.7e-05   24.4   0.2    7.1e-05   23.0   0.0    1.8  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00015   21.4   0.1    0.00043   19.9   0.0    1.8  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
  ------ inclusion threshold ------
       0.03   14.2   0.3        0.2   11.5   0.0    2.4  3  Rossmann-like   Rossmann-like domain
      0.097   13.1   0.0       0.29   11.6   0.0    1.8  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,


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 !  220.7   0.0   3.4e-69   8.7e-66       1     178 []     105     279 ..     105     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: 220.7 bits;  conditional E-value: 3.4e-69
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       +a+++a++r++++ad++v+eg+w ++k++ g+el+gkt+G+iGlGr+G +vakr+k ++m+v+ayd++ ++e+ ++e
  gi|488600295|ref|YP_007906766.1| 105 IAMIFAVARKIPQADRSVKEGKW-ERKKFIGTELRGKTLGVIGLGRVGYEVAKRAKMLEMHVLAYDPYISEEK-AKE 179
                                       689********************.9*******************************************99776.*** PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                        gve   +e++l++sD++++h+p t+et ++++++e+++mk+ga++iN+aRGg+vde+aL+e L +gk+aga+lDv+
  gi|488600295|ref|YP_007906766.1| 180 IGVEILPFEDVLRKSDFITIHVPKTKETVGMFSKREFELMKDGAYIINCARGGIVDEKALYESLINGKLAGAGLDVY 256
                                       ***************************************************************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                       e+ep+  d+pll+l+nv+ tPHi+
  gi|488600295|ref|YP_007906766.1| 257 ENEPPG-DNPLLKLDNVVTTPHIG 279
                                       ****99.66*************98 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   0.1   1.7e-42   4.4e-39       1     134 []       3     311 ..       3     311 .. 1.00

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 1.7e-42
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vl+++p+++e+++ +k++g++v+v ++l++e+l++ ++d+d+livrs tkvtaev+ea+++L++i+rag+GvDn+D+
  gi|488600295|ref|YP_007906766.1|   3 VLVSDPIPDEAIAMMKNAGIDVDVMTSLSQEDLIKVIPDYDGLIVRSGTKVTAEVIEAAKNLRIIGRAGAGVDNIDI 79 
                                       799**************999********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       + a+e+Gi+V+n+pg ++ s+AEl+                                                    
  gi|488600295|ref|YP_007906766.1|  80 KKATEKGIVVVNAPGGNSVSTAELAiamifavarkipqadrsvkegkwerkkfigtelrgktlgviglgrvgyevak 156
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|488600295|ref|YP_007906766.1| 157 rakmlemhvlaydpyiseekakeigveilpfedvlrksdfitihvpktketvgmfskrefelmkdgayiincarggi 233
                                       ***************************************************************************** PP

                                       ..............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ..............................................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                                                     a+T+eaq  ++ ++a ++++f kg +++nav
  gi|488600295|ref|YP_007906766.1| 234 vdekalyeslingklagagldvyeneppgdnpllkldnvvttphigASTKEAQISVGLTIAGEIINFSKGLPARNAV 310
                                       ***************************************************************************** PP

                                       S CS
                                       x RF
                        2-Hacid_dh 134 n 134
                                       n
  gi|488600295|ref|YP_007906766.1| 311 N 311
                                       8 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.81   2.1e+03      25      65 ..      21      64 ..      16      90 .. 0.68
   2 !   44.2   0.0   4.6e-15   1.2e-11       6      66 ..     457     516 ..     453     517 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.81
                                      TSEEEEEEEEEESTT...ECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT 25 giNidsieqrssedk...vagivfvvivvdeedleevlealkkl 65
                                      gi +d +++ s ed    + ++  +++  ++++++ev+ea k+l
  gi|488600295|ref|YP_007906766.1| 21 GIDVDVMTSLSQEDLikvIPDYDGLIVRSGTKVTAEVIEAAKNL 64
                                      56666665555555444555555556666666777777766655 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 4.6e-15
                                       EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                       + +D+PG+++rv++++++++iNi+ + +++++ k +gi  + ++vd+ + ++vle+  kl 
  gi|488600295|ref|YP_007906766.1| 457 LHEDKPGVIGRVGTLFGENNINIAGMIVGRHGGK-GGIQLMLLLVDDVPSKDVLEQMVKLD 516
                                       567*******************************.************99999999988875 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.8   4.6e+03      59      59 ..      67      67 ..      13     107 .. 0.60
   2 !   23.0   0.0   2.8e-08   7.1e-05       2     103 ..     142     242 ..     141     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                                      E CS
                     NAD_binding_2 59 v 59
                                      +
  gi|488600295|ref|YP_007906766.1| 67 I 67
                                      1 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 2.8e-08
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g+iGlG  G + a++ +  +++v +y+    + e++ + g++ +   e+++++ d++ + v+++k++  + ++  +
  gi|488600295|ref|YP_007906766.1| 142 LGVIGLGRVGYEVAKRAKMLEMHVLAYDPYI-SEEKAKEIGVE-ILPFEDVLRKSDFITIHVPKTKETVGMFSKrEF 216
                                       8***************************542.23344444554.456799****************99999988899 PP

                                       CC--TT-EEEE-S---HHHHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelake 103
                                       e +k g+++i+++   + d + l++ 
  gi|488600295|ref|YP_007906766.1| 217 ELMKDGAYIINCARGGIVDEKALYES 242
                                       ***********998877777777665 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1   2.8e+03      33      33 ..      71      71 ..      17     112 .. 0.60
   2 !   19.9   0.0   1.7e-07   0.00043       2      91 ..     137     225 ..     136     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                      E CS
                              IlvN 33 g 33
                                      g
  gi|488600295|ref|YP_007906766.1| 71 G 71
                                      1 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.7e-07
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHH.HHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqk.evy 77 
                                       l+gk++ viG G  G   a+  +   l++ v  ++   s +kAke g+e+l  +++ +k+d+++i +P + ++  ++
  gi|488600295|ref|YP_007906766.1| 137 LRGKTLGVIGLGRVGYEVAKRAKM--LEMHVLAYDPYISEEKAKEIGVEILPFEDVLRKSDFITIHVPKTKETvGMF 211
                                       789***************997665..5555666777779*****************************876542567 PP

                                       HHHTGGG--TT-EE CS
                              IlvN  78 eeeiepnlkegkal 91 
                                       +++  + +k+g+++
  gi|488600295|ref|YP_007906766.1| 212 SKREFELMKDGAYI 225
                                       77777777777743 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         1   2.6e+03      85     109 ..      74      98 ..      12     105 .. 0.58
   2 ?   11.5   0.0   7.6e-05       0.2      12      80 ..     141     205 ..     135     229 .. 0.86
   3 ?   -2.7   0.0       1.9   4.9e+03       5      21 ..     281     297 ..     277     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                     Rossmann-like  85 vkglaatgavraGtivahtsganGv 109
                                       v+++  ++a+ +G +v+ + g n v
  gi|488600295|ref|YP_007906766.1|  74 VDNIDIKKATEKGIVVVNAPGGNSV 98 
                                       5566667777777777777776665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.6e-05
                     Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdae 80 
                                       ++G+i+ GrvG  +++  +  + +v +       s+e+a++   +v++l+ edv ++++++ + vP ++
  gi|488600295|ref|YP_007906766.1| 141 TLGVIGLGRVGYEVAKRAKMLEMHVLAYDP--YISEEKAKEI--GVEILPFEDVLRKSDFITIHVPKTK 205
                                       579***********9999999988888765..6899999885..89********************875 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.9
                     Rossmann-like   5 dersarlsvGiisaGrv 21 
                                       ++++a++svG+  aG++
  gi|488600295|ref|YP_007906766.1| 281 STKEAQISVGLTIAGEI 297
                                       679999****9999975 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 ?   11.6   0.0   0.00011      0.29      22      77 ..     154     204 ..     151     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                       HHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C  22 iieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehd 77 
                                       ++++ +  +++v +yDP+++ee++++     gve++ ++e+ l+++d i i+++  
  gi|488600295|ref|YP_007906766.1| 154 VAKRAKMLEMHVLAYDPYISEEKAKE----IGVEIL-PFEDVLRKSDFITIHVPKT 204
                                       56666667889***********9987....689999.79************99763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3806.95
//
Query:       gi|488600296|ref|YP_007906767.1|  [L=336]
Description: RNA 3-phosphate cyclase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-76  255.2   0.0    4.4e-76  255.0   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
      4e-14   53.0   0.0    7.4e-14   52.1   0.0    1.4  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 !  255.0   0.0   4.9e-80   4.4e-76       2     217 ..       9     317 ..       8     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 255.0 bits;  conditional E-value: 4.9e-80
                                       TTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   2 gegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikagey 78 
                                       gegGgqiLR+++aLs++tgk+vrI++IRanR+kPGL++qhl++++ ++ +++aeveg ++ s+e++F+P+++k++ +
  gi|488600296|ref|YP_007906767.1|   9 GEGGGQILRSSIALSCITGKAVRITRIRANRPKPGLAPQHLKGIESAKMLCDAEVEGLKVRSMEVTFRPSDLKPKGL 85 
                                       8**************************************************************************** PP

                                       EEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  79 evdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGg 155
                                       e+digtAGs+tl+lq +l++ ++     +++++GgT+v++ap+vdy+++v+l++l+++g +++++e+  rG+ypkGg
  gi|488600296|ref|YP_007906767.1|  86 EIDIGTAGSVTLILQSILLPSILRG--CRMKIRGGTDVKWAPTVDYFRNVTLKALSELG-VRCNFEVITRGYYPKGG 159
                                       ********************99998..79******************************.7**************** PP

                                       EEEEEEEE-.-S---EB............................................................ CS
                                       xxxxxxxxxxxxxxxxx............................................................ RF
                               RTC 156 Gevelevepskklkpie............................................................ 172
                                       Gev++e+e+s +l+ ++                                                            
  gi|488600296|ref|YP_007906767.1| 160 GEVVVETEES-SLEGVDfndfkdtksktvygishcsnlpdhvasrqaksaerflrkngfesdiklevtkaystgsgi 235
                                       *******985.79999999********************************************************** PP

                                       .....................................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHH CS
                                       .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 .....................................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvi 212
                                                                            a++D+h +dq+++f+aLakgk++++++e+t+h +++++vi
  gi|488600296|ref|YP_007906767.1| 236 tlwsgykggsalgekgkraenvgqesameiakemnskAVFDRHIADQVMVFAALAKGKTSYTTSEITMHQKSNAYVI 312
                                       ***************************************************************************** PP

                                       HHHSS CS
                                       xxxxx RF
                               RTC 213 eqflg 217
                                       +qf+g
  gi|488600296|ref|YP_007906767.1| 313 KQFFG 317
                                       ***97 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   8.2e-18   7.4e-14       7     102 ..     185     269 ..     181     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 8.2e-18
                                       SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE-T CS
                        RTC_insert   7 krirGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealgek 83 
                                       k + G++++++++ +va+r++++a++ L+k + + +i+++      +++ s G+gi+L+  ++      g++algek
  gi|488600296|ref|YP_007906767.1| 185 KTVYGISHCSNLPDHVASRQAKSAERFLRKNGFESDIKLE-----VTKAYSTGSGITLWSGYK------GGSALGEK 250
                                       7899***************************988888888.....3567789**********6......58****** PP

                                       T--HHHHHHHHHHHHHHHH CS
                        RTC_insert  84 gvppedvGeeaaeeLleei 102
                                       g+++e vG+e a e+ +e+
  gi|488600296|ref|YP_007906767.1| 251 GKRAENVGQESAMEIAKEM 269
                                       **************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2455.83
//
Query:       gi|488600297|ref|YP_007906768.1|  [L=279]
Description: Zn-dependent hydrolase, including glyoxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   21.6   2.4     0.0015   18.6   2.4    2.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00069   19.2   0.0     0.0014   18.2   0.0    1.4  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 !   18.6   2.4   1.7e-07    0.0015       7     197 .]      23     190 ..      17     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.7e-07
                                       EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGC..TTHHCCEETCCEHHHHC CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglggl..veatdvpvgavaeeapa 81 
                                       n+ l+    + iLiD+G++   a +           ++v+ v+l+H H+DH+ ++  +  + +    +   + +   
  gi|488600297|ref|YP_007906768.1|  23 NCLLL----DSILIDAGLGDVGAVK-----------DRVEVVLLSHTHPDHVLDAWVFneMGRKVLSPEGFETDIDT 84 
                                       56666....5777777777777775...........89**************9999884445666677777777788 PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                       l ++ ad  a++++       +   +++ e +++++ +     + +  + + ++++v++ +g++ +  D  l++  +
  gi|488600297|ref|YP_007906768.1|  85 LANRLADELAEYWKE--FVKGVGLRGFKSEKYEEGLIFENPEIIAYKLPGHTLDMHVFLIDGRIMYGADIDLTRFGP 159
                                       888888777777774..555555556666666666666666666666666667888888888888888888888888 PP

                                       CCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 159 ridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       + +         + sd e+ ++s+++l++++ e+++ +H
  gi|488600297|ref|YP_007906768.1| 160 WYGN--------PESDLEQFRKSIEELRKMDFELYISSH 190
                                       8888........777777777777777777777777666 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 !   18.2   0.0   1.5e-07    0.0014       3      78 ..      30      90 ..      29     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-07
                                      EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2  3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78
                                      iLiDag++ ++           +++  ++++Vll+h H DH+ ++  + e+     +++ p+g   ++++   +la
  gi|488600297|ref|YP_007906768.1| 30 ILIDAGLGDVGA----------VKD--RVEVVLLSHTHPDHVLDAWVFNEMGR---KVLSPEGFETDIDTLANRLA 90
                                      677777773333..........345..89***************999999422...47777777777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1658.50
//
Query:       gi|488600298|ref|YP_007906769.1|  [L=437]
Description: NADPH:sulfur oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-67  225.6   0.3      1e-66  225.2   0.3    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.5e-26   91.6   7.1    6.8e-21   74.6   0.4    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      6e-21   74.8   0.1    1.8e-20   73.2   0.0    1.8  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    3.8e-15   55.9   3.2    2.5e-14   53.2   0.1    2.3  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.1e-14   53.9   0.5      0.083   12.4   0.0    4.1  4  DAO             FAD dependent oxidoreductase
    1.6e-11   43.6   3.5      0.024   13.3   0.1    4.1  4  HI0933_like     HI0933-like protein
    2.6e-08   34.0   0.0       0.01   16.1   0.0    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.9e-07   30.2   0.0     0.0016   17.8   0.0    2.3  2  Amino_oxidase   Flavin containing amine oxidoreductase
    9.5e-07   28.9   1.1        1.8    8.5   0.1    4.2  4  NAD_binding_9   FAD-NAD(P)-binding
    1.8e-06   27.3   0.3      0.062   12.4   0.0    3.4  3  FAD_binding_2   FAD binding domain
    2.1e-06   28.1   0.7     0.0014   19.0   0.3    2.4  2  NAD_binding_7   Putative NAD(P)-binding
    3.8e-06   26.6   0.1    7.7e-06   25.6   0.1    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.8e-05   24.1   0.2       0.13   11.4   0.0    3.3  3  Thi4            Thi4 family
    3.5e-05   24.6   0.1     0.0049   17.7   0.0    2.5  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00011   22.5   1.8      0.041   14.1   0.1    3.4  3  TrkA_N          TrkA-N domain
     0.0002   20.6   1.4       0.19   10.7   0.0    3.3  4  Lycopene_cycl   Lycopene cyclase protein
      0.002   17.3   0.4      0.026   13.7   0.0    2.6  4  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.003   17.5   1.7     0.0042   17.0   0.2    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.019   14.6   0.1      0.048   13.3   0.0    1.7  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.055   12.7   2.7        9.4    5.4   0.0    3.1  3  FAD_binding_3   FAD binding domain
       0.11   12.2   0.1       0.17   11.6   0.1    1.2  1  Cmyb_C          C-myb, C-terminal
       0.22   10.3   3.8        2.2    7.0   0.1    3.3  4  Trp_halogenase  Tryptophan halogenase
       0.29   10.2   6.8         10    5.0   0.2    3.8  4  GIDA            Glucose inhibited division protein A
       0.46    9.8   2.3         15    4.8   0.2    2.6  3  FAD_oxidored    FAD dependent oxidoreductase
        1.5    8.0   8.3        4.7    6.4   0.2    2.9  4  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 !  225.2   0.3   1.4e-69     1e-66       2     278 ..       2     276 ..       1     298 [. 0.91

  Alignments for each domain:
  == domain 1  score: 225.2 bits;  conditional E-value: 1.4e-69
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH..HHHHCHHHHCCCCHCCT CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias..evvkklnqgielllgee 74 
                                       +vvviGgG++G++ a ++++   + kvt++e+++ + +  c ++++++gv+e ++ +    +v   + gi+l+++++
  gi|488600298|ref|YP_007906769.1|   2 RVVVIGGGAGGMSSASRVRAlkPEWKVTVFEATNFVSHAPCGIPYVVEGVSELPKLMYypPEVFIEKRGIDLRMNTK 78 
                                       8*******************755*******9888888999999************999**666777889******99 PP

                                       CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHH.CCSS-TSEEEEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       Pyr_redox_2  75 vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaeal.klkllpkrivvvGg 150
                                       v+++ +++  vk+   ++g+e++i+ d+lv+AtG+sp ++gi+G   ++++ v+   +ae++ +++++ ++iv+vG+
  gi|488600298|ref|YP_007906769.1|  79 VTDVTRNS--VKYV--ENGEEKEIEWDYLVIATGASPIRPGIEGIDLEGIFTVDLPPDAERIvRYAEKAENIVIVGS 151
                                       ****8777..4442..248899***********************9999*********99982455666******** PP

                                       SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 151 GyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeid 227
                                       GyiG+E+A a++  +k+vt++e ++++l+++d+++++ +++++ek  v+++l+++v++++g+++ +e v +d+ e++
  gi|488600298|ref|YP_007906769.1| 152 GYIGLEMAEAFSARKKNVTVIEMLNHPLPNFDEDIAEVVKKEMEK-WVDLRLNEKVTAFEGKDR-VEKVVTDKGEYK 226
                                       *********************************************.5****************8.9988899999** PP

                                       ESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 228 adlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva 278
                                       ad+v+vavG +p+tel+ e+lg+++ e+g+i +d++++t+++++ya+GD+a
  gi|488600298|ref|YP_007906769.1| 227 ADMVIVAVGAKPNTELA-ERLGVKIGETGAIWTDRKMQTSMENVYACGDCA 276
                                       *****************.********************************* PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1    0.0006      0.43       1      31 [.       2      34 ..       2      39 .. 0.89
   2 !    8.2   0.1    0.0051       3.7      50      73 ..      66      90 ..      63      94 .. 0.88
   3 !   74.6   0.4   9.5e-24   6.8e-21       1      78 [.     145     220 ..     145     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0006
                                      EEEEECSSHHHHHHHHHHHHTT..SEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelg..kkVtvvers 31
                                      +vvv+GgG  g+  A+  ++l+   kVtv+e+ 
  gi|488600298|ref|YP_007906769.1|  2 RVVVIGGGAGGMSSASRVRALKpeWKVTVFEAT 34
                                      79*******************965699999975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0051
                                      HHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox 50 lekngievllntkveeiegsedg.v 73
                                      +ek+gi++++ntkv+ ++ ++ + v
  gi|488600298|ref|YP_007906769.1| 66 IEKRGIDLRMNTKVTDVTRNSVKyV 90
                                      5899**************9998766 PP

  == domain 3  score: 74.6 bits;  conditional E-value: 9.5e-24
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       ++v+vG+GyiglE+A+a+++ +k+Vtv+e+ +++l+++De++++++++++ek  ++++ln+kv+++eg+++ ve+v+
  gi|488600298|ref|YP_007906769.1| 145 NIVIVGSGYIGLEMAEAFSARKKNVTVIEMLNHPLPNFDEDIAEVVKKEMEKW-VDLRLNEKVTAFEGKDR-VEKVV 219
                                       59**************************************************9.****************9.99999 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       +
  gi|488600298|ref|YP_007906769.1| 220 T 220
                                       7 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 !   73.2   0.0   2.5e-23   1.8e-20       4     105 ..     322     424 ..     319     428 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 2.5e-23
                                       EEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEECTTHHH.HHHH CS
                     Pyr_redox_dim   4 vvftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivGpgage.liqe 78 
                                       ++f ++e++ +Gl+e+eA++ag  ++  ++ +ka +r ++y+  +k+f+K++ad++t+++lGa+i G++    +++ 
  gi|488600298|ref|YP_007906769.1| 322 TKFHELEIGRTGLNEKEAREAG--FDPQTTFIKAQTRVHYYPGgRKTFIKVIADRNTKRILGAQIAGYDSVLmRVNT 396
                                       7899******************..99999**************************************7654449*** PP

                                       HHHHHHTTSBHH.HHHTSBSSSSSTGGG CS
                     Pyr_redox_dim  79 lavaikagltve.dladtihihPtlsea 105
                                       +a++i+ g+t++ ++  +++++P+++ +
  gi|488600298|ref|YP_007906769.1| 397 MAAVIQTGMTTKdLFFADLAYAPPFAPT 424
                                       **********9966**********9944 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 ?    3.9   0.1     0.036        26       1      32 [.       4      36 ..       4      41 .. 0.76
   2 !   53.2   0.1   3.5e-17   2.5e-14      89     305 .]      64     273 ..      20     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.036
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagle.dylilEkgni 32
                                      ++iG+G+ G+++a  ++ ++ e ++++ E  n 
  gi|488600298|ref|YP_007906769.1|  4 VVIGGGAGGMSSASRVRALKPEwKVTVFEATNF 36
                                      79***********99988765325666666665 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 3.5e-17
                       Pyr_redox_3  89 evaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek....lvkhyskvkefhk 161
                                          ++  ++ +++++V++v++++ +++ + +++++e ++++iAtG    P +++i+G +     +v      + +  
  gi|488600298|ref|YP_007906769.1|  64 VFIEKRGIDLRMNTKVTDVTRNSVKYVENGEEKEIEWDYLVIATGA--SPIRPGIEGIDLegifTVDLPPDAERIVR 138
                                       346788999************************************9..**********9723222334444556666 PP

                       Pyr_redox_3 162 ya..gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevk 236
                                       ya   +++v++G +  + ++A  + ++ ++Vtv+   ++      +++  +  ++++++e+      +++  n++v+
  gi|488600298|ref|YP_007906769.1| 139 YAekAENIVIVGSGYIGLEMAEAFSARKKNVTVIEMLNH---PLPNFDEDIAEVVKKEMEKW-----VDLRLNEKVT 207
                                       6644789***************************98763...33445555666666666554.....7899****** PP

                       Pyr_redox_3 237 eikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       + + k++  kv t++g+   + d v++a+G kp++++ ++ ++++ e+g    t+ +++t +++++ +G
  gi|488600298|ref|YP_007906769.1| 208 AFEGKDRVEKVVTDKGEY--KADMVIVAVGAKPNTELAERLGVKIGETGA-IWTDRKMQTSMENVYACG 273
                                       *****9999999999864..56999********************88776.578899*********999 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00012     0.083       1      35 [.       2      39 ..       2      42 .. 0.84
   2 !   12.4   0.0   0.00012     0.086     156     203 ..      66     110 ..      64     125 .. 0.79
   3 !   12.3   0.0   0.00013     0.092       2      28 ..     146     174 ..     145     178 .. 0.91
   4 !   11.9   0.1   0.00017      0.12     161     208 ..     198     244 ..     186     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                      EEEEECTSHHHHHHHHHH.HHTT...EEEEESSSSTTSS CS
                               DAO  1 dvviiGGGiiGlstAyeL.arrg...Vtllekgdiagsg 35
                                      +vv+iGGG  G+s A    a ++   Vt++e+ ++++ +
  gi|488600298|ref|YP_007906769.1|  2 RVVVIGGGAGGMSSASRVrALKPewkVTVFEATNFVS-H 39
                                      59****************33345899******98877.4 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                                       HHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGG CS
                               DAO 156 aealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaaGaw 203
                                       +e++G++++ +t+vt++ ++   v+ ve  +++++  + d++V+a+Ga 
  gi|488600298|ref|YP_007906769.1|  66 IEKRGIDLRMNTKVTDVTRN--SVKYVEnGEEKEI--EWDYLVIATGAS 110
                                       589*************9665..4999964222243..5799******86 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00013
                                       EEEECTSHHHHHHHHHHHHTT..EEEEES CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllek 28 
                                       +vi+G+G+iGl  A + ++r+  Vt++e+
  gi|488600298|ref|YP_007906769.1| 146 IVIVGSGYIGLEMAEAFSARKknVTVIEM 174
                                       9****************988669****96 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00017
                                       -EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH.H CS
                               DAO 161 veilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.ll.g 208
                                       v+++++++vt++e + ++v +v  +t+ ge  +ad v++a Ga  + +l +
  gi|488600298|ref|YP_007906769.1| 198 VDLRLNEKVTAFEGK-DRVEKV--VTDkGEY-KADMVIVAVGAKPNtELaE 244
                                       99**********665.478888..6666985.4588******997774433 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   3.4e-05     0.024       2      33 ..       2      35 ..       1      39 [. 0.86
   2 !   11.9   0.0   9.1e-05     0.065     119     165 ..      66     110 ..      63     114 .. 0.86
   3 !    6.8   0.1    0.0033       2.4       2      34 ..     145     177 ..     144     183 .. 0.91
   4 !   10.0   0.1   0.00036      0.26     109     165 ..     184     237 ..     177     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                      SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVlllekak 33
                                      +v+viGgGa G+  A ++   k + +V+++e+++
  gi|488600298|ref|YP_007906769.1|  2 RVVVIGGGAGGMSSASRVraLKPEWKVTVFEATN 35
                                      69*************876548999*******976 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.1e-05
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       ++++g++lr++t+v++v++++  +  v+  +e+e+e d+lv+AtG  
  gi|488600298|ref|YP_007906769.1|  66 IEKRGIDLRMNTKVTDVTRNS--VKYVENGEEKEIEWDYLVIATGAS 110
                                       6899*************6654..457888799************975 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0033
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                       +++++G G  Gl  A++ ++r+k+V+++e  ++
  gi|488600298|ref|YP_007906769.1| 145 NIVIVGSGYIGLEMAEAFSARKKNVTVIEMLNH 177
                                       69**************************98765 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00036
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       edi ++ +ke+++  v+lrl+++v+++e  +d++ +v t +++e++ad +++A+G +
  gi|488600298|ref|YP_007906769.1| 184 EDIAEVVKKEMEK-WVDLRLNEKVTAFEG-KDRVEKVVT-DKGEYKADMVIVAVGAK 237
                                       5778888888765.7************66.555567777.89***********9876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05      0.01       1      29 [.       5      35 ..       5      38 .. 0.88
   2 !   15.0   0.0     3e-05     0.022       1      31 [.     148     178 ..     148     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrd 29
                                      ++G+G++G++ A++ +      +v+++e+ +
  gi|488600298|ref|YP_007906769.1|  5 VIGGGAGGMSSASRVRALkpEWKVTVFEATN 35
                                      8***************864588******976 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       IvG+G  Gl +A + + ++++v+++e+ +++
  gi|488600298|ref|YP_007906769.1| 148 IVGSGYIGLEMAEAFSARKKNVTVIEMLNHP 178
                                       9**************************9986 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.2e-06    0.0016     205     301 ..      38     162 ..       7     185 .. 0.75
   2 !    9.9   0.1   0.00056       0.4     222     262 ..     197     236 ..     179     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                                       E.........TTHTHHHHHHHHH......TTTTEEEETSEEEEEEEEETTCEEEEETTSTEE..EESEEEE-S-HHH CS
                     Amino_oxidase 205 p.........rgGlsqlpealae......elrgldirlntrVkeikregdgvtvtledgevv..eaDaVvvTvplgv 264
                                                  +G s+lp+ +        e+rg d+r+nt+V++++r++ ++     +ge+   e D+ v+++  + 
  gi|488600298|ref|YP_007906769.1|  38 ShapcgipyvVEGVSELPKLMYYppevfiEKRGIDLRMNTKVTDVTRNSVKYVE---NGEEKeiEWDYLVIATGASP 111
                                       455555555589999999999999999999*****************7777766...5555556************* PP

                                       HH........SSEEESCC.SH.....HHHHHHHHSEEEEEEEEEEEESSGG CS
                     Amino_oxidase 265 lk........ailfsPpl.pd.....ekaeairnlgfgsvnkvilefdrkf 301
                                       ++           f+  l pd       ae ++n+  +++  + le+ ++f
  gi|488600298|ref|YP_007906769.1| 112 IRpgiegidlEGIFTVDLpPDaerivRYAEKAENIVIVGSGYIGLEMAEAF 162
                                       *99999888866666666444555667778888888888888888888888 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00056
                                       TEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-H CS
                     Amino_oxidase 222 gldirlntrVkeikregdgvtvtledgevveaDaVvvTvpl 262
                                        +d+rln++V+  +  +d v   ++d  +++aD V+v+v  
  gi|488600298|ref|YP_007906769.1| 197 WVDLRLNEKVTAFEG-KDRVEKVVTDKGEYKADMVIVAVGA 236
                                       579***********6.77777777888889********975 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0044       3.2       1      37 [.       4      37 ..       4      42 .. 0.90
   2 ?    4.6   0.0      0.04        29     120     155 ..      75     109 ..      66     110 .. 0.84
   3 ?    3.7   0.0     0.075        54       1      25 [.     147     169 ..     147     180 .. 0.79
   4 !    8.5   0.1    0.0025       1.8     102     155 ..     185     236 ..     181     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0044
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      +++G+G+ G++ + r+ a    k + ++t+f+ +++ 
  gi|488600298|ref|YP_007906769.1|  4 VVIGGGAGGMSSASRVRAL---KPEWKVTVFEATNFV 37
                                      69**************999...69********98875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.04
                     NAD_binding_9 120 hraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       ++++v+d++++  ++ v   ++++++ d++v+A+G 
  gi|488600298|ref|YP_007906769.1|  75 MNTKVTDVTRNSVKY-VENGEEKEIEWDYLVIATGA 109
                                       68999**99887775.88899999**********95 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.075
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkksp 25 
                                       +ivG G  Gl ++e++ ar+  k+ 
  gi|488600298|ref|YP_007906769.1| 147 VIVGSGYIGLEMAEAFSARK--KNV 169
                                       7*****************96..322 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0025
                     NAD_binding_9 102 dlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       d++e + ++++++v++++ +++v++ e +++  +v  +d+ +++ad V++A+G 
  gi|488600298|ref|YP_007906769.1| 185 DIAEVVKKEMEKWVDLRL-NEKVTAFEGKDRVEKV-VTDKGEYKADMVIVAVGA 236
                                       556667778899998885.999**99988666555.778889**********95 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   8.7e-05     0.062       2      32 ..       3      35 ..       2      41 .. 0.80
   2 ?    4.9   0.0     0.016        11       2      29 ..     146     173 ..     145     177 .. 0.93
   3 !    6.3   0.0    0.0062       4.5     376     408 ..     256     281 ..     187     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.7e-05
                                      EEEE--SHHHHHHHHHHHH.TTT.-EEEEESSS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaae.aGl.kvavvekeq 32
                                      v+ViG+G++G+++A + +  +   kv+v e ++
  gi|488600298|ref|YP_007906769.1|  3 VVVIGGGAGGMSSASRVRAlKPEwKVTVFEATN 35
                                      9*************9887655556999888776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.016
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEE CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavve 29 
                                       ++++GsG  GL  A + + + ++v+v+e
  gi|488600298|ref|YP_007906769.1| 146 IVIVGSGYIGLEMAEAFSARKKNVTVIE 173
                                       79************************98 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0062
                                       EEBETTSBESTTEEESSBTEEE-STCEESSSST CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaaggvhg 408
                                       + td ++++        ++ YA+G +a   +h 
  gi|488600298|ref|YP_007906769.1| 256 IWTDRKMQT------SMENVYACGDCA-ETFHM 281
                                       455555555......************.77775 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.011       7.8       9      67 ..       2     106 ..       1     112 [. 0.59
   2 !   19.0   0.3     2e-06    0.0014       7      71 ..     143     236 ..     140     254 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                     NAD_binding_7   9 kvlvvGgGevAa...rkvrklleagakvtvvapevkeele..................................... 45 
                                       +v+v+GgG  ++   ++vr l ++  kvtv   +   +++                                     
  gi|488600298|ref|YP_007906769.1|   2 RVVVIGGGAGGMssaSRVRALKPE-WKVTVFEATN--FVShapcgipyvvegvselpklmyyppevfiekrgidlrm 75 
                                       79****998875333789988888.9****76663..3333345555566666666666666666666666665555 PP

                     NAD_binding_7  46 .........elvklaeeelekdlegadlvia 67 
                                                + vk+ e+  ek++e+  lvia
  gi|488600298|ref|YP_007906769.1|  76 ntkvtdvtrNSVKYVENGEEKEIEWDYLVIA 106
                                       5544444443344444444555655555555 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2e-06
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtv..............vapevkeeleelvklaeeelekd........... 58 
                                        +++++vG G ++++ ++ + + +++vtv              +            ++ ++e+ek+           
  gi|488600298|ref|YP_007906769.1| 143 AENIVIVGSGYIGLEMAEAFSARKKNVTViemlnhplpnfdedI-----------AEVVKKEMEKWvdlrlnekvta 208
                                       5789*************************444444444444443...........5555555555533333333333 PP

                     NAD_binding_7  59 ......leg.........adlviaatdd 71 
                                             +e+         ad+vi+a+  
  gi|488600298|ref|YP_007906769.1| 209 fegkdrVEKvvtdkgeykADMVIVAVGA 236
                                       3333342223334555558888888753 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 !   25.6   0.1   1.1e-08   7.7e-06       2      86 ..     145     236 ..     144     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.1e-08
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTT..TEEEES-HHHHHH. CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesg..rlsfttdvekave. 75 
                                       +i+++G+GY+Gl +a +++++ ++v+++ + ++   ++ ++  +++ +++e+ v  +++++   ++++ +vek v  
  gi|488600298|ref|YP_007906769.1| 145 NIVIVGSGYIGLEMAEAFSARKKNVTVIEMLNHPLPNFDEDIAEVVKKEMEKWVDLRLNEKvtAFEGKDRVEKVVTd 221
                                       79***************************************************998886551144556667766642 PP

                                       ....C-SEEEE---- CS
                    UDPG_MGDP_dh_N  76 ....eadvifiaVgT 86 
                                           +ad++++aVg 
  gi|488600298|ref|YP_007906769.1| 222 kgeyKADMVIVAVGA 236
                                       222368999999986 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00019      0.13      19      49 ..       2      33 ..       1      40 [. 0.83
   2 !    7.0   0.0    0.0042         3      11      48 ..     135     173 ..     131     177 .. 0.79
   3 ?    1.4   0.0      0.22   1.5e+02     166     222 ..     361     417 ..     332     420 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                      EEEEE--SHHHHHHH.HHHHHCTTS-EEEEES CS
                              Thi4 19 DvvivGaGssGLtaa.yylakkpdlkvailer 49
                                       vv++G+G+ G+++a ++ a kp+ kv+++e+
  gi|488600298|ref|YP_007906769.1|  2 RVVVIGGGAGGMSSAsRVRALKPEWKVTVFEA 33
                                      59**********8762566778********97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0042
                                       HHHHHTEE..EEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4  11 dllkyaes..DvvivGaGssGLtaayylakkpdlkvaile 48 
                                        ++ yae   ++vivG+G  GL  a  ++ + + +v+++e
  gi|488600298|ref|YP_007906769.1| 135 RIVRYAEKaeNIVIVGSGYIGLEMAEAFSAR-KKNVTVIE 173
                                       56778774338**************999888.66777777 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.22
                                       -GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHH CS
                              Thi4 166 tGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyvaGmev 222
                                        G    +++v++ ++++     ++ g  s+ + +   a v +t    ++l++a ++ 
  gi|488600298|ref|YP_007906769.1| 361 PGGRKTFIKVIADRNTKRILGAQIAGYDSVLMRVNTMAAVIQTGMTTKDLFFADLAY 417
                                       4666789999999999999999**************999999********9998775 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 ?    4.4   0.0     0.092        66       1      34 [.       1      34 [.       1      68 [. 0.80
   2 !   17.7   0.0   6.9e-06    0.0049       2      81 ..     145     245 ..     144     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.092
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECS CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldp 34
                                      +rv++iG+G  g   +  +++ +++++v+ +  +
  gi|488600298|ref|YP_007906769.1|  1 MRVVVIGGGAGGMSSASRVRALKPEWKVTVFEAT 34
                                      69**************9*****999999876555 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 6.9e-06
                                       EEEEETTSHHHHHHHHHHHHTTTTE...............EEEEEECSSHHHHHHHHHHTTHEEESS...HHHHHTC CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrle...............evvalldpdaeraeavaesfgveaysd...leellad 60 
                                       +++i+G+G+ig + ++++ +++++                +++ +++++ e+  +++ + +v a++    +e++++d
  gi|488600298|ref|YP_007906769.1| 145 NIVIVGSGYIGLEMAEAFSARKKNVtviemlnhplpnfdeDIAEVVKKEMEKWVDLRLNEKVTAFEGkdrVEKVVTD 221
                                       79*******************99999999999999999999999999999999999888888888877789999999 PP

                                       T...TESEEEE-S-GGGHHHHHHH CS
                      GFO_IDH_MocA  61 p...eidavivatpngtheelaka 81 
                                       +   ++d+viva+ ++   ela++
  gi|488600298|ref|YP_007906769.1| 222 KgeyKADMVIVAVGAKPNTELAER 245
                                       99999********99999888876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.082        59       1      30 [.       3      34 ..       3      53 .. 0.81
   2 !   14.1   0.1   5.8e-05     0.041       1      45 [.     146     190 ..     146     196 .. 0.81
   3 ?    1.8   0.1      0.39   2.8e+02      38      73 ..     202     237 ..     188     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.082
                                      EEEES-SHHHHHHHHHHHH.TT.EEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkd 30
                                      +++iG G  G+s a ++++ +  ++v+v +  
  gi|488600298|ref|YP_007906769.1|  3 VVVIGGGAGGMSSASRVRAlKPeWKVTVFEAT 34
                                      79*****************554799**99974 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.8e-05
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevv 45 
                                       i+i+G G +G ++ae +s+++k+v+vi+     + ++ e+ +evv
  gi|488600298|ref|YP_007906769.1| 146 IVIVGSGYIGLEMAEAFSARKKNVTVIEMLNHPLPNFDEDIAEVV 190
                                       89*****************8878****987766666666655555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.39
                                       HHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSH CS
                            TrkA_N  38 reeglevvvgdatdeevLeeagiekadaviaatgdd 73 
                                        +e+++++ g    e+v+ + g  kad+vi+a+g +
  gi|488600298|ref|YP_007906769.1| 202 LNEKVTAFEGKDRVEKVVTDKGEYKADMVIVAVGAK 237
                                       366688999999999999999999*******99865 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   0.0   0.00027      0.19       2      34 ..       3      35 ..       2      41 .. 0.92
   2 ?   -3.2   0.0       4.4   3.2e+03     104     141 ..      74     109 ..      72     115 .. 0.75
   3 !    6.4   0.0    0.0054       3.9       2      31 ..     146     173 ..     145     182 .. 0.78
   4 ?   -0.1   0.1      0.54   3.9e+02      92     145 ..     189     239 ..     183     253 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasp 34
                                      vvviG+G+ g+s A r+ + kp+ kv++ ea +
  gi|488600298|ref|YP_007906769.1|  3 VVVIGGGAGGMSSASRVRALKPEWKVTVFEATN 35
                                      8***************************99976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                     Lycopene_cycl 104 lleakvesveeeeageslvvleggrkirarlvvdargl 141
                                       +++ kv+ v+ +++  ++v   ++++i+    v a+g+
  gi|488600298|ref|YP_007906769.1|  74 RMNTKVTDVTRNSV--KYVENGEEKEIEWDYLVIATGA 109
                                       56788888888888..6777667779999999999884 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0054
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlie 31 
                                       +v++G+G  gl +A+    ++ + +v++ie
  gi|488600298|ref|YP_007906769.1| 146 IVIVGSGYIGLEMAEAF--SARKKNVTVIE 173
                                       8****************..55556666666 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.54
                     Lycopene_cycl  92 ellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                       ++++++ +    +l+ kv++ e ++     vv++ g + +a +v++a g a+++
  gi|488600298|ref|YP_007906769.1| 189 VVKKEMEKWVDLRLNEKVTAFEGKDR-VEKVVTDKG-EYKADMVIVAVG-AKPN 239
                                       45555544445678888888888888.344444444.578999999999.4433 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         2   1.4e+03     193     204 ..       2      13 ..       1      37 [. 0.62
   2 ?    5.1   0.0     0.015        11     293     339 ..      69     108 ..      53     111 .. 0.79
   3 !   13.7   0.0   3.7e-05     0.026     135     219 ..      90     171 ..      65     191 .. 0.72
   4 ?    0.0   0.0      0.52   3.7e+02     134     161 ..     217     239 ..     181     246 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2
                       K_oxygenase 193 riaVvGsGqSaa 204
                                       r++V+G+G  + 
  gi|488600298|ref|YP_007906769.1|   2 RVVVIGGGAGGM 13 
                                       788888886554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                       K_oxygenase 293 erlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                       + + l+ n++v+++++++       ++  e+gee+++e d++v+ATG
  gi|488600298|ref|YP_007906769.1|  69 RGIDLRMNTKVTDVTRNS-------VKYVENGEEKEIEWDYLVIATG 108
                                       347888888888888886.......56677899*************9 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 3.7e-05
                       K_oxygenase 135 veskdaegeeeelearnlvlgvGtepkiPevleklegkervvHss...eylerkee....llakkriaVvGsGqSaa 204
                                       v    ++gee+e+e   lv+++G +p  P + e ++  e ++  +   ++     +     +++++i++vGsG  + 
  gi|488600298|ref|YP_007906769.1|  90 V----ENGEEKEIEWDYLVIATGASPIRPGI-EGIDL-EGIFTVDlppDAE----RivryAEKAENIVIVGSGYIGL 156
                                       2....5799********************86.44553.5566554222333....23345999************** PP

                       K_oxygenase 205 eifedllrrqkkvel 219
                                       e++e   +r+k+v++
  gi|488600298|ref|YP_007906769.1| 157 EMAEAFSARKKNVTV 171
                                       ****99999887554 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.52
                       K_oxygenase 134 tveskdaegeeeelearnlvlgvGtepk 161
                                       +v +     ++ e++a  ++++vG +p+
  gi|488600298|ref|YP_007906769.1| 217 KVVT-----DKGEYKADMVIVAVGAKPN 239
                                       3333.....5789999999999999986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.2   1.6e+03       2      30 ..       3      33 ..       2      53 .. 0.71
   2 !   17.0   0.2   5.8e-06    0.0042       2      85 ..     146     233 ..     145     241 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.2
                                      EEEE--SCCHHHHHHHH..HHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavf..asagleVvlvdi 30
                                      v viG G  G + a+ +  ++ + +V++++ 
  gi|488600298|ref|YP_007906769.1|  3 VVVIGGGAGGMSSASRVraLKPEWKVTVFEA 33
                                      7899887777666654310444777777765 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.8e-06
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTT....TSS-HHHHCCCHHCEE.EES-H CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvek....gklkeeeveaalaris.fttdl 73 
                                       + ++G+G +G ++a++f +++ +V+++++ ++ l +  e i++ ++k +ek    +  ++ ++ +  +r++ + td 
  gi|488600298|ref|YP_007906769.1| 146 IVIVGSGYIGLEMAEAFSARKKNVTVIEMLNHPLPNFDEDIAEVVKKEMEKwvdlRLNEKVTAFEGKDRVEkVVTDK 222
                                       88***************************666666666666554444433210003333333333444443234444 PP

                                       HHHHC-SEEEE- CS
                           3HCDH_N  74 eeavdadlviEa 85 
                                        e+ +ad+vi a
  gi|488600298|ref|YP_007906769.1| 223 GEY-KADMVIVA 233
                                       444.56666655 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.8e-05     0.048       1      93 [.     146     251 ..     146     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-05
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT..CEEEEEECEEECCH..........SCC CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg..geeilrppealsae..........eks 64 
                                       i+i+G+G iG  +a   ++ + +vt+i   +  l ++ ++  ++ +++  + + lr +e+++a           +++
  gi|488600298|ref|YP_007906769.1| 146 IVIVGSGYIGLEMAEAFSARKKNVTVIEMLNhPLPNFDEDIAEVVKKEmeKWVDLRLNEKVTAFegkdrvekvvTDK 222
                                       89*****************999*****999999***************664445555555555479*******9999 PP

                                       CCS-ESEEEE-SSGGGHHHHHHHHGGGEC CS
                              ApbA  65 elepidlvivtvKayqteealeeikplld 93 
                                          ++d+viv+v a ++ e +e++   ++
  gi|488600298|ref|YP_007906769.1| 223 GEYKADMVIVAVGAKPNTELAERLGVKIG 251
                                       999************99999988766655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.1      0.28     2e+02       3      18 ..       2      17 ..       1      21 [. 0.89
   2 ?    4.2   0.0     0.029        21     117     169 ..      68     113 ..      63     127 .. 0.76
   3 ?    5.4   0.0     0.013       9.4       4      64 ..     146     208 ..     143     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.28
                                      EEEEE--SHHHHHHHH CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlal 18
                                       V+++G+G  G+++a+
  gi|488600298|ref|YP_007906769.1|  2 RVVVIGGGAGGMSSAS 17
                                      69**********9985 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.029
                                       HHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHH CS
                     FAD_binding_3 117 erglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvr 169
                                       +rg+++r++t+v+      +  +  v++ e+gee++++ +Ylv a G+ S++r
  gi|488600298|ref|YP_007906769.1|  68 KRGIDLRMNTKVT------DVTRNSVKYVENGEEKEIEWDYLVIATGA-SPIR 113
                                       6677777777777......444556789999************99997.4555 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.013
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEE..HHHHHHHHHTT-HHHHHH CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradgln..qrtmellrqlGledrila 64 
                                       ++IVG+G  Gl  a   s +  +v+++e  +   +++  d+ +  ++ me   +l l +++ a
  gi|488600298|ref|YP_007906769.1| 146 IVIVGSGYIGLEMAEAFSARKKNVTVIEMLNHPLPNFDEDIAEvvKKEMEKWVDLRLNEKVTA 208
                                       78***************999999*****99999988854444311344666666666666655 PP

>> Cmyb_C  C-myb, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00023      0.17      77     121 ..     161     205 ..     158     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            Cmyb_C  77 ALaaqekkyGpLkllpqtlahleeDlkeVlkeEtgsdivikeeee 121
                                       A+ a+ k    + +l+++l + +eD+ eV+k+E ++ + ++ +e+
  gi|488600298|ref|YP_007906769.1| 161 AFSARKKNVTVIEMLNHPLPNFDEDIAEVVKKEMEKWVDLRLNEK 205
                                       7788888888999********************996655553433 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0031       2.2       1      36 [.       2      36 ..       2      50 .. 0.84
   2 ?   -0.7   0.0      0.67   4.8e+02     166     209 ..      68     109 ..      64     112 .. 0.72
   3 ?    1.6   0.1      0.14     1e+02       1      33 [.     145     174 ..     145     201 .. 0.87
   4 ?   -0.2   0.0      0.49   3.5e+02     180     210 ..     208     237 ..     181     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0031
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseei 36
                                      ++v++GGG  G  +A+ ++     + +vt+ e+ ++
  gi|488600298|ref|YP_007906769.1|  2 RVVVIGGGAGGMSSASRVRALK-PEWKVTVFEATNF 36
                                      69******99999999887665.66*****998776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.67
                                       HCT-EEE.E--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGG CS
                    Trp_halogenase 166 arGvtrv.egkvvevqldedgrveslrledgreveadlfiDcsGf 209
                                       +rG++ + ++kv++v    +++v+ ++  +++e+e d  + ++G 
  gi|488600298|ref|YP_007906769.1|  68 KRGIDLRmNTKVTDV---TRNSVKYVENGEEKEIEWDYLVIATGA 109
                                       566664413344333...37889999999*********9999995 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.14
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlves 33 
                                       +ivivG G  G   A a++       +vt++e 
  gi|488600298|ref|YP_007906769.1| 145 NIVIVGSGYIGLEMAEAFSARK---KNVTVIEM 174
                                       69**********9999999888...46888885 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.49
                                       EE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
                    Trp_halogenase 180 qldedgrveslrledgreveadlfiDcsGfr 210
                                         + ++rve++ +++g+ ++ad++i + G +
  gi|488600298|ref|YP_007906769.1| 208 AFEGKDRVEKVVTDKGE-YKADMVIVAVGAK 237
                                       34569999999998887.99***99998876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.015        10       2      19 ..       3      20 ..       2      44 .. 0.72
   2 ?    2.5   0.0     0.087        62     115     150 ..      76     109 ..      65     118 .. 0.85
   3 ?    0.2   0.0      0.45   3.2e+02       2      28 ..     146     172 ..     145     184 .. 0.80
   4 ?    3.1   0.1     0.055        40     102     150 ..     191     236 ..     180     269 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.015
                                      EEEE-SSHHHHHHHHHHH CS
                              GIDA  2 viViGgGhAGceAAlaaa 19
                                      v+ViGgG  G+  A  + 
  gi|488600298|ref|YP_007906769.1|  3 VVVIGGGAGGMSSASRVR 20
                                      9***********997654 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.087
                                       ES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 115 eeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       + +v+++    ++vk v   ++++i+ +  viatG+
  gi|488600298|ref|YP_007906769.1|  76 NTKVTDVT--RNSVKYVENGEEKEIEWDYLVIATGA 109
                                       56788884..59***********************8 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.45
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                       ++++G G  G+e A a + +  +v+ i
  gi|488600298|ref|YP_007906769.1| 146 IVIVGSGYIGLEMAEAFSARKKNVTVI 172
                                       89**********999888877777766 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.055
                                       HHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 102 teklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       ++++e+  +l + +e+v+     +++v+ vvt++ge +ka+ v++a G+
  gi|488600298|ref|YP_007906769.1| 191 KKEMEKWVDLRL-NEKVTAF-EGKDRVEKVVTDKGE-YKADMVIVAVGA 236
                                       444444334443.4456666.447999999999885.89*********8 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.021        15       2      33 ..       3      36 ..       2      37 .. 0.78
   2 ?   -2.6   0.0       3.5   2.5e+03      97     124 ..      66      91 ..      62     109 .. 0.65
   3 ?    4.3   0.0      0.03        21      82     142 ..     176     233 ..     144     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.021
                      FAD_oxidored  2 vvVvGGgpaGvaAA..iaAaraGakvlLveergv 33
                                      vvV+GGg++G+  A  + A +   kv + e +++
  gi|488600298|ref|YP_007906769.1|  3 VVVIGGGAGGMSSAsrVRALKPEWKVTVFEATNF 36
                                      9**********99955667777777777777765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                      FAD_oxidored  97 laeagvtvllntrlvevekegkriesvt 124
                                       +++ g+++ +nt++++v+++   ++ v+
  gi|488600298|ref|YP_007906769.1|  66 IEKRGIDLRMNTKVTDVTRN--SVKYVE 91 
                                       57789999999999999987..333333 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.03
                      FAD_oxidored  82 n....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDA 142
                                       n     f+ ++a+ v +em   + v++ ln+++++ e ++ r+e+v++     + +++A+++i A
  gi|488600298|ref|YP_007906769.1| 176 NhplpNFDEDIAEVVKKEME--KWVDLRLNEKVTAFEGKD-RVEKVVTD----KGEYKADMVIVA 233
                                       13344699999999999996..46**************98.*******5....689999999855 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 ?    6.4   0.2    0.0066       4.7      30      57 ..       2      31 ..       1      38 [. 0.78
   2 ?   -3.8   0.0       8.9   6.4e+03      51      75 ..      74      98 ..      72     106 .. 0.73
   3 ?    6.3   0.1    0.0073       5.3      29      98 ..     144     233 ..     137     279 .. 0.76
   4 ?   -2.6   0.1       3.8   2.7e+03      33      54 ..     379     400 ..     362     408 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0066
                                      EEEEESTSHHHHHHHHHHHHTT-..EEEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglga..kVtvl 57
                                      +v+viGgG  G+++++  ++l+   kVtv+
  gi|488600298|ref|YP_007906769.1|  2 RVVVIGGGAGGMSSASRVRALKPewKVTVF 31
                                      79*************988887641156655 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.9
                                      T-EEEEEESSHHHHHHHHHTTTCEC CS
                       AlaDh_PNT_C 51 gakVtvlDvrparleqleslgakfv 75
                                        +++v+Dv  +  +++e+ ++k +
  gi|488600298|ref|YP_007906769.1| 74 RMNTKVTDVTRNSVKYVENGEEKEI 98
                                      5677788888888888887666655 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0073
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE....................HCHHHHHH CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev....................lksqeell 85 
                                        +++++G G  Gl+ +++ ++ + +Vtv+++  + l ++++  a++v+                      + ++   
  gi|488600298|ref|YP_007906769.1| 144 ENIVIVGSGYIGLEMAEAFSARKKNVTVIEMLNHPLPNFDEDIAEVVKKemekwvdlrlnekvtafegkDRVEKVVT 220
                                       4799**************************99998888888555545555566777777777776666433334444 PP

                                       HHHHHH-SEEEE- CS
                       AlaDh_PNT_C  86 aeavkeadvvigt 98 
                                       ++   +ad+vi +
  gi|488600298|ref|YP_007906769.1| 221 DKGEYKADMVIVA 233
                                       4445567777766 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.8
                                       EESTSHHHHHHHHHHHHTT-EE CS
                       AlaDh_PNT_C  33 viGgGvaGlqAiatakglgakV 54 
                                       ++G+ +aG  ++ + ++  a V
  gi|488600298|ref|YP_007906769.1| 379 ILGAQIAGYDSVLMRVNTMAAV 400
                                       6777777777776666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 2575.32
//
Query:       gi|488600299|ref|YP_007906770.1|  [L=318]
Description: transcriptional regulator, XRE family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-13   50.8   1.7    1.6e-12   47.3   0.4    2.6  2  HTH_3           Helix-turn-helix
    3.7e-07   30.0   2.0    6.2e-07   29.4   0.8    2.1  1  HTH_19          Helix-turn-helix domain
    1.2e-05   25.6   0.0      2e-05   24.8   0.0    1.4  1  HTH_31          Helix-turn-helix domain
    0.00047   20.1   0.0     0.0024   17.8   0.0    2.2  2  HTH_11          HTH domain
     0.0005   19.7   1.1      0.001   18.7   0.1    2.0  2  Sigma70_r4_2    Sigma-70, region 4
     0.0011   19.1   0.0     0.0029   17.8   0.0    1.7  1  NUMOD1          NUMOD1 domain
     0.0019   18.0   0.1     0.0043   16.9   0.1    1.6  1  HTH_25          Helix-turn-helix domain
      0.004   16.9   0.0      0.015   15.1   0.0    2.0  1  HTH_23          Homeodomain-like domain
     0.0055   16.9   0.0      0.023   14.9   0.0    2.1  1  HTH_17          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.047   13.5   0.1    1.9  1  MerR            MerR family regulatory protein
      0.027   14.4   0.0      0.055   13.3   0.0    1.5  1  Sigma70_ECF     ECF sigma factor
      0.032   14.1   0.2      0.069   13.0   0.2    1.5  1  UPF0228         Uncharacterised protein family (UPF0228)
      0.045   13.6   0.0       0.19   11.5   0.0    2.1  1  HTH_8           Bacterial regulatory protein, Fis family
      0.046   13.8   0.0       0.12   12.5   0.0    1.7  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.06   13.1   0.1       0.35   10.7   0.0    2.1  2  HTH_38          Helix-turn-helix domain
      0.078   13.0   1.1         20    5.3   0.0    3.1  3  HTH_6           Helix-turn-helix domain, rpiR family
       0.09   12.3   0.2       0.43   10.2   0.2    2.1  2  Sigma70_r4      Sigma-70, region 4
       0.12   12.5   0.3       0.57   10.3   0.0    2.3  2  MerR_1          MerR HTH family regulatory protein
       0.15   12.0   0.0       0.38   10.8   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.21   11.7   1.3       0.66   10.0   0.6    2.1  2  NUDIX           NUDIX 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 ?    1.8   0.0      0.29   2.6e+02      40      52 ..      60      73 ..      58      75 .. 0.85
   2 !   47.3   0.4   1.8e-15   1.6e-12       1      50 [.     131     179 ..     131     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.29
                                      HHHHHHHHHT.SEH CS
                             HTH_3 40 tlkklakaLg.vsl 52
                                       +kk+ak L+ v+l
  gi|488600299|ref|YP_007906770.1| 60 EMKKIAKLLNaVPL 73
                                      689*******8887 PP

  == domain 2  score: 47.3 bits;  conditional E-value: 1.8e-15
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50 
                                       ++e R++lgls+ e+A++lGvsr+t+ ++E G+   s+e+++kl++ Lg+
  gi|488600299|ref|YP_007906770.1| 131 IREVREELGLSLGEMAKYLGVSRRTVKKYEEGID-TSVENALKLEELLGT 179
                                       8*******************************55.*************97 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.8   6.9e-10   6.2e-07       2      53 ..     129     178 ..     128     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 6.9e-10
                            HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53 
                                       e+++e+Reelgl++ e+a+ lg+sr+   ++E g + ++s e+ lk+ e+lg
  gi|488600299|ref|YP_007906770.1| 129 EKIREVREELGLSLGEMAKYLGVSRRTVKKYEEG-I-DTSVENALKLEELLG 178
                                       89********************************.6.888888888877777 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.3e-08     2e-05       6      55 ..     131     178 ..     129     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.3e-08
                            HTH_31   6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55 
                                        r+ Re+ GLs+ e+A+ lgvs+ t+ ++E G  +  s +   +l ++lg
  gi|488600299|ref|YP_007906770.1| 131 IREVREELGLSLGEMAKYLGVSRRTVKKYEEGIDT--SVENALKLEELLG 178
                                       5999*****************************96..6666666666666 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.3   6.5e+03      36      46 ..      10      20 ..       9      26 .. 0.79
   2 !   17.8   0.0   2.7e-06    0.0024      16      35 ..     140     159 ..     129     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.3
                            HTH_11 36 IkaLeelgvpI 46
                                      +k+L+ +g+ +
  gi|488600299|ref|YP_007906770.1| 10 LKILKRAGFAV 20
                                      68889888776 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.7e-06
                            HTH_11  16 isgeeLAeeLnvSrrtvrrd 35 
                                       +s  e+A++L+vSrrtv ++
  gi|488600299|ref|YP_007906770.1| 140 LSLGEMAKYLGVSRRTVKKY 159
                                       899**************986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.1e-06     0.001      22      46 ..     135     159 ..     127     159 .. 0.91
   2 ?   -2.2   0.1       3.9   3.5e+03       6      24 ..     199     217 ..     195     221 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                                       HHTS---HHHHHHHHT--HHHHHHH CS
                      Sigma70_r4_2  22 ryleglsykEIAellgisegtVksr 46 
                                       r++ gls  E A++lg+s +tVk++
  gi|488600299|ref|YP_007906770.1| 135 REELGLSLGEMAKYLGVSRRTVKKY 159
                                       8899*******************86 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                       HHHTTS-HHHHHHHHHHHT CS
                      Sigma70_r4_2   6 ealaeLperqreifllryl 24 
                                       e + e+ e + ei++  ++
  gi|488600299|ref|YP_007906770.1| 199 EEKPEMEESEAEIVEQLRV 217
                                       5555666666666665554 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.2e-06    0.0029      18      36 ..     141     159 ..     141     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                            NUMOD1  18 SireAakyLgishntInky 36 
                                       S+ e+akyLg+s++t++ky
  gi|488600299|ref|YP_007906770.1| 141 SLGEMAKYLGVSRRTVKKY 159
                                       789***************9 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.8e-06    0.0043       2      37 ..     131     166 ..     130     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-06
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TT CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfda 37 
                                        r+ Re++glsl e+ak + ++ +++++ Ee+   +
  gi|488600299|ref|YP_007906770.1| 131 IREVREELGLSLGEMAKYLGVSRRTVKKYEEGIDTS 166
                                       699*************************99997555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.015      11      45 ..     131     162 ..     128     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                            HTH_23  11 llllae..GlsvreIAreLgvsrrTvyrwlkryreeG 45 
                                       ++ ++e  Gls  e A+ LgvsrrTv +    y eeG
  gi|488600299|ref|YP_007906770.1| 131 IREVREelGLSLGEMAKYLGVSRRTVKK----Y-EEG 162
                                       67788889******************75....4.555 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.6e-05     0.023       2      21 ..     140     159 ..     139     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                            HTH_17   2 ltveEaAelLgvsrstvyrl 21 
                                       l+  E+A++Lgvsr+tv ++
  gi|488600299|ref|YP_007906770.1| 140 LSLGEMAKYLGVSRRTVKKY 159
                                       6788*************875 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.3e-05     0.047       3      21 ..     143     161 ..     130     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHTTTHHHHHHHHH CS
                              MerR   3 gevAeltGvsprtLRyYEr 21 
                                       ge+A+ +Gvs rt+  YE+
  gi|488600299|ref|YP_007906770.1| 143 GEMAKYLGVSRRTVKKYEE 161
                                       99****************7 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.2e-05     0.055     145     171 ..     133     159 ..     123     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-05
                       Sigma70_ECF 145 elrkleGlsveEiAeklgvskrtverr 171
                                       e+r   Gls  E+A+ lgvs+rtv++ 
  gi|488600299|ref|YP_007906770.1| 133 EVREELGLSLGEMAKYLGVSRRTVKKY 159
                                       667778******************996 PP

>> UPF0228  Uncharacterised protein family (UPF0228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   7.7e-05     0.069      14      89 ..     118     198 ..     110     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.7e-05
                           UPF0228  14 veekyYivvdkdnitdvrkeleke.....knwtssipaikkgdeyiievseqaiedeevlaiLekydlqvkkfvwCy 85 
                                        +  yY+ +d ++i +vr+el  +     k + +s  ++kk +e i +  e+a++ ee+l +  +  + +k+fv  +
  gi|488600299|ref|YP_007906770.1| 118 APGGYYVKLDYEKIREVREELGLSlgemaKYLGVSRRTVKKYEEGIDTSVENALKLEELLGTYIIKAIDLKNFVKYE 194
                                       5778*****************998888855555666669**999999999*************9*********9766 PP

                           UPF0228  86 iefg 89 
                                        +++
  gi|488600299|ref|YP_007906770.1| 195 ENLE 198
                                       5554 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.19      21      35 ..     142     156 ..     126     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                       HHHHHHHHTS-HHHH CS
                             HTH_8  21 kskAArlLGisRrtL 35 
                                       + ++A++LG+sRrt+
  gi|488600299|ref|YP_007906770.1| 142 LGEMAKYLGVSRRTV 156
                                       579***********7 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 ?   12.5   0.0   0.00014      0.12      70     120 ..     127     177 ..     121     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                    MqsA_antitoxin  70 dpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvkllkll 120
                                       d ++i++vr++l+l+  e+a+ +G+   +  +ye+G   +    +kl +ll
  gi|488600299|ref|YP_007906770.1| 127 DYEKIREVREELGLSLGEMAKYLGVSRRTVKKYEEGIDTSVENALKLEELL 177
                                       6789********************************999888888887776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9   1.7e+03      23      31 ..      61      69 ..      59      70 .. 0.81
   2 ?   10.7   0.0   0.00039      0.35      19      37 ..     138     156 ..     129     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                            HTH_38 23 lreIArrLg 31
                                      +++IA++L+
  gi|488600299|ref|YP_007906770.1| 61 MKKIAKLLN 69
                                      679999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00039
                            HTH_38  19 eGlslreIArrLgrspsTI 37 
                                        Glsl e+A++Lg+s+ T+
  gi|488600299|ref|YP_007906770.1| 138 LGLSLGEMAKYLGVSRRTV 156
                                       58****************9 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.72   6.5e+02       3      27 ..      46      70 ..      44      74 .. 0.82
   2 ?    5.3   0.0     0.022        20      35      54 ..     140     159 ..     131     174 .. 0.83
   3 ?    4.0   0.1     0.056        50       2      25 ..     192     215 ..     191     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.72
                                      HHHHHHHH-----HHHHHHHHHHHH CS
                             HTH_6  3 llekiqskkekltksekkiaeyila 27
                                      +l  i s k ++++  kkia+ + a
  gi|488600299|ref|YP_007906770.1| 46 VLYNIDSFKLEMAQEMKKIAKLLNA 70
                                      6788999999999999999998865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.022
                                       --HHHHHHHTT--HHHHHHH CS
                             HTH_6  35 lsikalAkaaavSeativrf 54 
                                       ls+ ++Ak ++vS+ t+ + 
  gi|488600299|ref|YP_007906770.1| 140 LSLGEMAKYLGVSRRTVKKY 159
                                       7999************9886 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.056
                                       -HHHHHHHH-----HHHHHHHHHH CS
                             HTH_6   2 nllekiqskkekltksekkiaeyi 25 
                                       +++e ++++k ++ +se  i+e +
  gi|488600299|ref|YP_007906770.1| 192 KYEENLEEEKPEMEESEAEIVEQL 215
                                       57899****************987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         3   2.7e+03       5      18 ..      81      94 ..      80     102 .. 0.83
   2 ?   10.2   0.2   0.00047      0.43      20      40 ..     139     159 ..     131     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3
                                      S-HHHHHHHHHHHT CS
                        Sigma70_r4  5 Lpererevlelrfg 18
                                      L+  er v++ r+g
  gi|488600299|ref|YP_007906770.1| 81 LDFLERGVVYNRYG 94
                                      7788999**99995 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00047
                                       T--HHHHHHHHTS-HHHHHHH CS
                        Sigma70_r4  20 glTleEIgerlgiSrerVrqi 40 
                                       gl+l E ++ lg+Sr +V+  
  gi|488600299|ref|YP_007906770.1| 139 GLSLGEMAKYLGVSRRTVKKY 159
                                       89****************975 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 ?   -2.6   0.0       6.8   6.1e+03      34      51 ..     120     136 ..     110     139 .. 0.66
   2 ?   10.3   0.0   0.00064      0.57       2      22 ..     141     161 ..     140     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.8
                                       S-EEEEHHHHHHHHHHHH CS
                            MerR_1  34 grryYtdedierLkliky 51 
                                       g  yY + d e ++ +++
  gi|488600299|ref|YP_007906770.1| 120 G-GYYVKLDYEKIREVRE 136
                                       5.6777777777777764 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00064
                                       EHHHHHHHHTS-HHHHHHHHH CS
                            MerR_1   2 sigevakilgvtthtlrywek 22 
                                       s+ge ak lgv+ +t++ +e+
  gi|488600299|ref|YP_007906770.1| 141 SLGEMAKYLGVSRRTVKKYEE 161
                                       789****************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00042      0.38      18      39 ..     136     157 ..     123     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                                       EEEEHHHHHHHHHTTSSHHHHH CS
                         HTH_Crp_2  18 ielpltqeelAsmlGltretvs 39 
                                        el l+  e+A +lG++r tv 
  gi|488600299|ref|YP_007906770.1| 136 EELGLSLGEMAKYLGVSRRTVK 157
                                       4799999*************96 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   0.00073      0.66      48      73 ..     131     157 ..     131     225 .. 0.70
   2 ?   -0.6   0.0       1.4   1.3e+03      60      85 ..     255     280 ..     237     298 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00073
                                       HHHHHHHHSEEE.EEEEEEEEEEEEEE CS
                             NUDIX  48 rREleEEtGlea.ellellgrlhylap 73 
                                       +RE++EE+Gl+  e+ ++lg+ + + +
  gi|488600299|ref|YP_007906770.1| 131 IREVREELGLSLgEMAKYLGVSRRTVK 157
                                       6*********999*******5544333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                                       EEEEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX  60 ellellgrlhylapydgpygdeheil 85 
                                       + +++lgr+ +++++++ y  e+ ++
  gi|488600299|ref|YP_007906770.1| 255 KRVKVLGRVSEVLSTKAAYIVEKKVS 280
                                       45599999999999999888844443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2006.63
//
Query:       gi|488600300|ref|YP_007906771.1|  [L=544]
Description: thermosome subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-184  613.5  20.9   2.8e-184  613.3  20.9    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 !  613.3  20.9  1.6e-188  2.8e-184       1     490 [.      35     525 ..      35     526 .. 0.99

  Alignments for each domain:
  == domain 1  score: 613.3 bits;  conditional E-value: 1.6e-188
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++vk+tlGPkGmdKmlv++ g+vv+TnDG+tilke+++ehPaak+++e+a++q++evGDGTtt+v+Lage l++a
  gi|488600300|ref|YP_007906771.1|  35 IAEAVKSTLGPKGMDKMLVDSLGDVVITNDGVTILKEMDVEHPAAKMIIEVAKTQEDEVGDGTTTAVVLAGEFLRKA 111
                                       799************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+l+++++hpt i +gy+ a++ka+e L++ia++i+++  d+e+L+++a+t++++k  ++   +l++lvv+ +k++ 
  gi|488600300|ref|YP_007906771.1| 112 EELLEQEIHPTIIARGYRLAANKAMEVLDSIAEKIDVN--DEEKLKRIASTAITGKHAEYAVGYLAELVVQTIKAVA 186
                                       *******************************9999877..9********************************7777 PP

                                       CCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 155 ene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e+e   +++dl+++k++k +gg +ed++lv+G+v+dk+v++p+mpk++++ak+++l++ Le ++tet+++++++d+e
  gi|488600300|ref|YP_007906771.1| 187 EDEngkYKVDLDNVKLEKRQGGGIEDTKLVKGIVIDKEVVHPSMPKRIKDAKIAVLKTALEVKETETDAEIRITDPE 263
                                       7777*9*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                        l+k+ ++eek+l+++++ ++++g+nvv+cqkgiddla+ +lak+g+la+rrv+++d++++akatGa+++++l d++
  gi|488600300|ref|YP_007906771.1| 264 MLQKFIEQEEKMLKDMVDTLVNAGANVVFCQKGIDDLAQYYLAKAGVLAVRRVRQSDIDKIAKATGAKILTDLRDVK 340
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       pe+lGta+ vee+kig+ek+++ie++k++k++t+l+rg t++++de+er++ dAl+v+k a+e+++vv+GGGa e e
  gi|488600300|ref|YP_007906771.1| 341 PEDLGTAELVEERKIGDEKMVFIEGCKNPKAVTVLIRGGTEHIVDEVERSLTDALKVTKVAVESGYVVAGGGAPEAE 417
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       ++ klk++a ++ g+eqla+eafa+ALevip++LaeNaGldpi+++ ++r+ah++g+k++g+dv +g++++++e+gv
  gi|488600300|ref|YP_007906771.1| 418 ISLKLKQWAPTLGGREQLAAEAFANALEVIPRALAENAGLDPIDIIVEIRKAHEEGKKTYGVDVFDGKVKCMMEKGV 494
                                       ***************************************************************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiikak 490
                                       ++plkvk+qa++sAte+a +iLrid++i ak
  gi|488600300|ref|YP_007906771.1| 495 LEPLKVKKQAISSATEVAIMILRIDDVIAAK 525
                                       ****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3330.88
//
Query:       gi|488600301|ref|YP_007906772.1|  [L=117]
Description: hypothetical protein Asulf_00766 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   15.8   0.7      0.033   14.8   0.2    1.9  1  SlyX      SlyX


Domain annotation for each model (and alignments):
>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   1.9e-06     0.033      14      58 ..      26      70 ..      14      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                              SlyX 14 fqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58
                                      f  + ++eL + ++e  + id+l  ++ +l+ +lk+++es+++ +
  gi|488600301|ref|YP_007906772.1| 26 FEFKKVKELEAKIIEFSKLIDALSSEVLYLKSELKKMDESKETRK 70
                                      5557799999*************************9999987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1807  (0.100786); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 822.48
//
Query:       gi|488600302|ref|YP_007906773.1|  [L=1167]
Description: condensin subunit Smc [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  188.4  54.8    7.7e-55  185.7  54.8    2.5  1  SMC_N          RecF/RecN/SMC N terminal domain
    4.3e-31  107.6   0.1    1.7e-30  105.7   0.1    2.1  1  SMC_hinge      SMC proteins Flexible Hinge Domain
      4e-12   46.6  25.6      4e-12   46.6  25.6    5.0  2  AAA_15         AAA ATPase domain
    6.2e-08   32.3   0.0    1.2e-07   31.4   0.0    1.5  1  AAA_29         P-loop containing region of AAA domain
    5.3e-06   26.4   0.4    5.3e-06   26.4   0.4    5.1  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.1e-05   24.3  26.0    1.1e-05   24.3  26.0    5.4  5  AAA_13         AAA domain
    0.00017   22.1 164.5       0.82   10.1  76.6    7.6  1  AAA_23         AAA domain
    0.00035   20.7  25.3    0.00035   20.7  25.3    7.5  5  Tropomyosin_1  Tropomyosin like
     0.0043   16.9  16.9     0.0043   16.9  16.9    6.5  5  ERM            Ezrin/radixin/moesin family
     0.0047   17.0   5.5     0.0047   17.0   5.5    9.7 10  DUF1664        Protein of unknown function (DUF1664)
     0.0079   16.4   6.5     0.0079   16.4   6.5    9.9  8  DUF4164        Domain of unknown function (DUF4164)
  ------ inclusion threshold ------
      0.044   13.4   0.0      0.044   13.4   0.0    4.8  5  AAA_27         AAA domain
       0.35   11.2   2.6        6.5    7.1   0.0    3.9  4  AAA_16         AAA ATPase domain
       0.44   10.0   2.1        4.9    6.5   0.1    3.0  3  Mce4_CUP1      Cholesterol uptake porter CUP1 of Mce4, putati
        1.2    9.1  36.7        1.5    8.9   1.6    6.8  6  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
        1.4    9.1 103.4       0.16   12.2   6.2    8.0  9  ATG16          Autophagy protein 16 (ATG16)
        2.1    8.9  52.4        8.7    6.9   1.1   10.3  8  NPV_P10        Nucleopolyhedrovirus P10 protein
        3.3    7.3  13.7       0.93    9.1   0.1    4.6  5  DUF3251        Protein of unknown function (DUF3251)
        4.4    7.6  18.2        8.2    6.7   0.0    7.6  8  WXG100         Proteins of 100 residues with WXG
        5.2    7.4   8.4         84    3.6   0.1    4.7  3  Img2           Mitochondrial large subunit ribosomal protein 
        5.5    6.7 129.8       0.35   10.6  12.6    7.6  7  DUF4201        Domain of unknown function (DUF4201)
        5.8    6.5  92.3      0.078   12.7  11.3    6.5  6  Laminin_I      Laminin Domain I
        7.1    5.4 139.3      0.079   11.8  13.7    7.4  7  Spc7           Spc7 kinetochore protein


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 !  185.7  54.8   9.8e-58   7.7e-55       1     218 [.       2    1157 ..       2    1159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 9.8e-58
                                        EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT..TTTTTTCHCCCCCC--BTTCSST CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGer.sakklrseklsdlihkskekasv 74  
                                        ++k+++++nFks++ k+v++pf k+ft+i GpNGSGKsn++dAilF+LG + s++ lr++++ dli++   + ++
  gi|488600302|ref|YP_007906773.1|    2 YIKKIVLKNFKSFN-KKVEIPFFKGFTVISGPNGSGKSNIVDAILFCLGLTpSTRYLRADRVGDLIYS--GNGKL 73  
                                        79***********5.**********************************9868899***********7..8999* PP

                                        TEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEE...EETTEEE-HHHHHHHHHCTT-STT........... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx........... RF
                             SMC_N   75 kkaeveitfdnedkklkiekeevsisrrvkrkgesey...kingkevtkkevsellesagiske........... 135 
                                         +aev+++fdn++++       ++i+r++kr+ + +y   ++ngk+v+ +e+++ll++ gi+++           
  gi|488600302|ref|YP_007906773.1|   74 GEAEVTVIFDNDGEE-------IKITRKIKRTSKGNYtynYLNGKSVNLAEIQRLLQNFGIYSDaynvvmqgdvt 141 
                                        ************999.......99999999887755522368********************************* PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  142 riaemtpfqrrkiiddiagisefdekkakaieeleavrenierintilievsnqleqlkadreealrykslieek 216 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  217 elnlkylkinkflslnrrkrmikrdienlemrkdkilkeiidinsklnelntkadeisaeiyrladesyktiqne 291 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  292 iieisskreglkssiemkkkeikdiedektkllvsisklkeevskveeelqkfsiqkmsvqevlddleskkslii 366 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  367 sklnlmdsayselrdqllkkkeildelkerksskvnerdrllevirrigmeiediegeietlrkesitlneelke 441 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  442 lnkkykevekeleaaikrrneadnkifsirnqissleeekknlevelskikaqlsllessfskavelileaksrk 516 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  517 ampgvfgtvsqlcevdekfavalevsagnslqylvveneddaircikylkqidggratfiplnkikknfgdikld 591 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  592 rsvlkekgvidyainlikcekkfkpvfnfvyrdtlvvedidtakrlmdgrrivtldgdiveragtisggskqksk 666 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  667 gilatkelfekekkleeeitviesrkaemlgnlrlveeerrihqsnveeinsrlselsskisvaesklrdnenri 741 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  742 eelkekltykqkeraeiyermsgveeeiekideeirkisgeieeieakmrgseipaltrkleeikeeidrnsram 816 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  817 ysitknlensefklqqlkdlvlekeikideldrkienlkkeiendsqlyselgerlitlkekekevgesvkdlrd 891 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  892 krskllaeikklekdrdekrfevtgieetikakeeslkdieeqirelgeieydeeevqniprmehvkrrleeiel 966 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|488600302|ref|YP_007906773.1|  967 elkkfgdvnlkaiqdyeevkarkeelmskkltlekerseilekieryekmkrdtffetfnainmhfkeiisklae 1041
                                        *************************************************************************** PP

                                        .................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                        .................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 .................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177 
                                                                         ++SgGek+Lval+L+fAiqk+kpap+y +De+d+ LD  nv+
  gi|488600302|ref|YP_007906773.1| 1042 gegelyldnaddpfnsglymrvrvrdkpiqkieSMSGGEKSLVALSLIFAIQKFKPAPFYAFDEVDMFLDGINVE 1116
                                        *************************************************************************** PP

                                        HHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  178 kvaellkeksknaQfivislreemlekadklvgvtkvengv 218 
                                        kva+l+ e+sknaQfiv+slr+ mlekad++vgvt  +++ 
  gi|488600302|ref|YP_007906773.1| 1117 KVAKLISERSKNAQFIVVSLRKPMLEKADSIVGVTLSKDNS 1157
                                        ***********************************977765 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 !  105.7   0.1   2.1e-33   1.7e-30       2     116 ..     519     637 ..     518     638 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 2.1e-33
                         SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns 78 
                                       +gv+G++ +l+evde++ +A+e+ +gn+lq+lvve+e++a ++i++lk+ ++gratf+pl++ik++    + + + s
  gi|488600302|ref|YP_007906773.1| 519 PGVFGTVSQLCEVDEKFAVALEVSAGNSLQYLVVENEDDAIRCIKYLKQIDGGRATFIPLNKIKKNF--GDIKLDRS 593
                                       79************************************************************99983..33333333 PP

                         SMC_hinge  79 ......gavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                              + ++i+l++++++++++++++ +dtlvv+++d+A++l
  gi|488600302|ref|YP_007906773.1| 594 vlkekgVIDYAINLIKCEKKFKPVFNFVYRDTLVVEDIDTAKRL 637
                                       468889************************************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6  25.6   5.1e-15     4e-12       1     292 [.       1     304 [.       1     309 [. 0.66
   2 ?   -3.0  19.5         6   4.7e+03     177     298 ..     672     792 ..     580     824 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 5.1e-15
                            AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...............kkvikie 61 
                                       M+Ikki +kNF+s+ + vei++ + +tv+ G+N+sGKS+i++a+ + l  + +                 +      
  gi|488600302|ref|YP_007906773.1|   1 MYIKKIVLKNFKSFNKkVEIPFFKGFTVISGPNGSGKSNIVDAILFCLGLTPS-TrylradrvgdliysgN------ 70 
                                       **************999***************************777776622.23556666666666441...... PP

                            AAA_15  62 kedleifeniseskdikIdvefaek.ekakeyektlks..........kekkkadlllkkkesdlkktikdkklklk 127
                                                  +  + +++v f+++ e+ k+  k++++          ++k  +  +++++ + +  ++   +   +
  gi|488600302|ref|YP_007906773.1|  71 ----------GKLGEAEVTVIFDNDgEEIKITRKIKRTskgnytynylNGKSVNLAEIQRLLQNFGIYSDAYNVVMQ 137
                                       ..........3333444444442223333333333444000000000044444444455555555555555555555 PP

                            AAA_15 128 knelsdekisvekkkskkelpke.keeklekekeelkid..kedlkklikkleeslkkeeelknvlksaiiklllis 201
                                        + +     + +++ ++ ++    +e++++k k+  +++   e+++++   l+e  ++ e+lk   ++a+++  li+
  gi|488600302|ref|YP_007906773.1| 138 GDVTRIAEMTPFQRRKIIDDIAGiSEFDEKKAKAIEELEavRENIERINTILIEVSNQLEQLKADREEALRYKSLIE 214
                                       555555555555555544433331344444444444444559999999999999999999999************** PP

                            AAA_15 202 akRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk..kilkkkidkikkfny 276
                                       +k  + ++++ +k  +l++ k+ i+++      +e+l++  ++i++++ +i++kl+e  +  +++   i  + ++ y
  gi|488600302|ref|YP_007906773.1| 215 EKELNLKYLKINKFLSLNRRKRMIKRD------IENLEMRKDKILKEIIDINSKLNELNTkaDEISAEIYRLADESY 285
                                       *******99999999999999999999......67777777777777777777775555566778888899999999 PP

                            AAA_15 277 kgkkneeieik...ddeel 292
                                       k  +ne iei+   ++ ++
  gi|488600302|ref|YP_007906773.1| 286 KTIQNEIIEISskrEGLKS 304
                                       9999999999966655555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6
                            AAA_15 177 eeslkkee.......elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiq 246
                                       +e ++ke+       ++++   + +  l+l +++R + +++ e+++s l++l +ki+   +  kl  +++  ++e++
  gi|488600302|ref|YP_007906773.1| 672 KELFEKEKkleeeitVIESRKAEMLGNLRLVEEERRIHQSNVEEINSRLSELSSKISVAES--KL-RDNENRIEELK 745
                                       2233333334445555666667888888999999999999999999999999999877533..33.35566666667 PP

                            AAA_15 247 eklkeidkklaeelk..kilkkkidkikkfnykgkkneeieik.ddeelplnknG 298
                                       ekl+ ++k+ ae ++  + +++ i+ki        ++e ++i+ + ee++++++G
  gi|488600302|ref|YP_007906773.1| 746 EKLTYKQKERAEIYErmSGVEEEIEKI--------DEEIRKISgEIEEIEAKMRG 792
                                       777777777777777775555555555........22222222333333333333 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 !   31.4   0.0   1.5e-10   1.2e-07       2      46 ..       4      48 ..       3      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.5e-10
                            AAA_29  2 krlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      k++ l N  +f++  +i++  kg+t+++Gp+GsGKS ++DAi + L
  gi|488600302|ref|YP_007906773.1|  4 KKIVLKNFKSFNKkVEIPFF-KGFTVISGPNGSGKSNIVDAILFCL 48
                                      678899*******9999996.99*******************9876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.4   6.8e-09   5.3e-06       1      79 [.      26      96 ..      26     123 .. 0.64
   2 ?   -1.3   0.7       1.9   1.5e+03      73     140 ..     396     468 ..     341     505 .. 0.48
   3 ?   -0.6   6.5       1.2   9.2e+02      57     208 ..     715     860 ..     702     886 .. 0.86
   4 !   14.4   5.9   3.2e-05     0.025      95     296 ..     926    1135 ..     873    1135 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.8e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl......drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryr 73
                                      ++v+ GpNgsGKSn+ da+ +  +l      +                r+ +  + ++ + +++e +++ f+++g +++
  gi|488600302|ref|YP_007906773.1| 26 FTVISGPNGSGKSNIVDAILFCLGLtpstryL-------------RADRVGDLIYSGNGKLGEAEVTVI-FDNDGEEIK 90
                                      89********************7755555552.............444444444444444444444444.444444444 PP

                            AAA_21 74 yglrle 79
                                         +++
  gi|488600302|ref|YP_007906773.1| 91 ITRKIK 96
                                      433333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                            AAA_21  73 ryglrlersqv.....eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqf 140
                                       r + ++++++      ++   + e+ ++  ++l+k+s     +     +  ++++++ +++ + ++e+++++f
  gi|488600302|ref|YP_007906773.1| 396 RKSSKVNERDRlleviRRIGMEIEDIEGEIETLRKESITLNEELKELNKKYKEVEKELEAAIKRRNEADNKIF 468
                                       3333333333333333233333333333333333333333333333333333333333333344444333333 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                            AAA_21  57 pfefeieeflsqgvryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvs 133
                                       +++ +++e+ s+ ++ +  lr +++++       e+l+e+ ++++k+ +e + + + ++++i ++  + + ++ +++
  gi|488600302|ref|YP_007906773.1| 715 EINSRLSELSSKISVAESKLRDNENRI-------EELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIE 784
                                       555666666666677777777788888.......******************************************* PP

                            AAA_21 134 epndlqfgkaltditsrawsllllldglrke.rigllnifadyfgfakekrllqrlvrslklveielsdlgegeel 208
                                       e +++ +g+ +  +t+ +++++++ d    + ++ + n+ +++f+ + +k+l+ + + ++++ + ++++l++ +e+
  gi|488600302|ref|YP_007906773.1| 785 EIEAKMRGSEIPALTRKLEEIKEEIDRNSRAmYSITKNLENSEFKLQQLKDLVLEKEIKIDELDRKIENLKKEIEN 860
                                       ************************99988889********************************999999866554 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 3.2e-05
                            AAA_21   95 esgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigll 169 
                                        es     ++++e +   ++e++ + + + + + + l+ +e + ++fg+++++ + ++++ +  +++l+ +     
  gi|488600302|ref|YP_007906773.1|  926 ESLKDIEEQIRELGEIEYDEEEVQNIPRMEHVKRRLEEIELELKKFGDVNLKAIQDYEEVKARKEELMSK----- 995 
                                        3333333333333333344444444444444444444444444444444444444444444444333333..... PP

                            AAA_21  170 nifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer......................... 219 
                                                               ++ e e s ++e++e +++ +++  ++                         
  gi|488600302|ref|YP_007906773.1|  996 ----------------------KLTLEKERSEILEKIERYEKMKRDTFFEtfnainmhfkeiisklaegegelyl 1048
                                        ......................33333333333333333333333333334444555555555555555555555 PP

                            AAA_21  220 ..........gvvflengdgqelparelSdGtkrllalltallralkkg.sllliDEpEngLHPkllrrllellk 283 
                                                   ++ +   d     + ++S G k+l al ++++ +  k+ +++++DE++ +L+   ++++++l++
  gi|488600302|ref|YP_007906773.1| 1049 dnaddpfnsgLYMRVRVRDKPIQKIESMSGGEKSLVALSLIFAIQKFKPaPFYAFDEVDMFLDGINVEKVAKLIS 1123
                                        556666668777777777888889***********988888888877777************************9 PP

                            AAA_21  284 elsrngaQviltT 296 
                                        e s+ +aQ+i+++
  gi|488600302|ref|YP_007906773.1| 1124 ERSK-NAQFIVVS 1135
                                        9988.9****986 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.064        50       5      36 ..      14      44 ..       9      82 .. 0.86
   2 ?    3.0  28.0      0.04        31     277     454 ..     164     342 ..     148     354 .. 0.64
   3 !    9.1  20.3   0.00059      0.46     288     468 ..     351     496 ..     341     515 .. 0.54
   4 !   24.3  26.0   1.5e-08   1.1e-05     282     468 ..     675     859 ..     670     862 .. 0.89
   5 !    6.0  22.0    0.0049       3.8     281     510 ..     847    1086 ..     843    1093 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.064
                            AAA_13  5 fdfrgaeledfkriNliYGwNGaGKTtLSrll 36
                                      f+ ++ e++ fk + +i G NG+GK+ +  ++
  gi|488600302|ref|YP_007906773.1| 14 FN-KKVEIPFFKGFTVISGPNGSGKSNIVDAI 44
                                      44.5778999***************9876655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.04
                            AAA_13 277 FddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk 353
                                       Fd++ ++ +e+Le   e++e+    +l ++ +  ++ +++++ +  ++ l +e+e   ++Lk ++    ++rk++ k
  gi|488600302|ref|YP_007906773.1| 164 FDEKKAKAIEELEAVRENIERIN-TILIEVSNQLEQLKADREEALRYKSLIEEKELNLKYLKINKFLSLNRRKRMIK 239
                                       66666666666666666665554.35555555555555566667778888888888888899999999999999998 PP

                            AAA_13 354 svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveel...eseldeykkkykklekaiek 427
                                         ++e+++ + ++i k++ +in   ++ N k +++ +e  +++++  + + +e+    s+ + +k+ ++  +k+i++
  gi|488600302|ref|YP_007906773.1| 240 -RDIENLEMRKDKILKEIIDINSKLNELNTKADEISAEIYRLADESYKTIQNEIieiSSKREGLKSSIEMKKKEIKD 315
                                       .7888888888888888888888888888888888888888777766655444400033333444444444444444 PP

                            AAA_13 428 lekelkeeeaelkkleeeikeLekqlr 454
                                        e+e+++    + kl+ee++  e++l+
  gi|488600302|ref|YP_007906773.1| 316 IEDEKTKLLVSISKLKEEVSKVEEELQ 342
                                       444444444444444444444444443 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00059
                            AAA_13 288 LekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvel.esvkak 363
                                        ++                                 ++l+++++ + ++L+ + +a ++ r+++ k+ e+ +++k++
  gi|488600302|ref|YP_007906773.1| 351 VQE-------------------------------VLDDLESKKSLIISKLNLMDSAYSELRDQLLKKKEIlDELKER 396
                                       333...............................4455555555555555555555555555555555532455555 PP

                            AAA_13 364 iesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelk 440
                                        +s  ++ +++ e+i++    ++++e e e+++k+        l++el+e++kkyk++ek++e + k+ +e+ +++ 
  gi|488600302|ref|YP_007906773.1| 397 KSSKVNERDRLLEVIRRIGMEIEDIEGEIETLRKESIT-----LNEELKELNKKYKEVEKELEAAIKRRNEADNKIF 468
                                       55555555666666666666666666666655554333.....3455555566666666666666666666666666 PP

                            AAA_13 441 kleeeikeLekqlrdekpaaeeinkeLk 468
                                        ++++i+ Le++ ++ +   ++i  +L+
  gi|488600302|ref|YP_007906773.1| 469 SIRNQISSLEEEKKNLEVELSKIKAQLS 496
                                       6666666666666666665555555553 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 1.5e-08
                            AAA_13 282 eekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svel 357
                                        ek ++Le+ i+ +es+k+e+l +l  v +   e+++ ++++ee+++++++l++++  ++++l +  +++ + + +l
  gi|488600302|ref|YP_007906773.1| 675 FEKEKKLEEEITVIESRKAEMLGNLRLVEE---ERRIHQSNVEEINSRLSELSSKISVAESKLRDNENRIEElKEKL 748
                                       567899************988888854444...4567899**********************976666666533456 PP

                            AAA_13 358 esvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelke 434
                                       +  +++  +i + ++ ++e i+k  e + ++  e ee++ k++ +++  l+ +l+e k+++++ ++a+ + +k+l++
  gi|488600302|ref|YP_007906773.1| 749 TYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIEEIEAKMRGSEIPALTRKLEEIKEEIDRNSRAMYSITKNLEN 825
                                       777777889******************************************************************** PP

                            AAA_13 435 eeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                                       +e +l++l++ + e+e ++ +  + +e++ ke++
  gi|488600302|ref|YP_007906773.1| 826 SEFKLQQLKDLVLEKEIKIDELDRKIENLKKEIE 859
                                       *****************************99986 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.0049
                            AAA_13  281 feekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksv 355 
                                         ++k+e+L+k ie+  +  sel    + +++ ++++++  e +++l+++ ++l +++k+l++  ++Kr      +
  gi|488600302|ref|YP_007906773.1|  847 LDRKIENLKKEIENDSQLYSELG---ERLITLKEKEKEVGESVKDLRDKRSKLLAEIKKLEKDRDEKR------F 912 
                                        34444444444444444444333...4446667778889999******************99999999......5 PP

                            AAA_13  356 elesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeyk.......kkykklek 423 
                                        e++ +++ i++ ++++++i+e+i++  e+  + ee ++  + +  + ++ee+e el+++        ++y+++++
  gi|488600302|ref|YP_007906773.1|  913 EVTGIEETIKAKEESLKDIEEQIRELGEIEYDEEEVQNIPRMEHVKRRLEEIELELKKFGdvnlkaiQDYEEVKA 987 
                                        677788888888899999999999999999999999999999888889999999999877555556666666666 PP

                            AAA_13  424 aieklekelkeeeaelkkleeeikeLekqlrde.kpaaeein....keLkaf..GlgeleLkfeee...kkgYri 488 
                                          e+l  ++   e+e  ++ e+i+  ek  rd   ++ + in    +++++   G gel+L+ +++      Y  
  gi|488600302|ref|YP_007906773.1|  988 RKEELMSKKLTLEKERSEILEKIERYEKMKRDTfFETFNAINmhfkEIISKLaeGEGELYLDNADDpfnSGLYMR 1062
                                        666666666666666666666666666665554234555555222244555556899*******99998888988 PP

                            AAA_13  489 vrkggsqaa..etLSeGEktaIaf 510 
                                        vr +++  +  e++S GEk+++a+
  gi|488600302|ref|YP_007906773.1| 1063 VRVRDKPIQkiESMSGGEKSLVAL 1086
                                        8888776555599*********97 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1  76.6    0.0011      0.82       1     176 [.       5     311 ..       5     502 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                            AAA_23   1 kLkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks...........grgfeksdvei 65 
                                       k+ ++nf+sf +++ei F kg+t+I+GpNG+GK+ i+dAi ++L+  +++    +           ++++ +++v++
  gi|488600302|ref|YP_007906773.1|   5 KIVLKNFKSFnKKVEIPFFKGFTVISGPNGSGKSNIVDAILFCLGLTPSTRYL-RadrvgdliysgNGKLGEAEVTV 80 
                                       799*******88899****************************9986533322.23568889988655777888888 PP

                            AAA_23  66 esegkvkay.veltfenkdgry................................................trsiere 93 
                                        ++++++++ ++++++++++++                                                 r+i ++
  gi|488600302|ref|YP_007906773.1|  81 IFDNDGEEIkITRKIKRTSKGNytynylngksvnlaeiqrllqnfgiysdaynvvmqgdvtriaemtpfqRRKIIDD 157
                                       88888877788887777777777899999999999999999999999999999999999999998888888888888 PP

                            AAA_23  94 relskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer................feefelkdkke. 153
                                       +  +++  +++ ka++el  ++e+ ++i+++l    ++l+++    +e                           + 
  gi|488600302|ref|YP_007906773.1| 158 IAGISEFDEKKAKAIEELEAVRENIERINTILIEVSNQLEQLKADREEAlrykslieekelnlkyL---------Ki 225
                                       888888888888888888888888888888777667777777777777766655554333333330.........14 PP

                            AAA_23 154 ....................................rleelekeleeledekkllekl................... 175
                                                                           +l+el+++ +e+++e+  l ++                   
  gi|488600302|ref|YP_007906773.1| 226 nkflslnrrkrmikrdienlemrkdkilkeiidinsKLNELNTKADEISAEIYRLADEsyktiqneiieisskregl 302
                                       45555555555666666666666666666666666644444444444444333333335555555554444333333 PP

                            AAA_23 176 ........e 176
                                               +
  gi|488600302|ref|YP_007906773.1| 303 kssiemkkK 311
                                       333322221 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  10.9     0.028        22      11      69 ..     441     499 ..     438     513 .. 0.88
   2 ?   -1.9  14.1       4.4   3.4e+03      61     130 ..     699     747 ..     663     755 .. 0.36
   3 !   20.7  25.3   4.6e-07   0.00035       7     139 ..     725     859 ..     719     863 .. 0.93
   4 ?    3.8   5.3     0.074        58      22      61 ..     829     868 ..     826     887 .. 0.69
   5 ?    3.3  25.6      0.11        86      13     137 ..     890    1016 ..     884    1020 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.028
                     Tropomyosin_1  11 eaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeese 69 
                                       e  +k++e+e+++ ++ +++ e +++i s+ ++++ leee  +le +l++ k++++  e
  gi|488600302|ref|YP_007906773.1| 441 ELNKKYKEVEKELEAAIKRRNEADNKIFSIRNQISSLEEEKKNLEVELSKIKAQLSLLE 499
                                       56789999999999999***********************************9987655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                     Tropomyosin_1  61 akekaeesekkktnnealtrkiqlLEeeleesdkkLkettekLretdvkaeelERkvkaLeqerdewekk 130
                                        +   ee   +++n e                     e + +L+e + k    E k ++ e++ +e  +k
  gi|488600302|ref|YP_007906773.1| 699 LRLVEEERRIHQSNVE---------------------EINSRLSELSSKISVAESKLRDNENRIEELKEK 747
                                       2222233333333333.....................333333222222222222222222222222222 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 4.6e-07
                     Tropomyosin_1   7 leaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnne..altrk 81 
                                            a  k  + e+++ el ++ + k +e +++ ++++ +eee+ek++e++++   + ee e k   +e  altrk
  gi|488600302|ref|YP_007906773.1| 725 SKISVAESKLRDNENRIEELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIEEIEAKMRGSEipALTRK 801
                                       5556678899999************************************************99999999999***** PP

                     Tropomyosin_1  82 iqlLEeeleesdkkLkettekLretdvkaeelERkvkaLeqerdewekkyeeleekyk 139
                                       ++ + ee++++++ + + t+ L++++ k ++l   v + e + de ++k+e+l+++ +
  gi|488600302|ref|YP_007906773.1| 802 LEEIKEEIDRNSRAMYSITKNLENSEFKLQQLKDLVLEKEIKIDELDRKIENLKKEIE 859
                                       *****************************************************98765 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.074
                     Tropomyosin_1  22 kvKeleqenlekeqeiksLtkknqqleeevekleeklkea 61 
                                       k+++l +  leke +i +L +k+++l +e+e+ ++  +e 
  gi|488600302|ref|YP_007906773.1| 829 KLQQLKDLVLEKEIKIDELDRKIENLKKEIENDSQLYSEL 868
                                       5667777788888888888888888888888766554444 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.11
                     Tropomyosin_1   13 qekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakeka..eesekkktnnealtrkiqlL 85  
                                         +k ++l +++K+le+++ ek  e++ +++ +++ ee +  +ee+++e  e    ee+ ++    e ++r+++ +
  gi|488600302|ref|YP_007906773.1|  890 RDKRSKLLAEIKKLEKDRDEKRFEVTGIEETIKAKEESLKDIEEQIRELGEIEydEEEVQNIPRMEHVKRRLEEI 964 
                                        57889999****************************************98765115566677799********** PP

                     Tropomyosin_1   86 Eeelee.sdkkLkettekLretdvkaeelERkvkaLeqerdewekkyeeleek 137 
                                        E el +  d +Lk +++  +e+ ++ eel  k   Le+er e  +k+e  e+ 
  gi|488600302|ref|YP_007906773.1|  965 ELELKKfGDVNLK-AIQDYEEVKARKEELMSKKLTLEKERSEILEKIERYEKM 1016
                                        ****994577777.67789***********************99999988764 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  22.6     0.013        10       4     205 ..     239     432 ..     233     434 .. 0.84
   2 !    8.6  11.7    0.0018       1.4      13      97 ..     417     501 ..     412     518 .. 0.88
   3 ?   -1.7   2.2       2.6     2e+03      36      62 ..     672     698 ..     669     714 .. 0.59
   4 !   16.9  16.9   5.5e-06    0.0043       8     108 ..     714     816 ..     709     840 .. 0.81
   5 ?    0.2  31.4      0.68   5.3e+02       6     179 ..     843    1020 ..     838    1041 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                               ERM   4 erekreleerLkqlqeeaekaqeaLreseetaelLaek.arraeeeaelLeqkaaeaeeeiqrlkesaekeeeekek 79 
                                       +r+ ++le+r  ++ +e+   + +L+e + +a++   +  r a e  +  +++  e+  + + lk s e++++e ++
  gi|488600302|ref|YP_007906773.1| 239 KRDIENLEMRKDKILKEIIDINSKLNELNTKADEISAEiYRLADESYKTIQNEIIEISSKREGLKSSIEMKKKEIKD 315
                                       567788999999999999999999999999999996551677788889999999999******************** PP

                               ERM  80 lerklreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpskseseenveeseteeeeensee 156
                                       +e++ ++    +++l+ee+++ eee ++   + + ++e + + ++k   ++s+ +          ++  +e  ++  
  gi|488600302|ref|YP_007906773.1| 316 IEDEKTKLLVSISKLKEEVSKVEEELQKFSIQKMSVQEVLDDLESKKSLIISKLNL--------MDSAYSELRDQLL 384
                                       ***************************99999999999999888888888888831........1122223344455 PP

                               ERM 157 esaeletdeveklsleieeeRvtylekskrlqeqLkeLkseleqlkdee 205
                                       +++e+  +  ++ + ++ +eR  +le  +r+    ++ + e+e l+ e+
  gi|488600302|ref|YP_007906773.1| 385 KKKEILDE-LKERKSSKVNERDRLLEVIRRIGMEIEDIEGEIETLRKES 432
                                       66777755.77779999999**************************885 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0018
                               ERM  13 rLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreael 89 
                                       +++ ++ e+e  +++    +e+ ++L++k +++e+e e   ++++ea ++i  ++ + +  eeek++le +l + ++
  gi|488600302|ref|YP_007906773.1| 417 EIEDIEGEIETLRKESITLNEELKELNKKYKEVEKELEAAIKRRNEADNKIFSIRNQISSLEEEKKNLEVELSKIKA 493
                                       67788899999999999999999*************************************************99999 PP

                               ERM  90 eaarleee 97 
                                       +++ le+ 
  gi|488600302|ref|YP_007906773.1| 494 QLSLLESS 501
                                       99888765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.6
                               ERM  36 elLaekarraeeeaelLeqkaaeaeee 62 
                                       ++L ek +++eee    e ++ae+   
  gi|488600302|ref|YP_007906773.1| 672 KELFEKEKKLEEEITVIESRKAEMLGN 698
                                       567777777777777777777766433 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 5.5e-06
                               ERM   8 releerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerkl 84 
                                       +e++ rL +l +++  a+ +Lr++e+++e+L+ek+   ++e+ +  ++ + +eeei+++ e+ +k   e e++e+k+
  gi|488600302|ref|YP_007906773.1| 714 EEINSRLSELSSKISVAESKLRDNENRIEELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIEEIEAKM 790
                                       68999***********************************************************************9 PP

                               ERM  85 reae..leaarleeeserkeeeaerL 108
                                       r  e  +++++lee +e+ +++ + +
  gi|488600302|ref|YP_007906773.1| 791 RGSEipALTRKLEEIKEEIDRNSRAM 816
                                       96652245666666666655554443 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.68
                               ERM    6 ekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekekl 80  
                                        + +el +++++l++e+e+  +  +e  e+   L+ek +++ e  + L  k++++ +ei++l++++ ++  e   +
  gi|488600302|ref|YP_007906773.1|  843 KIDELDRKIENLKKEIENDSQLYSELGERLITLKEKEKEVGESVKDLRDKRSKLLAEIKKLEKDRDEKRFEVTGI 917 
                                        6689*********************************************************************** PP

                               ERM   81 erklreaeleaarleeeser.....keeeaerLke..eleeareaeeeakekllealstpskses.eenveeset 147 
                                        e+ ++++e+ ++++ee+ ++        + e+ ++  ++e++++++ee + +l+++   + k ++  e+v++ ++
  gi|488600302|ref|YP_007906773.1|  918 EETIKAKEESLKDIEEQIRElgeieY--DEEEVQNipRMEHVKRRLEEIELELKKFGDVNLKAIQdYEEVKARKE 990 
                                        ***************99888666443..44444443389999999999999999999999755552222222222 PP

                               ERM  148 eeeeenseeesaeletde...veklsleieeeRvt 179 
                                             + ++++  le++     ek+++ ++ +R t
  gi|488600302|ref|YP_007906773.1|  991 -----ELMSKKLTLEKERseiLEKIERYEKMKRDT 1020
                                        .....222233333333323333334444444555 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   0.3      0.14   1.1e+02      80     114 ..     166     200 ..     136     212 .. 0.64
   2 ?    5.6   4.8      0.02        15      54     116 ..     242     305 ..     224     311 .. 0.59
   3 ?    5.0   8.4     0.031        24      40     119 ..     289     364 ..     285     369 .. 0.78
   4 !    7.3   5.1     0.006       4.7      39     122 ..     372     451 ..     362     453 .. 0.81
   5 !    9.8   5.4   0.00096      0.75      52     122 ..     430     500 ..     425     502 .. 0.92
   6 !   17.0   5.5   6.1e-06    0.0047      40     118 ..     710     791 ..     705     794 .. 0.90
   7 !    9.4   1.2    0.0013         1      66     122 ..     793     849 ..     791     850 .. 0.95
   8 !    8.8   6.6    0.0021       1.6      37     122 ..     821     905 ..     815     907 .. 0.71
   9 ?    3.9   4.2     0.064        50      51     108 ..     883     940 ..     879     972 .. 0.84
  10 ?   -2.0   0.1       4.5   3.5e+03      55      81 ..     983    1009 ..     969    1041 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                           DUF1664  80 eiskeikeevtevredlseigedvesvkeavegle 114
                                       e +++  ee+++vre++++i++ + +v++  e+l+
  gi|488600302|ref|YP_007906773.1| 166 EKKAKAIEELEAVRENIERINTILIEVSNQLEQLK 200
                                       33344444555555555555555555555555543 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
                           DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevr.edlseigedvesvkeaveglesk 116
                                        e+l+  k+++ ++i  +++kl+e +  + ei++e+ ++  e  ++i++++ ++++  egl+s+
  gi|488600302|ref|YP_007906773.1| 242 IENLEMRKDKILKEIIDINSKLNELNTKADEISAEIYRLAdESYKTIQNEIIEISSKREGLKSS 305
                                       3555566666666666666666666666666666666554134556666666666666666655 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.031
                           DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       ++ + ++s++ e +++s++  k+    +i+ ++++  +    ++++keev++v+e+l++++ +  sv+e+  +lesk
  gi|488600302|ref|YP_007906773.1| 289 QNEIIEISSKREGLKSSIEMKKK----EIKDIEDEKTKLLVSISKLKEEVSKVEEELQKFSIQKMSVQEVLDDLESK 361
                                       55555666666677777776665....4677777777888888999*****************************99 PP

                           DUF1664 117 ler 119
                                        + 
  gi|488600302|ref|YP_007906773.1| 362 KSL 364
                                       665 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.006
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       + +a +++  ql + +e l + k++ ss++++ d+      e+++ i  e+++++++++++++++ +++e  ++l++
  gi|488600302|ref|YP_007906773.1| 372 MDSAYSELRDQLLKKKEILDELKERKSSKVNERDR----LLEVIRRIGMEIEDIEGEIETLRKESITLNEELKELNK 444
                                       45677777778877777787777777777776655....5678999999**************************** PP

                           DUF1664 116 kleriee 122
                                       k +++e+
  gi|488600302|ref|YP_007906773.1| 445 KYKEVEK 451
                                       **99996 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00096
                           DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       + s +l++  ++L+++ ++v+k+l++ ++  +e ++++ ++r+++s+++e+ ++++   ++++++l+ +e+
  gi|488600302|ref|YP_007906773.1| 430 KESITLNEELKELNKKYKEVEKELEAAIKRRNEADNKIFSIRNQISSLEEEKKNLEVELSKIKAQLSLLES 500
                                       55667889999******************************************************999986 PP

  == domain 6  score: 17.0 bits;  conditional E-value: 6.1e-06
                           DUF1664  40 sdavesvskqleqvseslaatkrhL...ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       ++ ve++ ++l ++s++++ +  +L   ++ri+++ +kl   ++  +ei e ++ v+e++++i+e++++++  +e++
  gi|488600302|ref|YP_007906773.1| 710 QSNVEEINSRLSELSSKISVAESKLrdnENRIEELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIEEI 786
                                       6779999***********9999999333479********************************************** PP

                           DUF1664 114 eskle 118
                                       e+k++
  gi|488600302|ref|YP_007906773.1| 787 EAKMR 791
                                       *9985 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.0013
                           DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       s+i  + +kl+e ke +   ++ + ++ ++l++ + +++++k++v + e k+++++ 
  gi|488600302|ref|YP_007906773.1| 793 SEIPALTRKLEEIKEEIDRNSRAMYSITKNLENSEFKLQQLKDLVLEKEIKIDELDR 849
                                       678999***********************************************9986 PP

  == domain 8  score: 8.8 bits;  conditional E-value: 0.0021
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       ++l++   ++ +ql+++  + +   ++L ++i+++ k++++ +++ +e+ e + +++e+ +e+ge v+ +++  ++l
  gi|488600302|ref|YP_007906773.1| 821 KNLENSEFKL-QQLKDLVLEKEIKIDELDRKIENLKKEIENDSQLYSELGERLITLKEKEKEVGESVKDLRDKRSKL 896
                                       3333333332.233333333333446899999999999999999999999999999999999999999999999999 PP

                           DUF1664 114 eskleriee 122
                                        ++++++e+
  gi|488600302|ref|YP_007906773.1| 897 LAEIKKLEK 905
                                       999999986 PP

  == domain 9  score: 3.9 bits;  conditional E-value: 0.064
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                        +  ++l++ + +L ++i++++k  de     + i+e +++ +e l++i+e+++++ e
  gi|488600302|ref|YP_007906773.1| 883 GESVKDLRDKRSKLLAEIKKLEKDRDEKRFEVTGIEETIKAKEESLKDIEEQIRELGE 940
                                       4556788899999999999999999999999999999999999999999999887755 PP

  == domain 10  score: -2.0 bits;  conditional E-value: 4.5
                           DUF1664   55 eslaatkrhLssridrvdkkldeqkei 81  
                                        e+++a k++L+s+  +++k+  e  e 
  gi|488600302|ref|YP_007906773.1|  983 EEVKARKEELMSKKLTLEKERSEILEK 1009
                                        555555555555544444333333222 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   2.1       1.2   9.6e+02      31      71 ..     165     205 ..     158     215 .. 0.62
   2 ?    1.1   3.1      0.62   4.8e+02      31      78 ..     232     279 ..     224     291 .. 0.84
   3 ?    1.9   2.6      0.36   2.8e+02      14      72 ..     296     358 ..     283     368 .. 0.72
   4 ?   -0.5   3.2         2   1.5e+03      34      66 ..     414     450 ..     375     452 .. 0.71
   5 !   16.4   6.5     1e-05    0.0079      11      66 ..     444     499 ..     434     507 .. 0.83
   6 ?   -0.9   2.9       2.6     2e+03      32      83 ..     676     727 ..     670     730 .. 0.79
   7 ?    1.1   8.0      0.62   4.8e+02       4      63 ..     732     791 ..     729     822 .. 0.72
   8 ?   -2.2   1.6       6.9   5.4e+03       6      69 ..     954    1017 ..     949    1022 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                           DUF4164  31 erkrdeleaeiealgedrsRLaeeLdqaearaarleevnrE 71 
                                       ++k++++ +e+ea++e  +R+   L ++++ +++l++  +E
  gi|488600302|ref|YP_007906773.1| 165 DEKKAKAIEELEAVRENIERINTILIEVSNQLEQLKADREE 205
                                       45555555666666666666666666666666666655444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.62
                           DUF4164  31 erkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLka 78 
                                       +r ++ ++++ie l+  + ++ +e+ + + ++++l+  ++E+s ++ +
  gi|488600302|ref|YP_007906773.1| 232 NRRKRMIKRDIENLEMRKDKILKEIIDINSKLNELNTKADEISAEIYR 279
                                       5666789999********************************998755 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.36
                           DUF4164  14 eaaldsLEkavdrrleaerkr....deleaeiealgedrsRLaeeLdqaearaarleevnrEv 72 
                                       + + + L ++++++ ++ ++      +l   i++l+e+ s+ +eeL + +    +++ev +++
  gi|488600302|ref|YP_007906773.1| 296 SSKREGLKSSIEMKKKEIKDIedekTKLLVSISKLKEEVSKVEEELQKFSIQKMSVQEVLDDL 358
                                       555566777777777766666443455556788999999999999998888888888877765 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2
                           DUF4164  34 r....deleaeiealgedrsRLaeeLdqaearaarle 66 
                                            +++e eie l+++   L eeL + + + +++e
  gi|488600302|ref|YP_007906773.1| 414 IgmeiEDIEGEIETLRKESITLNEELKELNKKYKEVE 450
                                       0444489999999999999999999999888888877 PP

  == domain 5  score: 16.4 bits;  conditional E-value: 1e-05
                           DUF4164  11 trLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarle 66 
                                       ++ ++  ++LE+a++rr ea++k  +++++i+ l+e+++ L+ eL + +a ++ le
  gi|488600302|ref|YP_007906773.1| 444 KKYKEVEKELEAAIKRRNEADNKIFSIRNQISSLEEEKKNLEVELSKIKAQLSLLE 499
                                       444444578**************************************999998887 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 2.6
                           DUF4164  32 rkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaieti 83 
                                       +k+++le+ei+ +++ ++ +  +L  +e + +  ++  +E+++rL  +  +i
  gi|488600302|ref|YP_007906773.1| 676 EKEKKLEEEITVIESRKAEMLGNLRLVEEERRIHQSNVEEINSRLSELSSKI 727
                                       5667888888888888888888888888888888888888888888777766 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.62
                           DUF4164   4 keleaaltrLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaa 63 
                                       ++l++  +r+e+  ++L+   ++r e  +  + +e+eie+++e+  ++  e+ + ea+ +
  gi|488600302|ref|YP_007906773.1| 732 SKLRDNENRIEELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIEEIEAKMR 791
                                       667777888888888888888899999999999999999999999999999998887754 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 6.9
                           DUF4164    6 leaaltrLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevn 69  
                                        +e + +rLe+   +L k  d  l+a ++ +e++a+ e+l + +  L++e  + + + +r e+++
  gi|488600302|ref|YP_007906773.1|  954 MEHVKRRLEEIELELKKFGDVNLKAIQDYEEVKARKEELMSKKLTLEKERSEILEKIERYEKMK 1017
                                        5666777777777777777777777777778888877777777777777666666666655555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.6e-05     0.044       1      47 [.       1      45 [.       1      65 [. 0.84
   2 ?    1.9   0.8      0.19   1.4e+02     159     200 ..     422     463 ..     391     490 .. 0.57
   3 ?   -1.2   0.2       1.7   1.3e+03     143     199 ..     722     778 ..     710     790 .. 0.58
   4 ?   -1.3   0.6       1.8   1.4e+03     150     150 ..     789     789 ..     727     849 .. 0.49
   5 ?   -1.4   0.4       1.9   1.5e+03     147     199 ..     885     930 ..     866     939 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                            AAA_27  1 MrlerLdLeryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAis 47
                                      M ++++ L+ + +f+ + ++ f    +++++i GpN +GKs +++Ai 
  gi|488600302|ref|YP_007906773.1|  1 MYIKKIVLKNFKSFNKKvEIPFF---KGFTVISGPNGSGKSNIVDAIL 45
                                      88999999999999765456665...9******************996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.19
                            AAA_27 159 revleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                       +  +e+L++e  +l ++ k+ +++++e ++ele+a k+ +ea
  gi|488600302|ref|YP_007906773.1| 422 EGEIETLRKESITLNEELKELNKKYKEVEKELEAAIKRRNEA 463
                                       444444444444444444444444444444444444444433 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.7
                            AAA_27 143 elgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       el++ +  a++ l++ ++ +e+L+++ +   k+r++  +++   +ee+e+ ++e+r+
  gi|488600302|ref|YP_007906773.1| 722 ELSSKISVAESKLRDNENRIEELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRK 778
                                       555555555655555555666665555444444444445666666666666666655 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.8
                            AAA_27 150 e 150
                                       +
  gi|488600302|ref|YP_007906773.1| 789 K 789
                                       2 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 1.9
                            AAA_27 147 lLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       +       +++lr+ + +L ae ++l k+r +k+ +++  +e++++ +++l++
  gi|488600302|ref|YP_007906773.1| 885 S-------VKDLRDKRSKLLAEIKKLEKDRDEKRFEVTGIEETIKAKEESLKD 930
                                       3.......344444444444555554444444444444444444444443333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0083       6.5      26      45 ..      26      45 ..      14      51 .. 0.89
   2 ?   -1.4   0.0       3.5   2.7e+03      36     107 ..     110     177 ..     110     234 .. 0.47
   3 ?   -0.8   0.1       2.2   1.7e+03      67     107 ..     374     417 ..     306     459 .. 0.60
   4 ?   -0.2   0.0       1.5   1.2e+03      86     145 ..     991    1052 ..     954    1080 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0083
                            AAA_16 26 lvllsGesGvGKsslvrell 45
                                       +++sG+ G+GKs +v+++l
  gi|488600302|ref|YP_007906773.1| 26 FTVISGPNGSGKSNIVDAIL 45
                                      689*************9886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                            AAA_16  36 GKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaa 107
                                       GKs  + e++ +l ++ gi+  + ++  + ++++  +a++  + +  + ++d a  +e+++ ++k  e+l+a
  gi|488600302|ref|YP_007906773.1| 110 GKSVNLAEIQ-RLLQNFGIYSDAYNVVMQGDVTR--IAEMTPF-QRRKIIDDIAGISEFDEKKAKAIEELEA 177
                                       7777777777.45555233333333333333333..3333322.3333333332333444444444444441 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.2
                            AAA_16  67 ipysalaqalareellrqlldeaesaeleawrekleeala....a 107
                                        +ys l ++l +++ + ++l e +s+++++ ++ l+e+++    +
  gi|488600302|ref|YP_007906773.1| 374 SAYSELRDQLLKKKEILDELKERKSSKVNERDR-LLEVIRrigmE 417
                                       345553333333333333333333333333333.33333333333 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.5
                            AAA_16   86 ldeaesaeleawrekleealaavpelagaea....srllellkrllallsrderplvlvlDdlq 145 
                                        + ++++  le  r +++e ++   +++++      ++++ ++k+++++l+++e    l lD+++
  gi|488600302|ref|YP_007906773.1|  991 ELMSKKLTLEKERSEILEKIERYEKMKRDTFfetfNAINMHFKEIISKLAEGEG--ELYLDNAD 1052
                                        33344555566666666666655555555558889999********88887677..78888887 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.31   2.4e+02      35      60 ..     180     205 ..     176     214 .. 0.89
   2 ?    6.5   0.1    0.0063       4.9      29      99 ..     248     316 ..     243     356 .. 0.85
   3 ?   -1.0   0.0       1.2   9.7e+02      42     103 ..     388     449 ..     379     465 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.31
                         Mce4_CUP1  35 esltdlnevLdelNprlpqlredire 60 
                                       e+++++n++L e+ ++l+ql++d +e
  gi|488600302|ref|YP_007906773.1| 180 ENIERINTILIEVSNQLEQLKADREE 205
                                       6899******************9776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0063
                         Mce4_CUP1  29 rGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdal 99 
                                       r +++ + + d+n+ L+elN++ ++++++i +lad  + Y+ + ++++++ ++    +++i+ +++e++++
  gi|488600302|ref|YP_007906773.1| 248 RKDKILKEIIDINSKLNELNTKADEISAEIYRLAD--ESYKTIQNEIIEISSKREGLKSSIEMKKKEIKDI 316
                                       567777899************************97..7799999999999888888888888888877665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.2
                         Mce4_CUP1  42 evLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaa 103
                                       e+Ldel +r  +  ++  +l ++    +   +d+   ++ +++ s T++e+ +eL++ + ++
  gi|488600302|ref|YP_007906773.1| 388 EILDELKERKSSKVNERDRLLEVIRRIGMEIEDIEGEIETLRKESITLNEELKELNKKYKEV 449
                                       55566655555555555555566666666666666666666666666666666666555544 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 ?    2.8   6.5      0.15   1.1e+02      40     105 ..     182     274 ..     168     294 .. 0.56
   2 ?    2.9   1.5      0.13     1e+02      36     100 ..     302     361 ..     283     410 .. 0.55
   3 ?    8.9   1.6    0.0019       1.5      29     109 ..     415     496 ..     390     502 .. 0.56
   4 ?    4.7   0.2     0.037        29      39      97 ..     712     772 ..     681     792 .. 0.56
   5 ?    6.0   0.4     0.014        11      68      99 ..     794     825 ..     751     862 .. 0.40
   6 ?    2.9   0.5      0.13     1e+02      40     109 ..     844     922 ..     829     980 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                      Baculo_PEP_C  40 ldaietqLnalsedlksllaeldt........................rldtlltnLtdalnalq...dtlrneLtn 89 
                                       ++ i+t L ++s++l++l a+ ++                         l+     +++ + +l+   d++ +e+  
  gi|488600302|ref|YP_007906773.1| 182 IERINTILIEVSNQLEQLKADREEalrykslieekelnlkylkinkflSLNRRKRMIKRDIENLEmrkDKILKEIID 258
                                       33333333333333333333333333333334455554455555666677777777777777777777777777777 PP

                      Baculo_PEP_C  90 lnsiltnLlssvtNin 105
                                       +ns+l++L+++   i 
  gi|488600302|ref|YP_007906773.1| 259 INSKLNELNTKADEIS 274
                                       7777777776655554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.13
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlss 100
                                       l++ ++  ++++++++++ ++ll +++ +l++ ++++++ l++++    ++++ L+ l+s       +
  gi|488600302|ref|YP_007906773.1| 302 LKSSIEMKKKEIKDIEDEKTKLLVSIS-KLKEEVSKVEEELQKFSiqkMSVQEVLDDLES-------K 361
                                       344444444555555555555555443.34444444444444444333333344444433.......3 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0019
                      Baculo_PEP_C  29 nvqilaqlatlldaietq...LnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvt 102
                                        ++i  +++  ++++ ++   Ln+  ++l++  +e++++l++++++ ++a n++  ++rn++ +l+ +  nL  ++ 
  gi|488600302|ref|YP_007906773.1| 415 GMEI-EDIEGEIETLRKEsitLNEELKELNKKYKEVEKELEAAIKRRNEADNKIF-SIRNQISSLEEEKKNLEVELS 489
                                       3333.33333333333320003333333444444444455555555555555555.788888888888888888887 PP

                      Baculo_PEP_C 103 NinstLn 109
                                        i++ L+
  gi|488600302|ref|YP_007906773.1| 490 KIKAQLS 496
                                       7777665 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.037
                      Baculo_PEP_C  39 lldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsiltnL 97 
                                        +++i+++L++ls++++ + ++l++   r+++l ++Lt + ++ + ++ +++ +++ ++  +
  gi|488600302|ref|YP_007906773.1| 712 NVEEINSRLSELSSKISVAESKLRDnenRIEELKEKLTYKQKERA-EIYERMSGVEEEIEKI 772
                                       456666666666666654444333333355555555554433333.3333333333333333 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.014
                      Baculo_PEP_C  68 lltnLtdalnalqdtlrneLtnlnsiltnLls 99 
                                        + +Lt++l +++++++ +  ++ si  nL +
  gi|488600302|ref|YP_007906773.1| 794 EIPALTRKLEEIKEEIDRNSRAMYSITKNLEN 825
                                       22233333333333222222222222222222 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.13
                      Baculo_PEP_C  40 ldaietqLnalsedlksllaeldt.............rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlss 100
                                       +d++++++++l+++++       +              l++  +++ ++++ l     +l  e++ l+++  +   +
  gi|488600302|ref|YP_007906773.1| 844 IDELDRKIENLKKEIE-------NdsqlyselgerliTLKEKEKEVGESVKDLRdkrSKLLAEIKKLEKDRDEKRFE 913
                                       3444444444444444.......333333334445555555555566666666555555666666666666666666 PP

                      Baculo_PEP_C 101 vtNinstLn 109
                                       vt+i++t++
  gi|488600302|ref|YP_007906773.1| 914 VTGIEETIK 922
                                       666666654 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.3       1.9   1.5e+03      80     118 ..     165     203 ..     150     224 .. 0.60
   2 ?   -1.1  17.0       2.5   1.9e+03      74     180 ..     226     340 ..     176     344 .. 0.73
   3 ?    4.9   6.1     0.035        28      99     154 ..     287     342 ..     281     364 .. 0.69
   4 ?    6.4  12.7     0.012       9.1      98     180 ..     377     452 ..     345     455 .. 0.57
   5 ?    9.3   8.2    0.0016       1.2      74     147 ..     437     510 ..     432     516 .. 0.83
   6 ?   11.9  14.5   0.00024      0.19      76     180 ..     671     775 ..     651     779 .. 0.92
   7 ?    8.9   2.4     0.002       1.6      81     132 ..     739     790 ..     738     794 .. 0.90
   8 ?   12.2   6.2    0.0002      0.16      71     151 ..     790     870 ..     778     878 .. 0.90
   9 ?    5.3   6.6     0.026        20      70     129 ..     880     939 ..     874     969 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.9
                             ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleekl 118
                                       ++k a+  eel+++    +  ++ l+e++++l++l++  
  gi|488600302|ref|YP_007906773.1| 165 DEKKAKAIEELEAVRENIERINTILIEVSNQLEQLKADR 203
                                       555555555555555555555555555555555555432 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                             ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerl........aeleaeraaletklkdr 142
                                       +k  sl+ +   ++ + ++l  ++ +  + +++ n++l +l++k+ e ++++        + +++e+ +++ k++ +
  gi|488600302|ref|YP_007906773.1| 226 NKFLSLNRRKRMIKRDIENLEMRKDKILKEIIDINSKLNELNTKADEISAEIyrladesyKTIQNEIIEISSKREGL 302
                                       556677777777888888888888888889999999998888888877766611111111556788999999999** PP

                             ATG16 143 eeelrekeklvqdlqDElsaLqlqlnqaEeklrklekE 180
                                       +  ++ k+k ++d+ DE + L +  +++ e+  k+e+E
  gi|488600302|ref|YP_007906773.1| 303 KSSIEMKKKEIKDIEDEKTKLLVSISKLKEEVSKVEEE 340
                                       ***********************************999 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.035
                             ATG16  99 elaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                       + ++ ++e +++ + l+++++ ++++++++e+e+++l   +++++ee+   e+ +q
  gi|488600302|ref|YP_007906773.1| 287 TIQNEIIEISSKREGLKSSIEMKKKEIKDIEDEKTKLLVSISKLKEEVSKVEEELQ 342
                                       45667777777777777777777777777777777777777777777776666555 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.012
                             ATG16  98 gelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEekl 174
                                       +el ++ll+++e l++l+e+ +++ ++       r +l + +++  +e+++ e  +++l+ E ++L+ +l+ + +k+
  gi|488600302|ref|YP_007906773.1| 377 SELRDQLLKKKEILDELKERKSSKVNE-------RDRLLEVIRRIGMEIEDIEGEIETLRKESITLNEELKELNKKY 446
                                       344444455555555555444444444.......5555555555555555555555566666666666666666666 PP

                             ATG16 175 rklekE 180
                                       +++ekE
  gi|488600302|ref|YP_007906773.1| 447 KEVEKE 452
                                       666555 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0016
                             ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelr 147
                                       +++++l++k +++ +el+++ k+r+e  +++ +  ++++ lee+ k+ e +l +++a+ + le   ++  e + 
  gi|488600302|ref|YP_007906773.1| 437 EELKELNKKYKEVEKELEAAIKRRNEADNKIFSIRNQISSLEEEKKNLEVELSKIKAQLSLLESSFSKAVELIL 510
                                       67788999999999999999999999999999999999999999999999999999999999988887777665 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 0.00024
                             ATG16  76 iqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekekl 152
                                       +++l +k ++l ee +    +++e+   l+ ++ee +  +++ +e ++rl el++++++ e kl+d+e++++e+++ 
  gi|488600302|ref|YP_007906773.1| 671 TKELFEKEKKLEEEITVIESRKAEMLGNLRLVEEERRIHQSNVEEINSRLSELSSKISVAESKLRDNENRIEELKEK 747
                                       567778889******************************************************************** PP

                             ATG16 153 vqdlqDElsaLqlqlnqaEeklrklekE 180
                                       +   q E +    +++ +Ee+ +k+ +E
  gi|488600302|ref|YP_007906773.1| 748 LTYKQKERAEIYERMSGVEEEIEKIDEE 775
                                       ***********************99998 PP

  == domain 7  score: 8.9 bits;  conditional E-value: 0.002
                             ATG16  81 qklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaer 132
                                       +++ +l+e l+  +k+r+e  +r   ++ee++k +e++++ + +++e+ea+ 
  gi|488600302|ref|YP_007906773.1| 739 NRIEELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIEEIEAKM 790
                                       6788999***************************************999876 PP

  == domain 8  score: 12.2 bits;  conditional E-value: 0.0002
                             ATG16  71 kqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelr 147
                                        + ++i++l+ kl +++ee     ++    ++ l + + +lq+l++   e+e +++el +++++l++++++  +   
  gi|488600302|ref|YP_007906773.1| 790 MRGSEIPALTRKLEEIKEEIDRNSRAMYSITKNLENSEFKLQQLKDLVLEKEIKIDELDRKIENLKKEIENDSQLYS 866
                                       567899****************************************************************9999888 PP

                             ATG16 148 ekek 151
                                       e+ +
  gi|488600302|ref|YP_007906773.1| 867 ELGE 870
                                       8765 PP

  == domain 9  score: 5.3 bits;  conditional E-value: 0.026
                             ATG16  70 skqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaele 129
                                       ++  +++++l +k+++l +e ++l k r e    ++  +e+++++ee+lk  ee+++el 
  gi|488600302|ref|YP_007906773.1| 880 KEVGESVKDLRDKRSKLLAEIKKLEKDRDEKRFEVTGIEETIKAKEESLKDIEEQIRELG 939
                                       356688999999999999999999999999999999999999999999999999999985 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   0.3     0.093        73      24      56 ..     169     201 ..     152     229 .. 0.69
   2 ?    5.7   1.9     0.027        21       8      56 ..     237     282 ..     236     297 .. 0.82
   3 ?    0.6   0.1       1.1   8.2e+02      13      59 ..     411     454 ..     406     459 .. 0.66
   4 ?    6.3   0.4     0.017        13      15      59 ..     462     503 ..     453     521 .. 0.77
   5 ?    6.9   1.1     0.011       8.7      29      56 ..     733     760 ..     707     835 .. 0.54
   6 ?    3.6   1.2      0.12        95       7      53 ..     831     877 ..     826     890 .. 0.74
   7 ?    5.0   0.5     0.042        33      12      64 ..     885     941 ..     881     956 .. 0.77
   8 ?    1.3   0.2      0.61   4.7e+02      12      54 ..     920     971 ..     915     982 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.093
                           NPV_P10  24 qqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                        ++++++++  ++++ +n+ L + s+qL++l++
  gi|488600302|ref|YP_007906773.1| 169 AKAIEELEAVRENIERINTILIEVSNQLEQLKA 201
                                       445556666666666677777777777777764 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                       +I+ di++++ + d + +++ d++++l++   ln+k d++sa++  l +
  gi|488600302|ref|YP_007906773.1| 237 MIKRDIENLEMRKDKILKEIIDINSKLNE---LNTKADEISAEIYRLAD 282
                                       58999999999999999999999999888...99999999999988865 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
                           NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                       i+ +   ++ ++ +++ +++++ +   lne+L +++++ +e+e+++e
  gi|488600302|ref|YP_007906773.1| 411 IRRIGMEIEDIEGEIETLRKESIT---LNEELKELNKKYKEVEKELE 454
                                       555555666677777777776666...77777777777777776655 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.017
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                       + d+k+ ++ +q+ +++e+ ++   l+ +L ++ aqL  le++ +
  gi|488600302|ref|YP_007906773.1| 462 EADNKIFSIRNQISSLEEEKKN---LEVELSKIKAQLSLLESSFS 503
                                       6799*****************9...66788888888887777443 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.011
                           NPV_P10  29 dvqenlpdvtelnekLdaqsaqLaelet 56 
                                       ++++n + ++el+ekL   +++ ae+ +
  gi|488600302|ref|YP_007906773.1| 733 KLRDNENRIEELKEKLTYKQKERAEIYE 760
                                       5555555555555555444333333333 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.12
                           NPV_P10   7 lvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLae 53 
                                        + ++ + + + k+d l+ +++++++++++ ++l ++L +   +L+e
  gi|488600302|ref|YP_007906773.1| 831 QQLKDLVLEKEIKIDELDRKIENLKKEIENDSQLYSELGERLITLKE 877
                                       55666667777899999999999999999988888877766555555 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.042
                           NPV_P10  12 dikavddkVdalqqqvddvqenlp....dvtelnekLdaqsaqLaeletkvenIqdi 64 
                                        +k++ dk + l +++++++++      +vt ++e + a  ++L+++e+++ +  +i
  gi|488600302|ref|YP_007906773.1| 885 SVKDLRDKRSKLLAEIKKLEKDRDekrfEVTGIEETIKAKEESLKDIEEQIRELGEI 941
                                       688888999999999988887765222269999***************998887766 PP

  == domain 8  score: 1.3 bits;  conditional E-value: 0.61
                           NPV_P10  12 dikavddkVdalqqqv.........ddvqenlpdvtelnekLdaqsaqLael 54 
                                        ika ++ ++ +++q+         ++  +n+p +++++ +L+++  +L+++
  gi|488600302|ref|YP_007906773.1| 920 TIKAKEESLKDIEEQIrelgeieydEEEVQNIPRMEHVKRRLEEIELELKKF 971
                                       4455555555555555333333333223345666666666666666666665 PP

>> DUF3251  Protein of unknown function (DUF3251)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.5     5e+03      11      42 ..     239     271 ..     234     293 .. 0.69
   2 ?    2.6   0.3      0.12        96       6      32 ..     326     352 ..     317     366 .. 0.78
   3 ?    2.1   0.2      0.18   1.4e+02       6      38 ..     424     454 ..     421     460 .. 0.84
   4 ?    9.1   0.1    0.0012      0.93       7      64 ..     467     525 ..     463     533 .. 0.85
   5 ?   -1.7   0.1       2.4   1.9e+03      11      65 ..     759     780 ..     717     799 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.5
                                       -S-------------HHHHHHH.HHHHHHHH-S CS
                           DUF3251  11 kqsvsklnqelktleqetvkie.qqnaLnaksk 42 
                                       k+ + +l+ +  ++ +e++ i+ + n+Ln k+ 
  gi|488600302|ref|YP_007906773.1| 239 KRDIENLEMRKDKILKEIIDINsKLNELNTKAD 271
                                       566666777777777777777623477777664 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                                       ------S-------------HHHHHHH CS
                           DUF3251   6 elrqlkqsvsklnqelktleqetvkie 32 
                                        + +lk++vsk+++el++   + + ++
  gi|488600302|ref|YP_007906773.1| 326 SISKLKEEVSKVEEELQKFSIQKMSVQ 352
                                       577899999999999999887776665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.18
                                       ------S-------------HHHHHHHHHHHHH CS
                           DUF3251   6 elrqlkqsvsklnqelktleqetvkieqqnaLn 38 
                                       e+  l+++  +ln+elk+l+++   +e++  L 
  gi|488600302|ref|YP_007906773.1| 424 EIETLRKESITLNEELKELNKKYKEVEKE--LE 454
                                       6778899999*************999987..54 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0012
                                       -----S-------------HHHHHHHHHHHH.HHH-SSSEEE-TTT---EEEE-SS-EE CS
                           DUF3251   7 lrqlkqsvsklnqelktleqetvkieqqnaL.nakskkgvyLlPgaktparlesqiGrl 64 
                                       +  +++++s l++e k+le e+ ki+ q  L     +k+v L  +ak+   + +  G++
  gi|488600302|ref|YP_007906773.1| 467 IFSIRNQISSLEEEKKNLEVELSKIKAQLSLlESSFSKAVELILEAKSRKAMPGVFGTV 525
                                       557899*******************9886651666689********9999988888887 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 2.4
                                       -S-------------HHHHHHHHHHHHHHH-SSSEEE-TTT---EEEE-SS-EEE CS
                           DUF3251  11 kqsvsklnqelktleqetvkieqqnaLnakskkgvyLlPgaktparlesqiGrlr 65 
                                        + +s +++e++++++e+ ki                                 +
  gi|488600302|ref|YP_007906773.1| 759 YERMSGVEEEIEKIDEEIRKI---------------------------------S 780
                                       444444444444444444444.................................3 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.66   5.2e+02      51      78 ..     173     200 ..     166     206 .. 0.78
   2 ?   -1.0   0.0       2.7   2.1e+03      55      78 ..     258     281 ..     249     285 .. 0.72
   3 ?   -2.7   0.1       9.1   7.1e+03       8      33 ..     336     361 ..     329     363 .. 0.72
   4 ?    1.3   0.0      0.51     4e+02      20      71 ..     432     450 ..     406     465 .. 0.55
   5 ?   -1.0   0.1       2.8   2.2e+03      10      41 ..     471     502 ..     469     505 .. 0.80
   6 ?    0.6   0.0      0.86   6.7e+02      58      85 ..     711     738 ..     704     739 .. 0.86
   7 ?    6.7   0.0      0.01       8.2      17      83 ..     766     832 ..     756     833 .. 0.90
   8 ?    2.3   0.0      0.25     2e+02      40      69 ..    1012    1041 ..     981    1047 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.66
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  51 aefeewkqaaqklvdaLeeisealkqaa 78 
                                       +e+e ++++++++++ L e+s++l+q +
  gi|488600302|ref|YP_007906773.1| 173 EELEAVRENIERINTILIEVSNQLEQLK 200
                                       5677788888888888888888888865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  55 ewkqaaqklvdaLeeisealkqaa 78 
                                        ++ ++++l+++ +eis ++ + a
  gi|488600302|ref|YP_007906773.1| 258 DINSKLNELNTKADEISAEIYRLA 281
                                       677788888888888888776655 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   8 elrqaaarfqkqaeeledelqrlkae 33 
                                       ++++  ++f+ q+ +++++l++l+++
  gi|488600302|ref|YP_007906773.1| 336 KVEEELQKFSIQKMSVQEVLDDLESK 361
                                       56666678888888888888888775 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  20 aeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeis 71 
                                       + +l +el++l++++++                                 ++
  gi|488600302|ref|YP_007906773.1| 432 SITLNEELKELNKKYKE---------------------------------VE 450
                                       33333333333333333.................................33 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGC CS
                            WXG100  10 rqaaarfqkqaeeledelqrlkaevdalqsgW 41 
                                       r  ++++ +++++le el+++ka+++ l+s++
  gi|488600302|ref|YP_007906773.1| 471 RNQISSLEEEKKNLEVELSKIKAQLSLLESSF 502
                                       66778889999999999999999998887765 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  58 qaaqklvdaLeeisealkqaanafedaD 85 
                                        ++++++  L+e+s+++  a ++++d +
  gi|488600302|ref|YP_007906773.1| 711 SNVEEINSRLSELSSKISVAESKLRDNE 738
                                       567999999999**99999999999987 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  17 qkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafed 83 
                                        ++ e++ +e++++ +e+++++++ +G+   a    +ee+k+++++  +a+ +i+++l+++  ++++
  gi|488600302|ref|YP_007906773.1| 766 EEEIEKIDEEIRKISGEIEEIEAKMRGSEIPALTRKLEEIKEEIDRNSRAMYSITKNLENSEFKLQQ 832
                                       567789999*************************************************999876665 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.25
                                        GCTHHHCHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100   40 gWsGaaadafqaefeewkqaaqklvdaLee 69  
                                         ++   +d+f+++f+ ++ ++++++ +L+e
  gi|488600302|ref|YP_007906773.1| 1012 RYEKMKRDTFFETFNAINMHFKEIISKLAE 1041
                                        6777889*******************9998 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 ?    2.5   0.5      0.24   1.9e+02      18      57 ..     315     354 ..     311     371 .. 0.83
   2 ?    2.4   0.3      0.25   1.9e+02      28      58 ..     416     450 ..     392     492 .. 0.75
   3 ?    3.6   0.1      0.11        84      29      46 ..     775     792 ..     749     828 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.24
                              Img2  18 dvkrggtkkltvirkieGDiaalredLrkaleelvkvnev 57 
                                       d++ ++tk l+ i k + ++++++e+L+k+  ++++v+ev
  gi|488600302|ref|YP_007906773.1| 315 DIEDEKTKLLVSISKLKEEVSKVEEELQKFSIQKMSVQEV 354
                                       677789999999999999*********9998877777775 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.25
                              Img2  28 tvirkieGDiaalred...Lrkalee.lvkvnevt 58 
                                        +i  ieG+i+ lr++   L++ l+e   k +ev+
  gi|488600302|ref|YP_007906773.1| 416 MEIEDIEGEIETLRKEsitLNEELKElNKKYKEVE 450
                                       57999999999999973334555554323333333 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.11
                              Img2  29 virkieGDiaalredLrk 46 
                                       +irki+G+i++++ ++r 
  gi|488600302|ref|YP_007906773.1| 775 EIRKISGEIEEIEAKMRG 792
                                       8***********999874 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8  10.5       2.8   2.2e+03      74     172 ..     156     246 ..     149     256 .. 0.65
   2 ?    8.9  22.7    0.0015       1.1      14     152 ..     227     363 ..     214     366 .. 0.91
   3 ?    4.3   3.3     0.038        30      84     126 ..     367     409 ..     363     415 .. 0.90
   4 ?   10.6  12.6   0.00045      0.35      57     139 ..     417     499 ..     411     501 .. 0.95
   5 ?    8.6  10.4    0.0019       1.5      55     155 ..     710     810 ..     701     815 .. 0.94
   6 ?    7.9  19.3    0.0031       2.4      22     123 ..     806     909 ..     800     915 .. 0.91
   7 ?   -1.7  15.2       2.6     2e+03      10     112 ..     909    1015 ..     908    1020 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.8
                           DUF4201  74 ktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdkt 150
                                       +++  +++  ek     +el++ +++++++++ l ++  +l+++k++r+ + + ++ ++++  +l++ ++ k +   
  gi|488600302|ref|YP_007906773.1| 156 DDIAGISEFDEKKAKAIEELEAVRENIERINTILIEVSNQLEQLKADREEALRYKSLIEEKELNLKYLKINK-FLS- 230
                                       566667777788888888888888888888888888888888888888888777777777766666555544.333. PP

                           DUF4201 151 kekveekrksvkkLrrkvkile 172
                                             +  + ++++r +++le
  gi|488600302|ref|YP_007906773.1| 231 ------LNRRKRMIKRDIENLE 246
                                       ......3333334444444444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0015
                           DUF4201  14 klislkhqlakiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvh.althlkeklhml 89 
                                       k +sl ++ + i++ +e++e   +++ l++ + ++ + ++ln+k +e ++e+ rl + + kt++ ++ ++  k+  l
  gi|488600302|ref|YP_007906773.1| 227 KFLSLNRRKRMIKRDIENLEMRKDKI-LKEIIDINSKLNELNTKADEISAEIYRLADESYKTIQnEIIEISSKREGL 302
                                       56788889999999999999999998.57889999**********************99999984689********* PP

                           DUF4201  90 eselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktke 152
                                       +s  +++kke+k++e++++kl  +++k+k+e +k++++ +k++ q+  ++v ++l D + +k+
  gi|488600302|ref|YP_007906773.1| 303 KSSIEMKKKEIKDIEDEKTKLLVSISKLKEEVSKVEEELQKFSIQK--MSVQEVLDDLESKKS 363
                                       *****************************************99876..669999999998886 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.038
                           DUF4201  84 eklhmleselselkkelkekeerlaklrkelykvklerdklrk 126
                                        kl+ ++s +sel+++l +k+e l++l+++ ++  +erd+l +
  gi|488600302|ref|YP_007906773.1| 367 SKLNLMDSAYSELRDQLLKKKEILDELKERKSSKVNERDRLLE 409
                                       599****************************999999999866 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00045
                           DUF4201  57 kIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkq 133
                                       +Ie+ + e++ l+k + +   +l++l +k +++e+el+++ k+ +e ++++ ++r +++++++e+++l+ + +k+k+
  gi|488600302|ref|YP_007906773.1| 417 EIEDIEGEIETLRKESITLNEELKELNKKYKEVEKELEAAIKRRNEADNKIFSIRNQISSLEEEKKNLEVELSKIKA 493
                                       6888899999******************************************************************* PP

                           DUF4201 134 qggllr 139
                                       q+ ll+
  gi|488600302|ref|YP_007906773.1| 494 QLSLLE 499
                                       *99985 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0019
                           DUF4201  55 nkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                       + ++ee n  L++l++k+     +l ++ ++  +l+++l  ++ke  e+ er   +++e++k  +e  k+  + e++
  gi|488600302|ref|YP_007906773.1| 710 QSNVEEINSRLSELSSKISVAESKLRDNENRIEELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIEEI 786
                                       56899************************************************************************ PP

                           DUF4201 132 kqqggllrvPaLlkDYdktkekve 155
                                       +++    + PaL++  ++ ke+++
  gi|488600302|ref|YP_007906773.1| 787 EAKMRGSEIPALTRKLEEIKEEID 810
                                       **************9999999887 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0031
                           DUF4201  22 lakiqeklekkeelgegLtlidF..eqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselsel 96 
                                        ++i+++++ +  ++ +L  ++F  +ql+  + + + kI+e + ++++lkk + ++++  ++l e+l +l+++ +e 
  gi|488600302|ref|YP_007906773.1| 806 KEEIDRNSRAMYSITKNLENSEFklQQLKDLVLEKEIKIDELDRKIENLKKEIENDSQLYSELGERLITLKEKEKEV 882
                                       6678889999999*********9555888888888889*************************************** PP

                           DUF4201  97 kkelkekeerlaklrkelykvklerdk 123
                                        ++ k++ +++ kl +e+ k++++rd 
  gi|488600302|ref|YP_007906773.1| 883 GESVKDLRDKRSKLLAEIKKLEKDRDE 909
                                       *************************96 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 2.6
                           DUF4201   10 klrlklislkhqlakiqeklekkeelgegLtlidFeqlqienq....alnkkIeernkeLkrlkkkttktvhalt 80  
                                        + r + +  +++++  +e l+  ee   +L +i+++  + +n+    + + ++ee + eLk+  +   k ++  +
  gi|488600302|ref|YP_007906773.1|  909 EKRFEVTGIEETIKAKEESLKDIEEQIRELGEIEYDEEEVQNIprmeHVKRRLEEIELELKKFGDVNLKAIQDYE 983 
                                        567788888999999999999999999999999**999999862222566677777889**************** PP

                           DUF4201   81 hlkeklhmleselselkkelkekeerlaklrk 112 
                                        ++k +  +l+s+  +l+ke +e+ e++++++k
  gi|488600302|ref|YP_007906773.1|  984 EVKARKEELMSKKLTLEKERSEILEKIERYEK 1015
                                        ************99999999999999998876 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.8     0.061        47     138     180 ..     163     205 ..     155     211 .. 0.88
   2 ?    1.4   2.8      0.28   2.2e+02      31      81 ..     231     281 ..     211     297 .. 0.52
   3 ?    1.0  13.8      0.37   2.9e+02      18     140 ..     282     399 ..     273     406 .. 0.92
   4 ?    7.9   8.7    0.0028       2.2      41     111 ..     417     487 ..     402     516 .. 0.55
   5 ?   12.7  11.3    0.0001     0.078      26     129 ..     711     811 ..     693     840 .. 0.78
   6 ?    9.1  16.9    0.0012      0.95      14     134 ..     844     964 ..     841    1015 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.061
                         Laminin_I 138 dftkqleeaeaelkaAqkLLsrvqtllqklqeenkaLkealrd 180
                                       +f +++++a +el+a ++  +r++t l +  +++++Lk + ++
  gi|488600302|ref|YP_007906773.1| 163 EFDEKKAKAIEELEAVRENIERINTILIEVSNQLEQLKADREE 205
                                       5889999******************************887555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.28
                         Laminin_I  31 klskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertl 81 
                                           +++ k++ie+le    ++ +e+     k+++   ka ++ ae+ r  
  gi|488600302|ref|YP_007906773.1| 231 LNRRKRMIKRDIENLEMRKDKILKEIIDINSKLNELNTKADEISAEIYRLA 281
                                       444445555555555555554444444444444444444444444443332 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.37
                         Laminin_I  18 nanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkl 94 
                                        ++++  ++e+ e  sk++  ks ie+++ke+++++ e  +L     +  ++ +kv++e ++ + +  + +e   +l
  gi|488600302|ref|YP_007906773.1| 282 DESYKTIQNEIIEISSKREGLKSSIEMKKKEIKDIEDEKTKLLVSISKLKEEVSKVEEELQKFSIQKMSVQEVLDDL 358
                                       4679999********************************************************************** PP

                         Laminin_I  95 adnikeilekvatlneneealpssklseelaeaqrlLeelrsRdft 140
                                       + + + i++k      n ++ + s+l  +l + + +L el++R  +
  gi|488600302|ref|YP_007906773.1| 359 ESKKSLIISKL-----NLMDSAYSELRDQLLKKKEILDELKERKSS 399
                                       *********99.....78999*********************9755 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0028
                         Laminin_I  41 kieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlnen 111
                                       +ie  e+e+e+L +e  +L +++++  +k ++v++e e+++++ +e++ ki  ++++i+ + e  ++l+ +
  gi|488600302|ref|YP_007906773.1| 417 EIEDIEGEIETLRKESITLNEELKELNKKYKEVEKELEAAIKRRNEADNKIFSIRNQISSLEEEKKNLEVE 487
                                       44444555555555555555555555555555555555555555555555555555555555444444332 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.0001
                         Laminin_I  26 keLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeil 102
                                       ++ +e  s  s+ +ski+++e +l + ++ +eeL +k+t   ++  +++++++   +++++ +e+i+k+  +i+ei 
  gi|488600302|ref|YP_007906773.1| 711 SNVEEINSRLSELSSKISVAESKLRDNENRIEELKEKLTYKQKERAEIYERMSGVEEEIEKIDEEIRKISGEIEEIE 787
                                       5567777888999999************************************************************* PP

                         Laminin_I 103 ekvatlneneealpssklseelaeaqr 129
                                       +k+   +     +  +kl+e  +e++r
  gi|488600302|ref|YP_007906773.1| 788 AKMRGSEI---PALTRKLEEIKEEIDR 811
                                       **943322...2234455555555554 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.0012
                         Laminin_I  14 pykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaek 90 
                                       + ++  ++e+l+ke+++  + +s+ ++++  l+++ +++ + ++ L  k  + la+ +k++++ ++   + +  +e 
  gi|488600302|ref|YP_007906773.1| 844 IDELDRKIENLKKEIENDSQLYSELGERLITLKEKEKEVGESVKDLRDKRSKLLAEIKKLEKDRDEKRFEVTGIEET 920
                                       5688999********************99999999****************************************** PP

                         Laminin_I  91 ikkladnikeilekvatlne.neealpssklseelaeaqrlLeel 134
                                       ik+ ++++k i e++ +l+e + ++  ++++ ++ + ++r Lee+
  gi|488600302|ref|YP_007906773.1| 921 IKAKEESLKDIEEQIRELGEiEYDEEEVQNIPRM-EHVKRRLEEI 964
                                       *********************8888888888877.4566667777 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   5.5      0.38     3e+02     195     240 ..     169     214 ..     150     227 .. 0.68
   2 ?    7.9  16.8    0.0016       1.2     144     252 ..     231     343 ..     223     350 .. 0.73
   3 ?    9.5  16.7   0.00053      0.41     143     258 ..     350     461 ..     345     464 .. 0.75
   4 ?   11.8  13.7    0.0001     0.079     163     261 ..     419     513 ..     412     520 .. 0.75
   5 ?    8.0  22.5    0.0014       1.1     149     281 ..     672     808 ..     663     816 .. 0.86
   6 ?    9.3  19.2   0.00059      0.46     157     261 ..     801     911 ..     797     920 .. 0.75
   7 ?   -2.2  15.3       1.9   1.5e+03     159     258 ..     922    1018 ..     913    1035 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.38
                              Spc7 195 sidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelk 240
                                       +   eeLe++re+++++++ + e +++l++l++++ee     + ++
  gi|488600302|ref|YP_007906773.1| 169 AKAIEELEAVRENIERINTILIEVSNQLEQLKADREEALRYKSLIE 214
                                       3345677777777777777777777777777777777655555544 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqe....aaeeles....idkeeLeelreelaelk 212
                                       l+++   +++d e+Le +++++ +   +++++ +el+ +++++ +     a    +      ++e+ e+ ++ + lk
  gi|488600302|ref|YP_007906773.1| 231 LNRRKRMIKRDIENLEMRKDKILKEIIDINSKLNELNTKADEISAeiyrLA----DesykTIQNEIIEISSKREGLK 303
                                       455555566666666666666666666666666666666666666333222....2443255999999999999999 PP

                              Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiae 252
                                       + ie kkke+++ ++++++l  +i++lke+ s++eee+++
  gi|488600302|ref|YP_007906773.1| 304 SSIEMKKKEIKDIEDEKTKLLVSISKLKEEVSKVEEELQK 343
                                       99********************************999986 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00053
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekk 219
                                       +++e l++le+ k+l+ ++ +++d+++ el+ +  + +e l++l+e++ +      +e   l e ++++  eie  +
  gi|488600302|ref|YP_007906773.1| 350 SVQEVLDDLESKKSLIISKLNLMDSAYSELRDQLLKKKEILDELKERKSSKV----NERDRLLEVIRRIGMEIEDIE 422
                                       68999999**********************9999999999999999665533....333344445666777777777 PP

                              Spc7 220 kelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                        e+++l+++  +l+e+++el+++++e+e+e+++a + ++
  gi|488600302|ref|YP_007906773.1| 423 GEIETLRKESITLNEELKELNKKYKEVEKELEAAIKRRN 461
                                       888888888888888888888888888888877766655 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.0001
                              Spc7 163 eeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                                       e ++   + l++e  +l+eel++l+++++e+e+    eLe++ ++ +e++++i + ++++++l+e++++le +++++
  gi|488600302|ref|YP_007906773.1| 419 EDIEGEIETLRKESITLNEELKELNKKYKEVEK----ELEAAIKRRNEADNKIFSIRNQISSLEEEKKNLEVELSKI 491
                                       455556677888888888888888888888654....8888888888888888888888888888888888888888 PP

                              Spc7 240 keqkseleeeiaeaervleeck 261
                                       k+q s le+  ++a +++ e k
  gi|488600302|ref|YP_007906773.1| 492 KAQLSLLESSFSKAVELILEAK 513
                                       8888888888877766655554 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0014
                              Spc7 149 egleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..id.keeLeelreelaelkaeieekkkel 222
                                       ++l e +++Le++   +++ + e+  +   +eee +  q+ +ee++s  ++ + ++  + ++l+++++ iee+k++l
  gi|488600302|ref|YP_007906773.1| 672 KELFEKEKKLEEEITVIESRKAEMLGNLRLVEEERRIHQSNVEEINSrlSElSSKISVAESKLRDNENRIEELKEKL 748
                                       56667788999999999999999999999999999999999999998875568999999999999999999999999 PP

                              Spc7 223 aelqeqleeleekieelkeqkseleeeiaeae.rvleeckgwsesevsrlkeevkaleel 281
                                       + +q++++e+ e+++ ++e+++++ eei++   ++ e + +++ se+ +l+ ++++++e+
  gi|488600302|ref|YP_007906773.1| 749 TYKQKERAEIYERMSGVEEEIEKIDEEIRKISgEIEEIEAKMRGSEIPALTRKLEEIKEE 808
                                       999999999999999999999999999999761556667899999999999999999887 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.00059
                              Spc7 157 lLekqeeeldellpeleeekaeleeeleklqe.....aaeelesid.keeLeelreelaelkaeieekkkelaelqe 227
                                       +Le+ +ee+d+   ++ +  ++le+   klq+      ++e++  +   ++e+l++e+++ ++ ++e+ ++l +l+e
  gi|488600302|ref|YP_007906773.1| 801 KLEEIKEEIDRNSRAMYSITKNLENSEFKLQQlkdlvLEKEIKIDElDRKIENLKKEIENDSQLYSELGERLITLKE 877
                                       45555566655555555555555554444444333543333333335679*************************** PP

                              Spc7 228 qleeleekieelkeqkseleeeiaeaervleeck 261
                                       + +e+ e++++l++++s+l +ei++ e+ ++e++
  gi|488600302|ref|YP_007906773.1| 878 KEKEVGESVKDLRDKRSKLLAEIKKLEKDRDEKR 911
                                       ******************************9987 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 1.9
                              Spc7  159 ekqeeeldellpeleeekaeleeeleklqe...aaeeles...id..keeLeelreelaelkaeieekkkelael 225 
                                        +++ee l+++ +++           ++l e    +ee+++   ++  k +Lee+  el++      +  ++++e+
  gi|488600302|ref|YP_007906773.1|  922 KAKEESLKDIEEQI-----------RELGEieyDEEEVQNiprMEhvKRRLEEIELELKKFGDVNLKAIQDYEEV 985 
                                        22222222222222...........22222322333333311122235667777777777777777777888999 PP

                              Spc7  226 qeqleeleekieelkeqkseleeeiaeaervle 258 
                                        ++++eel +k  +l++++se+ e+i++ e++++
  gi|488600302|ref|YP_007906773.1|  986 KARKEELMSKKLTLEKERSEILEKIERYEKMKR 1018
                                        999999999999999999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2639  (0.147192); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                       229  (0.0127726); expected 17.9 (0.001)
Passed Fwd filter:                       147  (0.00819901); 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: 3.68u 0.40s 00:00:04.08 Elapsed: 00:00:00.92
# Mc/sec: 3822.40
//
Query:       gi|488600303|ref|YP_007906774.1|  [L=241]
Description: condensin subunit ScpA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-18   66.2   6.3      1e-17   64.8   6.3    1.6  1  SMC_ScpA    Segregation and condensation protein ScpA
      0.001   18.3   0.0      0.002   17.4   0.0    1.4  1  Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
  ------ inclusion threshold ------
      0.028   14.1   1.7        0.1   12.2   1.5    2.0  2  FAM176      FAM176 family


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 !   64.8   6.3   1.8e-21     1e-17       1     238 [.      16     237 ..      16     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.8e-21
                                       HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXX...XXXXXXXXXXX CS
                          SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqvee...eedeeleleel 74 
                                       ++ ++e+d+++++v++v  +fl+ ++   +kl+l +s+  l+ a+ lv++Ka+ L +   +     ee+ e e+  +
  gi|488600303|ref|YP_007906774.1|  16 MAKRGEIDPWNIDVIDVASKFLEKLEKA-QKLDLRISGRVLLYAAILVRMKAEILANEALMTRggaEEEVE-EESYI 90 
                                       67899***********************.************************998865443311022222.46678 PP

                                       XXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SMC_ScpA  75 rdkL.iarLleYrkykeeaklfkeleaerlksfskarsdleefikeveevavkieksvfklieafnkllkrakival 150
                                       +d++ ++  +    ++e+   +  ++++     +k+  ++ +f  ++++   ++e     +     k+++++ +v+ 
  gi|488600303|ref|YP_007906774.1|  91 PDEIdFDTFP--FDFDEKPSERPDKKETENYDLPKR-RTVRRF-TTLDDLIKELEMA---ERVERRKRVRKK-VVRE 159
                                       9988688888..456665555555555555555666.566666.4566666666655...334445666555.3333 PP

                                       XXXXX...HHHHHHHHHHHH.................HHHTS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-E CS
                          SMC_ScpA 151 aekqiseleisieeqleellaqleqfl..qarlkevLldlrswvdlseLladnkledkkelvgvFlAlLeLiknqav 225
                                        e     l++++ee+ ee l ++e  l    r       ++  + +seL+ +   +++ke+v+ Fl +L L   +++
  gi|488600303|ref|YP_007906774.1| 160 VE---DPLKVPHEENIEETLIRIEAELlkYFR-------IKDAILFSELVGM---KERKEKVTYFLSILHLAYRKII 223
                                       34...4699*********99766643311222.......356799*******...9********************* PP

                                       EEEESSTTS.-EEE CS
                          SMC_ScpA 226 aleQeefld.dLqv 238
                                       +l Qe  ++ d+ +
  gi|488600303|ref|YP_007906774.1| 224 ELRQERIFEeDIEI 237
                                       *****976515665 PP

>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.3e-07     0.002       7      49 ..     194     237 ..     190     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-07
                                       T----------HHHHHHHHHHHHHHHHTSEEEEESSTT-.-EEE CS
                        Rad21_Rec8   7 slsllpagktRkeAArlFyelLvLatkgvIkvkQeaPYg.dIli 49 
                                        +s+l   k Rke +  F ++L La +++I++ Qe++++ dI i
  gi|488600303|ref|YP_007906774.1| 194 LFSELVGMKERKEKVTYFLSILHLAYRKIIELRQERIFEeDIEI 237
                                       568888899*****************************724555 PP

>> FAM176  FAM176 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.2   1.2e+03     107     119 ..      37      49 ..      25      51 .. 0.84
   2 ?   12.2   1.5   1.8e-05       0.1      78     126 ..     105     156 ..      52     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.2
                            FAM176 107 aeelerAqRlEeR 119
                                        e+le+Aq+l+ R
  gi|488600303|ref|YP_007906774.1|  37 LEKLEKAQKLDLR 49 
                                       599******9877 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.8e-05
                            FAM176  78 eeeedsseseaeeelsefertlsvnvftsa....eelerAqRlEeReriirEI 126
                                       e+ ++  +++++e+ +  +r  +v  ft       ele+A+R+E+R r+ + +
  gi|488600303|ref|YP_007906774.1| 105 EKPSERPDKKETENYDLPKRR-TVRRFTTLddliKELEMAERVERRKRVRKKV 156
                                       222223333333333333333.46666665333489**********9986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1303.41
//
Query:       gi|488600304|ref|YP_007906775.1|  [L=180]
Description: segregation and condensation protein B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-37  126.3   0.4      1e-36  126.0   0.4    1.1  1  SMC_ScpB        Segregation and condensation complex subunit 
    4.8e-06   26.5   0.0    0.00011   22.2   0.0    2.3  2  HTH_20          Helix-turn-helix domain
    3.1e-05   23.8   1.3     0.0022   17.9   0.1    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00064   19.6   0.3         15    5.6   0.1    4.0  4  MarR            MarR family
  ------ inclusion threshold ------
      0.014   15.8   0.2        3.2    8.2   0.0    3.1  3  Rrf2            Transcriptional regulator
      0.029   14.3   0.0       0.11   12.5   0.1    1.9  2  Cdc6_C          CDC6, C terminal winged helix domain
      0.061   12.9   0.1        3.5    7.2   0.0    2.0  2  E3_UFM1_ligase  E3 UFM1-protein ligase 1
      0.073   12.6   0.5       0.39   10.3   0.1    2.4  3  HTH_24          Winged helix-turn-helix DNA-binding
        0.4   10.7   1.8        6.1    6.9   0.1    3.1  4  HTH_Crp_2       Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.4   5.1e-40     1e-36       2     154 ..      12     156 ..      11     160 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 5.1e-40
                          SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkk 78 
                                       i+EAiLf+++ep+s +++a+i+ +++e ve++l +L  ey+ +d+ +e++e++g y +++kp++  +v ++ ++   
  gi|488600304|ref|YP_007906775.1|  12 IVEAILFSSSEPISPSKIARIVRVKTEIVEKVLRDLVHEYNIRDSSIEIIELKGSYLMRVKPNYTRFVDRFSEK--- 85 
                                       8*************************************************************************... PP

                          SMC_ScpB  79 trLsqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglksl 154
                                        +L++ + +tL +Ia++qp+  +e+++iRG +++++v++L e g+ie ++    +gr+ + +tT++F +y+gl++ 
  gi|488600304|ref|YP_007906775.1|  86 -DLDRGTRRTLVVIAIRQPIKLSELAKIRGNRCYEHVKKLEEIGFIETRK----EGRSKIITTTKYFAKYYGLEKS 156
                                       .*************************************************....9******************985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.11   2.1e+02      10      36 ..       8      35 ..       6      48 .. 0.81
   2 !   22.2   0.0   5.3e-08   0.00011      27      61 .]     106     137 ..      86     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                                      HHHHHHHHHH.STCTTB-HHHHHHHHTS CS
                            HTH_20 10 PvRrrilraL.araegltaselaerldl 36
                                      +vR  +++ L ++ e+ ++s +a+ +++
  gi|488600304|ref|YP_007906775.1|  8 EVRKIVEAILfSSSEPISPSKIARIVRV 35
                                      5666677777999**********98864 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 5.3e-08
                                       HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  27 aselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       +sela    ++ n ++ H+++Lee g++e+++egr
  gi|488600304|ref|YP_007906775.1| 106 LSELA---KIRGNRCYEHVKKLEEIGFIETRKEGR 137
                                       44444...499999*******************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 ?    4.8   0.1     0.013        26      18      47 ..      17      48 ..       5      59 .. 0.87
   2 !   17.9   0.1   1.1e-06    0.0022      27      63 ..     105     147 ..      95     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.013
                                      H..HHCCCHHCHHCCCTTSSCHCHHHHHHHHH CS
                              TrmB 18 l..klgpatadeiaeelgvprskvYevLrsLe 47
                                      l  +++p + ++ia+++ v    v +vLr L+
  gi|488600304|ref|YP_007906775.1| 17 LfsSSEPISPSKIARIVRVKTEIVEKVLRDLV 48
                                      4457889999********************98 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.1e-06
                                       HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEE CS
                              TrmB  27 eiaeelgvprskvYevLrsLedkGlVerekgr......pklYr 63 
                                       +++e +++  +++Ye +++Le+ G++e++k+       +++Y 
  gi|488600304|ref|YP_007906775.1| 105 KLSELAKIRGNRCYEHVKKLEEIGFIETRKEGrskiitTTKYF 147
                                       589999***********************97766676655665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0093        19      14      43 ..      20      49 ..      17      50 .. 0.90
   2 ?    1.4   0.0      0.16   3.2e+02      25      45 ..      66      86 ..      57      87 .. 0.82
   3 ?    1.8   0.0      0.12   2.4e+02       8      25 ..      94     111 ..      91     114 .. 0.88
   4 !    5.6   0.1    0.0076        15      37      51 ..     120     134 ..     118     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0093
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLek 43
                                      +++p+s s++a+ + v++  v +vl+ L++
  gi|488600304|ref|YP_007906775.1| 20 SSEPISPSKIARIVRVKTEIVEKVLRDLVH 49
                                      5799********************999975 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                                      HHHTS-HHHHHHHHHHHHHTT CS
                              MarR 25 kklgvskstvtrvldrLekkG 45
                                      + l+  k++ tr++dr  +k+
  gi|488600304|ref|YP_007906775.1| 66 SYLMRVKPNYTRFVDRFSEKD 86
                                      567788999*******98886 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.12
                                       HHHHHHHSTTEEHHHHHH CS
                              MarR   8 iLrilyeqgplsvseLak 25 
                                       +L+ ++ ++p+++seLak
  gi|488600304|ref|YP_007906775.1|  94 TLVVIAIRQPIKLSELAK 111
                                       688899999********8 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0076
                                       HHHHHHHTTSEEEEE CS
                              MarR  37 vldrLekkGlieRsk 51 
                                        +++Le+ G+ie +k
  gi|488600304|ref|YP_007906775.1| 120 HVKKLEEIGFIETRK 134
                                       69*********9665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0016       3.2      21      52 ..      19      50 ..       4      55 .. 0.87
   2 ?    1.7   0.0      0.16   3.3e+02      31      59 ..     106     134 ..      93     139 .. 0.81
   3 ?    2.0   0.0      0.13   2.6e+02      37      53 ..     156     172 ..     136     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrka 52
                                      +++ep+s ++ia+ + ++ +++ek+l+ L ++
  gi|488600304|ref|YP_007906775.1| 19 SSSEPISPSKIARIVRVKTEIVEKVLRDLVHE 50
                                      56778999********************9875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.16
                                       HHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2  31 iaerqnispsylekilakLrkaglvksvr 59 
                                       ++e  +i  + +   ++kL++ g++++++
  gi|488600304|ref|YP_007906775.1| 106 LSELAKIRGNRCYEHVKKLEEIGFIETRK 134
                                       66667788888889999999999999975 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.13
                                       S-HHHHHHHHHHHHHTT CS
                              Rrf2  37 ispsylekilakLrkag 53 
                                         p+y++  +++L+k+g
  gi|488600304|ref|YP_007906775.1| 156 SDPEYVREFFSELQKKG 172
                                       5799***********99 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.4e-05      0.11      37      66 ..     112     139 ..     105     148 .. 0.80
   2 ?   -1.7   0.0       1.4   2.9e+03      27      53 ..     146     172 ..     138     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-05
                                       --HHHHHHHHHHHHHTTSEEEEEEE-CC.C CS
                            Cdc6_C  37 ltqrevsdllseLemlgileleksskGrre 66 
                                       +  +++++++++Le  g++e++k+  Gr++
  gi|488600304|ref|YP_007906775.1| 112 IRGNRCYEHVKKLEEIGFIETRKE--GRSK 139
                                       56689*****************88..6654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                                       HHHHHTT-----HHHHHHHHHHHHHTT CS
                            Cdc6_C  27 slCesegvdpltqrevsdllseLemlg 53 
                                         ++ +g+++ + + v++  seL ++g
  gi|488600304|ref|YP_007906775.1| 146 YFAKYYGLEKSDPEYVREFFSELQKKG 172
                                       567888888888888888888888776 PP

>> E3_UFM1_ligase  E3 UFM1-protein ligase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0017       3.5     176     223 ..       8      55 ..       3      68 .. 0.88
   2 ?    3.9   0.0     0.018        35     185     251 ..      97     167 ..      90     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                    E3_UFM1_ligase 176 rqkakvrGalsaitkptllssllkkveleekllqslleeLikekeikG 223
                                       +++++v ++l +  +p++ s++++ v+++ ++++++l +L++e +i+ 
  gi|488600304|ref|YP_007906775.1|   8 EVRKIVEAILFSSSEPISPSKIARIVRVKTEIVEKVLRDLVHEYNIRD 55 
                                       56778899999999****************************999875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.018
                    E3_UFM1_ligase 185 lsaitkptllssllkkveleekllqslleeLikekeikGslkagre......lyiPtiy..skaqeewvesfykq 251
                                       + ai +p++ls+l+k   +  +  ++ +++L + + i+ + k+gr+       y+ ++y  +k+  e+v++f+++
  gi|488600304|ref|YP_007906775.1|  97 VIAIRQPIKLSELAK---IRGNRCYEHVKKLEEIGFIETR-KEGRSkiitttKYFAKYYglEKSDPEYVREFFSE 167
                                       679999999999988...6899999999999998888888.5555557777789999994446666899999875 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       1.1   2.1e+03      29      39 ..      24      34 ..      23      37 .. 0.73
   2 ?   10.3   0.1   0.00019      0.39      29      48 .]     112     131 ..     104     131 .. 0.80
   3 ?   -2.6   0.0       2.1   4.1e+03      11      19 ..     167     175 ..     165     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                            HTH_24 29 lSpstvnrrlk 39
                                      +Sps + r ++
  gi|488600304|ref|YP_007906775.1| 24 ISPSKIARIVR 34
                                      67777777765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                            HTH_24  29 lSpstvnrrlkrLeeeGlIk 48 
                                       +  + + +++k+Lee G+I+
  gi|488600304|ref|YP_007906775.1| 112 IRGNRCYEHVKKLEEIGFIE 131
                                       5567899***********97 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
                            HTH_24  11 lLqknpris 19 
                                       +Lqk++++s
  gi|488600304|ref|YP_007906775.1| 167 ELQKKGKLS 175
                                       678887765 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 ?    6.9   0.1    0.0031       6.1      21      61 ..      23      62 ..       6      65 .. 0.87
   2 ?   -1.8   0.0       1.6   3.3e+03      40      65 ..      77     106 ..      74     109 .. 0.59
   3 ?    0.4   0.1      0.32   6.3e+02      42      56 ..     121     137 ..     105     150 .. 0.72
   4 ?   -0.0   0.0      0.44   8.8e+02      35      52 ..     158     175 ..     143     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0031
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES- CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririld 61
                                      p++   +A+++ +  e v ++l++L  e  i+ +  i+i  
  gi|488600304|ref|YP_007906775.1| 23 PISPSKIARIVRVKTEIVEKVLRDLVHEYNIRDSS-IEIIE 62
                                      788899********************999999776.88765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                       HHHHHHHHTTSEE.ETEE...EEES-HHHH CS
                         HTH_Crp_2  40 rilseLkreglis.rgrr...irildleaL 65 
                                       r   +++++ l + ++r+   i i+++ +L
  gi|488600304|ref|YP_007906775.1|  77 RFVDRFSEKDLDRgTRRTlvvIAIRQPIKL 106
                                       666677777777754554544555555555 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.32
                                       HHHHHHTTSEE.E.TEE CS
                         HTH_Crp_2  42 lseLkreglis.r.grr 56 
                                        ++L++ g i+ r ++r
  gi|488600304|ref|YP_007906775.1| 121 VKKLEEIGFIEtRkEGR 137
                                       68999999999642223 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  35 retvsrilseLkreglis 52 
                                       +e v   +seL+++g +s
  gi|488600304|ref|YP_007906775.1| 158 PEYVREFFSELQKKGKLS 175
                                       78889999*****99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1143.60
//
Query:       gi|488600305|ref|YP_007906776.1|  [L=229]
Description: competence/damage-inducible protein cinA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  116.3   0.1    1.1e-33  115.9   0.1    1.1  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
       0.03   14.5   0.0      0.064   13.4   0.0    1.5  1  SOUL           SOUL heme-binding protein
      0.032   13.8   0.1      0.048   13.2   0.0    1.6  2  AA_kinase      Amino acid kinase family
      0.099   12.7   0.1        0.6   10.1   0.1    2.3  2  DUF218         DUF218 domain
       0.17   12.3   0.5          1    9.7   0.5    2.6  1  Radical_SAM    Radical SAM superfamily


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 !  115.9   0.1   3.1e-37   1.1e-33       2     139 ..       5     156 ..       4     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 3.1e-37
                                       EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHH CS
                     MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpeal 78 
                                       +i+vG+ellsg++ ++n+ ++a++l ++g++v+++ v+pDd +ei+e++++a e+ad++++tGG+G+t+dDvt e +
  gi|488600305|ref|YP_007906776.1|   5 IISVGNELLSGDTANSNSVYMAKKLVQMGHRVKRIIVIPDDVDEIAEEVRKASEKADFVLVTGGLGATHDDVTAEGI 81 
                                       8************************************************9998999********************* PP

                                       HHHHSEE-HHHHHHHHHHHHHHCC...................TTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHH CS
                     MoCF_biosynth  79 aklfekelegfeeafrrvslkpgk...................pvgvapgailsravgktiigLPGspkavkealee 136
                                       ak+f+ el+ +e + +r+++++++                   + g ap++i +     ++ ++PG+p ++++++ +
  gi|488600305|ref|YP_007906776.1|  82 AKAFNVELVVDEKTANRLRRFSRNeeairkvasvpkgseiipnDRGAAPAFIFR-----NVAVMPGVPAEMEDTFNK 153
                                       *********************999999*******99999999999999999996.....59**************** PP

                                       HHH CS
                     MoCF_biosynth 137 ill 139
                                       i++
  gi|488600305|ref|YP_007906776.1| 154 IIK 156
                                       994 PP

>> SOUL  SOUL heme-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.064      97     135 ..     189     226 ..     178     229 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                              SOUL  97 srVkleevpertvavrrFsGfateeevkeeaeeLreaLe 135
                                       ++V++ + p+  ++v++FsG+ ++ +v+e++++L e L+
  gi|488600305|ref|YP_007906776.1| 189 KDVSIGSYPKPGYVVIKFSGR-NKGRVEEAKKRLEELLK 226
                                       5899999*************9.999***********994 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.048      17      74 ..      45      96 ..       3     172 .. 0.81
   2 ?   -3.4   0.0       1.7   5.9e+03       3      10 ..     202     209 ..     201     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                      CHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHH CS
                         AA_kinase 17 easlrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeag 74
                                      +  ++++ae+++++ +++ + v+V+Gg + t+  +++  g+ + ++ + l ++++  +
  gi|488600305|ref|YP_007906776.1| 45 D--VDEIAEEVRKA-SEKADFVLVTGGLGATHDDVTA-EGIAKAFNVE-LVVDEKT-A 96
                                      4..899********.888888******6666666666.5999999983.3333332.2 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.7
                                       EEEEE-TT CS
                         AA_kinase   3 vVvKlGGs 10 
                                       vV+K+ G 
  gi|488600305|ref|YP_007906776.1| 202 VVIKFSGR 209
                                       79999986 PP

>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00017       0.6      30      89 ..      12      66 ..       3     111 .. 0.82
   2 ?   -0.9   0.0      0.43   1.5e+03      36      57 ..     124     145 ..      69     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                            DUF218 30 ivsGggadedvseaeamaeylrelgvp.eeailledrsrnTeenarfskellkersillVT 89
                                      ++sG   d+  s++ +ma+ l+++g   ++ i++ d     +e++r ++e ++   ++lVT
  gi|488600305|ref|YP_007906776.1| 12 LLSG---DTANSNSVYMAKKLVQMGHRvKRIIVIPDDVDEIAEEVRKASEKAD---FVLVT 66
                                      3444...568999**********998855356669999999999999999774...88888 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.43
                            DUF218  36 adedvseaeamaeylrelgvpe 57 
                                       +d++   a +++++++  gvp+
  gi|488600305|ref|YP_007906776.1| 124 NDRGAAPAFIFRNVAVMPGVPA 145
                                       3445566666777777777773 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5   0.00029         1      30      66 ..      45      79 ..      32     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                                      HHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 30 sveeileevkelkaekgvkevilgggepllypdfvel 66
                                      +v+ei+eev++++ ek +++v+++gg    ++d + +
  gi|488600305|ref|YP_007906776.1| 45 DVDEIAEEVRKAS-EK-ADFVLVTGGLGATHDDVTAE 79
                                      7999999999996.66.99*****9988888665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); 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: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1309.62
//
Query:       gi|488600306|ref|YP_007906777.1|  [L=221]
Description: 2,5-diamino-6-(5-phosphoribosylamino)pyrimidin-4(3H)-one reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-53  181.1   0.0    2.4e-53  181.0   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 !  181.0   0.0   1.3e-57   2.4e-53       1     198 [.       3     212 ..       3     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 1.3e-57
                                       -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS CS
                            RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearq 76 
                                       p+v +++a S+DGk++++++++ +i++ e+ ++v++lra +dai+vG+gtvl d+psltv+    r ++ + ++ ++
  gi|488600306|ref|YP_007906777.1|   3 PFVFVNIASSIDGKISDESRKQVRISCREDFQRVDRLRAFSDAIMVGIGTVLSDDPSLTVKDERLRYERvQAGKDEN 79 
                                       89***************************************************************9888777777** PP

                                       -EEEEEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC........E.....SE-HHHHHHHHHHTT--EEEE CS
                            RibD_C  77 pvrvVvdstlrvpldakvltddaptlvatteeadkekveklk........v.....rvdlkelleeLkergirsllv 140
                                       p+rvVvds+lr+pl+ak+l+d a+t+vatte+     +e++k        v     +vdl  l e L++ g+r+l+v
  gi|488600306|ref|YP_007906777.1|  80 PIRVVVDSRLRIPLNAKILDDRARTIVATTEK----GLERVKlieeraevVvfgreKVDLRLLCEYLYKIGVRRLMV 152
                                       ********************99*******994....55555554477775279999********************* PP

                                       EETHHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS.EEEEEEEEEEETTEE CS
                            RibD_C 141 eGGatLagsllraglvDelrlyiaPkllGg.agktlfdgegfka.lklklvksealgegv 198
                                       eGG+tL++sllr++++De+ +y+  +++Gg + +t++dge f   ++l+l ++++lgeg+
  gi|488600306|ref|YP_007906777.1| 153 EGGGTLINSLLREKMIDEFNIYYGNMIIGGrNSPTVVDGESFADpVRLELISCQKLGEGI 212
                                       ******************************************99**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1434.25
//
Query:       gi|488600307|ref|YP_007906778.1|  [L=289]
Description: 4-hydroxybenzoate polyprenyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  164.0  14.7    4.4e-48  163.8  14.7    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.05   13.3   1.9       0.37   10.5   0.0    3.2  3  DUF3188   Protein of unknown function (DUF3188)


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 !  163.8  14.7   4.9e-52   4.4e-48       1     251 [.      19     271 ..      19     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 4.9e-52
                              UbiA   1 llipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivll 77 
                                       +l++a+ g++laa g++  ++++l+l +++ ++++a+ +N+++DreiDa+++rt  R+l++G is+kea+i+a++ l
  gi|488600307|ref|YP_007906778.1|  19 ALPFAYTGAFLAADGWFGYRIFFLILTAFTGLRVFAMSINRIIDREIDALNPRTSSRHLPKGIISVKEAYIIAFLGL 95 
                                       578999*********************************************************************** PP

                              UbiA  78 ilgllllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl.....sllallla 149
                                       i+ +l + +l+n ++++l+ +  + ++vY+  +lKr+t l ++v+g+  + +p +gw+avt s+      + +++l+
  gi|488600307|ref|YP_007906778.1|  96 IVYFLSA-YLINRTAFMLSPIPAITAWVYP--YLKRYTCLSHFVLGLNLAYAPGGGWVAVTDSInifgsEFIPFMLG 169
                                       *******.**********************..*************************************99999999 PP

                              UbiA 150 lavflltwaialandlrdregDrkagiktlpvvlGrkaaril...lalllavlllallllllalllllylllallla 223
                                       + +++++++++++++l+d+e Drk+g++++ + +G  +a+i+   ++  ++++++  + +ll+++      ++l+ +
  gi|488600307|ref|YP_007906778.1| 170 IGIMFWVAGFDIIYALQDVEFDRKYGLHSIGAHFGSGVAKIVsaiSH--ILFFSI-SAYTLLFHVERKVIPYGLAGI 243
                                       99***************************************964333..333333.367999999999********* PP

                              UbiA 224 alallraarlvrrrdakkaakfflflss 251
                                       a++l+++++++r + ++k+ ++++f+s+
  gi|488600307|ref|YP_007906778.1| 244 AMLLIFEHYIIREKYDEKKIQLAFFYSN 271
                                       **********************988875 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.2e-05      0.37      24      45 ..      17      38 ..      13      39 .. 0.92
   2 ?   -0.3   0.2     0.097   8.7e+02      29      46 ..      90     107 ..      87     108 .. 0.76
   3 ?   -2.5   0.1      0.49   4.3e+03      31      37 ..     240     246 ..     236     252 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.2e-05
                           DUF3188 24 lqslPallvGlgLivsgavgrg 45
                                      l++lP + +G++L   g++g++
  gi|488600307|ref|YP_007906778.1| 17 LFALPFAYTGAFLAADGWFGYR 38
                                      89******************98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.097
                           DUF3188  29 allvGlgLivsgavgrgr 46 
                                       +++ Gl + +++a++++r
  gi|488600307|ref|YP_007906778.1|  90 IAFLGLIVYFLSAYLINR 107
                                       677888888888888776 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.49
                           DUF3188  31 lvGlgLi 37 
                                       l+G++ +
  gi|488600307|ref|YP_007906778.1| 240 LAGIAML 246
                                       4444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1729.82
//
Query:       gi|488600308|ref|YP_007906779.1|  [L=81]
Description: hypothetical protein Asulf_00773 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.8   0.3      0.044   13.2   0.0    2.1  2  zf-ribbon_3      zinc-ribbon domain
     0.0032   17.4   0.4      0.013   15.4   0.4    2.0  1  zinc_ribbon_4    zinc-ribbon domain
     0.0069   16.4   0.1     0.0092   16.0   0.1    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
      0.014   15.5   0.2      0.034   14.3   0.2    1.7  1  Zn-ribbon_8      Zinc ribbon domain
      0.041   14.0   0.1      0.041   14.0   0.1    2.5  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.051   13.6   0.9        6.2    6.9   0.1    2.0  2  CpXC             CpXC protein
      0.052   13.2   0.2      0.075   12.7   0.2    1.3  1  TackOD1          Thaumarchaeal output domain 1
       0.06   13.1   0.5       0.17   11.7   0.5    1.7  1  zinc_ribbon_2    zinc-ribbon domain
      0.095   13.1   0.6       0.12   12.7   0.6    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.15   11.5   1.7        1.2    8.6   1.7    2.0  1  Mu-like_Com      Mu-like prophage protein Com
       0.22   11.3   1.7        1.6    8.6   0.2    2.1  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        2.4    7.7   9.8       0.18   11.3   2.9    2.6  2  TF_Zn_Ribbon     TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0     3e-05     0.044       3      12 ..       6      15 ..       4      20 .. 0.68
   2 ?    3.0   0.0      0.05        74       2       9 ..      25      32 ..      24      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                       zf-ribbon_3  3 vrCPnCGapl 12
                                      ++CP+CG++l
  gi|488600308|ref|YP_007906779.1|  6 IKCPSCGEVL 15
                                      6788888755 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.05
                       zf-ribbon_3  2 tvrCPnCG 9 
                                      +++C+ CG
  gi|488600308|ref|YP_007906779.1| 25 EIQCSLCG 32
                                      78999999 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   8.9e-06     0.013       3      32 ..       6      32 ..       5      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.9e-06
                     zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCg 32
                                      i CpsC+ + e++d     +g++++Cs Cg
  gi|488600308|ref|YP_007906779.1|  6 IKCPSCGEVLELSD---MYEGMEIQCSLCG 32
                                      89************...5999********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 !   16.0   0.1   6.1e-06    0.0092      70     108 ..       5      45 ..       1      49 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.1e-06
                                       EEEETTTS-EEECHH..H..HHS-TTTSSS-EEEEESSSEEEE CS
                              HypA  70 kvrCreCgkefelee..k..alrCpkCgsadveivsGeellvk 108
                                       +++C +Cg+  el++  +  +++C  Cg +   iv+G+ellv 
  gi|488600308|ref|YP_007906779.1|   5 VIKCPSCGEVLELSDmyEgmEIQCSLCGLS--MIVKGDELLVL 45 
                                       689*********7765425677******96..599****9985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   2.3e-05     0.034       7      34 ..       7      33 ..       1      38 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs 34
                                      +C +Cg++ e l  + +  +++C  Cg 
  gi|488600308|ref|YP_007906779.1|  7 KCPSCGEVLE-LSDMYEGMEIQCSLCGL 33
                                      8*****8888.66699999999****95 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 ?   14.0   0.1   2.7e-05     0.041       2      11 ..       6      15 ..       6      19 .. 0.94
   2 ?   -0.8   0.1       1.1   1.7e+03       2       8 ..      26      32 ..      26      36 .. 0.81
   3 ?   -1.7   0.7       2.1   3.1e+03      12      21 ..      66      75 ..      64      75 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                            zf-ACC  2 tKCpsCgeml 11
                                      +KCpsCge+l
  gi|488600308|ref|YP_007906779.1|  6 IKCPSCGEVL 15
                                      8*******97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                            zf-ACC  2 tKCpsCg 8 
                                      ++C  Cg
  gi|488600308|ref|YP_007906779.1| 26 IQCSLCG 32
                                      6898887 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.1
                            zf-ACC 12 ykkeLernly 21
                                      + +e+e+ +y
  gi|488600308|ref|YP_007906779.1| 66 FEEEFEEEYY 75
                                      4678888776 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0079        12      37      49 ..       5      17 ..       2      22 .. 0.73
   2 ?    6.9   0.1    0.0041       6.2      37      84 ..      25      72 ..      20      80 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0079
                              CpXC 37 eatCpkCgatakl 49
                                       ++Cp+Cg+  +l
  gi|488600308|ref|YP_007906779.1|  5 VIKCPSCGEVLEL 17
                                      5778888877655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0041
                              CpXC 37 eatCpkCgataklea.pllyhdpekellillvpeserseeeeieeaeek 84
                                      e++C  Cg +  ++  +ll+ d ++ + i  +  +e++eee  ee++e+
  gi|488600308|ref|YP_007906779.1| 25 EIQCSLCGLSMIVKGdELLVLDTNEVYSIESLAFEEEEEEE-FEEEFEE 72
                                      79*******99998625778887777777766666665555.3333333 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2     5e-05     0.075     102     137 ..       4      39 ..       2      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                           TackOD1 102 elihhftCgnvgpeeeflkegkleCpkCktkLrhiG 137
                                       ++i++ +Cg+v + ++  ++ +++C+ C  ++   G
  gi|488600308|ref|YP_007906779.1|   4 KVIKCPSCGEVLELSDMYEGMEIQCSLCGLSMIVKG 39 
                                       689*************************88776555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   0.00011      0.17       1      20 [.       7      32 ..       7      33 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                     zinc_ribbon_2  1 fCpnCGaelqdnakF......CpyCG 20
                                      +Cp+CG+ l+  + +      C+ CG
  gi|488600308|ref|YP_007906779.1|  7 KCPSCGEVLELSDMYegmeiqCSLCG 32
                                      8******9998888877777777777 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   8.2e-05      0.12       3      37 ..       5      37 ..       3      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-05
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga...s 37
                                      +  CP Cg+  +l  ++ +       ++C  Cg    +
  gi|488600308|ref|YP_007906779.1|  5 VIKCPSCGEVLELSDMYEGM-----EIQCSLCGLsmiV 37
                                      568**********9999999.....6***99**94440 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 ?    8.6   1.7    0.0008       1.2       5      31 ..       6      32 ..       3      44 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0008
                       Mu-like_Com  5 lRCGeCaRLLaKaeAlDeltiKCPRCG 31
                                      ++C  C  +L  ++ ++ ++i+C  CG
  gi|488600308|ref|YP_007906779.1|  6 IKCPSCGEVLELSDMYEGMEIQCSLCG 32
                                      566667777777777777777777776 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0011       1.6       2      11 ..       6      15 ..       5      19 .. 0.83
   2 ?    2.2   0.1      0.11   1.6e+02       2      14 ..      26      38 ..      25      40 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                                      EE-SSS--EE CS
                    zf-C4_Topoisom  2 ekCPkCggdL 11
                                      +kCP+Cg+ L
  gi|488600308|ref|YP_007906779.1|  6 IKCPSCGEVL 15
                                      79*****866 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                                      EE-SSS--EEEEE CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlk 14
                                      ++C  Cg  +++k
  gi|488600308|ref|YP_007906779.1| 26 IQCSLCGLSMIVK 38
                                      58*****766665 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   2.9   0.00012      0.18       2      27 ..       7      33 ..       6      35 .. 0.82
   2 ?   -2.0   0.6       1.7   2.6e+03      38      38 ..      70      70 ..      59      80 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                      EETTTTCEECHEE.TSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD.pergelvCtdCGl 27
                                      kCP Cg    + D +e  e+ C+ CGl
  gi|488600308|ref|YP_007906779.1|  7 KCPSCGEVLELSDmYEGMEIQCSLCGL 33
                                      899999987566679999999999997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                      C CS
                      TF_Zn_Ribbon 38 p 38
                                       
  gi|488600308|ref|YP_007906779.1| 70 F 70
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 520.31
//
Query:       gi|488600309|ref|YP_007906780.1|  [L=130]
Description: secondary thiamine-phosphate synthase enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-40  137.5   0.0    2.3e-40  137.4   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 !  137.4   0.0   1.3e-44   2.3e-40       1     115 []      14     127 ..      14     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 1.3e-44
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssl 76 
                                       dit++v+e v++sg++eG+++++++htt++++inE  ++++ +D+e++l+klvp++  Y h+   ++nadaHl+++l
  gi|488600309|ref|YP_007906780.1|  14 DITSRVAEEVERSGIREGIAVIYTKHTTTGIVINEG-ESGLLKDIENMLSKLVPQNqGYIHD-RIDNNADAHLRAVL 88 
                                       8**********************************9.******************99*****.5567********** PP

                                       H-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEEE CS
                           UPF0047  77 lgssltipvedgklalGtwqsiylveldgpreRkvvvqv 115
                                       lg+s ++pv+dg+l+lGtwqsi+++eldgpr+R+vvv+v
  gi|488600309|ref|YP_007906780.1|  89 LGNSAVVPVSDGRLELGTWQSILFIELDGPRNRSVVVKV 127
                                       ************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 919.28
//
Query:       gi|488600310|ref|YP_007906781.1|  [L=166]
Description: hypothetical protein Asulf_00776 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   60.6   0.0      2e-16   59.9   0.0    1.3  1  MGS              MGS-like domain
    4.7e-13   49.2   0.0    7.3e-13   48.6   0.0    1.2  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
  ------ inclusion threshold ------
      0.041   13.5   0.0          1    9.0   0.0    2.3  2  STAS             STAS domain
       0.12   12.4   0.1        2.1    8.4   0.1    2.3  1  Lipin_N          lipin, N-terminal conserved region


Domain annotation for each model (and alignments):
>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   4.5e-20     2e-16       2      82 ..      13     101 ..      12     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 4.5e-20
                                       HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH...HHHHHHHTTSCCEEEEE--THHHHH CS
                               MGS   2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrv...eildaikngeidlvintlypfkatv 75 
                                       ++e+a kl+e+g+e++AT+GTa +l+  g+ v+ ++e tg  e ++ +     + +ai +geid+v++ lypf+ ++
  gi|488600310|ref|YP_007906781.1|  13 VAEFAAKLEEMGVEIIATEGTASYLESRGVRVKHLSEMTGLRETPELKTlypAVYEAIFSGEIDMVVVDLYPFEDMP 89 
                                       579*******************************************6669*************************99 PP

                                       H.....CHHHHH CS
                               MGS  76 a.....kdgyki 82 
                                               g+++
  gi|488600310|ref|YP_007906781.1|  90 CvenidVGGVSL 101
                                       755544445555 PP

>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   1.6e-16   7.3e-13       1      57 [.     105     160 ..     105     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.6e-16
                                       HHHTTTT-EEE-SGGGHHHHHHHHHCT.B-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   AICARFT_IMPCHas   1 AAKNhksVtvvvdpadYeevleelkkgevsletrkklaakaFahtaaYDaaiaeyls 57 
                                       A+KN+++V+ ++ p++Yeev+e+l +g v++e+r kla +aF++ a+YD aia+++ 
  gi|488600310|ref|YP_007906781.1| 105 ASKNYRQVMAISTPEQYEEVVENLVNG-VTEEFRLKLACEAFERIARYDMAIARWFC 160
                                       89**********************987.9**************************95 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.026   1.1e+02      77     117 .]      29      69 ..      17      69 .. 0.88
   2 ?    9.0   0.0   0.00023         1      54      78 ..      87     111 ..      86     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.026
                                       HHTT-EEEEES--HHHHHHHHHTTCGGCC..SEEESSHHHH CS
                              STAS  77 krigvevvlvnikpevreklektgffdeveeeklfltvhdA 117
                                        + g   +l +   +v++  e+tg+ +  e ++l++ v +A
  gi|488600310|ref|YP_007906781.1|  29 ATEGTASYLESRGVRVKHLSEMTGLRETPELKTLYPAVYEA 69 
                                       46788899999999*************99999999999887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00023
                                       EEEEEEEE-HHHHHHHHHHHHHHHH CS
                              STAS  54 dlsavsfiDssGvraLkeilkelkr 78 
                                       d+  v++iD+ Gv+ L+ + k++++
  gi|488600310|ref|YP_007906781.1|  87 DMPCVENIDVGGVSLLRAASKNYRQ 111
                                       8889*******************95 PP

>> Lipin_N  lipin, N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00046       2.1      10      33 ..      58      81 ..      50     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00046
                           Lipin_N 10 svkelykeinpatlsGaiDvivve 33
                                      ++k+ly  +  a +sG iD++vv+
  gi|488600310|ref|YP_007906781.1| 58 ELKTLYPAVYEAIFSGEIDMVVVD 81
                                      57889999999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1131.80
//
Query:       gi|488600311|ref|YP_007906782.1|  [L=395]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-49  165.6   0.2    1.2e-48  165.1   0.2    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    9.2e-37  126.2   0.2      3e-36  124.5   0.1    1.9  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.9e-29  101.7   0.1    3.5e-29  100.9   0.1    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    2.1e-20   73.4   0.0    3.4e-20   72.7   0.0    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
     0.0069   16.1   0.0      0.013   15.2   0.0    1.4  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina
  ------ inclusion threshold ------
       0.15   11.9   0.1       0.36   10.7   0.0    1.7  2  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.1   0.2     4e-52   1.2e-48       1     149 [.     231     379 ..     231     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 4e-52
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       g+Gf++am  +n +R+ va +a+g+a+ a+e a ey+++r+ fg++l d+ql ++k+a+m++e+eaarll+ +aa +
  gi|488600311|ref|YP_007906782.1| 231 GNGFAQAMMFFNTTRIPVAFQAVGIAQGAFELAFEYSKNREIFGRKLKDFQLTQDKFARMRTEIEAARLLAVQAAMQ 307
                                       68*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +d+g pd+  ++maK+++ ++a++v+d+a+q++Gg+Gy  eyp++r+yr+a++++++eGt e+ +++iar+l
  gi|488600311|ref|YP_007906782.1| 308 ADTGMPDPGLTAMAKYYCGKTAVKVCDEALQIFGGYGYIGEYPISRYYRHAKITELYEGTKEVEKEVIARSL 379
                                       **********************************************************************86 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.1     1e-39     3e-36       1     112 [.       8     117 ..       8     118 .. 0.96
   2 ?   -1.6   0.0       1.4   4.3e+03      39      77 ..     210     249 ..     189     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 1e-39
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       teeq+++++++refae+e+ap+a+e+d ++efp++++kk+ +lG++g+ +pe+ygG+gl++l+a++v+ee+ r+dag
  gi|488600311|ref|YP_007906782.1|   8 TEEQKDIKEAAREFAEKEIAPVAEEYDLKEEFPWDVYKKAVKLGFIGMGIPEKYGGQGLKMLDACLVVEEFFRVDAG 84 
                                       89*************************999*********************************************** PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasg 112
                                       ++++l   s+ +++++l fGteeqk++yLp+l++g
  gi|488600311|ref|YP_007906782.1|  85 IGMIL--ASTFGSEMLLYFGTEEQKQKYLPPLCEG 117
                                       87644..6789999*******************99 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                       HHHHTTCTSTTS-.GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N  39 klaelGllgitvp.eeygGagldyleaaivaeelaradag 77 
                                         ael + ++ vp e   G++++ +++a+++   +r  ++
  gi|488600311|ref|YP_007906782.1| 210 DTAELNFKNVRVPaENLVGQEGNGFAQAMMFFNTTRIPVA 249
                                       5689999999999656668877777777777777765544 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.1   1.2e-32   3.5e-29       2      97 .]     123     219 ..     122     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.2e-32
                                       EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS---..----EEEEEEE..GGGEEE CS
                     Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpd..rarglslflvprdapgvsv 75 
                                        a+TEp+aGsdva++k   ae+dg+e+vlnG+K++itn++ia++++vlar    ++  r++g+s+f+v++d++g++ 
  gi|488600311|ref|YP_007906782.1| 123 AAFTEPGAGSDVAGIKL-KAEKDGDEWVLNGTKTFITNGTIADWFVVLARtD-PNAkkRHEGMSVFIVEADSEGLER 197
                                       689*************9.67888888************************52.333477****************** PP

                                       -----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  76 rrieeklGlrglptgelvfedv 97 
                                       ++i++klG+r+ +t+el f++v
  gi|488600311|ref|YP_007906782.1| 198 TKIKNKLGIRSSDTAELNFKNV 219
                                       ********************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.0   1.1e-23   3.4e-20       3     133 ..     248     368 ..     246     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 1.1e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHH CS
                     Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtved 79 
                                       +a +a+G+A++a++ + e+ ++r    +g+kl+d++ tq + a+++++++AAr+l  +aa +    a++g +    d
  gi|488600311|ref|YP_007906782.1| 248 VAFQAVGIAQGAFELAFEYSKNREI--FGRKLKDFQLTQDKFARMRTEIEAARLLAVQAAMQ----ADTGMP----D 314
                                       7899*********************..***********************************....999999....6 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  80 raearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                           ++a+ +  ++a++++d++ +++Gg+++  e+p+ R++R a++++ +++++
  gi|488600311|ref|YP_007906782.1| 315 PGLTAMAKYYCGKTAVKVCDEALQIFGGYGYIGEYPISRYYRHAKITELYEGTK 368
                                       778889******************************************999875 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.3e-06     0.013     180     227 ..     149     196 ..     135     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.3e-06
                                       EEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEE CS
                            HpaB_N 180 vVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlk 227
                                       v +G+k ++T++ +ad+++vl    + +++  +   +f+v++d++Gl+
  gi|488600311|ref|YP_007906782.1| 149 VLNGTKTFITNGTIADWFVVLARTDPNAKKRHEGMSVFIVEADSEGLE 196
                                       889********************99999999999************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 ?   -4.0   0.0         4   1.2e+04      74      85 ..      84      95 ..      82     109 .. 0.60
   2 ?   10.7   0.0   0.00012      0.36      29      83 ..     179     240 ..     155     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4
                       HATPase_c_3 74 GiGlklAslslg 85
                                      GiG+ lAs   +
  gi|488600311|ref|YP_007906782.1| 84 GIGMILASTFGS 95
                                      888888876443 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                       HATPase_c_3  29 nrgktgeivieDdGkGmseeelknalrlatsskeakr.......kstslGkkGiGlklAsls 83 
                                       +++  + + +e d++G+++ ++kn+l + +s++ + +        ++ +G+ G G   A++ 
  gi|488600311|ref|YP_007906782.1| 179 RHEGMSVFIVEADSEGLERTKIKNKLGIRSSDTAELNfknvrvpAENLVGQEGNGFAQAMMF 240
                                       3344578999**********************9977544444546888*******5555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2793.96
//
Query:       gi|488600312|ref|YP_007906783.1|  [L=112]
Description: Putative sterol carrier protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-18   66.3   0.0    3.1e-18   66.1   0.0    1.1  1  SCP2      SCP-2 sterol transfer family
  ------ inclusion threshold ------
      0.052   13.6   0.0        8.5    6.5   0.0    2.2  2  DUF3895   Protein of unknown function (DUF3895)


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   3.5e-22   3.1e-18       4     101 .]      14     108 ..       4     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 3.5e-22
                                       HHHHHHHHHHHHHHCCH-EEEEEEECTC.TEEEEEET.TSTEEESSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHHH CS
                              SCP2   4 llerlkdpekkealkklagvlrfdltdlkgsltldlk.egqldvaakdegkadvtlslsledllelaegklnpqkaf 79 
                                       l ++  ++e k+++k ++gv++fd+ ++  ++++ ++ +g  + +++ + ++ +t+++s+e ++++++g+++p + f
  gi|488600312|ref|YP_007906783.1|  14 LGNQ--SDEIKNEMKGWGGVVQFDIDGE--KFYIKYNdDGTAEFVEGEANSPNFTVIASDEYWVKVMKGEEDPIMGF 86 
                                       3444..669*******************..79****94456666877779*************************** PP

                                       HTTSSEEEC-HHHHHHHHHHHH CS
                              SCP2  80 mqgkLkieGDielaqkleallk 101
                                       m+gk ki+G+i+  qkl++++k
  gi|488600312|ref|YP_007906783.1|  87 MTGKYKIQGNIMESQKLAGVMK 108
                                       *******************996 PP

>> DUF3895  Protein of unknown function (DUF3895)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0021        19      19      37 ..       3      21 ..       1      34 [. 0.84
   2 ?    6.5   0.0   0.00095       8.5      32      49 ..      80      97 ..      57     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0021
                           DUF3895 19 sAkelaeyLvrkgkasnes 37
                                      +Akel ++Lv+ g+ s+e 
  gi|488600312|ref|YP_007906783.1|  3 EAKELVKKLVELGNQSDEI 21
                                      69**************995 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00095
                           DUF3895 32 kasnesfstgryKiYgdv 49
                                      + +   f tg+yKi g++
  gi|488600312|ref|YP_007906783.1| 80 EDPIMGFMTGKYKIQGNI 97
                                      4555679*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 730.15
//
Query:       gi|488600313|ref|YP_007906784.1|  [L=89]
Description: nucleoid protein Alba [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   75.7   0.5    2.3e-21   75.4   0.5    1.1  1  Alba      Alba
    0.00065   19.7   0.1     0.0008   19.4   0.1    1.2  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 !   75.4   0.5   2.6e-25   2.3e-21       2      66 ..       5      66 ..       4      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.6e-25
                                      EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                              Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                      +++V++ +p+m+yv+++++++ n++ + Vv+ka+GraIs+Av+vaei+++rf+++ ++v++++++
  gi|488600313|ref|YP_007906784.1|  5 VVFVGN-KPVMNYVLATITQF-NEGVDKVVIKARGRAISRAVDVAEIVRNRFLPN-VKVEDIQIG 66
                                      799999.**************.******************************988.****99976 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 !   19.4   0.1     9e-08    0.0008      58      91 ..      25      60 ..      17      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9e-08
                             Rpp20 58 elkkeeVfvkatGrAiekalsvgrwfqeke..eykv 91
                                      ++  ++V++ka GrAi +a+ v++  +++   ++kv
  gi|488600313|ref|YP_007906784.1| 25 NEGVDKVVIKARGRAISRAVDVAEIVRNRFlpNVKV 60
                                      66789******************9987765344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 614.84
//
Query:       gi|488600314|ref|YP_007906785.1|  [L=173]
Description: hypothetical protein Asulf_00781 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1093.85
//
Query:       gi|488600315|ref|YP_007906786.1|  [L=144]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-46  157.9   0.0    1.4e-46  157.8   0.0    1.0  1  DUF371    Domain of unknown function (DUF371)


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.0   7.8e-51   1.4e-46       1     132 [.      10     143 ..      10     144 .] 0.93

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 7.8e-51
                                       EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS..-EEEEEEE CS
                            DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevge..ledeitgr 75 
                                       i arGHen++a+h++Tle+tkd+el+ rgdCI+gv+adk++++ls+ lke lke   ++++tle+ +  l++e+ g 
  gi|488600315|ref|YP_007906786.1|  10 IVARGHENIRATHRTTLEVTKDRELSLRGDCIVGVDADKSISELSSGLKERLKEGL-KCKITLELPDygLKEELFGF 85 
                                       689**************************************************986.6666666655449******* PP

                                       --TT-----SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHT.T-EEEEEEEE CS
                            DUF371  76 GspkltlenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkk.gaeltvelev 132
                                       Gs+klt+++++d+vvRkS++v++rTllvka+kaa+dl+re+v++L+  ++e+ + +e+
  gi|488600315|ref|YP_007906786.1|  86 GSEKLTFDHPTDIVVRKSSFVCGRTLLVKANKAARDLSREFVSHLRYpETEIFFIIEI 143
                                       **********************************************989999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1048.42
//
Query:       gi|488600316|ref|YP_007906787.1|  [L=125]
Description: hypothetical protein Asulf_00783 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   73.4   0.8    1.9e-20   73.2   0.8    1.1  1  DUF1284       Protein of unknown function (DUF1284)
  ------ inclusion threshold ------
      0.052   13.1   0.1       0.06   12.9   0.1    1.2  1  Peptidase_C8  Peptidase family C8


Domain annotation for each model (and alignments):
>> DUF1284  Protein of unknown function (DUF1284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.8   2.2e-24   1.9e-20       1     102 []      18     116 ..      18     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 2.2e-24
                           DUF1284   1 GYseeFvenmeeiveklkkeeeekielvegaDdiCsacpn.kkelC.eeeekvkelDrkvlealgleegeelkleel 75 
                                       GY+eeFv+n+++ +e+++k   ++ie+v gaDd+C acpn ++++C + ee+++elD  ++++l++++g+++ ++e+
  gi|488600316|ref|YP_007906787.1|  18 GYTEEFVDNLKSFLENVRK---QEIEIVVGADDVCIACPNlEDGICnKGEEDIMELDLLAMNLLKVKPGDRVGWAEV 91 
                                       9*************88855...45****************669***7779*************************** PP

                           DUF1284  76 lekvkekileekklkeiCgeCeWkelc 102
                                        +k++e +  + + + +C +Ce++++c
  gi|488600316|ref|YP_007906787.1|  92 ESKLDEIL--KIWKRYACFDCEYSHVC 116
                                       *****988..5667***********99 PP

>> Peptidase_C8  Peptidase family C8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.7e-06      0.06     112     155 ..       6      51 ..       3      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-06
                      Peptidase_C8 112 hsdqcvhivagetfrn..ydeikavlevilenepdilvgaeegsva 155
                                       h   c+h   ge + +   d++k+ le + ++e +i+vga++  +a
  gi|488600316|ref|YP_007906787.1|   6 HHLICLHFFKGEGYTEefVDNLKSFLENVRKQEIEIVVGADDVCIA 51 
                                       5667*******98865337**********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 958.62
//
Query:       gi|488600317|ref|YP_007906788.1|  [L=194]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  137.0  20.4      8e-40  136.7  20.4    1.0  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
  ------ inclusion threshold ------
        4.1    7.7   6.3       0.73   10.2   1.4    2.1  2  DUF1440          Protein of unknown function (DUF1440)


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 !  136.7  20.4     9e-44     8e-40      16     193 ..      15     185 ..       5     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 9e-44
                   Gpr1_Fun34_YaaH  16 kfaNPaPlgllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsy 92 
                                       + aNPaPlgl++f++tt +l+++n+g   + +  +++++ +fyGGl+q++aGi+e+   ntFgata++sYG Fwl++
  gi|488600317|ref|YP_007906788.1|  15 STANPAPLGLMGFGMTTVLLNIHNAGIYKLGA--MILAMGIFYGGLAQIIAGIMEWRKNNTFGATAFTSYGLFWLTL 89 
                                       68********************9999988876..9****************************************97 PP

                   Gpr1_Fun34_YaaH  93 .aailipgfgilaaYeedeeelnnalglyllgwfiftfllllatlrstvalfllfffldltflllaigeltgsakvl 168
                                         +il+p++g ++  e      n a+  y+ +w +ft +l++atlr + al ++f++l++ f++laig+ tgs+ ++
  gi|488600317|ref|YP_007906788.1|  90 vTLILMPSMGLTSPPE------NIAMVAYFSMWGLFTAVLFIATLRINRALQFVFLTLTILFFMLAIGDATGSTFIK 160
                                       257889*****99884......778889************************************************* PP

                   Gpr1_Fun34_YaaH 169 kAggvfgiiaaflawYnalaglatk 193
                                       + +g+ gi++++ a Y+ala+++++
  gi|488600317|ref|YP_007906788.1| 161 QLAGFEGIVCGLSAIYAALAQVLNE 185
                                       *********************9975 PP

>> DUF1440  Protein of unknown function (DUF1440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.4   8.1e-05      0.73      87     132 ..      80     127 ..      46     130 .. 0.72
   2 ?   -0.9   0.2      0.21   1.9e+03      63      96 ..     144     177 ..     131     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.1e-05
                           DUF1440  87 alfGllvtiavHlivlPllglvpalkelpleehvs..Eilghivwlws 132
                                       + +Gl+  ++v li++P +gl+ +++++ +   +s   +++ ++++++
  gi|488600317|ref|YP_007906788.1|  80 TSYGLFWLTLVTLILMPSMGLTSPPENIAMVAYFSmwGLFTAVLFIAT 127
                                       46899999*******************999888773345666666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.21
                           DUF1440  63 fsivfavlYvvvaevfpkiklwqGalfGllvtia 96 
                                       + +++a+  +  + ++++++  +G++ Gl+++ a
  gi|488600317|ref|YP_007906788.1| 144 LFFMLAIGDATGSTFIKQLAGFEGIVCGLSAIYA 177
                                       3456677777778888888889999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1143.08
//
Query:       gi|488600318|ref|YP_007906789.1|  [L=659]
Description: acetyl-coenzyme A synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  334.0   0.0    1.3e-99  333.7   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      1e-32  112.9   1.2      2e-32  112.0   1.2    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    1.5e-12   47.2   2.9    3.9e-12   45.9   2.9    1.8  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.7   0.0  2.1e-103   1.3e-99       2     422 ..      98     531 ..      97     532 .. 0.90

  Alignments for each domain:
  == domain 1  score: 333.7 bits;  conditional E-value: 2.1e-103
                                       HHHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEE CS
                       AMP-binding   2 eeqaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvv 75 
                                       ++qa+ +++k a+++    g+ ++lTY++l+++vnr+A++L+ lG++kgdrV i+lp+ pe+ +a+la++k+Ga+++
  gi|488600318|ref|YP_007906789.1|  98 DKQAKLRKNKLAYIWegePGDIRKLTYHDLYREVNRFANALKDLGIRKGDRVTIWLPMIPELPIAMLACAKIGAIHS 174
                                       7899999**********9999******************************************************** PP

                                       EEETTS-HHHHHHHHHHHTESEEE......E..TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCC CS
                       AMP-binding  76 plnptltaeelayiledseakvli......a..tvdsel.leklleaaakleavklvivldadellkeeelkeeees 143
                                       ++ +++++++l   ++d+eak+li      +  +   ++  ++++++ ++  + + viv+d+ +++   ++  +  +
  gi|488600318|ref|YP_007906789.1| 175 VVFSGFSEKALLDRIQDAEAKLLItadgfyRggK--VIElKSRADQILDQ-TTIENVIVYDRTNINPPMKEGRDHWW 248
                                       ************************9988763432..45545666666664.689999*******9999888888888 PP

                                       SCTT.S-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHH CS
                       AMP-binding 144 eeka.ekpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifgli 218
                                       +++   +++e+e  +++d+++i+YTSGTTGkPKGV++ h +++v ++++l+    f++kedd +++ +++ +i+g++
  gi|488600318|ref|YP_007906789.1| 249 QDVLgSRKCETEIMDANDTLFILYTSGTTGKPKGVIHAHgGYAVGTASTLH--FIFDIKEDDIWWCSADIGWITGHS 323
                                       877653788999***************************556666666653..3388899***************** PP

                                       HHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS- CS
                       AMP-binding 219 lelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggep 294
                                       + ++++l+ Gat v++++ ++ ++p++++e ie+++vtv++++P++++++++ g+++   +++dls lrl+ ++gep
  gi|488600318|ref|YP_007906789.1| 324 YIVYAPLILGATSVMYEGAPThPTPARWWEIIERYGVTVFYTAPTAIRMFMRLGEKY--PQNHDLSTLRLLGTVGEP 398
                                       *********************788****************************77776..4578************** PP

                                       EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEE CS
                       AMP-binding 295 lspellrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGell 368
                                       ++pe++ ++++  g+   ++++++++TEt++ ++  pl+    k+gs+ kp+pg+++ + D+e++ + +++  G l+
  gi|488600318|ref|YP_007906789.1| 399 INPEAWVWYYKYIGNeqcQIMDTWWQTETGMQMI-SPLPITPLKPGSATKPFPGIDADVFDPEGNSLHGRNAGGYLV 474
                                       **************9******************8.6667777799******************7777778888**** PP

                                       EEET..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 369 vrgp..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                       +++p   + +g ++ +e+   +++s  ++ + TGD +r+d +Gy++i gR++d++++
  gi|488600318|ref|YP_007906789.1| 475 IKKPwpAMLRGLWRAEERYINTYWSAyPNIYFTGDAARVDSEGYFWIQGRLDDVLNV 531
                                       ****667*****************84657*************************987 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   1.2   3.3e-36     2e-32       1      76 []     540     618 ..     540     618 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 3.3e-36
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsalvshpaV+eaaVvG+p+evkGea+vafVvlk+g  + e+l ++Lk+hv+ke+g++a+p++++fv++lpktrs
  gi|488600318|ref|YP_007906789.1| 540 EVESALVSHPAVSEAAVVGKPHEVKGEAIVAFVVLKSGiePsEQLIDDLKQHVAKEIGKIARPDEIYFVPDLPKTRS 616
                                       8***********************************99753355********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|488600318|ref|YP_007906789.1| 617 GK 618
                                       *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 !   45.9   2.9   6.5e-16   3.9e-12       6      53 ..      47      94 ..      42      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 6.5e-16
                                      HHHHH-HHHHHHHHHCC..S--SB--S-SECSTTTCT-EESTT-EE-HHH CS
                            ACAS_N  6 keSiedpeaFWaeqake..ldWekpfdkvldgskgpfikWFeGGklNicy 53
                                      ++  ++ e+FW+e+a+e  ++W++p+++vl++ ++p++kWF ++k Ni +
  gi|488600318|ref|YP_007906789.1| 47 RK-AQNIEWFWSEMAREvsIEWYEPYTQVLEW-NPPYAKWFINAKYNIVH 94
                                      44.4899*********999*************.9*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 4103.69
//
Query:       gi|488600319|ref|YP_007906790.1|  [L=203]
Description: hypothetical protein Asulf_00786 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   32.4   0.6    1.1e-07   31.5   0.6    1.5  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.11   12.4   0.2       0.24   11.4   0.2    1.5  1  DUF4250   Domain of unknown function (DUF4250)


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 !   31.5   0.6   1.3e-11   1.1e-07       1      38 [.      30      67 ..      30      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.3e-11
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                      r+si++d+e+ e+Ld l+++ ++S+SelIR+++ + +e
  gi|488600319|ref|YP_007906790.1| 30 RLSISIDSETREKLDILCKKKEKSKSELIRDLIDFGYE 67
                                      89*******************************98776 PP

>> DUF4250  Domain of unknown function (DUF4250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.7e-05      0.24      21      47 ..      41      67 ..      38      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                           DUF4250 21 ssldelcedldidkeeleekLasigYe 47
                                      + ld lc++ + +k+el+  L + gYe
  gi|488600319|ref|YP_007906790.1| 41 EKLDILCKKKEKSKSELIRDLIDFGYE 67
                                      689***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1277.17
//
Query:       gi|488600320|ref|YP_007906791.1|  [L=317]
Description: Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase-related deacylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   67.7   0.5    3.7e-18   66.0   0.5    1.8  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.6e-16   59.5   0.0    5.9e-16   58.3   0.0    1.6  1  M20_dimer      Peptidase dimerisation domain
     0.0005   19.8   0.2     0.0009   19.0   0.2    1.4  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.5   6.1e-22   3.7e-18       2     204 ..      54     313 ..      53     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 6.1e-22
                                       EEEES-BSSTTCGGGSSSTTSEEETTT.EEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwttpfslteedG.klyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgG 77 
                                       +  HlD+V        +++f  +   G + yG G++d k++++a+l+a+++          +  l+f++dEE g++G
  gi|488600320|ref|YP_007906791.1|  54 VSTHLDTVR------VKREFDFD---GvYAYGTGVCDAKASIAAMLKAAES---------VDYCLAFFCDEEEGGKG 112
                                       678******......22234444...6589******************977.........36689*******777** PP

                                       HHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                     Peptidase_M20  78 akallegleerekvdavfelhieepgileagklaigvv....................................... 115
                                       +k++++      ++d+ + ++i+ep+ ++    +   +                                       
  gi|488600320|ref|YP_007906791.1| 113 SKSFAK------DWDGGM-AVIMEPTSMHIASTH---Ygsidlvveiygrkshasipeagenaiekafelmielkkn 179
                                       ******......444444.346778888833333...2555888889999999999999999999999999999999 PP

                                       ..................................................EEEEEEEEEESHEEEC...CHHHHHHH CS
                                       ..................................................xxxxxxxxxxxxxxxx...xxxxxxxx RF
                     Peptidase_M20 116 ..................................................kvevelleggapvtln...dsplvkal 139
                                                                                         +v ve+         +   +++++ +l
  gi|488600320|ref|YP_007906791.1| 180 ftisplkiegggdeyiipdlcrikfdvllspesdvnssieviksiagkygNVIVEDAI-------DgfySGEVATIL 249
                                       9999*******************************99777766665544434444222.......244479****** PP

                                       HHHHHHHHTSCEEEEEESSSBHTHHHHTTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 140 aeaaeelfgekvelivsgpggtdarffagiptvmifgpgs.glaHspnEyvdledlekgikvlarl 204
                                       ++a+++  g +v+ + ++  +tda  +++   v++ gpg+ + +H++ E+v+led+ek+++vl+rl
  gi|488600320|ref|YP_007906791.1| 250 ERAISDC-GFEVRHTFMP-SWTDALNLKRKADVVVWGPGDlKYCHTEREKVKLEDIEKAVRVLVRL 313
                                       ******7.*999999888.9*******66668889****99**********************997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   9.9e-20   5.9e-16       3     103 ..     139     227 ..     137     231 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 9.9e-20
                                       B-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEE CS
                         M20_dimer   3 hkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeak 79 
                                       h G+++  +++ g++ H++ p+ag+NAiek+ +l+ el+++             t+++  iegG    +ipd ++ k
  gi|488600320|ref|YP_007906791.1| 139 HYGSIDLVVEIYGRKSHASIPEAGENAIEKAFELMIELKKN------------FTISPLKIEGGGDEYIIPDLCRIK 203
                                       89***************************************............************************ PP

                                       EEEEHHHHHHHHHHHHHHHHHHTS CS
                         M20_dimer  80 idiRllpgedpeevleeieeilek 103
                                       +d+ l+p++d+ + +e i++i++k
  gi|488600320|ref|YP_007906791.1| 204 FDVLLSPESDVNSSIEVIKSIAGK 227
                                       *******************99987 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   1.5e-07    0.0009      12      86 ..      49     120 ..      42     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-07
                                       SEEEEEEEE--B-TTT.....TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHH CS
                     Peptidase_M28  12 devlllgAHyDsvgvg.....rgp..ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkaf 81 
                                       d  +l++ H+D+v v+     +g      G+ D  +++aa+L+ a+ +            ++ff  EE+g  GSk f
  gi|488600320|ref|YP_007906791.1|  49 DSNFLVSTHLDTVRVKrefdfDGVyaYGTGVCDAKASIAAMLKAAESVDY---------CLAFFCDEEEGGKGSKSF 116
                                       67899**********86665522233344666666666666666666665.........89**************** PP

                                       HHHHC CS
                     Peptidase_M28  82 akakp 86 
                                       a +++
  gi|488600320|ref|YP_007906791.1| 117 A-KDW 120
                                       *.665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1847.03
//
Query:       gi|488600321|ref|YP_007906792.1|  [L=158]
Description: Acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-21   77.3   0.7    1.2e-21   77.1   0.7    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.3e-12   47.2   0.1    3.6e-12   46.5   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.6e-12   46.3   0.0    4.7e-12   45.9   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.1e-09   38.5   0.1    1.4e-09   38.1   0.1    1.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      6e-08   32.6   0.0    8.4e-08   32.1   0.0    1.3  1  FR47             FR47-like protein
    9.1e-08   32.9   0.1    1.1e-07   32.6   0.1    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00062   19.3   0.1    0.00087   18.8   0.1    1.2  1  Acetyltransf_15  Putative acetyl-transferase
     0.0019   18.3   0.4     0.0024   18.0   0.4    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0085   16.2   0.0      0.014   15.5   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.023   14.8   0.1    1.3  1  RRP7             Ribosomal RNA-processing protein 7 (RRP7) C-
       0.19   10.2   0.0        4.7    5.7   0.0    2.2  2  AstA             Arginine N-succinyltransferase beta subunit


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 !   77.1   0.7   7.6e-25   1.2e-21      11     117 .]      28     142 ..      18     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 7.6e-25
                                       HTH....HHHHHHHHHH.HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1  11 sff....ppnedaseee.feesfsleaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGs 79 
                                        ++      + ++ e   +++++++ +e +++++e++e+iGf+ +  ++     + +v++i++l+ +peyr+kG Gs
  gi|488600321|ref|YP_007906792.1|  28 AYRgleeYAYTKRKEIKnYFKWLRNRDEDGFMVLEGDEIIGFVACDTNWVsifDRLKVGEIHELVLHPEYRNKGFGS 104
                                       44433323333334444799********99999********************889********************* PP

                                       HHHHHHHHHHHHTTESEE.EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  80 aLlealeerareegikki.vlaveedndaairlYeklGF 117
                                        Ll++++e+a+++  k + +l+v e n +a+++Y+k GF
  gi|488600321|ref|YP_007906792.1| 105 FLLNKAVEYAKSKDRK-LaELWVGEKNYRARKFYMKNGF 142
                                       *************554.449******************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.1   2.2e-15   3.6e-12       6      75 ..      58     143 ..      52     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.2e-15
                                       EEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHH....TT...SEEEEE.EEEE..THH CS
                    Acetyltransf_7   6 fVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLlea....ae...kgiile.qlel..nae 63 
                                       f + ++++i+Gf+a+  ++         +ei++l+ +peyr+kG G+ Ll+     a+   ++     +l++  + +
  gi|488600321|ref|YP_007906792.1|  58 FMVLEGDEIIGFVACDTNWvsifdrlkvGEIHELVLHPEYRNKGFGSFLLNKaveyAKskdRK---LaELWVgeK-N 130
                                       456689********99999****9999999999*****************9534441132222...234555532.3 PP

                                       .HHHHHHHHTTEE CS
                    Acetyltransf_7  64 .kaikfYeklGFe 75 
                                        +a+kfY k+GF 
  gi|488600321|ref|YP_007906792.1| 131 yRARKFYMKNGFN 143
                                       59**********6 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   2.9e-15   4.7e-12      18     110 ..      39     146 ..      25     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 2.9e-15
                   Acetyltransf_10  18 spealrerie...egealllvaeeggkivGvielrdgs..........hisllfVdpeyrgqGigkaLleaveeeae 81 
                                       ++++++++++   + +   +++ eg++i+G+++ ++++          +i+ l+ +peyr +G g+ Ll+++ e+a+
  gi|488600321|ref|YP_007906792.1|  39 KRKEIKNYFKwlrNRDEDGFMVLEGDEIIGFVACDTNWvsifdrlkvgEIHELVLHPEYRNKGFGSFLLNKAVEYAK 115
                                       344444444334477777888889********9999999*************************************9 PP

                   Acetyltransf_10  82 kdgikl.eltvnasp.yavpfYeklGFkavg 110
                                        ++ kl el v +++  a++fY+k GF + g
  gi|488600321|ref|YP_007906792.1| 116 SKDRKLaELWVGEKNyRARKFYMKNGFNEKG 146
                                       999999*********99**********9865 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   8.5e-13   1.4e-09       1     125 [.       9     142 ..       9     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.5e-13
                                       .EEEE-GGGHHHHHHHHHHHTT----H......HHHHHHHHHHTT.SEEEEEEETTEEEEEEEEEEEEEEETTEEEE CS
                    Acetyltransf_9   1 eirelteedldevlellkyaFqdeespl...e.eireyfrkllee.srvlgaedngelvgqlallplelnvpGktlk 72 
                                       +ir+++ +dl++++++  +a+   e+++   + ei++yf+ l ++ ++ + + +++e++g +a+ +  +++ + +lk
  gi|488600321|ref|YP_007906792.1|   9 TIRKVDRSDLEAFVNIYIEAYRGLEEYAytkRkEIKNYFKWLRNRdEDGFMVLEGDEIIGFVACDTNWVSIFD-RLK 84 
                                       59**********************999988755777777776665269************9999888888876.79* PP

                                       EEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT- CS
                    Acetyltransf_9  73 aagvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGy 125
                                       ++ +     +pe+r++g+ s Ll++a+e++++++ +l+ l+      +++++Y + G+
  gi|488600321|ref|YP_007906792.1|  85 VGEIHELVLHPEYRNKGFGSFLLNKAVEYAKSKDRKLAELWVgeknyRARKFYMKNGF 142
                                       *****************************************98877666788888887 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   5.2e-11   8.4e-08      18      80 ..      82     145 ..      67     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.2e-11
                                       E-TTSSEEEEEE-GGG-SSSHHHHHH.HHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  18 rkdggelgalqvlpehrrrGlgsrlv.kalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       r+++ge+  l ++pe r++G+gs l  ka+ ++ ++  k + l+v+++N +++++y k Gf++ 
  gi|488600321|ref|YP_007906792.1|  82 RLKVGEIHELVLHPEYRNKGFGSFLLnKAVEYAKSKDRKLAELWVGEKNYRARKFYMKNGFNEK 145
                                       6789******************97651677777777889999*******************976 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1     7e-11   1.1e-07       3     138 .]       9     143 ..       8     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 7e-11
                    Acetyltransf_3   3 lLrplteeDlealfelrsdpe..vmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglr..dle 75 
                                       ++r++  +Dlea+++++ +    +++y    +++ e + +++  w ++ +e+g  +++ l+++++iG+v +   +++
  gi|488600321|ref|YP_007906792.1|   9 TIRKVDRSDLEAFVNIYIEAYrgLEEYA--YTKRKEIKNYFK--WLRNRDEDG--FMV-LEGDEIIGFVACDtnWVS 78 
                                       6899999999999987664332355552..456788899999..877666666..999.555548****88733333 PP

                    Acetyltransf_3  76 eedee.....aelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                           +     +e+  ++l+p++++kG+++  ++ ++eya +  + +  +  + ++N + ++ ++k Gf+
  gi|488600321|ref|YP_007906792.1|  79 I---FdrlkvGEIHeLVLHPEYRNKGFGSFLLNKAVEYA-KSKDRKLAELWVGEKNYRARKFYMKNGFN 143
                                       3...134577999779999********************.5555787888899**************96 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   5.3e-07   0.00087      46     136 ..      16     142 ..       5     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.3e-07
                   Acetyltransf_15  46 eeLvasvfivkkkyyslvs...........................................silieknvleiYtly 79 
                                         L a v i  + y++l++                                           si  + +v ei +l+
  gi|488600321|ref|YP_007906792.1|  16 SDLEAFVNIYIEAYRGLEEyaytkrkeiknyfkwlrnrdedgfmvlegdeiigfvacdtnwvSIFDRLKVGEIHELV 92 
                                       556677778888888888888888888888888888899999999999999999999999999999999******** PP

                   Acetyltransf_15  80 vsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgF 136
                                        +++yr+kG+   lL++++++ k     ++ +l  L + +k      +  +Y+++gF
  gi|488600321|ref|YP_007906792.1|  93 LHPEYRNKGFGSFLLNKAVEYAK----SKDRKLAELWVGEKNYR---ARKFYMKNGF 142
                                       ******************88774....44455555555554433...3345555555 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.4   1.5e-06    0.0024       1     137 [.      10     145 ..      10     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                    Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvaesdrivGyaylg.qfkkr.akd 75 
                                       ir + ++D++++ +iy e ++  +   + + + ++ + k+l ++    e  f+v+e d+i+G  +   +  +   + 
  gi|488600321|ref|YP_007906792.1|  10 IRKVDRSDLEAFVNIYIEAYRGLEEYAYTKRKEIKNYFKWLRNR---DEDGFMVLEGDEIIGFVACDtNWVSIfDRL 83 
                                       899*************7654433333444568899999999997...7888************99996666667889 PP

                    Acetyltransf_4  76 wkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelv 137
                                       + +e+  ++ +   +++g g+ l++  ++++k    +  +  +  +n  + +f+ + GF+  
  gi|488600321|ref|YP_007906792.1|  84 KVGEIHELVLHPEYRNKGFGSFLLNKAVEYAKSKDRKLAELWVGEKNYRARKFYMKNGFNEK 145
                                       999**99999999******************8887776666677778889999999999865 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.7e-06     0.014      26      59 ..      87     120 ..      58     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.7e-06
                   Acetyltransf_CG  26 dfthTeVpeelrGkGiAkkLvkaalddareeglk 59 
                                       +++  + ++e+r kG+++ L ++a+++a++++ k
  gi|488600321|ref|YP_007906792.1|  87 EIHELVLHPEYRNKGFGSFLLNKAVEYAKSKDRK 120
                                       67778889**********************9987 PP

>> RRP7  Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.4e-05     0.023       6      49 ..      14      63 ..      10     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                              RRP7  6 seeelqeevdeymeefdkeeeeekkeekkk......eeevDeDGfvtVtr 49
                                      ++ +l++ v+ y+e++   ee + +++k+        ++ DeDGf++ ++
  gi|488600321|ref|YP_007906792.1| 14 DRSDLEAFVNIYIEAYRGLEEYAYTKRKEIknyfkwLRNRDEDGFMVLEG 63
                                      6788999999999999999998888888886777776789******9987 PP

>> AstA  Arginine N-succinyltransferase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.021        34       3      31 ..       9      37 ..       8      75 .. 0.83
   2 ?    5.7   0.0    0.0029       4.7     121     144 ..      86     109 ..      81     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
                              AstA  3 viRparesDldallelaeesgvgltsLpa 31
                                      +iR++++sDl+a++++  e+ +gl +   
  gi|488600321|ref|YP_007906792.1|  9 TIRKVDRSDLEAFVNIYIEAYRGLEEYAY 37
                                      69**************9999999877654 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0029
                              AstA 121 selctlfldpeyrkgglgrllsrs 144
                                        e++ l+l+peyr++g g++l + 
  gi|488600321|ref|YP_007906792.1|  86 GEIHELVLHPEYRNKGFGSFLLNK 109
                                       5899**************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1095.00
//
Query:       gi|488600322|ref|YP_007906793.1|  [L=224]
Description: amino acid ABC transporter membrane protein, PAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   77.7  14.7    1.2e-21   77.3  14.7    1.2  1  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3  14.7   6.8e-26   1.2e-21       1     183 [.      37     218 ..      13     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 6.8e-26
                      BPD_transp_1   1 gillGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirra 74 
                                       g+++G +a+   +++n +   +++++++v++++P +v ++++++ +  ++i      ++ii+l + +++y+  i+ra
  gi|488600322|ref|YP_007906793.1|  37 GLIIGTIAGlgrVSKNPIPFAVSTFYVEVIRGTPLLVQILIIYFGLPAIGINLEPEPAGIIALSVCSGAYIAEIVRA 113
                                       789999999****************************999999776777677777888******************* PP

                      BPD_transp_1  75 alrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydys 151
                                       +++s+p +++eaar lG+s+ q +r+v++P+a++ i++ l++ f++ll++++ll+ +     +  l+    ++ +++
  gi|488600322|ref|YP_007906793.1| 114 GIESIPIGQMEAARSLGMSYLQAMRYVIFPQAFRNILPALGNEFIALLKDSSLLSVIS----IVELTRVGRQIVNTT 186
                                       **********************************************************....*************** PP

                      BPD_transp_1 152 eisnggvlalviavlllnlvadilqrlldprv 183
                                       +++++++l +++++l +++ +  l+ + ++r+
  gi|488600322|ref|YP_007906793.1| 187 FNAWTPFLGVALFYLMMTIPLSRLVSYSQKRL 218
                                       9999********************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1468.73
//
Query:       gi|488600323|ref|YP_007906794.1|  [L=275]
Description: amino acid ABC transporter substrate-binding protein, PAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-79  266.4   1.8    1.9e-79  266.2   1.8    1.0  1  SBP_bac_3        Bacterial extracellular solute-binding prote
    1.2e-14   54.5   0.1    4.8e-13   49.3   0.1    2.3  1  Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine
      3e-08   33.6   0.1    6.2e-08   32.5   0.1    1.5  1  Phosphonate-bd   ABC transporter, phosphonate, periplasmic su
    1.9e-06   28.0   0.4    5.2e-06   26.6   0.3    1.8  2  NMT1             NMT1/THI5 like
     0.0037   16.9   0.4       0.22   11.1   0.1    2.2  2  OpuAC            Substrate binding domain of ABC-type glycine
     0.0063   15.6   0.1      0.015   14.4   0.0    1.6  1  Lipoprotein_9    NLPA lipoprotein
  ------ inclusion threshold ------
      0.063   12.6   0.0      0.087   12.1   0.0    1.2  1  CLN6             Ceroid-lipofuscinosis neuronal protein 6
      0.093   12.3   0.0        7.4    6.0   0.0    2.3  2  YhfZ_C           YhfZ C-terminal domain
      0.093   12.1   0.1        3.4    7.0   0.1    2.1  2  NMT1_3           NMT1-like family


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 !  266.2   1.8   9.6e-83   1.9e-79       1     224 [.      52     274 ..      52     275 .] 0.95

  Alignments for each domain:
  == domain 1  score: 266.2 bits;  conditional E-value: 9.6e-83
                                       EEEEE-S-BTTTBEE-T.TS-EESHHHHHHHHHHHHCT-EEEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTE CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3   1 lrvgvdadypPfsykde.ngeltGfdvdlakaiakrlgvkvefvpvswdelipalksgkvDiaiaaititpeReekv 76 
                                       l+vg+d +ypPf++ de +g+++Gfd+dl+ +iakrlg++v+fv++ wd++ip+l s+k+D++++a+tit+eR+++v
  gi|488600323|ref|YP_007906794.1|  52 LTVGSDIAYPPFEFTDEkTGKYAGFDIDLMTEIAKRLGLEVKFVNTAWDGIIPGLLSKKYDVICSAMTITEERAKQV 128
                                       79******************************************99******************************* PP

                                       EEESESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC...TSEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  77 dFsqpyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk...gaeivefdtleealqaLkn 150
                                       dFs+pyf+a+qv+++r++d    +si+s++dL gkkv+vq+g+t + ++++ lk+   + ei++f+  +eal+a+++
  gi|488600323|ref|YP_007906794.1| 129 DFSEPYFEAKQVIITRADD----TSIQSVKDLDGKKVAVQQGTTGDFAAER-LKEkgiNLEIIRFEGTPEALMAIQK 200
                                       ****************665....5788888**************9855555.44457788889************** PP

                                       TSSSEEEEEHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHHHHTTHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 151 grvdavvadspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalaelkadgtlakisekWfg 224
                                       g +da++ d+ v++ +vkk+p+  +v+ ++++++e+y+iav+k+++ L++ainkal+e+k+dgt++ki+ekWfg
  gi|488600323|ref|YP_007906794.1| 201 GDADAAIIDNFVAYLAVKKDPKVYRVVEDPEFEPEYYGIAVNKDNKGLLEAINKALEEIKKDGTYDKIYEKWFG 274
                                       ***************************99999*****************************************9 PP

>> Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine-binding site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.1   2.4e-16   4.8e-13      22     112 ..      67     144 ..      52     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.4e-16
                                       --GGGGEESHHHHHHHHHHHHHT-EEEEEE-TT-----BETTTTEB-HHHHHHHTTS-SEE-SS-B--HHHHTTSEE CS
                   Lig_chan-Glu_bd  22 legneryeGfcidLlkelakklgfkYelklvedgkyGskkekkkewnGmigellekkadlavapltitaeReevvdF 98 
                                        e++ +y Gf idL++e+ak+lg++ ++               + w+G+i  ll+kk d++ +++tit+eR++ vdF
  gi|488600323|ref|YP_007906794.1|  67 DEKTGKYAGFDIDLMTEIAKRLGLEVKFVN-------------TAWDGIIPGLLSKKYDVICSAMTITEERAKQVDF 130
                                       344578******************999854.............37******************************** PP

                                       ESESEEE-EEEEEE CS
                   Lig_chan-Glu_bd  99 tkpfmelgisilik 112
                                       ++p+ e    i+++
  gi|488600323|ref|YP_007906794.1| 131 SEPYFEAKQVIITR 144
                                       *****999888876 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 !   32.5   0.1   3.1e-11   6.2e-08      71     219 ..     132     261 ..      79     273 .. 0.65

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.1e-11
                                       EEEEEEEETT--SEEEEEEEEETTSS.--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--H CS
                    Phosphonate-bd  71 eplatrvrsdGsasyrsviivradsd.iqsledLkgktiafvspsStsGylvpaalLvkeagldpeddfsevfsgsh 146
                                       ep    +          vii+rad++ iqs++dL+gk++a+ + +   G  + +  L ke+g+++e      +  + 
  gi|488600323|ref|YP_007906794.1| 132 EPYFEAK---------QVIITRADDTsIQSVKDLDGKKVAVQQGT--TGDFAAER-L-KEKGINLE----IIRFEGT 191
                                       5555555.........49******977*************96644..55555555.9.9*****65....5666679 PP

                                       HHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEEEE-.-EEEEETTS-HHHHHHHHHHHHH--- CS
                    Phosphonate-bd 147 daavlavlsgdadaaavsadaledlvaegpedkdelrviassppipn.dpvvvrkelseelkekiqdallslae 219
                                       ++a+ a+ +gdadaa +++++++  v+++p   +  rv++  +  p+ ++++v+k+  + l e+i +al ++++
  gi|488600323|ref|YP_007906794.1| 192 PEALMAIQKGDADAAIIDNFVAYLAVKKDP---KVYRVVEDPEFEPEyYGIAVNKD-NKGLLEAINKALEEIKK 261
                                       99*********************9999864...55555555443333156666666.44566666666666655 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.7   1.4e+03     116     149 ..      89     119 ..      72     139 .. 0.70
   2 !   26.6   0.3   2.6e-09   5.2e-06      74     167 ..     138     228 ..      86     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.7
                                       T--GGG-EEEE-.TT-HHHHHHCTSSSEEECEET CS
                              NMT1 116 ggdpsdvtlvnvggtslakalltgkvDaaiggye 149
                                       g+   +v++vn+  +  ++ ll++k D++  +++
  gi|488600323|ref|YP_007906794.1|  89 GL---EVKFVNTAWDGIIPGLLSKKYDVICSAMT 119
                                       44...68888887777788888888888874443 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 2.6e-09
                                       -EEEEEECCC-.-SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT.-HHHHHHCTSSSEEECEE CS
                              NMT1  74 lsglivlkdsg.ikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggt.slakalltgkvDaaiggy 148
                                        + +i+++d+  i+s+kDL+Gk+++++++  +  +  + l+++g++   +++++ +gt ++  a+ +g +Daai  +
  gi|488600323|ref|YP_007906794.1| 138 KQVIITRADDTsIQSVKDLDGKKVAVQQG-TTGDFAAERLKEKGIN---LEIIRFEGTpEALMAIQKGDADAAI--I 208
                                       456888888888****************5.5555666778999**5...55555555514445**********9..7 PP

                                       TTTHHHH.HHHTT--EEEE- CS
                              NMT1 149 enwegve.lesegkelrifa 167
                                        n+ ++  ++++ k +r+++
  gi|488600323|ref|YP_007906794.1| 209 DNFVAYLaVKKDPKVYRVVE 228
                                       77666551333333444444 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 !    5.7   0.1    0.0046       9.3      20     124 ..      81     172 ..      78     174 .. 0.74
   2 !   11.1   0.1   0.00011      0.22      16      96 ..     168     245 ..     164     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0046
                                       HHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEEEEEEESEEECEEEEEEHHH CS
                             OpuAC  20 lkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkglevlgplgagnteglavpkyv 96 
                                       ++++ +++G++v+ +n +  + ++ +l s++ Dv++++ t t      ++ +  k++   ++ ++++++ ++ +   
  gi|488600323|ref|YP_007906794.1|  81 MTEIAKRLGLEVKFVNTAW-DGIIPGLLSKKYDVICSAMTIT------EERA--KQVD-FSEPYFEAKQVIITR--- 144
                                       6777888899999999887.7779999999999999444433......2222..2222.257888888888887... PP

                                       HHHHTTTBHHHHCTHHGGTEEEEEHHCC CS
                             OpuAC  97 aekygiksisDLkkpaedlelgakgefl 124
                                       a+ + i+s++DL  +++++++g +g+f 
  gi|488600323|ref|YP_007906794.1| 145 ADDTSIQSVKDLDGKKVAVQQGTTGDFA 172
                                       4559********9999999999999986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEEEEEEESEEECEEEEE CS
                             OpuAC  16 laeilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkglevlgplgagnteglav 92 
                                       +++ +++ l++kG++ e  ++++t+ +  a+++Gd+D++  + +  ay a+kk +++ +  +v +p  +  ++g+av
  gi|488600323|ref|YP_007906794.1| 168 TGDFAAERLKEKGINLEIIRFEGTPEALMAIQKGDADAAIIDNF-VAYLAVKK-DPKVY-RVVEDPEFEPEYYGIAV 241
                                       56678899********************************4444.55888888.44333.33348************ PP

                                       EHHH CS
                             OpuAC  93 pkyv 96 
                                       +k+ 
  gi|488600323|ref|YP_007906794.1| 242 NKDN 245
                                       9986 PP

>> Lipoprotein_9  NLPA lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.4e-06     0.015      15      64 ..     170     220 ..     159     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.4e-06
                                       HHHHHHHHTTTEEEEEEEESSSSHHHHHHHTTSSSEEEEEE.HHHHHHHHH CS
                     Lipoprotein_9  15 ekvkkllkkkgldleiveFtdyvqpNkaladgeiDanaFQh.lpyLeqfnk 64 
                                        ++++ lk+kg++lei+ F    +  +a+++g+ Da + +  ++yL  ++ 
  gi|488600323|ref|YP_007906794.1| 170 DFAAERLKEKGINLEIIRFEGTPEALMAIQKGDADAAIIDNfVAYLAVKKD 220
                                       46899********************************99873578876554 PP

>> CLN6  Ceroid-lipofuscinosis neuronal protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05     0.087     150     202 ..       3      53 ..       1      60 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                              CLN6 150 llwyipfflilflyfsgcftkvkaeeklplsallllapsalyywylvtegqif 202
                                        +w++ + l++ + f+gc t++++ ++ p+++    a + +  +ylvteg ++
  gi|488600323|ref|YP_007906794.1|   3 KMWFVVVVLLIAIGFAGC-TQSETPKQTPAPTQT-PAENEIPKYYLVTEGMLT 53 
                                       7*****************.677888888888765.688999999*****9876 PP

>> YhfZ_C  YhfZ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.016        32      25     119 ..      72     163 ..      68     170 .. 0.57
   2 ?    6.0   0.0    0.0037       7.4      35      88 ..     174     227 ..     169     237 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                            YhfZ_C  25 kyeGLatglkaafeklgiplnlaymrGa.dkRlealkegrydfavvSrlaAeqaleegkeveialelGpetYvsahv 100
                                       ky G+   l ++++k  + l++ +++ a d  +  l +++yd +++S+++  ++ +++      +++ +  + +++v
  gi|488600323|ref|YP_007906794.1|  72 KYAGFDIDLMTEIAK-RLGLEVKFVNTAwDGIIPGLLSKKYD-VICSAMTITEERAKQ------VDFSEPYFEAKQV 140
                                       566666666666666.67777777777633445678888888.467777777766652......3566555544444 PP

                            YhfZ_C 101 lllrdgekseik...d..glrvgv 119
                                       ++ r  ++++i+   d  g +v+v
  gi|488600323|ref|YP_007906794.1| 141 IITRA-DDTSIQsvkDldGKKVAV 163
                                       44443.333333111233666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0037
                            YhfZ_C  35 aafeklgiplnlaymrGadkRlealkegrydfavvSrlaAeqaleegkeveial 88 
                                       + ++++gi+l++   +G  + l a+++g  d+a++ ++ A  a++++++v  ++
  gi|488600323|ref|YP_007906794.1| 174 ERLKEKGINLEIIRFEGTPEALMAIQKGDADAAIIDNFVAYLAVKKDPKVYRVV 227
                                       5678999****************************************9998776 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0017       3.4      94     164 ..     141     206 ..     130     208 .. 0.70
   2 ?    6.6   0.0    0.0023       4.6      22      67 ..     173     217 ..     165     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0017
                            NMT1_3  94 qlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalkdgqldga 164
                                        ++ ++d  i+s++dl+gk+v+v  +g++ +  a + l++ g++   l+++++ g+ e+  a+++g  d+a
  gi|488600323|ref|YP_007906794.1| 141 IITRADDTSIQSVKDLDGKKVAVQ-QGTTGD-FAAERLKEKGIN---LEIIRFEGTPEALMAIQKGDADAA 206
                                       344568999*************94.344443.455667888886...444455678888888888888876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0023
                            NMT1_3  22 seklakdqkvkasaqssaGsveNiqllkkgeadlailqsdvayeAy 67 
                                        e l k+++++ + +  +G+ e + +++kg+ad+ai+ + vay A+
  gi|488600323|ref|YP_007906794.1| 173 AERL-KEKGINLEIIRFEGTPEALMAIQKGDADAAIIDNFVAYLAV 217
                                       4455.6789*********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1525.36
//
Query:       gi|488600324|ref|YP_007906795.1|  [L=122]
Description: Formylmethanofuran dehydrogenase subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-08   34.6   0.0    1.8e-08   34.4   0.0    1.1  1  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.011   15.9   0.0       0.02   15.1   0.0    1.4  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      0.077   13.0   0.0       0.12   12.3   0.0    1.4  1  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
       0.14   12.4   0.0       0.18   12.1   0.0    1.3  1  FeoA             FeoA 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 !   34.4   0.0   4.1e-12   1.8e-08      10      83 ..      18      90 ..      10     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4.1e-12
                                      TBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC. CS
                   Molydop_binding 10 dqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwea 83
                                      +  h  t++++ ++  k +  v+ +npe A+++G k+Gd Veves   +v+++++ +++ +   + mp   +++
  gi|488600324|ref|YP_007906795.1| 18 RNSHQATAEKDEEEFEKLSA-VLFLNPEYAKKMGFKEGDVVEVESGGRAVRLKVMYSDTAPDEGAMMPNSIYSN 90
                                      55666667777777777776.**********************************************9998873 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 ?   15.1   0.0   4.4e-06      0.02      16      54 ..      38      77 ..      25      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-06
                                      EEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTS CS
                           CDC48_N 16 ivridpedmeelglepgdvveieg.krkTvaivwpaeped 54
                                      +  ++pe  +++g+++gdvve+e   r    +v+ +++  
  gi|488600324|ref|YP_007906795.1| 38 VLFLNPEYAKKMGFKEGDVVEVESgGRAVRLKVMYSDTAP 77
                                      6689*******************94554669999888764 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 ?   12.3   0.0   2.8e-05      0.12      14      34 ..      44      64 ..      43      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                                      CCHHHCCEECTCEEEEEECTT CS
                    MazE_antitoxin 14 evrfelgireGdevelevdgd 34
                                      e ++++g++eGd ve+e  g 
  gi|488600324|ref|YP_007906795.1| 44 EYAKKMGFKEGDVVEVESGGR 64
                                      7799************98765 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.1e-05      0.18      25      46 ..      35      64 ..       9      80 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
                                      H........HHHHHHT--TT-EEEEEEE-T CS
                              FeoA 25 l........rrLremGlvpGarievvarap 46
                                      l         + ++mG+ +G ++ev + ++
  gi|488600324|ref|YP_007906795.1| 35 LsavlflnpEYAKKMGFKEGDVVEVESGGR 64
                                      1555555558999************97544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 804.11
//
Query:       gi|488600325|ref|YP_007906796.1|  [L=398]
Description: formylmethanofuran dehydrogenase, subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.4   0.0       0.25   10.3   0.0    2.1  2  Molybdopterin    Molybdopterin oxidoreductase
      0.051   11.8   0.0       0.08   11.2   0.0    1.2  1  Fusion_gly       Fusion glycoprotein F0
      0.085   12.5   0.0       0.18   11.4   0.0    1.4  1  PGP_phosphatase  Mitochondrial PGP phosphatase
       0.19   11.7   1.4        5.2    7.0   0.0    2.9  3  DUF5043          Domain of unknown function (DUF5043)


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 ?    0.9   0.0     0.039   1.7e+02      70     125 ..      87     139 ..      54     192 .. 0.69
   2 ?   10.3   0.0   5.5e-05      0.25     329     404 ..     299     372 ..     236     386 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.039
                                       T-EEE-BEECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SE.EEEESS-HHHH CS
                     Molybdopterin  70 ggknlsfydwyadlppasaqqtigsdsrsnyessnpledlensdl.iilwGsNvree 125
                                         k  +f+d++   +++  ++ i     ++ + +++l ++ ++ + i+ wG+++++ 
  gi|488600325|ref|YP_007906796.1|  87 AEKKEAFIDDNSSFCLGDFVEMI----LKKEIPTTTLDEVKKNAYvIFYWGTDPYNS 139
                                       55555677777777777653333....334445556666666555377899999875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.5e-05
                                       CHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE.-CCGSEEEEE-TTS CS
                     Molybdopterin 329 ersnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaa.twyEkedlytndeg 404
                                       e +nl+ + +++   ++g++p ++ + e+ +   + ++   +v+d   t ta+ aD++LP+a t y + ++++ ++g
  gi|488600325|ref|YP_007906796.1| 299 EFKNLILNDEIDTALIIGTDPLNSLPFEVAR---KLSKIKKIVIDPKNTFTARTADVVLPSAiTGYDQGGTMVRSDG 372
                                       4457777777777888888888888888887...3355666899****************99344666666666655 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.8e-05      0.08     395     451 ..      11      67 ..       6      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.8e-05
                                       -SEEEETTEEEE--S-SS-TTTTCCGS----B---SHHHHHHHHHHHHHHHHHHHHH CS
                        Fusion_gly 395 cdtvsvdgivlklskklanveaknlsiklgppisveevdisaelskvnesleqskdl 451
                                       c+ + v   v+++ ++ a++  + ++ k +p++  +evd++++l+k+ e +++sk+l
  gi|488600325|ref|YP_007906796.1|  11 CTDIVVKDKVFNACRRGASIFRNAENNKAKPKVDGKEVDFDTALNKAIELISNSKNL 67 
                                       77889999999999*9**************************************985 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     4e-05      0.18      26      64 ..     320     357 ..     313     363 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                   PGP_phosphatase  26 frqlpieigkkkektikavvlDKDnclaapkedkvaeei 64 
                                       +++lp+e+ ++k ++ik +v+D  n+++a  +d v ++ 
  gi|488600325|ref|YP_007906796.1| 320 LNSLPFEV-ARKLSKIKKIVIDPKNTFTARTADVVLPSA 357
                                       7899****.9999******************99998865 PP

>> DUF5043  Domain of unknown function (DUF5043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3     0.038   1.7e+02     129     155 .]     106     132 ..     104     132 .. 0.93
   2 ?    7.0   0.0    0.0012       5.2       9      41 ..     158     190 ..     148     204 .. 0.90
   3 ?   -2.4   0.0      0.97   4.3e+03      19      41 ..     238     260 ..     229     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.038
                           DUF5043 129 ievklkeeivfklteeGkklnyilyvW 155
                                       +e+ lk+ei  +  +e kk  y++++W
  gi|488600325|ref|YP_007906796.1| 106 VEMILKKEIPTTTLDEVKKNAYVIFYW 132
                                       6889*********************99 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                           DUF5043   9 ktfnedgyvyqCdvaaskfvtlynksnklieve 41 
                                       + ++ed+++   dv++s++ +l +k+ ++i+v+
  gi|488600325|ref|YP_007906796.1| 158 RGYEEDRFLVVVDVRKSHTAKLAKKNARFIQVN 190
                                       6799**************************987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.97
                           DUF5043  19 qCdvaaskfvtlynksnklieve 41 
                                         + + s+f+ + nk n + +v+
  gi|488600325|ref|YP_007906796.1| 238 GLNSDYSRFLEMVNKMNEISNVY 260
                                       55567899999999999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2599.58
//
Query:       gi|488600326|ref|YP_007906797.1|  [L=156]
Description: formylmethanofuran dehydrogenase, subunit G [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-15   55.2   1.0    3.8e-15   55.2   1.0    2.1  1  FeS         Putative Fe-S cluster
    1.3e-08   34.8   5.1    1.3e-08   34.8   5.1    2.4  2  Fer4_10     4Fe-4S dicluster domain
    1.3e-06   28.0   3.4    1.3e-06   28.0   3.4    3.9  4  Fer4        4Fe-4S binding domain
    1.4e-05   25.6  16.7     0.0014   19.2   8.1    2.8  2  Fer4_7      4Fe-4S dicluster domain
    2.3e-05   24.4  12.0      7e-05   22.9   1.5    3.2  3  Fer4_21     4Fe-4S dicluster domain
    4.3e-05   23.4   3.5    4.3e-05   23.4   3.5    3.6  3  Fer4_6      4Fe-4S binding domain
     0.0004   20.5  17.5     0.0091   16.2  10.2    2.9  2  Fer4_9      4Fe-4S dicluster domain
    0.00075   19.5   2.8    0.00075   19.5   2.8    3.5  3  Fer4_2      4Fe-4S binding domain
     0.0028   18.1  13.1       0.01   16.3   5.6    2.4  2  Fer4_8      4Fe-4S dicluster domain
     0.0075   17.0   0.3     0.0075   17.0   0.3    2.8  3  Fer4_15     4Fe-4S single cluster domain
     0.0086   17.0  17.5       0.69   10.9   9.2    2.9  2  Fer4_16     4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.012   16.2   9.5      0.061   13.9   1.5    3.3  3  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
      0.041   13.9   1.1      0.041   13.9   1.1    2.6  2  YhfH        YhfH-like protein
       0.15   12.7   1.4       0.15   12.7   1.4    3.6  3  Fer4_4      4Fe-4S binding domain
       0.19   12.3  17.5      0.081   13.5   7.1    2.7  2  Fer4_17     4Fe-4S dicluster domain
       0.23   12.5  25.7       0.18   12.8   8.7    3.4  3  Fer4_3      4Fe-4S binding domain
        4.3    7.6   9.0          3    8.1   3.5    2.5  2  RIG-I_C-RD  C-terminal domain of RIG-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 !   55.2   1.0   3.6e-18   3.8e-15       1      33 []      12      44 ..      12      44 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.6e-18
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                      LP+tNC++CG+++Cm fA ++++ e +ledC+p
  gi|488600326|ref|YP_007906797.1| 12 LPKTNCKKCGEATCMSFAFKVINRERKLEDCTP 44
                                      9******************************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 ?    3.4   0.6      0.08        84      11      21 ..      16      26 ..      11      50 .. 0.63
   2 !   34.8   5.1   1.3e-11   1.3e-08       3      56 .]      74     147 ..      72     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.08
                           Fer4_10 11 rCgkCvka.CPa 21
                                      +C+kC +a C +
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGEAtC-M 26
                                      4555555445.3 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 1.3e-11
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.............tsvgakgeaseeeavrkkvekCtg.......cgaCveaCP 56 
                                       ++d++ C +C++Cv +CP+++             t ++ +  ++++ ++ ++++kC +       c aC e CP
  gi|488600326|ref|YP_007906797.1|  74 IVDEELCSGCANCVVVCPVHAsddpygmgsgygpTIDDPILRIEDGVVKVINMKKCRRygknrilCVACRENCP 147
                                       6899***************99*************************************999999999******9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4      0.38     4e+02       7      12 ..      16      21 ..      14      23 .. 0.66
   2 !   28.0   3.4   1.2e-09   1.3e-06       2      22 ..      74      94 ..      73      95 .. 0.95
   3 ?   -1.7   0.0       2.8     3e+03       2       8 ..     123     129 ..     122     130 .. 0.86
   4 !    9.4   1.2   0.00091      0.96      10      24 .]     138     152 ..     137     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.38
                                      TSSS-T CS
                              Fer4  7 kCigCG 12
                                       C +CG
  gi|488600326|ref|YP_007906797.1| 16 NCKKCG 21
                                      577777 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1.2e-09
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                      ++dee+C gC +Cv vCPv A
  gi|488600326|ref|YP_007906797.1| 74 IVDEELCSGCANCVVVCPVHA 94
                                      79*****************98 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.8
                                       EEETTTS CS
                              Fer4   2 videekC 8  
                                       vi++ kC
  gi|488600326|ref|YP_007906797.1| 123 VINMKKC 129
                                       7999999 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00091
                                       S-THHHHHSTTTEEE CS
                              Fer4  10 gCGaCvevCPvgAIt 24 
                                        C aC e CP +AI+
  gi|488600326|ref|YP_007906797.1| 138 LCVACRENCPSDAIR 152
                                       5669*********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 !   19.2   8.1   1.3e-06    0.0014       3      52 .]      15      94 ..      15      94 .. 0.62
   2 !   11.1   0.6   0.00044      0.47       3      20 ..     137     154 ..     135     156 .] 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                            Fer4_7  3 igCgaCvaa.Cpvkaieldeeenek........................gtekv........eidpekClgCgaCvavC 48
                                      ++C++C +a C++ a+++ ++e++                         g   +         +d+e C+gC +Cv vC
  gi|488600326|ref|YP_007906797.1| 15 TNCKKCGEAtCMSFAFKVINRERKLedctplfeekkyapqleelkkmlkG---IeeatetglIVDEELCSGCANCVVVC 90
                                      58999975449988888765543334455555444444455544444441...04445555578999************ PP

                            Fer4_7 49 Ptga 52
                                      P+ a
  gi|488600326|ref|YP_007906797.1| 91 PVHA 94
                                      *976 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00044
                            Fer4_7   3 igCgaCvaaCpvkaield 20 
                                       i C aC ++Cp++ai++ 
  gi|488600326|ref|YP_007906797.1| 137 ILCVACRENCPSDAIRFV 154
                                       6799***********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 ?    2.0   0.2      0.22   2.4e+02      10      28 ..      16      35 ..      13      55 .. 0.72
   2 !   22.9   1.5   6.6e-08     7e-05      26      54 ..      65      93 ..      59      96 .. 0.85
   3 ?    5.9   0.3     0.013        14      38      58 ..     136     152 ..     113     153 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.22
                           Fer4_21 10 gCgkCl.iaCedtshqaiei 28
                                      +C+kC   +C   + + i+ 
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGeATCMSFAFKVINR 35
                                      68888524688777777754 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 6.6e-08
                           Fer4_21 26 ieidaktvlkvvedeCvGCnlCssvCPve 54
                                      ie +++t l v e+ C GC+ C+ vCPv+
  gi|488600326|ref|YP_007906797.1| 65 IEEATETGLIVDEELCSGCANCVVVCPVH 93
                                      667778888999***************95 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.013
                           Fer4_21  38 edeCvGCnlCssvCPvedcie 58 
                                           + C  C + CP +d+i+
  gi|488600326|ref|YP_007906797.1| 136 R---ILCVACRENCP-SDAIR 152
                                       3...34666778899.58775 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.3      0.21   2.2e+02       8      16 ..      16      26 ..      14      27 .. 0.76
   2 !   23.4   3.5   4.1e-08   4.3e-05       4      23 ..      75      94 ..      74      95 .. 0.93
   3 ?    3.9   1.6     0.059        62       4      24 .]     124     151 ..     121     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.21
                            Fer4_6  8 kCigCgd..Cv 16
                                      +C  Cg+  C+
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGEatCM 26
                                      79999987776 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 4.1e-08
                            Fer4_6  4 idpdkCigCgdCvrvCPega 23
                                      +d+++C gC +Cv+vCP  a
  gi|488600326|ref|YP_007906797.1| 75 VDEELCSGCANCVVVCPVHA 94
                                      8****************876 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.059
                            Fer4_6   4 idpdkCi.......gCgdCvrvCPegai 24 
                                       i+  kC         C +C  +CP +ai
  gi|488600326|ref|YP_007906797.1| 124 INMKKCRrygknriLCVACRENCPSDAI 151
                                       6666666665555568888888999887 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   8.6   2.1e-05     0.022       3      50 ..      15      94 ..      14      95 .. 0.78
   2 !   16.2  10.2   8.6e-06    0.0091       2      51 .]      80     151 ..      79     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                            Fer4_9  3 tgCgaC.veaCpagvvvedaaerkarlraase................................eaCigCgaCveaCpk 48
                                      t+C++C ++ C + +++  + erk +  ++                                  e C gC  Cv +Cp 
  gi|488600326|ref|YP_007906797.1| 15 TNCKKCgEATCMSFAFKVINRERKLED-CTPLfeekkyapqleelkkmlkgieeatetglivdeELCSGCANCVVVCPV 92
                                      689999666697777766666666553.3333567788888999999999999999999999999*************8 PP

                            Fer4_9 49 ga 50
                                      +a
  gi|488600326|ref|YP_007906797.1| 93 HA 94
                                      75 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 8.6e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkgai 51 
                                       C gC +Cv +Cp ++  +  + +       ++                      ++ i C aC e Cp++ai
  gi|488600326|ref|YP_007906797.1|  80 CSGCANCVVVCPVHASDDPYGMGSGYGPTIDDpilriedgvvkvinmkkcrrygKNRILCVACRENCPSDAI 151
                                       ***********999999888888888888877899999999999999888888866688999*******997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3      0.11   1.2e+02       9      16 ..      16      25 ..      10      28 .. 0.65
   2 !   19.5   2.8   7.1e-07   0.00075       5      21 ..      75      91 ..      72      92 .. 0.92
   3 ?    5.5   1.2     0.019        20       5      21 ..     124     147 ..     121     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                            Fer4_2  9 rCigCg..aC 16
                                      +C  Cg  +C
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGeaTC 25
                                      4666665566 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.1e-07
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      vd++ C gC  Cv +CP
  gi|488600326|ref|YP_007906797.1| 75 VDEELCSGCANCVVVCP 91
                                      89*************** PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.019
                            Fer4_2   5 vdtdrCig.......CgaCvsaCP 21 
                                       ++  +C +       C aC+ +CP
  gi|488600326|ref|YP_007906797.1| 124 INMKKCRRygknrilCVACRENCP 147
                                       556666666666666779999999 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   5.6   9.7e-06      0.01       4      64 ..      16      93 ..      14      94 .. 0.75
   2 ?    6.2   0.8     0.013        14       7      17 ..     138     148 ..     121     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.7e-06
                            Fer4_8  4 kCieCg..aCq.............saC.pvlrrtkkhlldargeaaedvqeeqvlee..eealwsCttcgaCtevCpvg 64
                                      +C +Cg   C+             + C p+++++k  ++  + +++  +  e+++e+      + C++c +C++vCpv+
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGeaTCMsfafkvinrerklEDCtPLFEEKKYAPQLEELKKML-KGIEEATETglIVDEELCSGCANCVVVCPVH 93
                                      68888766788888888888888877888888888888888888887.44444433445566789************98 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                            Fer4_8   7 eCgaCqsaCpv 17 
                                        C aC+++Cp+
  gi|488600326|ref|YP_007906797.1| 138 LCVACRENCPS 148
                                       56666666664 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       8.5     9e+03       6      13 ..      15      22 ..      14      38 .. 0.54
   2 !   17.0   0.3   7.1e-06    0.0075       3      29 ..      75     101 ..      73     120 .. 0.84
   3 ?    2.0   0.6      0.33   3.5e+02      57      65 ..     144     152 ..     137     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.5
                           Fer4_15  6 daCigcgl 13
                                      ++C  cg 
  gi|488600326|ref|YP_007906797.1| 15 TNCKKCGE 22
                                      56776653 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.1e-06
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedgl 29 
                                       vD+++C gc++Cv ++p     d +g+
  gi|488600326|ref|YP_007906797.1|  75 VDEELCSGCANCVVVCPVHASDDPYGM 101
                                       9***************96665555665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.33
                           Fer4_15  57 raCPvdAIr 65 
                                       ++CP dAIr
  gi|488600326|ref|YP_007906797.1| 144 ENCPSDAIR 152
                                       58*****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 !   10.9   9.2   0.00066      0.69       4      66 ..      16      92 ..      14      93 .. 0.62
   2 !   10.3   0.8     0.001       1.1       5      19 ..     139     153 ..     135     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00066
                           Fer4_16  4 tCgkCaev.CPtnaikek.kekeieare....cisy......ntaekkdlaedeekck..kqeaitgCdiCqdvCPa 66
                                      +C+kC e+ C + a+k   +e+++e ++    +++y       +++ k+++e +e+     +e + gC++C+ vCP+
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGEAtCMSFAFKVInRERKLEDCTplfeEKKYapqleeLKKMLKGIEEATETGLivDEELCSGCANCVVVCPV 92
                                      67777654388877775423455554444444333367655566777777777777653244778***********7 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.001
                           Fer4_16   5 CgkCaevCPtnaike 19 
                                       C +C e CP++ai+ 
  gi|488600326|ref|YP_007906797.1| 139 CVACRENCPSDAIRF 153
                                       99***********85 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.23   2.5e+02       8      22 ..      16      30 ..      15      62 .. 0.86
   2 ?   13.9   1.5   5.8e-05     0.061       1      18 [.      75      92 ..      75     103 .. 0.87
   3 ?    4.2   0.1      0.06        63      44      56 ..     139     151 ..     117     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                           Fer4_13  8 acgaCvelaPdvFee 22
                                      +c++C+e+    F+ 
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGEATCMSFAF 30
                                      799999999888875 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.8e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD++ C++c++Cv ++P 
  gi|488600326|ref|YP_007906797.1| 75 VDEELCSGCANCVVVCPV 92
                                      9****************5 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.06
                           Fer4_13  44 aeeAadaCPvesI 56 
                                       + +  ++CP ++I
  gi|488600326|ref|YP_007906797.1| 139 CVACRENCPSDAI 151
                                       4445567777777 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.1   3.9e-05     0.041       3      22 ..       4      23 ..       3      26 .. 0.91
   2 ?    0.1   0.0       0.8   8.4e+02      11      21 ..     124     134 ..     121     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.9e-05
                              YhfH  3 kiveFfrnLPkKkCteCGke 22
                                      +++e ++ LPk  C +CG+ 
  gi|488600326|ref|YP_007906797.1|  4 TPMEVYKLLPKTNCKKCGEA 23
                                      589***************95 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.8
                              YhfH  11 LPkKkCteCGk 21 
                                       + +KkC   Gk
  gi|488600326|ref|YP_007906797.1| 124 INMKKCRRYGK 134
                                       579***98776 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.3      0.29     3e+02       3      12 ..      16      27 ..      14      28 .. 0.59
   2 ?   12.7   1.4   0.00014      0.15       2      16 ..      78      92 ..      77     103 .. 0.89
   3 ?    1.6   3.3      0.48   5.1e+02       4      16 ..     129     148 ..     126     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.29
                            Fer4_4  3 rCigCgs..Cva 12
                                      +C  Cg   C++
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGEatCMS 27
                                      677777444766 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C gC  Cv +CP+
  gi|488600326|ref|YP_007906797.1| 78 ELCSGCANCVVVCPV 92
                                      67************4 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.48
                            Fer4_4   4 C.......igCgsCvaaCPq 16 
                                       C       i C +C+  CP+
  gi|488600326|ref|YP_007906797.1| 129 CrrygknrILCVACRENCPS 148
                                       54444444578889999996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   7.1   7.7e-05     0.081       1      59 [.      16      93 ..      15      95 .. 0.53
   2 ?    3.6   2.6     0.092        97      48      59 ..     138     149 ..     122     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                           Fer4_17  1 rCiqCgy..ClpeCpsyeaydn...........epkkllraakl......glleeaeke......ekaslCieCgeCer 54
                                      +C +Cg   C+   + ++ ++            e+kk++ +++       g +ee             +lC++C +C+ 
  gi|488600326|ref|YP_007906797.1| 16 NCKKCGEatCMS--FAFKVINRerkledctplfEEKKYAPQLEElkkmlkG-IEE---AtetgliVDEELCSGCANCVV 88
                                      477777444777..4444444412223333333455555555445533422.222...23333433669********** PP

                           Fer4_17 55 kCPqg 59
                                      +CP +
  gi|488600326|ref|YP_007906797.1| 89 VCPVH 93
                                      ***87 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.092
                           Fer4_17  48 eCgeCerkCPqg 59 
                                        C  C++ CP++
  gi|488600326|ref|YP_007906797.1| 138 LCVACRENCPSD 149
                                       566777777765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1      0.85     9e+02       1       8 [.      17      26 ..      15      28 .. 0.75
   2 ?   12.8   8.7   0.00017      0.18       1      15 []      80      94 ..      80      94 .. 0.97
   3 ?    9.1   1.4    0.0027       2.8       3      15 .]     138     150 ..     128     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.85
                            Fer4_3  1 CtgCg..aCv 8 
                                      C  Cg  +C+
  gi|488600326|ref|YP_007906797.1| 17 CKKCGeaTCM 26
                                      7788866687 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00017
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gC  Cv+vCPv+A
  gi|488600326|ref|YP_007906797.1| 80 CSGCANCVVVCPVHA 94
                                      99***********98 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0027
                            Fer4_3   3 gCgaCvevCPvgA 15 
                                        C aC e CP++A
  gi|488600326|ref|YP_007906797.1| 138 LCVACRENCPSDA 150
                                       699********98 PP

>> RIG-I_C-RD  C-terminal domain of RIG-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.5    0.0028         3       3      37 ..      15      50 ..      13      87 .. 0.70
   2 ?    2.4   0.2      0.16   1.7e+02       2      22 ..     136     155 ..     135     156 .] 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0028
                        RIG-I_C-RD  3 llCkkCkkevcsssdirvienshhv.vvnpefkelv 37
                                       +CkkC +++c+s   +vi+       ++p f+e+ 
  gi|488600326|ref|YP_007906797.1| 15 TNCKKCGEATCMSFAFKVINRERKLeDCTPLFEEKK 50
                                      58*****************97765514666666443 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                        RIG-I_C-RD   2 kllCkkCkkevcsssdirvie 22 
                                       ++lC  C+++ c s+ ir +e
  gi|488600326|ref|YP_007906797.1| 136 RILCVACREN-CPSDAIRFVE 155
                                       689****865.999***9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 885.53
//
Query:       gi|488600327|ref|YP_007906798.1|  [L=303]
Description: GMP synthase (glutamine-hydrolyzing) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-30  105.0   0.0    3.2e-30  104.0   0.0    1.5  1  GMP_synt_C       GMP synthase C terminal domain
    3.8e-10   39.3   0.0    0.00066   18.9   0.0    2.2  2  NAD_synthase     NAD synthase
    7.2e-05   22.3   0.0    0.00014   21.3   0.0    1.4  1  Arginosuc_synth  Arginosuccinate synthase
     0.0008   19.0   0.0     0.0046   16.5   0.0    2.0  2  QueC             Queuosine biosynthesis protein QueC
     0.0015   17.4   0.0      0.078   11.8   0.0    2.1  2  tRNA_Me_trans    tRNA methyl transferase
      0.002   17.7   0.1      0.032   13.8   0.1    2.8  1  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0066   16.5   0.0      0.051   13.6   0.0    2.1  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
  ------ inclusion threshold ------
      0.034   13.8   0.1      0.061   13.0   0.1    1.3  1  Asn_synthase     Asparagine synthase


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   1.4e-33   3.2e-30      10      92 .]     221     302 ..     212     302 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1.4e-33
                                       GGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TT CS
                        GMP_synt_C  10 kkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskP 86 
                                        + wQ+fa+l+  k++Gv+gd+R ++y++ +Rav s+D+mtad ++++y+vL++i+ ri+ e+++v+rvvydit kP
  gi|488600327|ref|YP_007906798.1| 221 YDKWQCFAALVG-KATGVKGDNRVWGYIISVRAVGSRDGMTADPINIEYDVLRRIALRITGEIPEVARVVYDITPKP 296
                                       567*******98.9*************************************************************** PP

                                       TS-S-- CS
                        GMP_synt_C  87 patiEw 92 
                                       patiE+
  gi|488600327|ref|YP_007906798.1| 297 PATIEY 302
                                       *****7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.9e-07   0.00066       9      45 ..      11      47 ..       2      59 .. 0.76
   2 !   18.3   0.0   4.5e-07     0.001     146     177 ..     154     185 ..     136     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.9e-07
                                      HHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCG CS
                      NAD_synthase  9 lkeyvkkagakgvvlGlSGGvDSslvaalavkalgke 45
                                      ++e  ++ g  ++++ lSGGvDSs+  ala +a+g++
  gi|488600327|ref|YP_007906798.1| 11 IEEIRSRVGDGKAIIALSGGVDSSVCTALAYRAIGDK 47
                                      3333344566799*********************865 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.5e-07
                                       -SBETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 146 adlapiaellKtevkeLakelnvPervlkkpP 177
                                       + ++p+ el+K ev+e a++l+ Pe++ ++ P
  gi|488600327|ref|YP_007906798.1| 154 GVIEPLRELYKDEVREVARYLGLPEEISERMP 185
                                       5699*************************998 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   6.2e-08   0.00014       1      65 [.      24      86 ..      24      90 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.2e-08
                   Arginosuc_synth  1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefve 65
                                      ++a sGG+D sv+ +l    +g++ i v vd G     l e ++  + +++++ v +Da+eef +
  gi|488600327|ref|YP_007906798.1| 24 IIALSGGVDSSVCTALAYRAIGDKLIPVFVDTGLM--RLGEPERIKEIFSDMNLVFIDAREEFLK 86
                                      6899*****************************99..899999999999**************87 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     2e-06    0.0046       1      53 [.      22      75 ..      22     100 .. 0.81
   2 ?   -0.2   0.0      0.26   5.9e+02     149     178 ..     149     179 ..     121     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2e-06
                                      EEEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT-- CS
                              QueC  1 kavvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgv 53
                                      ka++ lSGG+DS++++ala +++ ++++ + +d g  +  e e  k+i++++++
  gi|488600327|ref|YP_007906798.1| 22 KAIIALSGGVDSSVCTALAYRAIgDKLIPVFVDTGLMRLGEPERIKEIFSDMNL 75
                                      79*****************88743888888888888888888888888888776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                                       TS--E.EE-TTTT--HHHHHHHHHHTTHHHH CS
                              QueC 149 dkkie.ieaPlidlsKaeivklgkelgvple 178
                                       d++++ +  Pl +l K e+ +++  lg+p e
  gi|488600327|ref|YP_007906798.1| 149 DYEFKgVIEPLRELYKDEVREVARYLGLPEE 179
                                       555544778***************9999866 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   3.5e-05     0.078       3      23 ..      23      43 ..      21      66 .. 0.76
   2 ?    3.6   0.0      0.01        23     163     186 ..     154     177 ..     149     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq 23
                                       ++alSgGVDSsv  al  ++
  gi|488600327|ref|YP_007906798.1| 23 AIIALSGGVDSSVCTALAYRA 43
                                      689**********87775543 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.01
                     tRNA_Me_trans 163 kllfPlgeltKeevrkiAkeagla 186
                                        ++ Pl el K+evr++A+  gl+
  gi|488600327|ref|YP_007906798.1| 154 GVIEPLRELYKDEVREVARYLGLP 177
                                       5677***************99986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.4e-05     0.032       3     117 ..      20     126 ..      18     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                              ThiI   3 qgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkev.lk 77 
                                        gk++  lSgG+DS V + l+ +  G +   v+++    t+    +  e++ e++++ +      lv +d +e  lk
  gi|488600327|ref|YP_007906798.1|  20 DGKAIIALSGGVDSSVCTALAYRAiGDKLIPVFVD----TGLMRLGEPERIKEIFSDMN------LVFIDAREEfLK 86 
                                       589999***********999887437777777775....55556677778888887766......777776655055 PP

                              ThiI  78 eilekvkekltivllkrkmlriAekvaeeegakalvtGes 117
                                        ++   +++++  ++   ++ri e+va+e++a+ l++G  
  gi|488600327|ref|YP_007906798.1|  87 ALKGVEDPEQKRKIIGELFVRIFERVAREKNADYLIQGTI 126
                                       555555666777778889******************9965 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.3e-05     0.051       2      42 ..      23      89 ..      22     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                      EEEE--SSCTCHHHHHHHHHHCTTH..........................EEEEEE-STB-HHHHH CS
                       PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpv..........................pvvfvdtghefpetie 42
                                       +++ sgG ds+V   La +a  ++                           +vf+d ++ef + ++
  gi|488600327|ref|YP_007906798.1| 23 AIIALSGGVDSSVCTALAYRAIGDKlipvfvdtglmrlgeperikeifsdmNLVFIDAREEFLKALK 89
                                      57899******************97555555555555555555555555555555555555555555 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.7e-05     0.061      16      39 ..      19      42 ..       7      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                      Asn_synthase 16 advpvGalLSGGlDSSliaalaar 39
                                      +d +  + LSGG+DSS+ +ala r
  gi|488600327|ref|YP_007906798.1| 19 GDGKAIIALSGGVDSSVCTALAYR 42
                                      67777889*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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 0.29s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1783.24
//
Query:       gi|488600328|ref|YP_007906799.1|  [L=531]
Description: CTP synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-125  416.1   0.9   7.6e-125  415.5   0.9    1.2  1  CTP_synth_N    CTP synthase N-terminus
    2.6e-57  193.7   0.0    4.3e-57  193.0   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    1.4e-07   31.5   0.0      7e-07   29.2   0.0    2.0  2  Peptidase_C26  Peptidase C26
    6.8e-06   26.2   0.0    3.6e-05   23.8   0.0    2.1  2  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0079   15.4   0.0      0.017   14.3   0.0    1.5  1  ArsA_ATPase    Anion-transporting ATPase


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 !  415.5   0.9  2.1e-128  7.6e-125       1     265 []       2     265 ..       2     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.5 bits;  conditional E-value: 2.1e-128
                                       EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHH CS
                       CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfl 77 
                                       kyi+vtGGv+SglGkGi+aas+g++l+ +g+kv  ik+DPYln+dagt++p++hGEvfvl+dG+e+DlDlG+YeRf+
  gi|488600328|ref|YP_007906799.1|   2 KYIFVTGGVMSGLGKGITAASIGRILTDMGYKVVPIKVDPYLNIDAGTMNPFQHGEVFVLKDGTEVDLDLGHYERFI 78 
                                       8**************************************************************************** PP

                                       T----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHH CS
                       CTP_synth_N  78 dikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfle 154
                                       ++++t e+n+ttGkiy sv+ekerrGdylG+tvq+iphvtdeik +i++va+k+ ad+++veigGtvgdie++ fle
  gi|488600328|ref|YP_007906799.1|  79 GEEVTGEHNVTTGKIYMSVLEKERRGDYLGSTVQIIPHVTDEIKMWIRNVAEKSGADICLVEIGGTVGDIEGMSFLE 155
                                       ****************************************************999********************** PP

                                       HHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--G CS
                       CTP_synth_N 155 airqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvek 231
                                       a+rq+k+e + e+++l+hvtl+p  +  ge+ktkptqhsvkelrs+G+qpdiiv r++++l e++k+kialfc+v+ 
  gi|488600328|ref|YP_007906799.1| 156 AVRQMKNEEKPEDFALVHVTLIPL-DLGGEQKTKPTQHSVKELRSIGLQPDIIVGRCKERLLESTKKKIALFCDVPV 231
                                       ***********************5.579************************************************* PP

                                       GGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 232 eavisvkdvesiyevpllleeqglaelileklkl 265
                                       eavis++d+e+iyevpl+l+e++++e++++klkl
  gi|488600328|ref|YP_007906799.1| 232 EAVISAHDAEEIYEVPLMLKEEKMDEYLIKKLKL 265
                                       *******************************987 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0   0.0   1.2e-60   4.3e-57       2     190 .]     299     521 ..     298     521 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 1.2e-60
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH.THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile.llknpdgilvsgGpgspgvegkieaikearenkiPiLGI 77 
                                       ++D+y s+ e+l+h ++ +g+kv++v +d++++e ++  + ++dgilv+gG+g++g egki ai++aren+iP+LGI
  gi|488600328|ref|YP_007906799.1| 299 VKDAYISIREALKHGGILAGCKVNMVLVDSEDLERYQdFELDVDGILVPGGFGHRGSEGKILAIQYARENDIPFLGI 375
                                       89*********************************997699************************************ PP

                                       THHHHHHHHHTTTEEE......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEE CS
                            GATase  78 CLGmQllaiefgrkvv......................kekekehhggtmrlgddet........allyglknevie 124
                                       C+G+Ql + ef+r+v                       ++ke +++ggtmrlgd e          +lyg  +++ e
  gi|488600328|ref|YP_007906799.1| 376 CFGFQLSVVEFARNVLgyedahsseladtkhpvidllpEQKEIDKLGGTMRLGDIEVtvkkgtkaFELYGR-EKIVE 451
                                       *************999999999999999999999****9999************8889*****99999**9.9**** PP

                                       EEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHHH CS
                            GATase 125 rhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflika 190
                                       rhrHryevnp+   ele++g++++++s+++ ++mei e+++ + f+++QFHPE++s+p  p+++f ++++a
  gi|488600328|ref|YP_007906799.1| 452 RHRHRYEVNPDyipELEKKGVVFSGTSDSG-RRMEILELPDkRfFFATQFHPEFKSRPYSPSPPFAGFVEA 521
                                       ***************************777.9*********879***********************9975 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.27   9.6e+02      41      67 ..     323     349 ..     301     356 .. 0.81
   2 !   29.2   0.0   1.9e-10     7e-07      97     216 .]     361     503 ..     351     503 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                     Peptidase_C26  41 vllpieedeedvkaildkldgllltGg 67 
                                       ++l  +ed e ++++   +dg+l++Gg
  gi|488600328|ref|YP_007906799.1| 323 MVLVDSEDLERYQDFELDVDGILVPGG 349
                                       445555688888888899********9 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.9e-10
                     Peptidase_C26  97 LiraalergvPilgiCrGlqllnvalGGtl..yqdieeqsgltdhrehe............q.....saashavkve 154
                                        i+ a e+++P lgiC G+ql  v +  ++  y+d+++ s+l d  +h             +          +v+v+
  gi|488600328|ref|YP_007906799.1| 361 AIQYARENDIPFLGICFGFQLSVVEFARNVlgYEDAHS-SELADT-KHPvidllpeqkeidKlggtmRLGDIEVTVK 435
                                       5788999**************99999888734566664.555555.444588888876665155555777899**** PP

                     Peptidase_C26 155 kgsllaellgseeievnslHhqaike.....laeelrveAvaeDgv..iEaieseeakafvlgvQwHPE 216
                                       kg+   el+g+e+i     H+  ++      l+++  v + ++D    +E +e+++++ f+++ Q+HPE
  gi|488600328|ref|YP_007906799.1| 436 KGTKAFELYGREKIVERHRHRYEVNPdyipeLEKKGVVFSGTSDSGrrMEILELPDKR-FFFATQFHPE 503
                                       **********9999999****999877777798888888887765334********55.*********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 !   23.8   0.0     1e-08   3.6e-05       7      55 ..      11     150 ..       4     301 .. 0.71
   2 ?   -0.3   0.0       0.3   1.1e+03      93     120 ..     397     420 ..     353     475 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1e-08
                                       STTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                              CbiA   7 kGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................. 54 
                                        +G GK  +aa+++r+l + g++V+++++Dp  n +a   g+ n  +                              
  gi|488600328|ref|YP_007906799.1|  11 MSGLGKGITAASIGRILTDMGYKVVPIKVDPYLNIDA---GTMNPFQHgevfvlkdgtevdldlghyerfigeevtg 84 
                                       69******************************88887...6666666567777777777777667777777777777 PP

                                       .................................................................C CS
                                       .................................................................x RF
                              CbiA  55 .................................................................d 55 
                                                                                                        +
  gi|488600328|ref|YP_007906799.1|  85 ehnvttgkiymsvlekerrgdylgstvqiiphvtdeikmwirnvaeksgadiclveiggtvgdieG 150
                                       777777777777777777777777777777777776666666666666666666666666665541 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.3
                                       CHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  93 lkealeelkqrygvpvlgviprdeavae 120
                                       +++ l+++    + pv++++p+ +++ +
  gi|488600328|ref|YP_007906799.1| 397 HSSELADT----KHPVIDLLPEQKEIDK 420
                                       44455554....7899999999988765 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.6e-06     0.017       1     107 [.       1     117 [.       1     137 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-06
                                       -EEEEEEE..STTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HH..... CS
                       ArsA_ATPase   1 lkvilvgG..KGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpe..... 70 
                                       +k+i+v+G    G GK   +a+++  l+++g+kv+ i +DP  ++     + +++ +  v +  + v++d       
  gi|488600328|ref|YP_007906799.1|   1 MKYIFVTGgvMSGLGKGITAASIGRILTDMGYKVVPIKVDPYLNIDAGTMNPFQHGEVFVLKDGTEVDLDLGhyerf 77 
                                       899***994447********************************987777778888888877655555555477777 PP

                                       ..HHHHHHHC.CHHGGGSCCHHHHHHHHHHHHHHTSSTTH CS
                       ArsA_ATPase  71 ..veleeakq.evqkeeeallgleeledvlaeelaslPGi 107
                                         +e+  +++  + k + ++l+ e   d l ++++++P +
  gi|488600328|ref|YP_007906799.1|  78 igEEVTGEHNvTTGKIYMSVLEKERRGDYLGSTVQIIPHV 117
                                       7655544333133445556677777778888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      821  (0.0457917); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3729.47
//
Query:       gi|488600329|ref|YP_007906800.1|  [L=62]
Description: hypothetical protein Asulf_00796 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-12   46.0   2.1    9.8e-12   45.3   2.1    1.4  1  Trm112p          Trm112p-like protein
    9.6e-05   22.4   0.0     0.0001   22.3   0.0    1.1  1  Elf1             Transcription elongation factor Elf1 like
    0.00041   20.7   0.2    0.00046   20.5   0.2    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0029   17.9   1.2      0.011   16.0   1.2    1.8  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
  ------ inclusion threshold ------
      0.016   15.1   0.3       0.21   11.5   0.0    2.2  2  zinc_ribbon_4    zinc-ribbon domain
      0.045   13.3   3.2        0.2   11.2   3.2    1.9  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.068   13.1   2.1       0.43   10.6   2.1    2.0  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.094   11.8   0.1      0.098   11.7   0.1    1.0  1  Tmemb_55A        Transmembrane protein 55A
       0.16   11.6   1.0       0.33   10.6   0.1    1.9  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.17   11.9   1.5       0.35   10.9   0.1    1.8  2  DUF1451          Zinc-ribbon containing domain


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 !   45.3   2.1   5.5e-15   9.8e-12       1      68 []       2      49 ..       2      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5.5e-15
                                      BTGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS
                           Trm112p  1 kllllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68
                                      k+ ll+iLaCp+ckg L     +ev++        ek    e     +i+ g+L+C++c+  YpI+dG
  gi|488600329|ref|YP_007906800.1|  2 KRQLLDILACPVCKGDL----TLEVEE--------EKD---E-----EIIAGTLICEKCNEKYPIEDG 49
                                      689************99....222222........222...3.....7889****************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 !   22.3   0.0   5.8e-08    0.0001      16      57 ..       3      46 ..       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.8e-08
                              Elf1 16 kklptkFdCpfCnheksvevkldkkek..iaevsCkvCgesfet 57
                                      ++l     Cp+C+ + ++ev+ +k e+   +++ C++C+e++ +
  gi|488600329|ref|YP_007906800.1|  3 RQLLDILACPVCKGDLTLEVEEEKDEEiiAGTLICEKCNEKYPI 46
                                      45788899*****************998889*********9975 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   2.6e-07   0.00046       3      36 ..       8      42 ..       6      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.6e-07
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigq.cvyCadCga 36
                                      ++ CP C+g+ +le ++ +++ei   + +C++C+ 
  gi|488600329|ref|YP_007906800.1|  8 ILACPVCKGDLTLEVEEEKDEEIIAgTLICEKCNE 42
                                      789******************99889*******96 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.2   5.9e-06     0.011       5      34 ..      10      46 ..       8      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.9e-06
                                      --TTTT-TTTEEETT........S-EEETTT.TB..X CS
                    Prim_Zn_Ribbon  5 pCPvCGGrDrFrfddkdgr....GtwfCrqC.gg..g 34
                                      +CPvC+G      ++++      Gt +C +C ++   
  gi|488600329|ref|YP_007906800.1| 10 ACPVCKGDLTLEVEEEKDEeiiaGTLICEKCnEKypI 46
                                      7***********66555555***********433554 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.11     2e+02       4       9 ..      10      15 ..       8      26 .. 0.76
   2 ?   11.5   0.0   0.00012      0.21       4      16 ..      36      48 ..      34      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                     zinc_ribbon_4  4 tCpsCk 9 
                                       Cp Ck
  gi|488600329|ref|YP_007906800.1| 10 ACPVCK 15
                                      677776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                     zinc_ribbon_4  4 tCpsCkakyeidd 16
                                       C++C+ ky i+d
  gi|488600329|ref|YP_007906800.1| 36 ICEKCNEKYPIED 48
                                      6**********98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.2   0.00011       0.2       2      25 ..      10      40 ..       9      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                      EETTTTCEE.C....HEETS..TTCEEESSS CS
                      TF_Zn_Ribbon  2 kCPnCgstn.l....veDpe..rgelvCtdC 25
                                       CP+C+++  l    + D+e   g+l+C++C
  gi|488600329|ref|YP_007906800.1| 10 ACPVCKGDLtLeveeEKDEEiiAGTLICEKC 40
                                      5******995676665553344799****** PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.1   0.00024      0.43       4      26 ..      10      41 ..       7      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                    PhnA_Zn_Ribbon  4 kCplCaSeytY.....edgal....lvCpeCa 26
                                      +Cp C+ + t+      d ++    l+C++C 
  gi|488600329|ref|YP_007906800.1| 10 ACPVCKGDLTLeveeeKDEEIiagtLICEKCN 41
                                      5************9994444333339*****6 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.5e-05     0.098      57      92 ..       7      48 ..       1      53 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                         Tmemb_55A 57 pvitCrvCqs..lidvegkleqhvvk....CevCneatpikn 92
                                       +++C vC+    ++ve+ ++  ++     Ce+Cne  pi +
  gi|488600329|ref|YP_007906800.1|  7 DILACPVCKGdlTLEVEEEKDEEIIAgtliCEKCNEKYPIED 48
                                      5789****8622678888888888744455*********986 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.71   1.3e+03       5       9 ..      11      15 ..       8      26 .. 0.81
   2 ?   10.6   0.1   0.00018      0.33       2      15 ..      34      47 ..      33      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.71
                            zf_UBZ  5 CerCg 9 
                                      C+ C+
  gi|488600329|ref|YP_007906800.1| 11 CPVCK 15
                                      99896 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00018
                            zf_UBZ  2 tylCerCgkeipes 15
                                      t +Ce+C+++ p++
  gi|488600329|ref|YP_007906800.1| 34 TLICEKCNEKYPIE 47
                                      789*******9987 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.39   7.1e+02     132     141 ..       8      17 ..       3      20 .. 0.79
   2 ?   10.9   0.1   0.00019      0.35     107     126 ..      27      46 ..      17      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.39
                           DUF1451 132 ippCpkCgat 141
                                       i +Cp C+++
  gi|488600329|ref|YP_007906800.1|   8 ILACPVCKGD 17 
                                       7889999875 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                           DUF1451 107 GevvglGtlvCekCgkelal 126
                                        e + +Gtl+CekC+++  +
  gi|488600329|ref|YP_007906800.1|  27 DEEIIAGTLICEKCNEKYPI 46 
                                       577889*********99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 434.64
//
Query:       gi|488600330|ref|YP_007906801.1|  [L=236]
Description: conserved hypothetical integral membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-55  185.1  10.9    9.3e-55  185.1  10.9    1.6  2  Vut_1     Putative vitamin uptake transporter
  ------ inclusion threshold ------
      0.032   14.9   2.1      0.032   14.9   2.1    3.0  3  DUF2809   Protein of unknown function (DUF2809)


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 ?   -2.4   0.7       0.6   5.3e+03      98     102 ..      36      40 ..       8      57 .. 0.41
   2 !  185.1  10.9     1e-58   9.3e-55       2     149 ..      60     225 ..      59     226 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.6
                             Vut_1  98 lrnig 102
                                       ++ ++
  gi|488600330|ref|YP_007906801.1|  36 TAMAI 40 
                                       21111 PP

  == domain 2  score: 185.1 bits;  conditional E-value: 1e-58
                             Vut_1   2 aGvllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa.......ealesvfgltprivlasli 71 
                                       +G++++ +tfl+tdi+ e yGk+ ark+v++gf++ ++++i+++l+l++ +        ale++f+l pri++asl+
  gi|488600330|ref|YP_007906801.1|  60 MGNIIYGSTFLVTDILCENYGKESARKAVMIGFFTLIFTTIIMQLCLAFIPdqsdtlsPALEQIFSLLPRITVASLT 136
                                       8*********************************************99999899999999***************** PP

                             Vut_1  72 aylvsqlldvyvfhrlkkltkgkklwlrnigStlvsqlvdtlifvtiaflg...........eqlleiilsqylikl 137
                                       ay++sq++dv++f+++k++tkgk+lwlrn++St+vsql+d+++f++iaf+g           e++ ei++++y++k+
  gi|488600330|ref|YP_007906801.1| 137 AYIISQFHDVWAFDFWKRKTKGKHLWLRNNASTMVSQLIDNAVFTWIAFVGfgifweqvfpwEVIAEIFITSYIMKF 213
                                       *************************************************88************************** PP

                             Vut_1 138 lialldtplvyl 149
                                       ++a+ldtp+vyl
  gi|488600330|ref|YP_007906801.1| 214 IVAVLDTPFVYL 225
                                       ***********7 PP

>> DUF2809  Protein of unknown function (DUF2809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.1   3.6e-06     0.032      13      81 ..       7      76 ..       2      80 .. 0.73
   2 ?   -0.8   0.1      0.27   2.4e+03      36      47 ..      91     102 ..      83     127 .. 0.54
   3 ?    1.6   2.4      0.05   4.5e+02       5      48 ..     170     213 ..     167     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-06
                           DUF2809 13 vlvvillyllvrllvp..kksplllalavllfavliEllQltqlpallglrattlgrlvLGstfdwsDlla 81
                                      +l+ ill++ +  +    +   +  + a  ++a++i  +Q++++++  gl  t +g+++ Gstf + D+l+
  gi|488600330|ref|YP_007906801.1|  7 ILWFILLIVNFSGITLayRLFGKSGLYAWTAMAIIIANIQVMKTIKFFGLV-TAMGNIIYGSTFLVTDILC 76
                                      5555555554444444222222223455678999*****************.*****************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                           DUF2809  36 alavllfavliE 47 
                                        +++l+f+ +i 
  gi|488600330|ref|YP_007906801.1|  91 GFFTLIFTTIIM 102
                                       455555555443 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.05
                           DUF2809   5 firkylGdvlvvillyllvrllvpkksplllalavllfavliEl 48 
                                       ++ + + +++++ + ++++ ++++++ p+ +++ +++ +++  +
  gi|488600330|ref|YP_007906801.1| 170 MVSQLIDNAVFTWIAFVGFGIFWEQVFPWEVIAEIFITSYIMKF 213
                                       6777788888999999**************99999999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1626.59
//
Query:       gi|488600331|ref|YP_007906802.1|  [L=397]
Description: tRNA-guanine transglycosylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  406.1   0.0   2.3e-120  402.0   0.0    1.9  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.0   0.0  1.3e-124  2.3e-120       3     345 ..      12     394 ..      10     396 .. 0.95

  Alignments for each domain:
  == domain 1  score: 402.0 bits;  conditional E-value: 1.3e-124
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EE CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpil 79 
                                        R+G ++++hg+++tP+f+pv+t ++v+gl  ++lk e+ga+++l+ntyhl+lrpg+e+++k gglhkf+++d pi+
  gi|488600331|ref|YP_007906802.1|  12 MRTGVVKTKHGKFNTPVFIPVATLASVRGLDNRDLK-EMGAEVLLANTYHLHLRPGDEVIKKLGGLHKFMNIDLPIV 87 
                                       6**********************************5.99************************************** PP

                                       EE-SHHHHHHH.........................E.....EEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-S CS
                               TGT  80 tdsggfqvfsl.........................k.....kiteegvsfqsridGskvlltpeesieiqeklgsD 126
                                       tdsggfq fsl                         k      +++ gv+f+++i+G+ v+ltp++s+eiq++lgsD
  gi|488600331|ref|YP_007906802.1|  88 TDSGGFQAFSLgfgmehgvgkiannifleglkdidfKgekwaYVDDRGVRFKNHISGEIVELTPRKSMEIQSNLGSD 164
                                       **********999***9999999888887776555415556566********************************* PP

                                       EEE-------SS--HHHHHHHHHHHHHHHHHHHHHH...SEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-SSSS CS
                               TGT 127 iimalddvvpspaskkrveksverTlrwldrcleah...qalfgivqGglyedlreesaeelakrdfdgyaigGlsv 200
                                       ii a+d+++++ ++kk+ e ++erT+rw+++cl+++   qa+fgivqGg y+dlre+sa+ +a+rdfdg+ igG s+
  gi|488600331|ref|YP_007906802.1| 165 IIFAFDECTSPLSDKKYTEIALERTHRWAEECLQYYnkkQAIFGIVQGGEYRDLRERSAKFMAERDFDGFGIGG-SL 240
                                       *********************************88888899*********************************.99 PP

                                       SSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEE..TTE.......EEE CS
                               TGT 201 geekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngralt..seg.......eln 268
                                       g++k+++ +++e v++llpe+kpr+l G+g  edl +++++GvDmfdcv+ptr ar+g++++  +eg       +++
  gi|488600331|ref|YP_007906802.1| 241 GKSKRDMHNILEWVIPLLPEEKPRHLLGIGAVEDLFNCIERGVDMFDCVAPTRWARRGHLYIspEEGgkpenkfRIH 317
                                       **************************************************************5513367777779** PP

                                       TTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                               TGT 269 lknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefa 345
                                       +knak++ d++p+d +C+C +C++y+rayl+hl+ ++e++  +L+++HN++++++l+++iR++I++g f e++++++
  gi|488600331|ref|YP_007906802.1| 318 IKNAKFRFDTNPVDRSCDCFVCQEYSRAYLRHLYVSNELTYFRLASYHNVYFIIRLVEKIRDSIESGAFYELKKRWL 394
                                       **************************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2548.81
//
Query:       gi|488600332|ref|YP_007906803.1|  [L=711]
Description: hypothetical protein Asulf_00800 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-05   23.0   0.7    0.00084   19.6   0.1    3.0  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00093   19.2   0.1     0.0042   17.0   0.1    2.1  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0088   16.4   0.0      0.036   14.4   0.0    2.0  1  DUF4198          Domain of unknown function (DUF4198)
  ------ inclusion threshold ------
      0.021   14.8   0.8      0.058   13.4   0.8    1.8  1  PGF-CTERM        PGF-CTERM motif
       0.17   11.3   0.0       0.29   10.6   0.0    1.3  1  DUF5046          Domain of unknown function (DUF5046)


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 !   19.6   0.1   2.3e-07   0.00084       5      72 ..      45     108 ..      41     113 .. 0.85
   2 ?   -2.8   0.0       2.3   8.3e+03      35      45 ..     196     206 ..     192     227 .. 0.81
   3 ?   -4.0   0.0         5   1.8e+04      37      45 ..     471     479 ..     468     483 .. 0.79
   4 ?   -1.0   0.0       0.6   2.1e+03      44      73 ..     656     685 ..     650     693 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.3e-07
                   CarboxypepD_reg   5 rVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltag 72 
                                       ++  + sg p++g+tV +       v   ttd+dG+ +  +  pg y + +s+ Gy +a++ ++++++ 
  gi|488600332|ref|YP_007906803.1|  45 KIIESlSGDPVEGVTVYIN-----GVEIGTTDEDGKITYVFNSPGVYLIGASKFGYTPAASLSLSVEPR 108
                                       5666669************.....677789******999999*****************9877777665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                   CarboxypepD_reg  35 dadGafrlrgl 45 
                                       +++G++r++g 
  gi|488600332|ref|YP_007906803.1| 196 EKSGYYRIEGY 206
                                       56899999875 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 5
                   CarboxypepD_reg  37 dGafrlrgl 45 
                                       dG+++l+g+
  gi|488600332|ref|YP_007906803.1| 471 DGKYTLKGV 479
                                       799999886 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.6
                   CarboxypepD_reg  44 glppgtysvtvsapGyatatreevtltagq 73 
                                       +lpp ty+ ++  +  +  + +ev++++g 
  gi|488600332|ref|YP_007906803.1| 656 NLPPLTYEAKIIVEAEDKKAESEVEVAVGL 685
                                       899988888776666666666678887775 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 !   17.0   0.1   1.2e-06    0.0042       4      58 ..      45      98 ..      45     118 .. 0.83
   2 ?   -3.9   0.0       4.1   1.5e+04      32      40 ..     470     478 ..     464     480 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-06
                   CarbopepD_reg_2  4 tVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktq 58
                                      +++++ +++p++g+tVy++g + gt Tde+G+ +     +g y + +s  Gy+++
  gi|488600332|ref|YP_007906803.1| 45 KIIESLSGDPVEGVTVYINGVEIGT-TDEDGKITYVFNSPGVYLIGASKFGYTPA 98
                                      5888999****************97.9****866655678************985 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.1
                   CarbopepD_reg_2  32 enGnFelkn 40 
                                        +G+++lk 
  gi|488600332|ref|YP_007906803.1| 470 VDGKYTLKG 478
                                       578888875 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     1e-05     0.036     144     209 ..      33      90 ..      27      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                           DUF4198 144 pydlkageelevqvl..ldGkPlagaeveveyggtryrdapdeikv.ktdadGvvtftlpkaGlwllea 209
                                       p+   +g+e+e+++   l G P++g++v +             +++ +td+dG++t+ + ++G++l+ a
  gi|488600332|ref|YP_007906803.1|  33 PSRAMVGDEVEIKIIesLSGDPVEGVTVYIN-----------GVEIgTTDEDGKITYVFNSPGVYLIGA 90 
                                       6667788889988888899999999999973...........344459******************987 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   1.6e-05     0.058       1      15 [.     688     702 ..     688     707 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                         PGF-CTERM   1 tPGFGavlAlaGLLa 15 
                                       tPGF++v+Al+  ++
  gi|488600332|ref|YP_007906803.1| 688 TPGFEVVIALISVAG 702
                                       9**********9876 PP

>> DUF5046  Domain of unknown function (DUF5046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     8e-05      0.29     189     235 ..     449     497 ..     407     507 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8e-05
                           DUF5046 189 lf.ygaaaGp..dgkslydvldaeGnvvlkglascysyysnslndlPddv 235
                                       l+ +g  +G   +++s+ dv+  +G+  lkg+ +  s   nsl  +P  v
  gi|488600332|ref|YP_007906803.1| 449 LLgFG-ITGFehNYSSIGDVVSVDGKYTLKGVVLTASLLDNSLPSVPVLV 497
                                       33344.3332459******************************9999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 4576.35
//
Query:       gi|488600333|ref|YP_007906804.1|  [L=317]
Description: Pyruvate-formate lyase-activating enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-15   57.1   0.0    5.8e-15   56.1   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    1.9e-07   31.4   0.3    3.7e-07   30.5   0.3    1.5  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.032   14.6   0.9      0.072   13.4   0.9    1.6  1  FpoO         F420H2 dehydrogenase subunit FpoO
       0.41   10.0   2.4        1.9    7.9   3.5    1.5  2  EURL         EURL 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 !   56.1   0.0   1.3e-18   5.8e-15       2     164 ..     104     259 ..     103     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.3e-18
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       v++ gCn++C +C+++e+    + gr++s++  +e + + +    +k +  +gg p  +  f+    r + ++ ++i
  gi|488600333|ref|YP_007906804.1| 104 VFYYGCNFDCLYCQNWEH---KKAGRIISLDVAVEYAMKDR----IKCICHFGGSPEPQLQFAIRFSRKVLKE-RDI 172
                                       6789*************6...*******************9....*****************99999999986.*** PP

                                       EEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                        i+ e ng+  +   +e ++   e    +v ++l+a++d    k++  g +++ +l++++++ + + ++v+ +++++
  gi|488600333|ref|YP_007906804.1| 173 MICWEWNGGGREkfvKEAVKISSESK-GTVKFDLKAWNDN-LYKIL-TGRSNKPTLKNFKLAYDIDPEVVSATTLLV 246
                                       **********6466666666666655.*************.*****.99***************9766655555555 PP

                                       TTTSH.HHHHHHH CS
                                       xxxxx.xxxxxxx RF
                       Radical_SAM 153 pGend.eeleell 164
                                       p + d +e+e ++
  gi|488600333|ref|YP_007906804.1| 247 PYYVDeKEVEGIA 259
                                       5555415555555 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.3   8.3e-11   3.7e-07       5     107 ..      99     193 ..      95     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 8.3e-11
                           Fer4_12   5 GvrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevke 81 
                                       G+ l++f  gCn+ C +C n e +  k+g+ ++ +    ++e ++k++i+ +  +GG P    + +  +++ ++v +
  gi|488600333|ref|YP_007906804.1|  99 GTNLAVFYYGCNFDCLYCQNWEHK--KAGRIISLD---VAVEYAMKDRIKCICHFGGSPEP--QLQFAIRFSRKVLK 168
                                       78899*************976665..556666644...4566778999***********99..99*********999 PP

                           Fer4_12  82 ekpekdiwlytgytleelskkekeel 107
                                       e     +w+++g   e++ k+   ++
  gi|488600333|ref|YP_007906804.1| 169 ERDIMICWEWNGGGREKFVKE-AVKI 193
                                       988789******999999865.4444 PP

>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   1.6e-05     0.072      36      71 ..      17      54 ..       9      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                              FpoO 36 lcekclkaakktydelskeeasgtaG..kcdlcgkktr 71
                                      lc +c+ +  +t+d+ s++  ++++G  kc lc + ++
  gi|488600333|ref|YP_007906804.1| 17 LCADCIRTNPETADKISRTLHKSVSGdrKCSLCENFCN 54
                                      9************************999*****98876 PP

>> EURL  EURL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.5   0.00042       1.9      18      61 ..       3      46 ..       1      58 [. 0.91
   2 ?   -3.0   0.0      0.88   3.9e+03       9      50 ..     202     245 ..     196     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00042
                              EURL 18 csvcklgtdketlsfchvcfelnieGvpksdllhtkslrGhkdc 61
                                      c +c  +t++et+ +c  c   n e   k +    ks+ G + c
  gi|488600333|ref|YP_007906804.1|  3 CLICNRETHTETIPLCADCIRTNPETADKISRTLHKSVSGDRKC 46
                                      99*************************997766669******99 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.88
                              EURL   9 sidln..ddnicsvcklgtdketlsfchvcfelnieGvpksdll 50 
                                       + dl+  +dn+  +    ++k tl   ++ ++++ e v+ ++ll
  gi|488600333|ref|YP_007906804.1| 202 KFDLKawNDNLYKILTGRSNKPTLKNFKLAYDIDPEVVSATTLL 245
                                       55665336899999999999999999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1974.51
//
Query:       gi|488600334|ref|YP_007906805.1|  [L=262]
Description: hypothetical protein Asulf_00803 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-21   74.6   0.0      1e-20   74.0   0.0    1.3  1  FMN_red         NADPH-dependent FMN reductase
    3.5e-11   43.2   0.0    4.3e-11   42.9   0.0    1.2  1  Flavodoxin_2    Flavodoxin-like fold
     0.0058   16.1   1.1      0.015   14.8   1.1    1.7  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
       0.22   11.6   8.6          1    9.4   0.1    3.3  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.63    9.7   6.2         10    5.8   1.4    3.5  3  RecR            RecR protein
        0.9    9.4   0.1        0.9    9.4   0.1    3.8  5  Rad50_zn_hook   Rad50 zinc hook motif
        3.8    7.3   6.7        5.1    6.9   0.0    2.7  3  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII


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 !   74.0   0.0     4e-24     1e-20       2     140 ..       4     142 ..       3     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 4e-24
                                       EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--...---HCHGHTCGGSHHHHHHHHHHHH-SCE CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc.alcdkdlesegqtsddvaellekiaaadal 76 
                                       k+l i+ + rk++n+  + +++a+al   +ae+e+i+l ++ i pc a + +   ++++ +ddv+e+l+ki ++d+l
  gi|488600334|ref|YP_007906805.1|   4 KLLSIVSTERKKGNSVLASKYIAKAL---NAELEIINLVKKdIRPCkACYRCLYGEDCKIDDDVEEILRKIDECDVL 77 
                                       7899**********************...79***************9555544544579****************** PP

                                       EEEEEECTTCE-HHHHHHHHCHT-..SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT- CS
                           FMN_red  77 iivtPeYngsysgllKnalDrlsr.trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elga 140
                                       +i++P+Y+  ++g lK+++Dr+ + ++  + +++K +++++ +g      + +++   vla +lg+
  gi|488600334|ref|YP_007906805.1|  78 LISSPVYWLDATGNLKAFIDRCFMsMKYFERFKNKKGVVLTFHGF-EDMKGWASATHLVLAkVLGV 142
                                       **********************99888888999999999988865.45555555555555555555 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.7e-14   4.3e-11       1     137 [.       3     123 ..       3     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.7e-14
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT.CHHHHHHH.HHHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek.padveseq.iekl 75 
                                       +k+L i++  r+  + +s la ++++++ +a+    ++++L +  +  +++ ++     y e  ++d + e+ + k+
  gi|488600334|ref|YP_007906805.1|   3 KKLLSIVSTERK--KGNSVLASKYIAKALNAE---LEIINLVKKDIRPCKA-CYR--CLYGEDcKIDDDVEEiLRKI 71 
                                       688999999998..455999999999988877...89******75544444.222..3555553599999999**** PP

                                       HCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS- CS
                      Flavodoxin_2  76 laadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgp 137
                                        ++d++++++P++w+     lK++iDr +   ++f          +++k+kk +v++  G+ 
  gi|488600334|ref|YP_007906805.1|  72 DECDVLLISSPVYWLDATGNLKAFIDRCFMSMKYF----------ERFKNKKGVVLTFHGFE 123
                                       ***********************************..........57888888887777766 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.1     6e-06     0.015       2      32 ..     185     213 ..     184     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6e-06
                                       EETTTTCEECHEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVledn 32 
                                       +CP+C +t  v+    g l C+ CG++l+ +
  gi|488600334|ref|YP_007906805.1| 185 QCPVCLNT--VFRVIDGKLDCPVCGSLLDTE 213
                                       8*****98..888888***********9976 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.5      0.24     6e+02      16      25 ..      48      58 ..      38      59 .. 0.86
   2 ?    4.5   0.1     0.014        37       1      11 [.     185     195 ..     185     200 .. 0.73
   3 ?    9.4   0.1    0.0004         1       2       9 ..     203     210 ..     202     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.24
                    DNA_ligase_ZBD 16 aiyRCt.nlsC 25
                                      a yRC  + +C
  gi|488600334|ref|YP_007906805.1| 48 ACYRCLyGEDC 58
                                      66****99999 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CPvC   v R
  gi|488600334|ref|YP_007906805.1| 185 QCPVCLNTVFR 195
                                       5****777666 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0004
                    DNA_ligase_ZBD   2 CPvCGsav 9  
                                       CPvCGs +
  gi|488600334|ref|YP_007906805.1| 203 CPVCGSLL 210
                                       *****965 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.4     0.004        10       9      24 ..      36      51 ..      33      60 .. 0.77
   2 ?    1.0   0.0      0.13   3.2e+02      30      36 ..     185     191 ..     171     193 .. 0.70
   3 ?    2.8   0.0     0.034        88      19      29 ..     203     213 ..     197     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.004
                                      HHHHHHH-EE-TTT-- CS
                              RecR  9 LqeakekvrhCsrCgn 24
                                      ++ +k+++r+C+ C+ 
  gi|488600334|ref|YP_007906805.1| 36 INLVKKDIRPCKACYR 51
                                      6669**********75 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                                       S-CCCCS CS
                              RecR  30 lCaICsd 36 
                                        C++C +
  gi|488600334|ref|YP_007906805.1| 185 QCPVCLN 191
                                       3666655 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.034
                                       -TTT--EESSS CS
                              RecR  19 CsrCgnlteed 29 
                                       C++Cg l +++
  gi|488600334|ref|YP_007906805.1| 203 CPVCGSLLDTE 213
                                       *****998877 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.6   9.3e+03      37      49 ..      20      32 ..      15      35 .. 0.62
   2 ?   -3.1   0.1       2.8   7.3e+03      32      41 ..      62      71 ..      61      73 .. 0.65
   3 ?    3.6   0.0     0.023        60      20      25 ..     184     189 ..     162     192 .. 0.75
   4 ?    9.4   0.1   0.00035       0.9      21      32 ..     202     213 ..     197     215 .. 0.86
   5 ?   -0.4   0.3      0.41   1.1e+03      34      46 ..     243     255 ..     239     260 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.6
                                      HHHHHHHHHHHHH CS
                     Rad50_zn_hook 37 Likelqsklerlp 49
                                      L++++ +k  + +
  gi|488600334|ref|YP_007906805.1| 20 LASKYIAKALNAE 32
                                      5666766666554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                                      HHHHHHHHHH CS
                     Rad50_zn_hook 32 ehrseLikel 41
                                      ++ +e+++++
  gi|488600334|ref|YP_007906805.1| 62 DDVEEILRKI 71
                                      5577888776 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.023
                                       EE-TTT CS
                     Rad50_zn_hook  20 gcCPlC 25 
                                       g CP+C
  gi|488600334|ref|YP_007906805.1| 184 GQCPVC 189
                                       59**** PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00035
                                       E-TTT--EE-HH CS
                     Rad50_zn_hook  21 cCPlCgReldee 32 
                                       +CP+Cg+ ld+e
  gi|488600334|ref|YP_007906805.1| 202 DCPVCGSLLDTE 213
                                       7********997 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHH CS
                     Rad50_zn_hook  34 rseLikelqskle 46 
                                        +e+ +el+ ++e
  gi|488600334|ref|YP_007906805.1| 243 YKEIKDELKRQTE 255
                                       4566666666665 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.0       1.7   4.4e+03       6      15 ..      45      54 ..      44      57 .. 0.64
   2 ?    6.9   0.0     0.002       5.1       6      21 ..     185     200 ..     182     201 .. 0.90
   3 ?    3.7   0.1     0.019        48       7      12 ..     203     208 ..     200     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                           zf-RRN7  6 pCgvCgcrsf 15
                                      pC +C  +++
  gi|488600334|ref|YP_007906805.1| 45 PCKACYRCLY 54
                                      7888855555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.002
                           zf-RRN7   6 pCgvCgcrsftlddGf 21 
                                       +C+vC ++ f+ +dG+
  gi|488600334|ref|YP_007906805.1| 185 QCPVCLNTVFRVIDGK 200
                                       7*************97 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.019
                           zf-RRN7   7 CgvCgc 12 
                                       C+vCg+
  gi|488600334|ref|YP_007906805.1| 203 CPVCGS 208
                                       *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1660.11
//
Query:       gi|488600335|ref|YP_007906806.1|  [L=282]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-71  240.3   0.0      2e-71  240.1   0.0    1.0  1  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.1   0.0   1.1e-75     2e-71       1     219 [.       8     263 ..       8     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 240.1 bits;  conditional E-value: 1.1e-75
                            DUF166   1 lvltsgeyGervvenilnepdfersl.....................ivavvevpe..eldefiedpeelLpe.lke 53 
                                       +v+++g +Ger+++n++n++++++s+                     iva++ +    ++++fied+e++Lp+ +++
  gi|488600335|ref|YP_007906806.1|   8 VVFYNGFFGERFIANLMNYSNSCPSFgacgldqcvqckqgaysfsknIVATFGLLSreNMPDFIEDAEDFLPKkIPK 84 
                                       699********************************************99999988777******************* PP

                            DUF166  54 aDiviaytlhpDlllelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCslee.egkpkid 126
                                       aDi++a+++hpD+l++l+ek+ke+++kalivp+e+p+   agl+k+lke++ e+g+e+a+pkpfC l++ e  p+i+
  gi|488600335|ref|YP_007906806.1|  85 ADIAVAINIHPDILMALPEKLKESGFKALIVPVEEPRwcsAGLAKQLKESCTEIGLEFAAPKPFCLLRKsEDTPTIN 161
                                       *********************************************************************9999**** PP

                            DUF166 127 eFlee..fGkPelevevkdgki....kkVeVlrsapCGstwyvakklkGkeveeaeeka...geahqsYpClAsmer 194
                                       +F++e  +G+Pe+ev+v+d +     k+ +V+rs+pCG+ wy+  kl+ +e+++++e +   +  h+s+pC+Asme+
  gi|488600335|ref|YP_007906806.1| 162 RFIDEmgIGYPEFEVDVEDSRGvkkiKNFRVIRSQPCGAGWYIGIKLREFEFKDMRELWdrvSSSHHSFPCTASMEK 238
                                       ******************65433234999***************************999999*************** PP

                            DUF166 195 dfelketklhkAgyihkeavekAlk 219
                                       d+e++et lh+Agy +++av+kA++
  gi|488600335|ref|YP_007906806.1| 239 DNEYNETLLHVAGYTARHAVDKAIG 263
                                       ***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 00:00:00.41
# Mc/sec: 2052.17
//
Query:       gi|488600336|ref|YP_007906807.1|  [L=767]
Description: Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   99.1   0.0    4.4e-28   98.2   0.0    1.4  1  DEAD        DEAD/DEAH box helicase
    1.3e-19   70.6   0.1    3.4e-17   62.8   0.1    2.5  2  Helicase_C  Helicase conserved C-terminal domain
    1.9e-09   38.1   0.0    4.3e-09   37.0   0.0    1.6  1  DUF1998     Domain of unknown function (DUF1998)
     0.0019   18.3   0.0      0.005   16.9   0.0    1.7  2  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
        0.2   12.0   0.0       0.54   10.6   0.0    1.8  1  AAA_19      AAA domain
       0.27   11.4   4.0         25    5.1   0.0    3.4  3  zf-RING_7   C4-type zinc ribbon domain
        3.7    6.4   5.9       0.32    9.9   0.3    1.8  2  VESA1_N     Variant erythrocyte surface antigen-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 !   98.2   0.0   1.7e-31   4.4e-28       2     173 ..      94     256 ..      93     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.7e-31
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       + Q+ ai+ +l+g++v++ a+TG GKT+af+ip++++v     ++  k +i+ Pt++La ++  +++ + +y++lr+
  gi|488600336|ref|YP_007906807.1|  94 NFQKDAIEFLLDGKNVVITAPTGFGKTEAFVIPMIERV-----RNYGKGIIIYPTKALAADQELKIRHYSEYCGLRA 165
                                       57*********************************999.....56679***************************** PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddll.stgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                         + g+++ar+ +++l+ + di++++p++ld +l +t +++  ++++ fl +DE + ++    +  +  ++++l++ 
  gi|488600336|ref|YP_007906807.1| 166 IRFDGDSTARERRDVLNGRFDILLTNPDMLDYHLrNTAEFRkvVKDLCFLAVDELHYYSGI-IGANLYYLIRRLKRF 241
                                       *99999999*******555*************99867776677*****************9.************533 PP

                                       CTTSTTTSEEEEEESSBSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 153 tcdgklqrqvivlSATlpkdv 173
                                             + q+ + SATl+ + 
  gi|488600336|ref|YP_007906807.1| 242 -----RNFQIACASATLS-NA 256
                                       .....4567********8.44 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.011        27      11      60 ..     129     182 ..     120     191 .. 0.73
   2 !   62.8   0.1   1.3e-20   3.4e-17       6     111 .]     294     396 ..     289     396 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                                       HHTTTTSEEEEEESSHH.HHHH...HHHHHHHT..TSTEEEESTTSTHHHHHHHHH CS
                        Helicase_C  11 kleeeggkilifvntid.rlek...vklllekk..gikvavlhgelpqnereeile 60 
                                       ++ ++ gk +i+ +t+   +++   ++     +  g+++++++g+ +++er+++l+
  gi|488600336|ref|YP_007906807.1| 129 ERVRNYGKGIIIYPTKAlAADQelkIRHYS--EycGLRAIRFDGDSTARERRDVLN 182
                                       556777888999999996444343333333..256*****************9996 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 1.3e-20
                                       HHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                        Helicase_C   6 llellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                       + +++ ++  ++k+lif n+ +++e + + l+++gi++a++ + l ++ r+e+ ++f++ge++v+++t+ +e G+di
  gi|488600336|ref|YP_007906807.1| 294 ISDIV-KSFPDKKVLIFGNSYRSVEYFAFTLNRQGIRAAIHKAGLRKDVRKEVERRFRDGEIKVVVSTSTLELGVDI 369
                                       45555.56689*************7777779999******************************************* PP

                                       TTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        +v++V+   +     ++iqr GR+gR+g
  gi|488600336|ref|YP_007906807.1| 370 GDVDVVVSEIVS--FPHFIQRLGRAGRMG 396
                                       *******54443..349**********86 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.7e-12   4.3e-09       1      82 [.     645     719 ..     645     720 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.7e-12
                           DUF1998   1 lehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCee. 76 
                                       leh+li+   +  +  +s++g+ ++         +  i+iyda+ gG+G+++ +++ le+ +r  ++++++c+C + 
  gi|488600336|ref|YP_007906807.1| 645 LEHVLIETSDMLTGGGSSQIGGIST--------PDGDIFIYDASFGGSGLSRLLFKRLERAFRISYDVLKNCKC-Gr 712
                                       6899999999999999999999997........4578*************************************.44 PP

                           DUF1998  77 .aGCpaC 82 
                                        +GCp+C
  gi|488600336|ref|YP_007906807.1| 713 iEGCPSC 719
                                       79***** 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 !   16.9   0.0     2e-06     0.005       6     146 ..      94     225 ..      89     255 .. 0.72
   2 ?   -1.9   0.0       1.1   2.8e+03      74     118 ..     241     294 ..     228     310 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                       + Q++aie ll      + k+++i ++TG GKT    + +ier+++  +  k +++ p+k+l    + +++++++ +
  gi|488600336|ref|YP_007906807.1|  94 NFQKDAIEFLL------DGKNVVITAPTGFGKTEAFvIPMIERVRNY-G--KGIIIYPTKALAADQELKIRHYSEYC 161
                                       55666665555......57899************9978888888884.4..79************998888888887 PP

                                       ...GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-S..EEEEETGGGTTS CS
                            ResIII  82 ykeigkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfd..viiiDEaHrlga 146
                                         +    ++gd+  +  +   +   +il+t+ ++ld ++    +++ e+++  +d  ++ +DE H +++
  gi|488600336|ref|YP_007906807.1| 162 GLR-AIRFDGDSTARerRDVLNGRFDILLTNPDMLDYHL----RNTAEFRKVVKDlcFLAVDELHYYSG 225
                                       664.3334444444422234678889*************....55556655555555677999999876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                       GGGGTGG........GEEEESSS-B--............-SEEEEEHHHHHHTH CS
                            ResIII  74 fkkflseayke....igkkvsgdkkka.....kekdstnkkilvttiqsldads 118
                                       f++f+  ++++    ++++ ++  +++      ek++ +++i++  +q l +++
  gi|488600336|ref|YP_007906807.1| 241 FRNFQIACASAtlsnAKEFAESLFDEKfewvkAEKRKGESHIVMLYTQNLFKAI 294
                                       545544444333332222222222222445555556677888888788777766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.54       1      38 [.      96     134 ..      96     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelg 38 
                                       q++a+e  l  k++++ta+ G GKT+  +  + + v++ 
  gi|488600336|ref|YP_007906807.1|  96 QKDAIEfLLDGKNVVITAPTGFGKTEAFVIPMIERVRNY 134
                                       88999889*****************98776555555554 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 ?    5.1   0.3      0.01        26      24      32 ..       6      14 ..       3      14 .. 0.92
   2 ?    5.1   0.0    0.0099        25       8      24 ..      35      55 ..      34      57 .. 0.82
   3 ?   -0.2   0.3      0.46   1.2e+03      20      29 ..     708     719 ..     687     720 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.01
                                      EE-TTT--E CS
                         zf-RING_7 24 vtCpeCGRI 32
                                      ++C+ CGRI
  gi|488600336|ref|YP_007906807.1|  6 FFCERCGRI 14
                                      69******9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0099
                                      B--CCHHHHHCCS....TB-E CS
                         zf-RING_7  8 elppqvlselrag....devv 24
                                      e++p+++selr+     de++
  gi|488600336|ref|YP_007906807.1| 35 EISPESYSELRNLfdtdDEII 55
                                      89*********9877766665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.46
                                       S..TB-EE-TTT CS
                         zf-RING_7  20 g..devvtCpeC 29 
                                       +  + +  Cp+C
  gi|488600336|ref|YP_007906807.1| 708 CkcGRIEGCPSC 719
                                       444778889999 PP

>> VESA1_N  Variant erythrocyte surface antigen-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3   0.00012      0.32     173     210 ..       5      42 ..       2      60 .. 0.80
   2 ?   -1.8   0.9      0.44   1.1e+03     161     182 ..     706     728 ..     702     762 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                           VESA1_N 173 kccckkcekckekcscvkeekkkleeevekdsyksayk 210
                                       k  c++c++ k+kc+c+ke+++k++ +  ++    +y+
  gi|488600336|ref|YP_007906807.1|   5 KFFCERCGRIKRKCICKKESTRKKNLRLLNEISPESYS 42 
                                       889****************8888887777776666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.44
                           VESA1_N 161 eeckcakaGkcckccck.kcekc 182
                                       ++ckc +   c  c+   +c++ 
  gi|488600336|ref|YP_007906807.1| 706 KNCKCGRIEGCPSCTYSyQCGNN 728
                                       45666555555555544455433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 5360.40
//
Query:       gi|488600337|ref|YP_007906808.1|  [L=440]
Description: NADPH:sulfur oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  187.6   0.3    4.3e-55  187.0   0.3    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    1.4e-22   80.0   1.0      2e-16   60.3   1.1    3.5  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    1.1e-17   64.3   0.0      5e-14   52.3   0.0    2.1  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
      1e-15   57.9   0.0    4.8e-15   55.8   0.0    2.0  2  Pyr_redox_dim    Pyridine nucleotide-disulphide oxidoreductas
    1.4e-10   41.2   0.0    1.9e-05   24.8   0.0    2.6  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    1.9e-10   40.0   0.1     0.0016   17.3   0.0    4.1  4  HI0933_like      HI0933-like protein
    2.7e-10   40.4   0.5      0.021   14.4   0.0    4.1  4  DAO              FAD dependent oxidoreductase
    3.5e-08   32.9   0.1     0.0072   15.4   0.0    3.8  4  FAD_binding_2    FAD binding domain
    1.7e-07   31.5   0.9      0.014   15.7   1.3    3.5  2  TrkA_N           TrkA-N domain
    1.5e-06   27.5   1.6      0.023   13.8   0.0    3.0  3  Lycopene_cycl    Lycopene cyclase protein
    1.2e-05   25.4   0.4      0.044   13.8   0.0    3.5  4  NAD_binding_9    FAD-NAD(P)-binding
    2.6e-05   23.5   1.5       0.19   10.8   0.7    3.3  2  GIDA             Glucose inhibited division protein A
    6.9e-05   22.8   0.2     0.0011   18.9   0.2    2.2  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0002   20.7   0.2      0.044   13.0   0.0    2.4  2  Thi4             Thi4 family
     0.0002   21.0   1.8    0.00026   20.6   0.2    1.9  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00031   20.1   0.5       0.67    9.2   0.3    2.5  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0015   17.5   0.3        1.3    7.8   0.1    2.6  3  Trp_halogenase   Tryptophan halogenase
     0.0018   18.7   0.3      0.048   14.1   0.2    2.4  2  NAD_binding_7    Putative NAD(P)-binding
     0.0024   17.2   2.4       0.14   11.3   0.1    2.5  2  FAD_binding_3    FAD binding domain
     0.0041   16.3   0.0       0.33   10.1   0.0    2.8  3  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.011   16.3   0.8        3.5    8.3   0.4    3.5  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.04   13.3   0.3       0.83    9.0   0.0    2.6  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.06   14.2   0.1        4.4    8.1   0.0    2.6  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.066   13.2   0.0          2    8.4   0.0    2.4  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.091   12.1   3.1        0.3   10.4   0.0    2.4  3  FAD_oxidored     FAD dependent oxidoreductase
       0.11   12.7   1.1        4.2    7.6   0.3    3.0  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.12   10.9   0.0       0.22   10.0   0.0    1.4  1  Mqo              Malate:quinone oxidoreductase (Mqo)
       0.43    9.9   1.5       0.51    9.7   0.1    1.8  2  ThiF             ThiF family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.0   0.3   6.7e-58   4.3e-55       2     294 .]       2     300 ..       1     300 [. 0.92

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 6.7e-58
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHHCCCCHC CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias....evvkklnqgielllg 72 
                                       +v++iGgG+AG+++a ++++     +v ++e+  ++ +  c ++  + g+ +  + +     + + + + gi++l++
  gi|488600337|ref|YP_007906808.1|   2 KVAIIGGGAAGMSCASRIKRlrPDWDVKVFEKSPYVSHAPCGIPFYVSGIVDSINNLCsydiD-FFRERRGIDVLTR 77 
                                       8*******************7669*******99999999999999999999998877689953.677789******* PP

                                       CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvv 148
                                       +ev+++  g +++++  +++g +e+++ dkl+ AtG+++  l+++ ++ +++  v+++++ e++k+  ++ ++iv+v
  gi|488600337|ref|YP_007906808.1|  78 TEVLEV--GDGELHV--LRDGRKERFEWDKLLFATGARAAPLNVQCEEIEGVLCVHYIENGEKVKRLVKNcRSIVIV 150
                                       ******..6666888..567999*******************888665566667799********999999****** PP

                                       S-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 149 GgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgee 225
                                       G+GyiGvE+A a+++lgk+v+l+e  + +l+++d e++  l+e+l+k  v+ ++ ++v++i+g+++ +e v +d+ e
  gi|488600337|ref|YP_007906808.1| 151 GSGYIGVEMAEAISRLGKNVVLIEKEEYPLPEYDVEIGSVLKERLQKV-VNARFSEKVEAIEGKDR-VERVVTDKGE 225
                                       ***********************************************5.*************9997.9989999999 PP

                                       EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 226 idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpelaqaAvqqG 294
                                       + +d+v+ a+G +p+ el+ ++lg++l ++g+i v+++++tn++++y +GD+a       g+ + + la+ A ++G
  gi|488600337|ref|YP_007906808.1| 226 YRCDMVISAIGSQPNIELA-KQLGVKLGKTGAIAVNSRMQTNIENVYSAGDCAettniitGKPDWIPLAVPANKMG 300
                                       *******************.*********************************99999999999999999998877 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0    0.0002      0.13       1      33 [.       2      36 ..       2      41 .. 0.88
   2 ?    2.4   0.0      0.38   2.4e+02      51      67 ..      68      84 ..      63      92 .. 0.81
   3 !   60.3   1.1   3.1e-19     2e-16       1      78 [.     146     221 ..     146     224 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0002
                                      EEEEECSSHHHHHHHHHHHHTT..SEEEEEESSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelg..kkVtvversdk 33
                                      kv+++GgG  g+ +A+ +++l+   +V+v+e s+ 
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKRLRpdWDVKVFEKSPY 36
                                      79*******************96559999998876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.38
                                      HHTTEEEECSEEEEEEE CS
                         Pyr_redox 51 ekngievllntkveeie 67
                                      e++gi+vl+ t+v e+ 
  gi|488600337|ref|YP_007906808.1| 68 ERRGIDVLTRTEVLEVG 84
                                      456***********997 PP

  == domain 3  score: 60.3 bits;  conditional E-value: 3.1e-19
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       ++v+vG+Gyig+E+A+a+++lgk+V ++e ++ +l+ +D e++++l+e+l+k  ++ ++++kve+ieg+++ ve+v+
  gi|488600337|ref|YP_007906808.1| 146 SIVIVGSGYIGVEMAEAISRLGKNVVLIEKEEYPLPEYDVEIGSVLKERLQKV-VNARFSEKVEAIEGKDR-VERVV 220
                                       69**************************************************9.****************9.99998 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       +
  gi|488600337|ref|YP_007906808.1| 221 T 221
                                       7 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 !   10.1   0.0   0.00055      0.35       2      21 ..       5      24 ..       4      39 .. 0.76
   2 !   52.3   0.0   7.7e-17     5e-14      93     305 .]      69     274 ..      56     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00055
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagl 21
                                      IiG+G+aG+++a  +k++  
  gi|488600337|ref|YP_007906808.1|  5 IIGGGAAGMSCASRIKRLRP 24
                                      9************9998764 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 7.7e-17
                       Pyr_redox_3  93 sfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek.lvkhyskv.kefhkya..gq 165
                                       +  +++ + +eV +v   + +   + +ke +e +k++ AtG    P   + +  e  l++hy ++ ++++ +    +
  gi|488600337|ref|YP_007906808.1|  69 RRGIDVLTRTEVLEVGDGELHVLRDGRKERFEWDKLLFATGARAAPLNVQCEEIEGvLCVHYIENgEKVKRLVknCR 145
                                       567899999******99999999999****************99997777666664478888776323333321257 PP

                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikeke 242
                                        +v++G +  +v++A  + r g++V ++ +++       ++++++  + ++rl+++v     ++ f ++v++i+ k+
  gi|488600337|ref|YP_007906808.1| 146 SIVIVGSGYIGVEMAEAISRLGKNVVLIEKEEY---PLPEYDVEIGSVLKERLQKVV-----NARFSEKVEAIEGKD 214
                                       899*************************99974...345689999********9975.....589***********9 PP

                       Pyr_redox_3 243 eeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +  +v t++g+  +  d v+ a+G +p++++ k+ +++l ++g +++++  ++tn+++++ aG
  gi|488600337|ref|YP_007906808.1| 215 RVERVVTDKGE-YR-CDMVISAIGSQPNIELAKQLGVKLGKTGAIAVNS-RMQTNIENVYSAG 274
                                       99999999985.45.4788999***********************9996.699*******999 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       4.7     3e+03      56      79 ..     143     166 ..     130     170 .. 0.78
   2 !   55.8   0.0   7.5e-18   4.8e-15       5     103 ..     324     420 ..     320     425 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.7
                                       ETTTTBEEEEEEECTTHHHHHHHH CS
                     Pyr_redox_dim  56 daktgkvlGahivGpgageliqel 79 
                                       + ++  ++G   +G +++e+i+ l
  gi|488600337|ref|YP_007906808.1| 143 NCRSIVIVGSGYIGVEMAEAISRL 166
                                       446778999999**9999999865 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 7.5e-18
                                       EESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                     Pyr_redox_dim   5 vftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                        f d+e++  Gl+e+eAk  g  +++++++++  + a++ ++ +++vK+v d  +g+vlG++++G+g++++i +++ 
  gi|488600337|ref|YP_007906808.1| 324 GFYDLEIGRAGLSEKEAKMHG--FETISVTITTKSTARYIPNGDITVKMVSDV-DGRVLGVQCIGKGVAKRIYAASS 397
                                       699******************..**************************9999.9********************** PP

                                       HHHTTSBHHH.HHTSBSSSSSTG CS
                     Pyr_redox_dim  82 aikagltved.ladtihihPtls 103
                                       ++ +++ ved +  ++ + P+ s
  gi|488600337|ref|YP_007906808.1| 398 LLYKKAMVEDfFFADLPYFPPES 420
                                       *********76999999999876 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 !   24.8   0.0     3e-08   1.9e-05       1      31 [.       5      37 ..       5      40 .. 0.91
   2 !   13.8   0.0   8.2e-05     0.052       1      30 [.     149     178 ..     149     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3e-08
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdrl 31
                                      I+G+G++G+++A+++++   + dv ++ek++++
  gi|488600337|ref|YP_007906808.1|  5 IIGGGAAGMSCASRIKRLrpDWDVKVFEKSPYV 37
                                      9***************965799*******9876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.2e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                       IvG+G  G  +A ++++ g++v+l+ek ++
  gi|488600337|ref|YP_007906808.1| 149 IVGSGYIGVEMAEAISRLGKNVVLIEKEEY 178
                                       9**************************875 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   0.0   2.5e-06    0.0016       2      33 ..       2      35 ..       1      39 [. 0.84
   2 ?    4.0   0.0     0.026        17     121     168 ..      69     114 ..      66     116 .. 0.83
   3 !    7.4   0.0    0.0024       1.6       2      33 ..     146     177 ..     145     182 .. 0.93
   4 !    6.1   0.1    0.0059       3.8     115     189 ..     191     253 ..     184     273 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-06
                                      SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVlllekak 33
                                      +v++iGgGaAG+ +A ++   + + +V ++ek +
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIkrLRPDWDVKVFEKSP 35
                                      79*************9995456788999999976 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.026
                                       HHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-G CS
                       HI0933_like 121 eagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiP 168
                                       ++g+++ ++tev +v   +++ + ++   +e++e dkl++AtG  ++P
  gi|488600337|ref|YP_007906808.1|  69 RRGIDVLTRTEVLEV--GDGELHVLRDGRKERFEWDKLLFATGARAAP 114
                                       689999*********..44554555557899*************9988 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0024
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                       +++++G G  G+  A+++++ gk+V+l+ek++
  gi|488600337|ref|YP_007906808.1| 146 SIVIVGSGYIGVEMAEAISRLGKNVVLIEKEE 177
                                       689**************************986 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0059
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT--SHHHHHHHHTT--EEE CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGstgkgyklaeqfghtivp 189
                                       l+++l ++ v+ r +++v+++e  +d++ rv t +++e+++d ++ A        +Gs+++ ++la+q+g+++ +
  gi|488600337|ref|YP_007906808.1| 191 LKERL-QKVVNARFSEKVEAIEG-KDRVERVVT-DKGEYRCDMVISA--------IGSQPN-IELAKQLGVKLGK 253
                                       44444.457999*********66.666688988.9************........555543.4566666655555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.3e-05     0.021       1      33 [.       2      38 ..       2      42 .. 0.84
   2 ?    4.2   0.0     0.043        27     157     206 ..      68     114 ..      59     136 .. 0.74
   3 !   13.3   0.1   7.1e-05     0.045       2      30 ..     147     177 ..     146     180 .. 0.93
   4 ?    3.5   0.1      0.07        45     161     209 ..     199     246 ..     189     276 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                                      EEEEECTSHHHHHHHHHHHHT.T...EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarr.g...Vtllekgdiag 33
                                      +v+iiGGG +G+s+A    r  +   V ++ek++ ++
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKRLrPdwdVKVFEKSPYVS 38
                                      59****************64335899******97776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.043
                                       HHTT-EEEESECEEEEEEEETCEEEEE..EECTEEEEEEEEEEE--GGGHHH CS
                               DAO 157 ealGveilegtevtgleeedgkvwgve..rttpgendaadavVnaaGawsdl 206
                                       e++G+++l++tev ++   dg ++ ++  r    e+++ d++  a+Ga +  
  gi|488600337|ref|YP_007906808.1|  68 ERRGIDVLTRTEVLEV--GDGELHVLRdgR---KERFEWDKLLFATGARAAP 114
                                       689***********99..345666663322...22346799******99753 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 7.1e-05
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                       +vi+G+G+iG+  A + +r g  V+l+ek++
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGknVVLIEKEE 177
                                       9*****************9999*******94 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.07
                                       -EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH.HT CS
                               DAO 161 veilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.ll.gl 209
                                       v+ ++ ++v+++e + ++v +v  +t+ ge + +d v+ a G + + +l ++
  gi|488600337|ref|YP_007906808.1| 199 VNARFSEKVEAIEGK-DRVERV--VTDkGEYR-CDMVISAIGSQPNiELaKQ 246
                                       667777889999654.478888..66669854.477******8877744333 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05    0.0072       2      34 ..       3      37 ..       2      43 .. 0.87
   2 ?   -0.2   0.0      0.64   4.1e+02     153     204 ..      60     113 ..      49     131 .. 0.76
   3 !    9.7   0.0   0.00062       0.4       2      33 ..     147     178 ..     146     179 .. 0.96
   4 ?    2.2   0.0      0.12        75     373     402 ..     254     277 ..     189     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                      EEEE--SHHHHHHHHHHHH.TTT.-EEEEESSSGG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaae.aGl.kvavvekeqef 34
                                      v +iG+G+AG+++A ++++ +   +v v ek +++
  gi|488600337|ref|YP_007906808.1|  3 VAIIGGGAAGMSCASRIKRlRPDwDVKVFEKSPYV 37
                                      89***************997666799999999885 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.64
                                       TCTEEEEESEEEEEEEECTT..EEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 153 kagvdfqerteadeLivedg..rvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ++++df+ + +  +++++++  +v   +++ +++gr++r++ ++++ atg+  +
  gi|488600337|ref|YP_007906808.1|  60 SYDIDFFRERRGIDVLTRTEvlEVGDGELHVLRDGRKERFEWDKLLFATGARAA 113
                                       566777777777777776666777777777779****************99876 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00062
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                       ++++GsG  G   A ++++ G++v+++eke++
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGKNVVLIEKEEY 178
                                       79***************************986 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.12
                                       S-EEEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 373 mgGvetdengrvldadgqpipGLYAaGeva 402
                                        g ++++ ++++      +i++ Y aG +a
  gi|488600337|ref|YP_007906808.1| 254 TGAIAVNSRMQT------NIENVYSAGDCA 277
                                       455777777787......**********99 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0077       4.9       1      31 [.       3      35 ..       3      50 .. 0.89
   2 !   15.7   1.3   2.1e-05     0.014       1      37 [.     147     183 ..     147     283 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0077
                                      EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkde 31
                                      ++iiG G  G+s a ++++ +  +dv v +k++
  gi|488600337|ref|YP_007906808.1|  3 VAIIGGGAAGMSCASRIKRlRPdWDVKVFEKSP 35
                                      68*****************765899*****998 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.1e-05
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveel 37 
                                       i+i+G G +G ++ae +s+ g+ +vv+i+k+e  + e+
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRlGK-NVVLIEKEEYPLPEY 183
                                       89*****************666.6*****999554443 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.6e-05     0.023       2      36 ..       3      37 ..       2      42 .. 0.92
   2 !    9.1   0.1   0.00091      0.58       2      35 ..     147     178 ..     146     185 .. 0.90
   3 ?    2.2   0.1      0.11        72      92     142 ..     190     237 ..     183     254 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      v++iG+G+Ag+s A r+ + +p+  v + e sp +
  gi|488600337|ref|YP_007906808.1|  3 VAIIGGGAAGMSCASRIKRLRPDWDVKVFEKSPYV 37
                                      89***************************999976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00091
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieasps 35 
                                       +v++G+G  g+ +A+ +  ++ g +vvlie  + 
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAI--SRLGKNVVLIEKEEY 178
                                       89***************..**********97665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.11
                     Lycopene_cycl  92 ellerlvengvklleakvesveeeeageslvvleggrkirarlvvdargla 142
                                       +l+erl +    + + kve++e ++    +vv++ g + r+ +v+ a g  
  gi|488600337|ref|YP_007906808.1| 190 VLKERLQKVVNARFSEKVEAIEGKDR-VERVVTDKG-EYRCDMVISAIG-S 237
                                       55666665556677889999999888.444444444.568999999988.3 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   6.8e-05     0.044       1      37 [.       4      37 ..       4      42 .. 0.91
   2 ?   -2.7   0.0         8   5.1e+03     129     154 ..      82     109 ..      74     110 .. 0.61
   3 ?    1.6   0.0      0.38   2.4e+02       1      20 [.     148     167 ..     148     180 .. 0.81
   4 ?    5.8   0.0      0.02        13     109     155 ..     193     237 ..     183     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-05
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      ai+G+G++G++++ r+ +    + + ++++f++s++ 
  gi|488600337|ref|YP_007906808.1|  4 AIIGGGAAGMSCASRIKRL---RPDWDVKVFEKSPYV 37
                                      8***************999...69*********9976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8
                     NAD_binding_9 129 eradgqavlladg..aslaadaVvLAlG 154
                                       e +dg   +l+dg  ++++ d++  A+G
  gi|488600337|ref|YP_007906808.1|  82 EVGDGELHVLRDGrkERFEWDKLLFATG 109
                                       4445554445555125689999999998 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.38
                     NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                       +ivG G  G+ ++e++ +  
  gi|488600337|ref|YP_007906808.1| 148 VIVGSGYIGVEMAEAISRLG 167
                                       7**************99874 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.02
                     NAD_binding_9 109 arlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       +rl ++v    ++++v+++e +++ ++ + +d+ ++++d V+ A+G 
  gi|488600337|ref|YP_007906808.1| 193 ERL-QKVVNARFSEKVEAIEGKDR-VERVVTDKGEYRCDMVISAIGS 237
                                       334.45556667899999997755.5666888999*********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 !    8.5   0.0    0.0014      0.91       1      21 [.       2      22 ..       2      42 .. 0.88
   2 !   10.8   0.7    0.0003      0.19       2      31 ..     147     176 ..     146     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                                      CEEEE-SSHHHHHHHHHHHHT CS
                              GIDA  1 dviViGgGhAGceAAlaaarl 21
                                      +v +iGgG AG+ +A  ++rl
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKRL 22
                                      699************999986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0003
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithk 31 
                                       ++++G G  G+e A a++rlG +v+Li ++
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGKNVVLIEKE 176
                                       89*************************443 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 ?    1.6   0.0      0.35   2.3e+02       1      19 [.       2      20 ..       2      39 .. 0.74
   2 !   18.9   0.2   1.7e-06    0.0011       2      86 ..     147     235 ..     146     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.35
                                      EEEEE--SCCHHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfa 19
                                      kva+iG G  G + a+ + 
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIK 20
                                      79**********9998764 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.7e-06
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH. CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav. 77 
                                       + ++G+G +G ++a+++ + g +Vvl++ +e  l +   +i + l++  +k  + ++ +++ ++ i+ ++ +e++v 
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGKNVVLIEKEEYPLPEYDVEIGSVLKERLQK--VVNARFSEKVEAIEGKDRVERVVt 221
                                       789*********************************999999977776544..334556666666665555555443 PP

                                       C.....-SEEEE-S CS
                           3HCDH_N  78 d.....adlviEav 86 
                                       d     +d+vi a+
  gi|488600337|ref|YP_007906808.1| 222 DkgeyrCDMVISAI 235
                                       32222278887776 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   6.9e-05     0.044      19      50 ..       2      34 ..       1      40 [. 0.92
   2 ?    5.2   0.1     0.016        10      19      49 ..     146     175 ..     134     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                                      EEEEE--SHHHHHHHHHHHHC.TTS-EEEEESS CS
                              Thi4 19 DvvivGaGssGLtaayylakk.pdlkvailers 50
                                       v+i+G+G++G+++a  + +  pd  v ++e+s
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKRLrPDWDVKVFEKS 34
                                      699****************988*********86 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailer 49 
                                        +vivG+G  G+  a  +++  + +v+++e+
  gi|488600337|ref|YP_007906808.1| 146 SIVIVGSGYIGVEMAEAISRL-GKNVVLIEK 175
                                       59******************9.999999997 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 ?   -1.1   0.1       1.9   1.2e+03       1      19 [.       1      19 [.       1      23 [. 0.87
   2 !   20.6   0.2     4e-07   0.00026       2      63 ..     146     206 ..     145     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                                      SEEEEE--STTHHHHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavl 19
                                      mk+++iG G  G+ +a  +
  gi|488600337|ref|YP_007906808.1|  1 MKVAIIGGGAAGMSCASRI 19
                                      89********999998765 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 4e-07
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTT CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgr 63 
                                        i+++G+GY+G+ +a +++++g++v+++ ++e    +   +  ++  + L+++v+++  s++
  gi|488600337|ref|YP_007906808.1| 146 SIVIVGSGYIGVEMAEAISRLGKNVVLIEKEEYPLPEYDVEIGSVLKERLQKVVNARF-SEK 206
                                       599***********************************99999999999999999988.444 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 !    8.7   0.0    0.0015      0.97      30      60 ..       2      34 ..       1      40 [. 0.79
   2 !    9.2   0.3     0.001      0.67      30      69 ..     146     185 ..     137     286 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                                      EEEEESTSHHHHHHHHHHHHTT..-EEEEEESS CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglg..akVtvlDvr 60
                                      kv +iGgG aG++ ++  k+l    +V+v++++
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKRLRpdWDVKVFEKS 34
                                      89**************99999622457777766 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.001
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                        ++++G G  G++ +++ ++lg +V+++++++  l + + 
  gi|488600337|ref|YP_007906808.1| 146 SIVIVGSGYIGVEMAEAISRLGKNVVLIEKEEYPLPEYDV 185
                                       5899*************************99877766665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0033       2.1       1      34 [.       2      34 ..       2      43 .. 0.86
   2 !    7.8   0.1     0.002       1.3       2      37 ..     147     179 ..     146     201 .. 0.90
   3 ?   -2.2   0.0       2.2   1.4e+03     178     209 ..     206     237 ..     191     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0033
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      k+ i+GGG aG   A+ +++    + +v++ e++
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKRLR-PDWDVKVFEKS 34
                                      799***************9998.44899888875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                                       EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlveseeig 37 
                                       ivivG G  G   A a+++ +    +v l+e+ee +
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLG---KNVVLIEKEEYP 179
                                       9********************...56*******987 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.2
                                       EEEE-T.TS-EEEEEETTS-EEE-SEEEE-SGG CS
                    Trp_halogenase 178 evqlde.dgrveslrledgreveadlfiDcsGf 209
                                       +v+  e ++rve++ +++g+ +  d++i + G 
  gi|488600337|ref|YP_007906808.1| 206 KVEAIEgKDRVERVVTDKGE-YRCDMVISAIGS 237
                                       44443449999999998887.999999988886 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 ?    2.4   0.0      0.33   2.1e+02       9      35 ..       2      30 ..       1     101 [. 0.81
   2 !   14.1   0.2   7.5e-05     0.048       8      71 ..     145     237 ..     140     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.33
                     NAD_binding_7  9 kvlvvGgGevAa...rkvrklleagakvtv 35
                                      kv ++GgG  ++   +++++l +   +v+v
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMscaSRIKRLRPD-WDVKV 30
                                      799******998222455554443.55555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.5e-05
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele.................elvklaeeelekdleg...... 61 
                                       +++++vG G ++ + ++ + + g++v+++ +e     +                 +   + +  +++++e       
  gi|488600337|ref|YP_007906808.1| 145 RSIVIVGSGYIGVEMAEAISRLGKNVVLIEKEE---YPlpeydveigsvlkerlqK---VVNARFSEKVEAiegkdr 215
                                       789*****************************5...22334556677666664432...333333333211111222 PP

                     NAD_binding_7  62 ............adlviaatdd 71 
                                                    d+vi a+  
  gi|488600337|ref|YP_007906808.1| 216 vervvtdkgeyrCDMVISAIGS 237
                                       2223333445557788888764 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.015       9.5       3      18 ..       2      17 ..       1      22 [. 0.87
   2 !   11.3   0.1   0.00023      0.14       4      35 ..     147     178 ..     145     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                                      EEEEE--SHHHHHHHH CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlal 18
                                      +V+I+G+G aG++ a+
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCAS 17
                                      79**********9986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00023
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       ++IVG+G  G+  a   s+ G +vvl+ek + 
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGKNVVLIEKEEY 178
                                       68***************************875 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.25   1.6e+02       5      37 ..       3      35 ..       1      41 [. 0.70
   2 !   10.1   0.0   0.00051      0.33     140     213 ..      92     166 ..      70     184 .. 0.81
   3 ?    1.0   0.0      0.28   1.8e+02     111     162 ..     200     241 ..     188     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.25
                       K_oxygenase  5 ligiGiGpsnLsLailleevkkelkalflerqp 37
                                      +++iG G++ +s a +++  + + ++ ++e++p
  gi|488600337|ref|YP_007906808.1|  3 VAIIGGGAAGMSCASRIKRLRPDWDVKVFEKSP 35
                                      567777777777777777777777777777766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00051
                       K_oxygenase 140 aegeeeelearnlvlgvG.tepkiPevleklegkervvHsseylerkee.llakkriaVvGsGqSaaeifedllrr 213
                                       ++g++e++e  +l+ ++G   + +  ++e++eg   +vH  e  e+ ++  ++ ++i++vGsG  + e++e + r 
  gi|488600337|ref|YP_007906808.1|  92 RDGRKERFEWDKLLFATGaRAAPLNVQCEEIEG-VLCVHYIENGEKVKRlVKNCRSIVIVGSGYIGVEMAEAISRL 166
                                       58999999999*******444557788999996.899999988888877577889************999887665 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.28
                       K_oxygenase 111 eqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepki 162
                                       +  rf+e+ve++e +++ e    +v +     ++ e+++  ++ ++G++p+i
  gi|488600337|ref|YP_007906808.1| 200 N-ARFSEKVEAIEGKDRVE----RVVT-----DKGEYRCDMVISAIGSQPNI 241
                                       3.68999999999999743....5665.....57899************998 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 ?    4.2   0.0       0.1        67       1      20 [.       2      21 ..       2      35 .. 0.86
   2 ?    8.3   0.4    0.0054       3.5       2      60 ..     147     211 ..     146     254 .. 0.79
   3 ?   -1.2   0.0         5   3.2e+03      27      74 ..     256     299 ..     231     304 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.1
                                      EEEEETTSHHHHHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasglla 20
                                      k++iiG+G  g + as++ +
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKR 21
                                      79***********9999765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0054
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..........-EEECECHHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..........vkvtavdneeaae 60 
                                       i i+G+G +g  +a+ +++ g   +++v++ ++++  + e   e+g          v++  +++ ea+e
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLG---KNVVLI-EKEEYPLPEYDVEIGsvlkerlqkvVNARFSEKVEAIE 211
                                       8899*****************...999988.66666665555555555555555555555555555555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5
                                       CEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHH CS
                     F420_oxidored  27 eivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedv 74 
                                        i  +nsr++  +e   ++    + + +++    + d++ lav+ +++
  gi|488600337|ref|YP_007906808.1| 256 AIA-VNSRMQTNIENVYSAGD--CAE-TTNIITGKPDWIPLAVPANKM 299
                                       444.66777777776655543..333.233333357888888877766 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 ?    1.4   0.0      0.28   1.8e+02      38      59 ..       2      23 ..       1      41 [. 0.82
   2 ?    9.0   0.0    0.0013      0.83      37      70 ..     145     178 ..     129     200 .. 0.82
   3 ?   -2.9   0.0       5.8   3.7e+03      41      55 ..     378     392 ..     358     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.28
                                      EEEEES-SHHHHHHHHHHHHTT CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafg 59
                                      +v+iiG G+ G + a r+k ++
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKRLR 23
                                      79**************999764 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                       + + i+G G IG ++a+ ++ +g +v+ +++ + 
  gi|488600337|ref|YP_007906808.1| 145 RSIVIVGSGYIGVEMAEAISRLGKNVVLIEKEEY 178
                                       6799**********************99987755 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.8
                                       EES-SHHHHHHHHHH CS
                      2-Hacid_dh_C  41 iiGlGrIGqavakrl 55 
                                       ++G+  IG+ vakr+
  gi|488600337|ref|YP_007906808.1| 378 VLGVQCIGKGVAKRI 392
                                       678888999999986 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 ?    3.3   0.0      0.22   1.4e+02       1      29 [.       1      29 [.       1      54 [. 0.86
   2 ?    8.1   0.0    0.0069       4.4       3      82 ..     147     247 ..     145     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.22
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEE CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevv 29
                                      ++vaiiG+G +g   +  +++ +++++v 
  gi|488600337|ref|YP_007906808.1|  1 MKVAIIGGGAAGMSCASRIKRLRPDWDVK 29
                                      69**********99999999988888765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0069
                                       EEEETTSHHHHHHHHHHHHTTTTE...............EEEEEECSSHHHHHHHHHHTTHEEESS...HHHHHTCT CS
                      GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrle...............evvalldpdaeraeavaesfgveaysd...leelladp 61 
                                       ++i+G+G+ig + ++++ +  ++                e+  +l+++ ++  +++ s +vea +    +e++++d+
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGKNVvliekeeyplpeydvEIGSVLKERLQKVVNARFSEKVEAIEGkdrVERVVTDK 223
                                       89****************99999999999999999965555555555555555556666666555555699999999 PP

                                       ...TESEEEE-S-GGGHHHHHHHH CS
                      GFO_IDH_MocA  62 ...eidavivatpngtheelakaa 82 
                                          ++d+vi a+ ++   elak++
  gi|488600337|ref|YP_007906808.1| 224 geyRCDMVISAIGSQPNIELAKQL 247
                                       988899999888888777777765 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.23   1.5e+02       1      20 [.       2      21 ..       2      39 .. 0.82
   2 ?    8.4   0.0    0.0031         2       2      33 ..     147     189 ..     146     263 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                                      -EEEE--SHHHHHHHHHHHT CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlae 20
                                      k+a++G+G+ G + A  +++
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKR 21
                                      79**********99987766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0031
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H...........H CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree...........e 33 
                                       i ++G+G  G  +A ++++ g++v+l+ +ee            
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGKNVVLIEKEEyplpeydveigS 189
                                       89*************************9999777766653331 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.18   1.2e+02       2      17 ..       3      18 ..       2      24 .. 0.86
   2 ?   10.4   0.0   0.00046       0.3       2      32 ..     147     177 ..     146     179 .. 0.94
   3 ?   -3.8   0.1       9.4     6e+03     101     140 ..     198     232 ..     189     234 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.18
                      FAD_oxidored  2 vvVvGGgpaGvaAAia 17
                                      v ++GGg+aG+ +A  
  gi|488600337|ref|YP_007906808.1|  3 VAIIGGGAAGMSCASR 18
                                      89*********99976 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00046
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                       +v+vG+g  Gv  A a  r G++v+L+e+++
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGKNVVLIEKEE 177
                                       8***************************976 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 9.4
                      FAD_oxidored 101 gvtvllntrlvevekegkriesvtveskegrktirAkvfi 140
                                        v+  + ++++++e ++ r+e v++     + ++r++++i
  gi|488600337|ref|YP_007906808.1| 198 VVNARFSEKVEAIEGKD-RVERVVTD----KGEYRCDMVI 232
                                       23333333444444444.89999884....5666666666 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.4   4.8e+03       1      19 [.       3      21 ..       3      30 .. 0.84
   2 ?    7.6   0.3    0.0065       4.2       1      34 [.     147     177 ..     147     246 .. 0.79
   3 ?    2.2   0.0      0.31     2e+02      45      94 ..     341     388 ..     330     391 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.4
                                      EEEE--SHHHHHHHHHHHC CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellar 19
                                      v iiG+G+ G + a  ++r
  gi|488600337|ref|YP_007906808.1|  3 VAIIGGGAAGMSCASRIKR 21
                                      679*****99998888876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0065
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSH CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrsk 34 
                                       ++i+G+G++G  +ae ++r ++   +++++++++
  gi|488600337|ref|YP_007906808.1| 147 IVIVGSGYIGVEMAEAISRLGK---NVVLIEKEE 177
                                       89*****************997...588888776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.31
                                       TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGHHHHHHHHHHHT- CS
                   Sacchrp_dh_NADP  45 lgvrfeaialdaenyeavLaallkegdlvvnlsppissldvlkaCietgv 94 
                                       +   fe+i++++  ++   a+++  gd+ v ++ ++ ++ +   Ci +gv
  gi|488600337|ref|YP_007906808.1| 341 KMHGFETISVTITTKST--ARYIPNGDITVKMVSDVDGRVLGVQCIGKGV 388
                                       45668888888888776..99***************99999999998887 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00034      0.22       4      38 ..       2      36 ..       1      42 [. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00034
                               Mqo  4 dvvliGaGimsatlgvllkelepelsievlerldk 38
                                       v +iG+G    + ++ +k+l+p+++++v+e+   
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCASRIKRLRPDWDVKVFEKSPY 36
                                      689****************************9765 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       7.2   4.6e+03      20      35 ..       2      17 ..       1      21 [. 0.81
   2 ?    9.7   0.1   0.00079      0.51      11      41 ..     135     167 ..     125     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.2
                                      EEEEE--SHHHHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                              ThiF 20 kvllvGaGglGsellk 35
                                      kv+++G G+ G  ++ 
  gi|488600337|ref|YP_007906808.1|  2 KVAIIGGGAAGMSCAS 17
                                      899*****99987765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00079
                                       HHHHHHHT..SEEEEE--SHHHHHHHHHHHHHT CS
                                       xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  11 dgqekLrd..skvllvGaGglGsellknLalsG 41 
                                       +  ++L +   ++++vG G +G e+++++ ++G
  gi|488600337|ref|YP_007906808.1| 135 EKVKRLVKncRSIVIVGSGYIGVEMAEAISRLG 167
                                       555666666779*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2970.83
//
Query:       gi|488600338|ref|YP_007906809.1|  [L=175]
Description: hypothetical protein Asulf_00807 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-10   40.6   6.9    9.3e-10   39.0   6.9    1.7  1  Rubrerythrin     Rubrerythrin
    0.00011   22.4   1.0    0.00033   20.9   1.0    1.7  1  Ferritin_2       Ferritin-like domain
     0.0019   18.6   1.7        1.2    9.5   0.2    2.1  2  DUF2383          Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
       0.13   12.0   4.2       0.51   10.1   0.8    2.0  2  DUF4303          Domain of unknown function (DUF4303)
       0.27   10.9   0.1       0.27   10.9   0.1    1.8  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   6.9   2.6e-13   9.3e-10       1     130 [.      52     163 ..      52     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.6e-13
                                       HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                       ++Le A+  E +   +Y++  ek k  ++  +++F++l++ E+eHa ++ kll+  +pe                 k
  gi|488600338|ref|YP_007906809.1|  52 KNLEQALELELTNAGFYRAAMEKSK--NEYFKAMFKALSKVESEHASVICKLLKIKKPEIP---------------K 111
                                       69***********************..9999**********************98666655...............8 PP

                                       TGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHe 130
                                       +   +++Le  ++   ++e+++++fy++ a++++++++k++f  l + E  H 
  gi|488600338|ref|YP_007906809.1| 112 IDASDDDLE-NVKESFERESKAIKFYTKSAQEAVEARVKEVFTVLVNIESTHL 163
                                       889999999.8899999**********************************96 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.0   9.2e-08   0.00033       6     126 ..      54     162 ..      51     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9.2e-08
                        Ferritin_2   6 LnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaavakptfdfafdpfade 82 
                                       L+ Al lE + a fY aa+e       +  ++  +++++ + k e +H++++ + l+    ++kp++    d+ +d+
  gi|488600338|ref|YP_007906809.1|  54 LEQALELELTNAGFYRAAME-------KSKNEYFKAMFKALSKVESEHASVICKLLK----IKKPEIPK-IDASDDD 118
                                       788****************9.......467788899********************6....55555543.4456666 PP

                        Ferritin_2  83 ksflalaavlEdvgvsAYlgaapllsnkelltaaasIlsvEArH 126
                                        + ++ ++  E  +++ Y   a+   ++ ++++   ++++E+ H
  gi|488600338|ref|YP_007906809.1| 119 LENVKESFERESKAIKFYTKSAQEAVEARVKEVFTVLVNIESTH 162
                                       66666677778888888888888888888888888888888877 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2   0.00034       1.2       5      48 ..      53      96 ..      50     107 .. 0.86
   2 !    8.7   0.1    0.0006       2.2       4      39 ..     120     155 ..     117     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00034
                                      HHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHH CS
                           DUF2383  5 aLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaae 48
                                      +L++ +e +     +y++a ek k++ +k++++  ++  +e+a+
  gi|488600338|ref|YP_007906809.1| 53 NLEQALELELTNAGFYRAAMEKSKNEYFKAMFKALSKVESEHAS 96
                                      67888888888899*******************99998888876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0006
                                       HHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHH CS
                           DUF2383   4 eaLndLietlkdgeegykeaaekvkdpqlktlleri 39 
                                       e++++  e++  ++++y++ a+++ ++++k++++  
  gi|488600338|ref|YP_007906809.1| 120 ENVKESFERESKAIKFYTKSAQEAVEARVKEVFTVL 155
                                       667777899999********************9865 PP

>> DUF4303  Domain of unknown function (DUF4303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00014      0.51      65     119 ..      36      93 ..      34      98 .. 0.89
   2 ?    3.4   0.1     0.016        59      70     119 ..     112     161 ..     102     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                           DUF4303  65 adWpyadfgdedfedvnkllaardnefeleek.....efeafrdklleamvkAlkeldke 119
                                       ++W ++++ +  +++++++  + ++e el +       +e+ ++++++am kAl+++++e
  gi|488600338|ref|YP_007906809.1|  36 EEWRDENDVE--LSEISRKNLEQALELELTNAgfyraAMEKSKNEYFKAMFKALSKVESE 93 
                                       7888888544..9999999999999999999999**9*******************9988 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.016
                           DUF4303  70 adfgdedfedvnkllaardnefeleekefeafrdklleamvkAlkeldke 119
                                        d +d+d+e v++ +++++   ++  k  ++  + + +   ++l + +++
  gi|488600338|ref|YP_007906809.1| 112 IDASDDDLENVKESFERESKAIKFYTKSAQEAVEARVKEVFTVLVNIEST 161
                                       5677888999********99999999999999999999999999887765 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   7.5e-05      0.27       5      14 ..       2      11 ..       1      12 [. 0.88
   2 ?   -1.7   0.1      0.66   2.4e+03       9      13 ..      22      26 ..      21      32 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.5e-05
                                      -EEE-TTT-- CS
                   Desulfoferrod_N  5 evYkCevCGn 14
                                       vY+C +CG+
  gi|488600338|ref|YP_007906809.1|  2 RVYRCRICGD 11
                                      69*******5 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.66
                                      -TTT- CS
                   Desulfoferrod_N  9 CevCG 13
                                      C  CG
  gi|488600338|ref|YP_007906809.1| 22 CPFCG 26
                                      66666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1253  (0.0698868); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1380.93
//
Query:       gi|488600339|ref|YP_007906810.1|  [L=651]
Description: molybdopterin molybdochelatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-57  191.6   0.0    1.2e-56  190.9   0.0    1.3  1  PBP_like        PBP superfamily domain
      3e-43  147.3   0.9    5.1e-43  146.6   0.9    1.3  1  MoeA_N          MoeA N-terminal region (domain I and II)
    9.9e-23   80.4   0.0      2e-22   79.4   0.0    1.5  1  MoCF_biosynth   Probable molybdopterin binding domain
    6.3e-17   61.5   0.0      2e-16   59.9   0.0    2.0  1  MoeA_C          MoeA C-terminal region (domain IV)
     0.0028   17.4   0.0       0.22   11.2   0.0    2.3  2  PBP_like_2      PBP superfamily domain
  ------ inclusion threshold ------
      0.041   13.5   0.0      0.087   12.4   0.0    1.5  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
       0.17   10.2   0.0       0.24    9.7   0.0    1.1  1  MAD             Mitotic checkpoint protein


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.9   0.0   4.6e-60   1.2e-56       5     192 ..     434     626 ..     431     627 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 4.6e-60
                                       HHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHH CS
                          PBP_like   5 aeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpk 81 
                                       +ek  +++v+++n Gs+gG+ a+++geadiag+hlld+ ++eyn+p+++k+  +  + lv++++reqg++v+kgnp+
  gi|488600339|ref|YP_007906810.1| 434 REKDASISVKIINAGSTGGILAVKRGEADIAGTHLLDE-SGEYNIPFIKKYGLK-SCYLVKGYIREQGIIVQKGNPL 508
                                       67778999*****************************6.99**********999.6********************* PP

                                       S--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT.........E-SSTTSEEESSHHHHHCCHCCETTCCEC CS
                          PBP_like  82 kitnwkdladaplrlvnRetGSGtrdlfdellkkegisk.........ssikgyaqearshlavaaaVaagradvgv 149
                                       +i+ ++dl+d ++r+vnR++GSGtr+lfd  lk+  ++k         ++++gy+ ea+sh +va  V  ++ad+g+
  gi|488600339|ref|YP_007906810.1| 509 GIKCIEDLVDLECRIVNRNRGSGTRVLFDMYLKEI-ADKkgiefrkivKKLRGYEIEAKSHTSVAVSVLMNKADAGL 584
                                       ********************************774.4446899999******************************* PP

                                       CCGG-HCCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 150 gieavaeelkgldfvplaeerydlvvrkealddpevqaflefl 192
                                       gi++va++ ++ldf+pl+ e+yd++++k+++ ++ vq+f+++l
  gi|488600339|ref|YP_007906810.1| 585 GIKTVADR-YSLDFIPLRGEEYDFLISKDRFSKDVVQEFIDVL 626
                                       ******99.7*******************************98 PP

>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.9     2e-46   5.1e-43      16     157 .]      26     174 ..      10     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 2e-46
                                       H-EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...................-S---TT-.E CS
                            MoeA_N  16 leeeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........saageeperllpgg.a 83 
                                       ++  ev+l +ea++rv+ ed +A++dvPpfd+S+mDGYAv a+++ +a+e++p        + ag++p+ ++++g a
  gi|488600339|ref|YP_007906810.1|  26 PTADEVEL-KEAYNRVVFEDYYARIDVPPFDRSTMDGYAVIASDTFQADEDSPvrlkvagrVSAGDHPSVVVEEGtA 101
                                       34455***.99**************************************************888888888888888* PP

                                       EEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHHHCT CS
                            MoeA_N  84 vrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragtrltpaeigllasvG 157
                                       v+i TGa++P+ga+aVv+ E+t+ +    e v++ ++v+pgen+ +aG+di aGe+++ragt+lt++eig+l s G
  gi|488600339|ref|YP_007906810.1| 102 VEISTGAVIPSGANAVVMEEYTSmD---GEYVNIyRPVAPGENIMPAGSDIMAGELIVRAGTVLTAREIGVLSSSG 174
                                       **********************653...23333469************************************9987 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.0   7.7e-26     2e-22       1     143 [.     187     323 ..     187     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 7.7e-26
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       av ++G+e++        gki+D n++ +++ l e g+e   ++v +Dde+ei+e + +al++ dvii++GGt++++
  gi|488600339|ref|YP_007906810.1| 187 AVFSTGNEIVspgreleFGKIYDINSYAIMASLMEDGAEPVFLGVARDDEKEIEEMINRALDY-DVIICSGGTSAGS 262
                                       57788888888888888****************************************999888.************* PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                        D+ ++ l +         +++++++s kpgkp++va++   ++   k+ +gLPG+p ++ ++  ++++p ++
  gi|488600339|ref|YP_007906810.1| 263 GDMIYKLLDRWDP------GVVVHGISVKPGKPTIVAML---GN---KPAFGLPGNPTSALMIYNVFVSPLIR 323
                                       ********99977......5************9998888...54...48*******************99987 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   7.9e-20     2e-16       1      72 []     336     407 ..     336     407 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 7.9e-20
                                       EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       karla +  s +gr e+l+v+l   + +y a+p++ + Sg+++sl++++g+i i+e+   +++G eVev l+
  gi|488600339|ref|YP_007906810.1| 336 KARLAVKTFSSHGRVEYLPVNLVMGKEGYSAYPVSGHYSGAITSLSRSDGFIRIDEDISIVDEGSEVEVTLF 407
                                       79*********************88889*****************************************986 PP

>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   8.6e-05      0.22      33      65 ..     435     467 ..     422     487 .. 0.86
   2 ?    3.7   0.0     0.016        41     132     164 ..     518     548 ..     488     596 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.6e-05
                        PBP_like_2  33 kaapgakvnyastGSgagikalrngdvdfagsd 65 
                                       ++ + ++v++   GS++gi+a++ g++d+ag++
  gi|488600339|ref|YP_007906810.1| 435 EKDASISVKIINAGSTGGILAVKRGEADIAGTH 467
                                       4557899************************99 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                        PBP_like_2 132 dgpIkvvhrsdgsgttflfstalaeqgpwtasg 164
                                       d   ++v r+ gsgt+ lf  +l+e ++ +  g
  gi|488600339|ref|YP_007906810.1| 518 DLECRIVNRNRGSGTRVLFDMYLKEIADKK--G 548
                                       66778999***************9985544..3 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 ?   12.4   0.0   3.4e-05     0.087      89     172 ..     500     594 ..     478     646 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                                       EEEETTSS..--SHHHHGG-EEEE--TT-TTTTHHH....HHHTCCCCT--HH....HHSSEE.EE--HHHHHHHHH CS
                    Phosphonate-bd  89 iivradsd..iqsledLkgktiafvspsStsGylvp....aalLvkeagldpe....ddfsev.fsgshdaavlavl 154
                                       iiv+++++  i+ +edL +    +v ++  sG+ v     + ++ +++g++      ++ +++  ++sh +++++vl
  gi|488600339|ref|YP_007906810.1| 500 IIVQKGNPlgIKCIEDLVDLECRIVNRNRGSGTRVLfdmyLKEIADKKGIEFRkivkKLRGYEiEAKSHTSVAVSVL 576
                                       799999966699999**9999999999999999865111133446667777664444456777789*********** PP

                                       TTSSSEEEEEHHHHHHHH CS
                    Phosphonate-bd 155 sgdadaaavsadaledlv 172
                                        ++ada+   ++++++++
  gi|488600339|ref|YP_007906810.1| 577 MNKADAGLGIKTVADRYS 594
                                       ********9999999887 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   9.3e-05      0.24     563     597 ..     540     574 ..     538     592 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.3e-05
                               MAD 563 lKevFkakiqEFRevvYmLlGYkidittnsqyRlt 597
                                       lKe+  +k  EFR++v  L GY i+     ++ ++
  gi|488600339|ref|YP_007906810.1| 540 LKEIADKKGIEFRKIVKKLRGYEIEAKSHTSVAVS 574
                                       8************************9988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 4237.48
//
Query:       gi|488600340|ref|YP_007906811.1|  [L=430]
Description: molybdenum cofactor synthesis domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-45  153.1   0.0    8.1e-45  152.4   0.0    1.4  1  MoeA_N         MoeA N-terminal region (domain I and II)
    4.1e-24   84.9   0.0      7e-24   84.1   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
    3.6e-20   71.9   1.6    1.1e-19   70.4   0.0    2.7  4  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.022   14.9   0.0    1.3  1  7TMR-HDED      7TM-HD extracellular


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 !  152.4   0.0   1.8e-48   8.1e-45       3     157 .]      21     184 ..      19     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.8e-48
                                       HHHHHHHHHHH-HH.-EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............... CS
                            MoeA_N   3 veealaiilaalel.eeeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........sa 70 
                                       v +al+++l++++l + eev+   +al+rv+ edv++++dvP+fd+Sa+DGYAv ae++ +as+++p        ++
  gi|488600340|ref|YP_007906811.1|  21 VYQALKLFLKNVPLlDWEEVDF-FNALNRVCYEDVYSKRDVPHFDRSAVDGYAVIAEDTYSASTSNPiifrvidsIE 96 
                                       77999999***95547788***.99**************************************************99 PP

                                       ....-S---TT-.EEEE-TTSB--TT--EEEEGGGE.E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB- CS
                            MoeA_N  71 ageeperllpgg.avrimTGaplPegadaVvpvEdteeeeaketvev.kavkpgenvrraGedikaGevllragtrl 145
                                        ge+++  +++g avr+ TG+plP++a+aVv++E+t+ +  ++t+ev ++v p +nv raGedi++Gev++++g+++
  gi|488600340|ref|YP_007906811.1|  97 IGEQKDVAIESGeAVRVSTGSPLPKNANAVVMIEYTS-QIDESTIEVySSVPPFKNVSRAGEDIRKGEVVVKRGEII 172
                                       9999999999999**********************95.444555666899*************************** PP

                                       -CCCHHHHHHCT CS
                            MoeA_N 146 tpaeigllasvG 157
                                       +p++igll + G
  gi|488600340|ref|YP_007906811.1| 173 QPHHIGLLSASG 184
                                       ********9987 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.0   1.6e-27     7e-24       1     142 [.     197     333 ..     197     335 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.6e-27
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       a++++G+el+         +i+Dtn ++l+ ++k+l + + + ++v+Dde+e+++ +++al++ad+ii++GGt++++
  gi|488600340|ref|YP_007906811.1| 197 AIVSTGNELVepyddikGAQIVDTNRYMLMGRIKQLNAIAMDFGIVRDDEKELTDVFEKALSSADIIIFSGGTSVGS 273
                                       79**************9889*************************************99999*************** PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpal 142
                                       +D++p+++++  +       + ++++s kpg p g++++    r  gk++i LPG+p+a   a+ +i+ p+l
  gi|488600340|ref|YP_007906811.1| 274 KDLVPQIVNRYRDG------VFVHGLSIKPGMPAGFTTC----R--GKPVILLPGFPVANYLAFNLIVPPVL 333
                                       *************6......***************9999....3..468*******************7776 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 ?   -2.5   0.0       1.4   6.1e+03      49      58 ..      69      78 ..      66      83 .. 0.83
   2 ?   -3.5   0.1       2.8   1.3e+04      60      69 ..     104     113 ..      99     114 .. 0.73
   3 ?   -2.9   0.0       1.8     8e+03      56      67 ..     154     165 ..     147     165 .. 0.76
   4 !   70.4   0.0   2.4e-23   1.1e-19       1      72 []     352     423 ..     352     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                                      -EEEEE-TT- CS
                            MoeA_C 49 nglivipegt 58
                                      +g++vi e+t
  gi|488600340|ref|YP_007906811.1| 69 DGYAVIAEDT 78
                                      9*****9998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                                       EE-TT-EEEE CS
                            MoeA_C  60 gleaGeeVev 69 
                                        +e+Ge V v
  gi|488600340|ref|YP_007906811.1| 104 AIESGEAVRV 113
                                       4999999987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.8
                                       TT--EE-TT-EE CS
                            MoeA_C  56 egtegleaGeeV 67 
                                       + +e++++Ge+V
  gi|488600340|ref|YP_007906811.1| 154 RAGEDIRKGEVV 165
                                       566789999987 PP

  == domain 4  score: 70.4 bits;  conditional E-value: 2.4e-23
                                       EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       ka ++++++s +g r++ Rv l+e dg++ a+p++++gSg++ssl +A+g+i++pe++eg+eaGeeVevil+
  gi|488600340|ref|YP_007906811.1| 352 KAYAGRRIPSSAGIRTLTRVYLEEVDGRIFAYPLRTSGSGIISSLCKADGIIEVPEEVEGYEAGEEVEVILI 423
                                       68899****************************************************************985 PP

>> 7TMR-HDED  7TM-HD extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     5e-06     0.022     189     215 ..     158     184 ..     149     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5e-06
                         7TMR-HDED 189 kikkGevIVrkGervteeqlekLealg 215
                                        i+kGev+V++Ge++ + ++ +L a g
  gi|488600340|ref|YP_007906811.1| 158 DIRKGEVVVKRGEIIQPHHIGLLSASG 184
                                       69********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 3075.22
//
Query:       gi|488600341|ref|YP_007906812.1|  [L=150]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-41  139.3   0.1    7.6e-41  139.1   0.1    1.0  1  DUF2240   Uncharacterized protein conserved in archaea (DUF22
     0.0018   18.4   0.1     0.0036   17.4   0.1    1.5  1  UBA_2     Ubiquitin associated domain (UBA)


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 !  139.1   0.1   8.5e-45   7.6e-41       2     143 ..       2     143 ..       1     144 [. 0.97

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 8.5e-45
                           DUF2240   2 lkiavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpde 78 
                                       l +++a++fk k+k+++s+sd+ + ls+d+kw+s  ++kk++++a  +gLl+ ++g+l p+fd+++v++P gFkpd 
  gi|488600341|ref|YP_007906812.1|   2 LSLVIASAFKSKGKKRMSKSDLTYLLSFDLKWFSHSTSKKVVEEAIRKGLLTFNEGMLEPTFDLKQVDVPVGFKPDV 78 
                                       5689************************************************************************8 PP

                           DUF2240  79 ellkekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                       + + +   fe+++d i++  gi+k evv+ in++qee+++l+ +e++ l++ak+ g+dv+ ++ +
  gi|488600341|ref|YP_007906812.1|  79 KKIFDLGVFEELVDLISERLGIDKSEVVSAINRKQEEMSNLLYAEVISLIYAKECGIDVKPYLPK 143
                                       7777********************************************************98765 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.1e-07    0.0036       3      33 ..      88     117 ..      86     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.1e-07
                             UBA_2   3 edvvsaLsktMGYdkdeIieaLekaekskss 33 
                                       e++v+ +s+++G dk e++ a+++++++ +s
  gi|488600341|ref|YP_007906812.1|  88 EELVDLISERLGIDKSEVVSAINRKQEE-MS 117
                                       899**********************998.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1090.39
//
Query:       gi|488600342|ref|YP_007906813.1|  [L=256]
Description: Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-49  166.1   0.1    9.7e-49  166.0   0.1    1.0  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    1.9e-06   27.4   0.0    2.4e-06   27.1   0.0    1.3  1  PfkB          pfkB family carbohydrate kinase
    4.1e-05   23.2   0.0    5.4e-05   22.8   0.0    1.3  1  Carb_kinase   Carbohydrate kinase
    0.00053   20.1   0.6     0.0032   17.6   0.1    2.0  2  DUF3612       Protein of unknown function (DUF3612)


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 !  166.0   0.1   2.2e-52   9.7e-49       1     242 [.      14     244 ..      14     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 2.2e-52
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       D+sG AGi+ D  ++ alg ++++++t++t qnt++  + + +p+e+ve+ql ++led++++ vKiG++++a++ + 
  gi|488600342|ref|YP_007906813.1|  14 DPSGCAGITLDSAVIRALGFHSCTIVTSITFQNTCKAIGHEVVPREVVEKQLLSILEDLNIAGVKIGVIHEAHTET- 89 
                                       9********************************************************************6655433. PP

                                       HHHHHHHTTS.SEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH CS
                      Phos_pyr_kin  78 vaeklkkykv.pvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk 153
                                         + l+  ++  vV+DPV+ +++g+++ +   ++ +++++++ a+vitPN  Eae+L+g ki++ +d++++a+kl++
  gi|488600342|ref|YP_007906813.1|  90 -LKLLN--DFdVVVWDPVFKSTTGHTFSD---ISRIAKRVCEVAKVITPNKYEAEVLSGVKIESIDDARACAEKLSE 160
                                       .34554..45579*************965...67778899************************************* PP

                                       TT-SEEEEEEGGS-SSSEEEEEEEE..TSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHH CS
                      Phos_pyr_kin 154 lgakaVlikGghlegeeavvtdvly..dgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyv 228
                                       +   +V+i+Gg leg+     dv+y   +++v++++ae  +  + +GtGC++s+a+++ l k ++l +A + A+ y+
  gi|488600342|ref|YP_007906813.1| 161 MLNVSVVITGGGLEGN-----DVVYdmIRDHVFTVSAEFSD-FEIRGTGCAYSTALTCFLTK-RKLDDACRLARLYL 230
                                       ************9553.....44443345677888888888.99****************98.78************ PP

                                       HHHHHCG-BSTSSS CS
                      Phos_pyr_kin 229 teaikealelgkga 242
                                        +++k+a  +gk +
  gi|488600342|ref|YP_007906813.1| 231 LSSVKSAKPVGKCH 244
                                       *******9999877 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   5.3e-10   2.4e-06     150     229 ..      89     172 ..      59     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.3e-10
                                       HHHHHHHHTTE.EEEEECESSSHH...HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSE CS
                              PfkB 150 elaeaaknggt.fdpnlldplgaq...fkeallellaladllkpneeElealtgekledieealaalhklkakgakt 222
                                       +l+ +        dp++ +++g          +++ + a +++pn +E+e l+g k+e+i++a a+++kl +  +  
  gi|488600342|ref|YP_007906813.1|  89 TLKLLNDFDVVvWDPVFKSTTGHTfsdISRIAKRVCEVAKVITPNKYEAEVLSGVKIESIDDARACAEKLSEMLNVS 165
                                       44444444444556666666665566444455666699*************************************77 PP

                                       EEEEEGG CS
                              PfkB 223 vvvtlGk 229
                                       vv+t G 
  gi|488600342|ref|YP_007906813.1| 166 VVITGGG 172
                                       7777664 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-08   5.4e-05     114     205 ..     122     218 ..       8     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-08
                                       TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEEST....TSEEEEC.TTEEEEE----GGG- CS
                       Carb_kinase 114 serkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkge....kdvivsp.egevlinstgssala 185
                                          + + ++TP+k E + L+++ +++ dd   +a++l+++ln+ v++ g     +dv+ +   + v+++s++ s   
  gi|488600342|ref|YP_007906813.1| 122 RVCEVAKVITPNKYEAEVLSGVKIESIDDARACAEKLSEMLNVSVVITGGglegNDVVYDMiRDHVFTVSAEFSDFE 198
                                       4445677***************************************9995333256666668999*********999 PP

                                       STTHHHHHHHHHHHHHHCTS CS
                       Carb_kinase 186 kGGsGDvLaGligalLaqne 205
                                         G+G   + ++ ++L   +
  gi|488600342|ref|YP_007906813.1| 199 IRGTGCAYSTALTCFLTKRK 218
                                       99999999999999998766 PP

>> DUF3612  Protein of unknown function (DUF3612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   7.1e-07    0.0032      83     158 ..       8      86 ..       2      90 .. 0.82
   2 ?    0.6   0.0      0.12   5.3e+02      76     126 ..     123     172 ..     111     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.1e-07
                           DUF3612  83 kdlagnnhvlcagidlnpa.ieaqgkdalslaeel..kkacvknggsaaipkaikkdlvsvakilninwvergiesd 156
                                         +ag +   cagi l+ a i a g  + ++++ +  +++c + g ++   + + k+l s+   lni+ v+ g+ ++
  gi|488600342|ref|YP_007906813.1|   8 LSIAGLDPSGCAGITLDSAvIRALGFHSCTIVTSItfQNTCKAIGHEVVPREVVEKQLLSILEDLNIAGVKIGVIHE 84 
                                       5667778888******987479********9987522678877777766667789******************9988 PP

                           DUF3612 157 ar 158
                                       a+
  gi|488600342|ref|YP_007906813.1|  85 AH 86 
                                       85 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                           DUF3612  76 ccesikvkdlagnnhvlcagidlnpaieaqgkdalslaeelkkacvknggs 126
                                       +ce  kv      +  + +g+ ++   +     a +l+e l+  +v +gg 
  gi|488600342|ref|YP_007906813.1| 123 VCEVAKVITPNKYEAEVLSGVKIESIDD-ARACAEKLSEMLNVSVVITGGG 172
                                       5888888877777777778888875444.4456788888888777766653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1685.43
//
Query:       gi|488600343|ref|YP_007906814.1|  [L=77]
Description: Thioredoxin-like protein and domains [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-28   98.1   1.1    2.7e-28   97.9   1.1    1.0  1  NifU      NifU-like domain


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 !   97.9   1.1   1.5e-32   2.7e-28       1      67 []       7      75 ..       7      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 1.5e-32
                                      HHHHHHH.HGGG--GG--EEEEEEEETT..EEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EEE CS
                              NifU  1 ieevleeeirPaLasdGGdielvdvdeg..vVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeVe 67
                                      +eev++++irPaL++dGG+i lvdv+e+  +Vkv+l GaC+gCp+s++tl++++e+ L++++pevk+V+
  gi|488600343|ref|YP_007906814.1|  7 VEEVIDKDIRPALMRDGGNIALVDVEEDkgIVKVQLLGACGGCPMSQLTLTMVVEQHLRRKIPEVKKVI 75
                                      89***********************99999*************************************95 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:                      376  (0.0209716); 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: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.42
# Mc/sec: 552.29
//
Query:       gi|488600344|ref|YP_007906815.1|  [L=137]
Description: hypothetical protein Asulf_00813 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.44u 0.44s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 789.23
//
Query:       gi|488600345|ref|YP_007906816.1|  [L=338]
Description: hypothetical protein Asulf_00814 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  138.2  26.6    5.2e-40  137.8  26.6    1.1  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 !  137.8  26.6   2.9e-44   5.2e-40       1     301 []      15     324 ..      15     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 2.9e-44
                   LPG_synthase_TM   1 illglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllraylig 77 
                                       ill++++s++ ++++++ +  + +++++++ld  +l++all+++  + ++alr ++l   lg+ris++++l+a+  +
  gi|488600345|ref|YP_007906816.1|  15 ILLAIGISLATIFIIFKLTETELTWKVISALDKKFLAVALLFHIAFWAFWALRLQYLSLNLGKRISFSYALQATISS 91 
                                       7899***********999****************************99*********9999**************** PP

                   LPG_synthase_TM  78 lfvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalall 154
                                        f+  +tP+++gGe++ra +l+   g+s+++a+a+v++erlld ++++ +++++++l g ++      +++++++ +
  gi|488600345|ref|YP_007906816.1|  92 SFLAAITPSSAGGEPLRAKMLSD-AGMSYGEATATVLAERLLDAIFFITALPFMVILSGFKVRF---GVYAGVIFTI 164
                                       ***********************.************************************9876...4455555555 PP

                   LPG_synthase_TM 155 llavlalllllllrrrlarlarvlkrlarllarfarklasakr......................klvlasprrlll 209
                                       ++ ++++ l++++ + + ++ ++ +++   ++  +       +                       l+   + r+l+
  gi|488600345|ref|YP_007906816.1| 165 TFIGFLV-LMYMIFKDQENIDKITSKISFIFRFWK-------KdvgsrvydvvkkellffrsaliDLAKIPKLRILV 233
                                       5444444.445555566677777777765544333.......233445668999999999999985555566789** PP

                   LPG_synthase_TM 210 afllslliwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaa 286
                                        ++l+ l+w++e+ +  +ll a++ ++ + ++++ +l+l++++++p++Pg +G++E ++   ++ + v++a+ ++++
  gi|488600345|ref|YP_007906816.1| 234 LLILTSLTWIFEFCVPSALLLAMKSHPYWIESIASQLFLIILSLIPLTPGASGIAETGMLYFYSYF-VNSAYMGTLV 309
                                       ******************************************************************.********** PP

                   LPG_synthase_TM 287 llyrlitlylllllG 301
                                        l+r+it+ + l++G
  gi|488600345|ref|YP_007906816.1| 310 GLWRIITYHTNLVVG 324
                                       ********9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 2357.71
//
Query:       gi|488600346|ref|YP_007906817.1|  [L=312]
Description: hypothetical protein Asulf_00815 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-16   59.4   0.4    5.5e-16   59.1   0.4    1.2  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    2.5e-13   50.5   0.0    3.2e-13   50.1   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.1e-09   38.3   0.5    2.6e-09   37.1   0.2    1.8  2  Glycos_transf_2  Glycosyl transferase family 2
    3.3e-07   29.9   0.0    4.9e-07   29.4   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> 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 !   59.1   0.4   1.2e-19   5.5e-16       1     181 [.      83     263 ..      83     294 .. 0.71

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.2e-19
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelas.pevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsg 76 
                                       +i++ D D+ + +d++ ++++ l++ +++ i++ p ++ n  n+ +e+  +++ +  + +       +r+  + G +
  gi|488600346|ref|YP_007906817.1|  83 YIAIFDVDSIPEEDFVVKCVEALERnDKAYIASSPRFISNPVNLCSETVEAEYHLINYLL--KK---SRFRQFNGLI 154
                                       799*********************83677799999***9999999999998884333332..22...2355699999 PP

                   Glyco_trans_2_3  77 aflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.eleklill 152
                                        +lr++ l e  + d  es+++ED d++ r+ ++Gy  ++v+ + v+e+ p ++++ + Qr+Rw+yG  +l+k++  
  gi|488600346|ref|YP_007906817.1| 155 GVLRAKHLYEH-RLD--ESAITEDADFATRMHALGYEAVLVETR-VFEQAPVRWKDLFSQRRRWYYGGlQLWKHFNF 227
                                       9*********9.888..9************************88.9*********************7433333333 PP

                   Glyco_trans_2_3 153 vrll......gylgsl.lwsalplhlallllfslla 181
                                       vr        +++ sl l+  + + + +l+l+++l 
  gi|488600346|ref|YP_007906817.1| 228 VRKAdfgfklHWILSLtLTYIIAIFIPFLILSPFLL 263
                                       333321111122222202222222223333333322 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 !   50.1   0.0   7.2e-17   3.2e-13      27     230 .]      29     217 ..       3     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 7.2e-17
                   Glyco_tranf_2_3  27 qeypr.vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravk...sdlvllvDdDtv 99 
                                        +yp  v++ +v d++d++            + ++v ++++++  g   ++ a+n++++++k   +d+++++D D++
  gi|488600346|ref|YP_007906817.1|  29 LKYPGeVRILYVLDRYDRK-----------IDVEGVEILHRENTRG--KRAGAINDGIDHFKdfnPDYIAIFDVDSI 92 
                                       4563336666666666666...........3345789999998544..577899******99888************ PP

                   Glyco_tranf_2_3 100 vePdtlkrllqff.ltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralgvltlnGsgslirrevlkel 175
                                        e d++ + + ++ + +k+ ++  p+f  n+ +l+s +   e+   +     + +  ++  +nG + + r++ l e 
  gi|488600346|ref|YP_007906817.1|  93 PEEDFVVKCVEALeRNDKAYIASSPRFISNPVNLCSETVEAEYHLINY----LLKKSRFRQFNGLIGVLRAKHLYEH 165
                                       *************9888999999*************998866544444....6666777777998888999998888 PP

                   Glyco_tranf_2_3 176 egldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                        +ld+ + +t+D++ + r+ + g+  + v+ + v e+ p  +k+++ qr+Rw+yg
  gi|488600346|ref|YP_007906817.1| 166 -RLDE-SAITEDADFATRMHALGYEAVLVETR-VFEQAPVRWKDLFSQRRRWYYG 217
                                       .8999.***********************999.99******************97 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 !   37.1   0.2   5.9e-13   2.6e-09      52     129 ..      49     130 ..       6     162 .. 0.75
   2 ?   -2.0   0.0       0.6   2.7e+03     102     129 ..     180     207 ..     176     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 5.9e-13
                                       C-TTEEEEEESSS-.HHHHHHHHHHHH--SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCC CS
                   Glycos_transf_2  52 edprvrvirreenv.Gkagalnaglraatgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetd 124
                                         ++v +++re+ +   aga+n g+++ +     yi+++D D++p++d++ k veale+++++ ++ ++++i+   +
  gi|488600346|ref|YP_007906817.1|  49 DVEGVEILHRENTRgKRAGAINDGIDHFKDFnpdYIAIFDVDSIPEEDFVVKCVEALERNDKAYIASSPRFISNPVN 125
                                       456899*****9996679*********9998888*************************777666555555555555 PP

                                       CCCHC CS
                   Glycos_transf_2 125 eiern 129
                                         + +
  gi|488600346|ref|YP_007906817.1| 126 LCSET 130
                                       55444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.6
                                       HHHHH.TTCEEEEEEEEEECCCCCCCHC CS
                   Glycos_transf_2 102 ealekdgadvvlgqrprifgetdeiern 129
                                        ++++ g+ +vl+ ++++++ + +++  
  gi|488600346|ref|YP_007906817.1| 180 TRMHALGYEAVLVETRVFEQAPVRWKDL 207
                                       5677888888999999999888888764 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 !   29.4   0.0   1.1e-10   4.9e-07      29     171 ..      79     214 ..      55     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.1e-10
                   Glyco_transf_21  29 akydllvisDsdvrvkpdyLeellaaledpkvglVts.lpvgsdakglaaaleaaflntlagvlqaklsglgfavGk 104
                                        + d++ i D d + ++d++ + ++ale+++ +++ s + + s++ +l+++ + a      ++l+   s+++  +G 
  gi|488600346|ref|YP_007906817.1|  79 FNPDYIAIFDVDSIPEEDFVVKCVEALERNDKAYIASsPRFISNPVNLCSETVEAEYHLINYLLKK--SRFRQFNGL 153
                                       5679*************************777766661666**********988888777778877..899999*** PP

                   Glyco_transf_21 105 smalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRqlrW 171
                                         +lr + L +    e+    + eD+ ++++++a G+  vl+++ +++++ p    +++l+++  rW
  gi|488600346|ref|YP_007906817.1| 154 IGVLRAKHLYEHRLDES---AITEDADFATRMHALGYEAVLVETRVFEQA-PV--RWKDLFSQRRRW 214
                                       ************66666...9*********************99988754.53..6*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.95s 00:00:01.56 Elapsed: 00:00:00.80
# Mc/sec: 1173.23
//
Query:       gi|488600347|ref|YP_007906818.1|  [L=347]
Description: Glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-36  125.9   0.6    2.2e-36  124.9   0.2    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
    1.7e-32  112.6   0.6    6.8e-32  110.7   0.1    2.0  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.3e-11   44.8   1.6    3.9e-07   30.2   0.7    2.3  2  Glyco_transf_4   Glycosyltransferase Family 4
    2.1e-10   40.9   0.0    5.9e-10   39.4   0.0    1.8  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00013   22.4   0.0     0.0057   17.1   0.0    2.3  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
       0.14   12.4   0.1        9.9    6.5   0.0    3.4  4  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.2   7.5e-40   2.2e-36       6     169 ..     168     323 ..     164     326 .. 0.93
   2 ?   -3.4   0.0         2   6.1e+03     140     155 ..     327     342 ..     327     343 .. 0.86

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 7.5e-40
                                       HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs 82 
                                       ++  +  +k+ ++l+vgrl+++Kg+ +li+a+++++k  + ++ l+++G+ge++++l++la++ +     +flg+++
  gi|488600347|ref|YP_007906818.1| 168 KFNCKNVKKQDFVLYVGRLVEYKGLPVLIEAMKKVQK--EFDCELIVIGDGEDRARLENLAKNIKA----RFLGRLP 238
                                       555566689*************************975..79*******************999888....******* PP

                                       SSSHHHHHHCESEEEEEESS..BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHH CS
                   Glycos_transf_1  83 redleellknadifvlpsis..EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklle 157
                                        ++++ ++++a ++vlps s  E+fGivllEAma+g+pviasn+ g++ev  +g   l+++ +  ++l+++i k+l+
  gi|488600347|ref|YP_007906818.1| 239 TKEVIGWMQKARVLVLPSFSrlEAFGIVLLEAMACGTPVIASNIAGVREVALEGG--LVFDDV--DDLSNKILKILT 311
                                       ***************************************************9998..999888..************ PP

                                       SHHHHHHHHHHH CS
                   Glycos_transf_1 158 deelrerlgena 169
                                       ++  +++l+ ++
  gi|488600347|ref|YP_007906818.1| 312 NDSFAKKLSAKG 323
                                       **9999998877 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2
                                       E-TT-HHHHHHHHHHH CS
                   Glycos_transf_1 140 vkpnnaealaeairkl 155
                                       vk++++e  +e+i+k+
  gi|488600347|ref|YP_007906818.1| 327 VKNYSWEVVSEKIEKI 342
                                       57889********997 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.53   1.6e+03      61      80 ..     119     140 ..     100     149 .. 0.73
   2 !  110.7   0.1   2.3e-35   6.8e-32       4     134 .]     180     312 ..     177     312 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.53
                                       ---.TH.HHHHHHH-SEEEE-- CS
                   Glyco_trans_1_4  61 Gfv.ed.laellaaadvfvaPs 80 
                                        +v e+ + ++l+++dv +a++
  gi|488600347|ref|YP_007906818.1| 119 ERVnEKvIVPVLESCDVIIATT 140
                                       4454225889999999999887 PP

  == domain 2  score: 110.7 bits;  conditional E-value: 2.3e-35
                                       EEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEE CS
                   Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvf 76 
                                       +l+vGrl+ ++kg+ +l+ea+++++k+ d++l+++Gdg+ r ++le+la+++  + +f+G++  +++  ++++a+v+
  gi|488600347|ref|YP_007906818.1| 180 VLYVGRLV-EYKGLPVLIEAMKKVQKEfDCELIVIGDGEdR-ARLENLAKNI--KARFLGRLptKEVIGWMQKARVL 252
                                       89*****5.56**************9988*********955.6**9888876..5*******9888*********** PP

                                       EE--....---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  77 vaPs....egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLled 134
                                       v+Ps    e fg++llEama+g+pv+a++++g++ev  e gl+++  d+++l ++il++l++
  gi|488600347|ref|YP_007906818.1| 253 VLPSfsrlEAFGIVLLEAMACGTPVIASNIAGVREVALEGGLVFD--DVDDLSNKILKILTN 312
                                       ******999**************************8867799999..************986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   2.1e-05     0.062       1      31 [.      20      49 ..      20      64 .. 0.85
   2 !   30.2   0.7   1.3e-10   3.9e-07      72     169 ..      66     167 ..      60     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                    Glyco_transf_4  1 vGGverhvleLaraLarrGheVtvvtpgddg 31
                                      +GGve hv+ L+r+L ++ ++Vtv++++  +
  gi|488600347|ref|YP_007906818.1| 20 IGGVEIHVEGLVRQLSKK-YNVTVISSNNTR 49
                                      7*****************.******987665 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.3e-10
                    Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglye.......krllkarlkplsrllralerrllrradrviavS 141
                                       + D+ H+h p +++ a++  ++    p+V+t+H+          +r+ ++   + +r+++++   +l ++d +ia++
  gi|488600347|ref|YP_007906818.1|  66 QADIYHSHVPSPFF-AWWVMKK-GYSPHVITYHNDVVvpstvngYRIPGNVGYLVERVNEKVIVPVLESCDVIIATT 140
                                       78***999988764.4444454.778************9999988888888889999999999999**********8 PP

                    Glyco_transf_4 142 eatadelrerygvppekitVipnGvDle 169
                                       ++ a     + ++  +k++V+pn+vDl+
  gi|488600347|ref|YP_007906818.1| 141 KSYAVTSPVLSRFI-DKVEVVPNAVDLK 167
                                       87666666644554.89*********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 !   39.4   0.0     2e-13   5.9e-10       5      90 ..     257     339 ..     251     341 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2e-13
                   Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaeh 81 
                                        sr e +  +l+Ea+acG++++++ + g++e   +g  +++f+d+++l  ki + l+n+  ++++++++ + v +++
  gi|488600347|ref|YP_007906818.1| 257 FSRLEAFGIVLLEAMACGTPVIASNIAGVREVALEG--GLVFDDVDDLSNKILKILTNDSFAKKLSAKGLKSV-KNY 330
                                       567788999************************999..**********************************5.699 PP

                   Glyco_trans_1_2  82 tydhraeql 90 
                                       +++   e++
  gi|488600347|ref|YP_007906818.1| 331 SWEVVSEKI 339
                                       999888877 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 ?    3.3   0.0     0.035     1e+02       1      29 [.      21      48 ..      21      66 .. 0.87
   2 !   17.1   0.0   1.9e-06    0.0057      73     159 ..      66     162 ..      61     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.035
                   Glyco_trans_4_4  1 gGigryvaelaraLaarGheVtvltpapa 29
                                      gG++++v+ l+r+L +  + Vtv+ ++ +
  gi|488600347|ref|YP_007906818.1| 21 GGVEIHVEGLVRQLSKK-YNVTVISSNNT 48
                                      8**************99.*****987665 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.9e-06
                   Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlhglllrrg....sgavrrlyraler.......rllrradavlvvse 138
                                       + d+ h+h p ++++a++   +   p+v+t+h++ +++      +  +++   +er        +l ++d++++++ 
  gi|488600347|ref|YP_007906818.1|  66 QADIYHSHVP-SPFFAWWVMKKGYSPHVITYHNDVVVPStvngYRIPGNVGYLVERvnekvivPVLESCDVIIATTK 141
                                       5799999998.7777888875778********8775544333322233333444444446777************** PP

                   Glyco_trans_4_4 139 aeaeelralgvpadrvvvvpn 159
                                       + a +   l +  d+v+vvpn
  gi|488600347|ref|YP_007906818.1| 142 SYAVTSPVLSRFIDKVEVVPN 162
                                       ********************9 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0033       9.9      11      38 ..      28      54 ..      20      74 .. 0.78
   2 ?    0.7   0.0       0.2   5.8e+02      60      75 ..     130     145 ..     129     153 .. 0.87
   3 ?   -0.7   0.0      0.54   1.6e+03      33      57 ..     198     224 ..     186     229 .. 0.75
   4 ?   -1.4   0.0       0.9   2.7e+03      21      43 ..     304     325 ..     260     329 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0033
                                      HHHHHHHHHTTEEEEEEESSHHHHHHHH CS
                            TrkA_N 11 rslaeeLseggkdvvvidkdeerveelr 38
                                      + l+++Ls+++ +v+vi ++  r+ e+ 
  gi|488600347|ref|YP_007906818.1| 28 EGLVRQLSKKY-NVTVISSNNTRCIEIP 54
                                      5799*****99.5**********99875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                                       GGGESEEEE-SSSHHH CS
                            TrkA_N  60 iekadaviaatgddea 75 
                                       +e++d++ia+t+++++
  gi|488600347|ref|YP_007906818.1| 130 LESCDVIIATTKSYAV 145
                                       689********99876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.54
                                       HHHHHHHTT.SE.EEES-TTSHHHHHH CS
                            TrkA_N  33 rveelreeg.le.vvvgdatdeevLee 57 
                                       +++++++e+ +e +v+gd+ d++ Le+
  gi|488600347|ref|YP_007906818.1| 198 AMKKVQKEFdCElIVIGDGEDRARLEN 224
                                       456666666655588899999988876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.9
                                       TEEEEEEESSHHHHHHHHHTTSE CS
                            TrkA_N  21 gkdvvvidkdeerveelreegle 43 
                                       + +++ i ++++ +++l+++gl+
  gi|488600347|ref|YP_007906818.1| 304 N-KILKILTNDSFAKKLSAKGLK 325
                                       2.466666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); 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:                         6  (0.000334653); expected 0.2 (1e-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 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2201.25
//
Query:       gi|488600348|ref|YP_007906819.1|  [L=207]
Description: Uncharacterized Rossmann fold enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-12   46.5   0.0    3.8e-12   46.2   0.0    1.2  1  MAF_flag10  Protein of unknown function DUF115


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 !   46.2   0.0   2.1e-16   3.8e-12      35     167 ..      59     184 ..      19     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 2.1e-16
                        MAF_flag10  35 PSLekn.lellkelrdkaviiaadtalkaLlke..gIkPDivvs.lDpqeasyevfkeaekkgdiplvfasgvnpel 107
                                       P L ++  e ++e   + v i+a+ a++a  +   +++PDi+v+ +++   s +++ e+ ++  i++++a+g+n++ 
  gi|488600348|ref|YP_007906819.1|  59 PILSEDdAEEIREF--EGVKITAGKAINAVREFipDFVPDIHVTdMEE---SDDLLVEIGER-CILVLHAHGDNIDR 129
                                       66655446666655..45668889999999886669********9999...88889999998.************** PP

                        MAF_flag10 108 lkkykgpkiflvtgstqa.lelleeekneilfgGgsvantaldlAvklgfkeIiliGqDla 167
                                       + ++ ++  ++v +++ + ++ +       +fgG++++++a  +A +++++ I liG+D+ 
  gi|488600348|ref|YP_007906819.1| 130 VMSVIPKIGYFVGTTQSIpFDKI------YNFGGFTDGDRAACMAKHFNANGIKLIGFDFE 184
                                       *9999888887776555456666......8*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.42s 00:00:00.98 Elapsed: 00:00:00.60
# Mc/sec: 1041.18
//
Query:       gi|488600349|ref|YP_007906820.1|  [L=1029]
Description: Isoleucyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-202  671.7   7.3     1e-201  671.3   7.3    1.1  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
    3.2e-32  111.6   0.9    9.3e-32  110.1   0.9    1.8  1  Anticodon_1      Anticodon-binding domain of tRNA
    4.3e-28   98.2   1.7    4.6e-09   35.5   0.0    4.2  3  tRNA-synt_1g     tRNA synthetases class I (M)
    8.7e-07   28.6   0.0    3.8e-05   23.2   0.0    2.6  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
    0.00018   21.7   0.5       0.13   12.5   0.0    3.4  3  DALR_1           DALR anticodon binding domain
    0.00025   20.1   0.0     0.0014   17.6   0.1    2.2  2  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0077   15.8   0.0      0.075   12.5   0.0    2.8  1  tRNA-synt_1_2    Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
       0.11   12.6   3.3       0.25   11.5   0.1    2.8  3  Cass2            Integron-associated effector binding protein
       0.16   11.3   0.1       0.41   10.0   0.1    1.6  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
       0.19   11.9   1.5       0.29   11.3   0.1    1.9  2  RFC1             Replication factor RFC1 C terminal domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.3   7.3  5.7e-205    1e-201       3     602 .]      19     627 ..      17     627 .. 0.95

  Alignments for each domain:
  == domain 1  score: 671.3 bits;  conditional E-value: 5.7e-205
                       tRNA-synt_1   3 yekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                        ++W+e++++++   k++  ++f +vdgPPy tG++H+G a++k+lkd + ry+rm G++v+ +pGwD++Gl+ie k
  gi|488600349|ref|YP_007906820.1|  19 EKFWKENKIYERV--KNRGDRKFFFVDGPPYTTGRIHLGTAWNKVLKDSILRYRRMMGYRVTDTPGWDMHGLPIEVK 93 
                                       589*********9..7777999******************************************************* PP

                       tRNA-synt_1  80 vekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgli 156
                                       ve++lg + kk+ +++g ++f+e + +++ + ++ +++q+k lGv++D+d++y+T++ ++ +a ++++++ +++gl+
  gi|488600349|ref|YP_007906820.1|  94 VEQELGFRSKKDIEDYGIDKFVEMCLNYALKNKKAMEEQFKMLGVWMDWDNPYMTIKADYINAAWWTIKQGYERGLL 170
                                       ***************************************************************************** PP

                       tRNA-synt_1 157 yrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv...... 227
                                        + + +vnw+++++tal+++Evey d+kd++i+v+fpl+++e  ++vi+TTtP+Tl++++avav+p l+y+      
  gi|488600349|ref|YP_007906820.1| 171 EKKQMVVNWCPRCETALADAEVEYWDEKDPSIYVKFPLKKEEG-YIVIWTTTPWTLPANMAVAVHPSLEYAkikakk 246
                                       *******************************************.****************************99987 PP

                       tRNA-synt_1 228 .itkeklilaeallkslvkke.sek.kiledergkeLegkevelpl.......vnrkipiiaddyvdkeaGtGvVki 294
                                         ++e lila+ l +++++k   ++ +i++++ g++L+g+e+e+pl       ++ +  + + ++v +e+ tG+V+i
  gi|488600349|ref|YP_007906820.1| 247 dGKEEILILAKELADNVLEKAgYDSwEIVDTFLGEDLVGLEYEHPLfefvpeqKKFRHAVYMAEFVSAEN-TGCVHI 322
                                       777889**************987767********************9***987777888999****9986.****** PP

                       tRNA-synt_1 295 aPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkp 371
                                       aP+h+ +Dye+g +++l++ n++d+ g++te+a++++g++v da++ ++e+lkekglll +e+i h +++c+r k p
  gi|488600349|ref|YP_007906820.1| 323 APGHGLEDYELGLEHGLDIFNPVDDRGVYTEKAGKYAGINVRDANQVIIEDLKEKGLLLAHEHIVHRYGHCWRCKSP 399
                                       ***************************************************************************** PP

                       tRNA-synt_1 372 iiyrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvree 447
                                       iiyr+teqWf +v+el+d++++++ek++++p + +e+r+++w+ n++dWciSRqr+WG +ip++v ++ +++ v+ +
  gi|488600349|ref|YP_007906820.1| 400 IIYRSTEQWFLKVSELKDKMIEEIEKTRWIPSWaGEARFKDWVGNAKDWCISRQRYWGIPIPVWVCEKCGKMKVVGD 476
                                       *********************************99************************************999888 PP

                       tRNA-synt_1 448 lkelvagreeeeaekkalekeakdkl...kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmll 521
                                       ++e+  +   + ++ k       d++    +  g++++++dv+DvWF+Sg    +tl+yp   +e++++ +pad+++
  gi|488600349|ref|YP_007906820.1| 477 INEIPWESDLDLHRPKV------DEVtfdCECGGKMKRVPDVFDVWFDSGVASWGTLKYPRF-REDFENLWPADFIT 546
                                       88877744444444443......333332345789***************************.************** PP

                       tRNA-synt_1 522 eGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrd 598
                                       eG D++rgW+++ +  s+  +g++P+k+vl+hg+++de+GrKmSKslgNv++p+dv+k++g+d+ Rl++++s v +d
  gi|488600349|ref|YP_007906820.1| 547 EGHDQTRGWFYSQLGASVIAFGKAPYKTVLMHGFTLDEQGRKMSKSLGNVVEPEDVVKEVGVDSFRLYVLSSAVWED 623
                                       ***************************************************************************99 PP

                       tRNA-synt_1 599 inls 602
                                       +++s
  gi|488600349|ref|YP_007906820.1| 624 LRFS 627
                                       9985 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 !  110.1   0.9   5.2e-35   9.3e-32       1     151 [.     669     821 ..     669     822 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 5.2e-35
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       drwils+l++l   +++aye+y+++++++a  +f+++d+++wy++lv+p  + e++++++  +++++l+v+++ +r+
  gi|488600349|ref|YP_007906820.1| 669 DRWILSRLENLNMVAKDAYENYSLHRIVRAFLNFVVEDFSRWYIQLVRPVVWEEKDSPSKLaVYTTILKVVDKASRI 745
                                       9****************************************************99988866699************* PP

                       Anticodon_1  77 laPfmPfitEelwqr.eeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselkvv 151
                                       +aP++P+++E ++ +  +   ++kesi+l+ +pe ++ l ++el ee+++++++iv+ + ++r++ k k +++l++ 
  gi|488600349|ref|YP_007906820.1| 746 IAPIAPYLAEWIYINfVKAFRDSKESIFLERFPEPDKGLiDNEL-EEMMDFVRDIVESASNARQKAKKKLRWPLRKL 821
                                       *************88733344899*********94445569898.9************************9999876 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 !   35.5   0.0   2.5e-12   4.6e-09       8     136 ..      46     193 ..      43     195 .. 0.79
   2 !   25.6   0.2   2.7e-09   4.8e-06     168     238 ..     392     461 ..     374     474 .. 0.87
   3 !   32.2   0.1   2.6e-11   4.6e-08     244     377 ..     512     636 ..     497     646 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2.5e-12
                                       B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HH............HHHH... CS
                      tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpe............elve... 68 
                                       pY++g++HlG + + +  D + Ry+r+ g+ v+   g D+hG pie+k e+e g   +            e++    
  gi|488600349|ref|YP_007906820.1|  46 PYTTGRIHLGTAWNKVLKDSILRYRRMMGYRVTDTPGWDMHGLPIEVKVEQElGFRSKkdiedygidkfvEMCLnya 122
                                       8***********************************************98654333331111111111122333111 PP

                                       .HHHHHHHHHHHHTT-..--SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                      tRNA-synt_1g  69 .kvheeikelfkklni..sfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                        k++++++e+fk l++   +d+ + t + +  +++   +k+ +e+gl+++k++ + +cp++e+ l+d +ve
  gi|488600349|ref|YP_007906820.1| 123 lKNKKAMEEQFKMLGVwmDWDNPYMTIKADYINAAWWTIKQGYERGLLEKKQMVVNWCPRCETALADAEVE 193
                                       1567888999999987335778889999999999999999***************************9986 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.7e-09
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       ++  ++s  ++++te++f+k+s++++k+ e ie+++   +   +   k+w+ +  kd++isr+  wGip+P
  gi|488600349|ref|YP_007906820.1| 392 HCWRCKSPIIYRSTEQWFLKVSELKDKMIEEIEKTRWIPSWAGEARFKDWVGN-AKDWCISRQRYWGIPIP 461
                                       788899999***********************777766777778899****99.9***************9 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 2.6e-11
                                       EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEE..EGGGHH..HHHTHHHHHHHHTT----S-EE CS
                      tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfi..gkdiik..FHtifwPaillgaelklpkkvv 316
                                       v+ VW+d  +    ++k+        e++++ W +        fi  g d ++  F +  + a +++ +    k+v 
  gi|488600349|ref|YP_007906820.1| 512 VFDVWFDSGVASWGTLKYPR----FREDFENLWPA-------DFIteGHDQTRgwFYS-QLGASVIAFGKAPYKTVL 576
                                       56677777777777777764....35677777733.......4441144444321332.234555667777789999 PP

                                       EE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHH CS
                      tRNA-synt_1g 317 ahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNs 377
                                        h++ l  +g+K+SkS g+vv ++++++++ +d +R y++++a   +Dl fsw+++ + +N+
  gi|488600349|ref|YP_007906820.1| 577 MHGFtLDEQGRKMSKSLGNVVEPEDVVKEVGVDSFRLYVLSSAV-WEDLRFSWDEVRN-INR 636
                                       9**9456789****************************998765.68******99754.554 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 ?    2.2   0.0     0.053        94      21      49 ..      50      78 ..      35      80 .. 0.90
   2 !   23.2   0.0   2.1e-08   3.8e-05     229     296 ..     563     631 ..     548     636 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.053
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvq 49
                                        +hlG a + v  D + r+ +++gY v+
  gi|488600349|ref|YP_007906820.1| 50 GRIHLGTAWNKVLKDSILRYRRMMGYRVT 78
                                      579***********************996 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2.1e-08
                                       HHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHH CS
                      tRNA-synt_1e 229 seaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeell 296
                                       s  af+  ++    +h   l  +g+kmsksL+n++  +dv+k++    +Rl++ls    + l f+ +++
  gi|488600349|ref|YP_007906820.1| 563 SVIAFGkAPYKTVLMHGFTLDEQGRKMSKSLGNVVEPEDVVKEVGVDSFRLYVLSSAVWEDLRFSWDEV 631
                                       5556664667778899999999*******************************9999888999886665 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.092   1.7e+02      68     106 ..      14      64 ..      10      67 .. 0.82
   2 !   12.5   0.0   7.2e-05      0.13      32     110 ..     666     745 ..     634     748 .. 0.80
   3 ?    2.5   0.2     0.089   1.6e+02      25      70 ..     812     862 ..     796     866 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHHCTSTTSCTHHH.............HHHHHHHHHHHHHHHH CS
                            DALR_1  68 LaatfhkfYnkervlkeeeeel............aaaRLaLvkavrqvLan 106
                                       +a+++ kf++++++ +  ++              ++ R+ L  a ++vL++
  gi|488600349|ref|YP_007906820.1|  14 VAEEIEKFWKENKIYERVKNRGdrkfffvdgppyTTGRIHLGTAWNKVLKD 64 
                                       7999**********9955544355788888888899999999999999986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.2e-05
                                       SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHH.HHHHHHHHHHHHHHHC..TSTTSCTHHH.HHHHHHHHHHHHHHH CS
                            DALR_1  32 eeeekeLlkalaqfpevleeaaeelephklae.ylyeLaatfhkfYnke..rvlkeeeeelaaaRLaLvkavrqvLa 105
                                        +e++ +l +l +++ v ++a e++++h++++ +l  + ++f+++Y +   +v+ ee++    ++La    + +v+ 
  gi|488600349|ref|YP_007906820.1| 666 RKEDRWILSRLENLNMVAKDAYENYSLHRIVRaFLNFVVEDFSRWYIQLvrPVVWEEKDS--PSKLAVYTTILKVVD 740
                                       557788999*********************9834666899******85445999888884..599999888888887 PP

                                       HHHHH CS
                            DALR_1 106 ngLdl 110
                                       ++ ++
  gi|488600349|ref|YP_007906820.1| 741 KASRI 745
                                       77655 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.089
                                       CCHCC.......S-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHH CS
                            DALR_1  25 ealal.......leeeeekeLlkalaqfpevleeaaeelephklaeylyeLaa 70 
                                       ++  l       + e +++++++a+ +++++l++ ++  e++++ e+ +eL a
  gi|488600349|ref|YP_007906820.1| 812 KK--LrwplrklIIESQDEKVARAVKELEDILKAQCNVKEVEVVSEFEKELVA 862
                                       22..2235555456679***********************9999999888876 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1     2e+03      22      54 ..      37      69 ..      22      79 .. 0.62
   2 !   17.6   0.1     8e-07    0.0014     264     325 ..     569     631 ..     459     643 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                      tRNA-synt_1f 22 kdevvvesGispSGliHiGnlrevltadlvara 54
                                      ++   v+    + G+iH+G++ + +  d + r 
  gi|488600349|ref|YP_007906820.1| 37 RKFFFVDGPPYTTGRIHLGTAWNKVLKDSILRY 69
                                      444445555557899****99876666666655 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 8e-07
                      tRNA-synt_1f 264 eaPek..vvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldlei 325
                                       +aP+k  ++  + l+++g+kms+S Gnv+ +ed+++ +  ++ r+++l++   + ++++ d e+
  gi|488600349|ref|YP_007906820.1| 569 KAPYKtvLMHGFTLDEQGRKMSKSLGNVVEPEDVVKEVGVDSFRLYVLSSAVWEDLRFSWD-EV 631
                                       4454422567788899999*****************************9998888888888.55 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 !   12.5   0.0   4.2e-05     0.075       8     141 ..     200     346 ..     193     375 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                     tRNA-synt_1_2   8 eGleiefkveeseeklevfttrpdtlfGvtfvalapehplvekl..aekkkelaafieevkkksesereletke... 79 
                                         + ++f+++++e  + ++tt p tl     va+ p+ + ++    ++ k+e+  + +e++++  +++  ++ e   
  gi|488600349|ref|YP_007906820.1| 200 PSIYVKFPLKKEEGYIVIWTTTPWTLPANMAVAVHPSLEYAKIKakKDGKEEILILAKELADNVLEKAGYDSWEivd 276
                                       55778999999988999999999999988888888888777766234445666666666666555555555444211 PP

                     tRNA-synt_1_2  80 .keGv.ftglkaihPitgek.......ipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvik 141
                                          G    gl+  hP+ +           +++a++v +e +tg+v   P+h  +D+e   +++l+i + + 
  gi|488600349|ref|YP_007906820.1| 277 tFLGEdLVGLEYEHPLFEFVpeqkkfrHAVYMAEFVSAE-NTGCVHIAPGHGLEDYELGLEHGLDIFNPVD 346
                                       13344345777778874322222345578*******966.89**********************9987665 PP

>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7     3e+03      24      43 ..      14      33 ..       8      61 .. 0.73
   2 ?   11.5   0.1   0.00014      0.25      49     123 ..     198     270 ..     188     309 .. 0.83
   3 ?   -0.2   0.1      0.57     1e+03      25      90 ..     866     931 ..     851     980 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                                      ...HHHHHHHHHHHHHHHCT CS
                             Cass2 24 lnkeigklwreflekgrlkk 43
                                        +ei+k+w+e +  +r k+
  gi|488600349|ref|YP_007906820.1| 14 VAEEIEKFWKENKIYERVKN 33
                                      46788888887665555444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                                       EEEEEEEC-TT-CCGEEEEEEEEE-TTSSS-TT-EEEEE--EEEEEEEEESSSTT-HHHHHHHHHHCHCCHCTEE CS
                             Cass2  49 rvfgiyhdyeseenkfsyyagvevpsdsevpeglvkkeiPggkYavftiegdfeedlaeaweaiygellpnsnye 123
                                       +  +iy++++ ++++  +++++++p    +p+++ + + P+ +Ya+++ ++d +e++  + ++++  +l++++y+
  gi|488600349|ref|YP_007906820.1| 198 KDPSIYVKFPLKKEEGYIVIWTTTPW--TLPANMAVAVHPSLEYAKIKAKKDGKEEILILAKELADNVLEKAGYD 270
                                       55689999988888888899999999..**********************9999******************998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.57
                                       ..HHHHHHHHHHHHHHHCTTSBSTEEEEEEEC-TT....-CCGEEEEEEEEE-TTSSS-TT-EEEEE--E CS
                             Cass2  25 nkeigklwreflekgrlkkikkdkrvfgiyhdyes....eenkfsyyagvevpsdsevpeglvkkeiPgg 90 
                                        k+ig l+++  +++   + + + ++ +i + + +     ++k++ +  +e++   +vpeg+ + e+ +g
  gi|488600349|ref|YP_007906820.1| 866 FKKIGPLFKDRAKEV--AEMIRNMDSASITEATRNgievFGQKYRLEEIAEIEA--KVPEGYEYSEFRSG 931
                                       567777777766655..7777787777777777777878889999999999999..99999999998776 PP

>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00023      0.41      22      86 ..     929     992 ..     912    1018 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                                       ETTEEEE-HHHHHHHHHHHHHHHHHH...........HHGGGSSS---HHHHHHHCT--....... CS
                   DNA_primase_lrg  22 kkGyaylpkeeleslllekfrkrlekalestkeslp.eleeeikederekleellealsesyvaed 86 
                                       + G++y++ e  e+ll+e++++++ + +++++++l+ ++ee+i+  + +++e++ + +s  y++++
  gi|488600349|ref|YP_007906820.1| 929 RSGWVYITTELDEELLKEAYAREIVRRVQEMRKELDlDVEEFIEVGI-SESEDFVKGFS-DYIKNE 992
                                       78********************************9966655555444.48888888888.444444 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1         2   3.6e+03     102     140 ..     109     146 ..     101     153 .. 0.67
   2 ?   11.3   0.1   0.00016      0.29      32     130 ..     803     906 ..     791     921 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2
                                       --HHHHHHTTT--SHHHHH..HHHHH-X...XXXXXXXXXX CS
                              RFC1 102 dgveevielmdeysLtked..vdslvelslvkgekkkedpl 140
                                        g+++++e+  +y L+ ++   ++ + l ++   ++ ++p+
  gi|488600349|ref|YP_007906820.1| 109 YGIDKFVEMCLNYALKNKKamEEQFKMLGVW---MDWDNPY 146
                                       3599***********9665435566666666...5555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00016
                                       HHTT-EE-SS-----.SHHHHHHHHHHHHHHHHHHHTTTTT------HHHHHTTTHHH....HHHHHS--------- CS
                              RFC1  32 aslvrgslegrisFp.swLGknSktnKnkRllqelqshlrlktsaskselrldylpll....kkklvkpLkeegkdg 103
                                       as +r++ ++++++p + L   S+ +K  R ++el+  l ++++ ++ e+  ++ + l    ++k + pL ++ +++
  gi|488600349|ref|YP_007906820.1| 803 ASNARQKAKKKLRWPlRKLIIESQDEKVARAVKELEDILKAQCNVKEVEVVSEFEKELvakpNFKKIGPLFKDRAKE 879
                                       56666777778888886777789*************999999999988877774444411114567889***99999 PP

                                       HHHHHHTTT--SHHHHHHHHHH-X... CS
                              RFC1 104 veevielmdeysLtkedvdslvelslv 130
                                       v e+i  md+ s+t    + +  + ++
  gi|488600349|ref|YP_007906820.1| 880 VAEMIRNMDSASITEATRNGIEVFGQK 906
                                       **************9999999888554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1029 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.92u 0.40s 00:00:01.32 Elapsed: 00:00:00.61
# Mc/sec: 5083.83
//
Query:       gi|488600350|ref|YP_007906821.1|  [L=56]
Description: hypothetical protein Asulf_00819 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 322.60
//
Query:       gi|488600351|ref|YP_007906822.1|  [L=260]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  188.6   0.4    1.2e-55  188.4   0.4    1.0  1  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.4   0.4   6.8e-60   1.2e-55       2     219 ..       5     242 ..       4     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 6.8e-60
                            DUF166   2 vltsgeyGervvenilnepdfersl...................ivavvevpeeldefiedpeelLpelkeaDivia 59 
                                       ++ sge+G+r+v n+ ++p+++++l                   i  v e++ + + +iedp+e+L+ l ++D++ia
  gi|488600351|ref|YP_007906822.1|   5 IIFSGEFGRRFVLNL-AYPESCPHLgacgiefcdkckdydfsdkIAFVRELNLSGQLYIEDPSEYLQDL-QSDVIIA 79 
                                       7899***********.99******9******************96666666667799**********65.68***** PP

                            DUF166  60 ytlhpDlllelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCsleeegkpkideFlee.. 131
                                       +++hpD+l+el+e a   ++kali+p e p+    glrk++ke ++e+gie+++pkpfCs++  g  +i++F++e  
  gi|488600351|ref|YP_007906822.1|  80 INIHPDVLIELPEAA---EAKALIIPIEDPSwcpLGLRKQIKEICDEIGIEFTAPKPFCSIRA-GGRHIKKFCDEfr 152
                                       **************5...59*************99**************************95.99*********99 PP

                            DUF166 132 fGkPelevevkdgkikkVeVlrsapCGstwyvakklkGkeveeaeekageahqs...YpClAsmerdfelketklhk 205
                                       +G+P +e++  ++ i++V+  r+  CG+++yvakk+kG+ + +++e ++  hq+   YpC+Asmerd e+ e+++h 
  gi|488600351|ref|YP_007906822.1| 153 IGTPDFEIKSAGNVIEDVKAFRD-TCGCAYYVAKKMKGYIITDKHELWKDVHQHqcaYPCMASMERDVEIVEAIFHL 228
                                       **********************7.6***********************988888889******************** PP

                            DUF166 206 AgyihkeavekAlk 219
                                       Agyi++  +++Al+
  gi|488600351|ref|YP_007906822.1| 229 AGYIMVYNFSRALG 242
                                       ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1919.91
//
Query:       gi|488600352|ref|YP_007906823.1|  [L=343]
Description: Phosphate uptake regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-06   25.4   0.0    2.7e-05   24.0   0.0    1.8  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.12   12.6   1.6         17    5.7   0.0    2.9  3  MazG            MazG nucleotide pyrophosphohydrolase domain
       0.12   12.0   1.3       0.72    9.5   0.0    2.1  2  Casc1_N         Cancer susceptibility candidate 1 N-terminus
       0.13   12.5   1.3        3.9    7.6   0.0    2.8  3  Imm5            Immunity protein Imm5


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 !   24.0   0.0     6e-09   2.7e-05       3      40 ..      29      66 ..      27      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6e-09
                                      ETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                      +G+s++v++Pke++    +++Gde++l   +d i++ p
  gi|488600352|ref|YP_007906823.1| 29 GGSSYMVSLPKEWVYRYKLKQGDELILNDFDDFIVIQP 66
                                      8*************************977666777666 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.9   8.4e+03      27      37 ..     162     172 ..     151     175 .. 0.69
   2 ?    5.7   0.0    0.0037        17       6      45 ..     207     246 ..     204     262 .. 0.80
   3 ?    4.6   0.5    0.0081        36      40      67 ..     312     339 ..     278     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHH CS
                              MazG  27 deleeELGDvL 37 
                                       ++l +E+ DvL
  gi|488600352|ref|YP_007906823.1| 162 KSLISEIEDVL 172
                                       45666666666 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHH CS
                              MazG   6 llaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflan 45 
                                       +++ ++ E +E+   + +   ++  eE++D+L+ +  + +
  gi|488600352|ref|YP_007906823.1| 207 MKRITVSEWDEMRSLLGSRIISKFCEEIADILFIMTRYLK 246
                                       566778888888888888999999*********8876665 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0081
                                       HHHHHHHHHHHH---HHHHHHHHHHHHH CS
                              MazG  40 vlflaniaeeeggidledvaetileKle 67 
                                       +l++++++e+ g+i++++ ++++l+K  
  gi|488600352|ref|YP_007906823.1| 312 LLQICRMLESIGEITFNKCVREMLKKNV 339
                                       5678899999****************75 PP

>> Casc1_N  Cancer susceptibility candidate 1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00016      0.72     113     158 ..     159     204 ..     134     218 .. 0.85
   2 ?    1.2   0.2     0.055   2.4e+02     103     137 ..     253     297 ..     239     339 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00016
                           Casc1_N 113 tlvlklieeLeelledtaeeelsekeveeykevilelrellnkkid 158
                                       +++ +li+e+e++led+++ ++ ek++  y+   ++l  l+ + ++
  gi|488600352|ref|YP_007906823.1| 159 QILKSLISEIEDVLEDNTDYNAFEKKIRSYENDFDRLYLLSVRIVN 204
                                       45789*****************************999887766655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.055
                           Casc1_N 103 edieevmetctlvlkl.........ieeLeelledtae.eelsek 137
                                       ++i+e m+ +++vl++         i++  e l + ++ +++ +k
  gi|488600352|ref|YP_007906823.1| 253 RSIKEHMKSIKQVLEMgfesfrasdISKTTEFLTEVEKvSNKIQK 297
                                       567777777777777766666644422222222211110111111 PP

>> Imm5  Immunity protein Imm5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00088       3.9      49      91 ..     154     193 ..     135     203 .. 0.85
   2 ?    2.0   0.0     0.046   2.1e+02      53      91 ..     230     267 ..     224     280 .. 0.84
   3 ?   -0.1   0.1      0.21   9.4e+02      76     103 ..     281     307 ..     260     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00088
                              Imm5  49 weevfaedqsplrlLekaedylyektdkeeiekeadklsndle 91 
                                        ++ f   q++ +l++++ed+l ++td++++ek++ +++nd +
  gi|488600352|ref|YP_007906823.1| 154 IKRMF---QILKSLISEIEDVLEDNTDYNAFEKKIRSYENDFD 193
                                       55555...678899*************************9988 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.046
                              Imm5  53 faedqsplrlLekaedylye.ktdkeeiekeadklsndle 91 
                                       f+e+  ++++L ++ +yl +   d+ +i+++++++++ le
  gi|488600352|ref|YP_007906823.1| 230 FCEE--IADILFIMTRYLKNhDFDRRSIKEHMKSIKQVLE 267
                                       5554..999*********99999*********99999887 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.21
                              Imm5  76 keeiekeadklsndlendsgeeaeetva 103
                                         e+  e++k+sn ++ +s+ee+e+ + 
  gi|488600352|ref|YP_007906823.1| 281 TTEFLTEVEKVSNKIQ-KSIEETEDGII 307
                                       4577888888888888.88888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2176.91
//
Query:       gi|488600353|ref|YP_007906824.1|  [L=391]
Description: tyrosine decarboxylase MnfA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-32  112.7   0.0      2e-32  112.3   0.0    1.1  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    5.1e-09   35.6   0.0    5.9e-09   35.4   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
     0.0054   16.0   0.0     0.0098   15.2   0.0    1.4  2  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.0   3.4e-36     2e-32      79     374 ..      73     338 ..      67     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 3.4e-36
                                       HHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEETTS- CS
                     Pyridoxal_deC  79 elevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsdqah 155
                                       +le  ++ +++ell+ +      e  g + +g++e+++ ++ A r+k++ ++k++            ++++  + ah
  gi|488600353|ref|YP_007906824.1|  73 KLEEKLIGMIGELLHGS------EVAGYICSGGTEANIQGIRAGRNKMRDKIKDSR----------NPNIVIPKSAH 133
                                       57888888888888888......3579999***********************998..........469999999** PP

                                       HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEE CS
                     Pyridoxal_deC 156 ssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlH 232
                                        s ek++ +lgv++r  +lde++k+ +++ ek++   +e+  + ++ v ++Gtt lg+ d + el ++ e+  + lH
  gi|488600353|ref|YP_007906824.1| 134 FSFEKIGDILGVEVRRAKLDEEYKVDVSEVEKLM---DEN--T-VCLVGIAGTTELGQIDPIVELSKLAEENCVELH 204
                                       ***************************9999976...445..3.48999**************************** PP

                                       EE-TTGGGGGGSGGGGG...GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTTTSEE CS
                     Pyridoxal_deC 233 vDAAyaGsaficpeirh...llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsdvaad 306
                                       vDAA++G  ++ p++ +   +++  + + Sit+ phK++++++  + +++++++ l  al++e  YL          
  gi|488600353|ref|YP_007906824.1| 205 VDAAFGG--LVIPFMNNpypFDFQNDGVSSITIDPHKMGMATIPSGGILFRNESYLR-ALEVETPYLT--------S 270
                                       *******..99999988888**********************************996.678*******........4 PP

                                       CCCGSSSSSG.HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECSTTBSSEEEEEE CS
                     Pyridoxal_deC 307 lgtkaiplsr.rvrilklwfvlralGveglqnqirksvelakyleklirkderfeivaevelglVcFrl 374
                                         ++++   r    ++  + vl  lG  g+++ + +++++ + l++++     fe v ++ +  V+F+ 
  gi|488600353|ref|YP_007906824.1| 271 RTQFTLTGTRpGTGVASAFAVLHGLGFDGMKKIVMECLKNTRLLTEEMISL-GFEPVIDPIMNVVSFKT 338
                                       5689999999999*********************************99865.599999*********85 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   9.8e-13   5.9e-09      66     179 ..      95     210 ..      74     341 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.8e-13
                                       EESSHHHHHHHHHHHCCCC....-TTTS..EEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH- CS
                       Aminotran_5  66 ftsGtteainlvalslars....lkpgd..eivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll 136
                                        +sG+tea+   +++ +++    +k+ +  +iv+ ++ h +     +++ +  g++v+ ++ldee ++d++e+ekl+
  gi|488600353|ref|YP_007906824.1|  95 ICSGGTEANIQGIRAGRNKmrdkIKDSRnpNIVIPKSAHFS----FEKIGDILGVEVRRAKLDEEYKVDVSEVEKLM 167
                                       57777775444433333332322443332257777666666....4599999************************* PP

                                       -TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTT CS
                       Aminotran_5 137 nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqa 179
                                       +e+t  +   +  +++G i+p+ e+ kla ++ + ++vDaa +
  gi|488600353|ref|YP_007906824.1| 168 DENTVCLVGIAGTTELGQIDPIVELSKLAEENCVELHVDAAFG 210
                                       ****************************************965 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.6e-06    0.0098      69     169 ..     121     208 ..      52     209 .. 0.83
   2 ?   -3.6   0.0      0.85   5.1e+03     202     216 ..     245     265 ..     229     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                                       -TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB-- CS
                   Beta_elim_lyase  69 qrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvv 145
                                        r++++++ + ah+ f   g i    gv++r +k +e+ k+d+ ++e++++e     + + l+ ++ T++   Gq+ 
  gi|488600353|ref|YP_007906824.1| 121 SRNPNIVIPKSAHFSFEKIGDI---LGVEVRRAKLDEEYKVDVSEVEKLMDE-----NTVCLVGIAGTTEL--GQI- 186
                                       6778888888899999988877...899999***9999**************.....589**********9..875. PP

                                       -HHHHHHHHHHHHHCT-EEEEEET CS
                   Beta_elim_lyase 146 sleelrevaaiakkygiplhlDgA 169
                                         + + e++++a+++ ++lh+D+A
  gi|488600353|ref|YP_007906824.1| 187 --DPIVELSKLAEENCVELHVDAA 208
                                       ..7788999**************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.85
                                       -SS-EEEEE-HH.......... CS
                   Beta_elim_lyase 202 anvGgvlafrddel.......e 216
                                       ++ Gg+l+ +++ +        
  gi|488600353|ref|YP_007906824.1| 245 IPSGGILFRNES-YlraleveT 265
                                       355777777766.224444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2348.39
//
Query:       gi|488600354|ref|YP_007906825.1|  [L=253]
Description: TIGR00245 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-66  224.6  22.9    1.3e-66  224.5  22.9    1.0  1  UPF0014   Uncharacterised protein family (UPF0014)


Domain annotation for each model (and alignments):
>> UPF0014  Uncharacterised protein family (UPF0014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.5  22.9     7e-71   1.3e-66       2     242 .]       7     243 ..       6     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 224.5 bits;  conditional E-value: 7e-71
                           UPF0014   2 lqlalalllvlialllslvlklglekelliaavrmvvQLllvGyvLklifalnsl.llvllillvmllvAaieaakr 77 
                                       ++la+a +l ++++++s+ +++++ +++ +aa+r + QL+l+++vL+++f+ + + +++l i+++m+l+A++++akr
  gi|488600354|ref|YP_007906825.1|   7 IKLAYASALAILVMAVSYLRRIEIGRDFSFAALRGFAQLMLLSIVLTYVFTSTIWhIFALPIFIAMALLAGYTSAKR 83 
                                       79*************************************************8755146778999************* PP

                           UPF0014  78 vkkklkklllivllsllvstlltlllllllviqpepwyepqylIPlaGmilGnamnaialalerllselksereeie 154
                                           ++k++li++ s+++++++ l+ +++l +   ++++p+++IPlaGm +Gnamn ++l+l+rllse++++r++ie
  gi|488600354|ref|YP_007906825.1|  84 --VGMPKATLITTPSIAIGATTSLAAMTVLKV---IPLQPKFVIPLAGMAFGNAMNICSLTLNRLLSEVRNNRSRIE 155
                                       ..578888999999999999999999999888...9***************************************** PP

                           UPF0014 155 alLalGatpkeAvkeivreairaaliPtinsmatvGlVsLPGmmtGqiLaGaspleAvkyqilimfmilastalstv 231
                                       a+LalGat+++Av+++ r++i++aliP+i++m+t+G++++PG+mtG+++aG++p++A+ yqi i+fmi++s ++++v
  gi|488600354|ref|YP_007906825.1| 156 AMLALGATAQQAVEQYERTSIKSALIPSIDNMRTLGIIFIPGAMTGMLMAGIDPTTAAVYQISIFFMIISSGIVAAV 232
                                       ***************************************************************************** PP

                           UPF0014 232 lvvlllyrrlf 242
                                        +++l+ +rlf
  gi|488600354|ref|YP_007906825.1| 233 NATYLTKKRLF 243
                                       *******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1488.83
//
Query:       gi|488600355|ref|YP_007906826.1|  [L=226]
Description: phosphate ABC transporter ATP-binding protein, PhoT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  120.9   0.0    6.9e-35  120.5   0.0    1.1  1  ABC_tran     ABC transporter
      8e-14   52.1   0.2    2.2e-06   27.7   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.5e-09   36.9   0.1    1.5e-05   24.6   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
      2e-05   24.2   0.0    4.1e-05   23.2   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
    2.2e-05   24.3   0.2    0.00019   21.2   0.2    2.0  1  AAA_30       AAA domain
    2.4e-05   24.8   0.0    3.9e-05   24.1   0.0    1.3  1  AAA_16       AAA ATPase domain
    3.8e-05   22.9   0.3     0.0012   18.0   0.1    2.2  2  T2SSE        Type II/IV secretion system protein
    0.00029   21.4   0.0    0.00059   20.4   0.0    1.5  1  AAA_23       AAA domain
     0.0003   20.8   0.0     0.0025   17.8   0.0    2.0  2  Rad17        Rad17 P-loop domain
    0.00064   20.0   0.2     0.0023   18.2   0.2    1.9  1  AAA_22       AAA domain
     0.0009   19.2   0.1     0.0015   18.5   0.1    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0014   17.6   0.2       0.15   10.8   0.0    2.6  2  ABC_ATPase   Predicted ATPase of the ABC class
     0.0021   17.4   0.0     0.0049   16.2   0.0    1.5  1  Zeta_toxin   Zeta toxin
     0.0021   18.0   0.2     0.0059   16.5   0.2    1.9  1  ATPase_2     ATPase domain predominantly from Archaea
     0.0021   18.2   0.0       0.08   13.2   0.0    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0057   16.7   0.1       0.83    9.7   0.0    2.2  2  AAA_14       AAA domain
     0.0077   16.0   0.0       0.53    9.9   0.0    2.1  2  AAA_15       AAA ATPase domain
     0.0086   16.0   0.4       0.24   11.3   0.0    2.2  2  NTPase_1     NTPase
     0.0089   16.6   0.1      0.012   16.1   0.1    1.6  1  AAA_18       AAA domain
  ------ inclusion threshold ------
      0.012   16.1   0.0        6.5    7.2   0.0    2.3  2  AAA          ATPase family associated with various cellular a
      0.018   14.2   0.3      0.025   13.7   0.3    1.5  1  NB-ARC       NB-ARC domain
      0.021   14.8   0.0      0.055   13.4   0.0    1.7  2  NACHT        NACHT domain
      0.028   14.2   0.0      0.042   13.6   0.0    1.5  1  AAA_24       AAA domain
       0.04   14.3   0.3       0.11   12.9   0.0    1.8  2  AAA_19       AAA domain
      0.051   13.7   0.1       0.16   12.2   0.0    1.8  2  AAA_33       AAA domain
      0.054   13.1   0.0        0.1   12.2   0.0    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.088   12.4   0.0       0.15   11.6   0.0    1.3  1  AAA_27       AAA domain
      0.093   11.5   0.0       0.15   10.8   0.0    1.3  1  Adeno_IVa2   Adenovirus IVa2 protein
        0.1   12.9   0.1        1.4    9.1   0.0    2.4  2  AAA_28       AAA domain
       0.13   11.1   0.0       0.17   10.7   0.0    1.3  1  AAA_PrkA     PrkA AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5   0.0   1.2e-37   6.9e-35       1     137 []      17     159 ..      17     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 1.2e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk v+lk+k+ e+++i G++G+GKStLl+++ +l++ + G+il+dg ++k+ +  +lr+++g+++q p +f++  v+
  gi|488600355|ref|YP_007906826.1|  17 LKGVNLKVKRREVMVIAGPSGSGKSTLLRCINRLTEIDGGDILVDGISIKKYNPIQLRRNVGMVFQFPVMFEGR-VK 92 
                                       799**********************************************************************9.** PP

                                       HH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +n           + ++ +ek+++++g+++l d  +    s+LSgG++qrva+ar+l+ +pk+lllDEpta
  gi|488600355|ref|YP_007906826.1|  93 DNiayglrllgktATEKSVEKLAREVGIENLLDADA----SKLSGGEQQRVAIARTLALEPKVLLLDEPTA 159
                                       ***********9888888************999999....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   3.6e-09   2.2e-06       1      83 [.      29     106 ..      29     121 .. 0.90
   2 !   22.9   0.0   1.1e-07   6.6e-05     233     298 ..     127     190 ..     112     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.6e-09
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       ++v+ Gp gsGKS+LL+++  l       ++++d+l +g +i+k+   + +++  + f+f + + +  + ++ yglr
  gi|488600355|ref|YP_007906826.1|  29 VMVIAGPSGSGKSTLLRCINRLTE-----IDGGDILVDGISIKKYNPIQLRRNVGMVFQFPVMFEGRVKDNIAYGLR 100
                                       68********************86.....899*******************************99999******999 PP

                            AAA_21  78 lersqv 83 
                                       l  +  
  gi|488600355|ref|YP_007906826.1| 101 LLGKTA 106
                                       876655 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.1e-07
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                       +a++lS G ++  a++  l+  +   ++ll+DEp ++L+P+ +r++  l+ k+ ++++  v+ +TH+
  gi|488600355|ref|YP_007906826.1| 127 DASKLSGGEQQRVAIARTLALEP---KVLLLDEPTASLDPENVRKIENLVlKLVRSRDLTVLWVTHD 190
                                       56777888888756666666655...9********************998677777**********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00049       0.3      24      44 ..      27      47 ..       3      52 .. 0.81
   2 !   24.6   0.0   2.5e-08   1.5e-05     112     212 ..     100     204 ..      82     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                      +++ +i Gp GSGKs ll  i
  gi|488600355|ref|YP_007906826.1| 27 REVMVIAGPSGSGKSTLLRCI 47
                                      56899***********99877 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 2.5e-08
                                       EETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 112 kingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael 182
                                       ++ gk++t+k v++l +++gi+         LSgGe++ va+a  +A++   p+ + llDe  a LD +nv+k+ +l
  gi|488600355|ref|YP_007906826.1| 100 RLLGKTATEKSVEKLAREVGIENLldadasKLSGGEQQRVAIARTLALE---PK-VLLLDEPTASLDPENVRKIENL 172
                                       667999***************8766666669**************9986...44.569******************9 PP

                                       HHH..HCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 183 lke..ksknaQfivislreemlekadklvgvt 212
                                       + +  +s +  ++ ++++ e+ ++    v v+
  gi|488600355|ref|YP_007906826.1| 173 VLKlvRSRDLTVLWVTHDVEQAKRIGDRVAVM 204
                                       87511455677888888888777775555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   6.8e-08   4.1e-05      14      40 ..      19      45 ..      15      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.8e-08
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllD 40
                                      g  ++++++++++++GpsGsGKSTll 
  gi|488600355|ref|YP_007906826.1| 19 GVNLKVKRREVMVIAGPSGSGKSTLLR 45
                                      5778999999***************95 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   3.1e-07   0.00019      16      68 ..      25     120 ..      20     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.1e-07
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaag...........................................grv 49 
                                       +++ v+v+ Gp G+GK+t+l+ ++++ e +g                                            r+
  gi|488600355|ref|YP_007906826.1|  25 KRREVMVIAGPSGSGKSTLLRCINRLTEIDGgdilvdgisikkynpiqlrrnvgmvfqfpvmfegrvkdniaygLRL 101
                                       5678**************************85666666666666666666666666666666666666666666666 PP

                            AAA_30  50 iglAptgkaAkvLaeelgi 68 
                                       +g + t+k  ++La+e+gi
  gi|488600355|ref|YP_007906826.1| 102 LGKTATEKSVEKLAREVGI 120
                                       6666666666666666665 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   0.0   6.5e-08   3.9e-05      25     127 ..      28     177 ..      14     196 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.5e-08
                            AAA_16  25 elvllsGesGvGKsslvrellralekd.......................ggif.....lrgkcdqlesaipy.sal 72 
                                       e++++ G+sG+GKs+l+r++ r  e d                       g++f     ++g+ +++   i+y + l
  gi|488600355|ref|YP_007906826.1|  28 EVMVIAGPSGSGKSTLLRCINRLTEIDggdilvdgisikkynpiqlrrnvGMVFqfpvmFEGRVKDN---IAYgLRL 101
                                       7899*****************7555558899999999999999999998855555466677777777...9995335 PP

                            AAA_16  73 aqalareellrqllde........aesaeleawrekleeala....................avpelagaeasrlle 121
                                       +   a+e+ +++l++e        a       ++ kl +  +                    ++++l+++  + + +
  gi|488600355|ref|YP_007906826.1| 102 LGKTATEKSVEKLAREvgienlldA-------DASKLSGGEQqrvaiartlalepkvllldePTASLDPENVRKIEN 171
                                       5555566777777777533333331.......222222222233333345557777777777777777777766666 PP

                            AAA_16 122 llkrll 127
                                       l+ +l+
  gi|488600355|ref|YP_007906826.1| 172 LVLKLV 177
                                       666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     2e-06    0.0012     116     149 ..      14      47 ..       5      66 .. 0.82
   2 ?    2.9   0.0     0.081        48     156     170 ..     205     219 ..     199     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyal 149
                                       ++i + ++  v++r +++++G+ gsGK+tll  +
  gi|488600355|ref|YP_007906826.1|  14 KEILKGVNLKVKRREVMVIAGPSGSGKSTLLRCI 47 
                                       5677778899********************9654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.081
                             T2SSE 156 sderivtvEDpvEiq 170
                                       +d rivtvEDp  i 
  gi|488600355|ref|YP_007906826.1| 205 KDGRIVTVEDPEKIL 219
                                       458********8775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   9.8e-07   0.00059      18      40 ..      26      48 ..       2      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.8e-07
                            AAA_23 18 skgltlItGpNGaGKTTildAik 40
                                       + + +I Gp G+GK+T+l++i 
  gi|488600355|ref|YP_007906826.1| 26 RREVMVIAGPSGSGKSTLLRCIN 48
                                      56789****************96 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.1e-06    0.0025      32      68 ..      14      50 ..       4      83 .. 0.84
   2 ?    0.7   0.0      0.71   4.2e+02     133     175 ..     149     191 ..     130     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.1e-06
                             Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLske 68
                                      ke lk   L+ +++++++i+GPsG gkst ++ + + 
  gi|488600355|ref|YP_007906826.1| 14 KEILKGVNLKVKRREVMVIAGPSGSGKSTLLRCINRL 50
                                      788999999999999***************9987664 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.71
                             Rad17 133 kklilvedlPnkfyrds.dalrevirkylrssealplilvitei 175
                                        k++l+++       +  ++++++++k +rs++  +++ v  ++
  gi|488600355|ref|YP_007906826.1| 149 PKVLLLDEPTASLDPENvRKIENLVLKLVRSRDL-TVLWVTHDV 191
                                       567777776666665555999*********9987.555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   3.8e-06    0.0023       4      30 ..      26      52 ..      22     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.8e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                      ++ ++v+ G+sG+GK+tllr + +  +
  gi|488600355|ref|YP_007906826.1| 26 RREVMVIAGPSGSGKSTLLRCINRLTE 52
                                      68899***************9988765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.4e-06    0.0015      90     123 ..      17      51 ..       2      66 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                       l+ ++ ++k  +++v++G+SG GKStL+  ++  +
  gi|488600355|ref|YP_007906826.1|  17 LKGVNLKVKRrEVMVIAGPSGSGKSTLLRCINRLT 51 
                                       5555556666699**************98887654 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 !   10.8   0.0   0.00025      0.15     243     265 ..      25      48 ..       5      51 .. 0.77
   2 ?    4.0   0.0      0.03        18     324     351 ..     132     159 ..     120     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                       -SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 243 pkG.vtlIvGggfhGKsTLLeAle 265
                                       ++  v++I+G+   GKsTLL+ ++
  gi|488600355|ref|YP_007906826.1|  25 KRReVMVIAGPSGSGKSTLLRCIN 48 
                                       3335*****************997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.03
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts 351
                                       SG   q ++i++ l ++ k+lL+DE t+
  gi|488600355|ref|YP_007906826.1| 132 SGGEQQRVAIARTLALEPKVLLLDEPTA 159
                                       8999999999999999999999999886 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.1e-06    0.0049      12      59 ..      23      70 ..      14      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.1e-06
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhP 59
                                      + +r  +++++G +G+GKs+l++ +++ +e +g+ + +d+ +++++ P
  gi|488600355|ref|YP_007906826.1| 23 KVKRREVMVIAGPSGSGKSTLLRCINRLTEIDGGDILVDGISIKKYNP 70
                                      55888999*******************999999999999999999998 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   9.9e-06    0.0059      17      48 ..      24      54 ..      12     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.9e-06
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienledkd 48
                                       +++e+++i Gp gsGK++Ll+  i++l + d
  gi|488600355|ref|YP_007906826.1| 24 VKRREVMVIAGPSGSGKSTLLRC-INRLTEID 54
                                      45699***************985.56665555 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 !   13.2   0.0   0.00013      0.08      18      84 ..     116     169 ..     104     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                           SbcCD_C  18 dedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                       +e g e  l++++++lSGGe+q +       a+a  +         +++++LDE  ++lD+e+++++
  gi|488600355|ref|YP_007906826.1| 116 REVGIENLLDADASKLSGGEQQRV-------AIARTLAL------EPKVLLLDEPTASLDPENVRKI 169
                                       455666668999999*****9543.......44455555......3789999********9999986 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    0.0014      0.83       2      22 ..      27      47 ..      26      71 .. 0.83
   2 ?    5.1   0.0     0.037        22       8      76 ..      97     160 ..      92     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                            AAA_14  2 rkilvitGaRrvGKTtllkql 22
                                      r+++vi G+  +GK+tll+ +
  gi|488600355|ref|YP_007906826.1| 27 REVMVIAGPSGSGKSTLLRCI 47
                                      6899*************8644 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.037
                            AAA_14   8 tGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                        G+R  GKT   ++ +++l    +++   nl d + +kl+  e+   +i + l   + ++l+lDE   +
  gi|488600355|ref|YP_007906826.1|  97 YGLRLLGKTAT-EKSVEKLA---REVGIENLLDADASKLSGGEQQRVAIARTLAL-EPKVLLLDEPTAS 160
                                       799******99.56666666...56666666666666666443333444444333.6799999997665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00088      0.53      24      48 ..      27      52 ..      17     117 .. 0.82
   2 ?    4.2   0.0     0.048        29     324     364 ..     149     189 ..     128     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00088
                            AAA_15 24 e.ltvliGkNnsGKSsilealdlFln 48
                                        ++v+ G+ +sGKS++l+ ++ + +
  gi|488600355|ref|YP_007906826.1| 27 ReVMVIAGPSGSGKSTLLRCINRLTE 52
                                      249******************98766 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.048
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++ll++EP a+L p++ + + +l ++l+++ +  v+  TH
  gi|488600355|ref|YP_007906826.1| 149 PKVLLLDEPTASLDPENVRKIENLVLKLVRSRDLTVLWVTH 189
                                       6799***************************9999999999 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0    0.0004      0.24       2      38 ..      30      68 ..      29      81 .. 0.75
   2 ?    2.9   0.1      0.15        90     111     156 ..     166     213 ..     134     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                                      EEEE--TTSSHHHHHHHHHHH..H...GGGEEEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlel..lkssgvkvgGfyteev 38
                                      ++i Gp+G+GK+Tl++ + +l  ++  ++ v+G+  +++
  gi|488600355|ref|YP_007906826.1| 30 MVIAGPSGSGKSTLLRCINRLteIDGGDILVDGISIKKY 68
                                      589***********9988765114555677888877665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                                       -HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE-- CS
                          NTPase_1 111 skkfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfevt 156
                                       ++k+++ v ++++ ++  vl+v h  +  +++ +++   kd+++++v 
  gi|488600355|ref|YP_007906826.1| 166 VRKIENLVLKLVRsRDLTVLWVTHDVEqAKRIGDRVAVMKDGRIVTVE 213
                                       567777788888767778888888877677888888888888888876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     2e-05     0.012       2      34 ..      31      61 ..      30     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf..gvnlrdvake 34
                                      +++G++G+GK+tl + +++++++  g    d++ +
  gi|488600355|ref|YP_007906826.1| 31 VIAGPSGSGKSTLLRCINRLTEIdgG----DILVD 61
                                      69***************999866663....33333 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 ?    7.2   0.0     0.011       6.5       1      20 [.      30      49 ..      30      78 .. 0.83
   2 ?    6.9   0.0     0.013       7.7       4      68 ..      97     158 ..      95     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                                      EEEESSTTSSHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavak 20
                                      +++ Gp G GK++l + + +
  gi|488600355|ref|YP_007906826.1| 30 MVIAGPSGSGKSTLLRCINR 49
                                      6789**********998855 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                                       ESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGG CS
                               AAA   4 yGppGtGKTllakavakelg....vefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEid 68 
                                       yG    GKT++ k+v k +      ++l  ++s+l       + ++ r  +  a++ a +p++l++DE  
  gi|488600355|ref|YP_007906826.1|  97 YGLRLLGKTATEKSVEKLARevgiENLLDADASKLS------GGEQQRVAI--ARTLAlEPKVLLLDEPT 158
                                       566668999998777555432225567888888888......444444444..344455699*****955 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   4.3e-05     0.025      18      49 ..      27      55 ..      14     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                                      SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlakqilnksdeveg 49
                                          v+ + G  G+GK+tl++ i++   e++g
  gi|488600355|ref|YP_007906826.1| 27 R--EVMVIAGPSGSGKSTLLRCINRL-TEIDG 55
                                      3..49****************99987.66655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.1e-05     0.055       2      20 ..      29      47 ..      28      54 .. 0.89
   2 ?   -1.9   0.0       4.7   2.8e+03      90     115 ..     154     179 ..     113     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-05
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      ++++ G++GsGK+tLl+ +
  gi|488600355|ref|YP_007906826.1| 29 VMVIAGPSGSGKSTLLRCI 47
                                      79**************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.7
                                       STT-SS-TCH.........HHHHHCT CS
                             NACHT  90 lDelvtdlgqkekqpvrtlLselirk 115
                                       lDe  + l++++ +++++l  +l+r 
  gi|488600355|ref|YP_007906826.1| 154 LDEPTASLDPENVRKIENLVLKLVRS 179
                                       34555555554555555555555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     7e-05     0.042       4      30 ..      29      54 ..      26     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkplfid 30
                                       ++i Gpsg+GK+tl++ + ++   id
  gi|488600355|ref|YP_007906826.1| 29 VMVIAGPSGSGKSTLLRCI-NRLTEID 54
                                      689**************99.7777665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00018      0.11       6      34 ..      21      51 ..      17      65 .. 0.76
   2 ?   -1.5   0.0       4.8   2.8e+03      93      93 ..     140     140 ..      87     199 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                            AAA_19  6 e.alkekvllvtaGp.GtGKTrvlkhivall 34
                                      + ++k++ ++v+aGp G+GK+++l++i +l 
  gi|488600355|ref|YP_007906826.1| 21 NlKVKRREVMVIAGPsGSGKSTLLRCINRLT 51
                                      5566666677777666********9987654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.8
                            AAA_19  93 e 93 
                                        
  gi|488600355|ref|YP_007906826.1| 140 A 140
                                       1 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00026      0.16       1      17 [.      29      45 ..      29      62 .. 0.88
   2 ?   -1.2   0.0       3.3     2e+03      76      78 ..     155     157 ..      97     206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                            AAA_33  1 lvllvGlpGsGKstlae 17
                                      ++++ G++GsGKstl++
  gi|488600355|ref|YP_007906826.1| 29 VMVIAGPSGSGKSTLLR 45
                                      67899**********97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.3
                            AAA_33  76 dat 78 
                                       d +
  gi|488600355|ref|YP_007906826.1| 155 DEP 157
                                       333 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 ?   12.2   0.0   0.00017       0.1       2      20 ..      29      47 ..      28      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                      EEEEEESTTCCHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhl 20
                                      v+v++G+ GsGK+tLl+ +
  gi|488600355|ref|YP_007906826.1| 29 VMVIAGPSGSGKSTLLRCI 47
                                      79**************866 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.15      19      49 ..      20      50 ..      16      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      ++++ +++++ +i Gp  +GKst+lr i++l
  gi|488600355|ref|YP_007906826.1| 20 VNLKVKRREVMVIAGPSGSGKSTLLRCINRL 50
                                      56777899*******************9987 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00026      0.15      88     107 ..      28      47 ..       7      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                        Adeno_IVa2  88 viGviyGPtGsGksqllrnl 107
                                        + vi GP GsGks llr +
  gi|488600355|ref|YP_007906826.1|  28 EVMVIAGPSGSGKSTLLRCI 47 
                                       4679**************75 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0024       1.4       2      19 ..      30      47 ..      29      57 .. 0.84
   2 ?    1.2   0.0      0.63   3.8e+02     109     155 ..     141     187 ..      84     194 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                            AAA_28  2 ivitGgestGKTtlleaL 19
                                       vi G++++GK+tll+ +
  gi|488600355|ref|YP_007906826.1| 30 MVIAGPSGSGKSTLLRCI 47
                                      59************9755 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.63
                            AAA_28 109 ydlvfllppapeidddgeRredleereaiderlrealrelgipviiv 155
                                       +++ + l+p   + d  +   d+e+ ++i++++++++r ++  v+ v
  gi|488600355|ref|YP_007906826.1| 141 IARTLALEPKVLLLDEPTASLDPENVRKIENLVLKLVRSRDLTVLWV 187
                                       33344444433332333333455555555555555555555555555 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00029      0.17      86     116 ..      25      57 ..      18     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                          AAA_PrkA  86 erkqilyllGPvggGksslverlkklleaa..p 116
                                       +r++++ + GP g+Gks+l   + +l e     
  gi|488600355|ref|YP_007906826.1|  25 KRREVMVIAGPSGSGKSTLLRCINRLTEIDggD 57 
                                       57889******************9999877543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1526.12
//
Query:       gi|488600356|ref|YP_007906827.1|  [L=99]
Description: transcriptional regulator, PadR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-20   70.4   0.3    1.2e-19   70.0   0.3    1.1  1  PadR      Transcriptional regulator PadR-like family
    4.5e-09   36.9   0.4    4.8e-09   36.9   0.4    1.1  1  RTP       Replication terminator protein
    7.2e-05   22.9   0.1    9.9e-05   22.4   0.1    1.4  1  HTH_34    Winged helix DNA-binding domain
     0.0048   16.6   0.0     0.0061   16.3   0.0    1.2  1  DUF4364   Domain of unknown function (DUF4364)
     0.0066   16.4   0.4     0.0085   16.1   0.4    1.4  1  HTH_45    Winged helix-turn-helix
     0.0086   16.0   0.0      0.013   15.4   0.0    1.4  1  HTH_12    Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.011   14.1   0.1      0.012   14.1   0.1    1.0  1  DUF505    Protein of unknown function (DUF505)
       0.14   12.1   0.0       0.23   11.4   0.0    1.4  1  MarR      MarR family


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 !   70.0   0.3   5.3e-23   1.2e-19       1      73 [.      15      83 ..      15      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 5.3e-23
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                      iL+++++++ yG +++kel+++  g + ls+G+lYp+L+++e++gl++s+++  ++g+ rk+Yr+T++G + l
  gi|488600356|ref|YP_007906827.1| 15 ILYHASKGEIYGAWMMKELARH--G-YSLSPGTLYPILHEMERDGLLQSKKVV-VNGKVRKVYRITEKGLKML 83
                                      899*******************..9.9***********************999.6**************8776 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.4   2.1e-12   4.8e-09       9     102 ..      10      96 ..       1      99 [] 0.87

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.1e-12
                                       HHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS.. CS
                               RTP   9 FlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeG 85 
                                       F++++++  + k + yg  ++ el     + gy+ ++ ++y  lhe+  dg+l+ +k +  + k+++  +Y++t++G
  gi|488600356|ref|YP_007906827.1|  10 FVRVHILYHASKGEIYGAWMMKELA----RHGYSLSPGTLYPILHEMERDGLLQSKKVVV-NGKVRK--VYRITEKG 79 
                                       9999***************998875....679*********************9998887.455554..69****** PP

                                       HHHHHHHHHHHHHHHHH CS
                               RTP  86 kekaklykkqvkidldr 102
                                          +++ kk+vk  + +
  gi|488600356|ref|YP_007906827.1|  80 LKMLEMAKKRVKELFSE 96 
                                       ************98876 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   4.4e-08   9.9e-05      25      79 ..      39      93 ..      11      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.4e-08
                            HTH_34 25 eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksl 79
                                      +++ g L+  l+ +e  g ++ +k ++++k r ++riT++G++  +  +k +k+l
  gi|488600356|ref|YP_007906827.1| 39 SLSPGTLYPILHEMERDGLLQSKKVVVNGKVRKVYRITEKGLKMLEMAKKRVKEL 93
                                      678999**************************************99999998876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.7e-06    0.0061      39      80 ..      48      93 ..      43      99 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.7e-06
                           DUF4364 39 alseLvesglieeeek....enktlykiTekGketlelfenripks 80
                                      +l+e++ +gl+++++     + +++y+iTekG ++le+ ++r+ + 
  gi|488600356|ref|YP_007906827.1| 48 ILHEMERDGLLQSKKVvvngKVRKVYRITEKGLKMLEMAKKRVKEL 93
                                      689999999999886556557789*****************99875 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   3.8e-06    0.0085      43      71 ..      58      88 ..      13      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.8e-06
                            HTH_45 43 Lvekgli..kkskekYvlTekGlelleklke 71
                                      L++k+++   k  + Y++TekGl++le  k+
  gi|488600356|ref|YP_007906827.1| 58 LQSKKVVvnGKVRKVYRITEKGLKMLEMAKK 88
                                      444555555557789***********98776 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 !   15.4   0.0   5.7e-06     0.013      20      66 .]      30      83 ..      13      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.7e-06
                            HTH_12 20 aeeLkkrgydigeravRyrLrkleerglt..rrvgya.....greltEkGleeL 66
                                       +eL   gy ++  ++   L  +e++gl   ++v  +       ++tEkGl++L
  gi|488600356|ref|YP_007906827.1| 30 MKELARHGYSLSPGTLYPILHEMERDGLLqsKKVVVNgkvrkVYRITEKGLKML 83
                                      5789999********************752356666633333458*******98 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.2e-06     0.012     367     414 ..      46      96 ..      30      99 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-06
                            DUF505 367 reaLysLesfeLiesev...eekgkevyvlTeyGekvledqekklrevsae 414
                                          L+++e  +L++s+    + k ++vy +Te+G k+le  +k+++e  +e
  gi|488600356|ref|YP_007906827.1|  46 YPILHEMERDGLLQSKKvvvNGKVRKVYRITEKGLKMLEMAKKRVKELFSE 96 
                                       5679**********9977778888***************999999887665 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    0.0001      0.23      21      51 ..      31      62 ..      23      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                      HHHHHHHT.S-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 21 seLakklg.vskstvtrvldrLekkGlieRsk 51
                                      +eLa++ + +s++t+  +l+++e++Gl++++k
  gi|488600356|ref|YP_007906827.1| 31 KELARHGYsLSPGTLYPILHEMERDGLLQSKK 62
                                      6777776438******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 643.30
//
Query:       gi|488600357|ref|YP_007906828.1|  [L=136]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-11   41.7   0.4    2.7e-10   40.0   0.1    2.0  2  MarR             MarR family
    2.3e-10   40.2   0.1    1.1e-09   38.1   0.0    1.9  2  MarR_2           MarR family
    3.7e-09   36.3   0.5    4.6e-07   29.6   0.1    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.3e-08   34.3   0.5    3.6e-08   32.8   0.0    2.1  2  HTH_24           Winged helix-turn-helix DNA-binding
    1.7e-08   34.8   0.2      4e-08   33.6   0.1    1.7  1  HTH_27           Winged helix DNA-binding domain
      1e-06   28.4   0.0    1.9e-06   27.6   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
    7.8e-06   25.8   0.1    1.2e-05   25.2   0.1    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    1.8e-05   24.7   0.1    5.3e-05   23.2   0.0    1.8  2  HTH_20           Helix-turn-helix domain
      2e-05   24.9   1.4    5.3e-05   23.5   1.4    1.7  1  Penicillinase_R  Penicillinase repressor
      3e-05   23.8   0.0    6.8e-05   22.6   0.0    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
    5.7e-05   22.9   0.7      8e-05   22.4   0.7    1.3  1  DUF4364          Domain of unknown function (DUF4364)
     0.0002   21.0   0.1    0.00048   19.7   0.1    1.6  1  GntR             Bacterial regulatory proteins, gntR family
    0.00021   21.2   0.1    0.00061   19.7   0.1    1.8  1  HTH_11           HTH domain
    0.00025   21.1   0.2     0.0005   20.2   0.2    1.6  1  HTH_34           Winged helix DNA-binding domain
    0.00028   20.6   1.3    0.00055   19.6   0.2    1.8  2  SMC_ScpB         Segregation and condensation complex subunit
    0.00038   20.1   0.1    0.00081   19.0   0.1    1.6  1  HTH_41           Helix-turn-helix domain
     0.0006   19.7   0.1     0.0026   17.7   0.0    2.0  2  HTH_36           Helix-turn-helix domain
    0.00086   19.2   1.1     0.0017   18.3   0.1    2.0  2  HTH_45           Winged helix-turn-helix
     0.0016   17.9   1.1     0.0025   17.3   1.0    1.6  1  RepL             Firmicute plasmid replication protein (RepL)
     0.0017   18.4   0.0     0.0027   17.7   0.0    1.3  1  S10_plectin      Plectin/S10 domain
     0.0054   16.6   1.4      0.026   14.4   1.4    2.1  1  TFIIE_alpha      TFIIE alpha subunit
     0.0078   16.0   2.1      0.035   13.9   0.1    2.6  3  HxlR             HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.015   15.3   0.2       0.03   14.3   0.2    1.6  1  PadR             Transcriptional regulator PadR-like family
      0.015   15.4   0.0      0.026   14.7   0.0    1.6  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.018   15.0   1.4      0.018   15.0   1.4    2.2  2  HTH_12           Ribonuclease R winged-helix domain
      0.023   14.8   0.1      0.044   13.9   0.1    1.4  1  HTH_28           Helix-turn-helix domain
      0.028   14.5   0.0        0.1   12.8   0.0    1.9  2  DprA_WH          DprA winged helix domain
      0.028   14.6   0.8      0.055   13.7   0.0    1.9  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.03   13.9   0.3      0.096   12.2   0.0    2.1  2  Sigma70_r4       Sigma-70, region 4
      0.033   13.7   0.0      0.082   12.5   0.0    1.6  1  HTH_CodY         CodY helix-turn-helix domain
      0.036   14.4   0.1       0.13   12.7   0.0    1.9  2  Rrf2             Transcriptional regulator
      0.041   13.3   0.3       0.21   10.9   0.0    1.9  2  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
      0.046   13.8   0.1       0.11   12.6   0.0    1.7  1  HTH_54           ParA helix turn helix domain
      0.071   13.2   0.0        1.6    8.9   0.0    2.3  2  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
      0.076   13.3   0.1       0.28   11.5   0.0    2.0  2  KORA             TrfB plasmid transcriptional repressor
        0.1   12.6   0.2       0.36   10.8   0.2    1.9  1  HTH_1            Bacterial regulatory helix-turn-helix protei
       0.11   12.5   0.0       0.21   11.6   0.0    1.4  1  HTH_29           Winged helix-turn helix


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 !   40.0   0.1   5.6e-13   2.7e-10       2      51 ..      27      75 ..      26      77 .. 0.93
   2 ?   -1.6   0.1       5.7   2.7e+03      30      42 ..     114     126 ..     101     128 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 5.6e-13
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      t  +f++L i+y++ p++++e+ +  g++k+tv+++l+ Le++G+++R++
  gi|488600357|ref|YP_007906828.1| 27 TFLEFKCLKIIYQN-PITQKEIIEETGMTKGTVSKALRSLEERGFVTRRR 75
                                      6679*******975.7********************************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.7
                                       -HHHHHHHHHHHH CS
                              MarR  30 skstvtrvldrLe 42 
                                       +k t+ ++l+++ 
  gi|488600357|ref|YP_007906828.1| 114 EKQTLQTLLKKML 126
                                       4566666666665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   2.2e-12   1.1e-09       3      55 ..      26      75 ..      25      79 .. 0.92
   2 ?   -0.7   0.0       2.8   1.4e+03      35      46 ..     115     126 ..     114     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.2e-12
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      lt  ++  L  ++ +p   +t++e+ +++g++k++vs++l+ L+++G+v+rr+
  gi|488600357|ref|YP_007906828.1| 26 LTFLEFKCLKIIYQNP---ITQKEIIEETGMTKGTVSKALRSLEERGFVTRRR 75
                                      68888999999999*9...9*******************************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHH CS
                            MarR_2  35 ksavsrilkrLv 46 
                                       k++++ +lk++ 
  gi|488600357|ref|YP_007906828.1| 115 KQTLQTLLKKML 126
                                       99*******995 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   9.6e-10   4.6e-07      13      58 ..      33      77 ..      25      98 .. 0.83
   2 ?    5.0   0.0     0.046        22       5      30 ..     109     134 ..     108     136 .] 0.85

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9.6e-10
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      +  +++ + p t +ei ee+g  + +v ++LrsLe++G+V+r++  
  gi|488600357|ref|YP_007906828.1| 33 CL-KIIYQNPITQKEIIEETGMTKGTVSKALRSLEERGFVTRRRVG 77
                                      54.4556899********************************9844 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.046
                                       HHHHHCCCHCHHHHHHCCCHHCHHCC CS
                              TrmB   5 GLseyEakvYlaLlklgpatadeiae 30 
                                       +++e E ++ ++Llk+   + d++  
  gi|488600357|ref|YP_007906828.1| 109 NFTEDEKQTLQTLLKKMLRNLDQVED 134
                                       69************998888877765 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 ?   -2.4   0.1       7.6   3.7e+03       8      15 ..       6      13 ..       5      18 .. 0.54
   2 !   32.8   0.0   7.4e-11   3.6e-08       9      48 .]      34      72 ..      29      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.6
                            HTH_24  8 ILelLqkn 15
                                      IL  + +n
  gi|488600357|ref|YP_007906828.1|  6 ILFMILQN 13
                                      55555444 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 7.4e-11
                            HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      L+++++np i+q+e+ e++g++++tv++ l+ Lee G+++
  gi|488600357|ref|YP_007906828.1| 34 LKIIYQNP-ITQKEIIEETGMTKGTVSKALRSLEERGFVT 72
                                      56666644.****************************996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.1   8.3e-11     4e-08       1      68 []      26      88 ..      26      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 8.3e-11
                            HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      lt+++   L  i+  +++ +++++++ + +++ ++s++l+ L+e+G+v+r    + +re rv++T++G
  gi|488600357|ref|YP_007906828.1| 26 LTFLEFKCLKIIY--QNPITQKEIIEETGMTKGTVSKALRSLEERGFVTRR---RVGREYRVEITEEG 88
                                      5777777788888..999999***************************555...557**********9 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0     4e-09   1.9e-06      18      51 ..      41      74 ..      38      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4e-09
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      + t +e+ ++tg++k tv+  L++L+e+G+v++ 
  gi|488600357|ref|YP_007906828.1| 41 PITQKEIIEETGMTKGTVSKALRSLEERGFVTRR 74
                                      56889**************************985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   2.5e-08   1.2e-05      20      55 ..      40      75 ..      15      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-08
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrgr 55
                                       p+tq+e+ +  G+t  tvs++l+ L+++g ++r+r
  gi|488600357|ref|YP_007906828.1| 40 NPITQKEIIEETGMTKGTVSKALRSLEERGFVTRRR 75
                                      59*******************************542 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.1e-07   5.3e-05      25      61 .]      42      78 ..      34      78 .. 0.91
   2 ?   -1.9   0.0       7.3   3.5e+03      38      48 ..     115     125 ..      98     133 .. 0.48

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.1e-07
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 25 ltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                       t +e+ e+ +++k t+s+ Lr Lee g+v+++r+gr
  gi|488600357|ref|YP_007906828.1| 42 ITQKEIIEETGMTKGTVSKALRSLEERGFVTRRRVGR 78
                                      56679999999************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHH CS
                            HTH_20  38 kntlsyHLrvL 48 
                                       k+tl   L+++
  gi|488600357|ref|YP_007906828.1| 115 KQTLQTLLKKM 125
                                       33443333443 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   1.4   1.1e-07   5.3e-05       4     107 ..      29     123 ..      26     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-07
                                       S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XX.XXXXXXXXXX CS
                   Penicillinase_R   4 lEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvsee.eavasavkql 79 
                                       lE + ++i+++ +++t ke++ee   +    + TV   lr L+++g+++r++ gr++  +  ++ee +av+++ +++
  gi|488600357|ref|YP_007906828.1|  29 LEFKCLKIIYQ-NPITQKEIIEETGMT----KGTVSKALRSLEERGFVTRRRVGREY--RVEITEEgKAVMRKFEKI 98 
                                       66777777775.589999999988877....9***********************98..555555426777777777 PP

                                       XXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                   Penicillinase_R  80 ldklfegsvkelvaafveee.klseddle 107
                                        +++     + l+ +f+e+e +  ++ l+
  gi|488600357|ref|YP_007906828.1|  99 ASEIN----EILLKNFTEDEkQTLQTLLK 123
                                       77777....56777777776444444444 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 !   22.6   0.0   1.4e-07   6.8e-05      11      46 ..      37      72 ..      32      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-07
                                      HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 11 LaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                        +++ +  e+ ee+g++++tvS  L+ L+e G+V+
  gi|488600357|ref|YP_007906828.1| 37 IYQNPITQKEIIEETGMTKGTVSKALRSLEERGFVT 72
                                      556778889*************************96 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.7   1.7e-07     8e-05      27      94 ..      49     115 ..      34     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.7e-07
                           DUF4364  27 eneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfenripksirekideylkenke 94 
                                       e+  ++  ++++al  L+e g+++ ++   + + +iTe+Gk +++ fe+ i+++i e + +++ e ++
  gi|488600357|ref|YP_007906828.1|  49 EETGMTKGTVSKALRSLEERGFVTRRRVGREYRVEITEEGKAVMRKFEK-IASEINEILLKNFTEDEK 115
                                       44455556899************************************85.777787777777666544 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   9.8e-07   0.00048      24      58 ..      42      75 ..      39      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.8e-07
                                      ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 24 LPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                      + +++e+ +e g ++ tv +ALr Le++g v+rr+
  gi|488600357|ref|YP_007906828.1| 42 I-TQKEIIEETGMTKGTVSKALRSLEERGFVTRRR 75
                                      5.789***************************996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.3e-06   0.00061       6      44 ..      34      70 ..      30      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-06
                            HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      l+++++  +pi+ +e+ ee+++++ tv + +++Lee g+
  gi|488600357|ref|YP_007906828.1| 34 LKIIYQ--NPITQKEIIEETGMTKGTVSKALRSLEERGF 70
                                      666644..45**************************994 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2     1e-06    0.0005      14      71 ..      41      94 ..      29     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1e-06
                            HTH_34 14 eadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71
                                       ++ +e+ e++++t+g  s+ l+ Le+ g+++++   ++      ++iT+eG++   k
  gi|488600357|ref|YP_007906828.1| 41 PITQKEIIEETGMTKGTVSKALRSLEERGFVTRRRVGREY----RVEITEEGKAVMRK 94
                                      47789999************************99865554....799*****975433 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 !   19.6   0.2   1.1e-06   0.00055      70     143 ..      15      86 ..      10      92 .. 0.79
   2 ?   -0.4   0.0       1.6   7.9e+02      19      39 ..     107     127 ..      91     134 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                          SMC_ScpB  70 kklvkekkktrLsqaaletLaiIaykqpvtraeieeiRGvn...sdsvvrtLlerglieekgrkeepgrpilYgtTe 143
                                       kklv ++ + +L+  + + L iI y++p+t++ei e  G +   +++++r+L erg++++++    +gr +  ++Te
  gi|488600357|ref|YP_007906828.1|  15 KKLVMRNLSGELTFLEFKCLKII-YQNPITQKEIIEETGMTkgtVSKALRSLEERGFVTRRR----VGREYRVEITE 86 
                                       55666656666777777777765.9*********9999986556999************999....78887777776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                          SMC_ScpB  19 LakilelskeeveealeeLke 39 
                                       L++++e +k++++++l+++ +
  gi|488600357|ref|YP_007906828.1| 107 LKNFTEDEKQTLQTLLKKMLR 127
                                       344443335555555555554 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.7e-06   0.00081      10      43 ..      45      78 ..      42      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                            HTH_41 10 eelakeleLSvGlvQkALklLeddkaislerrGr 43
                                      +e+++e ++  G+v kAL +Le+ + ++  r Gr
  gi|488600357|ref|YP_007906828.1| 45 KEIIEETGMTKGTVSKALRSLEERGFVTRRRVGR 78
                                      6899************************999998 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.3e-06    0.0026      25      54 ..      40      70 ..      34      71 .. 0.90
   2 ?   -1.5   0.0         5   2.4e+03      36      48 ..     112     124 ..      95     128 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.3e-06
                            HTH_36 25 fp.sqetlakrlglsknTvsraikeLeqlGy 54
                                      +p +q+ + + +g+ k Tvs+a+++Le+ G+
  gi|488600357|ref|YP_007906828.1| 40 NPiTQKEIIEETGMTKGTVSKALRSLEERGF 70
                                      566899999********************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5
                            HTH_36  36 glsknTvsraike 48 
                                       +  k+T ++ +k+
  gi|488600357|ref|YP_007906828.1| 112 EDEKQTLQTLLKK 124
                                       3446777777765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       7.2   3.5e+03       6      16 ..       5      15 ..       4      19 .. 0.76
   2 !   18.3   0.1   3.5e-06    0.0017      11      74 ..      33     100 ..      29     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.2
                            HTH_45  6 eIiadILeais 16
                                      +I++ IL++i+
  gi|488600357|ref|YP_007906828.1|  5 KILFMILQNIK 15
                                      58888888885 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.5e-06
                            HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli..kkskekY..vlTekGlelleklkelee 74 
                                        L++i ++  ++ +i+ +  ++  +++k L  L e+g++  +  + +Y  ++Te+G+ +++k++++ +
  gi|488600357|ref|YP_007906828.1|  33 CLKIIYQNPITQKEIIEETGMTKGTVSKALRSLEERGFVtrRRVGREYrvEITEEGKAVMRKFEKIAS 100
                                       68999999999999*************************7633455552269************9876 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.0   5.2e-06    0.0025      76     111 ..      42      77 ..       6     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-06
                              RepL  76 atnRelaeetgislktvsetlkileeanilkkkanG 111
                                       +t++e+ eetg+   tvs+ l+ lee +++ ++  G
  gi|488600357|ref|YP_007906828.1|  42 ITQKEIIEETGMTKGTVSKALRSLEERGFVTRRRVG 77 
                                       69*****************************99866 PP

>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.6e-06    0.0027      31      84 ..      49     102 ..      34     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.6e-06
                                       SSS---HHHHHHHHHHCCCCTSEEEEEETTEEEEEE-HHHHHHHHHHHXXXXSX CS
                       S10_plectin  31 eelnvpnlqvikalqSLksrgyvkeqfaWrhyYytLtneGieylreylhlpeei 84 
                                       ee+++++  v kal+SL++rg+v+++ + r y   +t+eG +++r+  ++++ei
  gi|488600357|ref|YP_007906828.1|  49 EETGMTKGTVSKALRSLEERGFVTRRRVGREYRVEITEEGKAVMRKFEKIASEI 102
                                       5667888899************************************99998886 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.4   5.3e-05     0.026       6      69 ..      18      91 ..      12     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-05
                                      HHHHCS-HHHH...HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE.EE.......TTTEE CS
                       TFIIE_alpha  6 vvrkfygeeav...lvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr.rd.......eeksw 69
                                      v+r+  ge  +   + l+++  +  +t  ++ +e+++ +  + k+L  L e ++v  +r  r+       e+k +
  gi|488600357|ref|YP_007906828.1| 18 VMRNLSGELTFlefKCLKIIY-QNPITQKEIIEETGMTKGTVSKALRSLEERGFVTRRRVgREyrveiteEGKAV 91
                                      666666665540114555555.7789999**************************98874233444344444444 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.1   5.2e+02      68      88 ..       3      23 ..       1      26 [. 0.84
   2 !   13.9   0.1   7.3e-05     0.035      30      81 ..      52     100 ..      38     110 .. 0.80
   3 ?   -1.1   0.1       3.5   1.7e+03      33      45 ..     119     131 ..     107     133 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.1
                                      CGGGGHHHHHHHHHHHHHHHH CS
                              HxlR 68 kGrslepvlqelkkwgeeyle 88
                                       G+ l  +lq++kk+++++l+
  gi|488600357|ref|YP_007906828.1|  3 IGKILFMILQNIKKLVMRNLS 23
                                      699999999999999998875 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.3e-05
                                       TS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHH CS
                              HxlR  30 kisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkk 81 
                                       ++++ + ++ Lr Le+ g++ r+ +         ++te+G++++  +++++ 
  gi|488600357|ref|YP_007906828.1|  52 GMTKGTVSKALRSLEERGFVTRRRVG---REYRVEITEEGKAVMRKFEKIAS 100
                                       6799999**************98654...4444579*******999998876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHH CS
                              HxlR  33 qkmLaqrLreLeq 45 
                                       q +L + Lr+L+q
  gi|488600357|ref|YP_007906828.1| 119 QTLLKKMLRNLDQ 131
                                       5667777777765 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   6.3e-05      0.03      27      74 ..      51      93 ..      34      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-05
                                      CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR 27 lelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      + + +G++ +aL++Le+ g+v+++++    g++ ++ ++T++G++ ++
  gi|488600357|ref|YP_007906828.1| 51 TGMTKGTVSKALRSLEERGFVTRRRV----GREYRV-EITEEGKAVMR 93
                                      45899******************966....455554.89999999887 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.3e-05     0.026      19      53 ..      42      76 ..      29     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.3e-05
                    B-block_TFIIIC 19 itqsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                      itq++++ e+++ +  + + l+sLe+ g+++++ +
  gi|488600357|ref|YP_007906828.1| 42 ITQKEIIEETGMTKGTVSKALRSLEERGFVTRRRV 76
                                      89******************************988 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 ?   15.0   1.4   3.8e-05     0.018      32      64 ..      55      90 ..      33      92 .. 0.68
   2 ?   -1.4   0.0       4.7   2.3e+03      18      26 ..      97     105 ..      95     130 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-05
                            HTH_12 32 eravRyrLrkleergltrrvgya...greltEkGle 64
                                      + +v   Lr+leerg++ r + +     e+tE G  
  gi|488600357|ref|YP_007906828.1| 55 KGTVSKALRSLEERGFVTRRRVGreyRVEITEEGKA 90
                                      3567889********99665555446779***9976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.7
                            HTH_12  18 eiaeeLkkr 26 
                                       +ia+e++++
  gi|488600357|ref|YP_007906828.1|  97 KIASEINEI 105
                                       566666654 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     9e-05     0.044      14      49 ..      43      75 ..      38      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-05
                            HTH_28 14 svreaArelgisrrtvyrWikryeegGiagLvprrr 49
                                      +++e+ +e g++  tv++ ++ +ee G+   v+rrr
  gi|488600357|ref|YP_007906828.1| 43 TQKEIIEETGMTKGTVSKALRSLEERGF---VTRRR 75
                                      799**********************999...99998 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00021       0.1      23      57 ..      39      73 ..      23      75 .. 0.89
   2 ?   -2.1   0.0       8.7   4.2e+03      11      30 ..     112     131 ..     110     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00021
                           DprA_WH 23 pePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                      + P++  +++++tg++ ++vs aL  LE  G v+r
  gi|488600357|ref|YP_007906828.1| 39 QNPITQKEIIEETGMTKGTVSKALRSLEERGFVTR 73
                                      57888889********************9999988 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.7
                           DprA_WH  11 ddlerrvLaaLgpePvhvDq 30 
                                       +d+++++ ++L    + +Dq
  gi|488600357|ref|YP_007906828.1| 112 EDEKQTLQTLLKKMLRNLDQ 131
                                       56677777777766666666 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   0.00011     0.055      20      53 ..      39      72 ..      32      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                                      HSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 20 kkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      ++++++k++ e+ +  + +Vs+ l+ Le+ G+v 
  gi|488600357|ref|YP_007906828.1| 39 QNPITQKEIIEETGMTKGTVSKALRSLEERGFVT 72
                                      456999**************************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002     0.096       5      41 ..      26      62 ..      24      69 .. 0.87
   2 ?   -2.6   0.0       8.2     4e+03       6      24 ..     111     119 ..     104     121 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                      S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqie 41
                                      L+  e ++l+  +  + T++EI e+ g+++++V+  +
  gi|488600357|ref|YP_007906828.1| 26 LTFLEFKCLKIIYQNPITQKEIIEETGMTKGTVSKAL 62
                                      67777789999999*******************9755 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.2
                                       -HHHHHHHHHHHTTT--HH CS
                        Sigma70_r4   6 pererevlelrfgeglTle 24 
                                       +e+          e++Tl+
  gi|488600357|ref|YP_007906828.1| 111 TED----------EKQTLQ 119
                                       344..........444444 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 ?   12.5   0.0   0.00017     0.082       6      40 ..      43      77 ..      40      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                          HTH_CodY  6 taskiaDriGitrsvivnaLrkLesaGiiesrsLG 40
                                      t  +i ++ G+t+  +  aLr Le  G +  r +G
  gi|488600357|ref|YP_007906828.1| 43 TQKEIIEETGMTKGTVSKALRSLEERGFVTRRRVG 77
                                      5567999*********************9999887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00026      0.13      24      59 ..      40      75 ..      33      79 .. 0.91
   2 ?   -1.4   0.0       6.3     3e+03      36      49 ..     116     129 ..      93     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00026
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      +p++ +ei e++++ +  ++k l+ L++ g+v+ +r
  gi|488600357|ref|YP_007906828.1| 40 NPITQKEIIEETGMTKGTVSKALRSLEERGFVTRRR 75
                                      5799****************************9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.3
                                       TS-HHHHHHHHHHH CS
                              Rrf2  36 nispsylekilakL 49 
                                       ++ ++ l+k+l++L
  gi|488600357|ref|YP_007906828.1| 116 QTLQTLLKKMLRNL 129
                                       44556666777666 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00044      0.21     103     136 ..      42      75 ..      38      79 .. 0.92
   2 ?    0.1   0.2      0.86   4.2e+02       7      39 ..      94     127 ..      86     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                                       EEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEE CS
                     RNA_pol_Rpc34 103 IwsrtiksklnLhksvvkkcLksLeskkyiksvk 136
                                       I +++i + +++ k  v k L+sLe ++ +  ++
  gi|488600357|ref|YP_007906828.1|  42 ITQKEIIEETGMTKGTVSKALRSLEERGFVTRRR 75 
                                       99**************************998765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.86
                                       -HHHHHHHHHHHHHCS.SSSSHCCHHHHHHHSTT CS
                     RNA_pol_Rpc34   7 klqelkkrlleelrka.seqklfsqqdLqddips 39 
                                       k +++++++ e l k+  e++  ++q+L++++++
  gi|488600357|ref|YP_007906828.1|  94 KFEKIASEINEILLKNfTEDEKQTLQTLLKKMLR 127
                                       6677888888888888877777777777776443 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00023      0.11      24      70 ..      38      81 ..      29      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                            HTH_54 24 yyqtyskaalaklpklsrrkvdkavsemeaeGyefekkeagstekYa 70
                                      y ++ ++ ++ +++++++ +v ka+  +e++G++ +++ +g  ++Y 
  gi|488600357|ref|YP_007906828.1| 38 YQNPITQKEIIEETGMTKGTVSKALRSLEERGFVTRRR-VG--REYR 81
                                      55578999999**********************98877.44..4444 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 ?    8.9   0.0    0.0034       1.6      26      58 ..      40      72 ..      33      72 .. 0.87
   2 ?    2.0   0.0      0.48   2.3e+02      11      44 ..      95     132 ..      90     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0034
                                      SSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
                             HTH_9 26 grltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                                      +  t +e++++t++++  V k+L +L  +++V+
  gi|488600357|ref|YP_007906828.1| 40 NPITQKEIIEETGMTKGTVSKALRSLEERGFVT 72
                                      666889********************9988885 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.48
                                       STTHHHHHHHHHHHH....SSBEHHHHHHHHSSTHHHH CS
                             HTH_9  11 FGevvakVvetLlrk....grltlrelvkktkLsldqV 44 
                                       F ++++ + e Ll++     ++tl+ l+kk   +ldqV
  gi|488600357|ref|YP_007906828.1|  95 FEKIASEINEILLKNftedEKQTLQTLLKKMLRNLDQV 132
                                       77899999999998622224677777777766555555 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00058      0.28      33      52 ..      43      62 ..      26      80 .. 0.91
   2 ?   -0.9   0.1       4.3   2.1e+03      10      35 ..      92     117 ..      84     125 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00058
                              KORA 33 kqadvatelgltkqavsqav 52
                                      +q+++++e+g+tk+ vs+a 
  gi|488600357|ref|YP_007906828.1| 43 TQKEIIEETGMTKGTVSKAL 62
                                      79***************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.3
                              KORA  10 ikgleelaeqtveiargvLVegkkqa 35 
                                       + + e++a +  ei  +   e++kq+
  gi|488600357|ref|YP_007906828.1|  92 MRKFEKIASEINEILLKNFTEDEKQT 117
                                       45555566666666666666666665 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00074      0.36      21      40 ..      49      68 ..      49      89 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00074
                                      HHHTS-HHHHHHHHHHHHHH CS
                             HTH_1 21 eeLglsqpavsrqikrLEee 40
                                      ee g++  +vs+++++LEe+
  gi|488600357|ref|YP_007906828.1| 49 EETGMTKGTVSKALRSLEER 68
                                      5789**************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 ?   11.6   0.0   0.00044      0.21      14      55 ..      43      81 ..      32      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn 55
                                      t ++i + +g+++ tv ++l+  ee G      rrr gr ++
  gi|488600357|ref|YP_007906828.1| 43 TQKEIIEETGMTKGTVSKALRSLEERG---FVTRRRVGREYR 81
                                      678999*********************...999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1529  (0.0852808); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 955.26
//
Query:       gi|488600358|ref|YP_007906829.1|  [L=457]
Description: putative efflux protein, MATE family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-60  201.3  37.5    4.7e-39  133.6   9.9    3.1  4  MatE             MatE
    3.6e-10   40.1  15.5    3.6e-10   40.1  15.5    5.6  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   9.9   5.2e-43   4.7e-39       1     161 []      24     183 ..      24     183 .. 0.99
   2 ?   -1.6   0.2       0.2   1.8e+03      74      92 ..     197     214 ..     189     223 .. 0.63
   3 !   81.7  19.6     5e-27   4.5e-23       1     161 []     244     409 ..     244     409 .. 0.99
   4 ?   -2.4   0.2      0.35   3.2e+03      41      63 ..     420     442 ..     411     454 .. 0.56

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 5.2e-43
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P++++nl+++l++l+d  +v++lg++al+a++i+++++++++++++gl++++++ +++++Gak++k+a ++++++++
  gi|488600358|ref|YP_007906829.1|  24 PMMVSNLVFTLYNLADGAWVAGLGADALSAIGIFFPLFMIFISLSMGLGIGASSAMSRRIGAKDKKNADNIAMHAIV 100
                                       9**************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       ++++++li++l+ ++  e++l+l++++ +vl+la +y ri++ g ++l+++++++gil+g g+t++++y++++++++
  gi|488600358|ref|YP_007906829.1| 101 TGFAVALILTLI-VIRLEHLLKLLGAEGNVLNLALEYSRIIVAGSVFLVFNNISTGILNGEGNTRRTMYANVAGTVI 176
                                       ************.999************************************************************* PP

                              MatE 155 niplnyl 161
                                       ni+l+++
  gi|488600358|ref|YP_007906829.1| 177 NIILDPI 183
                                       ****986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.2
                              MatE  74 qglilllllsliiallvll 92 
                                       +++++++++s +++++ ++
  gi|488600358|ref|YP_007906829.1| 197 YATVVSMAISSAVFIY-WF 214
                                       5556666666666666.33 PP

  == domain 3  score: 81.7 bits;  conditional E-value: 5e-27
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P+ +++l +s+   ++++++ r  gs+ +A+ + a++++s+ f++l+g+s a+t++vg ++Gakn +++++a+ +++
  gi|488600358|ref|YP_007906829.1| 244 PSSFSMLSMSIAMVFLNMIIVRAgGSDGIAVFTSAWRLISFGFIPLFGMSGAVTAVVGASFGAKNAEKLRTAYLHAI 320
                                       99*************************************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyisli 150
                                       +l++l+ ++i+ ++++ +++i+ +ft++e+   + +   + +ril  ++++  + +++ ++++g+g+ + +l+i+++
  gi|488600358|ref|YP_007906829.1| 321 KLTALIEVFIVSAMIITAPKIAFVFTYSEAsvrIYQELVNAMRILPAFLLFTPMGMMTVAMFQGIGRGENSLAITIL 397
                                       ******************************999999999999*********************************** PP

                              MatE 151 sl.llniplnyl 161
                                       ++ +l++ ++y+
  gi|488600358|ref|YP_007906829.1| 398 RTiILQLSFAYI 409
                                       **********97 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.35
                              MatE  41 lfvfllglstalttlvgqalGak 63 
                                        +++++ +++ +++l++  +G  
  gi|488600358|ref|YP_007906829.1| 420 GVLIGVTIGNVTASLIAFMWGTL 442
                                       33355555555556666555555 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 ?    0.1   0.6     0.088   7.9e+02       5      26 ..      51      72 ..      16      86 .. 0.72
   2 ?    2.7   0.2     0.013   1.2e+02      29      57 ..      93     124 ..      87     130 .. 0.75
   3 !   40.1  15.5     4e-14   3.6e-10       3      85 ..     138     223 ..     136     279 .. 0.75
   4 ?   -2.7   8.4      0.64   5.7e+03      46      67 ..     283     304 ..     245     348 .. 0.75
   5 !   10.6  10.7   4.9e-05      0.44       2      75 ..     362     438 ..     361     448 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.088
                   Polysacc_synt_C  5 lalsiiflslstvlssiLqglg 26
                                      l+ + if+ l++++ s+  glg
  gi|488600358|ref|YP_007906829.1| 51 LSAIGIFFPLFMIFISLSMGLG 72
                                      4555566666666666555554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.013
                   Polysacc_synt_C  29 kialkalvigalvklilnllli...plfgivG 57 
                                        ia+ a+v g++v lil+l+ i   +l+ ++G
  gi|488600358|ref|YP_007906829.1|  93 NIAMHAIVTGFAVALILTLIVIrleHLLKLLG 124
                                       67888899999999999999885554555555 PP

  == domain 3  score: 40.1 bits;  conditional E-value: 4e-14
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavln.lya 76 
                                       +i++ + +fl++++++++iL+g g ++++++a+v+g ++++il  ++i    +g+ Gaa+atv+++++++++  +++
  gi|488600358|ref|YP_007906829.1| 138 RIIVAGSVFLVFNNISTGILNGEGNTRRTMYANVAGTVINIILDPIFIyiLNLGVAGAAYATVVSMAISSAVFiYWF 214
                                       688999******************************************555779*************9988873555 PP

                   Polysacc_synt_C  77 lrrllgikl 85 
                                          ++ +++
  gi|488600358|ref|YP_007906829.1| 215 FGGKTFVDV 223
                                       544554444 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 0.64
                   Polysacc_synt_C  46 nllliplfgivGaaiatvlall 67 
                                       ++ +iplfg+ Ga+ a v a +
  gi|488600358|ref|YP_007906829.1| 283 SFGFIPLFGMSGAVTAVVGASF 304
                                       5668899999998888876654 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 4.9e-05
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvi.galvklilnllli..plfgivGaaiatvlallvvavlnly 75 
                                       ++il   ++f+ + +++ +++qg+gr    l ++++ +++++l + +++     fg +G++i+ +++ ++++++ ++
  gi|488600358|ref|YP_007906829.1| 362 MRILPAFLLFTPMGMMTVAMFQGIGRGENSLAITILrTIILQLSFAYIFAflLGFGFYGVLIGVTIGNVTASLIAFM 438
                                       8899999*******************8887766666266799999999995456688*******9999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2614.34
//
Query:       gi|488600359|ref|YP_007906830.1|  [L=447]
Description: hypothetical protein Asulf_00828 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-64  216.9  77.3    8.6e-54  182.8  47.2    2.0  2  MFS_1       Major Facilitator Superfamily
    1.9e-08   33.7  13.5    1.9e-08   33.7  13.5    2.9  3  Sugar_tr    Sugar (and other) transporter
    2.1e-06   26.9  23.6    0.00071   18.5   7.8    2.7  2  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8  47.2   1.4e-57   8.6e-54       2     352 ..      10     393 ..       9     394 .. 0.89
   2 !   48.1  22.1   1.3e-16   7.7e-13       3     166 ..     256     438 ..     255     446 .. 0.88

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 1.4e-57
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                        la fl+ ++ s +++alp ++++++g+++ ++++++t++ l +a + +p+Grl+d  Gr+rv+++g+++f +g+ll
  gi|488600359|ref|YP_007906830.1|  10 TLASFLTPFTLSSVNVALP-TIGSEFGVDAITLNWIATAFLLSSAMFLVPFGRLADIKGRKRVFVTGMTVFTAGSLL 85 
                                       6899***************.******************************************************555 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                         + s++  +l+++rvlqG+g++++f++g+a+++ +fp +erg+++g+  a++  G  +gp +gg+l++++gWr+vf
  gi|488600359|ref|YP_007906830.1|  86 SGV-SNSAeMLIAFRVLQGIGGAMVFATGIAILTSVFPIKERGKVLGINVASVYTGLSFGPFFGGILTQNFGWRSVF 161
                                       555.99999******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee....................................kgtgpap 195
                                       +++ ++++l++ ++l+ l +e  + k ++    +                                    +++ ++p
  gi|488600359|ref|YP_007906830.1| 162 LVNVPLGVLVVAIALWKLKAEWADAKGERFDITGsviyslmlvlimigvsesspilitaglallitfilwESRIEHP 238
                                       **********887667774444444444444444778*****************9999999**************** PP

                             MFS_1 196 lvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlg 272
                                       +++ +k+++++  + +  +a+ll+  +++++++ll lylq    l+   +ag++l +  +v a+l+++ag+lsdr+ 
  gi|488600359|ref|YP_007906830.1| 239 VLE-IKLFRRNMTFAFSNLAALLNYSATFAVTYLLSLYLQYIKALT-PQQAGAILVAQPVVQAMLSPFAGWLSDRIE 313
                                       ***.******9988767788888888********************.799999999999999999**********55 PP

                             MFS_1 273 rrrrlllallllllaalglallavt..ssavllll.vlvliGfglgfvfpsllalasdlappeeagtasglfntags 346
                                          ++++a ++++++a+gl++++ +  s+++ +++  l+l+Gfg+++++++ ++++++++ ++  g as+  +t++ 
  gi|488600359|ref|YP_007906830.1| 314 ---PRVVASAGMAVTAMGLFVFSGInsSTSISMIVaNLMLMGFGFALFSSPNTNAIMSSVEKKFYGIASATLSTMRV 387
                                       ...6888888888888888888888432222223235555************************************* PP

                             MFS_1 347 lggalg 352
                                       +g +l+
  gi|488600359|ref|YP_007906830.1| 388 VGQMLS 393
                                       **9997 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 1.3e-16
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       laa+l++ a ++++ +l+l+l+    ++p+++g +l++  +++a +s+++G+lsdr+ +r v  +g++++a gl+++
  gi|488600359|ref|YP_007906830.1| 256 LAALLNYSATFAVTYLLSLYLQYIKALTPQQAGAILVAQPVVQAMLSPFAGWLSDRIEPRVVASAGMAVTAMGLFVF 332
                                       67889999999999999999999999***********************************************3333 PP

                             MFS_1  80 l.fa..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg... 149
                                       + +   +s+ ++++  +l+G+g +++ +    +i   + k+  g a + ls++  +G +l +++  l+   ++g   
  gi|488600359|ref|YP_007906830.1| 333 SgINssTSISMIVANLMLMGFGFALFSSPNTNAIMSSVEKKFYGIASATLSTMRVVGQMLSMAIVMLVFaIYIGkvl 409
                                       343254555599999**********************************************6665555538888*** PP

                             MFS_1 150 ............Wravfyilaivsllafv 166
                                                    r +f i+ +++++++ 
  gi|488600359|ref|YP_007906830.1| 410 itpevyslliesTRTSFAIFSLLCFFGIF 438
                                       *********9999999********99944 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7  13.5   3.1e-12   1.9e-08      44     189 ..      37     176 ..       7     180 .. 0.89
   2 ?   -0.1   4.1     0.054   3.2e+02     281     417 ..     152     282 ..     151     294 .. 0.70
   3 ?   -2.5  14.6      0.28   1.7e+03      46     160 ..     285     399 ..     253     439 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.1e-12
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                        ++++ +i+ +fl+ +++  + +g l+d+ GRk +++++ ++f +g++l+++++   s e+li+ Rvl Gig  ++ 
  gi|488600359|ref|YP_007906830.1|  37 DAITLNWIATAFLLSSAMFLVPFGRLADIKGRKRVFVTGMTVFTAGSLLSGVSN---SAEMLIAFRVLQGIGGAMVF 110
                                       567889************************************************...99************998888 PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGG CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilll 189
                                       ++    +  + p k Rg++ +++  ++ +G  ++ +fg +l ++ +   wr  + +++ + +l++++ l
  gi|488600359|ref|YP_007906830.1| 111 ATGIAILTSVFPIKERGKVLGINVASVYTGLSFGPFFGGILTQNFG---WRSVFLVNVPLGVLVVAIAL 176
                                       88888889999****************************9988888...************99987655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.054
                                       HHHSS-THHHHHHHHHHHHHHHHHHHHH..HHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHH CS
                          Sugar_tr 281 fenlglsksllvtiivgvvnfvatfvai..flvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivf 355
                                       ++n g    +lv++ +gv+ +++ +  +     d  G R + ++G++++++++v++     ++v++s    i+++++
  gi|488600359|ref|YP_007906830.1| 152 TQNFGWRSVFLVNVPLGVLVVAIALWKLkaEWADAKGER-FDITGSVIYSLMLVLIM----IGVSES--SPILITAG 221
                                       678888899999999999888888877544789999999.999*********99994....555553..36777777 PP

                                       HHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-H CS
                          Sugar_tr 356 ialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggy 417
                                       +al i +  +       vl   lf  ++  +++ +a+ +n  a+f++++l    ++ i+ + 
  gi|488600359|ref|YP_007906830.1| 222 LALLITFILWESRIEHPVLEIKLFRRNMTFAFSNLAALLNYSATFAVTYLLSLYLQYIK-AL 282
                                       77777777655554445666666777777777777777777777777777666666666.55 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.28
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                        + g+i+ +  v++++ s fag+l+dr+  + +  ++ +++  g ++   +++ +s+ ++++  +l+G+g  l+s  
  gi|488600359|ref|YP_007906830.1| 285 QQAGAILVAQPVVQAMLSPFAGWLSDRIEPRVVASAGMAVTAMGLFVFSGINSSTSISMIVANLMLMGFGFALFSSP 361
                                       35688888888999999999999999999999999999999999999999999999999999999999999988887 PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglg 160
                                        +  i     kk  g+      ++ ++G++++  + + 
  gi|488600359|ref|YP_007906830.1| 362 NTNAIMSSVEKKFYGIASATLSTMRVVGQMLSMAIVML 399
                                       77777777778888888888888888888887654433 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   7.8   1.2e-07   0.00071     270     384 ..      49     162 ..      29     163 .. 0.88
   2 !   13.3   7.8   4.7e-06     0.028      11      81 ..     261     331 ..     254     440 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-07
                        MFS_1_like 270 vvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksl 346
                                        +++ ++++   +l ++ G  ++ +++++++++  ll ++ ++a +++ + vL+gi  ++++a+++     ++p + 
  gi|488600359|ref|YP_007906830.1|  49 LLSSAMFLVPFGRLADIKGRKRVFVTGMTVFTAGSLLSGVSNSAEMLIAFRVLQGIGGAMVFATGIAILTSVFPIKE 125
                                       567778888899***************************************************************** PP

                        MFS_1_like 347 eatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       ++++ g+ ++     G  +G ++GG+l + ++ + +F 
  gi|488600359|ref|YP_007906830.1| 126 RGKVLGINVASV-YTGLSFGPFFGGILTQNFGWRSVFL 162
                                       *******66543.346679************9999996 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.7e-06
                        MFS_1_like  11 ffaalgsllPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfls 81 
                                        ++a+ ++   l++yl+  k l++++ g i+++ p+++ + +p+ g+l+Dr++ r  v+++++ + a+ +++
  gi|488600359|ref|YP_007906830.1| 261 NYSATFAVTYLLSLYLQyIKALTPQQAGAILVAQPVVQAMLSPFAGWLSDRIEPRV-VASAGMAVTAMGLFV 331
                                       5777777777799****6678******************************98774.444444333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 2775.09
//
Query:       gi|488600360|ref|YP_007906831.1|  [L=187]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-14   51.9   0.1    8.1e-14   51.2   0.1    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    6.7e-14   51.2   0.3    1.5e-13   50.0   0.3    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
    7.9e-10   38.6   0.0    1.3e-09   37.8   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    0.00014   21.7   0.5    0.00026   20.9   0.5    1.4  1  HTH_11          HTH domain
    0.00036   20.5   0.0    0.00086   19.3   0.0    1.6  2  HTH_20          Helix-turn-helix domain
    0.00056   19.4   0.0     0.0014   18.1   0.0    1.7  1  Sigma70_r4      Sigma-70, region 4
    0.00057   19.8   0.1     0.0011   18.9   0.1    1.4  1  MarR            MarR family
     0.0031   17.3   0.0     0.0055   16.6   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0042   16.8   0.1     0.0081   15.9   0.1    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   14.6   0.3       0.18   11.2   0.1    2.0  2  DUF4618         Domain of unknown function (DUF4618)
      0.017   15.2   0.0      0.033   14.3   0.0    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.031   14.2   0.0      0.052   13.4   0.0    1.3  1  MarR_2          MarR family
      0.032   13.9   0.0      0.086   12.5   0.0    1.8  1  Sigma70_r4_2    Sigma-70, region 4
      0.048   14.0   0.0      0.099   13.0   0.0    1.5  1  FaeA            FaeA-like protein
      0.057   13.6   0.7        0.1   12.7   0.7    1.4  1  zf-RING_13      RING/Ubox like zinc-binding domain
      0.069   12.9   0.3       0.54   10.1   0.1    2.1  2  LexA_DNA_bind   LexA DNA binding domain
      0.076   12.8   0.1       0.18   11.6   0.1    1.6  1  HTH_10          HTH DNA binding domain
       0.12   12.4   0.3       0.23   11.5   0.3    1.5  1  HTH_35          Winged helix-turn-helix DNA-binding
       0.13   12.7   0.7       0.25   11.8   0.7    1.5  1  HTH_40          Helix-turn-helix domain
       0.16   12.4   3.3       0.36   11.3   3.3    1.6  1  DUF3795         Protein of unknown function (DUF3795)
       0.21   11.6   1.6       0.34   11.0   1.6    1.3  1  DUF2089         Protein of unknown function (DUF2089)
        5.4    7.2   6.4       0.93    9.6   0.1    2.5  2  FeoC            FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1     1e-16   8.1e-14       1      42 []       1      42 [.       1      42 [. 0.99

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1e-16
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +De DrkI+++Lq++++++ +e+Ae++G+S+  v +R+++Le
  gi|488600360|ref|YP_007906831.1|  1 MDEKDRKIISILQRNGKATLSEIAEEIGMSAMGVKKRLDKLE 42
                                      9****************************************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 !   50.0   0.3   1.9e-16   1.5e-13       1      45 [.       1      45 [.       1      46 [. 0.96

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.9e-16
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                      +de+drkI+++Lq+n++ + +e+Ae++g+S   v++rl++Le+ +
  gi|488600360|ref|YP_007906831.1|  1 MDEKDRKIISILQRNGKATLSEIAEEIGMSAMGVKKRLDKLEKGE 45
                                      8*****************************************965 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   1.7e-12   1.3e-09       4      74 ..      67     137 ..      64     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.7e-12
                                       EE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHT..TTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   4 slepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflrek..laslpgvartetsivle 74 
                                       ++e+   e+le++ ++++++p ++ ++++tG+y++++ + ++d ++le +  e+  l+s pg++r+e + + e
  gi|488600360|ref|YP_007906831.1|  67 EVESA--EALEKLLKRFENCPRIIKFFVTTGSYNLFALIFAEDYHSLESVSLERcsLRSQPGIRRFEIYPIQE 137
                                       55533..69********************************************999***********998766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.5   3.2e-07   0.00026       3      45 ..       6      47 ..       4      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.2e-07
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                      ++i+ +L + +g+ + +e+Aee+++S + v +++++Le+  ++
  gi|488600360|ref|YP_007906831.1|  6 RKIISIL-QRNGKATLSEIAEEIGMSAMGVKKRLDKLEKGEIK 47
                                      79*****.77777************************986555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-06   0.00086      13      52 ..       6      45 ..       2      51 .. 0.93
   2 ?   -2.5   0.0       6.7   5.5e+03       6      31 ..      50      75 ..      47      82 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCT CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeag 52
                                      r+i + L r++ +t+se+ae++++s   + ++L++Le+ +
  gi|488600360|ref|YP_007906831.1|  6 RKIISILQRNGKATLSEIAEEIGMSAMGVKKRLDKLEKGE 45
                                      89**********************************9875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.7
                                      HHS-HHHHHHHHHHSTCTTB-HHHHH CS
                            HTH_20  6 ALahPvRrrilraLaraegltasela 31
                                      AL++   ++i  a+   e  +a++l 
  gi|488600360|ref|YP_007906831.1| 50 ALLNVEKLKIITAIIAMEVESAEALE 75
                                      55555566666666222333444444 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.7e-06    0.0014       6      42 ..       2      39 ..       1      41 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                                      -HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  6 pererevlelrf.geglTleEIgerlgiSrerVrqiek 42
                                      +e++r++++      + Tl+EI+e+ g+S + V+ ++ 
  gi|488600360|ref|YP_007906831.1|  2 DEKDRKIISILQrNGKATLSEIAEEIGMSAMGVKKRLD 39
                                      78999999988889999*****************9975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.3e-06    0.0011       7      43 ..       7      43 ..       4      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLek 43
                                      +i+ il ++g +++se+a+ +g+s + v + ld+Lek
  gi|488600360|ref|YP_007906831.1|  7 KIISILQRNGKATLSEIAEEIGMSAMGVKKRLDKLEK 43
                                      58899*******************************9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.7e-06    0.0055       2      41 ..       3      43 ..       2      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.7e-06
                                      HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5  2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLre 41
                                      ++ +kI+++L++ g+++ +e+aee+g+s   v   L kL++
  gi|488600360|ref|YP_007906831.1|  3 EKDRKIISILQRnGKATLSEIAEEIGMSAMGVKKRLDKLEK 43
                                      56689***********************8777777777765 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 !   15.9   0.1   9.9e-06    0.0081       4      41 ..       7      44 ..       5      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.9e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeq 41
                                      +i+  l++ gk ++ e++e+ g S + + + L++Le+ 
  gi|488600360|ref|YP_007906831.1|  7 KIISILQRNGKATLSEIAEEIGMSAMGVKKRLDKLEKG 44
                                      89*********************************975 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.063        51      51      89 ..       6      44 ..       2      53 .. 0.86
   2 ?   11.2   0.1   0.00022      0.18      14      60 ..      48      94 ..      34     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.063
                           DUF4618 51 ktvisileksskkqleqakaeLqeweekeekklekLeqq 89
                                      +++isil+++ k  l ++ +e+   +  ++k+l kLe+ 
  gi|488600360|ref|YP_007906831.1|  6 RKIISILQRNGKATLSEIAEEIGMSAMGVKKRLDKLEKG 44
                                      689*******************************99985 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00022
                           DUF4618 14 heaeLtklnkeLvkeIqdtedstakkvrklLqqyeklktvisileks 60
                                        a L+ +  +++++I+ +e ++a+   klL+++e +  +i+ + + 
  gi|488600360|ref|YP_007906831.1| 48 LTALLNVEKLKIITAIIAMEVESAEALEKLLKRFENCPRIIKFFVTT 94
                                      345567788999****************************9987665 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.1e-05     0.033      16      48 ..       6      38 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                                      HHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHH CS
                             HTH_9 16 akVvetLlrkgrltlrelvkktkLsldqVkksL 48
                                      +k+++ L r+g+ tl+e+++++++s   Vkk L
  gi|488600360|ref|YP_007906831.1|  6 RKIISILQRNGKATLSEIAEEIGMSAMGVKKRL 38
                                      59***************************9976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.3e-05     0.052      13      47 ..      11      43 ..       4      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLva 47
                                       L r++    t +e+a++ g+s   v ++l++L++
  gi|488600360|ref|YP_007906831.1| 11 ILQRNGK--ATLSEIAEEIGMSAMGVKKRLDKLEK 43
                                      5677777..8***********************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.086      28      47 ..      19      38 ..       1      41 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      -HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrl 47
                                      +  EIAe++g+s   Vk+rl
  gi|488600360|ref|YP_007906831.1| 19 TLSEIAEEIGMSAMGVKKRL 38
                                      678***************98 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.099       4      41 ..       7      43 ..       4      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                      HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHH CS
                              FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLek 41
                                      +I++ l++ ++ ++ +eiA+ +g+sa  ++  L +Lek
  gi|488600360|ref|YP_007906831.1|  7 KIISILQR-NGKATLSEIAEEIGMSAMGVKKRLDKLEK 43
                                      68888888.999999*********************98 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 ?   12.7   0.7   0.00013       0.1      16      34 ..     157     175 ..     148     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                       TTS-EE-TTTHHHTTTSS- CS
                        zf-RING_13  16 acggwfcgncvpyhaghch 34 
                                       a  g fcg+c  y ag+c 
  gi|488600360|ref|YP_007906831.1| 157 APCGVFCGDCKRYEAGKCL 175
                                       56789*************5 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00066      0.54      27      57 ..      19      47 ..       6      50 .. 0.80
   2 ?    0.4   0.0      0.71   5.8e+02      34      52 ..      65      83 ..      62      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00066
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyie 57
                                      +  eia+++g++ + +v+++L +Le KG i+
  gi|488600360|ref|YP_007906831.1| 19 TLSEIAEEIGMS-AMGVKKRLDKLE-KGEIK 47
                                      889*******97.***********8.67665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.71
                                      HHTS-.HHHHHHHHHHHHH CS
                     LexA_DNA_bind 34 alglkSpsaveehLkaLer 52
                                      a+ ++S++a e+ Lk+ e+
  gi|488600360|ref|YP_007906831.1| 65 AMEVESAEALEKLLKRFEN 83
                                      68999*********99886 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00023      0.18      23      49 ..      17      43 ..      14      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                      ++tl+e+A+e+G s++ ++++L k e+
  gi|488600360|ref|YP_007906831.1| 17 KATLSEIAEEIGMSAMGVKKRLDKLEK 43
                                      589*******************99875 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00028      0.23       5      55 ..       6      56 ..       2      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                            HTH_35  5 adIiAaLrkrg.ttLaalsreaglssstlsnaltrpwpkgEalIAeaLgvpp 55
                                        Ii+ L+++g  tL+++++e g+s   +++ l++   kgE  +  +L+v+ 
  gi|488600360|ref|YP_007906831.1|  6 RKIISILQRNGkATLSEIAEEIGMSAMGVKKRLDK-LEKGEIKLTALLNVEK 56
                                      57999999997469****************99987.6899999999998875 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00031      0.25      12      78 ..      17      86 ..       7      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                            HTH_40 12 glsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiek.vgsek....lkpikealpe 78
                                      + ++ eIA+e g++   + + L + +e+ge i+l+ l++ e+ k I+++i+  v+s +    l + +e++p 
  gi|488600360|ref|YP_007906831.1| 17 KATLSEIAEEIGMSAMGVKKRLDK-LEKGE-IKLTALLNVEKLKIITAIIAMeVESAEalekLLKRFENCPR 86
                                      5799******************99.66776.************99998887543322253333333566655 PP

>> DUF3795  Protein of unknown function (DUF3795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.3   0.00045      0.36       2      19 ..     156     173 ..     155     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00045
                           DUF3795   2 iapCGldCeeCeayeake 19 
                                       iapCG+ C++C++yea++
  gi|488600360|ref|YP_007906831.1| 156 IAPCGVFCGDCKRYEAGK 173
                                       89************9975 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.6   0.00041      0.34      49     113 ..      17      77 ..       1      78 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                           DUF2089  49 rGnlkevekelgisYpTvrnrldeile.aLgyeeeeeeeeeeeerkeileklekgeisveeAlerL 113
                                       +  l+e+++e+g+s   v++rld++ + ++++++       + e+ +i++++ + e++  eAle+L
  gi|488600360|ref|YP_007906831.1|  17 KATLSEIAEEIGMSAMGVKKRLDKLEKgEIKLTALL-----NVEKLKIITAIIAMEVESAEALEKL 77 
                                       34699******************9976234444432.....4678999999999999999999987 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0011      0.93       8      44 ..      11      46 ..       6      52 .. 0.87
   2 ?   -1.1   1.7       2.6   2.1e+03      50      64 ..     156     170 ..     150     183 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                              FeoC  8 yleergrvslkeLsrhfkaspealeamLeqwvrkGrv 44
                                       l+++g++ l+e++ +  +s+  +++ L+ ++ kG +
  gi|488600360|ref|YP_007906831.1| 11 ILQRNGKATLSEIAEEIGMSAMGVKKRLDKLE-KGEI 46
                                      699***********************999986.5655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                              FeoC  50 taccsgsCkkCggke 64 
                                        a+c+  C  C+ +e
  gi|488600360|ref|YP_007906831.1| 156 IAPCGVFCGDCKRYE 170
                                       556666666666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1226.51
//
Query:       gi|488600361|ref|YP_007906832.1|  [L=351]
Description: putative permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-80  268.4  31.5    7.3e-80  268.3  31.5    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 !  268.3  31.5   4.1e-84   7.3e-80       4     293 ..      12     345 ..       9     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: 268.3 bits;  conditional E-value: 4.1e-84
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1   4 ealtlfasilleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkk 79 
                                       ++ +l ++++l++l++Lv++fli+ga+++++++++++ +Lg ++++l s+++a +++f+l+vCsc+++P+a++++k+
  gi|488600361|ref|YP_007906832.1|  12 GLKALEEYVALHVLTCLVPAFLIAGALMSMMNKAVLVSYLGaATSKLRSFPLAVISSFFLAVCSCTVIPIASGIYKR 88 
                                       567899*********************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                            ArsP_1  80 GaplgaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek.. 154
                                       ++++++a+++l++aPa+ni+a+++t ++lg++l++ari++a+++a+++g+vl+y f+++ + +a  + + + +e+  
  gi|488600361|ref|YP_007906832.1|  89 TNATAPAMMILWVAPATNILAVTYTGAILGVELALARIIAAISTAFIVGIVLYYFFDRNLEIEALPTNPGRLIERka 165
                                       *****************************************************************99988777779* PP

                                       ................................xxxxxxxxxxxxxxxxxxxxx.xxxx.......xxxxxxxxxxxx RF
                            ArsP_1 155 ................................ltlkpklealkafaknevkew.lelg.......kyLiiGvaiagv 191
                                                                       l l++ l+a k+f+ +e+k+w le++       ++L++Gv+i+gv
  gi|488600361|ref|YP_007906832.1| 166 filfvlliatlllpnylglgkpyifkvevfgvLILATMLYAVKSFSMEELKYWmLETWffvkviiPLLLLGVFIVGV 242
                                       ********************************999****************************************** PP

                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 192 iqafl.pesvllsllggnsvsssllamligvvlyvcslgevpfiaalfesglalGsalAfLlagpllslpellillk 267
                                       i ++l +++v+  +lgg+++++s+la +ig+++y+++++e+pf+++l+ +g+++G alA+Llagp lslp++l++  
  gi|488600361|ref|YP_007906832.1| 243 IGEILkNTDVIYVWLGGEGLRQSFLATIIGALSYFATMTEAPFVEMLMRLGMGSGAALALLLAGPGLSLPNMLAIGR 319
                                       *****889********************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ArsP_1 268 vlkkklvavllglvvvsvvlaglvin 293
                                       +++ +++++++++++v+++lag+v++
  gi|488600361|ref|YP_007906832.1| 320 LFGVRRAVIYVLTIIVLSTLAGYVYG 345
                                       ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2488.72
//
Query:       gi|488600362|ref|YP_007906833.1|  [L=77]
Description: small redox-active disulfide protein 2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-25   88.1   0.7    3.1e-25   88.0   0.7    1.0  1  Thioredoxin_3  Thioredoxin domain
    0.00019   21.6   0.9      0.011   15.9   0.0    2.0  2  Thioredoxin_4  Thioredoxin
     0.0085   15.9   0.0      0.083   12.7   0.0    2.1  2  1-cysPrx_C     C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
      0.018   15.3   0.9      0.049   13.8   0.9    1.7  1  Glutaredoxin   Glutaredoxin
      0.029   14.7   0.0      0.044   14.1   0.0    1.3  1  ArsD           Arsenical resistance operon trans-acting repre
      0.041   13.8   0.2      0.073   13.0   0.2    1.4  1  zinc_ribbon_4  zinc-ribbon 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 !   88.0   0.7     1e-28   3.1e-25       1      75 [.       1      75 [.       1      76 [. 0.98

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 1e-28
                                      EEEEEESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                     Thioredoxin_3  1 meikvlgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                      m+ikvlgpgC++C++++++vk+++++++++a++e vtd++e  k+gV  +Pa+ +dg++v++Gk+pse ei k++
  gi|488600362|ref|YP_007906833.1|  1 MKIKVLGPGCPRCKATYEVVKKVVEKERTDADIEYVTDMSEATKFGVLVTPAVWVDGEIVIQGKIPSESEILKFI 75
                                      89*********************************************************************9988 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.4    0.0012       3.7      24      50 ..       9      35 ..       5      37 .. 0.81
   2 !   15.9   0.0   3.8e-06     0.011     119     156 ..      26      66 ..      22      77 .] 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                                      T-HHHHHHHHHHHHHHHHHHHTTSEEE CS
                     Thioredoxin_4 24 rCphCakfeeeveklleeyidtGkvkf 50
                                       Cp C++  e v+k++e+   + ++++
  gi|488600362|ref|YP_007906833.1|  9 GCPRCKATYEVVKKVVEKERTDADIEY 35
                                      6*************9999744446665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.8e-06
                                       ----HHHH..HHHHHHHHHHT--SS-EEEETTEEE.-TT-- CS
                     Thioredoxin_4 119 eekldalv..eaeskeakkagiestPtfiingekv.eepqt 156
                                       +e+ da++  ++++ ea+k g+  tP + ++ge+v +++++
  gi|488600362|ref|YP_007906833.1|  26 KERTDADIeyVTDMSEATKFGVLVTPAVWVDGEIViQGKIP 66 
                                       4555555533899*********************6233333 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.096   2.9e+02      23      37 ..      13      23 ..       7      26 .. 0.75
   2 !   12.7   0.0   2.8e-05     0.083       5      23 ..      42      61 ..      39      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.096
                                      EE---SSHHHHHHHH CS
                        1-cysPrx_C 23 ivpPpateedavkry 37
                                      +   +at+e +vk++
  gi|488600362|ref|YP_007906833.1| 13 C---KATYE-VVKKV 23
                                      5...89***.99986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.8e-05
                                      HHHHT-.BB-TTT.TBT-EE CS
                        1-cysPrx_C  5 adkhgv.atPAnWkpGdkvi 23
                                      a+k+gv +tPA W+ G+ vi
  gi|488600362|ref|YP_007906833.1| 42 ATKFGVlVTPAVWVDGEIVI 61
                                      789*************9998 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   1.6e-05     0.049       7      60 .]       8      60 ..       1      60 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                      TSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH..TSSSSSEEEETTEEE CS
                      Glutaredoxin  7 ptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels..gvrtvPqvfidgkhv 60
                                      p+Cp Ck++ ++ k+  v+ e    d+d e+  ++ e +  gv   P v++dg+ v
  gi|488600362|ref|YP_007906833.1|  8 PGCPRCKATYEVVKKV-VEKE--RTDADIEYVTDMSEATkfGVLVTPAVWVDGEIV 60
                                      9************998.4444..444444788888888888************975 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 ?   14.1   0.0   1.5e-05     0.044      68      98 ..      45      75 ..      32      77 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                              ArsD 68 kgaeaLPlvlvdgeivktgrYptreelaewl 98
                                       g+ + P v vdgeiv +g+ p+++e+ +++
  gi|488600362|ref|YP_007906833.1| 45 FGVLVTPAVWVDGEIVIQGKIPSESEILKFI 75
                                      577788********************99876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.4e-05     0.073       5      23 ..      10      28 ..       9      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                     zinc_ribbon_4  5 CpsCkakyeiddeklpakg 23
                                      Cp+Cka+ye+  + + +++
  gi|488600362|ref|YP_007906833.1| 10 CPRCKATYEVVKKVVEKER 28
                                      *********9887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 569.13
//
Query:       gi|488600363|ref|YP_007906834.1|  [L=57]
Description: hypothetical protein Asulf_00832 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.42u 0.32s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 356.52
//
Query:       gi|488600364|ref|YP_007906835.1|  [L=135]
Description: hypothetical protein Asulf_00833 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.6   0.0     0.0045   16.5   0.0    1.1  1  Cir_Bir_Yir  Plasmodium variant antigen protein Cir/Yir/Bir
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.38   10.8   0.0    1.8  1  HMG_box_5    HMG (high mobility group) box 5


Domain annotation for each model (and alignments):
>> Cir_Bir_Yir  Plasmodium variant antigen protein Cir/Yir/Bir
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     5e-07    0.0045     191     228 ..      25      76 ..      10     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5e-07
                       Cir_Bir_Yir 191 dssynqvLstLsndYnnlkkkckkekkkipslpeikk..............t 228
                                       ds yn++LstL +d+n+  kk  + +++++++ ei++              +
  gi|488600364|ref|YP_007906835.1|  25 DSRYNKILSTLIEDFNYVIKKTAEGSDRYEEFAEIRSpridslcgkylsslS 76 
                                       799**************99998776777889998887666667666554330 PP

>> HMG_box_5  HMG (high mobility group) box 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.2e-05      0.38      52      81 ..      42      70 ..       2      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.2e-05
                         HMG_box_5 52 wikkaaedqkryerelsemrsaaaatasgk 81
                                       ikk+ae   rye e+ e+rs+   + +gk
  gi|488600364|ref|YP_007906835.1| 42 VIKKTAEGSDRYE-EFAEIRSPRIDSLCGK 70
                                      59**********9.89******98887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 833.31
//
Query:       gi|488600365|ref|YP_007906836.1|  [L=130]
Description: hypothetical protein Asulf_00834 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   56.4   0.0    3.8e-15   56.0   0.0    1.2  1  4HBT             Thioesterase superfamily
     0.0052   16.3   0.0     0.0072   15.9   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
     0.0089   16.2   0.0      0.011   15.9   0.0    1.2  1  DUF4442          Domain of unknown function (DUF4442)
  ------ inclusion threshold ------
      0.083   13.1   0.0        0.1   12.8   0.0    1.1  1  4HBT_3           Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   8.4e-19   3.8e-15       1      77 [.      42     115 ..      42     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 8.4e-19
                                       TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                       +G+ hg ++++l+D a ++a++s +    + ++++++idf +p+  gdelt+earv++ g++++++e +v ++++ +
  gi|488600365|ref|YP_007906836.1|  42 HGTAHGSYLMSLADFAFAIAANSDNI---RRAAISIKIDFYKPAYEGDELTAEARVVHGGKRIVFCELKVMRGNDIV 115
                                       79***********************8...599***************************************998865 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.6e-06    0.0072      53     118 ..      45     114 ..      37     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-06
                                       --HHHHHHHHHHHHH.HHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEE..EEEEE.EEEEEEEEEE CS
                   MaoC_dehydratas  53 ahGmltlaivaklve.eelgdnvvarvgeikvrFtkpVlpgdtlkvelevvg..krdvr.ktkkvevtke 118
                                       ahG + ++++  +++ +   dn++    +ik+ F kp + gd+l++e+ vv   kr v+ + k+++ +++
  gi|488600365|ref|YP_007906836.1|  45 AHGSYLMSLADFAFAiAANSDNIRRAAISIKIDFYKPAYEGDELTAEARVVHggKRIVFcELKVMRGNDI 114
                                       79999999986655504455558899999**************998776554449999967777666655 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.4e-06     0.011      20      98 ..      17      94 ..      12     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                                      --EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S--.-S.-EEEEE CS
                           DUF4442 20 gprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlaka.tg.dltava 96
                                      g+ i e++ g+a+vr   + +  N  gt H+  +++la++a+ + a+    d+ r    ++++d++++a +g +lta+a
  gi|488600365|ref|YP_007906836.1| 17 GVEILEISEGYAKVRGVVKEGYLNFHGTAHGSYLMSLADFAFAIAAN---SDNIRRAAISIKIDFYKPAyEGdELTAEA 92
                                      67899************************************987665...46777777889999999963342588887 PP

                                      E- CS
                           DUF4442 97 el 98
                                      ++
  gi|488600365|ref|YP_007906836.1| 93 RV 94
                                      75 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    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      10      73 ..      44     112 ..      35     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                                       C.-HHHHHHHHHHHHHHT..-S.SS....EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEETT CS
                            4HBT_3  10 agyGGyvlAlalraaqrtv.pdprl....hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqgg 73 
                                       +++G y+++la  a   +  +d+ +     s+ ++F +p+ +g +++ ++++v  G+++  ++ ++ +g 
  gi|488600365|ref|YP_007906836.1|  44 TAHGSYLMSLADFAFAIAAnSDN-IrraaISIKIDFYKPAYEGdELTAEARVVHGGKRIVFCELKVMRGN 112
                                       34999999887555553333332.2333469999999999999999999999999999998888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 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:                        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: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 899.64
//
Query:       gi|488600366|ref|YP_007906837.1|  [L=133]
Description: hypothetical protein Asulf_00835 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-10   40.0   0.0    4.3e-10   39.6   0.0    1.1  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.034   14.1   0.0    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
       0.13   12.4   0.0       0.53   10.4   0.0    2.1  3  CesT         Tir chaperone protein (CesT) family


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   7.1e-14   4.3e-10      20      72 ..      69     132 ..      55     133 .] 0.84

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 7.1e-14
                         DDE_Tnp_1  20 k...........edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldel 72 
                                       k           +d +wg++g+k++ g+kl  avd+r++ +l + i p+n+hds+ ++++l++l
  gi|488600366|ref|YP_007906837.1|  69 KqknrksnedlkKDYKWGHDGNKFFIGFKLAFAVDHRTKRPLLFLIYPANTHDSHIFEDVLEQL 132
                                       445556667777999***********************************************97 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.7e-06     0.034      10      81 ..      58     132 ..      51     133 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-06
                       DDE_Tnp_1_3  10 iDstklav..ChnkrikrhkvfkglakrGkssmGWfyGfkLhliindkGe.ilavkltpgnvdDrepveelakel 81 
                                       +D+ ++++   ++k  k++  +k+  k+G     +f GfkL   ++++ +  l + + p+n++D ++ e++ ++l
  gi|488600366|ref|YP_007906837.1|  58 VDTSRIDLdlNKQKNRKSNEDLKKDYKWGHDGNKFFIGFKLAFAVDHRTKrPLLFLIYPANTHDSHIFEDVLEQL 132
                                       566655540044455667788999999********************9863588999********9998887765 PP

>> CesT  Tir chaperone protein (CesT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         1     6e+03      60      70 ..       6      16 ..       2      20 .. 0.76
   2 ?   -1.4   0.0       0.4   2.4e+03      98     114 ..      28      44 ..      26      45 .. 0.83
   3 ?   10.4   0.0   8.8e-05      0.53      76     112 ..      97     133 .]      67     133 .] 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                                      HHHHHHHHHCH CS
                              CesT 60 llerlLeaNll 70
                                       l++lL++++ 
  gi|488600366|ref|YP_007906837.1|  6 KLRKLLNLSYI 16
                                      68999999875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.4
                                       C--HHHHHHHHHHHHHH CS
                              CesT  98 sldeeaLeallealval 114
                                        l+ee +  ++e+++ +
  gi|488600366|ref|YP_007906837.1|  28 KLEEESFRKAIEQMISS 44 
                                       578999999***99975 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 8.8e-05
                                       T-EEEEETTTTEEEEEEEEEGCC--HHHHHHHHHHHH CS
                              CesT  76 ggalgldeesglllLwarlelesldeeaLeallealv 112
                                       + a+++d+ + + lL   ++++  d++ +e++le+l+
  gi|488600366|ref|YP_007906837.1|  97 KLAFAVDHRTKRPLLFLIYPANTHDSHIFEDVLEQLL 133
                                       679*******************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.35s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 743.20
//
Query:       gi|488600367|ref|YP_007906838.1|  [L=328]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.1   0.0      0.073   12.5   0.0    1.2  1  GATase1_like  Putative glutamine amidotransferase


Domain annotation for each model (and alignments):
>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-06     0.073      31     103 ..     148     222 ..     133     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-06
                      GATase1_like  31 aklllealkdseyevtympaheaaekfPatleglaaydaii..lsdiGsntlllspatflesksvPnrlkllkdy 103
                                       +k+l+ +lkd ++ev  + +  a  k  + +e+l+ yd +   +  i  ++ +l ++ ++e+++v +   ll + 
  gi|488600367|ref|YP_007906838.1| 148 SKELKMTLKDVDFEVAGVDNRMAIIKARFYIETLENYDDVTfhIKAIQHESNVLANESWIEMQKVSKGKTLLVET 222
                                       578999********************************88633689*****************999888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2082.83
//
Query:       gi|488600368|ref|YP_007906839.1|  [L=84]
Description: hypothetical protein Asulf_00837 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00084   19.6   0.2     0.0012   19.1   0.2    1.2  1  DUF2568   Protein of unknown function (DUF2568)
  ------ inclusion threshold ------
      0.031   14.4   2.3       0.04   14.0   2.3    1.1  1  DHHC      DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DUF2568  Protein of unknown function (DUF2568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   1.3e-07    0.0012      16      79 ..       7      75 ..       5      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-07
                           DUF2568 16 vwGfrlgkgallkivlavllpllaavlWglfaaP......karvrlpgpvrlllellvfalaalalavag 79
                                      ++Gf++ +  l ++ +a ++ +l++++Wgl+ +          ++  + +r ll+l v++++++ l ++ 
  gi|488600368|ref|YP_007906839.1|  7 ITGFNIEDV-LRRVFIAFVVLMLMIAVWGLYSSIndliqiWVDYKYAPLYRTLLNLGVLVITIYVLNLLV 75
                                      678998655.999********************9888876688999999***********9999998765 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.3   4.5e-06      0.04      49     104 ..      18      73 ..      14      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-06
                              DHHC  49 kyFllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsl 104
                                       ++F++f++ +l+++++ l+ ++  l++++ + k    +++ l+  +l+i+++vl l
  gi|488600368|ref|YP_007906839.1|  18 RVFIAFVVLMLMIAVWGLYSSINDLIQIWVDYKYAPLYRTLLNLGVLVITIYVLNL 73 
                                       89********************************9999887776566666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 587.35
//
Query:       gi|488600369|ref|YP_007906840.1|  [L=100]
Description: putative pyrophosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-10   39.9   3.2    3.6e-10   39.9   3.2    1.4  2  MazG       MazG nucleotide pyrophosphohydrolase domain
    0.00037   20.9   1.5    0.00043   20.7   1.5    1.1  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase
    0.00078   19.7   1.7    0.00078   19.7   1.7    1.7  2  MazG-like  MazG-like family


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.5   8.8e+03      61      66 ..      12      17 ..       4      21 .. 0.51
   2 !   39.9   3.2     6e-14   3.6e-10       4      70 ..      28      97 ..      25      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                      HHHHHH CS
                              MazG 61 tileKl 66
                                      ++++K+
  gi|488600369|ref|YP_007906840.1| 12 ETVNKI 17
                                      344444 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 6e-14
                                      HHHHHHHHHHHHHHHHHHHTT-HH.......HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH- CS
                              MazG  4 etllaylleEvgEvaeaIkkedrd.......eleeELGDvLlqvlflaniaeeeggidledvaetileKlerRh 70
                                      + +l  l+eE gE+a+aI++e+ +       ele+E +Dv+lq++ la +     ++dle+++   +e l++Rh
  gi|488600369|ref|YP_007906840.1| 28 QLTLSQLIEELGELARAINSEKLRnkraekkELEDEFADVFLQLVKLADL----FDVDLEKAVLDKIEVLIKRH 97
                                      67899***************65555566666******************9....*********99999999998 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.5   7.2e-08   0.00043       2      77 ..       4      88 ..       3      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.2e-08
                                      HHHHHHCT----SS----.-HHHHHHHHHHHHHHHHHHHHHT-SC.......HHHHHHHHHHHHHHHHHHHHHHCT--C CS
                            PRA-PH  2 kefhrligerkpetPeas.taelaslraaligEEavElleaaseg.......dlaeladelaDllYvtygllvllGidl 72
                                      +ef++l  e++++  ++   ++ a+l +  + EE+ El  a + +       +++el de aD++ ++  l++l+++dl
  gi|488600369|ref|YP_007906840.1|  4 EEFQKLAIETVNKIDKKLnLNRDAQLTLSQLIEELGELARAINSEklrnkraEKKELEDEFADVFLQLVKLADLFDVDL 82
                                      68888888888888888855555666999999**********9777888888**************************9 PP

                                      H.HHHH CS
                            PRA-PH 73 d.avfe 77
                                      + av++
  gi|488600369|ref|YP_007906840.1| 83 EkAVLD 88
                                      724555 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.22   1.3e+03      61      73 ..      15      26 ..       7      38 .. 0.55
   2 !   19.7   1.7   1.3e-07   0.00078      14      68 ..      33      95 ..      28      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.22
                         MazG-like 61 eklkkklkkypve 73
                                      +k++kkl+ ++ +
  gi|488600369|ref|YP_007906840.1| 15 NKIDKKLN-LNRD 26
                                      34444444.4444 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.3e-07
                         MazG-like 14 ellksveelfkallk.......gseeeildeLAdviiylylLAdrlGidfee.ideklkkklk 68
                                      +l+++ +el +a+ +       ++++e+ de Adv++ l+ LAd +++d+e+ + +k++  +k
  gi|488600369|ref|YP_007906840.1| 33 QLIEELGELARAINSeklrnkrAEKKELEDEFADVFLQLVKLADLFDVDLEKaVLDKIEVLIK 95
                                      566677777776664567777899**********************************98777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1501  (0.0837191); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 592.69
//
Query:       gi|488600370|ref|YP_007906841.1|  [L=52]
Description: hypothetical protein Asulf_00840 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       555  (0.0309554); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 350.49
//
Query:       gi|488600371|ref|YP_007906842.1|  [L=64]
Description: hypothetical protein Asulf_00841 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 451.42
//
Query:       gi|488600372|ref|YP_007906843.1|  [L=111]
Description: hypothetical protein Asulf_00842 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   0.0    1.7e-09   37.5   0.0    1.3  1  HTH_45    Winged helix-turn-helix
    6.4e-09   35.6   0.0    1.1e-08   34.7   0.0    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0076   16.1   0.1      0.031   14.1   0.1    1.9  1  HxlR      HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.017   13.5   0.0      0.017   13.5   0.0    1.1  1  DUF505    Protein of unknown function (DUF505)
       0.15   12.0   0.0       0.21   11.5   0.0    1.3  1  MarR_2    MarR family


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   0.0   4.8e-13   1.7e-09       9      73 ..      34      98 ..      29     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 4.8e-13
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkele 73
                                      + IL a+++   + +++m +  L+  +l++ L+ L++ +l++k +e Y+lT kG+++l+ ++++ 
  gi|488600372|ref|YP_007906843.1| 34 STILFALDRYPMRFSQLMFETRLNPGILDRHLKSLMQFELVEKGDELYTLTPKGEKILNIINQIF 98
                                      568888888899999*********************************************99986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   3.2e-12   1.1e-08       4      47 .]      33      76 ..      30      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.2e-12
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                       + IL++L + ++ +++l+ e++l+++++++HLk L++  LVek
  gi|488600372|ref|YP_007906843.1| 33 VSTILFALDRYPMRFSQLMFETRLNPGILDRHLKSLMQFELVEK 76
                                      567***************************************97 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   8.7e-06     0.031       9      80 ..      35      98 ..      27     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.7e-06
                                      HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                              HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80
                                       il++l + ++Rfs+l  +   +   +L ++L+ L q +l+e+           Y+lt+kG+++ ++++++ 
  gi|488600372|ref|YP_007906843.1| 35 TILFALDRYPMRFSQLMFET-RLNPGILDRHLKSLMQFELVEKGD-------ELYTLTPKGEKILNIINQIF 98
                                      69999999********9888.899999*************99754.......36*************99875 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.7e-06     0.017     370     406 ..      65      96 ..       5     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-06
                            DUF505 370 LysLesfeLieseveekgkevyvlTeyGekvledqek 406
                                       L+sL  feL+     ekg+e y+lT++Gek+l+  ++
  gi|488600372|ref|YP_007906843.1|  65 LKSLMQFELV-----EKGDELYTLTPKGEKILNIINQ 96 
                                       5555555555.....56799************97665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     6e-05      0.21       9      54 ..      35      77 ..      29      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       +L+aL r p   ++ ++l  +++l ++ + r+lk L +  Lve+ 
  gi|488600372|ref|YP_007906843.1| 35 TILFALDRYP---MRFSQLMFETRLNPGILDRHLKSLMQFELVEKG 77
                                      58********...9************************99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 613.36
//
Query:       gi|488600373|ref|YP_007906844.1|  [L=286]
Description: archaeal flagellin N-terminal-like domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-42  144.6  12.4    3.6e-41  141.1   7.3    2.2  2  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
       0.88   10.2   3.4         24    5.6   0.1    3.1  3  YtkA            YtkA-like


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   7.3     4e-45   3.6e-41       1     159 [.      17     173 ..      17     178 .. 0.89
   2 !    6.5   0.2   0.00097       8.7     104     163 ..     215     270 ..     182     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 4e-45
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSE...EEEEEE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtine...itiyvk 74 
                                       Gf+g++++Iv+IA+V+VAAv+++v++++++f++qk+q++++++++q+ss++e+ gdv+ +++++  n    it+yv+
  gi|488600373|ref|YP_007906844.1|  17 GFTGLEAAIVLIAFVVVAAVFSYVMLGAGFFTTQKSQEVVHTGVQQASSSIELAGDVVVKGDDTIANAvdtITFYVT 93 
                                       8*********************************************************5555554444556****** PP

                                       --TTS--EEGGG-EEEEEESS.--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEE CS
                    Arch_flagellin  75 lnaGsspidlnkttisvtddg.qetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsv 150
                                       ++aGs+p+dl+kt+is+ dd+ +   + +    + +i  + +++ ++ +++ek+e+++++v ++  +++ta +  sv
  gi|488600373|ref|YP_007906844.1|  94 VTAGSTPVDLDKTIISYKDDDeFFSKIPW---AYASIVREPNEFPAD-NLVEKNELYKITVYLD--KKVTAVTGESV 164
                                       *********************66666666...999999999999999.***************5..77888888888 PP

                                       EEE-SSS-- CS
                    Arch_flagellin 151 evvpenGas 159
                                       ++++ +G+ 
  gi|488600373|ref|YP_007906844.1| 165 TITTGSGSL 173
                                       888888875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00097
                                       .................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--EEEE CS
                    Arch_flagellin 104 efgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGasttie 163
                                       ++g ++++ +dg+ t+++ + e+g  ++       ++ + +++++++e++p++Ga+++i 
  gi|488600373|ref|YP_007906844.1| 215 STGAITTTLADGTYTANYRYTEPGTAGTDYP----SSLPQTNEKIQLELKPPTGATLVIV 270
                                       5555555555666666666666666554332....356889***************9985 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.012   1.1e+02       9      37 ..      73     103 ..      54     115 .. 0.76
   2 ?   -0.3   0.0      0.19   1.7e+03      23      43 ..     147     167 ..     133     172 .. 0.67
   3 ?    5.6   0.1    0.0027        24      58      80 ..     218     239 ..     200     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.012
                              YtkA   9 velvspeepkagentivv..tvtqggkpVed 37 
                                       v + +++++++  +ti++  tvt+g +pV+ 
  gi|488600373|ref|YP_007906844.1|  73 VVVKGDDTIANAVDTITFyvTVTAGSTPVDL 103
                                       5566778888888888775459999999983 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.19
                              YtkA  23 tivvtvtqggkpVedadvkve 43 
                                       +i+v  +++ ++V++++v+++
  gi|488600373|ref|YP_007906844.1| 147 KITVYLDKKVTAVTGESVTIT 167
                                       455567777888888888776 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0027
                              YtkA  58 kvelkesedGvYeaevnfsmeGt 80 
                                        ++++   dG Y a++ ++++Gt
  gi|488600373|ref|YP_007906844.1| 218 AITTT-LADGTYTANYRYTEPGT 239
                                       44444.59**************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1590.55
//
Query:       gi|488600374|ref|YP_007906845.1|  [L=204]
Description: archaeal flagellin N-terminal-like domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-46  157.2   8.6    4.7e-46  157.0   8.6    1.0  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.0   8.6   2.6e-50   4.7e-46       1     163 [.      15     190 ..      15     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 2.6e-50
                                       X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.........EEE-SSSSSE CS
                    Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.........dsatngtine 68 
                                       Gf+g++++Iv+IA+V+VAAv+++v++++++f++qk+q++++++++q+ss++e+tgdv+         +++t+++ine
  gi|488600374|ref|YP_007906845.1|  15 GFTGLEAAIVLIAFVVVAAVFSYVMLGAGFFTTQKSQEVVHTGVQQASSSIELTGDVIatkdssdadTDGTSDEINE 91 
                                       8*********************************************************9999988887788888888 PP

                                       EEEEEE--TTS--EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--....TTT- CS
                    Arch_flagellin  69 itiyvklnaGsspidlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvn....eddg 141
                                       + + ++l+ G++p+d++k++i +t+ +  ++lt  ++ + ++ ++++   +gd++lek ek+e++++vn    +dd+
  gi|488600374|ref|YP_007906845.1|  92 VKLFIQLASGGTPVDVDKMVIALTTADAHKVLTKGSSATATTFAYTDLNGDGDNLLEKYEKFEIVIDVNsalgTDDD 168
                                       ***************************77777777777777777777777889********************9999 PP

                                       --TT-EEEEEEE-SSS--EEEE CS
                    Arch_flagellin 142 itagdevsvevvpenGasttie 163
                                       +t ++++++e++p++Gas+t+ 
  gi|488600374|ref|YP_007906845.1| 169 LTVNEKFQIEIKPPQGASLTVV 190
                                       ******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1183.55
//
Query:       gi|488600375|ref|YP_007906846.1|  [L=225]
Description: hypothetical protein Asulf_00845 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.7   0.0     0.0044   16.9   0.0    1.4  1  Arch_fla_DE  Archaeal flagella protein
  ------ inclusion threshold ------
      0.026   14.5   0.1        1.5    8.8   0.0    2.4  2  Slx4         Slx4 endonuclease
      0.075   13.4   0.1      0.075   13.4   0.1    2.9  3  FlaC_arch    Flagella accessory protein C (FlaC)
      0.084   13.2   0.2      0.084   13.2   0.2    2.5  2  CLZ          C-terminal leucine zipper domain of cyclic nucle


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.8e-07    0.0044      12      58 ..     135     181 ..     125     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.8e-07
                       Arch_fla_DE  12 dyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlk 58 
                                       d+++ + ++eW + +v r+g e++ ++++ ++ +g is ev+e +  
  gi|488600375|ref|YP_007906846.1| 135 DPISLHRLVEWTNEMVMRYGEETLIKLVEVFQMVGYISPEVKEVVVM 181
                                       667778899********************************987655 PP

>> Slx4  Slx4 endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00034       1.5      22      51 ..     135     161 ..     134     164 .. 0.86
   2 ?    3.1   0.0     0.021        94      24      54 ..     196     223 ..     194     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00034
                                       --EEHHHHHHHHHHH-GGGGGS-HHHHHHH CS
                              Slx4  22 ePIvLedltawLnteglglkevdpaelrew 51 
                                       +PI+L+ l++w n+  +   ++++++l + 
  gi|488600375|ref|YP_007906846.1| 135 DPISLHRLVEWTNEMVM---RYGEETLIKL 161
                                       8*************988...8888888765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.021
                                       EEHHHHHHHHHHH-GGGGGS-HHHHHHHHHH CS
                              Slx4  24 IvLedltawLnteglglkevdpaelrewcds 54 
                                       I+L +l+ +Ln e+     +d + l+ ++d+
  gi|488600375|ref|YP_007906846.1| 196 IDLYKLYIILNPEDT---SLDSKVLKLMLDK 223
                                       8999**********9...9999999999997 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 ?   13.4   0.1   1.7e-05     0.075      13      54 ..      12      54 ..       2      55 .. 0.82
   2 ?   -2.6   0.1       1.7   7.6e+03       4      12 ..     106     114 ..      95     120 .. 0.64
   3 ?   -1.4   1.4      0.71   3.2e+03      33      44 ..     191     199 ..     155     204 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                         FlaC_arch 13 steletvkkeneelsksveelkenVkd.llsLYEvVsnqvNPF 54
                                      +t  +t ++ + +l+++v++lk ++k+ l++L E+  n  NPF
  gi|488600375|ref|YP_007906846.1| 12 DTGTDTPESRIAKLEEEVNMLKGSIKKlLIDLREIMNNLENPF 54
                                      55778889999**************772579****99999999 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                         FlaC_arch   4 elEnklskl 12 
                                       ++E++++k+
  gi|488600375|ref|YP_007906846.1| 106 NVEERIPKV 114
                                       455555555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.71
                         FlaC_arch  33 lkenVkdllsLY 44 
                                       + +    +++LY
  gi|488600375|ref|YP_007906846.1| 191 ISDA---VIDLY 199
                                       3333...34444 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.9e-05     0.084      12      62 ..       3      51 ..       1      61 [. 0.82
   2 ?   -0.9   1.1      0.49   2.2e+03      15      35 ..      78      99 ..      77     118 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                               CLZ 12 dglLDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62
                                      +g +D+  a+     ++ e+++ +Le+++++L+  +++Ll ++ +  + L+
  gi|488600375|ref|YP_007906846.1|  3 EGKIDQIIADT--GTDTPESRIAKLEEEVNMLKGSIKKLLIDLREIMNNLE 51
                                      68888886444..57899**********************99988877776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.49
                               CLZ 15 LDee.aakagaeqkeleekver 35
                                      ++e+ ++k+g+e+k+ ee v+ 
  gi|488600375|ref|YP_007906846.1| 78 IEEDgEKKRGKEEKKGEEDVSG 99
                                      5677556667888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1581.17
//
Query:       gi|488600376|ref|YP_007906847.1|  [L=160]
Description: hypothetical protein Asulf_00846 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   39.5   1.8    7.4e-10   39.3   1.8    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.026   14.8   0.1      0.043   14.2   0.1    1.3  1  DUF4854         Domain of unknown function (DUF4854)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   1.8   8.3e-14   7.4e-10       3     163 ..       4     157 ..       2     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 8.3e-14
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS CS
                    Arch_flagellin   3 vgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGs 79 
                                        +i t  + IA +++  +++ ++  +  + +++ +s   + +e v+++++i+ ++  s+t++    ++i++k n Gs
  gi|488600376|ref|YP_007906847.1|   4 EVITTSLLVIASIIATIALINAVFPSLAQMASSFTSLANNLNERVETNVDIIFVIASSSTDT----VNIWIK-NIGS 75 
                                       67899999999999999999999999999999999999999999999999999999666665....9*****.**** PP

                                       --EE...GGG-EEEEEESS--EE--E....................T-EE-TT-EEEEEEE--TTT---TT-EEEEE CS
                    Arch_flagellin  80 spid...lnkttisvtddgqetlltadefgivvisdtdgsltng..devlekgekvelevnvneddgitagdevsve 151
                                       ++i    ++k+++++  +    ++  + ++ +++ +++ s+ ng  d+++e ge++ ++v++    +  + +e++ +
  gi|488600376|ref|YP_007906847.1|  76 NKIPntlIEKSDLFIYSSS---MYLHVPYNDSSPPTWTYSFENGdgDDYWENGETINITVQL----SSLPAGEYTAN 145
                                       *765222444444433333...3333355677777888888888*****************9....57888888888 PP

                                       EE-SSS--EEEE CS
                    Arch_flagellin 152 vvpenGasttie 163
                                       ++  nG+st  +
  gi|488600376|ref|YP_007906847.1| 146 FILYNGVSTKDT 157
                                       999999998765 PP

>> DUF4854  Domain of unknown function (DUF4854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.8e-06     0.043      62      93 ..      29      60 ..      18      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-06
                           DUF4854 62 sldsqastfeslakqlkkevkvenpivvvrvl 93
                                      sl ++as+f+sla++l++ v+++  i+ v++ 
  gi|488600376|ref|YP_007906847.1| 29 SLAQMASSFTSLANNLNERVETNVDIIFVIAS 60
                                      6889******************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1090.33
//
Query:       gi|488600377|ref|YP_007906848.1|  [L=157]
Description: hypothetical protein Asulf_00847 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00023   21.4   0.0    0.00028   21.1   0.0    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.042   14.0   0.0    1.2  1  DUP             DUP family
       0.56    9.6   4.3       0.35   10.3   2.0    1.8  2  Rax2            Cortical protein marker for cell polarity


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.7e-08   0.00028       4     158 ..       5     147 ..       2     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.7e-08
                                       H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS CS
                    Arch_flagellin   4 g.igtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGs 79 
                                       + i+t+I +  + l+ + +a  +        ++ ++  +++++ +++++ei ++  +s t++    i++ v  n Gs
  gi|488600377|ref|YP_007906848.1|   5 VlIATAISLALLMLIVYSFAIGASMFIEVAHSSREDLHKRAVDRIQTRIEIKSVEWNSLTRD----INVSVF-NSGS 76 
                                       447888888777777777777666666667788899999*****************999997....9*****.**** PP

                                       --EE.GGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-S CS
                    Arch_flagellin  80 spid.lnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpe 155
                                       ++id +  ++++v++++ ++ l +   ++ +  + ++++ n   +l++ge+++  +      ++ +g+ v  ++ ++
  gi|488600377|ref|YP_007906848.1|  77 TKIDnFGLMDVIVVYNE-AKYLRY---ETDWKATIENETIN-PGILDPGETLAMLIYG----PFEQGTVVWMKICTP 144
                                       **975899*********.555555...44444444444444.59*************5....8************** PP

                                       SS- CS
                    Arch_flagellin 156 nGa 158
                                       nG+
  gi|488600377|ref|YP_007906848.1| 145 NGV 147
                                       997 PP

>> DUP  DUP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.1e-06     0.042       7      76 ..      10      78 ..       4      83 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-06
                               DUP  7 rllvlvllilllvalvlqnlrafsksvsdekfkikllseiikekpavdakeWdtIaknmNqYLfenklwk 76
                                      ++++++l+++++ + +  ++   + + s e+ + + +  i ++ + ++  eW+  ++++N  +f+ +  k
  gi|488600377|ref|YP_007906848.1| 10 AISLALLMLIVYSFAIGASMFIEVAHSSREDLHKRAVDRIQTRIE-IKSVEWNSLTRDINVSVFNSGSTK 78
                                      334444444444434444555567777888877888888888888.9*****************988766 PP

>> Rax2  Cortical protein marker for cell polarity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.0   5.9e-05      0.35     163     191 ..       2      30 ..       1      59 [. 0.71
   2 ?   -0.7   0.0      0.13   7.8e+02      26     112 ..      71      87 ..      53     113 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.9e-05
                              Rax2 163 gfVVlIgLAlALgtvallgllgiilayir 191
                                       gf VlI+ A++L++ +l++  ++i a ++
  gi|488600377|ref|YP_007906848.1|   2 GFEVLIATAISLALLMLIVYSFAIGASMF 30 
                                       778****************9888866544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                              Rax2  26 sftladsdisqlwvagkssngssfllkydgskWssiddinlgesttirglqvlsltnshsssdlldknqvLlvtGql 102
                                       +f                                                                       +G+ 
  gi|488600377|ref|YP_007906848.1|  71 VFN----------------------------------------------------------------------SGST 77 
                                       333......................................................................3444 PP

                              Rax2 103 nlpdfGnasa 112
                                       ++ +fG + +
  gi|488600377|ref|YP_007906848.1|  78 KIDNFGLMDV 87 
                                       4444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 923.66
//
Query:       gi|488600378|ref|YP_007906849.1|  [L=240]
Description: putative ATPases involved in biogenesis of archaeal flagella [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-29  102.6   0.1    2.3e-29  102.4   0.1    1.0  1  ATPase      KaiC
      2e-12   47.0   3.3    2.2e-09   36.9   0.3    2.0  2  PAXNEB      PAXNEB protein
    1.5e-10   40.8   0.3    3.5e-10   39.6   0.3    1.6  1  Rad51       Rad51
      3e-06   27.0   0.3    6.4e-06   25.9   0.3    1.5  1  DUF835      Protein of unknown function (DUF835)
     0.0002   21.0   0.0    0.00042   19.9   0.0    1.5  1  AAA_25      AAA domain
    0.00031   20.4   0.1    0.00037   20.1   0.1    1.2  1  Elong_Iki1  Elongator subunit Iki1
    0.00033   20.9   0.0    0.00056   20.2   0.0    1.3  1  AAA_22      AAA domain
    0.00059   19.7   0.0    0.00083   19.2   0.0    1.1  1  MEDS        MEDS: MEthanogen/methylotroph, DcmR Sensory domai
     0.0026   17.3   0.3     0.0069   15.9   0.1    1.7  2  RecA        recA bacterial DNA recombination protein
     0.0093   15.7   0.2       0.05   13.3   0.0    2.0  2  IstB_IS21   IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.092   12.2   0.0       0.17   11.2   0.0    1.4  1  TniB        Bacterial TniB protein
       0.12   12.4   0.5        2.3    8.3   0.4    2.3  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 !  102.4   0.1   1.5e-32   2.3e-29       3     229 ..      15     235 ..      13     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.5e-32
                            ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdleklee 79 
                                       +g  ++D+ l gGip g+ +li Ge +tGK+++++qF++ g+ + g  + + t+e + ++l ++++sl  d+ ++ +
  gi|488600378|ref|YP_007906849.1|  15 SGNSEIDKKLGGGIPIGSLTLIEGENDTGKSVLSQQFTYGGLHQ-GHSVAYYTTENTIKSLLKQMESLSLDVSEFYA 90 
                                       566789***********************************999.******************************** PP

                            ATPase  80 egklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgv 156
                                        g l +  +  ++ e     ++++++ +++ +a+ ik+ +++ v+iDs+t ++++++e+ + e l +l+++   +g 
  gi|488600378|ref|YP_007906849.1|  91 WGYLRVFPIHFEGVE----WTHDQMKRILSLVANHIKTARENVVIIDSLTMFTTYSTEDDILEFLTRLKNFCD-KGK 162
                                       ******999999887....45899****************************9999999999*******9985.566 PP

                            ATPase 157 TailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhsk.kehpfeIte.egikvlee 229
                                       T +++  + +  ++ +  ++   ++d+ + L+++++ ++ v ++e+ k+Rg++  + +++ f++ +  g k+++ 
  gi|488600378|ref|YP_007906849.1| 163 TILITLHQ-HAFKEDTLVRIRS-ACDCHLFLRKEQVGDRYVNVIEVAKVRGARKTTgNIVSFQVRPgFGLKIMPL 235
                                       77777774.4556777889999.****************************977661566799998888888875 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.3   1.5e-12   2.2e-09      16      85 ..      10      78 ..       6      87 .. 0.88
   2 !   10.9   0.2   0.00013      0.19     194     280 ..     117     190 ..     101     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-12
                            PAXNEB 16 qlltStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlreL 85
                                      + + S+G++++Dk LgGG+p+Gs+ lie + +++ ++vL + F   G+ q+h+v + + +++ +++l+++
  gi|488600378|ref|YP_007906849.1| 10 KSILSSGNSEIDKKLGGGIPIGSLTLIEGE-NDTGKSVLSQQFTYGGLHQGHSVAYYTTENTIKSLLKQM 78
                                      5799***********************976.56669********************99988888777765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                            PAXNEB 194 llkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslvrk 270
                                       l++++ ++a ++  v  ++i sL   +        s++ d+l+FL+ L+ +  + + ++litl  + +  ++  + +
  gi|488600378|ref|YP_007906849.1| 117 LVANHIKTAREN--V--VIIDSLTMFTT------YSTEDDILEFLTRLKNFCDKGK-TILITLHQHAF--KEDTLVR 180
                                       333333333333..3..78888888777......46899************98765.789********..6666778 PP

                            PAXNEB 271 ieqlvDtvie 280
                                       i++ +D+ + 
  gi|488600378|ref|YP_007906849.1| 181 IRSACDCHLF 190
                                       9999998775 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.3   2.3e-13   3.5e-10      12     160 ..       8     152 ..       2     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.3e-13
                                       HHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---G..G CS
                             Rad51  12 krsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrp..e 86 
                                       +r+++  l+ G++++D+ LgGGi+ gs+t i Ge+ +Gk+ l+++++    l  +   +   ++y  te t+++  +
  gi|488600378|ref|YP_007906849.1|   8 ERKSI--LSSGNSEIDKKLGGGIPIGSLTLIEGENDTGKSVLSQQFTYGG-L--H---QGHSVAYYTTENTIKSllK 76 
                                       44444..689*******************************999876432.2..2...346799*******986333 PP

                                       GGHHHH....HHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHH CS
                             Rad51  87 rlveia....erykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRq 159
                                       ++ ++     e y     +v         +t+++ +++l+ +a++++  + +++i+Ds+t    t +s  +++ +  
  gi|488600378|ref|YP_007906849.1|  77 QMESLSldvsEFYAWGYLRVFPIHFEGVEWTHDQMKRILSLVANHIKTARENVVIIDSLTMF--TTYSTEDDILEFL 151
                                       44333343435555555555555555555666999***********************9743..4455555554444 PP

                                       H CS
                             Rad51 160 q 160
                                       +
  gi|488600378|ref|YP_007906849.1| 152 T 152
                                       4 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.3   4.3e-09   6.4e-06      60     132 ..     110     181 ..     102     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.3e-09
                            DUF835  60 nlekltetivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalL 132
                                       ++++++  + + +k a ++vv+iD+l + ++++  +++l+fl+ lk  +  k++t+++++ ++a++e  l  +
  gi|488600378|ref|YP_007906849.1| 110 QMKRILSLVANHIKTARENVVIIDSLTMFTTYSTEDDILEFLTRLKN-FCDKGKTILITLHQHAFKEDTLVRI 181
                                       7899******************************************6.5799*************99876655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.8e-07   0.00042      26     188 ..      24     170 ..      11     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.8e-07
                            AAA_25  26 vkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.... 97 
                                       ++g +p g+l+l+ G  +tGK++l  +  +  + +G+            V y+ +E++ + l + ++ +  ++    
  gi|488600378|ref|YP_007906849.1|  24 LGGGIPIGSLTLIEGENDTGKSVLSQQFTYGGLhQGH-----------SVAYYTTENTIKSLLKQMESLSLDVsefy 89 
                                       4566799**********************99996766...........89*********999999999999994333 PP

                            AAA_25  98 rddarllvldlagveslpLfakd...rggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalvea 171
                                       +       + + +v +++    +   ++++++ + v   +++i+  ++  +v+iD+l+ ++  + +  +d+ +++++
  gi|488600378|ref|YP_007906849.1|  90 A-------WGYLRVFPIHFEGVEwthDQMKRILSLV---ANHIKT-ARENVVIIDSLTMFTTYSTE--DDILEFLTR 153
                                       1.......3333333333322221102233344554...555555.4457********99999877..7899***** PP

                            AAA_25 172 leriarrtgaavllvhH 188
                                       l++++++ + +++ +h+
  gi|488600378|ref|YP_007906849.1| 154 LKNFCDKGKTILITLHQ 170
                                       *****988887777774 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   2.5e-07   0.00037      69     135 ..     109     172 ..      63     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.5e-07
                        Elong_Iki1  69 kklkelakeiksalspkssekkkkalviiDslnplaslikeeslaaflssllssp...svslvavYHtdv 135
                                       +++k++ + ++++++++     ++++viiDsl++  ++ +e+++ +fl++l +       +++ ++H+  
  gi|488600378|ref|YP_007906849.1| 109 DQMKRILSLVANHIKTA-----RENVVIIDSLTMFTTYSTEDDILEFLTRLKN-FcdkGKTILITLHQHA 172
                                       24778888888887433.....789********998999*********99975.2344999999999976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.8e-07   0.00056       6     122 ..      32     161 ..      31     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.8e-07
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............ 70 
                                       +++++ Ge  tGK++l +++++           + + v ++ ++  + k+ll+++ +   +  +             
  gi|488600378|ref|YP_007906849.1|  32 SLTLIEGENDTGKSVLSQQFTYGGLH-------QGHSVAYYTTEN-TIKSLLKQMESLSLDVSEFyawgylrvfpih 100
                                       578999****************9753.......444444444444.4899999988876655555799999999999 PP

                            AAA_22  71 ......erlsseellealeqalraravielliiDEaqhlr..s..eealeeLrsllnl..srkg 122
                                               ++ +++l+++++++++++   ++iiD    ++  s  +++le+L +l n+  +  g
  gi|488600378|ref|YP_007906849.1| 101 fegvewTHDQMKRILSLVANHIKTARE-NVVIIDSLTMFTtySteDDILEFLTRLKNFcdK--G 161
                                       99***9999******************.**********98773679999999999997431..2 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 !   19.2   0.0   5.5e-07   0.00083      20     155 ..      51     180 ..      41     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.5e-07
                              MEDS  20 fikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralakala 96 
                                       f   gl++g+ v+y+++++t   l++++++  ldv+++ + g l++ +       +g+   + +++++ + +a++++
  gi|488600378|ref|YP_007906849.1|  51 FTYGGLHQGHSVAYYTTENTIKSLLKQMESLSLDVSEFYAWGYLRVFPIHF----EGVEWTHDQMKRILSLVANHIK 123
                                       66679*************************************999998553....3333335556777777777776 PP

                              MEDS  97 dgyaglrvigemtwalrspaereelleyEallneliadepvtalClYdrrrfsaevlad 155
                                          + + +i   t         ++ le+  +l +++++ + t+l + +   f++++l  
  gi|488600378|ref|YP_007906849.1| 124 TARENVVIIDSLTMFTTYS-TEDDILEFLTRLKNFCDKGK-TILITLHQHAFKEDTLVR 180
                                       6677887777777655555.89*************99999.666666668888886544 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   4.6e-06    0.0069      29      96 ..       8      74 ..       2      90 .. 0.83
   2 ?   -1.7   0.0       1.1   1.6e+03     117     144 ..     112     139 ..     107     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.6e-06
                                      ----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HH CS
                              RecA 29 lkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpk 96
                                      ++ + +ssG+  +d  lG GG+p G ++ i G + +Gk+ l+ +      ++g  +a+  +e ++ + 
  gi|488600378|ref|YP_007906849.1|  8 ERKSILSSGNSEIDKKLG-GGIPIGSLTLIEGENDTGKSVLSQQFTYGGLHQGHSVAYYTTENTIKSL 74
                                      455679************.*************************999999999999999999988764 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHTTT--SEEEEE-TTT-- CS
                              RecA 117 eqaleiadalvrsgaidlivvdsvaalv 144
                                       ++ l ++   ++++  +++++ds++ ++
  gi|488600378|ref|YP_007906849.1| 112 KRILSLVANHIKTARENVVIIDSLTMFT 139
                                       5567777888888899999999987665 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   3.3e-05      0.05      51      95 ..      35      79 ..      31      87 .. 0.86
   2 ?   -0.3   0.1       0.5   7.5e+02     103     125 ..     121     143 ..     104     179 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                         IstB_IS21 51 vllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarr 95
                                      ++ G   +GKs l+  + + + ++g+sv ++++e+ +++l ++ +
  gi|488600378|ref|YP_007906849.1| 35 LIEGENDTGKSVLSQQFTYGGLHQGHSVAYYTTENTIKSLLKQME 79
                                      5679999**************************999988866655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.5
                         IstB_IS21 103 lkrllkvdllilDdlgllpldqa 125
                                         + ++ +++i+D l + +  + 
  gi|488600378|ref|YP_007906849.1| 121 HIKTARENVVIIDSLTMFTTYST 143
                                       44556778888888877655443 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.17      38     154 ..      34     162 ..      31     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                              TniB  38 lllvGdsnnGKtmivekFa.....rlhppekdedaekvpvlvvqapp.kpdekrlya.aiLealgaplk....arar 103
                                        l+ G+ ++GK+++ ++F+     + h+ +  +++++++ l+ q+ + + d +++ya   L+ +   ++    ++++
  gi|488600378|ref|YP_007906849.1|  34 TLIEGENDTGKSVLSQQFTygglhQGHSVAYYTTENTIKSLLKQMESlSLDVSEFYAwGYLRVFPIHFEgvewTHDQ 110
                                       5899**************84422233444456888999999999988356999**9855788777776511114556 PP

                              TniB 104 vskleqqvlrllrelkvrvLiiDEihnllags.arkqreflnalksLgnelk 154
                                       ++++ + v + +++ +  v+iiD +  + + s  ++  efl  lk+++++ k
  gi|488600378|ref|YP_007906849.1| 111 MKRILSLVANHIKTARENVVIIDSLTMFTTYStEDDILEFLTRLKNFCDKGK 162
                                       6677778888899999*********998875414567888888888887755 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0015       2.3       5      44 ..      34      77 ..      31     170 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd....k 44
                                       +i+G   +GK++l +q+ +  l +  s+ y++ ++  +    +
  gi|488600378|ref|YP_007906849.1| 34 TLIEGENDTGKSVLSQQFTYGGLHQGHSVAYYTTENTIKsllkQ 77
                                      689999999*********99999888889998888855533330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); 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:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1564.50
//
Query:       gi|488600379|ref|YP_007906850.1|  [L=218]
Description: hypothetical protein Asulf_00849 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   0.4      0.052   13.5   0.4    1.7  2  Protocadherin   Protocadherin
        0.4   10.8   4.0       0.14   12.2   0.6    2.1  2  ENT             ENT domain
       0.53   10.9   7.8        1.1   10.0   1.8    2.3  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
        1.1    9.7  14.3       0.25   11.9   2.8    2.2  2  APG6_N          Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> Protocadherin  Protocadherin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   1.2e-05     0.052      39     104 ..       9      74 ..       3     124 .. 0.77
   2 ?   -2.0   0.0      0.63   2.8e+03      19      31 ..     151     162 ..     134     209 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                     Protocadherin  39 kiliavlaGvvtvilvilivvlvRycrqkaksgykagkKeeedfvtPkqenkeekgkkkkkkkkkk 104
                                       ++ ++++ G+v+++lvi i++l    r+kaks+ +  kK   +f+   +++k++k++k k  ++k 
  gi|488600379|ref|YP_007906850.1|   9 TVDYSIIIGSVVAVLVISITALYDVKREKAKSEGNEPKKGILQFIVDFKGRKKRKEEKLKEIDEKL 74 
                                       566799******************99999999999999*999999999888887776666544433 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.63
                     Protocadherin  19 pldqdiagdpdve 31 
                                        +++di g+ dv+
  gi|488600379|ref|YP_007906850.1| 151 GMEEDI-GENDVK 162
                                       444444.444433 PP

>> ENT  ENT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.73   3.3e+03      57      63 ..      71      77 ..      59      94 .. 0.58
   2 ?   12.2   0.6   3.2e-05      0.14      28      54 ..     163     189 ..     155     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.73
                               ENT 57 Derlkti 63
                                      De+l+++
  gi|488600379|ref|YP_007906850.1| 71 DEKLREV 77
                                      4444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.2e-05
                               ENT  28 ekkkllteLrkeLsIsterHraelrrv 54 
                                        k +l+++L+keLsI+ e+  +++r  
  gi|488600379|ref|YP_007906850.1| 163 GKDSLIESLQKELSIKREEKLNLMRDL 189
                                       799****************99998876 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 ?    4.4   0.4     0.012        56      52      84 ..      62      93 ..      30     111 .. 0.72
   2 ?   10.0   1.8   0.00023       1.1      43      91 ..     157     205 ..     134     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                    HIP1_clath_bdg 52 eelekLkreleakraelarlkssLesseqsgeq 84
                                       + ekL +e+ +k  e++ +++ Le+se+ +++
  gi|488600379|ref|YP_007906850.1| 62 RKEEKL-KEIDEKLREVTGVEKELERSEEVSAE 93
                                      333444.36777777777777777777776655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00023
                    HIP1_clath_bdg  43 aerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaa 91 
                                        e+ ++ + + +e+L++el  kr+e  +l   Le ++   ++l+s+l++
  gi|488600379|ref|YP_007906850.1| 157 GENDVKGKDSLIESLQKELSIKREEKLNLMRDLEGQKLDTAELESELKE 205
                                       46788899999********************************999987 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   3.9     0.018        83      51      93 ..      51      93 ..      28     101 .. 0.59
   2 ?   11.9   2.8   5.6e-05      0.25      81     131 ..     165     215 ..     131     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.018
                            APG6_N 51 eleeeleklekeeeelleeLkelekereeleaelaaleeelea 93
                                      +   +++  +k +ee+l+e++e  +e   +e+el+  ee +++
  gi|488600379|ref|YP_007906850.1| 51 QFIVDFKGRKKRKEEKLKEIDEKLREVTGVEKELERSEEVSAE 93
                                      3333355566666677777777777777777777776665554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.6e-05
                            APG6_N  81 eaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyehaqn 131
                                       ++ +++l++el+ + ee+ + +r+   ++l+ +ele el+ + ++++h ++
  gi|488600379|ref|YP_007906850.1| 165 DSLIESLQKELSIKREEKLNLMRDLEGQKLDTAELESELKEILSRIKHYEK 215
                                       667899999999999999999999999999999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1408  (0.078532); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1499.59
//
Query:       gi|488600380|ref|YP_007906851.1|  [L=610]
Description: Type IV secretory pathway, VirB11 component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-45  154.7   0.0    3.5e-45  154.2   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
     0.0022   18.5   0.0     0.0059   17.1   0.0    1.7  1  ABC_tran  ABC transporter
     0.0055   16.4   0.1      0.012   15.3   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.028   14.9   0.3      0.028   14.9   0.3    2.3  2  AAA_23    AAA domain
      0.047   13.4   0.0       0.12   12.0   0.0    1.6  1  AAA_15    AAA ATPase domain
       0.11   12.8   0.0       0.31   11.3   0.0    1.8  1  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   0.0   1.2e-48   3.5e-45       3     262 ..     221     491 ..     219     499 .. 0.92

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 1.2e-48
                             T2SSE   3 illeallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvr 79 
                                        +le++++d+ + di  +  + ++v+ ++ +   + +e+ +++ l+r++ ++a   ++ i  + p++da lp +g r
  gi|488600380|ref|YP_007906851.1| 221 GILEPYIKDKYIEDITCNGLGPIFVEHKIFKGLKSVMEFRDEETLNRFAIKLAERIGKPITYKDPIVDAVLP-DGSR 296
                                       5789999******************9999996777777888999****************************.**** PP

                             T2SSE  80 lrvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                       +++v    + +  ++++iRk s+  l++ +++ +++++  ia  l   ++e ++  + G T sGKtt+l+a+ ++i 
  gi|488600380|ref|YP_007906851.1| 297 INIVYGNDISKngTNFTIRKFSETPLSILQIIENGTMDYMIAGYLWLLISEGMSGFICGETASGKTTTLNAITTFIS 373
                                       ****99887776799************************************************************** PP

                             T2SSE 155 ksderivtvEDpvEiqleganqvqlnak............kakvtfadllraaLRlrPDrimvGEiRdketleilkA 219
                                        +  +iv +ED+ E+q+ ++n ++ +++              +vt+ dll+aaLR+rP  i+vGEiR+ e   + +A
  gi|488600380|ref|YP_007906851.1| 374 PD-AKIVSIEDTPELQVPHKNWTREVTRgstrggkigegsGSDVTMFDLLKAALRQRPNYIIVGEIRGIEGNIAFQA 449
                                       99.*********************99999********999999****************************999*** PP

                             T2SSE 220 vnTGHlgslsTlHansaagalerLeqlgaeveaaelkssilav 262
                                       ++TGH++ +sT Ha ++ + ++rL     +v+++ + +  + +
  gi|488600380|ref|YP_007906851.1| 450 MQTGHPV-MSTFHAATVEKLIQRLTGEPINVPKTYIDNLNFVI 491
                                       *******.****************9776667777766655544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     2e-06    0.0059       8      60 ..     345     397 ..     341     404 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrke 60 
                                       ++eg    i Ge+ +GK+t l++++   +p++  + +++++  + +++ + +e
  gi|488600380|ref|YP_007906851.1| 345 ISEGMSGFICGETASGKTTTLNAITTFISPDAKIVSIEDTPELQVPHKNWTRE 397
                                       67788889***************************999887776566555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   4.1e-06     0.012      22      51 ..     347     377 ..     325     380 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.1e-06
                            AAA_29  22 kg.atlltGpsGsGKSTllDAiqalLvpakk 51 
                                       +g + ++ G++ sGK+T l Ai++ + p+ k
  gi|488600380|ref|YP_007906851.1| 347 EGmSGFICGETASGKTTTLNAITTFISPDAK 377
                                       566789********************99875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3      0.58   1.7e+03      74      74 ..     178     178 ..     119     278 .. 0.52
   2 ?   14.9   0.3   9.4e-06     0.028      24      41 ..     353     370 ..     350     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.58
                            AAA_23  74 y 74 
                                       +
  gi|488600380|ref|YP_007906851.1| 178 F 178
                                       0 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 9.4e-06
                            AAA_23  24 ItGpNGaGKTTildAikl 41 
                                       I+G++ +GKTT l+Ai+ 
  gi|488600380|ref|YP_007906851.1| 353 ICGETASGKTTTLNAITT 370
                                       9***************96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.1e-05      0.12      27      51 ..     352     376 ..     345     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                            AAA_15  27 vliGkNnsGKSsilealdlFlnnke 51 
                                       +++G+ +sGK++ l+a+  F++ + 
  gi|488600380|ref|YP_007906851.1| 352 FICGETASGKTTTLNAITTFISPDA 376
                                       79*******************9873 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.31       6      29 ..     349     372 ..     345     438 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                            AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                        +++++Ge+ +GKTt+l+ ++   
  gi|488600380|ref|YP_007906851.1| 349 MSGFICGETASGKTTTLNAITTFI 372
                                       6899*************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3714.01
//
Query:       gi|488600381|ref|YP_007906852.1|  [L=535]
Description: Archaeal flagella assembly protein J [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-16   59.3   1.7    4.5e-07   29.9   0.0    2.8  3  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
       0.21   11.6   2.0        3.8    7.5   0.1    2.4  2  P4Ha_N    Prolyl 4-Hydroxylase alpha-subunit, N-terminal regi


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.7e-10   1.6e-06       2     124 ..      40     166 ..      39     167 .. 0.95
   2 !   29.9   0.0     5e-11   4.5e-07       1     121 [.     292     419 ..     292     423 .. 0.85
   3 ?   -5.8   1.9         2   1.8e+04     112     123 ..     505     516 ..     503     519 .. 0.50

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.7e-10
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC.....T-TT.TS-HHHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale.....rtpssefpelvvqliragee 73 
                                       l+++a+ + a ++ ++++e  +e   + + ++ +k+i++  ++++   +  +     + +++ +++l+ ++++a+++
  gi|488600381|ref|YP_007906852.1|  40 LTYMASISTAQINRDKIFEKTSEKV-EYAPSKYFKKIKDLAQNWHYDYATACeliarKVKHERLKNLLNRFSNAISA 115
                                       789**********************.*******************88655555999988889*************** PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       g +  ++Le+ ++ +   r+ + ++ +++l  ++ +++allv++ l+++++
  gi|488600381|ref|YP_007906852.1| 116 GEPDRDFLEHEWKAFKTIRKDEFERSLESLKKWADAYTALLVSSSLISVII 166
                                       ***********************************************9987 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 5e-11
                                       HHHHHHHHHH.TT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHH CS
                             T2SSF   1 flrqlatlls.aGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirage 72 
                                       f+r+l++ +s aGv++veaL+++ +    g+l++ ++ +++rl++G +++  ++    + +s  +++l + ++ a+ 
  gi|488600381|ref|YP_007906852.1| 292 FIRNLGSIVSgAGVSVVEALSRIDQKN-LGELKDPVNILYKRLAMGLDPKICWDrfigECGSYIIHKLTSIFVDAVN 367
                                       89999999999****************.**************************88887777677************ PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHH...HHHHHHTTXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrk...llaallepllllvvallvllilla 121
                                        gg+ + v e +++   e+  lr k   + + +l+ ++ l+ a++ l+i+++
  gi|488600381|ref|YP_007906852.1| 368 LGGDADIVSEIVSSSNLEMVLLRMKrdlISSGFLGLIIPLHAAMASLVIFIT 419
                                       **************99999999966111566667777777777777777666 PP

  == domain 3  score: -5.8 bits;  conditional E-value: 2
                                       XXXXXXXXXXXX CS
                             T2SSF 112 allvllillail 123
                                       +l++++i+++++
  gi|488600381|ref|YP_007906852.1| 505 LLIISGIVMLVV 516
                                       344444444443 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3    0.0085        76      42      73 ..      48      83 ..      17      91 .. 0.74
   2 ?    7.5   0.1   0.00043       3.8      26      67 ..      95     135 ..      90     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0085
                            P4Ha_N 42 eeh...es.akedkeeylsnPlnaFklikRltsdWe 73
                                       ++   ++  ++++e++   P + Fk ik l+++W+
  gi|488600381|ref|YP_007906852.1| 48 TAQinrDKiFEKTSEKVEYAPSKYFKKIKDLAQNWH 83
                                      44333233466778889999***************6 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00043
                            P4Ha_N  26 eekkleklkrfleeleeehesakedkeeylsnPlnaFklikR 67 
                                        + k e+lk++l++++++  sa e  + +l++ ++aFk+i++
  gi|488600381|ref|YP_007906852.1|  95 RKVKHERLKNLLNRFSNAI-SAGEPDRDFLEHEWKAFKTIRK 135
                                       567899***********99.55666677************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3154.03
//
Query:       gi|488600382|ref|YP_007906853.1|  [L=71]
Description: hypothetical protein Asulf_00852 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   28.8   0.0    1.6e-06   28.4   0.0    1.1  1  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 !   28.4   0.0   8.8e-11   1.6e-06      35      94 ..       6      62 ..       2      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 8.8e-11
                                      -.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-E CS
                           DUF4352 35 aggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskaddlflgtlnpGkk 94
                                      +g  fl+v+v++kN+g+e++ + +   +++d++g+ y++++++ s  d+l l +l +G+k
  gi|488600382|ref|YP_007906853.1|  6 EGINFLVVEVKIKNIGEEKYILLP---TVVDSEGNIYSYSFYTHSLTDYLKLVELHKGEK 62
                                      6778****************9955...5789***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 516.12
//
Query:       gi|488600383|ref|YP_007906854.1|  [L=260]
Description: hypothetical protein Asulf_00854 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  103.2   2.3    2.3e-14   53.6   0.2    2.5  2  CBS              CBS domain
    6.6e-15   55.2   0.9    9.7e-14   51.4   0.9    2.4  1  ParBc            ParB-like nuclease domain
    3.4e-05   24.0   0.1    0.00026   21.1   0.1    2.1  1  ParBc_2          Putative ParB-like nuclease
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.53   10.2   0.0    2.0  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
       0.55   10.3   4.4         31    4.7   2.5    3.3  2  PRC              PRC-barrel domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.2   6.3e-18   2.3e-14       1      54 [.       6      59 ..       6      62 .. 0.96
   2 !   49.1   0.2   1.5e-16   5.5e-13       1      54 [.      65     118 ..      65     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 6.3e-18
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      V+d+mtr vvt++p+ t+e+a++l++++g++++PVVd+++k++G+++  Dll++
  gi|488600383|ref|YP_007906854.1|  6 VKDYMTRSVVTLSPENTVEDAINLIEKTGHDGFPVVDSEKKVIGYISSIDLLKK 59
                                      89***********************9999***********************97 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.5e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       ++dim r++ ++++ ++l++a++ m ++g+s lPVVdedgklvGi++ +D++r 
  gi|488600383|ref|YP_007906854.1|  65 IKDIMARQLYVAREFMDLRDAARVMFRTGHSKLPVVDEDGKLVGIISNSDVIRS 118
                                       68**********************66999***********************96 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.9   2.7e-17   9.7e-14       3      81 ..     150     221 ..     109     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.7e-17
                             ParBc   3 vplseirpnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivleidde 79 
                                       v+++++ p++ ++    +++++  v +I+ +Gl +Pi+v k+  +ry++i+G++R  Aakr+glk +++++le+ d 
  gi|488600383|ref|YP_007906854.1| 150 VEVDRLIPTQTKVF---ADELKGRVYEIR-RGLAEPILVVKKG-KRYYLIDGHHRAVAAKRMGLKHLEAYILEVPD- 220
                                       34444444444444...667777777777.************6.*****************************994. PP

                             ParBc  80 ea 81 
                                         
  gi|488600383|ref|YP_007906854.1| 221 -T 221
                                       .3 PP

>> ParBc_2  Putative ParB-like nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   7.1e-08   0.00026       2      86 ..     149     220 ..     148     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.1e-08
                                       EEEGGGCB-SBSEE-HHHHHHHHHHHHT------.---TT-BEEEEEE-STT-EEE-S-HHHHHHHHHTT-....-E CS
                           ParBc_2   2 eveiadLrPTQlavGldeveyklgeleelkekkkldkflekklvpvVigpdgelYliDhHHllrallesgvggaekk 78 
                                       +ve+++L PTQ  v  de++ ++ e+++            ++++ vV  +++++YliD+HH + a  + g   ++ +
  gi|488600383|ref|YP_007906854.1| 149 NVEVDRLIPTQTKVFADELKGRVYEIRRGL----------AEPILVV-KKGKRYYLIDGHHRAVAAKRMGL--KHLE 212
                                       589999************999999994443..........2345455.58999*********999988555..6666 PP

                                       EEEEEEEE CS
                           ParBc_2  79 vlvkvvad 86 
                                       +++  v d
  gi|488600383|ref|YP_007906854.1| 213 AYILEVPD 220
                                       66555555 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.41   1.5e+03      27      47 ..      32      52 ..       7      58 .. 0.74
   2 ?   10.2   0.0   0.00015      0.53      12      49 ..      75     113 ..      58     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.41
                   Acetyltransf_10 27 eegealllvaeeggkivGvie 47
                                      ++g+  + v++ ++k++G+i+
  gi|488600383|ref|YP_007906854.1| 32 KTGHDGFPVVDSEKKVIGYIS 52
                                      467777889999999999995 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00015
                   Acetyltransf_10  12 tfkefisp.ealrerieegealllvaeeggkivGvielr 49 
                                       + +ef++  +a r ++++g+ +l v++e+gk+vG+i+ +
  gi|488600383|ref|YP_007906854.1|  75 VAREFMDLrDAARVMFRTGHSKLPVVDEDGKLVGIISNS 113
                                       5577888757788888********************654 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.026        93      11      30 ..      37      56 ..      36      62 .. 0.86
   2 ?    4.7   2.5    0.0087        31      12      28 ..      97     115 ..      95     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.026
                                      T-EEEETTSSEEEEEEEEEE CS
                               PRC 11 GkeVytedGeklGkVkDvvi 30
                                      G +V++++ + +G ++ + +
  gi|488600383|ref|YP_007906854.1| 37 GFPVVDSEKKVIGYISSIDL 56
                                      89*************99865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0087
                                       -EEEETTSSEEEEE..EEE CS
                               PRC  12 keVytedGeklGkV..kDv 28 
                                       ++V++edG+ +G +  +Dv
  gi|488600383|ref|YP_007906854.1|  97 LPVVDEDGKLVGIIsnSDV 115
                                       79**********9966666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1792.92
//
Query:       gi|488600384|ref|YP_007906855.1|  [L=107]
Description: signal recognition particle, subunit SRP19 (srp19) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-22   80.1   1.9    2.3e-22   79.7   1.9    1.3  1  SRP19     SRP19 protein
  ------ inclusion threshold ------
      0.021   14.4   0.5      0.022   14.3   0.5    1.1  1  UMPH-1    Pyrimidine 5'-nucleotidase (UMPH-1)


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 !   79.7   1.9   2.6e-26   2.3e-22       1      91 [.       6      87 ..       6     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.6e-26
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC-..........SS CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvklkedgkevnekik 78
                                      vi+Pv ld++k+rkeGR++p++l+v n++++e++ a+k+l++++ ve+ek+yPr w+++ Gr+ v+++           
  gi|488600384|ref|YP_007906855.1|  6 VIWPVNLDKRKSRKEGRKIPRRLSVPNVKLNELVSACKELEIKYRVEEEKKYPRCWWESgGRIFVEKR----------A 74
                                      7******************************************************999889*****85..........5 PP

                                      -CHHHHHHHHHHH CS
                             SRP19 79 nkkellkkiaell 91
                                      +k++++++ia+++
  gi|488600384|ref|YP_007906855.1| 75 KKTHIMIEIAKKI 87
                                      6777777777776 PP

>> UMPH-1  Pyrimidine 5'-nucleotidase (UMPH-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   2.5e-06     0.022      32      96 ..      33      95 ..      20     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-06
                            UMPH-1 32 kklkeLyhkYrpieidpsltieekvkymveWwskshaLlieqklkkeeiaevvkeskialrdgve 96
                                       kl+eL    + +ei     +ee  ky   Ww+  + + +e++ kk +i   +++   +lr++ e
  gi|488600384|ref|YP_007906855.1| 33 VKLNELVSACKELEIKYR--VEEEKKYPRCWWESGGRIFVEKRAKKTHIMIEIAKKILELREKSE 95
                                      577888888888888765..6777788899*******************9999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1194  (0.066596); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 721.98
//
Query:       gi|488600385|ref|YP_007906856.1|  [L=329]
Description: putative DNA modification methylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-29  102.5   0.1    2.6e-28   99.0   0.1    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    1.5e-07   31.3   0.3    6.5e-05   22.8   0.0    2.3  2  N6_N4_Mtase      DNA methylase
    4.4e-07   30.1   0.4    4.4e-07   30.1   0.4    1.8  2  THUMP            THUMP domain
    4.3e-06   27.4   0.0    1.3e-05   25.8   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    7.2e-06   26.6   0.0    1.7e-05   25.4   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    0.00044   20.1   0.0    0.00079   19.3   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.37   10.3   0.0    1.8  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.1     1e-31   2.6e-28       2     185 ..     156     311 ..     155     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 1e-31
                                       SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH-- CS
                           UPF0020   2 gyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelk 78 
                                       ++++f++p++L ++LA+alv+ +g+++ ++llDPmCG+GtilIEa+l+g + +                        
  gi|488600385|ref|YP_007906856.1| 156 DKKPFFKPGALLPRLARALVNFTGITD-DTLLDPMCGTGTILIEAGLMGIDFV------------------------ 207
                                       6799*********************86.689********************99........................ PP

                                       EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH CS
                           UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrv 155
                                         g++  ++v+ g+ eN+ ++++   +++   da+++ l+++ v +ivt++PY ++ +s ++l +LY+   +e++rv
  gi|488600385|ref|YP_007906856.1| 208 --GIEAFKKVLYGCAENLIYYNLP--VNLIRGDARNISLRDDTVSAIVTDYPYLRSSKSFGELSELYERSFEEISRV 280
                                       ..******************9875..67778888888877889********************************** PP

                                       -TT..-EEEEEESSHHHHHCC---...ESEEEE CS
                           UPF0020 156 lrgggrlvlltsenkalekaleer...alrkvk 185
                                       l++     l++ +n ++e+ ++ +   +++++ 
  gi|488600385|ref|YP_007906856.1| 281 LKK--GKRLVIVSNIDVEERYSIEnyfKIERKL 311
                                       ***..4555555666776666544234455554 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.5e-08   6.5e-05     176     224 ..     162     214 ..      84     221 .. 0.82
   2 !    6.8   0.1     0.002         5       2      55 ..     248     290 ..     247     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.5e-08
                                       --HHHHHHHHHHHS-T....T-EEEETT-TTTHHHHHHHHTT-EEEEEESSHH CS
                       N6_N4_Mtase 176 kPvallerlIklstkk....gdivlDpFaGSGtTavaakelgrkfiGieieee 224
                                       kP all rl +++ +     +d+ lDp +G+Gt++++a  +g +f+Gie  ++
  gi|488600385|ref|YP_007906856.1| 162 KPGALLPRLARALVNFtgitDDTLLDPMCGTGTILIEAGLMGIDFVGIEAFKK 214
                                       55555555555555444444*****************************8665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.002
                                       EEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEE CS
                       N6_N4_Mtase   2 dlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifin 55 
                                         ivtd PY  +++           s+ e +e+ e+ ++e+ rvLk+++ ++i 
  gi|488600385|ref|YP_007906856.1| 248 SAIVTDYPYLRSSK-----------SFGELSELYERSFEEISRVLKKGKRLVIV 290
                                       67999999999988...........88899999999999999999999987773 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.4   1.7e-10   4.4e-07      75     142 ..      76     140 ..      18     142 .. 0.85
   2 ?   -2.7   0.1       2.2   5.7e+03      77      82 ..     279     284 ..     258     314 .. 0.56

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.7e-10
                                       HHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEE CS
                             THUMP  75 vkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisi 142
                                       +k+  +e+k + +Vrvk+ +k + ++ +e++r++G+++ +++    dl++ di++ v+i ++ + i+i
  gi|488600385|ref|YP_007906856.1|  76 FKDLNFEGK-RVCVRVKKLNKSLAISTVELERKLGAILYRNGA-IIDLKDSDITIKVYITDR-CHIGI 140
                                       455556665.******************************999.***************984.66655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                                       HHHHHC CS
                             THUMP  77 kkfeee 82 
                                       + ++++
  gi|488600385|ref|YP_007906856.1| 279 RVLKKG 284
                                       222222 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.5   1.2e+04      44      61 ..      65      82 ..      51      91 .. 0.57
   2 !   25.8   0.0   5.2e-09   1.3e-05       2      96 ..     186     284 ..     185     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                                      TTTTEEEEESBCCGBSSS CS
                   Methyltransf_25 44 eglnvefvqgdaedlpfe 61
                                      + +++++++  ++dl+fe
  gi|488600385|ref|YP_007906856.1| 65 DTVDIDYLERRFKDLNFE 82
                                      334555555556666555 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.2e-09
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE.......E CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs.......s 71 
                                       Ld  cGtG++++++    g  +++g++  ++ l  ++e++   +l v++++gda+++++ d+++ ++v        s
  gi|488600385|ref|YP_007906856.1| 186 LDPMCGTGTILIEAGLM-G-IDFVGIEAFKKVLYGCAENLIYYNLPVNLIRGDARNISLRDDTVSAIVTdypylrsS 260
                                       7889*********9977.5.************************************************955554432 PP

                                       STGGGSSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  72 galhhlsdedlekalkeiarvLkpg 96 
                                        ++  ls e +e+ ++ei+rvLk+g
  gi|488600385|ref|YP_007906856.1| 261 KSFGELS-ELYERSFEEISRVLKKG 284
                                       2244455.456999*********97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   6.6e-09   1.7e-05       1      96 []     186     289 ..     186     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 6.6e-09
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES.......- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse.......v 70 
                                       Ld  cGtG ++ +    g + vg++  k++l  + e+    +l v+++++da+++ ++d+++ ++v          +
  gi|488600385|ref|YP_007906856.1| 186 LDPMCGTGTILIEAGLMGIDFVGIEAFKKVLYGCAENLIYYNLPVNLIRGDARNISLRDDTVSAIVTDYpylrsskS 262
                                       6788***************************99988888888889********************998876665555 PP

                                       CCC-.CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  71 lhhv.edpekalkeiaRvLkpgGllvi 96 
                                       +  + e  e+ ++ei RvLk+g +lvi
  gi|488600385|ref|YP_007906856.1| 263 FGELsELYERSFEEISRVLKKGKRLVI 289
                                       55557899**************99886 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.1e-07   0.00079       5     111 ..     183     291 ..     181     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.1e-07
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                        ++lD+ CGtG++++e+  ++  ++++vGi+  ++++  + en+   +l  v++ +gd+ +++  l d+++  i+++
  gi|488600385|ref|YP_007906856.1| 183 DTLLDPMCGTGTILIEAG-LM--GIDFVGIEAFKKVLYGCAENLIYYNL-PVNLIRGDARNIS--LRDDTVSAIVTD 253
                                       579*************99.55..69*****************9775555.79***********..99********** PP

                   Methyltransf_31  82 evl........naladpdkileeiervlkpggillied 111
                                        +          +    +  +eei+rvlk+g +l+i +
  gi|488600385|ref|YP_007906856.1| 254 YPYlrssksfgELSELYERSFEEISRVLKKGKRLVIVS 291
                                       8888888455555555555666***********99764 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 ?   -1.6   0.0      0.67   1.7e+03     103     138 ..      90     131 ..      64     147 .. 0.60
   2 ?   10.3   0.0   0.00015      0.37       3      60 ..     184     239 ..     182     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.67
                   Methyltransf_15 103 leqllke....slklskniilfLPrnsdlnqlaa..ltaevl 138
                                       +++l k+    +++l +++   L rn  + +l++  +t++v+
  gi|488600385|ref|YP_007906856.1|  90 VKKLNKSlaisTVELERKLGAILYRNGAIIDLKDsdITIKVY 131
                                       444444455546667777777777888777775411444444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00015
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                       ++lD+++G+G   i+  l++   ++ie  ++ l+ +++N   Y  +  + l+ gd  +
  gi|488600385|ref|YP_007906856.1| 184 TLLDPMCGTGTILIEAGLMGIDFVGIEAFKKVLYGCAENLIYY--NLPVNLIRGDARN 239
                                       68*****************99**********************..7789999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2073.53
//
Query:       gi|488600386|ref|YP_007906857.1|  [L=133]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   47.7   0.5    1.4e-12   47.3   0.5    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00012   22.3   0.0    0.00014   22.2   0.0    1.1  1  Penicillinase_R  Penicillinase repressor
    0.00015   21.3   0.3    0.00027   20.4   0.3    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0011   18.9   0.1     0.0015   18.4   0.1    1.2  1  MarR             MarR family
     0.0031   17.3   0.0     0.0062   16.3   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
     0.0033   17.3   0.0     0.0062   16.4   0.0    1.4  1  MarR_2           MarR family
     0.0046   16.8   0.7     0.0064   16.3   0.7    1.3  1  TFIIE_alpha      TFIIE alpha subunit
     0.0066   16.7   0.1       0.19   11.9   0.1    2.1  2  baeRF_family5    Bacterial archaeo-eukaryotic release factor 
     0.0095   15.8   0.1       0.02   14.8   0.1    1.5  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.016   15.4   0.1    1.3  1  Rio2_N           Rio2, N-terminal
       0.01   15.7   0.0      0.018   14.9   0.0    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
      0.018   15.7   0.3      0.034   14.8   0.3    1.5  1  RTP              Replication terminator protein
      0.025   14.5   0.2       0.99    9.3   0.1    2.2  2  RuvB_C           RuvB C-terminal winged helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.5     1e-15   1.4e-12       3      66 ..      24      93 ..      21     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1e-15
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE-- CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravd 66
                                      +l L+  E +vYl+L+++    +de++e+   +rs +Y++L+ L++kGlV+re +       +++Y +++
  gi|488600386|ref|YP_007906857.1| 24 VLKLTISELEVYLTLIENPGIGVDELSEIMRKDRSGIYRSLQTLLEKGLVKREYRIlkhggyKYIYTPLE 93
                                      5678999**********************************************98899998777888876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     1e-07   0.00014       1     100 [.      27     125 ..      27     133 .] 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-07
                                       ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHH.HHHTTS-EEEEETTEEEEE----XXXXXXXXX CS
                   Penicillinase_R   1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrr.LvkKgllsrekegrafiYsplvseeeavasav 76 
                                       l+ +E+ev+ +l e+  + v+e+ e + ++++  y + +tll++ Lvk+++   ++ g ++iY+pl  e + ++  +
  gi|488600386|ref|YP_007906857.1|  27 LTISELEVYLTLIENPGIGVDELSEIMRKDRSGIYRSLQTLLEKgLVKREYRILKHGGYKYIYTPL--EIDTLKAIL 101
                                       5779**************************7778888777775447777777777889*******8..78999999* PP

                                       XXXXXXXXXXXXXXXXXXXXXXX.X CS
                   Penicillinase_R  77 kqlldklfegsvkelvaafveee.k 100
                                       k+ l++ f+ +++e+v +f+ +e k
  gi|488600386|ref|YP_007906857.1| 102 KEELERWFK-RLNEVVDKFTLDEfK 125
                                       ********5.9999*9999877644 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 !   20.4   0.3   1.9e-07   0.00027       3      48 .]      29      74 ..      27      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + +++++ +L +np+i   eL+e     +s + r l+ L e+Gl+k
  gi|488600386|ref|YP_007906857.1| 29 ISELEVYLTLIENPGIGVDELSEIMRKDRSGIYRSLQTLLEKGLVK 74
                                      67899999************************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.1e-06    0.0015       1      50 [.      27      76 ..      27      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      lt +++++  +l e++++ v eL + +  ++s + r l +L +kGl++R+
  gi|488600386|ref|YP_007906857.1| 27 LTISELEVYLTLIENPGIGVDELSEIMRKDRSGIYRSLQTLLEKGLVKRE 76
                                      78999999999*************************************96 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 !   16.3   0.0   4.5e-06    0.0062      17      50 ..      42      75 ..      38      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.5e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++ ++ el++     +S  +R LqtL e G+v++
  gi|488600386|ref|YP_007906857.1| 42 PGIGVDELSEIMRKDRSGIYRSLQTLLEKGLVKR 75
                                      5678999*************************98 PP

>> 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   4.5e-06    0.0062       3      54 ..      27      76 ..      25      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.5e-06
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      lt +++ v + L  +pg  + v el + ++ ++s + r l+ L ++GLv r+
  gi|488600386|ref|YP_007906857.1| 27 LTISELEVYLTLIENPG--IGVDELSEIMRKDRSGIYRSLQTLLEKGLVKRE 76
                                      7888888889999****..******************************997 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.7   4.6e-06    0.0064      14     102 ..      30     118 ..      13     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEE.EECCCHCCCHHHHH CS
                       TFIIE_alpha  14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywr.inyeklvdvvkrkl 89 
                                       +  +v   L+e+  +  ++l++ ++ d+  + + L  L e++lvk   r   + + yky +  ++ ++l  ++k++l
  gi|488600386|ref|YP_007906857.1|  30 SELEVYLTLIENPGIGVDELSEIMRKDRSGIYRSLQTLLEKGLVKREYRI-LKHGGYKYIYTpLEIDTLKAILKEEL 105
                                       55678888999999999***************************955544.566667777762699*********** PP

                                       HHHHHHHHHHHCC CS
                       TFIIE_alpha  90 eevvkkLeeklek 102
                                       e+  k+L+e+++k
  gi|488600386|ref|YP_007906857.1| 106 ERWFKRLNEVVDK 118
                                       ********99875 PP

>> baeRF_family5  Bacterial archaeo-eukaryotic release factor family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.069        95      56      87 ..      46      77 ..      39      93 .. 0.88
   2 !   11.9   0.1   0.00014      0.19      56      81 ..      94     119 ..      75     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.069
                     baeRF_family5 56 kdefeerfeenqqRwyKslaskleklakerew 87
                                      +de++e +++ ++  y+sl++ lek   +re 
  gi|488600386|ref|YP_007906857.1| 46 VDELSEIMRKDRSGIYRSLQTLLEKGLVKREY 77
                                      79999999999**************9888875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                     baeRF_family5  56 kdefeerfeenqqRwyKslasklekl 81 
                                        d++++ ++e+ +Rw+K+l++ ++k 
  gi|488600386|ref|YP_007906857.1|  94 IDTLKAILKEELERWFKRLNEVVDKF 119
                                       6899999*****************96 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 !   14.8   0.1   1.5e-05      0.02      13      37 ..      64      88 ..      62      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                      HHHHHHTT-B-TTS--EEETTEEEE CS
                            Trm5_N 13 RkkLlekglLdrnyKIksdddylyI 37
                                       ++Llekgl  r+y+I + ++y yI
  gi|488600386|ref|YP_007906857.1| 64 LQTLLEKGLVKREYRILKHGGYKYI 88
                                      589*****************99776 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   1.2e-05     0.016      27      79 ..      46     100 ..      41     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                            Rio2_N  27 telieeisrlkeeevkkrlsrllkaklisr..ktakydGYkLtyeGyDyLALktl 79 
                                       +++++ei r +++++ ++l++ll+++l++r  +  k  GYk +y  + +  Lk++
  gi|488600386|ref|YP_007906857.1|  46 VDELSEIMRKDRSGIYRSLQTLLEKGLVKReyRILKHGGYKYIYTPLEIDTLKAI 100
                                       57788999999*******************87778999***99988877777665 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 ?   14.9   0.0   1.3e-05     0.018      18      46 ..      46      74 ..      32      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 18 vcelaeelglsqstvShHLkkLreaGLVe 46
                                      v el+e++++ +s + + L  L e GLV+
  gi|488600386|ref|YP_007906857.1| 46 VDELSEIMRKDRSGIYRSLQTLLEKGLVK 74
                                      78**************************7 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   2.5e-05     0.034      44     111 ..      56     116 ..      48     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                                       -HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               RTP  44 nhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkekaklykkqvkidldrckkllekal 111
                                       ++s iyr+l+ l+e+g++kr+ ++ ++  ++ +++    +     +  +k+ +k +l+r  k l+ ++
  gi|488600386|ref|YP_007906857.1|  56 DRSGIYRSLQTLLEKGLVKREYRILKHGGYKYIYT--PLE-----IDTLKAILKEELERWFKRLNEVV 116
                                       5799********************99999997654..333.....34555666666666655555544 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 ?    9.3   0.1   0.00072      0.99      11      70 ..      35      87 ..      27      89 .. 0.80
   2 ?    8.9   0.0   0.00096       1.3       1      37 [.      69     105 ..      69     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00072
                                      HHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-HHHHHH CS
                            RuvB_C 11 yLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTkkglky 70
                                      yL l+    ++  +g++ l++i++ +++ i       Ll++gl++r    Ril + g+ky
  gi|488600386|ref|YP_007906857.1| 35 YLTLI----ENPGIGVDELSEIMRKDRSGIYRSLQ-TLLEKGLVKREY--RILKHGGYKY 87
                                      44444....5788******************9985.899******986..6777777776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00096
                                       TT---HHHHHHHHHHHHT.TT--B-HHHHHHHTT--H CS
                            RuvB_C   1 elGLdeldikyLkllkekfkggpvglktlaailgeek 37 
                                       e+GL + + ++Lk   +k+  +p+ ++tl ail+ee 
  gi|488600386|ref|YP_007906857.1|  69 EKGLVKREYRILKHGGYKYIYTPLEIDTLKAILKEEL 105
                                       68*******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); 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:                        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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1002.83
//
Query:       gi|488600387|ref|YP_007906858.1|  [L=183]
Description: GMP synthase (glutamine-hydrolyzing), N-terminal domain or A subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-35  122.8   0.0    1.7e-35  122.6   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    9.2e-12   45.2   2.3      3e-10   40.2   0.6    2.8  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
       0.23   11.3   0.3        2.1    8.2   0.2    2.4  2  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.0   2.8e-39   1.7e-35       2     187 ..       6     178 ..       5     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 2.8e-39
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                       ++ ny ++++ +++ l+ l+v++++++++++aee     k+ dg+++ gGp    ++++ + ++     +iPiLGIC
  gi|488600387|ref|YP_007906858.1|   6 VVYNYGQYNHLIHRTLRDLDVETKLIQNTTPAEEL----KDLDGLVIGGGPSIERAGNSFQYLE----LDIPILGIC 74 
                                       567999*************************9999....69****************9998765....59******* PP

                                       HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEE CS
                            GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelm 155
                                       LG+ ++a+ fg+kv k +  ++   + ++ + + +l+++ +++++++ +H +ev++    p+g++ +aks d + ++
  gi|488600387|ref|YP_007906858.1|  75 LGLHIIAEHFGGKVGKGNIGGYAEVEVNILQ-DDELFNEIPSRIKVWASHADEVKE---IPEGFIHLAKS-DICNYE 146
                                       ****************999999999999998.569*********************...*******9999.8899** PP

                                       EEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 156 eiiekknpfvgvQFHPEststpegpellfnfl 187
                                       +i++ ++p++g+Q+HPE+ ++  g+e+ +nf+
  gi|488600387|ref|YP_007906858.1| 147 AIRHPDKPIYGIQWHPEVYHSSYGEEIYRNFI 178
                                       *****************************983 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.026   1.6e+02      53      71 ..      37      55 ..      29      63 .. 0.82
   2 !   40.2   0.6   5.1e-14     3e-10     102     216 .]      64     163 ..      60     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.026
                     Peptidase_C26 53 kaildkldgllltGgqdve 71
                                      ++ l+ ldgl++ Gg+ +e
  gi|488600387|ref|YP_007906858.1| 37 AEELKDLDGLVIGGGPSIE 55
                                      566899*********9886 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 5.1e-14
                     Peptidase_C26 102 lergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkv.ekgsllaellgseeievnslHhqa 177
                                       le ++PilgiC+Gl +++  +GG++ +                + a+ +v++ + + l++e+ +  +i+v   H   
  gi|488600387|ref|YP_007906858.1|  64 LELDIPILGICLGLHIIAEHFGGKVGKGNIG------G-----Y-AEVEVNIlQDDELFNEIPS--RIKVWASHADE 126
                                       7889*******************98764331......1.....2.2445665156666677666..*********** PP

                     Peptidase_C26 178 ikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       +ke+ e++   A ++    Eai++++  ++++g+QwHPE
  gi|488600387|ref|YP_007906858.1| 127 VKEIPEGFIHLAKSDICNYEAIRHPD--KPIYGIQWHPE 163
                                       ***************999********..47********9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2   0.00035       2.1      27      87 ..      36      86 ..      12     105 .. 0.73
   2 ?    0.6   0.0     0.074   4.4e+02     159     184 ..     152     179 ..     107     183 .] 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00035
                                      SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETT CS
                               SNO 27 rkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelen 87
                                        e+l+++d+l+i GG s  +++  + ++       ++ + + ++lG C Gl +++++ ++
  gi|488600387|ref|YP_007906858.1| 36 PAEELKDLDGLVIGGGPS--IERAGNSFQ-------YL-ELDIPILGICLGLHIIAEHFGG 86
                                      4699************87..444444444.......22.2347899999999888887665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.074
                                       ETTEEEESS-GGGSTT..HCHHHHHHHH CS
                               SNO 159 qkkilatsfhPelaed..dirvhdyfve 184
                                        k i ++ +hPe+  +  +  ++  f+e
  gi|488600387|ref|YP_007906858.1| 152 DKPIYGIQWHPEVYHSsyGEEIYRNFIE 179
                                       4455666677776554113456666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1254.43
//
Query:       gi|488600388|ref|YP_007906859.1|  [L=438]
Description: CTP:L-myo-inositol-1-phosphate cytidylyltransferase/di-myo-inositol-1,3-phosphate-1-phosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-15   56.7   0.0    5.9e-15   56.0   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    7.5e-10   39.4   0.7    7.5e-10   39.4   0.7    2.7  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
    6.3e-05   22.7   0.0    0.00012   21.7   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
     0.0034   17.2   0.0     0.0057   16.4   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   1.3e-18   5.9e-15       1     105 [.      28     134 ..      28     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.3e-18
                                       EEEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC...TS-EEE-TTSS-S CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggd..eevlaalarl...gvrvvededpgkg 71 
                                       aviL +G +sR gg +K+ll++gg  +++r++  l+++ vde ++v+g   e++++ l++    ++r++++e+p+ g
  gi|488600388|ref|YP_007906859.1|  28 AVILSAGFGSRIGGyPKPLLKVGGIEIIKRTITLLSPH-VDEFIIVAGKyyEDIKQFLEKNcriKYRLIRNEHPEYG 103
                                       79************************************.**999998877888887777656668999********* PP

                                       HHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHH CS
                      NTP_transf_3  72 plaslaaalraaadadavlvlacDmPlltpelve 105
                                        ++sl+ a +++  +  ++++++D+++ ++e+v+
  gi|488600388|ref|YP_007906859.1| 104 NGYSLLLAKDHI--DGKFVLVMGDHIY-SKEFVD 134
                                       ***********9..5777788899987.666665 PP

>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.7   1.7e-13   7.5e-10       2      66 .]     272     334 ..     271     334 .. 0.90
   2 ?   -0.3   1.6      0.43   1.9e+03      11      39 ..     398     420 ..     339     435 .. 0.55

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.7e-13
                                       -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf   2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66 
                                       +Pn++T +++l ++++ ll+l++ p  la + + ++s++D++DG +AR   ++s++G ++Ds++D
  gi|488600388|ref|YP_007906859.1| 272 TPNMMTAISFLTGIASSLLVLFSLP--LAGIAYQLSSILDGCDGEIARASLKQSRFGGYIDSILD 334
                                       8****************98866655..777777899**************88899********99 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.43
                                       HHHHHHHHHGGGS-H..HHHHHHHHHHHH CS
                   CDP-OH_P_transf  11 lllsvlailllltyyplvlailllliasl 39 
                                       ++l++l ++ l +++ +++a     ia++
  gi|488600388|ref|YP_007906859.1| 398 IFLIMLLCI-LGMVNEIFWA-----IAII 420
                                       333333332.1122222333.....3333 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.7e-08   0.00012       1     242 [.      27     235 ..      27     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.7e-08
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kavIL+ G G+R+       +k+l+ v+g   +i+ t++ l+   ++e  +++  +  + +++ l+++ +  ++   
  gi|488600388|ref|YP_007906859.1|  27 KAVILSAGFGSRIG----GYPKPLLKVGGI-EIIKRTITLLS-PHVDE-FIIVAGKYYEDIKQFLEKNCR--IKYRL 94 
                                       79**********96....688999999998.*******9888.799**.666666777778888887755..55666 PP

                                       EEESS--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTT.SEEEEEEESS-CTTSEEEE CS
                   NTP_transferase  78 alepegk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakg.tvtfgivpveeateyGvie 152
                                       +  + ++ g   +++la++ ++ ++    vlv+ gDh+++   +e+v+ka++ +  + ++  + v+v+eat+   ++
  gi|488600388|ref|YP_007906859.1|  95 IRNEHPEyGNGYSLLLAKDHIDGKF----VLVM-GDHIYS---KEFVDKAVKLEGLIgDAKPAFVDVNEATK---VK 160
                                       66666667**************888....5665.799999...899******99999999999999999998...77 PP

                                       ECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-E CS
                   NTP_transferase 153 adeegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyW 229
                                       +++ g ve++  K +  +    +++G +v ++++l+ +     e + +e +++di++ka    k++++ + +++  W
  gi|488600388|ref|YP_007906859.1| 161 ISN-GVVEDIGKKLSSFD---CIDTGFFVLDRSILDGI-----EFRGEELTVSDIMKKA----KPKVS-ILSGY-FW 222
                                       766.78999998877766...89999999999999999.....7888888888888877....67777.55665.69 PP

                                       EEXSSHHHHHHHH CS
                   NTP_transferase 230 sDvGtldsllean 242
                                        Dv t d+l +an
  gi|488600388|ref|YP_007906859.1| 223 IDVDTKDDLRRAN 235
                                       9998888888776 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-06    0.0057       2      64 ..      27      85 ..      26      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
                                      EEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHG CS
                              IspD  2 vvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqlll 64
                                       +vi  AG+G+R++ g pK +l++ g  ++++t++ l   ++vd+ ++v  ++  e ++q+l 
  gi|488600388|ref|YP_007906859.1| 27 KAVILSAGFGSRIG-GYPKPLLKVGGIEIIKRTITLLS--PHVDEFIIVAGKYY-EDIKQFLE 85
                                      689*********97.9******************8664..58888887777766.55666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2759.26
//
Query:       gi|488600389|ref|YP_007906860.1|  [L=423]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-88  296.7   0.0    2.5e-88  296.6   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 !  296.6   0.0   1.4e-92   2.5e-88       4     417 .]       7     412 ..       4     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: 296.6 bits;  conditional E-value: 1.4e-92
                                       SS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE CS
                     EPSP_synthase   4 gkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfea 80 
                                       g++++g+  +p+sks+++ra++ A+L++  s+++n+L s D++++l+a+r +ga+   +   +e ++ +g  +++++
  gi|488600389|ref|YP_007906860.1|   7 GGEIDGKAVPPPSKSYTHRAFISASLSR-SSRVENPLISLDTLATLKACRFIGAAF--E--RNEGFRFRG-VEEIKT 77 
                                       6688999999***************986.59**********************744..4..456788888.789999 PP

                                       -HHHHTT-GGGGGGHHHHHHHHSEES..SEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS- CS
                     EPSP_synthase  81 peelvldlgnsgtalrlLtallalas..gevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lkl 154
                                       +    l+l nsgt++r+ t+ll+l +   ++vL+Gd+s+rkRP  +l+ aL++lGa+i++++    +p+ vkg  k+
  gi|488600389|ref|YP_007906860.1|  78 S--GYLNLMNSGTTIRIFTGLLSLSRsgRFSVLDGDPSLRKRPNLELVLALKKLGARIYGSSS-YAPPIWVKGvVKG 151
                                       8..68*******************555799*****************************9999.99*********** PP

                                       BEEEEETSSTTHHHHHHHHHHHTTSBS.EEEEES-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SS.B--EE CS
                     EPSP_synthase 155 kgveikaevsSqqvtsllllaallaeg.tteleelasepsiddtlkmlkkfgikietsgteesitvkGkek.lpgte 229
                                       ++vei+a +sSq+++sll   +l  ++ +++++e++s+p+id+tl++l + gi++e+  ++++  ++G+++     +
  gi|488600389|ref|YP_007906860.1| 152 GEVEISA-KSSQFISSLLFTLPLCDQDsEVRVKEVKSRPYIDITLDVLAASGINVEE--EGNTYFIDGGQEyR-LGK 224
                                       *****97.69*************9999******************************..888899******54.459 PP

                                       EE--B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEET.TS--BEEEEEB CS
                     EPSP_synthase 230 yvvegDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgps.glklkdvdiet 305
                                       y++++D ss +y l a+ i+gg v++ n+++ s qGd  ++d i+++mg e+++ ++  iv+ ++  l+++++d e+
  gi|488600389|ref|YP_007906860.1| 225 YIIPSDFSSIGYILSAG-IAGGSVRIYNAFP-SKQGDQVIVD-IIREMGGEVRWDKERGIVEAEKsDLEGIEIDAEN 298
                                       ***********988766.7888******987.5789977777.*************9*99999999*********** PP

                                       GSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEET...TEEE.EEEEEE.EB-EEEE-T CS
                     EPSP_synthase 306 lpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeee...dgli.iipaekqlkgaevesy 378
                                        pd++p+la+l a+a+g+t i+ i++lr ke dr+  ++ +L  lG+++e+ e   d    i +++ ++ +++v+s+
  gi|488600389|ref|YP_007906860.1| 299 FPDLVPVLAALSAIAKGKTKIKRISHLRIKEIDRIEGIVRNLGSLGVKTEVVEednDLSLiIWGGRDEF-HGTVDSF 374
                                       ***********************************************9875543335544255555555.59***** PP

                                       TSTTTTHHHHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
                     EPSP_synthase 379 dDhRiamalalaglvaegeveiddiectdksfpefeekL 417
                                       +DhR+a a++++gl ++g   i+++e++++sfp+++e++
  gi|488600389|ref|YP_007906860.1| 375 GDHRMALAFSILGLKSRG-LMIRNAEVVSVSFPGYFEVM 412
                                       *************88888.*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2830.38
//
Query:       gi|488600390|ref|YP_007906861.1|  [L=363]
Description: chorismate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-144  480.0   0.1   2.8e-144  479.8   0.1    1.0  1  Chorismate_synt  Chorismate synthase
  ------ inclusion threshold ------
      0.079   13.5   0.0       0.18   12.4   0.0    1.5  1  POTRA            Surface antigen variable number repeat
       0.41   10.3   0.1       0.41   10.3   0.1    1.7  2  UPF0181          Uncharacterised protein family (UPF0181)


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 !  479.8   0.1  4.7e-148  2.8e-144       1     326 [.       8     351 ..       8     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 479.8 bits;  conditional E-value: 4.7e-148
                                       SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE CS
                   Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallie 77 
                                       +r+tt+GeShgka+g+vidg+p++l+l+eediq+eLdrR+pg+ klt++r E+D+veilsGvfegkt+G+pi++++ 
  gi|488600390|ref|YP_007906861.1|   8 FRITTWGESHGKAVGCVIDGCPSNLKLSEEDIQRELDRRKPGK-KLTSKRMEEDRVEILSGVFEGKTTGAPISMIVY 83 
                                       89****************************************8.9******************************** PP

                                       -TTS-..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  78 NkdqrskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       N+d+rs++y ++k++pRpgHADlty lkY +rd+rgggrsSaReT++rva Gavakkl++++gi++ +y +++++i 
  gi|488600390|ref|YP_007906861.1|  84 NRDVRSEHYVKLKNTPRPGHADLTYFLKYRHRDWRGGGRSSARETVGRVAGGAVAKKLINAFGINVLGYAIEVAGIr 160
                                       **************************************************************************888 PP

                                       ............CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHH CS
                   Chorismate_synt 154 ............ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalm 218
                                                   ++++++p+r+pde+++e++ee++ e++kegds+Ggvve+v+++vp+GlGepvfdkl a+La a+m
  gi|488600390|ref|YP_007906861.1| 161 werdsddyhevfQRAERSPLRIPDESVSERAEERVVELMKEGDSAGGVVEIVATNVPPGLGEPVFDKLSARLAYAVM 237
                                       888888888776545777*********************************************************** PP

                                       TSTTEEEEEETTGGGGGGSBHHHHS--EEEE......SS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTT CS
                   Chorismate_synt 219 sipAvkgveiGsGfeaaelkGseanDeivlr......ktnnaGGieGGisnGepivvrvavKpipsiakeqktvdle 289
                                       ++pAvkgveiGsGf+ a++kGse nD+iv+r      ++n++GGi+GGis Ge+i+vr+a+Kp+psi+k+q+tvd+e
  gi|488600390|ref|YP_007906861.1| 238 GVPAVKGVEIGSGFRLAKMKGSESNDPIVIRdgkvrlEKNDCGGILGGISVGETIIVRCAIKPTPSISKRQRTVDIE 314
                                       *****************************55566668**************************************** PP

                                       S-E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 290 tkeevelevkgrhDpcvvpravvvveamvalvladal 326
                                       ++eeve+e++grhDpc+vprav+v+e+mval+lad++
  gi|488600390|ref|YP_007906861.1| 315 KMEEVEIEITGRHDPCIVPRAVPVLESMVALTLADFM 351
                                       ***********************************98 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.1e-05      0.18       8      43 ..      25      64 ..      22      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                                      EES....SSS-HHHHHTTTS.SSTTSBHCHHHHHHHHHHH CS
                             POTRA  8 feG...nkktkdeelrrele.lkegdvynpekleadkeal 43
                                      + G   n k+++e+++rel   k+g++++++++e+d+ ++
  gi|488600390|ref|YP_007906861.1| 25 IDGcpsNLKLSEEDIQRELDrRKPGKKLTSKRMEEDRVEI 64
                                      66777799***********548**************9755 PP

>> UPF0181  Uncharacterised protein family (UPF0181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   6.8e-05      0.41      15      40 ..     190     215 ..     188     216 .. 0.91
   2 ?   -4.2   0.3       2.4   1.4e+04      27      34 ..     285     292 ..     284     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.8e-05
                           UPF0181  15 qAVEkIqeLmaqGmssgeAIalVAqe 40 
                                       +A E++ eLm++G s+g  +++VA +
  gi|488600390|ref|YP_007906861.1| 190 RAEERVVELMKEGDSAGGVVEIVATN 215
                                       688*********************75 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 2.4
                           UPF0181  27 GmssgeAI 34 
                                       G+s ge I
  gi|488600390|ref|YP_007906861.1| 285 GISVGETI 292
                                       99****88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2342.40
//
Query:       gi|488600391|ref|YP_007906862.1|  [L=210]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   91.3  14.8      7e-26   91.0  14.8    1.0  1  Yip1      Yip1 domain
     0.0032   17.3  12.4     0.0043   16.8  12.4    1.2  1  DUF1282   Protein of unknown function (DUF1282)


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0  14.8   7.8e-30     7e-26       3     172 .]       9     201 ..       8     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 7.8e-30
                              Yip1   3 ldPrevfrrlkkeppilrapdlallllalltlllgllas...........lnlgqtlasgeevqgltlssllgaiig 68 
                                        +P+ +fr+ k+e+  +  p  ++++ a+++ + +                ++ + +a++     + + +++++i+g
  gi|488600391|ref|YP_007906862.1|   9 YNPDNFFRKAKAEGIGFIVPVAIVVISAVIATINA---YitadeiaritvEIINNKFAPD--PGAMYQTIYISTIAG 80 
                                       69*************33344444444444444444...3555888777775555555555..667777889999999 PP

                              Yip1  69 gylglllgllllalllhliakllggkgsfkqtlsvvgyallPlilgaliaillllllgt.................l 128
                                       ++++ ++g+++l+++   ++ l+gg+gsf qtl ++++++ P i++++i+i ++l +                   +
  gi|488600391|ref|YP_007906862.1|  81 SFITPIIGWVILSGFAQGLSALFGGEGSFSQTLKFTAFSFYPGIILSPISIKIALDYELllrtygvqallskpfvqT 157
                                       999999*********************************************99888888****************** PP

                              Yip1 129 lllvgllaliWslvllylglkaahnlskkkallaalillllliv 172
                                        +l+g++ ++W+l+++++++k+a nls kk++++a+++ll++i+
  gi|488600391|ref|YP_007906862.1| 158 QILIGIITILWQLFIWMFAIKHARNLSLKKSFIVAAMPLLIYIA 201
                                       ****************************************9985 PP

>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  12.4   4.8e-07    0.0043       4     171 ..      10     204 ..       8     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.8e-07
                           DUF1282   4 sPaeefeeikkreetgkvlyivlillllliglvvfiystfq..vlseiltkq..ankltlassliisvvfylal... 73 
                                        P++ f++ k ++    v+++++++ +++   +++i+ + +  +  ei +++  +++  +  ++ is++++ +    
  gi|488600391|ref|YP_007906862.1|  10 NPDNFFRKAKAEGIGFIVPVAIVVISAVIATINAYITADEIarITVEIINNKfaPDPGAMYQTIYISTIAGSFItpi 86 
                                       67777777777777777777777777777677777777654114456666668844555555555555444443366 PP

                           DUF1282  74 .gvlvlayliklmgrtydsqhsyskifafaayalvplflgglalglsllllva....................lvsl 129
                                        g+++l ++++  +  ++++ s+s+++ f+a+ + p +++ ++++ ++l                        l++ 
  gi|488600391|ref|YP_007906862.1|  87 iGWVILSGFAQGLSALFGGEGSFSQTLKFTAFSFYPGIILSPISIKIALDYELllrtygvqallskpfvqtqiLIGI 163
                                       69***************************************99997776444456667**************99999 PP

                           DUF1282 130 llllyvvvLlylGvptlmnirekdraiviallvlvvsllila 171
                                       + +l+ +++   +++   n+   ++++++a+++l +++ ++a
  gi|488600391|ref|YP_007906862.1| 164 ITILWQLFIWMFAIKHARNL-SLKKSFIVAAMPLLIYIALIA 204
                                       *******99999********.889********9999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1388.44
//
Query:       gi|488600392|ref|YP_007906863.1|  [L=506]
Description: Coenzyme F420-reducing hydrogenase, beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-39  134.6   0.1    2.5e-39  134.6   0.1    2.3  2  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    1.7e-28   97.3  61.5    5.9e-07   29.0   1.7    7.0  7  Fer4         4Fe-4S binding domain
    1.9e-19   70.0  54.1    1.5e-08   35.1   9.6    4.6  5  Fer4_7       4Fe-4S dicluster domain
    4.1e-19   68.4  49.7    2.1e-07   30.9   8.6    5.1  6  Fer4_10      4Fe-4S dicluster domain
    5.3e-19   68.1  83.5    1.9e-06   27.9   9.8    4.8  6  Fer4_9       4Fe-4S dicluster domain
    1.3e-17   63.0  60.1    1.5e-05   24.9   4.0    7.0  7  Fer4_6       4Fe-4S binding domain
    2.7e-15   57.0  40.2    4.7e-05   24.2   5.7    6.4  6  Fer4_16      4Fe-4S double cluster binding domain
    3.2e-13   49.6  51.7    3.3e-05   23.9  14.5    4.7  5  Fer4_21      4Fe-4S dicluster domain
    4.5e-13   49.4  38.0    0.00044   20.6   7.4    5.3  7  Fer4_8       4Fe-4S dicluster domain
    6.8e-13   48.6   0.0    1.5e-12   47.4   0.0    1.7  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
      2e-12   46.4  57.5    0.00012   21.9   4.0    7.0  7  Fer4_2       4Fe-4S binding domain
    4.9e-11   42.2  57.3     0.0028   18.0   1.0    7.2  7  Fer4_4       4Fe-4S binding domain
    6.1e-09   36.3  51.5     0.0057   17.2  11.2    6.2  9  Fer4_17      4Fe-4S dicluster domain
    0.00048   20.9  71.4      0.064   14.2   5.4    6.8  6  Fer4_3       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.062   14.0  39.2      0.065   14.0   0.6    6.8  5  Fer4_15      4Fe-4S single cluster domain
      0.084   13.3   0.2       0.31   11.5   0.0    2.0  2  Ret2_MD      RNA editing 3' terminal uridylyl transferase 2 m
       0.17   12.3   0.1        1.5    9.3   0.0    2.4  3  GST_N_3      Glutathione S-transferase, N-terminal domain
        0.3   11.7  52.3        0.7   10.5   2.6    6.5  6  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
        3.1    8.0  48.7       0.22   11.7   2.8    6.2  6  Fer4_18      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       9.9   9.4e+03      83      97 ..     192     206 ..     165     209 .. 0.50
   2 !  134.6   0.1   2.7e-42   2.5e-39       3     153 ..     340     484 ..     338     485 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.9
                       FrhB_FdhB_C  83 keleefirpsCkvCk 97 
                                       k +++   + C +C+
  gi|488600392|ref|YP_007906863.1| 192 KVIDSGLCSHCSTCT 206
                                       244446667777775 PP

  == domain 2  score: 134.6 bits;  conditional E-value: 2.7e-42
                       FrhB_FdhB_C   3 kvavvGtPCqiaalrklqk.kklkekilltiglfCggnfspealrklleelgvdpedvkklefrgkgkfrvelkd.e 77 
                                        v++vGtPC++ +lrk+q+ + +++++ + + lfC++nf++++l+++l ++g+d ++ +k ++ +kgkf+v+++d e
  gi|488600392|ref|YP_007906863.1| 340 GVGFVGTPCMVSGLRKIQNiESFRDRVGVAVALFCTENFYHNQLKEFLARKGIDLSKAVKTDI-TKGKFIVKFEDgE 415
                                       699*****************99*****************************************.9***********9 PP

                       FrhB_FdhB_C  78 keislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveageleleeld 153
                                       +++++kelee+i+++C++C d+t+  +DisvG+v      g +d g st++vrte+g+e++e ++e+g+ e++e+d
  gi|488600392|ref|YP_007906863.1| 416 VSFPVKELEEIIPSGCRMCIDFTGVESDISVGSV------G-SDAGFSTIIVRTERGREIIEYIKEKGYAEFREAD 484
                                       9*********************************......9.*****************************99875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.0   3.6e-06    0.0034       2      23 ..       8      29 ..       7      30 .. 0.88
   2 !   29.0   1.7   6.3e-10   5.9e-07       3      24 .]      48      69 ..      46      69 .. 0.92
   3 !   24.3   3.2     2e-08   1.9e-05       5      24 .]     111     130 ..     110     130 .. 0.95
   4 !   25.0   4.5   1.2e-08   1.1e-05       2      23 ..     140     161 ..     139     162 .. 0.92
   5 !   16.2   1.8   7.3e-06    0.0069       2      23 ..     193     214 ..     192     215 .. 0.90
   6 !   19.5   3.8   6.3e-07   0.00059       5      19 ..     227     241 ..     225     242 .. 0.92
   7 ?   -0.7   0.2       1.5   1.4e+03      10      16 ..     430     436 ..     429     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.6e-06
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      v+ ++ Ci+C+aC+ +C   AI
  gi|488600392|ref|YP_007906863.1|  8 VYTMDGCIFCKACERACKQKAI 29
                                      566789************9999 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 6.3e-10
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                       d++kC +CG+C++ CP+++I+
  gi|488600392|ref|YP_007906863.1| 48 LDYSKCNFCGECAKKCPYDVIE 69
                                      79******************96 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 2e-08
                                       TTTSSS-THHHHHSTTTEEE CS
                              Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                       +e Ci+C +Cv  CPvgAI+
  gi|488600392|ref|YP_007906863.1| 111 PENCIACQLCVLSCPVGAIS 130
                                       799***************96 PP

  == domain 4  score: 25.0 bits;  conditional E-value: 1.2e-08
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        id++kC +CG Cv  CP  A+
  gi|488600392|ref|YP_007906863.1| 140 SIDPDKCGACGVCVRNCPAMAL 161
                                       79****************9997 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 7.3e-06
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       vid  +C +C +C  +CPv  I
  gi|488600392|ref|YP_007906863.1| 193 VIDSGLCSHCSTCTAICPVYGI 214
                                       79****************9655 PP

  == domain 6  score: 19.5 bits;  conditional E-value: 6.3e-07
                                       TTTSSS-THHHHHST CS
                              Fer4   5 eekCigCGaCvevCP 19 
                                       e++Ci CGaC+ vCP
  gi|488600392|ref|YP_007906863.1| 227 ENDCIDCGACIRVCP 241
                                       689************ PP

  == domain 7  score: -0.7 bits;  conditional E-value: 1.5
                                       S-THHHH CS
                              Fer4  10 gCGaCve 16 
                                       gC  C++
  gi|488600392|ref|YP_007906863.1| 430 GCRMCID 436
                                       9****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 !   35.1   9.6   1.6e-11   1.5e-08       2      52 .]      14      67 ..      13      67 .. 0.89
   2 !   28.9  13.3   1.4e-09   1.3e-06       2      50 ..     114     158 ..     113     160 .. 0.92
   3 !   22.8  13.2   1.1e-07    0.0001       1      50 [.     145     211 ..     145     214 .. 0.70
   4 !   17.7  13.2   4.2e-06     0.004       2      49 ..     199     241 ..     198     245 .. 0.83
   5 ?   -2.7   0.1       9.7   9.2e+03       4       9 ..     430     435 ..     428     437 .. 0.65

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.6e-11
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52
                                      Ci C+aC++aC++kai ++ e  ++g+   +++++d++kC +Cg+C++ CP+++
  gi|488600392|ref|YP_007906863.1| 14 CIFCKACERACKQKAIAIEVEIMPDGRrmpKSYRLDYSKCNFCGECAKKCPYDV 67
                                      *****************9977666665556889******************986 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 1.4e-09
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       Ci C+ Cv  Cpv+ai+        g +++ idp+kC  Cg+Cv+ CP+
  gi|488600392|ref|YP_007906863.1| 114 CIACQLCVLSCPVGAISCSRN----GDAEISIDPDKCGACGVCVRNCPA 158
                                       ******************876....7789*******************7 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 1.1e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek................gt.ekveidpekClgCgaCvavCPt 50 
                                       +C  Cg Cv++Cp+ a++l + +                   g+ +k +id+  C++C  C a CP+
  gi|488600392|ref|YP_007906863.1| 145 KCGACGVCVRNCPAMALDLVDLNGTFsvkvelpekiidakyfGNlKKKVIDSGLCSHCSTCTAICPV 211
                                       7****************999753322222333333333333311455599****************7 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 4.2e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       C +C  C+a Cpv+ i+  ++  +  ++ +   +++C++CgaC++vCP
  gi|488600392|ref|YP_007906863.1| 199 CSHCSTCTAICPVYGITAGDK--PIDFPNW---ENDCIDCGACIRVCP 241
                                       ****************99886..2233444...478************ PP

  == domain 5  score: -2.7 bits;  conditional E-value: 9.7
                            Fer4_7   4 gCgaCv 9  
                                       gC+ C 
  gi|488600392|ref|YP_007906863.1| 430 GCRMCI 435
                                       566665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.8   0.00023      0.22       2      19 ..       7      24 ..       4      44 .. 0.70
   2 !   25.0  10.3   1.6e-08   1.5e-05       3      56 .]      47     125 ..      45     125 .. 0.94
   3 !   23.1  15.5   6.2e-08   5.9e-05       5      56 .]     110     157 ..     107     157 .. 0.95
   4 !   18.4   3.1   1.9e-06    0.0018       2      22 ..     139     159 ..     138     181 .. 0.83
   5 !   30.9   8.6   2.2e-10   2.1e-07       2      56 .]     192     241 ..     191     245 .. 0.84
   6 ?   -3.1   0.0       9.5   8.9e+03      44      48 ..     430     434 ..     422     437 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                           Fer4_10  2 vvidddtCirCgkCvkaC 19
                                      +v+  d Ci C++C +aC
  gi|488600392|ref|YP_007906863.1|  7 PVYTMDGCIFCKACERAC 24
                                      566777788888888888 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.6e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.........................tsvgakgeaseeeavrkkvekCtgcgaCvea 54 
                                       ++d ++C  Cg+C k CP+d+                         + +++ g + +      k+e+C++c  Cv +
  gi|488600392|ref|YP_007906863.1|  47 RLDYSKCNFCGECAKKCPYDViemiedrekmesivgdkvydasmfvELKKQLGLDRNRRSGFSKPENCIACQLCVLS 123
                                       57999***************************************9988888888999999999************** PP

                           Fer4_10  55 CP 56 
                                       CP
  gi|488600392|ref|YP_007906863.1| 124 CP 125
                                       *9 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 6.2e-08
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        ++ Ci C+ Cv +CP+       +  ++++++++++++kC +cg Cv+ CP
  gi|488600392|ref|YP_007906863.1| 110 KPENCIACQLCVLSCPV----GAISCSRNGDAEISIDPDKCGACGVCVRNCP 157
                                       5789*************....999999************************9 PP

  == domain 4  score: 18.4 bits;  conditional E-value: 1.9e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPad 22 
                                       + id+d+C  Cg Cv+ CPa 
  gi|488600392|ref|YP_007906863.1| 139 ISIDPDKCGACGVCVRNCPAM 159
                                       689****************94 PP

  == domain 5  score: 30.9 bits;  conditional E-value: 2.2e-10
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkve..kCtgcgaCveaCP 56 
                                        vid+  C +C +C++ CP+       +g++ ++++++   +  +C++cgaC+++CP
  gi|488600392|ref|YP_007906863.1| 192 KVIDSGLCSHCSTCTAICPV-------YGITAGDKPIDFPNWenDCIDCGACIRVCP 241
                                       6899****************.......777777777777544226***********9 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 9.5
                           Fer4_10  44 kCtgc 48 
                                        C +c
  gi|488600392|ref|YP_007906863.1| 430 GCRMC 434
                                       23322 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   3.7    0.0003      0.29      35      51 .]      13      29 ..       6      29 .. 0.82
   2 !   26.6  10.5   5.2e-09   4.9e-06       2      51 .]      14      68 ..      13      68 .. 0.78
   3 !   27.9   9.8     2e-09   1.9e-06       1      51 []      52     129 ..      52     129 .. 0.93
   4 !   21.1  12.4   2.7e-07   0.00025       1      49 [.     113     159 ..     113     161 .. 0.81
   5 !   23.4   8.7   5.3e-08     5e-05       1      48 [.     145     211 ..     145     215 .. 0.92
   6 !   25.5  10.1   1.1e-08   1.1e-05       2      48 ..     199     242 ..     198     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                            Fer4_9 35 aCigCgaCveaCpkgai 51
                                       Ci+C+aC+ aC+++ai
  gi|488600392|ref|YP_007906863.1| 13 GCIFCKACERACKQKAI 29
                                      59999999999999887 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 5.2e-09
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkgai 51
                                      C+ C+aC++aC+++++  +     +  r+ +      ++C +Cg+C+++Cp ++i
  gi|488600392|ref|YP_007906863.1| 14 CIFCKACERACKQKAIAIEVEIMPDGRRMPKSyrldySKCNFCGECAKKCPYDVI 68
                                      ***********888886655555544445444577889*************9976 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 2e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...........................eaCigCgaCveaCpkga 50 
                                       kC+ Cg+C ++Cp++v+++ + ++k++    ++                           e+Ci C+ Cv  Cp ga
  gi|488600392|ref|YP_007906863.1|  52 KCNFCGECAKKCPYDVIEMIEDREKMESIVGDKvydasmfvelkkqlgldrnrrsgfskpENCIACQLCVLSCPVGA 128
                                       7****************999999999975544489****************************************98 PP

                            Fer4_9  51 i 51 
                                       i
  gi|488600392|ref|YP_007906863.1| 129 I 129
                                       7 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 2.7e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       +C+ C+ Cv +Cp g+++ ++++          ++C  Cg Cv  Cp  
  gi|488600392|ref|YP_007906863.1| 113 NCIACQLCVLSCPVGAISCSRNGDAEISIDP--DKCGACGVCVRNCPAM 159
                                       6****************88777665554333..37************75 PP

  == domain 5  score: 23.4 bits;  conditional E-value: 5.3e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...................eaCigCgaCveaCpk 48 
                                       kC  Cg Cv+ Cpa++    + +++ +++ +                       C +C +C+++Cp 
  gi|488600392|ref|YP_007906863.1| 145 KCGACGVCVRNCPAMALDLVDLNGTFSVKVELPekiidakyfgnlkkkvidsGLCSHCSTCTAICPV 211
                                       7****************999999999997755589*****************99************6 PP

  == domain 6  score: 25.5 bits;  conditional E-value: 1.1e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                       C  C +C++ Cp   ++  +++    + +++  +Ci+CgaC+ +Cp+
  gi|488600392|ref|YP_007906863.1| 199 CSHCSTCTAICPVYGITAGDKPIDFPN-WEN--DCIDCGACIRVCPR 242
                                       *************99999999998886.333..6************8 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   2.5     0.008       7.6       9      24 .]      14      29 ..       6      31 .. 0.81
   2 !   13.1   3.2   8.3e-05     0.079       5      24 .]      49      68 ..      49      68 .. 0.94
   3 !   16.5   2.0     7e-06    0.0066       5      24 .]     110     129 ..     108     129 .. 0.94
   4 !   24.9   4.0   1.6e-08   1.5e-05       2      24 .]     139     161 ..     138     161 .. 0.93
   5 !   17.7   1.2   2.9e-06    0.0028       3      21 ..     193     211 ..     191     215 .. 0.89
   6 !   18.1   3.4   2.1e-06     0.002       7      20 ..     228     241 ..     227     246 .. 0.89
   7 ?   -1.1   0.3       2.5   2.4e+03      11      16 ..     430     435 ..     427     436 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.008
                            Fer4_6  9 CigCgdCvrvCPegai 24
                                      Ci C +C+r+C  +ai
  gi|488600392|ref|YP_007906863.1| 14 CIFCKACERACKQKAI 29
                                      888********86665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.3e-05
                            Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                      d++kC+ Cg+C++ CP+++i
  gi|488600392|ref|YP_007906863.1| 49 DYSKCNFCGECAKKCPYDVI 68
                                      789**************987 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 7e-06
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       +p++Ci C  Cv  CP gai
  gi|488600392|ref|YP_007906863.1| 110 KPENCIACQLCVLSCPVGAI 129
                                       699****************8 PP

  == domain 4  score: 24.9 bits;  conditional E-value: 1.6e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + idpdkC  Cg Cvr+CP+ a+
  gi|488600392|ref|YP_007906863.1| 139 ISIDPDKCGACGVCVRNCPAMAL 161
                                       689*****************996 PP

  == domain 5  score: 17.7 bits;  conditional E-value: 2.9e-06
                            Fer4_6   3 eidpdkCigCgdCvrvCPe 21 
                                       +id  +C +C  C+++CP 
  gi|488600392|ref|YP_007906863.1| 193 VIDSGLCSHCSTCTAICPV 211
                                       79****************6 PP

  == domain 6  score: 18.1 bits;  conditional E-value: 2.1e-06
                            Fer4_6   7 dkCigCgdCvrvCP 20 
                                       + Ci+Cg+C+rvCP
  gi|488600392|ref|YP_007906863.1| 228 NDCIDCGACIRVCP 241
                                       67************ PP

  == domain 7  score: -1.1 bits;  conditional E-value: 2.5
                            Fer4_6  11 gCgdCv 16 
                                       gC+ C+
  gi|488600392|ref|YP_007906863.1| 430 GCRMCI 435
                                       8****7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.8    0.0012       1.1       2      26 ..      14      38 ..      13      50 .. 0.81
   2 !   15.5   0.2   2.6e-05     0.024       1      21 [.      52      72 ..      52      99 .. 0.81
   3 !   15.0   2.8   3.8e-05     0.036       1      24 [.     113     136 ..     113     144 .. 0.81
   4 !   24.2   5.7     5e-08   4.7e-05       1      66 [.     145     211 ..     145     212 .. 0.88
   5 !   11.2   2.2   0.00056      0.53       2      14 ..     230     242 ..     229     247 .. 0.91
   6 ?   -0.5   0.0       2.6   2.5e+03      55      62 ..     429     436 ..     395     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeie 26
                                      C+ C++C  +C ++ai  + e + +
  gi|488600392|ref|YP_007906863.1| 14 CIFCKACERACKQKAIAIEVEIMPD 38
                                      999*************987666555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.6e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                      +C  Cg+Ca+ CP ++i++ +
  gi|488600392|ref|YP_007906863.1| 52 KCNFCGECAKKCPYDVIEMIE 72
                                      5999*************9762 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 3.8e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkeke 24 
                                       +C+ C+ C+ +CP++ai+  ++  
  gi|488600392|ref|YP_007906863.1| 113 NCIACQLCVLSCPVGAISCSRNGD 136
                                       6****************9874444 PP

  == domain 4  score: 24.2 bits;  conditional E-value: 5e-08
                           Fer4_16   1 rCgtCgkCaevCPtnaikek.kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       +Cg Cg C+  CP+ a++    + ++  + +  ++ ++ k + + ++k    + +  C +C+++CP+
  gi|488600392|ref|YP_007906863.1| 145 KCGACGVCVRNCPAMALDLVdLNGTFSVKVELPEKIIDAKYFGNLKKKVIDSGLCSHCSTCTAICPV 211
                                       5****************987455677777777779999999999999999999*************7 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.00056
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C++Cg+C+ vCP 
  gi|488600392|ref|YP_007906863.1| 230 CIDCGACIRVCPR 242
                                       ************6 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 2.6
                           Fer4_16  55 tgCdiCqd 62 
                                        gC++C d
  gi|488600392|ref|YP_007906863.1| 429 SGCRMCID 436
                                       79999976 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   7.4   5.2e-07   0.00049       6      59 .]      12      70 ..       8      70 .. 0.72
   2 !   23.9  14.5   3.5e-08   3.3e-05       5      53 ..     111     158 ..     107     166 .. 0.86
   3 !   17.6  11.2   3.2e-06    0.0031       2      55 ..     140     213 ..     137     216 .. 0.77
   4 !   17.2  11.6   4.3e-06     0.004       2      52 ..     193     241 ..     192     245 .. 0.86
   5 ?   -1.2   0.0       2.4   2.3e+03      43      53 ..     430     440 ..     418     446 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.2e-07
                           Fer4_21  6 dkCigCgkCliaCedtshqai..eidak..t...vlkvvedeCvGCnlCssvCPvedciem 59
                                      d Ci C+ C  aC+++++ ai  ei ++  +    +++  ++C  C  C++ CP  d+iem
  gi|488600392|ref|YP_007906863.1| 12 DGCIFCKACERACKQKAI-AIevEIMPDgrRmpkSYRLDYSKCNFCGECAKKCPY-DVIEM 70
                                      78************7655.4534333332131113466789*************6.99998 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.5e-08
                           Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       +++Ci C++C+++C+ +++ + + ++++ + +  d+C +C +C+  CP 
  gi|488600392|ref|YP_007906863.1| 111 PENCIACQLCVLSCPVGAISCSR-NGDAEISIDPDKCGACGVCVRNCPA 158
                                       799************87777765.466777999***************6 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 3.2e-06
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai..............eidaktvl..........kvv.edeCvGCnlCssvCPv 53 
                                        id+dkC  Cg C+  C+  + + +              +i     +          kv+ +  C  C  C+++CPv
  gi|488600392|ref|YP_007906863.1| 140 SIDPDKCGACGVCVRNCPAMALDLVdlngtfsvkvelpeKI-----IdakyfgnlkkKVIdSGLCSHCSTCTAICPV 211
                                       59***********************7777777766665533.....133334666657763679************9 PP

                           Fer4_21  54 ed 55 
                                        +
  gi|488600392|ref|YP_007906863.1| 212 YG 213
                                       65 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 4.3e-06
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       +id+  C +C  C+  C+  ++    +d+   ++  e++C+ C  C+ vCP
  gi|488600392|ref|YP_007906863.1| 193 VIDSGLCSHCSTCTAICPVYGI--TAGDKPIDFPNWENDCIDCGACIRVCP 241
                                       69999*************6443..35677788999**************** PP

  == domain 5  score: -1.2 bits;  conditional E-value: 2.4
                           Fer4_21  43 GCnlCssvCPv 53 
                                       GC +C++   v
  gi|488600392|ref|YP_007906863.1| 430 GCRMCIDFTGV 440
                                       99999876655 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   3.1    0.0066       6.2      47      64 ..      10      27 ..       4      29 .. 0.85
   2 !   12.9  12.4   0.00012      0.11       3      64 ..      12      66 ..      10      67 .. 0.82
   3 !   17.4   9.7   4.7e-06    0.0044       3      64 ..      51     127 ..      49     128 .. 0.67
   4 !    8.6   3.8    0.0027       2.5       3      18 ..     112     127 ..     110     138 .. 0.77
   5 !   20.6   7.4   4.7e-07   0.00044       3      63 ..     144     211 ..     142     214 .. 0.75
   6 !    9.5   2.3    0.0014       1.3       5      21 ..     199     215 ..     195     222 .. 0.73
   7 !   13.5   0.0   8.1e-05     0.076       4      18 ..     229     243 ..     227     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0066
                            Fer4_8 47 alwsCttcgaCtevCpvg 64
                                      +++ C  c+aC+++C+++
  gi|488600392|ref|YP_007906863.1| 10 TMDGCIFCKACERACKQK 27
                                      588999999999999876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      + Ci C aC+ aC       +    + g+++ +  + ++        +C+ cg+C+++Cp +
  gi|488600392|ref|YP_007906863.1| 12 DGCIFCKACERACKQKAIAIEVEIMPDGRRMPKSYRLDY-------SKCNFCGECAKKCPYD 66
                                      67***********85555558889999999995555555.......9*************86 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 4.7e-06
                            Fer4_8   3 ekCieCgaCqsaCp.....vlrrtkkhlldargeaae..............dvqeeqvleeeealwsCttcgaCtev 60 
                                       +kC+ Cg C ++Cp     +++++ k+     +++ +              +++++         ++C +c+ C+  
  gi|488600392|ref|YP_007906863.1|  51 SKCNFCGECAKKCPydvieMIEDREKMESIVGDKVYDasmfvelkkqlgldRNRRSG----FSKPENCIACQLCVLS 123
                                       79***********98888755555555555555555555555544443332233333....57899*********** PP

                            Fer4_8  61 Cpvg 64 
                                       Cpvg
  gi|488600392|ref|YP_007906863.1| 124 CPVG 127
                                       **97 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0027
                            Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                       e+Ci C++C  +Cpv 
  gi|488600392|ref|YP_007906863.1| 112 ENCIACQLCVLSCPVG 127
                                       5899999999999964 PP

  == domain 5  score: 20.6 bits;  conditional E-value: 4.7e-07
                            Fer4_8   3 ekCieCgaCqsaCp.............vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       +kC+ Cg C  +Cp             +++ +  + + da++  + ++   +        + C++c  Ct  Cpv
  gi|488600392|ref|YP_007906863.1| 144 DKCGACGVCVRNCPamaldlvdlngtfSVKVELpEKIIDAKYFGNLKKKVID-------SGLCSHCSTCTAICPV 211
                                       69************77777666666666666666677777766666344444.......599************7 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0014
                            Fer4_8   5 CieCgaCqsaCpvlrrt 21 
                                       C +C+ C++ Cpv+  t
  gi|488600392|ref|YP_007906863.1| 199 CSHCSTCTAICPVYGIT 215
                                       88888888888887665 PP

  == domain 7  score: 13.5 bits;  conditional E-value: 8.1e-05
                            Fer4_8   4 kCieCgaCqsaCpvl 18 
                                       +Ci CgaC   Cp +
  gi|488600392|ref|YP_007906863.1| 229 DCIDCGACIRVCPRW 243
                                       799999999999833 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 !   47.4   0.0   1.6e-15   1.5e-12       6      74 ..     262     327 ..     257     331 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.6e-15
                       FrhB_FdhB_N   6 stdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeella..aaGskYtlspnl 74 
                                       s+    r  +q+G +vt++++++Le giid+ + v+++ ++wr+k v ++++++l +  a G+kY+ + ++
  gi|488600392|ref|YP_007906863.1| 262 SK----RFTGQDGAMVTEIMASALEMGIIDASLFVDRD-EEWRTKIVTIRKPKQLEKstATGTKYSFADVM 327
                                       44....899*****************************.79***************99999****988775 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   2.0     0.018        17       2      21 ..       6      25 ..       5      26 .. 0.86
   2 !    7.9   1.4    0.0036       3.4       4      22 .]      47      65 ..      43      65 .. 0.87
   3 !   14.0   2.2   4.3e-05      0.04       7      21 ..     111     125 ..     107     126 .. 0.91
   4 !   21.9   4.0   1.3e-07   0.00012       3      22 .]     139     158 ..     137     158 .. 0.92
   5 !   15.2   2.1   1.8e-05     0.017       4      21 ..     193     210 ..     190     211 .. 0.89
   6 !   14.8   3.2   2.5e-05     0.023       9      21 ..     229     241 ..     225     242 .. 0.90
   7 ?   -1.3   0.2       3.2   3.1e+03      12      18 ..     430     436 ..     429     437 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.018
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++v+  d Ci C+aC  aC 
  gi|488600392|ref|YP_007906863.1|  6 HPVYTMDGCIFCKACERACK 25
                                      67888899999********5 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                        d  +C+ Cg C + CP+
  gi|488600392|ref|YP_007906863.1| 47 RLDYSKCNFCGECAKKCPY 65
                                      57999*************5 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 4.3e-05
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                       +++Ci+C  Cv +CP
  gi|488600392|ref|YP_007906863.1| 111 PENCIACQLCVLSCP 125
                                       899************ PP

  == domain 4  score: 21.9 bits;  conditional E-value: 1.3e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       + +d+d+C +Cg Cv +CPa
  gi|488600392|ref|YP_007906863.1| 139 ISIDPDKCGACGVCVRNCPA 158
                                       679****************8 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 1.8e-05
                            Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                       v+d+  C +C++C+  CP
  gi|488600392|ref|YP_007906863.1| 193 VIDSGLCSHCSTCTAICP 210
                                       79999********999** PP

  == domain 6  score: 14.8 bits;  conditional E-value: 2.5e-05
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                        Ci CgaC+ +CP
  gi|488600392|ref|YP_007906863.1| 229 DCIDCGACIRVCP 241
                                       6************ PP

  == domain 7  score: -1.3 bits;  conditional E-value: 3.2
                            Fer4_2  12 gCgaCvs 18 
                                       gC+ C++
  gi|488600392|ref|YP_007906863.1| 430 GCRMCID 436
                                       8999975 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   4.2    0.0022         2       2      16 ..      12      26 ..      11      27 .. 0.88
   2 ?    4.6   4.5      0.06        56       2      16 ..      51      65 ..      50      66 .. 0.89
   3 !   15.0   2.4   2.7e-05     0.026       1      17 []     111     127 ..     111     127 .. 0.92
   4 !   12.6   0.9   0.00017      0.16       1      15 [.     143     157 ..     143     168 .. 0.91
   5 !   13.6   1.9   8.1e-05     0.076       4      16 ..     199     211 ..     191     213 .. 0.90
   6 !   18.0   1.0   2.9e-06    0.0028       3      15 ..     229     241 ..     224     252 .. 0.87
   7 ?    0.9   0.2      0.93   8.8e+02       6      13 ..     430     437 ..     429     437 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0022
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + Ci C++C++aC+q
  gi|488600392|ref|YP_007906863.1| 12 DGCIFCKACERACKQ 26
                                      67999********97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.06
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C+ Cg C   CP+
  gi|488600392|ref|YP_007906863.1| 51 SKCNFCGECAKKCPY 65
                                      68************8 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.7e-05
                            Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                       +e+Ci C  Cv +CP+g
  gi|488600392|ref|YP_007906863.1| 111 PENCIACQLCVLSCPVG 127
                                       699************86 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00017
                            Fer4_4   1 qerCigCgsCvaaCP 15 
                                       +++C  Cg+Cv+ CP
  gi|488600392|ref|YP_007906863.1| 143 PDKCGACGVCVRNCP 157
                                       58999********** PP

  == domain 5  score: 13.6 bits;  conditional E-value: 8.1e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C +C  C+a+CP+
  gi|488600392|ref|YP_007906863.1| 199 CSHCSTCTAICPV 211
                                       ************6 PP

  == domain 6  score: 18.0 bits;  conditional E-value: 2.9e-06
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                        Ci+Cg+C+++CP
  gi|488600392|ref|YP_007906863.1| 229 DCIDCGACIRVCP 241
                                       4************ PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.93
                            Fer4_4   6 gCgsCvaa 13 
                                       gC+ C+++
  gi|488600392|ref|YP_007906863.1| 430 GCRMCIDF 437
                                       8****986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   3.4    0.0045       4.3      42      58 ..      10      26 ..       1      29 [. 0.84
   2 !   14.5   2.6     4e-05     0.038      42      60 ..      49      67 ..      26      68 .. 0.80
   3 !   17.2  11.2     6e-06    0.0057       1      58 [.      52     126 ..      52     129 .. 0.60
   4 !    8.6   2.4    0.0028       2.6      43      58 ..     143     158 ..     127     162 .. 0.71
   5 !   17.1   7.4   6.1e-06    0.0058       1      57 [.     145     210 ..     145     212 .. 0.64
   6 !    8.9   2.2    0.0023       2.1       2      18 ..     199     215 ..     198     225 .. 0.83
   7 !   10.7   1.9   0.00065      0.62      44      57 ..     228     241 ..     212     243 .. 0.75
   8 !    9.6   2.5    0.0014       1.3       2      14 ..     230     242 ..     229     249 .. 0.78
   9 ?   -1.9   0.1       5.3     5e+03       4      10 ..     430     436 ..     429     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0045
                           Fer4_17 42 kaslCieCgeCerkCPq 58
                                      +++ Ci C+ Cer+C q
  gi|488600392|ref|YP_007906863.1| 10 TMDGCIFCKACERACKQ 26
                                      7999***********87 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4e-05
                           Fer4_17 42 kaslCieCgeCerkCPqgl 60
                                        s+C+ CgeC++kCP+++
  gi|488600392|ref|YP_007906863.1| 49 DYSKCNFCGECAKKCPYDV 67
                                      6799*************96 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 6e-06
                           Fer4_17   1 rCiqCgyClpeCpsyea....ydnepk.....kllraakl............glleeaeke.....ekaslCieCge 51 
                                       +C+ Cg C+++Cp+  +     +++ +       +    +            gl +    +     +k ++Ci C++
  gi|488600392|ref|YP_007906863.1|  52 KCNFCGECAKKCPYDVIemieDREK-MesivgDKV----YdasmfvelkkqlGLDR----NrrsgfSKPENCIACQL 119
                                       6************965544322222.232222222....12333565544333222....1334678********** PP

                           Fer4_17  52 CerkCPq 58 
                                       C+ +CP 
  gi|488600392|ref|YP_007906863.1| 120 CVLSCPV 126
                                       ******6 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0028
                           Fer4_17  43 aslCieCgeCerkCPq 58 
                                        ++C  Cg C+r CP+
  gi|488600392|ref|YP_007906863.1| 143 PDKCGACGVCVRNCPA 158
                                       5678888888888885 PP

  == domain 5  score: 17.1 bits;  conditional E-value: 6.1e-06
                           Fer4_17   1 rCiqCgyClpeCpsyea...........ydnepkkllraaklglleeaeke.ekaslCieCgeCerkCP 57 
                                       +C  Cg C+++Cp ++              + p+k++ a ++g l++   +    +lC++C  C++ CP
  gi|488600392|ref|YP_007906863.1| 145 KCGACGVCVRNCPAMALdlvdlngtfsvKVELPEKIIDAKYFGNLKK---KvIDSGLCSHCSTCTAICP 210
                                       699**********9888444332221111112555555555543333...325789************9 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0023
                           Fer4_17   2 CiqCgyClpeCpsyeay 18 
                                       C++C+ C++ Cp y ++
  gi|488600392|ref|YP_007906863.1| 199 CSHCSTCTAICPVYGIT 215
                                       99999999999998765 PP

  == domain 7  score: 10.7 bits;  conditional E-value: 0.00065
                           Fer4_17  44 slCieCgeCerkCP 57 
                                       ++Ci Cg C r+CP
  gi|488600392|ref|YP_007906863.1| 228 NDCIDCGACIRVCP 241
                                       66777777777777 PP

  == domain 8  score: 9.6 bits;  conditional E-value: 0.0014
                           Fer4_17   2 CiqCgyClpeCps 14 
                                       Ci Cg+C+++Cp+
  gi|488600392|ref|YP_007906863.1| 230 CIDCGACIRVCPR 242
                                       8888888888887 PP

  == domain 9  score: -1.9 bits;  conditional E-value: 5.3
                           Fer4_17   4 qCgyClp 10 
                                       +C++C++
  gi|488600392|ref|YP_007906863.1| 430 GCRMCID 436
                                       7999986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   3.4    0.0024       2.3       1      15 []      14      28 ..      14      28 .. 0.94
   2 !    9.4   3.7    0.0023       2.2       1      14 [.      53      66 ..      53      67 .. 0.94
   3 !   14.2   5.4   6.7e-05     0.064       1      15 []     114     128 ..     114     128 .. 0.98
   4 ?    2.3   4.8      0.43     4e+02       4      12 ..     149     157 ..     144     160 .. 0.80
   5 !   11.0   3.9   0.00072      0.68       1      13 [.     199     211 ..     199     214 .. 0.89
   6 !   12.7   3.0   0.00021       0.2       1      12 [.     230     241 ..     230     243 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C aC+++C  +A
  gi|488600392|ref|YP_007906863.1| 14 CIFCKACERACKQKA 28
                                      ***********9887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0023
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ Cg C + CP++
  gi|488600392|ref|YP_007906863.1| 53 CNFCGECAKKCPYD 66
                                      ************96 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 6.7e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C++Cv +CPvgA
  gi|488600392|ref|YP_007906863.1| 114 CIACQLCVLSCPVGA 128
                                       9*************9 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.43
                            Fer4_3   4 CgaCvevCP 12 
                                       Cg Cv+ CP
  gi|488600392|ref|YP_007906863.1| 149 CGVCVRNCP 157
                                       888*****9 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00072
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C +C++C   CPv
  gi|488600392|ref|YP_007906863.1| 199 CSHCSTCTAICPV 211
                                       9***********7 PP

  == domain 6  score: 12.7 bits;  conditional E-value: 0.00021
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ CgaC +vCP
  gi|488600392|ref|YP_007906863.1| 230 CIDCGACIRVCP 241
                                       9*********** PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.3      0.32     3e+02       6      19 ..      12      25 ..       8      33 .. 0.85
   2 ?    1.8  12.0      0.44   4.1e+02       3      65 ..      48     130 ..      47     131 .. 0.79
   3 ?   14.0   0.6   6.9e-05     0.065       1      20 [.     139     158 ..     139     176 .. 0.89
   4 ?    3.7   0.5      0.11     1e+02       2      20 ..     193     211 ..     193     220 .. 0.88
   5 ?    6.1   0.2      0.02        19       6      20 ..     228     242 ..     227     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.32
                           Fer4_15  6 daCigcglCvaeap 19
                                      d Ci c +C ++++
  gi|488600392|ref|YP_007906863.1| 12 DGCIFCKACERACK 25
                                      88*******99996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.44
                           Fer4_15   3 vDrdaCigcglCvaeap.evfelded..glasvl..................lddgeiaegevpddeeeaaqeAara 58 
                                       +D ++C  cg C++ +p +v+e+ ed   + s++                  l d+++ +g+ +++   a q  + +
  gi|488600392|ref|YP_007906863.1|  48 LDYSKCNFCGECAKKCPyDVIEMIEDreKMESIVgdkvydasmfvelkkqlgL-DRNRRSGFSKPENCIACQLCVLS 123
                                       899*************5467776553224555559999999999999999954.56778899999999999999999 PP

                           Fer4_15  59 CPvdAIr 65 
                                       CPv+AI+
  gi|488600392|ref|YP_007906863.1| 124 CPVGAIS 130
                                       9999996 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 6.9e-05
                           Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                       + +D d+C  cg+Cv+++p 
  gi|488600392|ref|YP_007906863.1| 139 ISIDPDKCGACGVCVRNCPA 158
                                       78****************95 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.11
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       v+D  +C  c  C a +p 
  gi|488600392|ref|YP_007906863.1| 193 VIDSGLCSHCSTCTAICPV 211
                                       69999************94 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.02
                           Fer4_15   6 daCigcglCvaeape 20 
                                       + Ci cg+C++++p+
  gi|488600392|ref|YP_007906863.1| 228 NDCIDCGACIRVCPR 242
                                       67***********96 PP

>> Ret2_MD  RNA editing 3' terminal uridylyl transferase 2 middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.31      53      84 ..      21      51 ..       8      55 .. 0.75
   2 ?   -2.5   0.0       7.5   7.1e+03      47      65 ..     428     446 ..     423     470 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                           Ret2_MD 53 aiqvsskeqaieaigllPdGkiltkgmredyt 84
                                      +  +  k  aie + ++PdG+ ++k+ r dy 
  gi|488600392|ref|YP_007906863.1| 21 ERACKQKAIAIE-VEIMPDGRRMPKSYRLDYS 51
                                      444555556666.89***************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.5
                           Ret2_MD  47 tyGcriaiqvsskeqaiea 65 
                                        +Gcr+ i+ +  e+ i  
  gi|488600392|ref|YP_007906863.1| 428 PSGCRMCIDFTGVESDISV 446
                                       5799999998887776655 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 ?    9.3   0.0    0.0016       1.5       2      38 ..       9      46 ..       8      52 .. 0.88
   2 ?   -2.3   0.0       6.8   6.4e+03      20      45 ..     317     342 ..     315     344 .. 0.82
   3 ?   -0.9   0.0       2.4   2.3e+03      11      38 ..     466     494 ..     464     502 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                                      ES-TTSHHHHHHHHHHHHHT--EEEE---TTTT.HHHH CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgeh.deel 38
                                      y + ++ +++ +  a+++k +++ev+ ++ g++ + ++
  gi|488600392|ref|YP_007906863.1|  9 YTMDGCIFCKACERACKQKAIAIEVEIMPDGRRmPKSY 46
                                      89************************999999855554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.8
                                       HT--EEEE---TTTTHHHHHHH-TT- CS
                           GST_N_3  20 kglpvevvevtpgehdeellaknplg 45 
                                        g ++ +++v+p+ +++ ++ k + g
  gi|488600392|ref|YP_007906863.1| 317 TGTKYSFADVMPELRKAVFRSKKGVG 342
                                       5788999******9999998887765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHT--.EEEE---TTTTHHHH CS
                           GST_N_3  11 rrvrlaLnekglp.vevvevtpgehdeel 38 
                                       r++ ++++ekg++ ++++++++ e+ +++
  gi|488600392|ref|YP_007906863.1| 466 REIIEYIKEKGYAeFREADLSVVEKLANY 494
                                       56677888999966888888888887777 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   3.4      0.59   5.5e+02       4      16 ..      12      24 ..      10      26 .. 0.89
   2 ?    3.8   0.7     0.089        84       2      22 ..      49      70 ..      48      85 .. 0.78
   3 ?    7.8   2.6     0.005       4.7       4      17 ..     112     125 ..     111     129 .. 0.93
   4 ?    9.3   4.0    0.0017       1.6       1      18 [.     141     158 ..     141     159 .. 0.94
   5 ?    7.2   1.6    0.0078       7.4       1      17 [.     194     210 ..     194     218 .. 0.91
   6 ?   10.5   2.6   0.00074       0.7       4      18 ..     228     242 ..     227     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.59
                           Fer4_13  4 dtCiacgaCvela 16
                                      d Ci c+aC  ++
  gi|488600392|ref|YP_007906863.1| 12 DGCIFCKACERAC 24
                                      79*******9999 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.089
                           Fer4_13  2 DrdtCiacgaCvelaP.dvFee 22
                                      D ++C  cg C++ +P dv e+
  gi|488600392|ref|YP_007906863.1| 49 DYSKCNFCGECAKKCPyDVIEM 70
                                      66899**********9555555 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.005
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                       ++Ciac++Cv  +P
  gi|488600392|ref|YP_007906863.1| 112 ENCIACQLCVLSCP 125
                                       79***********9 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0017
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D d+C acg+Cv  +P 
  gi|488600392|ref|YP_007906863.1| 141 IDPDKCGACGVCVRNCPA 158
                                       899**************6 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0078
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D   C+ c +C +++P
  gi|488600392|ref|YP_007906863.1| 194 IDSGLCSHCSTCTAICP 210
                                       78889************ PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00074
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       + Ci+cgaC  ++P 
  gi|488600392|ref|YP_007906863.1| 228 NDCIDCGACIRVCPR 242
                                       67************6 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.5      0.51   4.8e+02      85      97 ..      14      26 ..       8      36 .. 0.69
   2 ?    4.7   0.6     0.036        34      58      95 ..      50      89 ..      40     103 .. 0.75
   3 ?    7.5  14.2    0.0049       4.6       6      97 ..      59     158 ..      58     163 .. 0.75
   4 ?    4.2   2.0     0.051        48      59      73 ..     144     158 ..     132     183 .. 0.82
   5 ?    5.0   1.7     0.029        27      54      73 ..     192     211 ..     177     219 .. 0.82
   6 ?   11.7   2.8   0.00024      0.22      58      72 ..     227     241 ..     218     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.51
                           Fer4_18 85 ciscllcidacdk 97
                                      ci c  c  ac++
  gi|488600392|ref|YP_007906863.1| 14 CIFCKACERACKQ 26
                                      7777777777765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.036
                           Fer4_18 58 agdcidcescvkvcPtgi..dirkGlqleciscllcidac 95
                                       ++c  c+ c k cP ++   i +  ++e i   +  da 
  gi|488600392|ref|YP_007906863.1| 50 YSKCNFCGECAKKCPYDVieMIEDREKMESIVGDKVYDAS 89
                                      578999*********9873336777778877777777775 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0049
                           Fer4_18   6 cvyvcPyarvqsvlydeetllvvydakrGekiagrkkekkalkekeerkekgagdcidcescvkvcPtg.id.irkG 80 
                                       c   cPy  +  +   e+   +v d++   ++  + k++  l ++ +   ++  +ci+c+ cv  cP+g i   r+G
  gi|488600392|ref|YP_007906863.1|  59 CAKKCPYDVIEMIEDREKMESIVGDKVYDASMFVELKKQLGLDRNRRSGFSKPENCIACQLCVLSCPVGaIScSRNG 135
                                       8889***999877766777777888888888877777777777777777788899*************844325888 PP

                           Fer4_18  81 ...lql...eciscllcidacdk 97 
                                          + +   +c +c+ c+  c  
  gi|488600392|ref|YP_007906863.1| 136 daeISIdpdKCGACGVCVRNCPA 158
                                       43323333469999999999965 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.051
                           Fer4_18  59 gdcidcescvkvcPt 73 
                                        +c +c++cv+ cP 
  gi|488600392|ref|YP_007906863.1| 144 DKCGACGVCVRNCPA 158
                                       6799*********96 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.029
                           Fer4_18  54 kekgagdcidcescvkvcPt 73 
                                       k  ++g c +c++c ++cP+
  gi|488600392|ref|YP_007906863.1| 192 KVIDSGLCSHCSTCTAICPV 211
                                       4556789************7 PP

  == domain 6  score: 11.7 bits;  conditional E-value: 0.00024
                           Fer4_18  58 agdcidcescvkvcP 72 
                                       ++dcidc++c++vcP
  gi|488600392|ref|YP_007906863.1| 227 ENDCIDCGACIRVCP 241
                                       68************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.29s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3070.37
//
Query:       gi|488600393|ref|YP_007906864.1|  [L=112]
Description: S-adenosylmethionine decarboxylase proenzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-35  121.2   0.0    2.3e-35  121.1   0.0    1.0  1  AdoMet_dc      S-adenosylmethionine decarboxylase
  ------ inclusion threshold ------
      0.067   13.4   0.1       0.24   11.6   0.0    1.8  2  QueF           QueF-like protein
       0.12   11.9   0.0       0.15   11.6   0.0    1.2  1  Fucose_iso_N2  L-fucose isomerase, second N-terminal domain


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.0   3.8e-39   2.3e-35       1     106 []       6     112 .]       6     112 .] 0.99

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 3.8e-39
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftc 77 
                                       h+++++yg+ +el++++e++++i++e+++++++t + +++ +f+p+Gv+++vliaeSh+siHtwpe+g + +D+ftc
  gi|488600393|ref|YP_007906864.1|   6 HIIAEFYGVPEELISKEETVRAIVEEVVDKAELTKVGSVYKQFNPHGVTGIVLIAESHVSIHTWPEYGLVNLDIFTC 82 
                                       9**************************************************************************** PP

                                       ST.HHHHHHHHHHHHHHT-SEEEEEEEEEE CS
                         AdoMet_dc  78 ge.ispekaleylieafkadrvtvdelkRG 106
                                       g+  ++eka+++++e+fk+++++   l+RG
  gi|488600393|ref|YP_007906864.1|  83 GDtSKTEKAFRLFVEKFKPKSYRHYILDRG 112
                                       ***********************9999998 PP

>> QueF  QueF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.1e-05      0.24      33      77 ..      18      63 ..      11      66 .. 0.86
   2 ?   -0.6   0.0      0.25   1.5e+03      19      32 ..      89     102 ..      70     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.1e-05
                              QueF 33 gifhEevvnrilddlvealk.PkwlevvgdfnpRGgididvvvete 77
                                       i++Ee v+ i++++v++++  k+ +v+ +fnp G   i+ ++e++
  gi|488600393|ref|YP_007906864.1| 18 LISKEETVRAIVEEVVDKAElTKVGSVYKQFNPHGVTGIVLIAESH 63
                                      5799*************998345569**********9999998876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.25
                              QueF  19 lkslklYlisfrnr 32 
                                       +k+++l++  f+ +
  gi|488600393|ref|YP_007906864.1|  89 EKAFRLFVEKFKPK 102
                                       57777777777655 PP

>> Fucose_iso_N2  L-fucose isomerase, second N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.6e-05      0.15      17      61 ..       2      46 ..       1      56 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                                      S--HHHHHHCT--EEEEE-THHHHHHHHTT-S-HHHHHHHHHHHH CS
                     Fucose_iso_N2 17 ivdadflqeylglraelvdmveilrrieeeiydkeeyekalaWvk 61
                                      iv ++++ e+ g+  el+++ e +r i ee+ dk+e+ k+ +  k
  gi|488600393|ref|YP_007906864.1|  2 IVGKHIIAEFYGVPEELISKEETVRAIVEEVVDKAELTKVGSVYK 46
                                      678999******************************999766555 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:                      424  (0.0236488); 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 0.33s 00:00:00.89 Elapsed: 00:00:00.57
# Mc/sec: 593.14
//
Query:       gi|488600394|ref|YP_007906865.1|  [L=340]
Description: putative methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-103  344.4   0.3   3.4e-103  344.1   0.3    1.1  1  DUF43            Branched-chain polyamine synthase A C-termin
    0.00013   21.8   0.1    0.00038   20.4   0.1    1.7  1  HTH_45           Winged helix-turn-helix
    0.00017   22.2   0.0    0.00039   21.1   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    0.00047   20.0   0.0      0.001   18.9   0.0    1.6  2  Methyltransf_31  Methyltransferase domain
     0.0056   16.7   0.1      0.028   14.5   0.0    2.2  2  HemN_C           HemN C-terminal domain
     0.0071   16.5   0.1        4.2    7.7   0.0    2.6  2  CotJB            CotJB protein
  ------ inclusion threshold ------
      0.032   14.1   0.0       0.85    9.5   0.0    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.036   14.7   0.0      0.078   13.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      0.038   14.5   0.0       0.12   12.9   0.0    1.9  1  AAA_assoc_C      C-terminal AAA-associated domain
      0.046   13.4   0.0       0.26   10.9   0.0    2.0  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.073   12.4   0.0       0.14   11.5   0.0    1.4  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
        0.1   12.3   0.6         17    5.2   0.1    2.7  2  Nucleolin_bd     Nucleolin binding domain
        0.1   12.4   0.9       0.14   12.0   0.1    1.6  2  N6-adenineMlase  Probable N6-adenine methyltransferase
       0.15   12.1   0.0        0.3   11.1   0.0    1.5  1  DUF1217          Protein of unknown function (DUF1217)


Domain annotation for each model (and alignments):
>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.1   0.3  2.6e-106  3.4e-103       1     242 [.      92     336 ..      92     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 344.1 bits;  conditional E-value: 2.6e-106
                                       HHHHHHHHHHTT-----GGGT---B-HHHHHHHHHHHHHTT-STT-EEEEES-TT-HHHHHHHHT--SEEEEE-S-H CS
                             DUF43   1 dllekfreiakdRPeaieeyDqgfvtpettvaRvallyerGDLegkeilvlGdDDLtslalaLtglpkkvvvvDiDe 77 
                                       ++lek++ei  +RPeaie+yDqgf+++e++++Rv+++y+rG+L+ + i+v+GdDDL s+a++Ltglpkkvv vDiDe
  gi|488600394|ref|YP_007906865.1|  92 EILEKYSEISNNRPEAIEKYDQGFISLEGVIRRVEFIYDRGELNSR-IFVVGDDDLLSIAASLTGLPKKVVAVDIDE 167
                                       79******************************************99.****************************** PP

                                       HHHHHHHHHHHHHT--EEEE---TTS---TTTSS-BSEEEE---SSHHHHHHHHHHHHHTB-STT-EEEEEE-TTT- CS
                             DUF43  78 RlikfiervakelglkieaivyDlrkplpeelkekFdvfitDPpetvealkaFlgRGiaaLkgegcagYlgltrres 154
                                       Rli+fi++ a+e+gl++ea+vyD+++p+ +e+ +kFdvf+tDP+et+ +lk+Fl+RG+++Lkg gc gY+g+t+ e+
  gi|488600394|ref|YP_007906865.1| 168 RLINFINKTAEEYGLNVEALVYDVQQPFMDEFRKKFDVFVTDPVETIPGLKLFLSRGVSTLKGPGCSGYFGITTLEA 244
                                       ***************************************************************************** PP

                                       -HHHHHHHHHHHHTS--EEEEEEEEEEEB---S-GGGSHHHHHSSS--....--SS---EEEEEEEE--TT-.---S CS
                             DUF43 155 sldkWkeiqklllemgvvitdlirnFneYenweykeetraikllpvkk....kpekiwyksalfrietlkgk.rkve 226
                                       s++kW+eiq+++++mg++itdl+r+Fn Y + e+k+++r++++lp+++    +++++wy+s+lfrie++ ++ + ve
  gi|488600394|ref|YP_007906865.1| 245 SRKKWYEIQRMIMDMGFIITDLRRHFNIYPQ-EEKNFFRFQEKLPIVErlgfNVDFNWYNSTLFRIEAVMDPkPLVE 320
                                       ******************************9.99************999999*****************998799** PP

                                       SS--S.S-S--XXXXX CS
                             DUF43 227 eevkkvedlykdeess 242
                                        e+  +e++ykd+es+
  gi|488600394|ref|YP_007906865.1| 321 GEMILDEKVYKDDESW 336
                                       **************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 !   20.4   0.1     3e-07   0.00038       6      66 ..       4      63 ..       2      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3e-07
                            HTH_45  6 eIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlell 66
                                       I+ +IL+++ +ge++  +++y  + s   + + L+ L+++gli+ +++k +lTekG++ +
  gi|488600394|ref|YP_007906865.1|  4 RIYNQILQSL-DGEKSVYELLYLQDASLPEVFEILNDLQSNGLIEIKDGKARLTEKGRQEV 63
                                      5899******.**********************************************9855 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     3e-07   0.00039      16      70 ..     150     208 ..     142     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3e-07
                                       HCTS.T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG..BSSSTTTEEEEEE CS
                   Methyltransf_25  16 akrl.g.kakvtgvDiseemleaareraeeeglnvefvqgdaed..lpfedgsfDlvvs 70 
                                       a+ l g  +kv++vDi+e++++ +++ aee glnve ++ d+++  +++  ++fD+ v 
  gi|488600394|ref|YP_007906865.1| 150 AASLtGlPKKVVAVDIDERLINFINKTAEEYGLNVEALVYDVQQpfMDEFRKKFDVFVT 208
                                       444435579*********************************99776777789999876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.1     4e+03      97     127 ..      36      64 ..      13      97 .. 0.57
   2 !   18.9   0.0     8e-07     0.001      18      81 ..     147     209 ..     142     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.1
                   Methyltransf_31  97 iervlkpggilliedprllaelpakveeesk 127
                                       i + l+++g + i d +  a+l +k ++e +
  gi|488600394|ref|YP_007906865.1|  36 ILNDLQSNGLIEIKDGK--ARLTEKGRQEVR 64 
                                       45556666766666666..333333333333 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 8e-07
                   Methyltransf_31  18 tfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.lekl.ledekfDlilsn 81 
                                       +  +a++ g  ++vv +Di+e+ i++ ++ a++ gl nve  + d+++ +  + +  +kfD+ +++
  gi|488600394|ref|YP_007906865.1| 147 LSIAASLTGLPKKVVAVDIDERLINFINKTAEEYGL-NVEALVYDVQQpFM-DeFR-KKFDVFVTD 209
                                       556677888899************************.8**********643.4466.9****9997 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.2e-05     0.028      41      65 ..      36      60 ..      20      61 .. 0.91
   2 ?   -1.7   0.0       2.5   3.1e+03      30      47 ..      82      99 ..      78     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                            HemN_C 41 aleklqeqGLLeldggrlrltprGr 65
                                      +l +lq +GL+e+ +g+ rlt++Gr
  gi|488600394|ref|YP_007906865.1| 36 ILNDLQSNGLIEIKDGKARLTEKGR 60
                                      5899********************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                            HemN_C 30 fgldleellaaaleklqe 47
                                      +g+++ e ++ +lek+ e
  gi|488600394|ref|YP_007906865.1| 82 TGVAINEFFKEILEKYSE 99
                                      566666666666666644 PP

>> CotJB  CotJB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0096        12      28      55 ..      91     118 ..      89     122 .. 0.91
   2 !    7.7   0.0    0.0033       4.2       4      36 ..     253     285 ..     250     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0096
                             CotJB  28 kealelfnkyskkrkelkkeYeekygPL 55 
                                       ke le+++++s++r e++++Y + +  L
  gi|488600394|ref|YP_007906865.1|  91 KEILEKYSEISNNRPEAIEKYDQGFISL 118
                                       689*******************999877 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0033
                             CotJB   4 lkeiqelsFavvdlnLYLDthPddkealelfnk 36 
                                        + i+ + F+++dl+   +++P++++ +  f++
  gi|488600394|ref|YP_007906865.1| 253 QRMIMDMGFIITDLRRHFNIYPQEEKNFFRFQE 285
                                       578**********************99988876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00066      0.85      14      58 ..       6      52 ..       3      62 .. 0.84
   2 ?    1.7   0.0      0.19   2.4e+02      32      55 ..     242     265 ..     240     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00066
                                      CHHHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 14 YlaLl..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      Y  +l    g+++++e+    + + + v e+L+ L + Gl+e+++g+
  gi|488600394|ref|YP_007906865.1|  6 YNQILqsLDGEKSVYELLYLQDASLPEVFEILNDLQSNGLIEIKDGK 52
                                      6666655568899999999999999******************9988 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.19
                                       TTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  32 lgvprskvYevLrsLedkGlVere 55 
                                       l+ +r k Ye+ r  +d+G++ + 
  gi|488600394|ref|YP_007906865.1| 242 LEASRKKWYEIQRMIMDMGFIITD 265
                                       677999**************9876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.1e-05     0.078      15      66 ..     154     207 ..     144     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                                       HHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT...-EEEEE CS
                   Methyltransf_11  15 akrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfedn...sfDlvv 66 
                                       +  g  ++vv+vD+++++++  ++ a+e gl+ve +v d+++ pf d+   +fD+ v
  gi|488600394|ref|YP_007906865.1| 154 T--GlpKKVVAVDIDERLINFINKTAEEYGLNVEALVYDVQQ-PFMDEfrkKFDVFV 207
                                       3..45599*********************************9.99997666899876 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 ?   12.9   0.0   9.5e-05      0.12      11      45 ..      30      64 ..      20      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.5e-05
                       AAA_assoc_C 11 vddLlpiveaaelLglveveegdielTelGrkfve 45
                                      + ++++i++ +++ gl+e+++g+ +lTe+Gr+ v+
  gi|488600394|ref|YP_007906865.1| 30 LPEVFEILNDLQSNGLIEIKDGKARLTEKGRQEVR 64
                                      56789999***********************9765 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 ?   -0.7   0.0      0.73   9.3e+02     216     256 ..      68     107 ..      55     111 .. 0.69
   2 ?   10.9   0.0    0.0002      0.26      40      90 ..     155     207 ..     147     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.73
                                       HHHH.HHTT-EEEEEEESEESHHHHHHCTT...SEEEEECC CS
                   MethyltransfD12 216 lkslsskfgvkvllsnsfkdtklfrelyksYnnesilevee 256
                                       lk+l + +++ ++ +     +++f+e++++Y++ s  ++e+
  gi|488600394|ref|YP_007906865.1|  68 LKHLGNIYCTACEGTGV-AINEFFKEILEKYSEISNNRPEA 107
                                       55555555666655555.56789999999999877666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0002
                                       ..SSCEEEEES-HHHHHHHHHHCCH...SHHHHHHHHH.TCTTGGC.TSHHHHH CS
                   MethyltransfD12  40 kqgkkvlinDinedlinlykalikn...nveelikelekllekeelenereyfy 90 
                                         +kkv++ Di e lin+ +++ ++   nve+l+ ++++  +++e+ ++ + f+
  gi|488600394|ref|YP_007906865.1| 155 GLPKKVVAVDIDERLINFINKTAEEyglNVEALVYDVQQ-PFMDEFRKKFDVFV 207
                                       4789****************99999*************7.99999877766665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.14     174     232 ..     146     208 ..     141     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                              PrmA 174 iLaiaaakLg.akkvvavDiDevAvkvakeNaelNkveakleva.lseellk..eekadviva 232
                                       +L+iaa++ g  kkvvavDiDe  ++  ++ ae  +++ +  v+ +++  ++  ++k+dv v 
  gi|488600394|ref|YP_007906865.1| 146 LLSIAASLTGlPKKVVAVDIDERLINFINKTAEEYGLNVEALVYdVQQPFMDefRKKFDVFVT 208
                                       69********5599********99998888888777776555542333333345688998875 PP

>> Nucleolin_bd  Nucleolin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.022        28       9      54 ..     166     207 ..     158     214 .. 0.76
   2 ?    5.2   0.1     0.013        17      25      56 ..     253     284 ..     246     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.022
                      Nucleolin_bd   9 DkrLvqRveqyLesnedseyvDvdamaaeLqrqYreYgRrkrnaFr 54 
                                       D+rL++ ++++     ++  ++v+a++ + q+ + +  R+k+  F 
  gi|488600394|ref|YP_007906865.1| 166 DERLINFINKT----AEEYGLNVEALVYDVQQPFMDEFRKKFDVFV 207
                                       44454444444....555569**************99999999995 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                      Nucleolin_bd  25 dseyvDvdamaaeLqrqYreYgRrkrnaFriq 56 
                                       ++ ++D++ + ++L+r +  Y    +n Fr q
  gi|488600394|ref|YP_007906865.1| 253 QRMIMDMGFIITDLRRHFNIYPQEEKNFFRFQ 284
                                       56789***********************9976 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011      0.14      50      96 ..     158     210 ..     129     213 .. 0.83
   2 ?   -3.2   0.1       4.9   6.3e+03      52      79 ..     261     287 ..     248     299 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                   N6-adenineMlase  50 ekvlLleiDkrFealyge........ekfvfYdlnnpeelpeelkgkfdviviDP 96 
                                       +kv+  +iD+r  +++++         +  +Yd+++p    +e+++kfdv+v+DP
  gi|488600394|ref|YP_007906865.1| 158 KKVVAVDIDERLINFINKtaeeyglnVEALVYDVQQPFM--DEFRKKFDVFVTDP 210
                                       789999*****9899888787888884589999999976..89***********9 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.9
                   N6-adenineMlase  52 vlLleiDkrFealygeekfvfYdlnnpe 79 
                                        ++ ++ ++F ++y++e+  f+ +++++
  gi|488600394|ref|YP_007906865.1| 261 FIITDLRRHF-NIYPQEEKNFFRFQEKL 287
                                       4556666677.77777777777666655 PP

>> DUF1217  Protein of unknown function (DUF1217)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024       0.3      95     136 ..     133     175 ..      85     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                       T--SHHHHHTSHHHHHHHHTTTT----------TTHH.HHHHH CS
                           DUF1217  95 tltsaydiLgdkaLskvvntvlgLpatsgaadldkqa.alikk 136
                                       +l+s   ++gd+ L +++    gLp+++ a+d+d++  ++i+k
  gi|488600394|ref|YP_007906865.1| 133 ELNSRIFVVGDDDLLSIAASLTGLPKKVVAVDIDERLiNFINK 175
                                       566777799***********************99995155554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2030.02
//
Query:       gi|488600395|ref|YP_007906866.1|  [L=108]
Description: hypothetical protein Asulf_00866 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-15   57.6   0.0    1.9e-15   56.9   0.0    1.3  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
      0.088   12.3   0.0      0.095   12.2   0.0    1.1  1  Antigen_Bd37   Glycosylphosphatidylinositol-anchored merozoit


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 !   56.9   0.0   2.1e-19   1.9e-15       2      94 ..      12      98 ..      11      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.1e-19
                                      TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEE CS
                     Nitro_FeMo-Co  2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievyk 80
                                      g++++  FGra+yF+iy+++++e  +v  +   + +     +g + ++l++ +vd+v+v+ iG r+++ l+++gi+v++
  gi|488600395|ref|YP_007906866.1| 12 GKEISKYFGRARYFYIYDTKSQEGGLVRIP---YITVL---PGDALKFLESLNVDAVVVNTIGNRSREYLQKRGIKVLE 84
                                      7899**************************...77655...89999********************************* PP

                                      S-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co 81 gaggtveealkevl 94
                                      g +g+ve+++  ++
  gi|488600395|ref|YP_007906866.1| 85 GFDGKVEDIISNFI 98
                                      **********9886 PP

>> Antigen_Bd37  Glycosylphosphatidylinositol-anchored merozoite surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.1e-05     0.095      37      83 ..      42      98 ..      33     108 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                      Antigen_Bd37 37 flrvvdtdll.....lkvdsakvekaGkkvkaylesiGik.....gesveesldnlm 83
                                      ++ v+ +d l     l+vd   v+  G++ + yl++ Gik     +++ve+ + n++
  gi|488600395|ref|YP_007906866.1| 42 YITVLPGDALkflesLNVDAVVVNTIGNRSREYLQKRGIKvlegfDGKVEDIISNFI 98
                                      66666666655555589**********************955555677777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 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:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 776.73
//
Query:       gi|488600396|ref|YP_007906867.1|  [L=674]
Description: Acyl-CoA synthetase (NDP forming) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-66  222.0   1.4    8.8e-66  221.5   1.4    1.2  1  ATP-grasp_5    ATP-grasp domain
    9.9e-44  148.5   0.2      2e-43  147.5   0.1    1.6  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.9e-25   89.6   0.1    6.2e-24   84.7   0.0    2.8  2  CoA_binding_2  CoA binding domain
    2.5e-16   60.1   0.3    2.3e-15   57.0   0.0    2.7  3  CoA_binding    CoA binding domain
      0.002   17.7   0.8     0.0053   16.3   0.8    1.8  1  ATP-grasp_2    ATP-grasp domain
     0.0057   16.2   0.0      0.012   15.1   0.0    1.5  1  CPSase_L_D2    Carbamoyl-phosphate synthase L chain, ATP bind
  ------ inclusion threshold ------
      0.052   14.4   0.0       0.45   11.3   0.0    2.5  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
       0.12   12.5   0.4        5.3    7.3   0.1    2.7  2  DUF5442        Family of unknown function (DUF5442)


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 !  221.5   1.4   3.9e-69   8.8e-66       9     221 ..       3     205 ..       1     206 [. 0.97

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 3.9e-69
                       ATP-grasp_5   9 lLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeil 85 
                                        L e e+k++le+ygi++++  +a++++eave+a++igypvv+K++s++i+hK+dvgGv lnl+++eevr+ +++++
  gi|488600396|ref|YP_007906867.1|   3 FLMENEVKDILEDYGIKTAKCLFARDEDEAVEYAKQIGYPVVMKVASRKIIHKSDVGGVLLNLNSEEEVRQGFRKLI 79 
                                       689*************************************************************************9 PP

                       ATP-grasp_5  86 ervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertk 162
                                       +        + +egv Vq+  k +g+E+ivgv+e ++FG v++fGlGG+ vevlkdv+++l pl++++a+e+++++k
  gi|488600396|ref|YP_007906867.1|  80 SI-------KDVEGVNVQPALK-KGIEVIVGVSENEQFGSVVMFGLGGVFVEVLKDVSMRLLPLSRKDAEEMVKEIK 148
                                       86.......469********98.9***************************************************** PP

                       ATP-grasp_5 163 askllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarir 221
                                        ++ll+g+r+  k d++al++ll++l + v++ ++I e+d+nP++v+e+g  ++Dar +
  gi|488600396|ref|YP_007906867.1| 149 GYRLLEGYRNY-KGDVKALVDLLLKLNDVVEE-QNIIEMDLNPIFVYEDGYAVADARAV 205
                                       ***********.********************.8899*******************976 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.0       6.8   1.5e+04      16      35 ..     298     317 ..     288     322 .. 0.66
   2 !  147.5   0.1     9e-47     2e-43       2     138 .]     371     507 ..     370     507 .. 0.97

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 6.8
                      Succ_CoA_lig  16 alldwaasrglgfskvvslG 35 
                                       ++++++a+++++ + +vs G
  gi|488600396|ref|YP_007906867.1| 298 QVMEQCAEKHVKGAVIVSSG 317
                                       56666666666666666665 PP

  == domain 2  score: 147.5 bits;  conditional E-value: 9e-47
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasr..glgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaar 76 
                                       G+i++++q G ++  +++++a++  ++gfsk+v +Gn++dv+  ++l++l +d++tkvi++y+E++++gr+f ++ r
  gi|488600396|ref|YP_007906867.1| 371 GDIGIVAQTGLFLGIIMAHVATShpSIGFSKIVGMGNKIDVEDYEVLDFLLDDEKTKVIGMYIEGLKNGRSFYEISR 447
                                       89*********999999998887456*************************************************** PP

                      Succ_CoA_lig  77 raarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       +a   kp+vv+ksGrs+ g++aa+sht+++ g+d+v++a+++qa ++rv+s+ee+f++++++
  gi|488600396|ref|YP_007906867.1| 448 EAE--KPIVVFKSGRSDYGKKAAMSHTASICGDDEVFSAMCKQANITRVYSFEEMFNVTKAF 507
                                       **8..*****************************************************9986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.15   3.4e+02      72     107 ..       9      45 ..       4      53 .. 0.83
   2 !   84.7   0.0   2.8e-27   6.2e-24       2     114 ..     228     352 ..     227     354 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.15
                                       HHHHHHH.--SEEEE-TT---HHHHHHHHHTT-EEE. CS
                     CoA_binding_2  72 vkealal.gakavwlqpgsedeeaaelaeeagirvvg 107
                                       vk++l+  g+k++ +  +  ++ea+e+a++ g +vv+
  gi|488600396|ref|YP_007906867.1|   9 VKDILEDyGIKTAKCLFARDEDEAVEYAKQIGYPVVM 45 
                                       66664444999999999999**********9999997 PP

  == domain 2  score: 84.7 bits;  conditional E-value: 2.8e-27
                                       -EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkea 75 
                                       ++a++Gas + gk+gy ++ +l++   +g +++pVnp++++il  k+y+s+ + p ++d++ +++p++ +p++++++
  gi|488600396|ref|YP_007906867.1| 228 SVAIIGASRTVGKPGYNIVWNLKQhgfRG-RIYPVNPNADKILDYKCYPSILDIPDEIDMAIIAVPAKLVPQVMEQC 303
                                       79**********************44444.8*********************868********************** PP

                                       HHH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  76 lalgakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       +++++k++++ ++          ++++ ++e+a++ gir+ g++ ++v 
  gi|488600396|ref|YP_007906867.1| 304 AEKHVKGAVIVSSgfseegeigaEYERRVLEIAKSSGIRIFGPNTTGVL 352
                                       **********9999********************************997 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   2.4e+03      25      51 ..      92     115 ..      83     147 .. 0.54
   2 !   57.0   0.0     1e-18   2.3e-15       3      96 .]     226     317 ..     224     317 .. 0.96
   3 ?   -3.1   0.0         6   1.3e+04      43      59 ..     645     661 ..     636     666 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                                       HHHECEEEEEEC-TTTTTCEETTEEEE CS
                       CoA_binding  25 klkygikavfgvnprkvgtevlglpvy 51 
                                        lk gi++++gv+++   ++ + + ++
  gi|488600396|ref|YP_007906867.1|  92 ALKKGIEVIVGVSEN---EQFGSVVMF 115
                                       455566666666665...333333333 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 1e-18
                                       TEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHH CS
                       CoA_binding   3 dtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqe 77 
                                       + +v++iGa+++ ++ +   +++ ++ g++  +++vnp+  ++++l+ ++y+s+ +++++  +d+a+i+vPa+ + +
  gi|488600396|ref|YP_007906867.1| 226 PESVAIIGASRTVGKPGyNIVWNLKQHGFRgRIYPVNPN--ADKILDYKCYPSILDIPDE--IDMAIIAVPAKLVPQ 298
                                       579**************88899********9********..*******************..*************** PP

                                       HHHHHHHTT-SEEEEESST CS
                       CoA_binding  78 avdelveagikgiviiteg 96 
                                       ++++++e+ +kg+vi+++g
  gi|488600396|ref|YP_007906867.1| 299 VMEQCAEKHVKGAVIVSSG 317
                                       ***************9876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6
                                       CEETTEEEESCHHHHHH CS
                       CoA_binding  43 tevlglpvyksvdelee 59 
                                        e +g pvy+++ ++++
  gi|488600396|ref|YP_007906867.1| 645 YEFNGFPVYPDIITAVN 661
                                       67889999988877665 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.8   2.4e-06    0.0053       2      78 ..       4      81 ..       3     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-06
                                      E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEE.E--SSSTCCCTTCEEE.ESSHHHHHHHHHCCTTS CS
                       ATP-grasp_2  2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvK.aQvlaGGRGKagGvkl.vkskeeakeaakellgk 78
                                      l E + k+il++yg+k+++   a++++ea e ak++g  + v+K a  ++  +   gGv l  +s+ee+++  ++l++ 
  gi|488600396|ref|YP_007906867.1|  4 LMENEVKDILEDYGIKTAKCLFARDEDEAVEYAKQIGYPV-VMKvASRKIIHKSDVGGVLLnLNSEEEVRQGFRKLISI 81
                                      678899********************************99.55526667777777888876356778888888888764 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.3e-06     0.012       5      46 ..       9      48 ..       6      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.3e-06
                                      HHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEET CS
                       CPSase_L_D2  5 akealkkinvpvvpssaapvetleealaiakeigyPviikaa 46
                                       k++l++ ++++++   a  ++++ea++ ak+igyPv++k a
  gi|488600396|ref|YP_007906867.1|  9 VKDILEDYGIKTAKCLFA--RDEDEAVEYAKQIGYPVVMKVA 48
                                      677888899999999888..9******************987 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.45       3      90 ..     229     313 ..     228     315 .. 0.75
   2 ?   -1.0   0.0       1.3     3e+03      51      72 ..     582     604 ..     534     611 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                       EEEETTSHH.HHHHHH.HHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   3 vaiiGaGki.gskhlr.plnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthee 77 
                                       vaiiGa +  g++  +  +n +  ++   + + p +++a+++   ++ ++y ++ ++++  eid++i+a+p+++  +
  gi|488600396|ref|YP_007906867.1| 229 VAIIGASRTvGKPGYNiVWNLK--QHGFRGRIYPVNPNADKI---LDYKCYPSILDIPD--EIDMAIIAVPAKLVPQ 298
                                       7888887777554432034444..444555566666677776...8999**********..**************** PP

                                       HHHHHHHTT-..EEE CS
                      GFO_IDH_MocA  78 lakaaleagk..hvl 90 
                                       ++++++e+++  +v+
  gi|488600396|ref|YP_007906867.1| 299 VMEQCAEKHVkgAVI 313
                                       ******999877777 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                                       ESS.HHHHHTCTTESEEEE-S-G CS
                      GFO_IDH_MocA  51 ysd.leelladpeidavivatpn 72 
                                       y+  +++ll+d+++d ++va+++
  gi|488600396|ref|YP_007906867.1| 582 YDTaINALLSDENVDSLVVAMWA 604
                                       333688999999***99999875 PP

>> DUF5442  Family of unknown function (DUF5442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0024       5.3      41      70 ..       6      35 ..       1      41 [. 0.87
   2 ?    2.3   0.0     0.083   1.9e+02       5      32 ..     348     373 ..     345     379 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0024
                           DUF5442 41 keklkeylkdisirtvnciikrfeddpqay 70
                                       +++k+ l d  i+t++c++ r ed+   y
  gi|488600396|ref|YP_007906867.1|  6 ENEVKDILEDYGIKTAKCLFARDEDEAVEY 35
                                      5789*********************98777 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.083
                           DUF5442   5 tcgavsengandflkfvakgaiikygdi 32 
                                       t g+++  + n f++  ak  iik gdi
  gi|488600396|ref|YP_007906867.1| 348 TTGVLN--TDNGFITTFAKMPIIKVGDI 373
                                       667776..7899***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (674 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 4095.93
//
Query:       gi|488600397|ref|YP_007906868.1|  [L=747]
Description: ERCC4-like helicase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   93.3   0.6    5.1e-25   88.0   0.1    3.4  3  Helicase_C      Helicase conserved C-terminal domain
    1.8e-20   73.7   0.1    5.1e-20   72.2   0.1    1.8  1  ERCC4           ERCC4 domain
      7e-18   65.0   0.1    9.8e-17   61.3   0.0    2.4  2  DEAD            DEAD/DEAH box helicase
    2.6e-16   60.1   0.0    1.8e-15   57.3   0.0    2.4  2  ResIII          Type III restriction enzyme, res subunit
    4.6e-14   52.7   0.6    3.3e-13   50.0   0.2    2.6  2  HHH_5           Helix-hairpin-helix domain
    1.7e-12   47.2   0.0    4.9e-11   42.6   0.0    2.7  2  HHH_2           Helix-hairpin-helix motif
    1.6e-05   24.5   0.2    9.4e-05   22.1   0.2    2.4  2  HHH             Helix-hairpin-helix motif
     0.0031   17.8   0.1      0.016   15.6   0.1    2.3  2  HHH_8           Helix-hairpin-helix domain
     0.0041   16.4   0.1      0.009   15.2   0.1    1.5  1  ERCC3_RAD25_C   ERCC3/RAD25/XPB C-terminal helicase
     0.0086   16.3   0.0       0.04   14.2   0.0    2.2  1  HHH_3           Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.041   14.5   5.0        8.6    7.0   0.0    4.6  5  5_3_exonuc      5'-3' exonuclease, C-terminal SAM fold
        8.7    7.0   7.6        1.3    9.7   0.5    3.2  3  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac


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 ?    1.1   0.0      0.33     5e+02      11      58 ..      71     122 ..      60     166 .. 0.79
   2 !   88.0   0.1   3.4e-28   5.1e-25       2     110 ..     364     481 ..     363     482 .. 0.93
   3 ?   -1.1   0.0       1.6   2.4e+03      10      44 ..     529     564 ..     521     573 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.33
                                       HHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHH CS
                        Helicase_C  11 kleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereei 58 
                                        l + ggk+l  ++t+  +e+ +++l +k+    + ++++l ge+  ++r e 
  gi|488600397|ref|YP_007906868.1|  71 RLLNYGGKALFLAPTKPLVEQhAEFL-RKNlkidADEIITLSGEIGPEKRAEL 122
                                       456899***********999866666.44446667888999999999888765 PP

  == domain 2  score: 88.0 bits;  conditional E-value: 3.4e-28
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT........STHHHHHHHHHHHHTTSSSE CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhge........lpqnereeileqfnkgesdv 69 
                                       kle+++e lk  +++ ++++f++++d++e  vk l++ ++i++a++ g+        + q+e++e++e+f+kge++v
  gi|488600397|ref|YP_007906868.1| 364 KLEKIKEVLKGLKDDMRAIVFCTYRDTAEVlVKELNRLENIRAARFVGQssriddkgMRQKEQIEVVEKFRKGEFNV 440
                                       788899999999**************9986777776666999999999999999999******************** PP

                                       EEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  70 LiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       L+at+v+e+G+dip  +lVi++++  +  ++iqr+GRtgR+
  gi|488600397|ref|YP_007906868.1| 441 LVATSVGEEGLDIPATDLVIFYEAVPSEIRAIQRKGRTGRF 481
                                       ****************************************7 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.6
                                       HHHTTTTSEEEEEESSHHHHHH..HHHHHHHTTSTEE CS
                        Helicase_C  10 lkleeeggkilifvntidrlek..vklllekkgikva 44 
                                       +k+ ee ++++i+v ++++ +    +l+ ++ +ik+ 
  gi|488600397|ref|YP_007906868.1| 529 YKRPEESKEVVIYVDSREMKSGvvKELF-KHAEIKIR 564
                                       467789999********95533433444.34456665 PP

>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.1   3.4e-23   5.1e-20       1     154 [.     542     658 ..     542     660 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 3.4e-23
                                       EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCC..SH CS
                             ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikd..gr 75 
                                       +Dsre ksg+ ++l   + +e+ i++l+  dy ++   +++               v verk+a+d+++si++  + 
  gi|488600397|ref|YP_007906868.1| 542 VDSREMKSGVVKEL--FKHAEIKIRNLEAADY-VL---SDR---------------VGVERKTAEDFIDSITSadRN 597
                                       8******9999995..45568***********.**...9**...............***************88779* PP

                                       HHHHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHH CS
                             ERCC4  76 leeqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaew 152
                                       +++q+ +lk+ +y+kpil++eg + y r                i++++i +a++++++d +++i++t+++ etae+
  gi|488600397|ref|YP_007906868.1| 598 IFNQLLELKK-SYQKPILIIEG-ELYGR----------------IHPNAIRGAIAAIAVDLSIPIIQTKNEIETAEI 656
                                       **********.***********.77887................********************************9 PP

                                       HH CS
                             ERCC4 153 la 154
                                       l 
  gi|488600397|ref|YP_007906868.1| 657 LL 658
                                       85 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   6.6e-20   9.8e-17      12     174 ..      46     195 ..      35     197 .. 0.80
   2 ?    0.6   0.0      0.29   4.3e+02      43      94 ..     374     430 ..     349     450 .. 0.63

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 6.6e-20
                                       HTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  12 lgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaar 88 
                                       l  ++ lv  +TG GKT ++l  + ++++    + g kal+++Pt+ L+eq+++ l+k +k id  +  +++g+   
  gi|488600397|ref|YP_007906868.1|  46 L-LRNTLVVLPTGLGKTVIALYVIASRLL----NYGGKALFLAPTKPLVEQHAEFLRKNLK-IDADEIITLSGEIGP 116
                                       3.4899**********************5....6889************************.888888888888888 PP

                                       HHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  89 dqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqviv 164
                                       +++++l  g ++i+v+tp+ + + +  g+l+l++v  + +DEa+r   +    fi +   ++    +   ++  ++ 
  gi|488600397|ref|YP_007906868.1| 117 EKRAEL-YGmARIIVSTPQVIENDIIAGRLSLEDVVHITFDEAHRAVGNYSYVFIAKHYLET----A---KNPLILG 185
                                       888888.555************97778*******************9996666666633333....1...1223677 PP

                                       EESSBSHHHH CS
                                       xxxxxxxxxx RF
                              DEAD 165 lSATlpkdvk 174
                                       ++A + +d++
  gi|488600397|ref|YP_007906868.1| 186 ITASPGSDIE 195
                                       7776666665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.29
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET........TSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig........gvaardqlskl 94 
                                         k+  +a++ +  r  ae  +++l+++ +   +r+  ++g        g ++++q++++
  gi|488600397|ref|YP_007906868.1| 374 GLKDDMRAIVFCTYRDTAEVLVKELNRLEN---IRAARFVGqssriddkGMRQKEQIEVV 430
                                       467778899999999999999999988888...444444441112223344455555555 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 !   57.3   0.0   1.2e-18   1.8e-15      25     169 ..      48     190 ..      27     192 .. 0.81
   2 ?   -1.2   0.0       1.2   1.8e+03      68     118 ..     350     405 ..     300     442 .. 0.65

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1.2e-18
                                       SEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B--. CS
                            ResIII  25 krglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkkkak 97 
                                       ++ l++++TG GKT++a + ++ rll+ g+  k+lfl+p+k l+eq  e ++k l+ +++e    ++++  +k+ + 
  gi|488600397|ref|YP_007906868.1|  48 RNTLVVLPTGLGKTVIAlYVIASRLLNYGG--KALFLAPTKPLVEQHAEFLRKNLKIDADEiitLSGEIGPEKRAE- 121
                                       5889*************5555566666555..****************9999999999888666555566665555. PP

                                       ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH....HHT---SEEEEEESS- CS
                            ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei....lekfkeavllglTATp 169
                                             ++i+v+t q + +d+        +l+ +    i +DEaHr+ ++ s+  i    le  k+ ++lg+TA p
  gi|488600397|ref|YP_007906868.1| 122 --LYGMARIIVSTPQVIENDI-----IAGRLSLEDVVHITFDEAHRAVGNYSYVFIakhyLETAKNPLILGITASP 190
                                       ..8999***************.....99999999999************87888885555666699********98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                       HHHHHHGGGGTGG.....GEEEESSS-B--...........-SEEEEEHHHHHHTH CS
                            ResIII  68 eqtleefkkflseayke.igkkvsgdkkka....kekdstnkkilvttiqsldads 118
                                       e + +++k++++ ++ e i+++++g k++     +   ++++++lv + ++l +++
  gi|488600397|ref|YP_007906868.1| 350 EVMFKAMKCTIDHPKLEkIKEVLKGLKDDMraivFCTYRDTAEVLVKELNRLENIR 405
                                       44555556666655555566666666666655555555555555555555555555 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.3   3.4e+03      37      52 ..     573     588 ..     559     595 .. 0.68
   2 !   50.0   0.2   2.2e-16   3.3e-13       5      55 ..     692     741 ..     689     743 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.3
                                       HHTSTTS-HHHHHHHH CS
                             HHH_5  37 LakipGiGkktAerii 52 
                                       L++  G+  ktAe  i
  gi|488600397|ref|YP_007906868.1| 573 LSDRVGVERKTAEDFI 588
                                       5565677777777544 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 2.2e-16
                                       HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                        s+s iGp++A++ll++ ++++e +a adv+eL k+p +G ktA++i + l
  gi|488600397|ref|YP_007906868.1| 692 SSISNIGPVIARNLLKH-FKTIERIATADVDELVKVPKVGVKTAKKIREIL 741
                                       69***************.*****************************8865 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.22   3.3e+02      14      33 ..     389     408 ..     388     417 .. 0.91
   2 !   42.6   0.0   3.3e-14   4.9e-11       7      58 ..     693     744 ..     689     746 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.22
                             HHH_2  14 ktAklLakrFksldaLkkas 33 
                                        tA+ L+k+ + l+++++a 
  gi|488600397|ref|YP_007906868.1| 389 DTAEVLVKELNRLENIRAAR 408
                                       59***************997 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 3.3e-14
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFene 58 
                                       +I ++G   A++L k+Fk+++++++a+++eL++v+ +G ++A++i+e ++++
  gi|488600397|ref|YP_007906868.1| 693 SISNIGPVIARNLLKHFKTIERIATADVDELVKVPKVGVKTAKKIREILTTP 744
                                       699*******************************************998876 PP

>> HHH  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       4.8   7.2e+03      19      29 ..     697     707 ..     693     708 .. 0.81
   2 !   22.1   0.2   6.3e-08   9.4e-05       2      30 .]     712     740 ..     711     740 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.8
                                       -SHHHHHHHHH CS
                               HHH  19 VGpktAeaIls 29 
                                       +Gp  A+  l 
  gi|488600397|ref|YP_007906868.1| 697 IGPVIARNLLK 707
                                       9*****98775 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 6.3e-08
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIlsy 30 
                                       +e++ +a+++eL+++P VG ktA +I+++
  gi|488600397|ref|YP_007906868.1| 712 IERIATADVDELVKVPKVGVKTAKKIREI 740
                                       799***********************986 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.1   6.1e+03      48      61 ..     690     703 ..     680     707 .. 0.73
   2 !   15.6   0.1   1.1e-05     0.016      42      68 .]     715     742 ..     702     742 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.1
                                       HCTTSTT--HHHHH CS
                             HHH_8  48 eltklpgiGkkiaa 61 
                                        ++++ +iG+ ia+
  gi|488600397|ref|YP_007906868.1| 690 IVSSISNIGPVIAR 703
                                       56899****99997 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.1e-05
                                       HHHH..TTHCTTSTT--HHHHHHHHHHHH CS
                             HHH_8  42 itsl..eeeltklpgiGkkiaakieeile 68 
                                       i+++  +e l k+p +G k+a+ki+eil+
  gi|488600397|ref|YP_007906868.1| 715 IATAdvDE-LVKVPKVGVKTAKKIREILT 742
                                       33333244.******************95 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 !   15.2   0.1   6.1e-06     0.009      89     166 ..     421     502 ..     413     560 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.1e-06
                     ERCC3_RAD25_C  89 tseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksne......ee 159
                                       ++++e++++++kf+k  ++n+++   vg++ +D+P    +i  ++   s  +  qr Gr  r +k++        + 
  gi|488600397|ref|YP_007906868.1| 421 MRQKEQIEVVEKFRKG-EFNVLVATSVGEEGLDIPATDLVIFYEAV-PSEIRAIQRKGRTGRFRKGKIIvliakgTR 495
                                       57899*********87.89****************99999987765.566667899998888777532222332244 PP

                     ERCC3_RAD25_C 160 fnaffYs 166
                                        +a+++s
  gi|488600397|ref|YP_007906868.1| 496 DEAYYWS 502
                                       4555554 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.7e-05      0.04      18      64 ..     693     741 ..     690     742 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                             HHH_3  18 klpGlgpklAknIvayReknG..pfksreeLlkvkglgpktfeqlagfl 64 
                                        ++ +gp++A+n++++ +     + ++++eL+kv+++g kt  ++++ l
  gi|488600397|ref|YP_007906868.1| 693 SISNIGPVIARNLLKHFKTIEriATADVDELVKVPKVGVKTAKKIREIL 741
                                       6788999999999999888762255678899999999999999988765 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       2.6   3.9e+03      41      87 ..     197     240 ..     192     280 .. 0.68
   2 ?    1.3   0.0      0.35   5.3e+02      30      67 ..     390     427 ..     387     448 .. 0.66
   3 ?   -2.0   0.0       3.7   5.6e+03      25      53 ..     578     607 ..     577     655 .. 0.70
   4 ?    7.0   0.0    0.0058       8.6      21      46 ..     692     717 ..     687     720 .. 0.89
   5 ?    4.0   0.1     0.052        77      17      34 ..     720     737 ..     718     742 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.6
                        5_3_exonuc  41 leeilenldelkekklkekLeenkeearlskkLatiktdvplelele 87 
                                       ++e++enl  ++e ++++++  + +     k+++ ik d+p e  l+
  gi|488600397|ref|YP_007906868.1| 197 IKEVVENLG-IEEVEVRTEFDPDVKPYIHEKEIVWIKVDIPDE--LK 240
                                       555555554.445566777777777777777777777777744..33 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.35
                        5_3_exonuc  30 tAakLlkeygsleeilenldelkekklkekLeenkeea 67 
                                       tA  L+ke + le+i ++    +++++ +k  ++ke++
  gi|488600397|ref|YP_007906868.1| 390 TAEVLVKELNRLENIRAARFVGQSSRIDDKGMRQKEQI 427
                                       9999***********99542222233444444444444 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.7
                        5_3_exonuc  25 giGektAakLlkeygsle.eilenldelke 53 
                                       g+  ktA   +  + s + +i+++l elk+
  gi|488600397|ref|YP_007906868.1| 578 GVERKTAEDFIDSITSADrNIFNQLLELKK 607
                                       666788888888888876345665555554 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0058
                        5_3_exonuc  21 pGvpgiGektAakLlkeygsleeile 46 
                                         ++ iG+  A +Llk+++++e i  
  gi|488600397|ref|YP_007906868.1| 692 SSISNIGPVIARNLLKHFKTIERIAT 717
                                       56899*****************9965 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.052
                        5_3_exonuc  17 sDnipGvpgiGektAakL 34 
                                       +D++  vp++G ktA+k+
  gi|488600397|ref|YP_007906868.1| 720 VDELVKVPKVGVKTAKKI 737
                                       79999**********986 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 ?   -0.9   0.1       1.7   2.5e+03       1       8 [.      92      99 ..      92     105 .. 0.90
   2 ?    9.7   0.5   0.00086       1.3      23      83 ..     226     287 ..     223     300 .. 0.87
   3 ?   -1.7   0.1       3.1   4.6e+03      27      52 ..     663     688 ..     654     692 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                    HIP1_clath_bdg  1 HAdLLrKn 8 
                                      HA+ LrKn
  gi|488600397|ref|YP_007906868.1| 92 HAEFLRKN 99
                                      *******9 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00086
                    HIP1_clath_bdg  23 eeverekkeleeelerlkeeaerkleeqkeelekLkrele.akraelarlkssLesseqsge 83 
                                       +e+   k ++ +el++++e+ ++ le + + lekL  ++  +++ el  +++sL+  +++++
  gi|488600397|ref|YP_007906868.1| 226 KEIVWIKVDIPDELKDVREKFQKALEIRLKRLEKLGINVSyNTKRELLAIQESLQMMAMESK 287
                                       56777889999*************************998736789**********9988776 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.1
                    HIP1_clath_bdg  27 rekkeleeelerlkeeaerkleeqke 52 
                                       re+k l++e+   + ++++ l+eq+e
  gi|488600397|ref|YP_007906868.1| 663 REQKLLSREVAVHSGKTKMDLKEQQE 688
                                       67778888888888999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (747 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 4804.09
//
Query:       gi|488600398|ref|YP_007906869.1|  [L=198]
Description: Phosphatidylglycerophosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   48.1   0.9    1.5e-12   48.1   0.9    2.6  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.9   8.1e-17   1.5e-12       3      66 .]      36      98 ..      34      98 .. 0.92
   2 ?   -2.3   4.4      0.44   7.9e+03      10      21 ..     155     165 ..     103     188 .. 0.60

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 8.1e-17
                                      HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      Pn+iT+++l+ +++a +l+ ++  +++ i+++li+ ++D++DG lAR  +++++lG +lD++ D
  gi|488600398|ref|YP_007906869.1| 36 PNIITIASLITGIYAGYLI-YAGRIYWSIVVILISQILDCTDGDLARISGKITELGGYLDRIFD 98
                                      ****************988.44448*************************************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHGG CS
                   CDP-OH_P_transf  10 rlllsvlailll 21 
                                       r+++++l + l+
  gi|488600398|ref|YP_007906869.1| 155 RIAIVMLGL-LF 165
                                       444444444.23 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1190.85
//
Query:       gi|488600399|ref|YP_007906870.1|  [L=247]
Description: putative sugar nucleotidyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   52.4   0.0      1e-13   51.9   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    1.6e-12   47.5   0.0    2.6e-12   46.8   0.0    1.5  1  NTP_transferase  Nucleotidyl transferase
    3.3e-06   27.0   0.1    5.3e-06   26.3   0.1    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


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 !   51.9   0.0   1.7e-17     1e-13       1      96 [.       3     108 ..       3     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.7e-17
                                       EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC...TS-EEE-TT CS
                      NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggd..eevlaalarl...gvrvveded 67 
                                       +viLA+G +sR+g   +  +K ll++g+k+l++r+++++r+ g+ +vvvv+g+  + ++++l+     ++++v+++d
  gi|488600399|ref|YP_007906870.1|   3 VVILAAGLGSRLGhitStkPKSLLRIGDKTLIRRIINTIRKYGIMDVVVVTGYkdRMIREHLRNAynmNIEFVHNAD 79 
                                       69***********665267********************************9955466666654444489******9 PP

                                       SS.-SHHHHHHHHHHHH.SSSCEEEEETT- CS
                      NTP_transf_3  68 pg.kgplaslaaalraaadadavlvlacDm 96 
                                       ++ ++ ++sl+   +a+ +   ++++  D+
  gi|488600399|ref|YP_007906870.1|  80 YDiTNNIYSLYLSKDAL-SGGDFYIINSDV 108
                                       98799999999888887.455555555555 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   4.4e-16   2.6e-12       3     145 ..       4     138 ..       2     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 4.4e-16
                                       EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEE CS
                   NTP_transferase   3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlial 79 
                                       vILa G G+RL  +t+t +k l+ +++k +li   ++++ + gi + +vv+t ++  +++e+l++++++++e     
  gi|488600399|ref|YP_007906870.1|   4 VILAAGLGSRLGHITSTKPKSLLRIGDK-TLIRRIINTIRKYGIMD-VVVVTGYKDRMIREHLRNAYNMNIEFVHNA 78 
                                       9***************************.*****************.999999999***********9997777777 PP

                                       ESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-C CS
                   NTP_transferase  80 epegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveea 145
                                            +   +++l+++ l   +    + ++++D+l+ +++  ++   ++++   ++++ +v++ + 
  gi|488600399|ref|YP_007906870.1|  79 DYDITNNIYSLYLSKDALSGGD----FYIINSDVLFHEKIFSILHTSKKNGL--ILAVDVVKKLNR 138
                                       77777**************999....8*********9988877766555554..555555555554 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   8.9e-10   5.3e-06       2     136 ..       2     138 ..       1     153 [. 0.74

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.9e-10
                                       EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG..CCEEEEE- CS
                              IspD   2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld..ksiqlvaG 73 
                                        vvi AAG G+R++   + +pK +l + ++tl+ + ++++ +++ +d +vv   +d++   e+l  +   +i+ v+ 
  gi|488600399|ref|YP_007906870.1|   2 EVVILAAGLGSRLGhitSTKPKSLLRIGDKTLIRRIINTIRKYGIMDVVVVTGYKDRM-IREHLRNAynMNIEFVHN 77 
                                       69**********86333689***************************99999999984.445555555567899988 PP

                                       -S....SHHHHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSEEEE CS
                              IspD  74 Gd....eRaesVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDtikr 136
                                        d    +   s + + +al+g + +++  D    +l +++i+++l +++  ++g+ila+ v   + r
  gi|488600399|ref|YP_007906870.1|  78 ADyditNNIYSLYLSKDALSGGDFYIINSD----VLFHEKIFSILHTSK--KNGLILAVDVVKKLNR 138
                                       763222455677777788888865555544....567888888888777..4888888877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.31s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1621.16
//
Query:       gi|488600400|ref|YP_007906871.1|  [L=153]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  162.2   3.3    7.3e-48  162.0   3.3    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 !  162.0   3.3   4.1e-52   7.3e-48       2     140 .]       8     147 ..       7     147 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 4.1e-52
                           UPF0179   2 itLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekteheCavheegvvaveveeapiealie 78 
                                       itL+g+++A+ G+eF++ g  +eCekC+lk+ Cl+L+++ kY+iv++r+ t++eC++h++gvvavev+e+pi+al+e
  gi|488600400|ref|YP_007906871.1|   8 ITLCGRTWANIGVEFTFIGGRDECEKCRLKRPCLRLKENAKYKIVSLRDGTVQECPLHDGGVVAVEVVELPIIALLE 84 
                                       9**************************************************************************** PP

                           UPF0179  79 skkavegskitleseeCdevecesyelcepeglkegekvkivevlgeiee.ckkgrslkkvel 140
                                       skk veg+ki++e+++C+ ++c++y+lc+p++l +ge+v++++++g+ +  c+kg s+k vel
  gi|488600400|ref|YP_007906871.1|  85 SKKSVEGAKIRYEKKHCEIFNCSMYNLCHPAELMDGEEVVVEKIIGDSPGvCEKGLSVKVVEL 147
                                       ***********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1011.77
//
Query:       gi|488600401|ref|YP_007906872.1|  [L=309]
Description: ADP-ribosylglycohydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-68  230.5   0.0    3.9e-68  230.3   0.0    1.0  1  ADP_ribosyl_GH  ADP-ribosylglycohydrolase
  ------ inclusion threshold ------
      0.065   13.6   0.1       0.16   12.3   0.0    1.6  2  TetR_C_11       Tetracyclin repressor-like, C-terminal domain
          1    9.5   4.6        0.4   10.8   1.9    1.6  2  VMA21           VMA21-like domain


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 !  230.3   0.0   6.6e-72   3.9e-68       1     290 [.      10     278 ..      10     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 6.6e-72
                                       HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S-----STTTTT.S-TT---HHHHHHHHHHHTEET.TEE-HHHHH CS
                    ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelgetpdktgfghfg.lkpgewtddtqmalllleslleaggldpedla 76 
                                       G++lG a+GDAlG+p+e++  dei+r yg  +      +f++   lk+gewtddt++++ll+es++++  +dp+d+a
  gi|488600401|ref|YP_007906872.1|  10 GCILGTAIGDALGMPTEGLKLDEIKRIYGYVD------DFYPSPdLKAGEWTDDTEQMILLAESIIDRVYFDPDDFA 80 
                                       9****************************999......5555554******************************** PP

                                       HHHHH.HHT.....T--SS--HHHHHHHHHTTTT-...-S-B...---BTTTGGG-HHHHHHTSS-HHHHHHHHHHH CS
                    ADP_ribosyl_GH  77 rrflaeWlee.pgdteprgignttrealrnlksgepppeaganangsagngalmRaaplgllyagdpeeaaelaeea 152
                                       +++++ W e+ +    + ++g+ttr+alrnl +g ++ +ag     sa++ga mR+ap+gl+y+ + + + ++a+ +
  gi|488600401|ref|YP_007906872.1|  81 DKLRN-WAERaF----RIRTGPTTRQALRNLIAGMQWDKAGVD---SATCGASMRVAPVGLVYHFSINLVEKYAVIS 149
                                       **888.***766....999**********************98...******************************* PP

                                       HHTTB--HHHHHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........HHHH CS
                    ADP_ribosyl_GH 153 arlTHnhpeavagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaeeavde 229
                                       +++TH ++ a+ ga+a+a ++a +l   +++e l++    +++ + +  la+++++  ++ d++       ++av++
  gi|488600401|ref|YP_007906872.1| 150 SSITHKNSSAIGGAVAVAVAVACILSDFNEDEMLEEV--LKRTRTFDPLLADKIEYSMEIRDEGL------DYAVEK 218
                                       ************************************9..8999****************999888......9***** PP

                                       H--SSBHHHHHHHHHHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GGGS-H CS
                    ADP_ribosyl_GH 230 lgsggyavealaaalyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGleaiPe 290
                                       lg+++ + + +++++y+ ++ ++df  ++++ +n GgDtd++ aiaGal Ga yG++aiPe
  gi|488600401|ref|YP_007906872.1| 219 LGNSIMTWDVVPMSFYCYFS-SKDFYSSVTKGANAGGDTDSISAIAGALSGAKYGFKAIPE 278
                                       ********************.99*************************************8 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.6e-05      0.16       5      42 ..      77     114 ..      74     121 .. 0.90
   2 ?   -3.0   0.0       1.5   8.7e+03      30      50 ..     169     189 ..     163     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                         TetR_C_11   5 GslrgDLrallralaealaspragallrallaeaqrdp 42 
                                       +++++ Lr +++++ +  ++p ++++lr l+a +q d 
  gi|488600401|ref|YP_007906872.1|  77 DDFADKLRNWAERAFRIRTGPTTRQALRNLIAGMQWDK 114
                                       678899****************************9775 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                         TetR_C_11  30 llrallaeaqrdpelaealre 50 
                                       +++++l++  +d+ l+e l +
  gi|488600401|ref|YP_007906872.1| 169 AVACILSDFNEDEMLEEVLKR 189
                                       677777888888888777765 PP

>> VMA21  VMA21-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.9   6.8e-05       0.4      13      55 ..     126     172 ..     121     175 .. 0.76
   2 ?   -2.7   0.0       1.1   6.5e+03      21      28 ..     236     243 ..     228     266 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.8e-05
                             VMA21  13 mvtlPlasfftskhllfeg....vfglsnssatlysgvlAVivvnlv 55 
                                       m ++P+++ + +   l+e+     + +++++++ ++g++AV+v+ + 
  gi|488600401|ref|YP_007906872.1| 126 MRVAPVGLVYHFSINLVEKyaviSSSITHKNSSAIGGAVAVAVAVAC 172
                                       889**********9999994444445555888999999998887654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                             VMA21  21 fftskhll 28 
                                       +f sk++ 
  gi|488600401|ref|YP_007906872.1| 236 YFSSKDFY 243
                                       33333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2166.12
//
Query:       gi|488600402|ref|YP_007906873.1|  [L=151]
Description: cytidyltransferase-related domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-24   85.9   0.2    3.3e-24   85.7   0.2    1.0  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.028   14.8   0.2      0.042   14.2   0.2    1.4  1  Urm1             Urm1 (Ubiquitin related modifier)
      0.046   13.6   0.1       0.48   10.3   0.1    2.1  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.2   5.5e-28   3.3e-24       1     143 []      12     140 ..      12     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 5.5e-28
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       +a GtF +iH GHlr le+akkl++e liv+v+  +++k+k kp++++e+R + +e++k vd++i  d+ ++ +  +
  gi|488600402|ref|YP_007906873.1|  12 IATGTFEIIHPGHLRFLEEAKKLGDE-LIVIVARTKNVKHKPKPVIPEEQRRKVVEAIKFVDRAILGDENDIFK-PI 86 
                                       689***********************.*99999998888888*******************************7.88 PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                        +lkpd  ++v+g+d++ d   +k lee l+++++  ++++       +k +++++++Ss ki+++
  gi|488600402|ref|YP_007906873.1|  87 IELKPD--IIVLGHDQHFD---EKWLEEELRKRNVPAKVVR-------IKVKEPCEFCSSAKIIQA 140
                                       9999**..********999...8999****99999999888.......9**************985 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2     7e-06     0.042      24      71 ..      56     102 ..      33     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-06
                                       E-SSSSS-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEH CS
                              Urm1  24 leieseevnleeliayikknlikerkevFlekdkvrPGilvLindaDw 71 
                                       +  e+++ ++ e i+++ + ++ +++++F    +++P i+vL  d+ +
  gi|488600402|ref|YP_007906873.1|  56 I-PEEQRRKVVEAIKFVDRAILGDENDIFKPIIELKPDIIVLGHDQHF 102
                                       2.4788899999******************************888755 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   8.1e-05      0.48       8      39 ..      10      41 ..       4     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.1e-05
                           FAD_syn  8 avvtlGnFDGvHlGHqallkkaveaakekglp 39
                                       v++ G F  +H GH   l++a+++ +e  + 
  gi|488600402|ref|YP_007906873.1| 10 RVIATGTFEIIHPGHLRFLEEAKKLGDELIVI 41
                                      58999*******************99776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1183.46
//
Query:       gi|488600403|ref|YP_007906874.1|  [L=195]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-54  181.7  11.0    8.6e-30  102.7   3.3    2.0  2  DUF2250          Uncharacterized protein conserved in archaea
    1.8e-09   37.5   1.8    3.7e-05   23.5   0.2    2.1  2  DUF4423          Domain of unknown function (DUF4423)
    3.4e-08   33.2   0.0    0.00015   21.5   0.0    2.4  2  MarR_2           MarR family
    7.5e-06   25.7   0.1     0.0003   20.6   0.0    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm
    7.6e-06   26.3   2.3    1.9e-05   25.0   0.1    2.6  3  HTH_27           Winged helix DNA-binding domain
    1.8e-05   24.6   0.0      0.013   15.4   0.0    2.2  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
    0.00032   20.7   0.9       0.25   11.5   0.1    2.6  3  CtsR_C           CtsR C-terminal dimerization domain
    0.00052   19.9   1.7      0.016   15.1   0.5    2.7  2  HTH_36           Helix-turn-helix domain
    0.00056   19.7   0.9        1.1    9.2   0.1    2.4  2  HTH_5            Bacterial regulatory protein, arsR family
     0.0014   18.7   1.0      0.069   13.3   0.1    2.3  2  B-block_TFIIIC   B-block binding subunit of TFIIIC
     0.0017   18.2   2.2       0.64    9.9   0.3    2.4  2  TFIIE_alpha      TFIIE alpha subunit
     0.0025   16.8   0.1     0.0041   16.1   0.1    1.4  1  DUF2397          Protein of unknown function (DUF2397)
     0.0026   17.7   0.9      0.064   13.2   0.1    2.6  3  MarR             MarR family
     0.0079   16.4   1.0       0.25   11.6   0.1    2.7  2  Rio2_N           Rio2, N-terminal
     0.0082   16.0   1.6       0.12   12.2   0.4    2.7  2  HxlR             HxlR-like helix-turn-helix
  ------ inclusion threshold ------
       0.01   15.9   0.1       0.92    9.6   0.0    2.4  2  HTH_20           Helix-turn-helix domain
      0.012   15.6   0.1        1.2    9.1   0.1    3.0  3  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.012   15.7   2.6       0.45   10.5   0.3    2.2  2  Replic_Relax     Replication-relaxation
      0.013   15.3   0.1       0.13   12.0   0.0    2.4  2  HTH_IclR         IclR helix-turn-helix domain
      0.018   14.7   0.1       0.19   11.3   0.0    2.1  2  SMC_ScpB         Segregation and condensation complex subunit
      0.019   15.3   0.3       0.12   12.7   0.1    2.1  2  Rrf2             Transcriptional regulator
      0.043   13.8   0.8       0.45   10.5   0.0    2.4  2  Cdc6_C           CDC6, C terminal winged helix domain
       0.11   12.5   1.1       0.77    9.8   0.1    2.0  2  DUF480           Protein of unknown function, DUF480


Domain annotation for each model (and alignments):
>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   3.3   1.1e-32   8.6e-30       5      91 ..       6      92 ..       2      94 .. 0.95
   2 !   84.1   0.9   7.2e-27   5.6e-24       7      92 ..     108     193 ..     102     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 1.1e-32
                           DUF2250  5 eedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHtYYrlt 83
                                      + ++l++++l hl++an dYaksi+k ++i+++e++++lk+LeelGL++r +g++ikrt a++K+++evhkhHtYY lt
  gi|488600403|ref|YP_007906874.1|  6 KLSPLHIYILIHLRRANIDYAKSISKITKIDQQEIEKALKELEELGLIDRSHGSAIKRTAARFKLSHEVHKHHTYYCLT 84
                                      678899************************************************************************* PP

                           DUF2250 84 reGelllr 91
                                      r Ge++ r
  gi|488600403|ref|YP_007906874.1| 85 RLGEHTSR 92
                                      *****977 PP

  == domain 2  score: 84.1 bits;  conditional E-value: 7.2e-27
                           DUF2250   7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHtYYrlt 83 
                                        + al+++++l+ka+ ++a  +a+ + ++++ v++ll kL +lGLl + ++k++k++++k K+k+e+++hHtYYrl+
  gi|488600403|ref|YP_007906874.1| 108 YDAALDIIEYLAKAECEHAGWLARVFSMKVSDVQSLLTKLLDLGLLSECKAKVLKKKHRKGKPKKETRTHHTYYRLS 184
                                       56799************************************************************************ PP

                           DUF2250  84 reGelllre 92 
                                       r Ge++lr 
  gi|488600403|ref|YP_007906874.1| 185 RLGEMMLRY 193
                                       *******97 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   4.8e-08   3.7e-05      39      91 ..      26      76 ..       8      81 .. 0.83
   2 !   13.5   0.1   5.7e-05     0.044      37      89 ..     124     174 ..     108     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.8e-08
                           DUF4423 39 peelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevks 91
                                       ++++k+++  i+++e+ekal+ L++lgl++++    +++t + ++ s+ev +
  gi|488600403|ref|YP_007906874.1| 26 AKSISKITK--IDQQEIEKALKELEELGLIDRSHGSAIKRTAARFKLSHEVHK 76
                                      467999999..***********************************9999865 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.7e-05
                           DUF4423  37 adpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssev 89 
                                       +   +la+ +   +++++v++ l  Ll+lgll + +++ +++ +++ + ++e+
  gi|488600403|ref|YP_007906874.1| 124 EHAGWLARVFS--MKVSDVQSLLTKLLDLGLLSECKAKVLKKKHRKGKPKKET 174
                                       4789*******..***********************99999988877766666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     2e-07   0.00015       3      61 ..       7      63 ..       5      64 .. 0.92
   2 !    9.4   0.0    0.0012      0.93       9      55 ..     113     157 ..     106     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-07
                                      --HHHHHHHHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdl.tvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      l+p +  +L +L+r+    +  ++ + + ++++++ + ++lk+L++ GL+ r+ g++ kR
  gi|488600403|ref|YP_007906874.1|  7 LSPLHIYILIHLRRAN---IdYAKSISKITKIDQQEIEKALKELEELGLIDRSHGSAIKR 63
                                      789999*********9...55********************************9887666 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                                       HHHHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   9 rvLaaLgrrpgrdl.tvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       +++ +L+ ++   +  +g lar + ++ s v+ +l +L + GL+ +++
  gi|488600403|ref|YP_007906874.1| 113 DIIEYLAKAE---CeHAGWLARVFSMKVSDVQSLLTKLLDLGLLSECK 157
                                       5566666666...55899*************************98876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.9e-07    0.0003      25      58 ..      26      59 ..      13      84 .. 0.86
   2 ?    3.0   0.0      0.12        94      28      56 ..     129     157 ..     114     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.9e-07
                                      HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      a+ i+++++++++ + ++L++Le+ Gl++r++g+
  gi|488600403|ref|YP_007906874.1| 26 AKSISKITKIDQQEIEKALKELEELGLIDRSHGS 59
                                      789****************************998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                                       HCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB  28 iaeelgvprskvYevLrsLedkGlVerek 56 
                                       +a+      s v++ L +L+d Gl    k
  gi|488600403|ref|YP_007906874.1| 129 LARVFSMKVSDVQSLLTKLLDLGLLSECK 157
                                       566666677899***********977655 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 !   25.0   0.1   2.5e-08   1.9e-05       1      58 [.       7      63 ..       7      73 .. 0.87
   2 ?   -2.5   0.0       9.9   7.7e+03      34      43 ..      78      87 ..      71      98 .. 0.61
   3 ?    0.0   0.2       1.6   1.2e+03      37      48 ..     142     153 ..     129     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.5e-08
                            HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                      l+++++ +L ++r r + + ++ +++ ++++++ i ++lk+L+e GL+ r++  a +r
  gi|488600403|ref|YP_007906874.1|  7 LSPLHIYILIHLR-RANIDYAKSISKITKIDQQEIEKALKELEELGLIDRSHGSAIKR 63
                                      6789999******.**********************************8887665444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.9
                            HTH_27 34 hisyslkkLt 43
                                      h+ y+l +L 
  gi|488600403|ref|YP_007906874.1| 78 HTYYCLTRLG 87
                                      5556666653 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.6
                            HTH_27  37 yslkkLtekGLv 48 
                                       + l kL   GL+
  gi|488600403|ref|YP_007906874.1| 142 SLLTKLLDLGLL 153
                                       667888888888 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.7e-05     0.013      50      95 ..      20      65 ..      15      84 .. 0.81
   2 !    7.2   0.0    0.0058       4.5      55      92 ..     125     162 ..     116     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                   Phage_rep_org_N 50 enipytaemlalifnreletvrlaLkvlkdlelieisedkvikikn 95
                                      ++  + a+ ++ i++ + ++++ aLk l++l+li+ s+  +ik ++
  gi|488600403|ref|YP_007906874.1| 20 RANIDYAKSISKITKIDQQEIEKALKELEELGLIDRSHGSAIKRTA 65
                                      555566899***************************9998888665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0058
                   Phage_rep_org_N  55 taemlalifnreletvrlaLkvlkdlelieisedkvik 92 
                                        a  la +f+ ++++v+  L+ l dl+l+   + kv+k
  gi|488600403|ref|YP_007906874.1| 125 HAGWLARVFSMKVSDVQSLLTKLLDLGLLSECKAKVLK 162
                                       56679***********************9988787776 PP

>> CtsR_C  CtsR C-terminal dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00033      0.25      12      45 ..      31      63 ..      21      76 .. 0.82
   2 ?   -2.6   0.0       8.1   6.3e+03      19      30 ..     108     119 ..      94     122 .. 0.70
   3 !    7.1   0.0    0.0074       5.7      20      44 ..     138     162 ..     134     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                            CtsR_C 12 sigdsiseqdaeaiiqrLleegliterEakLmka 45
                                      +i  +i++q++e+ ++ L e gli++  ++ +k 
  gi|488600403|ref|YP_007906874.1| 31 KIT-KIDQQEIEKALKELEELGLIDRSHGSAIKR 63
                                      454.5********************998887775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.1
                            CtsR_C  19 eqdaeaiiqrLl 30 
                                       + +a +ii+ L 
  gi|488600403|ref|YP_007906874.1| 108 YDAALDIIEYLA 119
                                       567788888886 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0074
                            CtsR_C  20 qdaeaiiqrLleegliterEakLmk 44 
                                       +d+++++ +Ll+ gl++e  ak++k
  gi|488600403|ref|YP_007906874.1| 138 SDVQSLLTKLLDLGLLSECKAKVLK 162
                                       799******************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 !   15.1   0.5   2.1e-05     0.016      29      55 .]      27      53 ..       5      53 .. 0.90
   2 ?    3.1   0.0      0.12        91      31      55 .]     129     153 ..     126     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                      + ++k ++++ + + +a+keLe+lG+i
  gi|488600403|ref|YP_007906874.1| 27 KSISKITKIDQQEIEKALKELEELGLI 53
                                      569999*******************98 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                            HTH_36  31 lakrlglsknTvsraikeLeqlGyi 55 
                                       la+ + ++++ v++ + +L +lG++
  gi|488600403|ref|YP_007906874.1| 129 LARVFSMKVSDVQSLLTKLLDLGLL 153
                                       677788999**************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 !    9.2   0.1    0.0014       1.1       7      46 ..      14      54 ..       8      55 .. 0.82
   2 !    9.2   0.0    0.0014       1.1       5      46 ..     112     154 ..     109     155 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                      HHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  7 ILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      IL  L++ +  ++  +++++++ q  +   Lk L+e+GL++
  gi|488600403|ref|YP_007906874.1| 14 ILIHLRRANiDYAKSISKITKIDQQEIEKALKELEELGLID 54
                                      555566644467889************************96 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                                       HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   5 lkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       l+I+ +La+ e   ++ la+ + +  s v   L kL ++GL++
  gi|488600403|ref|YP_007906874.1| 112 LDIIEYLAKAEcEHAGWLARVFSMKVSDVQSLLTKLLDLGLLS 154
                                       89*******99899***************************86 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   8.9e-05     0.069      22      67 ..      27      82 ..      25      85 .. 0.80
   2 ?    3.9   0.1     0.075        58      24      53 ..     129     158 ..     127     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.9e-05
                    B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqsii..........dsatkksistsll 67
                                      ++++k++k+d   + + lk Le+ gLI +               s++ ++++t+ +
  gi|488600403|ref|YP_007906874.1| 27 KSISKITKIDQQEIEKALKELEELGLIDRSHGSaikrtaarfkLSHEVHKHHTYYC 82
                                      5789***********************99877666777777766666677777666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.075
                    B-block_TFIIIC  24 LakeskqdprslfyrlksLekkgLIvkqsi 53 
                                       La+++ ++++++ ++l +L + gL    ++
  gi|488600403|ref|YP_007906874.1| 129 LARVFSMKVSDVQSLLTKLLDLGLLSECKA 158
                                       788999*****************9876555 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.3   0.00082      0.64      32      61 ..      28      57 ..      11     101 .. 0.74
   2 !    8.0   0.1    0.0032       2.5      13      76 ..     109     183 ..      96     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00082
                                      HHHHHHTS-HHHHHHHHHHHHHCTSEEEEE CS
                       TFIIE_alpha 32 dlakelkidlnelrklLnrLyearlvkykr 61
                                       ++k +kid++e+ k+L +L e +l++   
  gi|488600403|ref|YP_007906874.1| 28 SISKITKIDQQEIEKALKELEELGLIDRSH 57
                                      58999*********************9654 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE...........TTTEEEEEEEEE CS
                       TFIIE_alpha  13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd...........eekswykyywri 76 
                                       + a  +++ L++  +     la+  +++   + +lL +L + +l +  +++             e+ + + y+r+
  gi|488600403|ref|YP_007906874.1| 109 DAALDIIEYLAKAECEHAGWLARVFSMKVSDVQSLLTKLLDLGLLSECKAKVlkkkhrkgkpkKETRTHHTYYRL 183
                                       5566788888877777778899999****************9998754444333344556777777777777775 PP

>> DUF2397  Protein of unknown function (DUF2397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.3e-06    0.0041      30     110 ..      18     103 ..      11     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                           DUF2397  30 LrpedvlarlkedpefedyteeqlqadLdqLveWgnLeasqdtsrvttieefk......rkrfrYqltpagvevera 100
                                       Lr + +  + k+    ++ ++++++++L++L+e g +++s+  +  +t + fk      + +  Y lt++g+   r+
  gi|488600403|ref|YP_007906874.1|  18 LRRANIDYA-KSISKITKIDQQEIEKALKELEELGLIDRSHGSAIKRTAARFKlshevhKHHTYYCLTRLGEHTSRM 93 
                                       555555444.67778889999*********************9966666666422222288999************* PP

                           DUF2397 101 veeleealge 110
                                       +++l+    +
  gi|488600403|ref|YP_007906874.1|  94 LRDLLGDYLS 103
                                       ***9987665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   8.2e-05     0.064       6      51 ..      12      57 ..       7      63 .. 0.82
   2 ?   -2.9   0.0       8.4   6.6e+03      34      41 ..      90      97 ..      81      99 .. 0.63
   3 ?    2.3   0.0       0.2   1.6e+02      23      47 ..     129     153 ..     111     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.2e-05
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      + iL  l++ +  + + + k  ++++  + ++l++Le+ Gli+Rs+
  gi|488600403|ref|YP_007906874.1| 12 IYILIHLRRANIDYAKSISKITKIDQQEIEKALKELEELGLIDRSH 57
                                      5566666666666778999999**********************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.4
                                      HHHHHHHH CS
                              MarR 34 vtrvldrL 41
                                      ++r+l+ L
  gi|488600403|ref|YP_007906874.1| 90 TSRMLRDL 97
                                      56666655 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.2
                                       HHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  23 LakklgvskstvtrvldrLekkGli 47 
                                       La+ ++++ s v  +l++L + Gl+
  gi|488600403|ref|YP_007906874.1| 129 LARVFSMKVSDVQSLLTKLLDLGLL 153
                                       899999999999999****999997 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00033      0.25      28      57 ..      27      56 ..      16      64 .. 0.88
   2 ?    2.9   0.0      0.17   1.3e+02      31      60 ..     130     159 ..     112     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                            Rio2_N 28 elieeisrlkeeevkkrlsrllkaklisrk 57
                                      + i++i++++++e++k+l++l + +li r+
  gi|488600403|ref|YP_007906874.1| 27 KSISKITKIDQQEIEKALKELEELGLIDRS 56
                                      6899***********************995 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                            Rio2_N  31 eeisrlkeeevkkrlsrllkaklisrktak 60 
                                       +++ ++k ++v++ l +ll+ +l+s  +ak
  gi|488600403|ref|YP_007906874.1| 130 ARVFSMKVSDVQSLLTKLLDLGLLSECKAK 159
                                       566789999***************996654 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.4   0.00015      0.12       9      54 ..      13      58 ..      10     105 .. 0.78
   2 ?   -1.1   0.0       2.3   1.8e+03      58      72 ..     176     190 ..     152     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevy 54
                                       il++l + +  + +   ++ ki q+ + + L+eLe+ gli+r+  
  gi|488600403|ref|YP_007906874.1| 13 YILIHLRRANIDYAKSISKITKIDQQEIEKALKELEELGLIDRSHG 58
                                      688888888888888888999*********************9864 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                                       S-EEEEEE-TCGGGG CS
                              HxlR  58 PpkveYsltekGrsl 72 
                                         +  Y+l+  G+ +
  gi|488600403|ref|YP_007906874.1| 176 THHTYYRLSRLGEMM 190
                                       345668888888765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0012      0.92      27      56 ..      26      55 ..       7      59 .. 0.80
   2 ?    3.9   0.0      0.07        54      12      55 ..     111     154 ..     101     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                      HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 27 aselaerldlskntlsyHLrvLeeagLvev 56
                                      a+ + +   ++++++ + L++Lee gL+++
  gi|488600403|ref|YP_007906874.1| 26 AKSISKITKIDQQEIEKALKELEELGLIDR 55
                                      66677777899*****************87 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.07
                                       HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                        ++i  +La ae+  a+ la+ ++++ + +   L +L + gL+ 
  gi|488600403|ref|YP_007906874.1| 111 ALDIIEYLAKAECEHAGWLARVFSMKVSDVQSLLTKLLDLGLLS 154
                                       5899************************************9986 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 ?    9.1   0.1    0.0016       1.2      27      55 ..      29      57 ..      26      66 .. 0.79
   2 ?    0.2   0.0      0.99   7.7e+02      36      45 ..      88      97 ..      87     111 .. 0.87
   3 ?    1.8   0.0       0.3   2.4e+02      27      53 ..     129     155 ..     128     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                                      HHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2 27 lAsmlGltretvsrilseLkreglisrgr 55
                                      ++ +  + ++ + ++l+eL++ gli+r++
  gi|488600403|ref|YP_007906874.1| 29 ISKITKIDQQEIEKALKELEELGLIDRSH 57
                                      5666777889999*************753 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.99
                                      HHHHHHHHHH CS
                         HTH_Crp_2 36 etvsrilseL 45
                                      e++sr+l++L
  gi|488600403|ref|YP_007906874.1| 88 EHTSRMLRDL 97
                                      899*****98 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.3
                                       HHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2  27 lAsmlGltretvsrilseLkreglisr 53 
                                       lA+   +  + v  +l++L + gl+s 
  gi|488600403|ref|YP_007906874.1| 129 LARVFSMKVSDVQSLLTKLLDLGLLSE 155
                                       788899999999************995 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00058      0.45      14      65 ..      28      87 ..      15     108 .. 0.71
   2 ?    5.5   0.1      0.02        16      14      68 ..     128     190 ..     115     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00058
                      Replic_Relax 14 qiarllfashratarrrLarLrelgllsr.lrkrvggarg........gsepyvYaLtpkG 65
                                       i +++  +++  + ++L++L+elgl++r +   +++ ++         ++++ Y Lt +G
  gi|488600403|ref|YP_007906874.1| 28 SISKITKIDQQE-IEKALKELEELGLIDRsHGSAIKRTAArfklshevHKHHTYYCLTRLG 87
                                      567777777888.99**************88777766666444444444444444444444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                      Replic_Relax  14 qiarllfashratarrrLarLrelgllsr.lrkrvggarg........gsepyvYaLtpkGarl 68 
                                        +ar++ ++++  +++ L++L +lglls    k  +++++         ++++ Y L  +G+ +
  gi|488600403|ref|YP_007906874.1| 128 WLARVFSMKVSD-VQSLLTKLLDLGLLSEcKAKVLKKKHRkgkpkketRTHHTYYRLSRLGEMM 190
                                       689999999999.***************976666666666666766666666667777777655 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.93   7.2e+02      39      50 ..      44      55 ..      40      57 .. 0.85
   2 ?   12.0   0.0   0.00017      0.13       5      49 ..     111     154 ..     109     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.93
                                      HHHHHHTTSEE. CS
                          HTH_IclR 39 LqtLvelGyveq 50
                                      L+ L+elG++ +
  gi|488600403|ref|YP_007906874.1| 44 LKELEELGLIDR 55
                                      789*****9976 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00017
                                       HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR   5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       al+i+++la+a  e     lAr + +  S v  lL  L  lG++ 
  gi|488600403|ref|YP_007906874.1| 111 ALDIIEYLAKAECE-HAGWLARVFSMKVSDVQSLLTKLLDLGLLS 154
                                       89***********9.8***************************95 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.19      17      61 ..      27      72 ..      15     107 .. 0.81
   2 ?    1.7   0.0      0.23   1.8e+02     105     130 ..     134     159 ..     110     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                          SMC_ScpB 17 eeLakilelskeeveealeeLkeey.eeedrglelvevaggyrlvt 61
                                      ++++ki++++++e+e+al+eL+e    ++++g  ++++a +++l  
  gi|488600403|ref|YP_007906874.1| 27 KSISKITKIDQQEIEKALKELEELGlIDRSHGSAIKRTAARFKLSH 72
                                      6789999999999999999998864378888999999999888764 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.23
                          SMC_ScpB 105 eiRGvnsdsvvrtLlerglieekgrk 130
                                       +++ ++++s++ +Ll+ gl +e++ k
  gi|488600403|ref|YP_007906874.1| 134 SMKVSDVQSLLTKLLDLGLLSECKAK 159
                                       45556688888888888888877654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00016      0.12      12      61 ..      13      59 ..       4      74 .. 0.84
   2 ?    0.1   0.0       1.3     1e+03       8      55 ..     109     153 ..     104     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                       +l++L + + +    +++i++ ++i ++ +ek l++L++ gl+    G 
  gi|488600403|ref|YP_007906874.1| 13 YILIHLRRANIDY---AKSISKITKIDQQEIEKALKELEELGLIDRSHGS 59
                                      4555665555555...899*************************998886 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              Rrf2   8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglv 55 
                                       + al ++ yLak e e+   +  +a+ ++++ s ++ +l+kL   gl+
  gi|488600403|ref|YP_007906874.1| 109 DAALDIIEYLAKAECEH---AGWLARVFSMKVSDVQSLLTKLLDLGLL 153
                                       67888888998888876...7788888888888888888888887776 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 ?   10.5   0.0   0.00057      0.45      33      65 ..      31      63 ..      24      85 .. 0.82
   2 ?    1.3   0.2      0.43   3.4e+02      38      58 ..     136     156 ..     130     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00057
                                      T-----HHHHHHHHHHHHHTTSEEEEEEE-CC. CS
                            Cdc6_C 33 gvdpltqrevsdllseLemlgileleksskGrr 65
                                       +++++q+e+ + l+eLe lg++++ ++s  +r
  gi|488600403|ref|YP_007906874.1| 31 KITKIDQQEIEKALKELEELGLIDRSHGSAIKR 63
                                      688999*******************99877665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.43
                                       -HHHHHHHHHHHHHTTSEEEE CS
                            Cdc6_C  38 tqrevsdllseLemlgilele 58 
                                       + + v++ll++L +lg+l+  
  gi|488600403|ref|YP_007906874.1| 136 KVSDVQSLLTKLLDLGLLSEC 156
                                       567899999999999999755 PP

>> DUF480  Protein of unknown function, DUF480
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00099      0.77      43      91 ..      32      78 ..      25     131 .. 0.85
   2 ?    1.9   0.1      0.27   2.1e+02      43      81 ..     132     167 ..     120     193 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00099
                                      -----HHHHHHHHHHHHHTTSEEEE..--SS--EEEE-HHHHHT--HHH CS
                            DUF480 43 vmelsesevqealdeLkkkklvseaseagsRvekyehrleealklseae 91
                                      +++++++e+++al+eL++ +l+ ++  +gs +++   r++ ++++++++
  gi|488600403|ref|YP_007906874.1| 32 ITKIDQQEIEKALKELEELGLIDRS--HGSAIKRTAARFKLSHEVHKHH 78
                                      6789*******************99..8888888888888888777665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.27
                                       -----HHHHHHHHHHHHHTTSEEEE..--SS--EEEE-H CS
                            DUF480  43 vmelsesevqealdeLkkkklvseaseagsRvekyehrl 81 
                                       v +++ s+vq+ l++L + +l+se    +++v k +hr 
  gi|488600403|ref|YP_007906874.1| 132 VFSMKVSDVQSLLTKLLDLGLLSEC---KAKVLKKKHRK 167
                                       7788999999******999999987...44555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1252  (0.069831); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1199.41
//
Query:       gi|488600404|ref|YP_007906875.1|  [L=147]
Description: hypothetical protein Asulf_00875 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1066.88
//
Query:       gi|488600405|ref|YP_007906876.1|  [L=214]
Description: RNA:NAD 2-phosphotransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-28  100.4   0.0    1.6e-28  100.0   0.0    1.0  1  PTS_2-RNA      RNA 2'-phosphotransferase, Tpt1 / KptA family
  ------ inclusion threshold ------
       0.07   13.5   0.0       0.12   12.8   0.0    1.5  1  UvrA_DNA-bind  UvrA DNA-binding domain
       0.18   12.0   0.0       0.27   11.5   0.0    1.2  1  DUF4154        YfiR/HmsC-like


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 !  100.0   0.0   2.7e-32   1.6e-28       4     180 ..      35     198 ..      32     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 2.7e-32
                         PTS_2-RNA   4 vqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslkvtleeikevVesndKqRFelveleelliranqgh 80 
                                       ++l++ +s iLRh ++++gL+++e+G+v+ e+l +    k + ++   ik++V s++K R+el    +  ira  gh
  gi|488600405|ref|YP_007906876.1|  35 EKLGRFISGILRHFPDRFGLEMDENGWVDFEKLSKVVSRKYRWANKWLIKAIVYSDKKGRYELS---DGKIRARYGH 108
                                       6799****************************9996655555588889**************54...467******* PP

                         PTS_2-RNA  81 sikkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrksaevliyi 157
                                       s+ +  +    l+  e+ae+  +v+++gT+ ++ +++l + g+k+++++ +hl+t++ +    +   r+++ +++++
  gi|488600405|ref|YP_007906876.1| 109 SV-D--V---KLNDYEEAEN--DVLYYGTSEEEAHRLL-EIGIKPVNQKFVHLSTTIDKG-IEVALLRTDEPIILMV 175
                                       *5.2..2...3777766664..89**************.88**************98644.4556699********* PP

                         PTS_2-RNA 158 dvekaladgikfyvsengviLte 180
                                       d++ka ++gikf +++n ++L+e
  gi|488600405|ref|YP_007906876.1| 176 DAKKARTAGIKFLKANNHIVLSE 198
                                       *********************97 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 ?   12.8   0.0   1.9e-05      0.12      36      69 ..     102     135 ..      64     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                                       HHTTTS------------S-THHHHH----.... CS
                     UvrA_DNA-bind  36 vaehygidldtpfkeLpeeqkdilLyGsgeekik 69 
                                       + ++yg ++d+++++++e + d+l yG++ee+ +
  gi|488600405|ref|YP_007906876.1| 102 IRARYGHSVDVKLNDYEEAENDVLYYGTSEEEAH 135
                                       55689************************98765 PP

>> DUF4154  YfiR/HmsC-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.5e-05      0.27      47     134 ..     103     187 ..      77     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                                       TTS..-EEEEEEE-TT-TTHH-SEEEE-S-..-HHHHHHHHHHHTTS--EEEESSTSGGSSS-SEEEEESSSSEEEE CS
                           DUF4154  47 kkvrgrpievrrlddsseaeechvlyiges..earelaailkalagkpvLtvsdgegfaeqggminLvredgrlrfe 121
                                       +   g+++ v+  d++++  e +vly g+s  ea++l +i  +  +++ +  s +   +++g  ++L r+d+ + + 
  gi|488600405|ref|YP_007906876.1| 103 RARYGHSVDVKLNDYEEA--ENDVLYYGTSeeEAHRLLEIGIKPVNQKFVHLSTT---IDKGIEVALLRTDEPIILM 174
                                       444456666555555554..48*****9994455666777777778889999998...9****************** PP

                                       EEHHHHHHSSSEE CS
                           DUF4154 122 iNldaarraglki 134
                                       ++ ++ar ag+k+
  gi|488600405|ref|YP_007906876.1| 175 VDAKKARTAGIKF 187
                                       **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1423.18
//
Query:       gi|488600406|ref|YP_007906877.1|  [L=165]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-68  227.6   0.0    1.1e-67  227.4   0.0    1.0  1  DUF531           Protein of unknown function (DUF531)
  ------ inclusion threshold ------
      0.034   13.5   0.0      0.043   13.2   0.0    1.2  1  SPOUT_MTase_2    AF2226-like SPOUT RNA Methylase fused to THU
      0.063   13.1   0.0       0.12   12.2   0.0    1.5  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
       0.16   11.5   0.0       0.19   11.3   0.0    1.1  1  Q_salvage        Potential Queuosine, Q, salvage protein fami


Domain annotation for each model (and alignments):
>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.4   0.0   2.4e-71   1.1e-67       1     169 [.       1     161 [.       1     162 [. 0.96

  Alignments for each domain:
  == domain 1  score: 227.4 bits;  conditional E-value: 2.4e-71
                            DUF531   1 mltlglvntYDkkklheaHkRaiARaapicyafdfnLalldFplkkeekelvdvvaekttiGesGkylkelaeknrl 77 
                                       m++l+lvntYDk klhe+H+R+iARa+picya++f+LalldF ++++ekelv++++e+ttiG+  ky +++ e++++
  gi|488600406|ref|YP_007906877.1|   1 MISLCLVNTYDKLKLHEIHYRSIARAIPICYAYSFHLALLDFGFWNDEKELVKEIVEYTTIGDP-KYAESMLESGKI 76 
                                       899************************************************************9.************ PP

                            DUF531  78 lvldlpkkgfpaqfGevvattskpdekkaitpeevaeeilrkksvllliGlGrkGlPkellklakyhlditekgvsl 154
                                       +++d    ++pa+fG++vatts+p++  +++  e+ +++l+++s+++liGlGrkGlPk+llk++kyhldit+kgvsl
  gi|488600406|ref|YP_007906877.1|  77 HLID----KIPAHFGSIVATTSRPEKGLSVE--EL-KKLLKSESLTFLIGLGRKGLPKDLLKKSKYHLDITWKGVSL 146
                                       ****....****************9877665..55.56799************************************ PP

                            DUF531 155 EtctAigaiaaviat 169
                                       Etc+Aig+ia++i++
  gi|488600406|ref|YP_007906877.1| 147 ETCSAIGVIASTIYW 161
                                       ************986 PP

>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.5e-06     0.043     112     167 ..     103     159 ..      89     165 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.5e-06
                     SPOUT_MTase_2 112 eelaealrkakevvvlvG.sReGiPkGlfrfadfvvDlaP.gvtlateyaiaaalial 167
                                       eel++ l k++ ++ l+G  R+G+Pk l++ + + +D++  gv l t  ai  +  ++
  gi|488600406|ref|YP_007906877.1| 103 EELKKLL-KSESLTFLIGlGRKGLPKDLLKKSKYHLDITWkGVSLETCSAIGVIASTI 159
                                       5677777.567778888857******************95268888888887666555 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05      0.12     100     156 ..      84     138 ..      42     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                                       SS--EEEE--SS--SS-B-HHHHHHHHHH--S-EEEEE--TT---HHHHTT-SEEB- CS
                   Methyltrn_RNA_4 100 gkkplvvatsArkkentvsyeelrelleeeekpvlllfGtgwGlaeevlekadyiLe 156
                                        +   +vat+ r  e+ +s+eel++ll++e+ ++l+ +G   Gl +++l+k++y L+
  gi|488600406|ref|YP_007906877.1|  84 AHFGSIVATTSR-PEKGLSVEELKKLLKSESLTFLIGLGR-KGLPKDLLKKSKYHLD 138
                                       555678889888.67889*********5555555555553.7***********9986 PP

>> Q_salvage  Potential Queuosine, Q, salvage protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.1e-05      0.19      11      47 ..      31      67 ..      19     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                         Q_salvage 11 vdfifvvdlLNFsFWsekeeeerfaveykgkkytgYw 47
                                       ++ f + lL F+FW++++e  +  vey++    +Y 
  gi|488600406|ref|YP_007906877.1| 31 YAYSFHLALLDFGFWNDEKELVKEIVEYTTIGDPKYA 67
                                      5799**************9999999***986555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1117.98
//
Query:       gi|488600407|ref|YP_007906878.1|  [L=117]
Description: Sec-independent protein secretion pathway component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-09   35.3   0.3    5.2e-09   35.3   0.3    1.2  1  MttA_Hcf106  mttA/Hcf106 family


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.3   2.9e-13   5.2e-09       2      46 ..       3      47 ..       2     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.9e-13
                                      -HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH- CS
                       MttA_Hcf106  2 gapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleee 46
                                      g+ el i+ + a++l Gp+kLPE+ r LGk   e+kka k  e e
  gi|488600407|ref|YP_007906878.1|  3 GWGELGIVIILAIVLLGPDKLPEIFRTLGKIYAEYKKAKKRFELE 47
                                      899************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 782.12
//
Query:       gi|488600408|ref|YP_007906879.1|  [L=293]
Description: Pyruvate:ferredoxin oxidoreductase-related 2-oxoacid:ferredoxin oxidoreductase, beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   87.5   0.1    9.9e-25   87.1   0.1    1.2  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
      0.022   14.0   0.0      0.034   13.3   0.0    1.3  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.1   1.1e-28   9.9e-25       4     153 .]      40     194 ..      37     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.1e-28
                                       HHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHH...ST.TSEEEEEEEHHHHHHT.GGGHHHHHHTT-S CS
                      TPP_enzyme_C   4 cltlwaarllkvkrprsylt.sgglgtmGyglpaAiGakla...kp.drevvaivGDGgflmi.lqelatavrrnlp 74 
                                       c+++++  +     p s ++ + +  t+  + + A+G+k a   k  d+evv+ +GDGg+++i lq+l+ a++rn +
  gi|488600408|ref|YP_007906879.1|  40 CTSVYMGAY-----PHSAINiPVFNCTFASAASTATGIKGAlefKGiDAEVVVWAGDGGTYDIgLQALSGAAERNED 111
                                       566655555.....888888788999*************9655443589**************************** PP

                                       EEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSS CS
                      TPP_enzyme_C  75 itvvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkg 147
                                       i+++++nNe+y +tg q    +p+g+++ ++++gk ++ +d+a++   + ++ +a+ +  ++ +l  ++++a++ kg
  gi|488600408|ref|YP_007906879.1| 112 ILYICYNNEIYSNTGIQrsgATPYGAWTNTTVSGKREHRKDVAEILITHDVPyVATASAGYLRDLYSKVRKARKIKG 188
                                       ***********************************9****************999********************** PP

                                       EEEEEE CS
                      TPP_enzyme_C 148 paliev 153
                                       + +ie+
  gi|488600408|ref|YP_007906879.1| 189 FRYIEI 194
                                       **9996 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-06     0.034     111     177 ..      61     125 ..      51     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-06
                    DXP_synthase_N 111 gHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                       + +s + s+a+G++ a + kg + +vv   GDg+ t  + ++al  ++e ++++l i  +Ne   ++
  gi|488600408|ref|YP_007906879.1|  61 TFAS-AASTATGIKGALEFKGIDAEVVVWAGDGG-TYDIGLQALSGAAERNEDILYICYNNEIYSNT 125
                                       5555.5699************************9.8899****************999999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1749.60
//
Query:       gi|488600409|ref|YP_007906880.1|  [L=372]
Description: Pyruvate:ferredoxin oxidoreductase-related 2-oxoacid:ferredoxin oxidoreductase, alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-68  228.3   0.4    1.5e-67  227.8   0.4    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
      3e-21   75.7   0.1    5.5e-21   74.8   0.1    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    2.2e-05   24.4   0.0    5.4e-05   23.1   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
     0.0046   16.6   1.7     0.0081   15.8   1.7    1.4  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.8   0.4   3.3e-71   1.5e-67       2     220 ..      25     232 ..      24     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: 227.8 bits;  conditional E-value: 3.3e-71
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       aa++a+v+++a+YPITP+++++e++++l+++g++ ++++v +esE++a+sa++GA++aG r++TaTS++Gl++m+e+
  gi|488600409|ref|YP_007906880.1|  25 AAMNAKVRFVAGYPITPATSVIETISKLIDEGKM-KARFVAVESEHSAMSACVGASYAGLRTFTATSSHGLAYMHEM 100
                                       899******************************8.8***************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                       l++a+ +++Pvv++v++Ra+   g++i+ d sD +  rdtg+++++ +++qe++d++++A+++Ae+v++Pv+v+ Dg
  gi|488600409|ref|YP_007906880.1| 101 LHFAVNARTPVVMAVANRAIGP-GWNIWSDLSDSLSQRDTGWLQFYCSDIQEIYDTIAMAYRIAEQVMLPVMVCYDG 176
                                       ********************85.6***************************************************** PP

                                       HHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXX CS
                             POR_N 156 fllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaed 220
                                       f+lsh+ +++e+ + +        + ee+++   ++d+++p ++g   +p+ ++  r++ ++a++
  gi|488600409|ref|YP_007906880.1| 177 FVLSHSTKPIEVTPLD-------GFIEERDA--EGIDFDNPTTFGNISPPESYFSLRKAIHKAVE 232
                                       ****************.......55544444..48**************************9987 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 !   74.8   0.1   1.2e-24   5.5e-21       1     101 [.     265     360 ..     265     361 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.2e-24
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Ae v+v mG+va++a+ avd lR+eg+k Gll+++++ P P++ +k +l + k+v+v+dr+ s g+ G+l +e+++ 
  gi|488600409|ref|YP_007906880.1| 265 AEKVMVSMGAVASEARVAVDLLRDEGEKWGLLKVKSFKPLPKKIIKAML-SGKEVFVIDRSLSPGTGGILHHEMSSI 340
                                       89*********************************************99.8899*********************** PP

                                       TGGGTSEEEEEE--GGG----HHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditved 101
                                       l +      + + glgG d+t+e 
  gi|488600409|ref|YP_007906880.1| 341 LGDV----NSAILGLGGVDVTAEA 360
                                       9765....999**********986 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.2e-08   5.4e-05      13     107 ..     268     359 ..     263     372 .] 0.89

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.2e-08
                                       EEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCC CS
                   Transketolase_C  13 tlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeaf 89 
                                       ++v++G+  +ea  A++ L++eg +  ++ + ++kpl k+ i+  ++  g+ v+v + + + G g  + + ++  ++
  gi|488600409|ref|YP_007906880.1| 268 VMVSMGAVASEARVAVDLLRDEGEKWGLLKVKSFKPLPKKIIK--AMLSGKEVFVIDRSLSPGTGGILHHEMSS-IL 341
                                       689****************************************..88899999999********9988888888.99 PP

                                       TTCSSEEEEEEE-SSSSS CS
                   Transketolase_C  90 dgldapvkrvggpdviep 107
                                        +++ +++ +gg dv   
  gi|488600409|ref|YP_007906880.1| 342 GDVNSAILGLGGVDVTAE 359
                                       **************9444 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 !   15.8   1.7   1.8e-06    0.0081       2     102 ..      17     120 ..      16     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT......TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CH CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeq.....girvvlarhEqgaafaAdgyaratgkpgvvlvtsg 73 
                                       t+ ea + a  +++v+ v g+p +  +++++ +s+       + r+v + +E +a+ a +g + a   +  + +ts 
  gi|488600409|ref|YP_007906880.1|  17 TGNEASAYAAMNAKVRFVAGYPITPATSVIETISKLIdegkmKARFVAVESEHSAMSACVGASYAG--LRTFTATSS 91 
                                       6778888888999*************99999999876677999****************9998885..566666777 PP

                                       HHHHHCHHHHHHHHHHT--EEEEEEE--C CS
                      TPP_enzyme_N  74 pGatnaltalaeAkvdriPllvlsgdrpt 102
                                        G++ +   l+ A  +r+P+++ +++r+ 
  gi|488600409|ref|YP_007906880.1|  92 HGLAYMHEMLHFAVNARTPVVMAVANRAI 120
                                       8*********************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2257.71
//
Query:       gi|488600410|ref|YP_007906881.1|  [L=281]
Description: 2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate family/2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  105.4   0.0    7.1e-30  104.4   0.0    1.5  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
    1.6e-13   49.9  13.4    7.5e-07   28.7   3.3    2.4  2  Fer4      4Fe-4S binding domain
    4.1e-11   42.5  13.3    1.1e-05   25.3   2.2    2.5  2  Fer4_6    4Fe-4S binding domain
    5.1e-09   35.7  12.1    5.4e-05   23.0   3.8    2.5  2  Fer4_2    4Fe-4S binding domain
    4.5e-07   30.7   7.0    0.00079   20.3   1.1    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    6.1e-07   29.5   9.0    1.1e-06   28.6   9.0    1.4  1  Fer4_21   4Fe-4S dicluster domain
      8e-07   29.1   9.3    1.4e-06   28.3   9.3    1.4  1  Fer4_9    4Fe-4S dicluster domain
    2.5e-06   27.5  11.3    0.00013   22.0  12.0    2.2  2  Fer4_10   4Fe-4S dicluster domain
    5.6e-06   26.9  12.2    5.1e-05   23.8  12.7    2.1  3  Fer4_7    4Fe-4S dicluster domain
    0.00013   22.2  13.3      0.062   13.8   2.1    2.4  2  Fer4_4    4Fe-4S binding domain
    0.00059   20.3   8.8      0.038   14.5   1.1    2.3  2  Fer4_17   4Fe-4S dicluster domain
     0.0017   19.1   7.9       0.36   11.6   1.2    2.7  2  Fer4_15   4Fe-4S single cluster domain
     0.0034   17.9  10.9       0.11   13.0   1.5    2.7  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0089   16.9  17.6       0.33   12.0   5.3    2.3  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.025   15.0  14.3       0.51   10.8   3.2    2.4  3  Fer4_8    4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   5.9e-33   7.1e-30       1     176 [.      11     166 ..      11     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 5.9e-33
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldg 75 
                                       GGqGvvta+k++a+aa   Gyy q+ +++g+e+rG++++s  risdepi+++ +v+e+d++v++d+ +++   +++g
  gi|488600410|ref|YP_007906881.1|  11 GGQGVVTASKLIAEAAYLDGYYSQSMPFFGAERRGAPVVSFARISDEPIYRTSQVYEPDVVVIFDPVLINfpHVFSG 87 
                                       9********************************************************************88999*** PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC....CCHHHHHHHHHHHHHHTS-HHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggn...eraaNtvmlGalaallglplea 149
                                       lk++g++++ns ++ ++                   ++ vda  ia++        ++ N+ mlGal+++  +  ++
  gi|488600410|ref|YP_007906881.1|  88 LKEDGVVVVNSRDFLDARN-----------------IVMVDADGIAEKYDLVvagMPVYNIPMLGALSHV--VIYDS 145
                                       ***********54433332.................4589******9665555569**********9999..66678 PP

                                       HHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 150 leeaikkrfpkkkeviekNlkafragy 176
                                       ++ +i+++f++      k l af+++y
  gi|488600410|ref|YP_007906881.1| 146 MRYVIERKFGE------KALLAFDEAY 166
                                       88888888885......5777777776 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   2.5     3e-09   3.6e-06       1      24 []     215     238 ..     215     238 .. 0.95
   2 !   28.7   3.3   6.3e-10   7.5e-07       2      24 .]     245     267 ..     244     267 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3e-09
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       +v+d e+C  CG+C   CP g+I+
  gi|488600410|ref|YP_007906881.1| 215 PVVDRERCNECGTCSLYCPEGVIS 238
                                       69*******************995 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 6.3e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        id+e C gC++C++vCP  AI+
  gi|488600410|ref|YP_007906881.1| 245 DIDYEYCKGCMICMSVCPKRAIS 267
                                       69*******************95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   2.2     9e-09   1.1e-05       2      24 .]     215     237 ..     214     237 .. 0.96
   2 !   22.3   3.6   7.9e-08   9.5e-05       2      24 .]     244     266 ..     243     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9e-09
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       +++d+++C+ Cg C   CPeg+i
  gi|488600410|ref|YP_007906881.1| 215 PVVDRERCNECGTCSLYCPEGVI 237
                                       89*******************98 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 7.9e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       v id++ C gC+ C++vCP  ai
  gi|488600410|ref|YP_007906881.1| 244 VDIDYEYCKGCMICMSVCPKRAI 266
                                       679****************9887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   3.8   4.5e-08   5.4e-05       2      22 .]     214     234 ..     213     234 .. 0.93
   2 !   17.5   1.2   2.7e-06    0.0032       5      21 ..     246     262 ..     242     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-08
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       ++vvd++rC++Cg+C   CP+
  gi|488600410|ref|YP_007906881.1| 214 RPVVDRERCNECGTCSLYCPE 234
                                       589*****************5 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.7e-06
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       +d + C gC +C s+CP
  gi|488600410|ref|YP_007906881.1| 246 IDYEYCKGCMICMSVCP 262
                                       89999***********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 !   13.6   0.5   8.3e-05     0.099       1      18 [.     221     238 ..     221     247 .. 0.90
   2 !   20.3   1.1   6.6e-07   0.00079       2      25 ..     251     274 ..     250     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                       rC +Cg C   CP+++i+
  gi|488600410|ref|YP_007906881.1| 221 RCNECGTCSLYCPEGVIS 238
                                       6***************97 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 6.6e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekei 25 
                                       C++C  C++vCP +ai++ ke e+
  gi|488600410|ref|YP_007906881.1| 251 CKGCMICMSVCPKRAISGVKESEV 274
                                       *****************9977665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   9.0   9.6e-10   1.1e-06       2      57 ..     216     266 ..     215     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.6e-10
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       ++d+++C +Cg C + C+++ +  +      ++ +  + C GC +C+svCP + +i
  gi|488600410|ref|YP_007906881.1| 216 VVDRERCNECGTCSLYCPEGVISVVL----GMVDIDYEYCKGCMICMSVCP-KRAI 266
                                       699***************86555554....4789999**************.5665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   9.3   1.2e-09   1.4e-06       1      51 []     221     266 ..     221     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.2e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C++Cg+C   Cp gv++   +   + ++      C gC+ C+ +Cpk ai
  gi|488600410|ref|YP_007906881.1| 221 RCNECGTCSLYCPEGVISVVLGMVDIDYEY-----CKGCMICMSVCPKRAI 266
                                       6**********************9999954.....*************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 !   22.0  12.0   1.1e-07   0.00013       2      56 .]     215     262 ..     214     262 .. 0.96
   2 !   17.7   2.0   2.4e-06    0.0028       2      23 ..     244     265 ..     243     280 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +v+d+++C +Cg+C   CP          +    ++v++++e C gc  C+++CP
  gi|488600410|ref|YP_007906881.1| 215 PVVDRERCNECGTCSLYCPE-------GVISVVLGMVDIDYEYCKGCMICMSVCP 262
                                       5889****************.......9999999********************9 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.4e-06
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                       v id + C +C  C+++CP  +
  gi|488600410|ref|YP_007906881.1| 244 VDIDYEYCKGCMICMSVCPKRA 265
                                       56999**************944 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   2.4   7.3e-05     0.087      30      52 .]     214     236 ..     197     236 .. 0.84
   2 !   23.8  12.7   4.3e-08   5.1e-05       1      52 []     221     265 ..     221     265 .. 0.92
   3 !   15.0   3.4   2.3e-05     0.027       2      26 ..     251     275 ..     250     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                            Fer4_7  30 kveidpekClgCgaCvavCPtga 52 
                                       ++++d e+C  Cg C   CP g+
  gi|488600410|ref|YP_007906881.1| 214 RPVVDRERCNECGTCSLYCPEGV 236
                                       56789999*******99999886 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 4.3e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       rC +Cg C  +Cp ++i++           v+id+e+C gC  C++vCP+ a
  gi|488600410|ref|YP_007906881.1| 221 RCNECGTCSLYCPEGVISVVL-------GMVDIDYEYCKGCMICMSVCPKRA 265
                                       8*****************965.......469******************976 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.3e-05
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek 26 
                                       C gC  C+++Cp +ai+  +e++ k
  gi|488600410|ref|YP_007906881.1| 251 CKGCMICMSVCPKRAISGVKESEVK 275
                                       9***************998876554 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   3.7   6.7e-05      0.08       2      16 ..     220     234 ..     219     236 .. 0.92
   2 !   13.8   2.1   5.2e-05     0.062       2      16 ..     249     263 ..     248     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       erC++Cg C  +CP 
  gi|488600410|ref|YP_007906881.1| 220 ERCNECGTCSLYCPE 234
                                       8*************6 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.2e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e C gC+ C+++CP 
  gi|488600410|ref|YP_007906881.1| 249 EYCKGCMICMSVCPK 263
                                       89************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 !   14.5   1.1   3.2e-05     0.038      44      60 ..     220     236 ..     212     237 .. 0.92
   2 !    9.9   1.4   0.00092       1.1       2      18 ..     251     267 ..     250     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                           Fer4_17  44 slCieCgeCerkCPqgl 60 
                                       ++C+eCg C+ +CP+g+
  gi|488600410|ref|YP_007906881.1| 220 ERCNECGTCSLYCPEGV 236
                                       69************986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00092
                           Fer4_17   2 CiqCgyClpeCpsyeay 18 
                                       C +C  C+ +Cp  ++ 
  gi|488600410|ref|YP_007906881.1| 251 CKGCMICMSVCPKRAIS 267
                                       99*********987764 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   1.2    0.0003      0.36       2      20 ..     216     234 ..     216     238 .. 0.92
   2 !   10.5   0.8   0.00068      0.81       1      21 [.     244     264 ..     244     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       vvDr++C  cg C   +pe
  gi|488600410|ref|YP_007906881.1| 216 VVDRERCNECGTCSLYCPE 234
                                       69***************97 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00068
                           Fer4_15   1 VvvDrdaCigcglCvaeapev 21 
                                       V +D + C gc  C+ ++p++
  gi|488600410|ref|YP_007906881.1| 244 VDIDYEYCKGCMICMSVCPKR 264
                                       679***************985 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       8.8     1e+04      17      32 ..      82      97 ..      81     100 .. 0.83
   2 !   13.0   1.5   9.5e-05      0.11       1      18 [.     217     234 ..     217     235 .. 0.97
   3 !    9.8   1.4   0.00093       1.1       1      18 [.     246     263 ..     246     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.8
                           Fer4_13 17 PdvFeeddeggasvva 32
                                      P+vF   +e+g +vv 
  gi|488600410|ref|YP_007906881.1| 82 PHVFSGLKEDGVVVVN 97
                                      8999999999988875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.5e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VDr++C +cg+C   +P+
  gi|488600410|ref|YP_007906881.1| 217 VDRERCNECGTCSLYCPE 234
                                       9****************7 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00093
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D + C +c++C +++P+
  gi|488600410|ref|YP_007906881.1| 246 IDYEYCKGCMICMSVCPK 263
                                       78899************6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   4.4   0.00072      0.86       1      14 [.     222     235 ..     222     236 .. 0.95
   2 !   12.0   5.3   0.00027      0.33       1      15 []     251     265 ..     251     265 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00072
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ Cg+C   CP+g
  gi|488600410|ref|YP_007906881.1| 222 CNECGTCSLYCPEG 235
                                       ************98 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00027
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gC+ C+ vCP++A
  gi|488600410|ref|YP_007906881.1| 251 CKGCMICMSVCPKRA 265
                                       99***********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 ?   10.5   3.4   0.00053      0.63      50      65 .]     221     236 ..     206     236 .. 0.83
   2 ?   10.8   3.2   0.00042      0.51      50      64 ..     221     235 ..     218     245 .. 0.74
   3 ?    8.9   3.6    0.0017         2       3      63 ..     249     263 ..     247     277 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00053
                            Fer4_8  50 sCttcgaCtevCpvgi 65 
                                       +C++cg C+  Cp+g+
  gi|488600410|ref|YP_007906881.1| 221 RCNECGTCSLYCPEGV 236
                                       6888888888888875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
                            Fer4_8  50 sCttcgaCtevCpvg 64 
                                       +C++cg C+  Cp+g
  gi|488600410|ref|YP_007906881.1| 221 RCNECGTCSLYCPEG 235
                                       577777777777766 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0017
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       e+C +C+ C+s Cp                                              +
  gi|488600410|ref|YP_007906881.1| 249 EYCKGCMICMSVCP----------------------------------------------K 263
                                       44555555555555..............................................4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1761.12
//
Query:       gi|488600411|ref|YP_007906882.1|  [L=235]
Description: putative DNA binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-17   63.0   0.1    4.3e-17   61.6   0.0    1.8  2  HTH_10    HTH DNA binding domain
  ------ inclusion threshold ------
       0.05   13.2   0.1       0.15   11.7   0.0    1.8  2  HTH_24    Winged helix-turn-helix DNA-binding


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 ?   -3.1   0.0      0.79   7.1e+03      36      48 ..      51      63 ..      51      64 .. 0.83
   2 !   61.6   0.0   4.8e-21   4.3e-17       1      52 [.     167     218 ..     167     219 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.79
                            HTH_10 36 skstlsehLrkae 48
                                      s ++l++++++a+
  gi|488600411|ref|YP_007906882.1| 51 SYQALKDYIENAK 63
                                      6789999999997 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 4.8e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       L+ kq +vl  Ay  GYF+yP++++l+++A+++GI+kst + h+r ae+k++
  gi|488600411|ref|YP_007906882.1| 167 LSSKQKKVLIGAYMDGYFEYPKKTNLSSIANRFGIAKSTCLHHIRIAEQKIL 218
                                       789***********************************************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 ?   11.7   0.0   1.7e-05      0.15      20      42 ..     192     214 ..     188     216 .. 0.85
   2 ?   -1.8   0.0      0.26   2.3e+03       6      14 ..     219     227 ..     212     232 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
                            HTH_24  20 qreLAerlglSpstvnrrlkrLe 42 
                                        + +A r g+ +st++ +++  e
  gi|488600411|ref|YP_007906882.1| 192 LSSIANRFGIAKSTCLHHIRIAE 214
                                       578****************9666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.26
                            HTH_24   6 rkILelLqk 14 
                                        +I++++++
  gi|488600411|ref|YP_007906882.1| 219 SRIIREIKE 227
                                       456666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1754.81
//
Query:       gi|488600412|ref|YP_007906883.1|  [L=305]
Description: hypothetical protein Asulf_00883 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   11.8   0.0        0.4   10.9   0.0    1.3  1  LpqV      Putative lipoprotein LpqV


Domain annotation for each model (and alignments):
>> LpqV  Putative lipoprotein LpqV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.3e-05       0.4      64      89 ..      78     104 ..      70     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.3e-05
                              LpqV  64 dpksqiEpYLaslqssd.sagpgtfnt 89 
                                       +   qiEpYL+++q+ + s+  gtf++
  gi|488600412|ref|YP_007906883.1|  78 KRILQIEPYLEIVQKMQkSIEDGTFEE 104
                                       44479*********9875889999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2073.99
//
Query:       gi|488600413|ref|YP_007906884.1|  [L=328]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-60  202.8   0.4    6.8e-60  202.3   0.4    1.2  1  NRD1_2         NrpR regulatory domains NRD1 and 2
    2.1e-13   50.0   0.2      4e-13   49.1   0.2    1.5  1  HTH_12         Ribonuclease R winged-helix domain
    2.1e-06   27.6   0.0    5.2e-06   26.4   0.0    1.7  1  HTH_45         Winged helix-turn-helix
      0.002   18.3   0.0     0.0084   16.3   0.0    2.0  2  FUR            Ferric uptake regulator family
     0.0066   16.5   0.0      0.015   15.4   0.0    1.6  1  HemN_C         HemN C-terminal domain
  ------ inclusion threshold ------
      0.061   13.0   0.0       0.11   12.2   0.0    1.5  1  DUF4423        Domain of unknown function (DUF4423)
       0.14   11.2   0.1       0.21   10.6   0.1    1.2  1  Lipoprotein_1  Borrelia lipoprotein


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 !  202.3   0.4   2.7e-63   6.8e-60       2     236 ..      88     321 ..      87     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.3 bits;  conditional E-value: 2.7e-63
                                       --HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE..........E CS
                            NRD1_2   2 gfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegek..elevpegkv 76 
                                       g +++ +e++++++tf++ t++G+V + ++++dk+++++ale+l+ev++s+l++s++  +l+ege   ++e++egk+
  gi|488600413|ref|YP_007906884.1|  88 GEFSETLEYNMLHSTFNIYTMEGTVPTSVAILDKDQADRALEVLSEVLNSRLATSRYAVLLDEGEIagKTEIEEGKI 164
                                       778999***********************************************************99********** PP

                                       EEEEE-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEE CS
                            NRD1_2  77 giatvCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilA 153
                                       gi t++S+ +d ++l+ G++++++y+Gll++e++ pv+ telI+Y+gt+i+P  +fi+ ++Tsv++v+ +g+g+ + 
  gi|488600413|ref|YP_007906884.1| 165 GIGTISSTVMDIIMLNIGVILSVEYAGLLKYENGLPVGVTELINYSGTTISPGLLFIRGGYTSVYDVVVRGSGYAVI 241
                                       ***************************************************************************** PP

                                       EEEEEETTTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEE CS
                            NRD1_2 154 nlReipvsarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsgl 230
                                       ++R++  +a e+ve+ ++ ++++g+ +vl+i +  ++++g+p + +++++v+ +G+n +a+l e+g+k  ++++s+l
  gi|488600413|ref|YP_007906884.1| 242 AIRNFSPYAIEEVEKEVQLASARGLGKVLTITM--DRFFGIPAQ-KRAMLVFQAGINQLAPLYELGFKPVLEINSSL 315
                                       *********************************..*******77.999***************************** PP

                                       EEGGGS CS
                            NRD1_2 231 idisel 236
                                       i+++++
  gi|488600413|ref|YP_007906884.1| 316 IEFRKF 321
                                       ****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 !   49.1   0.2   1.6e-16     4e-13       1      66 []      13      78 ..      13      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.6e-16
                            HTH_12  1 veILkila.esdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                      veIL+ l+ + ++ + a+ei +++++rg + +er+vR rL ++ erg+++++g++  ++t+kGle+L
  gi|488600413|ref|YP_007906884.1| 13 VEILRALSsKGSNYVRAGEIVHKIRDRGLNFSERTVRNRLEAMAERGFVEKKGNS-WRITDKGLEML 78
                                      6999999725567899***************************************.99*******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 !   26.4   0.0     2e-09   5.2e-06      28      74 ..      40      86 ..       9      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2e-09
                            HTH_45 28 kanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkelee 74
                                        n s +++++ L+ + e+g+++k+++++++T+kGle+l++   +++
  gi|488600413|ref|YP_007906884.1| 40 GLNFSERTVRNRLEAMAERGFVEKKGNSWRITDKGLEMLSRSTVFDR 86
                                      35888899*******************************98776665 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.3e-06    0.0084      12      60 ..      14      63 ..      13      67 .. 0.93
   2 ?   -3.3   0.0       3.8   9.6e+03      31      59 ..     155     185 ..     148     195 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.3e-06
                                      HHHHHHHHHSS.SBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE CS
                               FUR 12 kilevleksee.hlsaeevykelkeedpeislaTVYrtLklleeaglvke 60
                                      +il+ l ++   ++ a e+++++++++ + s  TV + L+ ++e+g+v++
  gi|488600413|ref|YP_007906884.1| 14 EILRALSSKGSnYVRAGEIVHKIRDRGLNFSERTVRNRLEAMAERGFVEK 63
                                      689999999888************************************86 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                                       HHHHHTTTT--HHHHHHHHH..HHHHTTSEE CS
                               FUR  31 kelkeedpeislaTVYrtLk..lleeaglvk 59 
                                        + + e+ +i++ T+  t+   ++ ++g++ 
  gi|488600413|ref|YP_007906884.1| 155 GKTEIEEGKIGIGTISSTVMdiIMLNIGVIL 185
                                       5555667788888887766422445555555 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.8e-06     0.015      34      65 ..      43      75 ..      37      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.8e-06
                            HemN_C 34 leell.aaaleklqeqGLLeldggrlrltprGr 65
                                      ++e+  ++ le + e+G++e  g+++r t++G+
  gi|488600413|ref|YP_007906884.1| 43 FSERTvRNRLEAMAERGFVEKKGNSWRITDKGL 75
                                      666666999***********************6 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-05      0.11      46      85 ..      41      77 ..      27     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                           DUF4423 46 lrpkisaeevekalefLlklgllkkdedgkyrqteksltt 85
                                      l+  +s+  v++ le + + g+++k+++  +r t+k l++
  gi|488600413|ref|YP_007906884.1| 41 LN--FSERTVRNRLEAMAERGFVEKKGN-SWRITDKGLEM 77
                                      56..999********************8.*******9984 PP

>> Lipoprotein_1  Borrelia lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   8.1e-05      0.21     113     186 ..      92     163 ..      74     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.1e-05
                                       EEETTSCEEEE.EEEETTS-EEEEECESSTTSEEEEEEEECCCEEEEEEEETTEEEEEEEETTEEEEEEEETTSS CS
                     Lipoprotein_1 113 eklkknkldek.kltradGtrleysqitdadnatkakevlknsvkleGslvaekttlevkeGtvtlkkeiekdGk 186
                                       e+l+ n l++   +   +Gt      i d d+a +a evl +   l+  l++ + ++ + eG ++ k eie  Gk
  gi|488600413|ref|YP_007906884.1|  92 ETLEYNMLHSTfNIYTMEGTVPTSVAILDKDQADRALEVLSEV--LNSRLATSRYAVLLDEGEIAGKTEIEE-GK 163
                                       7888888876526788899999999***************875..59***********************84.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2190.73
//
Query:       gi|488600414|ref|YP_007906885.1|  [L=551]
Description: succinate dehydrogenase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-115  385.4   0.0   4.3e-115  385.1   0.0    1.1  1  FAD_binding_2   FAD binding domain
    1.6e-41  141.3   0.2    2.3e-41  140.8   0.2    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    4.3e-10   39.3   2.5      1e-05   24.9   2.1    3.0  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      2e-05   23.5   3.8      0.012   14.4   1.4    3.2  3  HI0933_like     HI0933-like protein
    9.3e-05   22.2   0.1     0.0076   15.9   0.1    2.4  2  DAO             FAD dependent oxidoreductase
    0.00013   21.5   3.7     0.0037   16.7   3.9    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0009   18.4   7.4      0.012   14.8   7.4    2.2  1  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
       0.01   15.1   0.6      0.091   12.0   0.7    2.2  2  Thi4            Thi4 family
      0.099   11.9   0.9        0.2   10.9   0.9    1.5  1  FAD_binding_3   FAD binding domain
       0.14   11.4   1.1        2.2    7.5   1.6    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.21   10.6   1.3       0.35    9.9   1.3    1.3  1  Lycopene_cycl   Lycopene cyclase protein
       0.38   11.0   4.0       0.59   10.4   2.5    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
        3.2    6.9   5.8          1    8.6   1.7    2.3  4  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.1   0.0  3.1e-118  4.3e-115       1     417 []       5     380 ..       5     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 385.1 bits;  conditional E-value: 3.1e-118
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       Dv+V+GsG+AGL++A++aa +G +v +v k+ + ++++++++Ggi av       ++ +ds +lh++dt+k++d la
  gi|488600414|ref|YP_007906885.1|   5 DVVVVGSGIAGLRCAIAAAMKGVSVGIVAKTYPIRCHSVCAEGGIGAVM------SE-EDSFDLHAWDTVKGSDFLA 74 
                                       9************************************************......44.4****************** PP

                                       -HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTC CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarka 154
                                       dq++ve+fv++ p+++  L ++g+p+sr++ g++++r lGg+sa+ rt++ aad+      tg++++++l+e+ + +
  gi|488600414|ref|YP_007906885.1|  75 DQDVVEFFVREIPKEILRLDNWGCPWSRDDSGRIALRILGGHSAK-RTVF-AADR------TGFHIVHTLYEKSLMY 143
                                       *********************************************.****.****......**************** PP

                                       TEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHH CS
                     FAD_binding_2 155 gvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdgla 231
                                       +++ + +++++ L ved+r+ G+++ n++sg+ ++iraka+vlatgG+gr           +  ++   +vt dg a
  gi|488600414|ref|YP_007906885.1| 144 DIQKYSEYFVTGLAVEDNRCAGVYAINLKSGEVEAIRAKATVLATGGAGR----------LYSFSSYSNTVTADGMA 210
                                       **************************************************..........***************** PP

                                       HHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHHHHH. CS
                     FAD_binding_2 232 lalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsraile 301
                                       +a+r+g++l+d  me++q+hPt+l+    +sgiL++ea+rgeGg+l++++G+rFm       +ela+rdvvsrai+ 
  gi|488600414|ref|YP_007906885.1| 211 IAYRSGVPLKD--MEFFQIHPTGLI----PSGILVSEACRGEGGYLLNSKGERFMeryaperMELAPRDVVSRAIW- 280
                                       ***********..************....***********************************************. PP

                                       HHHHTTTS.....CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES CS
                     FAD_binding_2 302 keiaeggs.....eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytm 373
                                        ei++g++     +++v ld++h l+++ +e++l+ ++e+a+++++      +dp ++pip       v+p++hytm
  gi|488600414|ref|YP_007906885.1| 281 SEIEQGRGfeseyGPYVLLDLTH-LGEDRIEERLPLVRETAIKFAG------VDPVEEPIP-------VRPTVHYTM 343
                                       ***********************.**********************......*********.......********* PP

                                       -EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 374 gGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                       gG+++++ +++       ipGL+A+Ge+a+ ++hganrlg+nsl
  gi|488600414|ref|YP_007906885.1| 344 GGIHVNY-CET------SIPGLFACGECACLSIHGANRLGSNSL 380
                                       ******7.899......9************************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.2   1.7e-44   2.3e-41       2     128 .]     431     551 .]     430     551 .] 0.98

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 1.7e-44
                                       HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-B CS
                    Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESr 78 
                                       +eL+++m+++  +fR+e+g+ +alk+++el++r++n++v+d+sk++N++l++a+e+  +le+Ae++a sAl+RkESr
  gi|488600414|ref|YP_007906885.1| 431 RELNQTMDRNLWIFRDEQGIMNALKKIRELKDRYRNIEVSDRSKIFNTDLTFAIEVGYMLEIAEVVALSALNRKESR 507
                                       79*************************************************************************** PP

                                       TTBEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                    Succ_DH_flav_C  79 GaHaredfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                       GaH+r+d+p+rdD nwlkhtl+      ++ ++ey pv++++ kp eRsY
  gi|488600414|ref|YP_007906885.1| 508 GAHFRTDYPKRDDGNWLKHTLV------RHGRIEYIPVKITKWKPVERSY 551
                                       **********************......4579*****************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 !   24.9   2.1   7.4e-09     1e-05       1     112 [.       4     193 ..       4     230 .. 0.74
   2 !   10.7   0.0   0.00016      0.22     255     279 ..     343     370 ..     316     382 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.4e-09
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH..HCHHHHHHHHHHHHH.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx.................. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll..skallgvaedaeias.................. 57 
                                       +dvvv+G+G+AGl++a+ +a +g+ v +v   +t + +  ++     + +v+++++ +                   
  gi|488600414|ref|YP_007906885.1|   4 HDVVVVGSGIAGLRCAIAAAMKGVSVGIV--AKTYPIRCHSVcaEGGIGAVMSEEDSFDlhawdtvkgsdfladqdv 78 
                                       59***************************..4545544222222345555555555555788888888888888888 PP

                                       ...........................................................HHHHCHHHHCCCCHC..C CS
                                       ...........................................................xxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2  58 ...........................................................evvkklnqgielllg..e 73 
                                                                                                  e  k+l  +i+++ +  +
  gi|488600414|ref|YP_007906885.1|  79 veffvreipkeilrldnwgcpwsrddsgrialrilgghsakrtvfaadrtgfhivhtlyE--KSLMYDIQKYSEyfV 153
                                       888889999999999999999999999999999999999999998888888888777653..355555666666333 PP

                                       TCEEEE.ESCEEEEETEEECTCEEEEEESEEEE---EEE- CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  74 evvkid.pgkkkvklekkkegdeekiaydklvlAtGsspr 112
                                       ++++++ + ++ v   ++k+g+ e i +++ vlAtG+  r
  gi|488600414|ref|YP_007906885.1| 154 TGLAVEdNRCAGVYAINLKSGEVEAIRAKATVLATGGAGR 193
                                       3444432333566666777799999999999999997655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                                       TTEEE--TTSBESSTTEEE-GGGC....T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       Pyr_redox_2 255 rggivvdeflrtnvpgiyaiGDva....g 279
                                        ggi v+ +++t++pg++a+G +a    +
  gi|488600414|ref|YP_007906885.1| 343 MGGIHVN-YCETSIPGLFACGECAclsiH 370
                                       4777776.99**************55553 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.4   8.6e-06     0.012       1      31 [.       4      34 ..       4      39 .. 0.91
   2 !    5.8   0.0    0.0035       4.8      99     165 ..     120     191 ..     114     219 .. 0.82
   3 ?    1.6   0.0     0.063        87     357     408 ..     343     392 ..     334     393 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.6e-06
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                                      +dv+v+G G AGl +Ai+aa +g +V ++ k
  gi|488600414|ref|YP_007906885.1|  4 HDVVVVGSGIAGLRCAIAAAMKGVSVGIVAK 34
                                      59************************98866 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0035
                                       TEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE....EEEEE...TTEEEEESEEEE----S CS
                       HI0933_like  99 grlFpvsdkaedivdallkelkeagvklrletevksvekeedg...kfrvktk..seeeleadklvlAtGGl 165
                                         +F ++++  +iv++l ++    +++ + e  v++++ e+++   ++ +++k  + e+++a+++vlAtGG+
  gi|488600414|ref|YP_007906885.1| 120 RTVFAADRTGFHIVHTLYEKSLMYDIQKYSEYFVTGLAVEDNRcagVYAINLKsgEVEAIRAKATVLATGGA 191
                                       568999999999*********9*****9999999999887765111556666433557899**********7 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.063
                                       EEEE-GGGB-TTT-BBTTSTTEEE-GGG..BSEEE-..TTTHHHHHHHHHHHHHHH CS
                       HI0933_like 357 aGGVdlkevssktmeskkvpgLffaGEv..lDvegv..tGGynlqaAwasgyaAGk 408
                                       +GG++++  +       ++pgLf +GE+  l ++g   +G   l  +++ g +AG+
  gi|488600414|ref|YP_007906885.1| 343 MGGIHVNYCE------TSIPGLFACGECacLSIHGAnrLGSNSLAECLVFGKVAGE 392
                                       5555554433......468********54488988534788888888888888886 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.5e-06    0.0076       1      29 [.       5      35 ..       5     108 .. 0.87
   2 ?    3.9   0.0     0.024        33     169     203 ..     153     191 ..     130     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      dvv++G+Gi+Gl +A ++a +g  V ++ k 
  gi|488600414|ref|YP_007906885.1|  5 DVVVVGSGIAGLRCAIAAAMKGvsVGIVAKT 35
                                      9******************999999998887 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.024
                                       EEEEEEEETCEEEEE..EECTEEEEEEEE..EEE--GGG CS
                               DAO 169 vtgleeedgkvwgve..rttpgendaada..vVnaaGaw 203
                                       vtgl  ed++ +gv+  + ++ge++a++a   V+a+G  
  gi|488600414|ref|YP_007906885.1| 153 VTGLAVEDNRCAGVYaiNLKSGEVEAIRAkaTVLATGGA 191
                                       8999888999999999888886665445555******65 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.9   2.7e-06    0.0037       1      31 [.       5      35 ..       5      38 .. 0.95
   2 ?    2.5   0.0     0.052        72      94     145 ..     138     190 ..     106     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                      DvvVvG+g+aG+ +AiaAa +G +v +v ++
  gi|488600414|ref|YP_007906885.1|  5 DVVVVGSGIAGLRCAIAAAMKGVSVGIVAKT 35
                                      9************************999875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.052
                      FAD_oxidored  94 eemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATgd 145
                                       e+ l   +++ + + ++++  +e++r+ +v + + + g  ++irAk ++ ATg 
  gi|488600414|ref|YP_007906885.1| 138 EKSLMY-DIQKYSEYFVTGLAVEDNRCAGVYAINLKsGeVEAIRAKATVLATGG 190
                                       444433.78888889999999999998888888888788***********9974 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   7.4   8.4e-06     0.012       1     150 [.       5     190 ..       5     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.4e-06
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSE.EE-T............................. CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnps.iggi............................. 47 
                                       dv+V+G G AG+ +A+aaa +G++v ++++ +   ++ +C +  ig++                             
  gi|488600414|ref|YP_007906885.1|   5 DVVVVGSGIAGLRCAIAAAMKGVSVGIVAKTYPIRCHSVCAEGgIGAVmseedsfdlhawdtvkgsdfladqdvvef 81 
                                       79**************************5555555555554320222233344444444444444467777777776 PP

                                       THHHHHHHHHHHT..-SHHHHHHHHEEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHT.STTE.EEEES-EEE CS
                              GIDA  48 akgllvrEidalg..gliikaadkagiqfrilNrskGpavralraqvdrelyskevteklen.epnl.eiieeevee 120
                                        + ++ +Ei +l+  g   +  d+ +i +ril    G + + +  ++dr  ++   t + ++   ++ +  e  v+ 
  gi|488600414|ref|YP_007906885.1|  82 FVREIPKEILRLDnwGCPWSRDDSGRIALRIL---GGHSAKRTVFAADRTGFHIVHTLYEKSlMYDIqKYSEYFVTG 155
                                       67777777777776666666677777777777...677777777777777775443333332322331344556777 PP

                                       EEECTTEEEEEE...ETTS..-EEEECEEEE--TT CS
                              GIDA 121 liveekkvkgvv...tedg..etikakavviatGt 150
                                       l ve+++++gv+   +++g  e+i+aka+v+atG 
  gi|488600414|ref|YP_007906885.1| 156 LAVEDNRCAGVYainLKSGevEAIRAKATVLATGG 190
                                       77777777776522234441145777788888876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7   6.6e-05     0.091      16      48 ..       2      33 ..       1      49 [. 0.89
   2 ?    0.1   0.0      0.29     4e+02     209     233 ..     352     377 ..     346     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.6e-05
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvaile 48
                                      +e Dvv+vG+G +GL +a   a k ++ v i+ 
  gi|488600414|ref|YP_007906885.1|  2 IEHDVVVVGSGIAGLRCAIAAAMK-GVSVGIVA 33
                                      799***************999999.88888875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
                                       CEEETTEEE-T.HHHHHHHT-EB--S CS
                              Thi4 209 revvpnlyvaG.mevaevdganRmGp 233
                                       +  +p+l+++G  +   ++ganR+G+
  gi|488600414|ref|YP_007906885.1| 352 ETSIPGLFACGeCACLSIHGANRLGS 377
                                       56789*****9446779*******96 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9   0.00014       0.2       2      32 ..       4      34 ..       3      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                       dV++VG+G aGl  a   +++Gv+v +v k
  gi|488600414|ref|YP_007906885.1|  4 HDVVVVGSGIAGLRCAIAAAMKGVSVGIVAK 34
                                      69************************99987 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.6    0.0016       2.2      30      57 ..       5      32 ..       2      56 .. 0.88
   2 ?    0.6   0.0      0.21   2.9e+02      29      79 ..     381     430 ..     371     456 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvl 57
                                       v+v+G G+aGl  + +a+  g +V ++
  gi|488600414|ref|YP_007906885.1|  5 DVVVVGSGIAGLRCAIAAAMKGVSVGIV 32
                                      69***********999999888888765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHC CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlk 79 
                                       a+ lv+G  vaG +A++ a + + +   +D +++r+  l s g +   ++k
  gi|488600414|ref|YP_007906885.1| 381 AECLVFGK-VAGEKAAEYAERSEFRSISTDEEEKRIYSLFSNGDESAYTIK 430
                                       66777775.9**********9999999999999998888776666555544 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3   0.00025      0.35       1      30 [.       5      32 ..       5      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                      Dvvv+G+G Agl+ A     a +g++v+++
  gi|488600414|ref|YP_007906885.1|  5 DVVVVGSGIAGLRCAIAA--AMKGVSVGIV 32
                                      9*************9988..999****999 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 ?   10.4   2.5   0.00042      0.59       1      24 [.       8      31 ..       8      36 .. 0.91
   2 ?   -2.0   0.0       3.3   4.5e+03      31      55 ..     113     136 ..     111     143 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                                      EE--SHHHHHHHHHHHCCTEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvll 24
                                      +vG+G++Gl +A ++a +g++v +
  gi|488600414|ref|YP_007906885.1|  8 VVGSGIAGLRCAIAAAMKGVSVGI 31
                                      8****************9999865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
                                       SSGGG-EECE..TTCEECTS---EEET CS
                     NAD_binding_8  31 lGGraasyev..pgvrvdygahifhgs 55 
                                       lGG++a ++v     r  +g hi+h+ 
  gi|488600414|ref|YP_007906885.1| 113 LGGHSAKRTVfaA-DR--TGFHIVHTL 136
                                       6777777766421.22..677777774 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.7   0.00073         1       1      29 [.       7      34 ..       7      39 .. 0.90
   2 ?   -2.6   0.0       1.8   2.5e+03     245     267 ..     167     190 ..     119     207 .. 0.63
   3 ?   -2.7   0.0         2   2.7e+03     293     305 .]     350     362 ..     347     362 .. 0.89
   4 ?   -3.4   0.0       3.2   4.4e+03     234     270 ..     453     491 ..     420     506 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00073
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEk 29
                                      +++G G aGl +ai++  +g+ ++ i+ k
  gi|488600414|ref|YP_007906885.1|  7 VVVGSGIAGLRCAIAAAMKGV-SVGIVAK 34
                                      79*******************.7889876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                       Pyr_redox_3 245 ykvktedgkkvev.kddvvlatGy 267
                                       y ++ ++g+   +  +  vlatG 
  gi|488600414|ref|YP_007906885.1| 167 YAINLKSGEVEAIrAKATVLATGG 190
                                       444444443222224455566665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2
                       Pyr_redox_3 293 teetnvpglflaG 305
                                        +et +pglf +G
  gi|488600414|ref|YP_007906885.1| 350 YCETSIPGLFACG 362
                                       689*******999 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 3.2
                       Pyr_redox_3 234 evkeikekeeey.kvktedgkkvevkddvvla.tGykpd 270
                                        +k+i+e + +y +++ +d +k+ ++d  +++ +Gy  +
  gi|488600414|ref|YP_007906885.1| 453 ALKKIRELKDRYrNIEVSDRSKIFNTDLTFAIeVGYMLE 491
                                       456666666666345556655555544444446777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 3276.61
//
Query:       gi|488600415|ref|YP_007906886.1|  [L=292]
Description: hypothetical protein Asulf_00886 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2086.06
//
Query:       gi|488600416|ref|YP_007906887.1|  [L=200]
Description: Uncharacterized metal-binding protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-64  214.8   0.3    5.3e-64  214.6   0.3    1.0  1  DUF1847   Protein of unknown function (DUF1847)


Domain annotation for each model (and alignments):
>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.6   0.3     3e-68   5.3e-64       6     156 ..      25     174 ..      21     175 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 3e-68
                           DUF1847   6 ekeileealeeykdeeekkiakaaaeveaegyakltRveeiiefakrmgykkiGiafCvglleeakalakileakgf 82 
                                         ++++eal++y d  e++ia +a +veaegy +++R++ei+efakr+g++k+G+afC+gl++ea++ ++ile++gf
  gi|488600416|ref|YP_007906887.1|  25 LMDVYDEALAQY-DGFEREIAVNAGKVEAEGYLNWCRIKEIAEFAKRCGFRKLGLAFCIGLRREARETVSILEKYGF 100
                                       568899******.9*************************************************************** PP

                           DUF1847  83 evvsviCkvgsvdkeelgieeeekvkkkkkeamCnPilQAellneaktdlnvvlGLCvGhDslfikyseapvtt 156
                                       ev+sv+Ck+g++dke +g+++e+k++kk +eamCnPi+QAe+ln+ +tdln++lGLCvGhD+lfi++s+apvt+
  gi|488600416|ref|YP_007906887.1| 101 EVFSVVCKTGAIDKEVIGLKREDKISKKDFEAMCNPIAQAEILNRLETDLNIILGLCVGHDTLFIMHSKAPVTC 174
                                       *************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1195.95
//
Query:       gi|488600417|ref|YP_007906888.1|  [L=438]
Description: Uncharacterized protein involved in propionate catabolism [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-107  358.1   0.0   6.3e-107  357.8   0.0    1.0  1  MmgE_PrpD  MmgE/PrpD family


Domain annotation for each model (and alignments):
>> MmgE_PrpD  MmgE/PrpD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.8   0.0  3.5e-111  6.3e-107       7     421 ..      11     416 ..       5     429 .. 0.95

  Alignments for each domain:
  == domain 1  score: 357.8 bits;  conditional E-value: 3.5e-111
                                       HHHH-----H..HHHHHHHHHHHHHHHHHHHHTT-HHHHTT-SSSTT-B-TT-EE-TTSS-EE-HHHHHHHHHHHHH CS
                         MmgE_PrpD   7 fvaelryddlpeevverakrlilDtlGvalaglrepavkkaleavkgtggpggatvigtgerlspvkAAfvnGaaih 83 
                                       ++   ++++l ++vver+k l+lD +G+ + + +e++++++++ +     +g++  i  g+r+ p++ A+++G+++h
  gi|488600417|ref|YP_007906888.1|  11 HII--DLKHLNSDVVERCKLLFLDLIGIPFRAEKEESSRALIRSIDIDRIKGDSIAIPYGFRTVPEYSALIMGTLSH 85 
                                       444..4567888***************************************************************** PP

                                       CTS-S-BEESSSEE-GGGGHHHHHHHHHHHHHHBHHHHHHHHHHHHHHHHHCCC--SCCCT....B-THHHHHHHHH CS
                         MmgE_PrpD  84 alDfdDthlaaelhhpsdvlpaalAvAealgasgkdlLtAivvGyEvqgrlglalsfnhyg...fhdtvtlgtfgaa 157
                                       +lDfdDth+++ +h++++++p +l+ ++ l+  gk++++A+v+Gy+++++lg+al+++++    fh t+t+g fg  
  gi|488600417|ref|YP_007906888.1|  86 SLDFDDTHRESSIHPGAVIIPSILSYSNDLD--GKKFIEAMVCGYDIACKLGMALNPEKHYargFHGTATCGVFGGV 160
                                       **************************99885..89********************9998888*************** PP

                                       HHHHHHTT--HHHHHHHHHHHHCT-B-BSGGGSTTT--CHHCHHHHHHHHHHHHHHHHHTT---TTTTT-TTTSHHH CS
                         MmgE_PrpD 158 aaaakLlgLdaeqianAlgiaatqaaglrqyrhagtkskklwaaGdAarnGveaallAkrGftGpsdilegewGfla 234
                                       aa++++ +Ld ++i +A+g a+++ +g++q++++g+++k+l +aG A+rn+v+a  lAk Gf G+++ +eg++Gfl+
  gi|488600417|ref|YP_007906888.1| 161 AAISRIFDLDFDRIKSAFGVALSMVSGSMQFLENGAWNKRL-HAGLASRNAVMAIELAKSGFIGAEKPIEGKYGFLN 236
                                       *****************************************.*********************************** PP

                                       HHSTT-----S.S-SS...SHHHHC-B---SSS-CCCHHHHHHHHHHHHHHCCTCCCEEEEEEEE-HHHHHHC---S CS
                         MmgE_PrpD 235 vlsggkdlelevkplgegesweienvlfKpypaerhthaaidaalklraelklkpddIesieirtseaalriigkkg 311
                                        +s+++d+e++v++lg  e++e++++ +K yp++r++h+a+d+al+l    +++p+ +++i +r+  a +ri+g++ 
  gi|488600417|ref|YP_007906888.1| 237 SYSENADPEKAVDGLG--ERFEVMHTGVKLYPCCRYIHPALDIALNL----EIDPESVDRIAVRMVTAGYRIVGEPI 307
                                       ***********99999..9**************************98....466899******************99 PP

                                       ....---SHHHHCT-CCHHHHHHHHCS---CCCCSCCCCTSCHHCCHHCCEEEEE-HHHHHHHTTT---EEEEETTS CS
                         MmgE_PrpD 312 ....ppenradadhSlqyvvAvalldgrvtledfederladpevqaLrekvevvedpeltadypekrsivvvvlkdg 384
                                           +p+n++da++Sl+y++A+al+++r t++d + e++ d++v+++++k++v++d el+ +ypek++   vvl+ +
  gi|488600417|ref|YP_007906888.1| 308 grkrDPRNAVDAQFSLPYALATALVRKRFTVDDLSRESIMDSRVREVMKKIDVQADGELDVEYPEKWA---VVLEID 381
                                       9999****************************************************************...666667 PP

                                       -B---EEESS-TTSGGHHHHHHHHHHHHHHHHHCCS- CS
                         MmgE_PrpD 385 grtleerveypkGhprnplsreeleeKfrrlaegvls 421
                                       g+++  r +yp+G+p+ p +  e+e+K+r+l++g+ +
  gi|488600417|ref|YP_007906888.1| 382 GEEY--RKDYPRGDPEDPADFSEVENKVRTLMNGRAE 416
                                       8766..56************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2922.51
//
Query:       gi|488600418|ref|YP_007906889.1|  [L=293]
Description: Citrate lyase beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-44  150.6   0.0    5.2e-44  150.0   0.0    1.2  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
    4.2e-18   65.6   0.0    4.4e-10   39.2   0.0    2.2  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
  ------ inclusion threshold ------
      0.011   14.2   0.4       0.18   10.2   0.0    2.1  2  PEPcase_2       Phosphoenolpyruvate carboxylase


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.0   0.0   8.7e-48   5.2e-44       1     221 []       5     222 ..       5     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 8.7e-48
                                       EEEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHH CS
                         HpcH_HpaI   1 riglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqd 77 
                                       r+ lf+pg+n + + k    ++D  ++DlEdav +++K++AR  v++a++ l++ +    + +VR+ns  +     d
  gi|488600418|ref|YP_007906889.1|   5 RSALFIPGNNYRAILKSEKIDFDIAIFDLEDAVPVNDKETARIFVRDAIERLKF-NGR--KKFVRINSDYDD----D 74 
                                       789***************************************************.655..9******99885....5 PP

                                       GG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEEEE-HH CS
                         HpcH_HpaI  78 le.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgvflGae 152
                                       l+ ++  g+++v++Pk e++ +++++++ l + e ++r   +e+r++  iEsa+gv+n  eIa +++++ ++++Ga 
  gi|488600418|ref|YP_007906889.1|  75 LNeIALRGLDGVMLPKSESERDIRNLERKLSRLE-DERN-LNEIRIIPLIESARGVMNSFEIAsSSDRIVALAFGAV 149
                                       555999****************************.5555.589********************************** PP

                                       HHHHHTT-TT...STTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSH.HHHHHHHHTTHCEEEEEEHHHHHHHH CS
                         HpcH_HpaI 153 Dlsadlgtkr...spegtevldareriltaaraagiaaldtvasdi.ddaegflaegalfvalGfdgkllinp 221
                                       D+ ++lg++    s+ + e+l+ar++i+ aa+aag++a+d+ ++++  d eg+l+e++l+ +lGfdgkl+i+p
  gi|488600418|ref|YP_007906889.1| 150 DYYRTLGRSYfkfSNTQIELLFARSMIVNAAKAAGLKAIDSPFFGMlIDMEGLLKESKLAFQLGFDGKLAIHP 222
                                       *******86422278888999********************888752799**********************8 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.3e-09   1.4e-05      11     147 ..       8     131 ..       5     161 .. 0.75
   2 !   39.2   0.0   7.3e-14   4.4e-10     249     319 ..     198     272 ..     173     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.3e-09
                    C-C_Bond_Lyase  11 LYmPatrediaekilkqklegltslvlclEDavseeeveaAeenlkellkelaeaekekekeelpllFvRvRspeql 87 
                                       L++P+++   ++ ilk++  +    +++lEDav  ++ e+A   +++++++l+ +            FvR+ s    
  gi|488600418|ref|YP_007906889.1|   8 LFIPGNN---YRAILKSEKIDFDIAIFDLEDAVPVNDKETARIFVRDAIERLKFNG--------RKKFVRINSDY-D 72 
                                       6777776...67788889999999****************************9954........456****8765.4 PP

                    C-C_Bond_Lyase  88 kellerlgealelltGfvlPkftse.sleeylealkkanek.lgkklllmPilEteevleke 147
                                       ++l e+    l+ l+G++lPk +se  +++  + l++++++   +++ ++P +E+++ + + 
  gi|488600418|ref|YP_007906889.1|  73 DDLNEIA---LRGLDGVMLPKSESErDIRNLERKLSRLEDErNLNEIRIIPLIESARGVMNS 131
                                       7787775...9**********977614666667777765540457799*******9877332 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 7.3e-14
                    C-C_Bond_Lyase 249 dldglirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedAldiles.akg.....gvfkseyankmnEvkph 319
                                       d++gl++E +l  + G+ GK +IhP++i++++++++ skee+e+A++i+es +++     gv++ e  ++m++ + +
  gi|488600418|ref|YP_007906889.1| 198 DMEGLLKESKLAFQLGFDGKLAIHPNHIKIINEVFSPSKEEFEEARKIVESyEAAkqrgeGVITFE--GRMVDFASY 272
                                       799**********************************************98432123434555555..888777665 PP

>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.1e-05      0.18     156     191 ..     101     136 ..      83     158 .. 0.81
   2 ?    2.2   0.2    0.0086        51      24      75 ..     233     288 ..     219     293 .] 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.1e-05
                                       .HHHHH-SS---TTSSEEEEEE-SHHHHHTHHHHHH CS
                         PEPcase_2 156 dlkvkelvgelkpesievIPLiEdkesllnideive 191
                                       + k++ l+ e + ++i++IPLiE +  ++n+ ei +
  gi|488600418|ref|YP_007906889.1| 101 ERKLSRLEDERNLNEIRIIPLIESARGVMNSFEIAS 136
                                       467788899999***************999988865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.0086
                                       B-TTTHHHHHHHHHSS----....EEEEE-SSB---TTHHHHHHHHHHC..TT--T CS
                         PEPcase_2  24 isgedEveEAykalselgvd....EvMwDfEGKevdehvvrkllseyeeffkekvl 75 
                                          ++E eEA k + ++++     E  + fEG+ vd    ++    +e + + ++ 
  gi|488600418|ref|YP_007906889.1| 233 SPSKEEFEEARKIVESYEAAkqrgEGVITFEGRMVDFASYKQARDVVETYLEIERR 288
                                       44567788887777765553222288999999999965555544444444445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2073.35
//
Query:       gi|488600419|ref|YP_007906890.1|  [L=293]
Description: Succinyl-CoA synthetase, alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-22   78.0   1.1    6.4e-22   78.0   1.1    2.0  2  CoA_binding    CoA binding domain
    5.2e-10   39.3   0.3    9.3e-10   38.4   0.3    1.4  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    5.5e-06   26.9   0.2      3e-05   24.5   0.0    2.2  2  CoA_binding_2  CoA binding domain
    5.4e-05   23.1   0.2    0.00011   22.1   0.1    1.5  1  Ligase_CoA     CoA-ligase
  ------ inclusion threshold ------
       0.06   13.6   0.0        1.7    8.9   0.0    2.1  2  EloA-BP1       ElonginA binding-protein 1


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   1.1   1.8e-25   6.4e-22       1      92 [.       6      96 ..       6      99 .. 0.96
   2 ?   -0.7   0.1      0.68   2.4e+03      12      46 ..     159     194 ..     148     236 .. 0.56

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1.8e-25
                                      CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC.TTTEEEEES-HHHHHHH CS
                       CoA_binding  1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt.evdvavitvPaesaqea 78
                                      d+++ v+++G++g+  +g  + +++l+yg+k+v+gv+p+k g++v g+pvy+sv+e++ +  e+d++v+++P +++++a
  gi|488600419|ref|YP_007906890.1|  6 DENKTVLIQGITGR--EGSARARFMLEYGTKVVAGVTPGKKGENVWGIPVYDSVEEVVGEFgEIDISVTFIPGPQVKDA 82
                                      57899*********..*********************************************66**************** PP

                                      HHHHHHTT-SEEEE CS
                       CoA_binding 79 vdelveagikgivi 92
                                      v+e+++ag+ ++v+
  gi|488600419|ref|YP_007906890.1| 83 VIEAINAGVGTVVM 96
                                      **********9996 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.68
                                       TSHHHHHHHHHHHHHHECEEEEEEC-TT.TTTCEET CS
                       CoA_binding  12 gglgiaglyhfkeklkygikavfgvnpr.kvgtevl 46 
                                       +g  +a ++   +k +yg++ ++ ++ +  +gt+  
  gi|488600419|ref|YP_007906890.1| 159 SGGQTATVSWLVSKHGYGVSTAVHTGTEpVLGTNLA 194
                                       444444444444555555554444433324555544 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 !   38.4   0.3   2.6e-13   9.3e-10       1     133 [.     150     286 ..     150     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.6e-13
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGne..advdvadlleylaedpetkvillylEsird.grkflsa 74 
                                       +G++a+is SG+  +++   ++++g g+s++v++G e  + +++a+++ + +ed+e ++i+++ E  +   ++ +++
  gi|488600419|ref|YP_007906890.1| 150 AGRVAVISRSGGQTATVSWLVSKHGYGVSTAVHTGTEpvLGTNLAEYVLMANEDDESEAIVIFGEIGGIaEEETAEV 226
                                       599**************9999999************733566889******************99666525778888 PP

                      Succ_CoA_lig  75 arraarkkpvvvlksGr...seagaraaashtgalagsdavvdaafrqaGvlrvdsleelfd 133
                                       + ++   kpv+++ +G    s      a++  +   gs++  ++a+++aGv++vds  e+++
  gi|488600419|ref|YP_007906890.1| 227 MDKVD--KPVIAYIAGAklpSGIRFSHASAIIEGKKGSYESKREALENAGVMVVDSPIEIVS 286
                                       88887..*********843333333333444445568999999************9988765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   8.4e-09     3e-05      13     114 ..      18     127 ..       9     129 .. 0.87
   2 ?   -0.7   0.0      0.53   1.9e+03      20      44 ..     166     192 ..     151     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.4e-09
                                       TSHHHHHHHHHHHHT--EEE.ESSS-..SEETTEES----T.......T--EEEE-S-HHHHGGGHHHHHHH--SEE CS
                     CoA_binding_2  13 gkfgykvlryllehglpvvp.Vnpke..eeilgekvyaslae.d..pepvdlvdvftppeatpeivkealalgakav 83 
                                       g+ g   +r++le g +vv+ V+p +  e ++g +vy s++e     +++d+ + f+p   + + v ea+ +g+ +v
  gi|488600419|ref|YP_007906890.1|  18 GREGSARARFMLEYGTKVVAgVTPGKkgENVWGIPVYDSVEEvVgeFGEIDISVTFIPGPQVKDAVIEAINAGVGTV 94 
                                       66777788999998887775599988889************8658889***************************** PP

                                       EE-TT..---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  84 wlqpg..sedeeaaelaeeagirvvgdrCilve 114
                                       ++  +    ++++  + +++g ++vg+++++++
  gi|488600419|ref|YP_007906890.1|  95 VMPVErvPLHDTLEIISHARGTTIVGPGSLGII 127
                                       **999877888888888889*********9996 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.53
                                       HHHHHH.HT--E.EEESSS-SEETTEE CS
                     CoA_binding_2  20 lrylle.hglpv.vpVnpkeeeilgek 44 
                                       +++l++ hg+ v ++V+   e +lg +
  gi|488600419|ref|YP_007906890.1| 166 VSWLVSkHGYGVsTAVHTGTEPVLGTN 192
                                       577877788777568888888888865 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1     3e-08   0.00011      59     152 ..     191     275 ..     155     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3e-08
                                       HHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTT CS
                        Ligase_CoA  59 tkriealkklaadpevkvilldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleea 135
                                       t+  e +    +d+e ++i++ +++G g +e++ ae+++++         +pv+a++aG++ + + + ++a a+ e+
  gi|488600419|ref|YP_007906890.1| 191 TNLAEYVLMANEDDESEAIVIFGEIG-GIAEEETAEVMDKVD--------KPVIAYIAGAKLPSGIRFSHASAIIEG 258
                                       566777888899**************.999998888887664........589************************ PP

                                       TSSEEE-SSHHHHHHHH CS
                        Ligase_CoA 136 gveiasskaqalraaka 152
                                       +   ++sk +al+ a++
  gi|488600419|ref|YP_007906890.1| 259 KKGSYESKREALENAGV 275
                                       ************99986 PP

>> EloA-BP1  ElonginA binding-protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.041   1.5e+02     102     141 ..     160     201 ..     142     206 .. 0.85
   2 ?    8.9   0.0   0.00048       1.7       1      42 [.     232     273 ..     232     275 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.041
                          EloA-BP1 102 gklaaktsfsiekksks..kkeeelkgatlYekLkeylLtee 141
                                       g ++a++s+ + k++    + +++ ++++l ++L ey+L  +
  gi|488600419|ref|YP_007906890.1| 160 GGQTATVSWLVSKHGYGvsTAVHTGTEPVLGTNLAEYVLMAN 201
                                       667899********9997767888889**********99765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00048
                          EloA-BP1   1 rPvipkefgsKvPtniRqrYlnlfideclkiyssedeAyerA 42 
                                       +Pvi   +g+K P  iR +    +i+     y+s+ eA+e+A
  gi|488600419|ref|YP_007906890.1| 232 KPVIAYIAGAKLPSGIRFSHASAIIEGKKGSYESKREALENA 273
                                       799*************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1931.77
//
Query:       gi|488600420|ref|YP_007906891.1|  [L=98]
Description: hypothetical protein Asulf_00891 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.6e-05   22.9   3.5      0.082   13.5   1.1    2.2  2  Fer4_7      4Fe-4S dicluster domain
     0.0063   16.5   7.5       0.27   11.4   1.1    2.4  2  Fer4_6      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.073   13.2   8.6        4.9    7.3  10.1    2.1  2  Fer4_10     4Fe-4S dicluster domain
      0.089   13.0   9.0        2.6    8.3   2.6    2.1  2  Fer4_9      4Fe-4S dicluster domain
       0.11   12.7   6.9       0.45   10.7   7.3    1.7  2  Fer4_21     4Fe-4S dicluster domain
        0.5   10.3   0.3        0.5   10.3   0.3    3.0  3  Fer4        4Fe-4S binding domain
       0.53   10.9   5.3        6.6    7.5   0.2    2.2  2  Fer4_4      4Fe-4S binding domain
        4.3    7.6   9.7        6.8    7.0   2.3    2.3  2  Fer4_2      4Fe-4S binding domain
        4.7    7.9  11.2         11    6.7   1.1    3.1  3  Antistasin  Antistasin family


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 !   13.5   1.1   4.1e-05     0.082      26      48 ..       7      31 ..       2      33 .. 0.87
   2 !    9.9   0.1   0.00057       1.1       4      20 ..      61      77 ..      60      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                            Fer4_7 26 kgtekveidpekClgCga..CvavC 48
                                       +t++++id++kC +C++  C+++C
  gi|488600420|ref|YP_007906891.1|  7 TRTMRIVIDHSKCETCDSydCAKAC 31
                                      4678999*********9888***** PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00057
                            Fer4_7  4 gCgaCvaaCpvkaield 20
                                      +C  C+  Cp++a+++ 
  gi|488600420|ref|YP_007906891.1| 61 ECLSCEIHCPHSAVKIF 77
                                      6999******9999876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   1.1   0.00013      0.27       2      20 ..      12      32 ..      11      39 .. 0.79
   2 !    8.7   0.7   0.00092       1.8      12      23 ..      62      73 ..      59      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                            Fer4_6  2 veidpdkCigC..gdCvrvCP 20
                                      ++id +kC  C  +dC+++C 
  gi|488600420|ref|YP_007906891.1| 12 IVIDHSKCETCdsYDCAKACS 32
                                      79******9663366*****7 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00092
                            Fer4_6 12 CgdCvrvCPega 23
                                      C  C+++CP+ a
  gi|488600420|ref|YP_007906891.1| 62 CLSCEIHCPHSA 73
                                      889******987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  10.1    0.0025       4.9       2      56 .]      12      70 ..      11      70 .. 0.61
   2 ?    6.4   0.5    0.0048       9.5      11      22 ..      61      72 ..      53      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0025
                           Fer4_10  2 vvidddtCirCg..kCvkaCPadl.......tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      +vid ++C  C   +C kaC  +l         +++k+ +  ++++         +c +C  +CP
  gi|488600420|ref|YP_007906891.1| 12 IVIDHSKCETCDsyDCAKAC--SLygtnilrI-KNGKPVTFFSDEDVArRDN---ECLSCEIHCP 70
                                      79*********9999*****..6767887743.3333333333333331334...4566666665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0048
                           Fer4_10 11 rCgkCvkaCPad 22
                                      +C  C   CP +
  gi|488600420|ref|YP_007906891.1| 61 ECLSCEIHCPHS 72
                                      799999999984 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.6    0.0013       2.6      21      47 ..       5      32 ..       1      36 [. 0.78
   2 ?    6.7  11.0     0.004         8       1      50 [.      18      73 ..      18      74 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                            Fer4_9 21 aaerkarlraaseeaCigCga..CveaCp 47
                                       ++r++r+ ++   +C +C +  C++aC 
  gi|488600420|ref|YP_007906891.1|  5 LKTRTMRIVIDHS-KCETCDSydCAKACS 32
                                      5667777776655.9****9999*****6 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.004
                            Fer4_9  1 kCtgCga..CveaC...pagvvvedaaerkarlraase....eaCigCgaCveaCpkga 50
                                      kC  C++  C +aC    +++ + ++++         +     +  +C +C+ +Cp+ a
  gi|488600420|ref|YP_007906891.1| 18 KCETCDSydCAKACslyGTNILRIKNGKPVTFFS---DedvaRRDNECLSCEIHCPHSA 73
                                      7****8667*****77733333333333333332...223452334677999****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 ?   10.7   7.3   0.00023      0.45       2      52 ..      13      70 ..      12      76 .. 0.68
   2 ?    5.2   0.8     0.012        23      10      24 ..      61      75 ..      57      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                           Fer4_21  2 ridedkCigCgk..CliaCedtshqaieidaktvl........kvvedeCvGCnlCssvCP 52
                                      +id++kC  C +  C++aC+  +++ ++i++ + +        + +++eC     C + CP
  gi|488600420|ref|YP_007906891.1| 13 VIDHSKCETCDSydCAKACSLYGTNILRIKNGKPVtffsdedvARRDNECLS---CEIHCP 70
                                      69********8555*************8887776622233221334555555...556677 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                           Fer4_21 10 gCgkCliaCedtshq 24
                                      +C +C i C+ ++++
  gi|488600420|ref|YP_007906891.1| 61 ECLSCEIHCPHSAVK 75
                                      577888888866655 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   0.5      0.01        20       1      11 [.      12      22 ..      12      24 .. 0.89
   2 ?   -0.0   0.6      0.44   8.8e+02      14      18 ..      27      31 ..      25      31 .. 0.93
   3 ?   10.3   0.3   0.00025       0.5      10      23 ..      61      74 ..      60      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.01
                                      EEEETTTSSS- CS
                              Fer4  1 vvideekCigC 11
                                      +vid +kC  C
  gi|488600420|ref|YP_007906891.1| 12 IVIDHSKCETC 22
                                      69******999 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.44
                                      HHHHS CS
                              Fer4 14 CvevC 18
                                      C+++C
  gi|488600420|ref|YP_007906891.1| 27 CAKAC 31
                                      ***** PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00025
                                      S-THHHHHSTTTEE CS
                              Fer4 10 gCGaCvevCPvgAI 23
                                       C  C+  CP+ A 
  gi|488600420|ref|YP_007906891.1| 61 ECLSCEIHCPHSAV 74
                                      59*********996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.2     0.015        30       3      15 ..      18      32 ..      16      42 .. 0.90
   2 ?    7.5   0.2    0.0033       6.6       5      15 ..      60      70 ..      60      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                            Fer4_4  3 rCigCgs..CvaaCP 15
                                      +C  C+s  C  aC+
  gi|488600420|ref|YP_007906891.1| 18 KCETCDSydCAKACS 32
                                      7999**999*****7 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0033
                            Fer4_4  5 igCgsCvaaCP 15
                                      ++C sC++ CP
  gi|488600420|ref|YP_007906891.1| 60 NECLSCEIHCP 70
                                      5899******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 ?    7.0   2.3    0.0034       6.8       2      20 ..      11      31 ..      10      32 .. 0.87
   2 ?    5.0   0.9     0.015        30      11      22 .]      60      71 ..      60      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0034
                            Fer4_2  2 pvvvdtdrCigCg..aCvsaC 20
                                      ++v+d  +C  C    C +aC
  gi|488600420|ref|YP_007906891.1| 11 RIVIDHSKCETCDsyDCAKAC 31
                                      589999******556****** PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.015
                            Fer4_2 11 igCgaCvsaCPa 22
                                      ++C +C   CP+
  gi|488600420|ref|YP_007906891.1| 60 NECLSCEIHCPH 71
                                      58****888*97 PP

>> Antistasin  Antistasin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.008        16      15      24 ..      13      22 ..      12      23 .. 0.89
   2 ?    2.5   1.5      0.12   2.3e+02       1      13 [.      22      35 ..      22      38 .. 0.83
   3 ?    6.7   1.1    0.0056        11       1      12 [.      62      71 ..      60      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.008
                        Antistasin 15 qtDenGCpiC 24
                                      ++D++ C++C
  gi|488600420|ref|YP_007906891.1| 13 VIDHSKCETC 22
                                      89******** PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                        Antistasin  1 CpslnCelrCp.yG 13
                                      C s++C + C+ yG
  gi|488600420|ref|YP_007906891.1| 22 CDSYDCAKACSlYG 35
                                      98988*****8666 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0056
                        Antistasin  1 CpslnCelrCpy 12
                                      C  l Ce++Cp+
  gi|488600420|ref|YP_007906891.1| 62 C--LSCEIHCPH 71
                                      6..44******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 633.93
//
Query:       gi|488600421|ref|YP_007906892.1|  [L=405]
Description: Succinyl-CoA synthetase, beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-35  120.5   0.2    9.9e-35  119.9   0.2    1.3  1  ATP-grasp_2   ATP-grasp domain
    2.3e-09   37.0   0.1    4.3e-09   36.1   0.1    1.3  1  Citrate_bind  ATP citrate lyase citrate-binding
    6.8e-09   35.8   0.5    1.5e-08   34.7   0.5    1.5  1  GARS_A        Phosphoribosylglycinamide synthetase, ATP-grasp
    1.1e-06   28.3   0.2    2.3e-06   27.2   0.2    1.6  1  ATP-grasp_5   ATP-grasp domain
    0.00043   19.9   0.2    0.00077   19.1   0.2    1.4  1  ATP-grasp     ATP-grasp domain
  ------ inclusion threshold ------
       0.05   13.2   0.0        0.1   12.2   0.0    1.4  1  RimK          RimK-like ATP-grasp domain
       0.15   11.5   0.1       0.27   10.7   0.1    1.3  1  CPSase_L_D2   Carbamoyl-phosphate synthase L chain, ATP bindi


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.2   3.8e-38   9.9e-35       1     201 [.       3     187 ..       3     188 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 3.8e-38
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellg 77 
                                       +l+Eyq+ke+l+k g+kvpe++vae+ e+++e a+k++    v+KaQ l+ GR Kag vk++++  e++e+ +el+ 
  gi|488600421|ref|YP_007906892.1|   3 KLYEYQGKELLKKEGIKVPEFFVAENIEQLKEFAEKMNPPF-VLKAQLLISGRMKAGAVKFASNIREVEEYGRELFE 78 
                                       69***********************************9988.*********************************** PP

                                       SEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETT..TTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTT CS
                       ATP-grasp_2  78 kelvtkqtgkeGkkvekvlveealdikkElYlsivlDra..skkvvviaSseGGvdiEevaakkPekiikvaidpak 152
                                        + +       G k +kvl+e+a+   +E+Y si++  a   k + +++S  GG+d+Ee      ++++++++d +k
  gi|488600421|ref|YP_007906892.1|  79 RQFK-------GFKAKKVLIEQAVS-GEEYYASIIVNPAynVKAPEILFSPYGGIDVEE------HEVFRFVVDYKK 141
                                       ****.......**********9997.67********9752167899************9......89********** PP

                                       B--HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                       ATP-grasp_2 153 glkeeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                       g++++   ++++    +    + +a++++kly++fv+ da++vE+NPL 
  gi|488600421|ref|YP_007906892.1| 142 GFDKTRFMDLIDGQVGD---PEAVADFLEKLYSVFVKADARIVEVNPLF 187
                                       ****9999998764433...46899**********************95 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 !   36.1   0.1   1.7e-12   4.3e-09      28     165 ..     255     383 ..     251     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.7e-12
                      Citrate_bind  28 pkgriwtlvaGGGasvvyaDtiadlglaselanYgeysGapseeqtyeyaktildlmtrekrpdgkvliiGggianf 104
                                       +kg i+    GGGas++ aD+++ +g    lanY++ sG+p  +++y++ k+i+      +  +g v + G+  a  
  gi|488600421|ref|YP_007906892.1| 255 KKGYIAFHGIGGGASMLSADAMIRKG--LVLANYADSSGNPPASKIYKLIKVIMAQ----EGIEGYV-LAGSVFASQ 324
                                       5788888889**************99..56*******************9999543....3345654.456666665 PP

                      Citrate_bind 105 tnvaatfkgiiraleelksklkehkvkiyvrrggpnyqeglkamkelgeelglpikvfgpe 165
                                        +  +  +++++a++el++kl e    i +  +g++ +e+ +++ke  +++++  +++g++
  gi|488600421|ref|YP_007906892.1| 325 -EQWHHAHAVVKAFRELENKLGE-GFPIVILLAGNKEKESHEILKEGLSKTKFRFEIYGRD 383
                                       .55566678**********9976.688999999**************************97 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.5   5.8e-12   1.5e-08       7      99 ..      10     105 ..       6     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.8e-12
                                       HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT....-EEEESSHHHHHHHHHHHCTS-TTCCC CS
                            GARS_A   7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagK....gvivakseeealkavkeilekkkfGea 79 
                                       k+llkk gi+ +e+ + ++ e++ke+ e+++ +  V+Ka+ l +g+     v+ a++ +e  ++ +e++e++  G  
  gi|488600421|ref|YP_007906892.1|  10 KELLKKEGIKVPEFFVAENIEQLKEFAEKMNPPF-VLKAQLLISGRmkagAVKFASNIREVEEYGRELFERQFKGFK 85 
                                       99***************************99999.*******9996445468999***************9999*9* PP

                                       CSSEEEEE---SEEEEEEEE CS
                            GARS_A  80 gekvviEelleGeEvsllal 99 
                                        +kv+iE+ ++GeE     +
  gi|488600421|ref|YP_007906892.1|  86 AKKVLIEQAVSGEEYYASII 105
                                       **************866555 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2     9e-10   2.3e-06      10     123 ..       4     110 ..       2     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 9e-10
                       ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeile 86 
                                       L+e++ kell+  gi+v+e+ +a++ e+  e ae+++ p vlK +   i+ + ++g v++    a+++r+  e  +e
  gi|488600421|ref|YP_007906892.1|   4 LYEYQGKELLKKEGIKVPEFFVAENIEQLKEFAEKMNPPFVLKAQL-LISGRMKAGAVKF----ASNIREVEEYGRE 75 
                                       99*****************************************985.599*********9....5555555555555 PP

                       ATP-grasp_5  87 rvkekspeariegvlVqemakrggrElivgvteDpvF 123
                                        +++++++ + ++vl+++ +   g E   ++   p +
  gi|488600421|ref|YP_007906892.1|  76 LFERQFKGFKAKKVLIEQAVS--GEEYYASIIVNPAY 110
                                       555578889999999999888..66666555555544 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   0.2     3e-07   0.00077       2      75 ..      14      98 ..      13     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3e-07
                                      HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEE.EECTCCGHHCHHHHC...........GTTCEEE CS
                         ATP-grasp  2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqs.vvrseedleqaleal...........keekviv 68
                                      +k g++vp+f ++e+ e+l+e+ae+++ p+v+K ++l  +G+ +   v+ +++++++ e+            k++kv++
  gi|488600421|ref|YP_007906892.1| 14 KKEGIKVPEFFVAENIEQLKEFAEKMNPPFVLK-AQLLISGRMKAgAVKFASNIREVEEYGrelferqfkgfKAKKVLI 91
                                      789******************************.666678885542344444444444433445777888888888888 PP

                                      EE----S CS
                         ATP-grasp 69 Eefvpfe 75
                                      E+ v+ e
  gi|488600421|ref|YP_007906892.1| 92 EQAVSGE 98
                                      8888755 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.9e-05       0.1       8      47 ..      10      47 ..       6      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                                      HHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE CS
                              RimK  8 lklLakakikvpntalardeedaekliekiklrfPvvvKs 47
                                       +lL k++ikvp++ +a++ e+++++ ek++   P v+K 
  gi|488600421|ref|YP_007906892.1| 10 KELLKKEGIKVPEFFVAENIEQLKEFAEKMN--PPFVLKA 47
                                      689***************************6..9999996 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 ?   10.7   0.1    0.0001      0.27       6      91 ..      10      97 ..       7     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
                                      HHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTT....TEEEESSHHHHHHHHHHHHHHHHHHHST CS
                       CPSase_L_D2  6 kealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGk....Gmrvarneeelaelvkkalaeakaafgn 80
                                      ke+lkk +++v + + a  e++e+  ++a+++  P ++ka   + G+      ++a+n  e++e  ++ ++     f  
  gi|488600421|ref|YP_007906892.1| 10 KELLKKEGIKVPEFFVA--ENIEQLKEFAEKMNPPFVLKAQLLISGRmkagAVKFASNIREVEEYGRELFERQFKGFKA 86
                                      67788888888888877..***********************9999855533699*****************99***** PP

                                      S-EEEEE--SS CS
                       CPSase_L_D2 81 kqvlvekslkg 91
                                      k+vl+e+ ++g
  gi|488600421|ref|YP_007906892.1| 87 KKVLIEQAVSG 97
                                      ******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2518.35
//
Query:       gi|488600422|ref|YP_007906893.1|  [L=338]
Description: putative DNA-binding protein with the Helix-hairpin-helix motif [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-10   41.2   0.0    2.1e-10   41.2   0.0    1.9  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4      0.63   1.1e+04       5      13 ..      16      24 ..      13      24 .. 0.83
   2 !   41.2   0.0   1.2e-14   2.1e-10       3     163 ..      47     208 ..      45     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.63
                                      SEESS--TT CS
                                      xxxxxxxxx RF
                       Radical_SAM  5 rgCnlrCsf 13
                                        C+ rC+f
  gi|488600422|ref|YP_007906893.1| 16 DVCHSRCTF 24
                                      67*****99 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 1.2e-14
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC..CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla..vp 76 
                                        ++ C+++C++C + +     ++g s s+eei++ ++++k ek+ v + ++++   ++ ++  e+l++  +l     
  gi|488600422|ref|YP_007906893.1|  47 LSNRCRFDCKYCRNAW-----YKGISASPEEIAKVFRIMK-EKNlVSGAFISSAVDSDPDNVMEKLLETGRLIrkFH 117
                                       5789***********7.....9*****************6.666699999988866666666666666666644534 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.........HHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaadde.........kvlklmnrghtfeevlealeklreagikr 144
                                          +++ + ++   +e++e+  +l  +rvs++le+++d          + ++ +       ++ + ++k++ea+   
  gi|488600422|ref|YP_007906893.1| 118 SGYLHLKIIPGSS-PEYIEEAIDLA-NRVSINLETTSDSrmneissvkRLKEDI-F-RKQRKIQREIKKAKEARRS- 189
                                       4444555555554.9*********9.*************777776554444444.4.4448888999999999666. PP

                                       EEEEEEEBTTTSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 vvdrivglpGendeeleel 163
                                        ++ i+ + Ge+d e+ ++
  gi|488600422|ref|YP_007906893.1| 190 QTTQIIAGIGESDLEILKI 208
                                       7888888888999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1445  (0.0805957); expected 358.6 (0.02)
Passed bias filter:                      857  (0.0477997); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2106.81
//
Query:       gi|488600423|ref|YP_007906894.1|  [L=190]
Description: hypothetical protein Asulf_00894 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   80.8   0.8    1.3e-22   80.0   0.5    1.6  2  bPH_3         Bacterial PH domain
    8.3e-11   41.3   7.4    2.4e-10   39.8   7.4    1.9  1  SHOCT         Short C-terminal domain
     0.0023   17.9   0.4     0.0051   16.8   0.4    1.6  1  GvpG          Gas vesicle protein G
  ------ inclusion threshold ------
      0.044   13.4   2.0       0.13   11.8   2.0    1.9  1  ArsR          ArsR transcriptional regulator
       0.44   11.4   4.3       0.75   10.6   3.3    1.9  2  DMAP_binding  DMAP1-binding Domain


Domain annotation for each model (and alignments):
>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.5   3.5e-26   1.3e-22       1      94 [.      12     105 ..      12     106 .. 0.97
   2 ?   -2.5   0.0       1.9   6.7e+03      57      76 ..     119     138 ..     116     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.5e-26
                             bPH_3   1 LkkdEkilyltkgqinakldkpglivvTnkRiifldpkmfggkdfeeipYksIksvdlkkgllgakitlet.sgkti 76 
                                       L ++Ek+l+ +k++++    kp++++vT++R+i+ld+k++g+++ +++pY++++ v++kkg +ga+++l+  +gkt+
  gi|488600423|ref|YP_007906894.1|  12 LYPNEKVLFSVKKKLK-TELKPKYLIVTDRRVIYLDQKILGRYELIDFPYEKLEFVKFKKGKIGAEFILQSeEGKTV 87 
                                       789**********999.579********************************************************* PP

                             bPH_3  77 tidnidksevrkiveair 94 
                                       ++ ++dk+e++ ++eair
  gi|488600423|ref|YP_007906894.1|  88 KLSWMDKNEAKDAIEAIR 105
                                       *****************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                             bPH_3  57 dlkkgllgakitletsgkti 76 
                                         kkgllg + ++  +++t+
  gi|488600423|ref|YP_007906894.1| 119 AKKKGLLGEEWSISKPKETV 138
                                       55889999998888887776 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   7.4   6.6e-14   2.4e-10       1      28 []     160     187 ..     160     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 6.6e-14
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       ++L+kLkeLy++G+I++EEFe+kK+kLL
  gi|488600423|ref|YP_007906894.1| 160 EKLKKLKELYEAGVISKEEFEEKKKKLL 187
                                       68*************************8 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   1.4e-06    0.0051      18      65 ..     146     190 .]     143     190 .] 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                              GvpG  18 qvqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrL 65 
                                       qv e++  q +d+     +L +L+   +aG I++eeF+++  +lLd++
  gi|488600423|ref|YP_007906894.1| 146 QVIEKTTPQKEDPI---EKLKKLKELYEAGVISKEEFEEKKKKLLDQI 190
                                       44455555555554...56777777789*****************986 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.0   3.7e-05      0.13      33     116 ..     101     189 ..      78     190 .] 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                              ArsR  33 eeeleeklgeeveealklLkkikliEsqWrmpepgekpekeYhtsY.....skvqanfqcsledlsdiievafmsde 104
                                        e +++ l++ + e +++ kk +l+ + W++++p+e+  +    +      +  + + +  l+ l ++ e+ ++s+e
  gi|488600423|ref|YP_007906894.1| 101 IEAIRDALNATAVEQISIAKKKGLLGEEWSISKPKETVARTLPMTQviektTPQKEDPIEKLKKLKELYEAGVISKE 177
                                       34566777788999*********************998877544321111022334445566677777777777777 PP

                              ArsR 105 eleelvekieke 116
                                       e+ee  +k+ ++
  gi|488600423|ref|YP_007906894.1| 178 EFEEKKKKLLDQ 189
                                       777777777665 PP

>> DMAP_binding  DMAP1-binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.9     1e+04      33      52 ..      69      86 ..      68     115 .. 0.54
   2 ?   10.6   3.3   0.00021      0.75      11      39 ..     160     188 ..     156     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.9
                      DMAP_binding 33 kklkLLreFlpnslkae.nqa 52
                                      kk k+ +eF+   l++e  ++
  gi|488600423|ref|YP_007906894.1| 69 KKGKIGAEFI---LQSEeGKT 86
                                      5666666777...44433222 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                      DMAP_binding  11 erLaeLeldlseGdiTeKgyekkklkLLr 39 
                                       e+L++L + ++ G i++++ e kk+kLL+
  gi|488600423|ref|YP_007906894.1| 160 EKLKKLKELYEAGVISKEEFEEKKKKLLD 188
                                       69**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1239.21
//
Query:       gi|488600424|ref|YP_007906895.1|  [L=289]
Description: hypothetical protein Asulf_00895 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0017   17.3   0.5     0.0017   17.3   0.5    1.5  2  DUF4781          Domain of unknown function (DUF4781)
  ------ inclusion threshold ------
        1.5    8.1  12.2        2.4    7.4  11.6    1.8  1  OST3_OST6        OST3 / OST6 family, transporter family
        1.6    8.6  13.7      0.067   13.1   1.7    2.7  3  DUF2975          Protein of unknown function (DUF2975)
        6.1    5.5  17.9    1.6e+02    0.8  17.9    2.0  1  DUF2207          Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF4781  Domain of unknown function (DUF4781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       0.5   2.3e+03     259     295 ..      20      56 ..      17      66 .. 0.77
   2 !   17.3   0.5   3.7e-07    0.0017     174     275 ..     126     228 ..     116     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.5
                           DUF4781 259 iIekaqnqkikdyretlrsnrsrkaFkkilketakkn 295
                                       iI++   + i++++e  +++++r  F +ilke  + +
  gi|488600424|ref|YP_007906895.1|  20 IIMNFIFKLINEIKEFFEKRSKRYLFLRILKEYDAIK 56 
                                       6777777889999999988889999999998866555 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.7e-07
                           DUF4781 174 aagataalsaaaaagkevsqaaqlavnginvssivisgtgvansvydlvlk.vaddeqlsaldvlqlsa.sllffth 248
                                        a+ +  l+a++++  +    + la++g++++ +++s  + a+ +y  ++k   d+ ql++l +l ++a  l++ft+
  gi|488600424|ref|YP_007906895.1| 126 VAVLSILLTAISKEKSIYIYWTLLAMEGAIIGYLIASYLSYAY-LYISFKKiGIDETQLTKLFLLIFAAiFLVLFTS 201
                                       455677888888888888888999**************99965.6777788677889*******9998626899*** PP

                           DUF4781 249 svvnlklAskiIekaqnqkikdyretl 275
                                       +++++ + s i ++++ + i+ +r+++
  gi|488600424|ref|YP_007906895.1| 202 KIISFPFISSIRKNTEIEVIEAFRNSI 228
                                       **********************99875 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 ?    7.4  11.6   0.00054       2.4     124     278 ..      50     200 ..      24     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00054
                         OST3_OST6 124 fdaealakfisertgvkirikrppnyskiiitallvlllvlllklrrklllkilksktlwavlslliillftsGymf 200
                                       ++ +a+ + i +  +++  + rp n+ ++ +t++++ ++++++  + k+   +l s tl+++ls++       G  f
  gi|488600424|ref|YP_007906895.1|  50 KEYDAIKRCIDSVSQKTSDYLRPKNIRRMYNTIIIISAIIFIVLPYLKYQ--NLDSSTLILLLSFISLGPIFIGLIF 124
                                       56788999999************************999999999888888..78*********************** PP

                         OST3_OST6 201 nqIrgvpfvakdekggisyfaggsqnQfgaEtqivally.gllallvilLiklvpriknakvqrvlvivllvlifll 276
                                              ++    k++ +y++      +++E+ i++ l    l+ + + + ++   i +++  +++ +++++++++l
  gi|488600424|ref|YP_007906895.1| 125 LVAVLSILLTAISKEKSIYIYWT---LLAMEGAIIGYLIaSYLSYAYLYISFKKIGIDETQLTKLFLLIFAAIFLVL 198
                                       98887777777778887899876...7999**999977413455555555555555666777777777777666666 PP

                         OST3_OST6 277 fs 278
                                       f 
  gi|488600424|ref|YP_007906895.1| 199 FT 200
                                       54 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         1   4.6e+03      35      47 ..      22      31 ..       9      44 .. 0.45
   2 ?   13.1   1.7   1.5e-05     0.067      48     112 ..      67     126 ..      54     141 .. 0.72
   3 ?    2.8   1.2     0.023     1e+02      62     109 ..     155     199 ..     153     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1
                           DUF2975 35 lvqlwkLlrsirk 47
                                      +     ++++i++
  gi|488600424|ref|YP_007906895.1| 22 MNF---IFKLINE 31
                                      222...3333333 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.5e-05
                           DUF2975  48 gevFspanvrrLrriglaliaaalllaagivalallaelelapgvvllllgvafaslvigllvlv 112
                                       +++  p+n+rr+ + + ++ a+++++++   +l + +   ++  ++lll  ++++ ++igl+ lv
  gi|488600424|ref|YP_007906895.1|  67 SDYLRPKNIRRMYNTIIIISAIIFIVLP---YLKYQNL--DSSTLILLLSFISLGPIFIGLIFLV 126
                                       5666777777777666655555555555...5555555..56788999999**********9887 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.023
                           DUF2975  62 iglaliaaalllaagivalallaelelapgvvllllgvafaslvigll 109
                                       i++ lia+ l++a +++ +  ++    +  ++  l++++fa+++++l+
  gi|488600424|ref|YP_007906895.1| 155 IIGYLIASYLSYAYLYISFKKIGI---DETQLTKLFLLIFAAIFLVLF 199
                                       777778888888888887777777...566777777888888888887 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8  17.9     0.036   1.6e+02     321     431 ..      20     129 ..       4     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.036
                           DUF2207 321 alldlLfdkseegkslkeikkyakkskk..kakkfkkalkkwksavkk...kergyfdkkgkkklkklsalglglii 392
                                        +++++f+       ++eik++++k +k  +  ++ k+++++k+ +++   k++ y++ k+ ++++  ++++ ++i+
  gi|488600424|ref|YP_007906895.1|  20 IIMNFIFKL------INEIKEFFEKRSKryLFLRILKEYDAIKRCIDSvsqKTSDYLRPKNIRRMYNTIIIISAIIF 90 
                                       568999944......5788888888777788888888888888888888889999***9988777666666666666 PP

                           DUF2207 393 lglilillallllvlllvfllilllillliaiivlllfs 431
                                       ++l  + + +l   +l+ +l++++l+ ++i++i+l+   
  gi|488600424|ref|YP_007906895.1|  91 IVLPYLKYQNLDSSTLILLLSFISLGPIFIGLIFLVAVL 129
                                       666666555555555555555555555555555444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1914.90
//
Query:       gi|488600425|ref|YP_007906896.1|  [L=68]
Description: hypothetical protein Asulf_00896 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-14   52.5   3.2    5.2e-14   52.2   3.2    1.1  1  DUF2283   Protein of unknown function (DUF2283)
  ------ inclusion threshold ------
      0.013   15.3   0.4        1.3    8.9   0.4    2.1  1  SHD1      SLA1 homology domain 1, SHD1
      0.063   12.9   0.1      0.066   12.8   0.1    1.0  1  DUF4998   Domain of unknown function


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 !   52.2   3.2   8.7e-18   5.2e-14       2      46 ..       4      48 ..       3      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 8.7e-18
                           DUF2283  2 itYDpeaDalYIylsegpveeseevdddiilDfDedGrlvGIEiL 46
                                      +++D+e+ a YI++++++++ se ++d++++D+De+G++vGIE+L
  gi|488600425|ref|YP_007906896.1|  4 VEFDDEVKAIYIRFKDEKIAISEPLADNVVIDVDEKGEIVGIEVL 48
                                      799*****************************************8 PP

>> SHD1  SLA1 homology domain 1, SHD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4   0.00022       1.3      22      46 ..      10      36 ..       3      68 .] 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00022
                              SHD1 22 VeAeflglkdgkirLhk..vnGvkiaV 46
                                      V A ++ +kd+ki +    +++v+i+V
  gi|488600425|ref|YP_007906896.1| 10 VKAIYIRFKDEKIAISEplADNVVIDV 36
                                      667777777777766543355555555 PP

>> DUF4998  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.1e-05     0.066      44      89 ..       7      60 ..       2      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                           DUF4998 44 dpkitkakifwnnkk........dsvevpverkegvdtveviidnLeEgsytFs 89
                                      d +++ + i ++++k        d v+++v++k +   +ev++++L+E++++F 
  gi|488600425|ref|YP_007906896.1|  7 DDEVKAIYIRFKDEKiaiseplaDNVVIDVDEKGEIVGIEVLLPKLDERQMEFV 60
                                      67788888888888888888889****************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 439.26
//
Query:       gi|488600426|ref|YP_007906897.1|  [L=84]
Description: hypothetical protein Asulf_00897 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-11   42.1   0.5    9.6e-11   41.9   0.5    1.1  1  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 !   41.9   0.5   5.4e-15   9.6e-11       1      54 [.       5      72 ..       5      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 5.4e-15
                           DUF4258  1 fsaHArermaeRgIseedieevlenGe.iieeys.............lvlgktsegrplhvvvapded 54
                                      +s+HA+ r  +RgI++edie +++  e iie +              lv ++++  ++++vv++++ d
  gi|488600426|ref|YP_007906897.1|  5 LSNHALHRANDRGIRREDIELTIREAEeIIEVKFgrkaafrqfgdkfLVVIFEEQKDEIVVVTELKVD 72
                                      69**********************9999********88776666666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 587.41
//
Query:       gi|488600427|ref|YP_007906898.1|  [L=60]
Description: hypothetical protein Asulf_00898 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 393.90
//
Query:       gi|488600428|ref|YP_007906899.1|  [L=40]
Description: hypothetical protein Asulf_00899 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.2   0.0       0.11   12.2   0.0    1.0  1  FAM184    Family with sequence similarity 184, A and B


Domain annotation for each model (and alignments):
>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.3e-06      0.11      86     117 ..       8      39 ..       2      40 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-06
                            FAM184  86 relkleaehsqkvvelsreveevkrkFeeklr 117
                                       +e++l+ e+ + v+ l+ ev+e++r Fe+ ++
  gi|488600428|ref|YP_007906899.1|   8 NEIALNPEFMAYVIGLEMEVKELRRIFENYIK 39 
                                       5789999*********************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 294.54
//
Query:       gi|488600429|ref|YP_007906900.1|  [L=126]
Description: hypothetical protein Asulf_00900 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 876.78
//
Query:       gi|488600430|ref|YP_007906901.1|  [L=408]
Description: phosphoglycerate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-102  341.3   0.3   7.3e-102  341.1   0.3    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 !  341.1   0.3  4.1e-106  7.3e-102       1     377 [.       8     385 ..       8     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: 341.1 bits;  conditional E-value: 4.1e-106
                                       GGGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHH CS
                               PGK   1 vkdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLse 77 
                                       ++d+d +gkr+l+R+D+N+p+ +  +i d+tr+++++pT+k+l  ++++vvll+H++r  g+k+ +sl+ +a+ Ls+
  gi|488600430|ref|YP_007906901.1|   8 LDDIDYSGKRILMRIDINAPIVN-STILDTTRFESHVPTLKEL--EDCRVVLLAHQSRA-GKKDFTSLETHAKTLSR 80 
                                       589******************87.*******************..89***********8.89*************** PP

                                       HHTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H..H.....HHHHHHHT-SEEEE--GGGTTS- CS
                               PGK  78 llgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde..e.....lakklasladvyVnDAFgtahra 147
                                       llgkeV +v+d++g+ + + i+e+  g  llLeNvrfy+eE+ +++  e     ++++l+ l+d+yVnDAF+++hr+
  gi|488600430|ref|YP_007906901.1|  81 LLGKEVDYVDDLFGSCAINRIKEMDTG-YLLLENVRFYAEETLKRDaiEhskslIVRRLSPLFDFYVNDAFSASHRS 156
                                       ************************965.799**********86554351445679********************** PP

                                       -TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHH CS
                               PGK 148 haStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlk 222
                                       +aS+vg++ v+++++G+l+ekE++alsk++ + e++ ++ilGGak+sd +kv++n+le+    k++++G++an Fl 
  gi|488600430|ref|YP_007906901.1| 157 QASLVGFPPVIPSVVGRLVEKEVAALSKAI-RSEKDKIFILGGAKISDSVKVLKNVLERGiaSKVVLTGVVANYFLM 232
                                       ***********99*****************.588899*********************9888*************** PP

                                       HTT-B-T...TSS--GGGHHH.HHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHH CS
                               PGK 223 aqgleig...kslveedklel.akellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktie 295
                                        +g+++g   +++vee+k  +  +e+l++ k+ ++ki+lp D+ v+ + +   +k  +ve++  d  ++Dig +ti+
  gi|488600430|ref|YP_007906901.1| 233 LDGVKLGpenEKVVEENKEGInDEEMLKTLKAYRDKIILPEDFGVEIDGK---RKDISVEEFRGDGRIMDIGVETIS 306
                                       *******87666677766444157899999****************7432...34568999*9************** PP

                                       HHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHH CS
                               PGK 296 lfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsL 372
                                       +++e+i + ++ v+nGp+Gvfe ekfa GT++++ka+++a +  +s+vGGg+  +a++++gl++k+shvStGGgAs+
  gi|488600430|ref|YP_007906901.1| 307 MLSEEIPKHSIAVINGPAGVFEDEKFALGTFEVLKAVSRA-E--FSLVGGGHISTAARMVGLDKKMSHVSTGGGASI 380
                                       ***************************************6.4..9******************************** PP

                                       HHHCT CS
                               PGK 373 elLeg 377
                                       ++L+g
  gi|488600430|ref|YP_007906901.1| 381 RYLSG 385
                                       ***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 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:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2326.44
//
Query:       gi|488600431|ref|YP_007906902.1|  [L=89]
Description: nucleoid protein Alba [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   74.1   0.3    7.3e-21   73.8   0.3    1.2  1  Alba      Alba
    0.00064   19.7   0.3    0.00083   19.3   0.3    1.3  1  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.3   8.2e-25   7.3e-21       1      67 []       4      67 ..       4      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 8.2e-25
                                      CEEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEEE CS
                              Alba  1 neiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltsss 67
                                      n ++V++ +p+m+yv+++l+++ n++ eeV +ka+GraIs+Av+vaei+++rf+++ + v+++++s+
  gi|488600431|ref|YP_007906902.1|  4 NAVFVGN-KPVMNYVLAVLTQF-NSGVEEVSVKARGRAISRAVDVAEIVRKRFLPD-VDVKDIKIST 67
                                      6799999.**************.*******************************99.***9999875 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   9.2e-08   0.00083      58      96 ..      25      68 ..      19      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.2e-08
                             Rpp20 58 elkkeeVfvkatGrAiekalsvgrwfqeke.....eykvrvetg 96
                                      +   eeV vka GrAi +a+ v++  +++         ++++t+
  gi|488600431|ref|YP_007906902.1| 25 NSGVEEVSVKARGRAISRAVDVAEIVRKRFlpdvdVKDIKISTE 68
                                      56789******************998766433222223444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 610.26
//
Query:       gi|488600432|ref|YP_007906903.1|  [L=342]
Description: aspartate semialdehyde dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-42  145.4   0.0    8.6e-42  143.3   0.0    1.8  2  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    2.3e-35  121.6   0.0    3.3e-35  121.1   0.0    1.2  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0013   18.3   0.0     0.0027   17.3   0.0    1.4  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
     0.0027   17.6   0.0     0.0047   16.8   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
       0.02   15.0   0.0       0.04   14.1   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.028   15.1   0.0      0.051   14.3   0.0    1.4  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


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 ?   -0.4   0.0      0.36   1.1e+03      38      63 ..      60      85 ..      21      98 .. 0.77
   2 !  143.3   0.0   2.9e-45   8.6e-42       1     183 [.     157     322 ..     157     323 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.36
                                      HHHHHSTTS.CTTTSSHHTTSEESTC CS
                   Semialdhyde_dhC 38 aelqrsdeakpgvfgvpiagNlipyi 63
                                       + ++ ++++p+v  ++i ++++p  
  gi|488600432|ref|YP_007906903.1| 60 VKDLEMQPMDPKVIDADIVFSALPSD 85
                                      45667888999999999999999865 PP

  == domain 2  score: 143.3 bits;  conditional E-value: 2.9e-45
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       LkPL+d  ++l++viv+t+qa+SGaG                     pgv+++ i++N++p+i++ee+k e+e  + 
  gi|488600432|ref|YP_007906903.1| 157 LKPLMD--LGLRKVIVSTMQALSGAGF--------------------PGVPSLGIMDNILPFIKGEEEKVETEPLKL 211
                                       8*****..56*****************....................9***************************** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS........TTEEEEESSHCHHS CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa........pevkvvvneeedrP 146
                                       l++ + ++ ++++ + vsa+c+rVPv++Gh+e+v+++++ +dv+veev +++++         pe+ ++v++e+drP
  gi|488600432|ref|YP_007906903.1| 212 LGKFDGERIRFADLK-VSASCHRVPVIDGHLESVWAEFN-RDVSVEEVVDAFESFkpldlptsPEKLIIVRNEPDRP 286
                                       ************997.**********************5.************************************* PP

                                       SHHHHTTC..SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 147 tpaavagg..tnsvsVGRirkdemgdeglklvvvgDNll 183
                                       +p++++++  ++s++VGRirkd   +  +k+ v+g+N++
  gi|488600432|ref|YP_007906903.1| 287 QPRLDRDEggGMSITVGRIRKDD--S-AIKYLVLGHNTV 322
                                       ******9999************9..3.499*******98 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 !  121.1   0.0   1.1e-38   3.3e-35       1     118 [.       4     126 ..       4     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 1.1e-38
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEE CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivf 71 
                                       k+a++GatG+vGq++++lL++h ++e++ l++s++  Gk + e v+       +e++kdl+++++d++ + ++divf
  gi|488600432|ref|YP_007906903.1|   4 KAAVLGATGMVGQKFIQLLSDHEWFEITSLIASEKRVGKFYGEEVNwvvsanVPEKVKDLEMQPMDPKVI-DADIVF 79 
                                       689************************************************99***********999988.****** PP

                                       E-SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGG CS
                    Semialdhyde_dh  72 lalpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreai 118
                                       +alp++++k+++p++a+ag+++ +++s++R+++d+++v+pevn++++
  gi|488600432|ref|YP_007906903.1|  80 SALPSDIAKKVEPEFAKAGFVIASNASAYRMDEDVPLVIPEVNPDHL 126
                                       *********************************************97 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.1e-07    0.0027      71     108 ..     226     263 ..     222     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.1e-07
                                       TEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHH CS
                           Gp_dh_C  71 kldglAvrVPtpnvsvvdlvvelekevtveevnaalke 108
                                       k++++  rVP++++++ ++  e++++v+veev +a++ 
  gi|488600432|ref|YP_007906903.1| 226 KVSASCHRVPVIDGHLESVWAEFNRDVSVEEVVDAFES 263
                                       6778899****************************985 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 !   16.8   0.0   1.6e-06    0.0047       1      69 [.       9      83 ..       9     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-06
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-.CCHHHHHHT.....T-SEEEES-- CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtd.vedlaealk.....gadaVvsalg 69
                                      GAtG vG++ ++ l +++ +e+t l+ +++++ ++  ee   vv+++v + v+dl+         +ad+V+sal 
  gi|488600432|ref|YP_007906903.1|  9 GATGMVGQKFIQLLSDHEWFEITSLIASEKRVGKFYGEEVNWVVSANVPEkVKDLEMQPMdpkviDADIVFSALP 83
                                      9**********9888888***************998654445677888532455443222344449999999993 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05      0.04       2      50 ..       4      50 ..       3     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSS CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellgl 50
                                      k av+Ga+G +G++ +++++++e +e+++ + +++   +gk  ge ++ 
  gi|488600432|ref|YP_007906903.1|  4 KAAVLGATGMVGQKFIQLLSDHEWFEITSLIASEK--RVGKFYGEEVNW 50
                                      679*****************************987..445555544433 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 ?   14.3   0.0   1.7e-05     0.051       2      39 ..       6      43 ..       5      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                      EEESTTSHHHHHHHHHHHHCTTTEEEEEEEE.SSTHHHH CS
                   DXP_reductoisom  2 viLGsTGSIGtqtLdvieenpdkfevvalaa.gsnvell 39
                                      ++LG+TG +G++ ++++++++  fe+++l a +++v ++
  gi|488600432|ref|YP_007906903.1|  6 AVLGATGMVGQKFIQLLSDHE-WFEITSLIAsEKRVGKF 43
                                      69****************998.9******9967777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 2206.41
//
Query:       gi|488600433|ref|YP_007906904.1|  [L=319]
Description: TIGR01210 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00095   19.6   0.0     0.0016   18.9   0.0    1.4  1  Radical_SAM    Radical SAM superfamily
     0.0021   18.0   0.0       0.49   10.5   0.0    2.7  2  Radical_SAM_C  Radical_SAM C-terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.7e-07    0.0016       3     158 ..      34     190 ..      32     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-07
                                       EESEESS-....-TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                       xxxxxxxx....xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlr....CsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakl 73 
                                        trgC ++    C+ C  + +     +++  ++++e ++ee+k+    k +  ++ +g   + +   +++ +++   
  gi|488600433|ref|YP_007906904.1|  34 RTRGCYRAqrdpCRMCGYSIDsdANVTDKNLEKQLEFVEEEIKKR-NPK-ILKIFTSGSFFDPRETSQKIRKKIYGM 108
                                       689999999999*******99887788888888889999999888.565.777777777666655555555555555 PP

                                       CCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  74 avpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                        v++++i   + + +  +e+++  ++     v +gle+++d++  +l+n+g +fee+ ea + l++ g+ +  + ++
  gi|488600433|ref|YP_007906904.1| 109 -VKEYSIEKLIVESR--PEFIRSADPEVYMEVGIGLESVNDFVRNELINKGFSFEEYTEAHDFLKSIGVSVKAYLLL 182
                                       .68999999999999..69999999999**************8899999*******************997666666 PP

                                       EBTTTSHH CS
                                       xxxxxxxx RF
                       Radical_SAM 151 glpGende 158
                                        +p  +++
  gi|488600433|ref|YP_007906904.1| 183 KPPFLSEK 190
                                       66666555 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 !   10.5   0.0   5.4e-05      0.49       2      38 ..     210     246 ..     209     249 .. 0.89
   2 !    4.7   0.0    0.0034        30      26      56 ..     284     314 ..     276     319 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.4e-05
                     Radical_SAM_C   2 dgvKlypllvikgTeLaelyksgeykplsleeyvdlv 38 
                                       d++ + p+ + kgT  ++l+ +g ++p  l  +vd++
  gi|488600433|ref|YP_007906904.1| 210 DIISINPTNIQKGTYVERLWYKGYFRPPWLWSAVDVL 246
                                       677788*********************9999999887 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0034
                     Radical_SAM_C  26 ykplsleeyvdlvadilellppdirvhRltg 56 
                                       +++ +  ++++l +d++e ++  + ++R+ +
  gi|488600433|ref|YP_007906904.1| 284 FSLTQNRDVLNLYCDCIEEWKDYMLIERIAR 314
                                       6677778999*******************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); 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: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1785.64
//
Query:       gi|488600434|ref|YP_007906905.1|  [L=279]
Description: hypothetical protein Asulf_00906 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  114.9  14.3    3.1e-33  114.9  14.3    1.4  2  Rhomboid     Rhomboid family
    3.2e-12   46.4   7.1    4.8e-12   45.8   7.1    1.2  1  zf-AN1       AN1-like Zinc finger
    1.5e-07   31.9   0.1    1.5e-07   31.9   0.1    2.8  3  DUF1751      Eukaryotic integral membrane protein (DUF1751)
  ------ inclusion threshold ------
        2.2    8.5   5.3        4.3    7.6   5.3    1.4  1  C5HCH        NSD Cys-His rich domain
        2.4    7.7   6.1         12    5.5   1.0    2.2  2  zf-ribbon_3  zinc-ribbon domain
        5.8    8.0   6.2        6.8    7.8   1.0    2.4  2  zf-C2H2_4    C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       3.1   9.4e+03      11      14 ..     100     103 ..      84     118 .. 0.53
   2 !  114.9  14.3     1e-36   3.1e-33       6     145 ..     127     270 ..     123     275 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.1
                                       HHGG CS
                          Rhomboid  11 ltsm 14 
                                       +t m
  gi|488600434|ref|YP_007906905.1| 100 ITIM 103
                                       1111 PP

  == domain 2  score: 114.9 bits;  conditional E-value: 1e-36
                                       -TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S.....-EESSHHHHH CS
                          Rhomboid   6 elwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses..plvGaSGaif 80 
                                       + w+l+tsmf+H+++ H+l+N+++ll+fG++lerr+G ++++ ++llsglag++++l+fs  s+s   ++G SGai+
  gi|488600434|ref|YP_007906905.1| 127 MPWQLITSMFFHVEFGHFLVNAIVLLFFGTELERRVGGKNYIKIFLLSGLAGNIGYLAFSLMSGSyaGALGSSGAIY 203
                                       78**********************************************************999887789******** PP

                                       HHHHHHHHHHHCCCCGS----HC.....CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHH CS
                          Rhomboid  81 gllgallvlvprnrkllrkliia..llllllfillnlvlgllpraggvsnlAHlgGllaGlllglll 145
                                       g++g l++  p+ r l++++i++   ++l++f+l++l++  l++ +gv+++AHl+Gll+Gl +g  +
  gi|488600434|ref|YP_007906905.1| 204 GIMGTLAIIAPEIRVLFFFFIPMsiRVALVIFALYDLLMLPLSSISGVAHIAHLSGLLVGLYYGDKF 270
                                       *********************99999************************************99655 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   7.1   1.6e-15   4.8e-12       1      38 [.       5      40 ..       5      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.6e-15
                            zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkHrlpedHdCkkl 38
                                      C++  C+k+++lpf C+yCg++FC++Hrlpe H+C++ 
  gi|488600434|ref|YP_007906905.1|  5 CDY--CGKEEYLPFVCKYCGGKFCAEHRLPEMHECEGR 40
                                      775..******************************986 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.42   1.2e+03      48      72 ..      82     106 ..      75     113 .. 0.81
   2 !   31.9   0.1   4.9e-11   1.5e-07       1      68 [.     121     188 ..     121     213 .. 0.88
   3 ?   -0.0   0.6      0.44   1.3e+03      49      93 ..     221     264 ..     215     267 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.42
                           DUF1751  48 lkFilvvnvitnllvvlltlllylv 72 
                                       +kF ++++ + n +v+ + ++++++
  gi|488600434|ref|YP_007906905.1|  82 IKFNAITAYGYNNIVLGIITIMFFI 106
                                       7999999999888888777777766 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 4.9e-11
                           DUF1751   1 PgallpypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltll 68 
                                       P++++  pw l+t++f+ +++ ++lv+++ ll++g+ lEr  g k ++k +l+ +++ n+  +++ l+
  gi|488600434|ref|YP_007906905.1| 121 PNKFIEMPWQLITSMFFHVEFGHFLVNAIVLLFFGTELERRVGGKNYIKIFLLSGLAGNIGYLAFSLM 188
                                       89999***************************************************999987777665 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.44
                           DUF1751  49 kFilvvnvitnllvvlltlllylvtkseelllvpisGlagilagf 93 
                                        F++ +++ ++l++++l+ ll+l  +s++ + ++i+ l g+l+g+
  gi|488600434|ref|YP_007906905.1| 221 FFFIPMSIRVALVIFALYDLLMLPLSSISGV-AHIAHLSGLLVGL 264
                                       3444455556666666666666666666633.6666666666665 PP

>> C5HCH  NSD Cys-His rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.3    0.0014       4.3       3      27 ..       4      30 ..       3      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                             C5HCH  3 qCsvCgkaat..sfCefCPssFCkeHe 27
                                      +C+ Cgk+      C++C   FC eH+
  gi|488600434|ref|YP_007906905.1|  4 KCDYCGKEEYlpFVCKYCGGKFCAEHR 30
                                      6*****98762268************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 ?    4.6   0.3    0.0074        22      18      24 ..       4      10 ..       2      11 .. 0.74
   2 ?    5.5   1.0    0.0039        12      18      25 ..      17      24 ..      16      25 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0074
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C yCG+
  gi|488600434|ref|YP_007906905.1|  4 KCDYCGK 10
                                      6888886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0039
                       zf-ribbon_3 18 vCpyCGtk 25
                                      vC+yCG+k
  gi|488600434|ref|YP_007906905.1| 17 VCKYCGGK 24
                                      7*****98 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4      0.11   3.3e+02       2       8 ..       4      10 ..       3      12 .. 0.88
   2 ?    7.8   1.0    0.0023       6.8       1      14 [.      16      29 ..      16      36 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                         zf-C2H2_4  2 kCpiCgk 8 
                                      kC++Cgk
  gi|488600434|ref|YP_007906905.1|  4 KCDYCGK 10
                                      8****98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0023
                         zf-C2H2_4  1 fkCpiCgksFsskk 14
                                      f C++Cg+ F+  +
  gi|488600434|ref|YP_007906905.1| 16 FVCKYCGGKFCAEH 29
                                      89********7555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1765.30
//
Query:       gi|488600435|ref|YP_007906906.1|  [L=386]
Description: hypothetical protein Asulf_00907 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  105.6  17.3    1.5e-13   50.9   2.5    4.1  4  CBS              CBS domain
     0.0041   17.9   0.5      0.029   15.2   0.1    2.6  3  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
  ------ inclusion threshold ------
      0.019   15.1   0.0       0.32   11.1   0.0    2.5  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
      0.071   12.9   0.0        1.2    9.0   0.0    2.5  2  RVT_3            Reverse transcriptase-like
       0.13   12.0   2.2       0.18   11.5   0.2    2.0  2  She2p            RNA binding protein She2p


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.6   6.7e-09   2.4e-05       5      53 ..      10      58 ..       3      62 .. 0.83
   2 ?   -2.7   0.0       2.4   8.6e+03      44      55 ..     111     122 ..      90     123 .. 0.81
   3 !   50.9   2.5   4.2e-17   1.5e-13       1      55 [.     131     185 ..     131     187 .. 0.94
   4 !   38.6   0.6   3.1e-13   1.1e-09       1      56 [.     210     264 ..     210     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.7e-09
                                      SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                       ++d+ +++ ++t+++++ ++ e+++ r + V+edg+++G+v ++Dl+r
  gi|488600435|ref|YP_007906906.1| 10 IRDDYDVISASETISKVISMLGESKHERALLVEEDGEIIGVVREKDLVR 58
                                      55666689999**********87666566599***************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.4
                                       EEEEHHHHHHHH CS
                               CBS  44 GivtlrDllral 55 
                                       G+++  D l+++
  gi|488600435|ref|YP_007906906.1| 111 GVIHINDFLQKI 122
                                       888888888876 PP

  == domain 3  score: 50.9 bits;  conditional E-value: 4.2e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +gd+m+++v+tv+  + +++al +mr++g+sr+ VVd+++k+vGi+t +D+++ +
  gi|488600435|ref|YP_007906906.1| 131 IGDVMNPEVITVKTYDGISKALATMRNHGISRVVVVDDENKVVGIITGKDIVDRV 185
                                       69*******************************889***************9876 PP

  == domain 4  score: 38.6 bits;  conditional E-value: 3.1e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT.BEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedg.klvGivtlrDllrall 56 
                                       V++im+r+v+tv  ++t+++a+ lm+e+++s+l VV   g  + G+v ++Dll++ l
  gi|488600435|ref|YP_007906906.1| 210 VESIMSRPVITVERNDTIAKAIGLMIENDISSL-VV-TRGsIPEGVVVKKDLLEYYL 264
                                       789******************************.99.5774699*********9975 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.5   5.3e+03      41      72 ..     205     236 ..     185     242 .. 0.70
   2 ?    3.3   0.1      0.04   1.4e+02      39      83 ..     266     304 ..     218     307 .. 0.72
   3 !   15.2   0.1     8e-06     0.029      17      83 ..     287     370 ..     274     372 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                                       EEEEEEEEC.TTEEEEEEEEESSHHHHHHHHHH CS
                   Ribosomal_S30AE  41 kvevtirla.kgkviraeeesedlyaaidlavd 72 
                                       +  + ++   + +vi++ e+++++ +ai l+++
  gi|488600435|ref|YP_007906906.1| 205 TLSIVVESImSRPVITV-ERNDTIAKAIGLMIE 236
                                       44455544456777776.457899999888776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.04
                                       E...EEEEEEEEECTTEEEEEEEEESSHHHHHHHHHHHHHHHHHHCHH CS
                   Ribosomal_S30AE  39 k...kkvevtirlakgkviraeeesedlyaaidlavdklerqlrkyke 83 
                                       +   k++ev+i ++kg+v+          + i++++d l++ lrk+k+
  gi|488600435|ref|YP_007906906.1| 266 TtipKEYEVQI-ITKGVVLDD--------SEIEKLLDELNKFLRKFKS 304
                                       13456788888.777888886........4488999999999999886 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 8e-06
                                       HHHHHHCCGGGG..........-EEEEEEE.....EE....EEEEEEEEEC.TTEEEEEEEEESSHHHHHHHHHHHH CS
                   Ribosomal_S30AE  17 yvekklekleky...f......ieadVtls.....kk....kkvevtirla.kgkviraeeesedlyaaidlavdkl 74 
                                        +ek l+ l+k+   f      +++ V+++     ++     +v +++  + ++ v++++ es  ++ a++++++kl
  gi|488600435|ref|YP_007906906.1| 287 EIEKLLDELNKFlrkFksslgkAHLFVYIKklrlyYReiplIHVMMRL--RsDHGVFFVTGESWGVEFAVHATLNKL 361
                                       466666777777444356666677777777777762256444466666..4468888888899************** PP

                                       HHHHHHCHH CS
                   Ribosomal_S30AE  75 erqlrkyke 83 
                                       erq+ k ke
  gi|488600435|ref|YP_007906906.1| 362 ERQVIKDKE 370
                                       ******997 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     9e-05      0.32      23      65 ..       8      52 ..       1      60 [. 0.81
   2 ?    1.0   0.0      0.12   4.2e+02      32      72 ..     143     184 ..     118     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9e-05
                    Acetyltransf_4 23 taitfeyev.ssveefekfleal.dsekeyvflvaesdrivGyay 65
                                      + i  +y+v s+ e + k +++l +s+ e+ +lv+e+++i+G  +
  gi|488600435|ref|YP_007906906.1|  8 KLIRDDYDViSASETISKVISMLgESKHERALLVEEDGEIIGVVR 52
                                      45566777758888999******77999**************976 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                    Acetyltransf_4  32 ssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkr 72 
                                       ++ + + k l+ + + + ++v  v+++ ++vG+ +++ + +r
  gi|488600435|ref|YP_007906906.1| 143 KTYDGISKALATMrNHGISRVVVVDDENKVVGIITGKDIVDR 184
                                       5555666777777667779999999999*****999988876 PP

>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00032       1.2      45      80 ..     145     180 ..     137     185 .. 0.91
   2 ?    0.6   0.0      0.13   4.6e+02      73     103 ..     274     304 ..     271     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00032
                             RVT_3  45 lqALlrGLqlalklgirrlvvegDsktvvqllngre 80 
                                       + ++  +L +  ++gi+r+vv  D  +vv  ++g+ 
  gi|488600435|ref|YP_007906906.1| 145 YDGISKALATMRNHGISRVVVVDDENKVVGIITGKD 180
                                       678999**************************9986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                             RVT_3  73 vqllngrekvksselanlldeirkllksfes 103
                                       vq +++   ++ se+++llde +k l++f+s
  gi|488600435|ref|YP_007906906.1| 274 VQIITKGVVLDDSEIEKLLDELNKFLRKFKS 304
                                       678888888999*****************86 PP

>> She2p  RNA binding protein She2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   4.9e-05      0.18      65     131 ..     234     300 ..     213     310 .. 0.87
   2 ?   -0.8   0.1      0.29     1e+03      38      53 ..     310     325 ..     304     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                             She2p  65 keeksleelvkllgsffikvleilDlLnyyltqslqkeiisktLnedlvlseetivaiedtynhfvk 131
                                         e+++++lv++ gs+   v+   DlL+yyl  ++ ke  ++ + + +vl+++ i+ + d  n f++
  gi|488600435|ref|YP_007906906.1| 234 MIENDISSLVVTRGSIPEGVVVKKDLLEYYLKTTIPKEYEVQIITKGVVLDDSEIEKLLDELNKFLR 300
                                       567888999999999999999999*********************************9999999985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.29
                             She2p  38 tlikfvkklRflndsl 53 
                                        l  ++kklR +   +
  gi|488600435|ref|YP_007906906.1| 310 HLFVYIKKLRLYYREI 325
                                       6788******886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2221.72
//
Query:       gi|488600436|ref|YP_007906907.1|  [L=642]
Description: acetyl-coenzyme A synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-96  324.1   0.0    1.3e-96  323.8   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    6.2e-30  104.0   1.2    1.3e-29  102.9   1.2    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    2.6e-15   56.1   0.2    1.1e-14   54.0   0.2    2.2  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
       0.17   11.9   0.0       0.32   11.0   0.0    1.3  1  MutS_V         MutS domain V


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 !  323.8   0.0  2.9e-100   1.3e-96       2     422 ..      83     518 ..      82     519 .. 0.86

  Alignments for each domain:
  == domain 1  score: 323.8 bits;  conditional E-value: 2.9e-100
                                       HHHHHHSTTSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EE CS
                       AMP-binding   2 eeqaaktpdkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavv 74 
                                       +++ + + dk+a+++    ++e +++TY+el++rv+r+A++Lr lGvk++d+V i++ + pe+++a+la++++Ga++
  gi|488600436|ref|YP_007906907.1|  83 DRHIESKGDKTAIIWqgepENEKERITYHELYRRVCRFANALRTLGVKEQDVVTIYMGMVPELLIAMLACARIGAIH 159
                                       67889999***********999******************************************************* PP

                                       EEEETTS-HHHHHHHHHHHTESEEE.........ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCC CS
                       AMP-binding  75 vplnptltaeelayiledseakvli.........atvdselleklleaaakleavklvivldadellkeeelkeeee 142
                                        ++  ++++ +l+  ++d++akv++         +    ++ +++ ++a ++  v++v+vl++ + + +     +  
  gi|488600436|ref|YP_007906907.1| 160 NVVFGGFSSTALRDRINDANAKVVVtmdgyyrrgKV---IETKRIVDKALEDCNVESVVVLERIGNDVSMVDGRDIW 233
                                       *************************99998764312...22333444444445566666666555444433333333 PP

                                       CSCTTS..-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHH.HHHHHHHHHHHC.SCCTTT-EEEESS-TTSCH CS
                       AMP-binding 143 seekae..kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnl.vanvaslkletr.fklkeddvvlsilplahif 215
                                       + + ++  +++e ++l+++++++i+YTSGTTGkPKGV + h+ + v +  +   ++  f+lk++d +++++++ +i+
  gi|488600436|ref|YP_007906907.1| 234 WHDLQKvpDKCECKALDSEHPLFILYTSGTTGKPKGVLHVHGGYnVGTHIT---TKWvFDLKDRDIFWCTADIGWIT 307
                                       333331446889999**************************7752222222...222488999************** PP

                                       HHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEE CS
                       AMP-binding 216 glilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllg 291
                                       g+++ ++++l++Gat+ ++++ ++ ++p++++  ie+++vtv++++P++++++++ g++    +++dlsslrl+ ++
  gi|488600436|ref|YP_007906907.1| 308 GHSYVVYGPLSNGATILIYEGAPDyPQPDRWWSIIEQYGVTVFYTAPTAIRYFMKLGEEW--LEKHDLSSLRLLGTV 382
                                       ************************777****************************86554..5678*********** PP

                                       SS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE CS
                       AMP-binding 292 geplspellrffralfge...evlegYGlTEttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdgee 364
                                       ge + pe+++++++ +g+   +v++++++TEt++vv+  lp    k k+gsv  p+pg+ v i De+ g+p     +
  gi|488600436|ref|YP_007906907.1| 383 GETIDPEAWKWYYKNVGNehcPVIDTWWQTETGMVVIApLP-GVTKLKPGSVTLPFPGILVDIRDEK-GNPA---DS 454
                                       *****************9******************87444.5555799****************98.8866...79 PP

                                       EEEEEEET..TS-SEBTT-HHHHHHHEEE...TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 365 Gellvrgp..gvmkgYlkkpeataeafds...egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                       Gel++  p   +++  +++pe+ a+ ++    +g+  + TGD +r d dGy++i+gR+++++k+
  gi|488600436|ref|YP_007906907.1| 455 GELVITNPwpAMFRNLWGEPERFAKQYWRsndSGElIYYTGDGARKDGDGYYWIIGRIDEVLKV 518
                                       *******9667*****************76643778**************************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 !  102.9   1.2     3e-33   1.3e-29       1      76 []     527     605 ..     527     605 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 3e-33
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       e+E al+sh+aV+eaaV+G+p+e+kG+++vafVvlk+g+e+   le++Lk hvr e+g++avp++++fv++lpktrs
  gi|488600436|ref|YP_007906907.1| 527 EIEGALISHEAVSEAAVIGKPHEIKGQVPVAFVVLKTGYEPsveLEKDLKTHVRNEIGAIAVPEEIYFVEQLPKTRS 603
                                       8***********************************99655578********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|488600436|ref|YP_007906907.1| 604 GK 605
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.2   2.6e-18   1.1e-14       9      55 .]      34      81 ..      28      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.6e-18
                                      HH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  9 iedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                       +d+ + W+e+ak  ++W++p++ vld+s++pf++W++GGk+Ni++Nc
  gi|488600436|ref|YP_007906907.1| 34 AQDYLTLWDEVAKSdIEWFEPYEDVLDDSNAPFYRWYVGGKINITHNC 81
                                      5777888******77********************************* PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.1e-05      0.32      69     119 ..     203     253 ..     192     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.1e-05
                                       HHHHTT--TTSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES CS
                            MutS_V  69 asilknatekslvilDElGRGtstydGlaialavaeyllekikaktlfatH 119
                                        + l++++ +s+v+l+ +G   s +dG  i +  ++ + +k ++k+l + H
  gi|488600436|ref|YP_007906907.1| 203 DKALEDCNVESVVVLERIGNDVSMVDGRDIWWHDLQKVPDKCECKALDSEH 253
                                       4567888999***********************************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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 0.32s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 3744.72
//
Query:       gi|488600437|ref|YP_007906908.1|  [L=230]
Description: hypothetical protein Asulf_00909 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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       0.12   12.3   0.0    1.2  1  Lipase_GDSL  GDSL-like Lipase/Acylhydrolase


Domain annotation for each model (and alignments):
>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.8e-06      0.12      51     149 ..      77     214 ..       9     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-06
                                       HHCCH..........ECTTTECHHHHHCTTS.EEEEE--CTCC-EECSSCTTTCEEHHHHHHHHHHHHHHHHHHHHT CS
                                       xxxxx..........xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL  51 lqqll..........nkyplkseqlkalhpd.lviislGtNDsnlgkkstdaakkeaeeyiknlreaikelkeegap 116
                                       + + l          ++y++++    ++ +d l++ + G +++        + ++ + e+ik lr+ ++ l++ + +
  gi|488600437|ref|YP_007906908.1|  77 FDGFLtyctdregrfHSYVQFFRNGVVEAVDgLMLRQHGEEQV-------IPGEALEGELIKALRDYLSVLNALNVK 146
                                       3333356777777778999************************.......*************************** PP

                                       TEEEEEEE-SSTCH...................................CTCCCCHCCHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx...................................xxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL 117 kaivvlvsppglgp...................................qeekdakklgekgnefvge 149
                                        +i v vs++g+++                                   + ek+ +++ + + +++g+
  gi|488600437|ref|YP_007906908.1| 147 PPIFVFVSLLGVSGyymahdkplflpeyesyvdrdtllvpevvvesydiEPEKVLRPCFDSIWNACGY 214
                                       ************99888888888888888888877777777777777777777777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1546.23
//
Query:       gi|488600438|ref|YP_007906909.1|  [L=875]
Description: hypothetical protein Asulf_00910 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-262  871.6  20.3     5e-262  871.4  20.3    1.0  1  UPF0182   Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  871.4  20.3  2.8e-266    5e-262       3     758 .]      14     752 ..      12     752 .. 0.97

  Alignments for each domain:
  == domain 1  score: 871.4 bits;  conditional E-value: 2.8e-266
                           UPF0182   3 lllavlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvflllalllllnlllaerlelleklerlr 79 
                                       ++la++++ll++ ++++ +yte+lwf++l+ +svf+  l+++++lfv++f++++++l ln +  +r          +
  gi|488600438|ref|YP_007906909.1|  14 IVLAIFVALLVFPSIVLYFYTEFLWFESLNLSSVFMAMLYYKVILFVIFFAFAFAMLSLNHFALRRV---------S 81 
                                       67888888999999*************************************************9999.........3 PP

                           UPF0182  80 ealekklkllllaialvlsllvglvassqwekvllflnstsfgvkDpifgkDisFYvFklPflelllslllalvlla 156
                                       +    ++ +l + ++++l+l+v+l++s+ w +++ f+ns +f+ kDpifg D+sFYvFklPf++++l+++l++++la
  gi|488600438|ref|YP_007906909.1|  82 HE-LDEPLKLPFWVNILLALIVALLFSRVWLQYVYFTNSVDFNLKDPIFGLDVSFYVFKLPFIQTILFFFLTVLILA 157
                                       33.44555566778999************************************************************ PP

                           UPF0182 157 liavllvyllsgeslgirl...kfaelskaarrhlsvllallllllalsywLdryellyskrgvvtGagYtdvnavl 230
                                       +++++++y +  + +  ++      ++ +a  +h s++la ++++ a+ ++++r++ll+s +g+v+GagYtdv+++l
  gi|488600438|ref|YP_007906909.1| 158 ILISAAYYAFIFRDV--KSfdeLRDNFPQAGYAHASLILAGIFIFTAAYFYFARFDLLTSPHGAVMGAGYTDVQVRL 232
                                       999999998877555..233555689*************************************************** PP

                           UPF0182 231 paktilavialvvavlllvaivlkklklplialallvllaillgvvlpalvqkfiVkPnelekEkpYiernIeaTre 307
                                       pa  ++a+++l++a++ ++   ++++  + i l++l+++++l  vv+pa+vqk+ V+Pne+  E++Yi++ I++Tr 
  gi|488600438|ref|YP_007906909.1| 233 PAMGLVALLSLLLAAVSIYLGHKRNIDAMPILLIVLAAVMLLSIVVAPAVVQKLKVEPNEIVVEEEYIRYGIDFTRF 309
                                       *******************99*****9999999999999999*********************************** PP

                           UPF0182 308 AygLdkveveefeaeaeltaedleenaetienirLlDprplletfrqlqqirnYYkFedldvdrYtidgeerqvvia 384
                                       AygL +v++  ++ae++l+ +++e+n+ ti+nir++D+rpll+++rq+qqir+YY+ +d+dvdrY idg+++q++i+
  gi|488600438|ref|YP_007906909.1| 310 AYGL-DVKKMYYSAENNLSVDTIERNRGTIDNIRIWDHRPLLSVYRQMQQIRTYYSINDVDVDRYYIDGRYTQLMIT 385
                                       ****.8*********************************************************************** PP

                           UPF0182 385 aREldysalpeeaktwvnkhlvYTHGyGvvaspvnkvteeGlpeflvkdipseeeeslkieepriYfGeltndyviv 461
                                       aREl+++ l+ +a+tw+nkhl+YTHGyGvvaspvn+vt+ Glp+++++dip+  ++++ ie+p+iY+Ge+t++yviv
  gi|488600438|ref|YP_007906909.1| 386 ARELSTDLLSPRAQTWLNKHLIYTHGYGVVASPVNSVTKVGLPDLIIEDIPP--KGKIAIERPEIYYGEITTNYVIV 460
                                       ***************************************************9..9********************** PP

                           UPF0182 462 gtkvkEfdypsgeenvyntYdGkgGvkigsllrrllfaiklkdlklllsseitseskilfrRnikeRvekvaPfLtl 538
                                       +tk+kEfdyp ge nv +tY+G+gGvk++s++++l++aik+ d+k+lls++it+es+++f+R+i +Rv+++aPfL +
  gi|488600438|ref|YP_007906909.1| 461 KTKQKEFDYPLGEGNVLTTYNGSGGVKLDSYFKKLIYAIKFADIKFLLSDYITTESRLMFHRDIIDRVSTLAPFLVY 537
                                       ***************************************************************************** PP

                           UPF0182 539 DsdpYlvvadgrlyWivDaYTtsdrYPySepeeatsgeeevnYiRNSVKvvvDAydGtvklYvvdeeDPiikawski 615
                                       D+dpY+ v+dg+ yWi+D YTt d++PyS +        ++nY+RN+VKv vD y+G  k+Yv++ e+P+ik  +k+
  gi|488600438|ref|YP_007906909.1| 538 DRDPYITVIDGKQYWIIDSYTTLDKFPYSAR------YPTFNYVRNPVKVFVDTYNGIPKFYVIQ-EEPVIKVLMKA 607
                                       *****************************99......678************************8.79********* PP

                           UPF0182 616 FpglfkplsempeeLrshlrYPedlFkvqsellakYHvtdpevFYnredlWevpke...eeeqpvePyYlilklpge 689
                                       Fp+lf+++++m+ee r+h+rYP dlF+vq++++a++H++d+++FYnred+We+p+e   e++ ++ePyY+il+lpg+
  gi|488600438|ref|YP_007906909.1| 608 FPDLFTSADKMSEEERAHIRYPIDLFEVQAHIYATFHMDDAKTFYNREDVWEIPEEileEDRIQMEPYYVILTLPGN 684
                                       ********************************************************99888889************* PP

                           UPF0182 690 ekeefillspftpssrenliawlaarsdgenygklllyelpkqelvyGpeqiearinqdpeisqqlsLw 758
                                       +k+ef+l++pftp+ r+n+iawlaar+d e+yg+l+lye+pk +l+yGp+qieari+q+++is+ ++Lw
  gi|488600438|ref|YP_007906909.1| 685 DKPEFLLMLPFTPKGRDNIIAWLAARCD-ESYGELRLYEFPKGQLIYGPMQIEARIDQNADISKLFTLW 752
                                       ***************************9.79*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (875 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); 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:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 5667.41
//
Query:       gi|488600439|ref|YP_007906910.1|  [L=1113]
Description: hypothetical protein Asulf_00911 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-13   49.7   0.1    1.1e-07   31.7   0.0    2.3  2  Glyco_hydro_cc   Glycosyl hydrolase catalytic core
    4.4e-10   39.4   1.9    1.5e-05   24.5   0.2    4.3  4  Glyco_hydro_42   Beta-galactosidase
      4e-06   26.0   0.3      0.001   18.1   0.2    2.9  2  Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
    4.6e-05   22.2   2.0     0.0015   17.3   0.3    2.1  2  Glyco_hydro_39   Glycosyl hydrolases family 39
    0.00011   21.3   0.0     0.0018   17.3   0.1    2.6  3  Glyco_hydro_53   Glycosyl hydrolase family 53
     0.0004   19.6   0.6      0.017   14.3   0.0    2.7  3  Glyco_hydro_10   Glycosyl hydrolase family 10
    0.00055   19.6   0.0      0.097   12.2   0.0    2.4  2  Glyco_hydro_32N  Glycosyl hydrolases family 32 N-terminal dom
  ------ inclusion threshold ------
        0.1   12.6   0.0        2.2    8.3   0.0    2.5  2  B12-binding      B12 binding domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_cc  Glycosyl hydrolase catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.2e-06    0.0094     136     179 ..     527     570 ..     499     592 .. 0.78
   2 !   31.7   0.0   4.9e-11   1.1e-07     103     198 ..     911    1003 ..     871    1013 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.2e-06
                    Glyco_hydro_cc 136 ckvdflavHwY..kgdfeelkehieelheaynkpiWvTEfalqses 179
                                         +d++++H +   +d+ +lke+ +++   ++kp+WvTEf+ ++e 
  gi|488600439|ref|YP_007906910.1| 527 KYIDIVNFHSFspYEDAIRLKERFGKY--VAGKPLWVTEFSATDEY 570
                                       589*******97667788899999999..899********988733 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 4.9e-11
                    Glyco_hydro_cc  103 e.kgvklvsPavaatnseegleWldeFleacskdckvdflavHwYkgdfeelk.ehieelheayn..kpiWvTEf 173 
                                        +  +v l++ a+    ++e +eW +eF++    +  +d+  +H Y  + ++++ + +++l e+y+  kpiWvTE 
  gi|488600439|ref|YP_007906910.1|  911 StAKVVLGGAATL---DKESIEWWEEFYSLGG-GNYFDIAGIHSYADEKDDFNvDDLKKLLEKYGinKPIWVTEV 981 
                                        3355556666664...45679*********99.99**********5557776437888888898888******** PP

                    Glyco_hydro_cc  174 alqsesgdasqeetkeflnevlawl 198 
                                        ++   +g+ s e+   f++++++ +
  gi|488600439|ref|YP_007906910.1|  982 GP---TGEMSREDGIMFAKAAIRAF 1003
                                        *6...67777777777777777665 PP

>> Glyco_hydro_42  Beta-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2   6.7e-09   1.5e-05      31     150 ..     341     464 ..     337     491 .. 0.76
   2 !    6.8   0.0    0.0016       3.7     144     366 ..     411     622 ..     402     627 .. 0.79
   3 ?    4.1   0.1     0.011        25      37     163 ..     770     906 ..     763     917 .. 0.61
   4 ?    4.1   0.0     0.011        24     213     336 ..     897    1015 ..     874    1026 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.7e-09
                                       TT-HHHH-SBTTB---HHHHHHHHHHHCTT-EEEEE-STTS--HHHHHH-GGGS-B-TTS-B--SSSS----TT-HH CS
                    Glyco_hydro_42  31 efaWaklePeegkydFewLdevldllekagikviLatptaapPaWlvkkyPeilavdadgskrkfgsrqhiclsspv 107
                                        f W k+ePe+gkydF+  dev+  ++++g+++ Lat      +W  +k+ +i +  +++  ++    ++  +++++
  gi|488600439|ref|YP_007906910.1| 341 PFIWDKIEPERGKYDFSEADEVVREAQAMGLNI-LATIWP-YAKWDQEKWGNIDRFVEKRDFPELPFSRYKPYNMQA 415
                                       689****************************97.566433.458***********99999999999999999***** PP

                                       HHHHHHHHHHHH.HHHHTT-TT....EEEEE-SSSTTTT.S--SHHHHH CS
                    Glyco_hydro_42 108 yrekvakiveal.aerYkdhpa....vilwhidnEygch.ecycetcee 150
                                       y+e v+++ve+   + ++d p     +  w++ nE ++   c  e  + 
  gi|488600439|ref|YP_007906910.1| 416 YKEFVKALVERYdGDGFNDMPGltkpIKYWEVINEPSTGiICKFEGKNA 464
                                       *****99999986556666655111156899999977655555554444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0016
                                       -SHHHHHHHHHHHHHHHSSHHHHHHHHTTTGGG---SSGGG---S-S-SS---HHHHHHHHHHHHHHHHHHHHHHHH CS
                    Glyco_hydro_42 144 ycetceeaFrkwlkekYgtidelneawgtafWsqeysdfeeielPselseeenpskildykrFssdqilefvkaeae 220
                                       y  ++ ++F k l e+Y+  d  n+  g +     ++ +e i+ Ps+    + ++k+  + +   +   e++k  +e
  gi|488600439|ref|YP_007906910.1| 411 YNMQAYKEFVKALVERYD-GDGFNDMPGLTK---PIKYWEVINEPSTGIICKFEGKNAGFFKGDAEDYFEVLKVTYE 483
                                       555666667777777776.667777666554...7889*********9999*********9999************* PP

                                       HHHHHSTT-EEE-EE-TT................--SS-HHHHGGGSSSEEEEE-HH---HHHHH-TTHHHHHHHHH CS
                    Glyco_hydro_42 221 ilreyspdipvttnfmgs...............afkdldyvklakeldivswdsYptrskeekeekldelalkhdly 282
                                       +++e+ +d+ v +  m +               ++k +++   +k++div + s+           +d+++lk+ + 
  gi|488600439|ref|YP_007906910.1| 484 AIKEADKDAKVLNGGMVPlppekgevsdgfygfWNKVFEMGG-SKYIDIVNFHSFSP--------YEDAIRLKERFG 551
                                       ************999999999988887777776666666555.77777777777766........678899999998 PP

                                       HHHTTT-.EEEEEE--S--SSSSS-----TTHHHHHHHHHHHTT-S-EEEC-SB--SSSTTTTS--SB-TTS.-B-H CS
                    Glyco_hydro_42 283 rslkkgkpflvmEqqpsavnwapvnkakapGavrlwslqavAhGadavlyFqwrqsrggsEkfhsgvlehvgsektr 359
                                       +++  gkp +v E ++             ++    ++ ++++ G++ + y  +r  + + E++  g l + + +++r
  gi|488600439|ref|YP_007906910.1| 552 KYV-AGKPLWVTEFSAT------------DEYRYVEASKSFGEGVERIFYTAYRAFPEAPEDLITGSLIDFEGNPKR 615
                                       888.9999999999887............666677777888899999999999999999999887776666668888 PP

                                       HHHHHHH CS
                    Glyco_hydro_42 360 vfrevke 366
                                        ++ vk+
  gi|488600439|ref|YP_007906910.1| 616 SYYAVKT 622
                                       8877776 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.011
                                       H-SBTTB---HHHHHHHHHHHCTT-EEEEE-STTS--HHHHHH-GGGS-B-TTS-B--SSSS-.---TT-HHHHHH. CS
                    Glyco_hydro_42  37 lePeegkydFewLdevldllekagikviLatptaapPaWlvkkyPeilavdadgskrkfgsrq.hiclsspvyrek. 111
                                       +e e+g ydF+  de +++++++g +++      +   W ++++ e   ++++g  +  g+ +  ++l s+ ++ + 
  gi|488600439|ref|YP_007906910.1| 770 IEKEKGVYDFSACDEGVKRAQQTGAEIVA-----T--IWPYTEWDEEAYKGREGYGEATGGGPfAYVLPSSRFKPYd 839
                                       78899********************9972.....2..5777777777777777776666655413444455555431 PP

                                       ...HHHHHHHHHHHHTT-TT.........EEEEE-SSSTTTT...S--SHHHHHHHHHHHHHHHSSH CS
                    Glyco_hydro_42 112 ...vakivealaerYkdhpa.........vilwhidnEygch...ecycetceeaFrkwlkekYgti 163
                                           ++ v+al erY  ++          +  w+i nE + +   + + +   +++ + +k++Y+ +
  gi|488600439|ref|YP_007906910.1| 840 iqaYKAFVRALVERYDGDGIddmpglkypIKYWEILNEPEAQhdnKYFFKGSGKEYFELVKATYEAV 906
                                       1114455666677776443111122222256677777766655644444555555556666666655 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.011
                                        HHHHHHHHHHHHHSTT-EEE-EE-TT........--SS-HHHHGGGSSSEEEEE-HH---HHHHH-TTHHHHHHH CS
                    Glyco_hydro_42  213 efvkaeaeilreyspdipvttnfmgs.......afkdldyvklakeldivswdsYptrskeekeekldelalkhd 280 
                                        e+vka +e+++e+ + + v     ++       +++++     +++ di+   sY        e++  ++   + 
  gi|488600439|ref|YP_007906910.1|  897 ELVKATYEAVKEADSTAKVVLGGAATldkesieWWEEFYSLGGGNYFDIAGIHSYAD------EKDDFNVDDLKK 965 
                                        555666677776666666653333323334444444444444556666666666666......444455555566 PP

                                        HHHHHTTT-.EEEEEE--S--SSSSS-----TTHH.HHHHHHHHHTT-S-EEEC-SB CS
                    Glyco_hydro_42  281 lyrslkkgkpflvmEqqpsavnwapvnkakapGav.rlwslqavAhGadavlyFqwr 336 
                                        l +++  +kp +v E  p        + ++++G + +  ++ a+A Ga  vl+F ++
  gi|488600439|ref|YP_007906910.1|  966 LLEKYGINKPIWVTEVGPT------GEMSREDGIMfAKAAIRAFANGA-EVLFFDYK 1015
                                        77888899********999......56778899662667899******.79999997 PP

>> Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   4.6e-07     0.001      46     117 ..      71     138 ..      63     144 .. 0.83
   2 !    4.6   0.0    0.0057        13     145     200 ..     205     264 ..     155     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.6e-07
                                       E......EEEEEEEEETTS-E.EEEEEEESSSSS-EE-SS---EE-TTS-B--EEEEEEEEETTEEE.EEEE. CS
                   Glyco_hydro_130  46 eLevyaRvvllYrkyvsdiaslrigledlkdGikktlepeevvlpedkqellgveDPRvvkinskyy.ltYtg 117
                                        L+v +++ + Y +  +d     i ++++ dGi+++   ++v++ +d+++ +g+ DP v++i ++++ + Y g
  gi|488600439|ref|YP_007906910.1|  71 VLKVNGKFLMYYVIPGEDE----IRIAESEDGIHFHNS-QVVIEKGDEYDKFGAVDPAVIQISENLFrMYYVG 138
                                       5788889999988888874....669*******99876.569********************88765266665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0057
                                       SSE..........EEEEE-SS-BTTBEEEEEE....SS-S---EEEEEESSSS-BEEEEE CS
                   Glyco_hydro_130 145 lielkkdeislatkdgalfpkkikgkylmfsr....vhtvsekifLavsddlvlwenele 200
                                        +++ kd  +++ +  + f+ k++++y +++       +  ++++L+ s+d +++++e+ 
  gi|488600439|ref|YP_007906910.1| 205 GVNITKDWGRIMERVSVPFVLKTDNEYRLYYTkvpdSPEEGIDVYLSTSKDGINFTGEKL 264
                                       566678889999999999999**999988776443333345689***********99876 PP

>> Glyco_hydro_39  Glycosyl hydrolases family 39
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.1    0.0055        12     128     199 ..     410     494 ..     406     545 .. 0.71
   2 !   17.3   0.3   6.5e-07    0.0015     128     212 ..     837     931 ..     832     966 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0055
                    Glyco_hydro_39 128 pkqvkeWkeLisllarryisRY.....GldevskWnFevWnePdl...kdF......dkvattkeylklYkaaaeal 190
                                       p +++++ke +++l+ ry +       Gl++  k+ +ev neP       F      + +++ ++y++  k++ ea+
  gi|488600439|ref|YP_007906910.1| 410 PYNMQAYKEFVKALVERYDGDGfndmpGLTKPIKY-WEVINEPSTgiiCKFegknagFFKGDAEDYFEVLKVTYEAI 485
                                       55667777777777777766411222255554443.57888886422212211111144578999************ PP

                    Glyco_hydro_39 191 kkvseelkv 199
                                       k+++++ kv
  gi|488600439|ref|YP_007906910.1| 486 KEADKDAKV 494
                                       ****99987 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.5e-07
                    Glyco_hydro_39 128 pkqvkeWkeLisllarryisRYGldevs..kWn...FevWnePdlk.d..FdkvattkeylklYkaaaealkkvsee 196
                                       p +++++k  +++l+ ry +  G+d++   k++   +e+ neP+ + d  ++ ++  key++l ka+ ea+k+++++
  gi|488600439|ref|YP_007906910.1| 837 PYDIQAYKAFVRALVERYDGD-GIDDMPglKYPikyWEILNEPEAQhDnkYFFKGSGKEYFELVKATYEAVKEADST 912
                                       667778888888888888664.555543123331115888***85313447778999*******************9 PP

                    Glyco_hydro_39 197 lkv..GGP.alctgldewi 212
                                        kv  GG  +l     ew 
  gi|488600439|ref|YP_007906910.1| 913 AKVvlGGAaTLDKESIEWW 931
                                       8864477622333333333 PP

>> Glyco_hydro_53  Glycosyl hydrolase family 53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.39   8.7e+02      53      83 ..     345     375 ..     321     380 .. 0.79
   2 ?   -0.4   0.0       0.2   4.6e+02     140     179 ..     449     494 ..     439     496 .. 0.75
   3 !   17.3   0.1   8.1e-07    0.0018     159     248 ..     895     985 ..     878    1073 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.39
                    Glyco_hydro_53  53 nkngelegvndldkaikiakrakaaGmkvll 83 
                                       +k +   g +d ++a ++++ a+a G+++l+
  gi|488600439|ref|YP_007906910.1| 345 DKIEPERGKYDFSEADEVVREAQAMGLNILA 375
                                       556667899*******************985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.2
                    Glyco_hydro_53 140 NEinsgllws.egk.....kenweklakllnsgikavkevstnikv 179
                                       NE ++g++ + egk     k + e + ++l+  ++a+ke ++++kv
  gi|488600439|ref|YP_007906910.1| 449 NEPSTGIICKfEGKnagffKGDAEDYFEVLKVTYEAIKEADKDAKV 494
                                       6666666554133366677778888899***************999 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 8.1e-07
                    Glyco_hydro_53 159 lakllnsgikavkevstnikvviHlangedaaskkaifkklskag.vdfDvigvsYYpfwsstleklk.snlkdlas 233
                                       + +l+++ ++avke ++++kvv+  a   d++s +++ ++ s  g   fD+ g+  Y   ++   +++ ++lk+l +
  gi|488600439|ref|YP_007906910.1| 895 YFELVKATYEAVKEADSTAKVVLGGAATLDKESIEWWEEFYSLGGgNYFDIAGIHSYADEKD---DFNvDDLKKLLE 968
                                       56899***********************************999963778****987764444...333256777777 PP

                    Glyco_hydro_53 234 ry..gkevivvEtsypy 248
                                       +y  +k + v+E++ + 
  gi|488600439|ref|YP_007906910.1| 969 KYgiNKPIWVTEVGPTG 985
                                       77336999999998554 PP

>> Glyco_hydro_10  Glycosyl hydrolase family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   7.7e-06     0.017      46     167 ..     344     493 ..     342     496 .. 0.73
   2 ?   -2.3   0.0      0.88     2e+03      49      75 ..     770     796 ..     768     801 .. 0.89
   3 ?    2.4   0.0     0.031        69     107     169 ..     844     916 ..     833     918 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.7e-06
                                       HHHHCSBTTBEE-HHHHHHHHHHHHTT-EEEEEEEEESS...S--HHHHTS.CCCHHH..........HHHHHHHHH CS
                    Glyco_hydro_10  46 wealepsegnftfekadklvdfakennmkvrGHtLvWhs...qlPdwvkke.ngskae..........eallkrlen 108
                                       w+++ep++g+++f++ad++v  a++ ++++   + +W        +w + +  ++k +              ++ ++
  gi|488600439|ref|YP_007906910.1| 344 WDKIEPERGKYDFSEADEVVREAQAMGLNIL--ATIWPYakwDQEKWGNIDrFVEKRDfpelpfsrykPYNMQAYKE 418
                                       99*********************99998886..5677544454556766664334444777778777666788999* PP

                                       HHHHHHHHTT...........TTESEEEEEES-B-TTS..CSBE-SHHHHHHTTHHHH...HHHHHHHHH-TTSE CS
                    Glyco_hydro_10 109 hiktvveryk...........gkiyawDVVNEavddng..gslresvwyqilGedyie...kAFeaAreadpdak 167
                                       ++k++very            + i+ w V+NE         + ++  + +   edy+e     +ea +ead dak
  gi|488600439|ref|YP_007906910.1| 419 FVKALVERYDgdgfndmpgltKPIKYWEVINEPSTGIIckFEGKNAGFFKGDAEDYFEvlkVTYEAIKEADKDAK 493
                                       ******************99999*********8655444445566666666666665422246666666666665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.88
                                       HCSBTTBEE-HHHHHHHHHHHHTT-EE CS
                    Glyco_hydro_10  49 lepsegnftfekadklvdfakennmkv 75 
                                       +e+++g ++f++ d+ v+ a++ + ++
  gi|488600439|ref|YP_007906910.1| 770 IEKEKGVYDFSACDEGVKRAQQTGAEI 796
                                       68899*****************99876 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHTT...........TTESEEEEEES-B-TTSCSBE-SHHHHHHTTHHHH...HHHHHHHHH-TTSEEE CS
                    Glyco_hydro_10 107 enhiktvveryk...........gkiyawDVVNEavddnggslresvwyqilGedyie...kAFeaAreadpdakLy 169
                                       + +++++very              i+ w + NE  ++++    +  + +  G++y+e     +ea +ead +ak +
  gi|488600439|ref|YP_007906910.1| 844 KAFVRALVERYDgdgiddmpglkYPIKYWEILNEPEAQHD----NKYFFKGSGKEYFElvkATYEAVKEADSTAKVV 916
                                       6677777777777777777776667999*****9988776....7899*****999652226899999999999865 PP

>> Glyco_hydro_32N  Glycosyl hydrolases family 32 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   4.3e-05     0.097      42     119 ..      92     172 ..      70     195 .. 0.80
   2 !    4.6   0.0    0.0092        21      17      60 ..     226     268 ..     223     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.3e-05
                                       EEEESSSSSBEEEEEEE-SSSGGCTTEEEEEEEEE-TT-EEEEEEEE-T......CSEEEEEEEEESSTTSSEEE-T CS
                   Glyco_hydro_32N  42 havSkDlvhWeelpvalapdeefdsngafSGsavvdddklvllYTgnvk......eeeqvQnlayskdkgreftkye 112
                                        a+S+D +h+++ +v +++ +e+d+ ga    +++ +++l+ +Y   ++        ++    a+s  +g++++k  
  gi|488600439|ref|YP_007906910.1|  92 IAESEDGIHFHNSQVVIEKGDEYDKFGAVDPAVIQISENLFRMYYVGWEedipggWGRNSLLTAIS-TDGIHWKK-- 165
                                       589***********************************9887665555558887523667777777.9999**99.. PP

                                       T--SB-. CS
                   Glyco_hydro_32N 113 enpviae 119
                                       e++++++
  gi|488600439|ref|YP_007906910.1| 166 ERKILSK 172
                                       7777775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0092
                                       ECTTEEEEEEEEETTSSSS-SBEEEEEEESSSSSBEEEEEEE-S CS
                   Glyco_hydro_32N  17 yykgeYhlFYqynpkgavwgnisWghavSkDlvhWeelpvalap 60 
                                       ++++eY l+Y   p +++ g i  + ++SkD ++++ +++ l++
  gi|488600439|ref|YP_007906910.1| 226 KTDNEYRLYYTKVPDSPEEG-IDVYLSTSKDGINFTGEKLILEN 268
                                       5789**********988888.77789*********999988765 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.17   3.8e+02      65      91 ..     475     501 ..     471     511 .. 0.84
   2 ?    8.3   0.0     0.001       2.2      64      97 ..     895     927 ..     891     938 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.17
                       B12-binding  65 leavkelvellkrirprvkvvvGGahp 91 
                                       +e  k + e++k++++++kv+ GG +p
  gi|488600439|ref|YP_007906910.1| 475 FEVLKVTYEAIKEADKDAKVLNGGMVP 501
                                       5666777788**************875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.001
                       B12-binding  64 qleavkelvellkrirprvkvvvGGahpsldpee 97 
                                       ++e vk++ e++k++++ +kvv+GGa+ +ld e 
  gi|488600439|ref|YP_007906910.1| 895 YFELVKATYEAVKEADSTAKVVLGGAA-TLDKES 927
                                       57889999999**************85.888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1113 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:                        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: 0.79u 0.31s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 6997.34
//
Query:       gi|488600440|ref|YP_007906911.1|  [L=871]
Description: ATPase, P-type (transporting), HAD superfamily, subfamily IC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  182.5   3.8    5.4e-54  182.5   3.8    3.3  4  E1-E2_ATPase     E1-E2 ATPase
    2.3e-34  118.7  12.7    2.3e-34  118.7  12.7    2.4  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.3e-21   77.9   0.3    4.8e-21   76.0   0.3    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.3e-17   63.2   0.0    3.5e-17   61.8   0.0    1.8  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    7.2e-12   45.6   2.5    1.7e-06   28.0   0.4    2.5  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    4.8e-11   42.6   0.0    1.2e-10   41.4   0.0    1.6  1  Cation_ATPase    Cation transport ATPase (P-type)
     0.0023   18.4   0.0     0.0052   17.2   0.0    1.6  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.018   14.9   0.3        0.5   10.3   0.1    2.7  2  RNA_pol_Rpb5_C   RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.69   1.5e+03     106     144 ..      47      85 ..      41     101 .. 0.63
   2 !  182.5   3.8   2.4e-57   5.4e-54       5     181 .]     117     304 ..     113     304 .. 0.97
   3 ?   -2.8   0.1       1.7   3.9e+03     113     134 ..     665     686 ..     632     715 .. 0.53
   4 ?   -0.4   1.0      0.31   6.9e+02     119     154 ..     743     775 ..     731     788 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.69
                                       ----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSST CS
                      E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflialllgksl 144
                                       +k +++ ++l+ +   l+ + ++ +l++ +++ ++  ++
  gi|488600440|ref|YP_007906911.1|  47 KKISEILRFLSHFNDPLIYILMVSGLITTFLLRYVDTTI 85 
                                       666777788888888877777777777777765554443 PP

  == domain 2  score: 182.5 bits;  conditional E-value: 2.4e-57
                                       -EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-...........G-TTE CS
                      E1-E2_ATPase   5 ptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek...........ekgdm 69 
                                        +a+vir   e+ei+akelvpGD+++l+ag++vpaD+r++e ++ +vdes+LTGEs+pvek           e+++m
  gi|488600440|ref|YP_007906911.1| 117 VKARVIRR-VEKEIPAKELVPGDVIVLEAGMKVPADARLFEVKNlTVDESLLTGESTPVEKfsetiqektavERNNM 192
                                       57777764.5899**********************************************************99**** PP

                                       E-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTH CS
                      E1-E2_ATPase  70 vfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslae 146
                                       vf+Gt v++g  kavV+atge+telgkia+ v+ +k  +tpl + ++ ++k+++++++++++l f+i +l+g ++++
  gi|488600440|ref|YP_007906911.1| 193 VFAGTLVLEGYGKAVVVATGENTELGKIAKTVKIEKGVETPLLRRIKHISKFIFFIIVVVSILNFIIGVLRGYDPTF 269
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 147 allralallvaaiPcaLplavplalalgarrlakk 181
                                       ++l +++l+vaaiP+ Lp++v+++la+g+r +ak+
  gi|488600440|ref|YP_007906911.1| 270 MFLASVSLAVAAIPESLPALVTMSLAIGVRDMAKR 304
                                       *********************************96 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 113 kkldklgkvlvpvvlliallvf 134
                                       +k++k+ ++l p+ +  +l+v+
  gi|488600440|ref|YP_007906911.1| 665 RKIQKILAWLLPTNVGEGLVVL 686
                                       4444555555544443222222 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHH CS
                      E1-E2_ATPase 119 gkvlvpvvlliallvflialllgkslaeallralal 154
                                       +++++++++l++++ fl++ + +++l   + r++a+
  gi|488600440|ref|YP_007906911.1| 743 FRIIWVAIVLVVCAYFLYFRYDENEL---IARTIAM 775
                                       45666666666666666665555544...4444443 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 ?   -1.9   0.1         1   2.3e+03     115     146 ..      51      82 ..      44     108 .. 0.68
   2 ?   -0.9   0.1       0.5   1.1e+03      92     141 ..     243     258 ..     195     293 .. 0.70
   3 !  118.7  12.7     1e-37   2.3e-34       2     182 .]     695     861 ..     694     861 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                   Cation_ATPase_C 115 slfkfsglfsnkllllaillslllqvlivyvp 146
                                       ++++f + f  +l+++ ++  l+ ++l+ yv 
  gi|488600440|ref|YP_007906911.1|  51 EILRFLSHFNDPLIYILMVSGLITTFLLRYVD 82 
                                       56677777766666666666666666666663 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.5
                   Cation_ATPase_C  92 tmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvl 141
                                        ++F ++v+++i+n                                   +
  gi|488600440|ref|YP_007906911.1| 243 KFIFFIIVVVSILNF----------------------------------I 258
                                       333333333333332..................................2 PP

  == domain 3  score: 118.7 bits;  conditional E-value: 1e-37
                   Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgi 78 
                                       lp+ ++qiLwin vt +l++++L++ep e++++k +P   +  l+++++l+ri+++++++++++++++f     ++ 
  gi|488600440|ref|YP_007906911.1| 695 LPILPVQILWINTVTAVLLGTTLVFEPREPNLLKLKPI--TGELLNPAILFRIIWVAIVLVVCAYFLYFR----YDE 765
                                       89***********************************8..999*********************999953....345 PP

                   Cation_ATPase_C  79 sekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgta 155
                                       +e         a+t+a +t+v+++if++l++rs + s++k    f+n+ ++l+il++++lq++ +y p++n +++ta
  gi|488600440|ref|YP_007906911.1| 766 NELI-------ARTIAMNTIVFFEIFYLLSSRSIDLSFIK-TLKFKNRAIYLGILAMIVLQLVATYSPHFNVILHTA 834
                                       6655.......**********************9999999.66679******************************* PP

                   Cation_ATPase_C 156 plsleewlialllalvvllvdelvKll 182
                                       pl++++wl ++ ++++v+l++el K++
  gi|488600440|ref|YP_007906911.1| 835 PLDASMWLEIVTVSSLVFLLAELEKYI 861
                                       *************************96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.3   2.1e-24   4.8e-21       1     210 []     320     625 ..     320     625 .. 0.75

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 2.1e-24
                                       SSEEEEESBTTTBCHHHHHHHHHHHH.........................CHHHHHHHHHH...........HHCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxx...........xxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.........................alalaaaletg...........sehp 41 
                                       ++t++ Dk+GTLt+ ++ v ++++                           +++ + + +t+           s  p
  gi|488600440|ref|YP_007906911.1| 320 VTTICTDKTGTLTQNKMKVIRIFAGGreydieskdsilsreelaehldiylTIKAGYICNTAiyflkdgepitSGDP 396
                                       579******************99999999999999999988888888888877777777777888888888887777 PP

                                       HHHHH..HHHHHHH............HHHHHHHHHETTTE....HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHH CS
                                       xxxxx..xxxxxxx............xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  42 igkal..vaaakar............sgaltgfatfigrg....ayaigkpewltaldippdlgaaigsaqsqgrtv 100
                                          al  va   ++             +al  +at   +g     y +g+ e + ++            a ++g+ v
  gi|488600440|ref|YP_007906911.1| 397 TEVALleVASLAGIkkqfkiideipfDPALRYMATAVKEGefveIYVKGSIERVLSM---------CRWALAEGKVV 464
                                       777774344444447777777777776666666665555577888888888877777.........33333333333 PP

                                       HHH.......................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEE CS
                                       xxx.......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 101 all.......................................qaralavftiadplkvkpeaaeavasLkaagievv 138
                                        l+                                       +   l++  + dp  +++e  ea+++ k+ag++v+
  gi|488600440|ref|YP_007906911.1| 465 ELDehrihkiasefalrglrvlafaykfvdleefgsiednldDLIFLGLQCMIDP--PREECYEAIKKCKEAGVRVI 539
                                       3334444445555666777777788************8877766777788888**..******************** PP

                                       EEESSEHHHHHHHHHHTT.......GGGESEEEEHHCES...........STTTSHHHHHHHHHHHTSTGGGEEEEE CS
                                       xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 139 lltgdnpetaeraanqlG.......ddyfdaviasdiet...........vakpspegkvaaireLqgkpeevamVG 197
                                       ++tgd+p+ta  +a++l+             +i++ +++           +a  +p++k+++++ Lq+ +e va+ G
  gi|488600440|ref|YP_007906911.1| 540 MITGDHPSTALFIAKELDingsvitG----DKIEKMNDEelkkvlkktnvFARILPKMKLRIVKLLQEMGEIVAVTG 612
                                       ******************88644442....222222222433345556667777*************77777***** PP

                                       SSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxx RF
                         Hydrolase 198 DgvnDaaalaaAg 210
                                       DgvnDa+al++A+
  gi|488600440|ref|YP_007906911.1| 613 DGVNDAPALKRAD 625
                                       ***********98 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0   1.6e-20   3.5e-17       1      68 [.       7      73 ..       7      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.6e-20
                   Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                      ++  +++ev++  + ++++G+t++eaa+rl  yG Ne+ke+kk s + ++l++f++pl+++L+v++l+
  gi|488600440|ref|YP_007906911.1|  7 WYRTPISEVFKLAK-SSPQGITDEEAAKRLILYGYNEIKEEKKISEILRFLSHFNDPLIYILMVSGLI 73
                                      77789999999998.9**************************************************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 !   17.0   0.1   1.7e-06    0.0037      19      82 ..     523     583 ..     519     598 .. 0.82
   2 !   28.0   0.4   7.6e-10   1.7e-06     196     255 .]     598     657 ..     592     657 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE--B-HH CS
                       Hydrolase_3  19 ktkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilykstiske 82 
                                       +  eaikk+ke+g+ v+  TG +++++l +++el+++  vi+  G  i++ +++ l k+ ++k+
  gi|488600440|ref|YP_007906911.1| 523 ECYEAIKKCKEAGVRVIMITGDHPSTALFIAKELDINGSVIT--GDKIEKMNDEEL-KKVLKKT 583
                                       6679*******************************9999987..888866666666.4555544 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 7.6e-10
                                       HHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHHH CS
                       Hydrolase_3 196 akelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVakal 255
                                       +k l+   e v++ GDg ND + L++a++gvAmg+++e +k+ A  +  + n   +++a+
  gi|488600440|ref|YP_007906911.1| 598 VKLLQEMGEIVAVTGDGVNDAPALKRADIGVAMGSGTEVAKESAEIILLDDNFATIVEAI 657
                                       56666667789999*********************************9999988877776 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 !   41.4   0.0   5.2e-14   1.2e-10       3      89 ..     378     455 ..     376     456 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.2e-14
                     Cation_ATPase   3 cNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKG 79 
                                       cN a +    +++e  ++G++tE+ALl++a+ +      +++++k++ eipF+   ++m++++k  + + v +yvKG
  gi|488600440|ref|YP_007906911.1| 378 CNTAIY--FLKDGEPITSGDPTEVALLEVASLA-----GIKKQFKIIDEIPFDPALRYMATAVK--EGEFVEIYVKG 445
                                       776666..788888899************9998.....899***********************..5699******* PP

                     Cation_ATPase  80 ApeiilkrCt 89 
                                       + e++l+ C 
  gi|488600440|ref|YP_007906911.1| 446 SIERVLSMCR 455
                                       *********5 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-06    0.0052      88     188 .]     522     622 ..     476     622 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                               HAD  88 pgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkv.....aalr 159
                                       ++ +e+++++++aG+rv++++g +   +  +++el+    ++ +     ++tg    ++k+  +e k      +   
  gi|488600440|ref|YP_007906911.1| 522 EECYEAIKKCKEAGVRVIMITGDHPSTALFIAKELD----INGS-----VITGD--KIEKMNDEELKKvlkktN--- 584
                                       5999********************************....7776.....66666..444444444443233332... PP

                               HAD 160 e..........wlaaegegidleevvay.GDspsDlpllr 188
                                                       +   +  e+va+ GD+++D p+l+
  gi|488600440|ref|YP_007906911.1| 585 VfarilpkmklR--IVKLLQEMGEIVAVtGDGVNDAPALK 622
                                       033355555332..333333334478888********996 PP

>> 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 ?    1.4   0.0      0.14     3e+02      41      61 ..     423     445 ..     401     452 .. 0.81
   2 ?   10.3   0.1   0.00022       0.5      11      38 ..     567     594 ..     564     613 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                                       SHHHHCC..T--TTSEEEEEEEE CS
                    RNA_pol_Rpb5_C  41 Dpvaryl..glkkGdvvkItrks 61 
                                       Dp++ry+   +k+G+ v+I  k+
  gi|488600440|ref|YP_007906911.1| 423 DPALRYMatAVKEGEFVEIYVKG 445
                                       9***9998889********8775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00022
                                       EEEEE-HHHHHHHHHHTT--TTCSS-EE CS
                    RNA_pol_Rpb5_C  11 khevlseeekkellkklkikeeqLPkis 38 
                                       k e++++ee k++lkk ++    LPk++
  gi|488600440|ref|YP_007906911.1| 567 KIEKMNDEELKKVLKKTNVFARILPKMK 594
                                       6789***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (871 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.25s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 6158.56
//
Query:       gi|488600441|ref|YP_007906912.1|  [L=78]
Description: hypothetical protein Asulf_00914 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-12   45.7   0.9    8.2e-12   45.2   0.7    1.4  1  DsrD      Dissimilatory sulfite reductase D (DsrD)
     0.0072   16.9   0.1      0.011   16.3   0.1    1.3  1  HTH_32    Homeodomain-like domain
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.018   15.0   0.1    1.3  1  HRDC      HRDC domain
      0.017   15.2   0.2      0.019   15.0   0.2    1.1  1  HTH_54    ParA helix turn helix domain
      0.032   14.2   0.4       0.07   13.1   0.4    1.6  1  HTH_36    Helix-turn-helix domain
      0.069   11.7   0.3      0.073   11.6   0.3    1.1  1  DUF5357   Family of unknown function (DUF5357)
       0.17   11.9   1.8       0.47   10.4   0.1    2.0  2  HTH_37    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DsrD  Dissimilatory sulfite reductase D (DsrD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.7   3.2e-15   8.2e-12       1      57 [.       8      59 ..       8      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.2e-15
                                      HHHHHHHHHSSCCCSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEETTEE CS
                              DsrD  1 akkaiveflekkkkKskfYfkDlekalPdakpreiKkvvneLVnegkLeywSsGSTt 57
                                      +k++++e+l +k+       +Dl+k+l  +k+re+ k++ eL+negk  ywSsGST 
  gi|488600441|ref|YP_007906912.1|  8 VKQKVLEKLAQKP----WSTRDLAKIL-KMKKREVDKICKELINEGKATYWSSGSTA 59
                                      5999*****9999....6679******.***************************97 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   4.3e-06     0.011      29      67 ..       4      43 ..       2      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-06
                            HTH_32 29 lsdevrariiallreeprWsprqlaarl..aeregvkvShs 67
                                      +++ev++++++ l ++  Ws+r la+ l  ++re +k+ ++
  gi|488600441|ref|YP_007906912.1|  4 FDEEVKQKVLEKLAQK-PWSTRDLAKILkmKKREVDKICKE 43
                                      589**********667.6********998777777777766 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   6.9e-06     0.018      28      66 ..       9      46 ..       8      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.9e-06
                                      -HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHHHH CS
                              HRDC 28 pdktLleiAeklPttleeLlqiegvgkrklekygeeile 66
                                      ++k+L+++A+k P ++ +L++i +++kr ++k  +e+++
  gi|488600441|ref|YP_007906912.1|  9 KQKVLEKLAQK-PWSTRDLAKILKMKKREVDKICKELIN 46
                                      789999**999.99*********************9986 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   7.4e-06     0.019      26      84 ..      19      75 ..       3      78 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                            HTH_54 26 qtyskaalaklpklsrrkvdkavsemeaeGyefekkeagstekYaltiqnvidlykhrg 84
                                      +++s   lak+ k+ +r+vdk  +e+ +eG +     +g ++ Y  t++ + ++ + r+
  gi|488600441|ref|YP_007906912.1| 19 KPWSTRDLAKILKMKKREVDKICKELINEGKATYWS-SG-STAYVTTVEKAEEMEAKRK 75
                                      679999************************987766.45.56899***99999888776 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   2.7e-05      0.07      27      51 ..      22      46 ..      12      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeq 51
                                      s ++lak l+++k+ v ++ keL+ 
  gi|488600441|ref|YP_007906912.1| 22 STRDLAKILKMKKREVDKICKELIN 46
                                      789********************97 PP

>> DUF5357  Family of unknown function (DUF5357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   2.9e-05     0.073     204     245 ..       7      50 ..       4      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                           DUF5357 204 klqplveeqlakkpWs..evErwLleadkevkslgkqvldknle 245
                                       +++++v e+la+kpWs  +  ++L   ++ev ++ k+++++  +
  gi|488600441|ref|YP_007906912.1|   7 EVKQKVLEKLAQKPWStrDLAKILKMKKREVDKICKELINEGKA 50 
                                       6788999*********88899*****************996544 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00018      0.47      23      53 ..      12      42 ..       6      47 .. 0.84
   2 ?    1.0   0.2      0.16   4.1e+02       8      20 ..      65      77 ..      62      78 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                                      HHHHHHHCT--HHHHHHHHT--HHHHHHHHT CS
                            HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllr 53
                                      + e+++++ +s++++a++l++++ +v+++ +
  gi|488600441|ref|YP_007906912.1| 12 VLEKLAQKPWSTRDLAKILKMKKREVDKICK 42
                                      6688999***************999998866 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
                                      -HHHHHHHHHHHH CS
                            HTH_37  8 edaeelkaKaqla 20
                                      e aee++aK++ a
  gi|488600441|ref|YP_007906912.1| 65 EKAEEMEAKRKEA 77
                                      789******9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1542  (0.0860059); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 426.85
//
Query:       gi|488600442|ref|YP_007906913.1|  [L=365]
Description: dissimilatory sulfite reductase beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-38  130.1   0.0    7.3e-38  129.6   0.0    1.2  1  NIR_SIR         Nitrite and sulphite reductase 4Fe-4S domain
    5.4e-13   48.6   0.0      1e-12   47.7   0.0    1.5  1  NIR_SIR_ferr    Nitrite/Sulfite reductase ferredoxin-like hal
    1.8e-06   27.5   5.7    1.4e-05   24.7   3.1    2.6  2  Fer4            4Fe-4S binding domain
     0.0016   19.0   9.9     0.0042   17.6   9.9    1.8  1  Fer4_7          4Fe-4S dicluster domain
     0.0019   18.9   0.1     0.0065   17.2   0.0    1.9  2  Fer4_15         4Fe-4S single cluster domain
     0.0022   18.5   2.5     0.0022   18.5   0.1    2.2  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
     0.0043   17.2   5.2     0.0043   17.2   5.2    1.8  2  Fer4_9          4Fe-4S dicluster domain
     0.0047   17.0   5.7      0.011   15.8   5.7    1.6  1  Fer4_10         4Fe-4S dicluster domain
     0.0055   16.7   2.0     0.0055   16.7   2.0    2.3  1  Fer4_2          4Fe-4S binding domain
  ------ inclusion threshold ------
      0.029   14.8   0.1      0.029   14.8   0.1    2.2  2  Fer4_8          4Fe-4S dicluster domain
      0.043   13.9   5.6      0.061   13.4   1.5    2.8  2  Fer4_6          4Fe-4S binding domain
       0.21   11.5   0.0       0.43   10.5   0.0    1.4  1  DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
       0.75   10.8   6.4        6.7    7.7   4.8    2.6  2  Fer4_16         4Fe-4S double cluster binding domain
        1.9    8.7  10.4       0.11   12.7   3.8    2.1  2  Fer4_21         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.0   5.7e-41   7.3e-38       5     157 ..     130     344 ..     127     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 5.7e-41
                                       CCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                           NIR_SIR   5 lrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei.. 79 
                                       l n+++++g+ +c++ ++D++  +ka++d+l +++++++lP  ++i++++c n+c+av+a+Di+lvg+++ ++++  
  gi|488600442|ref|YP_007906913.1| 130 LSNIVHTQGWIHCHTPAIDASGPVKALMDALFDHFKNMDLPGLCRISLACCLNMCGAVHASDISLVGIHRTPPMVdd 206
                                       6799************************************************************************* PP

                                       ..........................................................EEEEEE--B-SSSTC-TCE CS
                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  80 ..........................................................gfnilvGGglgrthgakkt 98 
                                                                                                 g++il GG+l+  ++ ++ 
  gi|488600442|ref|YP_007906913.1| 207 dvvrrtcelpstvagcptgalrpdmknktikvdkekcmycgncytmcpgmplfdpengGVAILAGGKLSDARSPARL 283
                                       ***************************************************************************** PP

                                       EEEE.EEEEGG.....GHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHHHCCTC CS
                                       xxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  99 sarl.gfvpee.....evlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekveeelgk 157
                                       s+++ +++p++     ev+++v+ai+e ++    ++++ +eR++++++r+G+ekF+ek++ e++ 
  gi|488600442|ref|YP_007906913.1| 284 SKVVvPYLPNNpprwpEVVDTVKAILEAWA----AEAKPHERIAEWIDRIGWEKFFEKTGIEFKV 344
                                       **99**************************....*************************999876 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 !   47.7   0.0     8e-16     1e-12       3      68 ..      48     112 ..      46     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 8e-16
                      NIR_SIR_ferr   3 qkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLae 68 
                                        + g+++y+vr+  p   ++  + r+l+dia+ky++g++r+T+r n+++   +e+++++++ee+++
  gi|488600442|ref|YP_007906913.1|  48 AESGDKIYTVRVGSP-RLLSIYTIRELCDIADKYCDGYLRFTSRNNIEFLLTDESKIDPLIEEVEK 112
                                       6789999********.555*******************************************9976 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.11   1.4e+02      18      24 .]     222     228 ..     219     228 .. 0.84
   2 !   24.7   3.1   1.1e-08   1.4e-05       1      19 [.     236     254 ..     236     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                       STTTEEE CS
                              Fer4  18 CPvgAIt 24 
                                       CP+gA++
  gi|488600442|ref|YP_007906913.1| 222 CPTGALR 228
                                       *****85 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.1e-08
                                       EEEETTTSSS-THHHHHST CS
                              Fer4   1 vvideekCigCGaCvevCP 19 
                                       +++d+ekC++CG+C+ +CP
  gi|488600442|ref|YP_007906913.1| 236 IKVDKEKCMYCGNCYTMCP 254
                                       689**************** 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   9.9   3.3e-06    0.0042       9      49 ..     219     254 ..     173     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                            Fer4_7   9 vaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       va Cp++a++ d +     ++++++d ekC++Cg+C + CP
  gi|488600442|ref|YP_007906913.1| 219 VAGCPTGALRPDMK-----NKTIKVDKEKCMYCGNCYTMCP 254
                                       5679******9887.....578******************9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.9   7.6e+03      57      64 ..     220     227 ..     217     228 .. 0.81
   2 !   17.2   0.0     5e-06    0.0065       1      41 [.     236     276 ..     236     287 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.9
                           Fer4_15  57 raCPvdAI 64 
                                       + CP++A+
  gi|488600442|ref|YP_007906913.1| 220 AGCPTGAL 227
                                       67****97 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5e-06
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfelde..dglasvllddgeiae 41 
                                       ++vD+++C+ cg+C++ +p +  +d    g+a +l ++g++++
  gi|488600442|ref|YP_007906913.1| 236 IKVDKEKCMYCGNCYTMCPGMPLFDPenGGVA-IL-AGGKLSD 276
                                       79****************88655555214555.44.4555555 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 ?   -1.1   0.6       2.2   2.8e+03      48      55 ..     219     226 ..     175     228 .. 0.69
   2 !   18.5   0.1   1.7e-06    0.0022       1      31 [.     238     268 ..     238     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.2
                           Fer4_13  48 adaCPves 55 
                                       +++CP+ +
  gi|488600442|ref|YP_007906913.1| 219 VAGCPTGA 226
                                       57788876 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.7e-06
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvv 31 
                                       VD+++C+ cg+C+ ++P +   d+e g +++
  gi|488600442|ref|YP_007906913.1| 238 VDKEKCMYCGNCYTMCPGMPLFDPENGGVAI 268
                                       9****************88777777666665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.4       5.6   7.2e+03       8      15 ..     180     187 ..     172     200 .. 0.66
   2 !   17.2   5.2   3.4e-06    0.0043       9      47 ..     219     254 ..     211     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.6
                            Fer4_9   8 CveaCpag 15 
                                       C ++C a 
  gi|488600442|ref|YP_007906913.1| 180 CLNMCGAV 187
                                       67777554 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.4e-06
                            Fer4_9   9 veaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47 
                                       v+ Cp+g+ ++d ++++++++++   +C+ Cg C+  Cp
  gi|488600442|ref|YP_007906913.1| 219 VAGCPTGALRPDMKNKTIKVDKE---KCMYCGNCYTMCP 254
                                       578****************9874...8***********9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   5.7   8.6e-06     0.011      18      56 .]     221     254 ..     211     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.6e-06
                           Fer4_10  18 aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        CP+     ga   ++++++++++ ekC+ cg+C+  CP
  gi|488600442|ref|YP_007906913.1| 221 GCPT-----GALRPDMKNKTIKVDKEKCMYCGNCYTMCP 254
                                       5888.....888888899999999999999999999998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.0   4.3e-06    0.0055       3      21 ..     236     254 ..     234     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       ++vd ++C+ Cg C++ CP
  gi|488600442|ref|YP_007906913.1| 236 IKVDKEKCMYCGNCYTMCP 254
                                       689***************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.0       1.3   1.6e+03      10      22 ..     179     191 ..     173     225 .. 0.77
   2 ?   14.8   0.1   2.3e-05     0.029       3      18 ..     241     256 ..     239     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                            Fer4_8  10 aCqsaCpvlrrtk 22 
                                       +C ++C ++++++
  gi|488600442|ref|YP_007906913.1| 179 CCLNMCGAVHASD 191
                                       8999997777654 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.3e-05
                            Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                       ekC+ Cg C ++Cp +
  gi|488600442|ref|YP_007906913.1| 241 EKCMYCGNCYTMCPGM 256
                                       79***********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 ?    1.0   0.1      0.39     5e+02      17      24 .]     220     227 ..     213     227 .. 0.84
   2 ?   13.4   1.5   4.8e-05     0.061       2      20 ..     236     254 ..     235     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.39
                            Fer4_6  17 rvCPegai 24 
                                       + CP+ga+
  gi|488600442|ref|YP_007906913.1| 220 AGCPTGAL 227
                                       55****97 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.8e-05
                            Fer4_6   2 veidpdkCigCgdCvrvCP 20 
                                       + +d++kC  Cg+C++ CP
  gi|488600442|ref|YP_007906913.1| 236 IKVDKEKCMYCGNCYTMCP 254
                                       789***************9 PP

>> DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00034      0.43      16      64 ..      69     116 ..      65     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00034
                    DNA_pol3_a_NII  16 slksllkkqepevegnkliikvpneiiaealkkkkldklleeyikfgFg 64 
                                        +++l++ ++ +++g    ++ +n+i+     + k+d+l+ee++k gF+
  gi|488600442|ref|YP_007906913.1|  69 TIRELCDIADKYCDGYLR-FTSRNNIEFLLTDESKIDPLIEEVEKLGFP 116
                                       589999999999999988.5****************************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       0.2   2.6e+02      11      24 ..     221     235 ..     219     242 .. 0.68
   2 ?    7.7   4.8    0.0052       6.7      50      65 ..     239     254 ..     230     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.2
                           Fer4_16  11 vCPtnaikek.keke 24 
                                        CPt+a++ + k+k+
  gi|488600442|ref|YP_007906913.1| 221 GCPTGALRPDmKNKT 235
                                       5*******9943344 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0052
                           Fer4_16  50 kqeaitgCdiCqdvCP 65 
                                        +e++++C++C ++CP
  gi|488600442|ref|YP_007906913.1| 239 DKEKCMYCGNCYTMCP 254
                                       3677889999999998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   1.2       2.1   2.7e+03      14      52 ..     180     223 ..     173     228 .. 0.54
   2 ?   12.7   3.8   8.3e-05      0.11      32      52 ..     234     254 ..     217     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.1
                           Fer4_21  14 CliaCedtshqaieida.ktvlkvvedeCv..GCnlCssv..CP 52 
                                       Cl +C       i++ + +++ ++v+d+ v   C+l s+v  CP
  gi|488600442|ref|YP_007906913.1| 180 CLNMCGAVHASDISLVGiHRTPPMVDDDVVrrTCELPSTVagCP 223
                                       66667644444444333033445566666544577776665577 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.3e-05
                           Fer4_21  32 tvlkvvedeCvGCnlCssvCP 52 
                                       +++kv +++C+ C  C+++CP
  gi|488600442|ref|YP_007906913.1| 234 KTIKVDKEKCMYCGNCYTMCP 254
                                       555666777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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):              14  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2240.76
//
Query:       gi|488600443|ref|YP_007906914.1|  [L=409]
Description: dissimilatory sulfite reductase alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-45  152.3   0.1    1.9e-44  151.0   0.1    1.6  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    3.2e-10   39.7   0.0      8e-10   38.4   0.0    1.7  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
    0.00054   20.4   3.4      0.025   15.1   0.0    2.9  3  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
     0.0027   18.2   3.3     0.0027   18.2   3.3    2.3  3  Fer4_7        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.083   13.1   4.9      0.068   13.3   2.5    2.1  2  Fer4_9        4Fe-4S dicluster domain
      0.087   13.0   1.4       0.17   12.0   1.4    1.4  1  ETF_QO        Electron transfer flavoprotein-ubiquinone oxido
       0.15   12.1   0.1         19    5.3   0.0    2.5  2  DUF4974       Domain of unknown function (DUF4974)
       0.61    9.8   3.2        1.6    8.4   3.2    1.7  1  zf-Tim10_DDP  Tim10/DDP family zinc finger
        2.2    9.1   5.9        6.2    7.6   0.0    3.1  3  Fer4_15       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.9   3.7e+03     103     125 ..      94     113 ..      65     122 .. 0.72
   2 !  151.0   0.1   9.4e-48   1.9e-44       1     152 [.     153     369 ..     153     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                                       EEEEGGGHHHHHHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR 103 gfvpeeevlevveaivevyrdhg 125
                                       g+  +    +++++i ++++++g
  gi|488600443|ref|YP_007906914.1|  94 GWFYTS---DALRTICDIWEKYG 113
                                       455555...55666666666665 PP

  == domain 2  score: 151.0 bits;  conditional E-value: 9.4e-48
                                       .SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGS.SEEEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                           NIR_SIR   1 sganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvavean.Diglvgvkkde 76 
                                       sg+ lr++++c+g ++ce+al+Dt el+++++ ++++e++++++P+KfK++++gcpn+cva++a+ D+++vg++kde
  gi|488600443|ref|YP_007906914.1| 153 SGSALRTPSACVGPARCEFALIDTLELCYDLTITYQDELHRPMWPYKFKFKIAGCPNDCVAAKARsDFAIVGTWKDE 229
                                       6899************************************************************************* PP

                                       CEE................................................................EEEEEE--B- CS
                                       xxx................................................................xxxxxxxxxx RF
                           NIR_SIR  77 kei................................................................gfnilvGGgl 89 
                                       ++i                                                                g+ il GG++
  gi|488600443|ref|YP_007906914.1| 230 IKInqeevkkyaeagvdiktqvvdncptkcieydeekkelkidnsncvrcmhcinvlpkalkpgderGAVILMGGKA 306
                                       ***************************************************************************** PP

                                       SSSTC-TCEEEEEEEEEGG....GHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  90 grthgakktsarlgfvpee....evlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekve 152
                                       ++ +g  + +++++f+++e    e++e++ea++++++    ++++ +eRl++l+er+G+ +F+e+++
  gi|488600443|ref|YP_007906914.1| 307 PILEGPVMGWVVVPFIKAEkpfdEIKELAEAVWDFWD----ENGKFRERLAELIERVGMMRFLEAIG 369
                                       **********************88*************....***********************985 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 !   38.4   0.0     4e-13     8e-10       8      68 ..      83     145 ..      79     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4e-13
                      NIR_SIR_ferr   8 gyymvrlrvpnGri.taeqlraladiaekygsgeirlTtrQn.lqlhgvpeedleeileeLae 68 
                                       +++++r++ p+G+  t++ lr ++di+ekygsg   ++   + ++l g +  +l++ ++eLa+
  gi|488600443|ref|YP_007906914.1|  83 EFHTMRVNQPAGWFyTSDALRTICDIWEKYGSGLTNMHGSTGdIILLGTTTQNLQPCFNELAK 145
                                       699************************************9999******************86 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.4       6.2   1.2e+04      49      56 ..     205     212 ..     204     213 .. 0.80
   2 ?    5.6   0.1     0.012        24      45      57 ..     249     261 ..     227     262 .. 0.78
   3 !   15.1   0.0   1.2e-05     0.025       1      32 [.     271     302 ..     271     338 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.2
                           Fer4_13  49 daCPvesI 56 
                                       ++CP +++
  gi|488600443|ref|YP_007906914.1| 205 AGCPNDCV 212
                                       79**9986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                           Fer4_13  45 eeAadaCPvesIg 57 
                                       ++ +d+CP+++I+
  gi|488600443|ref|YP_007906914.1| 249 TQVVDNCPTKCIE 261
                                       6789********6 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.2e-05
                           Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvva 32 
                                       +D+++C+ c+ C ++ P+  +  de ga++ +
  gi|488600443|ref|YP_007906914.1| 271 IDNSNCVRCMHCINVLPKALKPGDERGAVILM 302
                                       899**********************9998765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       8.3   1.6e+04       2       8 ..     163     169 ..     158     172 .. 0.52
   2 ?   -1.6   0.0       2.2   4.4e+03      11      22 ..     206     217 ..     204     239 .. 0.72
   3 !   18.2   3.3   1.4e-06    0.0027       9      47 ..     252     285 ..     252     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.3
                            Fer4_7   2 CigCgaC 8  
                                       C+g  +C
  gi|488600443|ref|YP_007906914.1| 163 CVGPARC 169
                                       4444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                            Fer4_7  11 aCpvkaieldee 22 
                                        Cp++++  + +
  gi|488600443|ref|YP_007906914.1| 206 GCPNDCVAAKAR 217
                                       588877776654 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.4e-06
                            Fer4_7   9 vaaCpvkaieldeeenekgtekveidpekClgCgaCvav 47 
                                       v++Cp+k+ie+dee     +++++id ++C+ C +C++v
  gi|488600443|ref|YP_007906914.1| 252 VDNCPTKCIEYDEE-----KKELKIDNSNCVRCMHCINV 285
                                       689********997.....5779*************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.3   4.6e+03      11      21 ..     206     216 ..     204     229 .. 0.60
   2 ?   13.3   2.5   3.4e-05     0.068      10      45 ..     253     285 ..     251     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
                            Fer4_9  11 aCpagvvveda 21 
                                        Cp++ v  +a
  gi|488600443|ref|YP_007906914.1| 206 GCPNDCVAAKA 216
                                       46666655555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.4e-05
                            Fer4_9  10 eaCpagvvvedaaerkarlraaseeaCigCgaCvea 45 
                                       + Cp++ +++d+ +++ ++++    +C+ C+ C+++
  gi|488600443|ref|YP_007906914.1| 253 DNCPTKCIEYDEEKKELKIDNS---NCVRCMHCINV 285
                                       68***************99775...8*******986 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   8.8e-05      0.17      47      81 ..     252     282 ..     224     289 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                                       HHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HH CS
                            ETF_QO  47 qryCPagvyeivedeeakekklqinaqnCvhCktC 81 
                                          CP    e+ e+    +k+l+i+ +nCv C  C
  gi|488600443|ref|YP_007906914.1| 252 VDNCPTKCIEYDEE----KKELKIDNSNCVRCMHC 282
                                       44688888887654....589***********999 PP

>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0096        19       9      26 ..      34      51 ..      30      58 .. 0.89
   2 ?    4.1   0.0     0.024        48      13      30 ..     174     190 ..     172     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0096
                                      HHHHHHHHHHHHT--EEE CS
                           DUF4974  9 LeeilkkLerwYnveivi 26
                                      ++++lk+Ler Y  +i++
  gi|488600443|ref|YP_007906914.1| 34 MKDLLKQLERSYEDKITY 51
                                      799*********999987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.024
                                       HHHHHHHHT--EEE-TTS CS
                           DUF4974  13 lkkLerwYnveivienee 30 
                                       +++Le  Y+ +i++++ e
  gi|488600443|ref|YP_007906914.1| 174 IDTLELCYDLTITYQD-E 190
                                       789************5.4 PP

>> zf-Tim10_DDP  Tim10/DDP family zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.2    0.0008       1.6      17      47 ..     249     279 ..     234     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0008
                      zf-Tim10_DDP  17 nkltekCfkkCi..gkypgssLdsseesCldnC 47 
                                       ++++++C +kCi  +    ++L+   ++C++ C
  gi|488600443|ref|YP_007906914.1| 249 TQVVDNCPTKCIeyD-EEKKELKIDNSNCVR-C 279
                                       789*********632.388999999999993.3 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         9   1.8e+04      56      62 ..      75      81 ..      73      82 .. 0.80
   2 ?    2.4   1.4      0.13   2.6e+02      54      65 ..     250     261 ..     211     262 .. 0.76
   3 ?    7.6   0.0    0.0031       6.2       2      33 ..     270     301 ..     269     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 9
                           Fer4_15 56 araCPvd 62
                                      a++CP+ 
  gi|488600443|ref|YP_007906914.1| 75 AKECPGV 81
                                      799*985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                           Fer4_15  54 eAaraCPvdAIr 65 
                                       + +++CP+++I+
  gi|488600443|ref|YP_007906914.1| 250 QVVDNCPTKCIE 261
                                       55799******7 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0031
                           Fer4_15   2 vvDrdaCigcglCvaeapevfeldedglasvl 33 
                                       ++D ++C  c  C+ ++p+  +  ++  a++l
  gi|488600443|ref|YP_007906914.1| 270 KIDNSNCVRCMHCINVLPKALKPGDERGAVIL 301
                                       69****************99987776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); 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):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2563.87
//
Query:       gi|488600444|ref|YP_007906915.1|  [L=245]
Description: uroporphyrinogen-III C-methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-53  179.8   0.0    8.7e-53  179.4   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.4   0.0   4.8e-57   8.7e-53       2     212 ..       7     213 ..       7     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 179.4 bits;  conditional E-value: 4.8e-57
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel.eleapmgkekepleeayeeiaealaealr 77 
                                       +ylVG+GpGdpellT++Al+++k+adv+l+d+ ++ + + ++l+    e+++  + + e  ++++eei+  ++ +++
  gi|488600444|ref|YP_007906915.1|   7 VYLVGAGPGDPELLTIKALNIIKSADVILYDK-LVGDDIVKFLKAMGkEIVYAGKSSHEKGGARQEEINNLMKHYAK 82 
                                       7****************************999.8777666777664444444444444555555************* PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                        gk Vv+l++GDP+v+g+g  ++e+l++  +gi++e+iPGvss++a+++ +giplt+ + ++svl   +++++  ++
  gi|488600444|ref|YP_007906915.1|  83 MGKIVVRLKGGDPFVFGRGCIEAEFLKK--EGIDFEIIPGVSSINAVPTNAGIPLTHPEISSSVL-VVTGRDNVLRW 156
                                       ****************************..9**********************************.77778899999 PP

                      TP_methylase 155 eallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       +++l+   t+v+l++ ++++++++ L+e  ++++tpvav+e++++e ++++ g+l+++
  gi|488600444|ref|YP_007906915.1| 157 KNALD-HSTIVILMGKDRIEQICKKLIELGKNPETPVAVIENGTLESQKTIFGSLSTI 213
                                       99999.55888888999************888899****************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 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:                        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 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1579.32
//
Query:       gi|488600445|ref|YP_007906916.1|  [L=627]
Description: threonyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  174.5   0.3    2.5e-51  173.3   0.3    1.7  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    1.3e-21   76.5   2.3    5.2e-21   74.6   2.3    2.1  1  HGTP_anticodon  Anticodon binding domain
    5.4e-20   72.1   0.4    1.3e-19   70.8   0.4    1.7  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.3   0.3   4.3e-55   2.5e-51       1     137 []       1     135 [.       1     135 [. 0.98

  Alignments for each domain:
  == domain 1  score: 173.3 bits;  conditional E-value: 4.3e-55
                                       -EEEEEEEEEEEEEEEEESSSS-...SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEE CS
                       tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae..eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvv 75 
                                       m+lLlihad +eye kk++ ++ae  +e+ek+ +lee+lv F++vEk+D+e   +vv+kav +i +va+kvka++++
  gi|488600445|ref|YP_007906916.1|   1 MKLLLIHADFMEYELKKET-PVAEkiDEDEKRRKLEEVLVSFTSVEKGDNE---EVVKKAVGNIIDVANKVKAERIL 73 
                                       9*****************9.99998999999********************...9********************** PP

                                       EEE-STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                       tRNA-Thr_ED  76 lypyaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                       +ypyaHLss+la++++ +eilkk+ee ++++g+ev+raPFGwyk+f+isckGhpL+elsre+
  gi|488600445|ref|YP_007906916.1|  74 VYPYAHLSSNLADAKTGVEILKKMEEVIRDSGFEVYRAPFGWYKAFNISCKGHPLSELSREV 135
                                       ************************************************************86 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   2.3   8.6e-25   5.2e-21       1      93 [.     510     604 ..     510     605 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 8.6e-25
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET... CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr... 74 
                                       q  +ip++e   +++++akk+a e+++ g+rv++dd++e++gkkir+a + ++p++ v+Geke+++g++tv  r   
  gi|488600445|ref|YP_007906916.1| 510 QLRIIPVSE---RFLDEAKKIALEIKEMGVRVDVDDRDETLGKKIRDAGRDWVPYVAVIGEKEIRDGKLTVTIRaes 583
                                       678******...**************************************************************875 PP

                                       ..TTCEE..EEEETTHHHHHHHH CS
                    HGTP_anticodon  75 ..dtreq..ervsldelveklke 93 
                                         +  eq  +++s +elv+ +k+
  gi|488600445|ref|YP_007906916.1| 584 smK--EQkrVSMSKEELVQRIKA 604
                                       433..333379999999999986 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 !   70.8   0.4   2.2e-23   1.3e-19       7     178 ..     285     489 ..     280     490 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2.2e-23
                                       TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                      tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.easlddsl 80 
                                       ++re+ L+  ++ +   +  d v+  k+LPlk+y++++  +R+E++ ++ GL R+r F++ d + +    +s+++++
  gi|488600445|ref|YP_007906916.1| 285 DKREFFLRFAACFGQFLIKHDAVITYKNLPLKMYELTRYsFRKEQRgELVGLRRLRAFTMPDMHTITRdMESAKQEF 361
                                       479*******************9999*********99855******8999******************88******* PP

                                       HHHHHHHHHHHHHTT.SCEEEEEEGTTSC..............................BTTSEEEEEEEEETTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............................xxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  81 rdlikaisriferlglefraiielmsaks..............................adykdkkefeavsesltk 127
                                        +  k+  ++++ +gle    +   + ++                              +    k ef+ v++ l+k
  gi|488600445|ref|YP_007906916.1| 362 LNQYKLSIEVLRGIGLEPDDYETAVRVTKdfyeenkefihslvdiikkpiliemwdrrfFYFVLKFEFNFVDC-LDK 437
                                       ****************984444443333311122334555555555555555555555322234555555555.*** PP

                                       EEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                      tRNA-synt_2b 128 gieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                       +  ++t+q +  + ++r g+t++de++++k++ +++ +  g veR + aile+
  gi|488600445|ref|YP_007906916.1| 438 ASALSTVQID-VENAKRYGITFVDEDGEKKHPLILHCSlSGaVERCMYAILEK 489
                                       **********.999************************6669*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3873.09
//
Query:       gi|488600446|ref|YP_007906917.1|  [L=119]
Description: hypothetical protein Asulf_00919 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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 0.32s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 752.83
//
Query:       gi|488600447|ref|YP_007906918.1|  [L=588]
Description: putative ATPase, RNase L inhibitor (RLI)-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  142.2   0.0    1.4e-20   74.2   0.0    2.5  2  ABC_tran      ABC transporter
    2.5e-17   63.6   7.9     0.0014   18.5   0.1    4.3  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.4e-14   52.2   4.4      1e-05   25.1   0.0    4.3  4  SMC_N         RecF/RecN/SMC N terminal domain
    3.6e-13   49.1   2.8    9.7e-13   47.7   2.8    1.8  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    5.8e-09   35.6  13.1    1.2e-05   25.1   2.8    2.4  2  Fer4_6        4Fe-4S binding domain
    3.8e-08   32.8   3.6    3.8e-08   32.8   3.6    2.9  3  Fer4          4Fe-4S binding domain
    2.2e-06   27.6   0.4      0.044   13.5   0.1    3.3  3  AAA_15        AAA ATPase domain
    7.7e-06   25.9   0.1       0.18   11.7   0.0    2.8  2  Rad17         Rad17 P-loop domain
    4.6e-05   23.8   0.0      0.018   15.4   0.0    2.5  2  AAA           ATPase family associated with various cellular 
    0.00013   22.1  10.6    0.00053   20.1   0.8    2.4  2  Fer4_10       4Fe-4S dicluster domain
    0.00033   21.2   0.6       0.66   10.5   0.0    3.1  2  AAA_18        AAA domain
    0.00039   21.0   3.6       0.22   12.0   0.0    2.8  2  AAA_23        AAA domain
    0.00051   19.7   0.6        1.1    9.1   0.1    2.3  2  AAA_29        P-loop containing region of AAA domain
    0.00061   20.1   1.0       0.16   12.2   0.0    2.7  2  AAA_22        AAA domain
    0.00063   19.9  10.3     0.0012   19.0  10.3    1.4  1  Fer4_9        4Fe-4S dicluster domain
    0.00065   19.6  11.6    0.00075   19.5   1.5    2.4  2  Fer4_2        4Fe-4S binding domain
    0.00076   19.6  10.3     0.0013   18.8  10.3    1.4  1  Fer4_21       4Fe-4S dicluster domain
    0.00089   19.7   0.1       0.85   10.0   0.0    2.6  2  AAA_16        AAA ATPase domain
    0.00096   19.5   0.0        1.9    8.9   0.0    2.8  2  RNA_helicase  RNA helicase
     0.0018   18.1   0.7       0.85    9.3   0.1    2.7  2  AAA_30        AAA domain
     0.0026   18.3   1.5     0.0026   18.3   1.5    2.3  3  Fer4_7        4Fe-4S dicluster domain
     0.0027   17.9   1.4       0.76    9.9   0.1    2.6  2  AAA_33        AAA domain
       0.01   16.1   0.1         14    6.0   0.0    3.4  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.012   15.8   0.2        2.1    8.5   0.0    2.8  2  AAA_28        AAA domain
      0.014   15.1   1.6        3.1    7.5   0.3    2.7  3  AAA_24        AAA domain
      0.021   14.9   0.1      0.049   13.7   0.1    1.5  1  RNR_N         Ribonucleotide reductase N-terminal
      0.029   14.5   0.2        1.2    9.3   0.0    2.8  2  MMR_HSR1      50S ribosome-binding GTPase
      0.033   14.2   1.2          8    6.5   0.0    3.3  3  AAA_14        AAA domain
      0.041   13.6   0.0        4.2    7.1   0.0    2.3  2  VirE          Virulence-associated protein E
      0.052   12.5   0.2       0.13   11.2   0.0    1.7  2  Spore_IV_A    Stage IV sporulation protein A (spore_IV_A)
      0.056   14.4   2.3      0.056   14.4   2.3    2.5  2  Fer4_16       4Fe-4S double cluster binding domain
       0.06   13.3   1.2        5.4    7.0   0.3    3.0  3  AAA_5         AAA domain (dynein-related subfamily)
       0.06   13.2   0.0         16    5.4   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
      0.087   12.3   0.2        5.1    6.6   0.0    2.3  2  AAA_7         P-loop containing dynein motor region
       0.14   11.6   0.0        3.9    6.8   0.0    2.4  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.14   11.7   0.6        2.8    7.5   0.2    2.4  2  SRP54         SRP54-type protein, GTPase domain
       0.16   11.7   0.1         11    5.7   0.0    3.3  3  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
       0.18   10.8   1.0         11    4.9   0.1    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.59   10.0   3.5         31    4.4   0.3    3.4  3  NTPase_1      NTPase
        2.3    8.7   8.9       0.87   10.1   2.0    2.4  2  Fer4_8        4Fe-4S dicluster domain
        3.4    8.4  14.9       0.25   11.9   3.4    2.3  2  Fer4_4        4Fe-4S binding domain
        6.5    7.9  16.2       0.84   10.7   5.1    2.4  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   1.5e-20   6.4e-18      10     137 .]      97     237 ..      94     237 .. 0.71
   2 !   74.2   0.0   3.4e-23   1.4e-20       7     137 .]     357     480 ..     351     480 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.5e-20
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..........B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..........qeleslrkeigvlpqepqlfpeltv 76 
                                       +g++v+++G+nG+GK+t +k+l+g+ kp+ G+ + d +++ e           +  +   + +v pq  +  p++  
  gi|488600447|ref|YP_007906918.1|  97 KGHVVGLLGPNGTGKTTAVKILSGQIKPNLGKDEADWEEIFErfagtelldyLKSLVDGIRTSVKPQYIEAIPRVY- 172
                                       799*****************************96665555555655555533222333334444455555555553. PP

                                       HHH.......HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx.......xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.......esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                         +        + +e   i+++++kl+lk+  ++ v    ++LSgG+ qr+a+a++ll+++++++lDE t+
  gi|488600447|ref|YP_007906918.1| 173 --KgkakdllSKADEigkIDEMVEKLSLKNSIERDV----RHLSGGELQRLAIAACLLRDADFYFLDEVTS 237
                                       ..0345778744444344777777777777666666....****************************985 PP

  == domain 2  score: 74.2 bits;  conditional E-value: 3.4e-23
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.... 79 
                                       ++k++e+++ivG+n +GKSt++k+lag l+++eG+i           ++  + + ++ pq  +  +++tv++     
  gi|488600447|ref|YP_007906918.1| 357 EIKQSEVLGIVGPNATGKSTFVKILAGVLEDDEGKI-----------ERDEELKTSYKPQYIKTESDMTVASFltki 422
                                       799*********************************...........445566667777777777777777766666 PP

                                       ....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                           + +   +++l+ l+++el d+++    + LSgG+ qrva++++ll++++l+llDEp+a
  gi|488600447|ref|YP_007906918.1| 423 npmvNTSYYKTEFLKPLRIEELMDRNL----KDLSGGELQRVAIVACLLRDADLYLLDEPSA 480
                                       666677777899***************....*****************************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 !   13.2   0.7   0.00013     0.058       2      21 ..     101     120 ..     100     142 .. 0.81
   2 !   18.5   0.1   3.4e-06    0.0014     142     287 ..     131     256 ..     121     271 .. 0.71
   3 !   17.1   0.0   8.7e-06    0.0037       3      24 ..     365     386 ..     363     427 .. 0.78
   4 !   17.4   0.0   7.3e-06    0.0031     233     303 .]     448     516 ..     407     516 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                            AAA_21   2 nvliGpNgsGKSnLLdaldl 21 
                                        +l GpNg+GK++  ++l++
  gi|488600447|ref|YP_007906918.1| 101 VGLLGPNGTGKTTAVKILSG 120
                                       689***************76 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.4e-06
                            AAA_21 142 kaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlre 218
                                       +++ +i++r++ ++ll+      +   l + +++  ++  ++ + r +++  ++ +   d+  ++++          
  gi|488600447|ref|YP_007906918.1| 131 ADWEEIFERFAGTELLD------YLKSLVDGIRTSVKPQYIEAIPRVYKGKAKDLLSKADEIGKIDE---------- 191
                                       56666666666666666......55555555555555555555555555555555555555433333.......... PP

                            AAA_21 219 rgvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                         v  l  ++  e+++r+lS G ++ la+++ llr++   +++++DE+ + L+     +++++++e+++
  gi|488600447|ref|YP_007906918.1| 192 -MVEKLSLKNSIERDVRHLSGGELQRLAIAACLLRDA---DFYFLDEVTSYLDIYQRISVAKVIREKAE 256
                                       .56666678889999***********89999999888...9*************999999999977665 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 8.7e-06
                            AAA_21   3 vliGpNgsGKSnLLdaldllar 24 
                                       +++GpN++GKS++ ++l ++  
  gi|488600447|ref|YP_007906918.1| 365 GIVGPNATGKSTFVKILAGVLE 386
                                       79***************88753 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 7.3e-06
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkll...rrllellkelsrngaQviltTHSpllld 303
                                       ++ +lS G ++  a+++ llr++   +l+l+DEp ++L+ +     +r+++ + ++++    ++++ H+ +l+d
  gi|488600447|ref|YP_007906918.1| 448 NLKDLSGGELQRVAIVACLLRDA---DLYLLDEPSAHLDVEQRtetARIIRRFALNTK--KSIFVVDHDIYLID 516
                                       5667899999999********99...9*************666555888888888888..78888877777775 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     0.087        37      23      40 ..      97     114 ..      85     130 .. 0.83
   2 !   25.1   0.0   2.4e-08     1e-05     135     201 ..     207     269 ..     147     283 .. 0.81
   3 ?    6.3   0.0     0.013       5.7      25      57 ..     362     394 ..     352     401 .. 0.79
   4 !   15.3   0.1   2.4e-05      0.01     135     197 ..     450     510 ..     405     530 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.087
                                       TSSEEEEEESTTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnl 40 
                                       + ++  ++GpNG GK+  
  gi|488600447|ref|YP_007906918.1|  97 KGHVVGLLGPNGTGKTTA 114
                                       55677899*******975 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.4e-08
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreem 201
                                         LSgGe + +a+a        + a +y+lDe+ + LD  ++  va++++ek ++  ++++ ++  +
  gi|488600447|ref|YP_007906918.1| 207 RHLSGGELQRLAIAAC----LLRDADFYFLDEVTSYLDIYQRISVAKVIREKAEEKPVLIVEHDLAI 269
                                       47*****886666544....68999*******************************99999887655 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.013
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklr 57 
                                       ++  ivGpN  GKs ++  +  vL +++ k  r
  gi|488600447|ref|YP_007906918.1| 362 EVLGIVGPNATGKSTFVKILAGVLEDDEGKIER 394
                                       5678************99998888877765545 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 2.4e-05
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivisl 197
                                       + LSgGe + va  ++ A    + a lyllDe  a+LD +++++ a++++  + +++  ++v+ +
  gi|488600447|ref|YP_007906918.1| 450 KDLSGGELQRVA--IV-AC-LLRDADLYLLDEPSAHLDVEQRTETARIIRrfALNTKKSIFVVDH 510
                                       479***966544..44.22.368899***********************9333344455666555 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 !   47.7   2.8   2.3e-15   9.7e-13       2      34 ..       5      34 ..       4      35 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.3e-15
                                      -EEEES---------TTHHHHHTTSEEEESS-- CS
                               RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlvrtgk 34
                                      r+A+vd+d+C+P KC+  +c+++cpv  vr+g 
  gi|488600447|ref|YP_007906918.1|  5 RIAVVDRDRCKPQKCSR-ECEKYCPV--VRSGA 34
                                      9****************.********..***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 !   15.8   2.7   2.6e-05     0.011       1      21 [.       6      29 ..       6      36 .. 0.86
   2 !   25.1   2.8   2.8e-08   1.2e-05       1      24 []      42      65 ..      42      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-05
                            Fer4_6  1 vveidpdkCi..gC.gdCvrvCPe 21
                                      ++++d+d+C    C ++C++ CP 
  gi|488600447|ref|YP_007906918.1|  6 IAVVDRDRCKpqKCsRECEKYCPV 29
                                      689******9888*888******5 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.8e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +++i +++C+gCg Cv+ CP++ai
  gi|488600447|ref|YP_007906918.1| 42 KAVISEELCVGCGICVKKCPFKAI 65
                                      689******************998 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1         4   1.7e+03       2       8 ..       8      14 ..       7      15 .. 0.87
   2 ?    2.2   0.8      0.43   1.8e+02      13      20 ..      22      29 ..      21      30 .. 0.89
   3 !   32.8   3.6   8.8e-11   3.8e-08       2      24 .]      44      66 ..      43      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4
                                      EEETTTS CS
                              Fer4  2 videekC 8 
                                      v+d ++C
  gi|488600447|ref|YP_007906918.1|  8 VVDRDRC 14
                                      89***** PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.43
                                      HHHHHSTT CS
                              Fer4 13 aCvevCPv 20
                                      +C++ CPv
  gi|488600447|ref|YP_007906918.1| 22 ECEKYCPV 29
                                      6******8 PP

  == domain 3  score: 32.8 bits;  conditional E-value: 8.8e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      vi ee+C+gCG+Cv+ CP+ AI+
  gi|488600447|ref|YP_007906918.1| 44 VISEELCVGCGICVKKCPFKAIS 66
                                      89*******************96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.023       9.7      28      44 ..     103     119 ..      92     207 .. 0.80
   2 !   13.5   0.1    0.0001     0.044      22      55 ..     361     404 ..     356     444 .. 0.67
   3 ?    4.4   0.0     0.059        25     324     368 ..     470     514 ..     466     515 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.023
                            AAA_15  28 liGkNnsGKSsileald 44 
                                       l G+N++GK++++++l 
  gi|488600447|ref|YP_007906918.1| 103 LLGPNGTGKTTAVKILS 119
                                       77************995 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0001
                            AAA_15  22 seeltvliGkNnsGKSsilealdlFlnnkekkn...........k 55 
                                       se +  ++G+N++GKS+++++l   l+ +e k             
  gi|488600447|ref|YP_007906918.1| 361 SE-VLGIVGPNATGKSTFVKILAGVLEDDEGKIerdeelktsykP 404
                                       44.7889***************98888663333444444444440 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.059
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                        +++l++EP ahL  ++ ++ ++ +++ a ++k+ +++  H  ++
  gi|488600447|ref|YP_007906918.1| 470 ADLYLLDEPSAHLDVEQRTETARIIRRFALNTKKSIFVVDHDIYL 514
                                       689******************************999998887666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00041      0.18      46      71 ..      99     124 ..      89     133 .. 0.80
   2 !   11.0   0.0   0.00071       0.3      41     102 ..     357     418 ..     347     444 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00041
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgi 71 
                                       +++ + GP G gk+t+vk+Ls +  +
  gi|488600447|ref|YP_007906918.1|  99 HVVGLLGPNGTGKTTAVKILSGQIKP 124
                                       466688**************987655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00071
                             Rad17  41 esrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrf 102
                                       e ++ ++L i GP   gkst vk+L+  l  +  +     +lk +   q   + +++ + s f
  gi|488600447|ref|YP_007906918.1| 357 EIKQSEVLGIVGPNATGKSTFVKILAGVLEDDEGKIERDEELKTSYKpQYIKTESDMTVAS-F 418
                                       5566679*******************98876655555555554433345555555555555.5 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.3e-05     0.018       3      41 ..     103     151 ..     101     194 .. 0.76
   2 ?    5.9   0.0     0.038        16       3      22 ..     366     385 ..     364     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.3e-05
                                       EESSTTSSHHHHHHHHHHHHTHE...........EEEEETTTCSSSSTTH CS
                               AAA   3 lyGppGtGKTllakavakelgve...........fleisgsellskyvge 41 
                                       l Gp GtGKT+++k +  +++ +           f ++ g+ell +y++ 
  gi|488600447|ref|YP_007906918.1| 103 LLGPNGTGKTTAVKILSGQIKPNlgkdeadweeiFERFAGTELL-DYLKS 151
                                       89*****************9755444455566667777777777.55554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.038
                                       EESSTTSSHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel 22 
                                       ++Gp  tGK++++k +a  l
  gi|488600447|ref|YP_007906918.1| 366 IVGPNATGKSTFVKILAGVL 385
                                       68**************9876 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3  13.0   7.8e-05     0.033       2      56 .]       7      61 ..       6      61 .. 0.75
   2 !   20.1   0.8   1.2e-06   0.00053       2      27 ..      43      69 ..      42      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-05
                           Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      +v+d+d+C   +C  +C k CP+    v+  +ea  +e + +   e C gcg Cv++CP
  gi|488600447|ref|YP_007906918.1|  7 AVVDRDRCkpQKCSrECEKYCPV----VRSGAEAVVIEDKAViSEELCVGCGICVKKCP 61
                                      68899***66599889*******....55555554444444426678***********9 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.2e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl.tsvg 27
                                      +vi ++ C++Cg Cvk CP+++ + vg
  gi|488600447|ref|YP_007906918.1| 43 AVISEELCVGCGICVKKCPFKAiSIVG 69
                                      78999***************7753333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0015      0.66       1      21 [.     101     121 ..     101     201 .. 0.75
   2 ?    7.7   0.2     0.012         5       3      44 ..     366     405 ..     364     571 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0015
                            AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                       ++l G+ G+GKtt  k Ls  
  gi|488600447|ref|YP_007906918.1| 101 VGLLGPNGTGKTTAVKILSGQ 121
                                       6899**************765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.012
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       + G+ ++GK+t+ k L+  l   +  +++ ++++l +++ p+
  gi|488600447|ref|YP_007906918.1| 366 IVGPNATGKSTFVKILAGVL--EDDEGKIERDEELKTSYKPQ 405
                                       89**************7766..77777777777777777666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.3    0.0045       1.9      21      36 ..     100     115 ..      83     120 .. 0.84
   2 !   12.0   0.0   0.00051      0.22      21      55 ..     363     399 ..     342     454 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0045
                            AAA_23  21 ltlItGpNGaGKTTil 36 
                                       ++ + GpNG+GKTT +
  gi|488600447|ref|YP_007906918.1| 100 VVGLLGPNGTGKTTAV 115
                                       67789*********86 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00051
                            AAA_23  21 ltlItGpNGaGKTTildAiklaLygetprlsrks..g 55 
                                       +  I+GpN +GK+T++  +  +L  + ++ +r++  +
  gi|488600447|ref|YP_007906918.1| 363 VLGIVGPNATGKSTFVKILAGVLEDDEGKIERDEelK 399
                                       567**************99999988777776665443 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0036       1.5      17      39 ..      92     115 ..      85     119 .. 0.86
   2 !    9.1   0.1    0.0025       1.1      19      39 ..     358     378 ..     345     386 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0036
                            AAA_29  17 ieidlkg.atlltGpsGsGKSTll 39 
                                       ++i +kg ++ l Gp+G+GK+T +
  gi|488600447|ref|YP_007906918.1|  92 LPIPRKGhVVGLLGPNGTGKTTAV 115
                                       67888898999***********75 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0025
                            AAA_29  19 idlkgatlltGpsGsGKSTll 39 
                                       i+++++  ++Gp+ +GKST++
  gi|488600447|ref|YP_007906918.1| 358 IKQSEVLGIVGPNATGKSTFV 378
                                       56666778***********98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.048        20      10      25 ..     103     118 ..      96     127 .. 0.83
   2 !   12.2   0.0   0.00037      0.16       7      90 ..     363     456 ..     357     508 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.048
                            AAA_22  10 vtGesGtGKTtllrrl 25 
                                       + G+ GtGKTt ++ l
  gi|488600447|ref|YP_007906918.1| 103 LLGPNGTGKTTAVKIL 118
                                       67*********99876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00037
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee....erpevv......fvtlpsstsskdllrellralglelka... 70 
                                       +l ++G+  tGK+t ++ l+  l+ ++   e                +++  s+++ +++l+++   ++ +  +   
  gi|488600447|ref|YP_007906918.1| 363 VLGIVGPNATGKSTFVKILAGVLEDDEGKIErdeeL----KtsykpqYIKTESDMTVASFLTKINPMVNTSYYKtef 435
                                       6679***************99997776666656432....233568899********************99999999 PP

                            AAA_22  71 .erlsseell.ealeqalrara 90 
                                        ++l+ eel+ + l + +    
  gi|488600447|ref|YP_007906918.1| 436 lKPLRIEELMdRNLKDLS-GGE 456
                                       999999999944444444.333 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0  10.3   2.8e-06    0.0012       4      51 .]      18      65 ..      13      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.8e-06
                            Fer4_9  4 gCga.CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C + C++ Cp      +a+  +++  + + e C+gCg Cv++Cp +ai
  gi|488600447|ref|YP_007906918.1| 18 KCSReCEKYCPVVRSGAEAVVIEDKAVISE-ELCVGCGICVKKCPFKAI 65
                                      465337777777777777777777766655.59************9887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.0     0.069        30       3      21 ..       7      28 ..       5      29 .. 0.83
   2 !   19.5   1.5   1.8e-06   0.00075       3      21 ..      43      61 ..      41      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.069
                            Fer4_2  3 vvvdtdrCi.g.Cg.aCvsaCP 21
                                      +vvd+drC  + C+  C + CP
  gi|488600447|ref|YP_007906918.1|  7 AVVDRDRCKpQkCSrECEKYCP 28
                                      789*****7678*55******* PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.8e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +v+ ++ C+gCg+Cv+ CP
  gi|488600447|ref|YP_007906918.1| 43 AVISEELCVGCGICVKKCP 61
                                      67889************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8  10.3     3e-06    0.0013       1      57 [.       7      65 ..       7      67 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3e-06
                           Fer4_21  1 AridedkCi..gCgk.CliaCed..tshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      A++d+d+C   +C + C + C+   ++ +a+ i++k+v  + e+ CvGC +C++ CP  ++i
  gi|488600447|ref|YP_007906918.1|  7 AVVDRDRCKpqKCSReCEKYCPVvrSGAEAVVIEDKAV--ISEELCVGCGICVKKCPF-KAI 65
                                      78999999422554336666664225666666665554..789**************7.776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     0.002      0.85      25      63 ..      99     133 ..      89     258 .. 0.62
   2 ?    7.2   0.0     0.014         6      24      69 ..     361     402 ..     350     553 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.002
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       ++v l G+ G+GK++ v+ l  +++ +    l  +  + 
  gi|488600447|ref|YP_007906918.1|  99 HVVGLLGPNGTGKTTAVKILSGQIKPN----LGKDEADW 133
                                       67889************9999999988....33333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdql.esaipy 69 
                                       +e++ ++G+ ++GKs+ v+ l+  le+d     +gk ++  e +++y
  gi|488600447|ref|YP_007906918.1| 361 SEVLGIVGPNATGKSTFVKILAGVLEDD-----EGKIERDeELKTSY 402
                                       378889************9999777777.....55555552222333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0045       1.9       3      32 ..     103     132 ..     101     148 .. 0.82
   2 ?    7.7   0.0      0.01       4.4       3      28 ..     366     391 ..     364     435 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0045
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkd 32 
                                       l Gp+g+GK+t++k L+ ++  +l+++++d
  gi|488600447|ref|YP_007906918.1| 103 LLGPNGTGKTTAVKILSGQIKPNLGKDEAD 132
                                       68*************999998777555544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.01
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkklkl 28 
                                       ++Gp+ +GKSt++k La  l+++ ++
  gi|488600447|ref|YP_007906918.1| 366 IVGPNATGKSTFVKILAGVLEDDEGK 391
                                       78*************99988865533 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1     0.002      0.85      19      40 ..      99     120 ..      94     129 .. 0.81
   2 ?    6.5   0.0     0.014         6      19      49 ..     362     392 ..     352     511 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                            AAA_30  19 rvavltGpAGtGKttalkalre 40 
                                        v+ l Gp GtGKtta+k l  
  gi|488600447|ref|YP_007906918.1|  99 HVVGLLGPNGTGKTTAVKILSG 120
                                       488899***********98865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrv 49 
                                        v  ++Gp  tGK+t +k l+ ++e+++g++
  gi|488600447|ref|YP_007906918.1| 362 EVLGIVGPNATGKSTFVKILAGVLEDDEGKI 392
                                       38899*******************9996554 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   3.1      0.42   1.8e+02      31      50 ..       7      29 ..       2      34 .. 0.79
   2 !   11.7  13.7   0.00071       0.3       4      52 .]      18      64 ..      13      64 .. 0.74
   3 !   18.3   1.5     6e-06    0.0026       2      21 ..      50      69 ..      49      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.42
                            Fer4_7 31 veidpekC..lgCga.CvavCPt 50
                                      +++d ++C  + C + C++ CP+
  gi|488600447|ref|YP_007906918.1|  7 AVVDRDRCkpQKCSReCEKYCPV 29
                                      5678899966689888*****97 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00071
                            Fer4_7  4 gC.gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C + C+++Cpv     + + +    +k++i++e C+gCg Cv+ CP++a
  gi|488600447|ref|YP_007906918.1| 18 KCsRECEKYCPVVRSGAEAV-VI--EDKAVISEELCVGCGICVKKCPFKA 64
                                      56348999999544444333.33..3689******************986 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 6e-06
                            Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                      C+gCg Cv+ Cp kai++  
  gi|488600447|ref|YP_007906918.1| 50 CVGCGICVKKCPFKAISIVG 69
                                      ****************9864 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.022       9.4       1      19 [.     100     118 ..     100     128 .. 0.84
   2 !    9.9   0.1    0.0018      0.76       4      35 ..     366     399 ..     363     513 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.022
                            AAA_33   1 lvllvGlpGsGKstlaerl 19 
                                       +v l G++G+GK+t ++ l
  gi|488600447|ref|YP_007906918.1| 100 VVGLLGPNGTGKTTAVKIL 118
                                       56688*********99855 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0018
                            AAA_33   4 lvGlpGsGKstlaerllkklg..avl.lssdtlrr 35 
                                       +vG++++GKst+++ l+  l       ++ d++++
  gi|488600447|ref|YP_007906918.1| 366 IVGPNATGKSTFVKILAGVLEddE-GkIERDEELK 399
                                       79************9987776532.2255555544 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 ?    5.3   0.0     0.053        22      25      47 ..     201     223 ..     190     252 .. 0.84
   2 ?    6.0   0.0     0.032        14      26      48 ..     445     467 ..     429     496 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.053
                           SbcCD_C  25 elsrssgtlSGGekqflaylala 47 
                                       +++r+++ lSGGe q la  a +
  gi|488600447|ref|YP_007906918.1| 201 SIERDVRHLSGGELQRLAIAACL 223
                                       47899*********998876654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.032
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaa 48 
                                       ++r+ + lSGGe q +a +a ++
  gi|488600447|ref|YP_007906918.1| 445 MDRNLKDLSGGELQRVAIVACLL 467
                                       7899999*****99998888763 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0     0.005       2.1       4      21 ..     103     120 ..     100     145 .. 0.83
   2 ?    4.2   0.0      0.11        45       4      20 ..     366     382 ..     364     412 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.005
                            AAA_28   4 itGgestGKTtlleaLaa 21 
                                       ++G+ +tGKTt ++ L+ 
  gi|488600447|ref|YP_007906918.1| 103 LLGPNGTGKTTAVKILSG 120
                                       89************9984 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       i+G+  tGK+t ++ La
  gi|488600447|ref|YP_007906918.1| 366 IVGPNATGKSTFVKILA 382
                                       89************999 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3    0.0073       3.1       4      22 ..     100     118 ..      97     128 .. 0.83
   2 ?   -2.3   0.0       7.2   3.1e+03     144     174 ..     163     193 ..     156     240 .. 0.74
   3 ?    5.8   0.0     0.023       9.7       5      22 ..     364     381 ..     360     424 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0073
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        + + Gp+g+GKTt +k l
  gi|488600447|ref|YP_007906918.1| 100 VVGLLGPNGTGKTTAVKIL 118
                                       6789**********99877 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.2
                            AAA_24 144 kytrlepklgkktanelkeevDlvlranlkr 174
                                       +y   +p + k+ a+ l +++D+++ ++   
  gi|488600447|ref|YP_007906918.1| 163 QYIEAIPRVYKGKAKDLLSKADEIGKIDEMV 193
                                       5666677777888888888888888887543 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.023
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       + i+Gp+ +GK+t++k l
  gi|488600447|ref|YP_007906918.1| 364 LGIVGPNATGKSTFVKIL 381
                                       679************987 PP

>> RNR_N  Ribonucleotide reductase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00011     0.049      14      69 ..     387     443 ..     382     449 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                             RNR_N  14 dgkiqlekDkeAleaYlkehvnpnt.vkfesleekldyLvendYyeeevlekYskef 69 
                                       d++ ++e D+e  ++Y  ++++ ++ ++++s+  k++ +v++ Yy++e+l+  + e+
  gi|488600447|ref|YP_007906918.1| 387 DDEGKIERDEELKTSYKPQYIKTESdMTVASFLTKINPMVNTSYYKTEFLKPLRIEE 443
                                       56667899*************9764399*********************98766655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.45   1.9e+02       2      22 ..     101     121 ..     100     133 .. 0.85
   2 ?    9.3   0.0    0.0027       1.2       3      55 ..     365     479 ..     363     532 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.45
                                       EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                       v+++G   +GK+t ++ l+g+
  gi|488600447|ref|YP_007906918.1| 101 VGLLGPNGTGKTTAVKILSGQ 121
                                       899************999987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0027
                                       EEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEEEEETTEE.......................... CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegrvklkgke.......................... 47 
                                       +ivG   +GKSt+++ l g     e k +  ++  t  ++++++ + +                             
  gi|488600447|ref|YP_007906918.1| 365 GIVGPNATGKSTFVKILAGvleddEgKIERDEELKTSYKPQYIKTESD-MTvasfltkinpmvntsyykteflkplr 440
                                       89***************9866654235566666677777777777622.1123333444444444455555555555 PP

                                       ...............................EEEEECGG CS
                          MMR_HSR1  48 ...............................ielvDtpG 55 
                                                                      ++l+D p 
  gi|488600447|ref|YP_007906918.1| 441 ieelmdrnlkdlsggelqrvaivacllrdadLYLLDEPS 479
                                       555555444445555555555555555554455555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.086        37       3      22 ..      99     118 ..      97     207 .. 0.83
   2 ?    0.2   0.0       1.7   7.3e+02      64      81 ..     226     243 ..     152     261 .. 0.75
   3 ?    6.5   0.0     0.019         8       2      27 ..     361     386 ..     360     431 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.086
                            AAA_14   3 kilvitGaRrvGKTtllkql 22 
                                       +++ + G+  +GKTt +k l
  gi|488600447|ref|YP_007906918.1|  99 HVVGLLGPNGTGKTTAVKIL 118
                                       78999**********99766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.7
                            AAA_14  64 kktylflDEiqevpewek 81 
                                       +  + flDE+  + ++++
  gi|488600447|ref|YP_007906918.1| 226 DADFYFLDEVTSYLDIYQ 243
                                       567899999998866665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.019
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell 27 
                                       +++l i+G+  +GK+t++k l+  l 
  gi|488600447|ref|YP_007906918.1| 361 SEVLGIVGPNATGKSTFVKILAGVLE 386
                                       57899*************98875554 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.081        34      52      75 ..      98     121 ..      89     138 .. 0.86
   2 ?    7.1   0.0    0.0098       4.2      48      89 ..     357     398 ..     343     421 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.081
                              VirE  52 DfvlvLvGkqgsgKstfleklgee 75 
                                        +v+ L G+ g+gK+t +++l+++
  gi|488600447|ref|YP_007906918.1|  98 GHVVGLLGPNGTGKTTAVKILSGQ 121
                                       58999****************654 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0098
                              VirE  48 giKfDfvlvLvGkqgsgKstfleklgeewftdslksvedkda 89 
                                        iK  +vl +vG+  +gKstf+++l++    d+ k + d++ 
  gi|488600447|ref|YP_007906918.1| 357 EIKQSEVLGIVGPNATGKSTFVKILAGVLEDDEGKIERDEEL 398
                                       589999*******************87766666555555555 PP

>> Spore_IV_A  Stage IV sporulation protein A (spore_IV_A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.3   1.9e+03      20      36 ..     101     117 ..      98     131 .. 0.82
   2 ?   11.2   0.0    0.0003      0.13      19      38 ..     363     382 ..     352     423 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.3
                        Spore_IV_A  20 igvvGpvRtGKStfikr 36 
                                       +g+ Gp  tGK t +k 
  gi|488600447|ref|YP_007906918.1| 101 VGLLGPNGTGKTTAVKI 117
                                       899**********9984 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0003
                        Spore_IV_A  19 yigvvGpvRtGKStfikrfm 38 
                                        +g+vGp  tGKStf+k + 
  gi|488600447|ref|YP_007906918.1| 363 VLGIVGPNATGKSTFVKILA 382
                                       48**************9654 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 ?   -0.3   2.8       5.1   2.2e+03       4      14 ..      18      29 ..      13      48 .. 0.79
   2 ?   14.4   2.3   0.00013     0.056       2      18 ..      50      66 ..      49      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 5.1
                           Fer4_16  4 tCgk.CaevCPt 14
                                      +C + C + CP+
  gi|488600447|ref|YP_007906918.1| 18 KCSReCEKYCPV 29
                                      677778888886 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00013
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C++Cg C++ CP +ai+
  gi|488600447|ref|YP_007906918.1| 50 CVGCGICVKKCPFKAIS 66
                                      ***************97 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3     0.013       5.4       4      23 ..     103     122 ..     100     128 .. 0.85
   2 ?   -2.3   0.0       9.2   3.9e+03      64      75 ..     225     236 ..     195     248 .. 0.73
   3 ?    3.6   0.0      0.14        60       4      59 ..     366     435 ..     364     490 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                                       EE--SSSSHHHHHHHGGGGB CS
                             AAA_5   4 LvGppGtgKselaerlaaal 23 
                                       L+Gp GtgK++ ++ l+  +
  gi|488600447|ref|YP_007906918.1| 103 LLGPNGTGKTTAVKILSGQI 122
                                       99**********99998655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.2
                                       -G-SEEEEESGG CS
                             AAA_5  64 regeilvlDEve 75 
                                       r ++ ++lDEv+
  gi|488600447|ref|YP_007906918.1| 225 RDADFYFLDEVT 236
                                       378889999997 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.14
                                       EE--SSSSHHHHHHHGGGGB...............S--EEEEE--TT--HHHHH--B--.........--- CS
                             AAA_5   4 LvGppGtgKselaerlaaal...............nreveyvqltrdtteedlkgrreikngttslvdspl 59 
                                       +vGp  tgKs++++ la +l                 + +y+   +d+t + ++ ++++ + +ts+ + ++
  gi|488600447|ref|YP_007906918.1| 366 IVGPNATGKSTFVKILAGVLeddegkierdeelktSYKPQYIKTESDMTVASFLTKINP-MVNTSYYKTEF 435
                                       689999*********99999888877777777776677788888888888888888887.66666655555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.036        16      98     125 ..      97     124 ..      88     135 .. 0.85
   2 ?    5.1   0.0     0.044        19      99     132 ..     360     394 ..     335     415 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.036
                                       TTSEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelel 125
                                       k++++ l+G+ G GK+t ++ l ++ + 
  gi|488600447|ref|YP_007906918.1|  97 KGHVVGLLGPNGTGKTTAVKILSGQIKP 124
                                       568899**************99998765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.044
                                       T.SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpelelktgevse 132
                                       + ++  +vG+   GKSt+++ l++ le   g++ +
  gi|488600447|ref|YP_007906918.1| 360 QsEVLGIVGPNATGKSTFVKILAGVLEDDEGKIER 394
                                       4478889***************9988877777765 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 ?    6.6   0.0     0.012       5.1      32      55 ..      97     120 ..      88     126 .. 0.80
   2 ?    3.3   0.0      0.12        53      34      58 ..     362     386 ..     357     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                             AAA_7  32 nkkpvllvGptGtGKtviikdllk 55 
                                       +++ v l Gp GtGKt+ +k l  
  gi|488600447|ref|YP_007906918.1|  97 KGHVVGLLGPNGTGKTTAVKILSG 120
                                       56677899*********9987655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                         + +vGp  tGK++ +k l   l+
  gi|488600447|ref|YP_007906918.1| 362 EVLGIVGPNATGKSTFVKILAGVLE 386
                                       44558***********997665555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0092       3.9      22      53 ..      98     130 ..      95     139 .. 0.81
   2 ?    1.9   0.0      0.29   1.2e+02      27      49 ..     366     388 ..     350     418 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0092
                      Mg_chelatase  22 gHnlllvGppGsGKtmlakrlps.llpplseee 53 
                                       gH + l+Gp G+GKt   k l++ + p+l ++e
  gi|488600447|ref|YP_007906918.1|  98 GHVVGLLGPNGTGKTTAVKILSGqIKPNLGKDE 130
                                       68999**************99862556666655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.29
                      Mg_chelatase  27 lvGppGsGKtmlakrlpsllppl 49 
                                       +vGp  +GK+   k l+++l + 
  gi|488600447|ref|YP_007906918.1| 366 IVGPNATGKSTFVKILAGVLEDD 388
                                       79****************99764 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0066       2.8       3      26 ..     100     123 ..      98     130 .. 0.81
   2 ?    2.0   0.0      0.33   1.4e+02       3      29 ..     363     389 ..     361     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                                       EEEEEESTTSSHHHHHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallk 26 
                                       v+ l+G++G+GKTt++  L+ ++k
  gi|488600447|ref|YP_007906918.1| 100 VVGLLGPNGTGKTTAVKILSGQIK 123
                                       67799*********9987776655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.33
                                       EEEEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkeg 29 
                                       v+ +vG++ +GK t +  La +l++++
  gi|488600447|ref|YP_007906918.1| 363 VLGIVGPNATGKSTFVKILAGVLEDDE 389
                                       5669***************99998775 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.026        11      35      61 ..      99     126 ..      96     141 .. 0.85
   2 ?    0.1   0.0       1.4   6.1e+02      55      93 ..     200     235 ..     164     245 .. 0.78
   3 ?    0.5   0.0       1.1   4.5e+02      31      57 ..     359     385 ..     342     415 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                            RuvB_N  35 hvl.lyGpPGlGkttlakiiakelgvkl 61 
                                       hv+ l Gp G Gktt  ki++ +++ +l
  gi|488600447|ref|YP_007906918.1|  99 HVVgLLGPNGTGKTTAVKILSGQIKPNL 126
                                       554489**************99887665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.4
                            RuvB_N  55 kelgvklkitsgPvlekagdlaalltnleekdvlfidei 93 
                                       + ++ ++++ sg  l++ + +aa l  l++ d  f+de+
  gi|488600447|ref|YP_007906918.1| 200 NSIERDVRHLSGGELQRLA-IAACL--LRDADFYFLDEV 235
                                       5667778888888888765.44444..678999999998 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.1
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakel 57 
                                       ++ + + ++Gp   Gk+t+ ki+a  l
  gi|488600447|ref|YP_007906918.1| 359 KQSEVLGIVGPNATGKSTFVKILAGVL 385
                                       445555589*************99766 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   0.1     0.038        16      28      51 ..      97     120 ..      89     128 .. 0.86
   2 ?    4.9   0.1     0.026        11      28      55 ..     360     387 ..     346     393 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.038
                                       -SEEEEEEE-TTSSHHHHHHHHHH CS
                              MeaB  28 raqvvGltGvPGaGkstlvealgl 51 
                                       + +vvGl G  G+Gk t+v+ l  
  gi|488600447|ref|YP_007906918.1|  97 KGHVVGLLGPNGTGKTTAVKILSG 120
                                       579****************98865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.026
                                       -SEEEEEEE-TTSSHHHHHHHHHHHHHC CS
                              MeaB  28 raqvvGltGvPGaGkstlvealglelrr 55 
                                       +++v+G+ G   +Gkst+v+ l+  l +
  gi|488600447|ref|YP_007906918.1| 360 QSEVLGIVGPNATGKSTFVKILAGVLED 387
                                       6899***************999877765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.072        31       3      24 ..     102     123 ..     100     127 .. 0.82
   2 ?   -0.6   0.0       2.6   1.1e+03      94     114 ..     175     196 ..     157     207 .. 0.70
   3 ?    4.1   0.1     0.093        40       3      27 ..     365     389 ..     363     393 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.072
                                       EEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellk 24 
                                        + Gp G+GKtT vk ++ ++k
  gi|488600447|ref|YP_007906918.1| 102 GLLGPNGTGKTTAVKILSGQIK 123
                                       577***********98877765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.6
                                       HHH-.EEEE---STTGGG-HHH CS
                          NTPase_1  94 sead.viviDEiGkmElkskkf 114
                                       + +d +   DEiGk+   ++k+
  gi|488600447|ref|YP_007906918.1| 175 KAKDlLSKADEIGKIDEMVEKL 196
                                       455646678*****98887765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.093
                                       EEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssg 27 
                                        i Gp  +GK+T+vk ++ +l++++
  gi|488600447|ref|YP_007906918.1| 365 GIVGPNATGKSTFVKILAGVLEDDE 389
                                       588***************9998876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   9.9      0.31   1.3e+02      10      63 ..      22      62 ..      13      64 .. 0.59
   2 ?   10.1   2.0     0.002      0.87       5      17 ..      50      62 ..      46      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.31
                            Fer4_8 10 aCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                       C++ Cpv+r+ ++      + ++     e         + C++cg C+++Cp 
  gi|488600447|ref|YP_007906918.1| 22 ECEKYCPVVRSGAEAVVIEDKAVIS----E---------ELCVGCGICVKKCPF 62
                                      5666666666665443333333222....2.........357888888888875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.002
                            Fer4_8  5 CieCgaCqsaCpv 17
                                      C++Cg C ++Cp+
  gi|488600447|ref|YP_007906918.1| 50 CVGCGICVKKCPF 62
                                      9999999999984 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   3.8       1.1   4.7e+02       2      16 ..      12      29 ..      11      33 .. 0.73
   2 ?   11.9   3.4    0.0006      0.25       2      16 ..      48      62 ..      47      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.1
                            Fer4_4  2 erC..igCgs.CvaaCPq 16
                                      +rC  + C + C+ +CP+
  gi|488600447|ref|YP_007906918.1| 12 DRCkpQKCSReCEKYCPV 29
                                      56644567755******4 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0006
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e C+gCg Cv  CP+
  gi|488600447|ref|YP_007906918.1| 48 ELCVGCGICVKKCPF 62
                                      67************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 ?    2.8   3.3      0.69   2.9e+02       3      13 ..      18      29 ..      14      34 .. 0.78
   2 ?   10.7   5.1     0.002      0.84       1      15 []      50      64 ..      50      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.69
                            Fer4_3  3 gCg.aCvevCPv 13
                                       C+  C++ CPv
  gi|488600447|ref|YP_007906918.1| 18 KCSrECEKYCPV 29
                                      59757******5 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.002
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv+ CP +A
  gi|488600447|ref|YP_007906918.1| 50 CVGCGICVKKCPFKA 64
                                      ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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):              42  [number of targets reported over threshold]
# CPU time: 0.81u 0.32s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 3473.45
//
Query:       gi|488600448|ref|YP_007906919.1|  [L=321]
Description: ABC-type Fe3+-hydroxamate transport system, periplasmic component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-44  150.1   0.1    8.8e-44  149.8   0.1    1.1  1  Peripla_BP_2   Periplasmic binding protein
  ------ inclusion threshold ------
      0.059   13.8   0.1        1.7    9.0   0.0    2.6  2  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
        0.2   11.4   0.3       0.47   10.2   0.3    1.7  1  SPOB_a         Sensor_kinase_SpoOB-type, alpha-helical 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 !  149.8   0.1   1.5e-47   8.8e-44       1     237 [.      59     293 ..      59     294 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 1.5e-47
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGG CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskglgltded 75 
                                       i+sl+ps+teil+a+Ga+d+vvgv  ++++p +  ++++    v+vg++++++vE+++alkPDlv++ +g    d +
  gi|488600448|ref|YP_007906919.1|  59 IVSLAPSNTEILFAIGAEDRVVGVTDYCNYPPEVLEKKKsgVLVSVGGYSTVNVERVLALKPDLVVATYGN-GLDTI 134
                                       9***************************999998777767788**************************99.99*** PP

                                       HHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EE CS
                      Peripla_BP_2  76 eellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyv 152
                                       e l+  gi++++++++ t+e++ + i  +g+++g+ d+a+++v+e+ sk++++++ i+ +k+  v+   ++d+  + 
  gi|488600448|ref|YP_007906919.1| 135 EALRNFGIDVIAFDPK-TIEDVMKDIILIGKATGKYDQAKEVVKEMYSKIERVRKEIAGKKKVRVAHILWHDP--VW 208
                                       ****************.67*****************************************9999999999999..** PP

                                       EE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH...HHHT-S--HHHHT-SHHHHTSHHH CS
                      Peripla_BP_2 153 vagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr...aeadnktgleflkenpllaelpAv 226
                                       v+g n++i+++++ +g+en+++    +++  +s E +l ++pdvi+vs+      ++++ ++e ++++  l +++Av
  gi|488600448|ref|YP_007906919.1| 209 VSGKNTFISEVIELAGGENVFDF---DGWRIVSIEDLLRANPDVIIVSSGsgmGGNEKNIVYEWIMSDSRLRNINAV 282
                                       ********************887...6*********************9989889999999**************** PP

                                       HTT-EEEE-HH CS
                      Peripla_BP_2 227 kngrVyaldss 237
                                       +ngrVy +d++
  gi|488600448|ref|YP_007906919.1| 283 ENGRVYVVDAD 293
                                       ******99875 PP

>> 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 ?    9.0   0.0   0.00028       1.7      15      71 ..      81     128 ..      65     217 .. 0.82
   2 ?    1.4   0.0      0.06   3.6e+02      44      71 ..     234     255 ..     210     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00028
                                       CHCHHCCCCCCCHHHTT-EEEEE.EEHCCH-H..HHHHHHHHCTGGG-TSEEEEE-- CS
                     Lipase_GDSL_2  15 ggrsypaylarllaarlgldvvnnlgvsGattallrllerlrdllrlkpdlvtiliG 71 
                                       g   y++y ++ l ++   + v   +v+G++t   +++    ++l+lkpdlv+ + G
  gi|488600448|ref|YP_007906919.1|  81 GVTDYCNYPPEVLEKKK--SGVL-VSVGGYST--VNVE----RVLALKPDLVVATYG 128
                                       567899**999999999..7788.99****99..5554....4558******98877 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.06
                                       H-H..HHHHHHHH.....CTGGG-TSEEEEE-- CS
                     Lipase_GDSL_2  44 attallrllerlr.....dllrlkpdlvtiliG 71 
                                       +           r     dllr++pd+++++ G
  gi|488600448|ref|YP_007906919.1| 234 W-----------RivsieDLLRANPDVIIVSSG 255
                                       3...........33334488999******9977 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 ?   10.2   0.3   7.8e-05      0.47      36      57 ..     166     187 ..     151     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.8e-05
                            SPOB_a  36 Lgkydkaeeyieevvkelkees 57 
                                       +gkyd+a+e+++e++  +++ +
  gi|488600448|ref|YP_007906919.1| 166 TGKYDQAKEVVKEMYSKIERVR 187
                                       79***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      789  (0.0440069); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1916.34
//
Query:       gi|488600449|ref|YP_007906920.1|  [L=818]
Description: hypothetical protein Asulf_00922 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-17   62.1   7.9    1.5e-07   30.9   0.2    3.7  3  SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
      8e-17   60.9   0.0    2.1e-16   59.5   0.0    1.7  1  PKD              PKD domain
    7.7e-10   39.2   0.0    3.9e-09   37.0   0.0    2.3  2  DUF4430          Domain of unknown function (DUF4430)
    1.2e-09   37.7   6.9       0.02   14.6   0.0    5.2  5  Prenyltrans      Prenyltransferase and squalene oxidase repea
    1.8e-07   30.5   0.5    0.00095   18.3   0.1    3.3  3  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
    2.6e-05   23.4   2.8      0.043   12.8   0.5    3.6  3  TED_complement   A-macroglobulin TED domain
  ------ inclusion threshold ------
      0.044   13.5   0.0       0.14   11.9   0.0    1.9  1  PKD_3            PKD-like domain
       0.07   13.2   0.8       0.14   12.2   0.8    1.4  1  DUF4366          Domain of unknown function (DUF4366)
      0.099   13.1   0.2        0.7   10.3   0.0    2.5  3  E1_DerP2_DerF2   ML domain
        0.1   12.3   0.0          4    7.1   0.0    2.5  2  Cytochrom_C550   Cytochrome c-550 domain
       0.11   11.4   0.0         16    4.3   0.0    3.3  2  Cobalamin_bind   Eukaryotic cobalamin-binding protein


Domain annotation for each model (and alignments):
>> SQHop_cyclase_C  Squalene-hopene cyclase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   5.8e-07   0.00095     203     270 ..     464     520 ..     450     535 .. 0.81
   2 !   15.4   0.5   4.5e-06    0.0074     185     227 ..     581     618 ..     538     631 .. 0.80
   3 !   30.9   0.2   9.1e-11   1.5e-07     190     291 ..     630     724 ..     627     736 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.8e-07
                                       -TTSHHHHHHHHHHHTT--TTSSBB--GGGGT-GGGTT-SSBBHHHHHHHHHHHHHTTGGGSHHHHHH CS
                   SQHop_cyclase_C 203 dleepvirkavdWlksvqnedGGWGesaesykdpklagkgestasqtaWallallaageveseavkrG 270
                                       + +++ i+ a++Wlks+qnedGG+ +              es   +t+Wa++a+++age  ++ +k G
  gi|488600449|ref|YP_007906920.1| 464 NASDERIQIALKWLKSIQNEDGGFSNPG-----------EESSIGKTSWAIMAIVSAGEDPHNWTKNG 520
                                       5678899****************97654...........3677789*************998888777 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.5e-06
                                       SHHHHHHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB CS
                   SQHop_cyclase_C 185 nyiyGtwsvlsalaavgedleepvirkavdWlksvqnedGGWG 227
                                       +++y t+  + al++vged      +++v+Wlk++qn+dGG+ 
  gi|488600449|ref|YP_007906920.1| 581 DFVYTTIWGILALTSVGEDV-----NRSVEWLKAQQNQDGGFA 618
                                       689***999********995.....689*************64 PP

  == domain 3  score: 30.9 bits;  conditional E-value: 9.1e-11
                                       HHHHHHHHHHTT--TTSHHHHHHHHHHHTT--TTSSBB--GGGGT-GGGTT-SSBBHHHHHHHHHHHHHTTGGGSHH CS
                   SQHop_cyclase_C 190 twsvlsalaavgedleepvirkavdWlksvqnedGGWGesaesykdpklagkgestasqtaWallallaagevesea 266
                                       t s+++al a+ge+ +++vi+ka+d+lk+ qn+dGG           +++g+++s +++ aWa+ al aag    e 
  gi|488600449|ref|YP_007906920.1| 630 TSSAIQALIAAGEPRDSDVIKKALDYLKQGQNDDGGM----------RYFGTSASNSASDAWAIQALTAAGLNPAEW 696
                                       8899*******************************95..........7899999999**************877665 PP

                                       HHHH...HHHHHHH--TTS-----S--E CS
                   SQHop_cyclase_C 267 vkrG...iaylletqkedGtWeeeaytg 291
                                        k     +++ll+ q++dG ++ ++y++
  gi|488600449|ref|YP_007906920.1| 697 KKNNisvVEHLLSLQTDDGYFRYTSYQT 724
                                       5544111689*********999888864 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   1.3e-19   2.1e-16       8      69 ..     250     311 ..     244     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.3e-19
                                       -BSSEEEEEEEES....-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EE CS
                               PKD   8 lvpgatvaftaav...pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsa 69 
                                       +v+g+ ++f+a++   +dg++++y+Wdfgd   + + s++ vth+++++G YeV++t++++ g +
  gi|488600449|ref|YP_007906920.1| 250 PVAGERITFNASLsydEDGDIISYLWDFGD---GHTASGKVVTHSFEKAGRYEVRLTVEDDKGVS 311
                                       799***************************...***************************99966 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         7   1.1e+04      20      34 ..      62      76 ..      53      81 .. 0.65
   2 !   37.0   0.0   2.4e-12   3.9e-09       3      73 ..     126     202 ..     125     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7
                           DUF4430 20 eaqsgehyitsIngl 34
                                      +++ ++++i  I+g+
  gi|488600449|ref|YP_007906920.1| 62 KTDDQAYFIPRITGV 76
                                      2233336**999998 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 2.4e-12
                           DUF4430   3 tvfdvleaaakkkedkteaqsge..hyitsIngl.eqdtakksyWmyevN..Gepsdv.Gagsyklkdgdkivfryt 73 
                                       t++ +l++a++  +++++ + +e  ++++ Ingl ++d +++s+Wmy vN  +ep     a +y+++ gd+iv++++
  gi|488600449|ref|YP_007906920.1| 126 TAYGALKKATETLGISYKPELKEwgIFVDCINGLcSKDLGETSGWMYWVNypDEPLPGiVATDYEISPGDRIVWYFS 202
                                       8999*************999999**************************966454433499***************7 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05      0.02       6      21 ..     473     488 ..     470     503 .. 0.90
   2 ?    1.2   0.0      0.19   3.1e+02      29      41 ..     582     594 ..     575     597 .. 0.86
   3 !   14.0   0.0   1.9e-05     0.031       2      44 .]     599     641 ..     598     641 .. 0.89
   4 !    6.8   0.7    0.0033       5.4       3      20 ..     649     666 ..     647     690 .. 0.85
   5 ?   -2.9   0.0       3.6   5.8e+03      10      18 ..     707     715 ..     703     715 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHSHTTS-BB CS
                       Prenyltrans   6 avefLlscQnedGGwg 21 
                                       a+ +L+s+QnedGG++
  gi|488600449|ref|YP_007906920.1| 473 ALKWLKSIQNEDGGFS 488
                                       678************6 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                                       BHHHHHHHHHHHH CS
                       Prenyltrans  29 dtyytywalaaLa 41 
                                       ++y t w+++aL 
  gi|488600449|ref|YP_007906920.1| 582 FVYTTIWGILALT 594
                                       89*********97 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHCT CS
                       Prenyltrans   2 dvekavefLlscQnedGGwggrpgsesdtyytywalaaLallG 44 
                                       dv++ ve+L+  Qn dGG++   g  sd+  t  a++aL+++G
  gi|488600449|ref|YP_007906920.1| 599 DVNRSVEWLKAQQNQDGGFAWAVGEQSDFDDTSSAIQALIAAG 641
                                       788889*************999999999999999999998887 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHHHSHTTS-B CS
                       Prenyltrans   3 vekavefLlscQnedGGw 20 
                                       ++ka+++L+  Qn+dGG 
  gi|488600449|ref|YP_007906920.1| 649 IKKALDYLKQGQNDDGGM 666
                                       89***************6 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 3.6
                                       HHHHSHTTS CS
                       Prenyltrans  10 LlscQnedG 18 
                                       Lls Q +dG
  gi|488600449|ref|YP_007906920.1| 707 LLSLQTDDG 715
                                       9*******9 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0019       3.1      42      92 ..     465     514 ..     445     517 .. 0.85
   2 !   18.3   0.1   5.8e-07   0.00095      45     102 ..     598     655 ..     584     665 .. 0.90
   3 ?    3.3   0.1     0.023        38       2      84 ..     650     738 ..     649     764 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0019
                   SQHop_cyclase_N  42 ddeeeeekiakylrsqqredGgWelypggpgdlsttveaYlALkllGdspd 92 
                                        ++e+++ + k+l s q+edGg++  pg+++ +  t  a +A+  +G +p+
  gi|488600449|ref|YP_007906920.1| 465 ASDERIQIALKWLKSIQNEDGGFSN-PGEESSIGKTSWAIMAIVSAGEDPH 514
                                       5677888999*************85.8899999999999999999998876 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 5.8e-07
                   SQHop_cyclase_N  45 eeeekiakylrsqqredGgWelypggpgdlsttveaYlALkllGdspdapalarAref 102
                                       e+ ++ +++l +qq++dGg++ + g+++d   t  a  AL  +G + d++ +++A ++
  gi|488600449|ref|YP_007906920.1| 598 EDVNRSVEWLKAQQNQDGGFAWAVGEQSDFDDTSSAIQALIAAGEPRDSDVIKKALDY 655
                                       66788999********************************************999776 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.023
                   SQHop_cyclase_N   2 kraaeallslqkpdG..hWvgeLeanvtitaeyillreflgedd...eeeeekiakylrsqqredGgWely.pggpg 72 
                                       k+a ++l + q++dG   + g   +n   +a +i   +  g +    ++++  ++++l+s q++dG ++   ++ + 
  gi|488600449|ref|YP_007906920.1| 650 KKALDYLKQGQNDDGgmRYFGTSASNSASDAWAIQALTAAGLNPaewKKNNISVVEHLLSLQTDDGYFRYTsYQTSN 726
                                       56666666666666633355566666666666665555553332111334456677888888888888766234444 PP

                   SQHop_cyclase_N  73 dlsttveaYlAL 84 
                                          +tv a +AL
  gi|488600449|ref|YP_007906920.1| 727 PGYMTVSAIMAL 738
                                       456677777776 PP

>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0021       3.5     113     140 ..     465     492 ..     440     504 .. 0.85
   2 !   12.8   0.5   2.6e-05     0.043     261     311 ..     583     638 ..     567     640 .. 0.77
   3 ?    0.8   0.0      0.13     2e+02     114     138 ..     645     669 ..     640     692 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                                       --HHHHHHHHHHHHTTB-TTS-B--SS- CS
                    TED_complement 113 ideeeiseslewLlseQkedGsFkeegs 140
                                        ++e i+ +l+wL s Q+edG F ++g+
  gi|488600449|ref|YP_007906920.1| 465 ASDERIQIALKWLKSIQNEDGGFSNPGE 492
                                       567889999**************99876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHHHHHTTSCHHHHHHHHHHHHTHTSTSSSS......S.HHHHHHHHHHHH CS
                    TED_complement 261 vettaYaLLallsekdleladkivkWLtkqrnsaGGFs......S.tqDtvvaLqaLs 311
                                       v tt + +Lal s ++   +++ v+WL +q+n++GGF+      S   Dt  a+qaL 
  gi|488600449|ref|YP_007906920.1| 583 VYTTIWGILALTSVGE--DVNRSVEWLKAQQNQDGGFAwavgeqSdFDDTSSAIQALI 638
                                       5577778888877655..78999**************633333343468999999986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.13
                                       -HHHHHHHHHHHHTTB-TTS-B--S CS
                    TED_complement 114 deeeiseslewLlseQkedGsFkee 138
                                       d + i+++l +L + Q++dG  +  
  gi|488600449|ref|YP_007906920.1| 645 DSDVIKKALDYLKQGQNDDGGMRYF 669
                                       6788999999999999999876654 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.6e-05      0.14      17      67 ..     252     305 ..     243     306 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.6e-05
                             PKD_3  17 vgreltiaPtvenaenaa...faWtieGkivsteptytfteeelgsyevtleve 67 
                                       +g+ +t++   ++ e+ +   ++W   +    + ++ t ++e++g yev+l+ve
  gi|488600449|ref|YP_007906920.1| 252 AGERITFNASLSYDEDGDiisYLWDFGDGHTASGKVVTHSFEKAGRYEVRLTVE 305
                                       678888888888777776788******999999*******************97 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8   8.5e-05      0.14      74     130 ..     750     812 ..     733     817 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-05
                           DUF4366  74 eevcactekcaagkvntdcpv.....eepepekeaepee..peeepekksn.nglllvvlavali 130
                                       +e  ++  k a+g+v++++       +e++pe++a+p++  +  +pekk+   g++l++la++++
  gi|488600449|ref|YP_007906920.1| 750 TE-TKEAVKEAKGEVEEETVGskevqPEAKPEATATPTSalT-ATPEKKTPgFGIILIILAMVVA 812
                                       22.233345566777766633556446666666777766643.3334433325555555555443 PP

>> E1_DerP2_DerF2  ML domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.5   8.9e+03      54      60 ..     216     222 ..     187     250 .. 0.57
   2 ?   -2.1   0.0         3   4.9e+03      17      41 ..     240     263 ..     234     271 .. 0.76
   3 ?   10.3   0.0   0.00043       0.7      24      67 ..     388     431 ..     361     439 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.5
                                       EEEEETT CS
                    E1_DerP2_DerF2  54 vevkvgg 60 
                                       +e+++g+
  gi|488600449|ref|YP_007906920.1| 216 IEISIGS 222
                                       3333332 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                                       EEEEEEESSECEECTSEEEEEEEEE CS
                    E1_DerP2_DerF2  17 vksveisppcplkrgqnltisadgs 41 
                                       + +++ +p+ ++++g+++t++a+ s
  gi|488600449|ref|YP_007906920.1| 240 IAKFDYTPE-NPVAGERITFNASLS 263
                                       456677778.99999****999984 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00043
                                       SSECEECTSEEEEEEEEEECSSBBSSEEEEEEEEETT.EEEEE-B CS
                    E1_DerP2_DerF2  24 ppcplkrgqnltisadgstsdeissglkaevevkvgg.wikvpfe 67 
                                        + ++  ++++++++d+++++e+++g ++ v +k++g w+ +p e
  gi|488600449|ref|YP_007906920.1| 388 RSFKIEVNSSVAVEIDFKVPKEVADGKRV-VVMKYNGtWVALPTE 431
                                       55688999********************9.88888888*****98 PP

>> Cytochrom_C550  Cytochrome c-550 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.076   1.2e+02      68      96 ..     546     574 ..     533     582 .. 0.83
   2 ?    7.1   0.0    0.0025         4      51     109 ..     629     688 ..     618     715 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.076
                                       SHHHHHHHHHS-B-TTSSSBGTTTSSSCC CS
                    Cytochrom_C550  68 nvaalvdylknPtsyDGeedlaelhpslk 96 
                                       ++ alv+  +nP  +DG + +ael + +k
  gi|488600449|ref|YP_007906920.1| 546 TILALVAADENPRNFDGIDLVAELKSKMK 574
                                       799***************98888877665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0025
                                       TSCSSHHHHHTSSS--SS..HHHHHHHHHS-B-TTSSSBGTTTSSSCCGTTTTGGGTTS-H CS
                    Cytochrom_C550  51 nvsLsledLalAtPpRdn..vaalvdylknPtsyDGeedlaelhpslksadiypelrnltd 109
                                       + s ++++L +A  pRd+  ++  +dylk+ +  DG   +  +  s + +d +  ++ lt 
  gi|488600449|ref|YP_007906920.1| 629 DTSSAIQALIAAGEPRDSdvIKKALDYLKQGQNDDGGMRYFGTSASNSASDAW-AIQALTA 688
                                       5666788999998888755599******************************9.6777765 PP

>> Cobalamin_bind  Eukaryotic cobalamin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0096        16      72     132 ..     480     542 ..     465     546 .. 0.79
   2 ?    3.4   0.0     0.019        30      93     124 ..     545     576 ..     539     721 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0096
                                       HHHHHHHHHS-SSS--HHHHHHHHHHHHHTT----H..HHHHHHHHHHHHHHHHHHHHHTTTS CS
                    Cobalamin_bind  72 lkeslqekllsslssstGqLALyilALkssCedlde..ekserlvsqLkkkleeekenieesh 132
                                       +++++    +   +ss+G+ ++ i+A+ s+ ed+ +  +++++ v   + +l+ e +++++ +
  gi|488600449|ref|YP_007906920.1| 480 IQNEDGGFSNPGEESSIGKTSWAIMAIVSAGEDPHNwtKNGKSPVDYIRDHLRGEMPKMGTAD 542
                                       4444444333334458********************9999999*************9998876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.019
                                       HHHHHHHHTT----HHHHHHHHHHHHHHHHHH CS
                    Cobalamin_bind  93 LyilALkssCedldeekserlvsqLkkkleee 124
                                        +ilAL ++ e++++  + +lv++Lk k+++ 
  gi|488600449|ref|YP_007906920.1| 545 RTILALVAADENPRNFDGIDLVAELKSKMKDD 576
                                       57888888888888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (818 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 5422.56
//
Query:       gi|488600450|ref|YP_007906921.1|  [L=611]
Description: WD40-like repeat protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-44  149.8  24.5    1.3e-09   38.3   0.1    8.8  9  PQQ_3      PQQ-like domain
    1.2e-34  119.9   0.1    8.2e-16   58.3   0.0    3.8  4  PQQ_2      PQQ-like domain
    5.3e-26   89.3  31.9    1.7e-08   34.0   0.1    9.4 10  PQQ        PQQ enzyme repeat
    1.3e-08   35.3   0.7    1.3e-08   35.3   0.7    4.2  5  DUF4430    Domain of unknown function (DUF4430)
  ------ inclusion threshold ------
      0.061   12.6   0.8         11    5.2   0.0    3.2  3  WD40_like  WD40-like domain
        4.2    7.7   8.0        7.4    7.0   0.2    5.0  5  DUF5122    Domain of unknown function (DUF5122) beta-propelle


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   3.9   2.7e-08   8.1e-05       3      40 .]      43      86 ..      42      86 .. 0.97
   2 !   10.7   0.1    0.0002      0.59       2      40 .]      88     125 ..      87     125 .. 0.85
   3 !   12.5   0.0   5.2e-05      0.15      12      37 ..     142     168 ..     132     170 .. 0.89
   4 !   13.6   0.0   2.5e-05     0.074       3      37 ..     172     210 ..     171     212 .. 0.83
   5 !   16.8   0.0   2.4e-06    0.0072       3      38 ..     215     249 ..     213     250 .. 0.94
   6 !   26.6   0.0   1.9e-09   5.8e-06       1      39 [.     251     288 ..     251     289 .. 0.92
   7 !   38.3   0.1   4.2e-13   1.3e-09       1      38 [.     290     329 ..     290     331 .. 0.97
   8 !   16.6   0.1   2.7e-06     0.008      12      37 ..     349     374 ..     332     376 .. 0.83
   9 ?   -4.0   0.2         6   1.8e+04      20      27 ..     477     484 ..     469     486 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.7e-08
                             PQQ_3  3 vlWsvqlpgpvnsspavdgglvyvgtg......dGtlyAlDaet 40
                                      + W+++l g v++sp++++g+++v+ +      +G+ly+l+a+t
  gi|488600450|ref|YP_007906921.1| 43 LAWKTELTGLVGASPVYWNGHIFVTNWygwgdwNGGLYSLNATT 86
                                      57****************************************98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                             PQQ_3   2 evlWsv.qlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                        + W+  q+ g+  ss+av g+ v+vg+  G ly ++a++
  gi|488600450|ref|YP_007906921.1|  88 SIEWRNsQITGA--SSVAVIGNSVVVGSLSGYLYFVNATS 125
                                       566777777766..99*********************975 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 5.2e-05
                             PQQ_3  12 pvnsspavdgglvyvgtg.dGtlyAlD 37 
                                        + ssp+++++++yv+t  +Gtl A++
  gi|488600450|ref|YP_007906921.1| 142 GIASSPLAYNNTIYVVTFsNGTLWAIN 168
                                       5789*********************97 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 2.5e-05
                             PQQ_3   3 vlWsvqlpgpvn..sspavdgglvyvgtg..dGtlyAlD 37 
                                       +lW+++++ +v   +sp +++g++++++    ++ly+l+
  gi|488600450|ref|YP_007906921.1| 172 ILWKFTTGNEVShyTSPSAYNGRIFFAGNdsVNRLYCLN 210
                                       79******9554449998888888888888*******97 PP

  == domain 5  score: 16.8 bits;  conditional E-value: 2.4e-06
                             PQQ_3   3 vlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDa 38 
                                       ++W+++++++++ +pa++ ++v+++t   +lyAl+ 
  gi|488600450|ref|YP_007906921.1| 215 EIWNFSVDSQITNTPAIGYNKVFFATK-SRLYALNM 249
                                       89************************8.******86 PP

  == domain 6  score: 26.6 bits;  conditional E-value: 1.9e-09
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       G + Wsv++ g   s++a++ g +y+g++ G+ly+++a+
  gi|488600450|ref|YP_007906921.1| 251 GSLAWSVSFNGT-MSTAAIAYGNIYIGSYEGKLYCFNAT 288
                                       7899******85.599*********************97 PP

  == domain 7  score: 38.3 bits;  conditional E-value: 4.2e-13
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg..dGtlyAlDa 38 
                                       G +lW+++  g++ sspav+gg+vy++t   +Gt+yA+Da
  gi|488600450|ref|YP_007906921.1| 290 GAELWNFTANGKIDSSPAVAGGIVYFATNnpQGTIYAVDA 329
                                       899************************************9 PP

  == domain 8  score: 16.6 bits;  conditional E-value: 2.7e-06
                             PQQ_3  12 pvnsspavdgglvyvgtgdGtlyAlD 37 
                                        + ssp ++++++y+g++ G ly+++
  gi|488600450|ref|YP_007906921.1| 349 NIMSSPYIANNRLYIGADSGYLYCFN 374
                                       677*********************97 PP

  == domain 9  score: -4.0 bits;  conditional E-value: 6
                             PQQ_3  20 dgglvyvg 27 
                                       dg++vy++
  gi|488600450|ref|YP_007906921.1| 477 DGDIVYFT 484
                                       78999975 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   2.8   3.7e-10   1.1e-06      58     184 ..      43     162 ..      42     169 .. 0.85
   2 !   34.4   0.0   5.3e-12   1.6e-08       3     102 ..     162     257 ..     160     260 .. 0.88
   3 !   58.3   0.0   2.8e-19   8.2e-16       3     138 ..     242     374 ..     241     377 .. 0.89
   4 !   15.2   0.0   4.2e-06     0.012       2      64 ..     321     385 ..     320     419 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.7e-10
                             PQQ_2  58 vlWettlegpvvgaplvaegrvvvva......sdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvg 128
                                       + W+t+l+g v ++p   +g+++v +       +g l+ l+a++G   W+  ++      + +++s av g+ vvvg
  gi|488600450|ref|YP_007906921.1|  43 LAWKTELTGLVGASPVYWNGHIFVTNwygwgdWNGGLYSLNATTGSIEWR-NSQ------ITGASSVAVIGNSVVVG 112
                                       78************************999965555***************.333......3466677777******* PP

                             PQQ_2 129 essgklvaldpkdGkvlWerel.aaprgtselsrvgdisgrpvvaegtVyassgqgr 184
                                         sg l+ +++++G    +++l ++p+          i+++p+  ++t+y+++++++
  gi|488600450|ref|YP_007906921.1| 113 SLSGYLYFVNATSGVIEKSYQLeTSPS-------WWGIASSPLAYNNTIYVVTFSNG 162
                                       ****************99999977776.......5679999999999*****99985 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 5.3e-12
                             PQQ_2   3 gvvsaldaatGaelWrvdlarplgggvsravlsggtlfva..tgggrlvaldaatGkvlWettlegpvvgaplvaeg 77 
                                       g++ a++  +  +lW+++ + + ++ +  ++  +g++f a  +  +rl++l+ ++G ++W++++++++ ++p +  +
  gi|488600450|ref|YP_007906921.1| 162 GTLWAIN--DSGILWKFTTGNEVSHYT-SPSAYNGRIFFAgnDSVNRLYCLN-ENGVEIWNFSVDSQITNTPAIGYN 234
                                       5666666..6789****9977788888.566689999998899********9.************************ PP

                             PQQ_2  78 rvvvvasdgqlialdaedGkrlWst 102
                                       +v++++ + +l+al+  dG ++Ws+
  gi|488600450|ref|YP_007906921.1| 235 KVFFAT-KSRLYALN-MDGSLAWSV 257
                                       **9997.99******.*******94 PP

  == domain 3  score: 58.3 bits;  conditional E-value: 2.8e-19
                             PQQ_2   3 gvvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrv 79 
                                       ++++al+  +G++ W+v+    ++g +s+a  + g +++++++g+l++++a++G++lW++t++g++ ++p va+g v
  gi|488600450|ref|YP_007906921.1| 242 SRLYALNM-DGSLAWSVS----FNGTMSTAAIAYGNIYIGSYEGKLYCFNATNGAELWNFTANGKIDSSPAVAGGIV 313
                                       78899997.8*******6....7888889999********************************************* PP

                             PQQ_2  80 vvva..sdgqlialdaedGkrlWstqqrseepae..lrssaspavagdtvvvgessgklvald 138
                                       ++++  + g+++a+da +G+ lW  ++ + +pa       +sp +a +++++g  sg l++++
  gi|488600450|ref|YP_007906921.1| 314 YFATnnPQGTIYAVDAFSGNMLWY-YRLT-PPAGnyYNIMSSPYIANNRLYIGADSGYLYCFN 374
                                       ***977778***************.6666.566668888888888999999999999998877 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 4.2e-06
                             PQQ_2   2 egvvsaldaatGaelWrvdlarp...lgggvsravlsggtlfvatgggrlvaldaatGkvlWettl 64 
                                       +g+++a+da +G+ lW  +l++p     +++s ++ ++++l+++ ++g l++++ ++G +  ++tl
  gi|488600450|ref|YP_007906921.1| 321 QGTIYAVDAFSGNMLWYYRLTPPagnYYNIMSSPYIANNRLYIGADSGYLYCFN-SSGLIEVNVTL 385
                                       689999999999999999887754446678888999999999999999999998.77777766666 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.9   5.6e+03      23      37 ..      44      58 ..      43      58 .. 0.87
   2 !    9.6   1.5   0.00031      0.91       7      25 ..      74      92 ..      70      92 .. 0.91
   3 !   16.6   0.1   1.9e-06    0.0056       1      37 [.     107     143 ..     107     144 .. 0.93
   4 !    9.5   0.4   0.00031      0.92       1      32 [.     152     182 ..     152     186 .. 0.91
   5 ?    3.5   0.0     0.025        75      10      32 ..     204     225 ..     193     231 .. 0.82
   6 !    7.1   0.0    0.0018       5.4       1      26 [.     234     257 ..     234     265 .. 0.85
   7 !   34.0   0.1   5.6e-12   1.7e-08       1      37 [.     271     307 ..     271     308 .. 0.97
   8 !   19.8   0.2   1.8e-07   0.00052       4      36 ..     315     348 ..     311     350 .. 0.84
   9 !    5.3   0.1    0.0068        20       1      17 [.     359     375 ..     359     377 .. 0.87
  10 ?   -2.7   0.0       2.4   7.1e+03      15      23 ..     473     481 ..     473     482 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                                      EEEEESSSCGSSESE CS
                               PQQ 23 lWrfktggpvlslpi 37
                                       W++++ g v ++p+
  gi|488600450|ref|YP_007906921.1| 44 AWKTELTGLVGASPV 58
                                      6*******9999985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00031
                                      ETTSEEEEEETTTCCEEEE CS
                               PQQ  7 sadGylyAlDadTGkvlWr 25
                                      + +G ly l+a+TG + Wr
  gi|488600450|ref|YP_007906921.1| 74 DWNGGLYSLNATTGSIEWR 92
                                      679***************7 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.9e-06
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                       + v++gs  Gyly ++a++G +  +++++  + ++ i
  gi|488600450|ref|YP_007906921.1| 107 NSVVVGSLSGYLYFVNATSGVIEKSYQLETSPSWWGI 143
                                       6799***************************999875 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00031
                                       TEEEEE.ETTSEEEEEETTTCCEEEEEESSSCG CS
                               PQQ   1 gvvylg.sadGylyAlDadTGkvlWrfktggpv 32 
                                       +++y+    +G+l+A++ d+  +lW+f tg++v
  gi|488600450|ref|YP_007906921.1| 152 NTIYVVtFSNGTLWAIN-DS-GILWKFTTGNEV 182
                                       6899999**********.**.6*******9987 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.025
                                       SEEEEEETTTCCEEEEEESSSCG CS
                               PQQ  10 GylyAlDadTGkvlWrfktggpv 32 
                                       ++ly l+ ++G ++W f +++ +
  gi|488600450|ref|YP_007906921.1| 204 NRLYCLN-ENGVEIWNFSVDSQI 225
                                       79*****.*******99988765 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0018
                                       TEEEEEETTSEEEEEETTTCCEEEEE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrf 26 
                                       ++v+ +++  +lyAl+  +G + W++
  gi|488600450|ref|YP_007906921.1| 234 NKVFFATKS-RLYALN-MDGSLAWSV 257
                                       567778777.9*****.*******97 PP

  == domain 7  score: 34.0 bits;  conditional E-value: 5.6e-12
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                       g++y+gs+ G+ly ++a++G +lW f ++g+++s+p+
  gi|488600450|ref|YP_007906921.1| 271 GNIYIGSYEGKLYCFNATNGAELWNFTANGKIDSSPA 307
                                       79*********************************97 PP

  == domain 8  score: 19.8 bits;  conditional E-value: 1.8e-07
                                       EEE.ETTSEEEEEETTTCCEEEEEESSSCGSSES CS
                               PQQ   4 ylg.sadGylyAlDadTGkvlWrfktggpvlslp 36 
                                       +++  + G++yA+Da +G++lW +++ +p  +++
  gi|488600450|ref|YP_007906921.1| 315 FATnNPQGTIYAVDAFSGNMLWYYRLTPPAGNYY 348
                                       5557778********************9988775 PP

  == domain 9  score: 5.3 bits;  conditional E-value: 0.0068
                                       TEEEEEETTSEEEEEET CS
                               PQQ   1 gvvylgsadGylyAlDa 17 
                                       +++y+g + Gyly ++ 
  gi|488600450|ref|YP_007906921.1| 359 NRLYIGADSGYLYCFNS 375
                                       679************94 PP

  == domain 10  score: -2.7 bits;  conditional E-value: 2.4
                                       EETTTCCEE CS
                               PQQ  15 lDadTGkvl 23 
                                       +D+++G+++
  gi|488600450|ref|YP_007906921.1| 473 YDLNDGDIV 481
                                       79****986 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       4.5   1.3e+04      26      44 ..     119     141 ..     107     143 .. 0.61
   2 ?    1.0   0.1      0.22   6.7e+02      43      57 ..     254     268 ..     248     273 .. 0.87
   3 ?   -0.6   0.2       0.7   2.1e+03      26      51 ..     273     301 ..     260     305 .. 0.67
   4 !   35.3   0.7   4.4e-12   1.3e-08      25      72 ..     432     485 ..     407     487 .. 0.83
   5 ?   -1.3   0.0       1.1   3.4e+03      45      67 ..     498     520 ..     490     520 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.5
                           DUF4430  26 hyitsIngl.eqdtakk...syW 44 
                                       +++++  g+ e++++     s+W
  gi|488600450|ref|YP_007906921.1| 119 YFVNATSGViEKSYQLEtspSWW 141
                                       57777777775555444444666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.22
                           DUF4430  43 yWmyevNGepsdvGa 57 
                                        W+ + NG++s+ ++
  gi|488600450|ref|YP_007906921.1| 254 AWSVSFNGTMSTAAI 268
                                       6**********9987 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.7
                           DUF4430  26 hyitsIngl..eqdtakk.syWmyevNGe 51 
                                       +yi s +g    ++ +++ + W ++ NG+
  gi|488600450|ref|YP_007906921.1| 273 IYIGSYEGKlyCFNATNGaELWNFTANGK 301
                                       566666666553444444599******98 PP

  == domain 4  score: 35.3 bits;  conditional E-value: 4.4e-12
                           DUF4430  25 e........hyitsIngleqdtakksyWmyevNGepsdvGagsyklkdgdkivfry 72 
                                                +++ sI g+  +++++ +Wmy vN+++++vG+++y l+dgd + f+y
  gi|488600450|ref|YP_007906921.1| 432 DswyatwgsLFVPSILGI--SNTNTLFWMYWVNDTQPSVGVNLYDLNDGDIVYFTY 485
                                       1455556679********..77788******************************9 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1.1
                           DUF4430  45 myevNGepsdvGagsyklkdgdk 67 
                                       ++++N e  + G++s ++++g+k
  gi|488600450|ref|YP_007906921.1| 498 TLKINVEVKSAGISSFTVSSGTK 520
                                       67788889999********9976 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.076   2.3e+02      86     224 ..     100     124 ..      80     168 .. 0.65
   2 ?    5.2   0.0    0.0036        11      78     109 ..     256     287 ..     188     303 .. 0.84
   3 ?    2.9   0.1     0.019        57      90     116 ..     356     383 ..     349     429 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.076
                         WD40_like  86 stvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennkiysLsesafivfdlfsqnieykisvkdik 162
                                       s v vi++ +++G+  G                                                            
  gi|488600450|ref|YP_007906921.1| 100 SSVAVIGNSVVVGSLSGY----------------------------------------------------------- 117
                                       445555555555555555........................................................... PP

                         WD40_like 163 tfeiienkdilligtegeililkknvilqkidvegkPecillvddylivGgsfkyllliNik 224
                                                                                              l  +N  
  gi|488600450|ref|YP_007906921.1| 118 -------------------------------------------------------LYFVNAT 124
                                       .......................................................5555554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0036
                         WD40_like  78 nekieedistvkviddklliGtnkGsiyvfsk 109
                                       + + +  +st+ +  ++++iG+++G++y+f+ 
  gi|488600450|ref|YP_007906921.1| 256 SVSFNGTMSTAAIAYGNIYIGSYEGKLYCFNA 287
                                       567788999999******************96 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.019
                         WD40_like  90 viddklliGtnkGsiyvfskd.lqleev 116
                                       + +++l+iG++ G +y+f+   l  ++v
  gi|488600450|ref|YP_007906921.1| 356 IANNRLYIGADSGYLYCFNSSgLIEVNV 383
                                       5689**************9762333333 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 ?    7.0   0.2    0.0025       7.4       3      30 ..     192     213 ..     192     214 .. 0.91
   2 ?   -0.8   0.0      0.64   1.9e+03      26      32 ..     247     253 ..     241     253 .. 0.88
   3 ?   -0.2   0.1      0.44   1.3e+03      11      30 ..     272     290 ..     268     291 .. 0.80
   4 ?   -0.7   0.0      0.61   1.8e+03      27      35 ..     297     305 ..     293     319 .. 0.79
   5 ?   -1.4   0.1         1     3e+03       4      30 ..     359     377 ..     357     379 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                           DUF5122   3 DGKIlVaGsftsyngssdfalvRLnaDG 30 
                                       +G+I+ aG+ +       ++l +Ln +G
  gi|488600450|ref|YP_007906921.1| 192 NGRIFFAGNDS------VNRLYCLNENG 213
                                       69999999999......89********9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.64
                           DUF5122  26 LnaDGsl 32 
                                       Ln+DGsl
  gi|488600450|ref|YP_007906921.1| 247 LNMDGSL 253
                                       9*****8 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.44
                           DUF5122  11 sftsyngssdfalvRLna.DG 30 
                                       + + + gs++  l ++na +G
  gi|488600450|ref|YP_007906921.1| 272 NIY-I-GSYEGKLYCFNAtNG 290
                                       555.5.99999******9887 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.61
                           DUF5122  27 naDGslDts 35 
                                       +a+G +D+s
  gi|488600450|ref|YP_007906921.1| 297 TANGKIDSS 305
                                       677777776 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 1
                           DUF5122   4 GKIlVaGsftsyngssdfalvRLnaDG 30 
                                       ++++++ +++        +l ++n+ G
  gi|488600450|ref|YP_007906921.1| 359 NRLYIGADSG--------YLYCFNSSG 377
                                       5666666666........589999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 3542.21
//
Query:       gi|488600451|ref|YP_007906922.1|  [L=294]
Description: hypothetical protein Asulf_00924 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-29  102.5   0.0    3.5e-29  102.1   0.0    1.2  1  ABC_tran     ABC transporter
    1.3e-07   32.0   2.2    6.2e-06   26.6   2.2    2.3  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    1.2e-05   25.6   0.3    0.00019   21.7   0.3    2.1  1  AAA_22       AAA domain
    0.00017   21.3   0.0     0.0003   20.5   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00048   20.0   0.5       0.83    9.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00068   19.1   0.0       0.11   11.9   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0016   18.8   0.0     0.0022   18.4   0.0    1.3  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.038   13.9   0.0      0.068   13.1   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.071   12.7   0.0       0.22   11.1   0.0    1.8  2  AAA_25       AAA domain
       0.18   11.9   0.0       0.63   10.2   0.0    1.9  2  AAA_33       AAA domain
       0.22   11.4   0.3        0.5   10.3   0.2    1.6  1  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0   2.2e-32   3.5e-29       2     137 .]      25     173 ..      24     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 2.2e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + v++++++ge++a+vGe+G+GKStL ++l+ l++pt Gei +dg dl +    +l+++r++++ +pq+  + l+p+
  gi|488600451|ref|YP_007906922.1|  25 DGVDIEINRGEVLALVGESGSGKSTLGRMLLMLVRPTRGEIYFDGLDLVRmkaGDLRRVRRRMQLIPQHpeDALDPR 101
                                       7899*****************************************999998999***************9999**** PP

                                       SBHHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        +++++          d   + +++ +++++l+++++++ p++LSgG+ qrv++ara++ +p+++++DEpt+
  gi|488600451|ref|YP_007906922.1| 102 WRIYDSiaeplrihGLDCSRDIIHNLIEMVGLREEHLYRYPHELSGGELQRVVIARAIAVEPEFIVCDEPTS 173
                                       *****9999999994444455555556666677799999*******************************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 !   26.6   2.2   3.8e-09   6.2e-06       8      65 .]     229     274 ..     224     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.8e-09
                         oligo_HPY   8 klfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +++d+plHPYT++L+rsv +  +  +            +   +GC+F++ Cp ++e+C
  gi|488600451|ref|YP_007906922.1| 229 DVLDRPLHPYTEMLVRSVEESFELTQ------------RSERSGCKFYSLCPKRMEIC 274
                                       89****************88733333............33345**************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   1.2e-07   0.00019       5     129 ..      34     202 ..      30     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee........................................erpe 41 
                                         +l+++GesG+GK+tl r+ll+    ++   e                                         ++ 
  gi|488600451|ref|YP_007906922.1|  34 GEVLALVGESGSGKSTLGRMLLMLV--RPTRGEiyfdgldlvrmkagdlrrvrrrmqlipqhpedaldprwriYDSI 108
                                       56899******************97..44444478999999999999999999999999998888888666655555 PP

                            AAA_22  42 vvfvtlpsstsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr...seeale 110
                                            + ++  s+d+ ++l + +gl+ ++     +el    l++ + ara    +e+++ DE    l+   ++ +++
  gi|488600451|ref|YP_007906922.1| 109 AEPLRIHGLDCSRDIIHNLIEMVGLREEHLYRYPHELSgGELQRVVIARAIavePEFIVCDEPTSmLDmsvQASIVN 185
                                       55888888889999999999999999888555666666689999988888899999******999666855599999 PP

                            AAA_22 111 eLrsllnlsrkgvqliLvG 129
                                        L+sl++  + g++ +++ 
  gi|488600451|ref|YP_007906922.1| 186 LLVSLHK--KLGMAYLFIT 202
                                       9999988..5555554444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.8e-07    0.0003      13      38 ..      25      50 ..      22      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                      dg +iei++ ++  l+G+sGsGKSTl
  gi|488600451|ref|YP_007906922.1| 25 DGVDIEINRGEVLALVGESGSGKSTL 50
                                      78899**9777**************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 !    9.4   0.0   0.00051      0.83       3      22 ..      38      57 ..      36     100 .. 0.83
   2 !    9.3   0.1   0.00056      0.91     255     301 ..     160     207 ..     103     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00051
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +l+G  gsGKS+L + l +l
  gi|488600451|ref|YP_007906922.1| 38 ALVGESGSGKSTLGRMLLML 57
                                      89************999888 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00056
                            AAA_21 255 lkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                       + ++ +++ DEp + L+ +++++++ ll +l++  g   ++ TH+ +l
  gi|488600451|ref|YP_007906922.1| 160 AVEPEFIVCDEPTSMLDMSVQASIVNLLVSLHKkLGMAYLFITHDLEL 207
                                       333489999*******************77777577778******987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0076        12      25      41 ..      35      51 ..      23      60 .. 0.81
   2 !   11.9   0.0   6.8e-05      0.11     109     211 ..     110     217 ..      89     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0076
                                      SEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnll 41
                                      ++ a+vG+ GSGKs l 
  gi|488600451|ref|YP_007906922.1| 35 EVLALVGESGSGKSTLG 51
                                      46799*********875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.8e-05
                                       EEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 109 seykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                          +i g ++++  +++l+e++g+ +e       +LSgGe + v +a  +A++   p  + + De  + LD +  + 
  gi|488600451|ref|YP_007906922.1| 110 EPLRIHGLDCSRDIIHNLIEMVGLREEhlyryphELSGGELQRVVIARAIAVE---P-EFIVCDEPTSMLDMSVQAS 182
                                       5567889999999999********9999999999******9999999888875...3.4999*************** PP

                                       HHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 179 vaellkekskn..aQfivislreemlekadklvgv 211
                                       +++ll + +k+  + ++ i+++ e+ + +   v v
  gi|488600451|ref|YP_007906922.1| 183 IVNLLVSLHKKlgMAYLFITHDLELARIVADRVAV 217
                                       ****9998888667788889888877766555554 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   1.3e-06    0.0022      22      98 ..      32     103 ..      24     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekd..ggif.....lrgkcdqlesaipysalaqalareellrqlldeaes 91 
                                       +r+e++ l+GesG+GKs+l r+ll  ++ +  +++f     +r k+            ++   r + ++ + +++e+
  gi|488600451|ref|YP_007906922.1|  32 NRGEVLALVGESGSGKSTLGRMLLMLVRPTrgEIYFdgldlVRMKAG----------DLRRV-R-RRMQLIPQHPED 96 
                                       56799*******************65554443244433333333333..........33444.3.556666666666 PP

                            AAA_16  92 aeleawr 98 
                                       a+ ++wr
  gi|488600451|ref|YP_007906922.1|  97 ALDPRWR 103
                                       6666665 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   4.2e-05     0.068      98     120 ..      33      55 ..      10      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-05
                                       TTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinall 120
                                       ++++ +lvG+SG GKStL  +ll
  gi|488600451|ref|YP_007906922.1|  33 RGEVLALVGESGSGKSTLGRMLL 55 
                                       45999*************87775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.22      30      50 ..      31      51 ..      24     128 .. 0.87
   2 ?   -1.5   0.0      0.96   1.6e+03     143     188 ..     163     203 ..     142     204 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + +ge+ +l+G +g+GK+tl 
  gi|488600451|ref|YP_007906922.1| 31 INRGEVLALVGESGSGKSTLG 51
                                      679****************95 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.96
                            AAA_25 143 vrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                       ++++v D  +++l+ + +     +++v+ l ++ +++g a l++ H
  gi|488600451|ref|YP_007906922.1| 163 PEFIVCDEPTSMLDMSVQ-----ASIVNLLVSLHKKLGMAYLFITH 203
                                       666666666666555554.....67788888888888888888887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00039      0.63       1      20 [.      36      55 ..      36      93 .. 0.91
   2 ?   -1.5   0.0       1.6   2.6e+03      18      40 ..     189     213 ..     186     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00039
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      ++ lvG +GsGKstl + ll
  gi|488600451|ref|YP_007906922.1| 36 VLALVGESGSGKSTLGRMLL 55
                                      6789***********98875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                            AAA_33  18 rllkklg..avllssdtlrrrlfgt 40 
                                       +l+kklg  + +++ d ++ r++++
  gi|488600451|ref|YP_007906922.1| 189 SLHKKLGmaYLFITHDLELARIVAD 213
                                       6899999989999999988888764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00031       0.5       2      23 ..      36      57 ..      35      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                      CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                      +++l Ge+GsGK+tL + l ++
  gi|488600451|ref|YP_007906922.1| 36 VLALVGESGSGKSTLGRMLLML 57
                                      789************8888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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: 00:00:00.47
# Mc/sec: 1886.70
//
Query:       gi|488600452|ref|YP_007906923.1|  [L=308]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   77.1   0.0    2.5e-21   76.6   0.0    1.2  1  ABC_tran   ABC transporter
    6.9e-16   58.5   0.6    1.2e-15   57.7   0.6    1.4  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    0.00038   20.4   0.1       0.11   12.2   0.0    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
     0.0038   16.9   0.0     0.0068   16.1   0.0    1.3  1  AAA_29     P-loop containing region of AAA domain
     0.0057   16.4   0.0       0.15   11.8   0.0    2.1  2  IstB_IS21  IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.015   15.7   0.1      0.024   15.0   0.1    1.6  1  AAA_16     AAA ATPase domain
      0.027   14.7   0.0       0.11   12.8   0.0    1.8  2  AAA_22     AAA domain
      0.042   13.4   0.1      0.084   12.4   0.0    1.5  2  AAA_7      P-loop containing dynein motor region
      0.088   12.8   0.2       0.17   11.9   0.2    1.5  1  AAA_5      AAA domain (dynein-related subfamily)
      0.088   12.2   0.0        8.8    5.7   0.0    2.0  2  SMC_N      RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   1.4e-24   2.5e-21       2     136 ..      25     181 ..      24     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.4e-24
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..pq 69 
                                       + vs++++ege +a++Ge+G+GKS L +++++ll       G+il++g +l e      +e+  +ei+++pq+  ++
  gi|488600452|ref|YP_007906923.1|  25 DGVSFHVSEGEALALIGESGSGKSVLGMTILRLLPEnvrVGGKILFNGLNLLElpeeGLREIRGREIAWVPQNpaTS 101
                                       78****************************99998878789**********99998777899999********9888 PP

                                       S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                       xxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  70 lfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                       l+p l+v+ +              ++ +++  +l+ ++++  ++++v++ p+++SgG++qr  +a+   ++p+l+++
  gi|488600452|ref|YP_007906923.1| 102 LNPVLRVGIQiaepmevhmgidrkTAIQRVVGLLRYFDINP-AEKRVNQYPHQYSGGMRQRALVAMGTSTQPRLIIA 177
                                       99999888889999999998866555555777777777766.7888899**************************** PP

                                       ESTT CS
                                       xxxx RF
                          ABC_tran 133 DEpt 136
                                       DEpt
  gi|488600452|ref|YP_007906923.1| 178 DEPT 181
                                       ***9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.6   6.8e-19   1.2e-15       1      65 []     233     292 ..     233     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 6.8e-19
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE  +++++f+eplHPY+kaLl+s+p+       l  ikg  ps  + +eGC+F+pRC +a+++C
  gi|488600452|ref|YP_007906923.1| 233 VEVCDARTFFEEPLHPYSKALLNSLPSR-----GLNPIKGYSPSMVNPPEGCRFHPRCDHATDKC 292
                                       89999*********************98.....46689*************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.3    0.0043       7.6       3      23 ..      38      58 ..      37      89 .. 0.77
   2 !   12.2   0.0   6.4e-05      0.11     188     298 ..     101     213 ..      69     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0043
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      +liG  gsGKS L  ++  l 
  gi|488600452|ref|YP_007906923.1| 38 ALIGESGSGKSVLGMTILRLL 58
                                      79***********99998885 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.4e-05
                            AAA_21 188 lvrslklveielsdlgegeeliasvderlrer....gvvflengdgqelparelSdGtkrllalltallralkkgsl 260
                                        ++++++v+i +   +e+   i++    +r +    ++ ++  +++ +  +++ S G+++  al+++  ++ +  +l
  gi|488600452|ref|YP_007906923.1| 101 SLNPVLRVGIQIAEPMEVHMGIDRKTAIQRVVgllrYFDINPAEKRVNQYPHQYSGGMRQR-ALVAMGTSTQP--RL 174
                                       46777777777777777777777777777777999999***********************.88877777776..9* PP

                            AAA_21 261 lliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                       ++ DEp  g +     r++el+ k++++ +  +++ TH+
  gi|488600452|ref|YP_007906923.1| 175 IIADEPTKGVDVTKKVRVAELFrKIKKNSKPSLLIITHD 213
                                       ************999999999985555566********9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.8e-06    0.0068      13      38 ..      25      50 ..      20      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.8e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                      dg ++++++ +a  l+G+sGsGKS l
  gi|488600452|ref|YP_007906923.1| 25 DGVSFHVSEGEALALIGESGSGKSVL 50
                                      67888998666*************87 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   8.5e-05      0.15      32      80 ..      18      70 ..       6      79 .. 0.75
   2 ?    2.5   0.0      0.06   1.1e+02     105     153 ..     168     218 ..     152     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.5e-05
                         IstB_IS21 32 krkvkeLatlsf.iekkenivllGpsGvGKshlaialgv...eavraglsvlf 80
                                      + +vk++ + sf +++ e+++l+G sG GKs l +++ +   e vr g ++lf
  gi|488600452|ref|YP_007906923.1| 18 NMTVKAVDGVSFhVSEGEALALIGESGSGKSVLGMTILRllpENVRVGGKILF 70
                                      55677777778758999****************98864322256666666666 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.06
                         IstB_IS21 105 rllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpfae 153
                                       + ++++l+i D+   g+   ++   ++lf+ i+k  + + +iit +lpfae
  gi|488600452|ref|YP_007906923.1| 168 TSTQPRLIIADEptKGVDVTKKVRVAELFRKIKKNSKPSLLIITHDLPFAE 218
                                       556788999998434777777888899*******9999999******9986 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   0.1   1.4e-05     0.024      23      51 ..      33      61 ..      27     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                      ++e++ l+GesG+GKs l  ++lr l ++
  gi|488600452|ref|YP_007906923.1| 33 EGEALALIGESGSGKSVLGMTILRLLPEN 61
                                      44899******************877776 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   5.9e-05      0.11       6      31 ..      35      60 ..      30      78 .. 0.87
   2 ?   -1.1   0.0       1.2   2.1e+03      91     100 ..     168     180 ..     139     215 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.9e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqlde 31
                                        l+++GesG+GK++l  ++l+ l+e
  gi|488600452|ref|YP_007906923.1| 35 EALALIGESGSGKSVLGMTILRLLPE 60
                                      6799************9999988865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                            AAA_22  91 v...ielliiDEa 100
                                       +   ++l+i DE 
  gi|488600452|ref|YP_007906923.1| 168 TstqPRLIIADEP 180
                                       2333567777774 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 ?   12.4   0.0   4.7e-05     0.084      24      60 ..      25      61 ..       8      72 .. 0.79
   2 ?   -3.3   0.0       3.1   5.6e+03      16      38 ..     186     208 ..     184     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.7e-05
                             AAA_7 24 yllelllknkkpvllvGptGtGKtviikdllkkldke 60
                                        ++ +++++  + l+G++G+GK+v+ +++l+ l+++
  gi|488600452|ref|YP_007906923.1| 25 DGVSFHVSEGEALALIGESGSGKSVLGMTILRLLPEN 61
                                      556789999*********************9999954 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.1
                             AAA_7  16 tvdtvrysyllelllknkkpvll 38 
                                        ++ vr+  l++++ kn+kp ll
  gi|488600452|ref|YP_007906923.1| 186 VTKKVRVAELFRKIKKNSKPSLL 208
                                       56789999999999999999887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   9.6e-05      0.17       2      27 ..      37      62 ..      36      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.6e-05
                                      EEEE--SSSSHHHHHHHGGGGBS--E CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnrev 27
                                      + L+G++G+gKs l + ++++l  +v
  gi|488600452|ref|YP_007906923.1| 37 LALIGESGSGKSVLGMTILRLLPENV 62
                                      569*******************7766 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0098        17      26      45 ..      36      55 ..      16      68 .. 0.82
   2 ?    5.7   0.0    0.0049       8.8     136     211 ..     153     226 ..      89     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0098
                                      EEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAil 45
                                        a++G+ GSGKs l   il
  gi|488600452|ref|YP_007906923.1| 36 ALALIGESGSGKSVLGMTIL 55
                                      5689*********9887776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0049
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE..EEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ..fivislreemlekadklvg 210
                                       + SgG ++ +   L +A+    +  l + De     D ++  +vael+++ +kn+   +++i+++  + e+    v 
  gi|488600452|ref|YP_007906923.1| 153 QYSGGMRQRA---L-VAMGTSTQPRLIIADEPTKGVDVTKKVRVAELFRKIKKNSKpsLLIITHDLPFAERLADRVA 225
                                       5566655433...3.25555566668999********************888875433999**99988887654444 PP

                                       E CS
                                       x RF
                             SMC_N 211 v 211
                                       v
  gi|488600452|ref|YP_007906923.1| 226 V 226
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1893.89
//
Query:       gi|488600453|ref|YP_007906924.1|  [L=284]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   23.3   2.5    6.1e-05   23.3   2.5    2.6  4  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 !   23.3   2.5   3.4e-09   6.1e-05       6      99 ..       2      85 ..       1     102 [. 0.90
   2 ?   -0.8   0.1       0.1   1.8e+03      24      39 ..      89     104 ..      76     127 .. 0.64
   3 ?   -1.9   0.2      0.22   3.9e+03       4      17 ..     167     180 ..     160     222 .. 0.71
   4 ?   -2.0   0.0      0.23   4.2e+03      60      90 ..     209     230 ..     184     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.4e-09
                              Gate  6 piillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpks 84
                                      p++++++++ +++ + +++ r+  +l+p+++  +  l+  +++++ t f++  +++++++++y        +++ ++ +
  gi|488600453|ref|YP_007906924.1|  2 PYVVAGIVMANIAIELGIFYRVLPVLKPFIKLSK--LSSGSCIAIATAFGSPQAAISMIAEIY-------RNRKISRTE 71
                                      89******************************77..***************************.......********* PP

                              Gate 85 alafllfvllytpcv 99
                                      a+++ + + +    v
  gi|488600453|ref|YP_007906924.1| 72 AYITSIATWFPQ-TV 85
                                      ***999998875.44 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.1
                              Gate  24 lgrigkllepvfaplg 39 
                                       +++i+ ++ p++ plg
  gi|488600453|ref|YP_007906924.1|  89 IAYIAPAIIPLLGPLG 104
                                       6777888888888888 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.22
                              Gate   4 agpiillasiliwf 17 
                                       a+pi ++a++l+ +
  gi|488600453|ref|YP_007906924.1| 167 ALPITIVAFVLLDV 180
                                       55666666666544 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.23
                              Gate  60 vvgtlgtlytsalgellqgfdtpksalafll 90 
                                       ++++l++++          + t+k+al++ll
  gi|488600453|ref|YP_007906924.1| 209 AYAALSEIM---------DTITFKQALIVLL 230
                                       444444444.........5555555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1590.20
//
Query:       gi|488600454|ref|YP_007906925.1|  [L=289]
Description: ABC-type dipeptide/oligopeptide/nickel transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-36  125.9   9.7    1.5e-36  125.9   9.7    2.6  3  BPD_transp_1     Binding-protein-dependent transport system i
    1.3e-05   25.0   0.3    1.3e-05   25.0   0.3    3.9  4  OppC_N           N-terminal TM domain of oligopeptide transpo
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.036   14.3   0.1    1.6  1  Arylesterase     Arylesterase
        5.3    6.6   9.2       0.18   11.4   0.2    2.3  3  DUF2208          Predicted membrane protein (DUF2208)


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   1.6     0.056   2.5e+02     157     180 ..      19      42 ..       5      44 .. 0.57
   2 ?   -1.2   0.2      0.31   1.4e+03      27      39 ..      84      96 ..      62      98 .. 0.44
   3 !  125.9   9.7   3.3e-40   1.5e-36       1     184 [.      99     282 ..      99     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.056
                      BPD_transp_1 157 gvlalviavlllnlvadilqrlld 180
                                       +v +++++++l+++++ +++++++
  gi|488600454|ref|YP_007906925.1|  19 TVNFIALLIILCLFLVAVFADVIS 42 
                                       444555556666666555555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.31
                      BPD_transp_1 27 llslPsfvlaill 39
                                       l + +f++ai++
  gi|488600454|ref|YP_007906925.1| 84 SLFVSVFAIAIIM 96
                                      1222233333333 PP

  == domain 3  score: 125.9 bits;  conditional E-value: 3.3e-40
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirraal 76 
                                       gi++G++aa ++++k+d++++++++vlls+P ++lai lv      +ilg +l   vi+++l+s+a y+r++r+ +l
  gi|488600454|ref|YP_007906925.1|  99 GIMFGSIAA-YFGGKVDEVIMRFVDVLLSFPGLILAITLV------GILGpSLKNLVIAIALTSWASYARIVRSCVL 168
                                       89*******.******************************......****777777********************* PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++ ++++v  a++lGas+  i++k+v+Pna+ pii ++ l +g+++   + l+flg    lg +  ++++g +++e+
  gi|488600454|ref|YP_007906925.1| 169 SIKEMEFVTQAKVLGASDVYILVKHVIPNAIAPIIVLATLDMGHIVLSITGLSFLG----LGAQPPTPEWGTMLNEG 241
                                       ********************************************************....***************** PP

                      BPD_transp_1 154 s..........nggvlalviavlllnlvadilqrlldprvr 184
                                                  +++ la+ i vl++nl+ d l +lldprvr
  gi|488600454|ref|YP_007906925.1| 242 KnfmttapwltIFPGLAIMITVLAFNLLGDGLRDLLDPRVR 282
                                       ****************************************8 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 !   25.0   0.3     3e-09   1.3e-05      17      51 .]      22      58 ..      19      60 .. 0.83
   2 ?   -1.0   1.8      0.39   1.7e+03      17      28 ..      89     100 ..      83     115 .. 0.54
   3 ?    1.0   0.6     0.092   4.1e+02      22      36 ..     130     144 ..     129     157 .. 0.86
   4 ?   -1.7   0.1      0.65   2.9e+03      19      35 ..     256     272 ..     256     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3e-09
                            OppC_N 17 vvglvilllllliaifaPliaPydpqdli.qn.llpP 51
                                      +++l i+l l+l+a+fa++i+Pydp +++    l++P
  gi|488600454|ref|YP_007906925.1| 22 FIALLIILCLFLVAVFADVISPYDPYEVNmKEkLQKP 58
                                      589**********************555533248888 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.39
                            OppC_N  17 vvglvillllll 28 
                                       v++ +i+++l +
  gi|488600454|ref|YP_007906925.1|  89 VFAIAIIMFLGI 100
                                       333344443333 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.092
                            OppC_N  22 illlllliaifaPli 36 
                                       ++l+++l+ i++P +
  gi|488600454|ref|YP_007906925.1| 130 LILAITLVGILGPSL 144
                                       588899999***987 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.65
                            OppC_N  19 glvilllllliaifaPl 35 
                                       gl+i +++l++ ++++ 
  gi|488600454|ref|YP_007906925.1| 256 GLAIMITVLAFNLLGDG 272
                                       78999999988777765 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     8e-06     0.036      11      53 ..      78     120 ..      73     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8e-06
                      Arylesterase  11 fyatndhyFgdnfllllemslqlawtavvYyspsevkvvasgl 53 
                                       +y t+ + F + f+  ++m l+ + +++  y +++v +v+ ++
  gi|488600454|ref|YP_007906925.1|  78 IYGTRISLFVSVFAIAIIMFLGIMFGSIAAYFGGKVDEVIMRF 120
                                       69*************************************9998 PP

>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.9     0.082   3.7e+02      88     111 ..      16      41 ..       6      57 .. 0.57
   2 ?   11.4   0.2   4.1e-05      0.18      67     149 ..      58     139 ..      45     161 .. 0.83
   3 ?   -3.0   0.1         1   4.5e+03      95     122 ..     183     210 ..     170     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.082
                           DUF2208  88 kasmitllllliviilffl..lyryi 111
                                         s++++++lli++ lf++  + ++i
  gi|488600454|ref|YP_007906925.1|  16 SISTVNFIALLIILCLFLVavFADVI 41 
                                       34445555555555554442144444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.1e-05
                           DUF2208  67 knalkliekDeelqkelkeqlkasmitllllliviilffllyryiiplassllgevleeklarflaflalFealfli 143
                                        n + l+ +D+   + l++++  + i+l+++++ i+++++l  +++++a++  g+v +e++ rf+  l+ F +l+l 
  gi|488600454|ref|YP_007906925.1|  58 PNLNHLLGTDQLGRDVLSRIIYGTRISLFVSVFAIAIIMFLGIMFGSIAAYFGGKV-DEVIMRFVDVLLSFPGLILA 133
                                       5788999999999999********************99999999999999888888.**************999988 PP

                           DUF2208 144 smflrl 149
                                        +++ +
  gi|488600454|ref|YP_007906925.1| 134 ITLVGI 139
                                       877763 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1
                           DUF2208  95 lllliviilffllyryiiplassllgev 122
                                       +++ ++i++  ++ ++i p+++  ++ +
  gi|488600454|ref|YP_007906925.1| 183 GASDVYILVKHVIPNAIAPIIVLATLDM 210
                                       4556788888888888888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1704.64
//
Query:       gi|488600455|ref|YP_007906926.1|  [L=312]
Description: ABC-type dipeptide/oligopeptide/nickel transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-40  136.8  15.3    6.6e-40  136.8  15.3    1.9  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        4.1    8.1   5.3       0.85   10.3   0.7    2.2  2  Renin_r       Renin receptor-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 ?   -1.3   0.0      0.17   1.5e+03     119     128 ..      16      25 ..       4      83 .. 0.63
   2 ?   -3.3   0.2      0.71   6.3e+03     103     118 ..      98     113 ..      93     115 .. 0.71
   3 !  136.8  15.3   7.4e-44   6.6e-40       2     185 .]     117     307 ..     116     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.17
                      BPD_transp_1 119 ggllggavll 128
                                       + +   ++l+
  gi|488600455|ref|YP_007906926.1|  16 IVASLLSFLI 25 
                                       1111111111 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.71
                      BPD_transp_1 103 lPnalppiitglilaf 118
                                       +P++l  i++++++a+
  gi|488600455|ref|YP_007906926.1|  98 FPASLQLIAASILIAV 113
                                       7777777777777765 PP

  == domain 3  score: 136.8 bits;  conditional E-value: 7.4e-44
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf........vilsilghlilpviillllsaapyvrl 70 
                                       i+lGil+al++n  +d++ r+l+ ++ s+P f+l++ll+l+f        ++  ++++ +lp+++l++ +a+ ++rl
  gi|488600455|ref|YP_007906926.1| 117 IPLGILSALKHNTAIDHICRILSLFGISMPNFWLGLLLILIFsvklrilpAFGYGAKNIVLPALTLGMSFAGTLTRL 193
                                       8*************************************************9999*********************** PP

                      BPD_transp_1  71 irraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailg 147
                                       +r + l++l ++++ +a+a+G++++ i+ +++l+na++p+it +++ +g++ +gav++e++++wpG+g+ ++++i +
  gi|488600455|ref|YP_007906926.1| 194 MRVSLLEVLHQQYIIVAKAKGLPEKLIITRHALKNAFIPVITAIGIYSGHAATGAVIVETIFAWPGVGSYFVSSIYA 270
                                       ***************************************************************************** PP

                      BPD_transp_1 148 ydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                       +dy+ i+ g vl ++++++l nl +d+++ +ldpr+r+
  gi|488600455|ref|YP_007906926.1| 271 RDYPVIQ-GFVLLVALFFILTNLTVDVIYLFLDPRIRY 307
                                       *******.****************************95 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3       1.2   1.1e+04      56      69 ..     147     160 ..     144     164 .. 0.74
   2 ?   10.3   0.7   9.5e-05      0.85      41      81 ..     263     303 ..     246     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                           Renin_r  56 niiLwlvvvlvlal 69 
                                       n +L+l ++l++++
  gi|488600455|ref|YP_007906926.1| 147 NFWLGLLLILIFSV 160
                                       67788888888776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.5e-05
                           Renin_r  41 lnlakkyssdYpaiFniiLwlvvvlvlaliaivvalasmdP 81 
                                       + +++ y  dYp+i   +L + ++++l+ +++ v  + +dP
  gi|488600455|ref|YP_007906926.1| 263 YFVSSIYARDYPVIQGFVLLVALFFILTNLTVDVIYLFLDP 303
                                       6788899*********************9999999888998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2287.86
//
Query:       gi|488600456|ref|YP_007906927.1|  [L=527]
Description: ABC-type dipeptide transport system, periplasmic component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-82  276.5   1.9    4.2e-82  276.1   1.9    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
       0.17   11.6   1.0       0.38   10.5   0.1    2.1  2  PAM2       Ataxin-2 C-terminal region


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 !  276.1   1.9   4.7e-86   4.2e-82       1     354 [.      87     428 ..      87     438 .. 0.88

  Alignments for each domain:
  == domain 1  score: 276.1 bits;  conditional E-value: 4.7e-86
                                       SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTE CS
                         SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddyt 77 
                                       +++p+LAes we+ d+gkt++f+L+kg+kFsDG++++A++v+f+++rl+  ++ + +  +      i++ve +d+yt
  gi|488600456|ref|YP_007906927.1|  87 KLIPQLAES-WEIKDNGKTIIFYLKKGIKFSDGSEFNADAVKFTIDRLKALKYYHWTEVDR-----IENVEIIDPYT 157
                                       689******.7********************************************998887.....*********** PP

                                       EEEEESSETT..TTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSS CS
                         SBP_bac_5  78 vrftlkkpna..lfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkl 152
                                       v ++ k+ ++    l  +a+++  i +++ ++ + + + +  +p+gtGP+k+ e++++q++v++ n++Y  g+kpkl
  gi|488600456|ref|YP_007906927.1| 158 VAIHYKEGQNgyIDLVAFAEFHLGIISPNSVEPKGNVTGKIVNPIGTGPWKVGEYVKNQYAVFVPNEYYH-GEKPKL 233
                                       ********8856244444444444444667888899*********************************8.****** PP

                                       SEEEEEE-.SHHHHHHHHHTTSSSEE.......ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHH CS
                         SBP_bac_5 153 driefkvipdsdaraaalqsGeiddv.......aepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkr 222
                                       +++++k+ipd+++r++al+sGeid +       ++ +p ++ +  +++g  + y+   + +t lafN ++ p d++ 
  gi|488600456|ref|YP_007906927.1| 234 EKLVVKIIPDAETRVLALRSGEIDAIvdhyhggSYYTPRNVLKSLQDEGFVI-YKNEIPMTTILAFNYENSPWDNEL 309
                                       ***********************99954333333333555555566666666.************************ PP

                                       HHHHHHHHS-HHHHHHHCTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEE CS
                         SBP_bac_5 223 vRqAlsyAiDreeivkavlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklk 298
                                       vR+A++yAi+r+ei + +  g  + a ++      p+ +e   ++  +y+pekAk+lLkeaGy+  +          
  gi|488600456|ref|YP_007906927.1| 310 VRKAVNYAINRDEISQLF-DGWVRGAEGAlYCDKAPYVKEVDIKY--EYNPEKAKELLKEAGYESIN---------- 373
                                       ***************999.99999999995666666665555554..79*****************9.......... PP

                                       EEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEE CS
                         SBP_bac_5 299 ltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillg 354
                                         l+l +++p+  ++aeliq+qlkk+Gi++e++++++   y+e++k+g++d+ +  
  gi|488600456|ref|YP_007906927.1| 374 AKLILRGENPDKVKLAELIQAQLKKVGINIEIEVLES-GPYKEKQKKGEYDLRFYY 428
                                       7899*********************************.*************97765 PP

>> PAM2  Ataxin-2 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.46   4.2e+03      12      16 ..     219     223 ..     218     223 .. 0.82
   2 ?   10.5   0.1   4.2e-05      0.38       6      16 ..     444     454 ..     443     456 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.46
                                       ----T CS
                              PAM2  12 EFVPs 16 
                                       +FVP+
  gi|488600456|ref|YP_007906927.1| 219 VFVPN 223
                                       7***6 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4.2e-05
                                       SSTTSS----T CS
                              PAM2   6 LNPnAkEFVPs 16 
                                       +NP+A+EF ++
  gi|488600456|ref|YP_007906927.1| 444 FNPDAPEFKYG 454
                                       8*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3200.79
//
Query:       gi|488600457|ref|YP_007906928.1|  [L=99]
Description: hypothetical protein Asulf_00930 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   15.0   0.0      0.026   14.9   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 ?   14.9   0.0   1.4e-06     0.026     132     170 ..       9      46 ..       2      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-06
                           DUF4198 132 vglglEivP.lthpydlkageelevqvlldGkPlagaeve 170
                                       +g ++Ei P + +p+  k+g+++++q+ ++Gk + g+   
  gi|488600457|ref|YP_007906928.1|   9 AGFEFEIMPeVLKPF--KSGDKMRIQLIFRGKSVNGVVKV 46 
                                       58899****889999..88****************75433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 747.12
//
Query:       gi|488600458|ref|YP_007906929.1|  [L=125]
Description: hypothetical protein Asulf_00931 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 867.49
//
Query:       gi|488600459|ref|YP_007906930.1|  [L=208]
Description: hypothetical protein Asulf_00932 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-28   97.8   0.0      1e-27   96.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    3.5e-26   91.7   0.0      9e-26   90.4   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    1.4e-24   86.7   0.1    1.9e-24   86.2   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
    9.3e-19   67.8   0.0    1.2e-18   67.5   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.4e-18   67.1   0.0    1.8e-18   66.7   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.9e-16   59.6   0.0    7.5e-16   58.7   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    1.8e-09   37.5   0.1    2.8e-09   36.8   0.1    1.2  1  MetW             Methionine biosynthesis protein MetW
    3.7e-09   36.4   0.2    1.2e-08   34.7   0.2    1.7  1  MTS              Methyltransferase small domain
    1.1e-08   35.0   0.0    1.5e-08   34.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    6.2e-08   32.3   0.1    7.8e-08   31.9   0.1    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    7.6e-08   32.2   0.0    9.9e-08   31.8   0.0    1.1  1  NodS             Nodulation protein S (NodS)
      2e-07   31.1   0.0    2.7e-07   30.7   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
    3.5e-07   29.9   0.0    4.4e-07   29.6   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    6.9e-07   28.9   0.0    9.6e-07   28.4   0.0    1.3  1  TehB             Tellurite resistance protein TehB
    2.5e-06   26.6   0.0    3.3e-06   26.3   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
    5.3e-06   26.3   0.0    1.1e-05   25.3   0.0    1.6  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    6.8e-06   25.3   0.0      1e-05   24.8   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
    9.5e-06   25.6   0.0    1.7e-05   24.8   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
    5.4e-05   23.0   0.1      0.001   18.8   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    0.00016   20.9   0.1    0.00019   20.6   0.1    1.1  1  DREV             DREV methyltransferase
     0.0012   18.1   0.2     0.0039   16.5   0.2    1.8  1  GidB             rRNA small subunit methyltransferase G
      0.004   17.5   0.3      0.019   15.3   0.1    2.1  2  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
     0.0069   16.2   0.0      0.043   13.7   0.0    2.0  1  Methyltransf_8   Hypothetical methyltransferase
     0.0091   15.5   0.7      0.032   13.7   0.1    2.2  2  Methyltransf_4   Putative methyltransferase
     0.0093   16.1   0.0      0.017   15.2   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.011   15.5   0.1       0.12   12.1   0.1    2.4  2  UPF0020          Putative RNA methylase family UPF0020
      0.011   15.5   0.1      0.014   15.1   0.1    1.3  1  Methyltransf_16  Lysine methyltransferase
      0.011   15.0   0.0      0.017   14.4   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
      0.043   13.6   0.0      0.075   12.8   0.0    1.3  1  DUF938           Protein of unknown function (DUF938)
      0.056   13.0   0.1       0.13   11.8   0.0    1.7  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.063   12.7   1.1       0.16   11.4   0.2    1.9  2  ComA             (2R)-phospho-3-sulfolactate synthase (ComA)
      0.082   13.2   0.0       0.19   12.1   0.0    1.7  1  Mur_ligase       Mur ligase family, catalytic domain
        0.2   12.0   3.3       0.22   11.9   0.8    2.2  2  Spore_SspJ       Small spore protein J (Spore_SspJ)


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 !   96.6   0.0   1.9e-30     1e-27       1      96 []      50     145 ..      50     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.9e-30
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvGcGtG ++  la+ g++vvg+Dls+ ml  a+eka+e+g+++ f   dae+l fedn+fD+v+ ++vl ++++p
  gi|488600459|ref|YP_007906930.1|  50 LDVGCGTGFVSLILAELGHEVVGIDLSEGMLSKAREKAEEKGHNILFKIDDAENLAFEDNTFDAVIERHVLWTLPNP 126
                                       8**************************************************************************** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                       eka+ke++RvL++gG+l++
  gi|488600459|ref|YP_007906930.1| 127 EKAIKEWVRVLRQGGKLIL 145
                                       ****************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   1.7e-28     9e-26       1      97 []      49     141 ..      49     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.7e-28
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd+GcGtG ++l la+ +  ++v+g+D+se+ml +are+aee+g n+ f   dae+l fed++fD+v+ +++l  l
  gi|488600459|ref|YP_007906930.1|  49 VLDVGCGTGFVSLILAELG--HEVVGIDLSEGMLSKAREKAEEKGHNILFKIDDAENLAFEDNTFDAVIERHVLWTL 123
                                       9***************995..*************************************************8666666 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +  + eka+ke+ rvL++gG
  gi|488600459|ref|YP_007906930.1| 124 P--NPEKAIKEWVRVLRQGG 141
                                       6..5669************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.1   3.5e-27   1.9e-24       3     119 ..      45     155 ..      43     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 3.5e-27
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       + ++vlD+GCGtG+ ++ la elg   evvGiD se ++++Are+a+++g  n+ F++ d+e+l   +ed++fD ++
  gi|488600459|ref|YP_007906930.1|  45 NRKKVLDVGCGTGFVSLILA-ELG--HEVVGIDLSEGMLSKAREKAEEKGH-NILFKIDDAENLA--FEDNTFDAVI 115
                                       5689****************.776..49*******************9999.8************..********** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedprllaelp 119
                                        + vl +l++p+k+++e  rvl++gg l++ +    +e  
  gi|488600459|ref|YP_007906930.1| 116 ERHVLWTLPNPEKAIKEWVRVLRQGGKLILIESENKEEKT 155
                                       *****************************99998333322 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   2.3e-21   1.2e-18       9     160 ..      35     188 ..      24     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.3e-21
                   Methyltransf_23   9 lsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepq 80 
                                       ++++l+++   l+ +++vLd+GcGtG ++ +l+e g++v+g+Dls+ + ++a+     k ++  ++  d+++ a+++
  gi|488600459|ref|YP_007906930.1|  35 VKEALKEM---LENRKKVLDVGCGTGFVSLILAELGHEVVGIDLSEGMLSKARekaeeKGHNILFKIDDAENLAFED 108
                                       34444444...689**************************************99999945555555555559999** PP

                   Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhi...sffsarslkel 154
                                       ++fd ++ r+vl ++p+p+++++   + l+ gG l+l e+ +  ke++ + +   + +a r++   + ++ r +k++
  gi|488600459|ref|YP_007906930.1| 109 NTFDAVIERHVLWTLPNPEKAIKEWVRVLRQGGKLILIESEN--KEEKTANHHYSEEIA-RKLpfgNGIDLRKFKKI 182
                                       ***************************************965..445555554445555.66644466777777777 PP

                   Methyltransf_23 155 leeaGl 160
                                       + + +l
  gi|488600459|ref|YP_007906930.1| 183 ADKCNL 188
                                       777766 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.0   3.3e-21   1.8e-18      46     171 ..      44     165 ..       9     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 3.3e-21
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                                        + +kvlDv +Gtg +++ l++      +vv++D++e mL+ +++k++e+g  ni f   +ae+L fed++fD v  
  gi|488600459|ref|YP_007906930.1|  44 ENRKKVLDVGCGTGFVSLILAELG---HEVVGIDLSEGMLSKAREKAEEKGH-NILFKIDDAENLAFEDNTFDAVIE 116
                                       23459**********999988764...589********************96.899********************* PP

                                       ES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH CS
                   Ubie_methyltran 123 sfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayelysk 171
                                        + l  +++ +ka+ke  rvl+ GG+l+ +e  + e ++ ++ y+    
  gi|488600459|ref|YP_007906930.1| 117 RHVLWTLPNPEKAIKEWVRVLRQGGKLILIESENKEEKTANHHYSEEIA 165
                                       *******************************999988888888866555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   1.4e-18   7.5e-16       1      99 []      50     143 ..      50     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.4e-18
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcGtG ++  l+e   + e++g+D+s+ ++ +a+ek  +++ n   +++  ++ ++ +d  ++fD+v+  +vl 
  gi|488600459|ref|YP_007906930.1|  50 LDVGCGTGFVSLILAEL--GHEVVGIDLSEGMLSKAREKAEEKGHNILFKIDDAENLAF-ED--NTFDAVIERHVLW 121
                                       8****************..**************88888888877655555555544443.33..5************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        l+++++++++  ++L++gG+l
  gi|488600459|ref|YP_007906930.1| 122 TLPNPEKAIKEWVRVLRQGGKL 143
                                       ********************97 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1   5.2e-12   2.8e-09       5     104 ..      37     139 ..      32     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 5.2e-12
                              MetW   5 eliaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvae....cvakGlsviqgdldkdlenfedksfd 77 
                                       e+++e+++++ +vld+GcG G +  +l+e  + +  G++l+e  + +    + +kG +++ +  d +   fed++fd
  gi|488600459|ref|YP_007906930.1|  37 EALKEMLENRKKVLDVGCGTGFVSLILAE-LGHEVVGIDLSEGMLSKarekAEEKGHNILFKIDDAENLAFEDNTFD 112
                                       56889****************98888865.9999999*99998876511115678999988877888889******* PP

                              MetW  78 yvvlsqtlqatrnpkevldellrigrr 104
                                        v+    l ++ np++ ++e +r+ r+
  gi|488600459|ref|YP_007906930.1| 113 AVIERHVLWTLPNPEKAIKEWVRVLRQ 139
                                       **********************99775 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.2   2.1e-11   1.2e-08      24     144 ..      40     152 ..      28     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.1e-11
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EE CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfd 99 
                                        e l+   ++kvlD+GcG+G++++ la+   e  v+ +d +   l  a+e +e++++++ +   d+ + ++e++ fd
  gi|488600459|ref|YP_007906930.1|  40 KEMLE--NRKKVLDVGCGTGFVSLILAELGHE--VVGIDLSEGMLSKAREKAEEKGHNILFKIDDAENlAFEDNTFD 112
                                       33344..4678*****************8887..9***********************9999999987356799*** PP

                                       EEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSC CS
                               MTS 100 livsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklg 144
                                       +++      ++   +l   e+ i+e  ++L++gG+L+++ +++ +
  gi|488600459|ref|YP_007906930.1| 113 AVIE-----RHVLWTLPNPEKAIKEWVRVLRQGGKLILIESENKE 152
                                       **96.....344445666788899999999999999999877665 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 !   34.6   0.0   2.8e-11   1.5e-08      67     172 ..      37     146 ..       9     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.8e-11
                                       HHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG- CS
                              PCMT  67 elle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeeka 141
                                       e l+  l++ ++vL+vG+G+G+ + +la+l  ++  vv+i+ ++ + ++a+++ ++++ +n+ +++ D ++   e  
  gi|488600459|ref|YP_007906930.1|  37 EALKemLENRKKVLDVGCGTGFVSLILAELG-HE--VVGIDLSEGMLSKAREKAEEKG-HNILFKIDDAENLAFEDN 109
                                       666667999*******************974.44..58***************99876.6999*****998888888 PP

                                       SEEEE...EE..SS.BBSS--HHHHHTEEEEEEEEEE CS
                              PCMT 142 PYdai...hv..ga.aapeiPealidQLkeGGrlvvP 172
                                        +da+   hv  +   +++  +++++ L +GG+l++ 
  gi|488600459|ref|YP_007906930.1| 110 TFDAVierHVlwTLpNPEKAIKEWVRVLRQGGKLILI 146
                                       89998333231122123345578***********983 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   1.4e-10   7.8e-08      48     203 ..      31     184 ..      16     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.4e-10
                                       HHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG- CS
                              CMAS  48 laKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl 124
                                        +K+     k  l++ +++Ld+GcG G +    +e  + +vvg+ lS+    +a+++ +e + +   +++ ++   +
  gi|488600459|ref|YP_007906930.1|  31 DKKVVKEALKEMLENRKKVLDVGCGTGFVSLILAEL-GHEVVGIDLSEGMLSKAREKAEEKGHNILFKIDDAENLAF 106
                                       556666666778999************999988877.*************************999999999999999 PP

                                       --.--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHHHHTSTTS.---BHH CS
                              CMAS 125 de.kvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglklkfidkeiFPgG.elpsie 199
                                       ++  +d+v+   ++      n ++ +k+  ++l+++G l+l     +++k+++ ++ + +  +k  F +G  l + +
  gi|488600459|ref|YP_007906930.1| 107 EDnTFDAVIERHVLW--TLPNPEKAIKEWVRVLRQGGKLILIESENKEEKTAN-HHYSEEIARKLPFGNGiDLRKFK 180
                                       8889***97766654..567888999************999887777776666.44454666666676663355555 PP

                                       HHHH CS
                              CMAS 200 eiee 203
                                       +i++
  gi|488600459|ref|YP_007906930.1| 181 KIAD 184
                                       5555 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   1.8e-10   9.9e-08      43     157 ..      45     158 ..      16     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.8e-10
                              NodS  43 siadalevGcaaGalterlapyckrltvvdvveeaiararervkessh.iswivsdvqqfst.dekfdlivvaevly 117
                                       +  ++l+vGc +G ++  la + + +  +d+ e  +++are+ +e+ h i + + d +++   d+ fd ++   vl+
  gi|488600459|ref|YP_007906930.1|  45 NRKKVLDVGCGTGFVSLILAELGHEVVGIDLSEGMLSKAREKAEEKGHnILFKIDDAENLAFeDNTFDAVIERHVLW 121
                                       34689**************************************9987648899999*999862678*********** PP

                              NodS 118 yiedvaelraavrnlvsllapdgqlvfGsardavcrrwGh 157
                                        + + +    a+++ v++l+ +g+l++  + ++  +   h
  gi|488600459|ref|YP_007906930.1| 122 TLPNPE---KAIKEWVRVLRQGGKLILIESENKEEKTANH 158
                                       999876...59***************98777766555555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0     5e-10   2.7e-07      11      78 ..      33      94 ..      29     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 5e-10
                   Methyltransf_32 11 elvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                                      ++v+++lke+   +++++v+DvG+G g+ s +la     ++++vvgid++e + +ka++ ae+ g+++
  gi|488600459|ref|YP_007906930.1| 33 KVVKEALKEM--LENRKKVLDVGCGTGFVSLILAE----LGHEVVGIDLSEGMLSKAREKAEEKGHNI 94
                                      5677777775..56679******************....7*********************9988655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   8.1e-10   4.4e-07     153     231 ..      37     115 ..      32     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8.1e-10
                              PrmA 153 ealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.keekad 228
                                       eal ++++++++vlDvG+G+G  ++  a Lg+ +vv++D+ e  ++ a+e ae  + +  +++  +e+l  +++++d
  gi|488600459|ref|YP_007906930.1|  37 EALKEMLENRKKVLDVGCGTGFVSLILAELGH-EVVGIDLSEGMLSKAREKAEEKGHNILFKIDDAENLAfEDNTFD 112
                                       68999**************************7.699***************99988888888765555443567888 PP

                              PrmA 229 viv 231
                                        ++
  gi|488600459|ref|YP_007906930.1| 113 AVI 115
                                       776 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.8e-09   9.6e-07      22     110 ..      35     125 ..       6     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.8e-09
                                       HHHHCCCS..-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-. CS
                              TehB  22 vveavkiv..kpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklder. 95 
                                       v+ea k +  +  kvld+gcg g  sl l+ lg++v  +d  e  ++  +e +e  + +ni  ++ d +++ ++++ 
  gi|488600459|ref|YP_007906930.1|  35 VKEALKEMleNRKKVLDVGCGTGFVSLILAELGHEVVGIDLSEGMLSKAREKAEE-KGHNILFKIDDAENLAFEDNt 110
                                       56666644224579****************************9999988776665.555699999999999996543 PP

                                       EEEEEEESSGGGS-G CS
                              TehB  96 ydfilstvvlmflea 110
                                       +d ++   vl  l +
  gi|488600459|ref|YP_007906930.1| 111 FDAVIERHVLWTLPN 125
                                       999999888877743 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 !   26.3   0.0     6e-09   3.3e-06     114     217 ..      43     145 ..      24     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6e-09
                                       -TT.-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---G...GGS-T.---EEE CS
                    Methyltransf_9 114 lkg.rtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgi...eqlpe.leafdt 185
                                       l++ +++ldvGcg+G+    +++e  + vvGid se  l +  a +k     ++ h++ + i   e+l    ++fd+
  gi|488600459|ref|YP_007906930.1|  43 LENrKKVLDVGCGTGFVSL-ILAELGHEVVGIDLSEGMLSK--AREKAE---EKGHNILFKIddaENLAFeDNTFDA 113
                                       344268*********9765.78899999********99875..444433...3334444555111555544689*** PP

                                       EEEES-GGG-S-HHHHHHHHHCTEEEEEEEEE CS
                    Methyltransf_9 186 vfsmGvlyhrrsPldhllqlkdqlvkgGelvl 217
                                       v    vl+    P   + +    l++gG+l+l
  gi|488600459|ref|YP_007906930.1| 114 VIERHVLWTLPNPEKAIKEWVRVLRQGGKLIL 145
                                       ******************************98 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0     2e-08   1.1e-05      28     150 ..      37     142 ..       8     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2e-08
                                       HHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--........... CS
                              TPMT  28 kfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsgvkeysageiellcg 104
                                       + l++  +++ ++vl  +CG +     lAe g+evvG++lse  ++k+ e+a++  k +++ +              
  gi|488600459|ref|YP_007906930.1|  37 EALKE-MLENRKKVLDVGCGTGFVSLILAELGHEVVGIDLSEGMLSKAREKAEE--KGHNILFKID----------- 99 
                                       33333.44556799999******************************7555544..3333333333........... PP

                                       -TTT---SS-..EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE CS
                              TPMT 105 dvFtlraeelgkfdliydraalvAlppelreryakslaelLkpdge 150
                                       d+ +l  e+  +fd++ +r +l  lp+  ++   k+  ++L+++g+
  gi|488600459|ref|YP_007906930.1| 100 DAENLAFEDN-TFDAVIERHVLWTLPNPEKA--IKEWVRVLRQGGK 142
                                       2222222232.35666666666666654433..4555566666666 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.9e-08     1e-05      13      80 ..      29      96 ..      22     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.9e-08
                                      E--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEE CS
                            RrnaAD 13 lknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkv 80
                                      +k+kkv++e+l+++ le+ ++vl++g G+G+ + +La+   +vv + l e ++   ++k + k++++  
  gi|488600459|ref|YP_007906930.1| 29 EKDKKVVKEALKEM-LENRKKVLDVGCGTGFVSLILAELGHEVVGIDLSEGMLSKAREKAEeKGHNILF 96
                                      79*********886.9******************************************99988888865 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   3.1e-08   1.7e-05       7      64 ..      38      93 ..      36     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.1e-08
                   Methyltransf_18  7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagle 64
                                      a+ +++e+ ++v+D+G+  g++++ l++ g  ++v+ +D++eg l+ka+e++e++g++
  gi|488600459|ref|YP_007906930.1| 38 ALKEMLENRKKVLDVGCGTGFVSLILAELG--HEVVGIDLSEGMLSKAREKAEEKGHN 93
                                      56789999******************9766..56*******************98874 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.9e-06     0.001     152     227 ..      11      81 ..       4      85 .. 0.80
   2 ?    2.3   0.0      0.21   1.1e+02      36      63 ..     127     154 ..     102     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                                       EE-SCCCTTSTTS-CHH..----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                       N6_N4_Mtase 152 Wdlseiqsnekkskgdt..kkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                       W   + +s+++++   +   +  + +k  + +++++k  +++ + vlD  +G+G    + +elg + +Gi+ +e  +
  gi|488600459|ref|YP_007906930.1|  11 W---DEHSENYEN---IpaHGI-KSEKDKKVVKEALKEMLENRKKVLDVGCGTGFVSLILAELGHEVVGIDLSEGML 80 
                                       4...333333333...332333.8999**********************************************9876 PP

                                       H CS
                       N6_N4_Mtase 227 e 227
                                        
  gi|488600459|ref|YP_007906930.1|  81 S 81 
                                       5 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHEEEEEEEEEEE-CCCHHT CS
                       N6_N4_Mtase  36 ekvlkevrrvLkddgsifiniddseikk 63 
                                       ek +ke+ rvL ++g +++  ++++ +k
  gi|488600459|ref|YP_007906930.1| 127 EKAIKEWVRVLRQGGKLILIESENKEEK 154
                                       6789999999999998877756655555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   3.6e-07   0.00019      94     186 ..      45     145 ..      28     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-07
                              DREV  94 edkklldlGaGdGeitkrvaptfeevyatelsetm....rdrlkkkkynvlsale....lqetdvkldlilclnlld 162
                                       + kk+ld+G G G ++ ++a+  +ev   +lse m    r++ + k++n+l +++    l+  d  +d +    +l 
  gi|488600459|ref|YP_007906930.1|  45 NRKKVLDVGCGTGFVSLILAELGHEVVGIDLSEGMlskaREKAEEKGHNILFKIDdaenLAFEDNTFDAVIERHVLW 121
                                       6799****************************988333355677899****99984212333466788888888888 PP

                              DREV 163 rcfdplklledirsalepngrviv 186
                                          +p k +++   +l+  g+ i+
  gi|488600459|ref|YP_007906930.1| 122 TLPNPEKAIKEWVRVLRQGGKLIL 145
                                       888888888888888888888775 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   7.3e-06    0.0039      43     160 ..      41     159 ..      34     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.3e-06
                                       GCS-CCC-.EEEETSTTTTTHHHHHHH-TTSE.EEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EE CS
                              GidB  43 ellkekrdkviDvGsGaGlPGipLaiarpelk.ltLleslekkiaFLeevkeelklenveivearaee.kqeeekyd 117
                                       e+l++ + kv+DvG G G+ +++La +  e+  + L e    k++     k+e k +n+ +  ++ae+   e +++d
  gi|488600459|ref|YP_007906930.1|  41 EMLENRK-KVLDVGCGTGFVSLILAELGHEVVgIDLSEGMLSKAR----EKAEEKGHNILFKIDDAENlAFEDNTFD 112
                                       4455555.8****************99888776888888777764....2334445567777888998777888999 PP

                                       EEEEC-S....SSHHHHHHHHCCCEEEEEEEEEEESS--HHHHHCCH CS
                              GidB 118 vvtsRAl....aslnelteillkllkegglilalKGksaedeleeke 160
                                       +v+ R +     + ++ ++   ++l++gg+++++  +++e+  ++++
  gi|488600459|ref|YP_007906930.1| 113 AVIERHVlwtlPNPEKAIKEWVRVLRQGGKLILIESENKEEKTANHH 159
                                       99999762222333444433344589999999998888877766655 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.5e-05     0.019      57      89 ..      44      76 ..      32      89 .. 0.86
   2 ?   -1.3   0.0       4.9   2.7e+03      83      93 ..     171     181 ..     167     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-05
                      AdoMet_MTase 57 eketsfvdvgcgngllvyvlaaegykgygidlr 89
                                      e+++   dvgcg g++  +la  g++  gidl 
  gi|488600459|ref|YP_007906930.1| 44 ENRKKVLDVGCGTGFVSLILAELGHEVVGIDLS 76
                                      4667789************************86 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.9
                      AdoMet_MTase  83 gygidlrkrkl 93 
                                       g gidlrk k 
  gi|488600459|ref|YP_007906930.1| 171 GNGIDLRKFKK 181
                                       78999999775 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   7.9e-05     0.043      71     163 ..      44     152 ..      29     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.9e-05
                                       -TTS-EEEES-TT-HHHHH--S.-..EEEEESS......-...SSTT.....EEES-TTS-S--TT-EEEEEEES-- CS
                    Methyltransf_8  71 kdnlvvadlGcGeakiaeavre.kekvrsfdlv......a...vner.....vvacdlakvPledesvdvavfclsl 132
                                       ++ + v d+GcG   ++    e  ++v  +dl       a    +e+         d  ++  ed++ d ++    l
  gi|488600459|ref|YP_007906930.1|  44 ENRKKVLDVGCGTGFVSLILAElGHEVVGIDLSegmlskArekAEEKghnilFKIDDAENLAFEDNTFDAVIERHVL 120
                                       556678888888887775544414678888875222221111111111111112346799*********99988777 PP

                                       -S.S-HHHHHHHHHHHEEEEEEEEEEEEGGG- CS
                    Methyltransf_8 133 mg.tnladflkeanrvlkvGGllkvaevksrf 163
                                        +  n ++ +ke  rvl++GG l + e + + 
  gi|488600459|ref|YP_007906930.1| 121 WTlPNPEKAIKEWVRVLRQGGKLILIESENKE 152
                                       6526999****************998876654 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       4.9   2.7e+03     131     165 ..      15      36 ..       2      42 .. 0.46
   2 !   13.7   0.1   5.9e-05     0.032       2      76 ..      46     114 ..      45     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.9
                                       HCSTTEEESSCCCSCCTCHCHHCCCSSTTCCCCCC CS
                    Methyltransf_4 131 eeeplferlskeeeleeeplsvlriatkyeqkvqs 165
                                       +e+  +e++             + i ++ ++kv++
  gi|488600459|ref|YP_007906930.1|  15 SEN--YENIPA-----------HGIKSEKDKKVVK 36 
                                       333..444444...........4444444444433 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.9e-05
                                       -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEE CS
                    Methyltransf_4   2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgsleki 76 
                                       ++ vl++GcG G + + lA+     +++Gi++++ ++ k+ +k+e++  +N++    da + l  ++ed++++ +
  gi|488600459|ref|YP_007906930.1|  46 RKKVLDVGCGTGFVSLILAELG--HEVVGIDLSEGMLSKAREKAEEK-GHNILFKIDDA-ENL--AFEDNTFDAV 114
                                       6779********9998888775..679**************999876.58999999999.666..6777777665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.1e-05     0.017      18      71 ..      42      95 ..      29     123 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                                      -S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHHTTEEEECS-CC CS
                              FtsJ 18 lfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...aplpgvttiqgdit 71
                                      ++++ k+v+D+g+++G  s  +l +lg  + vv++Dl ++   + +++ +    +i+
  gi|488600459|ref|YP_007906930.1| 42 MLENRKKVLDVGCGTGFVS-LILAELG--HEVVGIDLSEGmlsKAREKAEEKGHNIL 95
                                      5678899********9555.5555556..79******88867744455555555553 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00022      0.12      78     126 ..      69     115 ..       8     117 .. 0.86
   2 ?    0.9   0.0      0.56     3e+02     150     175 ..     131     156 ..     127     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                       -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEE CS
                           UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdviv 126
                                       +++g+Dl + ++ +are+ae+ g + l ++ +a++ +++  ++ +d+++
  gi|488600459|ref|YP_007906930.1|  69 EVVGIDLSEGMLSKAREKAEEKGHNILFKIDDAENLAFE--DNTFDAVI 115
                                       589*****************9877666666665555555..55799987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                                       HHHHHH-TT..-EEEEEESSHHHHHC CS
                           UPF0020 150 relkrvlrgggrlvlltsenkaleka 175
                                       +e  rvlr+gg+l+l+ senk+ ++a
  gi|488600459|ref|YP_007906930.1| 131 KEWVRVLRQGGKLILIESENKEEKTA 156
                                       677899***99999999999876555 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.7e-05     0.014      40      94 ..      39      92 ..      25     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                   Methyltransf_16 40 lganelsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnkn 94
                                      l++   ++++vl++G GtG v l++ael  + +v+  Dl+e +l   ++  e  ++
  gi|488600459|ref|YP_007906930.1| 39 LKEMLENRKKVLDVGCGTGFVSLILAEL--GHEVVGIDLSEgMLSKAREKAEEKGH 92
                                      455566889*******************..77777778776555555555554343 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.2e-05     0.017      48     177 ..      32     158 ..       9     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS-----TTEEEEES-TTTS CS
                    Methyltransf_2  48 slvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsageeervefvgGdffkd 123
                                       + v+k++l+++ le+ k+++DvG GtG +    +++  + +v+  Dl+e   ++A+e+   ++ +++ f   d  + 
  gi|488600459|ref|YP_007906930.1|  32 KKVVKEALKEM-LENRKKVLDVGCGTGFVSLILAEL--GHEVVGIDLSEgMLSKAREK-AEEKGHNILFKIDDAENL 104
                                       44566666654.9999***********765555554..56888899987467899999.555556777776666544 PP

                                       ---..--SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---H CS
                    Methyltransf_2 124 slP..eaDaillkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadpsgel 177
                                       +    + Da++  +vl  w+  +  k +k+  + l++gGk+i++e+  +++++++ 
  gi|488600459|ref|YP_007906930.1| 105 AFEdnTFDAVIERHVL--WTLPNPEKAIKEWVRVLRQGGKLILIESENKEEKTANH 158
                                       44433679*******9..788888999******************98776665544 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.075       7      44 ..      28      64 ..      24      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                            DUF938  7 aernrepilevLksylakttervLEiasGtGqHAvffA 44
                                      +e+ ++ + e+Lk++l+++++ vL+++ GtG     +A
  gi|488600459|ref|YP_007906930.1| 28 SEKDKKVVKEALKEMLENRKK-VLDVGCGTGFVSLILA 64
                                      68999***************6.*********7666655 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   0.00024      0.13       7      67 ..      55     107 ..      47     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                                       --STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEE CS
                    UDPG_MGDP_dh_N   7 GlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsft 67 
                                       G+G+v    +++lae+ghev+g+D +e   +k +++    +e+g + l k    +++l f+
  gi|488600459|ref|YP_007906930.1|  55 GTGFV----SLILAELGHEVVGIDLSEGMLSKAREK---AEEKGHNILFKIDD-AENLAFE 107
                                       55555....5679*************9877766654...34555444443333.5555555 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.2   6.5e+02     124     159 ..      17      54 ..      12      65 .. 0.69
   2 ?   11.4   0.2    0.0003      0.16     106     185 ..      73     159 ..      59     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                                       TSEEEEEES-SSHHHHTT..--CCHHHHHHHHHHHHTE CS
                              ComA 124 glkvlpevgkkdgelese..sdveklieeakrdleaGa 159
                                       + + +p  g+k+++ ++   + +++++e+ k+ l+ G+
  gi|488600459|ref|YP_007906930.1|  17 NYENIPAHGIKSEKDKKVvkEALKEMLENRKKVLDVGC 54 
                                       55667777777773333255778888888888887775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0003
                                       S---HHHHHHHHHHHCCTTSEEEEEES-SSH............HHHTT...--CCHHHHHHHHHHHHTECEEEE--T CS
                              ComA 106 lelpeeeklrliekakkeglkvlpevgkkdg............elese...sdveklieeakrdleaGaekviiEar 167
                                       ++l+e    ++ eka+++g ++l+++   ++            e++      ++ek i+e  r l++G + ++iE++
  gi|488600459|ref|YP_007906930.1|  73 IDLSEGMLSKAREKAEEKGHNILFKIDDAENlafedntfdaviERHVLwtlPNPEKAIKEWVRVLRQGGKLILIESE 149
                                       6888999999999999999999999999888888888888776333336669************************* PP

                                       TT--SSTTB-TTS-B-HH CS
                              ComA 168 esGitegvydekgevrtd 185
                                       +  + e+        + +
  gi|488600459|ref|YP_007906930.1| 150 N--KEEKT------ANHH 159
                                       4..43333......3333 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00034      0.19      15      52 ..      59     114 ..      49     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00034
                                       HHHHHHHTTSEEEEEESSHC........HHHTT-EEEE.S-HGGGG.........E CS
                        Mur_ligase  15 galflalkGykvdGsdfies........lialGaaavv.ghdaani.........v 52 
                                       ++l+la  G++v G d+ e         ++++G ++++  +da+n+         v
  gi|488600459|ref|YP_007906930.1|  59 VSLILAELGHEVVGIDLSEGmlskarekAEEKGHNILFkIDDAENLafedntfdaV 114
                                       689******************************88866155666544444444443 PP

>> Spore_SspJ  Small spore protein J (Spore_SspJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8    0.0004      0.22       9      25 ..      25      41 ..      23      47 .. 0.89
   2 ?   -0.8   0.1       3.7     2e+03       5      18 ..      81      94 ..      78     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0004
                        Spore_SspJ  9 gkksEKdknavdgaLEd 25
                                      g ksEKdk++v+ aL +
  gi|488600459|ref|YP_007906930.1| 25 GIKSEKDKKVVKEALKE 41
                                      77************987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.7
                        Spore_SspJ  5 nKDkgkksEKdkna 18
                                       K + k  EK +n 
  gi|488600459|ref|YP_007906930.1| 81 SKAREKAEEKGHNI 94
                                      57788888999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      796  (0.0443973); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1284.46
//
Query:       gi|488600460|ref|YP_007906931.1|  [L=109]
Description: nitrogen regulatory protein P-II family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-39  132.9   2.3    6.2e-39  132.7   2.3    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 !  132.7   2.3   3.5e-43   6.2e-39       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 3.5e-43
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       +eaiirpekle vk++Le++gv g+tvtev+GrG+qkg +  +rg+e++v+llpkvk+eivv+d  v++v++ai+++
  gi|488600460|ref|YP_007906931.1|   4 VEAIIRPEKLECVKKVLEDIGVAGMTVTEVRGRGEQKGIKLQFRGREMHVDLLPKVKMEIVVDDGMVDRVIDAIVES 80 
                                       79*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tg++GDGkiFv+pve+ +r+rtg
  gi|488600460|ref|YP_007906931.1|  81 ARTGNPGDGKIFVIPVESSTRVRTG 105
                                       ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 783.24
//
Query:       gi|488600461|ref|YP_007906932.1|  [L=462]
Description: ammonium transporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-134  448.0  39.8   2.7e-134  447.8  39.8    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.8  39.8  1.5e-138  2.7e-134       1     399 []      39     446 ..      39     446 .. 0.97

  Alignments for each domain:
  == domain 1  score: 447.8 bits;  conditional E-value: 1.5e-138
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-TTTTSCCG CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfignlglsaagv 77 
                                       ++ l++ +lv+fmqagfa+leag +r+knv n+++knl+d+av++++++++G++l++g++  ++g+ig+ g+++ag 
  gi|488600461|ref|YP_007906932.1|  39 VWTLICGFLVMFMQAGFAMLEAGFSRAKNVANVMMKNLMDFAVGTIAFFAIGFALMMGTD--LGGIIGTDGWFLAGN 113
                                       79*********************************************************9..*******88877777 PP

                                       CCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--....... CS
                   Ammonium_transp  78 qdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvl....... 147
                                         +  +  + ++f+l+faata+tivsga+aer kfs+y+++s++++ ++yp+++hw wg ggwl++  ++       
  gi|488600461|ref|YP_007906932.1| 114 AYDVSTIEI-WFFMLVFAATAATIVSGAIAERPKFSTYIIYSVIVSAIIYPVYGHWLWG-GGWLSTSDFMiklgvgy 188
                                       666665565.*************************************************.***************** PP

                                       ...-SSSTTTTHHHHHHHHHHHHHHHS-STTTTG.TTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH CS
                   Ammonium_transp 148 ..iDfAgstvVHlvggvagLaaalvlgkregrfe.gkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrara 221
                                          DfAgs+vVH++gg+++La+ +++g+r+g++  gk++ai+gh++ fav+Gtl+LwfgWfgFN+Gs+l+a++ + +
  gi|488600461|ref|YP_007906932.1| 189 gaLDFAGSGVVHALGGYIALAGCILIGPRIGKYVnGKPKAIPGHSMAFAVIGTLILWFGWFGFNPGSTLSAHELRIS 265
                                       **********************************9****************************************** PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Ammonium_transp 222 raavtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkek 298
                                       ++a +T+lAaaaga+ta+li++ k gk++v  ++nG+++GlVAiTa ca+v pw+A++iG+vAg++s +g+ ++ e+
  gi|488600461|ref|YP_007906932.1| 266 VIAANTNLAAAAGAVTAMLITWKKMGKPDVGITCNGAIGGLVAITAPCAWVAPWAAVLIGVVAGFISSYGY-WWLER 341
                                       ***********************************************************************.8**** PP

                                       HTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHC....SSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Ammonium_transp 299 lkidDsldvvavHgvgGiwGllavgifaaekvv....askisggllsgegkqlvvqligilvilayafvvtlillll 371
                                        +idD++++v+vHg+ G+wGl+a g+fa+  +     ++ i +gll+g+   +  q+i ++v +a+af++++ l+++
  gi|488600461|ref|YP_007906932.1| 342 RGIDDVVGAVPVHGFNGTWGLIALGLFADGTYGvyttEAPIVTGLLYGNAGFFACQMISAIVNFAWAFGTGFALFYI 418
                                       ******************************99899999999************************************ PP

                                       HHHHTTSB--HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 372 lklllgLrvseeeeevglDvaehgetay 399
                                       lk+++g+rv++eee +glD+aeh++  y
  gi|488600461|ref|YP_007906932.1| 419 LKKTVGIRVKPEEEILGLDIAEHAAISY 446
                                       ***********************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 2460.14
//
Query:       gi|488600462|ref|YP_007906933.1|  [L=188]
Description: adenosylcobinamide hydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-39  135.3   0.0    3.7e-39  134.8   0.0    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 !  134.8   0.0   2.1e-43   3.7e-39      10     192 .]      23     181 ..      16     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 2.1e-43
                              CbiZ  10 ssavlngGlrelravlnhqvpegyeredpeeyleeyleelglppektvgllTaadmenaaiaeeefedlevtavvTa 86 
                                       s+  l gG++++r+++nh+v ++++  dp +yl+++++ lg+  ++  gllT++ m+++++++++    evt++vTa
  gi|488600462|ref|YP_007906933.1|  23 STG-LLGGWKKVRYAFNHTVGDDFDYVDPVKYLRDVARGLGV--KSYFGLLTSVPMDKLSVQSCG----EVTVFVTA 92 
                                       566.55********************************9999..8********************....******** PP

                              CbiZ  87 GvesnavragdedeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsrysegatGTgTDaiavaa 163
                                       Gv +n+            +GTINii +++ + + +a+++a+it+tEAK++al+++g +      +tGT TDa++v++
  gi|488600462|ref|YP_007906933.1|  93 GV-RNPNE---------LIGTINIIAILDCRVSRSAMLNAIITVTEAKSKALLEMGHN------FTGTNTDAVIVLT 153
                                       **.77755.........58**************************************8......************* PP

                              CbiZ 164 dkegeeeltyaGkhtklGeliaraVyeAv 192
                                       +++g+  ++yaG++++lG+ + +aV  Av
  gi|488600462|ref|YP_007906933.1| 154 TERGRY-YRYAGPASDLGARLWEAVCGAV 181
                                       *99995.******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1146.73
//
Query:       gi|488600463|ref|YP_007906934.1|  [L=406]
Description: ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-31  107.1   0.0    4.1e-30  105.1   0.0    2.0  2  ABC_tran      ABC transporter
    1.6e-12   47.8   0.7      2e-05   24.6   0.1    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      8e-09   35.3   0.7    1.1e-07   31.6   0.3    2.4  1  SMC_N         RecF/RecN/SMC N terminal domain
    7.1e-05   22.5   0.0    0.00026   20.7   0.0    1.9  1  AAA_29        P-loop containing region of AAA domain
    0.00048   20.7   0.0     0.0013   19.3   0.0    1.6  1  AAA_23        AAA domain
     0.0031   17.9   0.0     0.0051   17.2   0.0    1.5  1  AAA_16        AAA ATPase domain
     0.0049   16.3   0.0      0.011   15.1   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0063   16.4   0.4      0.065   13.1   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
     0.0076   16.0   0.2       0.19   11.4   0.0    2.3  2  AAA_15        AAA ATPase domain
      0.008   15.8   0.0      0.017   14.7   0.0    1.5  1  AAA_27        AAA domain
  ------ inclusion threshold ------
      0.024   13.8   0.0      0.071   12.3   0.0    1.7  2  NB-ARC        NB-ARC domain
      0.039   13.9   0.0      0.097   12.6   0.0    1.7  2  NACHT         NACHT domain
      0.041   14.1   0.1       0.69   10.2   0.1    2.5  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.045   13.8   0.1       0.15   12.2   0.1    2.0  1  MMR_HSR1      50S ribosome-binding GTPase
      0.084   12.8   1.0       0.32   10.9   0.0    2.2  2  NTPase_1      NTPase
      0.091   13.0   0.0       0.26   11.6   0.0    1.7  1  AAA_22        AAA domain
       0.14   12.3   0.0       0.52   10.5   0.0    2.0  2  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.0   3.9e-33   4.1e-30       1     137 []      18     164 ..      18     164 .. 0.90
   2 ?   -0.6   0.0       1.7   1.7e+03      21      67 ..     267     329 ..     252     400 .. 0.63

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 3.9e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++++++++    va++G+nG+GKStLl+++ g l+p  G +lldg+++k+  + s++k++g+lpqe +   +l+v 
  gi|488600463|ref|YP_007906934.1|  18 LRDMTFEVSDHDFVALLGPNGSGKSTLLRTIFGILRPVRGVVLLDGRKIKT--IDSASKRMGFLPQE-TPETGLSVL 91 
                                       6899***********************************************..99************.888888899 PP

                                       HH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +               +s+++i+ al+ l+ ++++d  +++s  +LSgG+kq+v+lar+++++p+++llDEpta
  gi|488600463|ref|YP_007906934.1|  92 DIvllgrtpylsgikrASSVDINIALNALKEVGMED-FAQRSFLELSGGEKQKVMLARVFAQQPQIMLLDEPTA 164
                                       98999********99988888777766666666333.334666*****************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                       TSSHHHHHHHHTTSS--SEEEE................EETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  21 GaGKStLlkllagllkpteGei................lldgkdlkeqeleslrkeigvlpqe 67 
                                       G+GK  L  l    ++  +G i                 +d+++++ +++es ++++++++  
  gi|488600463|ref|YP_007906934.1| 267 GSGKDLLHILSEAGYRISAGVInaldsdweliteiggeSIDEAPFTPISEESHEQNLKMIENV 329
                                       666654444444445555555555555555555444444555555556666666666666554 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 !   24.6   0.1   1.9e-08     2e-05       1      51 [.      30      77 ..      30      85 .. 0.78
   2 !   21.3   0.0   1.8e-07   0.00019     220     288 ..     119     184 ..     102     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.9e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldl 51
                                      + +l GpNgsGKS+LL+++ ++   +r v+g    ++++ ++++ +s+  +
  gi|488600463|ref|YP_007906934.1| 30 FVALLGPNGSGKSTLLRTIFGI---LRPVRGVVLLDGRKIKTIDSASKRMG 77
                                      679****************999...77777777777777777776666555 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.8e-07
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrn 288
                                        +  + ++d  ++++ elS G k+   +l+ ++++ +   + l+DEp ++L+ +++ +++e+++e+ ++
  gi|488600463|ref|YP_007906934.1| 119 ALKEVGMEDFAQRSFLELSGGEKQK-VMLARVFAQQP--QIMLLDEPTAHLDISAQIEIMEIVREKVKE 184
                                       5556678888999999*********.67777776665..9***********************887664 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.3     1e-10   1.1e-07      23     189 ..      27     184 ..      18     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1e-10
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEE..EETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitf..dnedkklkiekeev 97 
                                       ++ f a++GpNGSGKs ll  i   +G      lr  +   l+   ++ + +++a+  + f  +++ ++     + v
  gi|488600463|ref|YP_007906934.1|  27 DHDFVALLGPNGSGKSTLLRTI---FG-----ILRPVRGVVLLDG-RKIKTIDSASKRMGFlpQETPETGLSVLDIV 94 
                                       57899*****************...89.....4899999999998.999**********996544444444555667 PP

                                       EEEEEEETTSE...EEEEETTEEE-HHHH.HHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxx...xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkge...seykingkevtkkev.sellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                        + r+ + +g    s++ in      kev +e +++  +   +LSgGek+ v+la +fA q      ++llDe  a+
  gi|488600463|ref|YP_007906934.1|  95 LLGRTPYLSGIkraSSVDINIALNALKEVgMEDFAQRSFL--ELSGGEKQKVMLARVFAQQ----PQIMLLDEPTAH 165
                                       7788877766544577777777766666633445555554..6***************965....3589******** PP

                                       S-HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkekskn 189
                                       LD +   ++ e+++ek k+
  gi|488600463|ref|YP_007906934.1| 166 LDISAQIEIMEIVREKVKE 184
                                       **************99876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.4e-07   0.00026      15      48 ..      21      54 ..      15      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-07
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                       t+e++ ++++ l Gp+GsGKSTll  i  +L p
  gi|488600463|ref|YP_007906934.1| 21 MTFEVSDHDFVALLGPNGSGKSTLLRTIFGILRP 54
                                      5677777779**************9777666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06    0.0013      14      42 ..      22      51 ..      13      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                            AAA_23 14 eidF.skgltlItGpNGaGKTTildAikla 42
                                      +++  ++ ++++ GpNG+GK+T+l+ i  +
  gi|488600463|ref|YP_007906934.1| 22 TFEVsDHDFVALLGPNGSGKSTLLRTIFGI 51
                                      5566678999**************998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.8e-06    0.0051      25      59 ..      29      64 ..      16     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggif.lrgk 59
                                        v l G+ G+GKs+l+r+++  l+  +g++ l g+
  gi|488600463|ref|YP_007906934.1| 29 DFVALLGPNGSGKSTLLRTIFGILRPVRGVVlLDGR 64
                                      4699*****************766666655535554 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     1e-05     0.011      24      70 ..      30      76 ..      12     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeee 70
                                       + l+Gp GsGK+ l + + ++l p+     l+ +ki+++ +++++ 
  gi|488600463|ref|YP_007906934.1| 30 FVALLGPNGSGKSTLLRTIFGILRPVRGVVLLDGRKIKTIDSASKRM 76
                                      35799*******************************99998854443 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   6.1e-05     0.065      83     120 ..      11      49 ..       2      71 .. 0.83
   2 ?    1.1   0.1       0.3   3.2e+02      14      97 ..     327     405 ..     314     406 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-05
                                       -TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  83 saktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       +  ++e l++++ +++d ++++l+G+ G GKStL+ ++ 
  gi|488600463|ref|YP_007906934.1|  11 RLGSSEVLRDMTFEVSDhDFVALLGPNGSGKSTLLRTIF 49 
                                       45566788888889988899***************9986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.3
                                       ES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  14 aNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegl 90 
                                        Nvd ++  +s    ++     + +L+   ++++  +iv+n++   +++ + ++ +e ++++  + ++v+++ +e l
  gi|488600463|ref|YP_007906934.1| 327 ENVDAVV--LSN--LSFGWGNFKNLLASEYAAKLGKLIVVNRTPFKSRNFTDSKAEEIYSRILEKAVVVNSE-EEVL 398
                                       5666543..232..25778888888999999999999999*9999999998888899999997777777666.7788 PP

                                       HHHHHHC CS
                       RsgA_GTPase  91 eelkell 97 
                                       ++l++ll
  gi|488600463|ref|YP_007906934.1| 399 DALRKLL 405
                                       8887765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00018      0.19      18      43 ..      22      48 ..      17      74 .. 0.83
   2 ?    2.2   0.1      0.11   1.2e+02     322     353 ..     152     183 ..     142     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsileal 43
                                      + ++s+  +  l G+N+sGKS++l+ +
  gi|488600463|ref|YP_007906934.1| 22 TFEVSDHdFVALLGPNGSGKSTLLRTI 48
                                      5555555699**************987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelan 353
                                       +++ i l++EP ahL ++aq ++++  +e ++
  gi|488600463|ref|YP_007906934.1| 152 QQPQIMLLDEPTAHLDISAQIEIMEIVREKVK 183
                                       5689******************9999887665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.6e-05     0.017      18      47 ..      20      49 ..      17      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAis 47
                                       ++f+ +++d+  ++GpN +GKst+lr i 
  gi|488600463|ref|YP_007906934.1| 20 DMTFEVSDHDFVALLGPNGSGKSTLLRTIF 49
                                      6889999*******************9985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05     0.071      16      41 ..      26      49 ..      15      58 .. 0.82
   2 ?   -2.3   0.0       1.8   1.9e+03      90     143 ..     140     197 ..     119     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                                      TTSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 16 delqslvvalvGmgGvGKttlakqil 41
                                       +   ++val G  G+GK+tl++ i+
  gi|488600463|ref|YP_007906934.1| 26 SDH--DFVALLGPNGSGKSTLLRTIF 49
                                      444..5*****************998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                                       TSHHHHHHHHCCCTTEEEEEEEE-SHHH....H.....HHHHCHTTSEEEEEESBCCC CS
                            NB-ARC  90 eslkrklvrlLltkrfllvlDDVweeed....wdkigvvlparenrlrvllTTRdeev 143
                                       e+ k +l r+  ++  +++lD    + d     + + +v+   +++++ ll   d ++
  gi|488600463|ref|YP_007906934.1| 140 EKQKVMLARVFAQQPQIMLLDEPTAHLDisaqIEIMEIVREKVKEGCSALLAIHDINL 197
                                       4467788888888888888885444433333344466666666666666666655555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.2e-05     0.097       2      21 ..      30      49 ..      29      54 .. 0.88
   2 ?   -3.1   0.0       6.2   6.5e+03      95     129 ..     164     194 ..     148     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-05
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                       v+l G++GsGK+tLl+ + 
  gi|488600463|ref|YP_007906934.1| 30 FVALLGPNGSGKSTLLRTIF 49
                                      5899*************996 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.2
                                       S-TCH.........HHHHHCTTTTT--EEEEEEEC CS
                             NACHT  95 tdlgqkekqpvrtlLselirkkllpeasllltvrp 129
                                       ++l+     +++  + e++r+k+  ++s ll+++ 
  gi|488600463|ref|YP_007906934.1| 164 AHLDI----SAQIEIMEIVREKVKEGCSALLAIHD 194
                                       44444....66777888888888888888887765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00066      0.69      21      88 ..     124     178 ..     108     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00066
                           SbcCD_C  21 gkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       g e   +rs+ +lSGGekq+++   ++        +      ++++++LDE  + lD   + +++e++
  gi|488600463|ref|YP_007906934.1| 124 GMEDFAQRSFLELSGGEKQKVMLARVF-------AQ------QPQIMLLDEPTAHLDISAQIEIMEIV 178
                                       555557899999******887754444.......34......47788888888888888777777766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.15       2      40 ..      31      75 ..      30     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      EEEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegr 40
                                      va++G   +GKStL+++++g     + ++    ++ +T+d   +r
  gi|488600463|ref|YP_007906934.1| 31 VALLGPNGSGKSTLLRTIFGilrpvRgVVLLDGRKIKTIDSASKR 75
                                      89****************985544422455566666666655555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0003      0.32       2      47 ..      31      78 ..      30      87 .. 0.80
   2 ?   -0.4   0.1      0.91   9.6e+02      94     153 ..     152     214 ..     136     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                                      EEEE--TTSSHHHHHHHHHHHH....G.GGEEEEEEEEE-------EE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss.g.vkvgGfyteevreggrrigF 47
                                      v++ Gp G+GK+Tl++ +   l+   g v ++G   + + +  +r+gF
  gi|488600463|ref|YP_007906934.1| 31 VALLGPNGSGKSTLLRTIFGILRPVrGvVLLDGRKIKTIDSASKRMGF 78
                                      5678******************74324145678888888888999998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.91
                                       HHH-EEEE--.-STTGGG-H.HHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEE CS
                          NTPase_1  94 seadviviDE.iGkmElksk.kfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvf 153
                                       ++++++++DE    +  +++ ++ e v+e +k++   l  ih  +   ++  +i   k++k++
  gi|488600463|ref|YP_007906934.1| 152 QQPQIMLLDEpTAHLDISAQiEIMEIVREKVKEGCSALLAIHDINlAASFASRILMVKKGKII 214
                                       566677777733456665554577888899998888888888887777888888888877775 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   0.00024      0.26       5      26 ..      28      49 ..      24      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                            AAA_22  5 agilvvtGesGtGKTtllrrll 26
                                      + ++++ G+ G+GK+tllr+++
  gi|488600463|ref|YP_007906934.1| 28 HDFVALLGPNGSGKSTLLRTIF 49
                                      67899**************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00049      0.52       2      21 ..      31      50 ..      30      85 .. 0.82
   2 ?   -3.0   0.0       6.8   7.2e+03      15      35 ..     146     166 ..     143     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                            AAA_33  2 vllvGlpGsGKstlaerllk 21
                                      v l G++GsGKstl++ +  
  gi|488600463|ref|YP_007906934.1| 31 VALLGPNGSGKSTLLRTIFG 50
                                      5678***********98754 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
                            AAA_33  15 laerllkklgavllssdtlrr 35 
                                       la+  +++ +  ll+++t++ 
  gi|488600463|ref|YP_007906934.1| 146 LARVFAQQPQIMLLDEPTAHL 166
                                       555556666688888888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2266.62
//
Query:       gi|488600464|ref|YP_007906935.1|  [L=315]
Description: ABC-type Fe3+-siderophore transport system, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-88  294.6  30.6    7.9e-88  294.4  30.6    1.0  1  FecCD            FecCD transport family
    2.3e-05   24.0  17.9    3.5e-05   23.4  17.9    1.4  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 !  294.4  30.6   8.8e-92   7.9e-88       8     312 .]      12     313 ..       1     313 [. 0.94

  Alignments for each domain:
  == domain 1  score: 294.4 bits;  conditional E-value: 8.8e-92
                             FecCD   8 lslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissgaa 84 
                                       + +++ +  ++   ++++l+g+ad++e++iv+++rlpr l+a+lvGa+L+++G+ +Q+++rNpLa+P+ilG+ sga+
  gi|488600464|ref|YP_007906935.1|  12 VFVSYLSLGYQNDLLLKVLTGNADKIERSIVIDTRLPRFLTAVLVGASLSASGCAMQALFRNPLAEPYILGVASGAS 88 
                                       22344444555667899999999****************************************************** PP

                             FecCD  85 lgavlalllllgslslfalplaaflgallalllvllla.rkrkgasplkliLaGiavsallsaltsllllllneeal 160
                                       +ga++a++l  g  +++  +++af++all++ lv+ +  ++r + +++ ++LaGia+++++s+ltsl++++  ++++
  gi|488600464|ref|YP_007906935.1|  89 VGAAIATVL--GFGTIQNKLILAFVSALLTSYLVYEIGtTSRFRDQTYAILLAGIAIASFFSGLTSLIIYF-FAQSM 162
                                       ********9..5778888999**************99978999999*************************.679** PP

                             FecCD 161 esilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavava 237
                                       ++++fw++Gs+s+ +ws+v+++l+++++++++ll+++ +l++l lgde A ++Gv+v+r+r  l++++a+lt++ava
  gi|488600464|ref|YP_007906935.1| 163 HKVVFWIMGSFSNPQWSEVYFALPITIAGIAYLLINSWNLNALLLGDEHAMAVGVDVNRFRKYLIAVIAVLTSSAVA 239
                                       ***************************************************************************** PP

                             FecCD 238 lvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                       ++G+igFvG+i+Ph++r+lvg++h+kllpl++l+++l++ l dl+a++++   elpvg++ta++G+pff+y+l+r
  gi|488600464|ref|YP_007906935.1| 240 VSGVIGFVGIIIPHTMRMLVGEEHQKLLPLTILFAMLFMPLIDLVAKTAT-TGELPVGAITAMLGGPFFVYILWR 313
                                       *************************************************7.79********************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 !   23.4  17.9   3.9e-09   3.5e-05      42     227 ..      87     280 ..      48     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.9e-09
                             ABC-3  42 alpGvalayllgvn....lllgailvgliaavalellkrktklkedt....aigivlsvfla.lglvlvslikkskv 109
                                       a  G a+a +lg+      l+ a++++l+ +  +  + ++++++  t    + gi +++f++ l  +++    +s  
  gi|488600464|ref|YP_007906935.1|  87 ASVGAAIATVLGFGtiqnKLILAFVSALLTSYLVYEIGTTSRFRDQTyailLAGIAIASFFSgLTSLIIYFFAQSMH 163
                                       44577888888876445577888888888888888899999999887333346999988886566667777777999 PP

                             ABC-3 110 dldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqa 186
                                       ++  +++G+    +  +++  + i++  +++ll+   +l ++ +  e+A++ g+ v++++ +l+a+ia+  + a+ +
  gi|488600464|ref|YP_007906935.1| 164 KVVFWIMGSFSNPQWSEVYFALPITIAGIAYLLINSWNLNALLLGDEHAMAVGVDVNRFRKYLIAVIAVLTSSAVAV 240
                                       9**************************************************************************** PP

                             ABC-3 187 vGviLvialliiPaatArrltrslesllivAillglvsvva 227
                                        Gvi  + + iiP  + ++++++ ++ll + il++++++ +
  gi|488600464|ref|YP_007906935.1| 241 SGVIGFVGI-IIPHTMRMLVGEEHQKLLPLTILFAMLFMPL 280
                                       ****99986.78************************98854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1805.12
//
Query:       gi|488600465|ref|YP_007906936.1|  [L=292]
Description: wyosine biosynthesis protein TYW1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-24   84.4   0.1    2.7e-23   82.1   0.0    2.1  2  Wyosine_form  Wyosine base formation
    2.4e-16   60.6   0.1    1.1e-15   58.4   0.0    2.1  2  Radical_SAM   Radical SAM superfamily
     0.0051   16.9   0.0      0.009   16.1   0.0    1.4  1  HAD_2         Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.32   1.9e+03       8      18 ..       7      17 ..       4      36 .. 0.81
   2 !   82.1   0.0   4.5e-27   2.7e-23       1      63 []     230     291 ..     230     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.32
                                      EEEE------- CS
                      Wyosine_form  8 EvKaytyvGss 18
                                      E+K+y  vG +
  gi|488600465|ref|YP_007906936.1|  7 ELKGYNIVGKH 17
                                      89999999976 PP

  == domain 2  score: 82.1 bits;  conditional E-value: 4.5e-27
                                       HHT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   1 kaepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       ka+pdF+E Kay+++G+sr+rL+++++P+h+e++dfa++le+ a  Y++++e++ Srvvll+r
  gi|488600465|ref|YP_007906936.1| 230 KANPDFIEAKAYMHLGHSRYRLERSAMPEHDEIRDFAEKLEKLAD-YRIVDESEISRVVLLER 291
                                       69*******************************************.**************975 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   1.9e-19   1.1e-15       2     161 ..      53     222 ..      52     228 .. 0.82
   2 ?   -2.0   0.0      0.68   4.1e+03      91     101 ..     266     276 ..     237     284 .. 0.65

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.9e-19
                                       EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE...............SSTGGG CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilg...............ggepll 59 
                                       ++   Cnl C++C+rp +        ++++++  e+i+++ + l+  +g+k+v                   gep+l
  gi|488600465|ref|YP_007906936.1|  53 SPALRCNLSCIHCWRPLSlmpeIDGWDDPQFIVEESIKAQQRLLSGFWGTKGVNTKkleeaykpnqvaislIGEPTL 129
                                       67789*****************7778888888888888888888755555555555566666666666666****** PP

                                       STTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                       Radical_SAM  60 ypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevleale 135
                                       yp ++el+++   +   +++++v+tngt p    ++rl ++    ++++l a+++  ++ l++  g+ ++++ ++le
  gi|488600465|ref|YP_007906936.1| 130 YPFIAELVDEFNSR---EMTTFVVTNGTNP--NAVDRLEPYQ---LYISLTAYSESSHKTLNKpHGNLWDKINRSLE 198
                                       *************8...************6..7777777765...**********95555555778999******** PP

                                       HHHHTTSETEEEEEEEBTTTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 136 klreagikrvvdrivglpGendeele 161
                                       ++ e++++ +v r+++++G n+  +e
  gi|488600465|ref|YP_007906936.1| 199 IMSEKDCR-TVLRLTLIKGINMN-VE 222
                                       ********.************97.45 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.68
                                       HHHHHHHHHTT CS
                                       xxxxxxxxxxx RF
                       Radical_SAM  91 eeklerllelg 101
                                        ekle+l++++
  gi|488600465|ref|YP_007906936.1| 266 AEKLEKLADYR 276
                                       45555555555 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-06     0.009      67     153 ..     112     202 ..      84     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-06
                             HAD_2  67 rkyneekkk....kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpe 139
                                       + y+ ++       e ++y+ + el++e ++++++  +vT++++ ++ + le  ++   ++    s++ + +KP+ +
  gi|488600465|ref|YP_007906936.1| 112 EAYKPNQVAisliGEPTLYPFIAELVDEFNSREMTTFVVTNGTNPNAVDRLEPYQLYISLTAYSESSHKTLNKPHGN 188
                                       555555555545557799*************************************98888888888888889***** PP

                             HAD_2 140 viekaleklklkke 153
                                       +  k+ ++l++ +e
  gi|488600465|ref|YP_007906936.1| 189 LWDKINRSLEIMSE 202
                                       ****9999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1752.20
//
Query:       gi|488600466|ref|YP_007906937.1|  [L=197]
Description: putative RNA-binding protein of the translin family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-10   40.5   2.1    8.5e-06   25.9   0.0    2.4  2  Translin  Translin family


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 !   13.8   0.5   2.3e-06     0.042       3      96 ..      23     102 ..      21     107 .. 0.76
   2 !   25.9   0.0   4.7e-10   8.5e-06     116     193 ..     106     181 ..     100     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHH.HGGGTH.H CS
                          Translin   3 reriikasrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayr.Yqrqisgg 78 
                                       re++ k+ rd+ + +  +i+ +hr         ++++++ ke+ ++l++i+            +++ + Y    +  
  gi|488600466|ref|YP_007906937.1|  23 REELLKLTRDLRRRATSAIAEVHRNS------LENAENMLKECFNHLEKIKYYE---------DDFPEiYYPITRDP 84 
                                       999********999999999999944......3456666677777777776655.........44433388889999 PP

                                       HHHHHHHHHHHHHHHHSS CS
                          Translin  79 lqeliealsfahYletqt 96 
                                       +qe+iea+ f + +++++
  gi|488600466|ref|YP_007906937.1|  85 IQEFIEAYVFFSIIKNRE 102
                                       **********98777765 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 4.7e-10
                                       SSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHHHHHHHHTS----HH...HHHHHTTHHHHHH CS
                          Translin 116 dafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflrelragfellnlkndsakdlrkKldvlkqsvk 192
                                       ++++++p+  l Gl+d++gEL R+a   + + + + ++ ++++f++++++++  ++ + d+   l+ Kld+++  ++
  gi|488600466|ref|YP_007906937.1| 106 PEVKVHPSPILTGLADCVGELRRYALEMMREMKVK-EANEMINFMEAIYSKLIEFDYP-DKIVPLKSKLDMVRLAIE 180
                                       5788999999******************9999977.9*******************99.445899999999987776 PP

                                       H CS
                          Translin 193 K 193
                                       +
  gi|488600466|ref|YP_007906937.1| 181 R 181
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      809  (0.0451224); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1425.31
//
Query:       gi|488600467|ref|YP_007906938.1|  [L=427]
Description: Adenylosuccinate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-161  536.2   4.8    8.4e-98  328.0   0.1    2.0  2  Adenylsucc_synt  Adenylosuccinate synthetase
  ------ inclusion threshold ------
      0.083   13.1   0.0       0.52   10.5   0.0    2.0  2  DUF1033          Protein of unknown function (DUF1033)
        0.1   12.9   0.0       0.25   11.6   0.0    1.6  1  KIX              KIX domain


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 !  211.5   1.3   3.4e-66   2.1e-62       1     156 [.       5     158 ..       5     159 .. 0.96
   2 !  328.0   0.1  1.4e-101   8.4e-98     190     419 .]     156     419 ..     153     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: 211.5 bits;  conditional E-value: 3.4e-66
                                       .EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHH CS
                   Adenylsucc_synt   1 vvvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpeall 77 
                                       v+vvG qwGDEGKGkivD+lae+ad+v+R++GG+nAGHtvvvd+kkyk+hl+pSGi++ g+ nviGng+v+dp++l+
  gi|488600467|ref|YP_007906938.1|   5 VIVVGGQWGDEGKGKIVDFLAEKADLVIRYAGGNNAGHTVVVDEKKYKFHLIPSGIIH-GKLNVIGNGTVIDPDVLI 80 
                                       68*******************************************************7.99**************** PP

                                       HHHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHH CS
                   Adenylsucc_synt  78 eEieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeee 154
                                       +Eie+le++g+++ +++l++s++ah +l+ hk  D+ e++   +kkiGtT++GiGp+y+dk+ar+gir+g+ +++e+
  gi|488600467|ref|YP_007906938.1|  81 SEIEQLEKMGIQVDESKLVVSSSAHTILQKHKDEDNPEKNPL-SKKIGTTGRGIGPCYRDKIARKGIRLGEYVEKEN 156
                                       ************************************999865.58***************************99887 PP

                                       HH CS
                   Adenylsucc_synt 155 le 156
                                       +e
  gi|488600467|ref|YP_007906938.1| 157 IE 158
                                       65 PP

  == domain 2  score: 328.0 bits;  conditional E-value: 1.4e-101
                                       HHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESS CS
                   Adenylsucc_synt 190 yaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSnttaggaltglglapkkidevlgvvKAy 266
                                         erlkp+++dt +++nea+++gkkvLfEGaqgtllDidhGtYPfvTsSn+taggaltg+g++p+kid+v+gv+KAy
  gi|488600467|ref|YP_007906938.1| 156 NIERLKPLIKDTCYIINEAIDSGKKVLFEGAQGTLLDIDHGTYPFVTSSNPTAGGALTGTGVGPTKIDSVIGVFKAY 232
                                       5799************************************************************************* PP

                                       EEESSSS--TTB--S..................................HHHHHHHHHTT-B-TTT--B-EEE-EEH CS
                   Adenylsucc_synt 267 ttrvGeGpfptelkd..................................evgeklrekGkEfgtttgrpRrcGwlDl 309
                                       ttrvG Gpfptel +                                    g+++r  GkE+gtttgrpRr+Gw+D 
  gi|488600467|ref|YP_007906938.1| 233 TTRVGGGPFPTELGTeeetnregrwedivkdydvilkealekanegdeyYQGKYMRLMGKEYGTTTGRPRRTGWFDG 309
                                       ************8436789999999*********************9888899************************ PP

                                       HHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT---GGG CS
                   Adenylsucc_synt 310 vllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgvrsfed 386
                                       v+ ryav++ng+t++a+tklDvl+gl++ik+cvaY++dgk++d+f  ++++l +v+pvyeelpgW+edis++rsf++
  gi|488600467|ref|YP_007906938.1| 310 VAGRYAVMINGMTSMAITKLDVLTGLKRIKICVAYEIDGKTTDRFILNTDRLYDVKPVYEELPGWDEDISEARSFDE 386
                                       ***************************************************************************** PP

                                       S-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
                   Adenylsucc_synt 387 lpenakkyvefieellgvpvkiisvGpereqti 419
                                       lpenak+y++++ee++g+++++isvGp+r+qti
  gi|488600467|ref|YP_007906938.1| 387 LPENAKNYLKRLEEICGAKISLISVGPRRDQTI 419
                                       *******************************98 PP

>> DUF1033  Protein of unknown function (DUF1033)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.2   1.2e+03      23      51 ..     265     294 ..     254     305 .. 0.76
   2 ?   10.5   0.0   8.7e-05      0.52      17      47 ..     371     401 ..     361     410 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.2
                           DUF1033  23 diveekefdefeealkyykkeWqklk.eey 51 
                                       d++ +++ ++ +e  +yy+ ++++l  +ey
  gi|488600467|ref|YP_007906938.1| 265 DVILKEALEKANEGDEYYQGKYMRLMgKEY 294
                                       778888899999999999999988641455 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.7e-05
                           DUF1033  17 legWeediveekefdefeealkyykkeWqkl 47 
                                       l gW+edi e+++fde+ e  k y k+ +++
  gi|488600467|ref|YP_007906938.1| 371 LPGWDEDISEARSFDELPENAKNYLKRLEEI 401
                                       679**************99999888877665 PP

>> KIX  KIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.2e-05      0.25      31      66 ..     248     283 ..     236     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                               KIX  31 dqealnDkRmeelieyarkvEkeafekakdrdeYYh 66 
                                       ++e+ +++R e++++    + kea eka++ deYY+
  gi|488600467|ref|YP_007906938.1| 248 EEETNREGRWEDIVKDYDVILKEALEKANEGDEYYQ 283
                                       6788999****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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 0.32s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2563.69
//
Query:       gi|488600468|ref|YP_007906939.1|  [L=264]
Description: 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-61  206.5   0.0    5.2e-61  206.3   0.0    1.1  1  DeoC        DeoC/LacD family aldolase
    0.00066   19.1   0.8      0.006   15.9   0.1    2.5  3  ThiG        Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.036   13.5   0.0          3    7.2   0.0    2.9  3  PEP_mutase  Phosphoenolpyruvate phosphomutase
        0.1   11.7   0.1       0.21   10.7   0.0    1.6  2  DUF561      Protein of unknown function (DUF561)


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 !  206.3   0.0   1.2e-64   5.2e-61       2     234 ..      20     233 ..      19     234 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.3 bits;  conditional E-value: 1.2e-64
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       +i+++D++ + +++++       e++ +++++++++ga+av +++g+++ ++++y+kd++l+v+l+ +t l++++++
  gi|488600468|ref|YP_007906939.1|  20 LIVPLDHGLSVGPIEGL------ENMPETINKVVEGGANAVIVHKGIVPFGHRGYGKDVGLIVHLSGSTSLSPDPND 90 
                                       69***************......9***************************************************** PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                       + + v+sveea++lGAdav+++v++   gs +e ++l+e++ +++ c e+g+pl++++y+r++ i d + +++ v+ 
  gi|488600468|ref|YP_007906939.1|  91 KKI-VCSVEEALKLGADAVSIHVNI---GSNTEPKQLEELGSISKSCMEWGMPLLAMMYPRGNGI-DPF-SEKSVKI 161
                                       ***.*********************...************************************8.666.8****** PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEES CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsG 229
                                       A+r++aelGaDiiK++++        +d ++f++v+k++pvp vv++GG+      dfl++vedA+  aga Gv++G
  gi|488600468|ref|YP_007906939.1| 162 ATRAGAELGADIIKTNYT--------GDPDSFRRVVKGCPVP-VVIAGGPrieRTIDFLKMVEDAM-HAGAKGVAIG 228
                                       ******************........****************.*******998888**********.********** PP

                                       HHHHT CS
                              DeoC 230 Raifq 234
                                       R+ifq
  gi|488600468|ref|YP_007906939.1| 229 RNIFQ 233
                                       ****9 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.52   2.3e+03     187     205 ..      40      58 ..      32      61 .. 0.76
   2 ?    0.6   0.0     0.063   2.8e+02     190     215 ..      97     122 ..      94     130 .. 0.85
   3 !   15.9   0.1   1.3e-06     0.006     164     233 ..     182     257 ..     154     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.52
                                       HHHHHHHHHTT-SEEEESH CS
                              ThiG 187 psdaaqamelGadavllnt 205
                                       p+ + +++e Ga+av++  
  gi|488600468|ref|YP_007906939.1|  40 PETINKVVEGGANAVIVHK 58 
                                       6677788888888888865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.063
                                       HHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 190 aaqamelGadavllntavaeakdpva 215
                                       + +a++lGadav +   + + ++p +
  gi|488600468|ref|YP_007906939.1|  97 VEEALKLGADAVSIHVNIGSNTEPKQ 122
                                       56899********9999999888866 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHH-SS-BEEES-......--SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH CS
                              ThiG 164 kealkiiieeakvPvivDAG......igspsdaaqamelGadavllntavaeakdpvamArafklaveaGrlayla 233
                                       +  ++ +++ + vPv++  G      i   + +  am  Ga++v +   + +a++p +m +a+++ ++    a +a
  gi|488600468|ref|YP_007906939.1| 182 PDSFRRVVKGCPVPVVIAGGpriertIDFLKMVEDAMHAGAKGVAIGRNIFQADNPTKMTKAIAMIIHENSSAESA 257
                                       566777888889999998885522223334556789****************************999877666655 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.095   4.2e+02      83     104 ..      35      56 ..      10      66 .. 0.76
   2 ?    2.0   0.0     0.027   1.2e+02     165     200 ..     100     145 ..      91     163 .. 0.75
   3 ?    7.2   0.0   0.00066         3     166     226 ..     167     234 ..     160     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.095
                        PEP_mutase  83 speevaetvrrliaaGvvgvni 104
                                         e++ et++++++ G+ +v++
  gi|488600468|ref|YP_007906939.1|  35 GLENMPETINKVVEGGANAVIV 56 
                                       4688999999999999988875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.027
                        PEP_mutase 165 YaeAGAdgvfvpgl..........qkdaeiaelvaavdvplnvvpl 200
                                        ++ GAd+v ++            ++  +i + + ++++pl +++ 
  gi|488600468|ref|YP_007906939.1| 100 ALKLGADAVSIHVNigsntepkqlEELGSISKSCMEWGMPLLAMMY 145
                                       5788999999999888988886655555577778888899988883 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.00066
                        PEP_mutase 166 aeAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgt.......lsvaelaelGvarislgnhllra 226
                                       ae GAd +      ++++ +++v+ ++vp+++  +++          v++   +G++ + +g ++++a
  gi|488600468|ref|YP_007906939.1| 167 AELGADIIKTNYTGDPDSFRRVVKGCPVPVVIAGGPRIertidflKMVEDAMHAGAKGVAIGRNIFQA 234
                                       799*****************************995332245788667888889999999999988877 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.78   3.5e+03     199     219 ..      96     116 ..      94     126 .. 0.69
   2 ?   10.7   0.0   4.7e-05      0.21     199     239 ..     213     253 ..     160     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.78
                            DUF561 199 tvplalslgasGiGigsavsk 219
                                       +v+ al+lga  + i  ++ +
  gi|488600468|ref|YP_007906939.1|  96 SVEEALKLGADAVSIHVNIGS 116
                                       566678888888877777655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.7e-05
                            DUF561 199 tvplalslgasGiGigsavsklndeeemvallseikkaisk 239
                                        v+ a+++ga G+ ig+++ + ++ ++m +++  i++  s+
  gi|488600468|ref|YP_007906939.1| 213 MVEDAMHAGAKGVAIGRNIFQADNPTKMTKAIAMIIHENSS 253
                                       356699**************************999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1453.45
//
Query:       gi|488600469|ref|YP_007906940.1|  [L=405]
Description: Site-specific recombinase XerD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   63.4   0.0    4.2e-17   62.5   0.0    1.4  1  Phage_integrase  Phage integrase family
    0.00023   21.1   0.3    0.00037   20.4   0.3    1.4  1  DZR              Double zinc ribbon
     0.0043   17.5   0.0     0.0089   16.5   0.0    1.6  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.042   14.1   0.0    2.0  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
      0.017   14.8   3.5      0.035   13.8   3.5    1.6  1  zinc_ribbon_2    zinc-ribbon domain
       0.16   12.7   0.4       0.32   11.8   0.4    1.4  1  zinc_ribbon_15   zinc-ribbon family
       0.43   10.1   3.8       0.88    9.1   3.8    1.4  1  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   1.6e-20   4.2e-17       3     169 ..     130     298 ..     129     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.6e-20
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE..EEECSSSSEEEEECTHHHH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvh..eregKgskeravplseeal 77 
                                       l e+ev r+++ +e     rdk+++++ ye GlR++El++L++kd+ + ++   +   +++  +  er++pl  + +
  gi|488600469|ref|YP_007906940.1| 130 LSEEEVFRMVEVAEH---PRDKAMIAVWYEAGLRVAELATLQIKDIVWYEQKDELRakIKVRGKTGERVIPLVLS-V 202
                                       789999********9...9**************************8876554444211233333446*****987.6 PP

                                       HHHHHHHHHHCHCCTTTSBSSBET....TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHH CS
                   Phage_integrase  78 ellkellskaleeaeksellfask....rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrv 150
                                       ++lk++++ +  +++ + ++f+s      g  +  q + + +k+++++agi k++ +H lRhs a+ L++     + 
  gi|488600469|ref|YP_007906940.1| 203 QYLKRWIDMHPFRDDLNAIVFCSFakqnYGGVIDYQPLLRKVKEIAKKAGIRKRVYTHILRHSRASVLANYLTEAQM 279
                                       99********999999********777777789************************************99877665 PP

                                       HHHHHT-SSCCHH.HHHHCC CS
                   Phage_integrase 151 vqkllGHssistt.qiYthv 169
                                         +++G+++ s   +iY+h+
  gi|488600469|ref|YP_007906940.1| 280 -CEYFGWEQGSDMpKIYVHL 298
                                       .6789****99999****97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   1.5e-07   0.00037      27      48 ..     320     345 ..     275     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                               DZR  27 a....edrCpsCgekvdpearfCpeC 48 
                                       +    ++rCp+C++ + p++rfC+ C
  gi|488600469|ref|YP_007906940.1| 320 DdklePKRCPRCNYLNAPTDRFCGRC 345
                                       0555599******************* 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 !   16.5   0.0   3.5e-06    0.0089       5      84 ..      35     112 ..      31     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.5e-06
                   Phage_int_SAM_4   5 frealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffykkvler 81 
                                       f ++l ++ +s+  i  Y++  +   ++++ k+  e ++++i+  l     +r++++ t +  ++a++ f++++ ++
  gi|488600469|ref|YP_007906940.1|  35 FKDYLVSESISPLRILRYVQIMRMTSEWVD-KPLTEWGRDEIIKVLGEIE-TRNYKVGTKNEFRKAMKKFFRWLHGE 109
                                       55556666666666667888888889999*.*****************88.***********************999 PP

                   Phage_int_SAM_4  82 ela 84 
                                        ++
  gi|488600469|ref|YP_007906940.1| 110 NWE 112
                                       996 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 ?   14.1   0.0   1.7e-05     0.042       4      81 ..      35     107 ..      32     110 .. 0.93
   2 ?   -2.1   0.0       1.9   4.9e+03      21      51 ..     236     268 ..     234     277 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1   4 fleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqfl 80 
                                       f++yL    ++sp  ++ Y++  r+ +++ ++     l++ +++++ + l e e ++++  + +  + a+++Ff++l
  gi|488600469|ref|YP_007906940.1|  35 FKDYLV-SESISPLRILRYVQIMRMTSEWVDK----PLTEWGRDEIIKVLGEIETRNYKVGTKNEFRKAMKKFFRWL 106
                                       888998.5678*********************....****************************************9 PP

                                       H CS
                   Phage_int_SAM_1  81 v 81 
                                        
  gi|488600469|ref|YP_007906940.1| 107 H 107
                                       5 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHH...TS--TTT--HHHHHH CS
                   Phage_int_SAM_1  21 aYrrdLrrflkflae..rgkesleqlttedvra 51 
                                       +Y+  Lr++ + +++   +k+  +++ ++++++
  gi|488600469|ref|YP_007906940.1| 236 DYQPLLRKVKEIAKKagIRKRVYTHILRHSRAS 268
                                       677777777777777333444455555555444 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.5   1.4e-05     0.035       1      19 [.     327     345 ..     327     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyC 19 
                                       +Cp+C + + ++++FC +C
  gi|488600469|ref|YP_007906940.1| 327 RCPRCNYLNAPTDRFCGRC 345
                                       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 ?   11.8   0.4   0.00012      0.32      56      85 ..     316     345 ..     302     346 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                    zinc_ribbon_15  56 eiekkessekkeCknCgkeveeefkyCpkC 85 
                                       e ++ ++ e k+C++C+    +  ++C +C
  gi|488600469|ref|YP_007906940.1| 316 EEKEDDKLEPKRCPRCNYLNAPTDRFCGRC 345
                                       3344455569******************** 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   3.8   0.00034      0.88       3      22 ..     326     345 ..     325     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00034
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyC 22 
                                       +rCP+C+  + ++ d++C  C
  gi|488600469|ref|YP_007906940.1| 326 KRCPRCNYlN-APTDRFCGRC 345
                                       69******99.*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2409.96
//
Query:       gi|488600470|ref|YP_007906941.1|  [L=323]
Description: hypothetical protein Asulf_00944 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1822.32
//
Query:       gi|488600471|ref|YP_007906942.1|  [L=161]
Description: hypothetical protein Asulf_00945 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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  12.7      0.015   15.4  12.7    1.2  1  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
      0.019   14.9   4.4      0.065   13.2   2.7    2.4  2  LrgA             LrgA family
      0.025   14.7   1.6       0.05   13.7   0.2    2.0  2  Jagunal          Jagunal, ER re-organisation during oogenesis
       0.03   13.6   8.4       0.04   13.2   8.4    1.2  1  SLAC1            Voltage-dependent anion channel
       0.47   10.1   7.4        2.3    7.9   6.9    2.0  1  NrsF             Negative regulator of sigma F
        1.5    8.6  10.8        3.4    7.4   3.4    2.1  2  DUF2157          Predicted membrane protein (DUF2157)
          3    7.4  13.9       0.32   10.5   5.6    2.0  2  ABC2_membrane_5  ABC-2 family transporter protein
        4.2    7.7   8.1        5.6    7.3   0.5    2.2  2  DUF1772          Domain of unknown function (DUF1772)
        5.2    7.4  17.4          2    8.7   0.4    3.9  4  YiaAB            yiaA/B two helix domain


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 ?   15.4  12.7   7.4e-06     0.015       5     131 ..      18     150 ..      14     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.4e-06
                   Polysacc_synt_C   5 lalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgi......vGaaiatvlallvvavlnly 75 
                                       +a+++i++++++v+  ++q+ +r + +lk+ ++ a+  ++  ++    + +      vG +++tv+++ +++v ++ 
  gi|488600471|ref|YP_007906942.1|  18 FAITLILAGVYVVYPDLFQAGDRIWSLLKVGIAVAA-SIAGIYIVYNTLEAkrgyltVGDLAGTVIGMGLMFVGLYL 93 
                                       799*************************98766555.55555555544433333355******************** PP

                   Polysacc_synt_C  76 alrrllgikl....ellrrllkpllaalvmgivvylllllllgllllaalalllavlvga 131
                                       +l   +   +    + + +++ + l+a+ m++    ++ +  +    aa+ +++a+++++
  gi|488600471|ref|YP_007906942.1|  94 MLGEAIENTFtgvaQTVLQFVPYGLSAISMFAG---IQAIQKNRKERAAVFIAIAAIFAI 150
                                       **********988766777779999*******9...666666666666344444443332 PP

>> LrgA  LrgA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.25     5e+02      12      31 ..      48      67 ..      36      74 .. 0.77
   2 ?   13.2   2.7   3.3e-05     0.065      14      70 ..      76     129 ..      70     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.25
                              LrgA 12 plpiPgsviGlllLlllLlt 31
                                      ++ + +s+ G+ +++ +L +
  gi|488600471|ref|YP_007906942.1| 48 GIAVAASIAGIYIVYNTLEA 67
                                      57899999999998887765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.3e-05
                              LrgA  14 piPgsviGlllLlllLltkivklekveeaadfllkhlallFvPagvgvmeyldllka 70 
                                        + g+viG+ l+++ L +  +  e +e++ +++ +   l FvP g + ++ +  ++a
  gi|488600471|ref|YP_007906942.1|  76 DLAGTVIGMGLMFVGLYL--MLGEAIENTFTGVAQT-VLQFVPYGLSAISMFAGIQA 129
                                       5789*************8..7778899999987766.689****9998888765543 PP

>> Jagunal  Jagunal, ER re-organisation during oogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.32   6.4e+02     104     144 ..      69     109 ..      40     117 .. 0.69
   2 ?   13.7   0.2   2.5e-05      0.05      84     123 ..     115     154 ..     104     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.32
                           Jagunal 104 ikllklyligtlvlgllpllygaveylkevleylkskease 144
                                         +l +  ++ +v+g++ +++g+  +l e++e + ++ a+ 
  gi|488600471|ref|YP_007906942.1|  69 RGYLTVGDLAGTVIGMGLMFVGLYLMLGEAIENTFTGVAQT 109
                                       45566666677788888888888888888888777777665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.5e-05
                           Jagunal  84 vwllSivpsllgllalkknkikllklyligtlvlgllpll 123
                                        + lS + ++ g++a++kn+ +   +++ +  ++++++++
  gi|488600471|ref|YP_007906942.1| 115 PYGLSAISMFAGIQAIQKNRKERAAVFIAIAAIFAIVSIF 154
                                       5889********************************9997 PP

>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   8.4     2e-05      0.04     131     244 ..      35     149 ..       5     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                             SLAC1 131 leeitpawllpvvgllvvallgallaesqnpslqllgilvvslllwglGlllalvlfvlylyrlithklppaelrpt 207
                                        ++   +w l  vg+ v+a++++ ++ + + +++   + v  l+   +G+ l +v + l+l   i + +   ++++ 
  gi|488600471|ref|YP_007906942.1|  35 FQAGDRIWSLLKVGIAVAASIAGIYIVYNTLEAKRGYLTVGDLAGTVIGMGLMFVGLYLMLGEAIENTFTGVAQTVL 111
                                       4555678****************9976644443333567777888889999999999999***************** PP

                             SLAC1 208 lfiplGplgqgalallllgkaapk........aaevlkvlallla 244
                                        f+p G  +++++a ++  ++ +k        +       a++ a
  gi|488600471|ref|YP_007906942.1| 112 QFVPYGLSAISMFAGIQAIQKNRKeraavfiaI------AAIF-A 149
                                       **************9876555544442222222......2222.2 PP

>> NrsF  Negative regulator of sigma F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.9    0.0011       2.3      22      97 ..      14      90 ..       8     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                              NrsF 22 llgaalalalvllllGlrpDlaealatpvfwlklalalllalaallaalrlarPgae.arrawlllalpvlllwlaa 97
                                      + +  +++++++ ++ + pDl +a    + +lk+++a++  +a+++++      +++    + l+  ++ + l++++
  gi|488600471|ref|YP_007906942.1| 14 VKASFAITLILAGVYVVYPDLFQAGDRIWSLLKVGIAVAASIAGIYIVYNTLEAKRGyLTVGDLAGTVIGMGLMFVG 90
                                      55667778888889999*****************************9998877777543333333333333333333 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.7     0.006        12      41     114 ..      18      96 ..       9      99 .. 0.66
   2 ?    7.4   3.4    0.0017       3.4      40     111 ..      81     152 ..      76     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.006
                           DUF2157  41 lGalllglGlilfvAanWqglsrlvkfllllvllllslllgavlwrdr...rvpprlgealllla..alllgaaial 112
                                        ++ l+++G+ ++   ++q+  r + +l + +++++s++++++++++    r++ ++g++++++   +l++++++ +
  gi|488600471|ref|YP_007906942.1|  18 FAITLILAGVYVVYPDLFQAGDRIWSLLKVGIAVAASIAGIYIVYNTLeakRGYLTVGDLAGTVIgmGLMFVGLYLM 94 
                                       68899999999999999977666665555555555555555555543333488888888777665114566666666 PP

                           DUF2157 113 vg 114
                                        g
  gi|488600471|ref|YP_007906942.1|  95 LG 96 
                                       65 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0017
                           DUF2157  40 vlGalllglGlilfvAanW.qglsrlvkfllllvllllslllgavlwrdrrvpprlgeallllaalllgaaia 111
                                       v+G+ l+ +Gl l+      ++++ +++++l +v+  ls++ ++   +   +++r  +a++++a  ++ a + 
  gi|488600471|ref|YP_007906942.1|  81 VIGMGLMFVGLYLMLGEAIeNTFTGVAQTVLQFVPYGLSAISMFAGIQAI-QKNRKERAAVFIAIAAIFAIVS 152
                                       4555566666655555554799*********************8777765.5666677777777777666654 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.1     0.057   1.1e+02     121     164 ..      17      60 ..       2      79 .. 0.53
   2 ?   10.5   5.6   0.00016      0.32      89     166 ..      81     155 ..      76     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.057
                   ABC2_membrane_5 121 liglvialiflaivlPlyfkfgvekgrivliiiifgiifllvai 164
                                        +++ ++l+ + +v+P +f  g +   ++ + i +++ + ++ i
  gi|488600471|ref|YP_007906942.1|  17 SFAITLILAGVYVVYPDLFQAGDRIWSLLKVGIAVAASIAGIYI 60 
                                       33444444446666666666666666654443333333322222 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                   ABC2_membrane_5  89 liliailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaif 165
                                       +i ++++++ l+l++++ i++++t   v  ++l ++ ++l +++++  ++ + +++k r +++i+i++i f +v+if
  gi|488600471|ref|YP_007906942.1|  81 VIGMGLMFVGLYLMLGEAIENTFT--GVAQTVLQFVPYGLSAISMFAGIQAIQKNRKERAAVFIAIAAI-FAIVSIF 154
                                       566788888899999*******99..8999999999999999999999999999999998888888887.5566666 PP

                   ABC2_membrane_5 166 s 166
                                       +
  gi|488600471|ref|YP_007906942.1| 155 K 155
                                       5 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.0     0.018        37      29      84 ..       5      62 ..       1      69 [. 0.57
   2 ?    7.3   0.5    0.0028       5.6      39      77 ..     113     153 ..      95     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                           DUF1772 29 rrlfkrgkavfpplallsalafayla...araasrgarllylaaaallllsivpyTllv 84
                                      +++fk+   v  ++a++ +la +y++     +a+++ + l+ + ++++++si+ + +++
  gi|488600471|ref|YP_007906942.1|  5 SNFFKAFDLVKASFAITLILAGVYVVypdLFQAGDRIWSLLKV-GIAVAASIAGIYIVY 62
                                      4555444444555666666666666667755566666666633.444455677766655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0028
                           DUF1772  39 fpplallsalafa.ylaaraasrgarllylaaaal.lllsi 77 
                                       f p +l ++++fa   a ++ +++++++++a+aa+ +++si
  gi|488600471|ref|YP_007906942.1| 113 FVPYGLSAISMFAgIQAIQKNRKERAAVFIAIAAIfAIVSI 153
                                       34456666666666688889999999999999999555555 PP

>> YiaAB  yiaA/B two helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.3   2.5e+03       6      17 ..      15      26 ..      13      33 .. 0.59
   2 ?    8.7   0.4     0.001         2       6      36 ..      44      75 ..      40      81 .. 0.86
   3 ?    5.8   2.3    0.0082        16      10      24 ..      81      95 ..      77     113 .. 0.76
   4 ?    2.6   0.6     0.083   1.7e+02      10      45 ..     117     154 ..     103     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                             YiaAB  6 wlsfllalvlll 17
                                      ++sf++ l+l +
  gi|488600471|ref|YP_007906942.1| 15 KASFAITLILAG 26
                                      566666555544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.001
                             YiaAB  6 wlsfllalvlllvGlwyl.pldlseKgfyamg 36
                                       l  ++a+++  +G++   +     +g++++g
  gi|488600471|ref|YP_007906942.1| 44 LLKVGIAVAASIAGIYIVyNTLEAKRGYLTVG 75
                                      56679***********99***********998 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0082
                             YiaAB 10 llalvlllvGlwylp 24
                                      +++++l++vGl+ + 
  gi|488600471|ref|YP_007906942.1| 81 VIGMGLMFVGLYLML 95
                                      89**********554 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.083
                             YiaAB  10 llalvlllvGlwylpldlseKg..fyamgllfllfsaf 45 
                                       +l+++ +++G+   + +  e++  f a++ +f++ s f
  gi|488600471|ref|YP_007906942.1| 117 GLSAISMFAGIQAIQKNRKERAavFIAIAAIFAIVSIF 154
                                       68888999999866777777753366666777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 925.99
//
Query:       gi|488600472|ref|YP_007906943.1|  [L=344]
Description: hypothetical protein Asulf_00946 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-11   43.8   1.7    7.5e-11   43.0   1.7    1.5  1  PPC           Bacterial pre-peptidase C-terminal domain
  ------ inclusion threshold ------
      0.035   14.1   0.0      0.064   13.3   0.0    1.4  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
      0.045   13.7   0.0      0.093   12.7   0.0    1.5  1  EMP24_GP25L   emp24/gp25L/p24 family/GOLD
       0.14   12.5   0.0       0.34   11.3   0.0    1.8  1  IL32          Interleukin 32


Domain annotation for each model (and alignments):
>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   1.7   1.7e-14   7.5e-11       2      70 .]      44     109 ..      43     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.7e-14
                                       EEEEEEEE-TT-EEEEEES-TT...SEEEEE-TT..-SS-EE-STT-TTS-TTS-EE-SSSEEEEEEE.. CS
                               PPC   2 vDvysfevpagdsltididggti.dldLylldsngtsvaaydansapsgsdeyieftapqaGtYyvaVss 70 
                                       v++y++ ++ag s+ti+++g +  d+dLy++d++ + +a    +s +++s e+++fta   G Y ++V+s
  gi|488600472|ref|YP_007906943.1|  44 VHYYKVQLSAGNSITISLSGPADaDFDLYIYDPSVNLIA----SSTSGDSEESCTFTASVSGYYLIEVTS 109
                                       89*******************955666*******55555....5888999******************85 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 ?   13.3   0.0   1.4e-05     0.064      51     125 ..     160     242 ..     149     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                      Baculo_PEP_C  51 sedlksllaeldtrldtlltnLtdalnalq.......dtlrneLtnlns.iltnLlssvtNinstLnnllqalnnld 119
                                       +++l+++l+ +++ + + +++Ltd l  l+       d l n+Lt ++s  + n+ + v   +++L+ l +a+ n+ 
  gi|488600472|ref|YP_007906943.1| 160 ANSLTEVLNGFKQFIIEKIQALTDFLGWLAslpfqavDWLFNKLTEITSaAVENIKNAVDAFIKSLTDLGTAIGNFF 236
                                       55666777777777777777777776666666676778889999998873589999999999999999999999998 PP

                      Baculo_PEP_C 120 lgalsq 125
                                        g +s+
  gi|488600472|ref|YP_007906943.1| 237 GGLFSA 242
                                       777665 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 ?   12.7   0.0   2.1e-05     0.093      13      83 ..      33     111 ..      30     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                       EMP24_GP25L  13 Cfyeelkk.gtlltgsyqvtdgg.........aaldvdlsvkdpdgngerlvkkkdresegdfsftakesgeykvCf 79 
                                       C++ el+  g++  +++q+  g+         a+ d+dl+++dp+   + + ++   +se++ +fta+ sg y + +
  gi|488600472|ref|YP_007906943.1|  33 CYFGELTYtGEVHYYKVQLSAGNsitislsgpADADFDLYIYDPSV--NLIASSTSGDSEESCTFTASVSGYYLIEV 107
                                       7777777656666777777777788888888877999999**5555..9999888888889************9877 PP

                       EMP24_GP25L  80 dnsf 83 
                                       ++ +
  gi|488600472|ref|YP_007906943.1| 108 TSCS 111
                                       6655 PP

>> IL32  Interleukin 32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.7e-05      0.34      41      99 ..     180     239 ..     157     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.7e-05
                              IL32  41 vlrrfqallrsLqqklrd.vlaWlkekaaacleAlvsavkavwkvledFcsslaqllrsl 99 
                                       +l  f + l sL  +  d ++  l e   a++e + +av+a+ k l+d  +++++ +  l
  gi|488600472|ref|YP_007906943.1| 180 ALTDFLGWLASLPFQAVDwLFNKLTEITSAAVENIKNAVDAFIKSLTDLGTAIGNFFGGL 239
                                       5667888888886555541556799999**************************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2133.36
//
Query:       gi|488600473|ref|YP_007906944.1|  [L=123]
Description: hypothetical protein Asulf_00947 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0067   16.4   2.5     0.0086   16.1   2.1    1.3  1  BCHF      2-vinyl bacteriochlorophyllide hydratase (BCHF)
  ------ inclusion threshold ------
      0.045   13.8   0.9      0.045   13.8   0.9    2.3  2  DUF1206   Domain of Unknown Function (DUF1206)


Domain annotation for each model (and alignments):
>> BCHF  2-vinyl bacteriochlorophyllide hydratase (BCHF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.1   9.6e-07    0.0086      19      70 ..      24      77 ..      16      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.6e-07
                              BCHF 19 liLaPiqflvflvslalvllylatg.egfalvtvsvllktlll.vlilitGaif 70
                                      ++  P+q+++fl++ +lv + l ++ +++ +++ s+ +k++ + +++++    +
  gi|488600473|ref|YP_007906944.1| 24 AMFEPVQWMLFLIGATLVGFGLYSAwKSYRIASYSISVKVAKFgFTLIVISFAW 77
                                      4678**************998887779************987634455555555 PP

>> DUF1206  Domain of Unknown Function (DUF1206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9     5e-06     0.045      46      68 ..      30      52 ..      29      53 .. 0.94
   2 ?    0.4   1.0     0.077   6.9e+02      44      55 ..      95     106 ..      66     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-06
                           DUF1206 46 rvllglvglgllgyglwqlveAv 68
                                      +++l l+g+ l+g+gl+++++ +
  gi|488600473|ref|YP_007906944.1| 30 QWMLFLIGATLVGFGLYSAWKSY 52
                                      7*******************987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.077
                           DUF1206  44 fGrvllglvglg 55 
                                       +  ++l+l+g  
  gi|488600473|ref|YP_007906944.1|  95 VLAFVLILAGGF 106
                                       333444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 789.49
//
Query:       gi|488600474|ref|YP_007906945.1|  [L=39]
Description: hypothetical protein Asulf_00948 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); 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: 0.30u 0.22s 00:00:00.52 Elapsed: 00:00:00.36
# Mc/sec: 321.76
//
Query:       gi|488600475|ref|YP_007906946.1|  [L=75]
Description: hypothetical protein Asulf_00949 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   12.4   0.5       0.21   12.2   0.5    1.1  1  TPPII_N   Tripeptidyl peptidase II N terminal


Domain annotation for each model (and alignments):
>> TPPII_N  Tripeptidyl peptidase II N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   1.2e-05      0.21      68     104 ..       5      41 ..       2      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                                       ----HHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHH CS
                           TPPII_N  68 gkakaDeYaEslRDfqcsqiakldlenAekiYnevva 104
                                        k   De +E l+ ++ + ++kl ++ Ae+i +e+ +
  gi|488600475|ref|YP_007906946.1|   5 KKVIEDEEVEELKKYKKAAMSKLLIDVAEDIVEEIYK 41 
                                       67778******************99999876555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1639  (0.0914161); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); 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: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 523.84
//
Query:       gi|488600476|ref|YP_007906947.1|  [L=341]
Description: hypothetical protein Asulf_00950 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.01   15.1   1.5      0.017   14.4   1.5    1.3  1  Glyco_transf_22  Alg9-like mannosyltransferase family
       0.25   11.5   1.6       0.43   10.7   0.4    2.0  2  UBA_2            Ubiquitin associated domain (UBA)
       0.69    9.7   5.8       0.55   10.1   0.3    2.5  3  DUF2100          Uncharacterized protein conserved in archaea


Domain annotation for each model (and alignments):
>> Glyco_transf_22  Alg9-like mannosyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.5   2.9e-06     0.017     179     254 ..     164     244 ..     135     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-06
                   Glyco_transf_22 179 iRptsallwlplvlflllrlvkkrsktf.....lfliialvllvlllvlvlviliDslfYgkfvftplnflkyNvls 250
                                        R   ++++l +    + ++ k++  ++     ++l ++++l ++l+  +  i +Ds f+  fvft  ++l y +++
  gi|488600476|ref|YP_007906947.1| 164 ERHAQVAIVLAVFAIAVAYVLKRKTLLIspfnfINLGFVIGLTAVLAYYLEYIRTDSTFWLAFVFTASEILSYQLFT 240
                                       5555555555555555555555544444667779999**********9*************************9998 PP

                   Glyco_transf_22 251 nlss 254
                                       ++ +
  gi|488600476|ref|YP_007906947.1| 241 AGRK 244
                                       7765 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.8   4.8e+03      25      42 ..     164     184 ..     160     185 .. 0.62
   2 ?   10.7   0.4   7.2e-05      0.43       1      31 [.     259     292 ..     259     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.8
                             UBA_2  25 ekaeks...kssneIkDAYlL 42 
                                       e+  +     ++ +I  AY L
  gi|488600476|ref|YP_007906947.1| 164 ERHAQVaivLAVFAIAVAYVL 184
                                       555554444556689999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.2e-05
                             UBA_2   1 IdedvvsaLsktMGYdkdeIieaLekaeks...k 31 
                                       I+e v  +++k M Y ++ + ea+++ + +    
  gi|488600476|ref|YP_007906947.1| 259 IEEGVLYKIEKGMAYARQSVDEAIKRLKGEhilV 292
                                       8999*********************988875554 PP

>> DUF2100  Uncharacterized protein conserved in archaea (DUF2100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.73   4.4e+03      77     110 ..      20      54 ..      18      62 .. 0.59
   2 ?    2.0   0.2     0.027   1.6e+02      41      99 ..     114     178 ..     112     191 .. 0.74
   3 ?   10.1   0.3   9.1e-05      0.55     153     195 ..     259     301 ..     251     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHHHHHHHHHTTT---X.X..XXXXS CS
                           DUF2100  77 eefckillkakkklekvLeefgveee.edieeldk 110
                                        e+ ++ l+ k+ l+kv +++g++e  +   e ++
  gi|488600476|ref|YP_007906947.1|  20 AEVNQTKLSDKDVLKKVKAKLGIKEFpQPTIETNH 54 
                                       55555556667777777777777665444444455 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.027
                                       EE--HHHHHHHHHHHHHHTHHHHH.TTTT.-EE-HHHHHH....HHHHHHHHHHHHHHHHHTTT- CS
                           DUF2100  41 gkidieelkkavyelieadeylyk.kaPe.helkkeeAee....fckillkakkklekvLeefgv 99 
                                       g i ++ +k+ +y  ie d  +y+ k+P  + +k+++ ee    f k +++ + ++  vL+ f +
  gi|488600476|ref|YP_007906947.1| 114 GTIGQKGMKDTIYLKIEVDGEVYTyKIPLvKSIKEKKEEEgvltFKKEVIERHAQVAIVLAVFAI 178
                                       67888999*********998888735675255665555545555888888888888888888876 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 9.1e-05
                                       XXSTTTTTSHHHHHHHHHHHHHHHHHHXXSXEEEEXS..SHHH CS
                           DUF2100 153 ipekalkgieKkveivkeeieklikklkpekvvvvveeddkad 195
                                       i e +l  ieK ++ +++ +++ ik+lk e+++v  +e  k +
  gi|488600476|ref|YP_007906947.1| 259 IEEGVLYKIEKGMAYARQSVDEAIKRLKGEHILVEDKEIKKPG 301
                                       789999**************************99777755544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2000.81
//
Query:       gi|488600477|ref|YP_007906948.1|  [L=98]
Description: hypothetical protein Asulf_00951 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   15.1   0.3      0.016   15.0   0.3    1.3  1  NinB      NinB protein


Domain annotation for each model (and alignments):
>> NinB  NinB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   8.9e-07     0.016      43      80 ..      54      91 ..       7      98 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.9e-07
                              NinB 43 aqNallwallkdiarqvewagekldaeeWKdlltaalk 80
                                      aqN  l     d++ +v++   k+ ae+WK++l  +  
  gi|488600477|ref|YP_007906948.1| 54 AQNIELRGKYLDLQAKVTFMADKIAAEKWKRILKLSKE 91
                                      899999999***********************986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 626.46
//
Query:       gi|488600478|ref|YP_007906949.1|  [L=103]
Description: hypothetical protein Asulf_00952 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 731.89
//
Query:       gi|488600479|ref|YP_007906950.1|  [L=312]
Description: hypothetical protein Asulf_00953 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   1.1        0.5   10.8   0.3    2.4  2  RNA_helicase     RNA helicase
       0.22   11.4   2.1         19    5.3   0.1    2.5  2  SF3a60_bindingd  Splicing factor SF3a60 binding domain


Domain annotation for each model (and alignments):
>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   5.5e-05       0.5       3      63 ..      26      78 ..      24     108 .. 0.65
   2 ?   -2.6   0.0      0.81   7.3e+03      78      93 ..     204     219 ..     180     227 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.5e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl.........klkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkd 63
                                      ++G++g GKStl   L k++l+k+                           d+  ++ +  idDf ++k+
  gi|488600479|ref|YP_007906950.1| 26 ITGEKGNGKSTLGWWLEKEILSKVgyeldfvkdM-----------------DKLLNHLIFTIDDFFSIKK 78
                                      89******************98884444444430.................4444444444444444443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.81
                      RNA_helicase  78 sstpyplnmasleekg 93 
                                         ++ ++ + +leek+
  gi|488600479|ref|YP_007906950.1| 204 IDAKRMMRVIKLEEKA 219
                                       2233334444455554 PP

>> SF3a60_bindingd  Splicing factor SF3a60 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2    0.0021        19       9      19 ..     190     200 ..     184     201 .. 0.90
   2 ?    5.3   0.1    0.0021        19      11      18 ..     298     305 ..     292     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0021
                   SF3a60_bindingd   9 seFYkrLkeIK 19 
                                       + FY+++++IK
  gi|488600479|ref|YP_007906950.1| 190 KQFYNEYRKIK 200
                                       68********9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0021
                   SF3a60_bindingd  11 FYkrLkeI 18 
                                       FY+rLke+
  gi|488600479|ref|YP_007906950.1| 298 FYNRLKEV 305
                                       ******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1896.44
//
Query:       gi|488600480|ref|YP_007906951.1|  [L=89]
Description: hypothetical protein Asulf_00954 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.53
# Mc/sec: 506.24
//
Query:       gi|488600481|ref|YP_007906952.1|  [L=214]
Description: hypothetical protein Asulf_00955 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-18   66.9   1.7    3.4e-18   66.4   1.7    1.2  1  DUF3800    Protein of unknown function (DUF3800)
  ------ inclusion threshold ------
       0.14   12.3   0.3       0.23   11.6   0.3    1.4  1  DASH_Dad3  DASH complex subunit Dad3


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 !   66.4   1.7   3.8e-22   3.4e-18       1     119 [.       6     189 ..       6     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 3.8e-22
                           DUF3800   1 liYiDESGdnklkdgsspyfvlggkkieeikkleekikelkkky................................. 44 
                                       +iYiDESGd++++ +s++y+v+++++ ++ +++++ +k++++k+                                 
  gi|488600481|ref|YP_007906952.1|   6 YIYIDESGDLGFTEKSTKYYVIAAVETKNPQQFSRMFKKIRRKMgkkkkdikefkfsktksstkemilkkiaeleiq 82 
                                       79**********************44446666666666666666666666666666669988886666666666666 PP

                           DUF3800  45 ............krlleriakflkkndlik...................sdeesdesilivldk...kkkkekakke 87 
                                                   +                +                       +++++ iv+dk   +   e+ + +
  gi|488600481|ref|YP_007906952.1|  83 fsavvlkkatvyQ----------------HlrekrqilhnyltgfivelIPFMDSRDFEIVIDKfisN---EADRTN 140
                                       6655555544431................022222233334444555576677889999999995542...333333 PP

                           DUF3800  88 l.eilld................esvkfvdSkesrglQlADlvagaifr 119
                                       + e+l d                 ++k+++S+++ glQ+AD+vagaif+
  gi|488600481|ref|YP_007906952.1| 141 FdEYLRDhvnyecwklglipprsLNIKHESSYSCSGLQVADFVAGAIFA 189
                                       332221134566788999*****************************97 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   2.6e-05      0.23      22      67 ..      52     101 ..      31     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                         DASH_Dad3  22 LaselkeLasn.....steeildgLReLErkiglvyTLlKaSVYsivlqqe 67 
                                        ++ +ke+  +     ++e il+++ eLE + + v+ L Ka VY+ + +++
  gi|488600481|ref|YP_007906952.1|  52 KKKDIKEFKFSktkssTKEMILKKIAELEIQFSAVV-LKKATVYQHLREKR 101
                                       44444444333445547999*************997.9******9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1332  (0.074293); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1358.35
//
Query:       gi|488600482|ref|YP_007906953.1|  [L=177]
Description: hypothetical protein Asulf_00956 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.4   7.6        0.1   12.3   0.8    2.0  2  Tetraspanin  Tetraspanin family
     0.0029   16.7   0.5     0.0034   16.5   0.5    1.1  1  PHO4         Phosphate transporter family
  ------ inclusion threshold ------
      0.033   14.3   9.6      0.044   13.9   9.6    1.1  1  ECF_trnsprt  ECF transporter, substrate-specific component
      0.077   12.2   8.4      0.096   11.9   8.4    1.0  1  Voltage_CLC  Voltage gated chloride channel
       0.21   11.7   9.3        2.1    8.5   0.1    2.1  2  GWT1         GWT1
       0.25   11.1   4.9       0.41   10.4   4.7    1.5  1  DUF2214      Predicted membrane protein (DUF2214)
       0.29   11.0   7.1        1.3    8.9   2.4    2.1  2  DUF2723      Protein of unknown function (DUF2723)
       0.37   10.3  14.2       0.18   11.3   0.5    2.0  2  DUF3169      Protein of unknown function (DUF3169)
       0.62    9.4   8.2        1.2    8.5   8.2    1.3  1  DUF373       Domain of unknown function (DUF373)
        3.2    7.6   8.2        5.6    6.8   0.4    2.5  3  DUF2976      Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.8   5.8e-05       0.1      10      72 ..      22      77 ..      16      83 .. 0.71
   2 !    9.4   1.1   0.00044      0.79      45     127 ..      91     172 ..      78     177 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.8e-05
                                      XXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 10 llfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigal 72
                                       ++ +++++++a ++ +    + + ++++   ++ed++    ++ +vG++lf+ gf+G++ +l
  gi|488600482|ref|YP_007906953.1| 22 SVIAIFSAFMVAGSFLI----DTTYFKNA---TNEDSNPFNKTFALVGAFLFVSGFAGIFLVL 77
                                      57888999999988666....33333444...4444444445599*************99876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00044
                                       ........XXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXX--HHH........HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  45 dpailaillivvGvllfllgflGcigalkenk....cllltfsllllvlfllelaagilgfvfsdkargkvseiinn 117
                                        +++l+ + +v+ + ++ ++f+ ++  +k  +     l l+f l+ ++  +++l +++++f+f+       +e+++ 
  gi|488600482|ref|YP_007906953.1|  91 LQKMLSFISVVLLSGIATVTFFSIYYLIKTAYnskdLLSLSFKLFGVMTYIAFLFVTFMIFHFEPL-----YEWVKP 162
                                       344444446666667888888887777776666667999*******************99999988.....889999 PP

                                       HHHHHHHHHH CS
                                       xxxxxxxxxx RF
                       Tetraspanin 118 aievkyrddl 127
                                        i++++ +  
  gi|488600482|ref|YP_007906953.1| 163 RIKQRLSKLK 172
                                       9988877665 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5   1.9e-06    0.0034      63     174 ..      23     152 ..       3     174 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                              PHO4  63 mlgmlaallgaavwlllatvl.......glPvStthslvGaliGaalaa.......eggeavkw........kklvk 117
                                       ++++++a + a+ +l+ +t++       + P  +t++lvGa++ ++ +a                       +  ++
  gi|488600482|ref|YP_007906953.1|  23 VIAIFSAFMVAGSFLIDTTYFknatnedSNPFNKTFALVGAFLFVSGFAgiflvlvD------SlakyldrfE-KLQ 92 
                                       4666777777777777777774444444689999******99866666533333331......2443454443.344 PP

                              PHO4 118 ivlswvlsPllggiiaallfllvkrlilvk...eklknalralpvlvlvtiailalsilf 174
                                        +ls +  +ll+gi+ +++f +   + +     + l+ +++++ v++++ +++++++i++
  gi|488600482|ref|YP_007906953.1|  93 KMLSFISVVLLSGIATVTFFSIYYLIKTAYnskDLLSLSFKLFGVMTYIAFLFVTFMIFH 152
                                       455666666667766666555554443322334777778888888877777777777765 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   9.6   2.4e-05     0.044       5     128 ..      23     153 ..      19     168 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHHHH..H.HEEE.STS......EEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH..CHT-SSTTH CS
                       ECF_trnsprt   5 itglliAisivlsl..l.gyiplpni......kitiihipvllggllfGpikGailgiitsvlkai..ltggtgals 70 
                                       ++++++A  + +s+    +y++  +       + t+  + ++   l+++ ++G++l ++ s++k++  +      ++
  gi|488600482|ref|YP_007906953.1|  23 VIAIFSAFMVAGSFliDtTYFKNATNedsnpfNKTFALVGAF---LFVSGFAGIFLVLVDSLAKYLdrF-EKLQKML 95 
                                       79***********88745777777558755445555555555...677889999999998888888443.3344555 PP

                                       HHHHHHHHHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCCHHH CS
                       ECF_trnsprt  71 sfvpiaflsriligliagllykkgkkknlkeivvsfilagvlgtivatllvlliilpl 128
                                       sf+ +  ls+i+++  +++ y ++  +n k  +  ++ +  ++t +a+l+v ++i+ +
  gi|488600482|ref|YP_007906953.1|  96 SFISVVLLSGIATVTFFSIYYLIKTAYNSKDLLSLSFKLFGVMTYIAFLFVTFMIFHF 153
                                       6669999999999999999999999999999888888888899999999988888544 PP

>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.4   5.3e-05     0.096     128     257 ..      21     149 ..       9     154 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHHHHHHHHCTTS-S-.T---...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHH CS
                       Voltage_CLC 128 pvfvasvvaalvlrlllgeepafgeveslfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrl 204
                                       ++++a + a +v+ ++l ++++f++ ++  + ++++ +++v   +++  ++++f  l+  ++++++++ekl++  +l
  gi|488600482|ref|YP_007906953.1|  21 ASVIAIFSAFMVAGSFLIDTTYFKNATNEDSNPFNKTFALVGAFLFVSGFAGIFLVLVDSLAKYLDRFEKLQK--ML 95 
                                       5688999999999999999999*98555445555555555555556677889999999999999999974444..33 PP

                                       HHHHHHHHHHHHC..CCSC.C.CSSSSCCHHHHHCTT-S-HHHHHH...HHHHHHH CS
                       Voltage_CLC 205 epalvgllvgllg..lllp.asvlgggyeliasllegstlllsllllllllllkll 257
                                         + v+ll g+ +  ++     ++++ y+  ++ll+ s +l+ +++ + +l++ ++
  gi|488600482|ref|YP_007906953.1|  96 SFISVVLLSGIATvtFFSIyY-LIKTAYN-SKDLLSLSFKLFGVMTYIAFLFVTFM 149
                                       333333333333300333313.4444443.33344333334555555555554444 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0012       2.1      86     129 ..      19      63 ..      12      68 .. 0.87
   2 ?    5.9   4.8     0.007        13      48     107 ..      92     153 ..      62     177 .] 0.49

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                              GWT1  86 pYvlwvvalnltllllflliel.lfvekeeekerkekatstvlea 129
                                       +Y  +++ +++++++ ++li++ +f ++++e++++ ++t +++ a
  gi|488600482|ref|YP_007906953.1|  19 KYASVIAIFSAFMVAGSFLIDTtYFKNATNEDSNPFNKTFALVGA 63 
                                       69999*****************98888888888888888887765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.007
                              GWT1  48 ketlkllikllllsilllll..llllelyvefvSRrlaNlpYvlwvvalnltllllfl.liel 107
                                       +++l+  i+++lls + +++   +++ +++ ++S+ l  l++ l+ v++ +++l++ + ++++
  gi|488600482|ref|YP_007906953.1|  92 QKMLSF-ISVVLLSGIATVTffSIYYLIKTAYNSKDLLSLSFKLFGVMTYIAFLFVTFmIFHF 153
                                       222222.22222222222220023334445569*********999665555555555515555 PP

>> DUF2214  Predicted membrane protein (DUF2214)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.7   0.00023      0.41      15     100 ..      26     113 ..      17     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                           DUF2214  15 llvaalaaeavllrre.lsaeevkrlalaDlvyglaallvlvtGllrvl.yfgkGlafYlhnplFwlKvglfvlvgl 89 
                                       ++ a+++a  +l+ ++ +++++ ++   ++ ++ l++++++v+G++ ++ +    la Yl       K+  f+ v+l
  gi|488600482|ref|YP_007906953.1|  26 IFSAFMVAGSFLIDTTyFKNATNEDSNPFNKTFALVGAFLFVSGFAGIFlVLVDSLAKYLDRFEKLQKMLSFISVVL 102
                                       334555555666666655667777777889999**************99788999999******************* PP

                           DUF2214  90 lslyPtltfir 100
                                       ls + t+tf++
  gi|488600482|ref|YP_007906953.1| 103 LSGIATVTFFS 113
                                       ********986 PP

>> DUF2723  Protein of unknown function (DUF2723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.014        26      44      86 ..      21      66 ..      12      71 .. 0.77
   2 ?    8.9   2.4   0.00074       1.3      23      86 ..      75     140 ..      69     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                           DUF2723 44 nllsalssaltilflfltitlllr...skakkiailgaglvgalaf 86
                                      + + a++sa+++   fl+ t   +   ++ ++ + ++ +lvga++f
  gi|488600482|ref|YP_007906953.1| 21 ASVIAIFSAFMVAGSFLIDTTYFKnatNEDSNPFNKTFALVGAFLF 66
                                      4566888999999888888888887776677778888999999887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00074
                           DUF2723  23 flllgrlfslladaekvalrvnllsalssaltilflfltitlllr..skakkiailgaglvgalaf 86 
                                        +l+  l ++l  +ek+  ++ ++s+++ +  + ++f++i  l++   ++k ++ l   l+g +++
  gi|488600482|ref|YP_007906953.1|  75 LVLVDSLAKYLDRFEKLQKMLSFISVVLLSGIATVTFFSIYYLIKtaYNSKDLLSLSFKLFGVMTY 140
                                       467888899999********************************9884455556666666665554 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5    0.0001      0.18      84     152 ..       4      72 ..       1      86 [. 0.67
   2 ?    3.7   7.6     0.021        38      93     157 ..      84     151 ..      78     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                           DUF3169  84 eddeeseeey.eqiekklsiglilssvslilsfllilasyslkiyeeesssklvlifliaivlfliilfl 152
                                       ++++e +  y + ++ k++ +++++s+++++  +li  +y  ++++e+s+    ++ l++++lf+  ++ 
  gi|488600482|ref|YP_007906953.1|   4 NIEKEKNNRYlDILN-KYASVIAIFSAFMVAGSFLIDTTYFKNATNEDSNPFNKTFALVGAFLFVSGFAG 72 
                                       567777788845555.555566666677777777777777777677766665555558888888876654 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.021
                           DUF3169  93 y.eqiekklsiglilss..vslilsfllilasyslkiyeeesssklvlif.liaivlfliilflkiiiq 157
                                       y ++ ek  ++  ++s+  +s i+ + +++++y  k++++ s++ l+l f l++++  +++lf++++i 
  gi|488600482|ref|YP_007906953.1|  84 YlDRFEKLQKMLSFISVvlLSGIATVTFFSIYYLIKTAYN-SKDLLSLSFkLFGVMTYIAFLFVTFMIF 151
                                       5566676555555544411567999999999999997777.4455666669888888888888888765 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   8.2   0.00065       1.2     225     326 ..      23     144 ..       9     153 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00065
                            DUF373 225 vvallllligiisgyislesvss.asvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllp 300
                                       v+a++++++ + s +i ++  ++ ++ +s+ +++++a++ +++ +  +a+++++l+  + +yl ++ ++++++l+ +
  gi|488600482|ref|YP_007906953.1|  23 VIAIFSAFMVAGSFLIDTTYFKNaTNEDSNPFNKTFALVGAFLFVSGFAGIFLVLVDSLAKYL-DRFEKLQKMLSFI 98 
                                       344444333332333332223334556778888888888888888888888899999999999.6677888888777 PP

                            DUF373 301 flvlaiglvl.ygasaylls...................lsilals 326
                                        +vl  g+ + + +s y l                    ++++a+ 
  gi|488600482|ref|YP_007906953.1|  99 SVVLLSGIATvTFFSIYYLIktaynskdllslsfklfgvMTYIAFL 144
                                       7777776666233333333347777777766666555543333333 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4    0.0031       5.6      11      71 ..       8      68 ..       3      84 .. 0.79
   2 ?    4.7   1.0     0.015        26      30      86 ..      61     122 ..      52     124 .. 0.59
   3 ?    3.6   2.4     0.031        56      33      80 ..     104     151 ..      80     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0031
                           DUF2976 11 ekggdllelikgylkdgvillgLvlaavaflaVakaalkkfneisegkaewgkfgltlvvG 71
                                      ek+  +l++++ y+  ++i  + ++a+  ++   +   ++ ++ +   ++++ +g++l v 
  gi|488600482|ref|YP_007906953.1|  8 EKNNRYLDILNKYASVIAIFSAFMVAGSFLIDTTYFKNATNEDSNPFNKTFALVGAFLFVS 68
                                      457889*********************9999998888888888888888888888887774 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.015
                           DUF2976  30 llgLvl.aa.vaflaVakaalkkfneisegkaewgkfgltlv...vGvvllvvviwLltkAa 86 
                                       +++ ++ ++ ++++ V    l+k+ +  e+ ++  +f+++++   ++ v  + + +L+++A 
  gi|488600482|ref|YP_007906953.1|  61 VGAFLFvSGfAGIFLVLVDSLAKYLDRFEKLQKMLSFISVVLlsgIATVTFFSIYYLIKTAY 122
                                       44433313325689999999999999866655555555554411144455555678888876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.031
                           DUF2976  33 LvlaavaflaVakaalkkfneisegkaewgkfgltlvvGvvllvvviw 80 
                                         +a+v f+ + + + + +n  +    ++  fg++  ++++ + ++i+
  gi|488600482|ref|YP_007906953.1| 104 SGIATVTFFSIYYLIKTAYNSKDLLSLSFKLFGVMTYIAFLFVTFMIF 151
                                       34789999***9999999*99999999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); 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:                        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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1083.98
//
Query:       gi|488600483|ref|YP_007906954.1|  [L=124]
Description: hypothetical protein Asulf_00957 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.4   0.0      0.012   15.8   0.0    1.2  1  TMEM131_like  Transmembrane protein 131-like


Domain annotation for each model (and alignments):
>> TMEM131_like  Transmembrane protein 131-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.9e-07     0.012      14      77 ..      49     113 ..      43     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.9e-07
                      TMEM131_like  14 slgkaasrtvtvvNkhkkeklkllsvtsdsie.fqssffeevvlpPggntslkvvFLPrelGase 77 
                                       slg+   +++ v+ +++ + + +l +   +i  f+ +  +e +  P gnt++++  +P+++G+ +
  gi|488600483|ref|YP_007906954.1|  49 SLGSHYVQKLKVHAEKECKIMAILYPKDAAIVyFHDVHGKEIETVPAGNTTVHIHIIPKQIGNLS 113
                                       677778888888887777777777776655434*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 791.41
//
Query:       gi|488600484|ref|YP_007906955.1|  [L=541]
Description: hypothetical protein Asulf_00958 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-09   36.7  26.0    0.00066   19.8   7.1    4.0  4  Pentapeptide_4  Pentapeptide repeats (9 copies)
    1.3e-07   31.1   5.7       0.23   11.1   0.1    6.3  8  Pentapeptide    Pentapeptide repeats (8 copies)
    1.3e-06   28.4  33.9      0.048   13.8   2.2    6.4  4  Pentapeptide_3  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.5   3.3e-06      0.02       8      69 ..     119     182 ..     108     187 .. 0.86
   2 !   19.8   7.1   1.1e-07   0.00066       6      68 ..     195     258 ..     191     261 .. 0.64
   3 !   15.4   0.7   2.6e-06     0.016       2      61 ..     247     307 ..     246     317 .. 0.84
   4 ?   -3.8   0.0       2.5   1.5e+04      47      58 ..     335     346 ..     330     356 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-06
                    Pentapeptide_4   8 fnncklsnvnFsearlrd.cnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.s 69 
                                        n+ ++++++Fs++++++   F e++ ++++F+++ + d    +  + +++F +  + +++f s
  gi|488600484|ref|YP_007906955.1| 119 VNDGQFNYIDFSNVKFHSyVIFFEVDVDEAVFERTEFYDFVQIHGTFSKLNFNAAKFHSAVFmS 182
                                       5777999999999999998889999999999999999999999999999999999999999944 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.1e-07
                    Pentapeptide_4   6 csfnncklsn.vnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf 68 
                                       + f ++k++n v+F + +++ + F  ++++ v+F +  +++vdf  +++++a F  +n  +  f
  gi|488600484|ref|YP_007906955.1| 195 AIFTKTKFENyVQFQNLKFNMAKFDFTKFDTVEFLNVEFQKVDFLRAKFTKAIFYSVNVLEGSF 258
                                       5566677766677777777777777777777777777777777777777777776666655555 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2.6e-06
                    Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFde.cnlsdvdfaevdlkrasFsgc 61 
                                        f ++  ++  ++++ F+ +r  ++ F ++++ +++F+  + +++v f+ +++ r+ F++ 
  gi|488600484|ref|YP_007906955.1| 247 IFYSVNVLEGSFEGAGFESIRVYNSKFIYANFIYATFEYvAEFREVVFYFANFSRTIFKNI 307
                                       5788888888999999999999999999999999999873579999999999999988875 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 2.5
                    Pentapeptide_4  47 dfaevdlkrasF 58 
                                       +f +  l+++sF
  gi|488600484|ref|YP_007906955.1| 335 SFIDFPLTNISF 346
                                       333444444444 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.3   1.8e+03      16      23 ..     127     134 ..     123     136 .. 0.42
   2 ?   -1.7   0.0       0.4   2.4e+03      11      24 ..     143     156 ..     140     157 .. 0.62
   3 ?    0.9   0.1     0.063   3.8e+02      13      26 ..     165     178 ..     162     183 .. 0.49
   4 ?   -0.4   0.0      0.15   9.1e+02      29      39 ..     193     203 ..     191     204 .. 0.50
   5 !    5.5   0.1    0.0022        13       6      38 ..     206     238 ..     205     238 .. 0.93
   6 !   11.1   0.1   3.9e-05      0.23       6      38 ..     216     248 ..     212     248 .. 0.92
   7 !    4.9   0.0    0.0034        21      19      34 ..     269     284 ..     257     286 .. 0.80
   8 !    9.0   0.0   0.00017         1      21      40 .]     287     306 ..     287     306 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.3
                                       CCCESEEE CS
                      Pentapeptide  16 anlsgAnL 23 
                                        ++s+ ++
  gi|488600484|ref|YP_007906955.1| 127 IDFSNVKF 134
                                       33444333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.4
                                       SCCEECCCESEEEC CS
                      Pentapeptide  11 anLsganlsgAnLt 24 
                                        + ++a ++++ ++
  gi|488600484|ref|YP_007906955.1| 143 VDVDEAVFERTEFY 156
                                       55667777777665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.063
                                       CEECCCESEEECT- CS
                      Pentapeptide  13 LsganlsgAnLtgA 26 
                                       +s+ n++ A++++A
  gi|488600484|ref|YP_007906955.1| 165 FSKLNFNAAKFHSA 178
                                       33334444444433 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.15
                                       TT-EECCEEEC CS
                      Pentapeptide  29 sgAdLsganLs 39 
                                       ++A ++ ++++
  gi|488600484|ref|YP_007906955.1| 193 NHAIFTKTKFE 203
                                       55555555555 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.0022
                                       -B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   6 AnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       +++++ +++ a +  ++++ +++ +  ++ +++
  gi|488600484|ref|YP_007906955.1| 206 VQFQNLKFNMAKFDFTKFDTVEFLNVEFQKVDF 238
                                       789*************************99998 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 3.9e-05
                                       -B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   6 AnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       A +  ++++ + + +  ++++++ +A+++ a++
  gi|488600484|ref|YP_007906955.1| 216 AKFDFTKFDTVEFLNVEFQKVDFLRAKFTKAIF 248
                                       78999999999********************98 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.0034
                                       ESEEECT-B-TT-EEC CS
                      Pentapeptide  19 sgAnLtgAnlsgAdLs 34 
                                       +++++++An++ A ++
  gi|488600484|ref|YP_007906955.1| 269 YNSKFIYANFIYATFE 284
                                       6899999999999886 PP

  == domain 8  score: 9.0 bits;  conditional E-value: 0.00017
                                       EEECT-B-TT-EECCEEECT CS
                      Pentapeptide  21 AnLtgAnlsgAdLsganLsg 40 
                                       A ++++ +++A++s++++++
  gi|488600484|ref|YP_007906955.1| 287 AEFREVVFYFANFSRTIFKN 306
                                       56778888888888888765 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   1.4   2.1e-05      0.12       9      46 ..     105     142 ..     104     144 .. 0.90
   2 ?   -0.9   6.3      0.31   1.9e+03       7      21 ..     171     184 ..     140     210 .. 0.57
   3 !    6.9   9.0    0.0011       6.8       5      44 ..     207     248 ..     192     283 .. 0.70
   4 !   13.8   2.2   8.1e-06     0.048       1      33 [.     278     310 ..     278     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                    Pentapeptide_3   9 aadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46 
                                       + +F ++ F+g++ +++ +F+ +dFs++ F+  v F +
  gi|488600484|ref|YP_007906955.1| 105 SIYFNFSEFHGDVWVNDGQFNYIDFSNVKFHSYVIFFE 142
                                       678****************************8898865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.31
                    Pentapeptide_3   7 sgaadFrgatFsgaa 21 
                                         a  F+ a+F +++
  gi|488600484|ref|YP_007906955.1| 171 NAA-KFHSAVFMSGT 184
                                       222.44444444444 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0011
                    Pentapeptide_3   5 nFsgaadFrgatFsgaas....FsnadFgsadFsgarFtgdvdF 44 
                                       +F++   F +a F+ + +    F n  F+ +dF +a Ft  + F
  gi|488600484|ref|YP_007906955.1| 207 QFQNL-KFNMAKFDFTKFdtveFLNVEFQKVDFLRAKFT-KAIF 248
                                       34444.444555555542234477777777777777776.5555 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 8.1e-06
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadF 33 
                                       F  a+F+  a Fr+++F+ a +Fs++ F + a F
  gi|488600484|ref|YP_007906955.1| 278 FIYATFEYVAEFREVVFYFA-NFSRTIFkNIAVF 310
                                       56799***************.9******888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 3153.28
//
Query:       gi|488600485|ref|YP_007906956.1|  [L=289]
Description: hypothetical protein Asulf_00959 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00012   22.3   0.1     0.0012   19.1   0.0    2.2  2  DUF3382     Domain of unknown function (DUF3382)
  ------ inclusion threshold ------
      0.063   13.1   2.9        5.4    6.9   1.4    3.3  3  DUF2976     Protein of unknown function (DUF2976)
       0.21   11.6   1.6         18    5.4   0.0    3.3  3  DUF4227     Protein of unknown function (DUF4227)


Domain annotation for each model (and alignments):
>> DUF3382  Domain of unknown function (DUF3382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.14   8.5e+02      42      91 ..      41      92 ..      27      99 .. 0.65
   2 !   19.1   0.0     2e-07    0.0012       9      80 ..     207     282 ..     203     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                           DUF3382 42 aiavavvfvgqLlrplllqalkarkklkkveskadgvlvl..tqrwiillll 91
                                      ++++++  ++ ++ + +++++k+ +++k +   ++++l +  +  +ii+l+l
  gi|488600485|ref|YP_007906956.1| 41 FFFIGLSGIFVIIANIYMSKFKKIAEEKTFIDFLNSSLLVsiFLSMIIILVL 92
                                      5666677788888888888888888777766655555543554444443333 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2e-07
                           DUF3382   9 aallalvlfvpilGl.qleldgtrlvlep...rwglvaiavavvfvgqLlrplllqalkarkklkkveskadgvlv 80 
                                       +++la++l+++++Gl + el+ + l +e    r+   ai  ++v +++L+++ l  ++++r++++k ++++++v +
  gi|488600485|ref|YP_007906956.1| 207 STILAIGLTYVFFGLsKSELSINFLGIEInsyRISAFAIYLGMVIIVSLFLKILHLRFSNRRESEKPKEHDEPVRN 282
                                       799************76666666565555779******************************99999998888765 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.4   0.00091       5.4      39      80 ..      49      90 ..      32      96 .. 0.76
   2 ?    0.7   0.0     0.077   4.6e+02      23      58 ..     121     157 ..     108     165 .. 0.67
   3 ?    2.3   0.0     0.024   1.4e+02      24      56 ..     240     272 ..     229     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00091
                           DUF2976 39 aflaVakaalkkfneisegkaewgkfgltlvvGvvllvvviw 80
                                       f+ +a+  ++kf+ i e+k     + + l+v + l +++i 
  gi|488600485|ref|YP_007906956.1| 49 IFVIIANIYMSKFKKIAEEKTFIDFLNSSLLVSIFLSMIIIL 90
                                      58899999********88888777788888888877665554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.077
                           DUF2976  23 ylkdgvillgLvlaavaflaVakaalkkfnei.segk 58 
                                       y+    ill   l   ++ ++a+   k++nei +e+k
  gi|488600485|ref|YP_007906956.1| 121 YFGSWTILLYYPLILRMIATIATFPKKQYNEIpDEEK 157
                                       4555555555555556777888888899999954444 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.024
                           DUF2976  24 lkdgvillgLvlaavaflaVakaalkkfneise 56 
                                       + + +i+lg+v+ +  fl++ +  +++ +e ++
  gi|488600485|ref|YP_007906956.1| 240 ISAFAIYLGMVIIVSLFLKILHLRFSNRRESEK 272
                                       45678999**********999887777666655 PP

>> DUF4227  Protein of unknown function (DUF4227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.5       0.3   1.8e+03       4      17 ..      84      97 ..      77     104 .. 0.75
   2 ?    5.4   0.0    0.0029        18       7      26 ..     116     135 ..     112     159 .. 0.89
   3 ?    3.2   0.0     0.014        84       6      43 ..     239     276 ..     237     287 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.3
                           DUF4227  4 lerlkvflLFtvlt 17
                                      l+++ +++LF    
  gi|488600485|ref|YP_007906956.1| 84 LSMIIILVLFARHL 97
                                      67888888887554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0029
                           DUF4227   7 lkvflLFtvltllfyyallw 26 
                                       + v++ F   t+l+yy l++
  gi|488600485|ref|YP_007906956.1| 116 IAVIIYFGSWTILLYYPLIL 135
                                       789*************8876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.014
                           DUF4227   6 rlkvflLFtvltllfyyallwlneeyepyhrYdePeGs 43 
                                       r+  f +++++ +++   l  l+  +++ ++ ++P+++
  gi|488600485|ref|YP_007906956.1| 239 RISAFAIYLGMVIIVSLFLKILHLRFSNRRESEKPKEH 276
                                       678899*****************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1260  (0.0702772); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2087.79
//
Query:       gi|488600486|ref|YP_007906957.1|  [L=56]
Description: hypothetical protein Asulf_00960 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   15.6   0.2       0.03   14.2   0.1    1.7  2  HxlR            HxlR-like helix-turn-helix
       0.04   12.3   0.1      0.041   12.3   0.1    1.0  1  Mlo             Mlo family
      0.045   13.7   0.1      0.083   12.9   0.0    1.5  2  HTH_45          Winged helix-turn-helix
      0.054   13.7   0.1      0.071   13.3   0.1    1.2  1  DUF3970         Protein of unknown function (DUF3970)
      0.099   12.5   0.0       0.12   12.3   0.0    1.2  1  Csm1_B          Csm1 subunit domain B
       0.18   11.6   1.4          3    7.7   0.2    1.9  2  Synaptonemal_3  Synaptonemal complex central element protein 


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 ?   14.2   0.1   9.9e-06      0.03      54      89 ..       3      39 ..       1      41 [. 0.84
   2 ?   -0.0   0.0      0.27     8e+02      26      37 ..      43      54 ..      37      56 .] 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.9e-06
                                      ESSSS-EEE.EEE-TCGGGGHHHHHHHHHHHHHHHHC CS
                              HxlR 54 ypevPpkve.YsltekGrslepvlqelkkwgeeylee 89
                                      ++++P+  e Y lt+ G+++ ++++e++k  e++ ++
  gi|488600486|ref|YP_007906957.1|  3 IHNTPTSSEvYVLTPLGKKIVQLIEEMEKEFEKWHSQ 39
                                      5677776655******************999999776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.27
                                      HHSTTS-HHHHH CS
                              HxlR 26 ralpkisqkmLa 37
                                      + l ki+++mL 
  gi|488600486|ref|YP_007906957.1| 43 KDLEKITNEMLE 54
                                      556678888876 PP

>> Mlo  Mlo family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.4e-05     0.041      17      56 ..      13      52 ..       3      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                               Mlo 17 avlvlisiliekllhklgkwlkkkkkkalleaLekikaeL 56
                                       vl  +   i +l++++ k ++k + +al++ Leki +e+
  gi|488600486|ref|YP_007906957.1| 13 YVLTPLGKKIVQLIEEMEKEFEKWHSQALFKDLEKITNEM 52
                                      5666677778899***********************9997 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.8e-05     0.083      52      75 ..       9      32 ..       2      34 .. 0.88
   2 ?   -2.5   0.0       1.7   5.1e+03       6      12 ..      47      53 ..      41      55 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                            HTH_45 52 skekYvlTekGlelleklkeleel 75
                                      s+e YvlT  G+++++ ++e+e+ 
  gi|488600486|ref|YP_007906957.1|  9 SSEVYVLTPLGKKIVQLIEEMEKE 32
                                      7899****************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                            HTH_45  6 eIiadIL 12
                                      +I+ ++L
  gi|488600486|ref|YP_007906957.1| 47 KITNEML 53
                                      3344444 PP

>> DUF3970  Protein of unknown function (DUF3970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.4e-05     0.071      11      35 ..      20      47 ..      15      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                           DUF3970 11 eEieeflksleknyevtytS...keytr 35
                                      + i+++++++ek++e+ +     k+  +
  gi|488600486|ref|YP_007906957.1| 20 KKIVQLIEEMEKEFEKWHSQalfKDLEK 47
                                      78**************997666666666 PP

>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.9e-05      0.12      46      80 ..      11      45 ..       6      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                                      EEEEEEE--HHHHHHHHHHHHHHHHHCCCCTSSS- CS
                            Csm1_B 46 hfylLlpntekvkekleeiekelnewllkefkgkL 80
                                      ++y+L+p  +k+ + +ee+eke+++w  +   ++L
  gi|488600486|ref|YP_007906957.1| 11 EVYVLTPLGKKIVQLIEEMEKEFEKWHSQALFKDL 45
                                      78************************887765555 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 ?    3.8   0.1     0.016        49      12      27 ..      16      31 ..       6      38 .. 0.55
   2 ?    7.7   0.2     0.001         3      18      32 ..      38      52 ..      32      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                    Synaptonemal_3 12 edfskeslqlnkdlek 27
                                        ++k+ +ql +++ek
  gi|488600486|ref|YP_007906957.1| 16 TPLGKKIVQLIEEMEK 31
                                      4444555555555554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.001
                    Synaptonemal_3 18 slqlnkdleklteqm 32
                                      s  l kdlek+t++m
  gi|488600486|ref|YP_007906957.1| 38 SQALFKDLEKITNEM 52
                                      56799*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 338.49
//
Query:       gi|488600487|ref|YP_007906958.1|  [L=113]
Description: transcriptional regulator, HxlR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   29.8   0.1    5.2e-07   29.4   0.1    1.1  1  HxlR      HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.065   13.8   0.3        0.2   12.2   0.0    1.8  2  DUF4706   Domain of unknown function (DUF4706)


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 !   29.4   0.1   5.8e-11   5.2e-07       2      88 ..      11      95 ..      10      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.8e-11
                                      HHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-.EEEEEE-TCGGGGHHHHHHH CS
                              HxlR  2 iggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPp.kveYsltekGrslepvlqel 79
                                      i++k ++ il++l + +kR+sel++ +    +k L + ++eL   gli+ +    +P+    Y+l++ G+++ ++l+++
  gi|488600487|ref|YP_007906958.1| 11 ITKKTNMTILFSLKDSPKRWSELEKSI---YKKDLHKGIKELLDLGLIQITLRFDTPTgSKAYELSPLGKKIVQLLEQI 86
                                      78999*******************987...99*******************99999973568****************9 PP

                                      HHHHHHHHH CS
                              HxlR 80 kkwgeeyle 88
                                      ++  ++y +
  gi|488600487|ref|YP_007906958.1| 87 EEEYTKYHS 95
                                      987777755 PP

>> DUF4706  Domain of unknown function (DUF4706)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.23   2.1e+03       9      20 ..       7      18 ..       2      45 .. 0.57
   2 ?   12.2   0.0   2.2e-05       0.2       5      44 ..      71     110 ..      69     113 .] 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.23
                           DUF4706  9 markImedkeei 20
                                      +a+kI + ++ +
  gi|488600487|ref|YP_007906958.1|  7 LAKKITKKTNMT 18
                                      667776655443 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.2e-05
                           DUF4706   5 slnsmarkImedkeeikekyepewerlspkeqdelidesl 44 
                                       +l+++ +kI++  e+i e+y++  ++ ++k+ ++ i+e l
  gi|488600487|ref|YP_007906958.1|  71 ELSPLGKKIVQLLEQIEEEYTKYHSKAPQKDPEKFINELL 110
                                       69******************************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 736.62
//
Query:       gi|488600488|ref|YP_007906959.1|  [L=204]
Description: hypothetical protein Asulf_00962 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0003   20.8   0.0    0.00052   20.1   0.0    1.3  1  DUF4145    Domain of unknown function (DUF4145)
  ------ inclusion threshold ------
       0.08   13.3   0.1       0.21   12.0   0.1    1.9  2  HEPN_Swt1  Swt1-like HEPN


Domain annotation for each model (and alignments):
>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.8e-08   0.00052       4      81 ..     102     185 ..      99     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.8e-08
                           DUF4145   4 ekllnaspkasavliRraLEkllkdkgiakgkd.....LknkiealvekgvipeklkelldairviGNdgaHelk.. 73 
                                       ek+  ++p +++v++ r +E ++++ + ++  +     ++ +i++l  k++i+++l + +++  +i+N   H+ k  
  gi|488600488|ref|YP_007906959.1| 102 EKISEVDPHTAIVYLGREIESIIREIYRKHFPTqrpqpIYFMIKDLETKEIISPELSSIIRRFWMIRNQVLHK-Kdv 177
                                       788899*********************444333455569*********************************8.512 PP

                           DUF4145  74 ditkedae 81 
                                       ++t+e+  
  gi|488600488|ref|YP_007906959.1| 178 KLTQEEMY 185
                                       56667665 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.29   2.6e+03      57      84 ..      70      98 ..      50     105 .. 0.60
   2 ?   12.0   0.1   2.3e-05      0.21      69     113 ..     150     196 ..      80     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.29
                         HEPN_Swt1 57 lrvite..nWkevFkkklsraerslaseLr 84
                                      lr ++    ++e +k+k++ + rsl s+L+
  gi|488600488|ref|YP_007906959.1| 70 LRSLSLmmDFEE-IKSKIEPEFRSLFSQLI 98
                                      444443445566.67777777777777665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.3e-05
                         HEPN_Swt1  69 kkklsraerslaseLrevRNkwaHqe..sfstddayraldtierllr 113
                                       k+ +s +  s++   + +RN++ H++  +++++++y  l    r+++
  gi|488600488|ref|YP_007906959.1| 150 KEIISPELSSIIRRFWMIRNQVLHKKdvKLTQEEMYEMLLLGLRIIK 196
                                       45667777899999**********88789********9987777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1446.62
//
Query:       gi|488600489|ref|YP_007906960.1|  [L=309]
Description: hypothetical protein Asulf_00963 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.02   15.5   0.1      0.096   13.4   0.0    2.2  2  TPR_6           Tetratricopeptide repeat
      0.023   15.1   3.4       0.04   14.4   0.8    2.2  2  RXLR            RXLR phytopathogen effector protein, Avirulen
      0.078   13.1   1.1       0.56   10.4   0.1    2.5  3  Nod1            Gef2-related medial cortical node protein Nod
        0.2   12.0   2.5        1.4    9.3   0.1    2.3  2  HEPN_Swt1       Swt1-like HEPN
       0.39   10.6   8.5        1.2    9.0   0.3    3.1  3  HEPN_RiboL-PSP  RiboL-PSP-HEPN


Domain annotation for each model (and alignments):
>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.7e-05     0.096      10      32 ..      44      66 ..      38      67 .. 0.83
   2 ?   -2.8   0.1       3.8   1.4e+04      21      29 ..     137     145 ..     132     146 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 10 yrklgdtdkAlealerlikeYPd 32
                                      +++l + ++A+e le+li++YP+
  gi|488600489|ref|YP_007906960.1| 44 LKSLSEFSNAVEQLEKLIRNYPN 66
                                      556668899*************8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.8
                                       HHHHHHHHH CS
                             TPR_6  21 ealerlike 29 
                                       +a ++l++e
  gi|488600489|ref|YP_007906960.1| 137 DAAKKLLDE 145
                                       445555555 PP

>> RXLR  RXLR phytopathogen effector protein, Avirulence activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   1.1e-05      0.04      45     139 ..      52     158 ..      35     160 .. 0.75
   2 ?    1.0   0.1      0.15   5.3e+02      91     116 ..     265     290 ..     198     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                              RXLR  45 srdaadkRfLRshkaeeddeeseeraagknlld..............vfvekklkkmlanekyakklFreWkanGft 107
                                       +++++ ++++R++   ++++ +ee +  k + +               f +       ++  +ak+l  +W ++++t
  gi|488600489|ref|YP_007906960.1|  52 NAVEQLEKLIRNYP--NKKDWEEESNLSKLAYHlitaisyhgeyiflYFPKLAKSRYASDFLHAKDLHIHWERYNQT 126
                                       55666667778777..5555555555555444566677888888765555555556789999*************** PP

                              RXLR 108 lkdieseLkqsearklkekYktlakqYaaylk 139
                                       +k+ie +   + a+kl + +++++++++ +l 
  gi|488600489|ref|YP_007906960.1| 127 RKRIEVKRYLDAAKKLLDEFYEIVEEFDWFLM 158
                                       ******99999999***********9999875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                              RXLR  91 ekyakklFreWkanGftlkdieseLk 116
                                       ++ ++++F++W +  +t+ + ++ L 
  gi|488600489|ref|YP_007906960.1| 265 PDDTTDIFDNWREIAITTARAANGLW 290
                                       45678899999999999999998875 PP

>> Nod1  Gef2-related medial cortical node protein Nod1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00015      0.56      27      84 ..      10      67 ..       3      69 .. 0.93
   2 ?   -0.1   0.1      0.25   9.1e+02     128     144 ..      79      95 ..      74      96 .. 0.88
   3 ?   -3.5   0.0         3   1.1e+04      86      98 ..     140     152 ..     121     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                              Nod1 27 fgsFlkYlkdkilekaGylLsekliqrLenldldlnskslkekavqqvkslleeLpes 84
                                      f  F kY++ +  ++ G  +  k    +en+   l s s +++av+q+ +l+++ p++
  gi|488600489|ref|YP_007906960.1| 10 FDEFEKYVNPFFINHQGPYIGMKQSCLFENIMEVLKSLSEFSNAVEQLEKLIRNYPNK 67
                                      788***************9999999999*************************99986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.25
                              Nod1 128 eayelveflsleadelf 144
                                        ay+l+  +s++ +++f
  gi|488600489|ref|YP_007906960.1|  79 LAYHLITAISYHGEYIF 95 
                                       589************99 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3
                              Nod1  86 lklLevvfsivse 98 
                                        klL+ +  iv+e
  gi|488600489|ref|YP_007906960.1| 140 KKLLDEFYEIVEE 152
                                       4677777777765 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3     0.054   1.9e+02      27     113 ..      54     144 ..      36     146 .. 0.70
   2 ?    9.3   0.1    0.0004       1.4      43      94 ..     214     266 ..     196     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.054
                         HEPN_Swt1  27 weeveaslekdeeekkesekeiskldvqdllrvitenWkevFkkklsraerslaseLrevRNkwaHqe....sfstd 99 
                                       +e++e+ ++++ ++k  +e++  ++ ++ l+++i+ + +++F    + a+ ++as+  ++++   H e    + +  
  gi|488600489|ref|YP_007906960.1|  54 VEQLEKLIRNYPNKKDWEEESNLSKLAYHLITAISYHGEYIFLYFPKLAKSRYASDFLHAKDLHIHWErynqTRKRI 130
                                       45555555555555544555556666778889999999998888666677889999999999999954344466667 PP

                         HEPN_Swt1 100 dayraldtierllr 113
                                       ++ r ld +++ll 
  gi|488600489|ref|YP_007906960.1| 131 EVKRYLDAAKKLLD 144
                                       88899998888885 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0004
                         HEPN_Swt1  43 esekeiskldvqdllrvite.nWkevFkkklsraerslaseLrevRNkwaHqe 94 
                                       ++++ ++k+ + +l + +++ +W++  ++  +++ + l++ L+ +RNk aH +
  gi|488600489|ref|YP_007906960.1| 214 DKQEPLHKQSLTNLTEGLYRvRWRDNGERVVTKEIKDLIKFLISLRNKKAHPD 266
                                       4566677777777777777789*999999999999****************64 PP

>> HEPN_RiboL-PSP  RiboL-PSP-HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.11   3.8e+02     101     125 ..      33      59 ..       2     105 .. 0.54
   2 ?    4.7   0.2     0.007        25     166     193 ..     124     151 ..     108     152 .. 0.85
   3 ?    9.0   0.3   0.00034       1.2     127     168 ..     198     270 ..     196     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
                    HEPN_RiboL-PSP 101 fklfgenisekink..afidtesnlks 125
                                        ++++eni e +++  +f++  + l++
  gi|488600489|ref|YP_007906960.1|  33 QSCLFENIMEVLKSlsEFSNAVEQLEK 59 
                                       455555555555552222222222222 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.007
                    HEPN_RiboL-PSP 166 dtdltkdeleeyidfikelvealdeile 193
                                       +++ +  e++ y+d +k+l+++++ei+e
  gi|488600489|ref|YP_007906960.1| 124 NQTRKRIEVKRYLDAAKKLLDEFYEIVE 151
                                       4788999******************998 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00034
                    HEPN_RiboL-PSP 127 vleeifkrlglekskkeskk................................kklnelvkrRNeIAHgndsdtd 168
                                       vl++i k+lg++++kk++ +                                  ++ l+++RN+ AH +d+ td
  gi|488600489|ref|YP_007906960.1| 198 VLRRISKNLGVKIIKKDKQEplhkqsltnlteglyrvrwrdngervvtkeikDLIKFLISLRNKKAHPDDT-TD 270
                                       6788889999999999999999999999999999999999999999999999***************9999.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2177.46
//
Query:       gi|488600490|ref|YP_007906961.1|  [L=113]
Description: transcriptional regulator, HxlR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   36.0   0.1    6.2e-09   35.6   0.1    1.3  1  HxlR      HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.075   13.6   0.2       0.37   11.4   0.0    2.1  2  RPAP3_C   Potential Monad-binding region of RPAP3
      0.077   13.0   0.1        0.2   11.7   0.1    1.8  1  HTH_45    Winged helix-turn-helix
      0.079   13.2   0.3        2.2    8.6   0.1    2.2  2  DUF3970   Protein of unknown function (DUF3970)
       0.09   11.4   0.3      0.092   11.4   0.3    1.0  1  DUF2748   Protein of unknown function (DUF2748)


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 !   35.6   0.1   1.7e-12   6.2e-09       8      88 ..      18      96 ..       4      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.7e-12
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-.EEEEEE-TCGGGGHHHHHHHHHHHHH CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPp.kveYsltekGrslepvlqelkkwgee 85
                                        il++l +g+kR+s+l++      +k+L++++ eL   glie+++++ +P+    Y+l++ G+++ ++l++++k  ee
  gi|488600490|ref|YP_007906961.1| 18 FKILIALNDGSKRWSQLEKLA---DKKTLSKSINELFDLGLIEATIIHDTPTgSKAYQLSPLGKKVVQLLEQIEKEFEE 93
                                      679****************98...89*************************83467*****************998888 PP

                                      HHH CS
                              HxlR 86 yle 88
                                      y +
  gi|488600490|ref|YP_007906961.1| 94 YHS 96
                                      865 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.37      68      92 ..       4      28 ..       1      30 [. 0.85
   2 ?    0.8   0.0       0.2   7.3e+02      37      39 ..      50      52 ..      24     104 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                           RPAP3_C 68 lvleiLdrLskvkRFdmlvmflsdq 92
                                       +leiL++Lsk+  F++l+ + + +
  gi|488600490|ref|YP_007906961.1|  4 NLLEILKKLSKTGNFKILIALNDGS 28
                                      589***************9987765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                           RPAP3_C 37 iFk 39
                                      +F+
  gi|488600490|ref|YP_007906961.1| 50 LFD 52
                                      332 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.6e-05       0.2      33      75 ..      40      90 ..       3      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                            HTH_45 33 ykllnkYLdmLvekgli........kkskekYvlTekGlelleklkeleel 75
                                       k+l+k ++ L + gli         + ++ Y+l   G+++++ l+++e+ 
  gi|488600490|ref|YP_007906961.1| 40 KKTLSKSINELFDLGLIeatiihdtPTGSKAYQLSPLGKKVVQLLEQIEKE 90
                                      68999***********99999998767999****************99875 PP

>> DUF3970  Protein of unknown function (DUF3970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.04   1.4e+02      10      26 ..       2      20 ..       1      29 [. 0.87
   2 ?    8.6   0.1   0.00061       2.2      11      36 ..      78     105 ..      73     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.04
                           DUF3970 10 qeEieeflkslek..nyev 26
                                      +e + e+lk+l+k  n+++
  gi|488600490|ref|YP_007906961.1|  2 KENLLEILKKLSKtgNFKI 20
                                      578899*******999987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00061
                           DUF3970  11 eEieeflksleknyevtytS..keytrt 36 
                                       + ++++l+++ek++e  +    ke+ + 
  gi|488600490|ref|YP_007906961.1|  78 KKVVQLLEQIEKEFEEYHSHlpKEPEKF 105
                                       6799**********96554466998875 PP

>> DUF2748  Protein of unknown function (DUF2748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   2.6e-05     0.092      20     109 ..       3      95 ..       1     110 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                           DUF2748  20 peleelakelvlsGklri..dand.kinfarlslpylsvslmfslreltdlkllketkkllssvlkkdtdssalddk 93 
                                        +l e+ k+l ++G+++i    nd    +++l + ++++ l  s +el dl l+++t    +   +k  + s l +k
  gi|488600490|ref|YP_007906961.1|   3 ENLLEILKKLSKTGNFKIliALNDgSKRWSQLEKLADKKTLSKSINELFDLGLIEATIIHDTPTGSKAYQLSPLGKK 79 
                                       55567788999999888632567724579****************************9888899999999******* PP

                           DUF2748  94 vrsevsklkkqikklq 109
                                       v + +++++k+ + + 
  gi|488600490|ref|YP_007906961.1|  80 VVQLLEQIEKEFEEYH 95 
                                       ***********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 717.50
//
Query:       gi|488600491|ref|YP_007906962.1|  [L=59]
Description: hypothetical protein Asulf_00965 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       371  (0.0206927); 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:                         0  (0); expected 0.2 (1e-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: 406.90
//
Query:       gi|488600492|ref|YP_007906963.1|  [L=40]
Description: hypothetical protein Asulf_00966 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 268.25
//
Query:       gi|488600493|ref|YP_007906964.1|  [L=66]
Description: hypothetical protein Asulf_00967 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 462.59
//
Query:       gi|488600494|ref|YP_007906965.1|  [L=89]
Description: hypothetical protein Asulf_00968 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.3   0.0      0.025   14.9   0.0    1.6  2  Biliv-reduc_cat  Biliverdin reductase, catalytic
  ------ inclusion threshold ------
       0.02   15.1   0.1      0.022   15.0   0.1    1.1  1  RecJ_OB          RecJ OB domain
      0.037   14.5   0.1      0.094   13.2   0.0    1.7  3  OAM_dimer        Dimerisation domain of d-ornithine 4,5-amino


Domain annotation for each model (and alignments):
>> Biliv-reduc_cat  Biliverdin reductase, catalytic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.48   2.9e+03      46      65 ..       7      28 ..       5      35 .. 0.69
   2 !   14.9   0.0   4.2e-06     0.025      46      85 ..      45      86 ..      42      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.48
                   Biliv-reduc_cat 46 dlfG..elsvtsatleedkekk 65
                                      +lfG  e+ v+ a+  e++ +k
  gi|488600494|ref|YP_007906965.1|  7 ELFGleEIEVVDAQTAEKDGQK 28
                                      6777556777777777766555 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.2e-06
                   Biliv-reduc_cat 46 dlfGelsvtsatl..eedkekkyskmtaklktadkrpltWie 85
                                       +fGe ++ sa    e ++ k y+k+ ak+ t+ ++ + Wi+
  gi|488600494|ref|YP_007906965.1| 45 GFFGEKAIESALKhgEKRDGKVYLKVPAKFITKGEKRVQWIN 86
                                      68*******9976113344578******************97 PP

>> RecJ_OB  RecJ OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   3.6e-06     0.022      32      86 ..       8      63 ..       6      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-06
                           RecJ_OB 32 vfllknvkvesarivgkeknhlklkledesgksleaiaFnlaeklee.lekgdkvd 86
                                      +f+l++++v +a++  k+++ + +   +++g +++ai+F  ++ +e+ l++g+k d
  gi|488600494|ref|YP_007906965.1|  8 LFGLEEIEVVDAQTAEKDGQKILVVYGKHNGVEIDAIGFFGEKAIESaLKHGEKRD 63
                                      799****************999999999999*********9988887777777655 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 ?   13.2   0.0   1.6e-05     0.094      37      66 ..       7      37 ..       2      45 .. 0.80
   2 ?   -2.5   0.0       1.2   7.3e+03      37      37 ..      60      60 ..      48      68 .. 0.51
   3 ?   -2.4   0.0       1.1   6.6e+03      10      17 ..      62      69 ..      58      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                      HCTTSEEEEEEEEEEEET.TEEEEEEEEE-- CS
                         OAM_dimer 37 kkmGledpeVvhkeelhe.eftffvvyGkvs 66
                                      +  Gle++eVv +++ ++ +   +vvyGk +
  gi|488600494|ref|YP_007906965.1|  7 ELFGLEEIEVVDAQTAEKdGQKILVVYGKHN 37
                                      568***************777899****975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                                      H CS
                         OAM_dimer 37 k 37
                                      +
  gi|488600494|ref|YP_007906965.1| 60 E 60
                                      2 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.1
                                      T--EEEEE CS
                         OAM_dimer 10 nDGvvqls 17
                                       DG+v l+
  gi|488600494|ref|YP_007906965.1| 62 RDGKVYLK 69
                                      58999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 598.33
//
Query:       gi|488600495|ref|YP_007906966.1|  [L=1358]
Description: hypothetical protein Asulf_00969 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-11   42.2   0.2      1e-10   41.0   0.2    1.6  1  DNA_pol_B       DNA polymerase family B
    4.1e-08   32.7   2.2    9.1e-08   31.6   0.8    2.3  2  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
     0.0027   17.4   0.1     0.0027   17.4   0.1    2.5  4  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 !   41.0   0.2   1.7e-14     1e-10     152     302 ..     505     636 ..     487     693 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.7e-14
                                       HHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS......T-EEEE CS
                         DNA_pol_B 152 ldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeee.klkviY 227
                                        d  Q a+Kv+ Ns YG +  +++  + +a A+ +T+  R mL k    +++k                e +++v Y
  gi|488600495|ref|YP_007906966.1| 505 GDPSQVAYKVLLNSCYGKLAESEGEWYNKACASAITSFVRAMLFKCL--MKAK----------------ElGVQVLY 563
                                       5789***************************************8764..4544................229***** PP

                                       EBSSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTSEEEEES CS
                         DNA_pol_B 228 GDTDSvfielkvkdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskanklliKG 302
                                        DTDS++++   k++  l +  ++l+   +e   +++lk e e++  +   ++ K+Y+ ++ ++ + +  ++iKG
  gi|488600495|ref|YP_007906966.1| 564 SDTDSMYVKATEKQIRLLQDYSNKLNPLPKELYGEDNLKDEGENII-CFFATKRKRYTKVIENE-DGSITVVIKG 636
                                       *******************************99999********96.56678888998887774.4444578888 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 !   31.6   0.8   1.5e-11   9.1e-08     229     293 ..     105     168 ..      56     189 .. 0.75
   2 ?   -2.1   0.0      0.27   1.6e+03      19      62 ..    1203    1247 ..    1195    1263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.5e-11
                                       TEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCE CS
                    DNA_pol_B_exo1 229 gvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggr 293
                                       + + + f+sEkel++ f+ef+++  P+ ++g+Ni  FDl  ++++ +++++  ++++      g+
  gi|488600495|ref|YP_007906966.1| 105 ELNFYLFNSEKELIESFFEFLRKN-PKHLIGHNIAHFDLGLLNQKRQKYKIEGFRFFAHNVGAGE 168
                                       334459****************65.**********************999988877765444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.27
                                        EE.EEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECC CS
                    DNA_pol_B_exo1   19 fY.ceapdgkeleevkeelkelyeelskkvtkivkvelvlkksly 62  
                                         Y + a d k+l e+ ++ + +y++  + ++k+++ve++l++++ 
  gi|488600495|ref|YP_007906966.1| 1203 AYvFNALDHKSLLEFVKQSDSYYNGVMNAFRKVKTVEVKLSTRYN 1247
                                        443566677888899999999*****9999999999999998764 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 !   17.4   0.1   4.5e-07    0.0027      36      89 ..     113     166 ..     105     181 .. 0.88
   2 ?   -4.0   0.4       1.6   9.8e+03     158     197 ..     757     797 ..     743     803 .. 0.70
   3 ?   -2.5   0.0      0.55   3.3e+03      24      51 ..     891     918 ..     882     919 .. 0.82
   4 ?   -4.3   0.0         2   1.2e+04     160     187 ..    1065    1092 ..    1057    1096 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.5e-07
                    DNA_pol_B_exo2  36 sekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsapkyfdegded 89 
                                       sekeli++ffe+++k+  +l+++n   fDl +l+++  k++++  ++f ++  +
  gi|488600495|ref|YP_007906966.1| 113 SEKELIESFFEFLRKNPKHLIGHNIAHFDLGLLNQKRQKYKIEGFRFFAHNVGA 166
                                       79*****************************************99999876554 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.6
                    DNA_pol_B_exo2 158 YcetDvlnTYlvylrlellr.gklseeeyaeeiaqvrelle 197
                                       Y ++  l+TYl  l+ e+ + ++l+++++++ ++ +++ l 
  gi|488600495|ref|YP_007906966.1| 757 YDRFLELKTYLSDLKAEKKKyDRLKTSKWQQFYELLKNELY 797
                                       55555577888777776654377888888888887777775 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.55
                    DNA_pol_B_exo2  24 kfkvkslgeeessekelikkffegvekk 51 
                                       + k+k l++e ++ek  i  ffe+++ +
  gi|488600495|ref|YP_007906966.1| 891 EAKLKRLEKEVKKEKPYIGLFFEVWKGY 918
                                       458999999999**********999865 PP

  == domain 4  score: -4.3 bits;  conditional E-value: 2
                    DNA_pol_B_exo2  160 etDvlnTYlvylrlellrgklseeeyae 187 
                                        +tD+ + Y v ++l+ l  ++ e+++ +
  gi|488600495|ref|YP_007906966.1| 1065 QTDIFKVYYVAIKLQNLMRQFIEDQFRK 1092
                                        6899999999999999999988888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1335  (0.0744604); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.83u 0.29s 00:00:01.11 Elapsed: 00:00:00.46
# Mc/sec: 8904.02
//
Query:       gi|488600496|ref|YP_007906967.1|  [L=181]
Description: hypothetical protein Asulf_00970 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   12.7   0.0       0.16   11.8   0.0    1.4  1  DUF4817   Helix-turn-helix domain (DUF4817)


Domain annotation for each model (and alignments):
>> DUF4817  Helix-turn-helix domain (DUF4817)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.7e-06      0.16      25      54 ..     125     154 ..     123     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.7e-06
                           DUF4817  25 afrrrFpnrsvPsrstirrlvkkfeetGsv 54 
                                       +f +++   ++P+ +ti r+ k+fe +G v
  gi|488600496|ref|YP_007906967.1| 125 KFLKKYDIAKIPDYRTIERILKEFEVSGIV 154
                                       577899999*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1286.47
//
Query:       gi|488600497|ref|YP_007906968.1|  [L=54]
Description: hypothetical protein Asulf_00971 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 343.21
//
Query:       gi|488600498|ref|YP_007906969.1|  [L=393]
Description: hypothetical protein Asulf_00972 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-96  322.8  42.6    4.5e-96  322.6  42.6    1.0  1  DUF401    Protein of unknown function (DUF401)


Domain annotation for each model (and alignments):
>> DUF401  Protein of unknown function (DUF401)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.6  42.6  2.5e-100   4.5e-96       4     387 ..       4     391 ..       2     393 .] 0.96

  Alignments for each domain:
  == domain 1  score: 322.6 bits;  conditional E-value: 2.5e-100
                            DUF401   4 vllllfsvivvlilikklsisllifvivailalkvlileillvtlksladsftieivvvvllalllGyseksfGdle 80 
                                       +l+l+ s++ +l+li+ ++is++i  ++ il +++l+l+++  +++s+ ds t  iv++v+la++lGys++++  +e
  gi|488600498|ref|YP_007906969.1|   4 SLALFISIAFILVLIRFINISVAILAGSFILGFLTLGLDVFSHIISSVLDSETLRIVTIVVLAFTLGYSMEYLKLFE 80 
                                       799999*********************************************************************** PP

                            DUF401  81 kvseelreifskyvdllvPlliGllPmPGGalisavilknllkeerisseklalknywfrhvivtfwPlyPavvlva 157
                                        +++ ++ + + ++ +l+Pl++G+lPmPGGalisa+++ +l+ke+r+s+e+++  nywfrh +v  wPlyP+ v++ 
  gi|488600498|ref|YP_007906969.1|  81 GLTNSVSRMTGMFSVVLIPLIVGFLPMPGGALISAIMIASLVKEYRLSPERATFINYWFRHLWVAVWPLYPSFVVGV 157
                                       ***************************************************************************** PP

                            DUF401 158 elvnvdyfkvalalfPvfvialtlG..ltltrkqerrlrksrslfdsli.nlyPliillilsvlllldkllalvvll 231
                                       ++    + +v +a++P+ ++a++ G  +t++ k   rlr + + f  li  +yP++ + +l++ l++d ll+lv++ 
  gi|488600498|ref|YP_007906969.1| 158 AVLKSSFAEVVMATYPIAILAILSGmaMTFSEKFSIRLRPTMKDFLMLIySFYPVLLVAVLAIGLKIDFLLTLVIAN 234
                                       *************************7778888999999877665555442678888888888899************ PP

                            DUF401 232 lavsiyavakledllkilkrvvdkkvilllfavyvykvvvensGvaeslaedv.rlnlsapillilltllvGiatGi 307
                                       +   i+ ++    ++ i++r++d  +i+l+fav++yk ++e +  ae +++++ +++++ p++ +++++l+G++tG+
  gi|488600498|ref|YP_007906969.1| 235 MVLFIHKRVDWGAIRSIFRRTIDFNIIILIFAVMIYKNLIETTSSAEIFFQHLnEWSVPVPVASFIMSFLIGFSTGV 311
                                       *************************************************888736********************** PP

                            DUF401 308 eqaavsialPlltevtssgivvakylvlviaaaviGvilsPvhlcvvlsakyfevevfdilkklllilvltlilval 384
                                       e +++s+alPllt +t+ g ++  +++lv+  ++ Gv+ sP+hlc+vl+a+yf+  ++ +++ l+  + l ++l ++
  gi|488600498|ref|YP_007906969.1| 312 EISYASVALPLLTGFTGVGEIIPENVMLVFGSGFLGVMTSPLHLCLVLTAQYFNARLYGVYRYLIPAVILEAALIWV 388
                                       *****************************************************************99********** PP

                            DUF401 385 vll 387
                                       ++ 
  gi|488600498|ref|YP_007906969.1| 389 IYV 391
                                       997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2477.15
//
Query:       gi|488600499|ref|YP_007906970.1|  [L=687]
Description: methionyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-152  506.2   0.1   4.9e-152  506.2   0.1    1.5  2  tRNA-synt_1g   tRNA synthetases class I (M)
    4.4e-26   90.8   0.2      1e-25   89.7   0.2    1.7  1  tRNA_bind      Putative tRNA binding domain
    1.9e-17   62.8  10.0    7.3e-11   41.0   0.0    4.6  4  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.5e-11   44.2   5.7    4.9e-10   39.2   0.0    2.9  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    2.1e-06   27.8   4.9    4.5e-06   26.7   4.9    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
       0.33   11.0   8.2       0.69   10.0   8.2    1.6  1  DZR            Double zinc ribbon
       0.41   10.9   0.1       0.41   10.9   0.1    3.4  3  zf-RING_7      C4-type zinc ribbon domain
       0.53   10.3   8.5       0.15   12.1   5.2    1.7  2  TERB2          Telomere-associated protein TERB2
        1.2    9.0   8.5       0.39   10.5   2.7    2.6  2  zinc_ribbon_2  zinc-ribbon domain
        1.2    8.1   6.5        1.9    7.5   6.5    1.2  1  Roughex        Drosophila roughex protein
        2.5    7.6  11.5         13    5.3   7.7    2.8  3  Sec62          Translocation protein Sec62
        2.6    7.8   6.1        5.3    6.8   6.1    1.5  1  DUF3464        Photosynthesis affected mutant 68


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 !  506.2   0.1  3.3e-155  4.9e-152       2     390 ..       3     387 ..       2     388 .. 0.97
   2 ?   -4.2   1.2       3.5   5.2e+03     198     227 ..     554     583 ..     530     591 .. 0.43

  Alignments for each domain:
  == domain 1  score: 506.2 bits;  conditional E-value: 3.3e-155
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelf 78 
                                       lvt++lpYangk H+Ghl+++++aD++++y r+ geev+fvcg+D hGtpi ++Aekeg++p+elv+ +he+++++f
  gi|488600499|ref|YP_007906970.1|   3 LVTCGLPYANGKAHIGHLRTYVPADVYVKYMRMFGEEVIFVCGSDCHGTPIVVNAEKEGLKPRELVDIYHEHFNRVF 79 
                                       8**************************************************************************** PP

                                       HHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.-T CS
                      tRNA-synt_1g  79 kklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.ee 154
                                       k+++i+fd++grt++e h++ +qei+k+l ++g+iy +eie +ycp+++rflpdryveg CP+c+ ++argd+c + 
  gi|488600499|ref|YP_007906970.1|  80 KEIDIEFDYFGRTDEEYHHRRTQEIVKRLIDNGYIYPREIELAYCPNCDRFLPDRYVEGICPYCG-ATARGDECdQG 155
                                       *****************************************************************.88******889 PP

                                       TSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS- CS
                      tRNA-synt_1g 155 cgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdl 231
                                       cg++lep e+ +p+++i+gs++++++++h+ffkl +f+++l +++  ++ + +en+ +++++w++ +Lkd++i+r+l
  gi|488600499|ref|YP_007906970.1| 156 CGRHLEPGEILEPRCKICGSRAVFRKQKHYFFKLTEFKDFLLDFL--SNLRGTENALNYARQWVSMELKDWCITRNL 230
                                       *********************************************..5667************************** PP

                                       SSS-EETTECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHTT CS
                      tRNA-synt_1g 232 dwGipvPgaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillgae 308
                                       +wG+++Pg e+ v+YVW+dA+igYis+t+  +++k  + +wk+ W  + ++e++hfig di+++H+ifwPa+l ga+
  gi|488600499|ref|YP_007906970.1| 231 EWGVKFPG-EDLVVYVWVDAPIGYISFTERACESK--NIDWKKIW-VHGDAEIIHFIGLDIVYHHCIFWPAMLRGAK 303
                                       *******6.689********************554..78******.779**************************** PP

                                       ----S-EEEE--EEE--------------H.HHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHH CS
                      tRNA-synt_1g 309 lklpkkvvaheyltvegkKlSkSrgvvvka.kealer.ldadllRYylaaeapekkDldfswedfvervNseLadkl 383
                                       + lp++v+a+++++v+gk +Sk+rg+vv+  +++l++ l++d+lRYyl+  ++++kDl+fswe f e++N+eL+++l
  gi|488600499|ref|YP_007906970.1| 304 YALPSSVIASGMVKVDGKTFSKTRGYVVWLeEDYLKSgLNTDFLRYYLVNYTSHQKDLNFSWEVFGEKINNELIANL 380
                                       *****************************956899999*************************************** PP

                                       HHHHHHH CS
                      tRNA-synt_1g 384 gnlvnRv 390
                                       gn+++Rv
  gi|488600499|ref|YP_007906970.1| 381 GNFLYRV 387
                                       ******8 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 3.5
                                       HH.HH-TTSHHHHHHHH.HHHHT----EE- CS
                      tRNA-synt_1g 198 wieeeekeleenvkkivkewlkegLkdlai 227
                                        ++e+++e++++ +k+ ++  +++ k + i
  gi|488600499|ref|YP_007906970.1| 554 SVNEDKEEQKKEQEKQEEQKEQKDQKAREI 583
                                       333333333333333333333333333333 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.2   6.8e-29     1e-25       1      96 []     593     685 ..     593     685 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 6.8e-29
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       lr+Gk+++ae++++++kL++l++d+G+e+ rq+v+g+++ y+pe++ +k v v++nlkp+kl+GveS+GMil+a+  
  gi|488600499|ref|YP_007906970.1| 593 LRIGKIVKAEKIKKSRKLMRLEIDIGDEI-RQVVAGIAEEYSPEDVEGKLVPVLVNLKPAKLMGVESRGMILAAD-- 666
                                       79***************************.*********************************************.. PP

                                       ESSCEEEEEESST--TTCE CS
                         tRNA_bind  78 dekevgilelpadveaGek 96 
                                        +++  +l ++++ve+G+k
  gi|488600499|ref|YP_007906970.1| 667 INGKPVLLHPDREVEPGSK 685
                                       799**************85 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   4.9e-14   7.3e-11      29     111 ..       6      86 ..       3     138 .. 0.73
   2 !   16.8   0.1     1e-06    0.0015     361     432 ..     166     237 ..     153     270 .. 0.82
   3 !    5.8   0.0    0.0023       3.5     549     602 .]     309     364 ..     298     364 .. 0.83
   4 ?   -4.2   2.7       2.3   3.5e+03     441     469 ..     552     580 ..     539     600 .. 0.52

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 4.9e-14
                       tRNA-synt_1  29 dgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekvr 105
                                        g Py++G+ HiGh  + +  d+ ++y rm G+ev +v G D++G +i  + ek+ g k + e  ++ +e+f+   +
  gi|488600499|ref|YP_007906970.1|   6 CGLPYANGKAHIGHLRTYVPADVYVKYMRMFGEEVIFVCGSDCHGTPIVVNAEKE-GLKPR-ELVDIYHEHFNRVFK 80 
                                       577*********************************************9999999.44443.456666666666666 PP

                       tRNA-synt_1 106 ewkaey 111
                                       e+  e+
  gi|488600499|ref|YP_007906970.1|  81 EIDIEF 86 
                                       655444 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1e-06
                       tRNA-synt_1 361 svpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswle.niqdWciSRqrwWGhrip 432
                                         p c+  +   ++r ++ +f +++e++d +l+ +++ + + +   +   +w+  + +dWci R++ WG++ p
  gi|488600499|ref|YP_007906970.1| 166 LEPRCKICGSRAVFRKQKHYFFKLTEFKDFLLDFLSNLRGTENA-LNYARQWVSmELKDWCITRNLEWGVKFP 237
                                       56788888889999999***************999998877665.445567775389*************987 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0023
                       tRNA-synt_1 549 evlvhglvrdeeGrKmSKslgNvi..dpldvikkygadalRltli.lsdvgrdinls 602
                                       +v+ +g+v   +G+  SK  g v+  + +++ + + +d lR++l+ +++  +d+n+s
  gi|488600499|ref|YP_007906970.1| 309 SVIASGMVK-VDGKTFSKTRGYVVwlEEDYLKSGLNTDFLRYYLVnYTSHQKDLNFS 364
                                       577777765.68*********997335566777789*********99******9986 PP

  == domain 4  score: -4.2 bits;  conditional E-value: 2.3
                       tRNA-synt_1 441 evvvreelkelvagreeeeaekkalekea 469
                                       ++ v+e+++e ++++e++e++k++ +++a
  gi|488600499|ref|YP_007906970.1| 552 KISVNEDKEEQKKEQEKQEEQKEQKDQKA 580
                                       34443344444433333333333322222 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 !   39.2   0.0   3.3e-13   4.9e-10      12     125 ..       3     118 ..       1     127 [. 0.85
   2 !    6.9   0.0    0.0024       3.5     239     294 ..     308     366 ..     273     373 .. 0.73
   3 ?   -1.6   1.0      0.93   1.4e+03     146     165 ..     556     575 ..     495     604 .. 0.58

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.3e-13
                                       EEEEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e  12 lYvCG.ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdl 87 
                                       l +CG p +  ++h+Gh R++v  D+  ++++++g +v fv         i+ +a++e+++ +el++ + e+f++ +
  gi|488600499|ref|YP_007906970.1|   3 LVTCGlPYANGKAHIGHLRTYVPADVYVKYMRMFGEEVIFVCGSDCHGTPIVVNAEKEGLKPRELVDIYHEHFNRVF 79 
                                       5678844567799****************************997777789*************************** PP

                                       HHTT----SB--BGGG.GHHHHHHHHHHHHHTTSEEE-T CS
                      tRNA-synt_1e  88 eaLnvlkptleprvse.kvdeiielvekliekgyaYavs 125
                                       +++++    +     e +     e+v++li++gy Y+ +
  gi|488600499|ref|YP_007906970.1|  80 KEIDIEFDYFGRTDEEyHHRRTQEIVKRLIDNGYIYPRE 118
                                       *****985554444441345789*************876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0024
                                       EEEEEE--EEETTBE--TTTT---BHH.HHHTT.S-HHHHHHHHHS.S-TTS-EEE-HH CS
                      tRNA-synt_1e 239 kyflhnghlkiegekmsksLknfitik.dvlkk.fdprqlRlllls.ahyrsqldfkee 294
                                          + +g++k++g+  sk  + ++ ++ d lk+  ++  lR++l++ + +++ l+f+ e
  gi|488600499|ref|YP_007906970.1| 308 SSVIASGMVKVDGKTFSKTRGYVVWLEeDYLKSgLNTDFLRYYLVNyTSHQKDLNFSWE 366
                                       556789****************99986268886478999***99872568889999866 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.93
                                       -HHHHHHT----S--S-SST CS
                      tRNA-synt_1e 146 nleelelgaegevseekkdk 165
                                       n ++ e+++e+e++ee+k++
  gi|488600499|ref|YP_007906970.1| 556 NEDKEEQKKEQEKQEEQKEQ 575
                                       11111222222222222222 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 !   26.7   4.9     3e-09   4.5e-06       1     147 [.     408     558 ..     408     610 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3e-09
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.raaqevllevletllrl 76 
                                       d  +ls +  +  ++++ +++++f+ + +a +e+   ++ ++y++ ++p+   +++ ++ +++ + +l ++++++ l
  gi|488600499|ref|YP_007906970.1| 408 DEKALSAIKTAMDKIKNGLANWEFKVVSDAFMEL--SSFGNNYFQNAQPWDLVKKDVEEaKRVVASCLQIARAIVLL 482
                                       6778999**************************8..99************9988877775559999*********** PP

                       Anticodon_1  77 laPfmPfitEelwqr.....eeeelgkkesimlaewpe.kaeel.....ekeleeeevellkei.vkairklrselk 141
                                        +P++P ++ e  +      e+e++++   +  +++   k++       +     e++e l+ i ++ i k+ + +k
  gi|488600499|ref|YP_007906970.1| 483 SYPVLPKTMKEFSKVfgmeiEKEKIDSAMAV--SKFVIsKPKIPfqkipD-----EKIEELQHImLERIKKAEEANK 552
                                       ************9667777644444444222..23332122111212222.....3334444442233333444444 PP

                       Anticodon_1 142 ikpsse 147
                                       i+ +++
  gi|488600499|ref|YP_007906970.1| 553 ISVNED 558
                                       443333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   8.2   0.00046      0.69       1      49 []     124     174 ..     124     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                               DZR   1 CpqCgeelppdar..fCseCgtklkavaaedrCps.Cgekvdpearf...CpeCG 49 
                                       Cp+C + lp++     C++Cg++ +     d C++ Cg+ ++p++     C+ CG
  gi|488600499|ref|YP_007906970.1| 124 CPNCDRFLPDRYVegICPYCGATAR----GDECDQgCGRHLEPGEILeprCKICG 174
                                       ***********9888**********....8***866*****99988877888888 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 ?   10.9   0.1   0.00027      0.41      22      33 .]     120     131 ..     102     131 .. 0.87
   2 ?    2.0   0.2      0.17   2.5e+02      26      31 ..     140     145 ..     139     145 .. 0.87
   3 ?   -1.9   0.6       2.7   4.1e+03      24      30 ..     168     174 ..     154     175 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                                       B-EE-TTT--EE CS
                         zf-RING_7  22 evvtCpeCGRIL 33 
                                       e+++Cp+C R+L
  gi|488600499|ref|YP_007906970.1| 120 ELAYCPNCDRFL 131
                                       689*******98 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                                       -TTT-- CS
                         zf-RING_7  26 CpeCGR 31 
                                       Cp+CG+
  gi|488600499|ref|YP_007906970.1| 140 CPYCGA 145
                                       ****96 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.7
                                       EE-TTT- CS
                         zf-RING_7  24 vtCpeCG 30 
                                       ++C  CG
  gi|488600499|ref|YP_007906970.1| 168 PRCKICG 174
                                       5565555 PP

>> TERB2  Telomere-associated protein TERB2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       3.2   4.7e+03       9      29 ..     261     281 ..     260     286 .. 0.88
   2 ?   12.1   5.2    0.0001      0.15      66     165 ..     497     593 ..     490     621 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                             TERB2   9 ssSvskdltelWvkegGkivd 29 
                                       ++S ++d +++Wv+ + +i +
  gi|488600499|ref|YP_007906970.1| 261 CESKNIDWKKIWVHGDAEIIH 281
                                       789999*********999987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0001
                             TERB2  66 sylsaaknekskksvalgkyvLppakvqeeirkkigrfiweqdnqslveqssevhsaeepeiakdslleekeeqask 142
                                        +  ++++ek+++ +a+ k+v+  +k+     +ki   + e+ +++++e  ++ + a++ ++++d+++++ke+++++
  gi|488600499|ref|YP_007906970.1| 497 VFGMEIEKEKIDSAMAVSKFVISKPKIP---FQKIPDEKIEELQHIMLERIKKAEEANKISVNEDKEEQKKEQEKQE 570
                                       5667789999999999*****9999976...3688889999999999999999999999999999999999999999 PP

                             TERB2 143 laksaeksatstsksekqlcsel 165
                                       ++k++++++ +  + e+ ++  l
  gi|488600499|ref|YP_007906970.1| 571 EQKEQKDQKAREISYEEFQRLDL 593
                                       99999988887777776666555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.7   0.00026      0.39       1      21 [.     123     145 ..     123     146 .. 0.96
   2 ?    0.8   0.3      0.28   4.3e+02       5      21 ..     156     175 ..     156     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                     zinc_ribbon_2   1 fCpnCGaelqdnakF..CpyCGt 21 
                                       +CpnC + l+d+ +   CpyCG+
  gi|488600499|ref|YP_007906970.1| 123 YCPNCDRFLPDRYVEgiCPYCGA 145
                                       8*********************7 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.28
                     zinc_ribbon_2   5 CGaelqdnakF...CpyCGt 21 
                                       CG+ l++++     C  CG+
  gi|488600499|ref|YP_007906970.1| 156 CGRHLEPGEILeprCKICGS 175
                                       99999999888888888885 PP

>> Roughex  Drosophila roughex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.5    0.0013       1.9     246     303 ..     525     583 ..     504     591 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                           Roughex 246 fadgadedgdedtdgsvee.kkddasepdlpdqnkeedkdeqeqqaeqeeqaqqqaeea 303
                                       f    de  +e     +e  kk + ++    +++kee+k eqe+q eq+eq++q+a e 
  gi|488600499|ref|YP_007906970.1| 525 FQKIPDEKIEELQHIMLERiKKAEEANKISVNEDKEEQKKEQEKQEEQKEQKDQKAREI 583
                                       55556666666665555542444444455567899********************9985 PP

>> Sec62  Translocation protein Sec62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.79   1.2e+03     120     140 ..     288     306 ..     273     317 .. 0.72
   2 ?    2.2   0.0     0.073   1.1e+02     106     135 ..     464     493 ..     457     500 .. 0.89
   3 ?    5.3   7.7    0.0085        13       5      83 ..     541     613 ..     534     641 .. 0.48

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.79
                             Sec62 120 ilavvlFPLWPaelrkgvyYL 140
                                       +   ++F  WPa+lr + y L
  gi|488600499|ref|YP_007906970.1| 288 VYHHCIF--WPAMLRGAKYAL 306
                                       5555666..******999977 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.073
                             Sec62 106 qlktlligllvvvailavvlFPLWPaelrk 135
                                       + k++++++l ++ ++++  +P+ P+++++
  gi|488600499|ref|YP_007906970.1| 464 EAKRVVASCLQIARAIVLLSYPVLPKTMKE 493
                                       568899999*******************97 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0085
                             Sec62   5 ffrakkvvralksekekkkskkkkeklkevkkkek....aekvfkelkksqlalrveklkekekkkkkeekkkkkkk 77 
                                       + r+kk+ +a+k + ++ k+++kke++k++++ke+    a++++  ++ ++l lr+ k  ++ek          kk+
  gi|488600499|ref|YP_007906970.1| 541 LERIKKAEEANKISVNEDKEEQKKEQEKQEEQKEQkdqkAREIS-YEEFQRLDLRIGKIVKAEK---------IKKS 607
                                       55666666555433332222222222222221111000022222.2222334455555544444.........4444 PP

                             Sec62  78 kkkvkl 83 
                                       +k ++l
  gi|488600499|ref|YP_007906970.1| 608 RKLMRL 613
                                       444444 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.1    0.0036       5.3       9      64 ..     542     596 ..     522     601 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0036
                           DUF3464   9 epkkkrkkkpkkkkkskkakkeekekakeeekkdkeekeeaaiPevVskRmirRva 64 
                                       e+ kk ++++k + +++k++++++ ++k+ee+k+++++++++i+ +  +R+  R++
  gi|488600499|ref|YP_007906970.1| 542 ERIKKAEEANKISVNEDKEEQKKE-QEKQEEQKEQKDQKAREISYEEFQRLDLRIG 596
                                       443444444455554444444444.5566666666667778899999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (687 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2646  (0.147582); expected 358.6 (0.02)
Passed bias filter:                     1052  (0.0586759); expected 358.6 (0.02)
Passed Vit filter:                       199  (0.0110993); 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: 1.00u 0.34s 00:00:01.34 Elapsed: 00:00:00.52
# Mc/sec: 3966.01
//
Query:       gi|488600500|ref|YP_007906971.1|  [L=202]
Description: hypothetical protein Asulf_00974 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   53.2   0.0    4.4e-14   52.4   0.0    1.4  1  SIS           SIS domain
    1.8e-12   47.5   1.4    1.5e-07   31.5   0.1    2.2  2  SIS_2         SIS domain
  ------ inclusion threshold ------
      0.045   13.4   0.0       0.06   13.0   0.0    1.3  1  DUF2529       Domain of unknown function (DUF2529)
      0.061   12.6   0.0      0.087   12.1   0.0    1.2  1  LSDAT_prok    SLOG in TRPM, prokaryote
       0.14   10.8   0.0       0.27    9.9   0.0    1.4  1  DHDPS         Dihydrodipicolinate synthetase family
       0.16   11.7   2.5       0.26   11.0   0.0    2.3  2  Gemini_AC4_5  Geminivirus AC4/5 conserved region


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 !   52.4   0.0   1.5e-17   4.4e-14       3     120 ..      40     154 ..      38     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.5e-17
                                       CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHT CS
                               SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelaker 79 
                                        + k i ++G G+s+a+a+ +a  l+++ +i   +++   l ++v   i+++d++i++s sget++ v  a++ake 
  gi|488600500|ref|YP_007906971.1|  40 ENGKAIHIFGVGRSGAVALCFAIRLKHFEKIF--GHKVWWLGDEVREKIENGDVLIIFSGSGETAEAVFIAQKAKEV 114
                                       5668899**********************996..55555566888999***************************** PP

                                       TSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHH CS
                               SIS  80 gakiiaITdskgsplareadlalyinaepetlvastkslta 120
                                       ga+i++IT+ ++s++ +++dl ++++ + e     +k l+a
  gi|488600500|ref|YP_007906971.1| 115 GARIVLITSFPESTIGKMSDLLITLPGGLEK-SKGWKYLQA 154
                                       ***********************99988777.555555555 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.4e-06     0.016      20      59 ..      31      66 ..      14      77 .. 0.80
   2 !   31.5   0.1     5e-11   1.5e-07      93     138 .]      80     123 ..      73     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.4e-06
                                      HHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT- CS
                             SIS_2 20 aiekaaeliadslenggkvlvfGsGhSaalaeelaaragg 59
                                      +i+     ++  +eng+ +++fG G S a a  +a r+  
  gi|488600500|ref|YP_007906971.1| 31 SIN----EFFRLIENGKAIHIFGVGRSGAVALCFAIRLKH 66
                                      444....466779*********************999865 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 5e-11
                                       HHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                             SIS_2  93 kqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                       ++++++  +++gDvL+++S sG+ a +v +a++ake+g++++ +ts
  gi|488600500|ref|YP_007906971.1|  80 DEVREK--IENGDVLIIFSGSGETAEAVFIAQKAKEVGARIVLITS 123
                                       556666..9*********************************9998 PP

>> DUF2529  Domain of unknown function (DUF2529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05      0.06      73     123 ..      82     132 ..      20     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                       -..---TT-EEEEEES-S--HHHHHHHHHHHHHT--EEEEESS---T..TGGG CS
                           DUF2529  73 k..eltetDrvllfsresndkealklakkleekgievvavsskvkeedaltel 123
                                          ++++ D  ++fs + +++ea+ +a+k++e g+ +v+++s ++++    ++
  gi|488600500|ref|YP_007906971.1|  82 VreKIENGDVLIIFSGSGETAEAVFIAQKAKEVGARIVLITSFPESTI--GKM 132
                                       14589999**********************************998763..444 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05     0.087     138     171 ..      80     113 ..      70     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                        LSDAT_prok 138 kdiresvkagrpilvvaGsgrladeiaaalrgds 171
                                       +++re++++g  +++  Gsg +a++++ a+++++
  gi|488600500|ref|YP_007906971.1|  80 DEVREKIENGDVLIIFSGSGETAEAVFIAQKAKE 113
                                       79***********************976665544 PP

>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   9.1e-05      0.27      69     102 ..      89     121 ..      79     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.1e-05
                                       TSSEEEEE---SSHHHHHHHHHCCCCCT-SEEEE CS
                             DHDPS  69 gripviagvGsnstseaiklakkaeeaGadgvla 102
                                       g + +i+  Gs  t+ea+ +a+ka+e+Ga  vl+
  gi|488600500|ref|YP_007906971.1|  89 GDV-LIIFSGSGETAEAVFIAQKAKEVGARIVLI 121
                                       444.566789******************987765 PP

>> Gemini_AC4_5  Geminivirus AC4/5 conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.6e-05      0.26      12      23 ..      14      25 ..       8      31 .. 0.80
   2 ?   -0.7   1.0      0.41   1.2e+03      17      28 ..      65      76 ..      63      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.6e-05
                      Gemini_AC4_5 12 iVkHvKhLtKil 23
                                       + H+ h++Kil
  gi|488600500|ref|YP_007906971.1| 14 LIDHIRHFPKIL 25
                                      689********9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.41
                      Gemini_AC4_5 17 KhLtKilwssir 28
                                      Kh+ Ki +   +
  gi|488600500|ref|YP_007906971.1| 65 KHFEKIFGHKVW 76
                                      9*****987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1288.14
//
Query:       gi|488600501|ref|YP_007906972.1|  [L=629]
Description: Prephenate dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-55  185.7   0.1    1.5e-54  184.6   0.1    1.6  2  PDT             Prephenate dehydratase
    1.2e-18   67.1   0.0    2.2e-18   66.2   0.0    1.4  1  PDH             Prephenate dehydrogenase
    1.6e-11   43.8   0.0    8.4e-11   41.5   0.0    2.3  2  ACT             ACT domain
    3.4e-11   43.3   3.1    5.4e-11   42.7   1.2    2.3  2  CM_2            Chorismate mutase type II
  ------ inclusion threshold ------
      0.039   13.3   0.3        1.6    8.0   0.0    3.2  4  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.087   13.4   0.0       0.66   10.6   0.0    2.5  2  ACT_4           ACT domain
      0.092   12.9   0.0       0.22   11.7   0.0    1.6  1  T2SS_PulS_OutS  Type II secretion system pilotin lipoprotein 
       0.17   12.5   0.0       0.56   10.8   0.0    1.9  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


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 ?   -3.2   0.0       2.7   6.1e+03      26      43 ..      59      76 ..      57      80 .. 0.81
   2 !  184.6   0.1   6.7e-58   1.5e-54       2     181 ..     365     538 ..     364     540 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.7
                                      EEEES-HHHHHHHHCTTS CS
                               PDT 26 lipvasieevfeavekge 43
                                      ++p++si++v++++ek +
  gi|488600501|ref|YP_007906972.1| 59 CVPMDSIDSVISKLEKLS 76
                                      689999999999999865 PP

  == domain 2  score: 184.6 bits;  conditional E-value: 6.7e-58
                                       EEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEE CS
                               PDT   2 aylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgEv 78 
                                       a+lGp g++s+++alk+  +++v +i ++s+ee+++ vek+e +y+++PiENs++G+V +++D L++  d++++gE+
  gi|488600501|ref|YP_007906972.1| 365 AVLGPMGSFSDEVALKLT-GSRVPFIYCSSVEEIVRMVEKDENTYGLIPIENSVHGTVLKSIDALMR-YDVEVFGET 439
                                       89***************9.************************************************.99******* PP

                                       EEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHH CS
                               PDT  79 vlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaael 155
                                        +++ h L++k+k +l ei++vyShpqa++Qc +f++++lp+++ ++++st++A+ +     +++ aai se aa+l
  gi|488600501|ref|YP_007906972.1| 440 KMEVIHVLASKKKLELTEIEEVYSHPQAMAQCAEFINNYLPKAKLRYTSSTSDAISM----LKDTSAAIVSENAARL 512
                                       *********************************************************....56788*********** PP

                                       TT-EEEECS-SS-S--EEEEEEEEET CS
                               PDT 156 yglkvleeniedkknntTRFlvlake 181
                                       y+l++l++ i+d +nn+TRF++++k+
  gi|488600501|ref|YP_007906972.1| 513 YNLYILRKGIQDMENNVTRFYIIRKQ 538
                                       ***********************986 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   9.8e-22   2.2e-18      43     230 ..      50     225 ..      30     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 9.8e-22
                                       GCCGSEEEE-S-GGGHHHHHHHHHH...HS-TT-EEEE--S--CHHHHHHHHHCC..GCEEEEEES---S-SSGGG- CS
                               PDH  43 vkeadivvlavPvevilevlkelap...hlkedalitDvgsvKekvvreleellkegksfvgghPmaGteksGvdaa 116
                                       +  +d+++l+vP++ i  v+ +l +   +  ++ li+D++svK  + + ++     +  + + hPm+G+        
  gi|488600501|ref|YP_007906972.1|  50 LFGFDVIFLCVPMDSIDSVISKLEKlstKFYKKPLIVDIASVKSDLDKLIR-----NFDVLSIHPMIGP-------D 114
                                       4457**********99999877766222666789*********98766555.....45679********.......3 PP

                                       -TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHH CS
                               PDH 117 reelfenavviLtPtektdkealekvkelleevgarvilmspeeHDrvvavvshlphvvaialaatlkekkndekei 193
                                       ++  + n +v+     +++    + + + l   ga +  ++   HD+ +a ++++ h++ ia+a+ lk   ++  + 
  gi|488600501|ref|YP_007906972.1| 115 SDLGLSNIIVVYESGREEG----KLILDELYRAGANISRLNYRLHDHKMAEIQGVAHFLLIAMANFLKDRMDK--ND 185
                                       4444666666665555555....5666667789********************************66654444..45 PP

                                       HHCGTCCH....HHHHCGGGS-HHHHHHHHHHTHHHHHHHH CS
                               PDH 194 rklasggf....rdvtRiaksnPelwadilleNkeavleal 230
                                        ++as++f    ++++Ri++++ +++++i+++  e++ e l
  gi|488600501|ref|YP_007906972.1| 186 LNYASPIFytlyKLASRIINQDWRMYYNIQKN-SEQLREEL 225
                                       89***99633337788*************975.55455544 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.4   5.3e+03      18      31 ..     137     150 ..     136     158 .. 0.83
   2 !   41.5   0.0   3.8e-14   8.4e-11       1      51 [.     548     598 ..     548     610 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                                       HHHHHHTTSEEEEE CS
                               ACT  18 fgaladrgiNidsi 31 
                                       +  l ++g Ni ++
  gi|488600501|ref|YP_007906972.1| 137 LDELYRAGANISRL 150
                                       567999****9875 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 3.8e-14
                                       EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEE CS
                               ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvd 51 
                                       t+l++gv+D+PG+L +v+ ++ + +iN++++e+r+s+ ++++++f+ +v+ 
  gi|488600501|ref|YP_007906972.1| 548 TSLFFGVEDKPGALKDVLEVFYEKNINLRKLESRPSGTGLGDYIFFSEVEK 598
                                       5899***********************************999999998875 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.4   3.1e+03      62      72 ..     241     251 ..     214     254 .. 0.64
   2 !   42.7   1.2   2.4e-14   5.4e-11       1      75 []     280     355 ..     280     355 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHH CS
                              CM_2  62 ifreiisasra 72 
                                        f+ei++as++
  gi|488600501|ref|YP_007906972.1| 241 RFKEIFEASKK 251
                                       37777777765 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 2.4e-14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH.HHS-HHHHHHHHHHHHHHHHHHHH CS
                              CM_2   1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee.galdeeaierifreiisasralqk 75 
                                       R  I  +D+ il+L+++R +  ke+++yKke++lp++  e e+  l++l++   l++ +++rif ei+   +a ++
  gi|488600501|ref|YP_007906972.1| 280 RGYIRVVDSLILRLIERRVRAGKEIAMYKKEKNLPIEISEIEEVKLKELASsTTLNRMMLNRIFGEIFHLTKAEEY 355
                                       566999*********************************************555**************99998875 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00073       1.6      38      76 ..       9      47 ..       2      64 .. 0.84
   2 ?   -0.3   0.0      0.27     6e+02      82     101 ..      92     111 ..      78     116 .. 0.81
   3 ?   -3.0   0.0       1.7   3.9e+03      37      70 ..     362     396 ..     351     408 .. 0.78
   4 ?    0.0   0.1      0.21   4.7e+02      58     123 ..     439     503 ..     433     511 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00073
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeee 76
                                      ++ i+G+G +G+ + k ++  g  v +yd  ++k+e +e
  gi|488600501|ref|YP_007906972.1|  9 KILIWGMGGMGTLFKKFFELRGYTVKGYDIDENKREVDE 47
                                      789****************************99777222 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.27
                                       ECSHHHHHHH-SEEEE-S-- CS
                      2-Hacid_dh_C  82 lvsleellaesDivslhlpl 101
                                       + +l++l+++ D++s+h  +
  gi|488600501|ref|YP_007906972.1|  92 KSDLDKLIRNFDVLSIHPMI 111
                                       569*************9765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.7
                                       SEEEEES.-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  37 ktvGiiG.lGrIGqavakrlkafgmkviaydrskk 70 
                                       k+++++G +G+   +va +l++ ++  i+ +  ++
  gi|488600501|ref|YP_007906972.1| 362 KRMAVLGpMGSFSDEVALKLTGSRVPFIYCSSVEE 396
                                       66777776999999999999999999999887754 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.21
                                       TT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEE CS
                      2-Hacid_dh_C  58 fgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgail 123
                                        +m+vi +  skkk e   e +  +   +++ + ++++ + lp  +  +   ++++++++k+++  
  gi|488600501|ref|YP_007906972.1| 439 TKMEVIHVLASKKKLE-LTEIEEVYSHPQAMAQCAEFINNYLPKAKLRYTSSTSDAISMLKDTSAA 503
                                       6788888888877665.6666666888899999999999999999999999999999999988754 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.3   9.6e+03      26      50 ..     139     162 ..     135     163 .. 0.74
   2 ?   10.6   0.0   0.00029      0.66      13      41 ..     554     582 ..     548     592 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.3
                             ACT_4  26 viseekanivsvnaktrkkdglaei 50 
                                        +  ++ani+ +n + ++  ++aei
  gi|488600501|ref|YP_007906972.1| 139 ELYRAGANISRLNYRLHD-HKMAEI 162
                                       556789999999999865.678887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00029
                             ACT_4  13 aedrkglLaditqviseekanivsvnakt 41 
                                       +ed++g+L+d+++v+ e+++n+++++++ 
  gi|488600501|ref|YP_007906972.1| 554 VEDKPGALKDVLEVFYEKNINLRKLESRP 582
                                       68**********************99886 PP

>> T2SS_PulS_OutS  Type II secretion system pilotin lipoprotein (PulS_OutS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.8e-05      0.22      29      86 ..     170     228 ..     154     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                                       HHHHHHHHHHHS--TTS--HHHHHHHHHHHHHHTT--G..GG-TTHHHHHHHHHHHHHHS CS
                    T2SS_PulS_OutS  29 lvaaikYLkqkCnrsdLpddatilkvalkvakqrgWdt..deyqslpqrserlYqgLlkd 86 
                                       l+a +++Lk + +++dL   + i  + +k+a +r  +     y  + ++se+l + L+k 
  gi|488600501|ref|YP_007906972.1| 170 LIAMANFLKDRMDKNDLNYASPIFYTLYKLA-SRIINQdwRMYYNIQKNSEQLREELVKS 228
                                       79*****************************.887777447899*********9999985 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.56      62      94 ..      53      88 ..      34      90 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                      -SEEEE-S-HHHHHHHHHHC...GHHHHTTSEEEEE CS
                     F420_oxidored 62 advvvlavkpedveevlsel...akdalkgklvisv 94
                                       dv++l+v++  +++v+s+l     +  k+ l++++
  gi|488600501|ref|YP_007906972.1| 53 FDVIFLCVPMDSIDSVISKLeklSTKFYKKPLIVDI 88
                                      69******************4433344455556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3747.59
//
Query:       gi|488600502|ref|YP_007906973.1|  [L=208]
Description: 3-dehydroquinate dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-27   94.8   0.2    1.1e-26   94.6   0.2    1.0  1  DHquinase_I  Type I 3-dehydroquinase


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 !   94.6   0.2   5.9e-31   1.1e-26       7     227 ..       6     196 ..       1     198 [. 0.84

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 5.9e-31
                                       SSHHHHHHHHHHHTTS-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHH CS
                       DHquinase_I   7 ktleeilaelesgkekaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellr 83 
                                       + + e  +++ ++   +D+vE+R+D +++    e++++  e l     +  i+t+r++a+gg + +++e  ++++l+
  gi|488600502|ref|YP_007906973.1|   6 SVVGEFSKRMIEM---CDIVEIRIDAVANA---EEIIKLSEDL----GKEKIITCRRRADGGYY-DGDESGRIKKLK 71 
                                       5555666677777...**********9655...5455555555....6689************9.9*********** PP

                                       HHHHCT-SEEEEEGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SS.. CS
                       DHquinase_I  84 taielgadyvDvElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaks.. 158
                                       +  +  ad+vD+E  +++    +++ +      +++I Syh  +  p  e l +l+e  +  g Di Kia+  +   
  gi|488600502|ref|YP_007906973.1|  72 KFSKY-ADFVDIES-DMD----DDVFDV---FDCRIIESYHGIN--PGYEYLSDLVEGKR--G-DIFKIAILGRRen 134
                                       ***95.9*******.555....467776...59**********9..677889**999654..6.*********9989 PP

                                       .HHHHHHHHHHHHHHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHH CS
                       DHquinase_I 159 .ieDvlrllsltseakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelre 227
                                        +eDv ++l+l s      +  +lIa+ mGe+ k++R++++++G p+++++++  +++a Gq++++e+  
  gi|488600502|ref|YP_007906973.1| 135 gKEDVKTILKLHS------EYDNLIAFVMGERFKFTRVISTMLGNPIIYCHAG--RKAAEGQISVEEAVA 196
                                       99*********73......3479****************************55..55*********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1456.75
//
Query:       gi|488600503|ref|YP_007906974.1|  [L=329]
Description: 3-dehydroquinate synthase II [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-123  412.2   3.1   3.8e-122  407.6   3.1    2.0  1  DHQS             3-dehydroquinate synthase II
     0.0045   17.0   0.0        1.8    8.7   0.0    2.7  2  OapA             Opacity-associated protein A LysM-like domai
  ------ inclusion threshold ------
        0.1   12.8   0.1        2.4    8.4   0.0    2.6  3  CTP_transf_like  Cytidylyltransferase-like
       0.16   12.0   0.0        1.7    8.7   0.0    2.5  2  FlpD             Methyl-viologen-reducing hydrogenase, delta 


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 !  407.6   3.1  8.4e-126  3.8e-122       1     352 []       2     329 .]       2     329 .] 0.97

  Alignments for each domain:
  == domain 1  score: 407.6 bits;  conditional E-value: 8.4e-126
                              DHQS   1 kevwikadeeeweerkelvtaaleagvdavlveeedaekvkelgkikviakeeddavlvgkddleklkkakkvaalv 77 
                                       ke+w+++d+++w++ ke v++ale g++ v+v+e  ++k+++lg+ikvi++++                     +++
  gi|488600503|ref|YP_007906974.1|   2 KEIWLRIDDDQWDDVKEGVKNALELGYSGVFVKEGFEDKIRQLGRIKVITDRN---------------------SFL 57 
                                       89***********************************************6553.....................589 PP

                              DHQS  78 eikskeeeeeaaeaakeadyvivelkdwtvIPlEnliAalqgeetkiiaavksaeeAklaletLEkGadgvllkted 154
                                       +++s+e++++a e++k++dy++++++dw+vIPlEnliA  ++ ++k+i++v+s+e AklaletLEkGadg++++++d
  gi|488600503|ref|YP_007906974.1|  58 TVSSSEDQDRAIELSKTMDYLFLDFSDWKVIPLENLIA--MKGRAKLIVHVDSVESAKLALETLEKGADGIIVSSKD 132
                                       9*************************************..67889******************************** PP

                              DHQS 155 veeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGmLvGsssrglfLvhsEtlespYvasR 231
                                        +e++++ e++++++  ++e++e+e+ +++++gmgdRvc+Dt+slm+ geGmLvG+ss+ +fLv sE++es+Yv+sR
  gi|488600503|ref|YP_007906974.1| 133 RDELSKFREIMSSMD--RVEMVEIEIDEIKPLGMGDRVCIDTISLMNVGEGMLVGNSSKFMFLVASESEESEYVSSR 207
                                       ***********8886..79********************************************************** PP

                              DHQS 232 PFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiEkRPlllveaeaegkkvstilQnaet 308
                                       PFRVNAG+v+aY++v g++T+YLseLkaGdev +v+++Gktr+++vGRvKiEkRP++l++ + +++k ++ilQnaet
  gi|488600503|ref|YP_007906974.1| 208 PFRVNAGSVNAYIRV-GDRTRYLSELKAGDEVEIVSYDGKTRRSYVGRVKIEKRPMILISGRISEEKGTIILQNAET 283
                                       ***************.************************************************************* PP

                              DHQS 309 irlvtedgkaisvteLkeGdevlvylee..kaRHfGikieEtiiEk 352
                                       i+lv+++g++isv+ LkeGd+vl+++++  k+RHfG +++E+i+E+
  gi|488600503|ref|YP_007906974.1| 284 IKLVNSKGEHISVSMLKEGDKVLGWVDRsgKGRHFGAEVDEFIVER 329
                                       ************************99874479************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 !    8.7   0.0    0.0004       1.8      23      52 ..     212     241 ..     206     265 .. 0.82
   2 !    5.3   0.0    0.0048        21      25      58 ..     281     314 ..     277     324 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0004
                              OapA  23 plsdvnalakveGadkplSnlksGqkvrik 52 
                                       +   vna  +v  + + lS+lk+G++v+i 
  gi|488600503|ref|YP_007906974.1| 212 NAGSVNAYIRVGDRTRYLSELKAGDEVEIV 241
                                       66789**********************984 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0048
                              OapA  25 sdvnalakveGadkplSnlksGqkvriklnaqgk 58 
                                       ++  +l++ +G+  ++S lk+G+kv   ++++gk
  gi|488600503|ref|YP_007906974.1| 281 AETIKLVNSKGEHISVSMLKEGDKVLGWVDRSGK 314
                                       6677899999**************9888887775 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.24   1.1e+03      43      97 ..      57     112 ..      41     124 .. 0.67
   2 ?    8.4   0.0   0.00052       2.4      24      58 ..     119     155 ..     103     201 .. 0.70
   3 ?    0.9   0.0      0.11   4.7e+02      46      95 ..     220     272 ..     211     317 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.24
                                       SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHH..HHHHHTTTTEEEEEEEHHHHHHH CS
                   CTP_transf_like  43 kplasaeeRlemlela.kevdevisvdpweltr..evlkklkpdklylvigadvledf 97 
                                        ++ s+e+  + +el  + +  ++ +++w++ +  +++  ++     l++  d++e++
  gi|488600503|ref|YP_007906974.1|  57 LTVSSSEDQDRAIELSkTMDYLFLDFSDWKVIPleNLIAMKGR--AKLIVHVDSVESA 112
                                       4577777777777888555666677888888885533333333..3677777877775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00052
                                       SSES.EEEEEESSTHCSST-.SCSSTHHHHHHHHHHH CS
                   CTP_transf_like  24 leed.livgvpsdeppkkkk.kplasaeeRlemlela 58 
                                       le+    ++v s++ +   k ++++s+ +R+em+e  
  gi|488600503|ref|YP_007906974.1| 119 LEKGaDGIIVSSKDRDELSKfREIMSSMDRVEMVEIE 155
                                       333352344677777776678*************965 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.11
                                       STHHHHHHHHHHHTTCTTEEEEEEESEHH.HHHHHTTTT..EEEEEEEHHHHH CS
                   CTP_transf_like  46 asaeeRlemlelakevdevisvdpweltr.evlkklkpd..klylvigadvle 95 
                                       + + +R++ l ++k  dev  v+ +  tr +++ + k++   ++l+ g ++ e
  gi|488600503|ref|YP_007906974.1| 220 IRVGDRTRYLSELKAGDEVEIVSYDGKTRrSYVGRVKIEkrPMILISGRISEE 272
                                       67789999999999999988888888777755555555554558887776654 PP

>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.2   8.8e+02      44      57 ..      20      33 ..      17      66 .. 0.87
   2 ?    8.7   0.0   0.00037       1.7      42      82 ..     113     153 ..     103     180 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                              FlpD 44 ilkalekGadgVlv 57
                                      + +ale G+ gV+v
  gi|488600503|ref|YP_007906974.1| 20 VKNALELGYSGVFV 33
                                      67899999999998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00037
                              FlpD  42 efilkalekGadgVlvlgChpgd.ChyvkGnekaerrveklk 82 
                                       ++ l+ lekGadg++v+    ++  ++ +      +rve+++
  gi|488600503|ref|YP_007906974.1| 113 KLALETLEKGADGIIVSSKDRDElSKF-REIMSSMDRVEMVE 153
                                       67799***********98887774344.33334444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2124.16
//
Query:       gi|488600504|ref|YP_007906975.1|  [L=264]
Description: 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-49  167.0   0.4    6.1e-49  166.8   0.4    1.1  1  DeoC      DeoC/LacD family aldolase
     0.0015   17.8   1.1     0.0041   16.3   0.2    2.0  2  DUF561    Protein of unknown function (DUF561)
     0.0056   16.0   2.1      0.068   12.5   0.5    2.1  2  ThiG      Thiazole biosynthesis protein ThiG
     0.0057   16.0   0.2       0.14   11.5   0.2    2.3  2  TMP-TENI  Thiamine monophosphate synthase
     0.0061   16.0   1.1      0.011   15.2   0.3    1.6  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 !  166.8   0.4   1.7e-52   6.1e-49       2     235 .]      18     228 ..      17     228 .. 0.95

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 1.7e-52
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       +i+++D+++  +++++        ++ +++ ++++  a+a++l++gv+   +  +  + al+++l+++t l +++ +
  gi|488600504|ref|YP_007906975.1|  18 LIVPMDHGITVGPIKGL------SNIDQMIGKVKE--ADAIVLHKGVAKNSKALKCYEGALIIHLSASTVLREPE-Y 85 
                                       79***************......688888888876..79********9999888888************999999.7 PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                       + + v+sve a++lGAdav+v++++   gse+e ++l+ +++++e c+++ +pl++++y+r++ i dek dp+ v +
  gi|488600504|ref|YP_007906975.1|  86 KRL-VTSVESAIKLGADAVSVHINV---GSEREGEQLEILGMISEICDDWAMPLLAMMYPRGKGI-DEK-DPKMVSH 156
                                       777.9********************...************************************8.777.8****** PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTHCEEEESH CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeagasGvlsGR 230
                                       A r++ elGaDi+K++++        +++e+f dv++++ +p vv++GG+  ++ +fl+ +++A+  agasGv++GR
  gi|488600504|ref|YP_007906975.1| 157 AVRIGYELGADIVKTNYT--------GSIESFADVVESSSIP-VVVAGGSkmNDLAFLQEIKEAM-IAGASGVAVGR 223
                                       ******************........****************.*******999999*********.*********** PP

                                       HHHTT CS
                              DeoC 231 aifqk 235
                                       ++fq+
  gi|488600504|ref|YP_007906975.1| 224 NVFQH 228
                                       ***97 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.22   7.7e+02     199     233 ..      91     127 ..      88     132 .. 0.70
   2 !   16.3   0.2   1.1e-06    0.0041     175     235 ..     177     243 ..     161     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.22
                            DUF561 199 tvplalslgasGiGigsavskl..ndeeemvallsei 233
                                       +v+ a++lga  + +  +v +    ++ e+  ++sei
  gi|488600504|ref|YP_007906975.1|  91 SVESAIKLGADAVSVHINVGSEreGEQLEILGMISEI 127
                                       6788999999999998888654015566677777776 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.1e-06
                            DUF561 175 lastyeiskkvslPvicasG..lsdvt....vplalslgasGiGigsavsklndeeemvallseikk 235
                                       + s   ++++ s+Pv+ a G  ++d++    ++ a+ +gasG+ +g++v + ++ + mv++l+ i++
  gi|488600504|ref|YP_007906975.1| 177 IESFADVVESSSIPVVVAGGskMNDLAflqeIKEAMIAGASGVAVGRNVFQHSNPKMMVKALKMIIH 243
                                       5566678889999999997744677653323567999************************998865 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.014        50     144     231 ..      15     103 ..       5     114 .. 0.74
   2 !   12.5   0.5   1.9e-05     0.068     166     225 ..     179     243 ..     156     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                                       T-SEBEEB..SSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHH CS
                              ThiG 144 GcaavmPl..aapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamAr 218
                                       G + ++P+  +  +G  +Gl+n  ++   ++ea+  +++  G+ + s+a +  e  +   l +++v +  +  ++ +
  gi|488600504|ref|YP_007906975.1|  15 GRTLIVPMdhGITVGPIKGLSNIDQMIGKVKEAD-AIVLHKGVAKNSKALKCYEGALIIHLSASTVLREPEYKRLVT 90 
                                       5555555422667788889988777666666666.589999******999999987777788888888888888888 PP

                                       HHHHHHHHHHHHH CS
                              ThiG 219 afklaveaGrlay 231
                                       +++ a++ G  a 
  gi|488600504|ref|YP_007906975.1|  91 SVESAIKLGADAV 103
                                       8888888887775 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHH-SS-BEEES---SH.....HHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 166 alkiiieeakvPvivDAGigsp.....sdaaqamelGadavllntavaeakdpvamArafklave 225
                                        +  ++e+ ++Pv+v  G         +++ +am  Ga++v +   v + ++p +m +a+k+ ++
  gi|488600504|ref|YP_007906975.1| 179 SFADVVESSSIPVVVAGGSKMNdlaflQEIKEAMIAGASGVAVGRNVFQHSNPKMMVKALKMIIH 243
                                       556678999******99965542222268899*****************************9886 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.03   1.1e+02      12      60 ..      85     135 ..      76     137 .. 0.73
   2 !   11.5   0.2   3.9e-05      0.14     138     179 ..     176     223 ..     167     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
                          TMP-TENI  12 neellevveealkggvtlvqlRek..eldarellelaeklaalcrkygvpl 60 
                                        ++l+  ve a+k g+++v +     +  + e le    + ++c++  +pl
  gi|488600504|ref|YP_007906975.1|  85 YKRLVTSVESAIKLGADAVSVHINvgSEREGEQLEILGMISEICDDWAMPL 135
                                       5789999********999988877444555667777777777777766665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.9e-05
                          TMP-TENI 138 gleglkelaealeiPvvaiGGitlenvaevl......eagadgvavvs 179
                                        +e +++++e+++iPvv+ GG +++++a +        aga+gvav +
  gi|488600504|ref|YP_007906975.1| 176 SIESFADVVESSSIPVVVAGGSKMNDLAFLQeikeamIAGASGVAVGR 223
                                       57889999**************98876544422233278888888866 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.32   1.1e+03     148     162 ..      91     105 ..      46     139 .. 0.68
   2 !   15.2   0.3     3e-06     0.011     181     225 ..     176     225 ..     157     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.32
                               NMO 148 earkvearGaDaliv 162
                                        +  ++++GaDa+ v
  gi|488600504|ref|YP_007906975.1|  91 SVESAIKLGADAVSV 105
                                       334445555555533 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3e-06
                               NMO 181 lfaLvpqvldavdiPviAaGG..iidr...rgvaaaLalGAsgvqigtrf 225
                                        ++  + v++  +iPv+ aGG  ++d    ++++ a+ +GAsgv++g   
  gi|488600504|ref|YP_007906975.1| 176 SIESFADVVESSSIPVVVAGGskMNDLaflQEIKEAMIAGASGVAVGRNV 225
                                       4444455666666********77555333389**************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1575.01
//
Query:       gi|488600505|ref|YP_007906976.1|  [L=269]
Description: 1,4-dihydroxy-6-naphthoate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-79  264.7   0.7    1.1e-78  264.5   0.7    1.0  1  VitK2_biosynth  Menaquinone biosynthesis
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.027   14.1   0.0    1.4  1  NS3             Non-structural protein NS3
      0.059   12.8   0.0       0.16   11.4   0.0    1.7  1  SBP_bac_3       Bacterial extracellular solute-binding protei


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.5   0.7   1.8e-82   1.1e-78       1     265 [.       4     256 ..       4     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 264.5 bits;  conditional E-value: 1.8e-82
                                       EEEEEESSHHHHHHHHHHHTTSS..SGCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEE CS
                    VitK2_biosynth   1 lrlGhspylNdlflfyaLvegkvdsegleveivledpetlnrallegelDvakiSsaayariaddyalLpdlsisal 77 
                                       l+++h+p+++d+f+fya+++  +d+  le+e+v+ed+e lnr++ e e+Dv++iS++ay  ++d+y++L+  s++++
  gi|488600505|ref|YP_007906976.1|   4 LKVAHTPDADDAFMFYAMTHDEIDTW-LEIEHVIEDIESLNRKAFEVEYDVTAISAYAYSFLSDRYQILS--SGASV 77 
                                       68***********************9.8******************************************..***** PP

                                       ESSSSEEEEESS-CCC-SSS..T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTS.SEEEEEC CS
                    VitK2_biosynth  78 Grvygvllvskvpleelegel.gkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlege.dagLlIg 152
                                       G++yg+++v+    ee++  l ++++a+pg++tT+ lLl l++        + ve++fdei +av+eg+ dagLlI+
  gi|488600505|ref|YP_007906976.1|  78 GDGYGPIVVAM---EEID--LrHREIAVPGRYTTANLLLNLAIDF------KPVEMRFDEIIPAVKEGRvDAGLLIH 143
                                       **********4...4554..4467*****************6655......59************************ PP

                                       CHHHTGGGGTTEEEEEHHHHHHHHHSS-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS CS
                    VitK2_biosynth 153 esaltyaeeglkkvlDLgelWeeltglPlvlglwvvrrdlaaeaakeleealreSveyalahldevaeyaaeraqem 229
                                       e+++ty+++ l++vlDL+e+W + ++lPl+lgl++++rdl+ae  ke+ +++reS++yal+++d +++ya+++++  
  gi|488600505|ref|YP_007906976.1| 144 EGQITYKDHNLVRVLDLWEWWHDKAKLPLPLGLNAIKRDLDAEVKKEFLRVMRESINYALKNVDIAMDYAMKYSRGL 220
                                       ***************************************************************************** PP

                                       .HHHHHHHHHHHCSHHHHS-CHHHHHHHHHHHHHHH CS
                    VitK2_biosynth 230 ddevlekhlelYvnelsydlgeegragleeflelaa 265
                                       d+e++ k+  +Yvn ++y++ e  +++le ++++++
  gi|488600505|ref|YP_007906976.1| 221 DKETATKFALMYVNRYTYEMPESVKKALELLYKMGE 256
                                       *********************************986 PP

>> NS3  Non-structural protein NS3
   #    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      33      83 ..     123     174 ..     113     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-06
                               NS3  33 ewnklivcikdeevdiklevkedqlirkiykwdsvldswdws.kqyklpkpl 83 
                                        ++++i  +k+  vd  l ++e q+  k ++   vld w+w   + klp pl
  gi|488600505|ref|YP_007906976.1| 123 RFDEIIPAVKEGRVDAGLLIHEGQITYKDHNLVRVLDLWEWWhDKAKLPLPL 174
                                       578899999*******************************861568999887 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.16      36      61 ..     113     138 ..     106     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                                       CT-EEEEEE-SGGGHHHHHHTTSSSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  36 lgvkvefvpvswdelipalksgkvDi 61 
                                       l ++++ v++ +de+ipa+k+g+vD+
  gi|488600505|ref|YP_007906976.1| 113 LAIDFKPVEMRFDEIIPAVKEGRVDA 138
                                       4445566668***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1772.76
//
Query:       gi|488600506|ref|YP_007906977.1|  [L=252]
Description: thiazole-adenylate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-74  248.7   2.4    5.1e-74  248.4   2.4    1.0  1  Thi4           Thi4 family
    2.8e-08   33.5   0.2    3.8e-08   33.1   0.2    1.1  1  FAD_oxidored   FAD dependent oxidoreductase
    3.3e-07   30.4   0.6    8.2e-07   29.2   0.6    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.5e-06   26.4   2.4     0.0008   18.6   0.3    2.9  3  FAD_binding_2  FAD binding domain
      4e-06   26.3   0.2      1e-05   25.0   0.1    1.6  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.2e-06   26.6   1.3    0.00035   20.3   0.5    2.1  2  DAO            FAD dependent oxidoreductase
    8.2e-05   22.0   0.6    0.00013   21.3   0.6    1.3  1  FAD_binding_3  FAD binding domain
    0.00016   20.5   0.4    0.00025   19.9   0.4    1.2  1  HI0933_like    HI0933-like protein
    0.00045   19.4   0.6    0.00087   18.5   0.2    1.7  2  GIDA           Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.066   13.8   0.1       0.19   12.3   0.1    1.8  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.084   12.1   0.3       0.21   10.8   0.3    1.6  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.17   11.1   0.0       0.63    9.3   0.0    1.7  2  Amino_oxidase  Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.4   2.4   3.4e-77   5.1e-74       1     235 []      10     233 ..      10     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 248.4 bits;  conditional E-value: 3.4e-77
                                       HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHH CS
                              Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelL 77 
                                       s+aive+y+ +l++  esDv+ivG+G+sGL +ayyl+   ++k++++e+++s+GGG+w+GG++f+++vv+++a  +L
  gi|488600506|ref|YP_007906977.1|  10 SKAIVEKYSAKLMDVLESDVAIVGGGPSGLVSAYYLGDM-GFKTVLFEKKLSLGGGIWGGGMMFNKVVVQEEATGIL 85 
                                       79*************************************.************************************* PP

                                       HHTT---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTC..TTTSS.- CS
                              Thi4  78 delgikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvela..hdtqscv 152
                                       d+lgi ye++++  +v da+++   l+ ++ +   +k++n + veD++v++  +vaG+vin+t ve++  h     +
  gi|488600506|ref|YP_007906977.1|  86 DDLGIGYENYDEKHYVVDAIELAGGLIYNASK--KAKVFNLINVEDVMVKN-GRVAGLVINYTPVEMSnlH-----I 154
                                       *****************************999..89***************.8**************9777.....* PP

                                       B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT-E CS
                              Thi4 153 DPlvirakvvvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdgan 229
                                       DP ++ +k+v+datGhd+++ +++++k  + +    +kgek +da  +e+ +v +t ev+p+l+vaGm va+v+g +
  gi|488600506|ref|YP_007906977.1| 155 DPITVSTKAVIDATGHDASVCSILARKGGDLE----LKGEKYMDAPLGERGVVDNTSEVFPGLFVAGMTVAAVYGHP 227
                                       ***************************99887....***************************************** PP

                                       B--SB- CS
                              Thi4 230 RmGpif 235
                                       RmGpif
  gi|488600506|ref|YP_007906977.1| 228 RMGPIF 233
                                       *****9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.2   2.6e-11   3.8e-08       1     144 [.      28     169 ..      28     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.6e-11
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq..rggarl 75 
                                       Dv +vGGgp+G++ A+    +G k++L e++  lGG   +g+++        ++ +tgi +++    ++  ++++  
  gi|488600506|ref|YP_007906977.1|  28 DVAIVGGGPSGLVSAYYLGDMGFKTVLFEKKLSLGGGIWGGGMMFNKV--VVQEEATGILDDLGIGYENydEKHY-- 100
                                       9***********************************999888433333..3346799999999888866323333.. PP

                      FAD_oxidored  76 k.krskwn.......tfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.grktirAkvfiDAT 143
                                         +    +       +++ +  ++v++ +  e +v v  ++++ + + +    + v++ +     +t++ k +iDAT
  gi|488600506|ref|YP_007906977.1| 101 VvD----AielagglIYNASKKAKVFNLINVE-DVMVKNGRVA-GLVIN---YTPVEMSNLHiDPITVSTKAVIDAT 168
                                       211....0122344488888888888877766.6655544444.44443...678888888877************* PP

                      FAD_oxidored 144 g 144
                                       g
  gi|488600506|ref|YP_007906977.1| 169 G 169
                                       8 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.6   5.5e-10   8.2e-07       1      33 [.      31      63 ..      31      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.5e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                      IvG+G sGlv Ay+L + gf+ +l+ek  +lGG
  gi|488600506|ref|YP_007906977.1| 31 IVGGGPSGLVSAYYLGDMGFKTVLFEKKLSLGG 63
                                      9*******************************9 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   5.3e-07    0.0008       1      45 [.      28      71 ..      28      88 .. 0.86
   2 !    6.1   0.1    0.0034       5.1     143     201 ..     107     170 ..      66     186 .. 0.74
   3 ?    0.5   0.0      0.17   2.5e+02     385     406 ..     203     224 ..     199     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.3e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-E CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgi 45
                                      Dv ++G+G +GL++A+ + + G k+++ ek+ + gg + w +G++
  gi|488600506|ref|YP_007906977.1| 28 DVAIVGGGPSGLVSAYYLGDMGFKTVLFEKKLSLGGGI-WGGGMM 71
                                      9*****************************99977754.666666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET..TTTCEE....EEEESEEEE---- CS
                     FAD_binding_2 143 llarlvesarkagvdfqerteadeLivedgrvtGavvenp..esgrev....rirakavvlatgG 201
                                       l+  l+ +a + + ++++ +++++++v++grv G v++    e ++ +    ++  kav++atg 
  gi|488600506|ref|YP_007906977.1| 107 LAGGLIYNA-SKKAKVFNLINVEDVMVKNGRVAGLVINYTpvEMSNLHidpiTVSTKAVIDATGH 170
                                       555555555.556899999******************96676333333668788888*****995 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.17
                                       STTEEESSBTEEE-STCEESSS CS
                     FAD_binding_2 385 ldadgqpipGLYAaGevaaggv 406
                                        d++ ++ pGL+ aG + a+ +
  gi|488600506|ref|YP_007906977.1| 203 VDNTSEVFPGLFVAGMTVAAVY 224
                                       4889999********9995544 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   6.8e-09     1e-05       2      64 ..      28     126 ..      27     191 .. 0.63
   2 ?   -0.6   0.0      0.41   6.1e+02     246     275 ..     191     217 ..     149     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.8e-09
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................. 57 
                                       dv+++GgGp Gl  a +l+  g+k++l+e    l+g + +gg++  k++++ ++ +  +                  
  gi|488600506|ref|YP_007906977.1|  28 DVAIVGGGPSGLVSAYYLGDMGFKTVLFEkklsLGGGIWGGGMMFNKVVVQEEATGI-LDdlgigyenydekhyvvd 103
                                       8***************************99999788888888888777777776663.3336666677777777766 PP

                                       ................HHHHCHH CS
                                       ................xxxxxxx RF
                       Pyr_redox_2  58 ................evvkkln 64 
                                                       +v++ +n
  gi|488600506|ref|YP_007906977.1| 104 aielaggliynaskkaKVFNLIN 126
                                       66555555554444433333333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.41
                                       HCCT-EEEETTEEE--TTSBESSTTEEE-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 246 eklglelderggivvdeflrtnvpgiyaiG 275
                                       + +  +l  + + vvd ++++  pg++++G
  gi|488600506|ref|YP_007906977.1| 191 KYMDAPL--GERGVVDNTSEV-FPGLFVAG 217
                                       5556666..667789999988.99999998 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.5   2.3e-07   0.00035       1      36 [.      28      64 ..      28      81 .. 0.86
   2 !    5.5   0.0    0.0073        11     141     206 ..     100     176 ..      76     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.3e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                      dv+i+GGG  Gl  Ay+L   g  ++l+ek+  +g g 
  gi|488600506|ref|YP_007906977.1| 28 DVAIVGGGPSGLVSAYYLGDMGfkTVLFEKKLSLG-GG 64
                                      9*****************66689*******98888.44 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0073
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEE........EEEEEEE--GGGHH.. CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgleeedgkvwgve.rttp.gend........aadavVnaaGawsd.. 205
                                        +vd+ +l+ +l   a ++ +++++  +v+++  ++g+v+g+  + tp +           + +av+ a+G+ ++  
  gi|488600506|ref|YP_007906977.1| 100 YVVDAIELAGGLIYNASKK-AKVFNLINVEDVMVKNGRVAGLViNYTPvEMSNlhidpitvSTKAVIDATGHDASvc 175
                                       4557777788888888777.999999999999999999999999444444332345666775578******998744 PP

                                       H CS
                               DAO 206 l 206
                                        
  gi|488600506|ref|YP_007906977.1| 176 S 176
                                       2 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.6   8.7e-08   0.00013       2      33 ..      27      58 ..      26      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.7e-08
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       dV+IVG+Gp+Gl++a  L   G ++vl ek 
  gi|488600506|ref|YP_007906977.1| 27 SDVAIVGGGPSGLVSAYYLGDMGFKTVLFEKK 58
                                      79**************************9995 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.4   1.6e-07   0.00025       2      39 ..      28      65 ..      27      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.6e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKi 39
                                      dv+++GgG++Gl  A  +++ g +++l+ek+ +lg  i
  gi|488600506|ref|YP_007906977.1| 28 DVAIVGGGPSGLVSAYYLGDMGFKTVLFEKKLSLGGGI 65
                                      8******************************9998655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   5.8e-07   0.00087       1      72 [.      28     121 ..      28     131 .. 0.63
   2 ?   -1.4   0.0      0.62   9.2e+02     108     150 ..     127     170 ..     112     183 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.8e-07
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..........ES-GGGTT--SSSSEEE-T............THHHHHHH CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..........thkldtiaelsCnpsiggi............akgllvrE 55 
                                       dv ++GgG +G+  A+ +  +G+k++L+               ++ +++ ++   gi             k  +v  
  gi|488600506|ref|YP_007906977.1|  28 DVAIVGGGPSGLVSAYYLGDMGFKTVLFekklslgggiWGGGMMFNKVVVQEEATGIlddlgigyenydEKHYVVDA 104
                                       799*************************6655555555333333333344444444444555555555555556666 PP

                                       HHHHT-SHHHHHHHHEE CS
                              GIDA  56 idalggliikaadkagi 72 
                                       i+  ggli +a +ka++
  gi|488600506|ref|YP_007906977.1| 105 IELAGGLIYNASKKAKV 121
                                       66666666666666655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.62
                                       STTEEEEES-EEEEEECTTEEEE.EEETTS-EEEECEEEE--TT CS
                              GIDA 108 epnleiieeeveeliveekkvkg.vvtedgetikakavviatGt 150
                                        +++ + +++v+ l+++ + v+   +  d  t+++kav+ atG 
  gi|488600506|ref|YP_007906977.1| 127 VEDVMVKNGRVAGLVINYTPVEMsNLHIDPITVSTKAVIDATGH 170
                                       45666777777777665555555233345667777788888885 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00013      0.19       2      31 ..      29      58 ..      28      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      v++vGgG +gl  A +l ++g k+ ++e +
  gi|488600506|ref|YP_007906977.1| 29 VAIVGGGPSGLVSAYYLGDMGFKTVLFEKK 58
                                      89*******************999999876 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 ?   10.8   0.3   0.00014      0.21       2      30 ..      31      58 ..      30      65 .. 0.87
   2 ?   -2.0   0.0       1.1   1.7e+03     293     305 .]     205     217 ..     150     217 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg 30
                                      I+G+GP Gl +a+ l ++g++  +  Ek+
  gi|488600506|ref|YP_007906977.1| 31 IVGGGPSGLVSAYYLGDMGFK-TVLFEKK 58
                                      9*******************5.6788886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                       Pyr_redox_3 293 teetnvpglflaG 305
                                       + +  +pglf+aG
  gi|488600506|ref|YP_007906977.1| 205 NTSEVFPGLFVAG 217
                                       2344467777766 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00042      0.63       2      31 ..      37      66 ..      36      68 .. 0.94
   2 ?   -0.8   0.0      0.49   7.3e+02     417     450 ..     208     246 ..     191     247 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00042
                                      HHHHHHHHHHHTTEEEEEEESSSSSBTTS- CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGGRir 31
                                      +GL+ A++L + Gf+++++E +  +GG i+
  gi|488600506|ref|YP_007906977.1| 37 SGLVSAYYLGDMGFKTVLFEKKLSLGGGIW 66
                                      9*************************9776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.49
                                       HCSTTEEE.SGGGCTTTTTS.H....HHHHHHHHHHHHH CS
                     Amino_oxidase 417 egdprlffAGehtsreypgt.v....egAilSGlraAar 450
                                       e  p+lf+AG  ++  y +  +     g +lSG+r+A+ 
  gi|488600506|ref|YP_007906977.1| 208 EVFPGLFVAGMTVAAVYGHPrMgpifGGMLLSGKRVAEL 246
                                       458999999999998887633322226888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1520.19
//
Query:       gi|488600507|ref|YP_007906978.1|  [L=299]
Description: hypothetical protein Asulf_00981 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-21   77.0   0.2    9.1e-21   74.9   0.1    2.0  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.16   12.1   0.1       0.25   11.4   0.1    1.3  1  DUF1644      Protein of unknown function (DUF1644)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.1     1e-24   9.1e-21       3     154 ..      21     171 ..      19     181 .. 0.89
   2 ?   -0.5   0.0      0.16   1.4e+03     125     160 ..     174     210 ..     169     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1e-24
                                       EESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlr.CsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlaklavpg 77 
                                       v+rgC+ + C fC  ++      + + +++ ei +e+++l+ + + +++ +lg  +pl++ d+ve++  l+++    
  gi|488600507|ref|YP_007906978.1|  21 VVRGCTWNkCAFCGMYK----DMKFEKRDKSEIFREIDRLReFFPYARTAFLGDSNPLVHNDIVEIINYLREKNPWI 93 
                                       789***999*******6....8*******************76666***************************8555 PP

                                       EEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                        r+t  + + ++    eekl +l+++g+drv++g e++dde vlkl+++g t e++++a +k+ ++ ++++++ i+g
  gi|488600507|ref|YP_007906978.1|  94 ERVTAYARAKTIArmsEEKLLALKDAGLDRVHIGMESGDDE-VLKLVKKGATAEDIIQAGKKAGKN-FEVSFYYILG 168
                                       5666666666666788*************************.************************.**87777777 PP

                                       BTT CS
                                       xxx RF
                       Radical_SAM 152 lpG 154
                                       l G
  gi|488600507|ref|YP_007906978.1| 169 LGG 171
                                       766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.16
                                       SHHHHHHHHHHHHHHTTSET..EEEEEEEBTTTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                       Radical_SAM 125 htfeevlealeklreagikr..vvdrivglpGendeel 160
                                        ++++ l++ e ++ea  ++   + +++++pG   e+l
  gi|488600507|ref|YP_007906978.1| 174 RSRSHALKSAEVINEA-KPDfvRIRTLTVIPGTDIEKL 210
                                       5677889999999999.888888888899999887765 PP

>> DUF1644  Protein of unknown function (DUF1644)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.8e-05      0.25     106     138 ..      15      47 ..       8      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                           DUF1644 106 rkylnekkrsCseesCsfvGnykelrkharreh 138
                                        + l +  r C+ ++C+f+G yk+++   r + 
  gi|488600507|ref|YP_007906978.1|  15 GSALIRVVRGCTWNKCAFCGMYKDMKFEKRDKS 47 
                                       55666778****************997777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.59
# Mc/sec: 1529.15
//
Query:       gi|488600508|ref|YP_007906979.1|  [L=618]
Description: ferrous iron transporter FeoB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-52  177.1   1.5      3e-52  176.3   1.5    1.4  1  FeoB_N       Ferrous iron transport protein B
    3.6e-23   82.0  15.3    1.8e-11   44.3   4.5    2.7  2  Gate         Nucleoside recognition
    9.3e-20   70.8   0.3      2e-19   69.8   0.3    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
    9.9e-10   38.0   0.7    9.9e-10   38.0   0.7    3.6  3  FeoB_C       Ferrous iron transport protein B C terminus
    0.00021   20.8   0.1    0.00036   20.0   0.1    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
    0.00047   20.3   1.6     0.0046   17.0   0.2    2.6  3  Dynamin_N    Dynamin family
     0.0011   18.9   1.2       0.63    9.9   0.1    2.6  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.016   15.7   0.4       0.04   14.4   0.4    1.6  1  FeoB_Cyto    FeoB cytosolic helical domain
      0.022   14.1   0.1      0.039   13.3   0.1    1.4  1  AIG1         AIG1 family
      0.042   13.4   0.2      0.074   12.6   0.2    1.5  1  GTP_EFTU     Elongation factor Tu GTP binding domain
      0.065   13.5   0.0       0.22   11.7   0.0    1.9  2  Roc          Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3   1.5   1.9e-55     3e-52       5     156 .]       2     150 ..       1     150 [. 0.98

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 1.9e-55
                                       EEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSE CS
                            FeoB_N   5 lvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdv 81 
                                       lvGnpnvGk+ +f +ltg++ +v+N+pG+tv+ + +klk  g++ +++D PG+Ysl a++eee+va+++ll e +d+
  gi|488600508|ref|YP_007906979.1|   2 LVGNPNVGKSLIFQHLTGKYATVSNYPGTTVDITVAKLK--GSNKTLIDTPGMYSLVAITEEERVAKKILL-EGADI 75 
                                       9***********************************999..99999************************9.567** PP

                                       EEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N  82 vvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                       vv+vvda+nl+r L +t+ql+e g +++l+ln ideaek g+eid k Lse+Lg+pvvkt+a++k gi+el+kai
  gi|488600508|ref|YP_007906979.1|  76 VVHVVDAKNLKRMLPFTIQLIEAGFNTILVLNAIDEAEKLGMEIDSKLLSERLGIPVVKTIATQKMGIDELKKAI 150
                                       ************************************************************************986 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   4.5   1.1e-14   1.8e-11       4     108 ..     337     427 ..     334     430 .. 0.92
   2 !   42.6   3.1   3.7e-14     6e-11       2     111 ..     491     591 ..     490     592 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.1e-14
                              Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfd 80 
                                       ++pi+  ++i  ++l++s++l r++ ll+  f++ g  l+++a+++ll+g++   ++  + ++++         + +
  gi|488600508|ref|YP_007906979.1| 337 IFPIVTTFFIAFSVLEDSGFLPRMASLLNSTFKKVG--LSGRAVIPLLLGLG---CGTMATIVTR---------TLE 399
                                       789*********************************..**************...6655555565.........*** PP

                              Gate  81 tpksalafllfvllytpcvatlavivre 108
                                       t+k+++++ l+++  +pc a+++v++++
  gi|488600508|ref|YP_007906979.1| 400 TKKERIIATLLLAVGIPCSAQMGVMMGI 427
                                       ************************9986 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 3.7e-14
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       + ++pi++l+s++iw+ + +++++ + ++l+     +g  l+ +a   ll gf+ +  +++ l  l       + +g
  gi|488600508|ref|YP_007906979.1| 491 KEVMPIFILISVFIWIGRITGVFDLLVNALAVPSTLIG--LPSQAGLILLYGFFRRDYGAAGLYDL-------VNKG 558
                                       7899**********************************..***********************666.......6*** PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrelgs 111
                                       +++  ++++++++++l +pc+a++ v+ +e g 
  gi|488600508|ref|YP_007906979.1| 559 IFSYNQVIVAMVTLTLFVPCIAQFSVMCKERGL 591
                                       ******************************996 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.3   1.2e-22     2e-19       3     113 ..       1     107 [.       1     108 [. 0.78

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1.2e-22
                                       EEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCTS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleead 77 
                                       ++vG+pNvGKS +++ ltg+ a vs++pgtT di+ +++k  g++ +l+DtpG+++     ee++++k++l le ad
  gi|488600508|ref|YP_007906979.1|   1 MLVGNPNVGKSLIFQHLTGKYATVSNYPGTTVDITVAKLK--GSNKTLIDTPGMYSlvAITEEERVAKKIL-LEGAD 74 
                                       58*************************************9..8899*******986533344557888888.5669* PP

                                       EEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  78 lillvvdaseeklkpldeeleelleeakkplilvln 113
                                       ++++vvda+ + lk++     +l+ ea+ ++ilvln
  gi|488600508|ref|YP_007906979.1|  75 IVVHVVDAK-N-LKRMLPFTIQLI-EAGFNTILVLN 107
                                       *******76.3.555544444443.34556666666 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 ?   -1.8   0.8       1.6   2.6e+03       1      19 [.     268     286 ..     268     292 .. 0.81
   2 !   38.0   0.7   6.1e-13   9.9e-10       2      53 .]     435     485 ..     434     485 .. 0.92
   3 ?   -1.0   2.0      0.92   1.5e+03       3      20 ..     596     613 ..     595     616 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.6
                            FeoB_C   1 lfslYllgilvallvalll 19 
                                       ++slY+l +++ ++ a +l
  gi|488600508|ref|YP_007906979.1| 268 VLSLYILYLFAGVFGAQFL 286
                                       6899999999999888665 PP

  == domain 2  score: 38.0 bits;  conditional E-value: 6.1e-13
                            FeoB_C   2 fslYllgilvallvalllkkttlkgepspfvmELPpYrlPslknvliktweR 53 
                                       ++++ +  l  +++a l+++  + ge+  f+mE+Pp+r+P+++n++ kt++R
  gi|488600508|ref|YP_007906979.1| 435 MIWITVISLTLIFTATLASRA-IEGEDIVFFMEIPPLRMPNFRNIIFKTVTR 485
                                       667778888999********7.***************************987 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.92
                            FeoB_C   3 slYllgilvallvalllk 20 
                                       +++++++ va++v++l +
  gi|488600508|ref|YP_007906979.1| 596 GIFIISLTVAFAVGYLTN 613
                                       7899**********9976 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 !   20.0   0.1   2.2e-07   0.00036       7      85 ..       1      82 [.       1     110 [. 0.70

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.2e-07
                                      EEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG.....GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE....E CS
                             SRPRB  7 llvGlsdsGKTslftrLttdsvkktvtSqessaalkv..ksekgskltliDfPGheklrqklleklkaksslkg....l 79
                                      +lvG  + GK ++f++Lt + ++   +S  + ++ ++   + kgs++tliD PG  +l     e+ +ak+ l      +
  gi|488600508|ref|YP_007906979.1|  1 MLVGNPNVGKSLIFQHLTGKYAT---VSNYPGTTVDItvAKLKGSNKTLIDTPGMYSLVAITEEERVAKKILLEgadiV 76
                                      589**************987543...34444444443225679**************9877776666665533212225 PP

                                      EEEEET CS
                             SRPRB 80 vfvvDS 85
                                      v+vvD+
  gi|488600508|ref|YP_007906979.1| 77 VHVVDA 82
                                      666664 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.45   7.4e+02       3      39 ..       2      38 ..       1      44 [. 0.77
   2 !   17.0   0.2   2.8e-06    0.0046      94     140 ..      35      84 ..      18     109 .. 0.82
   3 ?    1.1   0.0      0.23   3.7e+02      50     106 ..     148     203 ..     129     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.45
                                      EEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEE CS
                         Dynamin_N  3 vvGsqSsGKSSvlnaLlgedilprgpnptTrrplelq 39
                                      +vG+ + GKS +  +L+g+   ++    tT  +++ +
  gi|488600508|ref|YP_007906979.1|  2 LVGNPNVGKSLIFQHLTGKYATVSNYPGTTVDITVAK 38
                                      79****************9977766666666666555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.8e-06
                                       EEEETTS-SEEEEE---B-S..SSGTTSHHHHHHH.STTEEEEEEEETTS CS
                         Dynamin_N  94 kilsllvkgltlvDlPGlds..vnkrdqelvkeyi.kkadiilavtsanh 140
                                       ++ +l+ ++ tl+D+PG+ s    +++++++k+++ + adi+++v++a++
  gi|488600508|ref|YP_007906979.1|  35 TVAKLKGSNKTLIDTPGMYSlvAITEEERVAKKILlEGADIVVHVVDAKN 84 
                                       5667788999*********9854566669******************986 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.23
                                       ...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEE CS
                         Dynamin_N  50 avkeelkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlv 106
                                       +++ ++++++k++ +++ ++e++e+ t+ ++ +   iskk+i l il  ++++l++v
  gi|488600508|ref|YP_007906979.1| 148 KAIFNYRSDKKEIIKLNSMDEKLESITRLLD-QDYPISKKMIALLILLGDKDTLEMV 203
                                       566678888999*************999999.9999999999998887777777665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.2    0.0028       4.6     104     163 ..       2      54 ..       1      57 [. 0.79
   2 !    9.9   0.1   0.00039      0.63      30      97 ..      83     150 ..      71     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
                                       EECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETT.TEEEESS-SSSS CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelae.gglliDtPGfre 163
                                       lvG+  vGKS +  +l+++     + vs+       TT   ++ +l+  + +liDtPG+ +
  gi|488600508|ref|YP_007906979.1|   2 LVGNPNVGKSLIFQHLTGK----YATVSNYP----GTTVDITVAKLKGsNKTLIDTPGMYS 54 
                                       7899999999999999998....56677754....38888888888854789******976 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00039
                                       --HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  30 lslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                        +l+++  f +++ e+g + ++vln iD +e+     + k   e+lg++v+++ a++k g++elk+++
  gi|488600508|ref|YP_007906979.1|  83 KNLKRMLPFTIQLIEAGFNTILVLNAIDEAEKLGMEIDSKLLSERLGIPVVKTIATQKMGIDELKKAI 150
                                       3344444455788899****************9944556666789*******************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 ?   14.4   0.4   2.5e-05      0.04       6      47 ..     167     220 ..     164     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                         FeoB_Cyto   6 EkaiekleellkesnlkaklppRwlAlklLegDeelleelk...............e 47 
                                       ++++e++++ll+++    +++++ +Al +L gD++ le+++               +
  gi|488600508|ref|YP_007906979.1| 167 DEKLESITRLLDQD---YPISKKMIALLILLGDKDTLEMVRgeknyqkiveiakdsN 220
                                       67899999999996...************************5444444444443333 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.4e-05     0.039       5     113 ..       2     102 ..       1     114 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                       EESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCT CS
                              AIG1   5 lvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllse 81 
                                       lvG   +GkS     + gk a  s++  ++v  ++    ++ +g +   iDTPg+ +l + ++  ++ + + +l   
  gi|488600508|ref|YP_007906979.1|   2 LVGNPNVGKSLIFQHLTGKYATVSNYPGTTVDITV----AKLKGSNKTLIDTPGMYSLVAITE--EERVAKKIL--L 70 
                                       88888899998888888888888887666555554....4566777789*********99877..444555444..4 PP

                                       T-ESEEEEEEETTB-SHHHHHHHHHHHHHHCG CS
                              AIG1  82 egihalllvlslgrfteedekalktlkelFGe 113
                                       eg ++++ v++++++++    +++ +++ F +
  gi|488600508|ref|YP_007906979.1|  71 EGADIVVHVVDAKNLKRMLPFTIQLIEAGFNT 102
                                       899*********99998888888888887765 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 ?   12.6   0.2   4.5e-05     0.074      53     189 ..      29     151 ..       9     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.5e-05
                                       TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHH.......HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTT CS
                          GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFskevirg.......lrvlDgavlvvdaveGvepqteevlrlalkeg 122
                                       g T+++++++l+      + +liDtPG  + +  +++        l+ +D++v vvda++    +      ++++ g
  gi|488600508|ref|YP_007906979.1|  29 GTTVDITVAKLK----GSNKTLIDTPGMYSLVAITEEErvakkilLEGADIVVHVVDAKN--LKRMLPFTIQLIEAG 99 
                                       677777777777....667799*****999775554443456777888999999999984..45556667788899* PP

                                       TEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 123 vpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealv 189
                                        ++i+++N +D++ k  ++   + ++++l                 +pvv + a ++ g+++l +a++
  gi|488600508|ref|YP_007906979.1| 100 FNTILVLNAIDEAeKLGMEIDSKLLSERL----------------GIPVVKTIATQKMGIDELKKAIF 151
                                       ***********994333443344444444................24555555555555555544444 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 ?   11.7   0.0   0.00014      0.22       3      93 ..       1      86 [.       1     111 [. 0.56
   2 ?   -2.0   0.0       2.4     4e+03      30      83 ..     139     188 ..     131     225 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTC.EEEEEEEE-SGGCTTTT-HHHHCTS CS
                               Roc  3 vlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkk.vklniWDtaGqerfrslhplylrea 80
                                      +lvG+ +vGK+ ++++++ +  + ++ + + vd++  ++   kg  n++ +++   +++  +a  e+ r  +++ l++a
  gi|488600508|ref|YP_007906979.1|  1 MLVGNPNVGKSLIFQHLTGKYATVSNYPGTTVDITVAKL---KGS-NKTLIDTpGMYSL--VAITEEERVAKKILLEGA 73
                                      79***************9987766655555555544333...331.1111111011111..455666666666777777 PP

                                      CEEEEEEEGHHHH CS
                               Roc 81 alailvydsrsse 93
                                      ++++ v+d+++ +
  gi|488600508|ref|YP_007906979.1| 74 DIVVHVVDAKNLK 86
                                      7777777665544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                                       TTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEE CS
                               Roc  30 stigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaala 83 
                                       + +g+d l+k + + ++    +k++ +kln  D   +  +r l + y  +++++
  gi|488600508|ref|YP_007906979.1| 139 QKMGIDELKKAIFNYRS----DKKEIIKLNSMDEKLESITRLLDQDYPISKKMI 188
                                       55677776666543332....334557777777666666666666665444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.77u 0.28s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 3603.30
//
Query:       gi|488600509|ref|YP_007906980.1|  [L=224]
Description: hypothetical protein Asulf_00983 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  100.8   1.4    6.1e-29   99.9   1.4    1.5  1  Fe_dep_repr_C  Iron dependent repressor, metal binding and di
    7.3e-11   42.2   0.0    1.3e-10   41.4   0.0    1.4  1  FeoA           FeoA domain
     0.0052   16.7   0.2      0.012   15.6   0.1    1.6  2  HTH_45         Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   1.4     1e-32   6.1e-29       1      69 [.      47     115 ..      47     116 .. 0.99

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1e-32
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                       TekG++ A++++r hrl+er+L+d+lg+++e++++ A+++Eh +see++e++++llg+p++cPhg++ip
  gi|488600509|ref|YP_007906980.1|  47 TEKGKKRAEKIIRLHRLAERLLSDILGMEEEDVEKSACKFEHFISEEVEEAICTLLGHPRFCPHGSEIP 115
                                       9*******************************************************************9 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   2.2e-14   1.3e-10       2      72 ..     133     199 ..     132     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.2e-14
                                       EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEE CS
                              FeoA   2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlV 72 
                                       +Ls+l+ G++gei+ +    + +  ++ ++G+ pG++i+v++   f  ++++++g+t++aL++e+A++I+V
  gi|488600509|ref|YP_007906980.1| 133 KLSELNAGDEGEIKYVVGG-KGVSSKFIAFGIMPGEEIKVLRV--F-PTYIIQIGNTQFALDKELADSIYV 199
                                       69**************987.99*******************64..3.68********************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 !   15.6   0.1     2e-06     0.012      42      76 ..      30      64 ..      25      65 .. 0.93
   2 ?   -3.1   0.0       1.4   8.3e+03      50      62 ..     141     153 ..     127     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-06
                            HTH_45 42 mLvekglikkskekYvlTekGlelleklkeleela 76
                                      +L+++gli+ +++k  lTekG++  ek+ +l++la
  gi|488600509|ref|YP_007906980.1| 30 YLQDEGLIEVKNGKAFLTEKGKKRAEKIIRLHRLA 64
                                      799*************************9999986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                            HTH_45  50 kkskekYvlTekG 62 
                                       ++ + kYv+  kG
  gi|488600509|ref|YP_007906980.1| 141 DEGEIKYVVGGKG 153
                                       5677889988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1399.53
//
Query:       gi|488600510|ref|YP_007906981.1|  [L=99]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   25.9   0.1    1.5e-05   25.2   0.1    1.3  1  Rrf2            Transcriptional regulator
    0.00017   21.1   0.2    0.00033   20.2   0.2    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0046   16.8   0.0      0.011   15.6   0.0    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0076   16.2   0.6      0.013   15.4   0.1    1.8  2  HTH_12          Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.033   14.2   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      0.021   15.0   0.4      0.036   14.2   0.3    1.6  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.022   14.5   0.0      0.038   13.7   0.0    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.023   14.5   0.9      0.052   13.4   0.1    1.9  2  RuvB_C          RuvB C-terminal winged helix domain
      0.031   14.0   2.1        1.4    8.6   0.0    2.1  2  DUF4423         Domain of unknown function (DUF4423)
       0.04   13.8   0.0      0.078   12.9   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.071   12.4   0.0      0.078   12.3   0.0    1.1  1  FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protei
       0.67   10.1   3.0        1.5    9.0   0.3    2.1  2  Fib_alpha       Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1     1e-08   1.5e-05       2      58 ..       5      61 ..       4      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1e-08
                                      ---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2  2 klsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      kl++++e+al+ +++L++ ++++p+ + +++e  n++++ ++  l+ L+++g+++++
  gi|488600510|ref|YP_007906981.1|  5 KLKQESEIALRHIIVLQEVQKNQPIGIFKLSELLNMPKHRIRYSLRVLEQSGIIEAT 61
                                      6899**************************************************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 !   20.2   0.2   2.2e-07   0.00033       8      48 .]      19      59 ..      15      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.2e-07
                            HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +L+++qkn  i +  L+e l++++  +++ l+ Le++G+I+
  gi|488600510|ref|YP_007906981.1| 19 VLQEVQKNQPIGIFKLSELLNMPKHRIRYSLRVLEQSGIIE 59
                                      69**************************************7 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 !   15.6   0.0     7e-06     0.011      20      46 ..      33      59 ..      19      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7e-06
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 20 elaeelglsqstvShHLkkLreaGLVe 46
                                       l+e l++++  +++ L++L+++G++e
  gi|488600510|ref|YP_007906981.1| 33 KLSELLNMPKHRIRYSLRVLEQSGIIE 59
                                      59***********************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 !   15.4   0.1   8.8e-06     0.013      11      61 ..      26      70 ..      11      75 .. 0.77
   2 ?   -2.2   0.1       2.7   4.1e+03       7      10 ..      89      92 ..      79      98 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.8e-06
                            HTH_12 11 dkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEk 61
                                      ++pig  ++ e L+     i     Ry Lr+le+ g+++   y+ + + E 
  gi|488600510|ref|YP_007906981.1| 26 NQPIGIFKLSELLNMPKHRI-----RYSLRVLEQSGIIEATQYG-AVIKEG 70
                                      45677777777776665555.....****************998.777775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                            HTH_12  7 laes 10
                                      ++e 
  gi|488600510|ref|YP_007906981.1| 89 IEEL 92
                                      3333 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.2e-05     0.033      27      56 ..      31      60 ..      14      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 27 aselaerldlskntlsyHLrvLeeagLvev 56
                                         l e+l ++k  ++y LrvLe+ g++e 
  gi|488600510|ref|YP_007906981.1| 31 IFKLSELLNMPKHRIRYSLRVLEQSGIIEA 60
                                      567999**********************95 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   2.4e-05     0.036      16      72 ..      22      81 ..       4      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                           DUF2250 16 hlkkanvdYaksiakeleipleevrellkkLeelGLlerve.gktikrteakl..Kkkse 72
                                       ++k ++     +++ l++p++++r  l+ Le+ G++e  + g++ik+   k   K+k+e
  gi|488600510|ref|YP_007906981.1| 22 EVQKNQPIGIFKLSELLNMPKHRIRYSLRVLEQSGIIEATQyGAVIKEGAEKEfeKLKKE 81
                                      444444444446778999********************9998999999877632255555 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.038       1      53 [.      15      67 ..      15      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                          HTH_DeoR  1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGavs 53
                                      R+   l+ +++ + + + +l+ell+  +  iR  L+ Le++g+++ t  Gav+
  gi|488600510|ref|YP_007906981.1| 15 RHIIVLQEVQKNQPIGIFKLSELLNMPKHRIRYSLRVLEQSGIIEATQYGAVI 67
                                      78889***************************************988777765 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.5e-05     0.052      11      63 ..      16      67 ..      10      76 .. 0.78
   2 ?   -0.8   0.1      0.93   1.4e+03      33      45 ..      78      90 ..      75      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                                      HHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE CS
                            RuvB_C 11 yLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRil 63
                                       + +l+e  k++p+g+  l+++l+++k+ i      +L ++g Ie t+ G  +
  gi|488600510|ref|YP_007906981.1| 16 HIIVLQEVQKNQPIGIFKLSELLNMPKHRIRYSL-RVLEQSGIIEATQYGAVI 67
                                      5567888889*******************98554.788888888888877655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.93
                                      TT--HHHHHHTTH CS
                            RuvB_C 33 lgeeketiedviE 45
                                      l+ e +ti+++iE
  gi|488600510|ref|YP_007906981.1| 78 LKKEIDTIIKNIE 90
                                      5567788888888 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00091       1.4      40      75 ..      32      65 ..      11      72 .. 0.80
   2 ?    4.8   1.1     0.014        20     128     147 ..      72      91 ..      65      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00091
                           DUF4423 40 eelakrlrpkisaeevekalefLlklgllkkdedgk 75
                                       +l++ l+  +++ +++ +l+ L+++g+++ ++ g 
  gi|488600510|ref|YP_007906981.1| 32 FKLSELLN--MPKHRIRYSLRVLEQSGIIEATQYGA 65
                                      479999**..********************988765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.014
                           DUF4423 128 kedyekikkeirefrkkila 147
                                       ++++ek+kkei++ +k+i +
  gi|488600510|ref|YP_007906981.1|  72 EKEFEKLKKEIDTIIKNIEE 91 
                                       789************99976 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   5.2e-05     0.078      20      56 ..      26      62 ..      15      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      ++p  + +++e l+ p+ ++  +Lr Le+ G++e  +
  gi|488600510|ref|YP_007906981.1| 26 NQPIGIFKLSELLNMPKHRIRYSLRVLEQSGIIEATQ 62
                                      566666789************************9876 PP

>> FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.2e-05     0.078      39      93 ..      39      91 ..      14      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.2e-05
                    FAE1_CUT1_RppA 39 kldeesldflrkilersglgeetyvPravlelpekktlaeareEaeevlfgavde 93
                                      ++ ++++++  ++le+sg+ e t   + + e   +k +++ ++E ++++   ++e
  gi|488600510|ref|YP_007906981.1| 39 NMPKHRIRYSLRVLEQSGIIEATQYGAVIKE-GAEKEFEKLKKEIDTIIK-NIEE 91
                                      3456789****************99876655.566789999999998765.4555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.13   1.9e+02     101     124 ..      14      37 ..       3      48 .. 0.75
   2 ?    9.0   0.3     0.001       1.5      81     111 ..      66      96 ..      42      99 .] 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 101 esnirvLqnvlesneqkiqkLeqd 124
                                        ++i vLq+v +++   i kL + 
  gi|488600510|ref|YP_007906981.1|  14 LRHIIVLQEVQKNQPIGIFKLSEL 37 
                                       478999999999999888888765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                                       HHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                         Fib_alpha  81 ksskeleeeilrlketidaqesnirvLqnvl 111
                                        +++  e+e ++lk++id+ ++ni++L+  +
  gi|488600510|ref|YP_007906981.1|  66 VIKEGAEKEFEKLKKEIDTIIKNIEELKRRV 96 
                                       45677799999****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1636  (0.0912488); expected 358.6 (0.02)
Passed bias filter:                     1010  (0.0563333); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); 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 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 659.45
//
Query:       gi|488600511|ref|YP_007906982.1|  [L=143]
Description: hypothetical protein Asulf_00985 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-47  157.8   2.0    6.8e-47  157.7   1.3    1.4  2  DUF365    Domain of unknown function (DUF365)


Domain annotation for each model (and alignments):
>> DUF365  Domain of unknown function (DUF365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.44     8e+03      33      44 ..      18      29 ..       5      37 .. 0.65
   2 !  157.7   1.3   3.8e-51   6.8e-47       1      96 []      46     142 ..      46     142 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.44
                                      HHHTSTTBSS-H CS
                            DUF365 33 fekygdrvfltk 44
                                       +ky +r f  k
  gi|488600511|ref|YP_007906982.1| 18 PKKYMNRFFEGK 29
                                      456666666544 PP

  == domain 2  score: 157.7 bits;  conditional E-value: 3.8e-51
                                       EEEEE---STT-B--EEEEEEEEEEES-THHHHHHTSTTBSS-HHHHHHHHHHHHHT----S.S---EEEEEEEEEE CS
                            DUF365   1 mklvfyasredtGfvGeaeikrvvlsedpleifekygdrvfltkeelkkyvkskerwrkgkk.rkkawlvleledik 76 
                                       mk+vfy+s+edtGfvGea+ikr++l+edp+++fe+ygdr+fltk+elk y+ks+erwr+g+k rkk+w+++eledi+
  gi|488600511|ref|YP_007906982.1|  46 MKFVFYQSQEDTGFVGEAKIKRIILQEDPMKFFEIYGDRIFLTKDELKGYIKSQERWRSGQKdRKKLWMAIELEDIQ 122
                                       9**********************************************************9988************** PP

                                       E--S-B--SS---TT-EEEE CS
                            DUF365  77 kydkvvkPkrfvpvgGkylr 96 
                                       kydk+++P+rfvp+gG+y+r
  gi|488600511|ref|YP_007906982.1| 123 KYDKPIQPERFVPAGGQYIR 142
                                       ******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 987.02
//
Query:       gi|488600512|ref|YP_007906983.1|  [L=315]
Description: hypothetical protein Asulf_00986 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.8   0.0        2.7    8.1   0.0    2.4  2  Dehydratase_SU  Dehydratase small subunit
  ------ inclusion threshold ------
       0.73   10.2   4.6       0.42   11.0   0.3    2.5  3  Ribosomal_L12   Ribosomal protein L7/L12 C-terminal domain


Domain annotation for each model (and alignments):
>> Dehydratase_SU  Dehydratase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0012        11      55      80 ..     140     165 ..     135     169 .. 0.86
   2 !    8.1   0.0    0.0003       2.7      23      79 ..     212     268 ..     199     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0012
                    Dehydratase_SU  55 iAesagrkqlaknlrRaaElvkvpde 80 
                                       +  +  r++++ n++R +E+++++++
  gi|488600512|ref|YP_007906983.1| 140 VVTDSFRDRMQVNINRNSEIIEIDED 165
                                       6677889****************886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0003
                    Dehydratase_SU  23 sldditlekvlsgkvkaedlritpetLelqaqiAesagrkqlaknlrRaaElvkvpd 79 
                                        +dd+ ++ v+++ v+  ++ +++e ++  + i  ++ +k +++ l+R a l +++ 
  gi|488600512|ref|YP_007906983.1| 212 GYDDLRIKGVIDNGVSYYEIILNEENIKKLTGIGVEEAKKIVEESLEREAVLSELSS 268
                                       589***********************************************9988765 PP

>> Ribosomal_L12  Ribosomal protein L7/L12 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.93   8.3e+03      28      42 ..       2      16 ..       1      20 [. 0.70
   2 ?   11.0   0.3   4.7e-05      0.42      19      37 ..     238     256 ..     236     269 .. 0.82
   3 ?   -0.2   0.1      0.15   1.3e+03      47      60 ..     299     312 ..     295     315 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.93
                                      HHHHHHHTTTTSTEE CS
                     Ribosomal_L12 28 keaKdlVeaapkvvk 42
                                      k+ K+ ++a+ k++ 
  gi|488600512|ref|YP_007906983.1|  2 KDMKEKINALTKQIL 16
                                      777888877777765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.7e-05
                                       HHHHH---HHHHHHHHTTT CS
                     Ribosomal_L12  19 VreitglgLkeaKdlVeaa 37 
                                       ++++tg+g  eaK++Ve+ 
  gi|488600512|ref|YP_007906983.1| 238 IKKLTGIGVEEAKKIVEES 256
                                       89**************984 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHCT CS
                     Ribosomal_L12  47 keeAeeikkkLeea 60 
                                       keeAe+i   +e++
  gi|488600512|ref|YP_007906983.1| 299 KEEAEKILSMIEDI 312
                                       89****99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2270.71
//
Query:       gi|488600513|ref|YP_007906984.1|  [L=254]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   11.5   7.6      0.093   11.2   7.6    1.1  1  Borrelia_P83  Borrelia P83/100 protein


Domain annotation for each model (and alignments):
>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.6   5.2e-06     0.093     183     262 ..     148     220 ..     102     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.2e-06
                      Borrelia_P83 183 veklredkekdvelrrdivDlkeresqedakraqvlkeeldkkqkdadkakkkadtaednadkqrkevreklqeakn 259
                                       ++k++e++++d  l+++i  +  re     k+a    +e  ++ +++d+a+k+ad+ +   +  r+evr++++e   
  gi|488600513|ref|YP_007906984.1| 148 IKKMLEEEDEDCRLAKEIYGMNVREYIDVVKKAVISIKEEAEAYREIDEAEKDADKDR---EEDREEVRDEMKE--- 218
                                       689***********************99999999777777677777777777766532...2233333333333... PP

                      Borrelia_P83 260 lpe 262
                                        pe
  gi|488600513|ref|YP_007906984.1| 219 -PE 220
                                       .32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1649  (0.0919739); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); 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):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1622.15
//
Query:       gi|488600514|ref|YP_007906985.1|  [L=369]
Description: Aspartate/tyrosine/aromatic aminotransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-65  222.3   0.0    1.2e-65  222.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    3.4e-07   29.5   0.0    7.3e-07   28.5   0.0    1.5  1  Aminotran_5      Aminotransferase class-V
    6.6e-07   28.2   0.1    7.7e-07   28.0   0.1    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.6e-06   27.7   0.1    2.3e-06   27.1   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    5.6e-05   22.6   0.0      9e-05   21.9   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00011   21.2   0.1     0.0088   15.0   0.1    2.1  2  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.078   12.9   0.1       0.17   11.9   0.1    1.6  1  DUF1246          Protein of unknown function (DUF1246)
      0.093   12.8   0.2        1.9    8.7   0.0    2.9  3  LZ3wCH           Leucine zipper with capping helix domain


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 !  222.1   0.0   5.2e-69   1.2e-65       2     363 .]      30     362 ..      29     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 222.1 bits;  conditional E-value: 5.2e-69
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       ++inL+++e+++d++ + ++++ ka+      +++++ y+ + g +el+e +a+ +g      +  e +v  + Ga+
  gi|488600514|ref|YP_007906985.1|  30 EIINLTIGEPDFDTHLEIIERAYKAM------KEGYTHYTSNFGIAELREVIAERYG------VSEE-EVMITCGAS 93 
                                       79***********4445555555555......55***********************......5556.9******** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       +++     ++ ++  +e+++p+p++ sy ++ +l+ + v ++  +s+++f+l +e+l e +++      kt +++++
  gi|488600514|ref|YP_007906985.1|  94 EALLNTSLAF-IEENSEVVIPTPSFLSYFTYSKLCNARVKPVD-TSSNNFELKAEDLNETVSD------KTSLVFLN 162
                                       **********.9*******************************.88*****************......9******* PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                        p+NPtG+v++ +   +++++++ ++++l++De+Y   +++++       +++ + n+++ + +sK+++++G+R+Gy
  gi|488600514|ref|YP_007906985.1| 163 YPNNPTGAVLDQKAMNAIAEVCEDKGIILVSDEVYDSIYYDKK-----PGTLAGKENVVVINAFSKSLAMTGWRIGY 234
                                       *****************************************54.....89*************************** PP

                                       EEEEHHHHHHHHHHH..HHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 233 ilgnaavvsqlrkls..rpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmf 307
                                       i++n+++++ + k++  ++++ ++ +q+av  +++d l + + ++ m++++ krr++++d+L ++ +kv +++++++
  gi|488600514|ref|YP_007906985.1| 235 IIANKDLLDSILKVHqvNGVCAPAFAQKAVYDVIKDGLAE-EITKSMVREFRKRRDFVYDSL-KDVFKVSKPEGAFY 309
                                       ***********99972256677**************9975.6999*****************.88************ PP

                                       EEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 308 lltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelveal 363
                                        +  +++   +e+++kLl e gv+vtpg+ f+ + ++Ri++ + + e+le+++e++
  gi|488600514|ref|YP_007906985.1| 310 IFPQVENP--MEFAEKLLAETGVAVTPGNAFGSERNIRISY-ASSMENLEKAMEKI 362
                                       ******99..*******************************.***********997 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   3.2e-10   7.3e-07      44     177 ..      67     196 ..      45     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.2e-10
                                       HHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE. CS
                       Aminotran_5  44 aveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi. 119
                                        + e re +ae +++++ ee++ t G++ea+    l++   +++  e+v+ +    + +      +k ++a+vk + 
  gi|488600514|ref|YP_007906985.1|  67 GIAELREVIAERYGVSE-EEVMITCGASEALLNTSLAF---IEENSEVVIPTPSFLSYF----TYSKLCNARVKPVd 135
                                       57899***********6.**********9988877788...9**********9999999....55556699***995 PP

                                       EBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 120 pldeegeldldelekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvDaa 177
                                       +  ++ el+ ++l++++++kt+lv+++  +n tG + +   +++i++++ +kg++++ D +
  gi|488600514|ref|YP_007906985.1| 136 TSSNNFELKAEDLNETVSDKTSLVFLNYPNNPTGAVLDqkaMNAIAEVCEDKGIILVSDEV 196
                                       5667789****************************88722245667778889999999965 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   3.4e-10   7.7e-07      51     181 ..      65     202 ..      45     328 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.4e-10
                                       -HHHHHHHHHHHHHHT-.SEEEEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHH...HHHHHTHHHTTCEEEEE CS
                   Cys_Met_Meta_PP  51 nptrsvleeriaaLegg.eaalavssGma.AiaaailallkaGdeivvsddlYggtq...rllkkvlkklgievkfv 122
                                       n     l e ia+ +g+ e+ +++++G + A+ ++ la++++ +e+v+ +  + + +   +l++  +k +  +++ +
  gi|488600514|ref|YP_007906985.1|  65 NFGIAELREVIAERYGVsEEEVMITCGASeALLNTSLAFIEENSEVVIPTPSFLSYFtysKLCNARVKPVDTSSNNF 141
                                       555667888888888875777888999876899999***********999876655400155555555555555555 PP

                                       STTSHHHHHHHCCTTEEEEEEESS-TTTT----...HHHHHHHHHHTT-EEEEEGTTTHTTT CS
                   Cys_Met_Meta_PP 123 dtsdleelekaikentklvylEtptnpllkvvD...iekiaklakkagvlvvvDntfaspll 181
                                       +  ++e+l++ ++++t+lv+l  p np+  v+D   +++ia+++ ++g+++v D ++ s ++
  gi|488600514|ref|YP_007906985.1| 142 EL-KAEDLNETVSDKTSLVFLNYPNNPTGAVLDqkaMNAIAEVCEDKGIILVSDEVYDSIYY 202
                                       55.899***************************66667899999999*******99988754 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1     1e-09   2.3e-06       7     161 ..      48     209 ..      43     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1e-09
                                       HHHHHHHHTSS..-SSSSHHHHHHHHHHHHHHT.-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHH CS
                   DegT_DnrJ_EryC1   7 leaveevlksg..wltsgpeveeFEkafaaylg.vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanav 80 
                                       +e++ +++k g   +ts+  ++e+ + +a+  g ++  + ++ G +  +l  +   ++++ eV++p+ +F++     
  gi|488600514|ref|YP_007906985.1|  48 IERAYKAMKEGytHYTSNFGIAELREVIAERYGvSEEEVMITCGASEALLNTSLAFIEENSEVVIPTPSFLSYFTYS 124
                                       555666666664345557778888899999888645555555555555555566667888***************** PP

                                       HHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB---...HHHHHHHHHHCT-EEEEE-TT-TT- CS
                   DegT_DnrJ_EryC1  81 lelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVhlyGqvad...mdalkaiaakhglkvieDaAhAlGa 151
                                         ++a++ +vD   + + ++++++++ +  +t+ ++   p +  G+v d   m+a+ ++++++g+++++D  +   +
  gi|488600514|ref|YP_007906985.1| 125 KLCNARVKPVDTSSNNFELKAEDLNETVSDKTSLVFlnyPNNPTGAVLDqkaMNAIAEVCEDKGIILVSD--EVYDS 199
                                       *********************************9974446788999985444999999***********9..44555 PP

                                       EETTEECCCS CS
                   DegT_DnrJ_EryC1 152 tykgkkvGal 161
                                        y +kk G+l
  gi|488600514|ref|YP_007906985.1| 200 IYYDKKPGTL 209
                                       6666665555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     4e-08     9e-05      14     167 ..      47     194 ..      42     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4e-08
                                       HHHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-..-TTEEEEEETT-HHHHSST CS
                   Beta_elim_lyase  14 msdaq.aaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkill..qrgeevivtepahihfdet 87 
                                       ++++   a+  G   Y  + ++ +L + +ae +g      + +  a++++l + l+  + ++ev++  p+     + 
  gi|488600514|ref|YP_007906985.1|  47 IIERAyKAMKEGYTHYTSNFGIAELREVIAERYGVSEEEVMITCGASEALLNTSLAfiEENSEVVIPTPSFLSYFTY 123
                                       556665788889999********************99999999999*****97776558888888888888887777 PP

                                       THHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EE CS
                   Beta_elim_lyase  88 gaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygipl 164
                                         +   a vk++d  +++  ++++e+l++ + +      k++l+ l   nn   G v+  + ++++a++++++gi l
  gi|488600514|ref|YP_007906985.1| 124 SKL-CNARVKPVDTSSNN-FELKAEDLNETVSD------KTSLVFLNYPNNP-TGAVLDQKAMNAIAEVCEDKGIIL 191
                                       665.44677777777777.78888888888877......799*********5.9*********************99 PP

                                       EEE CS
                   Beta_elim_lyase 165 hlD 167
                                       + D
  gi|488600514|ref|YP_007906985.1| 192 VSD 194
                                       988 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.9e-06    0.0088      64     244 ..      82     272 ..      51     302 .. 0.69
   2 !    4.3   0.0    0.0069        15     314     362 ..     318     365 ..     297     366 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-06
                                       -TTSEEEEECHHHHHHHHHHHHHHHH..SSSSSEEEEE-SS--THHHHHTTTT-BTTEEEEEESTT-.--S..S-EE CS
                       Alliinase_C  64 tddryivvGtGstqLlqalvyalspeasseskpvkvvaavPyysvykeqtslldsklykweGdaaayvkkknpeefi 140
                                       +++  ++    s  Ll++ +  +  +++   ++ + +++  y  + + + + +d++  ++e +a++  ++ + +  +
  gi|488600514|ref|YP_007906985.1|  82 SEEEVMITCGASEALLNTSLAFIEENSEVVIPTPSFLSYFTYSKLCNARVKPVDTSSNNFELKAEDLNETVSDKTSL 158
                                       44555555555667888888888888888888889999999999999999999**************8888888999 PP

                                       EEEESS-TTT---..-----.......-TT-EEEEEE-TT....-STTTS---S-B--SE.EEEEHHHHHS-GGG-E CS
                       Alliinase_C 141 elvtsPnnPdgll..reavv.......kgseakviyDlay....YWPhytpitskadedi.mLftlskltGhaGsrl 203
                                        +   PnnP g++  ++a +       +++  +++ D +y    Y     p t +  e++ ++ ++sk    +G r+
  gi|488600514|ref|YP_007906985.1| 159 VFLNYPNNPTGAVldQKA-MnaiaevcEDKGIILVSDEVYdsiyYDK--KPGTLAGKENVvVINAFSKSLAMTGWRI 232
                                       9999******98633222.2222333244444455555552220433..35566666665156799*********** PP

                                       EEEEES-HHHHHHHHHHHHHHHSS--HHHHHHHHHHHHHHH CS
                       Alliinase_C 204 GWalvkdkevakklveyieknsiGvskesqlrvlkilkvvl 244
                                       G+ ++ +k++ + +++  + n +     +q  v  ++k  l
  gi|488600514|ref|YP_007906985.1| 233 GY-IIANKDLLDSILKVHQVNGVCAPAFAQKAVYDVIKDGL 272
                                       *9.67888899988888888888877777777777777544 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0069
                                       ..-HHHHHHTTTEEEEEGGGGTS-TTEEEEESSS-HHHHHHHHHHHHTS CS
                       Alliinase_C 314 dedcaevlrekkiltrsGevfeaesryvrlsllkrdddfdvllerlkkl 362
                                        e  +++l e+++    G+ f++e r++r+s  ++ ++ +  +e+++++
  gi|488600514|ref|YP_007906985.1| 318 MEFAEKLLAETGVAVTPGNAFGSE-RNIRISYASSMENLEKAMEKIRQF 365
                                       4556788999***********986.89*****************99875 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.6e-05      0.17      30      90 ..      71     132 ..      45     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                                       CCHHHHHTTTT-.SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC-HHHHHC-SS- CS
                           DUF1246  30 greklYekfkvi.devivldkfkdilkeevqeklreenailvPhgsfveYvgiekieelkvp 90 
                                        re + e+++v  +ev++    ++ l ++    + e+  +++P  sf +Y  ++k+ + +v+
  gi|488600514|ref|YP_007906985.1|  71 LREVIAERYGVSeEEVMITCGASEALLNTSLAFIEENSEVVIPTPSFLSYFTYSKLCNARVK 132
                                       56777788988856777777888888888899999999****************99888876 PP

>> LZ3wCH  Leucine zipper with capping helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00083       1.9       6      43 ..      48      87 ..      44      91 .. 0.90
   2 ?    0.4   0.0      0.32   7.1e+02      30      45 ..     136     151 ..     134     153 .. 0.85
   3 ?   -2.7   0.2       3.1   6.8e+03       3      19 ..     352     368 ..     351     369 .] 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00083
                            LZ3wCH  6 kkkatkkakeaanrWtd..nifdikswikekfpkskkeln 43
                                      +++a+k  ke   ++t    i ++++ i e++++s++e++
  gi|488600514|ref|YP_007906985.1| 48 IERAYKAMKEGYTHYTSnfGIAELREVIAERYGVSEEEVM 87
                                      7999*************7779****************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.32
                            LZ3wCH  30 wikekfpkskkelnee 45 
                                       + +++f+ + ++lne 
  gi|488600514|ref|YP_007906985.1| 136 TSSNNFELKAEDLNET 151
                                       5689**********96 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.1
                            LZ3wCH   3 ieekkkatkkakeaanr 19 
                                       +e ++ka +k ++ a+ 
  gi|488600514|ref|YP_007906985.1| 352 MENLEKAMEKIRQFAKA 368
                                       56777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2323.71
//
Query:       gi|488600515|ref|YP_007906986.1|  [L=72]
Description: hypothetical protein Asulf_00989 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 439.46
//
Query:       gi|488600516|ref|YP_007906987.1|  [L=55]
Description: hypothetical protein Asulf_00990 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-16   57.8  20.6    7.3e-09   35.1   6.6    2.1  2  Fer4           4Fe-4S binding domain
    4.7e-12   45.4  18.2    6.8e-06   25.9   4.5    2.1  2  Fer4_6         4Fe-4S binding domain
    5.1e-12   45.7  26.2    3.6e-08   33.4  14.4    1.8  2  Fer4_10        4Fe-4S dicluster domain
    2.6e-11   42.9  15.8    6.4e-07   29.1   4.2    2.1  2  Fer4_2         4Fe-4S binding domain
    3.2e-11   44.0   9.8    2.9e-05   24.9   1.9    2.0  2  Fer4_16        4Fe-4S double cluster binding domain
    2.4e-10   40.8  11.7    6.6e-10   39.4  11.8    1.6  1  Fer4_7         4Fe-4S dicluster domain
    5.1e-09   36.1  12.3    1.4e-08   34.8  12.3    1.6  1  Fer4_9         4Fe-4S dicluster domain
      3e-08   33.6  15.5    0.00073   19.9   3.9    2.1  2  Fer4_4         4Fe-4S binding domain
    5.7e-07   29.6  16.8    0.00084   19.4   4.3    2.0  2  Fer4_21        4Fe-4S dicluster domain
    7.9e-06   26.3  10.9     0.0029   18.1   0.9    2.0  2  Fer4_17        4Fe-4S dicluster domain
    1.8e-05   25.3  18.1     0.0074   17.1   4.0    2.2  2  Fer4_3         4Fe-4S binding domain
    0.00014   22.2  13.2      0.018   15.5   2.7    2.1  2  Fer4_8         4Fe-4S dicluster domain
      0.001   19.7  15.8      0.038   14.7   4.0    2.7  2  Fer4_15        4Fe-4S single cluster domain
     0.0042   17.6  14.9       0.16   12.5   5.2    2.2  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
     0.0044   17.8   9.4       0.16   12.8   0.5    2.0  2  Fer4_22        4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.14   12.3  14.2       0.67   10.2  14.2    1.8  1  Fer4_18        4Fe-4S dicluster domain
        1.8    9.1  10.7        4.3    7.9   2.6    2.0  2  Me-amine-dh_L  Methylamine dehydrogenase, L chain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   6.1   4.8e-10     5e-07       6      24 .]       7      25 ..       2      25 .. 0.90
   2 !   35.1   6.6   6.9e-12   7.3e-09       2      24 .]      31      53 ..      30      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.8e-10
                                      TTSSS-THHHHHSTTTEEE CS
                              Fer4  6 ekCigCGaCvevCPvgAIt 24
                                      + C gCG Cv+ CP gAI+
  gi|488600516|ref|YP_007906987.1|  7 DSCDGCGVCVDECPMGAIE 25
                                      89****************6 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 6.9e-12
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      v+d+e C+ CG C++vCP++AIt
  gi|488600516|ref|YP_007906987.1| 31 VVDPEICTECGSCIDVCPNEAIT 53
                                      8*********************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 !   25.9   4.5   6.4e-09   6.8e-06       7      24 .]       7      24 ..       1      24 [. 0.90
   2 !   25.9   5.8   6.5e-09   6.9e-06       1      24 []      29      52 ..      29      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.4e-09
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                      d+C+gCg Cv+ CP+gai
  gi|488600516|ref|YP_007906987.1|  7 DSCDGCGVCVDECPMGAI 24
                                      99***************8 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 6.5e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++++dp+ C+ Cg C++vCP  ai
  gi|488600516|ref|YP_007906987.1| 29 KAVVDPEICTECGSCIDVCPNEAI 52
                                      689*****************8887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4  14.4   3.4e-11   3.6e-08       7      56 .]       7      48 ..       2      48 .. 0.95
   2 !   23.2   3.9   5.1e-08   5.3e-05       1      21 [.      29      49 ..      29      55 .] 0.87

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.4e-11
                           Fer4_10  7 dtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      d+C +Cg Cv+ CP+        g+++ e++  +++e Ct+cg+C+++CP
  gi|488600516|ref|YP_007906987.1|  7 DSCDGCGVCVDECPM--------GAIELEDKAVVDPEICTECGSCIDVCP 48
                                      89*************........9*************************9 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 5.1e-08
                           Fer4_10  1 kvvidddtCirCgkCvkaCPa 21
                                      k+v+d++ C++Cg C ++CP 
  gi|488600516|ref|YP_007906987.1| 29 KAVVDPEICTECGSCIDVCPN 49
                                      5799****************8 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   3.8   4.4e-07   0.00047       4      21 ..       3      20 ..       1      21 [. 0.87
   2 !   29.1   4.2   6.1e-10   6.4e-07       2      22 .]      29      49 ..      28      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.4e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      +v+ d+C gCg Cv+ CP
  gi|488600516|ref|YP_007906987.1|  3 AVVGDSCDGCGVCVDECP 20
                                      667799************ PP

  == domain 2  score: 29.1 bits;  conditional E-value: 6.1e-10
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++vvd+++C++Cg+C+++CP+
  gi|488600516|ref|YP_007906987.1| 29 KAVVDPEICTECGSCIDVCPN 49
                                      579*****************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 !   24.9   1.9   2.8e-08   2.9e-05       2      29 ..       9      36 ..       8      37 .. 0.91
   2 !   23.6   2.9   6.8e-08   7.2e-05       2      20 ..      37      55 .]      36      55 .] 0.93

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.8e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeieare 29
                                      C +Cg C++ CP +ai+ + +++++++ 
  gi|488600516|ref|YP_007906987.1|  9 CDGCGVCVDECPMGAIELEDKAVVDPEI 36
                                      *******************999999865 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 6.8e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg C++vCP +ai+++
  gi|488600516|ref|YP_007906987.1| 37 CTECGSCIDVCPNEAITME 55
                                      ****************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 !   39.4  11.8   6.3e-13   6.6e-10       1      52 []       8      51 ..       8      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 6.3e-13
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C gCg Cv+ Cp++aiel+++        +++dpe C+ Cg+C++vCP +a
  gi|488600516|ref|YP_007906987.1|  8 SCDGCGVCVDECPMGAIELEDK--------AVVDPEICTECGSCIDVCPNEA 51
                                      5******************775........79*****************876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8  12.3   1.3e-11   1.4e-08       2      51 .]       9      52 ..       8      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.3e-11
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      C gCg Cv+ Cp+g+++ ++++  +         C++Cg+C+++Cp++ai
  gi|488600516|ref|YP_007906987.1|  9 CDGCGVCVDECPMGAIELEDKAVVDPE------ICTECGSCIDVCPNEAI 52
                                      ****************99999888875......4*************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 !   19.9   3.9   6.9e-07   0.00073       2      17 .]       7      22 ..       6      22 .. 0.93
   2 !   19.6   3.8   8.4e-07   0.00088       2      15 ..      35      48 ..      34      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.9e-07
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C gCg+Cv+ CP+g
  gi|488600516|ref|YP_007906987.1|  7 DSCDGCGVCVDECPMG 22
                                      79************86 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 8.4e-07
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e C++CgsC+++CP
  gi|488600516|ref|YP_007906987.1| 35 EICTECGSCIDVCP 48
                                      66************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   4.4   2.6e-06    0.0028      35      58 ..       3      25 ..       1      26 [. 0.89
   2 !   19.4   4.3     8e-07   0.00084      33      59 .]      29      54 ..      23      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                           Fer4_21 35 kvvedeCvGCnlCssvCPvedcie 58
                                      +vv d+C GC +C++ CP+ ++ie
  gi|488600516|ref|YP_007906987.1|  3 AVVGDSCDGCGVCVDECPM-GAIE 25
                                      5789**************7.9997 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 8e-07
                           Fer4_21 33 vlkvvedeCvGCnlCssvCPvedciem 59
                                      ++ v  + C+ C  C++vCP +++i+m
  gi|488600516|ref|YP_007906987.1| 29 KAVVDPEICTECGSCIDVCP-NEAITM 54
                                      44577899999999999999.699998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.9   2.7e-06    0.0029       2      21 ..       9      28 ..       8      36 .. 0.81
   2 !   14.6   2.2   3.4e-05     0.036      45      59 ..      36      50 ..      26      52 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                           Fer4_17  2 CiqCgyClpeCpsyeaydne 21
                                      C +Cg C++eCp++++  ++
  gi|488600516|ref|YP_007906987.1|  9 CDGCGVCVDECPMGAIELED 28
                                      999********998876655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.4e-05
                           Fer4_17 45 lCieCgeCerkCPqg 59
                                       C+eCg C  +CP++
  gi|488600516|ref|YP_007906987.1| 36 ICTECGSCIDVCPNE 50
                                      477777777777764 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   6.2   5.5e-05     0.058       1      15 []       9      23 ..       9      23 .. 0.98
   2 !   17.1   4.0   7.1e-06    0.0074       1      15 []      37      51 ..      37      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv+ CP gA
  gi|488600516|ref|YP_007906987.1|  9 CDGCGVCVDECPMGA 23
                                      ************998 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.1e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct Cg C +vCP+ A
  gi|488600516|ref|YP_007906987.1| 37 CTECGSCIDVCPNEA 51
                                      ************866 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.8   3.6e-05     0.038       4      18 ..       8      22 ..       5      36 .. 0.70
   2 !   15.5   2.7   1.7e-05     0.018      50      63 ..      36      49 ..      23      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                            Fer4_8  4 kCieCgaCqsaCpvl 18
                                      +C +Cg C ++Cp+ 
  gi|488600516|ref|YP_007906987.1|  8 SCDGCGVCVDECPMG 22
                                      577777777777754 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.7e-05
                            Fer4_8 50 sCttcgaCtevCpv 63
                                       Ct+cg+C +vCp+
  gi|488600516|ref|YP_007906987.1| 36 ICTECGSCIDVCPN 49
                                      59999999999997 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 !   14.7   4.0   3.6e-05     0.038       6      25 ..       7      27 ..       4      32 .. 0.73
   2 !   10.6   4.1   0.00071      0.75       2      20 ..      31      49 ..      30      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.6e-05
                           Fer4_15  6 daCigcglCvaeap.evfeld 25
                                      d C+gcg+Cv+e+p   +el+
  gi|488600516|ref|YP_007906987.1|  7 DSCDGCGVCVDECPmGAIELE 27
                                      89***********82344444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00071
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      vvD + C+ cg C++++p+
  gi|488600516|ref|YP_007906987.1| 31 VVDPEICTECGSCIDVCPN 49
                                      69***************95 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   2.1   0.00049      0.52       4      17 ..       7      20 ..       4      25 .. 0.91
   2 !   12.5   5.2   0.00016      0.16       1      18 [.      32      49 ..      32      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d+C +cg+Cv+ +P
  gi|488600516|ref|YP_007906987.1|  7 DSCDGCGVCVDECP 20
                                      89************ PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD + C++cg+C +++P+
  gi|488600516|ref|YP_007906987.1| 32 VDPEICTECGSCIDVCPN 49
                                      899**************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 !    9.6   2.8    0.0016       1.7      80      94 ..       7      21 ..       2      23 .. 0.87
   2 !   12.8   0.5   0.00015      0.16      78      94 ..      33      49 ..      25      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                           Fer4_22 80 sgCvGCgRCieacpv 94
                                       +C GCg C++ cp+
  gi|488600516|ref|YP_007906987.1|  7 DSCDGCGVCVDECPM 21
                                      57***********97 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      + + C+ Cg Ci++cp+
  gi|488600516|ref|YP_007906987.1| 33 DPEICTECGSCIDVCPN 49
                                      66789999999999986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  14.2   0.00064      0.67      60      96 ..       8      48 ..       3      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00064
                           Fer4_18 60 dcidcescvkvcPtg.idirkGlqle...ciscllcidacd 96
                                       c  c++cv+ cP+g i++ +   ++   c +c+ cid c 
  gi|488600516|ref|YP_007906987.1|  8 SCDGCGVCVDECPMGaIELEDKAVVDpeiCTECGSCIDVCP 48
                                      5999*********9768999988876667***********6 PP

>> Me-amine-dh_L  Methylamine dehydrogenase, L chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.6    0.0041       4.3      15      36 ..       3      24 ..       1      32 [. 0.86
   2 ?    7.4   0.9    0.0056       5.9      15      34 ..      31      50 ..      25      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0041
                                      T-EEEBGGGGT-BTTBB-TTSE CS
                     Me-amine-dh_L 15 aidGalcaccGGsvtscppGte 36
                                      a+ G  c+ cG +v++cp G+ 
  gi|488600516|ref|YP_007906987.1|  3 AVVGDSCDGCGVCVDECPMGAI 24
                                      67899**************985 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0056
                                      T-EEEBGGGGT-BTTBB-TT CS
                     Me-amine-dh_L 15 aidGalcaccGGsvtscppG 34
                                       +d  +c+ cG +++ cp  
  gi|488600516|ref|YP_007906987.1| 31 VVDPEICTECGSCIDVCPNE 50
                                      58999************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 374.25
//
Query:       gi|488600517|ref|YP_007906988.1|  [L=211]
Description: small GTP-binding protein domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-16   58.3   0.0    9.1e-16   58.0   0.0    1.2  1  MMR_HSR1       50S ribosome-binding GTPase
    1.5e-12   47.5   0.0    1.5e-05   24.7   0.0    3.1  2  GTP_EFTU       Elongation factor Tu GTP binding domain
      3e-06   26.8   0.0     0.0091   15.5   0.0    2.3  2  Arf            ADP-ribosylation factor family
    1.2e-05   25.3   0.0       0.11   12.4   0.0    2.1  2  RsgA_GTPase    RsgA GTPase
    0.00012   22.0   0.0    0.00019   21.4   0.0    1.3  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
    0.00047   19.7   0.1     0.0049   16.4   0.1    2.4  1  FeoB_N         Ferrous iron transport protein B
    0.00078   18.8   0.0      0.001   18.4   0.0    1.2  1  Septin         Septin
    0.00093   19.4   0.0       0.07   13.3   0.0    2.2  2  Roc            Ras of Complex, Roc, domain of DAPkinase
     0.0023   18.0   0.0       0.42   10.7   0.0    2.2  2  Dynamin_N      Dynamin family
     0.0024   17.6   0.0     0.0048   16.6   0.0    1.5  1  AAA_24         AAA domain
     0.0048   17.3   0.0     0.0082   16.6   0.0    1.5  1  AAA            ATPase family associated with various cellular
      0.008   15.6   0.0        0.2   11.1   0.0    2.3  1  SRPRB          Signal recognition particle receptor beta subu
     0.0081   16.7   0.1      0.045   14.3   0.1    2.1  1  AAA_18         AAA domain
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.022   14.7   0.0    1.5  2  ATPase_2       ATPase domain predominantly from Archaea
      0.015   14.5   0.0      0.025   13.8   0.0    1.3  1  NB-ARC         NB-ARC domain
      0.018   15.4   0.0      0.025   15.0   0.0    1.3  1  AAA_16         AAA ATPase domain
      0.026   14.9   0.0      0.044   14.2   0.0    1.4  1  RNA_helicase   RNA helicase
      0.071   13.6   0.0      0.098   13.2   0.0    1.3  1  ABC_tran       ABC transporter
      0.073   12.7   0.0        0.1   12.3   0.0    1.2  1  Guanylate_kin  Guanylate kinase
       0.11   13.1   0.0       0.22   12.1   0.0    1.5  1  MMR_HSR1_C     GTPase of unknown function C-terminal
       0.14   11.2   0.0       0.22   10.6   0.0    1.2  1  Parvo_NS1      Parvovirus non-structural protein NS1
       0.18   12.0   0.0       0.35   11.1   0.0    1.7  1  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 !   58.0   0.0   1.1e-18   9.1e-16       1     114 []      25     168 ..      25     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.1e-18
                                       EEEEEESTTSSHHHHHHHHHTS.....TEEESSSTTSSSSEEEEE...EEETT..EEEEEEECGGC........... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.....kaivsdkpgtTrdinegr...vklkg..keielvDtpGl........... 56 
                                       +++i+G pN+GK+tL n+++++        +sd p  Tr  + ++   ++++g   +i +vDtpGl           
  gi|488600517|ref|YP_007906988.1|  25 KIGIYGPPNAGKTTLANRILRDwtgdiMGSASDVPHETRRARLREgvrIEVNGksLNIDIVDTPGLatkidfheflk 101
                                       699****************9855444446899******99977753224444434789*******877777666655 PP

                                       S....S....HHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  57 i....e....gaseek.glgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       +    e    +a+e   g+ +a++ l++ d +llv+d+se+ +++++ ++   +e ++ pl++v+nk
  gi|488600517|ref|YP_007906988.1| 102 YgmdeEeakrRAKEATeGVIEAIKWLDDLDGVLLVMDSSEDPFTQVNVTIIGNIEARGLPLLIVANK 168
                                       1444312323222222577777777888*********99899**********9999*********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 !   18.6   0.0   1.3e-06    0.0011       4      80 ..      24      90 ..      21     104 .. 0.84
   2 !   24.7   0.0   1.8e-08   1.5e-05      87     190 ..     123     208 ..     117     211 .] 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                                      EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                          GTP_EFTU  4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80
                                      ++igi g  ++GKtTL  r+l +   + + +            ++E +r    +   i+++  +k+ +i ++DtPG 
  gi|488600517|ref|YP_007906988.1| 24 MKIGIYGPPNAGKTTLANRILRDWTGDIMGS--------ASDVPHETRRARLREGVRIEVN--GKSLNIDIVDTPGL 90
                                      689******************9977766622........3457899999988888899999..99999********4 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.8e-08
                                       HHHHHHT-SEEEEEEETTTBSTHHHH.HHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  87 virglrvlDgavlvvdaveGvepqte.evlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekyge 162
                                        i+ l  lDg++lv+d++e++ +q + +++  + ++g+p+ ++ NK+D ++a+  +i+++  q+             
  gi|488600517|ref|YP_007906988.1| 123 AIKWLDDLDGVLLVMDSSEDPFTQVNvTIIGNIEARGLPLLIVANKIDLPNASPARIKSAFPQHT------------ 187
                                       55668899************98887538999**********************999999888666............ PP

                                       TTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 163 kgekevpvvfgSalkgegvktllealve 190
                                              vv++Salkg ++++l +++ e
  gi|488600517|ref|YP_007906988.1| 188 -------VVPISALKGLNIDNLYKVMAE 208
                                       .......899999999999999888776 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00096      0.78       5      37 ..      15      46 ..      11      57 .. 0.79
   2 !   15.5   0.0   1.1e-05    0.0091      80     139 ..     128     182 ..     122     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00096
                                      HHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHS CS
                               Arf  5 laklklkkkelrilllGLDnaGKtTilkklkle 37
                                      l+ ++ kk +++i + G  naGKtT+ +++  +
  gi|488600517|ref|YP_007906988.1| 15 LKWFF-KKDKMKIGIYGPPNAGKTTLANRILRD 46
                                      44444.4889****************9998765 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.1e-05
                                       TTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHH CS
                               Arf  80 ektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrel 139
                                       ++ d+v+ v+Ds++   +++ +    +++ + e +  +ll++aNK+Dlp+a   + ++++
  gi|488600517|ref|YP_007906988.1| 128 DDLDGVLLVMDSSEDP-FTQVN---VTIIGNIEARGLPLLIVANKIDLPNAS-PARIKSA 182
                                       6678888888887643.33333...468889999***************985.4555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00013      0.11     104     162 ..      28      91 ..       8      96 .. 0.80
   2 !   11.0   0.0   0.00037       0.3      16     100 ..     130     209 ..     112     211 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                       EECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETT........TEEEESS-SSS CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelae........gglliDtPGfr 162
                                       + G+  +GK+tL n++l +    tg++  + +   h T++++l e  +        +  ++DtPG+ 
  gi|488600517|ref|YP_007906988.1|  28 IYGPPNAGKTTLANRILRD---WTGDIMGSASDVPHETRRARLREGVRievngkslNIDIVDTPGLA 91 
                                       789999**********999...99**************9999955333333445556679*****86 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00037
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHH CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkeglee 92 
                                       +d +l+v+  +e+ +++  ++ ++  +e++g++++iv nKiDl + +    ++k+++ +   +v+ +sa ++ ++++
  gi|488600517|ref|YP_007906988.1| 130 LDGVLLVMDSSEDPFTQVNVT-IIGNIEARGLPLLIVANKIDLPNASP--ARIKSAFPQH--TVVPISALKGLNIDN 201
                                       688889998887888777765.7899******************9999..6777777766..778888888889999 PP

                                       HHHHCTTS CS
                       RsgA_GTPase  93 lkellkdk 100
                                       l +++++k
  gi|488600517|ref|YP_007906988.1| 202 LYKVMAEK 209
                                       98888876 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 !   21.4   0.0   2.3e-07   0.00019      56     103 ..     160     209 ..     133     211 .] 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.3e-07
                      MMR_HSR1_Xtn  56 ipclyvlNKiDl..isleeldelarepnsvviSaekelnldeLkekiwee 103
                                       +p l+v NKiDl  +s + +++   ++ +v+iSa k+ln+d+L + + e+
  gi|488600517|ref|YP_007906988.1| 160 LPLLIVANKIDLpnASPARIKSAFPQHTVVPISALKGLNIDNLYKVMAEK 209
                                       699*********666677777777778999*************9988665 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 !   16.4   0.1     6e-06    0.0049       2     153 ..      25     203 ..      24     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6e-06
                                       EEEEEESTTSSHHHHHHHHHTTS..EEEEESTTSSSEEEEEEEEE........TTEEEEEEE----........... CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgak..qkvgNwpGvtvekkegklkl........kgkeveivDlPGi........... 57 
                                       ++ + G pn+Gkttl n++        +g  + v  e ++++l+         k+ +++ivD PG            
  gi|488600517|ref|YP_007906988.1|  25 KIGIYGPPNAGKTTLANRILRDWtgDIMGSASDVPHETRRARLREgvrievngKSLNIDIVDTPGLatkidfheflk 101
                                       68899************9976431145677777777776666655555555445578999*****977777644444 PP

                                       SSS.......SSSSHHHHHHHHHHHCTSSSEEEEEEEGGG...HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEE CS
                            FeoB_N  58 Ysl.......sayseeekvardflleeepdvvvnvvdatn...lernLyLtlqllelgvpvvlalnmideaekkgie 124
                                       Y +        a    e v + +   ++ d v+ v+d+++    + n++++ ++   g+p++++ n+id  +++  +
  gi|488600517|ref|YP_007906988.1| 102 YGMdeeeakrRAKEATEGVIEAIKWLDDLDGVLLVMDSSEdpfTQVNVTIIGNIEARGLPLLIVANKIDLPNASPAR 178
                                       44444433322222333344444446788888889888764445677778888888888888888999888888888 PP

                                       E-HHHHHHHHTS-EEEEBTTTTBTHHHHH CS
                            FeoB_N 125 idlkkLsekLgvpvvktsakkkegieell 153
                                       i  +      +  vv++sa k+ +i++l 
  gi|488600517|ref|YP_007906988.1| 179 IKSAFP----QHTVVPISALKGLNIDNLY 203
                                       875433....3467777887777777775 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.2e-06     0.001       6      80 ..      25      98 ..      20     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                      EEEEEEBTTSSCCCCCCTTSSSS------------------S-E.EEEEEEEETTCEEEEEEEE---BSSSSSHHC CS
                            Septin  6 tlmvvGesglGkttlintlfetdlieeekleeasekkkktveik.kkkvvieedgvklnltviDtpgfGdavdnsk 80
                                       + + G    Gkttl n ++++   +     +as+  ++t + + ++ v ie +g  ln+ ++Dtpg   ++d ++
  gi|488600517|ref|YP_007906988.1| 25 KIGIYGPPNAGKTTLANRILRDWTGDIM--GSASDVPHETRRARlREGVRIEVNGKSLNIDIVDTPGLATKIDFHE 98
                                      5667899999*********987666654..44455444444444378899******************99999765 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 !   13.3   0.0   8.6e-05      0.07       1      66 [.      25      90 ..      25     105 .. 0.86
   2 ?    4.0   0.0     0.067        54      81     120 .]     131     171 ..     123     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.6e-05
                                      EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG CS
                               Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGq 66
                                      K+ + G  ++GKt+l++r+++d   +   s   v   t+++   +gv+ + + k+++++i Dt G 
  gi|488600517|ref|YP_007906988.1| 25 KIGIYGPPNAGKTTLANRILRDWTGDIMGSASDVPHETRRARLREGVRIEVNGKSLNIDIVDTPGL 90
                                      78899****************999999999999998888887678999999999999999999885 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.067
                                       CEEEEEEEGHHHHCHHHHHHHHHHHCSS.S-EEEEEE-TTT CS
                               Roc  81 alailvydsrssenlkeWlkelkkvagk.spvilvgnkiDl 120
                                       + ++lv+ds+++   +  ++ + +   +  p+++v+nkiDl
  gi|488600517|ref|YP_007906988.1| 131 DGVLLVMDSSEDPFTQVNVTIIGNIEARgLPLLIVANKIDL 171
                                       6788899988877666667777776554169********95 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.023        19       1      20 [.      26      45 ..      26      55 .. 0.90
   2 !   10.7   0.0   0.00051      0.42     101     167 ..      80     168 ..      72     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.023
                                      EEEEEBTTTTHHHHHHHHHT CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                                      i + G  ++GK++++n +l+
  gi|488600517|ref|YP_007906988.1| 26 IGIYGPPNAGKTTLANRILR 45
                                      6788999**********996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00051
                                       -SEEEEE---B-SSSGTTS......................HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHS CS
                         Dynamin_N 101 kgltlvDlPGldsvnkrdq......................elvkeyikkadiilavtsanhdlsnsealflarevd 155
                                        ++ +vD+PGl    + ++                        + + +++ d +l+v++++ d  ++ +  +  +++
  gi|488600517|ref|YP_007906988.1|  80 LNIDIVDTPGLATKIDFHEflkygmdeeeakrrakeategvIEAIKWLDDLDGVLLVMDSSEDPFTQVNVTIIGNIE 156
                                       6899*********9999999**************9999866344455689999999999999988888888999999 PP

                                       TTBTTEEEEEE- CS
                         Dynamin_N 156 pkgkrtivvltk 167
                                        +g   ++v +k
  gi|488600517|ref|YP_007906988.1| 157 ARGLPLLIVANK 168
                                       999999988887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.9e-06    0.0048       2      22 ..      23      43 ..      22      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.9e-06
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      k+ki iyGp+ +GKTtla+++
  gi|488600517|ref|YP_007906988.1| 23 KMKIGIYGPPNAGKTTLANRI 43
                                      789***************987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     1e-05    0.0082       3      74 ..      28     137 ..      26     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
                                       EESSTTSSHHHHHHHHHHHH......THE...................................EEEEETTTCSSSS CS
                               AAA   3 lyGppGtGKTllakavakel......gve...................................fleisgsellsky 38 
                                       +yGpp  GKT+la+ + +++      +                                       +i+ +e+l   
  gi|488600517|ref|YP_007906988.1|  28 IYGPPNAGKTTLANRILRDWtgdimgS-AsdvphetrrarlregvrievngkslnidivdtpglATKIDFHEFL--K 101
                                       7******************63333330.1344455555666666644444444444444444444444444444..4 PP

                                       TTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH CS
                               AAA  39 vgesekkirelfkeakekakp.silfiDEidalaksr 74 
                                        g  e++ +   kea e      i ++D++d +    
  gi|488600517|ref|YP_007906988.1| 102 YGMDEEEAKRRAKEATEGV-IeAIKWLDDLDGVLLVM 137
                                       5666666666667776666.44777888888776666 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 !   11.1   0.0   0.00024       0.2       5      58 ..      25      89 ..      21     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                      EEEEE-STTSSHHHHHHHHHHSS---B---S..S-EEETTG............GGTT-SEEEETT CS
                             SRPRB  5 avllvGlsdsGKTslftrLttdsvkktvtSq..essaalkv.........ksekgskltliDfPG 58
                                      ++ + G+ ++GKT+l +r++ d + + + S    ++ + +           + k  +++++D PG
  gi|488600517|ref|YP_007906988.1| 25 KIGIYGPPNAGKTTLANRILRDWTGDIMGSAsdVPHETRRArlregvrieVNGKSLNIDIVDTPG 89
                                      56689*****************6655544442234444433444455544466777788888888 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   5.5e-05     0.045       1      19 [.      26      49 ..      26     155 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-05
                            AAA_18  1 IlltGtpGvGKttlakeL.....s 19
                                      I++ G+p +GKttla+++      
  gi|488600517|ref|YP_007906988.1| 26 IGIYGPPNAGKTTLANRIlrdwtG 49
                                      89*************998443330 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.6e-05     0.022      10      42 ..      13      45 ..       8      51 .. 0.87
   2 ?   -2.9   0.0       6.3   5.1e+03      71      83 ..     106     118 ..      91     148 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                          ATPase_2 10 eleeilerepneiyfiYGpegsGKtaLlkeiie 42
                                       ++++  ++ ++ + iYGp + GKt+L ++i+ 
  gi|488600517|ref|YP_007906988.1| 13 FILKWFFKKDKMKIGIYGPPNAGKTTLANRILR 45
                                      688999999999999*************99975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.3
                          ATPase_2  71 eeeekkklekalg 83 
                                       eee k+++++a+ 
  gi|488600517|ref|YP_007906988.1| 106 EEEAKRRAKEATE 118
                                       4444444444443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     3e-05     0.025       8      43 ..      14      46 ..       7      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                                      HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                      + ++ ++kd+++   ++++G +  GKttla+ il++
  gi|488600517|ref|YP_007906988.1| 14 ILKWFFKKDKMK---IGIYGPPNAGKTTLANRILRD 46
                                      778889888888...******************998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.1e-05     0.025      29      91 ..      28     109 ..      21     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
                            AAA_16  29 lsGesGvGKsslvrellralekd..................ggiflrgkcdqlesaipy......sa.laqalaree 80 
                                       ++G++  GK++l++++lr +++d                  +g+ ++ + ++      +       + la+ ++++e
  gi|488600517|ref|YP_007906988.1|  28 IYGPPNAGKTTLANRILRDWTGDimgsasdvphetrrarlrEGVRIEVNGKS------LnidivdTPgLATKIDFHE 98 
                                       89*********************44444444444443333322222222222......0222233344777777766 PP

                            AAA_16  81 llrqlldeaes 91 
                                       +l+   de+e+
  gi|488600517|ref|YP_007906988.1|  99 FLKYGMDEEEA 109
                                       66666666444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.4e-05     0.044       3      26 ..      28      51 ..      26      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                      +yGp++ GK+tla+++ +++++++
  gi|488600517|ref|YP_007906988.1| 28 IYGPPNAGKTTLANRILRDWTGDI 51
                                      8*****************999877 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.098      12      70 ..      24      80 ..      18     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                      SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepql 70
                                       k++i G+  aGK+tL++ +++  +   G+i     d+ + +++ +lr+ +++    ++l
  gi|488600517|ref|YP_007906988.1| 24 MKIGIYGPPNAGKTTLANRILRDWT---GDIMGSASDVPHeTRRARLREGVRIEVNGKSL 80
                                      589***************9999865...56644445555534555555555544444444 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013       0.1       7      76 ..      28     107 ..      23     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                       EESTTTSSHHHHHHHHHHHSTTTE.E..E--EEESS---TT.....S-TTTSEE..E--HHHHHHHHHTTTEEEEEE CS
                     Guanylate_kin   7 lvgpsgaGksslkkaLlselpekf.g..vsvshtTrdprkg.....evdGkdYy..FvskeemekdiskneflEaae 73 
                                       + gp  aGk +l + +l+       g  + v+h Tr  r       ev+Gk  +   v +  +  +i+ +efl ++ 
  gi|488600517|ref|YP_007906988.1|  28 IYGPPNAGKTTLANRILRDWTGDImGsaSDVPHETRRARLRegvriEVNGKSLNidIVDTPGLATKIDFHEFLKYGM 104
                                       78***************8865544355688*******997523333799*988733589999999999999999987 PP

                                       ETT CS
                     Guanylate_kin  74 fsg 76 
                                        ++
  gi|488600517|ref|YP_007906988.1| 105 DEE 107
                                       655 PP

>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00027      0.22       1      40 [.     165     201 ..     165     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrk 40 
                                       ++NK+Dl  ++   +++k+++p+++ vvp+sA   l + +
  gi|488600517|ref|YP_007906988.1| 165 VANKIDL--PNASPARIKSAFPQHT-VVPISALKGLNIDN 201
                                       79*****..777789*******777.******98777766 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   0.00026      0.22     104     135 ..      15      44 ..      11      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                         Parvo_NS1 104 lawlskqlgkrntvwfyGpantGktnlaeaIa 135
                                       l+w+ k+   +  +++yGp+n Gkt la+ I 
  gi|488600517|ref|YP_007906988.1|  15 LKWFFKK--DKMKIGIYGPPNAGKTTLANRIL 44 
                                       5566665..34469***************996 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   0.00043      0.35      10      28 ..      28      46 ..      20     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00043
                            AAA_22 10 vtGesGtGKTtllrrlleq 28
                                      ++G++ +GKTtl++r+l+ 
  gi|488600517|ref|YP_007906988.1| 28 IYGPPNAGKTTLANRILRD 46
                                      99*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1393.92
//
Query:       gi|488600518|ref|YP_007906989.1|  [L=116]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  140.2   1.5    2.1e-41  140.1   1.5    1.0  1  DUF2073   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
       0.15   11.4   0.0        0.4   10.1   0.0    1.6  2  DUF99     Protein of unknown function DUF99


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 !  140.1   1.5   2.3e-45   2.1e-41       1     104 [.      14     113 ..      14     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.1 bits;  conditional E-value: 2.3e-45
                           DUF2073   1 lekmtsmekirlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkekdkgllekllgkkes 77 
                                       le+m++mek+r+ild+vkegkivvlE+gL+peeeaklie tm ei++++F+Gie+e+yp+k+   ++++k++gk+  
  gi|488600518|ref|YP_007906989.1|  14 LERMSTMEKLRMILDEVKEGKIVVLESGLSPEEEAKLIELTMLEIDHENFVGIEVESYPRKTV--SFFQKIFGKS-- 86 
                                       79**********************************************************998..*********6.. PP

                           DUF2073  78 eerltvigPanqlktlkkdkdlisalv 104
                                       e rlt+igPan+lktl+k++d i alv
  gi|488600518|ref|YP_007906989.1|  87 EGRLTLIGPANRLKTLEKHEDQIKALV 113
                                       9************************98 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   4.4e-05       0.4     117     164 ..      11      56 ..       5      59 .. 0.81
   2 ?   -1.5   0.0      0.16   1.4e+03     117     134 ..      93     110 ..      72     114 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.4e-05
                                       TTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHHC-S CS
                             DUF99 117 pdeeeRlelieklgerieevektgeelyvravGieleeaaklvrkltl 164
                                       +d+ eR++++ekl +   ev+  +++++v   G+++ee akl++ ++l
  gi|488600518|ref|YP_007906989.1|  11 KDKLERMSTMEKLRMILDEVK--EGKIVVLESGLSPEEEAKLIELTML 56 
                                       566799999999954455544..599*****************99876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.16
                                       TTHHHHHHHHHHC.---E CS
                             DUF99 117 pdeeeRlelieklgerie 134
                                        ++++Rl+++ek  ++i+
  gi|488600518|ref|YP_007906989.1|  93 IGPANRLKTLEKHEDQIK 110
                                       345566666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 771.44
//
Query:       gi|488600519|ref|YP_007906990.1|  [L=105]
Description: Zn-ribbon containing protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   5.9    5.2e-16   59.1   0.2    2.0  2  DUF2072        Zn-ribbon containing protein
  ------ inclusion threshold ------
      0.013   14.9   0.2       0.12   11.7   0.1    1.9  2  AnfO_nitrog    Iron only nitrogenase protein AnfO (AnfO_nitro
      0.018   14.5   0.2      0.018   14.5   0.2    1.7  2  zf_C2H2_10     C2H2 type zinc-finger
      0.055   13.2   0.4      0.055   13.2   0.4    2.0  2  zinc_ribbon_2  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 !   45.9   2.8   1.4e-15   6.2e-12       1      45 [.       2      45 ..       2      54 .. 0.83
   2 !   59.1   0.2   1.2e-19   5.2e-16      78     133 .]      45     100 ..      37     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.4e-15
                           DUF2072  1 PHkCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvsee 45
                                      PH+CtkC++ + dg++ il+GC +CG +kFly+ + +k+++++ +
  gi|488600519|ref|YP_007906990.1|  2 PHQCTKCGEQYPDGDTRILSGC-KCGNNKFLYIPKVKKDSEEQIR 45
                                      9*********************.7*********998876655433 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 1.2e-19
                           DUF2072  78 kaekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegkYvvdlpsvlkk 133
                                       ++ +e+ ++  + sv+i+ pG+YelNle+Ll++de+v+al+e+gkYv++lps lkk
  gi|488600519|ref|YP_007906990.1|  45 REIEEQLTDIGIASVKIIAPGKYELNLERLLQSDEIVIALEEDGKYVIHLPSLLKK 100
                                       3334444555799***************************************9885 PP

>> AnfO_nitrog  Iron only nitrogenase protein AnfO (AnfO_nitrog)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.7e-05      0.12      89     141 ..      24      78 ..      18      83 .. 0.80
   2 ?    1.7   0.0     0.032   1.4e+02     123     141 ..      83     101 ..      78     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                       AnfO_nitrog  89 eiegkpeefLdevlekeeeeaeeakk..keesiplpeelkeGnYridlkeiqkkn 141
                                       ++ ++   ++ +v +++ee+ +e ++  +++ i+ ++   +G+Y ++l+++++++
  gi|488600519|ref|YP_007906990.1|  24 KCGNNKFLYIPKVKKDSEEQIREIEEqlTDIGIASVKIIAPGKYELNLERLLQSD 78 
                                       55666677788898777777666666679999*******************9987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.032
                       AnfO_nitrog 123 eelkeGnYridlkeiqkkn 141
                                         +++G+Y+i+l +++kk+
  gi|488600519|ref|YP_007906990.1|  83 ALEEDGKYVIHLPSLLKKK 101
                                       56799*******9999986 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 ?   14.5   0.2   4.1e-06     0.018       3      17 ..       3      17 ..       2      18 .. 0.94
   2 ?   -4.9   0.9         4   1.8e+04       7       9 ..      24      26 ..      23      27 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-06
                        zf_C2H2_10  3 fsCPKCqeklPDiDt 17
                                      + C KC+e+ PD Dt
  gi|488600519|ref|YP_007906990.1|  3 HQCTKCGEQYPDGDT 17
                                      89**********998 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 4
                        zf_C2H2_10  7 KCq 9 
                                      KC+
  gi|488600519|ref|YP_007906990.1| 24 KCG 26
                                      886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   1.2e-05     0.055       2      14 ..       5      17 ..       4      18 .. 0.93
   2 ?   -1.2   0.5      0.41   1.8e+03       4       7 ..      24      27 ..      24      28 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                     zinc_ribbon_2  2 CpnCGaelqdnak 14
                                      C++CG++ +d+++
  gi|488600519|ref|YP_007906990.1|  5 CTKCGEQYPDGDT 17
                                      **********986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.41
                     zinc_ribbon_2  4 nCGa 7 
                                      +CG+
  gi|488600519|ref|YP_007906990.1| 24 KCGN 27
                                      5776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 771.76
//
Query:       gi|488600520|ref|YP_007906991.1|  [L=383]
Description: putative aconitase subunit 1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-139  464.4   0.0     3e-139  464.2   0.0    1.0  1  DUF521         Protein of unknown function (DUF521)
  ------ inclusion threshold ------
      0.049   13.9   0.0       0.16   12.3   0.0    1.8  1  GCR1_C         Transcriptional activator of glycolytic enzyme
      0.051   14.1   0.0       0.11   13.0   0.0    1.5  1  CoA_binding_2  CoA binding domain
      0.064   13.5   0.0       0.16   12.3   0.0    1.6  1  DUF2958        Protein of unknown function (DUF2958)


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 !  464.2   0.0  6.8e-143    3e-139       1     401 []       1     379 [.       1     379 [. 0.95

  Alignments for each domain:
  == domain 1  score: 464.2 bits;  conditional E-value: 6.8e-143
                            DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvptt 77 
                                       m+L+keee++l+ +  e+ +kameilva+G+i++A+rL+pv+s+++sg+syk+igdagle++e+l+   ak+ ++++
  gi|488600520|ref|YP_007906991.1|   1 MYLSKEEEKLLESD-NETIRKAMEILVAIGKIFDADRLIPVKSVQISGISYKNIGDAGLEWFESLN---AKFVIKAM 73 
                                       9**********976.9**************************************************...******** PP

                            DUF521  78 lnpigvdlerweelgvdeefaekqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTn 154
                                       +np+g+d  rw+e+g+de f++kq+rii+a+ +lG++ t+tCtpy+  +  kkG+h+aw+ES+a+vyaNS+lG+rTn
  gi|488600520|ref|YP_007906991.1|  74 INPAGMDVIRWKEMGIDEGFYRKQMRIINALIRLGADKTLTCTPYYF-DSLKKGDHVAWAESNAIVYANSILGVRTN 149
                                       **********************************************8.899************************** PP

                            DUF521 155 reggpsalaaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKal 231
                                       re+g+sala++i+G+tp+yGlh+++nR ptv+v+v+ae +++ad+++lGy vG+k+ ++iP++   ++ +++ lK+l
  gi|488600520|ref|YP_007906991.1| 150 RESGISALASGIIGKTPNYGLHVKKNRSPTVIVDVKAEINSSADLAMLGYSVGEKLSNSIPYFIFRNSIEREWLKDL 226
                                       ****************************************************************99999******** PP

                            DUF521 232 gAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElre 308
                                       gA laa+g++alfh eg+TPe  ++e         e+  i+       lee+  + + ++dl+a+GcPhls +Elr+
  gi|488600520|ref|YP_007906991.1| 227 GAVLAAKGNTALFHAEGLTPEYGDFEIDS-----LEREVID------ELEEI--EFDCEPDLIAIGCPHLSSSELRQ 290
                                       *********************44444332.....4444444......34444..56889****************** PP

                            DUF521 309 laellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpg 385
                                       +a+ll  ++kkv++++w++tsr v ee+e++  ++k+e+ Gvkv++dtCmvvsp+++  ++++v++nSgKa++Ylp+
  gi|488600520|ref|YP_007906991.1| 291 IADLLFRNDKKVRKDVWLFTSRRVLEENEDV--ARKIESYGVKVFADTCMVVSPATE--NYECVMVNSGKALTYLPK 363
                                       *****************************99..**********************99..4***************** PP

                            DUF521 386 ltgvkvalgsleecve 401
                                       + gv v++g+++ec++
  gi|488600520|ref|YP_007906991.1| 364 HAGVMVKFGDIKECIK 379
                                       **************96 PP

>> GCR1_C  Transcriptional activator of glycolytic enzymes
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05      0.16       7      66 ..      50     112 ..      48     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                            GCR1_C   7 iktVedlwnEykeglngkpsikslekkygk...rWrkdskesklfsrRkkiidfierlieeeg 66 
                                        k++ d   E++e+ln k  ik +++  g    rW++   ++ ++++ ++ii++ +rl  +++
  gi|488600520|ref|YP_007906991.1|  50 YKNIGDAGLEWFESLNAKFVIKAMINPAGMdviRWKEMGIDEGFYRKQMRIINALIRLGADKT 112
                                       578889999***************99987633478877779*************999877755 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05      0.11      46     113 ..     261     340 ..     252     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                       ----T......T--EEEE-S-HHHHGGGHHHHHHH....-...-SEEEE-TT....---HHHHHHHHHTT-EEE.ES CS
                     CoA_binding_2  46 yaslae.d.pepvdlvdvftppeatpeivkealal....g...akavwlqpg....sedeeaaelaeeagirvvgdr 109
                                       + +l+e + + ++dl+ +  p +   + ++++++l    +    k vwl+ +    +e+e++a++ e++g++v  d 
  gi|488600520|ref|YP_007906991.1| 261 IDELEEiEfDCEPDLIAIGCP-HLSSSELRQIADLlfrnDkkvRKDVWLFTSrrvlEENEDVARKIESYGVKVFADT 336
                                       555555445677788888774.344444555555544441456899******************************* PP

                                       -HHH CS
                     CoA_binding_2 110 Cilv 113
                                       C+ v
  gi|488600520|ref|YP_007906991.1| 337 CMVV 340
                                       **98 PP

>> DUF2958  Protein of unknown function (DUF2958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.5e-05      0.16      60     107 ..     277     325 ..     271     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                           DUF2958  60 glglpelgsvsLselesirgplglpverDll.FeakrplsvyaeaAraa 107
                                        +g+p l+s +L++++++  +   +v++D++ F+++r l +  + Ar+ 
  gi|488600520|ref|YP_007906991.1| 277 AIGCPHLSSSELRQIADLLFRNDKKVRKDVWlFTSRRVLEENEDVARKI 325
                                       58***************************85489999998888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2392.94
//
Query:       gi|488600521|ref|YP_007906992.1|  [L=203]
Description: uracil-DNA glycosylase, family 4 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-41  139.4   0.0    1.2e-40  139.0   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 !  139.0   0.0   6.9e-45   1.2e-40       1     147 [.      30     177 ..      30     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 6.9e-45
                                       HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHH.CCCCCCCHHGCTEEEEESSS....SECGCTTCCC CS
                               UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllne.aglkrdleseqgvyitnvvkcrppgnrdtptsae 76 
                                       pgeg+ +a +v+vGeaPg+eed +g+pF+g+ag+ll +++++ ++l+r     ++v+itn++kcrpp nr +p ++e
  gi|488600521|ref|YP_007906992.1|  30 PGEGNCKALIVFVGEAPGREEDIHGRPFVGNAGKLLTEMISRkLNLSR-----KDVFITNILKCRPPNNR-DPLEEE 100
                                       7999********************************************.....*****************.****** PP

                                       CTCCHHHHHHHHHHHHSSEEEEESHHHHHH.......HH.HHSCESCCCSCT......SEEEEES-SSTTTTTTTTS CS
                               UDG  77 ikacaplleeeiellkprlivllGktaakall.....ge.klgklrgklleak.....irvlplphPsplnrnffks 142
                                       ikac+p+l ++++ ++p+++v+lG++ a+ ++     ++  ++k rgk++e +     ++v++++hP++++++    
  gi|488600521|ref|YP_007906992.1| 101 IKACKPYLIRQLKSIRPKAVVCLGRHSASLIFsffglEFnGISKERGKIYEVEvewgkMKVIAVYHPAAALYK---- 173
                                       ******************************8667887666888*********778899**************9.... PP

                                       HHHHH CS
                               UDG 143 npelk 147
                                        p+l+
  gi|488600521|ref|YP_007906992.1| 174 -PPLR 177
                                       .4443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1331.16
//
Query:       gi|488600522|ref|YP_007906993.1|  [L=171]
Description: transcriptional regulator, ArsR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-64  215.4   0.3    3.4e-64  215.2   0.3    1.0  1  ArsR      ArsR transcriptional regulator


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 !  215.2   0.3   1.9e-68   3.4e-64       1     158 [.       8     166 ..       8     167 .. 0.99

  Alignments for each domain:
  == domain 1  score: 215.2 bits;  conditional E-value: 1.9e-68
                              ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgeeveealklLkkikliEsqWrmpe.pgekpekeYht 76 
                                       +nd+veLvp+lq+f+++t+++vye+l+++W+t +el++++g++v+ealk+Lk+++++E +Wrmp+ pg++p+keYh+
  gi|488600522|ref|YP_007906993.1|   8 VNDIVELVPILQIFSTKTYREVYESLLEGWMTYNELRDRFGDSVDEALKILKHAGMLEVKWRMPKdPGDTPQKEYHV 84 
                                       8**************************************************************************** PP

                              ArsR  77 sYskvqanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrklglsplfiralakrsekldvkGq 153
                                       sY++++anf++sl+dl++i+ev+f+sd+ele++v++i++e++ g++s+ ++sr+l+l+plfira ak+s kl++kGq
  gi|488600522|ref|YP_007906993.1|  85 SYTHLSANFYTSLKDLNKILEVIFLSDDELEKIVSRIIEEINMGRMSVPHISRSLQLDPLFIRATAKKSLKLNIKGQ 161
                                       ***************************************************************************** PP

                              ArsR 154 rlelv 158
                                        +el+
  gi|488600522|ref|YP_007906993.1| 162 LVELS 166
                                       **986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1051.00
//
Query:       gi|488600523|ref|YP_007906994.1|  [L=79]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-16   59.6   0.3    4.3e-16   59.4   0.3    1.0  1  MJ1316    MJ1316 RNA cyclic group end recognition domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.3   2.4e-20   4.3e-16       2      76 .]       5      78 ..       4      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2.4e-20
                            MJ1316  2 rtaqdvlnRirWdkeldkskfvvgyldRfkgikevpleeiswied.flleeeegelaIPlHRiryikrkgevvWdR 76
                                      +t +d+ln  rW +++d +++vv y+dR+kg++e  + +i +i++ f++ +++  ++IP+HRi +++++gev W++
  gi|488600523|ref|YP_007906994.1|  5 KTLRDLLNFFRWNPDFDFDRVVVEYIDRPKGTSEFYGMDIEDIGHkFIYLKDS--TTIPMHRIVRVTYDGEVWWEK 78
                                      6899*****************************************87777766..79*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 497.39
//
Query:       gi|488600524|ref|YP_007906995.1|  [L=487]
Description: argininosuccinate lyase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  192.2   0.0    4.7e-56  190.5   0.0    1.8  2  Lyase_1          Lyase
    1.5e-11   44.8   0.1    7.7e-11   42.6   0.0    2.3  1  ASL_C2           Argininosuccinate lyase C-terminal
     0.0013   18.7   5.3      0.013   15.4   1.7    2.7  2  Apolipoprotein   Apolipoprotein A1/A4/E domain
     0.0043   16.4   0.3      0.051   12.9   0.1    2.2  2  EAP30            EAP30/Vps36 family
  ------ inclusion threshold ------
      0.014   15.2   2.9      0.014   15.2   2.9    1.6  2  DUF1351          Protein of unknown function (DUF1351)
       0.12   12.6   2.6        3.6    7.8   0.3    2.6  2  DUF5388          Family of unknown function (DUF5388)
       0.14   12.6   0.1       0.48   10.9   0.0    1.9  2  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_
       0.14   12.6   1.5       0.52   10.8   0.6    2.3  2  Spectrin         Spectrin repeat
       0.17   12.7   0.7       0.33   11.7   0.7    1.5  1  FIVAR            FIVAR domain
        0.9    9.6   3.4         24    5.1   0.0    3.3  3  TraY             TraY domain


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 !  190.5   0.0   2.6e-59   4.7e-56       2     312 .]       8     296 ..       7     296 .. 0.97
   2 ?   -1.3   0.0      0.62   1.1e+03     125     151 ..     387     413 ..     371     434 .. 0.65

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 2.6e-59
                                       EEEEETCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSS CS
                           Lyase_1   2 rftvkadklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqeg 78 
                                       rf+++ d+l  +f+ ++  +  +  +di +  a   ++   +v++ e a++i+++l  +++eg ++    l ++ e+
  gi|488600524|ref|YP_007906995.1|   8 RFEKSMDELALKFSSSMDDDRNIFYYDILVDLAHVLGLYHTGVLYREDASEIVEGLLRIRDEGFEN----LSKDYED 80 
                                       7899999999999999999999999999999999999************************99999....******* PP

                                       HHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEE CS
                           Lyase_1  79 sgtavnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvki 155
                                        + a++++l e+             k htg+S+nD v+T lrl++++++   +l  l +L++++ + a+++ d + +
  gi|488600524|ref|YP_007906995.1|  81 VHEAIEARLIELTE--------KGAKMHTGRSRNDEVATCLRLFARDRMLS-ILFRLIELRSVVLDLAVKHLDSLIP 148
                                       *******9999876........899************************55.************************* PP

                                       EEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEES CS
                           Lyase_1 156 GrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvka 232
                                       G+Th q A+P +l++ l ay++al+rd  r+ ++  r+++++lgg + + t ++ d+    + a+ l+ ++g   + 
  gi|488600524|ref|YP_007906995.1| 149 GFTHMQYAQPNRLAHHLLAYHDALKRDFDRILDSFWRVNLSPLGGSAFASTSFKLDRD---FTANLLG-FDG---IV 218
                                       **********************************************************...9999999.***...** PP

                                       SSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHH CS
                           Lyase_1 233 pnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagr 309
                                       +ns++av++rD+++e+++ ++ l+++Ls+++e+l+l ss e+++vels+  s+  SSiMP+K+NP+ +El++  a+r
  gi|488600524|ref|YP_007906995.1| 219 ENSMDAVASRDFLIEAVFDCSSLMLNLSRICEELILWSS-EFNFVELSDELSS-TSSIMPQKKNPDIAELIRARAAR 293
                                       **********************************99988.*********9999.9********************** PP

                                       HHH CS
                           Lyase_1 310 vvG 312
                                       v G
  gi|488600524|ref|YP_007906995.1| 294 VCG 296
                                       *98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.62
                                       HHHHHTHHHHHHHHHHHHHHHHHHTTT CS
                           Lyase_1 125 kalsekLlpaleqLidalkekakefkd 151
                                        a++ +  p+l++L++a+ke a+e+ d
  gi|488600524|ref|YP_007906995.1| 387 LAMNGRTDPTLNDLVEAVKEVAEEYLD 413
                                       444444556677777777777777655 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   4.3e-14   7.7e-11       1      50 [.     359     403 ..     359     433 .. 0.68

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 4.3e-14
                                       STTHHHHHHHHHHC.TS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH CS
                            ASL_C2   1 FstATdlADyLvrk.GlpFReAHeivgravrlaeekgkeleeltleelkei 50 
                                       F+tAT++AD+Lv+k ++pFR AH+ivg ++ +  +      + tl++l e+
  gi|488600524|ref|YP_007906995.1| 359 FLTATEIADMLVQKaNIPFRVAHRIVGWLAMNG-R-----TDPTLNDLVEA 403
                                       99***************************9982.3.....34444444422 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.027        49     112     150 ..      56      94 ..       3     101 .. 0.77
   2 !   15.4   1.7   7.3e-06     0.013      14      93 ..     398     478 ..     389     486 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.027
                                       HHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..---- CS
                    Apolipoprotein 112 vealkarlapyveelrqklaerleelkeslaphaeevee 150
                                       ++++ + l  +++e++++l +  e+++e +++++ e+ e
  gi|488600524|ref|YP_007906995.1|  56 ASEIVEGLLRIRDEGFENLSKDYEDVHEAIEARLIELTE 94 
                                       566667777777777788888888888888777777665 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.3e-06
                                       CCHHHCHHCHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHH CS
                    Apolipoprotein  14 eeleeqlaplaqelrdrl...skeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerla 87 
                                        +l e ++++a+e  d+l   +++l+++++++   le  ++r +p r+ev++++++++e+l+++    ++e+++r++
  gi|488600524|ref|YP_007906995.1| 398 NDLVEAVKEVAEEYLDNLdisEEDLNQAKNAV-NALERRKNRGSPSREEVEKMINSRIEALNKDY-RKVDEIADRIS 472
                                       45555555555544444422255566666666.56777777777777777777777777777663.34556666666 PP

                                       HCHHCC CS
                    Apolipoprotein  88 adaeel 93 
                                       a +e+l
  gi|488600524|ref|YP_007906995.1| 473 ASLEKL 478
                                       655555 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.1   1.8e+02      57     107 ..       3      44 ..       1     110 [. 0.70
   2 !   12.9   0.1   2.8e-05     0.051      97     193 ..     378     477 ..     337     485 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.1
                             EAP30  57 pafraqftkmcaslGvdplssk.kseslgflellglgdfyyeLavqivevcl 107
                                       +++r++f+k++++l +   ss+ ++ +           fyy + v ++ v+ 
  gi|488600524|ref|YP_007906995.1|   3 KGVRSRFEKSMDELALKFSSSMdDDRNI----------FYYDILVDLAHVLG 44 
                                       5789999999999999876555333333..........88888888887764 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.8e-05
                             EAP30  97 eLavqivevclatraengglisleelyalvnrarggvalvspdDllraiekllvlg........sglsvlqvggkkv 165
                                        +a++iv ++  + +  + l +l e ++ v  ++     +s++Dl +a ++   l         s  +v +     +
  gi|488600524|ref|YP_007906995.1| 378 RVAHRIVGWLAMNGRTDPTLNDLVEAVKEVAEEYLDNLDISEEDLNQAKNAVNALErrknrgspSREEVEK-----M 449
                                       67999999998776666699999999999999997768********9999985555556666657777766.....* PP

                             EAP30 166 vrSvptelntdqvevlevakrlvsllae 193
                                       + S  ++ln+d  +v e+a r+ + l++
  gi|488600524|ref|YP_007906995.1| 450 INSRIEALNKDYRKVDEIADRISASLEK 477
                                       ********************99776665 PP

>> DUF1351  Protein of unknown function (DUF1351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.2   7.5e+03     137     177 ..      73      87 ..      55     104 .. 0.56
   2 ?   15.2   2.9   7.9e-06     0.014      17      93 ..     399     476 ..     396     484 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.2
                           DUF1351 137 nktvslkkieeeieaakaekikkdreelekakaeieekaka 177
                                       n ++  + + e i                          +a
  gi|488600524|ref|YP_007906995.1|  73 NLSKDYEDVHEAI--------------------------EA 87 
                                       3333333333333..........................22 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.9e-06
                           DUF1351  17 eleaaveeivkkY.eglvvtedsvkdaKkeraeLnklkkaLddkRkevkkeysePideFeakikelekkikeaidki 92 
                                       +l +av+e++++Y ++l ++e+++++aK+    L + k++ +  R ev+k ++  i++ ++ + +++++ + +++++
  gi|488600524|ref|YP_007906995.1| 399 DLVEAVKEVAEEYlDNLDISEEDLNQAKNAVNALERRKNRGSPSREEVEKMINSRIEALNKDYRKVDEIADRISASL 475
                                       68899********9********************************************9998888777766666655 PP

                           DUF1351  93 d 93 
                                       +
  gi|488600524|ref|YP_007906995.1| 476 E 476
                                       4 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.9     0.003       5.4      36      68 ..     402     436 ..     398     438 .. 0.83
   2 ?    7.8   0.3     0.002       3.6      16      55 ..     423     463 ..     422     469 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.003
                           DUF5388  36 eavkklveslidsL..sesdkkrfkkqleiLEekD 68 
                                       eavk++ e+++d+L  se+d ++ k+ ++ LE++ 
  gi|488600524|ref|YP_007906995.1| 402 EAVKEVAEEYLDNLdiSEEDLNQAKNAVNALERRK 436
                                       79***********93346678899999999*9986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                           DUF5388  16 NHirNklqALa.aiGlaksqkeavkklveslidsLsesdkk 55 
                                       N  +N+++AL      ++  +e v+k+++s i+ L+++ +k
  gi|488600524|ref|YP_007906995.1| 423 NQAKNAVNALErRKNRGSPSREEVEKMINSRIEALNKDYRK 463
                                       7789******9777888889***************998776 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.3   5.9e+03      28      47 ..     350     373 ..     332     374 .. 0.67
   2 ?   10.9   0.0   0.00027      0.48      21     101 .]     380     459 ..     376     459 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.3
                   Phage_holin_6_1  28 l...klkkqgekakkiaei.akna 47 
                                           k+ k++ +a +ia++ +++a
  gi|488600524|ref|YP_007906995.1| 350 VmkeKISKGFLTATEIADMlVQKA 373
                                       145578888999999998888776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00027
                   Phage_holin_6_1  21 vkkikkllklkkqgekakkiaeiaknaVkaveqvakedakgeeKkeeAleklkellkekgi.sitddeleglIEaaV 96 
                                       +++i+ +l  + +g +  ++ ++++++ +++e+  ++   +ee +++A++++++l   k+  s++ +e+e++I + +
  gi|488600524|ref|YP_007906995.1| 380 AHRIVGWL--AMNGRTDPTLNDLVEAVKEVAEEYLDNLDISEEDLNQAKNAVNALERRKNRgSPSREEVEKMINSRI 454
                                       56666677..6777788889999999999999999995567888*******************************99 PP

                   Phage_holin_6_1  97 kelkk 101
                                       ++l+k
  gi|488600524|ref|YP_007906995.1| 455 EALNK 459
                                       99985 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1     2e+03      83     103 ..      72      92 ..      68     106 .. 0.63
   2 ?   10.8   0.6   0.00029      0.52      38     104 ..     410     476 ..     393     477 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  83 eelnerWeeLkelaaerkqkL 103
                                       e+l + +e+++e++++r  +L
  gi|488600524|ref|YP_007906995.1|  72 ENLSKDYEDVHEAIEARLIEL 92 
                                       445555555555555554444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  38 allkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLe 104
                                       + l+ ++  e++l+++++ v+al+  +++   + ++ ++ i++r+e+ln+ ++++ e a++  ++Le
  gi|488600524|ref|YP_007906995.1| 410 EYLDNLDISEEDLNQAKNAVNALERRKNRGSPSREEVEKMINSRIEALNKDYRKVDEIADRISASLE 476
                                       5566777789***********************************************9999888887 PP

>> FIVAR  FIVAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00019      0.33       5      61 ..     397     451 ..     394     459 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                       HHHHHCCHHHHHCSCCCCCC-CCHHHHHHHHHHHHHHHC...TSTTTTCCCHHHHHH CS
                             FIVAR   5 LkdsinqatntktssnysnydqdkkdaynnalsaAnailnktnnpnatveqVnqala 61 
                                       L+d+++  +++   ++y +  + + + +n+a++a+na+  + n  +++ e+V++ ++
  gi|488600524|ref|YP_007906995.1| 397 LNDLVEAVKEVA--EEYLDNLDISEEDLNQAKNAVNALERRKNRGSPSREEVEKMIN 451
                                       666666666655..8899999999999999999999997777888899999998776 PP

>> TraY  TraY domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.013        24      16      30 ..      97     111 ..      85     114 .. 0.88
   2 ?    3.5   0.2     0.042        76      31      42 ..     160     171 ..     154     175 .. 0.90
   3 ?   -2.8   0.0       3.7   6.6e+03      24      37 ..     463     476 ..     463     477 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                              TraY  16 saersgRSKrkEAql 30 
                                       +++++gRS+  E++ 
  gi|488600524|ref|YP_007906995.1|  97 AKMHTGRSRNDEVAT 111
                                       899*********985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.042
                              TraY  31 RLkdHLkrFpdi 42 
                                       RL++HL  ++d 
  gi|488600524|ref|YP_007906995.1| 160 RLAHHLLAYHDA 171
                                       9********996 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.7
                              TraY  24 KrkEAqlRLkdHLk 37 
                                       K  E++ R+++ L+
  gi|488600524|ref|YP_007906995.1| 463 KVDEIADRISASLE 476
                                       6689*****99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      812  (0.0452898); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3054.94
//
Query:       gi|488600525|ref|YP_007906996.1|  [L=408]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-59  198.7   0.1    1.1e-58  197.9   0.1    1.4  1  Asparaginase    Asparaginase, N-terminal
    1.2e-25   90.0   0.0    4.2e-25   88.2   0.0    1.9  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    5.5e-13   48.0   1.1    1.2e-12   46.9   1.1    1.5  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 !  197.9   0.1   1.9e-62   1.1e-58       1     182 [.      71     257 ..      71     266 .. 0.95

  Alignments for each domain:
  == domain 1  score: 197.9 bits;  conditional E-value: 1.9e-62
                                       EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.- CS
                      Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.y 76 
                                       +v +++tGGTias++d+++ga++ ++s+ee+++++pe+e+i++++s  l ni S+nm+p +w +l ++i++++++ y
  gi|488600525|ref|YP_007906996.1|  71 NVKIISTGGTIASKVDYRTGAVTSQFSSEEIVAEVPEIENICNIDSMLLYNILSENMKPVNWIELSKEIYSSIKDgY 147
                                       599**********************************************************************555* PP

                                       SEEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.... CS
                      Asparaginase  77 dgfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.... 149
                                       d+++v+hGTDTlaytA+a+s+ml + ++pv ++G+qr++++++sD+++Nl+ ++ va s+    +v++v++ +    
  gi|488600525|ref|YP_007906996.1| 148 DAVIVTHGTDTLAYTATAVSFMLST-PVPVLFVGAQRSSDRPSSDATMNLICSAHVARSE--LGEVAIVMHAStsdd 221
                                       ***********************99.********************************98..9************** PP

                                       ...EEETTTEEE-BSSSSS-EEETTT--SEEEETTE CS
                      Asparaginase 150 ...llranrvtKvhtssldaFespnlgplaevegsk 182
                                          ++ra +++K hts++daF+s+n +pl++v+  +
  gi|488600525|ref|YP_007906996.1| 222 ycyIHRAVKARKNHTSRRDAFQSVNQKPLGRVSYPD 257
                                       *******************************95443 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.63   3.8e+03      17      30 ..     140     153 ..     132     164 .. 0.78
   2 !   88.2   0.0   6.9e-29   4.2e-25       3     110 ..     285     390 ..     283     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.63
                                       HHHHHTT--EEEEE CS
                    Asparaginase_C  17 kallkkgakGvvle 30 
                                        + +k g+++v++ 
  gi|488600525|ref|YP_007906996.1| 140 YSSIKDGYDAVIVT 153
                                       4567999***9986 PP

  == domain 2  score: 88.2 bits;  conditional E-value: 6.9e-29
                                       EEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHH CS
                    Asparaginase_C   3 vvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkeler 79 
                                       v++k++pg++++vl+++ +kg++G vlegtG G+++s+++++++ + + + ++v+tsqc+ g+v + +y++g++l +
  gi|488600525|ref|YP_007906996.1| 285 VLVKFFPGLKPDVLEYYYSKGYRGFVLEGTGLGHVSSDWIDTIRGI-SDDSLIVMTSQCLWGRVCDRVYDTGRDLLN 360
                                       799*****************************************99.9999************************** PP

                                       HTEEE-TT--HHHHHHHHHHHCTT---HHHH CS
                    Asparaginase_C  80 lgvisaddmtpeaarikLmlllgkgldpaev 110
                                       +gvi+++dm pe a ik m+llg+  d +e 
  gi|488600525|ref|YP_007906996.1| 361 AGVIEGEDMLPEVALIKIMWLLGNY-DLEEA 390
                                       ***********************86.44444 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   1.1     2e-16   1.2e-12       4      49 ..       6      47 ..       4      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2e-16
                                      T-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT- CS
                            GatD_N  4 GDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieei 49
                                      G +++++ kg+++eGi+mP      +  ++lKLdnGYN+G++  ei
  gi|488600525|ref|YP_007906996.1|  6 GKKVRIKAKGKVFEGIVMPTR----SGNLILKLDNGYNVGFSEYEI 47
                                      889******************....***************987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 2285.67
//
Query:       gi|488600526|ref|YP_007906997.1|  [L=159]
Description: hypothetical protein Asulf_01000 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.4   0.3      0.071   12.9   0.3    1.2  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 ?   12.9   0.3     4e-06     0.071      72     147 ..       5      81 ..       1      84 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-06
                                       TTTS-HHHHHHHHHHHHHH.HHHHTCEECCECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHH CS
                         RNase_HII  72 eneinlneikaaltlavik.lleklgvkvdeilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkv 147
                                       +  i++nei++ +++ +i   + k+ ++ d+i +d  t    +   +e   ki +  e  ad++ +   +A iiAk 
  gi|488600526|ref|YP_007906997.1|   5 VPYIDRNEIREGVVEFLIAkGYSKSEIQDDYIEIDSQTIWIDIVVRVEGKNKIVILCESSADNLTISSRIAEIIAKL 81 
                                       56799********999998799999**********999988888888888888899*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 955.01
//
Query:       gi|488600527|ref|YP_007906998.1|  [L=280]
Description: methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  222.9   6.1    5.2e-66  222.2   4.9    1.7  2  Met_10           Met-10+ like-protein
    6.5e-08   32.3   0.0    1.1e-07   31.6   0.0    1.3  1  MTS              Methyltransferase small domain
    6.1e-07   30.1   0.0    1.4e-06   28.9   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    9.7e-07   28.3   0.0    1.2e-06   27.9   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    7.4e-06   25.8   0.0    1.3e-05   25.1   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
      1e-05   25.1   0.0    1.7e-05   24.4   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    3.3e-05   23.6   0.0    5.4e-05   22.9   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0011   19.5   0.0     0.0029   18.2   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
     0.0023   17.8   0.0     0.0035   17.2   0.0    1.2  1  PRMT5            PRMT5 arginine-N-methyltransferase
     0.0068   16.3   0.0      0.015   15.1   0.0    1.5  2  Methyltransf_23  Methyltransferase domain
     0.0076   15.8   0.0      0.022   14.4   0.0    1.7  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.036   13.7   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
      0.029   15.4   0.0      0.076   14.0   0.0    1.7  1  Methyltransf_24  Methyltransferase domain
      0.059   12.8   0.0       0.22   11.0   0.0    1.9  1  Methyltransf_4   Putative methyltransferase
      0.088   12.1   0.0       0.14   11.5   0.0    1.3  1  DNA_methylase    C-5 cytosine-specific DNA methylase
      0.091   12.4   0.0       0.14   11.8   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.19   10.7   0.0       0.28   10.1   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   4.9   4.9e-69   5.2e-66       2     199 .]      24     223 ..      23     223 .. 0.99
   2 ?   -0.7   0.0      0.98     1e+03      92     107 ..     238     253 ..     226     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 4.9e-69
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +feiiGdvvi+++++++ eyk +i + il+k+ +v+t+lrkv+ev+g++R++++e + G+  teti+kE+gcrf++D
  gi|488600527|ref|YP_007906998.1|  24 SFEIIGDVVIVDIPDDVVEYKDLIIRGILEKHkHVRTILRKVGEVDGVYRVARYEKIFGDS-TETIVKEHGCRFHVD 99 
                                       8*******************************9**************************99.*************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                        +kvy+s kl+ Erer+ klv+e e+V+ +fAG+Gpfai+iak +k+k+v+++++nP +v+y+++n+  Nkve++vk
  gi|488600527|ref|YP_007906998.1| 100 PTKVYYSVKLSGERERISKLVDERERVLVMFAGVGPFAIVIAKKAKPKEVVGVEINPVAVEYFRKNVVANKVEDIVK 176
                                       ***************************************************************************** PP

                                       EEES-GGG---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 155 pileDgrevir..eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       ++++D+rev++  +  +dr++m+ p+ a++F+d v +++k+gg ihy
  gi|488600527|ref|YP_007906998.1| 177 VFEGDVREVMPklDGRFDRILMPSPYIAENFVDVVGSKVKEGGYIHY 223
                                       **********988999******************************9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.98
                                       HHHHTT--TT-EEEET CS
                            Met_10  92 erlaklveegevVvdv 107
                                       er+++l+ ++ v+vdv
  gi|488600527|ref|YP_007906998.1| 238 ERVMRLFADNGVIVDV 253
                                       7999*********998 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0     1e-10   1.1e-07      31     108 ..     122     203 ..     113     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1e-10
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST..TS-EEEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve..ekkfdlivs 103
                                       ++++vl + +G+G+ ++++ak+ +  ev+ v+++  A+e  ++n+ ank+e  v+v++ dv e ++  +++fd i++
  gi|488600527|ref|YP_007906998.1| 122 ERERVLVMFAGVGPFAIVIAKKAKPKEVVGVEINPVAVEYFRKNVVANKVEdiVKVFEGDVREVMPklDGRFDRILM 198
                                       456799999****************************************************999886789*****99 PP

                                       ---ST CS
                               MTS 104 NPPfh 108
                                         P+ 
  gi|488600527|ref|YP_007906998.1| 199 PSPYI 203
                                       87765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.3e-09   1.4e-06       1      70 [.     126     198 ..     126     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.3e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaed.lpfedgsfDlvvs 70 
                                       vL + +G G +++ +ak+ + ++v+gv+i++ ++e+ r+++ ++++   v++ +gd+++ +p  dg+fD +++
  gi|488600527|ref|YP_007906998.1| 126 VLVMFAGVGPFAIVIAKKAKPKEVVGVEINPVAVEYFRKNVVANKVedIVKVFEGDVREvMPKLDGRFDRILM 198
                                       677789************978**********************999999********88689*********98 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.2e-09   1.2e-06      51     149 ..     124     221 ..      77     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.2e-09
                                       EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE. CS
                               TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDl. 126
                                        +vl  +++ G  ai  a+  ++ kev+  +i++ Ave  ++Nv  n+ve+iv++ e+d + ++ + + rfd i + 
  gi|488600527|ref|YP_007906998.1| 124 ERVLVMFAGVGPFAIVIAKK-AKPKEVVGVEINPVAVEYFRKNVVANKVEDIVKVFEGDVREVMPKLDGRFDRILMp 199
                                       56777788888889999998.777889999********************************************884 PP

                                       --SS--GGGHHHHHHHEEEEEEE CS
                               TRM 127 DPfGspapfldsavqsvkekglL 149
                                        P+  + +f+d +   vke+g++
  gi|488600527|ref|YP_007906998.1| 200 SPY-IAENFVDVVGSKVKEGGYI 221
                                       577.6789***999999999986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.2e-08   1.3e-05       7      83 ..     126     201 ..     121     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-08
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsn 81 
                                       vl   +G G +++++a++  + +evvG++i++ a+e+ r+n   ++++  v++ +gd+ e ++kl  d +fD il  
  gi|488600527|ref|YP_007906998.1| 126 VLVMFAGVGPFAIVIAKK-AKPKEVVGVEINPVAVEYFRKNVVANKVEdIVKVFEGDVREvMPKL--DGRFDRILMP 199
                                       556678999*******55.55699***********************9899************87..8****99877 PP

                   Methyltransf_31  82 ev 83 
                                       ++
  gi|488600527|ref|YP_007906998.1| 200 SP 201
                                       44 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.6e-08   1.7e-05     155     255 ..     116     220 ..     113     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.6e-08
                              PrmA 155 leklvkegeevlDvGtGSGiLaiaaa.kLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.eekadv 229
                                       + klv e+e+vl + +G G  ai+ a k   k+vv+v i++vAv+  ++N+  Nkve+ ++v+ ++++ +   k d 
  gi|488600527|ref|YP_007906998.1| 116 ISKLVDERERVLVMFAGVGPFAIVIAkKAKPKEVVGVEINPVAVEYFRKNVVANKVEDIVKVF-EGDVREvMPKLDG 191
                                       5678999999999999******9865167789****************************994.4444433233444 PP

                              PrmA 230 ivaNILae...vlielaedikklvkeggl 255
                                        +  IL     +  ++++ + + vkegg+
  gi|488600527|ref|YP_007906998.1| 192 RFDRILMPspyIAENFVDVVGSKVKEGGY 220
                                       44444432111334566666666666665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.1e-08   5.4e-05      41     148 ..     122     227 ..     115     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.1e-08
                                       CC-EEEETT-TTSHHHHHHHHTT-..SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRga..kkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefd 115
                                       e++rvL +faG G  ++  +  +a  k++v ve ++ av+  ++n+ + k+e+ ++++  d  e ++kl   +++fd
  gi|488600527|ref|YP_007906998.1| 122 ERERVLVMFAGVGPFAIV-IAKKAkpKEVVGVEINPVAVEYFRKNVVANKVEDIVKVFEGDVREVMPKL---DGRFD 194
                                       56899********99995.5555523799**************************************99...789** PP

                                       EEEE--SSSTTCH.HHHHHHHHHTT-EEEEEEE CS
                     Cons_hypoth95 116 ivflDPPyakellieevlelleekkllkenalv 148
                                        + +  Py +e+++  v ++++e + ++  ++ 
  gi|488600527|ref|YP_007906998.1| 195 RILMPSPYIAENFVDVVGSKVKEGGYIHYYTFA 227
                                       ************999999999988887766555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.8e-06    0.0029       6      67 ..     132     198 ..     129     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-06
                                       TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT.SS-TT-EEEEEE CS
                   Methyltransf_11   6 GtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaekl.pfednsfDlvvs 67 
                                       G G +a  +ak++  ++vvgv++++ ++++ +++++ +++   v++ ++d++++ p  d+ fD +++
  gi|488600527|ref|YP_007906998.1| 132 GVGPFAIVIAKKAkpKEVVGVEINPVAVEYFRKNVVANKVedIVKVFEGDVREVmPKLDGRFDRILM 198
                                       778888888877778***********************99998999*******66********9986 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.3e-06    0.0035      59     135 ..     117     188 ..     101     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.3e-06
                                       GTCC.-EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCCHC CS
                             PRMT5  59 kkksekklvilvvGaGRGplvdralkaleetkvtkvkivavEKnpnavvtLqkkvneekWeekveviksdmrelkae 135
                                       +k  +++  +lv+ aG Gp+   + k   ++k    ++v vE np av + +k+v  +k e+ v+v++ d+re+  +
  gi|488600527|ref|YP_007906998.1| 117 SKLVDERERVLVMFAGVGPFAIVIAK---KAK--PKEVVGVEINPVAVEYFRKNVVANKVEDIVKVFEGDVREVMPK 188
                                       34446778899999999998654444...333..5579**********************************98765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05     0.015       8      86 ..     108     196 ..     102     200 .. 0.75
   2 ?   -3.2   0.0         6   6.4e+03     107     121 ..     213     227 ..     204     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae........kakkaqkdqfdeq 74 
                                       +ls ++er+++  +++ rvL + +G+G ++ v++++ +  +v+gv+++p+ave  +        +++  +++   ++
  gi|488600527|ref|YP_007906998.1| 108 KLSGERERISKLVDERERVLVMFAGVGPFAIVIAKKAKpkEVVGVEINPVAVEYFRknvvankvEDIVKVFEGDVRE 184
                                       67778899998779999****************7765445*************988666666665555555555555 PP

                   Methyltransf_23  75 eaaepqgkfdlI 86 
                                         ++ +g+fd I
  gi|488600527|ref|YP_007906998.1| 185 VMPKLDGRFDRI 196
                                       556666666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                   Methyltransf_23 107 tllkpgGylllsepl 121
                                       + +k+gGy+   +++
  gi|488600527|ref|YP_007906998.1| 213 SKVKEGGYIHYYTFA 227
                                       667788887766653 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 ?   -1.9   0.0         2   2.1e+03      67      88 ..      24      45 ..      10      47 .. 0.76
   2 !   14.4   0.0     2e-05     0.022       3      65 ..     125     189 ..     123     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2
                   Methyltransf_15 67 lekikvdlvflSpPwGGpsYkk 88
                                      + +i  d+v++ +P   ++Yk+
  gi|488600527|ref|YP_007906998.1| 24 SFEIIGDVVIVDIPDDVVEYKD 45
                                      3456789999999999999986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellakl 65 
                                        +l +f+G G  +i +a++   ++v+++ein+  ++   +N  +  v+d +++  gdv e++ kl
  gi|488600527|ref|YP_007906998.1| 125 RVLVMFAGVGPFAIVIAKKakPKEVVGVEINPVAVEYFRKNVVANKVEDIVKVFEGDVREVMPKL 189
                                       67889********99999865679**********************************9976654 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.4e-05     0.036      75     131 ..     145     202 ..     124     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE---- CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnpPY 131
                                       +  +++g+++++ +v+  r+N  + +v+d++++ + d++++  + +g +d i+   PY
  gi|488600527|ref|YP_007906998.1| 145 KPKEVVGVEINPVAVEYFRKNVVANKVEDIVKVFEGDVREVMpKLDGRFDRILMPSPY 202
                                       33459***********************************9989999******99999 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.2e-05     0.076      17      76 ..     140     199 ..     129     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-05
                   Methyltransf_24  17 alrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDllfiD 76 
                                        +++++  ++v v+ +p    a +++r+    ++++d+v++ ++d +e++++l+ g++D +++ 
  gi|488600527|ref|YP_007906998.1| 140 IAKKAKPKEVVGVEINP---VAVEYFRKnvvaNKVEDIVKVFEGDVREVMPKLD-GRFDRILMP 199
                                       3455556789*******...6666677667779*********************.99*988765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.22      11      66 ..     132     188 ..     126     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                                       TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSE.EEEES-CCCHHHH CS
                    Methyltransf_4  11 GkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNl.rilrgdalkvlle 66 
                                       G G f + +Akk   k+++G+Ei+   v++  k++ a++++ + ++++gd  +v+++
  gi|488600527|ref|YP_007906998.1| 132 GVGPFAIVIAKKAKPKEVVGVEINPVAVEYFRKNVVANKVEDIvKVFEGDVREVMPK 188
                                       8999**********************************9998637888898777766 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 ?   11.5   0.0   0.00013      0.14       4      56 ..     127     180 ..     125     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                       EEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS- CS
                     DNA_methylase   4 idLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfkkvsigDitkidkk 56 
                                       + +faG+G f++  +++   + v+ +ei++ a++ +++n    + +Di k+ + 
  gi|488600527|ref|YP_007906998.1| 127 LVMFAGVGPFAIVIAKKAkPKEVVGVEINPVAVEYFRKNVVANKVEDIVKVFEG 180
                                       559*********98776659********************98888888776555 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    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      38      93 ..     123     179 ..     111     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                       -EEEEEET-TT-HHHHHH-BTT..EEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE-- CS
                              TPMT  38 glrvlvPlCGkaldlvwlAeqg..revvGvelselAvekffeeanlepkvkelsgvke 93 
                                        +rvlv   G +  ++ +A++   +evvGve+ + Ave  f+++    kv+ + +v+e
  gi|488600527|ref|YP_007906998.1| 123 RERVLVMFAGVGPFAIVIAKKAkpKEVVGVEINPVAVEY-FRKNVVANKVEDIVKVFE 179
                                       55777777777777777776542279***********98.688888899888887776 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00027      0.28     201     251 ..     122     174 ..     114     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                   tRNA_U5-meth_tr 201 skgdllelycGnGnfslalarnf..ekvlateiakssveaaqyniaankidnv 251
                                       +++ +l ++ G G f++ +a++   + v+  ei   +ve  ++n+ ank++++
  gi|488600527|ref|YP_007906998.1| 122 ERERVLVMFAGVGPFAIVIAKKAkpKEVVGVEINPVAVEYFRKNVVANKVEDI 174
                                       45568899************9873368***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1651.23
//
Query:       gi|488600528|ref|YP_007906999.1|  [L=280]
Description: putative metal-dependent hydrolase (urease superfamily) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-24   84.7   0.1      8e-24   84.4   0.1    1.1  1  TatD_DNase    TatD related DNase
    8.4e-05   22.9   2.6     0.0014   19.0   0.4    2.8  2  FumaraseC_C   Fumarase C C-terminus
  ------ inclusion threshold ------
      0.049   13.1   0.0      0.074   12.5   0.0    1.4  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.14   11.8   0.1        4.5    7.0   0.0    2.9  3  DUF1918       Domain of unknown function (DUF1918)
       0.16   12.4   0.0        9.1    6.8   0.0    2.5  2  DUF4350       Domain of unknown function (DUF4350)


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 !   84.4   0.1   2.2e-27     8e-24       1     254 [.      10     274 ..      10     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.2e-27
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG................GGHH.HHHHHHTT.TTTEEEEE- CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtss................kdsk.avlelakkypnkvyavlG 60 
                                       +D+H+Hl +++    + ++l+++++ag+++v+ v++ s                 d+   +++ a++   kv++vl 
  gi|488600528|ref|YP_007906999.1|  10 TDNHMHLYNNL----KLKALKQFRNAGGTHVFLVSLLSthydmvptsgedfrkiFDFHlSLVRKANEIV-KVHPVLA 81 
                                       5********55....899**************9999999999999999999865344445555555555.5****** PP

                                       --GGGGGC.........C.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEE CS
                        TatD_DNase  61 iHPnevde.........asedlleelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklpl 127
                                       +HP+e++          a e + e+l  + ++v++ k+vai + G+++y+++++ +e  +e++ + +++Ak++++++
  gi|488600528|ref|YP_007906999.1|  82 VHPAEITIlgerigyekACEIMKEALAIAgEYVAEGKAVAI-KSGRPHYKVSKKVWEMSNEIMGHAFSVAKDCDCAV 157
                                       ******9988888765433444499999999**********.*********************************** PP

                                       EEEEES.-HHHHHHHHHHCGGCCS...EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHH.HHS-GGG CS
                        TatD_DNase 128 viHlrk.aeedlleilkeaaeaka...kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelv.kavpldr 199
                                       +iH+++ + + + ei++ a+++++   +vv H     ++e +++   g++ s+ +   f+n     +++ +a + dr
  gi|488600528|ref|YP_007906999.1| 158 QIHTESyTSDGMKEIAEIARKSGIkveRVVKHFAPPAVKEFEEI---GLFPSVIA---FDN-----NILkAAEEGDR 223
                                       ******966655555555555555556*****977766666666...77777776...433.....34448899*** PP

                                       EEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 200 lLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                       + +ETD  y+++k   g+   p++v++ +++l+el  +  +  ++++ eN+++++
  gi|488600528|ref|YP_007906999.1| 224 FFVETD--YIDDKSRPGAILGPKTVPRRIRELYELGYE--DVAYKVCVENVEKIY 274
                                       ******..9***66666*****************9874..445688899999887 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4     4e-07    0.0014       2      23 ..      87     108 ..      87     121 .. 0.93
   2 ?    2.9   0.1     0.043   1.5e+02      16      34 ..     171     189 ..     169     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4e-07
                                       GGGGHHHHHHHHHHHHHHHHHH CS
                       FumaraseC_C   2 VTaLnphIGYekAakIAkeAlk 23 
                                       +T L   IGYekA +I keAl+
  gi|488600528|ref|YP_007906999.1|  87 ITILGERIGYEKACEIMKEALA 108
                                       799*****************97 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.043
                                       HHHHHHHHHT--HHHHHHH CS
                       FumaraseC_C  16 kIAkeAlkegktlreavle 34 
                                       +IA  A k+g+++  +v  
  gi|488600528|ref|YP_007906999.1| 171 EIAEIARKSGIKVERVVKH 189
                                       8************999975 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 ?   12.5   0.0   2.1e-05     0.074      64     150 ..      94     178 ..      12     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                                       S.HHHHHHHHHHHHHHHHHH..TBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTS CS
                      AP_endonuc_2  64 r.reesvdalkraielaaaL..GapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgv 137
                                          e++ + +k+a+ +a +    ++ + + +G   +++ +  +  we   e +  +  +a  +++  a++ +++s++
  gi|488600528|ref|YP_007906999.1|  94 IgYEKACEIMKEALAIAGEYvaEGKAVAIKSG---RPHYKVSKKVWEMSNEIMGHAFSVA--KDCDCAVQIHTESYT 165
                                       25577899999999999655448999999999...6666666679**************5..6999*********** PP

                                       SSTCHHHHHHHHH CS
                      AP_endonuc_2 138 elgdeelarllda 150
                                       ++g +e+a++ ++
  gi|488600528|ref|YP_007906999.1| 166 SDGMKEIAEIARK 178
                                       9999***999876 PP

>> DUF1918  Domain of unknown function (DUF1918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.63   2.3e+03       5      14 ..       4      13 ..       3      15 .. 0.80
   2 ?    0.7   0.0      0.12   4.1e+02      28      39 ..     120     131 ..     108     137 .. 0.78
   3 ?    7.0   0.0    0.0013       4.5       3      26 ..     218     241 ..     217     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.63
                                      TTEEEEES-T CS
                           DUF1918  5 vGDrlvvegr 14
                                       GDr+v+ ++
  gi|488600528|ref|YP_007906999.1|  4 RGDRIVTDNH 13
                                      59****9876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                                       -S-SSS-S-EEE CS
                           DUF1918  28 VrgedGaPPYlV 39 
                                       V  + G P+Y V
  gi|488600528|ref|YP_007906999.1| 120 VAIKSGRPHYKV 131
                                       55689*****99 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0013
                                       --TTEEEEES-TTTS--EEEEEEE CS
                           DUF1918   3 AkvGDrlvvegrtvgepereGeiv 26 
                                       A+ GDr+ ve   ++ + r G i+
  gi|488600528|ref|YP_007906999.1| 218 AEEGDRFFVETDYIDDKSRPGAIL 241
                                       899*******************98 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.04   1.4e+02      39      68 ..       8      39 ..       4      40 .. 0.82
   2 ?    6.8   0.0    0.0025       9.1       4      26 ..     166     188 ..     163     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.04
                           DUF4350 39 lvvapdlrlte.eelaallewvarGn.tlvla 68
                                      +v++++++l +   l+al ++  +G+ +++l+
  gi|488600528|ref|YP_007906999.1|  8 IVTDNHMHLYNnLKLKALKQFRNAGGtHVFLV 39
                                      578888886666889********999678887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0025
                           DUF4350   4 pnGtralaelLeaqGvevrrvrk 26 
                                        +G +  ae+++++G++v+rv k
  gi|488600528|ref|YP_007906999.1| 166 SDGMKEIAEIARKSGIKVERVVK 188
                                       6899***************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 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:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1928.38
//
Query:       gi|488600529|ref|YP_007907000.1|  [L=245]
Description: RecA-superfamily ATPases implicated in signal transduction [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-73  244.4   0.7      1e-72  244.3   0.7    1.0  1  ATPase    KaiC
     0.0082   15.7   0.0      0.014   15.0   0.0    1.4  1  AAA_25    AAA domain
  ------ inclusion threshold ------
      0.031   14.7   0.0      0.036   14.4   0.0    1.3  1  AAA_16    AAA ATPase domain
      0.043   12.9   0.0      0.067   12.2   0.0    1.3  1  T2SSE     Type II/IV secretion system protein
      0.048   13.4   0.1        0.1   12.4   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
       0.16   11.6   0.1       0.43   10.3   0.1    1.6  2  AAA_24    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 !  244.3   0.7   3.4e-76     1e-72       1     230 [.       6     242 ..       6     243 .. 0.98

  Alignments for each domain:
  == domain 1  score: 244.3 bits;  conditional E-value: 3.4e-76
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       ++tgI+g+Dei++gG+ ++r++l+tG +G+GKtif+ qFl++g+e y+epg+++++ee+++++re ++++Gw+le+l
  gi|488600529|ref|YP_007907000.1|   6 IPTGIPGFDEITHGGLIRDRSYLVTGPSGSGKTIFVGQFLVNGIEMYNEPGIMIATEERPQHIREYFSTFGWELERL 82 
                                       69*************************************************************************** PP

                            ATPase  78 eeegklaiidasesaeesaee.....kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlv 148
                                       e+e++lai+da++++++ +++      + +d+++li+++ ++ +ei+akr v+Ds t++   +++ +++R +l ++ 
  gi|488600529|ref|YP_007907000.1|  83 EDENMLAIVDATSTKIGLPSDekyidIRPFDTRSLIDQIINIQDEIGAKRAVLDSTTSIgFAINDVSKFRIELLKIS 159
                                       *****************999888888889************************************************ PP

                            ATPase 149 rvlkklgvTailvsekss.seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegi 224
                                       ++l+ lg+T++l++e+ s + ++++++gve+f+v+g+ivL +++ e+ +vR +ei k+Rg++hskk+hpfeIte+gi
  gi|488600529|ref|YP_007907000.1| 160 TTLEILGLTSLLTCEVLStEGDQISRFGVENFVVEGTIVLYYTKTENVRVRGIEIFKLRGSDHSKKIHPFEITENGI 236
                                       ***************98867789****************************************************** PP

                            ATPase 225 kvleek 230
                                       +v++e+
  gi|488600529|ref|YP_007907000.1| 237 VVHPEE 242
                                       ***987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.7e-06     0.014      17     150 ..       8     137 ..       2     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.7e-06
                            AAA_25  17 apppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlrav 93 
                                       + +p  + + +g l+++   l++G++g+GKt ++ +  +   +           + + +++++E++ +++r+ ++  
  gi|488600529|ref|YP_007907000.1|   8 TGIPGFDEITHGGLIRDRSYLVTGPSGSGKTIFVGQFLVNGIEM---------YNEPGIMIATEERPQHIREYFSTF 75 
                                       5566677788988899********************99988853.........455779999999999999999998 PP

                            AAA_25  94 geal...rddarllvldlagveslpLfakdrggtlltadvdaleaaieeveg...vrlvviDp 150
                                       g +l   +d   l+++d+ + +++ L ++++   +++ d++ l+++i  + +   ++  v+D+
  gi|488600529|ref|YP_007907000.1|  76 GWELerlEDENMLAIVDATS-TKIGLPSDEKYIDIRPFDTRSLIDQIINIQDeigAKRAVLDS 137
                                       85554347777888888533.577777777666665555555555555544433355555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.036      25      45 ..      25      45 ..      13     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                            AAA_16 25 elvllsGesGvGKsslvrell 45
                                      ++ l++G+sG+GK+  v ++l
  gi|488600529|ref|YP_007907000.1| 25 RSYLVTGPSGSGKTIFVGQFL 45
                                      899************999887 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05     0.067     127     151 ..      22      47 ..       9      69 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                             T2SSE 127 rerglilvsGgTgsGKttll.yallk 151
                                        +  + lv+G+ gsGKt+++   l++
  gi|488600529|ref|YP_007907000.1|  22 IRDRSYLVTGPSGSGKTIFVgQFLVN 47 
                                       566788************98444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.4e-05       0.1      23      38 ..      25      40 ..      12      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                            AAA_29 23 gatlltGpsGsGKSTl 38
                                       ++l+tGpsGsGK+ +
  gi|488600529|ref|YP_007907000.1| 25 RSYLVTGPSGSGKTIF 40
                                      269**********865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00014      0.43       3      22 ..      25      44 ..      23      69 .. 0.76
   2 ?   -1.5   0.0      0.58   1.7e+03     108     167 ..      69     128 ..      66     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      +++l++Gpsg+GKT ++ ++
  gi|488600529|ref|YP_007907000.1| 25 RSYLVTGPSGSGKTIFVGQF 44
                                      5789************9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.58
                            AAA_24 108 aeefrrllkklqelrk.nvifiahektrkdedpegeakytrlepklgkktanelkeevDlv 167
                                       +e f+ +   l+ l + n  +i  ++  k++ p  e ky  ++p       +++ ++ D++
  gi|488600529|ref|YP_007907000.1|  69 REYFSTFGWELERLEDeNMLAIVDATSTKIGLPSDE-KYIDIRPFDTRSLIDQIINIQDEI 128
                                       667777777888888889999999999999988777.777777665555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1609.46
//
Query:       gi|488600530|ref|YP_007907001.1|  [L=297]
Description: hypothetical protein Asulf_01004 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   46.8   0.0    5.8e-12   45.5   0.0    1.8  1  Thioredoxin_3  Thioredoxin domain
    0.00035   20.4   0.1    0.00061   19.6   0.1    1.3  1  Thioredoxin_9  Thioredoxin
      0.001   19.0   0.0     0.0018   18.2   0.0    1.4  1  Thioredoxin    Thioredoxin
     0.0017   18.7   0.1     0.0035   17.7   0.1    1.5  1  HEAT_2         HEAT repeats
  ------ inclusion threshold ------
      0.011   16.0   0.1          5    7.3   0.1    2.8  3  Thioredoxin_4  Thioredoxin
      0.024   14.8   0.1      0.057   13.6   0.1    1.6  1  RTP1_C1        Required for nuclear transport of RNA pol II C
      0.027   14.7   0.0      0.069   13.4   0.0    1.7  1  Glutaredoxin   Glutaredoxin
       0.05   14.0   0.0       0.53   10.7   0.0    2.3  1  Thioredoxin_2  Thioredoxin-like domain
       0.15   12.5   0.0       0.42   11.1   0.0    1.8  1  DUF836         Glutaredoxin-like domain (DUF836)


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 !   45.5   0.0   2.9e-15   5.8e-12       3      76 .]      83     158 ..      81     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.9e-15
                                       EEE.ESSSSTTCH.HHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHHHHHH CS
                     Thioredoxin_3   3 ikv.lgpgCakCp.klekavkeaaaekgikaevekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeirklle 76 
                                       +kv ++p C++C   ++k+++  +a+++i++e+ ++t fe++  ky++ svP ++++++++ +G  +s ee+ +++e
  gi|488600530|ref|YP_007907001.1|  83 FKVfISPFCPHCAnLVRKLIQLSLANPDISLEIFDATRFEKLaRKYEILSVPVTILNDRIRLVG-DKSIEELLNWVE 158
                                       79988999*****9999***********************************************.799999999985 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.1e-07   0.00061      19     116 ..      56     158 ..      43     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.1e-07
                                       HHHHHHHHHHH---HHHHHT--S.-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-S CS
                     Thioredoxin_9  19 mlrvykkvelseeteekiksiek.klkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltng 94 
                                       m  + +++++++e ++ +++iek k ++ v+  ++C+ +a+ v  l +++ +np+i+++i+   + ++l ++y    
  gi|488600530|ref|YP_007907001.1|  56 MITLSNSMSFDPEIKNNLERIEKiKASFKVFISPFCPHCANLVRKLIQLSLANPDISLEIFDATRFEKLARKYE--- 129
                                       66778888999999996666554266888999***************************************995... PP

                                       S--SSEEEEE-.......TT--EEEEEES CS
                     Thioredoxin_9  95 araiPtliild.......eegeelgvwge 116
                                         ++P+ i+ d       +  eel  w+e
  gi|488600530|ref|YP_007907001.1| 130 ILSVPVTILNDrirlvgdKSIEELLNWVE 158
                                       59999999888776766444777777765 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.9e-07    0.0018      24      78 ..      85     138 ..      59     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.9e-07
                                       EEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                       Thioredoxin  24 eFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlkl 78 
                                        F +p+C+hC +l  +l +l+ +   ++ l   d++  e+la+kye+ ++P  +l
  gi|488600530|ref|YP_007907001.1|  85 VFISPFCPHCANLVRKLIQLSLANP-DISLEIFDATRFEKLARKYEILSVPVTIL 138
                                       599**************99999988.9************************7755 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.7e-06    0.0035      21      84 ..     214     284 ..     192     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                            HEAT_2  21 iraLgrignp......ealpaLvelled.edpavRraaaeaLgaigdpealpaLkellddddddvvReaAa 84 
                                       +++L+++g +      ++l+++ + l+  +d+   + a++ Lg+igd++++++Lk+ll + +d   +ea  
  gi|488600530|ref|YP_007907001.1| 214 LENLAEMGKDvakakkKILELIQDRLNLeSDRVFLEDAVMILGKIGDSSDADFLKKLLSSVEDKGLKEALM 284
                                       3444444444553333667777777754267889999*********************9999998888765 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.2   4.4e+03     138     152 ..      28      42 ..      19      46 .. 0.80
   2 ?    7.3   0.1    0.0025         5      16      36 ..      82     102 ..      77     115 .. 0.80
   3 ?    5.4   0.0     0.009        18     127     165 ..     119     158 ..     114     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.2
                                       --SS-EEEETTEEE- CS
                     Thioredoxin_4 138 iestPtfiingekve 152
                                        e tP fi+n  +++
  gi|488600530|ref|YP_007907001.1|  28 YEYTPVFILNSIRYH 42 
                                       578******987775 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0025
                                       EEEEEE-TT-HHHHHHHHHHH CS
                     Thioredoxin_4  16 tvieyedlrCphCakfeeeve 36 
                                       +  ++ +  CphCa++ +++ 
  gi|488600530|ref|YP_007907001.1|  82 SFKVFISPFCPHCANLVRKLI 102
                                       56789*********9877665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.009
                                       HHHHHHHHHHT--SS-EEEETTEE.E-TT--HHHHHHHHT CS
                     Thioredoxin_4 127 eaeskeakkagiestPtfiingek.veepqtyeelkalid 165
                                       +++ k a+k +i s+P  i+n+++ + + +++eel  +++
  gi|488600530|ref|YP_007907001.1| 119 TRFEKLARKYEILSVPVTILNDRIrLVGDKSIEELLNWVE 158
                                       5667889****************987889****9999987 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.8e-05     0.057      15      90 ..     206     281 ..     195     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                           RTP1_C1  15 vrahglvlLrkliekkskeavldiekilkllleaLkdedsYvYLn.aikgLvaLadvfpeevlklLleeyeeeneke 90 
                                       +r  ++ lL++l+e  + + ++ ++kil+l+++ L+ e + v+L+ a+ +L +++d  ++++lk+Ll+ +e++  ke
  gi|488600530|ref|YP_007907001.1| 206 TRLGAMFLLENLAEMGK-DVAKAKKKILELIQDRLNLESDRVFLEdAVMILGKIGDSSDADFLKKLLSSVEDKGLKE 281
                                       6888999*******997.7888999***********99999***65**********************997766555 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.5e-05     0.069       3      52 ..      85     135 ..      83     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                                       EEESTSSHHHHHHHHHHHHTT.....GGEEEEEGCCSHHHHHHHHHHHTSSSSSE CS
                      Glutaredoxin   3 lftkptCpyCkkakrlLkelg.....vkfeeidvdkdeeireelkelsgvrtvPq 52 
                                       +f +p Cp+C++ +r L +l      ++ e++d +      e+l ++ ++ +vP+
  gi|488600530|ref|YP_007907001.1|  85 VFISPFCPHCANLVRKLIQLSlanpdISLEIFDATRF----EKLARKYEILSVPV 135
                                       89***************88884333344555555554....44444445555665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.53       9     108 ..      83     156 ..      76     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                     Thioredoxin_2   9 lvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                       + vf +p Cp C+ l ++l +l    +       +p+   ++ +i  a+  +          +larky++ ++P ++
  gi|488600530|ref|YP_007907001.1|  83 FKVFISPFCPHCANLVRKLIQL----SL-----ANPD---ISLEIFDATRFE----------KLARKYEILSVPVTI 137
                                       56899999****9999999999....22.....3444...677777777664..........799999999999999 PP

                     Thioredoxin_2  86 fldgkeivarlpGyvpaeeleal 108
                                       + d      rl+G  + eel+ +
  gi|488600530|ref|YP_007907001.1| 138 LNDRI----RLVGDKSIEELLNW 156
                                       99998....88888888887765 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00021      0.42       6      57 ..      87     140 ..      84     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                       E-TT-HHHHHHHHHHHHHCCCTT.EEEEEEETTT-CCCHCCCC.TTTTEEEECT CS
                            DUF836   6 skpgChlCeqakekLkelkleeg.leleviDIakdeeleakYg.leipvlaleg 57 
                                         p C+ C ++  kL +l+l++  ++le  D ++ e+l +kY+ l +pv  l++
  gi|488600530|ref|YP_007907001.1|  87 ISPFCPHCANLVRKLIQLSLANPdISLEIFDATRFEKLARKYEiLSVPVTILND 140
                                       5689*************9998877*********99*******845788877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); 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 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1829.72
//
Query:       gi|488600531|ref|YP_007907002.1|  [L=231]
Description: Flp pilus assembly protein TadD, contains TPR repeats [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-57  186.6  10.5    3.3e-14   52.0   0.3    6.7  7  TPR_1         Tetratricopeptide repeat
    2.4e-48  158.4   7.7    3.3e-11   42.4   0.1    6.7  7  TPR_2         Tetratricopeptide repeat
    7.7e-42  138.0  12.9    6.5e-10   38.4   0.2    6.8  7  TPR_8         Tetratricopeptide repeat
    1.3e-40  136.8   3.8    2.1e-09   36.9   0.1    6.1  6  TPR_11        TPR repeat
    1.8e-40  134.4   5.0    2.3e-07   30.7   0.0    6.1  6  TPR_17        Tetratricopeptide repeat
    4.4e-31  107.2   1.6    3.7e-09   37.0   0.0    4.3  5  TPR_19        Tetratricopeptide repeat
    3.3e-27   94.6   3.5    2.1e-11   44.0   0.0    4.8  4  TPR_12        Tetratricopeptide repeat
    3.5e-25   86.1   0.3    2.7e-05   23.9   0.0    5.5  5  TPR_7         Tetratricopeptide repeat
    5.7e-24   82.8   0.0    6.8e-05   23.4   0.0    6.1  6  TPR_14        Tetratricopeptide repeat
    1.5e-23   82.0   5.3     0.0002   21.1   0.0    5.3  5  TPR_10        Tetratricopeptide repeat
    6.5e-23   81.1   0.0    1.2e-08   35.4   0.0    3.4  3  TPR_16        Tetratricopeptide repeat
    2.4e-16   59.2   2.2    6.5e-05   23.3   0.0    5.2  5  TPR_6         Tetratricopeptide repeat
    6.6e-16   58.3  13.3    2.4e-08   34.1   0.9    3.1  5  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    1.1e-15   57.5   0.0    9.9e-05   22.4   0.0    3.8  4  TPR_9         Tetratricopeptide repeat
    2.9e-10   39.9   0.6      0.061   13.3   0.1    5.2  5  TPR_3         Tetratricopeptide repeat
    4.6e-09   36.2   3.1      0.083   13.0   0.1    4.5  4  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    3.3e-08   33.8   0.0      0.034   14.5   0.0    3.9  4  TPR_20        Tetratricopeptide repeat
    8.6e-08   31.6   0.4    0.00038   19.6   0.1    2.2  2  Paf67         RNA polymerase I-associated factor PAF67
    3.7e-05   23.3   3.4       0.09   12.2   0.2    3.3  4  DUF5112       Domain of unknown function (DUF5112)
    4.9e-05   22.7   0.1      0.012   14.9   0.1    2.4  3  TPR_15        Tetratricopeptide repeat
    5.8e-05   22.6   0.9        1.8    7.9   0.1    3.7  4  Coatomer_E    Coatomer epsilon subunit
    7.5e-05   23.2   0.0       0.02   15.3   0.0    2.8  3  BTAD          Bacterial transcriptional activator domain
    0.00018   21.0   1.8     0.0032   16.9   1.7    2.7  1  SNAP          Soluble NSF attachment protein, SNAP
    0.00021   20.7   0.6        2.4    7.3   0.4    3.8  4  FAT           FAT domain
    0.00054   19.8   0.9       0.77    9.5   0.0    3.7  3  TOM20_plant   Plant specific mitochondrial import receptor su
    0.00064   19.8  12.5      0.024   14.9   0.1    5.2  6  PPR           PPR repeat
    0.00073   19.5   4.1      0.004   17.2   3.5    2.4  2  SRP_TPR_like  Putative TPR-like repeat
     0.0012   17.8   1.2       0.03   13.3   0.3    2.1  2  NARP1         NMDA receptor-regulated protein 1
     0.0044   16.7   6.8          1    9.2   0.0    4.6  5  PPTA          Protein prenyltransferase alpha subunit repeat
     0.0065   16.2   0.9       0.02   14.6   0.0    2.4  1  PPR_1         PPR repeat
     0.0093   16.0   0.1       0.49   10.5   0.0    2.9  3  Rapsyn_N      Rapsyn N-terminal myristoylation and linker reg
  ------ inclusion threshold ------
      0.055   13.2   1.8        5.6    6.6   0.2    3.3  4  RPN7          26S proteasome subunit RPN7
      0.094   12.7   0.4       0.37   10.8   0.1    2.1  2  DUF627        Protein of unknown function (DUF627)
       0.17   11.2   0.0         20    4.4   0.0    2.7  3  TPR_MalT      MalT-like TPR region
        0.2   11.9   5.8        1.1    9.6   0.0    3.9  4  PPR_2         PPR repeat family
        0.2   12.4   0.0    2.2e+02    2.9   0.0    4.0  4  TPR_4         Tetratricopeptide repeat
       0.94    9.8   3.0        6.4    7.2   0.0    3.2  3  Dynein_light  Dynein light chain type 1


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 ?   -0.6   0.0       2.8   1.4e+03      20      29 ..      10      19 ..       9      20 .. 0.85
   2 ?    3.8   0.0      0.11        54      23      34 .]      29      40 ..      27      40 .. 0.89
   3 !   37.2   0.1   3.3e-12   1.6e-09       2      34 .]      42      74 ..      41      74 .. 0.95
   4 !   32.8   0.0   7.7e-11   3.7e-08       2      34 .]      76     108 ..      75     108 .. 0.96
   5 !   33.3   0.2   5.5e-11   2.6e-08       3      33 ..     111     141 ..     110     142 .. 0.96
   6 !   52.0   0.3   6.9e-17   3.3e-14       2      34 .]     144     176 ..     143     176 .. 0.97
   7 !   28.1   0.0   2.5e-09   1.2e-06       3      34 .]     179     210 ..     178     210 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.8
                                      HHHHHHHHHH CS
                             TPR_1 20 AleyyekALe 29
                                      A+e ++k Le
  gi|488600531|ref|YP_007907002.1| 10 AEEWFKKGLE 19
                                      8999999987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.11
                                      HHHHHHHHSTTH CS
                             TPR_1 23 yyekALelnPnn 34
                                       ++k +el+P+n
  gi|488600531|ref|YP_007907002.1| 29 SFKKSVELDPEN 40
                                      69********97 PP

  == domain 3  score: 37.2 bits;  conditional E-value: 3.3e-12
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                       a++nlG a++ +g+ +eA++++ kALe++ ++
  gi|488600531|ref|YP_007907002.1| 42 SAWNNLGIALYDKGMQEEAIQCFVKALEIDSKY 74
                                      69****************************876 PP

  == domain 4  score: 32.8 bits;  conditional E-value: 7.7e-11
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +al+nlG+a++ + +++eA++++e+ L+ n n+
  gi|488600531|ref|YP_007907002.1|  76 DALFNLGYALMMMRRFEEAEQCFERILKFNSND 108
                                       79****************************986 PP

  == domain 5  score: 33.3 bits;  conditional E-value: 5.5e-11
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                       a++nlG++ ++l ky+eA++  +kA+e+n +
  gi|488600531|ref|YP_007907002.1| 111 AWNNLGYVQYNLRKYEEAEKSISKAIEINSQ 141
                                       8****************************86 PP

  == domain 6  score: 52.0 bits;  conditional E-value: 6.9e-17
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        a+ynlG++y+ ++++d+A+++yek+Le++P+n
  gi|488600531|ref|YP_007907002.1| 144 SAWYNLGLLYYAMERFDDAIKCYEKVLEIDPKN 176
                                       59*****************************98 PP

  == domain 7  score: 28.1 bits;  conditional E-value: 2.5e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       a +n++ ++ ++gk+deA+e ++k++e +P+n
  gi|488600531|ref|YP_007907002.1| 179 AMNNIAIILGRKGKLDEAIELFDKVIEMEPDN 210
                                       679***************************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       4.7   2.3e+03      20      29 ..      10      19 ..       5      20 .. 0.81
   2 ?    2.4   0.0      0.44   2.1e+02      24      34 .]      30      40 ..      29      40 .. 0.92
   3 !   30.3   0.0   5.1e-10   2.5e-07       2      33 ..      42      73 ..      41      74 .. 0.93
   4 !   30.2   0.0   5.7e-10   2.8e-07       2      34 .]      76     108 ..      75     108 .. 0.95
   5 !   28.2   0.1   2.4e-09   1.2e-06       3      33 ..     111     141 ..     109     142 .. 0.94
   6 !   42.4   0.1   6.7e-14   3.3e-11       3      34 .]     145     176 ..     143     176 .. 0.96
   7 !   23.2   0.0   9.6e-08   4.6e-05       3      34 .]     179     210 ..     177     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.7
                             TPR_2 20 AleafekAle 29
                                      A+e+f+k le
  gi|488600531|ref|YP_007907002.1| 10 AEEWFKKGLE 19
                                      8889998886 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.44
                             TPR_2 24 fekAleldPnn 34
                                      f+k++eldP+n
  gi|488600531|ref|YP_007907002.1| 30 FKKSVELDPEN 40
                                      99*******97 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 5.1e-10
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                       a++nlG a+y +g  eeA+++f kAle+d +
  gi|488600531|ref|YP_007907002.1| 42 SAWNNLGIALYDKGMQEEAIQCFVKALEIDSK 73
                                      69***************************975 PP

  == domain 4  score: 30.2 bits;  conditional E-value: 5.7e-10
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +al+nlG+a++ + ++eeA+++fe+ l+ + n+
  gi|488600531|ref|YP_007907002.1|  76 DALFNLGYALMMMRRFEEAEQCFERILKFNSND 108
                                       69**************************99886 PP

  == domain 5  score: 28.2 bits;  conditional E-value: 2.4e-09
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a++nlG++ y+l +yeeA++   kA+e++ +
  gi|488600531|ref|YP_007907002.1| 111 AWNNLGYVQYNLRKYEEAEKSISKAIEINSQ 141
                                       8***************************976 PP

  == domain 6  score: 42.4 bits;  conditional E-value: 6.7e-14
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a+ynlGl+yy++ ++++A++++ek+le+dP+n
  gi|488600531|ref|YP_007907002.1| 145 AWYNLGLLYYAMERFDDAIKCYEKVLEIDPKN 176
                                       9*****************************97 PP

  == domain 7  score: 23.2 bits;  conditional E-value: 9.6e-08
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       a +n++ ++ ++g+++eA+e+f+k++e +P+n
  gi|488600531|ref|YP_007907002.1| 179 AMNNIAIILGRKGKLDEAIELFDKVIEMEPDN 210
                                       789***************************98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       2.5   1.2e+03      19      29 ..       9      19 ..       3      20 .. 0.83
   2 ?    6.0   0.0     0.033        16      15      34 .]      21      40 ..      18      40 .. 0.85
   3 !   26.9   0.1   6.7e-09   3.2e-06       2      33 ..      42      73 ..      41      74 .. 0.95
   4 !   20.6   0.0   6.8e-07   0.00033       2      33 ..      76     107 ..      75     108 .. 0.94
   5 !   26.5   0.2   9.2e-09   4.4e-06       3      33 ..     111     141 ..     109     142 .. 0.95
   6 !   38.4   0.2   1.3e-12   6.5e-10       2      34 .]     144     176 ..     143     176 .. 0.96
   7 !   22.6   0.0   1.6e-07   7.8e-05       3      34 .]     179     210 ..     178     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.5
                                      HHHHHHHHHHH CS
                             TPR_8 19 eAkeyyekale 29
                                      +A+e+++k le
  gi|488600531|ref|YP_007907002.1|  9 SAEEWFKKGLE 19
                                      799*****997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.033
                                      T-HHHHHHHHHHHHHHHHH. CS
                             TPR_8 15 gdyeeAkeyyekaleldpdn 34
                                      g+ +  + +++k +eldp+n
  gi|488600531|ref|YP_007907002.1| 21 GNVDDEIMSFKKSVELDPEN 40
                                      77778899**********86 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 6.7e-09
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      +a++nlg ++ ++g  eeA++++ kale+d +
  gi|488600531|ref|YP_007907002.1| 42 SAWNNLGIALYDKGMQEEAIQCFVKALEIDSK 73
                                      69****************************87 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 6.8e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a++nlg++++ + ++eeA++++e+ l+ + +
  gi|488600531|ref|YP_007907002.1|  76 DALFNLGYALMMMRRFEEAEQCFERILKFNSN 107
                                       699*************************9987 PP

  == domain 5  score: 26.5 bits;  conditional E-value: 9.2e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       a++nlg++  +l +yeeA++++ ka+e++ +
  gi|488600531|ref|YP_007907002.1| 111 AWNNLGYVQYNLRKYEEAEKSISKAIEINSQ 141
                                       8***************************987 PP

  == domain 6  score: 38.4 bits;  conditional E-value: 1.3e-12
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +a+ynlg++y  +++++ A+++yek+le+dp+n
  gi|488600531|ref|YP_007907002.1| 144 SAWYNLGLLYYAMERFDDAIKCYEKVLEIDPKN 176
                                       69*****************************97 PP

  == domain 7  score: 22.6 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       a++n++ i+  +g+++eA+e + k++e++pdn
  gi|488600531|ref|YP_007907002.1| 179 AMNNIAIILGRKGKLDEAIELFDKVIEMEPDN 210
                                       679***************************97 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   7.8e-09   3.8e-06      16      42 .]      29      55 ..      19      55 .. 0.90
   2 !   36.9   0.1   4.4e-12   2.1e-09       3      40 ..      50      87 ..      50      88 .. 0.95
   3 !   12.5   0.0   0.00018     0.088       9      40 ..      90     121 ..      90     122 .. 0.94
   4 !   25.5   0.5   1.6e-08   7.5e-06       9      41 ..     124     156 ..     124     157 .. 0.96
   5 !   30.2   0.1   5.4e-10   2.6e-07       4      42 .]     153     191 ..     152     191 .. 0.96
   6 !   14.8   0.0   3.5e-05     0.017       7      28 ..     190     211 ..     186     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 7.8e-09
                            TPR_11 16 aYkkAlkldPdnaeayynLGlayykqG 42
                                      ++kk ++ldP+n++a++nLG a+y +G
  gi|488600531|ref|YP_007907002.1| 29 SFKKSVELDPENPSAWNNLGIALYDKG 55
                                      7899********************998 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 4.4e-12
                            TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                                      a+y++G  eeAi+++ kAl++d+++ +a++nLG+a+++
  gi|488600531|ref|YP_007907002.1| 50 ALYDKGMQEEAIQCFVKALEIDSKYTDALFNLGYALMM 87
                                      69*********************************976 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00018
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       ++eeA +++++ lk+++++  a++nLG+++y+
  gi|488600531|ref|YP_007907002.1|  90 RFEEAEQCFERILKFNSNDGGAWNNLGYVQYN 121
                                       689***************************97 PP

  == domain 4  score: 25.5 bits;  conditional E-value: 1.6e-08
                            TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       kyeeA ++ +kA+++++++ +a+ynLGl+yy++
  gi|488600531|ref|YP_007907002.1| 124 KYEEAEKSISKAIEINSQDSSAWYNLGLLYYAM 156
                                       799999*************************86 PP

  == domain 5  score: 30.2 bits;  conditional E-value: 5.4e-10
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       yy+  ++++Ai++Y+k l++dP+n  a +n++ ++ ++G
  gi|488600531|ref|YP_007907002.1| 153 YYAMERFDDAIKCYEKVLEIDPKNTLAMNNIAIILGRKG 191
                                       9*******************************9999988 PP

  == domain 6  score: 14.8 bits;  conditional E-value: 3.5e-05
                            TPR_11   7 qGkyeeAieaYkkAlkldPdna 28 
                                       +Gk++eAie + k ++  Pdn 
  gi|488600531|ref|YP_007907002.1| 190 KGKLDEAIELFDKVIEMEPDNE 211
                                       8*******************95 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.6e-09   7.9e-07       2      34 .]      30      62 ..      29      62 .. 0.97
   2 !   21.0   0.0     6e-07   0.00029       1      34 []      63      96 ..      63      96 .. 0.95
   3 !   23.6   0.2     9e-08   4.4e-05       1      34 []      97     130 ..      97     130 .. 0.97
   4 !   23.5   0.0   9.5e-08   4.6e-05       4      34 .]     134     164 ..     132     164 .. 0.95
   5 !   30.7   0.0   4.7e-10   2.3e-07       1      34 []     165     198 ..     165     198 .. 0.97
   6 ?    3.7   0.0       0.2        97       1      15 [.     199     213 ..     199     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.6e-09
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      ++k++eldP n+ a+nnL+ +l+ +G  ++A+q
  gi|488600531|ref|YP_007907002.1| 30 FKKSVELDPENPSAWNNLGIALYDKGMQEEAIQ 62
                                      79*****************************98 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 6e-07
                            TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      ++ kale+d ++ da++nL+++l +  ++++A+q
  gi|488600531|ref|YP_007907002.1| 63 CFVKALEIDSKYTDALFNLGYALMMMRRFEEAEQ 96
                                      6779****************************98 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 9e-08
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ++++ l+ + n+  a+nnL+++++++ ++++A++
  gi|488600531|ref|YP_007907002.1|  97 CFERILKFNSNDGGAWNNLGYVQYNLRKYEEAEK 130
                                       89******************************86 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 9.5e-08
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                       ka+e++  ++ a++nL+ l++   ++++A++
  gi|488600531|ref|YP_007907002.1| 134 KAIEINSQDSSAWYNLGLLYYAMERFDDAIK 164
                                       9**************************9985 PP

  == domain 5  score: 30.7 bits;  conditional E-value: 4.7e-10
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y+k+le+dP+n  a+nn A +l ++G+l++A++
  gi|488600531|ref|YP_007907002.1| 165 CYEKVLEIDPKNTLAMNNIAIILGRKGKLDEAIE 198
                                       8*******************************86 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.2
                            TPR_17   1 lylkaleldPnnada 15 
                                       l+ k++e +P+n +a
  gi|488600531|ref|YP_007907002.1| 199 LFDKVIEMEPDNEVA 213
                                       799********9655 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00031      0.15      13      47 ..      29      63 ..      18      65 .. 0.86
   2 !   27.5   0.0     7e-09   3.4e-06       8      58 ..      58     108 ..      55     115 .. 0.91
   3 !   27.3   0.0     8e-09   3.9e-06       1      62 [.      85     147 ..      85     152 .. 0.93
   4 !   24.3   0.1     7e-08   3.4e-05       6      52 ..     124     170 ..     120     171 .. 0.95
   5 !   37.0   0.0   7.5e-12   3.7e-09       2      62 ..     154     213 ..     153     218 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00031
                            TPR_19 13 lleqalqedpknaearllLAeallalgqldeAeal 47
                                       +++  + dp+n+ a+ +L +al+  g  +eA+++
  gi|488600531|ref|YP_007907002.1| 29 SFKKSVELDPENPSAWNNLGIALYDKGMQEEAIQC 63
                                      589999**************************987 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 7e-09
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       +eA++ + +al+ d k+ +a+ +L  al+ + +++eAe++ +++++ + +d
  gi|488600531|ref|YP_007907002.1|  58 EEAIQCFVKALEIDSKYTDALFNLGYALMMMRRFEEAEQCFERILKFNSND 108
                                       69*******************************************988876 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 8e-09
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.arya 62 
                                       l+++ +++eA + +e++l+ + +++ a+ +L  ++++l  ++eAe+ ++++ e + +d +++ 
  gi|488600531|ref|YP_007907002.1|  85 LMMMRRFEEAEQCFERILKFNSNDGGAWNNLGYVQYNLRKYEEAEKSISKAIEINSQDsSAWY 147
                                       7899*************************************************9999856665 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 7e-08
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                       +y+eA +  ++a++ + +++ a+++L  +++a+ ++d+A+++ ++++
  gi|488600531|ref|YP_007907002.1| 124 KYEEAEKSISKAIEINSQDSSAWYNLGLLYYAMERFDDAIKCYEKVL 170
                                       79***************************************998876 PP

  == domain 5  score: 37.0 bits;  conditional E-value: 7.5e-12
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       +a++++++A++ +e++l+ dpkn  a  + A++l   g ldeA++l d++ e++pd  ++a
  gi|488600531|ref|YP_007907002.1| 154 YAMERFDDAIKCYEKVLEIDPKNTLAMNNIAIILGRKGKLDEAIELFDKVIEMEPD-NEVA 213
                                       6899****************************************************.6665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.1e-05      0.01      47      75 ..      43      71 ..      26      73 .. 0.82
   2 !   13.5   0.1   0.00014     0.067       5      31 ..      77     103 ..      73     110 .. 0.74
   3 !   39.3   0.2   1.2e-12     6e-10       5      76 ..     111     174 ..     108     175 .. 0.93
   4 !   44.0   0.0   4.3e-14   2.1e-11       3      74 ..     143     206 ..     141     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                            TPR_12 47 tlrnLgrlyralgryeeAlelleealaia 75
                                      + +nLg++++  g +eeA++ + +al+i+
  gi|488600531|ref|YP_007907002.1| 43 AWNNLGIALYDKGMQEEAIQCFVKALEID 71
                                      67889999889999999999998888886 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00014
                            TPR_12   5 alnnlaavlrrlgrydeAlellekale 31 
                                       al nl+ +l+ + r++eA++++e+ l 
  gi|488600531|ref|YP_007907002.1|  77 ALFNLGYALMMMRRFEEAEQCFERILK 103
                                       344888888888888888888888775 PP

  == domain 3  score: 39.3 bits;  conditional E-value: 1.2e-12
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a+nnl+ v + l +y+eA++   ka+ei       +    +++ +nLg ly+a++r+++A++ +e++l+i++
  gi|488600531|ref|YP_007907002.1| 111 AWNNLGYVQYNLRKYEEAEKSISKAIEIN-----SQ---DSSAWYNLGLLYYAMERFDDAIKCYEKVLEIDP 174
                                       799**************************.....33...46899*************************986 PP

  == domain 4  score: 44.0 bits;  conditional E-value: 4.3e-14
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       ++a++nl++++++++r+d+A++++ek+lei      p++ l   +++n+++++ + g+++eA+el+ +++++
  gi|488600531|ref|YP_007907002.1| 143 SSAWYNLGLLYYAMERFDDAIKCYEKVLEID-----PKNTL---AMNNIAIILGRKGKLDEAIELFDKVIEM 206
                                       57899**************************.....99855...8***********************9987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.7e-05     0.018       1      30 [.      43      72 ..      43      76 .. 0.92
   2 !   14.6   0.0   5.2e-05     0.025       1      33 [.      77     109 ..      77     111 .. 0.89
   3 !    9.7   0.1    0.0019      0.93       1      27 [.     111     137 ..     111     144 .. 0.82
   4 !   23.9   0.0   5.6e-08   2.7e-05       1      29 [.     145     173 ..     145     177 .. 0.91
   5 !   16.5   0.0   1.2e-05     0.006       1      34 [.     179     212 ..     179     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                             TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltk 30
                                      a++nL+ +  + G  eeAi+++ ++L++++
  gi|488600531|ref|YP_007907002.1| 43 AWNNLGIALYDKGMQEEAIQCFVKALEIDS 72
                                      79**********************999875 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.2e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                       aL+nL+ +   ++++eeA++++e+ L + + ++
  gi|488600531|ref|YP_007907002.1|  77 ALFNLGYALMMMRRFEEAEQCFERILKFNSNDG 109
                                       79**********************998877666 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0019
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLa 27 
                                       a++nL+ ++ +l++yeeA++   ++++
  gi|488600531|ref|YP_007907002.1| 111 AWNNLGYVQYNLRKYEEAEKSISKAIE 137
                                       79****************987766554 PP

  == domain 4  score: 23.9 bits;  conditional E-value: 5.6e-08
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++nL+ ly ++ ++++Ai++ye++L+++
  gi|488600531|ref|YP_007907002.1| 145 AWYNLGLLYYAMERFDDAIKCYEKVLEID 173
                                       799*********************88876 PP

  == domain 5  score: 16.5 bits;  conditional E-value: 1.2e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                       a +n+a +  r G+ +eAiel+ ++++++ d e+
  gi|488600531|ref|YP_007907002.1| 179 AMNNIAIILGRKGKLDEAIELFDKVIEMEPDNEV 212
                                       579*********************8888877665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0063       3.1      13      42 ..      19      48 ..      17      50 .. 0.92
   2 !   11.9   0.0   0.00069      0.33       2      43 ..      42      83 ..      41      84 .. 0.91
   3 !   16.9   0.0   1.7e-05    0.0084       3      42 ..      77     116 ..      75     118 .. 0.91
   4 !   14.8   0.0   8.1e-05     0.039       3      42 ..     111     150 ..     109     152 .. 0.93
   5 !   23.4   0.0   1.4e-07   6.8e-05       3      37 ..     145     179 ..     143     185 .. 0.93
   6 !   15.9   0.0   3.4e-05     0.017       8      39 ..     184     215 ..     182     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0063
                            TPR_14 13 alGdpdeAiallrralalaPddaeawllla 42
                                      ++G+ d+ i  +++ ++l+P+++ aw  l+
  gi|488600531|ref|YP_007907002.1| 19 EAGNVDDEIMSFKKSVELDPENPSAWNNLG 48
                                      789***********************8886 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00069
                            TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43
                                       a+  l+ al+  G  +eAi+++ +al+ + +  +a++ l+ 
  gi|488600531|ref|YP_007907002.1| 42 SAWNNLGIALYDKGMQEEAIQCFVKALEIDSKYTDALFNLGY 83
                                      688899************************999999998875 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.7e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       al  l+ al+  ++++eA+++++r+l+ + +d  aw  l+
  gi|488600531|ref|YP_007907002.1|  77 ALFNLGYALMMMRRFEEAEQCFERILKFNSNDGGAWNNLG 116
                                       677799******************************8887 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 8.1e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       a+  l+ + ++l++++eA++   +a++ + +d  aw+ l+
  gi|488600531|ref|YP_007907002.1| 111 AWNNLGYVQYNLRKYEEAEKSISKAIEINSQDSSAWYNLG 150
                                       6777999******************************998 PP

  == domain 5  score: 23.4 bits;  conditional E-value: 1.4e-07
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaea 37 
                                       a++ l+ +++a +++d+Ai++++++l+ +P++  a
  gi|488600531|ref|YP_007907002.1| 145 AWYNLGLLYYAMERFDDAIKCYEKVLEIDPKNTLA 179
                                       9******************************9876 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 3.4e-05
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       a +l + G++deAi+l++++++  Pd+++a +
  gi|488600531|ref|YP_007907002.1| 184 AIILGRKGKLDEAIELFDKVIEMEPDNEVAKF 215
                                       5666789*********************9976 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00028      0.14       6      31 ..      45      70 ..      42      72 .. 0.96
   2 !   13.9   0.0   7.5e-05     0.036       7      29 ..      80     102 ..      76     104 .. 0.93
   3 !   14.2   0.1     6e-05     0.029       6      31 ..     113     138 ..     111     141 .. 0.91
   4 !   18.4   0.1   2.9e-06    0.0014       7      31 ..     148     172 ..     147     172 .. 0.97
   5 !   21.1   0.0   4.1e-07    0.0002       4      31 ..     179     206 ..     178     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                            TPR_10  6 nNLanalrqrgrydeAealleealai 31
                                      nNL++al++ g  +eA + + +al+i
  gi|488600531|ref|YP_007907002.1| 45 NNLGIALYDKGMQEEAIQCFVKALEI 70
                                      9***********************97 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.5e-05
                            TPR_10   7 NLanalrqrgrydeAealleeal 29 
                                       NL+ al  ++r++eAe+ +e+ l
  gi|488600531|ref|YP_007907002.1|  80 NLGYALMMMRRFEEAEQCFERIL 102
                                       9*******************987 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 6e-05
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       nNL+ + +++++y+eAe+   +a++i
  gi|488600531|ref|YP_007907002.1| 113 NNLGYVQYNLRKYEEAEKSISKAIEI 138
                                       9****************988888876 PP

  == domain 4  score: 18.4 bits;  conditional E-value: 2.9e-06
                            TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                       NL+ +++++ r+d+A + +e++l+i
  gi|488600531|ref|YP_007907002.1| 148 NLGLLYYAMERFDDAIKCYEKVLEI 172
                                       9**********************97 PP

  == domain 5  score: 21.1 bits;  conditional E-value: 4.1e-07
                            TPR_10   4 slnNLanalrqrgrydeAealleealai 31 
                                       ++nN+a++l + g++deA +l+++++++
  gi|488600531|ref|YP_007907002.1| 179 AMNNIAIILGRKGKLDEAIELFDKVIEM 206
                                       8************************997 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.6e-05     0.017      22      65 ..      32      72 ..      18      75 .. 0.84
   2 !   26.3   0.0   1.7e-08   8.4e-06       2      67 ..      80     142 ..      79     144 .. 0.92
   3 !   35.4   0.0   2.5e-11   1.2e-08       1      67 [.     147     210 ..     147     211 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-05
                            TPR_16 22 aalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65
                                        +++d   P+++ A+++lg a++ +g  +eA++ + +al+ ++
  gi|488600531|ref|YP_007907002.1| 32 KSVELD---PENPSAWNNLGIALYDKGMQEEAIQCFVKALEIDS 72
                                      556667...************************99988887765 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.7e-08
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +l++a++  +++++A+  +e+ lk +   + +  A+++lg + + +  ++eA+  + +a++  +++
  gi|488600531|ref|YP_007907002.1|  80 NLGYALMMMRRFEEAEQCFERILKFN---SNDGGAWNNLGYVQYNLRKYEEAEKSISKAIEINSQD 142
                                       79999999******************...88888*******************9999999887776 PP

  == domain 3  score: 35.4 bits;  conditional E-value: 2.5e-11
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       ++l++++++  ++ddA++ +e +l+ d   P +  A+++ + ++ r+g l+eA++l+++ ++  pd+
  gi|488600531|ref|YP_007907002.1| 147 YNLGLLYYAMERFDDAIKCYEKVLEID---PKNTLAMNNIAIILGRKGKLDEAIELFDKVIEMEPDN 210
                                       89*************************...*****************************99988887 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.36   1.7e+02       6      26 ..      47      67 ..      46      71 .. 0.82
   2 !   14.6   0.1   8.2e-05      0.04       1      28 [.      76     103 ..      76     107 .. 0.95
   3 ?    2.6   0.0      0.54   2.6e+02       5      28 ..     114     137 ..     114     141 .. 0.83
   4 !   23.3   0.0   1.3e-07   6.5e-05       2      32 ..     145     175 ..     144     176 .. 0.94
   5 !   10.8   0.0    0.0013      0.64       6      32 ..     183     209 ..     179     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.36
                                      HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  6 lalsyrklgdtdkAlealerl 26
                                      l+ +++  g  ++A++ + + 
  gi|488600531|ref|YP_007907002.1| 47 LGIALYDKGMQEEAIQCFVKA 67
                                      899999988*******99665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                       dAl++l++++ ++ + ++A + +er++k
  gi|488600531|ref|YP_007907002.1|  76 DALFNLGYALMMMRRFEEAEQCFERILK 103
                                       8***********99***********987 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                       +l++ +++l ++++A +   + i+
  gi|488600531|ref|YP_007907002.1| 114 NLGYVQYNLRKYEEAEKSISKAIE 137
                                       5899****99*****887777665 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                       A y+l+l+y+++ + d+A++ +e++++  P+
  gi|488600531|ref|YP_007907002.1| 145 AWYNLGLLYYAMERFDDAIKCYEKVLEIDPK 175
                                       89*********88**************9997 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       +a  + + g+ d+A+e+++++i+  Pd
  gi|488600531|ref|YP_007907002.1| 183 IAIILGRKGKLDEAIELFDKVIEMEPD 209
                                       677777778*************99888 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 !   11.8   0.0   0.00044      0.21       3      81 ..      21     100 ..      19     101 .. 0.90
   2 !   23.6   0.4   9.1e-08   4.4e-05       2      81 ..      54     134 ..      53     135 .. 0.95
   3 !   34.1   0.9   4.9e-11   2.4e-08       2      81 ..      88     168 ..      87     169 .. 0.95
   4 !   15.5   0.2   3.1e-05     0.015      18      81 ..     138     202 ..     133     203 .. 0.85
   5 ?    2.2   0.0      0.45   2.2e+02       3      23 ..     191     211 ..     189     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00044
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +n ++ i+ + + ++ ++e+p++   l+ +ly  g  ++A++ + ka +++sk   +++ ++ +l  + ++eeA+++
  gi|488600531|ref|YP_007907002.1|  21 GNVDDEIMSFKKSVELDPENPSAWNNLGIALYDKGMQEEAIQCFVKAlEIDSKYTDALFNLGYALMMMRRFEEAEQC 97 
                                       567778888888999999999999999********************99999999********************99 PP

                                       H-S CS
                            ANAPC3  79 Lek 81 
                                       +e+
  gi|488600531|ref|YP_007907002.1|  98 FER 100
                                       987 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 9.1e-08
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       +++ ++Ai ++ ++l+ +++  ++++ l+++l  + ++++A + +++  k ns++ g++  ++ +++ L kyeeA++
  gi|488600531|ref|YP_007907002.1|  54 KGMQEEAIQCFVKALEIDSKYTDALFNLGYALMMMRRFEEAEQCFERIlKFNSNDGGAWNNLGYVQYNLRKYEEAEK 130
                                       678899*********999**********************************************************9 PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                        ++k
  gi|488600531|ref|YP_007907002.1| 131 SISK 134
                                       9877 PP

  == domain 3  score: 34.1 bits;  conditional E-value: 4.9e-11
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       ++++++A+ ++er+l+ ++++  +   l+++ y++ +y++A + ++ka ++ns++  ++y ++  +++++++++Ai+
  gi|488600531|ref|YP_007907002.1|  88 MRRFEEAEQCFERILKFNSNDGGAWNNLGYVQYNLRKYEEAEKSISKAiEINSQDSSAWYNLGLLYYAMERFDDAIK 164
                                       67899**********999999999999************************************************** PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                       ++ek
  gi|488600531|ref|YP_007907002.1| 165 CYEK 168
                                       *998 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 3.1e-05
                                       HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  18 aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                        +++++++ y l+l +y +++++ A++ ++k  ++++k+  +   +A  l   +k++eAi +++k
  gi|488600531|ref|YP_007907002.1| 138 INSQDSSAWYNLGLLYYAMERFDDAIKCYEKVlEIDPKNTLAMNNIAIILGRKGKLDEAIELFDK 202
                                       46777788888899999999999999999999999999999999999999999999999999887 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.45
                                       T-HHHHHHHHHHHH.HHH--H CS
                            ANAPC3   3 nnyknAiflaerllaaetesp 23 
                                       +++++Ai l++++ ++e++++
  gi|488600531|ref|YP_007907002.1| 191 GKLDEAIELFDKVIEMEPDNE 211
                                       567888888888887777766 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   0.00098      0.47      22      62 ..      34      74 ..      31      79 .. 0.89
   2 !   20.3   0.0   9.1e-07   0.00044       7      63 ..      87     143 ..      81     145 .. 0.90
   3 !   22.4   0.0     2e-07   9.9e-05      10      62 ..     124     176 ..     123     181 .. 0.93
   4 !   19.1   0.0   2.3e-06    0.0011       4      66 ..     152     214 ..     149     220 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00098
                             TPR_9 22 lllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62
                                      + l+P+ p+ +   G++l+  G  ++A++++  +l+++ + 
  gi|488600531|ref|YP_007907002.1| 34 VELDPENPSAWNNLGIALYDKGMQEEAIQCFVKALEIDSKY 74
                                      689****************************9999988755 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 9.1e-07
                             TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                         +++e+a ++ er+l ++++d + +   G +++ l  +++A +    +++++ ++ 
  gi|488600531|ref|YP_007907002.1|  87 MMRRFEEAEQCFERILKFNSNDGGAWNNLGYVQYNLRKYEEAEKSISKAIEINSQDS 143
                                       5689*****************************************999999988776 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 2e-07
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                       ++e+a + +   + ++++d + ++  Gll++ ++++  A+++ e  l+++p++
  gi|488600531|ref|YP_007907002.1| 124 KYEEAEKSISKAIEINSQDSSAWYNLGLLYYAMERFDDAIKCYEKVLEIDPKN 176
                                       688999999999***************************************76 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 2.3e-06
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                       ++   e+++ a++++e +l ++P+        +++l + G l +A++ ++  ++++pd++ a 
  gi|488600531|ref|YP_007907002.1| 152 LYYAMERFDDAIKCYEKVLEIDPKNTLAMNNIAIILGRKGKLDEAIELFDKVIEMEPDNEVAK 214
                                       677789****************************************************99885 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.1   5.5e+02       7      24 ..      47      64 ..      44      73 .. 0.81
   2 ?    3.7   0.0      0.13        65       2      24 ..      76      98 ..      75     100 .. 0.89
   3 ?    7.2   0.0     0.011       5.1       7      21 ..     115     129 ..     112     131 .. 0.92
   4 !   13.3   0.1   0.00012     0.061       4      28 ..     146     168 ..     144     176 .. 0.82
   5 !    8.1   0.0    0.0054       2.6      14      25 ..     190     201 ..     189     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.1
                                      HHHHHHHTT-HHHHHHH. CS
                             TPR_3  7 yAaefynkkkyqeArelf 24
                                      ++ ++y+k+  +eA++ f
  gi|488600531|ref|YP_007907002.1| 47 LGIALYDKGMQEEAIQCF 64
                                      67899****999999874 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHHTT-HHHHHHH. CS
                             TPR_3  2 dylysyAaefynkkkyqeArelf 24
                                      d l+ +++++ ++ +++eA++ f
  gi|488600531|ref|YP_007907002.1| 76 DALFNLGYALMMMRRFEEAEQCF 98
                                      67999***************985 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.011
                                       HHHHHHHTT-HHHHH CS
                             TPR_3   7 yAaefynkkkyqeAr 21 
                                       +++++yn  ky+eA+
  gi|488600531|ref|YP_007907002.1| 115 LGYVQYNLRKYEEAE 129
                                       89************7 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHTT-HHHHHHH..HHH CS
                             TPR_3   4 lysyAaefynkkkyqeArelfsYal 28 
                                       +y ++  +y ++++++A+    Y+ 
  gi|488600531|ref|YP_007907002.1| 146 WYNLGLLYYAMERFDDAIKC--YEK 168
                                       9*****************99..654 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0054
                                       TT-HHHHHHH.. CS
                             TPR_3  14 kkkyqeArelfs 25 
                                       k+k++eA+elf+
  gi|488600531|ref|YP_007907002.1| 190 KGKLDEAIELFD 201
                                       9*********98 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0051       2.5       2      30 ..      76     104 ..      75     109 .. 0.92
   2 ?    4.7   0.1     0.066        32      11      32 ..     119     140 ..     114     145 .. 0.81
   3 !   13.0   0.1   0.00017     0.083       4      35 ..     146     177 ..     143     181 .. 0.92
   4 !    7.8   0.0    0.0069       3.3      13      37 ..     189     213 ..     182     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHT-HHHHHHHHHHHHHH CS
                        Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLei 30 
                                       + l+ l ++ + +++++eA ++ +++L+ 
  gi|488600531|ref|YP_007907002.1|  76 DALFNLGYALMMMRRFEEAEQCFERILKF 104
                                       88*************************86 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.066
                                       HHHHT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEP 32 
                                       +y l++Y+eA + +   +ei  
  gi|488600531|ref|YP_007907002.1| 119 QYNLRKYEEAEKSISKAIEINS 140
                                       79**********9999999865 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEPenr 35 
                                        Y l l +y + ++++A ++ + +Lei+P+n 
  gi|488600531|ref|YP_007907002.1| 146 WYNLGLLYYAMERFDDAIKCYEKVLEIDPKNT 177
                                       5999999***********************96 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0069
                                       HHT-HHHHHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQa 37 
                                       + g+ +eA ++ d ++e+EP+n+ a
  gi|488600531|ref|YP_007907002.1| 189 RKGKLDEAIELFDKVIEMEPDNEVA 213
                                       668899****************866 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.9e-05     0.034       6      57 ..      25      76 ..      22      78 .. 0.93
   2 ?    2.1   0.0      0.52   2.5e+02      23      55 ..      76     108 ..      74     115 .. 0.86
   3 !    8.7   0.0    0.0045       2.2      10      43 ..     131     164 ..     123     171 .. 0.90
   4 ?    4.5   0.0     0.089        43      13      64 ..     168     219 ..     164     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-05
                            TPR_20  6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwed 57
                                       e+ ++++ ++ +p++  a  +l  al+ +g +eeA++ +++ l+ d+k++d
  gi|488600531|ref|YP_007907002.1| 25 DEIMSFKKSVELDPENPSAWNNLGIALYDKGMQEEAIQCFVKALEIDSKYTD 76
                                      577889999***************************************9976 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.52
                            TPR_20  23 darldlAlallaagryeeAleqLleilkrdrkw 55 
                                       da ++l  al++  r eeA + + +ilk ++++
  gi|488600531|ref|YP_007907002.1|  76 DALFNLGYALMMMRRFEEAEQCFERILKFNSND 108
                                       78999**************99999999888765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0045
                            TPR_20  10 eleaalaanpddldarldlAlallaagryeeAle 43 
                                       ++ +a++ n +d  a ++l l+++a +r ++A++
  gi|488600531|ref|YP_007907002.1| 131 SISKAIEINSQDSSAWYNLGLLYYAMERFDDAIK 164
                                       678999**************************86 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.089
                            TPR_20  13 aalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkql 64 
                                       + l+ +p++  a+ + A  l  +g+ +eA+e++ ++++ + + e  +  kq+
  gi|488600531|ref|YP_007907002.1| 168 KVLEIDPKNTLAMNNIAIILGRKGKLDEAIELFDKVIEMEPDNEVAKFNKQF 219
                                       667889*************************999999888777766666666 PP

>> Paf67  RNA polymerase I-associated factor PAF67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   7.9e-07   0.00038     161     199 ..      72     110 ..      57     138 .. 0.73
   2 !   10.9   0.0   0.00035      0.17     159     192 ..     138     171 ..     121     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.9e-07
                             Paf67 161 aahvsllYyvGfaylmlrrYkDAirtlsqillyisrtkq 199
                                       + +  +l+ +G+a +m+rr+++A +++++il + s    
  gi|488600531|ref|YP_007907002.1|  72 SKYTDALFNLGYALMMMRRFEEAEQCFERILKFNSNDGG 110
                                       55677899***********************99887643 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00035
                             Paf67 159 vpaahvsllYyvGfaylmlrrYkDAirtlsqill 192
                                       + +   s+ Y +G+ y  ++r+ DAi++ +++l 
  gi|488600531|ref|YP_007907002.1| 138 INSQDSSAWYNLGLLYYAMERFDDAIKCYEKVLE 171
                                       556677999********************99985 PP

>> DUF5112  Domain of unknown function (DUF5112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.2   0.00019      0.09      23      70 ..      60     107 ..      53     109 .. 0.87
   2 ?    5.3   0.1     0.024        12      36      67 ..     107     138 ..     104     145 .. 0.84
   3 !    7.2   0.1    0.0066       3.2      20      66 ..     125     171 ..     114     178 .. 0.89
   4 ?    4.1   0.0     0.058        28      26      72 ..     165     212 ..     160     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                           DUF5112  23 AekalklaegysagkaeAlNnlaFvaiarmdyeeaekllkeveektdn 70 
                                       A + +  a + ++++++Al nl++  ++  ++eeae++++++ +  +n
  gi|488600531|ref|YP_007907002.1|  60 AIQCFVKALEIDSKYTDALFNLGYALMMMRRFEEAEQCFERILKFNSN 107
                                       566677788889999***************************998877 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                           DUF5112  36 gkaeAlNnlaFvaiarmdyeeaekllkeveek 67 
                                       +   A Nnl++v+    +yeeaek ++++ e 
  gi|488600531|ref|YP_007907002.1| 107 NDGGAWNNLGYVQYNLRKYEEAEKSISKAIEI 138
                                       55679*******************99987765 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0066
                           DUF5112  20 klaAekalklaegysagkaeAlNnlaFvaiarmdyeeaekllkevee 66 
                                       +  Aek+++ a + +++ + A  nl+ +  a  ++++a k++++v e
  gi|488600531|ref|YP_007907002.1| 125 YEEAEKSISKAIEINSQDSSAWYNLGLLYYAMERFDDAIKCYEKVLE 171
                                       55799**************************99***********987 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.058
                           DUF5112  26 alklaegysagkaeAlNnlaFvaiarmdyeeaekllkevee.ktdnei 72 
                                        ++ + + + +++ A+Nn+a +   + + +ea +l+++v e + dne+
  gi|488600531|ref|YP_007907002.1| 165 CYEKVLEIDPKNTLAMNNIAIILGRKGKLDEAIELFDKVIEmEPDNEV 212
                                       55666666777888***********************99772567876 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.019       9.4     159     247 ..      20     108 ..      15     113 .. 0.77
   2 !   14.9   0.1   2.5e-05     0.012      17      97 ..     118     197 ..     111     203 .. 0.73
   3 ?   -0.6   0.0       1.3   6.1e+02     157     181 ..     188     212 ..     178     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
                            TPR_15 159 egqtdaAlrdyreAlalapdsselraallWlliDlgrrae.LrellkawkaraesdasLwgplaaAlllLgrpkkAL 234
                                       +g+ d+ +  +++ ++l+p++ ++ ++l  +l D g ++e ++  +ka++ ++ + ++    l+ Al+++ r ++A 
  gi|488600531|ref|YP_007907002.1|  20 AGNVDDEIMSFKKSVELDPENPSAWNNLGIALYDKGMQEEaIQCFVKALEIDS-KYTDALFNLGYALMMMRRFEEAE 95 
                                       56666777788999999999999999999999999999985555566666553.33333334788999999999999 PP

                            TPR_15 235 eylrkqakenrkd 247
                                       + +++ +k n++d
  gi|488600531|ref|YP_007907002.1|  96 QCFERILKFNSND 108
                                       9999999999888 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.5e-05
                            TPR_15  17 llykqgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliel.lydae 92 
                                       + y+ +++++A + + + a ++  s+d   W++l+ L  a++++d+a+k y++ l+++  +   ++++  +  ++ +
  gi|488600531|ref|YP_007907002.1| 118 VQYNLRKYEEAEKSISK-AIEI-NSQDSSAWYNLGLLYYAMERFDDAIKCYEKVLEIDPKNTLAMNNIAIIlGRKGK 192
                                       66888888888888844.4445.388889999999999999999999999999999887776666665555346666 PP

                            TPR_15  93 pkeaa 97 
                                        +ea+
  gi|488600531|ref|YP_007907002.1| 193 LDEAI 197
                                       66665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                            TPR_15 157 rqegqtdaAlrdyreAlalapdsse 181
                                        ++g+ d+A++++ ++++++pd++ 
  gi|488600531|ref|YP_007907002.1| 188 GRKGKLDEAIELFDKVIEMEPDNEV 212
                                       57899999*********99999764 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.018       8.8     214     241 ..      54      81 ..      10      84 .. 0.85
   2 !    7.9   0.1    0.0038       1.8     211     261 ..      85     134 ..      82     143 .. 0.83
   3 ?    4.5   0.1     0.041        20     211     241 ..     119     149 ..     113     155 .. 0.88
   4 ?    4.4   0.0     0.043        21     213     256 ..     155     198 ..     149     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.018
                                       TT-HHHHHHHHHHHHHH-TT-HHHHHHH CS
                        Coatomer_E 214 lgryeeAeslLkeaLdkdakdeetLiNl 241
                                        g  eeA +   +aL+ d+k+ ++L Nl
  gi|488600531|ref|YP_007907002.1|  54 KGMQEEAIQCFVKALEIDSKYTDALFNL 81 
                                       556799*********************8 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0038
                                       HHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHH CS
                        Coatomer_E 211 slllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsq 261
                                        +++ r+eeAe+  +  L+ +++d  +  Nl  +  +l k  e  e+++s+
  gi|488600531|ref|YP_007907002.1|  85 LMMMRRFEEAEQCFERILKFNSNDGGAWNNLGYVQYNLRKY-EEAEKSISK 134
                                       699*************************9999888888887.555667665 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.041
                                       HHHTT-HHHHHHHHHHHHHH-TT-HHHHHHH CS
                        Coatomer_E 211 slllgryeeAeslLkeaLdkdakdeetLiNl 241
                                       +  l +yeeAe+++ +a++ +++d  +  Nl
  gi|488600531|ref|YP_007907002.1| 119 QYNLRKYEEAEKSISKAIEINSQDSSAWYNL 149
                                       567899******************9998887 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.043
                                       HTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                        Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                       +++r+++A +  ++ L+ d+k+  ++ N+ +     gk +e++e
  gi|488600531|ref|YP_007907002.1| 155 AMERFDDAIKCYEKVLEIDPKNTLAMNNIAIILGRKGKLDEAIE 198
                                       56777777777777777777777777777777777777666654 PP

>> BTAD  Bacterial transcriptional activator 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      59     121 ..       5      66 ..       2      73 .. 0.87
   2 ?    4.3   0.0       0.1        49      75     122 ..     122     169 ..     110     185 .. 0.84
   3 ?   -1.0   0.0       4.3   2.1e+03      65      96 ..     180     211 ..     171     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  59 elrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                       e++l+a e+ +++ l+ G  ++ +   ++ v+++P +  ++  l  Al+  G q+eA++ + +
  gi|488600531|ref|YP_007907002.1|   5 EEKLSA-EEWFKKGLEAGNVDDEIMSFKKSVELDPENPSAWNNLGIALYDKGMQEEAIQCFVK 66 
                                       555555.5556779********************************************98865 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       l ++eea +  +++++ +  +  ++  l + +++++r  +A++ Ye++
  gi|488600531|ref|YP_007907002.1| 122 LRKYEEAEKSISKAIEINSQDSSAWYNLGLLYYAMERFDDAIKCYEKV 169
                                       5567788888888899999999999999999**************987 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-H CS
                              BTAD  65 lealaeaelrlGraeealaelealvaehPlrE 96 
                                       +  +a  + r G+ +ea++  ++ ++++P +E
  gi|488600531|ref|YP_007907002.1| 180 MNNIAIILGRKGKLDEAIELFDKVIEMEPDNE 211
                                       55555556677888888888888888888888 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.7   6.6e-06    0.0032     122     194 ..     137     216 ..      48     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-06
                                       HHHHHTT--.........HHHHHHHHHHHHHHHHHTT-HHHHHH.HHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS- CS
                              SNAP 122 elyekelgd.........lekAieaYekAaelyeqeeakalank.cllkvAelsaelekyekAieiyekvakkslen 188
                                       e+  +   d         l  A+e +++A + ye+       n+ ++ ++A +  +++k+++Aie+++kv++   +n
  gi|488600531|ref|YP_007907002.1| 137 EINSQ---DssawynlglLYYAMERFDDAIKCYEKVLEIDPKNTlAMNNIAIILGRKGKLDEAIELFDKVIEMEPDN 210
                                       33333...123344455566788888888888887764444444156789*************************** PP

                                       TTTGGG CS
                              SNAP 189 nllkys 194
                                       ++ k++
  gi|488600531|ref|YP_007907002.1| 211 EVAKFN 216
                                       ****98 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.018       8.9     259     294 ..      19      49 ..       3      58 .. 0.80
   2 ?    3.6   0.0     0.067        32     267     297 ..      56      86 ..      50      97 .. 0.80
   3 !    7.3   0.4     0.005       2.4     268     310 ..      91     132 ..      85     168 .. 0.52
   4 ?   -1.3   0.0       2.1     1e+03     266     289 ..     157     180 ..     153     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                                       CCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCH CS
                               FAT 259 qkldwseekieeilqsysaateidpswykawhtwal 294
                                       +       +++++  s+++++e+dp+   aw++++ 
  gi|488600531|ref|YP_007907002.1|  19 E-----AGNVDDEIMSFKKSVELDPENPSAWNNLGI 49 
                                       3.....345999********************9975 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.067
                                       .-SSCCHHHHCCHHCTCCCHSTTCCCCHHHH CS
                               FAT 267 kieeilqsysaateidpswykawhtwalfnf 297
                                        +ee+ q++ +a eid + ++a ++++++  
  gi|488600531|ref|YP_007907002.1|  56 MQEEAIQCFVKALEIDSKYTDALFNLGYALM 86 
                                       479999***************9999988765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.005
                                       -SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHHSSSS CS
                               FAT 268 ieeilqsysaateidpswykawhtwalfnfevvskeeeqkeee 310
                                       +ee++q++ +  +++ +   aw++++++  +  + ee +k+ +
  gi|488600531|ref|YP_007907002.1|  91 FEEAEQCFERILKFNSNDGGAWNNLGYVQYNLRKYEEAEKS-I 132
                                       56666666666666666666666666554443333333322.2 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.1
                                       ..-SSCCHHHHCCHHCTCCCHSTT CS
                               FAT 266 ekieeilqsysaateidpswykaw 289
                                       e+++++ ++y +  eidp+ + a 
  gi|488600531|ref|YP_007907002.1| 157 ERFDDAIKCYEKVLEIDPKNTLAM 180
                                       5689999*****999999877665 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 !    9.5   0.0    0.0016      0.77      48      98 ..      54     100 ..      49     111 .. 0.81
   2 ?    3.9   0.0     0.082        40      92     115 ..     155     178 ..     125     187 .. 0.79
   3 ?    4.6   0.1      0.05        24      96     116 ..     159     179 ..     152     225 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHH CS
                       TOM20_plant  48 kqmiqdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfek 98 
                                       k m ++ai+ + +al id k  dal+ +g a +   ++    eea++ fe+
  gi|488600531|ref|YP_007907002.1|  54 KGMQEEAIQCFVKALEIDSKYTDALFNLGYALMMMRRF----EEAEQCFER 100
                                       77999************************998765544....555555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHHHHHH-TT-HH CS
                       TOM20_plant  92 akenfekatqffqqavdedPdndl 115
                                       a e f+ a +++++  + dP+n+l
  gi|488600531|ref|YP_007907002.1| 155 AMERFDDAIKCYEKVLEIDPKNTL 178
                                       556777777777777777777765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHH-TT-HHH CS
                       TOM20_plant  96 fekatqffqqavdedPdndly 116
                                       f+ a +++++  + dP+n+l 
  gi|488600531|ref|YP_007907002.1| 159 FDDAIKCYEKVLEIDPKNTLA 179
                                       444444444444444444432 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       9.8   4.7e+03      19      29 ..      10      20 ..       8      22 .. 0.76
   2 ?    1.0   0.0       1.3   6.3e+02       2      25 ..      43      66 ..      42      71 .. 0.82
   3 ?    6.4   0.5     0.024        12      10      29 ..      85     104 ..      83     106 .. 0.84
   4 ?   -1.3   0.0         7   3.4e+03      13      21 ..     122     130 ..     111     137 .. 0.75
   5 ?    1.4   0.1      0.97   4.7e+02      12      28 ..     155     171 ..     151     173 .. 0.80
   6 !   14.9   0.1     5e-05     0.024       9      28 ..     186     205 ..     179     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 9.8
                               PPR 19 AlelfkeMkek 29
                                      A+e+fk+ +e 
  gi|488600531|ref|YP_007907002.1| 10 AEEWFKKGLEA 20
                                      89999986665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.3
                               PPR  2 tynslIsgycknGkleeAlelfke 25
                                      ++n l  ++  +G+ eeA+++f +
  gi|488600531|ref|YP_007907002.1| 43 AWNNLGIALYDKGMQEEAIQCFVK 66
                                      689998899999999999999965 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.024
                               PPR  10 ycknGkleeAlelfkeMkek 29 
                                       +   +++eeA+++f+++++ 
  gi|488600531|ref|YP_007907002.1|  85 LMMMRRFEEAEQCFERILKF 104
                                       566789**********9886 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 7
                               PPR  13 nGkleeAle 21 
                                        +k+eeA++
  gi|488600531|ref|YP_007907002.1| 122 LRKYEEAEK 130
                                       678999986 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.97
                               PPR  12 knGkleeAlelfkeMke 28 
                                          ++++A++++++ +e
  gi|488600531|ref|YP_007907002.1| 155 AMERFDDAIKCYEKVLE 171
                                       56799******998765 PP

  == domain 6  score: 14.9 bits;  conditional E-value: 5e-05
                               PPR   9 gycknGkleeAlelfkeMke 28 
                                        ++++Gkl+eA+elf++ +e
  gi|488600531|ref|YP_007907002.1| 186 ILGRKGKLDEAIELFDKVIE 205
                                       689*************9887 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 !   17.2   3.5   8.3e-06     0.004      23     114 ..      84     185 ..      48     187 .. 0.74
   2 ?    2.8   0.0      0.24   1.2e+02       3      44 ..     164     207 ..     162     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.3e-06
                      SRP_TPR_like  23 aliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkv...eaee.kvkvlksqvlYrlgsye 92 
                                       al+ + ++eea +  +      + ++       Yv Y l+ky++a k ++k+   ++++  +   +  ++Y ++ ++
  gi|488600531|ref|YP_007907002.1|  84 ALMMMRRFEEAEQCFERILkfnSNDGGAWNNLGYVQYNLRKYEEAEKSISKAieiNSQDsSAWYNLGLLYYAMERFD 160
                                       888999999988777766511133445677889************9988764222455523334456788899**** PP

                      SRP_TPR_like  93 kA...YklLskekkedelvvNllAv 114
                                       +A   Y+ + + + ++ l++N  A+
  gi|488600531|ref|YP_007907002.1| 161 DAikcYEKVLEIDPKNTLAMNNIAI 185
                                       **77777777888888888887775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                      SRP_TPR_like   3 eeyekilrlegkelkkfkvvali..klekyeeaLkllkkgsals 44 
                                       ++yek+l+++ k+      +a+i  + +k +ea++l +k  +++
  gi|488600531|ref|YP_007907002.1| 164 KCYEKVLEIDPKNTLAMNNIAIIlgRKGKLDEAIELFDKVIEME 207
                                       789******99999999888888556789999999998876554 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.031        15      16      82 ..      53     119 ..      47     141 .. 0.63
   2 !   13.3   0.3   6.2e-05      0.03     168     255 ..     121     206 ..     114     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.031
                                       HHTHHHHHHHHHHH...HGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT CS
                             NARP1  16 eagkleeAlehLee...kekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak 82 
                                       ++g+ eeA++ + +    +++ +D    + + +  l+ + r+eeAe+ +e++l+ n+++   +++l  ++
  gi|488600531|ref|YP_007907002.1|  53 DKGMQEEAIQCFVKaleIDSKYTDA---LFNLGYALMMMRRFEEAEQCFERILKFNSNDGGAWNNLGYVQ 119
                                       5666666666665522233444443...345577788899999999999999999988776666665555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.2e-05
                                       TTTTSSSSTTGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHH CS
                             NARP1 168 slktsgklsesdnedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkk 244
                                       +l++ +++++s ++  e +++ +   + y l   y  +++ + A+++ +k +e +p+ +  + + a il ++G l++
  gi|488600531|ref|YP_007907002.1| 121 NLRKYEEAEKSISKAIEINSQDS--SAWYNLGLLYYAMERFDDAIKCYEKVLEIDPKNTLAMNNIAIILGRKGKLDE 195
                                       55666666666655555555555..456889999999**************************************** PP

                                       HHHHHHHHHHC CS
                             NARP1 245 Aaevmeearkl 255
                                       A+e+ ++  ++
  gi|488600531|ref|YP_007907002.1| 196 AIELFDKVIEM 206
                                       ****9997666 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0021         1      10      21 ..      35      46 ..      31      47 .. 0.87
   2 ?   -2.1   0.0       7.4   3.6e+03       8      21 ..     101     114 ..      99     115 .. 0.67
   3 ?    5.3   0.1     0.035        17       5      21 ..     132     148 ..     130     149 .. 0.90
   4 ?    1.8   0.0      0.46   2.2e+02       6      15 ..     167     176 ..     167     176 .. 0.91
   5 ?    0.2   0.0       1.4     7e+02       3      15 ..     198     210 ..     196     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                                      HH-TT-CHHHHH CS
                              PPTA 10 ekdpkNYsaWny 21
                                      e+dp N saWn 
  gi|488600531|ref|YP_007907002.1| 35 ELDPENPSAWNN 46
                                      68********96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.4
                                       HHHH-TT-CHHHHH CS
                              PPTA   8 liekdpkNYsaWny 21 
                                       +++ +  +  aWn 
  gi|488600531|ref|YP_007907002.1| 101 ILKFNSNDGGAWNN 114
                                       56666666679995 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.035
                                       HHHHHHH-TT-CHHHHH CS
                              PPTA   5 tekliekdpkNYsaWny 21 
                                       ++k+ie + ++ saW+ 
  gi|488600531|ref|YP_007907002.1| 132 ISKAIEINSQDSSAWYN 148
                                       689************85 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.46
                                       HHHHHH-TT- CS
                              PPTA   6 ekliekdpkN 15 
                                       ek++e dpkN
  gi|488600531|ref|YP_007907002.1| 167 EKVLEIDPKN 176
                                       689******9 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 1.4
                                       HHHHHHHHH-TT- CS
                              PPTA   3 eltekliekdpkN 15 
                                       el +k+ie+ p+N
  gi|488600531|ref|YP_007907002.1| 198 ELFDKVIEMEPDN 210
                                       677899******9 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.1e-05      0.02      18      32 ..     188     202 ..     187     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-05
                                       HHTS-HHHHHHHHHH CS
                             PPR_1  18 CkaGrvdeAfelfde 32 
                                        ++G++deA+elfd+
  gi|488600531|ref|YP_007907002.1| 188 GRKGKLDEAIELFDK 202
                                       59***********97 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 !   10.5   0.0     0.001      0.49      13      61 ..      48      93 ..      45     105 .. 0.85
   2 ?    0.2   0.0       1.7   8.4e+02      24      50 ..      93     119 ..      90     139 .. 0.74
   3 ?    2.0   0.0      0.46   2.2e+02      22      65 ..     125     165 ..     113     178 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.001
                          Rapsyn_N 13 GLklyesndtekalrvWrkvLkktsdregkfrvLGcLitahsemGkyke 61
                                      G+ ly++  +e+a++ + k+L+  s+  + +  LG+   a + m ++ e
  gi|488600531|ref|YP_007907002.1| 48 GIALYDKGMQEEAIQCFVKALEIDSKYTDALFNLGY---ALMMMRRFEE 93
                                      899*************************99999998...4455666655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.7
                          Rapsyn_N  24 kalrvWrkvLkktsdregkfrvLGcLi 50 
                                       +a + + ++Lk  s+ +g ++ LG++ 
  gi|488600531|ref|YP_007907002.1|  93 EAEQCFERILKFNSNDGGAWNNLGYVQ 119
                                       566778889999999999999999864 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.46
                          Rapsyn_N  22 tekalrvWrkvLkktsdregkfrvLGcLitahsemGkykealef 65 
                                        e+a +   k+++  s+ +  +  LG L+ a   m ++ +a++ 
  gi|488600531|ref|YP_007907002.1| 125 YEEAEKSISKAIEINSQDSSAWYNLGLLYYA---MERFDDAIKC 165
                                       5555666667777777777777777777776...5566666664 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.53   2.6e+02      37      80 ..      42      86 ..      24      91 .. 0.74
   2 ?    2.9   0.1      0.16        77     120     138 ..      82     100 ..      47     108 .. 0.74
   3 ?    6.6   0.2     0.012       5.6      31      64 ..     138     171 ..     117     183 .. 0.80
   4 ?    0.1   0.0       1.1   5.5e+02      38      64 ..     179     205 ..     171     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.53
                                      HHHHHHHHHHHHCT-HHHHHHHHHT.CCCC--SHHHHHHHHHHHH CS
                              RPN7 37 rakldlaehYlkigdleeAlkaysr.ireyctslkhkidmllnli 80
                                       a+++l+   ++ g  eeA++++ + + +++  +++ +++ ++l+
  gi|488600531|ref|YP_007907002.1| 42 SAWNNLGIALYDKGMQEEAIQCFVKaLEIDSKYTDALFNLGYALM 86
                                      567777777888899999999999945556777888888877776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                                       HHHHHHTT-HHHHHHHHCT CS
                              RPN7 120 GlallairkfkeAaellld 138
                                       G al+++r+f+eA +++  
  gi|488600531|ref|YP_007907002.1|  82 GYALMMMRRFEEAEQCFER 100
                                       5567777777777777654 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                                       -HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  31 gkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                       + ++   a+++l+  Y+ +  ++ A+k+y++++e
  gi|488600531|ref|YP_007907002.1| 138 INSQDSSAWYNLGLLYYAMERFDDAIKCYEKVLE 171
                                       4555567899********************9876 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrire 64 
                                       a++++a    + g+l+eA++++ +++e
  gi|488600531|ref|YP_007907002.1| 179 AMNNIAIILGRKGKLDEAIELFDKVIE 205
                                       6667777777889********999776 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00077      0.37      61     106 ..      59     104 ..      56     106 .. 0.92
   2 ?   -1.7   0.0       6.1     3e+03       8      32 ..     190     214 ..     184     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00077
                            DUF627  61 asvecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                        +++cf +a e+ + y+  Lf+l+  l   + +++a +  +r L++
  gi|488600531|ref|YP_007907002.1|  59 EAIQCFVKALEIDSKYTDALFNLGYALMMMRRFEEAEQCFERILKF 104
                                       59**********************************9999988876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.1
                            DUF627   8 rgnhikALeiiedlisrhgedeksa 32 
                                       +g   +A+e+++++i  + ++e+++
  gi|488600531|ref|YP_007907002.1| 190 KGKLDEAIELFDKVIEMEPDNEVAK 214
                                       6666789999999998887776655 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.12        59      85     150 ..      80     137 ..      45     153 .. 0.55
   2 ?    3.8   0.0     0.065        32      35     109 ..      96     172 ..      90     183 .. 0.69
   3 ?    4.4   0.0     0.042        20      81     117 ..     178     214 ..     144     227 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.12
                          TPR_MalT  85 qqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGie 150
                                        ++  l++  r++eA++ +e++l++    g++    ++     l+ ++y   + eeAe+   ++ie
  gi|488600531|ref|YP_007907002.1|  80 NLGYALMMMRRFEEAEQCFERILKFNSNDGGA----WN----NLGYVQYNLRKYEEAEKSISKAIE 137
                                       23333333344556666666665555444444....22....224445555555555555555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.065
                          TPR_MalT  35 dllar.iaatavlGeasllqGdleaAlqalqeaekl.arqadslhvallallqqaeilvaqGrLheAletyeqalql 109
                                       + ++r +  +++ G+a+   G ++  l+ ++eaek  +++++   +   a + ++ ++ a  r+++A++ ye+ l+ 
  gi|488600531|ref|YP_007907002.1|  96 QCFERiLKFNSNDGGAWNNLGYVQYNLRKYEEAEKSiSKAIEINSQDSSAWYNLGLLYYAMERFDDAIKCYEKVLEI 172
                                       55555334567778888889999999999999997524444444444555566677777777999999999998875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.042
                          TPR_MalT  81 lallqqaeilvaqGrLheAletyeqalqlateqglqq 117
                                       la+  +a il  +G+L+eA+e++ + +++ ++++ ++
  gi|488600531|ref|YP_007907002.1| 178 LAMNNIAIILGRKGKLDEAIELFDKVIEMEPDNEVAK 214
                                       4556667777888888888888888888877776665 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       2.2     1e+03       6      26 ..      44      64 ..      40      66 .. 0.78
   2 ?    0.5   0.3       1.5   7.1e+02      13      29 ..      85     101 ..      83     106 .. 0.82
   3 ?    0.3   0.1       1.7   8.4e+02      13      28 ..     153     168 ..     147     170 .. 0.86
   4 ?    9.6   0.0    0.0022       1.1       2      28 ..     176     202 ..     175     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.2
                             PPR_2  6 yNtlIsglckkgkveeAfklf 26
                                      +N l  +l+ kg+ eeA++ f
  gi|488600531|ref|YP_007907002.1| 44 WNNLGIALYDKGMQEEAIQCF 64
                                      55555578899999***9998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.5
                             PPR_2  13 lckkgkveeAfklfneM 29 
                                       l+  +++eeA + f+  
  gi|488600531|ref|YP_007907002.1|  85 LMMMRRFEEAEQCFERI 101
                                       677899********975 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.7
                             PPR_2  13 lckkgkveeAfklfne 28 
                                       ++  +++++A+k +++
  gi|488600531|ref|YP_007907002.1| 153 YYAMERFDDAIKCYEK 168
                                       677899******9985 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0022
                             PPR_2   2 dvvtyNtlIsglckkgkveeAfklfne 28 
                                       ++ ++N +   l +kgk++eA++lf++
  gi|488600531|ref|YP_007907002.1| 176 NTLAMNNIAIILGRKGKLDEAIELFDK 202
                                       7788888888899************96 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.93   4.5e+02       2      20 ..      42      60 ..      41      64 .. 0.86
   2 ?    2.9   0.0      0.46   2.2e+02       3      26 .]      77     100 ..      76     100 .. 0.80
   3 ?    1.5   0.0       1.4   6.7e+02       3      20 ..     145     162 ..     143     163 .. 0.88
   4 ?   -0.6   0.0       6.6   3.2e+03       9      25 ..     185     201 ..     184     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.93
                             TPR_4  2 rallaLArallalGdldeA 20
                                       a  +L+ al++ G  +eA
  gi|488600531|ref|YP_007907002.1| 42 SAWNNLGIALYDKGMQEEA 60
                                      67789*********99999 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.46
                             TPR_4   3 allaLArallalGdldeAraller 26 
                                       al +L+ al    +++eA++ +er
  gi|488600531|ref|YP_007907002.1|  77 ALFNLGYALMMMRRFEEAEQCFER 100
                                       56777777777779*****99997 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.4
                             TPR_4   3 allaLArallalGdldeA 20 
                                       a ++L+ +++a  ++d+A
  gi|488600531|ref|YP_007907002.1| 145 AWYNLGLLYYAMERFDDA 162
                                       889*******99999888 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 6.6
                             TPR_4   9 rallalGdldeAralle 25 
                                         l + G ldeA +l++
  gi|488600531|ref|YP_007907002.1| 185 IILGRKGKLDEAIELFD 201
                                       56667799****88765 PP

>> Dynein_light  Dynein light chain type 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       3.7   1.8e+03       9      53 ..       2      45 ..       1      46 [. 0.79
   2 ?    7.2   0.0     0.013       6.4      10      32 ..      53      73 ..      49     113 .. 0.78
   3 ?    1.0   0.1       1.1   5.3e+02      15      46 ..     194     222 ..     189     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.7
                                      E-HHHHHHHHHHHHHHHHH-SSHH..HHHHHHHH.HHHHHH-S-EE CS
                      Dynein_light  9 mseemqeeaielakealekfkkekekdiaayikk.eldkkygptWh 53
                                      msee +  a e++k+ le  ++++  +i ++ k  eld +  ++W+
  gi|488600531|ref|YP_007907002.1|  2 MSEEEKLSAEEWFKKGLEAGNVDD--EIMSFKKSvELDPENPSAWN 45
                                      889999999999999999877777..88777776788888777785 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                                      -HHHHHHHHHHHHHHHHH-SSHH CS
                      Dynein_light 10 seemqeeaielakealekfkkek 32
                                      ++ mqeeai+++ +ale   ++k
  gi|488600531|ref|YP_007907002.1| 53 DKGMQEEAIQCFVKALEI--DSK 73
                                      678*************85..323 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHH-SSHH..HHHHHHHHHHHH CS
                      Dynein_light  15 eeaielakealekfkkekekdiaayikkeldk 46 
                                       +eaiel+ + +e  + +  +++a++ k+ l +
  gi|488600531|ref|YP_007907002.1| 194 DEAIELFDKVIEM-EPD--NEVAKFNKQFLIQ 222
                                       6899999999976.333..5999999988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 1360.94
//
Query:       gi|488600532|ref|YP_007907003.1|  [L=302]
Description: hypothetical protein Asulf_01006 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   21.5   5.8        3.1    8.3   0.1    5.3  4  TPR_8     Tetratricopeptide repeat
    0.00065   20.2   5.4      0.047   14.2   1.0    3.9  4  TPR_19    Tetratricopeptide repeat
     0.0035   17.6   0.0      0.056   13.7   0.1    2.6  3  CHASE8    Periplasmic sensor domain
     0.0061   16.8   2.4         10    6.5   0.1    4.1  4  TPR_12    Tetratricopeptide repeat
     0.0083   16.8   0.4        2.1    9.1   0.0    3.9  5  TPR_16    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.081   13.6   0.7         31    5.5   0.0    4.5  4  TPR_6     Tetratricopeptide repeat
      0.087   13.0  18.5       0.24   11.6   0.5    5.9  8  TPR_2     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.23     6e+02      13      24 ..     150     161 ..     149     164 .. 0.84
   2 !    7.6   0.3    0.0019       4.9      11      33 ..     185     207 ..     175     208 .. 0.85
   3 ?    2.2   0.0       0.1   2.6e+02      10      25 ..     221     236 ..     217     243 .. 0.54
   4 !    8.3   0.1    0.0012       3.1       9      27 ..     279     297 ..     273     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
                                       HTT-HHHHHHHH CS
                             TPR_8  13 klgdyeeAkeyy 24 
                                       ++gd+e A+  +
  gi|488600532|ref|YP_007907003.1| 150 EKGDFERAINIL 161
                                       68******9876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0019
                                       HHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  11 ylklgdyeeAkeyyekaleldpd 33 
                                       y++l+dy +A+  +++al  +++
  gi|488600532|ref|YP_007907003.1| 185 YMELKDYLAAEIQLKEALNFAEN 207
                                       9*****************98887 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.1
                                       HHHHTT-HHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyye 25 
                                       ++++++++e A++ +e
  gi|488600532|ref|YP_007907003.1| 221 ALKNQNKFEDAMKQLE 236
                                       4455555555555544 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0012
                                       HHHHHTT-HHHHHHHHHHH CS
                             TPR_8   9 siylklgdyeeAkeyyeka 27 
                                       +i  k gd e A +++eka
  gi|488600532|ref|YP_007907003.1| 279 RIAVKIGDSELARKCLEKA 297
                                       578899************9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         2   5.2e+03       2      11 ..     114     123 ..     113     128 .. 0.78
   2 ?    4.3   0.0     0.023        59       4      17 ..     151     164 ..     149     183 .. 0.67
   3 !   14.2   1.0   1.8e-05     0.047       6      55 ..     197     242 ..     185     255 .. 0.79
   4 ?    0.6   0.1      0.33   8.5e+02       5      21 ..     265     281 ..     261     299 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2
                            TPR_19   2 laegdyaeAl 11 
                                       +++gdy+ A+
  gi|488600532|ref|YP_007907003.1| 114 IDDGDYETAA 123
                                       6789999997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.023
                            TPR_19   4 egdyaeAlalleqa 17 
                                        gd+++A+++l+++
  gi|488600532|ref|YP_007907003.1| 151 KGDFERAINILSRL 164
                                       57777777777773 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.8e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                       ++ eAl++ e+    d +  e+++lL +al +++ +++A++ L+++  + 
  gi|488600532|ref|YP_007907003.1| 197 QLKEALNFAEN----DLDVKEIKMLLYDALKNQNKFEDAMKQLETIDTSS 242
                                       55566666666....6668999**********************997665 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.33
                            TPR_19   5 gdyaeAlalleqalqed 21 
                                       +d ++Al+ + +a+  +
  gi|488600532|ref|YP_007907003.1| 265 KDVDNALEKYDAAYRIA 281
                                       67777777777776554 PP

>> CHASE8  Periplasmic sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.3   8.4e+03      32      44 ..      43      55 ..      36      68 .. 0.53
   2 ?    0.3   0.0      0.33   8.4e+02      28      48 ..     153     173 ..     152     178 .. 0.87
   3 !   13.7   0.1   2.2e-05     0.056      31      81 ..     230     280 ..     228     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.3
                            CHASE8 32 AreiLaaLkaepe 44
                                      A++ L +Lk +p+
  gi|488600532|ref|YP_007907003.1| 43 AGKYLVMLKDRPK 55
                                      5555555555443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.33
                            CHASE8  28 DaaaAreiLaaLkaepeiaaa 48 
                                       D + A +iL+ Lk+++ i++ 
  gi|488600532|ref|YP_007907003.1| 153 DFERAINILSRLKQNEVIREL 173
                                       778999*********999875 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2.2e-05
                            CHASE8  31 aAreiLaaLkaepeiaaaavydaegkllaeyaresseakeeleallaslll 81 
                                        A + L+++ ++  i++ +v+ ++ kll ++a++s++ ++ le+  a +++
  gi|488600532|ref|YP_007907003.1| 230 DAMKQLETIDTSSPIEELKVLREKAKLLLSWAEKSKDVDNALEKYDAAYRI 280
                                       58899*********************************9999888777665 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      0.96   2.5e+03      16      41 ..      50      75 ..      43      79 .. 0.74
   2 ?    1.4   0.0      0.16   4.1e+02      29      68 ..     123     161 ..     117     165 .. 0.74
   3 ?    5.1   0.1     0.011        28      11      34 ..     183     206 ..     173     213 .. 0.60
   4 !    6.5   0.1     0.004        10      15      46 ..     263     292 ..     256     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.96
                            TPR_12 16 lgrydeAlellekaleiarrllGpdh 41
                                      l++  +Al +  k  e+++r++++++
  gi|488600532|ref|YP_007907003.1| 50 LKDRPKALYIIAKLSERISRYFDGEN 75
                                      66777888888888888888877665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                            TPR_12  29 aleiarrllGpdhpltattlrnLgrlyralgryeeAlell 68 
                                       al i + ++ + + ++ ++l+  g++  + g++e A+++l
  gi|488600532|ref|YP_007907003.1| 123 ALLITEFYHFGFKSQLKRILFKVGEI-TEKGDFERAINIL 161
                                       45555666777777788888888999.5999999999987 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.011
                            TPR_12  11 avlrrlgrydeAlellekaleiar 34 
                                         +++l++y  A+  l++al+ a+
  gi|488600532|ref|YP_007907003.1| 183 RRYMELKDYLAAEIQLKEALNFAE 206
                                       445555566666666666655554 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.004
                            TPR_12  15 rlgrydeAlellekaleiarrllGpdhpltat 46 
                                       + ++ d Ale +++a++ia ++  +d++l+  
  gi|488600532|ref|YP_007907003.1| 263 KSKDVDNALEKYDAAYRIAVKI--GDSELARK 292
                                       57899**************999..88877655 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       2.2   5.7e+03       8      19 ..     114     125 ..     110     130 .. 0.67
   2 ?   -1.5   0.0       1.7   4.3e+03      10      22 ..     151     163 ..     150     164 .. 0.74
   3 !    9.1   0.0    0.0008       2.1       2      59 ..     180     237 ..     179     243 .. 0.89
   4 ?    2.1   0.1      0.12   3.1e+02      47      63 ..     264     280 ..     254     286 .. 0.67
   5 ?   -0.0   0.0      0.56   1.4e+03       5      23 ..     279     297 ..     277     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.2
                            TPR_16   8 lragdyddAaaa 19 
                                       ++ gdy+ Aa +
  gi|488600532|ref|YP_007907003.1| 114 IDDGDYETAALL 125
                                       566777777744 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                            TPR_16  10 agdyddAaaalea 22 
                                        gd+++A++ l +
  gi|488600532|ref|YP_007907003.1| 151 KGDFERAINILSR 163
                                       5899999887765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0008
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                       +++r +++++dy +A+ +l++al  +  + d  e  +ll da+  q+ +++A  +++ 
  gi|488600532|ref|YP_007907003.1| 180 EWGRRYMELKDYLAAEIQLKEALNFAENDLDVKEIKMLLYDALKNQNKFEDAMKQLET 237
                                       57999*****************9999999***********************966665 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.12
                            TPR_16  47 qgrlaeAaalyraalra 63 
                                        ++++ A++ y+aa+r 
  gi|488600532|ref|YP_007907003.1| 264 SKDVDNALEKYDAAYRI 280
                                       35666666666666654 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 0.56
                            TPR_16   5 raalragdyddAaaaleaa 23 
                                       r+a++ gd + A++ le a
  gi|488600532|ref|YP_007907003.1| 279 RIAVKIGDSELARKCLEKA 297
                                       678999*******999865 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.9   7.3e+03       2       9 ..      56      63 ..      55      69 .. 0.81
   2 ?    5.5   0.0     0.012        31       3      29 ..     142     167 ..     140     168 .. 0.81
   3 ?    0.1   0.0      0.65   1.7e+03      10      26 ..     222     238 ..     216     243 .. 0.79
   4 ?    1.6   0.1      0.21   5.4e+02      25      25 ..     276     276 ..     253     297 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                                      HHHHHHHH CS
                             TPR_6  2 Alyklals 9 
                                      Aly +a++
  gi|488600532|ref|YP_007907003.1| 56 ALYIIAKL 63
                                      99**9986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlike 29 
                                       l+k ++  +k+ d ++A+ +l rl ++
  gi|488600532|ref|YP_007907003.1| 142 LFKVGEITEKG-DFERAINILSRLKQN 167
                                       56666666767.***********9886 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerl 26 
                                       ++++++ ++A++ le +
  gi|488600532|ref|YP_007907003.1| 222 LKNQNKFEDAMKQLETI 238
                                       55679999***999875 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.21
                                       H CS
                             TPR_6  25 r 25 
                                        
  gi|488600532|ref|YP_007907003.1| 276 A 276
                                       2 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.8   1.2e+04       8      21 ..      44      57 ..      42      62 .. 0.72
   2 ?   -3.3   0.0       5.4   1.4e+04      18      30 ..      77      89 ..      70      90 .. 0.69
   3 ?   -4.0   0.0         7   1.8e+04      15      21 ..     117     123 ..     116     125 .. 0.71
   4 ?    0.0   0.0      0.48   1.2e+03      14      23 ..     151     160 ..     150     166 .. 0.75
   5 ?   11.6   0.5   9.5e-05      0.24       3      34 .]     177     208 ..     175     208 .. 0.91
   6 ?    2.2   0.0     0.096   2.5e+02      10      25 ..     221     236 ..     220     238 .. 0.86
   7 ?    4.7   0.3     0.015        39      12      30 ..     262     280 ..     260     283 .. 0.89
   8 ?    3.5   0.1     0.036        92      13      27 ..     283     297 ..     279     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.8
                             TPR_2  8 GlayyklgdyeeAl 21
                                      G+ +  l+d  +Al
  gi|488600532|ref|YP_007907003.1| 44 GKYLVMLKDRPKAL 57
                                      66777788888876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.4
                             TPR_2 18 eeAleafekAlel 30
                                      e+  e+f k+l+l
  gi|488600532|ref|YP_007907003.1| 77 ERVFELFLKSLRL 89
                                      5556789999987 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 7
                             TPR_2  15 gdyeeAl 21 
                                       gdye A+
  gi|488600532|ref|YP_007907003.1| 117 GDYETAA 123
                                       7887774 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.48
                             TPR_2  14 lgdyeeAlea 23 
                                       +gd+e+A++ 
  gi|488600532|ref|YP_007907003.1| 151 KGDFERAINI 160
                                       6899999875 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 9.5e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ++ ++G+ y++l+dy  A+  +++Al  ++n+
  gi|488600532|ref|YP_007907003.1| 177 IYIEWGRRYMELKDYLAAEIQLKEALNFAEND 208
                                       68999*********************988875 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.096
                             TPR_2  10 ayyklgdyeeAleafe 25 
                                       a+ +++++e+A + +e
  gi|488600532|ref|YP_007907003.1| 221 ALKNQNKFEDAMKQLE 236
                                       7889*******99887 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.015
                             TPR_2  12 yklgdyeeAleafekAlel 30 
                                       +k++d + Ale +++A ++
  gi|488600532|ref|YP_007907003.1| 262 EKSKDVDNALEKYDAAYRI 280
                                       6899************987 PP

  == domain 8  score: 3.5 bits;  conditional E-value: 0.036
                             TPR_2  13 klgdyeeAleafekA 27 
                                       k gd e A++++ekA
  gi|488600532|ref|YP_007907003.1| 283 KIGDSELARKCLEKA 297
                                       679999********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.43
# Mc/sec: 2116.43
//
Query:       gi|488600533|ref|YP_007907004.1|  [L=421]
Description: tRNA(Ile2) 2-agmatinylcytidine synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-39  132.2   0.0    1.3e-37  128.3   0.0    2.2  2  DUF1743          Domain of unknown function (DUF1743)
    1.4e-05   25.0   0.4    3.8e-05   23.6   0.2    1.8  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    8.6e-05   22.7   0.0    0.00018   21.6   0.0    1.4  1  tRNA_anti_2      OB-fold nucleic acid binding domain
    0.00018   21.4   1.0    0.00036   20.4   1.0    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.014   15.4   1.6      0.014   15.4   1.6    1.8  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.051   13.3   0.1       0.12   12.1   0.1    1.7  1  YdjO             Cold-inducible protein YdjO
      0.073   13.2   1.6         16    5.7   0.5    2.8  2  Zn-ribbon_8      Zinc ribbon domain
       0.12   12.4   0.2       0.26   11.3   0.2    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.33   10.9   2.6       0.66    9.9   2.6    1.4  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.96    9.2   6.8        1.8    8.4   6.8    1.4  1  YacG             DNA gyrase inhibitor YacG


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 ?    1.4   0.0      0.18   3.2e+02      66     100 ..      43      83 ..      39     102 .. 0.79
   2 !  128.3   0.0   7.5e-41   1.3e-37       1     116 []     141     253 ..     141     253 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.18
                                       CCS-STTSS......EEEEEEES-HHHHHHHHHCSEE..S- CS
                           DUF1743  66 vlvPhtpdp......vlfGirgedpeallkaakeilskeee 100
                                        l+P  p +      v f +  +d+e+++++++++  +++ 
  gi|488600533|ref|YP_007907004.1|  43 RLNPTIPYKtrgngaVAFLVETDDVENVIEVVDDVIIEHSM 83 
                                       57788888888999999***************999886654 PP

  == domain 2  score: 128.3 bits;  conditional E-value: 7.5e-41
                                       TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEE CS
                           DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvl 76 
                                       grg+iGA+ a+g++   +d+tyEllaYr+per+g +r +de+s++eade +yp+ +d+vD+++++vv+vP+++dpvl
  gi|488600533|ref|YP_007907004.1| 141 GRGLIGALSAVGYDG--HDYTYELLAYRMPERFGtPRGIDEDSFYEADELYYPKIWDTVDWRNRIVVCVPKGKDPVL 215
                                       89***********55..58********************************************************** PP

                                       EEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  77 fGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       +Girg+d +a+ +a++ +++  ee+++ ++f tnq tdah
  gi|488600533|ref|YP_007907004.1| 216 YGIRGSDYNAINSAVEILRT--EEVDRKMMFITNQSTDAH 253
                                       ********************..****************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 ?   -3.0   0.0       4.3   7.7e+03      12      25 ..      52      65 ..      33      74 .. 0.62
   2 !   23.6   0.2   2.1e-08   3.8e-05       3      61 ..     271     331 ..     269     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.3
                                      EEEETTEEEEEEEE CS
                   tRNA_anti-codon 12 drsggkvifidlrD 25
                                      +r++g v+f++ +D
  gi|488600533|ref|YP_007907004.1| 52 TRGNGAVAFLVETD 65
                                      68888888876444 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 2.1e-08
                                       EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEEC CS
                   tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrr 61 
                                       ++G v+++   ++g+++f++++ + g++++++f   ++++++  +l eGd vrv+G  k+ 
  gi|488600533|ref|YP_007907004.1| 271 IRGTVVQKPYIHKGGHVFFTIKTKFGEVKCSAFEptKQFRDVVLKLIEGDEVRVFGAMKKN 331
                                       8899999988889*********************999*******************99986 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 !   21.6   0.0     1e-07   0.00018      16      78 ..     264     328 ..     256     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1e-07
                       tRNA_anti_2  16 aelkkavwvrGeisnlkr.kasghvYftLkDekakisavifr..sraaklkftledGmkVlvkgrl 78 
                                       +++++ + +rG + +    ++ ghv+ft+k +  ++++  f+  ++++ +  +l +G++V v g +
  gi|488600533|ref|YP_007907004.1| 264 KNFHS-YIIRGTVVQKPYiHKGGHVFFTIKTKFGEVKCSAFEptKQFRDVVLKLIEGDEVRVFGAM 328
                                       47855.9********97556799*******88899999999976777888899*********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 !   20.4   1.0     2e-07   0.00036      20      56 ..     342     378 ..     330     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2e-07
                    OrfB_Zn_ribbon  20 eevnpayTSktCseCgsknkealsgrtfkCpnCgfea 56 
                                       ++v  +y+  +C+ Cg+++k +  ++ f+C+nC+++a
  gi|488600533|ref|YP_007907004.1| 342 KLVRFRYSNPKCPICGKRMKSSGRNKPFRCKNCKTTA 378
                                       4566678999***********99999********987 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.5   6.2e+03      15      21 ..     199     206 ..     196     220 .. 0.74
   2 ?   15.4   1.6   7.7e-06     0.014      14      45 ..     345     376 ..     338     377 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.5
                     Zn_Tnp_IS1595  15 Wpng.fvC 21 
                                       W+n+ +vC
  gi|488600533|ref|YP_007907004.1| 199 WRNRiVVC 206
                                       99996669 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.7e-06
                     Zn_Tnp_IS1595  14 rWpng.fvCPhCgsrkayriktrglfqCkeCrk 45 
                                       r++   + CP Cg+r   + ++ + f+Ck C++
  gi|488600533|ref|YP_007907004.1| 345 RFRYSnPKCPICGKRMKSSGRN-KPFRCKNCKT 376
                                       44444477*****884444444.79******97 PP

>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.9e-05      0.12      39      54 ..     350     365 ..     345     369 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.9e-05
                              YdjO  39 ePtCplCkseMvkevr 54 
                                       +P+Cp+C+++M+++ r
  gi|488600533|ref|YP_007907004.1| 350 NPKCPICGKRMKSSGR 365
                                       79**********9977 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0097        17      23      36 ..     347     360 ..     336     362 .. 0.67
   2 ?    5.7   0.5    0.0091        16       6      22 ..     369     385 ..     368     404 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0097
                       Zn-ribbon_8  23 dapltaCPeCgsev 36 
                                       + ++++CP Cg+++
  gi|488600533|ref|YP_007907004.1| 347 RYSNPKCPICGKRM 360
                                       455788*****865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0091
                       Zn-ribbon_8   6 YrCeeCghefevlqsis 22 
                                       +rC++C+++ e +++ +
  gi|488600533|ref|YP_007907004.1| 369 FRCKNCKTTAESRVKEK 385
                                       8*******999776644 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   0.2   0.00015      0.26      47      96 ..     324     378 ..     313     385 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                       HHHHHHCC.T.TTT-EEE..EEEE--EEEETTTS-EEECHH.H.HHS-TTTSSS- CS
                              HypA  47 afellaegtv.legaeLe..ieevpvkvrCreCgkefelee.k.alrCpkCgsad 96 
                                       +f +++++t+ le+ e+   ++    + +C  Cgk+++++  +  +rC++C+++ 
  gi|488600533|ref|YP_007907004.1| 324 VFGAMKKNTInLEKMEVIklVRFRYSNPKCPICGKRMKSSGrNkPFRCKNCKTTA 378
                                       57888999988887665445566667789*********77743578*****9865 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 ?    9.9   2.6   0.00037      0.66       6      33 ..     352     377 ..     352     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                    Zn_ribbon_SprT   6 rCtgCgreythhlsirrhn.YrCrrCkgt 33 
                                       +C+ Cg   ++  s+ r +  rC+ Ck t
  gi|488600533|ref|YP_007907004.1| 352 KCPICG---KRMKSSGRNKpFRCKNCKTT 377
                                       6*****...******88889******965 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.8     0.001       1.8       2      28 ..     352     376 ..     351     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                              YacG   2 kCPtCkkevewseenpfrPFCSeRCkl 28 
                                       kCP+C+k+++ s   + +PF +++Ck+
  gi|488600533|ref|YP_007907004.1| 352 KCPICGKRMKSSG--RNKPFRCKNCKT 376
                                       7*******99988..889*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 2318.03
//
Query:       gi|488600534|ref|YP_007907005.1|  [L=152]
Description: SSU ribosomal protein S15P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   99.3   0.2    1.7e-28   98.4   0.2    1.5  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
      1e-14   54.5   1.1    1.6e-14   53.8   1.1    1.3  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
      0.047   14.2   0.1      0.064   13.8   0.1    1.3  1  YflT             Heat induced stress protein YflT
       0.11   12.8   0.2       0.18   12.1   0.2    1.6  1  DUF1884          Domain of unknown function (DUF1884)
       0.17   12.1   2.9       0.27   11.4   1.1    2.0  2  Cnn_1N           Centrosomin N-terminal motif 1


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 !   98.4   0.2   4.8e-32   1.7e-28       1      60 []       1      60 [.       1      60 [. 1.00

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 4.8e-32
                                      X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      Marmh+r++G+SgS+r yr ++p+W++l++eeve++iv+l+++G++pS+IG+iLRD+yGv
  gi|488600534|ref|YP_007907005.1|  1 MARMHARRRGSSGSKRVYRDSPPEWVELTAEEVEKKIVELHNEGYEPSMIGMILRDRYGV 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 !   53.8   1.1   4.6e-18   1.6e-14       5      80 ..      75     148 ..      70     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 4.6e-18
                                       HHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCT CS
                     Ribosomal_S15   5 ikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklg 79 
                                       +ke + +     + ++++  l++++ nl++hl+++kkD h++rgL+++++k+ +l  Y+k+k +  +++ +  ekl 
  gi|488600534|ref|YP_007907005.1|  75 LKEKGAKI----DYPEDLKSLIRKAINLRKHLETHKKDLHNKRGLQLIEAKIWRLSCYYKEKGIlpKDWSYDPEKLR 147
                                       55555555....78999**********************************************************98 PP

                                       S CS
                     Ribosomal_S15  80 l 80 
                                       +
  gi|488600534|ref|YP_007907005.1| 148 I 148
                                       7 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.8e-05     0.064       6      51 ..      29      74 ..      27     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                              YflT  6 neeellsaieelkaeGyneddiyvvakdkdrlerlaentdaetett 51
                                      + ee+ ++i el++eGy+ + i  +  d+  + ++++ t+ + +++
  gi|488600534|ref|YP_007907005.1| 29 TAEEVEKKIVELHNEGYEPSMIGMILRDRYGVPSVRQVTGKKLVQI 74
                                      579*************************998888887777666655 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2     5e-05      0.18       9      28 ..      31      50 ..      26     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                                      HHHHHHHHHHHHTT----EE CS
                           DUF1884  9 evieekineLkleGfePdii 28
                                      e++e+ki eL++eG+eP +i
  gi|488600534|ref|YP_007907005.1| 31 EEVEKKIVELHNEGYEPSMI 50
                                      89***************987 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 ?   -0.1   0.0       0.3   1.1e+03       4      15 ..      32      43 ..      21      46 .. 0.63
   2 ?   11.4   1.1   7.6e-05      0.27      24      64 ..      73     114 ..      69     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.3
                            Cnn_1N  4 EqeeqidkLkKE 15
                                      E e++i +L++E
  gi|488600534|ref|YP_007907005.1| 32 EVEKKIVELHNE 43
                                      455555555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.6e-05
                            Cnn_1N  24 yfLeerleklse.eqkeellkenielkveveslqkelkekkk 64 
                                       + L+e+  k++  e+ ++l+++ i+l+ ++e+ +k+l++k+ 
  gi|488600534|ref|YP_007907005.1|  73 QILKEKGAKIDYpEDLKSLIRKAINLRKHLETHKKDLHNKRG 114
                                       567777777765699***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); 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: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 951.70
//
Query:       gi|488600535|ref|YP_007907006.1|  [L=602]
Description: ATPase, PilT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-08   34.5   0.2    2.1e-08   33.6   0.2    1.4  1  T2SSE           Type II/IV secretion system protein
    1.1e-06   28.4   3.8    5.9e-06   26.0   1.4    2.8  2  KH_1            KH domain
    1.9e-05   24.4   0.1      0.015   14.9   0.0    3.3  3  AAA_25          AAA domain
    4.3e-05   23.3   0.0    8.2e-05   22.4   0.0    1.4  1  IstB_IS21       IstB-like ATP binding protein
    0.00025   20.8   3.2     0.0027   17.5   0.8    3.2  2  KH_2            KH domain
    0.00034   21.1   0.1     0.0019   18.7   0.0    2.3  2  PIN             PIN domain
     0.0028   17.4   0.0       0.26   11.0   0.0    2.4  2  AAA_30          AAA domain
     0.0037   17.5   0.0      0.053   13.8   0.0    2.4  2  AAA_22          AAA domain
     0.0051   16.7   0.0      0.015   15.2   0.0    1.8  1  NTPase_1        NTPase
     0.0072   16.1   0.6       0.79    9.5   0.0    3.0  3  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
     0.0079   16.6   0.0      0.023   15.1   0.0    1.8  1  AAA_16          AAA ATPase domain
     0.0091   15.9   0.0       0.88    9.5   0.0    2.4  2  Ploopntkinase3  P-loop Nucleotide Kinase3
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.041   14.4   0.0    2.0  1  AAA_18          AAA domain
      0.014   15.1   0.0      0.036   13.8   0.0    1.7  1  AAA_24          AAA domain
      0.015   14.6   0.0       0.05   12.9   0.0    1.9  1  ATPase          KaiC
      0.025   14.6   0.0      0.059   13.4   0.0    1.7  1  AAA_5           AAA domain (dynein-related subfamily)
      0.029   14.3   0.0       0.05   13.5   0.0    1.3  1  Rad17           Rad17 P-loop domain
       0.03   14.5   0.0      0.074   13.2   0.0    1.7  1  AAA_33          AAA domain
      0.031   14.0   0.0      0.069   12.9   0.0    1.6  1  AAA_29          P-loop containing region of AAA domain
      0.031   14.7   0.0      0.093   13.2   0.0    1.8  1  AAA             ATPase family associated with various cellula
      0.048   13.4   0.0      0.084   12.6   0.0    1.4  1  ATP_bind_1      Conserved hypothetical ATP binding protein
      0.048   12.9   0.0       0.11   11.7   0.0    1.6  1  Zeta_toxin      Zeta toxin
      0.065   12.1   0.0      0.096   11.5   0.0    1.1  1  PPV_E1_C        Papillomavirus helicase
      0.085   13.3   0.0       0.25   11.8   0.0    1.8  1  RNA_helicase    RNA helicase
       0.17   11.8   0.0       0.44   10.4   0.0    1.7  1  NACHT           NACHT domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   2.9e-11   2.1e-08      45     245 ..     188     380 ..     150     402 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.9e-11
                             T2SSE  45 aalerlisriaalakldisee.rplqdarlp..ekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkek 117
                                       ++l+ ++++i  +a++d +++ ++   +++    +  r+ ++  P + + e  ++R   +++++++++g++e+lk  
  gi|488600535|ref|YP_007907006.1| 188 EELRGIANEILESARQDDDSSiEIERHGAVVvqLRDLRIAIAEKPFSDKmEITAVR--PVAKVSIHEYGVDEELKR- 261
                                       45555555555555554333212223343334456778888889999998889999..455678999999887764. PP

                             T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfadllra 194
                                         ++++k       il++G+ g GK+t++ ++  ++ ++   + t+E p+ + ++++ ++q  + ++++ + + +  
  gi|488600535|ref|YP_007907006.1| 262 --RFIEKQ----RGILIAGPPGAGKSTFAASVADFLMEHGFLVKTMESPRDLMVRDE-VTQYSPLEGDMSLTADI-- 329
                                       ..667776....779************************99999*******999653.44555554445544443.. PP

                             T2SSE 195 aLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeq 245
                                       +L  rPD  +  E+R +  ++i   +     g ++  Ha  a++a++r+  
  gi|488600535|ref|YP_007907006.1| 330 LLLVRPDYTIYDELRKTSDFQIFADMRLAGVGMIGVTHATRAIDAVQRMVG 380
                                       56789*****************76666655666***************975 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.46   3.3e+02      21      41 ..      66      85 ..      65     109 .. 0.80
   2 !   26.0   1.4   8.2e-09   5.9e-06       4      40 ..     490     527 ..     487     542 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.46
                                      HHHHHHHHHT-EEEEESSTT. CS
                              KH_1 21 nIkeIreetgakIkvpksede 41
                                      +I++I e++g  +++  +e +
  gi|488600535|ref|YP_007907006.1| 66 RIRKIAEKKGLDVVFS-GERP 85
                                      79*****99*****99.5554 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 8.2e-09
                                       EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sed 40 
                                       i vP +++++i+G++G+nIk+I++e + +I+v + +++
  gi|488600535|ref|YP_007907006.1| 490 IRVPEDQISFILGRRGRNIKRIEDEVKISIDVQPlRSK 527
                                       78**********************77888888765554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.28     2e+02     127     155 ..      95     123 ..      63     130 .. 0.79
   2 !   14.9   0.0   2.1e-05     0.015      27      58 ..     261     292 ..     255     317 .. 0.81
   3 ?    3.5   0.0     0.063        45      70     107 ..     447     484 ..     438     521 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.28
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsral 155
                                        +++d++++++ eve++ l+  D +++++
  gi|488600535|ref|YP_007907006.1|  95 GGAIDEMIRRVAEVENATLITCDRVQHIV 123
                                       47899****************99999876 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.1e-05
                            AAA_25  27 kgllpagelallaGapgtGKttlaldlalava 58 
                                       ++++ ++  +l+aG+pg+GK+t+a ++a  ++
  gi|488600535|ref|YP_007907006.1| 261 RRFIEKQRGILIAGPPGAGKSTFAASVADFLM 292
                                       5788888889****************998776 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.063
                            AAA_25  70 eqgkVlyvsaEdsedelrrRlravgealrddarllvld 107
                                       eq+ V+ +++E + +e+++Rl++++ +l  d +++vl+
  gi|488600535|ref|YP_007907006.1| 447 EQVVVMPLVGERDPEEIKQRLEEILFELVTDFEVDVLN 484
                                       7888999******************9996666666665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.1e-07   8.2e-05      37      83 ..     257     303 ..     225     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                         IstB_IS21  37 eLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrv 83 
                                       e  +  fiek+ +i++ Gp+G+GKs +a++++   +++g+ v  +  
  gi|488600535|ref|YP_007907006.1| 257 EELKRRFIEKQRGILIAGPPGAGKSTFAASVADFLMEHGFLVKTMES 303
                                       556678*********************************99976543 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.36   2.6e+02       6      37 ..     193     227 ..     190     229 .. 0.69
   2 !   17.5   0.8   3.7e-06    0.0027      10      58 ..     470     519 ..     460     544 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.36
                                       HHHHT.ECET...EEEEEEECCSCEEEEEEEESCHH CS
                              KH_2   6 lavei.kkag...vskveIertanrviiviresqpg 37 
                                       +a+ei ++a     s++eIer + +v++ +r+ + +
  gi|488600535|ref|YP_007907006.1| 193 IANEIlESARqddDSSIEIER-HGAVVVQLRDLRIA 227
                                       55566676666679*****99.56777777666555 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.7e-06
                                       TECETEEEEEEEC.CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2  10 ikkagvskveIer.tanrviiviresqpgivIGkgGsnikkigkelrkdi 58 
                                       i ++ v ++e++  + +++ii + e q   ++G++G+nik+i+ e++  i
  gi|488600535|ref|YP_007907006.1| 470 ILFELVTDFEVDVlNDRKAIIRVPEDQISFILGRRGRNIKRIEDEVKISI 519
                                       33666888999885559**************************9998666 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.6e-06    0.0019       1     115 [.      12     119 ..      12     126 .. 0.85
   2 ?   -2.0   0.0       6.6   4.7e+03      14      34 ..     456     477 ..     449     481 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-06
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBC CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel..eelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpid 74 
                                       ivlDTs+li   +g+       k++e+   +++++++ ++aEl + ++  + s+   ++e+++ + +++   +  + 
  gi|488600535|ref|YP_007907006.1|  12 IVLDTSALI---DGRI-----SKIIEKSfdGKVIIPEPAVAELEAQANFgKMSGFRGLEEITRIRKIAEKKGLDVVF 80 
                                       799******...5555.....778888888*******************9777777777777777776666666677 PP

                                       HHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTH CS
                               PIN  75 aeiaeeaaeialkygllpnDaliaAtAkehgikliatfDed 115
                                       ++ +    +i+l +  +++D +i  +A+ ++++li t+D+ 
  gi|488600535|ref|YP_007907006.1|  81 SGERPGLDDIKLSK-GGAIDEMIRRVAEVENATLI-TCDRV 119
                                       99999999999998.9*******************.***86 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.6
                                       TSHHHHHHHHHHHTS.SEEEEE CS
                               PIN  14 geekaeaarklleel.eelvts 34 
                                       ge + e+++++lee+  elvt 
  gi|488600535|ref|YP_007907006.1| 456 GERDPEEIKQRLEEIlFELVTD 477
                                       6788999999999988888875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.057        41     101     158 ..      60     120 ..      55     145 .. 0.82
   2 !   11.0   0.0   0.00036      0.26      15      49 ..     265     298 ..     257     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.057
                            AAA_30 101 dtkqlaallkaaekagakvilvGDerQlasVea..Ggvlrdlvea.agigtaeLtevvRqk 158
                                       + ++++++ k+aek+g  v++ G +  l+ ++   Gg+++++++  a+ + a+L +  R +
  gi|488600535|ref|YP_007907006.1|  60 GLEEITRIRKIAEKKGLDVVFSGERPGLDDIKLskGGAIDEMIRRvAEVENATLITCDRVQ 120
                                       567889999*********************9754599999998764577888887777765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00036
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaaggrv 49 
                                       +++ r  ++ Gp+G+GK+t  +++++ + ++g+ v
  gi|488600535|ref|YP_007907006.1| 265 EKQ-RGILIAGPPGAGKSTFAASVADFLMEHGFLV 298
                                       444.478999**************99999888655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.81   5.8e+02     106     135 ..      61      89 ..      47      90 .. 0.68
   2 !   13.8   0.0   7.4e-05     0.053       4      33 ..     266     295 ..     261     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.81
                            AAA_22 106 eealeeLrsllnlsrkgvqliLvGtp.elrk 135
                                        e ++ +r++++  +kg+ +++ G + +l++
  gi|488600535|ref|YP_007907006.1|  61 LEEITRIRKIAE--KKGLDVVFSGERpGLDD 89 
                                       555666677777..**********9888876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.4e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeea 33 
                                       +++ +++ G++G+GK+t ++ +++ l e+ 
  gi|488600535|ref|YP_007907006.1| 266 KQRGILIAGPPGAGKSTFAASVADFLMEHG 295
                                       678899****************99997654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.1e-05     0.015       2      31 ..     270     299 ..     269     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       ++i GppG GK+T+   v++ l ++g+ v+
  gi|488600535|ref|YP_007907006.1| 270 ILIAGPPGAGKSTFAASVADFLMEHGFLVK 299
                                       789*********************999876 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 !    9.5   0.0    0.0011      0.79      34      56 ..     268     290 ..     255     311 .. 0.81
   2 ?   -1.5   0.1       2.7   1.9e+03      89     131 ..     371     411 ..     340     434 .. 0.71
   3 ?    3.2   0.1     0.095        68      96     118 ..     463     485 ..     459     497 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                            RuvB_N  34 dhvllyGpPGlGkttlakiiake 56 
                                         +l++GpPG Gk+t+a+ +a+ 
  gi|488600535|ref|YP_007907006.1| 268 RGILIAGPPGAGKSTFAASVADF 290
                                       569**************999864 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                            RuvB_N  89 fideihrlsraveevlysamedfrldivigkGpsarsikldlp 131
                                        id + r+   ve  + + + d    i i+ G+ a+  +l+++
  gi|488600535|ref|YP_007907006.1| 371 AIDAVQRMVGRVELGVIPQVVDTV--IFIDAGRIAKVYELKFN 411
                                       588888888888888888887776..57788888888777654 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.095
                            RuvB_N  96 lsraveevlysamedfrldivig 118
                                       +++ +ee+l+  + df++d++ +
  gi|488600535|ref|YP_007907006.1| 463 IKQRLEEILFELVTDFEVDVLND 485
                                       67889**************9865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.2e-05     0.023      22      57 ..     265     301 ..     255     398 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggif.lr 57 
                                          + +l+ G++G GKs+ + ++++ l ++g+++ + 
  gi|488600535|ref|YP_007907006.1| 265 EKQRGILIAGPPGAGKSTFAASVADFLMEHGFLVkTM 301
                                       44589*******************9998887666433 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0012      0.88       3      36 ..     267     300 ..     265     316 .. 0.74
   2 ?    3.8   0.0     0.065        47      37      63 ..     517     543 ..     496     546 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                    Ploopntkinase3   3 arliylvGqPGaGkstlmaeltkgfdrskveqee 36 
                                       +r i + G PGaGkst+ a++++ +  + +  ++
  gi|488600535|ref|YP_007907006.1| 267 QRGILIAGPPGAGKSTFAASVADFLMEHGFLVKT 300
                                       78899**************999887766555444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.065
                    Ploopntkinase3  37 etvphdvlvdrttGevvgaelGkrrea 63 
                                         +  + l+ +  Gev+ ae+G+ r++
  gi|488600535|ref|YP_007907006.1| 517 ISIDVQPLRSKRRGEVIEAEVGESRKQ 543
                                       45666779999************9987 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   5.7e-05     0.041       1      21 [.     270     290 ..     270     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                       Il++G+pG+GK+t+a  +++ 
  gi|488600535|ref|YP_007907006.1| 270 ILIAGPPGAGKSTFAASVADF 290
                                       99***********98777543 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     5e-05     0.036       4      28 ..     269     292 ..     266     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplf 28 
                                        ili Gp+g+GK+t+a++   ++l+
  gi|488600535|ref|YP_007907006.1| 269 GILIAGPPGAGKSTFAASV-ADFLM 292
                                       599**************99.77665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     7e-05      0.05       7      38 ..     254     286 ..     249     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7e-05
                            ATPase   7 glDeilkgGip.egrvvlitGepGtGKtifalq 38 
                                       g De lk+ +  ++r +li+G pG+GK++fa+ 
  gi|488600535|ref|YP_007907006.1| 254 GVDEELKRRFIeKQRGILIAGPPGAGKSTFAAS 286
                                       6788887776515688**************974 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.2e-05     0.059       2      60 ..     270     331 ..     269     353 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-05
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.........---- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvdsplv 60 
                                       +l+ GppG gKs++a ++a +l   +  v ++  +rd+  +d + ++++ +g+ sl+  +l 
  gi|488600535|ref|YP_007907006.1| 270 ILIAGPPGAGKSTFAASVADFLmehGFLVKTMESPRDLMVRDEVTQYSPLEGDMSLTADILL 331
                                       7999******************9887778888888888777777777777777777666655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     7e-05      0.05      30      66 ..     254     288 ..     235     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                             Rad17  30 evkewlkadvLesrkkriLLisGPsGCgkstvvkvLs 66 
                                        v+e lk  ++e++  r +Li+GP+G gkst    ++
  gi|488600535|ref|YP_007907006.1| 254 GVDEELKRRFIEKQ--RGILIAGPPGAGKSTFAASVA 288
                                       478999999**999..8899***********766555 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    0.0001     0.074       2      21 ..     270     289 ..     270     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                            AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                       +l+ G+pG+GKst+a +++ 
  gi|488600535|ref|YP_007907006.1| 270 ILIAGPPGAGKSTFAASVAD 289
                                       5789***********99964 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.7e-05     0.069      21      39 ..     267     284 ..     247     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.7e-05
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       ++  +l++Gp G+GKST+ 
  gi|488600535|ref|YP_007907006.1| 267 QR-GILIAGPPGAGKSTFA 284
                                       34.49************85 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.093       1      22 [.     270     291 ..     270     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                                       EEEESSTTSSHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel 22 
                                       +l+ GppG GK+++a +va  l
  gi|488600535|ref|YP_007907006.1| 270 ILIAGPPGAGKSTFAASVADFL 291
                                       699***************9865 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 ?   12.6   0.0   0.00012     0.084       1      27 [.     272     298 ..     272     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsv 27 
                                       ++Gp+G+GK+tf  +++++l++ g  v
  gi|488600535|ref|YP_007907006.1| 272 IAGPPGAGKSTFAASVADFLMEHGFLV 298
                                       79******************9988765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.11      15      44 ..     266     295 ..     253     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqg 44 
                                       +   il++G pGAGKs+ a+ ++d l ++g
  gi|488600535|ref|YP_007907006.1| 266 KQRGILIAGPPGAGKSTFAASVADFLMEHG 295
                                       55569**************99998776555 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013     0.096     260     287 ..     265     292 ..     258     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                          PPV_E1_C 260 PkknclvllGppntGkslfamslikfLk 287
                                        k+  +++ Gpp +Gks+fa s+  fL 
  gi|488600535|ref|YP_007907006.1| 265 EKQRGILIAGPPGAGKSTFAASVADFLM 292
                                       68899********************995 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00034      0.25       1      26 [.     270     295 ..     270     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i++ Gp+g GKSt+a ++a+ l+++ 
  gi|488600535|ref|YP_007907006.1| 270 ILIAGPPGAGKSTFAASVADFLMEHG 295
                                       6899*************998888765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00062      0.44       3      24 ..     270     291 ..     268     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       +++ G++G GK+t+++++a+ +
  gi|488600535|ref|YP_007907006.1| 270 ILIAGPPGAGKSTFAASVADFL 291
                                       899**************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3651.19
//
Query:       gi|488600536|ref|YP_007907007.1|  [L=116]
Description: phosphoribosyl-AMP cyclohydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-36  121.4   1.0    1.4e-35  120.9   1.0    1.2  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.035   14.4   0.0    1.4  2  DUF3239   Protein of unknown function (DUF3239)


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 !  120.9   1.0   1.6e-39   1.4e-35       1      74 []      35     108 ..      35     108 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 1.6e-39
                                       EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                            PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                       mlay+n+ea++kt+etg+a+y+SrsrkklWkKGetSgnvqkv +++ DcD+Da+++ veq+g+aCHtg+ +CF+
  gi|488600536|ref|YP_007907007.1|  35 MLAYANEEAIRKTFETGYAHYWSRSRKKLWKKGETSGNVQKVISVYADCDRDAIIYVVEQNGKACHTGEWTCFH 108
                                       9************************************************************************6 PP

>> DUF3239  Protein of unknown function (DUF3239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     4e-06     0.035      10      50 ..      15      56 ..       8      86 .. 0.77
   2 ?   -3.0   0.0      0.99   8.8e+03     101     119 ..      91     109 ..      89     111 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-06
                                      XXXX-EEEEEEEEE-SS-EEEEEEEE-BS.STTS---EEEEE CS
                           DUF3239 10 YdeyeLvPavvaevnprdvvllaLvdiak.deaaepeyalal 50
                                      + e+ L P vv +v+ rdv++la+++ +  +++ e+ ya  +
  gi|488600536|ref|YP_007907007.1| 15 FSESGLIPVVVQDVKTRDVLMLAYANEEAiRKTFETGYAHYW 56
                                      89999********************97651344455566555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.99
                                       HHHHHHHHS-HHHHHHHHH CS
                           DUF3239 101 vlkraekaIpeeeWklLek 119
                                       v+++  ka  + eW+  ++
  gi|488600536|ref|YP_007907007.1|  91 VVEQNGKACHTGEWTCFHN 109
                                       6777778888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 780.49
//
Query:       gi|488600537|ref|YP_007907008.1|  [L=235]
Description: RecA-superfamily ATPases implicated in signal transduction [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   81.2   1.1    8.9e-23   80.8   1.1    1.1  1  ATPase    KaiC
    0.00036   19.8   1.9       0.25   10.5   0.1    2.1  2  PAXNEB    PAXNEB protein
     0.0055   16.1   0.0     0.0091   15.4   0.0    1.4  1  DnaB_C    DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.018   14.7   2.1      0.037   13.8   2.1    1.6  1  DUF835    Protein of unknown function (DUF835)
      0.032   13.5   0.0      0.048   12.9   0.0    1.5  1  Rad51     Rad51
      0.057   13.2   0.0       0.11   12.4   0.0    1.4  1  MEDS      MEDS: MEthanogen/methylotroph, DcmR Sensory 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 !   80.8   1.1     3e-26   8.9e-23       2     225 ..       5     227 ..       4     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 3e-26
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       +tgI+ lD+ lkgG+p+++ +li  epG G  if+ + +++g+++ ge+++++t++ ++e++ +   sl + ++++ 
  gi|488600537|ref|YP_007907008.1|   5 RTGIPSLDTQLKGGLPSENLTLILAEPGVGEEIFSYHIVVEGLKR-GERVLYITTDYSKEAVLK---SLKMYFKEVD 77 
                                       7*****************************************999.***************976...5667788888 PP

                            ATPase  79 eegklaiidasesaeesaee..kdkedleel....ieelaeaikeikakrvviDsitglayeekeavaReilrqlvr 149
                                        + +l iid ++++++   e  + ++ ++ l    i ++ + +k+ +  rv++ ++t +  + + +++   l +l+ 
  gi|488600537|ref|YP_007907008.1|  78 FS-NLEIIDFFSQRTTLVLEntDMEAYIRGLrqdyIGSVLKLLKKENYDRVILNNLTFYIITYEFEEVQYFLENLKL 153
                                       87.899******999877665533444444411114455566777778**********9666666777788877776 PP

                            ATPase 150 vlkklg.vTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                         k ++ +T +l +e  +  +   + +v++ ++d vi Ldl+e+e+e++R l+i+k+      k+++ +e t++gi 
  gi|488600537|ref|YP_007907008.1| 154 LTKIKDsLTVLLMTE--NMFDVRIETAVKH-LSDAVIDLDLREVENEIQRRLKIIKLLNYVPPKNIMRYELTQRGIM 227
                                       665554145555555..345678899****.****************************99999********99996 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   8.2e-05      0.25      21      85 ..       6      69 ..       2      79 .. 0.72
   2 !    8.9   0.2   0.00024      0.73     207     282 ..     123     190 ..      95     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.2e-05
                            PAXNEB 21 tGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlreL 85
                                      tG+psLD+ L GGLp  ++ li ++     +++     + eG+  + +vl+++ d ++e++l++L
  gi|488600537|ref|YP_007907008.1|  6 TGIPSLDTQLKGGLPSENLTLILAEPG-VGEEIFSYHIVVEGLKRGERVLYITTDYSKEAVLKSL 69
                                      9******************99975522.2233333444567777777777777776666666665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00024
                            PAXNEB 207 nvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieLe 282
                                       n  R+++++L    +        + e++  FL  L+ l + + +  +  +  +++  +  + + +++l+D+vi L 
  gi|488600537|ref|YP_007907008.1| 123 NYDRVILNNLTFYII------TYEFEEVQYFLENLKLLTKIKDSLTVLLMTENMF--DVRIETAVKHLSDAVIDLD 190
                                       556888888887777......346789999**********666666777888999..999*************996 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     3e-06    0.0091       4      80 ..       6      82 ..       4     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-06
                                      SSTHHHH.HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHH CS
                                      xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  4 tgfkdLD.kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklr 80
                                      tg  +LD +l +Gl + +l++i a p++G   +  +i+ +  + +  +v+++  + s+e +++ l +  +e+d ++l+
  gi|488600537|ref|YP_007907008.1|  6 TGIPSLDtQLKGGLPSENLTLILAEPGVGEEIFSYHIVVEGLK-RGERVLYITTDYSKEAVLKSLKMYFKEVDFSNLE 82
                                      88999995667889999*********************98775.5669************999888888888887775 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.1   1.2e-05     0.037      67     125 ..     114     172 ..      83     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                            DUF835  67 tivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkeale 125
                                       ++ k lk+++   v++ +l + ++  +Fe+v  fl++lk  + +k+++ +l + +++++
  gi|488600537|ref|YP_007907008.1| 114 SVLKLLKKENYDRVILNNLTFYIITYEFEEVQYFLENLKLLTKIKDSLTVLLMTENMFD 172
                                       677889999999**********************************9999999999887 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.6e-05     0.048      20      59 ..       5      44 ..       1     132 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                                      --S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHH CS
                             Rad51 20 ttGskklDelLgGGietgsiteifGefrsGktqlchtlcv 59
                                       tG  +lD+ L+GG+++ ++t i+ e + G   +++ + v
  gi|488600537|ref|YP_007907008.1|  5 RTGIPSLDTQLKGGLPSENLTLILAEPGVGEEIFSYHIVV 44
                                      79****************************9999988876 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 ?   12.4   0.0   3.6e-05      0.11      21      66 ..      43      84 ..      39     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                              MEDS 21 ikaglargekvlyvasastldelrealrkagldvdaalesgqleil 66
                                      + +gl+rge+vly++++ + +++++ l+ +  +vd   +s+ lei+
  gi|488600537|ref|YP_007907008.1| 43 VVEGLKRGERVLYITTDYSKEAVLKSLKMYFKEVD---FSN-LEII 84
                                      669**********************9976555444...344.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1693.53
//
Query:       gi|488600538|ref|YP_007907009.1|  [L=165]
Description: hypothetical protein Asulf_01012 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-11   43.6   0.0    3.8e-11   43.4   0.0    1.0  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 !   43.4   0.0   2.1e-15   3.8e-11      20     145 ..      26     143 ..      17     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.1e-15
                                       CTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESS CS
                           CGI-121  20 eldfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvsss 96 
                                        ld+  ++a+++l++e l  Av +al    +g+  +++l  Ei+++L  +++I + ++ fg+++   ++ vv +s++
  gi|488600538|ref|YP_007907009.1|  26 GLDVSAINAKYVLNREILDFAVGKALKRWYSGERISRNLGVEIMLYLFATRQIRDVIQ-FGLKERGMKVYVVVISDR 101
                                       579999***************************************************9.******999******998 PP

                                       S--HHHHHHHHHHHS-SEEE--SHHHHHH--HHHHHHHTT--..TT--- CS
                           CGI-121  97 eadeeevlkslkevvegelvpleeeleeltdwkkikkiYklneleeeke 145
                                         d +e   ++ ++v+ e+++ e   +e   +kk+ +iY +ne  ee e
  gi|488600538|ref|YP_007907009.1| 102 --DINEAEFDCVDIVDCEEMETEL--NE-EKLKKFMEIYDINE--EELE 143
                                       ..5566666777888866664444..33.68***********4..3322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1075.83
//
Query:       gi|488600539|ref|YP_007907010.1|  [L=201]
Description: Molybdopterin converting factor, large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-23   82.5   0.0    3.5e-23   82.0   0.0    1.2  1  MoaE      MoaE protein


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0     2e-27   3.5e-23      13     112 ..      76     178 ..      65     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2e-27
                                       HHH-...-TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEETTSEE CS
                              MoaE  13 alva...spkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelevgeas 86 
                                       + v+    + +GA+ +FvG+vR+ +dgk+v +Leyeayep+  ++++ei + +++ +++e+v ++H+ G+++vge +
  gi|488600539|ref|YP_007907010.1|  76 KKVKrenAEYCGAIGIFVGFVRKFSDGKEVVRLEYEAYEPVFSEKVREIENILKSYPGVEGVKIFHKKGKINVGEDI 152
                                       4444333556************7777*************************************************** PP

                                       EEEEEEESSHHHHHHHHHHHHHHHHH CS
                              MoaE  87 vvvavssahRkeafeaceylidelKk 112
                                       v+v+++++hRk+ ++  ++ ++ +K+
  gi|488600539|ref|YP_007907010.1| 153 VYVVIMGRHRKDVWKPLSESMEIIKR 178
                                       *************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1305.70
//
Query:       gi|488600540|ref|YP_007907011.1|  [L=177]
Description: phosphoesterase, MJ0936 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   97.7   0.0      1e-27   97.4   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    9.7e-06   26.2   1.2    6.1e-05   23.6   1.2    1.9  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 !   97.4   0.0   1.1e-31     1e-27       2     156 ..       3     141 ..       2     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 1.1e-31
                     Metallophos_2   2 klaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaaelg 78 
                                       k+++iSD+H  l+ +++ l++l +  +d+i+h+GD+  ++ ev e+l++ +++ aVrGN D            ++++
  gi|488600540|ref|YP_007907011.1|   3 KIIAISDTHMDLWHPPKKLSELMDN-ADLIVHCGDF--TKYEVYETLKKEYDLFAVRGNAD-----------DNRIK 65 
                                       799******8888887777777666.6*********..***********************...........899** PP

                     Metallophos_2  79 tdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdgdp 154
                                       ++lpe  +++++g k++liH+   ++ +++++l ++a+e s  v+v+GH+H+  ve  gg l++ PGs++ pr +  
  gi|488600540|ref|YP_007907011.1|  66 KELPELTRFSVEGLKIGLIHQG--NYLNRFDDLGYKAKEMSVdVLVFGHIHRFVVESVGGKLLICPGSPTKPRLSIA 140
                                       **********************..9999999999997766666*****************************97765 PP

                     Metallophos_2 155 et 156
                                        +
  gi|488600540|ref|YP_007907011.1| 141 -S 141
                                       .4 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.2   6.8e-09   6.1e-05       2     123 ..       3     131 ..       2     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.8e-09
                                       EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS... CS
                       Metallophos   2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe... 75 
                                       +i+ i+D+H      +l+   k l++l +  ++dl++++GD++   ++e+     l++ ++    +++++GN +   
  gi|488600540|ref|YP_007907011.1|   3 KIIAISDTH-----MDLWHPPKKLSELMD--NADLIVHCGDFTKYEVYET-----LKKEYD----LFAVRGNADdnr 63 
                                       89*******.....666666666656533..58********999997777.....455566....6999******** PP

                                       .......................CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEE..EETTEEEEEEEESE CS
                       Metallophos  76 .......................gfeeellnkygylgifsepwrsdaevfnnlplas..lgsgslkvlllhGg 123
                                                              g   ++ln++++lg+ ++    d+ vf+++  ++   ++g  k+l+++G 
  gi|488600540|ref|YP_007907011.1|  64 ikkelpeltrfsveglkiglihqG---NYLNRFDDLGYKAKEMSVDVLVFGHIHRFVveSVGG--KLLICPGS 131
                                       *********999997777643322...777777777777777777788888887777555566..88888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1195.95
//
Query:       gi|488600541|ref|YP_007907012.1|  [L=180]
Description: hypothetical protein Asulf_01015 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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     0.0042   17.2   0.0    1.4  1  ATP12     ATP12 chaperone protein


Domain annotation for each model (and alignments):
>> ATP12  ATP12 chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-07    0.0042      25     104 ..       4      93 ..       1     112 [. 0.70

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-07
                                       EE-BET.TSEB--BSSHH...HHHHHHHHHH.........T-SSB--GGG-HHH.HHHHHHHH.TT..C.CCHHHHH CS
                             ATP12  25 rplrtp.tknilavpssk.klLAeaiaaEWdl.......saqqalikphllplt.slasraiDleaeda.ttreaiv 90 
                                       ++++ +  ++++++ ++  + + +ai +EW++       +a  +  ++ l   t +++s +iDl + ++ ++ ++ v
  gi|488600541|ref|YP_007907012.1|   4 KEIKETkVRKVIRLREKDlRRVQKAIHEEWKKmmfgerfKAAIEV-EEYLDDCTsRIVSGVIDLFSGNDpEDLDEAV 79 
                                       6666554677777766652457789*****998888533333322.34444444169999***98644449****** PP

                                       HHHHHHHHC-CCCE CS
                             ATP12  91 ktllryldtDtllc 104
                                       ++l+ryl tD  l 
  gi|488600541|ref|YP_007907012.1|  80 DNLMRYLATDRFLS 93 
                                       **********8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1262.82
//
Query:       gi|488600542|ref|YP_007907013.1|  [L=285]
Description: protoheme IX farnesyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-48  164.3  24.6    3.9e-48  164.0  24.6    1.1  1  UbiA             UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.48   10.2   2.0       0.65    9.8   0.2    2.1  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l


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 !  164.0  24.6   4.3e-52   3.9e-48       2     241 ..      19     257 ..      18     267 .. 0.89

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 4.3e-52
                              UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivlli 78 
                                       +i++++++++a+g s+++  l+ ++l++ la a++ alN+++Dr+iD +m+rt +RP++sGr+      i++++l++
  gi|488600542|ref|YP_007907013.1|  19 MITCIMSFLVASGFSFHPVELIKVFLAVSLAVAGTTALNMVLDRDIDILMPRTMKRPVPSGRLPETVCAIYGTLLFL 95 
                                       799************************************************************************** PP

                              UbiA  79 lgllllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfl 154
                                       +g++++ +++n ++ ++++l+l++  v+Yt ++lKr +++ +v+gg+a+++p ++gw+a+ g ++++ +l++++++l
  gi|488600542|ref|YP_007907013.1|  96 IGIAIS-YTINIYVSIVIFLGLFFDiVIYT-IMLKRKSPYSIVLGGLAGAMPSFAGWTAAKGYFDVAGMLISMIILL 170
                                       ******.*****************99****.9********************************************* PP

                              UbiA 155 ltwaialandlrdregDrkagiktlpvvlGrkaarillalllavllla..llllllalllllylllalllaalallr 229
                                       ++ a++++ +++  e++r+a+i++lp+++G ++a ++ +++ ++l+l+   ll+l++ +++ y++ ++++ +++l+r
  gi|488600542|ref|YP_007907013.1| 171 WIPAHIWYLSMHYEEDYRRANIPMLPLIAGMERASWI-IVFSVALMLFmvTLLFLVLPFGPAYFITSVIITTYFLYR 246
                                       ************99999*******************6.333333333344567888888888888888888888888 PP

                              UbiA 230 aarlvrrrdakk 241
                                       a+ + +   ++ 
  gi|488600542|ref|YP_007907013.1| 247 AIVFAKAP-SRI 257
                                       66655544.444 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 ?   -1.7   0.1      0.28   2.5e+03      34      50 ..      85     101 ..      82     104 .. 0.80
   2 ?    9.8   0.2   7.3e-05      0.65      19      48 ..     141     170 ..     138     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.28
                   Phage_holin_2_4  34 lialvGlavAliGlLvn 50 
                                       + a+ G ++ liG+ ++
  gi|488600542|ref|YP_007907013.1|  85 VCAIYGTLLFLIGIAIS 101
                                       56889999999998886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7.3e-05
                   Phage_holin_2_4  19 gGavvsfaGflasselialvGlavAliGlL 48 
                                        Ga+ sfaG+ a+     + G+++ +i lL
  gi|488600542|ref|YP_007907013.1| 141 AGAMPSFAGWTAAKGYFDVAGMLISMIILL 170
                                       69**********************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1843.78
//
Query:       gi|488600543|ref|YP_007907014.1|  [L=135]
Description: hypothetical protein Asulf_01017 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 906.70
//
Query:       gi|488600544|ref|YP_007907015.1|  [L=305]
Description: Sugar kinase, ribokinase family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-54  184.5   0.0    3.2e-54  184.3   0.0    1.0  1  PfkB          pfkB family carbohydrate kinase
    0.00014   21.3   0.0    0.00021   20.8   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
        0.3   10.9   0.5       0.55   10.1   0.5    1.4  1  DUF865        Herpesvirus-7 repeat of unknown function (DUF86


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 !  184.3   0.0   5.3e-58   3.2e-54       3     301 ..       6     294 ..       4     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 5.3e-58
                                       EEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   3 kvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       +vv +G ++ d i  ++k+  ++e   vk+ve +aGG+ aN+  +lar g ++afig vG D+ G+fll+ ++ egv
  gi|488600544|ref|YP_007907015.1|   6 DVVGFGAINLDKIYRVDKIpgKDEEGFVKDVELHAGGSSANTIAGLARFGLKTAFIGTVGSDEDGKFLLNDFEREGV 82 
                                       68889**************9888888*************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaea 154
                                       dt+ +  ++d r g ali+vd  g+r i++++g +  ++ +    + ++   a+l+++ +++++    +++e  + +
  gi|488600544|ref|YP_007907015.1|  83 DTSLIL-KQDGRSGNALIFVDDSGNRAILVDPGVNDTIRYD----SISKNFRAKLIHLTSFICK-NGIDSFESQKRI 153
                                       **8887.8889**********77**********99999997....57999*********96666.566777777777 PP

                                       HHHTTE...EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEG CS
                              PfkB 155 aknggt...fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlG 228
                                        ++g +   fdp l        + +l+ ++ +++++ p+++E+e l++++       ++a++++++ g k vvv+lG
  gi|488600544|ref|YP_007907015.1| 154 VEEGIAeisFDPGLIYVERG--LNELEGIIKKTTIFMPSRNEIELLMNMD------YVDAAKEIVSMGCKIVVVKLG 222
                                       77777779999999999996..999*************************......666667777789********* PP

                                       GGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSCC CS
                              PfkB 229 keGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslpt 301
                                       k+G++++++++e++v+a + +k+vDttGAGD+f++gf++++ +g +l ++ +++n  A+ ++qk ga+a +p+
  gi|488600544|ref|YP_007907015.1| 223 KDGCYISDGEKEFCVKA-YRTKPVDTTGAGDAFNAGFIYGYIKGYPLDKCGKIGNFSAMKNIQKVGARAGIPS 294
                                       *****************.88***********************************************998875 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.5e-08   0.00021     115     218 ..     179     269 ..     168     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.5e-08
                                       HTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE-- CS
                      Phos_pyr_kin 115 eLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaeri 191
                                        +++++t+  P   E+e L++       d  +aak+++++g+k V++k g+    +     ++ dge+++ ++a r+
  gi|488600544|ref|YP_007907015.1| 179 GIIKKTTIFMPSRNEIELLMN------MDYVDAAKEIVSMGCKIVVVKLGK----DGC---YISDGEKEFCVKAYRT 242
                                       48999**************99......78999******************8....233...456999********** PP

                                       --S--BTHHHHHHHHHHHHHHCTSSHH CS
                      Phos_pyr_kin 192 etknthGtGCtlssaiaaelakgesle 218
                                       +  +t G+G+++ +       kg++l 
  gi|488600544|ref|YP_007907015.1| 243 KPVDTTGAGDAFNAGFIYGYIKGYPLD 269
                                       ************998777777777665 PP

>> DUF865  Herpesvirus-7 repeat of unknown function (DUF865)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   9.2e-05      0.55      20      35 .]     243     258 ..     241     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.2e-05
                            DUF865  20 KPVKTTGTAVvFSAGF 35 
                                       KPV TTG    F AGF
  gi|488600544|ref|YP_007907015.1| 243 KPVDTTGAGDAFNAGF 258
                                       9**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.46
# Mc/sec: 2003.25
//
Query:       gi|488600545|ref|YP_007907016.1|  [L=354]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0025   17.6   0.0     0.0044   16.8   0.0    1.7  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
     0.0034   17.8   0.0       0.72   10.2   0.0    2.4  2  HAD          haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.17   11.8   2.9       0.19   11.7   0.1    2.3  3  GP24_25      Tail assembly gene products 24 & 25


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 !   16.8   0.0   7.4e-07    0.0044     202     229 ..     218     246 ..      57     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.4e-07
                                       -GGGEEEEESSGGGHHHHHHS.SEEEEET CS
                       Hydrolase_3 202 sleeviafGDgeNDieMLeaa.glgvAmg 229
                                       ++e++ia+GD+  D eMLe++ ++g A+ 
  gi|488600545|ref|YP_007907016.1| 218 PKERIIAIGDSISDFEMLEWVrKRGLAVS 246
                                       6899*****************85666654 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0036        22      99     141 ..      97     142 ..      32     169 .. 0.81
   2 !   10.2   0.0   0.00012      0.72     171     188 .]     219     236 ..     184     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0036
                               HAD  99 aaGdrvvvvSgglrplvepllaelg.adevlatelevdd...rltge 141
                                       ++ ++ vv+S +++++++  + + g  d++ +t+++vd+   +++ +
  gi|488600545|ref|YP_007907016.1|  97 RK-YKPVVISTSYDQFLKTSAGKIGiQDRLHGTRMDVDRlseYFDDR 142
                                       44.7899******************9999********9999888877 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00012
                               HAD 171 leevvayGDspsDlpllr 188
                                        e+++a+GDs+sD ++l+
  gi|488600545|ref|YP_007907016.1| 219 KERIIAIGDSISDFEMLE 236
                                       3569************96 PP

>> GP24_25  Tail assembly gene products 24 & 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.29   1.8e+03       8      29 ..      89     110 ..      84     114 .. 0.79
   2 ?   11.7   0.1   3.2e-05      0.19      43      94 ..     143     194 ..     132     202 .. 0.88
   3 ?   -3.0   0.1       1.1   6.6e+03      50      74 ..     287     305 ..     279     312 .. 0.47

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.29
                           GP24_25   8 dalraevkkkyaavliglsddv 29 
                                       da ++   +ky +v+i +s d 
  gi|488600545|ref|YP_007907016.1|  89 DAAMKILLRKYKPVVISTSYDQ 110
                                       5566667789******999875 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.2e-05
                           GP24_25  43 areavvellkefeeiaeleeddedeLvdeysdelekviakvfrliatdPkkl 94 
                                        re +  l++++ + +e++ d e+  v+e + +  + + ++f   ++  kk+
  gi|488600545|ref|YP_007907016.1| 143 DREVASSLIEKISKLPEIKVDVENRTVNESATRTIDFLNDLFWGNSDFSKKI 194
                                       6899999***********************************8777777766 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.1
                           GP24_25  50 llkefeeiaeleedde.deLvdeysd 74 
                                        lk f       ed + deL+d   +
  gi|488600545|ref|YP_007907016.1| 287 FLKLF-------EDKKwDELKDVVDE 305
                                       33333.......33333555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2570.36
//
Query:       gi|488600546|ref|YP_007907017.1|  [L=193]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-55  185.9   5.6    8.5e-55  185.6   5.6    1.0  1  DUF2150   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
       0.13   11.9   1.7        2.3    8.0   0.1    2.4  2  PPR_1     PPR repeat
        1.2    9.6   3.8         18    5.9   0.1    3.0  3  PPR       PPR repeat


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 !  185.6   5.6   1.4e-58   8.5e-55       2     183 ..       3     179 ..       2     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.6 bits;  conditional E-value: 1.4e-58
                           DUF2150   2 FYteeRwqNWlnrvkeedldle.edseeleaavllnlqdDvilavlkiikaveeeelskeeAleeleevreivleev 77 
                                       FYteeR++NW+nr++ee++d+e ++s    ++v++++ +D+++a+l+++++v+++el+k+eAl+e+eev  ++  e+
  gi|488600546|ref|YP_007907017.1|   3 FYTEERLSNWVNRINEEKIDFEnAES----FEVFDKMIEDFVVACLHLVRSVKNRELNKKEALKEIEEVYGVFNIEY 75 
                                       *********************97777....*********************************************** PP

                           DUF2150  78 eeddeekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidgeklpe 154
                                       +++de k e++++ ++s+ +++++++ y++g+ +k kd+++l+++a+++e+e+dl++a+ei+a++Gakvi geklpe
  gi|488600546|ref|YP_007907017.1|  76 TFNDEFKGEFFDFAKESMRIILESTKLYLQGKSSK-KDFNSLLSQAIKKEKEGDLNKAFEILARMGAKVIGGEKLPE 151
                                       *********************************97.****************************************9 PP

                           DUF2150 155 kvledl..eyglvaewldgidslaaamssse 183
                                        + + +  e+ ++ +wldgid+++++m  se
  gi|488600546|ref|YP_007907017.1| 152 -F-D-IsdEELVLLNWLDGIDAINTVMLLSE 179
                                       .4.3.333666679*************9876 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.013        80      25      33 ..      27      35 ..      24      36 .. 0.86
   2 ?    8.0   0.1   0.00039       2.3      19      33 ..     125     139 ..     125     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.013
                                      HHHHHHHHH CS
                             PPR_1 25 eAfelfdeM 33
                                      e fe+fd+M
  gi|488600546|ref|YP_007907017.1| 27 ESFEVFDKM 35
                                      679****** PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00039
                                       HTS-HHHHHHHHHHH CS
                             PPR_1  19 kaGrvdeAfelfdeM 33 
                                       k+G++++Afe++ +M
  gi|488600546|ref|YP_007907017.1| 125 KEGDLNKAFEILARM 139
                                       89**********998 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.014        81      18      28 ..      27      37 ..      26      38 .. 0.88
   2 ?   -3.0   0.0         2   1.2e+04      15      24 ..      63      72 ..      61      72 .. 0.71
   3 ?    5.9   0.1     0.003        18      12      26 ..     125     139 ..     124     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.014
                               PPR 18 eAlelfkeMke 28
                                      e +e+f++M+e
  gi|488600546|ref|YP_007907017.1| 27 ESFEVFDKMIE 37
                                      789******98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                               PPR 15 kleeAlelfk 24
                                      ++ee+  +f+
  gi|488600546|ref|YP_007907017.1| 63 EIEEVYGVFN 72
                                      5788888885 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.003
                               PPR  12 knGkleeAlelfkeM 26 
                                       k+G+l +A+e++ +M
  gi|488600546|ref|YP_007907017.1| 125 KEGDLNKAFEILARM 139
                                       89***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1337.09
//
Query:       gi|488600547|ref|YP_007907018.1|  [L=116]
Description: putative metal-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-09   36.5   0.0    4.2e-09   35.9   0.0    1.4  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 !   35.9   0.0   2.3e-13   4.2e-09       1      39 [.      56      97 ..      43      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.3e-13
                              SWIM  1 yrVtlddervrlnkatCsCpefqk...ngipCkHalAvllal 39
                                      +++ ++++ + +++++C+C +fq+   ++ pC H++A l+a 
  gi|488600547|ref|YP_007907018.1| 56 FFIVVGENEYIVEENFCTCEDFQInlkGKKPCSHIIAMLIAR 97
                                      566777777******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 803.87
//
Query:       gi|488600548|ref|YP_007907019.1|  [L=287]
Description: putative methyltransferase, YaeB/AF_0241 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-26   91.2   0.0    8.7e-26   90.5   0.0    1.3  1  TrmO      tRNA-methyltransferase O
    5.4e-12   45.5   0.0    8.1e-12   45.0   0.0    1.3  1  dUTPase   dUTPase
    0.00068   18.5   0.0      0.001   17.9   0.0    1.4  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)
  ------ inclusion threshold ------
      0.041   13.7   0.1       0.11   12.4   0.0    1.7  2  WIYLD     Ubiquitin-binding WIYLD domain


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 !   90.5   0.0   1.9e-29   8.7e-26      12     119 .]      14     116 ..       7     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 1.9e-29
                                       -EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS-EEEEEEEEE CS
                              TrmO  12 aeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpnpiglsvvkle 88 
                                        + eie+ +e+    a++gl+e   +w+l++fh +  ++ k  v+p+    +   Gvf+tRsp+R n+igls+vk+ 
  gi|488600548|ref|YP_007907019.1|  14 KKDEIEILEEF--IPAMDGLSEGMLIWVLYIFHLS--TE-KIRVHPKGDTRKPLRGVFSTRSPYRINKIGLSAVKIR 85 
                                       56789999999..99******************88..23.445555555555667********************** PP

                                       EEETTEEEEES----TT-EEEEEEE--HHHH CS
                              TrmO  89 kvegnvlevsgvDlldgtpvlDiKPYvpyaD 119
                                       k+e+n+++v g+D+l+++pv+DiKP+ + +D
  gi|488600548|ref|YP_007907019.1|  86 KIEKNIIKVDGLDALENSPVVDIKPFAEVYD 116
                                       **************************99988 PP

>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   1.8e-15   8.1e-12      27     112 ..     193     278 ..     181     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.8e-15
                                       ET.TEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTS..EEEEEEEE-SSS-EEE-TT-EEEEEE CS
                           dUTPase  27 kp.getvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrG..evkvvlfnltkkdvkikkgdRiAqLi 100
                                          ++ ++ +++  + l+++++a+  pRS l ++g  v++ v+d+ yrG  ev++v++n+ +  + +kk +Ri qL+
  gi|488600548|ref|YP_007907019.1| 193 FLeKGVYRATLNEIVSLSEDIMAFARPRSTLIRSGANVLTAVWDAGYRGrsEVGIVVYNSEG--IMLKKDARIVQLV 267
                                       5546677788899999*********************************8889999999888..************* PP

                                       EEEBECGEEEEE CS
                           dUTPase 101 fariltaeleev 112
                                       f+++ +  ++++
  gi|488600548|ref|YP_007907019.1| 268 FIKLTE-RTKPY 278
                                       *98776.55555 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.3e-07     0.001       3     110 ..     121     225 ..     119     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-07
                               DCD   3 gilpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklheldLtegavle 79 
                                       ++l++++i + i+++++ ++    e+qiqP+ +D  L k++ r++        ++ ++ + e    e+d +  + le
  gi|488600548|ref|YP_007907019.1| 121 SVLSAEDILKRIRNENLITDYIDLETQIQPNGFDCTLKKVS-RIKGMGRID-FDNSERVIPETLEIEFDENGWVFLE 195
                                       58999999999999999888888899***********8765.888654432.3344555666666678877777788 PP

                               DCD  80 kgcvYivplleslaLpadlsaaanpksstGR 110
                                       kg vY + l+e ++L++d+ a a p+s+  R
  gi|488600548|ref|YP_007907019.1| 196 KG-VYRATLNEIVSLSEDIMAFARPRSTLIR 225
                                       77.9***********************9766 PP

>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.4   6.4e+03      16      35 ..      75      94 ..      73      96 .. 0.79
   2 ?   12.4   0.0   2.4e-05      0.11      35      60 ..     185     211 ..     162     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.4
                             WIYLD 16 kelGfskeqvrpvlkkLLkv 35
                                      +++G s+ ++r++ k++ kv
  gi|488600548|ref|YP_007907019.1| 75 NKIGLSAVKIRKIEKNIIKV 94
                                      67899999999998888776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.4e-05
                             WIYLD  35 vYgkn.WeliEednYrvLadaifekqe 60 
                                       ++++n W ++E + Yr+ +++i + +e
  gi|488600548|ref|YP_007907019.1| 185 EFDENgWVFLEKGVYRATLNEIVSLSE 211
                                       59****************999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 2189.60
//
Query:       gi|488600549|ref|YP_007907020.1|  [L=279]
Description: hypothetical protein Asulf_01023 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-44  150.3  38.8    5.6e-22   78.4  18.2    2.0  2  EamA      EamA-like transporter family
    0.00055   19.4  10.3    0.00055   19.4  10.3    2.2  2  TPT       Triose-phosphate Transporter family
  ------ inclusion threshold ------
        0.6   10.2   0.0        0.6   10.2   0.0    3.4  4  TPPK_C    Thiamine pyrophosphokinase C terminal
        1.2    9.2  14.7       0.14   12.2   6.4    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 !   78.4  18.2   1.2e-25   5.6e-22       4     136 ..       7     132 ..       4     133 .. 0.94
   2 !   78.2  12.6   1.4e-25   6.2e-22       2     136 ..     140     275 ..     139     276 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.2e-25
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       +l++l +a++w+i+f+++k++l+++sp+t++++rf ia++l+++++l k   +      ++++ l +g + ++l++ 
  gi|488600549|ref|YP_007907020.1|   7 DLILLSVAFIWGITFPVIKVALNSISPITFNTIRFAIASLLFIPFLLRKSDFN------QIKIGLMIG-IVVFLGYT 76 
                                       688999***************************************99988777......778877777.57999*** PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        ++++++ t+a+na++its+ +v+t  ++++l++ k+t k++l i+l++lG++li+
  gi|488600549|ref|YP_007907020.1|  77 TQTIGIEFTTATNAGFITSTYVVLTPAIAYILYRVKITEKEVLWIILAFLGLYLIS 132
                                       ******************************************************97 PP

  == domain 2  score: 78.2 bits;  conditional E-value: 1.4e-25
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvl 77 
                                       +g+l+++l a+f+a+ +vl+    r+ +p++l+f ++l+  ++  ++++++e+   +++++  + +l+++++++t+l
  gi|488600549|ref|YP_007907020.1| 140 IGDLFVFLCAIFFAMEIVLISNYARNNDPVMLAFGQTLAVVLFSAPLTMFEERFAiSQINQDVIVALIITAVFATTL 216
                                       799***********************************************99999********************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       a ++++ya+  t +s a++i+s+e vf+ i+++++l+e+l++ q+lg++li+++v+ i+
  gi|488600549|ref|YP_007907020.1| 217 AKIAQNYAQGFTRSSDAAIIFSMEGVFSHIFAIIILNESLSVVQYLGAFLIIVSVIGIS 275
                                       *******************************************************9987 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   8.1       1.1   5.1e+03      22     163 ..      25     162 ..       8     166 .. 0.73
   2 !   19.4  10.3   1.2e-07   0.00055      29     139 ..     166     278 ..     143     279 .] 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                               TPT  22 KkilnvfpyPltvsavqllvgsvlilvlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSfthtvK 98 
                                       K +ln +  P+t  ++++++ s+l ++++        k + +++k  l++++v +lg  + ++ ++ ++   +  + 
  gi|488600549|ref|YP_007907020.1|  25 KVALNSI-SPITFNTIRFAIASLLFIPFLLR------KSDFNQIKIGLMIGIVVFLGYTTQTIGIEFTTATNAGFIT 94 
                                       5556655.48888888888888775554432......3345667777888899999999999999999999999999 PP

                               TPT  99 asePiFtvilsrlllgeklsllvylsLlpivgGvalas..vtElsF.nligfisAlisnltfslrnif 163
                                       ++  + t +++ +l++ k++ + +l ++    G+ l s    E++  +l+ f++A++  +  +l +++
  gi|488600549|ref|YP_007907020.1|  95 STYVVLTPAIAYILYRVKITEKEVLWIILAFLGLYLISgfSGEVNIgDLFVFLCAIFFAMEIVLISNY 162
                                       99999999999999999999999999999999998887333567654677888888777766665555 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.2e-07
                               TPT  29 pyPltvsavqllvgsvlilvlwal.glkkrpkisseflkailplalv.ktlghvlavvslskvaVSfthtvKasePi 103
                                       + P++++  q l+ ++++++l ++ +   + +i++++++a+++ a++  tl++++ + + + +  S + ++ ++e +
  gi|488600549|ref|YP_007907020.1| 166 NDPVMLAFGQTLAVVLFSAPLTMFeERFAISQINQDVIVALIITAVFaTTLAKIAQNYAQGFTRSSDAAIIFSMEGV 242
                                       6799999999999999988887775667799*****999888888762679************************** PP

                               TPT 104 FtvilsrlllgeklsllvylsLlpivgGvalasvtE 139
                                       F+ i+++++l+e+ls+  yl    i++ v+  s+tE
  gi|488600549|ref|YP_007907020.1| 243 FSHIFAIIILNESLSVVQYLGAFLIIVSVIGISLTE 278
                                       *********************999999999999998 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00013       0.6       6      24 ..     108     126 ..     107     126 .. 0.95
   2 ?   -2.2   0.1         1   4.5e+03      16      31 ..     143     158 ..     138     161 .. 0.73
   3 ?   -4.1   0.1       3.9   1.8e+04      27      35 ..     177     185 ..     176     187 .. 0.65
   4 ?   -0.1   0.2      0.22     1e+03      28      38 ..     203     213 ..     200     227 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                            TPPK_C   6 LYrsrisggallllvlAaL 24 
                                       LYr++i  + +l+++lA L
  gi|488600549|ref|YP_007907020.1| 108 LYRVKITEKEVLWIILAFL 126
                                       9****************76 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                            TPPK_C  16 llllvlAaLvAvaval 31 
                                       l   ++A+++A+ ++l
  gi|488600549|ref|YP_007907020.1| 143 LFVFLCAIFFAMEIVL 158
                                       5567789999987776 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 3.9
                            TPPK_C  27 vavallvsp 35 
                                       +av+l  +p
  gi|488600549|ref|YP_007907020.1| 177 LAVVLFSAP 185
                                       677777666 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.22
                            TPPK_C  28 avallvspagq 38 
                                       +val ++ ++ 
  gi|488600549|ref|YP_007907020.1| 203 IVALIITAVFA 213
                                       34444443333 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.4     3e-05      0.14       1     115 [.      10     131 ..      10     132 .. 0.70
   2 ?    1.5   0.9     0.066   2.9e+02      75     112 ..     234     271 ..     205     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                           TMEM234   1 lllvgilWGitnPllkrgskgleevkeksklsq.lllelkf...lllrlkyliplllNqsgSvlff.lllgkadlsl 72 
                                       ll v+++WGit P +k + + ++ ++ +  + + ++++l f   ll +  +    +  + g v+f  ++ + + + +
  gi|488600549|ref|YP_007907020.1|  10 LLSVAFIWGITFPVIKVALNSISPITFN--TIRfAIASLLFipfLLRKSDFNQIKIGLMIGIVVFLgYTTQTIGIEF 84 
                                       799*********************9866..33324455554454888888865444445666666535555555544 PP

                           TMEM234  73 avp....iaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       + +       s  +v+T  ++++l +  +++k vl ++l ++g++l+
  gi|488600549|ref|YP_007907020.1|  85 TTAtnagFITSTYVVLTPAIAYILYRVKITEKEVLWIILAFLGLYLI 131
                                       43311114557778888889999999999999999999999999997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.066
                           TMEM234  75 piaNslafvfTvltelllgekvlkkktvlgmllvvvgi 112
                                       +i  s++ vf  + + ++ ++ l+  ++lg +l++v++
  gi|488600549|ref|YP_007907020.1| 234 AIIFSMEGVFSHIFAIIILNESLSVVQYLGAFLIIVSV 271
                                       56668888888888988888888888999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1538.11
//
Query:       gi|488600550|ref|YP_007907021.1|  [L=333]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-52  177.7  22.9    3.1e-52  177.4  22.9    1.1  1  Cons_hypoth698  Conserved hypothetical protein 698


Domain annotation for each model (and alignments):
>> Cons_hypoth698  Conserved hypothetical protein 698
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.4  22.9   1.7e-56   3.1e-52       5     303 ..      31     314 ..      27     315 .. 0.90

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 1.7e-56
                    Cons_hypoth698   5 lllliavlalllakvellfaklsalllAillGillgnflklqeqlkaGvafskkklLrlgivllGfrltlsdiakvG 81 
                                       l++  ++la+ ++ ++   +++  l++A+++Gi++g +++ +++     +    + L +gi+l+G+++ + + +++ 
  gi|488600550|ref|YP_007907021.1|  31 LIITSGLLAYAISLID---PAFDTLFMALFMGIVFGSLYGGKKKEIISQKAL-SITLPVGIILYGSNIIFPKEIEIP 103
                                       6667778888888866...*****************9666554433333333.479********************* PP

                    Cons_hypoth698  82 lkgvlldiivlistfllvlllgakllkldkklalLvaaGssiCGasAilavepvikareeevalaiavivllgtvam 158
                                          +++++i++is  ++ ++l a++ +l++k ++L+ +G++iCGasAi++v+++i++++ e++++i +i+++g++++
  gi|488600550|ref|YP_007907021.1| 104 PAYIAVTLISTISL-GFSVYLLARANNLSNKFTTLLVCGNAICGASAIAIVSSIINPKNREFSTSIIIITVVGLTGA 179
                                       *9999999999986.55666666****************************************************** PP

                    Cons_hypoth698 159 llyPalatllsltdeefgvfaGasvhevaqVvaagelvseeaakiAvivKltRvlllapvvlllslllakreeeset 235
                                       ++yP+l+  l+l + +++++ G+++++++ V++a ++++e+++++A+ +K +R++++a vvll+s+l +  ++    
  gi|488600550|ref|YP_007907021.1| 180 VIYPSLYYSLNLPEIKYALLSGSTLQQTGLVKIATNQFGEHVETLALAIKAIRIAMIAVVVLLVSFLYS--DQ---- 250
                                       *****************************************************************6554..33.... PP

                    Cons_hypoth698 236 keakitiPwFvlgFlvvallntlvllpselvsalktlstlllvmalaAlglktdlkalkkaglkplll 303
                                          k+++Pw++++F++va l + +l+p e++ +++ lstl+++++la +g  ++l++++++gl pl++
  gi|488600550|ref|YP_007907021.1| 251 ---KFYVPWYIVAFILVAFL-SQNLIPYEVIVVFQPLSTLAFAITLASIGFSVNLSDIQNVGLSPLII 314
                                       ...68***********9987.6789999*************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2007.43
//
Query:       gi|488600551|ref|YP_007907022.1|  [L=744]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-56  188.0   0.5    1.5e-21   76.5   0.0    3.4  3  PAS              PAS fold
    3.4e-47  159.0   4.9    1.6e-20   73.2   0.1    3.6  3  PAS_9            PAS domain
    1.2e-39  134.9   0.0    3.1e-17   62.8   0.0    3.3  3  PAS_4            PAS fold
    7.8e-31  106.2   0.0      3e-12   46.6   0.0    3.5  3  PAS_3            PAS fold
      3e-28   98.2   0.1      1e-27   96.5   0.1    2.0  1  DUF835           Protein of unknown function (DUF835)
    1.7e-21   75.8   0.0    8.7e-09   35.2   0.0    3.5  3  PAS_8            PAS domain
    1.4e-15   57.7   1.4    4.3e-07   30.5   0.0    3.8  3  PAS_10           PAS domain
    6.3e-13   48.8   0.0    1.9e-09   37.5   0.0    3.1  3  MEKHLA           MEKHLA domain
    9.9e-13   48.3   0.2    2.9e-09   37.1   0.0    3.6  3  PAS_7            PAS fold
    4.4e-07   30.2   0.0    1.8e-06   28.2   0.0    2.1  1  HAMP             HAMP domain
    0.00012   21.7   0.1    0.00029   20.5   0.1    1.6  1  HTH_41           Helix-turn-helix domain
    0.00029   20.5   0.1    0.00088   19.0   0.1    1.8  1  LexA_DNA_bind    LexA DNA binding domain
    0.00056   19.5   0.6      0.002   17.7   0.0    2.3  1  GntR             Bacterial regulatory proteins, gntR family
     0.0021   17.1   1.7     0.0063   15.5   0.9    2.0  2  LMBR1            LMBR1-like membrane protein
     0.0023   18.4   0.0     0.0076   16.7   0.0    1.9  1  HTH_27           Winged helix DNA-binding domain
     0.0071   16.2   0.0      0.022   14.7   0.0    1.9  1  MarR_2           MarR family
     0.0081   16.5   0.0      0.039   14.3   0.0    2.2  1  Penicillinase_R  Penicillinase repressor
     0.0093   15.6   1.5     0.0093   15.6   1.5    1.9  2  Mt_ATP-synt_B    Mitochondrial ATP synthase B chain precursor
  ------ inclusion threshold ------
       0.01   15.9   0.5      0.046   13.8   0.5    2.2  1  Rsbr_N           Rsbr N terminal
      0.011   15.7   0.0      0.022   14.8   0.0    1.4  1  HTH_20           Helix-turn-helix domain
      0.012   15.7   0.0       0.21   11.8   0.0    3.0  2  PAS_11           PAS domain
      0.021   14.4   0.2      0.095   12.3   0.1    2.2  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.025   14.3   0.0      0.073   12.8   0.0    1.8  1  HTH_DeoR         DeoR-like helix-turn-helix domain
       0.03   14.5   0.0      0.081   13.2   0.0    1.7  1  PaaX             PaaX-like protein
      0.031   14.2   0.1       0.16   11.8   0.1    2.3  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.036   14.0   0.1       0.12   12.4   0.1    1.9  1  HTH_11           HTH domain
      0.047   13.7   0.4        0.4   10.7   0.0    2.6  2  HTH_45           Winged helix-turn-helix
      0.064   13.2   0.2       0.17   11.9   0.2    1.7  1  DUF4743          Domain of unknown function (DUF4743)
      0.072   13.1   0.0       0.18   11.8   0.0    1.7  1  HTH_36           Helix-turn-helix domain
      0.078   13.3   0.2         24    5.3   0.0    3.6  3  NUMOD1           NUMOD1 domain
      0.087   12.8   0.1       0.22   11.5   0.1    1.6  1  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.14   12.0   3.0        1.5    8.7   0.2    2.5  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        1.2    9.7   7.5        2.3    8.8   0.9    3.7  3  Syntaxin-6_N     Syntaxin 6, N-terminal
        1.4    9.0   9.8        4.6    7.3   0.3    3.2  3  UPF0242          Uncharacterised protein family (UPF0242) N-t
        2.5    8.2   9.0       0.14   12.3   1.8    2.5  2  Cep57_CLD_2      Centrosome localisation domain of PPC89


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 !   35.6   0.0   1.5e-11   7.5e-09       1     113 []     130     235 ..     130     235 .. 0.93
   2 !   72.7   0.0   4.4e-23   2.2e-20       3     113 .]     248     357 ..     246     357 .. 0.96
   3 !   76.5   0.0     3e-24   1.5e-21       3     113 .]     391     498 ..     389     498 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.5e-11
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r+++e++ d +f ++ed +i+y ++   ++l  s+ e+++++ll++i  +    ++  + ++l++++e+++ ++
  gi|488600551|ref|YP_007907022.1| 130 EKYRSLVENINDWVFEINEDLIITYSSSRCLDFLDRSPYEIINRPLLEFIDSQ----DRHSVMEVLAEKKEFSGLDV 202
                                       579***********************************************877....67788888889999999888 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++       + le+  +p+ d +g+ +g+ +v+rdi
  gi|488600551|ref|YP_007907022.1| 203 RLAN---QDVVLEISGKPFHDDSGNFKGYRCVARDI 235
                                       6555...9***************************8 PP

  == domain 2  score: 72.7 bits;  conditional E-value: 4.4e-23
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       l++ile+++d+i+ +D d+ri+ +N+ ae+++G+++ee++gk+l+ li++e++ + ae ++++ ++g  + ++ i++
  gi|488600551|ref|YP_007907022.1| 248 LVSILEHTIDAIVSLDLDTRIVSWNKGAEKMFGYTAEEMVGKPLSTLIPPEKHKDCAENFKKVVNEGFARDIEAIRI 324
                                       689*************************************************9999999999999999999999999 PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        + +g+++ ++++++ + d +ge++gf+ ++rdi
  gi|488600551|ref|YP_007907022.1| 325 SK-NGKIVVVDQTVTAIHDSQGELTGFVAIMRDI 357
                                       99.******************************8 PP

  == domain 3  score: 76.5 bits;  conditional E-value: 3e-24
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHH.HHHTT-ECCCCEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleql.leqgeesrageis 78 
                                       l  i+e++ d+i  +D d +i+ +N++ae+l+G++ree+lg+ +++ ++ee    l+++++++ ++ g+e+ ++e++
  gi|488600551|ref|YP_007907022.1| 391 LAKIVENSNDAIYSIDLDNKITSWNRTAERLFGWRREEILGQDVNIIVPEE----LKKEISNVkEKIGKENLTYETR 463
                                       678**********************************************99....6666666527899999****** PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + ++dg++i +ev+a pv+d +g+++ + +++rdi
  gi|488600551|ref|YP_007907022.1| 464 RITKDGKIIFVEVTAIPVYDSDGKLTRISFIARDI 498
                                       **********************************8 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   6.4e-09   3.3e-06       3     103 ..     142     236 ..     140     236 .. 0.82
   2 !   73.2   0.1   3.2e-23   1.6e-20       2     104 .]     257     359 ..     256     359 .. 0.96
   3 !   58.7   0.3   1.1e-18   5.6e-16       3     103 ..     401     499 ..     399     500 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.4e-09
                             PAS_9   3 gilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                        ++ +n+d  i+ y +   l++l  sp e++++++ +++  d+++++ + ++l +++ ++   +v l + +      
  gi|488600551|ref|YP_007907022.1| 142 WVFEINEDL-IItYSSSRCLDFLDRSPYEIINRPLLEFI--DSQDRHSVMEVLAEKK-EFSGLDVRLANQDV---VL 211
                                       567688***.666**************************..6666666666666666.37777777777765...77 PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDit 103
                                       +++  p++dd+g+++g+ ++ rDi+
  gi|488600551|ref|YP_007907022.1| 212 EISGKPFHDDSGNFKGYRCVARDIS 236
                                       7***********************7 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 3.2e-23
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetf 76 
                                       d+i+  + d ri+++N++a++++Gy++ee++gk++++l+  +++++ +e++++++++g   +r+ e + i kng+ +
  gi|488600551|ref|YP_007907022.1| 257 DAIVSLDLDTRIVSWNKGAEKMFGYTAEEMVGKPLSTLIppEKHKDCAENFKKVVNEGF--ARDIEAIRISKNGKIV 331
                                       67887789*******************************99999999999999999999..**************** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                        v+ t+++++d++gel+g+++i+rDite
  gi|488600551|ref|YP_007907022.1| 332 VVDQTVTAIHDSQGELTGFVAIMRDITE 359
                                       ***************************8 PP

  == domain 3  score: 58.7 bits;  conditional E-value: 1.1e-18
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                       +i  ++ d++i+++N++a+rl+G  +ee+lg+++  ++  ++e +++++++ e + k+  ++e+  i+k+g+ ++v+
  gi|488600551|ref|YP_007907022.1| 401 AIYSIDLDNKITSWNRTAERLFGWRREEILGQDVNIIV--PEELKKEISNVKEKIGKENLTYETRRITKDGKIIFVE 475
                                       5665669999****************************..99999999999999999******************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDit 103
                                       +ta+pv+d+dg+l++i +i rDi+
  gi|488600551|ref|YP_007907022.1| 476 VTAIPVYDSDGKLTRISFIARDIS 499
                                       ***********************9 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.2e-08   1.1e-05       1     109 [.     136     239 ..     136     240 .. 0.93
   2 !   62.8   0.0     6e-20   3.1e-17       1     109 [.     252     361 ..     252     362 .. 0.98
   3 !   42.9   0.0   9.2e-14   4.7e-11       1     106 [.     395     499 ..     395     502 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.2e-08
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +++++d+++ +++d+ ++y + +  + + ++p e+++++l e+   +d++ +     +vl++++  + l+++l   +
  gi|488600551|ref|YP_007907022.1| 136 VENINDWVFEINEDLIITYSSSRCLDFLDRSPYEIINRPLLEFIDSQDRHSV----MEVLAEKKEFSGLDVRLA-NQ 207
                                       689***************************************9887555555....5799**********9999.99 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++++e++  P++d+sG   g+ +++rDi+ r+
  gi|488600551|ref|YP_007907022.1| 208 DVVLEISGKPFHDDSGNFKGYRCVARDISLRK 239
                                       ****************************9886 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 6e-20
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       l+++ da++ ld d r++ +N+ a+++fg+++ee++Gk+l  l p+e   + +++ ++v+ ++ + + + ++   +g
  gi|488600551|ref|YP_007907022.1| 252 LEHTIDAIVSLDLDTRIVSWNKGAEKMFGYTAEEMVGKPLSTLIPPEKHKDCAENFKKVVNEGFARDIEAIRISkNG 328
                                       78999*******************************************************************99*** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + ++++ +++ ++d++Ge  g+++i+rDiTer+
  gi|488600551|ref|YP_007907022.1| 329 KIVVVDQTVTAIHDSQGELTGFVAIMRDITERK 361
                                       ********************************8 PP

  == domain 3  score: 42.9 bits;  conditional E-value: 9.2e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       +++++da++ +d d +++ +N++a++lfg+++ee+lG+ +  ++pee++ ++++  ++  +++ ++e+  ++++ g+
  gi|488600551|ref|YP_007907022.1| 395 VENSNDAIYSIDLDNKITSWNRTAERLFGWRREEILGQDVNIIVPEELKKEISNVKEKIGKENLTYETRRITKD-GK 470
                                       699*******************************************9999999999999888888877777777.** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiT 106
                                         ++e++++P+ d++G+   + +i+rDi+
  gi|488600551|ref|YP_007907022.1| 471 IIFVEVTAIPVYDSDGKLTRISFIARDIS 499
                                       ****************************8 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0019      0.99       2      88 ..     153     231 ..     152     232 .. 0.83
   2 !   46.6   0.0   5.9e-15     3e-12       2      88 ..     269     353 ..     268     354 .. 0.97
   3 !   45.9   0.0   9.9e-15   5.1e-12       2      86 ..     412     492 ..     411     495 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +y s r+ + l+ sp e++++   +l+++  +Dr  v+e l+e  +       ++R+ ++d   + +e ++++++d+
  gi|488600551|ref|YP_007907022.1| 153 TYSSSRCLDFLDRSPYEIINR--PLLEFIDSQDRHSVMEVLAEKKEFS---GLDVRLANQD---VVLEISGKPFHDD 221
                                       68899****************..**********999999998554444...4667777776...6899999999999 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g+   + +v
  gi|488600551|ref|YP_007907022.1| 222 SGNFKGYRCV 231
                                       9998777665 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 5.9e-15
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +++++  e+++Gy++ee+ gk   +  l+ pe  + + e++++++++g + ++e  ++ k+G+++ v+ ++++i+d+
  gi|488600551|ref|YP_007907022.1| 269 VSWNKGAEKMFGYTAEEMVGK--PLSTLIPPEKHKDCAENFKKVVNEGFARDIEAIRISKNGKIVVVDQTVTAIHDS 343
                                       89*******************..****************************************************** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +g+ + ++++
  gi|488600551|ref|YP_007907022.1| 344 QGELTGFVAI 353
                                       ****999987 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 9.9e-15
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       ++++++ e+++G+++ee+lg+     +++ pe++++  ++++e + ++e ++ e R+++kdG+++ ve +a +++d+
  gi|488600551|ref|YP_007907022.1| 412 TSWNRTAERLFGWRREEILGQ---DVNIIVPEELKKEISNVKEKI-GKENLTYETRRITKDGKIIFVEVTAIPVYDS 484
                                       68*******************...5799*****************.77789************************** PP

                             PAS_3  79 ngkpvrvi 86 
                                       +gk +r+ 
  gi|488600551|ref|YP_007907022.1| 485 DGKLTRIS 492
                                       ****9986 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.1     2e-30     1e-27       2     135 ..     526     652 ..     525     653 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 2e-30
                            DUF835   2 vkkkekakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekg 78 
                                       +++++ + eilsdl+k+g++++++tR+n+++i    k+e+++v++l+++e+ ntv+P+   +l+e+i+++  +++  
  gi|488600551|ref|YP_007907022.1| 526 EHSTDLCDEILSDLIKCGFDGYIFTRRNSEDI----KCEGARVFYLSEKENFNTVKPDPK-VLRESIIHMQGWNN-- 595
                                       56788899********************9996....7********************997.**************.. PP

                            DUF835  79 vvliDgleyLvlengFesvlkflltlkDavllk.ngtlilvidkealeekelalLkre 135
                                        v+iD l+y++++++F++vl+f++++kDa++l  +g++i++id++ ++e+el++Lk+e
  gi|488600551|ref|YP_007907022.1| 596 AVVID-LDYILMKTQFSEVLEFIQEIKDAFYLFsKGVVIFHIDPSLISESELKILKKE 652
                                       7****.***********************98866**********************98 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.011       5.6       1      35 [.     130     164 ..     130     197 .. 0.75
   2 !   29.3   0.0   1.2e-09   6.2e-07       2      52 ..     247     298 ..     246     313 .. 0.80
   3 !   35.2   0.0   1.7e-11   8.7e-09       1      51 [.     389     440 ..     389     453 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellG 35 
                                       e++r+l+e+++d ++ ++++  i++   + l++l 
  gi|488600551|ref|YP_007907022.1| 130 EKYRSLVENINDWVFEINEDLIITYSSSRCLDFLD 164
                                       79*************99987877776666666665 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1.2e-09
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvl 52 
                                       +l +++e+  d+i+ +dl++riv +N+ a++++Gy+ +++ g++l +l+p  
  gi|488600551|ref|YP_007907022.1| 247 YLVSILEHTIDAIVSLDLDTRIVSWNKGAEKMFGYTaEEMVGKPLSTLIPPE 298
                                       56689************999****************8888888887555543 PP

  == domain 3  score: 35.2 bits;  conditional E-value: 1.7e-11
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51 
                                       e+l  ++e+s+d+i  +dl+++i+ +N++a++l+G++ ++++g+++ +++p+
  gi|488600551|ref|YP_007907022.1| 389 EYLAKIVENSNDAIYSIDLDNKITSWNRTAERLFGWRrEEILGQDVNIIVPE 440
                                       79999*************9999***************999999999755554 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.76   3.9e+02      68     105 ..     198     235 ..     162     236 .. 0.71
   2 !   30.5   0.0   8.4e-10   4.3e-07       4     106 .]     251     358 ..     248     358 .. 0.83
   3 !   22.0   0.1   3.6e-07   0.00018       9     104 ..     399     497 ..     391     499 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.76
                            PAS_10  68 devevvvpkngkwvlvrylpyrdedgeiaGvvetfvDi 105
                                          +v  ++++ +  +  +p++d+ g+++G   +  Di
  gi|488600551|ref|YP_007907022.1| 198 SGLDVRLANQDVVLEISGKPFHDDSGNFKGYRCVARDI 235
                                       3444555677888888999***********99999998 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 8.4e-10
                            PAS_10   4 lLnstpieltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknveeviealrtgek..devevvvpkn 77 
                                       +L++t  +++ lD + +i  +++ a+k+f +++++ vG pl+++ p+++ k+  e ++++ ++    d + + ++kn
  gi|488600551|ref|YP_007907022.1| 251 ILEHTIDAIVSLDLDTRIVSWNKGAEKMFGYTAEEmVGKPLSTLIPPEKHKDCAENFKKVVNEGFarDIEAIRISKN 327
                                       78899999***************99999888765439**********9999998888888887652255666678** PP

                            PAS_10  78 gkwvlv..rylpyrdedgeiaGvvetfvDit 106
                                       gk+v+v  ++ +++d +ge  G v ++ Dit
  gi|488600551|ref|YP_007907022.1| 328 GKIVVVdqTVTAIHDSQGELTGFVAIMRDIT 358
                                       **966422799*******************7 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 3.6e-07
                            PAS_10   9 pieltflDdnlqirrFtpaakklfk.lipadvGrpladihpkkavknveeviealrtgekdevevvvpkngkwvlvr 84 
                                       + ++  +D +++i+ ++++a++lf  ++++ +G +++ i+p++ +k++ +v e++ +++  +++  ++k+gk++ v+
  gi|488600551|ref|YP_007907022.1| 399 NDAIYSIDLDNKITSWNRTAERLFGwRREEILGQDVNIIVPEELKKEISNVKEKIGKENLTYETRRITKDGKIIFVE 475
                                       5567789****************983566778****************************************97665 PP

                            PAS_10  85 y..lpyrdedgeiaGvvetfvD 104
                                       +   p++d dg+   +  +  D
  gi|488600551|ref|YP_007907022.1| 476 VtaIPVYDSDGKLTRISFIARD 497
                                       5116788998887666555555 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.86   4.4e+02      44      91 ..     145     192 ..     106     202 .. 0.74
   2 !   37.5   0.0   3.8e-12   1.9e-09      19     139 ..     237     355 ..     226     358 .. 0.85
   3 ?    6.2   0.0     0.017       8.8      17     131 ..     379     488 ..     365     499 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.86
                            MEKHLA  44 slkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLe 91 
                                       ++++d + +y+  + ld l+++  e+++ p+ + ++++++++  + L+
  gi|488600551|ref|YP_007907022.1| 145 EINEDLIITYSSSRCLDFLDRSPYEIINRPLLEFIDSQDRHSVMEVLA 192
                                       567889999*************99999999999999777666555554 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 3.8e-12
                            MEKHLA  19 Lles.sesaeelakaLfeapfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekva 94 
                                       L ++ +++++ l+  L ++ +a++s +l+++   +  N+ a +++ +t ee++  p+   + pe++++ ++ ++kv 
  gi|488600551|ref|YP_007907022.1| 237 LRKKaEQETAYLVSILEHTIDAIVSLDLDTR--IVSWNKGAEKMFGYTAEEMVGKPLSTLIPPEKHKDCAENFKKVV 311
                                       5555455567778888899999999998754..5556****************************9999******** PP

                            MEKHLA  95 eqgfvenysGvrisstGrrfsienavvWkvldeegkahGqAamfs 139
                                       ++gf+++ +++ris++G+ + ++++ v  + d++g+ +G  a+++
  gi|488600551|ref|YP_007907022.1| 312 NEGFARDIEAIRISKNGKIVVVDQT-VTAIHDSQGELTGFVAIMR 355
                                       ******************9999886.5699999999999877765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.017
                            MEKHLA  17 keLlessesaeelakaLfeapfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLekv 93 
                                       keL es+++ e lak + + ++a+ s +l+  +  +  N++a +l+  + ee+    ++ ++ +e k+e ++  ek+
  gi|488600551|ref|YP_007907022.1| 379 KELEESKRELEYLAKIVENSNDAIYSIDLD--NKITSWNRTAERLFGWRREEILGQDVNIIVPEELKKEISNVKEKI 453
                                       456666777788888888899999888875..556677*************************88899967777777 PP

                            MEKHLA  94 aeqgfvenysGvrisstGrrfsienavvWkvldeegka 131
                                        ++++  +y+  ri+++G+ + +e +++  v+d++gk 
  gi|488600551|ref|YP_007907022.1| 454 GKENL--TYETRRITKDGKIIFVE-VTAIPVYDSDGKL 488
                                       77777..58999******988776.6667888888776 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       9.1   4.7e+03      80     114 ..     203     242 ..     180     243 .. 0.61
   2 !   37.1   0.0   5.7e-12   2.9e-09       1     114 [.     252     364 ..     252     365 .. 0.91
   3 ?    7.1   0.0     0.011       5.8       1      35 [.     395     429 ..     395     482 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9.1
                             PAS_7  80 rerpdgrvievrgnplpd.....gGfVttytDiTerrrae 114
                                       r  ++  v+e+ g+p  d     +G+  +  Di+ r++ae
  gi|488600551|ref|YP_007907022.1| 203 RLANQDVVLEISGKPFHDdsgnfKGYRCVARDISLRKKAE 242
                                       4455667888888888543222245556666777777766 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 5.7e-12
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefg..agdveaeverrlaaaragkp 75 
                                       le+  ++i+ +D d+r+v wN+   +++++++e + vg+pl++l+   +++   +  ++ v++ ++r ++a+r  k+
  gi|488600551|ref|YP_007907022.1| 252 LEHTIDAIVSLDLDTRIVSWNKGAEKMFGYTAEEM-VGKPLSTLIPPEKHKDCAEnfKKVVNEGFARDIEAIRISKN 327
                                       6788899****************************.*********9988877777666779999999999**99999 PP

                             PAS_7  76 hsfererpdgrvievrgnplpdgGfVttytDiTerrrae 114
                                        ++ +   d +v  ++ ++ +  GfV++  DiTer++ae
  gi|488600551|ref|YP_007907022.1| 328 GKIVVV--DQTVTAIHDSQGELTGFVAIMRDITERKKAE 364
                                       988886..899**************************98 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.011
                             PAS_7   1 lenmsqGisvfDadlrLvawNrrylelldlpeelv 35 
                                       +en +++i  +D d++++ wNr   +l+++ +e +
  gi|488600551|ref|YP_007907022.1| 395 VENSNDAIYSIDLDNKITSWNRTAERLFGWRREEI 429
                                       5888999*********************9977655 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   3.5e-09   1.8e-06       1      48 [.      69     115 ..      69     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.5e-09
                                       HHHHTTHHHHHHHHHHHHHHTTTBTSSTCCTTSSSHHHHHHHHHHHHH CS
                              HAMP   1 llarrilrPLrrLaraarriaaGdldtrlpvsgrDEiGeLarafNaMl 48 
                                       + a++i+ P++r+++   ++a+G+  + + v+++DE+ eLa +fN M+
  gi|488600551|ref|YP_007907022.1|  69 FAAGSIVEPIKRVKEGFTKLANGEKAY-VKVNTGDELEELADSFNIMA 115
                                       6799*******************9777.9*****************96 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   5.6e-07   0.00029       1      43 [.     679     720 ..     679     721 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.6e-07
                            HTH_41   1 kvGdRlktIeelakeleLSvGlvQkALklLeddkaislerrGr 43 
                                       +vG+R ++I+el ++++L + ++ k L  L + + i++e+ Gr
  gi|488600551|ref|YP_007907022.1| 679 RVGNR-PSIKELMEKFGLARNTIKKRLSYLASRGLIKIEKEGR 720
                                       58999.9***********************************9 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.7e-06   0.00088      22      59 ..     680     716 ..     666     720 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                                       HSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind  22 tgypPsireiaralglkSpsaveehLkaLerKGyierd 59 
                                        g  Psi+e+++++gl+  ++++++L  L+ +G+i+++
  gi|488600551|ref|YP_007907022.1| 680 VGNRPSIKELMEKFGLA-RNTIKKRLSYLASRGLIKIE 716
                                       4788*************.9****************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 !   17.7   0.0     4e-06     0.002      25      62 ..     684     721 ..     677     723 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-06
                                       --HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR  25 PsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62 
                                       Ps +eL+++fg  r+t+ + L+ L+++gl+ +++ + +
  gi|488600551|ref|YP_007907022.1| 684 PSIKELMEKFGLARNTIKKRLSYLASRGLIKIEKEGRI 721
                                       89****************************99987655 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.85   4.4e+02     204     252 ..      93     141 ..      22     196 .. 0.72
   2 !   15.5   0.9   1.2e-05    0.0063     182     283 ..     349     468 ..     348     534 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.85
                             LMBR1 204 klyfeaaklntekeeaereledllkevkklrksisesdp.lrkyleeilk 252
                                       k+y+++ + + e+ee  + ++ +  e++++r+ i+e+++ +r+ +e+i +
  gi|488600551|ref|YP_007907022.1|  93 KAYVKVNTGD-ELEELADSFNIMAYEIMRQREVIKENEEkYRSLVENIND 141
                                       5555555555.777777788878888888888888888767777777665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
                             LMBR1 182 GlvelPrslwreiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilk...... 252
                                       G+v++ r++    +++ +  l+ +y e+++ ++e+ee++rele l k v+++++ i + d     l++ ++      
  gi|488600551|ref|YP_007907022.1| 349 GFVAIMRDITE--RKKAEMALRTAYKELEERTKELEESKRELEYLAKIVENSNDAIYSID-----LDNKITswnrta 418
                                       9********88..******************************88888888888887777.....222222355566 PP

                             LMBR1 253 ..................kvPeeiaeklksnenk.teeslaklekqlika 283
                                                          vPee+++++++ ++k  +e+l+ +++++ k 
  gi|488600551|ref|YP_007907022.1| 419 erlfgwrreeilgqdvniIVPEELKKEISNVKEKiGKENLTYETRRITKD 468
                                       6788888888888999999********99944444666777777666654 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 !   16.7   0.0   1.5e-05    0.0076       7      68 .]     669     730 ..     664     730 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-05
                            HTH_27   7 lvLhlir...hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +++++i+   + ++r ++++l+++  +   +i + l+ L  +GL+   + e+++r k v+lTdkG
  gi|488600551|ref|YP_007907022.1| 669 QLMRHIYmenRVGNRPSIKELMEKFGLARNTIKKRLSYLASRGLI---KIEKEGRIKIVELTDKG 730
                                       67888887777788999****************************...56677***********9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.2e-05     0.022       2      55 ..     662     717 ..     661     721 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-05
                                       T--HHHHHHHHHHHCTTTS..EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   2 gltpaqarvLaaLgrrpgr..dltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       +l++  ++++ +++ + +   + +++el +++gl + ++ ++l  L ++GL+  ++
  gi|488600551|ref|YP_007907022.1| 662 DLPGEVYQLMRHIYMENRVgnRPSIKELMEKFGLARNTIKKRLSYLASRGLIKIEK 717
                                       78888899999999999768888*****************************8764 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   7.5e-05     0.039       7      59 ..     669     721 ..     667     725 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
                   Penicillinase_R   7 evmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegra 59 
                                       + m+++++++++  +  ++el e+  la++T+k  l+ L  +gl++ ekegr 
  gi|488600551|ref|YP_007907022.1| 669 QLMRHIYMENRVGNRPSIKELMEKFGLARNTIKKRLSYLASRGLIKIEKEGRI 721
                                       689*********99999**********************************96 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       8.4   4.3e+03      98     120 ..     115     137 ..     102     142 .. 0.65
   2 !   15.6   1.5   1.8e-05    0.0093      32     121 ..     305     394 ..     303     402 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.4
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B  98 aferelqaklareikkkldtlvn 120
                                       a+e  +q ++++e ++k+ +lv+
  gi|488600551|ref|YP_007907022.1| 115 AYEIMRQREVIKENEEKYRSLVE 137
                                       45556666666666666666665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_B  32 kslgpsikefldkriekiqeelnqsrnlkeealkerieqekklqslveltkslfevskeqvaleaeaferelqakla 108
                                        +++++++e +  +ie+i+ + n  +    ++++ + +++ +l  +v++  +++e +k ++al   + e+e ++k  
  gi|488600551|ref|YP_007907022.1| 305 ENFKKVVNEGFARDIEAIRISKNGKIVVVDQTVTAIHDSQGELTGFVAIMRDITERKKAEMALRTAYKELEERTKEL 381
                                       689************************************************************************** PP

                                       HHHHHHHHHHHHH CS
                     Mt_ATP-synt_B 109 reikkkldtlvna 121
                                        e k+ l++l + 
  gi|488600551|ref|YP_007907022.1| 382 EESKRELEYLAKI 394
                                       *********9875 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5     9e-05     0.046      82     128 ..     110     157 ..      93     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-05
                                       HHHHHHHHHHHH...T--TT--HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            Rsbr_N  82 efrkvvlellseed.dvvkeeqslelleeieewidpivnelvneYsgs 128
                                       +f  + +e++++++  + +ee+  +l+e+i++w+ +i++ l+  Ys+s
  gi|488600551|ref|YP_007907022.1| 110 SFNIMAYEIMRQREvIKENEEKYRSLVENINDWVFEINEDLIITYSSS 157
                                       467788999999986666777899*********************986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.3e-05     0.022      26      61 .]     685     720 ..     669     720 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-05
                                       -HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  26 taselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                       + +el+e ++l++nt+ ++L  L++ gL++ ++egr
  gi|488600551|ref|YP_007907022.1| 685 SIKELMEKFGLARNTIKKRLSYLASRGLIKIEKEGR 720
                                       789*******************************97 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0004      0.21       6      88 ..     260     338 ..     257     362 .. 0.83
   2 ?   -1.4   0.0       4.7   2.4e+03       6      21 ..     463     478 ..     459     486 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvk 82 
                                       + ld+d +I+s ++    a+   g++ ee+vg+ + +L+ p+  ++ ++ +++v+++  +  +   R++  ++k+v 
  gi|488600551|ref|YP_007907022.1| 260 VSLDLDTRIVSWNK---GAEKMFGYTAEEMVGKPLSTLIPPEKHKDCAENFKKVVNEGFARDIEAIRISK-NGKIVV 332
                                       679***********...**************************************888888888899988.777777 PP

                            PAS_11  83 vktksk 88 
                                       v  +  
  gi|488600551|ref|YP_007907022.1| 333 VDQTVT 338
                                       644443 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.7
                            PAS_11   6 trldidgkIisvDtsa 21 
                                        r++ dgkIi v+ +a
  gi|488600551|ref|YP_007907022.1| 463 RRITKDGKIIFVEVTA 478
                                       57889*****999755 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   0.1   0.00019     0.095      19      48 .]     685     714 ..     682     714 .. 0.95
   2 ?   -2.3   0.0       6.4   3.3e+03      12      25 ..     715     728 ..     715     729 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                            HTH_24  19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       s++eL e+ gl ++t+++rl  L + GlIk
  gi|488600551|ref|YP_007907022.1| 685 SIKELMEKFGLARNTIKKRLSYLASRGLIK 714
                                       89**************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.4
                            HTH_24  12 LqknprisqreLAe 25 
                                       ++k++ri + eL +
  gi|488600551|ref|YP_007907022.1| 715 IEKEGRIKIVELTD 728
                                       68999**9999976 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 ?   12.8   0.0   0.00014     0.073      16      45 ..     685     714 ..     682     725 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                          HTH_DeoR  16 sveelvellgvSeaTiRRDLneLeeqgllt 45 
                                       s++el+e +g + +Ti + L++L+  gl++
  gi|488600551|ref|YP_007907022.1| 685 SIKELMEKFGLARNTIKKRLSYLASRGLIK 714
                                       79*************************975 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00016     0.081      28      70 .]     688     730 ..     680     730 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                              PaaX  28 rllaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdkg 70 
                                       +l++++G+  +++   ls la +G+++ ekegr  + +L+dkg
  gi|488600551|ref|YP_007907022.1| 688 ELMEKFGLARNTIKKRLSYLASRGLIKIEKEGRIKIVELTDKG 730
                                       79*******************************9999**9996 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   0.00032      0.16      25      59 ..     686     720 ..     682     729 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                                       HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                              TrmB  25 adeiaeelgvprskvYevLrsLedkGlVerekgrp 59 
                                       ++e+ e+ g+ r+++ + L+ L ++Gl+++ek+ +
  gi|488600551|ref|YP_007907022.1| 686 IKELMEKFGLARNTIKKRLSYLASRGLIKIEKEGR 720
                                       6899***************************9764 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00022      0.12      17      50 ..     685     719 ..     678     721 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
                            HTH_11  17 sgeeLAeeLnvSrrtvrrdIkaLeelg.vpIesep 50 
                                       s++eL+e++++ r t+ +++  L + g ++Ie+e 
  gi|488600551|ref|YP_007907022.1| 685 SIKELMEKFGLARNTIKKRLSYLASRGlIKIEKEG 719
                                       89*********************99999***9986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       3.3   1.7e+03      42      57 ..     118     133 ..     113     134 .. 0.89
   2 ?   10.7   0.0   0.00078       0.4      24      65 ..     688     733 ..     678     743 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.3
                            HTH_45  42 mLvekglikkskekYv 57 
                                       ++ ++++ik+++ekY+
  gi|488600551|ref|YP_007907022.1| 118 IMRQREVIKENEEKYR 133
                                       7999**********96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00078
                            HTH_45  24 kimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlel 65 
                                       ++m k  L  ++++k L++L ++gli    + + +  +lT+kG+++
  gi|488600551|ref|YP_007907022.1| 688 ELMEKFGLARNTIKKRLSYLASRGLIkiekEGRIKIVELTDKGKDY 733
                                       7899999******************9776333667789*****986 PP

>> DUF4743  Domain of unknown function (DUF4743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00033      0.17      21     120 ..     329     425 ..     307     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                                       EEEETTEEEEEEEHHHHHHHCT-TTTEEE-SS....EEEE-TT--SHHHHHHHHHHHHHHHHHTT...SS----S-E CS
                           DUF4743  21 pFvvegqqvGlirpdvaeklrkfpdvFevseke...aveLapslktyeeRtaaveevleelreegsfvalkgwRdEl 94 
                                       + vv +q+v  i+ +   +l+ f ++ +  +++    + L+ ++k+ eeRt+++ee  +el+     +++++  d  
  gi|488600551|ref|YP_007907022.1| 329 KIVVVDQTVTAIHDS-QGELTGFVAIMRDITERkkaEMALRTAYKELEERTKELEESKRELEYLA--KIVENSNDAI 402
                                       678888888888765.4568888887763333335699***********************9988..899999**** PP

                                       EEE-SSTTS---EEEEGGGTGGGT-- CS
                           DUF4743  95 YeVrasfsdppllkleRaaaplfGvk 120
                                       Y++  +    ++ + +R+a +lfG +
  gi|488600551|ref|YP_007907022.1| 403 YSIDLDN---KITSWNRTAERLFGWR 425
                                       *998755...59999********976 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00035      0.18      26      55 .]     684     713 ..     670     713 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                            HTH_36  26 psqetlakrlglsknTvsraikeLeqlGyi 55 
                                       ps + l++++gl +nT+ + +  L+  G+i
  gi|488600551|ref|YP_007907022.1| 684 PSIKELMEKFGLARNTIKKRLSYLASRGLI 713
                                       99**************************98 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.27   1.4e+02       4      18 ..     142     156 ..     142     158 .. 0.95
   2 ?   -0.2   0.0       2.5   1.3e+03       5      14 ..     481     490 ..     477     508 .. 0.77
   3 ?    5.3   0.0     0.048        24      17      35 ..     684     702 ..     684     704 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.27
                            NUMOD1   4 yvYDlntktigkFsS 18 
                                       +v+ +n ++i ++sS
  gi|488600551|ref|YP_007907022.1| 142 WVFEINEDLIITYSS 156
                                       9*************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.5
                            NUMOD1   5 vYDlntktig 14 
                                       vYD ++k+++
  gi|488600551|ref|YP_007907022.1| 481 VYDSDGKLTR 490
                                       9****99973 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.048
                            NUMOD1  17 sSireAakyLgishntInk 35 
                                       +Si+e+ +++g  +ntI+k
  gi|488600551|ref|YP_007907022.1| 684 PSIKELMEKFGLARNTIKK 702
                                       6****************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00042      0.22      21      61 ..     683     725 ..     668     728 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..ETEEEEES- CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis..rgrririld 61 
                                       + + +el +  Gl r t+ + ls L  +gli+  +++ri+i  
  gi|488600551|ref|YP_007907022.1| 683 RPSIKELMEKFGLARNTIKKRLSYLASRGLIKieKEGRIKIVE 725
                                       55667888899*********************74333499875 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 ?    8.7   0.2     0.003       1.5     109     156 ..      97     144 ..      78     146 .. 0.86
   2 ?    3.2   0.2      0.14        74      38     147 ..     255     401 ..     226     415 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                       EMP24_GP25L 109 kkekletleselkkleekldsikreqkylrereerlrdtnestnsrvv 156
                                       k ++ ++le+  + ++    +i+r+ + ++e+ee+ r ++e++n++v+
  gi|488600551|ref|YP_007907022.1|  97 KVNTGDELEELADSFNIMAYEIMRQREVIKENEEKYRSLVENINDWVF 144
                                       55667888889999999999*************************996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                       EMP24_GP25L  38 dvdlsvkdpdgngerlvkkkdresegdfsftak...........esgeykvCfdnsfstkss............... 88 
                                       ++d+ v    + + r+v+  ++ +e+ f +ta+            + ++k C +n ++  ++               
  gi|488600551|ref|YP_007907022.1| 255 TIDAIVS--LDLDTRIVSW-NKGAEKMFGYTAEemvgkplstliPPEKHKDCAENFKKVVNEgfardieairiskng 328
                                       5555555..4444566665.444444666666556666666666666666666664443333666666665555555 PP

                       EMP24_GP25L  89 kkvsfdiev..gseasd..............ykdsak.kekletleselkkleekldsikreqkylrereerlrdt 147
                                       k v +d +v   +   d              +++ +k ++ l t  +el++  + l+++kre++yl +  e+  d+
  gi|488600551|ref|YP_007907022.1| 329 KIVVVDQTVtaIH---DsqgeltgfvaimrdITERKKaEMALRTAYKELEERTKELEESKRELEYLAKIVENSNDA 401
                                       4444444441122...123466677777666555555589999999999999999999999999998766665555 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.9   9.8e+02      71      94 ..     108     131 ..      98     140 .. 0.79
   2 ?    8.8   0.9    0.0045       2.3      31      79 ..     358     408 ..     331     419 .. 0.75
   3 ?    1.2   0.0       1.1   5.5e+02      44      88 ..     647     707 ..     637     711 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.9
                      Syntaxin-6_N  71 pskfkidekelsrrrafveevree 94 
                                        + f+i + e+ r+r++++e +e+
  gi|488600551|ref|YP_007907022.1| 108 ADSFNIMAYEIMRQREVIKENEEK 131
                                       466999999999999999987776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0045
                      Syntaxin-6_N  31 tss.stseeldetrteLrkalrsiewdledLeetvriveknpsk.fkidek 79 
                                       t+  + +  l+ + +eL++  +++e+  ++Le   +ive++++  ++id +
  gi|488600551|ref|YP_007907022.1| 358 TERkKAEMALRTAYKELEERTKELEESKRELEYLAKIVENSNDAiYSIDLD 408
                                       333345778888999999999999999999999999**9998887888865 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.1
                      Syntaxin-6_N  44 teLrkalrsiewdledLeetv................riveknpskfkidekelsrrrafv 88 
                                       + L+k+++si+++  dL   v                  +++  +kf++  +++++r +++
  gi|488600551|ref|YP_007907022.1| 647 KILKKECESIKQKEHDLPGEVyqlmrhiymenrvgnrPSIKELMEKFGLARNTIKKRLSYL 707
                                       5589999999999999999996555555555444443222335588999999999997765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3     0.009       4.6     136     187 ..      96     147 ..      79     151 .. 0.88
   2 ?    6.1   1.0     0.021        11      81     131 ..     341     396 ..     303     466 .. 0.73
   3 ?   -1.1   0.1       3.4   1.7e+03      79     105 ..     643     667 ..     607     708 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.009
                           UPF0242 136 lkleleeqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEik 187
                                       +k +  ++L+e    ++ ++ +i  qr+v+++ +++   L   ++D  +Ei 
  gi|488600551|ref|YP_007907022.1|  96 VKVNTGDELEELADSFNIMAYEIMRQREVIKENEEKYRSLVENINDWVFEIN 147
                                       56677789999999999*********************************96 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.021
                           UPF0242  81 d......eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae 131
                                               g+  +   + e+++ e+ L+  +++ ee  ++l+e + +L+  l +i+e
  gi|488600551|ref|YP_007907022.1| 341 HdsqgelTGFVAIMRDITERKKAEMALRTAYKELEERTKELEESKRELE-YLAKIVE 396
                                       0344444456666668999999999999999999999999999999988.4555554 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.4
                           UPF0242  79 eldeglktkeealeelqeeeeeLkeel 105
                                       e +  lk+ +++ e  +++e++L  e+
  gi|488600551|ref|YP_007907022.1| 643 ESE--LKILKKECESIKQKEHDLPGEV 667
                                       333..4555555555555555544442 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8   0.00027      0.14      31      63 ..     358     390 ..     350     393 .. 0.92
   2 ?   -1.2   0.0       4.4   2.3e+03      43      58 ..     495     510 ..     484     513 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00027
                       Cep57_CLD_2  31 kERdsalrqLgvAyeelneLkaevealrkELke 63 
                                       +ER  a+++L+ Ay el+e + e+e  ++EL++
  gi|488600551|ref|YP_007907022.1| 358 TERKKAEMALRTAYKELEERTKELEESKRELEY 390
                                       59****************************986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.4
                       Cep57_CLD_2  43 AyeelneLkaevealr 58 
                                       A++ + +Lkae e lr
  gi|488600551|ref|YP_007907022.1| 495 ARDISSKLKAEKELLR 510
                                       7888899****99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1428  (0.0796475); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); 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):              35  [number of targets reported over threshold]
# CPU time: 0.95u 0.34s 00:00:01.29 Elapsed: 00:00:00.56
# Mc/sec: 4009.04
//
Query:       gi|488600552|ref|YP_007907023.1|  [L=47]
Description: hypothetical protein Asulf_01026 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   13.7   2.2      0.047   13.4   2.2    1.3  1  DUF131    Protein of unknown function DUF131


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.2   2.6e-06     0.047      41      61 ..      17      37 ..      14      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-06
                            DUF131 41 krlaktaiiLaIilmilllil 61
                                      ++l+k+++iL+I+l+ill ++
  gi|488600552|ref|YP_007907023.1| 17 GKLIKWSVILGIVLTILLAAI 37
                                      589**************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 269.65
//
Query:       gi|488600553|ref|YP_007907024.1|  [L=484]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-24   84.0  16.2    8.3e-24   84.0  16.2    1.7  1  Cons_hypoth698  Conserved hypothetical protein 698


Domain annotation for each model (and alignments):
>> Cons_hypoth698  Conserved hypothetical protein 698
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0  16.2   4.6e-28   8.3e-24      27     302 ..     140     452 ..     101     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 4.6e-28
                    Cons_hypoth698  27 salllAillGillgn.flklqeqlkaGvafskkklLrlgivllGfrltlsdiakvGlkgvlldiivlistfl..... 97 
                                       ++ ++A+++G+l+gn ++k  +++ +  a  +  +++++iv+lG++l l+ i + G+ + ll + v ++++      
  gi|488600553|ref|YP_007907024.1| 140 AYYIIALIIGLLIGNfAPKGFKEFMKRAARPE-WFIKIAIVALGAKLGLKAIEATGFAMHLLFAGVCATIAAyllfw 215
                                       4689***********55555555555555555.789********************987777666665555411122 PP

                    Cons_hypoth698  98 .lvlllgakllkldkklalLvaaGssiCGasAilavepvikareeevalaiavivllgtvamllyP.alatllsltd 172
                                        l+ +++ k++kl+k+ ++ +a+G siCG+sA +a++ +i+ar+    +  + iv++ ++ ++++P +l t   +++
  gi|488600553|ref|YP_007907024.1| 216 pLAYTMSRKVFKLSKEWSACLASGISICGVSAAIATAGAIRARPIVPVMISSLIVVFAVIELVILPgVLVTTWFHEP 292
                                       24567899************************************988888899*************5567777778* PP

                    Cons_hypoth698 173 eefgvfaGasvhevaqVvaagelvseeaak................iAvivKltRvlllapvvlllslllakreees 233
                                        ++g+  G++v+  +  +aag+ +++   +                 A+++K+   + ++   ++l+ ++ +  e++
  gi|488600553|ref|YP_007907024.1| 293 IAAGASLGLTVKTDGADAAAGAILDQLMISkaasmgiywdegwilaSAIMTKIWIDMFIGVWAFVLATVWVYYFERK 369
                                       *********************99998877778889*******************99999988888877665555544 PP

                    Cons_hypoth698 234 etkeakit.....iPwFvlg.Flvvallntlvllp........selvsalktlstlllvmalaAlglktdlkalkka 296
                                         ++ +++     +P+Fv+g F+++  + +l l            l  +  +l  ++++++++ +g+ td++alk+ 
  gi|488600553|ref|YP_007907024.1| 370 PGEKVQKMeiwwrFPKFVIGyFVAMFSVMGLGLAGilshesleFGLKPVEGALRHFFFMLTFTSIGIVTDFRALKEE 446
                                       4444422224466999998647888888888777677765554556666678999*********************9 PP

                    Cons_hypoth698 297 glkpll 302
                                       gl  l+
  gi|488600553|ref|YP_007907024.1| 447 GLGRLA 452
                                       986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1059  (0.0590663); 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:                         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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 3817.20
//
Query:       gi|488600554|ref|YP_007907025.1|  [L=78]
Description: hypothetical protein Asulf_01028 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-27   96.1   0.1    1.5e-27   96.0   0.1    1.0  1  DUF5395       Family of unknown function (DUF5395)
  ------ inclusion threshold ------
      0.051   13.8   0.0      0.062   13.5   0.0    1.1  1  Poly_export   Polysaccharide biosynthesis/export protein
      0.087   12.8   0.0       0.11   12.4   0.0    1.1  1  RepB-RCR_reg  Replication regulatory protein RepB
      0.094   12.9   0.1       0.14   12.3   0.1    1.4  1  DUF596        Protein of unknown function, DUF596


Domain annotation for each model (and alignments):
>> DUF5395  Family of unknown function (DUF5395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.1   3.4e-31   1.5e-27       2      78 ..       4      77 ..       3      78 .] 0.96

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 3.4e-31
                           DUF5395  2 lelrlvhdgekWiaeneelvvkgktleeLDenlakelkkrgdfkgksqvevfmkfDyetiPtwirqyaphYfnRvve 78
                                      + l+l hdg++Wia+n e+v+kg+tl+eLD+++++ ++k+  ++gk +v+v m+fDy++iP wi qy+p+Y+ Rv+ 
  gi|488600554|ref|YP_007907025.1|  4 IVLSLLHDGKQWIAKNGEIVAKGETLDELDKEIESVVRKK--YPGK-KVKVSMEFDYSSIPFWIIQYHPYYLYRVIY 77
                                      6689**********************************99..****.****************************96 PP

>> Poly_export  Polysaccharide biosynthesis/export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.4e-05     0.062      48      80 ..      20      52 ..       9      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                       Poly_export 48 GkikvaGltveelreeieekl.skylkdpqvtVr 80
                                      G+i ++G t++el +eie+ + +ky    +v+V+
  gi|488600554|ref|YP_007907025.1| 20 GEIVAKGETLDELDKEIESVVrKKY-PGKKVKVS 52
                                      99*******************5446.44455555 PP

>> RepB-RCR_reg  Replication regulatory protein RepB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05      0.11      15      46 ..      22      53 ..      16      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                      RepB-RCR_reg 15 iyrkGkPltdaekqrlsvsrkklthkeikvfi 46
                                      i+ kG+ l + +k+  sv rkk   k++kv +
  gi|488600554|ref|YP_007907025.1| 22 IVAKGETLDELDKEIESVVRKKYPGKKVKVSM 53
                                      899**************************965 PP

>> DUF596  Protein of unknown function, DUF596
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.1e-05      0.14       9      55 ..      23      70 ..       9      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
                                      EETTEEE---HHHHHHHHHHH--SSSEE--TS.-EE.HHHHHHHT-SS CS
                            DUF596  9 arkgefieGtteelvemfrksfPesdeeldle.dvdaeglWfvvecpa 55
                                        kge ++   +e   + rk +P ++ ++ +e d  +  +W + + p 
  gi|488600554|ref|YP_007907025.1| 23 VAKGETLDELDKEIESVVRKKYPGKKVKVSMEfDYSSIPFWIIQYHPY 70
                                      34566666666889999************9997788888998877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); 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: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 510.29
//
Query:       gi|488600555|ref|YP_007907026.1|  [L=366]
Description: Uncharacterized Fe-S center protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  118.9   0.2      4e-34  118.6   0.2    1.1  1  DUF362    Domain of unknown function (DUF362)
    2.2e-08   33.6  14.5    1.8e-05   24.4   6.3    2.5  2  Fer4      4Fe-4S binding domain
    1.1e-07   31.6  13.9    5.1e-05   23.2   4.9    2.6  2  Fer4_6    4Fe-4S binding domain
    2.8e-06   27.4  10.4     0.0002   21.4   2.5    2.4  2  Fer4_9    4Fe-4S dicluster domain
    0.00012   22.9   9.8    0.00083   20.2   1.9    2.5  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00014   22.4  14.8     0.0083   16.7  13.6    2.4  3  Fer4_7    4Fe-4S dicluster domain
    0.00039   20.5  13.0      0.083   13.0   1.2    2.5  2  Fer4_21   4Fe-4S dicluster domain
    0.00057   20.0  15.0      0.049   13.7  15.4    2.4  2  Fer4_10   4Fe-4S dicluster domain
     0.0013   17.9   0.7     0.0033   16.6   0.2    1.7  2  Lar_N     Lactate racemase N-terminal domain
     0.0026   17.8  14.2      0.005   16.9   5.2    2.6  2  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   16.4  15.9      0.056   14.4   5.1    2.9  2  Fer4_3    4Fe-4S binding domain
      0.036   14.6   4.0      0.036   14.6   4.0    2.6  2  Fer4_4    4Fe-4S binding domain
      0.076   13.2   7.7       0.16   12.2   7.7    1.5  1  Fer4_18   4Fe-4S dicluster domain
       0.61   10.6  15.5       0.17   12.4   2.9    2.5  3  Fer4_8    4Fe-4S dicluster domain
       0.67   10.5  15.4       0.76   10.4   4.2    2.4  2  Fer4_17   4Fe-4S dicluster domain
        3.1    8.4  13.9       0.68   10.5   4.2    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.2   3.6e-37     4e-34       1     202 [.      49     317 ..      49     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 3.6e-37
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxx..xxxxxxxxxxxxxxx.xx.x RF
                            DUF362   1 VaiKpNlgeagnpegatthpevvravvellkeagagkiivgdspgl.yv.srgka..hrevaeeagydelae.ga.d 71 
                                       Va+K ++g +g +++  +++ ++r +v+ +k++g gk++v++++gl +   r+ a    e+aee+gy++ +     +
  gi|488600555|ref|YP_007907026.1|  49 VAVKTHFGDRGTTKT--LRSVYIRTIVKEIKKRG-GKPFVTETTGLgLTrLRSSAigRIEIAEENGYTSQTLlAPiI 122
                                       9*******8888886..*****************.9*********96544555667789*********96666336* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx..... RF
                            DUF362  72 iadglegedevvvpvkgkhlkkelkiakavleaDviInlpklKgHalagvtgalKn.lfGcisgsgkaeiHs..... 142
                                       iadg  g d v+v+++g+hlk+ + +aka++ +D +++ +++K H++ag++g++Kn ++Gc+++ +k ++H      
  gi|488600555|ref|YP_007907026.1| 123 IADGVMGFDFVKVNINGRHLKD-VFVAKAFESVDKVVCATHFKLHMMAGMGGSIKNvGVGCVAKPSKYDLHCpnppy 198
                                       ***************9999888.****************************************************** PP

                                       .................................................xxxxxxxxxxxxxxxxxx.....xxx.. RF
                            DUF362 143 .................................................krdsekfaekiadlakal.....kpd.. 163
                                                                                        + + +++ e+i+++ak++     + +  
  gi|488600555|ref|YP_007907026.1| 199 inenctecgdcveicpagaiknfridhsiclkctgcsevckydavtiepWLGGREIGERIVECAKGVyevvgEENfa 275
                                       ***********************************************97555678***********66888633346 PP

                                       .xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx RF
                            DUF362 164 .lnvvdgikamegegpsggskelglv.....laStDpvalDaaaa 202
                                        +n++ +++++ +  p + +   +++     ++S+D+v +Da+++
  gi|488600555|ref|YP_007907026.1| 276 fFNFMIDVTPHCDCHPYSDN---NIIpdvgiFVSRDIVSVDAVCL 317
                                       67******776665554444...44445556*************7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   6.3   1.6e-08   1.8e-05       3      24 .]     198     219 ..     196     219 .. 0.90
   2 !   13.9   1.1   3.2e-05     0.035       2      24 .]     222     244 ..     221     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.6e-08
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       ++ e C+ CG Cve+CP gAI+
  gi|488600555|ref|YP_007907026.1| 198 YINENCTECGDCVEICPAGAIK 219
                                       67899****************6 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.2e-05
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        id + C +C  C evC ++A t
  gi|488600555|ref|YP_007907026.1| 222 RIDHSICLKCTGCSEVCKYDAVT 244
                                       599*****************975 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   4.9   4.6e-08   5.1e-05       6      24 .]     200     218 ..     198     218 .. 0.93
   2 !   13.3   1.6   6.1e-05     0.068       3      23 ..     222     242 ..     221     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.6e-08
                            Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                        ++C+ CgdCv +CP+gai
  gi|488600555|ref|YP_007907026.1| 200 NENCTECGDCVEICPAGAI 218
                                       689***************8 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.1e-05
                            Fer4_6   3 eidpdkCigCgdCvrvCPega 23 
                                       +id + C+ C  C  vC ++a
  gi|488600555|ref|YP_007907026.1| 222 RIDHSICLKCTGCSEVCKYDA 242
                                       699**************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 !   21.4   2.5   1.8e-07    0.0002      33      51 .]     196     218 ..     150     218 .. 0.80
   2 !   10.5   1.1   0.00048      0.54       2      17 ..     228     243 ..     219     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                            Fer4_9  33 e....eaCigCgaCveaCpkgai 51 
                                            e+C++Cg+Cve+Cp gai
  gi|488600555|ref|YP_007907026.1| 196 PpyinENCTECGDCVEICPAGAI 218
                                       2567789*************987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00048
                            Fer4_9   2 CtgCgaCveaCpagvv 17 
                                       C +C+ C e+C++++v
  gi|488600555|ref|YP_007907026.1| 228 CLKCTGCSEVCKYDAV 243
                                       5555555555555544 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.9   7.4e-07   0.00083       1      20 [.     202     221 ..     202     226 .. 0.90
   2 ?    7.0   1.2      0.01        12       2      18 ..     228     244 ..     227     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.4e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++Cg C+e+CP++aik+ 
  gi|488600555|ref|YP_007907026.1| 202 NCTECGDCVEICPAGAIKNF 221
                                       6****************975 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C +C+ C evC  +a++
  gi|488600555|ref|YP_007907026.1| 228 CLKCTGCSEVCKYDAVT 244
                                       99*********999876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   5.3   2.8e-05     0.031      33      52 .]     198     217 ..     179     217 .. 0.83
   2 !   16.7  13.6   7.4e-06    0.0083       2      52 .]     203     242 ..     202     242 .. 0.93
   3 !   10.7   2.6   0.00055      0.62       2      21 ..     228     247 ..     227     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                            Fer4_7  33 idpekClgCgaCvavCPtga 52 
                                       +  e+C+ Cg Cv+ CP+ga
  gi|488600555|ref|YP_007907026.1| 198 YINENCTECGDCVEICPAGA 217
                                       55799************997 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.4e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       C++Cg Cv+ Cp++ai+             +id++ Cl C+ C +vC ++a
  gi|488600555|ref|YP_007907026.1| 203 CTECGDCVEICPAGAIKN-----------FRIDHSICLKCTGCSEVCKYDA 242
                                       ****************96...........579***************9986 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00055
                            Fer4_7   2 CigCgaCvaaCpvkaielde 21 
                                       C +C  C ++C+++a+++++
  gi|488600555|ref|YP_007907026.1| 228 CLKCTGCSEVCKYDAVTIEP 247
                                       999999*****999999876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   4.7   0.00014      0.16      35      58 ..     197     219 ..     176     220 .. 0.81
   2 !   13.0   1.2   7.4e-05     0.083       2      30 ..     222     247 ..     221     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                           Fer4_21  35 kvvedeCvGCnlCssvCPvedcie 58 
                                       ++++++C+ C  C+++CP  ++i+
  gi|488600555|ref|YP_007907026.1| 197 PYINENCTECGDCVEICPA-GAIK 219
                                       6789**************5.8885 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.4e-05
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieida 30 
                                       rid++ C++C+ C  +C+   ++a++i++
  gi|488600555|ref|YP_007907026.1| 222 RIDHSICLKCTGCSEVCK---YDAVTIEP 247
                                       79***************9...67777665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7  15.4   4.4e-05     0.049       6      55 ..     200     238 ..     196     238 .. 0.70
   2 !   10.0   3.1   0.00064      0.72       3      19 ..     222     238 ..     220     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                        + C++Cg+Cv+ CPa        g++++   ++  + kCtgc    e+C
  gi|488600555|ref|YP_007907026.1| 200 NENCTECGDCVEICPA--------GAIKNFRIDHSICLKCTGC---SEVC 238
                                       478*************........6655555555566665555...5555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00064
                           Fer4_10   3 vidddtCirCgkCvkaC 19 
                                       +id + C++C+ C ++C
  gi|488600555|ref|YP_007907026.1| 222 RIDHSICLKCTGCSEVC 238
                                       6999************* 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 ?   -1.5   0.0       1.1   1.2e+03      38      85 ..      30      80 ..      22      88 .. 0.69
   2 !   16.6   0.2   2.9e-06    0.0033     143     185 ..     143     185 ..     138     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                             Lar_N 38 Lenpigsekleelvkekekvvivvs..D.iTRptpskiilpllleelkeag 85
                                      L++ i+++k+ +++ +++ v++ +   D  T +t ++++++++++e+k+ g
  gi|488600555|ref|YP_007907026.1| 30 LKRLIDESKILDFIDKGDIVAVKTHfgDrGTTKTLRSVYIRTIVKEIKKRG 80
                                      667777777777777777777765411313444555888999999998866 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.9e-06
                             Lar_N 143 tpveinklvaeadlviltGfiepHyfaGfsGGrKsilpGvasr 185
                                        +v + k++ + d+v++    + H++aG++G  K +  G+  +
  gi|488600555|ref|YP_007907026.1| 143 KDVFVAKAFESVDKVVCATHFKLHMMAGMGGSIKNVGVGCVAK 185
                                       5899**********************************98665 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   5.2   4.5e-06     0.005       2      22 .]     196     215 ..     195     215 .. 0.89
   2 ?    5.5   1.6     0.018        20       6      20 ..     224     238 ..     220     240 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       p++++++ C++Cg Cv  CPa
  gi|488600555|ref|YP_007907026.1| 196 PPYINEN-CTECGDCVEICPA 215
                                       5788877.************8 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.018
                            Fer4_2   6 dtdrCigCgaCvsaC 20 
                                       d  +C+ C  C  +C
  gi|488600555|ref|YP_007907026.1| 224 DHSICLKCTGCSEVC 238
                                       666788887788888 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   5.1     5e-05     0.056       1      15 []     203     217 ..     203     217 .. 0.97
   2 ?    6.8   3.0     0.013        15       1      15 []     228     242 ..     228     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct Cg Cve CP gA
  gi|488600555|ref|YP_007907026.1| 203 CTECGDCVEICPAGA 217
                                       ************998 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C  C evC ++A
  gi|488600555|ref|YP_007907026.1| 228 CLKCTGCSEVCKYDA 242
                                       999*77*****9988 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   4.0   3.2e-05     0.036       2      17 .]     201     216 ..     200     216 .. 0.92
   2 ?   -0.7   3.4       2.5   2.8e+03       3      14 ..     230     238 ..     226     241 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       e+C++Cg Cv +CP g
  gi|488600555|ref|YP_007907026.1| 201 ENCTECGDCVEICPAG 216
                                       89************75 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                            Fer4_4   3 rCigCgsCvaaC 14 
                                       +C+gC     +C
  gi|488600555|ref|YP_007907026.1| 230 KCTGC---SEVC 238
                                       45555...4444 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   7.7   0.00014      0.16      59      96 ..     201     239 ..     194     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                           Fer4_18  59 gdcidcescvkvcPtgidirkGlqle...ciscllcidacd 96 
                                        +c++c+ cv++cP g  i++ ++++   c++c+ c + c+
  gi|488600555|ref|YP_007907026.1| 201 ENCTECGDCVEICPAGA-IKN-FRIDhsiCLKCTGCSEVCK 239
                                       68************995.322.3332223888888888885 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   4.0   0.00029      0.32      49      64 ..     201     216 ..     164     218 .. 0.83
   2 ?   12.4   2.9   0.00015      0.17       4      64 ..     202     216 ..     199     227 .. 0.61
   3 ?    4.0   3.8      0.06        67      51      63 ..     228     240 ..     222     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                            Fer4_8  49 wsCttcgaCtevCpvg 64 
                                       ++Ct+cg C+e Cp g
  gi|488600555|ref|YP_007907026.1| 201 ENCTECGDCVEICPAG 216
                                       6788888888888875 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00015
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       +                                              Ct+cg C+e Cp g
  gi|488600555|ref|YP_007907026.1| 202 N----------------------------------------------CTECGDCVEICPAG 216
                                       4..............................................55555555555543 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.06
                            Fer4_8  51 CttcgaCtevCpv 63 
                                       C+ c  C+evC+ 
  gi|488600555|ref|YP_007907026.1| 228 CLKCTGCSEVCKY 240
                                       9999999999975 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.2   0.00068      0.76      44      59 ..     201     216 ..     188     218 .. 0.85
   2 ?    5.5   3.2     0.023        25      44      59 ..     226     241 ..     217     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00068
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       ++C+eCg C++ CP+g
  gi|488600555|ref|YP_007907026.1| 201 ENCTECGDCVEICPAG 216
                                       6899999999999976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.023
                           Fer4_17  44 slCieCgeCerkCPqg 59 
                                       s C++C +C+++C ++
  gi|488600555|ref|YP_007907026.1| 226 SICLKCTGCSEVCKYD 241
                                       5699999999999876 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.2   0.00061      0.68       1      18 [.     199     215 ..     199     216 .. 0.91
   2 ?    3.0   2.1      0.13   1.5e+02       1      16 [.     223     238 ..     223     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00061
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       ++ ++C++cg Cve++P 
  gi|488600555|ref|YP_007907026.1| 199 IN-ENCTECGDCVEICPA 215
                                       56.9*************5 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       +D + C  c+ C e++
  gi|488600555|ref|YP_007907026.1| 223 IDHSICLKCTGCSEVC 238
                                       78999*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2423.90
//
Query:       gi|488600556|ref|YP_007907027.1|  [L=256]
Description: Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-60  202.6   0.0      8e-60  202.2   0.0    1.0  1  ThiF             ThiF family
    0.00069   19.7   0.1     0.0012   18.9   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00085   19.6   0.0      0.002   18.4   0.0    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.023   15.3   0.0      0.047   14.3   0.0    1.5  1  PglD_N           PglD N-terminal domain
      0.029   14.8   0.0      0.061   13.8   0.0    1.5  1  NAD_binding_7    Putative NAD(P)-binding
      0.076   12.6   0.3       0.22   11.1   0.2    1.8  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.16   11.1   0.1       0.24   10.6   0.1    1.2  1  FAD_binding_3    FAD binding domain
          2    8.5   4.0       0.58   10.2   0.3    2.0  3  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do


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 !  202.2   0.0   3.6e-63     8e-60       3     240 ..      10     232 ..       8     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 3.6e-63
                                       HHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHH CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   3 rqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaeva 77 
                                       rql++  +ge+ qekL +skvl+vGaGglGs+++++L  +Gvg+lt+vD+D +e++Nl+Rq++    +iG +Kae+a
  gi|488600556|ref|YP_007907027.1|  10 RQLMIpyFGEEAQEKLLSSKVLIVGAGGLGSPVIMYLSSAGVGELTIVDFDAVEKTNLQRQVI-HAGKIGWNKAESA 85 
                                       8877777********************************************************.899********** PP

                                       HHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip 154
                                        e+++++npdv v++++e+i++ +v  ++++++DlVv + Dn+ +r+l+n+ac+ kgipli+++  +feg +++i  
  gi|488600556|ref|YP_007907027.1|  86 MEFVSKLNPDVYVRTLKEKIEPGNV-MDIINGHDLVVSCPDNFRTRFLLNDACRIKGIPLIHGAIFEFEGEAMTIT- 160
                                       **********************774.5************************************************6. PP

                                       CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 155 gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfen 231
                                       + ++cy+Cl+p     + ++k p +         i++t +v+++++a+e++k+l g  +l + ll +vdll++ + +
  gi|488600556|ref|YP_007907027.1| 161 DSSPCYRCLYP----EAYPEKTPGI---------IGATAGVIGSIQAVEAIKVLTGLGDLLDCLL-RVDLLSMELFK 223
                                       89********9....4555556888.........8********************9998888888.9*****99999 PP

                                       ECCEEEEEE CS
                                       xxxxxxxxx RF
                              ThiF 232 velerakks 240
                                       +e++r  ++
  gi|488600556|ref|YP_007907027.1| 224 IEIKRRDDC 232
                                       999777655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.5e-07    0.0012       7      54 ..      22      69 ..      17      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.5e-07
                                      HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHH CS
                      Shikimate_DH  7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelae 54
                                       e+l ++kvl++GaG +++ v+ +L+++gv +++++  +     +l +
  gi|488600556|ref|YP_007907027.1| 22 QEKLLSSKVLIVGAGGLGSPVIMYLSSAGVGELTIVDFDAVEKTNLQR 69
                                      4567799****************************9866655555555 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 !   18.4   0.0   8.9e-07     0.002       1     101 [.      30     149 ..      30     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.9e-07
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH....................TTTCEEEEE--TT CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka....................lgvrfeaialdae 57 
                                       vli+GaG+ G++v+ +l+  +    e+t++d++  +  +l  ++                    l++++  ++l  +
  gi|488600556|ref|YP_007907027.1|  30 VLIVGAGGLGSPVIMYLSSAGVG--ELTIVDFDAVEKTNLQRQVihagkigwnkaesamefvskLNPDVYVRTLKEK 104
                                       89*****************9976..9******999988888777999************999997777777777777 PP

                                       THHHHHHHHHTTSSEEEE-SSGGGHH.HHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  58 nyeavLaallkegdlvvnlsppissl.dvlkaCietgvhyvdtsi 101
                                        ++  +  +++++dlvv++  ++ ++  + +aC+ +g+  +  +i
  gi|488600556|ref|YP_007907027.1| 105 IEPGNVMDIINGHDLVVSCPDNFRTRfLLNDACRIKGIPLIHGAI 149
                                       7777777799999**********5552777899999988776555 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.1e-05     0.047       1      51 [.      29      89 ..      29      99 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                            PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflD.dn.kkteveg.........ypvlgkaiell 51
                                      k++I+GaGG g  v+  + + g   ++ ++D d+ +kt+++          ++  ++a+e+ 
  gi|488600556|ref|YP_007907027.1| 29 KVLIVGAGGLGSPVIMYLSSAG-VGELTIVDfDAvEKTNLQRqvihagkigWNKAESAMEFV 89
                                      799******************9.666666663331333322111222222244444444444 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 ?   13.8   0.0   2.7e-05     0.061       8      88 ..      28     143 ..      24     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleag.akvtvvapevkeele........elvklaeee..................... 54 
                                        kvl+vG+G ++   +  l +ag  ++t+v+ +  e+++        +++ +++ e                     
  gi|488600556|ref|YP_007907027.1|  28 SKVLIVGAGGLGSPVIMYLSSAGvGELTIVDFDAVEKTNlqrqvihaGKIGWNKAEsamefvsklnpdvyvrtlkek 104
                                       69*********************779****99963333355656666333344444445555554444444444444 PP

                     NAD_binding_7  55 .....lekdlegadlviaatddrelneriaeaakarril 88 
                                            + + ++g dlv+ ++d+   +  + +a++ ++i+
  gi|488600556|ref|YP_007907027.1| 105 iepgnVMDIINGHDLVVSCPDNFRTRFLLNDACRIKGIP 143
                                       33333455599**********998888888888877776 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 ?   11.1   0.2   9.8e-05      0.22       2      48 ..      29      76 ..      28     103 .. 0.87
   2 ?   -2.5   0.0       1.4   3.2e+03      35      60 ..     223     248 ..     214     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.8e-05
                                      EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS-- CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiye 48
                                      k+ ++G+G +G +  + l+++g  e+++vD d+    +l+++ i+   
  gi|488600556|ref|YP_007907027.1| 29 KVLIVGAGGLGSPVIMYLSSAGvGELTIVDFDAVEKTNLQRQVIHAGK 76
                                      799*******************779*******9998888888887655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                                       HHHHHCTTS-SS--TTHHHHHHHHCH CS
                    UDPG_MGDP_dh_N  35 kvdklnsgkipiyepgLeelvkkave 60 
                                       k++  +++++pi +  L++++ ++ e
  gi|488600556|ref|YP_007907027.1| 223 KIEIKRRDDCPICNGRLRQIYPENYE 248
                                       777788999***99999999988875 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00011      0.24       3      36 ..      29      63 ..      27      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                      EEEEE--SHHHHHHHHHHHHTTHH.EEEEESSSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvr.vvlvekrstt 36
                                      +VlIVGaG  G    + Ls+aGv   ++v+  + +
  gi|488600556|ref|YP_007907027.1| 29 KVLIVGAGGLGSPVIMYLSSAGVGeLTIVDFDAVE 63
                                      8**********************846677755554 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00026      0.58       2      36 ..      29      61 ..      28      74 .. 0.88
   2 ?   -1.5   0.0       1.1   2.5e+03       9      49 ..      74     116 ..      67     129 .. 0.67
   3 ?   -3.8   0.3       5.8   1.3e+04       6      19 ..     182     196 ..     181     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                                      EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSH CS
                           Ldh_1_N  2 kvavvGaaGgiGqslalllankkladelaLlDiak 36
                                      kv +vGa Gg G+++ + l + ++++ l+++D++ 
  gi|488600556|ref|YP_007907027.1| 29 KVLIVGA-GGLGSPVIMYLSSAGVGE-LTIVDFDA 61
                                      9******.****************99.9*999874 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                       TSHHHHHHHHHHHHT..TSSSEEEEE-SSHHHHHHHHHHHHHC CS
                           Ldh_1_N   9 aGgiGqslalllank..kladelaLlDiakekleGvaldlshi 49 
                                       aG+iG + a + ++   kl  ++ +  ++++  +G+++d+ ++
  gi|488600556|ref|YP_007907027.1|  74 AGKIGWNKAESAMEFvsKLNPDVYVRTLKEKIEPGNVMDIING 116
                                       4777766665554432466666777777777777888887654 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 5.8
                                       ETT.TSHHHHHHHHH CS
                           Ldh_1_N   6 vGa.aGgiGqslall 19 
                                       +Ga aG iG+  a+ 
  gi|488600556|ref|YP_007907027.1| 182 IGAtAGVIGSIQAVE 196
                                       565478888766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1406.11
//
Query:       gi|488600557|ref|YP_007907028.1|  [L=249]
Description: NAD-dependent protein deacetylase, SIR2 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-55  187.8   0.0    2.1e-55  187.4   0.0    1.2  1  SIR2          Sir2 family
     0.0012   18.5   0.0       0.19   11.5   0.0    2.2  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.065   13.6   0.0       0.15   12.4   0.0    1.6  1  XPG_I         XPG I-region
      0.065   13.4   0.2       0.13   12.4   0.2    1.4  1  Zn-ribbon_8   Zinc ribbon domain
       0.11   12.0   0.1       0.46   10.1   0.0    2.0  2  HTH_24        Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.4   0.0   5.8e-59   2.1e-55       1     177 []      22     196 ..      22     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 5.8e-59
                                       -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCC.TSS--HHHHHHHHHHHTTCEE CS
                              SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellae.eaepnaaHkalkklekkgkll 76 
                                       G GiS+esGip+fR+ +Gl++k+++ee+as   +++++   +e    +a+el+ + +aepn+aH+a+++le++g ++
  gi|488600557|ref|YP_007907028.1|  22 GSGISAESGIPTFRGVDGLWKKYNPEEVASIYGFKRNPSAFWE----FAKELILKsNAEPNPAHYAIAELEREGVVK 94 
                                       89************************************99999....5555555559******************** PP

                                       EEEES-SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEECCGGHCHHHCCTT.B-TTTCC.BEEEEE--CTSB-S.H CS
                              SIR2  77 rliTQNiDgLekkaGskkvvelHGslakakcvkcekkldkeelqeeieaekvpecekcgk.llkpdvvfFGealp.d 151
                                       ++iTQNiD+L+++aGs++v+elHGs++ ++c +ce+ +++e++ ++i +e++p cekcg+  lkp+vvfFGe l  d
  gi|488600557|ref|YP_007907028.1|  95 AVITQNIDMLHQRAGSRRVLELHGSMNYVDCLDCEAVYEWEYI-AKILKERQPVCEKCGGeFLKPRVVFFGEPLSyD 170
                                       ****************************************665.56667779******8659*************** PP

                                       HHHHHHHHHHH-SEEEEES--STSTT CS
                              SIR2 152 klkkliekveeadlllviGtSlkVap 177
                                        l++++e++++adl+lviG+Sl V+p
  gi|488600557|ref|YP_007907028.1| 171 VLTSAMEEARKADLFLVIGSSLVVYP 196
                                       ************************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 !    5.0   0.0    0.0053        19       1      25 [.       4      28 ..       4      35 .. 0.89
   2 !   11.5   0.0   5.3e-05      0.19      69     136 ..     173     239 ..     160     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHH-SSEEEEE-CHHCHT CS
                      TPP_enzyme_M  1 iekaaellkaakrpvilvGggvars 25
                                      i+k+ ++l+++k  v++ G+g++ +
  gi|488600557|ref|YP_007907028.1|  4 IKKISQMLNESKYAVVFTGSGISAE 28
                                      78999****************9965 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-..EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
                      TPP_enzyme_M  69 kaanealeeaDlvlalGarfddirttgsepefapea..kiihididpaeigknyqvdlaivgdvketlea 136
                                       ++a e +++aDl l++G+ +  +  + s pe+a+++  k+  i+ +p e +  +  d+ ++g+++e++++
  gi|488600557|ref|YP_007907028.1| 173 TSAMEEARKADLFLVIGSSLVVYPAA-SLPEIAKKSgaKLALINLEPVEKDFIF--DVVVYGKAGEVMKK 239
                                       56778889***********9886555.555555553369*****9999877665..88999999988875 PP

>> XPG_I  XPG I-region
   #    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      16      39 ..      82     105 ..      75     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHTTSSSEEE-SSSHHHH CS
                             XPG_I  16 AqcayLqkkglvdaviseDsDlll 39 
                                         +a+L+++g+v+avi++  D+l 
  gi|488600557|ref|YP_007907028.1|  82 YAIAELEREGVVKAVITQNIDMLH 105
                                       5689******************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   0.2   3.7e-05      0.13       8      35 ..     125     154 ..     121     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                       Zn-ribbon_8   8 CeeCghefe..vlqsisdapltaCPeCgse 35 
                                       C +C  ++e   +++i ++ +++C +Cg+e
  gi|488600557|ref|YP_007907028.1| 125 CLDCEAVYEweYIAKILKERQPVCEKCGGE 154
                                       *********98888888889999*****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 ?   10.1   0.0   0.00013      0.46      21      48 .]      67      94 ..      66      94 .. 0.90
   2 ?   -1.3   0.0      0.45   1.6e+03      19      29 ..     199     209 ..     196     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +eL  +++  p++ ++ + +Le+eG++k
  gi|488600557|ref|YP_007907028.1| 67 KELILKSNAEPNPAHYAIAELEREGVVK 94
                                      67888889999***************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.45
                            HTH_24  19 sqreLAerlgl 29 
                                       s  e+A+++g 
  gi|488600557|ref|YP_007907028.1| 199 SLPEIAKKSGA 209
                                       7789****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1731.30
//
Query:       gi|488600558|ref|YP_007907029.1|  [L=226]
Description: SSU ribosomal protein S3AE [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  233.8   0.7    1.6e-69  233.5   0.7    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.16   11.9   0.0    1.4  1  DoxA            TQO small subunit DoxA


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 !  233.5   0.7   1.8e-73   1.6e-69       2     202 .]      11     202 ..      10     202 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.5 bits;  conditional E-value: 1.8e-73
                                       S----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCS.HTSSSEEEEEEEEE CS
                    Ribosomal_S3Ae   2 kkkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtnde.keqafrklklkiee 77 
                                       ++ +v+Dk++ K+W+++ aP++fg +e+G t++       +asek+  rvvev+la+Ltnd+ +++ + kl +k+ +
  gi|488600558|ref|YP_007907029.1|  11 RQARVKDKWTLKKWFTLIAPEYFGMSELGVTPA-------DASEKVLDRVVEVTLAELTNDYsNQNPYKKLCFKVYR 80 
                                       6789*****************************.......***********************999*********** PP

                                       EESSEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  78 vqgknaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilt 154
                                       v+g+na+t+F   el rD+++sl+r+++s+Ie ++dv+t+Dgy+lrv++vafT +r   +k+sq +aIr++m+ei+ 
  gi|488600558|ref|YP_007907029.1|  81 VAGNNAYTEFFRYELGRDYINSLTRRRTSKIEDVIDVTTTDGYVLRVKPVAFTIRR---CKTSQRRAIRAIMHEIIA 154
                                       ********************************************************...****************** PP

                                       HHHHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                    Ribosomal_S3Ae 155 eeaseldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                       ++ se+++ ++++++i  ++ +ei+k+akkIyplr+veirK+++lk+P
  gi|488600558|ref|YP_007907029.1| 155 KTGSESKFIQFIQECILGKIPSEIYKNAKKIYPLRRVEIRKIELLKEP 202
                                       *****************77***************************98 PP

>> DoxA  TQO small subunit DoxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.8e-05      0.16      24      90 ..      67     132 ..      52     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                              DoxA  24 klaengtLvleitrveGpdvYgafvikiellnstgkvvlelnqeeLaslpssnIknkyvakvkqaky 90 
                                       +++  ++L ++++rv+G ++Y  f    el  +  + +++   +++ ++ +   ++ yv++vk+ ++
  gi|488600558|ref|YP_007907029.1|  67 NQNPYKKLCFKVYRVAGNNAYTEFFR-YELGRDYINSLTRRRTSKIEDVIDVTTTDGYVLRVKPVAF 132
                                       4555689**************99864.5677776666667777777777777777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1455.62
//
Query:       gi|488600559|ref|YP_007907030.1|  [L=741]
Description: cationic amino acid:proton symporter, ABT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-47  162.7  52.1    1.6e-47  162.3  52.1    1.2  1  AA_permease_2  Amino acid permease
    1.6e-45  155.6  46.3      2e-45  155.3  46.3    1.1  1  AA_permease    Amino acid permease
    1.4e-24   87.2   0.1    2.4e-17   63.8   0.0    2.4  2  Usp            Universal stress protein family
    3.4e-05   23.8   6.3    3.4e-05   23.8   6.3    3.2  3  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 !  162.3  52.1   3.6e-51   1.6e-47       1     411 [.      14     421 ..      14     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 3.6e-51
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l++++ +++ i  +ig+g+f+ +  +a+  gpali+ +++  li  ++ +l+yaEl+s +p  gG yv+ k+ f+  
  gi|488600559|ref|YP_007907030.1|  14 LGFFDITMIGIAGMIGAGVFALTgiAAGISGPALIIAFFFNGLIA-TITALAYAELGSSMPQAGGGYVWIKESFPQS 89 
                                       79*******************997555559******999999999.89********777****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                       ++f+++w+ wfa ++++a++++ ++++ + +l +   +    +++  ++ ++l+a +n++g+kes+k+  i++++k+
  gi|488600559|ref|YP_007907030.1|  90 AGFIAGWIDWFAHSVACALYAVTFGAFVAVILEGY-MPFILVSKVSSFLAVTLFAYVNYIGVKESGKVGGIITLTKV 165
                                       ***********************999999999764.3556778888899**************************** PP

                     AA_permease_2 153 llpliiliilglitvdgggfssl..stetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifi 225
                                       + +l+++ i+g++      fs++  +   + f+png +gvl++++ +  +f G+e +++  eevk+  k++p+a  +
  gi|488600559|ref|YP_007907030.1| 166 V-ILLVFTIFGVYRT----FSNPewVLRFTPFMPNGMQGVLAAMGLTYIAFEGYEIIVQSGEEVKNpeKNIPRAVLV 237
                                       5.7788887888875....333334557889********************************999889******** PP

                     AA_permease_2 226 gllivlvlyllvniaflgvvpddei.....anlsnlgsvaalffeavgg..kvvaiivvilialsllgaintavigs 295
                                       +l +++++y+lv++++lg++  d        +l++lg     + +++g+  +++++i+ +++ +s   a+n+ +++s
  gi|488600559|ref|YP_007907030.1| 238 SLWVATLIYILVAVSVLGGIDSDRPswmylGELGELG-----LIKTAGSimPFGFAILLFAGLVSTTSAMNATIYSS 309
                                       ********************99998565554555544.....6666674226************************* PP

                     AA_permease_2 296 srvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigali 371
                                       srv++a+ard +lPr ++ ++ ++ +p ++i++++i+ ++++l +       + ++++ +++++i+ + ++ +++++
  gi|488600559|ref|YP_007907030.1| 310 SRVAFAMARDSFLPRALSEIDvRRRTPRNSIFFSYIIISAMTLSLP------IEAVAASANIMFILLFVMVNLTLIL 380
                                       *************************************988864443......59*********************** PP

                     AA_permease_2 372 lrkkrphlkrpgki.lvaiigalfllfllvalffppkgpat 411
                                        r+k p+l+rp k+  v  + ++ +++ +v+++f+   ++ 
  gi|488600559|ref|YP_007907030.1| 381 MRYKAPNLNRPFKVpFVPYLPIVAVILQFVIGYFMISMLEH 421
                                       **********6665145555577777777777777655543 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3  46.3   4.5e-49     2e-45       1     476 [.      18     450 ..      18     453 .. 0.83

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 4.5e-49
                       AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfv 77 
                                       ++++i ++g+iG+g+f  +g++++  Gp ++++a+ + g++ ++++l+ +e+ + +p++gg y++++++  +++Gf 
  gi|488600559|ref|YP_007907030.1|  18 DITMIGIAGMIGAGVFALTGIAAGISGP-ALIIAFFFNGLIATITALAYAELGSSMPQAGGGYVWIKESFPQSAGFI 93 
                                       689*************************.888********************************************* PP

                       AA_permease  78 iGlnylfswitvlaleltaasiliqfwelvtdlpkawvt.....gavflvvlliinlvgvkvygeaefilalikiia 149
                                        G++ +f   ++ al  ++ + ++  +  ++ ++  ++      + + ++++  +n++gvk +g++  i++l k+++
  gi|488600559|ref|YP_007907030.1|  94 AGWIDWFAHSVACALYAVTFGAFVAVI--LEGYM-PFILvskvsSFLAVTLFAYVNYIGVKESGKVGGIITLTKVVI 167
                                       ****66666666666666666666555..44444.3333455559999999************************** PP

                       AA_permease 150 iiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvk 226
                                       ++ f i+g+ + +  +p+       l      f  ++p+g        ++++++++   + af G+e+++  ++Evk
  gi|488600559|ref|YP_007907030.1| 168 LLVFTIFGV-YRTFSNPEWV-----LR-----FTPFMPNG--------MQGVLAAMGLTYIAFEGYEIIVQSGEEVK 225
                                       ********4.4444444444.....23.....55669999........***************************** PP

                       AA_permease 227 dPeksiPkailqvviritifYvlsllligllvprndlgllndsasa.aspfvifikesgvsvlaplinaviltaals 302
                                       +Pek+iP+a+l  ++  t++Y+l+++++  +++ + ++ +     + ++++ ++++  +  ++a l  ++ l++++s
  gi|488600559|ref|YP_007907030.1| 226 NPEKNIPRAVLVSLWVATLIYILVAVSVLGGIDSDRPSWMYLGELGeLGLIKTAGS-IMPFGFAIL-LFAGLVSTTS 300
                                       **************************************999555556677666665.455555555.555689**** PP

                       AA_permease 303 sansslysasRvlyslakdglaPkvlkkvs.krgvPlraillsmiisllalllaslnlaapivfnfllaisaligli 378
                                       ++n+ +ys+sRv +++a+d  +P+ l+ ++ +r+ P ++i++s+ii  ++     l+l+    ++ + a++ +++++
  gi|488600559|ref|YP_007907030.1| 301 AMNATIYSSSRVAFAMARDSFLPRALSEIDvRRRTPRNSIFFSYIIISAMT----LSLP----IEAVAASANIMFIL 369
                                       ***********************6666665499***********9988877....4455....55669********* PP

                       AA_permease 379 vwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaayli 455
                                       ++++++l+++ +R +    +r     +fk +++p+++i+++  ++ +++ ++++  l             f+a+ ++
  gi|488600559|ref|YP_007907030.1| 370 LFVMVNLTLILMRYKAPNLNR-----PFKVPFVPYLPIVAV--ILQFVIGYFMISMLE----------HGFLALAVS 429
                                       **********99988555555.....9**999999887543..344444555555555..........778999999 PP

                       AA_permease 456 vllfliilvgvklhvknkrpq 476
                                       vl++++ +v++  + k k+ +
  gi|488600559|ref|YP_007907030.1| 430 VLWIVLGIVIYSSYSKEKVKE 450
                                       999999999999988887765 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   5.4e-21   2.4e-17       4     141 .]     471     599 ..     470     599 .. 0.95
   2 !   21.3   0.0   6.9e-08   0.00031      70     141 .]     656     728 ..     612     728 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 5.4e-21
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                       rIlVa+ +    k +le+    aka+++e+ +++v++ +++++ +++++ ++e+ +e  e  +          +  +
  gi|488600559|ref|YP_007907030.1| 471 RILVAYANPAIGKMLLEFSDFIAKAKNGEIKVMNVVKLPEQTPLKAGMKLVREQIEEIDELLRI---------PSSP 538
                                       89****888888899999999*********************************9999999886.........789* PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +  v+ + ++++++i+ +a e++a+l+V+G+rgr+  +++++GS+ + vl +apc+V+v+r
  gi|488600559|ref|YP_007907030.1| 539 AKGVIKVAHSVSDAIISEAAEYKANLVVLGWRGRTFRRDFVFGSTIDPVLLKAPCDVIVTR 599
                                       *********************************999999********************87 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.9e-08
                                       H...HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  70 a...akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       +   +++++e g+ + e+  ++ dp  +i+e+a++  +d++ vG++++  ++ ++ G + e++++++++ V++Vr
  gi|488600559|ref|YP_007907030.1| 656 KaviEACRKESGIDADEILKLSDDPIKGIAEIARN--YDMMFVGASDEPFFKNFIKGMFVEKLVKETNKTVVMVR 728
                                       12335689999999******************987..9************************************8 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 ?   -3.0   0.8       1.9   8.3e+03      34      46 ..     237     249 ..     234     254 .. 0.52
   2 ?   -4.4   1.7         4   1.8e+04      14      25 ..     366     377 ..     363     379 .. 0.76
   3 !   23.8   6.3   7.7e-09   3.4e-05       1      48 [.     392     445 ..     392     448 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                     AA_permease_C  34 vwmliglliYflY 46 
                                       v + + +liY+l+
  gi|488600559|ref|YP_007907030.1| 237 VSLWVATLIYILV 249
                                       4444555555543 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 4
                     AA_permease_C  14 IlvNiyLmlqLd 25 
                                       +++ +++m++L+
  gi|488600559|ref|YP_007907030.1| 366 MFILLFVMVNLT 377
                                       567788999986 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 7.7e-09
                     AA_permease_C   1 FkvPlvPflPalsIlvNi...yLmlqL...dsltwirfgvwmliglliYflYgi 48 
                                       FkvP+vP+lP++++++ +   y m+++   ++l+++  + w+++g++iY  Y++
  gi|488600559|ref|YP_007907030.1| 392 FKVPFVPYLPIVAVILQFvigYFMISMlehGFLALAVSVLWIVLGIVIYSSYSK 445
                                       9************976654446677661224556666677************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (741 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 4651.80
//
Query:       gi|488600560|ref|YP_007907031.1|  [L=275]
Description: hypothetical protein Asulf_01035 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-61  206.9   3.9    3.4e-61  206.4   3.9    1.2  1  MS_channel       Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.38   11.2   3.0        8.7    6.8   1.7    2.9  2  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_


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 !  206.4   3.9   3.8e-65   3.4e-61       2     206 .]      57     254 ..      56     254 .. 0.99

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 3.8e-65
                                       .HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEE CS
                        MS_channel   2 kilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVed 78 
                                       ki++++ii++++++v+ +lg n+s ll++ G++g+ +g+a+++++snlv+Gi+l+ ekp+kiGD + + +++G+Ved
  gi|488600560|ref|YP_007907031.1|  57 KIVYYGIITIAFITVMPTLGLNLSGLLVAGGIAGIIIGFASQSVVSNLVSGIFLISEKPIKIGDQISVDGVAGYVED 133
                                       89*************************************************************************** PP

                                       E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS- CS
                        MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdke 155
                                       i +++t +rt dg +v iPn++++ts+i+N+   + +rr+++++g++ys d   +ek+++++++ ++e+p  lk++e
  gi|488600560|ref|YP_007907031.1| 134 IHILSTVVRTYDGLYVRIPNEKVFTSSITNYVA-NVARRFEYVVGIRYSDD---AEKAIQIINRLIDEHPFALKNPE 206
                                       *********************************.*****************...*********************** PP

                                       EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 156 llvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       ++ +++e+gd+++n+ vr++ ++    e++s+++e+  +ikk+lee+giei
  gi|488600560|ref|YP_007907031.1| 207 PQIFVNELGDNAVNIVVRIWGPS---TEWYSIKTELLWKIKKELEENGIEI 254
                                       ***********************...9**********************97 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.7   0.00097       8.7       6      43 ..      21      58 ..      15      69 .. 0.81
   2 ?    2.4   0.0     0.024   2.1e+02      37      83 ..     208     254 ..     186     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00097
                   Phage_holin_6_1  6 vsvlviiitivlgllvkkikkllklkkqgekakkiaei 43
                                      v ++++i tiv+ ++++ i++ l  k + ++++ i++i
  gi|488600560|ref|YP_007907031.1| 21 VVLMMTIATIVARIVTTNIRRALTDKMKRDQLELILKI 58
                                      3356778899999**********888888889999888 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.024
                   Phage_holin_6_1  37 akkiaeiaknaVkaveqvakedakgeeKkeeAleklkellkekgisi 83 
                                       +  + e+ +naV++v  +   +++    k+e l k+k+ l+e gi+i
  gi|488600560|ref|YP_007907031.1| 208 QIFVNELGDNAVNIVVRIWGPSTEWYSIKTELLWKIKKELEENGIEI 254
                                       55788889999999999988888888888999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1687.38
//
Query:       gi|488600561|ref|YP_007907032.1|  [L=234]
Description: hypothetical protein Asulf_01036 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  166.5   0.1    3.7e-49  166.0   0.1    1.2  1  DUF432    Protein of unknown function (DUF432)


Domain annotation for each model (and alignments):
>> DUF432  Protein of unknown function (DUF432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.0   0.1     2e-53   3.7e-49       1     123 []      56     178 ..      56     178 .. 1.00

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 2e-53
                            DUF432   1 PvnlpkeitkyllveleeplvvepkseveiyvkvpveigvfikskkeveliDvfslskkkYaLYGspesGviaryvk 77 
                                       Pvnlpkeit++ll+++++p+++epk+++e+++++pveigvf+++kk+v++iD+fsl+k+kY+LYG+p++G+i+ry++
  gi|488600561|ref|YP_007907032.1|  56 PVNLPKEITNFLLIRFKKPVFIEPKTSMEVNLTFPVEIGVFLAAKKRVDVIDIFSLQKPKYTLYGNPRMGIICRYWE 132
                                       9**************************************************************************** PP

                            DUF432  78 sevyseppeldpleeavveleikNetdevvevskivfdalglklyy 123
                                       s+vys +p++d ++e+v++l+i+N++de++ev+++vfd++g+k+yy
  gi|488600561|ref|YP_007907032.1| 133 SDVYSDVPDVDGFREGVMRLRITNSSDEWIEVTNAVFDIFGMKIYY 178
                                       *********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1436.40
//
Query:       gi|488600562|ref|YP_007907033.1|  [L=187]
Description: hypothetical protein Asulf_01039 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy 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:                       884  (0.0493056); 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:                         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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1126.16
//
Query:       gi|488600563|ref|YP_007907034.1|  [L=432]
Description: Uncharacterized conserved protein (some members containing a von Willebrand factor type A (vWA) domain) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   0.0    2.5e-18   66.1   0.0    1.6  1  DUF58     Protein of unknown function DUF58
    3.5e-06   27.6   0.0      7e-06   26.7   0.0    1.5  1  VWA_2     von Willebrand factor type A domain


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 !   66.1   0.0   2.8e-22   2.5e-18       2      77 ..     178     252 ..     177     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 2.8e-22
                             DUF58   2 ldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarql 77 
                                       +++++lReY+pgD ++ IdWkatAR+gel+vref +e +++++++ld+  em++g ++  k+++a ++++ l+  l
  gi|488600563|ref|YP_007907034.1| 178 VEIDSLREYQPGDYVKYIDWKATARLGELIVREFLKEVEGDIYIILDAGFEMRKGVRN-AKIDYATTLTLQLISAL 252
                                       5889************************************************998764.77777777766666544 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   7.8e-10     7e-06       2      70 ..     220     288 ..     219     297 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.8e-10
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsd.gpevlipltkdkakilnalrnle 70 
                                        ++lD    mr g ++++++++a  ++ +l+++l++ rvgl++++d g++++i ++k++++i++a+r+l+
  gi|488600563|ref|YP_007907034.1| 220 YIILDAGFEMRKG-VRNAKIDYATTLTLQLISALKRYRVGLIVYDDfGVKHKIEPSKSPDRIKKAIRSLN 288
                                       68999*******9.89***************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2876.36
//
Query:       gi|488600564|ref|YP_007907035.1|  [L=309]
Description: MoxR-like ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-63  210.7   0.1    7.8e-63  210.2   0.1    1.2  1  AAA_3            ATPase family associated with various cellul
    1.7e-17   63.7   0.0    3.2e-17   62.8   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-16   60.5   0.4    2.5e-16   59.3   0.0    1.8  2  AAA_lid_2        AAA lid domain
    2.5e-08   34.4   0.0      6e-08   33.2   0.0    1.7  1  AAA              ATPase family associated with various cellul
      7e-07   28.6   0.0    2.1e-06   27.0   0.0    1.8  1  MCM              MCM P-loop domain
    1.4e-06   27.8   0.2      0.015   14.7   0.1    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    7.7e-06   25.7   0.7    0.00052   19.8   0.1    3.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00015   21.5   0.1     0.0023   17.6   0.1    2.1  1  Sigma54_activat  Sigma-54 interaction domain
      0.008   16.6   0.1      0.025   14.9   0.1    1.9  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.095   12.7   0.0       0.17   11.9   0.0    1.4  1  DNA_photolyase   DNA photolyase
       0.14   12.4   0.7        8.7    6.6   0.1    2.7  3  AAA_22           AAA domain
       0.21   11.3   0.4        1.1    9.0   0.0    2.2  3  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.2   0.1   5.2e-66   7.8e-63       1     131 []      37     167 ..      37     167 .. 1.00

  Alignments for each domain:
  == domain 1  score: 210.2 bits;  conditional E-value: 5.2e-66
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hvlleg+PG+akt+++ka+aka++l+f+r+q+t dl+P+di+G  +++++++ef++kkGp+fan++ladeinra+pk
  gi|488600564|ref|YP_007907035.1|  37 HVLLEGIPGVAKTTIAKAFAKAIGLKFSRVQITLDLMPADIVGGAYYDQRTSEFKIKKGPIFANVVLADEINRATPK 113
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       tqsalleam+erqvt+eg+t++lp+pfl++at nPie eG+y+lpeaqldrf++
  gi|488600564|ref|YP_007907035.1| 114 TQSALLEAMQERQVTIEGTTFELPDPFLLIATMNPIEAEGVYKLPEAQLDRFMM 167
                                       ****************************************************98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   2.2e-20   3.2e-17       1     138 []      37     165 ..      37     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.2e-20
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlL G pG++K+++a+ +a+a++ ++  vq+t d+ ++d++g+  ++   ++ + +++p+      + +++ DE++
  gi|488600564|ref|YP_007907035.1|  37 HVLLEGIPGVAKTTIAKAFAKAIGLKFSRVQITLDLMPADIVGGAYYDqrTSEFKIKKGPIF-----ANVVLADEIN 108
                                       79*********************************************955555566788888.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra ++++++Ll  + er++ +e  +++   ++      f +iat+np +  ++ +l +a ++Rf
  gi|488600564|ref|YP_007907035.1| 109 RATPKTQSALLEAMQERQVTIEGTTFEL-PDP------FLLIATMNPIEaEGVYKLPEAQLDRF 165
                                       ********************66666666.556......***********999999999999998 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       4.7   7.1e+03      38      54 ..      19      35 ..      17      38 .. 0.79
   2 !   59.3   0.0   1.6e-19   2.5e-16       2      73 .]     229     301 ..     228     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.7
                         AAA_lid_2 38 VtpeDvkeaaplVLaHR 54
                                      V +eDv e+   +L  R
  gi|488600564|ref|YP_007907035.1| 19 VGKEDVLELLAVALLSR 35
                                      77899999988888665 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 1.6e-19
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeiveei 73 
                                       +tr++ ++ lg+s+r a  +ll a++ lA+l+grdyV+p+Dvke+a  +LaHR+    e e +g ++e+ ++ei
  gi|488600564|ref|YP_007907035.1| 229 RTRTDDRVLLGASPR-ALEHLLFASKSLAFLRGRDYVVPDDVKELATSILAHRILikAEYEIDGLKAEDLIKEI 301
                                       589999*********.***************************************9888898888899988875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0     4e-11     6e-08       1     131 [.      38     172 ..      38     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4e-11
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETT.TCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgs.ell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                       vll G pG+ KT++aka ak +g +f +++ + +l+  ++vg +  + r    ++k+      +++ DEi + +++ 
  gi|488600564|ref|YP_007907035.1|  38 VLLEGIPGVAKTTIAKAFAKAIGLKFSRVQITlDLMpADIVGGAYYDQRTSEFKIKKGPiFANVVLADEINRATPKT 114
                                       79********************99998887752555577888887777777666777766559************** PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkieie 131
                                                  +++Ll+++++ +           +++++i++ n      + kl++a l +Rf +ki+++
  gi|488600564|ref|YP_007907035.1| 115 -----------QSALLEAMQERQVTiegttfelPDPFLLIATMNPieaegVYKLPEAQL-DRFMMKIQMG 172
                                       ...........*************9*******977799999999877777889999999.9999999876 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.4e-09   2.1e-06      52     175 ..      30     150 ..       2     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.4e-09
                                       SBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS..EEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEE CS
                               MCM  52 tklrgdinvllvgdpgtaKsqlLkyveklapr..avytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcc 126
                                       + l ++ +vll g pg+aK+++ k+ +k +    +          a+++     d++t+ef ++ G +      v++
  gi|488600564|ref|YP_007907035.1|  30 VALLSRGHVLLEGIPGVAKTTIAKAFAKAIGLkfSRVQITLDLMPADIVGGAYYDQRTSEFKIKKGPIFAN---VVL 103
                                       4566778******************99876430034444455677899999999************98764...9** PP

                                       EESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 127 iDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                        De+++ + +++sal+Eam + +++i   G +  L+    ++a +np++
  gi|488600564|ref|YP_007907035.1| 104 ADEINRATPKTQSALLEAMQERQVTIE--GTTFELPDPFLLIATMNPIE 150
                                       **************************8..66799999999999999984 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   0.1   9.9e-06     0.015       3      44 ..      16      57 ..      15      67 .. 0.92
   2 !   11.0   0.0   0.00014       0.2     109     161 ..     101     151 ..      75     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.9e-06
                      Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                      k v+G+e+  + l +a   + ++ll G pG  Kt +ak++++
  gi|488600564|ref|YP_007907035.1| 16 KAVVGKEDVLELLAVALLSRGHVLLEGIPGVAKTTIAKAFAK 57
                                      5799**********************************9865 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00014
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpc 161
                                       v++ DE+   + k+  +L e +++++vti+ +  ++e p  f l+a+mNp  +
  gi|488600564|ref|YP_007907035.1| 101 VVLADEINRATPKTQSALLEAMQERQVTIEGT--TFELPDPFLLIATMNPIEA 151
                                       7788*************************865..6788999*********876 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   3.5e-07   0.00052      34     115 ..      36     129 ..      10     134 .. 0.70
   2 ?    1.2   0.1      0.19   2.8e+02      72     105 ..     188     222 ..     176     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.5e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaa........lltnleek....dvlfideihrlsr 98 
                                        hvll G PG+ ktt+ak  ak +g k+          ++d+++           +++++    +v++ dei r ++
  gi|488600564|ref|YP_007907035.1|  36 GHVLLEGIPGVAKTTIAKAFAKAIGLKFSRVQITLDLMPADIVGgayydqrtSEFKIKKGpifaNVVLADEINRATP 112
                                       6***********************99887666555555566654111111102223444322227888899999999 PP

                            RuvB_N  99 aveevlysamedfrldi 115
                                       +++  l  am++ ++ i
  gi|488600564|ref|YP_007907035.1| 113 KTQSALLEAMQERQVTI 129
                                       99999999998888765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                            RuvB_N  72 agdlaalltnleekdvl.fideihrlsraveevly 105
                                       +gd+  +   ++++dvl +ide  r++ + e + y
  gi|488600564|ref|YP_007907035.1| 188 SGDFGEIQRIVDREDVLkLIDEAGRIKVSDEVISY 222
                                       67888888888999998679999999876665544 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.6e-06    0.0023      10     142 ..      23     147 ..      15     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-.. CS
                   Sigma54_activat  10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAeke.. 84 
                                       ++le ++ +  ++ +vl++G  G+ K+++a+a  +a        +++   +i+ +l+ +++ G   Ga+ + +++  
  gi|488600564|ref|YP_007907035.1|  23 DVLELLAVALLSRGHVLLEGIPGVAKTTIAKAFAKAIG------LKFSRVQITLDLMPADIVG---GAYYDQRTSef 90 
                                       56677777888889999999999999999999877665......3344445666777777766...66665444300 PP

                                       ..BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  85 ..kkGlfekadgGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                         kkG +      +++ Dei++ ++++Q+ Ll+++qe++v+  G++ e +  + +ia+ n
  gi|488600564|ref|YP_007907035.1|  91 kiKKGPI---FANVVLADEINRATPKTQSALLEAMQERQVTIEGTTFELPDPFLLIATMN 147
                                       0033333...2357788************************9999988887777776654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.7e-05     0.025       3      52 ..      19      73 ..      17     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..........g 52
                                      vG+e+ le L+ al     +r + vll G +Gv K+++++++++a+  +           
  gi|488600564|ref|YP_007907035.1| 19 VGKEDVLELLAVALL----SR-GHVLLEGIPGVAKTTIAKAFAKAIGLKfsrvqitldlM 73
                                      777777777766664....23.69********************9987755444444440 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.17      68     120 ..     254     307 ..     227     309 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       -EEEEESS...HHHHHHHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEE CS
                    DNA_photolyase  68 rLvvrrgd...padvlpelakelgasavvanreyepdererdeavkealrkagiev 120
                                       +L ++rg+   + d ++ela+++ a+++++++eye+d+ + ++ +ke+l++  +ev
  gi|488600564|ref|YP_007907035.1| 254 SLAFLRGRdyvVPDDVKELATSILAHRILIKAEYEIDGLKAEDLIKEILEE--VEV 307
                                       477788877888899**********************************97..444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0058       8.7       4      28 ..      34      58 ..      32     128 .. 0.82
   2 ?    3.7   0.0     0.048        71      78     116 ..     190     227 ..     157     252 .. 0.77
   3 ?   -3.7   0.0         9   1.4e+04      51      65 ..     291     306 ..     270     308 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0058
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                      ++g++++ G +G+ KTt ++ +++ 
  gi|488600564|ref|YP_007907035.1| 34 SRGHVLLEGIPGVAKTTIAKAFAKA 58
                                      5899*****************9986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.048
                            AAA_22  78 llealeqalraravielliiDEaqhlr.seealeeLrsll 116
                                        +  +++ +++ +v  l +iDEa ++  s+e+++++ +++
  gi|488600564|ref|YP_007907035.1| 190 DFGEIQRIVDREDV--LKLIDEAGRIKvSDEVISYIYEIS 227
                                       45778888888888..99********87899999996554 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9
                            AAA_22  51 t.sskdllrellralg 65 
                                       + + +dl +e+l++++
  gi|488600564|ref|YP_007907035.1| 291 GlKAEDLIKEILEEVE 306
                                       3346666666666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00072       1.1      12      42 ..      31      59 ..      25      72 .. 0.80
   2 ?   -1.2   0.0      0.93   1.4e+03      90     117 ..     100     127 ..      83     131 .. 0.80
   3 ?   -2.2   0.0       1.9   2.9e+03      90     101 ..     203     214 ..     181     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00072
                            AAA_30 12 alltsgdrvavltGpAGtGKttalkalreaw 42
                                      all+ g   ++l+G +G  Ktt+ ka ++a+
  gi|488600564|ref|YP_007907035.1| 31 ALLSRG--HVLLEGIPGVAKTTIAKAFAKAI 59
                                      444444..699***************99987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.93
                            AAA_30  90 tllivDEagmvdtkqlaallkaaekaga 117
                                       ++++ DE+  +  k+  all+a++++++
  gi|488600564|ref|YP_007907035.1| 100 NVVLADEINRATPKTQSALLEAMQERQV 127
                                       5778888888888888888888888665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.9
                            AAA_30  90 tllivDEagmvd 101
                                        l ++DEag + 
  gi|488600564|ref|YP_007907035.1| 203 VLKLIDEAGRIK 214
                                       455788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1957.84
//
Query:       gi|488600565|ref|YP_007907036.1|  [L=340]
Description: hypothetical protein Asulf_01042 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-09   36.9   0.0      8e-09   35.8   0.0    1.6  1  DUF4350          Domain of unknown function (DUF4350)
    0.00035   20.1   0.0    0.00054   19.5   0.0    1.3  1  ABC_transp_aux   ABC-type uncharacterized transport system
  ------ inclusion threshold ------
      0.026   13.9   0.0      0.044   13.2   0.0    1.2  1  DUF4159          Domain of unknown function (DUF4159)
        0.1   12.0   0.0        0.2   11.1   0.0    1.4  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 


Domain annotation for each model (and alignments):
>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   1.8e-12     8e-09       1      69 []      35     103 ..      35     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.8e-12
                           DUF4350   1 skspnGtralaelLeaqGvevrrvrkpfdale.gedgtllvvapdlrlteeelaallewvarGntlvlaa 69 
                                       ++ +nG++ +a++L  ++ ev++v  +++  +  +dg l++v+pd+ +++ e++++ +++++G+ l+la+
  gi|488600565|ref|YP_007907036.1|  35 NTKWNGCSEFARFL-MTKGEVIPVMYSYNTIDlKSDGALIIVGPDVGFSQLEAEEIDKFLENGGVLLLAD 103
                                       688***********.77889999********857*********************************986 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.2e-07   0.00054     177     235 ..      59     110 ..      22     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-07
                    ABC_transp_aux 177 YnveevdldsedilpedidvlviakptkdlseeelykldqflmnGgkllvfldpvaeeq 235
                                       Y+++++dl+s++       +l+i++p   +s+ e + +d+fl+nGg ll++ d  +++ 
  gi|488600565|ref|YP_007907036.1|  59 YSYNTIDLKSDG-------ALIIVGPDVGFSQLEAEEIDKFLENGGVLLLADDFGTANS 110
                                       555555555444.......59****************************9999887766 PP

>> DUF4159  Domain of unknown function (DUF4159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.8e-06     0.044      61     114 ..      77     129 ..      73     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.8e-06
                                       S------HHHHHHHHHHHTT-EEEEEE-SSSSHHHHHHHHHHHHH.S-TTS-EE- CS
                           DUF4159  61 gnvkfssaeakaLraYlrkGGfLliDdrgygaaeaerlrrelkkv.fPekpleel 114
                                       ++v fs+ ea++++++l++GG+Ll  d + g+a+   l++++ k  f  +ple++
  gi|488600565|ref|YP_007907036.1|  77 PDVGFSQLEAEEIDKFLENGGVLLLAD-DFGTANS-LLEKLAVKArFSSQPLEDI 129
                                       678999***************987666.3444444.5777777777777777765 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 ?   11.1   0.0   4.4e-05       0.2     145     197 ..     209     281 ..     203     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                   tRNA_synthFbeta 145 dlkgivealleslgiekvefepaehpalhpgrsAeikvdgk....................evGvlGelhpev 197
                                       +  +++e+l++ lg+++++f++a+h+ + p+    ++v+++                    e G++G++  +v
  gi|488600565|ref|YP_007907036.1| 209 ENRKFIENLVDYLGVKRFYFDEAHHSDFNPYSITTVYVQKEldrgkafnvfllvfalavliESGIAGKILNSV 281
                                       556789********************************99988888888888888888888777777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 2225.58
//
Query:       gi|488600566|ref|YP_007907037.1|  [L=622]
Description: hypothetical protein Asulf_01043 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-05   24.8   0.3      0.092   12.9   0.0    2.9  3  Big_3_5      Bacterial Ig-like domain (group 3)
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.065   13.5   0.0    1.4  1  DUF4129      Domain of unknown function (DUF4129)


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 ?   -1.3   0.0      0.29   2.6e+03      46      66 ..     243     263 ..     234     285 .. 0.69
   2 !    8.6   0.0   0.00023       2.1      46      76 ..     331     361 ..     312     368 .. 0.79
   3 !   12.9   0.0     1e-05     0.092       3      87 ..     384     461 ..     375     464 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.29
                                       TSEEEEEEE-SS-EEEEEEEE CS
                           Big_3_5  46 nGtAtltvsalaaGthsitAt 66 
                                       +G++ + +++ ++G+h i A+
  gi|488600566|ref|YP_007907037.1| 243 SGNVEMVYEFNKTGKHIIYAE 263
                                       488888888999999999985 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00023
                                       TSEEEEEEE-SS-EEEEEEEEEE-TTS---S CS
                           Big_3_5  46 nGtAtltvsalaaGthsitAtYsGdanyaas 76 
                                       +   +l+v+  + G  +itA Y G+ +y++ 
  gi|488600566|ref|YP_007907037.1| 331 TQAFSLNVTRSSEGLVDITAIYPGNETYQST 361
                                       44778999999*****************975 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 1e-05
                                       -EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS---S--E CS
                           Big_3_5   3 svtagqtvtltatVtaasggtptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitAtYsGdanyaastss 79 
                                       +v+++++v +  +V+a+     t + ++++++t+ g+  +++     ++t+++ + G++ + + + Gd+ y    s+
  gi|488600566|ref|YP_007907037.1| 384 EVSVNESVLFYGKVSAN----ETIQLQIFVNSTEAGALNAVK---DFNFTLRFPKSGKYRVAVYFPGDSMYREEWSN 453
                                       45556666666666666....677778888999999977777...79************************999998 PP

                                       EEEEEEES CS
                           Big_3_5  80 avtvtVtk 87 
                                       ++ + V+ 
  gi|488600566|ref|YP_007907037.1| 454 SAEILVKE 461
                                       88777765 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.2e-06     0.065      17      62 ..     563     607 ..     558     609 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-06
                           DUF4129  17 rpgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeeyr 62 
                                       + + TprE++r++ +  s  + l+ ++ ++e++ YG   a++ e++
  gi|488600566|ref|YP_007907037.1| 563 KKSLTPREVVREL-RNESFIDKLRFVTSIHEKVIYGKMSADEKERE 607
                                       5688*********.556777899999**********9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3766.64
//
Query:       gi|488600567|ref|YP_007907038.1|  [L=247]
Description: hypothetical protein Asulf_01044 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1520.49
//
Query:       gi|488600568|ref|YP_007907039.1|  [L=79]
Description: hypothetical protein Asulf_01045 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1095  (0.0610742); 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):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 497.39
//
Query:       gi|488600569|ref|YP_007907040.1|  [L=133]
Description: hypothetical protein Asulf_01046 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0044   17.1   0.0     0.0044   17.1   0.0    1.1  1  CoA_binding_3  CoA-binding domain
  ------ inclusion threshold ------
      0.034   14.5   1.1      0.055   13.8   1.1    1.5  1  EbsA           EbsA-like protein


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 !   17.1   0.0   4.9e-07    0.0044      15      63 ..      10      60 ..       2     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.9e-07
                     CoA_binding_3 15 lrlllrvlsawllvlll.lallsfs.lkdafSRlwlaywavvglvllivsr 63
                                      + +++r+ +++++vll+ + llsf+ ++++fSRl++ + +++ +v+  +  
  gi|488600569|ref|YP_007907040.1| 10 NPQMKRFWLSVCVVLLIaGNLLSFVrFQNDFSRLMFSSITFTMAVAFFAIL 60
                                      468999999***999862566777646899*****9877666665555442 PP

>> EbsA  EbsA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.1   6.2e-06     0.055      39     111 ..      45     111 ..      16     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-06
                              EbsA  39 iylksnlvlllflvlvilgfkryliieedkliikslrffkkkkielseIkkvevekkkielklkekksrtflm 111
                                       ++++++++++ f+++++l   ry +ie+++++         k+ +l +I+ + v  k++++klk  ++  + +
  gi|488600569|ref|YP_007907040.1|  45 FSSITFTMAVAFFAILMLRKPRYYYIEDQTIY------SATKRTKLTDIEDIDVDSKNLVIKLKLINPSSMSL 111
                                       567888899999999999999******99986......45677899****************98555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 938.90
//
Query:       gi|488600570|ref|YP_007907041.1|  [L=409]
Description: adenosylhomocysteinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-60  202.8   0.0    1.2e-29  103.4   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    2.8e-53  180.3   0.8    7.4e-53  178.9   0.4    1.9  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    1.7e-10   40.6   0.2    3.1e-10   39.7   0.2    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    2.4e-09   37.0   0.2    9.9e-09   35.0   0.2    1.8  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.035   14.0   1.2       0.71    9.7   0.9    2.4  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.04   13.2   2.4        0.1   11.9   2.4    1.6  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 !   98.3   0.0   1.4e-31   4.3e-28      11     138 ..       5     127 ..       1     135 [. 0.94
   2 !  103.4   0.0     4e-33   1.2e-29     175     286 ..     131     403 ..     126     409 .] 0.98

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.4e-31
                                       HHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  11 efGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaaaai 87 
                                       e G  +ie ae+ m  + ++re +++ekpl+g +i  +lh+ ++tavL++tLva Gaev  + Cn  s qd+++aa+
  gi|488600570|ref|YP_007907041.1|   5 ESGYGKIEWAERHMKVMEKIREIFSKEKPLEGYKIGMALHVEAKTAVLVKTLVAGGAEVAITGCNPLSSQDDVSAAL 81 
                                       668889*********************************************************************** PP

                                       CCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  88 aeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                        + g+  +a +g++ eey   ++++l+      +p++i+DdG Dl  l+h 
  gi|488600570|ref|YP_007907041.1|  82 RDMGIECYAKRGMSDEEYYSALNKVLDS-----KPDVIIDDGADLIFLLHG 127
                                       **************************54.....7***********999985 PP

  == domain 2  score: 103.4 bits;  conditional E-value: 4e-33
                                       CCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                         AdoHcyase 175 ellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD............................... 220
                                       +l++++ G seetttGv r+  ++++g L++p i+vnd++tk  fD                               
  gi|488600570|ref|YP_007907041.1| 131 DLAERVLGASEETTTGVIRIRAMEREGILSFPVIDVNDALTKYLFDnrygtgqstwdgvlratnmliagkkvvvagy 207
                                       578999*********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|488600570|ref|YP_007907041.1| 208 gwcgrgiamrakglgakviitevdeiraleavmdgfevmkmedaakvgdifitatgnrdvivedhfklmkdgailan 284
                                       ***************************************************************************** PP

                                       .....................................................S-HHHHHHHHHHHHHHHHHHHHTT CS
                                       .....................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 .....................................................hpsfvmsasftnqvlaqielfkke 244
                                                                                            hp  vm++sf++q+la   + +++
  gi|488600570|ref|YP_007907041.1| 285 sghfnveinipslerlskskrevrnwvteydlgdkrlyllaegrlvnlvsgdgHPIEVMDMSFSDQALAVRYIVENH 361
                                       ***************************************************************************** PP

                                       SSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 245 kkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyig 286
                                       +k e+kvy+lp +lD  varl+l+++g++++el+++q +y++
  gi|488600570|ref|YP_007907041.1| 362 EKLENKVYRLPEELDRMVARLKLKSMGVDIDELSESQKKYLS 403
                                       ****************************************96 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.69   2.1e+03      41      58 ..      55      72 ..      26      96 .. 0.76
   2 !  178.9   0.4   2.5e-56   7.4e-53       1     159 [.     177     334 ..     177     337 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.69
                                      HHHHCT-EEEEE-S-HHH CS
                     AdoHcyase_NAD 41 slkglGarvivtevdPic 58
                                      +l + Ga v +t  +P++
  gi|488600570|ref|YP_007907041.1| 55 TLVAGGAEVAITGCNPLS 72
                                      455667777777777765 PP

  == domain 2  score: 178.9 bits;  conditional E-value: 2.5e-56
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg+ +s  dg+ rat++l+aGk++vvaGyG  G+G a   kglGa+vi+tevd i al a+m+Gfev+++e+++k
  gi|488600570|ref|YP_007907041.1| 177 NRYGTGQSTWDGVLRATNMLIAGKKVVVAGYGWCGRGIAMRAKGLGAKVIITEVDEIRALEAVMDGFEVMKMEDAAK 253
                                       78*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +di++t+tGn+d+i  +h+k mkd ai++n Ghf+ ei++ +le+ +++k ev+  v ++ l d+ ++ llaeGrl
  gi|488600570|ref|YP_007907041.1| 254 VGDIFITATGNRDVIVEDHFKLMKDGAILANSGHFNVEINIPSLERLSKSKREVRNWVTEYDLGDK-RLYLLAEGRL 329
                                       ***************************************************************985.6899****** PP

                                       CHHHT CS
                     AdoHcyase_NAD 155 lnlgc 159
                                       +nl +
  gi|488600570|ref|YP_007907041.1| 330 VNLVS 334
                                       **976 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.2     1e-13   3.1e-10      22     127 ..     185     286 ..     169     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1e-13
                                       CCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C  22 ewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslh 98 
                                       +w+   + +   ++gk+v + G+G  G+ +a r+k++g+kvi++++ + +  e+   g+e++++e++ +  Di + +
  gi|488600570|ref|YP_007907041.1| 185 TWDGVLRATNMLIAGKKVVVAGYGWCGRGIAMRAKGLGAKVIITEVDEIRALEAVMDGFEVMKMEDAAKVGDIFITA 261
                                       5544455666689**********************************9988899999***************99887 PP

                                       S--STTTTTSBSHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C  99 lpltpetrhlinaeelakmkkgailiNta 127
                                       +     +r++i ++++++mk+gail N +
  gi|488600570|ref|YP_007907041.1| 262 TG----NRDVIVEDHFKLMKDGAILANSG 286
                                       65....99******************987 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.4   1.2e+03       6      66 ..      62     124 ..      59     130 .. 0.63
   2 !   35.0   0.2   3.3e-12   9.9e-09       2     102 ..     197     293 ..     196     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.4
                                       -EEEES-S...HHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE CS
                              IlvN   6 kiaviGyG...sqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmi 66 
                                       ++a+ G+    sq  +    lrd g++       +++ + +A ++ ++ +    + + ad++++
  gi|488600570|ref|YP_007907041.1|  62 EVAITGCNplsSQDDVS-AALRDMGIECYAKRGMSDEEYYSALNKVLDSKPDVIIDDGADLIFL 124
                                       67777774332555554.5799999998766666666677777766666655555556666655 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 3.3e-12
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       + gkk++v GyG  G+  a+  +  g +v+++  ++   + +A  +gfev+++++a+k  d+ ++ +    +++v+ 
  gi|488600570|ref|YP_007907041.1| 197 IAGKKVVVAGYGWCGRGIAMRAKGLGAKVIITEVDEI-RALEAVMDGFEVMKMEDAAKVGDIFITAT---GNRDVIV 269
                                       789****************************999888.677899*****************987765...4677887 PP

                                       HHTGGG--TT-EEEESSSHHHHTT CS
                              IlvN  79 eeiepnlkegkalafahGfnihfg 102
                                       e+  + +k+g++la +  fn+  +
  gi|488600570|ref|YP_007907041.1| 270 EDHFKLMKDGAILANSGHFNVEIN 293
                                       888899**************9865 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 ?    9.7   0.9   0.00024      0.71       1      43 [.     201     244 ..     201     270 .. 0.78
   2 ?    1.9   0.0     0.058   1.7e+02      17      70 ..     332     385 ..     327     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00024
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-H.HHHHHHHHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdise.ealekalekie 43 
                                       kv v G G  G+gia+ +   g +V +++++e +ale++++  e
  gi|488600570|ref|YP_007907041.1| 201 KVVVAGYGWCGRGIAMRAKGLGAKVIITEVDEiRALEAVMDGFE 244
                                       699***************************88244555555544 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.058
                                       HHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEE CS
                           3HCDH_N  17 vfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisft 70 
                                       ++   g+++ ++d+s +  + a + i ++ ekl++k     ee ++++ar++ +
  gi|488600570|ref|YP_007907041.1| 332 LVSGDGHPIEVMDMSFSDQALAVRYIVENHEKLENKVYRLPEELDRMVARLKLK 385
                                       556678888888888888888888888888888888887788888888888765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.4   3.4e-05       0.1      26     121 ..     197     279 ..     179     284 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                                       B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BT CS
                       AlaDh_PNT_C  26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlip 102
                                       ++  kv+v G G  G   +  akglgakV +++v++  ++ le++    +ev+     ++++a+k  d+ i++   +
  gi|488600570|ref|YP_007907041.1| 197 IAGKKVVVAGYGWCGRGIAMRAKGLGAKVIITEVDE--IRALEAVMDG-FEVM-----KMEDAAKVGDIFITA---T 262
                                       55679***************************9975..4445554444.3332.....344455555666655...3 PP

                                       TSS---SC-HHHHHTS-TT CS
                       AlaDh_PNT_C 103 GkkaPkLvteemvksMkpg 121
                                       G++   ++ e++ k Mk+g
  gi|488600570|ref|YP_007907041.1| 263 GNR--DVIVEDHFKLMKDG 279
                                       433..35555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2366.13
//
Query:       gi|488600571|ref|YP_007907042.1|  [L=494]
Description: Exopolyphosphatase-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   76.8   0.1    4.2e-21   75.4   0.1    1.8  1  TrkA_N           TrkA-N domain
    1.9e-12   47.8   0.8    1.9e-11   44.5   0.2    2.5  2  DHHA1            DHHA1 domain
    1.6e-11   44.3   0.6    4.3e-11   42.9   0.6    1.7  1  DHH              DHH family
    0.00023   21.4   0.0    0.00049   20.3   0.0    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0049   17.4   0.0      0.013   16.1   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.02   14.5   0.1      0.075   12.6   0.0    1.8  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.037   13.4   0.0      0.072   12.4   0.0    1.4  1  ThiF             ThiF family
      0.094   13.0   0.0       0.36   11.1   0.0    2.0  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.16   11.9   0.0       0.34   10.8   0.0    1.6  1  KR               KR domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.1   2.1e-24   4.2e-21       1     116 []      27     142 ..      27     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.1e-24
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       +++iG+G +G ++++eL ++gk+ +++d+++e++e l+++ +++++gda++e++L + + +++++v ++++d e+  
  gi|488600571|ref|YP_007907042.1|  27 YLVIGCGSLGFNVLKELARRGKKALAVDSSQEKIEVLKDQDFNALIGDASNEDFLLSFDYDRISVVFILIPDFEVVK 103
                                       68*****************7778****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                        a++l+++      iiara++ +++e l+ lgad+vi+p
  gi|488600571|ref|YP_007907042.1| 104 RAIKLIRNVSRSVFIIARASTGKEKEELEMLGADAVITP 142
                                       ********9999*************************97 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.35     7e+02      15      59 ..     154     194 ..     146     213 .. 0.73
   2 !   44.5   0.2   9.5e-15   1.9e-11      34     124 ..     372     465 ..     352     481 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.35
                                       HHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHH CS
                             DHHA1  15 leelkealaklkaeellekaeevkgvkvlvaevgeewdagalgia 59 
                                       l++ ++    +k++e+l++ +   g k+++    ++ d++al +a
  gi|488600571|ref|YP_007907042.1| 154 LDRIETLRRLKKFKEVLNSMK---GSKLAIFTH-DNPDPDALSSA 194
                                       566666667778888888764...888888887.99999999887 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 9.5e-15
                                       CEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS-HHHHHHHHHHHTT CS
                             DHHA1  34 aeevk.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkdgvdagelakeaaaklg 108
                                       ++  +   +vl+++ g   +++a+ +aad l++   +  + v+v++   d +++sar  + + ++ge++++a+ ++g
  gi|488600571|ref|YP_007907042.1| 372 NR--EiYPPVLISFAGFISEKDAITQAADLLLK--LEgISTVLVFGVVRDVIHLSARNVDVRMNIGEVLRKAFGDVG 444
                                       23..3499*************************..666666666666666*********77***************9 PP

                                       CCEEEETCEEEEEEE......H CS
                             DHHA1 109 ggGGGHdlAaGagip......a 124
                                         G GH+ A G++ip      +
  gi|488600571|ref|YP_007907042.1| 445 SAG-GHAHAGGGQIPlgifgeI 465
                                       999.**********95555541 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.6   2.2e-14   4.3e-11       2     101 .]     178     319 ..     177     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.2e-14
                                       EEEE-ECSSSHHHHHHHHHHHHC...............................................ECS--TC CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...............................................xxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialanl...............................................lvDhnek 31 
                                        +i++h npD D++ Sa+al+++                                               lvD +  
  gi|488600571|ref|YP_007907042.1| 178 LAIFTHDNPDPDALSSAMALKEIakklgveadilyygeishqenkamvnlleielvhakdvdiytyenfaLVDSSAV 254
                                       6799******************6666666677677776677777777777777777777777777777779998776 PP

                                       GGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  32 sqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                           +  + ++ +  i+iDHH  + ++e    ++ ++ +vgsta+i+++++ e +  +s+ +a++l  gi
  gi|488600571|ref|YP_007907042.1| 255 GVNNS--IPKDVKLNIVIDHHPAE-NVEAD--FVDIRDDVGSTATIMTNYMVEMNMVPSRMLATALFFGI 319
                                       66654..5999999*********8.55554..67789*****************************9998 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.5e-07   0.00049       4      89 ..      29     121 ..      26     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-07
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHC.....SEEEE-SSSHHHHHHH CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...akaaesieelvasl.....dvvitmvkagkavdev 72 
                                       +iG G +G n  ++l+++g k  +++ ++ek+e l ++    + + +s e+++ s       vv++++++ + v+  
  gi|488600571|ref|YP_007907042.1|  29 VIGCGSLGFNVLKELARRGKKALAVDSSQEKIEVLKDQDfnaLIGDASNEDFLLSFdydriSVVFILIPDFEVVKRA 105
                                       8*************************************87777888999****999999999************999 PP

                                       HHSHCCC--TT-EEEE- CS
                     NAD_binding_2  73 iegllealkkgdilidg 89 
                                       i+  +++++++ ++i  
  gi|488600571|ref|YP_007907042.1| 106 IKL-IRNVSRSVFIIAR 121
                                       975.5556665555544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.5e-06     0.013       4      84 ..      29     111 ..      27     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.5e-06
                                       EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHH.HHHC-EEECECHHHHHH.....H-SEEEE-S-.HHH CS
                     F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeela.eelgvkvtavdneeaae.....eadvvvlavk.ped 73 
                                       +iG+G++g+ +++ l+++g   ++ + a ++++ek+e l+ +++++ +   +ne+ +      +  vv++ ++ +e+
  gi|488600571|ref|YP_007907042.1|  29 VIGCGSLGFNVLKELARRG---KKAL-AVDSSQEKIEVLKdQDFNALIGDASNEDFLLsfdydRISVVFILIPdFEV 101
                                       79*****************...9999.77***********7788888888889988752222244467777764555 PP

                                       HHHHHHHCGHH CS
                     F420_oxidored  74 veevlselakd 84 
                                       v+ +++ + ++
  gi|488600571|ref|YP_007907042.1| 102 VKRAIKLI-RN 111
                                       56666555.44 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.8e-05     0.075       5      43 ..      29      67 ..      27      72 .. 0.94
   2 ?   -1.9   0.0       1.1   2.1e+03      95     122 ..      97     124 ..      96     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                                      EE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS CS
                    UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeighevigvDideekvdklnsgk 43
                                      viG G +G      la++g++ + vD ++ek++ l+ ++
  gi|488600571|ref|YP_007907042.1| 29 VIGCGSLGFNVLKELARRGKKALAVDSSQEKIEVLKDQD 67
                                      9*********************************99876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                       B-THHHHHHHHHHHHHHHCEEEEEE-S- CS
                    UDPG_MGDP_dh_N  95 aDlkyvesaarsiaealkkgkvvvvkST 122
                                       +D + v++a++ i ++ ++  ++   ST
  gi|488600571|ref|YP_007907042.1|  97 PDFEVVKRAIKLIRNVSRSVFIIARAST 124
                                       68999**********9999999999998 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.6e-05     0.072      19      47 ..      25      53 ..      11      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                                      SEEEEE--SHHHHHHHHHHHHHTTTEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknLalsGvgkltl 47
                                        +l++G+G lG ++lk+La+ G + l +
  gi|488600571|ref|YP_007907042.1| 25 FDYLVIGCGSLGFNVLKELARRGKKALAV 53
                                      5689*****************99887765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.36       2      60 ..      28      79 ..      27      91 .. 0.84
   2 ?   -2.6   0.0       3.2   6.3e+03      32      67 ..     161     195 ..     159     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHH CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenye 60
                                      l+iG+Gs G  v+++lar+++       +d s+ek e l+     ++f+a   da+n++
  gi|488600571|ref|YP_007907042.1| 28 LVIGCGSLGFNVLKELARRGKK---ALAVDSSQEKIEVLK----DQDFNALIGDASNED 79
                                      89*****************985...899999999977664....567777777777765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                                       SSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHH CS
                   Sacchrp_dh_NADP  32 rskeklealaakalgvrfeaialdaenyeavLaall 67 
                                       r ++k ++++++++g+++ + + d  +++a L++++
  gi|488600571|ref|YP_007907042.1| 161 RRLKKFKEVLNSMKGSKLAIFTHDNPDPDA-LSSAM 195
                                       567888899999999999999999999999.76655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.34       3      36 ..      27      59 ..      26     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                      EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS.. CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaa 36
                                      yl++G +G+LG  + + la++g++ l++ s +++
  gi|488600571|ref|YP_007907042.1| 27 YLVIG-CGSLGFNVLKELARRGKKALAVDSSQEK 59
                                      89998.8********************9998853 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3300.40
//
Query:       gi|488600572|ref|YP_007907043.1|  [L=92]
Description: putative pyrophosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-13   48.3   0.4    8.3e-13   48.3   0.4    1.5  2  MazG       MazG nucleotide pyrophosphohydrolase domain
    1.4e-05   25.4   0.8    1.8e-05   25.1   0.8    1.2  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase
    0.00013   22.1   1.2    0.00028   21.1   0.3    1.8  2  MazG-like  MazG-like family
     0.0078   16.4   0.3      0.013   15.7   0.3    1.3  1  dUTPase_2  dUTPase
  ------ inclusion threshold ------
       0.12   12.8   0.0         28    5.4   0.0    2.8  2  TPR_17     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   5.3e+03      55      69 ..       3      17 ..       1      20 [. 0.61
   2 !   48.3   0.4   2.3e-16   8.3e-13       5      68 ..      25      81 ..      21      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                                      HHHHHHHHHHHHHHH CS
                              MazG 55 ledvaetileKlerR 69
                                      ++d  ++i eK+ + 
  gi|488600572|ref|YP_007907043.1|  3 VSDLQRKIAEKYLEV 17
                                      556666777777655 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 2.3e-16
                                      HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
                              MazG  5 tllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaetileKler 68
                                       lla l eEvgE+aea++k+d +++eeEL Dv++ vl++an     +g+ +e+ +   +eK+++
  gi|488600572|ref|YP_007907043.1| 25 FLLAVLFEEVGELAEAVRKNDVEAIEEELCDVMFMVLSIANY----YGLMFERRL---YEKYIE 81
                                      5899*************************************8....888888655...666665 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.8   4.9e-09   1.8e-05      26      74 ..      24      73 ..       3      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.9e-09
                                      H.HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHH CS
                            PRA-PH 26 l.raaligEEavElleaasegdlaeladelaDllYvtygllvllGidlda 74
                                      l ++a + EE+ El ea+ ++d + + +el+D++++++  + ++G+ +++
  gi|488600572|ref|YP_007907043.1| 24 LfLLAVLFEEVGELAEAVRKNDVEAIEEELCDVMFMVLSIANYYGLMFER 73
                                      35789999*********************************999998775 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.31   1.1e+03      55      72 ..       2      17 ..       1      24 [. 0.62
   2 !   21.1   0.3   7.8e-08   0.00028      15      63 ..      30      79 ..      20      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.31
                         MazG-like 55 dfeeideklkkklkkypv 72
                                      d++++++k+++k    +v
  gi|488600572|ref|YP_007907043.1|  2 DVSDLQRKIAEKYL--EV 17
                                      66778888877754..34 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 7.8e-08
                         MazG-like 15 llksveelfkallkgseeeildeLAdviiylylLAdrlGidfee.idekl 63
                                      l ++v+el +a+ k++ e+i +eL+dv+ +++  A+  G+ fe+ + ek 
  gi|488600572|ref|YP_007907043.1| 30 LFEEVGELAEAVRKNDVEAIEEELCDVMFMVLSIANYYGLMFERrLYEKY 79
                                      678999****999******************************9998885 PP

>> dUTPase_2  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   3.6e-06     0.013      12     101 ..       6      82 ..       4      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                                       HHHHHSTTH.....HH-HHHHH....HHHHH.HHHHHHTTS.---SSSSTT---HHHHHHHHHHHHHHHHHHHHCHH CS
                         dUTPase_2  12 LderiekkwnlkkkrkklsdwleekllAllv.ElaElanetrsfKyWknkkksdlekvleElvDilHFllslalelk 87 
                                       L ++i++k  l+ ++ k ++++   llA+l  E++Ela+ +         +k+d e + eEl D++  +ls+a+ + 
  gi|488600572|ref|YP_007907043.1|   6 LQRKIAEKY-LEVDK-KSGELF---LLAVLFeEVGELAEAV---------RKNDVEAIEEELCDVMFMVLSIANYYG 68 
                                       667777777.44444.467888...7776663699999999.........5689********************999 PP

                                       CT-GGGGCSSCCCC CS
                         dUTPase_2  88 dekeeasvekelsk 101
                                          e+  +ek +++
  gi|488600572|ref|YP_007907043.1|  69 LMFERRLYEKYIED 82 
                                       88888766666655 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0078        28      16      33 ..      24      41 ..      10      42 .. 0.83
   2 ?    4.5   0.0     0.015        55       1      12 [.      75      86 ..      75      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0078
                            TPR_17 16 ynnLAelllknGdlmtAr 33
                                      +++LA+l+++ G+l++A+
  gi|488600572|ref|YP_007907043.1| 24 LFLLAVLFEEVGELAEAV 41
                                      689**********99996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                            TPR_17  1 lylkaleldPnn 12
                                      ly+k +e dP++
  gi|488600572|ref|YP_007907043.1| 75 LYEKYIEDDPSS 86
                                      7*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 584.32
//
Query:       gi|488600573|ref|YP_007907044.1|  [L=251]
Description: Phosphate/sulfate permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-46  156.5  24.1    4.8e-45  154.1  24.1    1.8  1  PHO4      Phosphate transporter family
  ------ inclusion threshold ------
       0.31   11.0   2.3       0.89    9.5   2.3    1.8  1  DUF2897   Protein of unknown function (DUF2897)


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1  24.1   5.4e-49   4.8e-45      47     336 ..       4     242 ..       1     243 [. 0.90

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 5.4e-49
                              PHO4  47 irkgivdvelfdpselmlgmlaallgaavwlllatvlglPvStthslvGaliGaalaaeggeavkwkklvkivlswv 123
                                       +++++vd++       + ++ + l+ + +  +l ++ +lPvS+ +++v +l+G +la   g +v+ ++l++iv swv
  gi|488600573|ref|YP_007907044.1|   4 VGSELVDLN-------IHIISISLIISSIAIILSNWKKLPVSSHQAIVSSLVGSGLAF--GVSVDFNTLIRIVESWV 71 
                                       555555322.......2466678888999999*************************5..468999*********** PP

                              PHO4 124 lsPllggiiaallfllvkrlilvkeklknalralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsaalv 200
                                       +sP+ +++++++++ +++ ++            +p                         ++e+++++l+++s++l+
  gi|488600573|ref|YP_007907044.1|  72 ISPVSAFFASVIVYRIMESVVS----------KMP-----------------------PLKVERAVRYLLLLSGSLI 115
                                       ********************55..........233.......................3368999************ PP

                              PHO4 201 sfahGanDvanaiGpllaalisiykaskevplwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaa 277
                                       ++  Gan+ a a Gp++   + +      +pl   ++g + + lG +l+G rv++tvG+ it +l+p++Gf+a+++a
  gi|488600573|ref|YP_007907044.1| 116 AYNTGANELATALGPIVC--YGL-----LTPLQAGIAGTALLWLGAYLLGSRVVETVGKGIT-SLDPFSGFSAQMGA 184
                                       ****************43..333.....47999*****************************.6************* PP

                              PHO4 278 altvllasklglPvStThvlvgavvGvGlakkresavnwklvrnivlaWvlTlpvsall 336
                                        ++vll++ lg+P+StT +++g+v GvG++k +++ ++   +++i+l+Wv+T   +++l
  gi|488600573|ref|YP_007907044.1| 185 GISVLLFTSLGMPISTTYCIIGGVTGVGILK-STKTIRSPFLKKIFLSWVITPLTAMIL 242
                                       *******************************.79******************9998876 PP

>> DUF2897  Protein of unknown function (DUF2897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.3    0.0001      0.89       8      36 ..      13      40 ..      12      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0001
                           DUF2897  8 IiilVlgvIvGnlavLkysAkmklpqfge 36
                                      I i+++++I++++a++ +  k klp +  
  gi|488600573|ref|YP_007907044.1| 13 IHIISISLIISSIAIILSNWK-KLPVSSH 40
                                      779**************9999.9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1455.16
//
Query:       gi|488600574|ref|YP_007907045.1|  [L=212]
Description: TIGR00153 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-38  130.4   3.1    6.2e-38  130.3   3.1    1.0  1  PhoU_div  Protein of unknown function DUF47
    0.00026   21.4   0.9    0.00026   21.4   0.9    2.7  2  PhoU      PhoU domain
  ------ inclusion threshold ------
        0.1   12.0   0.8       0.25   10.8   0.1    1.8  2  DUF3087   Protein of unknown function (DUF3087)


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   3.1     1e-41   6.2e-38       2     212 ..       7     208 ..       6     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 1e-41
                          PhoU_div   2 lflfgsspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRe 78 
                                       +fl g ++e+++++++++++e   ++ e lk  +e   +++ +l  ei+elEr +D i+r+i l l++g+flP  R 
  gi|488600574|ref|YP_007907045.1|   7 KFLVGGEKEEEIINLFKEHIEKLSEASETLKLAIE---SDDASLNYEICELERTGDIIRRDIALGLYEGAFLPGVRG 80 
                                       7999*******************************...89************************************* PP

                          PhoU_div  79 dllelveslDeildvlediamlvtlrkvefpeelkdeflallkktveaiealaevieeleklletalskkdiveeie 155
                                       +l +l+e lDe ld +ed+ +  +l + ++ + ++d  l++++++ +++  l e++++l +  +++ls  d+  +i 
  gi|488600574|ref|YP_007907045.1|  81 NLYRLAELLDECLDLIEDTSVYFSLLN-GLHPAIRDLCLRIAEINCKMVDYLYEAFNSLYQ--DSDLS--DKTIKIR 152
                                       ***************************.8*******************************9..89999..7889*** PP

                          PhoU_div 156 slEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisiil 212
                                        +E+eiD l+r++++k+f   +  +++e  +l ++ + l  +sd++ed ad i+++ 
  gi|488600574|ref|YP_007907045.1| 153 AKEQEIDGLKRQIHEKMFD-IEIKSFWEGSILLKFLDSLISISDKIEDSADLIQVLN 208
                                       ******************9.777******************************9985 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.9     0.048   2.8e+02      34      82 ..      15      61 ..      12      66 .. 0.47
   2 !   21.4   0.9   4.4e-08   0.00026       3      82 ..     119     204 ..     117     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.048
                                      HHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU 34 ddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82
                                      ++ei +l+ke +++l ea  + +   e  +++ sl   + +lER gD +
  gi|488600574|ref|YP_007907045.1| 15 EEEIINLFKEHIEKLSEASETLKLAIE-SDDA-SLNYEICELERTGDII 61
                                      666666666666664444433222222.2222.1222344666666655 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 4.4e-08
                                       HHHHHHHHHHHHHHHHH...HCT-H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH..HHHHHHHHHHH CS
                              PhoU   3 rmaeiveemlddaleal...eekdt...elarevierddeidrlekeiersllealakrqplae..dlrellsllri 71 
                                       r+aei  +m+d+++ea+   + +d    +   +++++++eid l ++i ++ ++ + +++ ++    l++l sl++i
  gi|488600574|ref|YP_007907045.1| 119 RIAEINCKMVDYLYEAFnslY-QDSdlsDKTIKIRAKEQEIDGLKRQIHEK-MFDIEIKSFWEGsiLLKFLDSLISI 193
                                       7889999*********97642.354123555666788**************.7777666666666678999999999 PP

                                       HHHHHHHHHHH CS
                              PhoU  72 ardlERigDha 82 
                                       +  +E  +D +
  gi|488600574|ref|YP_007907045.1| 194 SDKIEDSADLI 204
                                       99999999976 PP

>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.18   1.1e+03     137     159 ..      22      44 ..      16      48 .. 0.81
   2 ?   10.8   0.1   4.3e-05      0.25     112     161 ..     126     178 ..     120     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.18
                           DUF3087 137 lekeieqlkelieelgltleaed 159
                                        +++ie+l+e+ e l+l +e +d
  gi|488600574|ref|YP_007907045.1|  22 FKEHIEKLSEASETLKLAIESDD 44 
                                       57889999999999999999876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.3e-05
                           DUF3087 112 kilrFyyqglkqlyq...LddNtltlselekeieqlkelieelgltleaedfe 161
                                       k++ + y++ + lyq   L d t+++   e+ei+ lk +i+e+ +++e+++f 
  gi|488600574|ref|YP_007907045.1| 126 KMVDYLYEAFNSLYQdsdLSDKTIKIRAKEQEIDGLKRQIHEKMFDIEIKSFW 178
                                       56789999999999777799*****************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1225.18
//
Query:       gi|488600575|ref|YP_007907046.1|  [L=243]
Description: amino acid ABC transporter ATP-binding protein, PAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-39  133.0   0.0    1.2e-38  132.7   0.0    1.1  1  ABC_tran      ABC transporter
    3.5e-13   50.0   0.0      4e-06   26.9   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.8e-11   43.3   0.6    3.3e-07   30.0   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    2.1e-05   25.0   0.0      3e-05   24.5   0.0    1.3  1  AAA_16        AAA ATPase domain
    2.5e-05   24.8   0.3    0.00023   21.7   0.0    2.0  2  AAA_23        AAA domain
    8.4e-05   22.6   0.3    0.00023   21.1   0.3    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
    8.6e-05   22.2   0.0    0.00019   21.1   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
    8.8e-05   21.5   1.5       0.19   10.5   0.0    2.9  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0001   22.6   0.2    0.00059   20.1   0.2    1.9  1  AAA_22        AAA domain
    0.00036   20.3   0.1     0.0044   16.8   0.0    2.0  2  AAA_15        AAA ATPase domain
    0.00075   19.9   0.1       0.32   11.4   0.1    2.3  2  AAA           ATPase family associated with various cellular 
      0.001   19.0   0.2     0.0018   18.2   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
     0.0014   18.2   0.4       0.21   11.1   0.0    2.2  2  AAA_25        AAA domain
     0.0024   17.0   0.0     0.0043   16.2   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
     0.0039   16.9   0.1      0.016   15.0   0.0    1.8  2  AAA_30        AAA domain
     0.0046   16.2   0.0     0.0063   15.7   0.0    1.2  1  G-alpha       G-protein alpha subunit
     0.0048   17.1   0.0      0.006   16.7   0.0    1.5  1  AAA_33        AAA domain
     0.0066   16.4   0.1      0.025   14.5   0.1    1.9  2  Rad17         Rad17 P-loop domain
     0.0094   15.4   0.3          1    8.7   0.1    2.4  2  TniB          Bacterial TniB protein
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.036   13.8   0.0    1.7  2  AAA_24        AAA domain
      0.018   14.9   0.0       0.43   10.4   0.0    2.1  2  TK            Thymidine kinase
       0.02   15.1   0.4       0.31   11.3   0.4    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.024   14.6   0.0        1.7    8.6   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
      0.025   14.5   0.0      0.053   13.4   0.0    1.6  1  NACHT         NACHT domain
      0.032   14.3   0.1        1.5    8.9   0.0    2.3  2  AAA_14        AAA domain
      0.038   13.6   0.0       0.13   11.9   0.0    1.7  2  AAA_27        AAA domain
       0.04   14.5   0.1      0.084   13.4   0.1    1.6  1  AAA_18        AAA domain
      0.047   12.5   0.1       0.17   10.6   0.0    1.9  2  Adeno_IVa2    Adenovirus IVa2 protein
      0.047   13.3   0.3        2.3    7.7   0.1    2.3  2  CobU          Cobinamide kinase / cobinamide phosphate guanyl
      0.049   13.0   0.4       0.13   11.6   0.1    1.8  2  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.055   12.8   0.1       0.61    9.4   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.083   13.2   0.3       0.15   12.4   0.3    1.6  1  AAA_19        AAA domain
       0.12   11.5   0.3       0.43    9.7   0.3    1.9  1  NB-ARC        NB-ARC domain
       0.14   11.9   0.0       0.51   10.0   0.0    1.8  2  IstB_IS21     IstB-like ATP binding protein
       0.16   12.2   0.0        0.5   10.6   0.0    1.8  1  AAA_28        AAA domain
       0.17   10.5   0.0        5.8    5.4   0.0    2.0  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 !  132.7   0.0   2.5e-41   1.2e-38       1     137 []      20     168 ..      20     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 2.5e-41
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpelt 75 
                                       lk ++l++k+ge+v+i+G++G+GKSt+l+++ +l++pt+G+illdg +++    +++++r++ig+++q+ +lfp+l+
  gi|488600575|ref|YP_007907046.1|  20 LKGIDLQVKKGEVVVIIGPSGSGKSTFLRCINRLEEPTSGRILLDGVEITGdnVDINKVRQRIGMVFQQFNLFPHLN 96 
                                       789***********************************************9888999******************** PP

                                       HHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + en              e +++++++l+k+glk++ ++      ++LSgGq+qrva+aral+ +p+++l+DE t+
  gi|488600575|ref|YP_007907046.1|  97 AIENvmlapvkikkedkkEVEKRAKRLLEKVGLKDFMHKYP----AQLSGGQQQRVAIARALAMNPEIMLFDEVTS 168
                                       99999*******99777666667999999999999877777....****************************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 !   21.2   0.0   4.3e-07   0.00021       1      22 [.      32      53 ..      32      85 .. 0.80
   2 !   26.9   0.0     8e-09     4e-06     235     297 ..     138     197 ..     107     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.3e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + v+iGp gsGKS++L+++  l
  gi|488600575|ref|YP_007907046.1| 32 VVVIIGPSGSGKSTFLRCINRL 53
                                      579****************988 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 8e-09
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++lS G+++  a++ al+  +    + l+DE+ + L+P+l++++l+++k+l++ g   i++TH
  gi|488600575|ref|YP_007907046.1| 138 AQLSGGQQQRVAIARALAMNP---EIMLFDEVTSALDPELVKEVLDVMKQLATDGMTMIVVTH 197
                                       688999999989999999988...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 !   11.2   0.0   0.00035      0.18      25      44 ..      31      50 ..      12      55 .. 0.84
   2 !   30.0   0.1   6.7e-10   3.3e-07     119     205 ..     116     205 ..      97     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      ++ +i+Gp GSGKs +l  i
  gi|488600575|ref|YP_007907046.1| 31 EVVVIIGPSGSGKSTFLRCI 50
                                      5789***********99877 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 6.7e-10
                                       -HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 119 tkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn 189
                                        +k  ++lle++g++        +LSgG+++ va+a  +A++   p  ++l+De+ +aLD + vk+v +++k+  ++
  gi|488600575|ref|YP_007907046.1| 116 VEKRAKRLLEKVGLKDFmhkypaQLSGGQQQRVAIARALAMN---P-EIMLFDEVTSALDPELVKEVLDVMKQLATD 188
                                       345566677777765435555559************999975...4.4899*********************98877 PP

                                       .SEEEEE-SSHHHCCC- CS
                                       .xxxxxxxxxxxxxxxx RF
                             SMC_N 190 .aQfivislreemleka 205
                                        + +iv++++ ++ +++
  gi|488600575|ref|YP_007907046.1| 189 gMTMIVVTHEMGFAREV 205
                                       79*******99887765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     6e-08     3e-05      21     107 ..      29     155 ..      17     197 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6e-08
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekd.......ggiflrgkcdqlesaipysa.laqalareellrqllde. 88 
                                       +g  e+v+++G+sG+GKs+ +r++  +le+        +g+ ++g++++  + + ++  + q++     l+++++  
  gi|488600575|ref|YP_007907046.1|  29 KG--EVVVIIGPSGSGKSTFLRCIN-RLEEPtsgrillDGVEITGDNVDINKVRQRIGmVFQQFNLFPHLNAIENVm 102
                                       44..89*******************.577666876666555588888888555555444777775555555555557 PP

                            AAA_16  89 ........aesaeleawrekleeala..........................a 107
                                               ++++e+e  +++l+e ++                          a
  gi|488600575|ref|YP_007907046.1| 103 lapvkikkEDKKEVEKRAKRLLEKVGlkdfmhkypaqlsggqqqrvaiaralA 155
                                       77776666566666666666666666777777755555555444444444440 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.7e-07   0.00023      14      40 ..      21      51 ..      10      53 .. 0.77
   2 ?    1.2   0.0      0.89   4.4e+02     148     166 ..     105     127 ..      57     159 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.7e-07
                            AAA_23 14 e.idF...skgltlItGpNGaGKTTildAik 40
                                      + id+   +  +++I+Gp G+GK+T+l++i 
  gi|488600575|ref|YP_007907046.1| 21 KgIDLqvkKGEVVVIIGPSGSGKSTFLRCIN 51
                                      357777755679*****************95 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.89
                            AAA_23 148 l....kdkkerleelekeleele 166
                                            k++k+++e+  k l e+ 
  gi|488600575|ref|YP_007907046.1| 105 PvkikKEDKKEVEKRAKRLLEKV 127
                                       02222333344444433333333 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   4.7e-07   0.00023      18     164 ..      28     196 ..      19     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.7e-07
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialr....eesiskldefie.................... 70 
                                       ++ e+++i Gp gsGK+++l+  i++le+    +i ++ ++    +++i+k+++ i+                    
  gi|488600575|ref|YP_007907046.1|  28 KKGEVVVIIGPSGSGKSTFLR-CINRLEEPTSGRILLDGVEitgdNVDINKVRQRIGmvfqqfnlfphlnaienvml 103
                                       56799*************997.6899999899888775543222288999999999999****************** PP

                          ATPase_2  71 .....eeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkk..iiiiiDelqklidlglngael 140
                                            ++e+kk++ek ++  ++k+ l+ ++++  +++    ++   +i +       i+++De+  +     +   +
  gi|488600575|ref|YP_007907046.1| 104 apvkiKKEDKKEVEKRAKRLLEKVGLKDFMHKYPAQLSGGQQQRV-AIARALAMnpEIMLFDEVTSAL----D--PE 173
                                       ****99999999999999999999999988844444333333222.2333322234599********9....5..89 PP

                          ATPase_2 141 lvkeLlnliesltkekhlcvvicl 164
                                       lvke l+++++l  +  +++v+ +
  gi|488600575|ref|YP_007907046.1| 174 LVKEVLDVMKQLATDGMTMIVV-T 196
                                       *********9977776655554.3 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.8e-07   0.00019      16      42 ..      24      50 ..      17      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.8e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAi 42
                                      +++++  ++++++GpsGsGKST+l  i
  gi|488600575|ref|YP_007907046.1| 24 DLQVKKGEVVVIIGPSGSGKSTFLRCI 50
                                      556664459*************99655 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 !   10.5   0.0   0.00038      0.19     240     266 ..      25      52 ..      10      98 .. 0.86
   2 !    8.1   0.3     0.002         1     321     412 ..     138     213 ..     104     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlek 266
                                       + ++kG v++I+G+   GKsT L+ +++
  gi|488600575|ref|YP_007907046.1|  25 LQVKKGeVVVIIGPSGSGKSTFLRCINR 52 
                                       468999*****************99864 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.002
                                       SS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS CS
                        ABC_ATPase 321 edASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvgg 397
                                       ++ SG   q ++i++al ++ +++L+DE tsA           elv       + ++d +++l ++ g+++i+v+  
  gi|488600575|ref|YP_007907046.1| 138 AQLSGGQQQRVAIARALAMNPEIMLFDEVTSALD--------PELV-------KEVLDVMKQL-ATDGMTMIVVTHE 198
                                       4568999999999999999999999999999843........3444.......3445666666.5557777777777 PP

                                       -GCCTTT-SEEEEEE CS
                        ABC_ATPase 398 sgdyldvAdtvilme 412
                                       +g   +v+d+vi m+
  gi|488600575|ref|YP_007907046.1| 199 MGFAREVGDRVIFMD 213
                                       777777777777775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   1.2e-06   0.00059       4     129 ..      29     196 ..      25     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee........................................erp 40 
                                       +  ++v++G+sG+GK+t lr + +  +                                               e++
  gi|488600575|ref|YP_007907046.1|  29 KGEVVVIIGPSGSGKSTFLRCINRLEEPT----SgrilldgveitgdnvdinkvrqrigmvfqqfnlfphlnaiENV 101
                                       56789***************999987433....13356888888888888888888888888888888777665555 PP

                            AAA_22  41 evvfvtlpsst..sskdllrellralglelka..erlsseellealeqalrarav.ielliiDEaqh.lrseealee 111
                                        ++ v+++++   + ++ +++ll+++gl+     ++++++   ++    +ra a+ +e+++ DE+   l  +e+++e
  gi|488600575|ref|YP_007907046.1| 102 MLAPVKIKKEDkkEVEKRAKRLLEKVGLKDFMhkYPAQLSGGQQQRVAIARALAMnPEIMLFDEVTSaL-DPELVKE 177
                                       555555555444477777888888888766666555555555544444444444488899999999988.8888888 PP

                            AAA_22 112 Lrsllnl.srkgvqliLvG 129
                                       + + ++  +++g+++i+v 
  gi|488600575|ref|YP_007907046.1| 178 VLDVMKQlATDGMTMIVVT 196
                                       8887777778888888775 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.8e-06    0.0044      18      84 ..      24      98 ..      18     150 .. 0.60
   2 ?    2.9   0.2      0.14        72     287     364 ..     121     197 ..      72     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.8e-06
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef...........a 84
                                      ++++++  + v+iG+ +sGKS++l+ ++ + + +    +  i ++  ++   + + ++ + +I + f           +
  gi|488600575|ref|YP_007907046.1| 24 DLQVKKGeVVVIIGPSGSGKSTFLRCINRLEEPT----SGRILLDGVEITGDNVDINKVRQRIGMVFqqfnlfphlnaI 98
                                      334444379******************9988877....45555555555555555555555555555333333333330 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                            AAA_15 287 k.........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkeland 354
                                       k         d +  + ++ + G+q+ + ++  ++++         + i l++E    L p++ k++ + +k la d
  gi|488600575|ref|YP_007907046.1| 121 KrllekvglkDFMHKYPAQLSGGQQQRVAIARALAMN---------PEIMLFDEVTSALDPELVKEVLDVMKQLATD 188
                                       4555555555555555566666666666665444443.........36799999999999***************99 PP

                            AAA_15 355 nktQviitTH 364
                                       +    i+ TH
  gi|488600575|ref|YP_007907046.1| 189 GM-TMIVVTH 197
                                       97.8999999 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 ?    6.5   0.0     0.021        10       1      21 [.      33      53 ..      33      99 .. 0.67
   2 !   11.4   0.1   0.00064      0.32      22     112 ..     120     199 ..     107     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.021
                                      EEEESSTTSSHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavake 21
                                      v+++Gp G GK+++ + + + 
  gi|488600575|ref|YP_007907046.1| 33 VVIIGPSGSGKSTFLRCINRL 53
                                      5789**********9988554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00064
                                       HTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTT CS
                               AAA  22 lgvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvk 97 
                                       +++ + ++ +++++ ky  + +   ++ ++ a++ a +p i+++DE+ +    +          +v++ l +++++ 
  gi|488600575|ref|YP_007907046.1| 120 AKRLLEKVGLKDFMHKYPAQLSGGQQQRVAIARALAmNPEIMLFDEVTSALDPE----------LVKEVLDVMKQLA 186
                                       55555667778888999999999999999999999999***********99888..........8999999999998 PP

                                       TSSSTEEEEEEESSG CS
                               AAA  98 kkeskvivigatnrp 112
                                       ++   +++i++t+++
  gi|488600575|ref|YP_007907046.1| 187 TD--GMTMIVVTHEM 199
                                       85..47888888765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.7e-06    0.0018      86     121 ..      16      52 ..       4      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-06
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       ++e l+ +  ++k+ +++v++G+SG GKSt++  ++ 
  gi|488600575|ref|YP_007907046.1|  16 DHEVLKGIDLQVKKgEVVVIIGPSGSGKSTFLRCINR 52 
                                       556667777777776****************987765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00042      0.21      31      50 ..      28      47 ..      19      50 .. 0.90
   2 ?    5.2   0.1     0.029        14      79     147 ..     110     194 ..     102     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                            AAA_25 31 pagelallaGapgtGKttla 50
                                       +ge+++++G++g+GK+t++
  gi|488600575|ref|YP_007907046.1| 28 KKGEVVVIIGPSGSGKSTFL 47
                                      68****************97 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                            AAA_25  79 aEdsedelrrRlravgeal...............rddarllvldlagv.eslpLfakdrggtlltadvdaleaaiee 139
                                        Ed+  e+++R+++++e++                +++r+++  +  +  +++Lf++   ++l ++ v+++ +++++
  gi|488600575|ref|YP_007907046.1| 110 KEDKK-EVEKRAKRLLEKVglkdfmhkypaqlsgGQQQRVAIARALAMnPEIMLFDE-VTSALDPELVKEVLDVMKQ 184
                                       57777.9************99999999999999988899999998888888888753.3344446667777777776 PP

                            AAA_25 140 veg..vrlvv 147
                                        +     ++v
  gi|488600575|ref|YP_007907046.1| 185 LATdgMTMIV 194
                                       5443366665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.6e-06    0.0043     116     189 ..      17      87 ..       4      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.6e-06
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfa 189
                                       +++ + +   v++  ++++ G+ gsGK+t+l  +    + ++ ri++  D vEi  ++++  +++++  ++ f+
  gi|488600575|ref|YP_007907046.1|  17 HEVLKGIDLQVKKGEVVVIIGPSGSGKSTFLRCINRLEEPTSGRILL--DGVEITGDNVDINKVRQR-IGMVFQ 87 
                                       5667778888999999***************9776666666788887..999999999888888888.666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.1e-05     0.016      17      48 ..      29      60 ..      23      73 .. 0.83
   2 ?   -0.7   0.1         2   9.9e+02      81     121 ..     141     194 ..     115     199 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggr 48
                                      +  v+v+ Gp G+GK+t l+ ++++ e   gr
  gi|488600575|ref|YP_007907046.1| 29 KGEVVVIIGPSGSGKSTFLRCINRLEEPTSGR 60
                                      3459*****************99988766544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                            AAA_30  81 k.........grarlepg.tllivDEagmv.dtkqlaall...kaaekagakvil 121
                                                 +r +l+ + ++++ DE+  + d + ++++l   k+++++g+++i+
  gi|488600575|ref|YP_007907046.1| 141 SggqqqrvaiAR-ALAMNpEIMLFDEVTSAlDPELVKEVLdvmKQLATDGMTMIV 194
                                       244444454432.233333777777765554444444444000444444566555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-05    0.0063      23     120 ..      31     152 ..      14     204 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                                       EEEEEEEESTTSSHHHHHHHHHHHCS--...............--HHHHHCCHH.....HHHHHHHHHHHHHHHHHH CS
                           G-alpha  23 evkllllGqseSGKsTilkqlkllykkg...............fseeelatwra.....viqlnivrsiktileale 79 
                                       ev ++++G s+SGKsT+l+ + +l++++               +   ++++ r+     + q+n+  +++ i + + 
  gi|488600575|ref|YP_007907046.1|  31 EV-VVIIGPSGSGKSTFLRCINRLEEPTsgrilldgveitgdnV---DINKVRQrigmvFQQFNLFPHLNAIENVML 103
                                       44.889*******************9998887665555543332...222222222222334555555555555555 PP

                                       HT.T.......HHHC-SS-SCCC...S-HCHHHH..............H CS
                           G-alpha  80 sl.eselsesfelqelkerldpl...kkveasliaklssateee....q 120
                                        + +++ +++ e +++ +rl +    k++ ++  a+ls++++++    +
  gi|488600575|ref|YP_007907046.1| 104 APvKIKKEDKKEVEKRAKRLLEKvglKDFMHKYPAQLSGGQQQRvaiaR 152
                                       5322222111222222222222122244444444444444444455553 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.2e-05     0.006       1      18 [.      32      49 ..      32     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                            AAA_33  1 lvllvGlpGsGKstlaer 18
                                      +v+++G++GsGKst+++ 
  gi|488600575|ref|YP_007907046.1| 32 VVVIIGPSGSGKSTFLRC 49
                                      89*************985 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.1e-05     0.025      33      70 ..      18      55 ..      11     171 .. 0.71
   2 ?    0.9   0.0      0.77   3.8e+02      77     171 ..     103     195 ..      93     204 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-05
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                      e lk   L+ +k ++++i GPsG gkst ++ + +   
  gi|488600575|ref|YP_007907046.1| 18 EVLKGIDLQVKKGEVVVIIGPSGSGKSTFLRCINRLEE 55
                                      56777778889899****************99887544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.77
                             Rad17  77 lnpvslkepdnqksdfkgltekesr.flsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrds.da 151
                                       l pv++k+ d ++ + +++   e+  +   +  ++   L + + +++      l  + +++l +++ +    ++ + 
  gi|488600575|ref|YP_007907046.1| 103 LAPVKIKKEDKKEVEKRAKRLLEKVgLKDFMHKYPAQ-LSGGQQQRVA-IARALAMNPEIMLFDEVTSALDPELvKE 177
                                       4677777777777776665444432146778888876.7888777777.7788888999999999999988888777 PP

                             Rad17 152 lrevirkylrssealplilv 171
                                       + +v+++  + + +  +i+v
  gi|488600575|ref|YP_007907046.1| 178 VLDVMKQLATDGMT--MIVV 195
                                       88888776665554..4444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.058        29      36      61 ..      31      56 ..      19      68 .. 0.83
   2 !    8.7   0.1     0.002         1      85     158 ..     122     194 ..     113     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.058
                              TniB 36 pnlllvGdsnnGKtmivekFarlhpp 61
                                      + ++++G+s  GK++ ++   rl++p
  gi|488600575|ref|YP_007907046.1| 31 EVVVIIGPSGSGKSTFLRCINRLEEP 56
                                      5689***********99877777665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                              TniB  85 rlyaai.LealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipiv 158
                                       rl +++ L+ ++ ++ a+ +  ++++ +++   +++++++++DE+ ++l    +  +e+l ++k+L  +    iv
  gi|488600575|ref|YP_007907046.1| 122 RLLEKVgLKDFMHKYPAQLSGGQQQRVAIARALAMNPEIMLFDEVTSAL--DPELVKEVLDVMKQLATDGMTMIV 194
                                       5555544778888888888888888888888999***************..7788899******99877655555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.3e-05     0.036       4      22 ..      32      50 ..      29      67 .. 0.86
   2 ?   -2.7   0.0       8.4   4.2e+03     111     131 ..     178     198 ..     167     213 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                       ++i+Gpsg+GK+t+++ +
  gi|488600575|ref|YP_007907046.1| 32 VVVIIGPSGSGKSTFLRCI 50
                                      79*************9877 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.4
                            AAA_24 111 frrllkklqelrknvifiahe 131
                                       + +++k+l   + + i++ he
  gi|488600575|ref|YP_007907046.1| 178 VLDVMKQLATDGMTMIVVTHE 198
                                       333333333333333333333 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00086      0.43       2      59 ..      31      89 ..      30     114 .. 0.75
   2 ?    2.5   0.0      0.23   1.2e+02      91     120 ..     176     205 ..     144     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00086
                                TK  2 sielilgpmfaGKsteLlrrvkryqlaekkvvv...ikaakdnRysegkvvthdgisleak 59
                                      ++ +i+gp  +GKst+L r+++r+++ +   ++   +  + dn + + kv  ++g+ +++ 
  gi|488600575|ref|YP_007907046.1| 31 EVVVIIGPSGSGKSTFL-RCINRLEEPTSGRILldgVEITGDNVDIN-KVRQRIGMVFQQF 89
                                      6789**********985.9*****99887777612234455666664.7999998887766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                                TK  91 qdivelseklanegkivivagLdtdFerkl 120
                                       +++++++++la+ g+++iv   ++ F+r++
  gi|488600575|ref|YP_007907046.1| 176 KEVLDVMKQLATDGMTMIVVTHEMGFAREV 205
                                       4788999999****************9986 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   0.4   0.00063      0.31      32      89 ..     139     183 ..     115     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00063
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +lSGG++q    +a+a a    +        +++++++DE  s lD+e ++++l++++
  gi|488600575|ref|YP_007907046.1| 139 QLSGGQQQR---VAIARA----LAM------NPEIMLFDEVTSALDPELVKEVLDVMK 183
                                       566666632...222222....222......4889*******************9997 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 ?    8.6   0.0    0.0034       1.7       2      20 ..      33      51 ..      32      61 .. 0.87
   2 ?    3.9   0.0     0.099        49      64      89 ..     152     182 ..     118     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0034
                                      EEEE--SSSSHHHHHHHGG CS
                             AAA_5  2 vlLvGppGtgKselaerla 20
                                      v+++Gp+G+gKs++ + + 
  gi|488600575|ref|YP_007907046.1| 33 VVIIGPSGSGKSTFLRCIN 51
                                      789**********998765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.099
                                       -....G-SEEEEESGGG--.HHHHHHHHHHH CS
                             AAA_5  64 r....egeilvlDEverae.sevlnsLlsll 89 
                                       r    ++ei+++DEv+ a  +e ++++l ++
  gi|488600575|ref|YP_007907046.1| 152 RalamNPEIMLFDEVTSALdPELVKEVLDVM 182
                                       2334699*********998888888887665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.053       2      20 ..      32      50 ..      31      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      +v++ G++GsGK+t+l+ +
  gi|488600575|ref|YP_007907046.1| 32 VVVIIGPSGSGKSTFLRCI 50
                                      89**************977 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.003       1.5       2      22 ..      30      50 ..      29      80 .. 0.85
   2 ?    3.5   0.0      0.14        67      63      97 ..     156     195 ..      89     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.003
                            AAA_14  2 rkilvitGaRrvGKTtllkql 22
                                      ++++vi G+  +GK+t+l+ +
  gi|488600575|ref|YP_007907046.1| 30 GEVVVIIGPSGSGKSTFLRCI 50
                                      579**************8654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                            AAA_14  63 ekktylflDEiqev......pewekalkslvdegknldviv 97 
                                        + +++++DE+  +      +e+ +++k+l  +g    ++v
  gi|488600575|ref|YP_007907046.1| 156 MNPEIMLFDEVTSAldpelvKEVLDVMKQLATDG-MTMIVV 195
                                       357899*****99988888888888888888888.445555 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   0.00025      0.13      17      49 ..      21      53 ..       6      54 .. 0.83
   2 ?   -1.5   0.0       3.2   1.6e+03      72     115 ..     138     183 ..     128     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                            AAA_27 17 rsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      + +d++ ++ ++ +i+Gp  +GKst lr i++l
  gi|488600575|ref|YP_007907046.1| 21 KGIDLQVKKGEVVVIIGPSGSGKSTFLRCINRL 53
                                      4589999999******************99876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                            AAA_27  72 avleeadgeelefaRrkgrkkt..lldaddqalpeevlaallggld 115
                                       a l+  +++++++aR  + + +  l+d+  +al++e+++++l+ ++
  gi|488600575|ref|YP_007907046.1| 138 AQLSGGQQQRVAIARALAMNPEimLFDEVTSALDPELVKEVLDVMK 183
                                       5666777788888888766654116677777899999998887765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00017     0.084       1      25 [.      33      72 ..      33     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00017
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf...............g 25
                                      +++ G++G+GK+t+ + ++++++                 
  gi|488600575|ref|YP_007907046.1| 33 VVIIGPSGSGKSTFLRCINRLEEPtsgrilldgveitgdN 72
                                      789*************998886323555555554555443 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00035      0.17      63     107 ..       6      50 ..       1      63 [. 0.74
   2 ?   -1.2   0.0       1.4   6.8e+02     233     255 ..     187     209 ..     177     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                        Adeno_IVa2  63 diekldakllrddGelsslnyg.lqPviGviyGPtGsGksqllrnl 107
                                       +iekl +k+  +   l  ++++ ++  + vi GP GsGks +lr +
  gi|488600575|ref|YP_007907046.1|   6 EIEKLTKKFGDH-EVLKGIDLQvKKGEVVVIIGPSGSGKSTFLRCI 50 
                                       667777777766.567777777234567899************975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                        Adeno_IVa2 233 ctgfsvlvvlhnlnPrsdiagni 255
                                         g +++vv h++   +++++ +
  gi|488600575|ref|YP_007907046.1| 187 TDGMTMIVVTHEMGFAREVGDRV 209
                                       56899********9998887765 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.14        71       1      14 [.      33      46 ..      33      57 .. 0.86
   2 ?    7.7   0.1    0.0047       2.3      74     128 ..     147     201 ..     133     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                              CobU  1 ilvtGgarSGKSef 14
                                      ++++G++ SGKS+f
  gi|488600575|ref|YP_007907046.1| 33 VVIIGPSGSGKSTF 46
                                      579*********98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                              CobU  74 evvLvDcltlwltnllleeeaekveekleeeveellealkelkatvvlVsnEvgl 128
                                       +v++  +l++  + +l++e +++ + +l +ev +++++l++  +t+++V+ E+g+
  gi|488600575|ref|YP_007907046.1| 147 RVAIARALAMNPEIMLFDEVTSALDPELVKEVLDVMKQLATDGMTMIVVTHEMGF 201
                                       556666666666677787777778899999**********************996 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00025      0.13      35      57 ..      27      48 ..      10      50 .. 0.82
   2 ?   -1.4   0.0       2.4   1.2e+03     111     118 ..     173     180 ..     111     213 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                                      GGGS-.SEEEE--TTSSHHHHHH CS
                      FtsK_SpoIIIE 35 lkkmashllvaGatgsGKStaln 57
                                       kk +  ++++G +gsGKSt+l+
  gi|488600575|ref|YP_007907046.1| 27 VKKGE-VVVIIGPSGSGKSTFLR 48
                                      44555.789*************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                                       HHHHHHHH CS
                      FtsK_SpoIIIE 111 eLvkemee 118
                                       eLvke+ +
  gi|488600575|ref|YP_007907046.1| 173 ELVKEVLD 180
                                       23333333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0012      0.61      12      52 ..      20      60 ..      10      94 .. 0.78
   2 ?    1.4   0.0      0.35   1.7e+02      89     134 ..     139     190 ..      90     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                      Mg_chelatase 12 kraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplsee 52
                                       + +++ +  g  ++++Gp+GsGK+   ++++ l  p s +
  gi|488600575|ref|YP_007907046.1| 20 LKGIDLQVKKGEVVVIIGPSGSGKSTFLRCINRLEEPTSGR 60
                                      555666666667799**************999987766655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.35
                      Mg_chelatase  89 alvGggskpkpGeislahn.GvLfLDEl.....pefkrkvlevLRePledge 134
                                        l Gg+++    + +la n  ++++DE+     pe+ ++vl+v+++   dg 
  gi|488600575|ref|YP_007907046.1| 139 QLSGGQQQRVAIARALAMNpEIMLFDEVtsaldPELVKEVLDVMKQLATDGM 190
                                       4556666555555566665347778887555556888888888887655555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00031      0.15       9      38 ..      29      58 ..      23     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00031
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelg 38
                                      k +v++++++ G+GK++ l++i +l + + 
  gi|488600575|ref|YP_007907046.1| 29 KGEVVVIIGPSGSGKSTFLRCINRLEEPTS 58
                                      67899***************9987765555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00087      0.43      21      44 ..      31      54 ..      18     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00087
                                      EEEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnks 44
                                       vv + G  G+GK+t ++ i++  
  gi|488600575|ref|YP_007907046.1| 31 EVVVIIGPSGSGKSTFLRCINRLE 54
                                      4899*************9998864 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 ?   10.0   0.0     0.001      0.51      44      63 ..      27      46 ..      16      54 .. 0.85
   2 ?   -1.2   0.0       2.9   1.5e+03     102     143 ..     151     191 ..     131     207 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                         IstB_IS21 44 iekkenivllGpsGvGKshl 63
                                      ++k e +v++GpsG GKs +
  gi|488600575|ref|YP_007907046.1| 27 VKKGEVVVIIGPSGSGKSTF 46
                                      78899************965 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                         IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekryerrsi 143
                                       a +  +++++++ D++    ld +  +++++v+++      +
  gi|488600575|ref|YP_007907046.1| 151 ARALAMNPEIMLFDEVT-SALDPELVKEVLDVMKQLATDGMT 191
                                       33344556788888874.568888888888888776544333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     0.001       0.5       2      21 ..      33      52 ..      32      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      +vi+G++++GK+t l+ +++
  gi|488600575|ref|YP_007907046.1| 33 VVIIGPSGSGKSTFLRCINR 52
                                      8************9976654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.012       5.8      20      99 ..      34     121 ..      25     147 .. 0.60
   2 ?    3.1   0.0     0.059        30     526     579 ..     157     207 ..     144     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                            AAA_13  20 liYGwNGaGKTtLSrllrslelgetepkfangsieitnge.......eldirVfNrdFveenls..eqgelkpvftL 87 
                                       +i G  G+GK+t+ r ++ le+   + +     +eit ++       +   +Vf +     +l+  e+  l+pv + 
  gi|488600575|ref|YP_007907046.1|  34 VIIGPSGSGKSTFLRCINRLEEPT-SGRILLDGVEITGDNvdinkvrQRIGMVFQQFNLFPHLNaiENVMLAPVKIK 109
                                       788999*************97533.3333333334444422223232444466633223335554444556666655 PP

                            AAA_13  88 Geesiekqekie 99 
                                        e+++e +++ +
  gi|488600575|ref|YP_007907046.1| 110 KEDKKEVEKRAK 121
                                       555555555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.059
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                                       + +i  +D   S LD + +  v   +k+ +   ++   +++ TH + f +ev +
  gi|488600575|ref|YP_007907046.1| 157 NPEIMLFDEVTSALDPELVKEVLDVMKQLA---TDGMTMIVVTHEMGFAREVGD 207
                                       56788888889999*9*************9...99999************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      852  (0.0475208); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); 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):              36  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 1422.39
//
Query:       gi|488600576|ref|YP_007907047.1|  [L=110]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       291  (0.0162307); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 735.85
//
Query:       gi|488600577|ref|YP_007907048.1|  [L=263]
Description: CoA-substrate-specific enzyme activase, putative [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-67  228.2   5.8    1.4e-67  228.1   5.8    1.0  1  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
    0.00059   19.6   0.0       0.12   12.1   0.0    2.1  2  Peptidase_M22   Glycoprotease family
     0.0014   17.8   0.4       0.11   11.5   0.0    2.4  3  PilM_2          Type IV pilus assembly protein PilM;
      0.002   17.8   0.2        1.6    8.2   0.1    2.3  2  FGGY_N          FGGY family of carbohydrate kinases, N-termin
     0.0023   17.8   0.0      0.023   14.6   0.0    2.2  2  DEDD_Tnp_IS110  Transposase
     0.0041   16.6   2.2        1.4    8.3   0.0    3.0  3  ROK             ROK family
     0.0086   14.8   0.1      0.018   13.7   0.1    1.5  1  Acetate_kinase  Acetokinase family
  ------ inclusion threshold ------
      0.015   14.0   0.9        0.3    9.7   0.0    2.2  2  MutL            MutL protein
      0.019   13.8   0.3      0.019   13.8   0.3    2.2  3  MreB_Mbl        MreB/Mbl protein
      0.056   13.2   3.6       0.26   11.0   0.0    2.5  3  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
       0.74   10.3   5.1        4.7    7.7   0.1    2.7  2  FtsA            Cell division protein FtsA


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 !  228.1   5.8   8.3e-71   1.4e-67       2     265 ..       5     253 ..       4     255 .. 0.96

  Alignments for each domain:
  == domain 1  score: 228.1 bits;  conditional E-value: 8.3e-71
                                       EEEE-SSEEEEEEEETTTE.EEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCT CS
                       BcrAD_BadFG   2 GiDgGsTttkavlmdekge.vlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratl 77 
                                       GiD+Gs +tk++++de++  ++ r +++s+++++ +          al+e l+++g+ + d++ +  v+tgyGr+ +
  gi|488600577|ref|YP_007907048.1|   5 GIDIGSLATKVCIVDERKRiLAYRIKKTSSKIMESGL--------SALEECLSETGLRKGDLDVV--VATGYGRNLA 71 
                                       9******************56678889999***9996........7*****************65..********** PP

                                       CTTBSEEE-..HHHHHHHHHHHH-TT--EEEEEETTEEEEEEEE.TTEEEEEEEESS--TTSHHHHHHHHHHHT--T CS
                       BcrAD_BadFG  78 pekfekeiirseilvhgdGavalypgtrtvldigGqdskgiqid.kgkvenfqmndrcaageGrylgiiadelnmgl 153
                                        + f++  i+ ei++h++Ga  l+ + rtv+digGqdsk+i id +g v+nf+mnd+caag+Gr+l+++a++l++ +
  gi|488600577|ref|YP_007907048.1|  72 VSSFADFKIT-EITCHARGAKELFLDCRTVIDIGGQDSKAISIDeNGMVVNFTMNDKCAAGTGRFLEVMANVLGLDI 147
                                       *****99998.****************************************************************** PP

                                       TTHHHHHTT--S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-H CS
                       BcrAD_BadFG 154 reldglaekatkkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvakne 230
                                       +e+++l+ ++ ++  i+stc+vfae+e+++ ls+ge  +dIlag+ raia+rv++l++ +g v+d v++tGGvakn+
  gi|488600577|ref|YP_007907048.1| 148 NEMGELSLRSEREVNITSTCTVFAESEVISLLSQGENEIDILAGINRAIAKRVASLARHVGVVDD-VVMTGGVAKNA 223
                                       ***************************************************************66.*********** PP

                                       HHHHHH.....HHHH-S-EE--GGGGGHHHHHHHH CS
                       BcrAD_BadFG 231 aavkelrklvkenygevkininpdsiytgalGAal 265
                                       ++vk+l     e+ +  ki i+ ++++ ga GA +
  gi|488600577|ref|YP_007907048.1| 224 GVVKAL-----EEELSHKIHIPDEPQIIGAYGAGV 253
                                       ******.....777778999*************66 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0071        12      34      57 ..      41      64 ..      30      66 .. 0.85
   2 !   12.1   0.0   7.3e-05      0.12     144     258 ..     139     241 ..     116     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0071
                                      HHHHHHHHHHHTSTGGGEEEEEEE CS
                     Peptidase_M22 34 lplieealaeaglsledldaIavt 57
                                      l+++ee+l+e gl++ dld++++t
  gi|488600577|ref|YP_007907048.1| 41 LSALEECLSETGLRKGDLDVVVAT 64
                                      6899*****************998 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.3e-05
                                       HHHHHT..SSCCHHHHHHHCTCS.......EETTEEE.CHHHHHHHHHHST.T.HHHHHHHHHHHHHHHHHHHHHHH CS
                     Peptidase_M22 144 varllglpypggpkieklakegkkiefprplkgldfsfsGlktavlkelek.e.vedlaasfqeavvdhlvektera 218
                                       +a++lgl+++++ +++ l +e ++++++++ +    +f+  +++v+++l++ e   d+ a +++a+++ +++ + ++
  gi|488600577|ref|YP_007907048.1| 139 MANVLGLDINEMGELS-LRSE-REVNITSTCT----VFA--ESEVISLLSQgEnEIDILAGINRAIAKRVASLARHV 207
                                       5667777777666666.2222.2344333322....222..345555553332355999999999777777777766 PP

                                       HHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXX CS
                     Peptidase_M22 219 lklpkakelvilGGvaankrLrealeeeaeelglkliiPp 258
                                            ++++v+ GGva+n+++ +aleee ++   k++iP+
  gi|488600577|ref|YP_007907048.1| 208 ---GVVDDVVMTGGVAKNAGVVKALEEELSH---KIHIPD 241
                                       ...8899****************99865554...567776 PP

>> PilM_2  Type IV pilus assembly protein PilM;
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.014        23       1      35 [.       5      41 ..       5      50 .. 0.84
   2 ?   -2.3   0.0       1.1   1.8e+03     180     199 ..      96     115 ..      72     150 .. 0.72
   3 !   11.5   0.0   6.8e-05      0.11     258     304 ..     191     239 ..     184     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.014
                            PilM_2  1 GiDissssvklvelskkk..gslrvealaieplekda 35
                                      GiDi+s + k+  ++++k    +r+++  ++ +e++ 
  gi|488600577|ref|YP_007907048.1|  5 GIDIGSLATKVCIVDERKriLAYRIKKTSSKIMESGL 41
                                      9******999999998664578999999999998875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                            PilM_2 180 kvvaivdigasrttlsvlrd 199
                                        +  ++dig + ++   +++
  gi|488600577|ref|YP_007907048.1|  96 DCRTVIDIGGQDSKAISIDE 115
                                       47777888777665544443 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 6.8e-05
                            PilM_2 258 eisralqffltssqqn..kvdkilLaGGtaslpgleelleeelgisttv 304
                                        i+ra+   ++s  ++   vd ++++GG a+  g+ ++leeel+ ++++
  gi|488600577|ref|YP_007907048.1| 191 GINRAIAKRVASLARHvgVVDDVVMTGGVAKNAGVVKALEEELSHKIHI 239
                                       57788877777765554489***********************998877 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0018         3       2      35 ..       3      36 ..       2      49 .. 0.84
   2 !    8.2   0.1     0.001       1.6       4      26 ..     100     122 ..      98     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                                      EEEEEEESSEEEEEEEETTS-EEEEEEEE--EB- CS
                            FGGY_N  2 ilglDcGttstkaivldekgkvvasaqaelelss 35
                                        g+D+G   tk+ ++de ++++a   ++  +++
  gi|488600577|ref|YP_007907048.1|  3 SAGIDIGSLATKVCIVDERKRILAYRIKKTSSKI 36
                                      579********************98877776665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                                       EEEEESSEEEEEEEETTS-EEEE CS
                            FGGY_N   4 glDcGttstkaivldekgkvvas 26 
                                       ++D+G++ +kai +de+g vv+ 
  gi|488600577|ref|YP_007907048.1| 100 VIDIGGQDSKAISIDENGMVVNF 122
                                       79*****************9975 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.4e-05     0.023       1      53 [.       4      63 ..       4      88 .. 0.62
   2 ?    0.8   0.0      0.24   3.9e+02       3      40 ..     101     141 ..     100     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                    DEDD_Tnp_IS110  1 vGiDvakdkhdacvidaegkvllservpnd.....ee...glealleklaakagevlvvve 53
                                      +GiD+++   ++c++d e k++l  r++++     e+   +le++l++ + ++g+  vvv 
  gi|488600577|ref|YP_007907048.1|  4 AGIDIGSLATKVCIVD-ERKRILAYRIKKTsskimESglsALEECLSETGLRKGDLDVVVA 63
                                      6**************9.55555555666652223334111455555555555666666654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.24
                    DEDD_Tnp_IS110   3 iDvakdkhdacvidaegkvl...lservpndeegleallek 40 
                                       iD++ ++++a  id++g v+   ++ +++    ++ +++++
  gi|488600577|ref|YP_007907048.1| 101 IDIGGQDSKAISIDENGMVVnftMNDKCAAGTGRFLEVMAN 141
                                       9****************998543334666666666666655 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00089       1.4       2      48 ..       4      49 ..       3      66 .. 0.83
   2 ?    0.9   0.0      0.16   2.6e+02       4      23 ..     101     120 ..      98     130 .. 0.89
   3 !    5.6   0.2     0.006       9.8     199     260 ..     174     235 ..     160     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00089
                                      EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHC CS
                               ROK  2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvd 48
                                      +gidiG   +++++vde   ila +  +t+ + +e +l +a++e ++
  gi|488600577|ref|YP_007907048.1|  4 AGIDIGSLATKVCIVDERKRILAYRIKKTSSKIMESGL-SALEECLS 49
                                      69********************9998889999999999.66666554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                                       EEE-SSEEEEEEEETTS-EE CS
                               ROK   4 idiGgtkialalvdeegeil 23 
                                       idiGg++ +++ +de+g ++
  gi|488600577|ref|YP_007907048.1| 101 IDIGGQDSKAISIDENGMVV 120
                                       9***************9876 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.006
                                       HHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH-.-SEEEEEHCCCTSTTHHHHHHHHHHH CS
                               ROK 199 eiiklaekgdevaeevverlaeylakaiadlinlfd.pqaivlgGgvseadklleairklvkk 260
                                       e+i l  +g++   +++  + +++ak +a l+  +   + +v+ Ggv +  ++++a+++++++
  gi|488600577|ref|YP_007907048.1| 174 EVISLLSQGEN-EIDILAGINRAIAKRVASLARHVGvVDDVVMTGGVAKNAGVVKALEEELSH 235
                                       56666666443.457788899999999999998775279***************999998875 PP

>> Acetate_kinase  Acetokinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   1.1e-05     0.018     307     341 ..     192     229 ..     182     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                    Acetate_kinase 307 lakyigeyaavle...gkvDaivFTgGigenaalvrel 341
                                       ++++i++ +a+l    g vD +v TgG+++na  v++l
  gi|488600577|ref|YP_007907048.1| 192 INRAIAKRVASLArhvGVVDDVVMTGGVAKNAGVVKAL 229
                                       5667777777776333679*************999876 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00018       0.3       4      59 ..       6      65 ..       5      81 .. 0.64
   2 ?    2.7   0.2     0.023        37     327     368 ..     173     216 ..      89     229 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00018
                              MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgkt..........e 59
                                      iDiGS  Tkv +vd++k   r+l+   + T+ +   ++e   +alee  +++g            +
  gi|488600577|ref|YP_007907048.1|  6 IDIGSLATKVCIVDERK---RILAYRIKKTSSK---IMESGLSALEECLSETGLRkgdldvvvatG 65
                                      8**************76...8888887778775...554444444444444332244445555555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.023
                              MutL 327 merpktiPkteeela....ldealareavelaverHagtleelytp 368
                                       +e ++++ + e+e+     +++a+a+  ++la  rH+g +++++ +
  gi|488600577|ref|YP_007907048.1| 173 SEVISLLSQGENEIDilagINRAIAKRVASLA--RHVGVVDDVVMT 216
                                       33445555555555511114566677777777..999999888764 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   2.1e+03     150     167 ..       6      23 ..       5      47 .. 0.63
   2 ?   -0.8   0.1      0.31   5.1e+02     148     170 ..      99     121 ..      95     126 .. 0.81
   3 ?   13.8   0.3   1.2e-05     0.019     253     317 ..     188     253 ..     159     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                       EEE-SS-EEEEEEETTEE CS
                          MreB_Mbl 150 vdiGggttevavislggi 167
                                       +diG+ +t+v ++     
  gi|488600577|ref|YP_007907048.1|   6 IDIGSLATKVCIVDERKR 23 
                                       567777777766654444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.31
                                       EEEEE-SS-EEEEEEETTEEEEE CS
                          MreB_Mbl 148 mvvdiGggttevavislggivts 170
                                        v+diGg  ++   i  +g+v+ 
  gi|488600577|ref|YP_007907048.1|  99 TVIDIGGQDSKAISIDENGMVVN 121
                                       69*****9999888888888875 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHTS-HHHHHHH.HHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHH CS
                          MreB_Mbl 253 iveavkevLektppeLaadi.vdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtgk 317
                                       i+  +++++ k  + La  + v   +v+tGG a+  g+ k l+ee++ ++++ ++p    a G+g 
  gi|488600577|ref|YP_007907048.1| 188 ILAGINRAIAKRVASLARHVgVVDDVVMTGGVAKNAGVVKALEEELSHKIHIPDEPQIIGAYGAGV 253
                                       67778888888888888876556689*******************************999999986 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 ?   11.0   0.0   0.00016      0.26       3      61 ..       5      62 ..       3      68 .. 0.92
   2 ?   -2.3   0.1       1.9   3.1e+03       3      22 ..     100     118 ..      98     152 .. 0.71
   3 ?    2.9   0.1     0.049        80      25      70 ..     175     223 ..     159     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                        Hydant_A_N  3 gIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvr 61
                                      gID+G+  T ++++de  +++ ++++  t+ +++e  ++alee l+e++ r++++dvv+
  gi|488600577|ref|YP_007907048.1|  5 GIDIGSLATKVCIVDER-KRILAYRIKKTSSKIMESGLSALEECLSETGLRKGDLDVVV 62
                                      9**************99.8899999999999999999***************9999987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                        Hydant_A_N   3 gIDvGGTfTDavaldekeee 22 
                                        ID+GG    a+ +de+ + 
  gi|488600577|ref|YP_007907048.1| 100 VIDIGGQDSKAISIDEN-GM 118
                                       68999987777777766.43 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.049
                        Hydant_A_N  25 vlKllst...pdavaegirealeevleesiprtskidvvrmGTTvatNa 70 
                                       v+ lls+   + ++  gi +a+++   +   + + +d v+m + va Na
  gi|488600577|ref|YP_007907048.1| 175 VISLLSQgenEIDILAGINRAIAKRVASLARHVGVVDDVVMTGGVAKNA 223
                                       5556666666778999**9999999888888899*******99999998 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0029       4.7       1      38 [.       4      42 ..       4      64 .. 0.82
   2 ?    3.2   1.8     0.074   1.2e+02       2      86 ..     100     233 ..      99     250 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0029
                                      EEEEE-SSSEEEEEEETTE.EEEEEEES--HHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedga.lvhlrvigvggngitkdia 38
                                      a++DiG+  t+v ++++ + + ++r+ ++ ++ + ++++
  gi|488600577|ref|YP_007907048.1|  4 AGIDIGSLATKVCIVDERKrILAYRIKKTSSKIMESGLS 42
                                      79*********9999987646668888889999988855 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.074
                                       EEEE-SSSEEEEEEETTEEEE....EEEES--HHHHHHHHHHHHT--HHHHHHHHHHH--S--EEEEEHHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                              FtsA   2 lvDiGagktdvavaedgalvh....lrvigvggngitkdiakalrtaveeAerikikyGsalaekeigrkels.... 70 
                                       ++DiG++ ++++ ++++++v      +    g   + +  a++l+  ++e  +++ +          +++e++    
  gi|488600577|ref|YP_007907048.1| 100 VIDIGGQDSKAISIDENGMVVnftmNDKCAAGTGRFLEVMANVLGLDINEMGELSLR----------SEREVNitst 166
                                       799999999888887766554332222222244444444777777777777777733..........2223333344 PP

                                       ...................................................GGGGSTTHHHHHHHHH CS
                                       ...................................................xxxxxxxxxxxxxxxx RF
                              FtsA  71 ...................................................ggsalpnleelaeral 86 
                                                                                          g+++ +++++++e+ l
  gi|488600577|ref|YP_007907048.1| 167 ctvfaesevisllsqgeneidilaginraiakrvaslarhvgvvddvvmtgGVAKNAGVVKALEEEL 233
                                       4444555555555555555555566666666666666666666677777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        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: 00:00:00.51
# Mc/sec: 1553.91
//
Query:       gi|488600578|ref|YP_007907049.1|  [L=69]
Description: hypothetical protein Asulf_01055 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.0   4.1       0.07   13.6   4.1    1.3  1  DUF2061   Predicted membrane protein (DUF2061)


Domain annotation for each model (and alignments):
>> DUF2061  Predicted membrane protein (DUF2061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.1   3.9e-06      0.07       6      34 ..      23      51 ..      18      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-06
                           DUF2061  6 swrvihtvvtflvaylltgslalAgaial 34
                                      ++ ++ ++ tf+vay ++ s+++++ i  
  gi|488600578|ref|YP_007907049.1| 23 TYTLMSFFATFIVAYYISHSYVASFIISS 51
                                      89******************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 503.13
//
Query:       gi|488600579|ref|YP_007907050.1|  [L=177]
Description: Amidases related to nicotinamidase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-44  151.4   0.0    3.2e-44  151.2   0.0    1.0  1  Isochorismatase  Isochorismatase family


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 !  151.2   0.0   1.8e-48   3.2e-44       2     167 ..       3     165 ..       2     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 1.8e-48
                   Isochorismatase   2 alvviDmqndfv..eegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttga 76 
                                       a++v+Dmq+df+  +++  +   i+++ e  + +l++ar  ++ +ift+d h+    k d + r +++h++ +t ga
  gi|488600579|ref|YP_007907050.1|   3 AVIVVDMQKDFCypDGALYAGDHIKEIFEPLASFLEKAR-GSMSIIFTQDWHR----KDDKEFRIWPAHCIMNTAGA 74 
                                       99***********99999999*****************9.8899*********....99999*************** PP

                   Isochorismatase  77 elvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalsp 153
                                       e+++el+p   d++v K+r+saf+gtdld iL+elg ++i+laG+ t++CV++ta da+ +Gy+v +++D++ al+ 
  gi|488600579|ref|YP_007907050.1|  75 EIIDELNPSDEDYFVKKRRYSAFFGTDLDLILRELGCNEIILAGVLTNICVLHTAGDAVSRGYDVKLLKDCTVALTD 151
                                       ***************************************************************************** PP

                   Isochorismatase 154 elhdaalkrlkqaf 167
                                        ++++a+k++++  
  gi|488600579|ref|YP_007907050.1| 152 YDYEYAIKHMRDVL 165
                                       **********9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1247.54
//
Query:       gi|488600580|ref|YP_007907051.1|  [L=249]
Description: dinuclear metal center protein, YbgI/SA1388 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-54  185.8   0.2    1.2e-54  185.5   0.2    1.0  1  NIF3      NIF3 (NGG1p interacting factor 3)
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.048   13.7   0.0    1.7  2  APC_N_CC  Coiled-coil N-terminus of APC, dimerisation domain


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5   0.2   1.4e-58   1.2e-54       1     243 [.       6     237 ..       6     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 1.4e-58
                              NIF3   1 eivevleelaplelaeswDnvGlqvgdpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddyk 77 
                                       ei+++l+e+++++++++   +Glq++  + +v++v +++d+++e + +A+e g+dl+i+hH+li+++lk l++    
  gi|488600580|ref|YP_007907051.1|   6 EITDFLDEYLQINKFRDLSSNGLQIE-GKGSVETVGFTVDACMESFLKAKELGVDLLIVHHGLIWGGLKFLKGI--A 79 
                                       6899*********************6.999********************************************..* PP

                              NIF3  78 krllkkliknnislysaHtnlDaapg.Gvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelakk 153
                                       ++++k l++n+isly+aH++lDa+ + G+n +++k+l  +  e +  ++     e+ ++g+ ge+e+ ++++el k+
  gi|488600580|ref|YP_007907051.1|  80 RKRIKFLLENEISLYTAHLPLDAHDEvGNNIQIMKLLSGS-SEGFFAEH-----EGIKIGVFGEIEK-MEVSELKKR 149
                                       *************************************544.45554433.....499*********8.********* PP

                              NIF3 154 lkkklglekvrvagdldkkvkkvaicaGsGaslieeakakgaDlliTGelkhhealdakekgiavidvgHyatErvf 230
                                       + + l+ ++  ++    ++++k+ i++GsG+  ieea +   D+liTGe +h++++ ake +++vi +gHy+tE+v+
  gi|488600580|ref|YP_007907051.1| 150 VDSVLNTTSRVLN-FGRNEIEKISIISGSGSFAIEEASQ-ISDCLITGEYRHEAYHVAKELEFNVIFAGHYETETVG 224
                                       *****88665555.99******************99966.68*********************************** PP

                              NIF3 231 lealaelLkeklk 243
                                       l+al+e+L+e+++
  gi|488600580|ref|YP_007907051.1| 225 LKALMEKLNERFD 237
                                       **********986 PP

>> APC_N_CC  Coiled-coil N-terminus of APC, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.2   1.1e+04      14      22 ..     140     148 ..     137     151 .. 0.68
   2 ?   13.7   0.0   5.4e-06     0.048      14      50 ..     198     234 ..     195     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.2
                          APC_N_CC  14 kkenthlrr 22 
                                       k+e ++l++
  gi|488600580|ref|YP_007907051.1| 140 KMEVSELKK 148
                                       667777766 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.4e-06
                          APC_N_CC  14 kkenthlrrELedNSshLskLEtetsgmKevlkqlqg 50 
                                       + e+ h  +ELe N       Etet+g+K+++ +l+ 
  gi|488600580|ref|YP_007907051.1| 198 RHEAYHVAKELEFNVIFAGHYETETVGLKALMEKLNE 234
                                       67899999**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1727.07
//
Query:       gi|488600581|ref|YP_007907052.1|  [L=132]
Description: hypothetical protein Asulf_01058 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 934.84
//
Query:       gi|488600582|ref|YP_007907053.1|  [L=112]
Description: N-terminal domain of molybdenum-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-13   48.7   0.0    1.1e-12   47.7   0.0    1.5  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
    7.9e-05   22.6   0.0    0.00013   21.9   0.0    1.3  1  HTH_45    Winged helix-turn-helix
    0.00019   21.4   0.1    0.00028   20.8   0.1    1.3  1  HTH_29    Winged helix-turn helix
     0.0029   17.6   0.1     0.0061   16.6   0.1    1.6  1  DUF2089   Protein of unknown function (DUF2089)
  ------ inclusion threshold ------
      0.064   13.5   0.0       0.11   12.8   0.0    1.4  1  NUMOD1    NUMOD1 domain
       0.12   12.2   0.0       0.19   11.6   0.0    1.3  1  HTH_23    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   3.6e-16   1.1e-12       5      60 .]      28      88 ..      27      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.6e-16
                                      HHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE.....EEE-HHHH CS
                             HTH_1  5 rlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrg.....lrLTeaGe 60
                                      +++ a+  egs+  A ++Lg+s+  v++ i ++E+ lg++ ++R+ +g     ++LTe+Ge
  gi|488600582|ref|YP_007907053.1| 28 EILSAIKSEGSIMSASKKLGMSYRYVWDYIEKMERNLGEKVVIRDRGGsrgggTVLTERGE 88
                                      6899***************************************9444333456******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 !   21.9   0.0   4.3e-08   0.00013       9      74 ..      27      99 ..      26     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.3e-08
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvek...gli.....kkskekYvlTekGlelleklkelee 74
                                      a+IL+ai ++e +  +  +k  +sy+ +  Y++++  +   +++       +++  vlTe+G+elle ++++++
  gi|488600582|ref|YP_007907053.1| 27 AEILSAI-KSEGSIMSASKKLGMSYRYVWDYIEKMERNlgeKVVirdrgGSRGGGTVLTERGEELLELFNKIDS 99
                                      69*****.6666666679****************9865322334687776677888**************9976 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   9.4e-08   0.00028       2      60 ..      27      86 ..      27      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9.4e-08
                            HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvyrwlkrfe.egGlaalld.rrrsgrprnrlsee 60
                                      a++l +++ ++s ++ + k lg+s+r+v ++++ +e + G++  ++ r +s+ + ++l+e+
  gi|488600582|ref|YP_007907053.1| 27 AEILSAIKSEGS-IMSASKKLGMSYRYVWDYIEKMErNLGEKVVIRdRGGSRGGGTVLTER 86
                                      68999999*998.*********************973578888888788777777798886 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.1e-06    0.0061      45      84 ..      32      71 ..      27     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                           DUF2089 45 fikarGnlkevekelgisYpTvrnrldeileaLgyeeeee 84
                                       ik++G++ +  k+lg+sY  v   ++++ ++Lg +   +
  gi|488600582|ref|YP_007907053.1| 32 AIKSEGSIMSASKKLGMSYRYVWDYIEKMERNLGEKVVIR 71
                                      59********************************987655 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.6e-05      0.11      18      37 .]      38      57 ..      37      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                            NUMOD1 18 SireAakyLgishntInkyl 37
                                      Si +A+k+Lg s+++++ y+
  gi|488600582|ref|YP_007907053.1| 38 SIMSASKKLGMSYRYVWDYI 57
                                      8999***************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.3e-05      0.19       9      40 ..      28      59 ..      27      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                            HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                      +il + +   s+  ++++Lg+s+r v+ ++++
  gi|488600582|ref|YP_007907053.1| 28 EILSAIKSEGSIMSASKKLGMSYRYVWDYIEK 59
                                      677777775689999*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 807.37
//
Query:       gi|488600583|ref|YP_007907054.1|  [L=196]
Description: Uncharacterized membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-35  122.6  18.7    1.7e-35  122.3  18.7    1.0  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
        2.6    8.2   8.5       0.21   11.7   1.6    2.2  2  TMEM169   TMEM169 protein family


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 !  122.3  18.7   1.9e-39   1.7e-35       2     156 .]      21     189 ..      20     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 1.9e-39
                            SpoIIM   2 lllflvgillgallaa......snfaeqis......seskensalslflaifanNlrvalllfllGllllgiptilv 66 
                                        l+f+++i++g+++++      +   + i+      s    n++l++f+ if+nN + a++++++G+ ++gi+++ +
  gi|488600583|ref|YP_007907054.1|  21 SLVFIIAIFFGYVSSSlqpdqsE---KFIEsvfeslSFIDFNNPLEVFMIIFLNNSSKAFIAMVAGF-FFGIFPVSF 93 
                                       589*************5554321...2333666788888899999*********************6.********* PP

                            SpoIIM  67 llinGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal......rsrrkalkeakrellkll 137
                                       +++nG+++G++ ++  +  g+l +++++lPhgile+pa+iia+a+gl+lgk +      ++ ++ + ++k+ ++k++
  gi|488600583|ref|YP_007907054.1|  94 VFLNGYIIGVIIYVKGSELGILRVAVSLLPHGILEIPAVIIASAYGLYLGKLFylrvfrSRSIDMKLAMKEFIKKFI 170
                                       *********99777777755*******************************999999987778888889999999** PP

                            SpoIIM 138 lllvpllliAaliEafvtp 156
                                        +++p+lliAaliE+fvtp
  gi|488600583|ref|YP_007907054.1| 171 TVIIPILLIAALIETFVTP 189
                                       ******************8 PP

>> TMEM169  TMEM169 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.8     0.092   8.2e+02       7      40 ..      57      90 ..      51     105 .. 0.75
   2 ?   11.7   1.6   2.3e-05      0.21      17      76 ..     124     182 ..     111     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.092
                           TMEM169  7 slekGlhilllsllclPlvfvvsavvsfylGtlt 40
                                      ++++ l ++++ +l     + +++v  f++G++ 
  gi|488600583|ref|YP_007907054.1| 57 DFNNPLEVFMIIFLNNSSKAFIAMVAGFFFGIFP 90
                                      5666777888888888888888999999999765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.3e-05
                           TMEM169  17 lsllclPlvfvvsavvsfylGtltWyniflvyneersllhkillcPllillyPllivlvt 76 
                                         +l +P v+ +++++  ylG l +  +f   + +  l  k ++  ++ ++ P+l++++ 
  gi|488600583|ref|YP_007907054.1| 124 HGILEIPAVI-IASAYGLYLGKLFYLRVFRSRSIDMKLAMKEFIKKFITVIIPILLIAAL 182
                                       4677888775.56789**************************************998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); 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:                         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 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1187.87
//
Query:       gi|488600584|ref|YP_007907055.1|  [L=61]
Description: hypothetical protein Asulf_01061 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.15   12.1   0.0    1.2  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.3e-06      0.15       2      38 ..      14      51 ..      13      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-06
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      + i++d++  e++ ++++++g  S  e++R ++ +y++
  gi|488600584|ref|YP_007907055.1| 14 IRIKVDRKFEEKFMKIKEELGlNSNAEVVRYLVNRYYK 51
                                      669*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 443.09
//
Query:       gi|488600585|ref|YP_007907056.1|  [L=415]
Description: UbiD family decarboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-72  242.5   0.0    8.7e-72  242.2   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase
  ------ inclusion threshold ------
      0.033   14.1   0.0      0.068   13.1   0.0    1.5  1  DUF4250   Domain of unknown function (DUF4250)


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 !  242.2   0.0   9.7e-76   8.7e-72      51     405 ..      48     379 ..      37     380 .. 0.90

  Alignments for each domain:
  == domain 1  score: 242.2 bits;  conditional E-value: 9.7e-76
                                       EEEE-TTS-HCHHHHHHTS..-GHHHHHHHHHHHHHS..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTT CS
                              UbiD  51 pvltnlfgtrervalalgl..ssleeileklaellepkppippkvvesekapcqeevvlegddvdLskLPvltlwpg 125
                                       +++ n +++re++++ lg+  ++l e+l k+            + v  e+ p +      +++  L++LP+++++++
  gi|488600585|ref|YP_007907056.1|  48 KLAQNFIASREHLCKYLGIrrENLAEFLSKIDYN------GDIEIV--EDNPLK------KTNWTLKDLPIPKYFER 110
                                       68899*************9655555555555444......446778..458999......45689************ PP

                                       SSS-EEECEE.EEEE-TTT.T-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHH CS
                              UbiD 126 DgGpyitlgl.vitrdpet.gkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltl 200
                                       DgG+yit+g+ ++trd ++ +  n+ i+R++v+++ +l+ ++++ ++    +++a ++  e+l++ +a+G++P+ ++
  gi|488600585|ref|YP_007907056.1| 111 DGGRYITAGVvIATRDEDDvNAYNACIHRLMVKSEGELVARLVPPRHTYLMWKDAVERS-EDLKILIAVGCHPLFLF 186
                                       *********94557777778***************************************.9**************** PP

                                       HCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEE CS
                              UbiD 201 aAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfk 277
                                       aA++++P   +E+ +a+ l++  ++l + +   l  p  AEiv+  +i+ + +a+EGPf+d+tG+y++ r+e pv++
  gi|488600585|ref|YP_007907056.1| 187 AASTRVP-AGKEFGYASKLMN-GLKLYRIDG--LLTP-MAEIVISARITGR-KAEEGPFVDITGTYDKIRME-PVIE 256
                                       *******.669*********6.699997744..8888.9**********97.59***************996.**** PP

                                       EEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHH CS
                              UbiD 278 VtaithRkdpiypttvvgkppeedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvm 354
                                       +++i  R++pi++++++g   e+++l+g+++e+++++++++ v +vk+v l++ +  +++a+v+i+k ++g+ k+++
  gi|488600585|ref|YP_007907056.1| 257 IDRIFARENPIFYSILPGGY-EHQVLMGIPYEPVIFKAVSN-VCRVKNVILTAGSRHYFHAIVQIEKVTEGDGKNAI 331
                                       ***************99999.******************77.556******************************99 PP

                                       HHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CCCCEEEECCC CS
                              UbiD 355 ealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpdrDlviiegt 405
                                         ++++++  s+ K v vvDed+d+++ +++++aiatr+++drD+v+i+g+
  gi|488600585|ref|YP_007907056.1| 332 ISALSAHP--SI-KGVTVVDEDIDIYSHEDIEYAIATRFQADRDFVLIRGV 379
                                       99999999..88.***********************************987 PP

>> DUF4250  Domain of unknown function (DUF4250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.6e-06     0.068      20      47 ..      54      81 ..      48      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-06
                           DUF4250 20 yssldelcedldidkeeleekLasigYe 47
                                        s ++lc++l i +e+l e L++i+Y+
  gi|488600585|ref|YP_007907056.1| 54 IASREHLCKYLGIRRENLAEFLSKIDYN 81
                                      47899**********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2971.20
//
Query:       gi|488600586|ref|YP_007907057.1|  [L=217]
Description: Histidinol phosphatase and related hydrolases of the PHP family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-08   35.0   0.2    5.5e-08   33.3   0.2    2.2  1  PHP          PHP domain
  ------ inclusion threshold ------
      0.019   14.5   0.0      0.032   13.7   0.0    1.4  1  RNase_P_p30  RNase P subunit p30
      0.022   14.0   0.0      0.033   13.4   0.0    1.4  1  DUF1152      Protein of unknown function (DUF1152)


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 !   33.3   0.2   9.3e-12   5.5e-08       1      74 [.       3      86 ..       3     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 9.3e-12
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT...HHHHHHHHHHH.HTTTTSEEEEEEE.......... CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.. RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf...gyvefykaakk.kykagikpiiGleayvaddse.. 73
                                      dlHvH+ +s     l ++e++++ +e g + +a+TDh+++    + ++   ++k+ +++ ++ +++G+e++ ++ +   
  gi|488600586|ref|YP_007907057.1|  3 DLHVHSIFSDG--ELVPSEIARRMAEIGNEGMAVTDHADFSnikDLMKKLDQMKDyRDDYELDILFGVEVTHVPPRLig 79
                                      89*******44..3346**********************9955544455555544544579********8777665455 PP

                                      ....... CS
                                      ......x RF
                               PHP 74 ......k 74
                                             
  gi|488600586|ref|YP_007907057.1| 80 kavemaW 86
                                      5555551 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-06     0.032      11     145 ..      13     144 ..       2     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-06
                                       .......HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H...HHHHH CS
                       RNase_P_p30  11 dskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl..qrlsk 85 
                                       ++  +s+++++ ae g +g a++ + + ++ k+  ++     ++k+ +++ ++l++l +v+++   p+ +       
  gi|488600586|ref|YP_007907057.1|  13 GELVPSEIARRMAEIGNEGMAVTDHADFSNIKDLMKKL---DQMKDYRDD-YELDILFGVEVTHVPPRLIgkAVEMA 85 
                                       44445688899999999999999999988888888888...456666666.44999999999999999444455567 PP

                                       HHHH--EEEEE--S......HHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                       RNase_P_p30  86 vrqkfdllavrPtt......ekalraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                        r    +++v++ t      e  + +a+   ++Di+ ++       +++ k +++A+e+g+ +Ei+
  gi|488600586|ref|YP_007907057.1|  86 WREGAEIVVVHGETvaepvkEGTNYHAL-CEEIDILAHPG------FIDEKCLELARENGIYLEIT 144
                                       7899999999865522221166666665.458******99......79****************96 PP

>> DUF1152  Protein of unknown function (DUF1152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.6e-06     0.033     161     209 ..       4      48 ..       1      69 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-06
                           DUF1152 161 lavaGpGsDGELseeelleriseiakeggllgilgldeedaellekile 209
                                       l+v+++ sDGEL  +e+ +r++ei +eg+ +     d+ d + ++++++
  gi|488600586|ref|YP_007907057.1|   4 LHVHSIFSDGELVPSEIARRMAEIGNEGMAV----TDHADFSNIKDLMK 48 
                                       7999********************6655444....44555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1245.30
//
Query:       gi|488600587|ref|YP_007907058.1|  [L=96]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-38  129.7   2.8    3.8e-38  129.5   2.8    1.0  1  DUF211    Uncharacterized ArCR, COG1888
     0.0071   15.9   0.5     0.0083   15.7   0.5    1.2  1  DUF2067   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.073   13.1   0.1        0.1   12.6   0.1    1.2  1  MOEP19    KH-like RNA-binding domain
       0.15   11.9   0.4       0.35   10.7   0.2    1.6  2  SHD1      SLA1 homology domain 1, SHD1


Domain annotation for each model (and alignments):
>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   2.8   8.5e-42   3.8e-38       2      88 ..       4      90 ..       3      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 8.5e-42
                                      EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEE CS
                            DUF211  2 irrlvLDvlkphepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevva 80
                                       +rlvLDvlkpheps++ lakkl+ele++dgvni+++e+D++ten+kiti G+++++e+i+ +ieelg+vihSiDe+va
  gi|488600587|ref|YP_007907058.1|  4 FKRLVLDVLKPHEPSTLILAKKLSELENIDGVNISLYEIDQNTENVKITIVGDDMSFEDIKMVIEELGAVIHSIDEIVA 82
                                      69***************************************************************************** PP

                                      ESS----- CS
                            DUF211 81 Gkkiveev 88
                                      Gkk++e+v
  gi|488600587|ref|YP_007907058.1| 83 GKKLIETV 90
                                      ******87 PP

>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   1.9e-06    0.0083      12      56 ..      22      70 ..      13      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
                           DUF2067 12 flekise..kiksaeevkievegn..rllievyGtekeikdiirrikel 56
                                      + +k+se  +i+ +  + +e+++n  +++i ++G++ + +di+++i+el
  gi|488600587|ref|YP_007907058.1| 22 LAKKLSEleNIDGVNISLYEIDQNteNVKITIVGDDMSFEDIKMVIEEL 70
                                      6678888879999999******************************997 PP

>> MOEP19  KH-like RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.2e-05       0.1      34      81 ..      25      73 ..      21      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                            MOEP19 34 ripeiEqvsqtllevkalds.eglaeilifGrprykkrvkkmllslAew 81
                                      +++e+E +  + +++  +d+ +++++i+i+G+ +  +++k ++ +l+++
  gi|488600587|ref|YP_007907058.1| 25 KLSELENIDGVNISLYEIDQnTENVKITIVGDDMSFEDIKMVIEELGAV 73
                                      67888888888899999998899**********************9986 PP

>> SHD1  SLA1 homology domain 1, SHD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.59   2.6e+03      36      45 ..      29      38 ..      23      45 .. 0.80
   2 ?   10.7   0.2   7.7e-05      0.35      39      62 ..      46      69 ..      37      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.59
                              SHD1 36 LhkvnGvkia 45
                                      L  ++Gv i+
  gi|488600587|ref|YP_007907058.1| 29 LENIDGVNIS 38
                                      7788899886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.7e-05
                              SHD1 39 vnGvkiaVpvekmskeDleyvekv 62
                                      +++vki +  + ms eD+++v + 
  gi|488600587|ref|YP_007907058.1| 46 TENVKITIVGDDMSFEDIKMVIEE 69
                                      789****************99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 606.29
//
Query:       gi|488600588|ref|YP_007907059.1|  [L=160]
Description: hypothetical protein Asulf_01065 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-15   57.2   0.0    2.8e-15   56.6   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.5e-12   46.8   0.0    3.4e-12   46.4   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.2e-12   46.3   0.1    7.4e-12   45.5   0.1    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.5e-10   40.1   0.0    6.3e-10   39.9   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      3e-09   37.2   0.3    4.6e-09   36.6   0.2    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    3.2e-05   23.8   0.0    5.4e-05   23.1   0.0    1.4  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.076   13.1   0.0        6.2    6.9   0.0    2.4  2  EFP              Elongation factor P (EF-P) OB domain
      0.094   11.2   0.0       0.11   10.9   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


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 !   56.6   0.0   1.2e-18   2.8e-15      14     117 .]      46     143 ..      28     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.2e-18
                                       HHHHHHHHHHHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHH CS
                    Acetyltransf_1  14 ppnedaseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeera 89 
                                       pp ++++ e + ++  l+++ + ++a++++++iG+i + +++d      +   ++ + +y gk +G ++++++e+++
  gi|488600588|ref|YP_007907059.1|  46 PPIKREMIESWIDF--LHNNgHMFIAKHGDRVIGHIAVVPKDD-----SAEFVIFMHQDYEGKLIGGKMVKTVEKFL 115
                                       66666666664444..666658999******************.....9999************************* PP

                                       HHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  90 reegikkivlaveedndaairlYeklGF 117
                                       ++ gi+k+ + +e +n+ ai+lY+klGF
  gi|488600588|ref|YP_007907059.1| 116 KSLGIRKLKAVTERTNRNAIKLYQKLGF 143
                                       ********9989999************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   1.5e-15   3.4e-12      17     111 ..      48     148 ..      26     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.5e-15
                   Acetyltransf_10  17 ispealrerie..egealllvaeeggkivGviel..rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.. 87 
                                       i++e ++++i+  +++ ++++a+ g++++G+i++  +d+s    +f +++y g+ ig +++++ve+ ++  gi++  
  gi|488600588|ref|YP_007907059.1|  48 IKREMIESWIDflHNNGHMFIAKHGDRVIGHIAVvpKDDSAEFVIFMHQDYEGKLIGGKMVKTVEKFLKSLGIRKlk 124
                                       6778899999777999****************9985555555566*****************************995 PP

                   Acetyltransf_10  88 eltvnaspyavpfYeklGFkavge 111
                                       ++t + +++a+++Y+klGFk+ ++
  gi|488600588|ref|YP_007907059.1| 125 AVTERTNRNAIKLYQKLGFKKESA 148
                                       55555555************9866 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   3.3e-15   7.4e-12       1      76 []      62     145 ..      62     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.3e-15
                                       TTEEEEEEEETTEEEEEEEEEEESTCTEE.EEE-GGGTTSSHHHHHHHH.TT....SEEE.EE.EEEETHHHHHHHH CS
                    Acetyltransf_7   1 ekgevfVaeddgkivGfialslldaeitr.laVdpeyrgkGiGraLlea.ae....kgii.le.qlelnaekaikfY 69 
                                       ++g++f+a+++++++G ia+++ d++ ++ ++ +++y gk iG ++++  ++     gi+ l+ ++e ++++aik+Y
  gi|488600588|ref|YP_007907059.1|  62 NNGHMFIAKHGDRVIGHIAVVPKDDSAEFvIFMHQDYEGKLIGGKMVKTvEKflksLGIRkLKaVTERTNRNAIKLY 138
                                       589********************9444446*****************96322454566543222222233489**** PP

                                       HHTTEEE CS
                    Acetyltransf_7  70 eklGFee 76 
                                       +klGF++
  gi|488600588|ref|YP_007907059.1| 139 QKLGFKK 145
                                       *****95 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.8e-13   6.3e-10      30     138 .]      46     144 ..       8     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.8e-13
                    Acetyltransf_3  30 epltleeaeewlerawaeeseeegygwaivlkdtg.viGsvglrdleeedeeaelgymlapsfwgkGyateavrall 105
                                       +p ++e+ e+w++ ++++    +g  ++   k+++ viG + + + +++   ae+ + +++++ gk ++  +v+ + 
  gi|488600588|ref|YP_007907059.1|  46 PPIKREMIESWID-FLHN----NGHMFIA--KHGDrVIGHIAVVPKDDS---AEFVIFMHQDYEGKLIGGKMVKTVE 112
                                       2667778888888.5554....8877777..555426*******88887...************************* PP

                    Acetyltransf_3 106 eyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +++ + lg+++l av++ +N++ i++++klGf+
  gi|488600588|ref|YP_007907059.1| 113 KFL-KSLGIRKLKAVTERTNRNAIKLYQKLGFK 144
                                       ***.9999************************7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.2   2.1e-12   4.6e-09      35     145 ..      51     154 ..      24     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.1e-12
                    Acetyltransf_4  35 eefekflealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqni 111
                                       e++e +++ l   +  +f +   dr++G  +++   +  kd +ae  +++ ++d + + +g ++++ +e++lk  +i
  gi|488600588|ref|YP_007907059.1|  51 EMIESWIDFL-HNNGHMFIAKHGDRVIGHIAVV---P--KDDSAEFVIFM-HQDYEGKLIGGKMVKTVEKFLKSLGI 120
                                       5677777776.6778888888899999999988...5..678********.599*********************** PP

                    Acetyltransf_4 112 enllaeiaspnensiqfhkalGFelvgifkkcik 145
                                       ++l a +  +n n+i+++++lGF+++ ++ ++i+
  gi|488600588|ref|YP_007907059.1| 121 RKLKAVTERTNRNAIKLYQKLGFKKESAEGGYIY 154
                                       *************************999988876 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.4e-08   5.4e-05      24      80 ..      89     146 ..      72     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.4e-08
                                       EEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  24 lgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfeki 80 
                                        + + ++++ +++  g+++vk + k +   g+  + +v+  +N ++i+ly+klGf+k 
  gi|488600588|ref|YP_007907059.1|  89 EFVIFMHQDYEGKLIGGKMVKTVEKFLKSLGIRkLKAVTERTNRNAIKLYQKLGFKKE 146
                                       56788899999999***************998615699999**************997 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.03        68      26      54 .]      48      76 ..      47      76 .. 0.90
   2 ?    6.9   0.0    0.0028       6.2      11      39 ..      89     116 ..      85     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.03
                                      EEHHHHTTGCGG--TT-EEEEEEETTEEE CS
                               EFP 26 lpkeqlgdaakfLkEgmevtvllyegepi 54
                                      ++ e+++++++fL ++  + +  + +++i
  gi|488600588|ref|YP_007907059.1| 48 IKREMIESWIDFLHNNGHMFIAKHGDRVI 76
                                      67899*9************9999999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                                       TEEEEEETTT--EEEEEHHHHTTGCGG-- CS
                               EFP  11 deyvFMdnetYeqielpkeqlgdaakfLk 39 
                                       ++++FM++ +Ye   +  ++++  +kfLk
  gi|488600588|ref|YP_007907059.1|  89 EFVIFMHQ-DYEGKLIGGKMVKTVEKFLK 116
                                       7899***5.************9999***9 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 ?   10.9   0.0   5.1e-05      0.11     195     264 ..      63     138 ..      46     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                                       ETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH......HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 195 SaTKylgGhsdvvaGvivvkgkeelkkelkflq......nalGavlspfdawlllrGlkTLslRlerhqenAlkvA 264
                                        +  +++ h+d v+G i+v  k++ ++ + f++         G++++  + +l   G++ L+   er ++nA+k+ 
  gi|488600588|ref|YP_007907059.1|  63 NGHMFIAKHGDRVIGHIAVVPKDDSAEFVIFMHqdyegkLIGGKMVKTVEKFLKSLGIRKLKAVTERTNRNAIKLY 138
                                       55669999*********999988888877777767777556688999**************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
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 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1105.20
//
Query:       gi|488600589|ref|YP_007907060.1|  [L=59]
Description: hypothetical protein Asulf_01066 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   13.0   0.3       0.13   12.5   0.3    1.4  1  VP9       VP9 protein


Domain annotation for each model (and alignments):
>> VP9  VP9 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3     7e-06      0.13      34      60 ..      29      54 ..       8      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-06
                               VP9 34 elrdgvfiVrlkdkkvlklknGlkrLr 60
                                       + d +fiVr+ d++vlk++ G+kr r
  gi|488600589|ref|YP_007907060.1| 29 VFYDYHFIVRVSDEDVLKID-GVKRYR 54
                                      57899*************96.888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 443.53
//
Query:       gi|488600590|ref|YP_007907061.1|  [L=227]
Description: uridylate kinase, putative [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-27   95.6   0.7    7.5e-26   91.2   0.7    2.0  1  AA_kinase    Amino acid kinase family
  ------ inclusion threshold ------
      0.031   14.8   0.1       0.11   13.1   0.1    2.0  1  Pyr_redox    Pyridine nucleotide-disulphide oxidoreductase
      0.052   12.8   0.0      0.095   11.9   0.0    1.4  1  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase


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 !   91.2   0.7   1.2e-29   7.5e-26       2     241 .]       4     204 ..       3     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 1.2e-29
                                       EEEEEE-TT.CCC.CTCC..HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HH CS
                         AA_kinase   2 rvVvKlGGs.slt.dkee..aslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstlee 72 
                                       +vV+ lGGs +++ +     +++r +ae i+++ +++n++ vV+Ggg +++++++   + g ++++           
  gi|488600590|ref|YP_007907061.1|   4 TVVISLGGSiLFGeN--LdsSRIRGFAEAIERI-SKDNRVFVVVGGGWIAREYIKTarELGSNETFC---------- 67 
                                       79*******555544..346*************.**********************55555555555.......... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEE CS
                         AA_kinase  73 agevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigl 149
                                              d++++  +rl+a+ll+ ++++ +  +       +++             ++  el ++  v++++g +  
  gi|488600590|ref|YP_007907061.1|  68 -------DYMGIEVTRLNAMLLSLAVRNSPKVV------PKDF-------------REAYELSKHYPVVIMGGTF-- 116
                                       .......9*****************95554422......2444.............3444555666899999977.. PP

                                       ETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHH CS
                         AA_kinase 150 deegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhp 224
                                         +g+    ++D ++allAe ++A+ li++t+VdGVy+ dpkk+ +a+++++i+++ ++e    +e + g   v+++
  gi|488600590|ref|YP_007907061.1| 117 --PGH----TTDATSALLAEFVNAELLINATSVDGVYSEDPKKNRNAKRFERIKAKGLLEivARNEAVAGTNTVMDL 187
                                       ..777....9***************************************************9999999999999*** PP

                                       HHHHHHHCTT-EEEEEE CS
                         AA_kinase 225 aalaaarrggipvvItn 241
                                         +++++r++i+++I++
  gi|488600590|ref|YP_007907061.1| 188 LSVKIIERSKIKTYIIK 204
                                       ***************85 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.8e-05      0.11       3      28 ..      42      67 ..      40      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                      EEECSSHHHHHHHHHHHHTTSEEEEE CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvv 28
                                      vvvGgG+i+ E+ ++++elg++ t +
  gi|488600590|ref|YP_007907061.1| 42 VVVGGGWIAREYIKTARELGSNETFC 67
                                      9*******************987665 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.6e-05     0.095     134     167 ..      29      73 ..      15     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                                       HHHCCSS-TSEE.EEES-SHHHHHHHHHHHHHT-..........E CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..........x RF
                       Pyr_redox_2 134 ealklkllpkri.vvvGgGyiGvElAaalaklgk..........e 167
                                       ea+++  +++r+ vvvGgG i+ E+  ++++lg+          e
  gi|488600590|ref|YP_007907061.1|  29 EAIERISKDNRVfVVVGGGWIAREYIKTARELGSnetfcdymgiE 73 
                                       5555555564544********************944444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1400.18
//
Query:       gi|488600591|ref|YP_007907062.1|  [L=933]
Description: leucyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  218.8   2.0    8.6e-64  215.8   2.0    2.3  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.8e-25   88.9   3.7    1.5e-10   40.4   0.1    3.9  4  tRNA-synt_1g   tRNA synthetases class I (M)
    2.9e-19   69.5   0.9      1e-18   67.8   0.9    2.0  1  Anticodon_1    Anticodon-binding domain of tRNA
    5.1e-13   48.9   0.2    3.5e-12   46.2   0.1    2.3  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
      2e-10   40.5   0.0    3.6e-06   26.6   0.0    2.6  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
     0.0034   16.4   0.9     0.0086   15.1   0.0    2.0  2  tRNA-synt_1d   tRNA synthetases class I (R)
  ------ inclusion threshold ------
      0.038   14.5   0.0       0.11   13.1   0.0    1.7  1  Ccdc124        Coiled-coil domain-containing protein 124 /Oxs
       0.05   13.3   0.2        1.4    8.6   0.1    2.5  2  O-FucT         GDP-fucose protein O-fucosyltransferase
       0.14   12.1   0.6       0.48   10.4   0.6    1.9  1  RepB-RCR_reg   Replication regulatory protein RepB


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 !  215.8   2.0   4.3e-67   8.6e-64       1     601 [.      12     671 ..      12     672 .. 0.86

  Alignments for each domain:
  == domain 1  score: 215.8 bits;  conditional E-value: 4.3e-67
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       k++e+We+e++f++e     +k++f ++++ Py +G+lH Gh  + t+ d   r+ rmkG++vl+ +G+   G +i 
  gi|488600591|ref|YP_007907062.1|  12 KWQEMWEKEGIFHAE---PSDKPKFFITIPYPYLNGNLHAGHTRTFTIGDAFARFMRMKGYNVLFPMGFHVTGTPII 85 
                                       5899**********9...889******************************************************96 PP

                       tRNA-synt_1  78 akvekklgakekkerkklgr.....eefr...ekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkev 146
                                          e  + +++ k+ + +++     e+     +   ++++++++e  k++k++G s+D+ r   T d+ +++ +++ 
  gi|488600591|ref|YP_007907062.1|  86 GLAE-LIQKRDPKTFEVYTKfhdvpEDVLkklDTPEKIVEYFSKEALKAMKDIGYSIDWRRVFTTTDETYQKFIEWQ 161
                                       5443.4455555555544432212233330114557899************************************** PP

                       tRNA-synt_1 147 fvrladkgliyrgkklvnwstklktalselEveykdkkda..lihvafpladkeevklviaTTtPeTllgdtavavn 221
                                       f rl + gl+ +g+++v ++++ + ++ + +  + ++  +  ++ ++f l+d++   l  aT +PeT++g t + ++
  gi|488600591|ref|YP_007907062.1| 162 FYRLKELGLVVKGSHPVRYCPNDQNPVEDHDLLHGENATVvdFTVIKFRLDDGTI--LPCATLRPETVFGVTNIWLK 236
                                       ********************************77766654126778999988877..******************** PP

                       tRNA-synt_1 222 peldyv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkia 295
                                       p  +yv   +++e++++ e   ++l   e++ + +++++++eL gk++++p+++ kipi+  ++vd+++ tGvV   
  gi|488600591|ref|YP_007907062.1| 237 PT-EYViarVDDEQWLVSEEAFEKLKYTEKKVEFVRKINAEELFGKYATNPVTKDKIPILPAEFVDTDNATGVVMSV 312
                                       *9.***99999**************9999999********************************************* PP

                       tRNA-synt_1 296 PahdedDyevg...kkynl..............evinildedgtlteea............................ 327
                                       Pah + Dy +    kk +l              +++ i  ed +++e +                            
  gi|488600591|ref|YP_007907062.1| 313 PAHAPYDYIAIedlKKSDLaekyglkdvlenikPIVLIRIEDQEFSEGVpaekvirelgikdqsdpeleratkilyk 389
                                       ********8651112333455555598887774333444467777777799999*********************** PP

                       tRNA-synt_1 328 ............aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..lada 390
                                                   +e++g k+ + ++ + ++l ekg      +++ +  +c  + k ++  +++qWf + ++   +++
  gi|488600591|ref|YP_007907062.1| 390 kefhkgvlmditGEYSGTKISQIKDRLQRDLIEKGIGDVFYEFSEKPVVCRCGTKCVVKVVKDQWFLSYSNpeWKAK 466
                                       **********************************************99999999***************987899** PP

                       tRNA-synt_1 391 alkavekvqfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekka 464
                                       +l+++e++++vp+ +++++ + +e  +d +  R +  G+rip    +  ++  + ++      l++ ++    ++++
  gi|488600591|ref|YP_007907062.1| 467 VLRHLENMRIVPEYYKEEFRNKIEWLKDKACARRKGLGTRIPWdkeWLIESLSDSTIYMAYYILAKFINSGLLKAEN 543
                                       ******************************************64447777666666655555556666666677777 PP

                       tRNA-synt_1 465 lekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslal 541
                                       ++ke  d +  ++g+le  ++      sSg+ +  +++     ++++   +p d+ ++G D +   +   ++  +a+
  gi|488600591|ref|YP_007907062.1| 544 MTKELLDYVLLGEGSLELASE------SSGLDK-EIVE---VIRRDFVYWYPVDLRSSGKDLVANHLLFFLFHHIAI 610
                                       777888877777888877776......566654.5555...4588******************************** PP

                       tRNA-synt_1 542 tgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                       + +e + + + v+g v   eG+KmSKs+g  +  +  +  y+ad+ R++++ +s++ +d ++
  gi|488600591|ref|YP_007907062.1| 611 FPEELWpRAIAVNGYVS-LEGKKMSKSKGPLLTMKRAVADYSADVTRMYILyTSEYDSDADW 671
                                       *9996636788899875.78*******************************67777777665 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   1.7e-13   3.4e-10       2      81 ..      34     116 ..      33     119 .. 0.82
   2 !    8.5   0.0   0.00038      0.76      62     132 ..     118     190 ..     113     197 .. 0.85
   3 ?   -2.6   0.1      0.86   1.7e+03     169     239 ..     438     510 ..     434     515 .. 0.67
   4 !   40.4   0.1   7.3e-14   1.5e-10     289     371 ..     592     676 ..     578     683 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.7e-13
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH.TTS-HH..HHHHHHHHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek.egvtpe..elvekvheeik 75 
                                       ++t + pY ng+lH Gh ++  ++D+faR+ r++g++vlf  g    Gtpi   Ae  ++ +p+  e+ +k+h+  +
  gi|488600591|ref|YP_007907062.1|  34 FITIPYPYLNGNLHAGHTRTFTIGDAFARFMRMKGYNVLFPMGFHVTGTPIIGLAELiQKRDPKtfEVYTKFHDVPE 110
                                       89*************************************************98887413334442256677777766 PP

                                       HHHHHT CS
                      tRNA-synt_1g  76 elfkkl 81 
                                       +++kkl
  gi|488600591|ref|YP_007907062.1| 111 DVLKKL 116
                                       666665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00038
                                       -HHHHHHHHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G CS
                      tRNA-synt_1g  62 tpeelvekvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpd 132
                                       tpe++ve +++e  + +k+++ s d     +tt+e+ +++ +  f +lke gl+ +++  + ycp+d++   d
  gi|488600591|ref|YP_007907062.1| 118 TPEKIVEYFSKEALKAMKDIGYSIDwrRVFTTTDETYQKFIEWQFYRLKELGLVVKGSHPVRYCPNDQNPVED 190
                                       8999**************98766663356678888999999999999*******************9986666 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.86
                                       ........EEE..EEEEEE-GGG..GHHHHHHHH.HH-TT.SHHHHHHHH.HHHHT----EE-ESS-SSS-EET.T CS
                      tRNA-synt_1g 169 saisgskpevke.tehlffklsk..fekklkewieeeeke.leenvkkivkewlkegLkdlaisrdldwGipvP.g 239
                                          +g+k +vk  ++++f++ s+  ++ k+ +++  e+ +  +e  k+  ++ ++  Lkd a +r+   G ++P +
  gi|488600591|ref|YP_007907062.1| 438 VCRCGTKCVVKVvKDQWFLSYSNpeWKAKVLRHL--ENMRiVPEYYKEEFRNKIEW-LKDKACARRKGLGTRIPwD 510
                                       5567777776642567887776511555555666..33344888888888888888.9999999999999999943 PP

  == domain 4  score: 40.4 bits;  conditional E-value: 7.3e-14
                                       EGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS- CS
                      tRNA-synt_1g 289 gkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkD 363
                                       gkd +  H +f+    ++   e   p+++++++y+ +egkK+SkS+g + ++k a+  ++ad+ R y++++++ ++D
  gi|488600591|ref|YP_007907062.1| 592 GKDLVANHLLFFLFHHIAifPEELWPRAIAVNGYVSLEGKKMSKSKGPLLTMKRAVADYSADVTRMYILYTSEYDSD 668
                                       9***********9999998777779**************************************************** PP

                                       EEE-HHHH CS
                      tRNA-synt_1g 364 ldfswedf 371
                                       +d++ +++
  gi|488600591|ref|YP_007907062.1| 669 ADWRRKEV 676
                                       **998876 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 !   67.8   0.9     5e-22     1e-18       1     145 [.     706     826 ..     706     833 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 5e-22
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drw+ s+++++v+e++ a+e ++ ++a+++++  ++ d+ +wyl+                  ++l  +++ +l+ll
  gi|488600591|ref|YP_007907062.1| 706 DRWLMSRFQRIVRETNLAMEALQTRRAVNSAFFEMMADV-RWYLRRGG---------------KNLSVIIDDWLKLL 766
                                       9**************************************.****9853...............67899********* PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikps 145
                                       aPf+P+++Eelw    + l ++++i+ +++pe ++++ + e+ e + e+   i ++i++++++lk  ++
  gi|488600591|ref|YP_007907062.1| 767 APFIPHLCEELW----H-LRHDTFISTESYPEfDESKIDREA-ELSEEY---IKTLINDIKEILKFVKA 826
                                       ************....3.478899*******98887774444.447777...88888888888876655 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 !   46.2   0.1   1.8e-15   3.5e-12      12     126 ..     207     320 ..     204     346 .. 0.84
   2 ?   -1.1   0.0      0.59   1.2e+03     134     181 ..     361     417 ..     351     420 .. 0.59

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.8e-15
                     tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalapehplveklaekkkela.afieevkkksesereletkekeGvftgl 87 
                                       i+f++++ +  l   t rp+t+fGvt + l p   ++ ++ +++  ++ +  e++k ++++ + +++ + e +  g 
  gi|488600591|ref|YP_007907062.1| 207 IKFRLDDGT-ILPCATLRPETVFGVTNIWLKPTEYVIARVDDEQWLVSeEAFEKLKYTEKKVEFVRKINAEEL-FGK 281
                                       788888765.888999************************888877751556777777766666666665555.599 PP

                     tRNA-synt_1_2  88 kaihPitgekipiwvanyvlmeygtgavmavPahdqrDf 126
                                       +a++P+t++kipi  a++v ++  tg+vm+vPah   D+
  gi|488600591|ref|YP_007907062.1| 282 YATNPVTKDKIPILPAEFVDTDNATGVVMSVPAHAPYDY 320
                                       **********************************88876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.59
                     tRNA-synt_1_2 134 lpikqvik....pedee.kklee.seeayte...egilvnsg.efdglkskeakekia 181
                                       +p ++vi+    + d++  +le+ ++  y++   +g+l++ + e++g+k++++k+++ 
  gi|488600591|ref|YP_007907062.1| 361 VPAEKVIRelgiK-DQSdPELERaTKILYKKefhKGVLMDITgEYSGTKISQIKDRLQ 417
                                       6677777633322.222244443222222222339999998669****9999998765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   9.4e-05      0.19      21      54 ..      44      77 ..      33     159 .. 0.78
   2 !   26.6   0.0   1.8e-09   3.6e-06     207     298 ..     585     678 ..     574     681 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.4e-05
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEB CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvqfvqnv 54
                                       + h Gh+R++ + D ++r+++++gY+v f   +
  gi|488600591|ref|YP_007907062.1| 44 GNLHAGHTRTFTIGDAFARFMRMKGYNVLFPMGF 77
                                      578*************************996655 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.8e-09
                                       SEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHH.HH CS
                      tRNA-synt_1e 207 eidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRll.ll 281
                                        +d+ s G+DL+  h    l  + a f  + + +    ng++++eg+kmsks + ++t+k ++  +++ + R++ l+
  gi|488600591|ref|YP_007907062.1| 585 PVDLRSSGKDLVANHLLFFLFHHIAIFPeELWPRAIAVNGYVSLEGKKMSKSKGPLLTMKRAVADYSADVTRMYiLY 661
                                       68999*********************995678899999**********************************76267 PP

                                       SS-TTS-EEE-HHHHHH CS
                      tRNA-synt_1e 282 sahyrsqldfkeellee 298
                                       + +y s  d++ +++e+
  gi|488600591|ref|YP_007907062.1| 662 TSEYDSDADWRRKEVES 678
                                       899***99999888765 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 !   15.1   0.0   4.3e-06    0.0086      19      82 ..      30      93 ..      15     160 .. 0.66
   2 ?   -1.8   0.6       0.6   1.2e+03     126     184 ..     814     869 ..     784     915 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-06
                                      T-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHH CS
                      tRNA-synt_1d 19 kkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylek 82
                                      k k  +    P +  ++h+Gh r+  iGda +r + + Gy+v+        Gt    L+  ++k
  gi|488600591|ref|YP_007907062.1| 30 KPKFFITIPYPYLNGNLHAGHTRTFTIGDAFARFMRMKGYNVLFPMGFHVTGTPIIGLAELIQK 93
                                      5566666677888999**************************8644334445554444444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.6
                                       HCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC--CCCCCCCHHHHHHHHHCTT-EE CS
                      tRNA-synt_1d 126 qsgdedirklwkllvditrtelqklydrldvtlierGeslykeslneivkelkkkglvk 184
                                        ++ ++i k+ k    +  t  +  y++l v +   Ge   +  +++++ + k + l k
  gi|488600591|ref|YP_007907062.1| 814 INDIKEILKFVKAERVYLATADEWKYEALKVIS---GEKEVRSAIKKLMSDEKYRKLGK 869
                                       444444444444444444444444444444444...33333333333333333333332 PP

>> Ccdc124  Coiled-coil domain-containing protein 124 /Oxs1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.3e-05      0.11      57     117 ..     359     418 ..     313     421 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
                           Ccdc124  57 eAsgideaiaaLsvkkeekldrhpekrlkAaYka.feeeeLprlkeenpgLrlsQlkqllkk 117
                                       e    +++i  L++  +++ d   e+  k  Yk+ f +  L  +  e++g + sQ+k++l++
  gi|488600591|ref|YP_007907062.1| 359 EGVPAEKVIRELGI--KDQSDPELERATKILYKKeFHKGVLMDITGEYSGTKISQIKDRLQR 418
                                       44445788999999..577899**********754************************987 PP

>> O-FucT  GDP-fucose protein O-fucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.088   1.7e+02     240     272 ..     128     161 ..      93     205 .. 0.80
   2 ?    8.6   0.1   0.00068       1.4     227     282 ..     802     859 ..     766     887 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.088
                            O-FucT 240 eeialqlkgllkelkltsvfvAtdeiygge.elk 272
                                       +e+++++k++  +++ ++vf  tde+y+++ e +
  gi|488600591|ref|YP_007907062.1| 128 KEALKAMKDIGYSIDWRRVFTTTDETYQKFiEWQ 161
                                       5677888888888899***********9875544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00068
                            O-FucT 227 egkltpeecvpsleeialqlkgllkelkltsvfvAtd........eiyggeelkelkkefpnlv 282
                                       e +l++e+    +++++  +k++lk +k+++v++At         +  +ge  ke ++++++l+
  gi|488600591|ref|YP_007907062.1| 802 EAELSEEY----IKTLINDIKEILKFVKAERVYLATAdewkyealKVISGE--KEVRSAIKKLM 859
                                       33477777....89999999999999999*******966555555333333..45555555544 PP

>> RepB-RCR_reg  Replication regulatory protein RepB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00024      0.48      22      67 ..     851     896 ..     843     907 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                      RepB-RCR_reg  22 ltdaekqrlsvsrkklthkeikvfiknelkdslvqlCeeeGitqaq 67 
                                       + +a k+ +s  + +   ke++ f+kn  k++++++ +ee + +++
  gi|488600591|ref|YP_007907062.1| 851 VRSAIKKLMSDEKYRKLGKEVQNFVKNVIKEKITDFIDEEKLIKEN 896
                                       56788999999999999********************999877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (933 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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: 0.87u 0.31s 00:00:01.18 Elapsed: 00:00:00.55
# Mc/sec: 5096.55
//
Query:       gi|488600592|ref|YP_007907063.1|  [L=210]
Description: RNase HII [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  184.2   0.1    2.7e-54  184.0   0.1    1.0  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.0   0.1   1.5e-58   2.7e-54       1     197 [.       4     198 ..       4     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 184.0 bits;  conditional E-value: 1.5e-58
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH..SEEEEEEE-HHHHH.HHTTTS CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik..kkiekrklvaeeikyasenei 75 
                                       +GiDEaG+Gpv+Gp+vv++ a++k+r +el+ lgvkDSKkL+k++re++a+++k   +    k + ++++ + ++e 
  gi|488600592|ref|YP_007907063.1|   4 AGIDEAGKGPVIGPMVVCCYAIDKDRLNELERLGVKDSKKLTKKRREKIAEELKsiGSYRVLKFEPQQLD-ELMEEK 79 
                                       6*****************************************************3333333444444444.889999 PP

                                       -HHHHHHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHC.CEEEEETTGGGT-HHHHHHHHHHHHHHHH CS
                         RNase_HII  76 nlneikaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiik.ikvtvekkadekyllvaaASiiAkverde 151
                                       ++nei  ++ +++i++++++ v vd+ +v       +l++ l + +k  kv  e+kad ky++va ASiiAkverd 
  gi|488600592|ref|YP_007907063.1|  80 TINEILYDACEKLIRKVKPDMVFVDSFDVM----SSRLENRLGNTFKsCKVRCEHKADDKYPVVASASIIAKVERDK 152
                                       999999999999999998888888888887....7789999999***9***************************** PP

                                       HHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                         RNase_HII 152 elellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                       ++e+lk+ +g  d+gsGyasd++t  +l+++  +  + p ivr ++kt
  gi|488600592|ref|YP_007907063.1| 153 KIEKLKEIYG--DFGSGYASDPRTIDFLRDYLRKkgHFPPIVRKKWKT 198
                                       ********98..********************9989999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1333.89
//
Query:       gi|488600593|ref|YP_007907064.1|  [L=436]
Description: signal recognition particle subunit FFH/SRP54 (srp54) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-73  244.3   1.1    1.3e-72  243.5   1.1    1.4  1  SRP54            SRP54-type protein, GTPase domain
    2.3e-30  105.1   2.9    9.7e-30  103.1   2.8    2.1  1  SRP_SPB          Signal peptide binding domain
    1.3e-15   57.4   3.2    1.3e-15   57.4   3.2    2.7  1  SRP54_N          SRP54-type protein, helical bundle domain
    1.6e-06   28.2   0.0    4.9e-06   26.6   0.0    1.9  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.7e-05   24.5   0.8    7.6e-05   22.4   0.8    2.0  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    6.2e-05   22.8   0.7    0.00015   21.6   0.7    1.7  1  AAA_24           AAA domain
     0.0012   18.2   0.1     0.0038   16.6   0.0    1.9  2  6PF2K            6-phosphofructo-2-kinase
     0.0015   18.7   0.0     0.0027   17.9   0.0    1.5  1  AAA_33           AAA domain
     0.0019   18.5   0.1     0.0056   17.0   0.0    1.8  1  AAA_22           AAA domain
     0.0029   16.8   0.0     0.0058   15.8   0.0    1.9  1  G-alpha          G-protein alpha subunit
     0.0038   17.1   0.2      0.015   15.2   0.0    2.1  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0057   17.2   0.1      0.026   15.0   0.0    2.3  1  AAA_18           AAA domain
     0.0063   16.9   0.1     0.0063   16.9   0.1    3.2  4  AAA_17           AAA domain
     0.0067   16.5   0.2      0.032   14.3   0.2    2.2  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0072   16.6   0.3      0.069   13.5   0.0    2.7  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
  ------ inclusion threshold ------
      0.016   14.2   0.3      0.064   12.2   0.0    2.0  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.017   14.9   0.1      0.063   13.0   0.0    2.0  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.018   15.5   0.0      0.046   14.1   0.0    1.7  1  AAA_16           AAA ATPase domain
      0.018   14.9   0.0      0.035   14.0   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.025   14.0   0.0      0.052   13.0   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
      0.026   14.2   0.4      0.065   12.9   0.3    1.7  1  AAA_30           AAA domain
      0.027   14.4   3.5       0.09   12.7   0.1    2.6  2  NTPase_1         NTPase
      0.029   13.7   0.1      0.067   12.5   0.1    1.6  1  Zeta_toxin       Zeta toxin
       0.03   14.3   0.0      0.054   13.5   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
      0.072   12.8   0.2       0.64    9.8   0.1    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.09   12.2   0.3       0.27   10.7   0.3    1.8  1  Arf              ADP-ribosylation factor family
      0.095   12.7   0.0       0.18   11.7   0.0    1.6  1  DUF2400          Protein of unknown function (DUF2400)
      0.098   12.3   2.4       0.11   12.2   0.5    2.1  2  Thymidylate_kin  Thymidylate kinase
        0.1   11.5   0.1       0.18   10.6   0.1    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
        0.1   13.0   0.1       0.48   10.8   0.0    2.2  2  AAA              ATPase family associated with various cellul
       0.11   11.7   0.3       0.49    9.6   0.2    2.0  2  DUF1611          Domain of unknown function (DUF1611_C) P-loo
       0.13   12.0   1.4       0.29   10.8   0.1    2.2  1  PRK              Phosphoribulokinase / Uridine kinase family
       0.13   12.6   0.0       0.72   10.2   0.0    2.1  2  AAA_19           AAA domain
       0.16   11.1   1.0       0.29   10.2   0.4    1.7  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
       0.16   11.5   0.7       0.28   10.7   0.0    1.8  2  AAA_7            P-loop containing dynein motor region
       0.17   12.1   0.1       0.45   10.7   0.1    1.8  1  AAA_28           AAA domain
       0.18   11.0   7.5        2.7    7.1   0.3    3.5  4  ArsA_ATPase      Anion-transporting ATPase
       0.19   11.3   0.9        5.9    6.4   0.2    2.6  2  AAA_25           AAA domain
       0.25   11.2   8.3       0.84    9.5   1.0    3.1  2  AAA_31           AAA domain
       0.44   11.0   5.2         11    6.5   0.0    3.2  3  CelTOS           Cell-traversal protein for ookinetes and spo


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.5   1.1     3e-75   1.3e-72       3     196 .]      95     286 ..      93     286 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.5 bits;  conditional E-value: 3e-75
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeaveka 79 
                                        i+lvGlqG+GKTtt+aK+a+++k++g k+ +++aDt+R+aA++QLk+lae +++ +++ k+e+d+++++++++ek+
  gi|488600593|ref|YP_007907064.1|  95 KIMLVGLQGSGKTTTTAKMAKYFKDKGLKAGVITADTWRPAAYDQLKQLAEAYDIGFYGDKNEKDAVKIVRDGLEKM 171
                                       69*************************************************************************99 PP

                                       HHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSST CS
                             SRP54  80 keekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakg 156
                                       k+  +d++++DTaGr++ ++ l++e+ +i++v++pd +llvlda++gq a +qak+F++a+gi+g+++tk+Dg+akg
  gi|488600593|ref|YP_007907064.1| 172 KD--YDIIIIDTAGRHALEEGLINEMIEISRVANPDYKLLVLDAAIGQLASTQAKRFHDAIGIDGIVITKFDGTAKG 246
                                       98..************************************************************************* PP

                                       THHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 157 GaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       G+als+a+e+++Pi+f+g+Gek+ed+e+fdp  +vsrllg
  gi|488600593|ref|YP_007907064.1| 247 GGALSAAREIGIPIAFLGTGEKVEDFEKFDPAGFVSRLLG 286
                                       **************************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   2.8   2.2e-32   9.7e-30       1      99 []     315     416 ..     315     416 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 2.2e-32
                                       SSCTHHHHHHHHHHHCCCCCCHHHHCCC............H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHH CS
                           SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiP..gmsae.....akaeeeaekklkrieaiidSMTkeErdspekllkesR 70 
                                       +ftl+d+++q++ ++kmGp+sk+++m+P  g          + +e++++k++++++i+dSMT+eE ++p  ++++sR
  gi|488600593|ref|YP_007907064.1| 315 NFTLKDVYKQIEAMRKMGPVSKIIEMLPlgG---LglkidDDMMEATQEKMQKFKYIMDSMTEEEITNPA-IIDSSR 387
                                       59**************************433...23556533448889**********************.9999** PP

                                       HHHHHHHTTS-HHHHHHHHHHHHHHHHHT CS
                           SRP_SPB  71 krRiArGsGtsvqevnellkqfeqmkkmm 99 
                                       +rRiA GsGts q+v+ellk +++mk++m
  gi|488600593|ref|YP_007907064.1| 388 IRRIAIGSGTSPQDVKELLKYYKTMKSVM 416
                                       **************************987 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   3.2   2.9e-18   1.3e-15       4      75 .]       5      79 ..       3      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.9e-18
                                      HHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHHH CS
                           SRP54_N  4 klnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkdeL 75
                                       l+++++k++++s+id+ ++ee+++++++aLl aDV+v+ vk++ + +kk+a+  ++     + +++++kiv++eL
  gi|488600593|ref|YP_007907064.1|  5 ALKDVVRKIKSSSSIDKYLVEEIVRDIQRALLRADVNVRHVKQISDAIKKRALS-EDvlptFNVREHIIKIVYEEL 79
                                      6999**********************************************9999.555999899***********8 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 !   26.6   0.0   1.1e-08   4.9e-06       9      91 ..     103     247 ..     100     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.1e-08
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.............................. RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep.............................. 54 
                                       G+GKTt++a++a++++++gl+  ++ aD+ ++++   l++l     +                              
  gi|488600593|ref|YP_007907064.1| 103 GSGKTTTTAKMAKYFKDKGLKAGVITADTWRPAAYDqLKQLA----Eaydigfygdknekdavkivrdglekmkdyd 175
                                       99*******************************863522222....2345577777888888*************** PP

                                       ....................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-T CS
                                       ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....................................dlkrllellealgkkkalllkiagvvlnrvdgeneet 91 
                                                                           d+  +++l+++  k++ +++ i g+v++++dg +   
  gi|488600593|ref|YP_007907064.1| 176 iiiidtagrhaleeglinemieisrvanpdykllvlDA-AIGQLASTQAKRFHDAIGIDGIVITKFDGTAKGG 247
                                       *******************************9997766.44666666666766669999*******9986554 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 !   22.4   0.8   1.7e-07   7.6e-05       3     154 ..      96     244 ..      94     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.7e-07
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SS.CHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefge.vsiDaellretgveivelenGciCctlredllkeleal 76 
                                       ++l+G  GsGKTt   ++    + +glk  vi+ +     + D+  l++    +     G    + ++d++k +++ 
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAkyFKDKGLKAGVITADTWRpAAYDQ--LKQL---AEAYDIGFYGDKNEKDAVKIVRDG 167
                                       6899**************9887899***********95333333..3333...345567999999***********9 PP

                                       HHHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                              cobW  77 eereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                       +e+ +++d+i+i t G  a    ++ +  e+++ ++ d ++ v+Da ++ +  +++++ ++d +   d +v++K D 
  gi|488600593|ref|YP_007907064.1| 168 LEKMKDYDIIIIDTAGrHALEEGLINEMIEISRVANPDYKLLVLDA-AIGQLASTQAKRFHDAIGI-DGIVITKFDG 242
                                       99999***********877777777779******************.6667777888888888875.99999**997 PP

                                       HC CS
                              cobW 153 ld 154
                                         
  gi|488600593|ref|YP_007907064.1| 243 TA 244
                                       65 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.7   3.3e-07   0.00015       1      76 [.      92     184 ..      92     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.3e-07
                            AAA_24   1 kklkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..swedfldevvel................ 59 
                                       kk+ki+++G +g+GKTt+ +++  k +    +kGlk+  ++  ++ +  +++++++ +++                 
  gi|488600593|ref|YP_007907064.1|  92 KKAKIMLVGLQGSGKTTTTAKM-AKYF---KDKGLKA-GVITADTWRpaAYDQLKQLAEAYdigfygdknekdavki 163
                                       589*******************.3333...6777743.333333333336777777666669999************ PP

                            AAA_24  60 ....aaeladyktlviDtide 76 
                                            ++ +dy++++iDt++ 
  gi|488600593|ref|YP_007907064.1| 164 vrdgLEKMKDYDIIIIDTAGR 184
                                       ***99*************974 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.5e-06    0.0038      13      70 ..      93     156 ..      88     184 .. 0.75
   2 ?   -2.2   0.0       4.6     2e+03     124     154 ..     174     207 ..     148     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.5e-06
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS......---GGGGSTT- CS
                             6PF2K  13 klvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska......lsdaeffrpdn 70 
                                       k  i+lvGL   gKt+++ k+ +y k  g+++ v  +   r  a  +        d  f+  +n
  gi|488600593|ref|YP_007907064.1|  93 KAKIMLVGLQGSGKTTTTAKMAKYFKDKGLKAGVITADTWRPAAYDQlkqlaeAYDIGFYGDKN 156
                                       66799***************************99999999988877755544433444444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.6
                                       -EEEEEEEE...--HHHHHHHHHHHHTTTSGGGT CS
                             6PF2K 124 lkvlflesi...csdeeiikeNikevklsspDYk 154
                                       + ++++++    + +e +i+e i+   +  pDYk
  gi|488600593|ref|YP_007907064.1| 174 YDIIIIDTAgrhALEEGLINEMIEISRVANPDYK 207
                                       6667776651113467889999999999999998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     6e-06    0.0027       2      43 ..      96     142 ..      96     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqq 43 
                                       ++lvGl+GsGK+t   +++k  +     a +++ dt+r + + + +q
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAKYFKdkglkAGVITADTWRPAAYDQLKQ 142
                                       79***************97766666799********99988875554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.2e-05    0.0056       8     115 ..      96     198 ..      92     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                       ++++G  G+GKTt+ +++++ ++     +  +++v++ +   +    d l++l++a++ +  +  +++++ ++ +++
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAKYFK----DKGLKAGVITADTWRPA-AYDQLKQLAEAYDIGFYG-DKNEKDAVKIVRD 166
                                       789**************999984....23379999999999999.666669999999998888.99999999***** PP

                            AAA_22  85 alraravielliiDEaqh..lrseealeeLrsl 115
                                        l++ ++  ++iiD a +  l +e +++e  ++
  gi|488600593|ref|YP_007907064.1| 167 GLEKMKDYDIIIIDTAGRhaL-EEGLINEMIEI 198
                                       **999999******9866224.66666665555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-05    0.0058      23      80 ..      93     149 ..      46     424 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                                       EEEEEEEESTTSSHHHHHHHHHHHCS--.--HHHH.HC.CHHHHHHHHHHHHHHHHHHHHH CS
                           G-alpha  23 evkllllGqseSGKsTilkqlkllykkg.fseeel.at.wraviqlnivrsiktileales 80 
                                       + k++l+G ++SGK+T+  ++ +++k++  +   + a  wr+      ++++k++ ea++ 
  gi|488600593|ref|YP_007907064.1|  93 KAKIMLVGLQGSGKTTTTAKMAKYFKDKgLKAGVItADtWRP----AAYDQLKQLAEAYDI 149
                                       47**************98888877765535555443333666....555555666666655 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 !   15.2   0.0   3.3e-05     0.015       2      34 ..      96     128 ..      95     139 .. 0.92
   2 ?   -2.1   0.0       7.3   3.3e+03      81      96 ..     164     179 ..     149     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-05
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiK 34 
                                       + +vg +gsGKTt   k+ + +k++gl+ g+i 
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAKYFKDKGLKAGVIT 128
                                       679***************************996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.3
                              MobB  81 leellarlsevDlvlv 96 
                                       +++ l++++++D++++
  gi|488600593|ref|YP_007907064.1| 164 VRDGLEKMKDYDIIII 179
                                       4455666666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.9e-05     0.026       1      92 [.      96     192 ..      96     238 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.9e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...................gvnlrdvakenglllevdpealdeskrldedkld 58 
                                       I+l G +G+GKtt +   +k   f                    ++l+++a   ++ ++ d++        ++d ++
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAKY--FkdkglkagvitadtwrpaaYDQLKQLAEAYDIGFYGDKN--------EKDAVK 162
                                       89************9999886..2334556666777766666666666666666666666666........333333 PP

                            AAA_18  59 klldaleenssaleegknlvidghlaeleseaak 92 
                                        + d+le+    + + + ++id    + ++e ++
  gi|488600593|ref|YP_007907064.1| 163 IVRDGLEK----MKDYDIIIIDTAGRHALEEGLI 192
                                       33444444....3446666666666665555544 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       8.5   3.8e+03      30      35 ..      36      41 ..       5      76 .. 0.53
   2 !   16.9   0.1   1.4e-05    0.0063       1     114 [.      99     217 ..      99     229 .. 0.76
   3 ?   -1.7   0.0       8.1   3.6e+03      55      92 ..     291     328 ..     283     341 .. 0.73
   4 ?    0.7   0.2       1.4   6.4e+02      39      79 ..     346     386 ..     335     412 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8.5
                                      HHHHHH CS
                            AAA_17 30 lreeak 35
                                      lr+ ++
  gi|488600593|ref|YP_007907064.1| 36 LRADVN 41
                                      222222 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.4e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT...TSHSSHHHHC...TSHHHHHHHHHHHHHHHHHHHHHS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg...glakardemr...klpleekkelqkeaaekiaeeakk 71 
                                       +G+ GsGK+t  +k+++ ++ + l aG +  ++ ++    +l++  ++++       + +k+  k++ + ++++++ 
  gi|488600593|ref|YP_007907064.1|  99 VGLQGSGKTTTTAKMAKYFKDKGLKAGVITADTWRPAaydQLKQLAEAYDigfY-GDKNEKDAVKIVRDGLEKMKDY 174
                                       79*************************999999888833223333333333323.4455566788999999999999 PP

                                       SEEEEEE-SEEEETTEEEESSHHHHHHHH...SEEEEEE--HHH CS
                            AAA_17  72 kgvlvdghprikeqagfldglpkevleelkp.daiilleadpee 114
                                       + +++d+  r   ++g++ ++  e+ + ++p  ++++l+a   +
  gi|488600593|ref|YP_007907064.1| 175 DIIIIDTAGRHALEEGLINEMI-EISRVANPdYKLLVLDAAIGQ 217
                                       **********999999999988.589999994456667776655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 8.1
                                       HHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESS CS
                            AAA_17  55 kelqkeaaekiaeeakkkgvlvdghprikeqagfldgl 92 
                                       k+l++++++ +++e+ + ++ ++g +++k+  ++++ +
  gi|488600593|ref|YP_007907064.1| 291 KALLEKVERVVQQEDLDPEAFLKGNFTLKDVYKQIEAM 328
                                       66777788888888877778888888887777766655 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.4
                                       S.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
                            AAA_17  39 l.akardemrklpleekkelqkeaaekiaeeakkkgvlvdgh 79 
                                       l  k +d+m+++ +e+ +++   +++++ ee+ ++ +++d  
  gi|488600593|ref|YP_007907064.1| 346 LgLKIDDDMMEATQEKMQKFK-YIMDSMTEEEITNPAIIDSS 386
                                       444677888888877777754.56667777778888888865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2     7e-05     0.032       1      87 [.      95     217 ..      95     239 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-05
                                       EEEEEESTTSSHHHHHHHHHT....STEEESSSTTSSSSE.EEEEEEETTEE......................... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltg....ekaivsdkpgtTrdi.negrvklkgke......................... 47 
                                       ++++vG   +GK+t   ++ +    +  +++ +   T  +  + ++k    +                         
  gi|488600593|ref|YP_007907064.1|  95 KIMLVGLQGSGKTTTTAKMAKyfkdKGLKAGVITADTWRPaAYDQLK----Qlaeaydigfygdknekdavkivrdg 167
                                       5899***************9744331123333333333331222222....12223333333333444445555555 PP

                                       ........EEEEECGGCSSHHHHHHHHHHHHHHHHC.T..SEEEEEEETT..T CS
                          MMR_HSR1  48 ........ielvDtpGliegaseekglgkaflalee.a..dlillvvdas..e 87 
                                               i+++Dt+G   ++  e+gl +++ ++ + a  d  llv+da+  +
  gi|488600593|ref|YP_007907064.1| 168 lekmkdydIIIIDTAG---RHALEEGLINEMIEISRvAnpDYKLLVLDAAigQ 217
                                       55555555********...4477789999999877763569*******77431 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 ?   -0.9   0.1       4.7   2.1e+03      44      84 ..       5      41 ..       3      52 .. 0.65
   2 !   13.5   0.0   0.00015     0.069      11      62 ..     107     157 ..      94     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.7
                                      HHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGGTSE CS
                           PFOR_II 44 elkellkkvkkvvvldrnisfgseGqlveevkaalkkskvk 84
                                      +lk++++k+k+  ++d+         +v+++++al + +v+
  gi|488600593|ref|YP_007907064.1|  5 ALKDVVRKIKSSSSIDKYLV----EEIVRDIQRALLRADVN 41
                                      56666667777777777663....77888999888777333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S- CS
                           PFOR_II  11 vagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrni 62 
                                       +  t+ + ++ ++++g+k+G++   t rP  +++lk+l++ ++  +  d+n 
  gi|488600593|ref|YP_007907064.1| 107 T-TTTAKMAKYFKDKGLKAGVITADTWRPAAYDQLKQLAEAYDIGFYGDKNE 157
                                       2.344556789***************************99887766666665 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 ?   12.2   0.0   0.00014     0.064      31      66 ..      95     130 ..      87     136 .. 0.90
   2 ?   -1.6   0.0       2.3     1e+03     121     134 ..     173     186 ..     163     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                       EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB  31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                       ++ l G+ G+Gk t++ +++  ++++G + +v+  D
  gi|488600593|ref|YP_007907064.1|  95 KIMLVGLQGSGKTTTTAKMAKYFKDKGLKAGVITAD 130
                                       67789****************************988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                                       T-SEEEEEEESSTT CS
                              MeaB 121 GfDvvlietvGvGq 134
                                        +D+++i+t G   
  gi|488600593|ref|YP_007907064.1| 173 DYDIIIIDTAGRHA 186
                                       69*******99655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.063       2      33 ..      99     130 ..      98     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                       vG  GsGKtt + +++++++++g +  v+  D
  gi|488600593|ref|YP_007907064.1|  99 VGLQGSGKTTTTAKMAKYFKDKGLKAGVITAD 130
                                       899********************999998766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0    0.0001     0.046      27     121 ..      96     228 ..      89     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.0001
                            AAA_16  27 vllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekl 101
                                       ++l+G +G+GK++   + +++++++  ++ ++++++ +    ++y++l q++++   +   +d+ e++++   r+ l
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAKYFKDKglKAGVITADTWRP---AAYDQLKQLAEA-YDIGFYGDKNEKDAVKIVRDGL 168
                                       689*****************9999966455554444444...578888888855.7777777776666666665544 PP

                            AAA_16 102 eeala.........................................avpelagaeasrlle 121
                                       e+ ++                                         a+++la+ +a+r+++
  gi|488600593|ref|YP_007907064.1| 169 EK-MKdydiiiidtagrhaleeglinemieisrvanpdykllvldaAIGQLASTQAKRFHD 228
                                       44.3347776655555555555555555555555555555555556666666666666665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.7e-05     0.035       3      49 ..      94     140 ..      92     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-05
                                       EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                        APS_kinase   3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                       + ++l Gl gsGK+t + +++k+ ++kg ++ ++  d+ R   + +L
  gi|488600593|ref|YP_007907064.1|  94 AKIMLVGLQGSGKTTTTAKMAKYFKDKGLKAGVITADTWRPAAYDQL 140
                                       5689*****************************99999987666655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.052       4      41 ..      96     133 ..      94     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                       ++l Gl  sGK+t ++++ak++++++ +  vi  ++ +
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAKYFKDKGLKAGVITADTWR 133
                                       7899***************************9999877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   0.00015     0.065      22      99 ..      97     184 ..      91     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                            AAA_30  22 vltGpAGtGKttalkalreaweaag.grviglAptgkaAkv..Lae.....elgieastiakllkrlk......... 81 
                                       +l+G  G+GKtt+ +++++ ++++g +  ++ A t + A+   L++     ++g+ ++       +++         
  gi|488600593|ref|YP_007907064.1|  97 MLVGLQGSGKTTTTAKMAKYFKDKGlKAGVITADTWRPAAYdqLKQlaeayDIGFYGD-------KNEkdavkivrd 166
                                       789*********************8566678888888664322553222223333332.......222333334456 PP

                            AAA_30  82 grarlepgtllivDEagm 99 
                                       g +++++ +++i+D ag 
  gi|488600593|ref|YP_007907064.1| 167 GLEKMKDYDIIIIDTAGR 184
                                       555666678888888775 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1    0.0002      0.09       1      36 [.      95     129 ..      95     137 .. 0.86
   2 ?    2.0   0.1      0.38   1.7e+02      84     116 ..     163     194 ..     140     220 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEE CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyte 36 
                                       k+++ G +G+GKtT   k+++  k++g+k  G++t 
  gi|488600593|ref|YP_007907064.1|  95 KIMLVGLQGSGKTTTTAKMAKYFKDKGLKA-GVITA 129
                                       58999***********************96.55554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHH-EEEE---STTGGG-HHHHH CS
                          NTPase_1  84 lalealrkalseadviviDEiGkmElkskkfke 116
                                       ++ + l+k +++ d+i+iD  G+  l+   ++e
  gi|488600593|ref|YP_007907064.1| 163 IVRDGLEK-MKDYDIIIIDTAGRHALEEGLINE 194
                                       33333433.48899*****99986555544444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00015     0.067      16      58 ..      93     136 ..      88     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh 58 
                                       ++ i+l+G +G+GK+++ ++++++++ ++ ++ ++ +D+ R+  
  gi|488600593|ref|YP_007907064.1|  93 KAKIMLVGLQGSGKTTTTAKMAKYFKdKGLKAGVITADTWRPAA 136
                                       56799*******************99788888999999999765 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 ?   13.5   0.0   0.00012     0.054      21      54 ..      81     123 ..      12     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                                       ...........TTSEEEEEESTTSTHHHHHHHHHHHH-S.... CS
                            ResIII  21 s.........krdkrglikmaTGtGKTlvaaklierllkkgke 54 
                                                  ++ +++++   G+GKT + ak++++++ kg +
  gi|488600593|ref|YP_007907064.1|  81 RgigegldipLKKAKIMLVGLQGSGKTTTTAKMAKYFKDKGLK 123
                                       14444555555677999*****************999998653 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0014      0.64       2      22 ..      94     114 ..      93     146 .. 0.89
   2 ?    0.2   0.0       1.3   5.9e+02      40      61 ..     178     199 ..     154     253 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                         PduV-EutP   2 kkilliGkvgsGKttLtqalk 22 
                                        ki+l+G  gsGKtt t ++ 
  gi|488600593|ref|YP_007907064.1|  94 AKIMLVGLQGSGKTTTTAKMA 114
                                       59*************998775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                         PduV-EutP  40 viDtPGeylenrklysalivts 61 
                                       +iDt G ++ ++ l + +i +s
  gi|488600593|ref|YP_007907064.1| 178 IIDTAGRHALEEGLINEMIEIS 199
                                       4677776666666666666555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00059      0.27      13      35 ..      92     114 ..      81     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                                       TEEEEEEEESTTSSHHHHHHHHH CS
                               Arf  13 kelrilllGLDnaGKtTilkklk 35 
                                       k+++i+l+GL ++GKtT   k+ 
  gi|488600593|ref|YP_007907064.1|  92 KKAKIMLVGLQGSGKTTTTAKMA 114
                                       899**************887765 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00041      0.18       9      67 ..     269     328 ..     259     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00041
                           DUF2400   9 fkekedieiaallaallayGnrkqiikkleellelmdkspydfvl.eeeeekdlkelekf 67 
                                       +++ e  + a++++ ll  G  k++++k+e+++++ d +p++f++ + + ++  k++e++
  gi|488600593|ref|YP_007907064.1| 269 VEDFEKFDPAGFVSRLLGMGDIKALLEKVERVVQQEDLDPEAFLKgNFTLKDVYKQIEAM 328
                                       4444556679**********************************9888888877777664 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00024      0.11       3      28 ..     100     126 ..      98     131 .. 0.88
   2 ?   -2.6   0.1       8.5   3.8e+03     133     133 ..     389     389 ..     352     423 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                                       ESTTSSHHHHHHHHHHHHHHTTE..EE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.vv 28 
                                       Gl G+GKtt ++++++++k++g+k  v
  gi|488600593|ref|YP_007907064.1| 100 GLQGSGKTTTTAKMAKYFKDKGLKaGV 126
                                       99********************98644 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.5
                                       T CS
                   Thymidylate_kin 133 k 133
                                       +
  gi|488600593|ref|YP_007907064.1| 389 R 389
                                       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 ?   10.6   0.1   0.00041      0.18      15      46 ..      93     124 ..      85     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00041
                     TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdra 46 
                                       +++i++vG +GsGKt+++ k+ +  + +g +a
  gi|488600593|ref|YP_007907064.1|  93 KAKIMLVGLQGSGKTTTTAKMAKYFKDKGLKA 124
                                       678******************99999998554 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 ?   10.8   0.0    0.0011      0.48       1      68 [.      96     183 ..      96     208 .. 0.68
   2 ?   -1.3   0.0       6.3   2.8e+03     121     124 ..     384     388 ..     351     418 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                                       EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS.................STTHHHHHHHHHHHH.HHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg...vefleisgsellsk.................yvgesekkirelfke.akek 56 
                                       ++l+G  G GKT++   +ak ++    +   i + + +                   y  ++ek+  +++++ ++++
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAKYFKdkgLKAGVITADTWR-PaaydqlkqlaeaydigfYGDKNEKDAVKIVRDgLEKM 171
                                       689******************85222222222222222.12344455677778888777888888888888844555 PP

                                       STSEEEEEETGG CS
                               AAA  57 akpsilfiDEid 68 
                                       ++  i++iD + 
  gi|488600593|ref|YP_007907064.1| 172 KDYDIIIIDTAG 183
                                       544899998665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.3
                                       S.TTS CS
                               AAA 121 r.gRf 124
                                         +R+
  gi|488600593|ref|YP_007907064.1| 384 DsSRI 388
                                       22222 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0011      0.49      11      49 ..      92     129 ..      82     134 .. 0.82
   2 ?   -1.7   0.0       3.4   1.5e+03      36      51 ..     252     267 ..     250     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                           DUF1611  11 kakrvlvvGTdcavGKrttaleleealeerGlkaafvaT 49 
                                       k+ +++ vG  +  GK tt+ ++++ ++++Glka+++  
  gi|488600593|ref|YP_007907064.1|  92 KKAKIMLVGL-QGSGKTTTTAKMAKYFKDKGLKAGVITA 129
                                       5666777775.568********************99865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                           DUF1611  36 aleerGlkaafvaTgq 51 
                                       a++e G+ +af++Tg+
  gi|488600593|ref|YP_007907064.1| 252 AAREIGIPIAFLGTGE 267
                                       79999**********8 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00066      0.29       4      37 ..      98     131 ..      96     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00066
                               PRK   4 vagsSGaGkttvarklekifgrekvkaaeiegds 37 
                                       + g  G+Gktt+++k+ k f+ +++ka +i+ d 
  gi|488600593|ref|YP_007907064.1|  98 LVGLQGSGKTTTTAKMAKYFKDKGLKAGVITADT 131
                                       67888*********************98887664 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0016      0.72       9      62 ..      92     144 ..      87     234 .. 0.79
   2 ?   -0.4   0.0         3   1.4e+03      20      82 ..     286     352 ..     280     384 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                       k+  +++++  G+GKT+++ ++ +++++ g +k+  i++ +    A ++l++  
  gi|488600593|ref|YP_007907064.1|  92 KKAKIMLVGLQGSGKTTTTAKMAKYFKDKG-LKAGVITADTWRPAAYDQLKQLA 144
                                       5667889999********999988888877.66677776676666777776544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3
                            AAA_19  20 GtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal....ldfdd 82 
                                       G+G  + l ++v+ +v++++++pe +l   ft + + +  e+++++g   + i  l l    l++dd
  gi|488600593|ref|YP_007907064.1| 286 GMGDIKALLEKVERVVQQEDLDPEAFLKGNFTLKDVYKQIEAMRKMGPVSKIIEMLPLgglgLKIDD 352
                                       6777778889999999999999999999999988888888888777766665555544555533333 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00064      0.29      46      72 ..     102     128 ..      92     129 .. 0.91
   2 ?   -2.5   0.0       4.7   2.1e+03     288     297 ..     157     168 ..     156     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00064
                                       S-HSHHHHHHHHHHHTTTS..-EEEEE CS
                              LpxK  46 GGtGKTPlvialvkllqarglkvgvlS 72 
                                        G+GKT +++ ++k+++++glk+gv++
  gi|488600593|ref|YP_007907064.1| 102 QGSGKTTTTAKMAKYFKDKGLKAGVIT 128
                                       59***********************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                                       HHHHTTSTT... CS
                              LpxK 288 eKDavklaa..l 297
                                       eKDavk+ +  l
  gi|488600593|ref|YP_007907064.1| 157 EKDAVKIVRdgL 168
                                       677777764222 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00063      0.28      33      64 ..      93     124 ..      89     166 .. 0.82
   2 ?   -3.0   0.2       9.5   4.3e+03      80      95 ..     410     425 ..     404     430 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekyls 64 
                                       k +++lvG +G+GKt+++ ++ k ++++ ++ 
  gi|488600593|ref|YP_007907064.1|  93 KAKIMLVGLQGSGKTTTTAKMAKYFKDKGLKA 124
                                       6789****************999888666555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.5
                             AAA_7  80 diiesklekrrkgvyg 95 
                                       ++++s ++k +kg +g
  gi|488600593|ref|YP_007907064.1| 410 KTMKSVMKKMKKGKFG 425
                                       6788888888888887 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1     0.001      0.45       1      44 [.      95     145 ..      95     187 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                            AAA_28   1 kivitGgestGKTtlleaLaar....gyp..vv.pEaareileeklakged 44 
                                       ki+++G +++GKTt+++++a+     g +  v+ +++ r    ++l++  +
  gi|488600593|ref|YP_007907064.1|  95 KIMLVGLQGSGKTTTTAKMAKYfkdkGLKagVItADTWRPAAYDQLKQLAE 145
                                       799*****************7655554433355566666666666655555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.035        16       4      38 ..      96     130 ..      94     151 .. 0.90
   2 ?    1.7   0.0      0.27   1.2e+02     121     133 ..     170     182 ..     156     187 .. 0.84
   3 ?    7.1   0.3    0.0061       2.7     154     208 ..     323     379 ..     311     388 .. 0.77
   4 ?   -3.4   0.1       9.2   4.1e+03     141     157 ..     405     421 ..     398     427 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.035
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                       i++ G  G GKtt  a +a +  +kg k  +i+ D
  gi|488600593|ref|YP_007907064.1|  96 IMLVGLQGSGKTTTTAKMAKYFKDKGLKAGVITAD 130
                                       67788899********************9999998 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.27
                                       HCSSSSEEEEESB CS
                       ArsA_ATPase 121 keeeydvvvlDta 133
                                       k ++yd++++Dta
  gi|488600593|ref|YP_007907064.1| 170 KMKDYDIIIIDTA 182
                                       4689********9 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0061
                                       HHHHHHHHHHHHHHHHCCCSHCHHHHHH...HHHHHHHHHHHHHHHHHHHHTSTTTEE CS
                       ArsA_ATPase 154 klvklkeklsplakqlvkllglggvsie...ealeeleetkeeikkveeiltdperts 208
                                       k ++  +k++p++k + ++l+lgg  ++   +++e+ +e+++++k + + +t++e+t 
  gi|488600593|ref|YP_007907064.1| 323 KQIEAMRKMGPVSKII-EMLPLGGLGLKiddDMMEATQEKMQKFKYIMDSMTEEEITN 379
                                       3455556777877776.888998876666689***********************996 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 9.2
                                       GGGHHHHHHHHHHHHHH CS
                       ArsA_ATPase 141 llslpevleklleklvk 157
                                       ll+  ++++++++k+ k
  gi|488600593|ref|YP_007907064.1| 405 LLKYYKTMKSVMKKMKK 421
                                       44444455555554433 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.013       5.9      33      54 ..      93     114 ..      88     117 .. 0.88
   2 ?    2.7   0.0      0.18        82     131     153 ..     162     184 ..     128     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                            AAA_25  33 gelallaGapgtGKttlaldla 54 
                                       ++ ++l+G +g+GKtt +  +a
  gi|488600593|ref|YP_007907064.1|  93 KAKIMLVGLQGSGKTTTTAKMA 114
                                       6789************999887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                            AAA_25 131 daleaaieevegvrlvviDplsr 153
                                       + +++ +e++++++ ++iD+  r
  gi|488600593|ref|YP_007907064.1| 162 KIVRDGLEKMKDYDIIIIDTAGR 184
                                       44667788999999*****9866 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.0    0.0019      0.84      12      40 ..     103     131 ..      96     165 .. 0.88
   2 ?    5.0   0.6     0.046        21     105     126 ..     162     182 ..     141     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                       G GKTTt+ ++a+ +  +g k  ++ +D+
  gi|488600593|ref|YP_007907064.1| 103 GSGKTTTTAKMAKYFKDKGLKAGVITADT 131
                                       89*******************99999997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.046
                            AAA_31 105 eilkellekvkdeYDyiiiDcp 126
                                       +i+++ lek+k +YD+iiiD+ 
  gi|488600593|ref|YP_007907064.1| 162 KIVRDGLEKMK-DYDIIIIDTA 182
                                       44566677765.6*******85 PP

>> CelTOS  Cell-traversal protein for ookinetes and sporozoites
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.052        23      17      60 ..       6      50 ..       2      88 .. 0.73
   2 ?    6.5   0.0     0.024        11      36      81 ..     293     341 ..     287     344 .. 0.76
   3 ?   -1.9   0.1        10   4.5e+03      63      80 ..     400     419 ..     359     421 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.052
                            CelTOS 17 lseiira..dldskgdelvdliandlekelqknslvaasfLqsgfd 60
                                      l++++r+  +  s+   lv+ i++d+ ++l + + v++  +++  d
  gi|488600593|ref|YP_007907064.1|  6 LKDVVRKikSSSSIDKYLVEEIVRDIQRALLRAD-VNVRHVKQISD 50
                                      555555322455666789*************999.77666665433 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.024
                            CelTOS  36 iandlekelqknslvaasfLqsgfdvk...kkaKeiiKkvllevlksll 81 
                                       + + +e+++q+++l   +fL+ +f +k   k++ ++ K   ++ + ++l
  gi|488600593|ref|YP_007907064.1| 293 LLEKVERVVQQEDLDPEAFLKGNFTLKdvyKQIEAMRKMGPVSKIIEML 341
                                       66789****************9999995556666666666666555555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 10
                            CelTOS  63 kkaKeiiK..kvllevlksl 80 
                                       +++Ke  K  k++++v+k++
  gi|488600593|ref|YP_007907064.1| 400 QDVKELLKyyKTMKSVMKKM 419
                                       55666666556777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 3057.37
//
Query:       gi|488600594|ref|YP_007907065.1|  [L=518]
Description: Thioredoxin reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-41  141.2   3.4    5.3e-41  140.8   3.4    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    3.5e-29  100.7   0.0    6.4e-29   99.8   0.0    1.4  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    9.4e-12   44.8   0.2    1.6e-08   34.1   0.2    2.4  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    1.3e-11   44.5   1.2      4e-11   42.9   0.0    2.0  2  FAD_oxidored     FAD dependent oxidoreductase
    2.8e-11   43.8   2.0    0.00069   20.1   0.0    3.9  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    4.7e-11   42.8   1.7      5e-06   26.6   0.1    3.0  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    1.6e-10   41.1   4.6    0.00057   19.6   0.1    3.6  4  DAO              FAD dependent oxidoreductase
    1.3e-09   37.6   6.8    7.7e-06   25.2   0.1    4.1  4  FAD_binding_2    FAD binding domain
      1e-07   31.6   2.4     0.0011   18.4   0.0    2.5  3  FAD_binding_3    FAD binding domain
    1.5e-07   30.5   7.6      1e-05   24.4   0.3    3.6  4  HI0933_like      HI0933-like protein
    2.5e-07   30.2  10.8    2.7e-05   23.5   0.3    3.8  4  GIDA             Glucose inhibited division protein A
    6.9e-05   22.2   0.3    6.9e-05   22.2   0.3    3.6  3  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0001   22.7   0.4       0.64   10.5   0.1    2.4  2  NAD_binding_7    Putative NAD(P)-binding
    0.00018   20.9   0.7     0.0061   15.8   0.0    2.3  2  Thi4             Thi4 family
     0.0046   16.1   1.6       0.05   12.6   0.1    2.7  3  Lycopene_cycl    Lycopene cyclase protein
  ------ inclusion threshold ------
      0.012   15.5   1.1       0.19   11.6   0.0    2.3  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.023   14.3   1.0        5.6    6.5   0.0    2.6  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.029   14.0   1.6      0.055   13.1   0.2    2.0  2  ApbA             Ketopantoate reductase PanE/ApbA
      0.048   13.5   2.6      0.095   12.5   2.6    1.5  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
       0.15   12.1   0.0       0.26   11.3   0.0    1.4  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
       0.35   10.8   1.4        1.6    8.7   0.0    2.7  4  NAD_binding_9    FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   3.4   6.2e-44   5.3e-41       2     294 .]     165     466 ..     164     466 .. 0.86

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 6.2e-44
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.HCHHHHHHHHHHHHH.........HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.........xxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.skallgvaedaeias.........evvkklnqgie 68 
                                       d+++iGgGpAG++aa++ a+ gakvtl+ +e+ +l+g+ +  ++ + g+++++   +         ++v++l   i+
  gi|488600594|ref|YP_007907065.1| 165 DIAIIGGGPAGMSAAIFSARFGAKVTLM-DENPFLGGQLVKqTHRFFGSGKHRAGTRgikiaellrKEVEELD--ID 238
                                       89**************************.**********9954577777777766667*9**98886666665..55 PP

                                       CCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BC.....TCTTC.TTBEECCSECHHHHHHCCS CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  69 lllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssprdl.....gipGvaenvgklvrtldsaealklk 139
                                       ++++++v++i++g  + v+     +++  ki  +k+v+AtG+  r+l     ++pGv  ++  +v+tl+++ ++k  
  gi|488600594|ref|YP_007907065.1| 239 VRYETKVFGIYNGIiGAVER----DKKLLKIVPKKIVVATGAYERTLifennDLPGV--YGAGGVQTLMNVFGVKPG 309
                                       666666****9888555555....467889999*********888887899999***..777888************ PP

                                       S-TSEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 140 llpkrivvvGgGyiGvElAaalaklgke.vtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge 214
                                       ++    ++vG+G++G+ l+ +l+++g+e   +vea++r+        + ++++a  ++ Gv +++ +++k+++g+++
  gi|488600594|ref|YP_007907065.1| 310 NRG---LIVGSGNVGLILSYQLMQAGVEvSAVVEAMPRIG-------GYFVHAAKIRRlGVPIYVSHTIKRAIGKKK 376
                                       **9...**********************4459*******9.......888888777777*****************9 PP

                                       .......EEE...EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE...EETTEE..E--TTSBESSTTEEE-GG CS
                                       .......xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 .......kle...vvledgeeidadlvvvavGvrpstelleeklglel...derggi..vvdeflrtnvpgiyaiGD 276
                                              +le    v++++++id+d ++va+G++p +ell  ++g+++    e gg+  v ++f++t+v g+y++GD
  gi|488600594|ref|YP_007907065.1| 377 vegaeivRLEnwrEVEGSEKRIDCDFICVATGLSPTHELL-YQAGCQMkfvPELGGLvpVRNRFGETTVSGLYVAGD 452
                                       997766633344455555555*******************.*******8887889888899**************** PP

                                       GCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 277 vaggkggpelaqaAvqqG 294
                                       va    g+e a+ A+++G
  gi|488600594|ref|YP_007907065.1| 453 VA----GIEEATSAMMEG 466
                                       **....********9998 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 !   99.8   0.0   7.5e-32   6.4e-29       2      81 ..      15      95 ..      14      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 7.5e-32
                            Fer2_4  2 rpvtltfDGkevtvpeGdtvasAllangvdvp.rsckygrprgelcaggeCrnClVevegepnvracstpvedGlkvet 79
                                      r+vt++f+ k+++++eG+tvasAl+ang++++ rs+  +rprg +ca+g+C+ C++ev+g+pn+r c + v+dG+ ++t
  gi|488600594|ref|YP_007907065.1| 15 REVTIYFNQKPIKAYEGETVASALYANGITTFsRSFRFHRPRGFFCAIGKCSSCMMEVDGVPNIRVCKVYVRDGMMIRT 93
                                      79****************************999********************************************** PP

                            Fer2_4 80 qt 81
                                      q+
  gi|488600594|ref|YP_007907065.1| 94 QN 95
                                      *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 !   12.1   0.3   9.6e-05     0.082       2      27 ..     168     192 ..     139     206 .. 0.75
   2 !   34.1   0.2   1.9e-11   1.6e-08       2     305 .]     168     451 ..     166     451 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.6e-05
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylil 27 
                                       IiG+GPaG++aai   ++g  +++ +
  gi|488600594|ref|YP_007907065.1| 168 IIGGGPAGMSAAIFSARFGA-KVTLM 192
                                       77777777777777776666.34444 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 1.9e-11
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg.nignsiyrypkemtfispsftsekleipdlnaiseetspafslkeek 77 
                                       IiG+GPaG++aai   ++g  +++ ++ +  +g  + +  ++ +f+ +   +++ ++                    
  gi|488600594|ref|YP_007907065.1| 168 IIGGGPAGMSAAIFSARFGA-KVTLMDENpFLGGQLVK--QTHRFFGSG--KHRAGT-------------------- 219
                                       99999999999999999999.57777777577777765..677787743..222233.................... PP

                       Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkkedegfevetske..tyeAkkviiAtGefdkP...nklnipGeekl 149
                                        ++ +++e lr+ +++ +++++++++V  + +      ve +k+  ++  kk+++AtG +++    + ++ pG    
  gi|488600594|ref|YP_007907065.1| 220 -RGIKIAELLRKEVEELDIDVRYETKVFGIYNGI-IGAVERDKKllKIVPKKIVVATGAYERTlifENNDLPGVYGA 294
                                       .35568999*********************9764.56788888877999**********986522234456666555 PP

                       Pyr_redox_3 150 vkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrlee..lvke 224
                                         ++  ++ f    g++ +++G +n +    ++l+++g eV+ v++  ++        y + +    rl    +v++
  gi|488600594|ref|YP_007907065.1| 295 GGVQTLMNVFGVKPGNRGLIVGSGNVGLILSYQLMQAGVEVSAVVEAMPRIG-----GYFVHAAKIRRLGVpiYVSH 366
                                       56666667776688*******************************9976444.....34445544444443113333 PP

                       Pyr_redox_3 225 ekikvlfnaevkeikekeeeykvktedgkkvevkddvvla.tGykpdlsflkk....slfeldedgrpvlteeteet 296
                                       +  +++ +++v+  +    e + ++ +g++ +++ d++ + tG +p++++l +    ++f  +  g + + +   et
  gi|488600594|ref|YP_007907065.1| 367 TIKRAIGKKKVEGAEIVRLE-NWREVEGSEKRIDCDFICVaTGLSPTHELLYQagcqMKFVPELGGLVPVRNRFGET 442
                                       32234555555443332222.34444555566777777666**********99775444445566899999999*** PP

                       Pyr_redox_3 297 nvpglflaG 305
                                       +v+gl++aG
  gi|488600594|ref|YP_007907065.1| 443 TVSGLYVAG 451
                                       ********9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   4.7e-14     4e-11       1      58 [.     165     221 ..     165     269 .. 0.80
   2 ?    0.1   0.2      0.47     4e+02       3      41 ..     313     352 ..     313     372 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 4.7e-14
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtg 58 
                                       D+ ++GGgpaG+ AAi +ar Gakv L +e+++lGG+l ++    +   k +++ ++g
  gi|488600594|ref|YP_007907065.1| 165 DIAIIGGGPAGMSAAIFSARFGAKVTLMDENPFLGGQLVKQTHRFFGSGK-HRAGTRG 221
                                       9**************************************99965554433.4445555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakv.lLveergvlGGlltsg 41 
                                       ++vG+g  G++  ++  +aG +v ++ve  +++GG +  +
  gi|488600594|ref|YP_007907065.1| 313 LIVGSGNVGLILSYQLMQAGVEVsAVVEAMPRIGGYFVHA 352
                                       69*******************98579*********88765 PP

>> Pyr_redox  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   8.1e-07   0.00069       2      35 ..     166     199 ..     165     210 .. 0.89
   2 ?    3.3   0.0      0.14   1.2e+02      41      63 ..     223     245 ..     213     251 .. 0.89
   3 !   16.9   0.4   8.2e-06     0.007       2      74 ..     312     378 ..     311     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.1e-07
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       ++++GgG  g+ +A + a++g+kVt+++ ++ l 
  gi|488600594|ref|YP_007907065.1| 166 IAIIGGGPAGMSAAIFSARFGAKVTLMDENPFLG 199
                                       89**************************998776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHTTEEEECSEEE CS
                         Pyr_redox  41 easkilqeklekngievllntkv 63 
                                       +++++l++++e++ i+v+++tkv
  gi|488600594|ref|YP_007907065.1| 223 KIAELLRKEVEELDIDVRYETKV 245
                                       6899*****************98 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 8.2e-06
                                       EEEECSSHHHHHHHHHHHHTTSEE.EEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkV.tvversdkllrllDeeaskilqeklekngievllntkveeiegsedgve 74 
                                        ++vG+G++gl l   l + g +V  vve+++++          + + k++++g+ ++ ++++++  g+++ ve
  gi|488600594|ref|YP_007907065.1| 312 GLIVGSGNVGLILSYQLMQAGVEVsAVVEAMPRIG------GYFVHAAKIRRLGVPIYVSHTIKRAIGKKK-VE 378
                                       68**********************88*********......55566899***************9998777.44 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   5.9e-09     5e-06       1      40 [.     168     207 ..     168     230 .. 0.86
   2 !   14.2   0.2   4.4e-05     0.038       1      34 [.     314     348 ..     314     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.9e-09
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev 40 
                                       I+G+G +G++aA + a+ g++v+l + ++ lGG++   ++
  gi|488600594|ref|YP_007907065.1| 168 IIGGGPAGMSAAIFSARFGAKVTLMDENPFLGGQLVKQTH 207
                                       9********************************9876655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.4e-05
                                       EE--SHHHHHHHHHHHCCTEE.EEEE-SSSSSSGG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfd.vlllekrdrlGGr 34 
                                       IvG+G  Gl + y L +ag++   ++e+ +r+GG 
  gi|488600594|ref|YP_007907065.1| 314 IVGSGNVGLILSYQLMQAGVEvSAVVEAMPRIGGY 348
                                       9*******************94579********96 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   6.7e-07   0.00057       1      36 [.     165     201 ..     165     211 .. 0.92
   2 !   10.7   0.0   0.00033      0.28     149     207 ..     225     282 ..     211     302 .. 0.75
   3 !    9.9   0.8   0.00058      0.49       3      49 ..     313     361 ..     312     414 .. 0.73
   4 ?    0.5   0.0      0.41   3.5e+02     155     207 ..     354     415 ..     351     446 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.7e-07
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36 
                                       d++iiGGG +G+s+A + ar g  Vtl + ++++g g+
  gi|488600594|ref|YP_007907065.1| 165 DIAIIGGGPAGMSAAIFSARFGakVTLMDENPFLG-GQ 201
                                       8*****************99999********9999.65 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00033
                                       HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH CS
                               DAO 149 taalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.ll 207
                                       +  l++++e+l ++++++t+v g+  ++g ++ ver+++   ++  +++V+a+Ga+ + l+
  gi|488600594|ref|YP_007907065.1| 225 AELLRKEVEELDIDVRYETKVFGI--YNGIIGAVERDKKlLKIVP-KKIVVATGAYERtLI 282
                                       5568888*****************..5666777764444333345.78********66544 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00058
                                       EEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSEEEEESSSS CS
                               DAO   3 viiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrnsgllhsglr 49 
                                       +i+G+G +Gl   y+L ++g    +++e+ +++g g   +++++ + g+ 
  gi|488600594|ref|YP_007907065.1| 313 LIVGSGNVGLILSYQLMQAGvevSAVVEAMPRIG-GYFVHAAKIRRLGVP 361
                                       6*********************************.999999998887773 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.41
                                       HHHHTT-EEEESECEEE.EEEEETCEEEEE.......EECTEEEEEEEE..EEE--GGGHH.HH CS
                               DAO 155 aaealGveilegtevtg.leeedgkvwgve.......rttpgendaada..vVnaaGawsd.ll 207
                                       ++++lGv i+  +++++ + +  +kv g e       r+ +g+++++d+  + +a+G+  + +l
  gi|488600594|ref|YP_007907065.1| 354 KIRRLGVPIYVSHTIKRaIGK--KKVEGAEivrlenwREVEGSEKRIDCdfICVATGLSPThEL 415
                                       566667766666566553322..2344444444546533334443346666******9865533 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   9.1e-09   7.7e-06       1      39 [.     165     203 ..     165     213 .. 0.94
   2 !    8.3   0.1    0.0012         1     117     209 ..     199     284 ..     198     303 .. 0.82
   3 !    6.4   0.3    0.0049       4.1       3      36 ..     313     347 ..     312     396 .. 0.92
   4 ?   -0.5   0.0      0.58     5e+02     389     403 ..     441     455 ..     435     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 9.1e-09
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                       D+ +iG+G AG++AA+  a+ G+kv++++  +  gg+++
  gi|488600594|ref|YP_007907065.1| 165 DIAIIGGGPAGMSAAIFSARFGAKVTLMDENPFLGGQLV 203
                                       899******************************999865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0012
                                       TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES CS
                     FAD_binding_2 117 GglsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirak 193
                                       Gg+  + +t++  +  + ++ + g ++++ l ++++++++d++ +t++  +    +++ Gav e  ++++  +i+ k
  gi|488600594|ref|YP_007907065.1| 199 GGQLVK-QTHRFFGSGKHRAGTRGIKIAELLRKEVEELDIDVRYETKVFGI---YNGIIGAV-E--RDKKLLKIVPK 268
                                       666666.5666566655577788999*************************...67999995.5..69********* PP

                                       EEEE-----GG..... CS
                     FAD_binding_2 194 avvlatgGfgrallke 209
                                       ++v+atg+++r+l++e
  gi|488600594|ref|YP_007907065.1| 269 KIVVATGAYERTLIFE 284
                                       **********955544 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0049
                                       EEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGS CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGl.kvavvekeqefgg 36 
                                       +++GsG  GL  ++++ +aG    avve +++ gg
  gi|488600594|ref|YP_007907065.1| 313 LIVGSGNVGLILSYQLMQAGVeVSAVVEAMPRIGG 347
                                       79*******************6669*****99998 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.58
                                       EESSBTEEE-STCEE CS
                     FAD_binding_2 389 gqpipGLYAaGevaa 403
                                       +++++GLY aG va+
  gi|488600594|ref|YP_007907065.1| 441 ETTVSGLYVAGDVAG 455
                                       679**********93 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   0.0   1.2e-06    0.0011       2      31 ..     164     193 ..     163     196 .. 0.93
   2 !   12.1   0.7    0.0001     0.086       5      31 ..     313     340 ..     311     345 .. 0.85
   3 ?   -3.0   0.0       3.7   3.2e+03     144     163 ..     389     408 ..     357     411 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlve 31 
                                       td++I+G+GpaG+++a + ++ G +v+l +
  gi|488600594|ref|YP_007907065.1| 164 TDIAIIGGGPAGMSAAIFSARFGAKVTLMD 193
                                       899***********************9988 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0001
                                       EEE--SHHHHHHHHHHHHTTHHE.EEEE CS
                     FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrv.vlve 31 
                                       lIVG+G +Gl+l+  L +aGv+v  +ve
  gi|488600594|ref|YP_007907065.1| 313 LIVGSGNVGLILSYQLMQAGVEVsAVVE 340
                                       8*********************614565 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.7
                                       ECCTTEEEEEEEEEEEE--G CS
                     FAD_binding_3 144 dketgeeetvrakYlvGaDG 163
                                        + +g e++++++++  a G
  gi|488600594|ref|YP_007907065.1| 389 REVEGSEKRIDCDFICVATG 408
                                       45678999999999987766 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.3   1.2e-08     1e-05       2      36 ..     165     199 ..     164     205 .. 0.92
   2 !    5.5   0.0    0.0066       5.6     110     164 ..     223     276 ..     217     278 .. 0.84
   3 ?    2.5   0.4     0.056        48       4      36 ..     313     346 ..     311     353 .. 0.89
   4 ?   -2.4   0.0       1.7   1.5e+03     117     163 ..     353     408 ..     348     410 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-08
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       d+++iGgG+AG+ aAi  a+ g++V+l+++++ lg
  gi|488600594|ref|YP_007907065.1| 165 DIAIIGGGPAGMSAAIFSARFGAKVTLMDENPFLG 199
                                       89****************************98877 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0066
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE---- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGG 164
                                       +i ++l ke++e ++++r+et+v ++ +   g   v+  k+  ++  +k+v+AtG 
  gi|488600594|ref|YP_007907065.1| 223 KIAELLRKEVEELDIDVRYETKVFGIYNGIIG--AVERdKKLLKIVPKKIVVATGA 276
                                       7899**********************766555..444434788999********96 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.056
                                       EEE--SHHHHHHHHHHHHTT--E.EEE-SSSSS- CS
                       HI0933_like   4 iviGgGaAGlmaAisaakrgkrV.lllekakklg 36 
                                       +++G G  Gl  + ++ ++g +V +++e+++++g
  gi|488600594|ref|YP_007907065.1| 313 LIVGSGNVGLILSYQLMQAGVEVsAVVEAMPRIG 346
                                       69********************955999999998 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.7
                                       HHHHHHT-EEE-S--EEEE..ECETTE.EEEEE........TTEEEEESEEEE--- CS
                       HI0933_like 117 kelkeagvklrletevksv..ekeedgkfrvktk.......seeeleadklvlAtG 163
                                       +++++ gv +++++++k++  +k+ +g+  v+++       se+++ +d + +AtG
  gi|488600594|ref|YP_007907065.1| 353 AKIRRLGVPIYVSHTIKRAigKKKVEGAEIVRLEnwrevegSEKRIDCDFICVATG 408
                                       56788888888888888775533344444444433445555778888888888887 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   0.3   3.1e-08   2.7e-05       1      31 [.     165     195 ..     165     211 .. 0.86
   2 ?    5.0   0.1     0.013        11     112     157 ..     226     283 ..     214     289 .. 0.77
   3 ?   -1.1   0.1      0.87   7.4e+02       4      36 ..     314     346 ..     313     351 .. 0.88
   4 !    6.5   0.2    0.0044       3.7     354     386 ..     443     475 ..     435     479 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.1e-08
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithk 31 
                                       d+ +iGgG AG+ AA+ +ar Gakv+L+ ++
  gi|488600594|ref|YP_007907065.1| 165 DIAIIGGGPAGMSAAIFSARFGAKVTLMDEN 195
                                       789************************9544 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                                       EEEES-EEEEEECT..........TEEEEEEETTS-EEE..ECEEEE--TT-BT-EEE CS
                              GIDA 112 eiieeeveelivee..........kkvkgvvtedgetik..akavviatGtflkgkih 157
                                       e++++eveel+++           + + g v +d++ +k   k++v+atG++ +  i 
  gi|488600594|ref|YP_007907065.1| 226 ELLRKEVEELDIDVryetkvfgiyNGIIGAVERDKKLLKivPKKIVVATGAYERTLIF 283
                                       5778888888774488888888888888888888876542177********9988775 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.87
                                       EE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                              GIDA   4 ViGgGhAGceAAlaaarlGakvlLithkldtia 36 
                                       ++G G  G+  ++++ ++G++v  +++ + +i+
  gi|488600594|ref|YP_007907065.1| 314 IVGSGNVGLILSYQLMQAGVEVSAVVEAMPRIG 346
                                       89********************98888777765 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0044
                                       SSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHH CS
                              GIDA 354 kvkgLflAGqinGteGYeEaaaqGllAGinaar 386
                                       +v+gL++AG++ G e  + a+  G +AG+  a 
  gi|488600594|ref|YP_007907065.1| 443 TVSGLYVAGDVAGIEEATSAMMEGRIAGLDCAI 475
                                       689************8888999******98775 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   8.1e-08   6.9e-05      29      78 ..     164     221 ..     157     277 .. 0.80
   2 ?   -3.0   2.1       4.3   3.7e+03      22      42 ..     302     323 ..     293     355 .. 0.71
   3 ?   -0.2   0.1       0.6   5.1e+02      17      46 ..     447     477 ..     437     512 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.1e-08
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE........H CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev........l 78 
                                         + +iGgG aG++A+  ++++gakVt++D +p    ql +  ++f+           
  gi|488600594|ref|YP_007907065.1| 164 TDIAIIGGGPAGMSAAIFSARFGAKVTLMDENPFLGGQLVKQTHRFFGSgkhragtrG 221
                                       5789****************************98887777766666655455555543 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
                                       EETCB---.EEEEESTSHHHHH CS
                       AlaDh_PNT_C  22 gvpgvepa.kvlviGgGvaGlq 42 
                                        v gv+p+ + l++G G +Gl 
  gi|488600594|ref|YP_007907065.1| 302 NVFGVKPGnRGLIVGSGNVGLI 323
                                       566788873579*******984 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.6
                                       EETTCEETCB---EEEEESTSHHHHH.HHHH CS
                       AlaDh_PNT_C  17 gtlaGgvpgvepakvlviGgGvaGlq.Aiat 46 
                                         +aG v g+e+a+   + g +aGl  Ai+ 
  gi|488600594|ref|YP_007907065.1| 447 LYVAGDVAGIEEATSAMMEGRIAGLDcAIKL 477
                                       46799**************99**99725554 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 !   10.5   0.1   0.00075      0.64      10      43 ..     166     197 ..     163     274 .. 0.79
   2 !   10.1   0.0   0.00099      0.85       8      46 ..     310     381 ..     308     424 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00075
                     NAD_binding_7  10 vlvvGgGevAarkvrklleagakvtvvapevkee 43 
                                       + ++GgG+ +++ +   +++gakvt+++++   +
  gi|488600594|ref|YP_007907065.1| 166 IAIIGGGPAGMSAAIFSARFGAKVTLMDENP--F 197
                                       78*************************9993..3 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00099
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev.......keele.............................e 46 
                                        + l+vG G+v++   ++l++ag +v  v +++           +                             e
  gi|488600594|ref|YP_007907065.1| 310 NRGLIVGSGNVGLILSYQLMQAGVEVSAVVEAMpriggyfV---HaakirrlgvpiyvshtikraigkkkvegaE 381
                                       5679**********************999999755554431...1333445555554444444444444333332 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.1e-06    0.0061      16      55 ..     162     200 ..     150     209 .. 0.85
   2 ?    2.8   0.3     0.066        57      21      55 ..     313     347 ..     311     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.1e-06
                                       TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4  16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGG 55 
                                       + +D++i+G+G++G++aa   a+  + kv++++++  +GG
  gi|488600594|ref|YP_007907065.1| 162 IHTDIAIIGGGPAGMSAAIFSARF-GAKVTLMDENPFLGG 200
                                       569***************999998.******999877777 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.066
                                       EEE--SHHHHHHHHHHHHCTTS-E.EEEESSSS--T CS
                              Thi4  21 vivGaGssGLtaayylakkpdlkv.ailersvspGG 55 
                                       +ivG+G  GL  +y l ++ +++v a++e+   +GG
  gi|488600594|ref|YP_007907065.1| 313 LIVGSGNVGLILSYQLMQA-GVEVsAVVEAMPRIGG 347
                                       59***************99.8888457777766666 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   5.9e-05      0.05       1      34 [.     165     196 ..     165     206 .. 0.91
   2 ?    0.9   0.2      0.21   1.8e+02       3      35 ..     313     344 ..     313     372 .. 0.77
   3 ?   -0.8   0.0      0.71   6.1e+02     123     153 ..     390     418 ..     365     442 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieasp 34 
                                       D+++iG+GpAg+s A  +  a+ g kv+l++  p
  gi|488600594|ref|YP_007907065.1| 165 DIAIIGGGPAGMSAAIFS--ARFGAKVTLMDENP 196
                                       9************99999..*********98766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvv.lieasps 35 
                                       +++G+G  gl l  +l   ++g++v  ++ea p 
  gi|488600594|ref|YP_007907065.1| 313 LIVGSGNVGLILSYQL--MQAGVEVSaVVEAMPR 344
                                       59**************..6666766513455554 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.71
                     Lycopene_cycl 123 vleggr.kirarlvvdarglaslkkarrlglQ 153
                                        +eg + +i++ ++ +a+g   l++  +l++Q
  gi|488600594|ref|YP_007907065.1| 390 EVEGSEkRIDCDFICVATG---LSPTHELLYQ 418
                                       45555449***********...4445555555 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 ?   11.6   0.0   0.00023      0.19       2      32 ..     166     196 ..     165     243 .. 0.88
   2 ?    2.4   0.2      0.14   1.2e+02       4      28 ..     314     338 ..     313     358 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdise 32 
                                       +a+iG G  G + a   a+ g +V+l+d ++
  gi|488600594|ref|YP_007907065.1| 166 IAIIGGGPAGMSAAIFSARFGAKVTLMDENP 196
                                       8***************************976 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                                       EE--SCCHHHHHHHHHHTT-EEEEE CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlv 28 
                                       ++G+G +G  + +++++ag+eV  v
  gi|488600594|ref|YP_007907065.1| 314 IVGSGNVGLILSYQLMQAGVEVSAV 338
                                       89********************876 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0066       5.6       2      32 ..     165     195 ..     164     209 .. 0.94
   2 ?    5.5   0.4     0.013        11       5      36 ..     314     345 ..     311     428 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0066
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S- CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDid 32 
                                        i++iG G  G+  a+  a+ g +v+++D +
  gi|488600594|ref|YP_007907065.1| 165 DIAIIGGGPAGMSAAIFSARFGAKVTLMDEN 195
                                       59***************************88 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.013
                                       EE--STTHHHHHHHHHHCTSEEEEE-S-HHHH CS
                    UDPG_MGDP_dh_N   5 viGlGYvGlvtaavlaeighevigvDideekv 36 
                                       ++G+G vGl+ +  l ++g+ev  v     ++
  gi|488600594|ref|YP_007907065.1| 314 IVGSGNVGLILSYQLMQAGVEVSAVVEAMPRI 345
                                       89*******************98875555444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1         2   1.7e+03       1      31 [.     166     196 ..     166     212 .. 0.84
   2 ?   13.1   0.2   6.4e-05     0.055       2      29 ..     313     340 ..     313     361 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr 31 
                                       iai+G G  G   a   a+ ga+vtl++ ++
  gi|488600594|ref|YP_007907065.1| 166 IAIIGGGPAGMSAAIFSARFGAKVTLMDENP 196
                                       8999999999888888888999999998876 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.4e-05
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilr 29 
                                       +i+G+G +G +l ++L +ag +v  ++ 
  gi|488600594|ref|YP_007907065.1| 313 LIVGSGNVGLILSYQLMQAGVEVSAVVE 340
                                       69*********************99986 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.6   0.00011     0.095       6      31 ..      60      82 ..      56      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                      SSSSSS-TTEEEETTCTT.CEEETTT CS
                   DHODB_Fe-S_bind  6 CGvGaClgCvvktkggdggeykrvCk 31
                                      C++G C +C+++++g     + rvCk
  gi|488600594|ref|YP_007907065.1| 60 CAIGKCSSCMMEVDGV---PNIRVCK 82
                                      *************876...4899*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 ?   11.3   0.0    0.0003      0.26      44      79 ..      48      88 ..      10     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                            Fer2_3 44 ptlafr....asCregiCGscavainGkptl.aCtatikdl 79
                                      +++ f+      C  g C sc ++++G p++ +C+  ++d 
  gi|488600594|ref|YP_007907065.1| 48 RSFRFHrprgFFCAIGKCSSCMMEVDGVPNIrVCKVYVRDG 88
                                      555555444457****************9653899998875 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 ?    8.7   0.0    0.0019       1.6       1      44 [.     167     205 ..     167     209 .. 0.77
   2 ?   -2.4   0.0       4.8   4.1e+03       5      30 ..     217     239 ..     217     249 .. 0.76
   3 ?   -1.3   0.2       2.3     2e+03       2      19 ..     314     331 ..     313     342 .. 0.87
   4 ?   -2.5   0.0       5.4   4.6e+03     123     154 ..     381     408 ..     356     409 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwrt 44 
                                       ai+G+Gp+G++++   +     +   ++tl+d++++ g g+  ++
  gi|488600594|ref|YP_007907065.1| 167 AIIGGGPAGMSAAIFSA-----RFGAKVTLMDENPFlG-GQLVKQ 205
                                       8*********9986433.....3589999999999955.766555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                     NAD_binding_9   5 aGprGlavlerLlarakkkspleitl 30 
                                       aG rG+ ++e L ++    ++l+i++
  gi|488600594|ref|YP_007907065.1| 217 AGTRGIKIAELLRKEV---EELDIDV 239
                                       7999999998777774...7777766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.3
                     NAD_binding_9   2 ivGaGprGlavlerLlar 19 
                                       ivG G  Gl +  +L++ 
  gi|488600594|ref|YP_007907065.1| 314 IVGSGNVGLILSYQLMQA 331
                                       9**********9999986 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 5.4
                     NAD_binding_9 123 evvdleeradgqavlladgaslaadaVvLAlG 154
                                       e+v+le+     + ++ +++++++d + +A+G
  gi|488600594|ref|YP_007907065.1| 381 EIVRLENW----REVEGSEKRIDCDFICVATG 408
                                       44444433....23466778889999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        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):              21  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 3207.31
//
Query:       gi|488600595|ref|YP_007907066.1|  [L=159]
Description: hypothetical protein Asulf_01072 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   34.0  13.5    4.5e-08   32.6   3.0    2.7  3  Fer4      4Fe-4S binding domain
    1.7e-07   31.7   8.7    3.7e-07   30.6   8.7    1.6  1  Fer4_7    4Fe-4S dicluster domain
    2.8e-07   30.3  15.2    6.1e-07   29.3   2.4    2.6  3  Fer4_6    4Fe-4S binding domain
    6.3e-07   29.4  10.0    9.4e-07   28.9  10.0    1.3  1  Fer4_21   4Fe-4S dicluster domain
    1.4e-06   28.3  10.5    2.5e-06   27.5  10.5    1.5  1  Fer4_9    4Fe-4S dicluster domain
    1.5e-05   25.0  10.6    2.7e-05   24.2  10.6    1.5  1  Fer4_10   4Fe-4S dicluster domain
    0.00011   22.1   3.6    0.00011   22.1   3.6    2.4  2  Fer4_2    4Fe-4S binding domain
    0.00027   21.2   0.5    0.00027   21.2   0.5    2.3  2  Fer4_4    4Fe-4S binding domain
    0.00029   21.6  12.3      0.026   15.4   4.9    2.5  2  Fer4_3    4Fe-4S binding domain
     0.0014   19.5  10.3      0.029   15.3   2.7    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.016   15.7   0.8      0.016   15.7   0.8    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.034   14.9   0.2      0.034   14.9   0.2    2.5  2  Fer4_15   4Fe-4S single cluster domain
        0.1   13.4   4.0        0.1   13.4   4.0    1.8  2  Fer4_22   4Fe-4S dicluster domain
        2.8    8.5  12.3      0.065   13.7   2.8    2.2  2  Fer4_8    4Fe-4S dicluster domain
          3    8.1   9.4       0.28   11.4   1.3    2.1  2  Fer4_18   4Fe-4S dicluster domain
          7    7.3  13.1       0.64   10.6   2.7    2.5  2  Fer4_17   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.1   5.7e+03      17      21 ..      32      36 ..      31      37 .. 0.74
   2 !    8.0   1.2    0.0023       2.6      11      24 .]      39      52 ..      39      52 .. 0.89
   3 !   32.6   3.0   4.1e-11   4.5e-08       1      23 [.      60      82 ..      60      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.1
                                      HSTTT CS
                              Fer4 17 vCPvg 21
                                       CP +
  gi|488600595|ref|YP_007907066.1| 32 ECPQE 36
                                      69975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0023
                                      -THHHHHSTTTEEE CS
                              Fer4 11 CGaCvevCPvgAIt 24
                                      C  Cve C ++AI+
  gi|488600595|ref|YP_007907066.1| 39 CSPCVESCKYDAIE 52
                                      667**********6 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 4.1e-11
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +++d+ekC+gC++C++vCP  AI
  gi|488600595|ref|YP_007907066.1| 60 PKVDYEKCTGCMRCIKVCPGLAI 82
                                      689****************9998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   8.7   3.3e-10   3.7e-07       4      49 ..      38      78 ..      37      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.3e-10
                            Fer4_7  4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49
                                       C  Cv+ C+++aie+++      ++++++d+ekC+gC +C++vCP
  gi|488600595|ref|YP_007907066.1| 38 PCSPCVESCKYDAIEMKNI-----NDTPKVDYEKCTGCMRCIKVCP 78
                                      5***************987.....45688***************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   3.8    0.0045         5      10      24 .]      37      51 ..      31      51 .. 0.86
   2 !   29.3   2.4   5.4e-10   6.1e-07       2      20 ..      60      78 ..      59      82 .. 0.91
   3 ?   -2.9   0.0         8     9e+03       2       7 ..     142     147 ..     141     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0045
                            Fer4_6 10 igCgdCvrvCPegai 24
                                      i C +Cv  C ++ai
  gi|488600595|ref|YP_007907066.1| 37 IPCSPCVESCKYDAI 51
                                      36***********98 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 5.4e-10
                            Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                      + +d++kC+gC++C++vCP
  gi|488600595|ref|YP_007907066.1| 60 PKVDYEKCTGCMRCIKVCP 78
                                      78***************** PP

  == domain 3  score: -2.9 bits;  conditional E-value: 8
                            Fer4_6   2 veidpd 7  
                                       ve+dp 
  gi|488600595|ref|YP_007907066.1| 142 VEVDPA 147
                                       89**96 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9  10.0   8.3e-10   9.4e-07       4      52 ..      32      78 ..      29      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 8.3e-10
                           Fer4_21  4 dedkCigCgkCliaCedtshqaieidaktvl.kvvedeCvGCnlCssvCP 52
                                      +  + i C  C+ +C+   ++aie+++ + + kv  ++C+GC  C++vCP
  gi|488600595|ref|YP_007907066.1| 32 ECPQEIPCSPCVESCK---YDAIEMKNINDTpKVDYEKCTGCMRCIKVCP 78
                                      5556699*********...9***9997765516678************** 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  10.5   2.3e-09   2.5e-06       4      49 ..      38      80 ..      31      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.3e-09
                            Fer4_9  4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                       C  Cve+C+++++++++ + + +++    e+C+gC++C+++Cp  
  gi|488600595|ref|YP_007907066.1| 38 PCSPCVESCKYDAIEMKNINDTPKVDY---EKCTGCMRCIKVCPGL 80
                                      4*********************99966...58************75 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2  10.6   2.4e-08   2.7e-05      10      56 .]      37      78 ..      20      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.4e-08
                           Fer4_10 10 irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      i C  Cv++C     +++a++ ++++++ ++++ekCtgc  C+++CP
  gi|488600595|ref|YP_007907066.1| 37 IPCSPCVESC-----KYDAIEMKNINDTPKVDYEKCTGCMRCIKVCP 78
                                      78********.....79*****************************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 ?    3.3   3.2     0.089     1e+02      13      21 ..      39      47 ..      31      48 .. 0.83
   2 !   22.1   3.6   9.5e-08   0.00011       3      21 ..      60      78 ..      58      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.089
                            Fer4_2 13 CgaCvsaCP 21
                                      C++Cv +C 
  gi|488600595|ref|YP_007907066.1| 39 CSPCVESCK 47
                                      ********5 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 9.5e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      ++vd ++C+gC  C+++CP
  gi|488600595|ref|YP_007907066.1| 60 PKVDYEKCTGCMRCIKVCP 78
                                      689***************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 ?    1.9   3.9      0.38   4.3e+02       5      16 ..      31      48 ..      31      49 .. 0.87
   2 !   21.2   0.5   2.4e-07   0.00027       1      15 [.      64      78 ..      64      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.38
                            Fer4_4  5 igCgs......CvaaCPq 16
                                      i+C++      Cv +C++
  gi|488600595|ref|YP_007907066.1| 31 IECPQeipcspCVESCKY 48
                                      68999999999*****97 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.4e-07
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +e+C+gC++C+ +CP
  gi|488600595|ref|YP_007907066.1| 64 YEKCTGCMRCIKVCP 78
                                      59************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 !   10.5   0.8   0.00088      0.99       4      15 .]      39      50 ..      33      50 .. 0.94
   2 !   15.4   4.9   2.4e-05     0.026       1      13 [.      67      79 ..      67      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00088
                            Fer4_3  4 CgaCvevCPvgA 15
                                      C++Cve+C ++A
  gi|488600595|ref|YP_007907066.1| 39 CSPCVESCKYDA 50
                                      9*******9998 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.4e-05
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      CtgC++C +vCP 
  gi|488600595|ref|YP_007907066.1| 67 CTGCMRCIKVCPG 79
                                      ************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 !    7.1   3.0    0.0091        10       5      21 ..      39      58 ..      32      67 .. 0.74
   2 !   15.3   2.7   2.6e-05     0.029       1      17 [.      66      82 ..      66      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0091
                           Fer4_16  5 CgkCaevCPtnaikek...k 21
                                      C  C+e+C  +ai++k    
  gi|488600595|ref|YP_007907066.1| 39 CSPCVESCKYDAIEMKninD 58
                                      9*************993333 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.6e-05
                           Fer4_16  1 rCgtCgkCaevCPtnai 17
                                      +C++C +C++vCP  ai
  gi|488600595|ref|YP_007907066.1| 66 KCTGCMRCIKVCPGLAI 82
                                      5************9887 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.3   1.5e+03      37      55 ..      19      37 ..       8      38 .. 0.76
   2 ?   15.7   0.8   1.4e-05     0.016       1      17 [.      62      78 ..      62      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                           Fer4_13 37 seeekadaeeAadaCPves 55
                                      see  ++ + A+ +CP e+
  gi|488600595|ref|YP_007907066.1| 19 SEERLKKRNVAYIECPQEI 37
                                      4566677778999999875 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD ++C++c+ C +++P
  gi|488600595|ref|YP_007907066.1| 62 VDYEKCTGCMRCIKVCP 78
                                      899************** 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 ?   -0.8   0.7       2.4   2.7e+03      11      61 ..      39      48 ..      31      55 .. 0.65
   2 ?   14.9   0.2     3e-05     0.034       2      21 ..      61      80 ..      61      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.4
                           Fer4_15 11 cglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPv 61
                                      c  Cv+ +                                           
  gi|488600595|ref|YP_007907066.1| 39 CSPCVESC-----------------------------------------KY 48
                                      55565555.........................................44 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3e-05
                           Fer4_15  2 vvDrdaCigcglCvaeapev 21
                                      +vD ++C+gc +C++++p +
  gi|488600595|ref|YP_007907066.1| 61 KVDYEKCTGCMRCIKVCPGL 80
                                      59***************975 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6       3.3   3.7e+03      83      93 ..      37      47 ..      20      51 .. 0.70
   2 ?   13.4   4.0   9.2e-05       0.1      72      93 ..      57      78 ..      44      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.3
                           Fer4_22 83 vGCgRCieacp 93
                                      + C  C+e+c+
  gi|488600595|ref|YP_007907066.1| 37 IPCSPCVESCK 47
                                      44666666665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.2e-05
                           Fer4_22 72 efkekfgesgCvGCgRCieacp 93
                                      + + k++ ++C+GC RCi++cp
  gi|488600595|ref|YP_007907066.1| 57 NDTPKVDYEKCTGCMRCIKVCP 78
                                      445678999************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 ?    3.7  13.5     0.077        87      45      62 ..      61      78 ..      17      80 .. 0.77
   2 ?   13.7   2.8   5.8e-05     0.065       3      16 ..      65      78 ..      63     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.077
                            Fer4_8 45 eealwsCttcgaCtevCp 62
                                      +   ++Ct+c++C +vCp
  gi|488600595|ref|YP_007907066.1| 61 KVDYEKCTGCMRCIKVCP 78
                                      445789999999999999 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.8e-05
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      ekC++C++C + Cp
  gi|488600595|ref|YP_007907066.1| 65 EKCTGCMRCIKVCP 78
                                      45566666665555 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.5      0.24   2.7e+02      83      96 ..      31      47 ..      18      64 .. 0.68
   2 ?   11.4   1.3   0.00025      0.28      47      73 ..      53      79 ..      47      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.24
                           Fer4_18 83 lec...iscllcidacd 96
                                      +ec   i c+ c+++c+
  gi|488600595|ref|YP_007907066.1| 31 IECpqeIPCSPCVESCK 47
                                      44544467777777775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00025
                           Fer4_18 47 lkekeerkekgagdcidcescvkvcPt 73
                                      +k+ +++ + +  +c+ c  c+kvcP 
  gi|488600595|ref|YP_007907066.1| 53 MKNINDTPKVDYEKCTGCMRCIKVCPG 79
                                      45555666777889************4 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5  14.0      0.81     9e+02      42      57 ..      63      78 ..      32      80 .. 0.71
   2 ?   10.6   2.7   0.00057      0.64       1      17 [.      66      82 ..      66     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.81
                           Fer4_17 42 kaslCieCgeCerkCP 57
                                        ++C++C +C ++CP
  gi|488600595|ref|YP_007907066.1| 63 DYEKCTGCMRCIKVCP 78
                                      6789999999999998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00057
                           Fer4_17  1 rCiqCgyClpeCpsyea 17
                                      +C++C  C+++Cp +++
  gi|488600595|ref|YP_007907066.1| 66 KCTGCMRCIKVCPGLAI 82
                                      69999999999996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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):              16  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1130.33
//
Query:       gi|488600596|ref|YP_007907067.1|  [L=89]
Description: hypothetical protein Asulf_01073 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.9e-22   77.8   0.0    6.1e-22   77.8   0.0    1.0  1  SO_alpha_A3  Sarcosine oxidase A3 domain
    3.2e-15   56.2   1.7    4.4e-15   55.8   1.7    1.2  1  Fer2_BFD     BFD-like [2Fe-2S] binding domain


Domain annotation for each model (and alignments):
>> SO_alpha_A3  Sarcosine oxidase A3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   6.8e-26   6.1e-22       3      83 ..       4      84 ..       2      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 6.8e-26
                       SO_alpha_A3  3 rqFvdlqnDvtvkdielavregfesiehvKRYttlgmgtdQgklsavnaaaivaeltgkevaevgtttlRpPlapvkla 81
                                      r+ v+  +D+t+++i +a++egf++ie++KRYt++++g  Qgk   ++ ++i++++tgk+++e+g+tt+RpP+ pv+l 
  gi|488600596|ref|YP_007907067.1|  4 RRIVCRCEDITEEEIIHAIEEGFDNIESLKRYTGVTTGSCQGKGCLMHVLRILSQKTGKSLDEIGITTQRPPVNPVPLY 82
                                      7789999*********************************************************************997 PP

                       SO_alpha_A3 82 al 83
                                      +l
  gi|488600596|ref|YP_007907067.1| 83 IL 84
                                      76 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   1.7   4.9e-19   4.4e-15       1      50 [.       6      57 ..       6      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 4.9e-19
                          Fer2_BFD  1 iVCrCegvtegeIrdairraglttveevkrrtkagtg.Cgg..CrpaieeiLa 50
                                      iVCrCe++te+eI++ai ++g  ++e++kr+t+++tg C+g  C  ++ +iL 
  gi|488600596|ref|YP_007907067.1|  6 IVCRCEDITEEEIIHAI-EEGFDNIESLKRYTGVTTGsCQGkgCLMHVLRILS 57
                                      8****************.99*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.31s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 604.38
//
Query:       gi|488600597|ref|YP_007907068.1|  [L=356]
Description: Glycine/D-amino acid oxidases (deaminating) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-53  182.1   0.0    2.4e-53  181.9   0.0    1.0  1  DAO             FAD dependent oxidoreductase
    2.4e-08   33.5   0.0    4.5e-05   22.8   0.0    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      1e-07   32.0   0.1    2.6e-07   30.8   0.1    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.6e-07   29.0   0.1    7.9e-07   28.5   0.1    1.2  1  FAD_binding_2   FAD binding domain
    3.2e-06   26.1   0.2    0.00037   19.3   0.1    2.1  2  HI0933_like     HI0933-like protein
    1.2e-05   24.7   0.2    0.00025   20.4   0.1    2.1  2  FAD_binding_3   FAD binding domain
    0.00028   20.1   0.0    0.00043   19.5   0.0    1.3  1  GIDA            Glucose inhibited division protein A
    0.00089   18.6   0.1     0.0017   17.7   0.1    1.5  1  Thi4            Thi4 family
    0.00091   18.6   0.1     0.0015   17.8   0.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0011   19.5   1.2     0.0034   17.9   0.0    2.5  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.002   17.1   0.1          1    8.1   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.014   15.3   0.6      0.037   13.9   0.2    1.7  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.038   13.6   0.0      0.077   12.6   0.0    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.062   12.9   0.1       0.12   11.9   0.1    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.065   13.2   0.0        3.1    7.8   0.0    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
       0.16   11.2   0.0        2.2    7.5   0.0    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   0.0   2.2e-56   2.4e-53       2     352 .]       3     340 ..       2     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 2.2e-56
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       v +iG+G++Gl+ Ay+La+ g  Vt++ek+  +  gaSgrnsg +++ l   +   el++l+++++e +++ ++e +
  gi|488600597|ref|YP_007907068.1|   3 VGVIGAGVAGLFSAYFLAKNGaeVTVFEKR-YPLYGASGRNSGGITPMLG-RK---ELVKLAKRSIEIYDRTQSEVR 74 
                                       78****************************.6666************774.34...799****************** PP

                                       STTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHHHHH CS
                               DAO  77 ididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpakltaa 151
                                       +++ +r+ G+l +a ++e++++l+k++++++e+g++ + +d+ e++ l  +  + + + + fy ++g++ p+ ++++
  gi|488600597|ref|YP_007907068.1|  75 FNFLFRKDGYLKVAKTDEDMDKLEKEARMQKELGVKLREIDEYELKSLVDGfnT-KSVVGAFYGEGGVIFPWPVIWG 150
                                       ***************9999***********99***9999***889999987643.45555689999*********** PP

                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTTCTTTSEEEEEEEEEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gllkeldlpispvrgqvlv 226
                                       l r +++lGvei+ + ev  +e  + +   v  ++  ge+ ++d v n+ Gaws  + + l  l++  + v+ +++v
  gi|488600597|ref|YP_007907068.1| 151 LERGCKSLGVEIIPQKEVS-VEVSNSR-ISV--KAGnGEEYKFDFVLNCSGAWSASVnRSL-GLRCN-RIVKEEICV 221
                                       ***************8886.5555444.444..333377756799********98773333.56788.99******* PP

                                       EEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEE...EEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGG. CS
                               DAO 227 lkplseklvspaailpvpetdddgrgvyvtprkdgrvl...vGgtadeesgdddpevdeedidellealrklfPql. 299
                                       l+ l+        i+p+  + + ++gvy+ +++ g+v+   +G++    +++ + + +   + ++ + + +++P+l 
  gi|488600597|ref|YP_007907068.1| 222 LESLKP------FIDPY--IMNVSDGVYLSQSARGEVVggiIGSE---VDSPKT-SSSLSFLTKYAKLAVEMIPKLk 286
                                       *77655......55566..667789********9*9996644554...576777.8889999999**********85 PP

                                       .CGEEEEEEEEEEE.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 300 .gdvlrkwaGlrpl.pdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                         +vlr+waG+++   dglp++ge  +v+g++ + G ++ G+  apa G+++a++
  gi|488600597|ref|YP_007907068.1| 287 gLSVLRQWAGVYDSsGDGLPVVGE-DKVEGIIQLNGLGRQGMCIAPALGEIVADI 340
                                       56688********637********.5699************************95 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0     4e-08   4.5e-05       2      58 ..       2      72 ..       1     130 [. 0.59
   2 !    8.7   0.0   0.00079      0.89     193     253 ..     155     212 ..     150     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE........TTHCHHHCSHHHHCHHHHHHHHHHHHH..............H CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxx..............x RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve........legtclnggcllskallgvaedaeias..............e 58
                                      +v viG+G+AGl  a +la++ga+vt++e        ++++        s  ++ + +++e ++              e
  gi|488600597|ref|YP_007907068.1|  2 KVGVIGAGVAGLFSAYFLAKNGAEVTVFEkryplygaSGRN--------SGGITPMLGRKELVKlakrsieiydrtqsE 72
                                      788*************************5333333332222........444444444444444444444233343330 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00079
                                       HHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 193 lekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklgleld 253
                                        +  Gve+  +++v  ++  +++++v+ ++gee++ d v+ + G    +    ++lgl ++
  gi|488600597|ref|YP_007907068.1| 155 CKSLGVEIIPQKEV-SVEVSNSRISVKAGNGEEYKFDFVLNCSGAWSASVN--RSLGLRCN 212
                                       5677**********.6776677799*******************9888866..68888884 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   2.3e-10   2.6e-07       1      28 [.       5      32 ..       5      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.3e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      ++GaG++Gl  Ay+Lak+g++v+++ekr
  gi|488600597|ref|YP_007907068.1|  5 VIGAGVAGLFSAYFLAKNGAEVTVFEKR 32
                                      8**************************8 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   7.1e-10   7.9e-07       4      47 ..       5      48 ..       2      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 7.1e-10
                                      EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE- CS
                     FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgida 47
                                      ViG+G+AGL +A+ +a++G++v+v ek  +  ga+   +Ggi  
  gi|488600597|ref|YP_007907068.1|  5 VIGAGVAGLFSAYFLAKNGAEVTVFEKRYPLYGASGRNSGGITP 48
                                      9********************************99988888764 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   3.3e-07   0.00037       2      32 ..       2      32 ..       1      38 [. 0.93
   2 !    4.9   0.0    0.0079       8.9      48     166 ..      86     200 ..      54     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.3e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +v viG+G AGl+ A  +ak+g++V+++ek 
  gi|488600597|ref|YP_007907068.1|  2 KVGVIGAGVAGLFSAYFLAKNGAEVTVFEKR 32
                                      678**************************96 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0079
                                       EEEETT-SGGGEEES...STTTTHHHHHH...S-HHHHHHHHH.HTT--EEE-STTEEEETT.-CHHHHHHHHHHHH CS
                       HI0933_like  48 NvTnlseepeellsrypenpkflksalsr...ftnedlialve.elgvelkeedsgrlFpvsdkaedivdallkelk 120
                                        v  ++e++++l ++ ++ +k+l   l++   ++ + l++ ++ +  v  + ++ g +Fp       ++  l++ +k
  gi|488600597|ref|YP_007907068.1|  86 KVAKTDEDMDKLEKE-ARMQKELGVKLREideYELKSLVDGFNtKSVVGAFYGEGGVIFPWP-----VIWGLERGCK 156
                                       555555666666666.5556666555554000444444443331333456777888888887.....999******* PP

                                       HHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                       HI0933_like 121 eagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                       + gv++  ++ev+ ve ++++ ++vk+ ++ee++ d ++  +G  S
  gi|488600597|ref|YP_007907068.1| 157 SLGVEIIPQKEVS-VEVSNSR-ISVKAGNGEEYKFDFVLNCSGAWS 200
                                       ***********96.5565555.999999999999999988888776 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.2e-07   0.00025       3      35 ..       2      34 ..       1      48 [. 0.89
   2 ?    2.2   0.0     0.077        86     143     208 ..     177     245 ..     159     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      +V ++GaG aGl +a +L++ G +v++ ekr  
  gi|488600597|ref|YP_007907068.1|  2 KVGVIGAGVAGLFSAYFLAKNGAEVTVFEKRYP 34
                                      799***************************865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.077
                                       EECCTTEEEEEEEEEEEE--GTT-H.HHHHHTGG..EEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEE CS
                     FAD_binding_3 143 rdketgeeetvrakYlvGaDGgrSt.vrktlgie..fegeetvyeagvldvlfdadlsdiveplvlils 208
                                        + ++g+ e+ + +++  + G++S+ v ++lg++  ++ +e++  +++l+  +d  + ++ ++++l +s
  gi|488600597|ref|YP_007907068.1| 177 ISVKAGNGEEYKFDFVLNCSGAWSAsVNRSLGLRcnRIVKEEICVLESLKPFIDPYIMNVSDGVYLSQS 245
                                       36677888889999**********736678998755666777766666666666655545555555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.9e-07   0.00043       1     105 [.       2     107 ..       2     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.9e-07
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHE..EEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalggliikaadkag..iqfr 75 
                                       +v ViG+G AG+  A+ +a+ Ga+v+ + +++  +   s  +s ggi   l  +E+ +l    i++ d+++  ++f+
  gi|488600597|ref|YP_007907068.1|   2 KVGVIGAGVAGLFSAYFLAKNGAEVTVFEKRYP-LYGASGRNS-GGITPMLGRKELVKLAKRSIEIYDRTQseVRFN 76 
                                       588*************************55554.555555555.777777777888888888888888664226677 PP

                                       EESTTS-C.CC-EEEEEE-HHHHHHHHHHHH CS
                              GIDA  76 ilNrskGp.avralraqvdrelyskevtekl 105
                                        l r+ G   v ++   +d+ + +++++++l
  gi|488600597|ref|YP_007907068.1|  77 FLFRKDGYlKVAKTDEDMDKLEKEARMQKEL 107
                                       7777777424455555566666666666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.5e-06    0.0017      20      58 ..       3      40 ..       1      72 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                      v ++GaG +GL +ay lak+ + +v+++e++  + G ++
  gi|488600597|ref|YP_007907068.1|  3 VGVIGAGVAGLFSAYFLAKN-GAEVTVFEKRYPLYGASG 40
                                      779*****************.*********988776544 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 !   17.8   0.1   1.4e-06    0.0015      30      61 ..       2      33 ..       1      40 [. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                      kv viG+GvaGl ++   ++ ga+Vtv+++r 
  gi|488600597|ref|YP_007907068.1|  2 KVGVIGAGVAGLFSAYFLAKNGAEVTVFEKRY 33
                                      799**************************986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     3e-06    0.0034       1      31 [.       2      32 ..       2      71 .. 0.91
   2 ?   -2.9   0.1       9.1     1e+04      36      57 ..      88     111 ..      78     114 .. 0.55
   3 ?   -1.8   0.0       4.2   4.7e+03      51      64 ..     156     169 ..     151     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                      kv v+G+G+ gl  A +la+ g++Vtv+e +
  gi|488600597|ref|YP_007907068.1|  2 KVGVIGAGVAGLFSAYFLAKNGAEVTVFEKR 32
                                      688*************************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.1
                                       TTSSHHHHHHH.HHHHHHT.TEEE CS
                         Pyr_redox  36 rllDeeaskil.qeklekn.giev 57 
                                        + De++ k+  + +++k+ g+++
  gi|488600597|ref|YP_007907068.1|  88 AKTDEDMDKLEkEARMQKElGVKL 111
                                       556666666552233333346665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.2
                                       HHTTEEEECSEEEE CS
                         Pyr_redox  51 ekngievllntkve 64 
                                       + +g+e++ +++v 
  gi|488600597|ref|YP_007907068.1| 156 KSLGVEIIPQKEVS 169
                                       67899999999874 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0021       2.4       1      33 [.       2      31 ..       2      37 .. 0.91
   2 !    8.1   0.0   0.00092         1     162     219 ..     153     208 ..     149     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0021
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      k+ ++G+G aG  +A  lak +   +evt+ e+
  gi|488600597|ref|YP_007907068.1|  2 KVGVIGAGVAGLFSAYFLAKNG---AEVTVFEK 31
                                      699*****************99...88999887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00092
                                       HHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT- CS
                    Trp_halogenase 162 rvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLk 219
                                       r  ++ Gv+++  k v+v++ ++    s++  +g+e+++d+++ csG  +  +++ L 
  gi|488600597|ref|YP_007907068.1| 153 RGCKSLGVEIIPQKEVSVEVSNS--RISVKAGNGEEYKFDFVLNCSGAWSASVNRSLG 208
                                       55667788888888777766653..34788999**************99988887765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.3e-05     0.037       1      30 [.       2      31 ..       2      34 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdi 30
                                      kv+viGaG+ G   a+ +a++g eV++++ 
  gi|488600597|ref|YP_007907068.1|  2 KVGVIGAGVAGLFSAYFLAKNGAEVTVFEK 31
                                      79************************9875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.9e-05     0.077       1      29 [.       3      31 ..       3      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.9e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilr 29
                                      + ++GaG  G + a+ Lak+ga+vt+  +
  gi|488600597|ref|YP_007907068.1|  3 VGVIGAGVAGLFSAYFLAKNGAEVTVFEK 31
                                      579*********************98755 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00011      0.12       1      28 [.       1      28 [.       1      32 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      SEEEEE--STTHHHHHHHHHHCTSEEEE CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevig 28
                                      mk+ viG+G  Gl +a  la+ g ev++
  gi|488600597|ref|YP_007907068.1|  1 MKVGVIGAGVAGLFSAYFLAKNGAEVTV 28
                                      89************************97 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0028       3.1       2      37 ..       5      37 ..       4      44 .. 0.84
   2 ?    3.0   0.0     0.082        92     114     154 ..     157     197 ..     149     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0028
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdp.sep.g 37
                                      ++GaG++Gl  +  L+++       e+t+f++ +++ g
  gi|488600597|ref|YP_007907068.1|  5 VIGAGVAGLFSAYFLAKN-----GAEVTVFEKrYPLyG 37
                                      8***************99.....59******9555533 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.082
                     NAD_binding_9 114 gvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       ++ ve++ ++ v++e ++++  v   +g+++++d V  + G
  gi|488600597|ref|YP_007907068.1| 157 SLGVEIIPQKEVSVEVSNSRISVKAGNGEEYKFDFVLNCSG 197
                                       56799999999*************************99988 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.002       2.2       1      23 [.      10      32 ..      10      33 .. 0.95
   2 ?    1.7   0.0      0.11   1.2e+02     230     264 ..     166     200 ..      91     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.002
                                      HHHHHHHHHHHHTTEEEEEEESS CS
                     Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEar 23
                                      +aGL  A+ L+ +G +Vtv+E r
  gi|488600597|ref|YP_007907068.1| 10 VAGLFSAYFLAKNGAEVTVFEKR 32
                                      69*******************87 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                                       EEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHH CS
                     Amino_oxidase 230 rVkeikregdgvtvtledgevveaDaVvvTvplgv 264
                                       +  +++ +++ ++v+  +ge++++D V+ ++  + 
  gi|488600597|ref|YP_007907068.1| 166 KEVSVEVSNSRISVKAGNGEEYKFDFVLNCSGAWS 200
                                       33467789999***************987766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2134.88
//
Query:       gi|488600598|ref|YP_007907069.1|  [L=163]
Description: hydrogenase maturation protease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-13   50.0   0.1    3.1e-13   49.7   0.1    1.2  1  HycI           Hydrogenase maturation protease
  ------ inclusion threshold ------
      0.035   13.0   0.0      0.056   12.4   0.0    1.3  1  Peptidase_A25  Germination protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.1   3.4e-17   3.1e-13      27     129 ..      43     144 ..      20     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.4e-17
                                       GGGHHHHCC-SEEEEEEE--SSS-TT-EEEEECCHHHHHHTTC.CGCCCHCHHHHHHH.HHHC.CS--SEEEEEEE- CS
                              HycI  27 lelvgtleeadkliivDavdfglepGevkiikddevpkklkakkmsaHqlplaevlkl.leek.geipkevillgvq 101
                                       ++ ++++  +d  iivDa+  g+epG+++ +  de   +  ++   +H ++l  +l+  +e + +e+p  + +++v+
  gi|488600598|ref|YP_007907069.1|  43 FDVLDKILGYDLAIIVDAIRLGNEPGTIYEFSHDEFS-FIPFS--GTHGMNLITTLRVgMEVFgEEMPGDIRIIAVE 116
                                       677889999***************************9.67777..8***********834444268*********** PP

                                       -S-BST.CCS--HHHHCCHHHHHHHCCC CS
                              HycI 102 pesledvgielseevkkavekavelile 129
                                        e++e +g + +++vk+a++k+ve i+e
  gi|488600598|ref|YP_007907069.1| 117 VEDVESFGRDCTPKVKAAIPKVVERITE 144
                                       *************************986 PP

>> Peptidase_A25  Germination protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.2e-06     0.056      98     122 ..       2      26 ..       1      37 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-06
                     Peptidase_A25  98 sclvvGlGnwnvtPdalGPlvvenl 122
                                       +c++vG+Gn n+  dalG  v+e++
  gi|488600598|ref|YP_007907069.1|   2 KCVIVGIGNPNLCDDALGIRVIEEI 26 
                                       7********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1084.90
//
Query:       gi|488600599|ref|YP_007907070.1|  [L=485]
Description: F420-non-reducing hydrogenase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  108.4   0.0    1.1e-14   54.3   0.0    3.1  3  NiFeSe_Hases  Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0     6e-19   1.1e-14       1      79 [.      38     116 ..      38     129 .. 0.95
   2 !   13.3   0.0   1.6e-06     0.028     155     243 ..     142     229 ..     135     254 .. 0.81
   3 !   37.2   0.0   8.8e-14   1.6e-09     331     505 .]     298     459 ..     291     459 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 6e-19
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTTGGG CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLhalD 77 
                                       RG E++l g   +++   v+ iCGVC  vH +a+++a +  +g+++++ a+ ir+l   a++++dh v +Y L   D
  gi|488600599|ref|YP_007907070.1|  38 RGYEKFLAGLPIEEVPRTVSTICGVCRGVHHTAATKASDGVYGVEPTETAKKIRELFLNAHYVEDHAVILYALGLPD 114
                                       9**************************************************************************** PP

                                       TS CS
                      NiFeSe_Hases  78 wv 79 
                                       +v
  gi|488600599|ref|YP_007907070.1| 115 FV 116
                                       99 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTGGGGC CS
                      NiFeSe_Hases 155 eaLelqrkaakivaifggknPhpqslvvGGvtcaidllnaerlaevkslikevkefveevylpDvlaiakaYkdwak 231
                                       e L+ ++ a+ki  ++ggk  hp + + GG + +i+  + ++++++ + + e+ +   + +++Dv++  + Y + ++
  gi|488600599|ref|YP_007907070.1| 142 EILKKRKCAVKIFELLGGKPIHPVAGLPGGWSKKIEENERQEIEKLAKELVELGQITLQ-IFEDVILKNEKYMELVT 217
                                       57899999**************************8888888888888888777776555.57999999999998877 PP

                                       S--GGGGT-EEE CS
                      NiFeSe_Hases 232 igkglgkknfls 243
                                        +   ++ n++ 
  gi|488600599|ref|YP_007907070.1| 218 GDLYRTVLNYMG 229
                                       665555556654 PP

  == domain 3  score: 37.2 bits;  conditional E-value: 8.8e-14
                                       -BESHHHHHHHHHHTT-HHHHHHHHHHHHHHT-HGGGGSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTB--- CS
                      NiFeSe_Hases 331 mevGplarvlvayakgkeevkelvdkllkklglkvealfstlGRtaaRaleakliaellkewldelvenikkgdtet 407
                                       + vGpl r+ v+   +++ ++e+ +k+++ lg k+++   +l  + aRa+e   +ae++ e  ++  e+i++ d ++
  gi|488600599|ref|YP_007907070.1| 298 YSVGPLPRLNVSEGMNTPLAQEHYEKMFEVLGEKPAH--YILSFHWARAIELLNAAERVLELAQD--ESITNSDVRA 370
                                       689***********9999************9999855..57889*******99888887766553..3333333222 PP

                                       B--TT-SGGGS-SEEEEEEEEEETTEEEEEEEEEETT.EEEEEEEE-HHHHHH--S-TT----HHHHHHTT-B-SST CS
                      NiFeSe_Hases 408 aneekldkkevpkeakGvglveapRGaLsHwikikdg.kienYqavvPsTWnasPrdakgqkgayEaaLigtpvadp 483
                                               +  + + +Gvg++eapRG+L H+ k +d+  +e+ +++v +T n +  + + ++ a  + + + ++   
  gi|488600599|ref|YP_007907070.1| 371 --------ELGEVTGEGVGILEAPRGTLIHHYKTDDRgIVEEANLIVATTHNNAAINLAIRN-AAKKFVKNGEID-- 436
                                       ........22234689******************88626799***********999877655.556777777774.. PP

                                       TS-HHHHH.HHHHT--BHHHHH- CS
                      NiFeSe_Hases 484 ekPleilr.tihSfDPClACavH 505
                                       ek l+ +    + +D ClACa+H
  gi|488600599|ref|YP_007907070.1| 437 EKILNYVEmAFRPYDLCLACATH 459
                                       455555541589**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2752.25
//
Query:       gi|488600600|ref|YP_007907071.1|  [L=317]
Description: F420-non-reducing hydrogenase subunit G [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   96.4   0.0    1.8e-27   95.7   0.0    1.3  1  Oxidored_q6     NADH ubiquinone oxidoreductase, 20 Kd subunit
  ------ inclusion threshold ------
      0.076   12.5   0.0       0.13   11.7   0.0    1.3  1  Allexi_40kDa    Allexivirus 40kDa protein


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 !   95.7   0.0     2e-31   1.8e-27       1     130 [.      14     180 ..      14     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 2e-31
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHH.HHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskee.eieakekeadvlvveGavtrkpkealellkelaekakav 76 
                                       C+Gc+++l +l+e+l+d+le ie+++  +++ d k++  ++ ++k +dv++v+Gav  +  e+ +++k l++k k++
  gi|488600600|ref|YP_007907071.1|  14 CAGCEMALVDLSEKLIDALENIEIVWWTPTVVDLKYKdLENLEDKSIDVALVDGAV--RLSEQEHVIKILRQKTKVL 88 
                                       **************************99999999999755567789**********..99***************** PP

                                       EEESHHHHH-TGGGSTT-TEE......................................-HHHHHHHC.S-E.EEE- CS
                       Oxidored_q6  77 iavGtCAafGGipaaannpsv......................................geevgellevvpvdinip 115
                                       +a+G+CAa+GG+p++an +++                                        ev++l++vv+vd++i 
  gi|488600600|ref|YP_007907071.1|  89 VAFGACAAMGGVPGLANFHKReelletayintwstdnpdgvlpqteydvngskltlpefYGEVKALHQVVDVDYFIG 165
                                       *****************8866789999******************9999998887776625889************* PP

                                       SSS--HHHHHHHHHH CS
                       Oxidored_q6 116 GCPphpeailetlla 130
                                       GCPph ++++ ++ a
  gi|488600600|ref|YP_007907071.1| 166 GCPPHHDHVAVAVEA 180
                                       ********9988765 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.5e-05      0.13      15      48 ..     123     156 ..     113     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.5e-05
                      Allexi_40kDa  15 trnLlgyvPParynlPpatLPldeLyGqLhaLhq 48 
                                       t n  g +P + y++  + L l e+yG + aLhq
  gi|488600600|ref|YP_007907071.1| 123 TDNPDGVLPQTEYDVNGSKLTLPEFYGEVKALHQ 156
                                       55555779*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1874.85
//
Query:       gi|488600601|ref|YP_007907072.1|  [L=133]
Description: F420-non-reducing hydrogenase subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-51  171.3   0.0    8.3e-51  171.1   0.0    1.0  1  FlpD      Methyl-viologen-reducing hydrogenase, delta subunit
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.17   11.8   0.0    1.3  1  UPF0146   Uncharacterised protein family (UPF0146)


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 !  171.1   0.0   9.2e-55   8.3e-51       1     123 []       8     129 ..       8     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 9.2e-55
                              FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerr 77 
                                       i++++Cnwc+y+aadlag+ r+ yp++v+iirvpCsgrv+pefi++ l++ adgVl+ gChpgdChy++Gn+ka+rr
  gi|488600601|ref|YP_007907072.1|   8 IIVIACNWCTYQAADLAGSLRYPYPTTVKIIRVPCSGRVEPEFIIETLRN-ADGVLIGGCHPGDCHYKEGNYKAARR 83 
                                       89**********************************************86.************************** PP

                              FlpD  78 veklkelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                       +++++++l e+giepeRvrle++s +eg +faev++ef++ki+eLG
  gi|488600601|ref|YP_007907072.1|  84 FKLIQKMLVEMGIEPERVRLEWISGSEGLRFAEVMREFDAKIRELG 129
                                       *********************************************8 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.8e-05      0.17      64     109 ..      14      61 ..       9      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                                       -HHHHTTEEEEEEES--TTSHHHHHHH..HHHHT-EEEEE-BTTB--- CS
                           UPF0146  64 nleiYkgadliYslRpPaelqsaildv..akkvgAaliikpLlgedvv 109
                                       n   Y++adl  slR P      i++v  +++v+ + ii++L + d v
  gi|488600601|ref|YP_007907072.1|  14 NWCTYQAADLAGSLRYPYPTTVKIIRVpcSGRVEPEFIIETLRNADGV 61 
                                       5668*************99999999986689***********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 797.77
//
Query:       gi|488600602|ref|YP_007907073.1|  [L=297]
Description: Heterodisulfide reductase, subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  104.1   0.2    1.3e-16   60.6   0.0    2.2  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 !   41.8   0.0   5.4e-15   9.6e-11       3      84 ..       5      85 ..       3      86 .. 0.95
   2 !   60.6   0.0   7.2e-21   1.3e-16       1      83 [.     148     240 ..     148     242 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 5.4e-15
                               CCG  3 yfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelae.alakrnvetaeetgadaivtacpgC 80
                                      +f gC  +  ++p+++ al+ +  +lgvel++le++sCC+ +g+  + +   + ++ +rn++ aee+g+d i+t c++C
  gi|488600602|ref|YP_007907073.1|  5 LFLGC-NIPLRRPDLEVALRYVYPKLGVELVDLEGASCCPTWGTMPSVDLAGWcSVSARNMCIAEEKGVD-ILTVCGSC 81
                                      799**.89999*********************************9999998888****************.******** PP

                               CCG 81 llql 84
                                      +++l
  gi|488600602|ref|YP_007907073.1| 82 YGSL 85
                                      *987 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 7.2e-21
                               CCG   1 vayfdgChllraa........ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeet 68 
                                       +a+++gCh+l+++        +p+ +++l +l ea+g++ +++     CCG gg rs + e++++l +r++++++e+
  gi|488600602|ref|YP_007907073.1| 148 IAVQPGCHFLWPSevyvdkerNPFRPRVLIELCEAMGAKAPDYsTITDCCGTGGLRSTNLEKSLKLFERKIKSIKEE 224
                                       589****************************************9********************************8 PP

                               CCG  69 .gadaivtacpgCllq 83 
                                        ++d +vt c++Cllq
  gi|488600602|ref|YP_007907073.1| 225 vDPDLVVTSCSSCLLQ 240
                                       8*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1883.76
//
Query:       gi|488600603|ref|YP_007907074.1|  [L=178]
Description: CoB--CoM heterodisulfide reductase subunit C [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-10   38.9  16.6    3.5e-07   30.6   7.5    2.0  2  Fer4_17   4Fe-4S dicluster domain
    1.2e-08   35.2   5.9      3e-08   34.0   5.9    1.6  1  Fer4_8    4Fe-4S dicluster domain
    7.5e-08   32.4   9.8      2e-07   31.0   9.9    1.6  1  Fer4_10   4Fe-4S dicluster domain
    1.3e-07   31.6  10.4    3.1e-06   27.2  11.5    2.0  2  Fer4_9    4Fe-4S dicluster domain
    1.4e-06   28.4  11.1    0.00074   19.8   2.0    2.2  2  Fer4_4    4Fe-4S binding domain
    1.4e-06   27.9  16.0    0.00071   19.3   4.3    2.2  2  Fer4      4Fe-4S binding domain
    1.9e-06   28.4  20.9    2.2e-05   25.0  10.7    1.9  2  Fer4_7    4Fe-4S dicluster domain
    9.7e-06   25.4  14.3     0.0011   18.9   2.1    2.3  2  Fer4_2    4Fe-4S binding domain
      1e-05   25.4  14.3     0.0055   16.7   3.1    2.2  2  Fer4_6    4Fe-4S binding domain
    1.5e-05   25.9   9.7      0.023   15.6   1.0    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00027   21.0  13.7     0.0019   18.3  13.7    2.0  1  Fer4_21   4Fe-4S dicluster domain
     0.0011   19.8   4.7       0.51   11.2   0.2    2.2  2  Fer4_22   4Fe-4S dicluster domain
     0.0066   16.6   5.6        0.9    9.8   0.3    2.2  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.23   12.5  17.1        1.2   10.2   3.9    2.2  2  Fer4_3    4Fe-4S binding domain
        1.2    9.7  14.4        2.8    8.6   2.5    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.7     5e-07   0.00059      35      59 ..      20      46 ..       9      48 .. 0.75
   2 !   30.6   7.5     3e-10   3.5e-07       1      60 [.      32      92 ..      32      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5e-07
                           Fer4_17 35 eeaeke..ekaslCieCgeCerkCPqg 59
                                      ee+++   e++++Ci+Cg+C+ +CP  
  gi|488600603|ref|YP_007907074.1| 20 EEIKEHggENIDRCIQCGKCAGSCPVA 46
                                      444333458****************75 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 3e-10
                           Fer4_17  1 rCiqCgyClpeCpsyea.ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                      rCiqCg C+ +Cp   a   + +k+++ a++lg++ee+ + +    C++C++C++ CP ++
  gi|488600603|ref|YP_007907074.1| 32 RCIQCGKCAGSCPVALAgFLWFNKRFIHALTLGIKEEILDIPSPWACVSCNKCTEICPRDV 92
                                      7************97777999****************99999****************987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   5.9   2.5e-11     3e-08       2      65 .]      30      92 ..      28      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.5e-11
                            Fer4_8  2 lekCieCgaCqsaCpvlrr......tkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                      +++Ci+Cg C  +Cpv+ +      ++  +  + g ++e   +          w+C++c++Cte Cp ++
  gi|488600603|ref|YP_007907074.1| 30 IDRCIQCGKCAGSCPVALAgflwfnKRFIHALTLGIKEE-ILDIPS------PWACVSCNKCTEICPRDV 92
                                      579************777766664133444444444444.555555......9**************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 !   31.0   9.9   1.7e-10     2e-07       5      56 .]      29      89 ..      25      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                           Fer4_10  5 dddtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + d+Ci+CgkC  +CP+ l           +  +  ++ee  +   +++C  c +C+e+CP
  gi|488600603|ref|YP_007907074.1| 29 NIDRCIQCGKCAGSCPVALagflwfnkrFIHALTLGIKEEILDIPSPWACVSCNKCTEICP 89
                                      568**************88*******86444444444444444458**************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 !   14.5   2.6   2.6e-05     0.031      33      48 ..      27      45 ..      10      48 .. 0.71
   2 !   27.2  11.5   2.6e-09   3.1e-06       1      49 [.      32      91 ..      32      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                            Fer4_9 33 e...eaCigCgaCveaCpk 48
                                          ++Ci+Cg+C+  Cp 
  gi|488600603|ref|YP_007907074.1| 27 GeniDRCIQCGKCAGSCPV 45
                                      1344689999999999997 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 2.6e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase...........eaCigCgaCveaCpkg 49
                                      +C++Cg+C  +Cp  ++   ++++   +  +             +aC++C++C+e+Cp++
  gi|488600603|ref|YP_007907074.1| 32 RCIQCGKCAGSCPVALAGFLWFNKRFIHALTLGikeeildipspWACVSCNKCTEICPRD 91
                                      6***********9999999988888887655448889*********************98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.0   6.2e-07   0.00074       2      16 ..      31      45 ..      30      50 .. 0.93
   2 !   13.5   2.0   6.5e-05     0.078       4      16 ..      78      90 ..      75     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.2e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      +rCi+Cg+C  +CP+
  gi|488600603|ref|YP_007907074.1| 31 DRCIQCGKCAGSCPV 45
                                      8*************6 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.5e-05
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C+ C +C+ +CP 
  gi|488600603|ref|YP_007907074.1| 78 CVSCNKCTEICPR 90
                                      ************5 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   4.3     6e-07   0.00071       6      20 ..      31      45 ..      28      46 .. 0.92
   2 !   14.3   3.9   2.3e-05     0.027       8      22 ..      78      92 ..      77      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6e-07
                                      TTSSS-THHHHHSTT CS
                              Fer4  6 ekCigCGaCvevCPv 20
                                      ++Ci CG+C+  CPv
  gi|488600603|ref|YP_007907074.1| 31 DRCIQCGKCAGSCPV 45
                                      9*************8 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.3e-05
                                      SSS-THHHHHSTTTE CS
                              Fer4  8 CigCGaCvevCPvgA 22
                                      C+ C++C e+CP ++
  gi|488600603|ref|YP_007907074.1| 78 CVSCNKCTEICPRDV 92
                                      ************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 !   15.7   2.5   1.4e-05     0.016      33      50 ..      28      45 ..      13      47 .. 0.76
   2 !   25.0  10.7   1.8e-08   2.2e-05       1      52 []      32      92 ..      32      92 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                            Fer4_7 33 idpekClgCgaCvavCPt 50
                                       + ++C++Cg+C+  CP+
  gi|488600603|ref|YP_007907074.1| 28 ENIDRCIQCGKCAGSCPV 45
                                      467899999999999997 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.8e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.........gtekvei.dpekClgCgaCvavCPtga 52
                                      rCi+Cg+C+  Cpv    +  + n++         + e ++i +p+ C++C++C + CP ++
  gi|488600603|ref|YP_007907074.1| 32 RCIQCGKCAGSCPVALAGFLWF-NKRfihaltlgiKEEILDIpSPWACVSCNKCTEICPRDV 92
                                      8************766665443.22223336664433666775699*************875 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.1   9.5e-07    0.0011       6      21 ..      29      44 ..      24      45 .. 0.88
   2 !   11.9   4.6   0.00016      0.19       9      21 ..      77      89 ..      72      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.5e-07
                            Fer4_2  6 dtdrCigCgaCvsaCP 21
                                      + drCi+Cg+C  +CP
  gi|488600603|ref|YP_007907074.1| 29 NIDRCIQCGKCAGSCP 44
                                      569************* PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00016
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      +C++C++C+  CP
  gi|488600603|ref|YP_007907074.1| 77 ACVSCNKCTEICP 89
                                      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 !   16.7   3.1   4.6e-06    0.0055       6      21 ..      30      45 ..      29      49 .. 0.88
   2 !   14.1   3.4   3.1e-05     0.037       8      20 ..      77      89 ..      77      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.6e-06
                            Fer4_6  6 pdkCigCgdCvrvCPe 21
                                       d+Ci+Cg+C+  CP 
  gi|488600603|ref|YP_007907074.1| 30 IDRCIQCGKCAGSCPV 45
                                      59*************6 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.1e-05
                            Fer4_6  8 kCigCgdCvrvCP 20
                                      +C++C++C+ +CP
  gi|488600603|ref|YP_007907074.1| 77 ACVSCNKCTEICP 89
                                      6************ PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   2.2   4.7e-05     0.056       1      15 [.      32      46 ..      32      51 .. 0.91
   2 !   15.6   1.0   1.9e-05     0.023       2      15 ..      78      91 ..      77     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                           Fer4_16  1 rCgtCgkCaevCPtn 15
                                      rC++CgkCa +CP++
  gi|488600603|ref|YP_007907074.1| 32 RCIQCGKCAGSCPVA 46
                                      6************86 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.9e-05
                           Fer4_16  2 CgtCgkCaevCPtn 15
                                      C++C+kC+e+CP +
  gi|488600603|ref|YP_007907074.1| 78 CVSCNKCTEICPRD 91
                                      ************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 !   18.3  13.7   1.6e-06    0.0019       6      52 ..      31      89 ..      28      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                           Fer4_21  6 dkCigCgkCliaCedtshqai...........eidaktvlkvv.edeCvGCnlCssvCP 52
                                      d+Ci+CgkC+ +C+ +    +            + ++++l +     Cv Cn C+++CP
  gi|488600603|ref|YP_007907074.1| 31 DRCIQCGKCAGSCPVALAGFLwfnkrfihaltLGIKEEILDIPsPWACVSCNKCTEICP 89
                                      79************877777755544433332222333445532469************ PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.9   0.00083      0.99       1      94 [.      32      45 ..      18      48 .. 0.67
   2 !   11.2   0.2   0.00043      0.51      81      94 ..      77      90 ..      53      92 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00083
                           Fer4_22  1 rClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfge 79
                                      rC++Cg+C+  Cp                                                                  
  gi|488600603|ref|YP_007907074.1| 32 RCIQCGKCAGSCP------------------------------------------------------------------ 44
                                      4555555555555.................................................................. PP

                           Fer4_22 80 sgCvGCgRCieacpv 94
                                                    v
  gi|488600603|ref|YP_007907074.1| 45 --------------V 45
                                      ..............4 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00043
                           Fer4_22 81 gCvGCgRCieacpv 94
                                      +Cv C++C+e cp 
  gi|488600603|ref|YP_007907074.1| 77 ACVSCNKCTEICPR 90
                                      56666666666665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.3   0.00075       0.9      48      74 ..      20      46 ..       9      49 .. 0.77
   2 !    9.2   0.8    0.0011       1.3      60      75 ..      77      92 ..      65      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00075
                           Fer4_18 48 kekeerkekgagdcidcescvkvcPtg 74
                                      +e +e+  ++   ci+c++c   cP+ 
  gi|488600603|ref|YP_007907074.1| 20 EEIKEHGGENIDRCIQCGKCAGSCPVA 46
                                      5555666778889***********986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                           Fer4_18 60 dcidcescvkvcPtgi 75
                                       c++c++c ++cP ++
  gi|488600603|ref|YP_007907074.1| 77 ACVSCNKCTEICPRDV 92
                                      5************876 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.3    0.0051         6       1      13 [.      33      45 ..      33      46 .. 0.96
   2 ?   10.2   3.9     0.001       1.2       1      14 [.      78      91 ..      78      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0051
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C++Cg C  +CPv
  gi|488600603|ref|YP_007907074.1| 33 CIQCGKCAGSCPV 45
                                      ************7 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ C+ C e CP +
  gi|488600603|ref|YP_007907074.1| 78 CVSCNKCTEICPRD 91
                                      99**********76 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.5    0.0023       2.8       4      17 ..      31      44 ..      29      48 .. 0.89
   2 ?    6.4   4.2     0.011        13       6      17 ..      78      89 ..      76      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0023
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d+Ci cg+C+  +P
  gi|488600603|ref|YP_007907074.1| 31 DRCIQCGKCAGSCP 44
                                      69*********999 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                           Fer4_13  6 CiacgaCvelaP 17
                                      C++c++C e++P
  gi|488600603|ref|YP_007907074.1| 78 CVSCNKCTEICP 89
                                      ************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1140.31
//
Query:       gi|488600604|ref|YP_007907075.1|  [L=686]
Description: CoB--CoM heterodisulfide reductase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-18   64.9   0.1      1e-09   38.1   0.1    3.0  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.1e-17   63.4  28.1    3.3e-10   40.4  10.3    4.0  4  Fer4_7         4Fe-4S dicluster domain
    7.8e-17   60.3  46.4    4.5e-07   29.4   2.6    5.7  5  Fer4           4Fe-4S binding domain
    2.1e-12   47.0  36.8    1.9e-08   34.3   9.3    3.8  3  Fer4_9         4Fe-4S dicluster domain
    3.6e-11   43.0  30.8    1.4e-06   28.3  10.9    4.1  3  Fer4_10        4Fe-4S dicluster domain
    5.1e-11   42.0  40.3    4.4e-05   23.3   2.7    5.9  5  Fer4_2         4Fe-4S binding domain
    2.5e-10   40.0  51.3    3.4e-05   23.7   3.2    6.0  5  Fer4_6         4Fe-4S binding domain
    2.6e-10   41.1  24.5      0.001   20.0   0.9    5.2  4  Fer4_16        4Fe-4S double cluster binding domain
    1.6e-09   37.7  27.8    4.6e-07   29.9  10.2    4.3  3  Fer4_21        4Fe-4S dicluster domain
      3e-08   33.4   0.0    6.4e-08   32.4   0.0    1.5  1  FAD_oxidored   FAD dependent oxidoreductase
    1.8e-07   31.3   0.0    4.3e-07   30.1   0.0    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    2.9e-07   31.1  19.9     0.0029   18.3   1.4    4.2  2  Fer4_15        4Fe-4S single cluster domain
    3.6e-07   30.1   0.1     0.0003   20.5   0.0    2.4  2  DAO            FAD dependent oxidoreductase
      7e-07   28.3   0.8    1.2e-05   24.2   0.5    2.2  2  HI0933_like    HI0933-like protein
    7.5e-07   28.6   0.1    1.3e-06   27.8   0.1    1.3  1  FAD_binding_2  FAD binding domain
    4.1e-06   27.2  30.4    0.00056   20.4   0.6    4.8  4  Fer4_17        4Fe-4S dicluster domain
    7.3e-06   26.8  18.5      0.076   13.9   1.0    4.5  4  Fer4_22        4Fe-4S dicluster domain
    9.7e-06   26.1   0.4    0.00017   22.1   0.4    2.8  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.5e-05   23.1   0.1    6.5e-05   22.2   0.1    1.4  1  GIDA           Glucose inhibited division protein A
    4.4e-05   23.7  39.6     0.0083   16.6   2.7    5.5  4  Fer4_4         4Fe-4S binding domain
    0.00014   22.4  20.1      0.071   13.7   0.9    3.9  3  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
    0.00031   20.1   0.1    0.00062   19.1   0.1    1.5  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.002   18.5  19.3     0.0041   17.5   1.6    4.4  2  Fer4_8         4Fe-4S dicluster domain
     0.0032   16.8   0.5      0.021   14.1   0.2    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.019   15.9   5.8      0.019   15.9   5.8    6.5  4  Fer4_3         4Fe-4S binding domain
      0.023   13.9   0.1       0.04   13.2   0.1    1.3  1  FAD_binding_3  FAD binding domain
      0.075   12.3   0.0       0.14   11.4   0.0    1.4  1  Amino_oxidase  Flavin containing amine oxidoreductase
       0.18   11.7   0.0         14    5.6   0.0    2.7  2  NAD_binding_9  FAD-NAD(P)-binding
        0.2   11.9  18.8       0.46   10.7   3.2    3.8  3  Fer4_18        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   1.7e-12     1e-09       4      79 ..     145     242 ..     142     387 .. 0.80
   2 !   23.3   0.0   5.1e-08   3.2e-05     191     293 ..     475     589 ..     444     590 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.7e-12
                                       EEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx......... RF
                       Pyr_redox_2   4 vviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias......... 57 
                                       +viGgG+AG+ aal+la  g+kv+lve           l++t+++++c+    ++++++va +++i++         
  gi|488600604|ref|YP_007907075.1| 145 MVIGGGVAGMFAALDLADMGYKVYLVEknpsiggnmakLDKTFPTNDCSAcilTPVMVQVATNPNIELmtysevesv 221
                                       9*************************888888899999********9865555**************9999877544 PP

                                       .......HHHHCHHHHCCCCHCCTCEEEE CS
                                       .......xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .......evvkklnqgielllgeevvkid 79 
                                              +        ++++ ++++v+ d
  gi|488600604|ref|YP_007907075.1| 222 dgsignfK--------VKVRRKQTYVDWD 242
                                       43332220........2222222222222 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 5.1e-08
                                       HHHHHTTEEEEESCEEEEEEETTE.......EEEEEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EEEETTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                       Pyr_redox_2 191 ealekeGvevklgtsvkeidgnge.......klevvledgeeidadlvvvavGvrpstelle..eklglelderggi 258
                                        + ++ G++v  g +   i++ ++        +++ l++  e+ ad+vv+a+ v+ps  l++  +klg+++   g++
  gi|488600604|ref|YP_007907075.1| 475 TYCKELGIKVIYGRVS-GIERIPDgerlrvrAYDTGLQSPVEVIADMVVLATAVEPSEGLKDltRKLGINVGAEGFL 550
                                       4567789999977654.4444444445633333366777777***************99999*************** PP

                                       .E--TTS...BESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                       .xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 259 .vvdefl...rtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                        +   +l   +t+v giy +G  +g++++pe++  A ++
  gi|488600604|ref|YP_007907075.1| 551 kELHTKLypvETSVAGIYICGCAQGPRDIPESVAQAKAA 589
                                       75666667899**********777999999999999876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   4.6   3.3e-07    0.0002      23      51 ..     229     257 ..     190     258 .. 0.72
   2 !   29.9   4.8     1e-09   6.2e-07       1      52 []     243     325 ..     243     325 .. 0.72
   3 ?   -2.0   0.1       9.4   5.8e+03       7      13 ..     431     437 ..     400     459 .. 0.73
   4 !   40.4  10.3   5.3e-13   3.3e-10       1      52 []     615     663 ..     615     663 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.3e-07
                            Fer4_7  23 enekgtekveidpekClgCgaCvavCPtg 51 
                                       +++ +++++++d +kC+gCg Cv+vCP++
  gi|488600604|ref|YP_007907075.1| 229 KVKVRRKQTYVDWDKCTGCGDCVKVCPSK 257
                                       3344668999*****************97 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 1e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaield.eeenekgt..........ekveidpekClgC....................gaCva 46 
                                       +C+gCg Cv++Cp+k+ +   e  +e++           +k+++d e C  C                      C++
  gi|488600604|ref|YP_007907075.1| 243 KCTGCGDCVKVCPSKVPDEFnEGLSERKAiyiqfpqavpKKAVLDVEACRECggrklgtppeinektgkpklAPCEK 319
                                       7************99998551333333223334444455888**********7777777777777776665556*** PP

                            Fer4_7  47 vCPtga 52 
                                       vC tga
  gi|488600604|ref|YP_007907075.1| 320 VCKTGA 325
                                       ****97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 9.4
                            Fer4_7   7 aCvaaCp 13 
                                       +C + C 
  gi|488600604|ref|YP_007907075.1| 431 YCSKICC 437
                                       6777764 PP

  == domain 4  score: 40.4 bits;  conditional E-value: 5.3e-13
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       rC gCg Cv+ Cp++ai+++e+   +g+  ++i++  C gCg+C a+CP++a
  gi|488600604|ref|YP_007907075.1| 615 RCSGCGICVPLCPYSAISMEEK---DGKYIARINMALCKGCGVCTAACPVKA 663
                                       8******************887...788999******************987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   4.4   1.1e-09   7.1e-07       2      21 ..     238     257 ..     237     260 .. 0.91
   2 ?    0.6   0.2      0.93   5.7e+02       2      12 ..     285     295 ..     284     296 .. 0.87
   3 ?    1.5   1.3      0.49   3.1e+02      14      22 ..     317     325 ..     317     327 .. 0.93
   4 !   29.4   2.6   7.3e-10   4.5e-07       2      24 .]     610     632 ..     609     632 .. 0.94
   5 !   26.2   3.8   7.7e-09   4.7e-06       2      24 .]     643     665 ..     642     665 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.1e-09
                                       EEETTTSSS-THHHHHSTTT CS
                              Fer4   2 videekCigCGaCvevCPvg 21 
                                       ++d++kC+gCG Cv+vCP  
  gi|488600604|ref|YP_007907075.1| 238 YVDWDKCTGCGDCVKVCPSK 257
                                       89****************76 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.93
                                       EEETTTSSS-T CS
                              Fer4   2 videekCigCG 12 
                                       v d e C  CG
  gi|488600604|ref|YP_007907075.1| 285 VLDVEACRECG 295
                                       6799******9 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.49
                                       HHHHSTTTE CS
                              Fer4  14 CvevCPvgA 22 
                                       C++vC +gA
  gi|488600604|ref|YP_007907075.1| 317 CEKVCKTGA 325
                                       ********9 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 7.3e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       ++d ++C gCG+Cv  CP+ AI+
  gi|488600604|ref|YP_007907075.1| 610 EVDADRCSGCGICVPLCPYSAIS 632
                                       59*******************95 PP

  == domain 5  score: 26.2 bits;  conditional E-value: 7.7e-09
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        i++ +C gCG C  +CPv AIt
  gi|488600604|ref|YP_007907075.1| 643 RINMALCKGCGVCTAACPVKAIT 665
                                       6999******************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 !   17.7   5.3   4.8e-06     0.003      33      49 ..     230     257 ..     189     258 .. 0.67
   2 !   24.0   6.3   5.1e-08   3.2e-05       1      50 [.     243     325 ..     243     326 .. 0.89
   3 !   34.3   9.3   3.1e-11   1.9e-08       1      51 []     615     664 ..     615     664 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.8e-06
                            Fer4_9  33 e...........eaCigCgaCveaCpkg 49 
                                                   ++C+gCg+Cv++Cp++
  gi|488600604|ref|YP_007907075.1| 230 VkvrrkqtyvdwDKCTGCGDCVKVCPSK 257
                                       03334444566689************87 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 5.1e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.............eaCigCga....................Cve 44 
                                       kCtgCg Cv++Cp++v  e + +   r  ++ +             eaC +Cg                     C++
  gi|488600604|ref|YP_007907075.1| 243 KCTGCGDCVKVCPSKVPDEFNEGLSERKAIYIQfpqavpkkavldvEACRECGGrklgtppeinektgkpklapCEK 319
                                       7************999988777777666665557779**************************************** PP

                            Fer4_9  45 aCpkga 50 
                                       +C++ga
  gi|488600604|ref|YP_007907075.1| 320 VCKTGA 325
                                       ***986 PP

  == domain 3  score: 34.3 bits;  conditional E-value: 3.1e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +C gCg Cv+ Cp+ +++++++ +k   r+  +  C gCg C++aCp +ai
  gi|488600604|ref|YP_007907075.1| 615 RCSGCGICVPLCPYSAISMEEKDGKYIARINMA-LCKGCGVCTAACPVKAI 664
                                       5***************98877777777666554.9************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 !   22.6   6.9   1.4e-07   8.5e-05       4      49 ..     239     295 ..     236     326 .. 0.79
   2 ?   -2.6   0.2       9.9   6.1e+03      14      19 ..     431     436 ..     403     451 .. 0.72
   3 !   28.3  10.9   2.3e-09   1.4e-06       4      56 .]     611     660 ..     608     660 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-07
                           Fer4_10   4 idddtCirCgkCvkaCPadl........tsvgakgeaseeeavrk...kvekCtgcg 49 
                                       +d d+C++Cg+Cvk+CP+++        ++ +a++++ ++++ +k   +ve+C +cg
  gi|488600604|ref|YP_007907075.1| 239 VDWDKCTGCGDCVKVCPSKVpdefneglSERKAIYIQFPQAVPKKavlDVEACRECG 295
                                       6889**************99********77777777777766666334578888885 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.9
                           Fer4_10  14 kCvkaC 19 
                                        C k C
  gi|488600604|ref|YP_007907075.1| 431 YCSKIC 436
                                       466665 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 2.3e-09
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d+d+C +Cg Cv  CP+   s    +e++++   r+++  C gcg C++aCP
  gi|488600604|ref|YP_007907075.1| 611 VDADRCSGCGICVPLCPY---SAISMEEKDGKYIARINMALCKGCGVCTAACP 660
                                       799***************...88888999999999*****************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 ?   -1.6   0.1         6   3.7e+03      12      16 ..     191     195 ..     187     197 .. 0.64
   2 !   23.3   2.7   7.1e-08   4.4e-05       4      21 ..     238     255 ..     235     256 .. 0.93
   3 ?    1.5   3.9      0.63   3.9e+02       3      14 ..     284     295 ..     281     323 .. 0.78
   4 !   19.1   3.4   1.5e-06   0.00095       5      22 .]     611     628 ..     609     628 .. 0.93
   5 !   17.6   2.6   4.7e-06    0.0029       5      21 ..     644     660 ..     640     661 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6
                            Fer4_2  12 gCgaC 16 
                                        C+aC
  gi|488600604|ref|YP_007907075.1| 191 DCSAC 195
                                       46666 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 7.1e-08
                            Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                       +vd d+C+gCg Cv++CP
  gi|488600604|ref|YP_007907075.1| 238 YVDWDKCTGCGDCVKVCP 255
                                       6899************** PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.63
                            Fer4_2   3 vvvdtdrCigCg 14 
                                       +v d ++C +Cg
  gi|488600604|ref|YP_007907075.1| 284 AVLDVEACRECG 295
                                       7899*******8 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 1.5e-06
                            Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                       vd+drC gCg+Cv  CP+
  gi|488600604|ref|YP_007907075.1| 611 VDADRCSGCGICVPLCPY 628
                                       89***************5 PP

  == domain 5  score: 17.6 bits;  conditional E-value: 4.7e-06
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       ++ + C gCg C+ aCP
  gi|488600604|ref|YP_007907075.1| 644 INMALCKGCGVCTAACP 660
                                       78899************ PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   3.2   5.5e-08   3.4e-05       7      22 ..     242     257 ..     238     259 .. 0.87
   2 ?   -2.1   0.1       8.1     5e+03       6      13 ..     288     295 ..     284     295 .. 0.67
   3 ?    3.5   0.6      0.13        80      14      23 ..     316     325 ..     315     325 .. 0.91
   4 !   22.4   3.3   1.4e-07   8.9e-05       2      24 .]     609     631 ..     608     631 .. 0.95
   5 !   21.9   3.9   2.1e-07   0.00013       1      24 []     641     664 ..     641     664 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.5e-08
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       dkC+gCgdCv+vCP +
  gi|488600604|ref|YP_007907075.1| 242 DKCTGCGDCVKVCPSK 257
                                       9*************76 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.1
                            Fer4_6   6 pdkCigCg 13 
                                        ++C  Cg
  gi|488600604|ref|YP_007907075.1| 288 VEACRECG 295
                                       56677775 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.13
                            Fer4_6  14 dCvrvCPega 23 
                                       +C++vC +ga
  gi|488600604|ref|YP_007907075.1| 316 PCEKVCKTGA 325
                                       7******998 PP

  == domain 4  score: 22.4 bits;  conditional E-value: 1.4e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       +e+d+d+C gCg Cv  CP+ ai
  gi|488600604|ref|YP_007907075.1| 609 SEVDADRCSGCGICVPLCPYSAI 631
                                       79******************998 PP

  == domain 5  score: 21.9 bits;  conditional E-value: 2.1e-07
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +++i+  +C gCg C+++CP +ai
  gi|488600604|ref|YP_007907075.1| 641 IARINMALCKGCGVCTAACPVKAI 664
                                       689******************998 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.6   9.9e-06    0.0061       1      15 [.     243     257 ..     203     295 .. 0.74
   2 ?    0.9   0.2       1.5   9.2e+02       8      33 ..     317     340 ..     314     366 .. 0.73
   3 !   17.4   0.7     1e-05    0.0064       1      22 [.     615     636 ..     615     646 .. 0.84
   4 !   20.0   0.9   1.6e-06     0.001       2      21 ..     649     668 ..     648     682 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.9e-06
                           Fer4_16   1 rCgtCgkCaevCPtn 15 
                                       +C++Cg C++vCP++
  gi|488600604|ref|YP_007907075.1| 243 KCTGCGDCVKVCPSK 257
                                       355555555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.5
                           Fer4_16   8 CaevCPtnaikekkekeiearecisy 33 
                                       C +vC t+a +     +++++ +i +
  gi|488600604|ref|YP_007907075.1| 317 CEKVCKTGACDRS--INWDPEGEIVE 340
                                       999****999988..78887766654 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 1e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                       rC +Cg C+  CP +ai+++++
  gi|488600604|ref|YP_007907075.1| 615 RCSGCGICVPLCPYSAISMEEK 636
                                       6*****************9843 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 1.6e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekk 21 
                                       C++Cg C+ +CP++ai+   
  gi|488600604|ref|YP_007907075.1| 649 CKGCGVCTAACPVKAITLHG 668
                                       ****************9873 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.4   5.2e+03      17      41 ..      43      69 ..      41      71 .. 0.63
   2 !   19.0   0.7   1.8e-06    0.0011      32      52 ..     235     255 ..     219     259 .. 0.73
   3 !   29.9  10.2   7.4e-10   4.6e-07       2      58 ..     610     665 ..     609     666 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.4
                           Fer4_21 17 aCedtshqaieidaktvl..kvvedeC 41
                                      +C+d + + i+ d +  l  +vv   C
  gi|488600604|ref|YP_007907075.1| 43 MCSDPGQEMIKQDIRDGLidRVVVAAC 69
                                      799999999987644322225555555 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-06
                           Fer4_21  32 tvlkvvedeCvGCnlCssvCP 52 
                                       +++ v  d+C+GC  C++vCP
  gi|488600604|ref|YP_007907075.1| 235 KQTYVDWDKCTGCGDCVKVCP 255
                                       3334567************** PP

  == domain 3  score: 29.9 bits;  conditional E-value: 7.4e-10
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                        +d d+C gCg C+  C+ +++   e+d+k ++++    C GC +C++ CPv ++i+
  gi|488600604|ref|YP_007907075.1| 610 EVDADRCSGCGICVPLCPYSAISMEEKDGKYIARINMALCKGCGVCTAACPV-KAIT 665
                                       5899**************7666666777888889999**************9.8886 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0     1e-10   6.4e-08       3      39 ..     145     181 ..     144     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1e-10
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39 
                                       +V+GGg+aG+ AA+  a +G kv Lve+++ +GG+++
  gi|488600604|ref|YP_007907075.1| 145 MVIGGGVAGMFAALDLADMGYKVYLVEKNPSIGGNMA 181
                                       69*********************************97 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0     7e-10   4.3e-07       1      37 [.     146     182 ..     146     200 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7e-10
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37 
                                       ++G+G++G+ aA  La+ g++v l+ek++++GG++a 
  gi|488600604|ref|YP_007907075.1| 146 VIGGGVAGMFAALDLADMGYKVYLVEKNPSIGGNMAK 182
                                       8*********************************986 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.4   4.8e-06    0.0029       2      22 ..     238     258 ..     237     295 .. 0.74
   2 !    8.8  11.2    0.0042       2.6       2      65 ..     610     665 ..     610     666 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.8e-06
                           Fer4_15   2 vvDrdaCigcglCvaeapevf 22 
                                       +vD+d+C+gcg Cv+++p  +
  gi|488600604|ref|YP_007907075.1| 238 YVDWDKCTGCGDCVKVCPSKV 258
                                       69***************7544 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0042
                           Fer4_15   2 vvDrdaCigcglCvaea..pevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIr 65 
                                       +vD d+C gcg Cv ++  + +  +++dg+            ++++  + +      +aCPv+AI+
  gi|488600604|ref|YP_007907075.1| 610 EVDADRCSGCGICVPLCpySAISMEEKDGKY----------IARINMALCKGCGVCTAACPVKAIT 665
                                       59***************54445555556665..........2578888888888888899999886 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.9e-07    0.0003       4      35 ..     146     178 ..     144     182 .. 0.92
   2 !    7.0   0.0     0.006       3.7     152     205 ..     473     530 ..     465     574 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.9e-07
                                       EECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO   4 iiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                       +iGGG++G+++A++La  g  V l+ek++ +g g
  gi|488600604|ref|YP_007907075.1| 146 VIGGGVAGMFAALDLADMGykVYLVEKNPSIG-G 178
                                       9**************9989*********9998.5 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.006
                                       HHHHHHHTT-EEEESECEEEEEE.EETCEEEEE...EECTEEEE....EEEEEEE--GGGHH CS
                               DAO 152 laraaealGveilegtevtglee.edgkvwgve...rttpgend....aadavVnaaGawsd 205
                                       ++  +++lG+++++g +v g+e+ +dg   +v+   +   g ++    +ad vV+a+ +  +
  gi|488600604|ref|YP_007907075.1| 473 YYTYCKELGIKVIYG-RVSGIERiPDGERLRVRaydT---GLQSpvevIADMVVLATAVEPS 530
                                       667899*********.*****8877655555645430...554323445677****965543 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.5   1.9e-08   1.2e-05       3      36 ..     144     177 ..     142     183 .. 0.93
   2 ?    2.3   0.0     0.087        54      97     151 ..     182     236 ..     178     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.9e-08
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                        +viGgG AG++aA+ +a+ g +V l+ek++++g
  gi|488600604|ref|YP_007907075.1| 144 AMVIGGGVAGMFAALDLADMGYKVYLVEKNPSIG 177
                                       68*****************************998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.087
                                       STTEEEETT.-CHHHHH.HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTE CS
                       HI0933_like  97 dsgrlFpvsdkaedivd.allkelkeagvklrletevksvekeedgkfrvktksee 151
                                       + ++ Fp++d ++ i++ ++++ +++ +++l++ +ev+sv+ +  g+f+vk++ ++
  gi|488600604|ref|YP_007907075.1| 182 KLDKTFPTNDCSACILTpVMVQVATNPNIELMTYSEVESVDGSI-GNFKVKVRRKQ 236
                                       56789***9988888763788889999*************6655.55999994444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   2.1e-09   1.3e-06       3      39 ..     145     181 ..     144     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.1e-09
                                       EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                        ViG+G+AG+ AAl +a+ G kv +vek ++ gg+ a
  gi|488600604|ref|YP_007907075.1| 145 MVIGGGVAGMFAALDLADMGYKVYLVEKNPSIGGNMA 181
                                       59*******************************9876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.6   9.1e-07   0.00056      33      60 ..     231     258 ..     186     259 .. 0.57
   2 !   14.7   0.8   5.3e-05     0.033      34      58 ..     604     628 ..     576     630 .. 0.69
   3 !   16.6   9.9   1.4e-05    0.0085       1      57 [.     615     660 ..     615     664 .. 0.81
   4 !    9.1   2.0     0.003       1.8       2      17 ..     649     664 ..     648     680 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.1e-07
                           Fer4_17  33 lleeaekeekaslCieCgeCerkCPqgl 60 
                                       ++++ ++   +++C++Cg C+++CP+++
  gi|488600604|ref|YP_007907075.1| 231 KVRRKQTYVDWDKCTGCGDCVKVCPSKV 258
                                       2333344469***************987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.3e-05
                           Fer4_17  34 leeaekeekaslCieCgeCerkCPq 58 
                                       +e  + e  a++C++Cg C+  CP+
  gi|488600604|ref|YP_007907075.1| 604 VEPLISEVDADRCSGCGICVPLCPY 628
                                       4555555688999999999999997 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.4e-05
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                       rC++Cg C+p Cp+ ++ ++++  k+++++            ++ lC +Cg C+++CP
  gi|488600604|ref|YP_007907075.1| 615 RCSGCGICVPLCPYSAIsMEEKDGKYIARI------------NMALCKGCGVCTAACP 660
                                       7************99883444444677774............5679************ PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.003
                           Fer4_17   2 CiqCgyClpeCpsyea 17 
                                       C +Cg C+++Cp  ++
  gi|488600604|ref|YP_007907075.1| 649 CKGCGVCTAACPVKAI 664
                                       9999999999998666 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.0   0.00012     0.076      68      95 ..     230     257 ..     219     258 .. 0.82
   2 ?   -0.8   0.0       4.5   2.8e+03       8      20 ..     317     329 ..     314     360 .. 0.82
   3 !    9.7   0.4    0.0025       1.5      69      94 ..     603     628 ..     589     630 .. 0.88
   4 !   12.4   1.7   0.00036      0.22      68      95 ..     635     662 ..     629     663 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                           Fer4_22  68 hklsefkekfgesgCvGCgRCieacpvk 95 
                                        k++  ++ ++  +C+GCg C+++cp+k
  gi|488600604|ref|YP_007907075.1| 230 VKVRRKQTYVDWDKCTGCGDCVKVCPSK 257
                                       4666666777999************987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.5
                           Fer4_22   8 CtlvCptCsCfdv 20 
                                       C  vC t  C + 
  gi|488600604|ref|YP_007907075.1| 317 CEKVCKTGACDRS 329
                                       999****999654 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0025
                           Fer4_22  69 klsefkekfgesgCvGCgRCieacpv 94 
                                       k++ + +++++  C GCg C+  cp 
  gi|488600604|ref|YP_007907075.1| 603 KVEPLISEVDADRCSGCGICVPLCPY 628
                                       67777889999*************96 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00036
                           Fer4_22  68 hklsefkekfgesgCvGCgRCieacpvk 95 
                                       +k  ++ +++++  C GCg C++acpvk
  gi|488600604|ref|YP_007907075.1| 635 EKDGKYIARINMALCKGCGVCTAACPVK 662
                                       5667889999***************986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.4   2.8e-07   0.00017       3      72 ..     145     227 ..     143     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.8e-07
                                       EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS...TTSSHHHHHH.........HHHHHHHT.TEEEECSEEEEEE CS
                         Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkll...rllDeeaski.........lqeklekn.gievllntkveei 66 
                                       +v+GgG+ g+ +A  la++g kV++ve ++ +     +lD+++ ++         ++ ++  n +ie+++ ++ve++
  gi|488600604|ref|YP_007907075.1| 145 MVIGGGVAGMFAALDLADMGYKVYLVEKNPSIGgnmAKLDKTFPTNdcsaciltpVMVQVATNpNIELMTYSEVESV 221
                                       7*******************************988888898765532222222223444444468888888888888 PP

                                       EEETTS CS
                         Pyr_redox  67 egsedg 72 
                                       +gs  +
  gi|488600604|ref|YP_007907075.1| 222 DGSIGN 227
                                       877665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   1.1e-07   6.5e-05       3      32 ..     145     174 ..     143     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkl 32 
                                       +ViGgG AG+ AAl +a +G+kv L+ ++ 
  gi|488600604|ref|YP_007907075.1| 145 MVIGGGVAGMFAALDLADMGYKVYLVEKNP 174
                                       7*************************5543 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.4   1.8e-05     0.011       2      16 ..     242     256 ..     241     261 .. 0.92
   2 ?   -0.7   2.4       4.4   2.7e+03       3      16 ..     290     323 ..     289     324 .. 0.55
   3 !   11.9   2.9    0.0004      0.25       2      16 ..     614     628 ..     613     630 .. 0.93
   4 !   16.6   2.7   1.3e-05    0.0083       4      16 ..     649     661 ..     645     663 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       ++C+gCg Cv +CP+
  gi|488600604|ref|YP_007907075.1| 242 DKCTGCGDCVKVCPS 256
                                       89************7 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.4
                            Fer4_4   3 rCigCgs....................CvaaCPq 16 
                                        C +Cg                     C+ +C++
  gi|488600604|ref|YP_007907075.1| 290 ACRECGGrklgtppeinektgkpklapCEKVCKT 323
                                       5777763334444444444555556668888876 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.0004
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       +rC gCg Cv  CP+
  gi|488600604|ref|YP_007907075.1| 614 DRCSGCGICVPLCPY 628
                                       9*************7 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 1.3e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C gCg+C+aaCP+
  gi|488600604|ref|YP_007907075.1| 649 CKGCGVCTAACPV 661
                                       ************7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.3   0.00013     0.078       1      18 [.     239     256 ..     239     294 .. 0.87
   2 !   13.7   0.9   0.00011     0.071       1      17 [.     611     627 ..     611     643 .. 0.80
   3 ?    4.7   2.7     0.072        44       2      17 ..     645     660 ..     644     664 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD d+C++cg Cv+++P 
  gi|488600604|ref|YP_007907075.1| 239 VDWDKCTGCGDCVKVCPS 256
                                       899*************95 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD d+C++cg+Cv l+P
  gi|488600604|ref|YP_007907075.1| 611 VDADRCSGCGICVPLCP 627
                                       8**************** PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.072
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       +   C +cg+C +++P
  gi|488600604|ref|YP_007907075.1| 645 NMALCKGCGVCTAACP 660
                                       6677***********9 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1     1e-06   0.00062      31      72 ..     144     185 ..     135     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTT CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslga 72 
                                        +viGgGvaG+ A+   + +g kV++++++p+   ++ +l +
  gi|488600604|ref|YP_007907075.1| 144 AMVIGGGVAGMFAALDLADMGYKVYLVEKNPSIGGNMAKLDK 185
                                       589***************************987766666555 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.6   6.6e-06    0.0041      36      65 .]     232     258 ..     190     258 .. 0.66
   2 !   15.0  10.3   4.2e-05     0.026       2      64 ..     613     662 ..     612     663 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.6e-06
                            Fer4_8  36 vqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       v+++q    +  +++Ct+cg C++vCp ++
  gi|488600604|ref|YP_007907075.1| 232 VRRKQT---YVDWDKCTGCGDCVKVCPSKV 258
                                       333333...56799*************986 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.2e-05
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       +++C +Cg C   Cp +++  ++ +d ++ a        +      +  C +cg Ct +Cpv+
  gi|488600604|ref|YP_007907075.1| 613 ADRCSGCGICVPLCP-YSAISMEEKDGKYIARI------N------MALCKGCGVCTAACPVK 662
                                       789***********9.66666776666666555......3......789************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 !   14.1   0.2   3.3e-05     0.021     164     252 ..     141     235 ..     131     243 .. 0.74
   2 ?   -3.0   0.0       5.5   3.4e+03     294     305 .]     560     571 ..     519     571 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseieke.....esdpsyslkpdienrleelvke.ekikvlfnae 234
                                       +q  +ViGg+  ++ aAl+l+++g +V +v ++ +i  +     ++ p    +++i   +   v++  +i++++ +e
  gi|488600604|ref|YP_007907075.1| 141 KQAAMVIGGGVAGMFAALDLADMGYKVYLVEKNPSIGGNmakldKTFPTNDCSACILTPVMVQVATnPNIELMTYSE 217
                                       67899*************************99998876511111344555677777766665555556689999999 PP

                       Pyr_redox_3 235 vkeikekeeeykvktedg 252
                                       v++++ +  ++kvk +++
  gi|488600604|ref|YP_007907075.1| 218 VESVDGSIGNFKVKVRRK 235
                                       998888888888877664 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.5
                       Pyr_redox_3 294 eetnvpglflaG 305
                                        et v g++++G
  gi|488600604|ref|YP_007907075.1| 560 VETSVAGIYICG 571
                                       5999******99 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   5.8   3.1e-05     0.019       1      14 [.     244     257 ..     244     258 .. 0.94
   2 ?    5.6   1.0      0.06        37       1      15 []     291     325 ..     291     325 .. 0.75
   3 ?    7.9   4.9     0.011       6.9       1      15 []     616     630 ..     616     630 .. 0.94
   4 ?    8.6   7.9    0.0064         4       1      15 []     649     663 ..     649     663 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.1e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       CtgCg Cv+vCP++
  gi|488600604|ref|YP_007907075.1| 244 CTGCGDCVKVCPSK 257
                                       ************86 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.06
                            Fer4_3   1 CtgCg....................aCvevCPvgA 15 
                                       C  Cg                    +C++vC +gA
  gi|488600604|ref|YP_007907075.1| 291 CRECGgrklgtppeinektgkpklaPCEKVCKTGA 325
                                       66676677777777777777777767******998 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.011
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg Cv  CP+ A
  gi|488600604|ref|YP_007907075.1| 616 CSGCGICVPLCPYSA 630
                                       99**********976 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0064
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C gCg C  +CPv+A
  gi|488600604|ref|YP_007907075.1| 649 CKGCGVCTAACPVKA 663
                                       9************98 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.4e-05      0.04       4      33 ..     144     173 ..     141     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                        +++G+G aG+ +al L+  G +v lvek 
  gi|488600604|ref|YP_007907075.1| 144 AMVIGGGVAGMFAALDLADMGYKVYLVEKN 173
                                       579*************************96 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.14       1      31 [.     151     181 ..     151     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS- CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRir 31 
                                       +aG+ aA  L++ G++V ++E ++ +GG ++
  gi|488600604|ref|YP_007907075.1| 151 VAGMFAALDLADMGYKVYLVEKNPSIGGNMA 181
                                       69**************************986 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.023        14       2      42 ..     146     181 ..     145     190 .. 0.84
   2 ?    3.1   0.0      0.14        85     115     153 ..     480     525 ..     470     528 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.023
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42 
                                       ++G+G++G+ ++  L++        ++ l++++++ g g ++
  gi|488600604|ref|YP_007907075.1| 146 VIGGGVAGMFAALDLADM-----GYKVYLVEKNPSiG-GNMA 181
                                       9**************999.....599******98845.6665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                     NAD_binding_9 115 vtvevhraevvdleeradgqavll...adg....aslaadaVvLAl 153
                                       + ++v+ ++v  +e+ +dg +++    ++g     ++ ad VvLA+
  gi|488600604|ref|YP_007907075.1| 480 LGIKVIYGRVSGIERIPDGERLRVrayDTGlqspVEVIADMVVLAT 525
                                       5789999********9999544332243332211469********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.2   0.00075      0.46      48      75 ..     231     258 ..     192     267 .. 0.79
   2 ?    3.2   8.1      0.16     1e+02      54      92 ..     609     650 ..     593     667 .. 0.70
   3 ?    4.0   0.9     0.091        56      56      86 ..     644     674 ..     631     678 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00075
                           Fer4_18  48 kekeerkekgagdcidcescvkvcPtgi 75 
                                       k + +++  +  +c+ c+ cvkvcP ++
  gi|488600604|ref|YP_007907075.1| 231 KVRRKQTYVDWDKCTGCGDCVKVCPSKV 258
                                       4444555667789************987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.16
                           Fer4_18  54 kekgagdcidcescvkvcP...tgidirkGlqleciscllci 92 
                                       +e +a  c  c+ cv +cP   + ++ ++G  +  i+ +lc 
  gi|488600604|ref|YP_007907075.1| 609 SEVDADRCSGCGICVPLCPysaISMEEKDGKYIARINMALCK 650
                                       5566778************43334677899988877655552 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.091
                           Fer4_18  56 kgagdcidcescvkvcPtgidirkGlqleci 86 
                                        +++ c  c++c + cP++    +G+  e i
  gi|488600604|ref|YP_007907075.1| 644 INMALCKGCGVCTAACPVKAITLHGFTTEQI 674
                                       4667899**********98777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 4261.54
//
Query:       gi|488600605|ref|YP_007907076.1|  [L=130]
Description: Universal stress protein UspA-related nucleotide-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-18   66.8   0.3    5.5e-18   65.8   0.3    1.4  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 !   65.8   0.3   3.1e-22   5.5e-18       4     140 ..       2     129 ..       1     130 [] 0.85

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 3.1e-22
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                        I+Va+ +se  ++  ++A+e+ak r+ +li++h +   + +++ +  e +     ++e+a+         ae+ +v
  gi|488600605|ref|YP_007907076.1|   2 SIVVALSKSERRTRIMDFAVEEAKFRNEKLIIVHSLFGGSRTSEEEITEGESLLKWAEEKAK---------AEGIDV 69 
                                       69******************************998876666555554444444444444443.........468999 PP

                                       EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                               Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                       ++++ v+++++++ i+++ +e ++ +++vG r+rs   ++++GSv ++++ ++++pV+ +
  gi|488600605|ref|YP_007907076.1|  70 ETHLLVRGKEAGDDIIDFIREVKPKMVIVGVRRRSPTGKVIFGSVPQKIILNSDVPVVSI 129
                                       99999****************************************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 834.17
//
Query:       gi|488600606|ref|YP_007907077.1|  [L=187]
Description: chorismate lyase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-20   71.2   0.2    1.8e-18   66.9   0.2    2.0  1  DUF98     p-hydroxybenzoic acid synthase


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 !   66.9   0.2     1e-22   1.8e-18       1     143 [.      24     183 ..      24     187 .] 0.82

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1e-22
                                       HH--S-HHHHHHHHHSS-EEEEEEEEEEEE--HHHHHHHTS-TT-EEEEEEEEEEETTEEEEEEEEEEEGGGS-HHH CS
                             DUF98   1 LlgDGsvTrhlelltqekveveliemeaeeseeeeapkeveelkkpllrRqVwlrangqklayAeSwwneeelekyl 77 
                                       L++DGs+T ++e+ t+++v+v + +++++++  + a     + ++ ++ R+V l ++++ +a A+S ++ ++le  +
  gi|488600606|ref|YP_007907077.1|  24 LTTDGSITTIIEAYTGNRVDVITRDQRIIKAG-RYASLLRIDEEDDINFRVVSLISGNRVYAEAVSLTPLKRLEPGF 99 
                                       79*****************9999887777665.5666777788999******************************* PP

                                       HH....SSS-HHHHHHHTT--BEEEEEEEEEEE--..HH......HHH......HTSS-EEEEEEEEEEETTEEEEE CS
                             DUF98  78 ke....kdqpiwksLtkerlelfReirglalgead..eL......eea......fgekgpfwsRhYrlfhkgkpltv 136
                                       ++    +d+pi+++L+k+++e++R+i+++ + +    ++       ++      +g++  +++R Y+++++g++l++
  gi|488600606|ref|YP_007907077.1| 100 RDdltrADIPIGRILRKHKIEARRDINWIVVCRFReiWVmnipdfVKEfsrnidLGSDEIVLARSYNIIRRGEVLMN 176
                                       9999999********************9987654423331111112331111225678899**************** PP

                                       EEEEEEG CS
                             DUF98 137 irEvFsp 143
                                       i+E+F  
  gi|488600606|ref|YP_007907077.1| 177 ITEFFRA 183
                                       *****76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1244.32
//
Query:       gi|488600607|ref|YP_007907078.1|  [L=321]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-19   69.8   1.7      3e-19   69.8   1.7    2.0  3  AAA_17       AAA domain
    5.9e-14   52.4   3.3    5.9e-14   52.4   3.3    2.9  2  RNA_binding  RNA binding
    3.9e-11   43.6   0.6    3.9e-11   43.6   0.6    1.7  2  AAA_18       AAA domain
    0.00085   19.5   0.0     0.0018   18.5   0.0    1.5  1  AAA_33       AAA domain
  ------ inclusion threshold ------
      0.059   13.5   0.2       0.27   11.3   0.0    2.1  2  ADK          Adenylate kinase
       0.12   11.8   1.8       0.22   11.0   0.0    2.3  3  KTI12        Chromatin associated protein KTI12
       0.81   10.3   4.0        5.2    7.7   0.2    2.3  2  TetR_C_19    Tetracyclin repressor-like, C-terminal domain
       0.95   10.1   5.5        2.4    8.8   0.1    3.4  4  Pyr_redox    Pyridine nucleotide-disulphide oxidoreductase


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 !   69.8   1.7   1.3e-22     3e-19       1     136 []       7     138 ..       7     138 .. 0.82
   2 ?   -1.6   0.1       1.5   3.3e+03      71     110 ..     183     218 ..     145     233 .. 0.55
   3 ?   -1.7   0.1       1.6   3.5e+03      77      77 ..     229     229 ..     185     270 .. 0.60

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1.3e-22
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC..TSHHHHHHHHHHHHHHHH...HHHHHSS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr..klpleekkelqkeaaeki...aeeakkk 72 
                                       +G P sGK+t+  k++e +g++++ +Gd++ree++++gl+ ++++     ++l+ek+ ++++a + i   +e+ kk+
  gi|488600607|ref|YP_007907078.1|   7 IGYPLSGKSTAG-KIAESLGIPVVIMGDIVREEVRKRGLELNDENAGkiANELREKEGMDAIARRCIpriREKGKKG 82 
                                       599*******99.*************************977777666233577777777777766443327777889 PP

                                       EEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHHH CS
                            AAA_17  73 gvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesik 136
                                        v+vdg   + e    +++++ke+ +++   ++i +e d ++ ++r l+ r+r++d ++++++k
  gi|488600607|ref|YP_007907078.1|  83 IVVVDGIRGVAE----VERFKKEFGDDF---ILIAIESDIKNRFDRALR-RKRDDDVKSIDELK 138
                                       9*******9966....556899999999...9999******99999987.67999999999886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE- CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiillea 110
                                       + +v++++     e+++   ++  + +++++pda i +e+
  gi|488600607|ref|YP_007907078.1| 183 SIDVIIETRVYPTEDEE---KVV-KAIKNFFPDAEISIED 218
                                       34455555443222222...222.2344555555555554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.6
                                       E CS
                            AAA_17  77 d 77 
                                       +
  gi|488600607|ref|YP_007907078.1| 229 N 229
                                       1 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       0.9     2e+03      66      66 ..     124     124 ..      87     177 .. 0.61
   2 !   52.4   3.3   2.7e-17   5.9e-14       2     118 ..     186     288 ..     185     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.9
                                       H CS
                       RNA_binding  66 e 66 
                                       +
  gi|488600607|ref|YP_007907078.1| 124 R 124
                                       2 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 2.7e-17
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH..... CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei..... 73 
                                       + +++ v++TEdeekV +a++n++p+ e+           + +  +l+a+ ++      +++++ellr ++i     
  gi|488600607|ref|YP_007907078.1| 186 VIIETRVYPTEDEEKVVKAIKNFFPDAEI-----------SIEDDVLRARAKN------INHFRELLRMQKIldtar 245
                                       789**********************8853...........2344678888888......777777777777774333 PP

                                       HHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS...EEEEEEE CS
                       RNA_binding  74 keLlkeleervdekgklylrldKQaaylgklslvegdd...vIkvkik 118
                                       +e+lk++++     +++++ l+KQ a + ++++ve+d    +Ik++++
  gi|488600607|ref|YP_007907078.1| 246 NEMLKSVSG-----NEITILLNKQTATVSRINFVEEDAilsPIKITFR 288
                                       555555555.....*********************9999999998875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.6   1.8e-14   3.9e-11       1     121 [.       4     133 ..       4     148 .. 0.89
   2 ?   -1.7   0.0       1.8   4.1e+03      64      64 ..     208     208 ..     159     257 .. 0.60

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.8e-14
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssal 71 
                                       I+  G+p +GK+t +k  +++ g+     g+++r+ ++++gl+l ++++ ++ +++r++e++++ + +++ ++++  
  gi|488600607|ref|YP_007907078.1|   4 IAFIGYPLSGKSTAGKIAESL-GIpvvimGDIVREEVRKRGLELNDENAgKIANELREKEGMDAIARRCIPRIRE-K 78 
                                       7889************99776.7888***********************************************98.9 PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRgyeeakik 121
                                       ++ + +v+dg+++  e e++k+  +     + ++ + + +++R  +R++ ++ ++
  gi|488600607|ref|YP_007907078.1|  79 GKKGIVVVDGIRGVAEVERFKKEFGddfilIAIESDIKNRFDRALRRKRDDDVKS 133
                                       9999*****************9999**99999999999*****999986655444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
                            AAA_18  64 l 64 
                                       +
  gi|488600607|ref|YP_007907078.1| 208 F 208
                                       1 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   7.9e-07    0.0018       1     125 [.       3     132 ..       3     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.9e-07
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdtlrrrlfg.....tdqqsktdytrvldr..lyqilnelarkalsa 69 
                                       l+ ++G p sGKst  + +++ lg  v++  d++r+ +++     +d++  +  ++++++  + +i ++ + + +++
  gi|488600607|ref|YP_007907078.1|   3 LIAFIGYPLSGKSTAGK-IAESLGiPVVIMGDIVREEVRKrglelNDENAGKIANELREKegMDAIARRCIPRIREK 78 
                                       789***********877.899***************99998888766666665555544444666666666655655 PP

                            AAA_33  70 grn.vildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddr 125
                                       g+  +++  + +  +e +rf k +   +  + ++++e+d +   +R  +R+++ d++
  gi|488600607|ref|YP_007907078.1|  79 GKKgIVVVDGIRGVAEVERFKKEFG--D-DFILIAIESDIKNRFDRALRRKRDDDVK 132
                                       5544999*************99997..5.8899999999999999999999986654 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.27       2      38 ..       7      42 ..       6     136 .. 0.87
   2 ?   -0.1   0.1      0.39   8.7e+02     109     109 ..     214     214 ..     158     304 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                      EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevksg 38
                                      +G P +GK t a k+++++g++ +  Gd++R+ev++ 
  gi|488600607|ref|YP_007907078.1|  7 IGYPLSGKST-AGKIAESLGIPVVIMGDIVREEVRKR 42
                                      899*****99.679*******************9753 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.39
                                       E CS
                                       x RF
                               ADK 109 l 109
                                       +
  gi|488600607|ref|YP_007907078.1| 214 I 214
                                       2 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.7e-05      0.22       1      19 [.       1      19 [.       1      89 [. 0.89
   2 ?   -2.2   0.0         1   2.3e+03     188     218 ..     162     192 ..     148     218 .. 0.64
   3 ?   -0.9   0.1      0.39   8.7e+02     173     221 ..     212     259 ..     186     277 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.7e-05
                                      E.EEEEE--TTSSHHHHHH CS
                             KTI12  1 MpLvvltGlPssGKstrak 19
                                      M L+ + G+P+sGKst+ k
  gi|488600607|ref|YP_007907078.1|  1 MKLIAFIGYPLSGKSTAGK 19
                                      99*************9654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                                       --HHHHHHHHHHHHHHHHHHH....HTT--H CS
                             KTI12 188 eanflqeLdketseivkeileaqksavaidk 218
                                       +++  ++ ++++++++k+il+ +  + ++  
  gi|488600607|ref|YP_007907078.1| 162 NNSDFETFRSKVEAVLKSILKSIDVIIETRV 192
                                       4555666677777777777775554444444 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.39
                                       HTS--SSSTT-------HHHHHHHHHHHHHHHHHHH....HTT--HHH. CS
                             KTI12 173 kklkpnqatlskplaeanflqeLdketseivkeileaqksavaidkltl 221
                                        + + + ++l +++++ n  +eL +  ++i+++  +++ ++v+++++t+
  gi|488600607|ref|YP_007907078.1| 212 AEISIEDDVLRARAKNINHFRELLR-MQKILDTARNEMLKSVSGNEITI 259
                                       4455555555555555555555543.35555555555555555555543 PP

>> TetR_C_19  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0023       5.2      42      89 ..     134     181 ..     119     186 .. 0.82
   2 ?    3.5   0.5     0.045     1e+02      19      79 ..     198     262 ..     187     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0023
                         TetR_C_19  42 tkefkkkkkkerlkelyelidkskLnieseeelklllkilmavtfqti 89 
                                        +e k+++++e+   ++e +d+ +L ie++ +++++   + av+ + +
  gi|488600607|ref|YP_007907078.1| 134 IDELKERDRREESWGMKEAFDMADLTIENNSDFETFRSKVEAVLKSIL 181
                                       55667777777778899******************9998888876655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.045
                         TetR_C_19  19 eeenakffkniflnmnykiekkftkefkkkkkker....lkelyelidkskLnieseeelklllk 79 
                                       ee+  k +kn+f    ++ie+ + +   k+ ++ r    ++++++   ++ L+  s  e+  ll+
  gi|488600607|ref|YP_007907078.1| 198 EEKVVKAIKNFFPDAEISIEDDVLRARAKNINHFRellrMQKILDTARNEMLKSVSGNEITILLN 262
                                       7788899**************99988877777766767788888888888888888777777765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.22     5e+02      35      76 ..      44      83 ..      35      88 .. 0.77
   2 ?   -0.2   0.0      0.68   1.5e+03      11      44 ..      91     125 ..      81     133 .. 0.75
   3 ?   -2.2   0.1       2.9   6.6e+03      54      65 ..     183     194 ..     156     206 .. 0.55
   4 ?    8.8   0.1    0.0011       2.4      30      67 ..     236     269 ..     222     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.22
                                      STTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox 35 lrllDeeaskilqeklekngievllntkveeiegsedgvesv 76
                                      l l De a+ki  e  ek+g++ +  + + +i++++++  ++
  gi|488600607|ref|YP_007907078.1| 44 LELNDENAGKIANELREKEGMDAIARRCIPRIREKGKK--GI 83
                                      4567999999999999999*999999999999987775..33 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.68
                                       HHHHHHHHHH.TTSEEEEEESSSSSSTTSSHHHHH CS
                         Pyr_redox  11 glElAgalae.lgkkVtvversdkllrllDeeask 44 
                                       g+ + + +++ +g++  ++  ++ + + +D+++++
  gi|488600607|ref|YP_007907078.1|  91 GVAEVERFKKeFGDDFILIAIESDIKNRFDRALRR 125
                                       66666666444999999999999999999998876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.9
                                       TEEEECSEEEEE CS
                         Pyr_redox  54 gievllntkvee 65 
                                        i+v+ +t+v  
  gi|488600607|ref|YP_007907078.1| 183 SIDVIIETRVYP 194
                                       355555555544 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0011
                                       SSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEE CS
                         Pyr_redox  30 rsdkllrllDeeaskilqeklekngievllntkveeie 67 
                                       r+ k+l    ++a++++ ++++ n i++lln++++ + 
  gi|488600607|ref|YP_007907078.1| 236 RMQKIL----DTARNEMLKSVSGNEITILLNKQTATVS 269
                                       445555....899********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 1937.90
//
Query:       gi|488600608|ref|YP_007907079.1|  [L=679]
Description: Acyl-CoA synthetase (NDP forming) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-67  227.4   0.1    2.2e-67  226.8   0.1    1.3  1  ATP-grasp_5     ATP-grasp domain
    2.3e-41  140.8   0.1    5.2e-40  136.4   0.0    2.9  4  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
    4.1e-26   91.8   0.0    3.4e-25   88.8   0.0    2.5  2  CoA_binding_2   CoA binding domain
    9.6e-14   51.8   0.9    9.3e-13   48.7   0.1    2.7  3  CoA_binding     CoA binding domain
    6.1e-07   29.2   0.1    1.5e-06   27.9   0.1    1.7  1  ATP-grasp_2     ATP-grasp domain
     0.0037   17.7   0.0      0.069   13.6   0.0    2.7  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.032   13.7   0.0      0.087   12.3   0.0    1.7  1  CPSase_L_D2     Carbamoyl-phosphate synthase L chain, ATP bin
      0.049   13.6   0.0       0.13   12.2   0.0    1.7  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.054   13.2   0.0        2.2    8.0   0.0    2.7  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
      0.076   12.1   0.1        1.7    7.7   0.0    2.3  2  S-layer         S-layer protein
       0.11   12.6   0.2       0.72   10.0   0.0    2.5  3  Response_reg    Response regulator receiver domain
       0.14   12.3   0.1        0.5   10.5   0.1    2.0  1  DpaA_N          Dipicolinate synthase subunit A N-terminal do
       0.14   12.7   1.1       0.85   10.2   0.1    2.9  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.17   12.2   0.5        2.2    8.7   0.3    2.8  2  NUMOD1          NUMOD1 domain


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.8   0.1   1.7e-70   2.2e-67       9     222 .]       3     206 ..       1     206 [. 0.98

  Alignments for each domain:
  == domain 1  score: 226.8 bits;  conditional E-value: 1.7e-70
                       ATP-grasp_5   9 lLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeil 85 
                                        L+e+e+kell+ y+i++++  l+s+++eav+ a+e+g+pvv+K+vs++i+hK+d+gGv lnl+++eevr+a+++++
  gi|488600608|ref|YP_007907079.1|   3 FLSEYESKELLKRYNINCTPIFLCSNEDEAVNKAKELGFPVVMKVVSKSIIHKSDAGGVLLNLNSEEEVRQAFRKLI 79 
                                       699*************************************************************************9 PP

                       ATP-grasp_5  86 ervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertk 162
                                       +        +    v+Vq+ma+ +g+E++vgv+e ++FG  ilfG+GG+ +evl+d +++l pl++++a+e+i++tk
  gi|488600608|ref|YP_007907079.1|  80 AL-------EGAYAVTVQQMAE-KGIEVMVGVSENEQFGKFILFGMGGIFAEVLEDYSLRLIPLTREDAEEMIRETK 148
                                       97.......35679********.****************************************************** PP

                       ATP-grasp_5 163 askllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarirl 222
                                        +++lkg+r+  kad+++l ell+r+s++v+   +I+e+d+nP++++e+g +++Darir+
  gi|488600608|ref|YP_007907079.1| 149 GYRILKGYRNF-KADIENLTELLLRVSEMVER-ENIAEMDLNPVFAYEDGYMVVDARIRI 206
                                       ***********.******************99.99***********************97 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.7   9.8e+03      97     124 ..      72      99 ..      66     113 .. 0.59
   2 ?    0.1   0.0      0.51   6.6e+02      69      95 ..     294     321 ..     291     334 .. 0.83
   3 !  136.4   0.0     4e-43   5.2e-40       1     137 [.     370     502 ..     370     503 .. 0.98
   4 ?   -1.6   0.0       1.6   2.1e+03      71      92 ..     608     627 ..     575     637 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.7
                      Succ_CoA_lig  97 raaashtgalagsdavvdaafrqaGvlr 124
                                       r+a     al g +av  + +++ G+ +
  gi|488600608|ref|YP_007907079.1|  72 RQAFRKLIALEGAYAVTVQQMAEKGIEV 99 
                                       5555555556666666666555555544 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.51
                      Succ_CoA_lig  69 rkflsaarraark.kpvvvlksGrseag 95 
                                       +k l+++++aa+k k + ++ sG  ea 
  gi|488600608|ref|YP_007907079.1| 294 EKVLQVVEEAAEKtKGIFIISSGFREAE 321
                                       688999*****999********987765 PP

  == domain 3  score: 136.4 bits;  conditional E-value: 4e-43
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +Gk+al+sqSG++++ +++  ++  +gfs++++lGn++dvd+ d++++l+ed++t++i+ly+E+++  r+++  ++r
  gi|488600608|ref|YP_007907079.1| 370 AGKVALVSQSGGICHYIMHNFRD--VGFSYIIHLGNRCDVDFPDIIRFLNEDERTEIITLYIEGLDYSRELVTEIKR 444
                                       59*****************9997..8*************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                                       ++  kpv+++k+G+s+++ +  +shtg+lag+++++ + ++qaG+l+v++ ++l+d+a++
  gi|488600608|ref|YP_007907079.1| 445 CS--KPVIAMKAGKSKKADKVSKSHTGSLAGDYRLYVSSLHQAGALVVENPTQLIDVARI 502
                                       *9..*****************************************************986 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.6
                      Succ_CoA_lig  71 flsaarraarkkpvvvlksGrs 92 
                                       f+++ + ++  kpv+v+ s + 
  gi|488600608|ref|YP_007907079.1| 608 FIDVFKDMK--KPVIVVYSSTD 627
                                       666666664..99999987765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.2   2.8e+03      86     107 ..      24      45 ..      10      49 .. 0.77
   2 !   88.8   0.0   2.7e-28   3.4e-25       1     114 [.     228     352 ..     228     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.2
                                       -TT---HHHHHHHHHTT-EEE. CS
                     CoA_binding_2  86 qpgsedeeaaelaeeagirvvg 107
                                       ++ s ++ea+++a+e g +vv+
  gi|488600608|ref|YP_007907079.1|  24 FLCSNEDEAVNKAKELGFPVVM 45 
                                       5557789999*****9999997 PP

  == domain 2  score: 88.8 bits;  conditional E-value: 2.7e-28
                                       --EEEET--S-TTSHHHHHHHHHHH.HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle.hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeal 76 
                                       ++iaVvGas+np k gy v++ l + ++l+++p+npk  ei+g +vy+s+ae pe++dlv++++p+e+++++v+ea+
  gi|488600608|ref|YP_007907079.1| 228 KSIAVVGASSNPLKVGYSVIKSLSAnKKLRIYPINPKLNEIDGLRVYKSIAEIPEDLDLVVIAVPSEKVLQVVEEAA 304
                                       79**********************9777***********************968*********************** PP

                                       HH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  77 algakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       ++    +++ +g          + ++ + e+ae++gir+ g+++ +++
  gi|488600608|ref|YP_007907079.1| 305 EKTKGIFIISSGfreaeieygaEMQNRLKEVAEKNGIRIFGPNSFGMI 352
                                       996666666666******9999999999999************99875 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.2   1.6e+03      18      44 ..      85     112 ..      80     127 .. 0.72
   2 !   48.7   0.1   7.3e-16   9.3e-13       4      96 .]     228     316 ..     226     316 .. 0.93
   3 ?   -2.3   0.0       5.7   7.3e+03      44      60 ..     638     654 ..     627     658 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHECEEEEEEC-TT.TTTCE CS
                       CoA_binding  18 glyhfkeklkygikavfgvnpr.kvgte 44 
                                        +++++++ + gi++ +gv+++ ++g+ 
  gi|488600608|ref|YP_007907079.1|  85 YAVTVQQMAEKGIEVMVGVSENeQFGKF 112
                                       5566778888888888888877555554 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 7.3e-16
                                       EEEEEETTTSHHHHHHHHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding   4 tkviviGagglgiaglyhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeav 79 
                                       ++++v+Ga+ +  +++y++++ l+ + k  ++++np+   +e++gl vyks++e++e+   d  vi+vP+e++ ++v
  gi|488600608|ref|YP_007907079.1| 228 KSIAVVGASSNPLKVGYSVIKSLSANKKlRIYPINPK--LNEIDGLRVYKSIAEIPED--LDLVVIAVPSEKVLQVV 300
                                       78**************9998888888888********..*******************..***************** PP

                                       HHHHHTT-SEEEEESST CS
                       CoA_binding  80 delveagikgiviiteg 96 
                                       +e++e + kgi ii++g
  gi|488600608|ref|YP_007907079.1| 301 EEAAE-KTKGIFIISSG 316
                                       ***99.67999999876 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.7
                                       EETTEEEESCHHHHHHH CS
                       CoA_binding  44 evlglpvyksvdeleek 60 
                                       e l++pv+ s++ +++ 
  gi|488600608|ref|YP_007907079.1| 638 EALNIPVFSSIERASKA 654
                                       55699****99999886 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   1.2e-09   1.5e-06       2      92 ..       4      99 ..       3     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.2e-09
                                      E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSE...EEEE--SSSTCCCTTCEEE.ESSHHHHHHHHHCCT CS
                       ATP-grasp_2  2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekel...vvKaQvlaGGRGKagGvkl.vkskeeakeaakell 76
                                      l Ey++ke+l++y+++ +  +++++++ea ++ak+lg  ++   v K+ ++   +  agGv l  +s+ee+++a ++l+
  gi|488600608|ref|YP_007907079.1|  4 LSEYESKELLKRYNINCTPIFLCSNEDEAVNKAKELGFPVVmkvVSKSIIH---KSDAGGVLLnLNSEEEVRQAFRKLI 79
                                      78***********************************88721113445554...67899*9873688999******999 PP

                                      TSE....EE-TTS-TT-EEE CS
                       ATP-grasp_2 77 gke....lvtkqtgkeGkkv 92
                                        e    +  +q  ++G +v
  gi|488600608|ref|YP_007907079.1| 80 ALEgayaVTVQQMAEKGIEV 99
                                      64322214445556666555 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.4e-05     0.069      26     101 ..     241     318 ..     222     338 .. 0.80
   2 ?    0.4   0.0      0.65   8.3e+02      63      96 ..     367     401 ..     357     425 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                                       EEEEEEESTTTTTSBHHHHSG...GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSEEEESSST CS
                    Semialdhyde_dh  26 elvvllsssrsaGkklaeavk...aleegkdlkvedvdeeelkevdivflalpagvskelapklaeagvkviDlssd 99 
                                       ++ + + +s sa kkl+ + +   +l+e+  l+v +  +e+ +++d+v+ a+p++   ++++++ae+   ++  ss 
  gi|488600608|ref|YP_007907079.1| 241 KVGYSVIKSLSANKKLRIY-PinpKLNEIDGLRVYKSIAEIPEDLDLVVIAVPSEKVLQVVEEAAEKTKGIFIISSG 316
                                       5555555566667766655.34559999999***99888888***********************999999989999 PP

                                       TT CS
                    Semialdhyde_dh 100 fR 101
                                       fR
  gi|488600608|ref|YP_007907079.1| 317 FR 318
                                       88 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.65
                                       GCTT-SEEEE-SCHHHHHHHHHHHHHTTS.EEEES CS
                    Semialdhyde_dh  63 elkevdivflalpagvskelapklaeagv.kviDl 96 
                                       e+k+ ++++ ++++g+++ +++++++ g+ ++i l
  gi|488600608|ref|YP_007907079.1| 367 EMKAGKVALVSQSGGICHYIMHNFRDVGFsYIIHL 401
                                       56777899******************999666665 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.8e-05     0.087       5      44 ..       9      46 ..       6      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                                      HHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEE CS
                       CPSase_L_D2  5 akealkkinvpvvpssaapvetleealaiakeigyPviik 44
                                      +ke+lk+ n+++ p + +  ++++ea++ ake+g+Pv++k
  gi|488600608|ref|YP_007907079.1|  9 SKELLKRYNINCTPIFLC--SNEDEAVNKAKELGFPVVMK 46
                                      68999***********99..******************98 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.13      56     125 ..     270     339 ..     244     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                       TEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SE...ET.TTEEHHHHHHHHH-S- CS
                    NAD_Gly3P_dh_N  56 nlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGi...eegtlkllsevieeelkee 125
                                        l++++ +ae  ++ d++v++vPs+ + +v+++++++    + + +++ G+   e +    +++ ++e+ +++
  gi|488600608|ref|YP_007907079.1| 270 GLRVYKSIAEIPEDLDLVVIAVPSEKVLQVVEEAAEK---TKGIFIISSGFreaEIEYGAEMQNRLKEVAEKN 339
                                       68899999****************9999988888874...466677778885443345555666666665555 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 ?    1.9   0.0      0.13   1.7e+02      28      74 ..      29      74 ..      27      78 .. 0.75
   2 ?    8.0   0.0    0.0017       2.2       5      48 ..     609     650 ..     605     655 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGSCHHHHHH CS
                      TPP_enzyme_M 28 seelrelaeklgiPvvttlmgkgvipedhplylg.mlglhgskaanea 74
                                      ++e+++ a++lg+Pvv  +  k++i +++    g  l l + +++++a
  gi|488600608|ref|YP_007907079.1| 29 EDEAVNKAKELGFPVVMKVVSKSIIHKSDA--GGvLLNLNSEEEVRQA 74
                                      57888889*****************98776..4435555555666655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0017
                                       HHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGG CS
                      TPP_enzyme_M   5 aellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmg 48 
                                       ++  k  k+pvi+v + ++  +  +++++ +e+l+iPv+++   
  gi|488600608|ref|YP_007907079.1| 609 IDVFKDMKKPVIVVYSSTD--EDYNHFKSRIEALNIPVFSSIER 650
                                       6788999************..******************98765 PP

>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.086   1.1e+02      92     149 ..      49     108 ..      39     111 .. 0.79
   2 ?    7.7   0.0    0.0013       1.7     166     219 ..     275     330 ..     264     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.086
                           S-layer  92 dvsllsdekLskvlidedeektlksg..ssleLeegYeleikqiDvdgdkvwleLtkdge 149
                                       ++s+++++    vl++ ++e+ +++   + + Le  Y+++++q+   g +v++ ++ +++
  gi|488600608|ref|YP_007907079.1|  49 SKSIIHKSDAGGVLLNLNSEEEVRQAfrKLIALEGAYAVTVQQMAEKGIEVMVGVSENEQ 108
                                       56777777888888887666666554226789********************99988776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0013
                           S-layer 166 vyekdlgdeddvviiavhvdevfrgtedslvviegifqisddv..leieegdefgk 219
                                          +++ +  d+v+iav  ++v++  e+ +   +gif is  +   eie g e+++
  gi|488600608|ref|YP_007907079.1| 275 KSIAEIPEDLDLVVIAVPSEKVLQVVEEAAEKTKGIFIISSGFreAEIEYGAEMQN 330
                                       44567777889*****************************7774578888888766 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       7.5   9.6e+03      71      93 ..      20      40 ..      10      52 .. 0.50
   2 ?   -3.3   0.1       7.6   9.8e+03       8      37 ..      69      98 ..      67     107 .. 0.69
   3 ?   10.0   0.0   0.00056      0.72      10      89 ..     217     303 ..     214     312 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.5
                                      TSEEEEEESSTSHHHHHHHHHCT CS
                      Response_reg 71 elpviiltahseeedavealkag 93
                                       +p+ +++ ++e   +++a ++g
  gi|488600608|ref|YP_007907079.1| 20 CTPIFLCSNEDE--AVNKAKELG 40
                                      355555553333..444444433 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.6
                                      HHHHHHHHHHHHHTTEEEEEEESSHHHHHH CS
                      Response_reg  8 plvrellrqlleeegyeevaeaedgkeale 37
                                      + vr+++r+l+  eg   v++ + +++ +e
  gi|488600608|ref|YP_007907079.1| 69 EEVRQAFRKLIALEGAYAVTVQQMAEKGIE 98
                                      568888899988777656666555555554 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00056
                                       HHHHHHHHHHHTTEEEEEEESS....HHHHHHHH.HHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEE..S CS
                      Response_reg  10 vrellrqlleeegyeevaeaed....gkealell.keekvdlillDinmpgmdGlellkeireedpelpviilt..a 79 
                                       + +l+r++l+ + + +v++ ++    g ++++ l  ++k  ++ ++ ++ ++dGl+++k i e +++l  +++   +
  gi|488600608|ref|YP_007907079.1| 217 NTNLIREILNAKSIAVVGASSNplkvGYSVIKSLsANKKLRIYPINPKLNEIDGLRVYKSIAEIPEDLDLVVIAvpS 293
                                       678899999988888888777722223445555555666999999*******************9776665555115 PP

                                       STSHHHHHHH CS
                      Response_reg  80 hseeedavea 89 
                                       ++  ++++ea
  gi|488600608|ref|YP_007907079.1| 294 EKVLQVVEEA 303
                                       5555555555 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 ?   10.5   0.1   0.00039       0.5      15     113 ..     247     344 ..     244     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                                       HHHHHHTT-EEEEES-.TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE-BSS-SS-EE-HHHHHTS-TT- CS
                            DpaA_N  15 arkLaekgakvslygl.eleekiegvekaesleealedadviilPvpgtkdggeintpfseeklsleelleklkkgq 90 
                                       +++L+++  k+++y + ++ ++i+g++ ++s++e  ed d+++  vp  k  + ++   +e+   +  + +  ++ +
  gi|488600608|ref|YP_007907079.1| 247 IKSLSAN-KKLRIYPInPKLNEIDGLRVYKSIAEIPEDLDLVVIAVPSEKVLQVVEE-AAEKTKGIFIISSGFREAE 321
                                       6666665.5889998888999**************************7777777766.4444445667999999999 PP

                                       EEEESS--HHHHHHHHHCT-EEE CS
                            DpaA_N  91 llfgGiippelkelaeekgielv 113
                                       + +g  ++++lke+ae++gi+++
  gi|488600608|ref|YP_007907079.1| 322 IEYGAEMQNRLKEVAEKNGIRIF 344
                                       99999*************99985 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.2   6.7e+03      16      37 ..      90     108 ..      86     111 .. 0.81
   2 ?   10.2   0.1   0.00066      0.85      52      93 ..     275     314 ..     229     318 .. 0.85
   3 ?   -1.8   0.0       3.8   4.9e+03      26      50 ..     617     641 ..     613     658 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.2
                                       HHHHHTTS-GGCEEEEEESSCC CS
                     F420_oxidored  16 sgllaagaqpheivvansrnpe 37 
                                       ++++++g    e++v+ s n++
  gi|488600608|ref|YP_007907079.1|  90 QQMAEKG---IEVMVGVSENEQ 108
                                       6889999...9***99887764 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00066
                                       CECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored  52 avdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                       + + +e  e+ d vv+av+ e+v +v++e+ +++ kg ++is
  gi|488600608|ref|YP_007907079.1| 275 K-SIAEIPEDLDLVVIAVPSEKVLQVVEEA-AEKTKGIFIIS 314
                                       4.667778899*******************.88899999998 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.8
                                       GCEEEEEESSCCCHHHHHHHHC-EE CS
                     F420_oxidored  26 heivvansrnpekaeelaeelgvkv 50 
                                       + ++v+ s++ e  +++++++++  
  gi|488600608|ref|YP_007907079.1| 617 KPVIVVYSSTDEDYNHFKSRIEALN 641
                                       5578889999999999999988433 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.4   1.7e+03      13      26 ..     271     284 ..     258     286 .. 0.74
   2 ?    8.7   0.3    0.0017       2.2      11      26 ..     640     655 ..     619     660 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                            NUMOD1  13 igkFsSireAakyL 26 
                                       ++++ Si e  ++L
  gi|488600608|ref|YP_007907079.1| 271 LRVYKSIAEIPEDL 284
                                       69*****9976665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                            NUMOD1  11 ktigkFsSireAakyL 26 
                                       + i++FsSi +A+k+L
  gi|488600608|ref|YP_007907079.1| 640 LNIPVFSSIERASKAL 655
                                       338***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 4078.37
//
Query:       gi|488600609|ref|YP_007907080.1|  [L=162]
Description: hypothetical protein Asulf_01086 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-57  192.1   1.1    5.4e-57  191.9   1.1    1.0  1  Adenosine_kin  Adenosine specific kinase
  ------ inclusion threshold ------
      0.036   14.2   0.1      0.067   13.4   0.1    1.4  1  HupF_HypC      HupF/HypC family


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 !  191.9   1.1     6e-61   5.4e-57       1     154 []       6     160 ..       6     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 6e-61
                                       EEE---T.TEEEEEEEESS.TTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TT CS
                     Adenosine_kin   1 vkiekpe.evnvilgqshf.iktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigagh 75 
                                       v+ie+p+ ++++i+gq +f i+t +dly +l+++vpgik+++a++Ea  ++L+rv+gndeel+e+a+knal+iga+h
  gi|488600609|ref|YP_007907080.1|   6 VEIENPDlKYQIIVGQGNFaIFTTDDLYSTLIKAVPGIKCAVAMNEAV-PKLTRVTGNDEELKEIAAKNALKIGASH 81 
                                       7899**999**************************************9.9*************************** PP

                                       EEEEEEEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTT CS
                     Adenosine_kin  76 vfvillknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkig 152
                                       vfvi+ +nafP+nvlnaiks+p v+++f+ +anp+e+ivaete gr+vlg vDG++++++e+ee+kker+el +k+g
  gi|488600609|ref|YP_007907080.1|  82 VFVIVTSNAFPMNVLNAIKSHPAVCNVFVGSANPIEIIVAETELGRAVLGAVDGTAVNRIENEEEKKERRELYQKLG 158
                                       ***************************************************************************** PP

                                       S- CS
                     Adenosine_kin 153 Yk 154
                                       Y+
  gi|488600609|ref|YP_007907080.1| 159 YR 160
                                       *7 PP

>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.4e-06     0.067       4      60 ..      90     148 ..      89     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-06
                                       EEEEEEEE.EETTEEEEECT.TEEEEEEGTTCTTB-TT-EEEEET.TEEEEEE-HHHHHH CS
                         HupF_HypC   4 aiPgkvve.iedelAlvdvg.GvrrevslalveevkvGdyVLvhv.GfAiekideeeaee 60 
                                       a P+ v++ i+ + A+++v  G    +++ +  e + G  VL  v G+A+++i++ee ++
  gi|488600609|ref|YP_007907080.1|  90 AFPMNVLNaIKSHPAVCNVFvGSANPIEIIVA-ETELGRAVLGAVdGTAVNRIENEEEKK 148
                                       7899998747779*****999********988.5********99956*******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1063.95
//
Query:       gi|488600610|ref|YP_007907081.1|  [L=393]
Description: 3-hexulose-6-phosphate synthase /formaldehyde activating enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  238.2   1.4    6.1e-71  237.5   0.1    1.8  2  Fae             Formaldehyde-activating enzyme (Fae)
      5e-23   81.9   0.1    1.4e-22   80.4   0.1    1.7  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    0.00088   18.7   0.5     0.0077   15.6   0.5    2.2  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
    0.00092   18.4   0.1     0.0023   17.1   0.1    1.7  1  NanE            Putative N-acetylmannosamine-6-phosphate epim
     0.0018   18.0   0.1     0.0072   16.1   0.0    1.8  2  PRAI            N-(5'phosphoribosyl)anthranilate (PRA) isomer
  ------ inclusion threshold ------
      0.018   14.3   0.0      0.037   13.4   0.0    1.5  1  TMP-TENI        Thiamine monophosphate synthase
      0.022   14.6   0.1      0.048   13.4   0.1    1.6  2  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
      0.092   13.1   0.1       0.24   11.7   0.1    1.7  1  Radical_SAM     Radical SAM superfamily


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 !  237.5   0.1   2.7e-74   6.1e-71       1     158 [.       3     160 ..       3     161 .. 1.00
   2 ?   -1.0   0.1      0.67   1.5e+03      65      96 ..     245     277 ..     240     289 .. 0.69

  Alignments for each domain:
  == domain 1  score: 237.5 bits;  conditional E-value: 2.7e-74
                               Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfG 77 
                                       vGEal+geg evAhidliiGe+dgp+g Afan++++ s+ghtpllav+rpnl++kP +++v+kvt+k+++qael+fG
  gi|488600610|ref|YP_007907081.1|   3 VGEALIGEGFEVAHIDLIIGERDGPAGIAFANSISQLSMGHTPLLAVIRPNLMTKPPAVIVPKVTVKEMDQAELIFG 79 
                                       8**************************************************************************** PP

                               Fae  78 paQaavakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdka 154
                                       paQ+avaka+adaveegiipke+a+d+viivsvfi+p+ak+k+ki+ yny AtklA+krA++++P++d++l ekd++
  gi|488600610|ref|YP_007907081.1|  80 PAQYAVAKAIADAVEEGIIPKEKAEDYVIIVSVFIHPKAKNKDKIFYYNYGATKLALKRAMQNFPDVDTMLYEKDRS 156
                                       ***************************************************************************** PP

                               Fae 155 khpf 158
                                       +hpf
  gi|488600610|ref|YP_007907081.1| 157 AHPF 160
                                       **98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.67
                               Fae  65 tiknekqaellfGpaQa.avakavadaveegii 96 
                                       +++ +++a+ + G a    +aka+ +a + gi+
  gi|488600610|ref|YP_007907081.1| 245 AVNATANAVVISGLAPIpTIAKAIKEARKTGIL 277
                                       556666666666666542678888887777776 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 !   80.4   0.1   6.1e-26   1.4e-22       2     224 ..     173     375 ..     172     376 .. 0.88

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 6.1e-26
                                       EEEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHH CS
                         OMPdecase   2 nLclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekq 75 
                                        L++a+D+++ +e+ ++++++ +  +++++++++lv+++g      +++ ++rk++  +  ++D+K+ D Gn ++++
  gi|488600610|ref|YP_007907081.1| 173 YLQIAIDIPDLEEVRHVLRNIPDsDHIIFEVGTPLVKRYG-----TEIILELRKEKpkAFFVLDLKTLDTGNLEARM 244
                                       69*********************99***************.....9*********9999999*************** PP

                                       HHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHH CS
                         OMPdecase  76 atagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehka 148
                                       a        + a++v ++++a   ++++++++a+k+g   l ++++++    +++ +  k  g   ++ve  r+   
  gi|488600610|ref|YP_007907081.1| 245 A------VNATANAVVISGLAPIPTIAKAIKEARKTG--ILSVVDMLNVSRPAEVLQklKeeGMLPDVVELHRAID- 312
                                       *......7999*************************8..9999999999988888774534666666666666666. PP

                                       HTTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 149 edfvmGfvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                               + ++   +++ ++ ++ ++   ++   ++++g++++++ ++ig +gadi++vGR+I++a+d + +++r
  gi|488600610|ref|YP_007907081.1| 313 --------VENK---EQPPWKFVKEIKDSFDV-LVAVAGGLRPENVGEAIG-EGADILVVGRSITRARDIEGAVRR 375
                                       ........2233...23447788889999998.******************.77******************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 !   15.6   0.5   3.5e-06    0.0077     155     197 ..     323     363 ..     239     364 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 155 kvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                        v+++ d+  +d+ + v GG++ +n+ +++ +gad+lV+g+ +
  gi|488600610|ref|YP_007907081.1| 323 FVKEIKDS--FDVLVAVAGGLRPENVGEAIGEGADILVVGRSI 363
                                       45555555..999***************************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 !   17.1   0.1     1e-06    0.0023      83     187 ..     266     377 ..     243     382 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                                       HHHHHHHHH-...-EEEEE-SSHHHHHH.HHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---S CS
                              NanE  83 elikkikeky...qllmaDistleeglv.akklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrint 155
                                       + ik+ ++++   ++ m ++s   e l+  k+ G+      l   ++ e+k++p +++vk+++++   ++a      
  gi|488600610|ref|YP_007907081.1| 266 KAIKEARKTGilsVVDMLNVSRPAEVLQkLKEEGMLPDVVELHRAIDVENKEQPPWKFVKEIKDSFDVLVAVAGGLR 342
                                       455555555533334455556666665413555653333356777788999***********998555444444457 PP

                                       HHHHHHHHTT--SEEEE-HHHH-HHHH...HHHHH CS
                              NanE 156 PekakkaieiGvdavvvGsaitrleei...akkfv 187
                                       Pe+  +ai  G+d +vvG +itr ++i   +++f 
  gi|488600610|ref|YP_007907081.1| 343 PENVGEAIGEGADILVVGRSITRARDIegaVRRFL 377
                                       ***********************998833345555 PP

>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.62   1.4e+03      57      81 ..     285     311 ..     242     322 .. 0.65
   2 !   16.1   0.0   3.2e-06    0.0072     136     164 ..     321     351 ..     317     360 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.62
                                       SS-HHHHHHHHHH..CTECEEEE-CGG CS
                              PRAI  57 Nqpieevlriaqe..lgldvvQLHGde 81 
                                           +evl++++e  +  dvv LH+  
  gi|488600610|ref|YP_007907081.1| 285 VSRPAEVLQKLKEegMLPDVVELHRAI 311
                                       444456666666522345999999876 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.2e-06
                                       GGGGTTSXX...TTEEEESSXXTTTHHHHHT CS
                              PRAI 136 wsliskllks..lkviLAGGLtpeNvaeaik 164
                                       w++++++++s  + v +AGGL peNv eai 
  gi|488600610|ref|YP_007907081.1| 321 WKFVKEIKDSfdVLVAVAGGLRPENVGEAIG 351
                                       999****999989999*************98 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.6e-05     0.037     134     181 .]     316     363 ..     311     363 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                          TMP-TENI 134 aeplgleglkelaealeiPvvaiGGitlenvaevleagadgvavvsai 181
                                       +e   ++++ke+++++ + v + GG+++env e++  gad + v ++i
  gi|488600610|ref|YP_007907081.1| 316 KEQPPWKFVKEIKDSFDVLVAVAGGLRPENVGEAIGEGADILVVGRSI 363
                                       567789**********************************99998876 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.3   9.7e+03      83      99 ..     176     192 ..     172     200 .. 0.67
   2 ?   13.4   0.1   2.1e-05     0.048      66     162 ..     264     367 ..     212     372 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.3
                                       EEEEESSHHHHHHHHHH CS
                         QRPTase_C  83 ievevesleeleevlea 99 
                                       i +++  lee+++vl  
  gi|488600610|ref|YP_007907081.1| 176 IAIDIPDLEEVRHVLRN 192
                                       66777777777777654 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHT...-SEEEEES-.....-HHHHHHHHHHHHHHSTTSEEEEES CS
                         QRPTase_C  66 iveavksvreavdkevkievevesleeleevleae...adiimLDnf.....sveelkkaveelkeknkrvlievSG 134
                                       i +a+k++r+     v   ++v+  +e+ + l++e   +d++ L        + +   k+v+e+k    +vl+ v+G
  gi|488600610|ref|YP_007907081.1| 264 IAKAIKEARKTGILSVVDMLNVSRPAEVLQKLKEEgmlPDVVELHRAidvenKEQPPWKFVKEIKDSF-DVLVAVAG 339
                                       55666666665544442234455555555555555677888888876544433333446777664444.5******* PP

                                       S--TTTHHHHHCTT-SEEEECHHCHTB- CS
                         QRPTase_C 135 gvtlenveeyaksgvdvisvgalthsvk 162
                                       g+  env e   +g d++ vg  +++++
  gi|488600610|ref|YP_007907081.1| 340 GLRPENVGEAIGEGADILVVGRSITRAR 367
                                       *********************9988876 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011      0.24      32     104 ..     184     275 ..     178     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC......................CCTEEEEEEECS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxx RF
                       Radical_SAM  32 eeileevkelkaekgvkevilgggepllypdfvellerlakla......................vpgiritvetng 86 
                                       ee+ + ++ +   ++ +++i+  g+pl+ +  +e++++l+k++                      v+   ++v+++g
  gi|488600610|ref|YP_007907081.1| 184 EEVRHVLRNI---PDSDHIIFEVGTPLVKRYGTEIILELRKEKpkaffvldlktldtgnlearmaVNATANAVVISG 257
                                       4444444444...239****************************************888866666555555555555 PP

                                       SCHGHHHHHHHHHTT-SE CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  87 tlpdeeklerllelgvdr 104
                                       + p + ++++++e++ + 
  gi|488600610|ref|YP_007907081.1| 258 LAPIPTIAKAIKEARKTG 275
                                       555577777777777333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2447.21
//
Query:       gi|488600611|ref|YP_007907082.1|  [L=220]
Description: triosephosphate isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-14   54.1   0.1    3.2e-14   52.9   0.0    1.6  2  TIM           Triosephosphate isomerase
    1.8e-05   24.2   0.0    3.1e-05   23.4   0.0    1.4  1  ThiG          Thiazole biosynthesis protein ThiG
     0.0011   18.4   0.1     0.0017   17.8   0.1    1.2  1  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.013   15.0   0.2      0.048   13.1   0.0    2.0  3  His_biosynth  Histidine biosynthesis protein
      0.063   12.4   0.0       0.11   11.6   0.0    1.5  1  IGPS          Indole-3-glycerol phosphate synthase
      0.088   11.8   0.1       0.19   10.8   0.1    1.5  1  FMN_dh        FMN-dependent dehydrogenase


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 !   52.9   0.0   1.1e-17   3.2e-14       2     126 ..       3     122 ..       2     131 .. 0.80
   2 ?   -1.3   0.0      0.39   1.2e+03     159     200 ..     135     170 ..     120     184 .. 0.56

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.1e-17
                                       EEEEE-TBTS..-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BH CS
                               TIM   2 liagNwKmnk..tleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsa 76 
                                       +i+ N+K +k  + ++a el+k +++  ++ +  ++iap+fl ++++ k++    + ++aq v+a + G++TG +  
  gi|488600611|ref|YP_007907082.1|   3 IIVINFKAYKegSGKKALELAKIVEEISSKVDDYIAIAPNFLDMSEIMKAV---DVDVYAQHVDAIEYGSHTGRIVP 76 
                                       7899****9944455566666656655555555699******999887777...5********************** PP

                                       HHHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE--- CS
                               TIM  77 emlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEt 126
                                       emlkd+g+k  +i HsErr  + + d  v +K++   + gl+ i+C  + 
  gi|488600611|ref|YP_007907082.1|  77 EMLKDIGLKGSLINHSERRLKLADIDF-VIEKFR---NLGLTSIVCTNNV 122
                                       ********************9998765.445665...5699999998765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                                       EEEE--GGGSSSS--...--HHHHHHHHHHHHHHHHHHSTHHHHT CS
                               TIM 159 viAYePvWAiGtgkt...atpeqaqevhaairkelaekvskevae 200
                                       ++A eP   iG g +   a+pe +++ ++a++k         v++
  gi|488600611|ref|YP_007907082.1| 135 FVAIEPPELIGSGIPvskADPEIVRNSVEAVKK---------VNS 170
                                       567777777777754001344444444444443.........334 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     1e-08   3.1e-05     173     213 ..     169     209 ..     142     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1e-08
                                       H-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                              ThiG 173 eakvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                       + +v v+  AGi + +d ++a++lG+++vll++ + +akdp
  gi|488600611|ref|YP_007907082.1| 169 NSNVKVLCGAGISKHEDYVTALDLGTEGVLLASGIVKAKDP 209
                                       34899***********************************9 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   5.6e-07    0.0017     127     230 ..     103     208 ..      96     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.6e-07
                               NMO 127 evvarlkeagvvliptissvkearkvearGaDalivqGpeaGGh.qGtpevgd.kglfaLvpqvldavd.iPviAaG 200
                                       +v+++  ++g+  i+ +  v    +++a+G+D + ++ pe  G  ++ ++++d +   + v+ v+++ + + v+   
  gi|488600611|ref|YP_007907082.1| 103 FVIEKFRNLGLTSIVCTNNVATTAAAAALGPDFVAIEPPELIGSgIP-VSKADpEIVRNSVEAVKKVNSnVKVLCGA 178
                                       67888899999***************************997664155.66665444444555566655599****** PP

                               NMO 201 GiidrrgvaaaLalGAsgvqigtrfLltke 230
                                       Gi ++++  +aL lG +gv +++  + +k+
  gi|488600611|ref|YP_007907082.1| 179 GISKHEDYVTALDLGTEGVLLASGIVKAKD 208
                                       **********************98887776 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.7   2.1e+03      66     116 ..      23      30 ..       3      61 .. 0.57
   2 ?   -2.4   0.0      0.87   2.6e+03     151     167 ..     103     119 ..      87     121 .. 0.76
   3 ?   13.1   0.0   1.6e-05     0.048      60     109 ..     160     207 ..     151     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.7
                                       HHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                      His_biosynth  66 eeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                       ++i+ee                                           ++
  gi|488600611|ref|YP_007907082.1|  23 AKIVEE-------------------------------------------IS 30 
                                       222222...........................................22 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.87
                                       HHHHHHHHTT-SEEEEE CS
                      His_biosynth 151 elakkleelgageillt 167
                                        +++k+ +lg+ +i++t
  gi|488600611|ref|YP_007907082.1| 103 FVIEKFRNLGLTSIVCT 119
                                       46789999999999998 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                      His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknp 109
                                       +  ++v+++ ++  ++v  G GI++ ed  ++l++g + v +++  vk +
  gi|488600611|ref|YP_007907082.1| 160 NSVEAVKKVNSN--VKVLCGAGISKHEDYVTALDLGTEGVLLASGIVKAK 207
                                       456777787777..9999************************99988754 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.7e-05      0.11     156     254 .]     110     216 ..      96     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                                       CTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTT..TEE-......CHHHHHHCHCC-TTSEEEEESSS-SHHHH CS
                              IGPS 156 slglevLvEvhdeeeleralklgakiiGvNnRnLkt..levd......lntteeLaklvpkdvllvaeSGiktredv 224
                                       +lgl  +v +++ ++ ++a +lg +++ +   +L    + v+      + ++ e +k+v+++v + +  Gi+++ed 
  gi|488600611|ref|YP_007907082.1| 110 NLGLTSIVCTNNVATTAAAAALGPDFVAIEPPELIGsgIPVSkadpeiVRNSVEAVKKVNSNVKVLCGAGISKHEDY 186
                                       56666666666666666666666666666666664311222211111134566777888999*************** PP

                                       HHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 225 eklkeegvnafLvGeslmrqedvekairel 254
                                        +  + g +++L  + +++++d + a++el
  gi|488600611|ref|YP_007907082.1| 187 VTALDLGTEGVLLASGIVKAKDPRFALEEL 216
                                       **********************99998876 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   6.2e-05      0.19     263     302 ..     163     202 ..     152     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.2e-05
                                       HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                            FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                       e v++v+++++vl+  Gi++ +D + Al lG ++vll+  
  gi|488600611|ref|YP_007907082.1| 163 EAVKKVNSNVKVLCGAGISKHEDYVTALDLGTEGVLLASG 202
                                       567888889**************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1165.60
//
Query:       gi|488600612|ref|YP_007907083.1|  [L=328]
Description: 3-isopropylmalate dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-106  354.1   0.0   9.6e-106  353.8   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 !  353.8   0.0  5.3e-110  9.6e-106       1     348 []       3     322 ..       3     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 353.8 bits;  conditional E-value: 5.3e-110
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSS CS
                            Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkek 77 
                                       kia+++gdgiG+ev++a lkvl+a +   +  +e+  +++G ++ ++tge+lp+etl+++ke+++vl+ga g     
  gi|488600612|ref|YP_007907083.1|   3 KIAVIPGDGIGKEVMSACLKVLEAFD--FP--FEYVFAEAGDETKEKTGEALPDETLQICKESSAVLFGAAGETA-- 73 
                                       79**********************99..55..8888899*******************************98877.. PP

                                       SSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEE CS
                            Iso_dh  78 evrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdt 154
                                              +++Lr el++fanlrp+k++   +vk+       ++vd+v+vRe+t+ +Y g e e k+      v  ++
  gi|488600612|ref|YP_007907083.1|  74 ----ADVIVRLRLELETFANLRPAKSY--KGVKCLF-----DNVDIVVVRENTECLYKGLEFEVKKG-----VTEGI 134
                                       ....55699******************..4555544.....57******************999997.....78899 PP

                                       EEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGG CS
                            Iso_dh 155 klyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspk 230
                                         ++e+++eriar+afelA++ g+k+vt+++Kanv+k++  l+r+++ +va+ +y die+++ ++D+ +m+lv +p 
  gi|488600612|ref|YP_007907083.1| 135 RIITEKASERIARYAFELARRDGRKRVTALHKANVMKKTCgLFRDVCRRVAR-DYDDIEFSDYYIDAGCMYLVLDPW 210
                                       9**************************************99***********.************************ PP

                                       GGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT- CS
                            Iso_dh 231 qfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgl 307
                                       +fdVivt+N+fGDi+SD+ a lvG+lGl+pSa++g +k aifE+vHGsapdiagk++aNp+a+ilS +lmLr+ +g 
  gi|488600612|ref|YP_007907083.1| 211 RFDVIVTTNMFGDIVSDLIAGLVGGLGLAPSANIG-EKYAIFEPVHGSAPDIAGKGIANPSAMILSSTLMLRH-FGY 285
                                       ***********************************.68***********************************.*** PP

                                       HHHHHHHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 308 eeaAdkiekAvekvleagivTkDlageaakevstsefgdav 348
                                         +A++iekA+ek++++g++T Dl+g+     +t+e+++++
  gi|488600612|ref|YP_007907083.1| 286 ISEAERIEKALEKTIAEGKTTPDLGGNL----KTDEMVEEI 322
                                       **************************99....*****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 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:                        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: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 1741.92
//
Query:       gi|488600613|ref|YP_007907084.1|  [L=162]
Description: 3-isopropylmalate dehydratase, small subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   77.0   0.0    2.2e-21   76.6   0.0    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 !   76.6   0.0   1.2e-25   2.2e-21      72     129 ..      47     103 ..      10     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.2e-25
                                       TT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                       Aconitase_C  72 egaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefk 129
                                       +  ++vv++ +nfG+GSSRehA++al++ G+ka+ia+SF+rIf +n+i+ +l+ le k
  gi|488600613|ref|YP_007907084.1|  47 KAGDFVVAG-ENFGCGSSREHAPLALKATGVKAIIAKSFARIFFRNAINLALMVLECK 103
                                       355666666.*******************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 959.12
//
Query:       gi|488600614|ref|YP_007907085.1|  [L=208]
Description: hypothetical protein Asulf_01091 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-09   37.0   0.0    4.1e-09   36.0   0.0    1.6  1  S4               S4 domain
    8.8e-07   29.2   0.0    1.1e-06   28.8   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
      6e-05   22.9   0.1    8.6e-05   22.4   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00027   21.6   0.0    0.00043   20.9   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
      0.001   19.7   0.0     0.0017   19.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0034   16.5   0.0     0.0053   15.9   0.0    1.4  1  Fibrillarin      Fibrillarin
     0.0094   15.1   0.0      0.012   14.7   0.0    1.2  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.026   14.3   0.0    1.4  1  S4_2             S4 domain
      0.019   14.8   0.0      0.027   14.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      0.033   15.2   0.0      0.054   14.5   0.0    1.3  1  Methyltransf_24  Methyltransferase domain
      0.094   12.3   0.0       0.14   11.7   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.095   12.0   0.0       0.15   11.3   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
       0.11   12.2   0.0       0.15   11.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !   36.0   0.0     3e-12   4.1e-09       1      45 [.       1      45 [.       1      48 [. 0.94

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3e-12
                                      EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TT CS
                                S4  1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpg 45
                                      +RLd++l++ g+ s+r +A+ +I+ + V VNG  ++ ps+ V+ +
  gi|488600614|ref|YP_007907085.1|  1 MRLDDLLVKRGYFSTRQKAKIAIKNKLVFVNGALADRPSMDVELS 45
                                      8***************************************99865 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   8.3e-10   1.1e-06       5      95 ..      58     146 ..      55     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.3e-10
                                       HHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.....HHH..TTEEEECS-CCCSS CS
                              FtsJ   5 sayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.....apl..pgvttiqgditdpe 74 
                                       +  KL  ++ek +++k+g++v+Dlg++ Gg++ +++        vv++          + +  ++v++i +d+++ +
  gi|488600614|ref|YP_007907085.1|  58 GYWKLKRLNEKWNFIKRGDRVLDLGSSAGGFISYASSFA---DLVVGIEYSREfeedlKRVeqKNVRIIFADVFEVD 131
                                       668**********99********************9993...68****99655586553336678888888888776 PP

                                       HHHHHCHCHHHSSEEEEEE-- CS
                              FtsJ  75 tiekikealserkvdlvvsDg 95 
                                                   k+d+++ D+
  gi|488600614|ref|YP_007907085.1| 132 ISSFD------FKFDVILDDL 146
                                       55522......3577777776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   6.2e-08   8.6e-05       2     108 ..      73     171 ..      72     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.2e-08
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfD 76 
                                       ++g rvlDlG+ +G ++  + +     a+ vvGi++s e  e  +      + +nv+   +d++e + + +   kfD
  gi|488600614|ref|YP_007907085.1|  73 KRGDRVLDLGSSAGGFISYASS----FADlVVGIEYSREFEEDLKR----VEQKNVRIIFADVFEVDISsFD-FKFD 140
                                       67899*******9999888884....2333*******987444333....3347888888888887766455.89** PP

                   Methyltransf_31  77 lilsnevlnaladpdkileeiervlkpggill 108
                                       +il++ +l   +d+ k+l++ + vlk++g  l
  gi|488600614|ref|YP_007907085.1| 141 VILDDLTL-KPSDSYKALKRFIPVLKDKGLAL 171
                                       *****999.889999***********999765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.1e-07   0.00043       1      97 []      78     168 ..      78     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.1e-07
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG..BSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed..lpfedgsfDlvvssgalh 75 
                                       vLdlG   G ++ +++    +  v+g+++s e+ e  ++   ++  nv+++ +d+ +  ++  d +fD+++    l 
  gi|488600614|ref|YP_007907085.1|  78 VLDLGSSAGGFISYASSF--ADLVVGIEYSREFEEDLKRVE-QK--NVRIIFADVFEvdISSFDFKFDVILDD--LT 147
                                       9*********99998866..49***********99988766.33..688888888661144566789999984..44 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                        l+++d  kalk++  vLk++G
  gi|488600614|ref|YP_007907085.1| 148 -LKPSDSYKALKRFIPVLKDKG 168
                                       .5778999***********998 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   1.2e-06    0.0017       1      96 []      79     172 ..      79     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTS..S-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklp..fednsfDlvvssevlhhve 75 
                                       Ld+G+ +G +  +  + +  vvg+++s e+ +  k+  +++   v+++ ad+ ++     d +fD+++   +l    
  gi|488600614|ref|YP_007907085.1|  79 LDLGSSAGGFISYASSFADLVVGIEYSREFEEDLKRVEQKN---VRIIFADVFEVDisSFDFKFDVILDDLTLKPS- 151
                                       8**************999*************8886555544...88899999975511345699999999999998. PP

                                       CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                       d  kalk +  vLk  Gl ++
  gi|488600614|ref|YP_007907085.1| 152 DSYKALKRFIPVLKDKGLALF 172
                                       79***************9875 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.9e-06    0.0053      66     128 ..      70     127 ..      63     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-06
                                       -S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-T CS
                       Fibrillarin  66 lpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDA 128
                                         ik+g++vL lG+++G  +s+ s   +   +v ++e+s     +l +v +k  n+  i +D 
  gi|488600614|ref|YP_007907085.1|  70 NFIKRGDRVLDLGSSAGGFISYASSFAD---LVVGIEYSREFEEDLKRVEQK--NVRIIFADV 127
                                       579*********************9998...999********99*9999765..666666665 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   8.8e-06     0.012      80     182 ..      61     168 ..      47     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.8e-06
                              DREV  80 kllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlk...kkkynvls....alelqetd 149
                                       kl  ++ e+++  ++  ++ldlG+  G      +++ + v   e s +  + lk   +k+ +++     ++++   d
  gi|488600614|ref|YP_007907085.1|  61 KLKRLN-EKWNFIKRGDRVLDLGSSAGGFISYASSFADLVVGIEYSREFEEDLKrveQKNVRIIFadvfEVDISSFD 136
                                       555566.89999999***************9*********999*999987665511167777764222257899999 PP

                              DREV 150 vkldlilclnlldrcfdplklledirsalepng 182
                                       +k+d+il  +l  +  d++k l+    +l+ +g
  gi|488600614|ref|YP_007907085.1| 137 FKFDVILD-DLTLKPSDSYKALKRFIPVLKDKG 168
                                       ****9975.333455666666666666666555 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05     0.026       9      44 ..       2      37 ..       1      43 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                              S4_2  9 tLgqlLKlaglvesGgeaKafiaegeVkvNGevetr 44
                                      +L++lL + g+ ++  +aK+ i+++ V+vNG+  +r
  gi|488600614|ref|YP_007907085.1|  2 RLDDLLVKRGYFSTRQKAKIAIKNKLVFVNGALADR 37
                                      799999999999*******************98876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     2e-05     0.027      20     117 ..      72     172 ..      53     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlrev 91 
                                        ++g rvLd+G   G + ++++ +   v+g++ s+e  e ++     + +  + d f e +++  + kfd+I    +
  gi|488600614|ref|YP_007907085.1|  72 IKRGDRVLDLGSSAGGFISYASSFADLVVGIEYSREFEEDLKrveqkNVRIIFADVF-EVDISSFDFKFDVILDDLT 147
                                       57899**************9998888999*****98777766777743333333333.6677777779999987666 PP

                   Methyltransf_23  92 lehvpdppellrqiatllkpgGylll 117
                                       l   +   ++l+++   lk+ G++l+
  gi|488600614|ref|YP_007907085.1| 148 LKPSD-SYKALKRFIPVLKDKGLALF 172
                                       65544.46779999999999998887 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     4e-05     0.054      48     103 ..     117     172 ..      79     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-05
                   Methyltransf_24  48 ddrvrlikadsee.alaslaagsiDllfiDgghaaeavledleallprlapggvvlf 103
                                       +++vr+i ad +e  ++s++  ++D+++ D   + ++ +++l+ + p+l+++g+ lf
  gi|488600614|ref|YP_007907085.1| 117 QKNVRIIFADVFEvDISSFD-FKFDVILDDLTLKPSDSYKALKRFIPVLKDKGLALF 172
                                       467********994599999.99******************************9876 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.14       9      85 ..      70     148 ..      64     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                              MetW   9 elikpgsrvldlGcGdGellellkeekqvdgrGlelde...egvaecvakGlsviqgdl.dkdlenfedksfdyvvl 81 
                                       ++ik g rvldlG+  G ++++     ++   G+e ++   e ++++ +k + +i  d+ + d++ f d +fd+++ 
  gi|488600614|ref|YP_007907085.1|  70 NFIKRGDRVLDLGSSAGGFISYASSFADL-VVGIEYSRefeEDLKRVEQKNVRIIFADVfEVDISSF-DFKFDVILD 144
                                       789******************99887776.579999962225789999*****99999747788888.567998776 PP

                              MetW  82 sqtl 85 
                                         tl
  gi|488600614|ref|YP_007907085.1| 145 DLTL 148
                                       6665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    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      50     124 ..      61     135 ..      57     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       HHHHHHTTTT.--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG- CS
                              CMAS  50 Kldlilekle.lkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl 124
                                       Kl+++ ek + +k G+++Ld+G   G+ + +a + +   vvg+  S+e ++  k++ ++      ++v   d   +
  gi|488600614|ref|YP_007907085.1|  61 KLKRLNEKWNfIKRGDRVLDLGSSAGGFISYASS-FADLVVGIEYSREFEEDLKRVEQKNVRIIFADVFEVDISSF 135
                                       77777777764799**************999865.67789******998766554433333223344444444444 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.15      68     132 ..      69     126 ..      27     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                       HTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  68 llelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       +  +k+g+rvL++Gs +G      + +     +vv+ie+++e+     + lk+ +++nv ++++D
  gi|488600614|ref|YP_007907085.1|  69 WNFIKRGDRVLDLGSSAGGFISYASSF---ADLVVGIEYSREFE----EDLKRVEQKNVRIIFAD 126
                                       44599***********99766555554...34689*****9985....45777777888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1260.36
//
Query:       gi|488600615|ref|YP_007907086.1|  [L=179]
Description: dITPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-48  164.4   0.0      3e-48  164.2   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 !  164.2   0.0   1.7e-52     3e-48       2     186 ..       2     173 ..       1     174 [. 0.88

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 1.7e-52
                                       EEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTT CS
                        Ham1p_like   2 vfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLngl 76 
                                       +f+T+NkgK+ e+ ei ++ ++e++      ++++eE q +++ee+a+k a a+++ ++ p++++DsgL+++aLng+
  gi|488600615|ref|YP_007907086.1|   2 LFITSNKGKFDEAYEIGKKYGFEIEWR----KEKYEEFQgDSLEEIAYKSALALVNkIKEPFFIEDSGLFINALNGF 74 
                                       79**************98888887733....457779999*************99747888**************** PP

                                       BGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGG CS
                        Ham1p_like  77 PGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpi 153
                                       PG+ys+++ ++      +++ +l+ +e++e +r+A+f++v+a++d+  +++++f+GeveGei +e+rg++gfGyDp+
  gi|488600615|ref|YP_007907086.1|  75 PGPYSSYVFKT-----IGNDGILRLMEGVE-NRKAKFIAVIAYFDG--SRVRIFNGEVEGEISREKRGDKGFGYDPV 143
                                       ********754.....46677777776444.8************95..7779************************* PP

                                       EEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHH CS
                        Ham1p_like 154 FvpeegektfaelskeeknaiShRgkAleklle 186
                                       F +  g+ktfael  eekn++ShR++Ale++ e
  gi|488600615|ref|YP_007907086.1| 144 FLY--GDKTFAELG-EEKNEVSHRRRALERFFE 173
                                       *99..599*****9.89************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1297.76
//
Query:       gi|488600616|ref|YP_007907087.1|  [L=205]
Description: hypothetical protein Asulf_01093 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0013   19.0   0.0     0.0022   18.3   0.0    1.4  1  TrkA_N    TrkA-N domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-07    0.0022       2      40 ..       3      41 ..       3      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-07
                                      EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHT CS
                            TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelree 40
                                      ++ G Gr G+  +e+L +++k+++vid +++ +++ + +
  gi|488600616|ref|YP_007907087.1|  3 VVYGGGRYGSDAVEYLISEKKQFIVIDENPNCLANTKFK 41
                                      799***************8889********988776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1197.31
//
Query:       gi|488600617|ref|YP_007907088.1|  [L=347]
Description: putative acyl-CoA transferases/carnitine dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-87  292.8   0.0    4.2e-87  292.7   0.0    1.0  1  CoA_transf_3    CoA-transferase family III
  ------ inclusion threshold ------
      0.017   14.2   0.0      0.026   13.6   0.0    1.2  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.7   0.0   4.7e-91   4.2e-87       1     367 [.       2     345 ..       2     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: 292.7 bits;  conditional E-value: 4.7e-91
                      CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegre 77 
                                       L+ +rVl++++++ Gp++t++LA++GAeVIk+Epp +gDp+R+        + ++f a+nrnK+s++l+lk+e + +
  gi|488600617|ref|YP_007907088.1|   2 LSNIRVLEVAYFYPGPFCTQILAEHGAEVIKIEPP-TGDPMRY--------DRTLFSAFNRNKKSIVLNLKDEGDLK 69 
                                       799********************************.******6........689*********************** PP

                      CoA_transf_3  78 llkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdg 154
                                        + +Lv+k+DV++e frpgv++rlg++y+++r+ n  +iy+s+sg+Gq+ +  + p +D+++ + sG++ ++g +d+
  gi|488600617|ref|YP_007907088.1|  70 KFYELVKKSDVIVEGFRPGVAKRLGIDYDTVRKYNKGIIYCSISGFGQDSELLDIPVHDINVLSFSGICRISGIKDN 146
                                       ***************************************************************************** PP

                      CoA_transf_3 155 pPvkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaap. 230
                                        P  ++v++ D+ ++++a+++il+al++r +tG+G+ idvs++++a+a +  + + y+++   +      d++++p 
  gi|488600617|ref|YP_007907088.1| 147 VPRDPNVQISDFSSAVFAVISILMALIKRMKTGEGEYIDVSMMDSAAASIPLHSASYMNGSSDRM-----DFKSNPg 218
                                       ********************************************************999999988.....6766666 PP

                      CoA_transf_3 231 ygvyrtkdgwvaia.aatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaag 306
                                       y++y+t+dg+++++ + ++++w++lc++l+ +e+ +d  +a++ +   + +e++ +++e++++ ++ e+ ++l++++
  gi|488600617|ref|YP_007907088.1| 219 YEIYKTRDGHISLGiMDEPHFWRNLCRVLEIEEY-ADISYAERLE---RYDEIRSRISEIIMKFKTSEISDILRRNN 291
                                       **************6778889***********98.4555555555...59*************************** PP

                      CoA_transf_3 307 vpaapvntleevlddpqlaarglvvevddpdygevpvvglpvrlsetparvkraaPklGed 367
                                       +p++ vn   ++   + l++rg++ +++++       vg+p++++  +++   + P lG d
  gi|488600617|ref|YP_007907088.1| 292 IPFGVVNHFTDA--VELLKKRGILAKTENGI-----FVGFPAKYKYYTPKRDGKVPDLGGD 345
                                       ************..789*************9.....9*********999999999**9987 PP

>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.9e-06     0.026      34     151 ..     137     255 ..     134     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-06
                                       TBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTH CS
                    Complex1_49kDa  34 yiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvgvlskeealelgltGpvlRasGvkyDl 110
                                       ++ri G++ ++p++   +i++f + + + ++ l  l+++ ++      +v++++++ a     +   + +s  ++D+
  gi|488600617|ref|YP_007907088.1| 137 ICRISGIKDNVPRDPNVQISDFSSAVFAVISILMALIKRMKTGEGEYIDVSMMDSAAASIPLHSASYMNGSSDRMDF 213
                                       689*******************************************************9999*************** PP

                                       HHHSS-SSGGGS-------SS.BSHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa 111 RkaepYeaYdeldfdvpvgee.gDvydRylvrveEmrqSlkI 151
                                         +  Ye+Y++ d ++ +g      + R l+rv E+++ ++I
  gi|488600617|ref|YP_007907088.1| 214 KSNPGYEIYKTRDGHISLGIMdEPHFWRNLCRVLEIEEYADI 255
                                       *****************9865266899*********998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2157.63
//
Query:       gi|488600618|ref|YP_007907089.1|  [L=330]
Description: hypothetical protein Asulf_01095 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-07   29.6  13.3      0.013   15.9   4.1    3.8  3  TPR_19    Tetratricopeptide repeat
    1.7e-05   25.2  20.3       0.04   14.5   0.2    6.5  6  TPR_6     Tetratricopeptide repeat
    3.1e-05   23.7  39.3       0.65   10.3   0.7    7.4  7  TPR_2     Tetratricopeptide repeat
     0.0022   17.5  23.5     0.0022   17.5  23.5    2.2  2  SNAP      Soluble NSF attachment protein, SNAP
  ------ inclusion threshold ------
      0.096   12.8   2.5        6.2    7.1   0.0    3.9  3  TPR_9     Tetratricopeptide repeat
       0.83    9.9   7.4         30    5.0   0.8    3.9  3  PerC      PerC transcriptional activator
       0.95   10.5  16.2         12    7.0   0.1    5.3  6  TPR_14    Tetratricopeptide repeat
        3.6    7.8  19.5         23    5.3   0.5    5.8  6  TPR_7     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.1     6e-06     0.013       4      61 ..     127     188 ..     124     194 .. 0.87
   2 ?    4.9   0.0     0.017        39      37      63 ..     198     225 ..     192     230 .. 0.80
   3 !   13.2   0.3   4.4e-05     0.099      12      53 ..     280     321 ..     262     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6e-06
                            TPR_19   4 egdyaeAlalleqalqedpk.naearllL....AeallalgqldeAealLdalpeedpddary 61 
                                       +g+y +A++ +e+a q++     ++++++    A ++ ++ q+++  ++ ++l e ++d ++y
  gi|488600618|ref|YP_007907089.1| 127 SGNYRAAARKYEKAGQYEKAaENYLKAGMeesaAWCYEKADQYEKCAEIYERLAETKKD-SYY 188
                                       79************9996555666666777788**************************.887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                            TPR_19  37 algqldeAealLdalpeedpdd.aryas 63 
                                       ++g+l+ A ++L+++ ee+p   +++a+
  gi|488600618|ref|YP_007907089.1| 198 KAGNLERAGKCLEKYAEEEPWYwEDVAK 225
                                       89***************99964366555 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 4.4e-05
                            TPR_19  12 alleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       ++l +al+e+ ++++ +   Aea+ +lg  ++A+++++++ e
  gi|488600618|ref|YP_007907089.1| 280 NFLNYALKEAEQDDAWWKHVAEAYEKLGIDEKAKEAMKRYEE 321
                                       78999*********************************9876 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.1     0.094   2.1e+02      10      23 ..     137     150 ..     119     153 .. 0.74
   2 !   14.5   0.2   1.8e-05      0.04       6      28 ..     159     181 ..     158     182 .. 0.93
   3 ?    3.1   0.1     0.078   1.7e+02      11      31 ..     196     217 ..     185     217 .. 0.77
   4 ?    4.8   0.1     0.023        52       7      30 ..     224     247 ..     223     249 .. 0.82
   5 ?    1.9   0.0       0.2   4.4e+02      10      28 ..     265     283 ..     261     285 .. 0.84
   6 !    7.2   0.2     0.004       8.9       7      26 ..     300     319 ..     298     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.094
                                       HHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAleal 23 
                                       y+k+g+++kA e +
  gi|488600618|ref|YP_007907089.1| 137 YEKAGQYEKAAENY 150
                                       55688999988855 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       +a++y+k+++++k  e++erl +
  gi|488600618|ref|YP_007907089.1| 159 AAWCYEKADQYEKCAEIYERLAE 181
                                       59******************976 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.078
                                       HH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6  11 rk.lgdtdkAlealerlikeYP 31 
                                        k +g+ ++A + le+  +e P
  gi|488600618|ref|YP_007907089.1| 196 WKkAGNLERAGKCLEKYAEEEP 217
                                       44479***********999877 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeY 30 
                                       a++ ++ ++++kA+ea++  ++ Y
  gi|488600618|ref|YP_007907089.1| 224 AKLWEEVKNKEKAREAWKMALEYY 247
                                       556677569***********9998 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerlik 28 
                                        +klg  +++++a+e++++
  gi|488600618|ref|YP_007907089.1| 265 CKKLGMEEESRKAWENFLN 283
                                       56789************97 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.004
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealerl 26 
                                       a++y+klg  +kA+ea++r 
  gi|488600618|ref|YP_007907089.1| 300 AEAYEKLGIDEKAKEAMKRY 319
                                       99****99********9986 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.5    0.0036       8.2       8      27 ..     121     140 ..     118     140 .. 0.89
   2 !    7.1   7.0     0.003       6.6       4      27 ..     130     153 ..     128     155 .. 0.91
   3 !   10.3   0.7   0.00029      0.65       8      29 ..     160     181 ..     158     186 .. 0.90
   4 ?    3.8   0.3     0.035        78      13      32 ..     198     217 ..     194     217 .. 0.87
   5 !    9.3   0.8    0.0006       1.3       3      32 ..     219     248 ..     217     250 .. 0.88
   6 ?    4.8   0.0     0.017        37       4      28 ..     258     282 ..     256     286 .. 0.87
   7 !    7.5   1.3    0.0022       4.9       3      26 ..     295     318 ..     293     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0036
                             TPR_2   8 GlayyklgdyeeAleafekA 27 
                                       + +++ +g+y  A++ +ekA
  gi|488600618|ref|YP_007907089.1| 121 ASSLEGSGNYRAAARKYEKA 140
                                       5678899************9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.003
                             TPR_2   4 lynlGlayyklgdyeeAleafekA 27 
                                       + + ++ y+k+g+ye+A+e + kA
  gi|488600618|ref|YP_007907089.1| 130 YRAAARKYEKAGQYEKAAENYLKA 153
                                       5677999***************98 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00029
                             TPR_2   8 GlayyklgdyeeAleafekAle 29 
                                       +++y+k+++ye+++e +e+  e
  gi|488600618|ref|YP_007907089.1| 160 AWCYEKADQYEKCAEIYERLAE 181
                                       89****************9876 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.035
                             TPR_2  13 klgdyeeAleafekAleldP 32 
                                       k+g++e+A +++ek  e +P
  gi|488600618|ref|YP_007907089.1| 198 KAGNLERAGKCLEKYAEEEP 217
                                       89************888776 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0006
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       ++   ++++++ ++ e+A+ea++ Ale++ 
  gi|488600618|ref|YP_007907089.1| 219 YWEDVAKLWEEVKNKEKAREAWKMALEYYK 248
                                       677789999999***************986 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.017
                             TPR_2   4 lynlGlayyklgdyeeAleafekAl 28 
                                       +   ++++ klg  ee ++a+e  l
  gi|488600618|ref|YP_007907089.1| 258 WEDVANICKKLGMEEESRKAWENFL 282
                                       66789****************9766 PP

  == domain 7  score: 7.5 bits;  conditional E-value: 0.0022
                             TPR_2   3 alynlGlayyklgdyeeAleafek 26 
                                       ++   ++ay+klg  e+A+ea+++
  gi|488600618|ref|YP_007907089.1| 295 WWKHVAEAYEKLGIDEKAKEAMKR 318
                                       89999****************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 !   17.5  23.5   9.7e-07    0.0022      36     181 ..     128     281 ..     114     296 .. 0.79
   2 ?   -0.8   0.2      0.37   8.2e+02     118     140 ..     297     321 ..     291     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.7e-07
                                       HHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HH CS
                              SNAP  36 dlyeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfr 111
                                         y  AA++y  a ++e+A+e +lka  ++e++    e a++y + a++y++  ++++    l++A e++ ++g+++
  gi|488600618|ref|YP_007907089.1| 128 GNYRAAARKYEKAGQYEKAAENYLKAG-MEESAAWCYEKADQYEKCAEIYERLaETKKDSYYLKEAYEFWKKAGNLE 203
                                       569999*****************9965.67778999999999999999999986677888899************** PP

                                       HHHHHHHHHHH...HHHHTT.......--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              SNAP 112 raAklkkeiae...lyekel.......gdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiy 178
                                       ra+k  ++ ae    y +++       +++ekA ea++ A e+y++e  +     ++++vA++  +l+  e++ +++
  gi|488600618|ref|YP_007907089.1| 204 RAGKCLEKYAEeepWYWEDVaklweevKNKEKAREAWKMALEYYKKEAEEE--GVFWEDVANICKKLGMEEESRKAW 278
                                       ****9999998444344444444544477****************998654..567899999988887555555555 PP

                                       HHH CS
                              SNAP 179 ekv 181
                                       e+ 
  gi|488600618|ref|YP_007907089.1| 279 ENF 281
                                       543 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.37
                                       HHHHHHHHHTT..--HHHHHHHHHH CS
                              SNAP 118 keiaelyekel..gdlekAieaYek 140
                                       k++ae yek    ++ ++A++ Ye+
  gi|488600618|ref|YP_007907089.1| 297 KHVAEAYEKLGidEKAKEAMKRYEE 321
                                       6788888875433558888888875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.24   5.3e+02      32      49 ..     130     147 ..     115     151 .. 0.66
   2 ?    7.1   0.0    0.0027       6.2       5      60 ..     163     217 ..     160     245 .. 0.81
   3 ?    1.2   0.1      0.19   4.1e+02      30      55 ..     294     319 ..     271     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.24
                             TPR_9  32 rrdRGlllaqlGclsaAl 49 
                                       +r  ++ +++ G++++A+
  gi|488600618|ref|YP_007907089.1| 130 YRAAARKYEKAGQYEKAA 147
                                       455556666666666665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0027
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       +  ++++e++ +++erl   + d+ ++  +      + G+l+ A ++Le y++ +p
  gi|488600618|ref|YP_007907089.1| 163 YEKADQYEKCAEIYERLAETKKDSYYL-KEAYEFWKKAGNLERAGKCLEKYAEEEP 217
                                       788999999999999999999999665.5555778889999999999999999888 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.19
                             TPR_9  30 eerrdRGlllaqlGclsaAladLeay 55 
                                         +   + ++++lG  ++A +++ +y
  gi|488600618|ref|YP_007907089.1| 294 AWWKHVAEAYEKLGIDEKAKEAMKRY 319
                                       57888999*************99998 PP

>> PerC  PerC transcriptional activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8     0.013        30       7      30 ..     121     143 ..     117     187 .. 0.63
   2 ?    2.0   0.2      0.11   2.5e+02      66      87 ..     260     281 ..     197     284 .. 0.82
   3 ?    4.5   0.0     0.019        43      65      89 ..     297     321 ..     288     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.013
                              PerC   7 aekLeakGlyRRaadRWaevmvll 30 
                                       a  Le  G yR aa ++ +  ++ 
  gi|488600618|ref|YP_007907089.1| 121 ASSLEGSGNYRAAARKYEK-AGQY 143
                                       6667777777655555443.2333 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                              PerC  66 avdrtykelGlatvseevfRky 87 
                                        v ++ k+lG++ +s++ + ++
  gi|488600618|ref|YP_007907089.1| 260 DVANICKKLGMEEESRKAWENF 281
                                       4667889999999999999875 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.019
                              PerC  65 kavdrtykelGlatvseevfRkyke 89 
                                       k v ++y++lG++ + +e  ++y+e
  gi|488600618|ref|YP_007907089.1| 297 KHVAEAYEKLGIDEKAKEAMKRYEE 321
                                       67899***************99986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.2     0.032        72       6      43 ..     145     181 ..     119     182 .. 0.67
   2 ?    4.2   0.2     0.044        98       8      33 ..     160     185 ..     155     193 .. 0.78
   3 ?    7.0   0.1    0.0054        12       9      36 ..     194     221 ..     186     228 .. 0.80
   4 ?    0.9   0.1       0.5   1.1e+03       2      32 ..     218     248 ..     217     254 .. 0.71
   5 ?    0.5   0.1      0.65   1.5e+03       7      43 ..     261     301 ..     256     302 .. 0.74
   6 ?    1.1   0.2      0.43   9.6e+02       4      26 ..     296     321 ..     292     325 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.032
                            TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       ++ae +l +G  + A+ ++++a +++ + ae++ +la+
  gi|488600618|ref|YP_007907089.1| 145 KAAENYLKAGMEESAAWCYEKA-DQYEKCAEIYERLAE 181
                                       3455566666666666666666.567777777777765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.044
                            TPR_14   8 aeallalGdpdeAiallrralalaPd 33 
                                       a+ ++ ++++++ +++++r+ ++  d
  gi|488600618|ref|YP_007907089.1| 160 AWCYEKADQYEKCAEIYERLAETKKD 185
                                       66788999999999999999776555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0054
                            TPR_14   9 eallalGdpdeAiallrralalaPddae 36 
                                       e+   +G++++A ++l+++ +  P+ +e
  gi|488600618|ref|YP_007907089.1| 194 EFWKKAGNLERAGKCLEKYAEEEPWYWE 221
                                       455689*************999998876 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.5
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaP 32 
                                       + + + a++ ++  + ++A+++ + al+ + 
  gi|488600618|ref|YP_007907089.1| 218 WYWEDVAKLWEEVKNKEKAREAWKMALEYYK 248
                                       5566777777888888888888888887554 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.65
                            TPR_14   7 laeallalGdpdeAiallrr....alalaPddaeawlllaq 43 
                                        a ++  lG  +e++++ +     al+ a +d+++w + a+
  gi|488600618|ref|YP_007907089.1| 261 VANICKKLGMEEESRKAWENflnyALKEAEQDDAWWKHVAE 301
                                       56777777888888887777666688899999999987665 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.43
                            TPR_14   4 llalaeallalG...dpdeAiallrr 26 
                                       ++  aea++ lG   + +eA++ +++
  gi|488600618|ref|YP_007907089.1| 296 WKHVAEAYEKLGideKAKEAMKRYEE 321
                                       56779999999843345555555555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.014        31      10      27 ..     125     140 ..     119     141 .. 0.82
   2 ?    4.2   4.2     0.024        53       9      28 ..     137     154 ..     130     166 .. 0.85
   3 ?    5.3   0.5      0.01        23       6      31 ..     160     185 ..     157     187 .. 0.85
   4 ?   -0.2   0.0      0.58   1.3e+03       9      24 ..     196     211 ..     194     217 .. 0.83
   5 ?    3.2   0.2     0.047   1.1e+02      15      28 ..     240     251 ..     224     255 .. 0.88
   6 ?   -1.2   0.0       1.2   2.7e+03       6      19 ..     300     313 ..     296     321 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.014
                             TPR_7  10 srlGdyeeAielyeqsLa 27 
                                       +  G+y+ A++ ye+  a
  gi|488600618|ref|YP_007907089.1| 125 EGSGNYRAAARKYEK--A 140
                                       558***********9..4 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.024
                             TPR_7   9 ysrlGdyeeAielyeqsLal 28 
                                       y++ G+ye+A+e y +  a 
  gi|488600618|ref|YP_007907089.1| 137 YEKAGQYEKAAENYLK--AG 154
                                       999***********99..65 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.01
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                       a +y++  +ye+ +e+ye++ ++ kd
  gi|488600618|ref|YP_007907089.1| 160 AWCYEKADQYEKCAEIYERLAETKKD 185
                                       7899999************7787776 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.58
                             TPR_7   9 ysrlGdyeeAielyeq 24 
                                       + + G+ e+A +++e+
  gi|488600618|ref|YP_007907089.1| 196 WKKAGNLERAGKCLEK 211
                                       77899*****999998 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.047
                             TPR_7  15 yeeAielyeqsLal 28 
                                       ++ A+e+y++  + 
  gi|488600618|ref|YP_007907089.1| 240 WKMALEYYKK--EA 251
                                       899******9..65 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 1.2
                             TPR_7   6 arlysrlGdyeeAi 19 
                                       a++y++lG  e+A 
  gi|488600618|ref|YP_007907089.1| 300 AEAYEKLGIDEKAK 313
                                       67888877666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1973  (0.110045); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2246.25
//
Query:       gi|488600619|ref|YP_007907090.1|  [L=136]
Description: heat shock protein Hsp20 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-21   74.3   3.5    8.3e-21   74.1   3.5    1.1  1  HSP20       Hsp20/alpha crystallin family
    8.3e-13   47.7   0.3    1.4e-12   47.0   0.3    1.4  1  ArsA_HSP20  HSP20-like domain found in ArsA
  ------ inclusion threshold ------
        0.6    9.9   2.3          1    9.2   0.8    1.8  2  DUF2807     Putative auto-transporter adhesin, head GIN domai


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 !   74.1   3.5   1.4e-24   8.3e-21       1      99 [.      37     135 ..      37     136 .] 0.93

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 1.4e-24
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkas 75 
                                       d+++e+++++v +++pg++k++++v ved  +++++e++  eee  +++++ker++++  r++++P +v+ dk++a+
  gi|488600619|ref|YP_007907090.1|  37 DVIDEDDRIRVVAELPGFDKKDIEVYVEDSDLVIRAERKeeEEEVRKNYIRKERRYGETYRRIAIPMEVEVDKITAK 113
                                       67899**********************************7666667899**************************** PP

                                       EETTEEEEEEEBSS--..------ CS
                             HSP20  76 lkdGvLtvtvpkkepekkkkerki 99 
                                       +++G+L+v +pk+e+e  +k++ki
  gi|488600619|ref|YP_007907090.1| 114 YNNGILEVILPKSEKE--RKVIKI 135
                                       *************999..678877 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 !   47.0   0.3   2.3e-16   1.4e-12       1      62 [.      42     122 ..      42     123 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.3e-16
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig....................nfrRqitLPsvlarkevtsAkfedg 57 
                                       dd+++++++LP++dk++i+++ ++++L+I+++                       R+i+ P+ +  +++  Ak+++g
  gi|488600619|ref|YP_007907090.1|  42 DDRIRVVAELPGFDKKDIEVYVEDSDLVIRAErkeeeeevrknyirkerrygETYRRIAIPMEVEVDKI-TAKYNNG 117
                                       799*******************************************99999988899************.******* PP

                        ArsA_HSP20  58 vLeIr 62 
                                        Le+ 
  gi|488600619|ref|YP_007907090.1| 118 ILEVI 122
                                       ***95 PP

>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.8   0.00017         1      16      56 ..      39      80 ..      31     111 .. 0.77
   2 ?    0.5   0.1     0.077   4.6e+02      30      57 ..     105     132 ..      92     136 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00017
                                      EE-SS-.EEEEEEEHHHHCCEEEEEETTEEEEEE-TTTTSSB CS
                           DUF2807 16 tqgdeq.svviegdenllekvevevedgtLkirlekefestk 56
                                         d   +vv e +    +++ev ved  L+ir e++ e ++
  gi|488600619|ref|YP_007907090.1| 39 IDEDDRiRVVAELPGFDKKDIEVYVEDSDLVIRAERKEEEEE 80
                                      4444444888888888899****************6665555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.077
                                       HHHCCEEEEEETTEEEEEE-TTTTSSB. CS
                           DUF2807  30 nllekvevevedgtLkirlekefestkt 57 
                                         ++k++ + ++g L++ l k+ + +k 
  gi|488600619|ref|YP_007907090.1| 105 VEVDKITAKYNNGILEVILPKSEKERKV 132
                                       4589999999999999988877777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 791.65
//
Query:       gi|488600620|ref|YP_007907091.1|  [L=582]
Description: hypothetical protein Asulf_01098 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.5  18.9        0.2   11.6   1.3    3.6  3  Cauli_AT       Aphid transmission protein
  ------ inclusion threshold ------
      0.036   13.9   1.9        3.2    7.6   0.3    3.1  3  AHD            ANC1 homology domain (AHD)
      0.066   13.9   2.7       0.14   12.8   2.7    1.5  1  Pex14_N        Peroxisomal membrane anchor protein (Pex14p) c
      0.099   13.2  11.7          1   10.0   1.1    3.9  3  Syntaxin-6_N   Syntaxin 6, N-terminal
       0.11   11.8   3.2       0.34   10.2   3.2    1.7  1  Cthe_2159      Carbohydrate-binding domain-containing protein
       0.14   11.8   1.2          4    7.2   0.0    3.2  3  TFA2_Winged_2  TFA2 Winged helix domain 2
       0.19   11.8   9.0        9.3    6.3   0.2    3.4  3  THP2           Tho complex subunit THP2
       0.34   10.3   5.1       0.16   11.4   1.2    2.2  2  HBM            Helical bimodular sensor domain
       0.55   10.6   3.8       0.84   10.0   0.4    2.4  2  T4SS           Type IV secretion system proteins
       0.55   10.2   0.1       0.55   10.2   0.1    3.3  3  SLATT_fungal   SMODS and SLOG-associating 2TM effector domain
        0.7   10.0  17.7       0.56   10.3   0.5    4.1  4  PTS_IIA        PTS system, Lactose/Cellobiose specific IIA su
        1.7    8.7  17.0          3    7.9   0.9    4.1  4  DUF1664        Protein of unknown function (DUF1664)
        2.1    8.9   9.4         26    5.4   0.1    4.5  4  NPV_P10        Nucleopolyhedrovirus P10 protein
        2.6    8.3   6.6        0.6   10.3   0.2    3.0  3  OstA           OstA-like protein
        3.3    8.1  12.0       0.45   10.9   0.2    3.9  4  DUF2524        Protein of unknown function (DUF2524)
        3.8    6.7   4.8        1.1    8.5   0.8    2.0  2  DUF1343        Protein of unknown function (DUF1343)
        4.8    7.9   6.0         15    6.3   0.2    3.8  4  FliD_N         Flagellar hook-associated protein 2 N-terminus


Domain annotation for each model (and alignments):
>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   1.3   0.00019       0.2      97     157 ..      43     103 ..      23     107 .. 0.86
   2 !    9.7   2.8   0.00073      0.77      99     161 ..     284     345 ..     273     347 .. 0.83
   3 ?    4.7   0.9     0.025        27     100     161 ..     376     436 ..     362     444 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                          Cauli_AT  97 keggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirds 157
                                       k  g++ +k  +   +L++a++r  klee++  l+ k v    lke +k+ +e++   r +
  gi|488600620|ref|YP_007907091.1|  43 KLMGGELSKLKNVERILQKAEQRHAKLEERVATLERKGVDVTELKELLKEHKEKIDLARAK 103
                                       445778888899999**********************999999**********99877665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00073
                          Cauli_AT  99 ggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkai 161
                                       +++++  + ++l  L +++++  ++ee + +++e   +e+ l+e vk++ ++ +eir+++  +
  gi|488600620|ref|YP_007907091.1| 284 AEKEQITEETKLRLLAKIDEKLAEIEELKSQINETSSPEE-LREVVKEIRKEWREIRKEMDGL 345
                                       45555666677889******************99999987.5899************998765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.025
                          Cauli_AT 100 gedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkai 161
                                       +    ++t+l  tL++ + +i+k ee + k ++  + e ++ e  k l e + +++d  k++
  gi|488600620|ref|YP_007907091.1| 376 EAAGVDTTELEVTLEDFSAKIDKAEELVGKAEDMFE-EGKVAEGHKTLREAIMTLKDAFKNV 436
                                       5555678888899*************9999777666.5556677799999999999887775 PP

>> AHD  ANC1 homology domain (AHD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.4   2.6e+03      39      59 ..      34      54 ..      32      59 .. 0.79
   2 ?    7.6   0.3    0.0031       3.2       2      31 ..     304     333 ..     303     334 .. 0.93
   3 ?    3.8   0.1     0.046        49       8      38 ..     421     452 ..     417     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.4
                               AHD 39 estfDFDLcaLDdeTieklqk 59
                                      +++ DFD  +L    ++kl++
  gi|488600620|ref|YP_007907091.1| 34 NAAKDFDVAKLMGGELSKLKN 54
                                      677899999998777777775 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0031
                               AHD   2 kleeLkeLqkklmsltdrkvlqrivdiIee 31 
                                       kl+e  eL++++++   +++l+++v+ I++
  gi|488600620|ref|YP_007907091.1| 304 KLAEIEELKSQINETSSPEELREVVKEIRK 333
                                       78999**********************986 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.046
                               AHD   8 eLqkklmsltdr.kvlqrivdiIeetGlyeit 38 
                                        L++ +m+l+d  k +++iv+  +e+    i+
  gi|488600620|ref|YP_007907091.1| 421 TLREAIMTLKDAfKNVKEIVAELKEQHRHRIQ 452
                                       6999*******7689*****999998777766 PP

>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.7   0.00013      0.14      10      52 ..      57      99 ..      50     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                           Pex14_N 10 kFLqdpsVrsaplekkvaFLesKGLtqeEIeeaLkraereeea 52
                                      + Lq ++ r a le++va Le+KG++  E +e+Lk+ +++ + 
  gi|488600620|ref|YP_007907091.1| 57 RILQKAEQRHAKLEERVATLERKGVDVTELKELLKEHKEKIDL 99
                                      78999999****************************7665544 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.6      0.14   1.5e+02      46      94 ..      55     103 ..      45     130 .. 0.57
   2 ?   10.0   1.1   0.00097         1      10      68 ..     301     353 ..     291     376 .. 0.74
   3 ?    5.1   0.1     0.032        33      10      62 ..     392     445 ..     385     457 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                      Syntaxin-6_N  46 LrkalrsiewdledLeetvriveknpskfkidekelsrrrafveevree 94 
                                       +++ l+++e+    Lee v+++e++  ++   ++ l+++++ ++ +r +
  gi|488600620|ref|YP_007907091.1|  55 VERILQKAEQRHAKLEERVATLERKGVDVTELKELLKEHKEKIDLARAK 103
                                       3444555555555555555555554333333333344444444444433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00097
                      Syntaxin-6_N  10 Vqkslnkaeslyrrwerlledtss.stseeldetrteLrkalrsiewdledLeetvrive 68 
                                       + ++l ++e+l ++ +       + s+ eel+e  +e+rk+ r+i+++++ L   v++++
  gi|488600620|ref|YP_007907091.1| 301 IDEKLAEIEELKSQIN-------EtSSPEELREVVKEIRKEWREIRKEMDGLAGFVAVAK 353
                                       4444444444444444.......44679*************************9996653 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.032
                      Syntaxin-6_N  10 Vqkslnkaeslyrrwerlledtss.stseeldetrteLrkalrsiewdledLee 62 
                                          +++kae+l+++ e++ e+++  +  + l+e+   L+ a +++++ + +L+e
  gi|488600620|ref|YP_007907091.1| 392 FSAKIDKAEELVGKAEDMFEEGKVaEGHKTLREAIMTLKDAFKNVKEIVAELKE 445
                                       567899999999999998888877677888888888888888888888888876 PP

>> Cthe_2159  Carbohydrate-binding domain-containing protein Cthe_2159
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.2   0.00033      0.34      54     156 ..     434     538 ..     430     577 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00033
                         Cthe_2159  54 kkadkvvitladgtentlsdgseytkddeekaaifskddltlkGsGtLtvtgnyknGikskddLk..itsgtlnvtA 128
                                       k+++++v +l+++    +++g+  + +++ +a ++ ++  +++G+G   v gn    +  +d ++  +  g  +v+ 
  gi|488600620|ref|YP_007907091.1| 434 KNVKEIVAELKEQHRHRIQEGKIFSGNETGEAWVTGNGTAEFTGTGVVVVRGNGTLEVSPEDAIVtlVGFGVKSVEG 510
                                       78899999999999999999999999999**************************9999999965223447888999 PP

                         Cthe_2159 129 vddgikgkdsleikdgtltitaggdgik 156
                                       +  +i+g+ +  i++ ++t+  +g+ ik
  gi|488600620|ref|YP_007907091.1| 511 NVSAISGEGKAVIRGENITVRVEGEDIK 538
                                       999*****************99988776 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.18   1.9e+02      15      32 ..      77      94 ..      53     143 .. 0.72
   2 ?   -3.8   0.1        10   1.1e+04      34      42 ..     371     379 ..     370     380 .. 0.81
   3 ?    7.2   0.0    0.0038         4      22      42 ..     427     447 ..     425     464 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.18
                     TFA2_Winged_2 15 kaeGikvkdLkdswpdve 32
                                      +++G++v +Lk+  +  +
  gi|488600620|ref|YP_007907091.1| 77 ERKGVDVTELKELLKEHK 94
                                      466777777776444444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 10
                     TFA2_Winged_2  34 aleeLeaeg 42 
                                        +eeLea g
  gi|488600620|ref|YP_007907091.1| 371 KIEELEAAG 379
                                       599**9976 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0038
                     TFA2_Winged_2  22 kdLkdswpdveealeeLeaeg 42 
                                        +Lkd+ ++v+e + eL++++
  gi|488600620|ref|YP_007907091.1| 427 MTLKDAFKNVKEIVAELKEQH 447
                                       68****************954 PP

>> THP2  Tho complex subunit THP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.6     0.048        50      27      74 ..      57     104 ..      43     117 .. 0.82
   2 ?    6.3   0.2    0.0088       9.3      21      65 ..     306     350 ..     288     357 .. 0.77
   3 ?    5.3   0.1     0.018        19      36     101 ..     382     448 ..     357     462 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.048
                              THP2  27 eivvddekppkelqeilekyeeesedaeelraklekYldeiKmeraky 74 
                                       +i    e+  ++l+e +  +e +  d++el++ l+++ ++i ++rak 
  gi|488600620|ref|YP_007907091.1|  57 RILQKAEQRHAKLEERVATLERKGVDVTELKELLKEHKEKIDLARAKI 104
                                       444555677889999999****************************95 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0088
                              THP2  21 sdeevseivvddekppkelqeilekyeeesedaeelraklekYld 65 
                                       ++ e+ + ++++++ p+el e++++ ++e +++++  + l  ++ 
  gi|488600620|ref|YP_007907091.1| 306 AEIEELKSQINETSSPEELREVVKEIRKEWREIRKEMDGLAGFVA 350
                                       456667789*****************9999999887777776665 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.018
                              THP2  36 pkelqeilekyeeesedaeelraklekYldeiKmerakytl.eNkyllkdklkeltkevnrWrkewd 101
                                        +el+ +le+++++  +aeel  k e+ ++e K++  + tl e   +lkd +k++++ v++ ++++ 
  gi|488600620|ref|YP_007907091.1| 382 TTELEVTLEDFSAKIDKAEELVGKAEDMFEEGKVAEGHKTLrEAIMTLKDAFKNVKEIVAELKEQHR 448
                                       579999****************************9998888355678*********99999887765 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.64   6.8e+02      57      91 ..      59      94 ..      43     130 .. 0.56
   2 ?   11.4   1.2   0.00015      0.16      44     196 ..     299     453 ..     290     455 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.64
                                      HHHHHHH-.-SHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM 57 lqklkakf.kspenvrlLqeqlalvqeyrksfnelr 91
                                      lqk +++  k +e v  L+ ++ +v+e+++ ++e +
  gi|488600620|ref|YP_007907091.1| 59 LQKAEQRHaKLEERVATLERKGVDVTELKELLKEHK 94
                                      333322220223333444444444444444443333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM  44 aavqkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelra..ayesrnaaRqeldsaaeraleaidel 118
                                       a++++kl+e++++  +++++++ +e +  ++e+++   e+rk+++ l+   a+++ +++ ++ ++ + ++ + i+el
  gi|488600620|ref|YP_007907091.1| 299 AKIDEKLAEIEELKSQINETSSPEELREVVKEIRKEWREIRKEMDGLAGfvAVAKVENLVERSKQVGLKLGAKIEEL 375
                                       67999***************9999999999*****************983366778889999999999********* PP

                                       HHHHHCS-S-HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHHHHHHHHH-GG.GHHHH CS
                               HBM 119 eaevlqtpeadserlaqlqa.iaelkrqvqlaryqvrgYtfsenedseqaavtaldaalaeldqlrqalasdpraal 194
                                       ea  + t e +   l+ + a i+++++ v  a  +     ++e  ++ + a+  l  a ++++++ ++l +++r ++
  gi|488600620|ref|YP_007907091.1| 376 EAAGVDTTELE-VTLEDFSAkIDKAEELVGKAEDMFEEGKVAEGHKTLREAIMTLKDAFKNVKEIVAELKEQHRHRI 451
                                       ******99985.77777654399999999999999999999999999999999999999999999999999999999 PP

                                       HH CS
                               HBM 195 qq 196
                                       q+
  gi|488600620|ref|YP_007907091.1| 452 QE 453
                                       86 PP

>> T4SS  Type IV secretion system proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.51   5.4e+02      65     140 ..      27     103 ..      15     112 .. 0.74
   2 ?   10.0   0.4    0.0008      0.84     125     194 ..     292     361 ..     270     364 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.51
                              T4SS  65 aewqdvkdlvksggasgslssaaqslrdknkvydvcal.ltskeqaskaceqaankaaqdkalaeqaydkankrlkq 140
                                       + ++d+k++ k++   + +++++++l++ +++ + +++  ++ e++++++e++ +   + k+l+++ ++k++   ++
  gi|488600620|ref|YP_007907091.1|  27 EVVEDAKNAAKDFDVAKLMGGELSKLKNVERILQKAEQrHAKLEERVATLERKGVDVTELKELLKEHKEKIDLARAK 103
                                       44677777777776566678888888888888888866555555555899999999999999999999888766655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0008
                              T4SS 125 alaeqaydkankrlkqiqkLadqinnatDpKeiaDLqaRiqaeqallqneqiqlqllqklaeaeeklaeq 194
                                       ++  ++  k++++l++i++L++qin ++ p e  ++   i  e   + +e+  l  + ++a+ e+ +++ 
  gi|488600620|ref|YP_007907091.1| 292 ETKLRLLAKIDEKLAEIEELKSQINETSSPEELREVVKEIRKEWREIRKEMDGLAGFVAVAKVENLVERS 361
                                       4445567899**********************99999999999999999988888888888777766665 PP

>> SLATT_fungal  SMODS and SLOG-associating 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       1.5   1.6e+03      73     117 ..      60     107 ..      44     112 .. 0.62
   2 ?   -0.3   0.4      0.97     1e+03      86     119 ..     305     340 ..     281     341 .. 0.61
   3 ?   10.2   0.1   0.00052      0.55      59     112 ..     345     401 ..     344     437 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                      SLATT_fungal  73 ersrkrrkdlekvireieafeldageas..l.dvreeieelrrryeea 117
                                       +++++r+++le+ + ++e+  +d  e +  l +++e+i+ +r ++ ea
  gi|488600620|ref|YP_007907091.1|  60 QKAEQRHAKLEERVATLERKGVDVTELKelLkEHKEKIDLARAKILEA 107
                                       566777778888888888877776632223323446666666665555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.97
                      SLATT_fungal  86 ireieafeldageas..ldvreeieelrrryeeala 119
                                       + eie+ + +++e+s   + re ++e+r++ +e+++
  gi|488600620|ref|YP_007907091.1| 305 LAEIEELKSQINETSspEELREVVKEIRKEWREIRK 340
                                       445555444444322112345788888888888776 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00052
                      SLATT_fungal  59 iAglLArlrgsgePersrkrrkdlekvireieafeldage.........asldvreeieelrr 112
                                       +Ag++A+++ +++ ers++   +l   i+e+ea+ +d+ e         a      +i+++++
  gi|488600620|ref|YP_007907091.1| 345 LAGFVAVAKVENLVERSKQVGLKLGAKIEELEAAGVDTTElevtledfsA------KIDKAEE 401
                                       69*******************************99999853333322222......3333322 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         3   3.1e+03      34      56 ..      50      72 ..      29      92 .. 0.75
   2 ?   10.3   0.5   0.00053      0.56      13      56 ..     100     143 ..      99     153 .. 0.89
   3 ?    8.7   0.6    0.0016       1.7      21      49 ..     219     247 ..     212     250 .. 0.91
   4 ?    1.2   0.6      0.36   3.8e+02      13      48 ..     399     434 ..     390     452 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                           PTS_IIA 34 ellkeAeeelkeAhkaqteliqk 56
                                      ++lk+ e+ l++A + +++l ++
  gi|488600620|ref|YP_007907091.1| 50 SKLKNVERILQKAEQRHAKLEER 72
                                      46777778888888888877555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00053
                           PTS_IIA  13 ArslameAlkaakegdfeeaeellkeAeeelkeAhkaqteliqk 56 
                                       Ar +++eA ++ k+g++e+  el+keA++ + ++ ++ te+ + 
  gi|488600620|ref|YP_007907091.1| 100 ARAKILEAKRKFKSGEIEAGLELIKEAKDLMDDGYELATEITAL 143
                                       89*******************************99999988665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0016
                           PTS_IIA  21 lkaakegdfeeaeellkeAeeelkeAhka 49 
                                       ++++ e++f +a+e +++A+ee+k+A+k+
  gi|488600620|ref|YP_007907091.1| 219 IHKIYEKEFMKAKERFEKAREEFKRAKKV 247
                                       788999********************987 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.36
                           PTS_IIA  13 ArslameAlkaakegdfeeaeellkeAeeelkeAhk 48 
                                       A +l+ +A +  +eg++ e ++ l+eA   lk+A k
  gi|488600620|ref|YP_007907091.1| 399 AEELVGKAEDMFEEGKVAEGHKTLREAIMTLKDAFK 434
                                       344444555556666666666666666666666655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.0     0.036        38      48     102 ..      53     110 ..      41     124 .. 0.70
   2 ?    7.9   0.9    0.0028         3      59     115 ..     292     347 ..     278     354 .. 0.66
   3 ?    4.0   0.2     0.046        48      47     114 ..     339     407 ..     337     420 .. 0.84
   4 ?    4.3   1.4     0.036        38      56     116 ..     384     446 ..     362     454 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.036
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkk...ldeqkeiskeikeevtevredlseiged 102
                                       k++e++ ++ ++   +L++r++++++k   + e ke+ ke ke+++ +r ++ e +++
  gi|488600620|ref|YP_007907091.1|  53 KNVERILQKAEQRHAKLEERVATLERKgvdVTELKELLKEHKEKIDLARAKILEAKRK 110
                                       4556666666677778888888887764335566677777777777777777666555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0028
                           DUF1664  59 atkrhLssridrvdkkldeqkeiskeikee..vtevredlseigedvesvkeavegles 115
                                       +tk +L ++id+   kl e +e++++i+e    +e+re ++ei+++ +++++ + gl++
  gi|488600620|ref|YP_007907091.1| 292 ETKLRLLAKIDE---KLAEIEELKSQINETssPEELREVVKEIRKEWREIRKEMDGLAG 347
                                       566666555555...55555555555544311468888899999999888888887765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.046
                           DUF1664  47 skqleqvseslaatk.rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                        k+++ +   +a +k ++L +r ++v+ kl + +e  ++   + te++  l++++ ++++ +e+v + e
  gi|488600620|ref|YP_007907091.1| 339 RKEMDGLAGFVAVAKvENLVERSKQVGLKLGAKIEELEAAGVDTTELEVTLEDFSAKIDKAEELVGKAE 407
                                       577788887888887457999999999999999999999999999999999999999999999987766 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.036
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeisk..eikeevtevredlseigedvesvkeaveglesk 116
                                       +l+ t +++s++id+ ++ + + +++ +  +++e  +++re + ++++ +++vke+v +l+++
  gi|488600620|ref|YP_007907091.1| 384 ELEVTLEDFSAKIDKAEELVGKAEDMFEegKVAEGHKTLREAIMTLKDAFKNVKEIVAELKEQ 446
                                       566677777778877777776666665411466777888888888888888888888888654 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3       0.2   2.1e+02      18      49 ..      64      95 ..      49     107 .. 0.64
   2 ?    1.8   0.2      0.33   3.5e+02      28      60 ..     299     330 ..     287     360 .. 0.70
   3 ?    5.4   0.1     0.024        26      23      66 ..     368     411 ..     349     417 .. 0.87
   4 ?    1.7   0.1      0.35   3.7e+02      23      48 ..     422     447 ..     414     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.2
                           NPV_P10 18 dkVdalqqqvddvqenlpdvtelnekLdaqsa 49
                                      ++   l+++v+ ++ +  dvtel+e L +  +
  gi|488600620|ref|YP_007907091.1| 64 QRHAKLEERVATLERKGVDVTELKELLKEHKE 95
                                      34445667777777777777777776665555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.33
                           NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       ++++e+l +++el++++++ s   +el + v++
  gi|488600620|ref|YP_007907091.1| 299 AKIDEKLAEIEELKSQINETSS-PEELREVVKE 330
                                       4556666666666666665443.2444444444 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.024
                           NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       l ++++++++   d+tel+  L++ sa++++ e+ v + +d+  
  gi|488600620|ref|YP_007907091.1| 368 LGAKIEELEAAGVDTTELEVTLEDFSAKIDKAEELVGKAEDMFE 411
                                       6788999****9**********************9999999876 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.35
                           NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqs 48 
                                       l +++  +++ +++v+e+ ++L +q 
  gi|488600620|ref|YP_007907091.1| 422 LREAIMTLKDAFKNVKEIVAELKEQH 447
                                       66777778888888888888887764 PP

>> OstA  OstA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.5   1.6e+03      46      77 ..     371     400 ..     349     445 .. 0.63
   2 ?   -2.0   0.4       3.9   4.1e+03      13      31 ..     470     489 ..     467     491 .. 0.80
   3 ?   10.3   0.2   0.00057       0.6      18      81 ..     508     574 ..     504     579 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.5
                              OstA  46 kierleakgtatfrqkvdlvgeqirGkAerie 77 
                                       kie+lea g  +  ++++++ e+ ++k +++e
  gi|488600620|ref|YP_007907091.1| 371 KIEELEAAG--VDTTELEVTLEDFSAKIDKAE 400
                                       456666666..333444444444444433333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                              OstA  13 kkvavftGn.VvvtqGnltl 31 
                                       +++a ftG  Vvv++Gn tl
  gi|488600620|ref|YP_007907091.1| 470 NGTAEFTGTgVVVVRGNGTL 489
                                       67788999659999999887 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00057
                              OstA  18 ftGnVvvtq..GnltlkAdkvtvtqdkk.....skkierleakgtatfrqkvdlvgeqirGkAerieydsk 81 
                                        +GnV +    G+  ++++++tv+ + +      k++ +l+ +g    + k+ ++++++++ +e+iey+ +
  gi|488600620|ref|YP_007907091.1| 508 VEGNVSAISgeGKAVIRGENITVRVEGEdikliVKGYGTLKLEG----EGKYRVKKNPQEAMSEEIEYEGE 574
                                       579998875116789*********99999999966666666666....66******************964 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.2   4.4e+03       6      25 ..      54      73 ..      50      86 .. 0.71
   2 ?    3.5   0.0     0.087        92      10      36 ..     226     252 ..     216     265 .. 0.73
   3 ?   -1.8   0.4       3.9   4.1e+03      44      72 ..     306     332 ..     269     342 .. 0.57
   4 ?   10.9   0.2   0.00043      0.45       6      69 ..     391     452 ..     387     456 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.2
                           DUF2524  6 sveellqkceqaieeaeeqf 25
                                      +ve +lqk+eq   + ee+ 
  gi|488600620|ref|YP_007907091.1| 54 NVERILQKAEQRHAKLEERV 73
                                      67788888888766666655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.087
                           DUF2524  10 llqkceqaieeaeeqfeeakrqehynd 36 
                                        + k+++  e+a+e+f++ak+++  ++
  gi|488600620|ref|YP_007907091.1| 226 EFMKAKERFEKAREEFKRAKKVGIKDE 252
                                       445677777888888888888766555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.9
                           DUF2524  44 lkLEeavneLeklaksandqQreqLeRar 72 
                                        ++Ee+  ++++  +s+ ++ re ++  r
  gi|488600620|ref|YP_007907091.1| 306 AEIEELKSQINE--TSSPEELREVVKEIR 332
                                       233333333332..233344444444444 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00043
                           DUF2524   6 sveellqkceqaieeaeeqfeeakrqehyndeeYteAqlkLEeavneLeklaksandqQreqLe 69 
                                        +   ++k+e+ + +ae+ fee+k  e    +   eA + L +a++++++++    +q r +++
  gi|488600620|ref|YP_007907091.1| 391 DFSAKIDKAEELVGKAEDMFEEGKVAEGH--KTLREAIMTLKDAFKNVKEIVAELKEQHRHRIQ 452
                                       5677899****************998865..5679*******************9999998875 PP

>> DUF1343  Protein of unknown function (DUF1343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.93   9.8e+02     239     322 ..      68     152 ..      58     178 .. 0.67
   2 ?    8.5   0.8     0.001       1.1     267     349 ..     259     341 ..     206     343 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.93
                                       HHHHHHHTT--TTEEEECEEE--SSSTTTTS-EEEEEECES-TTT---TCHHCCHCHHHHHHHHGGSHHH.HHHHHH CS
                           DUF1343 239 klaeelnalklpgvkfrpvsftpteskhkgetceGvqlevtdrekfdpvelgllllkallelypeqfelk.afdkll 314
                                       kl e++ +l+ +gv +++++   +e+k k  + ++  le++++ k   +e gl+l+k +++l+ + +el+  ++ l+
  gi|488600620|ref|YP_007907091.1|  68 KLEERVATLERKGVDVTELKELLKEHKEKIDLARAKILEAKRKFKSGEIEAGLELIKEAKDLMDDGYELAtEITALC 144
                                       55666777788888888888888999999888888888887777888889999999999999987776666555555 PP

                                       TSTHHHHH CS
                           DUF1343 315 gteelreq 322
                                       ++++ r+ 
  gi|488600620|ref|YP_007907091.1| 145 AKTAERHR 152
                                       55444433 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
                                       TTS-EEEEEECES-TTT---TCHHCCHCHHHHHHHHGGSHHH....HHHHHHTSTHHHHHHHCCS-CHHCHHHCHCC CS
                           DUF1343 267 kgetceGvqlevtdrekfdpvelgllllkallelypeqfelk....afdkllgteelreqieagksveeiraswqke 339
                                       kg ++ G++l     + ++ ++++++++    ++++ + +l+      +kl+  eel++qi++ +s+ee+r+ +++ 
  gi|488600620|ref|YP_007907091.1| 259 KGYMVAGFDLAE---RWLERLRVHVINMAEKEQITE-ETKLRllakIDEKLAEIEELKSQINETSSPEELREVVKEI 331
                                       455555666655...667777777777777777776.555667775556888999********************** PP

                                       HHHHHHHHHC CS
                           DUF1343 340 lekFkkkrkk 349
                                        ++++++rk+
  gi|488600620|ref|YP_007907091.1| 332 RKEWREIRKE 341
                                       *******997 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 ?    6.3   0.2     0.014        15      10      56 ..      56     101 ..      52     137 .. 0.79
   2 ?    0.4   0.2       1.1   1.1e+03      23      52 ..     284     312 ..     274     347 .. 0.67
   3 ?   -0.4   0.0       1.8   1.9e+03       9      52 ..     354     397 ..     346     423 .. 0.73
   4 ?    0.1   0.0       1.2   1.3e+03      34      55 ..     423     445 ..     414     492 .. 0.47

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                                       XXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXX CS
                            FliD_N  10 kqlmkaerakldkleqkktklewkqsayrelnsklsnlksalsalsk 56 
                                       + +++  +++  kle++ ++le k  +++el+  l++ k++++ l++
  gi|488600620|ref|YP_007907091.1|  56 ERILQKAEQRHAKLEERVATLERKGVDVTELKELLKEHKEKID-LAR 101
                                       556666677889*************************999774.422 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                                       XXXXXXXXXXXHHHHHHHHHHHHHHHHHHH CS
                            FliD_N  23 leqkktklewkqsayrelnsklsnlksals 52 
                                        e+++ + e+k   + ++  kl+++++ l+
  gi|488600620|ref|YP_007907091.1| 284 AEKEQITEETKLRLLAKIDEKLAEIEE-LK 312
                                       556666666677777777776666665.22 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.8
                                       XXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHH CS
                            FliD_N   9 vkqlmkaerakldkleqkktklewkqsayrelnsklsnlksals 52 
                                       v++l++  ++   kl +k ++le+   + +el+  l++++ +++
  gi|488600620|ref|YP_007907091.1| 354 VENLVERSKQVGLKLGAKIEELEAAGVDTTELEVTLEDFSAKID 397
                                       56677777776677888999999999999999999999998774 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHHHH.X CS
                            FliD_N  34 qsayrelnsklsnlksalsal.s 55 
                                       ++a+ +l+ +++n+k+ +++l +
  gi|488600620|ref|YP_007907091.1| 423 REAIMTLKDAFKNVKEIVAELkE 445
                                       44455555555555553333321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1997  (0.111384); expected 358.6 (0.02)
Passed bias filter:                      772  (0.0430587); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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):              17  [number of targets reported over threshold]
# CPU time: 1.03u 0.36s 00:00:01.39 Elapsed: 00:00:00.56
# Mc/sec: 3135.86
//
Query:       gi|488600621|ref|YP_007907092.1|  [L=76]
Description: hypothetical protein Asulf_01099 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-05   22.4   0.0    0.00012   22.0   0.0    1.2  1  DUF772           Transposase domain (DUF772)
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.15   12.1   0.0    1.2  1  DDE_Tnp_1_assoc  DDE_Tnp_1-associated


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 !   22.0   0.0   1.3e-08   0.00012       1      48 [.      27      72 ..      27      76 .] 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-08
                            DUF772  1 GrpayppelmlkllllqylyglSdreleealrenlsfrwflgldleed 48
                                      Gr++ +p+l+  + +++  +g S r++e+ ++en+++   lg+d   +
  gi|488600621|ref|YP_007907092.1| 27 GRKSHDPVLLTAITYIMIRNGWSLRDAERWCEENMHLLEQLGYDK--P 72
                                      9*****************************************863..3 PP

>> DDE_Tnp_1_assoc  DDE_Tnp_1-associated
   #    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       8      57 ..      21      70 ..      14      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                   DDE_Tnp_1_assoc  8 pDpRrergkrhpladiLlialcaviagadsweeieefakekeewlrefl.e 57
                                       D+R + +k h+  ++L+ + + +i +  s+++ e++++e+ + l+++  +
  gi|488600621|ref|YP_007907092.1| 21 RDHRGRGRKSHD-PVLLTAITYIMIRNGWSLRDAERWCEENMHLLEQLGyD 70
                                      699999999998.567777777888899************99999887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.35s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 415.01
//
Query:       gi|488600622|ref|YP_007907093.1|  [L=167]
Description: hypothetical protein Asulf_01100 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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    6.4   6.3        2.6    6.2   6.3    1.1  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   6.3   0.00014       2.6      42     123 ..      72     156 ..      25     161 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00014
                           DUF2070  42 llfglp..alvaflltlpvlrilggrltykrs.lflalltelivviisllaillsallqalvllalvlslalvfalr 115
                                       ++ g+    l++++ltl ++  + ++  ++ +  +l l++ ++++i+++ ++++s   +  ++ +l + + +v ++ 
  gi|488600622|ref|YP_007907093.1|  72 FFTGMAatDLINAVLTLVFVYGYFKKARWSMWlGTLTLTISMYAAIVFTYGTIASGAWTGNLYGYLWFYIPFVPVVI 148
                                       33333333578888888888777666666666778888889999999999999998778888899999999999999 PP

                           DUF2070 116 llvlvavs 123
                                       l+v++++ 
  gi|488600622|ref|YP_007907093.1| 149 LFVVFSIW 156
                                       99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 931.38
//
Query:       gi|488600623|ref|YP_007907094.1|  [L=219]
Description: hypothetical protein Asulf_01101 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1489.59
//
Query:       gi|488600624|ref|YP_007907095.1|  [L=58]
Description: hypothetical protein Asulf_01102 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 381.38
//
Query:       gi|488600625|ref|YP_007907096.1|  [L=296]
Description: putative glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-21   74.8   0.1    1.3e-20   73.9   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.7e-07   31.4   0.0    4.2e-07   30.1   0.0    1.6  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.1e-05   25.0   0.7    0.00034   20.2   0.1    2.1  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0012   18.4   0.0      0.003   17.1   0.0    1.6  2  Glyco_transf_21  Glycosyl transferase family 21
     0.0052   16.7   0.1     0.0089   16.0   0.1    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 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 !   73.9   0.1   3.5e-24   1.3e-20       3     168 ..       2     162 ..       1     164 [. 0.78

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 3.5e-24
                                       EEEESS-..TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   3 viptyNe..ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       ++ ty     +  +e+++sl +q  y+d+eii++ Dg++ + + i ee+    p++ +  +e+n G+  ++n+g++ 
  gi|488600625|ref|YP_007907096.1|   2 IVATYHPnmFNHFKECIDSLQNQ-SYDDLEIICIVDGDENYYKMIKEEI----PDIEIHLNEKNLGLLLSRNRGAKL 73 
                                       67788777788999*********.**************55555555555....8*********************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       a gd+i+f+D+D + d++w+e+lv+ +e  +a ++ g+ +     + +++ +++ +++ ++ +  +   +  ++   
  gi|488600625|ref|YP_007907096.1|  74 AEGDIIAFIDDDAVADRKWIEELVKTYEL-DAIAAGGKLVPLWITKEPKWFPEE-FYWMIGATHLGFPDKIAEVRNT 148
                                       ****************************9.775555555554444444444444.3444555555555555588888 PP

                                       STCCCEEEEHHHHH CS
                   Glycos_transf_2 155 igsaallrrealee 168
                                        gs+  +rr+++ e
  gi|488600625|ref|YP_007907096.1| 149 FGSNISFRRDIFLE 162
                                       88888888888755 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   1.2e-10   4.2e-07       7     212 ..       2     209 ..       1     231 [. 0.75

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.2e-10
                   Glyco_tranf_2_3   7 lVptfneed..vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                       +V+t++ +      e+++sl +q+y+++e++ +vd+++    ++++e   + pd+++++  n++nlg    sr  n+
  gi|488600625|ref|YP_007907096.1|   2 IVATYHPNMfnHFKECIDSLQNQSYDDLEIICIVDGDENY-YKMIKE---EIPDIEIHL--NEKNLGL-LLSR--NR 69 
                                       688888877778899*******************987766.777877...89**99995..9999*96.6666..9* PP

                   Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavg.tpvfllnrstlvsalgalefaerhlrflaarralg 156
                                       + + +++d+++++DdD+v +   ++ l+ ++ l++ ++    +p +   + ++++   +  ++ +hl f+    +++
  gi|488600625|ref|YP_007907096.1|  70 GAKLAEGDIIAFIDDDAVADRKWIEELVKTYeLDAIAAGGKlVPLWITKEPKWFPEEFYWMIGATHLGFPDKIAEVR 146
                                       *******************************5444222222233455678899888777788888888888778888 PP

                   Glyco_tranf_2_3 157 vltlnGsgslirrevlkelegldp..lfllt......dDyelglrlrr.agfrtayvpgaavrev 212
                                        ++  Gs   +rr+++ el+g+ p  +++++         e + r+r+ +g  + y p+a+v++ 
  gi|488600625|ref|YP_007907096.1| 147 NTF--GSNISFRRDIFLELGGFNPsmGGIKGnrmlqgGETEFCERMRQrYGKGVMYNPDAIVYHK 209
                                       777..999999999999999777776666663333222234444555547777778888888887 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 !   20.2   0.1   9.6e-08   0.00034      14     104 ..      13      98 ..       1     112 [. 0.70
   2 ?    3.5   0.1     0.012        41     163     186 ..     148     171 ..     127     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.6e-08
                   Glyco_tranf_2_2  14 yieerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFl 88 
                                       + +e +  lq+++y  +++e+i + dg  + +    + i d +      + ++k  +l  +rNrGa+ ae+d++ F+
  gi|488600625|ref|YP_007907096.1|  13 HFKECIdsLQNQSY--DDLEIICIVDGDENYYKMIKEEIPDIEI-----HLNEKNLGLLLSRNRGAKLAEGDIIAFI 82 
                                       55666665556666..5678888888866653222233444444.....4456778********************* PP

                   Glyco_tranf_2_2  89 DaDcfissDkfekilk 104
                                       D D       +e ++k
  gi|488600625|ref|YP_007907096.1|  83 DDDAVADRKWIEELVK 98 
                                       ***9888777777776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                   Glyco_tranf_2_2 163 pssssilinrraflevGGyDErfr 186
                                         +s+i  +r  fle+GG++ ++ 
  gi|488600625|ref|YP_007907096.1| 148 TFGSNISFRRDIFLELGGFNPSMG 171
                                       56899**************98874 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 !   17.1   0.0   8.4e-07     0.003      27     121 ..      72     168 ..      50     170 .. 0.85
   2 ?   -2.8   0.0       1.1   3.9e+03      84     108 ..     208     233 ..     189     247 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.4e-07
                   Glyco_transf_21  27 eaakydllvisDsdvrvkpdyLeellaaledpkv...glVtslpvgsdakglaaaleaaflntlagvlqaklsglgf 100
                                       + a+ d++ + D+d++++++ +eel+++ e +++   g ++ l ++ ++k ++ ++   + +t+ g+ +   ++++ 
  gi|488600625|ref|YP_007907096.1|  72 KLAEGDIIAFIDDDAVADRKWIEELVKTYELDAIaagGKLVPLWITKEPKWFPEEFYWMIGATHLGFPDK-IAEVRN 147
                                       34999**********************998754411155667778999999*****99999*********.****** PP

                   Glyco_transf_21 101 avGksmalrreaLeaiGGfea 121
                                        +G+ + +rr+++ ++GGf++
  gi|488600625|ref|YP_007907096.1| 148 TFGSNISFRRDIFLELGGFNP 168
                                       *******************86 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                   Glyco_transf_21  84 lntlagvlqa.klsglgfavGksmal 108
                                       +++++++l   +l +  f +G s a+
  gi|488600625|ref|YP_007907096.1| 208 HKIFSRRLEKkFLLRRAFWQGYSKAV 233
                                       34444444444444445555544443 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.5e-06    0.0089       1     144 [.      78     229 ..      78     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.5e-06
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvm...nvanwl.eelaalffaedhgkdilvrealgrvvps 72 
                                       ii+++D+D v ++  ++e++  ++ +  +a++ g+ ++       +w+ ee++ +  a     +  + +++ +v   
  gi|488600625|ref|YP_007907096.1|  78 IIAFIDDDAVADRKWIEELVKTYElD-AIAAG-GKLVPLwitKEPKWFpEEFYWMIGA----THLGFPDKIAEVRNT 148
                                       68999999999999999999999844.34433.3333322336666664777775433....444466789999999 PP

                   Glyco_trans_2_3  73 vGsgaflrrsalqevg.......gwdgdessvsEDfdmglrl.qrkGyrvrfvpeslvkek.spltlraalrQrkRw 140
                                       +Gs++++rr+ + e+g       g++g+    +  ++++ r+ qr+G  v + p+++v+ k ++++l   +  r+  
  gi|488600625|ref|YP_007907096.1| 149 FGSNISFRRDIFLELGgfnpsmgGIKGNRMLQGGETEFCERMrQRYGKGVMYNPDAIVYHKiFSRRLEKKFLLRRAF 225
                                       9************99955555555555555************7799**********887665888877777777666 PP

                   Glyco_trans_2_3 141 ayGc 144
                                        +G+
  gi|488600625|ref|YP_007907096.1| 226 WQGY 229
                                       6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1897.17
//
Query:       gi|488600626|ref|YP_007907097.1|  [L=355]
Description: hypothetical protein Asulf_01104 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   47.8   0.0    3.1e-12   47.1   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.5e-12   46.7   0.1    6.3e-12   45.4   0.1    1.6  1  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 !   47.1   0.0   3.4e-16   3.1e-12       2     102 ..     189     290 ..     188     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 3.4e-16
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---.TH.HHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv.ed.laellaaa 73 
                                       p+i++vG +  +v ++d+lle ++ l   d++l+++G+g  + ++l++l +  +l ++v f+G++ +d +ae+++ +
  gi|488600626|ref|YP_007907097.1| 189 PKIIYVGGF-SEVYNLDILLESMKYLP--DFQLIMIGGGRlE-NKLNDLKKelNL-KNVYFLGYLpNDvVAEVMKLC 260
                                       89*******.6789*************..79******99854.577765554567.69*******8667******** PP

                                       SEEEE---.--SHHHHHHHHTT-EEEE-TG CS
                   Glyco_trans_1_4  74 dvfvaPse.gfglkllEamaaglpvVatdv 102
                                       dv v   e   +lk++E++a gl vV+ + 
  gi|488600626|ref|YP_007907097.1| 261 DVGVTLCEvPRQLKIYEYLATGLRVVVPES 290
                                       *******7689***************9754 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 !   45.4   0.1     7e-16   6.3e-12       7     164 ..     180     329 ..     175     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 7e-16
                                       HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsr 83 
                                       +++g+++k++ i++vg ++++ ++d l+++++ l     p+++l+++G+g  e++l +l +el+l +nv flg++++
  gi|488600626|ref|YP_007907097.1| 180 ERNGIKQKQPKIIYVGGFSEVYNLDILLESMKYL-----PDFQLIMIGGGRLENKLNDLKKELNL-KNVYFLGYLPN 250
                                       678999**************************87.....89************************.9********** PP

                                       SSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT.-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  84 edleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn.naealaeairkllede 159
                                       + + e++k +d+ v  ++  +  + ++E++a gl v++  +   ++ ++ +e  ++  ++ +a + ae i+++l+ +
  gi|488600626|ref|YP_007907097.1| 251 DVVAEVMKLCDVGVTLCEV-PRQLKIYEYLATGLRVVVPESVLSSKDFEFAE--YCTGTKmDARDVAENIKRALSMP 324
                                       ************9999887.55588888888888888766333333333333..45555555557777777777777 PP

                                       HHHHH CS
                   Glycos_transf_1 160 elrer 164
                                        +r++
  gi|488600626|ref|YP_007907097.1| 325 RKRDK 329
                                       66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2037.91
//
Query:       gi|488600627|ref|YP_007907098.1|  [L=313]
Description: hypothetical protein Asulf_01105 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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    1.4e-10   41.3   0.1    1.1  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
     0.0082   16.2   0.1        1.3    9.2   0.0    2.4  2  Rv2175c_C     Rv2175c C-terminal domain of unknown function
  ------ inclusion threshold ------
       0.14   12.5   0.1        0.3   11.4   0.0    1.6  1  RT_RNaseH     RNase H-like domain found in reverse transcript
       0.15   11.1   0.1       0.21   10.6   0.1    1.1  1  TelA          Toxic anion resistance protein (TelA)


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 !   41.3   0.1   3.2e-14   1.4e-10       1     244 [.       3     270 ..       3     286 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.2e-14
                                       EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESE.EE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEE CS
                      Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapn.lrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgey 76 
                                       +lvi+ DG++ + l++     p + + + + +  p+   +    ++ ++++++ TG++  eH++ +  +  +  +e 
  gi|488600627|ref|YP_007907098.1|   3 LLVIGWDGATYNHLEK---IKPEFYRKLHRQIFLPEpFWQKREVDSGAAWTTITTGKSFFEHKVLS--ISGKLENET 74 
                                       5788888888888888...5555544444444455447788888999*******************..777777775 PP

                                       EEEETTTTGG..................GGGCTTS-HHHHHHHTH..TTCEEEESE..TTTTSEBTTCT.SC..... CS
                      Phosphodiest  77 vvfvtededa..................prwwqgepiwdtaakar..glkaaalfw..pgsevdystyyylvs.... 127
                                         f++ ++ +                  + +++++p+  ++++ r   +  ++l+w  p + ++++ y++ vs    
  gi|488600627|ref|YP_007907098.1|  75 -LFRIFSKVDflipsnlfgkavrlwlmsKLFYKHPPLSTDVKFPRiwEIIPNSLVWsvPVTHPPKPVYGVWVSgipy 150
                                       .7777777777***999999987777776667778888888888788777778999999999999999999997766 PP

                                       ....TBHHSBTCT.CSTTS............CHHHHHHHHHHHHHHHCHTHSHHHHHCT...SSESEEEEEECCCHH CS
                      Phosphodiest 128 ....etppryleddfnakv............pledkvdkavlqtwldaafakvvlekel...ekpdlllvyleetDt 185
                                           ++ p+++e                   +   ++ k  ++++++++f++v++ k l    + ++ ++++  +D+
  gi|488600627|ref|YP_007907098.1| 151 pdsyGVYPKKIES-----MlkkmyygepkrgS---DLRK-YKKELFEQHFREVEAIKWLydnFEFNFAFIVFVLPDR 218
                                       6666444444433.....03333344433220...2222.3335566666655555555655567************ PP

                                       HHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEE CS
                      Phosphodiest 186 vgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmadvsddkvie 244
                                       + H    d  e+++ +  +D+  ++L++++ ++      n++++SDHGm++ +  k ++
  gi|488600627|ref|YP_007907098.1| 219 FMHVE-NDWDEIKKMYMAIDESTEELVRYINPD------NVLILSDHGMKQERRAKWMH 270
                                       ***77.67899**********************......***********996555555 PP

>> Rv2175c_C  Rv2175c C-terminal domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.1    0.0085        38      13      27 ..     188     202 ..     185     205 .. 0.85
   2 !    9.2   0.0   0.00028       1.3       8      30 ..     252     274 ..     249     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0085
                         Rv2175c_C  13 DgGfddeeilrWLFt 27 
                                        + f++ e+++WL+ 
  gi|488600627|ref|YP_007907098.1| 188 EQHFREVEAIKWLYD 202
                                       578**********96 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00028
                         Rv2175c_C   8 ltvLrDgGfddeeilrWLFteDe 30 
                                       + +L+D G+++e   +W+ t+D 
  gi|488600627|ref|YP_007907098.1| 252 VLILSDHGMKQERRAKWMHTHDS 274
                                       569******************96 PP

>> RT_RNaseH  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.6e-05       0.3      38      80 ..     217     259 ..     207     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                                       EE--HHHHTS-HHHHHHHHHHHHHHHHHHHHTS--EEEE-SS- CS
                         RT_RNaseH  38 rklsgaernystiekellAivaalkkfrhylqgrkftvitDhk 80 
                                        ++   e+ ++ i+k+ +Ai ++++++  y+   ++ +++Dh 
  gi|488600627|ref|YP_007907098.1| 217 DRFMHVENDWDEIKKMYMAIDESTEELVRYINPDNVLILSDHG 259
                                       5678899***********************************5 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   4.7e-05      0.21      46     137 ..     157     247 ..     152     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.7e-05
                              TelA  46 vgklLseLvkelkeldpdelkeekklgllp.lfkkaknkieklfakYekaeeqidkIvkeLekgqdellkdnaaLdq 121
                                         k+++++ k++   +p++ ++++k    + lf++  +++e+++  Y++ e +   Iv  L        +d  ++++
  gi|488600627|ref|YP_007907098.1| 157 YPKKIESMLKKMYYGEPKRGSDLRK-Y-KKeLFEQHFREVEAIKWLYDNFEFNFAFIVFVLPDRFMHVENDWDEIKK 231
                                       56899999**********9999988.3.345999******************************************* PP

                              TelA 122 lyeknleyfkeLekyi 137
                                       +y +  e  +eL  yi
  gi|488600627|ref|YP_007907098.1| 232 MYMAIDESTEELVRYI 247
                                       ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1977.22
//
Query:       gi|488600628|ref|YP_007907099.1|  [L=298]
Description: Glycosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   88.6   0.2    5.2e-25   87.9   0.2    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    2.2e-23   83.2   0.0    4.1e-23   82.3   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.2e-08   35.2   0.0    6.6e-08   32.7   0.0    2.0  2  Glyco_transf_4   Glycosyltransferase Family 4
    0.00096   19.5   0.0      0.002   18.4   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00097   19.6   0.0     0.0043   17.5   0.0    1.9  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.044   13.1   0.8       0.43    9.8   0.1    2.4  3  DUF3689          Protein of unknown function (DUF3689)


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.2   1.7e-28   5.2e-25      17     171 ..     125     273 ..     118     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 1.7e-28
                                       EEEEESS-TTT...TTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                   Glycos_transf_1  17 iilsvgrleke...KgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                       +il+v +l+++    gv  +i+++ ++kk++ ++v+l++aG+g++++elk+ a++      v++lg+ +  d++ +l
  gi|488600628|ref|YP_007907099.1| 125 TILTVTNLRYKnkfRGVVEVIEVINKIKKKTGNDVVLLVAGGGKYLDELKEFAKKFDF---VEVLGFRK--DVPDVL 196
                                       567777777765456999**************************************99...********..****** PP

                                       HCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHH CS
                   Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlge 167
                                        +adifv+ s+ ++f+ v+lEA aaglpvi+ n+gg++e    +  G++vk +  ++l + + kll++++ +++l++
  gi|488600628|ref|YP_007907099.1| 197 ASADIFVYVSYLDAFPSVILEAQAAGLPVICNNYGGLPESCGWA--GIVVKDK--KDLEQVLSKLLTNKKIQRKLRY 269
                                       ***************************************98765..5888888..********************99 PP

                                       HHHH CS
                   Glycos_transf_1 168 nark 171
                                       +++k
  gi|488600628|ref|YP_007907099.1| 270 KSYK 273
                                       9887 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 !   82.3   0.0   1.4e-26   4.1e-23       2     134 .]     124     260 ..     123     260 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.4e-26
                                       EEEEEES--.-G.G.GTHHHHHHHHHHHH.H..H.EEEEEES---...HHHHHHHTT-T.TEEEE---THHHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrl.ee.nvkgvdllleavpllrkk..d.vrlvivGdgp.rpeeleelaagleerveftGfvedlaellaa 72 
                                       p+il+v +l ++ +  gv  ++e + +++kk  + v l+++G+g+  + el+e a+++ + ve++Gf++d++++la+
  gi|488600628|ref|YP_007907099.1| 124 PTILTVTNLrYKnKFRGVVEVIEVINKIKKKtgNdVVLLVAGGGKyLD-ELKEFAKKF-DFVEVLGFRKDVPDVLAS 198
                                       7899999997777889*************997637*******998775.999888877.79**************** PP

                                       -SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLled 134
                                       ad+fv  s    f+ ++lEa aaglpv++ + gg++e +g +g++v+  d ++l + + +Ll++
  gi|488600628|ref|YP_007907099.1| 199 ADIFVYVSylDAFPSVILEAQAAGLPVICNNYGGLPESCGWAGIVVK--DKKDLEQVLSKLLTN 260
                                       ********999**************************99*******9..99*****99999986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.2e-11   6.6e-08      66     169 ..       9     110 ..       1     111 [. 0.86
   2 ?   -0.0   0.0      0.25   7.6e+02      58     109 ..     186     240 ..     144     286 .. 0.62

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.2e-11
                    Glyco_transf_4  66 rllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye.krllkarlkplsrllralerrllrradrviavS 141
                                       +l+  e++D+  +  p+a g+ ++ +   +++pl +t+ g+ + + +++ +++++  +lr + +++l++adr+i+ S
  gi|488600628|ref|YP_007907099.1|   9 NLIT-EEYDLYLTDEPFANGLLAFIISSIKNKPLTVTLRGWGDlTNAHNEYSNLKFFFLRLISNFVLSKADRIIVLS 84 
                                       4444.69***********998888888889************988888888888888888899999*********** PP

                    Glyco_transf_4 142 eatadelrerygvppekitVipnGvDle 169
                                       +ata el + y+++  + +Vi +++D++
  gi|488600628|ref|YP_007907099.1|  85 KATATELNKIYNLR--RFYVIERPIDVK 110
                                       ************87..5*********85 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.25
                    Glyco_transf_4  58 laflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye.....k 109
                                       l f++++  +l     D+  + s+  ++ +++  +++ g+p+++   g  +      
  gi|488600628|ref|YP_007907099.1| 186 LGFRKDVPDVLA--SADIFVYVSYLDAFPSVILEAQAAGLPVICNNYGGLPescgwA 240
                                       444444555555..5677766666666666655555688888887777666555551 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 !   18.4   0.0   6.8e-07     0.002      10      79 ..     210     277 ..     196     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.8e-07
                   Glyco_trans_1_2  10 spnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervla 79 
                                        +  +++Ea a+G +++++   gl+e   +   +i+++d ++l++ + +ll+n +  r+++ + ++++++
  gi|488600628|ref|YP_007907099.1| 210 AFPSVILEAQAAGLPVICNNYGGLPESCGWA--GIVVKDKKDLEQVLSKLLTNKKIQRKLRYKSYKKMKK 277
                                       566789*************99******9665..9***************************999999765 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   0.0   1.5e-06    0.0043      69     148 ..      10      96 ..       1     104 [. 0.79
   2 ?   -0.6   0.0      0.55   1.7e+03      81     106 ..     207     232 ..     175     245 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                   Glyco_trans_4_4  69 qrrerpdvvhahsp.taglaarlarrrrgiplvvtlhgll.....lrrgsgavrrlyralerrllrradavlvvsea 139
                                          e +d+  + +p   gl+a +++  ++ pl vtl+g+      ++++s  +  ++r +  ++l+ ad+++v+s a
  gi|488600628|ref|YP_007907099.1|  10 LITEEYDLYLTDEPfANGLLAFIISSIKNKPLTVTLRGWGdltnaHNEYSNLKFFFLRLISNFVLSKADRIIVLSKA 86 
                                       3478899999999626899999999889*********74433333778899999999******************** PP

                   Glyco_trans_4_4 140 eaeelra.lg 148
                                        a el   ++
  gi|488600628|ref|YP_007907099.1|  87 TATELNKiYN 96 
                                       ***9977555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.55
                   Glyco_trans_4_4  81 spt..aglaarlarrrrgiplvvtlhgl 106
                                       + +   +++++ a+ ++g+p++++ +g 
  gi|488600628|ref|YP_007907099.1| 207 Y-LdaFPSVILEAQ-AAGLPVICNNYGG 232
                                       2.222445555555.8899999887765 PP

>> DUF3689  Protein of unknown function (DUF3689)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.068     2e+02     109     131 ..      26      48 ..      19      54 .. 0.92
   2 ?    9.8   0.1   0.00014      0.43      50      86 ..      60      96 ..      49     153 .. 0.87
   3 ?   -2.6   0.0      0.91   2.7e+03     115     141 ..     263     288 ..     247     291 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.068
                           DUF3689 109 kgLlskilevlkkeptdssfrFw 131
                                       +gLl  i++ +k++p++ ++r w
  gi|488600628|ref|YP_007907099.1|  26 NGLLAFIISSIKNKPLTVTLRGW 48 
                                       79******************988 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00014
                           DUF3689 50 alkiQfLRLvhsfcdhsenkylllskeElnelkqiss 86
                                       lk  fLRL+ +f  ++ ++ ++lsk+  +el++i++
  gi|488600628|ref|YP_007907099.1| 60 NLKFFFLRLISNFVLSKADRIIVLSKATATELNKIYN 96
                                      59999************************99999954 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.91
                           DUF3689 115 ilevlkkeptdssfrFwlaravEsflR 141
                                       i ++l+ ++ +  ++ + a+avE ++R
  gi|488600628|ref|YP_007907099.1| 263 IQRKLRYKSYK-KMKKYNAVAVEKYVR 288
                                       33444444443.556666777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1780.83
//
Query:       gi|488600629|ref|YP_007907100.1|  [L=218]
Description: hypothetical protein Asulf_01107 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-15   56.8   0.0    3.2e-15   56.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
      1e-10   42.1   0.0    1.5e-10   41.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.4e-06   28.2   0.0    3.2e-06   27.0   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
    5.4e-06   27.1   0.0    8.4e-06   26.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.4e-05   25.7   0.0    2.8e-05   24.7   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.017   14.3   0.0    1.2  1  DREV             DREV methyltransferase
      0.024   13.6   0.0      0.039   12.9   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.027   13.8   0.0      0.074   12.3   0.0    1.6  1  CMAS             Mycolic acid cyclopropane synthetase


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 !   56.4   0.0   1.4e-18   3.2e-15      13     164 ..      25     183 ..      16     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.4e-18
                   Methyltransf_23  13 lerllpklraggrvLdiGcGtGillevlre.......ngf..svtgvDlspeaveiaekakkaqkdqfdeqeaaepq 80 
                                       ++++l+   ag++vLd+Gc  ++  +  r+        ++   + gvDl ++ v+++ +   ++  ++d ++ + p+
  gi|488600629|ref|YP_007907100.1|  25 IQEILK-YVAGKKVLDLGCVQHSSNKATRAdwlhgiiSRYasYCLGVDLLEKEVKKL-NELGYNIICADVEKMDLPE 99 
                                       334443.45689**********76444433233333312342556****99988888.55555555555555577** PP

                   Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl...kedrllldwlylvpagrhisffsarslkel 154
                                       + f++Iv+ e++eh+ +p + l + +++lk++G+l++++p+  +    +++ + +  + v+  +h+ ++++ +l +l
  gi|488600629|ref|YP_007907100.1| 100 KDFEVIVAGELIEHLANPGSFLENCRNHLKDDGLLIITTPNPFCfihFRRSIFGK--LKVNP-EHVAWYDEITLTQL 173
                                       *****************************************99966334555555..44666.9************* PP

                   Methyltransf_23 155 leeaGlevve 164
                                       l+++++e ve
  gi|488600629|ref|YP_007907100.1| 174 LKRYNFEPVE 183
                                       *******997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   6.9e-14   1.5e-10      15      96 .]      57     136 ..      38     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 6.9e-14
                                       H....HTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHH CS
                   Methyltransf_11  15 a....krgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRv 87 
                                       +    ++++ ++gvDl ++ +k  +e +       ++++ad+ek+ ++++ f ++v+ e ++h+++p ++l++++  
  gi|488600629|ref|YP_007907100.1|  57 HgiisRYASYCLGVDLLEKEVKKLNELG------YNIICADVEKMDLPEKDFEVIVAGELIEHLANPGSFLENCRNH 127
                                       25553455999********996665444......457**************************************** PP

                                       EEEEEEEEE CS
                   Methyltransf_11  88 LkpgGllvi 96 
                                       Lk +Gll+i
  gi|488600629|ref|YP_007907100.1| 128 LKDDGLLII 136
                                       *******96 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.4e-09   3.2e-06       4     114 ..      34     147 ..      32     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.4e-09
                   Methyltransf_31   4 glrvlDlGCGtGeltfelae.......elgp..kaevvGiDiseeaielArenaqklgldnveFeqgdieeleklle 71 
                                       g++vlDlGC + + + ++ +          +   +   G+D  e+ +++ +e    lg++      +d+e+++  l 
  gi|488600629|ref|YP_007907100.1|  34 GKKVLDLGCVQ-HSSNKATRadwlhgiI--SryASYCLGVDLLEKEVKKLNE----LGYN---IICADVEKMD--LP 98 
                                       67899999999.7777777677755321..2223448899999988888888....5665...999*****99..88 PP

                   Methyltransf_31  72 dekfDlilsnevlnaladpdkileeiervlkpggilliedpr......l 114
                                       ++ f +i++ e++ +la+p ++le+  + lk++g l+i++p+       
  gi|488600629|ref|YP_007907100.1|  99 EKDFEVIVAGELIEHLANPGSFLENCRNHLKDDGLLIITTPNpfcfihF 147
                                       899**************************************96555550 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   3.7e-09   8.4e-06      25      99 .]      69     134 ..      38     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.7e-09
                   Methyltransf_12  25 gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99 
                                       gvD+ ++ +    +kl++ + +n  + ++e+ dl +    + f ++va ++++hl+++ ++l+n+r++Lk++G l
  gi|488600629|ref|YP_007907100.1|  69 GVDLLEKEV----KKLNELG-YNIICADVEKMDLPE----KDFEVIVAGELIEHLANPGSFLENCRNHLKDDGLL 134
                                       555555555....4444444.344566666666554....59*******************************86 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.3e-08   2.8e-05      21      97 .]      64     132 ..      37     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.3e-08
                                       SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGGSSHHHHHHHHHHHHHHEEEE CS
                   Methyltransf_25  21 kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhhlsdedlekalkeiarvLkpg 96 
                                       ++  +gvD+ e+ +++ +e         +++++d+e+++++++ f ++v+ g+ ++hl ++    +l++++++Lk++
  gi|488600629|ref|YP_007907100.1|  64 ASYCLGVDLLEKEVKKLNELG------YNIICADVEKMDLPEKDFEVIVA-GElIEHLANPG--SFLENCRNHLKDD 131
                                       566778888888877777765......89*********************.666***99765..9***********9 PP

                                       E CS
                   Methyltransf_25  97 G 97 
                                       G
  gi|488600629|ref|YP_007907100.1| 132 G 132
                                       9 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.4e-06     0.017      96     192 ..      35     142 ..      21     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.4e-06
                              DREV  96 kklldlGaGdGeitkrvaptfee.........vyatelsetmrdrlkkkkynvlsa.le.lqetdvkldlilclnll 161
                                       kk+ldlG  +    k  +    +             +l e+  ++l+ ++yn++ a +e ++  + ++++i++ +l+
  gi|488600629|ref|YP_007907100.1|  35 KKVLDLGCVQHSSNKATRADWLHgiisryasyCLGVDLLEKEVKKLNELGYNIICAdVEkMDLPEKDFEVIVAGELI 111
                                       6777777776666666665555556555554466678899999**********97524545556789********** PP

                              DREV 162 drcfdplklledirsalepngrvivalvlPv 192
                                       +   +p+ +le+ r+ l+ +g  i++   P+
  gi|488600629|ref|YP_007907100.1| 112 EHLANPGSFLENCRNHLKDDGLLIITTPNPF 142
                                       *********************9999877776 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   0.0   1.8e-05     0.039      95     219 ..      13     138 ..       7     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                       --SEEHHHHHHHHGGGS.--TT-EEEEET-TTSH........HHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTT CS
                    Methyltransf_9  95 dteWrsdwkWdrvlphlsdlkgrtildvGcgnGy........hlwrmvgegaklvvGidPselfliqfeavrkllge 163
                                           r   k  r+++ l  + g+++ld+Gc +          +l+ ++++ a+ ++G+d  e      + v+kl   
  gi|488600629|ref|YP_007907100.1|  13 KNIIRNSEKRYRIQEILKYVAGKKVLDLGCVQHSsnkatradWLHGIISRYASYCLGVDLLE------KEVKKLN-- 81 
                                       555677889999******************75320011111134445555555555555333......3344443.. PP

                                       TSSEEEE---GGGS-T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEE CS
                    Methyltransf_9 164 dqrahllplgieqlpe.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvlet 219
                                       +   + +   +e+++   + f+++ +  ++ h   P   l + +++l+ +G l++ t
  gi|488600629|ref|YP_007907100.1|  82 ELGYNIICADVEKMDLpEKDFEVIVAGELIEHLANPGSFLENCRNHLKDDGLLIITT 138
                                       34456677899999987889**********************************977 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05     0.074      49     166 ..      20     138 ..       8     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEE....EEES-HHHHHHHHHHHHTS-SSS-EEEEES-G CS
                              CMAS  49 aKldlileklelkpGmtlLdiGcGWGslvrraverydvkvv....glTlSkeqaklakkrvdeldlerkvevklldy 121
                                       +K+ +i e l+  +G+++Ld+Gc   s  + + + +   ++    +  l  +  ++  k+++el+     ++  +d 
  gi|488600629|ref|YP_007907100.1|  20 EKRYRIQEILKYVAGKKVLDLGCVQHSSNKATRADWLHGIIsryaSYCLGVDLLEKEVKKLNELGY----NIICADV 92 
                                       677788889999999999999998665544333333222220011333444444444445555553....3333333 PP

                                       G..G---.--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEE CS
                              CMAS 122 e..dlde.kvdrvvsvgafehvgkenydtffkklkkllkedGllllht 166
                                       e  dl+e  ++ +v+ +++eh+   n   f +++ + lk+dGll++ t
  gi|488600629|ref|YP_007907100.1|  93 EkmDLPEkDFEVIVAGELIEHLA--NPGSFLENCRNHLKDDGLLIITT 138
                                       311566669************95..6789**************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1328.91
//
Query:       gi|488600630|ref|YP_007907101.1|  [L=491]
Description: Membrane protein involved in the export of O-antigen and teichoic acid [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-34  117.9  32.0      5e-34  117.9  32.0    2.7  3  Polysacc_synt    Polysaccharide biosynthesis protein
    7.9e-31  107.4  18.1    7.9e-31  107.4  18.1    2.0  1  Polysacc_synt_3  Polysaccharide biosynthesis protein
      3e-18   66.3  54.9    2.5e-17   63.3  21.3    3.4  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.5e-15   56.8  39.1    2.1e-12   46.4  28.9    2.4  2  MurJ             Lipid II flippase MurJ
    4.3e-08   33.0   8.9    4.3e-08   33.0   8.9    4.1  5  MatE             MatE
  ------ inclusion threshold ------
      0.062   13.3   0.1       0.16   12.0   0.1    1.7  1  DUF2148          Uncharacterized protein containing a ferredo


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 !  117.9  32.0   1.7e-37     5e-34       2     273 ..      20     294 ..      19     295 .. 0.92
   2 ?   -0.4  15.4       0.2     6e+02      91     192 ..     318     422 ..     303     467 .. 0.82
   3 ?   -1.5   0.2      0.45   1.3e+03      82     109 ..     458     485 ..     451     490 .. 0.67

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 1.7e-37
                     Polysacc_synt   2 lkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.......k 71 
                                       +++++++lls ++  l +++  + larilg+e+fG ++la+a+ ++++ +++lG+++a+ r+ia ++ +        
  gi|488600630|ref|YP_007907101.1|  20 ARNALFNLLSLIVGSLSGLLLSITLARILGAEQFGVYSLAIAVGSMAISFATLGIDNAVMRYIAFSHGRkdlegirA 96 
                                       79****************************************************************99999*99755 PP

                     Polysacc_synt  72 elvslillnvllvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvve 148
                                       +     +++++++l+v+ +l++l++ +a+++++++l+++  ++ l++l + +++ f +++f+gl+++ y + +q+v+
  gi|488600630|ref|YP_007907101.1|  97 HFYYFAKVKAVITLIVSTILITLSPKLAEIFNDERLSIPFALAGLIVL-VASFSNFLNSFFRGLQKFDYSFFRQIVY 172
                                       5555556789999**************************988888887.99************************** PP

                     Polysacc_synt 149 qlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvils.lklvrellsfsapltisslailly 224
                                       ++sr ++v+ + + fl   +avlg vla+ +++i+++++     +++  + + ++   +   +   +ti s+++ +y
  gi|488600630|ref|YP_007907101.1| 173 ETSRWVFVIPLALFFL-ASGAVLGSVLAYTTSLIFLFVLAI--KHRELIFGNkTHISPKVNNYMGFMTIASISGIVY 246
                                       *********9999999.8999*******9999888888888..6666666663455556777888999********* PP

                     Polysacc_synt 225 tyidsillglllgaeavGiYnaayqllvaisgllapivtaalfPvfsel 273
                                       +y+dsi++g+l +++ vG+Y+aay+++ ai g++++ +t +l P+f+++
  gi|488600630|ref|YP_007907101.1| 247 AYVDSIMIGYLMDTTYVGYYRAAYTIVFAIIGFASSLAT-VLLPTFTQI 294
                                       ***************************************.*******97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.2
                     Polysacc_synt  91 lfllllliaa....flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflf 163
                                       ++ll+++ ++    ++g+  l +  +++ l+++l++g+ s+   +f+++er    a  ++ + +  v+l  ++++ +
  gi|488600630|ref|YP_007907101.1| 318 VVLLSHFSKElistLYGRDFLPSASVMFYLSFALIPGTFSYLITIFNAKERADIRAYIVITSMVLNVALNYALIIKM 394
                                       5555555555555599999999999999999********************************************** PP

                     Polysacc_synt 164 ldivaavlgavlaalvggivslavlrkkf 192
                                       + i++a++++v++ +  + + +++l + +
  gi|488600630|ref|YP_007907101.1| 395 G-ITGAAIATVISRFFVISATIVLLNRVL 422
                                       *.***********9999888777776555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.45
                     Polysacc_synt  82 llvllvlvllfllllliaaflglpelav 109
                                       +l +l+++++++lll+    l +++l++
  gi|488600630|ref|YP_007907101.1| 458 ILEILLTLMIYFLLLVGLKALTKKDLRY 485
                                       4556777777777777777777776666 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4  18.1   2.7e-34   7.9e-31       2     292 ..      44     341 ..      43     342 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 2.7e-34
                   Polysacc_synt_3   2 LARLLspedFGvvaialvvislanlfvdmGlssaliqkedltee.....dlstvft....fnlvlgllialvlflla 69 
                                       LAR+L  e FGv+++a++v s+a  f+++G+++a+ +    ++       ++  f+    ++ v+ l+++++l+ l+
  gi|488600630|ref|YP_007907101.1|  44 LARILGAEQFGVYSLAIAVGSMAISFATLGIDNAVMRYIAFSHGrkdleGIRAHFYyfakVKAVITLIVSTILITLS 120
                                       9**********************************986533333222334455554222247899999********* PP

                   Polysacc_synt_3  70 pliasfynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigt 146
                                       p +a+++n+++l   + +++l ++++++s+  ++++r   kF+  f++++v  +   ++ i lAl+ l   A++ + 
  gi|488600630|ref|YP_007907101.1| 121 PKLAEIFNDERLSIPFALAGLIVLVASFSNFLNSFFRGLQKFDYSFFRQIVYETSRWVFVIPLALFFLASGAVLGSV 197
                                       ***************************************************************************** PP

                   Polysacc_synt_3 147 llssllslvllwlaskwrprlkfslkslk.elfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlas 222
                                       l++ +  + l++la+k+r  +  + ++++ ++ ++   ++++++  +++  +d+++iG++++++++G+Y  a+++++
  gi|488600630|ref|YP_007907101.1| 198 LAYTTSLIFLFVLAIKHRELIFGNKTHISpKVNNYMGFMTIASISGIVYAYVDSIMIGYLMDTTYVGYYRAAYTIVF 274
                                       ******************8887888888725668999***************************************9 PP

                   Polysacc_synt_3 223 lpvaeitsviakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWleav 292
                                       +++  + s++a+Vl+P++ +++   ++++++++++ r +a++++P +v+l  ++++l+++l+G+ +l+++
  gi|488600630|ref|YP_007907101.1| 275 AIIG-FASSLATVLLPTFTQISL--RDIENALERLNRYSAILAFPSVVLLSHFSKELISTLYGRDFLPSA 341
                                       9886.67899*********9986..59**************************************99875 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   2.3     0.052   1.6e+02      34      85 ..      29      86 ..       7     130 .. 0.54
   2 !   12.4  15.6   4.2e-05      0.13       3     135 ..     137     283 ..     135     290 .. 0.84
   3 !   63.3  21.3   8.5e-21   2.5e-17       2     142 ..     344     476 ..     343     477 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.052
                   Polysacc_synt_C 34 alvigalvklilnllli.....plfgivGaaiatvlallvva.vlnlyalrrllgikl 85
                                      +l++g l  l+l++ l       +fg++  aia     +  a + +  a++r++ ++ 
  gi|488600630|ref|YP_007907101.1| 29 SLIVGSLSGLLLSITLArilgaEQFGVYSLAIAVGSMAISFAtLGIDNAVMRYIAFSH 86
                                      4444444444444444411114566665544444333222220222345555555555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrr 79 
                                       a+  l+++++s+s++l+s + gl + ++ +   ++     +++ ++l  +f + Ga++++vla++++++++++++ +
  gi|488600630|ref|YP_007907101.1| 137 ALAGLIVLVASFSNFLNSFFRGLQKFDYSFFRQIVYETSRWVFVIPLALFFLASGAVLGSVLAYTTSLIFLFVLAIK 213
                                       6778999****************************************************************999999 PP

                   Polysacc_synt_C  80 llgikl.......ellrrllkpllaalvmgivvylllllllglllla........alalllavlvgalvYl 135
                                       +  + +         +++ +  + +a + giv  ++ ++++g l++         a ++++a+ +g +  l
  gi|488600630|ref|YP_007907101.1| 214 HRELIFgnkthisPKVNNYMGFMTIASISGIVYAYVDSIMIGYLMDTtyvgyyraAYTIVFAI-IGFASSL 283
                                       888888777777744777778888888888887779999999998888888887444777776.6666554 PP

  == domain 3  score: 63.3 bits;  conditional E-value: 8.5e-21
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalr 78 
                                       + +l++++i+ ++ + l +i+++  r++i +++++ +++++++ln+ li ++gi+Gaaiatv++ ++v+   +++l+
  gi|488600630|ref|YP_007907101.1| 344 MFYLSFALIPGTF-SYLITIFNAKERADIRAYIVITSMVLNVALNYALIIKMGITGAAIATVISRFFVISATIVLLN 419
                                       6677777777665.57788********************************************************** PP

                   Polysacc_synt_C  79 rllgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                       r lg+++  + ++l+pl+a+++m+iv  ll+l  ++ +     + +l++l+   +Y+lll+ l+
  gi|488600630|ref|YP_007907101.1| 420 RVLGLQP-KIGSCLRPLVATVIMFIV--LLVLPKPESIY----TGILEILLTLMIYFLLLVGLK 476
                                       *******.699999************..33333333333....67999999********99876 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.0     1e-06    0.0031     197     308 ..      16     128 ..       1     131 [. 0.88
   2 !   46.4  28.9   7.1e-16   2.1e-12     157     428 ..     185     446 ..     166     470 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-06
                              MurJ 197 lkkflklllptllgvsvsql.nllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekded 272
                                        +++ +++l+ ll+  v  l +ll++++lA+ l +  + +++ a ++  ++++  ++ i ++++  ++ s+ +kd +
  gi|488600630|ref|YP_007907101.1|  16 ARRVARNALFNLLSLIVGSLsGLLLSITLARILGAEQFGVYSLAIAVGSMAISFATLGIDNAVMRYIAFSHGRKDLE 92 
                                       478888999999988875552799***************************************************** PP

                              MurJ 273 evrdllsqairltllllipvsfgllvlskpivsllf 308
                                        +r+    + ++ +++++ vs +l+ ls+++ ++++
  gi|488600630|ref|YP_007907101.1|  93 GIRAHFYYFAKVKAVITLIVSTILITLSPKLAEIFN 128
                                       *****************************9988775 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 7.1e-16
                              MurJ 157 ilaLaiGvliGgvlqllvqlpalkkaglllkprfafrdegl.kkflklllptllgvsvsqlnllvdtalAsflaegs 232
                                        + La G ++G vl     l++l+   ++ ++++  ++  +  k+ + + ++++++ + ++ ++vd ++  +l+ ++
  gi|488600630|ref|YP_007907101.1| 185 LFFLASGAVLGSVLAYTTSLIFLFVLAIKHRELIFGNKTHIsPKVNNYMGFMTIASISGIVYAYVDSIMIGYLMDTT 261
                                       4579************************97776666666551699999***************************** PP

                              MurJ 233 vsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllfe 309
                                          ++ a   + +++  f+ s++tvlLP++ +  + +d +   + l+   r +++l++p++++l  +sk+++s+l+ 
  gi|488600630|ref|YP_007907101.1| 262 YVGYYRAAYTIVFAIIGFASSLATVLLPTFTQI-SLRDIE---NALERLNRYSAILAFPSVVLLSHFSKELISTLY- 333
                                       99999999999999999999***********55.555555...46666779*************************. PP

                              MurJ 310 rGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnillsllllpplgvvglalats 386
                                              d+   a+v++  +++Lip      l+++f A+e++   ++i + s+vln++l++ l++++g  g a+at+
  gi|488600630|ref|YP_007907101.1| 334 -----GRDFLPSASVMFYLSFALIPGTFS-YLITIFNAKERADIRAYIVITSMVLNVALNYALIIKMGITGAAIATV 404
                                       .....5799****************7755.5789******************************************* PP

                              MurJ 387 lsaliglvllyvllrkrlklteargiktflaklvvllalaav 428
                                       +s  + +   +vll++ l+l+++ g  +    + v+++++  
  gi|488600630|ref|YP_007907101.1| 405 ISRFFVISATIVLLNRVLGLQPKIGSCLRPLVATVIMFIVLL 446
                                       *****************9999887765544443333333333 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   8.9   1.4e-11   4.3e-08       4     146 ..      28     167 ..      27     186 .. 0.90
   2 ?    2.0   0.5     0.048   1.4e+02      76     124 ..     196     242 ..     188     247 .. 0.76
   3 !   13.9  12.4     1e-05     0.031       5     160 ..     239     388 ..     236     389 .. 0.89
   4 ?   -3.7   0.2       2.8   8.4e+03     129     134 ..     403     408 ..     391     423 .. 0.47
   5 ?   -2.3   0.5         1   3.1e+03      97      97 ..     451     451 ..     427     479 .. 0.48

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.4e-11
                              MatE   4 lenllesllslidtllvgrl.gskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglil 78 
                                       l+ ++ sl++l++++ ++r+ g++  +++s+a+ + s+ ++   lg+ +a+   ++ + G k+ ++++  +++  ++
  gi|488600630|ref|YP_007907101.1|  28 LSLIVGSLSGLLLSITLARIlGAEQFGVYSLAIAVGSMAISfATLGIDNAVMRYIAFSHGRKDLEGIRAHFYYFAKV 104
                                       67788899999********99*******************9899********************************* PP

                              MatE  79 llllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvply 146
                                        +++ li++ +++ +s++++ +f+++   +++a      ++l +++ ++++ l++++rg +k+  +++
  gi|488600630|ref|YP_007907101.1| 105 KAVITLIVSTILITLSPKLAEIFNDERLSIPFAL-----AGLIVLVASFSNFLNSFFRGLQKFDYSFF 167
                                       ***********************99997777774.....56666677899999999999999988876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.048
                              MatE  76 lilllllsliiallvllfseqilslftqdeevlelakrylrililgipa 124
                                        +l+   sli+ ++  l +++   +f+++ ++++++++y+ ++ +  + 
  gi|488600630|ref|YP_007907101.1| 196 SVLAYTTSLIFLFV--LAIKHRELIFGNKTHISPKVNNYMGFMTIASIS 242
                                       45666666666666..778888889****************99987665 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 1e-05
                              MatE   5 enllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                       +++   ++  +d++++g+l +++ ++ + +a +i++ ++ f+ +l+t l +  +q     + +++++al +    ++
  gi|488600630|ref|YP_007907101.1| 239 ASISGIVYAYVDSIMIGYLmDTTYVGYYRAAYTIVFAIIGFASSLATVLLPTFTQ----ISLRDIENALERLNRYSA 311
                                       6666678999***********************9999998888888888887776....578999999999999999 PP

                              MatE  81 llsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnip 157
                                       +l+++ ++l+  fs+ ++s + +  + l+ a+ +  + +  ip+   +  l +i+++ +++ + +yi++ s++ln+ 
  gi|488600630|ref|YP_007907101.1| 312 ILAFPSVVLLSHFSKELISTL-YGRDFLPSASVMFYLSFALIPGT--FSYLITIFNAKERADIRAYIVITSMVLNVA 385
                                       9******************99.66679*****9999999999999..555678************************ PP

                              MatE 158 lny 160
                                       lny
  gi|488600630|ref|YP_007907101.1| 386 LNY 388
                                       **9 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 2.8
                              MatE 129 lvlsgi 134
                                       +v+s++
  gi|488600630|ref|YP_007907101.1| 403 TVISRF 408
                                       111111 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 1
                              MatE  97 i 97 
                                        
  gi|488600630|ref|YP_007907101.1| 451 P 451
                                       3 PP

>> 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 ?   12.0   0.1   5.4e-05      0.16       9      36 ..      55      82 ..      51      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                           DUF2148  9 aiDlGiAlgsavkvaadlrvDnRvmysv 36
                                      +  l+iA+gs +   a l++Dn vm  +
  gi|488600630|ref|YP_007907101.1| 55 VYSLAIAVGSMAISFATLGIDNAVMRYI 82
                                      6779********************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3170.24
//
Query:       gi|488600631|ref|YP_007907102.1|  [L=619]
Description: anion transporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-93  313.6  39.9    3.8e-93  313.1  39.9    1.1  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    1.9e-39  135.7  47.3    1.9e-39  135.7  47.3    2.5  2  CitMHS         Citrate transporter
  ------ inclusion threshold ------
       0.86    8.4  48.8       0.45    9.3  29.1    3.0  2  DctM           Tripartite ATP-independent periplasmic transpo


Domain annotation for each model (and alignments):
>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.1  39.9   6.3e-97   3.8e-93      32     462 ..     141     598 ..     134     607 .. 0.92

  Alignments for each domain:
  == domain 1  score: 313.1 bits;  conditional E-value: 6.3e-97
                     Na_sulph_symp  32 rllaifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlLvfaalliaaavektgLgkRi 108
                                        +la  +++++ +i e++pl+++al++l +l+ l       ++++v++ + s++++L++++++iaaa++k++L++R+
  gi|488600631|ref|YP_007907102.1| 141 SVLALTVLMAIWWIGEAIPLPATALLPLVVLPFLEVS----QITDVAKSYASKVIFLFMGGFMIAAAMMKWNLHRRL 213
                                       578999*************************766543....47********************************** PP

                     Na_sulph_symp 109 AlvlvkivGkrt..liLgyalvladlllapatpsntAraggivfpvikslss..........afgsepekqserkig 173
                                       Al+++ ++G+++   +Lg+++ +a+l+++++++++t ++ +i++++i+++++          + g+++  ++ +  g
  gi|488600631|ref|YP_007907102.1| 214 ALIIIDFIGVTPrkIVLGFMIATAFLSMWISNTATTMMMMPIALAIIMQVATqgmelqkkgqLKGVDFTAGNFK-FG 289
                                       ************8889***********************************99999999998888888888777.** PP

                     Na_sulph_symp 174 aylmltvvqsasitsiaflTamApNllllglins..ilgveitwasWflaaiptgvillllvpll.lyvlyppeikk 247
                                         lml +++sasi+++a++ ++ pN++l+g++ +      eit+++W+++ ip+ v++l+++++l +y+l ppei+ 
  gi|488600631|ref|YP_007907102.1| 290 TALMLGIAYSASIGGVATIIGTPPNAILVGVLPKlfPDAPEITFTDWIVFGIPIVVVMLFITWFLmVYILNPPEIDV 366
                                       **********************************7667889**********************7527********** PP

                     Na_sulph_symp 248 keeakavaktelkelGpltarekallilfvlllllWifge...........sln.....idattvaivvlvillllr 308
                                        + +k+v+k+e ++lG  t+ ek+++i+fvl  l Wi ++                   +++ ++a++  + l+l++
  gi|488600631|ref|YP_007907102.1| 367 LPGGKEVIKREKEKLGKWTKGEKIVMIVFVLTALAWINSSpknlggmivpgI-RtylpfVNDYVIAMLSAIALFLIP 442
                                       ***************************************9776666666550.055567****************** PP

                     Na_sulph_symp 309 ........vldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhyl 377
                                                ldW+    ++ +W++lll+gg+ial+   ++sgl  w+g++l  +   ++p v++++i +l+ +  ++
  gi|488600631|ref|YP_007907102.1| 443 vdmkrgefALDWD--HAKEIPWGILLLFGGGIALSGAFTKSGLAVWVGEQLLFLKG-MHPIVVLAVITTLV-IFLTE 515
                                       9************..8999********************************97766.9**99999887765.55699 PP

                     Na_sulph_symp 378 faSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiig 454
                                       ++S+tA t+ ++pi+++ a a+ g++p  ++++ ala s+a f+lp+at+pn+ivfg+gy+ + +++r Gf+l++ig
  gi|488600631|ref|YP_007907102.1| 516 MTSNTAITTLMMPIMASFALAM-GVDPRGFMVAAALAASYA-FMLPVATPPNAIVFGTGYVTIPQMARNGFLLNLIG 590
                                       **********************.******************.*********************************** PP

                     Na_sulph_symp 455 llillllg 462
                                       +++l ++ 
  gi|488600631|ref|YP_007907102.1| 591 IVLLTIAC 598
                                       99887765 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7  47.3   3.1e-43   1.9e-39       2     300 .]     151     549 ..     150     551 .. 0.84
   2 ?    0.2   9.8     0.058   3.5e+02     109     170 ..     537     599 ..     532     611 .. 0.63

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 3.1e-43
                                       xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            CitMHS   2 vllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd. 73 
                                       +++i e+++l+++all+lv+l    v +i ++ + +as +i+l++g+++i+aa+ +++l++rla  ++ + g  ++ 
  gi|488600631|ref|YP_007907102.1| 151 IWWIGEAIPLPATALLPLVVLpfleVSQITDVAKSYASKVIFLFMGGFMIAAAMMKWNLHRRLALIIIDFIGVTPRk 227
                                       89********************888777778********************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxx RF
                            CitMHS  74 llvllvlltallsafvsndgvvlimipivlslakrlkklppl......................lliplalaanigg 128
                                       +++ ++++ta+ls+++sn++++++m+pi+l++  +++   +                       l++ +a++a+igg
  gi|488600631|ref|YP_007907102.1| 228 IVLGFMIATAFLSMWISNTATTMMMMPIALAIIMQVATQGMElqkkgqlkgvdftagnfkfgtaLMLGIAYSASIGG 304
                                       *******************************999988877778999*****************99999********* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 129 altpiGtpttraaarpglslpnlll.......................lalllvgllplvllfmfgvalalpvnapk 182
                                       ++t+iGtp            pn +l                       +++++v+l++ ++l+   v +  p+++  
  gi|488600631|ref|YP_007907102.1| 305 VATIIGTP------------PNAILvgvlpklfpdapeitftdwivfgIPIVVVMLFITWFLM---VYILNPPEIDV 366
                                       ********............9999977777777777777777776666555666666666665...56666666667 PP

                                       xxxxxxxxxxxxxxxxxx.............................................xxxxxxx....... RF
                            CitMHS 183 vkkqkaiieaiarsllpv.............................................atillla....... 207
                                           k++i++ +++l ++                                             +     a       
  gi|488600631|ref|YP_007907102.1| 367 LPGGKEVIKREKEKLGKWtkgekivmivfvltalawinsspknlggmivpgirtylpfvndyvI-----Amlsaial 438
                                       7778888888888888888888876666555555556666666666666666666666665541.....04455677 PP

                                       ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxxxxxxxx RF
                            CitMHS 208 ..................ykkveWsvlllfaGvfllvgaleqtGilealadllga...g.gplvalalvlglialls 262
                                                          k+++W++lllf+G + l+ga++++G++ ++++ l     g  p+v+la+++ l+ +l+
  gi|488600631|ref|YP_007907102.1| 439 flipvdmkrgefaldwdhAKEIPWGILLLFGGGIALSGAFTKSGLAVWVGEQL-LflkGmHPIVVLAVITTLVIFLT 514
                                       788*****************************************999999888.335645888999999999999** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 263 afisnvavaalmapialgmapalgllspsplalalavg 300
                                        ++sn+a+++lm+pi+++ a a+g   ++p  ++ a++
  gi|488600631|ref|YP_007907102.1| 515 EMTSNTAITTLMMPIMASFALAMG---VDPRGFMVAAA 549
                                       **********************99...66666665553 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.058
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxx RF
                            CitMHS 109 lkklppllliplalaaniggaltpiGtpttraaarpglslpnlll....................lalllvgllplv 165
                                       ++ +p+ +++++alaa+    ++p+ tp            pn ++                    ++      ++l+
  gi|488600631|ref|YP_007907102.1| 537 MGVDPRGFMVAAALAASYAF-MLPVATP------------PNAIVfgtgyvtipqmarngfllnlIG------IVLL 594
                                       56678889**********99.*******............888886666555555555444333322......2222 PP

                                       xxxxx RF
                            CitMHS 166 llfmf 170
                                       ++++ 
  gi|488600631|ref|YP_007907102.1| 595 TIACY 599
                                       22222 PP

>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.2  21.9         3   1.8e+04     263     413 ..     175     353 ..     139     362 .. 0.77
   2 ?    9.3  29.1   7.6e-05      0.45     256     377 ..     442     568 ..     295     606 .. 0.79

  Alignments for each domain:
  == domain 1  score: -6.2 bits;  conditional E-value: 3
                              DctM 263 evaaallstakttaavlfilaaagifaglltltgvplklselllslsggk.llfLilvnllvlvlGmfldttaaiii 338
                                       ev +++  +  ++  v+f+  +  ++a +++  +++ +l+ +++   g     +++  ++   +l m ++ ta+ ++
  gi|488600631|ref|YP_007907102.1| 175 EVSQITDVAKSYASKVIFLFMGGFMIAAAMMKWNLHRRLALIIIDFIGVTpRKIVLGFMIATAFLSMWISNTATTMM 251
                                       566666677788999**************************999877755555777778888899************ PP

                              DctM 339 lvpilaPaaaklgidp......................ihfgvvivlnlsigli.....tPPvGlalfvassiakvs 388
                                       + pi++++++++  +                       +++ + i + +sig +     tPP ++ + v+ +     
  gi|488600631|ref|YP_007907102.1| 252 MMPIALAIIMQVATQGmelqkkgqlkgvdftagnfkfgTALMLGIAYSASIGGVatiigTPPNAILVGVLPKLFPDA 328
                                       ***********999887778888888888888887777666666666666665433344677777777777777666 PP

                              DctM 389 veeivkalvPflvvlvvalvlitlv 413
                                        e ++   + f +++vv+++ it++
  gi|488600631|ref|YP_007907102.1| 329 PEITFTDWIVFGIPIVVVMLFITWF 353
                                       6666666666777777777776665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 7.6e-05
                              DctM 256 yrrltleevaaallstakttaavlfilaaagifaglltltgvplklselllslsggk.llfLilvnllvlvlGmfld 331
                                         +++ +e a    ++ ++   +l++  +  +++g++t +g++ +++e ll l+g   +++L++++ lv++l  + +
  gi|488600631|ref|YP_007907102.1| 442 PVDMKRGEFALDWDHAKEIPWGILLLFGGGIALSGAFTKSGLAVWVGEQLLFLKGMHpIVVLAVITTLVIFLTEMTS 518
                                       5566666666667777777888999999999**********************9988799***************** PP

                              DctM 332 ttaaiiilvpilaPaaaklgidp....ihfgvvivlnlsiglitPPvGla 377
                                        ta+ +++ pi+a  a ++g+dp    +++ +   ++ ++  +tPP +++
  gi|488600631|ref|YP_007907102.1| 519 NTAITTLMMPIMASFALAMGVDPrgfmVAAALAASYAFMLPVATPPNAIV 568
                                       ***********************777777777788888888889997775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3617.00
//
Query:       gi|488600632|ref|YP_007907103.1|  [L=162]
Description: putative metal-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   73.4   0.0    2.7e-20   72.7   0.0    1.3  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 !   72.7   0.0   1.5e-24   2.7e-20      13     138 ..      36     146 ..      32     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 1.5e-24
                           DUF2284  13 rvrlkCekgCknYgknlsCPPavptveefrkilkeYkkallvqtkaeledeeddkeemkevkeelekillelekeaf 89 
                                       r r+kC++gC+ Ygk+ sCPP+vp ++e +++lk Yk ++++++           ++++++k +++++l++le +++
  gi|488600632|ref|YP_007907103.1|  36 RARWKCMFGCEYYGKRKSCPPFVPGIDEAERFLKAYKLGFIIKVPF----G----QNYMATKIAVQRLLIRLEAKLL 104
                                       679**************************************99876....2....244678999*********9997 PP

                           DUF2284  90 eagypkalalsagsCtlCetCayeegepCrhpekarpsmealGidvfkt 138
                                       ++ yp  +++++g C+lC+ C   ++  C    +arp++++lGi+++++
  gi|488600632|ref|YP_007907103.1| 105 NS-YPMIFTVFPGGCDLCDSCDPDST--C----QARPTLSSLGINISDL 146
                                       66.89*****************9994..7....69***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 1103.77
//
Query:       gi|488600633|ref|YP_007907104.1|  [L=431]
Description: phenylacetate-CoA ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-32  109.7   0.4    1.5e-31  108.6   0.3    1.7  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    7.5e-20   70.9   0.2      1e-18   67.2   0.2    2.0  1  AMP-binding      AMP-binding enzyme
    0.00011   21.2   0.0       0.14   11.0   0.0    2.4  3  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 ?   -3.6   0.0       2.4   1.4e+04      56      71 ..     214     229 ..     200     231 .. 0.72
   2 !  108.6   0.3   2.4e-35   1.5e-31       1      96 []     333     429 ..     333     429 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHHSS- CS
                   AMP-binding_C_2  56 lekkiakklksklgvs 71 
                                        +++ +k++++k g++
  gi|488600633|ref|YP_007907104.1| 214 WSEETRKRIEEKTGIT 229
                                       4566777777777776 PP

  == domain 2  score: 108.6 bits;  conditional E-value: 2.4e-35
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvel 76 
                                       GvnvfPsqie+ l++i+ev+++Y+i+++re+elD++++++E+k+ +++d++++  +lek ia++lks+l+v ++vel
  gi|488600633|ref|YP_007907104.1| 333 GVNVFPSQIEHTLMQIPEVGEHYMIYLDRENELDVMTIQIELKDeSMVDKVSDILRLEKLIAEELKSSLNVWARVEL 409
                                       9*******************************************889****************************** PP

                                       E-TT-S---------EEE-S CS
                   AMP-binding_C_2  77 vepgtlprsegKakrviDkR 96 
                                       v+pgtl+r egKakrviD+R
  gi|488600633|ref|YP_007907104.1| 410 VNPGTLQRFEGKAKRVIDRR 429
                                       ******************99 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.2   1.7e-22     1e-18     167     423 .]      90     332 ..      82     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.7e-22
                                       E--SSSS-EEEEEEHHHHHHHHHHHH..HHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC. CS
                       AMP-binding 167 TSGTTGkPKGVmlshrnlvanvaslk..letrfklkeddvv.lsilplahifglilelllallsGatvvllpkdaa. 239
                                       +SGTTGkP  V ++ + + + v sl   l+ + +++++d + +++    +  gl  + ++a   Ga+v+ ++  ++ 
  gi|488600633|ref|YP_007907104.1|  90 SSGTTGKPTVVGYTENDIRNWVESLCraLNSC-GVERSDIMqIAYGYGLFTGGL-GFHYAAEKLGASVIPVSAGNTq 164
                                       7**************99999988875434444.345578774555555566665.*************999988884 PP

                                       CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHH.CHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEE CS
                       AMP-binding 240 ldpklllelieklkvtviagvPrvlealle.sgalk.aakkakdlsslrlvllggeplspellrffralfgeevleg 314
                                       ++    +el+++lk tvia++P+ + +++e     k       +  +lr+ ++g+ep s+e+ +++++++g + +++
  gi|488600633|ref|YP_007907104.1| 165 RQ----IELMKDLKTTVIACTPSYMLYIAEyM-MNKgVSF---EETKLRMGIFGAEPWSEETRKRIEEKTGITAYDV 233
                                       44....8*********************7743.3332222...5567****************************** PP

                                       EEEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHE CS
                       AMP-binding 315 YGlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeaf 389
                                       YG +E +g ++  ++ e+      +G  ++     ++i+D+etge +++ge+Gel+v              +t+ea+
  gi|488600633|ref|YP_007907104.1| 234 YGTSELSGPLF-TECIEK------QGLHIWgdMFLIEIIDPETGEQLGEGEKGELVVT------------TLTKEAL 291
                                       *********98.554444......566666223468999*****************96............5688888 PP

                                       EET.CCEEEEEEEEEEETTS.........EEEEEEECCCEEEET CS
                       AMP-binding 390 dse.grwlrTGDlgrldedG.........yleivgRkkdliklr 423
                                         +     rTGD+  ++e+           ++i+gR++d+i++r
  gi|488600633|ref|YP_007907104.1| 292 --PlI-RWRTGDITSFEEEKcacgrthprIMRIMGRSDDMIIVR 332
                                       ..334.45999999998655567788887799999999999986 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.37   2.2e+03       8      32 ..      14      39 ..      10      55 .. 0.57
   2 !   11.0   0.0   2.4e-05      0.14      75     115 ..      83     122 ..      77     193 .. 0.75
   3 !    7.6   0.0   0.00025       1.5     352     472 ..     271     401 ..     261     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.37
                                      THHHHHHHHHHHHHHHC.TTSHHHHH CS
                               GH3  8 naaevqeevLkeiLkrn.anteylkk 32
                                      + +e+qe+ L++i++++  n+ y +k
  gi|488600633|ref|YP_007907104.1| 14 DLKELQERRLRAIIHHAyTNSPYYRK 39
                                      56666666666666654234444433 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.4e-05
                                       S-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHHHHH CS
                               GH3  75 piklfalsSGTtsgksKliPvteeslkelallvlallaall 115
                                       ++++f  sSGTt gk+ ++ +te+  +++   ++++l+++ 
  gi|488600633|ref|YP_007907104.1|  83 QVVRFHASSGTT-GKPTVVGYTENDIRNWVESLCRALNSCG 122
                                       7899********.***********99998777666665554 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00025
                                       CCS-TTSEEEEEEESTT....S-SSEEECEEEEEEEEE....TTEE.EEEEEECCTEEE-SSSS-CCHHHHHHHHH. CS
                               GH3 352 eevevGkeYelvvTtfa....GLyRYrigDvvrvtgfy....nkaP.rleFvgRknvvlsidgeklteeelqkavee 419
                                       e++  G++ elvvTt +     L R r+gD+  + +       + P +++++gR++ ++ ++g  +  +++++ + +
  gi|488600633|ref|YP_007907104.1| 271 EQLGEGEKGELVVTTLTkealPLIRWRTGDITSFEEEKcacgRTHPrIMRIMGRSDDMIIVRGVNVFPSQIEHTLMQ 347
                                       678899999*****96533337**********9987541111568*889*************************995 PP

                                       HHHHHTT-EEEEEEEEE.ESS.SSSEEEEEEEEECS........S........HHHHHHHHHCS CS
                               GH3 420 aakeltglelvdftsfapdtsesepghyvlflElkkk...eepee........eecckeldesL 472
                                         +   g   + ++++  d + +e    ++ +Elk++   +   +        + +++el +sL
  gi|488600633|ref|YP_007907104.1| 348 IPEV--G---EHYMIYL-DRE-NELDVMTIQIELKDEsmvD---KvsdilrleKLIAEELKSSL 401
                                       5544..3...5799988.666.89999999****9765441...12345455444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2790.89
//
Query:       gi|488600634|ref|YP_007907105.1|  [L=136]
Description: hypothetical protein Asulf_01112 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-23   82.0   0.1    4.3e-23   81.6   0.1    1.1  1  DUF123    Domain of unknown function DUF123
    0.00021   21.5   0.6    0.00031   21.0   0.6    1.5  1  GIY-YIG   GIY-YIG catalytic domain


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.1   4.8e-27   4.3e-23       2      93 ..      26     111 ..      25     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 4.8e-27
                            DUF123   2 elkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvvaseerlEcalaeal.eaeap 77 
                                        ++kg+y+Y Gs +   +l++R+krH+s+ k    kl+WhiDyL++++++  a ++++s +++Ec++++ l e+ +p
  gi|488600634|ref|YP_007907105.1|  26 YFRKGYYIYCGSHMV--NLEKRIKRHFSRDK----KLRWHIDYLTKEMDVLFA-IMIRSGKKMECSISRVLcEEFEP 95 
                                       689***********9..9********66655....7*********88776554.5556*************555569 PP

                            DUF123  78 vagfGasDckcesHLl 93 
                                        +++GasDckc++H++
  gi|488600634|ref|YP_007907105.1|  96 YSRLGASDCKCKTHVF 111
                                       99************98 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.6   3.4e-08   0.00031      10      36 ..      28      55 ..       4      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.4e-08
                                      TTT--EEEEEE.SSHHHHHHHHHHHHHH CS
                           GIY-YIG 10 kenkliYvGst.knlekRlkqHnagkka 36
                                      +++ +iY+Gs+  nlekR+k+H++ +k+
  gi|488600634|ref|YP_007907105.1| 28 RKGYYIYCGSHmVNLEKRIKRHFSRDKK 55
                                      567789*****99*********876643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 863.92
//
Query:       gi|488600635|ref|YP_007907106.1|  [L=456]
Description: mannose-1-phosphate guanylyltransferase (GDP) /mannose-6-phosphate isomerase, type 2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-67  223.9   0.3    1.2e-66  223.2   0.3    1.3  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    7.3e-59  199.3   0.0    1.1e-58  198.8   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    6.7e-12   45.0   0.1    1.6e-11   43.8   0.1    1.6  1  Cupin_2          Cupin domain
    3.6e-07   30.7   0.0    9.2e-07   29.4   0.0    1.7  2  NTP_transf_3     MobA-like NTP transferase domain
      0.005   16.5   0.0      0.013   15.2   0.0    1.6  1  Cupin_3          Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.074   13.0   0.0       0.17   11.8   0.0    1.6  1  AraC_binding     AraC-like ligand binding domain
       0.13   11.5   0.0       0.19   11.0   0.0    1.3  1  Lyx_isomer       D-lyxose isomerase


Domain annotation for each model (and alignments):
>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.2   0.3   4.8e-70   1.2e-66       1     151 []     302     452 ..     302     452 .. 1.00

  Alignments for each domain:
  == domain 1  score: 223.2 bits;  conditional E-value: 4.8e-70
                   MannoseP_isomer   1 vGvedlvvvetkdavlvadkdkvqdvkkvveelkaegreeaelhrevyrPWGsyevldegeryqvkritvkPgekls 77 
                                       +Gvedl+v++t+da+l+a+k + q+vk++++ lk +g+e+ ++hr++yrPWGsy+vl++ge +++kritv P ++ls
  gi|488600635|ref|YP_007907106.1| 302 IGVEDLLVIDTDDALLIAKKGESQKVKEIYSMLKGRGDERIKVHRTAYRPWGSYTVLETGEGFKIKRITVLPSKRLS 378
                                       79*************************************************************************** PP

                   MannoseP_isomer  78 lqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGsylgeddivrled 151
                                       lq+h+hr+ehWvvv+G+a+v vd +++ll++ est+i++ga+hrlenpGkiple+ievq+G+ylgeddi r+ed
  gi|488600635|ref|YP_007907106.1| 379 LQRHYHRSEHWVVVSGIARVVVDGKEILLRQGESTFIKAGAVHRLENPGKIPLEVIEVQIGQYLGEDDIERFED 452
                                       ************************************************************************98 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.8   0.0   4.2e-62   1.1e-58       1     246 [.       6     270 ..       6     272 .. 0.95

  Alignments for each domain:
  == domain 1  score: 198.8 bits;  conditional E-value: 4.2e-62
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTET.ETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTSGGGTSEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgke.rliqatlsrlan.sgieeiivvltqehsflveeqlkegskfgvev 75 
                                       k++ILaGG+GtRLwPL+r+l +k++    ++ +l+q+t++r+   s+ e+i +v+++e +f++ + l+e+ ++  ++
  gi|488600635|ref|YP_007907106.1|   6 KTIILAGGRGTRLWPLSRELLPKQFIRILDNrSLFQKTVERARIfSSPEDIFIVTNREYKFRILDDLSEIGDIP-KE 81 
                                       68******************999997555555*********9877***************************99.** PP

                                       EEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST..THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEE CS
                   NTP_transferase  76 lialepegkgtAdAvalaaelledeksdelvlvLggDhlikd..ayeeavkkaiekaakgtvtfgivpveeateyGv 150
                                       +i+lep  k+t +A+++a+++++d+ +   v vL++Dh+++    y e +kka++ a  +++tfgi+p++++t+yG+
  gi|488600635|ref|YP_007907106.1|  82 NILLEPDAKNTLPAIYWAVKVIGDNCK---VAVLPSDHIMDSgdGYIESFKKAMKLADSYLITFGIKPTKPHTGYGY 155
                                       *************************97...***********999**************99***************** PP

                                       EEEC....TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEEC CS
                   NTP_transferase 151 iead....eegrverfvEKPkeakaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalafl 222
                                       i+++    ++ +v +f+EKP+ ++a +++++G Y++ns++++f+ + +l+e ++ ++e++++++k +ee ++ +  +
  gi|488600635|ref|YP_007907106.1| 156 IKPGrnlgQGYEVAEFKEKPDLETAMQYVEKG-YFWNSGMFMFRTDiFLDEVQKLAPEVAEAFEKDIEEAYRTVPEI 231
                                       ****7774444*********************.*************************************9999888 PP

                                       STTEE...............-EEEXSSHHHHHHHHHHHH CS
                   NTP_transferase 223 fkdae...............yWsDvGtldslleanekla 246
                                         d+                yW+D+G++d++++a +k++
  gi|488600635|ref|YP_007907106.1| 232 SIDYGimektnrsavvpldtYWNDLGSFDAIYDALDKDE 270
                                       88877999**************************99887 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.1   6.1e-15   1.6e-11       5      70 ..     372     436 ..     368     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 6.1e-15
                                       EETTE.EEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   5 lppGe.sapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       lp  + s ++h+H+   e  +V++G +++ vdg+e+ l++G+s +++ag  Hr++N+g+ p++++ v
  gi|488600635|ref|YP_007907106.1| 372 LPSKRlSLQRHYHRS--EHWVVVSGIARVVVDGKEILLRQGESTFIKAGAVHRLENPGKIPLEVIEV 436
                                       444555667888887..6899*************************************99**99876 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 !   29.4   0.0   3.6e-10   9.2e-07       2      97 ..       8     117 ..       7     137 .. 0.80
   2 ?   -2.7   0.0       2.7   6.8e+03     103     121 ..     258     276 ..     238     322 .. 0.52

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.6e-10
                                       EEEEESS-TTT....TT..THHHHCC.CCCCHHHHHHHHHCTT..-CEEEEECSHC...HHHHHHTTC...TS-EEE CS
                      NTP_transf_3   2 viLAGGrSsRm....gg..dKallpl.ggkpllervldalraa.gvdevvvvggde...evlaalarl...gvrvve 64 
                                       +iLAGGr++R+     +  +K+++++ ++++l++ +++++r   + +++++v+++e    +l++l +    + + + 
  gi|488600635|ref|YP_007907106.1|   8 IILAGGRGTRLwplsREllPKQFIRIlDNRSLFQKTVERARIFsSPEDIFIVTNREykfRILDDLSEIgdiPKENIL 84 
                                       8**********66643389**********************994489********9555444444433322333344 PP

                                       -TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-T CS
                      NTP_transf_3  65 dedpgkgplaslaaalraaadadavlvlacDmP 97 
                                        e+  k++l +++ a++ ++d+  v+vl+ D++
  gi|488600635|ref|YP_007907106.1|  85 LEPDAKNTLPAIYWAVKVIGDNCKVAVLPSDHI 117
                                       455689*************************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                       HHHHHHHCHHHHTSSEEEE CS
                      NTP_transf_3 103 lverllaaaaasgadvvvp 121
                                         +++ +a++++++  ++ 
  gi|488600635|ref|YP_007907106.1| 258 SFDAIYDALDKDENGNAIR 276
                                       4444444444333333333 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     5e-06     0.013      20      60 ..     380     419 ..     374     434 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5e-06
                                       EECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3  20 rltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgl 60 
                                       + +y ++E+  +++G  +v++ +g+++ lr+G + ++++g 
  gi|488600635|ref|YP_007907106.1| 380 QRHYHRSEHWVVVSGIARVVV-DGKEILLRQGESTFIKAGA 419
                                       678999***************.****************997 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.5e-05      0.17      17      74 ..     380     434 ..     374     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                                       EEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEE CS
                      AraC_binding  17 pphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwl 74 
                                       ++h h   ++ +v++G +r+ ++g++  l++G+  +++ g +H++e  +   +++ ++
  gi|488600635|ref|YP_007907106.1| 380 QRHYHRSEHW-VVVSGIARVVVDGKEILLRQGESTFIKAGAVHRLENPG--KIPLEVI 434
                                       5677776666.5779******************************9988..5555555 PP

>> Lyx_isomer  D-lyxose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.4e-05      0.19     132     186 ..     383     436 ..     369     456 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.4e-05
                        Lyx_isomer 132 lededvtvsvDGvkktvaageklrlkpGesitlepglyHkfwaekgkgkvlvgev 186
                                       +++++  v v G+++ v  g+++ l++Ges  ++ g  H+     gk  + v ev
  gi|488600635|ref|YP_007907106.1| 383 YHRSEHWVVVSGIARVVVDGKEILLRQGESTFIKAGAVHRLENP-GKIPLEVIEV 436
                                       467788899******************************98876.6666556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2679.27
//
Query:       gi|488600636|ref|YP_007907107.1|  [L=230]
Description: hypothetical protein Asulf_01114 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   15.1   0.2        3.3    7.8   0.0    2.7  2  P2        P2 response regulator binding domain


Domain annotation for each model (and alignments):
>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00018       3.3      40      80 ..      42      82 ..      34      83 .. 0.83
   2 ?    4.6   0.0    0.0019        33      41      80 ..     178     221 ..     176     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00018
                                      HHHHTT-SSSEEEEEEEESS-HHHHHHHHHTSSS-SEEEEE CS
                                P2 40 edieeekfdegfevvlltkeskeeikealasiseiesveve 80
                                       die   f +   v++ ++ ++e ++e++++is i ++e +
  gi|488600636|ref|YP_007907107.1| 42 GDIEHAIFLGKNLVFFDNHLPEESVREIINKISRIGKIESK 82
                                      578888886666777789*****************999865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0019
                                       HHHT...T-S.SSEEEEEEEESS-HHHHHHHHHTSSS-SEEEEE CS
                                P2  41 diee...ekf.degfevvlltkeskeeikealasiseiesveve 80 
                                       die+    k+ ++++  + ++  +k +++++++++++ie++ +e
  gi|488600636|ref|YP_007907107.1| 178 DIEKlgfRKIaEGEIYALSIKWGEKGNLYKKVRDVADIEKLLIE 221
                                       566666677878899999999******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1391.54
//
Query:       gi|488600637|ref|YP_007907108.1|  [L=166]
Description: hypothetical protein Asulf_01115 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1862  (0.103854); expected 358.6 (0.02)
Passed bias filter:                      943  (0.0525964); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 897.33
//
Query:       gi|488600638|ref|YP_007907109.1|  [L=155]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-41  140.3   2.2      6e-41  139.9   2.2    1.2  1  Sm_multidrug_ex  Putative small multi-drug export protein
  ------ inclusion threshold ------
       0.42    9.3   2.3       0.54    9.0   2.3    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
       0.79    9.5   4.4        1.5    8.6   4.4    1.4  1  Phage_holin_2_3  Bacteriophage holin family HP1


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 !  139.9   2.2     1e-44     6e-41       1     121 []      19     139 ..      19     139 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 1e-44
                   Sm_multidrug_ex   1 ElrgaiplgillgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaekksekiekygflGL 77 
                                       Elrg++pl++ +g++pl+a++++vl n+ pvp+il++l k+ +++ ++++++k+f+++ +++ekk++ +e+yg++GL
  gi|488600638|ref|YP_007907109.1|  19 ELRGGLPLALHYGFSPLEAYVLCVLSNAFPVPFILMLLGKVEKIMGRYETTSKIFNFFLRRGEKKKDVVERYGYAGL 95 
                                       9**************************************************************************** PP

                   Sm_multidrug_ex  78 llFvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                       +lFvaiPLp+TGawtGslia++lglk+ k+++ i++G+liag++
  gi|488600638|ref|YP_007907109.1|  96 TLFVAIPLPVTGAWTGSLIAFILGLKPLKSFAYIFIGILIAGVV 139
                                       *****************************************986 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.3   9.1e-05      0.54     360     432 ..      62     146 ..      55     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 9.1e-05
                           DUF2207 360 wksavkk..kergyfdkkgkkklkklsalglgliilglilillallllvll............lvfllilllillli 422
                                       ++  ++   k  ++f ++g+kk+  +  +g +++ l++++ l + ++   +            l  ++++++++l++
  gi|488600638|ref|YP_007907109.1|  62 IMGRYETtsKIFNFFLRRGEKKKDVVERYGYAGLTLFVAIPLPVTGAW--TgsliafilglkpLKSFAYIFIGILIA 136
                                       33344447788999*******999999999999999999877776554..2559999999*9988888888888888 PP

                           DUF2207 423 aiivlllfsr 432
                                       +++vl+l+ +
  gi|488600638|ref|YP_007907109.1| 137 GVVVLALSMG 146
                                       8888887654 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 ?    8.6   4.4   0.00025       1.5       7      39 ..     107     140 ..     105     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00025
                   Phage_holin_2_3   7 aAYisSavavvlGllsLseWAiv.iGIicgvvTf 39 
                                        A+++S++a++lGl  L+  A + iGI+++ v +
  gi|488600638|ref|YP_007907109.1| 107 GAWTGSLIAFILGLKPLKSFAYIfIGILIAGVVV 140
                                       699***********9******8846***986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 986.61
//
Query:       gi|488600639|ref|YP_007907110.1|  [L=293]
Description: ketopantoate reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  116.6   1.2    1.2e-33  116.0   1.2    1.3  1  ApbA_C         Ketopantoate reductase PanE/ApbA C terminal
    2.2e-26   92.3   0.3    4.5e-26   91.3   0.3    1.5  1  ApbA           Ketopantoate reductase PanE/ApbA
    0.00078   20.0   0.9     0.0019   18.7   0.1    2.0  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


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 !  116.0   1.2   1.9e-37   1.2e-33       1     125 []     170     291 ..     170     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.9e-37
                            ApbA_C   1 dirlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaan 77 
                                       +i +++w+K ++na+inp+ta+l++ ng++l ++ l  +++ +++E  +v+e++g  ++ + leeav++v+ kta+n
  gi|488600639|ref|YP_007907110.1| 170 NISERIWRKAIVNAVINPITAILKVENGRVL-DEGLWSIAKLVIEEGKQVMERLG--INVDGLEEAVREVAVKTARN 243
                                       68899**************************.888********************..99****************** PP

                            ApbA_C  78 rsSMlqDveagrktEidyinGavvklAeklgvetPvnellyellkale 125
                                       rsSMlqD++agr+tEidyinG++v+l +++g+++ +n ll++l+ka+e
  gi|488600639|ref|YP_007907110.1| 244 RSSMLQDIMAGRRTEIDYINGEIVRLSDEMGISACANLLLTNLVKAME 291
                                       *********************************************986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.3   7.5e-30   4.5e-26       1     148 [.       8     142 ..       8     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 7.5e-30
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SS CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvK 77 
                                       i i+G+GaiGsl+++ ++  g dv++++r++rle + k+Glr+++   e  l ++++         e++d+ iv+vK
  gi|488600639|ref|YP_007907110.1|   8 IQIMGSGAIGSLFGGLIQLSGFDVHFVARRKRLE-VLKKGLRIRGLI-EADLDVDVSEK------PENADITIVAVK 76 
                                       78*****************************998.99*******999.44444444444......4599******** PP

                                       GGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEEEECS--EEEEE CS
                              ApbA  78 ayqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgevhhagkgeikig 148
                                       ay+te+ ++e+ + +d+  vvl++qNGlg+ e+l  +l  +rv+ggvtt ga+ +++  +  ag+g + +g
  gi|488600639|ref|YP_007907110.1|  77 AYDTEN-AAELLSKVDCG-VVLTIQNGLGNVERLSRKL--KRVIGGVTTYGANIKDDIVF-YAGEGVTFVG 142
                                       ******.66778889998.*******************..89************997776.6777777666 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   3.3e-07    0.0019       1      84 [.       7      88 ..       7     101 .. 0.75
   2 ?   -1.4   0.0      0.59   3.5e+03      14      51 ..     207     241 ..     206     252 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.3e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S-HHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlavkped 73
                                      ki+i G+G +g+ +   ++ +g    ++ +++    +++e l++ l       +++   d +e  e+ad+ ++avk +d
  gi|488600639|ref|YP_007907110.1|  7 KIQIMGSGAIGSLFGGLIQLSG---FDVHFVA--RRKRLEVLKKGLRirglieADLDV-DVSEKPENADITIVAVKAYD 79
                                      799*********999999999*...5665442..445666676666665676556665.8888889************* PP

                                      HHHHHHHCGHH CS
                     F420_oxidored 74 veevlselakd 84
                                      +e++++ l  +
  gi|488600639|ref|YP_007907110.1| 80 TENAAELL--S 88
                                      ****9988..3 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.59
                                       HHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEE CS
                     F420_oxidored  14 lasgllaagaqpheivvansrnpekaeelaeelgvkvt 51 
                                       +a+ ++++g   ++++     n + +ee+ +e+ vk+ 
  gi|488600639|ref|YP_007907110.1| 207 IAKLVIEEG---KQVMERLGINVDGLEEAVREVAVKTA 241
                                       566666777...66666666666666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1573.52
//
Query:       gi|488600640|ref|YP_007907111.1|  [L=295]
Description: hypothetical protein Asulf_01118 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-22   77.9   3.5    1.4e-21   77.1   2.3    1.9  2  THUMP           THUMP domain
    0.00081   19.0   0.1     0.0099   15.5   0.0    2.3  2  ThiI            Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
       0.13   12.9   0.1       0.21   12.2   0.1    1.3  1  Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-termina


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 !   77.1   2.3   2.3e-25   1.4e-21       9     142 ..      35     157 ..      27     159 .. 0.86
   2 ?   -1.1   0.0      0.32   1.9e+03      61      77 ..     226     242 ..     201     264 .. 0.57

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 2.3e-25
                                       HTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-E CS
                             THUMP   9 egkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeket 85 
                                       e +++++ v++g+gri+v+++g       e + ++++ ++g+++     +v  ++   +++ a+ei + ++   k +
  gi|488600640|ref|YP_007907111.1|  35 EFGIKAS-VRGGYGRIYVDVGGN-----VESVARRISNVFGVVS----AHVSVKRDLNLEKNAEEIAEYYKNRIKGS 101
                                       5566655.6778999****9955.....8999999999995555....4677999999999999999887777666* PP

                                       EEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEE CS
                             THUMP  86 FaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisi 142
                                       FaVrvkr gkh +fts++  +++G+ ++e tg++Vdl+nP++ +rvei+++k+y+++
  gi|488600640|ref|YP_007907111.1| 102 FAVRVKRSGKH-DFTSMDASKIIGRKLKEITGARVDLKNPETEIRVEIRDSKLYLMT 157
                                       ***********.******************************************986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                                       ESSHHHHHHHHHHHHHH CS
                             THUMP  61 eadledileaakeivkk 77 
                                         ++ed+l +a ++++k
  gi|488600640|ref|YP_007907111.1| 226 KGGFEDLLSKAFSMDYK 242
                                       44444444444444443 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-06    0.0099       1      37 [.     169     204 ..     169     265 .. 0.70
   2 ?    1.6   0.1      0.03   1.8e+02     134     159 ..     261     286 ..     246     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                              ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlkn 37 
                                       g+q++vl+++S+   S  +++ ++kRGc v++++ + 
  gi|488600640|ref|YP_007907111.1| 169 GSQERVLCIISDE-KSLLSTWYAMKRGCDVDVLYSER 204
                                       79*********97.79****************98654 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.03
                              ThiI 134 avvnllilrPLigldKeeiiklAkei 159
                                       ++ +l++l PL+ +d  ei +  k i
  gi|488600640|ref|YP_007907111.1| 261 KNRKLPVLMPLLPFDDSEIDEKIKMI 286
                                       56789***********9997666655 PP

>> Fapy_DNA_glyco  Formamidopyrimidine-DNA glycosylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.5e-05      0.21       6      75 ..      56     128 ..      54     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHHHTT-EEEEEEE-SSHHHTSTHHHHHT....T-.SEEEEEEEEETTEEEEEE..EEEEEEE-T CS
                    Fapy_DNA_glyco   6 EVetvrrglrrhllgkkiakvevlkdktlrgspaafak....alkgrkiasvgrrGKyllleldggevlvvhlg 75 
                                        Ve v+r ++ ++ g   a+v+v++d +l+++++++a+    ++kg+  ++v+r GK+ +  +d ++ ++ +l+
  gi|488600640|ref|YP_007907111.1|  56 NVESVARRIS-NVFGVVSAHVSVKRDLNLEKNAEEIAEyyknRIKGSFAVRVKRSGKHDFTSMDASKIIGRKLK 128
                                       5999999996.6999999*****99999999666655555559***************9999977666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1870.71
//
Query:       gi|488600641|ref|YP_007907112.1|  [L=124]
Description: hypothetical protein Asulf_01119 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       742  (0.0413855); 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:                         0  (0); expected 0.2 (1e-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: 818.07
//
Query:       gi|488600642|ref|YP_007907113.1|  [L=192]
Description: haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED/haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-19   70.0   2.5    4.9e-18   65.8   2.5    2.2  1  HAD_2           Haloacid dehalogenase-like hydrolase
    4.6e-09   36.9   0.0    1.2e-05   25.8   0.0    2.1  2  Hydrolase       haloacid dehalogenase-like hydrolase
    5.2e-07   29.6   0.0      8e-07   29.0   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
    2.6e-05   24.7   0.1    9.3e-05   22.9   0.1    1.9  1  HAD             haloacid dehalogenase-like hydrolase
     0.0031   17.6   0.0     0.0082   16.2   0.0    1.7  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   2.5   1.4e-21   4.9e-18      37     177 ..      23     160 ..       5     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.4e-21
                             HAD_2  37 lrkliglslrellrklgeseeeee...kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreave 110
                                       +rk ig++   +l+++ + + e e   k+e l ++y+    k + +++dgv e++e ++++++k givT + +e++e
  gi|488600642|ref|YP_007907113.1|  23 IRKEIGIKEGFVLENIMSLNYE-ErmkKLEVL-KRYEIDSVK-NARLMDGVLEIIEFIESKNIKKGIVTRNCKESAE 96 
                                       4444444443333333332222.224244444.777777777.89******************************** PP

                             HAD_2 111 ekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagikvia 177
                                        + +++gi+  Fd i++ e+v+ k P+p ++   + k++  ++e+++vGD ++D+ a+k ag+k++ 
  gi|488600642|ref|YP_007907113.1|  97 IFSKKFGID--FDYIISREEVTPK-PSPLPVILSMIKTNSRPDETMMVGDFKFDLLAGKLAGVKTVL 160
                                       *******95..*********9865.***************************************985 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00035       1.2       1      17 [.       2      18 ..       2      49 .. 0.77
   2 !   25.8   0.0   3.2e-09   1.2e-05     116     210 .]      63     155 ..      44     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00035
                                      SSEEEEESBTTTBCHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgep 17
                                      i+ ++fD+dGTLt  + 
  gi|488600642|ref|YP_007907113.1|  2 IRNIAFDLDGTLTYFNL 18
                                      5779*********8774 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 3.2e-09
                                       THHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 116 plkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpee 192
                                       + ++++++ e ++ + +++i+ +++t + +e ae   +++G   fd +i+++++t  kpsp  +   + + + +p e
  gi|488600642|ref|YP_007907113.1|  63 NARLMDGVLEIIEFIESKNIKKGIVTRNCKESAEIFSKKFG-IDFDYIISREEVT-PKPSPLPVILSMIKTNSRPDE 137
                                       456999****************************88888**.6666677777666.888888888888888899*** PP

                                       EEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxx RF
                         Hydrolase 193 vamVGDgvnDaaalaaAg 210
                                       ++mVGD   D+ a++ Ag
  gi|488600642|ref|YP_007907113.1| 138 TMMVGDFKFDLLAGKLAG 155
                                       **************9997 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.2e-10     8e-07       4      74 ..     118     186 ..     115     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.2e-10
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       KP+p  +   + +++s p+e++m+GD  + D+++++ aG+k+vL +t ++++       h +++++ +l+e
  gi|488600642|ref|YP_007907113.1| 118 KPSPLPVILSMIKTNSRPDETMMVGDF-KFDLLAGKLAGVKTVLLRTEKNADFI-DGMIHLADHIISSLTE 186
                                       89999999999999*************.*******************9987744.4466999999999987 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   2.6e-08   9.3e-05       1     131 [.       5     113 ..       5     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.6e-08
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv 77 
                                       + fD+DgTL+  +  +  +           ++++  k    l + +++l+++++++ le  l++++   ++ ++ ++
  gi|488600642|ref|YP_007907113.1|   5 IAFDLDGTLTYFNLPFDRI-----------RKEIGIKEGFVL-ENIMSLNYEERMKKLEV-LKRYE---IDSVKNAR 65 
                                       579******9995443322...........344555544444.77889989999999985.66666...58999999 PP

                               HAD  78 aevirpklldp..galellaahraaGdrvvvvSgglrplvepllaelg..adevlate 131
                                              l+d   ++ e+++   +++++  +v+ + ++ +e++ +++g  +d++++ e
  gi|488600642|ref|YP_007907113.1|  66 -------LMDGvlEIIEFIE---SKNIKKGIVTRNCKESAEIFSKKFGidFDYIISRE 113
                                       .......8855556666666...*******************************9984 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.3e-06    0.0082       1      65 [.       5     117 ..       5     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.3e-06
                                       EEEESTTTSE...............................................ETTEE-TTHHHHHHHHHHTT CS
                       Hydrolase_6   1 flfDidGvLw...............................................rgdkaipgaaealnalraag 30 
                                       ++fD+dG+L                                                ++ ++++g+ e+++++++++
  gi|488600642|ref|YP_007907113.1|   5 IAFDLDGTLTyfnlpfdrirkeigikegfvlenimslnyeermkklevlkryeidsvKNARLMDGVLEIIEFIESKN 81 
                                       579******99***************************************99999999******************* PP

                                       -EEEEEE---SS-HHHHHHHH.HHTT----GGGEEE CS
                       Hydrolase_6  31 kpvvllTNnsskseeeyakkl.eklgvditeeqvvt 65 
                                       ++  ++T n ++s e + kk+  ++++ i++e+v  
  gi|488600642|ref|YP_007907113.1|  82 IKKGIVTRNCKESAEIFSKKFgIDFDYIISREEVTP 117
                                       *************99999999777888788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1186.53
//
Query:       gi|488600643|ref|YP_007907114.1|  [L=193]
Description: hypothetical protein Asulf_01121 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-11   42.2   0.0    1.1e-10   41.7   0.0    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 !   41.7   0.0   6.1e-15   1.1e-10       5      68 ..      33     100 ..      29     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 6.1e-15
                                       EEEEE.EEETTSEEEEEEES..SSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEE CS
                             NUDIX   5 avgvv.llnekgevLlvrrs..kkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrl 68 
                                       av +  ++ ++ +++++ rs   ++ +g  ++PgG  e +E+p+++A+RE+eEE+Gl+ +++++lg l
  gi|488600643|ref|YP_007907114.1|  33 AVLIPlFTYPRVKLIMIMRSknLRRSAGhIAFPGGIRESDENPKDTALREAEEELGLPTPNVDILGFL 100
                                       5555533334445788888878666677457**************************99*******44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1299.26
//
Query:       gi|488600644|ref|YP_007907115.1|  [L=439]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   82.7   0.4    1.6e-11   44.3   0.1    2.4  2  PAS_3        PAS fold
      1e-16   61.4   0.2    1.9e-16   60.5   0.2    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.6e-13   50.1   0.0    5.8e-07   29.7   0.0    2.8  2  PAS_9        PAS domain
    1.1e-12   47.9   0.0    1.9e-09   37.5   0.0    2.3  2  PAS          PAS fold
    3.9e-08   33.1   0.0     0.0013   18.7   0.0    2.6  2  PAS_8        PAS domain
    3.9e-08   33.5   0.0    0.00031   21.0   0.0    2.3  2  PAS_4        PAS fold
    4.3e-07   29.5   0.5    1.4e-06   27.9   0.5    1.9  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain
    7.8e-06   25.7   0.7    2.7e-05   24.0   0.3    2.1  2  HATPase_c_5  GHKL domain
    0.00051   19.6   0.1    0.00084   18.9   0.1    1.4  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.028   14.4   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
      0.019   15.0   0.1      0.045   13.8   0.1    1.7  1  HisKA        His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   3.3e-12   5.4e-09       3      80 ..      24      98 ..      22     105 .. 0.92
   2 !   44.3   0.1   9.8e-15   1.6e-11       1      71 [.     145     214 ..     145     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.3e-12
                             PAS_3  3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80
                                      yv++ +e+ +Gys ee+++    ++++ + eD++ +++a+  +l+++++y  e+R+++k G++r+++   +++   +g
  gi|488600644|ref|YP_007907115.1| 24 YVNKVFEDATGYSLEEIYDI-IPFYKIAYEEDIPTIKKAIRSVLSGNKEY-LEVRYVTKKGKIRYIRGFFKPF-EVDG 98
                                      89*****************9.9**********************999998.*******************999.5444 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 9.8e-15
                             PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyege.yRirrkdGeyrwvear 71 
                                       +iyv++++ e++Gys+ el++   +  +lvhp+ re v++ ++e +++ ++ +++ ++i++k+Ge+rwv ar
  gi|488600644|ref|YP_007907115.1| 145 FIYVNDAFAETVGYSKGELYEI--NPFMLVHPDHREMVYRRYKERISGERETDTYkWKIVTKSGEIRWVVAR 214
                                       59********************..**********************9999885555*************876 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 !   60.5   0.2   1.2e-19   1.9e-16       5      94 ..     342     425 ..     338     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.2e-19
                                       HHHHHHHHHHHHHHHHHSTTTEEEEEEEE..EETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfatkageieveika..seddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGl 78 
                                       ++  +++nl+dNa+k+ + a++++v+ika  ++d++ ++ +DnG+Gi++++ ++lfe  f++         g G+Gl
  gi|488600644|ref|YP_007907115.1| 342 GIDIVFRNLIDNALKH-SGAEKLKVKIKAykEKDKVIVEFSDNGKGIDEKIKERLFEdGFTT--------NGQGMGL 409
                                       566799**********.88999999999975448***********************99999........9****** PP

                                       HHHHH.HHHHTTTEEEE CS
                         HATPase_c  79 sivkk.lvelmgGeiwv 94 
                                       +ivk+ l++ +gG+i++
  gi|488600644|ref|YP_007907115.1| 410 YIVKEiLIS-YGGSIEI 425
                                       *****7777.*****98 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.5e-06    0.0041      15     104 .]      24     111 ..      12     111 .. 0.86
   2 !   29.7   0.0   3.5e-10   5.8e-07       9     104 .]     141     235 ..     136     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.5e-06
                             PAS_9  15 yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvlltaspvkdddg 90 
                                       y+N+ +++ +Gys ee+     +  +   +e+  ++++a+++  + + +  ev +++k+g+  +++  + p+  d++
  gi|488600644|ref|YP_007907115.1|  24 YVNKVFEDATGYSLEEIYDIIPFYKI-AYEEDIPTIKKAIRSVLSgNKEYLEVRYVTKKGKIRYIRGFFKPFEVDGE 99 
                                       9***************9999888888.788888888888888888899************************99987 PP

                             PAS_9  91 elvgiivilrDite 104
                                       + ++  + l+D+t+
  gi|488600644|ref|YP_007907115.1| 100 KAIL--GSLVDVTK 111
                                       7777..******95 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 3.5e-10
                             PAS_9   9 pdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvllta 82 
                                        + + +y+N+a+++  Gys+ e+   + ++l+  +p+++e + + +++  +   +  ++   +++k+ge  w  + a
  gi|488600644|ref|YP_007907115.1| 141 QNEKFIYVNDAFAETVGYSKGELYEINPFMLV--HPDHREMVYRRYKERISgerETDTYKWKIVTKSGEIRW--VVA 213
                                       45567***************************..777777777777777666999999**************..666 PP

                             PAS_9  83 spvkdd.dgelvgiivilrDite 104
                                       +p +   ++e   + ++l+Dite
  gi|488600644|ref|YP_007907115.1| 214 RPSRTViNDEPA-VCATLVDITE 235
                                       555444333333.348*****98 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0015       2.4       4      96 ..       4      94 ..       2     109 .. 0.79
   2 !   37.5   0.0   1.1e-12   1.9e-09       3     110 ..     126     230 ..     124     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                                      HHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEEC CS
                               PAS  4 raileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesrageisfkl 81
                                      + +l+ + ++ifv+    r  yvN+ +e+ +G+s ee+     +  i  e+d  + +++++ +l+ ++e   ++   k 
  gi|488600644|ref|YP_007907115.1|  4 KKMLDESLAGIFVI-VGDRYKYVNKVFEDATGYSLEEIYDIIPFYKIAYEEDIpTIKKAIRSVLSGNKEYLEVRYVTK- 80
                                      56667777777777.677788*******************99999999999989999999999999999999777554. PP

                                      TTSSEEEEEEEEEEE CS
                               PAS 82 rdgrpihlevraspv 96
                                       +g++++++   +p+
  gi|488600644|ref|YP_007907115.1| 81 -KGKIRYIRGFFKPF 94
                                      .58888887665555 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.1e-12
                                       HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEE CS
                               PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisf 79 
                                       +r +++ + +p  +v  + +++yvN+a++e  G+s  e+   + ++l+h+++++ ++++++++++  +e  +++ ++
  gi|488600644|ref|YP_007907115.1| 126 FRKMVDESQTPAYIV-QNEKFIYVNDAFAETVGYSKGELYEINPFMLVHPDHREMVYRRYKERISGERETDTYKWKI 201
                                       7999***********.**********************************9999*********************** PP

                                       ECTTSSEEEEEEEEEEEEETTEEEEEEEEEE CS
                               PAS  80 klrdgrpihlevraspvrdaggeilgflgvl 110
                                        ++ g++++++ r s ++  ++    ++ +l
  gi|488600644|ref|YP_007907115.1| 202 VTKSGEIRWVVARPSRTVINDEP--AVCATL 230
                                       ***********999988766654..555555 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00012      0.19       5      39 ..       5      39 ..       3      56 .. 0.84
   2 !   18.7   0.0   8.2e-07    0.0013       2      44 ..     125     163 ..     124     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                             PAS_8  5 alfesspdgiavvdlgdrivdvNqaalellGys.ad 39
                                       +++ s  gi+v+ +++   +vN+ +++ +Gys ++
  gi|488600644|ref|YP_007907115.1|  5 KMLDESLAGIFVIVGDR-YKYVNKVFEDATGYSlEE 39
                                      6899999****998555.**************9544 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 8.2e-07
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGysadlkgel 44 
                                        +r +++ s+ +  +v + + +++vN+a++e  Gys   kgel
  gi|488600644|ref|YP_007907115.1| 125 LFRKMVDESQTPAYIVQNEK-FIYVNDAFAETVGYS---KGEL 163
                                       6999*******888886555.*************98...4444 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.9e-07   0.00031      16     108 ..      21     112 ..       7     114 .. 0.92
   2 !   10.4   0.0   0.00035      0.58      15     107 ..     143     235 ..     131     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.9e-07
                             PAS_4  16 rvlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrde 91 
                                       r+ y+N+ +++  g++ ee+++  ++  ++ eed + +  a+r vl+g++ + ++ +++  g+ r++  ++ P+ + 
  gi|488600644|ref|YP_007907115.1|  21 RYKYVNKVFEDATGYSLEEIYDIIPFyKIAYEEDIPTIKKAIRSVLSGNKEYLEVRYVTKKGKIRYIRGFFKPF-EV 96 
                                       89********************999989****************************9999*************9.89 PP

                             PAS_4  92 sGevigvlvisrDiTer 108
                                       +Ge  ++l+ ++D+T  
  gi|488600644|ref|YP_007907115.1|  97 DGE-KAILGSLVDVTKN 112
                                       ***.***********76 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                             PAS_4  15 grvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepief..leelllpgeerhyelrllPlr 89 
                                        +++y+N a+ae +g++  el+   ++ l+ +++++ + r +++ ++ge+  ++  + +++ +ge r++    +P r
  gi|488600644|ref|YP_007907115.1| 143 EKFIYVNDAFAETVGYSKGELYEINPFMLVHPDHREMVYRRYKERISGERETDTykWKIVTKSGEIRWVVA--RPSR 217
                                       579************************988888**************987665511445555899999765..5666 PP

                             PAS_4  90 desGevigvlvisrDiTe 107
                                           +  +v+++++DiTe
  gi|488600644|ref|YP_007907115.1| 218 TVINDEPAVCATLVDITE 235
                                       688889999999999998 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 !   27.9   0.5   8.7e-10   1.4e-06      10      52 ..     247     290 ..     238     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.7e-10
                            SPOB_a  10 keliklL.rsqRHDflNhLQvIsGylqLgkydkaeeyieevvke 52 
                                       + +++l+ +  RHD lN+L vI+G+++L  +d ae++i +v k 
  gi|488600644|ref|YP_007907115.1| 247 NRYLTLInKIMRHDMLNDLAVIRGFVELIDVDFAEKIISRVDKT 290
                                       45555555557****************************99665 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.1   5.1e+03      73      90 ..     315     333 ..     314     335 .. 0.75
   2 !   24.0   0.3   1.7e-08   2.7e-05       6      87 ..     343     425 ..     339     436 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.1
                       HATPase_c_5  73 sireivkkykg.nlsieae 90 
                                        i++++k y+g +++++++
  gi|488600644|ref|YP_007907115.1| 315 RIEHVIKDYDGvDFELDID 333
                                       6999*****9966666655 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.7e-08
                       HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.kklesskskkeehGiGlksireiv 78 
                                       + +++ nl+dNA+  + +    k ++++++ ++k+++i++++ + +g   ++ ++l++   +++ +G+Gl  ++ei+
  gi|488600644|ref|YP_007907115.1| 343 IDIVFRNLIDNALKHSGAE---KLKVKIKAYKEKDKVIVEFSDNGKGideKIkERLFEDGFTTNGQGMGLYIVKEIL 416
                                       5689*********987663...678***************9999777432334566677777999************ PP

                       HATPase_c_5  79 kkykgnlsi 87 
                                        +y+g+++i
  gi|488600644|ref|YP_007907115.1| 417 ISYGGSIEI 425
                                       *****9986 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   5.1e-07   0.00084     132     162 ..     245     275 ..     201     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.1e-07
                         HisKA_4TM 132 risdalafvndlirhdlrndlvvirgyaeai 162
                                       r    l+++n+++rhd+ ndl virg+ e i
  gi|488600644|ref|YP_007907115.1| 245 RKNRYLTLINKIMRHDMLNDLAVIRGFVELI 275
                                       44557999*******************9988 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-05     0.028      36     108 ..     347     415 ..     328     419 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                       HATPase_c_2  36 veEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikgl 108
                                          ++ Na +h   e+   +v++++  +++++ ve++D+G+g d + +++  e++       +G+Gl+++k++
  gi|488600644|ref|YP_007907115.1| 347 FRNLIDNALKHSGAEKL--KVKIKAYKEKDKVIVEFSDNGKGIDEKIKERLFEDG--FTTNGQGMGLYIVKEI 415
                                       55566799999988766..9999999****************9998777777665..89999*******9976 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 ?   13.8   0.1   2.8e-05     0.045       8      57 ..     256     322 ..     249     327 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHC..........T-HSSCHHHHHHHHHHHH.........HHHHHHHH CS
                             HisKA   8 gvaHELrtPLsailgnaeaLkre........gklteelkeyletiesear.........rldhlved 57 
                                        + H++ + L++i+g++e++  +        ++ t +    l+ +e++ +         r++h+++d
  gi|488600644|ref|YP_007907115.1| 256 IMRHDMLNDLAVIRGFVELIDVDfaekiisrVDKTVRMINILKELERSWDslhyinlkeRIEHVIKD 322
                                       589****************955345556555444455555666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2927.24
//
Query:       gi|488600645|ref|YP_007907116.1|  [L=423]
Description: acetyl-CoA acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-98  329.4   0.5    2.4e-88  295.9   0.2    2.3  2  Thiolase_N     Thiolase, N-terminal domain
    9.5e-47  157.7   2.2    2.7e-46  156.2   0.5    2.2  2  Thiolase_C     Thiolase, C-terminal domain
    1.8e-06   27.7   0.1      4e-06   26.6   0.1    1.5  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.089   12.7   0.0       0.17   11.8   0.0    1.4  1  Imm52          Immunity protein 52
       0.29   11.0   3.4          1    9.3   0.1    2.7  3  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


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 !   31.5   0.0     3e-11   1.1e-07       2      42 ..       4      44 ..       3      49 .. 0.94
   2 !  295.9   0.2   6.6e-92   2.4e-88      44     260 .]      78     293 ..      70     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3e-11
                                      EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-G CS
                        Thiolase_N  2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdp 42
                                      viv+a rtp+g+fggslkdl+a eL+a+a+k+ll++ +++p
  gi|488600645|ref|YP_007907116.1|  4 VIVGAIRTPVGRFGGSLKDLQAYELGAIAIKGLLKELKLKP 44
                                      9***********************************99887 PP

  == domain 2  score: 295.9 bits;  conditional E-value: 6.6e-92
                                       GCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-E CS
                        Thiolase_N  44 evdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnapt 120
                                       +v evi+Gnvlq+++gqn+arqa++ ag+p+e+pa tvnkvc+Sglka+alaa +i++g+a++++agG+Esmsnap+
  gi|488600645|ref|YP_007907116.1|  78 KVCEVIMGNVLQSAQGQNPARQATILAGLPKETPAYTVNKVCGSGLKAIALAASEIKSGNAEIIIAGGMESMSNAPY 154
                                       6889************************************************************************* PP

                                       EETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTB CS
                        Thiolase_N 121 aestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdei 197
                                       a + ++r+g+++ + ++ d++++dgl++ f ++hmG+taen+a+ y+isReeqd+ A +sh +a +a+++g F++ei
  gi|488600645|ref|YP_007907116.1| 155 ALT-KARWGYRMFNGELIDIMVHDGLWEKFYGYHMGVTAENIAELYGISREEQDQLAYESHMRAIKAIDNGIFAQEI 230
                                       **8.9************************************************************************ PP

                                       E-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 198 vPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtAgnasqisDGaaavllmses 260
                                       vPv++++kkg+ +vd+de++r+++++ekLakl ++Fkk+GtvtAgnas+++DGa+a+l+mse+
  gi|488600645|ref|YP_007907116.1| 231 VPVEIQQKKGTVVVDTDEHPRRDTSLEKLAKLPTVFKKDGTVTAGNASGVNDGASALLVMSEE 293
                                       *************************************************************96 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.15   5.3e+02      88     119 ..      98     128 ..      91     132 .. 0.82
   2 !  156.2   0.5   7.5e-50   2.7e-46       1     123 []     300     422 ..     300     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHCTTSEEEEEEEETTTEEEEE CS
                        Thiolase_C  88 RivvtllselkkeggklgvaalCigggqgval 119
                                       R+ +t+l  l ke   ++v  +C +g +++al
  gi|488600645|ref|YP_007907116.1|  98 RQ-ATILAGLPKETPAYTVNKVCGSGLKAIAL 128
                                       54.57888999999*********999999887 PP

  == domain 2  score: 156.2 bits;  conditional E-value: 7.5e-50
                                       ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHH CS
                        Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaia 77 
                                       lkpla+i+sya  + dp+ +glgP++ai+++lkka+l++edi l+E+nEAFaaqaLav+++l+ld++ +N++G  i+
  gi|488600645|ref|YP_007907116.1| 300 LKPLARIVSYAGGAIDPAYMGLGPIPAIQRALKKAELKLEDIGLIELNEAFAAQALAVIRELNLDMSITNIHGSGIS 376
                                       589************************************************************************** PP

                                       H-B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                        Thiolase_C  78 lGHPlGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                       lGHP+G++GaRi++tl++e+ +++ ++g+aalCiggg+g a+v++k
  gi|488600645|ref|YP_007907116.1| 377 LGHPIGCTGARITTTLVKEMVRSKVEYGLAALCIGGGMGFAMVLQK 422
                                       *******************************************985 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   1.1e-09     4e-06     167     207 ..     111     151 ..     100     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.1e-09
                                       SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                     ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                       p++tv   C S+l+a+++a ++++sg+a++++aGG+e + +
  gi|488600645|ref|YP_007907116.1| 111 PAYTVNKVCGSGLKAIALAASEIKSGNAEIIIAGGMESMSN 151
                                       99***********************************8865 PP

>> Imm52  Immunity protein 52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.17      52      74 ..     227     249 ..     209     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                                       -SEEEEEEETEEEEEEEES-SS- CS
                             Imm52  52 apalveveakkqkGtlivstdek 74 
                                       a+++v+ve +++kGt++v tde+
  gi|488600645|ref|YP_007907116.1| 227 AQEIVPVEIQQKKGTVVVDTDEH 249
                                       799******************96 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 ?    9.3   0.1   0.00028         1       3      38 ..     115     150 ..     113     153 .. 0.87
   2 ?    1.6   0.0     0.073   2.6e+02      52      67 ..     280     295 ..     271     303 .. 0.78
   3 ?   -2.7   0.1       1.5   5.3e+03       7      24 ..     383     400 ..     382     413 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGG CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetls 38 
                                       +n++C + + a+++A++ i+sg+a+ ++  g e +s
  gi|488600645|ref|YP_007907116.1| 115 VNKVCGSGLKAIALAASEIKSGNAEIIIAGGMESMS 150
                                       799*******************99988777777776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.073
                                       B-EEEEEEEEEEESSS CS
                       ACP_syn_III  52 fGDGAgAvvleaseee 67 
                                       + DGA A+++  +e+ 
  gi|488600645|ref|YP_007907116.1| 280 VNDGASALLVMSEEKA 295
                                       57*******9987543 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.5
                                       GGHHHHHHHHHHHHHHTT CS
                       ACP_syn_III   7 CsgfvyalsvAdaliesg 24 
                                       C+g+ +   +++++++s 
  gi|488600645|ref|YP_007907116.1| 383 CTGARITTTLVKEMVRSK 400
                                       999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2627.49
//
Query:       gi|488600646|ref|YP_007907117.1|  [L=412]
Description: phenylacetate-CoA ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.0    5.3e-13   48.4   0.0    1.3  1  AMP-binding      AMP-binding enzyme
    3.9e-07   30.3   0.0    9.1e-05   22.7   0.0    3.1  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
     0.0024   16.8   0.0     0.0037   16.2   0.0    1.3  1  GH3              GH3 auxin-responsive promoter
  ------ inclusion threshold ------
      0.022   14.8   0.9        3.1    7.9   0.3    2.8  2  PRC              PRC-barrel 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 !   48.4   0.0   1.2e-16   5.3e-13     110     370 ..      15     284 ..       7     288 .. 0.72

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.2e-16
                                       HHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS................-TSCCCS-BTTSEEEEEEE--S CS
                       AMP-binding 110 lleaaakleavklvivldadellkeeelkeeeeseekae................kpeeeeelkpddlayiiYTSGT 170
                                       + ++++k+ + +++ v+++ ++++e+  +++ ++ ++ae                 p + + + +d ++ ++ ++GT
  gi|488600646|ref|YP_007907117.1|  15 IIKIQEKRLRETVKFVYENSPFYREKLKDIDLDKIKSAEdleklplttkeelrnaYPLKMSCVPKDRIVRVQMSGGT 91 
                                       55555666666677777777777766666665555544245566777777777884446668999************ PP

                                       SSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TT..SCHHHHHHHHHHHHTT-EEEE-TTCGCCHHH CS
                       AMP-binding 171 TGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilpla..hifglilelllallsGatvvllpkdaaldpk 243
                                       TG+P  + ++ +  v++ +++ l++    +++++dv+ +i p +  +  g+  + ++a +  a v+ +   ++++  
  gi|488600646|ref|YP_007907117.1|  92 TGQPVIIPYTRKD-VNQWKEMLLRDFmlAGITSRDVI-QITPAFglWNGGF-GFHFAADAIDAFVIPIGAGNTRN-- 163
                                       ****888887777.66667765554454445556665.5555542244454.66666666666555555444444.. PP

                                       HHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGG CS
                       AMP-binding 244 lllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTE 319
                                         ++++++++ tv++++ +   +++e +++    ++ ++l+ l  +llg+ep s+e+ r+++++f  + +++ GlTE
  gi|488600646|ref|YP_007907117.1| 164 -QIKFMKDFGTTVLCATASYPLRIAEvADEMG--VDVSELP-LSKMLLGAEPWSEEMRRKIESKFNVRAFDIPGLTE 236
                                       .379********************99776555..3333555.777899*****************99********** PP

                                       GSSECEE.CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                       AMP-binding 320 ttgvvtv.lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                       ++gv t+ ++++e+    g +     +  v++vD+etge+v+dgeeGe++  
  gi|488600646|ref|YP_007907117.1| 237 MGGVGTIgFECPER---NG-IHIWEDNYIVEVVDPETGERVEDGEEGEIVYT 284
                                       *****975555555...32.4444469**********************975 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 ?   -1.4   0.0      0.69   3.1e+03      34      71 ..     191     227 ..     181     229 .. 0.64
   2 !   22.7   0.0     2e-08   9.1e-05       1      93 [.     334     409 ..     334     410 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.69
                                       EEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS- CS
                   AMP-binding_C_2  34 DelevkvEvkegfsdelkelealekkiakklksklgvs 71 
                                       De+ v v     +s+ l   e  ++++++k++sk +v+
  gi|488600646|ref|YP_007907117.1| 191 DEMGVDVSEL-PLSKMLLGAEPWSEEMRRKIESKFNVR 227
                                       5554444333.345555666777788888888887775 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 2e-08
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelv 77 
                                       Gv+++Ps ie+vl +  +  ++Y+i v +      ++v  E +++            ++ia+ +k+ +g+++k+e v
  gi|488600646|ref|YP_007907117.1| 334 GVKFYPSDIESVLFS--HGVSNYKIEVGNG-----IRVIFEGDQD----------KIHEIARDIKEFVGFKPKLEAV 393
                                       788888888888866..3445788888753.....6666666664..........3579****************** PP

                                       -TT-S---------EE CS
                   AMP-binding_C_2  78 epgtlprsegKakrvi 93 
                                       + g l+r egKakr+i
  gi|488600646|ref|YP_007907117.1| 394 PFGVLERFEGKAKRLI 409
                                       **************97 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.2e-07    0.0037       7     112 ..      13     114 ..       7     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.2e-07
                                       HTHHHHHHHHHHHHHHH.CTTSHH....HHHC...TTHCHHHHHHHS--BEHHHHHHHHHHHHTTCC.CTSSSS-SE CS
                               GH3   7 knaaevqeevLkeiLkr.nantey....lkkfefssiksaedFkkkvPivtYedlepyieriakGeqnvLtsepikl 78 
                                       k++ ++qe+ L+e +k   +n+ +    lk+ ++++iksaed  +k+P++t e+l++     ++       +++i++
  gi|488600646|ref|YP_007907117.1|  13 KEIIKIQEKRLRETVKFvYENSPFyrekLKDIDLDKIKSAED-LEKLPLTTKEELRNAYPLKMS----CVPKDRIVR 84 
                                       666777777777777741345544111144556666688888.778999999999884444444....4558***** PP

                                       EEEECCEETTEEEEEEESHHHHHHHHHH.HHHHH CS
                               GH3  79 falsSGTtsgksKliPvteeslkelallvlalla 112
                                        ++s GTt g++ +iP+t++ +++++ +   ll 
  gi|488600646|ref|YP_007907117.1|  85 VQMSGGTT-GQPVIIPYTRKDVNQWKEM---LLR 114
                                       ********.***************9988...444 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0099        44      36      70 ..      81     112 ..      77     117 .. 0.73
   2 ?    7.9   0.3    0.0007       3.1      28      61 ..     364     399 ..     356     409 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0099
                                       EEEEEEEEETTT.....-EEEEEGG..CEECCCTEE CS
                               PRC  36 rvralvvsvggflgigekevliPfd.lavkigkdri 70 
                                       r++ ++ s+g +    +  v+iP++ ++v+  k ++
  gi|488600646|ref|YP_007907117.1|  81 RIVRVQMSGGTT----GQPVIIPYTrKDVNQWKEML 112
                                       667777777665....5********77777766665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0007
                                       EEEETTTTEEEEEEEEETTT.....-EEEEEGG... CS
                               PRC  28 vvidekegrvralvvsvggflgigekevliPfd..l 61 
                                       v+++ ++ +++++  + ++f g++ k  ++Pf+  +
  gi|488600646|ref|YP_007907117.1| 364 VIFEGDQDKIHEIARDIKEFVGFKPKLEAVPFGvlE 399
                                       89******************************9543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.32s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2502.79
//
Query:       gi|488600647|ref|YP_007907118.1|  [L=488]
Description: transporter, SSS family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-61  207.8  32.9    3.4e-61  207.3  32.9    1.2  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
       0.18   11.8   0.2       0.33   10.9   0.2    1.3  1  SLM4      Protein SLM4


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 !  207.3  32.9   3.8e-65   3.4e-61       1     405 [.      31     442 ..      31     443 .. 0.88

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 3.8e-65
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelga.lllvlllllllaerlr....nagalTlp 72 
                                       ++lagr+l+ + +  s +a++ s a f+G+ G ++  G++++++   + +l +++++l++a+ +     ++g lT+p
  gi|488600647|ref|YP_007907118.1|  31 FYLAGRNLGVLLVSFSFFATYFSTAAFLGGGGFGFVAGFQWSAFLTFFhILFAIIAWLVIAPPMKriaeKYGSLTIP 107
                                       8****************************************9876555155666667777887778999******** PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdti 149
                                        ++   f+  +   ++sa+++l+++ +++ +   g++ l+e +lG++y+ta+++ +a++++Yt+iGG++Avv td i
  gi|488600647|ref|YP_007907118.1| 108 GIFGMSFGRAS--QIVSAIVILVFFQFYMVSIYKGAGNLLEVMLGIDYKTALIITVAVVMIYTAIGGFRAVVVTDFI 182
                                       ********999..9*************************************************************** PP

                               SSF 150 qavlmlvgalilliivllevGgleslveklkeaapkv...vdl.....lt.pdslkllrdpltalslwlglvlGvag 217
                                       q+vl+l+g + l +  +  +Gg  +++e lk+a+  +    +l     l  p  ++      ++lsl  ++ + +  
  gi|488600647|ref|YP_007907118.1| 183 QGVLILAGGIALFVTLIAYLGGPVNAIESLKAAEIFKgsgENLfkfgeLApPPIMNAGMVIPFILSLTFAISIAQLA 259
                                       *******************************9998666644444433311233333333444555565666666666 PP

                               SSF 218 lphilvRflaakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnlla 294
                                        p  ++Rf+aakd + i+kg +   i+++++ + ++si+ f+  ++    +   + +++s++++p +++kl+p ++ 
  gi|488600647|ref|YP_007907118.1| 260 SPQLVIRFVAAKDERVIRKGAILTPILIGIFALCVFSIGPFGWLIIPQYDDP-VKYLKNSDLVIPFIAMKLFPAGIN 335
                                       6*********************9999999**********9999887775555.57899******************* PP

                               SSF 295 GlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklve 371
                                       +lll +++Aa mst++sl+ + +++ft+Dl  +++   +++e   + + ri v   + + ++ a+++++  ++ +v 
  gi|488600647|ref|YP_007907118.1| 336 ALLLTAIVAAAMSTINSLVHVIATTFTRDLIGSVVSVSEKTE---LLITRISVFAFALIPMIFAINPPDI-IVVIVG 408
                                       **********************************99885555...555677788889999**********.****** PP

                               SSF 372 lafaglasavlavillalfwkrvneqGAlaglii 405
                                       l f++++sa+l  +l al+   + e+ Ala++i+
  gi|488600647|ref|YP_007907118.1| 409 LSFSVITSAFLIPLLSALYDPEAKEKPALASMIV 442
                                       ********************************97 PP

>> SLM4  Protein SLM4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   3.7e-05      0.33     119     152 ..     312     345 ..     303     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.7e-05
                                       EEE-TTSSEEEEEEEETTS-HHHHHHHHHHHHHT CS
                              SLM4 119 vaqipesdLlllliadkeyPygllvlklkallea 152
                                       v+ +++sdL++ +ia k +P g+  l l a+++a
  gi|488600647|ref|YP_007907118.1| 312 VKYLKNSDLVIPFIAMKLFPAGINALLLTAIVAA 345
                                       88899***********************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3177.73
//
Query:       gi|488600648|ref|YP_007907119.1|  [L=271]
Description: shikimate dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   78.6   0.0    9.8e-22   77.0   0.0    1.8  2  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    5.6e-16   58.0   0.1    9.4e-16   57.3   0.1    1.4  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
    1.8e-07   31.3   0.1      3e-07   30.6   0.1    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00017   21.1   0.0     0.0003   20.3   0.0    1.5  1  adh_short        short chain dehydrogenase
     0.0032   18.0   0.0     0.0063   17.1   0.0    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0084   16.4   0.2      0.024   14.9   0.1    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.027   13.9   0.1      0.047   13.0   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.031   13.6   0.3      0.059   12.7   0.3    1.4  1  ThiF             ThiF family
      0.049   13.2   0.0      0.073   12.6   0.0    1.2  1  DUF1188          Protein of unknown function (DUF1188)
      0.074   12.7   0.1       0.13   11.9   0.1    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.11   12.9   0.2       0.25   11.8   0.2    1.5  1  NAD_binding_7    Putative NAD(P)-binding
       0.44    9.6   2.8       0.86    8.6   2.7    1.5  2  FAD_binding_2    FAD binding domain
        1.9    8.0   4.1        7.6    6.0   3.4    1.9  2  DAO              FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   7.1e-25   9.8e-22       1      83 []       5      85 ..       5      85 .. 0.98
   2 ?   -1.8   0.0       2.8   3.9e+03      62      65 ..     200     203 ..     168     232 .. 0.63

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 7.1e-25
                                      EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT- CS
                    Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigA 79
                                      +iG+p+khS+SP+++n+af+  +++++y+ +ev+++ +++ ++ ++ + ++G+nvTiPfKe+v ++ + l  +A+ai  
  gi|488600648|ref|YP_007907119.1|  5 IIGYPLKHSVSPEMQNSAFRYYNMDAEYVKLEVNPEGFSEEIRIIE-KRFNGANVTIPFKEEVAKYYE-LVGDARAIRT 81
                                      79*****************************************999.5*******************7.********** PP

                                      -SEE CS
                    Shikimate_dh_N 80 vNti 83
                                      +Nti
  gi|488600648|ref|YP_007907119.1| 82 ANTI 85
                                      ***8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.8
                                       HHHG CS
                    Shikimate_dh_N  62 avip 65 
                                       ++i+
  gi|488600648|ref|YP_007907119.1| 200 KAIQ 203
                                       3333 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 !   57.3   0.1   6.8e-19   9.4e-16       1      31 []     232     262 ..     232     262 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 6.8e-19
                                       HHHHHHHHHHHHHHHHHS----HHHHHHHHH CS
                             SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreall 31 
                                       G++MLv+Qga +Fe+WTG+++Pv vMr+a+l
  gi|488600648|ref|YP_007907119.1| 232 GIDMLVYQGAKAFEIWTGKKAPVGVMRDAAL 262
                                       99***************************96 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   2.2e-10     3e-07       7      83 ..     110     184 ..     104     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.2e-10
                                       HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E.T-EEEEGCGHHHHHHT-SEEEE- CS
                      Shikimate_DH   7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge.eiealkleelkellaeadvvisa 82 
                                       +e++k+ +vl++GaG  ++ v   L+++g+  v++ NRt +ra +l+eel+   ++ +++ eel+++  ++d+v+ a
  gi|488600648|ref|YP_007907119.1| 110 IEEIKNIRVLVVGAGGAGKAVSYGLVKNGAV-VLIHNRTESRALNLVEELRRFgRAIFIRREELEKV--NVDMVVNA 183
                                       4589999*******************99999.*****************965413455555555543..66667666 PP

                                       S CS
                      Shikimate_DH  83 t 83 
                                       t
  gi|488600648|ref|YP_007907119.1| 184 T 184
                                       6 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.2e-07    0.0003       3      53 ..     118     167 ..     116     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.2e-07
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEE CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakala 53 
                                       vlv+Ga+ G G+a+++ l+k+Ga v++ +r+e+++ ++++el++ g+ +++
  gi|488600648|ref|YP_007907119.1| 118 VLVVGAG-GAGKAVSYGLVKNGAVVLIHNRTESRALNLVEELRRFGRAIFI 167
                                       8999998.***********************************97655544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.6e-06    0.0063       2      71 ..     118     186 ..     117     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHH.H-SEEEE-S-H CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaae.eadvvvlavkp 71 
                                       + ++GaG  g+a+  gl+++g     ++ + +r++++a  l eel     + ++    ee+ + + d+vv a + 
  gi|488600648|ref|YP_007907119.1| 118 VLVVGAGGAGKAVSYGLVKNG---AVVL-IHNRTESRALNLVEELRrfgrA-IFI-RREELEKvNVDMVVNATPL 186
                                       5689*****************...5555.77***********999888642.333.4444444458888877776 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 !   14.9   0.1   1.7e-05     0.024       1      45 [.     118     163 ..     118     188 .. 0.78
   2 ?   -2.4   0.0       3.9   5.4e+03      72      97 ..     205     230 ..     198     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH....T CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka....l 45 
                                       vl++GaG+ G+av   l++++ v   + +  r+++++ +l++++    +
  gi|488600648|ref|YP_007907119.1| 118 VLVVGAGGAGKAVSYGLVKNGAV---VLIHNRTESRALNLVEELrrfgR 163
                                       89********************9...***************98854442 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.9
                                       EEEE-SSGGGHHHHHHHHHHHT-EEE CS
                   Sacchrp_dh_NADP  72 lvvnlsppissldvlkaCietgvhyv 97 
                                       +v + + +    ++++ + e+g+++v
  gi|488600648|ref|YP_007907119.1| 205 VVFDTVYNPMETKLIRVAKEKGCDVV 230
                                       66677777777888888888888775 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 ?   13.0   0.1   3.4e-05     0.047      26      72 ..     105     151 ..      88     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                                       TCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C  26 ekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72 
                                       e +++++e+++ +v ++G+G  G+av   l + g+ v++++r++++ 
  gi|488600648|ref|YP_007907119.1| 105 EPKFSIEEIKNIRVLVVGAGGAGKAVSYGLVKNGAVVLIHNRTESRA 151
                                       5678999***********************************98754 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   4.2e-05     0.059      12      41 ..     109     138 ..      96     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                                       HHHHHHTSEEEEE--SHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  12 gqekLrdskvllvGaGglGsellknLalsG 41 
                                       + e++++ +vl+vGaGg G  +   L++ G
  gi|488600648|ref|YP_007907119.1| 109 SIEEIKNIRVLVVGAGGAGKAVSYGLVKNG 138
                                       5689****************9988887776 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05     0.073      38     108 ..     110     187 ..      98     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                       T--E..EEEEEES-CCCHHHHHHHHCCCEEEEEEESSGGGG..GGSSST....HHHHHHHHTT.S---SEEEE---T CS
                           DUF1188  38 eeeleeknvlviGaYltGaaiakkLskkeevtlvDiephlk..ellekd....vefklsleev.ernadlviDltGl 107
                                        ee+++ +vlv+Ga   G+a++  L k+  v+l+  + + +  +l+e+       + ++ ee+ ++n+d+v+  t l
  gi|488600648|ref|YP_007907119.1| 110 IEEIKNIRVLVVGAGGAGKAVSYGLVKNGAVVLIHNRTESRalNLVEELrrfgRAIFIRREELeKVNVDMVVNATPL 186
                                       5789999**************************998776651155665555654444555666689*********88 PP

                                       T CS
                           DUF1188 108 G 108
                                       G
  gi|488600648|ref|YP_007907119.1| 187 G 187
                                       7 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   9.2e-05      0.13       1      38 [.     118     156 ..     118     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-05
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkk 38 
                                       ++++GaG+ G  + + L k+ga v + +r++ r+ +l++
  gi|488600648|ref|YP_007907119.1| 118 VLVVGAGGAGKAVSYGLVKNGAVVLIHNRTEsRALNLVE 156
                                       68**********************999999977655444 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 ?   11.8   0.2   0.00018      0.25       5      69 ..     113     184 ..     110     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele......elvklaeeel..ekdleg..adlviaat 69 
                                       +k+ +vlvvG+G  +    + l+++ga v +   +    +       el ++ +  +  +++le+  +d+v+ at
  gi|488600648|ref|YP_007907119.1| 113 IKNIRVLVVGAGGAGKAVSYGLVKNGAVVLIHNRTE---SRalnlveELRRFGRAIFirREELEKvnVDMVVNAT 184
                                       7899*********************99888877763...222223335555444444544555542277898887 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.7   0.00063      0.86       2      34 ..     118     150 ..     117     156 .. 0.87
   2 ?   -2.1   0.0       1.1   1.6e+03     293     339 ..     159     203 ..     149     216 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00063
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqef 34 
                                       v+V+G+G+AG a ++ + ++G+ v++ + ++++
  gi|488600648|ref|YP_007907119.1| 118 VLVVGAGGAGKAVSYGLVKNGAVVLIHNRTESR 150
                                       9*********************99998888775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                       HHHHHHHH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHHH CS
                     FAD_binding_2 293 dvvsrailekeiaeggseanvyldashgldaegleatleaineeaan 339
                                        +++rai+ +  + ++ + +++++a+  l+ +g++++l+   e+a++
  gi|488600648|ref|YP_007907119.1| 159 RRFGRAIFIRREELEKVNVDMVVNATP-LGMHGFKNELPL-PEKAIQ 203
                                       567788886666666667777777887.888888888776.555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.4    0.0055       7.6       1      29 [.     117     146 ..     117     151 .. 0.90
   2 ?    1.4   0.0      0.14   1.9e+02     166     227 ..     146     209 ..     143     240 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0055
                                       EEEEECTSHHHHHHHHHHHHTT.EEEEESS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg.Vtllekg 29 
                                       +v+++G+G +G ++ y L + g V+l+  +
  gi|488600648|ref|YP_007907119.1| 117 RVLVVGAGGAGKAVSYGLVKNGaVVLIHNR 146
                                       59*********************9999765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                                       SECEEEEEEEE.....TCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTT.CTTTSEEEEEEEEEEEE CS
                               DAO 166 gtevtgleeed.....gkvwgverttp.gendaadavVnaaGawsdllgll.keldlpispvrgqvlvl 227
                                       +te ++l+  +     g++  + r ++ +  + +d vVna+ ++     ++ +el+lp ++++g v+ +
  gi|488600648|ref|YP_007907119.1| 146 RTESRALNLVEelrrfGRAIFI-RREElEK-VNVDMVVNATPLGMH---GFkNELPLPEKAIQGVVFDT 209
                                       5555555221112223554444.5454443.35677****977743...23355555667777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1548.46
//
Query:       gi|488600649|ref|YP_007907120.1|  [L=176]
Description: adenylyl cyclase CyaB, putative [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-29  102.9   2.9    2.1e-29  102.7   2.9    1.0  1  CYTH          CYTH domain
     0.0011   19.1   1.4      0.035   14.3   0.0    3.2  4  PurS          Phosphoribosylformylglycinamidine (FGAM) syntha
  ------ inclusion threshold ------
      0.075   13.4   0.0       0.16   12.4   0.0    1.6  1  H-kinase_dim  Signal transducing histidine kinase, homodimeri


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 !  102.7   2.9   3.5e-33   2.1e-29       1     179 []       1     167 [.       1     167 [. 0.87

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 3.5e-33
                                       EEEEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEEEEEEEECSSST. CS
                              CYTH   1 miEvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgeeltlKgpgvdge. 76 
                                       miE+E Kf+++ +e+ +++++l+e+ a+ +  +e  d+Yy +p rd+a+tdea+RiR+   +g ++t+Kg ++d e 
  gi|488600649|ref|YP_007907120.1|   1 MIEIEAKFMIDDSEFSRIDNLLSEI-AELVIEKEEVDIYYKHPLRDFAKTDEAFRIRKD-VEGVTITYKGKKMDPEt 75 
                                       89****************9999999.888888889**********************44.77777*******99975 PP

                                       ..EEEEEEEECCCEEECCCC..HHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESS CS
                              CYTH  77 ..reevegevsreEyeepls..daaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiEleved 149
                                         ree+++          +   d + a +++++lg+e++a+v+k R +y+ +++ ++lD  +f+  +++EiE+ ++d
  gi|488600649|ref|YP_007907120.1|  76 ktREEIKVR---------IYgdDYDNARDMFRKLGFEEFATVRKIRKIYRMDNAIICLDTLDFG--KFIEIEVDTQD 141
                                       555555555.........54557777888***********************************..*********** PP

                                       HHHHHHHHHHHHHHHHHTTEEGGGBSCSHH CS
                              CYTH 150 eeevkeaaekllallrelglssaskirrsy 179
                                        ee k  + +   ++++++ls ++ ir+sy
  gi|488600649|ref|YP_007907120.1| 142 IEEGKRKISE---IAKKINLSGKN-IRKSY 167
                                       ***8877777...77777777776.88777 PP

>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.73   4.4e+03      69      69 ..      29      29 ..       2      45 .. 0.59
   2 ?    1.5   0.0     0.059   3.5e+02       4      19 ..      62      77 ..      60      94 .. 0.89
   3 ?   -0.3   0.0      0.21   1.2e+03      25      43 ..      98     117 ..      92     120 .. 0.74
   4 !   14.3   0.0   5.9e-06     0.035      36      70 ..     128     163 ..     123     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.73
                                      T CS
                              PurS 69 v 69
                                      v
  gi|488600649|ref|YP_007907120.1| 29 V 29
                                      2 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.059
                                      EEEEE-TTS--HHHHH CS
                              PurS  4 veVtlKkgvlDpqGka 19
                                      v++t+K +  Dp+ k+
  gi|488600649|ref|YP_007907120.1| 62 VTITYKGKKMDPETKT 77
                                      89**********9987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.21
                                       HHTTHTTEEEEE.EEEEEEE CS
                              PurS  25 kslgyeevedvr.vgkyiel 43 
                                       ++lg+ee   vr + k++++
  gi|488600649|ref|YP_007907120.1|  98 RKLGFEEFATVRkIRKIYRM 117
                                       68999999999835566655 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 5.9e-06
                                       EEEEEEEEEEE-SSHHHHHHHHHHHHHHT.TS-TTT CS
                              PurS  36 rvgkyieleleaedeeeaeeeveemcekl.LaNpvi 70 
                                         gk+ie+e++++d ee ++++ e+++k+ L   +i
  gi|488600649|ref|YP_007907120.1| 128 DFGKFIEIEVDTQDIEEGKRKISEIAKKInLSGKNI 163
                                       68**************************98876666 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05      0.16       9      28 ..      16      35 ..      14      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                      H-kinase_dim  9 krlDyLlnlvGElVitkarL 28
                                      +r+D+Ll  + ElVi+k ++
  gi|488600649|ref|YP_007907120.1| 16 SRIDNLLSEIAELVIEKEEV 35
                                      7***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1040.15
//
Query:       gi|488600650|ref|YP_007907121.1|  [L=256]
Description: FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   45.4   0.0    1.9e-11   44.1   0.0    1.8  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    7.7e-05   22.7   0.1    0.00016   21.7   0.1    1.6  1  FKBP26_C  FKBP26_C-terminal
  ------ inclusion threshold ------
      0.032   14.1   0.3        6.4    6.7   0.1    3.0  3  TrkA_C    TrkA-C domain
      0.038   13.7   0.4       0.12   12.1   0.2    2.0  2  DUF3553   Protein of unknown function (DUF3553)
        2.4    8.3   6.8        6.6    6.9   6.8    1.8  1  DUF809    Protein of unknown function (DUF809)


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 !   44.1   0.0   5.3e-15   1.9e-11       5      74 ..       2      94 ..       1     143 [. 0.74

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 5.3e-15
                                      B-TTCEEEEEEEEEETTSSEEEEH..........CC..HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTT CS
                            FKBP_C  5 akegdtVtvhykgkledgkvfdss..........rs..rakplefkvGsgqvikGfeealegmkvGekrtltippelaY 71
                                      +++gd+V++ y+++ledg+++ds+           +  r+ ++ + vG+++vi+G+++al+g + G k ++ ++pe a+
  gi|488600650|ref|YP_007907121.1|  2 IQKGDFVKISYTARLEDGTIIDSTdektaieaglTDklRYGDIIVAVGDRHVIEGLDDALVGKEIGFKGEIVVEPEKAF 80
                                      589*********************99999888862267***************************************** PP

                                      TT...........T CS
                            FKBP_C 72 ge...........k 74
                                      g+           +
  gi|488600650|ref|YP_007907121.1| 81 GAydpdkketvtiR 94
                                      *9555444444440 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   4.6e-08   0.00016       3      71 ..     151     215 ..     149     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.6e-08
                                       HHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEE CS
                          FKBP26_C   3 ekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdef 71 
                                       ek+k+l  +y     +++++ ei+d+ v +e+p   +F +   + k++  + i++ +e+v++V++v+ +
  gi|488600650|ref|YP_007907121.1| 151 EKVKALFLLY----TTKEVNAEIKDGRVIVEVPRGSSFDQYFLIGKFSAIDAIFRHLEDVNEVELVERY 215
                                       6666666665....345788***********************************************87 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0018       6.4      37      63 ..      29      55 ..      14      61 .. 0.80
   2 ?    3.8   0.0     0.014        52       2      17 ..     121     136 ..     121     145 .. 0.91
   3 ?   -1.5   0.0      0.62   2.2e+03      51      67 ..     185     201 ..     183     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0018
                                      EEES--TT-B--TT-EEEEEEEHHHHH CS
                            TrkA_C 37 eliipsgdtvLeeGDvllvvgspsdla 63
                                        i ++ +++L+ GD+++ vg+++ ++
  gi|488600650|ref|YP_007907121.1| 29 TAIEAGLTDKLRYGDIIVAVGDRHVIE 55
                                      556666799*************98776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
                                       EEEEEE--GGGTTSBH CS
                            TrkA_C   2 vevtvpagsplvGktl 17 
                                       ++v+v+ ++p++Gk++
  gi|488600650|ref|YP_007907121.1| 121 RRVVVDFNHPYAGKKI 136
                                       589**********998 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.62
                                       -EEEEEEEHHHHHHHHH CS
                            TrkA_C  51 Dvllvvgspsdlaelre 67 
                                       D+ +++g+ s+++++ +
  gi|488600650|ref|YP_007907121.1| 185 DQYFLIGKFSAIDAIFR 201
                                       78899*******99765 PP

>> DUF3553  Protein of unknown function (DUF3553)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7     6e+03       3      12 ..      69      78 ..      69      79 .. 0.82
   2 ?   12.1   0.2   3.5e-05      0.12      17      40 ..     112     137 ..     102     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                           DUF3553  3 pGdlVrhPkq 12
                                      +G++V+ P++
  gi|488600650|ref|YP_007907121.1| 69 KGEIVVEPEK 78
                                      6999999975 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.5e-05
                           DUF3553  17 lGqVqSaiagrvtvnFen..aGkkvi 40 
                                       +G+V  +i++rv v+F++  aGkk+i
  gi|488600650|ref|YP_007907121.1| 112 WGTVERVIGRRVVVDFNHpyAGKKII 137
                                       589**************977899998 PP

>> DUF809  Protein of unknown function (DUF809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.8    0.0019       6.6      90     129 ..     215     254 ..     192     256 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0019
                            DUF809  90 spiikgeiegkeekkegkgeiegkeekkegkgeiegkeek 129
                                        p ik e e k+e+ e   e +++ee k+ k e + kee+
  gi|488600650|ref|YP_007907121.1| 215 YPRIKPEAEEKKEEAEEAEEQKSQEEAKDTKEEQDTKEEN 254
                                       5899******99999999999*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2085  (0.116292); expected 358.6 (0.02)
Passed bias filter:                     1004  (0.0559987); expected 358.6 (0.02)
Passed Vit filter:                       163  (0.00909142); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 1620.94
//
Query:       gi|488600651|ref|YP_007907122.1|  [L=281]
Description: CBS domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-45  153.1  13.1    2.5e-15   56.6   0.3    4.2  4  CBS            CBS domain
     0.0069   15.4   0.1       0.32    9.9   0.0    2.2  2  TraI_2         Putative helicase
  ------ inclusion threshold ------
       0.05   13.4   0.5       0.19   11.5   0.1    2.3  2  SpoVIF         Stage VI sporulation protein F
      0.075   13.0   0.1          1    9.2   0.0    2.3  2  Peptidase_S55  SpoIVB peptidase S55
      0.089   12.7   0.2         17    5.3   0.0    2.6  2  H_kinase_N     Signal transduction histidine kinase


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.6   3.3e-16   1.2e-12       1      54 [.       3      55 ..       3      58 .. 0.94
   2 !   56.6   0.3     7e-19   2.5e-15       4      56 ..      64     115 ..      59     116 .. 0.91
   3 !   17.1   0.1   1.6e-06    0.0057       3      49 ..     125     171 ..     121     178 .. 0.82
   4 !   38.5   0.2   3.3e-13   1.2e-09       1      56 [.     223     277 ..     223     278 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3.3e-16
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      ++d+m+rdvv+++   t   a+++++++++s++PVV ++++lvGivt++D+lr+
  gi|488600651|ref|YP_007907122.1|  3 AEDVMNRDVVYITLPNTRDVAINIFKKHKISGIPVV-KNDRLVGIVTRKDILRK 55
                                      579**********************8888*******.8999***********96 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 7e-19
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       +mt+d+vtv  d++l+++++++++++++rlPV+ +++klvGi+tlrD+++ ++
  gi|488600651|ref|YP_007907122.1|  64 LMTPDPVTVQHDDSLRDVVDILANSNFRRLPVL-KEDKLVGIITLRDIINQIA 115
                                       5*********************9999*******.6777***********8775 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.6e-06
                                       HHSBSSCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlr 49 
                                        + t   v+v ++t+l  + e mr ++   l PV+d++g lvG++ ++
  gi|488600651|ref|YP_007907122.1| 125 RYVTNSTVCVWEETPLNVVGEVMRLTN-AELcPVLDDNGSLVGLIDEK 171
                                       55566779***************7344.5999************9876 PP

  == domain 4  score: 38.5 bits;  conditional E-value: 3.3e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+ +m  + v+v+p+t +++++++m++++++++PV d d++l+G+v++r l+++ll
  gi|488600651|ref|YP_007907122.1| 223 VKNFMK-KAVYVYPQTKVSKCAREMIKNDIDHIPVADADERLIGMVHDRELIKVLL 277
                                       566774.556****************999********999*************997 PP

>> TraI_2  Putative helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0     9e-05      0.32     275     324 ..       9      59 ..       3      62 .. 0.87
   2 !    3.2   0.0    0.0097        35     274     319 ..     227     274 ..     213     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9e-05
                            TraI_2 275 edglwlVsktaadevralLlsdgisgiPks.netlfdllqeagiieaapdg 324
                                        d +++  +++ d  ++  ++++isgiP   n++l+++  +++i+ +  ++
  gi|488600651|ref|YP_007907122.1|   9 RDVVYITLPNTRDVAINIFKKHKISGIPVVkNDRLVGIVTRKDILRKPDEE 59 
                                       678899999999999*************8659************9886655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0097
                            TraI_2 274 tedglwlVsktaadevralLlsdgisgiPks..netlfdllqeagiie 319
                                        ++++++  +t + +    +++++i++iP +   e+l+++  ++++i+
  gi|488600651|ref|YP_007907122.1| 227 MKKAVYVYPQTKVSKCAREMIKNDIDHIPVAdaDERLIGMVHDRELIK 274
                                       5678999999999999999999*******876689******9999886 PP

>> SpoVIF  Stage VI sporulation protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7     6e+03      52      65 ..      39      52 ..      34      55 .. 0.75
   2 ?   11.5   0.1   5.3e-05      0.19      27      72 .]      72     117 ..      61     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                            SpoVIF 52 kedkivkaivndkv 65
                                      k d++v +++ +++
  gi|488600651|ref|YP_007907122.1| 39 KNDRLVGIVTRKDI 52
                                      77888888888776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.3e-05
                            SpoVIF  27 lkdektlRqlikqvsklankpvskekedkivkaivndkvpkdlekl 72 
                                        + ++ lR++++ +++   ++++  kedk+v +i+  ++ ++++++
  gi|488600651|ref|YP_007907122.1|  72 VQHDDSLRDVVDILANSNFRRLPVLKEDKLVGIITLRDIINQIAEM 117
                                       678899*********************************9999877 PP

>> Peptidase_S55  SpoIVB peptidase S55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00029         1     175     192 ..      32      49 ..      30      57 .. 0.91
   2 ?    1.0   0.0       0.1   3.6e+02     179     191 ..      94     106 ..      92     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00029
                     Peptidase_S55 175 mSGsPiiqngklvGavth 192
                                       +SG P+++n++lvG vt 
  gi|488600651|ref|YP_007907122.1|  32 ISGIPVVKNDRLVGIVTR 49 
                                       69**************96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.1
                     Peptidase_S55 179 PiiqngklvGavt 191
                                       P+++++klvG +t
  gi|488600651|ref|YP_007907122.1|  94 PVLKEDKLVGIIT 106
                                       9**********99 PP

>> H_kinase_N  Signal transduction histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0073        26     107     128 ..      34      55 ..      19      66 .. 0.80
   2 ?    5.3   0.0    0.0049        17      65     136 ..     108     184 ..     101     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0073
                                       EEEE.EETEEEEEEEEE--GGG CS
                        H_kinase_N 107 aiPVrrrgkviAVltretnlss 128
                                        iPV++++++++++tr+  l +
  gi|488600651|ref|YP_007907122.1|  34 GIPVVKNDRLVGIVTRKDILRK 55 
                                       59**999*********877654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0049
                                       S--TT-EE-GGGSHHHHHHHH---------.-.------..---EEEEEE.EE.TEEEEEEEEE--GGGS----HHH CS
                        H_kinase_N  65 eDvVGevveeeeeplvdraleegrivrekd.p.dwsggv..pvreeaiPVrrr.gkviAVltretnlssartpsrle 136
                                       +D++ +++e e e++v+r +++ +++  ++ p +  g+v   ++ e+ PV  + g +++ +  +  ls++   + le
  gi|488600651|ref|YP_007907122.1| 108 RDIINQIAEMEIEDAVKRYVTNSTVCVWEEtPlNVVGEVmrLTNAELCPVLDDnGSLVGLIDEKIMLSESLIDEFLE 184
                                       799***************99999655444413134444478888******88878****999888888776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1582.23
//
Query:       gi|488600652|ref|YP_007907123.1|  [L=130]
Description: hypothetical protein Asulf_01130 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   27.2   0.1    4.1e-06   26.8   0.1    1.2  1  Mrr_cat         Restriction endonuclease
     0.0043   17.5   0.5      0.007   16.8   0.5    1.3  1  NERD            Nuclease-related domain
     0.0051   17.0   0.0      0.019   15.2   0.0    1.8  2  DUF2316         Uncharacterized protein conserved in bacteria
  ------ inclusion threshold ------
      0.019   15.6   1.4      0.031   14.9   1.1    1.5  1  Ribosomal_S20p  Ribosomal protein S20
      0.023   14.9   0.5      0.028   14.6   0.5    1.2  1  UPF0102         Uncharacterised protein family UPF0102
      0.035   13.4   1.1      0.043   13.1   1.1    1.1  1  PARG_cat        Poly (ADP-ribose) glycohydrolase (PARG)
      0.098   13.1   1.6        0.1   13.1   0.7    1.6  2  DUF234          Archaea bacterial proteins of unknown functio
       0.11   11.9   0.0       0.14   11.7   0.0    1.1  1  Peptidase_S9    Prolyl oligopeptidase family


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 !   26.8   0.1   1.8e-09   4.1e-06       5      60 ..       3      58 ..       2      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.8e-09
                                      -TTCHHHHHHHHHHHHSSS...EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS- CS
                           Mrr_cat  5 spkeFeklvaellealGyk...eveltgrsgDggiDliakkdplgserilvqaKryknk 60
                                      s++eFe+lv++++e+++++   +v    +++   iD+iak+  ++ + ++v aKry+++
  gi|488600652|ref|YP_007907123.1|  3 SWQEFEELVKDVFEKNDFEtrfRVVFRYKGRRSEIDIIAKR--FN-KILAVDAKRYNRN 58
                                      79*****************977666777788999*****98..44.789*******754 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   3.1e-06     0.007       3     106 ..       5      92 ..       3      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                              NERD   3 aegEravakeLkelked.eylvlhdvrlrpgtgeiDhlvispkgifviEvKnwsGwifgdkegrwtqkikkgfknpl 78 
                                       +e E+ v ++ +  k+d e ++   +r++++++eiD+++   ++i+ ++ K ++         +w++k+        
  gi|488600652|ref|YP_007907123.1|   5 QEFEELVKDVFE--KNDfETRFRVVFRYKGRRSEIDIIAKRFNKILAVDAKRYNR--------NWYRKS-----ALK 66 
                                       567899999999..5564444444455544455*******************883........477774.....555 PP

                              NERD  79 eqakrhakalkksllekgkgvpvesvvv 106
                                       ++a++h+k ++++   k+ ++ v++v+v
  gi|488600652|ref|YP_007907123.1|  67 REAEKHRKRCENYS--KLTNQRVYPVIV 92 
                                       67888888885555..777888888877 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 !   15.2   0.0   8.4e-06     0.019      33      81 ..      37      85 ..      30      88 .. 0.92
   2 ?   -1.2   0.0       1.1   2.5e+03      65      80 ..     100     115 ..      97     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.4e-06
                           DUF2316 33 LnlttekvekvLelkasrledvWilrdyLeekikeqgktpvpfsaLkgd 81
                                      +++  ++++k+L+++a+r +  W  +  L+++ +++ k  + +s+L+++
  gi|488600652|ref|YP_007907123.1| 37 IDIIAKRFNKILAVDAKRYNRNWYRKSALKREAEKHRKRCENYSKLTNQ 85
                                      56678899**************************************976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                           DUF2316  65 ikeqgktpvpfsaLkg 80 
                                       i  +g ++vpf aL++
  gi|488600652|ref|YP_007907123.1| 100 IFYEGCAVVPFDALND 115
                                       556788999**99986 PP

>> Ribosomal_S20p  Ribosomal protein S20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.1   1.4e-05     0.031       8      57 ..      46      96 ..      41      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.-HHHHHHHHHHHHHHHH CS
                    Ribosomal_S20p  8 KrirqnekrrlrNrsyksavrtaiKkvraaiea.dkekaqealkkaiskid 57
                                      K + + +kr  rN ++ksa++  + k+r+ +e+ +k + q  +++++s id
  gi|488600652|ref|YP_007907123.1| 46 KILAVDAKRYNRNWYRKSALKREAEKHRKRCENySKLTNQRVYPVIVSLID 96
                                      6677889************************8889999************9 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   1.2e-05     0.028       2      62 ..       8      73 ..       7     100 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHTT-EEEEE...EEEETTEEEEEEE..TTEEEEEEEEE-......-------HHHHH CS
                           UPF0102  2 EelaaeyLekkgyeiler...nwrcragEiDiia..tevlvfvEVKtRssekfgspaeavtprKqr 62
                                      Eel+ +++ek+ +e   r   +++ r+ EiDiia   + ++ v+ K  +++ +++ a   +++K r
  gi|488600652|ref|YP_007907123.1|  8 EELVKDVFEKNDFETRFRvvfRYKGRRSEIDIIAkrFNKILAVDAKRYNRNWYRKSALKREAEKHR 73
                                      7888888888888877662113444668******99557999999985444444333333333333 PP

>> PARG_cat  Poly (ADP-ribose) glycohydrolase (PARG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   1.9e-05     0.043     219     273 ..      20      71 ..      12      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                          PARG_cat 219 Yassfrfagdyv.dktprdslgrrkteivaiDAlefkkeekekqykkekilRelnK 273
                                       +++ fr+  +y+  ++++d + +r ++i+a+DA ++++    + y+k+ ++Re  K
  gi|488600652|ref|YP_007907123.1|  20 FETRFRVVFRYKgRRSEIDIIAKRFNKILAVDAKRYNR----NWYRKSALKREAEK 71 
                                       566677777777448899*****************766....89*********998 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7   4.5e-05       0.1      35      91 ..       6      56 ..       3      74 .. 0.81
   2 ?   -3.2   0.0       5.3   1.2e+04      26      37 ..     118     129 ..     112     130 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                            DUF234 35 vFEelvrelllelnkagklpfrftkvGrwWkkeeeiDivaldeeekkalfgEvKwkn 91
                                      +FEelv++++     ++ +++rf+ v r+  +++eiDi+a + ++  +l++  K  n
  gi|488600652|ref|YP_007907123.1|  6 EFEELVKDVFE----KNDFETRFRVVFRYKGRRSEIDIIAKRFNK--ILAVDAKRYN 56
                                      68888888776....677899999***************988777..8888887554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.3
                            DUF234  26 eelneyvgkvFE 37 
                                        +++ y+++ FE
  gi|488600652|ref|YP_007907123.1| 118 LNIDYYLAELFE 129
                                       567889999998 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.1e-05      0.14     111     165 ..      55     107 ..      41     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                                       THH.HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHH CS
                      Peptidase_S9 111 lte.eymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealkl 165
                                       +++ +y +   ++e e+++k++ +ys+l+n ++yp   +i++l Ddr  + e+  +
  gi|488600652|ref|YP_007907123.1|  55 YNRnWYRKSALKREAEKHRKRCENYSKLTNQRVYP---VIVSLIDDRLIFYEGCAV 107
                                       89989999999999****************66666...899******999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 766.72
//
Query:       gi|488600653|ref|YP_007907124.1|  [L=99]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-16   60.5   1.6    1.9e-16   60.1   1.6    1.2  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   1.6     1e-20   1.9e-16       1      61 [.      18      93 ..      18      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1e-20
                                      --HHHHHHHHHHHHHHHHHHTTCGCS--.....TT----S.......-EB-S--.....HHHHHTT-SSEETTEEE CS
                       Glu-tRNAGln  1 lseeEleklakelnsildyveqLqevdt.....tgveplthp.....vlReDev.....reelLknApetedgyfv 61
                                      ls++E+e++ +e++sil+y+e L++v       ++vep++++     v+R+D++     re +L nA+++e+gyf+
  gi|488600653|ref|YP_007907124.1| 18 LSDDEIERFRSEFESILEYFESLDDVRNefenfDDVEPTFQVlplrnVFRDDVAkdsldRESVLMNAKHKEEGYFK 93
                                      79*************************5556669******************8578998888*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 623.65
//
Query:       gi|488600654|ref|YP_007907125.1|  [L=457]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-150  499.6   0.0   9.6e-150  499.5   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 !  499.5   0.0  5.4e-154  9.6e-150       1     451 []      18     445 ..      18     445 .. 0.97

  Alignments for each domain:
  == domain 1  score: 499.5 bits;  conditional E-value: 5.4e-154
                                       HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B CS
                           Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenyp 77 
                                       +lv ++++ri++  ++ln ++ +++e+a  +A++ d+        g L+G+P++vKDni++kg+ tt++sk+l ny+
  gi|488600654|ref|YP_007907125.1|  18 DLVAELIERIKK--SDLN-AFISVNEKAVDDARRFDEGK----LSGKLAGIPVAVKDNISTKGMLTTCASKILHNYI 87 
                                       6899999*9999..8999.78889************876....5********************************* PP

                                       -SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSS CS
                           Amidase  78 aekDatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGG 154
                                       +++Da+vverLk++Ga+i+gkTnmdefamg++te+s+fg ++NP+dksr++GGSSGGsAA +A + +++++G+DtGG
  gi|488600654|ref|YP_007907125.1|  88 PPYDAHVVERLKQEGAIIIGKTNMDEFAMGTTTETSYFGVVKNPFDKSRVAGGSSGGSAACLAGDESVVSLGSDTGG 164
                                       ***************************************************************************** PP

                                       TTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCT CS
                           Amidase 155 SiRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeel 231
                                       SiR+PAsfcg++GlKPtyg+vSr+g++++++sl+++Gp+a++vedla+ll+vi+g+d++dst+s      +d+ ++ 
  gi|488600654|ref|YP_007907125.1| 165 SIRCPASFCGVYGLKPTYGLVSRYGLIPYANSLEQIGPFATCVEDLAILLEVIAGKDERDSTNSG-----KDFNSRD 236
                                       ****************************************************************8.....8****** PP

                                       T---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS CS
                           Amidase 232 kkslkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvry 308
                                         +   l+iGv++e++    +++v  ++++al+ +++  hev+ev+l sl++al++yy+i+++eassnlary+gvry
  gi|488600654|ref|YP_007907125.1| 237 LRDVGRLKIGVIREMSG---NEDVMSSFNEALEVVKK-HHEVEEVSLRSLKYALPAYYIIAMSEASSNLARYDGVRY 309
                                       ****************6...99999***999998876.6************************************** PP

                                       .---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSS CS
                           Amidase 309 .erlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtapt 384
                                         +l++ +++++++++ rae++g+evkrri+lg+yalsa++++kyylka kvr+l++++f +a+ ++D+l++Pt+p+
  gi|488600654|ref|YP_007907125.1| 310 gLALDRLSNWNDYFSEVRAEGFGDEVKRRIMLGSYALSAGYYGKYYLKALKVRTLVINDFERALSKYDLLIAPTMPS 386
                                       ***************************************************************************** PP

                                       S--BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                           Amidase 385 paprlgekdktidsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                        ++r+ge      +++++y+ ++ t   vp nl glp+ls+p+  ++ glPvG+q+ig++f+e+ +L
  gi|488600654|ref|YP_007907125.1| 387 LPFRIGEL----ADPLTMYKADVNT---VPINLSGLPSLSMPIFMRK-GLPVGMQIIGNYFSESLIL 445
                                       ********....58***********...***************9986.***************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 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:                        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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2596.50
//
Query:       gi|488600655|ref|YP_007907126.1|  [L=538]
Description: phosphoserine-tRNA(Cys) ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-56  190.2   0.0    8.7e-53  179.3   0.0    2.2  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    3.1e-15   56.0   0.4    2.1e-14   53.3   0.1    2.4  2  SepRS_C          O-phosphoseryl-tRNA synthetase C-terminal do
    3.7e-10   39.6   0.0    5.1e-07   29.4   0.0    2.4  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
  ------ inclusion threshold ------
      0.013   15.5   0.1      0.041   13.9   0.1    1.9  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
      0.066   13.3   0.0       0.15   12.1   0.0    1.5  1  Lambda_Bor       Bor protein
       0.11   11.5   0.2         17    4.3   0.1    2.7  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)


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 !    8.6   0.0   0.00039       1.2       9      48 ..      39      78 ..      32      86 .. 0.86
   2 !  179.3   0.0   2.9e-56   8.7e-53      14     237 ..     119     352 ..     104     357 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00039
                                      SCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHH CS
                      tRNA-synt_2d  9 krieagklhpltkvleeikeiflelgfeevegpevesefy 48
                                       +++ g+ hpl k+++++++ ++ lgf+ev +p + ++ +
  gi|488600655|ref|YP_007907126.1| 39 YSYSIGEEHPLFKTINDLRRAYITLGFKEVVNPVIVEDSH 78
                                      5677899************************999877765 PP

  == domain 2  score: 179.3 bits;  conditional E-value: 2.9e-56
                                       SB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHH CS
                      tRNA-synt_2d  14 gklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttav 90 
                                       ++++  ++ ++ i+ if+e+++  ++g+++   +  ++a+++++ +++  ++ +F+  k  k++ e+l+LR+h+t+ 
  gi|488600655|ref|YP_007907126.1| 119 AQKKLSEEEIDAIRMIFHEFKKGRIDGDDL--PYKLASAIEISDVKAVEIIDKVFPEFKALKPEPESLTLRSHMTTG 193
                                       34556678899******************9..8999***************************************** PP

                                       HHHHH....TTS-SSEEEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTST.EEEEE CS
                      tRNA-synt_2d  91 qirtl....ekkkppikiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellkklfgae.vkvrf 161
                                       +++tl    ++  +pik++si+r+fR+++ +Dat+l+++++++++vvde+v +++ k+v+e ll+++ g++ +k+r+
  gi|488600655|ref|YP_007907126.1| 194 WFITLskiaSRFPLPIKLFSIDRCFRKEQrEDATRLYTYFSASCVVVDEDVGVEEGKAVAEGLLRQF-GFKkFKFRL 269
                                       *****888666779***************9*************************************.9998***** PP

                                       EECEETTEEEEEEEEEEE.........CCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-S CS
                      tRNA-synt_2d 162 rpsyfpftePsaevdvyl.........vekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygie 229
                                       +++ ++++ P+++++v++         ++ +++w+E++++G+++p++l+++++  e++++++GlGveRlam+ y+++
  gi|488600655|ref|YP_007907126.1| 270 DEKRSKYYIPGTQTEVFAfhpkivgssTKYSDGWIEIATFGIYSPTALAQYDV--EYPVMNLGLGVERLAMILYDYS 344
                                       ****************999********99************************..********************** PP

                                       SGHHHHTT CS
                      tRNA-synt_2d 230 DiRelven 237
                                       D+Relv++
  gi|488600655|ref|YP_007907126.1| 345 DVRELVYP 352
                                       *****986 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 ?   -0.3   0.0      0.39   1.2e+03       2      12 ..     402     412 ..     402     412 .. 0.89
   2 !   53.3   0.1   6.9e-18   2.1e-14       1      31 []     435     465 ..     435     465 .. 1.00

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.39
                                       EEEEETTEEEE CS
                           SepRS_C   2 EvyVYdGnIlG 12 
                                       Ev  ++G I+G
  gi|488600655|ref|YP_007907126.1| 402 EVTAFEGEIYG 412
                                       77889*****9 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 6.9e-18
                                       EEEEEETTEEEEEES-TTTCCHHHHSEEEEE CS
                           SepRS_C   1 NEvyVYdGnIlGvPdtekwkearenGvsTGI 31 
                                       NEv+VY+G+IlGvP+t+kw +++e+G  TGI
  gi|488600655|ref|YP_007907126.1| 435 NEVVVYQGSILGVPRTDKWLHVFEHGFTTGI 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 !    7.6   0.0   0.00075       2.2       5      50 ..      36      81 ..      34      91 .. 0.87
   2 !   29.4   0.0   1.7e-10   5.1e-07      73     208 ..     185     327 ..     178     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00075
                   tRNA_synthFbeta  5 lPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldk 50
                                      +P+ +   ge+++ +k+ + lr++ + +G+ Ev++   v ++++++
  gi|488600655|ref|YP_007907126.1| 36 FPRYSYSIGEEHPLFKTINDLRRAYITLGFKEVVNPVIVEDSHVRR 81
                                      67888888999************************99998888765 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.7e-10
                   tRNA_synthFbeta  73 vlRtsLlpglLevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgi 149
                                       +lR+ ++ g   +l++  +r    ++lF i ++f+k++ e+  +  +++++  +  +         ++v++++ k++
  gi|488600655|ref|YP_007907126.1| 185 TLRSHMTTGWFITLSKIASRFPLPIKLFSIDRCFRKEQREDATRLYTYFSASCVVVD---------EDVGVEEGKAV 252
                                       7999************99999999*************55555444444444444444.........55********* PP

                   tRNA_synthFbeta 150 vealleslgiek..vefepaehpalhpgrsAei.........kvdgk........evGvlGelhpevleafdlkqrv 207
                                       +e ll+++g++k  ++++++  +++ pg + e+         +            e+  +G  +p  l+++d++++v
  gi|488600655|ref|YP_007907126.1| 253 AEGLLRQFGFKKfkFRLDEKRSKYYIPGTQTEVfafhpkivgS---StkysdgwiEIATFGIYSPTALAQYDVEYPV 326
                                       **********87335555688************5555555550...055555569*******************998 PP

                   tRNA_synthFbeta 208 y 208
                                       +
  gi|488600655|ref|YP_007907126.1| 327 M 327
                                       6 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 ?   13.9   0.1   1.4e-05     0.041       9      58 ..     182     228 ..     174     344 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                                       EEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTSTBCTTTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEksdsrGLlR 58 
                                       ++++L+   +++     + + + s+  LP+kl+ i +++R+E++     +R
  gi|488600655|ref|YP_007907126.1| 182 ESLTLRSHMTTGWFITLS-K-IASRFpLPIKLFSIDRCFRKEQR-EDA-TR 228
                                       667777666666554444.4.556444****************9.333.34 PP

>> Lambda_Bor  Bor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.9e-05      0.15      49      71 ..     295     317 ..     290     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                        Lambda_Bor  49 tqqtfvngLlgvvTlGIYtPrtt 71 
                                       + +   +g +++ T+GIY+P+  
  gi|488600655|ref|YP_007907126.1| 295 SSTKYSDGWIEIATFGIYSPTAL 317
                                       667788999***********975 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 ?    4.3   0.1    0.0059        17      93     127 ..     210     242 ..     209     272 .. 0.80
   2 ?    4.2   0.0    0.0062        18     287     308 ..     329     350 ..     319     406 .. 0.91
   3 ?   -2.9   0.0       0.9   2.7e+03      11      51 ..     490     531 ..     485     535 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0059
                                       EEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqieaemsfiee 127
                                       + f+i r+FR+E+ +    l  +t + a +  ++e
  gi|488600655|ref|YP_007907126.1| 210 KLFSIDRCFRKEQREDATRL--YTYFSASCVVVDE 242
                                       68***********9988888..7777776666665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0062
                                       EEEEHHHHHHHHCT-SSGGGCS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdvi 308
                                       lglG++Rl m+l + +++r+++
  gi|488600655|ref|YP_007907126.1| 329 LGLGVERLAMILYDYSDVRELV 350
                                       79*****************875 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.9
                                       HHCCSHHHHHHHHHHHHHHHHHHHHHHHT.T-EE----SEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       tRNA-synt_2  11 ldlrtekvskvlrlrstvtkavrkyleen.gfieietPiLsk 51 
                                       +++rt+ v++   +   + + +rky++++ g i+i  P+++ 
  gi|488600655|ref|YP_007907126.1| 490 MEIRTRVVESLSDINLGLQENIRKYITSKeGKIDIRGPMFVA 531
                                       677888888888888888899999998877999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 3511.19
//
Query:       gi|488600656|ref|YP_007907127.1|  [L=223]
Description: Endonuclease V [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-61  205.7   0.0    6.6e-61  205.4   0.0    1.0  1  Endonuclease_5  Endonuclease V
  ------ inclusion threshold ------
      0.023   14.1   0.1       0.28   10.6   0.0    2.3  2  DUF99           Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.0   7.3e-65   6.6e-61       2     197 .]      14     205 ..      13     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 7.3e-65
                                       HHHCC-------SGG-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHH CS
                    Endonuclease_5   2 elakkveledklkeklklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllk 78 
                                       e++k+v+l++    k++ v GvD +f  ++    +++ v++++p+++++ ++v v++ +fpYipg+L+FRE p +lk
  gi|488600656|ref|YP_007907127.1|  14 EMSKRVVLREIDLGKVEHVLGVDQAFLGDKI---ISVGVLMSFPEMKIMGSSVRVEREDFPYIPGYLMFREGPSALK 87 
                                       7889999999888889**********55444...99***************************************** PP

                                       HHCC-SS--SEEEEEC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEES CS
                    Endonuclease_5  79 aleklkqkpdvllvDGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrt 155
                                       ++++l q++ ++lvDG+GiaHprr+GlA+++G+ +++ptiG++Ks+l+g+++ep +++g+++pl+++ge+ig+a++t
  gi|488600656|ref|YP_007907127.1|  88 VVKELLQENTLILVDGSGIAHPRRCGLATYIGIETQTPTIGITKSRLFGEYTEP-RDTGDISPLTHNGEIIGYAMKT 163
                                       *************************************************99987.6889****************** PP

                                       STTS--EEEEEECSS-HHHHHHHHHHCS-T-SS-HHHHHHHH CS
                    Endonuclease_5 156 kknvkpiyvSvGhrisletalelvlallkkyrlPepirqAdl 197
                                       ++++kpi++S+G++i+  +a+e v+ +lk+y+lPepir Ad+
  gi|488600656|ref|YP_007907127.1| 164 CRRCKPIFISPGNMITPLQAVEAVKLCLKGYKLPEPIRIADR 205
                                       ****************************************96 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.031   2.8e+02       4      30 ..      31      52 ..      28      69 .. 0.77
   2 ?   10.6   0.0   3.1e-05      0.28     150     180 ..     178     208 ..     155     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.031
                                      EEEEEEEEE.....-SS-EEEEEEEEE CS
                             DUF99  4 rvlGiddsfferkkkdgksvlvGvvmr 30
                                      +vlG+d +f+     ++k++ vGv+m 
  gi|488600656|ref|YP_007907127.1| 31 HVLGVDQAFL-----GDKIISVGVLMS 52
                                      79*******3.....578999999986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 3.1e-05
                                       S-HHHHHHHHHHC-SSSSS-HHHHHHHHHHH CS
                             DUF99 150 ieleeaaklvrkltlegriPEPlRvAhliAs 180
                                       i++ +a ++v+ + +  ++PEP+R+A+ +++
  gi|488600656|ref|YP_007907127.1| 178 ITPLQAVEAVKLCLKGYKLPEPIRIADRLSK 208
                                       67888999999999999*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1652.18
//
Query:       gi|488600657|ref|YP_007907128.1|  [L=231]
Description: formate dehydrogenase family accessory protein FdhD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-42  143.8   0.0    8.1e-42  143.5   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 !  143.5   0.0   4.5e-46   8.1e-42       2     223 ..      15     219 ..      14     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 4.5e-46
                                       --EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S.........--------- CS
                         FdhD-NarQ   2 eEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatrakaedkeerrtakrvv 78 
                                       +E ++t+++ng +   lm++p++leela+Gf++segli+ ++ +++ie++ + +++ v+ +a      +  t+ ++ 
  gi|488600657|ref|YP_007907128.1|  15 KEIEVTVYINGLP-SHLMCSPNNLEELAIGFVVSEGLID-RDLVDEIEIHRKGNEIFVDVDA------NSFTL-ELR 82 
                                       7999*******76.689*********************9.6889999*99999888888333......23333.577 PP

                                       ------.---...--H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHH CS
                         FdhD-NarQ  79 tsgCglcgkesleelletlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnA 155
                                       +sgC  +g+ +  e+l  +e   ++ k+s ++l ++++ +    e +++t+g H+ a++  ++ l++ + DvGRHnA
  gi|488600657|ref|YP_007907128.1|  83 SSGC--VGVFKKGEVLPPVE---AKEKFSLDELKKALEYIDV--EEYRKTRGYHSSAIVG-KKGLIVRAIDVGRHNA 151
                                       8999..37777656664444...4569999*********996..779************9.788************* PP

                                       HHHHHHHHHT.TSS-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEE CS
                         FdhD-NarQ 156 lDkviGaallegldlsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvr 223
                                       +Dk+iG+al++++d+s+ +l++sgR+s  + +Ka+r gip++vs++++ + a+++++++gl  v f+ 
  gi|488600657|ref|YP_007907128.1| 152 VDKAIGMALRKNIDTSKVFLLISGRISRGIAAKAVRSGIPLVVSKASILDSAIDVCKKTGLSAVSFAS 219
                                       *****************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1700.44
//
Query:       gi|488600658|ref|YP_007907129.1|  [L=221]
Description: ABC-type transport system involved in cytochrome c biogenesis, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   86.1   9.3    3.1e-24   85.7   9.3    1.0  1  CcmB             CcmB protein
     0.0016   17.8  17.1      0.069   12.4  11.3    2.1  2  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.037   13.2  25.5        0.1   11.7  25.5    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.38   10.1  25.4      0.011   15.1  16.4    2.0  2  ABC2_membrane    ABC-2 type transporter
        9.2    4.9  16.7          3    6.5  13.9    1.5  2  Presenilin       Presenilin


Domain annotation for each model (and alignments):
>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   9.3   8.7e-28   3.1e-24       3     206 ..      11     211 ..      10     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 8.7e-28
                              CcmB   3 alllrdlrlalRakgelllgllFfllvvtllplavGPdtallsriapgilWvaallaslLsldrlfaadfedGsLel 79 
                                       ++ l+d ++++R+k  ++  +lF l+ ++l+ +++   ++ ++r ap+++W+  ++  +++  r+f+++ ++ +++ 
  gi|488600658|ref|YP_007907129.1|  11 TIALKDAKVEMRSKSTISFMILFSLMNIALFSISIS--SRDIQRTAPALIWIVFIFVGIVGYSRAFTKEYDEQTIDG 85 
                                       5778**************************999995..7889*********************************** PP

                              CcmB  80 lllapvplellvlaKalAhwlltglplvllapllalllnleaaalgllaltLllGtpalsllgavgaAltvgLkrgg 156
                                       l + + p ++ +l+K++ +  +  l+  ++ap++  ++nle++ l    + L  G  a+ ++++  + ltv  ++ +
  gi|488600658|ref|YP_007907129.1|  86 LRMFAKPQSI-LLGKIIYNTCILILLEFIIAPIFIAFFNLEIENLVDFFVILTAGNFAFIVTTTSMSLLTVKSRARE 161
                                       *******875.689*************************************************************** PP

                              CcmB 157 lLlslLvlPliiPvlifaveaveaaaegldveaalalllaltvvtlvlap 206
                                       +Ll+++ +P+i P++ +av+a++++ +g  +e+  + ++a   + + l  
  gi|488600658|ref|YP_007907129.1| 162 ILLPVILFPIIFPIINVAVTALTQVFHGFHYEVSRLYIIACYTLIISLIG 211
                                       ****************************9998876666665555444443 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 !    9.5   0.4   0.00015      0.55       2      45 ..      11      54 ..      10      58 .. 0.87
   2 !   12.4  11.3   1.9e-05     0.069      82     247 ..      59     208 ..      51     212 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00015
                   ABC2_membrane_2  2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqsea 45
                                      +ia k+ +  +rs++++ +++l+ l+  al  ++ ++++ q+ a
  gi|488600658|ref|YP_007907129.1| 11 TIALKDAKVEMRSKSTISFMILFSLMNIALFSISISSRDIQRTA 54
                                      89************************888888888888877766 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.9e-05
                   ABC2_membrane_2  82 avlipviaalfgadaiagEkergTlk..llLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivl 156
                                        +++ +++++  + a+++E+++ T+   ++++kP    +illgK+i + +i   ++++ +++   a ++i+ +  ++
  gi|488600658|ref|YP_007907129.1|  59 WIVFIFVGIVGYSRAFTKEYDEQTIDglRMFAKPQ---SILLGKIIYNTCI---LILLEFII---APIFIAFFNLEI 126
                                       445555566666899**********74478****6...6************...88888888...455555555555 PP

                   ABC2_membrane_2 157 .aledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindf 232
                                        +l d+++++ a  + ++ v+    ++ +S ++  +++a ++ l +++ + i++pi+  +v++l +++      +  
  gi|488600658|ref|YP_007907129.1| 127 eNLVDFFVILTAGNFAFI-VT----TTSMSLLTV-KSRAREILLPVIL-FPIIFPIINVAVTALTQVFHG---FHYE 193
                                       256666666666664444.33....444444444.4444454444444.446666666677777765544...6668 PP

                   ABC2_membrane_2 233 lsllsptsayntlln 247
                                       +s l +++ y+++++
  gi|488600658|ref|YP_007907129.1| 194 VSRLYIIACYTLIIS 208
                                       888888888877765 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  25.5   2.8e-05       0.1     154     306 ..      45     200 ..      10     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                   ABC2_membrane_3 154 eelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqllli.lll.. 227
                                        ++ ++++++ +li i++if++++  ++++ +E   +++ ++ +   +p +++l+ki+    + +l  ++i  ++  
  gi|488600658|ref|YP_007907129.1|  45 ISSRDIQRTAPALIWIVFIFVGIVGYSRAFTKEYDEQTIDGLRMF-AKPQSILLGKIIYNTCILILLEFIIaPIFia 120
                                       455677778888*********************************.***********88777766664443134345 PP

                   ABC2_membrane_3 228 afglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp...ledlpsalkwif 301
                                       +f+  ++++nl+ +++ +  + +a+i+ ++ +s l+ +s++  il++++++++++ ++++ +   ++ ++++   ++
  gi|488600658|ref|YP_007907129.1| 121 FFN--LEIENLVDFFVILTAGNFAFIVTTTSMSLLTVKSRAREILLPVILFPIIFPIINVAVtalTQVFHGFHYEVS 195
                                       666..******************************999988778888888888888888765342333445555555 PP

                   ABC2_membrane_3 302 siiPf 306
                                       ++  +
  gi|488600658|ref|YP_007907129.1| 196 RLYII 200
                                       55444 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1  16.4   3.1e-06     0.011      16     174 ..      22     173 ..      10     174 .. 0.81
   2 ?    0.3   3.9      0.11     4e+02      96     150 ..     162     213 ..     157     219 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                     ABC2_membrane  16 rdpslgllwrliqplllalvfgtvfgnlgnsedgl.nrpgllffsvlflafsaltsvapvferergvlerelvsply 91 
                                       r++s++  +++++ l+ + +f   ++    s d++ + p l+ + ++f++ +   s a++ e+++ +++ ++ +   
  gi|488600658|ref|YP_007907129.1|  22 RSKSTI-SFMILFSLMNIALFSISIS----SRDIQrTAPALIWIVFIFVG-IVGYSRAFTKEYDEQTIDGLRMFAK- 91 
                                       555444.5566666666666666666....56666455999999999999.5566666***************998. PP

                     ABC2_membrane  92 slsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalapsfedasqlaslv 168
                                        + +++l+k++++ ++ +l+ +i+  i++ +++l++++ + f+++l +  +a++     +s l+++ +   +l +++
  gi|488600658|ref|YP_007907129.1|  92 -PQSILLGKIIYNTCILILLEFIIAPIFIAFFNLEIENLVDFFVILTAGNFAFIVTTTSMSLLTVKSRAREILLPVI 167
                                       .*****************************99****97788888888888888888888888889999999999999 PP

                     ABC2_membrane 169 llplll 174
                                       l+p+++
  gi|488600658|ref|YP_007907129.1| 168 LFPIIF 173
                                       998876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                     ABC2_membrane  96 yvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgll 150
                                       ++l  +l+ +++ ++ +++  l+ +f  g++++  +  l+++ +++l++s +g+l
  gi|488600658|ref|YP_007907129.1| 162 ILLPVILFPIIFPIINVAVTALTQVFH-GFHYE--VSRLYIIACYTLIISLIGFL 213
                                       444444444555555444444444443.66665..55555666666666666554 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3      0.16   5.7e+02      98     137 ..      28      69 ..      25      78 .. 0.53
   2 ?    6.5  13.9   0.00082         3      48     161 ..      88     206 ..      50     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.16
                        Presenilin  98 slllLf.lvsglllaevlkaynipldyitlllllwnf.gvvG 137
                                       s+++Lf l+ ++l++  ++  +i  ++ +l+ +++ f g+vG
  gi|488600658|ref|YP_007907129.1|  28 SFMILFsLMNIALFSISISSRDIQRTAPALIWIVFIFvGIVG 69 
                                       444444144445555555666666666655555444424555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00082
                        Presenilin  48 eesdstgqkllnsllnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsgl.....llaevlkayni 119
                                          + ++  l++ ++n++ilil+ +++  ++++++ ++  +++  ++il++    f+v+++     ++++  +++ +
  gi|488600658|ref|YP_007907129.1|  88 MFAKPQSILLGKIIYNTCILILLEFIIAPIFIAFFNLEIENLVDFFVILTAGNFAFIVTTTsmsllTVKSRAREILL 164
                                       45566667788899**********************************99866555554440000044445555577 PP

                        Presenilin 120 pldyitlllllwnfgvvGviaifwkgplllqqaYlilisalm 161
                                       p+ ++ +++ ++n++v  +  +f      + + Y+i+  +l+
  gi|488600658|ref|YP_007907129.1| 165 PVILFPIIFPIINVAVTALTQVFHGFHYEVSRLYIIACYTLI 206
                                       7777788999*************************9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1580.09
//
Query:       gi|488600659|ref|YP_007907130.1|  [L=208]
Description: hypothetical protein Asulf_01137 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-33  114.9   0.0    4.6e-33  114.6   0.0    1.1  1  ABC_tran         ABC transporter
    1.6e-10   41.3   0.1    0.00015   21.7   0.4    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0002   20.9   0.1       0.26   10.7   0.1    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00066   19.5   0.0      0.052   13.2   0.0    2.1  2  AAA_15           AAA ATPase domain
    0.00074   19.3   0.0    0.00098   18.9   0.0    1.3  1  AAA_30           AAA domain
    0.00079   19.8   0.0      0.001   19.5   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.001   16.7   0.1     0.0013   16.3   0.1    1.1  1  DUF3584          Protein of unknown function (DUF3584)
     0.0053   17.3   0.5       0.01   16.3   0.1    1.7  2  AAA_23           AAA domain
     0.0057   16.4   0.1       0.01   15.6   0.1    1.3  1  AAA_29           P-loop containing region of AAA domain
      0.006   16.9   0.0       0.39   11.1   0.0    2.4  1  GTP_EFTU_D2      Elongation factor Tu domain 2
     0.0088   16.3   0.1      0.082   13.2   0.1    2.1  2  AAA_28           AAA domain
     0.0092   15.7   0.2       0.15   11.8   0.1    2.2  2  AAA_24           AAA domain
     0.0099   15.8   0.1       0.25   11.2   0.0    2.2  2  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.036   14.0   0.1    1.7  2  NACHT            NACHT domain
      0.015   15.7   0.2       0.11   12.9   0.2    2.2  1  AAA              ATPase family associated with various cellul
      0.025   14.9   0.1      0.056   13.7   0.1    1.7  1  AAA_22           AAA domain
      0.039   14.5   1.1      0.088   13.4   1.1    2.0  1  AAA_18           AAA domain
      0.046   12.4   0.0       0.15   10.7   0.0    1.8  2  AAA_13           AAA domain
      0.051   13.7   0.2       0.12   12.5   0.2    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
      0.064   12.9   0.0       0.15   11.7   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
      0.092   12.9   0.0        0.2   11.8   0.0    1.6  1  AAA_33           AAA domain
        0.1   12.1   0.1       0.42   10.1   0.0    1.9  3  Arf              ADP-ribosylation factor family
        0.1   12.2   0.0       0.13   11.9   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.12   12.0   0.0       0.26   10.9   0.0    1.6  1  Thymidylate_kin  Thymidylate kinase
       0.14   11.4   0.0       0.21   10.9   0.0    1.3  1  Zeta_toxin       Zeta toxin
       0.16   11.6   0.1       0.27   10.8   0.1    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   0.0   6.7e-36   4.6e-33       2     136 ..      20     157 ..      19     158 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 6.7e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       k+v++ +k+gekvaivG nG+GK+tLl++l+g+ kp +G +++ gk+  +    +lrk+ig+l++ ++l +elt++e
  gi|488600659|ref|YP_007907130.1|  20 KDVNFVVKRGEKVAIVGVNGSGKTTLLRILSGQIKPSAGYVEIFGKNPYM--DVELRKKIGFLSHSSHLYRELTAKE 94 
                                       89******************************************999999..899********************** PP

                                       H.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n          ++++++++l+ ++l + +++ v    +s+S+G+ qr+++a+all++p++l++DEp+
  gi|488600659|ref|YP_007907130.1|  95 NlifyaklmgVDESRVSEVLKLVNLWKARNDLV----RSFSKGMEQRLKIAKALLNDPDILICDEPS 157
                                       **********999********************....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.4   2.2e-07   0.00015       3      22 ..      33      52 ..      31      97 .. 0.81
   2 !   18.0   0.0     3e-06     0.002     234     300 ..     127     187 ..      73     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +++G NgsGK++LL++l++ 
  gi|488600659|ref|YP_007907130.1| 33 AIVGVNGSGKTTLLRILSGQ 52
                                      79***************864 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3e-06
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       +r++S G+ + l+++ all ++   ++l+ DEp  gL+ +  + +   +k+ ++    vi++THS +
  gi|488600659|ref|YP_007907130.1| 127 VRSFSKGMEQRLKIAKALLNDP---DILICDEPSDGLDVRGREFIRNYIKNFNK---TVIISTHSEE 187
                                       678899998888********99...9**************99**********99...********75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00038      0.26      27      41 ..      32      46 ..      17      50 .. 0.81
   2 !    8.4   0.0    0.0019       1.3     161     211 ..     150     198 ..      93     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                                      EEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnll 41
                                       aivG NGSGK+ ll
  gi|488600659|ref|YP_007907130.1| 32 VAIVGVNGSGKTTLL 46
                                      69**********987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0019
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                       + + De    LD + ++ + +++k+ +    +i+ +++ee ++ +d+++g 
  gi|488600659|ref|YP_007907130.1| 150 ILICDEPSDGLDVRGREFIRNYIKNFN--KTVIISTHSEEEIRLCDRVLGF 198
                                       667899999***************999..669**************99986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   7.6e-05     0.052      25      44 ..      31      50 ..      18     115 .. 0.86
   2 ?    4.8   0.0     0.028        19     343     366 ..     166     186 ..     130     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.6e-05
                            AAA_15 25 ltvliGkNnsGKSsileald 44
                                         ++G N+sGK+++l++l 
  gi|488600659|ref|YP_007907130.1| 31 KVAIVGVNGSGKTTLLRILS 50
                                      678**************994 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.028
                            AAA_15 343 vlikllkelandnktQviitTHSp 366
                                       ++i+++++  n+    vii+THS+
  gi|488600659|ref|YP_007907130.1| 166 EFIRNYIKNFNK---TVIISTHSE 186
                                       455555555555...5*******7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.4e-06   0.00098      20     108 ..      31     119 ..      22     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-06
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi..eastiakllkrlkgrarlepgtlliv 94 
                                        ++++G+ G+GKtt+l+ l   ++ + g v ++  +  +  +L++++g+  ++s + + l  +++++ +  ++l+ v
  gi|488600659|ref|YP_007907130.1|  31 KVAIVGVNGSGKTTLLRILSGQIKPSAGYVEIFGKNPYMDVELRKKIGFlsHSSHLYREL--TAKENLIFYAKLMGV 105
                                       57899**************9999999889*******************944455555555..333345556688888 PP

                            AAA_30  95 DEagmvdtkqlaal 108
                                       DE+ +    +l +l
  gi|488600659|ref|YP_007907130.1| 106 DESRVSEVLKLVNL 119
                                       88766655555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.5e-06     0.001      23      63 ..      28      69 ..      13     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      r+e v ++G  G+GK++l+r l  +++ + g++ + gk+   
  gi|488600659|ref|YP_007907130.1| 28 RGEKVAIVGVNGSGKTTLLRILSGQIKPSAGYVeIFGKNPYM 69
                                      336699***********************9999999998877 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     2e-06    0.0013      18      37 ..      30      49 ..      22      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-06
                           DUF3584 18 ghtnieGtNaaGKTtLlrLi 37
                                      +++ i+G+N++GKTtLlr++
  gi|488600659|ref|YP_007907130.1| 30 EKVAIVGVNGSGKTTLLRIL 49
                                      7899**************86 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.5e-05      0.01      21      39 ..      31      49 ..      11      51 .. 0.78
   2 ?   -2.0   0.0       6.2   4.3e+03     153     153 ..     125     125 ..      62     177 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                       ++I+G NG+GKTT+l+ +
  gi|488600659|ref|YP_007907130.1| 31 KVAIVGVNGSGKTTLLRIL 49
                                      569************9865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.2
                            AAA_23 153 e 153
                                       +
  gi|488600659|ref|YP_007907130.1| 125 D 125
                                       1 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.5e-05      0.01      12      39 ..      19      46 ..      17      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      f++  + +++ + + ++G +GsGK+Tll
  gi|488600659|ref|YP_007907130.1| 19 FKDVNFVVKRGEKVAIVGVNGSGKTTLL 46
                                      6666777776669**************8 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00057      0.39       1      73 [.      41     114 ..      25     115 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00057
                                       EEEEEEEEEESEEETTE.EEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGd.evrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G ++l r+ sG++k+   +v+i g n+    e + +i+ l  +   ++e+ a +n  + +++ g++++ +v+++l
  gi|488600659|ref|YP_007907130.1|  41 GKTTLLRILSGQIKPSAgYVEIFGkNPYMDVELRKKIGFLSHSSHLYRELTAKENLIFYAKLMGVDES-RVSEVL 114
                                       45566666666666653266665555554444888888888888888888888888888888888885.887776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   0.00012     0.082       1      22 [.      31      52 ..      31      68 .. 0.83
   2 ?    0.8   0.0      0.76   5.3e+02      54      79 ..     129     154 ..      88     157 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                            AAA_28  1 kivitGgestGKTtlleaLaar 22
                                      k++i+G  ++GKTtll+ L+ +
  gi|488600659|ref|YP_007907130.1| 31 KVAIVGVNGSGKTTLLRILSGQ 52
                                      79*****************954 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.76
                            AAA_28  54 afaervleeqleeeaaa.aankvlfcD 79 
                                        f +++++ +l+ ++a  +++++l+cD
  gi|488600659|ref|YP_007907130.1| 129 SFSKGMEQ-RLKIAKALlNDPDILICD 154
                                       45555554.344433334777777777 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00021      0.15       3      22 ..      30      49 ..      28      71 .. 0.83
   2 ?    1.7   0.0      0.26   1.8e+02     112     134 ..     165     188 ..     159     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                       k++i+G +g+GKTtl++ l
  gi|488600659|ref|YP_007907130.1| 30 EKVAIVGVNGSGKTTLLRIL 49
                                      699*************9877 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.26
                            AAA_24 112 rrllkk.lqelrknvifiahektr 134
                                       r+++++ +++++k+vi+  h++++
  gi|488600659|ref|YP_007907130.1| 165 REFIRNyIKNFNKTVIISTHSEEE 188
                                       5778877*************9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00037      0.25      91     126 ..      20      56 ..       4      98 .. 0.83
   2 ?    2.7   0.0      0.16   1.1e+02       4      39 ..     163     196 ..     160     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                                       HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       ++++ ++k  + +++vG  G GK+tL+  l ++ + +
  gi|488600659|ref|YP_007907130.1|  20 KDVNFVVKRgEKVAIVGVNGSGKTTLLRILSGQIKPS 56 
                                       56667777668999****************9986654 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                                       -S-EETTTTEES--EEEEEEESTTTT--HHHHHHHH CS
                       RsgA_GTPase   4 RknelvrpkvaNvdqllivvslkepelslnlldrfL 39 
                                       R  e++r+ + N ++ +i+++ +e+  + +l dr+L
  gi|488600659|ref|YP_007907130.1| 163 RGREFIRNYIKNFNKTVIISTHSEE--EIRLCDRVL 196
                                       778999************9998855..556677776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.2e-05     0.036       3      23 ..      32      52 ..      30      61 .. 0.85
   2 ?   -1.1   0.0       2.3   1.6e+03      64      88 ..     122     154 ..      87     191 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.2e-05
                                      EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklala 23
                                      v++ G +GsGKTtLl+ l  +
  gi|488600659|ref|YP_007907130.1| 32 VAIVGVNGSGKTTLLRILSGQ 52
                                      89*************987655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                                       S--SSS-C...CHHHHCCSCCCEE.....EEEE CS
                             NACHT  64 epaapvse...vwavllelperlL.....lilD 88 
                                       + ++ v+    +++ +l++++ lL     li D
  gi|488600659|ref|YP_007907130.1| 122 ARNDLVRSfskGMEQRLKIAKALLndpdiLICD 154
                                       444444333335555666666666555544443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00016      0.11       2      66 ..      33     155 ..      32     191 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                                       EEESSTTSSHHHHHHHHHHHHT..HE................................................... CS
                               AAA   2 llyGppGtGKTllakavakelg..ve................................................... 25 
                                        ++G  G GKT+l + +  +++  +                                                    
  gi|488600659|ref|YP_007907130.1|  33 AIVGVNGSGKTTLLRILSGQIKpsAGyveifgknpymdvelrkkigflshsshlyreltakenlifyaklmgvdesr 109
                                       579*****************863322333444444444445555554444444444444444444444444444444 PP

                                       ....EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  26 ....fleisgsellskyvgesekkirelfkeakeka.kpsilfiDE 66 
                                           +  +++ + ++++v   +k +++ +k ak+   +p il+ DE
  gi|488600659|ref|YP_007907130.1| 110 vsevLKLVNLWKARNDLVRSFSKGMEQRLKIAKALLnDPDILICDE 155
                                       4443333344444444666666666666666666666666666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   8.1e-05     0.056       8      99 ..      32     155 ..      27     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.1e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka............ 70 
                                       ++++G  G+GKTtllr l  q          +p+  +v++ +++     +l++++    ++++ +            
  gi|488600659|ref|YP_007907130.1|  32 VAIVGVNGSGKTTLLRILSGQI---------KPSAGYVEIFGKNpyMDVELRKKIGFLSHSSHLYreltakenlify 99 
                                       589***************9998.........5555555555555223333344444444444444444444444555 PP

                            AAA_22  71 ......................erlsseell.ealeqalrarav....ielliiDE 99 
                                                             +r+++ + + + +eq l+ +++    + +li DE
  gi|488600659|ref|YP_007907130.1| 100 aklmgvdesrvsevlklvnlwkARNDLVRSFsKGMEQRLKIAKAllndPDILICDE 155
                                       55555555556666666666665555555555555555555555666666666666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.1   0.00013     0.088       1      21 [.      32      52 ..      32     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      +++ G+ G+GKttl + Ls  
  gi|488600659|ref|YP_007907130.1| 32 VAIVGVNGSGKTTLLRILSGQ 52
                                      689***************654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00022      0.15      21      39 ..      34      52 ..      25      94 .. 0.90
   2 ?   -0.8   0.0      0.65   4.5e+02     550     571 ..     167     186 ..     137     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G NG+GKTtL r+l+ +
  gi|488600659|ref|YP_007907130.1| 34 IVGVNGSGKTTLLRILSGQ 52
                                      679************9976 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                            AAA_13 550 liksrllkkkkakQlfiLTHnl 571
                                       +i++++  k+  k ++i+TH+ 
  gi|488600659|ref|YP_007907130.1| 167 FIRNYI--KNFNKTVIISTHSE 186
                                       566666..44458899999985 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00017      0.12       1      23 [.      31      53 ..      31      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                                      EEEEEESTTSSHHHHHHHHHTST CS
                          MMR_HSR1  1 evaivGrpNvGKStLinaltgek 23
                                      +vaivG   +GK+tL++ l+g+ 
  gi|488600659|ref|YP_007907130.1| 31 KVAIVGVNGSGKTTLLRILSGQI 53
                                      69*****************9973 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.15       4      24 ..      32      52 ..      30      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                      EEEEESTTSSHHHHHHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaal 24
                                      +++vG++G+GKTt l  L+ +
  gi|488600659|ref|YP_007907130.1| 32 VAIVGVNGSGKTTLLRILSGQ 52
                                      789**********98777655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00029       0.2       3      19 ..      33      49 ..      32      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                            AAA_33  3 llvGlpGsGKstlaerl 19
                                       +vG++GsGK+tl++ l
  gi|488600659|ref|YP_007907130.1| 33 AIVGVNGSGKTTLLRIL 49
                                      689**********9866 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0006      0.42      11      35 ..      26      50 ..      17      59 .. 0.83
   2 ?   -3.4   0.0       8.3   5.7e+03     133     149 ..     107     123 ..      96     141 .. 0.61
   3 ?   -1.6   0.0       2.3   1.6e+03      64      81 ..     161     178 ..     159     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0006
                                      .TTEEEEEEEESTTSSHHHHHHHHH CS
                               Arf 11 kkkelrilllGLDnaGKtTilkklk 35
                                      +k+  ++ ++G  ++GKtT+l  l+
  gi|488600659|ref|YP_007907130.1| 26 VKRGEKVAIVGVNGSGKTTLLRILS 50
                                      4677899**************8875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.3
                                       HHHHHHHTTGGGSSSSS CS
                               Arf 133 eeelrellgleelkgkr 149
                                       e+ ++e l+l +l ++r
  gi|488600659|ref|YP_007907130.1| 107 ESRVSEVLKLVNLWKAR 123
                                       45555555555554444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.3
                                       EE-SSGGGGGGGGGGCTT CS
                               Arf  64 DvGGqeklRplWknYfek 81 
                                       Dv G+e +R++ kn+ ++
  gi|488600659|ref|YP_007907130.1| 161 DVRGREFIRNYIKNFNKT 178
                                       777777777777776443 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.13       6      41 ..      21      56 ..      19     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                      HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqsnsd 41
                                      D+ f + +G++++i+g +g Gkt++++ ls q + +
  gi|488600659|ref|YP_007907130.1| 21 DVNFVVKRGEKVAIVGVNGSGKTTLLRILSGQIKPS 56
                                      6668889*******************9999987544 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00038      0.26       3      63 ..      36     100 ..      34     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                                       ESTTSSHHHHHHHHHHHHHHT.TE..EEEESSSTTSHHHHHHHHHHHTCS---HHH..HHHHHHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkee.gik.vvltrepggteiGekirelllkeeeleeqt..eallfaa 63 
                                       G++G+GKtt +++l   +k + g+  ++ + +  + e+++ki  l   +  + e+t  e+l f+a
  gi|488600659|ref|YP_007907130.1|  36 GVNGSGKTTLLRILSGQIKPSaGYVeIFGKNPYMDVELRKKIGFLSHSSHLYRELTakENLIFYA 100
                                       9*************999886515556777778888888888866655555555555555666655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0003      0.21      19      49 ..      32      62 ..      15      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrl 49
                                      + ++G  G+GK++l++ l  ++++  ++v++
  gi|488600659|ref|YP_007907130.1| 32 VAIVGVNGSGKTTLLRILSGQIKPSAGYVEI 62
                                      5578******************999999987 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 ?   10.8   0.1   0.00039      0.27       4      20 ..      33      49 ..      30      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                                      EEEESTTCCHHHHHHHH CS
                              cobW  4 vltGflGsGKTtLlnhl 20
                                       ++G  GsGKTtLl+ l
  gi|488600659|ref|YP_007907130.1| 33 AIVGVNGSGKTTLLRIL 49
                                      699***********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1294.92
//
Query:       gi|488600660|ref|YP_007907131.1|  [L=400]
Description: hypothetical protein Asulf_01138 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-11   42.1   0.0    3.3e-05   23.4   0.1    2.2  2  Amino_oxidase   Flavin containing amine oxidoreductase
    1.3e-09   38.1   0.3    2.5e-09   37.2   0.3    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.3e-05   24.6   0.4      0.006   15.9   0.0    3.0  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0025   17.1   0.8     0.0054   16.0   0.2    1.9  3  FAD_binding_3   FAD binding domain
     0.0051   15.6   0.2       0.05   12.3   0.1    2.0  2  HI0933_like     HI0933-like protein
     0.0075   15.4   0.1      0.041   13.0   0.2    1.9  2  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
      0.037   13.6   0.1       0.86    9.1   0.4    2.1  2  DAO             FAD dependent oxidoreductase
      0.051   13.8   0.1       0.12   12.6   0.1    1.7  1  Minor_capsid_1  Minor capsid protein
       0.14   12.7   3.3        1.6    9.3   0.2    3.0  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.6e-08   3.3e-05       2      68 ..      11      79 ..      10      94 .. 0.89
   2 !   16.7   0.0   1.7e-06    0.0034     126     258 ..      99     231 ..      78     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                                      HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET..TTHHHHHHHHHTTCCCCEE CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg..agnpllellkelgledsls 68
                                       GL  A+ L+++G+ V v+E  +  GGR  +++  G+ i +Ga  + +     pl ++lk++g + + +
  gi|488600660|ref|YP_007907131.1| 11 GGLLSASILSEKGYAVDVYEKLGFYGGRFTSIKYRGFEISTGALHMIPhgRRGPLGKMLKRIGTDVEIV 79
                                      7******************************************99988789999999999999886654 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.7e-06
                                       HHHCCCCHHHHHHHHHCHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTS CS
                     Amino_oxidase 126 qktldeldldskslaesleelgrrepgdvev..wdrliepelfaklefasglfagdpselsaklalpllwelegfgg 200
                                       ++++++ +l+ +++++    +g+++  d ++  +d + +   +++l++++ ++    ++  + +++++ +++  + g
  gi|488600660|ref|YP_007907131.1|  99 SSFPRKTKLKYFKWLIGYKIFGIDRTMDEYAreMDDFTLKFFEKFLGWSLSIY----PDQIKFSDIYEIYKRVLKYG 171
                                       55666667777777777777777777774445566666666666777777776....88889999999998888888 PP

                                       CCCEETTHTHHHHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE CS
                     Amino_oxidase 201 slllprgGlsqlpealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvv 258
                                       +  +p gG + ++  lae  ++ +++i l ++V ++ +e+ +++   +dge+ ++D  ++
  gi|488600660|ref|YP_007907131.1| 172 GPGIPIGGCKKVVTELAEiiKSNDGNIYLKKPVEKLIYENKEIRSLKVDGEEKHYDIFIS 231
                                       88999**************************************999******99997665 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 !   37.2   0.3   1.3e-12   2.5e-09       1      65 [.       5      69 ..       5      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.3e-12
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHH CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrll 65
                                      I+GaGl+Gl+ A+ L+++g+ v+++ek    GGr +s+++ g+ + +ga  + + g+   + ++l
  gi|488600660|ref|YP_007907131.1|  5 IIGAGLGGLLSASILSEKGYAVDVYEKLGFYGGRFTSIKYRGFEISTGALHMIPHGRRGPLGKML 69
                                      9*********************************************9997777666666666655 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 !   15.9   0.0     3e-06     0.006       2      99 ..       2     108 ..       1     115 [. 0.66
   2 ?    2.9   0.0     0.027        53     189     249 ..     187     249 ..     180     257 .. 0.81
   3 ?    2.2   0.1     0.045        89     261     281 ..     354     374 ..     347     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...........HHHHCHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias...........evvkklnqgi 67 
                                       +v++iG+G +Gl  a  l+++g+ v ++e  +  ++gg + s +++g++  +  ++           + +k++++++
  gi|488600660|ref|YP_007907131.1|   2 RVAIIGAGLGGLLSASILSEKGYAVDVYE--KLGFYGGRFTSIKYRGFEISTGALHmiphgrrgplgKMLKRIGTDV 76 
                                       8***************************5..3334555555555555444444444444555556897778888888 PP

                                       CCCHCCT.CEEEEESCEEEEETEEECTCEEEEE CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  68 elllgee.vvkidpgkkkvklekkkegdeekia 99 
                                       e +  ++ +v++ +g+  ++++ ++   ++k++
  gi|488600660|ref|YP_007907131.1|  77 EIVDSKPeGVALQNGE-MIEIRSSSFPRKTKLK 108
                                       8888777777776666.5555444445555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.027
                                       HHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS..HCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                       Pyr_redox_2 189 leealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle..eklg 249
                                       l+e ++ ++ +++l++ v++++ ++++++    dgee  +d  +  +G +  +ell+  +++ 
  gi|488600660|ref|YP_007907131.1| 187 LAEIIKSNDGNIYLKKPVEKLIYENKEIRSLKVDGEEKHYDIFISNIGHSLTRELLGfsRQDV 249
                                       55666777778999999999999999999999999999****************997744444 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.045
                                       -TTSBESSTTEEE-GGGCTEC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 261 deflrtnvpgiyaiGDvaggk 281
                                       d  ++t+  +++++GD a+gk
  gi|488600660|ref|YP_007907131.1| 354 DTGYQTEFRNLFVVGDGAKGK 374
                                       66789***********99544 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   2.7e-06    0.0054       3      32 ..       2      31 ..       1      35 [. 0.89
   2 ?   -3.3   0.0       2.1   4.1e+03      16      48 ..      65      97 ..      65      98 .. 0.79
   3 ?   -3.5   0.0       2.3   4.5e+03     141     165 ..     349     372 ..     338     374 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-06
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                       V+I+GaG+ Gl++a++Lse+G  v + ek
  gi|488600660|ref|YP_007907131.1|  2 RVAIIGAGLGGLLSASILSEKGYAVDVYEK 31
                                      69********************98877776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                      HHHHHHHTTHHEEEEESSSSSCCSSS--EEEHH CS
                     FAD_binding_3 16 lallLseaGvrvvlvekrsttvvlpradglnqr 48
                                      l+++L++ G +v +v+   + v l  +++++ r
  gi|488600660|ref|YP_007907131.1| 65 LGKMLKRIGTDVEIVDSKPEGVALQNGEMIEIR 97
                                      578999999999999999888887777777655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.3
                                       EEEECCTTEEEEEEEEEEEE--GTT CS
                     FAD_binding_3 141 evrdketgeeetvrakYlvGaDGgr 165
                                       ++ +k+tg ++++r  ++vG DG++
  gi|488600660|ref|YP_007907131.1| 349 VMSGKDTGYQTEFRNLFVVG-DGAK 372
                                       55677777777777777777.6665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   2.5e-05      0.05       2      33 ..       2      33 ..       1      41 [. 0.90
   2 ?    1.0   0.0     0.068   1.4e+02     109     153 ..     181     224 ..     176     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +v++iG+G  Gl+ A  ++++g  V ++ek  
  gi|488600660|ref|YP_007907131.1|  2 RVAIIGAGLGGLLSASILSEKGYAVDVYEKLG 33
                                      69***************************965 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEE CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeel 153
                                       +++v+ l + +k+++ +++l++ v+++ +e++++ ++k++ +ee 
  gi|488600660|ref|YP_007907131.1| 181 KKVVTELAEIIKSNDGNIYLKKPVEKLIYENKEIRSLKVD-GEEK 224
                                       789999**************************99999994.4443 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2   2.1e-05     0.041       2      36 ..       3      37 ..       2      43 .. 0.90
   2 ?   -0.3   0.0      0.22   4.3e+02     138     185 ..     178     225 ..     166     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      v +iG+Gl+GL +A  ++e+G  v v ek +  gg
  gi|488600660|ref|YP_007907131.1|  3 VAIIGAGLGGLLSASILSEKGYAVDVYEKLGFYGG 37
                                      89************************999887666 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
                                       .HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTT CS
                     FAD_binding_2 138 vtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesg 185
                                       +  ++++  l+e +++++  ++ + ++++Li+e+++++   v  +e+ 
  gi|488600660|ref|YP_007907131.1| 178 GGCKKVVTELAEIIKSNDGNIYLKKPVEKLIYENKEIRSLKVDGEEKH 225
                                       56678888888999888999***************9999888755444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4   0.00043      0.86       1      29 [.       2      32 ..       2      44 .. 0.90
   2 ?    1.9   0.0     0.066   1.3e+02     146     203 ..     181     236 ..     175     278 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      +v+iiG+G  Gl  A  L+++g  V ++ek 
  gi|488600660|ref|YP_007907131.1|  2 RVAIIGAGLGGLLSASILSEKGyaVDVYEKL 32
                                      59**************************995 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.066
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGG CS
                               DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGaw 203
                                        k++  la+ ++++ ++i+++ +v++l  e++ +  +  + +ge++++d  +   G+ 
  gi|488600660|ref|YP_007907131.1| 181 KKVVTELAEIIKSNDGNIYLKKPVEKLIYENKEIRSL--KVDGEEKHYDIFISNIGHS 236
                                       689999********************84444445555..2335554456666666665 PP

>> Minor_capsid_1  Minor capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.8e-05      0.12      47     104 ..     220     278 ..     193     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                    Minor_capsid_1  47 nskqkkknavif.idkkysspliersvkdavvydGkeyiitkvipvyalsdeifsyEve 104
                                       ++++k+++  i+ i + ++  l  +s +d+v++ G +y i+  +p+++++   f + ve
  gi|488600660|ref|YP_007907131.1| 220 DGEEKHYDIFISnIGHSLTRELLGFSRQDVVESRGIKYSIALKEPFIGHTGICFPFDVE 278
                                       577777776665355678999*****************************999999997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2    0.0008       1.6       1      29 [.       2      30 ..       2      35 .. 0.92
   2 ?    2.3   0.0      0.13   2.5e+02      15      35 ..      66      86 ..      65     101 .. 0.81
   3 ?   -1.1   0.2       1.5   2.9e+03      44      78 ..     185     219 ..     181     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0008
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvve 29
                                      +v+++G+G+ gl  A++l+e g  V v e
  gi|488600660|ref|YP_007907131.1|  2 RVAIIGAGLGGLLSASILSEKGYAVDVYE 30
                                      79********************9998876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                                      HHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox 15 AgalaelgkkVtvversdkll 35
                                      +++l+++g +V +v+ +++  
  gi|488600660|ref|YP_007907131.1| 66 GKMLKRIGTDVEIVDSKPEGV 86
                                      5789***********998755 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedgvesvkl 78 
                                       ++l+e ++ n  +++l++ ve++  ++++++s+k+
  gi|488600660|ref|YP_007907131.1| 185 TELAEIIKSNDGNIYLKKPVEKLIYENKEIRSLKV 219
                                       67778888888889999999999888887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2450.33
//
Query:       gi|488600661|ref|YP_007907132.1|  [L=53]
Description: hypothetical protein Asulf_01139 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-13   48.9  14.2    1.1e-06   28.2   3.4    2.0  2  Fer4      4Fe-4S binding domain
    1.1e-11   44.3  13.6    9.1e-06   25.5   3.2    2.0  2  Fer4_6    4Fe-4S binding domain
    1.5e-09   37.4   9.8    2.2e-05   24.3   1.5    2.1  2  Fer4_2    4Fe-4S binding domain
    6.3e-09   35.8  11.5    3.9e-05   23.7   2.2    2.0  2  Fer4_21   4Fe-4S dicluster domain
    4.6e-08   33.5  12.0    1.2e-07   32.2  12.0    1.6  1  Fer4_7    4Fe-4S dicluster domain
    1.3e-07   31.6  23.4    1.4e-05   25.1  12.3    2.0  2  Fer4_10   4Fe-4S dicluster domain
    6.3e-07   29.5  10.0    9.7e-07   28.9  10.0    1.3  1  Fer4_9    4Fe-4S dicluster domain
      2e-06   27.9  13.8    0.00038   20.7   2.0    2.1  2  Fer4_4    4Fe-4S binding domain
    9.4e-06   26.5  10.6     0.0066   17.4   3.4    2.1  3  Fer4_16   4Fe-4S double cluster binding domain
    0.00038   21.0   8.5      0.043   14.4   1.6    2.2  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00056   20.7  14.1      0.036   15.0   4.0    2.4  2  Fer4_3    4Fe-4S binding domain
     0.0015   18.9  12.9        1.3    9.5  12.9    2.0  1  Fer4_8    4Fe-4S dicluster domain
     0.0062   17.0  13.2       0.13   12.8   2.0    2.1  2  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.074   13.8  11.1       0.34   11.7   1.6    2.2  2  Fer4_15   4Fe-4S single cluster domain
       0.18   12.6  11.0       0.85   10.5   2.3    2.0  2  Fer4_22   4Fe-4S dicluster domain
        0.4   10.9  10.4        3.1    8.0  10.4    1.9  1  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   3.1   2.4e-09   2.7e-06       3      23 ..       3      23 ..       1      24 [. 0.90
   2 !   28.2   3.4   9.6e-10   1.1e-06       2      23 ..      30      51 ..      29      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.4e-09
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      +  e+C+gC  C+ +CP++A 
  gi|488600661|ref|YP_007907132.1|  3 VKAERCVGCAFCMLICPYDAV 23
                                      678*****************7 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 9.6e-10
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      +ideekC +C +Cv  CP  AI
  gi|488600661|ref|YP_007907132.1| 30 EIDEEKCKACLKCVYYCPKSAI 51
                                      79*****************999 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   3.2   8.1e-09   9.1e-06       3      23 ..       2      22 ..       1      23 [. 0.93
   2 !   24.8   2.8   1.4e-08   1.5e-05       1      24 []      28      51 ..      28      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8.1e-09
                            Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                      e+++++C+gC  C+ +CP++a
  gi|488600661|ref|YP_007907132.1|  2 EVKAERCVGCAFCMLICPYDA 22
                                      899****************98 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.4e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++eid++kC  C +Cv  CP  ai
  gi|488600661|ref|YP_007907132.1| 28 KAEIDEEKCKACLKCVYYCPKSAI 51
                                      689*****************9998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.5   1.5e-06    0.0017       4      22 .]       2      20 ..       1      20 [. 0.90
   2 !   24.3   1.5     2e-08   2.2e-05       2      21 ..      28      47 ..      27      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                      +v ++rC+gC  C   CP+
  gi|488600661|ref|YP_007907132.1|  2 EVKAERCVGCAFCMLICPY 20
                                      5789**************5 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2e-08
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++++d+++C +C +Cv  CP
  gi|488600661|ref|YP_007907132.1| 28 KAEIDEEKCKACLKCVYYCP 47
                                      5789***************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 !   23.7   2.2   3.5e-08   3.9e-05      35      58 ..       2      24 ..       1      25 [. 0.86
   2 !   17.8   2.0   2.4e-06    0.0027       1      22 [.      29      50 ..      28      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.5e-08
                           Fer4_21 35 kvvedeCvGCnlCssvCPvedcie 58
                                      +v +++CvGC+ C+ +CP  d+++
  gi|488600661|ref|YP_007907132.1|  2 EVKAERCVGCAFCMLICPY-DAVK 24
                                      6889**************6.8776 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.4e-06
                           Fer4_21  1 AridedkCigCgkCliaCedts 22
                                      A ide+kC  C kC+  C++++
  gi|488600661|ref|YP_007907132.1| 29 AEIDEEKCKACLKCVYYCPKSA 50
                                      7788888888888888888765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2  12.0     1e-10   1.2e-07       1      52 []       7      50 ..       7      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      rC+gC +C+  Cp++a+++          k+eid+ekC  C +Cv  CP+ a
  gi|488600661|ref|YP_007907132.1|  7 RCVGCAFCMLICPYDAVKVFG--------KAEIDEEKCKACLKCVYYCPKSA 50
                                      8*****************965........589*****************976 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1  12.3   1.2e-08   1.4e-05       4      56 .]       3      47 ..       1      47 [. 0.80
   2 !   17.3   3.2   3.4e-06    0.0038       2      21 ..      29      48 ..      28      53 .] 0.87

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-08
                           Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + +++C++C+ C+  CP+        ++ +  ++ +++ ekC +c +Cv  CP
  gi|488600661|ref|YP_007907132.1|  3 VKAERCVGCAFCMLICPY--------DAVKVFGKAEIDEEKCKACLKCVYYCP 47
                                      6789**************........455555555555578***********9 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.4e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                      ++id+++C  C kCv  CP 
  gi|488600661|ref|YP_007907132.1| 29 AEIDEEKCKACLKCVYYCPK 48
                                      789****************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 !   28.9  10.0   8.7e-10   9.7e-07       1      51 []       7      51 ..       7      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 8.7e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C+gC  C+  Cp+++v+   ++++++       +C  C +Cv  Cpk ai
  gi|488600661|ref|YP_007907132.1|  7 RCVGCAFCMLICPYDAVKVFGKAEIDEE------KCKACLKCVYYCPKSAI 51
                                      6***********************9996......7*************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 !   20.7   2.0   3.4e-07   0.00038       2      16 ..       6      20 ..       5      22 .. 0.92
   2 !   12.8   4.3   0.00012      0.13       2      15 ..      34      47 ..      33      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.4e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      erC+gC  C+ +CP+
  gi|488600661|ref|YP_007907132.1|  6 ERCVGCAFCMLICPY 20
                                      9*************8 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00012
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e+C  C +Cv++CP
  gi|488600661|ref|YP_007907132.1| 34 EKCKACLKCVYYCP 47
                                      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 !   14.1   1.6   6.3e-05     0.071      50      66 ..       4      20 ..       2      21 .. 0.85
   2 !   17.4   3.4   5.9e-06    0.0066       1      31 [.       7      37 ..       7      38 .. 0.93
   3 !   15.1   2.7   2.9e-05     0.033       1      18 [.      35      52 ..      35      53 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-05
                           Fer4_16 50 kqeaitgCdiCqdvCPa 66
                                      k+e++ gC+ C+ +CP+
  gi|488600661|ref|YP_007907132.1|  4 KAERCVGCAFCMLICPY 20
                                      56899***********8 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 5.9e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeieareci 31
                                      rC++C  C+ +CP +a+k   ++ei+ ++c+
  gi|488600661|ref|YP_007907132.1|  7 RCVGCAFCMLICPYDAVKVFGKAEIDEEKCK 37
                                      6*****************9999999999996 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.9e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C+ C kC+  CP +ai 
  gi|488600661|ref|YP_007907132.1| 35 KCKACLKCVYYCPKSAIG 52
                                      6***************97 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.8    0.0004      0.45       3      17 ..       5      19 ..       3      27 .. 0.91
   2 !   14.4   1.6   3.8e-05     0.043       1      18 [.      31      48 ..      31      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                           Fer4_13  3 rdtCiacgaCvelaP 17
                                       ++C++c+ C  ++P
  gi|488600661|ref|YP_007907132.1|  5 AERCVGCAFCMLICP 19
                                      589***********9 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.8e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +D+++C ac +Cv  +P+
  gi|488600661|ref|YP_007907132.1| 31 IDEEKCKACLKCVYYCPK 48
                                      8****************7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   4.0   3.2e-05     0.036       1      15 []       8      22 ..       8      22 .. 0.95
   2 !   11.1   2.4   0.00057      0.64       1      15 []      36      50 ..      35      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gC  C+  CP++A
  gi|488600661|ref|YP_007907132.1|  8 CVGCAFCMLICPYDA 22
                                      ****88*******98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00057
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C  C  Cv  CP+ A
  gi|488600661|ref|YP_007907132.1| 36 CKACLKCVYYCPKSA 50
                                      777889******977 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5  12.9    0.0012       1.3       2      64 ..       5      49 ..       4      50 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      +e+C++C +C+  Cp + + k +     g+a+      ++       ++C +c +C+  Cp++
  gi|488600661|ref|YP_007907132.1|  5 AERCVGCAFCMLICP-YDAVKVF-----GKAEI-----DE-------EKCKACLKCVYYCPKS 49
                                      789***********9.3333333.....33333.....23.......4699999999999986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   2.0   0.00012      0.13      42      59 ..       4      21 ..       1      23 [. 0.76
   2 !   10.4   3.6   0.00067      0.75      44      58 ..      34      48 ..      23      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                      ka++C++C  C   CP++
  gi|488600661|ref|YP_007907132.1|  4 KAERCVGCAFCMLICPYD 21
                                      678888888888888876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00067
                           Fer4_17 44 slCieCgeCerkCPq 58
                                      ++C  C +C+++CP+
  gi|488600661|ref|YP_007907132.1| 34 EKCKACLKCVYYCPK 48
                                      68************8 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.4    0.0048       5.4       5      19 ..       5      19 ..       1      30 [. 0.81
   2 ?   11.7   1.6    0.0003      0.34       2      20 ..      30      48 ..      29      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0048
                           Fer4_15  5 rdaCigcglCvaeap 19
                                       ++C gc+ C+  +p
  gi|488600661|ref|YP_007907132.1|  5 AERCVGCAFCMLICP 19
                                      689*********997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      ++D+++C  c  Cv  +p+
  gi|488600661|ref|YP_007907132.1| 30 EIDEEKCKACLKCVYYCPK 48
                                      69***************97 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.3   0.00076      0.85      78      94 ..       4      20 ..       1      22 [. 0.77
   2 ?    8.4   1.2    0.0036         4      76      94 ..      30      48 ..      20      50 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00076
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      +++ CvGC  C+  cp 
  gi|488600661|ref|YP_007907132.1|  4 KAERCVGCAFCMLICPY 20
                                      56789999999999885 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0036
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                      +++e++C  C +C+  cp+
  gi|488600661|ref|YP_007907132.1| 30 EIDEEKCKACLKCVYYCPK 48
                                      5677788888888888876 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  10.4    0.0028       3.1      58      96 ..       5      47 ..       1      49 [. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0028
                           Fer4_18 58 agdcidcescvkvcPtg.idirkGlql...eciscllcidacd 96
                                      a  c+ c +c+ +cP + + +     +   +c +cl+c+  c 
  gi|488600661|ref|YP_007907132.1|  5 AERCVGCAFCMLICPYDaVKVFGKAEIdeeKCKACLKCVYYCP 47
                                      567************8525554444442227*******99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); 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 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 331.33
//
Query:       gi|488600662|ref|YP_007907133.1|  [L=341]
Description: putative butyrate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-98  327.7   0.1    8.5e-98  327.5   0.1    1.0  1  DUF1464   Protein of unknown function (DUF1464)


Domain annotation for each model (and alignments):
>> DUF1464  Protein of unknown function (DUF1464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.5   0.1  4.7e-102   8.5e-98       1     326 [.       5     328 ..       5     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: 327.5 bits;  conditional E-value: 4.7e-102
                           DUF1464   1 GiDPGtksydvvvvddlgkvvlekeiptdevekdpsvlvkaieearadivalpSGyGlPlkriselaereillltla 77 
                                       GiDPGt+sy++  ++d  +   + ei t+ v++dp+++ k+ ++ ++d+ a++SGyGlP+kr+sel+e++i+l+tl+
  gi|488600662|ref|YP_007907133.1|   5 GIDPGTSSYEIFILED-SEPHDRIEIETSAVREDPESVKKIFADLEVDVYAGLSGYGLPFKRFSELDEKDIFLMTLN 80 
                                       9***************.77899******************************************************* PP

                           DUF1464  78 eeseeglvGLrellkelaskelnaftiPgVieLptvPewRKvnkiDmGtADKlasavlavadeaeeeeyrelsFilv 154
                                       +++e++ +G+r+l+    + +l+ +tiP+Vi+LptvPe+RK+nkiDmGtADKl+s+vla+++    e+  +++Filv
  gi|488600662|ref|YP_007907133.1|  81 KDEEKA-IGMRSLIDVAIKLDLEIYTIPAVIHLPTVPEYRKINKIDMGTADKLCSVVLALYS---CEDVGTADFILV 153
                                       **9988.8*******8788899************************************8875...5799******** PP

                           DUF1464 155 EvGsgfnaviaVknGkivDGlGgti.lpGflsaGalDgEvAyllgkvakiekslifsgGvasiagea..elekklse 228
                                       E G+gfna+i V  Gki+DGlGg++ +p f+s+Ga+DgE+Ayllg    + k+l+fsgG++s    +  +++  +se
  gi|488600662|ref|YP_007907133.1| 154 ESGYGFNAFISVSRGKIIDGLGGSSsFPAFSSLGAMDGELAYLLG---DFPKRLLFSGGIKSYLHDMgiQVNS-ISE 226
                                       ************************99*******************...*************999998544443.333 PP

                           DUF1464 229 e...aferlke.vvksvaellsskykleeiivSGrlkrikelgkklesrleev..kllelaskaKeaaqGaAiiana 299
                                           ++  l e ++k v+++ +++   + i++SGr++  ++++k + +  e++  + le+++ +K++a GaAiian+
  gi|488600662|ref|YP_007907133.1| 227 MpedSLVWLAEyLLKGVRAVNVQN--TDRILMSGRNFLNSRFRKIFVEMAEDFtcERLEGFGISKQSAEGAAIIANG 301
                                       346688999999*******99998..666*********************9*944445567899************* PP

                           DUF1464 300 laGgryrelvdhleiekssgtvldyvk 326
                                       +aGg+y++lv hle++k+sg+vldy++
  gi|488600662|ref|YP_007907133.1| 302 IAGGEYKHLVTHLELDKASGSVLDYIT 328
                                       *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2402.00
//
Query:       gi|488600663|ref|YP_007907134.1|  [L=773]
Description: pyruvate formate-lyase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-195  649.5   0.0   7.6e-195  649.3   0.0    1.0  1  PFL-like     Pyruvate formate lyase-like
    8.3e-25   87.4   0.0      5e-24   84.9   0.0    2.4  2  Gly_radical  Glycine radical


Domain annotation for each model (and alignments):
>> PFL-like  Pyruvate formate lyase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  649.3   0.0  8.4e-199  7.6e-195       3     647 .]       2     636 ..       1     636 [. 0.98

  Alignments for each domain:
  == domain 1  score: 649.3 bits;  conditional E-value: 8.4e-199
                                       HHHHHHHHCC.HT.TS.E.EESHHHHHHHHHHHHCTTS-HHHHHHHHHHHHHHHS-----TT-SS---SSSSTTEEE CS
                          PFL-like   3 erierlkknytlyeakps.lelerarllteseketegepvdirrakalakilsnlplyIrddElIvGsqtkkprkra 78 
                                       +r+++l  n+    +kp  l++er+ l+tes+ketegep++ir+akal++il+n p+ I ++E++vG++  +p ++ 
  gi|488600663|ref|YP_007907134.1|   2 DRVNKLITNI----QKPPrLSIERCVLYTESMKETEGEPMPIRQAKALKHILENIPVQILPHEIVVGTMLPDPPGAI 74 
                                       5778888888....55666********************************************************** PP

                                       --TTTTCHHHHTTTTTCCCSSSSTEBEECHHHHHHHH.HHHHHTTTSHHHHHHHHCHHTTHHHHTSTSEE--CHGGS CS
                          PFL-like  79 ifPegsirmledeldtlaereadgfeideeekkilre.ifpyWkgktvnegvfdayteetkaaresgiitvglpdas 154
                                       +fPeg    + +el+ l++re ++  ++ee+++ilre i+pyW+ +++++ + + ++e ++ ++  +++   l +++
  gi|488600663|ref|YP_007907134.1|  75 LFPEGVGLRIINELESLPSRETNRLIVREEDARILREeIAPYWQSRNIEAFASQLMPEIIEVLYTGSVFV--LTEFA 149
                                       ******999***********************************************99999999999999..9**** PP

                                       SCEEEE--HHHHHTCHHHHHHHHHHHHHHHHCCTTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-SHH CS
                          PFL-like 155 grGhiipdyervlkyGldglieeikeklakldlddpeaiekaefykaviisleavieyaeryarlaeelaeqetdpk 231
                                       g +hi+++y+ +lk+G++ +iee +++  +l+ +++ +  k  fyk  +i+ ea+i ya+rya+lae++a++ +d +
  gi|488600663|ref|YP_007907134.1| 150 GISHIAVNYPYLLKRGFRWFIEESRRNVVELEDNGCWDAPKLVFYKTAEIVSEAMISYANRYAKLAEKMADE-ADDE 225
                                       **********************************************************************99.9*** PP

                                       HHHHHHHHHHHHHHTTTS--SSHHHHHHHHHHHHHHHHHHSSCCEEE-BSHHHHTHHHHHHHHHTTSS-HHHHHHHH CS
                          PFL-like 232 rkaeLleiaevcgrvpskpaetfqEAiQlvwfvhlalvkesngaamslgRldqylypyyekDleeGrlteeeaqeli 308
                                       r++eLl+iae+c+rvp++++e+f+EA+Q+vwfv+ al++e+ ++++s+gR+dqyl pyy kDl+eGr+++++a e++
  gi|488600663|ref|YP_007907134.1| 226 RREELLRIAEICRRVPAEKPESFHEAVQFVWFVQSALHQENYEQGISMGRIDQYLLPYYLKDLKEGRIDRKQAFEIL 302
                                       ***************************************************************************** PP

                                       HHHHHHHTTB-----HHHHCCCTTT----EEEEESB-TTSSB---HHHHHHHHHHHHH--SSSEEEEEE-TTS-HHH CS
                          PFL-like 309 dclwlklrevrklrseeyaelfagydpfqnltvGGqnedGrdavnelsyliLealenlklpePnlsvrvskklpeef 385
                                        +lw+k++e+    ++  + +f+g  + q lt+GG++++G+da+n+lsyl+Le+++ ++l +Pn++vrvs+k+p++f
  gi|488600663|ref|YP_007907134.1| 303 ANLWIKTNEIVPPFDSLLELYFSGQATNQALTIGGIDANGNDATNDLSYLMLEVTKAVPLRQPNVHVRVSSKTPDSF 379
                                       ************************999************************************************** PP

                                       HHHHHHHHHTTS--CEEEEHHHHHHHHHHTT--HHHHHTEEEETTTEEEECCCEES-S.SEEEECHHHHHHHHTTTC CS
                          PFL-like 386 lkkaaevsrkGlgspayenddviipallnrgvsledArdyaiaGCvepqipGkeeqff.aarinlakaLelalnnGr 461
                                       l+  a+++ +G + + ++nd+vi++al+++gv++ed  +y  +GCve+  +G++ +   aa inlakaLe+aln+G 
  gi|488600663|ref|YP_007907134.1| 380 LDVLADLIAEGKNNIGIFNDEVIFKALRSAGVEEEDLWNYSTVGCVEIAPFGNSFTSSdAALINLAKALEYALNEGT 456
                                       ****************************************************999999******************* PP

                                       ETTTTCB-S-----GGG--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--HHHHHTSTTHHHHT--GGGT- CS
                          PFL-like 462 dektgkqvgpktgdvtefksyeelmeafkkqleylvklyvealniihymhdkyapepllsalvddciergkdlgegG 538
                                       d + g ++g ++++    +s+ee+++af+kql++++k +v++ ni +y+ + + p+plls++++dc+e+g d++ gG
  gi|488600663|ref|YP_007907134.1| 457 DIMFGYRFGLEIKK---PESLEEVIDAFRKQLAHIIKKVVKGSNILEYANASVKPTPLLSLCIEDCFEKGVDVTLGG 530
                                       **********8876...579********************************************************* PP

                                       SSEECEEEEEE-HHHHHHHHHHHHHHHTTSTSS-HHHHHHHHHTTTTT-HHHHHHHHHS--TTSS-HHHHHHHHHHH CS
                          PFL-like 539 arynfsgpqgvGlanvaDSLsAIkklVFddkkvtleeLkealaanFegeeelrqlllnaPkYGndddevDeiakevv 615
                                       a+ynf+g+q+vG+a+vaDSL+AI  ++  +k ++l+e+ ea++ nF+g+eelr+lllnaPkYGnd + +D+ ak v 
  gi|488600663|ref|YP_007907134.1| 531 AKYNFTGIQAVGIADVADSLAAIELAI--KKGYSLDEIIEACRSNFNGYEELRSLLLNAPKYGNDSE-ADRYAKLVL 604
                                       *************************99..9**********************************976.********* PP

                                       HHHHHHHCTSB-TTSCEEEEEE--TTTHHHHH CS
                          PFL-like 616 etfaeevkkyknyrggkftaslltissnvpyg 647
                                       e ++eev +y+n rgg+fta+++++++nv +g
  gi|488600663|ref|YP_007907134.1| 605 EMYCEEVSRYRNFRGGRFTAGCYPMTTNVAFG 636
                                       ******************************98 PP

>> Gly_radical  Glycine radical
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.68   6.1e+03      79      99 ..     352     372 ..     296     372 .. 0.62
   2 !   84.9   0.0   5.6e-28     5e-24       2     106 .]     653     755 ..     652     755 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.68
                                       CCHCCCCCSCGGGCCEEEESS CS
                       Gly_radical  79 etLldAqehpekypqltiRVs 99 
                                        +L+   + p  +p++ +RVs
  gi|488600663|ref|YP_007907134.1| 352 LMLEVTKAVPLRQPNVHVRVS 372
                                       566677777888899999997 PP

  == domain 2  score: 84.9 bits;  conditional E-value: 5.6e-28
                                       TSTTSHHCCHHHCHCHHCCCCCCTSECGCETTEETTECCCCHHHHHHHCC-CCCCCCHHCCCCCC.T-SECEEEEET CS
                       Gly_radical   2 apganpmegrdkegplaslnSvakldyevaldgislnlkavpdalgkeeeerienlatlldgyfe.ggfhlnvnvvs 77 
                                       + g++p+ g+d+eg +a+++S+ kl+ye  ++g sl++++   +l   + ++ + +++l++++++ gg+h+++nv++
  gi|488600663|ref|YP_007907134.1| 653 NSGVSPSTGMDREGVTAAIKSACKLNYEMLSNGSSLTVNLDSGIL---GAKGKDVIKALIRSFVDlGGMHIQFNVLN 726
                                       579******************************************...888899999*******66*********** PP

                                       CCCHCCCCCSCGGGCCEEEESSSSEEECC CS
                       Gly_radical  78 retLldAqehpekypqltiRVsGYavnFv 106
                                       ++ L++Aqe+peky+ l++RV+G++++Fv
  gi|488600663|ref|YP_007907134.1| 727 QDLLKKAQEEPEKYRWLLVRVAGWSAYFV 755
                                       ****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 4632.05
//
Query:       gi|488600664|ref|YP_007907135.1|  [L=299]
Description: glycyl-radical enzyme activating protein family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   92.5   0.1    8.3e-26   91.3   0.1    1.6  1  Radical_SAM  Radical SAM superfamily
    1.2e-16   61.2   3.1    3.6e-14   53.2   1.9    3.2  2  Fer4_12      4Fe-4S single cluster domain
    8.6e-12   44.4   9.4    5.2e-06   26.0   2.2    2.4  2  Fer4         4Fe-4S binding domain
      5e-08   32.7  11.3    1.4e-05   24.9   1.8    2.5  2  Fer4_6       4Fe-4S binding domain
    1.2e-05   25.3   9.1    2.5e-05   24.3   9.1    1.6  1  Fer4_10      4Fe-4S dicluster domain
    1.7e-05   24.9   5.1      0.017   15.2   0.0    2.5  2  Fer4_14      4Fe-4S single cluster domain
    4.1e-05   23.4  20.8    0.00029   20.7   2.9    3.1  3  Fer4_2       4Fe-4S binding domain
    0.00026   21.5  16.8     0.0018   18.8  14.1    2.4  3  Fer4_7       4Fe-4S dicluster domain
    0.00037   20.6  12.6    0.00037   20.6  12.6    2.3  2  Fer4_9       4Fe-4S dicluster domain
    0.00052   20.9   7.1      0.048   14.6   0.1    2.5  2  Fer4_16      4Fe-4S double cluster binding domain
     0.0013   18.8  11.0     0.0013   18.8  11.0    1.9  2  Fer4_21      4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   16.1   8.2      0.023   15.4   0.5    2.5  2  Fer4_15      4Fe-4S single cluster domain
      0.024   15.1  11.4      0.066   13.7   0.1    2.5  2  Fer4_8       4Fe-4S dicluster domain
      0.033   14.7   0.9      0.033   14.7   0.9    2.9  2  Fer4_4       4Fe-4S binding domain
       0.17   12.4  12.1       0.43   11.2   2.1    2.5  3  Fer4_17      4Fe-4S dicluster domain
        1.5   10.0  22.3       0.47   11.5   6.2    2.8  2  Fer4_3       4Fe-4S binding domain
        1.5    9.7  13.5        3.1    8.7   2.1    2.6  2  Fer4_22      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.1   7.9e-29   8.3e-26       2     159 ..      23     229 ..      22     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 7.9e-29
                                       EEESEESS--TTTSCCTT.......................................................HHHH CS
                                       xxxxxxxxxxxxxxxxxx.......................................................xxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.......................................................vrre 23 
                                       v+++gC+lrC++C++pe+                                                        +  
  gi|488600664|ref|YP_007907135.1|  23 VFLKGCPLRCVWCHNPESqrfdidlayredmctgclscievcerdallwegervsvnsdlcngcgacvencsnNALI 99 
                                       799************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  24 grgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerll 98 
                                        +g+++  e++++ev++   ++++  ++v+++ggep ++ df  +l+rl+++  +gi+++v t+g++  +e +e+ l
  gi|488600664|ref|YP_007907135.1| 100 LYGYDIEAEDVIREVEKDLiFYRNsSGGVTFSGGEPYFQTDFLLELLRLCRE--RGISTAVDTSGYTR-WENIEKSL 173
                                       *******************999999***************************..7************6.******** PP

                                       HTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  99 elgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                                       +l  d +  +l+ +d+ ++l+ +  g ++  +le+lekl +   + vv+ri+ +p  n++ 
  gi|488600664|ref|YP_007907135.1| 174 NLV-DLFLYDLKDYDSQRHLRFT--GVDNRTILENLEKLVKT-AE-VVVRIPFIPSCNFQS 229
                                       *99.*************999999..499**************.89.9********888764 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 !   53.2   1.9   3.4e-17   3.6e-14       2     101 ..      15     171 ..      14     183 .. 0.89
   2 ?    4.0   0.0     0.052        55      81     123 ..     185     225 ..     173     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3.4e-17
                           Fer4_12   2 nGeGvrlslfvsgCnlsCkgCfnketwsfk............................................... 31 
                                       +G G+r+++f++gC+l+C  C+n+e ++f+                                               
  gi|488600664|ref|YP_007907135.1|  15 DGYGIRTTVFLKGCPLRCVWCHNPESQRFDidlayredmctgclscievcerdallwegervsvnsdlcngcgacve 91 
                                       799************************************************************************** PP

                           Fer4_12  32 .........sgkeft.kelleeiiedlkk..esiegltllGGEPllpenaeallelvkevkeekpekdiwlytgyt. 95 
                                                +g +++ +++++e+ +dl    +s  g+t++GGEP    +++ llel++ ++e+++  + + ++gyt 
  gi|488600664|ref|YP_007907135.1|  92 ncsnnalilYGYDIEaEDVIREVEKDLIFyrNSSGGVTFSGGEPYF--QTDFLLELLRLCRERGI-STAVDTSGYTr 165
                                       *********88888768888888888875226669***********..*****************.58999999974 PP

                           Fer4_12  96 leelsk 101
                                       +e+++k
  gi|488600664|ref|YP_007907135.1| 166 WENIEK 171
                                       666653 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.052
                           Fer4_12  81 eekpekdiwlytgytleelskkekeellkeidvlvdGkfeesl 123
                                          + + ++ +tg+ + +++++  e+l+k  +v+v  +f  s 
  gi|488600664|ref|YP_007907135.1| 185 DYDS-QRHLRFTGVDNRTILEN-LEKLVKTAEVVVRIPFIPSC 225
                                       4444.68999*********985.************99998665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.8   6.6e-08     7e-05       4      23 ..      50      69 ..      47      70 .. 0.91
   2 !   26.0   2.2   4.9e-09   5.2e-06       2      23 ..      77      98 ..      76      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.6e-08
                                      ETTTSSS-THHHHHSTTTEE CS
                              Fer4  4 deekCigCGaCvevCPvgAI 23
                                       e++C+gC  C+evC  +A+
  gi|488600664|ref|YP_007907135.1| 50 REDMCTGCLSCIEVCERDAL 69
                                      58**************9997 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 4.9e-09
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       ++ ++C gCGaCve C ++A+
  gi|488600664|ref|YP_007907135.1| 77 SVNSDLCNGCGACVENCSNNAL 98
                                      699****************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 !   12.3   2.3   0.00013      0.13       6      23 ..      51      68 ..      48      69 .. 0.87
   2 !   24.9   1.8   1.3e-08   1.4e-05       2      24 .]      76      98 ..      75      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                            Fer4_6  6 pdkCigCgdCvrvCPega 23
                                      +d C+gC  C+ vC  +a
  gi|488600664|ref|YP_007907135.1| 51 EDMCTGCLSCIEVCERDA 68
                                      89************8777 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.3e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      v ++ d+C+gCg+Cv +C  +a+
  gi|488600664|ref|YP_007907135.1| 76 VSVNSDLCNGCGACVENCSNNAL 98
                                      789***************98886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   9.1   2.4e-08   2.5e-05       5      55 ..      50      93 ..      46      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.4e-08
                           Fer4_10  5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                       +d C++C  C ++C       +  +  +e+e+v+++++ C gcgaCve C
  gi|488600664|ref|YP_007907135.1| 50 REDMCTGCLSCIEVC-------ERDALLWEGERVSVNSDLCNGCGACVENC 93
                                      6799***********.......6999************************* 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 !    9.3   2.8    0.0011       1.2       2      33 ..      24      53 ..      22      68 .. 0.84
   2 !   15.2   0.0   1.7e-05     0.017      26      91 ..     103     164 ..      78     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                           Fer4_14  2 fvrlsgCnlsCkgCdnketwkselgkpqteel 33
                                      f  l gC+l C++C n e+++++    + e++
  gi|488600664|ref|YP_007907135.1| 24 F--LKGCPLRCVWCHNPESQRFDIDLAYREDM 53
                                      4..49*************99998887777766 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.7e-05
                           Fer4_14  26 gkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtl 91 
                                         +++e+++ ++ kdl  ++ +  g++++GGeP    +++ ll+l++  +e++  ++  + t+g  
  gi|488600664|ref|YP_007907135.1| 103 YDIEAEDVIREVEKDLIFYRNSSGGVTFSGGEPY--FQTDFLLELLRLCRERG--ISTAVDTSGYT 164
                                       3344444554444466666666789********9..689*************9..66666665544 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.1       4.9   5.2e+03       8      13 ..      30      35 ..      27      37 .. 0.75
   2 !   14.4   2.3   2.8e-05      0.03       6      20 ..      50      64 ..      46      65 .. 0.89
   3 !   20.7   2.9   2.8e-07   0.00029       2      20 ..      75      93 ..      74      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.9
                            Fer4_2  8 drCigC 13
                                       rC+ C
  gi|488600664|ref|YP_007907135.1| 30 LRCVWC 35
                                      589888 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.8e-05
                            Fer4_2  6 dtdrCigCgaCvsaC 20
                                       +d+C+gC +C+ +C
  gi|488600664|ref|YP_007907135.1| 50 REDMCTGCLSCIEVC 64
                                      589************ PP

  == domain 3  score: 20.7 bits;  conditional E-value: 2.8e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                      +v v++d C+gCgaCv +C
  gi|488600664|ref|YP_007907135.1| 75 RVSVNSDLCNGCGACVENC 93
                                      6889*************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   6.6   0.00076       0.8      12      52 .]      28      68 ..      25      68 .. 0.71
   2 !   18.8  14.1   1.7e-06    0.0018       2      52 .]      54      97 ..      53      97 .. 0.92
   3 !   15.4   3.1     2e-05     0.021       2      18 ..      83      99 ..      82     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00076
                            Fer4_7 12 CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      Cp +++  ++ e+++   ++++++++C+gC +C++vC  +a
  gi|488600664|ref|YP_007907135.1| 28 CPLRCVWCHNPESQRFDIDLAYREDMCTGCLSCIEVCERDA 68
                                      666666555554444445678899*************8765 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.7e-06
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+gC  C ++C  +a+ ++ e       +v ++++ C gCgaCv+ C  +a
  gi|488600664|ref|YP_007907135.1| 54 CTGCLSCIEVCERDALLWEGE-------RVSVNSDLCNGCGACVENCSNNA 97
                                      ******************664.......79*****************8876 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2e-05
                            Fer4_7  2 CigCgaCvaaCpvkaie 18
                                      C gCgaCv++C+++a+ 
  gi|488600664|ref|YP_007907135.1| 83 CNGCGACVENCSNNALI 99
                                      ************99975 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   6.4   0.00033      0.35      26      50 ..      44      68 ..      25      69 .. 0.62
   2 !   20.6  12.6   3.5e-07   0.00037       2      50 ..      54      97 ..      53      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                            Fer4_9 26 arlraaseeaCigCgaCveaCpkga 50
                                      +   a++e+ C+gC +C+e+C+++a
  gi|488600664|ref|YP_007907135.1| 44 DIDLAYREDMCTGCLSCIEVCERDA 68
                                      2222334458************997 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.5e-07
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      CtgC +C+e+C+ ++   +  +  ++ +      C gCgaCve C ++a
  gi|488600664|ref|YP_007907135.1| 54 CTGCLSCIEVCERDALLWEGERVSVNSD-----LCNGCGACVENCSNNA 97
                                      **************99998888888874.....5***********9986 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 !    7.8   3.0    0.0058       6.2       2      17 ..      54      69 ..      28      80 .. 0.78
   2 !   14.6   0.1   4.5e-05     0.048       2      29 ..      83     109 ..      82     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0058
                           Fer4_16  2 CgtCgkCaevCPtnai 17
                                      C++C  C+evC  +a+
  gi|488600664|ref|YP_007907135.1| 54 CTGCLSCIEVCERDAL 69
                                      7778888888877776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.5e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare 29 
                                       C +Cg+C+e C  na+     + iea++
  gi|488600664|ref|YP_007907135.1|  83 CNGCGACVENCSNNALILY-GYDIEAED 109
                                       ***************8776.45555555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   5.5    0.0007      0.74      34      51 ..      47      64 ..      26      71 .. 0.72
   2 !   18.8  11.0   1.2e-06    0.0013       5      52 ..      51      94 ..      47     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0007
                           Fer4_21 34 lkvvedeCvGCnlCssvC 51
                                      l+++ed C+GC  C++vC
  gi|488600664|ref|YP_007907135.1| 47 LAYREDMCTGCLSCIEVC 64
                                      56789************* PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.2e-06
                           Fer4_21  5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52
                                      ed+C gC +C+ +Ce    +a+  ++++v  v +d C GC  C++ C 
  gi|488600664|ref|YP_007907135.1| 51 EDMCTGCLSCIEVCE---RDALLWEGERV-SVNSDLCNGCGACVENCS 94
                                      89*************...6***9988776.9****************6 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.9     0.089        93       6      19 ..      52      65 ..      49      69 .. 0.89
   2 ?   15.4   0.5   2.2e-05     0.023       1      20 [.      76      95 ..      76     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.089
                           Fer4_15  6 daCigcglCvaeap 19
                                      d C+gc  C+++++
  gi|488600664|ref|YP_007907135.1| 52 DMCTGCLSCIEVCE 65
                                      88*********996 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.2e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                      V v+ d+C gcg+Cv+++++
  gi|488600664|ref|YP_007907135.1| 76 VSVNSDLCNGCGACVENCSN 95
                                      7899*************975 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   7.3      0.15   1.5e+02      49      63 ..      52      66 ..      25      68 .. 0.82
   2 ?   13.7   0.1   6.2e-05     0.066       5      62 ..      83      94 ..      72     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.15
                            Fer4_8 49 wsCttcgaCtevCpv 63
                                      + Ct+c +C evC  
  gi|488600664|ref|YP_007907135.1| 52 DMCTGCLSCIEVCER 66
                                      67***********75 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.2e-05
                            Fer4_8  5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62
                                      C++CgaC ++C                                               
  gi|488600664|ref|YP_007907135.1| 83 CNGCGACVENC----------------------------------------------S 94
                                      55555555555..............................................4 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.8    0.0021       2.2       2      15 ..      52      65 ..      51      68 .. 0.90
   2 ?   14.7   0.9   3.1e-05     0.033       2      15 ..      81      94 ..      80     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0021
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      + C+gC sC+ +C+
  gi|488600664|ref|YP_007907135.1| 52 DMCTGCLSCIEVCE 65
                                      78***********8 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.1e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      + C+gCg+Cv  C+
  gi|488600664|ref|YP_007907135.1| 81 DLCNGCGACVENCS 94
                                      88********9997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.7     0.031        33       2      14 ..      54      66 ..      53      78 .. 0.83
   2 ?   10.8   2.4   0.00053      0.56      42      59 ..      79      96 ..      67      98 .. 0.77
   3 ?   11.2   2.1   0.00041      0.43       2      27 ..      83     112 ..      82     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.031
                           Fer4_17  2 CiqCgyClpeCps 14
                                      C++C  C+++C +
  gi|488600664|ref|YP_007907135.1| 54 CTGCLSCIEVCER 66
                                      9999999999976 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00053
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                      + +lC++Cg C++ C ++
  gi|488600664|ref|YP_007907135.1| 79 NSDLCNGCGACVENCSNN 96
                                      567888888888888765 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00041
                           Fer4_17   2 CiqCgyClpeCpsyea....ydnepkkllr 27 
                                       C++Cg+C+++C+ ++     yd e + ++r
  gi|488600664|ref|YP_007907135.1|  83 CNGCGACVENCSNNALilygYDIEAEDVIR 112
                                       899999999998755544445555555555 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.1    0.0045       4.8       1      14 [.      54      67 ..      54      68 .. 0.85
   2 ?   11.5   6.2   0.00045      0.47       1      15 []      83      97 ..      83      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0045
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      CtgC  C evC  +
  gi|488600664|ref|YP_007907135.1| 54 CTGCLSCIEVCERD 67
                                      ****88*****665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00045
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCgaCve C ++A
  gi|488600664|ref|YP_007907135.1| 83 CNGCGACVENCSNNA 97
                                      ***********9988 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.9     0.021        22      76      94 ..      48      66 ..      27      68 .. 0.84
   2 ?    8.7   2.1    0.0029       3.1      77      94 ..      78      95 ..      72      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                       + e +C+GC  Cie+c  
  gi|488600664|ref|YP_007907135.1| 48 AYREDMCTGCLSCIEVCER 66
                                      56789************86 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0029
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      +++  C GCg C+e+c +
  gi|488600664|ref|YP_007907135.1| 78 VNSDLCNGCGACVENCSN 95
                                      57889***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2140.64
//
Query:       gi|488600665|ref|YP_007907136.1|  [L=96]
Description: hypothetical protein Asulf_01143 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0048   17.5   0.1     0.0052   17.4   0.1    1.1  1  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.9e-07    0.0052      23     106 ..       3      83 ..       1      84 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.9e-07
                                       STTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCHHHHHHHCCHHHHHCCEEEEEE CS
                              ASCH  23 wdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.sleewrevheefyeeeseeyedelv 98 
                                       w++++ kv g++  +++   ++ +++  +vt+ ++ ++ +++ e+a++eg  s+e+ ++  +e+ +++    ++ +v
  gi|488600665|ref|YP_007907136.1|   3 WKKPRVKV-GGIYKAKTKLFSKDYFALLRVTRLRKERLGDISPEDAQAEGGySIEQFKRIWKEINGSWD---PEQEV 75 
                                       66676666.5555555555789999***************************************99995...6999* PP

                                       EEEEEEEE CS
                              ASCH  99 vveefelv 106
                                       +v efe +
  gi|488600665|ref|YP_007907136.1|  76 WVVEFEML 83 
                                       *****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 591.49
//
Query:       gi|488600666|ref|YP_007907137.1|  [L=122]
Description: hypothetical protein Asulf_01144 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   16.2   0.0      0.013   15.9   0.0    1.1  1  RXLR          RXLR phytopathogen effector protein, Avirulence
      0.031   14.3   1.3      0.036   14.1   0.6    1.4  2  DHR10         Designed helical repeat protein 10 domain
      0.065   13.3   2.3       0.11   12.6   1.5    1.8  1  Exonuc_VII_S  Exonuclease VII small subunit
      0.094   13.3   0.1       0.12   13.0   0.1    1.2  1  ArdA          Antirestriction protein (ArdA)


Domain annotation for each model (and alignments):
>> RXLR  RXLR phytopathogen effector protein, Avirulence activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   2.9e-06     0.013      82     134 ..      66     118 ..      36     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.9e-06
                              RXLR  82 kklkkmlanekyakklFreWkanGftlkdieseLkqsearklkekYktlakqY 134
                                         l+ ++++ ++a++l +eW +  + l++i +eL++++ + ++  Y+ l + Y
  gi|488600666|ref|YP_007907137.1|  66 DSLNGIVTDVDKANELLDEWLETKKRLEEIVKELEKEQISSIDGFYSILRQLY 118
                                       67999***********************************9999999776656 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.4   1.1e+04      51      54 ..      19      22 ..       5      30 .. 0.51
   2 ?   14.1   0.6     8e-06     0.036      24      63 ..      64     103 ..      62     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.4
                             DHR10 51 klee 54
                                      k ee
  gi|488600666|ref|YP_007907137.1| 19 KKEE 22
                                      2222 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8e-06
                             DHR10  24 kidalqvvekdlrsciklleeieaelakleeakkklkelr 63 
                                       ++d+l+ + +d+ ++ +ll+e+ +  ++lee  k+l++ +
  gi|488600666|ref|YP_007907137.1|  64 TVDSLNGIVTDVDKANELLDEWLETKKRLEEIVKELEKEQ 103
                                       789********************************99865 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 ?   12.6   1.5   2.4e-05      0.11       6      21 ..      90     105 ..      87     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                      Exonuc_VII_S   6 aeLeeIvekLEsgels 21 
                                       ++LeeIv++LE++++s
  gi|488600666|ref|YP_007907137.1|  90 KRLEEIVKELEKEQIS 105
                                       89***********996 PP

>> ArdA  Antirestriction protein (ArdA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.6e-05      0.12      17     111 ..      12     110 ..       7     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                              ArdA  17 eWldlpadaeelqealkai....s..aeeedeEwaihDye....glpeaslgeyesidelnelaklleeleehgeaf 83 
                                       e ++l a++ee+  +++++    +  + e  +++++         +  ++++ y ++d ln ++   +++++ +e +
  gi|488600666|ref|YP_007907137.1|  12 EFVSLIAKKEEIDGKISSLtipaGgtI-EVADDFFVYGALikkdDI--FEIHRYMTVDSLNGIV---TDVDKANELL 82 
                                       566666777777777776534431222.344566655544221123..5667799999999999...99999999** PP

                              ArdA  84 aawvehfgdleeledafeeeylgeydsl 111
                                         w+e+++ lee+++++e+e  +++d +
  gi|488600666|ref|YP_007907137.1|  83 DEWLETKKRLEEIVKELEKEQISSIDGF 110
                                       *******************998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1420  (0.0792013); expected 358.6 (0.02)
Passed bias filter:                      976  (0.0544369); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 760.04
//
Query:       gi|488600667|ref|YP_007907138.1|  [L=89]
Description: hypothetical protein Asulf_01145 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 595.21
//
Query:       gi|488600668|ref|YP_007907139.1|  [L=98]
Description: hypothetical protein Asulf_01146 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 719.80
//
Query:       gi|488600669|ref|YP_007907140.1|  [L=183]
Description: hypothetical protein Asulf_01147 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.1    9.4e-22   77.2   0.0    1.4  2  Mrr_cat    Restriction endonuclease
     0.0016   18.9   0.2     0.0098   16.3   0.0    2.1  2  NERD       Nuclease-related domain
  ------ inclusion threshold ------
       0.14   12.3   0.1        0.3   11.3   0.1    1.6  1  MTES_1575  REase_MTES_1575
       0.55   10.1   0.1       0.55   10.1   0.1    2.1  3  IF2_N      Translation initiation factor IF-2, N-terminal reg


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 !   77.2   0.0   2.1e-25   9.4e-22       6     114 ..       9     121 ..       5     122 .. 0.94
   2 ?   -3.4   0.0       2.1   9.4e+03      51      67 ..     138     157 ..     133     162 .. 0.62

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2.1e-25
                                       TTCHHHHHHHHHHHHSSS...EEE---B-T.TSSB--EE.EETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS. CS
                           Mrr_cat   6 pkeFeklvaellealGyk...eveltgrsg.DggiDlia.kkdplgserilvqaKryknkvgvkeVqeligalkkrg 77 
                                       + e+eklva+l++++Gy    +v+l grsg +++iD++a  k pl+  ri++++K y+ +++++ V +li+ + + g
  gi|488600669|ref|YP_007907140.1|   9 GVELEKLVAQLFKSKGYDvmhNVKLKGRSGvEHQIDVYAeYKCPLHLSRIVIECKAYDTPINKDIVMKLIQEVLDLG 85 
                                       5689************************998889****9456899999***************************** PP

                                       .SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  78 adkgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                       +d+gi+vtts+ft++A + a++  +++L+d ++L +l
  gi|488600669|ref|YP_007907140.1|  86 VDRGILVTTSYFTPDAVSTANG-YNVDLWDYTKLTSL 121
                                       **********************.9**********987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                                       EEEEE--...TS-B-HHHHH CS
                           Mrr_cat  51 lvqaKry...knkvgvkeVq 67 
                                       +++ K +   ++kv +k+V+
  gi|488600669|ref|YP_007907140.1| 138 YIEPKLSaeqSKKVAEKQVR 157
                                       55555554323677777776 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.2e-06    0.0098       2      58 ..       9      69 ..       8      83 .. 0.78
   2 ?   -0.4   0.0      0.34   1.5e+03       4      24 ..     151     169 ..     148     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-06
                              NERD  2 gaegEravakeLkelkedeylvlhdvrlrpgtg...eiDhlvispkg....ifviEvKnwsGwi 58
                                      g e E+ va+  k   +++y v+h+v+l++++g   +iD+ + +++      +viE+K+++  i
  gi|488600669|ref|YP_007907140.1|  9 GVELEKLVAQLFK---SKGYDVMHNVKLKGRSGvehQIDVYAEYKCPlhlsRIVIECKAYDTPI 69
                                      7778999999999...568*********99955778****998887523335899999988654 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                              NERD   4 egEravakeLkelkedeylvl 24 
                                        +E++v  +L+   e++++ l
  gi|488600669|ref|YP_007907140.1| 151 VAEKQVRGYLE--GEKYWNSL 169
                                       57899999999..77777654 PP

>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   6.7e-05       0.3       2      47 ..      13      66 ..      12      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.7e-05
                         MTES_1575  2 eeeVaeaLrergykvkpqvgvg.....gfriDlvvedp...gkyllaIecdgdk 47
                                      e+ Va+  +++gy+v ++v+++     +++iD+  e +   +  +++Iec  + 
  gi|488600669|ref|YP_007907140.1| 13 EKLVAQLFKSKGYDVMHNVKLKgrsgvEHQIDVYAEYKcplHLSRIVIECKAYD 66
                                      678999999************977777789*****99999999*******8765 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 ?   10.1   0.1   0.00012      0.55       8      36 ..       3      30 ..       2      33 .. 0.86
   2 ?   -1.7   0.0      0.61   2.7e+03      17      26 ..      70      79 ..      70      88 .. 0.60
   3 ?   -3.2   0.0       1.8   7.9e+03      39      50 ..     143     154 ..     143     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                             IF2_N  8 eLAkeLgvkskevikkLfkelGievkshs 36
                                      +L  e gv+ ++++++Lfk++G++ + h+
  gi|488600669|ref|YP_007907140.1|  3 QLSYEKGVELEKLVAQLFKSKGYD-VMHN 30
                                      67888899****************.6665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.61
                             IF2_N 17 skevikkLfk 26
                                      +k+++ kL +
  gi|488600669|ref|YP_007907140.1| 70 NKDIVMKLIQ 79
                                      5677777644 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.8
                             IF2_N  39 LDeetaeliaee 50 
                                       L++e+ +++ae+
  gi|488600669|ref|YP_007907140.1| 143 LSAEQSKKVAEK 154
                                       678888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1209.20
//
Query:       gi|488600670|ref|YP_007907141.1|  [L=219]
Description: hypothetical protein Asulf_01148 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-07   28.7   0.0    1.9e-06   27.6   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
      0.015   15.0   0.7      0.027   14.3   0.7    1.4  1  HTH_IclR         IclR helix-turn-helix domain
      0.016   15.6   0.0      0.056   13.8   0.0    1.9  3  Penicillinase_R  Penicillinase repressor
      0.036   14.3   0.2      0.072   13.3   0.2    1.4  1  SgrR_N           Sugar transport-related sRNA regulator N-ter
       0.17   11.7   0.1       0.41   10.4   0.1    1.6  1  HTH_DeoR         DeoR-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   5.4e-10   1.9e-06       6      64 ..      61     120 ..      60     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.4e-10
                                       HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE CS
                              TrmB   6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYra 64 
                                       +s+ Ea++++ Ll+ +++t+  +a+ l  +++k+ + L+ L  +Gl + +k gr   Y++
  gi|488600670|ref|YP_007907141.1|  61 ISDAEAEAFKLLLTMDSLTVASLASLLSCSEAKARKLLQGLTARGLARQVKvGRQIQYEP 120
                                       799*********************************************999444557765 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 ?   14.3   0.7   7.6e-06     0.027      18      51 ..      77     110 ..      65     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.6e-06
                                       S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  18 eltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                        lt++ lA  +  + ++++ lLq L+ +G+ +q 
  gi|488600670|ref|YP_007907141.1|  77 SLTVASLASLLSCSEAKARKLLQGLTARGLARQV 110
                                       599*****************************95 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   7.2e+03      33      46 ..      31      44 ..      12      47 .. 0.53
   2 ?   13.8   0.0   1.6e-05     0.056       1      67 [.      61     123 ..      61     144 .. 0.90
   3 ?   -3.2   0.0       2.9     1e+04      81      96 ..     197     212 ..     174     215 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                      --HHHHHHHHHHHH CS
                   Penicillinase_R 33 laysTVktllrrLv 46
                                       a+ TV   ++ Lv
  gi|488600670|ref|YP_007907141.1| 31 KAKLTVDACINALV 44
                                      25566766666665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.6e-05
                                       ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE---- CS
                   Penicillinase_R   1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvs 67 
                                       ++++Eae  ++l + +++tv+++ + l+      ++  + ll+ L+++gl ++ k gr+++Y p v+
  gi|488600670|ref|YP_007907141.1|  61 ISDAEAEAFKLLLTMDSLTVASLASLLSCS----EAKARKLLQGLTARGLARQVKVGRQIQYEPGVN 123
                                       799********************9999988....555688***********************9775 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.9
                                       XXXXXXXXXXXXXXXX CS
                   Penicillinase_R  81 dklfegsvkelvaafv 96 
                                          ++g+v+++v++++
  gi|488600670|ref|YP_007907141.1| 197 VDALTGNVNDFVSKLL 212
                                       4444556666666655 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 ?   13.3   0.2     2e-05     0.072      19      57 ..      77     114 ..      70     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                            SgrR_N  19 evtLqelAdvlfCsrRhartlLkkmqeegwleWqpevGR 57 
                                       ++t++ lA++l Cs+  ar lL+ +  +g+ + q +vGR
  gi|488600670|ref|YP_007907141.1|  77 SLTVASLASLLSCSEAKARKLLQGLTARGLAR-QVKVGR 114
                                       6799*********************9998643.666666 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 ?   10.4   0.1   0.00011      0.41       7      47 ..      70     110 ..      66     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                          HTH_DeoR   7 ellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47 
                                       +ll   ++l+v  l+ ll  Sea +R+ L+ L++ gl + +
  gi|488600670|ref|YP_007907141.1|  70 KLLLTMDSLTVASLASLLSCSEAKARKLLQGLTARGLARQV 110
                                       7899999*****************************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1566.44
//
Query:       gi|488600671|ref|YP_007907142.1|  [L=125]
Description: hypothetical protein Asulf_01149 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 834.18
//
Query:       gi|488600672|ref|YP_007907143.1|  [L=114]
Description: Plastocyanin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-17   62.7   0.0    3.4e-17   62.4   0.0    1.0  1  Cupredoxin_1  Cupredoxin-like domain
      4e-13   49.6   0.3    6.3e-12   45.8   0.3    2.0  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
     0.0083   15.5   0.0     0.0099   15.3   0.0    1.1  1  Mig-14        Mig-14


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 !   62.4   0.0   5.8e-21   3.4e-17       3     104 .]       8     113 ..       5     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 5.8e-21
                      Cupredoxin_1   3 aalavllllsskaa........aaaektveitvkdggfePskievkagekvklkiknkdktpeefesedlgeekvla 71 
                                       +al++ll  ++k +        +a++ +ve+++ d +f+P+++ +  g+  +++++n+d+  +++++ed   + +l+
  gi|488600672|ref|YP_007907143.1|   8 LALVMLLSGCAKPQapsqaqqpQAQQSVVEVKIRDFAFDPETVRISPGT--TVRWVNEDNARHTVTFEDGVASGDLK 82 
                                       5555555555544457777776788888********************8..99************************ PP

                      Cupredoxin_1  72 pgktttitiaplkpGeYeftcdmhmdakGkliV 104
                                       +g+t++ t+   ++G+Y+++c++h+ +kG++iV
  gi|488600672|ref|YP_007907143.1|  83 KGDTFERTF--SEKGTYNYYCQIHPAMKGTVIV 113
                                       *********..9********************9 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.3     1e-15   6.3e-12       4      99 .]      35     114 .]      32     114 .] 0.87

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1e-15
                                       EEEETTETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEE CS
                       Copper-bind   4 klgvesgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtY 80 
                                        ++v+  d++F+++++++++g++v +vn +   H v ++ +      ++  +k+         G++++ tf+e+gtY
  gi|488600672|ref|YP_007907143.1|  35 VVEVKIRDFAFDPETVRISPGTTVRWVNEDNARHTVTFEDGV-----ASGDLKK---------GDTFERTFSEKGTY 97 
                                       5789999***************************99997544.....3445555.........89************ PP

                                       EEEETTTTTTTSEEEEEEE CS
                       Copper-bind  81 kffCsPHaaagMkgkvtve 99 
                                       +++C+ H a  Mkg+v+ve
  gi|488600672|ref|YP_007907143.1|  98 NYYCQIHPA--MKGTVIVE 114
                                       ********4..7****996 PP

>> Mig-14  Mig-14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-06    0.0099     194     233 ..      30      70 ..       4      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
                            Mig-14 194 eape.wisveyinGgvdpetrelsPGsvlsflniqaaweda 233
                                       +a++  + v++ + + dpet  +sPG+ + ++n ++a++ +
  gi|488600672|ref|YP_007907143.1|  30 QAQQsVVEVKIRDFAFDPETVRISPGTTVRWVNEDNARHTV 70 
                                       45441578999999************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 770.13
//
Query:       gi|488600673|ref|YP_007907144.1|  [L=105]
Description: transcriptional regulator, ArsR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-13   49.3   0.5    4.9e-13   48.7   0.5    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    4.2e-12   46.0   0.1    5.6e-12   45.5   0.1    1.2  1  HTH_20          Helix-turn-helix domain
    8.2e-06   25.7   2.5      4e-05   23.5   2.5    1.9  1  PadR            Transcriptional regulator PadR-like family
    1.5e-05   24.8   0.2    2.2e-05   24.2   0.2    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    2.4e-05   24.2   0.7    3.7e-05   23.6   0.7    1.3  1  HTH_11          HTH domain
    5.2e-05   23.4   0.6    7.7e-05   22.8   0.6    1.3  1  HTH_34          Winged helix DNA-binding domain
    0.00017   21.1   1.7    0.00091   18.7   0.2    2.3  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00062   19.6   0.1     0.0011   18.9   0.1    1.5  1  MarR            MarR family
     0.0012   19.3   0.4     0.0018   18.8   0.4    1.3  1  Mga             Mga helix-turn-helix domain
     0.0022   17.8   1.6     0.0029   17.4   1.6    1.2  1  TFIIE_alpha     TFIIE alpha subunit
     0.0034   17.2   0.2     0.0045   16.8   0.2    1.3  1  HxlR            HxlR-like helix-turn-helix
     0.0073   16.2   0.0      0.011   15.6   0.0    1.4  1  MarR_2          MarR family
     0.0081   16.5   0.1      0.013   15.8   0.1    1.4  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.033   14.3   0.1    1.3  1  HTH_28          Helix-turn-helix domain
      0.027   14.3   0.0      0.053   13.3   0.0    1.5  1  HTH_10          HTH DNA binding domain
      0.033   14.2   0.2      0.058   13.4   0.2    1.4  1  BLACT_WH        Beta-lactamase associated winged helix domain
      0.038   13.8   0.1      0.064   13.1   0.1    1.3  1  HTH_23          Homeodomain-like domain
      0.045   13.3   0.0      0.081   12.5   0.0    1.4  1  HTH_CodY        CodY helix-turn-helix domain
      0.057   13.7   0.1      0.088   13.1   0.1    1.3  1  HTH_Tnp_1       Transposase
      0.099   12.8   0.2       0.17   12.1   0.1    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.5   5.4e-16   4.9e-13       1      47 []      27      73 ..      27      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 5.4e-16
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +p R+kILklL e+e +v ela+el +s+  +  HL+kL++aGLV++
  gi|488600673|ref|YP_007907144.1| 27 NPLRVKILKLLIEKEWYVYELAKELSISRQLLYLHLRKLEKAGLVSS 73
                                      699******************************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   6.2e-15   5.6e-12       5      55 ..      23      72 ..      16      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 6.2e-15
                                      HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +AL++P R +il++L  +++  + ela++l++s++ l+ HLr+Le+agLv 
  gi|488600673|ref|YP_007907144.1| 23 DALSNPLRVKILKLL-IEKEWYVYELAKELSISRQLLYLHLRKLEKAGLVS 72
                                      8**************.*********************************97 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   2.5   4.5e-08     4e-05       1      64 [.      33      87 ..      33      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.5e-08
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEE CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYr 64
                                      iL+ll e++ y ye++kel+ +           lY  L++Lek glv+s  + + e++++kyY 
  gi|488600673|ref|YP_007907144.1| 33 ILKLLIEKEWYVYELAKELSIS--------RQLLYLHLRKLEKAGLVSSDIRLE-ENKAKKYYW 87
                                      89****************9877........347*****************9995.9*******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 !   24.2   0.2   2.5e-08   2.2e-05      15      54 ..      34      73 ..      33      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.5e-08
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      l+Ll +++  ++e+a+el ++r+  Y  Lr+Le++GlV  
  gi|488600673|ref|YP_007907144.1| 34 LKLLIEKEWYVYELAKELSISRQLLYLHLRKLEKAGLVSS 73
                                      58999*********************************75 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.7   4.1e-08   3.7e-05       4      44 ..      32      75 ..      30      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.1e-08
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.....v 44
                                      +il+lL+e++  +   eLA+eL++Sr+  + ++++Le++g     +
  gi|488600673|ref|YP_007907144.1| 32 KILKLLIEKE--WYVYELAKELSISRQLLYLHLRKLEKAGlvssdI 75
                                      79****8888..99**************************666443 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.6   8.6e-08   7.7e-05       1      57 [.      29      84 ..      29      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.6e-08
                            HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprt 57
                                      +R ++l +L+++++    el ++l+++   L+ hl+kLekag ++ d+ ++++k + 
  gi|488600673|ref|YP_007907144.1| 29 LRVKILKLLIEKEWYV-YELAKELSISRQLLYLHLRKLEKAGLVSSDIRLEENKAKK 84
                                      6999***999998865.589999**************************99998765 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 ?    1.2   0.1      0.31   2.8e+02       3      14 ..      28      39 ..      26      41 .. 0.79
   2 !   18.7   0.2     1e-06   0.00091      22      47 ..      46      71 ..      46      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.31
                            HTH_24  3 etdrkILelLqk 14
                                       ++ kIL+lL +
  gi|488600673|ref|YP_007907144.1| 28 PLRVKILKLLIE 39
                                      66789****987 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1e-06
                            HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlI 47
                                      eLA++l +S++ +  +l++Le++Gl+
  gi|488600673|ref|YP_007907144.1| 46 ELAKELSISRQLLYLHLRKLEKAGLV 71
                                      8***********************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.2e-06    0.0011      19      49 ..      43      73 ..      27      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 19 svseLakklgvskstvtrvldrLekkGlieR 49
                                      +v eLak l++s+  +   l++Lek+Gl+++
  gi|488600673|ref|YP_007907144.1| 43 YVYELAKELSISRQLLYLHLRKLEKAGLVSS 73
                                      688**************************86 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.4   2.1e-06    0.0018      17      68 ..      29      80 ..      12      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-06
                                      HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHH.CHCCT-EEETT CS
                               Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikelnkl.Lkefdleltkk 68
                                      l  ++lk+l+ e+e  ++ela+el iS+  l+ ++++l+k  L + d++l+++
  gi|488600673|ref|YP_007907144.1| 29 LRVKILKLLI-EKEWYVYELAKELSISRQLLYLHLRKLEKAgLVSSDIRLEEN 80
                                      678999*999.89999**********************986588999999433 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.6   3.2e-06    0.0029      16      79 ..      31      92 ..      25     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.2e-06
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECC CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinye 79
                                      v++l+ L+ + e    +lakel+i ++ l   L +L +a+lv+   r +e+k  +kyyw  + +
  gi|488600673|ref|YP_007907144.1| 31 VKILKLLI-EKEWYVYELAKELSISRQLLYLHLRKLEKAGLVSSDIRLEENK-AKKYYWANEFK 92
                                      57888887.56667779**************************999998876.689***87665 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   0.2   5.1e-06    0.0045       8      59 ..      31      81 ..      24      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-06
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS- CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPp 59
                                      + il  l++++    el+++l +is+++L  +Lr+Le+ gl++ ++  e  +
  gi|488600673|ref|YP_007907144.1| 31 VKILKLLIEKEWYVYELAKEL-SISRQLLYLHLRKLEKAGLVSSDIRLEENK 81
                                      568888999999999******.9*******************9887655544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05     0.011      24      51 ..      44      71 ..      28      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 24 vgelarrlglsksavsrilkrLvaaGLv 51
                                      v ela++l +s++ +  +l++L++aGLv
  gi|488600673|ref|YP_007907144.1| 44 VYELAKELSISRQLLYLHLRKLEKAGLV 71
                                      679************************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.5e-05     0.013      28      57 ..      44      73 ..      30      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 28 seeiaerqnispsylekilakLrkaglvks 57
                                      + e+a++ +is++ l   l+kL+kaglv s
  gi|488600673|ref|YP_007907144.1| 44 VYELAKELSISRQLLYLHLRKLEKAGLVSS 73
                                      679*************************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.7e-05     0.033       2      41 ..      30      70 ..      29      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-05
                            HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWikryeegGi 41
                                      R +i+kll++ +  v e+A+el isr+ +y  ++++e+ G+
  gi|488600673|ref|YP_007907144.1| 30 RVKILKLLIEKEwYVYELAKELSISRQLLYLHLRKLEKAGL 70
                                      8899999998888999**********************886 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     6e-05     0.053      27      49 ..      45      67 ..      39      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                            HTH_10 27 keLAkelGIskstlsehLrkaes 49
                                       eLAkel Is++ l+ hLrk e+
  gi|488600673|ref|YP_007907144.1| 45 YELAKELSISRQLLYLHLRKLEK 67
                                      69******************886 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.5e-05     0.058      25      41 ..      58      74 ..      52      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-05
                          BLACT_WH 25 vlahLeKLeeeGkVkre 41
                                      +++hL+KLe+ G+V+++
  gi|488600673|ref|YP_007907144.1| 58 LYLHLRKLEKAGLVSSD 74
                                      789***********974 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.1e-05     0.064       7      46 ..      30      70 ..      26      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.1e-05
                            HTH_23  7 Rlrillllae.GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      R +il+ll e  + v e A+eL +sr+ +y  l++ ++ Gl
  gi|488600673|ref|YP_007907144.1| 30 RVKILKLLIEkEWYVYELAKELSISRQLLYLHLRKLEKAGL 70
                                      889******99*******************88888777886 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 ?   12.5   0.0   9.1e-05     0.081      10      36 ..      47      73 ..      42      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                          HTH_CodY 10 iaDriGitrsvivnaLrkLesaGiies 36
                                      +a ++ i r  +   LrkLe aG++ s
  gi|488600673|ref|YP_007907144.1| 47 LAKELSISRQLLYLHLRKLEKAGLVSS 73
                                      789999******************987 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.9e-05     0.088      11      57 ..      29      76 ..      26      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                         HTH_Tnp_1 11 fKariVreslepgksvsevArrhgvspnqLykWrrqyr.egeeaspae 57
                                       +++i+++  e    v e+A+++ +s++ Ly   r+ + +g+ +s+++
  gi|488600673|ref|YP_007907144.1| 29 LRVKILKLLIEKEWYVYELAKELSISRQLLYLHLRKLEkAGLVSSDIR 76
                                      5788999999*********************88777773555555555 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 ?   12.1   0.1   0.00019      0.17      23      50 ..      46      73 ..      42      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                    B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvk 50
                                      +Lake+ ++   l+ +l++Lek gL+  
  gi|488600673|ref|YP_007907144.1| 46 ELAKELSISRQLLYLHLRKLEKAGLVSS 73
                                      79***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        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: 00:00:00.48
# Mc/sec: 654.29
//
Query:       gi|488600674|ref|YP_007907145.1|  [L=68]
Description: hypothetical protein Asulf_01153 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.3   0.5      0.037   14.0   0.5    1.2  1  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
      0.036   13.7   1.5      0.046   13.4   1.5    1.1  1  DUF4988         Domain of unknown function
      0.042   14.1   0.1      0.047   14.0   0.1    1.1  1  DUF948          Bacterial protein of unknown function (DUF948
      0.059   12.9   1.3        7.5    6.2   0.0    3.1  3  YvrJ            YvrJ protein family


Domain annotation for each model (and alignments):
>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   8.2e-06     0.037      12      68 ..       6      62 ..       3      68 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.2e-06
                                      ETTEEEEEEEEEETTEEEEEEEEESBSSSSHCHHHHHHHTTSBSSHHHHHHHHHTSC CS
                    Lip_prot_lig_C 12 fdwGtvevrldvekgiIkdikiyGDffgpkdieeleekLigvkyekeaieealekid 68
                                      +++G++ v l+v  gi++ i i G ++  k i++l++ +i ++ + e+++  +++i 
  gi|488600674|ref|YP_007907145.1|  6 YEGGNFLVSLTVGFGIVSIIMILGFYLLIKSINDLKNSMISIENKVENVNTKVKEIA 62
                                      57899******************************************9999998875 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.5     1e-05     0.046       3      30 ..      35      62 ..      33      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                           DUF4988  3 ddvndlkdrvaaleeqvkelndniealk 30
                                      + +ndlk+ + ++e++v+++n++++ ++
  gi|488600674|ref|YP_007907145.1| 35 KSINDLKNSMISIENKVENVNTKVKEIA 62
                                      689*********************9986 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 ?   14.0   0.1     1e-05     0.047       5      51 ..      21      67 ..      17      68 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                            DUF948  5 IaAiAFvvLviflivvllklkktldeaaatieelekqvdpilkeved 51
                                      I+ i +++   +li+ ++ lk+ + ++++ +e+++ +v++i +++e+
  gi|488600674|ref|YP_007907145.1| 21 IVSIIMILGFYLLIKSINDLKNSMISIENKVENVNTKVKEIADQLEE 67
                                      667777778889999***************************99987 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.063   2.8e+02       4      10 ..      16      22 ..      15      23 .. 0.87
   2 ?    6.2   0.0    0.0017       7.5      26      35 ..      33      42 ..      29      43 .. 0.89
   3 ?    3.1   0.1     0.015        68      19      34 ..      47      62 ..      44      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.063
                              YvrJ  4 nvGFPIa 10
                                       vGF I+
  gi|488600674|ref|YP_007907145.1| 16 TVGFGIV 22
                                      59****8 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0017
                              YvrJ 26 LtksIeeLse 35
                                      L+ksI++L++
  gi|488600674|ref|YP_007907145.1| 33 LIKSINDLKN 42
                                      9*******97 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.015
                              YvrJ 19 iEkkLdeLtksIeeLs 34
                                      iE+k ++ ++ ++e +
  gi|488600674|ref|YP_007907145.1| 47 IENKVENVNTKVKEIA 62
                                      9********9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1693  (0.094428); expected 358.6 (0.02)
Passed bias filter:                      920  (0.0513135); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 448.73
//
Query:       gi|488600675|ref|YP_007907146.1|  [L=226]
Description: phosphoglycolate phosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  116.4   4.1    4.9e-22   78.9   0.7    2.1  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    3.6e-11   43.1   0.0    1.5e-10   41.0   0.0    1.8  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
    1.4e-07   32.0   1.6     0.0038   17.6   0.0    3.1  3  Hydrolase    haloacid dehalogenase-like hydrolase
    3.5e-06   27.6   3.3      0.049   14.0   0.0    3.7  3  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 !   39.2   0.2   1.4e-13   6.3e-10       1      74 [.       8      79 ..       8     128 .. 0.88
   2 !   78.9   0.7   1.1e-25   4.9e-22     176     254 ..     141     219 ..     119     220 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.4e-13
                                      EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEEE CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgkil 74
                                      +a+D+DGT+  +d +++ +++eai+klk   + vv+ATG+    ++  ++ +g + +vi+ NG+++  +++g+ +
  gi|488600675|ref|YP_007907146.1|  8 VAIDIDGTITYKDRSLNCRAVEAIRKLK---VPVVLATGNISCYARTTAKLIGASDIVICENGGVVrFEYDGEDI 79
                                      79*************************9...***********************************755555554 PP

  == domain 2  score: 78.9 bits;  conditional E-value: 1.1e-25
                                       TTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHH CS
                       Hydrolase_3 176 kgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVa 252
                                       ++ + i+ ++v Kg+alk+++ el+i+ e+ +a+GD+eNDi ++e ag+gvA++na+ ++k+ Ad v+  +n dGV+
  gi|488600675|ref|YP_007907146.1| 141 GFAYHITDANVGKGKALKYICDELGIPVEKFVAIGDSENDIDLIEIAGIGVAVANADIKLKERADIVVSRKNGDGVV 217
                                       56789***********************************************************************9 PP

                                       HH CS
                       Hydrolase_3 253 ka 254
                                       +a
  gi|488600675|ref|YP_007907146.1| 218 EA 219
                                       87 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.16     7e+02       6      45 ..       9      45 ..       7      81 .. 0.62
   2 !   41.0   0.0   3.4e-14   1.5e-10     137     246 ..     124     224 ..     117     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.16
                                      EE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS- CS
                              S6PP  6 vsdLDntlvdgdnealarlnelleaeerkdvllvfaTGRs 45
                                      ++d+D+t++ +d++   r  e     ++ +v +v+aTG  
  gi|488600675|ref|YP_007907146.1|  9 AIDIDGTITYKDRSLNCRAVEA---IRKLKVPVVLATGNI 45
                                      6799999995554433333333...336888888888854 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 3.4e-14
                                       HHHHHTTTS-EEEEEETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHH CS
                              S6PP 137 eqlLekreldvkviyssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeel 213
                                       +++L++++l+   ++ sg +  +   + +kg+Al+y+++ l+++ e+++  Gds+nD++l++    gV V+na+ + 
  gi|488600675|ref|YP_007907146.1| 124 KKILKEAGLEGVKLIDSGFAYHITDANVGKGKALKYICDELGIPVEKFVAIGDSENDIDLIEIAGIGVAVANADIK- 199
                                       678888888888888889999999999**********************************9999*********99. PP

                                       HHHHHHH--TTE..EE-SS-THHHHHHHHHHTT CS
                              S6PP 214 lqwllenakeneriylaeercaaGileglahfg 246
                                              +ke+  i++++ +  +G++e+ ++ +
  gi|488600675|ref|YP_007907146.1| 200 -------LKERADIVVSR-KNGDGVVEAFEFLN 224
                                       .......55555566655.45688888888766 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.1     0.009        41       3      18 ..       7      22 ..       5      25 .. 0.80
   2 !    8.3   0.0   0.00057       2.5     126     163 ..      27      62 ..      22      86 .. 0.82
   3 !   17.6   0.0   8.4e-07    0.0038     150     209 ..     125     187 ..     105     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.009
                                      EEEEESBTTTBCHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                         Hydrolase  3 tvvfDkdGTLttgeps 18
                                       v++D+dGT+t   +s
  gi|488600675|ref|YP_007907146.1|  7 GVAIDIDGTITYKDRS 22
                                      699********77655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00057
                                       HHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 126 avasLkaagievvlltgdnpetaeraanqlGddyfdav 163
                                       av+++++ +++vvl+tg+ +  a+ +a+ +G  + d+v
  gi|488600675|ref|YP_007907146.1|  27 AVEAIRKLKVPVVLATGNISCYARTTAKLIG--ASDIV 62 
                                       677888888**********************..22333 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 8.4e-07
                                       HHHHHTT...GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 150 raanqlG...ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       ++++++G    + +d  +a+ i+     + ++++++++eL+++ e+ +++GD+ nD+  ++ A
  gi|488600675|ref|YP_007907146.1| 125 KILKEAGlegVKLIDSGFAYHITDANVGKGKALKYICDELGIPVEKFVAIGDSENDIDLIEIA 187
                                       67777887743333666666666655558899*************************877666 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.087   3.9e+02       3      14 ..      10      21 ..       8      33 .. 0.78
   2 !   14.0   0.0   1.1e-05     0.049      90     140 ..      27      76 ..      21      85 .. 0.80
   3 !    9.9   0.1    0.0002      0.91     156     186 ..     155     183 ..      75     185 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.087
                               HAD  3 fDfDgTLldgds 14
                                       D+DgT++ +d 
  gi|488600675|ref|YP_007907146.1| 10 IDIDGTITYKDR 21
                                      6******98864 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.1e-05
                               HAD  90 alellaahraaGdrvvvvSgglrplvepllaelg.adevlatelevdd.rltg 140
                                       a+e+++   +  ++vv+ +g+++ +++ ++++ g +d v+++   v++  ++g
  gi|488600675|ref|YP_007907146.1|  27 AVEAIR---KLKVPVVLATGNISCYARTTAKLIGaSDIVICENGGVVRfEYDG 76 
                                       677888...9999*********************99999**944444344444 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0002
                               HAD 156 aalrewlaaegegidleevvayGDspsDlpl 186
                                       +al+      + gi+ e+ va+GDs++D+ l
  gi|488600675|ref|YP_007907146.1| 155 KALKY--ICDELGIPVEKFVAIGDSENDIDL 183
                                       33333..55678899999**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1579.22
//
Query:       gi|488600676|ref|YP_007907147.1|  [L=415]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-37  126.6   1.0    1.6e-36  125.8   1.0    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    5.1e-22   78.6   0.2      7e-22   78.1   0.2    1.2  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    1.7e-21   77.0   0.1    4.5e-21   75.6   0.1    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    6.6e-21   74.3   0.0    1.2e-20   73.5   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8   1.0   3.5e-40   1.6e-36      11     146 ..     242     383 ..     232     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 3.5e-40
                                       T--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------... CS
                     Acyl-CoA_dh_1  11 lnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd... 84 
                                       +  eRl+ aa+a+g+ar+ale a++y+ +rkafg+++ ++q v +++ae +++l+aar+l+y+aa+a+d  +     
  gi|488600676|ref|YP_007907147.1| 242 MIPERLTSAAGAIGTARAALEIAVKYSEKRKAFGRKIREFQGVNFMVAEAMTKLDAARALTYTAAKAVDLYDTGlsk 318
                                       5679**************************************************************88766666667 PP

                                       ...HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHH CS
                     Acyl-CoA_dh_1  85 ...raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniia 146
                                          r  +s aK++a+++ ++v+++amq+lGg Gy++ ypver++rd+r+ +i+ G++ei++ +i+
  gi|488600676|ref|YP_007907147.1| 319 ldpRRLVSEAKYYATDVGWDVVNKAMQILGGIGYTQVYPVERMLRDMRLSPIWTGSNEIMKVLIQ 383
                                       9999********************************************************98886 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.2   1.6e-25     7e-22       2     126 ..     248     368 ..     247     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.6e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       + aa a+G Araal+ +v++ ++r+   +g+k+++++ + + +aea ++ldAAral++ aa++  +l ++g + + +
  gi|488600676|ref|YP_007907147.1| 248 TSAAGAIGTARAALEIAVKYSEKRKA--FGRKIREFQGVNFMVAEAMTKLDAARALTYTAAKA-VDLYDTGLS-KLD 320
                                       67999*********************..*******************************9999.999999999.89* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaa 126
                                        r+  + a+ +a++   ++v++++++ Gg ++++ +p++R++RD++  
  gi|488600676|ref|YP_007907147.1| 321 PRRLVSEAKYYATDVGWDVVNKAMQILGGIGYTQVYPVERMLRDMRLS 368
                                       ********************************************9865 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.1     1e-24   4.5e-21       1     112 [.       9     120 ..       9     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1e-24
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHT.SGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-H CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeeg.efprelwkklaelGllgitvpeeygGagldyleaaivaeelarada 76 
                                       tee+ +lr++v+ef++   ++  +++d+++  +p e+++ +a+  llg+ +peeygG+gl+++++ i++ee++  + 
  gi|488600676|ref|YP_007907147.1|   9 TEEEIKLREEVKEFVASIDPELLRKMDKDEiDYPFEFLEGAAKRNLLGLRFPEEYGGRGLTWTAESIAMEEVGVLGN 85 
                                       799*************977999*****99999********************************************* PP

                                       HHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  77 glalllgvhsslvapailrfGteeqkrryLpklasg 112
                                       gl+ ++++  s+v++ai+rfG e +k+++L+++++g
  gi|488600676|ref|YP_007907147.1|  86 GLGCSYAM-VSIVGEAIYRFGEEWHKEEFLKPIIKG 120
                                       ***98877.567889*******************99 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   2.6e-24   1.2e-20       3      97 .]     127     220 ..     125     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 2.6e-24
                                       E---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE-- CS
                     Acyl-CoA_dh_M   3 alTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsvrr 77 
                                       +lTEp +Gsd  + +t+ ae+ g++++lnG+K++i +++ a+++l++art+ p+  +++ l+ flv+r + gv+v++
  gi|488600676|ref|YP_007907147.1| 127 GLTEPRGGSDFFGTTTK-AEKRGNKWILNGTKRFIAGGKVADFYLIYARTD-PSapGHKALTAFLVER-DMGVEVEE 200
                                       89********9999995.6666667************************44.44489**********6.568***** PP

                                       ---BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                       + + lG rg+ t+++vf+dv
  gi|488600676|ref|YP_007907147.1| 201 VYNLLGFRGMGTARIVFKDV 220
                                       ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2944.28
//
Query:       gi|488600677|ref|YP_007907148.1|  [L=492]
Description: Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-77  261.5   0.0    1.3e-77  261.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.4e-13   51.6   0.3    2.9e-13   50.6   0.3    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.2   0.0   1.4e-81   1.3e-77       2     422 ..       9     391 ..       8     392 .. 0.86

  Alignments for each domain:
  == domain 1  score: 261.2 bits;  conditional E-value: 1.4e-81
                                       HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       e++a+ +p+k +      g++  Y+e ++rv +lAa+L+++Gv+kg++Va++ +n++ ++ +++a+  aG+++ p+n
  gi|488600677|ref|YP_007907148.1|   9 ERAAKLFPEKEVA-G--VGERQNYSETYSRVLKLAAYLKKIGVEKGTVVAVADWNTLKFFELIYAVTAAGGIIYPVN 82 
                                       7889999999966.5..899********************************************************* PP

                                       TTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS CS
                       AMP-binding  79 ptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeee 155
                                        +l++e++ay l++s++++li  ++++  + l+++ +      + i +d+        +++eee e +         
  gi|488600677|ref|YP_007907148.1|  83 IRLPPEQIAYTLKKSDSQLLI--YSEDF-KPLANVFE-----GESISIDD-------LQYSEEEIE-W--------D 135
                                       *********************..54443.33333333.....22455552.......233333222.2........3 PP

                                       -BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH...HHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHT CS
                       AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk...letr..fklkeddvvlsilplahifglilelllalls 227
                                       +++dd  +i++TSGTTG PK+V ++h+ +++ + s++   + ++   kl+ +dv++   p++hi+++   +++a + 
  gi|488600677|ref|YP_007907148.1| 136 VRQDDYSVIMFTSGTTGLPKAVRYTHEKMLHGALSIAhqlVIHEtpAKLTGNDVMFPQIPIYHILAW-GTVFIAPYM 211
                                       578********************************9988744444566777****************.999999999 PP

                                       T-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                       AMP-binding 228 GatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffr 304
                                       G ++++  k+++      ++l+++++vt i++vP+++++lle    +      dls+l++ l+gg+p+ ++l+r+++
  gi|488600677|ref|YP_007907148.1| 212 GLKLIMGGKFDPVG---AVKLMKEEGVTWINAVPTMINMLLET--GE------DLSGLKI-LVGGSPVTSDLARKME 276
                                       ******99998833...369**********************7..35......9*****9.68************** PP

                                       HHHTCEEEEEEEEGGGSSECEE...CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEB CS
                       AMP-binding 305 alfgeevlegYGlTEttgvvtv...lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgY 378
                                       +++++ +  +YG T ++++ +     + + +  +   v  p+p +e kiv +e++     g  Ge+++r p++   Y
  gi|488600677|ref|YP_007907148.1| 277 SRGIK-FTTIYGATDMLAASIAiqtSYAKSKPGYMREVTHPVPFAEFKIVQPEGL----SGDMGEIFFRAPWLPGEY 348
                                       **998.*************95435533344444566789*************954....5899************** PP

                                       TT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 379 lkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       +k++e+t+ea++ e++w+ TGD+g + +dG +++++R kd ik+
  gi|488600677|ref|YP_007907148.1| 349 YKDEEKTREAYT-EDGWFITGDVGIIMPDGGIKVLDRVKDAIKS 391
                                       ***********9.867**************************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 !   50.6   0.3   3.3e-17   2.9e-13       2      76 .]     401     480 ..     401     480 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 3.3e-17
                                       HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------....HHHHHHHHH.HHHT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea....leeeLkahv.rkelgpyavpkkvvfvdelpktr 73 
                                       +Esa+++++ V+ +aVvG++de++ e++va++ + + ++a    ++++L + v + ++++++ p++++fv+e+p+t 
  gi|488600677|ref|YP_007907148.1| 401 LESAISEVEWVEYVAVVGKKDEKWDERPVAIIKPTEMQKAnveeVKNHLLKLVeEGRIAKWWIPEEIIFVEEMPLTS 477
                                       59********************************4323231222555555555555********************* PP

                                       TS- CS
                     AMP-binding_C  74 sGK 76 
                                       +GK
  gi|488600677|ref|YP_007907148.1| 478 TGK 480
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3116.99
//
Query:       gi|488600678|ref|YP_007907149.1|  [L=135]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-20   71.1   1.2      6e-20   71.1   1.2    2.0  3  MerR_1         MerR HTH family regulatory protein
    1.8e-16   60.4   1.7    1.8e-16   60.4   1.7    2.1  2  MerR-DNA-bind  MerR, DNA binding
    1.4e-14   53.6   0.5    4.9e-14   51.8   0.7    1.8  2  MerR           MerR family regulatory protein
    0.00032   20.6   0.9     0.0012   18.8   0.0    2.4  2  HTH_11         HTH domain
  ------ inclusion threshold ------
       0.01   16.0   1.8      0.032   14.4   0.1    2.3  2  HTH_17         Helix-turn-helix domain
      0.011   15.8   0.0      0.035   14.2   0.0    1.8  1  HTH_28         Helix-turn-helix domain
      0.012   15.6   0.6       0.12   12.4   0.2    2.5  2  HTH_3          Helix-turn-helix
      0.013   15.2   0.0        0.1   12.4   0.0    2.3  2  HTH_DeoR       DeoR-like helix-turn-helix domain
      0.033   14.4   0.7      0.053   13.8   0.7    1.3  1  NUMOD1         NUMOD1 domain
      0.041   13.7   0.7       0.58   10.0   0.0    2.4  2  HTH_23         Homeodomain-like domain
       0.05   13.3   1.2        3.3    7.5   0.0    3.0  3  HTH_41         Helix-turn-helix domain
      0.077   13.3   0.1      0.077   13.3   0.1    1.7  2  PAXIP1_C       PAXIP1-associated-protein-1 C term PTIP bindin
      0.081   12.6   3.4        2.5    7.8   0.0    2.8  2  Sigma70_r4_2   Sigma-70, region 4
       0.12   13.0   1.6       0.44   11.2   0.7    2.4  3  HTH_32         Homeodomain-like domain
       0.13   12.2   0.8        5.5    7.0   0.1    2.8  2  Terminase_5    Putative ATPase subunit of terminase (gpP-like
       0.13   12.0   0.0       0.28   11.0   0.0    1.6  1  HTH_psq        helix-turn-helix, Psq domain
       0.94    9.6   3.7        3.7    7.7   0.3    2.6  2  MRP-L20        Mitochondrial ribosomal protein subunit L20
        1.7    8.9   8.6      0.094   12.9   1.5    2.3  3  XhlA           Haemolysin XhlA


Domain annotation for each model (and alignments):
>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   1.2     6e-23     6e-20       1      67 [.      12      78 ..      12      80 .. 0.98
   2 ?   -1.6   0.1       3.1   3.1e+03      52      67 ..      91     107 ..      86     109 .. 0.58
   3 ?   -1.4   0.2       2.6   2.6e+03      45      45 ..     108     108 ..      92     123 .. 0.57

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 6e-23
                                      EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHHHHHHHHHHTT--GGG---XXX CS
                            MerR_1  1 ysigevakilgvtthtlrywekegllkpkrteggrryYtdedierLklikyLlkrGltlkgikklln 67
                                      y+i+e+a++++++t+t+ry+e+ gll pkrt g++r++t++d +rLkli + +  G+ l++ik++++
  gi|488600678|ref|YP_007907149.1| 12 YTISELAREFEISTRTIRYYEEVGLLSPKRTPGNQRRFTRKDRARLKLILRGKRLGFRLEEIKEMID 78
                                      9***************************************************************987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.1
                                       HHH.TT--GGG---XXX CS
                            MerR_1  52 Llk.rGltlkgikklln 67 
                                        lk    +lk+i + ++
  gi|488600678|ref|YP_007907149.1|  91 TLKyGEKKLKEIEEKIE 107
                                       44446667777766655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.6
                                       H CS
                            MerR_1  45 r 45 
                                       +
  gi|488600678|ref|YP_007907149.1| 108 E 108
                                       2 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   1.7   1.8e-19   1.8e-16       1      63 [.      54     117 ..      54     119 .. 0.91
   2 ?    1.9   0.2      0.33   3.3e+02      37      52 ..     119     134 ..     117     135 .] 0.86

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.8e-19
                                       HHHHHHHHHHHHTT--HHHHHHHHHHHHSTTTBHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind   1 leRLkfIrrarrlGFsLdeIrelLalyddrappcqdvr.allarklaeleeriaeLqalraeLa 63 
                                       ++RLk+I+r++rlGF L+eI+e++++yd ++p++ ++  +  ++kl+e+ee+i+eL+alr+++ 
  gi|488600678|ref|YP_007907149.1|  54 RARLKLILRGKRLGFRLEEIKEMIDMYDVSEPEQIKLTlKYGEKKLKEIEEKIEELKALREDIL 117
                                       58***************************7666666666*********************9875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  37 vrallarklaeleeri 52 
                                       +r++l ++l+ele ++
  gi|488600678|ref|YP_007907149.1| 119 LREILLKRLEELEGKR 134
                                       6899********9876 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.7   4.9e-17   4.9e-14       1      38 []      13      49 ..      13      49 .. 0.99
   2 ?   -1.9   0.0       2.9   2.9e+03       2      12 ..      73      83 ..      73      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.9e-17
                                      EHHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSEEE CS
                              MerR  1 tIgevAeltGvsprtLRyYEreGLipppeRtegGyRlY 38
                                      tI+e+A+ + +s+rt+RyYE+ GL+ +p Rt+g++R++
  gi|488600678|ref|YP_007907149.1| 13 TISELAREFEISTRTIRYYEEVGLL-SPKRTPGNQRRF 49
                                      8************************.**********98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                                      HHHHHHHHTTT CS
                              MerR  2 IgevAeltGvs 12
                                      I+e+ ++ +vs
  gi|488600678|ref|YP_007907149.1| 73 IKEMIDMYDVS 83
                                      89999999998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06    0.0012      11      33 ..       6      29 ..       1      31 [. 0.84
   2 ?   -0.7   0.2       1.5   1.4e+03      33      33 ..     113     113 ..      97     134 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                            HTH_11 11 eargp.isgeeLAeeLnvSrrtvr 33
                                      +++++  +++eLA+e+++S+rt+r
  gi|488600678|ref|YP_007907149.1|  6 KSKKNhYTISELAREFEISTRTIR 29
                                      5555559****************8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                            HTH_11  33 r 33 
                                       r
  gi|488600678|ref|YP_007907149.1| 113 R 113
                                       2 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.2e-05     0.032       2      42 ..      12      53 ..      12      53 .. 0.95
   2 ?    0.1   0.2      0.98   9.7e+02      32      48 ..      62      78 ..      54      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                            HTH_17  2 ltveEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsd 42
                                      +t++E+A+ + +s +t++ +   g l + +  G+++r++r+d
  gi|488600678|ref|YP_007907149.1| 12 YTISELAREFEISTRTIRYYEEVGLLSPKRtPGNQRRFTRKD 53
                                      8*************************88879********987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.98
                            HTH_17 32 iGrrwriprsdleewle 48
                                      +G+r+ ++ +++ e+++
  gi|488600678|ref|YP_007907149.1| 62 RGKRLGFRLEEIKEMID 78
                                      78899999999999885 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.5e-05     0.035      10      30 ..       9      29 ..       4      32 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                            HTH_28 10 aaGhsvreaArelgisrrtvy 30
                                      +++ +++e+Are+ is rt++
  gi|488600678|ref|YP_007907149.1|  9 KNHYTISELAREFEISTRTIR 29
                                      3555****************7 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00012      0.12       1      30 [.       3      32 ..       3      33 .. 0.91
   2 ?    0.6   0.0      0.61   6.1e+02      36      52 ..      68      84 ..      51      87 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriE 30
                                      lk++ k++ +++ eLA++  +s +ti+ +E
  gi|488600678|ref|YP_007907149.1|  3 LKKKSKKNHYTISELAREFEISTRTIRYYE 32
                                      56777899*********************9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.61
                                      SBHHHHHHHHHHHTSEH CS
                             HTH_3 36 PsletlkklakaLgvsl 52
                                       +le +k++ + ++vs 
  gi|488600678|ref|YP_007907149.1| 68 FRLEEIKEMIDMYDVSE 84
                                      45667777777777765 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   0.0    0.0001       0.1      11      32 ..       8      29 ..       3      30 .. 0.92
   2 ?   -0.2   0.0      0.89   8.8e+02      17      28 ..      73      84 ..      69      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                          HTH_DeoR 11 qqgklsveelvellgvSeaTiR 32
                                      ++ + ++ el+ ++++S+ TiR
  gi|488600678|ref|YP_007907149.1|  8 KKNHYTISELAREFEISTRTIR 29
                                      678899***************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.89
                          HTH_DeoR 17 veelvellgvSe 28
                                      ++e ++ ++vSe
  gi|488600678|ref|YP_007907149.1| 73 IKEMIDMYDVSE 84
                                      788899999996 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   5.4e-05     0.053       9      36 ..       4      31 ..       2      31 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-05
                            NUMOD1  9 ntktigkFsSireAakyLgishntInky 36
                                      ++k++   ++i+e+a+ + is +tI++y
  gi|488600678|ref|YP_007907149.1|  4 KKKSKKNHYTISELAREFEISTRTIRYY 31
                                      5666777789****************99 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00059      0.58      17      37 ..      11      31 ..       3      34 .. 0.86
   2 ?    1.4   0.2       0.3     3e+02       3      26 ..      52      76 ..      50      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                            HTH_23 17 GlsvreIAreLgvsrrTvyrw 37
                                       ++++e Are+ +s rT++ +
  gi|488600678|ref|YP_007907149.1| 11 HYTISELAREFEISTRTIRYY 31
                                      689***************965 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.3
                            HTH_23  3 sereRlrillllae.GlsvreIAre 26
                                      + r Rl+ +l  ++ G + +eI ++
  gi|488600678|ref|YP_007907149.1| 52 KDRARLKLILRGKRlGFRLEEIKEM 76
                                      6788999999999999999999776 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0033       3.3       8      23 ..      13      28 ..      11      30 .. 0.88
   2 ?    2.9   0.0     0.087        87       2      19 ..      66      83 ..      65      84 .. 0.86
   3 ?   -0.3   0.1      0.86   8.5e+02       5      16 ..      98     109 ..      93     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0033
                            HTH_41  8 tIeelakeleLSvGlv 23
                                      tI+ela e+e+S  ++
  gi|488600678|ref|YP_007907149.1| 13 TISELAREFEISTRTI 28
                                      9***********7665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.087
                            HTH_41  2 vGdRlktIeelakeleLS 19
                                       G Rl+ I+e++  +++S
  gi|488600678|ref|YP_007907149.1| 66 LGFRLEEIKEMIDMYDVS 83
                                      689*********988877 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.86
                            HTH_41   5 RlktIeelakel 16 
                                       +lk Iee ++el
  gi|488600678|ref|YP_007907149.1|  98 KLKEIEEKIEEL 109
                                       799999999886 PP

>> PAXIP1_C  PAXIP1-associated-protein-1 C term PTIP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.8e-05     0.077      65     122 ..       4      61 ..       2      65 .. 0.88
   2 ?   -1.4   0.5       2.7   2.7e+03      23      47 ..      75      98 ..      70     115 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-05
                          PAXIP1_C  65 eeeekeeeekkpkvpteFDFdeeseqatakkkllerrRtpgssqrssqkrvArldkvl 122
                                       +++ k+++ ++ +++ eF+    + +   +  ll+++Rtpg+++r ++k  Arl  +l
  gi|488600678|ref|YP_007907149.1|   4 KKKSKKNHYTISELAREFEISTRTIRYYEEVGLLSPKRTPGNQRRFTRKDRARLKLIL 61 
                                       567777888888899********99999999***********9999*******98776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                          PAXIP1_C 23 eivklYellekdgvleLqlkclprr 47
                                      e+ ++Y+ +++ + ++L lk   ++
  gi|488600678|ref|YP_007907149.1| 75 EMIDMYD-VSEPEQIKLTLKYGEKK 98
                                      5555565.35556666666554443 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 ?    7.8   0.0    0.0025       2.5      26      46 ..      11      31 ..      10      31 .. 0.91
   2 ?    3.5   1.6     0.055        55       2      24 ..     100     122 ..      99     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0025
                                      ---HHHHHHHHT--HHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksr 46
                                      ++++ E A++++is +t++++
  gi|488600678|ref|YP_007907149.1| 11 HYTISELAREFEISTRTIRYY 31
                                      6899**************975 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.055
                                       HHHHHHHTTS-HHHHHHHHHHHT CS
                      Sigma70_r4_2   2 qalrealaeLperqreifllryl 24 
                                        +++e ++eL   +  i++lr++
  gi|488600678|ref|YP_007907149.1| 100 KEIEEKIEELKALREDILMLREI 122
                                       5899****************987 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.32   3.2e+02      46      70 ..      11      29 ..       2      32 .. 0.72
   2 ?   11.2   0.7   0.00044      0.44       4      64 ..      26      82 ..      23     108 .. 0.80
   3 ?   -1.3   0.0       3.6   3.6e+03      34      41 ..     106     113 ..      93     132 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.32
                            HTH_32 46 rWsprqlaarlaeregvkvShstvy 70
                                      +++ ++la++       ++S +t++
  gi|488600678|ref|YP_007907149.1| 11 HYTISELAREF------EISTRTIR 29
                                      67777777766......89****98 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00044
                            HTH_32  4 rwlkRyneeGlegLkdrprrgrprklsdevrariiallreep.rWsprqlaarlaeregvkv 64
                                      r+++ y+e G   L +++ +g  r+++   rar++ +lr ++  + ++++ + + + +  +v
  gi|488600678|ref|YP_007907149.1| 26 RTIRYYEEVG--LLSPKRTPGNQRRFTRKDRARLKLILRGKRlGFRLEEIKEMI-DMY--DV 82
                                      7777787776..7779988999999*************5444577888898888.554..34 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.6
                            HTH_32  34 rariiall 41 
                                        ++++al+
  gi|488600678|ref|YP_007907149.1| 106 IEELKALR 113
                                       33333333 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0055       5.5      13      34 ..      11      32 ..      10      34 .. 0.91
   2 ?    2.5   0.1      0.14   1.3e+02      13      26 ..      67      80 ..      66     114 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0055
                       Terminase_5 13 GyrvaeIAeelglkeatVysWk 34
                                       y++ e A+e  ++ +t+ ++ 
  gi|488600678|ref|YP_007907149.1| 11 HYTISELAREFEISTRTIRYYE 32
                                      59*****************995 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                       Terminase_5 13 GyrvaeIAeelglk 26
                                      G+r  eI e++++ 
  gi|488600678|ref|YP_007907149.1| 67 GFRLEEIKEMIDMY 80
                                      66777777777653 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 ?   11.0   0.0   0.00028      0.28      18      36 ..      13      31 ..       9      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                           HTH_psq 18 SirkAArkYgiPrsTLwrr 36
                                      +i+++Ar+++i+++T++++
  gi|488600678|ref|YP_007907149.1| 13 TISELAREFEISTRTIRYY 31
                                      5899************976 PP

>> MRP-L20  Mitochondrial ribosomal protein subunit L20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3    0.0037       3.7     104     125 ..      11      32 ..       3      61 .. 0.83
   2 ?    2.3   0.3      0.17   1.7e+02      86      99 ..     101     114 ..      70     115 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0037
                           MRP-L20 104 kwsrkkLakkFgcsklfvsmvt 125
                                        +++++La++F++s+  +++  
  gi|488600678|ref|YP_007907149.1|  11 HYTISELAREFEISTRTIRYYE 32 
                                       79*************9998765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.17
                           MRP-L20  86 ltkedieeirrLra 99 
                                         +e+iee++ Lr+
  gi|488600678|ref|YP_007907149.1| 101 EIEEKIEELKALRE 114
                                       24678888888886 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.4   1.4e+03      30      44 ..       3      17 ..       2      21 .. 0.82
   2 ?   12.9   1.5   9.4e-05     0.094       5      46 ..      69     111 ..      68     113 .. 0.95
   3 ?   -2.7   0.1       7.2   7.1e+03       4      11 ..     125     132 ..     123     134 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                              XhlA 30 aeekiknleedlkkl 44
                                       ++k+k ++ ++++l
  gi|488600678|ref|YP_007907149.1|  3 LKKKSKKNHYTISEL 17
                                      578999999999998 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.4e-05
                              XhlA   5 rlerietkldnlee.rvdkleekaaeaeekiknleedlkkles 46 
                                       rle+i++++d+++  + +++++     e+k+k++ee++++l++
  gi|488600678|ref|YP_007907149.1|  69 RLEEIKEMIDMYDVsEPEQIKLTLKYGEKKLKEIEEKIEELKA 111
                                       89***********99889***********************96 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.2
                              XhlA   4 erleriet 11 
                                       +rle++e+
  gi|488600678|ref|YP_007907149.1| 125 KRLEELEG 132
                                       56666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1330  (0.0741815); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 831.85
//
Query:       gi|488600679|ref|YP_007907150.1|  [L=132]
Description: hypothetical protein Asulf_01158 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-16   58.6   0.2    9.8e-16   57.9   0.1    1.5  2  4HBT             Thioesterase superfamily
    4.3e-07   30.4   0.0      5e-07   30.2   0.0    1.1  1  4HBT_3           Thioesterase-like superfamily
    1.1e-05   25.5   0.2    1.5e-05   25.1   0.2    1.1  1  DUF4442          Domain of unknown function (DUF4442)
  ------ inclusion threshold ------
      0.088   12.4   0.1       0.11   12.0   0.1    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 ?   -3.3   0.0       2.8   1.2e+04      46      57 ..      26      37 ..      25      38 .. 0.72
   2 !   57.9   0.1   2.2e-19   9.8e-16       2      77 ..      45     120 ..      44     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                                      TTCEEEEEEEEE CS
                              4HBT 46 lgdeltvearvl 57
                                      lgd+  ve +v+
  gi|488600679|ref|YP_007907150.1| 26 LGDKTIVELEVS 37
                                      688888888876 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 2.2e-19
                                       SSB-HHHHHHHHHHHHHHHHHHTTST.TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   2 GvvhgGvylallDeaagaalrslggr.gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                       G+ hgGv++++lD+aag+a+++   + g+++v++e+++++l+pvr g ++++e++v+  g++++v + + ++ d+ +
  gi|488600679|ref|YP_007907150.1|  45 GTAHGGVLASILDSAAGLAVNRELYGsGKIAVTAEMKVNYLKPVRNG-KVVAEGEVVSWGSKIVVATSKAYQNDELV 120
                                       9***********************999********************.********************999999876 PP

>> 4HBT_3  Thioesterase-like 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       9      83 ..      44     127 ..      36     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                                       TC..-HHHHHHHHHHHHHHT........-S.SS...EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEETTE CS
                            4HBT_3   9 ga.gyGGyvlAlalraaqrtv.......pdprl...hslhvyFlrpgdagpviyhvervrdGrsfstrtvelsqggr 74 
                                        + ++GG++++++ +aa  +v        +  +   + + v++l+p+  g+v+ + e+v  G ++ + t +++q+++
  gi|488600679|ref|YP_007907150.1|  44 LGtAHGGVLASILDSAAGLAVnrelygsGK--IavtAEMKVNYLKPVRNGKVVAEGEVVSWGSKIVVATSKAYQNDE 118
                                       3424****************9777776533..34489**************************************** PP

                                       EEEEEEEEE CS
                            4HBT_3  75 piftatasf 83 
                                        ++++t+++
  gi|488600679|ref|YP_007907150.1| 119 LVAICTVTM 127
                                       ******997 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   3.3e-09   1.5e-05      30     131 ..      29     128 ..      23     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.3e-09
                                       EEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-T.TEEEEEEEEEEEE-S-.--S-EEEEEE-TTS-TT CS
                           DUF4442  30 raevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpd.thrwipkgmevdYlak.atgdltavaelepedvg 104
                                       ++ v+l+   +++ ++gt H++ ++++++ a+Gl +++ l   ++  +   m+v+Yl++  +g++ a+ e+    +g
  gi|488600679|ref|YP_007907150.1|  29 KTIVELEVSEKHHQALGTAHGGVLASILDSAAGLAVNRELYGsGKIAVTAEMKVNYLKPvRNGKVVAEGEV--VSWG 103
                                       66788899999*************************99986648999999*********667888776655..4555 PP

                                       --EEEEEEEEEEETTE.EEEEEEEEEE CS
                           DUF4442 105 ekeelvvevevrdekgeevvraeitlw 131
                                          ++vv+ +   +++e v+ +++t++
  gi|488600679|ref|YP_007907150.1| 104 --SKIVVATSKAYQNDELVAICTVTMY 128
                                       ..4455555555555557777777776 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.5e-05      0.11      52     101 ..      51      99 ..      36     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                                       B--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEE CS
                   MaoC_dehydratas  52 IahGmltlaivaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelev 101
                                       ++ ++l +a+  ++  e +g++ +a + e kv + kpV+ g  +  e ev
  gi|488600679|ref|YP_007907150.1|  51 VLASILDSAAGLAVNRELYGSGKIAVTAEMKVNYLKPVRNGKVVA-EGEV 99 
                                       666778899999999999*********************998663.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 938.18
//
Query:       gi|488600680|ref|YP_007907151.1|  [L=51]
Description: hypothetical protein Asulf_01159 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       499  (0.027832); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 349.46
//
Query:       gi|488600681|ref|YP_007907152.1|  [L=345]
Description: hypothetical protein Asulf_01160 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00013   21.8   0.1    0.00024   20.9   0.1    1.5  1  Phage_integrase  Phage integrase family
     0.0038   16.1   0.0      0.007   15.3   0.0    1.3  1  Mitofilin        Mitochondrial inner membrane protein
  ------ inclusion threshold ------
       0.13   12.7   1.0        9.2    6.7   0.1    2.7  2  ACP_PD           Acyl carrier protein phosphodiesterase


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 !   20.9   0.1   4.1e-08   0.00024       2     143 ..     139     290 ..     138     320 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.1e-08
                                       HHHHHHHHHHHHCCGC.......HHHHHHHHH.....HHHHHHHT--HHHHTT-BGGG....EECTTTEEEEEEEEC CS
                   Phage_integrase   2 vltedeverllaalee.......slkirdkll.....lellyetGlRisEllsLrvkd....ldlengvilvhereg 62 
                                       v+te++ver +++  +       s k +   l     + +   +G+R   +++Lrv++    l+l+  +ilv++++ 
  gi|488600681|ref|YP_007907152.1| 139 VITEKDVERVIKFFIKrwkagelSRKKT---LshvtqTLFGAYSGQRPYTIARLRVDQfeeaLKLKTPTILVEASQD 212
                                       7899999999999888898765533333...2333235555679************9833346799*********** PP

                                       SSSSEEEEECTHHHHHHHHHHHHHHCHCCTTTSBSSBET.TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHH CS
                   Phage_integrase  63 Kgskeravplseealellkellskaleeaeksellfask.rgkplsrqtvrkafkraveeagiekpltpHtlRhsfa 138
                                       K + e++vpl   +++ lk ll+ +  +++++e +f     ++ l+r +++     + +  ++  ++   +lR  fa
  gi|488600681|ref|YP_007907152.1| 213 KIRMEHYVPLHPDIVPFLKALLKIR--KKQGKEKMFDYNsYEQLLKRAKISLERGDLIKDPNKR-HFVVGDLR-KFA 285
                                       *************************..5555555565551344444445555555555555554.66666666.666 PP

                                       HHHHH CS
                   Phage_integrase 139 taLle 143
                                        +++ 
  gi|488600681|ref|YP_007907152.1| 286 EQMAD 290
                                       66665 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-06     0.007     543     580 ..     229     267 ..     226     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                         Mitofilin 543 yllSkllfkpkq.geldvagdDvesiLaRAeyyLeegdL 580
                                       +l+++l +++kq +e +++ +++e++L+RA+  Le+gdL
  gi|488600681|ref|YP_007907152.1| 229 FLKALLKIRKKQgKEKMFDYNSYEQLLKRAKISLERGDL 267
                                       689******99955559*********************9 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.013        78      11      45 ..      31      65 ..      25     100 .. 0.81
   2 ?    6.7   0.1    0.0015       9.2       8      40 ..     311     342 ..     309     345 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.013
                            ACP_PD 11 eysaepLeefvqrvyaqlekneealPerlqrllpr 45
                                      eys e+Le+++q+  + ++k+++++ e++++++++
  gi|488600681|ref|YP_007907152.1| 31 EYSREELEAYTQNRLKGISKKTRWWIEKASQTFWE 65
                                      799***************99999999998887765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0015
                            ACP_PD   8 nwseysaepLeefvqrvyaqlekneealPerlq 40 
                                       +ws+y+  pL+efv ++y +  +n + +P+++ 
  gi|488600681|ref|YP_007907152.1| 311 DWSNYK-HPLPEFVYQIYMESWENVHLVPKEAY 342
                                       8****6.9************9999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2185.52
//
Query:       gi|488600682|ref|YP_007907153.1|  [L=245]
Description: hypothetical protein Asulf_01161 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.2   1.0     0.0031   17.0   1.0    1.1  1  DUF3387        Domain of unknown function (DUF3387)
  ------ inclusion threshold ------
      0.051   14.1   0.1       0.11   13.1   0.1    1.6  1  MerR-DNA-bind  MerR, DNA binding
       0.79    9.8   8.7       0.67   10.1   1.7    2.5  3  DUF5101        Domain of unknown function (DUF5101)
        2.5    8.8   4.5        4.7    7.9   4.5    1.5  1  LPAM_1         Prokaryotic membrane lipoprotein lipid attachm


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 !   17.0   1.0   6.8e-07    0.0031      61     185 ..      38     165 ..      21     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.8e-07
                           DUF3387  61 egkkrFlklvka..Lkkay.alcapseeaeelrdevaffqavrailvKltaaeegkspdteeleaavrqlidkaias 134
                                       e  k+F+++v++  +k+ay +l++++e++ e+++e+ f +++  +l+   +++  ++  +e l+ ++  l+++    
  gi|488600682|ref|YP_007907153.1|  38 EEGKQFVENVTQieIKEAYeSLVNQEEQLIEEAKELGFNTEIIIALYDELKRNPFNQDVIELLKFHIDALMQEESIN 114
                                       5678999998862268999457888888***************99999888777777778999************** PP

                           DUF3387 135 eevvdifaaaglekpdisiLseefleevkkmkeknlavelLkklLadeika 185
                                       e   ++ + +  e + i  ++e+f e+ +  +++ + ++ + k L+++  +
  gi|488600682|ref|YP_007907153.1| 115 ESHKELANILADEIKAIGPINETFFEDYETFNRQTYRINHIAKTLNQKFGT 165
                                       **********************************************99765 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.4e-05      0.11       5      51 ..      65     110 ..      65     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHTT--HHHHHHHHHHHHS..TTTBHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind   5 kfIrrarrlGFsLdeIrelLalydd..rappcqdvrallarklaeleer 51 
                                       ++I  a++lGF  + I +l    d+  r+p  qdv +ll+ +++ l + 
  gi|488600682|ref|YP_007907153.1|  65 QLIEEAKELGFNTEIIIALY---DElkRNPFNQDVIELLKFHIDALMQE 110
                                       6899********99987777...555589***************99864 PP

>> DUF5101  Domain of unknown function (DUF5101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.7   0.00015      0.67      61      95 ..      45      79 ..      37      82 .. 0.86
   2 ?    3.5   0.5     0.016        73      62      90 ..      93     121 ..      86     129 .. 0.90
   3 ?   -3.5   0.0       2.5   1.1e+04      60      72 ..     174     187 ..     168     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                           DUF5101 61 EnqevvelkealeevleEnEklvkekvdLiaelei 95
                                      En+  +e+kea e +++ +E+l++e ++L  + ei
  gi|488600682|ref|YP_007907153.1| 45 ENVTQIEIKEAYESLVNQEEQLIEEAKELGFNTEI 79
                                      9***************************9776665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.016
                           DUF5101  62 nqevvelkealeevleEnEklvkekvdLi 90 
                                       nq+v+el +  +++l+ +E + + +++L+
  gi|488600682|ref|YP_007907153.1|  93 NQDVIELLKFHIDALMQEESINESHKELA 121
                                       99*********************999995 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.5
                           DUF5101  60 kEnqe.vvelkeal 72 
                                       kEn   + ++++al
  gi|488600682|ref|YP_007907153.1| 174 KENFVgIQDIRKAL 187
                                       67743266777776 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 ?    7.9   4.5     0.001       4.7       7      18 .]      12      23 ..      10      23 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.001
                            LPAM_1  7 algalllLsGCs 18
                                      +++++llL+GCs
  gi|488600682|ref|YP_007907153.1| 12 LILLALLLTGCS 23
                                      89*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1391.82
//
Query:       gi|488600683|ref|YP_007907154.1|  [L=45]
Description: hypothetical protein Asulf_01162 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.27s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 368.07
//
Query:       gi|488600684|ref|YP_007907155.1|  [L=56]
Description: hypothetical protein Asulf_01163 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.7   0.3        1.3    9.8   0.0    2.4  3  TPR_6     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1    0.0068   1.2e+02      15      28 ..       2      15 ..       1      17 [. 0.86
   2 ?    9.8   0.0   7.2e-05       1.3      19      32 ..      24      37 ..      22      37 .. 0.94
   3 ?   -2.5   0.0      0.61   1.1e+04      17      24 ..      40      47 ..      39      48 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0068
                                      HHHHHHHHHHHHHH CS
                             TPR_6 15 dtdkAlealerlik 28
                                      + d+A++ le l k
  gi|488600684|ref|YP_007907155.1|  2 NRDEARKVLEVLAK 15
                                      679*******9976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7.2e-05
                                      HHHHHHHHHHH-TT CS
                             TPR_6 19 AlealerlikeYPd 32
                                      A+e+++++i+e+P+
  gi|488600684|ref|YP_007907155.1| 24 ARELFNNFIQEFPE 37
                                      9************5 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.61
                                      HHHHHHHH CS
                             TPR_6 17 dkAleale 24
                                      d A++ ++
  gi|488600684|ref|YP_007907155.1| 40 DLAKTVFK 47
                                      66888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 358.75
//
Query:       gi|488600685|ref|YP_007907156.1|  [L=65]
Description: hypothetical protein Asulf_01164 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   32.3   0.0    9.7e-08   32.2   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 !   32.2   0.0   5.4e-12   9.7e-08       3      49 ..       6      52 ..       4      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.4e-12
                   HicB_lk_antitox  3 iaiek.dedsaygvvvPdlpGcfsagdtleeaianakeaielhlegli 49
                                      i i   +ed+ +  +vP+lpGc   g+t eea+++ k aiel++e++ 
  gi|488600685|ref|YP_007907156.1|  6 IEIFYsKEDEGF-TIVPELPGCSVFGETDEEALKEVKTAIELWIEAAK 52
                                      555541334444.579*****************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 470.55
//
Query:       gi|488600686|ref|YP_007907157.1|  [L=104]
Description: hypothetical protein Asulf_01165 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); 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: 00:00:00.47
# Mc/sec: 663.90
//
Query:       gi|488600687|ref|YP_007907158.1|  [L=88]
Description: hypothetical protein Asulf_01166 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 603.16
//
Query:       gi|488600688|ref|YP_007907159.1|  [L=89]
Description: hypothetical protein Asulf_01167 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.074   12.4   0.0        0.1   12.0   0.0    1.2  1  NucS             Endonuclease NucS
      0.078   13.4   0.0       0.13   12.7   0.0    1.4  2  DUF234           Archaea bacterial proteins of unknown functi
        0.1   12.3   0.0       0.13   11.9   0.0    1.1  1  MmcB-like        DNA repair protein MmcB-like
       0.22   11.1   0.0       0.22   11.1   0.0    1.1  1  Glyco_hydro_32N  Glycosyl hydrolases family 32 N-terminal dom


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.2e-05       0.1     105     156 ..      22      82 ..       5      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                              NucS 105 GseaelaeliiehpdLi.....eeGfkpv...areyava.iGivdiLgkdeegklvivelk 156
                                         eael++l+ie p Li      eG  p+     e+ ++ +G  diL+  e+g++ i+e k
  gi|488600688|ref|YP_007907159.1|  22 KAEAELQKLLIESPSLIpvdeiREGASPLvfaVAEFWLPgSGSTDILAFSENGDIAIIECK 82 
                                       479***********996443336999885222356665449******************98 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.7   7.5e+03      64      79 ..      13      28 ..       8      33 .. 0.61
   2 ?   12.7   0.0     3e-05      0.13      53      91 ..      48      85 ..      36      89 .] 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                            DUF234 64 WkkeeeiDivaldeee 79
                                      Wk  e iD  a +e +
  gi|488600688|ref|YP_007907159.1| 13 WKPVESIDTKAEAELQ 28
                                      6666777765555544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3e-05
                            DUF234 53 lpfrftkvGrwW.kkeeeiDivaldeeekkalfgEvKwkn 91
                                       p    +v ++W   +   Di+a++e+++ + ++E+K  +
  gi|488600688|ref|YP_007907159.1| 48 SPLV-FAVAEFWlPGSGSTDILAFSENGD-IAIIECKLAT 85
                                      4543.35666772577799*********6.*******876 PP

>> MmcB-like  DNA repair protein MmcB-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.9e-05      0.13      32      62 ..      53      83 ..      43      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                         MmcB-like 32 alpelsLasGrraDlvalskkgeiwiieiks 62
                                      a++e+ L+     D++a s++g+i iie k 
  gi|488600688|ref|YP_007907159.1| 53 AVAEFWLPGSGSTDILAFSENGDIAIIECKL 83
                                      7899***88889****************995 PP

>> Glyco_hydro_32N  Glycosyl hydrolases family 32 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.9e-05      0.22     157     197 ..       4      46 ..       1      76 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                                       EEEESSSSSEEEECCESEECC.T..TTEEEEEEEEEEECSTT- CS
                   Glyco_hydro_32N 157 lYkskdlkewelaselleskkek..ggmwEcpdlfeldekdee 197
                                       l +s+d k+w+ +++++++++ +  +  +E p l+++de +e+
  gi|488600688|ref|YP_007907159.1|   4 LIRSDDSKNWKPVESIDTKAEAElqKLLIESPSLIPVDEIREG 46 
                                       569***********9999988767799**********987533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 507.93
//
Query:       gi|488600689|ref|YP_007907160.1|  [L=146]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-24   87.2   0.7    1.2e-24   87.0   0.7    1.0  1  EVE             EVE domain
     0.0039   17.0   0.0     0.0057   16.5   0.0    1.4  1  Dev_Cell_Death  Development and cell death domain


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.7   1.3e-28   1.2e-24       1     143 [.       2     143 ..       2     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.3e-28
                                       -EEEEEEBHHTSHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEE......ETSSS...S-EEEEEEEEECEE CS
                               EVE   1 ayWllksepdefsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfY......hsgek...lqaivgiaeVvsea 68 
                                       ayWl+++++d  ++  +  k++++W gv++ +++n++ ++++GD++l+Y      +   +   +++iv+++e vse+
  gi|488600689|ref|YP_007907160.1|   2 AYWLCITNED--NWRVI--KQKNIW-GVPE-RHKNTIAKVRPGDKLLIYlkqernK---DtvkEPRIVAVYEAVSEV 69 
                                       6*********..99999..99****.****.99****************9975422...24579************* PP

                                       EE-GGGG-TTSTT--TTTBTTS-.-EEEEEEEEEEEEEEEEHHHHTTHG.TCTTSHHHHCC..T-SEEEE-HHHHHH CS
                               EVE  69 ypdetqfdpkskyydpkskkekp.wlrvdvkpvkklkrplslkelkaep.elegmkllrkg..rlsvrpvteedwel 141
                                        +d+  +     ++ pk +++++ +lr+++kp+k ++rp+++k l ++  +++++k ++ +    ++r++teed+++
  gi|488600689|ref|YP_007907160.1|  70 FKDSNRI-----FKSPKGMGNETfPLRIKLKPIKIFDRPVEFKPLIPKLkFITNKKKWSGHlmGKAMREITEEDYKV 141
                                       ****999.....778****999999********************995348899999999988999**********9 PP

                                       HH CS
                               EVE 142 il 143
                                       ++
  gi|488600689|ref|YP_007907160.1| 142 VA 143
                                       86 PP

>> Dev_Cell_Death  Development and cell death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.3e-07    0.0057       8      83 ..       9      95 ..       4     136 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-07
                    Dev_Cell_Death  8 nketkkecfrkklfglpaeklslvkkikpglkLfLfdyder........kLyGvfeAasdGglniepkafts....eks 74
                                      n++  +   +k++ g+p+++++++ k++pg kL+++  +er        ++  v+eA s+     +++ f+s     ++
  gi|488600689|ref|YP_007907160.1|  9 NEDNWRVIKQKNIWGVPERHKNTIAKVRPGDKLLIYLKQERnkdtvkepRIVAVYEAVSEVFK-DSNRIFKSpkgmGNE 86
                                      555566677899************************877772222222245666666665433.333344446666677 PP

                    Dev_Cell_Death 75 kfpaQvrfk 83
                                      +fp  +++k
  gi|488600689|ref|YP_007907160.1| 87 TFPLRIKLK 95
                                      777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1022.73
//
Query:       gi|488600690|ref|YP_007907161.1|  [L=218]
Description: putative metal-dependent hydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  145.3   0.2    3.2e-42  144.9   0.2    1.2  1  DUF45     Protein of unknown function DUF45
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.17   11.9   0.1    1.3  1  WLM       WLM domain


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.9   0.2   3.6e-46   3.2e-42       1     207 []      11     201 ..      11     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 144.9 bits;  conditional E-value: 3.6e-46
                             DUF45   1 knlrlrvepdgsvevsaPkgvseeeiedfvkkkakwiekklakleerakeaekelesgesfpl.lGkkyrlkvekgk 76 
                                       k++r++v p+g v+++aP++    +++ f++ +a+wi kk +++ee       e++ +e++ + +Gk y+l  +k+ 
  gi|488600690|ref|YP_007907161.1|  11 KYARIQVLPNGMVRIVAPPD---FDVDTFINDHAEWINKKKKEIEE----LAGEIKGKENLLIlNGKFYHLVKDKSF 80 
                                       6889**************96...68999******************....777777777777788999998888888 PP

                             DUF45  77 easvklkreelelavkkeeeeeklrkaleewlrkeakeeleerlaklaaklgvkprsvsikdmktrWGscsskgkir 153
                                             +  + e+ v k  + ++l+++l  +lr+    el++ ++ +++ lg+k+ ++ ik++kt+W+scssk +++
  gi|488600690|ref|YP_007907161.1|  81 ------EILDGEEGVVKYYSMRSLKRRLVSMLRE----ELKSTVSFYSRLLGIKYGRIFIKMQKTKWASCSSKANLS 147
                                       ......5555566666666666666666666665....7888999******************************** PP

                             DUF45 154 lnwrLvkappevidYVvvHElaHlleknHskrFwalvekllPdwkeakkeLkrk 207
                                       +n+ ++ +p+++ +Y+vvHElaHl+e++H+ +Fw+lv  ++P++k+a+keLk++
  gi|488600690|ref|YP_007907161.1| 148 FNLAMLALPEKLREYIVVHELAHLIEPKHTNAFWDLVGFYYPEYKNAEKELKKY 201
                                       ***************************************************985 PP

>> WLM  WLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.9e-05      0.17      87     108 ..     164     185 ..     158     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                               WLM  87 llHELaHnvygpHdakFyallk 108
                                        +HELaH +  +H + F++l+ 
  gi|488600690|ref|YP_007907161.1| 164 VVHELAHLIEPKHTNAFWDLVG 185
                                       68*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1350.63
//
Query:       gi|488600691|ref|YP_007907162.1|  [L=966]
Description: type I site-specific deoxyribonuclease, HsdR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-60  202.9   0.4    4.7e-59  199.8   0.0    2.6  2  SWI2_SNF2      SWI2/SNF2 ATPase
    5.5e-31  108.0   0.2    5.5e-31  108.0   0.2    3.7  4  HSDR_N         Type I restriction enzyme R protein N terminus
    8.1e-18   65.0   0.0    8.1e-18   65.0   0.0    3.1  3  ResIII         Type III restriction enzyme, res subunit
    7.3e-05   23.1   2.2    0.00086   19.6   0.0    3.3  2  Helicase_C     Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.022   13.5   0.1       0.11   11.2   0.1    2.2  1  SNF2_N         SNF2 family N-terminal domain
      0.026   14.9   0.1        6.3    7.2   0.0    3.1  2  AAA_assoc_2    AAA C-terminal domain
       0.19   11.6   3.2       0.24   11.2   0.7    2.5  2  ETC_C1_NDUFA5  ETC complex I subunit conserved region


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 !  199.8   0.0   1.8e-62   4.7e-59       2     220 ..     227     465 ..     226     470 .. 0.89
   2 ?   -0.8   0.0       0.4     1e+03      40      57 ..     570     588 ..     559     590 .. 0.78

  Alignments for each domain:
  == domain 1  score: 199.8 bits;  conditional E-value: 1.8e-62
                         SWI2_SNF2   2 Qyravekavervke.....gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakag 73 
                                       Qyrav+++ver+ +     +dr++G+iWH qG GK+ltm+f a k+++  l np +++++DR +L+kQls++++ ++
  gi|488600691|ref|YP_007907162.1| 227 QYRAVNAIVERAVSyakglTDRNKGLIWHWQGTGKTLTMTFSAVKIRD-LLGNPSIFFIVDRVELQKQLSDELKGLK 302
                                       ************999999999***************************.9************************988 PP

                         SWI2_SNF2  74 eekpkqaesrkeLkell.eke.sekiifttiqKfeeeek........eklevlsereniivlvDEaHRsqygelakk 140
                                        +  + +es  +Lke l +++ +++ ++t+i+Kf+eee         +++  + +r+++i l+DE+HR+qygela++
  gi|488600691|ref|YP_007907162.1| 303 ISC-EVIESIGHLKEVLsHADgKRGFFITLIHKFREEELaklreqmeKQHWSIMKRKDVICLIDEGHRTQYGELAAS 378
                                       776.69***********53335999*********944223345455466778899999******************* PP

                         SWI2_SNF2 141 lrkalpnaafigFTGTPilkkdkktkevFg....eyidkYtikeaveDgavvpilYesrlaklelkeeek...ldee 210
                                       +r +l+na+f++FTGTPi kk ++t + Fg     y+d+Y i ++++Dg +v+i Y+srl +++l++e+    l ++
  gi|488600691|ref|YP_007907162.1| 379 MRGILKNASFFAFTGTPIAKKGRDTYSAFGypdePYLDRYFILDSINDGFTVKIAYQSRLDDVHLDRENLeifLSSK 455
                                       *****************************988878********************************9966667777 PP

                         SWI2_SNF2 211 feeiteelee 220
                                       +eei ee++e
  gi|488600691|ref|YP_007907162.1| 456 LEEIPEEYRE 465
                                       7777766655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.4
                         SWI2_SNF2  40 kklle.eelknpkvvvvtD 57 
                                       + +++ ++++npk+++vtD
  gi|488600691|ref|YP_007907162.1| 570 EIITRfKKKENPKILIVTD 588
                                       456665689*********9 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 !  108.0   0.2   2.1e-34   5.5e-31       4     189 ..       4     179 ..       1     183 [. 0.86
   2 ?   -1.2   0.0      0.64   1.6e+03       2      60 ..     335     396 ..     334     490 .. 0.55
   3 ?   -0.3   0.2      0.34   8.6e+02      47     180 ..     669     705 ..     647     778 .. 0.61
   4 ?   -0.3   0.6      0.34   8.7e+02      11      86 ..     805     886 ..     796     908 .. 0.58

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 2.1e-34
                                       HHHHHH.HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH......-HHHHHHHH....TT CS
                            HSDR_N   4 EaeleqelidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgaln......ikkltkrla....ls 70 
                                       E+   ++ + e+l++ G++ +  k           +    +   ++++ ++l++ln      ik++ + l       
  gi|488600691|ref|YP_007907162.1|   4 EKSQSEDYLSEILESYGWKQKRLK-----------P----DILALDEFVDALKRLNdvseedIKEVLNFLEtrsfDV 65 
                                       666677788999999999885443...........3....3467899**********9877644444444477789* PP

                                       --HHHHHHHHHTS.-EEEETS-EEEEESS-SSSGGGS-EEEEE----SSSS---EEEEEEETTEEEEEEEE--TT.- CS
                            HSDR_N  71 dgnkefyellkeg.kvkfkegrkknikLiDkknlenNrfqvvnQvtvtgnqkrrpDivlfvnglplvviElKrpg.t 145
                                       +g  ++++++k+g ++k  eg+ k+i+LiD++nle+N+  + +Qv++   +  +pDi+lfvng+pl+viE+K+ + +
  gi|488600691|ref|YP_007907162.1|  66 EGSMQILDVIKRGvTIKDSEGNLKTIRLIDYDNLEANSLVFSRQVSF--RDAVIPDITLFVNGIPLAVIECKKMAkS 140
                                       *****************779***************************..6788*********************66* PP

                                       HHHHHHHHTSS---.---SSSGGGGG--EEEEE-SS-EEEEE-- CS
                            HSDR_N 146 ieeAinQikryrkeksdvsipqlfrYlqfgvisngketrfyakt 189
                                       ++e+++Qikry+ ++    +p+lf+Y+q+gv+  +k ++f+  +
  gi|488600691|ref|YP_007907162.1| 141 WKEGYSQIKRYE-QS----VPELFKYVQIGVSFADKLVYFPIVR 179
                                       ************.55....9****************99998665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.64
                                       SSHHHHHH.HHHHHHHHTT-EE.................----SHHHHHHHHHHHHHHHH........- CS
                            HSDR_N   2 lsEaeleqelidellrelGyqvlskkdveiegrrpe..vrkskaevaleknlreqlgaln........i 60 
                                       ++E+el +  + e+ +++ +++ + kdv    +++            l + +r+ l++          i
  gi|488600691|ref|YP_007907162.1| 335 FREEELAK--LREQMEKQHWSIMKRKDVICLIDEGHrtQ-----YGELAASMRGILKNASffaftgtpI 396
                                       56777777..77777888888887777765555444211.....2224444444444333444444441 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHH-HHHHHHHHTT--HHHHHHHHHTS-EEEETS-EEEEESS-SSSGGGS-EEEEE----SSSS--- CS
                            HSDR_N  47 leknlreqlgalnikkltkrlalsdgnkefyellkegkvkfkegrkknikLiDkknlenNrfqvvnQvtvtgnqkrr 123
                                       ++++lr++                                                                     
  gi|488600691|ref|YP_007907162.1| 669 IKEELRKK--------------------------------------------------------------------- 676
                                       33333333..................................................................... PP

                                       EEEEEEETTEEEEEEEE--TT-HHHHHHHHTSS---.---SSSGGGGG-.............-EEEEE-S CS
                            HSDR_N 124 pDivlfvnglplvviElKrpgtieeAinQikryrkeksdvsipqlfrYl.............qfgvisng 180
                                                                                i+q+f+++             +++visn+
  gi|488600691|ref|YP_007907162.1| 677 -----------------------------------------IEQAFNFFdfelsydrdvidrAVLVISNN 705
                                       .........................................44444444444444444444433333332 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.34
                                       HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH..-HHHHHHHH...TT--HHHHHHHHHT CS
                            HSDR_N  11 lidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgaln..ikkltkrla...lsdgnkefyellke 82 
                                       + d l+    y  +  ++  +e+ +  vr+  +++   ++l e l ++   i+k++k+     l+++++++ +llk+
  gi|488600691|ref|YP_007907162.1| 805 FYDLLFPVKNYAKDISDESIVERVDRIVRDWNERRRDIDELYEELLSIAevINKERKEREklkLNEKEYRVFKLLKS 881
                                       55555555555555555555555555555555555555555555555558866666555544477777777777776 PP

                                       S.-EE CS
                            HSDR_N  83 g.kvk 86 
                                         + k
  gi|488600691|ref|YP_007907162.1| 882 HlTDK 886
                                       64433 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 !   65.0   0.0   3.2e-21   8.1e-18       4     169 ..     223     395 ..     220     397 .. 0.83
   2 ?   -1.6   0.9      0.94   2.4e+03      67      75 ..     521     538 ..     445     590 .. 0.54
   3 ?   -0.5   0.6      0.42   1.1e+03     101     139 ..     738     789 ..     661     794 .. 0.73

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3.2e-21
                                       E-HHHHHHHHHHT...........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGG CS
                            ResIII   4 lreyQeeaienlleklks.....krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefk 75 
                                       +r++Q +a+++++e   s     +++++gli++  GtGKTl+++  + +++   ++  ++f+v+r +l +q+ +e+k
  gi|488600691|ref|YP_007907162.1| 223 PRYMQYRAVNAIVERAVSyakglTDRNKGLIWHWQGTGKTLTMTFSAVKIRDLLGNPSIFFIVDRVELQKQLSDELK 299
                                       79***********98888899999999****************9999999999999********************* PP

                                       GGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH............HHHTTT-S.EEEEETGGGTTS. CS
                            ResIII  76 kflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseee....eeeseellrdrfd.viiiDEaHrlgak 147
                                        ++ ++   + +++   k+   ++++ ++ +++t i+++ +++  +     e+++    +r+d + +iDE Hr+++ 
  gi|488600691|ref|YP_007907162.1| 300 GLKISCE--VIESIGHLKEVL-SHADGKRGFFITLIHKFREEELAKlreqMEKQHWSIMKRKDvICLIDEGHRTQYG 373
                                       ****996..777777777666.78888999999999**99999555776533333344444444779*********9 PP

                                       T...TTHHHHHT---SEEEEEESS- CS
                            ResIII 148 k...swreilekfkeavllglTATp 169
                                       +   s+r il++   a  +++T+Tp
  gi|488600691|ref|YP_007907162.1| 374 ElaaSMRGILKN---ASFFAFTGTP 395
                                       544488888777...6699*****9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.94
                                       HHHHHHHG.........G CS
                            ResIII  67 leqtleef.........k 75 
                                       ++q+l++f         +
  gi|488600691|ref|YP_007907162.1| 521 YKQALDKFlneneteivM 538
                                       344444443333333330 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.42
                                       ...-SEEEEEHHHHHHTH.....................HHHTTT-SEEEEE CS
                            ResIII 101 stnkkilvttiqsldadseee.............eeeseellrdrfdviiiD 139
                                       s+  ++++  +++lda++e++             e  + ++ ++ ++v++iD
  gi|488600691|ref|YP_007907162.1| 738 SEIYHVYLQRENQLDAEIEQKkdqfykealkfihETIDVQKIKKDYPVVVID 789
                                       4556888888888888887778888777777777777777777777788888 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   3.3e-07   0.00086       8     109 ..     527     622 ..     517     623 .. 0.69
   2 ?    0.2   0.9      0.35     9e+02      12      58 ..     692     753 ..     675     781 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                                       HHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGTSSSTST CS
                        Helicase_C   8 ellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesd.vLiatdvaerGidip 83 
                                       ++l  +e++ +i++  ++ d+ e +++l   ++++  +   el ++  eei+++f+k+e   +Li td++ +G d p
  gi|488600691|ref|YP_007907162.1| 527 KFL--NENETEIVMTFQQNDSRELLNYL---EKLRKKYGKNEL-KEIHEEIITRFKKKENPkILIVTDMLLTGFDAP 597
                                       444..33334444444444433224455...334444444443.78899*******888888*************** PP

                                       TESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  84 kvnlVinfdlprnvtsyiqriGRtgR 109
                                        ++++  +d p + +++ q+i Rt R
  gi|488600691|ref|YP_007907162.1| 598 ILQTL-YLDKPLKEHRLLQAIARTNR 622
                                       88876.68999999*********998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.35
                                       HTTTTSEEEEEESSHHHHHH........HHHH.......HHHTTSTEEEESTTSTHHHHHHH CS
                        Helicase_C  12 leeeggkilifvntidrlek........vkll.......lekkgikvavlhgelpqnereei 58 
                                       + ++++ +l+++n+id++ k         +ll       +ek+++ + ++h  l+ ++++++
  gi|488600691|ref|YP_007907162.1| 692 RDVIDRAVLVISNNIDEFRKlyfeirnlYRLLledklefKEKFDLLSEIYHVYLQRENQLDA 753
                                       566788999*******7754554544443444555445556667777777777777776654 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.3e-05      0.11     168     251 ..     349     462 ..     311     564 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                                       ...TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HH...HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xx RF
                            SNF2_N 168 kkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGTPiqnsledlygLlkfLreepfgekq...tf 241
                                       k+   +++++     +DEgh+ + ++  a++    L++      tGTPi  + +d y+ + +  e+ ++ +    + 
  gi|488600691|ref|YP_007907162.1| 349 KQHWSIMKRKDVICLIDEGHRTQYGELAASMRGI-LKNASFFAFTGTPIAKKGRDTYSAFGYPDEPYLDRYFildSI 424
                                       3333334444444568*******99888887777.99******************9987766655555543223344 PP

                                       HHHTHHHHH............................H CS
                                       xxxxxxxxx............................x RF
                            SNF2_N 242 dkllqrpie............................a 251
                                       +++++ +i+                            +
  gi|488600691|ref|YP_007907162.1| 425 NDGFTVKIAyqsrlddvhldrenleiflsskleeipeE 462
                                       44444444455555555555555555555555544443 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 ?    3.9   0.0     0.027        70      10      34 ..      38      62 ..      32      98 .. 0.83
   2 ?    7.2   0.0    0.0025       6.3       9      55 ..     531     576 ..     526     584 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.027
                                      XXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2 10 dalealaeladGDaRkaLnlLElaa 34
                                      dal+ l ++++ D++ +Ln LE+  
  gi|488600691|ref|YP_007907162.1| 38 DALKRLNDVSEEDIKEVLNFLETRS 62
                                      79999*****************755 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXX CS
                       AAA_assoc_2   9 ddalealaeladGDaRkaLnlLElaaeaaeakegkieitledleeal 55 
                                       ++  e ++++ + D R +Ln+LE + ++  + ++ +ei +e++++  
  gi|488600691|ref|YP_007907162.1| 531 ENETEIVMTFQQNDSRELLNYLEKLRKKYGK-NELKEIHEEIITRFK 576
                                       5566778888999**********87777765.788888888887665 PP

>> ETC_C1_NDUFA5  ETC complex I subunit conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   9.3e-05      0.24      21      63 ..     454     498 ..     451     502 .. 0.82
   2 ?   -1.9   0.1       1.2     3e+03      38      58 ..     761     781 ..     757     783 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.3e-05
                     ETC_C1_NDUFA5  21 kkLkkiPessvYRqsvEaltkhRlkiVee....eedvekiekkigag 63 
                                       +kL++iPe+  YR++vE+  k +l+ V+      + +e+i + i  +
  gi|488600691|ref|YP_007907162.1| 454 SKLEEIPEE--YREKVEQDLKRKLNKVKViledRNRIERIARDIASH 498
                                       689999997..*****************7755677788887777666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                     ETC_C1_NDUFA5  38 altkhRlkiVeeeedvekiek 58 
                                       +++k+ lk + e+ dv+ki+k
  gi|488600691|ref|YP_007907162.1| 761 QFYKEALKFIHETIDVQKIKK 781
                                       7889999***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (966 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1754  (0.0978303); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); 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):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 6150.50
//
Query:       gi|488600692|ref|YP_007907163.1|  [L=138]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-10   39.5   1.1    1.2e-09   38.7   1.1    1.4  1  PIN       PIN domain
    1.2e-05   26.1   0.2    1.8e-05   25.5   0.2    1.3  1  PIN_3     PIN domain
    0.00044   18.9   0.0    0.00047   18.8   0.0    1.2  1  CAS_CSE1  CAS/CSE protein, C-terminus
    0.00056   20.1   0.3     0.0012   19.1   0.3    1.5  1  PIN_2     PIN domain
     0.0049   16.8   0.1        1.6    8.7   0.0    2.1  2  DUF4411   Domain of unknown function (DUF4411)


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 !   38.7   1.1   3.4e-13   1.2e-09       2     120 ..       9     120 ..       8     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 3.4e-13
                                       EE-HHHHHHHH..TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                               PIN   2 vlDTsvliall..rgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida 75 
                                       ++DT+v+ia++     + +e ++ ll ++   lv +++ laE     ++       +ae+++++l + ++ i++ ++
  gi|488600692|ref|YP_007907163.1|   9 LIDTNVFIAAVkkGWTKTTELVLHLLSNPeFILVANDVLLAEYEKYGKA------FDAENFLEFL-KLRVIIVNPSD 78 
                                       79*********99999999999999999988888888888888766555......3444444444.667777788** PP

                                       HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       e  +  +e++ +    ++Da++ At++++++ li t+D++f+ ++
  gi|488600692|ref|YP_007907163.1|  79 EEIKACKEYFPE--NEVADAIHTATCLKTNAVLI-TNDKHFDPIK 120
                                       ***********9..6****************999.******8665 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2     5e-09   1.8e-05       1     116 []       7     115 ..       7     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5e-09
                             PIN_3   1 rvvlDtnvlldallfdsp.aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvalerk 76 
                                       r+++Dtnv+++a+    +   + +l +l + ++ lv+   ll E+e      ++ + f ++ +   +l  +v +   
  gi|488600692|ref|YP_007907163.1|   7 RFLIDTNVFIAAVKKGWTkTTELVLHLLSNPEFILVANDVLLAEYE------KYGKAFDAENFLE-FLKLRVII--V 74 
                                       789*******9999443379999***********************......2344445555544.33444532..2 PP

                             PIN_3  77 avapdaelrpllkcr....DpdDqkvlelAlaaradvlVTkdra 116
                                        +++++ ++            +D+ + +++l++  +vl+T d++
  gi|488600692|ref|YP_007907163.1|  75 NPSDEEIKACKE--YfpenEVADAIHTATCLKT-NAVLITNDKH 115
                                       333333333322..1335599************.8999**9985 PP

>> CAS_CSE1  CAS/CSE protein, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.3e-07   0.00047     328     407 ..       6      86 ..       3     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-07
                          CAS_CSE1 328 tkllaesealldrykklwaklleallkllekpeeeaaadedeiieeadvedlgfgv....aftkLntakkkeeDplp 400
                                       t++l +++ ++ + kk+w+k++e +l+ll++pe   + ++d +++e ++   +f +     f kL  +  +++D+  
  gi|488600692|ref|YP_007907163.1|   6 TRFLIDTNVFIAAVKKGWTKTTELVLHLLSNPEFILV-ANDVLLAEYEKYGKAFDAenflEFLKLRVIIVNPSDE-- 79 
                                       99*******************************9888.7888999998888888763222356666666666554.. PP

                          CAS_CSE1 401 eikdvkq 407
                                       eik  k+
  gi|488600692|ref|YP_007907163.1|  80 EIKACKE 86 
                                       3555555 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   3.3e-07    0.0012       2     115 ..      10     116 ..       9     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.3e-07
                             PIN_2   2 vdaNivvsallk..srikkrlilvekaleli..apeeaveeiekhkealvkksklseeeleellelletkikivees 74 
                                       +d+N+ ++a+ k  +++ +++++  ++ e+i  a + +++e ek+ +         +  +e++le l+ ++ iv+ s
  gi|488600692|ref|YP_007907163.1|  10 IDTNVFIAAVKKgwTKTTELVLHLLSNPEFIlvANDVLLAEYEKYGK---------AFDAENFLEFLKLRVIIVNPS 77 
                                       899*9999998888677777777777777661145567779999998.........445778888899999999997 PP

                             PIN_2  75 lyeskikeAkeriarvDpdDtpfvAlaLlleapiWTeDkdl 115
                                         ++ ik  ke  ++    D+   A+ L+++a + T+Dk +
  gi|488600692|ref|YP_007907163.1|  78 --DEEIKACKEYFPENEVADAIHTATCLKTNAVLITNDKHF 116
                                       ..6889999******************************98 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0     0.002       7.1       1      15 [.       8      22 ..       8      31 .. 0.85
   2 !    8.7   0.0   0.00043       1.6      80     128 ..      67     117 ..      45     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.002
                           DUF4411  1 YllDtnvfieakrry 15
                                      +l+Dtnvfi a ++ 
  gi|488600692|ref|YP_007907163.1|  8 FLIDTNVFIAAVKKG 22
                                      79*******998875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00043
                           DUF4411  80 gkvakwvivesekyskaakkefl...svaDpfliAaAlaknatvVTkEvkkp 128
                                        k++ + iv+ +  + +a ke+    +vaD+   A+ l+ na+++T+++  +
  gi|488600692|ref|YP_007907163.1|  67 LKLRVI-IVNPSDEEIKACKEYFpenEVADAIHTATCLKTNAVLITNDKHFD 117
                                       555555.45555555556677777999********************99844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.30s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 946.49
//
Query:       gi|488600693|ref|YP_007907164.1|  [L=86]
Description: transcriptional regulator, AbrB family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   27.4   2.1    3.4e-06   26.8   0.5    2.0  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0053   16.7   0.1     0.0062   16.5   0.1    1.4  1  MraZ            MraZ protein, putative antitoxin-like
  ------ inclusion threshold ------
      0.022   14.8   0.0        0.1   12.7   0.0    1.8  2  AbrB-like       AbrB-like transcriptional regulator


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 !   26.8   0.5   5.7e-10   3.4e-06       2      38 ..       5      42 ..       4      50 .. 0.84
   2 ?    0.2   0.1      0.13   7.5e+02      26      36 ..      67      77 ..      45      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.7e-10
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiil 38
                                      k++++g++ +Pke+r++++i++G e  +  +++   il
  gi|488600693|ref|YP_007907164.1|  5 KIDKKGRILLPKEIRDKMNIKPGEEFLVADVDEnAVIL 42
                                      899**********************9887777655555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.13
                                      EEEEEECTTCC CS
                    MazE_antitoxin 26 evelevdgdki 36
                                      e e+e++g++i
  gi|488600693|ref|YP_007907164.1| 67 EREIEEEGNRI 77
                                      67777777755 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     1e-06    0.0062       9      29 ..       5      25 ..       3      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                                      EB-TTSEEE--CHHHHHTTSC CS
                              MraZ  9 elDakGRlllPaklreeakle 29
                                      ++D+kGR+llP++ r++++ +
  gi|488600693|ref|YP_007907164.1|  5 KIDKKGRILLPKEIRDKMNIK 25
                                      79**************99987 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    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      34      61 ..       5      32 ..       3      41 .. 0.90
   2 ?    0.0   0.0      0.15   9.2e+02       8      27 ..      57      76 ..      49      85 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                         AbrB-like 34 sVqknGnLliGsaYTkklgLkpGdefeI 61
                                      ++ k G++l+ +   +k+++kpG+ef +
  gi|488600693|ref|YP_007907164.1|  5 KIDKKGRILLPKEIRDKMNIKPGEEFLV 32
                                      78899*********************76 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.15
                         AbrB-like  8 eAkGikldseakkskkkrGr 27
                                      +Ak i+l++ +++ ++++ r
  gi|488600693|ref|YP_007907164.1| 57 KAKSIDLENLEREIEEEGNR 76
                                      48888888765533333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 464.03
//
Query:       gi|488600694|ref|YP_007907165.1|  [L=339]
Description: hypothetical protein Asulf_01173 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2192.60
//
Query:       gi|488600695|ref|YP_007907166.1|  [L=446]
Description: Restriction endonuclease S subunits [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-54  182.6   0.8    8.8e-29  100.9   1.7    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 !   79.0   0.0   2.7e-26   4.8e-22       1     160 [.      32     204 ..      32     213 .. 0.86
   2 !  100.9   1.7   4.9e-33   8.8e-29       1     168 []     242     427 ..     242     427 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 2.7e-26
                                       ETT-EEEEHHHHEEEEE-----TTGGTTT--E....EEE-HH.HCCT...EE-HHHHCCTT---B-.TT-EEEE-S. CS
                       Methylase_S   1 pedwevvkLgdvfeikkgktpkkkelkengky....pyirag.ilnn...kvvkdglgykkkyilp.kgdilissr. 67 
                                       pedwevv+Lgd++++  g ++ k++++++g+       +++g +ln+   +++ +  ++ ++  ++ ++dilis   
  gi|488600695|ref|YP_007907166.1|  32 PEDWEVVRLGDLGTLTDGDWILKEDYTNEGVRliqiGNVGVGtFLNKsrrFISPERAKQLNCTFVDpEKDILISRMp 108
                                       89*********************8888888854444344444445559**99999999999999988*******889 PP

                                       SSTT-EEEESS...-BEE-TTEEEEEESTTT--HHHHHHHHH..HCHHHHHHHCCSSTTT---HHHHCC-EEEE--H CS
                       Methylase_S  68 atiGkvayrdk...kyylnqsvivlipknkkkineflylyll..lklkklkslsvgstqpkltkenlkkikIplPpl 139
                                        +iG++ +++    +y+++ ++  l++ n+k +++f+ + l   + l+++++l  g t+++++  nl+k+ IplPpl
  gi|488600695|ref|YP_007907166.1| 109 DPIGRACLAPRlpyPYIVAVDITILKVDNSKADRNFIVYALNfeATLERVERLASGATRKRISRRNLEKVLIPLPPL 185
                                       9*******9998889************885555699999988777888***************************** PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                       Methylase_S 140 eeQkkIakiLsqldntielek 160
                                       +eQ kIa+iLs++d+  ++ek
  gi|488600695|ref|YP_007907166.1| 186 PEQRKIAEILSTVDK--AIEK 204
                                       ***************..6655 PP

  == domain 2  score: 100.9 bits;  conditional E-value: 4.9e-33
                                       ETT-EEEEHHHHEEE.EE-----TT..GGTTT--EEEE-HHHCCT..........EE-HHHHCCTT---B-TT-EEE CS
                       Methylase_S   1 pedwevvkLgdvfei.kkgktpkkk..elkengkypyiragilnn..........kvvkdglgykkkyilpkgdili 64 
                                       p++wevv+Lgd++e   kg+tp +   +++e+g+  +i++++ ++           +++++ +  +  il++gdi++
  gi|488600695|ref|YP_007907166.1| 242 PKEWEVVRLGDLAETiTKGTTPTTYgfNFTESGV-NFIKVESIDEhgnfvwdniaHISEEANKVLSRSILKEGDIVF 317
                                       89************9777777777799******9.9*****555569******999999999999************ PP

                                       E-SSSTT-EEEESS...-BEE-TTEEEEEESTTT--.HHHHHHHHH..HCHHHHHHHCCSSTTT---HHHHCC-EEE CS
                       Methylase_S  65 ssratiGkvayrdk...kyylnqsvivlipknkkki.neflylyll..lklkklkslsvgstqpkltkenlkkikIp 135
                                       s+ +  G+va  +k   ++++nq +  +++k++ ++  ++l +yl+  +++k++  + v+s+q++l+++++k++ I 
  gi|488600695|ref|YP_007907166.1| 318 SIAGALGRVAVVTKevlPANTNQALAIIRLKKNVELaINYLKYYLAgpFIQKYIRTIAVQSAQANLSLTQVKNFLIT 394
                                       **************5554699999999999863333457777888889***************************** PP

                                       E--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Methylase_S 136 lPpleeQkkIakiLsqldntielekkikneier 168
                                       lPpl+eQ+kI +iLs++d+++ele+k+k+++er
  gi|488600695|ref|YP_007907166.1| 395 LPPLSEQQKITEILSTVDKKLELERKRKEKLER 427
                                       *******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2795.77
//
Query:       gi|488600696|ref|YP_007907167.1|  [L=57]
Description: hypothetical protein Asulf_01175 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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: 426.86
//
Query:       gi|488600697|ref|YP_007907168.1|  [L=556]
Description: hypothetical protein Asulf_01176 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3787.52
//
Query:       gi|488600698|ref|YP_007907169.1|  [L=505]
Description: Type I restriction-modification system methyltransferase subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.1e-109  365.0   0.1     4e-109  364.6   0.1    1.1  1  N6_Mtase         N-6 DNA Methylase
    3.9e-15   56.7   7.1    1.2e-14   55.1   4.2    2.6  2  HsdM_N           HsdM N-terminal domain
     0.0032   17.9   0.1      0.017   15.6   0.1    2.2  2  Eco57I           Eco57I restriction-modification methylase
     0.0042   16.9   0.0      0.016   15.0   0.0    2.1  3  Methyltransf_31  Methyltransferase domain
     0.0092   15.7   0.0      0.018   14.8   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020
     0.0097   15.5   0.0      0.024   14.2   0.0    1.6  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
       0.14   12.3   1.0       0.25   11.5   0.2    1.7  2  NAD2             Novel AID APOBEC clade 2


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 !  364.6   0.1  1.6e-112    4e-109       3     310 ..     157     470 ..     155     472 .. 0.94

  Alignments for each domain:
  == domain 1  score: 364.6 bits;  conditional E-value: 1.6e-112
                          N6_Mtase   3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee..dgktke 77 
                                       + +lGd+YE+l+++fa +++k+ Ge+fTP+ev+ liv++++p++  svyDpa+G + +l+ a +++k++  ++++k+
  gi|488600698|ref|YP_007907169.1| 157 DSILGDAYEWLIGYFAPQKAKE-GEVFTPSEVVDLIVRIVDPQPMDSVYDPAAGYARMLIRAYDYVKQKygEEEAKK 232
                                       679******************9.********************************************9965666777 PP

                          N6_Mtase  78 lsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe...kdkkfdvvvaNppfnqkewkektlek.... 147
                                       l +yGqe+n+tty++akmN ++hgi+    k + gdtl++p+f+   + +kfd+v+aNpp+nq+++ e++l+k    
  gi|488600698|ref|YP_007907169.1| 233 LFLYGQEVNPTTYAIAKMNAIVHGIKDI--KLEVGDTLKNPRFKegeTFRKFDIVIANPPWNQDGYGEEELKKaefy 307
                                       8889*********************865..799**********9888889****************77777763333 PP

                          N6_Mtase 148 derfreavapksnadlafllhiieslkpkGraavvlangvLfrggkegkIrkalvekdlveavialpeklFyntsip 224
                                       derf++++ pk++ad+a+++h+++s+k   +++vv++ng+Lfrggke +Irka++e dl+e+vi lpeklFynt++p
  gi|488600698|ref|YP_007907169.1| 308 DERFKYGFTPKQSADWAWIQHMLASAKR--KVGVVIDNGCLFRGGKERQIRKAILERDLIECVILLPEKLFYNTGAP 382
                                       6699999*****************9999..9********************************************** PP

                          N6_Mtase 225 tcilvlkkekae.rkgkvlfidaseefkkkd..rkknklteediekildtykekskevdkfskvveleeiaendynl 298
                                       ++i++++k+k+e rkgk+lfi+as+ef+k++  rk n+l e++ieki+++y+e+ k+ d+f++vv+leei+endynl
  gi|488600698|ref|YP_007907169.1| 383 GAIIIFNKQKPEnRKGKILFINASNEFEKHPevRKLNRLGEQHIEKIVNAYNEF-KDGDGFCRVVSLEEIRENDYNL 458
                                       **********999*****************999*********************.********************** PP

                          N6_Mtase 299 nvgryveteeee 310
                                       nv  yv ++ee 
  gi|488600698|ref|YP_007907169.1| 459 NVTLYVFPQEEI 470
                                       ******998775 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   4.2   4.8e-18   1.2e-14       6     136 ..      21     146 ..      16     147 .. 0.79
   2 ?    1.5   0.0      0.17   4.4e+02      60      93 ..     308     343 ..     272     363 .. 0.68

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4.8e-18
                                       HHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC..........--..--------......S-CCCSHHH CS
                            HsdM_N   6 wkaadiLRgkvdaseykeyilgLlFlKrlddveeereekllee.yken..aleeleeklksk..eafyipeelrWke 77 
                                       ++aad +R    + +yk yil LlFlKrl+d+++++ +++l++   e+  +++e e   k+k  + f  pe++ W+e
  gi|488600698|ref|YP_007907169.1|  21 KQAADLIR---TRVDYK-YILVLLFLKRLSDEWKKEYNEALKTlL-EKglDRKEAEVLAKDKsfHRFTYPEKYLWEE 92 
                                       68999999...556788.************************963.33353322222222223578999******** PP

                                       HHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS.......S-----SSHHHHHHHHHH CS
                            HsdM_N  78 lakkkdddelgenlnkafpaleelnkslkgvfmkd.dfnafalgeitkkspalLskviek 136
                                       l+k+    el   l +a++ l+e+n++l+gv++ + df +f++ +   ++ + L+++ e 
  gi|488600698|ref|YP_007907169.1|  93 LRKNIN--ELPVRLSEALKLLAEKNPELQGVVD-RlDFLEFTRHR---DNFDILVQLFEL 146
                                       ***755..5***********************7.78999998866...477777777665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                       -----....S-CCCSHHHHHHS..--HHHHHHHHHH CS
                            HsdM_N  60 klkskeafyipeelrWkelakk..kdddelgenlnk 93 
                                       +++ k++f  ++ + W+++ ++  + ++++g  +++
  gi|488600698|ref|YP_007907169.1| 308 DERFKYGFTPKQSADWAWIQHMlaSAKRKVGVVIDN 343
                                       233337799999******999987444457766666 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         7   1.8e+04      45      58 ..      78      90 ..      69     100 .. 0.61
   2 !   15.6   0.1   6.5e-06     0.017       2     104 ..     281     392 ..     280     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7
                            Eco57I 45 kylaliiparflas 58
                                       +  + +p+++l  
  gi|488600698|ref|YP_007907169.1| 78 SFHRFTYPEKYL-W 90
                                      455677888887.3 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.5e-06
                            Eco57I   2 kfdviiGNPPYqeseakkelkaleek.............akdiyqkFvekalkledkylaliiparflasgkglkef 65 
                                       kfd++i NPP+ +     e + ++               +++    ++++ l  +++ ++++i +  l +g   +++
  gi|488600698|ref|YP_007907169.1| 281 KFDIVIANPPWNQDG-YGEEELKK-AefyderfkygftpKQSADWAWIQHMLASAKRKVGVVIDNGCLFRGGKERQI 355
                                       9*********99887.33332222.246677788888885555566677777777999999999999878888999* PP

                            Eco57I  66 rekllkdkklkklvefedskevFkdveikggilvflkdk 104
                                       r+ +l+   ++ ++ ++++   F ++   g+i++f k+k
  gi|488600698|ref|YP_007907169.1| 356 RKAILERDLIECVILLPEKL--FYNTGAPGAIIIFNKQK 392
                                       ******99999999988766..**************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.5   6.5e+03      61      80 ..     125     142 ..     105     166 .. 0.61
   2 !   15.0   0.0   6.3e-06     0.016       6      84 ..     202     291 ..     197     353 .. 0.86
   3 ?   -3.2   0.0       2.5   6.4e+03      41      67 ..     448     474 ..     446     478 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.5
                   Methyltransf_31  61 gdieeleklledekfDlils 80 
                                        d+ e+    ++++fD+++ 
  gi|488600698|ref|YP_007907169.1| 125 LDFLEFTR--HRDNFDILVQ 142
                                       56666553..3688998664 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.3e-06
                   Methyltransf_31   6 rvlDlGCGtGeltfelae........elgpkae...vvGiDiseeaielArenaqklgldnveFeqgdieeleklle 71 
                                       +v+D+++G  + ++++++        e   +a+   ++G + +++    A+ na  +g++ +++e+gd  + +  ++
  gi|488600698|ref|YP_007907169.1| 202 SVYDPAAGYARMLIRAYDyvkqkygeE---EAKklfLYGQEVNPTTYAIAKMNAIVHGIKDIKLEVGDTLKNPR-FK 274
                                       79****************888743332...333677***********************************887.66 PP

                   Methyltransf_31  72 d....ekfDlilsnevl 84 
                                       +    +kfD++++n + 
  gi|488600698|ref|YP_007907169.1| 275 EgetfRKFDIVIANPPW 291
                                       6789********99554 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.5
                   Methyltransf_31  41 ielArenaqklgldnveFeqgdieele 67 
                                       +e  ren  +l+++ + F q++iee++
  gi|488600698|ref|YP_007907169.1| 448 LEEIRENDYNLNVTLYVFPQEEIEEID 474
                                       566677777788888888899999877 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.9e-06     0.018      64     134 ..     217     294 ..     172     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.9e-06
                                       S...HHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.....STTS---EEEE----- CS
                           UPF0020  64 e...lkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLr.....lkegevdvivtnpPYG 132
                                           +k++  ee+ ++l lyg + ++   + a+ Na   g++d i++++ d  k +     ++  ++d++++npP+ 
  gi|488600698|ref|YP_007907169.1| 217 AydyVKQKYGEEEAKKLFLYGQEVNPTTYAIAKMNAIVHGIKD-IKLEVGDTLKNPrfkegETFRKFDIVIANPPWN 292
                                       144578888888889999***********************98.5666666665555557777789*********97 PP

                                       -- CS
                           UPF0020 133 er 134
                                       + 
  gi|488600698|ref|YP_007907169.1| 293 QD 294
                                       64 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   9.4e-06     0.024      25      88 ..     235     298 ..     228     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.4e-06
                   Methyltransf_15  25 viaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkleki.kvdlvflSpPwGGpsYkk 88 
                                        ++ e+n+ + a+a+ Na v g++d i+l +gd ++  ++ + e+  k+d+v++ pPw   +Y +
  gi|488600698|ref|YP_007907169.1| 235 LYGQEVNPTTYAIAKMNAIVHGIKD-IKLEVGDTLKNPRFKEGETFrKFDIVIANPPWNQDGYGE 298
                                       68999*****************976.9********98877555555899*********8777765 PP

>> NAD2  Novel AID APOBEC clade 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   9.6e-05      0.25      98     176 ..      31     106 ..      18     108 .. 0.77
   2 ?   -2.4   0.0       1.7   4.5e+03      43      69 ..     399     426 ..     387     437 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.6e-05
                              NAD2  98 aekknvtLtifaaRlYyfwepdyqeaLrsLrqagarvkimdyeefekCWekfvynekepfkPWkkleensalldsrL 174
                                        + k + + +f  Rl   w+++y+eaL++L ++g   k  +    +k +++f y ek     W++l +n++ l  rL
  gi|488600698|ref|YP_007907169.1|  31 VDYKYILVLLFLKRLSDEWKKEYNEALKTLLEKGLDRKEAEVLAKDKSFHRFTYPEK---YLWEELRKNINELPVRL 104
                                       445566677899**********************99888888888899999999944...35999999998888887 PP

                              NAD2 175 ke 176
                                        e
  gi|488600698|ref|YP_007907169.1| 105 SE 106
                                       66 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                              NAD2  43 kgvllnqk.esklhaellfLskfvlrql 69 
                                       k ++ n + e + h+e++ L+++ ++++
  gi|488600698|ref|YP_007907169.1| 399 KILFINASnEFEKHPEVRKLNRLGEQHI 426
                                       4445555337778888888888744433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3347.49
//
Query:       gi|488600699|ref|YP_007907170.1|  [L=152]
Description: hypothetical protein Asulf_01178 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.089   12.8   0.2       0.11   12.6   0.2    1.1  1  RIG-I_C   RIG-I receptor C-terminal domain


Domain annotation for each model (and alignments):
>> RIG-I_C  RIG-I receptor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   5.9e-06      0.11      50     113 ..      35     100 ..       2     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-06
                           RIG-I_C  50 tqkYeqwvvklekkaa.keeerkkrvcaltcaehLrkYndALi.inddaRtsdAleyLekflndlk 113
                                       ++  ++ + +lek+++  +++++ +  ++++++ Lr++ d  + in++ R +dA e Le+ +n+l 
  gi|488600699|ref|YP_007907170.1|  35 SEVITNLLLDLEKELRgGQKQKQLSSADIATIQKLRYFKDKVHrINKNNRGIDAAELLENVYNTLL 100
                                       677778888999999965666666666699*********99966*******************953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1045.94
//
Query:       gi|488600700|ref|YP_007907171.1|  [L=77]
Description: hypothetical protein Asulf_01179 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0097   16.3   0.0      0.011   16.1   0.0    1.1  1  DUF2924   Protein of unknown function (DUF2924)


Domain annotation for each model (and alignments):
>> DUF2924  Protein of unknown function (DUF2924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.1e-07     0.011      17      68 ..      20      71 ..       9      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.1e-07
                           DUF2924 17 ekwrelfgeeapklnkeflekrlayriqelaeggLseearrrleelaeekek 68
                                      ++++++ +++  ++n e+++  + y  +++ eggL++e ++ lee++eek +
  gi|488600700|ref|YP_007907171.1| 20 DRFNAVKERAGVSMNAEVVRFLINYYYKNEVEGGLKKEIEKILEEVVEEKLR 71
                                      456666677777899********************************99444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 533.18
//
Query:       gi|488600701|ref|YP_007907172.1|  [L=48]
Description: hypothetical protein Asulf_01180 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   13.1   0.0        0.1   12.9   0.0    1.1  1  DndE      DNA sulphur modification protein DndE


Domain annotation for each model (and alignments):
>> DndE  DNA sulphur modification protein DndE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.6e-06       0.1       8      33 ..      16      41 ..      12      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-06
                              DndE  8 akeqLkkLkrrtgiepwnilcRiAlf 33
                                      + + L++Lkrrtg++ w  ++R  ++
  gi|488600701|ref|YP_007907172.1| 16 VVQALRELKRRTGLKYWAEVIRYCIM 41
                                      5678******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 322.52
//
Query:       gi|488600702|ref|YP_007907173.1|  [L=380]
Description: hypothetical protein Asulf_01181 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.2   0.0       0.22   11.2   0.0    1.5  1  Glyco_hydro_6  Glycosyl hydrolases family 6


Domain annotation for each model (and alignments):
>> Glyco_hydro_6  Glycosyl hydrolases family 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.2e-05      0.22     147     203 ..      38      96 ..      29     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.2e-05
                     Glyco_hydro_6 147 vkkLkalpnvavYlDaghsgwlgWeknleeaaellakvvkaa..agvakvdGfalnvsn 203
                                       v+ L+     ++Y+Da+  +   W ++ +++ e l+k  +++   ++ k++Gf++++  
  gi|488600702|ref|YP_007907173.1|  38 VDGLQLALVLQNYIDAASDACADWISDSKKISEVLEKARATTftCEYMKMQGFCTDIEE 96 
                                       67778877889*************************966666888899*******9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2724.22
//
Query:       gi|488600703|ref|YP_007907174.1|  [L=534]
Description: hypothetical protein Asulf_01182 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-13   48.6   6.2    7.9e-07   28.9   0.1    3.2  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
    1.2e-12   48.3   0.0    3.4e-12   46.9   0.0    1.8  1  AAA_19           AAA domain
    3.4e-12   46.4   7.8    3.6e-09   36.5   0.8    2.6  3  UvrD_C           UvrD-like helicase C-terminal domain
    1.3e-09   37.7   0.1    2.7e-09   36.7   0.1    1.5  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    0.00075   19.3   0.0     0.0043   16.8   0.0    2.1  2  AAA_30           AAA domain
     0.0012   18.5   2.6       0.01   15.4   2.6    2.2  1  AAA_12           AAA domain
     0.0015   18.4   0.0     0.0026   17.6   0.0    1.4  1  AAA_11           AAA domain
      0.002   17.9   0.5       0.26   11.0   0.1    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
      0.024   15.1   0.1      0.067   13.6   0.1    1.8  1  AAA              ATPase family associated with various cellul


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 !   21.3   0.3   8.3e-08   0.00016      18      67 ..       6      55 ..       3      99 .. 0.79
   2 !   28.9   0.1     4e-10   7.9e-07     214     311 ..     163     258 ..      77     262 .. 0.84
   3 ?   -1.4   0.2      0.67   1.3e+03     143     143 ..     377     377 ..     276     495 .. 0.54

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.3e-08
                                      EEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH CS
                     UvrD-helicase 18 veAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee 67
                                      ++  +G+GKT+ l + + + ike  i+ ++i+ v  Tn A eE + Ri  
  gi|488600703|ref|YP_007907174.1|  6 IYGPPGTGKTTKLLNEVKQDIKELDITLKDIMYVSTTNTAIEEVRGRIGI 55
                                      56679******************************************975 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 4e-10
                                       HHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT..... CS
                     UvrD-helicase 214 aeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasghee..... 285
                                         ++++ +e+kk++n +D++dll++l++   +++ +        +++  DE+QD     ++il++ + + +      
  gi|488600703|ref|YP_007907174.1| 163 VRIIRRWLEYKKQMNYIDYEDLLIYLYH---NPPYA------LTPVVKFDEAQDFADLEWEILRRTYIDVPPytplp 230
                                       567788899999***********99887...44433......3578889***************999887667999* PP

                                       ..EEEEE-GGG--GGGGTB-THHHHHHH CS
                     UvrD-helicase 286 ..lfmvGDpkQsIYgFRgAdielflkkk 311
                                         +++ GD++Q I +FRgA  e fl + 
  gi|488600703|ref|YP_007907174.1| 231 rrITIAGDDDQTILSFRGASAEKFLDFP 258
                                       ************************9875 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.67
                                       S CS
                     UvrD-helicase 143 a 143
                                        
  gi|488600703|ref|YP_007907174.1| 377 L 377
                                       1 PP

>> AAA_19  AAA 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   3.4e-12      14     146 .]       5     247 ..       2     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.7e-15
                            AAA_19  14 lvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.....atTiHrlal........ 77 
                                        + ++pGtGKT+ l   v+  +++ ++ +++i+ v+ t+ A +e+r r+ +++++      +T+H++al        
  gi|488600703|ref|YP_007907174.1|   5 KIYGPPGTGKTTKLLNEVKQDIKELDITLKDIMYVSTTNTAIEEVRGRI-GITKNnvgkyFKTLHGIALshlltfkk 80 
                                       589********************************************99.4444458888*******99******** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|488600703|ref|YP_007907174.1|  81 dvqlynaakntlklynfvetakikfcreikvryepeavssnapanqafeawsyviakyyhcfedvdrcfsafqrlyk 157
                                       ***************************************************************************** PP

                            AAA_19  78 .....................ldfddlltealelleeaeeekklqeee.llivDEfqdvdelqyrLlkallgek.kk 131
                                                            +d++dll     l  +  ++ +  + + ++  DE+qd  +l++++l++ + +   +
  gi|488600703|ref|YP_007907174.1| 158 dlpwlvriirrwleykkqmnyIDYEDLL---IYL--Y--HNPPY-ALTpVVKFDEAQDFADLEWEILRRTYIDVpPY 226
                                       ********99997766664444444433...333..4..44455.3355*******************998555333 PP

                            AAA_19 132 ......lllvGDpdQliyvfr 146
                                             +++ GD+dQ+i +fr
  gi|488600703|ref|YP_007907174.1| 227 tplprrITIAGDDDQTILSFR 247
                                       677777***********9996 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 ?   -1.7   0.0      0.72   1.4e+03     144     176 ..      15      47 ..       4     177 .. 0.56
   2 !   13.8   0.3   1.5e-05     0.029       1     106 [.     263     361 ..     263     371 .. 0.85
   3 !   36.5   0.8   1.8e-12   3.6e-09     210     344 ..     388     514 ..     364     519 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.72
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 144 gkatveriseelkklglsltDfikedtleygee 176
                                       ++++++++ +++k+l + l D +  +t+++  e
  gi|488600703|ref|YP_007907174.1|  15 TTKLLNEVKQDIKELDITLKDIMYVSTTNTAIE 47 
                                       556666666666666666666665555544333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   1 ivLekNyRStksLlkaankflenilnrralekek..ktvekgekivvleaeteeeEaekiaatikalleknekledi 75 
                                       ivLek +R ++++lk an++++++ +r    k k  ++v +g  + ++++++  + +++ a+++++       ++++
  gi|488600703|ref|YP_007907174.1| 263 IVLEKSWRVKENILKFANSIIKHVEKR----KSKkvEPVAEGGIVAYRSFANIYQLTDFAAKIANKYS-----DKTV 330
                                       79*******************999999....3333699999998999999988888877777766666.....99** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  76 avLvRsnkdadkiskaLkkegipfnvvdeek 106
                                        +L+ +n+  ++ + +L +++ pf+ +++e+
  gi|488600703|ref|YP_007907174.1| 331 FLLFYTNSMVHEAEIELYRLKQPFRRLKGES 361
                                       *******************999998877665 PP

  == domain 3  score: 36.5 bits;  conditional E-value: 1.8e-12
                                       xxxxxxxxxxxxxxxxxxxxxxx.....xxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 210 yadlfkelaeklaelkekseskr.....kkee.....klenlreLysllkelekkeeeeeveeklneileiatLses 276
                                       ++ l ++++ +l +  ek    +     k  +     + ++l +Lys+ + l+   ++ +      +i+++a     
  gi|488600703|ref|YP_007907174.1| 388 FKFLLRHMRAHLISKGEKE---NmlssfK--QcgtpiQFYTLTKLYSIQQLLDS--KTFNFAR-TLDIIKTA----- 451
                                       3333333333333332222...2343332..12345566666666666666666..4444333.34444444..... PP

                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 277 eleeskkk...ekipiiTiHqAKGlEFdvVflagleegtfPsyrskkekrleEEkRlfYVaiTRAkkrLfi 344
                                            ++k    + ++ TiH++KG E ++V++a++ + +        e+ ++  +R+fYVa+TRA++  ++
  gi|488600703|ref|YP_007907174.1| 452 -R--YTIKpaqVNLYVDTIHASKGREANIVIVANAINRKAL-----YENSIDDLRRVFYVAATRARDVCVV 514
                                       .2..2222212567788*****************7777653.....36677889************97666 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   1.3e-12   2.7e-09       2      51 ..     462     514 ..     461     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.3e-12
                          UvrD_C_2   2 ayaltihkaQGsefpaVivfdpd.laaarmgel....rrrlLYtavTRAreklil 51 
                                        y++tih ++G e+++Viv+++    a ++        rr +Y+a+TRAr+ +++
  gi|488600703|ref|YP_007907174.1| 462 LYVDTIHASKGREANIVIVANAInRKALYE--NsiddLRRVFYVAATRARDVCVV 514
                                       69*****************99996666664..24688*************87765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.2e-06    0.0043      23      81 ..       6      68 ..       2      93 .. 0.82
   2 ?   -1.4   0.0      0.81   1.6e+03     118     164 ..     232     278 ..     230     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                            AAA_30 23 ltGpAGtGKtt.alkalreaweaag...grviglAptgkaAkvLaeelgieastiakllkrlk 81
                                      + Gp+GtGKtt +l+++++ +++     ++++ ++ t++a ++++  +gi+ +++ k+ k+l 
  gi|488600703|ref|YP_007907174.1|  6 IYGPPGTGKTTkLLNEVKQDIKELDitlKDIMYVSTTNTAIEEVRGRIGITKNNVGKYFKTLH 68
                                      78*******99567888888888878999**************************99998776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.81
                            AAA_30 118 kvilvGDerQlasVeaGgvlrdlveaagigtaeLtevvRqkeseera 164
                                       ++ ++GD++Q     +G+  ++ ++  + + + L++ +R ke+  + 
  gi|488600703|ref|YP_007907174.1| 232 RITIAGDDDQTILSFRGASAEKFLDFPTDEEIVLEKSWRVKENILKF 278
                                       67889999999888888888888888888888999999987644433 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.6   5.3e-06      0.01      84     194 ..     380     514 ..     250     518 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.3e-06
                            AAA_12  84 ksyiNeeEaelvvklvek.llkkgsee....erkkigv.itpYr.aqvellkkklkekeeekseke........... 142
                                       ++   + E +++++++++ l++kg++e    + k+ g  i +Y  +++  +++ l++k  +    +           
  gi|488600703|ref|YP_007907174.1| 380 NKQLTYDEFKFLLRHMRAhLISKGEKEnmlsSFKQCGTpIQFYTlTKLYSIQQLLDSKTFNFAR-Tldiiktaryti 455
                                       3445555555555555431444444445555333333324444323444455555543332211.134555566666 PP

                            AAA_12 143 ......ievntvdgfQGrekdviilslVRsnekkeigflkderrl.NValTRAksklii 194
                                             + v+t+ +  Gre +++i+    +++      ++d rr+  Va TRA++ +++
  gi|488600703|ref|YP_007907174.1| 456 kpaqvnLYVDTIHASKGREANIVIVANAINRKALYENSIDDLRRVfYVAATRARDVCVV 514
                                       666667*******************9998887777778899998637******987665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0026      19      75 ..       3      54 ..       1     106 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                            AAA_11 19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerll 75
                                      i+ i GPPGtgKT+ ++  ++q +     +e   + + i + + +N+A+ e+  r+ 
  gi|488600703|ref|YP_007907174.1|  3 IRKIYGPPGTGKTTKLLNEVKQDI-----KELDITLKDIMYVSTTNTAIEEVRGRIG 54
                                      6779*********76666555552.....45789999***************99974 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0091        18       5      23 ..       8      33 ..       6      77 .. 0.67
   2 !   11.0   0.1   0.00013      0.26      99     232 ..     382     514 ..     380     516 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0091
                   Viral_helicase1  5 GvpGcGKStlirkllrts.......l 23
                                      G pG GK+t + + ++++       l
  gi|488600703|ref|YP_007907174.1|  8 GPPGTGKTTKLLNEVKQDikelditL 33
                                      78*********999999776644441 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                   Viral_helicase1  99 Qipfhsrnasfllahlpssl.shrvgrrttyllpsdvaeilsakvgteveversgelkvetepkgqekvlvyltftq 174
                                       Q ++ +   +fll+h   +l s+ ++ +  + +++ +++i+    +t+ ++ ++  +  + +++    +l +++ ++
  gi|488600703|ref|YP_007907174.1| 382 QLTYDE--FKFLLRHMRAHLiSKGEKENMLSSFKQCGTPIQFYT-LTKLYSIQQLLD--SKTFNFA-RTLDIIKTAR 452
                                       555554..456777777777777788888888888888888887.888888888888..5555555.4566666666 PP

                   Viral_helicase1 175 alkealgvr.evttvhevqGltfdkVtlvllketdlelis....esrenllvAlTRhrkslvi 232
                                        + +  +v+  v t h   G +++ V++    +  + l++    + r +++vA TR+r+ +v+
  gi|488600703|ref|YP_007907174.1| 453 YTIKPAQVNlYVDTIHASKGREANIVIVANAIN-RKALYEnsidDLRRVFYVAATRARDVCVV 514
                                       6666677777689***********999888855.5566666787779***********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 ?   13.6   0.1   3.3e-05     0.067       3      49 ..       6      49 ..       5      73 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                                      EESSTTSSHHH.HHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHH CS
                               AAA  3 lyGppGtGKTl.lakavakelgvefleisgsellskyvgesekkirel 49
                                      +yGppGtGKT+ l + v ++  ++ l i +++++  yv+ ++  i+e+
  gi|488600703|ref|YP_007907174.1|  6 IYGPPGTGKTTkLLNEVKQD--IKELDITLKDIM--YVSTTNTAIEEV 49
                                      69********8233333333..222444444444..555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1009  (0.0562775); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 3442.11
//
Query:       gi|488600704|ref|YP_007907175.1|  [L=370]
Description: hypothetical protein Asulf_01183 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-13   50.6   0.1    2.5e-13   50.0   0.1    1.2  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   1.4e-17   2.5e-13     102     202 ..     272     358 ..     238     367 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.4e-17
                                       HHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHHHH.HTHCHCHHHCC-S CS
                   DNA_primase_lrg 102 klakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekFdk.eyrynirhnyGke 177
                                       k  ++ + pC+++l+e+ +++ +l+h+ r ++++ l  + +s dei+++++++     ++Fd+ ++ry+++h+   +
  gi|488600704|ref|YP_007907175.1| 272 KGGRKKIRPCIQKLIEKAQDSINLEHYKRIAIVAELYVAEYSIDEIVSVFRNQ-----PDFDEkKTRYQVEHITA-K 342
                                       45556677********************************************8.....****************9.9 PP

                                       TT--------HHHHHHS....TT-- CS
                   DNA_primase_lrg 178 gkrtnyspysCekiltkpppgkgda 202
                                       g ++ y+p+ C++i+         +
  gi|488600704|ref|YP_007907175.1| 343 GINAPYKPFRCATIK---------Q 358
                                       **************4.........3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2415.44
//
Query:       gi|488600705|ref|YP_007907176.1|  [L=151]
Description: hypothetical protein Asulf_01184 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 933.87
//
Query:       gi|488600706|ref|YP_007907177.1|  [L=63]
Description: hypothetical protein Asulf_01185 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1375  (0.0766914); expected 358.6 (0.02)
Passed bias filter:                     1006  (0.0561102); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 372.81
//
Query:       gi|488600707|ref|YP_007907178.1|  [L=30]
Description: hypothetical protein Asulf_01186 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.48
# Mc/sec: 189.56
//
Query:       gi|488600708|ref|YP_007907179.1|  [L=302]
Description: 3-hydroxyacyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-61  205.2   0.4    9.4e-61  204.8   0.4    1.1  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    1.6e-24   86.3   0.2    6.4e-24   84.4   0.0    2.0  2  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    3.8e-05   23.9   0.5    0.00013   22.2   0.5    2.0  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    5.7e-05   22.8   0.2    0.00013   21.6   0.2    1.6  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0058   16.0   0.1      0.009   15.4   0.1    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.097   13.3   0.4        0.5   11.0   0.4    2.1  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.12   12.7   0.2        0.5   10.6   0.0    2.2  2  TrkA_N          TrkA-N domain
       0.14   12.2   0.0       0.37   10.8   0.0    1.9  1  ADH_zinc_N      Zinc-binding dehydrogenase
       0.22   11.0   0.0          1    8.8   0.0    1.9  1  ERAP1_C         ERAP1-like C-terminal domain


Domain annotation for each model (and alignments):
>> 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 !  204.8   0.4   4.7e-64   9.4e-61       1     179 [.       2     181 ..       2     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 204.8 bits;  conditional E-value: 4.7e-64
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH...HHHCCTTTTSS-HHHHCCCHHCEEEES-HH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek...sleklvekgklkeeeveaalarisfttdle 74 
                                       k++v+G G+mG++i++ fa++ +eV  +d++ee+l+k+++++      l++lvekgk++e+e+e++++ris++t++e
  gi|488600708|ref|YP_007907179.1|   2 KIGVVGFGLMGSQITQFFAQSRFEVIALDVNEEKLKKGMNAVIWgrfGLKRLVEKGKINEDEMEEIVNRISTSTNYE 78 
                                       69***************************************9998999***************************** PP

                                       HHHC-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE CS
                           3HCDH_N  75 eavdadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvr 151
                                       +++dadlviEav+E++ lK++v++++++++  dai+ snTSs+si++l++a+k+pe+++g+HFfnP+++ kLvE+vr
  gi|488600708|ref|YP_007907179.1|  79 DLKDADLVIEAVFEDIGLKKEVLEKISEVT--DAIIGSNTSSISITKLSSAVKSPEKFLGIHFFNPAQIQKLVELVR 153
                                       *****************************7..9******************************************** PP

                                       -TT--HHHHHHHHHHHHHTT-EEEEECS CS
                           3HCDH_N 152 gekTseetvatvvelakkigktpvvvkd 179
                                       g  Tse+++a+v+el+ ++gk+p+vvkd
  gi|488600708|ref|YP_007907179.1| 154 GLLTSEDVIAEVRELFSSLGKVPIVVKD 181
                                       **************************99 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 ?   -1.1   0.0       1.6   3.1e+03      50      93 ..      27      66 ..      23      70 .. 0.61
   2 !   84.4   0.0   3.2e-27   6.4e-24       1      91 [.     184     274 ..     184     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--BGGGTBS CS
                             3HCDH 50 vgldvakkilevlaeelgerayapsplleklveagrlgrktgkg 93
                                      + ldv++  l+  +++  + ++     l++lve+g++ + + ++
  gi|488600708|ref|YP_007907179.1| 27 IALDVNEEKLKKGMNAVIWGRFG----LKRLVEKGKINEDEMEE 66
                                      56666666665444444555565....78888888877766665 PP

  == domain 2  score: 84.4 bits;  conditional E-value: 3.2e-27
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+++R+   l +ea+ +v+egva+p+diD  m+lg+G+ mGp+e+ dlvgld+ ++i+e ++e ++++++ap+ ll
  gi|488600708|ref|YP_007907179.1| 184 GFATTRLGLMLGKEAMLMVQEGVATPQDIDIGMMLGYGYTMGPIETGDLVGLDTRLRIYESMYEMTKDPKWAPPRLL 260
                                       9**************************************************************************** PP

                                       HHHHHTT--BGGGT CS
                             3HCDH  78 eklveagrlgrktg 91 
                                        +lv+ag lg  + 
  gi|488600708|ref|YP_007907179.1| 261 VQLVDAGYLGDPSV 274
                                       **********8764 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.5   6.3e-08   0.00013       1      43 [.       2      58 ..       2     179 .. 0.71
   2 ?   -1.1   0.0      0.92   1.8e+03      43      62 ..     159     178 ..     124     202 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.3e-08
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..............E CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..............a 43
                                      kig++G G MGs++ + ++++ ++v++ ++++ek+++ +++                
  gi|488600708|ref|YP_007907179.1|  2 KIGVVGFGLMGSQITQFFAQSRFEVIALDVNEEKLKKGMNAViwgrfglkrlvekgK 58
                                      79***********************************99998555666666533332 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.92
                                       EEE-SSHHHHHHHCSEEEE- CS
                     NAD_binding_2  43 akaaesieelvasldvvitm 62 
                                        +++++++el++sl +v ++
  gi|488600708|ref|YP_007907179.1| 159 EDVIAEVRELFSSLGKVPIV 178
                                       22333333444444444444 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 !   21.6   0.2   6.4e-08   0.00013       1      56 [.       1      55 [.       1     115 [. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6.4e-08
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvk 56
                                      mki v+G G +G      +a+  +evi +D++eek +k  +  i     gL++lv+
  gi|488600708|ref|YP_007907179.1|  1 MKIGVVGFGLMGSQITQFFAQSRFEVIALDVNEEKLKKGMNAVI-WGRFGLKRLVE 55
                                      89*********************************998444332.22334444444 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 !   15.4   0.1   4.5e-06     0.009      38      73 ..       2      37 ..       1      59 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.5e-06
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                      ++G++G+G +G+++ + +++ +++via d++++k +
  gi|488600708|ref|YP_007907179.1|  2 KIGVVGFGLMGSQITQFFAQSRFEVIALDVNEEKLK 37
                                      79****************************977544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00025       0.5       1      68 [.       2      89 ..       2     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........................-EEECECH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........................vkvtavdn 55
                                      kig++G+G mg+ +++ ++++     e++ a + n+ek+++  +++                          ++++++n
  gi|488600708|ref|YP_007907179.1|  2 KIGVVGFGLMGSQITQFFAQSR---FEVI-ALDVNEEKLKKGMNAVIwgrfglkrlvekgkinedemeeivNRISTSTN 76
                                      7***************999998...9999.99*****999877666566666777777777666666666656666666 PP

                                      HHHHHH-SEEEE- CS
                     F420_oxidored 56 eeaaeeadvvvla 68
                                       e +++ad v+ a
  gi|488600708|ref|YP_007907179.1| 77 YEDLKDADLVIEA 89
                                      6666666666655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025       0.5       3      36 ..       5      38 ..       3      47 .. 0.88
   2 ?   -2.7   0.0       3.4   6.8e+03      91     107 ..      66      82 ..      57      93 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                                      EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHH CS
                            TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeervee 36
                                      ++G+G +G+++++ + + +  +v++ d +ee++++
  gi|488600708|ref|YP_007907179.1|  5 VVGFGLMGSQITQFFAQsRF-EVIALDVNEEKLKK 38
                                      9****************555.5*********9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                                       EEEEEESSGGGHHHHHH CS
                            TrkA_N  91 kiiaraqdpehaellkk 107
                                       +i+ r++++ + e lk+
  gi|488600708|ref|YP_007907179.1|  66 EIVNRISTSTNYEDLKD 82 
                                       45666666666555555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.37       3      66 ..      12      90 ..       7     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                      HHHHHHHHHHTT-EEEEEESSHHHHHHHHHT......TESEEEET.....TTC.HHHHHHHHHT...TTSSEEEEEESS CS
                        ADH_zinc_N  3 GlaavqlAkalGaeviavdsseeklelakkl......Gadeviny.....kea.dlverikelt...ggegvdvvfecv 66
                                      G+   q+ + + +evia d++eekl++ +        G ++++       +e+ ++v ri   t   + +++d+v+e+v
  gi|488600708|ref|YP_007907179.1| 12 GSQITQFFAQSRFEVIALDVNEEKLKKGMNAviwgrfGLKRLVEKgkineDEMeEIVNRISTSTnyeDLKDADLVIEAV 90
                                      4445566666667************999998889999999999988888888888999999999665456889999987 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00052         1     172     238 ..      52     123 ..      49     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00052
                                       HHHHHS..-HHHHHHHHHHHHC-SS.HHHHHHHHHHHCC-S-HHHHHHHHHHCTT.T..S-.GGGHHHHHHH CS
                           ERAP1_C 172 alaang..geaewdallerykdtsa.psekeaalralaatpdpellerllnfvle.sdevr.nqdlrallag 238
                                       +l+ +g  +e+e +++ +r +++++ ++ k+a l   a ++d  l++++l+ ++e +d++  +  +++ ++ 
  gi|488600708|ref|YP_007907179.1|  52 RLVEKGkiNEDEMEEIVNRISTSTNyEDLKDADLVIEAVFEDIGLKKEVLEKISEvTDAIIgSNTSSISITK 123
                                       67888889************888877899************************7343333214444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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 0.23s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2140.00
//
Query:       gi|488600709|ref|YP_007907180.1|  [L=258]
Description: short chain enoyl-CoA hydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-78  263.5   0.0    1.8e-78  263.4   0.0    1.0  1  ECH_1          Enoyl-CoA hydratase/isomerase
    3.7e-41  141.7   0.1    3.2e-35  122.2   0.1    2.0  2  ECH_2          Enoyl-CoA hydratase/isomerase
    0.00036   20.5   0.1       0.48   10.4   0.0    2.2  2  Peptidase_S49  Peptidase family S49
  ------ inclusion threshold ------
       0.15   11.9   0.0       0.42   10.5   0.0    1.7  1  Plectin        Plectin repeat


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.4   0.0   3.9e-82   1.8e-78       4     250 ..      13     257 ..      10     258 .] 0.98

  Alignments for each domain:
  == domain 1  score: 263.4 bits;  conditional E-value: 3.9e-82
                                       TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHH CS
                             ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlel 80 
                                       +++av++lnrPe++Nal+ +++tEl+qa e++e+   +r+ ++tG++kaFaaGad+ e+ ++++ +  ++ +    l
  gi|488600709|ref|YP_007907180.1|  13 DNIAVLTLNRPEKLNALDSKTRTELLQAVEEVENR--ARVLIITGSGKAFAAGADIGELSKRNPLDCIESAKLGTRL 87 
                                       79*******************************99..*************************999999999999*** PP

                                       HHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT- CS
                             ECH_1  81 wtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgk 157
                                       +tk+ ++++p iaa+nG+a+gGG+ela+acDi++a+++a+fg++e+++G+ipgaggtq+l+r vG   A++++l+g+
  gi|488600709|ref|YP_007907180.1|  88 FTKIEEMDIPSIAAINGYALGGGCELAMACDIRVASKKAKFGQPEINIGIIPGAGGTQRLPRLVGVGMAKKLVLTGE 164
                                       ***************************************************************************** PP

                                       EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHH CS
                             ECH_1 158 kisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddik 234
                                        isa+ea ++Glvd+ v e++l++ a+e+a+++ eksp a++++k aln   +++l  +le e  lf+ +fs++d k
  gi|488600709|ref|YP_007907180.1| 165 IISAEEAYRIGLVDELVDEDKLMDRAMEIARRICEKSPIAVAFAKRALNSSNSMNLHDGLEYELSLFSILFSTEDAK 241
                                       ***************************************************************************** PP

                                       HHHHHHHTCSH----- CS
                             ECH_1 235 eGlqaflEkrkpefed 250
                                       eG++aflEkrkpef++
  gi|488600709|ref|YP_007907180.1| 242 EGMNAFLEKRKPEFRG 257
                                       **************86 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   0.1   7.1e-39   3.2e-35       2     179 ..      16     188 ..      15     195 .. 0.93
   2 !   18.7   0.0   2.2e-07     0.001     249     317 ..     190     255 ..     185     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 7.1e-39
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                       +v+tLnrp++lNaL+ +  ++l +a++e+e  +++++++++g+g kaf AG D+ +l + +  +  e     +   +
  gi|488600709|ref|YP_007907180.1|  16 AVLTLNRPEKLNALDSKTRTELLQAVEEVE--NRARVLIITGSG-KAFAAGADIGELSKRNPLDCIE---SAKLGTR 86 
                                       799*************************96..566788999977.**************99998766...5788889 PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTG 154
                                       l   i+++  p +a ++G+++GgG+ l++ + +rv++++++f  PE++IG++P  Gg+  L+rl g  +++ l lTG
  gi|488600709|ref|YP_007907180.1|  87 LFTKIEEMDIPSIAAINGYALGGGCELAMACDIRVASKKAKFGQPEINIGIIPGAGGTQRLPRLVGvGMAKKLVLTG 163
                                       99**************************************************************887********** PP

                                       --B-HHHHHHTTS--EE--GGGHHH CS
                             ECH_2 155 arlkgadalaaglathyvpseklea 179
                                       + +++++a+ +gl + +v+++kl +
  gi|488600709|ref|YP_007907180.1| 164 EIISAEEAYRIGLVDELVDEDKLMD 188
                                       ********************99865 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                             ECH_2 249 akktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                       a ++++ + ++sP++++++ ++l+++++++ l++ l+ El l + l++++D  eG +a l ++  kP++
  gi|488600709|ref|YP_007907180.1| 190 AMEIARRICEKSPIAVAFAKRALNSSNSMN-LHDGLEYELSLFSILFSTEDAKEGMNAFLEKR--KPEF 255
                                       678899999********************5.***************************98554..5655 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00055       2.4       5      39 ..      94     128 ..      90     140 .. 0.89
   2 !   10.4   0.0   0.00011      0.48     119     149 ..     162     192 ..     152     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00055
                                       TT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EE CS
                     Peptidase_S49   5 akkPvvasaenvaaSggYylasaadkivanpstiv 39 
                                         +P +a ++++a  gg  la+a+d  va++++  
  gi|488600709|ref|YP_007907180.1|  94 MDIPSIAAINGYALGGGCELAMACDIRVASKKAKF 128
                                       579***************************99865 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                                       CCHEEEHHHHHHTTSSSEETSHHHHHHHHHH CS
                     Peptidase_S49 119 egrvltgqqAlklgLvdelgtvddavaelee 149
                                       +g++ ++++A + gLvdel   d+++++++e
  gi|488600709|ref|YP_007907180.1| 162 TGEIISAEEAYRIGLVDELVDEDKLMDRAME 192
                                       689999**********************998 PP

>> Plectin  Plectin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.4e-05      0.42      16      34 ..     161     179 ..     159     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.4e-05
                           Plectin  16 vtgerlsveeAvkrGllde 34 
                                       +tge +s eeA++ Gl+de
  gi|488600709|ref|YP_007907180.1| 161 LTGEIISAEEAYRIGLVDE 179
                                       699***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 1498.78
//
Query:       gi|488600710|ref|YP_007907181.1|  [L=387]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  187.6   1.0    2.2e-55  187.0   1.0    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    7.7e-29   99.8   0.1    5.9e-28   96.9   0.1    2.1  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.6e-28   98.1   0.3      9e-28   97.2   0.3    1.5  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
      2e-26   92.8   0.1    5.1e-26   91.6   0.1    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
     0.0056   16.4   0.1      0.027   14.1   0.1    2.1  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.0   1.0   6.1e-59   2.2e-55       1     149 [.     230     378 ..     230     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 6.1e-59
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       gkGf++ me +nh+R+ vaa+a+g+a+ a+e al+y+++rk+fgkp++++q+ ++k+aema++++aarll+y+aa++
  gi|488600710|ref|YP_007907181.1| 230 GKGFYYLMEFFNHTRPRVAAQAVGMAQGAFELALSYVKERKQFGKPIAAFQHTQFKIAEMATRIQAARLLTYQAAWQ 306
                                       79*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       ++ g+ ++  +smaK+fa e+a++vad a+ql+Gg+Gy  eypver+yrda++++++eGt eiq++iiar l
  gi|488600710|ref|YP_007907181.1| 307 CSIGERKPELSSMAKYFAGETAVYVADWAVQLHGGYGYIGEYPVERFYRDAKITELYEGTKEIQKQIIARML 378
                                       *********************************************************************975 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.26   9.3e+02      60      88 ..      37      66 ..      29      72 .. 0.76
   2 !   96.9   0.1   1.6e-31   5.9e-28       1      97 []     122     218 ..     122     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.26
                                      -EEEEEEE..GG.GEEE-----BSS-TTS- CS
                     Acyl-CoA_dh_M 60 glslflvprdap.gvsvrrieeklGlrglp 88
                                      +  + +v++ ++ g+s  +i+ek+G +gl 
  gi|488600710|ref|YP_007907181.1| 37 RYPMEVVKKARElGFSTIKIPEKYGGMGLT 66
                                      5556788855556***********988875 PP

  == domain 2  score: 96.9 bits;  conditional E-value: 1.6e-31
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvr 76 
                                       a+a+TEp+aGsdvasvkt  +erdg+e+++nG+K++itn+  ++++lvl+rt + + r++gl++++v+++++g++ +
  gi|488600710|ref|YP_007907181.1| 122 AMASTEPDAGSDVASVKT-KIERDGDEWIINGTKMFITNGSVCDFVLVLGRTYEGEkRHHGLTFAIVESNSKGFKAK 197
                                       79****************.89999999************************5555567******************* PP

                                       ----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  77 rieeklGlrglptgelvfedv 97 
                                       +i++klGlr  +t+e+v++dv
  gi|488600710|ref|YP_007907181.1| 198 KIKNKLGLRASDTAEIVLKDV 218
                                       *******************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.3   2.5e-31     9e-28       3     133 ..     247     367 ..     246     368 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 2.5e-31
                                       HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHH CS
                     Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtved 79 
                                       +aa+a+G+A++a++ ++++++er++  +g+++a ++ tq+++ae+a+r++AAr+l+++aa++   + +++       
  gi|488600710|ref|YP_007907181.1| 247 VAAQAVGMAQGAFELALSYVKERKQ--FGKPIAAFQHTQFKIAEMATRIQAARLLTYQAAWQ-CSIGERKP------ 314
                                       79***********************..***********************************.33344444...... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  80 raearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                          +++a+ +a e+a+ ++d++++++Gg+++  e+p++R++RDa++++ +++++
  gi|488600710|ref|YP_007907181.1| 315 -ELSSMAKYFAGETAVYVADWAVQLHGGYGYIGEYPVERFYRDAKITELYEGTK 367
                                       .469********************************************999875 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.1   1.4e-29   5.1e-26       1     108 [.       6     113 ..       6     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 1.4e-29
                                       THHHHHHHHHHHHHHHHHT.HHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-H CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeel.aphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelarada 76 
                                       t+eq +++ ++ref e+e  ++ ++e+d+e+++p e++kk+ elG+  i +pe+ygG+gl+ +e+++v+ee+ r++ 
  gi|488600710|ref|YP_007907181.1|   6 TPEQMDIKNAAREFSEKEFtPELIEECDREERYPMEVVKKARELGFSTIKIPEKYGGMGLTLFEEVLVTEEFYRVSP 82 
                                       79*****************66689****999********************************************** PP

                                       HHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHH CS
                     Acyl-CoA_dh_N  77 glalllgvhsslvapailrfGteeqkrryLpk 108
                                       g++ +  ++s+ +++ ++ fG+eeqk++yL+ 
  gi|488600710|ref|YP_007907181.1|  83 GMGNAC-LSSTFGTELLILFGSEEQKEKYLRW 113
                                       *98855.56778889***************85 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   7.5e-06     0.027     169     270 ..     139     225 ..      81     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.5e-06
                                       -EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEE.EETT-TTEEEEE-------S..-TTT CS
                            HpaB_N 169 vrvveetddGivVrGakvlaTgaaladeilvlptramlkeedkdyavafa.vpvdapGlklicresfedkleesefd 244
                                        ++ e++ d  +++G+k+++T++ ++d +lvl   ++ + e++ + + fa v+++++G k       ++k       
  gi|488600710|ref|YP_007907181.1| 139 TKI-ERDGDEWIINGTKMFITNGSVCDFVLVLGR-TY-EGEKRHHGLTFAiVESNSKGFKAKKI---KNK------- 202
                                       333.444455689******************988.56.44555555555427899999874222...211....... PP

                                       -TTTTT----EEEEEEEEEEEEGGGE CS
                            HpaB_N 245 yplssrfdendalvvfDdVfVPwerV 270
                                        +l       +a +v+ dV VP e++
  gi|488600710|ref|YP_007907181.1| 203 LGLR---ASDTAEIVLKDVRVPEENI 225
                                       2233...2346667777888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2562.49
//
Query:       gi|488600711|ref|YP_007907182.1|  [L=131]
Description: putative nucleic-acid-binding protein containing a Zn-ribbon [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   32.8   1.3    7.4e-08   32.3   1.3    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    0.00031   20.6   0.8    0.00041   20.2   0.8    1.2  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
       0.07   12.6   0.1      0.078   12.4   0.1    1.1  1  tRNA-synt_2d   tRNA synthetases class II core domain (F)


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 !   32.3   1.3   1.2e-11   7.4e-08       1      64 [.      58     116 ..      58     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.2e-11
                                       EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                       wve+ g G+v++ftvv   p gf+  + y++++ ++ + vr+m++      ++v++G+rVra +
  gi|488600711|ref|YP_007907182.1|  58 WVEIDGYGVVETFTVVQSVPSGFEWIKAYTIAIARFGN-VRVMGWGN----ESVKVGDRVRAYT 116
                                       9************************************9.******98....4689******976 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.8   6.9e-08   0.00041       1      33 [.      23      54 ..      23      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.9e-08
                           DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgs 33
                                      w+++  g++  + C  CG+ ++PP+a C+ C+ 
  gi|488600711|ref|YP_007907182.1| 23 WKGLEYGKIYKTVCE-CGREYYPPQAECSFCRK 54
                                      788888899999999.***************64 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 ?   12.4   0.1   1.3e-05     0.078     168     197 ..      42      69 ..      32     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                       TEEEEEEEEEEECCSSSSEEEEEEEEEE-H CS
                      tRNA-synt_2d 168 ftePsaevdvylvekkkkwlEllgaGmvrp 197
                                       ++ P+ae++     k+++w+E+ g G+v+ 
  gi|488600711|ref|YP_007907182.1|  42 YYPPQAECSFCR--KETEWVEIDGYGVVET 69 
                                       8999***99855..*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 842.43
//
Query:       gi|488600712|ref|YP_007907183.1|  [L=385]
Description: Acetyl-CoA acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   97.6   1.5      2e-27   96.2   1.5    1.7  1  Thiolase_N     Thiolase, N-terminal domain
    6.1e-08   32.6   6.5    5.6e-06   26.1   2.8    2.6  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
    6.9e-07   28.9   0.9    4.1e-05   23.2   0.1    3.1  3  Thiolase_C     Thiolase, C-terminal domain
     0.0024   17.7   0.7       0.14   12.0   0.3    2.5  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


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 !   96.2   1.5   4.5e-31     2e-27      13     260 .]      10     221 ..       3     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 4.5e-31
                                       ETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHH CS
                        Thiolase_N  13 kfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSgl 89 
                                        ++  ++d++++eL+ ea+k++l++a++++++v+  +vG v + + + ++a  +    g++ + p ++v+ +c+ g 
  gi|488600712|ref|YP_007907183.1|  10 CSKFGVRDTTIQELAFEAVKEALDDANITQDDVNISVVGSVGTRNYELMPAVPVNEYCGFSGKGP-IRVESACATGS 85 
                                       4455569*****************************************************77766.69********* PP

                                       HHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTT..TTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHH CS
                        Thiolase_N  90 kavalaaqsiaageadvvvagGvEsmsnaptaestdv..rsglklgdekakdllipdgladafneehmGltaenlak 164
                                       +av++a  sia+g a+v++a+GvE+m++++t +s +v  r+g  l +    +++ p            +++a    +
  gi|488600712|ref|YP_007907183.1|  86 SAVYTAYASIASGVAEVAIAIGVEKMTEVETPVSLAVggRAGNYLWEFHQYGTTFPA---------YYAMHASSHMA 153
                                       ***************************998877644411688888888889999999.........889999999** PP

                                       HHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BT CS
                        Thiolase_N 165 kykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtA 241
                                       ky+ + e+ + +Avk h++a++++ka+ +++ei              d ++ ++s+v a +L+              
  gi|488600712|ref|YP_007907183.1| 154 KYGTTEEQMALVAVKAHRNAVKNPKAH-LQKEI--------------DVETVLNSRVIAYPLKLF------------ 203
                                       ***************************.*****..............99****************............ PP

                                       TSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 242 gnasqisDGaaavllmses 260
                                        ++s+isDGa+av+l+ses
  gi|488600712|ref|YP_007907183.1| 204 -DCSPISDGASAVILASES 221
                                       .***************996 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 !    7.7   0.0   0.00051       2.3      88     120 ..      20      49 ..      16      66 .. 0.78
   2 !   26.1   2.8   1.3e-09   5.6e-06     159     213 ..      64     119 ..      46     128 .. 0.82
   3 ?   -3.2   0.0       1.1   5.1e+03     129     129 ..     236     236 ..     207     268 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEE CS
                     ketoacyl-synt  88 qqrllleaawealedagltpeeldgsrvgvfiG 120
                                        q l+ ea++eal da++t+++++ s vg    
  gi|488600712|ref|YP_007907183.1|  20 IQELAFEAVKEALDDANITQDDVNISVVG---S 49 
                                       689*****************876654444...3 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.3e-09
                                       HHHHT--SS.EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHH CS
                     ketoacyl-synt 159 syalglrGp.svtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavag 213
                                       +  +g+ G   + v++AC+++  av  a+ s+ sg a+va+a Gve +++ e+ ++
  gi|488600712|ref|YP_007907183.1|  64 NEYCGFSGKgPIRVESACATGSSAVYTAYASIASGVAEVAIAIGVEKMTEVETPVS 119
                                       5556777743689**********************************998776555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.1
                                       H CS
                     ketoacyl-synt 129 l 129
                                       +
  gi|488600712|ref|YP_007907183.1| 236 I 236
                                       1 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.028   1.3e+02      11      44 ..      11      44 ..       5      48 .. 0.83
   2 ?   -0.8   0.0      0.26   1.2e+03       9      43 ..     151     186 ..     145     191 .. 0.76
   3 !   23.2   0.1   9.2e-09   4.1e-05      36     104 ..     271     357 ..     244     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.028
                                      EEEE--GGGGGGHHHHHHHHHHHHHT--GGGESE CS
                        Thiolase_C 11 aevgvdpeilglgPayaikkvlkkagltvedidl 44
                                      ++ gv +++++     a+k++l++a +t +d+++
  gi|488600712|ref|YP_007907183.1| 11 SKFGVRDTTIQELAFEAVKEALDDANITQDDVNI 44
                                      5667777777778889***************987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.26
                                       EEEEEE--GGGGGGHHHHHHHHHHHHHT--G.GGES CS
                        Thiolase_C   9 syaevgvdpeilglgPayaikkvlkkagltv.edid 43 
                                       ++a+ g+++e+++l  + a ++++k+   ++ ++id
  gi|488600712|ref|YP_007907183.1| 151 HMAKYGTTEEQMALVAVKAHRNAVKNPKAHLqKEID 186
                                       678889999999999999999999976555413455 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 9.2e-09
                                       T--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHHHHHHHHH CS
                        Thiolase_C  36 gltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGaRivvtll 94 
                                          v+++d+  +++ F+   + + ++l++                      vN  GG  a GHPl a+G+ +v  ++
  gi|488600712|ref|YP_007907183.1| 271 DNPVNQLDIATVHDCFTIAEIIAYEDLGFCRkgeggrfiedgesdfggkIPVNTFGGLKAKGHPLAATGTAMVYEIV 347
                                       345899**********************99999*************987779************************* PP

                                       HHHHHCTTSE CS
                        Thiolase_C  95 selkkeggkl 104
                                       ++l++e gkl
  gi|488600712|ref|YP_007907183.1| 348 KQLREEAGKL 357
                                       *****98876 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.3   3.2e-05      0.14       3      39 ..      77     113 ..      75     117 .. 0.94
   2 ?    3.4   0.0     0.016        70      52      65 ..     208     221 ..     193     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                       +++aC++   a+ +A a i+sg a+ ++ ig e++++
  gi|488600712|ref|YP_007907183.1|  77 VESACATGSSAVYTAYASIASGVAEVAIAIGVEKMTE 113
                                       5789******************************987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.016
                                       B-EEEEEEEEEEES CS
                       ACP_syn_III  52 fGDGAgAvvlease 65 
                                        +DGA Av+l  + 
  gi|488600712|ref|YP_007907183.1| 208 ISDGASAVILASES 221
                                       68********9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2533.69
//
Query:       gi|488600713|ref|YP_007907184.1|  [L=162]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   40.1   0.2    3.3e-10   39.4   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.7e-06   28.0   0.1    5.2e-06   26.5   0.0    1.8  2  HTH_28          Helix-turn-helix domain
    2.5e-06   27.3   0.2    5.7e-06   26.2   0.2    1.6  1  HTH_11          HTH domain
    9.5e-06   25.3   0.0    2.1e-05   24.2   0.0    1.6  1  HTH_23          Homeodomain-like domain
    1.1e-05   25.0   0.0    2.3e-05   23.9   0.0    1.6  1  RepL            Firmicute plasmid replication protein (RepL)
    2.1e-05   24.1   0.1      4e-05   23.2   0.1    1.5  1  Sigma70_r4_2    Sigma-70, region 4
    0.00027   20.9   0.0    0.00045   20.1   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00028   20.6   1.3      0.002   17.9   1.3    2.1  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00071   19.5   0.2     0.0018   18.2   0.1    1.8  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0016   18.3   0.2      0.036   13.9   0.1    2.3  2  DUF4224         Domain of unknown function (DUF4224)
     0.0016   18.4   0.0     0.0029   17.7   0.0    1.5  1  HTH_20          Helix-turn-helix domain
     0.0019   17.6   0.0     0.0033   16.8   0.0    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0051   16.8   0.0      0.011   15.7   0.0    1.6  1  HTH_29          Winged helix-turn helix
     0.0061   16.1   0.0      0.011   15.2   0.0    1.4  1  Sigma70_r4      Sigma-70, region 4
      0.007   16.2   0.3      0.023   14.6   0.2    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0077   16.4   0.1      0.022   14.9   0.0    1.9  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.026   14.3   0.1    1.7  1  HTH_8           Bacterial regulatory protein, Fis family
       0.02   14.9   0.2       0.02   14.9   0.2    1.7  1  HTH_3           Helix-turn-helix
      0.024   14.5   0.0      0.043   13.7   0.0    1.4  1  MarR_2          MarR family
      0.029   14.3   0.1      0.093   12.7   0.0    1.9  2  HTH_36          Helix-turn-helix domain
       0.03   13.9   1.8      0.036   13.6   0.1    2.0  2  GerE            Bacterial regulatory proteins, luxR family
      0.055   13.3   0.0      0.097   12.5   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.074   13.5   0.3        0.2   12.1   0.3    1.9  1  HTH_40          Helix-turn-helix domain
      0.091   12.7   0.3       0.26   11.3   0.0    2.0  2  HTH_6           Helix-turn-helix domain, rpiR family
        0.1   12.8   0.0       0.25   11.6   0.0    1.6  1  NIPSNAP         NIPSNAP
        0.1   12.9   0.1       0.23   11.9   0.1    1.6  1  FaeA            FaeA-like protein
       0.11   12.3   0.0       0.21   11.4   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.11   12.7   0.0        0.2   11.9   0.0    1.4  1  DUF5361         Family of unknown function (DUF5361)
       0.16   12.3   1.2       0.28   11.5   0.1    1.9  1  KORA            TrfB plasmid transcriptional repressor
       0.18   11.6   0.5       0.42   10.4   0.1    1.8  1  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 !   39.4   0.2   5.5e-13   3.3e-10       1      47 [.       6      50 ..       6      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 5.5e-13
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ld+ d+kI+e++ k  + +q+e+Ae +g+++ tv  r+k LeeeG+I
  gi|488600713|ref|YP_007907184.1|  6 LDDVDKKIIEYILK--GKTQSEVAELTGVTLRTVQNRMKALEEEGYI 50
                                      79************..******************************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 !   26.5   0.0   8.7e-09   5.2e-06       4      40 ..      12      48 ..      11      54 .. 0.95
   2 ?   -1.9   0.0       6.3   3.8e+03      32      42 ..      58      68 ..      57      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.7e-09
                            HTH_28  4 eiikllaaGhsvreaArelgisrrtvyrWikryeegG 40
                                      +ii+++++G++++e+A++ g++ rtv+  +k++ee+G
  gi|488600713|ref|YP_007907184.1| 12 KIIEYILKGKTQSEVAELTGVTLRTVQNRMKALEEEG 48
                                      89*********************************99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.3
                            HTH_28 32 WikryeegGia 42
                                      W+  y++ G+ 
  gi|488600713|ref|YP_007907184.1| 58 WVADYQKLGLT 68
                                      99999999975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   9.5e-09   5.7e-06       4      51 ..      12      56 ..      10      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.5e-09
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                      +i+e +l+ +   + +e Ae ++v+ rtv++++kaLee g+ I  + g
  gi|488600713|ref|YP_007907184.1| 12 KIIEYILKGK---TQSEVAELTGVTLRTVQNRMKALEEEGYIIKLKEG 56
                                      7888887777...789************************99988776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.5e-08   2.1e-05      10      45 ..      13      48 ..      11      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.5e-08
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      i+   ++G++++e+A++ gv+ rTv++  k+ +eeG
  gi|488600713|ref|YP_007907184.1| 13 IIEYILKGKTQSEVAELTGVTLRTVQNRMKALEEEG 48
                                      6777788************************99999 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.8e-08   2.3e-05      76     114 ..      21      59 ..       6      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.8e-08
                              RepL  76 atnRelaeetgislktvsetlkileeanilkkkanGvlv 114
                                       +t+ e+ae tg+ l+tv++ +k+lee ++++k  +G  v
  gi|488600713|ref|YP_007907184.1|  21 KTQSEVAELTGVTLRTVQNRMKALEEEGYIIKLKEGYWV 59 
                                       6999**************************999988765 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 !   23.2   0.1   6.6e-08     4e-05       9      47 ..       4      41 ..       1      43 [. 0.92

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.6e-08
                                      TTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2  9 aeLperqreifllryleglsykEIAellgisegtVksrl 47
                                       eL   +++i++ + l+g+++ E+Ael+g++ +tV++r+
  gi|488600713|ref|YP_007907184.1|  4 KELDDVDKKIIEYI-LKGKTQSEVAELTGVTLRTVQNRM 41
                                      5789999******7.**********************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   7.5e-07   0.00045      23      65 ..      22      65 ..      11      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.5e-07
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.EEEEES-HHHH CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.rg.rririldleaL 65
                                      tq e A++ G+t  tv   +++L++eg+i   + +   + d ++L
  gi|488600713|ref|YP_007907184.1| 22 TQSEVAELTGVTLRTVQNRMKALEEEGYIIkLKeG-YWVADYQKL 65
                                      89**************************9954414.888888887 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.3   3.4e-06     0.002       1      42 []       6      45 ..       6      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.4e-06
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LD++D+kI+e + +    + +e+Ae +G++  tv++R+++Le
  gi|488600713|ref|YP_007907184.1|  6 LDDVDKKIIEYILKG--KTQSEVAELTGVTLRTVQNRMKALE 45
                                      8************87..6788********************8 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     3e-06    0.0018       5      52 ..      77     125 ..      73     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3e-06
                                       E-GGGTTHHHHHHHHHHTSTTEEEEEEESS.SSSEEEEEEESSHHHHHH CS
                    AsnC_trans_reg   5 lepghpeqleefeealaelpeVvecyrvtG.dydyllkvvvrdlealer 52 
                                       l+ +++  ++ + e++++l+ V+ ++ v G +yd+ l+v+ +d+e++++
  gi|488600713|ref|YP_007907184.1|  77 LDMDSKNKIDMIVEHMKTLDFVENVFEVVGsPYDLCLIVRYKDIEEYRK 125
                                       44334568999*******************99**************975 PP

>> DUF4224  Domain of unknown function (DUF4224)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   6.1e-05     0.036       3      38 ..      22      59 ..      22      60 .. 0.88
   2 ?    2.2   0.0      0.28   1.7e+02      14      29 ..     125     140 ..     107     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                           DUF4224  3 tpeElaeLTGykrrsaQ..akwLranGipfvvradGrp 38
                                      t++E+aeLTG+  r  Q  +k+L ++G+ ++   ++++
  gi|488600713|ref|YP_007907184.1| 22 TQSEVAELTGVTLRTVQnrMKALEEEGYIIKLKEGYWV 59
                                      899*********9999977899******9998887775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.28
                           DUF4224  14 krrsaQakwLranGip 29 
                                       k + + ++w+r+n  +
  gi|488600713|ref|YP_007907184.1| 125 KEKRKFMEWFRKNNMR 140
                                       3778899****99765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.8e-06    0.0029      19      59 ..      17      55 ..       6      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.8e-06
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +   +g t se+ae+ +++  t+ +++++Lee g++   +e
  gi|488600713|ref|YP_007907184.1| 17 I--LKGKTQSEVAELTGVTLRTVQNRMKALEEEGYIIKLKE 55
                                      4..578899*************************9866555 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.5e-06    0.0033      17      50 ..      10      43 ..       7      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-06
                      HTH_Tnp_ISL3 17 eayilelllesrsvkavArqlgvSwtTVwrildr 50
                                      + +i+e  l++++ ++vA+++gv+ +TV++++++
  gi|488600713|ref|YP_007907184.1| 10 DKKIIEYILKGKTQSEVAELTGVTLRTVQNRMKA 43
                                      77999999***********************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 !   15.7   0.0   1.8e-05     0.011       4      45 ..      13      54 ..      11      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegG.laall 45
                                      ++  + +G  t s++A+l+g++ rtv++  k+ ee+G + +l+
  gi|488600713|ref|YP_007907184.1| 13 IIEYILKGK-TQSEVAELTGVTLRTVQNRMKALEEEGyIIKLK 54
                                      666677887.9**************************766665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.9e-05     0.011       5      42 ..       6      42 ..       4      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                                      S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqiek 42
                                      L++ +++++e+  ++g T++E++e  g+++ +V  ++k
  gi|488600713|ref|YP_007907184.1|  6 LDDVDKKIIEYI-LKGKTQSEVAELTGVTLRTVQNRMK 42
                                      666666666644.6777****************99987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   3.9e-05     0.023      21      58 ..      19      56 ..       1      67 [. 0.86
   2 ?   -1.0   0.0       2.9   1.7e+03      36      54 ..      82     100 ..      81     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      + +t +e+ae +gv   +v++ ++ Le+ G++ + k+ 
  gi|488600713|ref|YP_007907184.1| 19 KGKTQSEVAELTGVTLRTVQNRMKALEEEGYIIKLKEG 56
                                      67899***************************999876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                                       CHCHHHHHHHHHHCTSEEE CS
                              TrmB  36 rskvYevLrsLedkGlVer 54 
                                       ++k+  +++ ++  ++Ve 
  gi|488600713|ref|YP_007907184.1|  82 KNKIDMIVEHMKTLDFVEN 100
                                       7789999999999999986 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.7e-05     0.022      17      51 ..      19      53 ..      16      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-05
                    B-block_TFIIIC 17 sGitqsdLakeskqdprslfyrlksLekkgLIvkq 51
                                      +G tqs++a +++   r +  r+k+Le+ g+I k+
  gi|488600713|ref|YP_007907184.1| 19 KGKTQSEVAELTGVTLRTVQNRMKALEEEGYIIKL 53
                                      799*****************************997 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.4e-05     0.026       2      41 ..       6      43 ..       5      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH CS
                             HTH_8  2 leevEkelIeaALertgGnkskAArlLGisRrtLyrKLkk 41
                                      l++v+k++Ie  L+     +s++A+l G++ rt+ +++k+
  gi|488600713|ref|YP_007907184.1|  6 LDDVDKKIIEYILKGKT--QSEVAELTGVTLRTVQNRMKA 43
                                      56777777777777555..9*******************7 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   3.4e-05      0.02       7      30 ..      18      41 ..      11      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-05
                                      HTTHHHHHHHHHHTSSHHHHHHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriE 30
                                       +g +q e+Ae++Gv+ +t+++ +
  gi|488600713|ref|YP_007907184.1| 18 LKGKTQSEVAELTGVTLRTVQNRM 41
                                      68*****************99765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.2e-05     0.043      23      53 ..      22      52 ..      10      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLver 53
                                      t++e+a+ +g++  +v+++ k L++ G++ +
  gi|488600713|ref|YP_007907184.1| 22 TQSEVAELTGVTLRTVQNRMKALEEEGYIIK 52
                                      9***************************965 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00016     0.093      27      55 .]      22      50 ..       5      50 .. 0.94
   2 ?   -1.6   0.0       4.7   2.8e+03      25      42 ..     142     160 ..     130     161 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +q+  a+++g+  +Tv++  k Le+ Gyi
  gi|488600713|ref|YP_007907184.1| 22 TQSEVAELTGVTLRTVQNRMKALEEEGYI 50
                                      68889***********************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.7
                            HTH_36  25 fpsqetlakrl.glsknTv 42 
                                       +  q  +a+++ + +++T+
  gi|488600713|ref|YP_007907184.1| 142 NHLQTIIASKTyKNHRRTI 160
                                       5556667777734458887 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     6e-05     0.036       7      40 ..      10      43 ..       4      46 .. 0.88
   2 ?   -1.5   0.2       3.1   1.8e+03      29      41 ..     148     160 ..     145     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                                      HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHH CS
                              GerE  7 ErevLrllaeGksnkeIAeelniSekTVkvhksn 40
                                       +++ +++ +Gk+  e+Ae  ++  +TV++ ++ 
  gi|488600713|ref|YP_007907184.1| 10 DKKIIEYILKGKTQSEVAELTGVTLRTVQNRMKA 43
                                      67899***********************998876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.1
                                       S-HHHHHHHHHHH CS
                              GerE  29 iSekTVkvhksni 41 
                                       i+ kT k+h++ i
  gi|488600713|ref|YP_007907184.1| 148 IASKTYKNHRRTI 160
                                       8899999**9976 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016     0.097      20      48 ..      22      50 ..      13      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyv 48
                                      t se+A+ tg++  tv + ++ L+e+Gy+
  gi|488600713|ref|YP_007907184.1| 22 TQSEVAELTGVTLRTVQNRMKALEEEGYI 50
                                      569*************************7 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00034       0.2       7      47 ..      15      55 ..      11     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00034
                            HTH_40  7 elleeglsieeIAkerglkesTIegHLaelieegeeidler 47
                                      e + +g++  e+A+  g++  T+++ +  l eeg+ i+l++
  gi|488600713|ref|YP_007907184.1| 15 EYILKGKTQSEVAELTGVTLRTVQNRMKALEEEGYIIKLKE 55
                                      66789****************************98777644 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00044      0.26       9      31 ..       1      23 [.       1      50 [. 0.83
   2 ?   -1.9   0.0       5.6   3.3e+03      15      34 ..     124     143 ..     118     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                                      HH-----HHHHHHHHHHHH-S-- CS
                             HTH_6  9 skkekltksekkiaeyilaspdk 31
                                      ++k++l + +kki+eyil+ + +
  gi|488600713|ref|YP_007907184.1|  1 MRKKELDDVDKKIIEYILKGKTQ 23
                                      5799**************98765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.6
                                       -HHHHHHHHHHHH-S---TT CS
                             HTH_6  15 tksekkiaeyilaspdkaie 34 
                                        k  +k +e+ +++   + +
  gi|488600713|ref|YP_007907184.1| 124 RKEKRKFMEWFRKNNMRINH 143
                                       56778889998888777666 PP

>> NIPSNAP  NIPSNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00041      0.25      42      88 ..     104     148 ..      82     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                                       EESBSSEEEEEEEES-HHHHHHHHHHHHH-HHH.HHHHHHHHTT..EE CS
                           NIPSNAP  42 eiGalnqvlhlwaydslaarearraalaadpew.eaavekavdldlik 88 
                                        +G+ + +  +++y++ +++++++ +++   ew +++ ++ ++l++i 
  gi|488600713|ref|YP_007907184.1| 104 VVGSPYDLCLIVRYKDIEEYRKEKRKFM---EWfRKNNMRINHLQTII 148
                                       689999**********************...99999999999998885 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00038      0.23       3      47 ..      11      52 ..       9      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00038
                                      HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEE CS
                              FaeA  3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikr 47
                                       +I+ey+ +   + + +e+A+ +g++   +   ++ Le eg i +
  gi|488600713|ref|YP_007907184.1| 11 KKIIEYILK---GKTQSEVAELTGVTLRTVQNRMKALEEEGYIIK 52
                                      579****99...55568************************9866 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.21       3      52 ..      11      58 ..      10      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGav 52
                                      ++i+e++ +  + s  e++el gv+  T+ + ++ Lee+g +++   G+ 
  gi|488600713|ref|YP_007907184.1| 11 KKIIEYILKGKTQS--EVAELTGVTLRTVQNRMKALEEEGYIIKLKEGYW 58
                                      68888888877664..9***************************988875 PP

>> DUF5361  Family of unknown function (DUF5361)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00033       0.2       4      44 ..      52      92 ..      49     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                           DUF5361  4 DlAEtYqiydyrqlplrkvavlalGLredsRikmklsgekv 44
                                       l E Y + dy++l l+ +av+ + L  ds+ k+ +  e++
  gi|488600713|ref|YP_007907184.1| 52 KLKEGYWVADYQKLGLTVLAVIFIDLDMDSKNKIDMIVEHM 92
                                      6889***************************9998865554 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00048      0.28      21      51 ..      11      40 ..       3      48 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00048
                              KORA 21 veiargvLVegkkqadvatelgltkqavsqa 51
                                       +i+  +L +gk+q++va+ +g+t + v++ 
  gi|488600713|ref|YP_007907184.1| 11 KKIIEYIL-KGKTQSEVAELTGVTLRTVQNR 40
                                      55665555.9**************9999875 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0007      0.42       3      16 ..      24      37 ..      22      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0007
                                      HHHHHHHTTTHHHH CS
                              MerR  3 gevAeltGvsprtL 16
                                      +evAeltGv+ rt+
  gi|488600713|ref|YP_007907184.1| 24 SEVAELTGVTLRTV 37
                                      69**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1174.76
//
Query:       gi|488600714|ref|YP_007907185.1|  [L=200]
Description: Multimeric flavodoxin WrbA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-35  121.7   0.0    2.8e-35  121.3   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    2.5e-15   56.7   0.0    3.2e-15   56.4   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
     0.0076   16.5   0.0      0.012   15.8   0.0    1.3  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 !  121.3   0.0   4.8e-39   2.8e-35       1     144 [.       1     146 [.       1     155 [. 0.93

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 4.8e-39
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHTCGGSHHHHHHHHHHHH-SCE CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlesegqtsddvaellekiaaadal 76 
                                       mkil+i+GS++ ++nt +l+e ++++++++gae+e+++l+d+ i+ c  cdk l+ e++++dd++++lek+++ada+
  gi|488600714|ref|YP_007907185.1|   1 MKILAINGSPN-RRNTHALLEIILSEAEKMGAETEILNLRDYsIKECIGCDKCLKGECSQKDDINKVLEKMKEADAI 76 
                                       9*********5.9**********************************778877777799****************** PP

                                       EEEEEECTTCE-HHHHHHHHCHT-..SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEE CS
                           FMN_red  77 iivtPeYngsysgllKnalDrlsr.trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvp 144
                                       +i+ P+Y+g+++g+ Kn++Dr ++ + g+  l+++++a+v+++g r+gg++ +     v+a   g+i+v+
  gi|488600714|ref|YP_007907185.1|  77 VIGVPTYFGNVPGIVKNLIDRSRMaRMGGFWLKNRVFAPVVTSGLRNGGAEYAIMSLLVYAlGQGMIPVS 146
                                       **********************99999999*******************999999888888678888776 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   5.4e-19   3.2e-15       1     102 [.       1      97 [.       1     125 [. 0.81

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 5.4e-19
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHC....C.HHHHTTCHHHHHHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaa....k.layeekpadveseq 71 
                                       mkiL in++p+    +++al++ +++++ek g +e ++++L +        ++++ +    k + +     + + ++
  gi|488600714|ref|YP_007907185.1|   1 MKILAINGSPNR--RNTHALLEIILSEAEKMG-AETEILNLRDYsI-----KECIGCdkclKgECS----QKDDINK 65 
                                       9*********99..899***************.9*********632.....334444322212222....3334444 PP

                                       .HHHHHCSSEEEEEEE-BTTB--HHHHHHHHH CS
                      Flavodoxin_2  72 .iekllaadaivlqfPlwwfgvPailKgwiDr 102
                                        +ek+++adaiv+++P ++ +vP i+K+ iDr
  gi|488600714|ref|YP_007907185.1|  66 vLEKMKEADAIVIGVPTYFGNVPGIVKNLIDR 97 
                                       46*****************************9 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.1e-06     0.012      33      70 ..      62      99 ..      49     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-06
                      Flavodoxin_5 33 dvekesedlesydavvigasvyygkllpelakFvekhr 70
                                      d++k  e+++++da+vig + y g++++ +++++++ r
  gi|488600714|ref|YP_007907185.1| 62 DINKVLEKMKEADAIVIGVPTYFGNVPGIVKNLIDRSR 99
                                      44456689**************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1288.57
//
Query:       gi|488600715|ref|YP_007907186.1|  [L=347]
Description: hypothetical protein Asulf_01195 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-09   35.4   7.1    8.6e-09   35.4   7.1    2.6  2  Fer4_21      4Fe-4S dicluster domain
    1.5e-07   31.5  15.5    3.8e-07   30.2   9.9    2.6  2  Fer4_9       4Fe-4S dicluster domain
    1.7e-06   28.5  22.2    1.4e-05   25.6  12.7    2.8  3  Fer4_7       4Fe-4S dicluster domain
    1.7e-05   24.8   9.7    1.7e-05   24.8   9.7    2.9  3  Fer4_10      4Fe-4S dicluster domain
    2.3e-05   24.0  16.2    6.9e-05   22.5   3.8    2.8  2  Fer4         4Fe-4S binding domain
    0.00025   20.9   0.2      0.001   18.9   0.2    2.1  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0056   17.1   3.9     0.0056   17.1   3.9    3.4  3  Fer4_4       4Fe-4S binding domain
     0.0089   15.6   0.3       0.42   10.2   0.0    3.0  3  HTH_24       Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.035   14.2   0.0    1.6  1  Sigma70_r3   Sigma-70 region 3
      0.022   14.6   2.0      0.029   14.2   0.4    2.0  1  TFIIE_alpha  TFIIE alpha subunit
      0.025   15.5  17.1       0.21   12.5   1.1    3.6  3  Fer4_16      4Fe-4S double cluster binding domain
      0.042   13.9   2.4      0.042   13.9   2.4    3.6  2  Fer4_2       4Fe-4S binding domain
      0.044   14.5   9.4      0.078   13.7   0.8    3.2  2  Fer4_15      4Fe-4S single cluster domain
       0.16   12.4   0.0       0.35   11.3   0.0    1.5  1  FaeA         FaeA-like protein
        1.1    9.3   0.0        1.1    9.3   0.0    3.4  3  FeoC         FeoC like transcriptional regulator
        1.2    9.8  23.5          2    9.0  11.3    3.1  2  Fer4_17      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.4     0.048        54       3      18 ..     237     252 ..     220     261 .. 0.69
   2 !   35.4   7.1   7.7e-12   8.6e-09       1      58 [.     276     334 ..     273     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.048
                           Fer4_21   3 idedkCigCgkCliaC 18 
                                       +d+   ++C+ C   C
  gi|488600715|ref|YP_007907186.1| 237 VDNRVTVNCNCCSDCC 252
                                       3444445555555555 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 7.7e-12
                           Fer4_21   1 AridedkCigCgkCliaCedtshqai.....eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       A +ded+CigC+ C+  C+    +ai     e+++k +++vv+++C GC +C+  C  +++i+
  gi|488600715|ref|YP_007907186.1| 276 AYVDEDECIGCQTCIDRCH---FDAIemyrpEGSKKFKARVVAENCFGCGVCVVGCE-QEAIK 334
                                       789****************...6777444555566668899***************8.57776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.052        58      34      44 ..     243     253 ..     209     279 .. 0.77
   2 !   30.2   9.9   3.4e-10   3.8e-07       1      51 []     282     333 ..     282     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.052
                            Fer4_9  34 eaCigCgaCve 44 
                                        +C  C +C e
  gi|488600715|ref|YP_007907186.1| 243 VNCNCCSDCCE 253
                                       45777777754 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 3.4e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.eaCigCgaCveaCpkgai 51 
                                       +C+gC++C++ C ++++++ + e+  + +a+   e+C+gCg Cv  C+++ai
  gi|488600715|ref|YP_007907186.1| 282 ECIGCQTCIDRCHFDAIEMYRPEGSKKFKARVVaENCFGCGVCVVGCEQEAI 333
                                       5****************9999998888876655799*************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 !   12.4  13.0   0.00017      0.19       3      52 .]     243     297 ..     241     297 .. 0.71
   2 !   25.6  12.7   1.2e-08   1.4e-05       2      51 ..     283     331 ..     282     332 .. 0.88
   3 !   16.0   2.0   1.2e-05     0.013       2      22 ..     318     338 ..     317     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                            Fer4_7   3 igCgaCvaaC......pvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       ++C+ C + C      +   + ++   + k + ++++d+++C+gC+ C+++C ++a
  gi|488600715|ref|YP_007907186.1| 243 VNCNCCSDCCefflsaKFANVPMETLLE-KSRYEAYVDEDECIGCQTCIDRCHFDA 297
                                       68********444433233333333333.3447899****************9986 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.2e-08
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       CigC+ C + C  +aie+   e  +++ k+++++e+C gCg+Cv  C  +
  gi|488600715|ref|YP_007907186.1| 283 CIGCQTCIDRCHFDAIEMYRPEG-SKKFKARVVAENCFGCGVCVVGCEQE 331
                                       ******************87755.45599******************765 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.2e-05
                            Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                       C gCg Cv+ C ++ai+l+ +
  gi|488600715|ref|YP_007907186.1| 318 CFGCGVCVVGCEQEAIKLKAV 338
                                       ****************99876 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       3.5   3.9e+03      39      49 ..     184     194 ..     166     198 .. 0.75
   2 ?   -1.3   2.8       2.2   2.5e+03      11      19 ..     244     252 ..     232     262 .. 0.62
   3 !   24.8   9.7   1.5e-08   1.7e-05       3      55 ..     277     328 ..     275     329 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                           Fer4_10  39 rkkvekCtgcg 49 
                                       ++ +++C++ g
  gi|488600715|ref|YP_007907186.1| 184 DESYWHCIQFG 194
                                       56789999866 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                           Fer4_10  11 rCgkCvkaC 19 
                                       +C+ C + C
  gi|488600715|ref|YP_007907186.1| 244 NCNCCSDCC 252
                                       344444444 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 1.5e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       ++d+d Ci+C++C + C  ++     +++e s++ + r++ e+C gcg Cv  C
  gi|488600715|ref|YP_007907186.1| 277 YVDEDECIGCQTCIDRC--HFdAIEMYRPEGSKKFKARVVAENCFGCGVCVVGC 328
                                       789**************..99889999************************999 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   3.8   6.1e-08   6.9e-05       2      24 .]     277     299 ..     276     299 .. 0.94
   2 !   14.9   4.6   1.5e-05     0.017       3      24 .]     313     334 ..     311     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.1e-08
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       ++de+ CigC +C++ C ++AI+
  gi|488600715|ref|YP_007907186.1| 277 YVDEDECIGCQTCIDRCHFDAIE 299
                                       89***************999996 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.5e-05
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       +  e C gCG Cv  C  +AI+
  gi|488600715|ref|YP_007907186.1| 313 VVAENCFGCGVCVVGCEQEAIK 334
                                       7789****************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 !   18.9   0.2   9.1e-07     0.001      23      63 ..      39      80 ..       7      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.1e-07
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEE CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYr 63
                                       ++de+ae+l+ +  +v e+L++L +kG+V  +  r + +Yr
  gi|488600715|ref|YP_007907186.1| 39 GSTDEVAEKLDMDIGRVREILENLFKKGVVIPKNFRnREYYR 80
                                      5689**************************988844244555 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   5.1       3.8   4.2e+03       6      15 ..     244     253 ..     243     261 .. 0.89
   2 !    8.4   3.7    0.0029       3.3       2      16 ..     281     295 ..     280     296 .. 0.87
   3 !   17.1   3.9     5e-06    0.0056       2      16 ..     316     330 ..     315     331 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.8
                            Fer4_4   6 gCgsCvaaCP 15 
                                       +C +C ++C+
  gi|488600715|ref|YP_007907186.1| 244 NCNCCSDCCE 253
                                       8********8 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0029
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + CigC  C++ C +
  gi|488600715|ref|YP_007907186.1| 281 DECIGCQTCIDRCHF 295
                                       78*********9975 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5e-06
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+C+gCg+Cv  C+q
  gi|488600715|ref|YP_007907186.1| 316 ENCFGCGVCVVGCEQ 330
                                       89***********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 ?    1.1   0.0      0.26   2.9e+02       3      16 ..      16      29 ..      14      36 .. 0.77
   2 !   10.2   0.0   0.00037      0.42      21      47 ..      42      68 ..      40      69 .. 0.93
   3 ?    0.2   0.0      0.52   5.8e+02      34      47 ..     214     227 ..     208     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.26
                            HTH_24  3 etdrkILelLqknp 16
                                      e+ +kILe+L+ + 
  gi|488600715|ref|YP_007907186.1| 16 ELLKKILEYLMSEE 29
                                      6679******9865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00037
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlI 47
                                       e+Ae+l++ ++ v++ l++L ++G++
  gi|488600715|ref|YP_007907186.1| 42 DEVAEKLDMDIGRVREILENLFKKGVV 68
                                      69***********************98 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.52
                            HTH_24  34 vnrrlkrLeeeGlI 47 
                                        ++ ++r ee+Gl+
  gi|488600715|ref|YP_007907186.1| 214 ALEIIERAEEDGLV 227
                                       567899******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 ?   14.2   0.0   3.1e-05     0.035      22      42 ..      40      60 ..      38      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                                      XHHHHHHHHTXXHHHHHHHHH CS
                        Sigma70_r3 22 tpeEiAeeLglseekVrevle 42
                                      +++E+Ae+L++++ +Vre+le
  gi|488600715|ref|YP_007907186.1| 40 STDEVAEKLDMDIGRVREILE 60
                                      689****************98 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   2.6e-05     0.029       1      62 [.      16      73 ..      16      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                       TFIIE_alpha  1 ellkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                                      ellk ++   + ee +++  vL      + +++a++l +d+  +r++L +L+++++v  k  
  gi|488600715|ref|YP_007907186.1| 16 ELLKKILEYLMSEEEAKIAAVLP----GSTDEVAEKLDMDIGRVREILENLFKKGVVIPKNF 73
                                      57788888888888888888877....45699**********************99966655 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 ?    3.3   1.0      0.14   1.6e+02      41      65 ..     230     253 ..     203     254 .. 0.63
   2 ?   12.5   1.1   0.00019      0.21       2      20 ..     283     301 ..     282     316 .. 0.82
   3 ?    8.7   1.6    0.0029       3.3       1      20 [.     317     336 ..     317     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                           Fer4_16  41 laedeekckkqeaitgCdiCqdvCP 65 
                                       ++++ +k   +  +  C+ C d+C 
  gi|488600715|ref|YP_007907186.1| 230 WPNT-AKIVDNRVTVNCNCCSDCCE 253
                                       3333.33333455599999999996 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00019
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++C+ C++ C  +ai++ 
  gi|488600715|ref|YP_007907186.1| 283 CIGCQTCIDRCHFDAIEMY 301
                                       ****************987 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0029
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C +Cg C+  C ++aik k
  gi|488600715|ref|YP_007907186.1| 317 NCFGCGVCVVGCEQEAIKLK 336
                                       599**************998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.4   3.8e-05     0.042       3      20 ..     276     293 ..     273     295 .. 0.89
   2 ?    9.8   3.2   0.00076      0.86       5      20 ..     313     328 ..     310     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.8e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       ++vd+d CigC +C++ C
  gi|488600715|ref|YP_007907186.1| 276 AYVDEDECIGCQTCIDRC 293
                                       799***********9988 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00076
                            Fer4_2   5 vdtdrCigCgaCvsaC 20 
                                       v++++C gCg Cv  C
  gi|488600715|ref|YP_007907186.1| 313 VVAENCFGCGVCVVGC 328
                                       6789********9989 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 ?   13.7   0.8     7e-05     0.078       2      18 ..     277     293 ..     276     311 .. 0.84
   2 ?    4.5   1.2     0.053        59       6      19 ..     316     329 ..     312     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7e-05
                           Fer4_15   2 vvDrdaCigcglCvaea 18 
                                       +vD+d+Cigc  C++++
  gi|488600715|ref|YP_007907186.1| 277 YVDEDECIGCQTCIDRC 293
                                       69*************99 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.053
                           Fer4_15   6 daCigcglCvaeap 19 
                                       ++C gcg+Cv  ++
  gi|488600715|ref|YP_007907186.1| 316 ENCFGCGVCVVGCE 329
                                       78********9884 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.35       4      46 ..      20      69 ..      18      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                      HHHHHHHH........S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA  4 eIleylnsi.......kapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                      +Ileyl s          p+ T e+A+ l + +  +R  Le+L k+g + 
  gi|488600715|ref|YP_007907186.1| 20 KILEYLMSEeeakiaaVLPGSTDEVAEKLDMDIGRVREILENLFKKGVVI 69
                                      6888888877777766679**************************99875 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0     0.001       1.1      16      47 ..      40      71 ..      17      77 .. 0.87
   2 ?    0.4   0.6      0.64   7.1e+02      43      60 ..     235     251 ..     220     255 .. 0.60
   3 ?   -1.1   0.4       1.9   2.1e+03      54      63 ..     280     289 ..     265     302 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                              FeoC 16 slkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                      s +e + +++++   ++ +Le + +kG v  +
  gi|488600715|ref|YP_007907186.1| 40 STDEVAEKLDMDIGRVREILENLFKKGVVIPK 71
                                      7799***********************99765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.64
                              FeoC  43 rvekvaataccsgsCkkC 60 
                                       ++ +   t+ c ++C+ C
  gi|488600715|ref|YP_007907186.1| 235 KIVDNRVTVNC-NCCSDC 251
                                       55555555555.555555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.9
                              FeoC  54 sgsCkkCggk 63 
                                       ++ C +C+  
  gi|488600715|ref|YP_007907186.1| 280 EDECIGCQTC 289
                                       4455555432 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  15.4      0.31   3.5e+02       4      57 ..     244     294 ..     243     297 .. 0.66
   2 ?    9.0  11.3    0.0018         2       1      59 [.     282     331 ..     282     332 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.31
                           Fer4_17   4 qCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                       +C +C + C ++   ++  + +++   l++ ++ e+    ++Ci+C+ C  +C 
  gi|488600715|ref|YP_007907186.1| 244 NCNCCSDCCEFFLSAKF-ANVPMET-LLEKSRY-EAYVDEDECIGCQTCIDRCH 294
                                       7******8888888666.3333333.1212222.3345669************5 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                       +Ci+C+ C++ C + ++    + +  +        + +++ +a++C +Cg C+  C q+
  gi|488600715|ref|YP_007907186.1| 282 ECIGCQTCIDRCHFDAIEMY-RPEGSK--------KFKARVVAENCFGCGVCVVGCEQE 331
                                       6*********9987666332.222223........333456999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2171.58
//
Query:       gi|488600716|ref|YP_007907187.1|  [L=273]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  104.7  43.3    3.8e-20   72.5  16.2    2.1  2  EamA      EamA-like transporter family
     0.0029   17.0  23.6       0.72    9.1  22.2    3.0  2  TPT       Triose-phosphate Transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5  16.2   4.2e-24   3.8e-20       3     136 ..       3     137 ..       1     138 [. 0.98
   2 !   38.6  19.1   1.2e-13   1.1e-09       3     136 ..     143     271 ..     141     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 4.2e-24
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvla 78 
                                       g+++al+a+++w++++v+ +++l+k++ ++ tf+  l++++ ll+++ + ++ + a+l++k++++l+  g+l  +++
  gi|488600716|ref|YP_007907187.1|   3 GYIFALVASMLWGLNAVFVRKALEKTDAFSGTFFIVLVSAVCLLMMSIFDKSLFnANLTQKNLIFLAAGGILQYFFG 79 
                                       99*************************************************************************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        +l + + k +++s+a   +s+  +f++il++l+lgek+++++ +gi+ +++G ++++
  gi|488600716|ref|YP_007907187.1|  80 RSLTYFSAKIVGSSRAFTGSSTRIMFSAILGILILGEKVSFMKAFGIIAMIAGMYILS 137
                                       *******************************************************987 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 1.2e-13
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                       g+ + +++ +f++++ +++k+++++  ++ l+ + ++++++ +l++++ + ++      + +  +ll++ +  +la 
  gi|488600716|ref|YP_007907187.1| 143 GLHISIAGGFFYGLASIVIKAGMAE--SVVLSNLISILSALPFLALLASRNINT-----SKFNRFLLFSGFTLFLAT 212
                                       566678999**********998543..444444445555555555555555555.....56666788888******* PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlll..gekltlkqllgivlillGvllil 136
                                       l +++al+  ++ +++++++l Pvf++i+s+l+    e+++l++++g++++++G ++++
  gi|488600716|ref|YP_007907187.1| 213 LSYYKALSLAPVVVVVPLSNLYPVFAVIFSYLFIqsLERIGLRTFAGACIAVFGGIIVY 271
                                       **********************************6569**************9988775 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.7    0.0015        13     145     196 ..       2      50 ..       1      66 [. 0.71
   2 !    9.1  22.2     8e-05      0.72      34     285 ..      40     266 ..      30     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0015
                               TPT 145 igfisAlisnltfslrnifsKkllkklkdldalnlfaiitilslllllPval 196
                                        g+i Al++ +   l  +f +k+l+k+   da    ++i ++s++ ll +++
  gi|488600716|ref|YP_007907187.1|   2 DGYIFALVASMLWGLNAVFVRKALEKT---DAFSGTFFIVLVSAVCLLMMSI 50 
                                       58999*********************3...4555555555555555554444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 8e-05
                               TPT  34 vsavqllvgsvlilvlwalglkkrpkisseflkailpla.lvktlghvlavvslskvaVSfthtvKasePiFtvils 109
                                       vsav ll+ s++   l++      ++++++ l+ +   + l  ++g  l+ +s + v  S + t  ++  +F++il 
  gi|488600716|ref|YP_007907187.1|  40 VSAVCLLMMSIFDKSLFN------ANLTQKNLIFLAAGGiLQYFFGRSLTYFSAKIVGSSRAFTGSSTRIMFSAILG 110
                                       333333333333333333......33334444444444423457899****************************** PP

                               TPT 110 rlllgeklsllvylsLlpivgGvalasvtElsFnligfisAlisnltfslrnifsKkllkklkdldalnlfaiitil 186
                                       +l+lgek+s+++   ++ +++G+ + s+  l    +g+   ++  ++  l +i+ K  + +  ++  +nl +i+++l
  gi|488600716|ref|YP_007907187.1| 111 ILILGEKVSFMKAFGIIAMIAGMYILSMERL----SGLHISIAGGFFYGLASIVIKAGMAE--SVVLSNLISILSAL 181
                                       ****************************976....599999999****************9..35555555555554 PP

                               TPT 187 slllllPvallvegvlktpsllkstkvslkevllllllsgvlfhlynqvaymvLervspvthsv.antvKrvvvIvl 262
                                        +l l      + +      ++++     +++   ll sg+  +l     y++L+  +pv   v  + +  v+ +++
  gi|488600716|ref|YP_007907187.1| 182 PFLAL------LAS-----RNINT-----SKFNRFLLFSGFTLFLATLSYYKALSL-APVVVVVpLSNLYPVFAVIF 241
                                       44443......333.....22222.....234445667777777776666666664.34444331344555666666 PP

                               TPT 263 svlvfk..npvsllnaiGtavaivG 285
                                       s l+++  +++ l +  G+++a++G
  gi|488600716|ref|YP_007907187.1| 242 SYLFIQslERIGLRTFAGACIAVFG 266
                                       6666653346777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2075.63
//
Query:       gi|488600717|ref|YP_007907188.1|  [L=278]
Description: 1,4-Dihydroxy-2-naphthoyl-CoA synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-60  205.0   0.0    1.5e-60  204.7   0.0    1.1  1  ECH_1     Enoyl-CoA hydratase/isomerase
    4.1e-17   62.7   0.0    9.5e-17   61.5   0.0    1.7  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.7   0.0   1.6e-64   1.5e-60       2     248 ..      13     269 ..      12     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 204.7 bits;  conditional E-value: 1.6e-64
                                       EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHC.HHHHHHHCC CS
                             ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeek.akqallkee 76 
                                       +++ +a i++nrP   Na  + ++ El++a+ ++  dk++++vv tG gdkaF+ G+d+  +  +++  + ++++ +
  gi|488600717|ref|YP_007907188.1|  13 KKDRIATITINRPGRYNACRPITIYELTKAFIDAWADKEIGVVVFTGaGDKAFCTGGDQSIRDVGGYkGDMKEYRGT 89 
                                       6788*******************************************************977666665555555555 PP

                                       HHHH.....HH....HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHH CS
                             ECH_1  77 vlel.....wt....klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkv 144
                                       +  l     w+    +++++pkpvia vnG+aigGG++  + cD+ ia+++a+fg++  ++G++++ +gt  l r+v
  gi|488600717|ref|YP_007907188.1|  90 IATLplevgWQfvtfLIRHIPKPVIARVNGYAIGGGHVWQVNCDLSIASETAKFGQAGPRVGSFDPGFGTGDLWRNV 166
                                       443322222764444689*********************************************************** PP

                                       HHHHHHHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHH.HHHHHHHHHH CS
                             ECH_1 145 GkskAeeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakle.dalaeqleae 220
                                       G +kA+ei++l++ ++aqeal++Glv+kvvp ++l ee ++++ +l+eksp+al++lk a+ a+++    ++ l + 
  gi|488600717|ref|YP_007907188.1| 167 GLKKAKEIWYLCRIYTAQEALEMGLVNKVVPPDKLDEEVRKWCDELLEKSPTALKMLKYAFLAETDgLGGITELGVG 243
                                       *****************************************************************999999888877 PP

                                       HHHHHHHCTSHHHHHHHHHHHTCSH--- CS
                             ECH_1 221 aklfestfskddikeGlqaflEkrkpef 248
                                          ++++ ++  + eG++af+Ekr p+f
  gi|488600717|ref|YP_007907188.1| 244 GLSLYYMSDE--SVEGRNAFMEKRMPDF 269
                                       7666666655..56************98 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   1.1e-20   9.5e-17       2     178 ..      18     202 ..      17     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.1e-20
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B-..-HHHHHHHHCS-THH....HHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgD..vralyeaakegkkee....eef 72 
                                       ++it+nrp   Na     + +l++a+ +  +d+e+ +vv +gag+kafC GgD  +r +   + + k+ +    +  
  gi|488600717|ref|YP_007907188.1|  18 ATITINRPGRYNACRPITIYELTKAFIDAWADKEIGVVVFTGAGDKAFCTGGDqsIRDVGGYKGDMKEYRgtiaTLP 94 
                                       78***********************99999**********************9555555433333322212222333 PP

                                       HHHHHH.HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT--.--TTHHHHHHCSSTTHH CS
                             ECH_2  73 freeYk.lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlf.PDvGgsyfLsrlpgelG 147
                                        +  ++ +  li ++pkpv+a ++G+++GgG    v++ + +++e+++f     ++G f P  G+  +   +  + +
  gi|488600717|ref|YP_007907188.1|  95 LEVGWQfVTFLIRHIPKPVIARVNGYAIGGGHVWQVNCDLSIASETAKFGQAGPRVGSFdPGFGTGDLWRNVGLKKA 171
                                       44455525689**************************************9999999977577777766666655666 PP

                                       HHHHHH---B-HHHHHHTTS--EE--GGGHH CS
                             ECH_2 148 lylalTGarlkgadalaaglathyvpsekle 178
                                       + +    +  ++++al++gl +++vp +kl+
  gi|488600717|ref|YP_007907188.1| 172 KEIWYLCRIYTAQEALEMGLVNKVVPPDKLD 202
                                       6666666777777777777777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2163.05
//
Query:       gi|488600718|ref|YP_007907189.1|  [L=299]
Description: 3-hydroxyacyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-68  229.6   0.2    3.3e-68  229.1   0.2    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    4.9e-26   91.2   0.0    1.8e-25   89.3   0.0    1.9  2  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
      4e-05   23.8   0.4    8.9e-05   22.7   0.4    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00023   21.2   0.3    0.00068   19.6   0.3    1.7  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    0.00035   21.1   0.3     0.0011   19.5   0.3    1.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0055   17.0   0.3     0.0091   16.3   0.2    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.008   16.0   0.0      0.012   15.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.018   14.6   0.0    1.2  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.016   14.8   0.7      0.028   14.0   0.6    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.062   12.6   0.6       0.13   11.6   0.3    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.065   12.5   0.0      0.086   12.1   0.0    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
       0.07   13.3   3.2       0.18   12.1   0.6    2.2  2  DUF2666          Protein of unknown function (DUF2666)
      0.076   12.5   0.1      0.098   12.1   0.1    1.2  1  adh_short        short chain dehydrogenase
       0.11   11.7   0.1       0.17   11.2   0.1    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
       0.12   12.3   0.1       0.27   11.2   0.0    1.7  2  ADH_zinc_N       Zinc-binding dehydrogenase
       0.15   12.7   0.4       0.37   11.4   0.4    1.7  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> 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 !  229.1   0.2   2.9e-71   3.3e-68       1     179 [.       9     190 ..       9     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 229.1 bits;  conditional E-value: 2.9e-71
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH...HHHCCTTTTSS-HHHHCCCHHCEEEES-HH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek...sleklvekgklkeeeveaalarisfttdle 74 
                                       k++v+GaG+mG+gia+v+a++g+e+vlvdi+ee+l+ka + i++    leklv+kgk++eee++++lari+++t+++
  gi|488600718|ref|YP_007907189.1|   9 KIGVLGAGVMGHGIAQVCARSGYETVLVDIKEEFLKKAVDIIKSgpfGLEKLVQKGKINEEEMHEVLARIKTSTSMD 85 
                                       69******************************************9999***************************** PP

                                       HHHC-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE CS
                           3HCDH_N  75 eavdadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvr 151
                                        ++d+d+ iE+++E++elK+kv+++l+ki+k+++i+asnTS+++is+la+a++r++r+ig+H+fnPpp+mkL+Evvr
  gi|488600718|ref|YP_007907189.1|  86 VLKDVDFLIESIPEDIELKKKVYTQLDKICKAETIFASNTSGIMISDLASAVDRKDRFIGMHWFNPPPVMKLIEVVR 162
                                       ***************************************************************************** PP

                                       -TT--HHHHHHHHHHHHHTT-EEEEECS CS
                           3HCDH_N 152 gekTseetvatvvelakkigktpvvvkd 179
                                       g+ Ts+et++ +vel+kk+gk+pv++ d
  gi|488600718|ref|YP_007907189.1| 163 GALTSDETFNITVELSKKLGKVPVEAAD 190
                                       ************************9876 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 ?   -1.1   0.0       2.7   3.1e+03      62      90 ..      42      70 ..       2      76 .. 0.49
   2 !   89.3   0.0   1.6e-28   1.8e-25       1      93 [.     193     285 ..     193     294 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.7
                                      HHHHTTTHGGHH-HHHHHHHHTT--BGGG CS
                             3HCDH 62 laeelgerayapsplleklveagrlgrkt 90
                                      + ++  +     +  leklv++g++ +++
  gi|488600718|ref|YP_007907189.1| 42 FLKKAVDIIKSGPFGLEKLVQKGKINEEE 70
                                      33333333333345566777777766655 PP

  == domain 2  score: 89.3 bits;  conditional E-value: 1.6e-28
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+++R +  +l ea+rl+e g+a +++iD +++ ++G+pmGpfel+dl+gld++ +i e+++ee+ +++yap+  l
  gi|488600718|ref|YP_007907189.1| 193 GFFTTRFINCWLVEAIRLFETGIAGIKEIDDMCKMAFGFPMGPFELMDLIGLDTMFHIGEYMYEETRDPHYAPPVTL 269
                                       9**************************************************************************** PP

                                       HHHHHTT--BGGGTBS CS
                             3HCDH  78 eklveagrlgrktgkg 93 
                                       +kl+ +g +g k+ k+
  gi|488600718|ref|YP_007907189.1| 270 KKLILSGYIGDKKLKK 285
                                       **********998664 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.4   7.9e-08   8.9e-05       1      87 [.       9     122 ..       9     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.9e-08
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..........................EEE-SSHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..........................akaaesiee 51 
                                       kig++G GvMG+ +a+ ++++gy++++++ ++e ++++v+                               +++  +
  gi|488600718|ref|YP_007907189.1|   9 KIGVLGAGVMGHGIAQVCARSGYETVLVDIKEEFLKKAVDIIksgpfgleklvqkgkineeemhevlaRIKTSTSMD 85 
                                       79*****************************9888877765444588888888888888888888874333444457 PP

                                       HHHHCSEEEE-SSSHHHHH.HHHHSHCCC--TT-EEE CS
                     NAD_binding_2  52 lvasldvvitmvkagkavd.eviegllealkkgdili 87 
                                       +++++d+ i  ++++ + + +v+++l + +k+++i+ 
  gi|488600718|ref|YP_007907189.1|  86 VLKDVDFLIESIPEDIELKkKVYTQLDKICKAETIFA 122
                                       8888888888888887765156666777777776665 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 !   19.6   0.3   6.1e-07   0.00068       1     106 [.       9     128 ..       9     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.1e-07
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H...............HHHHHHHHHSSBTTTBTT----TTEEEES- CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree...............elieeineehenvkyLpgiklpenlvattd 62 
                                       ki+vlGaG  G  +A+v+a+ g e++l   +e                l + +++ + n++ + +  + + ++ +t 
  gi|488600718|ref|YP_007907189.1|   9 KIGVLGAGVMGHGIAQVCARSGYETVLVDIKEeflkkavdiiksgpfGLEKLVQKGKINEEEMHE--VLARIKTSTS 83 
                                       79********************8888888888788866666666666444455555666664443..4456666665 PP

                                       HHHHHTT--EEEE---HHH..HHHHHHHHCCC--TT-EEEE---SE CS
                    NAD_Gly3P_dh_N  63 laealkgadiivlvvPsqa..lrevlkklkgllkkkailvsliKGi 106
                                       + ++lk++d+++  +P  +   ++v ++l+++ k+++i++s + Gi
  gi|488600718|ref|YP_007907189.1|  84 M-DVLKDVDFLIESIPEDIelKKKVYTQLDKICKAETIFASNTSGI 128
                                       5.68999999999**9864226899999999999999999999998 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 !   19.5   0.3   9.8e-07    0.0011       1      66 [.       9      94 ..       9     120 .. 0.77
   2 ?   -1.8   0.0       4.5     5e+03      38      72 ..     116     149 ..      93     161 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.8e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........................-EEECECH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........................vkvtavdn 55
                                      kig++GaG mg+++a+ ++++g   +e v++ + ++e ++++ + ++                        +++++++ 
  gi|488600718|ref|YP_007907189.1|  9 KIGVLGAGVMGHGIAQVCARSG---YETVLV-DIKEEFLKKAVDIIKsgpfgleklvqkgkineeemhevlARIKTSTS 83
                                      7*********************...888867.99999999988888866666666666666666666666655555556 PP

                                      HHHHHH-SEEE CS
                     F420_oxidored 56 eeaaeeadvvv 66
                                       +++++ d+++
  gi|488600718|ref|YP_007907189.1| 84 MDVLKDVDFLI 94
                                      66666655555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                                       CHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HH CS
                     F420_oxidored  38 kaeelaeelgvkvtavdneeaaeeadvvvlavkpe 72 
                                       kae + ++   +++ +d + a+++ d  ++ +++ 
  gi|488600718|ref|YP_007907189.1| 116 KAETIFASNTSGIMISDLASAVDRKDR-FIGMHWF 149
                                       444444444456666667777766664.4555555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   8.1e-06    0.0091       1      45 [.      10      57 ..      10      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.1e-06
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH......T CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka......l 45
                                      + ++GaG +G+++a+++ar++ +  e +++d ++e l+++++ +      l
  gi|488600718|ref|YP_007907189.1| 10 IGVLGAGVMGHGIAQVCARSG-Y--ETVLVDIKEEFLKKAVDIIksgpfgL 57
                                      689****************98.5..79************998774444443 PP

>> Methyltransf_31  Methyltransferase domain
   #    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      13     113 ..      14     127 ..      14     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                   Methyltransf_31  13 GtGeltfelae.elgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieelekl.led.....ekfDlilsn 81 
                                       G+G  ++ +a+  ++++ e v++Di+ee +++A  + ++  +  +  +++g i+e e++ +        + D++ + 
  gi|488600718|ref|YP_007907189.1|  14 GAGVMGHGIAQvCARSGYETVLVDIKEEFLKKAVDIIKSGPFGlEKLVQKGKINEEEMHeVLAriktsTSMDVLKDV 90 
                                       7888899999665566889*******************999995555666999999987644357777777777666 PP

                   Methyltransf_31  82 evl.....naladpdkileeiervlkpggilliedpr 113
                                       ++l      ++  ++k++ ++ +  k ++i+++++  
  gi|488600718|ref|YP_007907189.1|  91 DFLiesipEDIELKKKVYTQLDKICKAETIFASNTSG 127
                                       66688888***********************998877 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 ?   14.6   0.0   1.6e-05     0.018       6      67 ..      18      82 ..      11     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTT...SEEEE--TTSHHHHHHHHHHHHHHH CS
                      adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelg...aevlecDVtdeeqvealveevvekf 67
                                      +G++iA+ +a+ G+e vl+d++ee  k++ ++ ++++   +++++    +ee+++++ ++++ ++
  gi|488600718|ref|YP_007907189.1| 18 MGHGIAQVCARSGYETVLVDIKEEFLKKAVDIIKSGPfglEKLVQKGKINEEEMHEVLARIKTST 82
                                      89***********************6666666666553444456666666666677766666554 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 ?   14.0   0.6   2.5e-05     0.028       2      57 ..       9      63 ..       8      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkk 57
                                      ki v+G+G +G   a v a+ g e ++vDi ee  +k   + i+    gLe+lv+k
  gi|488600718|ref|YP_007907189.1|  9 KIGVLGAGVMGHGIAQVCARSGYETVLVDIKEEFLKKA-VDIIKSGPFGLEKLVQK 63
                                      8*****************************99866553.34444444556666555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00011      0.13      37      70 ..       8      41 ..       4      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                      k++G++G+G +G+ +a++++  g + + +d +++
  gi|488600718|ref|YP_007907189.1|  8 KKIGVLGAGVMGHGIAQVCARSGYETVLVDIKEE 41
                                      89***************************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 ?   12.1   0.0   7.7e-05     0.086     143     180 ..       8      46 ..       3     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrll.ra 180
                                       k+i v G+G+ G  +A++ a+ g+e++lv+  +++l +a
  gi|488600718|ref|YP_007907189.1|   8 KKIGVLGAGVMGHGIAQVCARSGYETVLVDIKEEFLkKA 46 
                                       578888888888888888888888888888888888444 PP

>> DUF2666  Protein of unknown function (DUF2666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   0.00016      0.18      36      90 ..      29      85 ..      18      93 .. 0.75
   2 ?    1.8   0.2      0.23   2.6e+02      29      54 ..      89     114 ..      85     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHH.HHTT--HHHHHHH.TTT--S--S....HHHHHHHHHHHHT-.... CS
                           DUF2666 36 sieetvskkik.dylpfDlekleei.adeikkkkkgrvkeedisevleklkspattk 90
                                      s  etv   ik ++l+  ++ ++   ++  k ++kg+++ee+++evl+++k+ ++  
  gi|488600718|ref|YP_007907189.1| 29 SGYETVLVDIKeEFLKKAVDIIKSGpFGLEKLVQKGKINEEEMHEVLARIKTSTSMD 85
                                      556899999973599888888876515555679*****************9886555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHTT--HH CS
                           DUF2666  29 eiarlLasieetvskkikdylpfDle 54 
                                       ++  l+ si e ++ k k y ++D  
  gi|488600718|ref|YP_007907189.1|  89 DVDFLIESIPEDIELKKKVYTQLDKI 114
                                       7788999******9999999999964 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   0.1   8.8e-05     0.098       6      74 ..      13      81 ..       8     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-05
                                      ESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHH CS
                         adh_short  6 tGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkk 74
                                       Ga+  +G+ ia+ +a++G+++v+vd++ee l+++++ +k+   g + l+ ++ ++ +ee+ +++++++  
  gi|488600718|ref|YP_007907189.1| 13 LGAG-VMGHGIAQVCARSGYETVLVDIKEEFLKKAVDIIKSGpfGLEKLVQKGKIN-EEEMHEVLARIKTS 81
                                      5554.68******************************9999877777777777777.55566666666544 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00015      0.17      30      70 ..       9      50 ..       2      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.T CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.l 70
                                      k+ v+G+Gv G   ++++++ g +++++D++++ l++  + +
  gi|488600718|ref|YP_007907189.1|  9 KIGVLGAGVMGHGIAQVCARSGYETVLVDIKEEFLKKAVDiI 50
                                      788*****************************9998876643 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.27       2      63 ..      18      94 ..      17     126 .. 0.80
   2 ?   -3.1   0.0       6.6   7.4e+03      66      86 ..     165     185 ..     155     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                      HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT......TESEEEET.....TTC.HHHHHHHHHT...TTSSEEEEE CS
                        ADH_zinc_N  2 vGlaavqlAkalGaeviavdsseeklelakkl......Gadeviny.....kea.dlverikelt...ggegvdvvf 63
                                      +G+   q+++ +G e++ vd++ee l++a ++      G + ++       +e+ ++ +rik  t     ++vd+ +
  gi|488600718|ref|YP_007907189.1| 18 MGHGIAQVCARSGYETVLVDIKEEFLKKAVDIiksgpfGLEKLVQKgkineEEMhEVLARIKTSTsmdVLKDVDFLI 94
                                      799********************977666555666666999988888888888888999999988443123555555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.6
                                       SCSHHHHHHHHHCEEEEEEEE CS
                        ADH_zinc_N  66 vGsgatleaalkllkpgGrlv 86 
                                       + s +t++  ++l k+ G++ 
  gi|488600718|ref|YP_007907189.1| 165 LTSDETFNITVELSKKLGKVP 185
                                       556777777777777777765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00033      0.37       1      39 [.       9      48 ..       9      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllD 39
                                      k+ v+G+G+ g   A++ a+ g ++ +v+ ++++l ++ D
  gi|488600718|ref|YP_007907189.1|  9 KIGVLGAGVMGHGIAQVCARSGYETVLVDIKEEFLkKAVD 48
                                      688********************************66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1706.17
//
Query:       gi|488600719|ref|YP_007907190.1|  [L=177]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   65.0   4.2    6.4e-18   64.0   4.2    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
      1e-15   57.3   0.1    1.8e-15   56.4   0.1    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    5.1e-15   55.5  11.3    2.7e-14   53.2  10.6    2.2  2  Arc_trans_TRASH  Archaeal TRASH domain
    7.8e-09   35.3   0.6    2.3e-08   33.9   0.3    1.9  1  MarR             MarR family
    2.9e-08   33.5   1.6    2.9e-08   33.5   1.6    1.9  2  HTH_11           HTH domain
    2.2e-07   30.8   1.0    6.5e-07   29.3   1.0    1.8  1  HTH_Mga          M protein trans-acting positive regulator (M
    5.5e-06   26.2   0.0    1.6e-05   24.7   0.0    1.7  1  MarR_2           MarR family
    1.4e-05   24.9   0.8    3.4e-05   23.7   0.3    1.9  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    8.7e-05   22.3   0.3    0.00025   20.8   0.0    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm
    9.5e-05   22.4   0.0    0.00018   21.5   0.0    1.4  1  HTH_20           Helix-turn-helix domain
    0.00022   21.4   0.1     0.0012   19.1   0.0    2.0  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00024   20.8   1.6      0.014   15.2   0.1    2.4  2  HTH_30           PucR C-terminal helix-turn-helix domain
    0.00047   20.2   0.0    0.00092   19.3   0.0    1.4  1  HTH_28           Helix-turn-helix domain
     0.0005   19.8   0.1     0.0011   18.7   0.1    1.6  1  HTH_23           Homeodomain-like domain
    0.00054   19.8   2.4    0.00056   19.7   0.7    1.8  1  RuvB_C           RuvB C-terminal winged helix domain
    0.00083   19.2   1.7     0.0031   17.3   0.3    2.1  2  HxlR             HxlR-like helix-turn-helix
    0.00096   19.0   0.1     0.0025   17.6   0.0    1.8  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0011   18.7   3.1     0.0013   18.4   0.8    2.2  2  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0012   18.5   0.1      0.003   17.2   0.1    1.7  1  Sigma70_r4_2     Sigma-70, region 4
     0.0013   18.4   0.0     0.0031   17.1   0.0    1.6  1  GntR             Bacterial regulatory proteins, gntR family
     0.0025   17.3   0.8     0.0049   16.3   0.1    1.8  1  Sigma70_r4       Sigma-70, region 4
     0.0037   17.4   0.1     0.0072   16.5   0.1    1.5  1  HTH_34           Winged helix DNA-binding domain
      0.004   17.1   1.5      0.011   15.6   1.5    1.8  1  HTH_12           Ribonuclease R winged-helix domain
      0.005   16.9   0.5     0.0096   16.0   0.1    1.7  1  DUF2250          Uncharacterized protein conserved in archaea
     0.0056   16.7   0.1      0.019   15.0   0.1    1.9  1  HTH_7            Helix-turn-helix domain of resolvase
     0.0056   17.0   0.1     0.0093   16.3   0.1    1.5  1  Penicillinase_R  Penicillinase repressor
     0.0057   17.0   0.5      0.014   15.7   0.1    1.8  1  Rrf2             Transcriptional regulator
     0.0068   16.2   0.4     0.0068   16.2   0.4    2.5  3  TFIIE_alpha      TFIIE alpha subunit
      0.008   16.1   0.1      0.019   14.9   0.1    1.6  1  HTH_36           Helix-turn-helix domain
       0.01   15.9   0.0       0.01   15.9   0.0    2.6  3  FeoC             FeoC like transcriptional regulator
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.018   15.0   0.0    1.4  1  HTH_29           Winged helix-turn helix
      0.011   16.3   0.1      0.018   15.7   0.1    1.2  1  RPA_C            Replication protein A C terminal
      0.012   15.4   0.1      0.026   14.3   0.1    1.6  1  LexA_DNA_bind    LexA DNA binding domain
      0.014   15.6   2.5      0.027   14.7   0.7    2.2  2  UPF0122          Putative helix-turn-helix protein, YlxM / p1
      0.014   15.1   0.1      0.029   14.1   0.1    1.5  1  HTH_39           Helix-turn-helix domain
      0.015   15.3   0.8      0.033   14.2   0.8    1.5  1  HTH_45           Winged helix-turn-helix
      0.017   14.7   0.2       0.04   13.5   0.2    1.7  1  GerE             Bacterial regulatory proteins, luxR family
      0.023   14.5   0.1      0.064   13.1   0.1    1.7  1  HTH_10           HTH DNA binding domain
      0.029   14.2   0.0       0.16   11.8   0.0    1.9  2  HTH_IclR         IclR helix-turn-helix domain
      0.033   14.8   2.4      0.062   13.9   1.0    2.1  2  Mga              Mga helix-turn-helix domain
      0.054   12.8   0.0       0.08   12.2   0.0    1.3  1  EAP30            EAP30/Vps36 family
       0.06   13.7   0.4       0.19   12.1   0.1    1.9  2  FaeA             FaeA-like protein
      0.072   13.6   0.9       0.26   11.8   0.1    2.1  2  HTH_27           Winged helix DNA-binding domain
      0.086   12.3   0.0       0.16   11.4   0.0    1.4  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.086   12.8   0.0       0.18   11.8   0.0    1.5  1  HTH_1            Bacterial regulatory helix-turn-helix protei
      0.095   13.2   1.3       0.18   12.3   1.3    1.6  1  HTH_40           Helix-turn-helix domain
        0.1   12.7   0.3       0.22   11.6   0.3    1.5  1  YhdB             YhdB-like protein
       0.14   12.4   1.2       0.65   10.3   0.1    2.2  2  Rio2_N           Rio2, N-terminal
        0.6   10.5   3.1          1    9.7   2.1    1.8  2  DUF3268          zinc-finger-containing domain
       0.89    9.6  11.1        2.6    8.1   0.8    2.3  2  zf-C2H2_6        C2H2-type zinc finger
        2.8    8.5   8.2        2.8    8.5   0.1    2.3  2  zf-H2C2_2        Zinc-finger double domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   4.2   1.8e-20   6.4e-18       2      48 .]       4      50 ..       3      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.8e-20
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      de+d+kIL++L++n+ris +e+A+ l+++++tv+ r++rLe++G+Ik
  gi|488600719|ref|YP_007907190.1|  4 DEIDIKILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIK 50
                                      9*********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1   5.2e-18   1.8e-15       1      42 []       3      44 ..       3      44 .. 0.99

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 5.2e-18
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +DeiD+kIL++L e++Ris++e+A+ ++++++tv  R++rLe
  gi|488600719|ref|YP_007907190.1|  3 IDEIDIKILNILKENSRISFTEIAKNLNITRQTVKSRIERLE 44
                                      6****************************************8 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       3.2   1.1e+03       6      17 ..     126     137 ..     126     140 .. 0.84
   2 !   53.2  10.6   7.7e-17   2.7e-14       1      35 [.     141     175 ..     141     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 3.2
                   Arc_trans_TRASH   6 keivgePivykl 17 
                                       +eiv++P+ +kl
  gi|488600719|ref|YP_007907190.1| 126 SEIVDKPLSLKL 137
                                       59*****99987 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 7.7e-17
                   Arc_trans_TRASH   1 CDYCGkeivgePivyklknkvYyvCCktCkselkk 35 
                                       CDYCGk   ++P++yk +n+ Y++CCktC++e+kk
  gi|488600719|ref|YP_007907190.1| 141 CDYCGKTSIDDPLIYKKHNRFYVLCCKTCLEEFKK 175
                                       **********************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.3   6.4e-11   2.3e-08       6      51 ..       8      53 ..       5      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 6.4e-11
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      ++iL il+e+  +s +e+ak l++++ tv   + rLek+G i+R+ 
  gi|488600719|ref|YP_007907190.1|  8 IKILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKRYT 53
                                      689*****************************************96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   1.6   8.1e-11   2.9e-08       4      46 ..       9      54 ..       7      57 .. 0.86
   2 ?   -1.6   0.1       7.4   2.6e+03      33      43 ..      74      84 ..      74      94 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 8.1e-11
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpI 46
                                      +il +L ++++ is  e+A+ Ln++r+tv  +I++Le+ g    + I
  gi|488600719|ref|YP_007907190.1|  9 KILNIL-KENSRISFTEIAKNLNITRQTVKSRIERLEKDGiikrYTI 54
                                      899***.55556****************************6555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.4
                            HTH_11 33 rrdIkaLeelg 43
                                      +r++k++ee +
  gi|488600719|ref|YP_007907190.1| 74 YRRLKDIEEVL 84
                                      68888888876 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   1.0   1.8e-09   6.5e-07       5      44 ..       5      43 ..       1      49 [. 0.91

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.8e-09
                           HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdiseL 44
                                      + ++k+l++L e +++++ +e+ak+L++++ t++s+i+ L
  gi|488600719|ref|YP_007907190.1|  5 EIDIKILNILKE-NSRISFTEIAKNLNITRQTVKSRIERL 43
                                      5689********.************************988 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   4.6e-08   1.6e-05      10      53 ..      10      51 ..       6      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.6e-08
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +L+ L  + +  ++ +e+a+ l++++++v  +++rL++ G + r
  gi|488600719|ref|YP_007907190.1| 10 ILNILKENSR--ISFTEIAKNLNITRQTVKSRIERLEKDGIIKR 51
                                      6677777776..9*****************************88 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 !   23.7   0.3   9.7e-08   3.4e-05      21      61 ..      19      58 ..       7      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 9.7e-08
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES- CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririld 61
                                      +++ +e+A  l++tr+tv   + +L+++g+i+r + i++ d
  gi|488600719|ref|YP_007907190.1| 19 RISFTEIAKNLNITRQTVKSRIERLEKDGIIKRYT-IEVAD 58
                                      67889***************************987.99988 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   7.2e-07   0.00025       5      55 ..       2      52 ..       1      63 [. 0.92
   2 ?   -1.6   0.0       7.3   2.6e+03      23      23 ..     101     101 ..      77     124 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.2e-07
                                      HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                       + e ++k+   L ++ + + +eia++l++ r++v + +++Le+ G+++r 
  gi|488600719|ref|YP_007907190.1|  2 EIDEIDIKILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKRY 52
                                      5789999**99999**********************************985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.3
                                       C CS
                              TrmB  23 a 23 
                                       +
  gi|488600719|ref|YP_007907190.1| 101 S 101
                                       1 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   5.2e-07   0.00018      14      57 ..       9      52 ..       4      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5.2e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +il  L+++   +++e+a+ l ++++t+  +++ Le+ g++++ 
  gi|488600719|ref|YP_007907190.1|  9 KILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKRY 52
                                      788999999999*****************************986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.3e-06    0.0012      13      52 ..      10      49 ..       9      52 .. 0.92
   2 ?   -0.6   0.0       4.4   1.5e+03      25      45 ..      77      97 ..      66     109 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.3e-06
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      I+ + +e++ ++ +++a+ Ln+   +V   +++LekdG +
  gi|488600719|ref|YP_007907190.1| 10 ILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGII 49
                                      7788899999****************************76 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.4
                                      HHHHHHHHTS-HHHHHHHHHH CS
                    Fe_dep_repress 25 tkdlaerLnvspssVsemlkk 45
                                       kd+ e+L++ + s  e + k
  gi|488600719|ref|YP_007907190.1| 77 LKDIEEVLEINKISDREYILK 97
                                      455556666555554444444 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     4e-05     0.014      14      37 ..      21      44 ..      14      45 .. 0.90
   2 ?    4.5   0.1     0.083        29      30      55 ..      74     100 ..      74     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_30 14 nisatAkaLhvHrnTlryRLrrie 37
                                      + ++ Ak L++ r+T++ R++r+e
  gi|488600719|ref|YP_007907190.1| 21 SFTEIAKNLNITRQTVKSRIERLE 44
                                      67899*****************98 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.083
                                       HHHHHHHHHHHS--.TTSHHHHHHHHH CS
                            HTH_30  30 ryRLrrieellgld.lddpddrlaLyl 55 
                                       + RL+ iee+l ++ ++d +  l+L++
  gi|488600719|ref|YP_007907190.1|  74 YRRLKDIEEVLEINkISDREYILKLEI 100
                                       57**********987788887777765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.6e-06   0.00092      14      41 ..      21      48 ..       9      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.6e-06
                            HTH_28 14 svreaArelgisrrtvyrWikryeegGi 41
                                      s +e+A+ l+i+r+tv++ i r+e+ Gi
  gi|488600719|ref|YP_007907190.1| 21 SFTEIAKNLNITRQTVKSRIERLEKDGI 48
                                      889**********************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   3.2e-06    0.0011      16      46 ..      16      48 ..       8      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.2e-06
                            HTH_23 16 e..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      e  ++s +eIA+ L+++r+Tv   ++r +++G+
  gi|488600719|ref|YP_007907190.1| 16 EnsRISFTEIAKNLNITRQTVKSRIERLEKDGI 48
                                      3458999***************88888877886 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 !   19.7   0.7   1.6e-06   0.00056       4      46 ..       3      42 ..       2      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-06
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHH CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedviEP 46
                                      +de+dik+L++lk   +++ ++ + +a+ l+++++t+ + iE 
  gi|488600719|ref|YP_007907190.1|  3 IDEIDIKILNILK---ENSRISFTEIAKNLNITRQTVKSRIER 42
                                      589*********9...79************************7 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   8.9e-06    0.0031      14      55 ..      14      55 ..       7      59 .. 0.80
   2 ?    0.9   0.1       1.1     4e+02       8      34 ..      64      92 ..      60     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.9e-06
                                      HTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES CS
                              HxlR 14 llk.gkkRfselkralpkisqkmLaqrLreLeqdglierevyp 55
                                      l +  +  f+e++++l +i++++  +r+ +Le+dg+i+r +++
  gi|488600719|ref|YP_007907190.1| 14 LKEnSRISFTEIAKNL-NITRQTVKSRIERLEKDGIIKRYTIE 55
                                      4442334599******.**********************8765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.1
                                      HHHHHHHTTS-EEHHHHHHH..STTS-HH CS
                              HxlR  8 llilvellkgkkRfselkra..lpkisqk 34
                                      l il+  ++  +R +++++   + kis +
  gi|488600719|ref|YP_007907190.1| 64 LFILRVRTEDYRRLKDIEEVleINKISDR 92
                                      67888888899999999986114566655 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.2e-06    0.0025       5      46 ..       8      50 ..       4      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.2e-06
                                      HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +kIL++L e++  +++e+a+ l++++ tv     +L++ G+++
  gi|488600719|ref|YP_007907190.1|  8 IKILNILKENSrISFTEIAKNLNITRQTVKSRIERLEKDGIIK 50
                                      69*******6659****************************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 !   18.4   0.8   3.7e-06    0.0013       4      46 ..       9      51 ..       7      53 .. 0.96
   2 ?   -1.1   0.0       4.6   1.6e+03       7      23 ..     107     123 ..     106     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.7e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +il  lk+   +s +e++  l+++ +T+   ++ Le++g+++R
  gi|488600719|ref|YP_007907190.1|  9 KILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKR 51
                                      79***************************************99 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.6
                          HTH_DeoR   7 ellkqqgklsveelvel 23 
                                         +++q+ ++vee++  
  gi|488600719|ref|YP_007907190.1| 107 SEIAEQDWIEVEEVIPV 123
                                       56889999999999765 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 !   17.2   0.1   8.4e-06     0.003      28      49 ..      21      42 ..      13      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.4e-06
                                      -HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrlsR 49
                                      s  EIA+ l+i+ +tVksr+ R
  gi|488600719|ref|YP_007907190.1| 21 SFTEIAKNLNITRQTVKSRIER 42
                                      778*****************98 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.7e-06    0.0031       8      56 ..       5      51 ..       3      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.7e-06
                                      HHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR  8 rLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                      +++ +Il+  l+ ++++ s  e+a+ ++++r+tv   + rLe +g++ r
  gi|488600719|ref|YP_007907190.1|  5 EIDIKILN-ILKENSRI-SFTEIAKNLNITRQTVKSRIERLEKDGIIKR 51
                                      67777777.9999****.****************************987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.4e-05    0.0049      22      43 ..      21      42 ..      17      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                                      -HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 22 TleEIgerlgiSrerVrqiekr 43
                                      ++ EI++ l+i+r +V++++ r
  gi|488600719|ref|YP_007907190.1| 21 SFTEIAKNLNITRQTVKSRIER 42
                                      789***************9876 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.1e-05    0.0072       3      46 ..       8      51 ..       6      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-05
                            HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                      +++l +L ++++++f+e+ + l++t     + ++ Lek g i++
  gi|488600719|ref|YP_007907190.1|  8 IKILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKR 51
                                      689*************************************9985 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 !   15.6   1.5   3.2e-05     0.011       1      51 [.       8      52 ..       8      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.2e-05
                            HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrv 51
                                      ++IL+il+e+++ i+  eia++L+     i  ++v  r+  le++g+++r 
  gi|488600719|ref|YP_007907190.1|  8 IKILNILKENSR-ISFTEIAKNLN-----ITRQTVKSRIERLEKDGIIKRY 52
                                      68**********.*********96.....888999**************96 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.7e-05    0.0096       7      58 ..       4      55 ..       1      64 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-05
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegk 58
                                      de ++k+l++lk+        iak+l+i ++ v++ +++Le+ G+++r++ +
  gi|488600719|ref|YP_007907190.1|  4 DEIDIKILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKRYTIE 55
                                      566788888888888777789***************************9855 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 !   15.0   0.1   5.5e-05     0.019      22      39 ..      20      37 ..       8      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.5e-05
                                      --STTTSSSS---SSSS- CS
                             HTH_7 22 isiskIAkevnisRsTvY 39
                                      is ++IAk +ni+R+Tv+
  gi|488600719|ref|YP_007907190.1| 20 ISFTEIAKNLNITRQTVK 37
                                      7889************96 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   2.7e-05    0.0093       6      59 ..       8      57 ..       3      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.7e-05
                                      SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
                   Penicillinase_R  6 aevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegra 59
                                       ++++il e+++++ +e+ + l+ +    ++TVk+ ++rL+k g+++r++ + a
  gi|488600719|ref|YP_007907190.1|  8 IKILNILKENSRISFTEIAKNLNIT----RQTVKSRIERLEKDGIIKRYTIEVA 57
                                      689*******************988....******************9986655 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.9e-05     0.014      15      56 ..      12      50 ..       5      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.9e-05
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                       +L   +e++ +s +eia++ ni ++ ++  +++L+k g++k
  gi|488600719|ref|YP_007907190.1| 12 NIL---KENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIK 50
                                      444...444459****************************98 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   1.9e-05    0.0068      15      58 ..       7      50 ..       2      58 .. 0.93
   2 ?   -0.7   0.2       3.7   1.3e+03      57      65 ..      72      81 ..      43     110 .. 0.63
   3 ?    1.2   0.1      0.95   3.3e+02      14      42 ..     116     142 ..     104     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                       +++l++L e++ ++  ++ak+l+i ++ +++ + rL +++++k
  gi|488600719|ref|YP_007907190.1|  7 DIKILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIK 50
                                      579***************************************98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.7
                                      EEEEEEEE.T CS
                       TFIIE_alpha 57 vkykrrrd.e 65
                                       +y+r +d e
  gi|488600719|ref|YP_007907190.1| 72 EDYRRLKDiE 81
                                      4555555531 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.95
                                       HHHHHHHHHHCTTSEBHHHHHHHHTS-HH CS
                       TFIIE_alpha  14 eavlvldvLlekgevteedlakelkidln 42 
                                       e+ +v+ vL  k+e+ +  l+ +l+++  
  gi|488600719|ref|YP_007907190.1| 116 EVEEVIPVL--KSEIVDKPLSLKLEFKCD 142
                                       444555555..599999999999998865 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   5.5e-05     0.019      27      55 .]      21      49 ..      16      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.5e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s+  +ak+l++ ++Tv + i  Le+ G+i
  gi|488600719|ref|YP_007907190.1| 21 SFTEIAKNLNITRQTVKSRIERLEKDGII 49
                                      7889*********************9998 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.8e-05      0.01       7      47 ..      12      52 ..       8      60 .. 0.89
   2 ?   -0.4   0.2       3.6   1.3e+03      54      62 ..     138     146 ..      77     156 .. 0.62
   3 ?   -1.6   0.9       8.5     3e+03      55      64 ..     164     173 ..     153     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.8e-05
                              FeoC  7 eyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                      + l+e+ r+s+ e+++ ++++ +++++ +e +++ G +++ 
  gi|488600719|ref|YP_007907190.1| 12 NILKENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKRY 52
                                      5689*****************************99988875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.6
                              FeoC  54 sgsCkkCgg 62 
                                       + +C  Cg+
  gi|488600719|ref|YP_007907190.1| 138 EFKCDYCGK 146
                                       445666665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 8.5
                              FeoC  55 gsCkkCggke 64 
                                        +Ck C ++ 
  gi|488600719|ref|YP_007907190.1| 164 LCCKTCLEEF 173
                                       5899997765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   5.2e-05     0.018       9      41 ..      14      48 ..       9      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.2e-05
                            HTH_29  9 aeGvs..tvsqiAkllglsrrtvyrwlkrfeegGl 41
                                       ++ s  +  +iAk+l+++r+tv   ++r e++G+
  gi|488600719|ref|YP_007907190.1| 14 LKENSriSFTEIAKNLNITRQTVKSRIERLEKDGI 48
                                      44444445789***********************7 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 ?   15.7   0.1   5.2e-05     0.018      53      97 ..       9      49 ..       3      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.2e-05
                                      HHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 53 qvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                       +ln++k+    +  +++ eia++l++  ++vk+ ++ L+++Gii
  gi|488600719|ref|YP_007907190.1|  9 KILNILKE----NSRISFTEIAKNLNITRQTVKSRIERLEKDGII 49
                                      57778777....7779****************************9 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   7.5e-05     0.026      27      58 ..      21      51 ..      10      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.5e-05
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyier 58
                                      s  eia++l+++  ++v+++ ++Le+ G+i+r
  gi|488600719|ref|YP_007907190.1| 21 SFTEIAKNLNIT-RQTVKSRIERLEKDGIIKR 51
                                      678*********.9****************97 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.7   7.6e-05     0.027      34      64 ..      20      52 ..      10      95 .. 0.82
   2 ?   -0.4   0.1         4   1.4e+03      35      46 ..     105     116 ..      90     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-05
                           UPF0122 34 lSlsEiAeefnvsrqavydnikrtek..lleky 64
                                      +S++EiA + n++rq+v   i+r ek  ++++y
  gi|488600719|ref|YP_007907190.1| 20 ISFTEIAKNLNITRQTVKSRIERLEKdgIIKRY 52
                                      79*********************9874455555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 4
                           UPF0122  35 SlsEiAeefnvs 46 
                                        lsEiAe+  ++
  gi|488600719|ref|YP_007907190.1| 105 RLSEIAEQDWIE 116
                                       389999986665 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.2e-05     0.029       5      42 ..       9      48 ..       7      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.2e-05
                            HTH_39  5 rilaaLrqhgsittleamrelditr..laaRIkeLrekGy 42
                                      +il++L++ ++i+  e  ++l+itr    +RI +L+++G+
  gi|488600719|ref|YP_007907190.1|  9 KILNILKENSRISFTEIAKNLNITRqtVKSRIERLEKDGI 48
                                      79***********************9999**********7 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   9.4e-05     0.033       6      51 ..       5      51 ..       3      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.4e-05
                            HTH_45  6 eIiadILeais.egeakkTkimykanLsykllnkYLdmLvekglikk 51
                                      eI + IL++++ +++ + T+i ++ n++ +++++ ++ L + g+ik 
  gi|488600719|ref|YP_007907190.1|  5 EIDIKILNILKeNSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKR 51
                                      677789999987888999***************************86 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   0.00011      0.04      21      41 ..      23      43 ..      20      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                                      HHHHHHHTS-HHHHHHHHHHH CS
                              GerE 21 keIAeelniSekTVkvhksni 41
                                      +eIA++lni  +TVk+ ++++
  gi|488600719|ref|YP_007907190.1| 23 TEIAKNLNITRQTVKSRIERL 43
                                      79**************99876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00018     0.064      23      49 ..      19      45 ..      16      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                            HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                      r++  e+Ak l+I+++t++ ++++ e+
  gi|488600719|ref|YP_007907190.1| 19 RISFTEIAKNLNITRQTVKSRIERLEK 45
                                      78999*****************99886 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   0.00045      0.16       7      50 ..       9      51 ..       8      52 .. 0.92
   2 ?   -0.5   0.0       3.2   1.1e+03      20      27 ..     105     112 ..      99     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00045
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       iL++l e  +  +++e+A+++ +++ tv   +  L++ G++++
  gi|488600719|ref|YP_007907190.1|  9 KILNILKENSR-ISFTEIAKNLNITRQTVKSRIERLEKDGIIKR 51
                                      699***99999.8******************9999999999876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.2
                                       BHHHHHHH CS
                          HTH_IclR  20 tlselArr 27 
                                       +lse+A++
  gi|488600719|ref|YP_007907190.1| 105 RLSEIAEQ 112
                                       79999997 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   0.00018     0.062      17      65 ..       6      56 ..       3      66 .. 0.86
   2 ?   -0.7   0.0       6.4   2.3e+03      48      60 ..      74      86 ..      56      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00018
                                      HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH..HCHCCT-EE CS
                               Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikelnk..lLkefdlel 65
                                      +++++l  l e+ ++s++e+a++l i + t+k  i++l+k   +k + +e+
  gi|488600719|ref|YP_007907190.1|  6 IDIKILNILKENSRISFTEIAKNLNITRQTVKSRIERLEKdgIIKRYTIEV 56
                                      78999*********************************9843477777765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 6.4
                                      HHHHHHHHHHCHC CS
                               Mga 48 krkikelnklLke 60
                                      +r +k+++++L+ 
  gi|488600719|ref|YP_007907190.1| 74 YRRLKDIEEVLEI 86
                                      8899999999874 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00023      0.08     186     232 ..       9      49 ..       1      51 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                             EAP30 186 rlvsllaekssgggvtaselaeeeenlgwsvarakeaLeelereGll 232
                                       +++++l+e+s+   ++ +e+a++   l+++++ +k+ +e+le++G++
  gi|488600719|ref|YP_007907190.1|   9 KILNILKENSR---ISFTEIAKN---LNITRQTVKSRIERLEKDGII 49 
                                       56677777777...9*****555...*******************87 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00055      0.19       5      48 ..      10      52 ..       7      56 .. 0.89
   2 ?   -1.4   0.0       9.1   3.2e+03      32      40 ..      91      99 ..      74     112 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00055
                                      HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE CS
                              FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrs 48
                                      Il+ l++ ++    +eiA+ l ++   +++ +e Lek g ikr 
  gi|488600719|ref|YP_007907190.1| 10 ILNILKE-NSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKRY 52
                                      7777777.8888899***************************96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 9.1
                                      HHHHHHHHH CS
                              FaeA 32 aRyYLeqLe 40
                                       R Y+ +Le
  gi|488600719|ref|YP_007907190.1| 91 DREYILKLE 99
                                      455655555 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00075      0.26       7      50 ..       9      51 ..       4      55 .. 0.85
   2 ?   -0.1   0.1       3.8   1.3e+03      16      34 ..      72      90 ..      63     119 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00075
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                       +L+ ++ ++ r + +++++ ln++ +++ + +++L++ G ++r
  gi|488600719|ref|YP_007907190.1|  9 KILNILK-ENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKR 51
                                      5888888.7777777***********************998855 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.8
                            HTH_27 16 rrrkkladlcgrlnvedsh 34
                                      ++  +l+d+ ++l +++++
  gi|488600719|ref|YP_007907190.1| 72 EDYRRLKDIEEVLEINKIS 90
                                      4444555555555555443 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00044      0.16      27      51 ..      18      43 ..       7      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                      HTH_Tnp_ISL3 27 s.rsvkavArqlgvSwtTVwrildry 51
                                      s +s++++A+ l+++  TV+ ++ r+
  gi|488600719|ref|YP_007907190.1| 18 SrISFTEIAKNLNITRQTVKSRIERL 43
                                      369******************99885 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0005      0.18      15      39 ..      21      45 ..       7      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0005
                                      SHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 15 sftrAAeeLglsqpavsrqikrLEe 39
                                      sft+ A+ L+++  +v  +i rLE+
  gi|488600719|ref|YP_007907190.1| 21 SFTEIAKNLNITRQTVKSRIERLEK 45
                                      99**********************7 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.3   0.00052      0.18      12      76 ..      19      84 ..      11     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00052
                            HTH_40 12 glsieeIAkerglkesTIegHLaelieeg....eeidlerlvseeeekeIeeaiekvgseklkpikeal 76
                                        s+ eIAk+ +++++T+ + + +l ++g    + i++ ++    +++  +  ++  + ++lk+i e l
  gi|488600719|ref|YP_007907190.1| 19 RISFTEIAKNLNITRQTVKSRIERLEKDGiikrYTIEVADI---FRKNLFILRVRTEDYRRLKDIEEVL 84
                                      57899***********************9554322333222...3334444444444455566666655 PP

>> YhdB  YhdB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00064      0.22      20      62 ..      63     105 ..      59     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00064
                              YhdB  20 nLLiLmvrtkDdllskkiehfLhaynfekdeavveksleaLlr 62 
                                       nL iL vrt+D    k ie++L+  + +  e +++ + ++L r
  gi|488600719|ref|YP_007907190.1|  63 NLFILRVRTEDYRRLKDIEEVLEINKISDREYILKLEISSLSR 105
                                       89*********************99999888888877777766 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0018      0.65      20      59 ..      15      54 ..       2      58 .. 0.86
   2 ?    0.8   0.1       1.6   5.7e+02       6      36 ..      71     106 ..      66     126 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0018
                            Rio2_N 20 rnhevVptelieeisrlkeeevkkrlsrllkaklisrkta 59
                                      ++ + +++++i+++ +++++ vk+r++rl k ++i+r t+
  gi|488600719|ref|YP_007907190.1| 15 KENSRISFTEIAKNLNITRQTVKSRIERLEKDGIIKRYTI 54
                                      555668999***************************9765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.6
                            Rio2_N   6 kedfrvLtavEmgm.....rnhevVptelieeisrl 36 
                                        ed+r L+ +E         + e++ + +i+++srl
  gi|488600719|ref|YP_007907190.1|  71 TEDYRRLKDIEEVLeinkiSDREYILKLEISSLSRL 106
                                       678888888886541111133444444555555555 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         8   2.8e+03      53      78 ..      25      49 ..      11      54 .. 0.52
   2 ?    9.7   2.1    0.0029         1       4      36 ..     140     169 ..     137     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 8
                           DUF3268 53 lAnaelrklrkeahaaFdklwksgal 78
                                      +A ++l  +r++ ++  ++l k g++
  gi|488600719|ref|YP_007907190.1| 25 IA-KNLNITRQTVKSRIERLEKDGII 49
                                      33.23455555555555555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0029
                           DUF3268   4 rCpyCGekvilvsaseiYkerskgkllylCpkC 36 
                                       +C+yCG+++i  ++  iYk++++   +  C++C
  gi|488600719|ref|YP_007907190.1| 140 KCDYCGKTSI--DDPLIYKKHNRF-YVLCCKTC 169
                                       8*****9875..899***555444.45567999 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.8    0.0075       2.6       2      10 ..     139     147 ..     138     147 .. 0.93
   2 ?    5.9   3.7     0.038        13       3      14 ..     165     176 ..     164     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0075
                         zf-C2H2_6   2 heCsvCsks 10 
                                       ++C++C+k+
  gi|488600719|ref|YP_007907190.1| 139 FKCDYCGKT 147
                                       8******97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.038
                         zf-C2H2_6   3 eCsvCsksFpsl 14 
                                       +C++C+++F+++
  gi|488600719|ref|YP_007907190.1| 165 CCKTCLEEFKKY 176
                                       8********987 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 ?    8.5   0.1     0.008       2.8      14      23 ..     138     147 ..     125     149 .. 0.81
   2 ?    2.2   3.7      0.79   2.8e+02      13      26 .]     161     175 ..     154     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.008
                         zf-H2C2_2  14 pyeCplCdka 23 
                                       +++C++C+k+
  gi|488600719|ref|YP_007907190.1| 138 EFKCDYCGKT 147
                                       49*******8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.79
                         zf-H2C2_2  13 kp.yeCplCdkaFkt 26 
                                       +  ++C+ C   Fk+
  gi|488600719|ref|YP_007907190.1| 161 FYvLCCKTCLEEFKK 175
                                       3337*******9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                       135  (0.0075297); 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):              51  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1051.76
//
Query:       gi|488600720|ref|YP_007907191.1|  [L=154]
Description: aspartate carbamoyltransferase, regulatory subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-31  108.1   4.8    2.7e-31  107.6   4.8    1.2  1  PyrI          Aspartate carbamoyltransferase regulatory chain
    4.1e-16   58.6   3.2    7.6e-16   57.8   3.2    1.4  1  PyrI_C        Aspartate carbamoyltransferase regulatory chain
  ------ inclusion threshold ------
       0.08   12.5   0.7       0.19   11.3   0.0    1.9  2  TF_Zn_Ribbon  TFIIB zinc-binding


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 !  107.6   4.8   4.6e-35   2.7e-31       2      94 .]       8      99 ..       7      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 4.6e-35
                                      -----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEE CS
                              PyrI  2 kvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatin 80
                                       ++ki++G+ViDHI+ g a+ vlk+L+++  ks+e+v++++nv+s k+gkKdi+k+egk++ ++el+k+aliap+atin
  gi|488600720|ref|YP_007907191.1|  8 VISKIKDGTVIDHITPGLAILVLKILGIKP-KSSEAVSMAMNVESAKMGKKDIVKVEGKYIGDQELNKIALIAPEATIN 85
                                      699**************************8.7777******************************************** PP

                                      EEETTEEEEEE--. CS
                              PyrI 81 iIkdgevveKkkve 94
                                      +I+++e+++K++v+
  gi|488600720|ref|YP_007907191.1| 86 LIQNYEIIRKFNVK 99
                                      **********9985 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   3.2   1.3e-19   7.6e-16       2      43 ..     104     147 ..     103     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.3e-19
                                       EESSS--S-TTBGGGT.TS-.-EEEE.EETTTTEEEETTT--EE CS
                            PyrI_C   2 iegvlkCpNpnCItnn.epveskFkv.edkekvklkCkYCekei 43 
                                       +e+++kCpNpnCI+n+ ep++s+F++  d+++vk  C YC++++
  gi|488600720|ref|YP_007907191.1| 104 VENIIKCPNPNCISNSnEPIKSRFRIfLDESRVKAVCDYCGRKL 147
                                       89**************99***********************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 ?   -1.8   0.4      0.39   2.4e+03       2       5 ..     109     112 ..     108     121 .. 0.74
   2 ?   11.3   0.0   3.2e-05      0.19       7      28 ..     124     146 ..     122     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.39
                                       EETT CS
                      TF_Zn_Ribbon   2 kCPn 5  
                                       kCPn
  gi|488600720|ref|YP_007907191.1| 109 KCPN 112
                                       7876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.2e-05
                                       TCEE.CHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon   7 gstn.lveDpergelvCtdCGlV 28 
                                       +s++ + +D++r   vC  CG  
  gi|488600720|ref|YP_007907191.1| 124 KSRFrIFLDESRVKAVCDYCGRK 146
                                       688999***************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 915.89
//
Query:       gi|488600721|ref|YP_007907192.1|  [L=305]
Description: aspartate carbamoyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-51  173.1   0.0    6.3e-51  172.3   0.0    1.4  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    2.5e-29  102.4   0.0    4.2e-29  101.6   0.0    1.4  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 !  172.3   0.0     7e-55   6.3e-51       1     147 [.       5     145 ..       5     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 7e-55
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       rhl+s++dl+k++i +ll++a+++++     k+ k+l+gk+la+lF+epStRTr+Sfe+A+krlGg+v++++++   
  gi|488600721|ref|YP_007907192.1|   5 RHLISIDDLTKDDILYLLKQAERFEDIA-MGKRCKYLEGKILANLFFEPSTRTRMSFETAMKRLGGDVINMTAH--- 77 
                                       8************************765.59*****************************************55... PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       + ssv+kg  E+l+Dt+rv+s+y+daiv+Rhp  g+  ++   ++++vp+iNagdg+g+HPtQ+L+Dl+ti 
  gi|488600721|ref|YP_007907192.1|  78 EASSVAKG--ETLADTIRVVSNYADAIVLRHPleGS--ARFASENSTVPIINAGDGAGQHPTQTLLDLYTIM 145
                                       67999***..**********************7666..88778889************************96 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 !  101.6   0.0   4.7e-33   4.2e-29       1     155 [.     151     295 ..     151     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 4.7e-33
                                       CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEE CS
                            OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvy 76 
                                       +g+kia++Gd k++++++slik+l+ ++ +++l++P+ l+   e+le +       +g+i+   +le+++++ Dv+y
  gi|488600721|ref|YP_007907192.1| 151 EGCKIALMGDlKYSRTVHSLIKALTLFNTTIYLISPPMLKLPAEFLEGL-------NGRIEEV-ELEDVISEIDVLY 219
                                       599***********************************99988888555.......4455554.7899********* PP

                                       E--SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHH CS
                            OTCace  77 tdvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlht 149
                                        ++++     ker+   e++kk+ + y ++++++++ak+ +iv+H+LP  r +E++ +V++ +++ +f+qa +++ +
  gi|488600721|ref|YP_007907192.1| 220 VTRIQ-----KERFpdeEEYKKVSGsYVINRNIISRAKESMIVMHPLP--RINEIDVDVDSTEHAKYFKQAFYGVPI 289
                                       *****.....6666666999999999**********************..99************************* PP

                                       HHHHHH CS
                            OTCace 150 ikAllv 155
                                       ++A+l+
  gi|488600721|ref|YP_007907192.1| 290 RMAILY 295
                                       *****8 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:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1848.35
//
Query:       gi|488600722|ref|YP_007907193.1|  [L=279]
Description: hypothetical protein Asulf_01202 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); 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:                         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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1866.10
//
Query:       gi|488600723|ref|YP_007907194.1|  [L=205]
Description: putative Zn-dependent hydrolases of the beta-lactamase fold protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-31  107.1   0.1    9.9e-31  106.8   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    2.6e-18   66.3   0.4    9.5e-18   64.4   0.4    1.7  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.4e-05   25.2   2.6    0.00061   19.8   2.6    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.038   14.3   0.0      0.074   13.4   0.0    1.5  1  DUF5417        Family of unknown function (DUF5417)


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.1   2.2e-34   9.9e-31       1     163 []       9     178 ..       9     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 2.2e-34
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql.aenvkvlee......... 67 
                                       e+t+l h+ f +++  ++i++DP++    +    e+aD + +++++ dH ++  +++l +++++v+ +         
  gi|488600723|ref|YP_007907194.1|   9 EITFLKHAGFKIKG-SKTIYIDPYD----LPDGLEKADYIFVTHDHFDHKDIGSIRRLsKHDTTVVIPsgcllegyr 80 
                                       69*********986.59*******8....677789***********************8666676666788888888 PP

                     Lactamase_B_3  68 ......geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvgg 138
                                             ge+ +++g+++++v++++ +++ +++g ++g+++e+dg++iyh G+++     +e k   ++D+ l+Pvgg
  gi|488600723|ref|YP_007907194.1|  81 tceldiGEEEDLNGVKVKTVPAYNIDKPFHPKGIGVGYIIEMDGVRIYHAGDTDF---IPEMKDV-EADIALIPVGG 153
                                       888888999*********************************************9...7888888.99********* PP

                     Lactamase_B_3 139 pltlgqeealelakrLkpklvlPmh 163
                                       ++t++ e+a+++++ +k+k+v+Pmh
  gi|488600723|ref|YP_007907194.1| 154 KYTMDMEQAKKAIEVIKAKVVVPMH 178
                                       ************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.4   2.1e-21   9.5e-18      20     201 .]      29     179 ..      12     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.1e-21
                                       S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEE CS
                     Lactamase_B_2  20 qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesf 96 
                                        P  l d l++ d +++th+H+DH  ++ ++r+l++++ +++ p g+l +                ++ eld+ge+ 
  gi|488600723|ref|YP_007907194.1|  29 DPYDLPDGLEKADYIFVTHDHFDHK-DIGSIRRLSKHDTTVVIPSGCLLEGY--------------RTCELDIGEEE 90 
                                       666788999***************9.*******8776667766665554444..............4458******* PP

                                       EECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHH CS
                     Lactamase_B_2  97 elgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemi 173
                                       +l+  g++++++pa    ++     +g  +G++ie +g r+y++gDt +ipe+  + ++ ad++l++++        
  gi|488600723|ref|YP_007907194.1|  91 DLN--GVKVKTVPAYNIDKP--FHPKGIGVGYIIEMDGVRIYHAGDTDFIPEM--KDVE-ADIALIPVG-------- 152
                                       **9..799******999999..5667889**********************88..4565.*********........ PP

                                       HHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 174 rhmgHltpeeaveaaadlgakrlvliHi 201
                                        + +++++e+a +a++ ++ak++v++H+
  gi|488600723|ref|YP_007907194.1| 153 -GKYTMDMEQAKKAIEVIKAKVVVPMHY 179
                                       .899***********************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 !   19.8   2.6   1.4e-07   0.00061      34     197 .]      29     178 ..      12     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-07
                                       HHHHHTSGGGGEEEEE-SBSSHHH..HTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEE CS
                       Lactamase_B  34 elaalglkpkdvdavilTHlHlDH..iGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdv 108
                                       ++++l  ++++ d++++TH H+DH  iG  + l ++   +v+     ++ +++ e+d +++               +
  gi|488600723|ref|YP_007907194.1|  29 DPYDLPDGLEKADYIFVTHDHFDHkdIGSIRRLSKHDTTVVIPSGCLLEGYRTCELDIGEE---------------E 90 
                                       67889999999*************9999999999999999999999999999999966444...............6 PP

                                       EETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC......TTCEEE-SHCHHHHHHH CS
                       Lactamase_B 109 deeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl.....tlrgaevrdpsdaekyld 180
                                       d+++  + + +      + +p   ++++++e++g ++  +GD+ +++e  +++      + +g +++d  +a+k+++
  gi|488600723|ref|YP_007907194.1|  91 DLNGVKVKTVPAYNIDKPFHPKGIGVGYIIEMDGVRIYHAGDTDFIPEMKDVEAdialiPVGGKYTMDMEQAKKAIE 167
                                       77777777777777777778888899999*************************99999999999999999999995 PP

                                       HHHHHHHHCHSEEEESS CS
                       Lactamase_B 181 sllklaglkaevlvpgH 197
                                               ka+v+vp H
  gi|488600723|ref|YP_007907194.1| 168 ------VIKAKVVVPMH 178
                                       ......55667777666 PP

>> DUF5417  Family of unknown function (DUF5417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.074      42      85 ..      87     130 ..      77     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                           DUF5417  42 dellekagwesdgcpnyedddefgnagyscgylieiddvarfka 85 
                                        e  +  g +   +p y+ d  f   g  +gy+ie+d v  ++a
  gi|488600723|ref|YP_007907194.1|  87 GEEEDLNGVKVKTVPAYNIDKPFHPKGIGVGYIIEMDGVRIYHA 130
                                       5666778899999**************************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1270.87
//
Query:       gi|488600724|ref|YP_007907195.1|  [L=62]
Description: hypothetical protein Asulf_01204 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.031   14.2   1.3       0.12   12.3   0.0    2.0  2  zf-C2HCIx2C  Zinc-finger


Domain annotation for each model (and alignments):
>> zf-C2HCIx2C  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.9e-06      0.12       4      38 ..       8      41 ..       3      42 .. 0.86
   2 ?    1.0   0.3     0.022     4e+02      22      37 ..      46      61 ..      44      62 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-06
                       zf-C2HCIx2C  4 kellkeideLletyCegCflkkhfrkekgktyahs 38
                                      ke+ ++ deL+ +  ++  lk+++rk+ gk+ya++
  gi|488600724|ref|YP_007907195.1|  8 KEVPDDSDELMMQVASS-QLKANYRKSLGKEYARR 41
                                      78888999999988766.5*************975 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.022
                       zf-C2HCIx2C 22 flkkhfrkekgktyah 37
                                      ++kk ++k++  ++a+
  gi|488600724|ref|YP_007907195.1| 46 EIKKALKKKEEERKAK 61
                                      5899999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 397.48
//
Query:       gi|488600725|ref|YP_007907196.1|  [L=200]
Description: hypothetical protein Asulf_01205 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   82.2  13.6      4e-23   81.9  13.6    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 !   81.9  13.6   2.2e-27     4e-23       1     193 []      15     195 ..      15     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.2e-27
                              LysE   1 lslllspGpqnllvlkqgikrgfkggilvalgvligdavlil.lgllGlalLlkaapivlsilrllGgayLlwlgvl 76 
                                       ls++++pGp ++  +++g ++   +g+l+  g++i+++  il l  +G++ + +   +v  ++ ++Gg++L++++ +
  gi|488600725|ref|YP_007907196.1|  15 LSGVMAPGPLFASAVSEGMNKK-YAGFLLSSGHAIVEIPIILiLFFFGVSIITE---QVKVFVGVFGGIFLIYMAHK 87 
                                       5899**************9999.78899999******98765166789999988...9999**************** PP

                              LysE  77 alrdakekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsl 153
                                        l ++ + + ++        ++++ +gl+ s++NP++i++w+ ++  l++ ae+ g +g++++ +++ + ++ w+ +
  gi|488600725|ref|YP_007907196.1|  88 ELTSKSKLDGSTD-------MRSIFTGLAMSIANPYFIIWWFTIGLILVTTAEKFGIMGLIVFIIVHELCDFGWLGF 157
                                       *999888875332.......45689*************************99************************* PP

                              LysE 154 laflaarlsrrlsskkvlriinvvvgvlligfavkllleg 193
                                       ++++++   +   ++   + ++++ ++++++f+++++++g
  gi|488600725|ref|YP_007907196.1| 158 VSLISSKTVEVWDKSA--KTLSTISAIIFVIFGIYFIYSG 195
                                       **99998888777775..68*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1366.82
//
Query:       gi|488600726|ref|YP_007907197.1|  [L=136]
Description: hypothetical protein Asulf_01206 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-14   51.7   0.1    1.1e-13   51.4   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.2e-13   51.1   0.1    1.4e-13   50.9   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    9.7e-11   42.0   0.4    1.6e-10   41.3   0.4    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      3e-06   27.4   0.2    3.2e-06   27.4   0.2    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00013   21.8   0.0    0.00023   21.1   0.0    1.4  1  Nudix_hydro      Nudix hydrolase domain
    0.00031   20.8   0.0     0.0005   20.1   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.052   13.7   0.0       0.13   12.5   0.0    1.6  1  3D               3D domain
      0.094   12.7   0.0       0.16   12.0   0.0    1.3  1  FR47             FR47-like protein
       0.13   12.1   0.0       0.16   11.8   0.0    1.2  1  Acetyltransf_18  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.1   5.5e-17   1.1e-13      31     117 .]      30     111 ..       3     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 5.5e-17
                                       TTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHH CS
                    Acetyltransf_1  31 eaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveednda 107
                                        ++  +va  +ge+iG + ++++         i sl+V++e+r++++G+ L+++++e+a   g++ ++l+v +++  
  gi|488600726|ref|YP_007907197.1|  30 YHKKVFVADVGGEIIGGAVAYWNEK-----FKIGSLFVKEEFRKQNIGRNLVKKCIEFANAIGFDSVWLEVPVNQGN 101
                                       3447899**************9999.....***************************************99888888 PP

                                       HHHHHHH.TTE CS
                    Acetyltransf_1 108 airlYek.lGF 117
                                        + +Y k +GF
  gi|488600726|ref|YP_007907197.1| 102 LVSYY-KsMGF 111
                                       89999.66**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   6.9e-17   1.4e-13      31     118 ..      32     123 ..      23     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 6.9e-17
                   Acetyltransf_10  31 alllvaeeggkiv.Gviel.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYek 103
                                       ++++va++gg+i+ G++++  ++ +i+ lfV++e+r+q ig++L+++++e a+  g     l+v  ++ + v++Y++
  gi|488600726|ref|YP_007907197.1|  32 KKVFVADVGGEIIgGAVAYwNEKFKIGSLFVKEEFRKQNIGRNLVKKCIEFANAIGFDSvWLEVPVNQgNLVSYYKS 108
                                       679**********55558877777****************************99999999999999999******** PP

                   Acetyltransf_10 104 lGFkavgeeqeenGi 118
                                       +GF+ ++  + + Gi
  gi|488600726|ref|YP_007907197.1| 109 MGFRIHEVIKHFYGI 123
                                       ****99888888777 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.4     8e-14   1.6e-10       3      75 ..      32     112 ..      30     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 8e-14
                                       EEEEEEEETTEEEEEEEEEEES.TCTEEEEE-GGGTTSSHHHHHHHH.TT....SEEEEE.EEEE...THH.HHHHH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld.aeitrlaVdpeyrgkGiGraLlea.ae....kgiile.qlel...nae.kaikf 68 
                                       ++vfVa+ +g+i+G ++++ ++ + i+ l+V++e+r++ iGr L++  +e     g   +  ++l   +++ + +++
  gi|488600726|ref|YP_007907197.1|  32 KKVFVADVGGEIIGGAVAYWNEkFKIGSLFVKEEFRKQNIGRNLVKKcIEfanaIG---FdSVWLevpVNQgNLVSY 105
                                       689**********877777766677777*****************95322322223...23345532322235577* PP

                                       HHHTTEE CS
                    Acetyltransf_7  69 YeklGFe 75 
                                       Y+++GF+
  gi|488600726|ref|YP_007907197.1| 106 YKSMGFR 112
                                       ******8 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.2   1.6e-09   3.2e-06      58     154 ..      41     131 ..       2     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.6e-09
                    Acetyltransf_4  58 drivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGF 134
                                       ++i+G a +    +   ++  + s +++ +  +k+ +gr+l++ +++++ + ++ +   e+ +++ n +  +k++GF
  gi|488600726|ref|YP_007907197.1|  41 GEIIGGAVAY---W--NEKFKIGSLFVK-EEFRKQNIGRNLVKKCIEFANAIGFDSVWLEVPVNQGNLVSYYKSMGF 111
                                       5555544443...3..445556678887.78********************************************** PP

                    Acetyltransf_4 135 elvgifkkcikkngrwiDmi 154
                                       ++    k ++ ++ + + m+
  gi|488600726|ref|YP_007907197.1| 112 RIHEVIKHFYGIGKHAYSMV 131
                                       **************999986 PP

>> Nudix_hydro  Nudix hydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.1e-07   0.00023      27      69 ..      74     116 ..      52     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
                       Nudix_hydro  27 skLkaslsqwreegkrgvwlkvpieqselvpiavkeGFefHha 69 
                                       + +k+ ++  ++ g  +vwl+vp +q +lv+   + GF++H+ 
  gi|488600726|ref|YP_007907197.1|  74 NLVKKCIEFANAIGFDSVWLEVPVNQGNLVSYYKSMGFRIHEV 116
                                       567778888889999**************************86 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 !   20.1   0.0   2.5e-07    0.0005      14      57 ..      47      87 ..      34      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.5e-07
                   Acetyltransf_CG 14 fleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeg 57
                                       + Y    ++++++   +V+ee+r ++i++ Lvk+++++a + g
  gi|488600726|ref|YP_007907197.1| 47 AVAYW---NEKFKIGSLFVKEEFRKQNIGRNLVKKCIEFANAIG 87
                                      45563...45799999***********************99876 PP

>> 3D  3D domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.4e-05      0.13       6      47 ..      11      47 ..      10      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                                      -TTTS-TT-EEEEEECCEETTTCCEEEEEEEEE--TT--SSE CS
                                3D  6 DpsviplGtpvlvegepllagkkpvyrlviaqDtGgaIkGnr 47
                                      D ++  lG  v+v++     +++p ++ v+++D+Gg I G  
  gi|488600726|ref|YP_007907197.1| 11 DLEYEILGLSVFVDI-----STRPYHKKVFVADVGGEIIGGA 47
                                      6667779999*****.....789****************965 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.9e-05      0.16      23      79 ..      56     113 ..      44     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                                       SEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-H.HHHHHHHHHT-EE CS
                              FR47  23 elgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNt.psirlyeklGfek 79 
                                        +g+l v++e+r++  g+ lvk+ ++   + g +++ + v+ N+ +  + y+++Gf+ 
  gi|488600726|ref|YP_007907197.1|  56 KIGSLFVKEEFRKQNIGRNLVKKCIEFANAIGFDSVWLEVPVNQgNLVSYYKSMGFRI 113
                                       6899*******************99999998877766666555525678999999986 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.1e-05      0.16      25     100 ..      31     112 ..      20     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                   Acetyltransf_18  25 eqklvvveedgeivGyglarktrkglkiGPlvAen....eeiAeaLlkalvanaeg...kkvridvpeenkaliell 94 
                                       ++k++v + +gei G ++a+ + +++kiG l+ ++    ++i ++L+k++++ a+    ++v + vp ++ +l+++ 
  gi|488600726|ref|YP_007907197.1|  31 HKKVFVADVGGEIIGGAVAYWN-EKFKIGSLFVKEefrkQNIGRNLVKKCIEFANAigfDSVWLEVPVNQGNLVSYY 106
                                       5788999999*****8888877.799******975222279*********98776554789**************** PP

                   Acetyltransf_18  95 eklgfk 100
                                       +++gf+
  gi|488600726|ref|YP_007907197.1| 107 KSMGFR 112
                                       ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1075.67
//
Query:       gi|488600727|ref|YP_007907198.1|  [L=454]
Description: Na+/proline symporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-29  101.5  30.7    1.1e-28  100.3  30.7    1.6  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3  30.7   5.9e-33   1.1e-28       1     406 []      31     414 ..      31     414 .. 0.81

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 5.9e-33
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpd 73 
                                       y+l+gr+++g+v +l+  a+  sa  +vGl G+ +asG++ + +el  l++ l+ll   a++      +   +T  d
  gi|488600727|ref|YP_007907198.1|  31 YYLGGRRIGGIVSALTYSATTYSAFMMVGLVGLTYASGVGSLGFELFYLVGTLFLLSYYAPKIWklgkERAYITPGD 107
                                       9************************************************************999566555569999* PP

                               SSF  74 ylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiq 150
                                       ++  R+++    ++++++++++ ++ ++sv+l+g   +ie+   ++++ a+l+ a l+a + ++GGl+ v +td iq
  gi|488600727|ref|YP_007907198.1| 108 MMVDRYGKLV-PKIMAVIVSIA-LIPYISVQLIGVSLIIEKNSTISFTHAILASAFLIAFWAFLGGLRGVAWTDAIQ 182
                                       ******9776.88888887765.668*************************************************** PP

                               SSF 151 avlmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRfla 227
                                       +v ml+ a+  ++ +++ + g   ++ ++  +      l+ p+ + +   +++ +++   + +     p + +R++ 
  gi|488600727|ref|YP_007907198.1| 183 GVFMLIMAVSAVMWAFSMLNGT--FFGEISRIGD---LLIVPNKIWTPERFIALTVP---WFFFALTNPQVFQRIYV 251
                                       ******9999999999888753..4555555554...44556554333335666666...66666789********9 PP

                               SSF 228 akdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAa 304
                                         d +a+   +++l + ++l++     + + + +l  +      + ++  + + p+    ++p+ la l++  ++Aa
  gi|488600727|ref|YP_007907198.1| 252 PRDERALK-KMVILFGTFGLIYTI--LVTFLGLELRVMTEIGSFPLLKDRDAVTPTFL-GIMPPSLAVLISLSIFAA 324
                                       99998775.588999999999865..777888888888666777899999*****986.689999999999999*** PP

                               SSF 305 imstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasav 381
                                        + t +s++l  +s++++Dl  + r +           ++i ++vv  +ai l   +    ++   ++ ++ l  + 
  gi|488600727|ref|YP_007907198.1| 325 AITTANSIVLTLASMISRDLLGSNRINT----------GQI-LIVVLTIAITLFSIQRPGYIVN-LAVLSSTLLLCQ 389
                                       *******************976544444..........333.3344445554443333332444.456677788888 PP

                               SSF 382 lavillalfwkrvneqGAlagliiG 406
                                       l++il    wk   e+ A++ li+G
  gi|488600727|ref|YP_007907198.1| 390 LPLILGVFHWKSGGEKAAISTLIVG 414
                                       8888877779999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2739.76
//
Query:       gi|488600728|ref|YP_007907199.1|  [L=46]
Description: hypothetical protein Asulf_01208 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 274.59
//
Query:       gi|488600729|ref|YP_007907200.1|  [L=40]
Description: hypothetical protein Asulf_01209 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   26.8   0.2    3.6e-06   26.6   0.2    1.0  1  HTH_23      Homeodomain-like domain
    0.00035   20.6   0.2    0.00038   20.5   0.2    1.0  1  HTH_28      Helix-turn-helix domain
     0.0039   17.2   0.0     0.0044   17.0   0.0    1.0  1  HTH_29      Winged helix-turn helix
  ------ inclusion threshold ------
      0.026   14.0   0.1       0.03   13.8   0.1    1.2  1  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 !   26.6   0.2   8.1e-10   3.6e-06      11      43 ..       3      35 ..       3      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.1e-10
                            HTH_23 11 llllaeGlsvreIAreLgvsrrTvyrwlkryre 43
                                      ++ l++G++ +eIA+   v+ r vy+++k y+e
  gi|488600729|ref|YP_007907200.1|  3 IRQLDRGAPLKEIAAVIRVTLRKVYQIKKQYKE 35
                                      688999*************************65 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   8.5e-08   0.00038       6      38 ..       3      35 ..       3      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.5e-08
                            HTH_28  6 ikllaaGhsvreaArelgisrrtvyrWikryee 38
                                      i++l +G + +e+A+   ++ r vy+  k+y e
  gi|488600729|ref|YP_007907200.1|  3 IRQLDRGAPLKEIAAVIRVTLRKVYQIKKQYKE 35
                                      78999**************************98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.7e-07    0.0044       5      38 ..       3      35 ..       2      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.7e-07
                            HTH_29  5 llllaeGvstvsqiAkllglsrrtvyrwlkrfee 38
                                      ++ l++G +  ++iA++ +++ r+vy ++k + e
  gi|488600729|ref|YP_007907200.1|  3 IRQLDRGAP-LKEIAAVIRVTLRKVYQIKKQYKE 35
                                      68899***9.*********************987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.7e-06      0.03      17      43 ..       5      32 ..       1      35 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-06
                                      H.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 17 f.geglTleEIgerlgiSrerVrqiekr 43
                                        ++g +l+EI+++  +++  V qi+k+
  gi|488600729|ref|YP_007907200.1|  5 QlDRGAPLKEIAAVIRVTLRKVYQIKKQ 32
                                      457999*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 270.73
//
Query:       gi|488600730|ref|YP_007907201.1|  [L=544]
Description: hypothetical protein Asulf_01210 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-37  129.3   0.1    2.3e-37  128.6   0.1    1.3  1  AAA_12           AAA domain
    7.5e-29  101.3   0.0    1.1e-13   51.6   0.0    2.3  2  AAA_11           AAA domain
    3.8e-14   52.8   0.0    2.9e-13   50.0   0.0    2.4  2  AAA_30           AAA domain
    9.3e-11   42.2   0.0    1.9e-10   41.2   0.0    1.6  1  AAA_19           AAA domain
    3.5e-08   33.5   0.0      0.026   14.2   0.0    3.2  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    2.3e-05   24.1   0.4    5.6e-05   22.9   0.4    1.7  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    0.00014   21.4   0.0      0.022   14.2   0.0    2.6  2  PhoH             PhoH-like protein
    0.00052   19.9   0.1     0.0079   16.1   0.0    2.6  2  Helicase_RecD    Helicase
    0.00062   19.4   0.0       0.48    9.9   0.0    2.2  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
     0.0011   18.7   0.0      0.011   15.4   0.0    2.5  3  SRP54            SRP54-type protein, GTPase domain
     0.0021   17.5   0.0      0.013   14.9   0.0    2.3  3  ATPase           KaiC
     0.0025   18.3   0.0     0.0056   17.2   0.0    1.6  1  ABC_tran         ABC transporter
     0.0027   18.1   0.0       0.01   16.2   0.0    1.9  1  AAA_16           AAA ATPase domain
     0.0074   16.0   0.0      0.018   14.8   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.019   15.4   0.9      0.037   14.4   0.2    2.1  1  AAA              ATPase family associated with various cellul
      0.025   14.1   0.0       0.05   13.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.026   14.3   0.0       0.06   13.1   0.0    1.6  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.029   14.7   0.3        0.4   11.0   0.3    2.6  1  AAA_22           AAA domain
      0.052   13.4   0.0        0.1   12.5   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
      0.053   13.1   0.0       0.11   12.0   0.0    1.5  1  AAA_25           AAA domain
      0.056   13.2   0.2       0.13   12.0   0.2    1.7  1  AAA_24           AAA domain
       0.08   13.1   0.1       0.37   10.9   0.0    2.0  2  AAA_33           AAA domain
      0.086   12.2   0.9        0.5    9.7   0.2    2.1  2  UvrD_C           UvrD-like helicase C-terminal domain
       0.18   12.3   0.8       0.67   10.5   0.0    2.3  2  AAA_18           AAA domain


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.6   0.1   3.1e-40   2.3e-37      15     198 ..     343     513 ..     332     514 .. 0.93

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 3.1e-40
                            AAA_12  15 ekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkrele.......aqealeepleplvfidvekseeekekkek 84 
                                       +k+  L+  YR++++I +f+s+++Y+gk+k +es+k+ +le         + + +p + ++f++v++ +e  +   k
  gi|488600730|ref|YP_007907201.1| 343 SKPLWLRNHYRSNEKIINFASRYVYGGKIKPHESCKNIKLEvdcadkgFRWFIIDPGRTVIFVSVDSRDEPMK---K 416
                                       567899***************************99999999999999888888999999******97777776...6 PP

                            AAA_12  85 syiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgfQGrekdviil 161
                                       s +N++Ea++v ++v++ll++g+e+    +gvitpY aq + +++ ++          +ev+tvd+fQGre+dvi++
  gi|488600730|ref|YP_007907201.1| 417 SRVNPKEAAVVGDIVRTLLDAGVED----VGVITPYIAQRDQIREIIS----------VEVDTVDAFQGRERDVIVF 479
                                       9********************9998....*******************..........9****************** PP

                            AAA_12 162 slVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                       s+      +++ f  ++rr+NVa+TRA++k+i+vGn+
  gi|488600730|ref|YP_007907201.1| 480 STTAV---RNLRFACEKRRFNVAVTRARKKIIVVGNR 513
                                       *9755...6899***********************97 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   1.1e-15   8.3e-13       2     121 ..     136     242 ..     135     260 .. 0.84
   2 !   51.6   0.0   1.5e-16   1.1e-13     176     258 ..     248     326 ..     237     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.1e-15
                            AAA_11   2 lndsqreai..ksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76 
                                       l++ q +a+  +  l+e+e+  + GPPGtgKT++i++  + +          ++++r+ +++++N AvD+ le++l+
  gi|488600730|ref|YP_007907201.1| 136 LDEYQSDAVvaSLSLEENEVMRVIGPPGTGKTTFIAYCAKIA---------MDEGKRVFIASHTNRAVDNALEKILE 203
                                       7889999998788899999******************99999.........699*********************** PP

                            AAA_11  77 glldsegekykpkivRvgneeeriseavksvsleekvekrlekee 121
                                         +d + +ky   +vRvg+   ++s +v+++ le++  +  ++ +
  gi|488600730|ref|YP_007907201.1| 204 --FDLHRSKY---VVRVGRYW-KTSGDVRKILLEYMAMRDVTSLM 242
                                       ..66666666...9*******.89***********9988776643 PP

  == domain 2  score: 51.6 bits;  conditional E-value: 1.5e-16
                            AAA_11 176 elskeleeaeesleeevldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpk 252
                                       +l ke+ ++e++   e+l++++iv +Tl ++g   l ++   fd+v+IDEA+qa+  s+l  ++++ + +v vGDp 
  gi|488600730|ref|YP_007907201.1| 248 SLAKEYSKIERKS-LEILSKSRIVGSTLIKSGMYPLVDQ--HFDLVLIDEASQALISSALLSISQE-SSFVVVGDPF 320
                                       5667777777775.89***********************..8***********************9.9********* PP

                            AAA_11 253 QLpatv 258
                                       QL ++ 
  gi|488600730|ref|YP_007907201.1| 321 QLSPVL 326
                                       ****85 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   3.9e-16   2.9e-13       2     138 ..     136     332 ..     135     380 .. 0.79
   2 ?   -1.4   0.0       2.2   1.6e+03      46      82 ..     439     485 ..     426     512 .. 0.63

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 3.9e-16
                            AAA_30   2 lnaeQaaaveallt.sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgi...easti 73 
                                       l++ Q++av a l+ +++ v+ + Gp+GtGKtt ++  ++++ ++g+rv+++++t++a ++ L++ l++   +++ +
  gi|488600730|ref|YP_007907201.1| 136 LDEYQSDAVVASLSlEENEVMRVIGPPGTGKTTFIAYCAKIAMDEGKRVFIASHTNRAVDNaLEKILEFdlhRSKYV 212
                                       6788999887665537788*****************************************98887666544455555 PP

                            AAA_30  74 akllkrlk............................................................grarlepg. 89 
                                        ++ + +k                                                                ++++ 
  gi|488600730|ref|YP_007907201.1| 213 VRVGRYWKtsgdvrkilleymamrdvtslmhfdldslakeyskierksleilsksrivgstliksgmyP--LVDQHf 287
                                       555555557778888888888899999999999999999999999*******************98652..466778 PP

                            AAA_30  90 tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlr 138
                                       +l+++DEa+ + +++  all++ ++   + ++vGD+ Ql++V + g+ +
  gi|488600730|ref|YP_007907201.1| 288 DLVLIDEASQALISS--ALLSISQE--SSFVVVGDPFQLSPVLRTGWNS 332
                                       *********987764..56766655..8999***********9877755 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                            AAA_30  46 ggrviglAptgkaAkvLaeelgieastiakllkrlk..........g 82 
                                        ++v +++p  ++ ++++e + +e +t++ +  r +          +
  gi|488600730|ref|YP_007907201.1| 439 VEDVGVITPYIAQRDQIREIISVEVDTVDAFQGRERdvivfsttavR 485
                                       46777788888888888888888888888888776655555554440 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   2.6e-13   1.9e-10       9     144 ..     152     325 ..     140     327 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 2.6e-13
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae................. 68 
                                       +++v+ v+++pGtGKT+ +    +++ ++g    +++ +++ t+rA+++  e++ +++++                 
  gi|488600730|ref|YP_007907201.1| 152 ENEVMRVIGPPGTGKTTFIAYCAKIAMDEG----KRVFIASHTNRAVDNALEKILEFDLHrskyvvrvgrywktsgd 224
                                       6789**************************....89**************999966666566666666666555555 PP

                            AAA_19  69 ..atTiHrlal......................ldfddlltealelle..........eaeeekklqeee.llivDE 110
                                                 +                       ++ +++ + le+l           ++     + +++ l+++DE
  gi|488600730|ref|YP_007907201.1| 225 vrK-------IlleymamrdvtslmhfdldslaKEYSKIERKSLEILSksrivgstliKSGMYPLVDQHFdLVLIDE 294
                                       551.......0555555555666666555555533444444444444477777888765555566666668****** PP

                            AAA_19 111 fqdvdelqyrLlkallgekkklllvGDpdQliyv 144
                                       +++      +Ll+    e+  +++vGDp Ql +v
  gi|488600730|ref|YP_007907201.1| 295 ASQA-LISSALLSISQ-ESS-FVVVGDPFQLSPV 325
                                       *985.44556666544.555.*********9876 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 ?    2.4   0.0      0.15   1.1e+02       4      21 ..     159     176 ..     157     211 .. 0.74
   2 !   14.2   0.0   3.5e-05     0.026      54     107 ..     279     329 ..     252     389 .. 0.73
   3 !   13.0   0.0   8.2e-05     0.061     180     233 ..     459     510 ..     415     511 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.15
                   Viral_helicase1   4 hGvpGcGKStlirkllrt 21 
                                        G pG GK+t i   ++ 
  gi|488600730|ref|YP_007907201.1| 159 IGPPGTGKTTFIAYCAKI 176
                                       588*******99766655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.5e-05
                   Viral_helicase1  54 lmalvkstkgkililDEylllhaGyill.laalskaklvilfGDplQipfhsrna 107
                                         +lv++ +++++++DE+ ++    i   l+ +s+ + ++++GDp+Q +   r +
  gi|488600730|ref|YP_007907201.1| 279 MYPLVDQ-HFDLVLIDEASQAL---ISSaLLSISQESSFVVVGDPFQLSPVLRTG 329
                                       4556665.8*********8887...5555******************98776554 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 8.2e-05
                   Viral_helicase1 180 lgvrevttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhrkslvil 233
                                        +v ev tv   qG + d+ ++ ++   +l  ++e +  + vA TR+rk+++++
  gi|488600730|ref|YP_007907201.1| 459 ISV-EVDTVDAFQGRERDVIVFSTTAVRNLRFACE-KRRFNVAVTRARKKIIVV 510
                                       344.599***********99999998888887776.999***********9875 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 !   22.9   0.4   7.5e-08   5.6e-05       3      52 .]     462     510 ..     460     510 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.5e-08
                          UvrD_C_2   3 yaltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAreklilv 52 
                                        ++t+  +QG e +++++      + r ++  +r + +avTRAr+k i+v
  gi|488600730|ref|YP_007907201.1| 462 EVDTVDAFQGRERDVIVFSTTAVRNLR-FACEKRRFNVAVTRARKKIIVV 510
                                       589***********9988666666666.5559***************998 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.9e-05     0.022      13      44 ..     145     179 ..     132     205 .. 0.70
   2 ?    4.5   0.0     0.028        21     122     159 ..     289     323 ..     226     341 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                                       HHHHH..H-SEEEEE--TTSSTT.HHHHHHHHHHH CS
                              PhoH  13 lealk..kndivfaiGpaGtGKt.ylavalaveal 44 
                                       + +l+  +n+++ +iGp GtGKt ++a ++ +++ 
  gi|488600730|ref|YP_007907201.1| 145 VASLSleENEVMRVIGPPGTGKTtFIAYCAKIAMD 179
                                       34444449**************7366666655543 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.028
                                       EEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE------ CS
                              PhoH 122 fvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqid 159
                                       +v++DEA   +++ +   l  + ++s +vv+Gd+ q  
  gi|488600730|ref|YP_007907201.1| 289 LVLIDEA---SQALISSALLSISQESSFVVVGDPFQLS 323
                                       5888988...56778899999*************9975 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   1.1e-05    0.0079       2      89 ..     158     243 ..     157     316 .. 0.63
   2 ?   -2.7   0.0       6.2   4.7e+03      12      56 ..     425     469 ..     424     502 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqriey 78 
                                       +++ +G+GK++ ++  ++ ++ egk ++++++ ++++v++ +e +  +++  + k+  +  +  k++  vrk  +ey
  gi|488600730|ref|YP_007907201.1| 158 VIGPPGTGKTTFIAYCAKIAMDEGK-RVFIASHTNRAVDNALEKI-LEFDLHRSKYVVRVGRYWKTSGDVRKILLEY 232
                                       56889**********9999999987.*************999988.4555555555444444444445555666666 PP

                     Helicase_RecD  79 iapdellklke 89 
                                       +a++++ +l +
  gi|488600730|ref|YP_007907201.1| 233 MAMRDVTSLMH 243
                                       66666555543 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.2
                     Helicase_RecD  12 aalGlalaaliaegksnilvtapskenvktlfeflakglealglk 56 
                                       a++G ++  l+ +g  ++ v  p  ++ +++ e +  ++++++  
  gi|488600730|ref|YP_007907201.1| 425 AVVGDIVRTLLDAGVEDVGVITPYIAQRDQIREIISVEVDTVDAF 469
                                       567777777778877888888887777777777776666665543 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 !    9.9   0.0   0.00064      0.48      13      68 ..     153     205 ..     140     241 .. 0.79
   2 !    7.4   0.0    0.0036       2.7     230     294 ..     251     321 ..     217     322 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00064
                                       SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH.H CS
                     UvrD-helicase  13 ggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee.a 68 
                                       ++ + v+  +G+GKT+ +a+     ++e+    +r+++   Tn+A +   e+i e +
  gi|488600730|ref|YP_007907201.1| 153 NEVMRVIGPPGTGKTTFIAYCAKIAMDEG----KRVFIASHTNRAVDNALEKILEfD 205
                                       556779999*********98766666666....9************99999998852 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0036
                                       EEHHHHHHHHHHHHHH.........CHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT..EEEEE-GGG CS
                     UvrD-helicase 230 lDfsdllhallellee.........neelaealrerykeiliDEyQDTnkiQyrilkllasghee..lfmvGDpkQ 294
                                        ++s++  + le+l +         ++ +   + ++++ +liDE+     +Q+ i + l s  +e  +++vGDp Q
  gi|488600730|ref|YP_007907201.1| 251 KEYSKIERKSLEILSKsrivgstliKSGMYPLVDQHFDLVLIDEA-----SQALISSALLSISQEssFVVVGDPFQ 321
                                       6788888888888888899988888888888999**********7.....56666665555554455******977 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.6   4.2e+03     173     193 ..     127     147 ..     123     148 .. 0.83
   2 !   15.4   0.0   1.4e-05     0.011       3      36 ..     155     188 ..     153     201 .. 0.87
   3 ?   -1.0   0.0       1.5   1.1e+03      72      97 ..     275     300 ..     258     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.6
                                       EE-SSSTTGEEE--HHHHHHH CS
                             SRP54 173 igvGekiedleefdperlvsr 193
                                        + G+kie l+e +++++v +
  gi|488600730|ref|YP_007907201.1| 127 RTSGQKIEGLDEYQSDAVVAS 147
                                       588*********999999876 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.4e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllva 36 
                                       v+ ++G+ G+GKTt +a  a++ ++egk+v +++
  gi|488600730|ref|YP_007907201.1| 155 VMRVIGPPGTGKTTFIAYCAKIAMDEGKRVFIAS 188
                                       66789************************99876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHTTSSEEEEEE--SSTT CS
                             SRP54  72 akeavekakeekidvvlvDTaGrlqn 97 
                                       +k ++    ++++d+vl+D a +  +
  gi|488600730|ref|YP_007907201.1| 275 IKSGMYPLVDQHFDLVLIDEASQALI 300
                                       566777778899*******9876655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-05     0.013       5      55 ..     133     187 ..     129     212 .. 0.77
   2 ?   -2.7   0.0       4.1     3e+03     147     175 ..     229     260 ..     220     269 .. 0.73
   3 ?   -1.6   0.0       1.9   1.4e+03      48      65 ..     399     416 ..     394     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                            ATPase   5 IeglDeilk......gGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvt 55 
                                       IeglDe  +        + e++v+ + G pGtGKt+f + +  k a++ g++ vf++
  gi|488600730|ref|YP_007907201.1| 133 IEGLDEYQSdavvasLSLEENEVMRVIGPPGTGKTTFIA-YCAKIAMDEGKR-VFIA 187
                                       8999998766777777899******************64.777777774555.4554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.1
                            ATPase 147 lvrvlkklgvTailvsekss...seeaaggyg 175
                                       l++ +++++vT+++  + +s   +++++++  
  gi|488600730|ref|YP_007907201.1| 229 LLEYMAMRDVTSLMHFDLDSlakEYSKIERKS 260
                                       67789999999999888877665555665555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.9
                            ATPase  48 gepgvfvtveepaedlre 65 
                                       g+ ++fv+v+++ e +++
  gi|488600730|ref|YP_007907201.1| 399 GRTVIFVSVDSRDEPMKK 416
                                       8899*******9998876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.5e-06    0.0056       5      44 ..     147     186 ..     145     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.5e-06
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeill 44 
                                       sl+l+e+e++ ++G+ G+GK+t+++  a+   ++  ++ +
  gi|488600730|ref|YP_007907201.1| 147 SLSLEENEVMRVIGPPGTGKTTFIAYCAKIAMDEGKRVFI 186
                                       89***********************999988765555544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-05      0.01      25      88 ..     154     231 ..     140     324 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesa............ipysa.laqalareellrqlld 87 
                                       e++ ++G++G+GK++ +  +++ + ++g  +f++ ++ +   +              y++ + ++ ++++ +r++l 
  gi|488600730|ref|YP_007907201.1| 154 EVMRVIGPPGTGKTTFIAYCAKIAMDEGkRVFIASHTNRAVDNalekilefdlhrSKYVVrVGRYWKTSGDVRKILL 230
                                       67779****************99999977899888877772222233333332222222223333333344444444 PP

                            AAA_16  88 e 88 
                                       e
  gi|488600730|ref|YP_007907201.1| 231 E 231
                                       4 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.4e-05     0.018      29      81 ..     135     187 ..     114     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                         IstB_IS21  29 sldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfv 81 
                                       +ld+ + +++++   +e++e + ++Gp+G+GK+ + +  ++ a+ +g++v+  
  gi|488600730|ref|YP_007907201.1| 135 GLDEYQSDAVVASLSLEENEVMRVIGPPGTGKTTFIAYCAKIAMDEGKRVFIA 187
                                       6677777777777778999***************99999999*****999765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2     5e-05     0.037       3      23 ..     158     181 ..     156     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5e-05
                                       EESSTTSSHHHHHHHHHHHH...T CS
                               AAA   3 lyGppGtGKTllakavakel...g 23 
                                       ++GppGtGKT+++   ak +   g
  gi|488600730|ref|YP_007907201.1| 158 VIGPPGTGKTTFIAYCAKIAmdeG 181
                                       79**********999998864432 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   6.7e-05      0.05      23      89 ..     142     209 ..     123     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                             AAA_7  23 syllell.lknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr 89 
                                       + ++  l l+++  + ++Gp GtGKt+ i  + k   +e   + + + +++   n l +i+e  l++ 
  gi|488600730|ref|YP_007907201.1| 142 DAVVASLsLEENEVMRVIGPPGTGKTTFIAYCAKIAMDEGKRVFIASHTNRAVDNALEKILEFDLHRS 209
                                       555544405555556689************97777776888888888888888999999999888775 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 ?   13.1   0.0     8e-05      0.06       1      27 [.     158     184 ..     158     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsv 27 
                                       v+Gp+G GKttf+  +++i++++g++v
  gi|488600730|ref|YP_007907201.1| 158 VIGPPGTGKTTFIAYCAKIAMDEGKRV 184
                                       89******************9998876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00053       0.4       7      29 ..     155     177 ..     150     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                            AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                       ++ v+G++GtGKTt ++  ++ +
  gi|488600730|ref|YP_007907201.1| 155 VMRVIGPPGTGKTTFIAYCAKIA 177
                                       5669**********998776655 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 ?   12.5   0.0   0.00014       0.1      15      70 ..     148     202 ..     142     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie 70 
                                       l+ e+ne++ + Gp g GKt+++   ++   d +k ++++ +  +++ +++ e+i 
  gi|488600730|ref|YP_007907201.1| 148 LSLEENEVMRVIGPPGTGKTTFIAYCAKIAMDEGK-RVFIASHTNRAVDNALEKIL 202
                                       677899************************99887.66666666665555544443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.11      30      65 ..     150     186 ..     144     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                            AAA_25  30 lpagelallaGapgtGKttlaldlalava..tGkpwlg 65 
                                       l ++e+  ++G+pgtGKtt+    ++++a  +Gk ++ 
  gi|488600730|ref|YP_007907201.1| 150 LEENEVMRVIGPPGTGKTTFIAY-CAKIAmdEGKRVFI 186
                                       5689999************9754.45555478888776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00017      0.13       5      22 ..     156     173 ..     152     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       + ++Gp+g+GKTt+++  
  gi|488600730|ref|YP_007907201.1| 156 MRVIGPPGTGKTTFIAYC 173
                                       6699**********9987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0005      0.37       3      18 ..     157     172 ..     155     222 .. 0.86
   2 ?   -0.8   0.0       2.1   1.6e+03      61     100 ..     464     506 ..     412     517 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                            AAA_33   3 llvGlpGsGKstlaer 18 
                                        ++G+pG+GK+t++  
  gi|488600730|ref|YP_007907201.1| 157 RVIGPPGTGKTTFIAY 172
                                       589**********875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                            AAA_33  61 elarkalsagrnvildatnlsrrer....arflklarrlgvpvr 100
                                       ++++  + ++r+vi+ +t + r+ r    +r +++a     + +
  gi|488600730|ref|YP_007907201.1| 464 DTVDAFQGRERDVIVFSTTAVRNLRfaceKRRFNVAVTRA-RKK 506
                                       6777778888998887775555444455555555555333.333 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 ?    0.8   0.0      0.35   2.6e+02       3      22 ..     348     367 ..     346     462 .. 0.76
   2 ?    9.7   0.2   0.00067       0.5     326     345 ..     491     510 ..     478     514 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.35
                                       xxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   3 LekNyRStksLlkaankfle 22 
                                       L   yRS++++++ a++++ 
  gi|488600730|ref|YP_007907201.1| 348 LRNHYRSNEKIINFASRYVY 367
                                       55669**********99983 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00067
                                       xxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 326 EEkRlfYVaiTRAkkrLfis 345
                                        EkR f Va+TRA+k++++ 
  gi|488600730|ref|YP_007907201.1| 491 CEKRRFNVAVTRARKKIIVV 510
                                       59***************996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0009      0.67       3      52 ..     158     204 ..     157     233 .. 0.70
   2 ?   -1.8   0.0       5.6   4.2e+03      24      48 ..     263     288 ..     248     316 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0009
                            AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrl 52 
                                       + G+pG+GKtt+  + +k     ++ + v+  +++   vd++ l++ +++
  gi|488600730|ref|YP_007907201.1| 158 VIGPPGTGKTTFIAYCAKIA--MDEGKRVFIASHTNRAVDNA-LEKILEF 204
                                       78**********99998876..55555555555555555555.4444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.6
                            AAA_18  24 f...gvnlrdvakenglllevdpealde 48 
                                       +   ++++++++ ++g++  vd++   +
  gi|488600730|ref|YP_007907201.1| 263 IlskSRIVGSTLIKSGMYPLVDQH--FD 288
                                       255568899999999999999998..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 3034.65
//
Query:       gi|488600731|ref|YP_007907202.1|  [L=394]
Description: L-threonine synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-77  259.3   1.1    5.3e-77  259.1   1.1    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.1   1.1     3e-81   5.3e-77       2     294 .]      64     364 ..      63     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: 259.1 bits;  conditional E-value: 3e-81
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       +l +g+TPl r++ l++el++  +++K E+lnp+gSfKdRg++  ++++ e  g+k v++as+GN+ ++lA++aa++
  gi|488600731|ref|YP_007907202.1|  64 SLNEGGTPLFRAEYLERELNIHrIYVKHEGLNPSGSFKDRGMTVGVTKAIEL-GKKAVACASTGNTSASLAMYAAKA 139
                                       7889************************************************.************************ PP

                                       T-EEEEEEETTS-H.HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHH CS
                              PALP  78 Glkvtivvpadasp.ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileq 153
                                       +lk+++++pa++ + +kva+  +++a+v+ ++g++d a+++++e+ ++ e++yl+++  np + eg++ti++Ei+++
  gi|488600731|ref|YP_007907202.1| 140 NLKAYVLLPAGKVAlGKVAQALMHNAKVIGIKGNFDKALELVREISRQ-ENFYLLNSV-NPFRLEGQKTIAFEIVDE 214
                                       *************88*********************************.*********.9***************** PP

                                       TTTTEEEEEEE-SSSHHHHHHHHHHHH....HSTT....-EEEEEEECTTCGGTTCC.S..S.SS..B.SSS.CCST CS
                              PALP 154 lggkpdavvvpvGgGgliaGiaaglke....rrpd....vrvigvepegsdalarsl.ragrrvtvpvsdtiadgla 221
                                       lg +pd v++pvG++g+i++i++g++e    +       +++ g++++g+++++r++ + +++ +  +++tia++++
  gi|488600731|ref|YP_007907202.1| 215 LGYVPDRVILPVGNAGNISAIYKGFRElktlG--LidsiPKMTGIQAKGANPIYRAFvESKKVIEPVTPETIATAIR 289
                                       ***************************77663..14478*****************9444444444455******** PP

                                       CS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 222 vg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       +g  +++++a+ ++ ++++ + +vsdee+++a++ la +egi vep+saa++a+l  +  +e++ +++vv+i tg
  gi|488600731|ref|YP_007907202.1| 290 IGnpVNARKALNAIYESNGLAEEVSDEEIISAQKILAGKEGIGVEPASAASVAGLIKLAGREIDVDETVVCITTG 364
                                       **9999*************************************************6667778888899***9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2555.11
//
Query:       gi|488600732|ref|YP_007907203.1|  [L=905]
Description: ATP dependent helicase, Lhr family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-30  104.9   0.3    9.5e-30  103.7   0.1    1.7  2  DEAD           DEAD/DEAH box helicase
    9.3e-26   90.8   0.0    1.8e-25   89.8   0.0    1.5  1  DEAD_assoc     DEAD/H associated
    1.9e-22   79.7   0.2    1.1e-20   74.0   0.1    2.8  2  Helicase_C     Helicase conserved C-terminal domain
    2.6e-10   40.6   0.0    5.7e-10   39.5   0.0    1.6  1  ResIII         Type III restriction enzyme, res subunit
     0.0023   17.7   0.1      0.017   15.0   0.0    2.4  2  AAA_11         AAA domain
      0.003   17.1   0.2     0.0058   16.2   0.2    1.6  1  UvrD-helicase  UvrD/REP helicase N-terminal domain
     0.0078   15.0   0.0      0.013   14.3   0.0    1.3  1  SNF2_N         SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.046   13.7   0.5       0.69   10.0   0.0    3.0  3  HypA           Hydrogenase/urease nickel incorporation, metal
      0.056   12.9   0.0        2.5    7.5   0.0    2.4  2  PhoH           PhoH-like protein
      0.058   13.5   0.5        2.4    8.3   0.5    3.4  3  PRC            PRC-barrel domain
        1.2    9.1   4.1        5.6    7.0   0.0    4.0  4  HTH_Crp_2      Crp-like helix-turn-helix domain
          2    9.0   5.4       0.79   10.3   0.3    2.9  3  FeoB_Cyto      FeoB cytosolic helical domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.1   6.4e-33   9.5e-30       2     175 ..      30     199 ..      29     200 .. 0.87
   2 ?   -3.1   0.0       3.8   5.7e+03      48     103 ..     257     311 ..     247     315 .. 0.61

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 6.4e-33
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       + Q++a++ il+g+d l+ a+TGsGKT+ ++ip++ +++   + +g   l+++P+++L +++l++++++ k++++++
  gi|488600732|ref|YP_007907203.1|  30 ELQKRAFKVILEGKDTLIVAPTGSGKTESAIIPIFYRMLL-GEYEGIFLLYITPLKALNRDMLRRISTLAKELEISI 105
                                       67*********************************88876.899***************************988777 PP

                                       EEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldng.vdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                        +  +g++ +++++k + + ++++++tp+ l+ l++ +kl+  l++v ++V+DE++++ d++++ +++  l++l++i
  gi|488600732|ref|YP_007907203.1| 106 AVR-HGDTLSSERRKQSLRpPQVLITTPETLQILFQGRKLRkaLKNVHYVVIDEIHEIADSERGVQLSIALERLREI 181
                                       644.5566655555554445***************88888888*******************************766 PP

                                       CTTSTTTSEEEEEESSBSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 153 tcdgklqrqvivlSATlpkdvkk 175
                                        +      ++i lSAT ++++++
  gi|488600732|ref|YP_007907203.1| 182 AS-----FTTIGLSATTKESISR 199
                                       44.....559******9977765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
                                       -EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  48 pkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvg 103
                                          li + tr+ ae    +lk++++ +++   ++  + + + +++ ++ +++ ++ 
  gi|488600732|ref|YP_007907203.1| 257 GSGLIFVNTRQTAEALGLRLKQIMD-VEVHHGSLSREARLEAERKFMEGELKALIC 311
                                       4678888899999999999998888.233333333344445555555444555555 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   1.2e-28   1.8e-25       1     190 [.     595     762 ..     595     763 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 1.2e-28
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +P+d+ + +E  ++     + v++++fG++vne+l++++a  l++r g +v++ +++++i l+ +  e    +++++
  gi|488600732|ref|YP_007907203.1| 595 VPSDKVVTIEGGEN-----TAVINACFGHKVNETLGRIIALLLTARKGRNVSIEIDPYRIKLTPASCE----EVRDI 662
                                       79999999998765.....78*****************************************553323....35689 PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavre 154
                                       l  l+ + +ee+ e+al +++l++++  + A++++ l+++ +         r++ ++L+  +r   d+p+++eavre
  gi|488600732|ref|YP_007907203.1| 663 LLNLRREGVEELAERALLDTKLLQWKVIHSARKFGYLSKNFDL-------SRVNLSRLVVRLR---DTPIYREAVRE 729
                                       999*************************************988.......8899999988888...*********** PP

                        DEAD_assoc 155 vledqlDlerlaellrriaageirvvevetprpSpf 190
                                       ++ +++D+er +e+++r+ + ++++v    ++ Sp+
  gi|488600732|ref|YP_007907203.1| 730 IFLEKMDIERSKEIIERLGK-DLKIVV--YNKLSPI 762
                                       *******************9.888888..8888887 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 ?    2.3   0.0      0.13     2e+02      27      58 ..      89     120 ..      63     138 .. 0.71
   2 !   74.0   0.1   7.3e-24   1.1e-20       5     108 ..     248     347 ..     244     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHTTSTEEEESTTSTHHHHHHH CS
                        Helicase_C  27 drlekvklllekkgikvavlhgelpqnereei 58 
                                       d+l +++ l ++ +i++av hg++ ++er++ 
  gi|488600732|ref|YP_007907203.1|  89 DMLRRISTLAKELEISIAVRHGDTLSSERRKQ 120
                                       34433455555559********8777666654 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 7.3e-24
                                       HHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                        Helicase_C   5 allellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                                       +++e++   ee+g  lifvnt++++e + l l k+ + v v+hg+l+ + r+e+ ++f +ge + Li+t+ +e Gid
  gi|488600732|ref|YP_007907203.1| 248 TIKEII---EEHGSGLIFVNTRQTAEALGLRL-KQIMDVEVHHGSLSREARLEAERKFMEGELKALICTSSMELGID 320
                                       566676...899999********997544444.4459**************************************** PP

                                       STTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtg 108
                                       i  v++Vi+++ pr+vt++iqr+GR+g
  gi|488600732|ref|YP_007907203.1| 321 IGHVDVVIQYNSPREVTRLIQRVGRAG 347
                                       **************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   3.8e-13   5.7e-10       3     170 ..      27     194 ..      10     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 3.8e-13
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEE.EESSHHHHHHHHHHGGGG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflf.lvprkslleqtleefkkf 77 
                                       el+e Q++a + +l      + k  li+++TG+GKT  a + + +r+l  ++e  fl+ + p k+l   +l++++ +
  gi|488600732|ref|YP_007907203.1|  27 ELNELQKRAFKVIL------EGKDTLIVAPTGSGKTESAiIPIFYRMLLGEYEGIFLLyITPLKALNRDMLRRISTL 97 
                                       45556666666665......55789**************7888888888777776654389999**********999 PP

                                       TGG....GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.... CS
                            ResIII  78 lseaykeigkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.... 148
                                       ++e       + +gd+ ++  ++++    ++l+tt ++l+      +  + ++  ++  +++iDE H +++++    
  gi|488600732|ref|YP_007907203.1|  98 AKELEI-SIAVRHGDTLSSerRKQSLRPPQVLITTPETLQILF---QGRKLRKALKNVHYVVIDEIHEIADSErgvq 170
                                       988753.4444555555554444478889**************...9999999999999************855444 PP

                                       ...TTHHHHHT---SEEEEEESS-S CS
                            ResIII 149 ...swreilekfkeavllglTATpe 170
                                          + ++ l+ + +++ +gl+AT +
  gi|488600732|ref|YP_007907203.1| 171 lsiALER-LREIASFTTIGLSATTK 194
                                       4444444.666777*********86 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.017       2      62 ..      28     132 ..      27     256 .. 0.81
   2 ?   -2.6   0.0       2.5   3.7e+03      51     114 ..     561     621 ..     548     655 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                            AAA_11   2 lndsqreaiksalseseitliqGPPGtgKT.ktivellsqll................................... 42 
                                       ln+ q++a+k +l+ ++ tli  P G+gKT ++i+ ++ ++l                                   
  gi|488600732|ref|YP_007907203.1|  28 LNELQKRAFKVILEGKD-TLIVAPTGSGKTeSAIIPIFYRMLlgeyegifllyitplkalnrdmlrristlakelei 103
                                       8****************.************99999999999889988888888888888877777666666555544 PP

                            AAA_11  43 sr.........rkseeeksakpriLvCap 62 
                                       s          ++ +++  ++p++L+++p
  gi|488600732|ref|YP_007907203.1| 104 SIavrhgdtlsSERRKQSLRPPQVLITTP 132
                                       00444455553335677888888888877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                            AAA_11  51 ksakpriLvCapSNaAvDellerllrglldsegekykpkivRvgneeeriseavksvsleekve 114
                                       ++ak  +L   ++N    e++ r +++ ++++ e+ + k+v +  +e   ++av + +  +kv+
  gi|488600732|ref|YP_007907203.1| 561 QDAKDYLLSRFETNEKAAETVIRTIKEHVEQKFEVPSDKVVTIEGGE---NTAVINACFGHKVN 621
                                       45555555555667777777777777777777777777777777777...56666666555555 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 !   16.2   0.2   3.9e-06    0.0058       2     101 ..      29     163 ..      28     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-06
                                       SHHHHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH......... CS
                     UvrD-helicase   2 npeqreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee......... 67 
                                       n+ q++a +    g+++l++A  GsGKT   +  i + +  +e+e   +l +T  ++  + +  Ri +         
  gi|488600732|ref|YP_007907203.1|  29 NELQKRAFKVilEGKDTLIVAPTGSGKTESAIIPIFYRMLLGEYEGIFLLYITPLKALNRDMLRRISTlakeleisi 105
                                       667777777666899*************877667777777777*************************999999999 PP

                                       ........................HHHHCCHHCTT-H...........HHHHHHHHCTTSEEEEHHHHH CS
                     UvrD-helicase  68 ........................alkkaeqessdde...........rlrlalqnlseanisTlHsfc 101
                                                               +           +           +lr+al+n++ + i  +H+++
  gi|488600732|ref|YP_007907203.1| 106 avrhgdtlsserrkqslrppqvliT-----------TpetlqilfqgrKLRKALKNVHYVVIDEIHEIA 163
                                       9999986666655555555555444...........044444444455999999999999999999886 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 !   14.3   0.0   8.4e-06     0.013     103     198 ..      81     171 ..      19     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.4e-06
                                       --H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S- CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 103 vPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvew 178
                                        P  +l +   + i + +++ ++ + v +g++      ++  ++ l+  +v+itt ++l+   + +k r++lk+v  
  gi|488600732|ref|YP_007907203.1|  81 TPLkALNRDMLRRISTLAKELEISIAVRHGDT----LSSERRKQSLRPPQVLITTPETLQILFQGRKLRKALKNV-- 151
                                       55545555566778888999999999999986....33455788999*************999999999*99976.. PP

                                       SEEEES-GGGT--TTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 179 krvvlDEghtlknstskaae 198
                                       ++vv+DE h +  s++ ++ 
  gi|488600732|ref|YP_007907203.1| 152 HYVVIDEIHEIADSERGVQL 171
                                       69*********999654433 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.3   3.5e+03      28      45 ..     541     558 ..     540     564 .. 0.84
   2 ?   -0.8   0.1         1   1.5e+03       7      41 ..     578     613 ..     574     626 .. 0.79
   3 ?   10.0   0.0   0.00046      0.69      64      97 ..     791     827 ..     753     835 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                                       EEEEEEETTCT--HHHHH CS
                              HypA  28 kvkvevGelsgvepeaLe 45 
                                       +v vevG+l+ v  + ++
  gi|488600732|ref|YP_007907203.1| 541 EVAVEVGRLRRVIADRIR 558
                                       699********9988776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHCC.TT..EEEEEEEEEETTCT--H CS
                              HypA   7 aesivevveeeake.aaarkvtkvkvevGelsgvep 41 
                                       ae ++++++e++++  ++ + + v++e Ge + v +
  gi|488600732|ref|YP_007907203.1| 578 AETVIRTIKEHVEQkFEVPSDKVVTIEGGENTAVIN 613
                                       688999999999554788888889999999887765 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00046
                                       EEEE--EEEETTTS-EEECHHH...HHS-TTTSSS-E CS
                              HypA  64 ieevpvkvrCreCgkefeleek...alrCpkCgsadv 97 
                                       +e++  +++C +Cg+++++  +   + +Cp+C+s  +
  gi|488600732|ref|YP_007907203.1| 791 LENEVTVIHCINCGYTIRTPIRlidRPECPRCKSGMI 827
                                       67788899********996653234679*****9766 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0017       2.5       2      37 ..      25      60 ..      24      79 .. 0.85
   2 ?    2.7   0.0     0.051        76     132     163 ..     736     767 ..     733     802 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
                                      ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHH CS
                              PhoH  2 ikpktkeQkeylealkkndivfaiGpaGtGKtylav 37
                                      i+  ++ Qk++++++ + + + +++p+G+GKt  a+
  gi|488600732|ref|YP_007907203.1| 25 IHELNELQKRAFKVILEGKDTLIVAPTGSGKTESAI 60
                                      7788999*********9999************7776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.051
                                       -HHHHHHHHTTB-TT-EEEEEE---------- CS
                              PhoH 132 tkeqmkmfltRlGenskvvvtGdvtqidlpkg 163
                                         e+ k+++ RlG++ k+vv   ++ i l ++
  gi|488600732|ref|YP_007907203.1| 736 DIERSKEIIERLGKDLKIVVYNKLSPISLASR 767
                                       568899**************999888887754 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.54   8.1e+02      33      61 ..     302     335 ..     300     345 .. 0.81
   2 ?    8.3   0.5    0.0016       2.4      12      42 ..     474     505 ..     468     557 .. 0.87
   3 ?   -1.4   0.0       1.7   2.6e+03      20      44 ..     622     646 ..     615     655 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.54
                                       TTTEEEEEEEEETTT.......-EEEEEGG.... CS
                               PRC  33 kegrvralvvsvggflgi..gekevliPfd...l 61 
                                        eg++ al+ + ++ lgi  g+ +v+i ++   +
  gi|488600732|ref|YP_007907203.1| 302 MEGELKALICTSSMELGIdiGHVDVVIQYNsprE 335
                                       58999************99999999999996543 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                                       -EEEETT.SSEEEEEEEEEEETTTTEEEEEEE CS
                               PRC  12 keVyted.GeklGkVkDvvidekegrvralvv 42 
                                       ++V++++ G+k+Gk+ +  + + +g+v a++ 
  gi|488600732|ref|YP_007907203.1| 474 YTVVDITtGRKIGKIDESFLSTFTGEVFAIKG 505
                                       79*************99999999***999976 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.7
                                       SEEEEEEEEEEETTTTEEEEEEEEE CS
                               PRC  20 eklGkVkDvvidekegrvralvvsv 44 
                                       e lG++  +++  + gr ++++++ 
  gi|488600732|ref|YP_007907203.1| 622 ETLGRIIALLLTARKGRNVSIEIDP 646
                                       6677777777777777777777664 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0038       5.6      32      54 ..       7      29 ..       6      41 .. 0.84
   2 ?   -0.7   0.0      0.96   1.4e+03      32      44 ..     191     203 ..     187     212 .. 0.88
   3 ?   -1.5   0.2       1.7   2.5e+03      33      50 ..     654     671 ..     625     686 .. 0.62
   4 ?   -1.1   0.0       1.3   1.9e+03      32      52 ..     704     724 ..     699     736 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0038
                                      TSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 32 GltretvsrilseLkreglisrg 54
                                      Gl+re + r++++Lk +g+++ +
  gi|488600732|ref|YP_007907203.1|  7 GLSREALDRLMNALKLAGIHELN 29
                                      89*****************9943 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.96
                                       TSSHHHHHHHHHH CS
                         HTH_Crp_2  32 Gltretvsrilse 44 
                                        +t e++sr++se
  gi|488600732|ref|YP_007907203.1| 191 ATTKESISRLISE 203
                                       6899*****9986 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.7
                                       SSHHHHHHHHHHHHHTTS CS
                         HTH_Crp_2  33 ltretvsrilseLkregl 50 
                                       ++ e v  il  L+reg+
  gi|488600732|ref|YP_007907203.1| 654 ASCEEVRDILLNLRREGV 671
                                       455666666666666666 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.3
                                       TSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  32 GltretvsrilseLkreglis 52 
                                        l+r+ +sr+  +L++  + +
  gi|488600732|ref|YP_007907203.1| 704 DLSRVNLSRLVVRLRDTPIYR 724
                                       589********9999977666 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00053      0.79       5      65 ..     197     256 ..     194     268 .. 0.85
   2 ?   -1.2   0.1         2     3e+03      49      67 ..     576     594 ..     557     603 .. 0.57
   3 ?   -2.0   0.1       3.6   5.4e+03      57      77 ..     738     758 ..     719     760 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                         FeoB_Cyto   5 iEkaiekleellkesnlkaklppRwlAlklLegDeelleelkedpelraeveearkeleae 65 
                                       i + i++   ++k+   k++++ R +   ++e+D+++ e+l+  +e++a ++++++ +e++
  gi|488600732|ref|YP_007907203.1| 197 ISRLISENAVVIKDI-RKKDYSFRVIQPEVIEDDKKISERLSIPQEISADLRTIKEIIEEH 256
                                       555566666667776.8899***********************9**********9999987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                         FeoB_Cyto  49 pelraeveearkeleaelg 67 
                                       ++ ++ ++++++++e++++
  gi|488600732|ref|YP_007907203.1| 576 KAAETVIRTIKEHVEQKFE 594
                                       3334444555566666554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.6
                         FeoB_Cyto  57 earkeleaelgedledvIvda 77 
                                       e +ke+ ++lg+dl+ v++++
  gi|488600732|ref|YP_007907203.1| 738 ERSKEIIERLGKDLKIVVYNK 758
                                       556777788999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (905 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 5353.22
//
Query:       gi|488600733|ref|YP_007907204.1|  [L=127]
Description: putative Fe-S-cluster oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   58.1   2.2    1.4e-15   57.7   2.2    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 !   57.7   2.2     8e-20   1.4e-15       4      85 .]      11      97 ..       4      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 8e-20
                          CxxCxxCC  4 eCgaCCkelkvklteedlerlkaaevaeeeeeskkiak.....adgrCvfldeetklCkiYeeRpkicrlfpas..eke 75
                                       Cg+CC+e+++ l + d+er++  +++e+e+  +         +dgrC fl+++   C+iY  Rp+ cr++p+   e++
  gi|488600733|ref|YP_007907204.1| 11 FCGKCCYETEMPLSKSDIERITSLGYNESEFAVEVNGVkqlrnVDGRCFFLEDN--ICTIYPYRPEGCRIYPFIydEER 87
                                      4*************************88887654332256777***********..8****************987777 PP

                          CxxCxxCC 76 ellaraetCa 85
                                      +  +++e C+
  gi|488600733|ref|YP_007907204.1| 88 DRIIVDEICP 97
                                      7778888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 775.02
//
Query:       gi|488600734|ref|YP_007907205.1|  [L=382]
Description: hypothetical protein Asulf_01214 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  122.8   3.7    2.1e-19   70.4   0.7    2.1  2  Asn_synthase  Asparagine synthase
  ------ inclusion threshold ------
       0.01   15.8   1.3       0.01   15.8   1.3    2.7  2  Trigger_C     Bacterial trigger factor protein (TF) C-terminu
      0.044   13.7   0.0      0.091   12.7   0.0    1.6  1  GATase_7      Glutamine amidotransferase domain


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 !   54.5   0.1   2.4e-18   1.4e-14      21     140 ..     153     264 ..     135     268 .. 0.91
   2 !   70.4   0.7   3.6e-23   2.1e-19     202     307 ..     266     368 ..     261     373 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2.4e-18
                      Asn_synthase  21 GalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee 97 
                                       ++ +SGGlDSSl+a++ +  +      +s++    +++e k+ ++ a+ +g +    +++ ++l+++ ++v +++e 
  gi|488600734|ref|YP_007907205.1| 153 CIAFSGGLDSSLLASIYDLSL------VSVTA---SDEEEKWLRKSAKMIGRDIEIRRFDLDDLVEVTRKVSRAIES 220
                                       6789************97754......78888...899***************9999******************** PP

                      Asn_synthase  98 ..pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfyk 140
                                         p+  +  ip yl ++ ak+ g+  +  G+GaDElfgGY   y 
  gi|488600734|ref|YP_007907205.1| 221 tnPVQVSIGIPIYLTMEFAKSLGYDSIVFGQGADELFGGYM-KYL 264
                                       ****************************************8.554 PP

  == domain 2  score: 70.4 bits;  conditional E-value: 3.6e-23
                      Asn_synthase 202 egedelhrelyldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPe 278
                                       +g+de+++e++ d++++ +++l+r  ++s  + + + +P+l ++l+++al++p+elk+r+gi KyiLRe++ ++lPe
  gi|488600734|ref|YP_007907205.1| 266 AGHDEMKEEMLKDVREIGKNNLVRDAKISYKNEIKLQTPYLQWDLIKLALSIPAELKVRDGIRKYILREVALDFLPE 342
                                       689************************************************************************** PP

                      Asn_synthase 279 eileRpKegfsapvgewklkgelrelaee 307
                                       ei++R+K++ +++++++   + l++la++
  gi|488600734|ref|YP_007907205.1| 343 EIAKREKKAIQYSTKAS---AMLKKLARK 368
                                       ************99999...567777776 PP

>> Trigger_C  Bacterial trigger factor protein (TF) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.074   4.4e+02     100     127 ..     121     148 ..     116     151 .. 0.88
   2 ?   15.8   1.3   1.8e-06      0.01      78     139 ..     319     381 ..     307     382 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.074
                                       HHHHHHHTT----HHHHHHHHHHHCCCT CS
                         Trigger_C 100 leeiakeekievteeelkeeleelasqy 127
                                       +e++++++++  + +++ke++++l + y
  gi|488600734|ref|YP_007907205.1| 121 FEDVFDVHEVDTDVDQVKERIAKLLEGY 148
                                       689999****************998877 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.8e-06
                                       HCCCHCHHCHHHHHHHHHHHHHHHHHHHHTT----.HHHHHHHHHHHCCCTTSXHHHHHHHHH CS
                         Trigger_C  78 seeelreelkeeAekrVklgLvleeiakeekievt.eeelkeeleelasqygmepeevkeflk 139
                                        e ++r+  ++ + + V l+++ eeiak+ek  +    +  ++l++la++ +m+++e++e+l+
  gi|488600734|ref|YP_007907205.1| 319 AELKVRDGIRKYILREVALDFLPEEIAKREKKAIQySTKASAMLKKLARKKNMNVKEFIEMLN 381
                                       57789999*********************997776345799********************95 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.5e-05     0.091      70     107 ..      47      82 ..      13      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                          GATase_7  70 alerlnGmfAfaiwdeeekrlllaRDrlGikPLyyged 107
                                       +  +ln  ++++ +  ++  ++l RD lG kPLyy ++
  gi|488600734|ref|YP_007907205.1|  47 LPLKLNKFYSVVAFRPSH--IYLSRDVLGGKPLYYSQS 82 
                                       555666677777777777..***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2559.99
//
Query:       gi|488600735|ref|YP_007907206.1|  [L=151]
Description: hypothetical protein Asulf_01215 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   14.5   2.8       0.18   12.5   1.4    2.1  2  PrgI      PrgI family protein
        0.1   11.8   0.0       0.13   11.5   0.0    1.2  1  RE_SinI   SinI restriction endonuclease


Domain annotation for each model (and alignments):
>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.061   5.5e+02      24      52 ..       6      31 ..       4      53 .. 0.76
   2 ?   12.5   1.4   2.1e-05      0.18      19      69 ..      82     134 ..      69     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.061
                              PrgI 24 flvlallvaiglylllrafleelasvlvi 52
                                      f++ ++lv ++++l++++++   a v+ i
  gi|488600735|ref|YP_007907206.1|  6 FYIPFILVTFAVILIVERIT---ARVVSI 31
                                      56667777788888887777...555544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                              PrgI  19 lRQliflvlallvaiglylllrafl..eelasvlvillavPvaalgfykkdgl 69 
                                       +RQli+ + ++++ +  y++l++fl  e ++s++ ++ a  ++ + +  + g+
  gi|488600735|ref|YP_007907206.1|  82 FRQLIIASTVFFIILSPYMFLSEFLlkEYITSPFSMVFATAIFYFMMKNVYGY 134
                                       5************************8777777777777766666644444444 PP

>> RE_SinI  SinI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.5e-05      0.13      70     107 ..      20      57 ..      15      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.5e-05
                           RE_SinI  70 ipstvpdeivsvvlqkayevseeelekikeehrlsmga 107
                                       i + +   +vs++++k  e  ee+  ki e+h+ls+ a
  gi|488600735|ref|YP_007907206.1|  20 IVERITARVVSIIFRKDLEEMEEQQRKIAEYHELSLLA 57 
                                       55678889***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1107.29
//
Query:       gi|488600736|ref|YP_007907207.1|  [L=340]
Description: hypothetical protein Asulf_01216 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   92.8  29.5    4.1e-26   92.1  29.5    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 !   92.1  29.5   2.3e-30   4.1e-26       2     235 ..      23     327 ..      21     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 2.3e-30
                              TauE   2 llagllaGfvagllGiGggliavPlLll.l.l.......................ppavavatsllavvatslsgal 53 
                                       +l+++ +G++ + +G+ gg++a    +  l +                          ++  +++l+  ++sls+++
  gi|488600736|ref|YP_007907207.1|  23 FLWAIWVGWIFSTVGAFGGIMAGVGHISiLgIgkygtslkgtpikigmyndagkyITDHIRFSNTLMTWLNSLSSTI 99 
                                       899************************9554389999*****************97777999*************** PP

                              TauE  54 ahrrrgnvdwrlllllllgsliGallGallll.llpsellkllfgvlllllallmllrkkr................ 113
                                        ++ ++++ w++++ ++lg+++Ga+++++     l  +l+k lfg++  +++++m+++ ++                
  gi|488600736|ref|YP_007907207.1| 100 NWYTQKRLVWPAAIAMGLGMVLGAQVAVWGTGgKLGVALYKGLFGLATWAVSIYMFYQVTPrakaskskgreaakrf 176
                                       *****99*******************9998777888999****************9944445577999********* PP

                              TauE 114 ..........................srak......grerrptaillvligglvGllsGllGiGgGfllvpllllll 158
                                                                    +      g++   +  l ++ g+l+G++++l+G+GgGf++vp+++  l
  gi|488600736|ref|YP_007907207.1| 177 qqrveelrkagrlgelegitnvkyslD--RvefdffGERFVAKNYLPFFYGLLIGFIAALIGVGGGFMIVPFFTA-L 250
                                       *****9999999999999888777662..144667777777888889999999*********************7.7 PP

                              TauE 159 glplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlfallllvlgvk 235
                                       g+p+  + a+s+l ++++  ++++g ++ g v +  ++++ +g+l+G+++G r+ ++l+   l +lf+ll +++g +
  gi|488600736|ref|YP_007907207.1| 251 GWPMYITPAVSALTVFLNQCSALAGWFARGLVFPIGIVIAWAGILIGSYIGPRTQKYLPMDSLFILFGLLAFYVGTR 327
                                       *************************98899988888888***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); 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:                         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 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2253.09
//
Query:       gi|488600737|ref|YP_007907208.1|  [L=282]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-51  174.3   0.0    3.4e-51  174.1   0.0    1.1  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 !  174.1   0.0   1.9e-55   3.4e-51       2     204 ..      36     241 ..      35     243 .. 0.94

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 1.9e-55
                            DUF169   2 LaealrlktePVavkfsdekpelpekke.kieekk......rlCqmvalarakgktvvftaetlgCpgGaaalGfke 71 
                                       L+++lrlk++PVavk++ +++e++e+ + k    k      ++C ++a+ r++g++v+  +e+lgC+++++ +G+k+
  gi|488600737|ref|YP_007907208.1|  36 LRNLLRLKYYPVAVKYFYSEEEVEEFRKnK--Y-KigihpfTFCHFSAVSRQRGEIVFSRRENLGCSNARYLFGWKD 109
                                       899*******************66655423..2.236688************************************* PP

                            DUF169  72 lp.eklksgegylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrl 147
                                        + +++ks+++y++++e+a++fv+++prl++g  k++++apL+ka+fePd+++++++  q ++L + +  + + ++ 
  gi|488600737|ref|YP_007907208.1| 110 FDeNEIKSHKKYTRDLEQAERFVKTKPRLPEGL-KALATAPLHKAPFEPDLIHIICDVLQSYHLYNDYASAMDVHPI 185
                                       999************************996655.******************************************* PP

                            DUF169 148 nvsfpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemv 204
                                       + +f +n+a+C  +v ++y +++ ni ++++g+++++k++++e+++ iP+e++e  v
  gi|488600737|ref|YP_007907208.1| 186 QPNFMMNSAVCGGAV-WTYVNKRINIVPMCSGSYTAGKTEQGEINVFIPWEHFEPTV 241
                                       *************99.*************************************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1670.15
//
Query:       gi|488600738|ref|YP_007907209.1|  [L=121]
Description: desulfoferrodoxin ferrous iron-binding domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-30  103.5   0.5    8.4e-30  103.2   0.5    1.1  1  Desulfoferrodox  Desulfoferrodoxin
     0.0053   16.3   0.0     0.0069   15.9   0.0    1.1  1  F_bP_aldolase    Fructose-bisphosphate aldolase class-II


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.5   9.4e-34   8.4e-30       2      96 .]       7     118 ..       6     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 9.4e-34
                                       SHTTTHTTSEEEEEESEEEETTEEEEEEEESS.SS--BSSSS-EEEEEEEEEETTSS......EEEE-TBS...... CS
                   Desulfoferrodox   2 adekeekHvPvieadevvkagelfevkvkvgk.ipHpneeeHyIewielyleeegek......rvelsaed...... 65 
                                       ad+k+ekHvPvie++   k+++l++vkv vgk ipHpn++eH+I+wiel + ++g+k      r+e+++++      
  gi|488600738|ref|YP_007907209.1|   7 ADWKSEKHVPVIEIE---KSDDLVDVKVVVGKeIPHPNTTEHHIKWIELLFLPDGAKfpvhigRTEFNTHGestqgp 80 
                                       79***********76...7899***********************************************999***** PP

                                       .......ESEEEEEEEESSSEEEEEEEEETTTEEEEEE CS
                   Desulfoferrodox  66 .......epevtftvklkkekklvalsyCnlHGlWese 96 
                                              ep+++f++k++k +kl+a+s+Cn+HGlW+se
  gi|488600738|ref|YP_007907209.1|  81 ntstvytEPTAVFRFKTEKPGKLIAVSFCNIHGLWKSE 118
                                       ******99***************************985 PP

>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.6e-07    0.0069     145     186 ..      78     118 ..      63     121 .] 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.6e-07
                                       ---TT-TTTS--HHHHHHHHHHHH-EEEE--SS---SS--SS CS
                     F_bP_aldolase 145 dgvvaeeklyTdpeeaeefveetgvdalAvaiGnvHGvykpk 186
                                       +g  +++++yT+p  + +f +e   +++Av++ n+HG  k++
  gi|488600738|ref|YP_007907209.1|  78 QG-PNTSTVYTEPTAVFRFKTEKPGKLIAVSFCNIHGLWKSE 118
                                       22.33455************9999*************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 745.01
//
Query:       gi|488600739|ref|YP_007907210.1|  [L=118]
Description: hypothetical protein Asulf_01219 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-24   85.3   0.4    3.6e-24   85.1   0.4    1.0  1  Response_reg  Response regulator receiver domain
     0.0051   16.2   0.1     0.0064   15.9   0.1    1.1  1  MTD           methylene-5,6,7,8-tetrahydromethanopterin dehyd
  ------ inclusion threshold ------
      0.049   13.7   0.1       0.16   12.0   0.1    1.8  2  B12-binding   B12 binding domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.4     6e-28   3.6e-24       1     111 [.       3     109 ..       3     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 6e-28
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vlivdDd  +re+lr +l   +y +v ea++g+ea++++k+ k+d++++D  mp mdG+ ++++i e dp+ +v++l
  gi|488600739|ref|YP_007907210.1|   3 VLIVDDDSGIREILRLMLS--EY-TVLEASNGDEAVKHYKNFKPDVVIMDAVMPVMDGVAATRRILEIDPNAKVVAL 76 
                                       8*****************9..78.89*************************************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ta+ + + a e+l+ag ++ l Kpf+++ +l+++
  gi|488600739|ref|YP_007907210.1|  77 TAYYT-TKAREMLEAGSVEALEKPFSKKIILEIV 109
                                       **997.8899****************99988876 PP

>> MTD  methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.1e-06    0.0064      22     104 ..       7      90 ..       2      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                                       STTS--SSEEEEEEEEET--SHHHHHHHHHHHHHH--SEEEEE-S-TTSHHHHHHHHHHH.HSSS-EEEEEEGGGGG CS
                               MTD  22 DeradRedievrvvgsgaklkkeeveevveklkefdpdlvivisPnaaapgptkarells.ekdvpaivisDapgkk 97 
                                       D+ +   +i   +++  + l+ ++ +e+v++ k+f+pd+vi+ +  + + g ++ r +l+ + +  ++ ++   ++k
  gi|488600739|ref|YP_007907210.1|   7 DDDSGIREILRLMLSEYTVLEASNGDEAVKHYKNFKPDVVIMDAVMPVMDGVAATRRILEiDPNAKVVALTAYYTTK 83 
                                       4444444777788899999999************************************9624456677777778888 PP

                                       GHHHHHH CS
                               MTD  98 ekdelee 104
                                       +++ le+
  gi|488600739|ref|YP_007907210.1|  84 AREMLEA 90 
                                       8888776 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.8e-05      0.16      37      99 ..      27      88 ..       9      95 .. 0.78
   2 ?    4.8   0.0    0.0047        28      51      70 ..      70      89 ..      59     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                       B12-binding 37 nven.edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetl 99
                                      +++n ++ v+  + +kpdvv + a +   +++v+++ + l +i+p++kvv+  a  ++ ++e+l
  gi|488600739|ref|YP_007907210.1| 27 EASNgDEAVKHYKNFKPDVVIMDA-VMPVMDGVAATRRIL-EIDPNAKVVALTAYYTTKAREML 88
                                      445579999999************.999999999988876.89999999975555555555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0047
                       B12-binding 51 kpdvvglSalltsqleavke 70
                                      ++ vv+l+a++t++ +++ e
  gi|488600739|ref|YP_007907210.1| 70 NAKVVALTAYYTTKAREMLE 89
                                      7888*********9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 763.42
//
Query:       gi|488600740|ref|YP_007907211.1|  [L=144]
Description: hypothetical protein Asulf_01221 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 786.00
//
Query:       gi|488600741|ref|YP_007907212.1|  [L=336]
Description: hypothetical protein Asulf_01222 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.5  14.6      0.011   16.0   6.6    2.3  2  Bactofilin  Polymer-forming cytoskeletal
  ------ inclusion threshold ------
       0.54    8.8  13.2        1.2    7.7  13.2    1.5  1  FapA        Flagellar Assembly Protein A
        5.1    7.2   0.0        5.1    7.2   0.0    2.9  3  ETRAMP      Malarial early transcribed membrane protein (ETRA


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   4.1    0.0017        10      15      72 ..      56     115 ..      37     118 .. 0.81
   2 !   16.0   6.6   1.8e-06     0.011      10      79 ..     101     173 ..      99     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0017
                        Bactofilin  15 vegdlridGkveGdi.eakgklvvgeggkvegn.ika.eevvvaGtvkGnveaee.kvelkk 72 
                                       + g + +d+ v+Gd+  a+g++ v +  kv g+ i a ++v+++G v G++ + + +++++k
  gi|488600741|ref|YP_007907212.1|  56 SGGRVIVDAPVSGDLiVAGGEVEVLD--KVAGDlIAAgGKVDLRGDVGGKLIVAGgSLRIEK 115
                                       558899999999*9977788888855..789997777788*********9988876887776 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-06
                        Bactofilin  10 kGeleve.gdlridGkv.eGdieakgklvvgeggkvegnika..eevvvaGtvkGnveaeekvelkktakveGd 79 
                                        G+l v  g+lri+ +v +  i ++g++v+g++++++g++ +  ++++ aG ++Gn+++    ++++++ v+G+
  gi|488600741|ref|YP_007907212.1| 101 GGKLIVAgGSLRIEKNVgKFVIASGGEVVIGKNSRIDGDVFVagGKIENAGIIEGNITVF-GKTFENKGFVKGE 173
                                       5776655599***99996666799***************77645779999*********9.6678888888886 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  13.2    0.0002       1.2     218     318 ..      57     152 ..      35     182 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0002
                              FapA 218 sgditikGvvesatieAggnItikgGiigkgkskikAggnisakfv.enaeveaggdievekqilnslikaggkiiv 293
                                       +g++ +   v++  i Agg++++   ++g     i Agg++  +    +  + agg++ +ek++ +  i +gg++++
  gi|488600741|ref|YP_007907212.1|  57 GGRVIVDAPVSGDLIVAGGEVEVLDKVAG---DLIAAGGKVDLRGDvGGKLIVAGGSLRIEKNVGKFVIASGGEVVI 130
                                       45555555555555555555555555555...555555555555432444455555555555555555555555555 PP

                              FapA 294 ngrkgkivggnikalkevkakklGs 318
                                        g+++ i g    a+ ++++   G 
  gi|488600741|ref|YP_007907212.1| 131 -GKNSRIDGDVFVAGGKIENA--GI 152
                                       .44555555555555555544..22 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00085       5.1       1      44 [.      11      51 ..      11      93 .. 0.76
   2 ?    0.1   2.4      0.15   8.8e+02      56      75 ..     232     251 ..     225     253 .. 0.73
   3 ?   -1.7   4.5      0.53   3.1e+03      56      77 ..     244     265 ..     240     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00085
                            ETRAMP  1 MKvtkvllffafLlavnlltpeslcdevnkkkekakkaikkidd 44
                                      M+++ ++ +++  l++ +l+ ++ + ev+     ++  ik+ +d
  gi|488600741|ref|YP_007907212.1| 11 MNIMEIAKLLFAVLIITVLAIPATSVEVK---SGDQVHIKQPKD 51
                                      9*****55555555566666666665555...355555665555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                            ETRAMP  56 iiistiatalallvasalGl 75 
                                       i i + a++++ll+ s++G+
  gi|488600741|ref|YP_007907212.1| 232 IAIIVSAIIVVLLFISVIGI 251
                                       45666666777777788886 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.53
                            ETRAMP  56 iiistiatalallvasalGlgi 77 
                                       ++is+i++  all+ sa+ + i
  gi|488600741|ref|YP_007907212.1| 244 LFISVIGIPSALLILSAFTIAI 265
                                       6799999999999999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1347  (0.0751297); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2140.05
//
Query:       gi|488600742|ref|YP_007907213.1|  [L=201]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-18   67.6  16.1      4e-09   36.7   7.4    2.0  2  VIT1      VIT family
     0.0093   16.1   5.3     0.0093   16.1   5.3    2.2  2  DUF3792   Protein of unknown function (DUF3792)
  ------ inclusion threshold ------
      0.073   12.4   0.1      0.091   12.1   0.1    1.1  1  ApoL      Apolipoprotein L


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   2.3     1e-12   6.1e-09       2      69 ..      32      99 ..      31     123 .. 0.89
   2 !   36.7   7.4   6.7e-13     4e-09     136     209 ..     120     192 ..     100     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1e-12
                              VIT1  2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkr 69
                                      r +v+G+ DG++++++l++G   ++  ss++++ aG+a  lA  iS g G+Y + + e+ +  +e++r
  gi|488600742|ref|YP_007907213.1| 32 RYFVIGFFDGVLTILGLIMGAHLSGEASSQLIVSAGIATGLALGISSGWGAYEAERVEQTISLREKQR 99
                                      679******************999999*******************************9999888777 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 6.7e-13
                              VIT1 136 kaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaa 209
                                        + l+ +++ +  ++iPl+py+f++    al+ +ia+ l+ l+++Ga+ ++++++++++s+lrm++ G+++ ++
  gi|488600742|ref|YP_007907213.1| 120 ISSLVHGIAPIPAAIIPLIPYMFLP-SEVALIPAIAIGLVSLFIVGAFMGRISKKNIIISGLRMAFAGIATLII 192
                                       5677778888889************.899***************************************988765 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   2.3      0.12   7.2e+02      44      74 ..      43      73 ..      28      81 .. 0.48
   2 !   16.1   5.3   1.5e-06    0.0093      30      85 ..     141     196 ..     116     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                           DUF3792 44 ililsvfigGflagkkakkkgllnGllvGll 74
                                      ++il++++g+ l+g  + +     G+++Gl+
  gi|488600742|ref|YP_007907213.1| 43 LTILGLIMGAHLSGEASSQLIVSAGIATGLA 73
                                      3334444444444443333333333333333 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-06
                           DUF3792  30 tslsekvlsililiililsvfigGflagkkakkkgllnGllvGllyflillllsll 85 
                                       + l+++v  i +++i ++s+fi G ++g+++kk+ +++Gl ++++ ++ l+++++l
  gi|488600742|ref|YP_007907213.1| 141 MFLPSEVALIPAIAIGLVSLFIVGAFMGRISKKNIIISGLRMAFAGIATLIIVTVL 196
                                       4477777778899*****************************99999998888766 PP

>> ApoL  Apolipoprotein L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.5e-05     0.091     106     166 ..      37     103 ..      13     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                              ApoL 106 gavSgiLtilGlaL.APvtaGlSLvL..s...atGlgLGaaaavTsvstsiveessnssakaeasrl 166
                                       g   g+LtilGl + A ++ ++S  L  s   atGl LG+ +      ++ ve++ +   k++a  +
  gi|488600742|ref|YP_007907213.1|  37 GFFDGVLTILGLIMgAHLSGEASSQLivSagiATGLALGISSGWGAYEAERVEQTISLREKQRALLI 103
                                       7788********9956677778866633344479********************9999999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1320.34
//
Query:       gi|488600743|ref|YP_007907214.1|  [L=100]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-31  108.8   1.0    2.3e-31  108.7   1.0    1.0  1  DUF5611   Domain of unknown function (DUF5611)


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   1.0   1.3e-35   2.3e-31       1     103 []       1      97 [.       1      97 [. 0.97

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 1.3e-35
                                       -EEE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHH CS
                           DUF5611   1 mreYkiKrGfkkeeeerlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaald 77 
                                       mr+Yk+KrG+k++  erl+e +e+yf ge+++eg++++++fgai +l++++  ++k l+v+ ++++  + ++++al+
  gi|488600743|ref|YP_007907214.1|   1 MRKYKFKRGYKPTP-ERLEEHIEKYF-GEFKREGEVYITKFGAIGELRMWF--EGKLLCVESKTNP--NVAEDIALN 71 
                                       9*************.***********.8***********************..***********76..4899***** PP

                                       HHHHHHHHHHHHH---GGGHHHHH-- CS
                           DUF5611  78 tvkkfndFLeeaTGydaKeRkkkakk 103
                                       t k++n+FLe++TGy+aKeR+k++kk
  gi|488600743|ref|YP_007907214.1|  72 TLKTYNRFLEDLTGYTAKERQKMLKK 97 
                                       ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 688.84
//
Query:       gi|488600744|ref|YP_007907215.1|  [L=297]
Description: LPPG:FO 2-phospho-L-lactate transferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  161.5   0.0    2.9e-47  161.3   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 !  161.3   0.0   1.6e-51   2.9e-47       3     260 ..       4     266 ..       2     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 1.6e-51
                                       EEE-CHHHHHHHHHHCCSSCEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C..........HH CS
                           UPF0052   3 vlgGGtGlskllrglkevtaeltavvtvaDdggssGelrrelgllaigDirnvlval...idder..........ll 66 
                                       +l+GGtG++kl+ g+ke+ ++  +vv++a+d++ sG         +++Di++v++ l   id+ +          ++
  gi|488600744|ref|YP_007907215.1|   4 ILSGGTGTPKLIWGMKEIYDDFFVVVNTAEDVWVSG-------NKICPDIDSVIYVLsemIDTSKwwgikddsfiTH 73 
                                       79**********************************.......9*************77777777999999989989 PP

                                       HHHCH-B-SS.....SSSSTT-BHHHHHHHHHHHHHS-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-EEE CS
                           UPF0052  67 eeLfqyRfkg.....dgdlaghslgnllLaalaeltgsleeaiealskilkvrgrvlPatddpvelsaeledGeeit 138
                                       ++L ++ +++     d d a+h+ ++ lL+       +l +a+++l+k+++++++v+P+++++v++ +e++dG++  
  gi|488600744|ref|YP_007907215.1|  74 NQLRRLGVDEgmmigDLDRATHIARTELLKR-----MDLVNATKELRKRFGIKQDVYPMCNEEVSTYIETADGRMHF 145
                                       99999966669999888**************.....89************************************666 PP

                                       STTTGGGG-S...-EEEEEEESTT-.---HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE- CS
                           UPF0052 139 geskisearklkapikrvflepega.eaapevleaikeAdlivlgpGslytSiiPiLlvpgiaealreskakkvlvs 214
                                       +e ++ ++++  +++k vf+e  ++  +++ev +++keA+++++gp++++tSi+Pi+ v+g +e lre  + +v+vs
  gi|488600744|ref|YP_007907215.1| 146 QEFWVVRKGE--PEVKGVFIENIDKaVIPEEVEKRLKEAEAVIIGPSNPITSIGPIISVRGYREILRE--KFVVAVS 218
                                       *****55555..99***8887766625888999*********************************55..9****** PP

                                       -SB--TTTSTT-BHHHHHHHHHHCH-.....SS....S........-SEEEEE-S---H CS
                           UPF0052 215 nimtqkGetdgfsvsdhvkaieravg.....kgvakay........vdavlvntsevpe 260
                                       +i++        s+s+++ + ++a+g     +              +d++++++++++ 
  gi|488600744|ref|YP_007907215.1| 219 PIIG------SRSFSGPAGKFMKALGyevssR-----GvvdiyqefLDVLVIDEEDFDF 266
                                       ***9......****************655552.....2345557779999999995443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1913.64
//
Query:       gi|488600745|ref|YP_007907216.1|  [L=325]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   24.5   0.4    5.8e-05   23.3   0.4    1.7  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.18   11.4   0.0    1.1  1  DUF4559       Domain of unknown function (DUF4559)


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 !   23.3   0.4   6.4e-09   5.8e-05       4      81 ..     104     179 ..      92     208 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.4e-09
                                       HHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEE CS
                      NTP_transf_2   4 lleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrek 78 
                                       +++++ + +   v k+ ++GS+  G+  ++SD+D++ +++ +++     +++ k++ ++ +l+e     + +++++ 
  gi|488600745|ref|YP_007907216.1| 104 VKRIVDFFNTipVDKMGVTGSRLIGLESEDSDVDFVMYGSYWFK----GREKIKRSIERGVLKEPSEETWNFIFEKR 176
                                       5566666666669*************************999965....34455555555444444444444443333 PP

                                       CCC CS
                      NTP_transf_2  79 led 81 
                                       + +
  gi|488600745|ref|YP_007907216.1| 177 KVN 179
                                       333 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     2e-05      0.18     152     201 ..      52     102 ..      48     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                           DUF4559 152 klMHSpdlkvss.qdmkeymkkilrLledlktvpeleeaeeaieellkilk 201
                                       klMHS  +++++ ++m++y +k+  +l    ++ e+ + ee+i e+ k  +
  gi|488600745|ref|YP_007907216.1|  52 KLMHSNAIEFAKkENMEYYNSKLGIFLIPNSKISEVYKPEERISEIVKSDD 102
                                       79********86257999999**99999777**************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1866.74
//
Query:       gi|488600746|ref|YP_007907217.1|  [L=192]
Description: putative archaeal Zn-finger protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   18.4   0.2     0.0012   18.4   0.2    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
  ------ inclusion threshold ------
      0.054   13.8   0.1       0.65   10.3   0.1    2.3  1  MlaD             MlaD protein
      0.091   12.2   0.2       0.16   11.4   0.2    1.4  1  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
       0.13   12.5   0.3       0.25   11.7   0.3    1.5  1  DUF3268          zinc-finger-containing domain
        0.3   10.7   3.1       0.92    9.1   0.2    2.2  2  RecR             RecR protein
       0.32   11.3   2.6       0.76   10.1   2.6    1.6  1  C1_2             C1 domain
       0.53   10.3   8.8       0.51   10.3   1.1    3.9  5  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a


Domain annotation for each model (and alignments):
>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.6      0.12     3e+02       5      12 ..       2       9 ..       1      11 [. 0.89
   2 !   18.4   0.2   4.7e-07    0.0012       2      19 ..      20      37 ..      19      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                      -EEE-TTT CS
                   Desulfoferrod_N  5 evYkCevC 12
                                       vY C vC
  gi|488600746|ref|YP_007907217.1|  2 KVYYCDVC 9 
                                      79****** PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.7e-07
                                      -TT-EEE-TTT--EEEEC CS
                   Desulfoferrod_N  2 eklevYkCevCGniVeVl 19
                                      ek++ YkCe CGn V+++
  gi|488600746|ref|YP_007907217.1| 20 EKTNLYKCEECGNYVTIT 37
                                      67899**********997 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00025      0.65      25      43 ..      80      97 ..      58     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                              MlaD 25 GvtvGrVtsitldpdtrrv 43
                                      G ++G+Vtsi+l +d++r+
  gi|488600746|ref|YP_007907217.1| 80 GFKIGEVTSIEL-EDGKRI 97
                                      99**********.555554 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   6.3e-05      0.16      27      60 ..      18      55 ..       3      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
                       Vps36-NZF-N 27 pnastplPpClaCG....vkpdlelikksikasasskk 60
                                      ++++t+l +C+ CG    + p+ e++ ++i++s+ +++
  gi|488600746|ref|YP_007907217.1| 18 VREKTNLYKCEECGnyvtITPEKEIVVNAIISSEGESE 55
                                      3789**********99999************9987665 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   9.8e-05      0.25      25      52 ..      19      46 ..       2      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                           DUF3268 25 skgkllylCpkCdayvgvhkgtkiplGt 52
                                      ++++ ly C++C+ yv + ++++i +  
  gi|488600746|ref|YP_007907217.1| 19 REKTNLYKCEECGNYVTITPEKEIVVNA 46
                                      456689**************99987655 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3     0.048   1.2e+02      15      24 ..       2      11 ..       1      17 [. 0.77
   2 ?    9.1   0.2   0.00036      0.92       8      25 ..      16      33 ..      14      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.048
                                      H-EE-TTT-- CS
                              RecR 15 kvrhCsrCgn 24
                                      kv +C +C+ 
  gi|488600746|ref|YP_007907217.1|  2 KVYYCDVCRE 11
                                      6789999985 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00036
                                      HHHHHHHH-EE-TTT--E CS
                              RecR  8 aLqeakekvrhCsrCgnl 25
                                      +L++ k+++  C++Cgn+
  gi|488600746|ref|YP_007907217.1| 16 SLVREKTNLYKCEECGNY 33
                                      7888899**********8 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.6    0.0003      0.76      20      40 ..       5      33 ..       2      35 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                              C1_2 20 nCsaCgrk.....idgff.....YsCseC.df 40
                                       C++C+++     +   +     Y+C+eC ++
  gi|488600746|ref|YP_007907217.1|  5 YCDVCREStmhslV---RektnlYKCEECgNY 33
                                      7*******876663...033479******556 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.19   4.9e+02      22      38 ..      28      44 ..      18      52 .. 0.75
   2 ?   10.3   1.1    0.0002      0.51      17      36 ..      61      83 ..      58      87 .. 0.83
   3 ?   -0.8   0.0      0.61   1.6e+03      30      41 ..      90     102 ..      80     113 .. 0.57
   4 ?    0.3   0.1      0.28   7.3e+02      20      39 ..     140     157 ..     135     163 .. 0.72
   5 ?   -1.5   0.0         1   2.7e+03      22      28 ..     169     175 ..     169     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                                      EC.TCEEEEEECTTCCCC CS
                    MazE_antitoxin 22 re.Gdevelevdgdkiil 38
                                      +e G+ v+++++++ i++
  gi|488600746|ref|YP_007907217.1| 28 EEcGNYVTITPEKE-IVV 44
                                      678999*****995.443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
                                      HHC..CEECTCEEEEEECTT.CC CS
                    MazE_antitoxin 17 fel..gireGdevelevdgd.ki 36
                                       +   ++++Gde+++ev+++ ki
  gi|488600746|ref|YP_007907217.1| 61 LKEgeNVEKGDELVVEVEEGfKI 83
                                      555569************99776 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.61
                                       EECTT.CCCCCCC CS
                    MazE_antitoxin  30 evdgd.kiilrpl 41 
                                       e +++ +i l+p 
  gi|488600746|ref|YP_007907217.1|  90 ELEDGkRIDLSPS 102
                                       3333346666554 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.28
                                       CEECTCEEEEEECTTCCCCC CS
                    MazE_antitoxin  20 gireGdevelevdgdkiilr 39 
                                       +ir+G ++ +e +  +  ++
  gi|488600746|ref|YP_007907217.1| 140 EIRVGEDIDIENK--RFRIT 157
                                       6999999999766..35555 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1
                                       ECTCEEE CS
                    MazE_antitoxin  22 reGdeve 28 
                                       reGd+v+
  gi|488600746|ref|YP_007907217.1| 169 REGDTVM 175
                                       79***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1465.09
//
Query:       gi|488600747|ref|YP_007907218.1|  [L=74]
Description: hypothetical protein Asulf_01229 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.17   11.8   0.0    1.2  1  KH_7      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 ?   11.8   0.0   9.7e-06      0.17       7      40 ..      14      48 ..       8      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.7e-06
                              KH_7  7 lkekieekl.PkevkitdveFEGPelViYtknpkl 40
                                       +e i + l P++++  + +FEG e+++ +k pk+
  gi|488600747|ref|YP_007907218.1| 14 FAEIISRALkPDDTQWNETTFEGDEIILRVKTPKI 48
                                      55666655449*****************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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 0.30s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 490.33
//
Query:       gi|488600748|ref|YP_007907219.1|  [L=434]
Description: Single-stranded DNA-specific exonuclease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-18   65.1   0.0      4e-17   62.9   0.0    2.2  2  DHHA1            DHHA1 domain
     0.0004   20.6   0.1    0.00091   19.4   0.1    1.6  1  DHH              DHH family
  ------ inclusion threshold ------
       0.13   11.1   0.0        0.2   10.4   0.0    1.2  1  Late_protein_L1  L1 (late) protein


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       0.7   4.2e+03     123     135 ..     205     217 ..     202     252 .. 0.70
   2 !   62.9   0.0   6.6e-21     4e-17      11     137 ..     301     427 ..     295     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.7
                                       EHCHHHHHHHHHH CS
                             DHHA1 123 paekleealeale 135
                                       ++++lee+le+++
  gi|488600748|ref|YP_007907219.1| 205 KEDELEEFLEKVR 217
                                       4556666666654 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 6.6e-21
                                       HHHHHHCHHHHHHHHHHHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEE CS
                             DHHA1  11 lekeleelkealaklkaeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkv 85 
                                       l k  e ++++l++l+  e++++ eevk g +  +  +++   +g ++++ ++      + p i++ +k +   +kv
  gi|488600748|ref|YP_007907219.1| 301 LDKGYEIWRKFLTELLD-EIVKRKEEVKeGECMRYLVMDNAPTTGPIATVLSRYIF--SDrPFIAVNIKRD--VAKV 372
                                       55555558999999875.66677788885777777777555555******999999..8846666666655..9*** PP

                                       EEEESSH...SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHH CS
                             DHHA1  86 sarskkd...gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeea 137
                                       s r++ +    vd+ge++++aa+++gg+GGGH+ AaGa+ip++++e+++++++++
  gi|488600748|ref|YP_007907219.1| 373 SSRTTMRmseIVDLGEIMNKAAKAVGGRGGGHRVAAGANIPPDRVEDFIKEVDRL 427
                                       *****99********************************************9976 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.5e-07   0.00091       7      71 ..      25     115 ..      21     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-07
                                       ECSSSHHHHHH.HHHHHH............................CECS--TCGGCGCCHHCCCSEEEEEEE-S-- CS
                                       xxxxxxxxxxx.xxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   7 hknpDtDsigS.aialan............................llvDhneksqavegeakeeaedviiiDHHrl 54 
                                       + ++D+D+i++ +i+ +                             +l+D+++   + +    + + d i+iDHH +
  gi|488600748|ref|YP_007907219.1|  25 FTHYDVDGITAgSIMAKSllrfnkkfhlsflnglnnginyekddlvILLDMGSGYPDIVS---SIEADFIVIDHHFP 98 
                                       789********888887788888888888888888888888888888*****99999987...8999********98 PP

                                       -SS---SS--EEEE-SS CS
                                       xxxxxxxxxxxxxxxxx RF
                               DHH  55 geefetlapilflnepv 71 
                                         +++  + ++ +n+++
  gi|488600748|ref|YP_007907219.1|  99 LGKIDAQSSFVHVNPHL 115
                                       77555554444444443 PP

>> Late_protein_L1  L1 (late) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.4e-05       0.2     291     334 ..      33      76 ..      18      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.4e-05
                                       EEE-SEEESTT-SSSSEEE-SS-SSSSSSBEGGGEEEEEEEEST CS
                   Late_protein_L1 291 tpsGslvssdaqlfnrpyWlqraqGknnGilWenqlfvtvvDnt 334
                                        ++Gs+++     fn+ + l+   G nnGi +e++ +v ++D  
  gi|488600748|ref|YP_007907219.1|  33 ITAGSIMAKSLLRFNKKFHLSFLNGLNNGINYEKDDLVILLDMG 76 
                                       6789****99999********************99999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 2441.33
//
Query:       gi|488600749|ref|YP_007907220.1|  [L=621]
Description: carbon-monoxide dehydrogenase, catalytic subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-137  457.4   0.6   7.2e-137  457.2   0.6    1.0  1  Prismane  Prismane/CO dehydrogenase family


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.2   0.6    4e-141  7.2e-137       2     510 ..      48     601 ..      47     602 .. 0.97

  Alignments for each domain:
  == domain 1  score: 457.2 bits;  conditional E-value: 4e-141
                                       EE-SSTCT-ECSC.S.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHTSTTTB-SHHHHHHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane   2 fCrqCengpCrit.knkrGvCGkdadtavardlliavlkgaaahaahareladtliakalfktltnvnfddekklkr 77 
                                        C++C++gpCri+ kn++G+CG+da+++v+r+++   + g+ a++ ha e+a+tl+a+a++kt   ++++d +klk+
  gi|488600749|ref|YP_007907220.1|  48 SCQLCSMGPCRISdKNPHGACGIDAAGMVMRNFVHKNMLGTEAYTYHAVEAAKTLKATAEGKT--PFEIKDVDKLKF 122
                                       6*************************************************************9..************ PP

                                       HHHHHCHHHCCSSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane  78 laealgieeelkdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlgyadeevveflaktlagl 154
                                       +a +lgie    d++e+a+kva+++++dls+ e  + ++++ ++p ++k+l+++++i+++++ +ev ++ ++ ++++
  gi|488600749|ref|YP_007907220.1| 123 FASKLGIEGG--DVNEIAKKVADYVIADLSSVE--QSKLVEIFAPDKRKELWKDLGIFPNGVFHEVLTVGSSSMTNV 195
                                       ******9955..5*****************885..9***************************************** PP

                                       TSTHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTC CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 155 esdpldllskalrlGlld.lkgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqtegkg 230
                                       +s++++l +k++ +++++ ++++++l+ ++++lfGtP+p+++ ++lg+ld+d+vnI+v GH++   ++l++ +e+++
  gi|488600749|ref|YP_007907220.1| 196 DSNYVSLAKKSMAMSIATcMSAQIALEFIQDILFGTPKPHESFADLGILDPDYVNIAVDGHEPFVGAALIKLAESEE 272
                                       ***************************************************************************** PP

                                       CCCCCC.....GCCCCCCHHHHHHHHHCC....EEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCE CS
                                       xxxxxx.....xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 231 lnvyth.....gemLpghcctalklkyrh....lvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktr 298
                                       ++++++     g++++g + t+++l +r     ++g+vGn++ qe a++tg+vd++  d+nC +p ++++++ y+ +
  gi|488600749|ref|YP_007907220.1| 273 IQNKAKeagakGLRIIGFIETGQELIQRFdspvFAGIVGNWIVQEFALATGCVDVFAADMNCALPTIPEYQR-YGVK 348
                                       ************************6666689**************************************777.**** PP

                                       EEEECTTB-.TTSEEE-..-CTTCHHHHHHHHHHHHCCHCCTTCGG.-...........................HH CS
                                       xxxxxxxxx.xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........................xx RF
                          Prismane 299 littsevak.pgakhie..eeekadkdaseiiekAielakareekkve...........................id 345
                                       ++ +s+ ++  g+++    e+ek ++ a+++i++Ai+++k+r+++k                             +d
  gi|488600749|ref|YP_007907220.1| 349 IVPVSKLVRfRGIDEGLdyEPEKVEEIARKLIDMAIDNFKQRDKSKAVriekkqkivvgfspeaileavgeievlLD 425
                                       *********999887644788999******************884444688999*********************** PP

                                       HHHTTSS-EEEEE-B---TTCGCC..HHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHC........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                          Prismane 346 aiksGtIkgvvlvvGCdnakkgrd..yytelakelikrdvlvltaGCakyalnklglgtieaaelageg........ 412
                                       aiksG+Ikg+v++v+C++ k+g +  +++++akelikrd+lvl++GC++ al+ +gl++++a + age+        
  gi|488600749|ref|YP_007907220.1| 426 AIKSGAIKGIVALVSCTTLKNGPHdlNTVTIAKELIKRDILVLSLGCGNAALQVAGLTSMDAVSEAGENlkavcekl 502
                                       **********************999******************************************99******** PP

                                       .EESEEEEESCCCHHHHHHHHHHHHHHTTSSGGGSSEEEEECC--SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 413 .iPrvLdvGsCvdnyrivvialklaealgvdindLplaalalewyeqKAvailltllalGinihlgptlpafgspnv 488
                                        iP+vL++G+C+d++r++ +   +a+algvdi++Lp+a+ a+e++eqKA++++++++a+G+ +h++p++p++gs+ v
  gi|488600749|ref|YP_007907220.1| 503 nIPPVLSFGTCTDTGRAAYLLRVVADALGVDIPQLPVAVTAPEYMEQKATIDAVFAVAYGLVTHVSPVPPVTGSADV 579
                                       ***************************************************************************** PP

                                       HHHHHCHHHHHHCEEEECHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 489 lkvlvedfedriggivtveedp 510
                                       +k+l+ed+e+ +gg++ veedp
  gi|488600749|ref|YP_007907220.1| 580 VKLLTEDIEKVTGGKIVVEEDP 601
                                       *********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3823.76
//
Query:       gi|488600750|ref|YP_007907221.1|  [L=360]
Description: hypothetical protein Asulf_01232 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.8   0.1      0.028   14.1   0.1    1.2  1  DUF2913     Protein of unknown function (DUF2913)
      0.035   14.5   0.6        0.1   13.0   0.1    2.0  2  RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N 
      0.044   13.5   0.1       0.09   12.5   0.1    1.5  1  GlutR_N     Glutamyl-tRNAGlu reductase, N-terminal domain


Domain annotation for each model (and alignments):
>> DUF2913  Protein of unknown function (DUF2913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.8e-06     0.028      54     148 ..     147     242 ..     143     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-06
                           DUF2913  54 vakdLkrwqkqgrskGknaqLkalleriseqykevaeeekeldskleallaeleekew.vvitdeevvdklkldsdg 129
                                       + k+++r+ + +rs  + ++L+++l ++s++  ++++   + ++  e++++++   e+     d   +dk++ ++d 
  gi|488600750|ref|YP_007907221.1| 147 ILKQVTRISESARSVNTVDGLENTLFEVSKIQMSFFKRFSTFKDINEEIFSSIVRFETlARKLDGWFNDKIQEFRDF 223
                                       78999********************************99999888888888888888757778899999******** PP

                           DUF2913 130 qeslvvcakqleqhfdeeg 148
                                        +slv  ++++eq ++   
  gi|488600750|ref|YP_007907221.1| 224 HQSLVYYESKFEQTLNGIR 242
                                       *************998555 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.66   3.9e+03      74      90 ..      11      27 ..       6      32 .. 0.80
   2 ?   13.0   0.1   1.7e-05       0.1       2      94 ..     121     220 ..     120     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.66
                        RasGEF_N_2 74 qelnfveeeldkWiekk 90
                                      +e++ v  e+++W+e k
  gi|488600750|ref|YP_007907221.1| 11 DEMEDVLGEIKSWFEVK 27
                                      56778999*****9865 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.7e-05
                        RasGEF_N_2   2 fekWgiellvnqLydqsrevvaaaleiLeeacddkeslevlvelkpslqhlgeigslLllkllstssGfkylqel.. 76 
                                       +e++ ie+ ++q++ + +++++   eiL++++   es++++  +    + l    s + + +++  s fk ++e+  
  gi|488600750|ref|YP_007907221.1| 121 IEAFKIEVTLRQCNLSVESISKEETEILKQVTRISESARSVNTVDGLENTLF-EVSKIQMSFFKRFSTFKDINEEif 196
                                       6899***************************887777776666444444442.348899*************9999* PP

                        RasGEF_N_2  77 ......nfveeeldkWiekkneeY 94 
                                             +++ ++ld W+++k +e+
  gi|488600750|ref|YP_007907221.1| 197 ssivrfETLARKLDGWFNDKIQEF 220
                                       *9**999***********998876 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 ?   12.5   0.1   1.5e-05      0.09      95     133 ..     135     173 ..      85     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                           GlutR_N  95 sGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfq 133
                                        + +S+   E++Il+Qv +  e a++ +t++   ++lf+
  gi|488600750|ref|YP_007907221.1| 135 LSVESISKEETEILKQVTRISESARSVNTVDGLENTLFE 173
                                       57899999**********************999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1227  (0.0684366); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2138.86
//
Query:       gi|488600751|ref|YP_007907222.1|  [L=62]
Description: hypothetical protein Asulf_01233 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-06   28.7   2.8    1.5e-06   28.7   2.8    1.0  1  Rubrerythrin  Rubrerythrin
    1.6e-05   24.9   2.9    1.9e-05   24.6   2.9    1.1  1  Ferritin      Ferritin-like domain
  ------ inclusion threshold ------
      0.047   13.9   0.3      0.058   13.6   0.3    1.1  1  Ferritin_2    Ferritin-like domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   2.8   2.5e-10   1.5e-06       1      56 [.       5      57 ..       5      62 .] 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.5e-10
                                      HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Rubrerythrin  1 eiLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnkllekl 56
                                      eiL+kA+  E +a++ Y  + + a+   p++ael+  l+ +EreH ++ln+  +++
  gi|488600751|ref|YP_007907222.1|  5 EILDKALELEKEAIEEYLKMKKDAD---PETAELLDFLISQEREHIRMLNERKKAI 57
                                      89***********************...*********************9976665 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.9   3.2e-09   1.9e-05      81     135 ..       3      53 ..       2      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.2e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  81 veevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleal 135
                                       v+e+l +ale+ek+++e++ ++ + a+    p ta++l+ ++ ++ eh+++l++ 
  gi|488600751|ref|YP_007907222.1|   3 VLEILDKALELEKEAIEEYLKMKKDAD----PETAELLDFLISQEREHIRMLNER 53 
                                       89*******************999887....66*******************985 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   9.8e-06     0.058       2      59 ..       3      52 ..       2      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.8e-06
                        Ferritin_2  2 dvdiLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflka 59
                                       ++iL  Al lE  +++ Y ++ +          d+e+ e++  + ++e++H+++l++
  gi|488600751|ref|YP_007907222.1|  3 VLEILDKALELEKEAIEEYLKMKK--------DADPETAELLDFLISQEREHIRMLNE 52
                                      579****************99977........689*******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); 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: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 404.53
//
Query:       gi|488600752|ref|YP_007907223.1|  [L=69]
Description: hypothetical protein Asulf_01234 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0078   14.6   0.4      0.008   14.6   0.4    1.0  1  DUF2194   Uncharacterised protein conserved in bacteria (DUF2
  ------ inclusion threshold ------
      0.024   14.4   0.1      0.082   12.7   0.1    1.7  1  FTH       FTH domain


Domain annotation for each model (and alignments):
>> DUF2194  Uncharacterised protein conserved in bacteria (DUF2194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.4     9e-07     0.008     382     414 ..      15      48 ..       7      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9e-07
                           DUF2194 382 aeeikrdy.gitdaeFYykvWWpdmkklseeyni 414
                                        ++i + + +++d  +Yy++WW d  ++s++  +
  gi|488600752|ref|YP_007907223.1|  15 VKKIMKVFeDVEDLIHYYNIWWADFSNYSQSDVV 48 
                                       5788999999*****************9987555 PP

>> FTH  FTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.1e-06     0.082      80     113 ..      20      54 ..       6      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.1e-06
                               FTH  80 lssfpiehlfhFeefei.kldkfsvedaikirdil 113
                                        + +++e+l+h  ++   ++++ s +d++ki d++
  gi|488600752|ref|YP_007907223.1|  20 KVFEDVEDLIHYYNIWWaDFSNYSQSDVVKIMDDM 54 
                                       333499*********999*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 446.56
//
Query:       gi|488600753|ref|YP_007907224.1|  [L=287]
Description: SPFH domain, Band 7 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-30  105.7   2.4    3.6e-30  105.3   2.4    1.1  1  Band_7    SPFH domain / Band 7 family
    1.8e-05   24.6   0.1    3.5e-05   23.6   0.0    1.5  1  Band_7_1  SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   2.4     4e-34   3.6e-30       2     176 ..      48     226 ..      47     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 4e-34
                            Band_7   2 iieegevgvvvrfGklsr.vlepGlhfilPfgrsvtvvsvrvqtldvsv..sltvptkDglpvtidvtviyrv.pdd 74 
                                       +i+  evgvv   G +++  l  Glh++ Pf+++v++++++  tl++     ++++t++glpv +d+ v+y++ p++
  gi|488600753|ref|YP_007907224.1|  48 VIDSTEVGVVKELGVVKDeELTEGLHIVKPFITEVIRMPIYEKTLEMVGerHIKALTSEGLPVYFDMAVQYKInPTK 124
                                       7999******8899999999*****************************************************9999 PP

                            Band_7  75 apklvaaveresanldnlirrvlesalrevisemtleellsn.reelaeelknelneqlrkyGvevldvritdidpp 150
                                       a+ +++++    +n++  +++ +++++r +++++++e+l+ + r +++ +++++l e+++ yG+ ++ v i++id+p
  gi|488600753|ref|YP_007907224.1| 125 ASDVYKSL----KNYEVWMESRIRAHARDMVAQYKAEDLYTEgRTKIQGDFEKKLSEEFEPYGIIITAVLIRNIDLP 197
                                       99999999....****************************8879********************************* PP

                            Band_7 151 pevaqalaakqaaeaea...qaeiaraea 176
                                       + v++a++ak++a +ea   q  i+++e 
  gi|488600753|ref|YP_007907224.1| 198 QSVESAIEAKIQAKQEAermQFVIQKEEL 226
                                       *****************888444444443 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.9e-09   3.5e-05     137     209 ..     139     210 ..     124     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.9e-09
                          Band_7_1 137 lkslivtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       + s i  +  d++a+ k   l  ++++ ++    +++l+ee++ yG+ ++++ i+ni+lp++ve a++++ ++
  gi|488600753|ref|YP_007907224.1| 139 MESRIRAHARDMVAQYKAEDLYTEGRT-KIQGDFEKKLSEEFEPYGIIITAVLIRNIDLPQSVESAIEAKIQA 210
                                       566777888888888887777666665.56677899*******************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1670.82
//
Query:       gi|488600754|ref|YP_007907225.1|  [L=66]
Description: hypothetical protein Asulf_01236 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       235  (0.0131073); 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:                         0  (0); expected 0.2 (1e-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: 521.49
//
Query:       gi|488600755|ref|YP_007907226.1|  [L=124]
Description: hypothetical protein Asulf_01237 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   1.8     0.0053   16.1   1.8    1.1  1  Rh5       Rh5 coiled-coil domain
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.21   11.7   0.0    1.2  1  HisKA     His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> Rh5  Rh5 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.8   5.9e-07    0.0053      31      97 ..      42     110 ..      32     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.9e-07
                               Rh5  31 tklenpeyefykksfkkdynsYkkkkkeyvnClknkfkklkkkindikssi..kkelykiscynsnkcn 97 
                                       + l +p+  fy k+++k+ ++Y++  k + + lk++ k+l ++++d+++     ++l++ +cy+ +  +
  gi|488600755|ref|YP_007907226.1|  42 DVLSYPLFIFYSKNVEKEKKKYRNLVKRLFEGLKKNLKTLRSIVEDVIKLGraAYSLKNLHCYDYEPVK 110
                                       6789999*****************************************975115778999998765554 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 ?   11.7   0.0   2.3e-05      0.21      30      63 ..      59      93 ..      37      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                                      ...T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                             HisKA 30 e.gklteelkeyletiesearrldhlvedlLdlsr 63
                                      e +k++  +k+++e ++++ + l+++ved+  l+r
  gi|488600755|ref|YP_007907226.1| 59 EkKKYRNLVKRLFEGLKKNLKTLRSIVEDVIKLGR 93
                                      24689999**********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1215  (0.0677673); expected 358.6 (0.02)
Passed bias filter:                      805  (0.0448993); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 824.04
//
Query:       gi|488600756|ref|YP_007907227.1|  [L=361]
Description: hypothetical protein Asulf_01238 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-107  357.2   0.0   8.3e-107  357.0   0.0    1.0  1  DUF917    Protein of unknown function (DUF917)


Domain annotation for each model (and alignments):
>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.0   0.0  4.6e-111  8.3e-107       2     350 .]       8     355 ..       7     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 357.0 bits;  conditional E-value: 4.6e-111
                                       GHHHHHHHHHHTTTT-SS-HHHHHHHHTT-SBTT--EEEE-GGG--SEE..EEEEEEE-HHH.HTT-SS-HH....H CS
                            DUF917   2 dlealatGaavLGtGGGGspysgylllrqaleegksvrvvsldelpddalvvvvgamGsptv.ieeklpsgdellea 77 
                                       +l+++ +G++vLGtGGGG+p++g  ++++ l++gk+  +  lde+pdd +v++++++Gs++   +e+++++ e  ++
  gi|488600756|ref|YP_007907227.1|   8 ELRDIIEGCTVLGTGGGGDPKEGWEMIEKELKSGKKFMLAGLDEVPDDGIVAMPYFVGSVSGkKVESVYEEGEGARS 84 
                                       689*******************************99************************97257999999****** PP

                                       HHHHHHHHT--EEEEE-SSSSCCHHHHHHHHHHHHT-EEESB-SSSS--SSGGGSHHHHTT----SEEEE-SSS-EE CS
                            DUF917  78 vealekllgrkidavislEiGGlNglvallaaaklglpvvDaDgmGRAfPelqqttfavagisltPlaladekgnvv 154
                                       ++ le+++g+++ +vis+E+GG+N++val++aaklglp+vD+D +GR++Pelq+tt+++ gi +tP+ +++  g+++
  gi|488600756|ref|YP_007907227.1|  85 YRLLEEYMGKEFWGVISTELGGANTAVALVTAAKLGLPIVDGDPAGRSVPELQHTTYYILGIGMTPFSVVTPLGDEI 161
                                       ***************************************************************************** PP

                                       EEEE.---HHHHHHHHHHCTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--...-SHHHHHHHHHH CS
                            DUF917 155 llkkaqsdkavErllRaalvemgsfagvaaypmtgaelkraavpgtlslalriGravaearea.kdvveailealgg 230
                                       +++k+++d ++E+++R +++++g  +gv  +p++g+ l++++++g +s al+iG+a+++are+ +d+++a++ a + 
  gi|488600756|ref|YP_007907227.1| 162 VISKVKDDFQAEKIVRGIVASIGTDVGVTSHPIPGKLLRDSVIKGAISYALKIGEALRAAREEgEDPIKALIGAGN- 237
                                       ********99***************************************************9988***********. PP

                                       -EEEEEEEEE--------------EEEET.......EEEEEEESSSEEEEE..ET-SEETTSEEEEEHHB-SSSSB- CS
                            DUF917 231 gakvlfkGkivdverrteggfdvgevtiegldedegrelkiefqNEnllaeedgevlatvPDlIsvldaetgepigt 307
                                       g+  lfkG  ++ ++++eggf++ge++++g++e eg++++++f+NEnl+ +++gev +t+PDlI+vl + +g+p+++
  gi|488600756|ref|YP_007907227.1| 238 GFL-LFKGIASKSSWKDEGGFTIGEFELNGTGEFEGETYRVWFKNENLISWRNGEVDVTIPDLICVL-TPDGHPVTN 312
                                       677.***************************************************************.999****** PP

                                       TTTT.TS-EEEEEE---GGGS..SHHHH-S-....-....--- CS
                            DUF917 308 eelryGlrVtVlalpasekwrteeglelvgPkaFGydleykpl 350
                                       +++++G + ++++lpa+++wrt++gle++gPk+ G+++ey+p+
  gi|488600756|ref|YP_007907227.1| 313 PNVQEGEEYAIVGLPAPQLWRTPKGLEIFGPKSLGLEIEYTPI 355
                                       ****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2265.02
//
Query:       gi|488600757|ref|YP_007907228.1|  [L=223]
Description: Hydantoin racemase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   44.7   0.0    1.8e-11   44.3   0.0    1.1  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase
     0.0068   15.8   0.0       0.01   15.2   0.0    1.3  1  AroM          AroM protein
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.53   10.4   0.0    1.7  2  DUF5500       Family of unknown function (DUF5500)


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0     3e-15   1.8e-11      50     215 ..      46     199 ..      11     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3e-15
                                       .T..THHHHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEECHHHHHHHHHHHSS-EEEEEE-HHHHHCT CS
                      Asp_Glu_race  50 sgddpvlklleaakkLekagadaiviaCnTahavadelqkkikiPvlgiveataealkatgvkkvglLgTrgtlksg 126
                                       +++ +  klle +++L+ka  daivi+C+     + el++++ +Pv g  e t++ ++   ++++ ++g+  ++ s 
  gi|488600757|ref|YP_007907228.1|  46 QKTIACSKLLEKIDELKKA--DAIVINCFAD-PCLFELRENLAVPVFGAGETTMHVAA--MLGEFSVIGPGDNMIS- 116
                                       3444556999999999987..9*********.9999************7777777774..5********8877776. PP

                                       HHHHHHHHHGT..EEE....T-CCCHHCCHCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHH CS
                      Asp_Glu_race 127 lyqkeleanqg.ievvvpseelqssvnqaiyeelkaGevteearrailkllerlaergadaviLGCTelplllekae 202
                                       + + + ++ +g ++ ++  ++++ sv     e+++aGe +   ++a ++++ +++++gada+iLGCT +  + e+++
  gi|488600757|ref|YP_007907228.1| 117 WTRIQAKE-YGlFDKLISVKKIRFSV-----EDVIAGEEEL--YKATKEACTDAIDDGADAIILGCTGFTSIAERLK 185
                                       56666688.48343344444444444.....4888887755..4777777777778***************999987 PP

                                       HCC-TT..SEEEEH CS
                      Asp_Glu_race 203 alekek.svpvidp 215
                                       +    + ++pv++p
  gi|488600757|ref|YP_007907228.1| 186 EEIWHEyQIPVLEP 199
                                       65554468999887 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-06      0.01      74     206 ..      53     199 ..      25     211 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-06
                              AroM  74 rlqaaiakleeegvdlilllcTgefpelea..kapliepqrileslvaalvkkkqlgvivPleeqaeq...aekkwe 145
                                       +l ++i++l+++ + +i  ++   + el++   +p++ + +   ++ a l +  + +vi P  ++++    ++k++ 
  gi|488600757|ref|YP_007907228.1|  53 KLLEKIDELKKADAIVINCFADPCLFELREnlAVPVFGAGETTMHVAAML-G--EFSVIGPGDNMISWtriQAKEYG 126
                                       56666777766644444444444555555544555555555555443333.3..57777777777654222455555 PP

                              AroM 146 elak.....evvvavaspygseeel....aeaarelaeqgadlivldciGYt...eemkaavaealgkpVlla 206
                                         +k     +++++v + ++ eeel    +ea ++  + gad i+l c G+t   e+ k+++ +++++pVl +
  gi|488600757|ref|YP_007907228.1| 127 LFDKlisvkKIRFSVEDVIAGEEELykatKEACTDAIDDGADAIILGCTGFTsiaERLKEEIWHEYQIPVLEP 199
                                       554455455677777777766666611115556667789************944457899999999***9866 PP

>> DUF5500  Family of unknown function (DUF5500)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   8.8e-05      0.53      43      82 ..      26      65 ..      17      71 .. 0.87
   2 ?   -2.2   0.0      0.76   4.6e+03      74      94 ..     133     154 ..     122     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.8e-05
                           DUF5500 43 nshytmfvldhgsvrierpsqsevdcaslmetlkrirlrn 82
                                      n  + +f ld g   ie  +q  + c+ l+e +  ++  +
  gi|488600757|ref|YP_007907228.1| 26 NDEFEVFSLDEGPETIESFTQKTIACSKLLEKIDELKKAD 65
                                      77899**************************998877655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.76
                           DUF5500  74 tlkrirlr.nswvasedeldvs 94 
                                       ++k+ir+  +  +a e+el  +
  gi|488600757|ref|YP_007907228.1| 133 SVKKIRFSvEDVIAGEEELYKA 154
                                       5788887624566888888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1463.86
//
Query:       gi|488600758|ref|YP_007907229.1|  [L=318]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-33  114.4   0.0    7.3e-33  114.0   0.0    1.2  1  ABC_tran   ABC transporter
    4.3e-19   68.8   0.0    8.4e-19   67.9   0.0    1.5  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    1.1e-06   28.7   1.0    0.00056   19.8   0.1    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    1.4e-05   25.4   0.1    0.00012   22.4   0.1    2.0  1  AAA_22     AAA domain
    2.8e-05   23.7   0.1     0.0012   18.3   0.0    2.1  2  SMC_N      RecF/RecN/SMC N terminal domain
     0.0034   17.1   0.1     0.0058   16.3   0.1    1.3  1  AAA_29     P-loop containing region of AAA domain
     0.0058   17.0   0.0     0.0093   16.4   0.0    1.3  1  AAA_16     AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.02   14.8   0.1    1.4  1  DUF1344    Protein of unknown function (DUF1344)
       0.02   14.1   0.0      0.022   13.9   0.0    1.1  1  G-alpha    G-protein alpha subunit
      0.097   12.7   0.0        2.7    8.0   0.0    2.2  2  AAA_5      AAA domain (dynein-related subfamily)
        0.1   11.9   0.0       0.17   11.2   0.0    1.3  1  AIG1       AIG1 family
       0.17   12.2   0.1       0.53   10.6   0.1    1.8  1  SbcCD_C    Putative exonuclease SbcCD, C subunit
       0.22   10.9   0.2        2.7    7.3   0.1    2.3  2  TniB       Bacterial TniB protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   5.3e-36   7.3e-33       2     137 .]      29     177 ..      28     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 5.3e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       ++v+++++ ge+ ++vGe+G+GKSt  +++++l++pt G+i +++ +++    +el++ r +++++ q+  ++l+p+
  gi|488600758|ref|YP_007907229.1|  29 DDVTFTINDGETFGLVGESGSGKSTTGRTILRLYEPTDGKIFFNDIEITAlpkKELRKIRPKMQIIYQDpySSLNPR 105
                                       89******************************************9999999999***************999***** PP

                                       SBHHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       ltv +         + ++  +k+l+ l+ ++l ++++++ p +LSgGq qrva+aral  +p++l+lDEpt+
  gi|488600758|ref|YP_007907229.1| 106 LTVFDIvaeplkehHCEDVEDKVLELLEAVGLSEEHARKYPDELSGGQCQRVAIARALSLNPEFLVLDEPTS 177
                                       *********9999856666777777777777888999999******************************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 !   67.9   0.0   6.1e-22   8.4e-19       1      65 []     228     294 ..     228     294 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 6.1e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd..klekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+g++ ++fd+plHPYT++Ll+s+p +d++ +  +   ++ge ps+ + ++GC+F++RCpf+++ C
  gi|488600758|ref|YP_007907229.1| 228 VEIGSIGQVFDNPLHPYTRLLLDSIPIPDPKARsiEKGIVAGEIPSPMDPPKGCRFHTRCPFVKDVC 294
                                       8********************************6666669*************************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0015         2       3      41 ..      42      76 ..      41     115 .. 0.66
   2 !   19.8   0.1   4.1e-07   0.00056     234     301 ..     146     211 ..      80     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsgggg 41
                                      +l+G  gsGKS+  +++  l       +++++++ ++  
  gi|488600758|ref|YP_007907229.1| 42 GLVGESGSGKSTTGRTILRLYE----PTDGKIFFNDIEI 76
                                      69***************88743....3333333333333 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 4.1e-07
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                       ++elS G+ +  a++ al   +    +l++DEp + L+ ++++ +l ll++l++  +   ++ +H+  +
  gi|488600758|ref|YP_007907229.1| 146 PDELSGGQCQRVAIARALSLNP---EFLVLDEPTSALDVSVQAQVLNLLENLQKeMNLTYLFISHDLGV 211
                                       4577888888867777777666...9***********************99999899999999999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   8.5e-08   0.00012      10     128 ..      43     205 ..      37     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.5e-08
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlpsstsskdllrellralglelka......... 70 
                                       ++GesG+GK+t+ r++l+ ++     ++             ++t+  ++++++++ ++  +++++ ++         
  gi|488600758|ref|YP_007907229.1|  43 LVGESGSGKSTTGRTILRLYEP----TDgkiffndI-----EITALPKKELRKIRPKMQIIYQDPYSSlnprltvfd 110
                                       79*****************953....2223334440.....555555556666666666666666666666666666 PP

                            AAA_22  71 ...............................erlsseell.ealeqalrarav...ielliiDEaqh.lr...seea 108
                                                                      +r+  +el   ++++ + ara    +e+l++DE    l+   ++++
  gi|488600758|ref|YP_007907229.1| 111 ivaeplkehhcedvedkvlelleavglseehARKYPDELSgGQCQRVAIARALslnPEFLVLDEPTSaLDvsvQAQV 187
                                       666666667777888888888888888888888889999999999999999999999*******9999989555999 PP

                            AAA_22 109 leeLrsllnlsrkgvqliLv 128
                                       l+ L +l++  + +++ +++
  gi|488600758|ref|YP_007907229.1| 188 LNLLENLQK--EMNLTYLFI 205
                                       999988888..887777666 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     0.031        43      27      41 ..      41      55 ..      19      63 .. 0.71
   2 !   18.3   0.0   8.6e-07    0.0012     122     212 ..     127     222 ..      74     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.031
                                      EEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnll 41
                                        +vG+ GSGKs   
  gi|488600758|ref|YP_007907229.1| 41 FGLVGESGSGKSTTG 55
                                      359*********765 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 8.6e-07
                                       HHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.. CS
                                       xxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                             SMC_N 122 evsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.. 189
                                       +v elle +g+s+e       +LSgG+ + va+a  ++++   p  + +lDe  +aLD +  ++v +ll++ +k+  
  gi|488600758|ref|YP_007907229.1| 127 KVLELLEAVGLSEEharkypdELSGGQCQRVAIARALSLN---P-EFLVLDEPTSALDVSVQAQVLNLLENLQKEmn 199
                                       5667777777777777777779***********9988775...4.499**********************8888733 PP

                                       SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 190 aQfivislreemlekadklvgvt 212
                                         ++ is++ ++++   + vgv+
  gi|488600758|ref|YP_007907229.1| 200 LTYLFISHDLGVVRYLANRVGVM 222
                                       56799999998888887777775 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   0.1   4.2e-06    0.0058      13      55 ..      29      72 ..      25      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.2e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      d+ t++i+  +++ l+G+sGsGKST    i  l  p+  k+ fN
  gi|488600758|ref|YP_007907229.1| 29 DDVTFTINDGETFGLVGESGSGKSTTGRTILRLYEPTDgKIFFN 72
                                      66788898555999***********8777777776766666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.7e-06    0.0093      25     164 ..      39     196 ..      23     205 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekd.........ggiflrgkcdql...esaipysa.laqalareellrqllde 88 
                                       e   l+GesG+GKs+  r++lr +e +         ++ +l  k  +    +++i y+  + ++  r +++  ++++
  gi|488600758|ref|YP_007907229.1|  39 ETFGLVGESGSGKSTTGRTILRLYEPTdgkiffndiEITALPKKELRKirpKMQIIYQDpYSSLNPRLTVFDIVAEP 115
                                       567799***************98888765333333222222222222244444466644466666666677777777 PP

                            AAA_16  89 aesaeleawrekleealaavpelagaea.....srllellkrll.allsrderplvlvlDdlqwadeaslql.laaL 158
                                       +++   e+  +k +e l+ +  l+ ++a     +    +++r + a++ +   p  lvlD+   a + s q+   +L
  gi|488600758|ref|YP_007907229.1| 116 LKEHHCEDVEDKVLELLE-AVGLSEEHArkypdELSGGQCQRVAiARALS-LNPEFLVLDEPTSALDVSVQAqVLNL 190
                                       666677777776666666.3333333332334322222233333333333.23567777777766665555555555 PP

                            AAA_16 159 lrlles 164
                                       l++l+ 
  gi|488600758|ref|YP_007907229.1| 191 LENLQK 196
                                       555554 PP

>> DUF1344  Protein of unknown function (DUF1344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.4e-05      0.02      15      60 .]      30      75 ..      21      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                           DUF1344 15 alsitLdDGktYklpeefdidgLkvGvkVvVfYtvvdgkrvitdlq 60
                                        + t +DG+t+ l  e   ++ ++G +++  Y+ +dgk + +d++
  gi|488600758|ref|YP_007907229.1| 30 DVTFTINDGETFGLVGESGSGKSTTGRTILRLYEPTDGKIFFNDIE 75
                                      578999**************************************96 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.022      28      85 ..      43     116 ..      20     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                                       EEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHH...HHHHHHHHHHHHHHHHHHHTT... CS
                           G-alpha  28 llGqseSGKsTilkqlkllykkg.............fseeelatwra...viqlnivrsiktilealeslesel 85 
                                       l+G+s+SGKsT+ + + +ly+++               ++el+++r+   +i++  ++s++  l  ++   ++l
  gi|488600758|ref|YP_007907229.1|  43 LVGESGSGKSTTGRTILRLYEPTdgkiffndieitaLPKKELRKIRPkmqIIYQDPYSSLNPRLTVFDIVAEPL 116
                                       89******************999999984444444422222222222333666666666665444444444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.002       2.7       4      23 ..      43      62 ..      41      76 .. 0.88
   2 ?    2.2   0.0      0.12   1.6e+02      61      91 ..     161     193 ..     143     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.002
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      LvG++G+gKs+  + +++++
  gi|488600758|ref|YP_007907229.1| 43 LVGESGSGKSTTGRTILRLY 62
                                      9*************999987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                                       ----.G-SEEEEESGGG--.HHHHHHHHHHHHS CS
                             AAA_5  61 raar.egeilvlDEverae.sevlnsLlsllee 91 
                                       ra   ++e lvlDE + a   +v++ +l+lle+
  gi|488600758|ref|YP_007907229.1| 161 RALSlNPEFLVLDEPTSALdVSVQAQVLNLLEN 193
                                       333378999******999989**********97 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.17       5      22 ..      43      60 ..      39      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                      EESSTTSSHHHHHHHHHT CS
                              AIG1  5 lvGktgnGkSaTgNsilg 22
                                      lvG +g+GkS+Tg +il+
  gi|488600758|ref|YP_007907229.1| 43 LVGESGSGKSTTGRTILR 60
                                      9***************96 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00038      0.53      63      89 ..     166     192 ..     133     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                       ++++++LDE  s lD   +a++l+lle
  gi|488600758|ref|YP_007907229.1| 166 NPEFLVLDEPTSALDVSVQAQVLNLLE 192
                                       589**********************98 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.2   2.7e+02      40      62 ..      43      65 ..      35      79 .. 0.83
   2 ?    7.3   0.1     0.002       2.7     114     156 ..     161     201 ..     131     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                              TniB 40 lvGdsnnGKtmivekFarlhppe 62
                                      lvG+s  GK++  +   rl++p+
  gi|488600758|ref|YP_007907229.1| 43 LVGESGSGKSTTGRTILRLYEPT 65
                                      89********9988877777766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                              TniB 114 llrelkvrvLiiDEihnllagsarkqreflnalksLgnelkip 156
                                          +l+++ L++DE  ++l   ++ q ++ln+l +L+ e++++
  gi|488600758|ref|YP_007907229.1| 161 RALSLNPEFLVLDEPTSAL--DVSVQAQVLNLLENLQKEMNLT 201
                                       44567899***********..6777889*********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2113.50
//
Query:       gi|488600759|ref|YP_007907230.1|  [L=322]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   98.0   0.1    8.5e-28   97.6   0.1    1.1  1  ABC_tran   ABC transporter
    4.2e-19   68.8   0.4    7.6e-19   68.0   0.4    1.5  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    1.9e-06   28.0   1.3    1.7e-05   24.8   0.3    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
     0.0077   15.6   0.1      0.024   14.0   0.1    1.8  2  AIG1       AIG1 family
  ------ inclusion threshold ------
      0.017   15.4   0.3       0.15   12.3   0.3    2.1  1  AAA_22     AAA domain
      0.073   13.2   0.7       0.26   11.3   0.1    1.9  2  DUF87      Helicase HerA, central domain
      0.074   13.1   0.0       0.13   12.3   0.0    1.3  1  Mrr_cat    Restriction endonuclease
       0.11   12.5   0.0       0.25   11.3   0.0    1.6  2  ResIII     Type III restriction enzyme, res subunit
       0.12   11.9   0.0       0.21   11.1   0.0    1.3  1  AAA_7      P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.1   4.3e-31   8.5e-28       1     136 [.      24     181 ..      24     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 4.3e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..x RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..p 68 
                                       l+ vslk+++ e+ +++Ge+G+GKS  ++ +++l        Gei ++g+++ e    + +++  k i+v++q+  +
  gi|488600759|ref|YP_007907230.1|  24 LNGVSLKIRKEEIFGLIGETGCGKSVTAMSILRLQPSnaeVYGEIIFKGENILEkseeEMRKIRGKDISVVFQDpmT 100
                                       789******************************9877666779********999888888899999********999 PP

                                       -S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEE CS
                                       xxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpklll 131
                                       +l+p  +++++              es ++++k+l+++gl +  +++++s p++LSgG++qrv +a+al ++p+ll+
  gi|488600759|ref|YP_007907230.1| 101 SLNPLFKIKDQmvdvittheglskeESLRHAKKYLKSVGLAD-VERILNSYPHELSGGMRQRVLIAMALSSNPSLLI 176
                                       9********************998888888************.899999**************************** PP

                                       EESTT CS
                                       xxxxx RF
                          ABC_tran 132 lDEpt 136
                                       +DEpt
  gi|488600759|ref|YP_007907230.1| 177 ADEPT 181
                                       ****9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.4   3.8e-22   7.6e-19       1      65 []     233     296 ..     233     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 3.8e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE +++++lf++  HPY+kaLl++vp+++r+k+ l+ +kg++psl + ++GC+F+pRC  ++++C
  gi|488600759|ref|YP_007907230.1| 233 VEVANTEELFENTIHPYSKALLSVVPDPRRRKH-LKPLKGSVPSLINPPDGCRFHPRCDCMKDAC 296
                                       8********************************.******************************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 ?    2.0   0.0     0.076   1.5e+02       1      23 [.      36      58 ..      36      97 .. 0.71
   2 !   24.8   0.3   8.5e-09   1.7e-05     233     302 ..     150     217 ..     107     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.076
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + +liG  g+GKS     +  l+
  gi|488600759|ref|YP_007907230.1| 36 IFGLIGETGCGKSVTAMSILRLQ 58
                                      578**********7766666664 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 8.5e-09
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                        ++elS G+++   ++ al + +   sll+ DEp + L+  +++ +l+l+ +++++ g  v+l TH+  ++
  gi|488600759|ref|YP_007907230.1| 150 YPHELSGGMRQRVLIAMALSSNP---SLLIADEPTTALDVTIQKQILGLIlELKESYGFSVLLITHDLGVV 217
                                       57899*******66666666666...9********************999666666***********8876 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.2e-05     0.024       5      54 ..      39      94 ..      37     125 .. 0.77
   2 ?   -2.9   0.0       1.7   3.4e+03      36      63 ..     218     245 ..     215     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                      EESSTTSSHHHHHHHHHTS--..........SS--TTTS---SS-EEEEEEETTEEEEEE CS
                              AIG1  5 lvGktgnGkSaTgNsilgkka..........FesklsaqsvtkkcqkksrtwdgkkinVi 54
                                      l+G tg+GkS T+ sil+ +           F    + +++ +k++++ r+ +gk+i+V+
  gi|488600759|ref|YP_007907230.1| 39 LIGETGCGKSVTAMSILRLQPsnaevygeiiF----KGENILEKSEEEMRKIRGKDISVV 94
                                      89**************8876644455433334....445899999999999999999998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                                       -SS-EEEEEEETTEEEEEEE--SCCCTT CS
                              AIG1  36 tkkcqkksrtwdgkkinViDTPglfdls 63 
                                        + c ++  + +g+ ++V +T +lf+  
  gi|488600759|ref|YP_007907230.1| 218 AEICDRAGVMYAGNVVEVANTEELFENT 245
                                       5567777778888899999999888865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   7.5e-05      0.15       7      38 ..      36      89 ..      31     216 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee......................e 38
                                      i  ++Ge+G+GK++++  +l+  +  a+                         +
  gi|488600759|ref|YP_007907230.1| 36 IFGLIGETGCGKSVTAMSILRLQPSNAEVYGeiifkgenilekseeemrkirgK 89
                                      56699***********99999987655554466666666666666655555551 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   0.00013      0.26      19      45 ..      34      56 ..      23      70 .. 0.83
   2 ?   -0.2   0.0      0.43   8.6e+02     142     182 ..      98     153 ..      65     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                             DUF87 19 nklvtrHlAilgsTGsGKSntvavLle 45
                                      +++    ++ +g+TG GKS t+ ++l+
  gi|488600759|ref|YP_007907230.1| 34 EEI----FGLIGETGCGKSVTAMSILR 56
                                      444....999**************997 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.43
                             DUF87 142 pveklleelk...............kekeelrklknqaiarlldkledllrkggsf 182
                                       p+ +l+   k               +++e+lr++k+ +++  l+++e++l+++ + 
  gi|488600759|ref|YP_007907230.1|  98 PMTSLNPLFKikdqmvdvittheglSKEESLRHAKKYLKSVGLADVERILNSYPHE 153
                                       33333333334444446666666655555666666666666666666666666655 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.4e-05      0.13      32      75 ..     109     152 ..     104     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.4e-05
                                       TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTT CS
                           Mrr_cat  32 gDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkk 75 
                                       +D+ +D+i ++++l++e+ l  aK+y ++vg  +V++++ +  +
  gi|488600759|ref|YP_007907230.1| 109 KDQMVDVITTHEGLSKEESLRHAKKYLKSVGLADVERILNSYPH 152
                                       7999********************************99887766 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 ?   11.3   0.0   0.00013      0.25      19     121 ..      29     129 ..      15     180 .. 0.67
   2 ?   -2.5   0.0       2.3   4.6e+03      56      75 ..     231     250 ..     194     260 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                       ....TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESS CS
                            ResIII  19 lkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke....igkkvsg 91 
                                       lk+++++ + +  +TG+GK+++a+++ + l+ ++ e    ++  ++++le+ +ee++k+  ++ +      +++++ 
  gi|488600759|ref|YP_007907230.1|  29 LKIRKEEIFGLIGETGCGKSVTAMSILR-LQPSNAEVYGEIIFKGENILEKSEEEMRKIRGKDISVvfqdPMTSLNP 104
                                       4446777777999*********998765.555555556667789999******999999988755454333333444 PP

                                       S-B--.......-SEEEEEHHHHHHTH... CS
                            ResIII  92 dkkkakekdstnkkilvttiqsldadseee 121
                                         k++     +++  ++tt + l+++++ +
  gi|488600759|ref|YP_007907230.1| 105 LFKIK-----DQMVDVITTHEGLSKEESLR 129
                                       44444.....44444555555566655444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                       -EEEEESSHHHHHHHHHHGG CS
                            ResIII  56 kflflvprkslleqtleefk 75 
                                       +++ ++++++l e t++ ++
  gi|488600759|ref|YP_007907230.1| 231 NVVEVANTEELFENTIHPYS 250
                                       67777777777777766555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0001      0.21      30      62 ..      31      63 ..      16      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkeky 62
                                      ++++  + l+G+tG+GK+v+++++l+  +++  
  gi|488600759|ref|YP_007907230.1| 31 IRKEEIFGLIGETGCGKSVTAMSILRLQPSNAE 63
                                      566667779**************9988776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2353.51
//
Query:       gi|488600760|ref|YP_007907231.1|  [L=284]
Description: ABC-type dipeptide/oligopeptide/nickel transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-37  128.8   8.6    1.9e-37  128.8   8.6    2.2  3  BPD_transp_1  Binding-protein-dependent transport system inne
    2.8e-11   43.2   0.3    2.8e-11   43.2   0.3    3.2  3  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
      0.069   13.3   0.1       0.13   12.4   0.1    1.5  1  DUF1148       Protein of unknown function (DUF1148)
       0.17   12.2   0.1       0.17   12.2   0.1    3.2  5  Ost5          Oligosaccharyltransferase subunit 5
        1.5    9.4  13.3        2.1    8.9   0.0    3.1  3  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 ?    0.7   0.3       0.1   3.7e+02     157     175 ..      18      36 ..       4      45 .. 0.60
   2 ?   -2.8   0.1       1.2   4.4e+03     151     165 ..      81      94 ..      63      96 .. 0.43
   3 !  128.8   8.6   5.4e-41   1.9e-37       1     185 []      97     281 ..      97     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.1
                      BPD_transp_1 157 gvlalviavlllnlvadil 175
                                       + l ++ia++l+ ++a +l
  gi|488600760|ref|YP_007907231.1|  18 VGLSIIIALILIAILAPVL 36 
                                       3444555555555555544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                      BPD_transp_1 151 seisnggvlalviav 165
                                       ++ + +g+ +++ia+
  gi|488600760|ref|YP_007907231.1|  81 TSLM-IGFSVVAIAL 94 
                                       2222.2333333333 PP

  == domain 3  score: 128.8 bits;  conditional E-value: 5.4e-41
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g++lG++a+ + ++k+d +++++++v+l++P+++la+l+       + lg +++  +++l+l  +++y+rl+r +++
  gi|488600760|ref|YP_007907231.1|  97 GVPLGLIAG-YVGRKIDLVIMRITDVFLAFPPLLLALLIA------TTLGRGMFNaILALALSWWPWYTRLMRGMVV 166
                                       89*******.******************************......******9998999999999************ PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++ ++ +veaa+a+   +w+i+ ++vlPn+++p+i ++ + +g+++ +a+ l+flg    lg +  ++ +g ++se+
  gi|488600760|ref|YP_007907231.1| 167 SVKERPYVEAAKAMDIAEWKIMLRHVLPNSISPVIIQATMDIGSAILEAAGLSFLG----LGVQPPTPDWGLMVSEG 239
                                       ********************************************************....***************** PP

                      BPD_transp_1 154 s..........nggvlalviavlllnlvadilqrlldprvrk 185
                                                  +++ la+ i v+++nl+ d++ +++dpr+r+
  gi|488600760|ref|YP_007907231.1| 240 KnyflnywwypVFPGLAIFITVMAFNLLGDAVREAIDPRLRR 281
                                       ***************************************995 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.3   7.9e-15   2.8e-11       5      51 .]       5      56 ..       3      56 .. 0.83
   2 ?   -7.3   8.8         5   1.8e+04      17      31 ..      84      98 ..      81     157 .. 0.76
   3 ?   -1.1   0.1      0.53   1.9e+03      19      32 ..     254     267 ..     253     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 7.9e-15
                            OppC_N  5 dawrrFkrNklAvvglvilllllliaifaPliaPydp.....qdliqn....llpP 51
                                      +++r +++Nkl +vgl i+++l+liai+aP++aPy+           n    l+pP
  gi|488600760|ref|YP_007907231.1|  5 EILRVLLKNKLSIVGLSIIIALILIAILAPVLAPYPEqamgeP----NlkerLQPP 56
                                      57899******************************87665322....234459998 PP

  == domain 2  score: -7.3 bits;  conditional E-value: 5
                            OppC_N 17 vvglvilllllliai 31
                                      ++g+ ++++ lli +
  gi|488600760|ref|YP_007907231.1| 84 MIGFSVVAIALLIGV 98
                                      888888888888853 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.53
                            OppC_N  19 glvilllllliaif 32 
                                       gl+i++++ ++ ++
  gi|488600760|ref|YP_007907231.1| 254 GLAIFITVMAFNLL 267
                                       78888887776555 PP

>> DUF1148  Protein of unknown function (DUF1148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.6e-05      0.13      52      92 ..     122     163 ..     112     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                           DUF1148  52 fessprflldvdmadclsra.wnkwpgialtwwcwyirdrva 92 
                                       f + p +ll + +a  l r  +n   ++al+ww wy r    
  gi|488600760|ref|YP_007907231.1| 122 FLAFPPLLLALLIATTLGRGmFNAILALALSWWPWYTRLMRG 163
                                       5567889999999****99638999***********986544 PP

>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.5       1.8   6.3e+03      21      52 ..      23      31 ..      14      37 .. 0.51
   2 ?   12.2   0.1   4.6e-05      0.17      42      71 ..      69      98 ..      63     100 .. 0.91
   3 ?   -3.1   0.9       2.7   9.7e+03      49      59 ..     129     139 ..     121     149 .. 0.50
   4 ?   -2.8   0.1       2.2   7.9e+03       5      29 ..     199     223 ..     196     225 .. 0.59
   5 ?   -0.8   0.0      0.55     2e+03      11      28 ..     251     268 ..     249     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                              Ost5 21 ligllltalfflyevtstkkkrslvkelllal 52
                                      +i+l+l+a                       +
  gi|488600760|ref|YP_007907231.1| 23 IIALILIA-----------------------I 31
                                      33333333.......................3 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.6e-05
                              Ost5 42 rslvkelllalvASlflGfGvvflllavGV 71
                                      r++++ +++++  Sl++Gf+vv+++l +GV
  gi|488600760|ref|YP_007907231.1| 69 RDILSRVIYGARTSLMIGFSVVAIALLIGV 98
                                      6789999**********************9 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.7
                              Ost5  49 llalvASlflG 59 
                                       llal+ + +lG
  gi|488600760|ref|YP_007907231.1| 129 LLALLIATTLG 139
                                       33333344444 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.2
                              Ost5   5 ppvppslqptlafvllligllltal 29 
                                       p++ ++++ + +++l ++gl +++l
  gi|488600760|ref|YP_007907231.1| 199 PVIIQATMDIGSAILEAAGLSFLGL 223
                                       5555555666666666667666654 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.55
                              Ost5  11 lqptlafvllliglllta 28 
                                       ++p la++ +++++ l++
  gi|488600760|ref|YP_007907231.1| 251 VFPGLAIFITVMAFNLLG 268
                                       578899999999998876 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00058       2.1      12      59 ..       1      48 [.       1      68 [. 0.86
   2 ?    0.5   9.1      0.24   8.6e+02      23      78 ..      84     139 ..      79     162 .. 0.53
   3 ?   -0.7   0.3      0.56     2e+03      40      79 ..     222     261 ..     192     267 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00058
                              FtsX 12 mkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsse 59
                                      m+++++l++ll   l i+ ++++i+l+l +++a +l  + ++ ++ ++
  gi|488600760|ref|YP_007907231.1|  1 MRRNEILRVLLKNKLSIVGLSIIIALILIAILAPVLAPYPEQAMGEPN 48
                                      78999**************************99999888877777554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.24
                              FtsX  23 teillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllll 78 
                                       + ++ ++++al+iG+ lgl+a ++  +  l ++  + + + ++++ ++++i+  l 
  gi|488600760|ref|YP_007907231.1|  84 MIGFSVVAIALLIGVPLGLIAGYVGRKIDLVIMRITDVFLAFPPLLLALLIATTLG 139
                                       66788999999999999999988844444444443333333333333333333222 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.56
                              FtsX  40 gllaaqllsdvllssvfsselkisidlitvliiivlllll 79 
                                       gl +  +  d++l +  + +  ++  + +v+ ++++++ +
  gi|488600760|ref|YP_007907231.1| 222 GLGVQPPTPDWGLMVSEGKNYFLNYWWYPVFPGLAIFITV 261
                                       4444455555554443334444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1936.58
//
Query:       gi|488600761|ref|YP_007907232.1|  [L=339]
Description: ABC-type dipeptide/oligopeptide/nickel transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-41  139.9  14.3    7.4e-41  139.9  14.3    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.7     0.055   9.9e+02     160     175 ..      13      28 ..       3      43 .. 0.50
   2 !  139.9  14.3   4.1e-45   7.4e-41       1     184 [.     115     338 ..     115     339 .] 0.99

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.055
                      BPD_transp_1 160 alviavlllnlvadil 175
                                        +v++++ +++v++++
  gi|488600761|ref|YP_007907232.1|  13 LAVFVIFGVITVVFFI 28 
                                       2222222222222222 PP

  == domain 2  score: 139.9 bits;  conditional E-value: 4.1e-45
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       gi+lG+++a+++ +++d+++r++ i + slP+f+++i+l+l+f                                  
  gi|488600761|ref|YP_007907232.1| 115 GIPLGVYSAVKKDSWVDNFSRIFAISGVSLPTFWFGIILQLAFfkylqllplagrvdsvillehpleiitglylvds 191
                                       89*************************************************************************** PP

                      BPD_transp_1  44 .......vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitg 113
                                              v+ ++l+h ilp+++l+++  + ++r +r++++++l+++++++a a+G++ ++i++k++l+na+ p++ +
  gi|488600761|ref|YP_007907232.1| 192 litgnipVFVNALHHIILPALTLAMYPVGLITRQVRSMMVEVLQENYIKTAFAYGLPSRKIYFKYALKNAIAPALIT 268
                                       ***************************************************************************** PP

                      BPD_transp_1 114 lilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       ++l++++ l+ga+l+e++++wpGlg+    +il++dy++ + g++++++  ++++nlv+d++q +ldpr++
  gi|488600761|ref|YP_007907232.1| 269 VGLSVAYTLTGAFLTEIIFNWPGLGRYAAYSILSMDYPAVL-GVTIVAATTYVIVNLVVDLIQVYLDPRIK 338
                                       *****************************************.***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2492.42
//
Query:       gi|488600762|ref|YP_007907233.1|  [L=541]
Description: ABC-type dipeptide transport system, periplasmic component [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-97  327.5   4.5    1.6e-97  326.9   4.5    1.3  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 !  326.9   4.5  8.9e-102   1.6e-97       2     373 ..      92     454 ..      91     458 .. 0.92

  Alignments for each domain:
  == domain 1  score: 326.9 bits;  conditional E-value: 8.9e-102
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       ++p+LA+s we ++Dg++++f+LRkgvkF+ G++ltAeDv++s+er+++++ +++  ++      ++++e+vddyt+
  gi|488600762|ref|YP_007907233.1|  92 LKPWLATS-WESNEDGTEWIFHLRKGVKFHSGNELTAEDVKWSIERTVRMGLGASFIWD-----PVESIEVVDDYTI 162
                                       68******.7********************************************99777.....59*********** PP

                                       EEEESSETTTTTTHCHHHHHHHGC.....CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTT.SC CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiak.....kaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgg.gk 149
                                       +f+lk p +l l+  + + a i       k  ++e+ +d  ++ +  g+GPY++++++p  ++vl+++++Ywgg + 
  gi|488600762|ref|YP_007907233.1| 163 KFKLKYPANLPLIASSSYGAYIMDskllsKIGDDETIADYLNKGHDAGSGPYTIEKYEPKTEVVLKKFDEYWGGwSD 239
                                       *******997777777777777778898888899999999999999**************************88899 PP

                                       SSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHH CS
                         SBP_bac_5 150 pkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqA 226
                                        ++d  ++k++pd++ r +++ sGei+++ ++p++di++l++++++ v +++ +++  y ++Nt+kpp+d+k vRqA
  gi|488600762|ref|YP_007907233.1| 240 DQFDIAIIKIVPDASLREQMVASGEIHIARDLPLDDIPKLQQDPNVVV-KQKSSYQELYAMLNTRKPPLDNKLVRQA 315
                                       9**********7777777777***************************.**************************** PP

                                       HHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEE CS
                         SBP_bac_5 227 lsyAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlll 303
                                       lsyA+++e+ivk vl+ y+++a++++pp++ g+ e+ k++  +ydpekAk+lL++aGy++g+         kl+l++
  gi|488600762|ref|YP_007907233.1| 316 LSYAVPYEDIVKYVLHDYGKAAKGPIPPGMLGYFEDLKTY--TYDPEKAKELLEQAGYPNGG--------FKLVLTY 382
                                       **************************************98..78*****************7........479**** PP

                                       ETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHH..HHCTTESEEEEEEECTTSTTHHHHHHHHSTT CS
                         SBP_bac_5 304 asgspaekaiaeliqqqlkkiGikvevktvdwaatyler..vkdgdfdmillgwgadypdpdnflnpflsss 373
                                       ++g++ae ++ae++++++ k+Gi+ve++++ w++++  +     +  d++++ w+++yp+p++fl ++++s 
  gi|488600762|ref|YP_007907233.1| 383 TNGDEAEAKVAEILKAEWGKLGIDVEIRPMNWEQQWALAksDPMKAQDVFIFYWWPTYPTPYDFLFSMFHSE 454
                                       ******************************996333222225667789******************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3686.21
//
Query:       gi|488600763|ref|YP_007907234.1|  [L=165]
Description: CRISPR-associated exonuclease, Cas4 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-50  171.9   1.8    1.2e-50  171.7   1.8    1.0  1  Cas_Cas4  Domain of unknown function DUF83
    0.00059   19.8   0.5     0.0011   19.0   0.2    1.6  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.043   14.3   0.1       0.12   12.8   0.0    1.8  2  DUF1284   Protein of unknown function (DUF1284)


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 !  171.7   1.8   2.1e-54   1.2e-50       2     161 ..       9     164 ..       8     165 .] 0.99

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 2.1e-54
                          Cas_Cas4   2 gtkiqyyliCkrklwlisheitleensetvelGkllheesyerekkevelsesikiDvvekekeklvvvEvKkskkk 78 
                                       gt+++yy+iCk+klwl+sh+it+e++s+ v+lGkl+h e ++r++kev++ + i+iDvv+  ++ l++ E+Kks+k+
  gi|488600763|ref|YP_007907234.1|   9 GTQVNYYFICKTKLWLFSHNITMEHESDAVKLGKLIHREVFKRDEKEVQI-GPIAIDVVR-VGNILEIREIKKSRKM 83 
                                       99************************************************.*********.999************* PP

                          Cas_Cas4  79 eeaaklQllyYlllLekkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCa 155
                                       e++  +Q lyYl++L+k g++++ +v+ +pk +++ e+el++e++ ++++++ +ie+ii+s  +pk++++kiC+kCa
  gi|488600763|ref|YP_007907234.1|  84 EDSYIYQTLYYLYFLKKFGIDAR-AVISFPKRRENIEIELSREDETKIKEILMDIEKIINS-PMPKPEYRKICRKCA 158
                                       ***********************.*************************************.8************** PP

                          Cas_Cas4 156 yaelCl 161
                                       y+e+C+
  gi|488600763|ref|YP_007907234.1| 159 YFEFCF 164
                                       *****9 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.25   1.5e+03       6      42 ..      11      46 ..      10      57 .. 0.66
   2 !   19.0   0.2   1.8e-07    0.0011     134     254 ..      63     163 ..      28     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.25
                          PDDEXK_1  6 rletfleCplrfflryllglreeeeleapdlGtlvHa 42
                                      +++ +  C+ +  l    +++ e+e +a  lG l+H+
  gi|488600763|ref|YP_007907234.1| 11 QVNYYFICKTKLWL-FSHNITMEHESDAVKLGKLIHR 46
                                      55666666666444.3444445677777789999996 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-07
                          PDDEXK_1 134 iDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkk 210
                                       iD v   +  l+i + K ++   k ++    ++  Q+l Yl+ l++       g +a+a++ +       ++++  +
  gi|488600763|ref|YP_007907234.1|  63 IDVVRVGN-ILEIREIKKSR---KMED----SYIYQTLYYLYFLKKF------GIDARAVISFP------KRRENIE 119
                                       45554333.48888888666...6665....4556*******99987......22999999999......7888888 PP

                          PDDEXK_1 211 malteeeleallqeleelaeeilagefparpskk.CeyCpyksvC 254
                                       ++l++e+ +++++ l ++ e+i +  +p  +++k C+ C+y + C
  gi|488600763|ref|YP_007907234.1| 120 IELSREDETKIKEILMDI-EKIINSPMPKPEYRKiCRKCAYFEFC 163
                                       889999999999999995.***********************999 PP

>> DUF1284  Protein of unknown function (DUF1284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.56   3.3e+03      50      62 ..      47      59 ..      28      88 .. 0.59
   2 ?   12.8   0.0     2e-05      0.12      62     102 .]     120     163 ..     101     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.56
                           DUF1284 50 kvkelDrkvleal 62
                                      +v ++D+k ++  
  gi|488600763|ref|YP_007907234.1| 47 EVFKRDEKEVQIG 59
                                      5555555554443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2e-05
                           DUF1284  62 lgleegeelkleellekvkekile...ekklkeiCgeCeWkelc 102
                                       ++l+ ++e k++e+l  +++ i++   + ++++iC++C + e+c
  gi|488600763|ref|YP_007907234.1| 120 IELSREDETKIKEILMDIEKIINSpmpKPEYRKICRKCAYFEFC 163
                                       5788899999999999888887652225579***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 996.11
//
Query:       gi|488600764|ref|YP_007907235.1|  [L=324]
Description: CRISPR-associated protein, Cas1 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-88  296.9   0.1    1.4e-88  296.7   0.1    1.0  1  Cas_Cas1  CRISPR associated protein Cas1


Domain annotation for each model (and alignments):
>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.7   0.1     8e-93   1.4e-88       1     282 [.       6     278 ..       6     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: 296.7 bits;  conditional E-value: 8e-93
                                       EEEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.S CS
                          Cas_Cas1   1 lyvteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.e 76 
                                       +y+ ++g+ l++ ++++++e+++  kk ip++ i  i+ +g++s+++kal+lla++g+ ++f++++g y+g+++p e
  gi|488600764|ref|YP_007907235.1|   6 YYILSDGK-LKRYENTIYFENKDG-KKPIPINAIYAIYALGSLSVTSKALSLLASEGVCIHFFNRSGFYVGSFYPrE 80 
                                       69******.*************99.9*************************************************** PP

                                       SSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHH CS
                          Cas_Cas1  77 esgnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrg 153
                                       +  ++++ ++Q++++ deekrl lak++v+g + n+ kvl ++  ++          e+e++l++l++a+++ e++g
  gi|488600764|ref|YP_007907235.1|  81 TLISGDMVVKQVQHHIDEEKRLFLAKAFVEGSILNMSKVLAYYGLND-------FRVEVENALQSLANAKTVAEIMG 150
                                       *******************************************9988.......66778888899999********* PP

                                       HHHHHHHHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHH CS
                          Cas_Cas1 154 iEGeaakaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLa 230
                                        E++a++aY++afd++l ++fef +Rsr+pp+++vNa++sfg++llys+vls+i++++L+P+i++LHe++++r+sLa
  gi|488600764|ref|YP_007907235.1| 151 AEATARNAYYSAFDSIL-KNFEFGKRSRQPPENEVNAMISFGNSLLYSTVLSEIYHTQLHPAISYLHEPSERRFSLA 226
                                       *****************.6********************************************************** PP

                                       HHHHHHHHHHHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHHH CS
                          Cas_Cas1 231 lDLmEefRpllvDrlvlslinkrqlkekdFekeengvlLteegrkkfleafe 282
                                       lD++E f+p++vDr+++ l+nk++++e dF+++ ++vlL+e+g++kfl+a++
  gi|488600764|ref|YP_007907235.1| 227 LDIAELFKPMIVDRTIFYLVNKGIVSEGDFNRDLKSVLLNESGKRKFLSAYN 278
                                       **************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2133.73
//
Query:       gi|488600765|ref|YP_007907236.1|  [L=87]
Description: CRISPR-associated protein, Cas2 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   79.8   0.5    1.4e-22   79.7   0.5    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
      0.047   13.4   0.1      0.055   13.2   0.1    1.2  1  DUF835       Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.5   1.6e-26   1.4e-22       1      72 [.       1      69 [.       1      73 [. 0.96

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 1.6e-26
                                      EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCH CS
                       CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekq 72
                                      m+v+vvYD+  +  r+++++k+l++y ++++Q+SVFege+++a+le++k  +++iid++ed + iy+l +++
  gi|488600765|ref|YP_007907236.1|  1 MYVIVVYDV--NVDRVNRIKKFLRRY-LTWIQNSVFEGEITPADLEEVKMGIREIIDEDEDMVVIYRLPSSK 69
                                      9********..***************.****************************************98765 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.1e-06     0.055      42      81 ..      23      62 ..       3      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-06
                            DUF835 42 vkviwltkveeentvsPtnlekltetivkflkeaekgvvl 81
                                        ++w+ ++  e+++ P++le+ +  i + ++e+e+ vv+
  gi|488600765|ref|YP_007907236.1| 23 RYLTWIQNSVFEGEITPADLEEVKMGIREIIDEDEDMVVI 62
                                      45789999999************************96654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 594.31
//
Query:       gi|488600766|ref|YP_007907237.1|  [L=239]
Description: CRISPR-associated protein, Cas6 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-40  139.2   2.3    3.8e-39  134.6   1.0    2.0  2  Cas_Cas6     CRISPR associated protein Cas6
  ------ inclusion threshold ------
      0.022   15.4   2.0        0.7   10.6   2.0    2.4  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.0    0.0065        59      27      71 ..      32      80 ..      12      83 .. 0.77
   2 !  134.6   1.0   4.2e-43   3.8e-39       1     145 [.      89     231 ..      89     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0065
                                      S....--TCEE.EEESS-BBEEEEEEETTCCEEEEE-TTSTTHHHHHHH CS
                          Cas_Cas6 27 e....itssevvfktlSPivvrstkkengkkktyylspddeeFsellke 71
                                           +t s+ +f t+S ++v+ ++ + +k k + l+p+ ++F   l++
  gi|488600766|ref|YP_007907237.1| 32 LslelHTPSTFKFFTFSRLLVEGKNFRVEKGKMRLLNPNVRFFFSTLQK 80
                                      334456667788**********99788888888889***9999998876 PP

  == domain 2  score: 134.6 bits;  conditional E-value: 4.2e-43
                                       HHHCS-EEEETTEEEEEEEEEE----S--TCEE.EEESS-BBEEEEEEETTCCEEEEE-TTSTTHHHHHHHHHHHHH CS
                          Cas_Cas6   1 gllknkeirlgnnefkveevellkepeitssevvfktlSPivvrstkkengkkktyylspddeeFsellkenlkkky 77 
                                       gll+++e+++g+++f v+e+++lke+ei  +e  f tlSPi v +   +ng+++ ++l pd+ +F+e+lk+nl +ky
  gi|488600766|ref|YP_007907237.1|  89 GLLEKPEVKIGDAKFVVSEIKVLKEKEIGRKER-FITLSPINVTTV-VDNGRRRIVDLYPDSLKFYENLKKNLVRKY 163
                                       699************************977766.**********66.89**************************** PP

                                       HHHHSS...SS---EEEEE.EEEE......TEEEEEEEEEEEEEE-HHHHHHHHHC-SCS-CCCT-S-EE CS
                          Cas_Cas6  78 kalygee.keeklsikpdk.kvkkivvkkketyirGylgrfelegdpellklaydaGlGeknsqGFGmve 145
                                        a+yg+e ++ +++i++ + k+k+i  + k+t++r++++ f  eg++ell+++y+aG+Ge+ns+GFGmv+
  gi|488600766|ref|YP_007907237.1| 164 VAYYGREpEDDDFRIRVLRsKMKRI--QVKNTFHRCVEMVFDAEGSKELLEIGYKAGFGERNSMGFGMVK 231
                                       *******99999*****99777775..55679************************************97 PP

>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.0   7.8e-05       0.7       2      86 .]      35     230 ..      34     230 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.8e-05
                                       EEEEEE-EE.................TEEESS..--HHHHHHHHHHH..HHHHTSS..................... CS
                       CRISPR_Cas6   2 rfltPtrfk.................krkgll..psprlvfssllrr..wnalaglkgk.................. 39 
                                       +++tP  fk                 k k++l  p++r +fs+l ++  +     + +                   
  gi|488600766|ref|YP_007907237.1|  35 ELHTPSTFKfftfsrllvegknfrveKGKMRLlnPNVRFFFSTLQKHigV--ALVEGLLekpevkigdakfvvseik 109
                                       66777777777777777766666665233333468888888886666331..2222111222222222222222222 PP

                                       ...............EECHHHHHH..................................................... CS
                       CRISPR_Cas6  40 ...............ptveeeleg..................................................... 48 
                                                                                                                    
  gi|488600766|ref|YP_007907237.1| 110 vlkekeigrkerfitL-------Spinvttvvdngrrrivdlypdslkfyenlkknlvrkyvayygrepedddfrir 179
                                       2211122222222220.......022222222233333333333333333333333333344333333334444444 PP

                                       .............EEEEEEEE--HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                       CRISPR_Cas6  49 .............GfvGevkysgeleelekllrfaeylgvGkktafGlGkv 86 
                                                     f   v+   + e  ++ll+++  +g G + ++G+G+v
  gi|488600766|ref|YP_007907237.1| 180 vlrskmkriqvknTFHRCVEMVFDAEGSKELLEIGYKAGFGERNSMGFGMV 230
                                       333333333333344444444335555566*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1514.98
//
Query:       gi|488600767|ref|YP_007907238.1|  [L=761]
Description: CRISPR-associated helicase, Cas3 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-18   67.2   0.1    6.1e-18   65.2   0.0    2.0  2  DEAD             DEAD/DEAH box helicase
    2.1e-13   50.6   0.1    5.6e-13   49.2   0.1    1.8  1  HD               HD domain
    8.9e-08   32.5   0.0    2.3e-07   31.1   0.0    1.7  1  Helicase_C       Helicase conserved C-terminal domain
    3.4e-07   30.4   0.0    8.5e-07   29.1   0.0    1.7  2  ResIII           Type III restriction enzyme, res subunit
    8.5e-06   26.0   0.0    3.7e-05   24.0   0.0    1.9  2  HD_6             HD domain
     0.0018   18.4   0.0     0.0035   17.4   0.0    1.5  1  Na_H_antiport_2  Na+-H+ antiporter family
  ------ inclusion threshold ------
      0.069   12.6   0.0       0.35   10.3   0.0    2.1  2  PhoH             PhoH-like protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0   2.4e-21   6.1e-18       2     171 ..      16     182 ..      15     188 .. 0.80
   2 ?   -1.4   0.1      0.68   1.7e+03      39      73 ..     233     266 ..     198     291 .. 0.60

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 2.4e-21
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       ++Q+ a++++++g++++++a+TGsGKT+++lip +  +   ++    + ++  Ptr L+e + ++++k+ ++ +lrv
  gi|488600767|ref|YP_007907238.1|  16 EYQKIAMENLVEGKSLIIRAPTGSGKTEVALIPFIYGL---NDFLPSQLIYSLPTRTLVESIGERATKYASFKKLRV 89 
                                       68*********************************999...579999************************999999 PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.........HCTSSHCTTE..EEEEEETHHHHHHTTTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddll.........stgklnlsqv..rflVlDEadrlldqgfsdfinr 144
                                           g++a+    s l  + di+v+t ++ +            + g++ +  v   + V+DE+++l  ++  ++  +
  gi|488600767|ref|YP_007907238.1|  90 ATHHGKKAT----SSL-FEEDIIVTTIDQTAGAYlsvplsmpkRWGNIFVGGVasALTVFDEVHTLDPEKGLQTAAA 161
                                       866554444....444.4557888888777664336677776545555566664478************88888888 PP

                                       HHHHSHHHCTTSTTTSEEEEEESSBSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 145 ilnqlpqitcdgklqrqvivlSATlpk 171
                                       i+ q +      kl    i++SATlp+
  gi|488600767|ref|YP_007907238.1| 162 IAMQSA------KLGFPSIIMSATLPD 182
                                       888883......344459*******93 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.68
                                       HHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  39 vyetkgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       v++ k ++  k ++v+ t e a+  + +l++ ++y
  gi|488600767|ref|YP_007907238.1| 233 VLN-KAENCRKLVVVVNTVERAQRLYLDLREKTDY 266
                                       222.4445555566666666666666555555555 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   2.2e-16   5.6e-13      10     121 ..     582     750 ..     567     751 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.2e-16
                                       HHHHHHHHHHHH..HHHHHHHHHHHHHTTTTHHHHTS..HHH...........HHH...CTCCHHHHHHHHHHHHHH CS
                                HD  10 klarrlaedlge..eedrellllaaLlHDiGkgpfgdafekk...........eee...fekflaHekvgaeilrev 70 
                                       ++++ +a++ g+  +e+++l+++++ lHD+Gk  +  ++ k              +    ++++ H+ v+a+ l+ +
  gi|488600767|ref|YP_007907238.1| 582 YVIKNFADYFGYeyNEFVDLIKCITALHDLGKLNIT-WQKKVswdskiplahsD-KnnvSGGLPPHAPVSAKALQPY 656
                                       344444555555889*******************99.99999**9999877642.2679999*************** PP

                                       HHHHHHH...HHHHHHHHHTTCCHHHHHHHH....................................H....HHHCC CS
                                HD  71 ekrlgld...ledvaklirehheswegkkrp....................................r....glaer 104
                                       +++l++d   +++++ +i++hh +w++++++                                    +    ++a+r
  gi|488600767|ref|YP_007907238.1| 657 LESLFDDedvFKAFYLAIAHHHAPWVREYKEyslipdfdkfieevwsvpkelikahdsagrldftylDlideNEAYR 733
                                       ****999*********************999*******************9999999988887766615667***** PP

                                       TSCHHHHHHHHHHHHHH CS
                                HD 105 qlslearivklaDrlaa 121
                                        + l+++++++ Drla+
  gi|488600767|ref|YP_007907238.1| 734 LYGLLSKLLRISDRLAT 750
                                       ***************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 !   31.1   0.0   8.9e-11   2.3e-07      10     111 .]     234     339 ..     223     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 8.9e-11
                                       HHHTTTTSEEEEEESSHHHHHHHHHH...HHHTTSTEEEESTTSTHHHHHHHHHHHH.....TTSSS.EEEESGGGT CS
                        Helicase_C  10 lkleeeggkilifvntidrlekvkll...lekkgikvavlhgelpqnereeileqfn.....kgesd.vLiatdvae 77 
                                       l++ e+ +k +++vnt++r+++  l    +ek ++ ++ lh++   ++r +  +        +g+   + i+t+v+e
  gi|488600767|ref|YP_007907238.1| 234 LNKAENCRKLVVVVNTVERAQR--LYldlREKTDYPILLLHSRYLEEDRAKKEKFLEevfgkNGKGEcIFISTQVVE 308
                                       466788899*********9974..3333367779*********999998854433333335589999899******* PP

                                       SSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        G+di   + Vi  ++   v+ +iqr+GR++R g
  gi|488600767|ref|YP_007907238.1| 309 VGMDIS--SPVILSEAA-PVDALIQRAGRCARWG 339
                                       *****6..677777766.69************86 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.3e-10   8.5e-07       3     168 ..      13     179 ..      11     182 .. 0.71
   2 ?   -3.2   0.1       2.8   7.1e+03      56      63 ..     242     249 ..     198     291 .. 0.58

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.3e-10
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       +++eyQ+ a+enl+      + k ++i ++TG+GKT va + +i+ l    + ++ +   p+++l+e   e+ +k++
  gi|488600767|ref|YP_007907238.1|  13 NPYEYQKIAMENLV------EGKSLIIRAPTGSGKTEVAlIPFIYGLNDFLP-SQLIYSLPTRTLVESIGERATKYA 82 
                                       7899*********8......5678***************9999999999888.5999999***************** PP

                                       GG........GEEEESSS-B--.......-SEEEEEHHHHHHTH..............HHHTTT-S.......EEEE CS
                            ResIII  79 seayke....igkkvsgdkkkakekdstnkkilvttiqsldadseee......eeeseellrdrfd.......viii 138
                                       s ++ +    +     g+k +   ++  + +i+vtti++   +          +++ +               + ++
  gi|488600767|ref|YP_007907238.1|  83 SFKKLRvathH-----GKKAT---SSLFEEDIIVTTIDQTAGAY-LSvplsmpKRWGNI------FvggvasaLTVF 144
                                       **987533222.....22222...245678*******9999999.33344444443333......14555557**** PP

                                       ETGGGTTS.TTTHHH..HHT---...SEEEEEESS CS
                            ResIII 139 DEaHrlgakkswrei..lekfke...avllglTAT 168
                                       DE+H l  +k  + +  + + ++   +  + ++AT
  gi|488600767|ref|YP_007907238.1| 145 DEVHTLDPEKGLQTAaaIAMQSAklgFPSIIMSAT 179
                                       *****999874444311222222234445556666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.8
                                       -EEEEESS CS
                            ResIII  56 kflflvpr 63 
                                       k +++v++
  gi|488600767|ref|YP_007907238.1| 242 KLVVVVNT 249
                                       33333333 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.63   1.6e+03     116     165 ..      89     153 ..      81     168 .. 0.60
   2 !   24.0   0.0   1.4e-08   3.7e-05      37     127 ..     586     685 ..     557     749 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.63
                                       HHTTTS---HHHHHTSS-HHHHTT...............HHHHHHHHHHHHHHHHCT-TTS-S.. CS
                              HD_6 116 vggHHGkppkeeeekaekkssaae...............dweeaqkelleaaaeflgaaaallle 165
                                       v+ HHGk  +++  +++   ++ +               +w +++   ++ a+++++++ +l++e
  gi|488600767|ref|YP_007907238.1|  89 VATHHGKKATSSLFEEDIIVTTIDqtagaylsvplsmpkRWGNIFVGGVASALTVFDEVHTLDPE 153
                                       788***55444433332222222245666666666666666666666666666666666666555 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.4e-08
                                       HHHHHC.TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH....... CS
                              HD_6  37 llarllrgleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle....... 106
                                       ++a+ + g e +++ +l+ +++alHDlGK++   q+kv+  ++   +++ +++ +   ++H+ ++a  l+       
  gi|488600767|ref|YP_007907238.1| 586 NFADYF-GYEYNEFVDLIKCITALHDLGKLNITWQKKVSWDSKIPLAHSDKNNVSGGLPPHAPVSAKALQpyleslf 661
                                       355555.99999999***********************7666655555555555669***********888999999 PP

                                       ...HHHHHHHHHHHTTTS---HHH CS
                              HD_6 107 ...evarslaaavggHHGkppkee 127
                                          +v +++  a++ HH   ++e 
  gi|488600767|ref|YP_007907238.1| 662 ddeDVFKAFYLAIAHHHAPWVREY 685
                                       997777777777777777444433 PP

>> Na_H_antiport_2  Na+-H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.4e-06    0.0035      29      86 ..     133     191 ..     129     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.4e-06
                   Na_H_antiport_2  29 lvgGlvgglsleetieafa..sGlgggaevAlsyallGafAvaisksgltdllvkkvikl 86 
                                       +vgG+ ++l++ + ++++   +Gl++ a +A+  a lG f  +i ++ l+d+++++v ++
  gi|488600767|ref|YP_007907238.1| 133 FVGGVASALTVFDEVHTLDpeKGLQTAAAIAMQSAKLG-FPSIIMSATLPDVFIERVGER 191
                                       79****************877****************9.777888889******998765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00014      0.35       8      67 ..      17      76 ..      13      92 .. 0.87
   2 ?   -1.7   0.0      0.64   1.6e+03     139     163 ..     406     430 ..     402     458 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----S CS
                              PhoH  8 eQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGf 67
                                       Qk ++e+l + + +++ +p+G+GKt +a+   +  l++   +++i++ p+ +  e++G 
  gi|488600767|ref|YP_007907238.1| 17 YQKIAMENLVEGKSLIIRAPTGSGKTEVALIPFIYGLNDFLPSQLIYSLPTRTLVESIGE 76
                                      59999999999999*****************99999999999999999888887777775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.64
                                       HHTTB-TT-EEEEEE---------- CS
                              PhoH 139 fltRlGenskvvvtGdvtqidlpkg 163
                                       f  RlGe +++v  G+ ++++++++
  gi|488600767|ref|YP_007907238.1| 406 FYQRLGELARAVYEGSKAKVEQNVR 430
                                       78899**9**999999999887743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 4574.84
//
Query:       gi|488600768|ref|YP_007907239.1|  [L=350]
Description: hypothetical protein Asulf_01250 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2087.31
//
Query:       gi|488600769|ref|YP_007907240.1|  [L=120]
Description: hypothetical protein Asulf_01251 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   13.0   0.0       0.21   12.1   0.0    1.5  1  SAM_1     SAM domain (Sterile alpha motif)


Domain annotation for each model (and alignments):
>> SAM_1  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.2e-05      0.21      18      47 ..      56      84 ..      48      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                                      GGGHHHHHTTTSSHHHHTTSCHHHHHHCTT CS
                             SAM_1 18 gqYadlFrageidgdaLlllteddLeklgv 47
                                       +Y+   r+g+  g+ L +l+e+dLe+l+ 
  gi|488600769|ref|YP_007907240.1| 56 RRYETIARRGY-KGKELSRLSEKDLEELMG 84
                                      5888889****.***************653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); 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: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 681.39
//
Query:       gi|488600770|ref|YP_007907241.1|  [L=317]
Description: CRISPR-associated autoregulator, Csa2 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-72  242.5   0.0    4.7e-72  242.3   0.0    1.0  1  DevR       CRISPR-associated negative auto-regulator DevR/Csa
      0.007   16.4   0.0      0.016   15.2   0.0    1.5  1  SBDS_C     SBDS protein C-terminal domain
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.17   11.3   0.0    1.4  1  RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> DevR  CRISPR-associated negative auto-regulator DevR/Csa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.3   0.0   7.8e-76   4.7e-72       1     267 [.       9     277 ..       9     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 242.3 bits;  conditional E-value: 7.8e-76
                                       EEEEEE-------------------EEEEEE--TT--EEEEEE-THHHHHHHHHHHHHHHHTSTTSSBHHHHTT--- CS
                              DevR   1 isgrvvvnveaLNmdesvGNytehrkvpvvlkeeykvrtvpaiSgeslkHayfetlvklakennlpvcelckrvegd 77 
                                       i gr+++++++LN++++vGN+te r v+++++++ k +t++ iSge+lkH+++e+++ l ++n  ++c++ck ++ +
  gi|488600770|ref|YP_007907241.1|   9 ILGRATWQLHSLNNEGTVGNVTEPRSVRIIDPNTKKAVTTDGISGEMLKHIHTEIMWALDDKN--NLCDACKVLNPE 83 
                                       679************************************************************..7*********** PP

                                       ---TT--EEEBTTSEESS-HHHHHHH-HHHHHH-EEEGGGT..EEE--SEEE--BEE-TTTTTTT-----------. CS
                              DevR  78 ggvikfatekklkekelkvekeiikecvveDvfGfLitekeksvkRkspvkfsyavpveesekavvdaqfharydl. 153
                                       ++++  +t+k+++++ ++++k+++++c ++Dv+GfL++   ++++Rks+v+f++a++++e++    d ++har++l 
  gi|488600770|ref|YP_007907241.1|  84 KFNFAIKTKKVTTKDVEDALKQALETCDICDVQGFLLE--RPTASRKSTVEFGWALGIPEVY---RDIHTHARHALg 155
                                       *************************************9..5559******************...5**********9 PP

                                       ......------------------HHHHHSSEEEEEEEEEGGGTTS-TTS--EE---S-HHHHHHHHHHHHHTHHHH CS
                              DevR 154 ......lenrarkkgeeeekqnifqvEehsalYalsfvlDldriGkpevkkskieyvleeeerkkRikaalkallnl 224
                                               ++++ + e+ ++q++++++++s++Ya+  v++ +riG +ev++sk++y  ++  r++R+k alka+ +l
  gi|488600770|ref|YP_007907241.1| 156 ekgrggRNQENEGETEGVSTQMVYHRPTRSGVYAVISVFQPWRIGLNEVRQSKYTYDADDSARERRYKLALKAYQLL 232
                                       9998875555566667899********************************************************** PP

                                       HH--------------EEEEEEEE--SSS-----..-TTTTHHHH CS
                              DevR 225 LsgsfgakrarllPvfeveslvaavskkpfpvfp..irledyvee 267
                                       + ++ ga++++ lP++e++s+v+++s+ p+pv+   + ++dyv+e
  gi|488600770|ref|YP_007907241.1| 233 FARPEGAMTTTRLPHVEDFSGVIVYSTEPIPVPIisPLKNDYVNE 277
                                       **********************************97888****97 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.7e-06     0.016      12      66 ..      36      94 ..      33     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-06
                                      HEEBTTTTB---HHHHH.HHHHHTT----TTS-CCCCHHHHHHHHT.TTS-..-EE-EE CS
                            SBDS_C 12 klvnpqtkrpytttmIe.kalkelgtsvktnksaksQalevikaLi.qeip..iqrarm 66
                                      ++++p+tk++ tt  I+ ++lk+++t++      k+   ++ k L+ ++++  i+ +++
  gi|488600770|ref|YP_007907241.1| 36 RIIDPNTKKAVTTDGISgEMLKHIHTEIMWALDDKNNLCDACKVLNpEKFNfaIKTKKV 94
                                      78***********9998478899999999999999999999999987666633444443 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 ?   11.3   0.0   2.9e-05      0.17      38      63 ..      81     108 ..       3     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                         RNA_pol_L  38 dkdklilevetdgsl..kPeealkeAlk 63 
                                       +++k+++ ++t+ ++  ++e+alk+Al+
  gi|488600770|ref|YP_007907241.1|  81 NPEKFNFAIKTKKVTtkDVEDALKQALE 108
                                       789*********999788********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2128.15
//
Query:       gi|488600771|ref|YP_007907242.1|  [L=228]
Description: CRISPR-associated protein Cas5, subtype I-A/APERN [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       448  (0.0249875); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1325.56
//
Query:       gi|488600772|ref|YP_007907243.1|  [L=65]
Description: hypothetical protein Asulf_01254 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.078   13.1   0.2       0.13   12.3   0.2    1.3  1  CIDR1_gamma  Cysteine-Rich Interdomain Region 1 gamma


Domain annotation for each model (and alignments):
>> CIDR1_gamma  Cysteine-Rich Interdomain Region 1 gamma
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   7.5e-06      0.13       2      34 ..       5      41 ..       5      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-06
                       CIDR1_gamma  2 tIdVlmidrrgkfikeylkn....lfkesrLFkgirk 34
                                      tI+V + dr ++ +k ++++    l ++ rLF+++r+
  gi|488600772|ref|YP_007907243.1|  5 TIKVRVPDRFEEIFKREVEElakaLIEKERLFEKLRE 41
                                      7*******************99999*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 430.35
//
Query:       gi|488600773|ref|YP_007907244.1|  [L=151]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-22   79.1   0.0    5.4e-22   78.6   0.0    1.3  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.086   13.6   0.0       0.15   12.8   0.0    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 !   78.6   0.0   6.1e-26   5.4e-22       1     118 [.       4     131 ..       4     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 6.1e-26
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHS.........SCHCHHHHHHHHHHHHHHHT CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlar.........rkskrekaaelvelllllsa 67 
                                       +++D+s li++++g +ka ++ + l     +l+++++v++E+ y   r           ++  k+ +++ l+ ll++
  gi|488600773|ref|YP_007907244.1|   4 VLIDSSLLIEYFKGNPKAVEIFENLKTSpVALLINPIVFSEVSYLFLRystkksrfdFTPEVVKSSKIETLFVLLNS 80 
                                       68****************9999999988*************************9999889999************** PP

                                       SEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                               PIN  68 lkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                       + il++++ei+  a+ i+ kygllpnDali+At+k +gik +++ D df++
  gi|488600773|ref|YP_007907244.1|  81 FGILDLTKEIVILAENIMVKYGLLPNDALILATCKFYGIKYLISLDGDFKE 131
                                       ****************************************999******98 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   1.7e-05      0.15       1      55 [.       3      56 ..       3     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                             PIN_3  1 rvvlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelayp 55
                                      rv++D++ l++++   +p a  i++ l+t ++ l++ p ++ E+ + + r ++++
  gi|488600773|ref|YP_007907244.1|  3 RVLIDSSLLIEYFK-GNPKAVEIFENLKTSPVALLINPIVFSEVSYLFLRYSTKK 56
                                      8*************.678***************************9996655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1076.68
//
Query:       gi|488600774|ref|YP_007907245.1|  [L=80]
Description: hypothetical protein Asulf_01256 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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    9.8   5.0         35    4.2   1.9    2.9  3  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 ?    4.1   0.0    0.0022        39      62      85 ..       1      25 [.       1      32 [. 0.79
   2 ?    1.5   0.1     0.014   2.5e+02      19      30 ..      36      47 ..      27      52 .. 0.62
   3 ?    4.2   1.9     0.002        35      22      34 ..      64      76 ..      46      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0022
                    Synaptonemal_3 62 ledeflkC.kavlcsladeqekkvh 85
                                      +edefl+    ++cs  d+ e+ ++
  gi|488600774|ref|YP_007907245.1|  1 MEDEFLNNfMQIICSGVDNGEVTIR 25
                                      699999752679******9998875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.014
                    Synaptonemal_3 19 lqlnkdleklte 30
                                      ++lnk +e+l  
  gi|488600774|ref|YP_007907245.1| 36 VDLNKVVERLEK 47
                                      455555555543 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.002
                    Synaptonemal_3 22 nkdleklteqmed 34
                                       k+lekl+e++ed
  gi|488600774|ref|YP_007907245.1| 64 GKNLEKLLEEIED 76
                                      499********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 525.27
//
Query:       gi|488600775|ref|YP_007907246.1|  [L=85]
Description: hypothetical protein Asulf_01257 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-26   90.9   0.3    3.5e-26   90.7   0.3    1.0  1  UPF0175          Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
      0.031   14.0   0.0      0.063   13.0   0.0    1.6  1  HTH_psq          helix-turn-helix, Psq domain
      0.046   13.9   0.1      0.069   13.3   0.1    1.2  1  Endonuc-dimeris  T4 recombination endonuclease VII, dimerisat


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 !   90.7   0.3   5.9e-30   3.5e-26       1      74 [.       8      80 ..       8      81 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 5.9e-30
                           UPF0175  1 ipdellqalklteeelerelrialAvklYeegrlSlgkAaelaglsrveflelLarrgiplinydeeeleeDle 74
                                      ip+el+  l+ + +el + +r+ lA++lY+eg++SlgkA+e+agls++e++e+La++gi+ ++ydee+l+eD+e
  gi|488600775|ref|YP_007907246.1|  8 IPQELARILGVKASELPKVVRLYLAIELYREGKVSLGKASEIAGLSKWEMMEILASKGIS-LQYDEEDLKEDIE 80
                                      8***********************************************************.7**********98 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 ?   13.0   0.0   1.1e-05     0.063       5      25 ..      29      49 ..      27      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                           HTH_psq  5 laaAleavvnGkmSirkAArk 25
                                      l +A+e +++Gk+S+ kA+ +
  gi|488600775|ref|YP_007907246.1| 29 LYLAIELYREGKVSLGKASEI 49
                                      568***************987 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 ?   13.3   0.1   1.2e-05     0.069      13      42 ..      49      80 ..      44      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                      HHTS-HHHHHHHHHHTT-..---TTS-HHHHH CS
                   Endonuc-dimeris 13 FSRLkkeEqkeellslGi..kYnesdkKsdLi 42
                                         L k E++e l s+Gi  +Y+e d K d++
  gi|488600775|ref|YP_007907246.1| 49 IAGLSKWEMMEILASKGIslQYDEEDLKEDIE 80
                                      5668999**********8557*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 510.85
//
Query:       gi|488600776|ref|YP_007907247.1|  [L=160]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   33.0   2.8    4.7e-08   32.7   0.5    2.1  2  DUF3368   Domain of unknown function (DUF3368)


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 ?   -0.1   0.1     0.047   8.5e+02       8      27 ..      10      29 ..      10      37 .. 0.82
   2 !   32.7   0.5   2.6e-12   4.7e-08       1      45 [.     113     158 ..     113     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.047
                           DUF3368  8 LllAKqrGlIpsvkplldaL 27
                                      L+ + + G+++ +k+l+ ++
  gi|488600776|ref|YP_007907247.1| 10 LITLAKIGKLSTLKELFGEI 29
                                      67788999999999998765 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 2.6e-12
                           DUF3368   1 vtGTLGiLllAKqrGlIps.vkplldaLiqaGfrispklyaevLrl 45 
                                       v G+L+++  AK++G+I +   +++  L+ +G+r s+++++++ +l
  gi|488600776|ref|YP_007907247.1| 113 VAGSLAVIYIAKKKGIIKEdFDEIVKILRLKGIRFSDEVVRKLKEL 158
                                       78***************************************99875 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:                      416  (0.0232026); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1070.53
//
Query:       gi|488600777|ref|YP_007907248.1|  [L=393]
Description: putative flavoprotein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   0.0    2.3e-13   50.6   0.0    1.4  1  Flavodoxin_1   Flavodoxin
    6.6e-08   32.8   0.0    1.2e-07   32.0   0.0    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00015   21.5   0.0    0.00032   20.4   0.0    1.5  1  PGM_PMM_I      Phosphoglucomutase/phosphomannomutase, alpha/b
    0.00068   19.2   0.0     0.0015   18.1   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.029   14.0   0.1       0.12   12.0   0.0    1.9  2  Peripla_BP_6   Periplasmic binding protein
       0.11   12.3   0.4        1.5    8.5   0.4    2.2  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 !   50.6   0.0   7.6e-17   2.3e-13       1     143 []     253     384 ..     253     384 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 7.6e-17
                                       EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGH.HHHHHHHHHH CS
                      Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppenge.sffqdllelk 76 
                                       i+Y+++  +teklA++la+++ ++g +++++++++    +  i++e+l ++ ++   +G+p++++  ++ ++ +  +
  gi|488600777|ref|YP_007907248.1| 253 IVYDTMWHSTEKLARALADGAASAGAKVRMFHIRKDP--WAAIMTEILDAKAIA---VGSPTMHNTvFPPVAGFLAY 324
                                       89***********************999999999988..78*************...9****99999999******9 PP

                                       CHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTST.HGHHHHHHHH CS
                      Flavodoxin_1  77 gdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednq.egqeeafrkW 143
                                       ++      l+ ++    ++G++++ +   a+k+++  +eel +e++ + l++   ++ e++e+af+++
  gi|488600777|ref|YP_007907248.1| 325 MK-----GLKPKNKIGMAFGSYGWGG--GAVKEINRVFEELKFEVVEP-LQVRFRPTgEELEAAFNAG 384
                                       74.....57789999***********..********************.***************9875 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0     4e-11   1.2e-07       7     155 ..      35     169 ..      30     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4e-11
                                       EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                       Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                       n+yli  d++  L+Dt  +  ++ +++   ++ ++p ++d++i  H  +DH G l+++++ ++ +v+++ + + +++
  gi|488600777|ref|YP_007907248.1|  35 NAYLI-LDDKIALVDTVKHKFYGEMME-RIKKLIDPSQIDYIIANHVETDHSGSLADIKRVAKDAVVVCTKRGMEGI 109
                                       99***.8***************99996.777889******************************************* PP

                                       CHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
                       Lactamase_B  84 meeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallag 155
                                         + ++  + +             v++ ++++ +g   +     + +h ++++  + +++ +l++ Da+ ++
  gi|488600777|ref|YP_007907248.1| 110 SKHFNTNGWDFN------------VVKSGDELKLGKKTLMFLEMTMLHWPDSMATYVKEDELLLSNDAFGQH 169
                                       ****99887765............9*******************************************9844 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 !   20.4   0.0   1.1e-07   0.00032      25      93 ..     234     302 ..     224     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHHHCHHCSTS-EEEEEE-S-TTH.HHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECE CS
                         PGM_PMM_I  25 klgqaiaeylkaeakkkkvvvGrDtRvss.relaealaaglaanGvevillgllptPavsfairklkada 93 
                                       ++++a+ e+ +  +++ kvv+ +Dt  +s ++la+ala g+a++G++v +++++  P ++ +++ l+a+a
  gi|488600777|ref|YP_007907248.1| 234 RIINAYKEWAEF-KTEDKVVIVYDTMWHStEKLARALADGAASAGAKVRMFHIRKDPWAAIMTEILDAKA 302
                                       556666666666.4899*******98655278****************************9999999877 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 !   18.1   0.0   4.9e-07    0.0015       4     101 ..      46     134 ..      45     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.9e-07
                                       EES--TT.HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   4 LiDagpd.lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       L+D++   + + ++ +    +++ ++++id ++  h + DH   l ++++ ++ ++ ++++k+ ++ ++++f  + +
  gi|488600777|ref|YP_007907248.1|  46 LVDTVKHkFYGEMMERI---KKLIDPSQIDYIIANHVETDHSGSLADIKRVAK-DAVVVCTKRGMEGISKHFNTNGW 118
                                       56777666666644333...3577899***********************665.56688************877666 PP

                                       HTTTTEEEEEE-TTSEEEECST CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdg 101
                                       + +       ++ g++++lg+ 
  gi|488600777|ref|YP_007907248.1| 119 DFN------VVKSGDELKLGKK 134
                                       655......5555555555543 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.2   6.5e+03     153     195 ..      60      99 ..      42     106 .. 0.49
   2 ?   12.0   0.0   3.9e-05      0.12      53     175 ..     231     371 ..     230     383 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHCCTEE.EEEEEEE-TTHHHHHHHHHHHHTTT-SEEE CS
                      Peripla_BP_6 153 aalkaaakaaGge.vvgeepvplgttdfsaqvlqikaagadavl 195
                                       + +k+++  + ++ ++      + +td s  ++ ik+   dav+
  gi|488600777|ref|YP_007907248.1|  60 ERIKKLIDPSQIDyII----ANHVETDHSGSLADIKRVAKDAVV 99 
                                       4444444444444222....222335555555555555555554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.9e-05
                                       SHHHHHHHHHHHHH...CT--SEEEE-BSHHHHHHHHHHHHH......HT-EEEE.....SS........-HHCCTT CS
                      Peripla_BP_6  53 dpdraaeaarrlvd...qdgvdalvgplssavaaavaevlak......dgvpvig.....pa........gltgekc 107
                                       +p+r ++a++++ +   +d+v ++++++  + ++ +a +la+      ++v +++     +a        + +   +
  gi|488600777|ref|YP_007907248.1| 231 NPERIINAYKEWAEfktEDKVVIVYDTMWHS-TEKLARALADgaasagAKVRMFHirkdpWAaimteildAKAIAVG 306
                                       6788888888887744469999999998887.455555555545555566666666666422233333221222577 PP

                                       STTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TT CS
                      Peripla_BP_6 108 spyvfslgpsysaqasalveylakelggkkvalvyadyafgregiaalkaaakaaGgevvgeepvplg 175
                                       sp + ++ + +   +++++ y++    + k+++    y +g  +++ + ++++++ +evv++ +v + 
  gi|488600777|ref|YP_007907248.1| 307 SPTMHNTVFPP---VAGFLAYMKGLKPKNKIGMAFGSYGWGGGAVKEINRVFEELKFEVVEPLQVRFR 371
                                       88888888887...677777755544588*******************************99888764 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4   0.00051       1.5      16     142 ..     262     362 ..     250     371 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00051
                                       HHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHH CS
                           FMN_red  16 trklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllK 92 
                                       t+kla+++a+ ++ aga+v ++++++                   d  a++   i +a a+ +++P+ + ++ ++  
  gi|488600777|ref|YP_007907248.1| 262 TEKLARALADGAASAGAKVRMFHIRK-------------------DPWAAIMTEILDAKAIAVGSPTMHNTVFPPVA 319
                                       66666666666666666666666666...................34578899999999999999999999999999 PP

                                       HHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EE CS
                           FMN_red  93 nalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaiv 142
                                        +l ++     +   ++K++++++  g  +gg +a+ +   v+ el+  v
  gi|488600777|ref|YP_007907248.1| 320 GFLAYMK----GLKPKNKIGMAFGSYG--WGG-GAVKEINRVFEELKFEV 362
                                       9999996....6677777776663333..455.44455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2327.07
//
Query:       gi|488600778|ref|YP_007907249.1|  [L=200]
Description: Multimeric flavodoxin WrbA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-34  118.7   0.0    2.3e-34  118.4   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    3.2e-07   30.3   0.0    3.6e-07   30.1   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 !  118.4   0.0   2.5e-38   2.3e-34       3     148 ..       2     151 ..       1     157 [. 0.92

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 2.5e-38
                                       EEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-SC CS
                           FMN_red   3 ilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaada 75 
                                       il+i+GS+r ++ t+ ++++a+++l+++g+e+e+++++++ i  c   ++c+k++e  +   dd+ el+  +++a++
  gi|488600778|ref|YP_007907249.1|   2 ILGICGSPR-KKATEHVLREALAMLEKDGIETEFFTVRKKeISFCqhcDYCLKKKE--CRIRDDMYELYPLMKEAEG 75 
                                       89******8.778********************************99888887775..68***************** PP

                                       EEEEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSEE CS
                           FMN_red  76 liivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraav 148
                                        i++tP+Yng++s+++K+++Dr+++    + + +r+K+++++avgg+r gg++++ q  + +   +g i+v+++ +
  gi|488600778|ref|YP_007907249.1|  76 YIFATPVYNGGVSAQIKAVMDRTRAivVENMDVFRHKIGMAIAVGGDRIGGQELAIQQIHTFFiLNGIIPVSGGFF 151
                                       ***********************99**9***********************************5577777766655 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.1e-11   3.6e-07       3     103 ..       2      98 ..       1     156 [. 0.80

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.1e-11
                                       EEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT...CHHHHHHHHHHHH CS
                      Flavodoxin_2   3 iLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek...padveseqiekll 76 
                                       iL i ++pr+  + + ++++++++ lek g  e + + + +  + ++++ d+      +++   + d ++     ++
  gi|488600778|ref|YP_007907249.1|   2 ILGICGSPRK--KATEHVLREALAMLEKDG-IETEFFTVRKKEISFCQHCDYC---LKKKEcriRDDMYELY-PLMK 71 
                                       678999**99..788***************.8888888888766666664443...2222233236666666.**** PP

                                       CSSEEEEEEE-BTTB--HHHHHHHHHH CS
                      Flavodoxin_2  77 aadaivlqfPlwwfgvPailKgwiDrv 103
                                       +a+ +++++P+++ gv+a+ K+ +Dr 
  gi|488600778|ref|YP_007907249.1|  72 EAEGYIFATPVYNGGVSAQIKAVMDRT 98 
                                       *************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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 0.33s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1232.29
//
Query:       gi|488600779|ref|YP_007907250.1|  [L=385]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.0    5.5e-52  176.0   0.0    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    2.2e-32  112.0   0.1    3.8e-32  111.3   0.1    1.4  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.3e-29  102.2   0.1      2e-29  101.6   0.1    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.1e-21   77.5   0.0    3.6e-21   75.9   0.0    1.8  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.088   12.5   0.0       0.14   11.8   0.0    1.3  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0   0.0   1.5e-55   5.5e-52       1     149 [.     232     380 ..     232     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 1.5e-55
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       ++Gf++++e ++ +R+ +aa+alg+a+ a++++++y+++rk+fg+p++ +q++++++a++++ +e +rll+y+ a+ 
  gi|488600779|ref|YP_007907250.1| 232 NRGFYQVLEFFDESRIEIAAQALGIAQGAFDRTVKYVKERKQFGQPIGGFQALQHRIADLRTLIECTRLLIYKSAWN 308
                                       79*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +d+g+ d+  +smaK++a ++a++v+d+a+q++Gg+Gy  ey ver+yrd+++++i+eGt e+q+n+ia+ +
  gi|488600779|ref|YP_007907250.1| 309 YDQGRIDPGLTSMAKYMAGKVAVKVCDEAIQMHGGYGYIGEYDVERFYRDSKITEIYEGTKEVQLNTIAKDV 380
                                       *********************************************************************987 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.1   1.1e-35   3.8e-32       1     112 [.       7     118 ..       7     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.1e-35
                                       THHHHHHHHHHHHHHHHHT.HHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-H CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeel.aphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelarada 76 
                                       t+eq+++++++refae+e  +++a+e+de++efp elwkk++elG++gi++peeygGag+++le+++v+ee+ rad+
  gi|488600779|ref|YP_007907250.1|   7 TQEQKDIQKAAREFAENEFtKERAEEADEKEEFPFELWKKACELGFIGIHFPEEYGGAGMGILENVLVVEEFCRADS 83 
                                       78*****************888999999999********************************************** PP

                                       HHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  77 glalllgvhsslvapailrfGteeqkrryLpklasg 112
                                        l++++ ++ +  +++++rfG+e+ k + Lpk+a g
  gi|488600779|ref|YP_007907250.1|  84 TLGSAIILS-DFSSEVVMRFGSEDLKSEVLPKVAGG 118
                                       **9988775.57779******************988 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.1   5.5e-33     2e-29       3      97 .]     125     220 ..     123     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 5.5e-33
                                       E---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEEE-- CS
                     Acyl-CoA_dh_M   3 alTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvsvrr 77 
                                       + TEp+aGsd++++kt  ae+dg+e+v+nG+K++itn++ia++++vla t+ ++  r+rg+++flv +da+g+s ++
  gi|488600779|ref|YP_007907250.1| 125 CYTEPEAGSDLTAIKT-KAEKDGDEWVINGTKTFITNGTIADYYIVLAVTDPDAkpRYRGFTTFLVRKDAEGLSTNK 200
                                       89**************.77788888************************44333688******************** PP

                                       ---BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                       i +k+G+r  pt+e+ f++v
  gi|488600779|ref|YP_007907250.1| 201 IGKKMGIRASPTAEVIFKNV 220
                                       ******************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.86   3.1e+03      52      73 ..      15      37 ..       2      46 .. 0.58
   2 !   75.9   0.0   9.9e-25   3.6e-21       3     133 ..     249     369 ..     247     370 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.86
                                      HHHHHHHHHHHHHHHHH.HHTT- CS
                     Acyl-CoA_dh_2 52 dAAralleraaaraeal.aaagk 73
                                      +AAr++ e+ +++  a  a++++
  gi|488600779|ref|YP_007907250.1| 15 KAAREFAENEFTKERAEeADEKE 37
                                      47777777777764443244444 PP

  == domain 2  score: 75.9 bits;  conditional E-value: 9.9e-25
                                       HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHH CS
                     Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtved 79 
                                       iaa+alG+A++a++ +v++++er++  +g+++  ++a+q+++a++++ ++  r+l+++ a+      ++g+     d
  gi|488600779|ref|YP_007907250.1| 249 IAAQALGIAQGAFDRTVKYVKERKQ--FGQPIGGFQALQHRIADLRTLIECTRLLIYKSAWN----YDQGRI----D 315
                                       89***********************..***********************************....555554....4 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  80 raearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                           ++a+ +a + a++++d++++++Gg+++  e+ ++R++RD ++++++++++
  gi|488600779|ref|YP_007907250.1| 316 PGLTSMAKYMAGKVAVKVCDEAIQMHGGYGYIGEYDVERFYRDSKITEIYEGTK 369
                                       68899*********************************************9876 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.9e-05      0.14     179     227 ..     149     197 ..     128     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                                       EEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEE CS
                            HpaB_N 179 ivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlk 227
                                        v++G+k ++T++ +ad+ +vl +  + ++   +    f v+ da+Gl+
  gi|488600779|ref|YP_007907250.1| 149 WVINGTKTFITNGTIADYYIVLAVTDPDAKPRYRGFTTFLVRKDAEGLS 197
                                       69**********************88855557777889*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2434.15
//
Query:       gi|488600780|ref|YP_007907251.1|  [L=419]
Description: 3-isopropylmalate dehydratase, large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-100  336.5   0.5    2.4e-63  214.8   0.1    2.1  2  Aconitase       Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.068   12.1   0.0       0.12   11.3   0.0    1.5  1  Neisseria_PilC  Neisseria PilC beta-propeller domain
      0.081   11.6   0.0       0.14   10.8   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 !  214.8   0.1     4e-67   2.4e-63       2     305 ..       8     286 ..       7     291 .. 0.89
   2 !  121.3   0.0   8.7e-39   5.2e-35     334     461 .]     287     411 ..     285     411 .. 0.96

  Alignments for each domain:
  == domain 1  score: 214.8 bits;  conditional E-value: 4e-67
                         Aconitase   2 kiwdahlvee..eg.iayv.pdrvllqdvtgvqalvdlaaa..reavrrlggtlatidhlvpvdlvidhsvgaeeal 72 
                                       ki+++   +e   g   +   dr +++d+tg+ a++ +++   + +v+++++ +   dh+vp+d     s+      
  gi|488600780|ref|YP_007907251.1|   8 KIFSKASGKEvkAGeFVFAeIDRAMIHDITGPLAIKVFNEItnNGKVWDPSKIVIAFDHQVPAD-----SI------ 73 
                                       666544333332332334378*****************8772245679****************.....66...... PP

                         Aconitase  73 eknledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgie 149
                                               +  +e+ + L+++ak+ gi  +++ +GI Hq+++E g +lpg++vvg DSHT+m+g+lG++ +G+G+++
  gi|488600780|ref|YP_007907251.1|  74 --------NA-AENHKLLRKFAKEQGILNYDVYEGIAHQIMVERGHVLPGMLVVGADSHTCMYGALGAFSTGIGSTD 141
                                       ........22.356789************************************************************ PP

                         Aconitase 150 aeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaE 226
                                       + +v++  +l++k+p+++++ ++Gkl++ v +kD++l++ig ++++g++ ++ Ef+G++v+++ + +r+T+aNMa+E
  gi|488600780|ref|YP_007907251.1| 142 MGSVFALGKLWFKVPETIRFIVEGKLQKRVYSKDVILKLIGLVGADGANYCACEFTGSTVREMGMSERLTMANMAIE 218
                                       ***************************************************************************** PP

                         Aconitase 227 vGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpl 303
                                       +G ++g++++d+ t +YL       +   ++ y++ +    + +deda+y++++eld+ +lep+va p+r++++v++
  gi|488600780|ref|YP_007907251.1| 219 MGGKAGIIEPDKVTENYLG------EI--IDGYENPDW---VFSDEDASYKRIVELDATKLEPQVAKPHRVDNVVDV 284
                                       *******************......33..467777555...559*******************************99 PP

                         Aconitase 304 se 305
                                        e
  gi|488600780|ref|YP_007907251.1| 285 GE 286
                                       54 PP

  == domain 2  score: 121.3 bits;  conditional E-value: 8.7e-39
                         Aconitase 334 lkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvga 410
                                       ++ +kvd+++igSCTN++ ed+++ a++l+     g kv++gv+++v P+++ + +++ ++Gl +i+ +aG+ v  +
  gi|488600780|ref|YP_007907251.1| 287 VEGVKVDQVFIGSCTNGRFEDLKISAEMLE-----GEKVARGVRLIVIPATRSIYRKALKDGLIDIFVDAGAIVEFP 358
                                       67899*************************.....****************************************** PP

                         Aconitase 411 gCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLaSPelvvaaAlaG 461
                                        C++C+g   + + +ge++vs+sNRNF gRqg p+++ yL+SP+ ++a+A+ G
  gi|488600780|ref|YP_007907251.1| 359 SCGPCMGgSFGLIGNGEVSVSTSNRNFVGRQGsPEGKIYLVSPATAAATAIYG 411
                                       *******7778889*****************8799999*************87 PP

>> Neisseria_PilC  Neisseria PilC beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.1e-05      0.12      77     131 ..      90     145 ..      33     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
                                       ----------HHHHHHHH---EEEEE.EETTEEEEEEEEE-TTS-SEEEEEE-SSC CS
                    Neisseria_PilC  77 rklaekGyvGgadrfyvdGsfvladi.dfdkakhtvliGalrlGGkGlfaldlsdp 131
                                         l    y G a++  v+ + vl  +   + + ht ++Gal++   G+ + d+   
  gi|488600780|ref|YP_007907251.1|  90 GILNYDVYEGIAHQIMVERGHVLPGMlVVGADSHTCMYGALGAFSTGIGSTDMGSV 145
                                       44555679***************998789999***********9999999888763 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.3e-05      0.14     288     357 ..     289     360 ..     262     374 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.3e-05
                            DUF521 288 eekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtC 357
                                         kvd v++G c    +e+l+  ae+l+g+k++ +v+l+v+ + r+++++a + gl+++  +aG+ v   +C
  gi|488600780|ref|YP_007907251.1| 289 GVKVDQVFIGsCTNGRFEDLKISAEMLEGEKVARGVRLIVIpATRSIYRKALKDGLIDIFVDAGAIVEFPSC 360
                                       56789999985677789999999**************998746789******************98765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2573.78
//
Query:       gi|488600781|ref|YP_007907252.1|  [L=181]
Description: putative hydrolase of the alpha/beta superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-06   27.7   0.1     0.0022   17.7   0.0    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold
    5.7e-05   23.8   0.0    9.7e-05   23.1   0.0    1.4  1  Abhydrolase_6  Alpha/beta hydrolase family
    0.00028   20.2   0.0       0.29   10.3   0.0    2.9  2  Hydrolase_4    Serine aminopeptidase, S33
     0.0012   18.6   0.0     0.0017   18.1   0.0    1.1  1  Abhydrolase_5  Alpha/beta hydrolase family
     0.0051   16.3   0.0       0.56    9.6   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.011   15.4   0.0       0.64    9.6   0.0    2.1  1  FSH1           Serine hydrolase (FSH1)
      0.034   13.7   0.0      0.047   13.2   0.0    1.2  1  DLH            Dienelactone hydrolase family
        0.1   12.7   0.0       0.13   12.4   0.0    1.2  1  Abhydrolase_4  TAP-like protein
        0.2   11.2   0.0       0.22   11.0   0.0    1.2  1  PE-PPE         PE-PPE domain


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 !    8.3   0.0   0.00078       1.6      72      92 ..      82     102 ..      35     113 .. 0.84
   2 !   17.7   0.0   1.1e-06    0.0022     206     251 ..     117     164 ..     105     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00078
                                       TSSEEEEEETHHHHHHHHHHH CS
                     Abhydrolase_1  72 ddkltlvGhSmGGmialayaa 92 
                                        +++++vG+S+G+ +a+++++
  gi|488600781|ref|YP_007907252.1|  82 FESVAVVGYSFGSVVASNLLE 102
                                       47899************9998 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.1e-06
                                       C..THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                     Abhydrolase_1 206 e..lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHl 251
                                       +  lkn   p lvi + +D+++p+++++++a++l+  r+vv++ + H+
  gi|488600781|ref|YP_007907252.1| 117 SigLKNSETPKLVIVAKHDQIIPYEESVEIASWLNPPRRVVEVETDHF 164
                                       255799999************************888799999999997 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.9e-08   9.7e-05      16      96 ..      38     125 ..      20     180 .. 0.58

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.9e-08
                                       HHHH.HHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC..EE. CS
                     Abhydrolase_6  16 vapL.aallaagvhvlapDlpGhGrsdpppldledladlaalldelaagggpvvlvGHSlGGalalaaaplalvvg. 90 
                                        +++  +l  ag+++la+D++      p  +++ +++d  a l+ l+++   v +vG+S+G ++a+    l+   + 
  gi|488600781|ref|YP_007907252.1|  38 IMRIsEELNDAGITTLAFDYR-----KPFRDGVGEVEDAIACLRFLRERFESVAVVGYSFGSVVASN---LLEANSl 106
                                       4455556667779*******9.....677777777777766666665446889**************...6644445 PP

                                       EEES-.............. CS
                     Abhydrolase_6  91 vlldp.............p 96 
                                       vl++p             +
  gi|488600781|ref|YP_007907252.1| 107 VLISPlrkinsiglknseT 125
                                       *****55555444444441 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00015      0.29      59     114 ..      68     116 ..      34     121 .. 0.75
   2 !    5.0   0.0    0.0065        13     190     215 ..     123     148 ..     119     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                       Hydrolase_4  59 vdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkik 114
                                       v+D+ a ++ ++e+ +   + ++G S G+++a ++l+ ++     l+l++P+ ki+
  gi|488600781|ref|YP_007907252.1|  68 VEDAIACLRFLRERFES--VAVVGYSFGSVVASNLLEANS-----LVLISPLRKIN 116
                                       67888888888877765..59*************997655.....48888887776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0065
                       Hydrolase_4 190 itlPllllhGeaDkvvdpeasrelye 215
                                        ++P l++ +++D+++++e+s e++ 
  gi|488600781|ref|YP_007907252.1| 123 SETPKLVIVAKHDQIIPYEESVEIAS 148
                                       579****************9987765 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.6e-07    0.0017      57     146 ..      83     169 ..      69     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.6e-07
                     Abhydrolase_5  57 ekfvvgGhslGGvvasrfaaeee..kiegvvflasYPekdelselskkvlsivgteDgvlnvkslekakkflpkdtk 131
                                       e   v G+s+G vvas++ + ++   i ++  + s      l++ +++ l iv+++D+++++++  + +  l    +
  gi|488600781|ref|YP_007907252.1|  83 ESVAVVGYSFGSVVASNLLEANSlvLISPLRKINSIG----LKNSETPKLVIVAKHDQIIPYEESVEIASWLNPPRR 155
                                       667899**************99844566666666654....899999****************************** PP

                     Abhydrolase_5 132 vvsieGgnhagfGsY 146
                                       vv++e  +h   G+Y
  gi|488600781|ref|YP_007907252.1| 156 VVEVET-DHFYTGKY 169
                                       **9995.56666666 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0083        16      40      82 ..      63     101 ..      54     106 .. 0.83
   2 !    9.6   0.0   0.00028      0.56     138     170 ..     121     151 ..     102     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0083
                                       GGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHH CS
                      Peptidase_S9  40 lgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaal 82 
                                        g  e++D ia++++l +++    e +a+ G S+G +++  +l
  gi|488600781|ref|YP_007907252.1|  63 DGVGEVEDAIACLRFLRERF----ESVAVVGYSFGSVVASNLL 101
                                       577899**********9988....569********88776655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00028
                                       GG-----EEEEEEETT-SSS-THHHHHHHHHHH CS
                      Peptidase_S9 138 dnvkaypplLlihGlaDdrvppaealklvaaLq 170
                                       +n   ++p L+i++ +D+ +p++e++++++ L+
  gi|488600781|ref|YP_007907252.1| 121 KN--SETPKLVIVAKHDQIIPYEESVEIASWLN 151
                                       33..899*******************9999887 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00032      0.64     158     201 ..     121     164 ..      51     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                              FSH1 158 dkiqtptLhvlGelDtvvdeerseaLaeafknsskvlkHpggHf 201
                                       ++ +tp L ++ + D++++ e+s ++a   +  ++v++ + +Hf
  gi|488600781|ref|YP_007907252.1| 121 KNSETPKLVIVAKHDQIIPYEESVEIASWLNPPRRVVEVETDHF 164
                                       34589999999999999999999999999999999999999998 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.047      73     168 ..      61     148 ..      35     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                               DLH  73 vaeekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapila 149
                                           + + ++++a+a l+  + +  + v+vvG+ +G  +a +l   +      v   +   + + +  +++++p l+
  gi|488600781|ref|YP_007907252.1|  61 F--RDGVGEVEDAIACLRFLR-ERFESVAVVGYSFGSVVASNLLEAN----SLVLISP-LRKINSIGLKNSETPKLV 129
                                       4..566778899999999999.6669**********98888777666....6888889.77788888999******* PP

                               DLH 150 lfgeeDefipadeveklee 168
                                       +++++D++ip +e  ++++
  gi|488600781|ref|YP_007907252.1| 130 IVAKHDQIIPYEESVEIAS 148
                                       **********998766665 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.3e-05      0.13      31      91 ..     121     180 ..      90     181 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                     Abhydrolase_4  31 akgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYL 91 
                                       +++++p L++ +++D + Pye   ++a+ l+  + v++ +++H  ++++ + + ++v+++L
  gi|488600781|ref|YP_007907252.1| 121 KNSETPKLVIVAKHDQIIPYEESVEIASWLNPPRRVVEVETDHF-YTGKYDFLARTVREFL 180
                                       34479***************************999999999997.4566666667777776 PP

>> PE-PPE  PE-PPE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.22      31      99 ..      63     133 ..      42     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                            PE-PPE  31 eGtenLeaairaela...agekvvvfGySqgalvasnekarla.alsepaapdqlsfvlvgnpnrpnggllar 99 
                                       +G+ ++e+ai          e+v+v+GyS g++vasn ++     l +p +  +++ + + n + p+ +++a 
  gi|488600781|ref|YP_007907252.1|  63 DGVGEVEDAIACLRFlreRFESVAVVGYSFGSVVASNLLEANSlVLISPLR--KINSIGLKNSETPKLVIVAK 133
                                       5666666555543222226678*************9865432202233333..55655555666555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1185.99
//
Query:       gi|488600782|ref|YP_007907253.1|  [L=183]
Description: putative domain HDIG [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   43.2   0.1    4.8e-11   42.9   0.1    1.3  1  HD        HD domain
    1.4e-05   24.6   0.1    2.7e-05   23.7   0.1    1.4  1  HDOD      HDOD domain
     0.0034   17.1   0.1       0.44   10.3   0.0    2.1  2  HD_4      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 !   42.9   0.1     8e-15   4.8e-11       2      96 ..      20      97 ..      19     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 8e-15
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                                HD  2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldled 80
                                      + H++++  ++++la++lg  ed+e+++++++lHDi    +g+           +  H   gaeil+ ++ ++     +
  gi|488600782|ref|YP_007907253.1| 20 IKHCIATSAIMKELAKELG--EDEEKWEIIGILHDIDYEMVGE----------DMTQHGLKGAEILKSEGVDD-----E 81
                                      68*****************..****************999887..........6888****************.....9 PP

                                      HHHHHHTTCCHHHHHH CS
                                HD 81 vaklirehheswegkk 96
                                      +++++r h++   g++
  gi|488600782|ref|YP_007907253.1| 82 IVEVVRTHNHTLFGNY 97
                                      ********99988663 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   4.6e-09   2.7e-05      88     161 ..      12      84 ..       3      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.6e-09
                                       -SS-HHHHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHHHH---HHHHH CS
                              HDOD  88 egadlkklwehslavAlvarelaeelgledpeeaflaGLLhdiGklvllsllpeeleellekvaeeelslleae 161
                                       ++++ ++l +h++a++++++ela+elg ++ e+  + G+Lhdi   ++ + + ++  +++e  ++e+++++ +e
  gi|488600782|ref|YP_007907253.1|  12 KHVKSENLIKHCIATSAIMKELAKELGEDE-EKWEIIGILHDIDYEMVGEDMTQHGLKGAEILKSEGVDDEIVE 84 
                                       5788999*********************99.*************999999999999999999999986665444 PP

>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0021        13      14      35 ..      13      34 ..       4      53 .. 0.72
   2 !   10.3   0.0   7.4e-05      0.44      11      83 ..      53     127 ..      44     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0021
                              HD_4 14 kltgepllahalevAailaelg 35
                                      + ++e+l++h+++++ai++el 
  gi|488600782|ref|YP_007907253.1| 13 HVKSENLIKHCIATSAIMKELA 34
                                      55789*************9994 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.4e-05
                              HD_4  11 gqrkltgepllahalevAailaelgldaetviAalLhdvv..edalsleeirerfGeevarLvegvsklkrlqkv 83 
                                        + +  ge++++h+l+ A+il++ g+d+e v     h+     +  +  ei+ +  ++v+ L+ +++ +k+ +  
  gi|488600782|ref|YP_007907253.1|  53 IDYEMVGEDMTQHGLKGAEILKSEGVDDEIVEVVRTHNHTlfGNYSKPVEIALQSADSVSGLIVACALVKKGKLS 127
                                       5567789**********************7655555444411555677888888889999999888877665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1241.70
//
Query:       gi|488600783|ref|YP_007907254.1|  [L=255]
Description: Pyrroline-5-carboxylate reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   87.7   1.5    7.8e-25   87.1   0.5    1.8  1  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
    2.5e-19   69.6   0.5    5.7e-19   68.5   0.2    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.7e-11   44.0   1.0      7e-11   42.0   0.4    2.2  2  ApbA             Ketopantoate reductase PanE/ApbA
      2e-11   44.3   0.7    4.6e-11   43.1   0.2    1.7  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    8.6e-11   41.7   0.2    1.6e-10   40.8   0.1    1.5  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    1.1e-09   37.9   0.0    1.7e-09   37.3   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    2.6e-07   30.7   0.3    9.9e-06   25.6   0.3    2.4  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    1.6e-05   25.0   0.0    3.3e-05   24.0   0.0    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.8e-05   25.2   0.0    7.5e-05   23.2   0.0    1.9  2  CoA_binding_2    CoA binding domain
    6.5e-05   23.2   0.3    0.00026   21.2   0.3    2.2  1  TrkA_N           TrkA-N domain
    7.2e-05   22.7   0.3    0.00014   21.8   0.3    1.6  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00054   19.0   0.3     0.0012   18.0   0.3    1.5  1  PDH              Prephenate dehydrogenase
     0.0012   19.2   0.1      0.015   15.6   0.0    2.1  2  AlaDh_PNT_N      Alanine dehydrogenase/PNT, N-terminal domain
     0.0016   17.8   0.2      0.003   16.9   0.2    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0017   18.8   0.0      0.033   14.7   0.0    2.4  2  XdhC_C           XdhC Rossmann domain
     0.0017   17.8   0.4      0.009   15.5   0.2    2.2  2  adh_short        short chain dehydrogenase
      0.002   17.0   0.0       0.29    9.8   0.0    2.1  2  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
     0.0035   17.7   0.5      0.008   16.6   0.3    1.7  1  NAD_binding_7    Putative NAD(P)-binding
     0.0046   17.5   0.1      0.014   15.9   0.1    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0062   16.1   0.6       0.22   11.1   0.1    2.6  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
  ------ inclusion threshold ------
      0.011   15.9   0.1        1.7    8.9   0.1    2.8  1  UPF0180          Uncharacterised protein family (UPF0180)
      0.013   15.0   0.0      0.024   14.2   0.0    1.4  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.013   14.7   0.2      0.035   13.3   0.2    1.4  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.015   15.6   0.1      0.032   14.5   0.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.017   15.1   0.0      0.039   13.9   0.0    1.6  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.022   14.7   0.4      0.046   13.6   0.1    1.7  2  KR               KR domain
      0.023   14.7   0.1      0.047   13.7   0.1    1.6  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
      0.027   14.6   1.3        3.1    7.9   0.5    3.2  2  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
       0.03   14.2   0.1      0.089   12.7   0.1    2.1  1  LpxI_N           LpxI N-terminal domain
       0.03   13.7   0.0      0.072   12.4   0.0    1.6  1  ThiF             ThiF family
       0.03   13.9   0.0        0.1   12.2   0.0    1.9  2  DUF364           Putative heavy-metal chelation
      0.035   13.6   0.0      0.047   13.1   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
       0.05   13.9   0.1         11    6.4   0.0    2.7  2  B5               tRNA synthetase B5 domain
      0.066   13.9   0.8       0.31   11.8   0.1    2.4  2  CoA_binding      CoA binding domain
      0.069   12.8   0.1       0.34   10.5   0.0    2.0  2  MEIOC            Meiosis-specific coiled-coil domain-containi
      0.081   13.2   0.5       0.32   11.3   0.0    2.2  2  HutP             HutP
       0.16   12.4   0.0        0.3   11.6   0.0    1.4  1  Glyco_tran_10_N  Fucosyltransferase, N-terminal
       0.17   12.5   0.1       0.78   10.4   0.0    2.1  2  Corona_NS2       Coronavirus non-structural protein NS2


Domain annotation for each model (and alignments):
>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.5   1.7e-27   7.8e-25       1     100 [.     153     252 ..     153     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.7e-27
                                       CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHSHHHHHHHH--TTSHHHHHH CS
                        P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllesepaelrdkvtspgGtTiagl 77 
                                       Ek++d +ta sGs+pA+v+ +ie+++ ag + Gl+ e++++ a  +++ + + l++++p+e + kvt+p+GtTi+gl
  gi|488600783|ref|YP_007907254.1| 153 EKEVDLMTAFSGSAPAFVAKIIESFIYAGLNSGLNAEVSKKCALSVFKATSEALKTQSPEEFIIKVTTPAGTTIQGL 229
                                       899*************************************************998767******************* PP

                                       HHHHHTTHHHHHHHHHHHHHHHH CS
                        P5CR_dimer  78 keleegglraavieaveaaakrs 100
                                       ++l+e++++ a+ +a++a+a+r+
  gi|488600783|ref|YP_007907254.1| 230 RKLMEHRVDFAIVDALQATARRA 252
                                       ********************997 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.2   1.2e-21   5.7e-19       1      96 [.      10      97 ..      10      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.2e-21
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      ki+++GaGn+g a+a++l ++g   +e++v+  r +  +e+l++ +g +vt   n +a++ead+v+++vkp+d++++++
  gi|488600783|ref|YP_007907254.1| 10 KIAVLGAGNLGYAIAKRLKESG---YEVIVT-GRREAVLESLKK-MGCRVTN--NRDAVSEADFVIITVKPKDLDSLID 81
                                      7*********************...****66.999998988855.5778888..************************* PP

                                      HCGHHHHTTSEEEEESS CS
                     F420_oxidored 80 elakdalkgklvisvla 96
                                      e+ +d  +gk++is +a
  gi|488600783|ref|YP_007907254.1| 82 EI-RDCAEGKIIISFVA 97
                                      **.999********987 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.4   1.5e-13     7e-11       1     100 [.      11      94 ..      11     117 .. 0.89
   2 ?   -2.5   0.0       7.3   3.5e+03     115     130 ..     210     225 ..     198     242 .. 0.48

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.5e-13
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-S CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtv 76 
                                       ia+lGaG +G  +a +L++ g++v++ +r++  le+lkk G+r+t ++           +a+     +++d vi+tv
  gi|488600783|ref|YP_007907254.1|  11 IAVLGAGNLGYAIAKRLKESGYEVIVTGRREaVLESLKKMGCRVTNNR-----------DAV-----SEADFVIITV 71 
                                       89**********************************************...........333.....567******* PP

                                       SGGGHHHHHHHHGGGECTCEEEEE CS
                              ApbA  77 Kayqteealeeikplldpntvvll 100
                                       K  ++++ ++ei++  + + ++++
  gi|488600783|ref|YP_007907254.1|  72 KPKDLDSLIDEIRDCAEGK-IIIS 94 
                                       **************99998.4444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.3
                                       STTSEEEEEEEE-EEE CS
                              ApbA 115 lpkprvlggvtthgat 130
                                        p++ ++  +t+ g t
  gi|488600783|ref|YP_007907254.1| 210 SPEEFIIKVTTPAGTT 225
                                       3333333333333332 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 !   43.1   0.2   9.7e-14   4.6e-11       1     103 [.      10     109 ..      10     118 .. 0.87
   2 ?   -1.6   0.0       5.5   2.6e+03      27      95 ..     198     224 ..     183     244 .. 0.52

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 9.7e-14
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHC CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegll 77 
                                       ki+++G G++G  +a++l+++gy+v+v  r+++ +e+l + g+++ ++ +++v+++d+vi+ vk  k+ d++i+++ 
  gi|488600783|ref|YP_007907254.1|  10 KIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCRV-TNNRDAVSEADFVIITVKP-KDLDSLIDEI- 83 
                                       79***********************************99999965.56699************85.99*******5. PP

                                       CC--TT-EEEE-S---HHHHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelake 103
                                       + +++g+i+i +  ++  + ++++++
  gi|488600783|ref|YP_007907254.1|  84 RDCAEGKIIISFVAMKKLEDIRMNAK 109
                                       66999*****9888777777666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.5
                                       EE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HH CS
                     NAD_binding_2  27 vynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdilidgstsspe 95 
                                       v+  t+e+++                                          + ++++++i ++t + +
  gi|488600783|ref|YP_007907254.1| 198 VFKATSEALK------------------------------------------TQSPEEFIIKVTTPAGT 224
                                       4444443333..........................................33444444444444333 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 !   40.8   0.1   3.4e-13   1.6e-10       2      84 ..       6      86 ..       5     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.4e-13
                                      HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHH CS
                              IlvN  2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeee 80
                                      l++ kiav+G G+ G a a+ l++sg +v+v+ r+++  +++ k+ g +v++ ++av++ad+v+i +  +  ++++ +e
  gi|488600783|ref|YP_007907254.1|  6 LDSSKIAVLGAGNLGYAIAKRLKESGYEVIVTGRREA-VLESLKKMGCRVTNNRDAVSEADFVIITVKPKDLDSLI-DE 82
                                      7789****************************99998.999*********************99988666555555.55 PP

                                      TGGG CS
                              IlvN 81 iepn 84
                                      i++ 
  gi|488600783|ref|YP_007907254.1| 83 IRDC 86
                                      6655 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 !   37.3   0.0   3.6e-12   1.7e-09      31     101 ..       3      73 ..       1      93 [. 0.92

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3.6e-12
                                       BS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S-- CS
                      2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpl 101
                                        k+l  ++++++G+G++G a+akrlk+ g +vi++ r++   e+ +++g+++++  ++++e+D+v++++  
  gi|488600783|ref|YP_007907254.1|   3 EKSLDSSKIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCRVTNNRDAVSEADFVIITVKP 73 
                                       578999********************************99999***********************99875 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 !   25.6   0.3   2.1e-08   9.9e-06       1      41 [.      10      50 ..      10     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.1e-08
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeinee 41
                                      kiavlGaG+ G a+Ak l+e g ev + +r+e+++e++++ 
  gi|488600783|ref|YP_007907254.1| 10 KIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKM 50
                                      7*******************************998888764 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     7e-08   3.3e-05       9      84 ..       5      72 ..       1      90 [. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7e-08
                                      ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisata 84
                                      sl+++k+ ++GaG+++  +ak L ++g++ v+v++R  +  ++l +++       +++++ +++++ead vi+ ++
  gi|488600783|ref|YP_007907254.1|  5 SLDSSKIAVLGAGNLGYAIAKRLKESGYE-VIVTGRREAVLESL-KKM------GCRVTNNRDAVSEADFVIITVK 72
                                      7899************************9.******98777777.334......5678999999999999998765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.6e-07   7.5e-05       2      78 ..      10      86 ..       9     118 .. 0.79
   2 ?   -0.5   0.0       3.6   1.7e+03      57      84 ..     207     241 ..     147     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.6e-07
                                      -EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEE...S----T.....T--EEEE-S-HHHHGGGHHHHH CS
                     CoA_binding_2  2 tiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgek...vyaslaed.pepvdlvdvftppeatpeivkeal 76
                                      +iaV+G     g+ gy +++ l+e+g++v++   +e  ++  k   +  + ++d +++ d v + ++p+++ ++++e+ 
  gi|488600783|ref|YP_007907254.1| 10 KIAVLG----AGNLGYAIAKRLKESGYEVIVTGRREAVLESLKkmgCRVTNNRDaVSEADFVIITVKPKDLDSLIDEIR 84
                                      699999....6888******************9999666665534333333334699********************97 PP

                                      HH CS
                     CoA_binding_2 77 al 78
                                      ++
  gi|488600783|ref|YP_007907254.1| 85 DC 86
                                      76 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.6
                                       -.......EEEE-S-HHHHGGGHHHHHHH--SEEE CS
                     CoA_binding_2  57 d.......lvdvftppeatpeivkealalgakavw 84 
                                       +       ++ v tp+ +t + ++++ + ++  ++
  gi|488600783|ref|YP_007907254.1| 207 KtqspeefIIKVTTPAGTTIQGLRKLMEHRVDFAI 241
                                       13333345777888888888888877777766655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   5.6e-07   0.00026       1      51 [.      11      62 ..      11     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.6e-07
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEE.S-TTS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvv.gdatd 51
                                      i+++G+G++G+++a++L+e g++ v+v  ++e+++e+l++ g++v +  da +
  gi|488600783|ref|YP_007907254.1| 11 IAVLGAGNLGYAIAKRLKEsGYE-VIVTGRREAVLESLKKMGCRVTNnRDAVS 62
                                      79*****************7785.****************9998765456655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   3.1e-07   0.00014       1      44 [.      10      53 ..      10     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.1e-07
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                      k+av+GaG +G  ia+ + ++g+eV ++ ++e+ le+ +++  +
  gi|488600783|ref|YP_007907254.1| 10 KIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCR 53
                                      69*******************************99998876544 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   2.5e-06    0.0012       1      82 [.      23      99 ..      23     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.5e-06
                                      HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE-- CS
                               PDH  1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvg 79
                                      +a+ l+++g +v+v+g+ +   ++ ++  +g   +++   +av+ead+v++ v ++ +   + e+     e+ +i+   
  gi|488600783|ref|YP_007907254.1| 23 IAKRLKESGYEVIVTGRREAVLESLKK--MGCRVTNNR--DAVSEADFVIITVKPKDLDSLIDEIRD-CAEGKIIISFV 96
                                      799**************9999999998..555555555..47****************999999999.66666666555 PP

                                      S-- CS
                               PDH 80 svK 82
                                       +K
  gi|488600783|ref|YP_007907254.1| 97 AMK 99
                                      555 PP

>> AlaDh_PNT_N  Alanine dehydrogenase/PNT, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.2e-05     0.015      20      95 ..      24      99 ..      21     118 .. 0.80
   2 ?    1.3   0.0      0.84     4e+02      72     119 ..     199     247 ..     179     254 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.2e-05
                                      HHHHHHTT-EEEEETTTTGGGTC-HHHHHHTTEEEESCHHHHCTTSSEEEESS--.....CHCGGGS-TTCEEEEE--G CS
                       AlaDh_PNT_N 20 vkkLvkaGhevlVesgaGegagfsdeeYeeaGaeivesaeevlaeadlilkVkeps....eeelellkegqtlisflhl 94
                                      +k+L+++G+ev+V            e  +++G+++++++++v +++ +i+ Vk+ +     +e++ + eg+++isf+ +
  gi|488600783|ref|YP_007907254.1| 24 AKRLKESGYEVIVTGRR----EAVLESLKKMGCRVTNNRDAVSEADFVIITVKPKDldslIDEIRDCAEGKIIISFVAM 98
                                      7999********96555....55668899********99888888888999999966677889999**********988 PP

                                      G CS
                       AlaDh_PNT_N 95 a 95
                                       
  gi|488600783|ref|YP_007907254.1| 99 K 99
                                      7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.84
                                       S--.CHCGGGS-TTCEEEEE--GGC.HHHHHHHHHHCTEEEEEGGG-BS CS
                       AlaDh_PNT_N  72 kepseeelellkegqtlisflhlaa.npellealaekgvtaialElvpr 119
                                        + ++e l++ ++++ +i +  +a+   + l++l+e++v    +++++ 
  gi|488600783|ref|YP_007907254.1| 199 FKATSEALKTQSPEEFIIKVTTPAGtTIQGLRKLMEHRVDFAIVDALQA 247
                                       4445566666677777777777774477777777777777777777666 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 !   16.9   0.2   6.3e-06     0.003      28      99 ..       8      71 ..       4      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.3e-06
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE-- CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtv 99
                                       +k+ v+G+G  G + ++  k+ g +V v+  r+a+le l+++g + v+       + ++av+ead vi tv
  gi|488600783|ref|YP_007907254.1|  8 SSKIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCR-VT-------NNRDAVSEADFVIITV 71
                                      689*****************************************99.33.......3456677777777776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.1e-05     0.033       2      57 ..      12      77 ..      11     109 .. 0.74
   2 ?    1.9   0.0      0.62   2.9e+02      84     111 ..     202     228 ..     191     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.1e-05
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG............-GGG-TT-SE......-EEEE--S-HHHH CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa............tkerfpeade......tavvvlthdhklD 57
                                      +++Gag+ + a+a+ +++ g++v+v   re++             +        +      ++v++  +  +lD
  gi|488600783|ref|YP_007907254.1| 12 AVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLeslkkmgcrvtnN--------RdavseaDFVIITVKPKDLD 77
                                      799***************************7555666665544332........03444435555555555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.62
                                       HCTTS.--.......TTEESS-S--S-- CS
                            XdhC_C  84 rlerlraaglseeelarlhaPiGldiga 111
                                       + e+l + + +ee + ++++P+G  i++
  gi|488600783|ref|YP_007907254.1| 202 TSEAL-KTQSPEEFIIKVTTPAGTTIQG 228
                                       45556.45568889999******99987 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.9e-05     0.009       3      42 ..      11      49 ..       9      85 .. 0.82
   2 ?    0.1   0.0         1   4.8e+02      24      65 ..      63     105 ..      54     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevak 42
                                      + v Ga+  +G+aiak+l ++G++v+v++r+e+ le ++k
  gi|488600783|ref|YP_007907254.1| 11 IAVLGAG-NLGYAIAKRLKESGYEVIVTGRREAVLESLKK 49
                                      5677776.7**********************998877665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                                       T-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHH CS
                         adh_short  24 Gakvvvvdrseekleevakelkee.gakalaiqvDvtdreeve 65 
                                        a+ v++  ++++l  +++e++++ + k+++  v +++ e+++
  gi|488600783|ref|YP_007907254.1|  63 EADFVIITVKPKDLDSLIDEIRDCaEGKIIISFVAMKKLEDIR 105
                                       5677788888899999999999988778777777777666664 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 !    9.8   0.0   0.00062      0.29     268     340 ..       4      82 ..       2     114 .. 0.83
   2 ?    5.5   0.0     0.013       6.1     148     209 ..     115     250 ..      90     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00062
                                       HHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.......SEEEES.CHHHHHHHH CS
                    Oxidored_nitro 268 eylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleeg......epeviddadleeleeli 338
                                       + l   ++a+ g + + +a+a+ lke G ev+++g ++a  +  +++ +++ ++      ++ vi+++  ++l +li
  gi|488600783|ref|YP_007907254.1|   4 KSLDSSKIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCRVTNNrdavseADFVIITVKPKDLDSLI 80 
                                       678889***************************99999988888999999888866666644566666666666666 PP

                                       HH CS
                    Oxidored_nitro 339 ke 340
                                        e
  gi|488600783|ref|YP_007907254.1|  81 DE 82 
                                       55 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.013
                                       EEEEEETTCGH......GHHHHHHHHHHHHTE............................................. CS
                    Oxidored_nitro 148 vnilgeynlgp......gdlrelkelleklGl............................................. 173
                                        nil ey l++       d +e++ +l+klG                                              
  gi|488600783|ref|YP_007907254.1| 115 SNILCEYGLAFtayyceFDDDEIESILSKLGDvykakdekevdlmtafsgsapafvakiiesfiyaglnsglnaevs 191
                                       58999999998888888899999999999999999999999999999999999999999999999999999999999 PP

                                       .......................EEEEEECTSB-HHHHGGGGG-SEEEEESHHCHHHHH CS
                    Oxidored_nitro 174 .......................evnavftggtsleelraagraklnlvlcprsanyaa 209
                                                               ++++++ gt+++ lr++ + ++ +++ + +++ a 
  gi|488600783|ref|YP_007907254.1| 192 kkcalsvfkatsealktqspeefIIKVTTPAGTTIQGLRKLMEHRVDFAIVDALQATAR 250
                                       999999999999999999999999999999***********999999999888777555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   1.7e-05     0.008       5      99 ..       6     103 ..       5     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk..laeeelekdlegadlviaatddrelneria 79 
                                       l+  k+ v G+G++++  +++l e+g +v+v   + ++ le+l k  ++ ++ ++ +++ad+vi++++ ++l + i 
  gi|488600783|ref|YP_007907254.1|   6 LDSSKIAVLGAGNLGYAIAKRLKESGYEVIVTGRR-EAVLESLKKmgCRVTNNRDAVSEADFVIITVKPKDLDSLID 81 
                                       5678999************************9999.444554444224555558889**********9999999997 PP

                     NAD_binding_7  80 e..aakarrilvnvadkpelcd 99 
                                       e  ++ + +i +  +  ++l d
  gi|488600783|ref|YP_007907254.1|  82 EirDCAEGKIIISFVAMKKLED 103
                                       6557888888888877777766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     3e-05     0.014       1      38 [.      10      47 ..      10      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrll 38
                                      k++v+G+G++g   A+ l+e g +V v  r++ +l  l
  gi|488600783|ref|YP_007907254.1| 10 KIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESL 47
                                      79*******************************99544 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 !   11.1   0.1   0.00047      0.22       2      47 ..      10      55 ..       9      61 .. 0.90
   2 ?   -0.3   0.0       1.4   6.8e+02      68      85 ..      55      72 ..      38      84 .. 0.72
   3 ?    2.4   0.0      0.21     1e+02      97     138 ..     196     235 ..     178     245 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS- CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy 47
                                      ki+v+G+G +G   a  l e g evi+    e+  ++l++  + ++
  gi|488600783|ref|YP_007907254.1| 10 KIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCRVT 55
                                      8**************************9999999999988877765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                                      S-HHHHHHC-SEEEE--- CS
                    UDPG_MGDP_dh_N 68 tdvekaveeadvifiaVg 85
                                      t+ + av+ead ++i+V 
  gi|488600783|ref|YP_007907254.1| 55 TNNRDAVSEADFVIITVK 72
                                      445667999999999995 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.21
                                       THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHH CS
                    UDPG_MGDP_dh_N  97 lkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkilee 138
                                       l+  ++++++++      +  ++k T+p gt+ + ++k++e+
  gi|488600783|ref|YP_007907254.1| 196 LSVFKATSEALKTQS--PEEFIIKVTTPAGTTIQGLRKLMEH 235
                                       333333333333222..3344556677777776666666554 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0035       1.7      12      40 ..      23      69 ..      10     107 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0035
                           UPF0180 12 vkeaLrekGYeVvdlet..................eedaqsvdaiVv 40
                                      +++ L+e+GYeV+  +                    ++  ++d +++
  gi|488600783|ref|YP_007907254.1| 23 IAKRLKESGYEVIVTGRreavleslkkmgcrvtnnRDAVSEADFVII 69
                                      55666666666666555333322222222222221123555555555 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 ?   14.2   0.0   5.2e-05     0.024       5      40 ..      18      53 ..      14      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-05
                                      SHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHH CS
                      adh_short_C2  5 gIGraiAkalaeeGaevvltdlneeakkrveelaee 40
                                       +G+aiAk+l+e G+ev++t ++e+  ++++++  +
  gi|488600783|ref|YP_007907254.1| 18 NLGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCR 53
                                      58*********************9985555555433 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 ?   13.3   0.2   7.4e-05     0.035       2      34 ..      10      42 ..       9      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegt 34
                                      +++v+G+G  G+a a++l+++g++v++ +++++
  gi|488600783|ref|YP_007907254.1| 10 KIAVLGAGNLGYAIAKRLKESGYEVIVTGRREA 42
                                      577778888888888888888888777754333 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.8e-05     0.032       1      76 [.      11      95 ..      11     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.8e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...........TTTCEEEEE--TTTHHHHHHHH.. CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka...........lgvrfeaialdaenyeavLaal.. 66
                                      + ++GaG+ G a+a+ l++++ +  e++v +r ++ le l++ +           ++ +f +i++ +++ +++++++  
  gi|488600783|ref|YP_007907254.1| 11 IAVLGAGNLGYAIAKRLKESG-Y--EVIVTGRREAVLESLKK-MgcrvtnnrdavSEADFVIITVKPKDLDSLIDEIrd 85
                                      689***************997.6..8**********999975.459999999999999999999999999998877777 PP

                                      HTTSSEEEE- CS
                   Sacchrp_dh_NADP 67 lkegdlvvnl 76
                                      ++eg+++++ 
  gi|488600783|ref|YP_007907254.1| 86 CAEGKIIISF 95
                                      7777888875 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.2e-05     0.039       2      52 ..      19      85 ..      17     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.2e-05
                                      HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET...............TTC.HHHHHHHH CS
                        ADH_zinc_N  2 vGlaavqlAkalGaeviavdsseeklelakklGadeviny...............kea.dlverike 52
                                      +G a  + +k +G evi++ + e  le +kk+G+ ++ n+               k+  +l ++i++
  gi|488600783|ref|YP_007907254.1| 19 LGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCRVTNNRdavseadfviitvkpKDLdSLIDEIRD 85
                                      56777777899999*************************9666555555555555444445555555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.8e-05     0.046       8      70 ..      15      69 ..      10     110 .. 0.82
   2 ?   -2.3   0.0       7.4   3.5e+03     124     157 ..     152     187 ..     147     203 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.8e-05
                                      TTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHH CS
                                KR  8 GlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavea 70
                                      G+G+LG ++a+ l e+g + +++++R+       +a +++l+++g++v+  +  vs++d v  
  gi|488600783|ref|YP_007907254.1| 15 GAGNLGYAIAKRLKESGYE-VIVTGRR-------EAVLESLKKMGCRVTNNRDAVSEADFVII 69
                                      79**************976.6789999.......5799**********999988888887655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.4
                                       TTS--SEEEEEEEHHHHH--..TT-HHHHHHHHHHH CS
                                KR 124 edesldffvlfSSiagllgs..agqanYaaaNaflD 157
                                        ++++d+++ fS  a  + +   +   Ya  N+ l+
  gi|488600783|ref|YP_007907254.1| 152 DEKEVDLMTAFSGSAPAFVAkiIESFIYAGLNSGLN 187
                                       568889999998766544330034444555555555 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1    0.0001     0.047      25      92 ..      10      77 ..       3     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
                                      EEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB CS
                     AdoHcyase_NAD 25 vavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttGnkdii 92
                                      ++ v G G++G   a+ lk+ G  vivt             G +v++  ++v++ad+v+ t   kd+ 
  gi|488600783|ref|YP_007907254.1| 10 KIAVLGAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKMGCRVTNNRDAVSEADFVIITVKPKDLD 77
                                      45689***********************87654444444569*****************999888874 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5    0.0067       3.1       2      25 ..      10      32 ..       9      74 .. 0.90
   2 ?    3.3   0.0      0.18        83      95     131 ..     196     232 ..     192     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0067
                                      EEEEETTTSHHHHHHHHHHHHTTS CS
                           Ldh_1_N  2 kvavvGaaGgiGqslalllankkl 25
                                      k+av+Ga G+ G+++a  l+++++
  gi|488600783|ref|YP_007907254.1| 10 KIAVLGA-GNLGYAIAKRLKESGY 32
                                      9******.*********9998865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHH CS
                           Ldh_1_N  95 akIvkeiveaiakvapnaivlvvsNPvdiltevlkka 131
                                        +++k+  ea++  +p+ +++ v+ P+ ++ + l k 
  gi|488600783|ref|YP_007907254.1| 196 LSVFKATSEALKTQSPEEFIIKVTTPAGTTIQGLRKL 232
                                       5799***********************9988887775 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00019     0.089       7      43 ..      15      51 ..      10     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                            LpxI_N  7 GsGrlPllvaeaakaagrevvvvalegeadeelekiv 43
                                      G+G+l  ++a+++k++g+ev+v + ++++ e+l+k  
  gi|488600783|ref|YP_007907254.1| 15 GAGNLGYAIAKRLKESGYEVIVTGRREAVLESLKKMG 51
                                      9**************************9999999864 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015     0.072      14      43 ..       4      33 ..       2      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                      HHHHTSEEEEE--SHHHHHHHHHHHHHTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 14 ekLrdskvllvGaGglGsellknLalsGvg 43
                                      + L +sk++++GaG lG  ++k L  sG +
  gi|488600783|ref|YP_007907254.1|  4 KSLDSSKIAVLGAGNLGYAIAKRLKESGYE 33
                                      68999*******************999975 PP

>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022       0.1      11      69 ..       8      70 ..       2      88 .. 0.88
   2 ?   -2.0   0.0         5   2.4e+03     104     140 ..     117     153 ..     113     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                            DUF364 11 gkkVvvVGy....fapvlkklkekgaeltvlelnpnlleeeegdl.pdeaaeellpeadvviit 69
                                      + k++v G+    +  ++k+lke+g+e++v  +++  le  ++     + +  +++ead viit
  gi|488600783|ref|YP_007907254.1|  8 SSKIAVLGAgnlgY-AIAKRLKESGYEVIVTGRREAVLESLKKMGcRVTNNRDAVSEADFVIIT 70
                                      67888888877665.699*****************9999988877899***************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5
                            DUF364 104 vlfdyGvdviagvvvtdpdkllraiaeGggtkhlkrk 140
                                       +l +yG+ + a     d d++ +++++ g +++ k +
  gi|488600783|ref|YP_007907254.1| 117 ILCEYGLAFTAYYCEFDDDEIESILSKLGDVYKAKDE 153
                                       7899999999999999999999999988888887765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.047       2      33 ..      12      42 ..      11     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-ST CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlss 33
                                       V+Ga G +G a++k+l+e gyevi+  r++ 
  gi|488600783|ref|YP_007907254.1| 12 AVLGA-GNLGYAIAKRLKESGYEVIVTGRREA 42
                                      56776.***********************932 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.053        25      18      37 ..      40      58 ..      17      92 .. 0.79
   2 ?    6.4   0.0     0.024        11      14      39 ..     130     155 ..     104     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.053
                                      HHHHHHHHHHTT-E.EESST CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                                B5 18 eeeiikiLkrlgceriekdk 37
                                      +e + + Lk++gc++++ + 
  gi|488600783|ref|YP_007907254.1| 40 REAVLESLKKMGCRVTN-NR 58
                                      588999*******9533.33 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                                       S---HHHHHHHHHHTT-E.EESSTTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  14 idlseeeiikiLkrlgceriekdkdl 39 
                                       ++++++ei+ iL++lg  ++ kd+++
  gi|488600783|ref|YP_007907254.1| 130 CEFDDDEIESILSKLGDVYKAKDEKE 155
                                       8999************7655555554 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00065      0.31       4      93 ..       9      95 ..       7      98 .. 0.75
   2 ?   -0.7   0.0         5   2.4e+03      50      59 ..     198     207 ..     148     245 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00065
                                      EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTT.CEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHH CS
                       CoA_binding  4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvg.tevlglpvyksvdeleektevdvavitvPaesaqeavde 81
                                      +k++v Gag+lg a++ + ke  +y+ ++v g  +  +   +  g  v  + ++++ +  +d  +itv ++   + +de
  gi|488600783|ref|YP_007907254.1|  9 SKIAVLGAGNLGYAIAKRLKES-GYE-VIVTGRREAVLEsLKKMGCRVT-NNRDAVSE--ADFVIITVKPKDLDSLIDE 82
                                      79*********88877666665.333.2455555553332555599999.77777777..8****************** PP

                                      HHH.TT-SEEEEE CS
                       CoA_binding 82 lve.agikgivii 93
                                        + a+ k i+ +
  gi|488600783|ref|YP_007907254.1| 83 IRDcAEGKIIISF 95
                                      9999999999877 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 5
                                       EESCHHHHHH CS
                       CoA_binding  50 vyksvdelee 59 
                                       v+k+ +e+ +
  gi|488600783|ref|YP_007907254.1| 198 VFKATSEALK 207
                                       3333333333 PP

>> MEIOC  Meiosis-specific coiled-coil domain-containing protein MEIOC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00071      0.34      53     138 ..      69     159 ..      39     164 .. 0.74
   2 ?   -0.5   0.0       1.7   8.2e+02      58      73 ..     235     250 ..     217     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00071
                             MEIOC  53 lpanpsrvdrLivdqlreha..rvitLlakmErLrgvplhanisaaleehle....aikkvqarrkeeiinainrqr 123
                                       ++ +p  +d Li d++r+ a  ++i  +  m +L ++ ++a+i +a+ + l     a +  ++   ++ i++i  + 
  gi|488600783|ref|YP_007907254.1|  69 ITVKPKDLDSLI-DEIRDCAegKIIISFVAMKKLEDIRMNAKIVRAMSNILCeyglAFTAYYCEFDDDEIESILSKL 144
                                       567888889885.99999874468888889*****************987642222666666666666666666666 PP

                             MEIOC 124 qgaarvqedkdvlal 138
                                         + +++++k+v ++
  gi|488600783|ref|YP_007907254.1| 145 GDVYKAKDEKEVDLM 159
                                       666677777777655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                             MEIOC  58 srvdrLivdqlrehar 73 
                                        rvd  ivd l+  ar
  gi|488600783|ref|YP_007907254.1| 235 HRVDFAIVDALQATAR 250
                                       6899999999988887 PP

>> HutP  HutP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00067      0.32      33      83 ..     159     210 ..     143     230 .. 0.84
   2 ?   -1.2   0.0       5.1   2.4e+03      68      88 ..     234     254 ..     222     255 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00067
                                       EEEEEESS...HHHHHHHHHHHHHHTTSS-SS.SHHHHHHHHHHHHHHHHHH CS
                              HutP  33 avevggeaeelskkivesavvaAkregvikee.hreehavahAvleAlsqvt 83 
                                       ++ ++g+a   + ki+es + a +++g+  e   +   +v +A+ eAl+  +
  gi|488600783|ref|YP_007907254.1| 159 MTAFSGSAPAFVAKIIESFIYAGLNSGLNAEVsKKCALSVFKATSEALKTQS 210
                                       6789999999******************988857778899*******98655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.1
                                       HHHHHHHHHHHHHHHHTTSHH CS
                              HutP  68 ehavahAvleAlsqvtrkavg 88 
                                       eh v  A+++Al+  +r+a+g
  gi|488600783|ref|YP_007907254.1| 234 EHRVDFAIVDALQATARRAMG 254
                                       688888999999999998876 PP

>> Glyco_tran_10_N  Fucosyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00063       0.3      29      61 ..      48      78 ..      30     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00063
                   Glyco_tran_10_N 29 niseCelttdrslleeadavvfhhrdlvkklkd 61
                                      +  +C++t++r++++ead v++ ++   k+l  
  gi|488600783|ref|YP_007907254.1| 48 KKMGCRVTNNRDAVSEADFVIITVKP--KDLDS 78
                                      5579******************9887..55555 PP

>> Corona_NS2  Coronavirus non-structural protein NS2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       9.6   4.5e+03      61      89 ..     148     176 ..     140     183 .. 0.78
   2 ?   10.4   0.0    0.0017      0.78      58     100 ..     204     246 ..     182     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 9.6
                        Corona_NS2  61 ekpghekfitsftaygrtvqqavsklvee 89 
                                        k   ek +  +ta+  +    v+k++e 
  gi|488600783|ref|YP_007907254.1| 148 YKAKDEKEVDLMTAFSGSAPAFVAKIIES 176
                                       56777888888999988888888888886 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0017
                        Corona_NS2  58 kscekpghekfitsftaygrtvqqavsklveeavdfilfratq 100
                                       ++ +    e+fi  +t+   t  q + kl+e  vdf ++ a q
  gi|488600783|ref|YP_007907254.1| 204 EALKTQSPEEFIIKVTTPAGTTIQGLRKLMEHRVDFAIVDALQ 246
                                       4445567799**999999999999*************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 1664.53
//
Query:       gi|488600784|ref|YP_007907255.1|  [L=133]
Description: Holliday junction resolvase - archaeal type [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-30  103.5   0.0    5.7e-30  103.2   0.0    1.1  1  Hjc        Archaeal holliday junction resolvase (hjc)
    0.00033   20.2   0.0    0.00066   19.2   0.0    1.5  1  AHJR-like  REase_AHJR-like
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.19   12.0   0.0    1.4  1  UPF0102    Uncharacterised protein family UPF0102


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 !  103.2   0.0   9.6e-34   5.7e-30       2      92 ..       8      98 ..       7      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 9.6e-34
                                      HHHHHHHHHHHTT-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEEE CS
                               Hjc  2 yERelvkiLrergfavvRsagSggatkplpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllavk 80
                                      +ER+l++ L+e+gfa++R +gSg +  p+pD+iA++g+++++iEvK+++k ++y++++q++ l+ f++ +g+e ++++k
  gi|488600784|ref|YP_007907255.1|  8 FERDLIHKLWENGFAAIRTPGSGTVAYPVPDIIAGNGKKYIAIEVKMRSKLPLYIEEQQIKDLAMFSSLFGAECFIGLK 86
                                      8************************99**************************************************** PP

                                      ETTTEEEEEEGG CS
                               Hjc 81 lqgkewkllvve 92
                                      l++++w++++++
  gi|488600784|ref|YP_007907255.1| 87 LPREDWRFFRID 98
                                      *********986 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.1e-07   0.00066      15      76 ..      11      71 ..       1      75 [. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-07
                         AHJR-like 15 slaeqyrekGyevllhPnredlPdfLksYrpDliarkdeeaviiEvksrrs...saseqyLqela 76
                                      +l++++ e+G+  +  P++ ++        pD+ia +++++++iEvk r++    + eq++++la
  gi|488600784|ref|YP_007907255.1| 11 DLIHKLWENGFAAIRTPGSGTVAY----PVPDIIAGNGKKYIAIEVKMRSKlplYIEEQQIKDLA 71
                                      355555678888888888888743....37*******************9877677888887776 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.1e-05      0.19      29      68 ..      38      74 ..      37     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                                      EEEE..TTEEEEEEEEE-......-------HHHHHHHHHHH CS
                           UPF0102 29 Diia..tevlvfvEVKtRssekfgspaeavtprKqrrlrraa 68
                                      Diia  ++ ++ +EVK+Rs+         +++++++ l+   
  gi|488600784|ref|YP_007907255.1| 38 DIIAgnGKKYIAIEVKMRSKL-----PLYIEEQQIKDLAMFS 74
                                      9*****889*********644.....4445555554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 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:                        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: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 884.07
//
Query:       gi|488600785|ref|YP_007907256.1|  [L=329]
Description: Zn-dependent hydrolase, including glyoxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-15   58.0   3.2    4.7e-15   56.1   3.2    1.8  1  Lactamase_B  Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.026   13.9   0.0      0.036   13.5   0.0    1.1  1  DUF3387      Domain of unknown function (DUF3387)
      0.036   14.4   0.6      0.074   13.3   0.5    1.6  2  DUF5082      Domain of unknown function (DUF5082)


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 !   56.1   3.2   7.9e-19   4.7e-15       6     197 .]      38     238 ..      34     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 7.9e-19
                                       SEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       +n+y++    g ++iD G+ + ++   l  e+ +lg+ ++ ++ + +TH+H+DHiG l +   ++  ++ +++  ++
  gi|488600785|ref|YP_007907256.1|  38 SNVYIM----GEFVIDGGFISKEKAGELagEIERLGYRIDSLTFI-ITHHHIDHIGILLWYDIRAIMHPSENEFLLF 109
                                       666666....77888888877777777778888888888888876.6****************************** PP

                                       CCHCHHHHHHHHHCCHH...................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEE CS
                       Lactamase_B  81 alfmeeaddaasrkgll...................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvv 138
                                       + ++ +  + +  ++++                   +   ++      + +  ++    ++ +++++pgh++gh+++
  gi|488600785|ref|YP_007907256.1| 110 YTNPQHFVKPYLEWSSRygidlemlrplaeffrsgsR---VKGEANSLKKDFRIEYETPEGMEIIHTPGHSPGHICI 183
                                       ***************************8888864321...2222333333444445555667899************ PP

                                       EETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 139 eygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       +++ +k+lf+GD++l+  t +i+      + + +++++++++sl+kl   +++ ++p+H
  gi|488600785|ref|YP_007907256.1| 184 YIPKEKILFSGDLVLSVTTTHIGY----YPGYGQDPVGDQIESLRKLLSYEIDEIYPAH 238
                                       ************************....88888899999999999*************9 PP

>> DUF3387  Domain of unknown function (DUF3387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-06     0.036     172     240 ..     220     291 ..     218     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-06
                           DUF3387 172 velLkklLadeikarsrkNlvkskkFserLeelikkYnnraltsaevie...eLielakeikeekkrgeelg 240
                                       +e L+klL+ ei ++        k+ ++r++eli+ Y+nr  +    i+   + i++ak+i+ ++ ++e+l+
  gi|488600785|ref|YP_007907256.1| 220 IESLRKLLSYEIDEIYPAHEDTIKNAEQRIHELIEHYENRLEEVYSGIDgicNVIDVAKNISWSAGSFEKLD 291
                                       899***************99999******************7776666688899********9999999986 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.6   9.6e+03      94     108 ..      62      76 ..      58      81 .. 0.63
   2 ?   13.3   0.5   1.2e-05     0.074      74     119 ..     230     275 ..     217     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                           DUF5082  94 eeEIerLenqiseaq 108
                                         EIerL   i +++
  gi|488600785|ref|YP_007907256.1|  62 AGEIERLGYRIDSLT 76 
                                       457777766666655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.2e-05
                           DUF5082  74 nlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqln 119
                                       ++++ y + +d +++++++i e Ie +en ++e ++ +d + + ++
  gi|488600785|ref|YP_007907256.1| 230 EIDEIYPAHEDTIKNAEQRIHELIEHYENRLEEVYSGIDGICNVID 275
                                       6788899999*****************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2369.27
//
Query:       gi|488600786|ref|YP_007907257.1|  [L=241]
Description: glucose-6-phosphate isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  166.9   0.7    3.5e-49  166.5   0.7    1.1  1  GPI       Glucose-6-phosphate isomerase (GPI)
     0.0021   18.3   0.2     0.0033   17.6   0.2    1.4  1  ARD       ARD/ARD' family
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.023   14.3   0.0    1.2  1  Cupin_1   Cupin


Domain annotation for each model (and alignments):
>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.5   0.7   5.8e-53   3.5e-49       4     180 ..      17     190 ..      14     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 5.8e-53
                               GPI   4 ardlaavladeealkaltetldddvaYevsdslktaeegerlaadqliydvtvilPgkiGeEriktrGHyHkevdrr 80 
                                       a dl++vl+++e l++     ++ ++ +++d+  ++e+ e + +++l+yd+t   PgkiG+E ikt GHyH+e   +
  gi|488600786|ref|YP_007907257.1|  17 AFDLKPVLKNPEELEE-----NFPAYEMFRDVYFSEEDRELILNKRLRYDYTFTNPGKIGDEFIKTFGHYHPEIGDG 88 
                                       5699*******88888.....787888899*******************************************99** PP

                               GPI  81 strPEvYevlkGealmlLek..PeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlvpkdagqdYdvi 155
                                        t+PE+Ye ++G+a+++L+k   +++ ++dv++v  ++++ +i+PPnygHv in++++ + +an+v++d++++Yd++
  gi|488600786|ref|YP_007907257.1|  89 ITYPEIYEIIEGRAIFVLQKhgESFGEIEDVVIVYAEEGDKIIIPPNYGHVMINPTDNMIKTANWVCRDFSSIYDPY 165
                                       ********************86678**************************************************** PP

                               GPI 156 akarGmaayiieegevlrkrkndda 180
                                       +++rG  +y+  +g v+ +r n + 
  gi|488600786|ref|YP_007907257.1| 166 KQMRGGVYYYTINGWVKNERYNAPE 190
                                       ***9999999988888888877766 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   5.6e-07    0.0033      94     144 ..      93     149 ..      29     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.6e-07
                               ARD  94 eirliveGtgyFdvrskdeaw......irvlvekGDLivlPagiyhrFtltednkvk 144
                                       ei  i+eG ++F++++++e++      + v  e+GD i++P++  h     +dn +k
  gi|488600786|ref|YP_007907257.1|  93 EIYEIIEGRAIFVLQKHGESFgeiedvVIVYAEEGDKIIIPPNYGHVMINPTDNMIK 149
                                       67779***********9999944444333678**************99999999888 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.8e-06     0.023      55     107 ..      92     146 ..      80     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-06
                                       -EEEEEEESEEEEEEEETTSS...EEEEEE....EETTEEEEE-TT-EEEEEEESSSSE CS
                           Cupin_1  55 teiayvlqGegrvgfvvpgng..nrdfhkk....lreGdvfvvPaglvhfqynsgdepa 107
                                       +ei  +++G++   fv ++ g  +  ++ +     +eGd +++P+++ h+++n +  ++
  gi|488600786|ref|YP_007907257.1|  92 PEIYEIIEGRAI--FVLQKHGesFGEIEDVvivyAEEGDKIIIPPNYGHVMINPT--DN 146
                                       677778999988..555555544666666677789******************95..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1600.34
//
Query:       gi|488600787|ref|YP_007907258.1|  [L=269]
Description: hypothetical protein Asulf_01269 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.0    6.9e-12   45.3   0.0    1.3  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.022   14.6   1.4        1.5    8.7   0.1    2.6  3  T6PP_N        Trehalose-6-phosphate phosphatase N-terminal he
      0.065   12.8   0.9      0.085   12.4   0.7    1.4  1  Filament      Intermediate filament protein


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 !   45.3   0.0   1.2e-15   6.9e-12       2     193 ..      20     207 ..      19     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.2e-15
                                       HHHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC..HTTCSHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypded..erearreesvdalkr 74 
                                       +a+++aG+dg+E++  +++ +  +   +++   l +++++  ++ a +s+  + + + ++        +  ++++  
  gi|488600787|ref|YP_007907258.1|  20 DACEKAGYDGIEFWVETPHFWIKRvsLKHKNSSLVEMIKDSRIK-AIHSPVLDLNPVSVNdgV----CDLTLRETLY 91 
                                       8999******************99**9****************9.444444444444443223....5566****** PP

                                       HHHHHHHHTBSEEEEEBCCGBCTTTSGHH..HHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHH CS
                      AP_endonuc_2  75 aielaaaLGapllvlhpGtagagpkgsee..eawerlaeslneladyaekegvklalEtlagsgvelgd..eelarl 147
                                        i la+++G+ ++++h+G + +  ++  +  ++++ l + l+ + +y + ++vkl+lE+  +  ++l    ee++++
  gi|488600787|ref|YP_007907258.1|  92 SINLARKVGVNIVTVHAG-RRSAVRE--PvwSDYASLNNYLRIASKYSRIKNVKLCLENSEPRINYLCKsaEEVKEF 165
                                       ******************.3344444..34599999999*********9***************98888******** PP

                                       HHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESS CS
                      AP_endonuc_2 148 ldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakg 193
                                       +++ +   + +++D+ H++   + + + + +l dr+  +H++ ++ 
  gi|488600787|ref|YP_007907258.1| 166 MEKYE---LYFTFDVNHAIKG-NYFSRSFLELIDRMENIHVSGYDA 207
                                       *****...9**********88.778888888888888888865554 PP

>> T6PP_N  Trehalose-6-phosphate phosphatase N-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.6   3.6e+03      34      58 ..      83     107 ..      51     115 .. 0.68
   2 ?    4.2   0.1    0.0065        39      34      88 ..     142     196 ..     134     204 .. 0.86
   3 ?    8.7   0.1   0.00025       1.5      25      86 ..     208     267 ..     207     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.6
                            T6PP_N  34 vesLknakesLeadcetgtevlelr 58 
                                         +L+++++s++ +++ g ++++++
  gi|488600787|ref|YP_007907258.1|  83 DLTLRETLYSINLARKVGVNIVTVH 107
                                       4467777777777777666666655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0065
                            T6PP_N  34 vesLknakesLeadcetgtevlelrtteeekvrldikdEieeLekDlkFLefiqs 88 
                                         +L+n+   ++  c++ +ev e+ ++ e  +++d++  i++     +FLe i+ 
  gi|488600787|ref|YP_007907258.1| 142 KLCLENSEPRINYLCKSAEEVKEFMEKYELYFTFDVNHAIKGNYFSRSFLELIDR 196
                                       5679999999999999999999999999**************9999999998765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00025
                            T6PP_N  25 kgieirehfvesLknakesLeadcetgtevlelrtteeekvrldikdEieeLekDlkFLefi 86 
                                       kg++i +   e +k+++e+L++   +++ ++el+    +  r+d+k  ie L + l +L++i
  gi|488600787|ref|YP_007907258.1| 208 KGRHISAIGFEDIKRVLEELSDMGFNKKITVELDDL--AYGRMDLKRKIEMLARELDYLRKI 267
                                       6888888899999********545588877888777..99*******************975 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   1.4e-05     0.085     110     140 ..     238     268 ..     155     269 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 110 kdldeatlarvdLekkvesLkeelaflkkvh 140
                                        +ld++   r+dL +k+e L  el++l+k++
  gi|488600787|ref|YP_007907258.1| 238 VELDDLAYGRMDLKRKIEMLARELDYLRKIF 268
                                       589**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1814.58
//
Query:       gi|488600788|ref|YP_007907259.1|  [L=644]
Description: Secreted protein containing C-terminal beta-propeller domain distantly related to WD-40 repeats [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-103  346.6   0.1   1.2e-101  341.1   0.1    2.1  1  Beta_propel  Beta propeller domain
     0.0018   17.9   0.0     0.0036   16.9   0.0    1.4  1  PQQ_2        PQQ-like domain


Domain annotation for each model (and alignments):
>> Beta_propel  Beta propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.1   0.1  1.3e-105  1.2e-101       1     507 [.     125     629 ..     125     634 .. 0.88

  Alignments for each domain:
  == domain 1  score: 341.1 bits;  conditional E-value: 1.3e-105
                       Beta_propel   1 ySeTNvqvegVdEaDivktDGkyiyvvsg.skvvivdaeaeelklvseiklee......kfkieelyldgdrLvvis 70 
                                       yS+TNvqv+g+dE+DivktDGk+iy+ s+    + + +e+ ++++++ +  e+       ++  el+l +  Lvvi+
  gi|488600788|ref|YP_007907259.1| 125 YSTTNVQVAGIDEPDIVKTDGKNIYFSSRfYPFRYMPYENLKTRVIAAFPPENltelfkLEDSGELLLMNGLLVVIG 201
                                       9**************************5544445555555555555554222222244444567************* PP

                       Beta_propel  71 seeeeeeseaeeeeepilskeetkvliyDisdkenpkllreleldGsyvssRkigdklylvsskeaeeeeenekeae 147
                                       +                      ++++y+    en k l +++l+ +yvs+R+  +k+ylv++          + ++
  gi|488600788|ref|YP_007907259.1| 202 HD---------------------HISAYST---ENGKELWKIKLESEYVSARLYSGKIYLVTR----------SWID 244
                                       98.....................4555554...5679**************************..........5667 PP

                       Beta_propel 148 eakleellPkvseeeeklvacediylpdesesssyl.vvtsldlakdkavdskavl..gsgeevYvseenlYlas.. 219
                                         +   + P + e +  +v+c++iy+p  +  s+++  v+ ++ +  k  +s++++   s + vY+s++++Y+++  
  gi|488600788|ref|YP_007907259.1| 245 SYQPCPIKPVTVEGKPYTVSCREIYHPVVPVYSDVVyNVMIINESG-KIEKSTSFVgsISRSVVYMSSNAIYVTYhq 320
                                       7778888999988888889********9988887553677777665.4445555552567789************** PP

                       Beta_propel 220 .......................................................................eeyeee 225
                                                                                                              e+y+ e
  gi|488600788|ref|YP_007907259.1| 321 tidpadmmysflmenkdllpekvidriktlkeyniskrakyveiqeilneykrmlskderlkfenefwnrmEKYRDE 397
                                       **********************************************************************999999* PP

                       Beta_propel 226 eeksedkTeiykfalsdgkveyaasgeVpGtllnqFsldeydgyLRvattleteeseaetsnnvyvLdeklkevGkl 302
                                       ++++ +kT+i+k+++   ++e+ a geVpG llnqFs+dey+g+LRva+t         ++n +yvLd+++++vG +
  gi|488600788|ref|YP_007907259.1| 398 HKRELEKTQIVKIST---DLEPLAVGEVPGDLLNQFSMDEYKGFLRVAVT-------LGDTNDLYVLDSNMNVVGYI 464
                                       *************87...589*****************************.......5789**************** PP

                       Beta_propel 303 eglapgEriysvRFmgdraYlVTfrqtDPLFviDLsdpanPkilGeLkIpGySeYLhpydenhLlGiGkeadeegee 379
                                        +++++Eri++vRF+ d++Y+VTfrqtDP+Fv+DLs+p +P+i GeLkIpG+S+YLhp++++ +lGiGke       
  gi|488600788|ref|YP_007907259.1| 465 MDFGEDERIFAVRFIADKGYVVTFRQTDPFFVMDLSNPYKPEIKGELKIPGFSSYLHPISDTIILGIGKE------- 534
                                       *********************************************************************9....... PP

                       Beta_propel 380 eqglklslFDVsDpanpkevakvvigdrgsdsealydhkAllfdkeknllaipvseesnsessssqgayvykvdaek 456
                                        +++k+slFDVsD+++pke++++++++   ++++l++h+A+l dk+++++ +p            +g y+++++ ++
  gi|488600788|ref|YP_007907259.1| 535 GSKVKISLFDVSDVESPKEIDRYILDEW--WTDVLNNHHAFLLDKKHEIFFLPGG----------KGGYIFSYK-DD 598
                                       379**********************555..5**********************99..........899******.89 PP

                       Beta_propel 457 gfklkgkitheelakeetlkkakdlyeysskvrRslyigdklytvseskik 507
                                       ++k + ++++                    +  R++yi+d ly++ ++ + 
  gi|488600788|ref|YP_007907259.1| 599 KLKMERAVDM--------------------QAVRAIYINDFLYVIGDKIVV 629
                                       9999999999....................479************998775 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     4e-07    0.0036      33      83 ..     191     239 ..     166     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4e-07
                             PQQ_2  33 vlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvva 83 
                                       +l +g l+v  g + ++a+++++Gk+lW+ +le++ v+a  +  g++++v+
  gi|488600788|ref|YP_007907259.1| 191 LLMNGLLVVI-GHDHISAYSTENGKELWKIKLESEYVSA-RLYSGKIYLVT 239
                                       4577888887.****************************.99999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1172  (0.065369); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 4050.66
//
Query:       gi|488600789|ref|YP_007907260.1|  [L=119]
Description: hypothetical protein Asulf_01271 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   87.8   1.4    5.7e-25   87.7   1.4    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.076   13.1   0.0      0.094   12.8   0.0    1.1  1  B12-binding   B12 binding domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   1.4   6.4e-29   5.7e-25       1     111 [.       5     111 ..       5     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 6.4e-29
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vl+vdDd l+r +l+++l   +y ev eae+gk+a+e++ ++k+d++l+D++mp mdG++++kei ++dp+ +++++
  gi|488600789|ref|YP_007907260.1|   5 VLLVDDDDLLRGILASMLS--DY-EVIEAENGKAAVEKYFQHKPDIVLMDVMMPVMDGVKATKEILKKDPKAKILAI 78 
                                       89****************9..89.8899************************************************* PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ta +      e+l+aga d++ Kp+++++L +++
  gi|488600789|ref|YP_007907260.1|  79 TAFAP-IRGDEMLEAGALDIIPKPITRKKLNEIV 111
                                       ***96.7899********************9987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05     0.094      31      86 ..      27      77 ..      14      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                       B12-binding 31 Vqllganven.edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvv 86
                                      V    +++en ++ v++  ++kpd+v++ + +   +++vk++ e lk+  p++k+++
  gi|488600789|ref|YP_007907260.1| 27 V----IEAENgKAAVEKYFQHKPDIVLMDV-MMPVMDGVKATKEILKKD-PKAKILA 77
                                      4....344556788888999**********.***********9998775.8888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 789.61
//
Query:       gi|488600790|ref|YP_007907261.1|  [L=194]
Description: archaeoflavoprotein AfpA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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    4.2e-18   65.6   0.0    1.8  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 !   65.6   0.0   2.4e-22   4.2e-18       1     106 [.       9     132 ..       9     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 2.4e-22
                                       EEEEEEE-SSCGGGCH.HHHHHHHHH..TTEEEEEEESCHHHHCCHHG..GS.....TCSSHHHHHHCT........ CS
                      Flavoprotein   1 kkillgiTGsvaaika.lellekLkk..egievqvvltkaAkkfiske..klklaa.redpilhielrr........ 63 
                                       +++++giTG+ + +++ l +++++++  ++ e++v+l+ka++++++    +    +  + + + + +++        
  gi|488600790|ref|YP_007907261.1|   9 MRVAWGITGAGDRLEEiLAIMKEINSkyDDLEIRVYLSKAGEQVMKFYriY----NdLKSSFEKVYVEKnanspfla 81 
                                       79*************98999999999999*****************33331....2233444444444456667888 PP

                                       ......TESEEEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE CS
                      Flavoprotein  64 ......wadllviaPasantlakianGiadnlltlilra..takkpiliaP 106
                                             ++++++iaPa+ant aki +Giad+llt+ +++  +a +p +i+P
  gi|488600790|ref|YP_007907261.1|  82 gqiqtgKFEFMIIAPATANTTAKISLGIADTLLTNSALMglKAYVPLYILP 132
                                       888889****************************99988888889999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1254.87
//
Query:       gi|488600791|ref|YP_007907262.1|  [L=563]
Description: hypothetical protein Asulf_01273 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-30  107.1   5.3    1.4e-30  107.1   5.3    2.9  3  DUF262    Protein of unknown function DUF262
    3.6e-06   26.9   4.9    5.2e-06   26.4   3.3    2.2  2  DUF1524   Protein of unknown function (DUF1524)
    3.3e-05   23.7   0.0    7.8e-05   22.5   0.0    1.6  1  HNH_4     HNH endonuclease
      9e-05   21.8   1.9    0.00039   19.8   1.9    1.8  1  DndB      DNA-sulfur modification-associated


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 !  107.1   5.3   3.1e-34   1.4e-30       4     220 ..      14     251 ..      10     252 .. 0.71
   2 ?    0.1   0.1      0.17   7.7e+02      81     164 ..     301     323 ..     260     380 .. 0.56
   3 ?    1.6   0.9     0.059   2.6e+02      96     157 ..     473     541 ..     417     559 .. 0.58

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 3.1e-34
                            DUF262   4 llskskrg..lriPdfQRpyvWeeeqveeLiedllalkgyplGsivlw........................skaad 54 
                                       l+++++++  l +P++QR + W++eq+e+L++++  +++yp+G +++w                         + ++
  gi|488600791|ref|YP_007907262.1|  14 LINNEEEQggLWLPNIQRYFIWSKEQIERLFDSI--MREYPIGNLLIWktkepvkmrkfidnyrdglkltdfYVPKN 88 
                                       555555545899**********************..**********************************8844455 PP

                            DUF262  55 sageleviDGQQRltTltlllaatkeesekriknleaeiek.......ekeeededrlkrreresdkellqkllrse 124
                                       ++ +l+v+DGQQRl++l+++l++      ++ ++l++++          k+e + ++ +    ++ + ++++++ ++
  gi|488600791|ref|YP_007907262.1|  89 EKIKLLVLDGQQRLQSLFIALKG-----SYNGDELYFNVLSgkeekedVKFEFKFINPTKADIKQGWVKVKDIVYDN 160
                                       599********************.....3333333333333222222222222333333444445555555555555 PP

                            DUF262 125 klslee..keelaelnsltkkdl...akeekrneeknlikayevieeilksallsalktklslieielese.....d 191
                                        +++e   ++ ++ +   tk+ l   +++ekr  +kn++k+++ +++            k +++  el+s       
  gi|488600791|ref|YP_007907262.1| 161 REYDEIaeNIVEKIE---TKRPLsplSEKEKRLIRKNVLKLIKEFRD------------KENIAYTELDSVdnpeiY 222
                                       544444122222222...3333355699999**************98............456666666644444448 PP

                            DUF262 192 dedqayeiFerlNsrGvpLtasellkall 220
                                       + +++ eiF+r Ns+G+pL++s+l+ +ll
  gi|488600791|ref|YP_007907262.1| 223 TLNDVVEIFIRANSGGTPLSKSDLMFSLL 251
                                       8889********************99986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                            DUF262  81 esekriknleaeiekekeeededrlkrreresdkellqkllrseklsleekeelaelnsltkkdlakeekrneeknl 157
                                        +ek++k+l+++ e                                                              +
  gi|488600791|ref|YP_007907262.1| 301 RKEKNLKELQNNWEE-------------------------------------------------------------I 316
                                       222222222222221.............................................................1 PP

                            DUF262 158 ikayevi 164
                                       +k ++ i
  gi|488600791|ref|YP_007907262.1| 317 KKSIKEI 323
                                       1111111 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.059
                            DUF262  96 ekeeededrlkrreresdkellqkllrseklsleekeelaelnsltkkdl.......akeekrneeknl 157
                                       ++ e+ ++ +k++  ++d+     ll+ e++++e+k++l +++  +k+d        +k+ +  + +n+
  gi|488600791|ref|YP_007907262.1| 473 INPETGRKIMKYKWWDRDQIANLMLLSAEENRDEKKDKLPQEWLRDKDDEyfeihliPKDRELWKIENY 541
                                       222333333344444444444444555555555555555555544444444455555333333333344 PP

>> DUF1524  Protein of unknown function (DUF1524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.3     1e+04      98     123 ..     200     226 ..     199     234 .. 0.74
   2 !   26.4   3.3   1.2e-09   5.2e-06      26     137 ..     435     553 ..     416     555 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.3
                           DUF1524  98 kpfleKrd.lykksslrlnrklaekde 123
                                       k+f++K + +y++ +   n ++++ ++
  gi|488600791|ref|YP_007907262.1| 200 KEFRDKENiAYTELDSVDNPEIYTLND 226
                                       689999998888888888888776665 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1.2e-09
                           DUF1524  26 yilakelesalreedeeegeakkltiEHilPqslaekw......egagqedeekreelvndlgNLtlltkslN.... 92 
                                       y+++  ++++ +   +  +e +  +++Hi+Pqs  ++        g++  + ++ ++  ++++NL+ll+ ++N    
  gi|488600791|ref|YP_007907262.1| 435 YLIFALWYQDVNF--KPAYEGNLPWVDHIFPQSKLKEIkeinpeTGRKIMKYKWWDR--DQIANLMLLSAEENrdek 507
                                       3333233433332..2233334567********999666777544444444444444..89************9998 PP

                           DUF1524  93 .sslsnkpfleKrdlykksslrlnrklaekdewdeeaiearqeaLa 137
                                        ++l   + ++K+d+y + +l+ +++  +k e  e++ie r++ ++
  gi|488600791|ref|YP_007907262.1| 508 kDKLPQEWLRDKDDEYFEIHLIPKDRELWKIENYEKFIEVRKKLIV 553
                                       88888777799999**998888888777888889999999988775 PP

>> HNH_4  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.7e-08   7.8e-05      21      54 ..     458     512 ..     447     513 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.7e-08
                                       EEESSTTTT---....................BSGGGEEEES-GGGGT.SSSSSS CS
                             HNH_4  21 iDHilPrsrskd....................DsvsNkVLvlrdaNqe.KsnrtP 54 
                                       +DHi+P+s+ k                     D++ N+ L ++++N++ K++++P
  gi|488600791|ref|YP_007907262.1| 458 VDHIFPQSKLKEikeinpetgrkimkykwwdrDQIANLMLLSAEENRDeKKDKLP 512
                                       9***********************************************9****99 PP

>> DndB  DNA-sulfur modification-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.9   8.6e-08   0.00039      40     301 ..      27     324 ..       7     381 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.6e-08
                              DndB  40 lraqRkln..ksrvkeIakYllensdeyifsaltasv...deeleflpls.ssq.kekvGvlkipmdaeil..ivDG 107
                                        ++qR  +  k+ ++ +++ ++     y +++l   +    e +++ ++  + +   k+  + +p++++i+  ++DG
  gi|488600791|ref|YP_007907262.1|  27 PNIQRYFIwsKEQIERLFDSIMRE---YPIGNLL--IwktKEPVKMRKFIdNYRdGLKLTDFYVPKNEKIKllVLDG 98 
                                       445553330033345555555332...3333333..12223555555555344444899999******77777**** PP

                              DndB 108 QHRraAieealkeepelgeeeipvvlfvelgleksqqlFadlNkyakridkslll....lyderdpl..aliakkll 178
                                       Q+R++++  alk + + +e  + v+   ++  e  +  F+ +N +   i+++       +yd+r+ +  a+++ + +
  gi|488600791|ref|YP_007907262.1|  99 QQRLQSLFIALKGSYNGDELYFNVLSG-KEEKEDVKFEFKFINPTKADIKQGWVKvkdiVYDNREYDeiAENIVEKI 174
                                       ************888788888998887.7778889999*****7777777664323333888775430033333333 PP

                              DndB 179 eevpifaglvemeksslskkseklfTlstlveatkellkn........................qsaskealdekie 231
                                       e + +++ l+e+ek+ + k+  kl+  +++++  ++ +++                          +  +++d   +
  gi|488600791|ref|YP_007907262.1| 175 ETKRPLSPLSEKEKRLIRKNVLKLI--KEFRDKENIAYTEldsvdnpeiytlndvveifiransGGTPLSKSDLMFS 249
                                       4444477888888888888888887..77777777777776666666633333333333222221333344444444 PP

                              DndB 232 lasefwnavaetipewelveekkisskelRedsilghsvglqalgrllk..allkek.....pddwketlsaLaeid 301
                                       l+ + w++v e +  ++++ee + ++ ++ +d++l +s++l + g+  +  +++kek     +++w+e ++ ++ei+
  gi|488600791|ref|YP_007907262.1| 250 LLTANWEEVEEDL--TNFLEELNGTAFDFGRDFVLKTSLILIGAGAKYDvmKFRKEKnlkelQNNWEEIKKSIKEIK 324
                                       4445555555543..56666777777999999999999988888876651146666689999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 3282.92
//
Query:       gi|488600792|ref|YP_007907263.1|  [L=161]
Description: putative methyltransferase, YaeB/AF_0241 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-40  137.7   0.0    2.4e-40  137.4   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 !  137.4   0.0   1.4e-44   2.4e-40       1     119 []      21     133 ..      21     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 1.4e-44
                                       TS-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SS CS
                              TrmO   1 giPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRp 77 
                                       g+P+qp+ a+ + + +e++pey  +e+l++le+fsh++l+++fh    kk  ++ ++p+++++ r Gvf+tR+p Rp
  gi|488600792|ref|YP_007907263.1|  21 GTPIQPTAARGIDGAVEVFPEY--AEGLKDLEGFSHIILIYHFHLV--KK-PSLKVKPFMDNQIR-GVFSTRAPSRP 91 
                                       79********************..********************88..23.34556899998777.*********** PP

                                       S-EEEEEEEEEEEETTEEEEES----TT-EEEEEEE--HHHH CS
                              TrmO  78 npiglsvvklekvegnvlevsgvDlldgtpvlDiKPYvpyaD 119
                                       npig+svv+l ++egn+l++++vD++dgtp+lDiKPYvp++D
  gi|488600792|ref|YP_007907263.1|  92 NPIGISVVHLVRIEGNILYIRDVDIVDGTPLLDIKPYVPEFD 133
                                       ****************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1035.25
//
Query:       gi|488600793|ref|YP_007907264.1|  [L=102]
Description: putative nucleotidyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-20   71.2   1.8    7.7e-20   71.0   1.8    1.0  1  NTP_transf_2    Nucleotidyltransferase domain
    4.8e-13   49.0   0.5      6e-13   48.7   0.5    1.1  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0065   16.7   0.0     0.0075   16.5   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   1.8   1.3e-23   7.7e-20       1      94 [.      14     101 ..      14     102 .] 0.96

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 1.3e-23
                                       HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEE CS
                      NTP_transf_2   1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtre 77 
                                       lkk+ +elke+++v+++ +fGSy+rG+ +k+SDiD+lv +   ++       l k +e ++ l+ellg++vdlv ++
  gi|488600793|ref|YP_007907264.1|  14 LKKHEKELKEKFGVKEIGVFGSYVRGEQKKDSDIDILVEFYPQTE-----MDLIKFVELEEYLSELLGIKVDLVMKS 85 
                                       699****************************************87.....88************************* PP

                                       ECCCCTEEEEEECEEEH CS
                      NTP_transf_2  78 kledpllvksileerpl 94 
                                        l+ p++ k il+e ++
  gi|488600793|ref|YP_007907264.1|  86 ALK-PRIGKRILKEVVY 101
                                       ***.***9999999877 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.5     1e-16     6e-13       4      83 ..      18      98 ..       9     102 .] 0.85

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1e-16
                                      TTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS-..--HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHH CS
                           Polbeta  4 keilekekeielaylFGSrakgkareeSDiDlavllkek..ldleeelelaaelediklgkkvDlvdlneapplllyei 80
                                      ++ l+++ +++ + +FGS+++g+++++SDiD+ v +  +   dl + +el++ l+++ lg kvDlv  ++ +p + ++i
  gi|488600793|ref|YP_007907264.1| 18 EKELKEKFGVKEIGVFGSYVRGEQKKDSDIDILVEFYPQteMDLIKFVELEEYLSEL-LGIKVDLVMKSALKPRIGKRI 95
                                      344455569*************************999997889999***********.9********99999******* PP

                                      HHS CS
                           Polbeta 81 lke 83
                                      lke
  gi|488600793|ref|YP_007907264.1| 96 LKE 98
                                      995 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-06    0.0075       9      54 ..       9      58 ..       4      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                                      HHHHHHHHHHHHH-TT...-EEEE-HHHHTT-S.EESSEEEEEEBTTBST CS
                    DNA_pol_B_palm  9 alealvkkaakeldpe...vevivcGSYRRgae.ssGDvDvlitkkdaks 54
                                       +++++kk+ kel+++    e+ v GSY Rg++ +  D+D+l+    +++
  gi|488600793|ref|YP_007907264.1|  9 GIKRILKKHEKELKEKfgvKEIGVFGSYVRGEQkKDSDIDILVEFYPQTE 58
                                      577888888889988855457889****999761568******8655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 760.06
//
Query:       gi|488600794|ref|YP_007907265.1|  [L=156]
Description: hypothetical protein Asulf_01278 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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    7.1  12.5        1.8    6.8  12.5    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  12.5   9.9e-05       1.8      16     148 ..       4     138 ..       2     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 9.9e-05
                           DUF2070  16 vsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrs.lflalltelivviisllail 91 
                                       + l++ +l+al++ +la+l+s     ++f +p +  ++l +p+l++++gr t+  + + l+++   +++i   + ++
  gi|488600794|ref|YP_007907265.1|   4 RFLIFNVLVALVYMVLAILIS-----FIFAFPGFGVLILPQPFLDVVRGRWTLAYNpVSLSAIPWAFYII--AIHCV 73 
                                       568999999999999996665.....8***********************55555556666666666666..34444 PP

                           DUF2070  92 lsallqalvllalvls............lalvfalrllvlvavsdesllkavlpaliqpllailllvly 148
                                       ++ +l      +++ +            +++ + + +l+l+  sd +l   +l ++  p+  i ++++ 
  gi|488600794|ref|YP_007907265.1|  74 YYNYL----GKSYLSDvlsdvkapvlggISVLVLNLILILTGCSDIDLHILLLNYMSEPIYWISAILVN 138
                                       44333....3333333333567788888999999******************99999999888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1037.58
//
Query:       gi|488600795|ref|YP_007907266.1|  [L=207]
Description: hypothetical protein Asulf_01279 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-24   85.0  15.6    7.4e-24   84.3  15.6    1.3  1  BioY         BioY family
  ------ inclusion threshold ------
       0.12   12.4  15.3        1.6    8.7  14.9    2.5  1  Colicin_V    Colicin V production protein
       0.21   11.7  25.0       0.42   10.7  25.0    1.5  1  ECF_trnsprt  ECF transporter, substrate-specific component
       0.54   10.1  14.9        1.9    8.3  14.9    2.0  1  CbiM         Cobalt uptake substrate-specific transmembrane r


Domain annotation for each model (and alignments):
>> BioY  BioY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3  15.6   1.7e-27   7.4e-24       2     128 ..      31     189 ..      30     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.7e-27
                              BioY   2 gpvpitlqtlavllaglllgprrgalavllYlllGalglPvfag.ggGlavllgptgGYllGFlvaalvvgll.... 73 
                                       g +p t+q+l+v+l+glllgp +g++++++Yl+l a+gl + ag +gG+av++gpt+GYll F++a+++ g++    
  gi|488600795|ref|YP_007907266.1|  31 GVIPYTMQNLGVVLSGLLLGPYWGFISQIIYLILIAIGLQLGAGfKGGIAVFFGPTAGYLLTFPIASALSGYFrrif 107
                                       679*****************************************77***************************9999 PP

                              BioY  74 ....kk.laelllallagllviyalGvlwlal...v....ls..............laaalaagvlpfipgdlv.ka 123
                                           k+ +  ++l  +++ + +y+ G+++++    +    ++              l a+++a+ ++++p d++   
  gi|488600795|ref|YP_007907266.1| 108 wddsKRgYFLTWLGSVIAFIPVYLAGFAVFYRfatInpayMKfavnassilgsfdpLIAVFIATTVIYMPQDFIiDH 184
                                       98752355555667777999999999999888544133331133334445555556777788888999999985145 PP

                              BioY 124 vlaal 128
                                       vla++
  gi|488600795|ref|YP_007907266.1| 185 VLAIA 189
                                       55544 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  14.9   0.00036       1.6       6     131 ..      40     153 ..      37     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00036
                         Colicin_V   6 llilllsallGlrrGfvrevlsllgwvvafvvasllypslaellae........................lilspal 58 
                                       l+++l ++llG ++Gf+ ++++l+ +++++ +++ +   +a ++++                        +      
  gi|488600795|ref|YP_007907266.1|  40 LGVVLSGLLLGPYWGFISQIIYLILIAIGLQLGAGFKGGIAVFFGPtagylltfpiasalsgyfrrifwdD------ 110
                                       789*******************************************4444444444444444444444432...... PP

                         Colicin_V  59 aaiiaflllfllvllivsllgallsklvsktglglldrllGaifGllkglllvvllllllalvplpkvqewlq 131
                                                                     +  g +  +lG ++ ++ ++l  +++++ +a+++    + +++
  gi|488600795|ref|YP_007907266.1| 111 ------------------------------SKRGYFLTWLGSVIAFIPVYLAGFAVFYRFATINPAYMKFAVN 153
                                       ..............................5555566666666666666666665555555555444432333 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  25.0   9.4e-05      0.42       5     151 ..      15     173 ..       9     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.4e-05
                                       HHHHHHHHHHHHHHHHEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHH.......HHHHHHHCHT-SSTTHHHH. CS
                       ECF_trnsprt   5 itglliAisivlsllgyiplpnikitiihipvllggllfGpikGailgii.......tsvlkailtggtgalssfv. 73 
                                        ++++++i + ls    +++++i+ t   + v+l+gll+Gp +G+i  ii       +  l+a ++gg ++  +f+ 
  gi|488600795|ref|YP_007907266.1|  15 SMAVFTGITAQLS----FKIGVIPYTMQNLGVVLSGLLLGPYWGFISQIIyliliaiGLQLGAGFKGGIAV--FFGp 85 
                                       589**********....9********************************766655555555555333322..3446 PP

                                       .HHHHHHHHCHHHHHHHHHHCCCHTTHHHH...HHHHHHHHCCCCCHHHHHHHCCC..HHHHS.............. CS
                       ECF_trnsprt  74 .piaflsriligliagllykkgkkknlkei...vvsfilagvlgtivatllvllii..lplylklktakaiaiag.. 142
                                         ++ l+  ++  + g+ +++    ++ ++   ++++++a + ++++++ +++ ++   p y+k++ ++a+ i+g  
  gi|488600795|ref|YP_007907266.1|  86 tAGYLLTFPIASALSGYFRRIFWDDSKRGYfltWLGSVIAFIPVYLAGFAVFYRFAtiNPAYMKFA-VNASSILGsf 161
                                       677777777777777777777777777666556677777777777777777666666666666444.4455555554 PP

                                       ....--HHHHHH CS
                       ECF_trnsprt 143 ...kallaailg 151
                                           a+++a ++
  gi|488600795|ref|YP_007907266.1| 162 dplIAVFIATTV 173
                                       444333333333 PP

>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  14.9   0.00042       1.9      38     185 ..       9     178 ..       2     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00042
                              CbiM  38 rvpllallaafifaaqminipip.ggtslHllgavlaaiLlGpwaaflavavvlllqallfgdGGitaLGaNilnma 113
                                       +++l++ +a f  +   ++++i   + ++  lg+vl ++LlGp+ +f++ ++ l+l a+ ++ G     G+ ++   
  gi|488600795|ref|YP_007907266.1|   9 KMVLATSMAVFTGITAQLSFKIGvIPYTMQNLGVVLSGLLLGPYWGFISQIIYLILIAIGLQLGAGFKGGIAVFFGP 85 
                                       3677888***************9999***********************9999999999887665555555555333 PP

                              CbiM 114 vigvllaylvyrllsrla.........sskkrvalaaflaallsvvlaallvalelalsgleas............. 168
                                        +g ll + +  +ls+           ++    +l++++ a++ v+la+++v   +a  + ++              
  gi|488600795|ref|YP_007907266.1|  86 TAGYLLTFPIASALSGYFrrifwddskRGYFLTWLGSVI-AFIPVYLAGFAVFYRFATINPAYMkfavnassilgsf 161
                                       333333333333332222333444221222223344444.6899999999998888887554435666666665554 PP

                              CbiM 169 lsltaalaamllvhlpv 185
                                        +l a++ a  ++++p 
  gi|488600795|ref|YP_007907266.1| 162 DPLIAVFIATTVIYMPQ 178
                                       44444444444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1420.72
//
Query:       gi|488600796|ref|YP_007907267.1|  [L=405]
Description: ATPase component of various ABC-type transport systems, containing duplicated ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-33  115.5   0.0    1.1e-15   58.4   0.0    3.0  2  ABC_tran        ABC transporter
    1.4e-20   74.4   7.1    2.7e-08   34.0   0.1    4.1  4  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
      1e-07   32.1   1.8     0.0025   17.6   0.2    3.4  4  AAA_15          AAA ATPase domain
    2.3e-06   27.2   2.7     0.0069   15.8   0.2    3.5  4  SMC_N           RecF/RecN/SMC N terminal domain
    2.9e-06   26.9   3.8    0.00017   21.3   0.3    2.7  2  AAA_29          P-loop containing region of AAA domain
    2.9e-06   27.9   1.4    8.5e-05   23.1   0.1    2.5  2  AAA_23          AAA domain
    3.7e-06   27.5   0.0      0.025   15.1   0.0    2.5  2  AAA_18          AAA domain
      7e-06   26.5   0.1    0.00042   20.7   0.0    2.4  2  AAA_16          AAA ATPase domain
    1.6e-05   24.3   0.7       0.11   11.6   0.1    2.2  2  PIF1            PIF1-like helicase
    2.1e-05   24.8   0.4       0.17   12.2   0.0    2.7  2  AAA_22          AAA domain
    2.5e-05   24.3   0.3      0.013   15.5   0.0    2.4  2  NACHT           NACHT domain
    3.5e-05   24.2   0.3        0.4   11.1   0.1    3.1  2  AAA             ATPase family associated with various cellula
    8.5e-05   21.7   0.1      0.051   12.6   0.0    2.3  2  T2SSE           Type II/IV secretion system protein
    0.00011   21.5   0.2       0.38    9.9   0.0    2.6  3  NB-ARC          NB-ARC domain
    0.00012   22.0   0.2       0.31   11.0   0.1    2.3  2  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
    0.00021   21.3   4.2      0.039   13.9   0.2    2.9  2  NTPase_1        NTPase
    0.00042   20.2   0.6       0.03   14.2   0.2    2.5  2  MobB            Molybdopterin guanine dinucleotide synthesis 
    0.00045   20.0   0.1      0.049   13.4   0.0    2.6  2  AAA_30          AAA domain
    0.00055   20.1   0.0        1.2    9.3   0.0    2.6  2  AAA_33          AAA domain
    0.00069   19.4   0.3        1.7    8.4   0.1    2.5  2  PduV-EutP       Ethanolamine utilisation - propanediol utilis
     0.0018   15.9   0.2       0.63    7.5   0.1    2.1  2  DUF3584         Protein of unknown function (DUF3584)
     0.0028   17.3   2.2       0.76    9.3   0.1    2.4  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
     0.0029   17.4   0.5       0.73    9.6   0.1    2.4  2  ATP_bind_1      Conserved hypothetical ATP binding protein
     0.0033   17.6   0.0       0.16   12.2   0.0    2.8  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
     0.0035   16.1   0.1        1.8    7.1   0.0    3.4  4  AAA_13          AAA domain
     0.0041   16.5   0.0        2.6    7.4   0.0    2.3  2  Mg_chelatase    Magnesium chelatase, subunit ChlI
     0.0045   16.3   0.0        0.2   10.9   0.0    2.3  2  Zeta_toxin      Zeta toxin
     0.0049   16.8   1.1        1.6    8.6   0.0    2.5  2  ATPase_2        ATPase domain predominantly from Archaea
     0.0083   15.3   0.0        1.1    8.4   0.0    2.2  2  G-alpha         G-protein alpha subunit
     0.0095   15.5   0.0       0.63    9.5   0.0    2.4  2  Ploopntkinase1  P-loop Nucleotide Kinase1
  ------ inclusion threshold ------
      0.012   15.5   2.2       0.95    9.3   0.0    2.5  2  dNK             Deoxynucleoside kinase
      0.013   15.8   0.4        2.5    8.3   0.0    2.3  2  AAA_28          AAA domain
      0.017   14.9   0.3        1.8    8.2   0.1    2.6  2  AAA_24          AAA domain
      0.022   14.8   0.4       0.92    9.6   0.0    2.6  2  MMR_HSR1        50S ribosome-binding GTPase
      0.022   14.4   0.0       0.41   10.3   0.0    2.2  2  ATP-synt_ab     ATP synthase alpha/beta family, nucleotide-bi
      0.024   13.6   0.1       0.91    8.4   0.0    2.2  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
      0.027   14.5   3.3        8.5    6.4   0.0    3.5  3  AAA_14          AAA domain
      0.027   14.8   0.2        2.2    8.6   0.0    2.8  3  AAA_19          AAA domain
      0.036   14.1   0.2        2.6    8.0   0.1    3.1  2  AAA_5           AAA domain (dynein-related subfamily)
      0.044   13.5   0.3       0.17   11.6   0.0    2.0  2  PRK             Phosphoribulokinase / Uridine kinase family
      0.081   11.8   1.0        1.4    7.7   0.0    2.6  3  DUF2791         P-loop Domain of unknown function (DUF2791)
      0.082   11.7   0.4        0.4    9.5   0.1    1.9  2  DLIC            Dynein light intermediate chain (DLIC)
      0.082   12.4   0.1        1.6    8.2   0.0    2.2  2  AAA_7           P-loop containing dynein motor region
        0.1   12.5   0.2       0.71    9.8   0.0    2.1  2  RsgA_GTPase     RsgA GTPase
       0.13   12.1   0.0        4.2    7.1   0.0    2.3  2  DEAD            DEAD/DEAH box helicase
       0.15   11.4   0.1          1    8.6   0.0    2.1  2  FtsK_SpoIIIE    FtsK/SpoIIIE family
       0.17   10.6   0.2       0.41    9.4   0.1    1.5  2  ABC_ATPase      Predicted ATPase of the ABC class
       0.34   10.5   1.1        2.6    7.6   0.1    2.3  2  SRP54           SRP54-type protein, GTPase domain
       0.67   10.2   3.2        1.1    9.5   0.2    2.5  2  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 !   58.4   0.0     3e-18   1.1e-15       2     136 ..      22     155 ..      21     156 .. 0.80
   2 !   52.5   0.4     2e-16   7.3e-14       1     136 [.     236     355 ..     236     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 3e-18
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqepqlfpe 73 
                                       +n+ ++   gek+ + G  G+GK+tL+k+++gl         +G++ + g+++       +rk++  +pq+p+ +  
  gi|488600796|ref|YP_007907267.1|  22 ENLYFTADYGEKIFVRGCVGSGKTTLFKIISGLIPVfyncrISGDVMVFGENSPA----NFRKHVYLVPQNPEEQI- 93 
                                       68999****************************9889778888888777777776....9***********54443. PP

                                       SBHHHHHHHTCHHHHHHHSTTGG..TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvrenesdeeiekalsklglke..lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                         + e   ++ei  + + l+l++   +d+ +++++s+LS G+kq v l  a+++k++ ++lDEp+
  gi|488600796|ref|YP_007907267.1|  94 --IFED-VEDEIFSVSHDLNLVKrfNADHLISKKTSELSDGEKQLVTLITAFASKRECIILDEPF 155
                                       ..3343.3444444444444444333667777888*****************************7 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 2e-16
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       l+ ++l+l++ge + ivG+nG+GK+tLlk+++g lk + G i             + + +i+   q  +  f e tv
  gi|488600796|ref|YP_007907267.1| 236 LNSINLDLRRGEAISIVGDNGSGKTTLLKAISGILK-ADGVI-------------VRKGRISLSLQYpNYSFTERTV 298
                                       689********************************9.58888.............6678888888884445666667 PP

                                       HHH.HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +e+   +++i k +   g+    ++ + ++p+sLS G+ + v++ +al  k +++llDEpt
  gi|488600796|ref|YP_007907267.1| 299 AEElSFSKDILKTIMGSGILT--EELLPKHPHSLSAGESKLVSVLKAL--KGDIVLLDEPT 355
                                       777677777777776666655..88899999***************98..779*******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 !    9.6   0.2    0.0019       0.7       9      26 ..      41      60 ..      38     120 .. 0.76
   2 !   34.0   0.1   7.3e-11   2.7e-08     235     282 ..     126     170 ..      91     180 .. 0.86
   3 !   25.1   0.2   3.8e-08   1.4e-05       4      48 ..     251     294 ..     249     318 .. 0.70
   4 ?    7.1   0.0     0.011         4     237     298 ..     330     383 ..     326     387 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                            AAA_21  9 gsGKSnLLdaldllarl..d 26
                                      gsGK++L++++++l  +  +
  gi|488600796|ref|YP_007907267.1| 41 GSGKTTLFKIISGLIPVfyN 60
                                      9************9666551 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 7.3e-11
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell 282
                                       +elSdG k+l  l+ta+++ +     +++DEp ++LHPk++++l++ +
  gi|488600796|ref|YP_007907267.1| 126 SELSDGEKQLVTLITAFASKR---ECIILDEPFSHLHPKRVEKLIDYV 170
                                       478****************99...99******************9766 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 3.8e-08
                            AAA_21   4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsl 48 
                                       ++G+NgsGK++LL+a++++   ++ v+ ++   s + +++ +++ 
  gi|488600796|ref|YP_007907267.1| 251 IVGDNGSGKTTLLKAISGILK-ADGVIVRKGRISLSLQYPNYSFT 294
                                       9*****************987.55555555555555555555555 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.011
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       lS G  +l    +++l alk  +++l+DEp    ++++  r+++l+k+l +     i++TH+
  gi|488600796|ref|YP_007907267.1| 330 LSAGESKL----VSVLKALKG-DIVLLDEPTVAQNYEFGMRIIGLIKKLGK---SAIIATHD 383
                                       55555555....666777766.************************99966...78999997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       7.3   2.7e+03      33      44 ..      41      52 ..      38     111 .. 0.79
   2 !    9.5   0.2     0.002      0.74     294     349 ..     125     171 ..      85     173 .. 0.72
   3 !   17.6   0.2   6.8e-06    0.0025      20      49 ..     242     272 ..     235     313 .. 0.74
   4 ?    1.6   0.0      0.48   1.8e+02     324     364 ..     346     382 ..     340     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.3
                            AAA_15 33 nsGKSsileald 44
                                      +sGK+++ +++ 
  gi|488600796|ref|YP_007907267.1| 41 GSGKTTLFKIIS 52
                                      689999999886 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                            AAA_15 294 lnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllk 349
                                        ++ ++G ++l+ li+   +a+k+        +++++EP  hLHp+  + li++ +
  gi|488600796|ref|YP_007907267.1| 125 TSELSDGEKQLVTLITA--FASKR-------ECIILDEPFSHLHPKRVEKLIDYVL 171
                                       56678888888888875..44444.......67*******************9876 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 6.8e-06
                            AAA_15  20 dlsee.ltvliGkNnsGKSsilealdlFlnn 49 
                                       dl       ++G N+sGK+++l+a+  +l+ 
  gi|488600796|ref|YP_007907267.1| 242 DLRRGeAISIVGDNGSGKTTLLKAISGILKA 272
                                       444445789****************877774 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.48
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                        +i+l++EP + + +++ + +i l+k+l ++     ii TH
  gi|488600796|ref|YP_007907267.1| 346 GDIVLLDEPTVAQNYEFGMRIIGLIKKLGKSA----IIATH 382
                                       689*************************9999....78888 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 ?   -0.7   0.0       2.2   7.9e+02      28      44 ..      35      51 ..      27      56 .. 0.84
   2 !    8.6   0.0    0.0031       1.1     135     187 ..     126     174 ..      67     199 .. 0.80
   3 !   15.8   0.2   1.9e-05    0.0069      26      49 ..     248     271 ..     231     296 .. 0.81
   4 ?   -0.7   0.0       2.2     8e+02     136     207 ..     329     392 ..     290     400 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.2
                                      EEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnlldAi 44
                                      ++ G  GSGK+ l+  i
  gi|488600796|ref|YP_007907267.1| 35 FVRGCVGSGKTTLFKII 51
                                      688999*****998766 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0031
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks 187
                                       ++LS Gek+Lv l   fA    k++++ +lDe  ++L  k+v+k+ +++ + +
  gi|488600796|ref|YP_007907267.1| 126 SELSDGEKQLVTLITAFAS---KRECI-ILDEPFSHLHPKRVEKLIDYVLSYR 174
                                       48*********98888875...45665.89***************99987665 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.9e-05
                                       EEEEEESTTSSHHHHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLG 49 
                                         +ivG NGSGK+ ll Ai+ +L 
  gi|488600796|ref|YP_007907267.1| 248 AISIVGDNGSGKTTLLKAISGILK 271
                                       568****************87765 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.2
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadk 207
                                       +LS Ge +Lv++       k+ +  ++llDe   a   +   ++  l+k+  k+   i+ +++ ++ e ad 
  gi|488600796|ref|YP_007907267.1| 329 SLSAGESKLVSV------LKALKGDIVLLDEPTVAQNYEFGMRIIGLIKKLGKS--AIIATHDFRLAEMADV 392
                                       677777777654......222333455555555555555555555555555533..3555555555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.025       9.2      24      39 ..      33      48 ..      22      56 .. 0.81
   2 !   21.3   0.3   4.6e-07   0.00017      18      48 ..     242     272 ..     234     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.025
                            AAA_29 24 atlltGpsGsGKSTll 39
                                       +++ G  GsGK+Tl+
  gi|488600796|ref|YP_007907267.1| 33 KIFVRGCVGSGKTTLF 48
                                      678999********97 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4.6e-07
                            AAA_29  18 eidlkgatlltGpsGsGKSTllDAiqalLvp 48 
                                       ++++ +a+ ++G++GsGK+Tll Ai+ +L +
  gi|488600796|ref|YP_007907267.1| 242 DLRRGEAISIVGDNGSGKTTLLKAISGILKA 272
                                       555444999****************999866 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.31   1.1e+02      29      39 ..      41      51 ..      35      55 .. 0.88
   2 !   23.1   0.1   2.3e-07   8.5e-05      22      43 ..     249     270 ..     233     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.31
                            AAA_23 29 GaGKTTildAi 39
                                      G+GKTT++  i
  gi|488600796|ref|YP_007907267.1| 41 GSGKTTLFKII 51
                                      9*******877 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2.3e-07
                            AAA_23  22 tlItGpNGaGKTTildAiklaL 43 
                                         I+G+NG+GKTT+l Ai  +L
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISGIL 270
                                       57****************9887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     7e-05     0.025       1      62 [.      34     104 ..      34     164 .. 0.79
   2 !   10.4   0.1     0.002      0.74       1      23 [.     249     271 ..     249     346 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.............gvnlrdvakenglllevdpealdeskrldedkldklld 62 
                                       I++ G+ G+GKttl k +s +  +             g+n+  +++++ +l +++pe    ++++ ed+ d++++
  gi|488600796|ref|YP_007907267.1|  34 IFVRGCVGSGKTTLFKIISGLIPVfyncrisgdvmvfGENSPANFRKHVYLVPQNPE----EQIIFEDVEDEIFS 104
                                       899***************998633477788888888899999999998888888888....66666666555554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.002
                            AAA_18   1 IlltGtpGvGKttlakeLskrlg 23 
                                       I + G  G+GKttl k++s  l+
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISGILK 271
                                       6799*************976653 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.28     1e+02      25      41 ..      32      48 ..      16      55 .. 0.81
   2 !   20.7   0.0   1.1e-06   0.00042      23     105 ..     245     341 ..     232     383 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.28
                            AAA_16 25 elvllsGesGvGKsslv 41
                                      e ++++G  G+GK++l 
  gi|488600796|ref|YP_007907267.1| 32 EKIFVRGCVGSGKTTLF 48
                                      5689***********95 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.1e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdql.........esa.....ipysa.laqalareellrq 84 
                                       r+e++ ++G+ G+GK++l++++   l++dg+i+ +g+   +         e       +++s  +++++  +++l++
  gi|488600796|ref|YP_007907267.1| 245 RGEAISIVGDNGSGKTTLLKAISGILKADGVIVRKGRISLSlqypnysftE-RtvaeeLSFSKdILKTIMGSGILTE 320
                                       4489********************999999999777766663222222221.0233334445556666666666666 PP

                            AAA_16  85 lldeaesaeleawrekleeal 105
                                       +l ++   +l+a   kl ++l
  gi|488600796|ref|YP_007907267.1| 321 ELLPKHPHSLSAGESKLVSVL 341
                                       666655555555555555555 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00031      0.11      13      46 ..      20      55 ..      16      61 .. 0.79
   2 !   10.8   0.1   0.00053      0.19       8      53 ..     234     277 ..     230     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                                      H........HCTS-EEEEESTTSSCHHHHHHHHHHC CS
                              PIF1 13 iieavln..ekgklfFvtGsgGtgKtflwkallkkl 46
                                      iie ++   + g+ +Fv G  G+gKt l+k ++  +
  gi|488600796|ref|YP_007907267.1| 20 IIENLYFtaDYGEKIFVRGCVGSGKTTLFKIISGLI 55
                                      555544322889*******************99876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00053
                                       HHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCE CS
                              PIF1   8 kvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkiv 53 
                                       +++++i   +  ++g+ + + G  G+gKt l+ka++ +l++ g iv
  gi|488600796|ref|YP_007907267.1| 234 TILNSI--NLDLRRGEAISIVGDNGSGKTTLLKAISGILKADGVIV 277
                                       444444..4455899*************************998877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0021      0.77       8      99 ..      34     153 ..      29     180 .. 0.59
   2 !   12.2   0.0   0.00046      0.17       5      29 ..     246     270 ..     242     353 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0021
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsstsskdllrellralglelka.. 70 
                                       ++v G++G+GKTtl + +    +  ++ +             ++ +   + +p+  + + +++++  ++ +  ++  
  gi|488600796|ref|YP_007907267.1|  34 IFVRGCVGSGKTTLFKIISGLIPVFYNCRIsgdvmvfgenspANFRKHVYLVPQNPEEQIIFEDVEDEIFSVSHDln 110
                                       6788**********998887776544433355555555443333332233333333444455555555555444477 PP

                            AAA_22  71 ..erlsseellealeqalrarav............ielliiDE 99 
                                         +r + ++l+++ +  l++  +            +e++i+DE
  gi|488600796|ref|YP_007907267.1| 111 lvKRFNADHLISKKTSELSDGEKqlvtlitafaskRECIILDE 153
                                       7766666666655555555555556666666666667777777 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00046
                            AAA_22   5 agilvvtGesGtGKTtllrrlleql 29 
                                          + ++G  G+GKTtll+ +   l
  gi|488600796|ref|YP_007907267.1| 246 GEAISIVGDNGSGKTTLLKAISGIL 270
                                       56789**************987666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.019       7.1       3      20 ..      34      51 ..      32      55 .. 0.86
   2 !   15.5   0.0   3.4e-05     0.013       3      27 ..     249     273 ..     247     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.019
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                      ++++G  GsGKTtL + +
  gi|488600796|ref|YP_007907267.1| 34 IFVRGCVGSGKTTLFKII 51
                                      799***********8765 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.4e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaeg 27 
                                       + + G++GsGKTtLl+ +   ++++
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISGILKAD 273
                                       6799*************99877765 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    0.0028         1       3      75 ..      36     110 ..      34     167 .. 0.70
   2 !   11.1   0.1    0.0011       0.4       3      26 ..     251     285 ..     249     355 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0028
                                       EESSTTSSHHHHHHHHHHHHTHEE.EEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...T CS
                               AAA   3 lyGppGtGKTllakavakelgvef.leisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...s 75 
                                       + G  G GKT+l k +   + v + ++isg  ++  + ++s++++r+ +  + ++ +  i+f D  d++++ +   +
  gi|488600796|ref|YP_007907267.1|  36 VRGCVGSGKTTLFKIISGLIPVFYnCRISGDVMV--FGENSPANFRKHVYLVPQNPEEQIIFEDVEDEIFSVShdlN 110
                                       56889**************986555899988888..88889999999998887666558888887777777663332 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
                                       EESSTTSSHHHHHHHHHHHHTHE...........E CS
                               AAA   3 lyGppGtGKTllakavakelgve...........f 26 
                                       ++G  G GKT+l ka+   l+++            
  gi|488600796|ref|YP_007907267.1| 251 IVGDNGSGKTTLLKAISGILKADgvivrkgrislS 285
                                       689***************99876333333434330 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 !    6.8   0.0    0.0083         3     130     154 ..      32      56 ..       7      64 .. 0.83
   2 !   12.6   0.0   0.00014     0.051     115     156 ..     232     273 ..     202     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0083
                             T2SSE 130 glilvsGgTgsGKttllyallkein 154
                                         i v G  gsGKttl  ++   i+
  gi|488600796|ref|YP_007907267.1|  32 EKIFVRGCVGSGKTTLFKIISGLIP 56 
                                       5799************999988776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                             T2SSE 115 kekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       +++i + ++  +r+   i + G  gsGKttll a+  +++++
  gi|488600796|ref|YP_007907267.1| 232 SKTILNSINLDLRRGEAISIVGDNGSGKTTLLKAISGILKAD 273
                                       4677788888889999999*****************999987 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    0.0023      0.83       6      40 ..      18      51 ..      15      64 .. 0.88
   2 ?   -2.0   0.0       4.5   1.6e+03      81     110 ..     123     152 ..      74     155 .. 0.73
   3 !    9.9   0.0     0.001      0.38      22      40 ..     248     266 ..     234     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                                      HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC  6 ekviekLlekdelqslvvalvGmgGvGKttlakqi 40
                                      +k+ie+L    + +   +++ G  G+GKttl+k i
  gi|488600796|ref|YP_007907267.1| 18 RKIIENLYFTADYG-EKIFVRGCVGSGKTTLFKII 51
                                      68889998888888.789*************9866 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                                       TTSSSS-STTSHHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  81 ddleekeeveslkrklvrlLltkrfllvlD 110
                                       ++++e +++e+    l  +  +kr  ++lD
  gi|488600796|ref|YP_007907267.1| 123 KKTSELSDGEKQLVTLITAFASKRECIILD 152
                                       345555555656777888888888888888 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.001
                                       EEEEEESTTSSHHHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqi 40 
                                        +++vG  G+GKttl+k i
  gi|488600796|ref|YP_007907267.1| 248 AISIVGDNGSGKTTLLKAI 266
                                       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 !    8.7   0.0    0.0046       1.7      18      39 ..      28      51 ..      15      58 .. 0.75
   2 !   11.0   0.1   0.00086      0.31      18      44 ..     243     271 ..     226     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0046
                                      H..TEEEEEEESTTSSHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrgl 39
                                      +  g+ i+ +G +G+GKTtl + +
  gi|488600796|ref|YP_007907267.1| 28 AdyGEKIFVRGCVGSGKTTLFKII 51
                                      2446679*************9976 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00086
                                       H..TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  18 l..gdvilLeGdLGaGKTtlvrglakalg 44 
                                       l  g++i + Gd G+GKTtl +++   l+
  gi|488600796|ref|YP_007907267.1| 243 LrrGEAISIVGDNGSGKTTLLKAISGILK 271
                                       13477899**************9987665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.5    0.0069       2.5       1      23 [.      33      55 ..      33     196 .. 0.89
   2 !   13.9   0.2   0.00011     0.039       2      30 ..     249     277 ..     248     283 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0069
                                      EEEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlell 23
                                      k+f+ G  G+GKtTl+k ++ l+
  gi|488600796|ref|YP_007907267.1| 33 KIFVRGCVGSGKTTLFKIISGLI 55
                                      699*************9988776 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00011
                                       EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                       + i G  G+GKtTl+k ++  lk +gv v
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISGILKADGVIV 277
                                       6799********************99988 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 ?    3.8   0.0      0.14        50       3      17 ..      35      49 ..      33      64 .. 0.70
   2 !   14.2   0.2   8.2e-05      0.03       2      30 ..     249     277 ..     248     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                              MobB  3 givgksgsGKTtLle 17
                                       + g+ gsGKTtL +
  gi|488600796|ref|YP_007907267.1| 35 FVRGCVGSGKTTLFK 49
                                      566999******964 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.2e-05
                              MobB   2 lgivgksgsGKTtLleklipelkarglrv 30 
                                       ++ivg +gsGKTtLl+ +  +lka g+ v
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISGILKADGVIV 277
                                       79*********************999866 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.12        42      22      39 ..      35      52 ..      25      57 .. 0.83
   2 !   13.4   0.0   0.00013     0.049      22      48 ..     250     276 ..     242     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                            AAA_30 22 vltGpAGtGKttalkalr 39
                                      ++ G  G+GKtt+ k + 
  gi|488600796|ref|YP_007907267.1| 35 FVRGCVGSGKTTLFKIIS 52
                                      78999********99876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00013
                            AAA_30  22 vltGpAGtGKttalkalreaweaaggr 48 
                                        ++G  G+GKtt+lka+  +++a+g  
  gi|488600796|ref|YP_007907267.1| 250 SIVGDNGSGKTTLLKAISGILKADGVI 276
                                       689*******************99933 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0033       1.2       2      81 ..      34     157 ..      34     179 .. 0.71
   2 !    8.0   0.0    0.0079       2.9       4      29 ..     251     278 ..     249     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0033
                            AAA_33   2 vllvGlpGsGKstlaerllkklg...avllssdt........................................... 32 
                                       +++ G  GsGK+tl + +    +    +++s d+                                           
  gi|488600796|ref|YP_007907267.1|  34 IFVRGCVGSGKTTLFKIISGLIPvfyNCRISGDVmvfgenspanfrkhvylvpqnpeeqiifedvedeifsvshdln 110
                                       6899**********998876666888899999999999999988777777777777777777776666666666555 PP

                            AAA_33  33 lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnls 81 
                                       l +r  +++  sk + ++++d  +q +  l++  +s++  +ild ++  
  gi|488600796|ref|YP_007907267.1| 111 LVKRFNADHLISK-KTSELSDGEKQLV-TLITAFASKRECIILDEPFSH 157
                                       5555554444444.3455655555555.888877777777888999876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0079
                            AAA_33   4 lvGlpGsGKstlaerllkklg..avlls 29 
                                       +vG +GsGK+tl++ +   l+  +v+++
  gi|488600796|ref|YP_007907267.1| 251 IVGDNGSGKTTLLKAISGILKadGVIVR 278
                                       7999*********988554444455555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0046       1.7       2      23 ..      32      53 ..      31      61 .. 0.88
   2 !    8.4   0.1    0.0046       1.7       4      23 ..     249     268 ..     247     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0046
                         PduV-EutP  2 kkilliGkvgsGKttLtqalkg 23
                                      +ki++ G vgsGKttL + ++g
  gi|488600796|ref|YP_007907267.1| 32 EKIFVRGCVGSGKTTLFKIISG 53
                                      58999************99987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0046
                         PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                       i ++G  gsGKttL +a++g
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISG 268
                                       6789*************987 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0031       1.1      21      43 ..      35      61 ..      28      96 .. 0.76
   2 !    7.5   0.1    0.0017      0.63      18      37 ..     247     266 ..     238     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0031
                           DUF3584 21 nieGtNaaGKTtLlr....LiPlFYGe 43
                                       + G  ++GKTtL +    LiP+FY  
  gi|488600796|ref|YP_007907267.1| 35 FVRGCVGSGKTTLFKiisgLIPVFYNC 61
                                      578999*******98555689****65 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0017
                           DUF3584  18 ghtnieGtNaaGKTtLlrLi 37 
                                       +   i+G N++GKTtLl+ i
  gi|488600796|ref|YP_007907267.1| 247 EAISIVGDNGSGKTTLLKAI 266
                                       56789***********9865 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.2     0.009       3.3       4      18 ..      35      49 ..      33      56 .. 0.86
   2 !    9.3   0.1    0.0021      0.76       3      20 ..     249     266 ..     247     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.009
                                      EEEESTTCCHHHHHH CS
                              cobW  4 vltGflGsGKTtLln 18
                                       + G +GsGKTtL +
  gi|488600796|ref|YP_007907267.1| 35 FVRGCVGSGKTTLFK 49
                                      688**********76 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                                       EEEEESTTCCHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhl 20 
                                       + ++G  GsGKTtLl+++
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAI 266
                                       679999*********987 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 ?    5.9   0.1     0.027       9.7       1      18 [.      36      53 ..      36      62 .. 0.83
   2 !    9.6   0.1     0.002      0.73       1      24 [.     251     274 ..     251     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                        ATP_bind_1  1 vvGpaGsGKttfvgalse 18
                                      v G++GsGKtt+ + +s 
  gi|488600796|ref|YP_007907267.1| 36 VRGCVGSGKTTLFKIISG 53
                                      67*********9987765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.002
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrg 24 
                                       +vG  GsGKtt+ +a+s il++ g
  gi|488600796|ref|YP_007907267.1| 251 IVGDNGSGKTTLLKAISGILKADG 274
                                       799**************9998875 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00043      0.16      23      87 ..     118     169 ..     103     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00043
                           SbcCD_C  23 ekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                       +  +s+++++lS Gekq l++l+ a      + s+       + ++LDE Fs l ++++++l+++
  gi|488600796|ref|YP_007907267.1| 118 DHLISKKTSELSDGEKQ-LVTLITA------FASK------RECIILDEPFSHLHPKRVEKLIDY 169
                                       44589999********5.4444444......2222......25799********99999999986 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.18        64      23      53 ..      38      63 ..      28     102 .. 0.78
   2 ?    2.3   0.0      0.14        52     495     511 ..     123     139 ..     115     156 .. 0.89
   3 !    7.1   0.0    0.0048       1.8      21      39 ..     251     269 ..     247     306 .. 0.85
   4 ?   -2.4   0.0       3.8   1.4e+03     526     573 ..     345     386 ..     336     391 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.18
                            AAA_13 23 GwNGaGKTtLSrllrslelgetepkfangsi 53
                                      G  G+GKTtL ++++ l      p f n+ i
  gi|488600796|ref|YP_007907267.1| 38 GCVGSGKTTLFKIISGL-----IPVFYNCRI 63
                                      667***********998.....355666665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                            AAA_13 495 qaaetLSeGEktaIafl 511
                                       +++ +LS+GEk +++++
  gi|488600796|ref|YP_007907267.1| 123 KKTSELSDGEKQLVTLI 139
                                       57899**********86 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0048
                            AAA_13  21 iYGwNGaGKTtLSrllrsl 39 
                                       i G NG+GKTtL ++++ +
  gi|488600796|ref|YP_007907267.1| 251 IVGDNGSGKTTLLKAISGI 269
                                       669*********9999876 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 3.8
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnlef 573
                                       k  iv +D P      ++ + +++lik+        k  +i TH + +
  gi|488600796|ref|YP_007907267.1| 345 KGDIVLLDEPTVAQNYEFGMRIIGLIKKLG------KSAIIATHDFRL 386
                                       7789999999999999999999****9997......777999999875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.011         4      22      48 ..      31      57 ..      16      68 .. 0.85
   2 !    7.4   0.0     0.007       2.6      22      47 ..     246     271 ..     225     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpp 48
                                      g ++++ G  GsGKt l k +++l+p 
  gi|488600796|ref|YP_007907267.1| 31 GEKIFVRGCVGSGKTTLFKIISGLIPV 57
                                      5679999*****************996 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.007
                      Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsllp 47 
                                       g  + +vG  GsGKt l k+++++l 
  gi|488600796|ref|YP_007907267.1| 246 GEAISIVGDNGSGKTTLLKAISGILK 271
                                       5567899*****************95 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.17        63      19      36 ..      34      51 ..      20      58 .. 0.84
   2 !   10.9   0.0   0.00054       0.2      15      60 ..     245     290 ..     233     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                        Zeta_toxin 19 illgGqpGAGKselaell 36
                                      i++ G  G+GK++l + +
  gi|488600796|ref|YP_007907267.1| 34 IFVRGCVGSGKTTLFKII 51
                                      8999*********98876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00054
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60 
                                       r  +i ++G  G+GK++l++++   l+++g +vr  + +l  ++P+
  gi|488600796|ref|YP_007907267.1| 245 RGEAISIVGDNGSGKTTLLKAISGILKADGVIVRKGRISLSLQYPN 290
                                       5578999****************99987777777555555555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.018       6.6      22     131 ..      33     158 ..      21     174 .. 0.56
   2 !    8.6   0.0    0.0044       1.6      20      47 ..     246     273 ..     234     382 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.018
                          ATPase_2  22 iyfiYGpegsGKtaLlkei......ienledkdkyviyyialreesiskldefieeeeekkklekal.........g 83 
                                        +f+ G  gsGKt+L+k i        n + +++  ++  +    + +++    ++ ee+  +e++          +
  gi|488600796|ref|YP_007907267.1|  33 KIFVRGCVGSGKTTLFKIIsglipvFYNCRISGDVMVFGENSPANFRKHVYLVPQNPEEQIIFEDVEdeifsvshdL 109
                                       58999**********98651111112233344446666666666666666665443333333333335555555667 PP

                          ATPase_2  84 iavpkaeleeilkeksklvfkaielllekikkkgkk.iiiiiDelqkli 131
                                       + v+++++++++++k+ ++    ++l   i+  + k   ii+De +   
  gi|488600796|ref|YP_007907267.1| 110 NLVKRFNADHLISKKTSELSDGEKQLVTLITAFASKrECIILDEPFSHL 158
                                       7777777777777554444444444444444433333667777766655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0044
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledk 47 
                                        e + i G  gsGKt+Llk i   l+  
  gi|488600796|ref|YP_007907267.1| 246 GEAISIVGDNGSGKTTLLKAISGILKAD 273
                                       5567899************997777554 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.025       9.1      25      44 ..      33      52 ..      16     173 .. 0.90
   2 !    8.4   0.0    0.0029       1.1      25      50 ..     248     274 ..     231     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.025
                                      EEEEEESTTSSHHHHHHHHH CS
                           G-alpha 25 kllllGqseSGKsTilkqlk 44
                                      k+ + G+ +SGK+T++k + 
  gi|488600796|ref|YP_007907267.1| 33 KIFVRGCVGSGKTTLFKIIS 52
                                      89999***********9775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0029
                                       EEEEEESTTSSHHHHHHHHH.HHCS-- CS
                           G-alpha  25 kllllGqseSGKsTilkqlk.llykkg 50 
                                        + ++G ++SGK+T+lk +  +l+ +g
  gi|488600796|ref|YP_007907267.1| 248 AISIVGDNGSGKTTLLKAISgILKADG 274
                                       47899*************996666655 PP

>> Ploopntkinase1  P-loop Nucleotide Kinase1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0017      0.63      16      55 ..      30      69 ..      20      75 .. 0.91
   2 ?    3.1   0.0      0.16        57      16      57 ..     245     286 ..     239     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                    Ploopntkinase1 16 rgelyyvkgsngsgkstvpsylaekdpeayvvtldgkvll 55
                                       ge  +v+g+ gsgk+t+   ++   p  y +  +g v++
  gi|488600796|ref|YP_007907267.1| 30 YGEKIFVRGCVGSGKTTLFKIISGLIPVFYNCRISGDVMV 69
                                      69999***************************99999986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.16
                    Ploopntkinase1  16 rgelyyvkgsngsgkstvpsylaekdpeayvvtldgkvlltv 57 
                                       rge   + g ngsgk+t+   ++       v++++g++ l++
  gi|488600796|ref|YP_007907267.1| 245 RGEAISIVGDNGSGKTTLLKAISGILKADGVIVRKGRISLSL 286
                                       89999999*********9999988887778888888888765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0026      0.95       1      21 [.      34      54 ..      34      62 .. 0.85
   2 ?    5.1   0.6     0.048        17       1      20 [.     249     268 ..     249     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                                      EEEEESTTSSHHHHHHHHHCC CS
                               dNK  1 ivveGnIgaGKstlvklLskk 21
                                      i v G +g+GK+tl k++s  
  gi|488600796|ref|YP_007907267.1| 34 IFVRGCVGSGKTTLFKIISGL 54
                                      6799************99865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.048
                                       EEEEESTTSSHHHHHHHHHC CS
                               dNK   1 ivveGnIgaGKstlvklLsk 20 
                                       i++ G  g+GK+tl+k +s 
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISG 268
                                       8999***********98875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1      0.05        18       1      19 [.      33      51 ..      33      64 .. 0.87
   2 ?    8.3   0.0    0.0069       2.5       2      20 ..     249     267 ..     248     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.05
                            AAA_28  1 kivitGgestGKTtlleaL 19
                                      ki + G+ ++GKTtl + +
  gi|488600796|ref|YP_007907267.1| 33 KIFVRGCVGSGKTTLFKII 51
                                      68899**********8765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0069
                            AAA_28   2 ivitGgestGKTtlleaLa 20 
                                       i i+G  ++GKTtll+a++
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAIS 267
                                       7899************997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.093        34       4      28 ..      33      58 ..      31      98 .. 0.84
   2 ?    8.2   0.1    0.0049       1.8       5      22 ..     249     266 ..     245     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.093
                            AAA_24  4 kiliyGpsgiGKTtlakel.gpkplf 28
                                      ki++ G  g+GKTtl k + g  p+f
  gi|488600796|ref|YP_007907267.1| 33 KIFVRGCVGSGKTTLFKIIsGLIPVF 58
                                      89999**********98775555555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0049
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       i i+G++g+GKTtl+k +
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAI 266
                                       789***********9977 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.32   1.2e+02       2      21 ..      34      53 ..      33      67 .. 0.85
   2 ?    9.6   0.0    0.0025      0.92       2      22 ..     249     269 ..     248     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.32
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      + + G   +GK+tL++ ++g
  gi|488600796|ref|YP_007907267.1| 34 IFVRGCVGSGKTTLFKIISG 53
                                      6788999********98876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0025
                                       EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                       + ivG   +GK+tL++a++g 
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISGI 269
                                       78****************983 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 ?    2.5   0.0      0.27        97       8      35 ..      25      52 ..      19     226 .. 0.92
   2 ?   10.3   0.0    0.0011      0.41      12      45 ..     244     277 ..     234     402 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.27
                                      HS-EBTT-EEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  8 lfpivqGqrtlipgafgvGktvisqsls 35
                                       f+   G+++ + g  g Gkt++ + +s
  gi|488600796|ref|YP_007907267.1| 25 YFTADYGEKIFVRGCVGSGKTTLFKIIS 52
                                      5778889***************998876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                                       BTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  12 vqGqrtlipgafgvGktvisqslskqsnsddaii 45 
                                        +G+ + i+g++g Gkt++++++s   ++d +i+
  gi|488600796|ref|YP_007907267.1| 244 RRGEAISIVGDNGSGKTTLLKAISGILKADGVIV 277
                                       689*********************9987775655 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 ?    2.8   0.0      0.14        49      13      47 ..      15      49 ..       8      57 .. 0.88
   2 ?    8.4   0.0    0.0025      0.91      15      58 ..     232     275 ..     221     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHH CS
                              MeaB 13 peakellerllakaGraqvvGltGvPGaGkstlve 47
                                       ++++++e+l  +a   +++ + G+ G+Gk tl +
  gi|488600796|ref|YP_007907267.1| 15 GNSRKIIENLYFTADYGEKIFVRGCVGSGKTTLFK 49
                                      57999***************************975 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                                       HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT- CS
                              MeaB  15 akellerllakaGraqvvGltGvPGaGkstlvealglelrrrGk 58 
                                       +k++l+ +  +  r + + + G  G+Gk tl++a+   l++ G 
  gi|488600796|ref|YP_007907267.1| 232 SKTILNSINLDLRRGEAISIVGDNGSGKTTLLKAISGILKADGV 275
                                       79999******************************999998886 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4      0.12        45       5      27 ..      34      55 ..      31     119 .. 0.82
   2 ?    2.7   0.1      0.32   1.2e+02      43      72 ..     122     153 ..      83     181 .. 0.62
   3 ?    6.4   0.0     0.023       8.5       3      24 ..     247     268 ..     245     323 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.12
                            AAA_14  5 lvitGaRrvGKTtllkqlikell 27
                                      ++++G+  +GKTtl +++i+ l+
  gi|488600796|ref|YP_007907267.1| 34 IFVRGCVGSGKTTL-FKIISGLI 55
                                      6899**********.56666555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.32
                            AAA_14  43 dkkladpe....kllelileklke..ekktylflDE 72 
                                        kk ++ +    +l +li     +  +k+++++lDE
  gi|488600796|ref|YP_007907267.1| 122 SKKTSELSdgekQLVTLIT----AfaSKRECIILDE 153
                                       2332222212223334444....1335899*****9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.023
                            AAA_14   3 kilvitGaRrvGKTtllkqlik 24 
                                       +++ i+G   +GKTtllk +  
  gi|488600796|ref|YP_007907267.1| 247 EAISIVGDNGSGKTTLLKAISG 268
                                       678999***********98754 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.38   1.4e+02      12      30 ..      33      51 ..      26      61 .. 0.83
   2 ?   -1.1   0.0       6.1   2.2e+03      99     128 ..     142     173 ..     100     181 .. 0.68
   3 ?    8.6   0.0    0.0059       2.2      11      38 ..     247     274 ..     239     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.38
                            AAA_19 12 vllvtaGpGtGKTrvlkhi 30
                                       ++v +  G+GKT++ k i
  gi|488600796|ref|YP_007907267.1| 33 KIFVRGCVGSGKTTLFKII 51
                                      5789999******987655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 6.1
                            AAA_19  99 klqeeellivDE.fqdvd.elqyrLlkallge 128
                                       +  ++e++i DE f+ +  +   +L++ +l  
  gi|488600796|ref|YP_007907267.1| 142 FASKRECIILDEpFSHLHpKRVEKLIDYVLSY 173
                                       34456688889877888877778888777654 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0059
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelg 38 
                                       + + +++  G+GKT++lk+i  +l++ g
  gi|488600796|ref|YP_007907267.1| 247 EAISIVGDNGSGKTTLLKAISGILKADG 274
                                       567899*************999888766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.4   1.5e+02       2      23 ..      34      55 ..      33      64 .. 0.82
   2 ?    8.0   0.1    0.0071       2.6       4      27 ..     251     274 ..     248     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.4
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                      +++ G  G+gK++l + ++ ++
  gi|488600796|ref|YP_007907267.1| 34 IFVRGCVGSGKTTLFKIISGLI 55
                                      5677999********9999887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0071
                                       EE--SSSSHHHHHHHGGGGBS--E CS
                             AAA_5   4 LvGppGtgKselaerlaaalnrev 27 
                                       +vG+ G+gK++l + ++  l++  
  gi|488600796|ref|YP_007907267.1| 251 IVGDNGSGKTTLLKAISGILKADG 274
                                       79***************9995543 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.4   1.6e+03       4      20 ..      36      52 ..      34      64 .. 0.81
   2 ?   11.6   0.0   0.00046      0.17       2      30 ..     249     277 ..     248     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.4
                               PRK  4 vagsSGaGkttvarkle 20
                                      v g  G+Gktt+ + + 
  gi|488600796|ref|YP_007907267.1| 36 VRGCVGSGKTTLFKIIS 52
                                      67888******987765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00046
                               PRK   2 IgvagsSGaGkttvarklekifgrekvka 30 
                                       I++ g+ G+Gktt+ +++  i++  +v  
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISGILKADGVIV 277
                                       9*********************9777763 PP

>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.31   1.1e+02      52      69 ..      34      51 ..       8      55 .. 0.77
   2 ?   -1.8   0.0       2.8     1e+03     215     237 ..     176     198 ..     175     200 .. 0.86
   3 ?    7.7   0.0    0.0037       1.4      53      86 ..     250     283 ..     229     303 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.31
                           DUF2791 52 rfirGeYGsGKtFllqll 69
                                       f+rG  GsGKt l +++
  gi|488600796|ref|YP_007907267.1| 34 IFVRGCVGSGKTTLFKII 51
                                      49**********999887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.8
                           DUF2791 215 giidddnaydylkllaafvrkaG 237
                                       +ii +d+ yd+lk + ++vr  G
  gi|488600796|ref|YP_007907267.1| 176 TIIFSDKRYDFLKRFSRVVRVGG 198
                                       57889999**********99766 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0037
                           DUF2791  53 firGeYGsGKtFllqllreralergfvvaeadls 86 
                                        i+G+ GsGKt ll+++  + ++ g++v + ++s
  gi|488600796|ref|YP_007907267.1| 250 SIVGDNGSGKTTLLKAISGILKADGVIVRKGRIS 283
                                       599************************9998887 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.92   3.4e+02      26      47 ..      32      53 ..      29      55 .. 0.84
   2 ?    9.5   0.1    0.0011       0.4      23      49 ..     244     270 ..     235     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.92
                              DLIC 26 ksvlvlGedgsGkttliaklqG 47
                                       +++v G  gsGkttl   + G
  gi|488600796|ref|YP_007907267.1| 32 EKIFVRGCVGSGKTTLFKIISG 53
                                      678999**********987776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                              DLIC  23 PsgksvlvlGedgsGkttliaklqGve 49 
                                         g ++ ++G++gsGkttl+  + G+ 
  gi|488600796|ref|YP_007907267.1| 244 RRGEAISIVGDNGSGKTTLLKAISGIL 270
                                       5678899**************999985 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.47   1.7e+02      32      51 ..      30      49 ..      22      56 .. 0.84
   2 ?    8.2   0.0    0.0043       1.6      30      64 ..     243     277 ..     234     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.47
                             AAA_7 32 nkkpvllvGptGtGKtviik 51
                                       + ++++ G +G+GKt++ k
  gi|488600796|ref|YP_007907267.1| 30 YGEKIFVRGCVGSGKTTLFK 49
                                      67789999********9876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0043
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekyls 64 
                                       l+++  + +vG+ G+GKt+++k +   l+ + +++
  gi|488600796|ref|YP_007907267.1| 243 LRRGEAISIVGDNGSGKTTLLKAISGILKADGVIV 277
                                       67888999*************99888777766655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.9   7.1e+02     101     120 ..      33      52 ..      15      57 .. 0.76
   2 ?    9.8   0.0    0.0019      0.71      86     122 ..     232     269 ..     202     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.9
                                       EEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinall 120
                                        +++ G  G GK+tL + + 
  gi|488600796|ref|YP_007907267.1|  33 KIFVRGCVGSGKTTLFKIIS 52 
                                       45667999*******98775 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +k+ l++++  l+  + + +vG  G GK+tL++a+ + 
  gi|488600796|ref|YP_007907267.1| 232 SKTILNSINLDLRRgEAISIVGDNGSGKTTLLKAISGI 269
                                       4556677777777769999**************99875 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.011       4.2      12      33 ..      25      50 ..      17      86 .. 0.85
   2 ?    2.5   0.0      0.29   1.1e+02      11      30 ..     242     262 ..     233     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                                      H....TTCEEEEEESTTSSHHHHHHH CS
                                      x....xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 12 l....gggdvlvaaeTGsGKTlafli 33
                                      +     g++++v++ +GsGKT+ f i
  gi|488600796|ref|YP_007907267.1| 25 YftadYGEKIFVRGCVGSGKTTLFKI 50
                                      444447899*************9976 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.29
                                       HH.TTCEEEEEESTTSSHHHH CS
                                       xx.xxxxxxxxxxxxxxxxxx RF
                              DEAD  11 il.gggdvlvaaeTGsGKTla 30 
                                        l +g+ + + ++ GsGKT+ 
  gi|488600796|ref|YP_007907267.1| 242 DLrRGEAISIVGDNGSGKTTL 262
                                       44467888999********86 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.5   5.5e+02      41      56 ..      33      48 ..      17      55 .. 0.79
   2 ?    8.6   0.0    0.0028         1      22      58 ..     230     265 ..     220     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                                      SEEEE--TTSSHHHHH CS
                      FtsK_SpoIIIE 41 hllvaGatgsGKStal 56
                                       + v G  gsGK+t  
  gi|488600796|ref|YP_007907267.1| 33 KIFVRGCVGSGKTTLF 48
                                      578999*******965 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0028
                                       EEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE  22 lgkeisgnplvldlkkmashllvaGatgsGKStalnt 58 
                                        g + + n + ldl+  +  + ++G  gsGK+t l++
  gi|488600796|ref|YP_007907267.1| 230 YGSKTILNSINLDLRRGE-AISIVGDNGSGKTTLLKA 265
                                       555666677888999999.999************997 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0011      0.41     242     265 ..     243     267 ..     239     271 .. 0.86
   2 ?   -3.5   0.0       9.3   3.4e+03     341     354 ..     346     359 ..     338     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                                       E-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                       +++G  + IvG +  GK+TLL+A++
  gi|488600796|ref|YP_007907267.1| 243 LRRGeAISIVGDNGSGKTTLLKAIS 267
                                       56676788***************96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.3
                                       -SEEEEEGGGS-HH CS
                        ABC_ATPase 341 akllLiDEDtsAtN 354
                                        +++L+DE t A+N
  gi|488600796|ref|YP_007907267.1| 346 GDIVLLDEPTVAQN 359
                                       5789*********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 ?    0.9   0.1      0.84   3.1e+02       4      17 ..      34      47 ..      32      53 .. 0.84
   2 ?    7.6   0.1     0.007       2.6       4      28 ..     249     273 ..     247     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.84
                                      EEEEESTTSSHHHH CS
                             SRP54  4 illvGlqGaGKTtt 17
                                      i + G  G+GKTt 
  gi|488600796|ref|YP_007907267.1| 34 IFVRGCVGSGKTTL 47
                                      67789*******97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.007
                                       EEEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkke 28 
                                       i +vG +G+GKTt l  ++ +lk++
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAISGILKAD 273
                                       679**********999888877765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3       2.4   8.8e+02       1      17 [.      33      49 ..      33      53 .. 0.85
   2 ?    9.5   0.2    0.0031       1.1       2      19 ..     249     266 ..     248     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.4
                                      EEEEESSTTSSHHHHHH CS
                               Roc  1 KvvlvGdsgvGKtsllk 17
                                      K+ + G  g+GKt+l+k
  gi|488600796|ref|YP_007907267.1| 33 KIFVRGCVGSGKTTLFK 49
                                      778889999******87 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0031
                                       EEEESSTTSSHHHHHHCH CS
                               Roc   2 vvlvGdsgvGKtsllkrf 19 
                                       + +vGd+g+GKt+llk +
  gi|488600796|ref|YP_007907267.1| 249 ISIVGDNGSGKTTLLKAI 266
                                       679***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); 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: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 2460.72
//
Query:       gi|488600797|ref|YP_007907268.1|  [L=236]
Description: hypothetical protein Asulf_01281 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   8.5       0.69   10.2   0.0    2.4  2  DUF1772   Domain of unknown function (DUF1772)


Domain annotation for each model (and alignments):
>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   6.1    0.0076   1.4e+02       1      78 [.      37     109 ..      37     143 .. 0.73
   2 ?   10.2   0.0   3.9e-05      0.69      36      90 ..     173     236 .]     154     236 .] 0.65

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0076
                           DUF1772   1 GlilafslfvvPallslpasssl.....llkqwrrlfkrgkavfpplallsalafaylaaraasrgarllylaaaal 72 
                                       G+++++s+f+  +ll +     l     l+++   l+     ++p++a+ s++ ++ l+++a ++   +ly++ ++l
  gi|488600797|ref|YP_007907268.1|  37 GFNFTLSMFTATILLCSLY---LaltsnLNRLINSLY----FALPFIAFFSVSTLL-LTSNAYGAMLNALYIL-SLL 104
                                       7888888887777773331...122333666666666....899999999999998.6668888888888855.555 PP

                           DUF1772  73 .lllsiv 78 
                                        l+   +
  gi|488600797|ref|YP_007907268.1| 105 sLS--SI 109
                                       354..33 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 3.9e-05
                           DUF1772  36 kavfpplallsalafa.yla..........araasrgarllylaaaal.lllsivpyTllvmvPtNn 90 
                                        ++f ++++l al++  +++            ++   + +++++a+a+ ++  ++++++++++ +Nn
  gi|488600797|ref|YP_007907268.1| 173 VKAFVSILILRALSVSeAIYmrdinlalerE-QKFGWREAYLILASAVlFC--LAVFSFFLNISINN 236
                                       4555556666666666555578888888742.3333333444343444266..99*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1491.12
//
Query:       gi|488600798|ref|YP_007907269.1|  [L=628]
Description: Archaeal serine protease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-11   43.7   0.5    4.3e-11   42.7   0.5    1.5  1  Lon_C          Lon protease (S16) C-terminal proteolytic doma
    8.4e-06   25.9   2.5      0.042   14.0   0.1    4.0  3  HEPN           HEPN domain
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.015   15.2   0.1    3.3  3  PaREP1         Archaeal PaREP1/PaREP8 family
      0.035   13.6   0.0      0.069   12.6   0.0    1.4  1  PEP_mutase     Phosphoenolpyruvate phosphomutase
       0.11   10.3   1.2        1.4    6.7   0.0    2.0  2  DUF4175        Domain of unknown function (DUF4175)
       0.12   12.2   0.0       0.26   11.1   0.0    1.5  1  Abhydrolase_3  alpha/beta hydrolase fold
        0.4   11.3   0.0        0.4   11.3   0.0    3.7  4  DUF4398        Domain of unknown function (DUF4398)


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 !   42.7   0.5   1.7e-14   4.3e-11      92     173 ..      92     173 ..      27     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.7e-14
                                       TT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEE CS
                             Lon_C  92 ekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvil 168
                                       +k+d    + + +    GPsaG  +++a++s+l++ k+++dv mtG i   G + p+GG+  k+ aa   g k  ++
  gi|488600798|ref|YP_007907269.1|  92 TKYDFFFTIKADSPIVGGPSAGGVMTVAVISALKDLKIENDVYMTGMIYPDGFIGPVGGIPYKMKAAADMGAKIFLI 168
                                       44455555555555567************************************************************ PP

                                       EGGGG CS
                             Lon_C 169 Pkene 173
                                       Pk  +
  gi|488600798|ref|YP_007907269.1| 169 PKGQR 173
                                       *9754 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0046        12       5      34 ..     275     304 ..     272     308 .. 0.91
   2 !   14.0   0.1   1.6e-05     0.042       2      37 ..     439     474 ..     438     524 .. 0.83
   3 ?    2.9   0.0     0.044   1.1e+02      70     111 ..     563     604 ..     542     609 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0046
                                       HHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              HEPN   5 lrrAeedleaAellleegdydlacfhaqqa 34 
                                       l+rA++ +e Ae+++ +gdy  a +++ qa
  gi|488600798|ref|YP_007907269.1| 275 LNRAKQLMEMAEESYGNGDYYTATSKYFQA 304
                                       78*********************9988776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaek 37 
                                       + +++ Ae+d+++A++ leeg+y+ a+  a   + k
  gi|488600798|ref|YP_007907269.1| 439 QSLIDGAEDDMDSARKQLEEGFYAGAAVSAMNGMVK 474
                                       67999*********************9988666655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.044
                                       -HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHH CS
                              HEPN  70 seelreeleeLekayiesrYpdakeeyteedaeealkdaeev 111
                                         +++  leeL+++  ++  p   + +t++d+e++++  e++
  gi|488600798|ref|YP_007907269.1| 563 VVKVEYNLEELNNYSEPAASPTVPKLPTSNDVEKIIEGIEAI 604
                                       66788889**************9999**********998887 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    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      50      75 ..     231     256 ..     216     264 .. 0.66
   2 ?   15.2   0.1     6e-06     0.015       3      43 ..     275     315 ..     273     358 .. 0.81
   3 ?   -0.9   1.7      0.57   1.5e+03       6      29 ..     445     468 ..     441     556 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                            PaREP1  50 eeaeekerwstkellkavaklleelg 75 
                                       + +++ +  ++ ellk++a+ +e+  
  gi|488600798|ref|YP_007907269.1| 231 KPKGKVNLFKYSELLKKLADRMEKDT 256
                                       66667777777777777777776654 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 6e-06
                            PaREP1   3 leeaekeleeAeellekGdlrqAaeKaykAvkalvkalaek 43 
                                       l+ a++++e Aee + +Gd+  A  K+++A  +l k++ e+
  gi|488600798|ref|YP_007907269.1| 275 LNRAKQLMEMAEESYGNGDYYTATSKYFQAKIELRKIYYEM 315
                                       678999************************99999998887 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.57
                            PaREP1   6 aekeleeAeellekGdlrqAaeKa 29 
                                       ae+ ++ A++ le+G +  Aa  a
  gi|488600798|ref|YP_007907269.1| 445 AEDDMDSARKQLEEGFYAGAAVSA 468
                                       566666777777777766666433 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.7e-05     0.069     163     219 ..     156     214 ..     153     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                        PEP_mutase 163 raYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvp.lkgtlsvael.aelGvarisl 219
                                       +a a+ GA+ +++p +q+  +++e v++ ++pl+vv  ++++l++ e  +elGv+++ +
  gi|488600798|ref|YP_007907269.1| 156 KAAADMGAKIFLIPKGQRIVKVQETVEERKGPLIVVRtQTKDLDLYEYgKELGVKVVEV 214
                                       7999*********************************5566799888746899999976 PP

>> DUF4175  Domain of unknown function (DUF4175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0   0.00055       1.4     682     733 ..     247     310 ..     238     324 .. 0.73
   2 ?    2.0   0.5     0.015        38     697     722 ..     441     466 ..     422     475 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00055
                           DUF4175 682 elqkelke...........qGk.eagdaLdeAeraMkdAeeaLgqgdlaeAvdaqgrALeaLrk 733
                                       +l +++++            G  +++d+L++A++ M+ Aee+ g+gd  +A+ +  +A  +Lrk
  gi|488600798|ref|YP_007907269.1| 247 KLADRMEKdtrnlyqtvesYGVrNSPDELNRAKQLMEMAEESYGNGDYYTATSKYFQAKIELRK 310
                                       444444444444333555555414556************************9988888777776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.015
                           DUF4175 697 aLdeAeraMkdAeeaLgqgdlaeAvd 722
                                         d Ae++M+ A+++L++g  a+A+ 
  gi|488600798|ref|YP_007907269.1| 441 LIDGAEDDMDSARKQLEEGFYAGAAV 466
                                       5689***************9888864 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0001      0.26      67     109 ..      99     143 ..      81     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                                       TETTCEEEEEEETHHHHHHHHHHHHHHHTT.---EEEEEEESE.- CS
                     Abhydrolase_3  67 gadpsrivlaGdSaGGnlaaavalrardeg.epkvagqvliyP.v 109
                                        +++++ +++G SaGG ++ av  +++d + e+ v  + +iyP +
  gi|488600798|ref|YP_007907269.1|  99 TIKADSPIVGGPSAGGVMTVAVISALKDLKiENDVYMTGMIYPdG 143
                                       57788889********************98677799999999961 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016       0.4       5      57 ..     255     306 ..     254     314 .. 0.85
   2 ?   -0.4   0.1      0.69   1.8e+03      29      60 ..     358     391 ..     353     395 .. 0.41
   3 ?   -1.0   0.6       1.1   2.8e+03      28      40 ..     444     456 ..     416     468 .. 0.56
   4 ?   -0.6   0.1      0.83   2.1e+03       5      18 ..     495     508 ..     484     523 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                           DUF4398   5 dAraaleaAraagaeeyApaeleeAreaLaqAeaamaekdyeeAdhlaylAer 57 
                                       d+r  ++++++ g ++  p+el++A++ ++ Ae+  +++dy +A   + +A+ 
  gi|488600798|ref|YP_007907269.1| 255 DTRNLYQTVESYGVRN-SPDELNRAKQLMEMAEESYGNGDYYTATSKYFQAKI 306
                                       6788888888888765.6889*************9999999999988888875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.69
                           DUF4398  29 AreaLaqAea...amaekdyeeAdhlaylAerdae 60 
                                       A+e +  Ae    ++  ++++    ++ l+++++e
  gi|488600798|ref|YP_007907269.1| 358 AQERVTLAENylyLARTSENR-MIYYLALSKERVE 391
                                       444444444443222222222.3344444444444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                           DUF4398  28 eAreaLaqAeaam 40 
                                        A++ ++ A+++ 
  gi|488600798|ref|YP_007907269.1| 444 GAEDDMDSARKQL 456
                                       3444444444443 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.83
                           DUF4398   5 dAraaleaAraaga 18 
                                       +Ar+a e+A ++  
  gi|488600798|ref|YP_007907269.1| 495 SARKASEQAISEAE 508
                                       33444333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3788.34
//
Query:       gi|488600799|ref|YP_007907270.1|  [L=409]
Description: TIGR00297 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  168.5  18.1    1.6e-49  168.5  18.1    2.7  2  DUF92     Integral membrane protein DUF92


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.6     0.027   4.8e+02     171     189 ..     111     149 ..      63     150 .. 0.66
   2 !  168.5  18.1   8.8e-54   1.6e-49       2     234 ..     188     400 ..     187     402 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.027
                             DUF92 171 l....................lillltlaGllGsllDSl 189
                                                            l++l ++ Gl++sl++S+
  gi|488600799|ref|YP_007907270.1| 111 FsfayfvfyfkvlgfnlnyefLFFLSLIGGLTASLVESV 149
                                       022333334444666667776666677778888888886 PP

  == domain 2  score: 168.5 bits;  conditional E-value: 8.8e-54
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       ++l+l ++a++++  + sG+++a+l+g+l+++  + ++ff +ll F+++gs +tk++++ K+  ++ e ++gaR++ 
  gi|488600799|ref|YP_007907270.1| 188 ISLILSIFAMKSGIADESGLMSATLIGTLMIVF-TDIRFFGILLSFYIIGSFATKYRYSLKQklGVGEPAGGARGYA 263
                                       6899************************99999.8999*********************99955666777999**** PP

                             DUF92  77 qVlanslvalllally..lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGlla 151
                                       +V+ansl al++a+ y  ++++l+lv +vas+Aa+++DT+aSE+Gk++   + +lit++k+v++G++Gg+s+ G l 
  gi|488600799|ref|YP_007907270.1| 264 NVFANSLPALFFAMNYgvFGGELFLVSFVASIAAALGDTMASEIGKTSD--RVYLITNFKRVNAGVSGGISVKGELS 338
                                       ****************765599***********************7774..6************************* PP

                             DUF92 152 sllGalliall.avlllllellillltlaGllGsllDSlLGatlqasvvdkrtgkvvegeggekvvsGldlLdNnaV 227
                                       ++lG++++a+l ++l++l+ + +++++++GllG  +DS+LGatl+++                       +L+N++V
  gi|488600799|ref|YP_007907270.1| 339 AFLGSFIVAMLaIALSILTVKQAMVALISGLLGVHVDSVLGATLEKK----------------------GYLTNSGV 393
                                       *********883444444444999999********************......................56777777 PP

                             DUF92 228 Nllsall 234
                                       N+l++l 
  gi|488600799|ref|YP_007907270.1| 394 NFLATLS 400
                                       7777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2404.61
//
Query:       gi|488600800|ref|YP_007907271.1|  [L=204]
Description: Undecaprenyl pyrophosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-25   88.3   0.0      1e-24   87.4   0.0    1.7  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   5.6e-29     1e-24     115     224 .]      98     203 ..       7     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 5.6e-29
                                       TSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTT CS
                      Prenyltransf 115 kklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytakalpdpDlliRtsGeeRlSnFllwqla 190
                                        ++ +n+++ Y +++eiv+av+++++e++e k +  ei+e+++ekhl    + ++pDl+iR +  e++ +Fllwq++
  gi|488600800|ref|YP_007907271.1|  98 CGFWINFIIGYEGKSEIVDAVKKIAAEVKEGKLRiGEITEKDIEKHLKI--K-NPPDLIIRAG--EKIPEFLLWQSI 169
                                       34889*******************9999777776556699********8..4.79******98..78********** PP

                                       T-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 191 yselyfldvlWPdfskedllealleyqkrerrfg 224
                                       yselyfld+ W +f+  d+l++++eyq+rerrfg
  gi|488600800|ref|YP_007907271.1| 170 YSELYFLDADWRNFRYIDFLRCIREYQRRERRFG 203
                                       ********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1332.83
//
Query:       gi|488600801|ref|YP_007907272.1|  [L=168]
Description: putative nucleotide kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-49  166.3   1.4    5.9e-49  166.2   1.4    1.0  1  NTPase_1         NTPase
    5.8e-08   33.4   0.1    3.7e-07   30.8   0.1    2.0  1  AAA_18           AAA domain
    2.7e-07   30.9   1.1    1.3e-05   25.4   0.3    2.9  2  AAA_22           AAA domain
    4.8e-07   30.3   0.4    2.1e-06   28.2   0.2    2.0  2  AAA              ATPase family associated with various cellul
    1.6e-06   27.6   0.2    2.5e-06   27.0   0.2    1.3  1  ATPase           KaiC
    5.1e-05   22.8   0.4    0.00042   19.9   0.4    2.0  1  Pox_A32          Poxvirus A32 protein
    7.9e-05   23.1   0.8    0.00042   20.8   0.6    2.1  1  AAA_17           AAA domain
     0.0001   22.1   0.1     0.0014   18.4   0.0    2.5  2  AAA_30           AAA domain
    0.00015   21.8   0.8    0.00038   20.4   0.7    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0002   21.2   2.5     0.0031   17.3   2.5    2.8  1  AAA_24           AAA domain
    0.00022   20.5   0.2    0.00053   19.3   0.2    1.8  1  NB-ARC           NB-ARC domain
    0.00031   20.8   0.1    0.00085   19.4   0.1    2.0  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0006   20.2   0.0      0.034   14.5   0.0    2.3  2  RNA_helicase     RNA helicase
    0.00065   20.1   0.0     0.0012   19.3   0.0    1.7  1  AAA_16           AAA ATPase domain
    0.00082   19.4   1.9      0.037   14.0   1.9    2.6  1  AAA_14           AAA domain
    0.00095   19.1   0.1     0.0049   16.8   0.0    2.0  2  NACHT            NACHT domain
      0.001   19.2   0.3       0.48   10.5   0.0    2.3  2  ADK              Adenylate kinase
     0.0021   17.8   0.4      0.048   13.4   0.0    2.4  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0022   18.5   0.1     0.0038   17.8   0.1    1.8  1  ABC_tran         ABC transporter
     0.0039   17.5   0.7       0.34   11.2   0.0    2.8  3  AAA_19           AAA domain
      0.005   16.1   0.0      0.044   13.0   0.0    1.8  2  KAP_NTPase       KAP family P-loop domain
     0.0054   16.5   0.3       0.66    9.7   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
     0.0076   16.1   0.1      0.096   12.5   0.0    2.3  3  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.01   15.5   0.1      0.047   13.3   0.0    2.0  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.013   14.8   0.2      0.044   13.0   0.2    2.0  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.014   15.7   0.0      0.035   14.4   0.0    1.7  1  AAA_28           AAA domain
      0.015   15.0   0.4       0.16   11.7   0.1    2.1  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.028   14.1   0.3        4.6    6.9   0.0    2.2  2  CoaE             Dephospho-CoA kinase
      0.028   14.1   0.4        4.5    7.0   0.0    2.6  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.06   12.0   0.0      0.098   11.3   0.0    1.4  1  GvpD             GvpD gas vesicle protein
      0.087   12.8   0.3        1.2    9.2   0.0    2.5  3  AAA_5            AAA domain (dynein-related subfamily)
      0.098   12.6   1.3        1.4    8.9   0.1    2.9  3  AbfS_sensor      Sensor histidine kinase (AbfS) sensor domain
        0.1   12.3   0.0        4.1    7.1   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
       0.11   12.0   0.6        7.9    5.8   0.0    2.5  3  TniB             Bacterial TniB protein
       0.12   12.6   0.0       0.32   11.2   0.0    1.7  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.13   12.5   0.0       0.22   11.7   0.0    1.8  1  AAA_33           AAA domain
       0.15   11.1   0.0       0.31   10.0   0.0    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.16   11.7   0.1       0.31   10.8   0.1    1.4  1  AAA_29           P-loop containing region of AAA domain
        0.2   11.2   0.1        4.1    6.9   0.0    2.3  2  AAA_25           AAA domain


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 !  166.2   1.4   1.3e-51   5.9e-49       1     168 []       2     164 ..       2     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 1.3e-51
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE- CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvd 77 
                                       k++iTG+pG+GKtTl+k++ + +k+ ++  gGf+t+e re+g r+gF   dl +gee +La+v++ +++rvgky v 
  gi|488600801|ref|YP_007907272.1|   2 KIAITGRPGSGKTTLCKRIFDSIKD-EFDCGGFITKERREKGIRVGFLFHDLVTGEEFWLASVKSDSRIRVGKYGVI 77 
                                       689********************65.5************************************************** PP

                                       HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE CS
                          NTPase_1  78 vesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfe 154
                                       ++++e++ ++ +++ + +++v++iDEiG+mElks+kf e+ve+vL+++   +++ih r++++l++++r++   +vf 
  gi|488600801|ref|YP_007907272.1|  78 LDNIEKI-SDRIKE-YAKKEVLIIDEIGPMELKSRKFVEEVERVLHRDGTNIFTIHYRSNHSLIQKVRKS--YQVFV 150
                                       ******8.788876.689**************************************************98..9**** PP

                                       --TTTTTTHHHHHH CS
                          NTPase_1 155 vteenrdalleeil 168
                                       ++e+nrd ++eei+
  gi|488600801|ref|YP_007907272.1| 151 IDEHNRDMVFEEIV 164
                                       ************95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1     8e-10   3.7e-07       1      82 [.       3     102 ..       3     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 8e-10
                            AAA_18   1 IlltGtpGvGKttlakeL....skrlgf.............gvnlrdvakenglllevdpealdeskrldedkldkl 60 
                                       I++tG pG+GKttl+k++    +++  f             g+++++++ +  + +e++ + +++  r++ +k  ++
  gi|488600801|ref|YP_007907272.1|   3 IAITGRPGSGKTTLCKRIfdsiKDE--FdcggfitkerrekGIRVGFLFHDLVTGEEFWLASVKSDSRIRVGKYGVI 77 
                                       89****************8766333..233555777777777777777777555555555588889*********** PP

                            AAA_18  61 ldaleenss...aleegknlvidgh 82 
                                       ld++e++s+    +++ ++l+id +
  gi|488600801|ref|YP_007907272.1|  78 LDNIEKISDrikEYAKKEVLIIDEI 102
                                       *******99**999999*****986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3   2.9e-08   1.3e-05       8     117 ..       3     121 ..       2     138 .. 0.73
   2 ?    0.7   0.0       1.3     6e+02      83     102 ..     139     156 ..     130     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.9e-08
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlpsstsskdl.lrellralglelkaerlsse 76 
                                       +++tG +G+GKTtl++r++++ + e +          e+   v +    + + +++ l  + ++   +  +  +   
  gi|488600801|ref|YP_007907272.1|   3 IAITGRPGSGKTTLCKRIFDSIKDEFDCGGfitkerrEKGIRVGFLFHDLVTGEEFwLASVKSDSRIRVGK-YGVIL 78 
                                       68*******************96555544488888543333345566666688888667777777666666.77777 PP

                            AAA_22  77 ellealeqalraravielliiDEaqhlr..seealeeLrslln 117
                                       + +e++ + ++++a++e+liiDE+  +   s + +ee+ + l 
  gi|488600801|ref|YP_007907272.1|  79 DNIEKISDRIKEYAKKEVLIIDEIGPMElkSRKFVEEVERVLH 121
                                       8888888888888889*******99987766777777744433 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.3
                            AAA_22  83 eqalraravielliiDEaqh 102
                                        q +r+ +   +++iDE  +
  gi|488600801|ref|YP_007907272.1| 139 IQKVRKSYQ--VFVIDEHNR 156
                                       455555555..9****9665 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 !   28.2   0.2   4.5e-09   2.1e-06       3      74 ..       5     109 ..       3     123 .. 0.72
   2 ?   -1.6   0.0       7.5   3.5e+03      48      66 ..     137     153 ..     123     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 4.5e-09
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS....................................STTHHH CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsellsk....................................yvgese 43 
                                       ++G pG GKT+l+k +  +++ e   +++  ++ k                                      g   
  gi|488600801|ref|YP_007907272.1|   5 ITGRPGSGKTTLCKRIFDSIKDE---FDCGGFITKerrekgirvgflfhdlvtgeefwlasvksdsrirvgKYGVIL 78 
                                       78*****************9864...344444433344445555555555666666666666677777777889999 PP

                                       HHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA  44 kkirelfkeakekakpsilfiDEidalaksr 74 
                                       ++i+++ +++ke ak+ +l+iDEi  +  ++
  gi|488600801|ref|YP_007907272.1|  79 DNIEKISDRIKEYAKKEVLIIDEIGPMELKS 109
                                       ************9978********9886555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.5
                                       HHHHHHHHTSTSEEEEEET CS
                               AAA  48 elfkeakekakpsilfiDE 66 
                                        l+++++++    +++iDE
  gi|488600801|ref|YP_007907272.1| 137 SLIQKVRKSY--QVFVIDE 153
                                       5667776665..8999998 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   5.4e-09   2.5e-06      22     169 ..       3     137 ..       1     157 [. 0.76

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.4e-09
                            ATPase  22 vlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaee 98 
                                       + itG pG+GKt+++++ ++ ++++  + g f+t e +++ +r     +G  +++l   +++ +  + ++++ +  +
  gi|488600801|ref|YP_007907272.1|   3 IAITGRPGSGKTTLCKR-IFDSIKDEFDCGGFITKERREKGIR-----VGFLFHDLVTGEEFWLASVKSDSRIRVGK 73 
                                       78*************99.899999989999********99997.....78889999998888888777776554443 PP

                            ATPase  99 ..kdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvlkklgvTailvseksssee 169
                                            +++    e++ + ike+   + ++iD i+++     e + R+ + ++ rvl+  + T+i++   +s+++
  gi|488600801|ref|YP_007907272.1|  74 ygVILDNI----EKISDRIKEYAKkEVLIIDEIGPM-----ELKSRKFVEEVERVLHR-DGTNIFTIHYRSNHS 137
                                       33444444....45555555555437899*******.....66678888888888764.568999988777544 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.4     9e-07   0.00042      15     152 ..       2     149 ..       1     164 [. 0.70

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9e-07
                           Pox_A32  15 rlalvGgsGsGktvyLlsLlrtlvkkykhifLltpvknse..YdkyvwPdhin.......kvtseeeleY.sLsatk 81 
                                       ++a++G  GsGkt+  + ++ ++ +++     +t    ++    ++++ d ++        v+s+ ++   +  +++
  gi|488600801|ref|YP_007907272.1|   2 KIAITGRPGSGKTTLCKRIFDSIKDEFDCGGFITKERREKgiRVGFLFHDLVTgeefwlaSVKSDSRIRVgKYGVIL 78 
                                       799************************88777777444431256899999875333322256666665431344667 PP

                           Pox_A32  82 ekieklakkeknqkeaerfLlilDDlGdkqtksktLlellnvgRhlnvsiilLcq.tykh.vpvngrasithl 152
                                       ++iek++ +   ++ a++ +li+D++G +++ks+  +e +    h    +i+ ++ + +h + ++ r+s   +
  gi|488600801|ref|YP_007907272.1|  79 DNIEKISDR--IKEYAKKEVLIIDEIGPMELKSRKFVEEVERVLHRDGTNIFTIHyRSNHsLIQKVRKSYQVF 149
                                       888888883..334467888999*************9999999999988888876233342344455555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.6     9e-07   0.00042       1      99 [.       6     123 ..       6     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9e-07
                                       EE-TTSSHHHHHHHHHHHH..............TEEEEEHHHHHHHHHHTTT....SHSSHHHHCTSHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..............gfthlsaGdllreeakrgg....lakardemrklpleekkelqk 59 
                                       +G PGsGK+t+c+++ + +                + +  G l+ + ++ ++    ++k+++++r ++  +  +  +
  gi|488600801|ref|YP_007907272.1|   6 TGRPGSGKTTLCKRIFDSIkdefdcggfitkerREKGIRVGFLFHDLVTGEEfwlaSVKSDSRIRVGKYGVILDNIE 82 
                                       699************8755222233322222225555666666666666665775458899999999999999999* PP

                                       HHHHHHHHHHHSSEEEEEE-.SEEEETTEEEESSHHHHHHH CS
                            AAA_17  60 eaaekiaeeakkkgvlvdgh.prikeqagfldglpkevlee 99 
                                       ++ ++i+e akk+ +++d   p+  ++++f++++++   ++
  gi|488600801|ref|YP_007907272.1|  83 KISDRIKEYAKKEVLIIDEIgPMELKSRKFVEEVERVLHRD 123
                                       ******************99899999999999999855554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.1e-06    0.0014      22     104 ..       4     109 ..       2     130 .. 0.74
   2 ?    0.6   0.0      0.86   3.9e+02      75      97 ..     118     154 ..     111     156 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.1e-06
                            AAA_30  22 vltGpAGtGKttalkalreaweaa.g..........................grviglAptgkaAkvLaeelgieas 71 
                                       ++tG++G+GKtt+ k + + ++++                            ++  +++ ++    +++ + g+  +
  gi|488600801|ref|YP_007907272.1|   4 AITGRPGSGKTTLCKRIFDSIKDEfDcggfitkerrekgirvgflfhdlvtgEEFWLASVKSDSRIRVG-KYGVILD 79 
                                       69***************9999999557788888888888777777777777555555555555555565.7799999 PP

                            AAA_30  72 tiakllkrlkgrarlepgtllivDEagmvdtkq 104
                                       +i+k+ +r k+   ++++++li+DE+g +  k+
  gi|488600801|ref|YP_007907272.1|  80 NIEKISDRIKE---YAKKEVLIIDEIGPMELKS 109
                                       99999988876...6789*********986554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.86
                            AAA_30  75 kllkrlk.............grarlepg.tllivDEa 97 
                                       ++l+r +               ++++++ +++++DE 
  gi|488600801|ref|YP_007907272.1| 118 RVLHRDGtniftihyrsnhsLIQKVRKSyQVFVIDEH 154
                                       55555555555555555566334667777******96 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 !   20.4   0.7   8.4e-07   0.00038      24     131 ..       4     106 ..       2     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.4e-07
                          ATPase_2  24 fiYGpegsGKtaLlkeiienledkdkyviyyialreesiskl.defie.....eeeekkklekalgiavpkaeleei 94 
                                        i+G+ gsGKt+L k+i    +d  +   ++++ r+e+  ++   f +     ee    +++    i+v+       
  gi|488600801|ref|YP_007907272.1|   4 AITGRPGSGKTTLCKRIFDSIKDEFDCGGFITKERREKGIRVgFLF-HdlvtgEEFWLASVKSDSRIRVG------- 72 
                                       699******************8888888888877776665551555.33433333333333333344444....... PP

                          ATPase_2  95 lkeksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                          k   +  +ie++ + ik+ +kk ++iiDe+  + 
  gi|488600801|ref|YP_007907272.1|  73 ---KYGVILDNIEKISDRIKEYAKKEVLIIDEIGPME 106
                                       ...44558899*********************87665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.5   6.6e-06    0.0031       4     130 ..       2     131 ..       1     165 [. 0.59

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.6e-06
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfi.......dtekGlksldadkfpdieswedfldevvelaaelady 66 
                                       ki+i+G +g+GKTtl+k++             +         ekG  ++ +   + +++ e +l  v+++++   + 
  gi|488600801|ref|YP_007907272.1|   2 KIAITGRPGSGKTTLCKRIfdsikdeF---D-CggfitkeRREKGI-RVGFLFHDLVTGEEFWLASVKSDSRIRVGK 73 
                                       9******************76643321...1.12333344444555.444444445556666667777776666666 PP

                            AAA_24  67 ktlviDtideleelclaevirqnekaeskedkgdgkG.ygelaeefrrllkklqelrknvifiah 130
                                         +++D+i+++ + +++++++   + +++       G   +  ++f++ ++++ + +++ if+ h
  gi|488600801|ref|YP_007907272.1|  74 YGVILDNIEKISDRIKEYAKKEVLIIDEI-------GpMELKSRKFVEEVERVLHRDGTNIFTIH 131
                                       66666666666666666665555554444.......33444455555555555555555555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   1.1e-06   0.00053      23      55 ..       3      32 ..       1     167 [. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                                      EEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEE CS
                            NB-ARC 23 valvGmgGvGKttlakqilnksdevegrFdsva 55
                                      +a+ G++G+GKttl k i+ +   ++ +Fd   
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFDS---IKDEFDCGG 32
                                      79*****************98...888888655 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   0.1   1.8e-06   0.00085       1      54 [.       2      53 ..       2     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.8e-06
                                      EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECG CS
                          MMR_HSR1  1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtp 54
                                      ++ai Grp +GK+tL ++++++ k +     + T++ +e+ ++     + + D++
  gi|488600801|ref|YP_007907272.1|  2 KIAITGRPGSGKTTLCKRIFDSiKDEFDCGGFITKERREKGIR---VGFLFHDLV 53
                                      69*******************9778889999999999888776...335555554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.5e-05     0.034       1      26 [.       3      28 ..       3      61 .. 0.84
   2 ?    3.7   0.0      0.17        79      41      64 ..      85     108 ..      72     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.5e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      i ++G++g GK+tl+k++ +++ +++
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFDSIKDEF 28
                                      5699**************99999887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.17
                      RNA_helicase  41 ddfwdgYtgqevvvidDfgqvkde 64 
                                       +d  + Y ++ev++id++g ++ +
  gi|488600801|ref|YP_007907272.1|  85 SDRIKEYAKKEVLIIDEIGPMELK 108
                                       566789************988755 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.6e-06    0.0012      28      59 ..       4      37 ..       2     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.6e-06
                            AAA_16 28 llsGesGvGKsslvrellralekd..ggiflrgk 59
                                       ++G +G+GK++l ++++++++++   g f++ +
  gi|488600801|ref|YP_007907272.1|  4 AITGRPGSGKTTLCKRIFDSIKDEfdCGGFITKE 37
                                      79********************998625554443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   1.9   8.1e-05     0.037       5     107 ..       3     141 ..       1     164 [. 0.57

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.1e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikell...........vkkesilyinldderd..............kkladpe...... 50 
                                       ++itG   +GKTtl+k+++++              ++e+ + + +  +++              +     +      
  gi|488600801|ref|YP_007907272.1|   3 IAITGRPGSGKTTLCKRIFDSIKdefdcggfitkERREKGIRVGFLFHDLvtgeefwlasvksdS-----Rirvgky 74 
                                       6799999***********97766555666665552233333333333222444444444332221.....1222333 PP

                            AAA_14  51 ....kllelileklke.ekktylflDEiqev....pewekalkslvdeg.knldvivtGSnskllsk 107
                                           +++e i +++ke  kk++l++DEi  +    +++ + + +++ ++ +n+  i   Sn +l++k
  gi|488600801|ref|YP_007907272.1|  75 gvilDNIEKISDRIKEyAKKEVLIIDEIGPMelksRKFVEEVERVLHRDgTNIFTIHYRSNHSLIQK 141
                                       3334444444444333567788888888765666666777676666644477777777777766654 PP

>> NACHT  NACHT 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    0.0049       3      26 ..       3      26 ..       2      33 .. 0.90
   2 ?   -0.4   0.0         2   9.2e+02      74      90 ..      86     102 ..      71     165 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawae 26
                                      ++++G++GsGKTtL +++ + +++
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFDSIKD 26
                                      689***************999886 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2
                                       HHHCCSCCCEEEEEE-S CS
                             NACHT  74 avllelperlLlilDgl 90 
                                         + e +++ +li+D +
  gi|488600801|ref|YP_007907272.1|  86 DRIKEYAKKEVLIIDEI 102
                                       44555555556666654 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0011      0.48       1      38 [.       5      42 ..       5      58 .. 0.70
   2 ?    7.3   0.1      0.01       4.8     122     144 ..      67     100 ..      27     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksg 38
                                      + G Pg+GK t ++++ ++ +      G + +++ ++g
  gi|488600801|ref|YP_007907272.1|  5 ITGRPGSGKTTLCKRIFDSIKDEFDCGGFITKERREKG 42
                                      679*************9987655444444444444555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.01
                                       T...........GSHHHHHHHHHHHHHHHHHHHH CS
                                       x...........xxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 122 g...........DneetvkkRletykkqtkplid 144
                                                   Dn e++++R+++y k+   +id
  gi|488600801|ref|YP_007907272.1|  67 SrirvgkygvilDNIEKISDRIKEYAKKEVLIID 100
                                       045556677777****************999998 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00011     0.048       2      21 ..       4      23 ..       3      39 .. 0.89
   2 ?    2.2   0.0      0.28   1.3e+02      53      72 ..      84     103 ..      76     113 .. 0.75
   3 ?   -2.1   0.0       5.8   2.7e+03      56      70 ..     140     153 ..     104     155 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                       + G pG+GK+tl+++++++
  gi|488600801|ref|YP_007907272.1|  4 AITGRPGSGKTTLCKRIFDS 23
                                      689**************987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.28
                   Viral_helicase1  53 flmalvkstkgkililDEyl 72 
                                       +    ++  k+++li+DE++
  gi|488600801|ref|YP_007907272.1|  84 ISDRIKEYAKKEVLIIDEIG 103
                                       55555556779*******97 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.8
                   Viral_helicase1  56 alvkstkgkililDE 70 
                                       ++v+ +++++ ++DE
  gi|488600801|ref|YP_007907272.1| 140 QKVR-KSYQVFVIDE 153
                                       2222.3466666666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   8.2e-06    0.0038      13      37 ..       2      26 ..       1     156 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.2e-06
                                      EEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                      k+ai+G+ G+GK+tL+k +    k+
  gi|488600801|ref|YP_007907272.1|  2 KIAITGRPGSGKTTLCKRIFDSIKD 26
                                      689**************99988775 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00075      0.34      13      36 ..       3      26 ..       1      31 [. 0.86
   2 ?    3.6   0.1      0.17        79      96     125 ..      87     116 ..      49     130 .. 0.77
   3 ?    0.3   0.0       1.8   8.3e+02      97     111 ..     139     154 ..     108     164 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00075
                            AAA_19 13 llvtaGpGtGKTrvlkhivallve 36
                                      +++t+ pG+GKT++ k i   +++
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFDSIKD 26
                                      689***********9999887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                            AAA_19  96 eekklqeeellivDEfqdvdelqyrLlkal 125
                                       + k+  ++e+li+DE+  ++    ++++++
  gi|488600801|ref|YP_007907272.1|  87 RIKEYAKKEVLIIDEIGPMELKSRKFVEEV 116
                                       3344546779*****999888888887776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.8
                            AAA_19  97 ekklqeee.llivDEf 111
                                        +k+++ + ++++DE 
  gi|488600801|ref|YP_007907272.1| 139 IQKVRKSYqVFVIDEH 154
                                       2344555557777775 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 !   13.0   0.0   9.6e-05     0.044      23      47 ..       3      27 ..       1      95 [. 0.85
   2 ?    2.2   0.0      0.19        88     160     184 ..      80     104 ..      35     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.6e-05
                        KAP_NTPase 23 vgLygkWGsGKssllnkledelkef 47
                                      ++++g  GsGK++l++++ d++k++
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFDSIKDE 27
                                      7899*******************98 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.19
                        KAP_NTPase 160 lladmektLdalqkrlVvviDdLDr 184
                                       +++++ + +++  k+ V++iD++  
  gi|488600801|ref|YP_007907272.1|  80 NIEKISDRIKEYAKKEVLIIDEIGP 104
                                       6788999999999999999999865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.066        30      50      64 ..       3      17 ..       1      25 [. 0.88
   2 !    9.7   0.0    0.0014      0.66      96     124 ..      81     109 ..      77     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.066
                         IstB_IS21 50 ivllGpsGvGKshla 64
                                      i+++G +G GK+ l 
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLC 17
                                      89**********986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                         IstB_IS21  96 dgklaralkrllkvdllilDdlgllpldq 124
                                        +k++ ++k+++k ++li+D++g  +l++
  gi|488600801|ref|YP_007907272.1|  81 IEKISDRIKEYAKKEVLIIDEIGPMELKS 109
                                       5788999****************887765 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   0.0   0.00021     0.096       1      21 [.       5      25 ..       5      30 .. 0.85
   2 ?    0.4   0.0         1   4.7e+02      76     103 ..      78     106 ..      73     118 .. 0.81
   3 ?   -0.4   0.1       1.7   7.9e+02     177     225 ..     110     157 ..      84     166 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                        ATP_bind_1  1 vvGpaGsGKttfvgalseile 21
                                      ++G +GsGKtt+++++ + ++
  gi|488600801|ref|YP_007907272.1|  5 ITGRPGSGKTTLCKRIFDSIK 25
                                      68************9987665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1
                        ATP_bind_1  76 resldwldeeleke.eddyllfDtPGQie 103
                                        +++++++++++++ +++ l++D  G +e
  gi|488600801|ref|YP_007907272.1|  78 LDNIEKISDRIKEYaKKEVLIIDEIGPME 106
                                       57889999999999788999999766555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.7
                        ATP_bind_1 177 leffedvealslllekee.ekykklaeaiaelleefalvlrflplsseke 225
                                        +f+e+ve++     ++    + +++ ++ + + + + v  f+ ++ +++
  gi|488600801|ref|YP_007907272.1| 110 RKFVEEVERVLHRDGTNIfTIHYRSNHSLIQKVRKSYQV--FVIDEHNRD 157
                                       344444444433333333544555555555555555555..555555555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0    0.0001     0.047       3      22 ..       3      22 ..       1      44 [. 0.86
   2 ?    0.1   0.0       1.1   5.2e+02     103     122 ..     135     154 ..      77     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                      EEEEESTTCCHHHHHHHHHC CS
                              cobW  3 tvltGflGsGKTtLlnhlle 22
                                      + +tG +GsGKTtL +++ +
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFD 22
                                      679***********999874 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                       SHHHHHCCCECEEEEEEETT CS
                              cobW 103 eeelksdltldavvavvDak 122
                                       +++l ++++ +  v+v+D +
  gi|488600801|ref|YP_007907272.1| 135 NHSLIQKVRKSYQVFVIDEH 154
                                       66777778888888888864 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   9.6e-05     0.044       5      30 ..       4      27 ..       2     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.6e-05
                           DUF2075  5 lVtGvaGtGKtvvllnllaeleddee 30
                                       +tG++G+GKt +  +++  +  ++e
  gi|488600801|ref|YP_007907272.1|  4 AITGRPGSGKTTLCKRIFDSI--KDE 27
                                      69*****************99..222 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.5e-05     0.035       1      19 [.       2      20 ..       2      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.5e-05
                            AAA_28  1 kivitGgestGKTtlleaL 19
                                      ki+itG +++GKTtl++++
  gi|488600801|ref|YP_007907272.1|  2 KIAITGRPGSGKTTLCKRI 20
                                      79**************986 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00035      0.16       3      22 ..       2      21 ..       1      26 [. 0.88
   2 ?    1.5   0.0       0.5   2.3e+02      79     133 ..      83     137 ..      75     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                         PduV-EutP  3 killiGkvgsGKttLtqalk 22
                                      ki + G+ gsGKttL++++ 
  gi|488600801|ref|YP_007907272.1|  2 KIAITGRPGSGKTTLCKRIF 21
                                      78899************985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.5
                         PduV-EutP  79 vfppgfasvfnkeviGi..itkidlaedeenieaveelLksaGaekifevsavekeg 133
                                        +++ + +  +kev+ i  i  ++l  +++ +e ve+ L+  G  +if++   +++ 
  gi|488600801|ref|YP_007907272.1|  83 KISDRIKEYAKKEVLIIdeIGPMELK-SRKFVEEVERVLHRDGT-NIFTIHYRSNHS 137
                                       56677777777777644335556666.77889999999999996.688887666554 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0099       4.6       3      22 ..       3      22 ..       1      33 [. 0.85
   2 ?    5.4   0.1     0.028        13     134     175 ..     114     155 ..     107     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0099
                                      EEEEESTTSSHHHHHHHHHH CS
                              CoaE  3 vgltGgiasGKstvanlfad 22
                                      +++tG  +sGK+t+++++ d
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFD 22
                                      89************997654 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
                                       HHHHHHHHCCTSTHHHHHHHHHHS--HHHHHHH-SEEEE-.S CS
                              CoaE 134 lqveRlvardgvseeevkaiiaaQlseeerlaladvvldNds 175
                                       ++veR+++rdg++   ++ + ++ l ++ r++   +v+d ++
  gi|488600801|ref|YP_007907272.1| 114 EEVERVLHRDGTNIFTIHYRSNHSLIQKVRKSYQVFVIDEHN 155
                                       78****************************999999998765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0097       4.5      36      59 ..       3      26 ..       2      43 .. 0.81
   2 ?    4.7   0.0     0.051        23      66      97 ..      75     106 ..      60     123 .. 0.76
   3 ?   -2.0   0.0       5.7   2.6e+03      17     102 ..     144     162 ..     132     165 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0097
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgv 59
                                      + ++G PG Gkttl+k i + ++ 
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFDSIKD 26
                                      5689**********9988776655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.051
                            RuvB_N  66 gPvlekagdlaalltnleekdvlfideihrls 97 
                                       g +l++   ++  +++  +k+vl idei  ++
  gi|488600801|ref|YP_007907272.1|  75 GVILDNIEKISDRIKEYAKKEVLIIDEIGPME 106
                                       556677777888889999**********8765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.7
                            RuvB_N  17 eklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfidei 93 
                                       +                                                                  + +v+ ide 
  gi|488600801|ref|YP_007907272.1| 144 K------------------------------------------------------------------SYQVFVIDEH 154
                                       2..................................................................3455556663 PP

                            RuvB_N  94 hrlsravee 102
                                        r + + ee
  gi|488600801|ref|YP_007907272.1| 155 NR-DMVFEE 162
                                       33.444444 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021     0.098      13      39 ..       3      29 ..       1      48 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                              GvpD 13 llikGaPGtGktlftlrgldvlrresd 39
                                      + i G+PG+Gkt++  r +d++++e d
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFDSIKDEFD 29
                                      5699********************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 ?    9.2   0.0    0.0025       1.2       4      25 ..       5      26 ..       2      35 .. 0.84
   2 ?    0.5   0.1       1.2   5.5e+02      63      74 ..      91     102 ..      62     122 .. 0.76
   3 ?   -1.2   0.0         4   1.8e+03      56      75 ..     135     155 ..     107     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                                      EE--SSSSHHHHHHHGGGGBS- CS
                             AAA_5  4 LvGppGtgKselaerlaaalnr 25
                                      + G pG+gK++l +r+   +++
  gi|488600801|ref|YP_007907272.1|  5 ITGRPGSGKTTLCKRIFDSIKD 26
                                      78************99776655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                                       --G-SEEEEESG CS
                             AAA_5  63 aregeilvlDEv 74 
                                         ++e+l++DE+
  gi|488600801|ref|YP_007907272.1|  91 YAKKEVLIIDEI 102
                                       337888889988 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4
                                       .--------.G-SEEEEESGG CS
                             AAA_5  56 dsplvraar.egeilvlDEve 75 
                                       + +l +++r + +++v+DE +
  gi|488600801|ref|YP_007907272.1| 135 NHSLIQKVRkSYQVFVIDEHN 155
                                       444555555445677777755 PP

>> AbfS_sensor  Sensor histidine kinase (AbfS) sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.3   5.9e+02      15      31 ..      87     103 ..      80     111 .. 0.83
   2 ?   -0.4   0.0       2.4   1.1e+03       7      27 ..     110     130 ..     106     141 .. 0.83
   3 ?    8.9   0.1     0.003       1.4      16      34 ..     140     158 ..     136     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.3
                                       TS-HHHHTTEEEEETTS CS
                       AbfS_sensor  15 rlphkarrnVflvDrqG 31 
                                       r ++ a+++V ++D+ G
  gi|488600801|ref|YP_007907272.1|  87 RIKEYAKKEVLIIDEIG 103
                                       77888999******987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.4
                                       HHHHHHHHTS-HHHHTTEEEE CS
                       AbfS_sensor   7 eeltewlerlphkarrnVflv 27 
                                       +++ e +er  h    n+f +
  gi|488600801|ref|YP_007907272.1| 110 RKFVEEVERVLHRDGTNIFTI 130
                                       678899999999999999987 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.003
                                       S-HHHHTTEEEEETTS-BT CS
                       AbfS_sensor  16 lphkarrnVflvDrqGrdL 34 
                                       +++ +  +Vf++D+ +rd+
  gi|488600801|ref|YP_007907272.1| 140 QKVRKSYQVFVIDEHNRDM 158
                                       56677889**********7 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0089       4.1      24      47 ..       2      25 ..       1      38 [. 0.85
   2 ?    3.2   0.0      0.14        65      90     109 ..      90     109 ..      77     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0089
                                      -EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat 24 svlitGesGtGKellaraiheask 47
                                      ++ itG  G+GK++l + i+++ k
  gi|488600801|ref|YP_007907272.1|  2 KIAITGRPGSGKTTLCKRIFDSIK 25
                                      688****************98655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                                       HHTTTSEEEEETGGGS-HHH CS
                   Sigma54_activat  90 ekadgGtlfLDeigelplel 109
                                       e a++ +l +Deig ++l+ 
  gi|488600801|ref|YP_007907272.1|  90 EYAKKEVLIIDEIGPMELKS 109
                                       679999*********99876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.017       7.9      38      58 ..       3      23 ..       1      38 [. 0.84
   2 ?    4.1   0.1     0.058        27     116     139 ..      90     113 ..      73     126 .. 0.73
   3 ?   -2.5   0.0       6.4   2.9e+03     119     129 ..     145     155 ..     131     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                              TniB 38 lllvGdsnnGKtmivekFarl 58
                                      + + G++  GKt+++++  ++
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLCKRIFDS 23
                                      689*************97665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.058
                              TniB 116 relkvrvLiiDEihnllagsarkq 139
                                       +  k +vLiiDEi  ++  s++  
  gi|488600801|ref|YP_007907272.1|  90 EYAKKEVLIIDEIGPMELKSRKFV 113
                                       456789*******98876655555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.4
                              TniB 119 kvrvLiiDEih 129
                                       + +v +iDE +
  gi|488600801|ref|YP_007907272.1| 145 SYQVFVIDEHN 155
                                       45788999965 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   0.00069      0.32       1      22 [.       2      23 ..       2      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00069
                                      EEEEESSTTSSHHHHHHCHCT- CS
                               Roc  1 KvvlvGdsgvGKtsllkrfved 22
                                      K+ + G  g+GKt+l+kr+ ++
  gi|488600801|ref|YP_007907272.1|  2 KIAITGRPGSGKTTLCKRIFDS 23
                                      899***************9875 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   0.00047      0.22       4      20 ..       5      21 ..       3     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00047
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      + G pGsGK+tl +r+ 
  gi|488600801|ref|YP_007907272.1|  5 ITGRPGSGKTTLCKRIF 21
                                      6799*********9986 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00068      0.31      31      53 ..       2      24 ..       1      30 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00068
                                      EEEEEE-TTSSHHHHHHHHHHHH CS
                              MeaB 31 vvGltGvPGaGkstlvealglel 53
                                      ++ +tG PG+Gk tl +++  ++
  gi|488600801|ref|YP_007907272.1|  2 KIAITGRPGSGKTTLCKRIFDSI 24
                                      689*************9987665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00068      0.31      26      38 ..       4      16 ..       2      24 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00068
                            AAA_29 26 lltGpsGsGKSTl 38
                                       +tG+ GsGK+Tl
  gi|488600801|ref|YP_007907272.1|  4 AITGRPGSGKTTL 16
                                      79**********8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0089       4.1      36      50 ..       3      17 ..       2      24 .. 0.89
   2 ?    2.2   0.0      0.25   1.1e+02     126     151 ..      77     102 ..      37     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0089
                            AAA_25 36 allaGapgtGKttla 50
                                      ++++G+pg+GKttl+
  gi|488600801|ref|YP_007907272.1|  3 IAITGRPGSGKTTLC 17
                                      5799*********97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                            AAA_25 126 ltadvdaleaaieevegvrlvviDpl 151
                                       +   ++++ ++i+e+++ ++++iD +
  gi|488600801|ref|YP_007907272.1|  77 ILDNIEKISDRIKEYAKKEVLIIDEI 102
                                       34568999999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); 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: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 1049.01
//
Query:       gi|488600802|ref|YP_007907273.1|  [L=352]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-103  344.4   0.0   1.1e-102  344.1   0.0    1.0  1  TRM            N2,N2-dimethylguanosine tRNA methyltransferase
     0.0013   18.7   0.4     0.0039   17.1   0.1    1.8  2  RNHCP          RNHCP domain
     0.0029   17.3   0.0     0.0044   16.7   0.0    1.2  1  Cons_hypoth95  Conserved hypothetical protein 95
     0.0095   15.5   0.0      0.015   14.8   0.0    1.3  1  MTS            Methyltransferase small domain
  ------ inclusion threshold ------
      0.015   14.7   0.0      0.023   14.1   0.0    1.2  1  PrmA           Ribosomal protein L11 methyltransferase (PrmA)
      0.046   13.6   0.0      0.087   12.7   0.0    1.4  1  PulG           Type II secretory pathway pseudopilin


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 !  344.1   0.0  3.6e-106  1.1e-102      18     374 ..      12     343 ..       2     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 344.1 bits;  conditional E-value: 3.6e-106
                                       --SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHH CS
                               TRM  18 eeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNv 94 
                                       + VFYNP+++f+RD +++v   + + ++k ++ +++ldaLsasG+R+iR  lE      v  NDi e+Ave+ik+N 
  gi|488600802|ref|YP_007907273.1|  12 NGVFYNPRMKFCRDFDIAV---FRAIHEK-ERMVRYLDALSASGIRGIRACLE--AGYDVSFNDIDERAVETIKRNL 82 
                                       67*****************...7777777.6889*******************..5667888*************** PP

                                       HHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHH CS
                               TRM  95 klneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkY 171
                                       +ln +e   ++ ++dAn+l+  ++krf +iD+DPfGspa+f+dsa+   k   +L+vTaTDt++L+G+s+ ++lrkY
  gi|488600802|ref|YP_007907273.1|  83 ELNGIEA--EVYNKDANILM--REKRFFHIDIDPFGSPAEFIDSACIYPK---YLSVTATDTSALCGSSTASGLRKY 152
                                       ******7..45555******..6778889****************87655...6*********************** PP

                                       SSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--E CS
                               TRM 172 gavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClse 248
                                       g +a+k+e++ Ev+lR l++ + +e akY+kav +l+++++++++rv+++ +++++ vk++++k g+++hC +Cl++
  gi|488600802|ref|YP_007907273.1| 153 GVFAVKTEYYPEVGLRALIGRIFNESAKYDKAVRVLVAFAKEHFYRVHIEFRRSPNAVKRTFSKYGYLFHCPKCLRR 229
                                       ***************************************************************************96 PP

                                       EEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EEHH CS
                               TRM 249 ekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyydls 325
                                        +v  + +   ++++cg+k+ ++GPlwlg+l+d++fve++             k+v + ++li+ E +++p++ydl+
  gi|488600802|ref|YP_007907273.1| 230 YHVR-IGEG-MDKCECGEKMIMIGPLWLGELHDQNFVEKLESDE---------KEVSRYINLIRGE-IQTPFFYDLH 294
                                       5554.4443.68889**********************9975443.........46999********.********** PP

                                       HHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHH CS
                               TRM 326 qlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvev 374
                                       +++++l++s p+l++v++al+elg+ +srt ++++++kT+a+++++  v
  gi|488600802|ref|YP_007907273.1| 295 HITKKLNTSPPKLDSVIEALRELGYSASRTRFSGTSFKTDADISEIGRV 343
                                       ********************************************99776 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.96   2.9e+03      28      49 ..     123     144 ..     122     147 .. 0.87
   2 !   17.1   0.1   1.3e-06    0.0039      22      53 ..     219     250 ..     205     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.96
                             RNHCP  28 sCLlskHvdeepgdraseCkgl 49 
                                       +C++ k + ++  d ++ C+++
  gi|488600802|ref|YP_007907273.1| 123 ACIYPKYLSVTATDTSALCGSS 144
                                       6999999999*******99875 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.3e-06
                             RNHCP  22 krnHCpsCLlskHvdeepgdraseCkglmepi 53 
                                       +  HCp+CL   Hv +  g  ++eC+ +m  i
  gi|488600802|ref|YP_007907273.1| 219 YLFHCPKCLRRYHVRIGEGMDKCECGEKMIMI 250
                                       456**********************9999655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0044      31     107 ..      29     103 ..       7     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                                       HHHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS CS
                     Cons_hypoth95  31 alFnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallkl 107
                                       a+F  ++++ +  r+LD  + sG  g+ A       + + + d++av+++k+nle  ++e+  +++++da   ++++
  gi|488600802|ref|YP_007907273.1|  29 AVFRAIHEKERMVRYLDALSASGIRGIRACLEAGYDVSFNDIDERAVETIKRNLELNGIEA--EVYNKDANILMREK 103
                                       89999**9*9*********************999**********************99885..77777776665544 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     5e-06     0.015      56      98 ..      63     105 ..      12     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5e-06
                                       .EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-E CS
                               MTS  56 aevtlvdvdarAlesakenleanklevevvasdvleeveekkf 98 
                                        +v + d+d rA+e  k+nle n++e+ev+++d+   + ek+f
  gi|488600802|ref|YP_007907273.1|  63 YDVSFNDIDERAVETIKRNLELNGIEAEVYNKDANILMREKRF 105
                                       469999***************************9877777766 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.6e-06     0.023     165     214 ..      43      92 ..      29     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.6e-06
                              PrmA 165 vlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakle 214
                                        lD    SGi  i a + +  +v   DiDe Av+  k+N+elN++ea++ 
  gi|488600802|ref|YP_007907273.1|  43 YLDALSASGIRGIRACLEAGYDVSFNDIDERAVETIKRNLELNGIEAEVY 92 
                                       567778899999*999999999999*********************9883 PP

>> PulG  Type II secretory pathway pseudopilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.9e-05     0.087      45      75 ..      73     103 ..      68     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                              PulG  45 mAvqtkqdeLslNGvevtikktqeeisvyed 75 
                                        Av+t +++L+lNG+e ++ +++ +i ++e+
  gi|488600802|ref|YP_007907273.1|  73 RAVETIKRNLELNGIEAEVYNKDANILMREK 103
                                       59********************999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); 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:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2092.68
//
Query:       gi|488600803|ref|YP_007907274.1|  [L=74]
Description: hypothetical protein Asulf_01287 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   14.3   0.1      0.012   14.2   0.1    1.1  1  PFL-like  Pyruvate formate lyase-like
      0.073   13.1   0.5       0.18   11.9   0.1    1.8  2  DUF2680   Protein of unknown function (DUF2680)


Domain annotation for each model (and alignments):
>> PFL-like  Pyruvate formate lyase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.4e-06     0.012     282     319 ..      32      69 ..      22      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-06
                                       HHHHTHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTTB- CS
                          PFL-like 282 ldqylypyyekDleeGrlteeeaqelidclwlklrevr 319
                                       +d + ypy+   l+eG+l++ee +e+++ + +kl+e++
  gi|488600803|ref|YP_007907274.1|  32 VDNFVYPYIGSYLAEGKLSKEEGKEIFQFCEMKLKEIK 69 
                                       79*********************************987 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.41   3.7e+03      19      27 ..       3      11 ..       2      14 .. 0.77
   2 ?   11.9   0.1     2e-05      0.18      27      54 ..      43      70 ..      39      74 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.41
                           DUF2680 19 lrKqivdKy 27
                                      l+ +++dK+
  gi|488600803|ref|YP_007907274.1|  3 LKDELIDKL 11
                                      577899986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2e-05
                           DUF2680 27 yVeaGllTkeqgekikkniDkrlkylke 54
                                      y   G+l ke g++i +  + +lk+ ke
  gi|488600803|ref|YP_007907274.1| 43 YLAEGKLSKEEGKEIFQFCEMKLKEIKE 70
                                      7789********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 490.05
//
Query:       gi|488600804|ref|YP_007907275.1|  [L=116]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-11   42.6   0.4    6.1e-11   42.0   0.1    1.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
    5.5e-05   22.9   0.0    9.9e-05   22.1   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
    0.00023   21.3   0.0    0.00043   20.4   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00038   20.9   0.1     0.0025   18.3   0.0    2.0  2  HTH_27          Winged helix DNA-binding domain
    0.00045   20.1   0.0    0.00069   19.5   0.0    1.4  1  MarR_2          MarR family
    0.00072   19.4   0.0     0.0013   18.6   0.0    1.4  1  MarR            MarR family
      0.002   18.4   0.0      0.013   15.8   0.0    2.0  2  Rrf2            Transcriptional regulator
     0.0021   18.1   0.8     0.0061   16.6   0.1    1.9  2  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
  ------ inclusion threshold ------
      0.014   14.9   0.3      0.046   13.3   0.0    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.035   14.3   0.1       0.44   10.8   0.0    2.2  2  Ribosomal_S25   S25 ribosomal protein
      0.042   13.7   0.1      0.083   12.8   0.1    1.5  1  TFIIE_alpha     TFIIE alpha subunit
      0.075   12.8   0.5       0.15   11.9   0.5    1.5  1  CvfB_WH         CvfB-like winged helix domain
      0.083   13.1   0.2       0.19   12.0   0.1    1.8  2  UPF0122         Putative helix-turn-helix protein, YlxM / p13
      0.084   12.9   0.0       0.17   11.9   0.0    1.6  1  HTH_20          Helix-turn-helix domain
       0.12   12.3   1.2       0.16   11.8   0.1    1.9  2  Clathrin        Region in Clathrin and VPS
       0.13   12.4   0.0       0.34   11.1   0.0    1.7  2  HTH_28          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.2   4.8e+03      20      33 ..       2      15 ..       1      18 [. 0.74
   2 !   42.0   0.1   5.4e-14   6.1e-11       3      60 ..      23      84 ..      20      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.2
                                      HCCCHHCHHCCCTT CS
                              TrmB 20 lgpatadeiaeelg 33
                                      ++++t +e+ eel+
  gi|488600804|ref|YP_007907275.1|  2 HERKTLEELREELK 15
                                      67788888888876 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 5.4e-14
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TT CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....pk 60
                                       lG++ +E+++Y+ L+  +++++dei+e+ g+++s++Y+ + +L +kGl +r+k +      +
  gi|488600804|ref|YP_007907275.1| 23 ILGMNATEVEIYFGLI-GKEMSIDEISERFGIEKSSAYKCVGKLYRKGLLKRKKMNfsngyNY 84
                                      79*************9.889**********************************997665444 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   8.9e-08   9.9e-05      17      50 ..      40      73 ..      18      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 8.9e-08
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       e+++ e+++r+g+ kS+++ ++  L + G++++
  gi|488600804|ref|YP_007907275.1| 40 KEMSIDEISERFGIEKSSAYKCVGKLYRKGLLKR 73
                                      68******************************98 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.9e-07   0.00043      25      56 ..      44      75 ..      39      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.9e-07
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyveyek 56
                                        +++er ++++ss+ + + kL ++G+++ +k
  gi|488600804|ref|YP_007907275.1| 44 IDEISERFGIEKSSAYKCVGKLYRKGLLKRKK 75
                                      579*************************9887 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 ?    0.5   0.0      0.81   9.1e+02      16      31 ..       2      17 ..       1      24 [. 0.82
   2 !   18.3   0.0   2.2e-06    0.0025      17      52 ..      40      75 ..      26      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.81
                            HTH_27 16 rrrkkladlcgrlnve 31
                                      ++rk+l++l++ l+ +
  gi|488600804|ref|YP_007907275.1|  2 HERKTLEELREELKND 17
                                      7899999999998765 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.2e-06
                            HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                       ++++ ++++r  +e+s++ +++ kL +kGL++r++
  gi|488600804|ref|YP_007907275.1| 40 KEMSIDEISERFGIEKSSAYKCVGKLYRKGLLKRKK 75
                                      578999**************************6654 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.1e-07   0.00069       3      54 ..      26      74 ..       3      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.1e-07
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      ++ ++  + + L   +   +++ e+ +r+g++ks++ + + +L ++GL+ r+
  gi|488600804|ref|YP_007907275.1| 26 MNATEVEIYFGLIGKE---MSIDEISERFGIEKSSAYKCVGKLYRKGLLKRK 74
                                      4445555555555555...9*****************************987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.2e-06    0.0013      17      51 ..      41      75 ..      39      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      ++s+ e+ +++g++ks++ + + +L++kGl++R+k
  gi|488600804|ref|YP_007907275.1| 41 EMSIDEISERFGIEKSSAYKCVGKLYRKGLLKRKK 75
                                      6899*****************************87 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.89     1e+03      39      62 ..       4      27 ..       2      31 .. 0.81
   2 !   15.8   0.0   1.2e-05     0.013      25      57 ..      41      73 ..      33      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.89
                                      HHHHHHHHHHHHHTTSEEEETTT- CS
                              Rrf2 39 psylekilakLrkaglvksvrGkg 62
                                      ++ le + ++L++ ++++++ G +
  gi|488600804|ref|YP_007907275.1|  4 RKTLEELREELKNDKILTAILGMN 27
                                      567888889999999999988865 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.2e-05
                                      -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvks 57
                                       +s++ei+er++i++s + k + kL ++gl+k 
  gi|488600804|ref|YP_007907275.1| 41 EMSIDEISERFGIEKSSAYKCVGKLYRKGLLKR 73
                                      49****************************986 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.99   1.1e+03      18      27 ..       4      13 ..       1      23 [. 0.76
   2 !   16.6   0.1   5.4e-06    0.0061      10      53 ..      33      76 ..      25      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.99
                    Sulfolobus_pRN 18 catleeleek 27
                                        tleel+e 
  gi|488600804|ref|YP_007907275.1|  4 RKTLEELREE 13
                                      5799999986 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.4e-06
                    Sulfolobus_pRN 10 illilsrrcatleeleektGiekeellvyltrlykrGlisrkWr 53
                                      i + l  + ++++e+ e+ Giek      + +ly++Gl+ rk  
  gi|488600804|ref|YP_007907275.1| 33 IYFGLIGKEMSIDEISERFGIEKSSAYKCVGKLYRKGLLKRKKM 76
                                      55566667799******************************965 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 ?   -1.1   0.1       1.3   1.5e+03       6      14 ..       4      12 ..       2      24 .. 0.72
   2 ?   13.3   0.0   4.1e-05     0.046      18      48 .]      42      72 ..      39      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                            HTH_24  6 rkILelLqk 14
                                      rk Le+L++
  gi|488600804|ref|YP_007907275.1|  4 RKTLEELRE 12
                                      677777776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.1e-05
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +s+ e++er g+ +s   +++ +L ++Gl+k
  gi|488600804|ref|YP_007907275.1| 42 MSIDEISERFGIEKSSAYKCVGKLYRKGLLK 72
                                      899*************************986 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.36     4e+02      40      59 ..       3      22 ..       1      35 [. 0.83
   2 ?   10.8   0.0   0.00039      0.44      61      88 ..      46      73 ..      39      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.36
                     Ribosomal_S25 40 dketydkllkevpkyklitp 59
                                      + +t+++l +e ++ k++t 
  gi|488600804|ref|YP_007907275.1|  3 ERKTLEELREELKNDKILTA 22
                                      67899999999999999996 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00039
                     Ribosomal_S25 61 vvserlkingslArraLreleekglikl 88
                                       +ser+ i+ s A ++  +l +kgl+k+
  gi|488600804|ref|YP_007907275.1| 46 EISERFGIEKSSAYKCVGKLYRKGLLKR 73
                                      69***********************997 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.4e-05     0.083      18      93 ..      33     106 ..      13     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.4e-05
                                       HHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEE.ECCCHCCCHHHHHHHHH CS
                       TFIIE_alpha  18 vldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywri.nyeklvdvvkrkleevv 93 
                                       + + L+   e++ +++++  +i++    k + +Ly ++l k  r++ +  + y+y +   n++kl+   k ++ +  
  gi|488600804|ref|YP_007907275.1|  33 IYFGLI-GKEMSIDEISERFGIEKSSAYKCVGKLYRKGLLK--RKKMNFSNGYNYLYISeNPQKLMSLAKSRIAQWC 106
                                       344444.5688899*************************86..5555677777777765267889999999888765 PP

>> CvfB_WH  CvfB-like winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   0.00013      0.15      21      52 ..      43      74 ..      37      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                           CvfB_WH 21 dPeeIkavfgmSKkaFKrAvGaLlkqgkIeie 52
                                      + +eI+++fg+ K++  + vG+L+++g+ + +
  gi|488600804|ref|YP_007907275.1| 43 SIDEISERFGIEKSSAYKCVGKLYRKGLLKRK 74
                                      679**********99999********998765 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00017      0.19      30      57 ..      38      65 ..      18      83 .. 0.86
   2 ?   -1.4   0.0       2.5   2.8e+03      15      29 ..      68      82 ..      63      92 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                           UPF0122 30 yadDlSlsEiAeefnvsrqavydnikrt 57
                                      + +++S+ Ei e+f +++++ y ++ + 
  gi|488600804|ref|YP_007907275.1| 38 IGKEMSIDEISERFGIEKSSAYKCVGKL 65
                                      56899******************99764 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                           UPF0122 15 qsLLTekqanylely 29
                                      + LL  k++n+ + y
  gi|488600804|ref|YP_007907275.1| 68 KGLLKRKKMNFSNGY 82
                                      468888888877665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.17      21      56 ..      38      73 ..      17      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       +++++  e+ er+++ k+++++ + +L + gL+++
  gi|488600804|ref|YP_007907275.1| 38 IGKEMSIDEISERFGIEKSSAYKCVGKLYRKGLLKR 73
                                      5899*****************************987 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.9   3.3e+03      30      53 ..       7      28 ..       5      33 .. 0.54
   2 ?   11.8   0.1   0.00015      0.16      34      66 ..      70      99 ..      53     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.9
                                      HCCHHHCHTS--HHHHHHHHHHHH CS
                          Clathrin 30 Lekvlkedskenpalqtallelya 53
                                      Le++++e   +n ++ ta+l ++a
  gi|488600804|ref|YP_007907275.1|  7 LEELREEL--KNDKILTAILGMNA 28
                                      56666433..44455555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                                      HHCHTS--HHHHHHHHHHHHHTT-HHHHHHTTS CS
                          Clathrin 34 lkedskenpalqtallelyakyddpqeleeflk 66
                                      l+  +++ +++ + +++ly+ +++ q+l++  k
  gi|488600804|ref|YP_007907275.1| 70 LL--KRKKMNFSNGYNYLYISENP-QKLMSLAK 99
                                      43..66789**************6.****8765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0003      0.34      12      41 ..      41      70 ..      37      76 .. 0.80
   2 ?   -2.5   0.0       5.1   5.7e+03      27      34 ..     100     107 ..      96     111 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                            HTH_28 12 GhsvreaArelgisrrtvyrWikryeegGi 41
                                       +s++e+++++gi  ++ y+ + ++   G+
  gi|488600804|ref|YP_007907275.1| 41 EMSIDEISERFGIEKSSAYKCVGKLYRKGL 70
                                      57*****************99988777554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.1
                            HTH_28  27 rtvyrWik 34 
                                       +++ +W+ 
  gi|488600804|ref|YP_007907275.1| 100 SRIAQWCE 107
                                       77888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 759.31
//
Query:       gi|488600805|ref|YP_007907276.1|  [L=381]
Description: Nicotinic acid phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  116.8   0.0    1.1e-33  116.4   0.0    1.2  1  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
    0.00052   20.0   0.0     0.0011   18.9   0.0    1.6  1  QRPTase_N   Quinolinate phosphoribosyl transferase, N-termina
  ------ inclusion threshold ------
      0.027   14.8   0.0       0.22   11.9   0.0    2.1  2  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   1.9e-37   1.1e-33       1     169 []     108     295 ..     108     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 1.9e-37
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveav 70 
                                       +At+++ ++  a + kv +++TR+ +P+l +  +++++iGG+d       +++lg++++ +++++ i+ +g++v+a+
  gi|488600805|ref|YP_007907276.1| 108 VATQAFVAKLSAGDRKVLSFGTRRQHPALSACIERSAYIGGVDgvsnfsaEKYLGINSIGTMPHALIISVGDQVKAW 184
                                       89*************************************************************************** PP

                                       HHHHHHHTTTSE..EEEEESSHHHHHHHHHHT....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEES CS
                         QRPTase_C  71 ksvreavdkevk..ievevesleeleevleae....adiimLDnfsv..eelkkaveel.keknkr....vlievSG 134
                                       + ++e+v++ v+    ++++++e++e+v+ +e    +d ++LD++s+   +++k++ee+ +e ++r    v+i  SG
  gi|488600805|ref|YP_007907276.1| 185 RFFDEVVSEDVPrtYLIDTYFDEKTEAVMVVEnlerVDAVRLDTPSTrrGNMRKIIEEVrWELDIRnrkdVKIVLSG 261
                                       *******99999999***************777777*********997799*******999999989999******* PP

                                       S--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 135 gvtlenveeyaksgvdvisvgalthsvkalDislk 169
                                       g++  ++ e+++ + d+++vg+++ ++k++D++++
  gi|488600805|ref|YP_007907276.1| 262 GLSVRDIVELRDLV-DAFGVGTMIAGAKPIDFAMD 295
                                       ************98.******************96 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 !   18.9   0.0   1.9e-07    0.0011      17      89 .]      36     106 ..      27     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-07
                                       EEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  17 kakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrlS 89 
                                       k+ ae+ +  +g++aGl  + e+++ l  + v  + ++G  + +++ ++ ieG++ ++ + E  +L l+ ++S
  gi|488600805|ref|YP_007907276.1|  36 KVVAEVTTSRWGIFAGLNDVIELLKGL-PIDVYSM-PEGCLFFPHQPVMFIEGRYLDFARFETPLLGLICHAS 106
                                       5678899999**************988.7777666.***********************************98 PP

>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.14   8.1e+02      37      54 ..      45      62 ..      16      65 .. 0.77
   2 ?   11.9   0.0   3.7e-05      0.22      88     124 ..      66     102 ..      62     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                        NAPRTase_N 37 eyaivagleevieylenl 54
                                      + +i+agl++vie l+ l
  gi|488600805|ref|YP_007907276.1| 45 RWGIFAGLNDVIELLKGL 62
                                      5689*********99877 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.7e-05
                        NAPRTase_N  88 evaveeeevvfpgepeirveGpwieaillEtplLaiv 124
                                       +++++e+  +fp++p + +eG  ++   +EtplL ++
  gi|488600805|ref|YP_007907276.1|  66 VYSMPEGCLFFPHQPVMFIEGRYLDFARFETPLLGLI 102
                                       578888888*************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2342.99
//
Query:       gi|488600806|ref|YP_007907277.1|  [L=96]
Description: putative pyrophosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   46.8   0.2    5.6e-12   45.7   0.0    1.6  2  MazG       MazG nucleotide pyrophosphohydrolase domain
    4.5e-05   23.6   0.0    6.3e-05   23.2   0.0    1.2  1  MazG-like  MazG-like family
    0.00012   22.5   0.1    0.00014   22.2   0.1    1.2  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.54   3.3e+03      12      23 ..       4      15 ..       3      20 .. 0.68
   2 !   45.7   0.0   9.3e-16   5.6e-12       3      66 ..      23      79 ..      21      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.54
                                      HHHHHHHHHHHT CS
                              MazG 12 eEvgEvaeaIkk 23
                                       E +E+++ I  
  gi|488600806|ref|YP_007907277.1|  4 REFQEMIRRIYF 15
                                      588888888854 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 9.3e-16
                                      HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH CS
                              MazG  3 petllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaetileKl 66
                                       e ++++++eEvgE+aea++k+d +++ eE++D+  ++++lan+    +gid+e+ +   ++K+
  gi|488600806|ref|YP_007907277.1| 23 REKTMLWVVEEVGELAEAVRKDDVENIGEEIADITAWIFSLANL----YGIDVEKEI---VKKY 79
                                      5789***************************************9....***999755...5555 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     1e-08   6.3e-05      16      62 ..      31      78 ..      23      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1e-08
                         MazG-like 16 lksveelfkallkgseeeildeLAdviiylylLAdrlGidfee.idek 62
                                      +++v+el +a+ k++ e+i +e+Ad+ +  + LA+  Gid+e+ i +k
  gi|488600806|ref|YP_007907277.1| 31 VEEVGELAEAVRKDDVENIGEEIADITAWIFSLANLYGIDVEKeIVKK 78
                                      47899999*999*****************************9998876 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   2.3e-08   0.00014      28      73 ..      27      72 ..       3      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.3e-08
                                      HHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CH CS
                            PRA-PH 28 aaligEEavElleaasegdlaeladelaDllYvtygllvllGidld 73
                                        +++EE+ El ea+ ++d +++ +e+aD+   +  l+ l+Gid +
  gi|488600806|ref|YP_007907277.1| 27 MLWVVEEVGELAEAVRKDDVENIGEEIADITAWIFSLANLYGIDVE 72
                                      55899*************************9999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 579.51
//
Query:       gi|488600807|ref|YP_007907278.1|  [L=271]
Description: imidazole glycerol phosphate synthase subunit hisF [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-89  297.0   0.2    9.1e-89  296.8   0.2    1.0  1  His_biosynth  Histidine biosynthesis protein
    3.8e-06   26.5   0.1     0.0044   16.5   0.0    2.1  2  NMO           Nitronate monooxygenase
    1.4e-05   24.6   0.2    0.00095   18.6   0.1    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    7.1e-05   22.2   0.2        0.1   11.9   0.0    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
    7.4e-05   22.0   0.0     0.0098   15.0   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    0.00026   20.4   0.1        0.4   10.0   0.0    2.3  2  TMP-TENI      Thiamine monophosphate synthase
    0.00079   18.7   0.0       0.03   13.5   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0038   16.3   0.2       0.47    9.4   0.0    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain


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 !  296.8   0.2   4.1e-92   9.1e-89       1     228 [.       5     253 ..       5     254 .. 0.96

  Alignments for each domain:
  == domain 1  score: 296.8 bits;  conditional E-value: 4.1e-92
                                       EEEEEEEE...ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SS CS
                      His_biosynth   1 riipalDl...kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfi 74 
                                       riip+lD+   ++G  V  vkG +f +lr+agdpvelakry++egadel+++D++a+ +gr+++ d++e++ +evfi
  gi|488600807|ref|YP_007907278.1|   5 RIIPCLDVtldEKGATV--VKGIEFVNLREAGDPVELAKRYNDEGADELVFLDITASPHGRKTMVDVIERTSDEVFI 79 
                                       8*******877566666..8********************************************************* PP

                                       EEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE......C............ CS
                      His_biosynth  75 pvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr......g............ 133
                                       p++vGGGI+s+ed+++ll+agadkv+i+t+av np++++e ++ fgsq+iv+aiD+rr      g            
  gi|488600807|ref|YP_007907278.1|  80 PLTVGGGIKSVEDIHSLLSAGADKVSINTSAVLNPDIVRESSDIFGSQCIVIAIDCRRnfdldkGenfveledgska 156
                                       **********************************************************666665167777888899* PP

                                       .EEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHH CS
                      His_biosynth 134 .ykvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkel 209
                                        y+v+i+g+r+ tg+dav++ak++eelgageillt+++rdGt++G+d+++t++++e+v+ipviasGG+g++e+++e 
  gi|488600807|ref|YP_007907278.1| 157 wYEVVIYGGRKPTGIDAVSWAKQVEELGAGEILLTSMNRDGTKDGFDIPITRKISEEVNIPVIASGGAGKVEHFYEG 233
                                       ***************************************************************************** PP

                                       HHTTC.SEEEESHHHHTTSS CS
                      His_biosynth 210 ksegv.davivgsalyegel 228
                                       +++g+ da++++s+++++e+
  gi|488600807|ref|YP_007907278.1| 234 FADGKaDACLAASIFHYREI 253
                                       *****************987 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.9e-06    0.0044     178     224 ..      63     109 ..      37     116 .. 0.85
   2 !    8.1   0.0   0.00066       1.5     143     205 ..     171     227 ..     167     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                               NMO 178 dkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                        k  + ++++  d v iP+   GGi   +++   L++GA  v i t 
  gi|488600807|ref|YP_007907278.1|  63 RKTMVDVIERTSDEVFIPLTVGGGIKSVEDIHSLLSAGADKVSINTS 109
                                       3567788888888889***************************9986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00066
                               NMO 143 issvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidr 205
                                       i +v  a++ve++Ga  + ++ ++  G +  +++       +  ++ + v+iPviA GG  + 
  gi|488600807|ref|YP_007907278.1| 171 IDAVSWAKQVEELGAGEILLTSMNRDGTKDGFDI------PITRKISEEVNIPVIASGGAGKV 227
                                       5677778888888888888777776666553444......5789999************8765 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 !   18.6   0.1   4.2e-07   0.00095     126     170 ..      65     109 ..      64     112 .. 0.92
   2 ?    4.0   0.0     0.013        30     130     148 ..     206     224 ..     201     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.2e-07
                                       GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--H CS
                      G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnk 170
                                       ++ +vi+++++e+ ip+  GG i++ ed++++l+aGa+ vs  ++
  gi|488600807|ref|YP_007907278.1|  65 TMVDVIERTSDEVFIPLTVGGGIKSVEDIHSLLSAGADKVSINTS 109
                                       5789************************************98765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                                       HHCTSTTS...EEEEESS- CS
                      G3P_antiterm 130 vikeikkelkipiiaGGLi 148
                                       ++++i++e++ip+ia+G  
  gi|488600807|ref|YP_007907278.1| 206 ITRKISEEVNIPVIASGGA 224
                                       7899************955 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   4.6e-05       0.1     135     214 ..      38     117 ..      16     131 .. 0.78
   2 !    8.4   0.0   0.00051       1.2     135     205 ..     175     246 ..     168     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHTT-SEBEEBSSSTTS----S-H.HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTS CS
                              ThiG 135 vlarrleevGcaavmPlaapiGsglGllnk.ealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaea 210
                                        la+r ++ G+  ++ l     s +G +++  +++   +e+ +P+ v  Gi s +d+   +  Gad v +nt+    
  gi|488600807|ref|YP_007907278.1|  38 ELAKRYNDEGADELVFLD-ITASPHGRKTMvDVIERTSDEVFIPLTVGGGIKSVEDIHSLLSAGADKVSINTSAVLN 113
                                       467777777777776553.2345566555414678889999******************************987666 PP

                                       SSHH CS
                              ThiG 211 kdpv 214
                                        d+v
  gi|488600807|ref|YP_007907278.1| 114 PDIV 117
                                       6655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00051
                                       HHHHHHHHTT-SEBE.EBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT.-SEEEESH CS
                              ThiG 135 vlarrleevGcaavm.PlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelG.adavllnt 205
                                         a+++ee+G+  ++       G+  G   +   + i ee+++Pvi   G g+ ++  + +  G ada+l ++
  gi|488600807|ref|YP_007907278.1| 175 SWAKQVEELGAGEILlTSMNRDGTKDGFDIPI-TRKISEEVNIPVIASGGAGKVEHFYEGFADGkADACLAAS 246
                                       56899999999766514556679999988775.57899******************99999888346666544 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.4e-06    0.0098     141     227 ..      37     121 ..      29     131 .. 0.79
   2 !    4.9   0.0    0.0053        12     139     198 ..     172     230 ..     164     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                               Dus 141 lelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                       +elak+ +++Ga++l+    t+    ++t   + I+   ++v ip+ + G+Ik++ed++  l+  Gad v i   a 
  gi|488600807|ref|YP_007907278.1|  37 VELAKRYNDEGADELVFLDITASPHGRKT-MVDVIERTSDEVFIPLTVGGGIKSVEDIHSLLSA-GADKVSINTSAV 111
                                       56666666666666666555555555543.3577888889999********************9.************ PP

                                       CSTTHHHHHH CS
                               Dus 218 gnPwlfaest 227
                                        nP +++es 
  gi|488600807|ref|YP_007907278.1| 112 LNPDIVRESS 121
                                       ****998743 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0053
                                       .HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHH CS
                               Dus 139 nalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaeda 198
                                       +a+  ak ve+ Ga ++ +    ++++ +   d+   +++ ++v+ipvia G+  ++e  
  gi|488600807|ref|YP_007907278.1| 172 DAVSWAKQVEELGAGEILLTSM-NRDGTKDGFDIPITRKISEEVNIPVIASGGAGKVEHF 230
                                       6777888888888888888432.222333378888999**************98877765 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00018       0.4     136     177 ..      64     106 ..      24     110 .. 0.76
   2 !    8.3   0.0   0.00058       1.3     117     160 ..     180     225 ..     170     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                          TMP-TENI 136 plgleglkelaealeiPvvaiGGitl.envaevleagadgvav 177
                                          ++ ++++++++ iP+ + GGi+  e+++++l agad v++
  gi|488600807|ref|YP_007907278.1|  64 KTMVDVIERTSDEVFIPLTVGGGIKSvEDIHSLLSAGADKVSI 106
                                       445678888999999*********85499**********9986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00058
                          TMP-TENI 117 adYigvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGit 160
                                       +  +g+G i  T+   d   +  ++   ++++e+++iPv+a GG  
  gi|488600807|ref|YP_007907278.1| 180 VEELGAGEILLTSMNRDGtkDGFDIPITRKISEEVNIPVIASGGAG 225
                                       5557888888888877774566678899****************75 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.3e-05      0.03     233     278 ..      65     112 ..      59     122 .. 0.76
   2 ?    3.1   0.0     0.021        46     234     282 ..     207     254 ..     202     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHTTT...S-EEEESS--SHHHHHHHHHHTECEEEESHHHHH CS
                            DHO_dh 233 virelykrlkke..ipiIgvGGiesgeDalekieaGAslvqvytalvf 278
                                       ++ ++ +r+++e  ip+   GGi+s eD    + aGA  v + t  v 
  gi|488600807|ref|YP_007907278.1|  65 TMVDVIERTSDEvfIPLTVGGGIKSVEDIHSLLSAGADKVSINTSAVL 112
                                       455555666655337888899*********************998854 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.021
                                       HHHHHHHTTT.S-EEEESS--SHHHHHHHHHHT.ECEEEESHHHHHHGTC CS
                            DHO_dh 234 irelykrlkkeipiIgvGGiesgeDalekieaG.Aslvqvytalvfegpk 282
                                        r+++++++  ip+I++GG    e  +e +  G A ++   + +++++  
  gi|488600807|ref|YP_007907278.1| 207 TRKISEEVN--IPVIASGGAGKVEHFYEGFADGkADACLAASIFHYREIP 254
                                       577888888..********9888888887766656666666666666655 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00021      0.47     197     234 ..      68     105 ..      32     109 .. 0.68
   2 !    5.0   0.0    0.0045        10     200     238 ..     208     247 ..     183     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00021
                                       HHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 197 aevaeaakkagvpviaDGGikysgdivkAlaaGadavm 234
                                         + ++ ++  +p+   GGik+ +di   l+aGad v 
  gi|488600807|ref|YP_007907278.1|  68 DVIERTSDEVFIPLTVGGGIKSVEDIHSLLSAGADKVS 105
                                       33333445556777777777777777777777777764 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0045
                                       HHHHCTCT-EEEEES---SHHHHHHHHHTT.-SEEEESCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             IMPDH 200 aeaakkagvpviaDGGikysgdivkAlaaG.adavmlGsl 238
                                        ++ ++ ++pvia GG  + ++    +a G ada++  s+
  gi|488600807|ref|YP_007907278.1| 208 RKISEEVNIPVIASGGAGKVEHFYEGFADGkADACLAASI 247
                                       5678999****************99999996666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 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:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1564.87
//
Query:       gi|488600808|ref|YP_007907279.1|  [L=90]
Description: Acylphosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  105.6   0.4    1.4e-30  105.5   0.4    1.0  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.029   14.5   0.0      0.039   14.1   0.0    1.2  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 !  105.5   0.4   1.6e-34   1.4e-30       1      85 []       4      88 ..       4      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 1.6e-34
                   Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeee 79
                                      vr++v+G+VQgvgFR+f+r+lAkelg+kGyv+Nlsdg+V +vaege e++ekf++el++gp  a v++++vee++ ++e
  gi|488600808|ref|YP_007907279.1|  4 VRIYVSGIVQGVGFRYFTRKLAKELGVKGYVKNLSDGRVLAVAEGESEQIEKFISELRKGPRGAVVRDIKVEEYQPNGE 82
                                      689**************************************************************************** PP

                   Acylphosphatase 80 fkdFei 85
                                      +++F i
  gi|488600808|ref|YP_007907279.1| 83 HDSFVI 88
                                      ****87 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 ?   14.1   0.0   4.3e-06     0.039      27      80 ..      22      76 ..      17      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-06
                                      HHHHHHHTEEEEEE.EETTEEEEEEEEEHHHHHHHHHHHHT-TTEEEEEEEEEEE CS
                              BLUF 27 renNkelgitGvLl.ydegvflQvLEGeeeaveelyerIkkDpRhkdvevleeee 80
                                      r+  kelg+ G++   ++g++l v EGe+e++e+ +++++k pR   v+ ++ ee
  gi|488600808|ref|YP_007907279.1| 22 RKLAKELGVKGYVKnLSDGRVLAVAEGESEQIEKFISELRKGPRGAVVRDIKVEE 76
                                      666789999999962579**************************98888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.43
# Mc/sec: 635.07
//
Query:       gi|488600809|ref|YP_007907280.1|  [L=63]
Description: hypothetical protein Asulf_01293 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-14   51.4  28.2    1.1e-07   31.4   4.7    2.5  3  Fer4      4Fe-4S binding domain
    1.2e-12   47.7  15.7    1.6e-12   47.3  15.7    1.2  1  Fer4_10   4Fe-4S dicluster domain
    1.2e-09   38.2  14.3    1.5e-09   37.9  14.3    1.2  1  Fer4_9    4Fe-4S dicluster domain
    1.9e-09   38.0  16.8    4.1e-09   36.9  16.9    1.5  1  Fer4_7    4Fe-4S dicluster domain
    4.6e-09   36.0  24.7    3.1e-08   33.3   4.0    2.5  3  Fer4_6    4Fe-4S binding domain
    1.5e-08   34.6  17.2    2.4e-08   34.0  17.2    1.4  1  Fer4_21   4Fe-4S dicluster domain
      2e-08   33.8  23.5    1.1e-06   28.4   3.0    2.6  3  Fer4_2    4Fe-4S binding domain
    6.7e-07   29.7  21.0    1.2e-05   25.7   4.3    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    8.4e-07   29.8  18.3    0.00047   21.0   1.6    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    7.8e-05   22.9  21.7    0.00032   21.0   2.3    2.6  3  Fer4_4    4Fe-4S binding domain
    0.00028   21.0  18.2      0.026   14.7   7.1    2.1  2  Fer4_18   4Fe-4S dicluster domain
    0.00059   20.2  19.3      0.042   14.3   4.6    2.1  2  Fer4_8    4Fe-4S dicluster domain
     0.0011   19.7  19.1      0.047   14.4  19.1    2.7  1  Fer4_15   4Fe-4S single cluster domain
     0.0022   18.8  28.2      0.016   16.1  10.2    2.6  2  Fer4_3    4Fe-4S binding domain
     0.0025   18.3  18.3      0.086   13.4   3.8    2.1  2  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.022   14.9   9.4      0.028   14.6   9.4    1.3  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
       0.65   10.9  17.8       0.24   12.3   2.8    2.1  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 !   31.4   4.7     1e-10   1.1e-07       1      21 [.       4      24 ..       4      27 .. 0.91
   2 !   31.2  10.2   1.2e-10   1.3e-07       2      24 .]      36      58 ..      35      58 .. 0.95
   3 ?   -2.9   0.2       6.9   7.2e+03      15      18 ..      59      62 ..      59      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1e-10
                                      EEEETTTSSS-THHHHHSTTT CS
                              Fer4  1 vvideekCigCGaCvevCPvg 21
                                      +v+d++kC+ CG+C++vCP  
  gi|488600809|ref|YP_007907280.1|  4 IVVDKDKCTSCGECINVCPAS 24
                                      69*****************75 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.2e-10
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       +++e Ci C  CvevCPvgAI+
  gi|488600809|ref|YP_007907280.1| 36 PVNPEECIECCSCVEVCPVGAIK 58
                                      59********************6 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.9
                                      HHHS CS
                              Fer4 15 vevC 18
                                      v+vC
  gi|488600809|ref|YP_007907280.1| 59 VDVC 62
                                      6888 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3  15.7   1.5e-15   1.6e-12       2      56 .]       4      53 ..       3      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.5e-15
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v+d+d+C+ Cg+C ++CPa     ++++++++e+ + +++e+C++c +Cve+CP
  gi|488600809|ref|YP_007907280.1|  4 IVVDKDKCTSCGECINVCPA-----SVYEFDDDEKSEPVNPEECIECCSCVEVCP 53
                                      789*****************.....*****************************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9  14.3   1.4e-12   1.5e-09       1      51 []      10      57 ..      10      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.4e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kCt+Cg+C+++Cpa v++ d+ e+   ++ +   +Ci+C +Cve+Cp gai
  gi|488600809|ref|YP_007907280.1| 10 KCTSCGECINVCPASVYEFDDDEKSEPVNPE---ECIECCSCVEVCPVGAI 57
                                      7*****************9999999998774...7*************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 !   36.9  16.9   3.9e-12   4.1e-09       1      52 []      10      56 ..      10      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3.9e-12
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+ Cg C ++Cp+++ e+d++e+        ++pe+C+ C +Cv+vCP+ga
  gi|488600809|ref|YP_007907280.1| 10 KCTSCGECINVCPASVYEFDDDEKS-----EPVNPEECIECCSCVEVCPVGA 56
                                      7*******************98544.....459*****************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   4.0   2.9e-11   3.1e-08       1      23 [.       3      25 ..       3      26 .. 0.93
   2 !   12.3   8.6   0.00013      0.13       4      24 .]      37      57 ..      37      57 .. 0.94
   3 ?   -2.8   0.1       7.9   8.4e+03      16      19 ..      59      62 ..      59      63 .] 0.65

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.9e-11
                            Fer4_6  1 vveidpdkCigCgdCvrvCPega 23
                                      ++++d+dkC++Cg+C++vCP+ +
  gi|488600809|ref|YP_007907280.1|  3 FIVVDKDKCTSCGECINVCPASV 25
                                      69******************986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      ++p+ Ci C  Cv vCP gai
  gi|488600809|ref|YP_007907280.1| 37 VNPEECIECCSCVEVCPVGAI 57
                                      68999***************8 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.9
                            Fer4_6 16 vrvC 19
                                      v+vC
  gi|488600809|ref|YP_007907280.1| 59 VDVC 62
                                      5688 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0  17.2   2.3e-11   2.4e-08       2      58 ..       5      58 ..       2      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.3e-11
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieid.aktvlkvvedeCvGCnlCssvCPvedcie 58
                                      ++d+dkC +Cg+C+ +C+  s+   e+d +++  +v  +eC+ C  C++vCPv ++i+
  gi|488600809|ref|YP_007907280.1|  5 VVDKDKCTSCGECINVCPA-SV--YEFDdDEKSEPVNPEECIECCSCVEVCPV-GAIK 58
                                      589***************5.33..3454144566899***************9.9997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   3.0     1e-09   1.1e-06       3      22 .]       4      23 ..       2      23 .. 0.94
   2 !   13.5   9.7   5.6e-05     0.059       5      21 ..      37      53 ..      36      54 .. 0.93
   3 ?   -2.1   0.0         5   5.3e+03       8      10 ..      60      62 ..      56      63 .] 0.56

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1e-09
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +vvd d+C++Cg C+++CPa
  gi|488600809|ref|YP_007907280.1|  4 IVVDKDKCTSCGECINVCPA 23
                                      89*****************8 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.6e-05
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      v+++ Ci+C +Cv +CP
  gi|488600809|ref|YP_007907280.1| 37 VNPEECIECCSCVEVCP 53
                                      79999************ PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5
                            Fer4_2  8 drC 10
                                      d C
  gi|488600809|ref|YP_007907280.1| 60 DVC 62
                                      444 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 !   25.7   4.3   1.2e-08   1.2e-05       1      27 [.       6      33 ..       6      36 .. 0.88
   2 !   10.3   8.4   0.00076       0.8       1      17 [.      37      53 ..      37      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.2e-08
                           Fer4_13  1 VDrdtCiacgaCvelaPd.vFeeddegg 27
                                      VD+d+C++cg C +++P  v+e dd+++
  gi|488600809|ref|YP_007907280.1|  6 VDKDKCTSCGECINVCPAsVYEFDDDEK 33
                                      9****************54999999854 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00076
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      V+ ++Ci+c +Cve++P
  gi|488600809|ref|YP_007907280.1| 37 VNPEECIECCSCVEVCP 53
                                      899*************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.6   4.5e-07   0.00047       1      24 [.      10      33 ..      10      40 .. 0.81
   2 !   14.7   9.4   4.3e-05     0.045       2      20 ..      42      60 ..      41      63 .] 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.5e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkeke 24
                                      +C++Cg+C++vCP+++ + + +++
  gi|488600809|ref|YP_007907280.1| 10 KCTSCGECINVCPASVYEFDDDEK 33
                                      6*************9988775544 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.3e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++C  C+evCP++aik +
  gi|488600809|ref|YP_007907280.1| 42 CIECCSCVEVCPVGAIKVD 60
                                      ****************976 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.3     3e-07   0.00032       1      16 [.       8      23 ..       8      31 .. 0.90
   2 !   10.0   8.6   0.00097         1       1      17 []      39      55 ..      39      55 .. 0.92
   3 ?   -1.5   0.0       4.9   5.1e+03      12      15 ..      60      63 .]      59      63 .] 0.57

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-07
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +++C+ Cg C+++CP 
  gi|488600809|ref|YP_007907280.1|  8 KDKCTSCGECINVCPA 23
                                      69*************4 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00097
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      +e Ci+C sCv +CP+g
  gi|488600809|ref|YP_007907280.1| 39 PEECIECCSCVEVCPVG 55
                                      689************86 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.9
                            Fer4_4 12 aaCP 15
                                      ++C+
  gi|488600809|ref|YP_007907280.1| 60 DVCE 63
                                      6675 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   3.5    0.0001      0.11      58      75 ..       8      25 ..       4      30 .. 0.87
   2 !   14.7   7.1   2.5e-05     0.026      51      74 ..      32      55 ..      25      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                           Fer4_18 58 agdcidcescvkvcPtgi 75
                                      + +c++c+ c++vcP  +
  gi|488600809|ref|YP_007907280.1|  8 KDKCTSCGECINVCPASV 25
                                      678************976 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.5e-05
                           Fer4_18 51 eerkekgagdcidcescvkvcPtg 74
                                      e+ +  +  +ci+c scv+vcP+g
  gi|488600809|ref|YP_007907280.1| 32 EKSEPVNPEECIECCSCVEVCPVG 55
                                      455566778*************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 !   14.3   4.6     4e-05     0.042      49      64 ..       9      24 ..       7      25 .. 0.77
   2 !   11.9   6.8   0.00023      0.24      48      64 ..      39      55 ..      26      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4e-05
                            Fer4_8 49 wsCttcgaCtevCpvg 64
                                      ++Ct+cg+C +vCp +
  gi|488600809|ref|YP_007907280.1|  9 DKCTSCGECINVCPAS 24
                                      5788888888888876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00023
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                       ++C +c +C+evCpvg
  gi|488600809|ref|YP_007907280.1| 39 PEECIECCSCVEVCPVG 55
                                      67899999999999986 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 !   14.4  19.1   4.4e-05     0.047       1      66 []       4      59 ..       4      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeape.vfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      +vvD+d+C++cg C+ ++p  v e+d+d ++           ++v+++e  +    +++CPv+AI v
  gi|488600809|ref|YP_007907280.1|  4 IVVDKDKCTSCGECINVCPAsVYEFDDDEKS-----------EPVNPEECIECCSCVEVCPVGAIKV 59
                                      89****************8526677777776...........6899999999999**********87 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   5.0   0.00013      0.14       1      12 [.      11      22 ..      11      25 .. 0.95
   2 !   16.1  10.2   1.5e-05     0.016       1      15 []      42      56 ..      42      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                            Fer4_3  1 CtgCgaCvevCP 12
                                      Ct Cg C +vCP
  gi|488600809|ref|YP_007907280.1| 11 CTSCGECINVCP 22
                                      ************ PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C  CvevCPvgA
  gi|488600809|ref|YP_007907280.1| 42 CIECCSCVEVCPVGA 56
                                      ****99********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   3.8   8.2e-05     0.086      44      60 ..       9      25 ..       7      26 .. 0.79
   2 !   11.2   6.3   0.00038       0.4      41      58 ..      37      54 ..      25      56 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-05
                           Fer4_17 44 slCieCgeCerkCPqgl 60
                                      ++C++CgeC  +CP+++
  gi|488600809|ref|YP_007907280.1|  9 DKCTSCGECINVCPASV 25
                                      57888999988888765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00038
                           Fer4_17 41 ekaslCieCgeCerkCPq 58
                                       + ++CieC  C+++CP 
  gi|488600809|ref|YP_007907280.1| 37 VNPEECIECCSCVEVCPV 54
                                      37799***********96 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 ?   14.6   9.4   2.6e-05     0.028      46      93 ..      17      60 ..       4      63 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                                      HHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE- CS
                            ETF_QO 46 eqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqniewv 93
                                      +  +CPa+vye+ +de+       +n ++C+ C +C    p   i+  
  gi|488600809|ref|YP_007907280.1| 17 CINVCPASVYEFDDDEK----SEPVNPEECIECCSCVEVCPVGAIKVD 60
                                      5679********98884....4469***********887787777765 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.6   0.00056      0.59      79      94 ..       8      23 ..       4      25 .. 0.66
   2 ?   12.3   2.8   0.00023      0.24       1      16 [.      10      25 ..      10      41 .. 0.71
   3 ?    3.8   7.5       0.1   1.1e+02       1      14 [.      41      54 ..      41      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00056
                           Fer4_22 79 esgCvGCgRCieacpv 94
                                      + +C+ Cg Ci++cp+
  gi|488600809|ref|YP_007907280.1|  8 KDKCTSCGECINVCPA 23
                                      5667777777777765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                           Fer4_22  1 rClsCgaCtlvCptCs 16
                                      +C sCg+C  vCp+ +
  gi|488600809|ref|YP_007907280.1| 10 KCTSCGECINVCPASV 25
                                      6999999999999754 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.1
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C++C +C  vCp 
  gi|488600809|ref|YP_007907280.1| 41 ECIECCSCVEVCPV 54
                                      599*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 416.84
//
Query:       gi|488600810|ref|YP_007907281.1|  [L=77]
Description: hypothetical protein Asulf_01294 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-23   82.8   0.0    1.5e-23   82.6   0.0    1.0  1  DUF5619   Domain of unknown function (DUF5619)


Domain annotation for each model (and alignments):
>> DUF5619  Domain of unknown function (DUF5619)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   8.2e-28   1.5e-23       1      85 []       1      75 [.       1      76 [. 0.94

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 8.2e-28
                                      -EEE----S.S---HHHHHHHH---TT---E.EEEEEEEE-----EES---SSSSSH...HHHHHHHTT--EEEEETTE CS
                           DUF5619  1 meeiklniegsdldfekAkklAkeiAeelleepmllsWkdrkrgkesPevecgeadkkpgwlvYgesrGakLeidindg 79
                                      m+++k++++  d+df+ A+k+A+ iA+    + ml+sW+d k+g++ P+v+c+++d+   wlvYg+srG++L i+in+ 
  gi|488600810|ref|YP_007907281.1|  1 MDTVKVSVD-RDVDFNLARKMADVIAD----DGMLVSWFDGKKGTHFPDVKCCGEDS---WLVYGKSRGGSLLIEINE- 70
                                      899****99.9***************9....89*********************666...******************. PP

                                      EEEEEE CS
                           DUF5619 80 eyvFiy 85
                                       y+F+y
  gi|488600810|ref|YP_007907281.1| 71 -YKFLY 75
                                      .88776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 515.22
//
Query:       gi|488600811|ref|YP_007907282.1|  [L=156]
Description: LSU ribosomal protein L11P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-26   90.8   0.1    7.4e-26   89.8   0.1    1.6  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    1.5e-22   79.9   0.9    2.7e-22   79.0   0.9    1.4  1  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 !   89.8   0.1   8.2e-30   7.4e-26       6      65 .]       3      62 ..       1      62 [. 0.98

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 8.2e-30
                   Ribosomal_L11_N  6 kvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrsf 65
                                      +vv++ vp+G+A+p+PplGpa+GplGln+k++++ +n+aTk+++gl +pVki v +drsf
  gi|488600811|ref|YP_007907282.1|  3 RVVEVLVPGGEASPGPPLGPAIGPLGLNVKQVVDRINAATKEYQGLSVPVKIIVHDDRSF 62
                                      689********************************************************9 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 !   79.0   0.9   3.1e-26   2.7e-22       2      70 .]      68     135 ..      67     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 3.1e-26
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                        Pp+++l+k+++gi kgs+k+gke+vG++sl++++eIAk+Kk +  ++ +l+++vk++lgt+ smG++V
  gi|488600811|ref|YP_007907282.1|  68 IPPVTALVKRELGITKGSSKTGKEFVGDISLEKIKEIAKMKKAQVLSY-DLKSVVKEVLGTCLSMGVTV 135
                                       5*****************************************887788.******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1044.07
//
Query:       gi|488600812|ref|YP_007907283.1|  [L=150]
Description: LSU ribosomal protein L24A [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-22   78.9   0.3      4e-22   77.9   0.3    1.5  1  Spt5-NGN       Early transcription elongation factor of RNA p
    2.8e-05   23.9   2.7    4.2e-05   23.3   0.4    2.3  2  KOW            KOW motif
    0.00014   22.3   4.1    0.00015   22.2   0.6    2.4  2  NusG           Transcription termination factor nusG
  ------ inclusion threshold ------
      0.014   15.4   0.5       0.02   14.9   0.4    1.4  1  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
       0.02   15.2   0.8       0.11   12.8   0.8    2.1  1  DUF3912        Protein of unknown function (DUF3912)


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 !   77.9   0.3   1.1e-25     4e-22       2      84 .]       4      82 ..       3      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 1.1e-25
                          Spt5-NGN  2 iwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEv 80
                                      ++ +k+ta+qE+ va  ++      +kk +l +++++ p+e+kGyi+vEA++ ++v +a++g+p+v+g+v+g+v + E+
  gi|488600812|ref|YP_007907283.1|  4 FFLLKTTANQEKVVANLMEMV----IKKYQLPVYAIMSPKEVKGYIFVEAENVEDVLKAIRGVPHVKGLVKGEVGFHEI 78
                                      89**********999999877....8999************************************************** PP

                          Spt5-NGN 81 edll 84
                                      e++l
  gi|488600812|ref|YP_007907283.1| 79 EHFL 82
                                      **98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.4   1.2e-08   4.2e-05       4      32 .]      96     124 ..      93     124 .. 0.95
   2 ?   -0.3   0.1      0.34   1.2e+03       3       9 ..     139     145 ..     139     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.2e-08
                                       EEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW   4 hVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                        V+++sGp+kG++ +V++vd+ k+ ++v+
  gi|488600812|ref|YP_007907283.1|  96 KVEIISGPFKGEISVVKRVDETKNEITVE 124
                                       59************************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                                       SEEEESS CS
                               KOW   3 dhVkVvs 9  
                                       dhV++++
  gi|488600812|ref|YP_007907283.1| 139 DHVRIID 145
                                       8****95 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.6   4.3e-08   0.00015       3      79 ..       4      71 ..       2      82 .. 0.72
   2 ?    0.5   0.2      0.24   8.7e+02      34      67 ..     109     146 ..      75     150 .] 0.46

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.3e-08
                                      EEEEEE-TTTHHHHHHHH...HHHCT-EEE-SCEEEEEEETTEEECSSTTEEEEEE---CHHHHHHHCSTTEEEE-EET CS
                                      xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              NusG  3 WYvlqvepgkekkvkenL...leeeglevivPaeekveirqgkkkklfpgyifikadmndkllmairktpgVtgfvrvg 78
                                      +++l++  ++ek v++ +   +++ +l v+  +  k+          ++gyif++a+  ++ l+air +p+V g+v  +
  gi|488600812|ref|YP_007907283.1|  4 FFLLKTTANQEKVVANLMemvIKKYQLPVYAIMSPKE----------VKGYIFVEAENVEDVLKAIRGVPHVKGLV--K 70
                                      6778888888777776664444444444444444444..........58***************************..3 PP

                                      T CS
                                      x RF
                              NusG 79 g 79
                                      g
  gi|488600812|ref|YP_007907283.1| 71 G 71
                                      3 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.24
                                       EEEEEE.TTEEE.....CSSTTEEEEEE---CHHHHHHHC CS
                                       xxxxxx.xxxxx.....xxxxxxxxxxxxxxxxxxxxxxx RF
                              NusG  34 ekveir.qgkkk.....klfpgyifikadmndkllmairk 67 
                                       ++v+ r ++  k      l+  ++ i ++++ +++++i+k
  gi|488600812|ref|YP_007907283.1| 109 SVVK-RvDET-KneitvELIDAVVPIPITVKADHVRIIDK 146
                                       2222.21222.13566655555555555555555566655 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 ?   14.9   0.4   5.5e-06      0.02      12      73 ..      11      74 ..       3     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.5e-06
                     Nit_Regul_Hom 12 enlgkvinalseagitGfylieYkGlsPqewkgflle..edpesaikiikdlseeavlintvvd 73
                                       n  kv+  l e+ i  + l  Y  +sP+e kg+     e+ e ++k+i+ + +   l++  v 
  gi|488600812|ref|YP_007907283.1| 11 ANQEKVVANLMEMVIKKYQLPVYAIMSPKEVKGYIFVeaENVEDVLKAIRGVPHVKGLVKGEVG 74
                                      577899***************************76543499********998776666655555 PP

>> DUF3912  Protein of unknown function (DUF3912)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8     3e-05      0.11       7      52 ..      94     129 ..      90     146 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                           DUF3912   7 GqkvyvkdGPyrnklGvvkkkeqedddhftvviddqdidvelkdil 52 
                                       G kv +  GP+++ + vvk++   d+ +        +i+vel d +
  gi|488600812|ref|YP_007907283.1|  94 GYKVEIISGPFKGEISVVKRV---DETKN-------EITVELIDAV 129
                                       7789999*************4...44433.......3444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 913.62
//
Query:       gi|488600813|ref|YP_007907284.1|  [L=60]
Description: protein translocase subunit secE/sec61 gamma [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-10   40.8   0.1    1.6e-10   40.8   0.1    1.0  1  SecE         SecE/Sec61-gamma subunits of protein translocati
  ------ inclusion threshold ------
      0.051   13.9   0.3      0.067   13.5   0.3    1.2  1  Sigma_reg_N  Sigma factor regulator N-terminal


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 !   40.8   0.1   1.8e-14   1.6e-10       4      54 ..      10      59 ..       7      60 .] 0.92

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.8e-14
                                      HHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE  4 fkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfsklinll 54
                                      + + ++ lk   +P+r+E+++tt+v l++++++g+++f++ l++  lin l
  gi|488600813|ref|YP_007907284.1| 10 LHDYYNLLKMTRKPDREEFITTTKVALAVMFVVGIIGFGIYLIL-ELINKL 59
                                      5688999************************************9.888766 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   7.4e-06     0.067       3      38 ..      19      54 ..      17      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.4e-06
                       Sigma_reg_N  3 ilkkakrksilrivlislivlllifvilvvtllyla 38
                                      + +k  r  +++++ ++l+v++++ +i + ++l+l+
  gi|488600813|ref|YP_007907284.1| 19 MTRKPDREEFITTTKVALAVMFVVGIIGFGIYLILE 54
                                      667888999*******************99998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 411.02
//
Query:       gi|488600814|ref|YP_007907285.1|  [L=255]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.0    6.6e-05   22.7   0.0    1.8  1  HxlR           HxlR-like helix-turn-helix
    0.00012   22.1   0.0    0.00027   21.1   0.0    1.5  1  HTH_34         Winged helix DNA-binding domain
     0.0003   21.2   0.0     0.0011   19.5   0.0    1.9  2  HTH_27         Winged helix DNA-binding domain
      0.005   16.7   0.1      0.017   15.0   0.1    1.9  2  MarR           MarR family
  ------ inclusion threshold ------
      0.026   14.5   0.1       0.31   11.0   0.0    2.5  2  PadR           Transcriptional regulator PadR-like family
      0.035   13.5   0.3      0.075   12.4   0.1    1.6  2  DUF1670        Protein of unknown function (DUF1670)
      0.037   13.9   0.0      0.087   12.7   0.0    1.6  1  MarR_2         MarR family
      0.065   13.3   0.0       0.14   12.2   0.0    1.6  1  OTT_1508_deam  OTT_1508-like deaminase


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 !   22.7   0.0   2.9e-08   6.6e-05       7      72 ..      25      88 ..      21     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.9e-08
                                      HHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGG CS
                              HxlR  7 kllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsl 72
                                      k+ + + l+kg   f +++r +  isqk L+++++  e  +li+ ev p+   k  Y++t++Gr+ 
  gi|488600814|ref|YP_007907285.1| 25 KVFLYIFLIKGA-DFADIARYV-RISQKNLTKHIKDFEFIRLIKSEVSPKDRRKKIYEVTPFGRDF 88
                                      555556666665.599**9999.*****************************************86 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.2e-07   0.00027       5      67 ..      26      87 ..      24      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67
                                      v+ y    + adf+++   +++++ nL +h+k +e  + i+ + + k++ ++ ++++Tp Gr+
  gi|488600814|ref|YP_007907285.1| 26 VFLYIFLIKGADFADIARYVRISQKNLTKHIKDFEFIRLIKSEVSPKDR-RKKIYEVTPFGRD 87
                                      5566666789**************************************9.999*********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 !   19.5   0.0   4.8e-07    0.0011      22      68 .]      39      85 ..      30      85 .. 0.95
   2 ?   -2.1   0.0       2.6   5.8e+03      21      31 ..     233     243 ..     223     254 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                            HTH_27 22 adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      ad+++++ +++ +  + +k  +   L++++ +++drr k +++T+ G
  gi|488600814|ref|YP_007907285.1| 39 ADIARYVRISQKNLTKHIKDFEFIRLIKSEVSPKDRRKKIYEVTPFG 85
                                      8*******************************************965 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                            HTH_27  21 ladlcgrlnve 31 
                                       l++l +r++ e
  gi|488600814|ref|YP_007907285.1| 233 LMELKERHKEE 243
                                       44444444333 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   7.8e-06     0.017      19      58 ..      37      76 ..      32      77 .. 0.93
   2 ?   -2.1   0.0       1.8   3.9e+03      15      57 ..     158     167 ..     150     170 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.8e-06
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR 19 svseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                        +++a+ + +s+ ++t+ ++  e   li+++ sp+DrR+
  gi|488600814|ref|YP_007907285.1| 37 DFADIARYVRISQKNLTKHIKDFEFIRLIKSEVSPKDRRK 76
                                      6789***********************************8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                       STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                              MarR  15 qgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57 
                                       +                                 R+ +p+D +
  gi|488600814|ref|YP_007907285.1| 158 S---------------------------------RRINPQDLK 167
                                       4.................................556666654 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.31      38      72 ..      56      88 ..      40      90 .. 0.79
   2 ?   -0.5   0.0      0.55   1.2e+03       1      15 [.     208     222 ..     208     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                      HHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR 38 LkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                       k++e  +l++se ++  +++++k+Y++T+ Gr+ 
  gi|488600814|ref|YP_007907285.1| 56 IKDFEFIRLIKSEVSP--KDRRKKIYEVTPFGRDF 88
                                      5667777889999886..69************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.55
                                       HHHHHCCS-EEHHHH CS
                              PadR   1 iLalleeqpsyGyei 15 
                                       iL +l  qp yG  +
  gi|488600814|ref|YP_007907285.1| 208 ILDVLPSQPVYGPVV 222
                                       7999999****9655 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.3e-05     0.075     159     200 ..      31      71 ..       6      92 .. 0.76
   2 ?   -3.0   0.0       1.7   3.7e+03     168     186 ..     117     132 ..     100     137 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                           DUF1670 159 lylkgyetteiarrtnHseeaidRYikafekvklLkekkles 200
                                        ++kg ++++iar ++ s++ + + ik+fe ++l+k++ +++
  gi|488600814|ref|YP_007907285.1|  31 FLIKGADFADIARYVRISQKNLTKHIKDFEFIRLIKSE-VSP 71 
                                       4589****************************999877.333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                           DUF1670 168 eiarrtnHseeaidRYika 186
                                       +++rr+   +e i RYi +
  gi|488600814|ref|YP_007907285.1| 117 DVERRV---NEVIGRYIVS 132
                                       344443...4667777755 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.9e-05     0.087      24      61 ..      38      75 ..      23      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-05
                                      HHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 24 vgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                       +++ar+ ++s+ ++++++k+++   L+  + +p D+R
  gi|488600814|ref|YP_007907285.1| 38 FADIARYVRISQKNLTKHIKDFEFIRLIKSEVSPKDRR 75
                                      78***********************************9 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 ?   12.2   0.0   6.2e-05      0.14      22      43 ..     192     213 ..     171     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                     OTT_1508_deam  22 pryIgcSKpaCylCelylrahg 43 
                                            cSK+ C +C+l+l+ ++
  gi|488600814|ref|YP_007907285.1| 192 LDAAICSKKGCSVCNLILDVLP 213
                                       55567*************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1894.96
//
Query:       gi|488600815|ref|YP_007907286.1|  [L=79]
Description: hypothetical protein Asulf_01300 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 545.07
//
Query:       gi|488600816|ref|YP_007907287.1|  [L=80]
Description: hypothetical protein Asulf_01301 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 627.69
//
Query:       gi|488600817|ref|YP_007907288.1|  [L=163]
Description: hypothetical protein Asulf_01302 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.085   12.7   0.0       0.12   12.2   0.0    1.2  1  Helicase_RecD  Helicase


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.6e-06      0.12      93     148 ..      16      71 ..       8      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.6e-06
                     Helicase_RecD  93 llvvDEAAaiplpllkkl.lekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkre 148
                                       ++ +DEA  i  + l++l + +++  +l+   hGYE + r+f+ + l +l ++++++
  gi|488600817|ref|YP_007907288.1|  16 AIAIDEAIKIAHTSLSSLfIAGNRISILTKIKHGYEVA-RAFTSHQLLTLLENTHHQ 71 
                                       689***************455555566666779***76.788766555554443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1040.54
//
Query:       gi|488600818|ref|YP_007907289.1|  [L=101]
Description: hypothetical protein Asulf_01303 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 686.46
//
Query:       gi|488600819|ref|YP_007907290.1|  [L=140]
Description: putative nucleic-acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   26.3   0.0    1.4e-05   25.9   0.0    1.2  1  PIN_3     PIN domain
    0.00058   20.4   0.6    0.00079   19.9   0.6    1.2  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.045   13.1   0.4      0.056   12.8   0.4    1.1  1  DUF5305   Family of unknown function (DUF5305)


Domain annotation for each model (and alignments):
>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.3e-09   1.4e-05       3     116 .]       4     115 ..       2     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.3e-09
                             PIN_3   3 vlDtnvlldallfdsp..aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvalerka 77 
                                       ++D nv++d+l ++    a+ ++++++ +g+i+ +vs+ +   ++   ar  + ++ ++++a + +++ ++     +
  gi|488600819|ref|YP_007907290.1|   4 FFDVNVFMDVLERRRGwkASLAVVQLVRNGKIEGYVSALTPPIIYFLRARYTDENR-AREDARRILREFRIVP--LT 77 
                                       79**********888799*******************9887776644455544444.4444444455554432..56 PP

                             PIN_3  78 vapdaelrpllkcrDpdDqkvlelAlaaradvlVTkdra 116
                                       ++      +++++ D++D      Al + a+vl+T++++
  gi|488600819|ref|YP_007907290.1|  78 EEIILNSYEESRIDDFEDCIQFHSALST-AEVLITRNIK 115
                                       66677777789999*************9.********86 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.6   1.3e-07   0.00079       2     118 ..       4     119 ..       3     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBC CS
                               PIN   2 vlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpid 74 
                                       ++D +v+ ++l+++ + +a+++ ++ +     e ++sal+   +++  ar     ++++++++++ +l++++i+p++
  gi|488600819|ref|YP_007907290.1|   4 FFDVNVFMDVLERRRGWKASLAVVQLVrngkIEGYVSALTPPIIYFLRAR---YTDENRAREDARRILREFRIVPLT 77 
                                       89*********7777777777777766777*999***9999755555555...77788888888888********** PP

                                       HHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTH.HHH CS
                               PIN  75 aeiaeeaaeialkygllpnDaliaAtAkehgikliatfDed.frr 118
                                       +ei +  +e ++    +  D++    A+++   li t++ + f+ 
  gi|488600819|ref|YP_007907290.1|  78 EEIILNSYEESRID--DFEDCIQFHSALSTAEVLI-TRNIKdFEA 119
                                       *******9999997..9*************99999.987443655 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   9.4e-06     0.056     135     194 ..      48     105 ..      38     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.4e-06
                           DUF5305 135 rriiftsskaekyelelekilkeYdewIvkgslppdlgdekvievdsledLvdvaielne 194
                                       ++ ++  +++++++ + ++il+e+  +Iv ++++  l+ ++  ++d++ed ++++  l +
  gi|488600819|ref|YP_007907290.1|  48 YFLRARYTDENRAREDARRILREF--RIVPLTEEIILNSYEESRIDDFEDCIQFHSALST 105
                                       4444556778999***********..7*************************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 912.47
//
Query:       gi|488600820|ref|YP_007907291.1|  [L=101]
Description: hypothetical protein Asulf_01307 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00094   19.2   2.0     0.0013   18.7   2.0    1.2  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
     0.0029   17.5   2.7     0.0037   17.2   2.7    1.1  1  DASH_Spc19      Spc19
     0.0066   16.3   0.4     0.0066   16.3   0.4    1.2  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
  ------ inclusion threshold ------
      0.011   15.9   1.7       0.02   15.0   1.7    1.5  1  Cnn_1N          Centrosomin N-terminal motif 1
      0.022   15.0   2.0       0.13   12.5   2.0    2.0  1  KxDL            Uncharacterized conserved protein
      0.024   15.3   0.8       0.04   14.5   0.8    1.4  1  SlyX            SlyX
      0.029   14.6   0.7      0.039   14.2   0.7    1.2  1  Spc24           Spc24 subunit of Ndc80
      0.031   14.2   4.2      0.037   14.0   2.0    1.9  2  Prefoldin_2     Prefoldin subunit
      0.036   12.6   0.1      0.036   12.6   0.1    1.0  1  Herpes_UL6      Herpesvirus UL6 like
       0.05   12.0   5.8      0.057   11.8   5.8    1.1  1  MAD             Mitotic checkpoint protein
       0.05   12.8   0.2      0.063   12.5   0.2    1.1  1  DLP_helical     Dynamin-like helical domain
      0.058   12.2   1.4      0.066   12.0   1.4    1.1  1  AAA_32          AAA domain
       0.12   11.4   0.4       0.11   11.5   0.4    1.0  1  Pox_F11         Poxvirus F11 protein
       0.19   12.3   5.8       0.19   12.3   4.9    1.5  1  RPA_interact_M  Replication protein A interacting middle
        0.2   11.1   0.7       0.23   10.8   0.7    1.1  1  FliD_C          Flagellar hook-associated protein 2 C-terminu
       0.29    9.5   0.5       0.34    9.3   0.5    1.0  1  Hemagglutinin   Haemagglutinin
       0.45   10.5   5.7       0.92    9.5   5.6    1.4  1  DUF1640         Protein of unknown function (DUF1640)
        2.3    8.2  14.1       0.24   11.3   5.3    2.9  3  Pox_A_type_inc  Viral A-type inclusion protein repeat


Domain annotation for each model (and alignments):
>> 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 !   18.7   2.0   1.3e-06    0.0013      40      91 ..      13      62 ..       5      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                    CENP-F_leu_zip 40 qekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqk 91
                                      q+ +  + E+ ++e+  lk e++ l+++l+elel+L++ +   e+++ el++
  gi|488600820|ref|YP_007907291.1| 13 QNVMAQNTESLRKEIFRLKREMDSLKRRLEELELELTHRSV--EDIKSELKE 62
                                      66788899****************************98664..455555555 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.7   3.7e-06    0.0037      58     105 ..       9      55 ..       2      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                                       HHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                        DASH_Spc19  58 aeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskk 105
                                       ++ i+  +++++e ++ke+ +l+r+ ++Lk +le +e+ l +++  ++
  gi|488600820|ref|YP_007907291.1|   9 RDHIQNVMAQNTESLRKEIFRLKREMDSLKRRLEELELELTHRS-VED 55 
                                       678999***********************************943.322 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   6.7e-06    0.0066      56     138 ..       8      57 ..       1      98 [. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.7e-06
                                       CHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH CS
                    Apolipoprotein  56 yrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklae 132
                                       +rd +q+ ++qn+e lr+++  + +e+ ++l++++eel+  l+  +                               
  gi|488600820|ref|YP_007907291.1|   8 DRDHIQNVMAQNTESLRKEIFRLKREM-DSLKRRLEELELELTHRS------------------------------- 52 
                                       456666666666666666666666665.556666666665555443............................... PP

                                       HHHHHH CS
                    Apolipoprotein 133 rleelk 138
                                        +e++k
  gi|488600820|ref|YP_007907291.1|  53 -VEDIK 57 
                                       .33333 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 ?   15.0   1.7   2.1e-05      0.02       7      40 ..      18      52 ..       5      68 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                            Cnn_1N  7 eqidkLkKENFdLKLriyfLeerleklse.eqkee 40
                                      ++ + L+KE F LK +   L+ rle+l+   ++++
  gi|488600820|ref|YP_007907291.1| 18 QNTESLRKEIFRLKREMDSLKRRLEELELeLTHRS 52
                                      55667777777777777777777777766423333 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.0   0.00013      0.13      35      84 ..      12      66 ..       2      67 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                              KxDL 35 lnalsqerlaklrarfkqgtkllkevkk.....dLesifkkirslkaklakkyPe 84
                                      +++ + +  ++lr+++ + ++ + ++k+     +Le +++ ++ +k++l+++yP+
  gi|488600820|ref|YP_007907291.1| 12 IQNVMAQNTESLRKEIFRLKREMDSLKRrleelELELTHRSVEDIKSELKEEYPD 66
                                      455555555566665555555555555511112345799***************8 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8     4e-05      0.04      19      62 ..      20      63 ..      12      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXX CS
                              SlyX 19 ieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaeee 62
                                       e+L +++++  +++d l+r+l++l+ +l +++ ++ +se +ee
  gi|488600820|ref|YP_007907291.1| 20 TESLRKEIFRLKREMDSLKRRLEELELELTHRSVEDIKSELKEE 63
                                      68899999999999999999999999998777777666655555 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   3.9e-05     0.039       9      44 ..      16      54 ..       9      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                             Spc24  9 iakelsdleselesleselaelkeeleeleeesee...k 44
                                      +a++ ++l +e+ +l+ e ++lk++leele e      +
  gi|488600820|ref|YP_007907291.1| 16 MAQNTESLRKEIFRLKREMDSLKRRLEELELELTHrsvE 54
                                      6889999***********************998874330 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.0   3.7e-05     0.037      57     100 ..       6      49 ..       5      54 .. 0.91
   2 ?    1.1   0.1      0.38   3.8e+02      56      70 ..      49      63 ..      47      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                                       EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  57 kqdkeevkeeLeerketlekeiktlekqleklekeleelkeelq 100
                                       ++d++ +++   ++ e+l kei +l++++++l+++leel+ el 
  gi|488600820|ref|YP_007907291.1|   6 LRDRDHIQNVMAQNTESLRKEIFRLKREMDSLKRRLEELELELT 49 
                                       578999999999***************************98875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.38
                                      EEE-HHHHHHHHHHH CS
                       Prefoldin_2 56 vkqdkeevkeeLeer 70
                                       ++++e++k+eL+e+
  gi|488600820|ref|YP_007907291.1| 49 THRSVEDIKSELKEE 63
                                      688999999999886 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.6e-05     0.036     364     412 ..      10      59 ..       3      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.6e-05
                        Herpes_UL6 364 nsvikcleeqineqfdtiekLkkenelllkklkelekeLerlreeakk.e 412
                                       +++ +++ +  +++ ++i +Lk+e + l+++l+ele eL++   e+ k e
  gi|488600820|ref|YP_007907291.1|  10 DHIQNVMAQNTESLRKEIFRLKREMDSLKRRLEELELELTHRSVEDIKsE 59 
                                       689999**********************************9988887632 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.8   5.7e-05     0.057     435     478 ..      14      55 ..       1      62 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                               MAD 435 dassskeevdslkkkleeLelerqrLreqkeelElelerreLqg 478
                                       +    +++ +sl+k++  L+ e ++L+++ eelElel +r+++ 
  gi|488600820|ref|YP_007907291.1|  14 NV--MAQNTESLRKEIFRLKREMDSLKRRLEELELELTHRSVED 55 
                                       33..568899****************************998765 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   6.4e-05     0.063      66     130 ..      10      74 ..       6      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                       DLP_helical  66 svirdvlerqlpeaeerleelekevekleesakriekelaelkkeieearielreelk..ayfsdLi 130
                                       + i++v+ ++ +  ++++ +l++e++ l+ +++++e  l+ +++ +e+ + el+ee    ++ +dL+
  gi|488600820|ref|YP_007907291.1|  10 DHIQNVMAQNTESLRKEIFRLKREMDSLKRRLEELE--LELTHRSVEDIKSELKEEYPdiDFDDDLL 74 
                                       569***************************999886..66688999*******99975223555665 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   6.7e-05     0.066     176     235 ..       8      67 ..       1      76 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.7e-05
                            AAA_32 176 erkeleekseeleeeleeilrelrelekeakeklkelerevakeaveplleelkekykdl 235
                                       +r+++++ +++ +e+l++ + +l++  +++k++l+ele e++++ ve++ +elke+y d 
  gi|488600820|ref|YP_007907291.1|   8 DRDHIQNVMAQNTESLRKEIFRLKREMDSLKRRLEELELELTHRSVEDIKSELKEEYPDI 67 
                                       68889999999999999999999999999****************************875 PP

>> Pox_F11  Poxvirus F11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00011      0.11     192     260 ..       3      74 ..       1     101 [] 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                           Pox_F11 192 kvyvrdldevadalvekvaekerkatklvedivkarveLEksrfeit.kelrtllkelneryndvya..dmi 260
                                       k+y+rd d++++++ ++    ++++ +l  ++  ++  LE  ++e+t + +  +  el+e+y d+    d++
  gi|488600820|ref|YP_007907291.1|   3 KTYLRDRDHIQNVMAQNTESLRKEIFRLKREMDSLKRRLEELELELThRSVEDIKSELKEEYPDIDFddDLL 74 
                                       89****************************99999999*******993456************996534444 PP

>> RPA_interact_M  Replication protein A interacting middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.9   0.00019      0.19       4      57 ..      13      66 ..      10      77 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                    RPA_interact_M  4 qeivsdElekLkrssesseklad.dDm..seseelllemerllyedirqElireeld 57
                                      q+++ +  e L+++  +++     +D     +eel+le+ +   edi++El +e  d
  gi|488600820|ref|YP_007907291.1| 13 QNVMAQNTESLRKEIFRLK---ReMDSlkRRLEELELELTHRSVEDIKSELKEEYPD 66
                                      6666666666666655555...11333559*********************887654 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 ?   10.8   0.7   0.00024      0.23     190     227 ..      14      51 ..       2      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                                       SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHH CS
                            FliD_C 190 gtlqtasknltkqikdldkkiedldkrletleerlkkq 227
                                       +++++++++l k+i +l++++++l++rle+le +l+++
  gi|488600820|ref|YP_007907291.1|  14 NVMAQNTESLRKEIFRLKREMDSLKRRLEELELELTHR 51 
                                       678899999*********************99999875 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5   0.00034      0.34     382     441 ..      11      72 ..       5      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00034
                                       HHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHHHHHHHHHHHHHHHH.H.HHHHHHHHHHHHH CS
                     Hemagglutinin 382 sliekenkqleavgkelnelekrieeldkkvddgfldvityniell.v.llenerildfeds 441
                                        + + + ++ e++ ke+ +l+++++ l+++++++ l++    +e +   l e+   +df+d+
  gi|488600820|ref|YP_007907291.1|  11 HIQNVMAQNTESLRKEIFRLKREMDSLKRRLEELELELTHRSVEDIkSeLKEEYPDIDFDDD 72 
                                       57788899999999999999999999999999999998887777441313333346777665 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.6   0.00093      0.92      63     121 ..       9      64 ..       7      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00093
                           DUF1640  63 rkevqisersefaalrseteklqreleklkqkLreeidklkadirldlnleKgrireel 121
                                       r+ +q+   +  ++lr+e  +l+re++ lk +L+e   +l++     +++ K++ +ee 
  gi|488600820|ref|YP_007907291.1|   9 RDHIQNVMAQNTESLRKEIFRLKREMDSLKRRLEELELELTHR---SVEDIKSELKEEY 64 
                                       5667788889999**********************99999998...6777777777775 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.48   4.8e+02       5      16 ..      22      33 ..      21      33 .. 0.69
   2 ?   11.3   5.3   0.00024      0.24       1      18 [.      32      49 ..      32      50 .. 0.94
   3 ?    2.1   0.3       0.2     2e+02      10      19 ..      53      62 ..      51      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.48
                    Pox_A_type_inc  5 rlRsRIsDLErq 16
                                      +lR +I  L+r+
  gi|488600820|ref|YP_007907291.1| 22 SLRKEIFRLKRE 33
                                      577777777776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                    Pox_A_type_inc  1 rEmsrlRsRIsDLErqLs 18
                                      rEm++l++R ++LE +L+
  gi|488600820|ref|YP_007907291.1| 32 REMDSLKRRLEELELELT 49
                                      8*************9996 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.2
                    Pox_A_type_inc 10 IsDLErqLse 19
                                      ++D++++L e
  gi|488600820|ref|YP_007907291.1| 53 VEDIKSELKE 62
                                      79******76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1733  (0.096659); expected 358.6 (0.02)
Passed bias filter:                     1104  (0.0615762); expected 358.6 (0.02)
Passed Vit filter:                       209  (0.0116571); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 692.47
//
Query:       gi|488600821|ref|YP_007907292.1|  [L=119]
Description: hypothetical protein Asulf_01308 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-05   25.2   1.1      3e-05   23.9   0.3    2.1  2  Cdc6_C    CDC6, C terminal winged helix domain
  ------ inclusion threshold ------
      0.043   13.8   0.1        1.9    8.5   0.1    2.1  2  PadR      Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.34     3e+03       9      26 ..       8      24 ..       3      25 .. 0.68
   2 !   23.9   0.3   3.4e-09     3e-05      37      83 ..      70     114 ..      52     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.34
                                      CHCSSS-EEHHHHHHHHH CS
                            Cdc6_C  9 rksgkeevttgevyevYk 26
                                      r + ++ + +++v+ vY+
  gi|488600821|ref|YP_007907292.1|  8 R-RASRKIELRDVEMVYE 24
                                      3.6777777788877775 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.4e-09
                                       --HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHHH CS
                            Cdc6_C  37 ltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvle 83 
                                       +  +++++++++Le l+++++ +++kGr  grtr+i  ++d + +l+
  gi|488600821|ref|YP_007907292.1|  70 MGYTRFYEIINKLERLRLIDVVMGKKGR--GRTRYILRKYDRELMLK 114
                                       5679***********************9..9****999999888776 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0064        58      24      39 ..      52      65 ..      42      72 .. 0.83
   2 ?    8.5   0.1   0.00021       1.9      27      60 ..      68     101 ..      65     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0064
                                      TT-CCTTHHHHHHHHH CS
                              PadR 24 egllelseGslYpaLk 39
                                      +g  ++s G++Y++Lk
  gi|488600821|ref|YP_007907292.1| 52 DG--DVSSGEIYRILK 65
                                      45..899********8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00021
                                       CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-E CS
                              PadR  27 lelseGslYpaLkrLekeglveseweesgegppr 60 
                                       +++ +++ Y + ++Le+ +l++  + ++g+g++r
  gi|488600821|ref|YP_007907292.1|  68 VNMGYTRFYEIINKLERLRLIDVVMGKKGRGRTR 101
                                       5678999*****************9998777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 894.34
//
Query:       gi|488600822|ref|YP_007907293.1|  [L=257]
Description: hypothetical protein Asulf_01309 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-09   36.9   0.0    1.7e-05   25.2   0.0    2.2  2  AAA_16         AAA ATPase domain
    7.9e-07   29.4   0.0    1.3e-06   28.8   0.0    1.2  1  AAA_22         AAA domain
    3.9e-05   22.9   0.0     0.0012   18.1   0.0    2.1  2  DUF815         Protein of unknown function (DUF815)
    0.00067   20.1   0.0     0.0017   18.8   0.0    1.6  1  AAA            ATPase family associated with various cellular
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.096   12.2   0.0    2.0  2  AAA_7          P-loop containing dynein motor region
      0.026   13.8   0.0      0.038   13.3   0.0    1.2  1  Zeta_toxin     Zeta toxin
      0.032   14.6   0.0      0.048   14.0   0.0    1.4  1  AAA_19         AAA domain
      0.049   13.4   0.0      0.072   12.8   0.0    1.2  1  RP854          Uncharacterized protein RP854
      0.058   13.6   0.0       0.38   10.9   0.0    2.1  1  AAA_33         AAA domain
       0.08   12.8   0.2       0.15   12.0   0.2    1.3  1  DAO_C          C-terminal domain of alpha-glycerophosphate ox
      0.083   11.8   0.0       0.12   11.3   0.0    1.1  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


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 !   25.2   0.0   1.1e-08   1.7e-05       2      78 ..      26     100 ..      25     104 .. 0.86
   2 !    9.7   0.0   0.00065       1.1     125     164 ..     118     159 ..     105     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.1e-08
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                       l+ Re+++ +L+  l+++ ++ +   ++l G +++GK+s +r++lr++ ++ +i ++ +c      ++y ++ ++++
  gi|488600822|ref|YP_007907293.1|  26 LIHRERQMVALAMNLRPALKNLSpVHTILFGSPATGKTSTLRTILREVDDH-AIITYVRCPLA--RTSYRVFSRIFE 99 
                                       788*************77777666*********************999988.99999999988..677877888884 PP

                            AAA_16  78 r 78 
                                       r
  gi|488600822|ref|YP_007907293.1| 100 R 100
                                       4 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00065
                            AAA_16 125 rll.allsrderplvlvlDdlqwade.aslqllaaLlrlles 164
                                       +l+ + l ++ +pl++ lDd+  ++  a  ++l+aLl++ e 
  gi|488600822|ref|YP_007907293.1| 118 ELIcEGLLEKNKPLIVALDDFNFLERnAGNEILYALLKAHEE 159
                                       4555444444999*********5555388999*****99886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   7.8e-10   1.3e-06       7     133 ..      51     174 ..      48     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.8e-10
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralgl.elkaerlsseelle 80 
                                       +++++G + tGKT +lr++l++          +++ +  +v +p   +s  +++++++ +   +  + + s  +++e
  gi|488600822|ref|YP_007907293.1|  51 HTILFGSPATGKTSTLRTILREV---------DDHAIitYVRCPLARTSYRVFSRIFERVYGyPPPNTGISIARMYE 118
                                       689*******************9.........5555557********99999999998876414444788999999* PP

                            AAA_22  81 aleqalraravielliiDEaqhlrs....eealeeLrsllnlsrkgvqliLvGtpel 133
                                       ++ + l ++ ++ ++ +D++ +l +    +e+l  L + ++     + +iLv t+ +
  gi|488600822|ref|YP_007907293.1| 119 LICEGLLEKNKPLIVALDDFNFL-ErnagNEILYALLKAHEEFGVRIGIILVTTERI 174
                                       ***********99999*******.522335555555444442666677788777655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   7.1e-07    0.0012       6      81 ..       3      77 ..       1     105 [. 0.80
   2 ?    3.2   0.0     0.026        42      97     134 ..     119     156 ..     112     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.1e-07
                            DUF815  6 frweekeegalepveevdevklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg 81
                                      f w++++  + e+v +++ v  ++L+  ++q  al  n +  l++l+  + +L+G+  tGK s+++++l+e+ ++ 
  gi|488600822|ref|YP_007907293.1|  3 FLWRDETLFRDESVFDPEYVP-ETLIHRERQMVALAMNLRPALKNLSPVHTILFGSPATGKTSTLRTILREVDDHA 77
                                      666644444456666666664.789999*******************************************98876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.026
                            DUF815  97 klvellrerperfilfvDDLsFeeeeeeyksLksvLeG 134
                                        ++e l e+++ +i+ +DD  F e+++    L ++L  
  gi|488600822|ref|YP_007907293.1| 119 LICEGLLEKNKPLIVALDDFNFLERNAGNEILYALLKA 156
                                       567778899999***********999999988888865 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     1e-06    0.0017       2     116 ..      53     177 ..      52     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                                       EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS.................STTHHHHHHHHHHHH.HHHTST CS
                               AAA   2 llyGppGtGKTllakavakelg..vefleisgsellsk.................yvgesekkirelfke.akekak 58 
                                       +l+G p tGKT++ + + +e++  + +  + ++  + +                   g s +++ el+ e + ek+k
  gi|488600822|ref|YP_007907293.1|  53 ILFGSPATGKTSTLRTILREVDdhAIITYVRCPLARTSyrvfsrifervygypppNTGISIARMYELICEgLLEKNK 129
                                       79******************964333444555555534567778888999988885555555555555442333336 PP

                                       SEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                               AAA  59 psilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkld 116
                                       p i+ +D++  l ++        +++++ +Ll++ +++  +   + +i++t++  +ld
  gi|488600822|ref|YP_007907293.1| 130 PLIVALDDFNFLERNA-------GNEILYALLKAHEEFGVR---IGIILVTTERIELD 177
                                       9*********997777.......999999999999999994...55666665544554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.9e-05     0.096      34      81 ..      50      97 ..      29     102 .. 0.76
   2 ?    0.5   0.0      0.22   3.6e+02      98     127 ..     127     155 ..     125     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdi 81
                                       +++l G+  tGKt++++++l+++d+  +++ +    a+ts + + +i
  gi|488600822|ref|YP_007907293.1| 50 VHTILFGSPATGKTSTLRTILREVDDHAIITYVRCPLARTSYRVFSRI 97
                                      467999*******************66665555555556655555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                             AAA_7  98 ggkklvvFvDDlnmpakekygaqppiellR 127
                                       ++k l+v +DD+n  +++  g+    +ll+
  gi|488600822|ref|YP_007907293.1| 127 KNKPLIVALDDFNFLERNA-GNEILYALLK 155
                                       68999********988875.5555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.3e-05     0.038      13      45 ..      46      78 ..      36     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                        Zeta_toxin 13 qerPklillgGqpGAGKselaellkdelerqgn 45
                                      + +P+  +l G+p+ GK+++++ + +e++ +  
  gi|488600822|ref|YP_007907293.1| 46 NLSPVHTILFGSPATGKTSTLRTILREVDDHAI 78
                                      568************************974443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     3e-05     0.048       7      63 ..      46     102 ..      41     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerla 63 
                                       +l+  + ++ + p tGKT +l++i++++ +   +   ++ l+    r  +++ er+ 
  gi|488600822|ref|YP_007907293.1|  46 NLSPVHTILFGSPATGKTSTLRTILREVDDHAIITYVRCPLARTSYRVFSRIFERVY 102
                                       556667899******************999998888888888877888888888774 PP

>> RP854  Uncharacterized protein RP854
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.4e-05     0.072     146     176 ..      87     117 ..      71     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                             RP854 146 acadfltflkifseiysymppntlisfvrvr 176
                                       a + +  f +if  +y y ppnt is+ r+ 
  gi|488600822|ref|YP_007907293.1|  87 ARTSYRVFSRIFERVYGYPPPNTGISIARMY 117
                                       55678899*******************9975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.38       3     120 ..      53     208 ..      52     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                            AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdtlrrrlfg.....tdqqsktdytrvldrlyqilnelarkalsag 70 
                                       +l G p++GK+  ++ +l++ +     + ++ + +r+ +++     + +     +++   ++ ++ + +++  l+++
  gi|488600822|ref|YP_007907293.1|  53 ILFGSPATGKTSTLRTILREVDdhaiITYVRCPLARTSYRVfsrifE-RVYGYPPPNTGISIARMYELICEGLLEKN 128
                                       789***************99998877666888887774444334321.22222222333334444444466666777 PP

                            AAA_33  71 rnvil...datnlsrrer....arflklarrlgvp.......................vrivvvetdeetlkeRlak 117
                                       +++i+   d  +l+r++      ++lk+ +++gv+                       ++i +   de+++++ la+
  gi|488600822|ref|YP_007907293.1| 129 KPLIValdDFNFLERNAGneilYALLKAHEEFGVRigiilvtterielddktgavfhpDEIYFPLYDEDEIRDILAQ 205
                                       77887787777777554444446777777778888555555555555555555555555666666666666666666 PP

                            AAA_33 118 Raa 120
                                       R +
  gi|488600822|ref|YP_007907293.1| 206 RVR 208
                                       555 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   8.9e-05      0.15      86     117 ..     199     230 ..     196     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-05
                                       HHHHHHTTS-HHHH-HHHHHHHHHHHHHHHHH CS
                             DAO_C  86 lvDvlaRRtrlafldadaalealpevaelmae 117
                                       + D+la R+rl f d   + +a ++++el a+
  gi|488600822|ref|YP_007907293.1| 199 IRDILAQRVRLGFYDGAITDDAFERIVELTAR 230
                                       68**************************9886 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.3e-05      0.12      12      41 ..      46      75 ..      37      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                     TrwB_AAD_bind 12 eretqhilivGttGsGKtqalekllraira 41
                                      +    h++++G+  +GKt +l+ +lr++  
  gi|488600822|ref|YP_007907293.1| 46 NLSPVHTILFGSPATGKTSTLRTILREVDD 75
                                      55668********************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 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:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1656.68
//
Query:       gi|488600823|ref|YP_007907294.1|  [L=162]
Description: hypothetical protein Asulf_01310 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00074   19.8   0.4       0.15   12.4   0.0    2.3  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
     0.0011   19.4   0.0       0.89   10.1   0.0    2.2  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.16   12.0   0.0    1.1  1  eIF3_p135        Translation initiation factor eIF3 subunit 1


Domain annotation for each model (and alignments):
>> 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 !    5.5   0.2    0.0035        21      21      74 ..      36      86 ..      34      90 .. 0.92
   2 !   12.4   0.0   2.4e-05      0.15      15      35 ..     117     137 ..     108     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0035
                                      HHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHH CS
                   Phage_int_SAM_1 21 aYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalr 74
                                      +Y+ +L++ lk l+    +++   + + ++++ +++++ g+s + ++r + +lr
  gi|488600823|ref|YP_007907294.1| 36 DYNERLKKELKILER---SKISDRNKNLILKYMNYRLADGVSVARVHREIVSLR 86
                                      799999999999999...99999999**********************999998 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.4e-05
                                       -HHHHHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  15 spnTlraYrrdLrrflkflae 35 
                                        p+T+++Y+rdLr++l++  +
  gi|488600823|ref|YP_007907294.1| 117 KPATVNEYERDLRMLLRMIGK 137
                                       699**************9998 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 !   10.1   0.0   0.00015      0.89      30      77 ..      45      91 ..      35      97 .. 0.84
   2 !    7.4   0.0     0.001       6.2       7      42 ..     109     150 ..     105     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                   Phage_int_SAM_4 30 lrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffykk 77
                                      l+ l++ ++++ +k+ i  Y+ny +  + +s++++++ + +l+ + +k
  gi|488600823|ref|YP_007907294.1| 45 LKILERSKISDRNKNLILKYMNYRL-ADGVSVARVHREIVSLRLLCEK 91
                                      56667669999999***********.**************99988665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.001
                   Phage_int_SAM_4   7 ealrlaglserTiksYlsaikrflrflkkk......apeelt 42 
                                        +++  g ++ T++ Y + ++ +lr + k       ++++++
  gi|488600823|ref|YP_007907294.1| 109 AKIETYGWKPATVNEYERDLRMLLRMIGKNelagriRVRDVK 150
                                       57889999******************9843555555444444 PP

>> eIF3_p135  Translation initiation factor eIF3 subunit 135
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05      0.16     113     170 ..      39      97 ..       4     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                         eIF3_p135 113 kkkesewtkltpeslweqiekevkarfryeleedsieeelk.kislLReiclkvGiqll 170
                                       ++ ++e++ l+++++  + ++ + ++ +y+l +     +++ +i  LR +c k+G++l+
  gi|488600823|ref|YP_007907294.1|  39 ERLKKELKILERSKISDRNKNLILKYMNYRLADGVSVARVHrEIVSLRLLCEKFGVELE 97 
                                       2237789999*********************665544455559*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1109.19
//
Query:       gi|488600824|ref|YP_007907295.1|  [L=250]
Description: hypothetical protein Asulf_01311 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-09   35.3   0.0    1.5e-08   34.6   0.0    1.3  1  Phage_integrase  Phage integrase family
     0.0012   18.1   3.4      0.002   17.4   3.4    1.3  1  zf-RanBP         Zn-finger in Ran binding protein and others
  ------ inclusion threshold ------
      0.053   14.0   0.2       0.11   13.0   0.0    1.7  2  EDS1_EP          Enhanced disease susceptibility 1 protein EP
       0.23   10.9   1.4        1.3    8.5   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   3.4e-12   1.5e-08      32     168 ..       5     147 ..       1     150 [. 0.80

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 3.4e-12
                                       HHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHH..CHCCTTTSBSSBET....T CS
                   Phage_integrase  32 etGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellska..leeaeksellfask....r 102
                                       + G R  Ell+Lrv+d++ +   i+vh+r++K+   r  p  +   +++ ++l+++   +  +   +l ++      
  gi|488600824|ref|YP_007907295.1|   5 DLGCRPEELLTLRVGDFERDSYGIRVHIRRSKT--TRRSPHLSFSIPYVVRWLEVHplRDDPDAPMWLDLHNfnrrI 79 
                                       5699**********************9998766..455666667778889999999533333334455343344438 PP

                                       SSB--HHHHHHHHHHHHHHCT-S..SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHH.HHHHC CS
                   Phage_integrase 103 gkplsrqtvrkafkraveeagie..kpltpHtlRhsfataLleagvdlrvvqkllGHssistt.qiYth 168
                                        kp+   ++++++ ++ ++agi+  k+++p ++Rh+ +  +  a +  +++ k  GH   s   ++Y +
  gi|488600824|ref|YP_007907295.1|  80 VKPIDIYAYNRILDKLFKKAGIQkrKRFSPYKFRHT-SITMWSAVLTEQELVKRSGHVVGSKAlRRYSK 147
                                       899999****************************98.67799999999999999999888877777765 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 !   17.4   3.4   4.4e-07     0.002       6      27 ..     180     201 ..     180     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.4e-07
                                       E-SSS--EEESSSSB-TTT--B CS
                          zf-RanBP   6 dCskClvqNfawstkCvaCqap 27 
                                       +C+ C+  N++++++C  C+a+
  gi|488600824|ref|YP_007907295.1| 180 QCNLCGEFNEPHRQRCWKCKAV 201
                                       8*******************95 PP

>> EDS1_EP  Enhanced disease susceptibility 1 protein EP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05      0.11      41      97 ..      50     104 ..      24     128 .. 0.79
   2 ?   -3.1   0.0       2.4   1.1e+04      42      58 ..     216     232 ..     204     240 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                           EDS1_EP  41 evveevekkelkeefelrkkwleagtnyrrlvEPLdiAeYyrkgkkgdYvkkgrskr 97 
                                        vv  +e ++l+++   ++ wl++ ++ rr+v P+di +Y r  +k  + k g +kr
  gi|488600824|ref|YP_007907295.1|  50 YVVRWLEVHPLRDDP-DAPMWLDLHNFNRRIVKPIDIYAYNRILDK-LFKKAGIQKR 104
                                       567777777887765.5689********************998777.6666665554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                           EDS1_EP  42 vveevekkelkeefelr 58 
                                       +ve v  ++++++++ +
  gi|488600824|ref|YP_007907295.1| 216 IVEAVIDEPMQNQMKEK 232
                                       45555444444443333 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.077   3.5e+02       3      11 ..     179     188 ..     179     190 .. 0.77
   2 ?    8.5   0.1    0.0003       1.3       3      14 ..     193     204 ..     192     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.077
                       zf-ribbon_3   3 vrCPnCGa.p 11 
                                       v+C+ CG+ +
  gi|488600824|ref|YP_007907295.1| 179 VQCNLCGEfN 188
                                       6899999855 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0003
                       zf-ribbon_3   3 vrCPnCGaplss 14 
                                       +rC++C+a+l++
  gi|488600824|ref|YP_007907295.1| 193 QRCWKCKAVLDP 204
                                       69******9897 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      779  (0.0434492); 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: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1543.55
//
Query:       gi|488600825|ref|YP_007907296.1|  [L=38]
Description: hypothetical protein Asulf_01312 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-05   21.8   0.0    0.00011   21.5   0.0    1.1  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
     0.0032   17.2   0.1     0.0042   16.8   0.0    1.3  1  HTH_23        Homeodomain-like domain
     0.0066   16.2   0.0     0.0075   16.0   0.0    1.1  1  HTH_10        HTH DNA binding domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.013   15.5   0.0    1.1  1  HTH_7         Helix-turn-helix domain of resolvase
      0.018   15.0   0.0      0.018   15.0   0.0    1.0  1  Mor           Mor transcription activator family
      0.035   13.7   0.0      0.037   13.6   0.0    1.1  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.087   12.9   0.0        0.1   12.7   0.0    1.1  1  HTH_22        HTH domain
      0.087   12.4   0.0      0.087   12.4   0.0    1.2  1  GerE          Bacterial regulatory proteins, luxR family
       0.11   11.9   0.0       0.12   11.8   0.0    1.0  1  RepL          Firmicute plasmid replication protein (RepL)
       0.13   12.3   0.0       0.14   12.2   0.0    1.1  1  HTH_6         Helix-turn-helix domain, rpiR family


Domain annotation for each model (and alignments):
>> 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 !   21.5   0.0   6.4e-08   0.00011      20      48 ..       2      29 ..       1      29 [. 0.90

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.4e-08
                      HTH_Tnp_ISL3 20 ilelllesrsvkavArqlgvSwtTVwril 48
                                      i+++     +v++vA++ g+S+ TVw il
  gi|488600825|ref|YP_007907296.1|  2 IFHEIVAQ-AVREVAEEEGISEETVWKIL 29
                                      78888888.*****************996 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   2.4e-06    0.0042      20      39 ..      11      30 ..       4      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                            HTH_23 20 vreIAreLgvsrrTvyrwlk 39
                                      vre+A+e g+s+ Tv+++l 
  gi|488600825|ref|YP_007907296.1| 11 VREVAEEEGISEETVWKILP 30
                                      89***************985 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.2e-06    0.0075      26      49 ..      11      34 ..       6      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                            HTH_10 26 lkeLAkelGIskstlsehLrkaes 49
                                      ++e+A+e GIs+ t++++L k+++
  gi|488600825|ref|YP_007907296.1| 11 VREVAEEEGISEETVWKILPKVKE 34
                                      689****************99876 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 ?   15.5   0.0   7.3e-06     0.013      22      44 ..       9      31 ..       8      32 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.3e-06
                                      --STTTSSSS---SSSS--SS-- CS
                             HTH_7 22 isiskIAkevnisRsTvYRylad 44
                                      ++++++A+e +is +Tv ++l++
  gi|488600825|ref|YP_007907296.1|  9 QAVREVAEEEGISEETVWKILPK 31
                                      6899*****************98 PP

>> Mor  Mor transcription activator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     1e-05     0.018      66     100 ..       2      36 ..       1      38 [] 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                                       HHHH--SS-HHHHHHHHT--HHHHHHHHHHHHH-- CS
                               Mor  66 ifnefkGnnvaeLarkYglseqwiykiikrvrkee 100
                                       if+e   ++v+e+a++ g+se++++ki+ +v+++ 
  gi|488600825|ref|YP_007907296.1|   2 IFHEIVAQAVREVAEEEGISEETVWKILPKVKERA 36 
                                       999***************************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 ?   13.6   0.0   2.1e-05     0.037      21      39 ..      12      30 ..       9      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                            HTH_24 21 reLAerlglSpstvnrrlk 39
                                      re+Ae+ g+S  tv++ l 
  gi|488600825|ref|YP_007907296.1| 12 REVAEEEGISEETVWKILP 30
                                      9**************9885 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.7e-05       0.1      42      62 ..       9      29 ..       6      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                            HTH_22 42 gavekvAekLgiSraTvYryL 62
                                      +av +vAe+ giS+ Tv + L
  gi|488600825|ref|YP_007907296.1|  9 QAVREVAEEEGISEETVWKIL 29
                                      79***************9876 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05     0.087      19      34 ..      10      25 ..       5      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                                      -HHHHHHHHTS-HHHH CS
                              GerE 19 snkeIAeelniSekTV 34
                                       + e+Aee +iSe+TV
  gi|488600825|ref|YP_007907296.1| 10 AVREVAEEEGISEETV 25
                                      689************9 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.6e-05      0.12      74      97 ..       7      30 ..       3      36 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                              RepL 74 liatnRelaeetgislktvsetlk 97
                                      + + +Re+aee gis +tv + l 
  gi|488600825|ref|YP_007907296.1|  7 VAQAVREVAEEEGISEETVWKILP 30
                                      55689**************98775 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.8e-05      0.14      30      54 ..       4      28 ..       2      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-05
                                      ---TT--HHHHHHHTT--HHHHHHH CS
                             HTH_6 30 dkaielsikalAkaaavSeativrf 54
                                      +++++ +++++A++ ++Se t+ ++
  gi|488600825|ref|YP_007907296.1|  4 HEIVAQAVREVAEEEGISEETVWKI 28
                                      789999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 271.05
//
Query:       gi|488600826|ref|YP_007907297.1|  [L=66]
Description: hypothetical protein Asulf_01313 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   0.1       0.26   11.1   0.1    2.0  1  HTH_23    Homeodomain-like domain
      0.087   13.2   0.0       0.15   12.5   0.0    1.5  1  CENP-S    CENP-S protein


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 ?   11.1   0.1   2.9e-05      0.26      14      30 ..      24      43 ..      12      45 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.9e-05
                            HTH_23 14 lae...GlsvreIAreLgvs 30
                                      l +   Gl+++++A++L+vs
  gi|488600826|ref|YP_007907297.1| 24 LIKkinGLTWEQAAKHLNVS 43
                                      443466*************9 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05      0.15      23      59 ..      17      57 ..       9      66 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                            CENP-S 23 eveatkqfiaaltelvykqle...nla.kDLeaFakHAkRs 59
                                      ++e++ + i+ +  l+++q++   n++   L +F +HA+R 
  gi|488600826|ref|YP_007907297.1| 17 RREISDELIKKINGLTWEQAAkhlNVSiPGLFVFLEHARRV 57
                                      6799***************65333444258*********94 PP



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:                      387  (0.0215851); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 510.63
//
Query:       gi|488600827|ref|YP_007907298.1|  [L=109]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-11   42.2   0.1      8e-11   41.6   0.1    1.3  1  HxlR            HxlR-like helix-turn-helix
    2.6e-09   36.9   0.0    3.9e-09   36.3   0.0    1.3  1  MarR            MarR family
    3.2e-09   36.5   0.0      6e-09   35.7   0.0    1.5  1  MarR_2          MarR family
    8.3e-08   32.1   0.6    1.2e-07   31.6   0.2    1.6  2  PadR            Transcriptional regulator PadR-like family
    8.7e-08   31.6   0.1    8.7e-08   31.6   0.1    2.1  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.2e-07   30.4   0.0    5.4e-07   29.7   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain
    3.9e-07   29.9   0.7      2e-06   27.6   0.1    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
    2.2e-06   28.0   0.0    3.7e-06   27.3   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
      4e-06   26.7   0.0    7.8e-06   25.8   0.0    1.5  1  HTH_45          Winged helix-turn-helix
      1e-05   25.3   0.0    1.8e-05   24.5   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    2.3e-05   24.7   0.0    3.9e-05   23.9   0.0    1.3  1  Rrf2            Transcriptional regulator
    4.7e-05   23.4   0.7     0.0077   16.3   0.1    2.4  2  DUF2250         Uncharacterized protein conserved in archaea 
    4.7e-05   23.5   0.2    0.00011   22.3   0.1    1.7  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    5.3e-05   23.3   0.0    0.00015   21.8   0.0    1.7  2  HTH_28          Helix-turn-helix domain
    8.3e-05   22.4   0.1    0.00016   21.5   0.0    1.5  1  TFIIE_alpha     TFIIE alpha subunit
    8.3e-05   22.5   0.0     0.0002   21.3   0.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00012   22.1   0.2    0.00036   20.5   0.0    1.7  2  HTH_20          Helix-turn-helix domain
    0.00028   20.5   0.5    0.00052   19.6   0.0    1.7  2  GntR            Bacterial regulatory proteins, gntR family
    0.00071   19.3   0.0     0.0025   17.6   0.0    1.8  1  AphA_like       Putative AphA-like transcriptional regulator
    0.00082   19.5   0.0      0.001   19.2   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0032   17.2   0.1       0.15   11.9   0.1    2.2  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
     0.0097   16.0   0.5       0.19   11.9   0.0    2.7  3  Mrr_N           Mrr N-terminal domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.012   15.7   0.0    1.3  1  Replic_Relax    Replication-relaxation
       0.01   15.5   0.4      0.034   13.8   0.0    1.8  2  DUF4423         Domain of unknown function (DUF4423)
      0.011   15.5   0.1      0.027   14.2   0.1    1.6  1  LexA_DNA_bind   LexA DNA binding domain
      0.014   15.1   0.0      0.021   14.6   0.0    1.6  1  DUF4364         Domain of unknown function (DUF4364)
      0.022   14.7   0.0       0.03   14.3   0.0    1.2  1  Dimerisation2   Dimerisation domain
      0.026   14.3   0.0      0.054   13.3   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
      0.026   14.3   0.0      0.038   13.8   0.0    1.3  1  RQC             RQC domain
      0.035   13.7   0.1      0.078   12.6   0.0    1.6  2  SMC_ScpB        Segregation and condensation complex subunit 
      0.048   13.9   0.0      0.094   12.9   0.0    1.7  1  Rio2_N          Rio2, N-terminal
      0.061   13.5   0.1       0.79    9.9   0.0    2.0  2  Trp_repressor   Trp repressor protein
      0.061   13.2   0.2       0.15   12.0   0.2    1.7  1  WD40_alt        Alternative WD40 repeat motif
      0.069   12.8   0.1       0.12   12.0   0.1    1.4  1  HTH_53          Zap  helix turn helix N-terminal domain
      0.072   13.1   0.0       0.13   12.3   0.0    1.5  1  BLACT_WH        Beta-lactamase associated winged helix domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.1   1.6e-13     8e-11      10      73 ..      10      73 ..       6      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.6e-13
                                      HHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE.SSSS-EEEEEE-TCGGGGH CS
                              HxlR 10 ilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevy.pevPpkveYsltekGrsle 73
                                      +l +l +g++R++el++++  is   L++ L++L+++glier    +  Pp v Y++tekGr + 
  gi|488600827|ref|YP_007907298.1| 10 VLGALKNGEMRYTELAEEV-RISPAGLTKVLKKLQKEGLIERMQDnSAYPPPVYYRITEKGRRVL 73
                                      7889***************.**********************8751568*************875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   7.5e-12   3.9e-09      15      53 ..      16      54 ..       3      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 7.5e-12
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                      +g+++ +eLa+ + +s++ +t+vl++L k+GlieR+++ 
  gi|488600827|ref|YP_007907298.1| 16 NGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIERMQDN 54
                                      6899*********************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.2e-11     6e-09       3      55 ..       3      52 ..       1      56 [. 0.92

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.2e-11
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      lt  ++ vL+aL +++   ++ +ela++ ++s++ ++++lk+L++ GL+er  
  gi|488600827|ref|YP_007907298.1|  3 LTNNDLNVLGALKNGE---MRYTELAEEVRISPAGLTKVLKKLQKEGLIERMQ 52
                                      6788899********9...9******************************974 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.2   2.4e-10   1.2e-07      25      74 ..      26      74 ..      10      75 .. 0.88
   2 ?   -2.4   0.0       9.5   4.9e+03      12      23 ..      93     104 ..      83     108 .. 0.59

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.4e-10
                                      T-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR 25 gllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                      +++++s++ l ++Lk+L+kegl+e+ +++s   pp  yYr+T++Grr l+
  gi|488600827|ref|YP_007907298.1| 26 EEVRISPAGLTKVLKKLQKEGLIERMQDNS-AYPPPVYYRITEKGRRVLK 74
                                      34799999999***************9986.89**************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.5
                                       HHHHHHHHHCCS CS
                              PadR  12 Gyeiikeleels 23 
                                         eii+e+++++
  gi|488600827|ref|YP_007907298.1|  93 ADEIIEEFRRRL 104
                                       446666666665 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 !   31.6   0.1   1.7e-10   8.7e-08       5      48 .]       7      49 ..       3      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.7e-10
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d+++L +L+ n+ + ++eLAe++ +Sp+ +++ lk+L++eGlI+
  gi|488600827|ref|YP_007907298.1|  7 DLNVLGALK-NGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIE 49
                                      555555554.6********************************7 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0     1e-09   5.4e-07      11      71 ..      15      75 ..       8      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1e-09
                            HTH_34 11 svdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71
                                      ++ e+ ++el e+++++ + L + lkkL+k g ie++ + +   p   +riT++Gr   k+
  gi|488600827|ref|YP_007907298.1| 15 KNGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIERMQDNSAYPPPVYYRITEKGRRVLKQ 75
                                      478999**************************************************98776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   3.9e-09     2e-06      16      64 ..      13      65 ..       2      68 .. 0.85
   2 ?    0.7   0.0      0.94   4.8e+02       7      32 ..      74     100 ..      73     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.9e-09
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TTEEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....pklYra 64
                                      a lk+g+++ +e+aee+ ++ +   +vL++L + Gl+er + +     p +Yr 
  gi|488600827|ref|YP_007907298.1| 13 A-LKNGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIERMQDNsayppPVYYRI 65
                                      4.58*************************************9999997667765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.94
                                       HHHC.CCHCHHHHHHCCCHHCHHCCCT CS
                              TrmB   7 seyE.akvYlaLlklgpatadeiaeel 32 
                                       +++E a+ +  L++ ++  adei ee 
  gi|488600827|ref|YP_007907298.1|  74 KQNEaAELFMNLIEVDERLADEIIEEF 100
                                       556625789999999999999999875 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 !   27.3   0.0   7.2e-09   3.7e-06       1      68 []       3      69 ..       3      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 7.2e-09
                            HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre....krvrlTdkG 68
                                      lt+++  vL  ++  +++++ ++l++ + ++ +   ++lkkL + GL+er++d     +    + +r+T+kG
  gi|488600827|ref|YP_007907298.1|  3 LTNNDLNVLGALK--NGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIERMQDN---SAypppVYYRITEKG 69
                                      5677777777777..9999********************************996...324699********9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.5e-08   7.8e-06      10      71 ..       9      78 ..       8      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.5e-08
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli........kkskekYvlTekGlelleklke 71
                                      ++L a+++ge + T++  ++ +s   l k L++L+++gli              Y++TekG+++l++ + 
  gi|488600827|ref|YP_007907298.1|  9 NVLGALKNGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIermqdnsaYPPPVYYRITEKGRRVLKQNEA 78
                                      579999**********************************876544322245679**********98765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   3.6e-08   1.8e-05       5      46 ..       8      49 ..       7      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.6e-08
                                      HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      l +L +L +ge+  +elaee+++s++ +   LkkL ++GL+e
  gi|488600827|ref|YP_007907298.1|  8 LNVLGALKNGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIE 49
                                      568999**********************************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   7.6e-08   3.9e-05      17      56 ..      11      49 ..       6      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 7.6e-08
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      L + +++e ++ +e+ae++ isp  l k+l+kL+k+gl++
  gi|488600827|ref|YP_007907298.1| 11 LGALKNGE-MRYTELAEEVRISPAGLTKVLKKLQKEGLIE 49
                                      55556666.99****************************8 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.5e-05    0.0077       7      57 ..       4      53 ..       1      56 [. 0.90
   2 ?    5.4   0.0      0.04        20      78      92 ..      61      75 ..      60      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                      ++++l+vl  lk+ +  Y   +a+e++i+    +++lkkL++ GL+er++ 
  gi|488600827|ref|YP_007907298.1|  4 TNNDLNVLGALKNGEMRYTE-LAEEVRISPAGLTKVLKKLQKEGLIERMQD 53
                                      67789*************85.799************************985 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.04
                           DUF2250 78 tYYrltreGelllre 92
                                       YYr+t++G  +l++
  gi|488600827|ref|YP_007907298.1| 61 VYYRITEKGRRVLKQ 75
                                      5***********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 !   22.3   0.1   2.2e-07   0.00011      24      54 ..      20      50 ..      13      56 .. 0.88
   2 ?   -2.1   0.0       9.3   4.8e+03      14      30 ..      63      80 ..      62      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.2e-07
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyvey 54
                                      + ++lae+  +sp+  ++ lkkL+k+G++e 
  gi|488600827|ref|YP_007907298.1| 20 RYTELAEEVRISPAGLTKVLKKLQKEGLIER 50
                                      6799************************986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.3
                                      HHHHH.HHSSB-HHHHHH CS
                    Fe_dep_repress 14 Ytlse.ekkvvktkdlae 30
                                      Y++ e ++ v k+ + ae
  gi|488600827|ref|YP_007907298.1| 63 YRITEkGRRVLKQNEAAE 80
                                      788887778877777666 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     3e-07   0.00015       3      41 ..       8      47 ..       8      58 .. 0.89
   2 ?   -1.8   0.0       7.1   3.6e+03      15      22 ..      75      82 ..      68      83 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3e-07
                            HTH_28  3 leiikllaaGh.svreaArelgisrrtvyrWikryeegGi 41
                                      l ++ +l++G+ +++e+A+e+ is+  + + +k+++++G+
  gi|488600827|ref|YP_007907298.1|  8 LNVLGALKNGEmRYTELAEEVRISPAGLTKVLKKLQKEGL 47
                                      57899*****99*************************994 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.1
                            HTH_28 15 vreaArel 22
                                      ++eaA+++
  gi|488600827|ref|YP_007907298.1| 75 QNEAAELF 82
                                      67788876 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.1e-07   0.00016      16      86 ..       8      74 ..       3      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.1e-07
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHH CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvk 86
                                       +vl +L  +ge+   +la+e++i +  l k+L +L++++l++  r +d++     +y+ri+  k   v+k
  gi|488600827|ref|YP_007907298.1|  8 LNVLGALK-NGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIE--RMQDNSAYPPPVYYRITE-KGRRVLK 74
                                      56888887.********************************85..999*************85.4455555 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 !   21.3   0.0   3.9e-07    0.0002      22      53 ..      19      50 ..       2      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.9e-07
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisr 53
                                      +  +elA+ + +++  ++++l++L++egli+r
  gi|488600827|ref|YP_007907298.1| 19 MRYTELAEEVRISPAGLTKVLKKLQKEGLIER 50
                                      7789**************************95 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     7e-07   0.00036      14      56 ..       9      50 ..       6      51 .. 0.95
   2 ?   -1.4   0.0       4.9   2.5e+03      10      47 ..      99     106 ..      87     109 .] 0.51

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7e-07
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       +l aL  ++++  +elae++++s++ l + L++L++ gL+e+
  gi|488600827|ref|YP_007907298.1|  9 NVLGAL-KNGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIER 50
                                      79999*.**********************************96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20  10 PvRrrilraLaraegltaselaerldlskntlsyHLrv 47 
                                       +                               +++L++
  gi|488600827|ref|YP_007907298.1|  99 E------------------------------FRRRLEE 106
                                       3..............................3444444 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     1e-06   0.00052      27      62 ..      21      56 ..      11      57 .. 0.89
   2 ?   -2.1   0.1         6   3.1e+03       8      15 ..      91      98 ..      87     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-06
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                        eLa+e  +s   + ++L++L+ egl+er q +++
  gi|488600827|ref|YP_007907298.1| 21 YTELAEEVRISPAGLTKVLKKLQKEGLIERMQDNSA 56
                                      579***************************997765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6
                                      HHHHHHHT CS
                              GntR  8 rLredIls 15
                                      rL ++I++
  gi|488600827|ref|YP_007907298.1| 91 RLADEIIE 98
                                      45555443 PP

>> AphA_like  Putative AphA-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.9e-06    0.0025      14      94 ..       8      81 ..       4      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-06
                         AphA_like 14 LvvLGlieraplryselagavrhlvsriagPsldLlgsslellreeGLveav.dGeGmednalLaiteaGrrelqaLlt 91
                                      L vLG+++ + +ry ela+ vr  +s++       l + l  l++eGL+e + d +     +   ite+Grr l++  +
  gi|488600827|ref|YP_007907298.1|  8 LNVLGALKNGEMRYTELAEEVR--ISPA------GLTKVLKKLQKEGLIERMqDNSAYPPPVYYRITEKGRRVLKQNEA 78
                                      78*******************9..3443......356789**********99345667788999********9998766 PP

                         AphA_like 92 anl 94
                                      a+l
  gi|488600827|ref|YP_007907298.1| 79 AEL 81
                                      665 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 !   19.2   0.0     2e-06     0.001      22      54 ..      22      54 ..      15      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2e-06
                    B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqsii 54
                                      ++La e++++p  l+++lk+L+k gLI++ + +
  gi|488600827|ref|YP_007907298.1| 22 TELAEEVRISPAGLTKVLKKLQKEGLIERMQDN 54
                                      689*************************98865 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 !   11.9   0.1    0.0003      0.15      59      88 ..      42      74 ..       1      75 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                           DUF1495 59 LielGLveeeeeseglk...lYklteeGieive 88
                                      L + GL+e++++++ +    +Y++te+G+++ +
  gi|488600827|ref|YP_007907298.1| 42 LQKEGLIERMQDNSAYPppvYYRITEKGRRVLK 74
                                      557899999999877666669********9865 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.68   3.5e+02       8      33 ..      10      30 ..       7      41 .. 0.60
   2 !   11.9   0.0   0.00037      0.19      59      86 ..      40      74 ..      38      75 .. 0.76
   3 ?   -2.3   0.0       9.8     5e+03      27      30 ..      92      95 ..      83     107 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.68
                             Mrr_N  8 lLealadgsehrlkeirervaerfgl 33
                                      +L al++g+ +   e+ e+v+    +
  gi|488600827|ref|YP_007907298.1| 10 VLGALKNGEMRY-TELAEEVR----I 30
                                      677777777775.66666654....3 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00037
                             Mrr_N 59 tyLkkagllespk.......rgvwkiTekGrevlk 86
                                      ++L+k+gl+e+ +         +++iTekGr+vlk
  gi|488600827|ref|YP_007907298.1| 40 KKLQKEGLIERMQdnsayppPVYYRITEKGRRVLK 74
                                      689999999998865444434579*********98 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.8
                             Mrr_N 27 vaer 30
                                      +a++
  gi|488600827|ref|YP_007907298.1| 92 LADE 95
                                      3332 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.0   2.4e-05     0.012      28      74 ..      36      78 ..      20     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-05
                      Replic_Relax 28 rrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqra 74
                                       ++L++L+++gl++r++ +  +a     p  Y +t+kG+r+l++++a
  gi|488600827|ref|YP_007907298.1| 36 TKVLKKLQKEGLIERMQDN--SAY--PPPVYYRITEKGRRVLKQNEA 78
                                      578************9998..222..3466677*********44433 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.7e-05     0.034      29      74 ..      11      54 ..       7      59 .. 0.91
   2 ?   -0.5   0.1       1.7   8.9e+02     132     146 ..      91     105 ..      71     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-05
                           DUF4423 29 llplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedg 74
                                      l +lk+++  + ela+ +r  is +   k l+ L+k gl+++ +d+
  gi|488600827|ref|YP_007907298.1| 11 LGALKNGEMRYTELAEEVR--ISPAGLTKVLKKLQKEGLIERMQDN 54
                                      66899999***********..*********************9884 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                           DUF4423 132 ekikkeirefrkkil 146
                                         + + i+efr+++ 
  gi|488600827|ref|YP_007907298.1|  91 RLADEIIEEFRRRLE 105
                                       556778888888875 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.3e-05     0.027      30      62 ..      23      54 ..      20      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-05
                                      HHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG- CS
                     LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyierdpgk 62
                                      e+a++++++ p++  + Lk+L++ G+ier++ +
  gi|488600827|ref|YP_007907298.1| 23 ELAEEVRIS-PAGLTKVLKKLQKEGLIERMQDN 54
                                      8999***97.*******************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 ?   14.6   0.0     4e-05     0.021      36      74 ..      35      77 ..       3     109 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                           DUF4364 36 lqqalseLvesglieeeekenkt....lykiTekGketlelfe 74
                                      l+++l++L ++glie +++++      +y+iTekG+++l++ e
  gi|488600827|ref|YP_007907298.1| 35 LTKVLKKLQKEGLIERMQDNSAYpppvYYRITEKGRRVLKQNE 77
                                      6789***********9875443233348********9987644 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.8e-05      0.03      18      84 ..       5      73 ..       3      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-05
                     Dimerisation2 18 AceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkee...kkalYsntelastyL 84
                                        +L+v  +Lk+ ++++  e+aee+ +s+ G++  l+ +   gL er ++++    +  Y+ te  ++ L
  gi|488600827|ref|YP_007907298.1|  5 NNDLNVLGALKN-GEMRYTELAEEVRISPAGLTKVLKKLQKEGLIERMQDNSaypPPVYYRITEKGRRVL 73
                                      568999999*99.********************************9775544222234556666655555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0    0.0001     0.054      15      50 ..      15      50 ..       8      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       ++e++ +elA++  ++++     L+ L+++G++e+
  gi|488600827|ref|YP_007907298.1| 15 KNGEMRYTELAEEVRISPAGLTKVLKKLQKEGLIER 50
                                      46789****************************997 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.4e-05     0.038      64     104 ..      35      80 ..      29      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHHHTTSEEEE......SSS.BEEE-CCGHHHHTSSS--E CS
                               RQC  64 wrrlirqLiaegyLeedve....eyg.vlkltekarevlkgeekvk 104
                                       +++++++L +eg++e  ++      + ++++tek+r+vlk++e  +
  gi|488600827|ref|YP_007907298.1|  35 LTKVLKKLQKEGLIERMQDnsayPPPvYYRITEKGRRVLKQNEAAE 80 
                                       67899*********6666667865568*************988554 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 ?   12.6   0.0   0.00015     0.078     111     156 ..      35      80 ..      24      85 .. 0.84
   2 ?   -1.3   0.0       2.8   1.5e+03      22      43 ..      85     106 ..      75     109 .] 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                          SMC_ScpB 111 sdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglkslee 156
                                        ++v+++L+++glie+ + +++   p+ Y++Tek  + ++ ++ +e
  gi|488600827|ref|YP_007907298.1|  35 LTKVLKKLQKEGLIERMQDNSAYPPPVYYRITEKGRRVLKQNEAAE 80 
                                       6799******************999********9766666666555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.8
                          SMC_ScpB  22 ilelskeeveealeeLkeeyee 43 
                                       ++e++++ ++e++ee+++++ee
  gi|488600827|ref|YP_007907298.1|  85 LIEVDERLADEIIEEFRRRLEE 106
                                       4555666677777777776654 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00018     0.094       4      61 ..       3      57 ..       1      80 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                            Rio2_N  4 LskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisr..ktaky 61
                                      L+++d+ vL a+  g  ++      +++e  r++  +++k+l++l k++li+r  ++  y
  gi|488600827|ref|YP_007907298.1|  3 LTNNDLNVLGALKNGEMRYT-----ELAEEVRISPAGLTKVLKKLQKEGLIERmqDNSAY 57
                                      88899999999988877664.....45555688889999**************7556666 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0015      0.79      39      75 ..       8      44 ..       5      53 .. 0.89
   2 ?    1.5   0.0      0.65   3.3e+02      14      32 ..      73      91 ..      64      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0015
                     Trp_repressor 39 lqvvkeLLkeelsqreIaeelgvSiAtItRvsrsLkt 75
                                      l+v+ +L ++e+ ++e+aee+ +S A  t v ++L++
  gi|488600827|ref|YP_007907298.1|  8 LNVLGALKNGEMRYTELAEEVRISPAGLTKVLKKLQK 44
                                      678888999**********************999984 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.65
                     Trp_repressor 14 eneeeleellelllTpdEr 32
                                       +++e+ el+  l+ +dEr
  gi|488600827|ref|YP_007907298.1| 73 LKQNEAAELFMNLIEVDER 91
                                      5789999999999999998 PP

>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00029      0.15       5      29 ..       6      30 ..       3      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                          WD40_alt  5 teKnvlGdqeqlkvrvseLeeEVrt 29
                                       + nvlG   +  +r +eL eEVr+
  gi|488600827|ref|YP_007907298.1|  6 NDLNVLGALKNGEMRYTELAEEVRI 30
                                      688********************96 PP

>> HTH_53  Zap  helix turn helix N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00024      0.12      13      39 ..      15      41 ..       9      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            HTH_53 13 hGGrmaLeeLlgeveLseaqLkevLee 39
                                      + G m   eL +ev +s+a L++vL++
  gi|488600827|ref|YP_007907298.1| 15 KNGEMRYTELAEEVRISPAGLTKVLKK 41
                                      68***********************86 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00026      0.13      24      43 ..      34      53 ..      21      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                          BLACT_WH 24 gvlahLeKLeeeGkVkregd 43
                                      g+  +L+KL++eG+++r +d
  gi|488600827|ref|YP_007907298.1| 34 GLTKVLKKLQKEGLIERMQD 53
                                      67889**********99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 755.82
//
Query:       gi|488600828|ref|YP_007907299.1|  [L=100]
Description: hypothetical protein Asulf_01315 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 614.16
//
Query:       gi|488600829|ref|YP_007907300.1|  [L=144]
Description: hypothetical protein Asulf_01316 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   11.7   0.5       0.33   10.6   0.2    1.7  2  Vac_Fusion  Chordopoxvirus multifunctional envelope protein A


Domain annotation for each model (and alignments):
>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.27   4.8e+03       7      18 ..      25      36 ..      21      38 .. 0.74
   2 ?   10.6   0.2   1.8e-05      0.33       2      39 ..      61      98 ..      60     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.27
                                      HHHHHHHHHHHH CS
                        Vac_Fusion  7 erllvlekdfql 18
                                      +r+++l + + l
  gi|488600829|ref|YP_007907300.1| 25 LRIITLLTAYSL 36
                                      588888888776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-XXXX CS
                        Vac_Fusion  2 lkdleerllvlekdfqlvikcckrvnealkRlEnHleT 39
                                      l+++ ++++ l  +++ + +   +++ea++Rl   leT
  gi|488600829|ref|YP_007907300.1| 61 LQKMLQKIMGLSSKHEGIREFIEESEEAVRRLHGKLET 98
                                      578999**************************999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 917.90
//
Query:       gi|488600830|ref|YP_007907301.1|  [L=215]
Description: hypothetical protein Asulf_01317 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   12.9   0.0       0.18   11.8   0.0    1.6  1  HSDR_N_2  Type I restriction enzyme R protein N terminus (HSD


Domain annotation for each model (and alignments):
>> 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 ?   11.8   0.0     1e-05      0.18      25      66 ..      63     103 ..      58     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                          HSDR_N_2  25 avekelqlgskkkraDivvykkdkkpllivecKapsvkisee 66 
                                        +e e +++ k++ +Di + +++  p+ ive+K+ +vk+ + 
  gi|488600830|ref|YP_007907301.1|  63 GIEAEAEITLKNGVVDIRIKREN-VPVAIVEVKTGKVKLIQS 103
                                       55666677778999*****9988.*************98543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1465.27
//
Query:       gi|488600831|ref|YP_007907302.1|  [L=49]
Description: looped-hinge helix DNA binding domain, AbrB family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    2.5e-07   30.5   0.0    1.1  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    1.2e-05   25.7   0.2    1.3e-05   25.6   0.2    1.0  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
      0.038   14.3   0.0      0.044   14.1   0.0    1.1  1  TOBE            TOBE domain
      0.069   13.4   0.0      0.069   13.4   0.0    1.1  1  PGDYG           PGDYG protein


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 !   30.5   0.0   5.6e-11   2.5e-07       3      40 ..      11      48 ..       9      49 .] 0.92

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.6e-11
                                      ETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                      v+ +++v++ k+vr+ lg+++Gd+v+++++gd  i+++
  gi|488600831|ref|YP_007907302.1| 11 VTQKYQVTLTKDVRDVLGVKPGDKVVFVQKGDAVIVKK 48
                                      7899***************************9888775 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   2.8e-09   1.3e-05       2      43 ..       9      48 ..       8      49 .] 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.8e-09
                    PrlF_antitoxin  2 stltergqttiPasvRkaLklkkgrdkiaytilddgkvvisr 43
                                      s +t+++q t+ + vR++L++k+  dk++++ +++  v++++
  gi|488600831|ref|YP_007907302.1|  9 SSVTQKYQVTLTKDVRDVLGVKP-GDKVVFV-QKGDAVIVKK 48
                                      78********************9.78**996.5555666665 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.044      35      63 ..      17      45 ..      11      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                              TOBE 35 ArvtrrsaeeLgLapGeeVfalikaakvh 63
                                      +++t++ ++ Lg++pG++V+++ k  +v+
  gi|488600831|ref|YP_007907302.1| 17 VTLTKDVRDVLGVKPGDKVVFVQKGDAVI 45
                                      789******************99988887 PP

>> PGDYG  PGDYG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.5e-05     0.069      61      95 ..      14      49 .]       3      49 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                             PGDYG 61 afsiars.aagdvlrgaaGdwllqyapGdygvveaa 95
                                      +++++ +    dvl  ++Gd ++  ++Gd  +v++a
  gi|488600831|ref|YP_007907302.1| 14 KYQVTLTkDVRDVLGVKPGDKVVFVQKGDAVIVKKA 49
                                      44444330457*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 310.93
//
Query:       gi|488600832|ref|YP_007907303.1|  [L=189]
Description: hypothetical protein Asulf_01319 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.0   4.8        1.6    8.5   1.8    2.1  2  PCRF             PCRF domain
      0.049   14.0   2.0        1.1    9.7   0.1    2.5  2  Snapin_Pallidin  Snapin/Pallidin
      0.068   12.0   2.2      0.089   11.6   2.2    1.3  1  TssC             Type VI secretion system, TssC, VipB
      0.081   13.5   0.1       0.16   12.5   0.1    1.5  1  Stimulus_sens_1  Stimulus-sensing domain
      0.094   12.9   0.4        1.6    9.0   0.2    2.5  2  DUF2795          Protein of unknown function (DUF2795)
       0.11   12.6   0.1       0.21   11.7   0.1    1.5  1  TaqI_C           TaqI-like C-terminal specificity domain


Domain annotation for each model (and alignments):
>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3   0.00061       1.8      15      78 ..      58     121 ..      46     130 .. 0.72
   2 ?    8.5   1.8   0.00054       1.6      26      82 ..     129     185 ..     114     189 .] 0.57

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00061
                                       GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GG...GTHHHHHH CS
                              PCRF  15 pevwedqekakklskelaeleeivealeeleealedleeakelleedeelaelaee...eleeleke 78 
                                       ++++  ++++ +l++e+++ ++++++++++e++ +++++ +  l  d++ ael  +   e+eel+++
  gi|488600832|ref|YP_007907303.1|  58 NQLA-LKNDIIQLAREIEAADPTLSTVKRIEARIRKIKKRRLPL--DPDTAELLMKalvEFEELKRQ 121
                                       3333.4678889***************************55555..777777664423356666554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00054
                                       STTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-...-GGGTHHHHHHHHHH CS
                              PCRF  26 klskelaeleeivealeeleealedleeakelleedeela.elaeeeleelekeleel 82 
                                        +  + ++l++i++++ee++++ e+ +e++ ++ +d++ + +la++  ++l++++ee+
  gi|488600832|ref|YP_007907303.1| 129 FVRVNRSKLQNILTTVEEVKKLFEEYREMEGFF-TDKNKKkALARDIESRLNSAIEEV 185
                                       445566778888888888888888888877777.443333134444344444444443 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00038       1.1      24      71 ..      54      96 ..      45     101 .. 0.83
   2 ?    3.5   0.2     0.032        94      43      78 ..     115     150 ..     105     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00038
                   Snapin_Pallidin 24 elrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkr 71
                                       ++++Q +L++++ +l+++++    a++  +l+++k+  +++++ikkr
  gi|488600832|ref|YP_007907303.1| 54 TTTANQLALKNDIIQLAREIE---AADP--TLSTVKRIEARIRKIKKR 96
                                      5789**************997...5555..667888888888888876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.032
                   Snapin_Pallidin  43 LkeleeaqeaevlpdlkeyakKLvnikkrmsslner 78 
                                       ++el++ +  e  ++++  + KL+ni   ++++++ 
  gi|488600832|ref|YP_007907303.1| 115 FEELKRQAMGERTEFVRVNRSKLQNILTTVEEVKKL 150
                                       45555544445588999999******9999999875 PP

>> TssC  Type VI secretion system, TssC, VipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.2     3e-05     0.089      27     119 ..      76     169 ..      49     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
                              TssC  27 lnperkarkkiflteeekkeereelk.kklelwiellessesveelvekskekaeeaeellkknlkkaveevrelek 102
                                        +p+  + k+i  + ++ k+ r  l   + el +++l + e+++      +++  +++++  +n+ ++veev++l +
  gi|488600832|ref|YP_007907303.1|  76 ADPTLSTVKRIEARIRKIKKRRLPLDpDTAELLMKALVEFEELKRQAMGERTEFVRVNRSKLQNILTTVEEVKKLFE 152
                                       556666666666666666666666652567888888888888888777777888888899999************** PP

                              TssC 103 syrsvalfykntesdkv 119
                                        yr+++ f+ + +++k 
  gi|488600832|ref|YP_007907303.1| 153 EYREMEGFFTDKNKKKA 169
                                       *********88877764 PP

>> Stimulus_sens_1  Stimulus-sensing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.4e-05      0.16      50     109 ..      73     134 ..      46     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-05
                   Stimulus_sens_1  50 ppeeselssllerfwdwlqslllreelpvyeergaangka...ypevqralageaaavvRrna 109
                                        + ++ + s+++r+  +++++  + +lp+  ++++  +ka   ++e +r++ ge++++vR+n+
  gi|488600832|ref|YP_007907303.1|  73 IEAADPTLSTVKRIEARIRKI-KKRRLPLDPDTAELLMKAlveFEELKRQAMGERTEFVRVNR 134
                                       335667778999999999999.9999**********99999999999**************96 PP

>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.13   3.8e+02       9      35 ..      17      47 ..      16      49 .. 0.75
   2 ?    9.0   0.2   0.00054       1.6      10      36 ..      63      89 ..      61      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                           DUF2795  9 tKdeLveyArrng....ApdevleaLeaLPd 35
                                      +K  L+++A  +     +++ +l++L ++++
  gi|488600832|ref|YP_007907303.1| 17 DKAGLIRRATGKSishlVSEYLLDILGRIEK 47
                                      7888999998777444448999999999985 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00054
                           DUF2795 10 KdeLveyArrngApdevleaLeaLPdr 36
                                      K ++++ Ar+  A d++l+ +++++ r
  gi|488600832|ref|YP_007907303.1| 63 KNDIIQLAREIEAADPTLSTVKRIEAR 89
                                      89**********************966 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 ?   11.7   0.1   6.9e-05      0.21       7      60 ..     116     186 ..     110     189 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                            TaqI_C   7 kdikrysieikgnYldlikkklkneka.....kelfe............ekpKilvrdiskkldaaydeka 60 
                                       +++kr  +  +++++++ ++kl+n        k+lfe            +k+K l rdi+++l+ a++e a
  gi|488600832|ref|YP_007907303.1| 116 EELKRQAMGERTEFVRVNRSKLQNILTtveevKKLFEeyremegfftdkNKKKALARDIESRLNSAIEEVA 186
                                       6899*******************9986777778888888899999999999*************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1291  (0.0720062); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1188.04
//
Query:       gi|488600833|ref|YP_007907304.1|  [L=73]
Description: hypothetical protein Asulf_01320 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 471.35
//
Query:       gi|488600834|ref|YP_007907305.1|  [L=54]
Description: hypothetical protein Asulf_01321 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 351.89
//
Query:       gi|488600835|ref|YP_007907306.1|  [L=221]
Description: hypothetical protein Asulf_01322 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.2   0.2       0.14   12.5   0.2    1.5  1  UPF0102   Uncharacterised protein family UPF0102
        0.2   11.0   0.0       0.22   10.9   0.0    1.1  1  CytoC_RC  Photosynthetic reaction centre cytochrome C subunit


Domain annotation for each model (and alignments):
>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.5e-05      0.14      23      47 ..      72      99 ..      53     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                                      ETTEEEEEEE...TTEEEEEEEEE-... CS
                           UPF0102 23 cragEiDiia...tevlvfvEVKtRsse 47
                                       ++g +Di++   +e++++vEVKt + +
  gi|488600835|ref|YP_007907306.1| 72 IEYGVVDIVVkyrGEIIAVVEVKTGKVK 99
                                      466889*******99*********6443 PP

>> CytoC_RC  Photosynthetic reaction centre cytochrome C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.4e-05      0.22      76     116 ..     152     193 ..      83     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.4e-05
                          CytoC_RC  76 eWvaPeeGctyChneedladdelYt.kvvarrmiqmtqkina 116
                                       + v P+ Gc yC ++  + +  + +     r+m++m  +in 
  gi|488600835|ref|YP_007907306.1| 152 DKVIPNPGCRYCTANCSYGNGRNLKgADPVRNMLKMLDNINV 193
                                       5688************99987665516678**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1387.34
//
Query:       gi|488600836|ref|YP_007907307.1|  [L=49]
Description: looped-hinge helix DNA binding domain, AbrB family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   28.8   0.1    1.3e-06   28.7   0.1    1.0  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
    6.2e-05   22.8   0.2    7.6e-05   22.5   0.2    1.1  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.024   14.9   0.0      0.025   14.9   0.0    1.1  1  TOBE            TOBE domain


Domain annotation for each model (and alignments):
>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   2.2e-10   1.3e-06       2      43 ..       9      48 ..       8      49 .] 0.88

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.2e-10
                    PrlF_antitoxin  2 stltergqttiPasvRkaLklkkgrdkiaytilddgkvvisr 43
                                      s++t+++q t+ + vR++L+++   dki+++i+d g+v++ +
  gi|488600836|ref|YP_007907307.1|  9 SNVTKKFQVTLTKDVRDILGVNA-GDKIVFVIKD-GEVIVRK 48
                                      89********************8.78****9975.6777766 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 !   22.5   0.2   1.3e-08   7.6e-05       3      40 ..      11      48 ..      11      49 .] 0.93

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-08
                                      ETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                      v+++ +v++ k+vr+ lg+++Gd+++++++++  i+r+
  gi|488600836|ref|YP_007907307.1| 11 VTKKFQVTLTKDVRDILGVNAGDKIVFVIKDGEVIVRK 48
                                      6789999999**********************999886 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.2e-06     0.025      33      64 .]      15      46 ..       6      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.2e-06
                              TOBE 33 LtArvtrrsaeeLgLapGeeVfalikaakvhl 64
                                       ++++t++ ++ Lg+ +G++++++ik ++v++
  gi|488600836|ref|YP_007907307.1| 15 FQVTLTKDVRDILGVNAGDKIVFVIKDGEVIV 46
                                      6899************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.29s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 359.09
//
Query:       gi|488600837|ref|YP_007907308.1|  [L=53]
Description: hypothetical protein Asulf_01324 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.5   0.1      0.044   13.5   0.1    1.1  1  PRKCSH_1  Glucosidase II beta subunit-like protein


Domain annotation for each model (and alignments):
>> PRKCSH_1  Glucosidase II beta subunit-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.5e-06     0.044      95     119 ..       8      32 ..       4      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-06
                                       EEEEEEE-SS-EEEEEEEEETTEEE CS
                          PRKCSH_1  95 aiveveCGdenelvsvseaekCeYl 119
                                        i+ v+C + n+lv +se   C+Y 
  gi|488600837|ref|YP_007907308.1|   8 IIAAVRCSKLNKLVPISECTECDYF 32 
                                       5899********************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); 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 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 362.01
//
Query:       gi|488600838|ref|YP_007907309.1|  [L=160]
Description: hypothetical protein Asulf_01325 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   19.3   5.2      0.001   19.3   5.2    2.1  2  DUF3267        Putative zincin peptidase
  ------ inclusion threshold ------
        1.1    8.4   6.3       0.65    9.2   2.4    2.3  3  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.1      0.13   1.1e+03      79      91 ..      14      26 ..       2      51 .. 0.52
   2 !   19.3   5.2   1.2e-07     0.001       1     100 [.      47     154 ..      47     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                           DUF3267 79 lllllalnaagsa 91
                                      ++++++l++a+s+
  gi|488600838|ref|YP_007907309.1| 14 AAFIFILMIAPSV 26
                                      3334444443333 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-07
                           DUF3267   1 llvlvilHEllHglffklfgkkpkkkvkfgiklliayatsseallskkqfiiillaPfvllgilllllalllpsstl 77 
                                       ++++ ilHE+ H++++ +fg+k  +++ +   l  + +t+++++ +  q i  ++ P  ++ ++l +++l+    +l
  gi|488600838|ref|YP_007907309.1|  47 FICVAILHEGGHMFAYTIFGVKFTYHFDL---LSLLHVTAESPPPPTVQLISLAMGP--IFQAVLGYIFLFSDWDFL 118
                                       57899***************999999999...6666777777776888888888889..556888888888775545 PP

                           DUF3267  78 .............llllllalnaagsagDllialll 100
                                                     ++l+l++ ++gs+ D++ ++++
  gi|488600838|ref|YP_007907309.1| 119 kkfregfldknltNITLFLIIVLLGSFLDIYGIIVI 154
                                       6999*******99889999999*******7766555 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.25   2.2e+03      19      40 ..      19      40 ..      18      42 .. 0.78
   2 ?    9.2   2.4   7.3e-05      0.65       2      28 ..      42      69 ..      41      77 .. 0.81
   3 ?    0.5   0.0     0.034     3e+02      86     107 ..      91     112 ..      85     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.25
                                      XXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 19 lvAklcgvkveefsigfGpkll 40
                                      +++ +  vk   f i fG++++
  gi|488600838|ref|YP_007907309.1| 19 ILMIAPSVKRLPFRIWFGKSIV 40
                                      66667778888999****9997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 7.3e-05
                                      XXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  2 filllgilv.vvHElGHflvAklcgvkv 28
                                      fi ll+i+v ++HE GH+++   +gvk+
  gi|488600838|ref|YP_007907309.1| 42 FIYLLFICVaILHEGGHMFAYTIFGVKF 69
                                      666666666267**************98 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.034
                                       XXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  86 qrllivlAGplanfilailvfv 107
                                        +l+ +++Gp++  +l++++++
  gi|488600838|ref|YP_007907309.1|  91 VQLISLAMGPIFQAVLGYIFLF 112
                                       5667788999999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1058.45
//
Query:       gi|488600839|ref|YP_007907310.1|  [L=154]
Description: hypothetical protein Asulf_01326 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.092   13.1   6.1        4.1    7.8   0.0    2.2  2  MgtC      MgtC family
        2.9    8.2  12.5        4.3    7.7   2.6    2.1  2  SpoVAB    Stage V sporulation protein AB


Domain annotation for each model (and alignments):
>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00046       4.1      85     120 ..      39      74 ..      31      75 .. 0.91
   2 ?    6.0   3.5    0.0017        15      48      98 ..      91     140 ..      80     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00046
                              MgtC  85 vtaaiGllvglglyllavvatvlvllllallreler 120
                                        t+++G+ +g+g ++l++ + ++++ +  l++e+++
  gi|488600839|ref|YP_007907310.1|  39 DTFLVGFYLGVGGIILGIYIGFIIIYVRFLKKEVKK 74 
                                       599************************999999875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0017
                              MgtC  48 rvaaqvvsgigflgagvilkekegakvkglTTaaslwvtaaiGllvglgly 98 
                                         +a++  g+++l+a +il+ ++    k +TT   + ++ + Gll  +gl 
  gi|488600839|ref|YP_007907310.1|  91 SYIAGIYGGLTVLAANLILSAND-IYSKTITTITFIGMMILFGLLGLAGLT 140
                                       45788999999999999994444.389999999999888888888777753 PP

>> SpoVAB  Stage V sporulation protein AB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.6    0.0013        12      21      67 ..       8      63 ..       1      69 [. 0.60
   2 ?    7.7   2.6   0.00048       4.3      47      99 ..      83     135 ..      65     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0013
                            SpoVAB 21 llyeeavilGavlgnllsvfeiklplg.........aillallglfaGiFvGclal 67
                                      l y e++il  +l   + ++ +k  ++          + l + g++ Gi++G++++
  gi|488600839|ref|YP_007907310.1|  8 LKYPEILILPPTLFVSIGLYLMKSDVSvehldtflvGFYLGVGGIILGIYIGFIII 63
                                      556666666655555555543322222223332222466779**********9986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00048
                            SpoVAB  47 gaillallglfaGiFvGclalaLaEvlnvlpilarriklkkglgililalalG 99 
                                       + +   +++ +aGi+ G+ +la   +l +  i+++ i   + +g++il+  lG
  gi|488600839|ref|YP_007907310.1|  83 TLWNQFMISYIAGIYGGLTVLAANLILSANDIYSKTITTITFIGMMILFGLLG 135
                                       4566778999*************************************998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 944.98
//
Query:       gi|488600840|ref|YP_007907311.1|  [L=76]
Description: hypothetical protein Asulf_01327 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0057   16.7   0.9     0.0061   16.6   0.9    1.1  1  Rootletin        Ciliary rootlet component, centrosome cohesi
     0.0087   16.2   0.5      0.013   15.6   0.5    1.4  1  COG5             Golgi transport complex subunit 5
     0.0088   15.9   4.5     0.0088   15.9   4.5    1.9  2  CdvA             CdvA-like coiled-coil domain
     0.0088   15.6   1.1      0.011   15.3   1.1    1.1  1  MscS_porin       Mechanosensitive ion channel porin domain
  ------ inclusion threshold ------
      0.012   15.7   2.2      0.019   15.0   1.4    1.7  1  YojJ             Bacterial membrane-spanning protein N-termin
      0.016   15.7   2.0      0.022   15.2   2.0    1.3  1  PhoU             PhoU domain
       0.02   15.0   1.5      0.023   14.8   1.5    1.1  1  COG2             COG (conserved oligomeric Golgi) complex com
       0.02   15.4   0.9       0.57   10.8   0.2    2.1  2  MerR-DNA-bind    MerR, DNA binding
      0.025   15.0   0.8       0.64   10.5   0.2    2.1  2  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.036   14.1   0.1      0.041   13.9   0.1    1.1  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.038   13.7   5.1       0.04   13.6   5.1    1.0  1  AAA_15           AAA ATPase domain
      0.061   13.8   2.8      0.073   13.6   2.8    1.1  1  DUF16            Protein of unknown function DUF16
      0.071   13.5   4.8       0.18   12.2   0.5    2.5  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.08   12.8   1.9       0.13   12.2   0.3    2.0  2  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
      0.089   12.8   0.6      0.098   12.7   0.6    1.1  1  Phasin           Poly(hydroxyalcanoate) granule associated pr
      0.089   13.4   1.7       0.23   12.0   1.7    1.7  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.13   13.2   1.3        3.4    8.6   0.3    2.2  2  HHH_9            HHH domain
       0.15   12.1   1.3       0.18   11.9   1.3    1.2  1  DUF1664          Protein of unknown function (DUF1664)
       0.16   11.9   2.0        9.7    6.1   0.4    2.3  2  HSBP1            Heat shock factor binding protein 1
       0.17   11.2   1.2       0.18   11.1   1.2    1.0  1  DctP             Bacterial extracellular solute-binding prote
        0.2   11.0   1.7       0.21   11.0   1.7    1.1  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
        0.2   12.1   1.4       0.24   11.9   0.4    1.6  2  DUF1599          Nucleotide modification associated domain 1
       0.22   11.4   4.0        7.9    6.4   0.1    2.6  3  MtrG             Tetrahydromethanopterin S-methyltransferase,
       0.24   12.0   0.9       0.54   10.8   1.0    1.7  1  YtxH             YtxH-like protein
       0.27   10.8   3.3        6.2    6.4   0.3    2.5  2  YvrJ             YvrJ protein family
       0.52   10.6   5.3         12    6.2   0.1    2.5  2  XhlA             Haemolysin XhlA
       0.58   10.5   8.4        8.6    6.7   8.4    2.5  1  ABC_tran_CTD     ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.9   9.1e-06    0.0061      11      55 ..       3      47 ..       1      74 [. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.1e-06
                         Rootletin 11 qqrqaqLvskLqaKvlqYkkrcseleqrllektselektkltlll 55
                                      ++ + ++++kL++K+ +  k+++el++ ++e+ +e  ++ l+l +
  gi|488600840|ref|YP_007907311.1|  3 KKTYEDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEK 47
                                      6899***************************77777666654333 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5     2e-05     0.013      68     114 ..       4      50 ..       1      66 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHH CS
                              COG5  68 kslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhq 114
                                       k++++++++l+++le++ + ++ l + ++e y+e+ +   +l+++ q
  gi|488600840|ref|YP_007907311.1|   4 KTYEDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEKIEQ 50 
                                       56677999999999999999999999999999999999999988876 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.5   1.3e-05    0.0088      16      61 ..       2      47 ..       1      50 [. 0.93
   2 ?    0.6   0.1      0.71   4.7e+02      44      56 ..      61      73 ..      51      76 .] 0.61

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                              CdvA 16 pkstyeeikekleealkklkekakelkeklkkrlkeledqikslek 61
                                       k+tye+i ekl+++l+k+ +k +el e ++++  e+ +   +lek
  gi|488600840|ref|YP_007907311.1|  2 AKKTYEDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEK 47
                                      589*********************************9999888886 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.71
                              CdvA 44 klkkrlkeledqi 56
                                      ++k+rl+ le +i
  gi|488600840|ref|YP_007907311.1| 61 RIKERLDNLEGKI 73
                                      4556666666555 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 !   15.3   1.1   1.6e-05     0.011      33     105 ..       4      70 ..       2      76 .] 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                        MscS_porin  33 dkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqln 105
                                       + +++ +e+l+k++++ Pk+++el ++++++       ++   + l le +eq   ++ + +++ +e+l +l+
  gi|488600840|ref|YP_007907311.1|   4 KTYEDIMEKLRKKLEKIPKKIQELDESIHEE------YYEILNDFLELEKIEQPTVNEVESQLRIKERLDNLE 70 
                                       6788889999999999999999999999999......333333446666666666666666666666665555 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 ?   15.0   1.4   2.9e-05     0.019       8      47 ..       7      46 ..       2      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-05
                              YojJ  8 eelkeklkeeLeqiekeleevlkaldeedeClLcelesir 47
                                      e + ekl+++Le+i k+++e  ++++ee   +L ++ ++ 
  gi|488600840|ref|YP_007907311.1|  7 EDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELE 46
                                      67889************************99999775443 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.0   3.4e-05     0.022       8      62 ..       2      56 ..       1      70 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-05
                                      HHHHHHHHHHHHHCT-HHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHH CS
                              PhoU  8 veemlddalealeekdtela.revierddeidrlekeiersllealakrqplaedl 62
                                      +++  +d +e l++k  e + +++ e+d++i + ++ei ++ le+ +++qp  +++
  gi|488600840|ref|YP_007907311.1|  2 AKKTYEDIMEKLRKKL-EKIpKKIQELDESIHEEYYEILNDFLELEKIEQPTVNEV 56
                                      5677788999999987.6666********************776667777754433 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 ?   14.8   1.5   3.5e-05     0.023      67     130 ..       6      70 ..       4      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-05
                              COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllkldevvekle 130
                                       +++ +e+++++l+++ kk++++ e+++e  +e+ +   e +++e+   + +++ l+++e++++le
  gi|488600840|ref|YP_007907311.1|   6 YEDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEKIEQPTvNEVESQLRIKERLDNLE 70 
                                       68899***************************************999899999999999999998 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00085      0.57      33      59 ..       5      31 ..       2      33 .. 0.85
   2 ?    3.7   0.0      0.14        92      23      53 ..      42      74 ..      37      76 .] 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00085
                                      BHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind 33 pcqdvrallarklaeleeriaeLqalr 59
                                      + +d  + l++kl+++ ++i+eL++  
  gi|488600840|ref|YP_007907311.1|  5 TYEDIMEKLRKKLEKIPKKIQELDESI 31
                                      5678899****************9865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.14
                                      HHHHHHSTTTBHHHHH..HHHHHHHHHHHHHHH CS
                     MerR-DNA-bind 23 lLalyddrappcqdvr..allarklaeleeria 53
                                      +L+l + ++p+  +v+    ++++l+ le +i+
  gi|488600840|ref|YP_007907311.1| 42 FLELEKIEQPTVNEVEsqLRIKERLDNLEGKIN 74
                                      5666555677777777667899*******9996 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00096      0.64      37      66 ..      10      40 ..       3      54 .. 0.75
   2 ?    4.1   0.1     0.099        66      34      61 ..      50      76 .]      44      76 .] 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00096
                           NPV_P10 37 vtelnekLdaqsaqLaeletkv.enIqdiLn 66
                                      +++l +kL++++++++el++++ e+  +iLn
  gi|488600840|ref|YP_007907311.1| 10 MEKLRKKLEKIPKKIQELDESIhEEYYEILN 40
                                      367999**************88345778888 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.099
                           NPV_P10 34 lpdvtelnekLdaqsaqLaeletkvenI 61
                                       p+v+e++++L ++ + L++le k++ I
  gi|488600840|ref|YP_007907311.1| 50 QPTVNEVESQL-RIKERLDNLEGKINGI 76
                                      46777777777.4677777777777655 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 ?   13.9   0.1   6.2e-05     0.041      31      95 ..       8      74 ..       3      76 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                      Baculo_PEP_C 31 qilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsilt 95
                                       i+ +l + l++i +++++l+e++++   e+ +++ +l +  + ++n+++    ++++L+nl+ +++
  gi|488600840|ref|YP_007907311.1|  8 DIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEKIEQPTVNEVEsqLRIKERLDNLEGKIN 74
                                      577889999999999999999999999999999999999999999****954456789****99988 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   5.1     6e-05      0.04     235     294 ..      10      73 ..       1      75 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                            AAA_15 235 eeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieik.....ddeelpl 294
                                        e+l++kl++i +k++e+d+ + ee+ +il+++++  +k++ + ++++e +++     d+ e ++
  gi|488600840|ref|YP_007907311.1|  10 MEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLEL-EKIEQPTVNEVESQLRikerlDNLEGKI 73 
                                       468999****************99999866666665.7888888888776666666776666555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.8   0.00011     0.073      40     104 .]       7      71 ..       2      71 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                                       HHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC- CS
                             DUF16  40 eakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsieg 104
                                       e+ ++kl ++++k+ +k+++++e i+e   e+     el+k+++     +e+  +i++RlD++eg
  gi|488600840|ref|YP_007907311.1|   7 EDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEKIEQPTVNEVESQLRIKERLDNLEG 71 
                                       4455566667777777777777777776666666666666776644444555567********97 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00028      0.18      16      38 ..      10      32 ..       3      45 .. 0.81
   2 ?    3.3   0.3      0.17   1.1e+02       9      37 ..      45      73 ..      43      76 .] 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                         FlaC_arch 16 letvkkeneelsksveelkenVk 38
                                      +e ++k++e++ k+++el+e++ 
  gi|488600840|ref|YP_007907311.1| 10 MEKLRKKLEKIPKKIQELDESIH 32
                                      78899999999999999999985 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                         FlaC_arch  9 lsklst.eletvkkeneelsksveelkenV 37
                                      l+k++  +++ v++++  +++ +++l+ ++
  gi|488600840|ref|YP_007907311.1| 45 LEKIEQpTVNEVESQL-RIKERLDNLEGKI 73
                                      5666666666666665.3666666665444 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 ?   12.2   0.3   0.00019      0.13      23      43 ..       9      29 ..       3      31 .. 0.84
   2 ?   -0.3   0.1       1.5     1e+03      35      44 ..      63      72 ..      54      73 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                      HHHHHHHHHHHHHHHHHHHHH CS
                    Matrilin_ccoil 23 eiqaLtqkLeavtkRlealEn 43
                                        ++L +kLe + k+++ l+ 
  gi|488600840|ref|YP_007907311.1|  9 IMEKLRKKLEKIPKKIQELDE 29
                                      4689***************97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                                      HHHHHHHHHH CS
                    Matrilin_ccoil 35 tkRlealEnk 44
                                       +Rl  lE k
  gi|488600840|ref|YP_007907311.1| 63 KERLDNLEGK 72
                                      4678888766 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 ?   12.7   0.6   0.00015     0.098      55     121 ..       2      73 ..       1      76 [] 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                            Phasin  55 aeekleevresvkskveevkekaeeqwdklekafdervaka..Lsrlgvpsredvea...LsarvdeLtkel 121
                                       a+++ e++ e++++k+e++ +k++e  +++ +   e +++   L++++ p+ ++ve+   +++r+d+L+ ++
  gi|488600840|ref|YP_007907311.1|   2 AKKTYEDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFleLEKIEQPTVNEVESqlrIKERLDNLEGKI 73 
                                       6788999999***************999**9999999999722579*********96444789999999876 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.7   0.00035      0.23      37      65 ..       4      37 ..       2      75 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00035
                      Syntaxin-6_N 37 eeldetrteLrkalrsiewdledLeetv.....r 65
                                      + +++ +++Lrk+l++i +++++L+e++     +
  gi|488600840|ref|YP_007907311.1|  4 KTYEDIMEKLRKKLEKIPKKIQELDESIheeyyE 37
                                      56788999********************444441 PP

>> HHH_9  HHH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0       0.2   1.3e+02      52      64 ..       3      15 ..       1      18 [. 0.88
   2 ?    8.6   0.3    0.0051       3.4       7      37 ..      30      60 ..      25      74 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.2
                             HHH_9 52 eptleDIleeLak 64
                                      ++t eDI+e+L+k
  gi|488600840|ref|YP_007907311.1|  3 KKTYEDIMEKLRK 15
                                      579********97 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0051
                             HHH_9  7 avHPEsYalakkllkklgldlkeligeeall 37
                                      ++H E Y++ +  l+  +++  ++ + e++l
  gi|488600840|ref|YP_007907311.1| 30 SIHEEYYEILNDFLELEKIEQPTVNEVESQL 60
                                      59**********9999888776655444433 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.3   0.00027      0.18      48     119 ..       4      75 ..       1      76 [] 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       k  e+++e+l++  +++ ++i+++d+++ e    + +   e++++++ + +  e    +ke   +le+k++ 
  gi|488600840|ref|YP_007907311.1|   4 KTYEDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEKIEQPTVNEVESQLRIKERLDNLEGKING 75 
                                       456778888888888899999999998876554444444567777665444444444688899999998875 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 ?    6.1   0.4     0.015       9.7      20      44 ..       8      32 ..       3      34 .. 0.82
   2 ?    5.2   0.1     0.029        20      33      44 ..      63      74 ..      61      76 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                             HSBP1 20 tmsdqilsriDdMssriDdLEksia 44
                                      ++ +++ ++++ + ++i +L++si 
  gi|488600840|ref|YP_007907311.1|  8 DIMEKLRKKLEKIPKKIQELDESIH 32
                                      5667788999999999999999996 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                             HSBP1 33 ssriDdLEksia 44
                                       +r+D+LE  i+
  gi|488600840|ref|YP_007907311.1| 63 KERLDNLEGKIN 74
                                      6899***99987 PP

>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.2   0.00027      0.18     211     268 ..       1      58 [.       1      69 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                       EEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEGEHHHH CS
                              DctP 211 vnkktwdsLpedlqaileeaakeatelqrklveeleeealqklkeagvevieltpedl 268
                                       + kkt++ + e+l++ le++ k+ +el   + ee+ e + ++l+ +++e  ++++++ 
  gi|488600840|ref|YP_007907311.1|   1 MAKKTYEDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEKIEQPTVNEVES 58 
                                       5699*********************************999999999999966666654 PP

>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.7   0.00031      0.21      38      93 ..       6      58 ..       1      73 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                                      HHHHHHHHHH..........HHGGGSSS---HHHHHHHCT--.............T CS
                   DNA_primase_lrg 38 lekfrkrlekalestkeslpeleeeikederekleellealsesyvaedvqeeeds 93
                                      +e ++++l k+le++ ++ +el+e+i+e++ e+l ++le  +   +++++ +e +s
  gi|488600840|ref|YP_007907311.1|  6 YEDIMEKLRKKLEKIPKKIQELDESIHEEYYEILNDFLELEK---IEQPTVNEVES 58
                                      688999999999999999999999999999988888887655...33333333333 PP

>> DUF1599  Nucleotide modification associated domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00036      0.24      15      52 ..       4      40 ..       1      41 [. 0.76
   2 ?   -2.0   0.0       7.7   5.1e+03      37      37 ..      60      60 ..      45      72 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                           DUF1599 15 ssltDqiliKakR.irsleekgeakvdEgiadeyidiiN 52
                                      + ++D i+ K+++ ++++  k+ ++ dE+i++ey +i+N
  gi|488600840|ref|YP_007907311.1|  4 KTYED-IMEKLRKkLEKIP-KKIQELDESIHEEYYEILN 40
                                      66788.8888864144444.69999************99 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.7
                           DUF1599 37 a 37
                                       
  gi|488600840|ref|YP_007907311.1| 60 L 60
                                      1 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.7     0.015        10      12      27 ..      10      25 ..       1      42 [. 0.69
   2 ?   -1.1   0.0       2.6   1.7e+03      19      23 ..      45      49 ..      30      61 .. 0.53
   3 ?    6.4   0.1     0.012       7.9      13      27 ..      60      74 ..      47      76 .] 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                              MtrG 12 fnevkkrLdeieekve 27
                                       +++ k+L++i +k++
  gi|488600840|ref|YP_007907311.1| 10 MEKLRKKLEKIPKKIQ 25
                                      4566677777777775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                              MtrG 19 Ldeie 23
                                      L++ie
  gi|488600840|ref|YP_007907311.1| 45 LEKIE 49
                                      44444 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.012
                              MtrG 13 nevkkrLdeieekve 27
                                       ++k+rLd++e k++
  gi|488600840|ref|YP_007907311.1| 60 LRIKERLDNLEGKIN 74
                                      479**********96 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0   0.00082      0.54      31      73 ..       3      41 ..       1      74 [. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00082
                              YtxH 31 kekaddlkekakelleeakekakekaedlkekvkekadelkek 73
                                      k++++d+ ek+ + le++     +k+++l e++ e+  e+ ++
  gi|488600840|ref|YP_007907311.1|  3 KKTYEDIMEKLRKKLEKI----PKKIQELDESIHEEYYEILND 41
                                      555666666666665555....777777777777776655544 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0094       6.2      19      32 ..      20      33 ..       7      33 .. 0.83
   2 ?    5.0   0.2     0.026        17      18      31 ..      61      74 ..      60      76 .] 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0094
                              YvrJ 19 iEkkLdeLtksIee 32
                                      i kk+ eL +sI+e
  gi|488600840|ref|YP_007907311.1| 20 IPKKIQELDESIHE 33
                                      55889999999986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                              YvrJ 18 RiEkkLdeLtksIe 31
                                      Ri ++Ld+L   I+
  gi|488600840|ref|YP_007907311.1| 61 RIKERLDNLEGKIN 74
                                      9999******9998 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.5     0.021        14      17      41 ..       7      31 ..       3      52 .. 0.59
   2 ?    6.2   0.1     0.017        12       8      21 ..      61      74 ..      53      76 .] 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                              XhlA 17 eervdkleekaaeaeekiknleedl 41
                                      e+ ++kl +k ++  +ki++l e +
  gi|488600840|ref|YP_007907311.1|  7 EDIMEKLRKKLEKIPKKIQELDESI 31
                                      4444455555555555555555544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                              XhlA  8 rietkldnleervd 21
                                      ri+++ldnle +++
  gi|488600840|ref|YP_007907311.1| 61 RIKERLDNLEGKIN 74
                                      67777777777665 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 ?    6.7   8.4     0.013       8.6       5      26 ..      12      33 ..       8      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                      ABC_tran_CTD  5 keqreleeleaeIeaLEeeiae 26
                                      k +++le+++++I++L+e i e
  gi|488600840|ref|YP_007907311.1| 12 KLRKKLEKIPKKIQELDESIHE 33
                                      889999********99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2423  (0.135144); expected 358.6 (0.02)
Passed bias filter:                     1357  (0.0756874); expected 358.6 (0.02)
Passed Vit filter:                       173  (0.00964917); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 444.42
//
Query:       gi|488600841|ref|YP_007907312.1|  [L=111]
Description: hypothetical protein Asulf_01328 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 638.28
//
Query:       gi|488600842|ref|YP_007907313.1|  [L=103]
Description: hypothetical protein Asulf_01329 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00011   22.1   0.3    0.00011   22.0   0.3    1.1  1  DUF4020   Domain of unknown function (DUF4020)
     0.0071   16.5   0.0      0.012   15.8   0.0    1.3  1  DUF5371   Family of unknown function (DUF5371)


Domain annotation for each model (and alignments):
>> DUF4020  Domain of unknown function (DUF4020)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.3   1.3e-08   0.00011      26      68 ..      28      69 ..      23     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-08
                           DUF4020 26 kerikfarllarevkslpkkaqrklWdaWlevylreRgklggi 68
                                      ++ +++a+ +  + ++l  k +rk W+ Wl  y+ eR ++  i
  gi|488600842|ref|YP_007907313.1| 28 ENLMRWAERVGLDPAGLGAKTTRKTWESWLMFYFSER-RIEII 69
                                      6789*********************************.55333 PP

>> DUF5371  Family of unknown function (DUF5371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-06     0.012      30      54 ..      74      98 ..      69     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                           DUF5371 30 dAlsiAveHYleCeYtdlneemwtk 54
                                        l  AveHYl+ ++t+ +  m++k
  gi|488600842|ref|YP_007907313.1| 74 HTLLTAVEHYLNMPFTENDRRMMEK 98
                                      56889************88899888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 656.20
//
Query:       gi|488600843|ref|YP_007907314.1|  [L=269]
Description: hypothetical protein Asulf_01330 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0061   16.8   1.3       0.27   11.5   0.0    3.0  3  DUF948           Bacterial protein of unknown function (DUF94
  ------ inclusion threshold ------
       0.02   15.1   0.0        1.9    8.7   0.0    2.7  2  P22_AR_C         P22AR C-terminal domain
      0.057   14.0   0.7        2.4    8.7   0.0    3.2  3  YtxH             YtxH-like protein
      0.058   14.1   0.1      0.058   14.1   0.1    2.7  3  CDH1_2_SANT_HL1  CDH1/2 SANT-Helical linker 1
       0.15   11.6   0.0       0.24   10.9   0.0    1.3  1  DUF4328          Domain of unknown function (DUF4328)
       0.16   12.6   0.5       0.73   10.5   0.4    2.2  1  DUF3502          Domain of unknown function (DUF3502)
       0.29   11.6   5.4       0.36   11.3   0.3    2.7  3  DUF16            Protein of unknown function DUF16
       0.31   11.6   2.1       0.36   11.4   0.1    2.1  3  Carbpep_Y_N      Carboxypeptidase Y pro-peptide
       0.49   10.4   6.8        3.8    7.6   2.3    3.1  2  DUF1664          Protein of unknown function (DUF1664)
        1.5    9.2   5.9        3.3    8.0   0.2    3.0  4  ATP-synt_ab_C    ATP synthase alpha/beta chain, C terminal do
        2.1    8.8   5.3        2.9    8.4   1.1    2.3  2  DUF3456          TLR4 regulator and MIR-interacting MSAP


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00017      0.27       2      37 ..      24      59 ..      24      83 .. 0.86
   2 ?    0.1   0.0      0.62     1e+03      27      53 ..     128     154 ..      98     177 .. 0.59
   3 ?    2.1   0.1      0.14   2.3e+02      62      80 ..     222     240 ..     216     252 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                            DUF948  2 AglIaAiAFvvLviflivvllklkktldeaaatiee 37
                                      +g I AiA ++Lvi+  + ++  +++++e+++ i++
  gi|488600843|ref|YP_007907314.1| 24 SGTIQAIATIILVIVTYKYVRLTRELVNETRREIQS 59
                                      6889***************************99975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.62
                            DUF948  27 tldeaaatieelekqvdpilkevedll 53 
                                       t de+++ +++  +++ + + e+ d  
  gi|488600843|ref|YP_007907314.1| 128 THDELREKLKTAVRNLAERILELPDFK 154
                                       444444444444444444444444333 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                            DUF948  62 dvneklekvdplteavadl 80 
                                       +v+e+++kv++lt+++ ++
  gi|488600843|ref|YP_007907314.1| 222 EVKEEVKKVQELTDELLKI 240
                                       5666666666666654443 PP

>> P22_AR_C  P22AR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.065   1.1e+02      43      62 ..     153     172 ..     151     182 .. 0.76
   2 ?    8.7   0.0    0.0012       1.9      23      60 ..     228     265 ..     225     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.065
                          P22_AR_C  43 lapkaYsiakEYsstlrdar 62 
                                       ++  +++++kEY+ ++    
  gi|488600843|ref|YP_007907314.1| 153 FKKRCHQMVKEYNDNASAED 172
                                       56689*******99887655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                          P22_AR_C  23 vrsvellrelepaLraigsnlapkaYsiakEYsstlrd 60 
                                       ++ +el+ el+++L  i s+l  ++  i+  Y+  lrd
  gi|488600843|ref|YP_007907314.1| 228 KKVQELTDELLKILATIVSELDNEILKIWRKYKIELRD 265
                                       6889***************************9988876 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.36   5.9e+02      25      59 ..      52      84 ..      46     128 .. 0.67
   2 ?    8.7   0.0    0.0015       2.4      24      70 ..     130     237 ..     127     242 .. 0.74
   3 ?    1.5   0.1      0.28   4.6e+02      27      45 ..     220     238 ..     219     252 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.36
                              YtxH 25 etRkdlkek.addlkekakelleeakekakekaedl 59
                                      etR++++ k +++l +k+      +ke ak + edl
  gi|488600843|ref|YP_007907314.1| 52 ETRREIQSKrMEELVNKI---MIPLKEHAKANYEDL 84
                                      677777655455554444...444555554444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                              YtxH  24 ketRkdlkek..........addlkekakelleeakeka...................................... 52 
                                        e+R++lk +          + d+k++  ++++e +++a                                      
  gi|488600843|ref|YP_007907314.1| 130 DELREKLKTAvrnlaerileLPDFKKRCHQMVKEYNDNAsaedkltgsqledfpeiligdiidrtenfreqdifrrf 206
                                       59999999997777777777777777777777777777788888888888888888888887777777777777777 PP

                              YtxH  53 .............kekaedlkekvkekadel 70 
                                                    +e++++ ++kv+e +del
  gi|488600843|ref|YP_007907314.1| 207 wqryrneligfldREEVKEEVKKVQELTDEL 237
                                       7777777777777777777777777777765 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.28
                              YtxH  27 Rkdlkekaddlkekakell 45 
                                       R+++ke++++++e ++ell
  gi|488600843|ref|YP_007907314.1| 220 REEVKEEVKKVQELTDELL 238
                                       6666677666666666654 PP

>> CDH1_2_SANT_HL1  CDH1/2 SANT-Helical linker 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.2   1.9e+03      46      85 ..      63     103 ..      46     106 .. 0.44
   2 ?   14.1   0.1   3.5e-05     0.058      26      72 ..     124     176 ..     112     190 .. 0.78
   3 ?   -0.8   0.1       1.5   2.5e+03       3      18 ..     197     213 ..     195     260 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                   CDH1_2_SANT_HL1  46 gellkerCeealeee.keekee.eeeekeekkkrergpsfkl 85 
                                        el+++     l+e+ k++ e+ +++e + k +++r  +fkl
  gi|488600843|ref|YP_007907314.1|  63 EELVNK-IMIPLKEHaKANYEDlANREYGYKFRTKRIRTFKL 103
                                       333322.22233333222222213333344444555566665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
                   CDH1_2_SANT_HL1  26 daiacdAeLqeKplsdLkklgell......kerCeealeeekeekeeeeeeke 72 
                                       ++i +  eL+eK ++ +++l+e +      k+rC+++++e++++ + e++ ++
  gi|488600843|ref|YP_007907314.1| 124 EKIKTHDELREKLKTAVRNLAERIlelpdfKKRCHQMVKEYNDNASAEDKLTG 176
                                       7888999***************8744444468*********777776666554 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                   CDH1_2_SANT_HL1   3 Ftdaei.RrFvksykkf 18 
                                       F +++i RrF + y+  
  gi|488600843|ref|YP_007907314.1| 197 FREQDIfRRFWQRYRNE 213
                                       66666556776666642 PP

>> DUF4328  Domain of unknown function (DUF4328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.24       8      69 ..      12      73 ..       6      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                           DUF4328  8 ealrladalvelagllalllllaaavvflvWlrraranaealapgrhrrspgwavggwlvPv 69
                                      ++ r+ d+l+   g ++ +++++ ++v  +++r +r+ +++ + + ++ +  ++v  +++P+
  gi|488600843|ref|YP_007907314.1| 12 SISRAIDWLNDNSGTIQAIATIILVIVTYKYVRLTRELVNETRREIQSKRMEELVNKIMIPL 73
                                      677899***************************************99999999999999996 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00045      0.73      58     107 ..     208     257 ..      67     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                           DUF3502  58 aka.spalgFtfDsspvkteiaalsnvveeykkaletGlvDpeetlpkfne 107
                                       + + + ++gF +D ++vk+e++++++ ++e  k l t + + ++++ k+  
  gi|488600843|ref|YP_007907314.1| 208 QRYrNELIGF-LDREEVKEEVKKVQELTDELLKILATIVSELDNEILKIWR 257
                                       3334889999.6*********************999987788877766655 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.5   2.4e+03      55      63 ..      60      68 ..      37     108 .. 0.57
   2 ?   11.3   0.3   0.00022      0.36      29      79 ..     112     162 ..      92     186 .. 0.82
   3 ?    1.8   0.2       0.2   3.3e+02      73     100 ..     222     249 ..     209     255 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                                      HHHHHHHHH CS
                             DUF16 55 qkvekqgek 63
                                      + +e++ +k
  gi|488600843|ref|YP_007907314.1| 60 KRMEELVNK 68
                                      222222222 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00022
                                       -..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                             DUF16  29 kdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln 79 
                                        ++ kq+   i +k+++++e  +kl+ +v+++ e+i el    k  ++ ++
  gi|488600843|ref|YP_007907314.1| 112 MKDFKQDYPSIYEKIKTHDELREKLKTAVRNLAERILELPDFKKRCHQMVK 162
                                       4578999******************************99887777777665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.2
                                       HHHH.......HHHHHHHHHHHHHHHHH CS
                             DUF16  73 aqgeelnkvdetleliletLqkinkRlD 100
                                         +ee++kv+e  + +l++L++i   lD
  gi|488600843|ref|YP_007907314.1| 222 EVKEEVKKVQELTDELLKILATIVSELD 249
                                       3445566777777777777777666666 PP

>> Carbpep_Y_N  Carboxypeptidase Y pro-peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         9   1.5e+04      53      69 ..      60      76 ..      49      82 .. 0.60
   2 ?   -1.6   0.0       2.3   3.8e+03      59      61 ..     133     135 ..     101     174 .. 0.56
   3 ?   11.4   0.1   0.00022      0.36      49      84 ..     223     259 ..     212     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9
                       Carbpep_Y_N 53 ekknnvfekiskvlnep 69
                                      +  +++++ki  +l+e 
  gi|488600843|ref|YP_007907314.1| 60 KRMEELVNKIMIPLKEH 76
                                      34445555555555554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                       Carbpep_Y_N  59 fek 61 
                                        ek
  gi|488600843|ref|YP_007907314.1| 133 REK 135
                                       222 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00022
                       Carbpep_Y_N  49 lee.eekknnvfekiskvlneplkeltseakkiWsem 84 
                                       ++e  +k++++ ++  k+l+  ++el++e+ kiW   
  gi|488600843|ref|YP_007907314.1| 223 VKEeVKKVQELTDELLKILATIVSELDNEILKIWRKY 259
                                       4454799***************************865 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.3    0.0023       3.8       8     120 ..      30     150 ..      23     154 .. 0.66
   2 ?    3.0   0.1     0.062     1e+02      87     120 ..     221     255 ..     213     259 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0023
                           DUF1664   8 vpaavvgavgYgyvwwkGwklsdlmfvTkrslsd.....avesvskqleqvs....eslaatkrhL...ssridrvd 72 
                                       +++++++ v Y yv+       +l+  T+r +++      v+++   l++      e+la+        ++ri +  
  gi|488600843|ref|YP_007907314.1|  30 IATIILVIVTYKYVRL----TRELVNETRREIQSkrmeeLVNKIMIPLKEHAkanyEDLANREYGYkfrTKRIRTFK 102
                                       5666777777777773....4566666666544311000333333223222122224444433221223789***** PP

                           DUF1664  73 kkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                        +l++++ + k+ k++  ++ e++++ +e  e++k+av++l++++ ++
  gi|488600843|ref|YP_007907314.1| 103 LNLNDTTILMKDFKQDYPSIYEKIKTHDELREKLKTAVRNLAERILEL 150
                                       *******************************************99776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.062
                           DUF1664  87 eevtevredlseigedv.esvkeavegleskleri 120
                                       eev+e  ++++e+ +++ + + ++v++l++++ +i
  gi|488600843|ref|YP_007907314.1| 221 EEVKEEVKKVQELTDELlKILATIVSELDNEILKI 255
                                       44444444555555544144567788888888766 PP

>> ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.3   2.1e+03      76     103 ..      55      82 ..      28     103 .. 0.61
   2 ?    8.0   0.2    0.0021       3.3      90     124 ..     111     145 ..      84     147 .. 0.82
   3 ?   -3.8   0.0       9.1   1.5e+04      95     114 ..     154     173 ..     151     180 .. 0.60
   4 ?    3.0   0.1     0.074   1.2e+02      84     125 ..     208     247 ..     196     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                     ATP-synt_ab_C  76 ddipvekvkefekelleyleeekkeile 103
                                        +i+ ++++e+ ++++  l+e++k  +e
  gi|488600843|ref|YP_007907314.1|  55 REIQSKRMEELVNKIMIPLKEHAKANYE 82 
                                       3444444444444444444444444444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                     ATP-synt_ab_C  90 lleyleeekkeileeieekkklsdeleeklkeaik 124
                                       l++ +++++++i+e+i+++ +l ++l+++++++++
  gi|488600843|ref|YP_007907314.1| 111 LMKDFKQDYPSIYEKIKTHDELREKLKTAVRNLAE 145
                                       678899*************9999999998887765 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 9.1
                     ATP-synt_ab_C  95 eeekkeileeieekkklsde 114
                                       +++ +++++e++++ + +d+
  gi|488600843|ref|YP_007907314.1| 154 KKRCHQMVKEYNDNASAEDK 173
                                       45555666666666555555 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.074
                     ATP-synt_ab_C  84 kefekelleyleeekkeileeieekkklsdeleeklkeaike 125
                                       +++++el+ +l++e  e+ ee+++ ++l+del + l+++++e
  gi|488600843|ref|YP_007907314.1| 208 QRYRNELIGFLDRE--EVKEEVKKVQELTDELLKILATIVSE 247
                                       57788888888877..899999999*****999999998876 PP

>> DUF3456  TLR4 regulator and MIR-interacting MSAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.1    0.0018       2.9      87     131 ..     124     167 ..      43     182 .. 0.74
   2 ?    2.3   0.2      0.13   2.1e+02      97     138 ..     223     258 ..     195     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0018
                           DUF3456  87 kelkelkdkevkvdlgipselkdep.aevkelkkaCeelveeyEde 131
                                       +++k+  + e++ +l+   +  +e+  e+ + kk C+++v ey d+
  gi|488600843|ref|YP_007907314.1| 124 EKIKT--HDELREKLKTAVRNLAERiLELPDFKKRCHQMVKEYNDN 167
                                       23333..44555566666677777889****************997 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                           DUF3456  97 vkvdlgipselkdepaevkelkkaCeelveeyEdeleelfke 138
                                       v      ++e+k+ ++ ++el k  +++v e ++e+ ++ ++
  gi|488600843|ref|YP_007907314.1| 223 V------KEEVKKVQELTDELLKILATIVSELDNEILKIWRK 258
                                       2......34555556888999999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1597  (0.0890736); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1523.42
//
Query:       gi|488600844|ref|YP_007907315.1|  [L=370]
Description: Micrococcal nuclease (thermonuclease)-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-24   86.2   3.5    3.5e-24   85.3   3.5    1.5  1  LTD             Lamin Tail Domain
      4e-22   78.7   0.0    5.7e-22   78.2   0.0    1.2  1  SNase           Staphylococcal nuclease homologue
  ------ inclusion threshold ------
          1    7.8  11.9        1.9    6.8   7.5    2.0  2  Neisseria_TspB  Neisseria meningitidis TspB protein
        1.5    9.4   5.9          2    9.0   0.6    3.1  3  RHS_repeat      RHS Repeat
        4.5    6.0   8.7       0.26   10.1   3.6    1.4  2  Nucleo_P87      Nucleopolyhedrovirus capsid protein P87


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 !   85.3   3.5   9.8e-28   3.5e-24       2     110 ..     259     370 .]     258     370 .] 0.96

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 9.8e-28
                               LTD   2 aaaagdvvIsevmedgagnnan....efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgt 73 
                                       +a++++v +  +++d+agn++     e+v ++N++ ++++L+gw l+d++g+ y+fp+   t  +ge+v v++gsgt
  gi|488600844|ref|YP_007907315.1| 259 TASTATVDFYYIHYDAAGNDQYnlndEYVVIANNGAASINLQGWVLQDEAGHtYVFPSY--TFGPGEVVYVHTGSGT 333
                                       57888999999*****999998***********************************99..5*************** PP

                               LTD  74 tsasngskasssavwnnggdavaLydasgevvdsvgy 110
                                       ++a + +++s +a+wnn+gd+++L+da+g++ d v++
  gi|488600844|ref|YP_007907315.1| 334 DTAGHLYWGSDRAIWNNDGDTAYLFDAAGNLTDVVSW 370
                                       ***********************************98 PP

>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   1.6e-25   5.7e-22       1     107 [.     117     235 ..     117     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 1.6e-25
                                       EEEETTEE-STSSBTTT............TTSTTHHHHHHHHHHHHHHCSSEEEEE-S...SBSTTSEEEEEEEETT CS
                             SNase   1 kvrLvgidaPetakpkk............tvqpfgkeAkeflkklvlqkkvvvleldk...kkDkygrllayvylnk 62 
                                       +vr++gid+Peta  k+            +++ +g  Ak+++++++   k +++eld     +++ygrllay+y++ 
  gi|488600844|ref|YP_007907315.1| 117 RVRMLGIDTPETAASKNkpyeydditnlsCLAYWGLMAKQYTESKLE-GKYIYIELDPiarMRGYYGRLLAYIYYDS 192
                                       79***********99999*****************************.555555555559889************** PP

                                       EEHHHHHHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGGC CS
                             SNase  63 knineeLvkeGlArvyevyekneekkkellkaeeeAkkkrkglWs 107
                                       +++ +eLvk+G+Arvy+  e n+e++ e+ +++  A ++ +glW 
  gi|488600844|ref|YP_007907315.1| 193 TDFTAELVKQGYARVYT--EGNFERESEYVAYQSTAMENSVGLWT 235
                                       **************776..4489*********************7 PP

>> Neisseria_TspB  Neisseria meningitidis TspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   7.5   0.00054       1.9     334     390 ..      25      82 ..      15      87 .. 0.84
   2 ?    3.1   0.1    0.0076        27     298     339 ..     214     255 ..     200     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00054
                    Neisseria_TspB 334 saeapnaqplpevspaenpannpdpdenpgtrpnpepdpdlnpdanpd.tdgqpgtrp 390
                                       s ++p   p p ++p   p+ +  p + p t+p p   p + p a p  t  qp  +p
  gi|488600844|ref|YP_007907315.1|  25 SIQTPTPTPTPAITPMHTPTPQHTPTQMPATTPTPMHTPHMTPTATPSlTPWQPSETP 82 
                                       6778999999999999999999999999999999999999999999974566777665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0076
                    Neisseria_TspB 298 drngnpvqvvatfgrdaqgnttvdvqviprpdltpasaeapn 339
                                       +r+ + v   +t   ++ g  t+ v+v   p ltpas+ +p 
  gi|488600844|ref|YP_007907315.1| 214 ERESEYVAYQSTAMENSVGLWTCSVEVASTPTLTPASTPTPT 255
                                       566777778888889999*******************98875 PP

>> RHS_repeat  RHS Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.2   1.1e+04      20      24 ..     136     140 ..     128     144 .. 0.82
   2 ?    1.7   0.1      0.11   3.8e+02      21      27 ..     271     277 ..     256     277 .. 0.76
   3 ?    9.0   0.6   0.00055         2       2      29 ..     334     365 ..     334     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.2
                        RHS_repeat  20 YtYDa 24 
                                       Y+YD+
  gi|488600844|ref|YP_007907315.1| 136 YEYDD 140
                                       99996 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                        RHS_repeat  21 tYDaqGr 27 
                                       +YDa+G+
  gi|488600844|ref|YP_007907315.1| 271 HYDAAGN 277
                                       8999997 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00055
                        RHS_repeat   2 DaaGrL.....tevtdpsGrvttYtYDaqGrlt 29 
                                       D aG+L     +++ + +G++ +Y  Da+G+lt
  gi|488600844|ref|YP_007907315.1| 334 DTAGHLywgsdRAIWNNDGDT-AYLFDAAGNLT 365
                                       56777777777889999**99.**********9 PP

>> Nucleo_P87  Nucleopolyhedrovirus capsid protein P87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.6   7.3e-05      0.26     297     361 ..      23      83 ..      12     140 .. 0.62
   2 ?   -3.0   0.2      0.66   2.4e+03     333     354 ..     241     261 ..     212     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.3e-05
                        Nucleo_P87 297 eqslqspaqtpapers.lqsPeqtparrkstkmteeslqsPaqtpawqtpattptretssdteaik 361
                                       + s+q+p++tp+p +  +++P+++++ ++ +  t++ + +P+ tp+ +tp  tp +      e+++
  gi|488600844|ref|YP_007907315.1|  23 KISIQTPTPTPTPAITpMHTPTPQHTPTQMPATTPTPMHTPHMTPT-ATPSLTPWQ----PSETPT 83 
                                       5688888888885542234443333335555556666666666665.555555443....333333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.66
                        Nucleo_P87 333 lqsPaqtpawqtpattptrets 354
                                         +P+ tpa +tp++tpt++ s
  gi|488600844|ref|YP_007907315.1| 241 ASTPTLTPA-STPTPTPTNTAS 261
                                       457777887.778888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2431.04
//
Query:       gi|488600845|ref|YP_007907316.1|  [L=204]
Description: hypothetical protein Asulf_01332 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-17   63.5   0.4    3.1e-17   62.5   0.2    1.6  1  DUF553    Transglutaminase-like domain


Domain annotation for each model (and alignments):
>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.2   1.7e-21   3.1e-17      63     149 ..       8      89 ..       2      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.7e-21
                            DUF553  63 lietpkeilktkkgiCrDYaiLTaalLlnl.niskvylvsvtfenskvgHaavavkidgtyfvlDqklpiikideyl 138
                                       ++ + k  ++++ ++CrDYa+LTa lL+nl   s++y++s+        H+a+ +k++ ++++lDqklp++++d +l
  gi|488600845|ref|YP_007907316.1|   8 RVDKGKPYIEYRLAMCRDYAKLTAVLLHNLfPNSQIYFISIP------WHVAAGIKVNKKLYILDQKLPVLTLDAWL 78 
                                       5556677899*******************8446788999988......7**************************** PP

                            DUF553 139 kkllkkvkiit 149
                                         + +++  i 
  gi|488600845|ref|YP_007907316.1|  79 RVWNRRTATIY 89 
                                       77666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1329.00
//
Query:       gi|488600846|ref|YP_007907317.1|  [L=181]
Description: putative nucleotidyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-10   40.9   0.0    3.6e-10   40.0   0.0    1.5  1  NTP_transf_2   Nucleotidyltransferase domain
    1.4e-08   34.7   0.0    2.5e-08   33.9   0.0    1.5  1  Polbeta        Polymerase beta, Nucleotidyltransferase
     0.0012   18.7   0.1     0.0033   17.3   0.1    1.7  1  MarR           MarR family
     0.0034   17.3   0.0      0.005   16.8   0.0    1.4  1  Adenyl_cycl_N  Adenylate cyclase NT domain
     0.0041   17.0   0.2      0.007   16.2   0.2    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.011   15.5   0.0       0.04   13.8   0.0    2.0  3  HTH_5          Bacterial regulatory protein, arsR family
      0.011   15.6   0.2      0.026   14.4   0.2    1.5  1  MarR_2         MarR family
      0.028   14.2   0.0      0.064   13.0   0.0    1.7  1  MdcG           Phosphoribosyl-dephospho-CoA transferase MdcG
      0.032   14.3   0.0      0.055   13.5   0.0    1.4  1  KorB           KorB domain
      0.032   14.2   0.0      0.058   13.4   0.0    1.4  1  HTH_29         Winged helix-turn helix
      0.069   13.6   0.0       0.15   12.5   0.0    1.6  1  DUF1697        Protein of unknown function (DUF1697)


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 !   40.0   0.0   2.2e-13   3.6e-10       9      80 ..      90     153 ..      79     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.2e-13
                                       HHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                      NTP_transf_2   9 kelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80 
                                       +e    ++++ ++GS+ +G+++++SDiD+ + ++++        g+++ a+i+ +l+  lg +v++++ ++ +
  gi|488600846|ref|YP_007907317.1|  90 RE--EwIVSLGVYGSFSKGENREDSDIDIWIRVDSH-------PGEKEVARIERELSNELGKRVHILILTPER 153
                                       23..369*****************************.......889********************9777665 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.5e-11   2.5e-08      11      70 ..      92     150 ..      80     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.5e-11
                                       HHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT CS
                           Polbeta  11 keielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln 70 
                                       + i  + ++GS+ kg+ re+SDiD+ + ++++   +e ++++ el++  lgk+v +++l 
  gi|488600846|ref|YP_007907317.1|  92 EWIVSLGVYGSFSKGENREDSDIDIWIRVDSHPGEKEVARIERELSNE-LGKRVHILILT 150
                                       46788889****************************************.99***999987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1     2e-06    0.0033       4      52 ..      11      59 ..       9      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                       ++++L+ + e+++  v e a  l  sk+ v+ +l+ Le++G ++++k 
  gi|488600846|ref|YP_007907317.1| 11 ERIETLEFILEREAVGVEEVATSLRRSKGFVSQFLRLLEEEGILRKQKR 59
                                      6778999999************************************986 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.1e-06     0.005      80     134 ..      82     136 ..      52     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.1e-06
                     Adenyl_cycl_N  80 ekekkekakeaaieglylmGStgsiaqsekSDlDiWvchrselsaeelelLekKl 134
                                        +++  k++e  i +l + GS++     e+SD+DiW+ ++s+  ++e++++e+ l
  gi|488600846|ref|YP_007907317.1|  82 LQTSLVKHREEWIVSLGVYGSFSKGENREDSDIDIWIRVDSHPGEKEVARIEREL 136
                                       333344446778999999999999999**************99999999988754 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   0.2   4.3e-06     0.007      12      62 ..      14      64 ..       7      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.3e-06
                                      CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                              TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62
                                      ++   +l+++   ++e+a  l +++  v + Lr Le+ G+ +++k+++ + 
  gi|488600846|ref|YP_007907317.1| 14 ETLEFILEREAVGVEEVATSLRRSKGFVSQFLRLLEEEGILRKQKRKYAVL 64
                                      5666789**************************************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 ?   13.8   0.0   2.4e-05      0.04      16      47 .]      25      56 ..      10      56 .. 0.81
   2 ?   -3.2   0.0       5.1   8.2e+03      20      27 ..     135     142 ..     134     143 .. 0.83
   3 ?   -3.2   0.0         5   8.2e+03      15      23 ..     162     170 ..     157     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                        v e a  l+ s++ vS+ L+ L+e+G+++k
  gi|488600846|ref|YP_007907317.1| 25 VGVEEVATSLRRSKGFVSQFLRLLEEEGILRK 56
                                      558899999********************976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                                       HHHHHHTS CS
                             HTH_5  20 elaeelgl 27 
                                       el++elg+
  gi|488600846|ref|YP_007907317.1| 135 ELSNELGK 142
                                       89999986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5
                                       SEEHHHHHH CS
                             HTH_5  15 elcvcelae 23 
                                       +   cela+
  gi|488600846|ref|YP_007907317.1| 162 PIFYCELAN 170
                                       556799997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.6e-05     0.026      10      54 ..      15      57 ..       8      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       L ++  r+   + v e+a  l+ sk+ vs+ l+ L++ G ++++
  gi|488600846|ref|YP_007907317.1| 15 TLEFILEREA--VGVEEVATSLRRSKGFVSQFLRLLEEEGILRKQ 57
                                      6889999998..99**************************99987 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.9e-05     0.064     127     173 ..     109     155 ..      52     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                              MdcG 127 hesSDLDLlirvasalqlarlldllaaleaaa.vrlDgeielpsggav 173
                                       +e+SD+D++irv+s+   ++++++ ++l++    r+ + i +p+    
  gi|488600846|ref|YP_007907317.1| 109 REDSDIDIWIRVDSHPGEKEVARIERELSNELgKRVHILILTPE-RIA 155
                                       89******************999999998885589999999888.444 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.4e-05     0.055       4      35 ..      25      56 ..      22      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                              KorB  4 vkqadIAkaLGksksfvslylklldvpdylre 35
                                      v ++++A  L +sk fvs++l ll+ +  lr+
  gi|488600846|ref|YP_007907317.1| 25 VGVEEVATSLRRSKGFVSQFLRLLEEEGILRK 56
                                      56789*******************99998886 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.6e-05     0.058       7      49 ..      20      59 ..      18      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                            HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrr 49
                                      l +e+v+ v ++A  l+ s+  v  +l++ ee+G+  l++++r
  gi|488600846|ref|YP_007907317.1| 20 LEREAVG-VEEVATSLRRSKGFVSQFLRLLEEEGI--LRKQKR 59
                                      6789**9.**************************6..544443 PP

>> DUF1697  Protein of unknown function (DUF1697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.5e-05      0.15      54      91 ..     126     163 ..     116     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.5e-05
                           DUF1697  54 aeleakiekaleeefgfevpvlvrtaeeleaivaanPf 91 
                                       ++  a+ie++l++e+g +v++l++t+e ++++ ++ P 
  gi|488600846|ref|YP_007907317.1| 126 EKEVARIERELSNELGKRVHILILTPERIARLRENDPI 163
                                       555689****************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1244.44
//
Query:       gi|488600847|ref|YP_007907318.1|  [L=146]
Description: putative conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   82.2   5.3    3.8e-23   81.9   5.3    1.1  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   5.3   2.1e-27   3.8e-23       2     117 ..      26     141 ..      25     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.1e-27
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHC..CHHHT...-HHHHHH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLle..elkkelkeseelree 76 
                                       ++ ++rAe+ le+Ae++l+++ yd+++  ++ a++++++A+l++ g++ +++ ++ + le  ++kk++  ++e+ + 
  gi|488600847|ref|YP_007907318.1|  26 RQSMKRAERWLEEAEKSLNNELYDSCLISSYLAMFHSARAVLYRDGWREKSHFCIARYLEemYVKKGKL-EREWVDL 101
                                       6789********************************************************999999998.******* PP

                                       HHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  77 leeLekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                       l++L++ ++  +Y+  ++  t+e+ae+al++a e++e +e+
  gi|488600847|ref|YP_007907318.1| 102 LDRLRETRHADQYDVSYFA-TREEAESALNIAFEFVERMEK 141
                                       ******************8.****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1006.97
//
Query:       gi|488600848|ref|YP_007907319.1|  [L=106]
Description: hypothetical protein Asulf_01335 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0032   17.0   0.0     0.0039   16.7   0.0    1.2  1  AHJR-like       REase_AHJR-like
     0.0041   17.3   0.0     0.0059   16.8   0.0    1.1  1  Tn7_Tnp_TnsA_N  TnsA endonuclease N terminal


Domain annotation for each model (and alignments):
>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.4e-07    0.0039       7      68 ..      12      76 ..       7     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.4e-07
                         AHJR-like  7 elererleslaeqyrekGye..vllhPnredlPdfLksYrpDliar.kdeeaviiEvksrrssas 68
                                      + ++e++++la+ yr +  +  v+++ +    P  ++s+rpD+i+  ++  + iiE+ ++ +   
  gi|488600848|ref|YP_007907319.1| 12 TEHDEAVKKLASRYRRQHPSatVYADASGFLKPRMIGSHRPDIIVVfRNGRGRIIEIETEDTINT 76
                                      568999*********99765115556666677**********99753888999****99887433 PP

>> Tn7_Tnp_TnsA_N  TnsA endonuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.5e-07    0.0059       5      86 ..      24     100 ..      22     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.5e-07
                    Tn7_Tnp_TnsA_N   5 direQ.PltlqiakelgikhpkvrevpsvmtpDfLvtlkdstgeellavevKyseeleeertrekleiereyweekg 80 
                                        +r Q P    +a+ +g+ +p   ++   + pD++v ++++   +  ++e+ +++ ++ e  r + +  r y++ kg
  gi|488600848|ref|YP_007907319.1|  24 RYRRQhPSATVYADASGFLKP---RMIGSHRPDIIVVFRNG---RGRIIEIETEDTINTEHARAQARSFRGYANLKG 94 
                                       5899*****************...88899***********9...556****************************** PP

                    Tn7_Tnp_TnsA_N  81 ipfrii 86 
                                       ++f ++
  gi|488600848|ref|YP_007907319.1|  95 FKFDVF 100
                                       ***875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 633.72
//
Query:       gi|488600849|ref|YP_007907320.1|  [L=152]
Description: hypothetical protein Asulf_01336 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 1020.00
//
Query:       gi|488600850|ref|YP_007907321.1|  [L=76]
Description: hypothetical protein Asulf_01337 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 511.09
//
Query:       gi|488600851|ref|YP_007907322.1|  [L=55]
Description: hypothetical protein Asulf_01338 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.025   14.5   0.0    1.2  1  MORN      MORN repeat


Domain annotation for each model (and alignments):
>> MORN  MORN repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-06     0.025       7      23 .]       4      20 ..       2      20 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-06
                              MORN  7 nGkrhGkGvytwpdGdr 23
                                      +Gk hGkGv + ++G++
  gi|488600851|ref|YP_007907322.1|  4 KGKAHGKGVAYDANGSV 20
                                      69*************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 348.20
//
Query:       gi|488600852|ref|YP_007907323.1|  [L=246]
Description: hypothetical protein Asulf_01339 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   21.3   0.5    0.00077   19.3   0.1    2.3  2  HTH_5        Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.035   14.2   0.0    1.6  1  HTH_20       Helix-turn-helix domain
       0.05   13.5   0.0      0.083   12.8   0.0    1.4  1  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
      0.063   13.8   0.2        1.8    9.1   0.0    3.1  3  HTH_27       Winged helix DNA-binding domain
      0.071   13.0   0.7       0.22   11.4   0.1    2.1  2  TrmB         Sugar-specific transcriptional regulator TrmB


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 ?   -1.3   0.0      0.58   2.1e+03      14      27 ..      42      55 ..      29      59 .. 0.61
   2 !   19.3   0.1   2.2e-07   0.00077      22      46 ..     183     207 ..     183     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.58
                                      SSEEHHHHHHHHTS CS
                             HTH_5 14 gelcvcelaeelgl 27
                                      ge+++ e + el++
  gi|488600852|ref|YP_007907323.1| 42 GEKKARETVYELKK 55
                                      66666666666654 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.2e-07
                                       HHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  22 aeelglsqstvShHLkkLreaGLVe 46 
                                       +e++++ +s vShH +kL++aG V 
  gi|488600852|ref|YP_007907323.1| 183 SEKFKKERSRVSHHISKLEKAGAVI 207
                                       6899******************886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.8e-06     0.035      38      61 .]     190     213 ..     154     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.8e-06
                                       HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  38 kntlsyHLrvLeeagLvevvregr 61 
                                       ++ +s+H+ +Le+ag+v  v++gr
  gi|488600852|ref|YP_007907323.1| 190 RSRVSHHISKLEKAGAVIKVKSGR 213
                                       6679*************9999987 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.3e-05     0.083      58     121 ..      62     121 ..      44     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                       Cas_APE2256  58 ieklsdlgreeFreglrnLveklarevknkkregekvlinaTgGfKpeiavltlvallladevy 121
                                        ++++  ++ +  ++  +L++ ++re    k eg+ v+ina+g++   +++ +++a + +++++
  gi|488600852|ref|YP_007907323.1|  62 EVEVARIDKRNVIRAAMQLIDIIKRE----KAEGNDVIINASGSLRTLAVAGYIAACVTSSRIF 121
                                       45555555555555555566555555....89***************99999999998887776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.9   6.9e+03      34      44 ..      15      25 ..       9      26 .. 0.78
   2 ?   -2.3   0.0       1.8   6.4e+03      35      48 ..      98     111 ..      96     117 .. 0.83
   3 ?    9.1   0.0   0.00051       1.8      32      68 .]     190     223 ..     151     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                            HTH_27 34 hisyslkkLte 44
                                       i++s+++L e
  gi|488600852|ref|YP_007907323.1| 15 RIVESIRALRE 25
                                      57899999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                            HTH_27  35 isyslkkLtekGLv 48 
                                       +s sl+ L  +G++
  gi|488600852|ref|YP_007907323.1|  98 ASGSLRTLAVAGYI 111
                                       56799999999998 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00051
                            HTH_27  32 dshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                        s +s  ++kL+++G v +    +++r++r+ lT+ G
  gi|488600852|ref|YP_007907323.1| 190 RSRVSHHISKLEKAGAVIKV---KSGRNVRIILTPLG 223
                                       56778889*********666...778********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 ?   -2.1   0.1         1   3.7e+03      22      34 ..      47      59 ..      44      60 .. 0.66
   2 ?   11.4   0.1   6.1e-05      0.22      29      58 ..     183     212 ..     179     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                                      CCHHCHHCCCTTS CS
                              TrmB 22 patadeiaeelgv 34
                                      + t++e+ +el+v
  gi|488600852|ref|YP_007907323.1| 47 RETVYELKKELEV 59
                                      5677777777765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.1e-05
                                       CCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  29 aeelgvprskvYevLrsLedkGlVerekgr 58 
                                       +e+ + +rs+v   +++Le++G V ++k+ 
  gi|488600852|ref|YP_007907323.1| 183 SEKFKKERSRVSHHISKLEKAGAVIKVKSG 212
                                       688999********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1560.17
//
Query:       gi|488600853|ref|YP_007907324.1|  [L=79]
Description: hypothetical protein Asulf_01340 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 500.30
//
Query:       gi|488600854|ref|YP_007907325.1|  [L=339]
Description: hypothetical protein Asulf_01341 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-50  170.2   0.1    7.2e-50  169.8   0.1    1.2  1  RmuC       RmuC family
  ------ inclusion threshold ------
      0.012   15.9   0.3         55    4.2   0.0    4.0  4  YvfG       YvfG protein
       0.05   13.3   1.5        1.3    8.8   0.2    2.6  3  DUF713     Protein of unknown function (DUF713)
       0.16   12.3   1.6         14    6.2   0.0    3.8  4  FlaC_arch  Flagella accessory protein C (FlaC)
       0.24   11.6   0.9        8.2    6.7   0.0    3.1  3  XhlA       Haemolysin XhlA
       0.27   11.6   3.7        6.4    7.1   0.6    2.8  3  Muted      Organelle biogenesis, Muted-like protein
        6.3    7.3   6.8         30    5.1   0.6    3.1  3  Latarcin   Latarcin precursor


Domain annotation for each model (and alignments):
>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.8   0.1   2.8e-53   7.2e-50      34     271 ..      90     321 ..      50     337 .. 0.92

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 2.8e-53
                              RmuC  34 slkeqlkelqelneqlgdeaenLtkaLknsktrGnwGEvqLerilessgleegeeyetqvslkdeegelrpDvvvkl 110
                                        ++e l++l+e +++l+  +++L+++++ +++r ++GE+qLe +l+++ ++++ +++++       g   pD+ + +
  gi|488600854|ref|YP_007907325.1|  90 GIQEDLGKLKEASSDLKGITSDLKSMFQVKQARAKFGELQLEMLLKDIFPSKRLNFQKNIGA----G--IPDACILV 160
                                       4699*************************************************999888873....3..8******* PP

                              RmuC 111 pggkklviDsKvpleaYerlveaeddeereealkahaksvkkhikeLseKdYeele.sldyvlmFiPiEsayaeale 186
                                        +g++l+iDsK+ple+++++ eae++ee++++ ++++++v+khi+e++ K Y   e +ld+++mF+P++ ++  +++
  gi|488600854|ref|YP_007907325.1| 161 EEGRYLCIDSKFPLENFRKYSEAENAEEKSKYWNEFLRDVRKHIEEIKGK-YVGKEnTLDFAFMFVPSDVIFYHIVS 236
                                       **************************************************.998866******************** PP

                              RmuC 187 adpeLleealrkkVvlasPttLlalLrtvamlwrqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksy 263
                                       + pe++ ea ++ V+lasP+ L a+L++v+  ++ e+++++aeei++++  +   + ++g +le+l +++++a +++
  gi|488600854|ref|YP_007907325.1| 237 ESPEIAVEASKSGVILASPSVLPAYLNLVSARIKAEEISERAEEIQRKMDLMGGYIDELGSRLETLFRHINNAYNNV 313
                                       **********************************************************************9999999 PP

                              RmuC 264 dkavkkle 271
                                        ++ ++ +
  gi|488600854|ref|YP_007907325.1| 314 SRVQQSYT 321
                                       99554443 PP

>> YvfG  YvfG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.038        98      35      53 ..      61      79 ..      26      82 .. 0.86
   2 ?    4.2   0.0     0.021        55       9      36 ..     174     200 ..     169     207 .. 0.87
   3 ?   -1.2   0.0       1.1   2.7e+03      29      55 ..     258     284 ..     256     291 .. 0.82
   4 ?    2.8   0.0     0.058   1.5e+02      55      67 ..     303     315 ..     298     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.038
                                      HHHHHHHHHSSS-HHHHHH CS
                              YvfG 35 vvvssllaDrlaknavllk 53
                                      +v   +    +a+na+++k
  gi|488600854|ref|YP_007907325.1| 61 SVFENIFSSAIARNADVIK 79
                                      6778899999*******98 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.021
                                       HHHHHHHHHC-SS.S-CCHHHHHHHHHH CS
                              YvfG   9 ienlkeyieqneayedkiqalnaYYkvv 36 
                                       +en+++y e  +a e+k +  n + + v
  gi|488600854|ref|YP_007907325.1| 174 LENFRKYSEAENA-EEKSKYWNEFLRDV 200
                                       79***********.99999999998877 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHSSS-HHHHHHHH CS
                              YvfG  29 lnaYYkvvvssllaDrlaknavllkRi 55 
                                       l aY   v + + a+ ++  a+ ++R 
  gi|488600854|ref|YP_007907325.1| 258 LPAYLNLVSARIKAEEISERAEEIQRK 284
                                       668999999999999999999999885 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHH CS
                              YvfG  55 irhLeeaYqkvkr 67 
                                        rh+++aY+ v r
  gi|488600854|ref|YP_007907325.1| 303 FRHINNAYNNVSR 315
                                       69********987 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   3.8e+03     135     156 ..      86     106 ..      57     132 .. 0.56
   2 ?    8.8   0.2   0.00049       1.3      27      52 ..     187     212 ..     184     223 .. 0.88
   3 ?    2.7   0.0     0.036        92      72     110 ..     284     322 ..     257     325 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                            DUF713 135 ldeleldkekleelrelfskld 156
                                       l+el  + e+l +l+e+ s l+
  gi|488600854|ref|YP_007907325.1|  86 LKELGIQ-EDLGKLKEASSDLK 106
                                       4444443.44555555555444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00049
                            DUF713  27 eekEqewsdwlkklrepivklknrfs 52 
                                       eek + w+++l+++r++i ++k ++ 
  gi|488600854|ref|YP_007907325.1| 187 EEKSKYWNEFLRDVRKHIEEIKGKYV 212
                                       89*******************99986 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.036
                            DUF713  72 dleelqselsnLakkvlsaynkLeeafeklkelsekfed 110
                                       +++ +   + +L + + +++  +++a++++++++++++d
  gi|488600854|ref|YP_007907325.1| 284 KMDLMGGYIDELGSRLETLFRHINNAYNNVSRVQQSYTD 322
                                       555555667788899999999999999999999999988 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.19   4.8e+02      20      37 ..      27      44 ..      24      49 .. 0.82
   2 ?   -1.7   0.0       1.6   4.1e+03      25      34 ..     199     208 ..     188     210 .. 0.73
   3 ?    0.7   0.2      0.28   7.2e+02      16      36 ..     264     284 ..     260     288 .. 0.81
   4 ?    6.2   0.0    0.0053        14       6      50 ..     289     334 ..     284     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.19
                         FlaC_arch 20 kkeneelsksveelkenV 37
                                      ++++ + + ++eel+++V
  gi|488600854|ref|YP_007907325.1| 27 ERSLADFKVKIEELNQSV 44
                                      677788889999999998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                         FlaC_arch  25 elsksveelk 34 
                                       +++k +ee+k
  gi|488600854|ref|YP_007907325.1| 199 DVRKHIEEIK 208
                                       5666677665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.28
                         FlaC_arch  16 letvkkeneelsksveelken 36 
                                       l +++ + ee+s+  ee++++
  gi|488600854|ref|YP_007907325.1| 264 LVSARIKAEEISERAEEIQRK 284
                                       557788899*****9999876 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0053
                         FlaC_arch   6 EnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsn.q 50 
                                          +++l ++let+ + +++  ++v +++++  dl + Y ++sn +
  gi|488600854|ref|YP_007907325.1| 289 GGYIDELGSRLETLFRHINNAYNNVSRVQQSYTDLRGYYSTISNfD 334
                                       556789999*********************************9965 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.16     4e+02      33      49 ..      97     113 ..      88     116 .. 0.77
   2 ?   -1.3   0.1         1   2.6e+03      21      44 ..     184     207 ..     175     210 .. 0.56
   3 ?    6.7   0.0    0.0032       8.2       1      46 [.     273     318 ..     273     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                              XhlA  33 kiknleedlkklesnqk 49 
                                       k+k++  dlk ++s +k
  gi|488600854|ref|YP_007907325.1|  97 KLKEASSDLKGITSDLK 113
                                       78888888888888776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                              XhlA  21 dkleekaaeaeekiknleedlkkl 44 
                                       +  eek+    e +  + + ++++
  gi|488600854|ref|YP_007907325.1| 184 ENAEEKSKYWNEFLRDVRKHIEEI 207
                                       344555555555555555555555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0032
                              XhlA   1 eikerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                       ei er e+i++k d ++  +d+l  + ++    i n+ +++++ ++
  gi|488600854|ref|YP_007907325.1| 273 EISERAEEIQRKMDLMGGYIDELGSRLETLFRHINNAYNNVSRVQQ 318
                                       69999*******************************9999998876 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.2   5.7e+03      75      86 ..     106     117 ..      82     137 .. 0.54
   2 ?    7.1   0.6    0.0025       6.4     100     136 ..     183     219 ..     174     224 .. 0.85
   3 ?    4.1   0.0     0.021        53      44      88 ..     274     320 ..     263     331 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                             Muted  75 eaalekverllq 86 
                                       +  +++ + + q
  gi|488600854|ref|YP_007907325.1| 106 KGITSDLKSMFQ 117
                                       333333333322 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0025
                             Muted 100 qekeeerkaeweeflkelqekkeevDeefeekveelk 136
                                        e+ ee+ + w+efl+++++  ee+  ++  k+++l+
  gi|488600854|ref|YP_007907325.1| 183 AENAEEKSKYWNEFLRDVRKHIEEIKGKYVGKENTLD 219
                                       456789999******************9999999886 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.021
                             Muted  44 ikklvnelkeql..lpkclesmkenLselnkkleaalekverllqke 88 
                                       i++ ++e++ ++  +   ++++ ++L++l + +++a ++v+r++q  
  gi|488600854|ref|YP_007907325.1| 274 ISERAEEIQRKMdlMGGYIDELGSRLETLFRHINNAYNNVSRVQQSY 320
                                       44444455444411223456677888888888888888888888764 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.69   1.8e+03      28      52 ..      93     117 ..      77     136 .. 0.62
   2 ?    5.1   0.6     0.012        30      44      78 ..     174     208 ..     171     211 .. 0.86
   3 ?    3.8   0.2      0.03        76       5      37 ..     265     317 ..     263     334 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.69
                          Latarcin  28 emvnnlRkvqgRLeemvenlrkved 52 
                                       e++ +l++    L+ +  +l+ +++
  gi|488600854|ref|YP_007907325.1|  93 EDLGKLKEASSDLKGITSDLKSMFQ 117
                                       4444444455555555555554444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                          Latarcin  44 venlrkvedledtEEARgafkklkdkfkkmgeklk 78 
                                       +en rk  + e+ EE   +++++ ++++k +e++k
  gi|488600854|ref|YP_007907325.1| 174 LENFRKYSEAENAEEKSKYWNEFLRDVRKHIEEIK 208
                                       69*************99988888888888888877 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.03
                          Latarcin   5 VseeleaeeLdele....................rgainrklmemvnnlRkvq 37 
                                       Vs+ + aee+ e                       + ++r++ + +nn+ +vq
  gi|488600854|ref|YP_007907325.1| 265 VSARIKAEEISERAeeiqrkmdlmggyidelgsrLETLFRHINNAYNNVSRVQ 317
                                       88899999998876456666666666666665554555666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                     1071  (0.0597356); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2103.81
//
Query:       gi|488600855|ref|YP_007907326.1|  [L=513]
Description: putative hydrolase of the metallo-beta-lactamase superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   42.2   0.0    8.1e-06   25.5   0.0    2.6  3  Lactamase_B_2  Beta-lactamase superfamily domain
    1.8e-05   24.6   0.3    6.4e-05   22.8   0.1    2.0  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    0.00012   22.2   0.0    0.00031   20.8   0.0    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.03   14.2   0.0       0.29   11.0   0.0    2.3  2  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 !   25.5   0.0   1.8e-09   8.1e-06      31      73 ..      87     125 ..      81     143 .. 0.88
   2 !   13.7   0.0   7.2e-06     0.032      58     171 ..     163     274 ..     151     295 .. 0.81
   3 ?   -2.6   0.0       0.7   3.2e+03     153     200 ..     439     487 ..     434     488 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.8e-09
                                       EEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTT CS
                     Lactamase_B_2  31 idaVllthaHyDHlaglltlrelrpkklplyapkgvlavlean 73 
                                       ++aVll+haH+DH+ ++  l e    ++p++a+++++a+l+a 
  gi|488600855|ref|YP_007907326.1|  87 VEAVLLSHAHVDHCGNISLLDE----SIPVMASPMTMAILKAM 125
                                       79************98888888....499**********9986 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.2e-06
                                       EEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEE..CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEEC CS
                     Lactamase_B_2  58 lplyapkgvlavleanfvylaleeepavnvheldwgesfel..gdggleitatparhksgrrldrnagdtlGlrieg 132
                                        +++++ g+ ++l++ ++y   +e  + ++++l++g+  ++  ++  ++i + ++ h+           + ++++  
  gi|488600855|ref|YP_007907326.1| 163 RDFICTGGIPDELAKFMCYKPGQES-KNARKKLNPGNICHVndHNLSFDIDVYEVDHSIYG--------ATAYILW- 229
                                       5799***************999999.9**************55455566777888888777........8888887. PP

                                       TTEEEEEESS-S---......HHHHHHHCT-SEEEEE-S-SSTTH CS
                     Lactamase_B_2 133 ggkrvyyigDtgyip......eeigerlggadllllditayedde 171
                                       g+ +++y+gD           +e  +r +ga +l++++t+ + +e
  gi|488600855|ref|YP_007907326.1| 230 GDSAIAYTGDIRMHGkyadrsKEFIKRAKGASVLIIEGTRASRNE 274
                                       999********955555547777889*************998877 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.7
                                       HHCT-SEEEEE-S-SSTTHHHH...HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 153 rlggadllllditayeddemir...hmgHltpeeaveaaadlgakrlvliH 200
                                       r++g++++l d +++ +   ir     gH++ ++   +++++++ + +++H
  gi|488600855|ref|YP_007907326.1| 439 RVYGFEMVL-DNGRLVPSF-IRgfhASGHASKGDLRWVIEQIDPDVIIPVH 487
                                       667777666.888888854.5568888999999999999999999999999 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.6   7.2e+03       6      21 ..      85     101 ..      82     107 .. 0.65
   2 !   22.8   0.1   1.4e-08   6.4e-05      11      41 ..     460     490 ..     454     492 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                             RMMBL   6 arieeid.fSgHadkne 21 
                                       + +e +    +H d+ +
  gi|488600855|ref|YP_007907326.1|  85 LNVEAVLlSHAHVDHCG 101
                                       56677776778888755 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.4e-08
                             RMMBL  11 idfSgHadknellelirklkprnvilvHGee 41 
                                       ++ SgHa k +l+ +i+++ p  +i+vH e 
  gi|488600855|ref|YP_007907326.1| 460 FHASGHASKGDLRWVIEQIDPDVIIPVHTEN 490
                                       778*************************995 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     7e-08   0.00031      40      67 ..      82     109 ..      62     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7e-08
                                       SGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                       Lactamase_B  40 lkpkdvdavilTHlHlDHiGglgglvea 67 
                                       ++ ++v+av+l+H+H+DH+G+   l e 
  gi|488600855|ref|YP_007907326.1|  82 YPKLNVEAVLLSHAHVDHCGNISLLDES 109
                                       67899***************99888776 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 ?   11.0   0.0   6.5e-05      0.29      31      70 ..      81     118 ..      10     146 .. 0.77
   2 ?    0.4   0.0      0.12   5.2e+02     150     163 .]     474     487 ..     466     487 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.5e-05
                     Lactamase_B_3  31 eppaeeaDlvlisqaledHahletlkqlaenvkvleeges 70 
                                        +p+ ++++vl+s+a+ dH+    l    e ++v++++ +
  gi|488600855|ref|YP_007907326.1|  81 IYPKLNVEAVLLSHAHVDHCGNISLLD--ESIPVMASPMT 118
                                       45779***************7655544..67777777655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                     Lactamase_B_3 150 lakrLkpklvlPmh 163
                                       ++++++p++++P+h
  gi|488600855|ref|YP_007907326.1| 474 VIEQIDPDVIIPVH 487
                                       7899********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 2780.93
//
Query:       gi|488600856|ref|YP_007907327.1|  [L=47]
Description: hypothetical protein Asulf_01343 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 299.24
//
Query:       gi|488600857|ref|YP_007907328.1|  [L=59]
Description: hypothetical protein Asulf_01344 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.6      0.069   13.1   0.1    2.1  2  TPR_10    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.019   15.3   0.3       0.22   11.9   0.1    1.9  2  TPR_12    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0014        12      24      40 ..       1      17 [.       1      21 [. 0.90
   2 !   13.1   0.1   7.7e-06     0.069       6      30 ..      28      52 ..      23      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0014
                            TPR_10 24 lleealairrrllGpdH 40
                                      +le+a+ i r+l++ d+
  gi|488600857|ref|YP_007907328.1|  1 MLEDAYTIMRELYEKDP 17
                                      68***********9886 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.7e-06
                            TPR_10  6 nNLanalrqrgrydeAealleeala 30
                                       N +  +++ +r++e +++l++al+
  gi|488600857|ref|YP_007907328.1| 28 LNFGTFYYEAYRLKETLRYLRKALE 52
                                      699********************96 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     0.029   2.6e+02      26      40 ..       2      16 ..       1      20 [. 0.81
   2 ?   11.9   0.1   2.4e-05      0.22       2      32 ..      23      53 ..      22      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.029
                            TPR_12 26 lekaleiarrllGpd 40
                                      le a+ i+r+l+++d
  gi|488600857|ref|YP_007907328.1|  2 LEDAYTIMRELYEKD 16
                                      788999999999876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.4e-05
                            TPR_12  2 vatalnnlaavlrrlgrydeAlellekalei 32
                                       a+++ n +++++++ r+ e l++l+kale 
  gi|488600857|ref|YP_007907328.1| 23 FAIMALNFGTFYYEAYRLKETLRYLRKALEH 53
                                      578888***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 388.31
//
Query:       gi|488600858|ref|YP_007907329.1|  [L=834]
Description: hypothetical protein Asulf_01345 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   52.4   0.0    4.7e-08   33.1   0.0    3.3  3  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-06   29.1   0.4    0.00023   21.6   0.0    3.3  2  AAA              ATPase family associated with various cellul
    1.6e-05   25.2   0.0    0.00051   20.3   0.0    3.2  3  AAA_22           AAA domain
    0.00017   21.1   0.0    0.00045   19.8   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
     0.0006   19.6   0.0     0.0013   18.4   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0034   17.1   0.1      0.012   15.4   0.0    2.0  2  AAA_24           AAA domain
     0.0041   17.7   0.1      0.024   15.2   0.0    2.4  1  AAA_18           AAA domain
     0.0079   16.2   0.1       0.57   10.2   0.0    3.5  3  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.049   13.1   0.0    1.6  1  PhoH             PhoH-like protein
      0.028   13.8   0.0        0.1   11.9   0.0    1.9  2  ATPase           KaiC
      0.028   14.0   0.0      0.061   12.9   0.0    1.5  1  AAA_25           AAA domain
       0.03   14.7   0.0       0.22   11.9   0.0    2.4  2  AAA_16           AAA ATPase domain
      0.031   14.5   0.0      0.075   13.2   0.0    1.6  1  AAA_33           AAA domain
      0.044   13.5   0.0        0.1   12.3   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
      0.048   14.3   0.0       0.11   13.2   0.0    1.5  1  TPR_16           Tetratricopeptide repeat
      0.065   13.0   0.0       0.22   11.2   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.068   12.5   0.0       0.14   11.5   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.078   12.9   0.0        0.2   11.6   0.0    1.7  1  NACHT            NACHT domain
      0.092   13.1   0.1        2.3    8.5   0.0    2.9  3  AAA_19           AAA domain
       0.11   12.5   0.0       0.29   11.2   0.0    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.11   13.0   0.0       0.38   11.2   0.0    1.9  1  ABC_tran         ABC transporter
       0.11   12.8   0.0        0.3   11.5   0.0    1.7  1  RNA_helicase     RNA helicase
        0.4   11.1   2.0        2.5    8.5   0.0    2.9  2  Ribosomal_S13    Ribosomal protein S13/S18
       0.41   11.0   6.1        1.1    9.6   0.9    3.6  3  DUF349           Domain of Unknown Function (DUF349)


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.3   5.5e+03      12      34 ..     110     132 ..     104     179 .. 0.57
   2 !   15.6   0.0   1.7e-05     0.012       2      19 ..     363     380 ..     362     395 .. 0.91
   3 !   33.1   0.0   6.4e-11   4.7e-08      65     138 .]     622     700 ..     537     700 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.3
                                       HHHHHHHGGGGBS--EEEEE--T CS
                             AAA_5  12 Kselaerlaaalnreveyvqltr 34 
                                       K +++  la++l+ ++++ +++r
  gi|488600858|ref|YP_007907329.1| 110 KVTVISTLAHVLKPNWFIPLNHR 132
                                       44555555555555555444443 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.7e-05
                                       EEEE--SSSSHHHHHHHG CS
                             AAA_5   2 vlLvGppGtgKselaerl 19 
                                       v+L GppGtgK++la+ +
  gi|488600858|ref|YP_007907329.1| 363 VILYGPPGTGKTWLAKNF 380
                                       9**************976 PP

  == domain 3  score: 33.1 bits;  conditional E-value: 6.4e-11
                                       G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---.............-EEEEEESS--.-TT-TTHH CS
                             AAA_5  65 egeilvlDEverae.sevlnsLlslleerrllleeggelvkaknddller.......frviatanpldrslnelspa 133
                                        +  l++DE++r + s ++++L++lle +++l++e+   v   +++  ++       +++i+t+n++drs + ++ a
  gi|488600858|ref|YP_007907329.1| 622 PKFFLIIDEINRGDiSRIFGELITLLEPDKRLFAENELIV-SLPYS--KTkfgippnLYIIGTMNTADRSIALIDVA 695
                                       67789***************************77665555.55554..224678999******************** PP

                                       HHTT- CS
                             AAA_5 134 lrsRf 138
                                       lr+Rf
  gi|488600858|ref|YP_007907329.1| 696 LRRRF 700
                                       ****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 !   21.6   0.0   3.1e-07   0.00023       1      37 [.     363     399 ..     363     454 .. 0.80
   2 ?    3.9   0.0     0.092        69      58     125 ..     621     701 ..     577     707 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.1e-07
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk 37 
                                       v+lyGppGtGKT lak  + e   e ++i  +++l++
  gi|488600858|ref|YP_007907329.1| 363 VILYGPPGTGKTWLAKNFVDENAPETYKIAKKDVLEN 399
                                       79*****************998777888887777744 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.092
                                       TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...................SSTEEEEEEESS... CS
                               AAA  58 kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkk...................eskvivigatnr... 111
                                       +p   l+iDEi +   sr          +  +L+t l+  k+                      ++ +ig+ n+   
  gi|488600858|ref|YP_007907329.1| 621 APkFFLIIDEINRGDISR----------IFGELITLLEPDKRLfaenelivslpysktkfgiPPNLYIIGTMNTadr 687
                                       354789999999987777..........88888888888888888888888888888889997789*****999666 PP

                                       .GGGSTHHHHSTTSS CS
                               AAA 112 .pdkldpallrgRfd 125
                                        +  +d al+ +Rf 
  gi|488600858|ref|YP_007907329.1| 688 sIALIDVALR-RRFG 701
                                       6667999999.6886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.2   1.7e+03      48      71 ..      13      43 ..       5      85 .. 0.70
   2 !   20.3   0.0   6.9e-07   0.00051       5      41 ..     360     387 ..     355     409 .. 0.80
   3 ?   -0.3   0.0       1.6   1.2e+03      80     114 ..     612     645 ..     535     659 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.2
                            AAA_22 48 psst..sskdllrellralglelka.....e 71
                                      ++++  +++++l ++ ++l +el++     +
  gi|488600858|ref|YP_007907329.1| 13 SEEKlaTWRKILDDVKNKLIEELEElkdsdY 43
                                      4444448888888888888888887543332 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 6.9e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                       ++ ++++G++GtGKT+l++++++++          pe
  gi|488600858|ref|YP_007907329.1| 360 KKQVILYGPPGTGKTWLAKNFVDEN---------APE 387
                                       56689*****************998.........333 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.6
                            AAA_22  80 ealeqalraravielliiDEaqhlrseealeeLrs 114
                                       +++   l+++ +  +liiDE+ + +  +++ eL +
  gi|488600858|ref|YP_007907329.1| 612 SKVGSSLNNAPK-FFLIIDEINRGDISRIFGELIT 645
                                       445555555555.799***9988432444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   6.1e-07   0.00045      26      64 ..     353     391 ..     344     396 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.1e-07
                             AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkldkekyls 64 
                                       l+++l++kk+v+l+Gp GtGKt ++k+++++  +e+y++
  gi|488600858|ref|YP_007907329.1| 353 LNKILNSKKQVILYGPPGTGKTWLAKNFVDENAPETYKI 391
                                       578999*********************999998899986 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 !   18.4   0.0   1.8e-06    0.0013      44      75 ..     357     388 ..     346     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavrag 75 
                                       +++k+ ++l Gp+G+GK++la  +  e + + 
  gi|488600858|ref|YP_007907329.1| 357 LNSKKQVILYGPPGTGKTWLAKNFVDENAPET 388
                                       678999***************99877766555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.9   5.1e+03      95     110 ..      37      53 ..      19      64 .. 0.55
   2 !   15.4   0.0   1.6e-05     0.012       2      23 ..     360     383 ..     359     399 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.9
                            AAA_24  95 k.edkgdgkGygelaee 110
                                       + +d  + +G++++ + 
  gi|488600858|ref|YP_007907329.1|  37 ElKDSDYERGWKDVLKL 53 
                                       13555666677666554 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.6e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakel..g 23 
                                       k+++++yGp+g+GKT lak++  +
  gi|488600858|ref|YP_007907329.1| 360 KKQVILYGPPGTGKTWLAKNFvdE 383
                                       7899****************9641 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   3.2e-05     0.024       1      78 [.     363     443 ..     363     462 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf...........gvnlrdvakenglllevdpe......aldeskrldedkldkl 60 
                                       ++l G+pG+GKt lak+  +++              +n+++ ++  +       +      +l+e k ++ ++  ++
  gi|488600858|ref|YP_007907329.1| 363 VILYGPPGTGKTWLAKNFVDEN-ApetykiakkdvLENVKFFWWSIN-------PrkwdytQLEEGKGIELWY-GQW 430
                                       79****************8884.346775555554555555555544.......3444444699999999999.999 PP

                            AAA_18  61 ldaleenssaleegknlv 78 
                                        +a+ee+s+     +++v
  gi|488600858|ref|YP_007907329.1| 431 KRAFEEISD-----GDIV 443
                                       999999987.....4444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       0.6   4.5e+02      45      77 ..     328     357 ..     317     363 .. 0.67
   2 !   10.2   0.0   0.00076      0.57       2      27 ..     360     385 ..     359     402 .. 0.78
   3 ?   -0.6   0.0       1.7   1.3e+03      61      75 ..     619     633 ..     595     641 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.6
                            AAA_14  45 kladpekllelileklkeekktylflDEiqevp 77 
                                       kl   ++l+e+il+k+ + ++t +++DE  ++ 
  gi|488600858|ref|YP_007907329.1| 328 KLG-IKDLIEEILNKI-P-EETNFVFDELNKIL 357
                                       333.336788888886.3.67789****98875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00076
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell 27 
                                       +k +++ G+  +GKT+l+k++++e+ 
  gi|488600858|ref|YP_007907329.1| 360 KKQVILYGPPGTGKTWLAKNFVDENA 385
                                       57799*****************9998 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.7
                            AAA_14  61 keekktylflDEiqe 75 
                                       ++  k +l++DEi +
  gi|488600858|ref|YP_007907329.1| 619 NNAPKFFLIIDEINR 633
                                       3356889*****976 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.5e-05     0.049      13      37 ..     354     378 ..     345     383 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                                       HHHHHH-SEEEEE--TTSSTTHHHH CS
                              PhoH  13 lealkkndivfaiGpaGtGKtylav 37 
                                        ++l++++ v+  Gp GtGKt+la 
  gi|488600858|ref|YP_007907329.1| 354 NKILNSKKQVILYGPPGTGKTWLAK 378
                                       56788999***************95 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.7   3.5e+03     143     176 ..     245     276 ..     236     285 .. 0.82
   2 ?   11.9   0.0   0.00014       0.1      14      46 ..     355     387 ..     344     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.7
                            ATPase 143 ilrqlvrvlkklgvTailvsekssseeaaggygv 176
                                         +ql ++lk+     i++s++  + +++ g g+
  gi|488600858|ref|YP_007907329.1| 245 SYHQLWKFLKEVSKGDIIISNR--GRKSIIGIGI 276
                                       5689999************995..6677777776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                            ATPase  14 gGipegrvvlitGepGtGKtifalqFlikgaek 46 
                                         + +++ v ++G pGtGKt +a++F+ + a +
  gi|488600858|ref|YP_007907329.1| 355 KILNSKKQVILYGPPGTGKTWLAKNFVDENAPE 387
                                       5567889999****************9877655 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   8.1e-05     0.061      29      55 ..     356     382 ..     331     461 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-05
                            AAA_25  29 llpagelallaGapgtGKttlaldlal 55 
                                       +l  ++ ++l+G+pgtGKt+la + + 
  gi|488600858|ref|YP_007907329.1| 356 ILNSKKQVILYGPPGTGKTWLAKNFVD 382
                                       66778889*************977665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.22      25      46 ..     361     382 ..     344     404 .. 0.78
   2 ?   -2.1   0.0       5.8   4.3e+03     121     147 ..     609     634 ..     564     651 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                            AAA_16  25 elvllsGesGvGKsslvrellr 46 
                                         v+l+G++G+GK+ l++ + +
  gi|488600858|ref|YP_007907329.1| 361 KQVILYGPPGTGKTWLAKNFVD 382
                                       6799************988765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.8
                            AAA_16 121 ellkrllallsrderplvlvlDdlqwa 147
                                       ++l++  + l + ++++ l++D++ + 
  gi|488600858|ref|YP_007907329.1| 609 DELSKVGSSLNN-APKFFLIIDEINRG 634
                                       455555555566.55699999988765 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    0.0001     0.075       2      34 ..     363     397 ..     363     436 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlr 34 
                                       v+l G+pG+GK+ la++ + +++  ++ +++ +++
  gi|488600858|ref|YP_007907329.1| 363 VILYGPPGTGKTWLAKNFVDENApeTYKIAKKDVL 397
                                       7899***************9998663334444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014       0.1      10      46 ..     348     384 ..     341     396 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  10 elleqikkvaktdlsvlitGesGtGKellaraiheas 46 
                                        ++++++k+ +++ +v++ G  GtGK+ la+   +++
  gi|488600858|ref|YP_007907329.1| 348 FVFDELNKILNSKKQVILYGPPGTGKTWLAKNFVDEN 384
                                       5788999***********************9877655 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00014      0.11       7      40 ..     147     177 ..     145     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllll 40 
                                       +++ +++++A++++++ lk+     d ++A+++l
  gi|488600858|ref|YP_007907329.1| 147 LANTKNFEEAVNVFQQILKKE---RDLVRASYAL 177
                                       567799***************...9999999988 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.22      31      56 ..     358     383 ..     339     401 .. 0.74
   2 ?   -1.9   0.0       3.3   2.5e+03     135     156 ..     682     703 ..     610     706 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiake 56 
                                       ++   v+lyGpPG Gkt lak   +e
  gi|488600858|ref|YP_007907329.1| 358 NSKKQVILYGPPGTGKTWLAKNFVDE 383
                                       566789*************9755444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                            RuvB_N 135 lvgattragllssPlrdrfgiv 156
                                       + +a    +l+   lr rfg++
  gi|488600858|ref|YP_007907329.1| 682 MNTADRSIALIDVALRRRFGFI 703
                                       3334444566677777777765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.14      23      42 ..     361     380 ..     356     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                      Mg_chelatase  23 HnlllvGppGsGKtmlakrl 42 
                                        +++l+GppG+GKt lak +
  gi|488600858|ref|YP_007907329.1| 361 KQVILYGPPGTGKTWLAKNF 380
                                       679**************986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00027       0.2       2      28 ..     362     388 ..     361     401 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegk 28 
                                       +vil G++G GKT L++ ++++ a ++
  gi|488600858|ref|YP_007907329.1| 362 QVILYGPPGTGKTWLAKNFVDENAPET 388
                                       699*****************9877665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0031       2.3       9      31 ..     359     381 ..     353     392 .. 0.83
   2 ?   -0.1   0.0       1.5   1.1e+03     101     132 ..     621     653 ..     527     655 .. 0.54
   3 ?   -1.0   0.0       2.7     2e+03     109     128 ..     721     740 ..     693     745 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhiv 31 
                                       ++k +++ ++pGtGKT + k  v
  gi|488600858|ref|YP_007907329.1| 359 SKKQVILYGPPGTGKTWLAKNFV 381
                                       578899**********8877665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                            AAA_19 101 qeeellivDEfqdvd..elqyrLlkallgekkkl 132
                                         ++ li+DE+   d      +L+  l  ++k+l
  gi|488600858|ref|YP_007907329.1| 621 APKFFLIIDEINRGDisRIFGELITLLE-PDKRL 653
                                       2345999999975444155566665555.44445 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.7
                            AAA_19 109 DEfqdvdelqyrLlkallge 128
                                       DE+ d++el+ ++lkal ++
  gi|488600858|ref|YP_007907329.1| 721 DEAGDIKELAISVLKALNER 740
                                       99**************9854 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   0.00038      0.29       5      42 ..     344     383 ..     341     393 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE   5 eetealgkklakal..gdvilLeGdLGaGKTtlvrglaka 42 
                                       eet+ +  +l k l  ++ ++L+G+ G+GKT l+++++ +
  gi|488600858|ref|YP_007907329.1| 344 EETNFVFDELNKILnsKKQVILYGPPGTGKTWLAKNFVDE 383
                                       5666777778887776788****************99875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00052      0.38       3      49 ..     352     396 ..     350     436 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00052
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdl 49 
                                       +++  l+  + v + G+ G+GK+ L+k +  +  p+  +i   +kd+
  gi|488600858|ref|YP_007907329.1| 352 ELNKILNSKKQVILYGPPGTGKTWLAKNFVDENAPETYKI--AKKDV 396
                                       56667899999*********************99988777..44444 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    0.0004       0.3       1      26 [.     363     388 ..     363     412 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++lyGp+g+GK+ lak+++++ + + 
  gi|488600858|ref|YP_007907329.1| 363 VILYGPPGTGKTWLAKNFVDENAPET 388
                                       689**************998876443 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2       1.1   8.4e+02      36      80 ..       2      47 ..       1      60 [. 0.75
   2 ?    8.5   0.0    0.0033       2.5      20      61 ..     576     621 ..     558     645 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                     Ribosomal_S13 36 dvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdGk 80
                                      d+++  r  +l+ee++ + ++i++  +++ i+++   +  d++ G 
  gi|488600858|ref|YP_007907329.1|  2 DLENLLRKYKLSEEKLATWRKILDDVKNKLIEELEeLKDSDYERGW 47
                                      5666677788999999998888888777778877767778888774 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0033
                     Ribosomal_S13  20 ikGiGrrkakiilkkadvdedkrige....lteeeiekieeivenk 61 
                                        kGi r + +++l++a+v+++ r+ge    lte+e++k+   ++n 
  gi|488600858|ref|YP_007907329.1| 576 FKGICRDAHNALLNHAGVEKEWRVGEnlptLTEDELSKVGSSLNNA 621
                                       69**********************9877779********9999993 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.9    0.0014       1.1      34      62 ..      27      57 ..       8      59 .. 0.88
   2 ?    1.4   0.0      0.55   4.1e+02      29      50 ..      72      93 ..      64     106 .. 0.78
   3 ?   -0.9   0.1       2.9   2.2e+03       4      22 ..     151     169 ..     148     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                            DUF349 34 kKealieeaealakstt..dwksatkrlkel 62
                                       K++liee+e+l++s+    wk+  k lke+
  gi|488600858|ref|YP_007907329.1| 27 VKNKLIEELEELKDSDYerGWKDVLKLLKEI 57
                                      69**********9995268999999999997 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.55
                            DUF349 29 eenlekKealieeaealakstt 50
                                       +n   +ea++e ++++++s+t
  gi|488600858|ref|YP_007907329.1| 72 LKNESTREAIVEFIKNIETSDT 93
                                      689999***********77742 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.9
                            DUF349   4 krFraacdafferrkahfe 22 
                                       k+F++a++ f + +k+ ++
  gi|488600858|ref|YP_007907329.1| 151 KNFEEAVNVFQQILKKERD 169
                                       5677777777776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      778  (0.0433934); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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: 0.91u 0.35s 00:00:01.26 Elapsed: 00:00:00.53
# Mc/sec: 4731.37
//
Query:       gi|488600859|ref|YP_007907330.1|  [L=437]
Description: McrBC 5-methylcytosine restriction system component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-62  209.6   0.1    7.5e-62  209.3   0.1    1.1  1  McrBC     McrBC 5-methylcytosine restriction system component
  ------ inclusion threshold ------
      0.014   15.9   0.1        0.7   10.5   0.0    2.5  2  CAAP1     Caspase activity and apoptosis inhibitor 1


Domain annotation for each model (and alignments):
>> McrBC  McrBC 5-methylcytosine restriction system component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.3   0.1   8.3e-66   7.5e-62       1     320 []      59     380 ..      59     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 209.3 bits;  conditional E-value: 8.3e-66
                             McrBC   1 lkagnyvGviqlksgaileIlPKlfendes...kelarklLlkmLsylknlrfkesslaalesaklpLseilillfl 74 
                                       +ka ny Gv ++ s   +eI PK+  +++s   k++    Ll+mL+y++ l+++++++a+l+  k +++e+++ lf+
  gi|488600859|ref|YP_007907330.1|  59 IKALNYAGVAKVGSI-KIEIIPKFLIGKDSeeiKPKVMSNLLQMLRYTRRLNIRKVEFAELDF-KSDFFEVFVHLFA 133
                                       6899*********77.*******9888887455555599999******************985.566********** PP

                             McrBC  75 qelqrllkkglyseYqsveenlsalkGrllvkeqlkknlaqkhkfeveydefsednaenRilksalelllkllrsse 151
                                       ++l +llk +  + Y++  ++l+++k r++  ++   n+a+ h++ + y e s d++ nR+lk++  l+l+l+rs+e
  gi|488600859|ref|YP_007907330.1| 134 KNLLNLLKVKHDRGYVRRYDELRFVKERIDT-RKYGANPAKLHRIPCIYHERSMDTPINRTLKYTSYLMLRLVRSRE 209
                                       ******************************9.78899**************************************** PP

                             McrBC 152 tlkelrellsilkevarskisekdlqkvqlnrlfarykkvlqlaevilknqsplakqgkqkalglLfdmeklFEeyv 228
                                       + + l++++sil+ v+ ++ s +  ++++++rl+a+++  ++++ ++l++ s + ++++ + ++l+++me lFEe++
  gi|488600859|ref|YP_007907330.1| 210 NYRLLKQIISILDPVELTPVSPDLVKRISFSRLNAEFEPFINFCWLFLRGCSLTLQASNVEFFSLMIPMERLFEEFI 286
                                       ***************************************************************************** PP

                             McrBC 229 aklLr.....kelskdakvktqeqskyllkaegeaefklkpDllikkkkeesivlDtKwKklekekakkkgisqsDl 300
                                        +++r        + +  + +q++  +l++++g+ +f+l+pD+ i+  +  + ++DtK+K l+ e ++++g+sq+Dl
  gi|488600859|ref|YP_007907330.1| 287 GEVIRdnpriVPENVRGSILIQKRIGHLATKNGKRKFELRPDIRIEGVG--KAIVDTKYKLLSLE-ERNYGVSQQDL 360
                                       *****9996555666778999**********************996665..6**********866.99********* PP

                             McrBC 301 YQllaYaqayqaeqgkLvYP 320
                                       YQ++aY++     +  L+YP
  gi|488600859|ref|YP_007907330.1| 361 YQMYAYCKESDTTKCLLIYP 380
                                       *******************9 PP

>> CAAP1  Caspase activity and apoptosis inhibitor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.025   2.2e+02      29      55 ..      76     102 ..      70     110 .. 0.88
   2 ?   10.5   0.0   7.8e-05       0.7      13      44 ..     212     243 ..     206     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.025
                             CAAP1  29 kllPdiLKklsleelkelCleqLegls 55 
                                       +++P++L + + ee+k + ++ L+++ 
  gi|488600859|ref|YP_007907330.1|  76 EIIPKFLIGKDSEEIKPKVMSNLLQML 102
                                       589********************9995 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.8e-05
                             CAAP1  13 elleqlFkvlkekklkkllPdiLKklsleelk 44 
                                        ll+q+ ++l + +l+   Pd +K +s++ l 
  gi|488600859|ref|YP_007907330.1| 212 RLLKQIISILDPVELTPVSPDLVKRISFSRLN 243
                                       69**************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2782.21
//
Query:       gi|488600860|ref|YP_007907331.1|  [L=29]
Description: hypothetical protein Asulf_01347 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-05   24.1   0.2    2.2e-05   24.1   0.2    1.0  1  UPF0175       Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
       0.12   11.7   0.6      0.094   12.0   0.6    1.0  1  V-ATPase_H_N  V-ATPase subunit H


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 !   24.1   0.2   2.5e-09   2.2e-05      52      75 .]       2      24 ..       1      24 [. 0.93

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.5e-09
                           UPF0175 52 elLarrgiplinydeeeleeDlet 75
                                      e+La+++ip ++yd+e+l+eD+et
  gi|488600860|ref|YP_007907331.1|  2 EILASKNIP-LQYDDEDLKEDIET 24
                                      89*******.7***********96 PP

>> V-ATPase_H_N  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6     1e-05     0.094     298     315 .]      12      29 .]       1      29 [] 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                      V-ATPase_H_N 298 kfsDeditedleyLkeeL 315
                                       +++Ded++ed+e+L++ L
  gi|488600860|ref|YP_007907331.1|  12 QYDDEDLKEDIETLEKLL 29 
                                       58************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (29 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 193.70
//
Query:       gi|488600861|ref|YP_007907332.1|  [L=45]
Description: hypothetical protein Asulf_01348 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); 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 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 312.53
//
Query:       gi|488600862|ref|YP_007907333.1|  [L=170]
Description: hypothetical protein Asulf_01349 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.088   12.7   0.0       0.17   11.8   0.0    1.4  1  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)


Domain annotation for each model (and alignments):
>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.5e-06      0.17      79     123 ..      87     132 ..      73     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.5e-06
                       Cas_APE2256  79 klarevknkkregekvlinaTgGfKpeiavltl.vallladevyYi 123
                                       k+++ ++  k++g++v+i +T G K+ +a +++ ++ ++ d+v+Y+
  gi|488600862|ref|YP_007907333.1|  87 KITSLIRDLKQNGYSVAIDVTPGRKALVAGALIpISKIGVDHVFYL 132
                                       5778899999****************877555438999999**996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1141.45
//
Query:       gi|488600863|ref|YP_007907334.1|  [L=335]
Description: hypothetical protein Asulf_01350 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-06   27.9   0.3    4.1e-06   27.1   0.3    1.4  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.3   2.3e-10   4.1e-06       3     125 ..     110     250 ..     108     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.3e-10
                             PIN_4   3 lDTnvlLhdpealksfkeehdvviPitVleELdklKkgsse....relarlarqanrlldelleke........... 64 
                                        DTn++ h + +  sf ++++v +  tV eE+++  + +       el++l++ +  llde ++k+           
  gi|488600863|ref|YP_007907334.1| 110 PDTNIIYHRFISNSSFFKQNEVLLVDTVKEEIEASLNYKYSphqiSELKSLVKYQEFLLDEWVNKRmkrsrkvayia 186
                                       6********************************98877777777966666666666666666555544444444444 PP

                             PIN_4  65 ........sgrlkvqtsaeelpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgi 125
                                               +  + ++ ++++ ++    se+nD+ I++ + ++++e+ +   vL++ D+ +    + +g+
  gi|488600863|ref|YP_007907334.1| 187 lreyktvrDLAVEIEGVEKSTND----SEHNDRIIIKSVRRFEKER-NVLPVLLTADVSMVDICELEGV 250
                                       43333322444444444444443....569***************8.89999******99766665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2061.96
//
Query:       gi|488600864|ref|YP_007907335.1|  [L=233]
Description: haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED/haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    2.4e-38  132.0   0.0    1.1  1  HAD_2            Haloacid dehalogenase-like hydrolase
    2.2e-18   67.3   0.4    4.7e-17   63.0   0.4    2.0  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.5e-12   47.4   0.0    3.4e-12   46.2   0.0    1.6  1  Hydrolase_like   HAD-hyrolase-like
    2.4e-08   34.6   0.1      3e-08   34.3   0.1    1.2  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.016   14.8   0.1        3.2    7.3   0.0    2.3  2  PGP_phosphatase  Mitochondrial PGP phosphatase
      0.019   15.1   0.0       0.16   12.1   0.0    2.4  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
      0.031   13.8   0.0          2    7.8   0.0    2.3  2  DUF705           Protein of unknown function (DUF705)
      0.054   13.3   0.0         15    5.4   0.0    2.8  2  Acid_PPase       Acid Phosphatase
      0.059   13.3   0.1       0.42   10.5   0.1    2.3  1  NT5C             5' nucleotidase, deoxy (Pyrimidine), cytosol


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 !  132.0   0.0   1.2e-41   2.4e-38       1     176 [.      20     200 ..      20     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 1.2e-41
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkli..glslrellrklgeseeeee.....kieellrkyn 70 
                                       +iFD+D+Tl d +e+ + a + ++e+ g +  +eeel +++  g++  e l+++++    ++     k+ee  r+y+
  gi|488600864|ref|YP_007907335.1|  20 VIFDMDNTLFDFVEAKLRACRAVVEHLGAG--DEEELLRYFlrGMHGFEDLENIADYMLDKGvysqeKYEECCRIYE 94 
                                       7***********************999775..44444444311444434444444433222255568********** PP

                             HAD_2  71 eekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekalek 147
                                       e k + +++py++v+e+Le L++ g+kl++vT+ ++  + + l++ g+ +yFdv+v++++++k+KP+p++i+ alek
  gi|488600864|ref|YP_007907335.1|  95 EVKLN-SIEPYPHVRETLERLRDLGLKLAVVTDAMNGHAVSRLRKAGLLHYFDVVVSADMTGKRKPEPDSIKFALEK 170
                                       *****.*********************************************************************** PP

                             HAD_2 148 lklkkeeviyvGDsp.tDieaakkagikvi 176
                                       l+++++e+i vGDs  +Diea+k++g+ ++
  gi|488600864|ref|YP_007907335.1| 171 LGVDAKEAILVGDSVrRDIEAGKRLGMMTV 200
                                       ***************************987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.4   2.3e-20   4.7e-17       1     210 []      17     196 ..      17     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.3e-20
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       +++v+fD+d+TL +      ++ + +                 +     a ++++ l  f +       + g +++ 
  gi|488600864|ref|YP_007907335.1|  17 VRAVIFDMDNTLFDFVEAKLRACRAV----------------VEH--LGAGDEEELLRYFLR------GMHGFEDLE 69 
                                       5899*********8884433333333................111..222222333333333......445555544 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                       +         + +    sq + +  +  r+++++++    +++p ++e++++L++ g++++++t     +a + +++
  gi|488600864|ref|YP_007907335.1|  70 NIA-----DYMLDKGVYSQEKYEECC--RIYEEVKLNSI-EPYPHVRETLERLRDLGLKLAVVTDAMNGHAVSRLRK 138
                                       444.....444555777788888888..88888888744.7************************************ PP

                                       TT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 155 lG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                       +G  +yfd+v+++d ++  kp+p+  + a+++L+++ +e + VGD+v  D++a+++ g
  gi|488600864|ref|YP_007907335.1| 139 AGlLHYFDVVVSADMTGKRKPEPDSIKFALEKLGVDAKEAILVGDSVRrDIEAGKRLG 196
                                       ******************************************************9876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   1.7e-15   3.4e-12       3      73 ..     157     225 ..     156     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.7e-15
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEE CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddla 73 
                                       +KPep +++fale+lg+d +e +++GD+++ Di+++++ G+++v  + G  +  +  e+  ++++v++++ 
  gi|488600864|ref|YP_007907335.1| 157 RKPEPDSIKFALEKLGVDAKEAILVGDSVRRDIEAGKRLGMMTVYAAYGDRNFFE--EKSREADFVIESIS 225
                                       7************************************************977755..45678888888876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   1.5e-11     3e-08       1     185 [.      20     190 ..      20     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.5e-11
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       ++fD+D TL+d   + l  r   r   ++l++  +e+ll +++r +  +++++   + + l +g + +e  +e++r+
  gi|488600864|ref|YP_007907335.1|  20 VIFDMDNTLFDFVEAKL--R-ACRAVVEHLGAGDEEELLRYFLRGMHGFEDLENI-ADYMLDKGVYsQEKYEECCRI 92 
                                       79**********54442..2.4445556678888888888886666666444433.44446677777********** PP

                               HAD  77 vaevirpkl.ldpgalellaahraaGdrvvvvSgglrplvepllaelg....adevlatelevddrltgelglegkp 148
                                       ++ev++  +  +p+++e l++ r+ G +++vv+ ++   +   l++ g    +d v++       ++tg+ + ++++
  gi|488600864|ref|YP_007907335.1|  93 YEEVKLNSIePYPHVRETLERLRDLGLKLAVVTDAMNGHAVSRLRKAGllhyFDVVVSA------DMTGK-RKPEPD 162
                                       *****99966569*******999************9999999999999999********......*****.777777 PP

                               HAD 149 vrgegkvaalrewlaaegegidleevvayGDsp.sDlp 185
                                       + +     al++       g d +e + +GDs+  D++
  gi|488600864|ref|YP_007907335.1| 163 SIK----FALEK------LGVDAKEAILVGDSVrRDIE 190
                                       777....78888......9999999*******856665 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0016       3.2      37      53 ..      13      29 ..       5      46 .. 0.84
   2 ?    5.5   0.0    0.0059        12     134     163 ..     173     202 ..     105     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0016
                   PGP_phosphatase 37 kektikavvlDKDncla 53
                                      ++++++av++D Dn+l 
  gi|488600864|ref|YP_007907335.1| 13 TTRKVRAVIFDMDNTLF 29
                                      5789***********96 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0059
                   PGP_phosphatase 134 eeadeiavvgDRllTdvllanmmGslgvwl 163
                                        +a+e ++vgD +  d+ ++++ G ++v+ 
  gi|488600864|ref|YP_007907335.1| 173 VDAKEAILVGDSVRRDIEAGKRLGMMTVYA 202
                                       46999*******************998876 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2   2.3e+03       1      18 [.      20      37 ..      20      59 .. 0.69
   2 ?   12.1   0.0   8.2e-05      0.16      13      43 ..     101     131 ..      95     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                                      EEEESTTTSEETTEE-TT CS
                       Hydrolase_6  1 flfDidGvLwrgdkaipg 18
                                      ++fD+d +L ++ +a   
  gi|488600864|ref|YP_007907335.1| 20 VIFDMDNTLFDFVEAKLR 37
                                      689999999986665433 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.2e-05
                                       TEE-TTHHHHHHHHHHTT-EEEEEE---SS- CS
                       Hydrolase_6  13 dkaipgaaealnalraagkpvvllTNnssks 43 
                                        +++p++ e+l++lr+ g +++++T   + +
  gi|488600864|ref|YP_007907335.1| 101 IEPYPHVRETLERLRDLGLKLAVVTDAMNGH 131
                                       589**********************654433 PP

>> DUF705  Protein of unknown function (DUF705)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.001         2     134     164 ..      17      47 ..       6      63 .. 0.78
   2 ?    3.8   0.0     0.017        33     158     227 ..     106     174 ..      95     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                            DUF705 134 khvvvfDlDstLitdeeevelR.dhavydsLd 164
                                          v+fD+D+tL  d +e++lR + av++ L 
  gi|488600864|ref|YP_007907335.1|  17 VRAVIFDMDNTLF-DFVEAKLRaCRAVVEHLG 47 
                                       4579*******97.899999996678888775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.017
                            DUF705 158 avydsLdelkerh.vlvLWsYGnaehvaeslrevglerslFkiilsgGrtveeekldalkkrflkekivld 227
                                        v ++L++l++ +  l +       h +  lr++gl  ++F++++s   t +++  +    +f  ek+ +d
  gi|488600864|ref|YP_007907335.1| 106 HVRETLERLRDLGlKLAVVTDAMNGHAVSRLRKAGLL-HYFDVVVSADMTGKRKP-EPDSIKFALEKLGVD 174
                                       566777777777755666666677899999******9.9******9877655443.334555666666555 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.013        26       4      17 ..      18      31 ..      15      48 .. 0.86
   2 ?    5.4   0.0    0.0074        15      42     150 ..      99     202 ..      70     213 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                                      SEEEE-STTTSSSS CS
                        Acid_PPase  4 klivFDLDyTLWpf 17
                                      ++++FD+D TL +f
  gi|488600864|ref|YP_007907335.1| 18 RAVIFDMDNTLFDF 31
                                      689********987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0074
                                       -EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT-G..........GGESEEEESSS-H..HHHHHHH CS
                        Acid_PPase  42 eelklypdveeileelkskevklavaSrtdepdlarelLklleindakekekklldvfddveiykgsk..tkhfekl 116
                                       ++++ yp+v+e le+l++ + klav   + +++   +l k+  ++          dv+ + ++  + k     ++ +
  gi|488600864|ref|YP_007907335.1|  99 NSIEPYPHVRETLERLRDLGLKLAVVTDAMNGHAVSRLRKAGLLH--------YFDVVVSADMTGKRKpePDSIKFA 167
                                       578889999999999998888888887776665544433222222........333333334433333112345566 PP

                                       HHHH---GGG.EEEEES-HHHHHHHHTTT-EEEE- CS
                        Acid_PPase 117 kkktgieyed.mlfFDdesrnievesrlgvtfvlv 150
                                        +k g++ ++ +l  D  +r+ie  +rlg++ v+ 
  gi|488600864|ref|YP_007907335.1| 168 LEKLGVDAKEaILVGDSVRRDIEAGKRLGMMTVYA 202
                                       66777754441344455666777777777776665 PP

>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00021      0.42      46      98 ..      82     134 ..      15     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                              NT5C  46 kPeqreslyrfltepglFadlepipgarevLeeladeg.rlvvitaallqfyda 98 
                                         e++e+  r + e +l +++ep p  re+Le+l d g +l v+t a+  +  +
  gi|488600864|ref|YP_007907335.1|  82 SQEKYEECCRIYEEVKL-NSIEPYPHVRETLERLRDLGlKLAVVTDAMNGHAVS 134
                                       45677777777777665.78******************9******998876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1586.21
//
Query:       gi|488600865|ref|YP_007907336.1|  [L=107]
Description: hypothetical protein Asulf_01352 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-06   26.0   0.1    9.6e-06   25.6   0.1    1.1  1  Mrr_cat     Restriction endonuclease
     0.0012   18.8   0.0     0.0014   18.6   0.0    1.1  1  Hjc         Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.013   16.0   0.0    1.2  1  NERD        Nuclease-related domain
      0.039   14.0   0.1        0.1   12.7   0.1    1.7  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


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 !   25.6   0.1   2.1e-09   9.6e-06      10      80 ..      12      79 ..       7      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.1e-09
                                      HHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..SE CS
                           Mrr_cat 10 eklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrgadk 80
                                      ek v + l++lG+k+v+++g ++ g  D++a + p g  +++vq+K y+++  ++e ++l+ ++kkr+   
  gi|488600865|ref|YP_007907336.1| 12 EKKVVNWLKKLGFKNVRRSG-GSRGPHDIYAVS-PSG-VKTYVQVKSYSARLTKEERRRLRNVAKKRKGFA 79
                                      7889999********99998.555779**9987.446.8**************************998655 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.1e-07    0.0014       2      78 ..      11      82 ..      10      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.1e-07
                                      HHHHHHHHHHHTT-EEE.EBSCSSSSSSSS-SEEEEET.TEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEE CS
                               Hjc  2 yERelvkiLrergfavv.RsagSggatkplpDviAirg.dvvlviEvKsskkeriylkkeqvekllefarkaggellla 78
                                      +E+ +v+ L++ gf+ v Rs gS g      D+ A+   +v   + vKs +     l ke+ ++l + a+k +g++ + 
  gi|488600865|ref|YP_007907336.1| 11 AEKKVVNWLKKLGFKNVrRSGGSRGP----HDIYAVSPsGVKTYVQVKSYS---ARLTKEERRRLRNVAKKRKGFAAYV 82
                                      5999**********766156778887....8*****97256899****999...899***************9998875 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.0   2.9e-06     0.013       1      72 [.       7      76 ..       7      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                              NERD  1 kgaegEravakeLkelkedeylvlhdvrlrpg.tgeiDhlvispkgifv.iEvKnwsGwifgd..kegrwtqkikk 72
                                      +g+ +E++v ++Lk+l  +    +++vr  +g +g  D+ ++sp+g+   ++vK++s +++++  ++ r ++k++k
  gi|488600865|ref|YP_007907336.1|  7 RGRIAEKKVVNWLKKL--G----FKNVRRSGGsRGPHDIYAVSPSGVKTyVQVKSYSARLTKEerRRLRNVAKKRK 76
                                      5899**********44..5....9999998885559***********999*******9777773333333333355 PP

>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.2e-05       0.1       2      22 ..      13      34 ..      13      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                                      HCHHHHHHHTT-EEEEE.ETTE CS
                        HicA_toxin  2 reviklLeklGfevvrq.kGSH 22
                                      ++v+  L+klGf+ vr+ +GS+
  gi|488600865|ref|YP_007907336.1| 13 KKVVNWLKKLGFKNVRRsGGSR 34
                                      689************7746675 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 732.61
//
Query:       gi|488600866|ref|YP_007907337.1|  [L=394]
Description: DNA-methyltransferase (dcm) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-66  223.3   0.0    5.9e-66  223.1   0.0    1.1  1  DNA_methylase    C-5 cytosine-specific DNA methylase
    1.1e-05   25.1   0.2    1.8e-05   24.4   0.2    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00054   19.5   0.1    0.00078   18.9   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0012   18.6   0.0     0.0017   18.1   0.0    1.2  1  Met_10           Met-10+ like-protein
     0.0012   19.5   0.0     0.0033   18.1   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
      0.005   16.6   0.0     0.0081   16.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0066   16.0   0.0       0.01   15.4   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.025   14.2   0.0      0.043   13.4   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.16   12.7   0.0       0.65   10.8   0.0    1.9  2  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.1   0.0     3e-69   5.9e-66       3     334 ..      24     386 ..      22     387 .. 0.80

  Alignments for each domain:
  == domain 1  score: 223.1 bits;  conditional E-value: 3e-69
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS-.....GS--...-SEEEE---GG CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkidkk.....klpe.d.iDlLvgGfPCq 72 
                                        id f+G+GG++lg+e+ag+++v+ ++ d+k++ tY++n k+ + +D+tki++      k ++ d iDl++gG+PCq
  gi|488600866|ref|YP_007907337.1|  24 AIDVFCGAGGLSLGFEQAGVDVVLGIDFDPKCISTYNQNLKNGVVKDVTKIRDVsnfvsKHADsDrIDLVIGGPPCQ 100
                                       59***************************************9999999999987888985555457*********** PP

                                       GTECTSE.......E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGG..CCSHHHHHHHHHHHHHTEEEEEE CS
                     DNA_methylase  73 pfSvaGk.......qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkh..dkgktlkvilekleelGYevsyk 140
                                        fS  G        +    d+r +L+ ++ +++ke +P++f++ENV+g+ +   + g+  ++i++  ++lGY+ +++
  gi|488600866|ref|YP_007907337.1| 101 TFSPVGRiklrslgRDPESDERTKLWRYFFKFVKELSPEFFVMENVPGMANIiyNGGNLAEHIVSFARKLGYNAEWR 177
                                       ******99999888889999999**************************996314459999999999********** PP

                                       EEEGGGTT-SB--EEEEEEEEEGGG----------SS---GGG.....TSGGGTTS-EE..BTTTB--GGGSSSTT- CS
                     DNA_methylase 141 llnasdyGvpQnReRvfivgirkdlelnvlvkvkefrfpkkkdleasktlrdlleekse..ldeektalsdklveke 215
                                       +l+as++GvpQ+R+R+fi+g + +++     +++e++ +k+   ++ +++ dl++ +     +e ++ +s  l++ +
  gi|488600866|ref|YP_007907337.1| 178 ILDASEFGVPQRRKRLFIIGRKGNRP----INWPEKKIKKPI--TVWEAISDLPKVPHGfrENEIEYDFSGRLTPYQ 248
                                       *********************99885....568888888886..688888888887766778888888888888888 PP

                                       EE--.......S---HHHTS--.......................B--TTS...-B----S-STT--B-TTS---EE CS
                     DNA_methylase 216 ekikkttkaseegypkelsrnr.......................idkveelkglsatrrksgrgeklekelaeagk 269
                                       + +++  +  + +  +                             +          + +r+  ++++ +k + ++++
  gi|488600866|ref|YP_007907337.1| 249 KLMRQGAGDVLYNHMTRW---HneddlrafsllpeggryvdlpdeL----------KRYRDDIFKDRYRKLIRNQPS 312
                                       888765555553333322...1244667888887766665554442..........222222222223333333333 PP

                                       EETTEEE--T..........TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHHH CS
                     DNA_methylase 270 lqknkerfkp.........viekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakeik 334
                                        + +++ +k+          + +  +R++++rEaarlq+fPd+f+f ++ ++a++qiGnsVp+ +++a+a +i 
  gi|488600866|ref|YP_007907337.1| 313 WTIDAHISKDsyryiypskKGGPGPHRTISVREAARLQSFPDTFIFLPTLTHAFRQIGNSVPPLLAKAVASAIL 386
                                       333333333344444455778899**********************************************9986 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 !   24.4   0.2     9e-09   1.8e-05       3      81 ..      23      99 ..      21     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9e-09
                   Methyltransf_15  3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpP 80
                                      v +D+f+GaGG +  f +   + v +i+ +++ +   ++N +  gv + +t +  dv + ++k   +  ++dlv+  pP
  gi|488600866|ref|YP_007907337.1| 23 VAIDVFCGAGGLSLGFEQAgVDVVLGIDFDPKCISTYNQNLKN-GVVKDVTKIR-DVSNFVSKHADS-DRIDLVIGGPP 98
                                      579**************99678899****************98.5888888775.888887774433.347*****999 PP

                   Methyltransf_15 81 w 81
                                      +
  gi|488600866|ref|YP_007907337.1| 99 C 99
                                      6 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   3.9e-07   0.00078     164     222 ..      23      81 ..       8      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.9e-07
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell 222
                                         +Dv +G+G L+++  + g + v+++D D+  ++  ++N++   v++  ++   ++ +
  gi|488600866|ref|YP_007907337.1|  23 VAIDVFCGAGGLSLGFEQAGVDVVLGIDFDPKCISTYNQNLKNGVVKDVTKIRDVSNFV 81 
                                       568**************************************988888877664333333 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.7e-07    0.0017     102     172 ..      22      90 ..       8     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.7e-07
                                       -EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EEEE CS
                            Met_10 102 evVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqladrv 172
                                        v +dvf G G +++   + + ++ vl+id +P+ +   ++n+k N v k v+ i  D+ +++  +   dr+
  gi|488600866|ref|YP_007907337.1|  22 IVAIDVFCGAGGLSLGFEQAGVDV-VLGIDFDPKCISTYNQNLK-NGVVKDVTKI-RDVSNFVSkHADSDRI 90 
                                       4779**************966665.*****************98.5555666455.6777777535555543 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.6e-06    0.0033       2      68 ..      25      93 ..      24     105 .. 0.74
   2 ?   -2.9   0.0       6.1   1.2e+04      16      59 ..     167     185 ..     158     194 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS...SSTTTEEEE CS
                   Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp...fedgsfDlv 68
                                      +d+ cG G l+l + ++ g   v+g+D++++++ + +++++ +g+ +      d++++     +++++Dlv
  gi|488600866|ref|YP_007907337.1| 25 IDVFCGAGGLSLGFEQA-GVDVVLGIDFDPKCISTYNQNLK-NGVvKDVTKIRDVSNFVskhADSDRIDLV 93
                                      699*************9.6899******************6.45544444445555542121345566666 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.1
                                       HCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS CS
                   Methyltransf_25  16 akrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp 59 
                                       a++                          g+n+e++  da+++ 
  gi|488600866|ref|YP_007907337.1| 167 ARK-------------------------LGYNAEWRILDASEFG 185
                                       333.........................3456666666665554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.1e-06    0.0081       3      79 ..      20      94 ..      18     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.1e-06
                   Methyltransf_31  3 kglrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlil 79
                                      + ++ +D+ CG+G l++ +  ++g   + v GiD++++ i+  ++n+++  ++ v+ ++ d+ +  +k+   +++Dl++
  gi|488600866|ref|YP_007907337.1| 20 SRIVAIDVFCGAGGLSLGFE-QAGV--DvVLGIDFDPKCISTYNQNLKNGVVKDVT-KIRDVSNfVSKHADSDRIDLVI 94
                                      567889*********99999.4432..349****************9988888776.6677777555554447888876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.1e-06      0.01      35     108 ..      24     100 ..       8     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.1e-06
                                       EEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  35 vlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvleeveekkfdlivsNPPf 107
                                       ++D+ cGaG l++ + ++  ++ v  +d d + +   ++nl++  ++    ++ v + v ++++ +++dl++  PP 
  gi|488600866|ref|YP_007907337.1|  24 AIDVFCGAGGLSLGFEQAGVDV-VLGIDFDPKCISTYNQNLKNGVVKdvtkIRDVSNFVSKHADSDRIDLVIGGPPC 99 
                                       79*************9998885.889*****************999977333333334455566899*********6 PP

                                       T CS
                               MTS 108 h 108
                                       +
  gi|488600866|ref|YP_007907337.1| 100 Q 100
                                       5 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.2e-05     0.043      42     123 ..      21      99 ..      13     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                       +   +D+f+G G+l+l     g++ ++ ++ d++ +++ ++nl++  +++   + ++d ++ ++k+ + + ++d+v 
  gi|488600866|ref|YP_007907337.1|  21 RIVAIDVFCGAGGLSLGFEQAGVDVVLGIDFDPKCISTYNQNLKNGVVKD--VTKIRDVSNFVSKH-ADSDRIDLVI 94 
                                       55679*******9877777789***********************99887..56666777777777.566789***9 PP

                                       E--SS CS
                     Cons_hypoth95 119 lDPPy 123
                                         PP 
  gi|488600866|ref|YP_007907337.1|  95 GGPPC 99 
                                       99996 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00033      0.65       2      71 ..      26      94 ..      25     104 .. 0.93
   2 ?   -1.4   0.0         2   3.9e+03      19      57 ..     172     210 ..     156     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                   Methyltransf_12  2 eiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvv 71
                                      ++ cG G l+  ++++  +++++ g+D++p+ i    + l+    +++++++   + ++++++++  Dlv+
  gi|488600866|ref|YP_007907337.1| 26 DVFCGAGGLSLGFEQA--GVDVVlGIDFDPKCISTYNQNLKNGVVKDVTKIRDVSNFVSKHADSDRIDLVI 94
                                      677*************..999999***************************99999999999999999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                   Methyltransf_12  19 pdieytgvDispsaiedakeklakrennnnnnveleald 57 
                                        ++e   +D s+  +++++++l  ++++ n  +++ ++ 
  gi|488600866|ref|YP_007907337.1| 172 YNAEWRILDASEFGVPQRRKRLFIIGRKGNRPINWPEKK 210
                                       567777899999999999999999999998888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2277.90
//
Query:       gi|488600867|ref|YP_007907338.1|  [L=247]
Description: hypothetical protein Asulf_01354 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-09   36.1   0.0    9.9e-09   35.6   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    4.4e-08   32.6   0.0      9e-08   31.6   0.0    1.6  1  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
        0.1   13.0   2.7        0.2   12.0   2.7    1.5  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   1.7e-12   9.9e-09       2     105 ..      40     170 ..      39     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.7e-12
                                       HHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                           HhH-GPD   2 sailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............ 66 
                                       ++il  +t+ e + +++++l+++  +p++ +la++d  +L+ +++++G+   ++   +e+A+ +v            
  gi|488600867|ref|YP_007907338.1|  40 AEILLHRTRAEQVIPLYNNLVAL--CPDAFSLAAIDRGELHRMLKSAGLR-WRIDLMHEMAKTIVeryngeipekre 113
                                       6899*******************..59*********************99.************************** PP

                                       .....................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHH CS
                                       .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 .....................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleel 105
                                                            g+p+  +  D+++ ri++r++ i+ k + +   kk++e 
  gi|488600867|ref|YP_007907338.1| 114 elmklpgvseyiasavrcfayGYPE--PLLDTNTVRIAGRVFDIEVK-DSSRRSKKMREF 170
                                       *********************9999..*****************885.777777776665 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.5e-11     9e-08       1      30 []     103     132 ..     103     132 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.5e-11
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       +++g+ip  reeL++lPGV ++ A a++++
  gi|488600867|ref|YP_007907338.1| 103 RYNGEIPEKREELMKLPGVSEYIASAVRCF 132
                                       799************************997 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.7   3.4e-05       0.2       1      13 [.     195     207 ..     195     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                     EndIII_4Fe-2S   1 CTARkPkCeaCPL 13 
                                       C+ R+P C aCPL
  gi|488600867|ref|YP_007907338.1| 195 CKKRNPECFACPL 207
                                       999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1696.39
//
Query:       gi|488600868|ref|YP_007907339.1|  [L=1248]
Description: hypothetical protein Asulf_01355 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   31.2   0.0    6.7e-07   29.6   0.0    1.8  2  Helicase_C      Helicase conserved C-terminal domain
     0.0064   16.5   0.0      0.034   14.2   0.0    2.2  2  ResIII          Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.079   12.8   0.0    1.7  1  DUF5594         Domain of unknown function (DUF5594)
      0.082   13.0   0.0       0.27   11.4   0.0    1.9  1  MerR_1          MerR HTH family regulatory protein
       0.18   11.5   0.0        1.7    8.4   0.0    2.1  2  DEAD            DEAD/DEAH box helicase
       0.68   10.0   7.4          4    7.6   0.4    3.1  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


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 ?   -4.0   0.0         6   1.8e+04      11      53 ..     597     637 ..     588     651 .. 0.62
   2 !   29.6   0.0   2.3e-10   6.7e-07      42     110 ..     990    1065 ..     952    1066 .. 0.75

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6
                                       HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHH CS
                        Helicase_C  11 kleeeggkilifvntidrlekvklllekkgikvavlhgelpqn 53 
                                       ++ee+++ il f++t   + +++++  ++g ++ +l  el ++
  gi|488600868|ref|YP_007907339.1| 597 TEEEIKSSILSFIETSGLIRNFRIF--HHGGEFFTLEIELDKK 637
                                       5677778888888888777666777..4555555555444444 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 2.3e-10
                                        TEEEESTTSTHHHHHHHHHHHHTTS.......SSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C   42 kvavlhgelpqnereeileqfnkge.......sdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109 
                                        +v+ l +++++ e   il++  +ge        d + +t++ ++G+d+p ++l+i  + p+++++y+q+ GR+gR
  gi|488600868|ref|YP_007907339.1|  990 NVVELSSRISSTEIPVILDELEEGErrdpsenPDAIFTTSMFGTGVDVPHLSLMIVNGQPKTTSQYVQATGRVGR 1064
                                        55666666666666666666665544455543679**************************************** PP

                                        T CS
                        Helicase_C  110 a 110 
                                        a
  gi|488600868|ref|YP_007907339.1| 1065 A 1065
                                        8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.1e-05     0.034       4      47 ..     401     448 ..     349     458 .. 0.68
   2 ?   -1.2   0.0       0.6   1.8e+03     134     169 ..     806     861 ..     753     863 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                       E-HHHHHHHHHHT..........TTSEEEEEESTTSTHHHHHHHHHHH CS
                            ResIII   4 lreyQeeaienlleklks....krdkrglikmaTGtGKTlvaaklier 47 
                                       + + Q   i  +le+l +    +r+k  l+++aTG GKT  +++l++ 
  gi|488600868|ref|YP_007907339.1| 401 WWPFQLAFILMVLESLANpasrDREKTDLLWIATGGGKTEAYLALMAF 448
                                       33444455555555555599989999****************999975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.6
                                       S..........EEEEETGGGTTS...T...TTHHHHHT---.....SEEEEEESS- CS
                            ResIII 134 d..........viiiDEaHrlgak..k...swreilekfke.....avllglTATp 169
                                                  +i+ DE H + +   +    ++ ++e +++      + ++ TAT+
  gi|488600868|ref|YP_007907339.1| 806 SidvspfsppeLIVQDELHLIEGPlgSmfgLYETVVEGLQNisgvkPKYIASTATI 861
                                       133555667789*******9988644144455555333333222335555557776 PP

>> DUF5594  Domain of unknown function (DUF5594)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05     0.079      19      86 ..     259     324 ..     251     336 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                           DUF5594  19 eevaavldrtvrvevlpyenlllptrlrisaarigigedlrryafdlnlyltwdddeivrllrpegea 86 
                                       e+ a  +d  vr +++p      p     +  r   g+  + +a+ l     wd+dei+r+l+p  +a
  gi|488600868|ref|YP_007907339.1| 259 EDCAEFFDCDVRSDFVPLYPSSAPNFEWDEEMRREFGDPPELFAYRLS--EMWDEDEIERFLGPVVDA 324
                                       678999******************99999999999****999999987..57************7665 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 ?   11.4   0.0     9e-05      0.27      28      49 ..     956     978 ..     946     980 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-05
                                       -EE.-TTS-EEEEHHHHHHHHHH CS
                            MerR_1  28 pkr.teggrryYtdedierLkli 49 
                                         r  +ggr++Y+++++erLk+i
  gi|488600868|ref|YP_007907339.1| 956 AIReLGGGRALYREDTVERLKQI 978
                                       556689***************99 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00058       1.7      20      79 ..     431     502 ..     410     523 .. 0.73
   2 ?    0.3   0.0      0.18   5.3e+02     119     170 ..     812     862 ..     754     867 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00058
                                       EESTTSSHHHHHHHHHHHHHHHS...........TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                              DEAD  20 aaeTGsGKTlaflipvlqivyet...........kgktgpkalivePtreLaeqtlnnlkkfkkyid.lrvl 79 
                                        ++TG GKT+a+l  +  i++ +            +  g+ ++    +r L+ q+++++ ++   ++ lrv+
  gi|488600868|ref|YP_007907339.1| 431 WIATGGGKTEAYLALMAFIMALRrvrarrgkaseSTGGGTAVITRYTLRLLTIQQFRRILRMVTAAEfLRVM 502
                                       568********9877775554336777888887433444455555788889999998888877765555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                                       CTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldq..gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +s  +++V DE + +     ++   ++++++ l++i+  ++ +   i+ +AT++
  gi|488600868|ref|YP_007907339.1| 812 FSPPELIVQDELHLIEGPlgSMFGLYETVVEGLQNISGVKP-K--YIASTATIK 862
                                       67778999*****9999887777788999999966666544.4..899999997 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2    0.0053        16       1       7 [.     567     573 ..     567     576 .. 0.86
   2 ?    7.6   0.4    0.0013         4       5      25 ..     671     694 ..     670     695 .. 0.92
   3 ?   -2.6   0.1         2     6e+03      16      21 ..     746     751 ..     740     751 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0053
                    DNA_ligase_ZBD   1 hCPvCGs 7  
                                       +CPvCG+
  gi|488600868|ref|YP_007907339.1| 567 RCPVCGT 573
                                       5*****8 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0013
                    DNA_ligase_ZBD   5 CGsavvReeg...eaiyRCtnlsC 25 
                                       C s+v R+ +   +  ++C+n++C
  gi|488600868|ref|YP_007907339.1| 671 CRSEVGRKSNiprDFEIYCPNPHC 694
                                       9999999998888*********** PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2
                    DNA_ligase_ZBD  16 aiyRCt 21 
                                         yRC+
  gi|488600868|ref|YP_007907339.1| 746 IYYRCP 751
                                       459**7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.87u 0.29s 00:00:01.15 Elapsed: 00:00:00.48
# Mc/sec: 7752.30
//
Query:       gi|488600869|ref|YP_007907340.1|  [L=602]
Description: hypothetical protein Asulf_01356 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   38.9   0.0    2.6e-09   37.7   0.0    1.7  1  DUF1998          Domain of unknown function (DUF1998)
  ------ inclusion threshold ------
        9.1    6.3   6.8        4.5    7.3   0.0    3.1  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.9e-13   2.6e-09       1      83 []     484     580 ..     484     580 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.9e-13
                           DUF1998   1 lehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaek...aaelleellraalelieec.d 73 
                                       l+hali  l+l++++++++l+++++ ++d       +iliy+++pg  G         +++ e+lr+  e+++ c +
  gi|488600869|ref|YP_007907340.1| 484 LSHALILTLSLHAGYSSASLRERVYINRDA---TSGGILIYTTSPGEDGSMGGltgSLKVFREILRKSSERLKLCsN 557
                                       69***********************88775...9***********999984443334556788*********99*62 PP

                           DUF1998  74 ...Cee..........aGCpaCl 83 
                                          C e          ++C++Cl
  gi|488600869|ref|YP_007907340.1| 558 dplCLEvrktpervngSACHSCL 580
                                       689977999*************7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00051       4.5      27      49 ..     117     139 ..     112     150 .. 0.76
   2 ?    1.0   0.2     0.046   4.2e+02      30      49 ..     179     199 ..     170     202 .. 0.72
   3 ?   -1.4   0.4      0.26   2.3e+03      18      43 ..     563     588 ..     560     593 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00051
                    OrfB_Zn_ribbon  27 TSktCseCgsknkealsgrtfkC 49 
                                        S +C++Cg+k++ +  + +  C
  gi|488600869|ref|YP_007907340.1| 117 NSERCPVCGRKDDSSAVRFVAAC 139
                                       79*********998554444455 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.046
                    OrfB_Zn_ribbon  30 tCseCgsknke.alsgrtfkC 49 
                                       +C+ Cg+k +  +  + +f+C
  gi|488600869|ref|YP_007907340.1| 179 ECHDCGKKTTMkEIYNIKFRC 199
                                       799999887664455555555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.26
                    OrfB_Zn_ribbon  18 kveevnpayTSktCseCgsknkeals 43 
                                       +v +  ++   + C+ C  +++++ +
  gi|488600869|ref|YP_007907340.1| 563 EVRKTPERVNGSACHSCLLISETSCE 588
                                       56666777788899999888777544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3909.68
//
Query:       gi|488600870|ref|YP_007907341.1|  [L=153]
Description: hypothetical protein Asulf_01357 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   67.5   0.1    1.2e-18   67.3   0.1    1.1  1  PLDc_2          PLD-like domain
    9.4e-08   31.5   0.1    1.1e-07   31.3   0.1    1.0  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    0.00019   21.5   0.0    0.00035   20.6   0.0    1.5  1  PLDc            Phospholipase D Active site motif
    0.00085   19.0   1.5     0.0026   17.4   1.5    1.7  1  FAM83           FAM83 A-H
  ------ inclusion threshold ------
      0.037   13.6   1.1      0.059   12.9   1.1    1.4  1  PP_kinase_C_1   Polyphosphate kinase C-terminal domain 1
      0.038   12.9   0.0      0.048   12.6   0.0    1.2  1  Dak1            Dak1 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 !   67.3   0.1   3.9e-22   1.2e-18       3     125 ..      27     144 ..      25     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 3.9e-22
                            PLDc_2   3 qliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetll 79 
                                       ++i+sA++++ + +y + sd ++ ++l+ka +rgv v+i + s  ++  a + +    l+el l+ + e r    ++
  gi|488600870|ref|YP_007907341.1|  27 EMIRSAEREVVMTVYVM-SDVSVTNSLKKAIERGVSVEIFVYS--PQ-IAIKPE---ALQEL-LKMKKEFRNLVIHN 95 
                                       78***************.***********************99..33.333333...33344.33344433332222 PP

                            PLDc_2  80 ...gslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakel 125
                                          ++lHaK++++dg+ v+vGS+N t  g+ +n+El++ +++ ++a+ +
  gi|488600870|ref|YP_007907341.1|  96 iedKILHAKVLVVDGRKVLVGSANPTMGGMLKNYELGLLVDNGKIAQNI 144
                                       33499****************************************9987 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   3.7e-11   1.1e-07       3     119 ..      13     143 ..      11     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.7e-11
                                       EEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS.......----GGGSSSSEEE CS
                    Regulator_TrmB   3 wvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp.......dedleeldleevat 72 
                                       wv  ++++  + + e+I+sAe e+++ +       +   l++a+ergv+V++ +y+       ++ +e l++++++ 
  gi|488600870|ref|YP_007907341.1|  13 WVGYGFRSFHSVVNEMIRSAEREVVMTVYVMSDVSVTNSLKKAIERGVSVEIFVYSpqiaikpEALQELLKMKKEFR 89 
                                       67778888889999**********************************************99888888889999998 PP

                                       EEE-S---S.EE....EEETTTEEEEE-SSS-...EEEE--HHHHHHHHHHHHH CS
                    Regulator_TrmB  73 evrvrrsgapll....vivDrkrgvvaprevl...rdkeeeyaiifkekelihv 119
                                       ++ +++  + +l    ++vD+++++v ++++    + k+ e ++++++ +++++
  gi|488600870|ref|YP_007907341.1|  90 NLVIHNIEDKILhakvLVVDGRKVLVGSANPTmggMLKNYELGLLVDNGKIAQN 143
                                       88888887766677779*********9998777677777777888877777666 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00035       4      23 ..     100     119 ..      97     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                                       EE---EEEETTTEEEEE--- CS
                              PLDc   4 thHqKivivDdrvafvGgaN 23 
                                        +H+K ++vD+r ++vG+aN
  gi|488600870|ref|YP_007907341.1| 100 ILHAKVLVVDGRKVLVGSAN 119
                                       69*****************9 PP

>> FAM83  FAM83 A-H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.5   8.7e-07    0.0026     126     211 ..      21     105 ..      16     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.7e-07
                             FAM83 126 ikevvrkliqkaqkviavvmdvftDvdilkdlleaaskrkvpvyilLdeknlklflemceklqvnkqhlknlrvRsv 202
                                          vv ++i++a++ + + ++v++Dv + + l +a  +r+v+v i + + ++    e +++l   k++++nl +  +
  gi|488600870|ref|YP_007907341.1|  21 FHSVVNEMIRSAEREVVMTVYVMSDVSVTNSLKKA-IERGVSVEIFVYSPQIAIKPEALQELLKMKKEFRNLVIHNI 96 
                                       5679************************9999876.5688*******************99999999*******999 PP

                             FAM83 203 kGetyltrs 211
                                       + + ++++ 
  gi|488600870|ref|YP_007907341.1|  97 EDKILHAKV 105
                                       998877665 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.1     2e-05     0.059       6     112 ..       7     109 ..       2     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                                       HHHS-EEEECTTB-SCHHHHHHHHHHC-TTEEEEEEEES-S-S--HHHHHHHHHHHTT-EEEEEES--SSS--HHHH CS
                     PP_kinase_C_1   6 irkkdillhhPyesfesvvelleeAaedpkvlaikitlYrvakdskivkaLieAaengkqvtvlvElkArfdeenNi 82 
                                       i++ +  + + ++sf+svv+ + ++ae     ++ +t+Y ++ d ++ ++L++A e+g +v ++v       + + +
  gi|488600870|ref|YP_007907341.1|   7 ITTGEKWVGYGFRSFHSVVNEMIRSAER----EVVMTVYVMS-DVSVTNSLKKAIERGVSVEIFVYSPQIAIKPEAL 78 
                                       6667777888899997777655555554....5678999766.5669****************99654444444555 PP

                                       HHHHHHHHHT-E.EEE--TT--B--EEEEEE CS
                     PP_kinase_C_1  83 ewakkleeagvk.vvygvvglkvhaklllvv 112
                                       +   k++++  + v++ +++   hak+l+v 
  gi|488600870|ref|YP_007907341.1|  79 QELLKMKKEFRNlVIHNIEDKILHAKVLVVD 109
                                       5555555554331566666666677777775 PP

>> Dak1  Dak1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05     0.048     102     157 ..      27      81 ..      21      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                                       HHHHHTT-.-EEEEEE--B-SSSSSTTCSSSB--THHHHHHHHHHHHHHHT--HHHH CS
                              Dak1 102 ekakaegi.kvetvvvdDDvavedseekagrRGvagtvlveKiaGaaAeegasLeev 157
                                       e++++ +   v tv+v  Dv+v++s +ka  RGv+ +++v+    + A + + L+e+
  gi|488600870|ref|YP_007907341.1|  27 EMIRSAEReVVMTVYVMSDVSVTNSLKKAIERGVSVEIFVYSP--QIAIKPEALQEL 81 
                                       555554432678999************************9853..344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 984.69
//
Query:       gi|488600871|ref|YP_007907342.1|  [L=992]
Description: hypothetical protein Asulf_01358 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (992 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.53
# Mc/sec: 5664.69
//
Query:       gi|488600872|ref|YP_007907343.1|  [L=88]
Description: hypothetical protein Asulf_01359 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); 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:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 753.84
//
Query:       gi|488600873|ref|YP_007907344.1|  [L=1526]
Description: hypothetical protein Asulf_01360 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-22   78.4   0.0    8.1e-19   68.1   0.0    2.9  3  DEAD        DEAD/DEAH box helicase
    2.5e-15   56.8   0.0    6.5e-13   49.0   0.0    2.9  2  Helicase_C  Helicase conserved C-terminal domain
    5.2e-08   33.1   0.0      0.001   19.1   0.0    2.6  2  ResIII      Type III restriction enzyme, res subunit
    0.00049   20.4   0.0       0.35   11.1   0.0    3.3  2  AAA_22      AAA domain
    0.00056   19.6   0.0      0.048   13.3   0.0    2.8  3  SRP54       SRP54-type protein, GTPase domain
      0.008   15.9   0.0        3.2    7.4   0.0    2.4  2  SWI2_SNF2   SWI2/SNF2 ATPase
  ------ inclusion threshold ------
       0.13   12.0   0.4        5.5    6.7   0.0    2.8  2  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
        0.3   11.3   2.8         12    6.1   0.1    3.6  3  BET         Bromodomain extra-terminal - transcription regula


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 !   68.1   0.0   3.6e-22   8.1e-19       2     173 ..     657     832 ..     656     835 .. 0.79
   2 ?   -3.8   0.0       4.3   9.6e+03      80     126 ..     951    1000 ..     937    1028 .. 0.59
   3 !    6.9   0.0    0.0022       4.9      16      76 ..    1282    1339 ..    1271    1389 .. 0.72

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 3.6e-22
                                       HHHHHHHHHHHTTCEEE........EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvl........vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkf 70 
                                       ++Q++a+ l+l+  ++         v  +TGsGK+ +f+ ++++      + tg+ +++v+P+++L++++++ l++ 
  gi|488600873|ref|YP_007907344.1| 657 PYQRKAVALLLSAYSLNrstspfgvVVLPTGSGKSVIFQSAAIALH----KLTGTVTIVVSPLQALIHDHVEGLRRK 729
                                       6788888888855333344445566999***************444....79999*******************998 PP

                                       TTTSTSEEE.EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                              DEAD  71 kkyidlrvl.liiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq..gfsdfinr 144
                                       +  +  ++   + ++++ +  l++++ ++ +++ tp+r+ +   +  l + +v f++lDE+++l+ +   f++ ++ 
  gi|488600873|ref|YP_007907344.1| 730 GVRVA-KIDsNTSSEERFNAILDAISGDIVLLYVTPERFERDELRVILGCGNVGFVILDEIHCLSTWgsTFRPSYKY 805
                                       88533.2221233344446666666555999*********966678899******************999******* PP

                                       HHHHSHHHCTTSTTTSEEEEEESSBSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 145 ilnqlpqitcdgklqrqvivlSATlpkdv 173
                                       +++ +++ +++  l   +  +SATlpkdv
  gi|488600873|ref|YP_007907344.1| 806 MARMIASESENRFLP--IYGFSATLPKDV 832
                                       *****7776666566..*********887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.3
                                        EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH....CTTEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxx RF
                              DEAD   80 liiggvaardqlskldngvdivvgtpgrlddllstgkln....lsqvrflV 126 
                                         + g+ + +++++++ ++++  v  p++   ++ t+ +     l +vrf+V
  gi|488600873|ref|YP_007907344.1|  951 YFHGQMDLDEKVEVI-SKLERAVKSPSKPRIVVATKAFGmgvdLPNVRFVV 1000
                                        445555555555555.55555555555555555444433333377777777 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0022
                                        EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                              DEAD   16 dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idl 76  
                                        + ++ + TGsGKT+  +  +   vy+    +   ++iv P r    +++++++ ++ y +d+
  gi|488600873|ref|YP_007907344.1| 1282 KAVIFGLTGSGKTEKLAELAAYYVYK---YSDRAVVIVLPDRR-SSDIVSRIRDYLGYdVDI 1339
                                        5566778*******999999989986...77778999999987.567888888877765553 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.019        44      13      70 ..     703     760 ..     693     863 .. 0.78
   2 !   49.0   0.0   2.9e-16   6.5e-13      21     109 ..     920    1020 ..     897    1022 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
                                       TTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEE CS
                        Helicase_C  13 eeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvL 70 
                                       +  g  ++++++ +  +++ v+ l ++kg++va+++++++++er  ++ +  +g++ +L
  gi|488600873|ref|YP_007907344.1| 703 KLTGTVTIVVSPLQALIHDhVEGL-RRKGVRVAKIDSNTSSEERFNAILDAISGDIVLL 760
                                       456667788888888776555555.6889***************877766657766555 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 2.9e-16
                                        EEESSHH......HHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH.....TTSSSEEEESGGGTSSSTST CS
                        Helicase_C   21 ifvntid......rlek.vklllekkgikvavlhgelpqnereeileqfn.....kgesdvLiatdvaerGidip 83  
                                        +f+ +++      +++  ++ ++e  g +v+++hg++  +e+ e++++         + ++++at++ ++G+d+p
  gi|488600873|ref|YP_007907344.1|  920 VFASFVRspiiheNVDYiARSIEEGIGEEVLYFHGQMDLDEKVEVISKLEravksPSKPRIVVATKAFGMGVDLP 994 
                                        5555555443323332234555555599*********************87776434555*************** PP

                                        TESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C   84 kvnlVinfdlprnvtsyiqriGRtgR 109 
                                        +v++V++ ++ +++++y q iGR+gR
  gi|488600873|ref|YP_007907344.1|  995 NVRFVVHAHVSQSLEEYYQEIGRAGR 1020
                                        ************************** PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.6e-07     0.001       2     169 ..     653     828 ..     652     830 .. 0.69
   2 !   11.3   0.0   0.00011      0.25      24      64 ..    1280    1320 ..    1212    1390 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.6e-07
                                       -EE-HHHHHHHHHHT......TTS..EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGG CS
                            ResIII   2 lelreyQeeaienlleklkskrdk..rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkk 76 
                                       ++ r+yQ +a+  ll++++ +r +   g+++++TG+GK+++  +++ +l+k  +   ++++ p ++l+    e +++
  gi|488600873|ref|YP_007907344.1| 653 FRYRPYQRKAVALLLSAYSLNRSTspFGVVVLPTGSGKSVIFQSAAIALHKLTG-TVTIVVSPLQALIHDHVEGLRR 728
                                       5689***********88876666566899*************999999998766.5899999999999999888877 PP

                                       GTGG.....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...... CS
                            ResIII  77 flseayke.igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..... 147
                                            +k   +++ +++ + +    s ++ +l +t +++ +d+      +  l+ ++  ++i DE H l+       
  gi|488600873|ref|YP_007907344.1| 729 KGVRVAKIdSNTSSEERFNAILDAISGDIVLLYVTPERFERDE-----LRVILGCGNVGFVILDEIHCLSTWgstfr 800
                                       7666655434444444444446677888888888999999999.....77888888888999999998887654444 PP

                                       TTTHHHHHT-...--...SEEEEEESS- CS
                            ResIII 148 kswreilekf...ke...avllglTATp 169
                                        s++  ++++   +e     + g++AT+
  gi|488600873|ref|YP_007907344.1| 801 PSYKYMARMIaseSEnrfLPIYGFSATL 828
                                       1333322222111222323344677775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                                        TSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH CS
                            ResIII   24 dkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk 64  
                                          +++i   TG+GKT  +a+l++++  k++ + ++++ p +
  gi|488600873|ref|YP_007907344.1| 1280 GDKAVIFGLTGSGKTEKLAELAAYYVYKYSDRAVVIVLPDR 1320
                                        447777888*******************9999888888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.011        24       4     103 ..     676     792 ..     673     810 .. 0.68
   2 !   11.1   0.0   0.00016      0.35       9     106 ..    1284    1373 ..    1280    1408 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee....................erpevvfvtlpsstsskdllrel 60 
                                       t  ++vv+ ++G+GK++  +  +  l++    +                     +r++v   ++ s tss++ ++++
  gi|488600873|ref|YP_007907344.1| 676 TSPFGVVVLPTGSGKSVIFQSAAIALHKL---TGtvtivvsplqalihdhveglRRKGVRVAKIDSNTSSEERFNAI 749
                                       567899999**********9999999532...224667777777777777777655555566666666667777777 PP

                            AAA_22  61 lralglelkaerlsseellealeqalraravielliiDEaqhl 103
                                       l a+  +      + e++ +   + +  ++ ++++i+DE++ l
  gi|488600873|ref|YP_007907344.1| 750 LDAISGDIVLLYVTPERFERDELRVILGCGNVGFVILDEIHCL 792
                                       7777765555445566665555555555555699999999877 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                            AAA_22    9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83  
                                        v++G +G+GKT  l++l+  ++        +++ v + lp    s+d+ +++   lg + +    + ++ ++ +e
  gi|488600873|ref|YP_007907344.1| 1284 VIFGLTGSGKTEKLAELAAYYVYK-----YSDRAVVIVLPDRR-SSDIVSRIRDYLGYDVDI---NIKQARNVVE 1349
                                        8***********999999988533.....48999999999999.99999***9999977777...5555555554 PP

                            AAA_22   84 qalraravielliiDEaqh.lr.se 106 
                                        +  +  +  e++i+D+a+  l  ++
  gi|488600873|ref|YP_007907344.1| 1350 NLDELLR-YEVIILDDADTaLAkTP 1373
                                        4444444.499******99775533 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.032        73      72     111 ..    1126    1164 ..    1107    1181 .. 0.82
   2 ?   -3.0   0.0       2.1   4.8e+03      47      97 ..    1224    1273 ..    1222    1275 .. 0.77
   3 !   13.3   0.0   2.2e-05     0.048       5      35 ..    1284    1316 ..    1281    1323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.032
                                        HHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHH CS
                             SRP54   72 akeavekakeekidvvlvDTaGrlqndkelmeelkkikkv 111 
                                        + +a+  ++e + dv+l+DT      +++lme l+k ++ 
  gi|488600873|ref|YP_007907344.1| 1126 IDDALVFFDE-ESDVILLDTNSPKMFKAALMERLRKWENE 1164
                                        5566666665.67*********************998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.1
                                        HHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTT CS
                             SRP54   47 QLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqn 97  
                                        QL+ + +++  ++  k++++++ +++ + +e+  +++++ +l+D  G  ++
  gi|488600873|ref|YP_007907344.1| 1224 QLERFLKEIS-SLPLKEQNKKAHETLGRYLEEGIANEFEKILLDRIGSIEE 1273
                                        7777777766.333366677899999999***************9887766 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 2.2e-05
                                        EEEESTTSSHHHHHHHHHHHHHHT..TS-EEEE CS
                             SRP54    5 llvGlqGaGKTttlaKLaallkke..gkkvllv 35  
                                        +++Gl+G+GKT  la Laa++  +   + v++v
  gi|488600873|ref|YP_007907344.1| 1284 VIFGLTGSGKTEKLAELAAYYVYKysDRAVVIV 1316
                                        789*****************9988655666665 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0043       9.7      14     130 ..     673     790 ..     658     811 .. 0.60
   2 !    7.4   0.0    0.0014       3.2      16      60 ..    1278    1322 ..    1264    1362 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0043
                         SWI2_SNF2  14 kegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka...geekpkqaesrkeLk 87 
                                       +++++  Gv+   +GSGKs+    +a +l++  +   ++v v   + L +   + +++      +  ++++s+++++
  gi|488600873|ref|YP_007907344.1| 673 NRSTSPFGVVVLPTGSGKSVIFQSAAIALHK-LTGTVTIV-VSPLQALIHDHVEGLRRKgvrVAKIDSNTSSEERFN 747
                                       345677899999*******998888888888.44444444.444444444444444443222233345677777777 PP

                         SWI2_SNF2  88 ellekesekiiftti..qKfeeeekeklevlsereni.ivlvDEaH 130
                                         l++ s++i++  +  ++fe++   +l+v+    n+ +v+ DE H
  gi|488600873|ref|YP_007907344.1| 748 AILDAISGDIVLLYVtpERFERD---ELRVILGCGNVgFVILDEIH 790
                                       77766677777665511455432...34444444433377777777 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                         SWI2_SNF2   16 gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkd 60  
                                        +  ++ vi+  +GSGK+ + + la+  + +  +++ v+v+ DR+ 
  gi|488600873|ref|YP_007907344.1| 1278 RLGDKAVIFGLTGSGKTEKLAELAAYYVYKYSDRAVVIVLPDRRS 1322
                                        446789***************99999999778889999999**74 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 ?    6.7   0.0    0.0024       5.5      85     125 ..    1121    1161 ..    1086    1199 .. 0.80
   2 ?    2.1   0.1     0.063   1.4e+02      68     161 ..    1324    1428 ..    1314    1436 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0024
                                        EEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHS CS
                         QRPTase_C   85 vevesleeleevleaeadiimLDnfsveelkkaveelkekn 125 
                                        ++ +s +++     +e d+i+LD+ s++++k a+ e+ +k+
  gi|488600873|ref|YP_007907344.1| 1121 IDLKSIDDALVFFDEESDVILLDTNSPKMFKAALMERLRKW 1161
                                        6777777777788899****************998764443 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.063
                                        HHHHHHHHHHTTTSEEEEEESSHHHHHHHHH..HT-SEEEEES-.........-HHHHHHHHHHHHHHSTT...S CS
                         QRPTase_C   68 eavksvreavdkevkievevesleeleevle..aeadiimLDnf.........sveelkkaveelkeknkr...v 128 
                                        ++v+++r++++  v   +++++  ++ e l    + ++i LD           +v +l+++++  ++       +
  gi|488600873|ref|YP_007907344.1| 1324 DIVSRIRDYLGYDVD--INIKQARNVVENLDelLRYEVIILDDAdtalaktpiDVSTLERIAKFNRKVYFAfdpM 1396
                                        688899999988865..444444444444442334569****996666655555555555555444433336767 PP

                                        EEEEESS--TTTHHHHHCTT-SEEEECHHCHTB CS
                         QRPTase_C  129 lievSGgvtlenveeyaksgvdvisvgalthsv 161 
                                        ++ + G++  + +e++ + +v v+ +  l  +v
  gi|488600873|ref|YP_007907344.1| 1397 ILAAFGNLR-QVLENFEECNVAVLRSVELPVKV 1428
                                        777778775.46777777777777666666555 PP

>> BET  Bromodomain extra-terminal - transcription regulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.57   1.3e+03      41      49 ..     848     856 ..     840     856 .. 0.86
   2 ?    2.3   0.0     0.086   1.9e+02      18      36 ..     891     909 ..     888     915 .. 0.80
   3 ?    6.1   0.1    0.0054        12       4      45 ..    1036    1072 ..    1035    1075 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.57
                               BET  41 dEiElDida 49 
                                        EiE+D+d+
  gi|488600873|ref|YP_007907344.1| 848 REIEIDFDS 856
                                       59*****96 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.086
                               BET  18 pgeklgrvveIIqerepel 36 
                                       +++kl++vv+ I++ +++l
  gi|488600873|ref|YP_007907344.1| 891 DEDKLRKVVNVIKQLRDTL 909
                                       689**********987554 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0054
                               BET    4 yeeKkeLseeInkLpgeklgrvveIIqerepelqsdedEiEl 45  
                                        ++eK++L ++I+    ++ ++ v+II + +++  ++ dEi +
  gi|488600873|ref|YP_007907344.1| 1036 FDEKRQLIRHITY---DQVNKLVKIIGNFRAS--NERDEIAI 1072
                                        79******99999...**********998866..67788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.96u 0.31s 00:00:01.27 Elapsed: 00:00:00.50
# Mc/sec: 9249.60
//
Query:       gi|488600874|ref|YP_007907345.1|  [L=273]
Description: hypothetical protein Asulf_01361 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.1   0.0       0.15   11.4   0.0    1.2  1  DUF2119   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2119  Uncharacterized protein conserved in archaea (DUF2119)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.2e-06      0.15       3      88 ..      31     119 ..      29     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.2e-06
                           DUF2119   3 gpvrlfvgGlHGdEgkdtskileklkeedlsegllvipn.lekskY.iSTldkeyyesee.gkklidlveklkpeiY 76 
                                       ++ rlf++G   +  +d++kilek++e d++ + ++ p+ + k ++  S  d+     ++ +++l++ ve +  +i+
  gi|488600874|ref|YP_007907345.1|  31 KIARLFIAGNFSRRFDDAKKILEKVSEMDFKADYFLTPSgFVKIPWkFSGFDEALKDGKRwAARLLEGVEINAKQIF 107
                                       689***************************999888775377766547999999988764389999*********** PP

                           DUF2119  77 vElHsYskenyk 88 
                                       + + sYs+ n+ 
  gi|488600874|ref|YP_007907345.1| 108 IGVDSYSSSNLA 119
                                       ******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1876.04
//
Query:       gi|488600875|ref|YP_007907346.1|  [L=153]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-08   34.5   2.6    2.1e-08   34.5   2.6    2.0  2  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 !   34.5   2.6   1.2e-12   2.1e-08       1      37 [.       1      41 [.       1      64 [. 0.71
   2 ?   -2.1   0.1      0.31   5.6e+03      47      57 ..      87      98 ..      75     103 .. 0.45

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.2e-12
                            DUF104  1 MskvIeavYEnGvLKPLek.....vdLkEGeevkikIeeake 37
                                      M+ +Ie+vYEn v+KPL++     v+L++Ge++ ++I+  ++
  gi|488600875|ref|YP_007907346.1|  1 MKVIIEVVYENSVFKPLKPleslgVSLSDGEKLTVEIKV-ES 41
                                      888**************994444457******9888887.33 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.31
                            DUF104 47 k.eadeeeleel 57
                                      + ++++ ++ el
  gi|488600875|ref|YP_007907346.1| 87 NnNVEKFTIYEL 98
                                      233333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1096.73
//
Query:       gi|488600876|ref|YP_007907347.1|  [L=149]
Description: hypothetical protein Asulf_01363 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.0     0.0069   15.9   0.0    1.1  1  H2O2_YaaD  Peroxide stress protein YaaA


Domain annotation for each model (and alignments):
>> H2O2_YaaD  Peroxide stress protein YaaA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.9e-07    0.0069      83     167 ..      27     112 ..      26     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-07
                         H2O2_YaaD  83 vvYkaldaeslseedleyaqehlrIlSglYGlLrpldliqp.YRLemgtklanekdLyefWgekltealneeevlvn 158
                                       +vY +l a+++ e + ++  ++ +IlS+ YG L p +li++ Y + ++    n   ++e  ++  ++ l + + +v 
  gi|488600876|ref|YP_007907347.1|  27 DVYIGLFARTCIEYAEKFYPNNYVILSAKYGFLSPDELIPEdYNVTFNDPKTNPIGVEELRKQVEEKGLMKYDEIVV 103
                                       68999**********************************85487777776665545555555555555555335555 PP

                         H2O2_YaaD 159 LaSkeyska 167
                                       +a ++y ++
  gi|488600876|ref|YP_007907347.1| 104 VAGSNYVNI 112
                                       555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1099.23
//
Query:       gi|488600877|ref|YP_007907348.1|  [L=165]
Description: Transposase-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   89.0   0.1    3.1e-25   88.6   0.1    1.2  1  DDE_3            DDE superfamily endonuclease
      7e-07   29.1   0.0    8.3e-07   28.8   0.0    1.2  1  DDE_1            DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.031   14.2   0.2      0.055   13.4   0.1    1.7  2  P-mevalo_kinase  Phosphomevalonate kinase
      0.042   14.0   0.0      0.077   13.2   0.0    1.4  1  rve              Integrase core domain
      0.078   11.8   0.0        0.1   11.4   0.0    1.2  1  Trp_syntA        Tryptophan synthase alpha chain


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 !   88.6   0.1   8.6e-29   3.1e-25      44     146 .]      34     131 ..       8     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 8.6e-29
                             DDE_3  44 ldekgglafvtfeetlnaedfaeflerlletalqakkivlilDnasiHkseslrelveeeadrlellylPpySPelN 120
                                       ++ +g + ++ f+e+ ++edf+ fl+++ +  +++ +iv+ilDn ++H+++ +re +e+   ++ l+ylPpySP+lN
  gi|488600877|ref|YP_007907348.1|  34 YSLNG-ESVIEFSERNRSEDFISFLRKIRDVNPEK-RIVIILDNFRTHHAKRVREEAEK--LNIALVYLPPYSPDLN 106
                                       44444.667788999999****************8.***********************..**************** PP

                             DDE_3 121 piEivwsklkrellkrrsfksldeLk 146
                                       piE+vw+++kr + +  s  +++eLk
  gi|488600877|ref|YP_007907348.1| 107 PIENVWKSVKRFVSE-VSPLNIEELK 131
                                       *************99.8888888886 PP

>> DDE_1  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.3e-10   8.3e-07      67     151 ..      57     142 ..      27     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.3e-10
                             DDE_1  67 dkrle..aekrkilLlldssrshetvel.leselqniklvflPassasllqPldqgvvselKarYrrqllqalleeq 140
                                        ++++  +++++i+++ld++r+h++  + +e e+ ni lv+lP+ s + l P++  v++ +K+ + +    ++ e++
  gi|488600877|ref|YP_007907348.1|  57 LRKIRdvNPEKRIVIILDNFRTHHAKRVrEEAEKLNIALVYLPPYSPD-LNPIE-NVWKSVKRFVSEVSPLNIEELK 131
                                       44445567899*************99999999***********88876.68997.5899999887777777777777 PP

                             DDE_1 141 nrlskeqkklt 151
                                       +++ k  kklt
  gi|488600877|ref|YP_007907348.1| 132 ETIVKAFKKLT 142
                                       77777666665 PP

>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.5e-05     0.055      61     103 ..      39      79 ..       7      90 .. 0.82
   2 ?   -2.7   0.0       1.6   5.7e+03      25      25 ..     132     132 ..     113     156 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                   P-mevalo_kinase  61 kemikwgeekrkkdpglFcraaiekieaakkdvliisDiRrkt 103
                                       +++i+++e++r++d   F+r++ + ++  +k ++ii D  r++
  gi|488600877|ref|YP_007907348.1|  39 ESVIEFSERNRSEDFISFLRKIRD-VNP-EKRIVIILDNFRTH 79 
                                       679******************998.445.55777777655544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.6
                   P-mevalo_kinase  25 v 25 
                                        
  gi|488600877|ref|YP_007907348.1| 132 E 132
                                       2 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.2e-05     0.077      47     116 ..      49     116 ..      37     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                               rve  47 dastvlalleravarfggvepervlsDngseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlk 116
                                        +++ + +l++  +   ++   +++ Dn ++  +k++re +++l+i + + +p++p+ n  +E+ ++ +k
  gi|488600877|ref|YP_007907348.1|  49 RSEDFISFLRKIRDVNPEK-RIVIILDNFRTHHAKRVREEAEKLNIALVYLPPYSPDLNP-IENVWKSVK 116
                                       6677777777555555554.7999*********************************997.577777666 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05       0.1     119     192 ..      70     144 ..      45     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                                       EEETT.SBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHH CS
                         Trp_syntA 119 livpD.lPleeaeelveaakkkglelvflvapttsderlkevveqaegfvYvvsraGvTgaenavaaevdelver 192
                                       +i+ D   +++a++++e+a+k +++lv l + + + + +++v ++++ fv  vs   +   ++++ +  ++l e 
  gi|488600877|ref|YP_007907348.1|  70 VIILDnFRTHHAKRVREEAEKLNIALVYLPPYSPDLNPIENVWKSVKRFVSEVSPLNIEELKETIVKAFKKLTES 144
                                       45555256789999*****************999*******************9998888888777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      756  (0.0421663); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1114.98
//
Query:       gi|488600878|ref|YP_007907349.1|  [L=160]
Description: Transposase-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-18   67.2   0.5    1.5e-18   67.2   0.5    1.6  2  HTH_32         Homeodomain-like domain
    2.3e-11   43.1   1.0    7.3e-10   38.3   0.2    2.6  2  HTH_33         Winged helix-turn helix
      3e-11   42.8   1.6    7.3e-11   41.5   0.1    2.3  3  HTH_23         Homeodomain-like domain
    4.1e-11   42.7   0.1    2.4e-10   40.3   0.0    2.1  2  HTH_29         Winged helix-turn helix
    1.1e-10   41.5   0.5    7.1e-10   38.9   0.0    2.2  2  HTH_28         Helix-turn-helix domain
    2.7e-05   24.6   0.0    4.5e-05   23.9   0.0    1.4  1  LZ_Tnp_IS481   leucine-zipper of insertion element IS481
    0.00013   21.8   0.0    0.00097   18.9   0.0    2.2  2  DUF746         Domain of Unknown Function (DUF746)
    0.00037   20.5   1.3        0.4   10.8   0.1    2.8  3  HTH_7          Helix-turn-helix domain of resolvase
    0.00038   20.6   0.9     0.0029   17.8   0.0    2.9  3  HTH_17         Helix-turn-helix domain
     0.0004   20.4   2.0    0.00068   19.7   0.6    2.2  2  HTH_Tnp_IS630  Transposase
     0.0028   17.9   0.3     0.0074   16.5   0.0    1.8  2  HTH_Tnp_Tc3_2  Transposase
      0.009   16.0   0.1        2.7    7.9   0.0    2.1  2  DinB           DinB family
  ------ inclusion threshold ------
      0.025   14.7   0.4       0.47   10.6   0.1    2.1  2  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos
      0.027   14.5   0.6        6.5    6.9   0.2    3.0  3  HTH_19         Helix-turn-helix domain
      0.028   14.5   0.8       0.62   10.2   0.0    2.6  2  HTH_3          Helix-turn-helix
      0.032   14.6   0.9        0.2   12.0   0.2    2.3  2  Gp-FAR-1       Nematode fatty acid retinoid binding protein (
      0.042   13.9   0.0        1.1    9.4   0.0    2.5  2  HTH_20         Helix-turn-helix domain
       0.11   12.9   0.0       0.46   10.9   0.0    1.9  2  HTH_26         Cro/C1-type HTH DNA-binding domain
       0.12   12.2   0.5       0.22   11.4   0.2    1.5  2  DUF1854        Domain of unknown function (DUF1854)
       0.14   12.5   0.8       0.84   10.0   0.0    2.2  2  HTH_31         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.3   6.6e+03      47      58 ..      13      24 ..       3      36 .. 0.54
   2 !   67.2   0.5   1.6e-21   1.5e-18       1      73 []      60     131 ..      60     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.3
                            HTH_32 47 Wsprqlaarlae 58
                                      + +++l +r+++
  gi|488600878|ref|YP_007907349.1| 13 LPAEELDKRIKK 24
                                      444555555433 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 1.6e-21
                            HTH_32   1 TvsrwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       T + wlkR+n++G+egL ++  +grp+kl++e++++++++l +e++W+++++++ +++++gvk+S  +v+riL
  gi|488600878|ref|YP_007907349.1|  60 TGYAWLKRWNSSGYEGLIPEFGGGRPSKLTEEQKEELREML-KEREWTTKEVQELIEAEFGVKYSSWQVRRIL 131
                                       789**************************************.667***********9999************8 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.1        94      22      35 ..      56      69 ..      54      71 .. 0.84
   2 !   38.3   0.2   8.2e-13   7.3e-10       5      42 ..     105     142 ..     101     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.1
                            HTH_33 22 ysvsgvyrlLkrlG 35
                                      +++++ y +Lkr+ 
  gi|488600878|ref|YP_007907349.1| 56 VTKATGYAWLKRWN 69
                                      678899******96 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 8.2e-13
                            HTH_33   5 WtlarlaqlieerfgvsysvsgvyrlLkrlGfsyqkPr 42 
                                       Wt++++++lie +fgv+ys+ +v+r+L+   + y kP 
  gi|488600878|ref|YP_007907349.1| 105 WTTKEVQELIEAEFGVKYSSWQVRRILRSFRMKYAKPY 142
                                       **********************************9995 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.1   8.2e-14   7.3e-11       2      49 ..      29      76 ..      28      77 .. 0.96
   2 ?   -2.8   0.0       7.1   6.3e+03      14      25 ..     100     112 ..      98     113 .. 0.69
   3 ?   -1.0   0.1       1.9   1.7e+03      33      42 ..     126     135 ..     126     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 8.2e-14
                            HTH_23  2 asereRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGlegl 49
                                       ++++Rl  ++ l +G+sv+e+A++ gv++ T y wlkr++ +G egl
  gi|488600878|ref|YP_007907349.1| 29 TRVLKRLYFIRYLHKGMSVEEAADLVGVTKATGYAWLKRWNSSGYEGL 76
                                      6899*******************************************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.1
                            HTH_23  14 lae.GlsvreIAr 25 
                                       l+e  ++++e+ +
  gi|488600878|ref|YP_007907349.1| 100 LKErEWTTKEVQE 112
                                       5555799999865 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.9
                            HTH_23  33 Tvyrwlkryr 42 
                                       +v+r+l+ +r
  gi|488600878|ref|YP_007907349.1| 126 QVRRILRSFR 135
                                       699***9985 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   2.7e-13   2.4e-10       8      62 ..      41      93 ..      34      94 .. 0.91
   2 ?   -0.1   0.0       1.1   9.9e+02      28      39 ..     126     137 ..     120     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.7e-13
                            HTH_29  8 laeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlseeqe 62
                                      l +G+s v ++A l+g+++ t y wlkr++  G ++l++  ++grp++ l+eeq+
  gi|488600878|ref|YP_007907349.1| 41 LHKGMS-VEEAADLVGVTKATGYAWLKRWNSSGYEGLIPEFGGGRPSK-LTEEQK 93
                                      5689*8.********************************8899***96.****97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                            HTH_29  28 tvyrwlkrfeeg 39 
                                       +v+r+l+ f+++
  gi|488600878|ref|YP_007907349.1| 126 QVRRILRSFRMK 137
                                       699999999875 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   7.9e-13   7.1e-10       2      50 ..      34      82 ..      33      86 .. 0.88
   2 ?    0.4   0.1      0.84   7.5e+02      18      37 ..     114     135 ..      96     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 7.9e-13
                            HTH_28  2 RleiikllaaGhsvreaArelgisrrtvyrWikryeegGiagLvprrrr 50
                                      Rl  i++l +G+sv eaA ++g++  t y W+kr+++ G +gL p  ++
  gi|488600878|ref|YP_007907349.1| 34 RLYFIRYLHKGMSVEEAADLVGVTKATGYAWLKRWNSSGYEGLIPEFGG 82
                                      56679999************************************96443 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.84
                            HTH_28  18 aArelgi..srrtvyrWikrye 37 
                                       + +e+g+  s+ +v+r ++ ++
  gi|488600878|ref|YP_007907349.1| 114 IEAEFGVkySSWQVRRILRSFR 135
                                       6678999777789999998776 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     5e-08   4.5e-05      13      61 ..      32      80 ..      22     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5e-08
                      LZ_Tnp_IS481 13 GrvllvrrvvedrrtvaqvarelGvslrtaykwlarfraeGldGlldrs 61
                                       + l   r +++  +v ++a  +Gv++ t+y wl r+ + G +Gl+   
  gi|488600878|ref|YP_007907349.1| 32 LKRLYFIRYLHKGMSVEEAADLVGVTKATGYAWLKRWNSSGYEGLIPEF 80
                                      44566678899999*******************************9753 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-06   0.00097       5      37 ..      37      69 ..      33      71 .. 0.93
   2 ?   -0.1   0.0      0.92   8.2e+02      16      37 ..     114     135 ..     111     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                            DUF746  5 lIrlLsqplslaeaadllgtdegiiakwvreFr 37
                                      +Ir+L   +s++eaadl+g+ +++   w++++ 
  gi|488600878|ref|YP_007907349.1| 37 FIRYLHKGMSVEEAADLVGVTKATGYAWLKRWN 69
                                      9***************************99995 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.92
                            DUF746  16 aeaadllgtdegiiakwvreFr 37 
                                        ea + ++ +   +++ +r Fr
  gi|488600878|ref|YP_007907349.1| 114 IEAEFGVKYSSWQVRRILRSFR 135
                                       57777888899999*******9 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 ?   -2.7   0.1       7.4   6.6e+03       1       6 [.       2       7 ..       2       8 .. 0.86
   2 !    8.0   0.0    0.0033         3      17      37 ..      40      60 ..      21      65 .. 0.87
   3 !   10.8   0.1   0.00045       0.4       1      20 [.      83     102 ..      83     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.4
                                     S---SS CS
                             HTH_7 1 GRpskl 6
                                     GR++ +
  gi|488600878|ref|YP_007907349.1| 2 GRKRIY 7
                                     9**988 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0033
                                      STTTT--STTTSSSS---SSS CS
                             HTH_7 17 LleeGisiskIAkevnisRsT 37
                                       l +G+s+ + A+ v+++++T
  gi|488600878|ref|YP_007907349.1| 40 YLHKGMSVEEAADLVGVTKAT 60
                                      5789****************9 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00045
                                       S---SS-HHHHGGGGSSTTT CS
                             HTH_7   1 GRpsklskndinrvvkLlee 20 
                                       GRpskl++++ ++++++l+e
  gi|488600878|ref|YP_007907349.1|  83 GRPSKLTEEQKEELREMLKE 102
                                       9*****************97 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.8   5.2e+03      44      44 ..      19      19 ..       2      39 .. 0.55
   2 !   17.8   0.0   3.2e-06    0.0029       2      34 ..      45      84 ..      45     104 .. 0.83
   3 ?   -0.6   0.0       1.7   1.5e+03       3      10 ..     106     113 ..     105     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.8
                            HTH_17 44 e 44
                                      +
  gi|488600878|ref|YP_007907349.1| 19 D 19
                                      2 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.2e-06
                            HTH_17  2 ltveEaAelLgvsrstvyrlir.......rgelpaakiGr 34
                                      ++veEaA+l gv ++t y +++       +g +p ++ Gr
  gi|488600878|ref|YP_007907349.1| 45 MSVEEAADLVGVTKATGYAWLKrwnssgyEGLIPEFGGGR 84
                                      89*******************7666666688888887666 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.7
                            HTH_17   3 tveEaAel 10 
                                       t++E++el
  gi|488600878|ref|YP_007907349.1| 106 TTKEVQEL 113
                                       99***998 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.4   1.2e+03      61      81 ..       6      26 ..       1      34 [. 0.55
   2 !   19.7   0.6   7.6e-07   0.00068       8      48 ..      34      74 ..      27     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                     HTH_Tnp_IS630 61 lkedvkknpdallkerakkfg 81
                                      + e vk+ p   l +r+kk++
  gi|488600878|ref|YP_007907349.1|  6 IYEVVKHLPAEELDKRIKKLE 26
                                      444555555555555555543 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 7.6e-07
                     HTH_Tnp_IS630  8 rlkvidyiesGggitkaskvfkvgratvyrWlkreelaatk 48
                                      rl  i y+  G ++++a  + +v++at y Wlkr + +  +
  gi|488600878|ref|YP_007907349.1| 34 RLYFIRYLHKGMSVEEAADLVGVTKATGYAWLKRWNSSGYE 74
                                      677899****************************9877654 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.9   2.6e+03       3      23 ..       5      25 ..       3      45 .. 0.54
   2 !   16.5   0.0   8.2e-06    0.0074       6      60 ..      97     152 ..      95     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.9
                     HTH_Tnp_Tc3_2  3 rIvrlvrkdPritlreLanel 23
                                      rI+++v++ P   l + +++l
  gi|488600878|ref|YP_007907349.1|  5 RIYEVVKHLPAEELDKRIKKL 25
                                      677777777664444444444 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 8.2e-06
                     HTH_Tnp_Tc3_2   6 rlvrkdPritlreLanelkee.GksvsreTirrrLrkaglkkrkprkkplLskknr 60 
                                       r++ k+++ t +e+++ ++ e G++ s+  +rr+Lr++ +k  kp +k   +++n+
  gi|488600878|ref|YP_007907349.1|  97 REMLKEREWTTKEVQELIEAEfGVKYSSWQVRRILRSFRMKYAKPYQKDYRKPENA 152
                                       5667899**************************************98876666665 PP

>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0083       7.5      18      38 ..       3      23 ..       2      36 .. 0.88
   2 !    7.9   0.0     0.003       2.7      56     101 ..      62     117 ..      40     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0083
                                      HHHHHHHHCT--CCCTT--SS CS
                              DinB 18 rdrtldaiaaLpdeelkaeng 38
                                      r+r++++++ Lp+eel+++++
  gi|488600878|ref|YP_007907349.1|  3 RKRIYEVVKHLPAEELDKRIK 23
                                      799**************8765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.003
                                       HHHHHHHHH............SSSGGGT---------HHHHHHHHHHHHHHHHCT- CS
                              DinB  56 elwlsrleg..........eegapavddqterkeleeldalrealderliafldql 101
                                       ++wl+r               g+p++  +++++el e+ + re+ +++++++ +++
  gi|488600878|ref|YP_007907349.1|  62 YAWLKRWNSsgyeglipefGGGRPSKLTEEQKEELREMLKEREWTTKEVQELIEAE 117
                                       6677776666777777777789****************************998766 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 ?   10.6   0.1   0.00052      0.47      25      48 ..      43      66 ..      16      74 .. 0.73
   2 ?    2.5   0.0      0.17   1.5e+02       7      39 ..      87     121 ..      83     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                                      --S-HHHHHHHHTS-HHHHHHHHH CS
                       HTH_Tnp_1_2 25 ekltldeiaeevgvsrsTlykWkk 48
                                      + ++++e a+ vgv ++T y W+k
  gi|488600878|ref|YP_007907349.1| 43 KGMSVEEAADLVGVTKATGYAWLK 66
                                      4589******************96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
                                       HS-HHHH.HHHHHHHHHHH--S-HHHHH.HHHTS- CS
                       HTH_Tnp_1_2   7 eLtakQk.kaaellvendyekltldeia.eevgvs 39 
                                       +Lt++Qk  + e+l e+++ ++ ++e+  +e gv+
  gi|488600878|ref|YP_007907349.1|  87 KLTEEQKeELREMLKEREWTTKEVQELIeAEFGVK 121
                                       477777725789*******6666666541466665 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.32   2.9e+02      27      50 ..      20      42 ..       8      43 .. 0.76
   2 ?    3.8   0.0     0.066        60      10      28 ..      42      60 ..      33      67 .. 0.79
   3 ?    6.9   0.2    0.0072       6.5       4      22 ..      96     114 ..      94     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.32
                            HTH_19 27 skisaiEngkkdvpsaelllkiae 50
                                      ++i ++E++ + v+++  + ++++
  gi|488600878|ref|YP_007907349.1| 20 KRIKKLEKDTR-VLKRLYFIRYLH 42
                                      68999999988.887666666665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.066
                            HTH_19 10 elgltqeelaerlgisrsk 28
                                      ++g++ ee a+ +g++++ 
  gi|488600878|ref|YP_007907349.1| 42 HKGMSVEEAADLVGVTKAT 60
                                      89************99765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0072
                            HTH_19   4 LkeaReelgltqeelaerl 22 
                                       L+e+ +e+ +t +e++e +
  gi|488600878|ref|YP_007907349.1|  96 LREMLKEREWTTKEVQELI 114
                                       9***************943 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00069      0.62       7      25 ..      42      60 ..      39      60 .. 0.92
   2 ?    2.0   0.1      0.25   2.3e+02       1      19 [.      96     114 ..      96     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00069
                                      HTTHHHHHHHHHHTSSHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrst 25
                                       +g+s ee+A+++Gv+++t
  gi|488600878|ref|YP_007907349.1| 42 HKGMSVEEAADLVGVTKAT 60
                                      68**************987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.25
                                       HHHHHHHTTHHHHHHHHHH CS
                             HTH_3   1 lkelRkqlglsqeeLAekl 19 
                                       l+e++k++ ++ +e++e++
  gi|488600878|ref|YP_007907349.1|  96 LREMLKEREWTTKEVQELI 114
                                       7999*******99999986 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.61   5.5e+02      62      98 ..      16      50 ..       4      64 .. 0.65
   2 ?   12.0   0.2   0.00022       0.2      16      45 ..      86     116 ..      71     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.61
                          Gp-FAR-1 62 aklkekvdkLspeakeFvkkliakgrkleaqvlagek 98
                                      ++l+++++kL+ +++  v k + ++r l++ +  +e 
  gi|488600878|ref|YP_007907349.1| 16 EELDKRIKKLEKDTR--VLKRLYFIRYLHKGMSVEEA 50
                                      578888888888888..44445566666655555554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
                          Gp-FAR-1  16 knltdeekaqlkevvkn.ykgyknedellaa 45 
                                       ++lt+e+k++l+e+ k+   + k ++el++a
  gi|488600878|ref|YP_007907349.1|  86 SKLTEEQKEELREMLKErEWTTKEVQELIEA 116
                                       79***************7778*******986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.29   2.6e+02      36      50 ..      13      27 ..       4      34 .. 0.82
   2 ?    9.4   0.0    0.0012       1.1      12      40 ..      34      60 ..      30      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.29
                                      S-HHHHHHHHHHHHH CS
                            HTH_20 36 lskntlsyHLrvLee 50
                                      l+  +l++++++Le+
  gi|488600878|ref|YP_007907349.1| 13 LPAEELDKRIKKLEK 27
                                      677789999999997 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHH CS
                            HTH_20 12 RrrilraLaraegltaselaerldlsknt 40
                                      R+ + r+L   +g++++e a++++++k+t
  gi|488600878|ref|YP_007907349.1| 34 RLYFIRYL--HKGMSVEEAADLVGVTKAT 60
                                      66678888..****************987 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 ?   -1.2   0.0       3.3     3e+03       9      32 ..      43      66 ..      41      68 .. 0.83
   2 ?   10.9   0.0   0.00052      0.46       2      31 ..      96     131 ..      95     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.3
                            HTH_26  9 rgitkseLargtgisaatlsrlvk 32
                                      +g+++ e a  +g+++at + ++k
  gi|488600878|ref|YP_007907349.1| 43 KGMSVEEAADLVGVTKATGYAWLK 66
                                      889999999999999999888876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00052
                            HTH_26   2 LrelmadrgitkseLargtg......isaatlsrlv 31 
                                       Lre++++r+ t++e+++ ++       s+ ++ r++
  gi|488600878|ref|YP_007907349.1|  96 LREMLKEREWTTKEVQELIEaefgvkYSSWQVRRIL 131
                                       9***************95553333337777777765 PP

>> DUF1854  Domain of unknown function (DUF1854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.4   4.8e+03      41      41 ..      28      28 ..      11      53 .. 0.59
   2 ?   11.4   0.2   0.00024      0.22      35      77 ..      85     128 ..      83     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.4
                           DUF1854 41 e 41
                                      +
  gi|488600878|ref|YP_007907349.1| 28 D 28
                                      1 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00024
                           DUF1854  35 ladLdeesrklleeeLarrefvp.eIkrIksvsekagpstweve 77 
                                       +++L+ee+++ l+e L++re++  e++++++ +  +++s+w+v 
  gi|488600878|ref|YP_007907349.1|  85 PSKLTEEQKEELREMLKEREWTTkEVQELIEAEFGVKYSSWQVR 128
                                       689*****************97538*****************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 ?   10.0   0.0   0.00094      0.84      13      30 ..      43      60 ..      16      68 .. 0.87
   2 ?    0.6   0.3      0.82   7.4e+02       5      33 ..      95     129 ..      94     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00094
                            HTH_31 13 aGLsqeevAerlgvsest 30
                                       G+s ee+A+++gv+++t
  gi|488600878|ref|YP_007907349.1| 43 KGMSVEEAADLVGVTKAT 60
                                      49************9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.82
                            HTH_31   5 lLralReraGLsqeevAerlg......vsestlsr 33 
                                       +Lr++ +++ ++ +ev e++       +s  +++r
  gi|488600878|ref|YP_007907349.1|  95 ELREMLKEREWTTKEVQELIEaefgvkYSSWQVRR 129
                                       68887788889999999988766665555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1694  (0.0944838); expected 358.6 (0.02)
Passed bias filter:                     1106  (0.0616878); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); 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 0.30s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1131.34
//
Query:       gi|488600879|ref|YP_007907350.1|  [L=368]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   92.8   0.0    5.3e-26   91.4   0.0    1.7  2  AGOG      N-glycosylase/DNA lyase


Domain annotation for each model (and alignments):
>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0     0.092   1.7e+03      94     123 ..      91     120 ..      86     139 .. 0.69
   2 !   91.4   0.0     3e-30   5.3e-26       7     231 ..     133     351 ..     127     360 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.092
                                       HHHHHHHHHHHCCHHHTTTHHHHHHHHHTH CS
                              AGOG  94 reakikRiekivefledleleelksylenl 123
                                       ++ +++R+e ++++  + + ++++++ + +
  gi|488600879|ref|YP_007907350.1|  91 LKLRVERLETVERVEASFQPKKVETPQSSV 120
                                       566888999998888888888888877443 PP

  == domain 2  score: 91.4 bits;  conditional E-value: 3e-30
                                       CHHHHHHHHHCCTSHHHHHHHHHHCCC-H.HHHHHHHHHHHHT-SS-TT-HH.HHHHHHHHHHCTS--SSHHHHHHH CS
                              AGOG   7 lgieevlkleekvDpQykaveelveklgedelfvklvilNaLvSYqLsgrGE.ewWkefskyfsekeiknileefik 82 
                                       + +e   +++++  p +k ++e +e++g    f+ l+i+ +L  +qL g+ E ++W ++ +++++++  n  +e+  
  gi|488600879|ref|YP_007907350.1| 133 IPVEIWDRVVQE-EPEWKHMREFLESYGF-GRFAVLMIAAGLNDFQLKGKAEvAYWPKMRELLKRNNTPNSPRELES 207
                                       555555566666.799*************.88889999**************77*********************** PP

                                       HHHH-TTS-TTHHHHHHHHHHHCCH.HHTTTHHHHHHHH.HTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHH CS
                              AGOG  83 flekskgnrrlreakikRiekivef.ledleleelksyl.enleelleelakilgskkesKTvvFavKmlyYalria 157
                                       +l +   n rl + k++R++++ ++ l +  ++ +  ++ en  +++++la+++ ++++ KT+vFa+K l+ al  +
  gi|488600879|ref|YP_007907350.1| 208 ILAEFYANERLPDLKLRRLNRFLSSrLAEWLWNAMPGEVtENFLRIWYDLAATMRQERSVKTIVFAMKCLGIALL-M 283
                                       *********************9765257889999*9999899*********************************.8 PP

                                       HTS-----TTS-----HHHHHHHHHTTS-SS-HHHHHHTHCCHCS.HHHHHHHH.....HHHHT--HHHHHHHHHHH CS
                              AGOG 158 lgeeiplpfeipiPvDvRiakltktsglielknekklarkelvqeevieaWkev.....sreseiPplhlDsllWvl 229
                                       +ge     ++ipiPvD+R+   tk +g++              +e+v ++W +v     +r  ei  +hlDsl+W +
  gi|488600879|ref|YP_007907350.1| 284 AGESNFCFERIPIPVDYRVREFTKRTGVVVRD-----------DEDVRTFWGKVleelrGRGLEINMIHLDSLIWQI 349
                                       899899999***************88888664...........466778999994444456689***********77 PP

                                       CC CS
                              AGOG 230 gk 231
                                       g 
  gi|488600879|ref|YP_007907350.1| 350 GV 351
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2290.51
//
Query:       gi|488600880|ref|YP_007907351.1|  [L=193]
Description: hypothetical protein Asulf_01367 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-09   38.1   0.0    5.8e-09   36.3   0.0    1.8  1  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 !   36.3   0.0   3.2e-13   5.8e-09      10     114 ..      70     182 ..      32     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 3.2e-13
                                       TTEEEEEEEEEEEEEETTS-CEET........T-.SEEEEEEEEEEE.-SSS-EEEEGGGEEEEETTEEE-BEEESC CS
                           DUF4352  10 gdlevtVnsveytksvgkneylqp........daggeflivdvtvkN.kgkealtvnssqfkLkdgdgkeydadlsa 77 
                                       g +e+tV ++  +k + + ++ ++        ++g+e+l+v+v+++   gk +l +++++fk + ++g+ y++++  
  gi|488600880|ref|YP_007907351.1|  70 GTFEITVLDY--MKGEEAYRIIKSgnmfnpeaEEGYEYLLVKVKFRYaSGKTSLPISEYSFKAY-SNGAGYSPAFVV 143
                                       5677888888..333333444444777778889*************99***************9.889999999987 PP

                                       CCCTTB.--EEEE-TT-EEEEEEEEEESTT-CG.EEEEE CS
                           DUF4352  78 sskadd.lflgtlnpGkkvtGklvFdvpkgkkk.leLey 114
                                         +    +   +l pG++++G+++F+vp+gk+  l +ey
  gi|488600880|ref|YP_007907351.1| 144 LPESFPeFKTVNLMPGGEIEGWIAFVVPEGKEAlLAYEY 182
                                       55554469999*******************997655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1139.19
//
Query:       gi|488600881|ref|YP_007907352.1|  [L=261]
Description: hypothetical protein Asulf_01368 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.073   13.6   0.1       0.21   12.1   0.1    1.8  1  HTH_27       Winged helix DNA-binding domain
       0.15   12.0   0.3       0.35   10.8   0.0    1.7  2  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.4e-05      0.21      38      68 .]     221     248 ..     220     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                            HTH_27  38 slkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +l+kL+  G++er    +++r+ r+ lT++G
  gi|488600881|ref|YP_007907352.1| 221 VLDKLESEGYIERV---KEGRYNRIVLTEEG 248
                                       699********888...789**********9 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.9e-05      0.35      73     124 ..      80     130 ..      47     135 .. 0.66
   2 ?   -2.3   0.0      0.42   3.8e+03      60      84 ..     201     225 ..     179     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.9e-05
                       Cas_APE2256  73 lrnLveklarevknkkregekvlinaTgGfKpeiavltlvallladevyYih 124
                                       ++  + k+++ + ++k++g +v+in+++ f   +av++ +a  + d ++Y  
  gi|488600881|ref|YP_007907352.1|  80 FESVLSKISELIVQEKMRGARVYINISA-FGRLVAVAASLAGWYHDCIVYYV 130
                                       456788999999999***********97.55555555555555555555544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.42
                       Cas_APE2256  60 klsdlgreeFreglrnLveklarev 84 
                                       +++ ++r e+++++++L + + +++
  gi|488600881|ref|YP_007907352.1| 201 RVERKDRREYQRAINKLNRLVLDKL 225
                                       4667777777777777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1642.28
//
Query:       gi|488600882|ref|YP_007907353.1|  [L=96]
Description: hypothetical protein Asulf_01369 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.3   0.2       0.24   11.2   0.2    2.2  2  UvrD_C_2  UvrD-like helicase C-terminal domain
      0.061   12.9   0.4       0.16   11.5   0.1    1.7  2  AAA_12    AAA domain


Domain annotation for each model (and alignments):
>> 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 ?   11.2   0.2   2.7e-05      0.24      41      52 .]       2      13 ..       1      13 [. 0.94
   2 ?    0.6   0.0     0.055     5e+02      17      30 ..      44      57 ..      43      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.7e-05
                          UvrD_C_2 41 avTRAreklilv 52
                                      avTRA++kli+v
  gi|488600882|ref|YP_007907353.1|  2 AVTRAKKKLIVV 13
                                      9*********98 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.055
                          UvrD_C_2 17 aVivfdpdlaaarm 30
                                      aV+++dp++ + + 
  gi|488600882|ref|YP_007907353.1| 44 AVFLADPSMFSNEL 57
                                      79*****9777654 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.8e-05      0.16     184     198 ..       2      16 ..       1      17 [. 0.91
   2 ?   -0.6   0.0     0.097   8.7e+02      40      49 ..      54      63 ..      29      89 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.8e-05
                            AAA_12 184 alTRAkskliivGnk 198
                                       a+TRAk+kli+vG++
  gi|488600882|ref|YP_007907353.1|   2 AVTRAKKKLIVVGSR 16 
                                       99***********86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.097
                            AAA_12 40 kgkLkdaesv 49
                                      +++L+ ae+ 
  gi|488600882|ref|YP_007907353.1| 54 SNELERAEKE 63
                                      3333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 619.14
//
Query:       gi|488600883|ref|YP_007907354.1|  [L=61]
Description: hypothetical protein Asulf_01370 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 409.50
//
Query:       gi|488600884|ref|YP_007907355.1|  [L=69]
Description: hypothetical protein Asulf_01371 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.4   3.0     0.0044   16.4   3.0    1.0  1  DUF4763   Domain of unknown function (DUF4763)
  ------ inclusion threshold ------
      0.011   15.7   1.2      0.014   15.4   1.2    1.2  1  DUF1128   Protein of unknown function (DUF1128)


Domain annotation for each model (and alignments):
>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.0   4.9e-07    0.0044      45     107 ..       4      65 ..       1      67 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.9e-07
                           DUF4763  45 eeeeldLdeiydelekiKqrvlelrskLalnvpecPeidecvdedlelelltseqpeileLqr 107
                                       + +++ L+eiy e++ki++++++l++ ++ +  +  e++  + ++l++e l+ e+++  eL+r
  gi|488600884|ref|YP_007907355.1|   4 TVNDTLLQEIYSEVKKIREKLELLEELII-PSEKVSEQELQEIRKLKEESLKGEHVDWGELKR 65 
                                       677889****************9998888.435556666666666666777777777777666 PP

>> DUF1128  Protein of unknown function (DUF1128)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.2   1.5e-06     0.014       7      44 ..      11      48 ..       5      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-06
                           DUF1128  7 enleymieeikekLkmvnaavlkaedfseekyedlkdl 44
                                      +++   +++i+ekL+++   ++ +e++se++ +++++l
  gi|488600884|ref|YP_007907355.1| 11 QEIYSEVKKIREKLELLEELIIPSEKVSEQELQEIRKL 48
                                      5677889****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1328  (0.0740699); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 525.30
//
Query:       gi|488600885|ref|YP_007907356.1|  [L=86]
Description: hypothetical protein Asulf_01372 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   31.4   0.1    1.9e-07   31.2   0.1    1.0  1  EVE       EVE domain
  ------ inclusion threshold ------
       0.12   12.5   1.1       0.25   11.5   1.1    1.5  1  Bombesin  Bombesin-like peptide


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 !   31.2   0.1   2.2e-11   1.9e-07      56     135 ..       3      81 ..       1      84 [. 0.85

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.2e-11
                                       -EEEEEEEEECEEEE-GGGG-TTSTT--TTTBTTS-.-EEEEEEEEEEEEEEEEHHHHTTHG.TCTTSHHHHCC..T CS
                               EVE  56 qaivgiaeVvseaypdetqfdpkskyydpkskkekp.wlrvdvkpvkklkrplslkelkaep.elegmkllrkg..r 128
                                       ++iv+++e vse+ +d++++     ++ p+ ++++  +lr+++kpvk +++p+++k l ++  ++++++ ++ +   
  gi|488600885|ref|YP_007907356.1|   3 PRIVAVYEAVSEVFKDSKKI-----FKTPEGMGNESfPLRIKLKPVKIFDEPVEFKPLIPKLkFIKNKQKWTGHlmG 74 
                                       89***************999.....7779999999999********************9953377888888887666 PP

                                       -SEEEE- CS
                               EVE 129 lsvrpvt 135
                                        ++r+++
  gi|488600885|ref|YP_007907356.1|  75 KAIREIP 81 
                                       6677766 PP

>> Bombesin  Bombesin-like peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   2.8e-05      0.25       6      12 ..      69      75 ..      67      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                          Bombesin  6 vGHlMGK 12
                                      +GHlMGK
  gi|488600885|ref|YP_007907356.1| 69 TGHLMGK 75
                                      9*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 585.35
//
Query:       gi|488600886|ref|YP_007907357.1|  [L=70]
Description: hypothetical protein Asulf_01373 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 438.25
//
Query:       gi|488600887|ref|YP_007907358.1|  [L=535]
Description: hypothetical protein Asulf_01374 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   68.8   6.1    9.9e-10   38.2   3.2    2.9  3  N6_Mtase         N-6 DNA Methylase
    1.6e-08   35.0   2.3    1.9e-08   34.8   0.4    2.2  2  Eco57I           Eco57I restriction-modification methylase
    1.6e-06   28.2   1.2    1.6e-06   28.2   1.2    2.3  2  TaqI_C           TaqI-like C-terminal specificity domain
      6e-06   25.9   0.0    0.00095   18.8   0.0    2.9  2  MTS              Methyltransferase small domain
    0.00018   21.3   0.1      0.031   14.0   0.0    2.6  2  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
       0.03   14.2   0.0      0.066   13.1   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
       0.19   12.5   0.0       0.53   11.0   0.0    1.8  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.6e-10   4.1e-07      18      64 ..       4      50 ..       1      58 [. 0.86
   2 !   38.2   3.2   3.9e-13   9.9e-10     122     254 ..      85     219 ..      56     243 .. 0.78
   3 ?   -0.6   0.0      0.25   6.4e+02     251     275 ..     305     329 ..     297     363 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.6e-10
                          N6_Mtase 18 aeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqa 64
                                       +e +k+ G++fTP+ v  ++v+l+ + +++ ++Dp++G+g + ++ 
  gi|488600887|ref|YP_007907358.1|  4 NKEIKKRYGQYFTPSYVADFMVSLISKPKNTLILDPCAGTGIFPISL 50
                                      577899*******************7777778*********887765 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 3.9e-13
                          N6_Mtase 122 kdkkfdvvvaNppfnqkew......kektlekderfreavapksnadlafllhiieslkpkGraavvlangvLfr.g 191
                                        +++fdv++ Npp+    w      +++  +k ++++ ++   s   +af+ h i++lk++G   ++ +  v++  +
  gi|488600887|ref|YP_007907358.1|  85 PNEQFDVIIGNPPYVR--WrnipteWKELFKKSKYWSAIMNGLSDLTYAFIYHSINMLKENGELIFITP--VFWTqT 157
                                       578***********75..333566567778888889999***********************9866655..666638 PP

                          N6_Mtase 192 gkegkIrkalvekdlveavialpe.klFyntsiptcilvlkkekaerkgkvlfidaseefkkkd 254
                                        +++++r +l++  +ve +i+l e k+F +  +  +i+++k  k++ ++ + +i+ +++ k + 
  gi|488600887|ref|YP_007907358.1| 158 VHGARLRDYLTKYGHVEVLINLNEmKIFKE--VSSTIIIFKYIKKKVEKPIKIINLHTKDKLTV 219
                                       88899*****************87589976..567788888777779999****9999887764 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.25
                          N6_Mtase 251 kkkdrkknklteediekildtykek 275
                                       + ++   +klt+e+ eki+ +yk++
  gi|488600887|ref|YP_007907358.1| 305 SLENIDIKKLTPEEREKIIYVYKAR 329
                                       555566799*************998 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.4   7.4e-12   1.9e-08       2      98 ..      88     195 ..      87     203 .. 0.83
   2 ?   -2.7   0.1       3.2   8.2e+03      30      46 ..     361     377 ..     342     409 .. 0.46

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 7.4e-12
                            Eco57I   2 kfdviiGNPPYqeseak.kelkaleek..........akdiyqkFvekalkle..dkylaliiparflasgkglkef 65 
                                       +fdviiGNPPY + +++  e+k+l +k           +d+   F+ +++++   ++ l +i+p  ++ +   ++++
  gi|488600887|ref|YP_007907358.1|  88 QFDVIIGNPPYVRWRNIpTEWKELFKKskywsaimngLSDLTYAFIYHSINMLkeNGELIFITPVFWT-QTVHGARL 163
                                       7***********98876356666655578999999998899999*******987778899*******9.8888999* PP

                            Eco57I  66 rekllkdkklkklvefedskevFkdveikggil 98 
                                       r+ l k  ++++l+++++ k +Fk+v+ +  i 
  gi|488600887|ref|YP_007907358.1| 164 RDYLTKYGHVEVLINLNEMK-IFKEVSSTIIIF 195
                                       ****************9999.***987554444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                            Eco57I  30 diyqkFvekalkledky 46 
                                       + y+k +    kl ++y
  gi|488600887|ref|YP_007907358.1| 361 NFYNKLISFKEKLLKRY 377
                                       34444444444444444 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 ?   -1.7   0.4       1.1   2.9e+03      22      68 ..     196     244 ..     178     253 .. 0.62
   2 !   28.2   1.2   6.1e-10   1.6e-06      20     120 .]     359     485 ..     341     485 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                            TaqI_C  22 dlikkklkneka.kelfeekpKilvrdisk.kld.aaydekayyvlntly 68 
                                       ++ikkk++++ +  +l++ k K+ v +++k kl   ++  ++ y+++ +y
  gi|488600887|ref|YP_007907358.1| 196 KYIKKKVEKPIKiINLHT-KDKLTVNHLKKvKLLiETLKGEESYIQEGVY 244
                                       455555555554455555.6777766666643323556666666665555 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 6.1e-10
                            TaqI_C  20 Yldlikkklkneka..........kelfe............ekpKilvrdiskkld.....aaydekayyvlntlyl 69 
                                       Y ++++k ++ +++            +++             ++Ki+v+  ++  +     +ay e  yy+ +++  
  gi|488600887|ref|YP_007907358.1| 359 YPNFYNKLISFKEKllkrynygieIPWWHwvflrnkhllekYNEKIFVPSKERYDSkgyfrFAYVEGPYYATQDVTT 435
                                       555555555444433222222222222224444444444445599*997655433234555**************** PP

                            TaqI_C  70 liakdelevslkyllgiLNSklikfyykkiystlrggysrlkrkeleklPi 120
                                       + +k+ ++  +ky+l++LNS+ ++ y+      +rgg   ++ + l+++Pi
  gi|488600887|ref|YP_007907358.1| 436 ICIKNTVREGIKYILALLNSEPYQEYILYKG-FSRGGVFDFSERPLADIPI 485
                                       ************************9987766.56799999*********98 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.7e-07   0.00095      21     124 ..      22     114 ..      19     118 .. 0.81
   2 ?    3.5   0.0     0.018        46     116     143 ..     127     154 ..     121     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.7e-07
                                       HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS- CS
                               MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekk 97 
                                       +++++ ++k ++  +lD ++G+G+  ++l k+  + +++++++d         +l  n+ e+e++ +d l+  ++++
  gi|488600887|ref|YP_007907358.1|  22 DFMVSLISKPKNTLILDPCAGTGIFPISLRKAGFK-NIVAYEIDE--------TL-PNHSEIEILRRDFLKLKPNEQ 88 
                                       6888999998999999*******999999998877.688888874........44.56678**************** PP

                                       EEEEEE---STTTCHCHHHHHHHHHHH CS
                               MTS  98 fdlivsNPPfhagkatelavaeeliae 124
                                       fd+i+ NPP+ + ++   + ++el+++
  gi|488600887|ref|YP_007907358.1|  89 FDVIIGNPPYVRWRN-IPTEWKELFKK 114
                                       *********998777.44455566665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHEEEEEEEEEEEETTS CS
                               MTS 116 avaeeliaeAkeaLkegGeLliVanrkl 143
                                       +++ ++i ++ ++Lke+GeL++++  + 
  gi|488600887|ref|YP_007907358.1| 127 DLTYAFIYHSINMLKENGELIFITPVFW 154
                                       577899***************9976554 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0095        24      17      44 ..      21      48 ..      17      54 .. 0.88
   2 !   14.0   0.0   1.2e-05     0.031     103     136 ..      71     103 ..      56     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0095
                                      HHHHHHHTT--TTS-EEETT-TTSHHHH CS
                           UPF0020 17 AaalvrlagwkpgepllDPmCGsGtilI 44
                                      A  +v l    +++ +lDP  G+G ++I
  gi|488600887|ref|YP_007907358.1| 21 ADFMVSLISKPKNTLILDPCAGTGIFPI 48
                                      667888888889999**********999 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                                       GGEEEEE--GGG--STTS---EEEE--------- CS
                           UPF0020 103 dliefsqadaakLrlkegevdvivtnpPYGerlg 136
                                        +ie+   d+ kL+ +++++dvi++npPY +  +
  gi|488600887|ref|YP_007907358.1|  71 SEIEILRRDFLKLK-PNEQFDVIIGNPPYVRWRN 103
                                       568888999*****.999***********76555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-05     0.066      21      89 ..      31      95 ..      13     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                   Methyltransf_23 21 raggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae.kakkaqkdqfdeqeaaepqgkfdlIvlr 89
                                      +++  +Ld  +GtGi+  +lr+ gf +++++++++ + +  e ++    + +       +p+++fd+I+ +
  gi|488600887|ref|YP_007907358.1| 31 PKNTLILDPCAGTGIFPISLRKAGFkNIVAYEIDETLPNHSEiEILRRDFLKL------KPNEQFDVIIGN 95
                                      5556689******************99******99888876665555555555......799999999877 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.53       1      71 [.      36      95 ..      36     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71
                                      +Ld ++GtG + + l k+ g +++++ +i+e++ ++          ++e+++ d+ +l+ ++++fD+++ +
  gi|488600887|ref|YP_007907358.1| 36 ILDPCAGTGIFPISLRKA-GFKNIVAYEIDETLPNHS---------EIEILRRDFLKLK-PNEQFDVIIGN 95
                                      89***************9.69*********9987642.........6888999999998.56799999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3511.56
//
Query:       gi|488600888|ref|YP_007907359.1|  [L=293]
Description: hypothetical protein Asulf_01375 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-11   42.0   2.3    8.8e-11   41.6   2.3    1.2  1  Endonuc-HincII  Restriction endonuclease HincII
  ------ inclusion threshold ------
      0.041   13.8   1.4       0.11   12.4   1.4    1.8  1  PBECR3          phage-Barnase-EndoU-ColicinE5/D-RelE like nuc


Domain annotation for each model (and alignments):
>> Endonuc-HincII  Restriction endonuclease HincII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   2.3   9.9e-15   8.8e-11      15     235 ..      28     268 ..      14     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 9.9e-15
                    Endonuc-HincII  15 sgtlsghaagepfdkhvykelkkelskqtfrqyeylndlysknpav.igfkerlklfns...ptvlfllsrgk..aa 85 
                                           sg a+g pf+    ++l+ e+  +tf q eyl ++  +  +   +  + ++++      t  +++sr +  +a
  gi|488600888|ref|YP_007907359.1|  28 MSRASGSASGLPFEEWTKNKLN-ECGFKTFLQEEYLLEVVRELKEKgHSNSQIERIIRDtwwGTSNYMISRNQlnHA 103
                                       45679**********9998885.7999*********98875433220222222233322111566778888753278 PP

                    Endonuc-HincII  86 tekwsle.nlfeekqndtadilv.....vkdefyel..vdvktrniskkaqapniisayklaqtcakmldnke..fd 152
                                        ++  l+ n     q+  adi++     + d++ ++  ++vk+ n+ + ++ pniisa ++ +    +l+ k    d
  gi|488600888|ref|YP_007907359.1| 104 FNQHALNqNDPPAYQQSIADIILfygndLVDNINDIvaINVKSHNLDRPSRDPNIISAKRIIDYMKDILETKPsiID 180
                                       89999973556788999***98722222235556663357899***************************985337* PP

                    Endonuc-HincII 153 sfsinylevdwklegeklvcvdthfaelfksnpeel.yinwaaamqiqfhvsdldqlfegnk....eewakrylkhf 224
                                       + ++ ++++ ++  +      +    ++f+ + +++  in+ aa+qiq+hv+d+ +l   +k    e  a+++ k +
  gi|488600888|ref|YP_007907359.1| 181 KVNLWFIGIYYRQSSGYASIEEIYIKDFFRLDVKKIpTINFDAAIQIQWHVKDMVELESQDKltfiESLAEEFNKRW 257
                                       ************9999999999999******9999857**************9865544444222367788888888 PP

                    Endonuc-HincII 225 vtqakkraedm 235
                                       v   ++r+ ++
  gi|488600888|ref|YP_007907359.1| 258 VEFVDRRTASI 268
                                       88888887665 PP

>> PBECR3  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.4   1.2e-05      0.11      23      84 ..      92     166 ..      72     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                            PBECR3  23 kilidpgaikHilkrH.gnqstekdrgqi....dianipdiiknPDkviyggknkk.......eksieyvKki.n 84 
                                       +++i+ + ++H+ ++H  nq+++  ++q      + + +d ++n + ++ +++++        +++i+++K+i +
  gi|488600888|ref|YP_007907359.1|  92 NYMISRNQLNHAFNQHaLNQNDPPAYQQSiadiILFYGNDLVDNINDIVAINVKSHnldrpsrDPNIISAKRIiD 166
                                       6789************99*****9999996655233336777777777777777666777888899999999943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1661.05
//
Query:       gi|488600889|ref|YP_007907360.1|  [L=145]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   84.0   0.7    1.1e-23   83.9   0.7    1.0  1  EVE             EVE domain
      0.004   17.0   0.0     0.0048   16.8   0.0    1.3  1  Dev_Cell_Death  Development and cell death domain
  ------ inclusion threshold ------
      0.089   12.7   0.1        5.2    7.0   0.0    2.3  2  DUF4609         Domain of unknown function (DUF4609)


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 !   83.9   0.7   1.8e-27   1.1e-23       1     143 [.       2     142 ..       2     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 1.8e-27
                                       -EEEEEEBHHTSHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEE..ETSSS...S-EEEEEEEEECEEEE-G CS
                               EVE   1 ayWllksepdefsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfY..hsgek...lqaivgiaeVvseaypde 72 
                                       +yWl+++ ++  ++  +  k +++W gv++ +++ ++ ++k+GD++l+Y  +++ek    ++iv+++e vse+ +d+
  gi|488600889|ref|YP_007907360.1|   2 KYWLCITTEE--NWRVI--KDKNIW-GVPE-RHKSTIARVKPGDKLLIYlkQEREKkvlVPRIVAVYEAVSEVFRDS 72 
                                       7*********..9***9..99****.****.66666666**********98444445899***************** PP

                                       GGG-TTSTT--TTTBTTS-.-EEEEEEEEEEEEEEEEHHHHTTHG.TCTTSHHHHCC..T-SEEEE-HHHHHHHH CS
                               EVE  73 tqfdpkskyydpkskkekp.wlrvdvkpvkklkrplslkelkaep.elegmkllrkg..rlsvrpvteedwelil 143
                                       +++     ++ p+ +++++ +lr+++kpv+ +++p+++k l ++  +++++k ++ +    +vr+++eed++li+
  gi|488600889|ref|YP_007907360.1|  73 KKI-----FKTPAGMGNETfPLRIKLKPVRIFDEPVEFKPLIPKLkFVKNKKKWTGHlmGKAVREIPEEDYKLIV 142
                                       999.....7779999999999********************995437799999999988999************7 PP

>> Dev_Cell_Death  Development and cell death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     8e-07    0.0048      14      83 ..      15      94 ..       4     135 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8e-07
                    Dev_Cell_Death 14 ecfrkklfglpaeklslvkkikpglkLfLfdyderk.......LyGvfeAasdGglniepkafts....ekskfpaQvr 81
                                         +k++ g+p++++s++ ++kpg kL+++  +er+       +  v+eA s+     ++k f++     +++fp  ++
  gi|488600889|ref|YP_007907360.1| 15 VIKDKNIWGVPERHKSTIARVKPGDKLLIYLKQEREkkvlvprIVAVYEAVSEVFR-DSKKIFKTpagmGNETFPLRIK 92
                                      5567899***********************77776422333335688998887543.3445554456667777888777 PP

                    Dev_Cell_Death 82 fk 83
                                      +k
  gi|488600889|ref|YP_007907360.1| 93 LK 94
                                      77 PP

>> DUF4609  Domain of unknown function (DUF4609)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00087       5.2      34      57 ..       7      30 ..       5      35 .. 0.86
   2 ?    3.4   0.0     0.012        70       9      21 ..      48      60 ..      44      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00087
                           DUF4609 34 sigseeqrTirEqadwGpysRHRn 57
                                      ++  e+ r i++++ wG  +RH++
  gi|488600889|ref|YP_007907360.1|  7 ITTEENWRVIKDKNIWGVPERHKS 30
                                      5667889***************85 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                           DUF4609  9 sskkkvviPqiii 21
                                        +kkv +P+i+ 
  gi|488600889|ref|YP_007907360.1| 48 EREKKVLVPRIVA 60
                                      45788******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 906.33
//
Query:       gi|488600890|ref|YP_007907361.1|  [L=83]
Description: hypothetical protein Asulf_01377 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   31.3   0.0    2.3e-07   30.7   0.0    1.3  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 !   30.7   0.0   1.3e-11   2.3e-07       2      55 ..      21      73 ..      20      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.3e-11
                                      HCHHHHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHH CS
                        HicA_toxin  2 reviklLeklGfevvrqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkq 55
                                      ++++k+ e +Gf++++ kGSH+++++++ ++i+ + +  +   kp+++k++lk 
  gi|488600890|ref|YP_007907361.1| 21 EDLCKAAELFGFKFRGGKGSHRVYVREGVKEILNFQNV-KGKAKPYQVKQLLKV 73
                                      69************************999996655544.7************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 607.10
//
Query:       gi|488600891|ref|YP_007907362.1|  [L=80]
Description: hypothetical protein Asulf_01378 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-13   49.8   0.0    3.5e-13   49.7   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 !   49.7   0.0     2e-17   3.5e-13       1      63 [.       4      67 ..       2      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2e-17
                   HicB_lk_antitox  1 ypiaiek.dedsaygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssiee 63
                                      y i i   +ed+ y  vvP+lpGc   gdt eea++++k aiel++e++ ++g+eip+p   e 
  gi|488600891|ref|YP_007907362.1|  4 YTIEIFYsEEDEGYIAVVPELPGCSAFGDTEEEALKEIKTAIELWIETAKKEGREIPKPMGKEL 67
                                      555555437889*********************************************9975544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); 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 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 564.23
//
Query:       gi|488600892|ref|YP_007907363.1|  [L=138]
Description: hypothetical protein Asulf_01379 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  123.9   2.7    3.5e-36  123.4   2.7    1.2  1  DUF365    Domain of unknown function (DUF365)


Domain annotation for each model (and alignments):
>> DUF365  Domain of unknown function (DUF365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   2.7   1.9e-40   3.5e-36       1      82 [.      40     126 ..      40     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 1.9e-40
                                       EEEEE---STT-B--EEEEEEEEEEES-THHHHHHTSTTBSS-HHHHHHHHHHHHHT.....----SS---EEEEEE CS
                            DUF365   1 mklvfyasredtGfvGeaeikrvvlsedpleifekygdrvfltkeelkkyvkskerw.....rkgkkrkkawlvlel 72 
                                       +k+vfy+s+edtGfvGea+ikr++l+edp+++fe ygdr+fltkeelk+y+ks+erw     ++gk++kk+wl++el
  gi|488600892|ref|YP_007907363.1|  40 IKFVFYQSHEDTGFVGEAKIKRIILQEDPMKFFEVYGDRIFLTKEELKEYIKSQERWksgwkSRGKEKKKLWLAIEL 116
                                       59*******************************************************8888878999********** PP

                                       EEEEE--S-B CS
                            DUF365  73 edikkydkvv 82 
                                       edikky+k  
  gi|488600892|ref|YP_007907363.1| 117 EDIKKYEKQS 126
                                       ******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 933.93
//
Query:       gi|488600893|ref|YP_007907364.1|  [L=161]
Description: hypothetical protein Asulf_01380 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   20.2  15.7      0.074   13.0   8.9    2.1  2  Rhomboid         Rhomboid family
  ------ inclusion threshold ------
        1.9    8.8  15.4        3.3    8.0   7.0    2.3  2  DUF2304          Uncharacterized conserved protein (DUF2304)


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 !   11.2   3.8   3.1e-05      0.28      71     121 ..      16      66 ..       1      75 [. 0.74
   2 !   13.0   8.9   8.3e-06     0.074      71     146 ..      54     145 ..      53     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                                       -EESSHHHHHHHHHHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHCT CS
                          Rhomboid  71 plvGaSGaifgllgallvlvprnrkllrkliiallllllfillnlvlgllp 121
                                        ++G+SG++++l+g++++ v  n  +  k   +  ++++++ +++v   ++
  gi|488600893|ref|YP_007907364.1|  16 ETIGFSGIVSALVGLYAFSVALNLYQKSKGCKFSFFFVFLLGVSVVAFTYG 66 
                                       579*****************9999988888888555555555555544444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.3e-06
                                       -EESSHHHHHHHHHHHHHHHHCCCCGS----HC..............CCCCCCCCCCHHHCTSS.....STTTHHHH CS
                          Rhomboid  71 plvGaSGaifgllgallvlvprnrkllrkliia...........llllllfillnlvlgllpra.....ggvsnlAH 131
                                       +l+G S + f++ g+++    +  + + ++ ++           +lll+l  +l +++gl+p       g ++ +AH
  gi|488600893|ref|YP_007907364.1|  54 FLLGVSVVAFTYGGYVIRILVSILTVIAFFYVFqnlkpkssdimILLLFLAPYLMAIVGLFPVSivtdgGFINIWAH 130
                                       578999999999888887777766666666666678889887544444444456666666666699999******** PP

                                       HHHHHHHHHHHHHHC CS
                          Rhomboid 132 lgGllaGlllgllll 146
                                        +G+  G+++ l+l+
  gi|488600893|ref|YP_007907364.1| 131 YAGIFLGYWIPLVLW 145
                                       *********998876 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.2    0.0015        14       4      44 ..      23      63 ..      20      65 .. 0.90
   2 ?    8.0   7.0   0.00037       3.3       2      68 ..      70     135 ..      69     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0015
                           DUF2304  4 iiliivsvllllliirlvrkkklkleysllwlllalilivl 44
                                      i++ +v+++++ + ++l++k+k     +++ +ll++ ++ +
  gi|488600893|ref|YP_007907364.1| 23 IVSALVGLYAFSVALNLYQKSKGCKFSFFFVFLLGVSVVAF 63
                                      78999*****************9999999999999998876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00037
                           DUF2304   2 lqiiliivsvllllliirlvrkkklkleysllwlllalilivlslfpqiltvlanllGvgrgtnllf 68 
                                       ++i++ i++v+++++++++++ k  ++   ll+l    +++++ lfp  +     ++ +      +f
  gi|488600893|ref|YP_007907364.1|  70 IRILVSILTVIAFFYVFQNLKPKSSDIMILLLFL-APYLMAIVGLFPVSIVTDGGFINIWAHYAGIF 135
                                       899****************999999988877755.55667778999977666555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1146.99
//
Query:       gi|488600894|ref|YP_007907365.1|  [L=42]
Description: hypothetical protein Asulf_01381 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       168  (0.00937029); 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:                         0  (0); expected 0.2 (1e-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: 324.40
//
Query:       gi|488600895|ref|YP_007907366.1|  [L=82]
Description: hypothetical protein Asulf_01382 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   32.0   0.0    1.5e-07   31.8   0.0    1.1  1  SNase     Staphylococcal nuclease homologue


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 !   31.8   0.0   8.4e-12   1.5e-07      18      65 ..      17      66 ..       3      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 8.4e-12
                                      TTSTTHHHHHHHHHHHHHHCSSEEEEE-S..SBSTTSEEEEEEEETTEEH CS
                             SNase 18 tvqpfgkeAkeflkklvlqkkvvvleldk..kkDkygrllayvylnkkni 65
                                      +++ +g++A++ +++l+ +k+vv++ +++   +D ygrllay+y+++k++
  gi|488600895|ref|YP_007907366.1| 17 YLAVWGRKAEDSARELLEGKQVVIQTDERacLRDVYGRLLAYIYIDGKDF 66
                                      7788********************99999999**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 606.65
//
Query:       gi|488600896|ref|YP_007907367.1|  [L=54]
Description: hypothetical protein Asulf_01383 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00041   20.8   0.3    0.00047   20.6   0.3    1.1  1  SNase     Staphylococcal nuclease homologue
  ------ inclusion threshold ------
      0.065   13.7   0.0      0.068   13.6   0.0    1.1  1  Tfb2_C    Transcription factor Tfb2 (p52) C-terminal domain


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 !   20.6   0.3   5.2e-08   0.00047      69     107 ..       1      37 [.       1      38 [. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.2e-08
                                       HHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGGC CS
                             SNase  69 LvkeGlArvyevyekneekkkellkaeeeAkkkrkglWs 107
                                       ++ eG+Ar y+  e+++ k++ ++++ee+A+ +r  lW+
  gi|488600896|ref|YP_007907367.1|   1 MIAEGYAR-YY-CEAEFSKRDYYSQLEEKARVNRAWLWN 37 
                                       899*****.44.344789********************8 PP

>> Tfb2_C  Transcription factor Tfb2 (p52) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.6e-06     0.068      23      58 ..      14      51 ..       6      54 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.6e-06
                            Tfb2_C 23 dFesqadfeevleyakelgvllwede..ekrllvvkee 58
                                      +F++++ + ++ e a+ ++++lw+ +  e r+l+v+ +
  gi|488600896|ref|YP_007907367.1| 14 EFSKRDYYSQLEEKARVNRAWLWNYSppELRILAVNYD 51
                                      79999******************976568899999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 366.98
//
Query:       gi|488600897|ref|YP_007907368.1|  [L=52]
Description: hypothetical protein Asulf_01384 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 357.72
//
Query:       gi|488600898|ref|YP_007907369.1|  [L=312]
Description: hypothetical protein Asulf_01385 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   28.5   0.0      2e-06   27.6   0.0    1.5  1  DDE_Tnp_1     Transposase DDE domain
  ------ inclusion threshold ------
      0.023   14.6   1.0        1.2    9.0   0.1    2.5  2  Phage_Mu_Gam  Bacteriophage Mu Gam like protein
        3.9    8.0   5.9        5.7    7.4   2.2    2.9  2  Latarcin      Latarcin precursor


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 !   27.6   0.0   3.3e-10     2e-06      35     186 ..     164     309 ..     144     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.3e-10
                         DDE_Tnp_1  35 gyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr...kgklvlaDaGYa.saelldtleekgvdyiirlk 107
                                       gy ++++ ++ +  +++v+i p+n++  + +++++ +   +   k k+v+aDaG++  +++l  l   ++ ++i+lk
  gi|488600898|ref|YP_007907369.1| 164 GYMVCTLLNLTNFSVVDVKIYPKNKAKKEIWDEMVITNLGTesgKIKVVIADAGFFaYNNILLPLN-YRIIHVIKLK 239
                                       8999*****************************6666555679*************8899999999.99999***** PP

                         DDE_Tnp_1 108 kntklyrk...............gaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevae 169
                                       kn   +++               ++ ++  + l  ++++ i ++++  +++                        +e
  gi|488600898|ref|YP_007907369.1| 240 KNIDREELkrmvegiltnvrwfdSRYNRILSSLLEDFEYIIKKTVEGIDRY------------------------EE 292
                                       ***999989999988888886654555555566667777666666666666........................8* PP

                         DDE_Tnp_1 170 lyrlRwqiErvFkwlkr 186
                                       ++  R+ iE +Fk+l++
  gi|488600898|ref|YP_007907369.1| 293 FAEMRSKIELIFKELRQ 309
                                       **************998 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1    0.0074        44       6      45 ..      89     128 ..      85     135 .. 0.86
   2 ?    9.0   0.1    0.0002       1.2     100     130 ..     224     266 ..     188     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH CS
                      Phage_Mu_Gam   6 walrkiaelkreleeieaeaneeiaaikekleaeleplkk 45 
                                       +++ ++ e +++l++i+ ++n+ i++  ++  +e++ l++
  gi|488600898|ref|YP_007907369.1|  89 KTFSNYEEFRKKLQRIKVKINNIIKRNVAEKVDEIYGLDT 128
                                       67899********************999998888888776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0002
                                       HHHHHHHCT-GCC--------HHHH..................T CS
                      Phage_Mu_Gam 100 lLealkelgfkefIkvkeevnkeaLkkkvk.............g 130
                                       +L  l +  + ++Ik k+ +++e+Lk +v+             +
  gi|488600898|ref|YP_007907369.1| 224 ILLPL-NYRIIHVIKLKKNIDREELKRMVEgiltnvrwfdsryN 266
                                       55555.3556789****************977766655555550 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.2   0.00095       5.7       6      75 ..       7     113 ..       4     120 .. 0.68
   2 ?    0.8   0.1      0.11   6.5e+02      20      40 ..     245     273 ..     131     310 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00095
                          Latarcin   6 seeleaeeLdelergainrklmemvnnlRkvqgR..........................................L 40 
                                        e +++ e++e e    +r +   ++++   + R                                          L
  gi|488600898|ref|YP_007907369.1|   7 VEKINKGEMTEDE----FRIIALEFDKVVSEKARgmfktkekyddyiieyyivetmrfffgfppilfyailrdhkeL 79 
                                       5666666666666....333444444444444445555555566666666666666666666666666666666669 PP

                          Latarcin  41 eemvenlrkvedledtEEARgafkklkdkfkkmge 75 
                                        e ++ l+ ++ +++ EE R   + +k k++++++
  gi|488600898|ref|YP_007907369.1|  80 RETLN-LKVLKTFSNYEEFRKKLQRIKVKINNIIK 113
                                       98885.899********************999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                          Latarcin  20 gainrklmemvnnlRkvqgR........L 40 
                                       +++ r +   + n+R    R        L
  gi|488600898|ref|YP_007907369.1| 245 EELKRMVEGILTNVRWFDSRynrilsslL 273
                                       33322222333444444444555544431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2073.45
//
Query:       gi|488600899|ref|YP_007907370.1|  [L=343]
Description: hypothetical protein Asulf_01386 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-21   74.8   0.3    1.3e-20   74.0   0.1    1.5  2  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.053   13.3   0.9      0.099   12.4   0.9    1.4  1  DUF4505    Domain of unknown function (DUF4505)
      0.066   12.9   0.0       0.39   10.4   0.0    2.1  1  DDE_Tnp_4  DDE superfamily endonuclease


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 ?   -2.4   0.0      0.52   3.1e+03     117     143 ..      21      47 ..       4      97 .. 0.57
   2 !   74.0   0.1   2.1e-24   1.3e-20       3     206 ..     119     317 ..     117     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.52
                         DDE_Tnp_1 117 aeskrrgrlrkhdrnkiltksqkrrnk 143
                                       ++ + + +++k+  ++ +t ++k+ ++
  gi|488600899|ref|YP_007907370.1|  21 IDKLENRETKKALARNKITPVNKAIEF 47 
                                       444445555566666666666666655 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 2.1e-24
                         DDE_Tnp_1   3 krevlivDattvrvpgtk........edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqllde 71 
                                       k+++li+D+t++    ++        +  +wgy+++ ++ g+k+ i++d ++ ++l +++ p+nvh+s+ ++ +l++
  gi|488600899|ref|YP_007907370.1| 119 KPSLLILDWTDISLDLNPfrkrdlknKPYKWGYSTKGFFLGMKMMILIDYKTLTPLFFHVYPANVHESRIYPLILEM 195
                                       7899**********9999*******9999************************************************ PP

                         DDE_Tnp_1  72 lrpr....kgklvlaDaGYa.saelldtleekgvdyiirlkkntklyrk......gaeskrrgrlrkhdrnkiltks 137
                                       l++      g+ +++D+G+   +++l  ++  g+ ++i ++ n+++ r+      +    ++++ + + +++ ++ +
  gi|488600899|ref|YP_007907370.1| 196 LKRKklirFGDAIIMDRGFYgYKNYLIGIR-YGIIPLILPRVNFRYRRLeglisyP-LFIFNSKNIEKEKRRYRKLV 270
                                       **99**************884699999999.999999999*********9988642.34455566666666666666 PP

                         DDE_Tnp_1 138 qkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqll 206
                                       +k++                          ++l +lR+ +E v+k  k  ++l rl++++++ v  +++
  gi|488600899|ref|YP_007907370.1| 271 KKLFKG----------------------LKMNLKTLRAIVEDVIKLGKEAYSLKRLHCYDYEPVIKRAC 317
                                       666665......................789***************************99987766665 PP

>> DUF4505  Domain of unknown function (DUF4505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   1.6e-05     0.099      28      55 ..      88     115 ..      77     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                           DUF4505  28 kvknftscfkdkkflefffkrlklnetg 55 
                                        v nfts fk ++f++f f+ l++n+  
  gi|488600899|ref|YP_007907370.1|  88 SVYNFTSKFKAEQFINFVFSILNVNSKR 115
                                       478*********************9764 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.5e-05      0.39      21      93 ..     151     223 ..     138     310 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.5e-05
                         DDE_Tnp_4  21 ysnykkkntlkvlivvdpngkiifvskgypGsvsDkeilens.gllkalkea.vkpgdvilaDkgFklsekllvp 93 
                                       ys++    ++k++i++d +       + yp+ v+ ++i+    ++lk+  ++ +  gd i+ D+gF + +++l+ 
  gi|488600899|ref|YP_007907370.1| 151 YSTKGFFLGMKMMILIDYKTLTPLFFHVYPANVHESRIYPLIlEMLKR--KKlIRFGDAIIMDRGFYGYKNYLIG 223
                                       555555559*******************************99888888..6778889*********998877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2549.84
//
Query:       gi|488600900|ref|YP_007907371.1|  [L=30]
Description: hypothetical protein Asulf_01387 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       161  (0.00897987); expected 358.6 (0.02)
Passed bias filter:                      115  (0.00641419); 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: 0.32u 0.28s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 217.07
//
Query:       gi|488600901|ref|YP_007907372.1|  [L=308]
Description: hypothetical protein Asulf_01388 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1924.79
//
Query:       gi|488600902|ref|YP_007907373.1|  [L=196]
Description: hypothetical protein Asulf_01389 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0027   18.1   0.2     0.0042   17.5   0.2    1.4  1  HEPN_Apea  Apea-like HEPN


Domain annotation for each model (and alignments):
>> HEPN_Apea  Apea-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   2.3e-07    0.0042      11      94 ..      33     150 ..      23     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-07
                         HEPN_Apea  11 kralewfgeaireeddedaildlvialEaldll....ldkkeeitekis.................lrsnaylkedk 66 
                                       +r  +w + a++++d   +++   ia++al+ +    ++++++i +k++                            
  gi|488600902|ref|YP_007907373.1|  33 ERVRKWREVAQEQTDPFLKFIVEYIAFNALFRAkyghKETERNIIDKLKgdipmevfdaakikqlrD---------- 99 
                                       44444555555556667777777899****5559998666667999998666665555533322220.......... PP

                         HEPN_Apea  67 eerkel..........................kkkikklYdlRSkivHggkik..k 94 
                                            l                          +++i+ +Y  R+++ Hg+k +  +
  gi|488600902|ref|YP_007907373.1| 100 -----LtpianlrnvrlnrgtreitpemldhpENSIEAIYVTRNNLFHGDKDYsfE 150
                                       .....123334444455666666679999999******************888431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1212.76
//
Query:       gi|488600903|ref|YP_007907374.1|  [L=160]
Description: hypothetical protein Asulf_01390 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-29  100.3   1.2    1.1e-28  100.2   1.2    1.0  1  DUF4411        Domain of unknown function (DUF4411)
  ------ inclusion threshold ------
      0.021   14.6   0.1      0.095   12.5   0.1    2.0  2  DUF5615        Domain of unknown function (DUF5615)
      0.032   14.7   0.2      0.053   14.0   0.2    1.4  1  PIN            PIN domain
      0.066   13.0   0.0       0.12   12.1   0.0    1.5  1  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN 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 !  100.2   1.2   2.4e-32   1.1e-28       1     160 [.      10     159 ..      10     160 .] 0.88

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 2.4e-32
                           DUF4411   1 YllDtnvfieakrryYs.fdifpsfWewleeeveegkllsikeVkrElergedelskWakenesieklesaedlavv 76 
                                       Y++D+ ++i+  r y + ++if+ +W +lee+v+e+ l+s  eV+rE+  g d +s+W+k+++ i  +++++d + +
  gi|488600903|ref|YP_007907374.1|  10 YVIDADALINIGRWYPRdMKIFEPIWAKLEELVDEELLISHYEVYREVSSGYDYISEWCKKHSRI--FKDVDD-EQI 83 
                                       9*********98888779**********************************************4..444444.556 PP

                           DUF4411  77 eevgkvakwvivesekyskaakkeflsvaDpfliAaAlaknatvVTkEvkkpnkkknkvkIPdvcealgikcidlfe 153
                                        ++ kv++++   +++y + ++++  ++aDp++iA+A +++a++VT+E k  +k+    +IP v++a+gi+ ++++e
  gi|488600903|ref|YP_007907374.1|  84 SIFEKVREVY---DKNYWDRNITNPNPWADPWIIALAVQNKAIIVTNENK--EKP---NRIPSVARAFGINSLKPIE 152
                                       7788888885...7778888888888************************..333...47***************** PP

                           DUF4411 154 llrelgl 160
                                       +++e g+
  gi|488600903|ref|YP_007907374.1| 153 FFKEIGI 159
                                       ***9876 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.29   1.3e+03      40      51 ..      64      75 ..      62      81 .. 0.86
   2 ?   12.5   0.1   2.1e-05     0.095      28      55 ..     100     128 ..      78     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.29
                           DUF5615 40 ileyAkeedrii 51
                                      i e++k++ ri+
  gi|488600903|ref|YP_007907374.1| 64 ISEWCKKHSRIF 75
                                      789*****9995 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                           DUF5615  28 relgleg.asDeeileyAkeedriivTkD 55 
                                       r++ +++ + D+ i+++A ++++iivT+ 
  gi|488600903|ref|YP_007907374.1| 100 RNITNPNpWADPWIIALAVQNKAIIVTNE 128
                                       556666669******************85 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.2e-05     0.053       1     114 [.      10     129 ..      10     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                       EEE-HHHHHHHH.....TTSHHHHHHHHHHHTS......SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.H CS
                               PIN   1 ivlDTsvliall.....rgeekaeaarklleel......eelvtsalvlaEllyvlarrkskrekaaelvellll.l 65 
                                       +v+D+ +li++      +   +   ++ ++++l      e l++   v+ E+  ++ +   +++ +++ +  ++   
  gi|488600903|ref|YP_007907374.1|  10 YVIDADALINIGrwyprD---MK-IFEPIWAKLeelvdeELLISHYEVYREVSSGYDY--ISEWCKKHSRIFKDVdD 80 
                                       689999999998774422...33.2344555554446866666677899999999999..77777777777777767 PP

                                       HTSEEEEBCHHHHHHHHHHHHHHH.SBHHHHHHHHHHHHHT-EEE.ESST CS
                               PIN  66 salkilpidaeiaeeaaeialkyg.llpnDaliaAtAkehgikliatfDe 114
                                       ++++i++   e++++ +  ++  +   ++D +i+A+A +++++++ t+ +
  gi|488600903|ref|YP_007907374.1|  81 EQISIFEKVREVYDKNYWDRNITNpNPWADPWIIALAVQNKAIIV-TNEN 129
                                       8888888445555554444444448*****************777.9765 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.8e-05      0.12      90     113 ..     108     131 ..      67     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                     RNase_Zc3h12a  90 yddrlilelAeekdGvivsndnyr 113
                                       + d  i+ lA +++++iv+n+n++
  gi|488600903|ref|YP_007907374.1| 108 WADPWIIALAVQNKAIIVTNENKE 131
                                       56999****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 992.87
//
Query:       gi|488600904|ref|YP_007907375.1|  [L=358]
Description: hypothetical protein Asulf_01391 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   59.5   0.0    1.6e-14   53.9   0.0    2.3  2  Peptidase_M78  IrrE N-terminal-like domain
    5.3e-14   52.0   0.3    5.6e-10   39.1   0.1    2.8  2  HTH_3          Helix-turn-helix
    6.5e-11   42.4   0.0    5.6e-08   33.0   0.0    2.5  2  HTH_31         Helix-turn-helix domain
    9.1e-10   38.4   2.4    1.2e-06   28.4   0.1    4.1  5  HTH_19         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.6   0.0       0.13   12.8   0.0    2.3  2  HTH_26         Cro/C1-type HTH DNA-binding domain
       0.02   14.9   0.0       0.19   11.8   0.0    2.3  3  BetR           BetR domain
      0.057   13.2   0.1       0.19   11.5   0.0    1.9  2  Peptidase_U49  Peptidase U49
      0.065   13.0   2.8      0.045   13.5   0.8    1.8  2  DUF4895        Domain of unknown function (DUF4895)


Domain annotation for each model (and alignments):
>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.036        82      92     118 ..      14      39 ..      11      41 .. 0.86
   2 !   53.9   0.0   7.1e-18   1.6e-14       3     121 ..     161     278 ..     159     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.036
                     Peptidase_M78  92 flalaatqrkdleerlaeyfgVSkeav 118
                                       +++l +++++++ee la+++gV++e +
  gi|488600904|ref|YP_007907375.1|  14 LKKLRENSGYTEEE-LASKLGVTTEKI 39 
                                       67888999*****8.*******99865 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 7.1e-18
                     Peptidase_M78   3 rlgidvlaldlgakdldgfrfdnsetkvivlnsnhsptrqrftlaHElgHlllhherdkfreegdskaqerlerean 79 
                                       +l+i +++ +l+a d++ f++ +    vivln+++ p  + f+l HE +Hll  ++++++       ++   er ++
  gi|488600904|ref|YP_007907375.1| 161 KLSILIMEYPLKADDVRAFCIFSD-LAVIVLNESDEPSIKLFSLFHEVAHLLKRESGICS--IDIEAERYDVERFCD 234
                                       799******************998.********************************762..222233333455577 PP

                     Peptidase_M78  80 afAaelllPeeaflalaatqrkdlee..rlaeyfgVSkeavavr 121
                                        fAae+l+P e++l  a   + ++e+  +la+ +gVS +++  r
  gi|488600904|ref|YP_007907375.1| 235 KFAAEFLVPAEDLLTEAGSIKLTDERikKLARLYGVSVQVMMLR 278
                                       77*********************999*************98766 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.1   2.5e-13   5.6e-10       1      53 [.      14      66 ..      14      68 .. 0.97
   2 !   10.1   0.0    0.0003      0.67      30      52 ..     250     272 ..     250     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.5e-13
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53
                                      lk+lR+  g++ eeLA klGv+   i + E+Ge + +l+ +kkla+ ++v+l+
  gi|488600904|ref|YP_007907375.1| 14 LKKLRENSGYTEEELASKLGVTTEKIVKVEKGEDSFTLTQIKKLADIYKVPLA 66
                                      89*************************************************97 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0003
                                       HTTSSCSBHHHHHHHHHHHTSEH CS
                             HTH_3  30 EnGernPsletlkklakaLgvsl 52 
                                       E G  + + e++kkla+ +gvs 
  gi|488600904|ref|YP_007907375.1| 250 EAGSIKLTDERIKKLARLYGVSV 272
                                       7899999**************97 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.5e-11   5.6e-08       4      58 ..      12      65 ..      11      68 .. 0.95
   2 !    6.7   0.0     0.004       8.9      35      58 ..     250     272 ..     248     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.5e-11
                            HTH_31  4 alLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldp 58
                                      +lL+ lRe +G + ee+A  lgv+  ++ ++E G+    ++ ++ +la+++ ++ 
  gi|488600904|ref|YP_007907375.1| 12 HLLKKLRENSGYTEEELASKLGVTTEKIVKVEKGED-SFTLTQIKKLADIYKVPL 65
                                      589*********************************.6**************986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.004
                            HTH_31  35 EqGrrgrpspavlealaralgldp 58 
                                       E G +   + + + +lar++g+++
  gi|488600904|ref|YP_007907375.1| 250 EAGSI-KLTDERIKKLARLYGVSV 272
                                       88999.59**************97 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   5.3e-10   1.2e-06       4      62 ..      14      71 ..      12      72 .. 0.92
   2 ?   -1.9   0.2       1.5   3.5e+03      40      55 ..     142     157 ..     134     168 .. 0.57
   3 ?   -1.9   0.0       1.6   3.5e+03      28      50 ..     184     209 ..     183     213 .. 0.67
   4 !    6.5   0.0    0.0037       8.3      33      57 ..     250     273 ..     247     282 .. 0.87
   5 ?   -0.8   0.0      0.73   1.6e+03      29      52 ..     277     297 ..     275     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.3e-10
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqg 62
                                      Lk++Re+ g+t eela++lg++  ki + E+g+   ++   ++k+a +++++l +++++
  gi|488600904|ref|YP_007907375.1| 14 LKKLRENSGYTEEELASKLGVTTEKIVKVEKGED-SFTLTQIKKLADIYKVPLAAFFSK 71
                                      9*******************************64.7778899**********9999876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                            HTH_19  40 psaelllkiaealgid 55 
                                       p+ ++ + i+e+++  
  gi|488600904|ref|YP_007907375.1| 142 PKEKKAREILEFYKEV 157
                                       5555555555555443 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.6
                            HTH_19  28 kisaiEngkkdvpsaell...lkiae 50 
                                        ++ i  +++d+ps++l+     +a+
  gi|488600904|ref|YP_007907375.1| 184 DLAVIVLNESDEPSIKLFslfHEVAH 209
                                       57889999999999666633355555 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0037
                            HTH_19  33 Engkkdvpsaelllkiaealgidle 57 
                                       E g++ +++ e+++k+a+++g++++
  gi|488600904|ref|YP_007907375.1| 250 EAGSI-KLTDERIKKLARLYGVSVQ 273
                                       88999.8899*************87 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.73
                            HTH_19  29 isaiEngkkdvpsaelllkiaeal 52 
                                       ++++E g   ++++++++k+ e++
  gi|488600904|ref|YP_007907375.1| 277 LRMLELG---KITRDRYQKFREEF 297
                                       7899999...66788888888777 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05      0.13       2      54 ..      14      65 ..      13      70 .. 0.93
   2 ?   -0.8   0.0      0.98   2.2e+03      13      27 ..     261     275 ..     255     277 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctp 54
                                      L++l    g+t  eLa ++g++  ++ +  kg+ ++ +l+ + k++d+ ++ +
  gi|488600904|ref|YP_007907375.1| 14 LKKLRENSGYTEEELASKLGVTTEKIVKVEKGE-DSFTLTQIKKLADIYKVPL 65
                                      7888899999***********************.9*************98865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.98
                            HTH_26  13 kseLargtgisaatl 27 
                                       +++Lar +g+s + +
  gi|488600904|ref|YP_007907375.1| 261 IKKLARLYGVSVQVM 275
                                       578888888887766 PP

>> BetR  BetR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.4e-05      0.19      27      69 ..      27      69 ..       4      85 .. 0.83
   2 ?   -1.1   0.0       0.8   1.8e+03      45      47 ..     252     254 ..     233     273 .. 0.52
   3 ?   -0.3   0.0      0.46     1e+03      45      69 ..     252     276 ..     247     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.4e-05
                              BetR 27 lladiLglslSqanRKlkGsipwnlaqlekvAktfgvpaaiLl 69
                                      +la  Lg+ + +  +  kG+ +++l q++k+A+ ++vp a  +
  gi|488600904|ref|YP_007907375.1| 27 ELASKLGVTTEKIVKVEKGEDSFTLTQIKKLADIYKVPLAAFF 69
                                      56677888888888888*********************99887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.8
                              BetR  45 Gsi 47 
                                       Gsi
  gi|488600904|ref|YP_007907375.1| 252 GSI 254
                                       344 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.46
                              BetR  45 GsipwnlaqlekvAktfgvpaaiLl 69 
                                       Gsi  + + ++k+A+ +gv+ ++++
  gi|488600904|ref|YP_007907375.1| 252 GSIKLTDERIKKLARLYGVSVQVMM 276
                                       788888899**********988765 PP

>> Peptidase_U49  Peptidase U49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.1   2.5e+03     120     137 ..      35      52 ..      24      63 .. 0.63
   2 ?   11.5   0.0   8.3e-05      0.19     103     141 ..     201     243 ..     198     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                     Peptidase_U49 120 steeslreEleaDSfAle 137
                                       +te++++ E+  DSf l 
  gi|488600904|ref|YP_007907375.1|  35 TTEKIVKVEKGEDSFTLT 52 
                                       566666666666666544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.3e-05
                     Peptidase_U49 103 yillHEvaHvvlqeekk....steeslreEleaDSfAlellls 141
                                       + l+HEvaH    e++       +e+ + E+ +D fA e+l+ 
  gi|488600904|ref|YP_007907375.1| 201 FSLFHEVAHLLKRESGIcsidIEAERYDVERFCDKFAAEFLVP 243
                                       5689******9999988777778999*************9875 PP

>> DUF4895  Domain of unknown function (DUF4895)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8     2e-05     0.045      98     185 ..     132     220 ..     102     259 .. 0.78
   2 ?   -3.9   0.0       4.4   9.8e+03     169     180 ..     325     336 ..     317     346 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                           DUF4895  98 GedelleKeilkEkvkgkeflsFakkvdekilekl.lklnekklkiari.llsdegvnvlvipesvdeefrsLlaEi 172
                                       G  ++l+ ei kEk k+ e l F k v e+ l  l +++  k  ++    ++sd +v vl   ++ + +  sL++E+
  gi|488600904|ref|YP_007907375.1| 132 GFRKYLRIEIPKEK-KAREILEFYKEVLENKLSILiMEYPLKADDVRAFcIFSDLAVIVLNESDEPSIKLFSLFHEV 207
                                       66789999999999.789********9888877652777777777755589**********9999999********* PP

                           DUF4895 173 vrvlrkkyGaanl 185
                                       + +l++  G+  +
  gi|488600904|ref|YP_007907375.1| 208 AHLLKRESGICSI 220
                                       *********9833 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.4
                           DUF4895 169 laEivrvlrkky 180
                                       ++E+++ +rkk 
  gi|488600904|ref|YP_007907375.1| 325 VSEVSKAYRKKE 336
                                       578999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2425.63
//
Query:       gi|488600905|ref|YP_007907376.1|  [L=89]
Description: hypothetical protein Asulf_01392 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-09   37.3   0.1    2.2e-09   37.2   0.1    1.1  1  DUF86        Protein of unknown function DUF86
  ------ inclusion threshold ------
      0.084   12.2   0.3      0.083   12.3   0.3    1.1  1  Tropomyosin  Tropomyosin


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 !   37.2   0.1   2.5e-13   2.2e-09       1      47 [.      13      60 ..      13      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.5e-13
                                      HHHHHHHHCCHH...T.STSCCGSHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF86  1 ikealeklkefteeld.eeeflsdeleydavernlqvigEaaidiakh 47
                                      ++ea+ek++++t +++  e+f+++ +  dav+rnl++igEaa++ + +
  gi|488600905|ref|YP_007907376.1| 13 MLEAIEKIERYTSSIEdLEDFMREDMVVDAVLRNLEIIGEAAKKHPRR 60
                                      89*************99**************************99887 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   9.2e-06     0.083     126     170 ..      10      57 ..       2      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-06
                       Tropomyosin 126 esdLeraeeraeaaeskiveLeeeLk...vvgnnlksLevseekaser 170
                                        +d+ +a e++e+  s i++Le+ ++   vv + l++Le+  e+a + 
  gi|488600905|ref|YP_007907376.1|  10 VQDMLEAIEKIERYTSSIEDLEDFMRedmVVDAVLRNLEIIGEAAKKH 57 
                                       578889*****************998666899********99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 572.37
//
Query:       gi|488600906|ref|YP_007907377.1|  [L=107]
Description: putative nucleotidyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-16   58.0   0.7      1e-15   57.8   0.7    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
    3.6e-11   43.0   0.1    4.9e-11   42.6   0.1    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
       0.08   12.4   0.1      0.094   12.2   0.1    1.0  1  ROK           ROK 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 !   57.8   0.7   1.7e-19     1e-15       6      92 ..      25     104 ..      14     107 .] 0.86

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.7e-19
                                       HHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC. CS
                      NTP_transf_2   6 eelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled. 81 
                                       ++lke+++v+++ +fGS+ rG+ +++SDiD++v ++e+v         ++++   +fleellg++vd+vt++   + 
  gi|488600906|ref|YP_007907377.1|  25 RILKERFKVKSIGVFGSVTRGEQKETSDIDIIVEFSEPVG--------WEIVDLKEFLEELLGVRVDVVTKNAAMRk 93 
                                       6899**********************************76........*********************77665554 PP

                                       CTEEEEEECEE CS
                      NTP_transf_2  82 pllvksileer 92 
                                       pll ksi+ e 
  gi|488600906|ref|YP_007907377.1|  94 PLLWKSIEREV 104
                                       66666666555 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   8.2e-15   4.9e-11       5      82 ..      25     101 ..      14     107 .] 0.81

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 8.2e-15
                                       TTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT.TS-HHHHHHH CS
                           Polbeta   5 eilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln.eapplllyei 80 
                                        il+++ +++ + +FGS+ +g+++e SDiD+ v ++e     e ++l++ le++ lg +vD+v+ n + ++ ll + 
  gi|488600906|ref|YP_007907377.1|  25 RILKERFKVKSIGVFGSVTRGEQKETSDIDIIVEFSEP-VGWEIVDLKEFLEEL-LGVRVDVVTKNaAMRKPLLWKS 99 
                                       4677778*******************************.556679*********.99*******9965555555444 PP

                                       HH CS
                           Polbeta  81 lk 82 
                                       ++
  gi|488600906|ref|YP_007907377.1| 100 IE 101
                                       44 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.6e-05     0.094      38     103 ..      12      85 ..       5      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHCCCHCCHTEEEEE.EEEESSEE.......ETTCCEBSSGGC.GCCCCTTHHHHHHHHHTS-EEEE CS
                               ROK  38 tlvdaiaelvdeaerkadeliav.gigspGli.......sdksgkivstpn.itwenfdlvekleerlnvpveve 103
                                        l+++i+ +++e +r ++e+ +v +ig++G +        ++   iv+  + ++we +dl+e lee l+v v v 
  gi|488600906|ref|YP_007907377.1|  12 NLEEVIQ-ILKENDRILKERFKVkSIGVFGSVtrgeqkeTSDIDIIVEFSEpVGWEIVDLKEFLEELLGVRVDVV 85 
                                       5655555.55566688889997768*******99998875566667766664889*************9998664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 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:                        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 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 682.21
//
Query:       gi|488600907|ref|YP_007907378.1|  [L=435]
Description: Uncharacterized protein with SCP/PR1 domains [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.1   8.5    2.1e-09   37.4   8.5    1.3  1  zf-AN1    AN1-like Zinc finger
    6.4e-05   23.8   0.0    0.00017   22.4   0.0    1.8  2  CAP       Cysteine-rich secretory protein family
  ------ inclusion threshold ------
      0.022   14.9   2.5      0.039   14.1   2.5    1.4  1  FYVE      FYVE zinc finger
       0.16   11.9   0.0       0.38   10.6   0.0    1.6  1  DUF1952   Domain of unknown function (DUF1952)
       0.84   10.0   9.2        1.4    9.2   9.2    1.4  1  C1_2      C1 domain


Domain annotation for each model (and alignments):
>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   8.5   5.8e-13   2.1e-09       1      38 [.       4      39 ..       4      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 5.8e-13
                            zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkHrlpedHdCkkl 38
                                      C+   C+k+++lp+kCryCg+ FC+++rlp +HdCk+ 
  gi|488600907|ref|YP_007907378.1|  4 CD--WCGKNTYLPYKCRYCGGFFCEDCRLPPNHDCKNI 39
                                      66..6*******************************96 PP

>> CAP  Cysteine-rich secretory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   4.8e-08   0.00017       1     111 [.     169     286 ..     169     298 .. 0.86
   2 ?   -3.3   0.0       4.3   1.5e+04      57      82 ..     340     365 ..     315     368 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.8e-08
                                       HHHHHHHHHHTT----EE-HHHHHHHHHHHHHHHHH.T---S-GGG--HHHHHHTT-T..............EEEEE CS
                               CAP   1 leahNeyRaaaglppLkwdatLekaAqdhardcaashsdsssspeggdllkyaenagk..............eniaa 63 
                                       l+++Ne R+++ lpp++  +t    Aq +a+d+ +++++ +++peg++++ y ++ g               +  ++
  gi|488600907|ref|YP_007907378.1| 169 LNYLNEERKKRELPPVELMQT--GIAQFRAEDMIQRDYFGHYDPEGFPPFHYYTKMGGiyameencgyyrviGGSTR 243
                                       799**************9886..78********************************9999*999999888778888 PP

                                       ES--CCCHHHHHHTSHH................HHHHHT-SS--EEEEEEE CS
                               CAP  64 aseaaedavdsWysepgtynkgketegs...ighftnllwpkstkvGcava 111
                                       ++e++ ++vds  +  +     ++   s   +gh+  ll+p ++ v ++v+
  gi|488600907|ref|YP_007907378.1| 244 YNEIPDKVVDSVRRMIY-----ND---SlsdWGHRDSLLDPGNNFVDIGVS 286
                                       89999999999988888.....23...235699*******98887755555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.3
                                       -TEEEEEES--CCCHHHHHHTSHH.. CS
                               CAP  57 gkeniaaaseaaedavdsWysepgty 82 
                                       +ke +++ s ++ d+v++ + +p++y
  gi|488600907|ref|YP_007907378.1| 340 SKEFTNRHSYELGDVVAGVIPSPYYY 365
                                       22556666777777777777777765 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.5   1.1e-05     0.039      11      40 ..       3      29 ..       1      75 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                      B-TTT--B--SSS--EE-TTT--EE-STTS CS
                              FYVE 11 kCeiCakkFsllrrrhhCrlCGkvvCekCs 40
                                      +C+ C k+  l    + Cr CG  +Ce+C 
  gi|488600907|ref|YP_007907378.1|  3 RCDWCGKNTYL---PYKCRYCGGFFCEDCR 29
                                      67777777655...689************8 PP

>> DUF1952  Domain of unknown function (DUF1952)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.38      15      47 ..     224     256 ..     211     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                           DUF1952  15 eWGaveedeGvyrldGavvrfrelePlkvGslr 47 
                                          a+ee+ G yr+ G   r+ e++ ++v s+r
  gi|488600907|ref|YP_007907378.1| 224 GIYAMEENCGYYRVIGGSTRYNEIPDKVVDSVR 256
                                       333678899********************9987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.2    0.0004       1.4      20      46 ..       3      28 ..       1      29 [. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0004
                              C1_2 20 nCsaCgrkidgffYsCseCdfslhvrC 46
                                      +C++Cg+++ +  Y+C  C  +++++C
  gi|488600907|ref|YP_007907378.1|  3 RCDWCGKNT-YLPYKCRYCGGFFCEDC 28
                                      8*******6.777*******9999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2537.77
//
Query:       gi|488600908|ref|YP_007907379.1|  [L=187]
Description: hypothetical protein Asulf_01397 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.03   13.4   0.2      0.037   13.1   0.2    1.2  1  Effector_1  Effector from type III secretion system


Domain annotation for each model (and alignments):
>> Effector_1  Effector from type III secretion system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.1e-06     0.037     225     309 ..      72     159 ..      36     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-06
                        Effector_1 225 ltteqkaklkde.lngYadeleaiveqLaelkvllrklsvsvvegd.deydeaftakkgsfevvg.qddWistLqtL 298
                                        ++    ++kd  ++ Y + ++ + e L+ l++ l+k+ +++  g  ++ +e  +  k  f+v +  ++   +L  L
  gi|488600908|ref|YP_007907379.1|  72 YSNRDLESIKDDfIKDYYNLFKYLHERLQRLNSNLAKVIFETLYGLgENLEEQLNGDKTFFSVYNlVTEMNRKLGEL 148
                                       5566666777653799**************************999625688889999999*****9999******** PP

                        Effector_1 299 EdavveGlssg 309
                                        d v++ ++s+
  gi|488600908|ref|YP_007907379.1| 149 HDRVISLEKSS 159
                                       *****976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1266.68
//
Query:       gi|488600909|ref|YP_007907380.1|  [L=163]
Description: hypothetical protein Asulf_01398 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1038.42
//
Query:       gi|488600910|ref|YP_007907381.1|  [L=101]
Description: hypothetical protein Asulf_01399 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 670.98
//
Query:       gi|488600911|ref|YP_007907382.1|  [L=615]
Description: DNA polymerase elongation subunit (family B) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   72.8   0.7    3.2e-09   36.0   0.0    3.0  2  DNA_pol_B  DNA polymerase family B


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.8e-13   3.2e-09      43      86 ..     276     318 ..     242     320 .. 0.81
   2 !   33.0   0.3   1.5e-12   2.7e-08     118     389 ..     319     552 ..     315     602 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.8e-13
                                       -S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE- CS
                         DNA_pol_B  43 gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlva 86 
                                       + +G+++l+P+ g+y+ +v+ lDF S+YP ii+++Nl+++ +  
  gi|488600911|ref|YP_007907382.1| 276 KDKGGLILQPEPGIYE-NVAQLDFTSMYPTIIVKYNLSPESISG 318
                                       469************7.69********************98865 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 1.5e-12
                                       ---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHH CS
                         DNA_pol_B 118 regllpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemL 194
                                       r+g l+++Lk ll  R + k ++k++k e     +     alK +  + +G+tG++n ++ ++a+ + +T iGRe+L
  gi|488600911|ref|YP_007907382.1| 319 RRGFLSTILKPLLGLRIKTK-RMKKSKPE-----VAGIDTALKWMLVTCFGYTGFRNAKFGSIAVHEAITGIGREIL 389
                                       79**************9998.58999888.....556678************************************* PP

                                       HHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEE CS
                         DNA_pol_B 195 ektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdveellkigkelaeevseklfkkplklefek 271
                                       +k  ++ve+          +       +++vi    DS+f++    +++e  ki +e    + e++++  + l    
  gi|488600911|ref|YP_007907382.1| 390 LKSIKVVEAG---------VD-----AGVEVIHAMVDSIFVRNPNGKLKE--KIERETGMLLDEDRYFWIVFLPKKD 450
                                       ********87.........22.....399999999999999877765554..3334444455555555555554444 PP

                                       EEEEEEEEETTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHH CS
                         DNA_pol_B 272 vykkllLisKKkYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkd 348
                                        + +       +Y+gl  +     ++l  +Gv   +rd  +++++   ++  ll k+ ++ ++l +  e+l++i  +
  gi|488600911|ref|YP_007907382.1| 451 GFGNA-----ARYYGLLES-----GELKLRGVMARKRDTPEYIRRSQLEMFSLLRKA-RTIEELCTLEEKLNRIYRK 516
                                       44443.....388888877.....888999999999999999988888888777777.3444444445555555555 PP

                                       HHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHH CS
                         DNA_pol_B 349 vleeleenkvplekfvlskelskepenyksknlphlevakr 389
                                        ++e+++   + e+f++ +++s++  +y+  +l +++++k+
  gi|488600911|ref|YP_007907382.1| 517 YRTEMRHA--NPEEFLIRRRISRT--SYTRSSL-EASAVKE 552
                                       55555544..57899999999995..5544442.2333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 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:                        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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 4266.05
//
Query:       gi|488600912|ref|YP_007907383.1|  [L=360]
Description: Cdc6-related protein, AAA superfamily ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   32.7   0.0    3.1e-07   30.7   0.0    1.9  2  AAA_22    AAA domain
      4e-07   30.6   0.1    6.5e-06   26.6   0.0    2.5  2  AAA_16    AAA ATPase domain
     0.0023   18.4   0.0     0.0046   17.4   0.0    1.5  1  AAA       ATPase family associated with various cellular acti
  ------ inclusion threshold ------
      0.051   12.7   0.0      0.086   12.0   0.0    1.3  1  DUF815    Protein of unknown function (DUF815)
      0.079   13.1   0.0       0.15   12.2   0.0    1.5  1  TIP49_C   TIP49 AAA-lid domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   8.7e-11   3.1e-07       8     112 ..      56     147 ..      55     170 .. 0.89
   2 ?   -1.6   0.0      0.81   2.9e+03      93     119 ..     254     284 ..     199     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8.7e-11
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                       +v++G++ tGKT ++r++ +++         + +  +v+++   ++++l++ +++a++  +     +   + e++ +
  gi|488600912|ref|YP_007907383.1|  56 TVCIGPPATGKTSCVRKIISSA---------EIRAGYVNASLVRTRSELATGIFKAVTGLTPP--RRGVSFSELMGR 121
                                       59*******************9.........89999**********************65555..7778888***** PP

                            AAA_22  85 alraravielliiDEaqhlrseealeeL 112
                                       a+++++   l++iD+a  l +e++l+e+
  gi|488600912|ref|YP_007907383.1| 122 AFDSADS-LLIVIDDATAL-NEKILNEV 147
                                       *******.***********.99999998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.81
                            AAA_22  93 elliiDEaqhlr.seealeeLrsllnl...s 119
                                       e + +D+a++   + + l   rsl+nl   +
  gi|488600912|ref|YP_007907383.1| 254 ERIGVDDAEKAYeKGKWLFLTRSLSNLsrdE 284
                                       6677888888654566666668888875444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.8e-09   6.5e-06       3      58 ..      31      86 ..      30     104 .. 0.83
   2 ?    0.9   0.1      0.14   5.1e+02     117     146 ..     113     138 ..      85     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.8e-09
                            AAA_16  3 vGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrg 58
                                        R+++l++L+s l++  sg     ++++G++++GK+s vr++  ++e + g++ ++
  gi|488600912|ref|YP_007907383.1| 31 AFRDAQLRALASNLKPMLSGMNaVDTVCIGPPATGKTSCVRKIISSAEIRAGYV-NA 86
                                      56******************999999******************9999985555.33 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                            AAA_16 117 srllellkrllallsrderplvlvlDdlqw 146
                                        ++ el+ r+++ + +    l++v+Dd+  
  gi|488600912|ref|YP_007907383.1| 113 VSFSELMGRAFDSADS----LLIVIDDATA 138
                                       5566666666655555....*******865 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   1.3e-06    0.0046       4      71 ..      59     140 ..      56     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                       ESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS............STTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA   4 yGppGtGKTllakavakelgve..fleisgsellsk............yvgesekkirelfkeakekakpsilfiDE 66 
                                       +Gpp tGKT++++ ++++++++  +++ s+ + +s+            +   +  +++el+ +a  +a+   ++iD+
  gi|488600912|ref|YP_007907383.1|  59 IGPPATGKTSCVRKIISSAEIRagYVNASLVRTRSElatgifkavtglTPPRRGVSFSELMGRAFDSADSLLIVIDD 135
                                       8*****************98662245555555555577777777655533333444445555554444346677777 PP

                                       GGGHH CS
                               AAA  67 idala 71 
                                       + al+
  gi|488600912|ref|YP_007907383.1| 136 ATALN 140
                                       66665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05     0.086      33      77 ..      33      77 ..      14      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                            DUF815 33 idkqkealventeqfleglpannvLLwGarGtGKSslvkallney 77
                                       d+q +al +n + +l+g++a + + +G   tGK s+v+ +++++
  gi|488600912|ref|YP_007907383.1| 33 RDAQLRALASNLKPMLSGMNAVDTVCIGPPATGKTSCVRKIISSA 77
                                      588999*********************************998765 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.2e-05      0.15      18      62 ..     221     266 ..     215     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                           TIP49_C  18 ldlLakigtetS.LRYaiqLltpasilakkrkkkevevedveevee 62 
                                       +d+ + ++ et  LR  +  l +a i+a +++k+++ v+d e+++e
  gi|488600912|ref|YP_007907383.1| 221 IDFATGMAFETAdLRLGLYILRMAGIIADREGKERIGVDDAEKAYE 266
                                       56666666666449*****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2398.77
//
Query:       gi|488600913|ref|YP_007907384.1|  [L=146]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-23   83.7   0.7    1.4e-23   83.6   0.7    1.0  1  EVE             EVE domain
     0.0001   22.1   0.0    0.00015   21.7   0.0    1.3  1  Dev_Cell_Death  Development and cell death domain


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.7   1.5e-27   1.4e-23       1     144 [.       2     144 ..       2     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1.5e-27
                                       -EEEEEEBHHTSHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEE......ETSSSS-EEEEEEEEECEEEE- CS
                               EVE   1 ayWllksepdefsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfY......hsgeklqaivgiaeVvseaypd 71 
                                       ayWl++++++  +++ +  k++++W gv++ +++n++ ++k+GD++l+Y      + + k+++ivg +e +se+ +d
  gi|488600913|ref|YP_007907384.1|   2 AYWLCITNEE--NWKVI--KEKNVW-GVPE-RHKNTIAKVKPGDKLLIYlkqeriKDDVKEPRIVGAYEATSEVFKD 72 
                                       6*********..*****..9*****.****.99****************998775444449**************** PP

                                       GGGG-TTSTT--TTTBTTS-.-EEEEEEEEEEEEEEEEHHHHTTHG.TCTTSHHHHCC..T-SEEEE-HHHHHHHHH CS
                               EVE  72 etqfdpkskyydpkskkekp.wlrvdvkpvkklkrplslkelkaep.elegmkllrkg..rlsvrpvteedwelile 144
                                       ++ +     ++ p  +++++ +lr+++kpvk +++++++k l ++  +++++k ++ +    ++r+++eed++li++
  gi|488600913|ref|YP_007907384.1|  73 SKRV-----FKTPPGMGNETfPLRIKLKPVKIFEKSVEFKPLIPKLkFITNKKKWSGHlmGKAMREIPEEDYKLIVS 144
                                       *999.....6779999999999********************995348899999999988999************85 PP

>> Dev_Cell_Death  Development and cell death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.6e-08   0.00015       6      90 ..       7     108 ..       3     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-08
                    Dev_Cell_Death   6 icnketkkecfrkklfglpaeklslvkkikpglkLfLf........dyderkLyGvfeAasdGglniepkafts... 71 
                                       i n+e  k   +k++ g+p+++++++ k+kpg kL+++        d++e ++ G +eA+s+  ++ +++ f++   
  gi|488600913|ref|YP_007907384.1|   7 ITNEENWKVIKEKNVWGVPERHKNTIAKVKPGDKLLIYlkqerikdDVKEPRIVGAYEATSEV-FKDSKRVFKTppg 82 
                                       5577777788899*************************5555555455555788888888875.4444555655788 PP

                    Dev_Cell_Death  72 .ekskfpaQvrfk......ikkkckP 90 
                                         +++fp  +++k        +++kP
  gi|488600913|ref|YP_007907384.1|  83 mGNETFPLRIKLKpvkifeKSVEFKP 108
                                       88888998888874443333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1054.79
//
Query:       gi|488600914|ref|YP_007907385.1|  [L=450]
Description: hypothetical protein Asulf_01405 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-11   41.8   0.3    1.2e-10   41.1   0.3    1.3  1  CoiA            Competence protein CoiA-like family
  ------ inclusion threshold ------
      0.032   14.0   1.0        3.4    7.5   0.1    3.1  3  zinc_ribbon_5   zinc-ribbon domain
       0.09   12.1   0.1        2.6    7.4   0.0    2.5  2  zf-TFIIB        Transcription factor zinc-finger
       0.11   12.5   0.3       0.44   10.7   0.0    2.1  2  DUF1272         Protein of unknown function (DUF1272)
       0.22   11.5   3.3       0.86    9.6   0.1    2.9  3  DUF1610         Domain of unknown function (DUF1610)
       0.53   10.1   0.1       0.53   10.1   0.1    2.7  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger


Domain annotation for each model (and alignments):
>> CoiA  Competence protein CoiA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.3     4e-14   1.2e-10      27      85 ..      23      79 ..       7      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 4e-14
                              CoiA 27 qkkerfyCpaCksklvikiGsqkipHFaHkkke..aCrvstepEseyHlsgKrqlyqWlkr 85
                                       k  ++yCp Ck++ +++ G+++++HFaHk     +C     +Es+ H   K++ly  l++
  gi|488600914|ref|YP_007907385.1| 23 EKGLKYYCPECKGEFIVRKGKIRAWHFAHKGGIppSCS----GESAKHALMKHKLYYLLSN 79
                                      455679************************87511666....**************98876 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.027        81       4      19 ..      29      44 ..      26      47 .. 0.81
   2 ?   -0.6   0.0      0.38   1.1e+03       4      10 ..      88      94 ..      86      97 .. 0.82
   3 ?    7.5   0.1    0.0011       3.4      12      37 .]     221     248 ..     219     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.027
                     zinc_ribbon_5  4 rCpdCdtkFklvdskl 19
                                       Cp+C+  F +   k+
  gi|488600914|ref|YP_007907385.1| 29 YCPECKGEFIVRKGKI 44
                                      5********8887776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                     zinc_ribbon_5  4 rCpdCdt 10
                                       C+ C++
  gi|488600914|ref|YP_007907385.1| 88 HCERCGS 94
                                      5999997 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0011
                     zinc_ribbon_5  12 Fklvds.klKksgkkVrC.akCaevFda 37 
                                       F++ d  ++K   kkVr  +kC+ +F +
  gi|488600914|ref|YP_007907385.1| 221 FRIIDNmNIKSWIKKVRAkGKCGTIFNV 248
                                       6654432799999****779******86 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00087       2.6      20      32 ..      28      40 ..      18      46 .. 0.85
   2 ?    2.0   0.1     0.045   1.3e+02      17      26 ..      84      93 ..      57      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00087
                          zf-TFIIB 20 dyCpqCrGvWldr 32
                                      +yCp+C+G ++ r
  gi|488600914|ref|YP_007907385.1| 28 YYCPECKGEFIVR 40
                                      79******98866 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.045
                          zf-TFIIB 17 veidyCpqCr 26
                                      + +++C++C+
  gi|488600914|ref|YP_007907385.1| 84 YVVYHCERCG 93
                                      6799*****7 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.44      36      54 ..      22      40 ..      20      43 .. 0.88
   2 ?   -2.2   0.0       1.5   4.5e+03       7      12 ..      88      93 ..      83     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                           DUF1272 36 aeevlenvCPncgGelvkR 54
                                      ae+ l+  CP+c Ge++ R
  gi|488600914|ref|YP_007907385.1| 22 AEKGLKYYCPECKGEFIVR 40
                                      5778999*********998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                           DUF1272  7 nCecCd 12
                                      +Ce+C 
  gi|488600914|ref|YP_007907385.1| 88 HCERCG 93
                                      577775 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00029      0.86       8      22 ..      19      33 ..      17      36 .. 0.88
   2 ?   -2.2   0.1       1.4   4.3e+03      14      23 ..      84      93 ..      83      93 .. 0.88
   3 ?    1.2   0.0      0.12   3.6e+02       9      18 ..     248     257 ..     248     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00029
                           DUF1610  8 laprEravvFpCPNC 22
                                      +  +E++ +++CP+C
  gi|488600914|ref|YP_007907385.1| 19 ILNAEKGLKYYCPEC 33
                                      6779*********** PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                           DUF1610 14 avvFpCPNCG 23
                                      +vv+ C  CG
  gi|488600914|ref|YP_007907385.1| 84 YVVYHCERCG 93
                                      8999998888 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.12
                           DUF1610   9 aprEravvFp 18 
                                       ++rE++v+F+
  gi|488600914|ref|YP_007907385.1| 248 VERENGVIFA 257
                                       68*******6 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00018      0.53       3      17 ..      29      43 ..      27      49 .. 0.90
   2 ?   -1.0   0.1      0.54   1.6e+03       3       9 ..      88      94 ..      86      95 .. 0.84
   3 ?   -2.2   0.2       1.3   3.8e+03      20      24 ..     366     370 ..     364     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                                      E-SSS--EEEEEE-S CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkrgk 17
                                       CP+C+g+ ++++gk
  gi|488600914|ref|YP_007907385.1| 29 YCPECKGEFIVRKGK 43
                                      6************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.54
                                      E-SSS-- CS
                    zf-C4_Topoisom  3 kCPkCgg 9 
                                       C+ Cg+
  gi|488600914|ref|YP_007907385.1| 88 HCERCGS 94
                                      6****97 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.3
                                       EEEEE CS
                    zf-C4_Topoisom  20 kFvGC 24 
                                       +F+GC
  gi|488600914|ref|YP_007907385.1| 366 EFYGC 370
                                       7**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2827.48
//
Query:       gi|488600915|ref|YP_007907386.1|  [L=214]
Description: hypothetical protein Asulf_01406 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   40.6   7.6    1.3e-10   40.6   7.6    2.1  2  SHOCT         Short C-terminal domain
  ------ inclusion threshold ------
      0.045   14.6   1.6       0.11   13.4   1.6    1.6  1  DMAP_binding  DMAP1-binding Domain
       0.56   10.3   4.4        0.5   10.4   2.8    1.7  2  GvpG          Gas vesicle protein G


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 ?   -1.0   0.4      0.28   1.7e+03      19      26 ..     162     169 ..     158     171 .. 0.53
   2 !   40.6   7.6   2.2e-14   1.3e-10       1      28 []     184     211 ..     184     211 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.28
                             SHOCT  19 EFeakKak 26 
                                       E +++K +
  gi|488600915|ref|YP_007907386.1| 162 ELNRRKSE 169
                                       44555555 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 2.2e-14
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       ++L+kLkeL+++G++t+EEFe+kK+kLL
  gi|488600915|ref|YP_007907386.1| 184 EKLKKLKELHDAGILTDEEFEEKKKKLL 211
                                       68*************************8 PP

>> DMAP_binding  DMAP1-binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.6   1.8e-05      0.11       8      39 ..     181     212 ..     180     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                      DMAP_binding   8 dvrerLaeLeldlseGdiTeKgyekkklkLLr 39 
                                       dv e+L++L +  + G +T+++ e kk+kLL+
  gi|488600915|ref|YP_007907386.1| 181 DVFEKLKKLKELHDAGILTDEEFEEKKKKLLD 212
                                       7889**************************97 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.36   2.1e+03      31      42 ..     154     165 ..     145     179 .. 0.55
   2 ?   10.4   2.8   8.3e-05       0.5      28      65 ..     177     214 .]     164     214 .] 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.36
                              GvpG  31 enlrkeLaaLqq 42 
                                       e+l  +La+L++
  gi|488600915|ref|YP_007907386.1| 154 EALYEKLAELNR 165
                                       334444444443 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.3e-05
                              GvpG  28 ddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrL 65 
                                        +++++  +L +L+   daG  ++eeF+++  +lLd L
  gi|488600915|ref|YP_007907386.1| 177 SEEADVFEKLKKLKELHDAGILTDEEFEEKKKKLLDML 214
                                       46678999***************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1502.61
//
Query:       gi|488600916|ref|YP_007907387.1|  [L=266]
Description: hypothetical protein Asulf_01407 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-08   34.0   0.2    3.2e-08   33.2   0.2    1.3  1  NucS      Endonuclease NucS
  ------ inclusion threshold ------
       0.14   12.0   0.2        1.4    8.8   0.0    2.2  2  DUF3215   Protein of unknown function (DUF3215)


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.2   3.5e-12   3.2e-08     105     187 ..      10      89 ..       4     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.5e-12
                              NucS 105 GseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivelkrrkaevdaveqLkryvellkedsvl 181
                                        +e el  +i ++ d +eeG ++++ e+a++ Gi d L+ d  g+lvi+e+k    e    + L+ y e  k ++v 
  gi|488600916|ref|YP_007907387.1|  10 SNEKELHSIIEKELDALEEGLELLQYEFATSKGIPDFLCVDSGGRLVIIEVKVGEDENILFQALRYYSEISKIKYV- 85 
                                       5799************************************************996666566666666777777888. PP

                              NucS 182 dkvrGv 187
                                         v  +
  gi|488600916|ref|YP_007907387.1|  86 --VANM 89 
                                       ..4444 PP

>> DUF3215  Protein of unknown function (DUF3215)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.073   6.6e+02      46      60 ..     129     143 ..     117     146 .. 0.77
   2 ?    8.8   0.0   0.00016       1.4       9      38 ..     222     255 ..     219     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.073
                                       CEEEEESSSEEEEEE CS
                           DUF3215  46 Gyavledsdvlvhvf 60 
                                        yavl+d+d+ + ++
  gi|488600916|ref|YP_007907387.1| 129 EYAVLQDKDGKMGIY 143
                                       599999999988776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00016
                                       SEEEEEETTS-EEEEEEGGG....CTHHHHHHHC CS
                           DUF3215   9 iGtltfDennnlvdasGiGk....erieDilels 38 
                                       +Gt ++Den ++++ s i      + i+Dile+ 
  gi|488600916|ref|YP_007907387.1| 222 VGTTVLDENGRVIEDSFIRVeepeTDISDILEKI 255
                                       8***************998778889999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1811.22
//
Query:       gi|488600917|ref|YP_007907388.1|  [L=219]
Description: hypothetical protein Asulf_01408 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-24   84.7   1.3    8.2e-24   84.1   0.7    1.5  2  LTD       Lamin Tail Domain
    8.8e-17   61.5   0.0    1.2e-16   61.1   0.0    1.2  1  SNase     Staphylococcal nuclease homologue


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 ?   -2.3   0.0      0.64   5.8e+03      25      31 ..      49      55 ..      10      77 .. 0.62
   2 !   84.1   0.7   9.2e-28   8.2e-24       4     110 ..     107     219 .]     104     219 .] 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.64
                               LTD 25 fvelyNt 31
                                      +v l+N 
  gi|488600917|ref|YP_007907388.1| 49 YVYLENG 55
                                      3333333 PP

  == domain 2  score: 84.1 bits;  conditional E-value: 9.2e-28
                               LTD   4 aagdvvIsevmedgagnnan.......efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsg 72 
                                        a ++ I ev++d++g + +       e++ ++N++s +++L+gw+l+d++g  ytf n    l+ag++v+v++g g
  gi|488600917|ref|YP_007907388.1| 107 GAISIEIVEVHYDAGGPDVDdrdmlndEYIVIVNSGSISINLEGWRLRDEAGFtYTFSNVA--LDAGGTVTVHTGIG 181
                                       566899********9999889******************************98****8885..************** PP

                               LTD  73 ttsasngskasssavwnnggdavaLydasgevvdsvgy 110
                                        + + + +++++s+vwnn+ d+++Ly+a+ge+vd +++
  gi|488600917|ref|YP_007907388.1| 182 GDYDGHLHWNRKSPVWNNDHDTAYLYNAEGELVDKYSW 219
                                       ************************************98 PP

>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   1.4e-20   1.2e-16      23     107 ..      13      98 ..       4      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.4e-20
                                       HHHHHHHHHHHHHHCSSEEEEE-S...SBSTTSEEEEEEEET.TEEHHHHHHHTTSSEE---BTTSTTTHHHHHHHH CS
                             SNase  23 gkeAkeflkklvlqkkvvvleldk...kkDkygrllayvyln.kknineeLvkeGlArvyevyekneekkkellkae 95 
                                       g +A ef+k+ +   k v++e+d+    +++ygrllayvyl+ ++++ + Lv+ G+Arvy  +  +++k+  +l++e
  gi|488600917|ref|YP_007907388.1|  13 GWKAYEFTKSIIE-GKYVYIEFDEtagFTGYYGRLLAYVYLEnGTDFTAMLVEGGYARVYV-EG-EFKKESYYLQLE 86 
                                       789*********9.666666666669999************999**************776.33.589********* PP

                                       HHHHHTT-GGGC CS
                             SNase  96 eeAkkkrkglWs 107
                                       eeAk++r+glWs
  gi|488600917|ref|YP_007907388.1|  87 EEAKRERRGLWS 98 
                                       ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1581.41
//
Query:       gi|488600918|ref|YP_007907389.1|  [L=273]
Description: hypothetical protein Asulf_01409 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1893.01
//
Query:       gi|488600919|ref|YP_007907390.1|  [L=172]
Description: hypothetical protein Asulf_01410 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.0   0.2       0.44   10.2   0.1    1.9  2  SPECT1    Plasmodium host cell traversal SPECT1


Domain annotation for each model (and alignments):
>> SPECT1  Plasmodium host cell traversal SPECT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   2.5e-05      0.44      43     100 ..      23      83 ..      15      94 .. 0.76
   2 ?   -1.5   0.0     0.098   1.8e+03     153     173 ..     124     144 ..     119     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.5e-05
                            SPECT1  43 ydteeklnileGlleefvenskGvifnsseekkkvekdk...fkkvcdlilkkvkklvels 100
                                       y ++ k+  ++   +   e +kG+i n++++ ++v ++k   f k   l+l+k+ +  ++ 
  gi|488600919|ref|YP_007907390.1|  23 YRIKLKFGTINIYTDSVKELEKGIIENLPRKTEQVTRKKatpFEKFWKLLLEKLGTPTHIR 83 
                                       555556555555566666889*********99999888766689*********98766655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.098
                            SPECT1 153 slvnfistiydkfvqklndli 173
                                       +lv  + ++y++f++k  dl 
  gi|488600919|ref|YP_007907390.1| 124 KLVYEVWENYKSFKVKRADLC 144
                                       677778899999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1330.34
//
Query:       gi|488600920|ref|YP_007907391.1|  [L=377]
Description: hypothetical protein Asulf_01411 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-06   28.8   0.0    3.2e-06   27.5   0.0    1.6  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 !   27.5   0.0   1.8e-10   3.2e-06      39     112 .]     116     175 ..      98     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.8e-10
                    Transglut_core  39 gsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsgeeekeqsvasedaHawvevylegygWvplDp 112
                                        s+++ ++ + + G c + aslf+ + + +G ++R+v +  ++             H wve  + ++ W+++Dp
  gi|488600920|ref|YP_007907391.1| 116 LSNNPYWIAFFKVGACGELASLFSEVSKQAGFETRIVRTEGED-------------HTWVELKI-DDEWIHADP 175
                                       56678888899**************************555443.............********.********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2402.81
//
Query:       gi|488600921|ref|YP_007907392.1|  [L=410]
Description: Site-specific recombinase XerD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-16   59.0   0.0    1.4e-15   57.5   0.0    1.7  2  Phage_integrase  Phage integrase family
    6.9e-05   23.2   1.8    0.00015   22.2   0.6    2.3  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
     0.0014   18.0   6.1     0.0034   16.8   6.1    1.6  1  GAS              Growth-arrest specific micro-tubule binding
     0.0057   16.5   0.6      0.011   15.6   0.6    1.4  1  Sec34            Sec34-like family
  ------ inclusion threshold ------
      0.013   15.8   1.3       0.22   11.8   0.2    3.4  3  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
       0.05   14.0   2.7       0.19   12.1   2.5    2.3  1  FlaC_arch        Flagella accessory protein C (FlaC)
      0.063   13.3   1.5       0.13   12.3   1.5    1.6  1  Laminin_II       Laminin Domain II
      0.071   13.2   5.4       0.23   11.5   4.0    2.1  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.34   10.7   1.4       0.46   10.2   0.3    1.8  2  G10              G10 protein
        9.2    7.0  11.7         20    5.9   2.0    3.8  4  YabA             Initiation control protein YabA


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 ?   -4.0   0.0         6   1.1e+04       6      35 ..       7      37 ..       6      40 .. 0.81
   2 !   57.5   0.0   7.8e-19   1.4e-15       2     158 ..     117     292 ..     116     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6
                                      HHHHHHHHCCGC.HHHHHHHHHHHHHHHHT- CS
                   Phage_integrase  6 deverllaalee.slkirdklllellyetGl 35
                                      +eve+ l++++  s++++++ l+ ++  +Gl
  gi|488600921|ref|YP_007907392.1|  7 EEVEKWLNNVKGgSKPTYRAGLTLFCQWCGL 37
                                      6899999999998888888888888877765 PP

  == domain 2  score: 57.5 bits;  conditional E-value: 7.8e-19
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE....EEECSSSSEEEEECTH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvh....eregKgskeravplse 74 
                                       v+t++ v++l++++ +   +rd++++ +l++ G+ +s l+sL+++d++ e +  +++      + K+++e    +++
  gi|488600921|ref|YP_007907392.1| 117 VITPEIVKKLVDHAST---LRDRAIILFLFQGGFDVSTLCSLNYGDVKNELEAEKIPmmihVVREKEEVEYFTFVGR 190
                                       689999**********...************************999765544433333322777788888889999* PP

                                       HHHHHHHHHHHHH...CHCCTTTSBSSBET.....TSSB--HHHHHHHHHHHHHHCT-S..........SC--TTHH CS
                   Phage_integrase  75 ealellkellska...leeaeksellfask.....rgkplsrqtvrkafkraveeagie..........kpltpHtl 133
                                        a+e+lk +l+++    ee ++++ lf++      +g+++s   ++ ++++++ +ag+           +p +pH l
  gi|488600921|ref|YP_007907392.1| 191 DAVEVLKAYLNDRrakGEELKYDTPLFIKDkakrrKGERISPHHIQNMLRETAIKAGLItkeemdkvdfNPYRPHAL 267
                                       *************998888889999***9999999*********************9988999************** PP

                                       HHHHHHHHHHHCTSHHHHHHHHT-S CS
                   Phage_integrase 134 RhsfataLleagvdlrvvqkllGHs 158
                                       R +f++ L  +g+d+  v  ++GHs
  gi|488600921|ref|YP_007907392.1| 268 RAAFSSILRLNGFDPVLVDFMMGHS 292
                                       ************************7 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 !   22.2   0.6   8.2e-08   0.00015      44      77 ..      62      95 ..       6      96 .. 0.93
   2 ?   -3.2   0.0       6.9   1.2e+04      14      36 ..     318     339 ..     311     355 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.2e-08
                   Phage_int_SAM_4 44 edieaYlnyLanerklsastqknalnalsffykk 77
                                      + ++++ nyL+ne+k++++t+  ++ a ++fyk+
  gi|488600921|ref|YP_007907392.1| 62 ARLMEFYNYLINEKKVAKKTATLYFTAVRSFYKW 95
                                      6789*****************************9 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.9
                   Phage_int_SAM_4  14 lserTiksYlsaikrflrflkkk 36 
                                       ls +T   ++s i++ l+ +k k
  gi|488600921|ref|YP_007907392.1| 318 LSISTAVKDVSEIEEKLNTYK-K 339
                                       556666666666665555555.4 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 !   16.8   6.1   1.9e-06    0.0034      28     102 ..     320     394 ..     312     409 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                       I +  +++ e+++k +  +k l+++++enkrl+e+ +++ eev  +++  ++  +  + l  lk+ +  +++  k
  gi|488600921|ref|YP_007907392.1| 320 ISTAVKDVSEIEEKLNTYKKILEDVQAENKRLREQFNALWEEVRIMNELFAQIVENPEMLSTLKEMYGIVKEMEK 394
                                       555667899*********************************************999999999999877766555 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   6.1e-06     0.011      13      76 ..     321     384 ..     311     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.1e-06
                             Sec34  13 delleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldp 76 
                                        + +++++e++e+L++ ++  ++v+++ ++l+e+ + l ee + ++el  +i e+ ++ + l++
  gi|488600921|ref|YP_007907392.1| 321 STAVKDVSEIEEKLNTYKKILEDVQAENKRLREQFNALWEEVRIMNELFAQIVENPEMLSTLKE 384
                                       566899**********************************************988666655555 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 ?   11.8   0.2   0.00012      0.22       3      32 ..      66      95 ..      15      97 .. 0.76
   2 ?   -0.3   0.0      0.77   1.4e+03      38      56 ..     224     242 ..     216     247 .. 0.79
   3 ?   -1.9   0.0       2.4   4.3e+03      23      35 ..     324     336 ..     305     354 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      HHHHHHHHTT-S-HHHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  3 qfleyLikerglspnTlraYrrdLrrflkf 32
                                      +f++yLi+e+ ++++T   Y  ++r+f k+
  gi|488600921|ref|YP_007907392.1| 66 EFYNYLINEKKVAKKTATLYFTAVRSFYKW 95
                                      566666666666666666666666666555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.77
                                       S--TTT--HHHHHHHHHS- CS
                   Phage_int_SAM_1  38 kesleqlttedvraflael 56 
                                        ++ e++++++++++l+e+
  gi|488600921|ref|YP_007907392.1| 224 RRKGERISPHHIQNMLRET 242
                                       5666899********9987 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHHH CS
                   Phage_int_SAM_1  23 rrdLrrflkflae 35 
                                       ++d++++++ l++
  gi|488600921|ref|YP_007907392.1| 324 VKDVSEIEEKLNT 336
                                       3444444444444 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.5   0.00011      0.19       2      40 ..     327     365 ..     326     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       + e+E+kl+  +  le v++en+ l+++ + l e+V+ +
  gi|488600921|ref|YP_007907392.1| 327 VSEIEEKLNTYKKILEDVQAENKRLREQFNALWEEVRIM 365
                                       679******************************999755 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.5   7.1e-05      0.13      26      81 ..     314     368 ..     305     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II  26 lentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       +e  + ++s++ ++v e++ek++ ++k+++d++ + k L ++ + L + ++ +++l
  gi|488600921|ref|YP_007907392.1| 314 VE-AQLSISTAVKDVSEIEEKLNTYKKILEDVQAENKRLREQFNALWEEVRIMNEL 368
                                       44.34578999999********************************9998887776 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 ?    0.5   0.0      0.31   5.5e+02      60     105 ..     159     223 ..     139     265 .. 0.72
   2 ?   11.5   4.0   0.00013      0.23      69     128 ..     319     378 ..     305     408 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.31
                           UPF0242  60 alkeklekskleekeaklteld..........eglktkeealeelqeeeeeLkee.........l 105
                                       ++k++le++k++  ++++ e++          + +++ +  l++++++ eeLk            
  gi|488600921|ref|YP_007907392.1| 159 DVKNELEAEKIPMMIHVVREKEeveyftfvgrDAVEVLKAYLNDRRAKGEELKYDtplfikdkaK 223
                                       57788899999999999999999988888888888888889999999999998775655444440 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                           UPF0242  69 kleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqeklea 128
                                        +++  + ++e +e+l+t ++ le++q+e+++L+e+++a  ee++ ++e  +q+ e  e+
  gi|488600921|ref|YP_007907392.1| 319 SISTAVKDVSEIEEKLNTYKKILEDVQAENKRLREQFNALWEEVRIMNELFAQIVENPEM 378
                                       4666778899999***********************888888887776655555554444 PP

>> G10  G10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.9   8.8e+03      74      87 ..      66      79 ..      64      82 .. 0.77
   2 ?   10.2   0.3   0.00026      0.46      12      56 ..     323     367 ..     314     386 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.9
                               G10 74 elydyllkekyada 87
                                      e y+yl++ek + +
  gi|488600921|ref|YP_007907392.1| 66 EFYNYLINEKKVAK 79
                                      78999999887655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00026
                               G10  12 ppegfekiedtleeleaklreaekeskeskkkeeslWkiarinhe 56 
                                       + ++ ++ie++l+++++ l+++++e+k+ +++ ++lW+ +ri +e
  gi|488600921|ref|YP_007907392.1| 323 AVKDVSEIEEKLNTYKKILEDVQAENKRLREQFNALWEEVRIMNE 367
                                       5678899*******************************9999876 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.7   4.9e+03      51      78 ..      42      69 ..      37      70 .. 0.81
   2 ?    1.5   0.0      0.26   4.6e+02      71      94 ..     137     163 ..     110     166 .. 0.78
   3 ?    5.9   2.0     0.011        20      16      52 ..     319     355 ..     305     368 .. 0.67
   4 ?    3.2   1.4     0.076   1.4e+02      10      52 ..     365     409 ..     356     410 .] 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.7
                                      HHXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA 51 rleeeekkekekkkelsegkenLarlYe 78
                                      +l+e+e+++k++++e ++ +  L + Y+
  gi|488600921|ref|YP_007907392.1| 42 LLDEAEEDRKKSRRERGKPEARLMEFYN 69
                                      5677888888899999999999999986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                                       XXXXXXXXXXXXX...XXXXXXXXXXX CS
                              YabA  71 enLarlYeeGFHi...CnvlyGsrrke 94 
                                         +  l++ GF +   C+++yG+ ++e
  gi|488600921|ref|YP_007907392.1| 137 AIILFLFQGGFDVstlCSLNYGDVKNE 163
                                       556679999**87666999***98876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  16 qleelleeleelkeelaelleenaeLeleneklrerl 52 
                                       ++++ +++++e++e+l++  +  +++++en++lre++
  gi|488600921|ref|YP_007907392.1| 319 SISTAVKDVSEIEEKLNTYKKILEDVQAENKRLREQF 355
                                       4566677777777777777777777888888888776 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.076
                                       HHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  10 leeleeqleelleeleelkee..laelleenaeLeleneklrerl 52 
                                       ++el  q+ e  e l++lke   +++ +e+n  L++   +l+e l
  gi|488600921|ref|YP_007907392.1| 365 MNELFAQIVENPEMLSTLKEMygIVKEMEKNPMLRMKLMELKESL 409
                                       56677788888888889988633678899********99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1567  (0.0874003); expected 358.6 (0.02)
Passed bias filter:                      922  (0.0514251); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3056.08
//
Query:       gi|488600922|ref|YP_007907393.1|  [L=78]
Description: hypothetical protein Asulf_01413 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-15   55.0   0.1      9e-15   54.6   0.1    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 !   54.6   0.1     5e-19     9e-15       2      49 .]      25      72 ..      24      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 5e-19
                           DUF2283  2 itYDpeaDalYIyl..segpveeseevdddiilDfDedGrlvGIEiLnAS 49
                                      ++YD+eaD+lYI +  +++   ++e  d++i+l+f ++++lvGI+iLnAS
  gi|488600922|ref|YP_007907393.1| 25 VDYDKEADVLYISFerPQKA-TDTEVTDEGILLRF-RENKLVGITILNAS 72
                                      89*************65555.556555********.*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 522.81
//
Query:       gi|488600923|ref|YP_007907394.1|  [L=69]
Description: hypothetical protein Asulf_01414 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   0.0      0.035   14.4   0.0    1.0  1  PBECR2    phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2
      0.051   13.8   0.1      0.051   13.8   0.1    1.0  1  DUF4443   Domain of unknown function (DUF4443)


Domain annotation for each model (and alignments):
>> PBECR2  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     4e-06     0.035      20      86 ..       8      69 .]       3      69 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-06
                            PBECR2 20 ktgepvviseelfehlaegekrgrerylplLaetledPdeIwldeeeskklrrrylkrfkdrglfav 86
                                      k g p+ ++ee+  h+ e++ ++ + + + +  ++edPd I+ +++++       +++++d++l+av
  gi|488600923|ref|YP_007907394.1|  8 KNGVPIRLTEERWFHIVENH-DELAGLSDEVLLAVEDPDFIVNGWTDE----FLAVRKINDKYLVAV 69
                                      56899****99999***888.88999*******************994....888899988777765 PP

>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.7e-06     0.051      45      93 ..       4      55 ..       1      69 [] 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-06
                           DUF4443 45 ilivkngepvfpederp..lrdtmeelamnieev.lnfsdgdlivvtwaenp 93
                                      i + kng p+   +er   + +  +ela   +ev l + d d+iv  w+++ 
  gi|488600923|ref|YP_007907394.1|  4 IAVSKNGVPIRLTEERWfhIVENHDELAGLSDEVlLAVEDPDFIVNGWTDEF 55
                                      6688*******99999722468899**988877725899*********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 486.16
//
Query:       gi|488600924|ref|YP_007907395.1|  [L=147]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-23   82.2   0.5    3.9e-23   82.1   0.5    1.0  1  EVE             EVE domain
      0.004   17.0   0.0     0.0054   16.6   0.0    1.3  1  Dev_Cell_Death  Development and cell death domain
  ------ inclusion threshold ------
      0.088   12.7   0.1        1.9    8.5   0.0    2.2  2  DUF4609         Domain of unknown function (DUF4609)


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 !   82.1   0.5   6.6e-27   3.9e-23       1     144 [.       2     144 ..       2     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 6.6e-27
                                       -EEEEEEBHHTSHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEE....ETSSS....S-EEEEEEEEECEEE CS
                               EVE   1 ayWllksepdefsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfY....hsgek....lqaivgiaeVvseay 69 
                                       +yWl+++ ++  +++ +  k++++W gv++ +++n++ ++k+GD++l+Y        k    +++iv+++e vse+ 
  gi|488600924|ref|YP_007907395.1|   2 TYWLCITTEE--NWNVI--KEKNIW-GVPE-RHKNTIAKVKPGDKLLIYlkqeRD--KdkvvEPRIVAVYEAVSEVF 70 
                                       6*********..9****..99****.****.99****************996633..23479*************** PP

                                       E-GGGG-TTSTT--TTTBTTS-.-EEEEEEEEEEEEEEEEHHHHTTHG.TCTTSHHHHCC..T-SEEEE-HHHHHHH CS
                               EVE  70 pdetqfdpkskyydpkskkekp.wlrvdvkpvkklkrplslkelkaep.elegmkllrkg..rlsvrpvteedweli 142
                                       +d++++     ++ p+ ++++  +lr+++k v+ +++p+++k l ++  ++++++ ++ +    ++r+++eed+ li
  gi|488600924|ref|YP_007907395.1|  71 RDSKKI-----FKTPAGMGSESfPLRIKLKSVRIFDKPVEFKPLIPKLkFIKNKQKWTGHliGKAMREIPEEDYGLI 142
                                       ***999.....6779999989989********************99534889999*****99999************ PP

                                       HH CS
                               EVE 143 le 144
                                       ++
  gi|488600924|ref|YP_007907395.1| 143 MS 144
                                       96 PP

>> Dev_Cell_Death  Development and cell death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.1e-07    0.0054      13      84 ..      14      96 ..       4     129 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.1e-07
                    Dev_Cell_Death 13 kecfrkklfglpaeklslvkkikpglkLfLfdyder........kLyGvfeAasdGglniepkafts....ekskfpaQ 79
                                      +   +k++ g+p+++++++ k+kpg kL+++  +er        ++  v+eA s+     ++k f++     +++fp  
  gi|488600924|ref|YP_007907395.1| 14 NVIKEKNIWGVPERHKNTIAKVKPGDKLLIYLKQERdkdkvvepRIVAVYEAVSEVFR-DSKKIFKTpagmGSESFPLR 91
                                      4556899************************888872222222235555555554322.22333333566666777777 PP

                    Dev_Cell_Death 80 vrfki 84
                                      +++k+
  gi|488600924|ref|YP_007907395.1| 92 IKLKS 96
                                      77764 PP

>> DUF4609  Domain of unknown function (DUF4609)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00031       1.9      35      57 ..       8      30 ..       4      34 .. 0.85
   2 ?    1.8   0.0     0.036   2.2e+02       6      21 ..      46      61 ..      44      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00031
                           DUF4609 35 igseeqrTirEqadwGpysRHRn 57
                                      +  e+   i+E++ wG  +RH+n
  gi|488600924|ref|YP_007907395.1|  8 TTEENWNVIKEKNIWGVPERHKN 30
                                      56677889*************98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.036
                           DUF4609  6 kqksskkkvviPqiii 21
                                      kq   k kvv P+i+ 
  gi|488600924|ref|YP_007907395.1| 46 KQERDKDKVVEPRIVA 61
                                      788899********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 941.82
//
Query:       gi|488600925|ref|YP_007907396.1|  [L=433]
Description: Site-specific recombinase XerD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-06   27.6   0.0    6.2e-06   26.1   0.0    1.7  2  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.16   2.8e+03      48      74 ..      91     115 ..      86     152 .. 0.64
   2 !   26.1   0.0   3.4e-10   6.2e-06      51     145 ..     181     280 ..     158     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.16
                                       EECTTTEEEEEEEECSSSSEEEEECT.H CS
                   Phage_integrase  48 ldlengvilvheregKgskeravpls.e 74 
                                       l++++++++v   ++K + ++++p + +
  gi|488600925|ref|YP_007907396.1|  91 LRFNDRELRV---NIKIRDSHEHPNTfN 115
                                       6788888888...556666655554432 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 3.4e-10
                                       TTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHH....CHCCTTTSBSSBET...TSSB--HHHHHHHHHHHHH CS
                   Phage_integrase  51 engvilvheregKgskeravplseealellkellska....leeaeksellfask...rgkplsrqtvrkafkrave 120
                                           + v ++ +K +++    l+ee + +lke+l+++     + + +s ++ +++   rg+++s+ ++ +++++a +
  gi|488600925|ref|YP_007907396.1| 181 VPTMVVVRPAISKVGHQYFTFLGEEGCTYLKEYLEERmrmgEKMDRNSPIITPRAasfRGRHISTINIGDIIRQAIR 257
                                       456677779999*************************887433333333555555888******************* PP

                                       HCT-SSC--TTHHHHHHHHHHHHHC CS
                   Phage_integrase 121 eagiekpltpHtlRhsfataLleag 145
                                       +ag +  ++p  lRh+f t+Ll a+
  gi|488600925|ref|YP_007907396.1| 258 RAGFD--WRPYVLRHYFDTQLLLAE 280
                                       *****..*************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2594.78
//
Query:       gi|488600926|ref|YP_007907397.1|  [L=748]
Description: hypothetical protein Asulf_01417 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   20.9  33.3       0.66   10.3   1.3    6.6  6  DUF5122          Domain of unknown function (DUF5122) beta-pr
     0.0012   18.9   0.0      0.012   15.7   0.0    2.3  2  VRR_NUC          VRR-NUC domain
  ------ inclusion threshold ------
      0.014   16.0  18.2      0.065   13.9   7.9    2.6  2  DUF4398          Domain of unknown function (DUF4398)
      0.017   15.1   0.1      0.052   13.6   0.0    1.8  1  HSDR_N_2         Type I restriction enzyme R protein N termin
      0.023   13.6   0.4        1.7    7.5   0.0    3.0  3  Tri3             15-O-acetyltransferase Tri3
      0.026   13.8   6.7        8.8    5.7   0.0    5.5  8  mRNA_decap_C     mRNA-decapping enzyme C-terminus
      0.029   14.7   1.4         10    6.5   0.2    3.0  3  Nif11            Nif11 domain
      0.031   13.9   0.1       0.06   13.0   0.1    1.4  1  DpnII-MboI       REase_DpnII-MboI
      0.073   13.1   0.1       0.14   12.2   0.1    1.5  1  Replic_Relax     Replication-relaxation
      0.082   13.3   6.9       0.65   10.4   2.4    2.5  2  DUF1771          Domain of unknown function (DUF1771)
      0.084   12.6   0.4       0.18   11.5   0.4    1.5  1  TSP_3            Thrombospondin type 3 repeat
      0.084   12.6   1.4    1.2e+02    2.6   0.0    4.3  4  RHS              RHS protein
       0.11   12.7   1.6       0.26   11.5   0.4    2.2  2  USP8_dimer       USP8 dimerisation domain
       0.14   12.3   8.7        1.3    9.2   1.0    3.0  3  HEPN             HEPN domain
       0.23   11.3  17.3        6.1    6.7   0.0    6.8  7  DUF2064          Uncharacterized protein conserved in bacteri
        2.7    8.0   4.9         10    6.1   0.2    2.7  2  Clathrin_H_link  Clathrin-H-link
        4.7    7.3   8.4         14    5.8   0.5    2.6  2  PTS_IIA          PTS system, Lactose/Cellobiose specific IIA 


Domain annotation for each model (and alignments):
>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.8   0.00089      0.94       2      27 ..      75     101 ..      74     102 .. 0.91
   2 !   10.3   0.6   0.00063      0.66       3      32 ..     131     161 ..     129     162 .. 0.89
   3 !   10.3   1.3   0.00062      0.66       2      32 ..     182     213 ..     181     213 .. 0.93
   4 ?   -1.1   0.2       2.4   2.5e+03       2      15 ..     234     247 ..     233     266 .. 0.80
   5 !    7.7   0.4    0.0042       4.4       2      32 ..     288     317 ..     287     317 .. 0.91
   6 ?    3.4   0.5     0.092        98       3      32 ..     338     368 ..     336     368 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00089
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLn 27 
                                       +DG  ++aG++ sy  g++d +l++++
  gi|488600926|ref|YP_007907397.1|  75 SDGGYIIAGWTDSYgVGNYDVYLIKID 101
                                       8***********999********9987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00063
                           DUF5122   3 DGKIlVaGsftsy.ngssdfalvRLnaDGsl 32 
                                       DG  ++aG ++s   gs+d +l++ +a+G+l
  gi|488600926|ref|YP_007907397.1| 131 DGGYIIAGVTSSFgKGSYDVYLIKTDANGNL 161
                                       88899999999667***************98 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00062
                           DUF5122   2 pDGKIlVaGsftsy.ngssdfalvRLnaDGsl 32 
                                       +DG  ++aG++ts   g+ d ++++ +a+G+l
  gi|488600926|ref|YP_007907397.1| 182 NDGGYIIAGYTTSLgEGGKDVYIIKTDANGNL 213
                                       7***********668***************97 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.4
                           DUF5122   2 pDGKIlVaGsftsy 15 
                                       +DG  +++G++ s 
  gi|488600926|ref|YP_007907397.1| 234 SDGGYIIVGTTKSF 247
                                       79999999998855 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0042
                           DUF5122   2 pDGKIlVaGsftsyngssdfalvRLnaDGsl 32 
                                       +DG  ++aG ++s  g +d +l++  a+G l
  gi|488600926|ref|YP_007907397.1| 288 SDGGYIIAGFSWSF-GAGDVYLIKTSANGKL 317
                                       8***********55.*************976 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.092
                           DUF5122   3 DGKIlVaGsftsy..ngssdfalvRLnaDGsl 32 
                                       DG  +++G+++    +  +d++l++ +++G+l
  gi|488600926|ref|YP_007907397.1| 338 DGGYIIVGWTG-ElrSRIGDIYLIKTDSNGNL 368
                                       9999*******.448***************97 PP

>> VRR_NUC  VRR-NUC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.012      51      81 ..     658     687 ..     633     705 .. 0.82
   2 ?   -0.1   0.0      0.93   9.9e+02      46      63 ..     721     738 ..     713     740 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                       HHSSTS-SEEEEETTTTE..EEEEEEE-TT..- CS
                           VRR_NUC  51 glrsGvPDLilwieeqkryvflliEvKgpg..d 81 
                                       ++++ +PD++++i+++      +iEvKgp+  +
  gi|488600926|ref|YP_007907397.1| 658 QRGASRPDIVVFIDKNT---SIAIEVKGPTgsQ 687
                                       345889**********9...6********9542 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.93
                                       HHCHHHHSSTS-SEEEEE CS
                           VRR_NUC  46 ledyrglrsGvPDLilwi 63 
                                        e y gl+ ++PD+++ +
  gi|488600926|ref|YP_007907397.1| 721 QETYEGLKRTYPDIVIIR 738
                                       47799**********976 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   7.9   6.2e-05     0.065       6      70 ..     420     482 ..     415     494 .. 0.70
   2 ?    8.7   2.8    0.0025       2.6       4      56 ..     482     535 ..     479     543 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                           DUF4398   6 AraaleaAraaga.eeyApaeleeAreaLaqAeaamaekdyeeAdhlaylAerdaelAearAkaak 70 
                                       A +a+++A++    ++    +  eA+  L qAe+a ++++y++A+ la+ A++   lA ++A +a 
  gi|488600926|ref|YP_007907397.1| 420 ANSAINSAKEVISsAKTKGFDVSEAESLLTQAEQAFNDERYSDAKSLAEKARE---LALQTADQAE 482
                                       77778888877777777777788888888888888888888888888888887...4444444443 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0025
                           DUF4398   4 adAraaleaAraaga.eeyApaeleeAreaLaqAeaamaekdyeeAdhlaylAe 56 
                                       ++A   + +A+++   ++   ++  eA+e L+qAe++ ++++ye+A  la  +e
  gi|488600926|ref|YP_007907397.1| 482 ENALNTIISAKENISlAKSKGLDVSEAEELLKQAEQEFNAGNYETAYNLATKTE 535
                                       4555555556666666666666799*************9*****9999998766 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 ?   13.6   0.0   4.9e-05     0.052      31      86 ..     656     711 ..     650     734 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                          HSDR_N_2  31 qlgskkkraDivvykkdkkpllivecKapsvki.seevleqlksYlealkaeylvvt 86 
                                       ++++  +r+Divv+ ++ ++ +++e+K p+ +   ++  + +++Y ++++   +v+ 
  gi|488600926|ref|YP_007907397.1| 656 EYQRGASRPDIVVFIDK-NTSIAIEVKGPTGSQeLQTIADKVMRYKQHFNHLIIVLF 711
                                       5778899********77.***********999855667799999*999987777665 PP

>> Tri3  15-O-acetyltransferase Tri3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.038        40      18      49 ..      68      99 ..      56     108 .. 0.89
   2 ?    7.5   0.0    0.0016       1.7      16      50 ..     121     155 ..     104     170 .. 0.79
   3 ?   -2.7   0.0         2   2.1e+03      18      50 ..     175     207 ..     156     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.038
                              Tri3 18 prvlqrravGaeaivGieksnakGqydlylva 49
                                      +  +q+ + G  +i G  +s   G+yd+yl+ 
  gi|488600926|ref|YP_007907397.1| 68 AYSVQQTSDGGYIIAGWTDSYGVGNYDVYLIK 99
                                      5678999***********************95 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                              Tri3  16 tdprvlqrravGaeaivGieksnakGqydlylvat 50 
                                        ++  +q+   G  +i G+ +s  kG yd+yl+ t
  gi|488600926|ref|YP_007907397.1| 121 DKAYSVQQTKDGGYIIAGVTSSFGKGSYDVYLIKT 155
                                       46778999999**********************88 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2
                              Tri3  18 prvlqrravGaeaivGieksnakGqydlylvat 50 
                                       +  +q+   G  +i G   s  +G  d+y++ t
  gi|488600926|ref|YP_007907397.1| 175 AYSVQQTNDGGYIIAGYTTSLGEGGKDVYIIKT 207
                                       456889999999******************987 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 ?   -3.0   0.0       4.4   4.7e+03      14      22 ..      95     103 ..      95     104 .. 0.82
   2 ?    1.5   0.0      0.17   1.8e+02      14      22 ..     150     158 ..     150     158 .. 0.89
   3 ?   -1.7   0.0       1.8   1.9e+03      14      22 ..     202     210 ..     202     210 .. 0.86
   4 ?    0.1   0.0      0.46   4.9e+02      14      21 ..     256     263 ..     256     264 .. 0.88
   5 ?   -3.3   0.0       5.6   5.9e+03      14      20 ..     306     312 ..     306     314 .. 0.78
   6 ?   -2.3   0.0       2.7   2.9e+03      21      31 ..     321     331 ..     317     338 .. 0.80
   7 ?    4.0   0.1      0.03        31      14      22 ..     357     365 ..     357     365 .. 0.94
   8 ?    5.7   0.0    0.0084       8.8      19      30 ..     548     559 ..     546     566 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.4
                      mRNA_decap_C  14 iHLIknDss 22 
                                       ++LIk D++
  gi|488600926|ref|YP_007907397.1|  95 VYLIKIDAK 103
                                       69***9975 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                      mRNA_decap_C  14 iHLIknDss 22 
                                       ++LIk+D++
  gi|488600926|ref|YP_007907397.1| 150 VYLIKTDAN 158
                                       69*****86 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.8
                      mRNA_decap_C  14 iHLIknDss 22 
                                       ++ Ik+D++
  gi|488600926|ref|YP_007907397.1| 202 VYIIKTDAN 210
                                       699****86 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.46
                      mRNA_decap_C  14 iHLIknDs 21 
                                       ++LIk+D+
  gi|488600926|ref|YP_007907397.1| 256 VYLIKTDP 263
                                       69*****6 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 5.6
                      mRNA_decap_C  14 iHLIknD 20 
                                       ++LIk+ 
  gi|488600926|ref|YP_007907397.1| 306 VYLIKTS 312
                                       69***96 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 2.7
                      mRNA_decap_C  21 ssFLntIHeAY 31 
                                       + F n I eAY
  gi|488600926|ref|YP_007907397.1| 321 KTFSNDIDEAY 331
                                       67999999**9 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.03
                      mRNA_decap_C  14 iHLIknDss 22 
                                       i+LIk+Ds+
  gi|488600926|ref|YP_007907397.1| 357 IYLIKTDSN 365
                                       9******97 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.0084
                      mRNA_decap_C  19 nDssFLntIHeA 30 
                                       nD++F  tIH+A
  gi|488600926|ref|YP_007907397.1| 548 NDQDFAPTIHNA 559
                                       9*********99 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.016        17      25      47 ..     423     445 ..     421     445 .. 0.91
   2 ?    6.5   0.2    0.0098        10      17      47 ..     479     509 ..     461     509 .. 0.81
   3 ?   -2.7   0.0       7.4   7.8e+03      34      41 ..     631     638 ..     620     639 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                             Nif11  25 acsdheevvalAkeaGyefteee 47 
                                       a+ ++ ev+  Ak +G++++e+e
  gi|488600926|ref|YP_007907397.1| 423 AINSAKEVISSAKTKGFDVSEAE 445
                                       678999**************987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0098
                             Nif11  17 palreqlkacsdheevvalAkeaGyefteee 47 
                                       ++  + l+++ ++ e + lAk++G +++e+e
  gi|488600926|ref|YP_007907397.1| 479 DQAENALNTIISAKENISLAKSKGLDVSEAE 509
                                       55567899999*****************987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.4
                             Nif11  34 alAkeaGy 41 
                                       ++A+e+Gy
  gi|488600926|ref|YP_007907397.1| 631 RYAREEGY 638
                                       689****9 PP

>> DpnII-MboI  REase_DpnII-MboI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.7e-05      0.06      36     136 ..     638     730 ..     620     739 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                        DpnII-MboI  36 vQdllhalLkpiFpdirdeewlpsyagkssraDfll...kslkiviEvKytrkskkekklieelaaDialYksdsky 109
                                        +d l a Lk  Fp+        +y+ ++sr+D+++   k+ +i+iEvK  + s++ +++ +++     +Yk  +++
  gi|488600926|ref|YP_007907397.1| 638 YRDTLFAWLKSRFPNTIM-----EYQRGASRPDIVVfidKNTSIAIEVKGPTGSQELQTIADKVM----RYK--QHF 703
                                       567777777777766555.....58999999998875668999*******888877777777765....675..447 PP

                        DpnII-MboI 110 ktLicfvYdperrienpeklekdleke 136
                                       ++Li++++d   + + +++  ++l+++
  gi|488600926|ref|YP_007907397.1| 704 NHLIIVLFDVRVSSTRYQETYEGLKRT 730
                                       9********999888888888888754 PP

>> Replic_Relax  Replication-relaxation
   #    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     111     178 ..     633     704 ..     585     707 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                      Replic_Relax 111 aRetpdaa.lteWresaktkafgkkaktllkPDaflsweedg.fflEvDtgtesl..ktlvrKirkYeelae 178
                                       aRe    + l +W +s+ +++  + +++  +PD ++ +++++ +++Ev   t s+  +t++ K+ +Y ++++
  gi|488600926|ref|YP_007907397.1| 633 AREEGYRDtLFAWLKSRFPNTIMEYQRGASRPDIVVFIDKNTsIAIEVKGPTGSQelQTIADKVMRYKQHFN 704
                                       4433333468899988888886666899******99999967999999966665544************987 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.4   0.00062      0.65      16      61 ..     445     490 ..     441     493 .. 0.90
   2 ?    4.5   0.1     0.044        46      15      40 ..     508     533 ..     504     538 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
                           DUF1771  16 nelfekAaeAyrrGdgaaAkelseqGkehgekmeeanreAaeaIfe 61 
                                        +l+ +A +A++      Ak l+e+++e+  +    +++A + I  
  gi|488600926|ref|YP_007907397.1| 445 ESLLTQAEQAFNDERYSDAKSLAEKARELALQTADQAENALNTIIS 490
                                       57899*************************9999999999888875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.044
                           DUF1771  15 rnelfekAaeAyrrGdgaaAkelseq 40 
                                         el+++A + +++G+ + A  l+ +
  gi|488600926|ref|YP_007907397.1| 508 AEELLKQAEQEFNAGNYETAYNLATK 533
                                       5799***************9988865 PP

>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00017      0.18      15      33 ..     540     558 ..     538     559 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                             TSP_3  15 DfDnDgvqddlDNCprnan 33 
                                       D+D+Dgv++d+D  p++ n
  gi|488600926|ref|YP_007907397.1| 540 DVDKDGVPNDQDFAPTIHN 558
                                       9***********8887755 PP

>> RHS  RHS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.12   1.3e+02      16      25 ..     155     164 ..     155     168 .. 0.88
   2 ?    1.7   0.0      0.21   2.2e+02      16      25 ..     207     216 ..     207     221 .. 0.86
   3 ?   -0.1   0.0      0.77   8.1e+02      16      27 ..     311     322 ..     311     325 .. 0.84
   4 ?    2.6   0.0      0.11   1.2e+02      16      27 ..     362     373 ..     362     379 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                               RHS  16 tDanGeivWa 25 
                                       tDanG++ W+
  gi|488600926|ref|YP_007907397.1| 155 TDANGNLEWQ 164
                                       9********9 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.21
                               RHS  16 tDanGeivWa 25 
                                       tDanG++ W 
  gi|488600926|ref|YP_007907397.1| 207 TDANGNLQWY 216
                                       9********6 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.77
                               RHS  16 tDanGeivWaae 27 
                                       t+anG++ W+ +
  gi|488600926|ref|YP_007907397.1| 311 TSANGKLQWQKT 322
                                       89*******965 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.11
                               RHS  16 tDanGeivWaae 27 
                                       tD+nG++ W+ +
  gi|488600926|ref|YP_007907397.1| 362 TDSNGNLQWQKT 373
                                       9********966 PP

>> USP8_dimer  USP8 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.9   6.3e+03      36      48 ..     425     437 ..     415     463 .. 0.57
   2 ?   11.5   0.4   0.00025      0.26      34      64 ..     504     534 ..     480     543 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.9
                        USP8_dimer  36 rsaeklfkkAeey 48 
                                       +sa++++  A+ +
  gi|488600926|ref|YP_007907397.1| 425 NSAKEVISSAKTK 437
                                       4444444444433 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00025
                        USP8_dimer  34 llrsaeklfkkAeeyrlegdeEkAYvlymky 64 
                                        +++ae+l+k+Ae+    g+ E+AY l +k 
  gi|488600926|ref|YP_007907397.1| 504 DVSEAEELLKQAEQEFNAGNYETAYNLATKT 534
                                       5789*********************999885 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       6.1   6.4e+03      98     114 ..     417     433 ..     410     436 .. 0.77
   2 ?    9.2   1.0    0.0012       1.3       6      39 ..     442     475 ..     440     488 .. 0.94
   3 ?    7.0   0.2    0.0059       6.2       6      31 ..     506     531 ..     504     534 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.1
                                       HHHHHHHHHHHHHHHHH CS
                              HEPN  98 eedaeealkdaeevlel 114
                                       +  a +a++ a+ev+  
  gi|488600926|ref|YP_007907397.1| 417 RVIANSAINSAKEVISS 433
                                       56688999999999865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                              HEPN   6 rrAeedleaAellleegdydlacfhaqqaaekal 39 
                                       ++Ae+ l +Ae+++++++y++a + a+ a e+al
  gi|488600926|ref|YP_007907397.1| 442 SEAESLLTQAEQAFNDERYSDAKSLAEKARELAL 475
                                       689*****************************98 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0059
                                       HHHHHHHHHHHHHHHTT-HHHHHHHH CS
                              HEPN   6 rrAeedleaAellleegdydlacfha 31 
                                       ++Aee l++Ae+ +++g y+ a + a
  gi|488600926|ref|YP_007907397.1| 506 SEAEELLKQAEQEFNAGNYETAYNLA 531
                                       68******************998765 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 ?   -0.0   0.4       0.7   7.4e+02      96     107 ..      74      85 ..      66      91 .. 0.85
   2 ?    2.5   0.1      0.11   1.2e+02      95     108 ..     128     141 ..     121     149 .. 0.83
   3 ?    2.3   0.1      0.13   1.4e+02      95     108 ..     180     193 ..     172     201 .. 0.85
   4 ?    6.7   0.0    0.0058       6.1      95     117 ..     232     252 ..     224     256 .. 0.81
   5 ?    1.1   0.2      0.31   3.3e+02      96     107 ..     287     298 ..     280     307 .. 0.84
   6 ?    3.5   0.0     0.056        59      95     108 ..     335     348 ..     327     358 .. 0.81
   7 ?   -1.6   0.0       2.1   2.2e+03      57      74 ..     727     744 ..     713     746 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.7
                                       BTTSSEEEEEEE CS
                           DUF2064  96 aeDGGYyllGlk 107
                                       ++DGGY++ G +
  gi|488600926|ref|YP_007907397.1|  74 TSDGGYIIAGWT 85 
                                       78******9988 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        ++DGGY++ G+++
  gi|488600926|ref|YP_007907397.1| 128 QTKDGGYIIAGVTS 141
                                       579*********96 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.13
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        ++DGGY++ G+++
  gi|488600926|ref|YP_007907397.1| 180 QTNDGGYIIAGYTT 193
                                       579********996 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0058
                                       EBTTSSEEEEEEEG-G...GGGT CS
                           DUF2064  95 paeDGGYyllGlkkrlapaelFe 117
                                        ++DGGY+++G +k  +  +lF 
  gi|488600926|ref|YP_007907397.1| 232 QTSDGGYIIVGTTK--SFGDLFH 252
                                       679**********8..4567886 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.31
                                       BTTSSEEEEEEE CS
                           DUF2064  96 aeDGGYyllGlk 107
                                       ++DGGY++ G++
  gi|488600926|ref|YP_007907397.1| 287 TSDGGYIIAGFS 298
                                       78********98 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.056
                                       EBTTSSEEEEEEEG CS
                           DUF2064  95 paeDGGYyllGlkk 108
                                        ++DGGY+++G + 
  gi|488600926|ref|YP_007907397.1| 335 QTKDGGYIIVGWTG 348
                                       579********985 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 2.1
                                       HHTT-SEEEEE-SS-TT- CS
                           DUF2064  57 feageepvlliGsDcpql 74 
                                       ++ ++  +++i  D p++
  gi|488600926|ref|YP_007907397.1| 727 LKRTYPDIVIIRKDFPSV 744
                                       4778889*********98 PP

>> Clathrin_H_link  Clathrin-H-link
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.8      0.11   1.2e+02       4      40 ..     443     478 ..     440     485 .. 0.83
   2 ?    6.1   0.2    0.0099        10       4      34 ..     507     536 ..     504     540 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                   Clathrin_H_link   4 GaddlyvqqFeqllaqgnykeAakvAaespqgiLRtp 40 
                                        a++l++q  eq ++ ++y++A  +A ++ + +L t+
  gi|488600926|ref|YP_007907397.1| 443 EAESLLTQA-EQAFNDERYSDAKSLAEKARELALQTA 478
                                       677777655.9***************99998888776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0099
                   Clathrin_H_link   4 GaddlyvqqFeqllaqgnykeAakvAaespq 34 
                                        a++l+ q  eq +++gny+ A ++A ++++
  gi|488600926|ref|YP_007907397.1| 507 EAEELLKQ-AEQEFNAGNYETAYNLATKTES 536
                                       67777755.5999*************98876 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.7     0.043        46      29      60 ..     441     472 ..     418     496 .. 0.58
   2 ?    5.8   0.5     0.013        14      21      46 ..     497     522 ..     489     536 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.043
                           PTS_IIA  29 feeaeellkeAeeelkeAhkaqteliqkeasg 60 
                                       ++eae+ll++Ae+++++ + + ++ ++++a++
  gi|488600926|ref|YP_007907397.1| 441 VSEAESLLTQAEQAFNDERYSDAKSLAEKARE 472
                                       44566666666666655555555555555443 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                           PTS_IIA  21 lkaakegdfeeaeellkeAeeelkeA 46 
                                       l++ k  d++eaeellk+Ae+e++++
  gi|488600926|ref|YP_007907397.1| 497 LAKSKGLDVSEAEELLKQAEQEFNAG 522
                                       5566777999************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.86u 0.34s 00:00:01.20 Elapsed: 00:00:00.53
# Mc/sec: 4262.38
//
Query:       gi|488600927|ref|YP_007907398.1|  [L=32]
Description: hypothetical protein Asulf_01418 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); 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:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.55 Elapsed: 00:00:00.39
# Mc/sec: 249.16
//
Query:       gi|488600928|ref|YP_007907399.1|  [L=148]
Description: hypothetical protein Asulf_01419 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0037   16.8   5.8     0.0057   16.2   5.8    1.3  1  TryThrA_C  Tryptophan-Threonine-rich plasmodium antigen C ter
  ------ inclusion threshold ------
      0.099   12.5   1.1       0.15   12.0   1.1    1.2  1  LMP        LMP repeated region


Domain annotation for each model (and alignments):
>> TryThrA_C  Tryptophan-Threonine-rich plasmodium antigen C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   5.8   6.3e-07    0.0057       3     107 ..       5     112 ..       4     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.3e-07
                         TryThrA_C   3 kkwlkkleeeWekFneslenekkkwlekkekeweewlkeienK..Wl..hynekldeeyksdilkksskwdeeqwee 75 
                                       +k++++++e+  +F++sl+ + k+ ++++eke + ++ke+ +   W   ++ +++     +++   s  w  ++w e
  gi|488600928|ref|YP_007907399.1|   5 NKYVNRVKENLLRFKNSLNGDLKEKVKETEKEIDGFVKEMDSNgyWRvvRFFRNILLFAYKKLEGVSIPWH-NNWME 80 
                                       7899************************************9864455114445555555555555666665.77888 PP

                         TryThrA_C  76 wiktegkkliekdwkkwikenesnlnkwlvke 107
                                        +  e+ k ++++w  w ++  +nl ++l ++
  gi|488600928|ref|YP_007907399.1|  81 GLVGEISKRMKNKWMSWSAKGAKNLLNLLLRR 112
                                       888999************99999998887665 PP

>> LMP  LMP repeated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1   1.6e-05      0.15      52      94 ..       7      50 ..       3      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                               LMP 52 kvteitkkLekFnkdkeakFke.LeqtRkdieeFlkdvknnpnY 94
                                       v  ++++L +F+++ + + ke +++t k+i+ F+k++  n ++
  gi|488600928|ref|YP_007907399.1|  7 YVNRVKENLLRFKNSLNGDLKEkVKETEKEIDGFVKEMDSNGYW 50
                                      58899**********99999754899***********9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 774.90
//
Query:       gi|488600929|ref|YP_007907400.1|  [L=328]
Description: Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase-related flavin-dependent oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-69  234.2   0.6    3.4e-67  227.1   0.6    2.0  1  Bac_luciferase  Luciferase-like monooxygenase
     0.0029   18.3   0.0        2.1    9.0   0.0    2.5  2  DUF3502         Domain of unknown function (DUF3502)
  ------ inclusion threshold ------
       0.08   11.8   0.1       0.12   11.2   0.1    1.2  1  Phage_min_cap2  Phage minor capsid protein 2


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 !  227.1   0.6   5.7e-71   3.4e-67       6     314 .]      14     305 ..       3     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 227.1 bits;  conditional E-value: 5.7e-71
                    Bac_luciferase   6 flptrqggalgaas..........aslrylvelaraaEelGfdavwvaehhggpgga.....ldaftllaalaaaTe 67 
                                       +lp r ++ + a +          +s+ y++e+a +aE+ G d+vw+++h ++p +      l+a+t++ a+a+aTe
  gi|488600929|ref|YP_007907400.1|  14 WLPSRESAKAVADGsyfdreeeerPSYSYVKEVALKAEKIGVDSVWIPDHMLNPIKGghapaLEAWTVAVAIAEATE 90 
                                       5556665555555567777778889***************************9988899****************** PP

                    Bac_luciferase  68 rirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGv...dhderyarlrEfvevlrrlwrg 141
                                       ++ +  ++++   r PavlA++aatLd++s+ Rf+l +g+g+++ e++++G+   +hder++r+ E++e++rrlwr+
  gi|488600929|ref|YP_007907400.1|  91 KVIIAHTTLCEAFRPPAVLAKMAATLDDVSNHRFWLSIGAGWYKREYEAYGLpfyEHDERVRRAGEAIEIIRRLWRE 167
                                       ****999988888**************************************************************99 PP

                    Bac_luciferase 142 eevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpa 218
                                       + ++f+G+++++ ++ l p+p+   iP++ a++s+a++ l a+ adg+l+ g + eea++ ie+++++ ++agrd +
  gi|488600929|ref|YP_007907400.1| 168 NGITFKGKYYQIINGVLEPKPK--KIPLWYAGVSEASRNLVAEKADGWLMRGCSVEEARKNIEDMKKRLKKAGRDEE 242
                                       999******************4..38*************************************************** PP

                    Bac_luciferase 219 dirvgisltvivadteeeAraearaliagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvG 295
                                       +++++i + + ++dt+eeA+ ++++l+                           +++  ++           t+lvG
  gi|488600929|ref|YP_007907400.1| 243 EMEFAIPALTFIRDTDEEALNHMEKLT-------------------------GGRRNVLDR--T------LDTGLVG 286
                                       ***********************8888.........................222222222..2......25799** PP

                    Bac_luciferase 296 tpeqvaerlaayaeagvde 314
                                       +pe+vae+++ ++eag+d+
  gi|488600929|ref|YP_007907400.1| 287 SPETVAEKIRKFEEAGIDH 305
                                       *****************97 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0016       9.8      83     116 ..     206     241 ..     199     248 .. 0.82
   2 !    9.0   0.0   0.00035       2.1      89     119 ..     278     308 ..     242     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0016
                           DUF3502  83 vveeykkaletG.lv.DpeetlpkfneklkaaGidk 116
                                       v e+    l+ G +v +  +++++++++lk+aG d+
  gi|488600929|ref|YP_007907400.1| 206 VAEKADGWLMRGcSVeEARKNIEDMKKRLKKAGRDE 241
                                       56666677888988899****************996 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00035
                           DUF3502  89 kaletGlvDpeetlpkfneklkaaGidkvia 119
                                       + l tGlv   et+++ + k ++aGid+++ 
  gi|488600929|ref|YP_007907400.1| 278 RTLDTGLVGSPETVAEKIRKFEEAGIDHILL 308
                                       5799****77778889999*********975 PP

>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1     2e-05      0.12      25     114 ..     227     316 ..     223     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2e-05
                    Phage_min_cap2  25 iediarrikktgeltntaewqieklaelgllnreilkliskltgksekelrkllkeagdkaiksddkelaiykeagl 101
                                       ied+ +r+kk+g+ ++  e++i  l+ ++  ++e l++ +kltg  ++ l+++l++    + + +++++++ +eag+
  gi|488600929|ref|YP_007907400.1| 227 IEDMKKRLKKAGRDEEEMEFAIPALTFIRDTDEEALNHMEKLTGGRRNVLDRTLDTGLVGSPETVAEKIRKFEEAGI 303
                                       89******************************************************999999999999********9 PP

                    Phage_min_cap2 102 epkplekseelqq 114
                                       +++ l+   +l++
  gi|488600929|ref|YP_007907400.1| 304 DHILLQLTPTLKE 316
                                       9966555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1978.59
//
Query:       gi|488600930|ref|YP_007907401.1|  [L=364]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-43  148.2   1.4    4.2e-43  147.1   1.4    1.6  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.2e-21   77.5   0.5    2.7e-21   76.3   0.2    1.7  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.6e-21   76.3   0.3      5e-21   74.7   0.1    1.9  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      3e-19   69.6   1.2    3.7e-19   69.3   0.3    1.7  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.1   1.4   9.5e-47   4.2e-43       1     150 []     215     363 ..     215     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 9.5e-47
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       gkG+rva+  l+ +R+  aa+ lg+a+ ++e++l+y+++r afg++++++q+v+++lae+aa++ea++ l+y+aae+
  gi|488600930|ref|YP_007907401.1| 215 GKGLRVALGILAPGRIPFAAMGLGIAEGCFEHVLNYVKKRGAFGQKILNFQAVQFMLAEVAADIEATKILIYHAAEL 291
                                       79**************************************************************************9 PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrll 150
                                       +++++ + + a+m+Kl+ +ela +vad a++l+Gg+G+l  + v+r+yrda++l i+eGtse++++ii+r+ll
  gi|488600930|ref|YP_007907401.1| 292 AKENDVT-VLAAMTKLKSAELAKKVADVAVELHGGYGILSNTLVDRAYRDAKTLDIAEGTSEMMKLIISRALL 363
                                       8888888.**************************************************************985 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.2     6e-25   2.7e-21       5     111 ..       5     106 ..       2     108 .. 0.88
   2 ?   -2.7   0.0         2   9.1e+03      22      33 ..     287     298 ..     267     334 .. 0.50

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 6e-25
                                       HHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHH CS
                     Acyl-CoA_dh_N   5 ealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglall 81 
                                       e+  ++v ef++++    a e+d+++e++++++++l    l+g+  p+ ygG+g++y+ea  ++eela+++a++a +
  gi|488600930|ref|YP_007907401.1|   5 EEAAKEVVEFVKTK----AVEIDRNNEMDKSVLEELFGKKLMGVIAPQRYGGLGMGYVEASRLVEELAKVSAAVAHS 77 
                                       45556666666665....568999999*********999***********************************999 PP

                                       HHHHHHTTHHHHHHHS-HHHHHHHHHHHHT CS
                     Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklas 111
                                       + vh+ ++a ail+fG+eeqkr+yL+ l s
  gi|488600930|ref|YP_007907401.1|  78 VFVHN-IAADAILKFGSEEQKRKYLKSLTS 106
                                       99*98.8889***************99876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                       HHHHHHHHTSGH CS
                     Acyl-CoA_dh_N  22 haaewdeegefp 33 
                                       haae  +e+ + 
  gi|488600930|ref|YP_007907401.1| 287 HAAELAKENDVT 298
                                       444444333333 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.1   1.1e-24     5e-21       1      97 []     111     203 ..     111     203 .. 0.91
   2 ?   -1.6   0.0       0.7   3.1e+03      30      52 ..     278     304 ..     262     326 .. 0.67

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.1e-24
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrr 77 
                                       a+a+TEp++Gsdva+     ae++g++y+ nG+K++itn+++a++++v+ar +++  +rgl+ ++v+ ++ g++v +
  gi|488600930|ref|YP_007907401.1| 111 AVAITEPSGGSDVANAIKLRAEKKGDKYIMNGTKMFITNSTHADIFIVVAR-TGEG-RRGLTALIVE-KNDGIEVIK 184
                                       689*********98766546999999*************************.4555.8*********.5779***** PP

                                       ---BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                       + +  G+rg   g ++f+dv
  gi|488600930|ref|YP_007907401.1| 185 L-NPSGMRGSGLGTVRFKDV 203
                                       9.58**************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.7
                                       EEEEEEEEETTTT....-SEEEEEEET CS
                     Acyl-CoA_dh_M  30 lnGeKiwitnaai....atlalvlart 52 
                                       ++ +Ki i +aa+    ++++++ a+t
  gi|488600930|ref|YP_007907401.1| 278 IEATKILIYHAAElakeNDVTVLAAMT 304
                                       566777777777665556666666662 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.9   1.3e+04      14      28 ..       7      21 ..       5      32 .. 0.61
   2 !   69.3   0.3   8.3e-23   3.7e-19       3     128 ..     232     346 ..     230     352 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.9
                                      HHHHHHHHHHHHHCT CS
                     Acyl-CoA_dh_2 14 alaefvelarervra 28
                                      a++e+ve+++++   
  gi|488600930|ref|YP_007907401.1|  7 AAKEVVEFVKTKAVE 21
                                      677778888777653 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 8.3e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHH CS
                     Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtved 79 
                                       +aa+ lG+A++++++++ ++++r    +g+k+  ++a+q+ lae+aa+++A + l+++aa+        +ke+  + 
  gi|488600930|ref|YP_007907401.1| 232 FAAMGLGIAEGCFEHVLNYVKKRGA--FGQKILNFQAVQFMLAEVAADIEATKILIYHAAEL-------AKEN--DV 297
                                       89***********************..***********************************.......3333..33 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCT CS
                     Acyl-CoA_dh_2  80 raearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaa 128
                                       +  a+++++  +ela +++d ++e++Gg++++++  ++R++RDa+++ +
  gi|488600930|ref|YP_007907401.1| 298 TVLAAMTKLKSAELAKKVADVAVELHGGYGILSNTLVDRAYRDAKTLDI 346
                                       788999***************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2513.46
//
Query:       gi|488600931|ref|YP_007907402.1|  [L=241]
Description: hypothetical protein Asulf_01422 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-09   37.0   0.1    1.1e-08   34.8   0.0    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
    4.2e-05   23.5   0.0    0.00012   22.1   0.0    1.8  1  HTH_20          Helix-turn-helix domain
    6.4e-05   22.9   0.7    0.00016   21.6   0.0    2.0  2  HTH_45          Winged helix-turn-helix
    8.1e-05   22.1   0.1    0.00044   19.7   0.1    2.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0058   16.7   0.1      0.057   13.5   0.0    2.5  3  Mrr_N           Mrr N-terminal domain
      0.007   16.5   0.0      0.022   14.9   0.0    2.0  1  HTH_34          Winged helix DNA-binding domain
     0.0093   15.8   0.3      0.059   13.2   0.0    2.3  3  HxlR            HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.034   14.3   0.0      0.094   12.9   0.0    1.7  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.045   13.5   0.0       0.08   12.6   0.0    1.4  1  Ribosomal_S19e  Ribosomal protein S19e
      0.057   13.1   0.4       0.19   11.4   0.0    2.0  2  RP-C            Replication protein C N-terminal domain
      0.065   13.1   0.0       0.13   12.1   0.0    1.5  1  MarR_2          MarR family
      0.082   12.7   0.3        0.5   10.2   0.3    2.3  1  DUF1495         Winged helix DNA-binding domain (DUF1495)


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 ?   -1.3   0.1       1.4   2.1e+03      16      27 ..     118     126 ..     102     131 .. 0.55
   2 !   34.8   0.0   7.4e-12   1.1e-08       2      45 ..     169     212 ..     168     213 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.4
                                       EEHHHHHHHHTS CS
                             HTH_5  16 lcvcelaeelgl 27 
                                       +c++e    l+l
  gi|488600931|ref|YP_007907402.1| 118 CCFSE---VLKL 126
                                       33333...3333 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 7.4e-12
                                       HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5   2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       + R+kIL  L + ++ +++l++++gl  ++++ H kkL +aGLV
  gi|488600931|ref|YP_007907402.1| 169 EIRIKILLELFKCPKRFSQLSNITGLDGGNLRFHIKKLVDAGLV 212
                                       78*****************************************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 !   22.1   0.0   7.7e-08   0.00012       7      59 ..     166     217 ..     155     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.7e-08
                                       HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                       L+++ R +il +L  + +  +s+l    +l+  +l++H+++L++agLv + + 
  gi|488600931|ref|YP_007907402.1| 166 LSNEIRIKILLEL-FKCPKRFSQLSNITGLDGGNLRFHIKKLVDAGLVVQHKK 217
                                       8999999999999.9999999***************************88775 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       6.2   9.3e+03       9      15 ..      10      16 ..       4      27 .. 0.53
   2 !   21.6   0.0   1.1e-07   0.00016       7      72 ..     170     237 ..     167     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.2
                            HTH_45  9 adILeai 15
                                       +ILe+ 
  gi|488600931|ref|YP_007907402.1| 10 KEILEIK 16
                                      4555533 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.1e-07
                            HTH_45   7 IiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli..kkskekYvlTekGlelleklkel 72 
                                       I + IL  + +  ++ +++     L+  +l+  +++Lv+ gl+  +k++++Y +Te+G+ +le+l ++
  gi|488600931|ref|YP_007907402.1| 170 IRIKILLELFKCPKRFSQLSNITGLDGGNLRFHIKKLVDAGLVvqHKKGGEYIITEQGRVFLERLVNV 237
                                       555565555566677777777788888899999*********97666999*************99775 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   0.1     3e-07   0.00044       2      47 ..     168     212 ..     167     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3e-07
                            HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       +e+++kIL +L k p+   ++L+  +gl  ++++ ++k+L+++Gl+
  gi|488600931|ref|YP_007907402.1| 168 NEIRIKILLELFKCPK-RFSQLSNITGLDGGNLRFHIKKLVDAGLV 212
                                       7899999999999555.799************************98 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.89   1.3e+03      23      54 ..      80     111 ..      75     120 .. 0.79
   2 ?   -3.1   0.0       5.8   8.7e+03      40      54 ..     125     141 ..     120     144 .. 0.51
   3 !   13.5   0.0   3.8e-05     0.057      54      86 ..     199     232 ..     196     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.89
                             Mrr_N  23 irervaerfglseeeraellpsgkqtrfknrv 54 
                                       + e++++ + l+e e     ++g  + ++nr+
  gi|488600931|ref|YP_007907402.1|  80 LDEALRDGMDLKELEALYEEKKGMVSQLENRA 111
                                       56778888888888888888888889999987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.8
                             Mrr_N  40 ellpsgkq..trfknrv 54 
                                       +ll++  q  ++fkn +
  gi|488600931|ref|YP_007907402.1| 125 KLLKKQHQvlKLFKNTI 141
                                       33333334466666655 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3.8e-05
                             Mrr_N  54 vgWartyLkkagllespk.rgvwkiTekGrevlk 86 
                                       +++ +++L+ agl+ + k  g + iTe+Gr +l+
  gi|488600931|ref|YP_007907402.1| 199 LRFHIKKLVDAGLVVQHKkGGEYIITEQGRVFLE 232
                                       689999*******999985677********9986 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05     0.022      16      76 ..     184     238 ..     170     241 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                            HTH_34  16 dfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaL 76 
                                        f++l++ +++  gnL  h+kkL +ag ++ +k+  g+     + iT++Gr   ++ v+ L
  gi|488600931|ref|YP_007907402.1| 184 RFSQLSNITGLDGGNLRFHIKKLVDAGLVVQHKK--GG----EYIITEQGRVFLERLVNVL 238
                                       69*************************9876664..33....5789999998777777666 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.98   1.5e+03      27      47 ..      41      61 ..      19      90 .. 0.68
   2 ?   -1.2   0.0       1.3   1.9e+03      12      36 ..      60      84 ..      49     114 .. 0.59
   3 !   13.2   0.0   3.9e-05     0.059       8      73 ..     172     231 ..     166     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.98
                                      HSTTS-HHHHHHHHHHHHHTT CS
                              HxlR 27 alpkisqkmLaqrLreLeqdg 47
                                      +l++i  ++++++ +eL +++
  gi|488600931|ref|YP_007907402.1| 41 KLGEILISIISAQNKELLSER 61
                                      445555555555555544443 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                                      HHHTTS-EEHHHHHHHSTTS-HHHH CS
                              HxlR 12 vellkgkkRfselkralpkisqkmL 36
                                        l kg  Rf+   +++ k   + L
  gi|488600931|ref|YP_007907402.1| 60 ERLQKGCSRFEVCMTNFSKFLDEAL 84
                                      4555566666555555444444444 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGH CS
                              HxlR   8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsle 73 
                                       + il el+k +kRfs+l+++  ++    L  ++++L   gl+   v ++ +   eY +te+Gr   
  gi|488600931|ref|YP_007907402.1| 172 IKILLELFKCPKRFSQLSNIT-GLDGGNLRFHIKKLVDAGLV---VQHKKGG--EYIITEQGRVFL 231
                                       679**************9766.99****************98...4556666..899999999754 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 ?   12.9   0.0   6.3e-05     0.094      22      50 ..     186     214 ..     185     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-05
                    B-block_TFIIIC  22 sdLakeskqdprslfyrlksLekkgLIvk 50 
                                       s+L+++++ d+ +l  ++k+L + gL+v 
  gi|488600931|ref|YP_007907402.1| 186 SQLSNITGLDGGNLRFHIKKLVDAGLVVQ 214
                                       689************************96 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05      0.08      66     132 ..     170     236 ..     150     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                       GS----SS-SSS-------THHHHHHHHHTTSSS--SSS---SS.-HHHHHTHHHHH--SS--S--XX CS
                    Ribosomal_S19e  66 vGverlrkvYGgkkrrgvrpshfvkasgsvirkilqqLeklglv.kkekkkgrrltkkGqrlldriae 132
                                       + ++ l + + + kr  ++ s+ +   g  +r  +++L ++glv +++k++  ++t++G+ +l+r+ +
  gi|488600931|ref|YP_007907402.1| 170 IRIKILLELFKCPKR-FSQLSNITGLDGGNLRFHIKKLVDAGLVvQHKKGGEYIITEQGRVFLERLVN 236
                                       555555555555555.455555566677889999**********77777777789*********9876 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 ?   -2.9   0.3         3   4.6e+03     156     170 ..       8      22 ..       4      27 .. 0.53
   2 ?   11.4   0.0   0.00013      0.19      76     103 ..     187     214 ..     183     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3
                              RP-C 156 lrerltllrrdiakl 170
                                       lr+++  ++r+i+kl
  gi|488600931|ref|YP_007907402.1|   8 LRKEILEIKREIEKL 22 
                                       455555555555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00013
                              RP-C  76 qLsralglsestlrrhlaaLveaGliir 103
                                       qLs+ +gl    lr h+++Lv+aGl++ 
  gi|488600931|ref|YP_007907402.1| 187 QLSNITGLDGGNLRFHIKKLVDAGLVVQ 214
                                       89999********************986 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     9e-05      0.13      10      53 ..     174     214 ..     170     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9e-05
                                       HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                       +L++L   p    + ++l   +gl+ +++  ++k+Lv+aGLv++
  gi|488600931|ref|YP_007907402.1| 174 ILLELFKCPK---RFSQLSNITGLDGGNLRFHIKKLVDAGLVVQ 214
                                       6788888887...99***************************86 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00033       0.5      38      89 ..     187     233 ..     159     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00033
                           DUF1495  38 kpsnvkGaleGmgkrynsessLielGLveeeeeseglklYklteeGieivev 89 
                                       + sn++G l G + r++ ++ L+  GLv   ++++g   Y +te+G+ + e+
  gi|488600931|ref|YP_007907402.1| 187 QLSNITG-LDGGNLRFHIKK-LVDAGLVV--QHKKG-GEYIITEQGRVFLER 233
                                       5678888.99999***9875.*******4..44444.4599*****998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1546.45
//
Query:       gi|488600932|ref|YP_007907403.1|  [L=119]
Description: hypothetical protein Asulf_01423 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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      0.013   15.5   0.0    1.1  1  Y2_Tnp    Putative transposase


Domain annotation for each model (and alignments):
>> Y2_Tnp  Putative transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   7.4e-07     0.013      78     132 ..       4      59 ..       1      73 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.4e-07
                            Y2_Tnp  78 eefssllkkaskkgfvvhakkave.kerkvleyLarYisrpaisnkRlvstdeekv 132
                                       ++ ++ll++++ ++++v++++ +e ++   l++L+ +++r+ ++ k l+++d++ +
  gi|488600932|ref|YP_007907403.1|   4 KKYKALLEDENVRRWYVNVSRGAEvTADVNLKRLSNFCERVGLNPKDLLKMDDKAL 59 
                                       567889999999************99999***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 785.09
//
Query:       gi|488600933|ref|YP_007907404.1|  [L=261]
Description: Iron-regulated ABC transporter ATPase subunit SufC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-23   81.5   0.0    1.1e-22   81.0   0.0    1.2  1  ABC_tran        ABC transporter
    1.8e-08   34.6   0.5    0.00027   20.9   0.1    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    1.1e-05   24.9   0.3     0.0028   17.1   0.1    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
    0.00034   21.2   1.4     0.0011   19.5   1.5    1.9  1  AAA_23          AAA domain
    0.00048   19.8   0.0    0.00088   19.0   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
     0.0023   17.8   0.1     0.0034   17.3   0.1    1.2  1  RsgA_GTPase     RsgA GTPase
     0.0091   16.1   0.1      0.016   15.3   0.1    1.7  1  MMR_HSR1        50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.012   15.4   0.3      0.031   14.0   0.1    1.7  2  AAA_15          AAA ATPase domain
      0.024   14.7   0.2      0.053   13.6   0.2    1.5  1  Dynamin_N       Dynamin family
      0.067   12.9   0.0       0.12   12.1   0.0    1.3  1  IstB_IS21       IstB-like ATP binding protein
      0.089   12.4   0.0       0.17   11.4   0.0    1.4  1  AAA_25          AAA domain
       0.87    9.3   2.6         22    4.7   0.2    2.7  3  Cytidylate_kin  Cytidylate kinase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   7.7e-26   1.1e-22       1     136 [.      24     168 ..      24     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 7.7e-26
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTS..S--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagl..lkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       l+nv+l ++ege+ a++G+nG+GKS+Ll+++ g+  +k t+G+i ++g+d+++ +  e+++  +g+ +q+p   +++
  gi|488600933|ref|YP_007907404.1|  24 LQNVNLYIQEGETFALFGPNGSGKSSLLSAIVGNpvYKITSGRIIFKGQDITSmTADERVKLGMGIAFQTPPKVSGV 100
                                       79*******************************833566*************9889999999********8888888 PP

                                       BHHHH.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++ +           s+e+i+++++ l+++e+ ++ +    + +SgG+ +r +l +++l ++++l+lDEp 
  gi|488600933|ref|YP_007907404.1| 101 KLIDVlrhcariggRSEEDIYRYAEMLKMDEFLERSI---NYGFSGGEVKRSELLQLILMNRDFLMLDEPD 168
                                       76666788*****************************...789**************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.8e-07   0.00027       3      51 ..      38      78 ..      37      99 .. 0.72
   2 !   12.2   0.0   7.8e-05      0.12     238     283 ..     142     192 ..     113     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldl 51
                                      +l GpNgsGKS+LL a+         +++   + sg+  +++++  + +
  gi|488600933|ref|YP_007907404.1| 38 ALFGPNGSGKSSLLSAIV--------GNPVYKITSGRIIFKGQDITSMT 78
                                      799**************4........35555555555555555555555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.8e-05
                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell........k 283
                                       S G  +   ll ++l  +   ++l +DEp++g + + +  + + +        k
  gi|488600933|ref|YP_007907404.1| 142 SGGEVKRSELLQLILMNR---DFLMLDEPDSGVDLENIDLIGKTIrellerdkK 192
                                       666666668888899888...9*************9997777666322244332 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.9e-06    0.0028      26      44 ..      36      54 ..      19      80 .. 0.85
   2 !    6.2   0.0    0.0041       6.1     159     187 ..     159     187 ..     113     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.9e-06
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                        a+ GpNGSGKs+ll Ai
  gi|488600933|ref|YP_007907404.1| 36 TFALFGPNGSGKSSLLSAI 54
                                      44799*************9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0041
                                       -SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkeks 187
                                       + + +lDe d+  D +n+  + + ++e  
  gi|488600933|ref|YP_007907404.1| 159 RDFLMLDEPDSGVDLENIDLIGKTIRELL 187
                                       4599*******************999753 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.5   7.3e-07    0.0011      18      39 ..      33      54 ..      21     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.3e-07
                            AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                      +   ++++GpNG+GK+++l Ai
  gi|488600933|ref|YP_007907404.1| 33 EGETFALFGPNGSGKSSLLSAI 54
                                      456899***************9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.9e-07   0.00088      17      42 ..      29      54 ..      21      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.9e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAi 42
                                      + i++ +++ l Gp+GsGKS+ll Ai
  gi|488600933|ref|YP_007907404.1| 29 LYIQEGETFALFGPNGSGKSSLLSAI 54
                                      556655599**************997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.3e-06    0.0034      82     127 ..      16      62 ..       2      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                                       --TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  82 vsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       +++++k+ l++++ ++++ +t +l G+ G GKS+L+ a++++   k+
  gi|488600933|ref|YP_007907404.1|  16 LKVDSKTVLQNVNLYIQEgETFALFGPNGSGKSSLLSAIVGNPVYKI 62 
                                       5667778899999999998********************99865554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.1e-05     0.016       2      42 ..      37      80 ..      36     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                      EEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvk 42
                                      +a++G   +GKS+L++a++g+   k   +++ ++ +di+  + +
  gi|488600933|ref|YP_007907404.1| 37 FALFGPNGSGKSSLLSAIVGNpvyKITSGRIIFKGQDITSMTAD 80
                                      689*****************975444557777777777776655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     2e-05     0.031      14      43 ..      24      54 ..      23      84 .. 0.89
   2 ?   -1.1   0.0      0.78   1.2e+03     214     233 ..     175     194 ..     118     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileal 43
                                      l++v + ++e  +  l G+N+sGKSs+l a+
  gi|488600933|ref|YP_007907404.1| 24 LQNVNLYIQEGeTFALFGPNGSGKSSLLSAI 54
                                      5778888888856699**************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.78
                            AAA_15 214 kssllgklkekileealqek 233
                                       + +l+gk+++++le  ++e 
  gi|488600933|ref|YP_007907404.1| 175 NIDLIGKTIRELLERDKKED 194
                                       34555666666666544433 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.5e-05     0.053       2      25 ..      38      61 ..      37      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                                      EEEEBTTTTHHHHHHHHHTS--S- CS
                         Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilp 25
                                      a++G   sGKSS+l a++g ++  
  gi|488600933|ref|YP_007907404.1| 38 ALFGPNGSGKSSLLSAIVGNPVYK 61
                                      689****************99865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.9e-05      0.12      43      68 ..      30      55 ..      17      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                         IstB_IS21 43 fiekkenivllGpsGvGKshlaialg 68
                                      +i++ e ++l+Gp G GKs l  a+ 
  gi|488600933|ref|YP_007907404.1| 30 YIQEGETFALFGPNGSGKSSLLSAIV 55
                                      89*****************9998875 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   0.00012      0.17      25      53 ..      26      54 ..       7      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                            AAA_25 25 lvkgllpagelallaGapgtGKttlaldl 53
                                       v  ++ +ge+ +l+G+ g+GK+ l++ +
  gi|488600933|ref|YP_007907404.1| 26 NVNLYIQEGETFALFGPNGSGKSSLLSAI 54
                                      6677899******************9865 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.014        22       2      18 ..      38      54 ..      37      71 .. 0.81
   2 ?   -0.5   0.0      0.56   8.4e+02     111     126 ..      63      78 ..      53      85 .. 0.79
   3 ?    3.3   0.1     0.038        57     163     190 ..     182     209 ..     168     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                                      EEE-STTSSHHHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaral 18
                                      a+ GP gsGKss+  a+
  gi|488600933|ref|YP_007907404.1| 38 ALFGPNGSGKSSLLSAI 54
                                      677*********97665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.56
                                       BSSBEEEEESSIIIII CS
                    Cytidylate_kin 111 kkarvvveGRDigtvv 126
                                       +++r+++ G Di+++ 
  gi|488600933|ref|YP_007907404.1|  63 TSGRIIFKGQDITSMT 78 
                                       57899*******9864 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHCTSSS-S---TT-EE CS
                    Cytidylate_kin 163 llaeikeRDklDkerevgpLklaedali 190
                                        ++e+ eRDk+  er+ ++L +++   i
  gi|488600933|ref|YP_007907404.1| 182 TIRELLERDKKEDERKKSGLLITHTGKI 209
                                       578999************9988766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1757.42
//
Query:       gi|488600934|ref|YP_007907405.1|  [L=373]
Description: ABC-type transport system involved in Fe-S cluster assembly, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-52  178.4   0.1    1.9e-52  178.1   0.1    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
       0.14   12.0   0.1        1.5    8.7   0.0    2.5  3  DUF4774   Domain of unknown function (DUF4774)


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 !  178.1   0.1   2.1e-56   1.9e-52       2     218 .]     123     345 ..     122     345 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 2.1e-56
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       q ++++i++eeg+e++ii   +gc            g++e+fv++nAkl+++++++w++d+ + ++++a ++++  +
  gi|488600934|ref|YP_007907405.1| 123 QKVHNIIIAEEGSELNII---SGCtshpgvtsgmhiGISEFFVKKNAKLTFTMIHSWESDIEVRPRSAALVEENGVF 196
                                       789***************...888888888888899*********************************9999999* PP

                           UPF0051  67 elttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkik 143
                                        +++v ++    ++ + + +  ++++a ++++++a +++ +d++++++++++++s++i+s++++k ++ ++ rg+i 
  gi|488600934|ref|YP_007907405.1| 197 ISNYVLMNPVKLVQMYPTAYVKKNGTAIFSSIIVALENSVVDSGSRAILEEEGASAEIVSRTISK-GGDIIARGHI- 271
                                       *******9986655555555569******************************************.599*******. PP

                           UPF0051 144 vrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       v   a   ++h e+r L+l++k+ +++iPele++  +v +sH+A++Gki+ee++fYL+sRGl+++eA++ i+rgf
  gi|488600934|ref|YP_007907405.1| 272 V-GSAPDVRGHLECRGLMLDEKGMIHAIPELEARYPNVDLSHEAAIGKIAEEEIFYLQSRGLTRDEATAAIIRGF 345
                                       5.55**********************************************************************9 PP

>> DUF4774  Domain of unknown function (DUF4774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00016       1.5       2      22 ..     179     199 ..     178     201 .. 0.91
   2 ?   -2.6   0.0      0.58   5.2e+03      27      38 ..     215     224 ..     213     227 .. 0.46
   3 ?   -0.7   0.1      0.14   1.2e+03       8      32 ..     240     263 ..     236     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00016
                           DUF4774   2 slevkpvGkAvaGkgGvAisa 22 
                                       ++ev+p ++A ++++Gv is+
  gi|488600934|ref|YP_007907405.1| 179 DIEVRPRSAALVEENGVFISN 199
                                       69***************8886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.58
                           DUF4774  27 aivkkGkkglal 38 
                                       a+v   k+g+a+
  gi|488600934|ref|YP_007907405.1| 215 AYV--KKNGTAI 224
                                       344..3344433 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.14
                           DUF4774   8 vGkAvaGkgGvAisaPvgtaivkkG 32 
                                       ++ A+ +++G A++  v++ i+k+G
  gi|488600934|ref|YP_007907405.1| 240 GSRAILEEEG-ASAEIVSRTISKGG 263
                                       5678888888.89999999999544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2176.41
//
Query:       gi|488600935|ref|YP_007907406.1|  [L=277]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-66  222.8  25.7    8.2e-66  222.3  25.7    1.2  1  SPP             Signal-peptide peptidase, presenilin aspartyl
    4.4e-10   39.6  16.6    7.6e-10   38.8  16.6    1.4  1  Peptidase_A22B  Signal peptide peptidase


Domain annotation for each model (and alignments):
>> SPP  Signal-peptide peptidase, presenilin aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.3  25.7   9.2e-70   8.2e-66       3     281 ..      10     272 ..       8     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 222.3 bits;  conditional E-value: 9.2e-70
                               SPP   3 lfvvvqvlalllavplesaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivvavifyvflv 79 
                                       ++v++ +la+ll+   e a+++a+e+P++v+ns++y  ++l+ft+f+l+v+k+ k li   ++y  +   ifyv+  
  gi|488600935|ref|YP_007907406.1|  10 IYVLSAILAILLTPNYEDAGMKAFENPEDVMNSIYYFGMILLFTAFILLVVKYRKDLIQ-FLLYGLMLISIFYVMYP 85 
                                       79***************************************************999865.56677777777887665 PP

                               SPP  80 llsivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvyk 156
                                        l ++          s++++++l+ +l+++p W vidl  ++l+vGv+++fGisl+  pa+vll++lavyd isvyk
  gi|488600935|ref|YP_007907406.1|  86 FLGVL----------SIIPSMVLLAVLIKKPSWIVIDLTALLLSVGVTTIFGISLSPQPALVLLTVLAVYDFISVYK 152
                                       55554..........899*********************************************************** PP

                               SPP 157 tkhmialaegvvdlklPillvvPetlaysfveeafeeaeeaearnvlfiGlGdavlPsilvvsaavfleshilagle 233
                                       t hm++la+   d+klP+l+v+P + +y +  e +e++++     + f+G+Gd+v+P ilvvs +vf +++ l  ++
  gi|488600935|ref|YP_007907406.1| 153 TGHMVSLADSLTDMKLPMLFVIPFSRSYRL--ENLENSKN----RAVFMGVGDVVIPNILVVSLQVFDNAPQLFFIK 223
                                       ***********************9999877..45667666....3479***************************** PP

                               SPP 234 lavllalaGtlvGllvlsi.lvlrgrpaaGlPllnsGaiaGfligvlaa 281
                                       l +l +l+G++ Gl++l++ l  ++ +++GlP+ln GaiaG+li vl++
  gi|488600935|ref|YP_007907406.1| 224 LSALFSLIGGVFGLVLLIYvLEKKEGAHPGLPFLNFGAIAGYLIYVLMS 272
                                       **************9886615567789*****************99976 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8  16.6   8.5e-14   7.6e-10      81     255 ..      79     256 ..       3     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 8.5e-14
                                       XXXXXXXXXXXXXXXX------S--XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Peptidase_A22B  81 flaielkaaeivalllsiviavlwllkrhwilndilglalailviellrlp.slkvgalLLvglflYDifwVFgtdv 156
                                       ++++ +    +++++ s+v++ + + k+ wi+ d+ +l l++ v  +  +  s + + +LL++l +YD   V+ t  
  gi|488600935|ref|YP_007907406.1|  79 IFYVMYPFLGVLSIIPSMVLLAVLIKKPSWIVIDLTALLLSVGVTTIFGISlSPQPALVLLTVLAVYDFISVYKTGH 155
                                       22256677788899999999999999999********9999988888777635677889999*************** PP

                                       XXXXXX...XXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXX CS
                    Peptidase_A22B 157 mvevAk...eldiPillklPq.....lsneieeaskfsiLGlGDivlPGllialllrfdiskkkttaeskeaqgkYf 225
                                       mv++A    ++++P+l+++P      l+n  + +++   +G+GD+v+P +l+  l  fd+  +    +         
  gi|488600935|ref|YP_007907406.1| 156 MVSLADsltDMKLPMLFVIPFsrsyrLENLENSKNRAVFMGVGDVVIPNILVVSLQVFDNAPQLFFIK------LSA 226
                                       *****877799*********98776334444445556679*******************987766543......445 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Peptidase_A22B 226 vvtlvaYvlgLlitivalalfkaaQPALLY 255
                                       + +l++ v+gL++ i +l+  + a P L +
  gi|488600935|ref|YP_007907406.1| 227 LFSLIGGVFGLVLLIYVLEKKEGAHPGLPF 256
                                       667888888888888888888888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1711.89
//
Query:       gi|488600936|ref|YP_007907407.1|  [L=30]
Description: hypothetical protein Asulf_01427 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       153  (0.00853366); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); 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: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 205.26
//
Query:       gi|488600937|ref|YP_007907408.1|  [L=383]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   90.4   0.3    1.1e-25   89.3   0.3    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.3e-10   40.7   1.2    4.7e-10   39.7   0.0    2.0  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.013   15.5   3.7      0.046   13.7   3.7    2.0  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.018   14.9   0.3      0.055   13.4   0.3    1.9  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.054   13.7   0.4       0.16   12.1   0.1    2.0  2  DUF2387         Probable metal-binding protein (DUF2387)
      0.078   13.1   1.4       0.16   12.1   1.4    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.081   12.2   0.1       0.14   11.4   0.1    1.3  1  AurF            P-aminobenzoate N-oxygenase AurF
        1.7    8.1   4.8        1.1    8.8   0.3    2.6  3  zf-ribbon_3     zinc-ribbon domain
        3.1    7.6   6.2        4.8    7.0   1.2    2.6  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 !   89.3   0.3   5.7e-29   1.1e-25       1      67 [.     280     347 ..     280     349 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 5.7e-29
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       fr+l+e++eyk+ e+G++v++v+p y+S++C++Cg ++k+ ++s+ +f+C +Cgf++++D++A++N+ 
  gi|488600937|ref|YP_007907408.1| 280 FRRLQEMIEYKCLERGVPVVYVEPKYSSQRCPRCGTIDKRnRKSQALFQCVSCGFQHNADYVASLNLS 347
                                       89****************************************************************95 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       1.9   3.7e+03      62      80 ..      75      93 ..      54     106 .. 0.58
   2 !   39.7   0.0   2.4e-13   4.7e-10       6     106 ..     159     250 ..     154     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.9
                        OrfB_IS605 62 sklkksknykkasrklarl 80
                                      + +k  kn +k + k + l
  gi|488600937|ref|YP_007907408.1| 75 RVAKSYKNNRKKRHKFTAL 93
                                      3333333334555555444 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 2.4e-13
                        OrfB_IS605   6 vevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhr 82 
                                       v ve p+p g++ +g+D+G+nnL++ +++       +g+++ s+ + ++k +  lq+k   s     a+rkl+ l+ 
  gi|488600937|ref|YP_007907408.1| 159 VLVEAPEPSGSNPVGVDIGVNNLVAASNGF----KVNGKPVESRRRHFRKLRSSLQKKGTSS-----AKRKLKQLSG 226
                                       44558999******************9997....789********************95555.....8********* PP

                        OrfB_IS605  83 krsrrrkhllhklathliktlkev 106
                                       + +r ++  lh+++++ ++tl e 
  gi|488600937|ref|YP_007907408.1| 227 RERRWVNTILHQISRAFVDTLSEG 250
                                       ********************9874 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.7   2.3e-05     0.046      19      46 .]     308     335 ..     303     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrkq 46 
                                       ++CP+Cg   k  r ++  lfqC +C+ q
  gi|488600937|ref|YP_007907408.1| 308 QRCPRCGTIdKRNRKSQ-ALFQCVSCGFQ 335
                                       68*****9976666666.9*******987 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 ?   13.4   0.3   2.7e-05     0.055       2      18 ..     308     324 ..     307     326 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                                       SB-TTT--BBEEEECTT CS
                      zf-FPG_IleRS   2 epCpRCwryiervgqag 18 
                                       ++CpRC+++++r ++++
  gi|488600937|ref|YP_007907408.1| 308 QRCPRCGTIDKRNRKSQ 324
                                       89*********998866 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.6   1.3e+04      51      64 ..      70      83 ..      57      90 .. 0.61
   2 ?   12.1   0.1   8.1e-05      0.16      11      42 ..     310     338 ..     307     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.6
                           DUF2387 51 kelktrvnkdeeke 64
                                      +  ++rv+k+ +++
  gi|488600937|ref|YP_007907408.1| 70 VRARDRVAKSYKNN 83
                                      45566777665433 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.1e-05
                           DUF2387  11 CPrCsemDkirmweedeveyrECvsCgftdel 42 
                                       CPrC + Dk    +   +    CvsCgf  + 
  gi|488600937|ref|YP_007907408.1| 310 CPRCGTIDKR---NRKSQALFQCVSCGFQHNA 338
                                       ********95...56778999*******8765 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 ?   12.1   1.4   8.2e-05      0.16      16      40 .]     308     333 ..     306     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                     Auto_anti-p27  16 etCpvCgvPLmrdr.kggkvyCvaCd 40 
                                       + Cp+Cg++  r+r  +    Cv+C+
  gi|488600937|ref|YP_007907408.1| 308 QRCPRCGTIDKRNRkSQALFQCVSCG 333
                                       78************7578888****6 PP

>> AurF  P-aminobenzoate N-oxygenase AurF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   6.9e-05      0.14     207     278 ..     217     286 ..     214     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHS-HHHHHHHHHHHHHHHHHHHS--HHHHHHHHHT-TTHHHHHHHHHHHHTT--S----.HHHHHH CS
                              AurF 207 lrrrvprlsraerallrlllalalrafasslvnppvyalagldpaeavraelianphsretlrdaaaklrkl 278
                                       ++r++++ls +er+++  +l +++raf+++l + ++ +l++l++ +++   +  ++ ++   ++a+++l+++
  gi|488600937|ref|YP_007907408.1| 217 AKRKLKQLSGRERRWVNTILHQISRAFVDTLSEGDYVVLEKLNGIRDRCNVR--KEYRATFHNWAFRRLQEM 286
                                       68999***********************************777666555544..444445555556666555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00055       1.1       3      16 ..     308     320 ..     306     322 .. 0.82
   2 ?    0.1   0.1      0.29   5.8e+02       4       9 ..     328     333 ..     326     335 .. 0.81
   3 ?   -2.3   0.0       1.6   3.3e+03      11      19 ..     361     369 ..     358     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00055
                       zf-ribbon_3   3 vrCPnCGaplssdd 16 
                                       +rCP+CG++ +++ 
  gi|488600937|ref|YP_007907408.1| 308 QRCPRCGTI-DKRN 320
                                       69*****99.8765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
                       zf-ribbon_3   4 rCPnCG 9  
                                       +C +CG
  gi|488600937|ref|YP_007907408.1| 328 QCVSCG 333
                                       688998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.6
                       zf-ribbon_3  11 plssddnvC 19 
                                       ++ +dd+ C
  gi|488600937|ref|YP_007907408.1| 361 NVGADDRLC 369
                                       5889****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.056   1.1e+02      16      22 ..     309     315 ..     309     317 .. 0.86
   2 ?    7.0   1.2    0.0024       4.8       1      11 [.     327     337 ..     327     340 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.056
                      Rubredoxin_2  16 rCpsCgs 22 
                                       rCp Cg+
  gi|488600937|ref|YP_007907408.1| 309 RCPRCGT 315
                                       8****85 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0024
                      Rubredoxin_2   1 YvCsqCGfesa 11 
                                       ++C +CGf+++
  gi|488600937|ref|YP_007907408.1| 327 FQCVSCGFQHN 337
                                       89*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); 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: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2161.99
//
Query:       gi|488600938|ref|YP_007907409.1|  [L=339]
Description: glycerol 3-phosphate dehydrogenase (NAD(P)+) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  117.2   0.1    1.2e-33  116.3   0.1    1.4  1  NAD_Gly3P_dh_C   NAD-dependent glycerol-3-phosphate dehydroge
    1.9e-22   79.9   1.0      3e-22   79.3   0.1    1.8  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    2.1e-06   28.2   0.3    1.3e-05   25.7   0.1    2.5  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.9e-05   24.3   0.0    3.8e-05   23.4   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.001   19.3   0.0     0.0028   17.8   0.0    1.8  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0018   17.3   0.2     0.0037   16.3   0.0    1.5  2  PDH              Prephenate dehydrogenase
     0.0088   15.9   0.5      0.057   13.3   0.1    2.5  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.012   15.1   0.1       0.11   12.0   0.1    2.3  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.051   13.1   0.0       0.17   11.4   0.0    1.9  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.085   13.0   0.3        4.3    7.7   0.0    3.3  3  Antimicrobial_8  Uperin family


Domain annotation for each model (and alignments):
>> NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.1   6.9e-37   1.2e-33       1     140 [.     179     332 ..     179     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 6.9e-37
                                       -HHHHHHHHHHHHHHHHHHHHHHHTT.H....-HHHHHHHHHHHHHHHHHHHHHHTSSGGGGGSTTTHHHHHHHHHS CS
                    NAD_Gly3P_dh_C   1 DviGvelagalKNviAiaaGivdglg.l....gdntkaalitrglaEmarlakalgakpetflglaglgDlivtcts 72 
                                       D+ G+e+ +alKNv++ia+ +v g + l     +n+k+++ tr+++E+a+l++  g++++t++gl+g+gDli+t+ +
  gi|488600938|ref|YP_007907409.1| 179 DIWGTEITSALKNVYSIAIAWVRGHEkLygveMSNAKGVITTRAINEIAKLLELTGGNRDTVFGLSGFGDLIATFRG 255
                                       999**********************643566688******************************************* PP

                                       CT.HHHHHHHHHHCT--HHHHHHHHC.C...--HHHHHHHHHHHHHHH...TT.....G.HHHHHHHHHHHS---HH CS
                    NAD_Gly3P_dh_C  73 gksRNrrfGeelgkgesleeiekeln.q...vleGvetakevyellkk...kgv....emplleavykilyegkspe 138
                                       g  RN ++Ge+lg+g +++e+ +el+ +   v+eG++ta+++y+l+k+   kg     e+pll+++y++ly++k++ 
  gi|488600938|ref|YP_007907409.1| 256 G--RNGMLGEMLGRGLNVREAFDELQrRgvgVVEGYQTAEKAYRLMKDlekKGKtdieEFPLLKSIYDVLYRDKKVA 330
                                       *..***********9999998886663355699************8873322214569*****************99 PP

                                       HH CS
                    NAD_Gly3P_dh_C 139 el 140
                                       e+
  gi|488600938|ref|YP_007907409.1| 331 EV 332
                                       87 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 !   79.3   0.1   1.7e-25     3e-22       1     151 [.       2     155 ..       2     161 .. 0.88
   2 ?   -1.9   0.1       1.6   2.8e+03      10      34 ..     181     205 ..     180     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.7e-25
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H..HHHHHHHHHSSBTTTBTT----.TTEEEES-HHHHHTT--EEE CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree..elieeineehenvkyLpgiklp.enlvattdlaealkgadiiv 74 
                                       ++++lGaG+ G+al   l++ g++vrlw+ e   e ++++++ +++ +   +++l+  ++   +d+++a+++adii+
  gi|488600938|ref|YP_007907409.1|   2 NVTILGAGAMGSALTVPLTDSGNNVRLWGTEYdvEILKKVERGEKHPR--IDVRLEgVKIFYPEDIEKAVRDADIIL 76 
                                       59**************************99885567777777766666..34555525799999************* PP

                                       E---HHHHHHHHHHHCCC--TT-EEEE---SE..ET.TTEEHHHHHHHHH-S--.EEEEESS--HHHHHTT--EEEE CS
                    NAD_Gly3P_dh_N  75 lvvPsqalrevlkklkgllkkkailvsliKGi..eegtlkllsevieeelkeek.vavlsGpslAeEvakgkptavv 148
                                       l+v++  +  +++k+++++ ++ ilv ++KG+   +g+  ++ e+i ++ ++++  + ++Gps+A+Evak++pt+vv
  gi|488600938|ref|YP_007907409.1|  77 LAVSTDGVLPIFRKIADHI-ENEILVTIAKGLieIDGKILTVPEAIWTVKDIKNrTVAITGPSIAREVAKRMPTKVV 152
                                       *******************.7899********866688899999999999988889********************9 PP

                                       EEE CS
                    NAD_Gly3P_dh_N 149 ias 151
                                        +s
  gi|488600938|ref|YP_007907409.1| 153 FSS 155
                                       987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHTTT--EEEE-S-HHH CS
                    NAD_Gly3P_dh_N  10 wGtalAkvlaenghevrlwvreeel 34 
                                       wGt +  +l++  +    wvr +e 
  gi|488600938|ref|YP_007907409.1| 181 WGTEITSALKNVYSIAIAWVRGHEK 205
                                       9999999999888888888887654 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   7.4e-09   1.3e-05       2      96 ..       3     105 ..       2     106 .. 0.80
   2 ?   -2.1   0.0       3.4     6e+03      38      60 ..     139     161 ..     129     174 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7.4e-09
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEE.EEESSCCCHHHHHHHHC............-EEECECHHHHHHH-SEE CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivv.ansrnpekaeelaeelg............vkvtavdneeaaeeadvv 65 
                                       + i+GaG mg+al+  l+ +g   +++++ +++ + e +++ + + +                + d e+a+++ad++
  gi|488600938|ref|YP_007907409.1|   3 VTILGAGAMGSALTVPLTDSG---NNVRLwGTEYDVEILKKVE-RGEkhpridvrlegvKIFYPEDIEKAVRDADII 75 
                                       78*******************...8877614444444444444.33368999999999544456799********** PP

                                       EE-S-HHHHHHHHHHCGHHHHTTSEEEEESS CS
                     F420_oxidored  66 vlavkpedveevlselakdalkgklvisvla 96 
                                       +lav +  v  + +++ +d  +++++++++ 
  gi|488600938|ref|YP_007907409.1|  76 LLAVSTDGVLPIFRKI-ADHIENEILVTIAK 105
                                       ****************.88899999999985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                                       CHHHHHHHHC-EEECECHHHHHH CS
                     F420_oxidored  38 kaeelaeelgvkvtavdneeaae 60 
                                        a+e a+++  kv  ++  +aae
  gi|488600938|ref|YP_007907409.1| 139 IAREVAKRMPTKVVFSSVGDAAE 161
                                       34444444444444444444444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.1e-08   3.8e-05       1     104 [.       3     106 ..       3     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.1e-08
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT......CEEEEEECEEECCHSCCCCS-ESE CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseg......geeilrppealsaeekselepidl 71 
                                       ++ilGaGa+Gs l + L+  g++v l++ +  +e lkk     + ++      g +i++p+           +++d+
  gi|488600938|ref|YP_007907409.1|   3 VTILGAGAMGSALTVPLTDSGNNVRLWGTEYDVEILKKVERGEKHPRidvrleGVKIFYPEDIEK-----AVRDADI 74 
                                       68**************************9988886666554444444323444444444444444.....4599*** PP

                                       EEE-SSGGGHHHHHHHHGGGECTCEEEEEESSS CS
                              ApbA  72 vivtvKayqteealeeikplldpntvvlllqNG 104
                                       ++++v +  +    ++i+++++++ + +++  G
  gi|488600938|ref|YP_007907409.1|  75 ILLAVSTDGVLPIFRKIADHIENE-ILVTIAKG 106
                                       *********************998.66666655 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.6e-06    0.0028       2     112 ..       3     135 ..       2     171 .. 0.71
   2 ?   -2.7   0.0       3.3     6e+03      31     102 ..     291     300 ..     271     336 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSH.HHHHHHHHTT..............EEE-SSHHHHHHHCSEEEE-S CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtk.ekveelvaeg..............akaaesieelvasldvvitmv 63 
                                       + ++G G MGs +   l+++g +v ++  +   ++ + v++g              +   e+ie++v+++d++++ v
  gi|488600938|ref|YP_007907409.1|   3 VTILGAGAMGSALTVPLTDSGNNVRLWGTEYdVEILKKVERGekhpridvrlegvkIFYPEDIEKAVRDADIILLAV 79 
                                       7899***********************9775223344444447889********8888889**************** PP

                                       SSHHHHHHHHHS........HCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEE CS
                     NAD_binding_2  64 kagkavdevieg........llealkkgdilidgstsspedtrelakelkekglkfl 112
                                       + +  v  + ++        +l +++kg i idg    + +++   k++k++ + + 
  gi|488600938|ref|YP_007907409.1|  80 STD-GVLPIFRKiadhieneILVTIAKGLIEIDGKILTVPEAIWTVKDIKNRTVAIT 135
                                       875.33333333111233356666688888888888888888777777777776665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.3
                                       SHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHH CS
                     NAD_binding_2  31 tkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdilidgstsspedtrelak 102
                                       t+ek+                                                               +l k
  gi|488600938|ref|YP_007907409.1| 291 TAEKAY--------------------------------------------------------------RLMK 300
                                       222222..............................................................2222 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.1e-06    0.0037      38      76 ..      63     102 ..      42     107 .. 0.86
   2 ?   -3.2   0.0       1.9   3.4e+03       6      45 ..     128     165 ..     125     166 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                                       S-.GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEE CS
                               PDH  38 dd.ieavkeadivvlavPvevilevlkelaphlkedalit 76 
                                       +d  +av++adi++lav  + +l++ +++a h++++ l+t
  gi|488600938|ref|YP_007907409.1|  63 EDiEKAVRDADIILLAVSTDGVLPIFRKIADHIENEILVT 102
                                       4423689*****************************9987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.9
                                       HHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-.GGGGCC CS
                               PDH   6 rrkgfkvtvigydideekaeaalelglvdeatdd.ieavke 45 
                                       +++   v ++g +i  e a++     +v+    d  e+vk+
  gi|488600938|ref|YP_007907409.1| 128 KNRT--VAITGPSIAREVAKRM-PTKVVFSSVGDaAEKVKD 165
                                       5555..8888888888888877.777777777766777776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   3.2e-05     0.057       1      33 [.       2      34 ..       2     104 .. 0.72
   2 ?   -1.5   0.0       1.1     2e+03     147     169 ..     283     305 ..     282     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdisee 33
                                      +v+++GaG mG+ ++  +  +g +V+l  ++ +
  gi|488600938|ref|YP_007907409.1|  2 NVTILGAGAMGSALTVPLTDSGNNVRLWGTEYD 34
                                      69************************9877443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                       EEEEE-TT--HHHHHHHHHHHHH CS
                           3HCDH_N 147 vEvvrgekTseetvatvvelakk 169
                                       v vv+g +T+e++   +++l kk
  gi|488600938|ref|YP_007907409.1| 283 VGVVEGYQTAEKAYRLMKDLEKK 305
                                       56899999999988877776544 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.4e-05      0.11       6     104 ..       2     115 ..       1     127 [. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                                       -EEEES-SHHHHHHHHHHHHTT--EEE.EE-TT-...HHHHHHHH........TT...-EEEEHHHHHHT-SEEEE- CS
                              IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvv.glregs...ksvkkAke........eg...fevltvaeavkkadvvmil 67 
                                       +++++G G+ G a +  l dsg +v + g + +    k+v++ ++        eg   f   ++++av++ad++++ 
  gi|488600938|ref|YP_007907409.1|   2 NVTILGAGAMGSALTVPLTDSGNNVRLwGTEYDVeilKKVERGEKhpridvrlEGvkiFYPEDIEKAVRDADIILLA 78 
                                       699**********************8734444444442333333311222222451114456788999999999999 PP

                                       S-HHHHHHHHHHHTGGG--TT-EEEESSSH.HHHTTSS CS
                              IlvN  68 iPDelqkevyeeeiepnlkegkalafahGf.nihfgli 104
                                       +       ++ ++i+++++++  ++ a+G+ +i  + +
  gi|488600938|ref|YP_007907409.1|  79 VSTDGVLPIF-RKIADHIENEILVTIAKGLiEIDGKIL 115
                                       9988889999.789999999999999999634555555 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 ?   11.4   0.0   9.5e-05      0.17       1      86 [.       1      81 [.       1      86 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.5e-05
                                      SEEEEE--STTHHHHHHHHHHCTSEE..EEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighev..igvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77
                                      m+++++G+G +G    + l   g++v   g   d e  +k+++g+    +p ++  ++ +    +++   d+ekav++a
  gi|488600938|ref|YP_007907409.1|  1 MNVTILGAGAMGSALTVPLTDSGNNVrlWGTEYDVEILKKVERGE---KHPRIDVRLEGV----KIFYPEDIEKAVRDA 72
                                      899********************7772256677777777777766...456666555444....59999********** PP

                                      SEEEE---- CS
                    UDPG_MGDP_dh_N 78 dvifiaVgT 86
                                      d+i++aV T
  gi|488600938|ref|YP_007907409.1| 73 DIILLAVST 81
                                      *******99 PP

>> Antimicrobial_8  Uperin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0024       4.3       1      11 [.      83      93 ..      83      97 .. 0.84
   2 ?   -2.6   0.0       4.4   7.8e+03       2       9 ..     156     163 ..     156     163 .. 0.80
   3 ?    1.3   0.0      0.26   4.7e+02       9      16 ..     185     192 ..     185     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                   Antimicrobial_8  1 GVGDliRKiVs 11
                                      GV+ ++RKi+ 
  gi|488600938|ref|YP_007907409.1| 83 GVLPIFRKIAD 93
                                      9********95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.4
                   Antimicrobial_8   2 VGDliRKi 9  
                                       VGD+  K+
  gi|488600938|ref|YP_007907409.1| 156 VGDAAEKV 163
                                       9**97776 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.26
                   Antimicrobial_8   9 iVsaIKNV 16 
                                       i sa KNV
  gi|488600938|ref|YP_007907409.1| 185 ITSALKNV 192
                                       679****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.68u 0.38s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 1742.22
//
Query:       gi|488600939|ref|YP_007907410.1|  [L=387]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-50  170.4   0.1    4.9e-50  169.6   0.1    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.2e-31  109.7   0.2    2.5e-31  108.7   0.2    1.5  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    2.5e-25   89.3   0.0      5e-25   88.3   0.0    1.5  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    2.9e-23   81.9   0.2      5e-23   81.1   0.2    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
      0.049   13.3   0.0      0.099   12.3   0.0    1.4  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina
      0.066   13.5   0.3       0.22   11.8   0.0    1.9  2  PHP            PHP domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.6   0.1   1.6e-53   4.9e-50       1     150 []     233     383 ..     233     383 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.6 bits;  conditional E-value: 1.6e-53
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraae. 76 
                                       gkGf+++me ++ +R+ vaa+ +g+a+ al  a+ey+++rkafg p+ ++q++++klae+a+++eaar l+yraa+ 
  gi|488600939|ref|YP_007907410.1| 233 GKGFYYMMEFFDRSRVWVAAQGVGIAKGALKLAVEYVKQRKAFGVPISNFQFIQFKLAELATKIEAARTLTYRAAAv 309
                                       79************************************************************************998 PP

                                       --------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH. CS
                     Acyl-CoA_dh_1  77 aldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrll 150
                                       ++++gkpd++ +smaK++a e+a+e +d a+q +Gg+Gy +eyp+  +yrda++++i+eGt ei ++i+ar+ll
  gi|488600939|ref|YP_007907410.1| 310 MIEKGKPDPMLSSMAKWYAGEVAVETCDWALQFHGGYGYIDEYPINEFYRDAKITEIYEGTKEIEKLIVARNLL 383
                                       99*********************************************************************985 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.2   8.3e-35   2.5e-31       1     113 []       7     119 ..       7     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 8.3e-35
                                       THHHHHHHHHHHHHHHHHT.HHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-H CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeel.aphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelarada 76 
                                       teeqe++r+++refae+e   + a+e+d+e+++prel+kk+a+lG+ ++++peeygG g +++e++iv+ee+++++ 
  gi|488600939|ref|YP_007907410.1|   7 TEEQEDIRRAAREFAEKEFtIELAQECDREEKYPRELVKKCAKLGFHAVSLPEEYGGGGYGPIEQMIVMEEFSAVNP 83 
                                       89*****************889******************************************************* PP

                                       HHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  77 glalllgvhsslvapailrfGteeqkrryLpklasge 113
                                       glal+  +    +++++l +G+eeqk++++pkl+sg+
  gi|488600939|ref|YP_007907410.1|  84 GLALACLTP-IFGVEILLYHGSEEQKEEWIPKLCSGD 119
                                       *87755443.34559********************96 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       5.4   1.6e+04      53      64 ..      16      27 ..      12      49 .. 0.55
   2 !   88.3   0.0   1.7e-28     5e-25       2     133 ..     249     371 ..     248     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.4
                                      HHHHHHHHHHHH CS
                     Acyl-CoA_dh_2 53 AAralleraaar 64
                                      AAr++ e+ ++ 
  gi|488600939|ref|YP_007907410.1| 16 AAREFAEKEFTI 27
                                      666666665543 PP

  == domain 2  score: 88.3 bits;  conditional E-value: 1.7e-28
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       ++aa+ +G+A++al+ +ve++++r+   +g++++ ++ +q++lae+a++++AAr+l++raaa    ++++gk+    
  gi|488600939|ref|YP_007907410.1| 249 WVAAQGVGIAKGALKLAVEYVKQRKA--FGVPISNFQFIQFKLAELATKIEAARTLTYRAAAV---MIEKGKP---- 316
                                       79************************..***********************************...7899999.... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                       d   +++a+ +a e a++ +d++ + +Gg+++ +e+p+  ++RDa++++++++++
  gi|488600939|ref|YP_007907410.1| 317 DPMLSSMAKWYAGEVAVETCDWALQFHGGYGYIDEYPINEFYRDAKITEIYEGTK 371
                                       68899**********************************************9876 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.2   1.7e-26     5e-23       1      97 []     123     221 ..     123     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 1.7e-26
                                       EEE---SS-SS-GGG---EE.EEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---...----EEEEEEE..GGGE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvktta.aerdggeyvlnGeKiwitnaaiatlalvlartekpd...rarglslflvprdapgv 73 
                                       ++a TEp+ Gsd as+kt+a  ++d  e+v+nG+K++itn++ a+++lv a+t + d   r++ +s f+v+++++g 
  gi|488600939|ref|YP_007907410.1| 123 GMANTEPDCGSDSASIKTRAvLDGD--EWVINGTKQFITNGTVADFILVTAKTREVDwkeRHKAMSYFIVETNREGY 197
                                       5899**************6655555..5************************666667889**************** PP

                                       EE-----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  74 svrrieeklGlrglptgelvfedv 97 
                                       + ++i+ klG+r  +t+e+ +++v
  gi|488600939|ref|YP_007907410.1| 198 KATKIRGKLGIRASDTAEISLSNV 221
                                       ********************9987 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05     0.099     180     228 ..     150     199 ..     145     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                       EEEEEEEEEE-.--SSEEEE---.SS-..TTSGGG-EEEEEETT-TTEEE CS
                            HpaB_N 180 vVrGakvlaTgaaladeilvlpt.ramlkeedkdyavafavpvdapGlkl 228
                                       v++G+k ++T++ +ad ilv    r+   +e  +   +f+v+++ +G k 
  gi|488600939|ref|YP_007907410.1| 150 VINGTKQFITNGTVADFILVTAKtREVDWKERHKAMSYFIVETNREGYKA 199
                                       89******************987566655666777778********9875 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.75   2.2e+03     144     165 ..      10      30 ..       4      32 .. 0.81
   2 ?   11.8   0.0   7.5e-05      0.22      18     116 ..      41     228 ..      34     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.75
                                       HHHHHHHHHHHHHC.T-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                               PHP 144 eekaeealeelakifgdyiEin 165
                                       +e +++a++e+a++ ++ iE+ 
  gi|488600939|ref|YP_007907410.1|  10 QEDIRRAAREFAEK-EFTIELA 30 
                                       4559999******9.*****85 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHHHCT-SEEEEEEEEBTT........HHHHHHHHHHHHTT.TTSEEEEEEE.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx............ RF
                               PHP  18 eelvkkakelglkaiaiTDhgnlf........gyvefykaakkkyk.agikpiiGleayvaddse............ 73 
                                        elvkk+++lg++a+ + +  +           ++e+++a++   + a ++pi+G+e+ +  +se            
  gi|488600939|ref|YP_007907410.1|  41 RELVKKCAKLGFHAVSLPEEYGGGgygpieqmIVMEEFSAVNPGLAlACLTPIFGVEILLYHGSEeqkeewipklcs 117
                                       79******************99999999999988899999866333588********99999999999999999999 PP

                                       .........................................................................E... CS
                                       ...............................................................xxxxxxxxxxxxxx RF
                               PHP  74 ...............................................................kerpshltllaknq 87 
                                                                                                      + +     ++  n+
  gi|488600939|ref|YP_007907410.1| 118 gdaimgmantepdcgsdsasiktravldgdewvingtkqfitngtvadfilvtaktrevdwkeRHKAMSYFIVETNR 194
                                       99999999999999999999999999999999999999999999999999999999999998866666666777799 PP

                                       .EHHHH............HHHHHHHHH..........HHHH CS
                                       xxxxxx............xxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  88 eGyknl............lkllskaylegfyrkpridkell 116
                                       eGyk              + ++s + +       r++k+ l
  gi|488600939|ref|YP_007907410.1| 195 EGYKATkirgklgirasdTAEISLSNV-------RVPKSNL 228
                                       999988888888877777777777776.......5666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2169.04
//
Query:       gi|488600940|ref|YP_007907411.1|  [L=395]
Description: Acetyl-CoA acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-25   88.2   0.0    1.1e-21   77.4   0.0    2.3  2  Thiolase_N     Thiolase, N-terminal domain
    1.1e-07   31.7   0.4    2.5e-07   30.5   0.4    1.7  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
    2.1e-06   27.4   0.0    6.1e-05   22.7   0.0    2.5  2  Thiolase_C     Thiolase, C-terminal domain
     0.0015   18.4   0.0     0.0077   16.1   0.0    2.1  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
     0.0034   17.5   0.0        2.5    8.3   0.0    2.5  2  4PPT_N         4'-phosphopantetheinyl transferase N-terminal 


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 !   77.4   0.0   3.1e-25   1.1e-21       6     197 ..      10     188 ..       5     200 .. 0.87
   2 !    8.6   0.0   0.00029         1     243     260 .]     207     224 ..     205     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 3.1e-25
                                       EEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEE CS
                        Thiolase_N   6 aartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvn 82 
                                          +++    gs kd+++ eL+ e +k +l++a+++++++d  +vGn     ++++i   +a  a++  +  +++v+
  gi|488600940|ref|YP_007907411.1|  10 VGHSKF----GSRKDVNIPELAWESIKPALDSANIEQKDIDFFVVGNAGVWSSEAAIPALMAEYADL-APKGSMRVE 81 
                                       444555....55**************************************99999999999999999.88899**** PP

                                       HGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT..TGGSSSSEEEEEHHHHHHTEETTTTSEHHH CS
                        Thiolase_N  83 kvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr..sglklgdekakdllipdgladafneehmGl 157
                                        +c+ g++a+  + q+i++geadvv++ G E+m ++p  +  +++   g  + + +  +l+ p            +l
  gi|488600940|ref|YP_007907411.1|  82 AACATGNAAIRVGYQAIKSGEADVVLVLGIEKMQESPNPTVIELIgrFGSYFWEFENFGLTFPG---------YYAL 149
                                       *********************************9999888888872244445555555666666.........7899 PP

                                       HHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTB CS
                        Thiolase_N 158 taenlakkykisReeqdefAvkshqkaaaaqkagkFkdei 197
                                       ++  +  ky+++ e+ +++Avk+h  +a+++ a+ F++e+
  gi|488600940|ref|YP_007907411.1| 150 HGTAYMMKYGATEEDYARVAVKNHYYGAKNPYAQ-FQKEV 188
                                       **********************************.****9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00029
                                       SB--BEEEEEEEEEEEHH CS
                        Thiolase_N 243 nasqisDGaaavllmses 260
                                       ++s+i+DG+a+v+l+se+
  gi|488600940|ref|YP_007907411.1| 207 DCSPITDGSACVILASEE 224
                                       79*************986 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 !   30.5   0.4   7.1e-11   2.5e-07     168     206 ..      77     115 ..       7     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 7.1e-11
                                       EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                     ketoacyl-synt 168 svtvdtACsSslvavhaavqslrsgeadvalaGGvelll 206
                                       s+ v++AC+++++a+ + +q+++sgeadv+l+ G e + 
  gi|488600940|ref|YP_007907411.1|  77 SMRVEAACATGNAAIRVGYQAIKSGEADVVLVLGIEKMQ 115
                                       899*******************************99875 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.045   1.6e+02      27      50 ..      30      53 ..      19      90 .. 0.89
   2 !   22.7   0.0   1.7e-08   6.1e-05      25      99 ..     260     356 ..     250     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.045
                                      HHHHHHHHHT--GGGESEEEE--S CS
                        Thiolase_C 27 aikkvlkkagltvedidlfEinEA 50
                                       ik +l+ a ++ +did+f +  A
  gi|488600940|ref|YP_007907411.1| 30 SIKPALDSANIEQKDIDFFVVGNA 53
                                      57889*************987665 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.7e-08
                                       HHHHHHHHHHHT--GGG....ESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH- CS
                        Thiolase_C  25 ayaikkvlkkagltved....idlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialG 79 
                                        ya++ + k+ag++++     +d   +++ F+a  + + ++l +++                    vNv GG  a G
  gi|488600940|ref|YP_007907411.1| 260 RYAAELAYKRAGIDMDApykyLDGANVHDCFTAPEIIAYEDLRFAKrgegvqlirdeqtyiggrIPVNVDGGLKAKG 336
                                       578888889999987533333999999*****99999999999999999********999999888*********** PP

                                       B-TTTHHHHHHHHHHHHHHH CS
                        Thiolase_C  80 HPlGasGaRivvtllselkk 99 
                                       HP+Ga+G+ ++v + ++l  
  gi|488600940|ref|YP_007907411.1| 337 HPIGATGVSQAVEAYKQLLS 356
                                       **********9999888754 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 !   16.1   0.0   2.2e-06    0.0077       3      39 ..      80     116 ..      78     130 .. 0.89
   2 ?   -1.1   0.0      0.49   1.7e+03      53      64 ..     212     223 ..     208     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                       ++aaC++  +a+ v  ++i+sg+a  vLv g e++ +
  gi|488600940|ref|YP_007907411.1|  80 VEAACATGNAAIRVGYQAIKSGEADVVLVLGIEKMQE 116
                                       689*****************************99876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.49
                                       -EEEEEEEEEEE CS
                       ACP_syn_III  53 GDGAgAvvleas 64 
                                        DG ++v+l  +
  gi|488600940|ref|YP_007907411.1| 212 TDGSACVILASE 223
                                       699999999876 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 !    6.5   0.0    0.0026       9.2      11      37 ..     247     276 ..     242     286 .. 0.79
   2 !    8.3   0.0   0.00068       2.5       3      27 ..     352     376 ..     350     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0026
                            4PPT_N  11 akRkaeFl...aGRicAraalarlgleavp 37 
                                        +R+++F+   ++R++A  a++r g+++ +
  gi|488600940|ref|YP_007907411.1| 247 LSRRSDFTsleSARYAAELAYKRAGIDMDA 276
                                       5799999844459************99854 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00068
                            4PPT_N   3 eelirkavakRkaeFlaGRicAraa 27 
                                       ++l++ka + R+ae   GR++A++ 
  gi|488600940|ref|YP_007907411.1| 352 KQLLSKAEPGRQAEIKHGRWLAHNV 376
                                       6899******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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:                         5  (0.000278878); expected 0.2 (1e-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: 2881.23
//
Query:       gi|488600941|ref|YP_007907412.1|  [L=163]
Description: putative nucleic-acid-binding protein containing a Zn-ribbon [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-16   57.6   0.1    1.2e-15   57.2   0.1    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    2.6e-14   52.7   0.3    4.1e-14   52.1   0.3    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.058   13.4   0.0      0.079   13.0   0.0    1.4  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.11   12.5   0.8       0.27   11.3   0.1    1.8  2  CpXC           CpXC protein


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 !   57.2   0.1   2.8e-19   1.2e-15       1      63 [.      85     146 ..      85     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.8e-19
                                       EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE CS
                     OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVrav 63 
                                       wvels++G +++ tv   +pp+fa++ Py+v++ +Ld+g+ri+a+l g++    r Gm+Vr++
  gi|488600941|ref|YP_007907412.1|  85 WVELSKEGQLETLTVLFVRPPSFANYDPYTVAIAKLDDGPRITAWLKGDP-TKARPGMKVRVE 146
                                       ***********************************************976.5579******97 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.3   9.2e-18   4.1e-14       1      37 []      48      84 ..      48      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 9.2e-18
                           DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgsddle 37
                                      +++++eg+L++++C++CG+++fPP+  Cp C+ d+++
  gi|488600941|ref|YP_007907412.1| 48 FEGLKEGKLLATKCKKCGRLFFPPQKDCPSCRTDEMD 84
                                      69******************************99985 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   0.0   1.8e-05     0.079      69     101 ..      57      87 ..      21      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                                       -EEEETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsadveivs 101
                                       + ++C++Cg+ f   +k   Cp+C + +++ v+
  gi|488600941|ref|YP_007907412.1|  57 LATKCKKCGRLFFPPQK--DCPSCRTDEMDWVE 87 
                                       5689*****99997644..7******9998775 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   6.1e-05      0.27      13      47 ..      34      68 ..      29      75 .. 0.84
   2 ?   -1.1   0.2      0.41   1.8e+03       3       8 ..      75      80 ..      73      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.1e-05
                              CpXC 13 eiwtsidadedpelkeklldgslfeatCpkCgata 47
                                      ++  +i +++ + + e l +g+l+ ++C kCg+ +
  gi|488600941|ref|YP_007907412.1| 34 RVKFIISVEKIKPFFEGLKEGKLLATKCKKCGRLF 68
                                      56668888888999999***************986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.41
                              CpXC  3 CpaCgk 8 
                                      Cp+C++
  gi|488600941|ref|YP_007907412.1| 75 CPSCRT 80
                                      555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 923.24
//
Query:       gi|488600942|ref|YP_007907413.1|  [L=653]
Description: 3-hydroxyacyl-CoA dehydrogenase /Enoyl-CoA hydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-68  228.9   0.9    6.5e-68  228.2   0.9    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    8.9e-65  218.5   0.6    1.5e-64  217.7   0.0    1.6  2  ECH_1           Enoyl-CoA hydratase/isomerase
    3.9e-50  168.4   1.1    6.1e-24   84.5   0.0    3.6  3  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    7.9e-33  114.4   0.1    4.3e-30  105.3   0.0    2.7  3  ECH_2           Enoyl-CoA hydratase/isomerase
      1e-06   28.8   0.0      2e-06   27.9   0.0    1.4  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    1.2e-05   24.9   0.1    2.2e-05   24.1   0.1    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    0.00059   20.4   0.9     0.0079   16.8   0.9    2.7  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00075   19.7   0.3     0.0027   17.9   0.3    2.0  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.016   14.8   1.4      0.064   12.8   0.5    2.4  2  Glyco_hydro_4   Family 4 glycosyl hydrolase
      0.051   12.6   1.1        5.6    5.9   0.9    2.4  2  SDH_sah         Serine dehydrogenase proteinase
       0.11   12.4   0.4       0.23   11.3   0.0    1.8  2  Rossmann-like   Rossmann-like domain
       0.14   11.7   0.0       0.39   10.4   0.0    1.8  2  ApbA            Ketopantoate reductase PanE/ApbA
       0.25   11.4   0.5        1.5    9.0   0.2    2.2  2  FeoC            FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> 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 !  228.2   0.9   4.7e-71   6.5e-68       1     179 [.       3     183 ..       3     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: 228.2 bits;  conditional E-value: 4.7e-71
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77 
                                       k+av+GaG mG+gia+v a ag++V + di++++l+kale+i+k lek+v+kgk+kee+++++l+r++ft d++ea+
  gi|488600942|ref|YP_007907413.1|   3 KIAVLGAGAMGHGIAYVSALAGYDVWVRDIDQKFLDKALENIKKMLEKAVAKGKMKEEKAKEVLDRLHFTLDMKEAI 79 
                                       69*************************************************************************** PP

                                       .C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-T CS
                           3HCDH_N  78 .dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrge 153
                                        +a+lviEav+E ++lK+kvf+e++k+a+p++ +a+nTS+lsi+e+a+ ++rpe+++glHFfnP+p+m+LvEv++ge
  gi|488600942|ref|YP_007907413.1|  80 eGAELVIEAVPEIMDLKKKVFEEVQKYASPECYFATNTSGLSITEIANITDRPEKFMGLHFFNPVPIMQLVEVIKGE 156
                                       ***************************************************************************** PP

                                       T--HHHHHHHHHHHHHTT-EEEEE.CS CS
                           3HCDH_N 154 kTseetvatvvelakkigktpvvv.kd 179
                                       kT+++t++  v+++k+igktpvvv kd
  gi|488600942|ref|YP_007907413.1| 157 KTADSTIEYGVNFVKSIGKTPVVVkKD 183
                                       ************************666 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       1.8   2.4e+03     177     203 ..      34      60 ..      31      78 .. 0.73
   2 !  217.7   0.0   1.1e-67   1.5e-64       2     250 ..     400     652 ..     399     653 .] 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                                       GGHHHHHHHHHHHHHHSCHHHHHHHHH CS
                             ECH_1 177 eqlleealelaeklaekspaalrqlke 203
                                       +++l++ale ++k++ek+ a  ++  e
  gi|488600942|ref|YP_007907413.1|  34 QKFLDKALENIKKMLEKAVAKGKMKEE 60 
                                       567889999999999888776665444 PP

  == domain 2  score: 217.7 bits;  conditional E-value: 1.1e-67
                                       EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHC....HHHHHH CS
                             ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeek....akqall 73 
                                       + + +a+i lnrP+ +Nals ell+El  al++l +d + r+ ++tG gdkaF+aG dl+e+++       a+ a++
  gi|488600942|ref|YP_007907413.1| 400 KDDKIAKIILNRPHRLNALSFELLDELEMALKQLAKD-ESRVLIITGsGDKAFSAGFDLQEALADPStlrpANSAMV 475
                                       5678*********************************.99**********************9875456669999** PP

                                       HCCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHH CS
                             ECH_1  74 keevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAe 150
                                           +e +t++   pkpviaa+nG+a+gGG+el lacD++i+++  ++gl+e+ +Glipg ggtq++a+ +G +kA+
  gi|488600942|ref|YP_007907413.1| 476 AARGQEVFTLIERFPKPVIAAINGYAFGGGCELTLACDFRIMSKAGKIGLTETAIGLIPGWGGTQRMAKLIGLAKAK 552
                                       ***************************************************************************** PP

                                       HHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             ECH_1 151 eilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfest 227
                                       e++ l+k+++a+ea+ +Glv+k+v  +++ +e ++la+ lae +p +lr +k a+n  +e   + + ++ea  f   
  gi|488600942|ref|YP_007907413.1| 553 ELIFLAKRLTADEAEAIGLVNKAVDPDKFWDEVMALANALAEMPPISLRVAKYAINYGYELPVEVGQAIEAAYFGIA 629
                                       ***************************************************************************** PP

                                       CTSHHHHHHHHHHHTCSH----- CS
                             ECH_1 228 fskddikeGlqaflEkrkpefed 250
                                       +s++d+ eG+ af E+rkpef++
  gi|488600942|ref|YP_007907413.1| 630 TSTEDVMEGVRAFFERRKPEFKG 652
                                       *********************97 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 ?    1.3   0.1      0.39   5.4e+02      42      95 ..      15      66 ..       4      68 .. 0.66
   2 !   84.5   0.0   4.4e-27   6.1e-24       1      97 []     186     276 ..     186     276 .. 0.93
   3 !   79.2   0.0     2e-25   2.7e-22       6      97 .]     295     386 ..     293     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.39
                                      CHHHHHHHHHHHHHHHHHHHHHHHTTTH.GGHH-HHHHHHHHTT--BGGGTBSSS CS
                             3HCDH 42 Gpfelldlvgldvakkilevlaeelger.ayapsplleklveagrlgrktgkgfy 95
                                      G+  ++ l+g dv  + ++   +++ ++   + +++lek v +g++ +++ k+++
  gi|488600942|ref|YP_007907413.1| 15 GIAYVSALAGYDVWVRDID---QKFLDKaLENIKKMLEKAVAKGKMKEEKAKEVL 66
                                      6666777777776544443...33333322333479**********999999876 PP

  == domain 2  score: 84.5 bits;  conditional E-value: 4.4e-27
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+vnR+l+p+l  a++ v +gva+ e+iDa+m++++ +pmGp+el d vgld+ ++  e +  +       ++++l
  gi|488600942|ref|YP_007907413.1| 186 GFIVNRCLVPYLALAIDDVGRGVATKEEIDATMKYKYAFPMGPIELGDFVGLDILYYGGEQWSLV------PNADIL 256
                                       9*********************************************************9844444......3446** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       ++ +e+++lg ktg+gfy++
  gi|488600942|ref|YP_007907413.1| 257 KEKIEKKELGMKTGRGFYDW 276
                                       ******************97 PP

  == domain 3  score: 79.2 bits;  conditional E-value: 2e-25
                                       HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHH CS
                             3HCDH   6 RvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklve 82 
                                       R++ap++n a  l+e gvas+e+iD am+lg+++p Gp el d++gldv +k le l+ee + +  +p++ll+k+v 
  gi|488600942|ref|YP_007907413.1| 295 RLIAPMVNIASGLIEMGVASAEEIDLAMKLGTNMPKGPCELGDEIGLDVILKKLEELYEEKKLDVLKPTELLKKMVA 371
                                       99**************************************************************9************ PP

                                       TT--BGGGTBSSSBC CS
                             3HCDH  83 agrlgrktgkgfyky 97 
                                       +g+lg+k+g+gfy y
  gi|488600942|ref|YP_007907413.1| 372 EGKLGKKSGEGFYSY 386
                                       *************98 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.86   1.2e+03     221     256 ..      31      69 ..      22     100 .. 0.72
   2 !  105.3   0.0   3.1e-33   4.3e-30       2     183 ..     405     587 ..     404     594 .. 0.90
   3 !    7.1   0.0    0.0024       3.3     251     310 ..     587     645 ..     579     652 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.86
                                       HHHHHT.-S-TTTHHHHHH....T..--SHHHHHHHHHH CS
                             ECH_2 221 aidrlfsadsveeiveaLek...aeaeedewakktletl 256
                                        id+ f ++ +e+i + Lek   + + ++e ak++l+ l
  gi|488600942|ref|YP_007907413.1|  31 DIDQKFLDKALENIKKMLEKavaKGKMKEEKAKEVLDRL 69 
                                       677777777788888888775543334444555555444 PP

  == domain 2  score: 105.3 bits;  conditional E-value: 3.1e-33
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THH.HHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkee.eeffreeY 77 
                                       + i+Lnrp+ lNaLs e++++l+ alk+ +kd+  ++++++g+g+kaf+AG D+++   + ++ + ++ + + ++  
  gi|488600942|ref|YP_007907413.1| 405 AKIILNRPHRLNALSFELLDELEMALKQLAKDE-SRVLIITGSGDKAFSAGFDLQEALADPSTLRPANsAMVAARGQ 480
                                       5799************************98876.578899**************98887777765554488999999 PP

                                       HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH CS
                             ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalT 153
                                       ++  li+++pkpv+a ++G++ GgG+ l++ + fr++++  ++   EtaIGl+P  Gg+  +++l g + ++ l   
  gi|488600942|ref|YP_007907413.1| 481 EVFTLIERFPKPVIAAINGYAFGGGCELTLACDFRIMSKAGKIGLTETAIGLIPGWGGTQRMAKLIGlAKAKELIFL 557
                                       *****************************************************************887889999999 PP

                                       ---B-HHHHHHTTS--EE--GGGHHHHHHH CS
                             ECH_2 154 Garlkgadalaaglathyvpseklealeea 183
                                       ++rl++ +a a+gl ++ v+ +k+ +   a
  gi|488600942|ref|YP_007907413.1| 558 AKRLTADEAEAIGLVNKAVDPDKFWDEVMA 587
                                       ******************998887444444 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0024
                                       HHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS CS
                             ECH_2 251 ktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvd 310
                                       + +++l+++ P+sl+v+  +++ g +l  ++   + E +    +++++D++eGvra +  
  gi|488600942|ref|YP_007907413.1| 587 ALANALAEMPPISLRVAKYAINYGYELP-VEVGQAIEAAYFGIATSTEDVMEGVRAFFER 645
                                       56789**********************7.888888888888888889*********8644 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 !   27.9   0.0   1.4e-09     2e-06       1     107 [.       3     121 ..       3     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.4e-09
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.......HHHHHHHHHSSBTTTBTT...----TTEEEES-HHHHH CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree.......elieeineehenvkyLpg...iklpenlvattdlaeal 67 
                                       kiavlGaG+ G  +A v a +g +v +   ++       e i+++ e+   +  +++    ++ + l++t d++ea+
  gi|488600942|ref|YP_007907413.1|   3 KIAVLGAGAMGHGIAYVSALAGYDVWVRDIDQkfldkalENIKKMLEKAVAKGKMKEekaKEVLDRLHFTLDMKEAI 79 
                                       7*********************7775555555999988877777777777777777622245667899********* PP

                                       TT--EEEE---HHH..HHHHHHHHCCC--TT-EEEE---SEE CS
                    NAD_Gly3P_dh_N  68 kgadiivlvvPsqa..lrevlkklkgllkkkailvsliKGie 107
                                       +ga++++ +vP  +   ++v+++++++ +++  ++  + G++
  gi|488600942|ref|YP_007907413.1|  80 EGAELVIEAVPEIMdlKKKVFEEVQKYASPECYFATNTSGLS 121
                                       ***********8542268899999998888887777777775 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   1.6e-08   2.2e-05       2      85 ..       3      90 ..       2     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.6e-08
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHH.HHHHHCHT...TTEEEES-HHHHHHC CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLee.lvkkaves...grlsfttdvekavee 76
                                      ki+v+G+G +G   a v a +g +v + Did++  dk  ++  ++ e+  ++  +k++ ++   +rl+ft+d+++a+e 
  gi|488600942|ref|YP_007907413.1|  3 KIAVLGAGAMGHGIAYVSALAGYDVWVRDIDQKFLDKALENIKKMLEKAVAKgKMKEEKAKevlDRLHFTLDMKEAIEG 81
                                      9********************************999999888888888765412332222212279************* PP

                                      -SEEEE--- CS
                    UDPG_MGDP_dh_N 77 advifiaVg 85
                                      a++++ aV+
  gi|488600942|ref|YP_007907413.1| 82 AELVIEAVP 90
                                      *****9997 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.9   5.7e-06    0.0079       1      70 [.       3      90 ..       3     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.7e-06
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......................-EEECECHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......................vkvtavdnee 57
                                      ki+++GaG mg+++a   + ag   ++++ + + +++ ++++ e+++                      +  ++ d +e
  gi|488600942|ref|YP_007907413.1|  3 KIAVLGAGAMGHGIAYVSALAG---YDVW-VRDIDQKFLDKALENIKkmlekavakgkmkeekakevldRLHFTLDMKE 77
                                      7*********************...****.5599999999999999999999999999999999999987777779999 PP

                                      HHHH-SEEEE-S- CS
                     F420_oxidored 58 aaeeadvvvlavk 70
                                      a+e a+ v+ av+
  gi|488600942|ref|YP_007907413.1| 78 AIEGAELVIEAVP 90
                                      9999999998887 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   1.9e-06    0.0027       1      84 [.       3     111 ..       3     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelv 53 
                                       ki+++G G MG+ +a   + agy+v v + +++ +++++++                         ++ + +++e++
  gi|488600942|ref|YP_007907413.1|   3 KIAVLGAGAMGHGIAYVSALAGYDVWVRDIDQKFLDKALENIkkmlekavakgkmkeekakevldrLHFTLDMKEAI 79 
                                       79*****************************9888888877556777778888888888888888877778888888 PP

                                       HHCSEEEE-SSSHHHHHHHHHS.HCCC--TT- CS
                     NAD_binding_2  54 asldvvitmvkagkavdevieg.llealkkgd 84 
                                       +++++vi  v++  + ++ +++ + ++++++ 
  gi|488600942|ref|YP_007907413.1|  80 EGAELVIEAVPEIMDLKKKVFEeVQKYASPEC 111
                                       88888888888888887766664666655555 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   4.6e-05     0.064      21      72 ..      17      67 ..       3     108 .. 0.71
   2 ?   -1.9   0.0       1.5   2.1e+03      20      73 ..     409     463 ..     403     465 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                                      HTTTTCTEEEEEEE-SSHHHHHHHHHHHHHHHHHCTTTCEEEEESSHHHHHT CS
                     Glyco_hydro_4 21 kkteelsvselaLvDideerldaiqtlakklveeagadlkieattdrkealk 72
                                          +l + +++  Did++ ld++ +++kk+ e+a a+ k++   + ke+l 
  gi|488600942|ref|YP_007907413.1| 17 AYVSALAGYDVWVRDIDQKFLDKALENIKKMLEKAVAKGKMKEE-KAKEVLD 67
                                      556789999*********99999999999999999988887543.2333333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                                       HHTTTTCTEEEEEEE-SSHHHHHHH.HHHHHHHHHHCTTTCEEEEESSHHHHHTT CS
                     Glyco_hydro_4  20 lkkteelsvselaLvDideerldai.qtlakklveeagadlkieattdrkealkd 73 
                                       l++ ++l+   + L+D  e  l++  ++  ++l+    +d +++a  d++eal d
  gi|488600942|ref|YP_007907413.1| 409 LNRPHRLNALSFELLDELEMALKQLaKDESRVLIITGSGDKAFSAGFDLQEALAD 463
                                       5677889999999999777666555055566778888899999999999999987 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.9     0.004       5.6     191     235 ..      38      80 ..      28     112 .. 0.68
   2 ?    4.3   0.0     0.012        17     116     163 ..     487     534 ..     470     544 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.004
                           SDH_sah 191 kkaikqveefvyell.kdkydeekakeiakklteGrwthdypltve 235
                                       +ka++++++++ + + k k+ eekake+ ++l   ++t d   ++e
  gi|488600942|ref|YP_007907413.1|  38 DKALENIKKMLEKAVaKGKMKEEKAKEVLDRL---HFTLDMKEAIE 80 
                                       68888888888876669**********98887...46666655555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
                           SDH_sah 116 kehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqyp 163
                                       +  + ++   +  ya+ GG+ ++la d  i+ +   +G  +  +g +p
  gi|488600942|ref|YP_007907413.1| 487 ERFPKPVIAAINGYAFGGGCELTLACDFRIMSKAGKIGLTETAIGLIP 534
                                       4566677778999********************999999888888776 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.3       9.1   1.2e+04      14      33 ..       5      24 ..       3      29 .. 0.60
   2 ?   11.3   0.0   0.00017      0.23      25      85 ..      37      99 ..      34     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 9.1
                     Rossmann-like 14 GiisaGrvGtalgaalerag 33
                                       +++aG +G  +++  + ag
  gi|488600942|ref|YP_007907413.1|  5 AVLGAGAMGHGIAYVSALAG 24
                                      56777777776666555444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00017
                     Rossmann-like 25 lgaaleraghvvvgisaisaasreraerrlPdvp.vlevedvaaraellllavPda.elpglv 85
                                      l +ale ++ ++    a  +  +e+a++ l      l++++ ++ ael++ avP+  +l + v
  gi|488600942|ref|YP_007907413.1| 37 LDKALENIKKMLEKAVAKGKMKEEKAKEVLDRLHfTLDMKEAIEGAELVIEAVPEImDLKKKV 99
                                      7899**************************9987369*****************842455444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00028      0.39       1      35 [.       4      39 ..       4     140 .. 0.69
   2 ?   -4.1   0.0       8.1   1.1e+04     107     133 ..     290     316 ..     289     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea 35
                                      ia+lGaGa+G  +a+  a ag+dv++ + ++  l++
  gi|488600942|ref|YP_007907413.1|  4 IAVLGAGAMGHGIAYVSALAGYDVWVRDIDQkFLDK 39
                                      89************99999****9876666644444 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 8.1
                                       HHHHHTTTSTTSEEEEEEEE-EEEEEE CS
                              ApbA 107 heeelrealpkprvlggvtthgatreg 133
                                       ++++lr + p  ++ +g+++ g+++ +
  gi|488600942|ref|YP_007907413.1| 290 KYDALRLIAPMVNIASGLIEMGVASAE 316
                                       567788888888999999999987765 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0011       1.5      26      50 ..      39      63 ..      29      68 .. 0.85
   2 ?   -0.8   0.0       1.2   1.7e+03      33      49 ..     364     380 ..     358     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                              FeoC 26 aspealeamLeqwvrkGrvekvaat 50
                                         e +++mLe  v+kG+ ++++a+
  gi|488600942|ref|YP_007907413.1| 39 KALENIKKMLEKAVAKGKMKEEKAK 63
                                      556899*************999875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                              FeoC  33 amLeqwvrkGrvekvaa 49 
                                        +L  +v+ G++ k+  
  gi|488600942|ref|YP_007907413.1| 364 ELLKKMVAEGKLGKKSG 380
                                       5899********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      833  (0.046461); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.83u 0.33s 00:00:01.15 Elapsed: 00:00:00.50
# Mc/sec: 3908.27
//
Query:       gi|488600943|ref|YP_007907414.1|  [L=247]
Description: electron transfer flavoprotein beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-43  148.5   0.1    2.5e-43  148.1   0.1    1.1  1  ETF            Electron transfer flavoprotein domain
  ------ inclusion threshold ------
      0.021   15.4   0.0      0.042   14.4   0.0    1.5  1  Biotin_carb_N  Biotin carboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.1   2.8e-47   2.5e-43       5     180 ..      27     204 ..      24     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 2.8e-47
                                       E-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHH CS
                               ETF   5 aehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakal 81 
                                       + +g  + +n++d++a+e+A ++kek ggev +v vG+ ++e++lr++la mGad++i v  ++    da++ta+++
  gi|488600943|ref|YP_007907414.1|  27 DQRGLVYDINDWDRYAVEEAIQIKEKVGGEVLVVGVGS-KCEDTLRKCLA-MGADRAIKVPYDTSM--DAYQTAELI 99 
                                       55667789******************99**********.788999*****.************985..********* PP

                                       HHHHHHC--SEEEEESSCCH...HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEE CS
                               ETF  82 aalikkedpdlvlagataig...kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavlt 155
                                       +++ik+e++dl++ag ++++   + v++ lA +L++p++t vt+leve+g+++v+R++eg  g+ e v ++lp+++t
  gi|488600943|ref|YP_007907414.1| 100 KEAIKDEKFDLIMAGYQSQDlnnALVGALLAGMLDLPYATGVTALEVEDGSIKVKRELEG--GYGEEVVLPLPCLVT 174
                                       *******************779**************************999*********..888889999****** PP

                                       E-TTSS--.....--S-TT---EEEE--HH CS
                               ETF 156 vrpgafep.....aaimaakkkeveeveva 180
                                       v++g++ep      +i++ak+ke +ev+++
  gi|488600943|ref|YP_007907414.1| 175 VQSGINEPryvsiMGIKRAKSKEMKEVALE 204
                                       *************************99875 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 ?   14.4   0.0   4.7e-06     0.042      40      82 ..      73     115 ..      40     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-06
                                       HHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE--S CS
                     Biotin_carb_N  40 lhvreadeavelgpasasesYlniekivkaakesgadavhpGy 82 
                                         +  ad+a++++ +++ ++Y  +e i +a+k+++ d +  Gy
  gi|488600943|ref|YP_007907414.1|  73 CLAMGADRAIKVPYDTSMDAYQTAELIKEAIKDEKFDLIMAGY 115
                                       455679************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1722.94
//
Query:       gi|488600944|ref|YP_007907415.1|  [L=317]
Description: electron transfer flavoprotein alpha subunit apoprotein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-37  128.8   0.4    5.1e-37  127.5   0.1    1.7  1  ETF              Electron transfer flavoprotein domain
    7.8e-33  112.4   0.4    1.7e-32  111.3   0.2    1.7  2  ETF_alpha        Electron transfer flavoprotein FAD-binding d
     0.0051   17.4   0.0      0.037   14.7   0.0    2.1  2  PIG-L            GlcNAc-PI de-N-acetylase
     0.0052   16.5   0.4          2    8.1   0.0    3.5  4  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
     0.0095   16.4   0.1       0.02   15.4   0.1    1.5  1  DUF1048          Protein of unknown function (DUF1048)
  ------ inclusion threshold ------
      0.056   13.5   0.0      0.093   12.8   0.0    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.5   0.1   1.7e-40   5.1e-37       1     178 [.       3     170 ..       3     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 1.7e-40
                                       EEEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-..CHHHHHHCT-SEEEEEE-GGGSS--CC CS
                               ETF   1 vlvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeea..lrealaamGadkvilvddpalagydae 75 
                                       v+v+aeh+  g+lnpv+ e+l+ A ++k+    + +avv+G+    ++   +++la + adkv++v+d++l++y++e
  gi|488600944|ref|YP_007907415.1|   3 VFVVAEHR-MGELNPVSIELLNLANAIKK---DSSVAVVLGK----DVkgFADELA-KFADKVYMVQDDSLENYNPE 70 
                                       689****9.9*****************87...67788889**....34469*****.******************** PP

                                       HHHHHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-T.SSS CS
                               ETF  76 atakalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevvea.dlp 151
                                       +++++l ++ +ke+pd+vl+++t++g +++p lAa+L++p++tdv++++++ ++l+v +  ++g+ ++  +   + +
  gi|488600944|ref|YP_007907415.1|  71 TYTDVLMQIFAKEKPDVVLLPNTSFGIDLGPYLAAKLNAPIATDVVAVDAS-DGLKVSKYFFQGKLMTDLKLKeADT 146
                                       **************************************************9.77*****************999*** PP

                                       EEEEE-TTSS----S-TT---EEEE-- CS
                               ETF 152 avltvrpgafepaaimaakkkeveeve 178
                                        vltvr g+f+     ++  ++vee++
  gi|488600944|ref|YP_007907415.1| 147 YVLTVRQGVFKE---GEEVNGAVEELD 170
                                       ***********9...344455555555 PP

>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.5   1.3e+04      27      45 ..     102     120 ..      97     124 .. 0.74
   2 !  111.3   0.2   5.8e-36   1.7e-32       1      84 []     192     275 ..     192     275 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.5
                                       HHHHHHT-EEEE-HHHHTT CS
                         ETF_alpha  27 elaealgaavgasRavvda 45 
                                        la++l+a ++   ++vda
  gi|488600944|ref|YP_007907415.1| 102 YLAAKLNAPIATDVVAVDA 120
                                       5888888888877777665 PP

  == domain 2  score: 111.3 bits;  conditional E-value: 5.8e-36
                                       .-TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHH CS
                         ETF_alpha   1 vdLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqh 77 
                                       vd+++a++vv++GrG+++++n+el+e+lae lg+ v+ sR+v+d+gw+p++rq+G +Gktv+Pkly+ + +sGa qh
  gi|488600944|ref|YP_007907415.1| 192 VDITQADIVVTVGRGIEDASNIELAEQLAEMLGGVVAGSRPVIDNGWLPKDRQIGISGKTVKPKLYLGLAVSGAFQH 268
                                       699************************************************************************** PP

                                       HGGGTT- CS
                         ETF_alpha  78 laGmkes 84 
                                       ++Gmk+s
  gi|488600944|ref|YP_007907415.1| 269 VMGMKDS 275
                                       *****97 PP

>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.037      70     111 ..      47      92 ..       6      97 .. 0.76
   2 ?    0.3   0.0      0.35     1e+03      12      42 ..     130     160 ..     128     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       .EEEEECC....CBTT-STTS-CHHHHHHHHHHHHHH--SEEEEE- CS
                             PIG-L  70 dedvffld....fpDgslesydedellddlaklieryrPdvvltld 111
                                       de + f d    ++D sle y+ ++++d+l +++++ +Pdvvl ++
  gi|488600944|ref|YP_007907415.1|  47 DELAKFADkvymVQDDSLENYNPETYTDVLMQIFAKEKPDVVLLPN 92 
                                       33444444777799****************************9986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHTT-EEEEEECE--TT---S CS
                             PIG-L  12 lfaggtiaklvaagvevkivcltaGdagspl 42 
                                       +f g ++++l+ ++++++++++ +G  ++ +
  gi|488600944|ref|YP_007907415.1| 130 FFQGKLMTDLKLKEADTYVLTVRQGVFKEGE 160
                                       5667788888888999999999998555333 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 !    8.1   0.0   0.00067         2       4      38 ..      24      56 ..      21      59 .. 0.93
   2 ?   -2.5   0.0       1.3   3.8e+03      34      46 ..     103     115 ..     102     127 .. 0.82
   3 ?    3.3   0.0     0.021        63      14      43 ..     199     228 ..     194     245 .. 0.86
   4 ?    0.3   0.0      0.17   5.1e+02     105     137 .]     277     308 ..     253     308 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00067
                                      HHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHH CS
                      TPP_enzyme_M  4 aaellkaakrpvilvGggvarsgaseelrelaekl 38
                                      +a+++k+ + +++++G+ v+  g ++el+++a+k+
  gi|488600944|ref|YP_007907415.1| 24 LANAIKKDSSVAVVLGKDVK--GFADELAKFADKV 56
                                      799*****************..**********986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                                       HHHHHT-EEEEEG CS
                      TPP_enzyme_M  34 laeklgiPvvttl 46 
                                       la kl++P++t +
  gi|488600944|ref|YP_007907415.1| 103 LAAKLNAPIATDV 115
                                       7999999999865 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.021
                                       EEEEE-CHHCHTTGHHHHHHHHHHHT-EEE CS
                      TPP_enzyme_M  14 pvilvGggvarsgaseelrelaeklgiPvv 43 
                                       +v+ vG g+ ++   e +++lae lg  v+
  gi|488600944|ref|YP_007907415.1| 199 IVVTVGRGIEDASNIELAEQLAEMLGGVVA 228
                                       689999999999999999999999987765 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.17
                                       EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M 105 kiihididpaeigknyqvdlaivgdvketleaL 137
                                        ii i+ dp+     + ++++ivgd+ e++ aL
  gi|488600944|ref|YP_007907415.1| 277 LIIAINKDPEAPIFGV-AQYGIVGDIFEVVPAL 308
                                       3667777775444433.5788888887777665 PP

>> DUF1048  Protein of unknown function (DUF1048)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   6.6e-06      0.02      50      91 ..      18      58 ..       2      67 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.6e-06
                                      HHHHHHHHHHHHHTT--HHHHH-S-HHHHHHHCCTTSHC.HH CS
                           DUF1048 50 lkevldLfEeaaadgkevkevvGedvaaFadelvkdsktkya 91
                                        e+l+L  +a  ++ +v+ v+G+dv+ Fadel+k + + y+
  gi|488600944|ref|YP_007907415.1| 18 SIELLNL-ANAIKKDSSVAVVLGKDVKGFADELAKFADKVYM 58
                                      4444444.345668899****************987665454 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.1e-05     0.093      17     134 ..      25     146 ..      12     151 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                   Glyco_trans_4_2  17 akeLakrgyeVhvitpkkga..kdeleaegi.hvhrlkvdrkg.pleylkafklkklikkikPDvvhahyakpygll 89 
                                       a++++k +  V+v+  k+ +   del a+ + +v+ +++d+      +     l+++++k+kPDvv + +++  + l
  gi|488600944|ref|YP_007907415.1|  25 ANAIKK-DSSVAVVLGKDVKgfADEL-AKFAdKVYMVQDDSLEnYNPETYTDVLMQIFAKEKPDVVLLPNTSFGIDL 99 
                                       555555.6666666665555433333.3333355666544333222233334689***************9776667 PP

                   Glyco_trans_4_2  90 gslaarlsgvipvvlsvwGldvlkfpkksk...lkklllklalkkatk 134
                                       g  +a +++  p++++v   d  ++ k sk     kl+  l lk a++
  gi|488600944|ref|YP_007907415.1| 100 GPYLAAKLN-APIATDVVAVDASDGLKVSKyffQGKLMTDLKLKEADT 146
                                       765555555.8**99999888877766665666888899999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 2309.71
//
Query:       gi|488600945|ref|YP_007907416.1|  [L=490]
Description: putative Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-11   44.2   0.2    5.1e-11   43.2   0.2    1.6  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 !   43.2   0.2   2.9e-15   5.1e-11       2     167 .]     176     369 ..     175     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.9e-15
                                       EEESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS................. CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                       Radical_SAM   2 vvtrgCnlr.CsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly................. 60 
                                       ++++gC  r CsfC+ +     +g +  +++  +++e+++l +++g++++ lg ++ ++                  
  gi|488600945|ref|YP_007907416.1| 176 ETYKGCYWRkCSFCIERI----HGEPNQRDPMAVIAEIEAL-YNQGCRYFRLGNQTDFMSymgdfshevprpnaekm 247
                                       7889**9999*******6....7******************.8**********999999977777777776666666 PP

                                       TTHHHHHHHHHHTCCCTEEEEEEECSSCHG.HHHHHHHHHTT......-SEEEEEEBSSSHHHHHHHHTCTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  61 pdfvellerlaklavpgiritvetngtlpd.eeklerllelg......vdrvslgleaaddekvlklmnrghtfeev 130
                                       ++f++++ r++ +  + ++i  + + t  + +e  +++ +         ++ ++gle+ad++ v + +     ++ev
  gi|488600945|ref|YP_007907416.1| 248 WNFHREIWRRCPK-IRTLHIDNVNPKTISEwREESREIIKCItvyqtpGNVAAMGLESADER-VIEENSLAAHPDEV 322
                                       4444444444444.356666666666665585555555555555559***************.55555599****** PP

                                       HHHHHHHHHTTSET..........EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 131 lealeklreagikr..........vvdrivglpGendeeleellell 167
                                       l+a+e+++++g  +            +++ gl+Ge++e++e+ +e+l
  gi|488600945|ref|YP_007907416.1| 323 LDAIELINRYGKFVgynglpyflpGLNFVAGLKGETRETFEKNYEFL 369
                                       ***********5555555555666******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2943.06
//
Query:       gi|488600946|ref|YP_007907417.1|  [L=415]
Description: ORC complex protein Cdc6/Orc1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   91.9   0.1    4.5e-26   90.7   0.1    1.7  1  Cdc6_C           CDC6, C terminal winged helix domain
      7e-12   46.1   0.0    8.3e-11   42.6   0.0    2.3  1  AAA_16           AAA ATPase domain
    1.1e-10   41.9   0.0    2.7e-10   40.6   0.0    1.6  1  AAA_22           AAA domain
    1.4e-09   38.5   0.1    4.1e-09   36.9   0.1    1.8  1  AAA              ATPase family associated with various cellul
    5.4e-06   26.5   0.3    1.4e-05   25.1   0.3    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
    2.9e-05   24.0   0.0    5.3e-05   23.2   0.0    1.4  1  NACHT            NACHT domain
    6.7e-05   22.7   0.1       0.13   12.0   0.0    2.9  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.4e-05   22.2   0.0    0.00016   21.1   0.0    1.5  1  TniB             Bacterial TniB protein
    9.6e-05   21.7   0.1    0.00027   20.2   0.0    1.7  2  DUF815           Protein of unknown function (DUF815)
     0.0061   16.9   0.0      0.017   15.4   0.0    1.7  1  AAA_assoc_2      AAA C-terminal domain
     0.0072   16.3   0.0      0.016   15.2   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
     0.0089   15.0   0.0      0.015   14.3   0.0    1.3  1  Kinesin          Kinesin motor domain
     0.0091   16.1   0.4      0.061   13.4   0.4    2.1  1  AAA_2            AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.017   14.2   0.0      0.031   13.3   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.024   13.4   0.2        5.2    5.7   0.1    2.2  2  AAA_32           AAA domain
      0.024   14.3   0.0       0.09   12.5   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
      0.025   13.9   0.1       0.17   11.2   0.0    2.1  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.027   13.6   0.0      0.049   12.8   0.0    1.4  1  NB-ARC           NB-ARC domain
      0.033   13.7   0.0      0.064   12.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.039   13.9   0.0       0.11   12.5   0.0    1.8  1  Microtub_bd      Microtubule binding
      0.043   14.4   0.0       0.13   12.8   0.0    1.9  1  AAA_18           AAA domain
      0.053   12.8   0.2        0.8    9.0   0.0    2.5  3  Zeta_toxin       Zeta toxin
      0.076   13.2   0.1       0.31   11.2   0.1    2.0  1  TIP49_C          TIP49 AAA-lid domain
       0.12   11.9   0.1       0.33   10.5   0.1    1.8  1  GerE             Bacterial regulatory proteins, luxR family
       0.13   12.3   0.0       0.25   11.3   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   12.1   3.5        6.8    6.4   0.1    2.7  3  DEAD             DEAD/DEAH box helicase
       0.15   11.3   0.8        2.8    7.1   0.0    2.1  2  KAP_NTPase       KAP family P-loop 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 !   90.7   0.1   6.7e-29   4.5e-26       1      83 [.     304     384 ..     304     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 6.7e-29
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                       L +++ll+   g++ +ttgevy vYkslC++ g+d+ltqr++sdl+seL+mlgi+++   skGr +grtr+i+L+v+
  gi|488600946|ref|YP_007907417.1| 304 LFSMILLHM-AGRTKFTTGEVYTVYKSLCKKVGMDVLTQRRISDLISELDMLGIINSIIISKGR-YGRTREIKLDVP 378
                                       678999999.*****************************************************9.************ PP

                                       CHHHHH CS
                            Cdc6_C  78 pddvle 83 
                                        d v++
  gi|488600946|ref|YP_007907417.1| 379 IDSVKK 384
                                       ***986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   1.3e-13   8.3e-11       2     163 ..      32     169 ..      31     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.3e-13
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                       l+ R+e++e+++s+l ++ +g++ +++l++G+ G+GK++ vr + ++lek        +++++        +  ++ 
  gi|488600946|ref|YP_007907417.1|  32 LPHRKEQIEAIASVLVSALRGETpSNILIYGMTGTGKTATVRFVGNELEKY----SLRTNTRC--------YMHYI- 95 
                                       788*************99999999*********************999988....44444444........22333. PP

                            AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslql 154
                                       +   ++ ++++   + l+     l ++l+   +++g    r++e+++ ++++ ++   ++++vlD+++++     ++
  gi|488600946|ref|YP_007907417.1|  96 N---CEIIDTQ--YRVLAT----LAKNLGRNVPMTGWPTDRVYEEVRYAIDKREQ---TVIIVLDEIDKLVKKGDDV 160
                                       2...2222222..211222....22222223334444449**********55554...6****************** PP

                            AAA_16 155 laaLlrlle 163
                                       l++L r  +
  gi|488600946|ref|YP_007907417.1| 161 LYSLSRINS 169
                                       **9998754 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   4.1e-13   2.7e-10       4     125 ..      54     178 ..      51     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.1e-13
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                                       t + ++++G +GtGKT ++r + ++l++++  ++ r    ++++    ++  +l  l+++lg++    +  +++++e
  gi|488600946|ref|YP_007907417.1|  54 TPSNILIYGMTGTGKTATVRFVGNELEKYSLRTNTRCYMHYINCEIIDTQYRVLATLAKNLGRNVPMTGWPTDRVYE 130
                                       66789*********************99988888777778***********************9999889999999* PP

                            AAA_22  81 aleqalraravielliiDEaqhlr..seealeeLrsllnl.srkgvql 125
                                        ++ a+++r  ++++++DE+++l    +++l  L+++    +r+ v+l
  gi|488600946|ref|YP_007907417.1| 131 EVRYAIDKREQTVIIVLDEIDKLVkkGDDVLYSLSRINSElERSRVSL 178
                                       **********************97644888888855533234444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   6.2e-12   4.1e-09       1     112 [.      58     188 ..      58     207 .. 0.68

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.2e-12
                                       EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS.................STTHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsellsk.................yvgesekkirelfk 51 
                                       +l+yG  GtGKT++++ v +el           ++  i++  +                    + g   +++ e ++
  gi|488600946|ref|YP_007907417.1|  58 ILIYGMTGTGKTATVRFVGNELekyslrtntRCYMHYINCEIID-TqyrvlatlaknlgrnvpMTGWPTDRVYEEVR 133
                                       699******************84333333221223333333333.13667777888888889955555555555555 PP

                                       HHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...G CS
                               AAA  52 eakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...p 112
                                        a  k+ +++i+++DEid+l+k+         ++v+  L +  +++++  s+v +ig+tn+    
  gi|488600946|ref|YP_007907417.1| 134 YAIDKReQTVIIVLDEIDKLVKKG--------DDVLYSLSRINSELER--SRVSLIGITNDlkfK 188
                                       543333246*************99........8899999988888888..58********95533 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 !   25.1   0.3   2.1e-08   1.4e-05      11     148 ..      46     167 ..      34     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.1e-08
                          ATPase_2  11 leeilerepneiyfiYGpegsGKtaLlkeiienledkdk...yviyyialreesiskldefieeeeekkklekalgi 84 
                                       l + l+ e+ + ++iYG  g GKta ++ + ++le+++     + y+  ++ e i++        ++   l+k lg 
  gi|488600946|ref|YP_007907417.1|  46 LVSALRGETPSNILIYGMTGTGKTATVRFVGNELEKYSLrtnTRCYMHYINCEIIDTQ------YRVLATLAKNLGR 116
                                       345678899999****************999999886653333333333333322222......2335567777777 PP

                          ATPase_2  85 avpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnl 148
                                       +vp +             ++  e++  +i k+ + +ii++De+ kl+    ++  +++++L ++
  gi|488600946|ref|YP_007907417.1| 117 NVPMTGW---------PTDRVYEEVRYAIDKREQTVIIVLDEIDKLV----KKGDDVLYSLSRI 167
                                       7777555.........668999*************************....6677888888765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     8e-08   5.3e-05       3      99 ..      58     159 ..      56     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8e-08
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C....CHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse....vwa 74 
                                       +++ G  G GKT+ ++ +  ++ +  l  ++ +++ ++++  + ++ ++  +la+ l ++ p  + p ++    v+ 
  gi|488600946|ref|YP_007907417.1|  58 ILIYGMTGTGKTATVRFVGNELEKYSLRTNTRCYMHYINCEIIDTQYRVlATLAKNLGRNVPMTGWPTDRvyeeVRY 134
                                       799**************************99**************9999999**********999999998889999 PP

                                       HHCCSCCCEEEEEE-STT-SS-TCH CS
                             NACHT  75 vllelperlLlilDglDelvtdlgq 99 
                                        + ++++ + ++lD +D+lv++ + 
  gi|488600946|ref|YP_007907417.1| 135 AIDKREQTVIIVLDEIDKLVKKGDD 159
                                       9******************996655 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 !   12.0   0.0   0.00019      0.13      22      59 ..      44      81 ..      23      93 .. 0.73
   2 !    7.1   0.0    0.0061         4      52     106 ..     109     163 ..     103     170 .. 0.89
   3 ?   -1.7   0.0       3.2   2.1e+03     129     131 ..     374     376 ..     352     411 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                            RuvB_N 22 fieaakkreealdhvllyGpPGlGkttlakiiakelgv 59
                                       +  +  r+e+   +l+yG  G Gkt+  + + +el+ 
  gi|488600946|ref|YP_007907417.1| 44 SVLVSALRGETPSNILIYGMTGTGKTATVRFVGNELEK 81
                                      334455799**************************986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0061
                            RuvB_N  52 iiakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevlys 106
                                        +ak+lg ++ +t  P+     ++   + + e++ ++ +dei +l ++ ++vlys
  gi|488600946|ref|YP_007907417.1| 109 TLAKNLGRNVPMTGWPTDRVYEEVRYAIDKREQTVIIVLDEIDKLVKKGDDVLYS 163
                                       5789999999999999988888998889999999999*****************7 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.2
                            RuvB_N 129 dlp 131
                                       +l+
  gi|488600946|ref|YP_007907417.1| 374 KLD 376
                                       432 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.4e-07   0.00016      17     158 ..      37     176 ..      24     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.4e-07
                              TniB  17 keilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekd.edaekvpvlvvqappkpdekrlyaaiLe 92 
                                       ++i +    L+++ + + ++n+l++G + +GKt+ v+ F  ++ ++ +  +++++ + ++++    ++ r  a + +
  gi|488600946|ref|YP_007907417.1|  37 EQIEAIASVLVSALRGETPSNILIYGMTGTGKTATVR-FVGNELEKYSlRTNTRCYMHYINCEIIDTQYRVLATLAK 112
                                       45555556677888888999**************995.77666666552777899********************** PP

                              TniB  93 algaplkar.arvskleqqvlrllrel.kvrvLiiDEihnllagsarkqreflnalksLgnelkipiv 158
                                       +lg ++  + + +++ +++v   +++  ++ ++++DEi++l+    +k   +l +l +++ el+ + v
  gi|488600946|ref|YP_007907417.1| 113 NLGRNVPMTgWPTDRVYEEVRYAIDKReQTVIIVLDEIDKLV----KKGDDVLYSLSRINSELERSRV 176
                                       **999877635888999999888876516677889*****98....6666777777777777766554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.1e-07   0.00027      33      83 ..      35      85 ..      22      89 .. 0.88
   2 ?   -2.5   0.1       3.5   2.3e+03      85     119 ..     154     188 ..     132     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.1e-07
                            DUF815 33 idkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLr 83
                                       ++q ea+ +     l+g++ +n+L++G  GtGK ++v+++ ne+++ +Lr
  gi|488600946|ref|YP_007907417.1| 35 RKEQIEAIASVLVSALRGETPSNILIYGMTGTGKTATVRFVGNELEKYSLR 85
                                      5678888888888999*****************************999887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.5
                            DUF815  85 ievekedlkelpklvellrerperfilfvDDLsFe 119
                                       ++   + l +l+++ ++l++++  +i    DL F+
  gi|488600946|ref|YP_007907417.1| 154 VKKGDDVLYSLSRINSELERSRVSLIGITNDLKFK 188
                                       44445667788888888888888888888888875 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.6e-05     0.017      13      57 ..     240     283 ..     231     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeakegkieitledleealqr 57 
                                       +a+a+  +GDaRkaL lL +  e ae+ eg  ++t +++++a+ +
  gi|488600946|ref|YP_007907417.1| 240 SAIAAHEHGDARKALDLLRVSGEIAER-EGASRVTVDHVKKAVRK 283
                                       57889999**************99986.9***********99965 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 !   15.2   0.0   2.4e-05     0.016       4      43 ..      34      74 ..      31      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                                      E-HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHH CS
                            ResIII  4 lreyQeeaienll.eklkskrdkrglikmaTGtGKTlvaak 43
                                       r+ Q+eai ++l ++l  +   ++li   TGtGKT +   
  gi|488600946|ref|YP_007907417.1| 34 HRKEQIEAIASVLvSALRGETPSNILIYGMTGTGKTATVRF 74
                                      5899*******997777779999*************99754 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.2e-05     0.015      55      92 ..      35      72 ..       5      86 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHHHHHHHHHHTTSE.EEEEEEESTTSSHHHHH CS
                           Kinesin 55 qeevyeetakplvesvleGyn.atifaYGqtgsGKTyTm 92
                                       +e  e  +++++ s+l+G   + i+ YG+tg+GKT T+
  gi|488600946|ref|YP_007907417.1| 35 RKEQIEA-IASVLVSALRGETpSNILIYGMTGTGKTATV 72
                                      3344444.5566667777765288************997 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.4   9.2e-05     0.061       4      94 ..      56     159 ..      53     178 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-05
                                       --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.......... CS
                             AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.......... 70 
                                       ++il+ g tg+Gkt + + + + l+        r + + ++       +++ +i+  ++ v a              
  gi|488600946|ref|YP_007907417.1|  56 SNILIYGMTGTGKTATVRFVGNELEK----YSLRTNTRCYMH------YINCEIIDTQYRVLATLAKnlgrnvpmtg 122
                                       67888888888888888888887773....455555555555......44444444444433221112224445555 PP

                                       .....................EEEEETGGG-------------HH CS
                             AAA_2  71 .....................ivllDEidKihpkessgadvSreg 94 
                                                            i+ lDEidK  +k        +++
  gi|488600946|ref|YP_007907417.1| 123 wptdrvyeevryaidkreqtvIIVLDEIDKLVKK--------GDD 159
                                       667778888888888888888**********993........333 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 ?   13.3   0.0   4.7e-05     0.031     103     156 ..      27      82 ..      11      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                             T2SSE 103 ltlddlgaeealkekiaevlrkavr..erglilvsGgTgsGKttllyallkeinks 156
                                       +t d l  ++++ e+ia+vl +a+r  +  +il+ G Tg+GKt ++  + +e++k+
  gi|488600946|ref|YP_007907417.1|  27 YTPDYLPHRKEQIEAIASVLVSALRgeTPSNILIYGMTGTGKTATVRFVGNELEKY 82 
                                       555666677778899999999998722457***************99888888876 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.009         6      32      68 ..      57      93 ..      40      99 .. 0.92
   2 ?    5.7   0.1    0.0078       5.2     477     510 ..     250     283 ..     230     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.009
                            AAA_32 32 NifvlGesgtGrttlvkrlleeiakkeptpdDwcYvn 68
                                      Ni + G +gtG+t +v+ + +e +k     +  cY++
  gi|488600946|ref|YP_007907417.1| 57 NILIYGMTGTGKTATVRFVGNELEKYSLRTNTRCYMH 93
                                      9***********************9999999999997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0078
                            AAA_32 477 fseiadllrEAdywakkegaevveaehVekAlee 510
                                        ++  dllr +  +a++ega+ v+ +hV+kA+++
  gi|488600946|ref|YP_007907417.1| 250 ARKALDLLRVSGEIAEREGASRVTVDHVKKAVRK 283
                                       567899*************************976 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.09      20      59 ..      53      98 ..      33     110 .. 0.63
   2 ?   -1.5   0.0       2.7   1.8e+03      96     114 ..     144     162 ..     136     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                      TSSS-EEEECSTTSSHHHHHHHHHH....HSTTTTS..-EEEEETT CS
                   Sigma54_activat 20 ktdlsvlitGesGtGKellaraihe....askrkek..pfvavnca 59
                                      +t++++li G +GtGK+   r + +     s r+++   +  +nc 
  gi|488600946|ref|YP_007907417.1| 53 ETPSNILIYGMTGTGKTATVRFVGNelekYSLRTNTrcYMHYINCE 98
                                      5679*************99988855333333333321145566765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                                       EEEEETGGGS-HHHHHHHH CS
                   Sigma54_activat  96 tlfLDeigelplelQekLl 114
                                       ++ LDei +l  ++   L 
  gi|488600946|ref|YP_007907417.1| 144 IIVLDEIDKLVKKGDDVLY 162
                                       7899999999887766554 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.17      30      57 ..      45      73 ..      33      75 .. 0.81
   2 ?   -0.1   0.0      0.74   4.9e+02     136     165 ..     130     160 ..     119     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                                      EEEEEGGGS-..SEEEE--TTSSHHHHHH CS
                      FtsK_SpoIIIE 30 plvldlkkma.shllvaGatgsGKStaln 57
                                      +lv+ l++ + s++l+ G tg+GK+ +++
  gi|488600946|ref|YP_007907417.1| 45 VLVSALRGETpSNILIYGMTGTGKTATVR 73
                                      55666666666**************9987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.74
                                       HHHHHHHHTT---B-TT-............. CS
                      FtsK_SpoIIIE 136 geiaedpldifgdvflvlDnyddlaaene.r 165
                                       +e+  +++++++ v +vlD+ d+l +++   
  gi|488600946|ref|YP_007907417.1| 130 EEVRYAIDKREQTVIIVLDEIDKLVKKGDdV 160
                                       56666788889999**********9999852 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.3e-05     0.049       3     112 ..      37     150 ..      35     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHHHHC..TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCC.....CCCBTEEEEEEEESXXHHHHHHHXX CS
                            NB-ARC   3 ksvekviekLle..kdelqslvvalvGmgGvGKttlakqilnksdev.....egrFdsvawvvvsktdkseeileti 72 
                                       +++e+++  L+    +e     + ++Gm G GKt  ++ + n++++      ++++  ++ +     d+++++l t+
  gi|488600946|ref|YP_007907417.1|  37 EQIEAIASVLVSalRGETP-SNILIYGMTGTGKTATVRFVGNELEKYslrtnTRCYMHYINC--EIIDTQYRVLATL 110
                                       5667777777654333333.4789*************9999987654111113455555555..556789999999* PP

                                       HHHHHCCCTTSSSS-STTSHHHHHHHHCCCT..TEEEEEEEE CS
                            NB-ARC  73 lkeLslseddleekeeveslkrklvrlLltk..rfllvlDDV 112
                                       +k+L+++   +   ++     ++++ ++ ++   +++vlD +
  gi|488600946|ref|YP_007907417.1| 111 AKNLGRN-VPMTGWPTDR-VYEEVRYAIDKReqTVIIVLDEI 150
                                       ****988.5555555455.68888888887775667888876 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   9.7e-05     0.064      34      66 ..      56      88 ..      39     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylslt 66
                                       ++l++G tGtGKt++++ + ++l+k ++ ++t
  gi|488600946|ref|YP_007907417.1| 56 SNILIYGMTGTGKTATVRFVGNELEKYSLRTNT 88
                                      689***************999999976665554 PP

>> Microtub_bd  Microtubule binding
   #    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      69     102 ..      40      74 ..       9     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                       CCCHHHHHHHH.TT--EEEEEEES........... CS
                       Microtub_bd  69 eeisqlvqsal.dgynvcifaygqTGsGKtyTmeg 102
                                       e i+ ++ sal  ++  +i+ yg TG GKt T+  
  gi|488600946|ref|YP_007907417.1|  40 EAIASVLVSALrGETPSNILIYGMTGTGKTATVRF 74 
                                       45556666788566789***************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0002      0.13       1      80 [.      58     148 ..      58     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf..gvnlrdvakenglllevdpe........aldeskrldedkldklldalee 66 
                                       Il+ G+ G+GKt   + + ++l ++   +n r++    ++++ ++++         l ++  +  + +d++ ++++ 
  gi|488600946|ref|YP_007907417.1|  58 ILIYGMTGTGKTATVRFVGNELeKYslRTNTRCYMHYINCEIIDTQYrvlatlakNLGRNVPMTGWPTDRVYEEVRY 134
                                       99****************99988889977777777777777666666555544444555555555555555555555 PP

                            AAA_18  67 nssaleegknlvid 80 
                                       +++++e+   +v+d
  gi|488600946|ref|YP_007907417.1| 135 AIDKREQTVIIVLD 148
                                       55555555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0012       0.8      12      42 ..      51      81 ..      41      88 .. 0.87
   2 ?   -1.4   0.0       1.8   1.2e+03     140     194 ..     102     162 ..      99     166 .. 0.62
   3 ?    0.1   0.0      0.63   4.2e+02     131     168 ..     259     298 ..     249     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdeler 42
                                      ++e+P  il+ G +G GK+++ + + +ele+
  gi|488600946|ref|YP_007907417.1| 51 RGETPSNILIYGMTGTGKTATVRFVGNELEK 81
                                      6799*******************99999965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                        Zeta_toxin 140 vldRyeeevae..gRlvpkee..hdeafeglresvealeeek..qldrvk.ikdrdgktvly 194
                                       ++ R+++++a+  gR+vp +    d+++e++r ++++ e++    ld++   +++++  vly
  gi|488600946|ref|YP_007907417.1| 102 TQYRVLATLAKnlGRNVPMTGwpTDRVYEEVRYAIDKREQTViiVLDEIDkLVKKGD-DVLY 162
                                       567777775555789888886335888888888888866666444444443333333.5555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.63
                        Zeta_toxin 131 vkkelSrlgvldRyeee.vaeg.Rlvpkeehdeafeglre 168
                                       v+ e++  + ++R+  + v+++ R++++++  ea++ l+ 
  gi|488600946|ref|YP_007907417.1| 259 VSGEIAEREGASRVTVDhVKKAvRKIECDNVVEAVRTLPT 298
                                       5566777777788888865555699999999999888765 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00047      0.31      33      60 ..     253     280 ..     250     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00047
                           TIP49_C  33 aiqLltpasilakkrkkkevevedveev 60 
                                       a+ Ll ++  +a+++++ +v+v++v+++
  gi|488600946|ref|YP_007907417.1| 253 ALDLLRVSGEIAEREGASRVTVDHVKKA 280
                                       899**********************997 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0005      0.33      22      55 ..     262     294 ..     259     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                       HHHHHHTS-HHHHHHHHHHHHHHHT-SSHHHHHH CS
                              GerE  22 eIAeelniSekTVkvhksnimkKLnvksrvelvr 55 
                                       eIAe+ + S  TV  h++ + +K+++ + ve+vr
  gi|488600946|ref|YP_007907417.1| 262 EIAEREGASRVTVD-HVKKAVRKIECDNVVEAVR 294
                                       9************8.9****************98 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00038      0.25       3      44 ..      35      80 ..      33      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                                      SHHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  3 seeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalg 44
                                      ++e++ea+++ l +al     + il++G  G+GKT+ vr + ++l+
  gi|488600946|ref|YP_007907417.1| 35 RKEQIEAIASVLVSALrgetPSNILIYGMTGTGKTATVRFVGNELE 80
                                      57899999999999888544445****************9988875 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1      0.01       6.8       4      31 ..      38      72 ..      35     137 .. 0.78
   2 ?    6.1   0.1     0.013       8.3     120     150 ..     140     168 ..     102     182 .. 0.78
   3 ?   -2.7   0.0       6.3   4.2e+03      65     106 ..     325     365 ..     320     402 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.01
                                      HHHHHHHHH.......TTCEEEEEESTTSSHHHHH CS
                                      xxxxxxxxx.......xxxxxxxxxxxxxxxxxxx RF
                              DEAD  4 Qaeaiplil.......gggdvlvaaeTGsGKTlaf 31
                                      Q eai  +l       +  ++l+ + TG+GKT+  
  gi|488600946|ref|YP_007907417.1| 38 QIEAIASVLvsalrgeTPSNILIYGMTGTGKTATV 72
                                      66777777766664433379************974 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                                       TTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 120 sqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       +q  ++VlDE+d+l ++  +d++   l++++
  gi|488600946|ref|YP_007907417.1| 140 EQTVIIVLDEIDKLVKK--GDDVLYSLSRIN 168
                                       67779**********99..566655566664 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.3
                                       HHHHHHTTTSTSEEEEEETTSSHHHHHHHHH.TT.CSEEEEEHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxx RF
                              DEAD  65 nnlkkfkkyidlrvlliiggvaardqlskld.ng.vdivvgtpg 106
                                       + +k+++k++++ v   +++ + +d +s+ld  g ++ ++   g
  gi|488600946|ref|YP_007907417.1| 325 TVYKSLCKKVGMDV---LTQRRISDLISELDmLGiINSIIISKG 365
                                       55555555554444...345555555555542224444444444 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0042       2.8       2      47 ..      36      82 ..      35     119 .. 0.81
   2 ?    2.1   0.5      0.14        91     162     185 ..     130     153 ..     124     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0042
                        KAP_NTPase  2 dlyasaladilseptl..atpivvgLygkWGsGKssllnkledelkef 47
                                      +  ++a+a +l++  l  +tp+ + +yg  G+GK++ + ++ +el++ 
  gi|488600946|ref|YP_007907417.1| 36 KEQIEAIASVLVSA-LrgETPSNILIYGMTGTGKTATVRFVGNELEKY 82
                                      67789999999944.6689****************9999988888775 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                        KAP_NTPase 162 admektLdalqkrlVvviDdLDrc 185
                                       ++   ++d+ ++++++v+D++D +
  gi|488600946|ref|YP_007907417.1| 130 EEVRYAIDKREQTVIIVLDEIDKL 153
                                       556668999999**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); 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 0.33s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2622.47
//
Query:       gi|488600947|ref|YP_007907418.1|  [L=180]
Description: Molecular chaperone (small heat shock protein) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-11   42.4   0.0    5.3e-11   41.9   0.0    1.3  1  ArsA_HSP20      HSP20-like domain found in ArsA
    7.8e-11   42.0   3.9    1.7e-09   37.7   3.9    2.1  1  HSP20           Hsp20/alpha crystallin family
    2.7e-05   25.1   0.1    4.4e-05   24.4   0.1    1.3  1  CS              CS domain
  ------ inclusion threshold ------
       0.02   15.3   0.0      0.032   14.6   0.0    1.3  1  PIH1_CS         PIH1 CS-like domain
       0.11   13.2   0.0       0.21   12.3   0.0    1.4  1  DNA_repr_REX1B  DNA repair REX1-B


Domain annotation for each model (and alignments):
>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   1.5e-14   5.3e-11       2      63 .]     100     164 ..      99     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.5e-14
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkignfrRq....itLPsvlarkevtsAkfedgvLeIrF 63 
                                        e+++ +++P+v+ke+idl  ++++L Ik++ ++R+    + LP  +  + + +A++++gvLe+ +
  gi|488600947|ref|YP_007907418.1| 100 EEVQIIAEMPGVNKEDIDLNATETTLEIKADGENRKyfetVELPAEVIPESA-KARYNNGVLEVVM 164
                                       6788899****************************99999**********77.**********986 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   3.9   4.8e-13   1.7e-09       1     101 [.      94     179 ..      94     180 .] 0.93

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 4.8e-13
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       d++e++ee ++ +++pg++ke+++++ +++++ +k+  e              +rk+  +++LP +v +++ ka ++
  gi|488600947|ref|YP_007907418.1|  94 DVMETDEEVQIIAEMPGVNKEDIDLNATETTLEIKADGE--------------NRKYFETVELPAEVIPESAKARYN 156
                                       6899********************************999..............3678888***************** PP

                                       TTEEEEEEEBSS--..-------- CS
                             HSP20  78 dGvLtvtvpkkepekkkkerkiqi 101
                                       +GvL+v ++kk+p+k+ +++ki+i
  gi|488600947|ref|YP_007907418.1| 157 NGVLEVVMKKKHPKKE-QKKKIDI 179
                                       **********999976.9999999 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.2e-08   4.4e-05       7      76 .]      97     166 ..      93     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-08
                                       EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                                CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliegeLfgpIdpeesswtieskkveitLkK 76 
                                       +t++eV +  ++++v  +k+d++++ +e++l++k  g+ +k +   eL +++ pe+++ +  +  +e+++kK
  gi|488600947|ref|YP_007907418.1|  97 ETDEEVQIIAEMPGV--NKEDIDLNATETTLEIKAdGEnRKYFETVELPAEVIPESAKARYNNGVLEVVMKK 166
                                       799***********9..******************977677777888***********************99 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     9e-06     0.032      34      87 ..     103     157 ..      95     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9e-06
                           PIH1_CS  34 aieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvk 87 
                                        i  e+P++   ++++l+ +e++le+++++   kyf +++Lp +v  ++++A++++
  gi|488600947|ref|YP_007907418.1| 103 QIIAEMPGV-NKEDIDLNATETTLEIKADGenRKYFETVELPAEVIPESAKARYNN 157
                                       566689999.6799************8888889*********************96 PP

>> DNA_repr_REX1B  DNA repair REX1-B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.7e-05      0.21      12      52 ..       5      48 ..       3      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                    DNA_repr_REX1B 12 eRaeiYkefeegfkaylk..sgaeee.ykqlvkevTeefseiSk 52
                                      +R ++Y+++++ f+++ +  s + +e ++++ k++T++f+ei +
  gi|488600947|ref|YP_007907418.1|  5 RRRKTYRDWDDIFDEMFEmfSFPFSEeFDEIFKRITRDFNEIFR 48
                                      899************999655554445*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1178.95
//
Query:       gi|488600948|ref|YP_007907419.1|  [L=729]
Description: AAA family ATPase, CDC48 subfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-101  336.2   0.0    1.7e-50  170.9   0.0    2.7  2  AAA              ATPase family associated with various cellul
    2.5e-32  110.4   8.2    3.2e-18   65.2   2.0    3.0  2  AAA_lid_3        AAA+ lid domain
    2.1e-31  107.9   0.3    7.8e-31  106.1   0.3    2.0  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.7e-19   69.3   0.1    3.5e-19   68.3   0.1    1.6  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    2.1e-17   63.3   0.0    8.6e-09   35.3   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      3e-16   60.0   0.0    7.4e-08   32.7   0.0    3.1  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.2e-14   53.7   0.1    7.1e-06   26.5   0.0    3.8  2  AAA_16           AAA ATPase domain
    8.6e-13   48.5   0.5    9.2e-05   22.5   0.0    3.6  2  AAA_5            AAA domain (dynein-related subfamily)
    4.5e-12   45.8   3.1    1.1e-05   25.3   0.2    3.2  2  Vps4_C           Vps4 C terminal oligomerisation domain
      9e-12   44.8   0.0    0.00018   20.9   0.0    2.9  2  TIP49            TIP49 P-loop domain
    4.1e-11   43.3   0.5     0.0023   18.2   0.1    4.1  2  AAA_22           AAA domain
    7.2e-10   39.2   0.0    0.00028   21.1   0.0    2.5  2  AAA_33           AAA domain
    1.4e-09   38.1   0.0     0.0004   20.4   0.0    2.6  2  AAA_14           AAA domain
    8.9e-08   32.7   0.4       0.02   15.4   0.0    3.4  2  AAA_18           AAA domain
    1.3e-07   31.5   0.0     0.0075   16.0   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    1.7e-07   31.6   0.0      0.024   15.0   0.0    3.0  2  RNA_helicase     RNA helicase
      3e-07   30.0   0.4      0.032   13.6   0.0    3.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.3e-07   30.2   0.2       0.11   12.2   0.0    4.2  2  Sigma54_activat  Sigma-54 interaction domain
    4.1e-07   29.7   0.0      0.018   14.5   0.0    2.9  2  AAA_7            P-loop containing dynein motor region
    7.2e-07   29.1   0.1      0.059   13.1   0.0    3.0  2  AAA_24           AAA domain
    8.5e-07   28.4   0.0      0.037   13.2   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    1.5e-06   28.5   0.0      0.071   13.4   0.0    2.5  2  AAA_28           AAA domain
    1.9e-06   27.8   0.0      0.039   13.8   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    6.1e-06   26.2   0.1        0.5   10.2   0.0    3.7  3  Bac_DnaA         Bacterial dnaA  protein
    6.9e-06   26.6   0.0       0.15   12.6   0.0    3.1  2  ABC_tran         ABC transporter
    1.1e-05   24.7   0.0      0.079   12.0   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
    1.1e-05   24.8   0.1      0.078   12.2   0.0    2.6  2  Zeta_toxin       Zeta toxin
    1.7e-05   24.8   0.0       0.18   11.8   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    2.7e-05   23.6   3.1       0.57    9.5   0.1    3.8  3  ATPase           KaiC
    3.1e-05   24.4   1.6       0.48   10.8   0.0    4.1  3  AAA_17           AAA domain
    3.3e-05   24.0   0.0       0.23   11.6   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
      5e-05   22.7   0.0       0.23   10.7   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    7.9e-05   22.6   1.9        4.5    7.2   0.0    4.7  4  NTPase_1         NTPase
    8.1e-05   22.2   0.1       0.44   10.0   0.0    2.6  2  PhoH             PhoH-like protein
     0.0001   21.9   6.4        1.3    8.6   0.3    4.0  4  AAA_25           AAA domain
    0.00011   21.5   0.2       0.89    8.7   0.0    3.3  3  NB-ARC           NB-ARC domain
    0.00011   22.1   2.7       0.77    9.6   0.0    3.6  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00014   21.8   0.2        1.9    8.4   0.0    3.9  4  NACHT            NACHT domain
    0.00023   21.5   1.2        1.4    9.3   0.0    3.2  3  AAA_19           AAA domain
    0.00033   20.5   0.8        1.1    9.0   0.0    2.8  3  AAA_11           AAA domain
    0.00043   20.0   0.0        0.9    9.2   0.0    2.6  2  AAA_30           AAA domain
     0.0021   17.4   0.0        1.5    7.9   0.0    3.0  3  KAP_NTPase       KAP family P-loop domain
     0.0021   18.2   2.5          3    7.9   0.0    3.9  3  Cytidylate_kin2  Cytidylate kinase-like family
     0.0026   17.5   0.1        2.8    7.6   0.0    2.7  2  Cytidylate_kin   Cytidylate kinase
     0.0026   17.9   0.1        1.8    8.7   0.0    3.1  3  SKI              Shikimate kinase
     0.0031   17.5   0.1        2.1    8.2   0.0    3.4  3  Rad17            Rad17 P-loop domain
     0.0032   17.3   0.0       0.05   13.3   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0041   16.6   0.0        7.8    5.9   0.0    3.8  4  TniB             Bacterial TniB protein
     0.0068   15.5   0.0        2.2    7.3   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.012   15.2   0.0        1.4    8.6   0.0    3.6  4  Zot              Zonular occludens toxin (Zot)
      0.014   15.1   0.0        5.5    6.6   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.014   15.4   0.0        5.2    7.0   0.0    2.7  2  ResIII           Type III restriction enzyme, res subunit
       0.03   14.3   2.0      0.091   12.7   2.0    1.8  1  DUF327           Protein of unknown function (DUF327)
       0.04   13.7   0.0         12    5.8   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.049   13.5   0.1         20    5.0   0.0    3.1  3  CPT              Chloramphenicol phosphotransferase-like prot
      0.057   12.3   0.0        5.9    5.7   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
      0.072   12.5   0.2         11    5.3   0.0    2.5  2  IPT              Isopentenyl transferase
      0.095   11.8   0.0        7.9    5.5   0.0    2.4  2  PIF1             PIF1-like helicase
       0.14   12.5   0.9        1.7    9.0   0.1    3.0  3  B5               tRNA synthetase B5 domain
          3    7.8   5.1         10    6.0   0.1    2.9  2  RNA_pol_Rpb5_C   RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.0   5.6e-53   1.7e-50       1     131 [.     214     343 ..     214     344 .. 0.98
   2 !  162.6   0.0     2e-50     6e-48       1     131 [.     489     619 ..     489     620 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 5.6e-53
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTl+akava+e++++f+++sg+e++sky gese+++re+f+eake+  p i+fiDEid++a++r++ 
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAHFITLSGPEIMSKYYGESEQRLREIFEEAKENT-PAIIFIDEIDSIAPKREEV 289
                                       79******************************************************8.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLl+ +dg++++ ++vivi+atnrpd +dpal+r gRfdr+iei+
  gi|488600948|ref|YP_007907419.1| 290 TGEVERRVVAQLLALMDGLESR-GEVIVIAATNRPDAIDPALRRpGRFDREIEIG 343
                                       *********************7.66***************************996 PP

  == domain 2  score: 162.6 bits;  conditional E-value: 2e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +llyGppGtGKTllakava+e++++f++++g+ellsk+vgesek++re+f++a++ a p ilf+DEid+la++r   
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNANFISVKGPELLSKWVGESEKHVREMFRKARQVA-PAILFFDEIDSLAPRRgGI 564
                                       69******************************************************9.****************777 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++s+++ervv+qLlteldg+++ ++ v+vi+atnrpd +dpallr gR++r+i i+
  gi|488600948|ref|YP_007907419.1| 565 GDSQVTERVVSQLLTELDGLEELKD-VVVIAATNRPDIVDPALLRpGRIERHILIP 619
                                       79********************755.***************************987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.5   2.9e-15   8.8e-13       1      34 [.     366     406 ..     366     429 .. 0.77
   2 !   65.2   2.0   1.1e-20   3.2e-18       2      44 ..     642     699 ..     641     700 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.9e-15
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr.......g 34 
                                       dv+l+eLA +T G++GADl+al +eAa++A+r        +
  gi|488600948|ref|YP_007907419.1| 366 DVNLEELADLTVGFVGADLEALAKEAAMHAIRKmletgkiD 406
                                       9*******************************944444330 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 1.1e-20
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrr...............gikeitmedfe 44 
                                       +d++eLAe+TeGySGAD++alcreA++lAlr+               ++ ++t ++fe
  gi|488600948|ref|YP_007907419.1| 642 IDFDELAEKTEGYSGADIEALCREAGMLALREklkaglskeeiskvaKEIKVTRKHFE 699
                                       8*******************************55554444444443334457777776 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 !  106.1   0.3   2.6e-33   7.8e-31       1      84 [.       5      88 ..       5      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 2.6e-33
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +LrV ea+ +dvgrgi+ridpe+m+++++++gdv+ei gk++  aivwp++ped+gkgiIr+dg +R+nagv+i+dkV+
  gi|488600948|ref|YP_007907419.1|  5 TLRVGEAYYRDVGRGIARIDPEVMDRYDIQSGDVIEIIGKNSVPAIVWPGYPEDKGKGIIRIDGSLRNNAGVGIDDKVR 83
                                      69***************************************9************************************* PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      ++k++
  gi|488600948|ref|YP_007907419.1| 84 IKKVS 88
                                      **986 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 !   68.3   0.1   1.2e-21   3.5e-19       4      64 .]     107     166 ..     104     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.2e-21
                                       CCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCCE CS
                           CDC48_2   4 gdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpvev 64 
                                       g+ +ayl r+++grp+ kG+++++e +g+++++vV+st P+g+v+++++T iel +kpve+
  gi|488600948|ref|YP_007907419.1| 107 GG-EAYLLRVLEGRPIKKGQKIRVEIFGHTLTFVVTSTRPSGVVIVSRSTAIELKDKPVEE 166
                                       56.78******************************************************95 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 !   35.3   0.0   2.9e-11   8.6e-09      35     103 ..     213     289 ..     205     330 .. 0.87
   2 !   24.7   0.0   5.4e-08   1.6e-05      35      97 ..     488     558 ..     478     565 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.9e-11
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                        vllyGpPG Gkt +ak +a+e+++++ + sgP +      e ++ l  ++ + +e+   ++fidei  ++++ eev
  gi|488600948|ref|YP_007907419.1| 213 GVLLYGPPGTGKTLIAKAVANEVDAHFITLSGPEImskyygESEQRLREIFEEAKENtpAIIFIDEIDSIAPKREEV 289
                                       69*******************************994433333456799999988876336*************9998 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 5.4e-08
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrls 97 
                                        +llyGpPG Gkt lak +a+e ++++ +  gP l      e ++ +  ++ + ++    +lf dei  l+
  gi|488600948|ref|YP_007907419.1| 488 GILLYGPPGTGKTLLAKAVANESNANFISVKGPELlskwvgESEKHVREMFRKARQVapAILFFDEIDSLA 558
                                       69*******************************87333333344555566655544322578888887765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.5e-10   7.4e-08       6     105 ..     214     307 ..     209     314 .. 0.91
   2 !   23.6   0.0   1.5e-07   4.5e-05       6     105 ..     489     583 ..     484     585 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.5e-10
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++aka+a+  ++    ++i++   e++     + + ++++  ++   +a+e+   i+++DEid i
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDA----HFITLSGPEIMS----KYYGESEQRLREIFEEAKENTpaIIFIDEIDSI 282
                                       6899******************96....************....999999**************999********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e+ + +v r  V+  LL +++g
  gi|488600948|ref|YP_007907419.1| 283 APKrEEVTGEVERR-VVAQLLALMDG 307
                                       **988888888886.66678888887 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 1.5e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt+laka+a+  ++    ++i +   ell     + + +++++ +++  +a +    i+++DEid  
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNA----NFISVKGPELLS----KWVGESEKHVREMFRKARQVApaILFFDEIDSL 557
                                       8999******************96....************....88888888999999999998889********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +p+ + +g     e V+  LL  l+g
  gi|488600948|ref|YP_007907419.1| 558 APRrGGIGDSQVTERVVSQLLTELDG 583
                                       **998888888888888888876665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.4e-08   7.1e-06      17     139 ..     204     316 ..     198     318 .. 0.69
   2 !   21.3   0.0   9.3e-07   0.00028      16      63 ..     478     522 ..     476     593 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.4e-08
                            AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                       ++v  + p  vll+G++G+GK+ +++++++++ ++   f++    +  ++  y    q l r e++++ +   e++ 
  gi|488600948|ref|YP_007907419.1| 204 QQVGIDPPKGVLLYGPPGTGKTLIAKAVANEVDAH---FITLSGPEI-MSKYYGESEQRL-R-EIFEEAK---ENTP 271
                                       5555666799*******************988876...666666665.222222233444.3.4444444...4456 PP

                            AAA_16  94 leawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                                       +  + +++++ +    e++g+ ++r+ ++l +l++ l+++++ +++
  gi|488600948|ref|YP_007907419.1| 272 AIIFIDEIDSIAPKREEVTGEVERRVVAQLLALMDGLESRGE-VIV 316
                                       66677777777778888888888***********99888777.443 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 9.3e-07
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       +++++   p  +ll+G++G+GK+ l+++++++ +++   f++ k  +l
  gi|488600948|ref|YP_007907419.1| 478 FKAINIKPPKGILLYGPPGTGKTLLAKAVANESNAN---FISVKGPEL 522
                                       56666666799*******************988877...777777776 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 !   21.4   0.1   6.3e-07   0.00019       1     136 [.     213     332 ..     213     333 .. 0.74
   2 !   22.5   0.0   3.1e-07   9.2e-05       2     134 ..     489     606 ..     488     609 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.3e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ +a  + + + +  +++ +++     +          +  ++ ++a+  +++i+++DE++
  gi|488600948|ref|YP_007907419.1| 213 GVLLYGPPGTGKTLIAKAVANEVDAHFITLSGPEIMSKYYGESE---------QRLREIFEEAKenTPAIIFIDEID 280
                                       59******************************998776543333.........34478888888899********** PP

                                       G--...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 rae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        +     ev++++ +    + l l++g e  ++        + via++n++d     ++palr+
  gi|488600948|ref|YP_007907419.1| 281 SIApkrEEVTGEVERRVVAQLLALMDGLESRGE--------VIVIAATNRPD----AIDPALRR 332
                                       987222345555555555555555555444433........99999999999....88888876 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.1e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+ la+ +a   n+++  v +++      l+ ++    g+ + +  ++ r+ar   ++il++DE++ 
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNANFISVKGPE------LLSKWV---GESEKHVREMFRKARqvAPAILFFDEIDS 556
                                       89***************************9998......889999...566666666667777799*********** PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                       + +   ++  s   er ++   ++el + ++   l+++ via++n++d     ++pal
  gi|488600948|ref|YP_007907419.1| 557 LAPRRGGIGDSQVTERVVS-QLLTELDGLEE---LKDVVVIAATNRPD----IVDPAL 606
                                       **99999999999999998.33444444443...45599999999999....555555 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 !   19.4   0.1   2.5e-06   0.00075       9      45 ..     402     438 ..     399     454 .. 0.89
   2 !   25.3   0.2   3.8e-08   1.1e-05      25      60 ..     689     724 ..     677     724 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.5e-06
                            Vps4_C   9 pgaiemtwmdipsdkllePpvtlkDflkalkkarptV 45 
                                        g+i + +++ip + l e +vt++Dfl+alk+  p+ 
  gi|488600948|ref|YP_007907419.1| 402 TGKIDIEVEEIPDEVLAEIKVTREDFLEALKNIEPSA 438
                                       6889999*****9999999****************96 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 3.8e-08
                            Vps4_C  25 lePpvtlkDflkalkkarptVskeDLekheeFTkef 60 
                                       +e +vt+k+f+ka++k +p+ ++eDLe++++  ++f
  gi|488600948|ref|YP_007907419.1| 689 KEIKVTRKHFEKAMEKIKPSLTNEDLERYKKIVEDF 724
                                       577**************************9976665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   7.4e-07   0.00022      51      97 ..     212     256 ..     207     282 .. 0.89
   2 !   20.9   0.0   5.9e-07   0.00018      51     108 ..     487     543 ..     475     546 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.4e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                       ++vLl Gp+gtGkt +a a+++e+    +f++lsg e+ s     +e
  gi|488600948|ref|YP_007907419.1| 212 KGVLLYGPPGTGKTLIAKAVANEVD--AHFITLSGPEIMSKYYGESE 256
                                       89*********************97..89*********998766665 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.9e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrksig 108
                                       +++Ll Gp+gtGkt la a+++e +    f++++g e+ s  v  +e  + + +rk+ +
  gi|488600948|ref|YP_007907419.1| 487 KGILLYGPPGTGKTLLAKAVANESN--ANFISVKGPELLSKWVGESEKhVREMFRKARQ 543
                                       89********************966..89**************9999537789999865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   7.6e-06    0.0023       8      62 ..     214     268 ..     209     321 .. 0.72
   2 !   17.8   0.0     1e-05     0.003       8      48 ..     489     520 ..     483     595 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.6e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellr 62 
                                       ++++G++GtGKT+ ++ ++++ d++ +++  +pe++ +++  s+  ++++++e  +
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAH-FITLSGPEIMsKYYGESEQRLREIFEEAKE 268
                                       689******************9644.333355555555555555555555555444 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48 
                                       ++++G++GtGKT+l++ ++++          ++ +++v+ p
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANES---------NANFISVKGP 520
                                       89******************98.........6666655554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   9.2e-07   0.00028       2      79 ..     214     321 ..     214     347 .. 0.75
   2 !   15.6   0.0   4.4e-05     0.013       2      46 ..     489     535 ..     489     598 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.2e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll G+pG+GK+  a+ ++++ +  +++ls ++++++++g+ +q+++                              
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDahFITLSGPEIMSKYYGESEQRLReifeeakentpaiifideidsiapkreeVT 290
                                       7899***************999999***************9998888667766777777777777777766554322 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatn 79 
                                        +v+ r+ ++l +l +   s+g  +++ atn
  gi|488600948|ref|YP_007907419.1| 291 GEVERRVVAQLLALMDGLESRGEVIVIAATN 321
                                       3355556666666666666666666666665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.4e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                       +ll G+pG+GK+ la+ ++++    ++ +  ++l+++ +g+ +++ +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNanFISVKGPELLSKWVGESEKHVR 535
                                       6789***************9999777888888888888886666554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.3e-06    0.0004       5      84 ..     214     290 ..     211     318 .. 0.79
   2 !   14.8   0.0   7.5e-05     0.022       5      76 ..     489     557 ..     486     593 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81 
                                       +++ G+  +GKT ++k +++e      +++ ++  +   k + ++e+ l++i+e++ke+   ++f+DEi  +   ++
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVD---AHFITLSGPEIMSKYYGESEQRLREIFEEAKENTPAIIFIDEIDSIAPKRE 287
                                       7899**************98877...9999999999888888877766667777666779999******99855555 PP

                            AAA_14  82 alk 84 
                                        + 
  gi|488600948|ref|YP_007907419.1| 288 EVT 290
                                       444 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.5e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k +++e+     +++ ++  +   k   ++e ++ e++++  ++    +lf+DEi  +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESN---ANFISVKGPELLSKWVGESEkHVREMFRKA-RQVAPAILFFDEIDSL 557
                                       7899**************98877...777777766666666555552445555554.4447899******865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00028     0.084       1      25 [.     214     256 ..     214     322 .. 0.61
   2 !   15.4   0.0   6.7e-05      0.02       1      25 [.     489     527 ..     489     593 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00028
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..................g 25 
                                       +ll G+pG+GKt +ak+++++                      
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAhfitlsgpeimskyygesE 256
                                       799***************9984222344444444444444441 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 6.7e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.............g 25 
                                       Ill G+pG+GKt lak+++++  ++             +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESnANfisvkgpellskwV 527
                                       99****************887522235444444444440 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00022     0.066      45      70 ..     209     234 ..     198     243 .. 0.86
   2 !   16.0   0.0   2.5e-05    0.0075      44      77 ..     483     516 ..     471     556 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00022
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgve 70 
                                       +  ++++l Gp+G+GK+ +a a++ e
  gi|488600948|ref|YP_007907419.1| 209 DPPKGVLLYGPPGTGKTLIAKAVANE 234
                                       556789****************9976 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.5e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavragls 77 
                                       i+  ++i+l Gp+G+GK+ la a++ e  ++ +s
  gi|488600948|ref|YP_007907419.1| 483 IKPPKGILLYGPPGTGKTLLAKAVANESNANFIS 516
                                       5566789*****************9987666555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.1e-05     0.024       1      31 [.     214     244 ..     214     290 .. 0.77
   2 !   13.1   0.0   0.00031     0.092       1      26 [.     489     514 ..     489     546 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.1e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...klkkk 31 
                                       ++lyGp+g+GK+++ak +a+++  ++        
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAHFitlS---G 244
                                       689******************999884431...3 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00031
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i+lyGp+g+GK++lak +a++   ++
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNANF 514
                                       789**************988766554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00016     0.049      25      43 ..     214     232 ..     206     237 .. 0.90
   2 !   13.6   0.0   0.00011     0.032      25      43 ..     489     507 ..     480     515 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt++ak+++
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVA 232
                                       89*************9875 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVA 507
                                       89*************9875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00083      0.25      23      51 ..     212     237 ..     200     327 .. 0.83
   2 !   12.2   0.0   0.00036      0.11      23      56 ..     487     517 ..     473     600 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00083
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkek 51 
                                         vl+ G  GtGK+l+a+a+ ++ +   +
  gi|488600948|ref|YP_007907419.1| 212 KGVLLYGPPGTGKTLIAKAVANEVD---A 237
                                       679****************987654...4 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00036
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                         +l+ G  GtGK+lla+a+ ++s+   ++f++v
  gi|488600948|ref|YP_007907419.1| 487 KGILLYGPPGTGKTLLAKAVANESN---ANFISV 517
                                       679*****************98876...556655 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 !   14.5   0.0   6.1e-05     0.018      33      64 ..     211     241 ..     201     290 .. 0.81
   2 !   11.6   0.0   0.00048      0.14      31      62 ..     484     514 ..     475     519 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.1e-05
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekyls 64 
                                        k vll+Gp GtGKt+i+k + +++d  ++++
  gi|488600948|ref|YP_007907419.1| 211 PKGVLLYGPPGTGKTLIAKAVANEVD-AHFIT 241
                                       5789*******************999.44443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00048
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkeky 62 
                                       k  k +ll+Gp GtGKt+++k + ++ +  ++
  gi|488600948|ref|YP_007907419.1| 484 KPPKGILLYGPPGTGKTLLAKAVANESN-ANF 514
                                       556789***************9999887.444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00029     0.088       5      29 ..     214     240 ..     211     291 .. 0.64
   2 !   13.1   0.0    0.0002     0.059       5      23 ..     489     509 ..     486     521 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00029
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfi 29 
                                       +l+yGp+g+GKT +ak    + ++ fi
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVanEVDAHFI 240
                                       89*************998654444444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0002
                            AAA_24   5 iliyGpsgiGKTtlakel..g 23 
                                       il+yGp+g+GKT lak    +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVanE 509
                                       89*************987554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00021     0.061      53     116 ..     211     279 ..     201     330 .. 0.63
   2 !   13.2   0.0   0.00012     0.037      20      81 ..     444     514 ..     429     554 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                            DUF815  53 annvLLwGarGtGKSslvkallneyaeegLrli..evekedl....kelpklvellrerperfilfvDDL 116
                                        + vLL+G  GtGK  + ka+ ne+ ++ + l   e+  +      + l +++e+ + +++  i+f+D +
  gi|488600948|ref|YP_007907419.1| 211 PKGVLLYGPPGTGKTLIAKAVANEVDAHFITLSgpEIMSKYYgeseQRLREIFEEAK-ENTPAIIFIDEI 279
                                       5789**********************9996664337766555100034444444433.455678898876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
                            DUF815  20 eevdevklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg 81 
                                        ev ++++dd+ g+++ k++l+e +e         + ++ +p + +LL+G  GtGK  l ka+ ne +++ 
  gi|488600948|ref|YP_007907419.1| 444 VEVPNITWDDVGGLEQAKQELKEAVEwplkypelfKAINIKPPKGILLYGPPGTGKTLLAKAVANESNANF 514
                                       5667788999999999999999887633322221123455677789*******************998765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00024     0.071       2      49 ..     214     266 ..     213     301 .. 0.77
   2 !   12.7   0.0   0.00037      0.11       2      35 ..     489     527 ..     488     553 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00024
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalpwv 49 
                                       + + G+++tGKT +++a a++     ++   pE++ +++ e  ++ +++ +++
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEvdahFITLSgPEIMSKYYGESEQRLREIFEEA 266
                                       6799***************6554425555588888888877776666655554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00037
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareil 35 
                                       i + G+++tGKT l++a a++   ++  v  pE   + +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANEsnaNFISVkgPELLSKWV 527
                                       7899***************76534322223555554444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00075      0.22       2      28 ..     214     240 ..     213     302 .. 0.86
   2 !   13.8   0.0   0.00013     0.039       2     112 ..     489     599 ..     488     604 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00075
                             AAA_3   2 vllegvPGlaktllvkalakaldlefk 28 
                                       vll g PG++ktl++ka+a+ +d++f 
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAHFI 240
                                       7999*******************9985 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00013
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappkt 78 
                                       +ll g PG++ktll+ka+a+  +++f  ++  p+ll    +G +  e++ +e+  k+  v   +l+ dei+  +p+ 
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNANFISVK-GPELLSK-WVGES--EKHVREMFRKARQVAPAILFFDEIDSLAPRR 561
                                       7999**********************9997.6888855.56664..5556677777778899999999999888875 PP

                             AAA_3  79 ....qsalleameerqvtvegethklpepflvlatqnP 112
                                           +s + e +  + +t  +   +l++  ++ at+ P
  gi|488600948|ref|YP_007907419.1| 562 ggigDSQVTERVVSQLLTELDGLEELKDVVVIAATNRP 599
                                       22224566666666666666666677777666666655 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0017      0.51      37     176 ..     214     355 ..     210     373 .. 0.69
   2 ?    0.4   0.1       1.7   4.9e+02     160     194 ..     381     420 ..     367     446 .. 0.77
   3 !   10.2   0.0    0.0017       0.5      37     110 ..     489     558 ..     480     632 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       +++yg+ G Gkt + ka++nev +++     + l++ e +++     +++  e f e   ++  ++ iD+i  +a k
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAHF-----ITLSGPEIMSKYYGESEQRLREIFEEAKENTpAIIFIDEIDSIAPK 285
                                       79****************99986655.....5678888888888777777777777766655156779999999987 PP

                                       HH.........HHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
                          Bac_DnaA 113 ek.........tqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                                        +         +  +l+ +++ l   g+ +v+++   P +++    r   rf++   ++i  pd++ rl+il+
  gi|488600948|ref|YP_007907419.1| 286 REevtgeverrVVAQLLALMDGLESRGEVIVIAATNRPDAIDPAL-RRPGRFDRE--IEIGVPDRDGRLEILQ 355
                                       532211111112334666666777788889999999998886543.335677765..4555577777777776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                                       EEE-----HHHHHHHHHHHHHHTT--.....--TTHHHHH CS
                          Bac_DnaA 160 vvdieppdletrlailkkkieaekle.....vpeevlefi 194
                                        +d+e   +e ++  ++k++e+ k++     +p+evl  i
  gi|488600948|ref|YP_007907419.1| 381 GADLEALAKEAAMHAIRKMLETGKIDieveeIPDEVLAEI 420
                                       36899999999999999*9998888866666788887665 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0017
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGT CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqfla 110
                                       +++yg+ G Gkt L ka++ne  +n+     + +++ e l++ v   +++  e f++  + +  +L  D+i  la
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNANF-----ISVKGPELLSKWVGESEKHVREMFRKARQvAPAILFFDEIDSLA 558
                                       79***************999866655.....45667777788887777777777776544244577777777776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0024      0.73       8      67 ..     208     265 ..     204     319 .. 0.77
   2 !   12.6   0.0    0.0005      0.15       7      80 ..     482     569 ..     480     599 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0024
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                       + + + v + G+ G+GK+ ++k++a++++  +  i+l g ++ ++   +++++++ +++e
  gi|488600948|ref|YP_007907419.1| 208 IDPPKGVLLYGPPGTGKTLIAKAVANEVD--AHFITLSGPEIMSKYYGESEQRLREIFEE 265
                                       566677899******************97..56777788777777777777777777766 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0005
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx... RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren... 79 
                                       ++k+ + + + G+ G+GK+ L+k++a++++  +  i ++g +l ++   +++k+++ ++ +  q+ p +   ++   
  gi|488600948|ref|YP_007907419.1| 482 NIKPPKGILLYGPPGTGKTLLAKAVANESN--ANFISVKGPELLSKWVGESEKHVREMFRKaRQVAPAILFFDEids 556
                                       5677778899******************97..578888999999988888888888777776677777665555566 PP

                                       ............H CS
                                       ............x RF
                          ABC_tran  80 ............e 80 
                                                    
  gi|488600948|ref|YP_007907419.1| 557 laprrggigdsqV 569
                                       6666666654432 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00027     0.079     117     139 ..     214     236 ..     208     240 .. 0.91
   2 !   10.2   0.0   0.00097      0.29     117     137 ..     489     509 ..     482     513 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavp 139
                                       v++yGp+ tGkt +a+a a+ v+
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVD 236
                                       89*****************9886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00097
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       +++yGp+ tGkt la+a a+ 
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANE 509
                                       89***************9985 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0016      0.48      15      49 ..     210     242 ..     201     254 .. 0.85
   2 !   12.2   0.0   0.00026     0.078      14      51 ..     484     519 ..     475     525 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                        Pk +ll G pG GK+ +a+++++e+  +  +++l
  gi|488600948|ref|YP_007907419.1| 210 PPKGVLLYGPPGTGKTLIAKAVANEV--DAHFITL 242
                                       6999*********************9..5555555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00026
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       + Pk ill G pG GK+ la+++++e   + n++ +++
  gi|488600948|ref|YP_007907419.1| 484 KPPKGILLYGPPGTGKTLLAKAVANES--NANFISVKG 519
                                       679***********************8..899998865 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0018      0.54      20      47 ..     212     241 ..     187     262 .. 0.73
   2 !   11.8   0.0   0.00061      0.18      19      51 ..     486     520 ..     453     526 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0018
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..- CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..e 47 
                                       + +lL+G+ G+GKT +++++a++++ +  +
  gi|488600948|ref|YP_007907419.1| 212 KGVLLYGPPGTGKTLIAKAVANEVDAHfiT 241
                                       349*******************99877433 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00061
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        + ilL+G+ G+GKT l++++a++ + +  +vk P
  gi|488600948|ref|YP_007907419.1| 486 PKGILLYGPPGTGKTLLAKAVANESNANfiSVKGP 520
                                       3349******************9998877777766 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0019      0.57      11      37 ..     202     229 ..     200     238 .. 0.85
   2 ?    3.2   0.0      0.16        49     109     154 ..     257     308 ..     242     319 .. 0.67
   3 !    8.6   0.0    0.0036       1.1      22      38 ..     489     505 ..     482     522 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                            ATPase  11 il.kgGipegrvvlitGepGtGKtifal 37 
                                       i+ + Gi   + vl++G pGtGKt++a+
  gi|488600948|ref|YP_007907419.1| 202 IFqQVGIDPPKGVLLYGPPGTGKTLIAK 229
                                       554568888889*************997 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.16
                            ATPase 109 eelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                       ++l+e+ +e k+     + iD i+++    +e + +v R+ + ql+  + +l
  gi|488600948|ref|YP_007907419.1| 257 QRLREIFEEAKEntpAIIFIDEIDSIapkREEVTGEVERRVVAQLLALMDGL 308
                                       4455555554443325566666666632155666677899999999999776 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0036
                            ATPase  22 vlitGepGtGKtifalq 38 
                                       +l++G pGtGKt++a+ 
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKA 505
                                       89************986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0055       1.7       1      26 [.     217     242 ..     217     293 .. 0.74
   2 !   10.8   0.0    0.0016      0.48       1      53 [.     492     545 ..     492     643 .. 0.74
   3 ?   -0.3   0.6       4.6   1.4e+03      31      67 ..     672     707 ..     664     722 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0055
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                       +G+PG GK+ +++ ++ +++ ++++ 
  gi|488600948|ref|YP_007907419.1| 217 YGPPGTGKTLIAKAVANEVDAHFITL 242
                                       7***************9997666543 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0016
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklplee 53 
                                       +G+PG GK+ +++ ++ + +  ++s  G  l +    ++ +  r+ +rk+ ++ 
  gi|488600948|ref|YP_007907419.1| 492 YGPPGTGKTLLAKAVANESNANFISVkGPELLSKWVGESEKHVREMFRKARQVA 545
                                       7***************99988887766666655555444445666676665554 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 4.6
                                       HHHHHTTTSHSSHHHHCTSHHHH..HHHHHHHHHHHHHH CS
                            AAA_17  31 reeakrgglakardemrklplee..kkelqkeaaekiae 67 
                                       re   + gl  +++e++k+ +e+  ++++ ++a+eki+ 
  gi|488600948|ref|YP_007907419.1| 672 REKL-KAGL--SKEEISKVAKEIkvTRKHFEKAMEKIKP 707
                                       3333.3444..6777777655552255667788888875 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0035       1.1      24      82 ..     214     283 ..     209     289 .. 0.62
   2 !   11.6   0.0   0.00078      0.23      24      83 ..     489     559 ..     478     561 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0035
                                       EEEEEETT--HHHHHHCC--TTS-E....E--SSTTHHH....H-HHHHHHHT...TTSEEEEEE-TT-- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw....leifvverla....klpldlleqa...kggtLylkdiadls 82 
                                       v+l G++G+gk+l+A++ +++        + + ++ +      +   +++e+a   +++++++ +i+++ 
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAHfitlSGPEIMSKYYgeseQRLREIFEEAkenTPAIIFIDEIDSIA 283
                                       9****************99864331111122222222111111355888888755566788888888765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00078
                                       EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..........HHHHHH...TTTSEEEEEE-TT--H CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp..........ldlleq...akggtLylkdiadlsk 83 
                                       ++l G++G+gk+l A++ +++s  +   ++  +l               +++ +   + +++L++ +i++l +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNANFISVKGPELL--SkwvgesekhvREMFRKarqVAPAILFFDEIDSLAP 559
                                       799***************99987743322222222..122344445556666663335999*******99975 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00076      0.23       4      36 ..     214     239 ..     211     293 .. 0.69
   2 !    9.6   0.0    0.0016      0.48       4      43 ..     489     521 ..     486     558 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00076
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavy 36 
                                       vl  G +GtGKt+++ ++++e+        a++
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEV-------DAHF 239
                                       6789****************99.......2333 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhpl 43 
                                       +l  G +GtGKt+++ ++++e        +a+++sv +p+
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANES-------NANFISVKGPE 521
                                       6789************999998.......55555555554 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     0.019       5.6       2      32 ..     214     244 ..     213     259 .. 0.84
   2 ?    1.4   0.2       0.9   2.7e+02      81     117 ..     255     292 ..     244     305 .. 0.73
   3 ?    2.5   0.0      0.42   1.2e+02      80     123 ..     430     473 ..     416     481 .. 0.78
   4 ?    7.2   0.0     0.015       4.5       2      32 ..     489     519 ..     488     554 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.019
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + k v+++++ + ++++G
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAHFITLSG 244
                                       6788***************999877666655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.9
                                       HHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHH CS
                          NTPase_1  81 feelalealrkal.seadviviDEiGkmElkskkfkea 117
                                        e+   e++++a  +++ +i iDEi ++  k +++  +
  gi|488600948|ref|YP_007907419.1| 255 SEQRLREIFEEAKeNTPAIIFIDEIDSIAPKREEVTGE 292
                                       567777888888756677*******7766665555555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                          NTPase_1  80 sfeelalealrkalseadviviDEiGkmElkskkfkeaveevLk 123
                                       +++++  +a+r+ l e   i  D +G +E   +++keave  Lk
  gi|488600948|ref|YP_007907419.1| 430 ALKNIEPSAMREVLVEVPNITWDDVGGLEQAKQELKEAVEWPLK 473
                                       5555666666666666667888*****************97665 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.015
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       +++ GppG+GKt l k v+++ + + ++v+G
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNANFISVKG 519
                                       6788***************999888788877 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0026      0.76      22      41 ..     214     233 ..     207     240 .. 0.86
   2 !   10.0   0.0    0.0015      0.44      22      42 ..     489     509 ..     476     516 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0026
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt++a a+a 
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVAN 233
                                       6789***********99985 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0015
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       +   Gp GtGKt+la a+a e
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANE 509
                                       6779***********999865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0077       2.3      36      54 ..     214     232 ..     209     238 .. 0.86
   2 ?    6.4   0.1     0.019       5.8     128     177 ..     257     306 ..     236     325 .. 0.86
   3 ?   -2.1   0.0       8.1   2.4e+03      72     124 ..     312     371 ..     304     393 .. 0.65
   4 !    8.6   0.3    0.0042       1.3      36      53 ..     489     506 ..     485     593 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0077
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt +a  +a
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVA 232
                                       69***********997665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                       + ++++ ++++e + ++ + iD ++++ +  e+   +v +++v++l  + +
  gi|488600948|ref|YP_007907419.1| 257 QRLREIFEEAKE-NTPAIIFIDEIDSIAPKREEVTGEVeRRVVAQLLALMD 306
                                       557889999999.88******************999999*****9988765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 8.1
                            AAA_25  72 gkVlyvsaEdsedelrrRlravg.eal.......rddarllvldlagveslpLfakdrggt 124
                                       g V++++a ++ d + + lr+ g  ++       ++d+rl +l+++++ s+pL+++ + ++
  gi|488600948|ref|YP_007907419.1| 312 GEVIVIAATNRPDAIDPALRRPGrFDReieigvpDRDGRLEILQIHTR-SMPLADDVNLEE 371
                                       566666666666666666666553233446677777899999998886.888876655444 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0042
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll+G+pgtGKt la  +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAV 506
                                       69***********99655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0033      0.99      23      45 ..     214     236 ..     208     243 .. 0.86
   2 !    8.7   0.0     0.003      0.89      23      44 ..     489     510 ..     480     518 .. 0.89
   3 ?   -1.7   0.2       4.4   1.3e+03     210     236 ..     694     722 ..     686     727 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0033
                                       EEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                       v l+G +G GKt +ak + n+ d
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVD 236
                                       679***************99944 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.003
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       + l+G +G GKt lak + n+s
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANES 510
                                       679***************9995 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.4
                                       -T.CSCCHHHHHHHHHHCTGCC.TS--SS CS
                            NB-ARC 210 tk.ktveewkkvleklesklle.veksts 236
                                       t+ ++++ ++k++ +l+++ le  +k+ +
  gi|488600948|ref|YP_007907419.1| 694 TRkHFEKAMEKIKPSLTNEDLErYKKIVE 722
                                       44499999999999999999997776655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0027      0.82      22     122 ..     213     317 ..     201     320 .. 0.54
   2 !    9.6   0.0    0.0026      0.77      15      45 ..     481     511 ..     475     518 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0027
                          ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal..........giavpk 88 
                                        +++YGp g GKt + k ++++ +  ++      +  e+ ++++ e+  e++ ++ +e+a+           i+   
  gi|488600948|ref|YP_007907419.1| 213 GVLLYGPPGTGKTLIAKAVANEVDA-HF---ITLSGPEIMSKYYGES--EQRLREIFEEAKentpaiifidEIDSIA 283
                                       5789********9888888887733.33...3334444444444444..2222222222223332333444333333 PP

                          ATPase_2  89 aeleeilkeksklvfkaielllekikkkgkkiii 122
                                        + ee+  e  + v +++ +l++ ++ +g  i+i
  gi|488600948|ref|YP_007907419.1| 284 PKREEVTGEVERRVVAQLLALMDGLESRGEVIVI 317
                                       3344455566666677777777777776665554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0026
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienle 45 
                                       ++ +p + +++YGp g GKt L k ++++++
  gi|488600948|ref|YP_007907419.1| 481 INIKPPKGILLYGPPGTGKTLLAKAVANESN 511
                                       5666777899*************99999874 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.029       8.7       3      23 ..     214     234 ..     212     239 .. 0.89
   2 ?   -1.2   0.0       5.7   1.7e+03      65     115 ..     255     307 ..     245     342 .. 0.57
   3 !    8.4   0.0    0.0064       1.9       3      23 ..     489     509 ..     487     515 .. 0.89
   4 ?    2.2   0.0      0.52   1.6e+02      56     112 ..     521     581 ..     510     633 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.029
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT  ++ +a +
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANE 234
                                       799*************99976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.7
                                       --SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCT CS
                             NACHT  65 paapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirk 115
                                       ++++ +e++++     + + + +D +D ++ + ++     e++ v +l   l+ +
  gi|488600948|ref|YP_007907419.1| 255 SEQRLREIFEEAK-ENTPAIIFIDEIDSIAPKREEvtgeVERRVVAQL-LALMDG 307
                                       5555555444433.3344445578888888877777774333333333.355555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0064
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT L++ +a +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANE 509
                                       7899************99875 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.52
                                       HHHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..............HHHH CS
                             NACHT  56 dllfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.....kekqpvrtlLsel 112
                                       +ll +   e++++v+e++    +++  + l +D +D l+   g       +++ v +lL+el
  gi|488600948|ref|YP_007907419.1| 521 ELLSKWVGESEKHVREMFRKARQVAPAI-LFFDEIDSLAPRRGGigdsqVTERVVSQLLTEL 581
                                       5777778899999999555555555555.559999999987777754444444444444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0065         2      11      32 ..     212     233 ..     205     242 .. 0.83
   2 ?   -1.1   0.0         7   2.1e+03      96     125 ..     264     293 ..     247     306 .. 0.66
   3 !    9.3   0.0    0.0047       1.4       4      32 ..     480     508 ..     478     544 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0065
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                       k +l+ ++pGtGKT + k++ +
  gi|488600948|ref|YP_007907419.1| 212 KGVLLYGPPGTGKTLIAKAVAN 233
                                       56899*********99887765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 7
                            AAA_19  96 eekklqeeellivDEfqdvdelqyrLlkal 125
                                       ee k +  +++++DE+  + +   ++  ++
  gi|488600948|ref|YP_007907419.1| 264 EEAKENTPAIIFIDEIDSIAPKREEVTGEV 293
                                       33344445699****999987766665555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0047
                            AAA_19   4 avealkekvllvtaGpGtGKTrvlkhiva 32 
                                       a++  + k +l+ ++pGtGKT + k++ +
  gi|488600948|ref|YP_007907419.1| 480 AINIKPPKGILLYGPPGTGKTLLAKAVAN 508
                                       56556678899**********98777655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0046       1.4      20      41 ..     214     235 ..     195     273 .. 0.78
   2 !    9.0   0.0    0.0036       1.1      20      42 ..     489     511 ..     474     550 .. 0.71
   3 ?   -1.4   0.2       5.5   1.6e+03     152     192 ..     680     720 ..     640     725 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0046
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                       +l+ GPPGtgKT    ++ +++
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEV 235
                                       6999********7776666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0036
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                        l+ GPPGtgKT    ++ ++ +
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESN 511
                                       5899********88888887775 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.5
                            AAA_11 152 lkkskekskskleqerrklkkerkelskeleeaeesleeev 192
                                       +k++ +k +++ +++r++ +k+ ++++ +l++++ +  +++
  gi|488600948|ref|YP_007907419.1| 680 SKEEISKVAKEIKVTRKHFEKAMEKIKPSLTNEDLERYKKI 720
                                       34455555555555666666666665555555555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0     0.003       0.9      21      42 ..     214     235 ..     201     244 .. 0.82
   2 !    8.0   0.0     0.007       2.1      22      41 ..     490     509 ..     476     519 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.003
                            AAA_30  21 avltGpAGtGKttalkalreaw 42 
                                       ++l Gp+GtGKt + ka+++ +
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEV 235
                                       6899************997655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.007
                            AAA_30  22 vltGpAGtGKttalkalrea 41 
                                       +l Gp+GtGKt + ka+++ 
  gi|488600948|ref|YP_007907419.1| 490 LLYGPPGTGKTLLAKAVANE 509
                                       789***********999765 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.8   5.5e+02      20      45 ..     211     236 ..     201     244 .. 0.82
   2 !    7.9   0.0    0.0052       1.5     160     196 ..     258     293 ..     238     300 .. 0.74
   3 ?    5.1   0.0     0.038        11      17      63 ..     483     559 ..     473     715 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                        KAP_NTPase  20 pivvgLygkWGsGKssllnkledelk 45 
                                       p  v Lyg+ G+GK+ + + + +e +
  gi|488600948|ref|YP_007907419.1| 211 PKGVLLYGPPGTGKTLIAKAVANEVD 236
                                       55689**********99888877765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0052
                        KAP_NTPase 160 lladmektLdalqkrlVvviDdLDrceteevlqllea 196
                                        l +++++ ++ +++ +++iD++D++ +++   + e+
  gi|488600948|ref|YP_007907419.1| 258 RLREIFEEAKE-NTPAIIFIDEIDSIAPKREEVTGEV 293
                                       45555555555.9*************99987776666 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.038
                        KAP_NTPase  17 latpivvgLygkWGsGKssllnkledelkefa..............................kpvrflfaefnawsf 63 
                                        ++p  + Lyg+ G+GK+ l + + +e + +                               +p  ++f e++++++
  gi|488600948|ref|YP_007907419.1| 483 IKPPKGILLYGPPGTGKTLLAKAVANESNANFisvkgpellskwvgesekhvremfrkarqvAPAILFFDEIDSLAP 559
                                       57788899*************99999999886677777777777777666666666666666555555555555555 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0      0.01         3       8      53 ..     220     267 ..     216     308 .. 0.80
   2 ?    6.4   0.0      0.03       9.1       8      54 ..     495     541 ..     489     592 .. 0.81
   3 ?    0.5   0.2       1.9   5.7e+02      29      55 ..     680     706 ..     669     724 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.01
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde.r 53 
                                        G+g++ i++a+A++   +f+    +e ++k  g se+ + e ++e +
  gi|488600948|ref|YP_007907419.1| 220 PGTGKTLIAKAVANEVDAHFITLSGPEIMSKYYGESEQRLrEIFEEaK 267
                                       59*********************9999999999999999966666632 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.03
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevders 54 
                                        G+g++ +++a+A++ + +f++ + +e ++k  g se++v+e+  ++
  gi|488600948|ref|YP_007907419.1| 495 PGTGKTLLAKAVANESNANFISVKGPELLSKWVGESEKHVREMFRKA 541
                                       69**************************************6655522 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.9
                   Cytidylate_kin2  29 dreiieevakelglseeeveevdersr 55 
                                       ++e i +vake +++++++e++ e+ +
  gi|488600948|ref|YP_007907419.1| 680 SKEEISKVAKEIKVTRKHFEKAMEKIK 706
                                       677789999999999999977777333 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0092       2.8       4      27 ..     217     240 ..     214     244 .. 0.90
   2 ?    7.0   0.0     0.014       4.3       3      28 ..     491     516 ..     489     518 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0092
                                       E-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                        GP g+GK  +a+a+a++++++++
  gi|488600948|ref|YP_007907419.1| 217 YGPPGTGKTLIAKAVANEVDAHFI 240
                                       6*******************9997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +a+a+a++ ++++++
  gi|488600948|ref|YP_007907419.1| 491 LYGPPGTGKTLLAKAVANESNANFIS 516
                                       67*******************99986 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0061       1.8       1      44 [.     220     268 ..     220     270 .. 0.72
   2 ?    5.5   0.0     0.059        18       1      22 [.     495     516 ..     495     542 .. 0.85
   3 ?   -1.1   0.0         6   1.8e+03      20      40 ..     641     661 ..     636     718 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0061
                                       TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT...S-HHHHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg...ksiaeifeeege 44 
                                       +G+GK+ ++k++A++++ +fi l   e+++k  g   ++ +eifee  e
  gi|488600948|ref|YP_007907419.1| 220 PGTGKTLIAKAVANEVDAHFITLsgPEIMSKYYGeseQRLREIFEEAKE 268
                                       69*******************9833345566555333556777777665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.059
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ ++k++A++ + +fi 
  gi|488600948|ref|YP_007907419.1| 495 PGTGKTLLAKAVANESNANFIS 516
                                       69*****************996 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 6
                                       EEEHHHHHHHHHTS-HHHHHH CS
                               SKI  20 fiDlDeliekrtgksiaeife 40 
                                        iD Del ek++g s a+i +
  gi|488600948|ref|YP_007907419.1| 641 KIDFDELAEKTEGYSGADIEA 661
                                       589999999999988877754 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0       0.1        30      48      79 ..     214     245 ..     209     280 .. 0.81
   2 ?   -1.7   0.0         8   2.4e+03     120     175 ..     391     446 ..     383     453 .. 0.74
   3 !    8.2   0.0     0.007       2.1      46     112 ..     487     554 ..     461     570 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.1
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                       +L+ GP+G gk+ + k ++ e   +++  + p
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAHFITLSGP 245
                                       5889*************999988877776665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8
                             Rad17 120 lklqklGddlrtdkklilvedlPnkfyrdsdalrevirkylrssealplilvitei 175
                                         +    + l+t k  i ve++P++   + +  re  +++l+  e+ ++  v+ e+
  gi|488600948|ref|YP_007907419.1| 391 AAMHAIRKMLETGKIDIEVEEIPDEVLAEIKVTREDFLEALKNIEPSAMREVLVEV 446
                                       45666667788888889999999999999988888888888887776665555555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.007
                             Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvslke.pdnqksdfkgltekesrflsqiesfkel 112
                                       + +L+ GP+G gk+   k ++ e   +++    p +l +     ++ ++ ++ k  +  + i  f e+
  gi|488600948|ref|YP_007907419.1| 487 KGILLYGPPGTGKTLLAKAVANESNANFISVKGPELLSKwVGESEKHVREMFRKARQVAPAILFFDEI 554
                                       456889***********************999998876514458889999999999999999888887 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.77   2.3e+02       5      71 ..     218     279 ..     214     283 .. 0.55
   2 !   13.3   0.0   0.00017      0.05       4      74 ..     492     557 ..     489     560 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.77
                   Viral_helicase1   5 GvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ + + ++++   + +t + p  e+ ++   + + ++ r  + f++a+ +  +  i+++DE+
  gi|488600948|ref|YP_007907419.1| 218 GPPGTGKTLIAKAVANEVdaHFITLSGP--EIMSK---YYGESEQRLREIFEEAKEN--TPAIIFIDEI 279
                                       78******99999999955333333222..33333...3333333333333333333..2567777776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00017
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylll 74 
                                        G pG GK+ l + ++++s  ++ +++   ell++++ +++++  ++++++ + +  +    il++DE+ +l
  gi|488600948|ref|YP_007907419.1| 492 YGPPGTGKTLLAKAVANESnANFISVKG-PELLSKWVGESEKHVREMFRKARQVA--P---AILFFDEIDSL 557
                                       588****************977777777.8************9999999877744..3...69*****8655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.053        16      35      57 ..     211     233 ..     198     243 .. 0.83
   2 ?   -1.7   0.0       5.4   1.6e+03     116     132 ..     267     283 ..     245     306 .. 0.70
   3 ?    5.9   0.0     0.026       7.8      25      60 ..     476     511 ..     459     521 .. 0.82
   4 ?    0.2   0.0       1.4   4.2e+02     109     132 ..     535     558 ..     523     600 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.053
                              TniB  35 mpnlllvGdsnnGKtmivekFar 57 
                                       ++ +ll+G++ +GKt i++  a+
  gi|488600948|ref|YP_007907419.1| 211 PKGVLLYGPPGTGKTLIAKAVAN 233
                                       6789*************997665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.4
                              TniB 116 relkvrvLiiDEihnll 132
                                       +e  + ++ iDEi+++ 
  gi|488600948|ref|YP_007907419.1| 267 KENTPAIIFIDEIDSIA 283
                                       4455789999**99986 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.026
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlhp 60 
                                       eL+++ + k ++ +ll+G++ +GKt +++  a++ +
  gi|488600948|ref|YP_007907419.1| 476 ELFKAINIKPPKGILLYGPPGTGKTLLAKAVANESN 511
                                       5666667777899**************998887665 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.4
                              TniB 109 qqvlrllrelkvrvLiiDEihnll 132
                                       +++ r  r++ + +L +DEi++l 
  gi|488600948|ref|YP_007907419.1| 535 REMFRKARQVAPAILFFDEIDSLA 558
                                       4445666789999******99875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.024       7.1     131     156 ..     213     238 ..     186     246 .. 0.88
   2 !    7.3   0.0    0.0073       2.2     127     155 ..     484     512 ..     361     520 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks 156
                                        +l+ G+ g+GKt ++ a+ +e++++
  gi|488600948|ref|YP_007907419.1| 213 GVLLYGPPGTGKTLIAKAVANEVDAH 238
                                       58999*****************9987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0073
                             T2SSE 127 rerglilvsGgTgsGKttllyallkeink 155
                                       +  + il+ G+ g+GKt l+ a+ +e n+
  gi|488600948|ref|YP_007907419.1| 484 KPPKGILLYGPPGTGKTLLAKAVANESNA 512
                                       236789**************999988776 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.9   8.6e+02     136     173 ..      62      96 ..      52     107 .. 0.76
   2 ?    8.6   0.0    0.0045       1.4       4      64 ..     215     280 ..     214     304 .. 0.80
   3 ?    1.0   0.0      0.96   2.9e+02       4      17 ..     490     503 ..     489     558 .. 0.73
   4 ?   -1.6   0.0         6   1.8e+03      64      95 ..     529     560 ..     508     579 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.9
                               Zot 136 alaekavklkrkaaigikgryrltraleddhaktekvt 173
                                       +++ +   l++ a++gi ++ r++ + +   + +ekvt
  gi|488600948|ref|YP_007907419.1|  62 GIIRIDGSLRNNAGVGIDDKVRIKKVST---KMAEKVT 96 
                                       5666677889999*********999886...4455554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0045
                               Zot   4 lvtGapGsgKts..gavkkdllp.alk.egRkiitnidGlrlerieqvlgekvs.tarlirid.npe 64 
                                       l +G+pG+gKt+  +av +++   ++  +g +i+ +  G   +r++ +++e+++ t+ +i+id + +
  gi|488600948|ref|YP_007907419.1| 215 LLYGPPGTGKTLiaKAVANEVDAhFITlSGPEIMSKYYGESEQRLREIFEEAKEnTPAIIFIDeI-D 280
                                       679********733579998877533358**********************9999******9941.2 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.96
                               Zot   4 lvtGapGsgKtsga 17 
                                       l +G+pG+gKt+ a
  gi|488600948|ref|YP_007907419.1| 490 LLYGPPGTGKTLLA 503
                                       56899999999754 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 6
                               Zot  64 egaetlkefakwatidkgallviDEcqeifpv 95 
                                       e+++ + e++  a+    a+l++DE   + p 
  gi|488600948|ref|YP_007907419.1| 529 ESEKHVREMFRKARQVAPAILFFDEIDSLAPR 560
                                       55666677777777568899999999877555 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 ?    6.1   0.0     0.025       7.5      18      67 ..     215     270 ..     212     309 .. 0.79
   2 ?    6.6   0.0     0.018       5.5      18      64 ..     490     542 ..     485     702 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.025
                                       EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHHSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpegt 67 
                                       l+ g  g+Gkt i+++++++ +++        i     Ge ++ ++e++ee +e+t
  gi|488600948|ref|YP_007907419.1| 215 LLYGPPGTGKTLIAKAVANEVDAHfitlsGpEIMSKYYGESEQRLREIFEEAKENT 270
                                       678999**************9777666652356666699********999999976 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
                                       EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE........ESEEHHHHHHHHHHCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg........iGergnevaevleefp 64 
                                       l+ g  g+Gkt ++++++++sn++   i v         +Ge ++ v+e++++ +
  gi|488600948|ref|YP_007907419.1| 490 LLYGPPGTGKTLLAKAVANESNAN--FISVKgpellskwVGESEKHVREMFRKAR 542
                                       688999**************9888..44444466666676666666666555544 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 ?    5.2   0.0     0.064        19      23      49 ..     210     236 ..     187     270 .. 0.85
   2 ?    7.0   0.0     0.017       5.2      17      51 ..     479     513 ..     430     554 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.064
                                       TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  23 rdkrglikmaTGtGKTlvaaklierll 49 
                                         k +l+  + GtGKTl+a +++ ++ 
  gi|488600948|ref|YP_007907419.1| 210 PPKGVLLYGPPGTGKTLIAKAVANEVD 236
                                       5677889999********988877765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                                       ......TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklierllkk 51 
                                       +++++k  k +l+  + GtGKTl+a +++ +   +
  gi|488600948|ref|YP_007907419.1| 479 KAINIKPPKGILLYGPPGTGKTLLAKAVANESNAN 513
                                       334448899999***********997777665553 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.0   0.00031     0.091      28      77 ..     677     726 ..     670     729 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHH CS
                            DUF327  28 etlekeeeeeseeelkelleeidkqgerLaesrtiedlkkYkklvkeflk 77 
                                         l+kee ++  +e+k   +  +k+ e+++ s t edl++Ykk v +f k
  gi|488600948|ref|YP_007907419.1| 677 AGLSKEEISKVAKEIKVTRKHFEKAMEKIKPSLTNEDLERYKKIVEDFHK 726
                                       558889999999***********************************976 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 ?    5.8   0.0     0.039        12      18      39 ..     207     228 ..     201     243 .. 0.76
   2 ?    5.3   0.0     0.055        16      19      39 ..     483     503 ..     476     508 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.039
                            AAA_29  18 eidlkgatlltGpsGsGKSTll 39 
                                        id+   +ll Gp G+GK+ + 
  gi|488600948|ref|YP_007907419.1| 207 GIDPPKGVLLYGPPGTGKTLIA 228
                                       4444444***********8665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.055
                            AAA_29  19 idlkgatlltGpsGsGKSTll 39 
                                       i++   +ll Gp G+GK+ l 
  gi|488600948|ref|YP_007907419.1| 483 IKPPKGILLYGPPGTGKTLLA 503
                                       4443449**********8765 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.066        20       4      33 ..     214     243 ..     212     268 .. 0.89
   2 ?   -1.5   0.0       6.6     2e+03      62      84 ..     382     404 ..     355     435 .. 0.60
   3 ?    4.1   0.0      0.12        37       4      33 ..     489     518 ..     487     547 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.066
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL G + +GK+ +a+a+ + +d+ ++ l 
  gi|488600948|ref|YP_007907419.1| 214 VLLYGPPGTGKTLIAKAVANEVDAHFITLS 243
                                       89*********************9999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.6
                                       -HHHHHHHHHHHHHHHHHHHTT- CS
                               CPT  62 gpeldlllaalyeavaamaraGn 84 
                                         +  l+ +a ++a++ m+++G+
  gi|488600948|ref|YP_007907419.1| 382 ADLEALAKEAAMHAIRKMLETGK 404
                                       44445666788888888888885 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.12
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       ilL G + +GK+ la+a+ + +++ ++ ++
  gi|488600948|ref|YP_007907419.1| 489 ILLYGPPGTGKTLLAKAVANESNANFISVK 518
                                       89******************9999998876 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.074        22      60      79 ..     209     228 ..     193     250 .. 0.87
   2 ?    5.7   0.0      0.02       5.9      57      79 ..     481     503 ..     452     510 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.074
                       AFG1_ATPase  60 epvrglYlwGgvGrGKtylm 79 
                                        p++g+ l+G+ G GKt + 
  gi|488600948|ref|YP_007907419.1| 209 DPPKGVLLYGPPGTGKTLIA 228
                                       79***************875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                       AFG1_ATPase  57 ksvepvrglYlwGgvGrGKtylm 79 
                                        + +p++g+ l+G+ G GKt l 
  gi|488600948|ref|YP_007907419.1| 481 INIKPPKGILLYGPPGTGKTLLA 503
                                       4678****************985 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.067        20       5      32 ..     215     242 ..     212     244 .. 0.88
   2 ?    5.3   0.0     0.038        11       5      31 ..     490     516 ..     487     519 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.067
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       l++G+ +tGKt  a ++a+e  a  i+l
  gi|488600948|ref|YP_007907419.1| 215 LLYGPPGTGKTLIAKAVANEVDAHFITL 242
                                       89****************9988777765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.038
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++G+ +tGKt  a ++a+e  a  i+
  gi|488600948|ref|YP_007907419.1| 490 LLYGPPGTGKTLLAKAVANESNANFIS 516
                                       89*****************99998887 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0       0.1        30      13      47 ..     202     236 ..     199     243 .. 0.82
   2 ?    5.5   0.0     0.026       7.9      14      44 ..     478     508 ..     473     517 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
                                       H......HCTS-EEEEESTTSSCHHHHHHHHHHCH CS
                              PIF1  13 iieavlnekgklfFvtGsgGtgKtflwkallkklr 47 
                                       i ++v  + +k + ++G  GtgKt + ka+ + + 
  gi|488600948|ref|YP_007907419.1| 202 IFQQVGIDPPKGVLLYGPPGTGKTLIAKAVANEVD 236
                                       556666677888999*************9998775 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.026
                                       ......HCTS-EEEEESTTSSCHHHHHHHHH CS
                              PIF1  14 ieavlnekgklfFvtGsgGtgKtflwkallk 44 
                                        +a++ + +k + ++G  GtgKt l ka+ +
  gi|488600948|ref|YP_007907419.1| 478 FKAINIKPPKGILLYGPPGTGKTLLAKAVAN 508
                                       56677788999**************999876 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       7.5   2.3e+03      13      46 ..     419     448 ..     390     475 .. 0.65
   2 ?   -0.9   0.0       6.9   2.1e+03      17      54 ..     570     604 ..     560     607 .. 0.65
   3 ?    9.0   0.1    0.0057       1.7      15      65 ..     678     728 ..     655     728 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 7.5
                                       TS---HHHHHHHHHHTT-E.EESSTTCEEEE--T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  13 GidlseeeiikiLkrlgceriekdkdlllVtvPs 46 
                                        i++++e+  + Lk+++         ++lV+vP+
  gi|488600948|ref|YP_007907419.1| 419 EIKVTREDFLEALKNIEPS----AMREVLVEVPN 448
                                       3555556666666655433....34455566665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 6.9
                                       -HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  17 seeeiikiLkrlgceriekdkdlllVtvPswRsDlere 54 
                                       +e  + ++L++l+    +++ + + V   + R+D++++
  gi|488600948|ref|YP_007907419.1| 570 TERVVSQLLTELDG---LEELKDVVVIAATNRPDIVDP 604
                                       55556666666654...2333445666777799*9986 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0057
                                       ---HHHHHHHHHHTT-E.EESSTTCEEEE--TT.-TT--SHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                                B5  15 dlseeeiikiLkrlgceriekdkdlllVtvPsw.RsDlereeDliEEvaRly 65 
                                        ls+eei k+ k+++++r ++ ++ ++   Ps   +Dler+  ++E+   +y
  gi|488600948|ref|YP_007907419.1| 678 GLSKEEISKVAKEIKVTR-KHFEKAMEKIKPSLtNEDLERYKKIVEDFHKMY 728
                                       589**************9.66666666666665379***********98877 PP

>> 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 ?    6.0   0.1     0.035        10      39      60 ..      22      44 ..      19      49 .. 0.77
   2 ?    2.8   0.2      0.36   1.1e+02      15      36 ..     679     700 ..     674     708 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.035
                                      TTSHHH.HCCT--TTSEEEEEEE CS
                    RNA_pol_Rpb5_C 39 ksDpva.rylglkkGdvvkItrk 60
                                      + Dp +   +++++Gdv++I+ k
  gi|488600948|ref|YP_007907419.1| 22 RIDPEVmDRYDIQSGDVIEIIGK 44
                                      5677443889**********977 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.36
                                       E-HHHHHHHHHHTT--TTCSS- CS
                    RNA_pol_Rpb5_C  15 lseeekkellkklkikeeqLPk 36 
                                       ls+ee+ ++ k++k++++++ k
  gi|488600948|ref|YP_007907419.1| 679 LSKEEISKVAKEIKVTRKHFEK 700
                                       89***************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (729 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); 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: 0.98u 0.35s 00:00:01.33 Elapsed: 00:00:00.53
# Mc/sec: 4113.78
//
Query:       gi|488600949|ref|YP_007907420.1|  [L=223]
Description: transcriptional regulator, ArsR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-18   65.1   0.2    2.5e-15   56.1   0.2    2.4  2  HTH_5            Bacterial regulatory protein, arsR family
    3.6e-14   52.5   0.0    4.7e-10   39.4   0.0    2.3  2  HTH_20           Helix-turn-helix domain
      2e-12   46.8   0.6    4.4e-06   26.5   0.0    2.7  2  TrmB             Sugar-specific transcriptional regulator Trm
    3.3e-10   39.7   0.2    0.00037   20.3   0.0    2.5  2  MarR_2           MarR family
    8.6e-10   38.0   0.6    0.00046   19.7   0.1    3.2  2  HTH_24           Winged helix-turn-helix DNA-binding
    3.6e-07   30.4   0.0      0.019   15.3   0.0    2.3  2  Rrf2             Transcriptional regulator
    7.5e-07   28.6   0.0    4.6e-05   22.9   0.0    2.5  2  HTH_47           winged helix-turn-helix
    8.3e-07   28.7   0.3      0.022   14.5   0.1    2.5  2  LexA_DNA_bind    LexA DNA binding domain
    2.1e-06   27.4   0.1    0.00023   20.8   0.0    2.2  2  DDRGK            DDRGK domain
    3.1e-05   24.4   0.1      0.008   16.7   0.0    2.3  2  HTH_27           Winged helix DNA-binding domain
    3.5e-05   23.6   0.3      0.055   13.2   0.0    2.8  4  DUF4423          Domain of unknown function (DUF4423)
    5.3e-05   23.1   0.0    0.00045   20.1   0.0    2.1  2  MarR             MarR family
    0.00011   22.2   0.1       0.68   10.1   0.0    2.4  2  DUF2250          Uncharacterized protein conserved in archaea
    0.00019   21.8   0.1        1.7    9.0   0.0    3.1  3  Penicillinase_R  Penicillinase repressor
    0.00025   21.2   0.0      0.045   13.9   0.0    2.3  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00041   20.3   0.0        1.2    9.2   0.0    2.4  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00048   19.9   0.3       0.25   11.2   0.0    3.6  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    0.00059   19.9   0.0      0.011   15.9   0.0    2.5  2  DprA_WH          DprA winged helix domain
     0.0012   18.7   0.1      0.095   12.7   0.1    3.4  3  PadR             Transcriptional regulator PadR-like family
     0.0023   17.6   0.1       0.62    9.8   0.0    2.7  2  TFA2_Winged_2    TFA2 Winged helix domain 2
      0.003   17.6   0.0        3.1    8.0   0.0    2.5  2  FeoC             FeoC like transcriptional regulator
     0.0032   17.3   1.6        1.6    8.6   0.1    2.5  2  TFIIE_alpha      TFIIE alpha subunit
     0.0037   17.4   0.1          2    8.7   0.0    2.3  2  PaaX             PaaX-like protein
      0.004   16.4   0.0       0.63    9.2   0.0    2.1  2  DDE_Tnp_2        Archaeal putative transposase ISC1217
      0.006   16.5   2.5      0.011   15.7   0.2    2.2  2  BLACT_WH         Beta-lactamase associated winged helix domai
     0.0075   16.5   0.1        5.7    7.2   0.0    2.4  2  AlkA_N           AlkA N-terminal domain
     0.0076   15.4   0.1     0.0094   15.1   0.1    1.3  1  RE_HaeIII        HaeIII restriction endonuclease
     0.0076   16.0   0.0        0.4   10.5   0.0    2.6  2  FtsK_gamma       Ftsk gamma domain
     0.0098   15.5   0.1       0.08   12.6   0.0    2.4  3  GntR             Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
       0.02   15.6   0.0       0.49   11.1   0.0    2.3  2  RPA_C            Replication protein A C terminal
      0.022   14.6   0.0        8.8    6.2   0.0    2.3  2  DUF742           Protein of unknown function (DUF742)
      0.026   14.1   0.2        4.4    6.9   0.0    2.7  3  ArsR             ArsR transcriptional regulator
      0.027   15.0   1.0      0.063   13.8   0.9    1.9  1  AF0941-like      AF0941-like
       0.03   14.1   0.0        2.5    8.0   0.0    2.5  2  HTH_IclR         IclR helix-turn-helix domain
      0.032   14.2   0.3         10    6.2   0.0    2.7  2  HTH_11           HTH domain
      0.038   14.0   0.0         13    5.9   0.0    2.5  2  HTH_45           Winged helix-turn-helix
      0.049   13.8   0.1       0.19   11.9   0.0    2.1  1  HTH_28           Helix-turn-helix domain
      0.058   13.0   0.0       0.88    9.2   0.1    2.3  2  RP-C             Replication protein C N-terminal domain
      0.066   12.5   0.0      0.088   12.1   0.0    1.2  1  DUF2235          Uncharacterized alpha/beta hydrolase domain 
      0.075   13.0   0.1          3    7.9   0.0    2.6  2  HTH_36           Helix-turn-helix domain
      0.081   13.0   0.1        4.9    7.3   0.0    2.4  2  HTH_29           Winged helix-turn helix
       0.09   12.7   0.2        3.6    7.6   0.0    2.8  3  TBPIP            TBPIP/Hop2 winged helix domain
      0.097   13.1   0.1          3    8.4   0.1    2.9  2  HTH_40           Helix-turn-helix domain
       0.11   12.4   0.7       0.29   11.0   0.7    1.7  1  HSBP1            Heat shock factor binding protein 1
       0.13   12.1   0.8        4.4    7.2   0.1    2.5  2  IF2_N            Translation initiation factor IF-2, N-termin


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 !   56.1   0.2   6.2e-18   2.5e-15       2      47 .]      13      58 ..      12      58 .. 0.96
   2 ?    6.9   0.0     0.014       5.5       8      46 ..     171     209 ..     168     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 6.2e-18
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                        R++IL+lLa+++++v+e++ +l++ + +v +HL kL++aGL+++
  gi|488600949|ref|YP_007907420.1| 13 DSRRRILSLLAKKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKS 58
                                      57*****************************************985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                                       HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   8 LklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       L  L++g +++ e+aee+gl+   v     +L++ G+V+
  gi|488600949|ref|YP_007907420.1| 171 LLGLSKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIVR 209
                                       66699****************999999999999999996 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.2e-12   4.7e-10       2      56 ..       5      58 ..       4      63 .. 0.95
   2 !   10.9   0.0    0.0009      0.36      16      56 ..     171     210 ..     154     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.2e-12
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +i+eAL++ +Rrril++L  +++  +se+  +l ++++ +  HL++Le+agL+++
  gi|488600949|ref|YP_007907420.1|  5 TILEALGNDSRRRILSLL-AKKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKS 58
                                      699***************.**********************************86 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0009
                                       HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56 
                                       l  L ++++++a e+ae+++l+ +++ + ++ L   g+v+ 
  gi|488600949|ref|YP_007907420.1| 171 LLGL-SKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIVRE 210
                                       5557.899*************************99**9986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.6e-06    0.0022      16      66 ..      20      70 ..      18      72 .. 0.93
   2 !   26.5   0.0   1.1e-08   4.4e-06      18      55 ..     172     211 ..     165     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.6e-06
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                       Ll+++p  ++ei+ +l+     v e L++Le++Gl++  +  +++Y +++
  gi|488600949|ref|YP_007907420.1| 20 SLLAKKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKSFEDGRRRYYYIN 70
                                      79***************************************9999998875 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1.1e-08
                                       H..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  18 l..klgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                                       l  ++g  +a eiaee g+p++ v +++++L++kG+V+ +
  gi|488600949|ref|YP_007907420.1| 172 LglSKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIVREV 211
                                       44489********************************876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.3e-07   0.00037       6      61 ..      14      63 ..       6      65 .. 0.85
   2 !   17.0   0.0     1e-05    0.0041      12      55 ..     172     212 ..     167     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.3e-07
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      + +r+L  L+  p   + v+e+  +l++ + av  +l++L++aGL+   +   D+R
  gi|488600949|ref|YP_007907420.1| 14 SRRRILSLLAKKP---CYVSEISFALKMAPKAVIEHLEKLEKAGLIKSFE---DGR 63
                                      5678888898888...9*****************************7553...344 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1e-05
                                       HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       + L  + g + ++ e+a+++gl+   v ++++rL  +G v+++ 
  gi|488600949|ref|YP_007907420.1| 172 LGL--SKGAR-SAVEIAEEFGLPYTEVEKAIERLKNKGIVREVM 212
                                       444..44443.******************************984 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   0.1   1.2e-06   0.00046       2      48 .]      12      57 ..      11      57 .. 0.92
   2 !   14.6   0.0   4.4e-05     0.017      19      48 .]     180     209 ..     173     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-06
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++ +r+IL+lL k+p +  +e++ +l + p +v ++l++Le++GlIk
  gi|488600949|ref|YP_007907420.1| 12 NDSRRRILSLLAKKP-CYVSEISFALKMAPKAVIEHLEKLEKAGLIK 57
                                      68899********77.5589**************************8 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.4e-05
                            HTH_24  19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       s  e+Ae+ gl+ + v + ++rL+++G+++
  gi|488600949|ref|YP_007907420.1| 180 SAVEIAEEFGLPYTEVEKAIERLKNKGIVR 209
                                       567*************************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0    0.0003      0.12      23      58 ..      24      59 ..      17      72 .. 0.87
   2 !   15.3   0.0   4.7e-05     0.019      26      57 ..     179     210 ..     167     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0003
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      ++p+ ++ei+   ++ p+ +   l+kL+kagl+ks 
  gi|488600949|ref|YP_007907420.1| 24 KKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKSF 59
                                      346889****************************96 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.7e-05
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2  26 vsseeiaerqnispsylekilakLrkaglvks 57 
                                        s+ eiae+++++ + +ek +++L+++g+v+ 
  gi|488600949|ref|YP_007907420.1| 179 RSAVEIAEEFGLPYTEVEKAIERLKNKGIVRE 210
                                       4889**************************86 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.19        76      51      77 ..      31      57 ..      28      58 .. 0.87
   2 !   22.9   0.0   1.2e-07   4.6e-05      37      77 ..     169     209 ..     158     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.19
                                      HHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 51 diAeriglpfdrvaaiaraLaeaglla 77
                                      +i+  +++  ++v++ +++L++agl++
  gi|488600949|ref|YP_007907420.1| 31 EISFALKMAPKAVIEHLEKLEKAGLIK 57
                                      56677899999**************97 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.2e-07
                                       HHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47  37 lwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77 
                                       + +L l+ G+rs ++iAe+ glp  +v++++++L+++g+++
  gi|488600949|ref|YP_007907420.1| 169 IVLLGLSKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIVR 209
                                       67899*********************************997 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.6e-05     0.022      28      58 ..      29      58 ..      16      65 .. 0.86
   2 !   11.8   0.0   0.00039      0.15      27      58 ..     180     210 ..     177     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.6e-05
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyier 58
                                      + ei+ al+++ p+av ehL++Le+ G+i+ 
  gi|488600949|ref|YP_007907420.1| 29 VSEISFALKMA-PKAVIEHLEKLEKAGLIKS 58
                                      789*******9.*****************85 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00039
                                       -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind  27 sireiaralglkSpsaveehLkaLerKGyier 58 
                                       s  eia+++gl     ve+  ++L++KG+++ 
  gi|488600949|ref|YP_007907420.1| 180 SAVEIAEEFGLP-YTEVEKAIERLKNKGIVRE 210
                                       6679*******9.778*************984 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   5.7e-07   0.00023     110     159 ..      23      72 ..      13      78 .. 0.94
   2 ?    4.7   0.0     0.051        20     117     151 ..     182     215 ..     128     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.7e-07
                                       H-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---X CS
                             DDRGK 110 ekKvvlleelavkfklktqevierikeLeeqgsltGvlDdrGkyiyitde 159
                                        kK + + e+++ +k+  + vie +++Le+ g ++   D r +y yi ++
  gi|488600949|ref|YP_007907420.1|  23 AKKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKSFEDGRRRYYYINQN 72 
                                       68999******************************************986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.051
                                       HHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT- CS
                             DDRGK 117 eelavkfklktqevierikeLeeqgsltGvlDdrG 151
                                        e+a +f+l  +ev + i+ L+++g +  v+ d G
  gi|488600949|ref|YP_007907420.1| 182 VEIAEEFGLPYTEVEKAIERLKNKGIVREVMRD-G 215
                                       699**********************99999866.5 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 !   16.7   0.0     2e-05     0.008      22      61 ..      30      66 ..      16      74 .. 0.86
   2 ?    5.5   0.0      0.06        24      21      50 ..     181     210 ..     167     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-05
                            HTH_27 22 adlcgrlnvedshisyslkkLtekGLvertgdeadrrekr 61
                                      ++++++l++   ++++ l+kL+++GL+++ +d   +r++ 
  gi|488600949|ref|YP_007907420.1| 30 SEISFALKMAPKAVIEHLEKLEKAGLIKSFED---GRRRY 66
                                      79*************************77755...55544 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.06
                            HTH_27  21 ladlcgrlnvedshisyslkkLtekGLver 50 
                                       + ++++   + ++ + +++++L +kG v +
  gi|488600949|ref|YP_007907420.1| 181 AVEIAEEFGLPYTEVEKAIERLKNKGIVRE 210
                                       568889999999**************9943 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0064       2.5      39      76 ..      29      64 ..      16     104 .. 0.78
   2 ?   -1.4   0.0       4.2   1.7e+03     122     146 ..      87     111 ..      68     129 .. 0.63
   3 ?   -1.3   0.0       3.8   1.5e+03     131     151 ..     144     164 ..     108     171 .. 0.66
   4 !   13.2   0.0   0.00014     0.055      25      75 ..     169     216 ..     145     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0064
                           DUF4423 39 peelakrlrpkisaeevekalefLlklgllkkdedgky 76
                                      ++e++ +l+  +  + v + le L+k+gl+k  edg+ 
  gi|488600949|ref|YP_007907420.1| 29 VSEISFALK--MAPKAVIEHLEKLEKAGLIKSFEDGRR 64
                                      678888888..9999999*************9999753 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.2
                           DUF4423 122 ltlaiskedyekikkeirefrkkil 146
                                        +++  + d++k+ ke r++  +i+
  gi|488600949|ref|YP_007907420.1|  87 SVISREAPDLDKAIKEARRLFDEIN 111
                                       4444444444555555554444444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.8
                           DUF4423 131 yekikkeirefrkkilaiaee 151
                                       + k++++ ++f  ++ +++e 
  gi|488600949|ref|YP_007907420.1| 144 FSKFSEMFERFLDEVERFVED 164
                                       455666666666666666655 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00014
                           DUF4423  25 virellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkded.gk 75 
                                       ++  ll l +++++  e+a+ ++  ++  eveka+e+L++ g++++    gk
  gi|488600949|ref|YP_007907420.1| 169 IV--LLGLSKGARSAVEIAEEFG--LPYTEVEKAIERLKNKGIVREVMRdGK 216
                                       44..58999999***********..******************998755455 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.1e-06   0.00045      12      50 ..      21      59 ..      14      63 .. 0.88
   2 ?    0.1   0.0       1.9   7.7e+02      19      48 ..     180     209 ..     174     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-06
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      l  + p++vse+  +l++ + +v + l +Lek+Gli++ 
  gi|488600949|ref|YP_007907420.1| 21 LLAKKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKSF 59
                                      445689******************************976 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.9
                                       EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  19 svseLakklgvskstvtrvldrLekkGlie 48 
                                       s  e+a+ +g+  + v +++ rL  kG ++
  gi|488600949|ref|YP_007907420.1| 180 SAVEIAEEFGLPYTEVEKAIERLKNKGIVR 209
                                       566899999999999999999999999886 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 !   10.1   0.0    0.0017      0.68      21      56 ..      25      60 ..       8      71 .. 0.83
   2 !    9.8   0.0    0.0022      0.86      25      56 ..     181     212 ..     160     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                           DUF2250 21 nvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      ++ Y   i+  l++  + v e l+kLe++GL++  e
  gi|488600949|ref|YP_007907420.1| 25 KPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKSFE 60
                                      57788999999*********************9765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0022
                           DUF2250  25 aksiakeleipleevrellkkLeelGLlerve 56 
                                       a  ia+e+ +p +ev++++++L++ G++ +v 
  gi|488600949|ref|YP_007907420.1| 181 AVEIAEEFGLPYTEVEKAIERLKNKGIVREVM 212
                                       56799***********************9985 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0042       1.7      23      67 ..      32      72 ..      16     102 .. 0.80
   2 ?    1.7   0.1      0.79   3.2e+02      61     109 ..     122     169 ..     117     172 .. 0.77
   3 ?    7.4   0.0     0.013       5.3      26      60 ..     183     217 ..     175     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0042
                                      HHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE---- CS
                   Penicillinase_R 23 vveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvs 67
                                      +  +l    ++a++ V   l++L+k gl+++ ++gr+  Y+ +++
  gi|488600949|ref|YP_007907420.1| 32 ISFAL----KMAPKAVIEHLEKLEKAGLIKSFEDGRRRYYYINQN 72
                                      44433....456999999*******************99987665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.79
                                       EEE----XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                   Penicillinase_R  61 iYsplvseeeavasavkqlldklfegsvkelvaafveee.klseddleeL 109
                                       iY+ l++ +ea++++  +++++++ ++++e+  +f++e     edd+e++
  gi|488600949|ref|YP_007907420.1| 122 IYRNLMNLREAQERF--SMIQNYIFSKFSEMFERFLDEVeRFVEDDYERI 169
                                       677777777777666..5788888899********999767778887765 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.013
                                       T--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
                   Penicillinase_R  26 eleeekelaysTVktllrrLvkKgllsrekegraf 60 
                                       e++ee  l y+ V   ++rL +Kg++++     +f
  gi|488600949|ref|YP_007907420.1| 183 EIAEEFGLPYTEVEKAIERLKNKGIVREVMRDGKF 217
                                       466777888*****************987665555 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 !   13.9   0.0   0.00011     0.045      19      53 ..      23      57 ..      16      62 .. 0.86
   2 ?    5.0   0.0     0.071        28      19      53 ..     175     209 ..     163     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00011
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                       kk+  +++++ +L+ +p  V e l+kLek+G+++
  gi|488600949|ref|YP_007907420.1| 23 AKKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIK 57
                                      57788899************************986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.071
                                       HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53 
                                       +k+  +  ++ae+ +     V + +++L+++G v 
  gi|488600949|ref|YP_007907420.1| 175 SKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIVR 209
                                       566667789***********************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 !    9.2   0.0    0.0029       1.2      25      55 ..      30      63 ..       3      73 .. 0.78
   2 !    8.9   0.0    0.0038       1.5      26      53 ..     183     211 ..     170     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0029
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TE CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis..r.gr 55
                                       e++  l + +  v   l +L+++gli+    gr
  gi|488600949|ref|YP_007907420.1| 30 SEISFALKMAPKAVIEHLEKLEKAGLIKsfEdGR 63
                                      68888999********************752343 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0038
                                       HHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                         HTH_Crp_2  26 elAsmlGltretvsrilseLkreglis.r 53 
                                       e+A+  Gl    v +++ +Lk++g+++  
  gi|488600949|ref|YP_007907420.1| 183 EIAEEFGLPYTEVEKAIERLKNKGIVReV 211
                                       8************************9952 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.13        53       6      41 ..      16      50 ..       4      51 .. 0.50
   2 !   11.2   0.0   0.00064      0.25      16      42 .]     177     203 ..     171     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      r+IL++L + +   ++e++ ++ +++ +v++ +++L
  gi|488600949|ref|YP_007907420.1| 16 RRILSLLAKKP-CYVSEISFALKMAPKAVIEHLEKL 50
                                      34444443332.234555555666666665555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00064
                     HTH_AsnC-type  16 aRisyaeLAervGlSestvlrRvrrLe 42 
                                       + +s  e+Ae+ Gl  ++v + ++rL+
  gi|488600949|ref|YP_007907420.1| 177 GARSAVEIAEEFGLPYTEVEKAIERLK 203
                                       67899********************95 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-05     0.011      11      57 ..      12      58 ..       2      62 .. 0.92
   2 ?    1.1   0.0       1.1   4.3e+02      11      42 ..     164     195 ..     160     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-05
                           DprA_WH 11 ddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                       d +rr+L++L+  P+ v +++ ++ + + +v  +L  LE aGl+++
  gi|488600949|ref|YP_007907420.1| 12 NDSRRRILSLLAKKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKS 58
                                      589*****************************************986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.1
                           DprA_WH  11 ddlerrvLaaLgpePvhvDqLvrrtglpaaev 42 
                                       dd er vL  L+  +++  +++++ glp  ev
  gi|488600949|ref|YP_007907420.1| 164 DDYERIVLLGLSKGARSAVEIAEEFGLPYTEV 195
                                       5667888899999999999*********9888 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   0.00024     0.095       1      68 [.      18      72 ..      18      78 .. 0.76
   2 ?    0.1   0.0         2   7.9e+02      31      44 ..     119     132 ..     104     133 .. 0.76
   3 ?   -0.5   0.0       3.1   1.2e+03      31      49 ..     192     210 ..     179     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00024
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHC CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTda 68
                                      iL+ll+++p y  ei  +l+   +         +   L++Lek gl++s ++     ++r+yY ++++
  gi|488600949|ref|YP_007907420.1| 18 ILSLLAKKPCYVSEISFALKMAPK--------AVIEHLEKLEKAGLIKSFED-----GRRRYYYINQN 72
                                      677777777777777777777733........35578************976.....58999999986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHT CS
                              PadR  31 eGslYpaLkrLeke 44 
                                        + +Y++L+ L++ 
  gi|488600949|ref|YP_007907420.1| 119 ISDIYRNLMNLREA 132
                                       5679******9875 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHTTSEEE CS
                              PadR  31 eGslYpaLkrLekeglves 49 
                                       ++++ +a +rL+++g+v +
  gi|488600949|ref|YP_007907420.1| 192 YTEVEKAIERLKNKGIVRE 210
                                       5556678899999999976 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0016      0.62      24      61 .]      36      70 ..      13      70 .. 0.82
   2 ?    4.9   0.0     0.053        21      28      48 ..     192     213 ..     192     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                     TFA2_Winged_2 24 LkdswpdveealeeLeaegeilvlrtkkdgqpkiVfwN 61
                                      Lk +++ v e+le+Le+ g i       dg+ ++ + N
  gi|488600949|ref|YP_007907420.1| 36 LKMAPKAVIEHLEKLEKAGLIKSF---EDGRRRYYYIN 70
                                      788999**************9999...88899999987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.053
                     TFA2_Winged_2  28 wpdveealeeLeaegei.lvlr 48 
                                       +  ve+a+e L+++g +  v+r
  gi|488600949|ref|YP_007907420.1| 192 YTEVEKAIERLKNKGIVrEVMR 213
                                       6789*********998866664 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0077       3.1      12      46 ..      24      58 ..      20      64 .. 0.87
   2 ?    7.1   0.0     0.014       5.5      13      50 ..     177     214 ..     174     223 .] 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0077
                              FeoC 12 rgrvslkeLsrhfkaspealeamLeqwvrkGrvek 46
                                      ++   ++e+s ++k+ p+a+   Le +++ G ++ 
  gi|488600949|ref|YP_007907420.1| 24 KKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKS 58
                                      6677789**********************999876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                              FeoC  13 grvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50 
                                       g  s  e++ +f    + +e+ +e +  kG v++v ++
  gi|488600949|ref|YP_007907420.1| 177 GARSAVEIAEEFGLPYTEVEKAIERLKNKGIVREVMRD 214
                                       556889***************************99776 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0077       3.1      12      59 ..      12      58 ..       3     102 .. 0.77
   2 !    8.6   0.1     0.004       1.6       8      61 ..     159     212 ..     153     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0077
                                      -HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                       TFIIE_alpha 12 geeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvky 59
                                      +++   +l  L++k +    +++  lk+ ++ + + L +L +a+l+k 
  gi|488600949|ref|YP_007907420.1| 12 NDSRRRILSLLAKKPCYV-SEISFALKMAPKAVIEHLEKLEKAGLIKS 58
                                      366778888888777766.57*************************84 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.004
                                       HHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEE CS
                       TFIIE_alpha   8 rkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykr 61 
                                        +f +++   ++   l+kg  +  ++a+e ++  +e+ k++ rL+++++v  ++
  gi|488600949|ref|YP_007907420.1| 159 ERFVEDDYERIVLLGLSKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIVREVM 212
                                       556666666666666679999999************************998666 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.025        10      44      65 ..      47      68 ..      35      72 .. 0.87
   2 !    8.7   0.0    0.0051         2      24      55 ..     179     210 ..     173     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.025
                              PaaX 44 lsRlakaGwlvrekegrrsfYr 65
                                      l  l+kaG++++ ++grr +Y 
  gi|488600949|ref|YP_007907420.1| 47 LEKLEKAGLIKSFEDGRRRYYY 68
                                      6789*************99995 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0051
                              PaaX  24 gsLirllaelGiseslvRaalsRlakaGwlvr 55 
                                       +s +++ +e+G+  + v  a+ Rl+++G +++
  gi|488600949|ref|YP_007907420.1| 179 RSAVEIAEEFGLPYTEVEKAIERLKNKGIVRE 210
                                       6779************************9875 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 ?    5.2   0.0     0.026        10      45      75 ..      28      58 ..       4      62 .. 0.81
   2 !    9.2   0.0    0.0016      0.63      13      74 ..     146     209 ..     133     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.026
                         DDE_Tnp_2 45 rateiaqeveldyetvlknldklanidllev 75
                                        +ei+ ++++  ++v++ l+kl+++ l++ 
  gi|488600949|ref|YP_007907420.1| 28 YVSEISFALKMAPKAVIEHLEKLEKAGLIKS 58
                                      468***********************99986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                         DDE_Tnp_2  13 alekaiqelilaltglrkdvavrlvlgaviGgrat..eiaqeveldyetvlknldklanidlle 74 
                                        + ++ ++ + +++    d   r+vl ++  g  +  eia e+ l y +v k++++l+n  +++
  gi|488600949|ref|YP_007907420.1| 146 KFSEMFERFLDEVERFVEDDYERIVLLGLSKGARSavEIAEEFGLPYTEVEKAIERLKNKGIVR 209
                                       3566666666666777778888999988875433335*********************987654 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   2.8e-05     0.011      19      43 ..      37      61 ..      35      65 .. 0.85
   2 ?    0.4   0.2       1.7   6.7e+02      29      44 ..     199     214 ..     194     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-05
                          BLACT_WH 19 paAergvlahLeKLeeeGkVkregd 43
                                      ++A + v+ hLeKLe+ G++k+ +d
  gi|488600949|ref|YP_007907420.1| 37 KMAPKAVIEHLEKLEKAGLIKSFED 61
                                      789999**************98554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                          BLACT_WH  29 LeKLeeeGkVkregdk 44 
                                        e+L++ G V++++ +
  gi|488600949|ref|YP_007907420.1| 199 IERLKNKGIVREVMRD 214
                                       689********99865 PP

>> AlkA_N  AlkA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.014       5.7      45      83 ..      72     108 ..      30     111 .. 0.76
   2 ?    7.1   0.0     0.016       6.2      21      58 ..     152     189 ..     139     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
                            AlkA_N  45 kGvvevrhepeksalkvrlslsdlraleaviarvrrllD 83 
                                       +  vev+ +p  ++++ ++ + ++++l+++i++ rrl+D
  gi|488600949|ref|YP_007907420.1|  72 NMRVEVSIAP--HMFQTSVISREAPDLDKAIKEARRLFD 108
                                       3445555555..99************************9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.016
                            AlkA_N  21 araiegvEavdedsygRtlrldgakGvvevrhepeksa 58 
                                       +r +++vE++ ed y+R + l+  kG  ++ + +e+  
  gi|488600949|ref|YP_007907420.1| 152 ERFLDEVERFVEDDYERIVLLGLSKGARSAVEIAEEFG 189
                                       58999*****************9999988888877644 PP

>> RE_HaeIII  HaeIII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.4e-05    0.0094     130     188 ..     107     165 ..      42     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                         RE_HaeIII 130 fgipcseeywnevepifdelkeekekkkkwseledkeedvyvPllkafidelerayekd 188
                                       f+    +++++++++i+  l + +e ++++s +++   + +  +++ f+de+er  e+d
  gi|488600949|ref|YP_007907420.1| 107 FDEINRSNFFRNISDIYRNLMNLREAQERFSMIQNYIFSKFSEMFERFLDEVERFVEDD 165
                                       55556679**********************************************88776 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.29   1.1e+02      40      58 ..      47      65 ..      41      70 .. 0.86
   2 !   10.5   0.0     0.001       0.4       7      51 ..     166     210 ..     162     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.29
                        FtsK_gamma 40 idqLeeeGiVgpaegskpR 58
                                      +++Le++G++ + e  ++R
  gi|488600949|ref|YP_007907420.1| 47 LEKLEKAGLIKSFEDGRRR 65
                                      699********99998887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.001
                        FtsK_gamma   7 feeavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgp 51 
                                       +e++v l +++g  S+  +  ++ + Y+   + i++L+++GiV +
  gi|488600949|ref|YP_007907420.1| 166 YERIVLLGLSKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIVRE 210
                                       78888888999999999**************************76 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.9   2.4e+03      39      64 .]       4      29 ..       2      29 .. 0.79
   2 ?   -1.0   0.0       3.5   1.4e+03      34      56 ..      36      58 ..      28      62 .. 0.71
   3 !   12.6   0.0    0.0002      0.08      29      60 ..     183     214 ..     180     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.9
                                      HHHHHHHHHHHHTTSEEEETTCEEEE CS
                              GntR 39 ttvReALrrLeaeglverrqgrGtfV 64
                                      +t+ eAL + +++ ++    ++ ++V
  gi|488600949|ref|YP_007907420.1|  4 NTILEALGNDSRRRILSLLAKKPCYV 29
                                      78999999888888888888887776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.5
                                      HTS-HHHHHHHHHHHHHTTSEEE CS
                              GntR 34 fgVsrttvReALrrLeaeglver 56
                                      ++     v e L +Le +gl+ +
  gi|488600949|ref|YP_007907420.1| 36 LKMAPKAVIEHLEKLEKAGLIKS 58
                                      55555667777999999999875 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.0002
                                       HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR  29 eLaaefgVsrttvReALrrLeaeglverrqgr 60 
                                       e+a+efg   t v +A+ rL+ +g+v    + 
  gi|488600949|ref|YP_007907420.1| 183 EIAEEFGLPYTEVEKAIERLKNKGIVREVMRD 214
                                       89************************866665 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.93   3.7e+02      70      97 ..      29      56 ..      19      62 .. 0.92
   2 ?   11.1   0.0    0.0012      0.49      71      97 ..     182     208 ..     179     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.93
                                      HHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 70 vdeiaqklrlsvndvkqavdeLsneGii 97
                                      v+ei+ +l++  + v + +++L+++G+i
  gi|488600949|ref|YP_007907420.1| 29 VSEISFALKMAPKAVIEHLEKLEKAGLI 56
                                      6899999*******************99 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0012
                                       HHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C  71 deiaqklrlsvndvkqavdeLsneGii 97 
                                        eia++++l+  +v++a++ L n+Gi+
  gi|488600949|ref|YP_007907420.1| 182 VEIAEEFGLPYTEVEKAIERLKNKGIV 208
                                       58***********************97 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.022       8.8      43      86 ..      13      57 ..       3      67 .. 0.80
   2 ?    6.1   0.0     0.024       9.4      45      85 ..     168     208 ..     155     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.022
                            DUF742 43 pehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldagllt 86
                                      + +r+il L ++ p  V e++ +lk+   +v   l  L +agl++
  gi|488600949|ref|YP_007907420.1| 13 DSRRRILSLLAKkPCYVSEISFALKMAPKAVIEHLEKLEKAGLIK 57
                                      67899***9999899*********996666655667777777766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.024
                            DUF742  45 hrailrLcreplsVaelaAelklPvgvvrvLlsdLldagll 85 
                                       +  +l L +  +s +e+a e  lP + v   +  L ++g +
  gi|488600949|ref|YP_007907420.1| 168 RIVLLGLSKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIV 208
                                       3445778888***************9988777666666665 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.011       4.4       9      58 ..       5      57 ..       1      61 [. 0.83
   2 ?   -0.2   0.0       1.7   6.7e+02      72     128 ..     101     159 ..      90     165 .. 0.66
   3 ?    4.0   0.0     0.088        35      14      58 ..     162     209 ..     155     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                              ArsR  9 pllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliE 58
                                      ++l+++++++ +++++ l k+ +  +e++  l+     v e l+ L+k++li 
  gi|488600949|ref|YP_007907420.1|  5 TILEALGNDSRRRILSLLAKKPCYVSEISFALKMApkaVIEHLEKLEKAGLIK 57
                                      699******************99999998655443225889999999999996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.7
                              ArsR  72 keYhtsYskv.qanfqcsledlsdiievafmsdeeleelvekiekeveeg.ntsisdls 128
                                       ke +  ++++ + nf  +++d+   ++     +e ++ + + i ++ +e  + ++ ++ 
  gi|488600949|ref|YP_007907420.1| 101 KEARRLFDEInRSNFFRNISDIYRNLMNLREAQERFSMIQNYIFSKFSEMfERFLDEVE 159
                                       55555666653467888888877777777777777777777777766665566666655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.088
                              ArsR  14 fdsetkkkvyeelskeWlteeeleeklg...eeveealklLkkikliE 58 
                                       ++++  + v+  lsk+  ++ e++e++g   +eve+a++ Lk+ +++ 
  gi|488600949|ref|YP_007907420.1| 162 VEDDYERIVLLGLSKGARSAVEIAEEFGlpyTEVEKAIERLKNKGIVR 209
                                       567778889999***************95555799*******999986 PP

>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   0.00016     0.063      36      90 ..     107     161 ..      81     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHCT CS
                       AF0941-like  36 ieelfrsdvedvleklkagdieeeeakknlklLkvyvvsqLdehykrvlelledk 90 
                                         e+ rs++   + +++ + ++  ea++ +++++ y+ s+ +e ++r l+ +e  
  gi|488600949|ref|YP_007907420.1| 107 FDEINRSNFFRNISDIYRNLMNLREAQERFSMIQNYIFSKFSEMFERFLDEVERF 161
                                       345667777777888889999*************************999877654 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.15        58       7      49 ..      17      57 ..       3      58 .. 0.75
   2 ?    8.0   0.0    0.0062       2.5      20      49 ..     180     209 ..     170     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.15
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +iL +la+ p    +se++ ++ +++ +v  +L  L++ G+++
  gi|488600949|ref|YP_007907420.1| 17 RILSLLAKKPC--YVSEISFALKMAPKAVIEHLEKLEKAGLIK 57
                                      35555555544..599999999999999999999999999986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0062
                                       BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  20 tlselArrtglpkStvhRlLqtLvelGyve 49 
                                       +  e+A+++glp + v   +  L + G+v+
  gi|488600949|ref|YP_007907420.1| 180 SAVEIAEEFGLPYTEVEKAIERLKNKGIVR 209
                                       567************************998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.047        19       3      44 ..      16      55 ..      14      68 .. 0.85
   2 ?    6.2   0.0     0.025        10      12      44 ..     175     207 ..     168     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.047
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      + il lL  a++p   +e++  L++  ++v  ++++Le++g+
  gi|488600949|ref|YP_007907420.1| 16 RRILSLL--AKKPCYVSEISFALKMAPKAVIEHLEKLEKAGL 55
                                      7789999..55569999***********************93 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.025
                            HTH_11  12 argpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                       ++g  s+ e+Aee+++  + v + I++L+ +g+
  gi|488600949|ref|YP_007907420.1| 175 SKGARSAVEIAEEFGLPYTEVEKAIERLKNKGI 207
                                       67778999*********************9994 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.039        16      11      51 ..      18      58 ..      16      71 .. 0.83
   2 ?    5.9   0.0     0.033        13      15      55 ..     174     216 ..     169     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.039
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikk 51
                                      IL+ + ++    ++i  +  +  k + + L++L + glik 
  gi|488600949|ref|YP_007907420.1| 18 ILSLLAKKPCYVSEISFALKMAPKAVIEHLEKLEKAGLIKS 58
                                      8888889999999**************************54 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.033
                            HTH_45  15 isegeakkTkimykanLsykllnkYLdmLvekglikk..skek 55 
                                       +s+g  +  +i  +  L y  ++k ++ L +kg++++  +++k
  gi|488600949|ref|YP_007907420.1| 174 LSKGARSAVEIAEEFGLPYTEVEKAIERLKNKGIVREvmRDGK 216
                                       667788888999999*******************954235555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00047      0.19       5      41 ..     169     207 ..     167     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00047
                            HTH_28   5 iikl.laaGh.svreaArelgisrrtvyrWikryeegGi 41 
                                       i++l l +G  s+ e+A+e+g+ ++ v + i r+   Gi
  gi|488600949|ref|YP_007907420.1| 169 IVLLgLSKGArSAVEIAEEFGLPYTEVEKAIERLKNKGI 207
                                       6666455786699********************999998 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 ?    9.2   0.1    0.0022      0.88      76     114 ..      31      68 ..       5     134 .. 0.78
   2 ?    1.8   0.0      0.42   1.7e+02      73     105 ..     180     214 ..     178     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirrDspngkRyar 114
                                       ++s al+++++++ +hl +L +aGli   +    +Ry +
  gi|488600949|ref|YP_007907420.1|  31 EISFALKMAPKAVIEHLEKLEKAGLIKSFEDG-RRRYYY 68 
                                       57899********************9654333.345544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.42
                              RP-C  73 sNaqLsralglsestlrrhlaaLveaGli..irrD 105
                                       s+ ++++++gl+ + +++ + +L + G++  ++rD
  gi|488600949|ref|YP_007907420.1| 180 SAVEIAEEFGLPYTEVEKAIERLKNKGIVreVMRD 214
                                       788999*******************9998444555 PP

>> DUF2235  Uncharacterized alpha/beta hydrolase domain (DUF2235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022     0.088      57     122 ..      95     190 ..      62     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                           DUF2235  57 llsslksaleklldgafgsgldehvveaYeflmrnyepgDe.................................Iyl 100
                                        l +  + +++l+d++  s++ +++ + Y+ lm+  e +++                                 I+l
  gi|488600949|ref|YP_007907420.1|  95 DLDKAIKEARRLFDEINRSNFFRNISDIYRNLMNLREAQERfsmiqnyifskfsemferfldeverfveddyerIVL 171
                                       3566668889999*******************999888765777777777777777777777777777777777*** PP

                           DUF2235 101 fGFSRGAytaRalagmlekvGl 122
                                       +G S+GA   R+ +++ e++Gl
  gi|488600949|ref|YP_007907420.1| 172 LGLSKGA---RSAVEIAEEFGL 190
                                       ******7...677777777777 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0075         3      29      55 .]      30      56 ..      12      56 .. 0.91
   2 ?    2.6   0.0      0.34   1.3e+02      30      55 .]     183     208 ..     170     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0075
                            HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                      + ++ +l++  + v+ ++ +Le++G+i
  gi|488600949|ref|YP_007907420.1| 30 SEISFALKMAPKAVIEHLEKLEKAGLI 56
                                      67888999999**************98 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.34
                            HTH_36  30 tlakrlglsknTvsraikeLeqlGyi 55 
                                        +a+ +gl    v +ai  L  +G++
  gi|488600949|ref|YP_007907420.1| 183 EIAEEFGLPYTEVEKAIERLKNKGIV 208
                                       589999999999***********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 ?    3.4   0.0      0.19        77       7      49 ..      22      64 ..      15      70 .. 0.76
   2 ?    7.3   0.0     0.012       4.9       4      41 ..     170     207 ..     168     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.19
                            HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfeegG.laalldrrr 49
                                      l+++ ++ vs+i  +l + ++ v  +l+  e+ G +++  d+rr
  gi|488600949|ref|YP_007907420.1| 22 LAKKPCY-VSEISFALKMAPKAVIEHLEKLEKAGlIKSFEDGRR 64
                                      4455566.999999********************4444555554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.012
                            HTH_29   4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41 
                                       +ll l++G  +  +iA+  gl ++ v ++++r  ++G+
  gi|488600949|ref|YP_007907420.1| 170 VLLGLSKGARSAVEIAEEFGLPYTEVEKAIERLKNKGI 207
                                       46666666667*************************97 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0091       3.6      15      61 ..      25      69 ..      15      70 .. 0.77
   2 ?   -1.9   0.0       8.5   3.4e+03      18      28 ..     118     128 ..     109     132 .. 0.80
   3 ?    1.9   0.0      0.53   2.1e+02      33      47 ..     193     207 ..     180     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0091
                             TBPIP 15 rPfsvqdvvanlqkklgKtavqkaLdeLvdegkiieKeyGKqkiYla 61
                                      +P  v++++ +l+  +  +av + L++L+++g+i++ e G    Y +
  gi|488600949|ref|YP_007907420.1| 25 KPCYVSEISFALK--MAPKAVIEHLEKLEKAGLIKSFEDGRRRYYYI 69
                                      5666666666664..45678999************988888777765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.5
                             TBPIP  18 svqdvvanlqk 28 
                                       +++d++ nl +
  gi|488600949|ref|YP_007907420.1| 118 NISDIYRNLMN 128
                                       78999999976 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.53
                             TBPIP  33 tavqkaLdeLvdegk 47 
                                       t v ka++ L+++g 
  gi|488600949|ref|YP_007907420.1| 193 TEVEKAIERLKNKGI 207
                                       789********9985 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0075         3       9      41 ..      22      55 ..      15     167 .. 0.88
   2 ?    1.1   0.0       1.3   5.4e+02      13      40 ..     179     206 ..     170     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0075
                            HTH_40  9 l.eeglsieeIAkerglkesTIegHLaelieege 41
                                      l ++ + + eI+   +++++ +++HL +l ++g 
  gi|488600949|ref|YP_007907420.1| 22 LaKKPCYVSEISFALKMAPKAVIEHLEKLEKAGL 55
                                      447778899********************99985 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.3
                            HTH_40  13 lsieeIAkerglkesTIegHLaelieeg 40 
                                        s  eIA+e gl  + +e+ + +l ++g
  gi|488600949|ref|YP_007907420.1| 179 RSAVEIAEEFGLPYTEVEKAIERLKNKG 206
                                       5677999999999999998888887776 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   0.00074      0.29      11      45 ..     129     164 ..     125     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00074
                             HSBP1  11 LqqlqdkFqtmsdqilsriDdMssr.iDdLEksiad 45 
                                       L + q++F+ + + i+s+  +M +r +D+ E+ ++d
  gi|488600949|ref|YP_007907420.1| 129 LREAQERFSMIQNYIFSKFSEMFERfLDEVERFVED 164
                                       6788******************88868999987765 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 ?    7.2   0.1     0.011       4.4       6      28 ..      29      50 ..      25      58 .. 0.87
   2 ?    2.7   0.1      0.28   1.1e+02       8      30 ..     183     207 ..     181     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                             IF2_N  6 VyeLAkeLgvkskevikkLfkel 28
                                      V+e+   L++ +k vi++L+k l
  gi|488600949|ref|YP_007907420.1| 29 VSEISFALKMAPKAVIEHLEK-L 50
                                      8999999************66.6 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.28
                             IF2_N   8 eLAkeLg...vkskevikkLfkelGi 30 
                                       e+A+e g   +++++ i++L k +Gi
  gi|488600949|ref|YP_007907420.1| 183 EIAEEFGlpyTEVEKAIERL-KNKGI 207
                                       89999995555566669999.55887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); 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: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1249.89
//
Query:       gi|488600950|ref|YP_007907421.1|  [L=260]
Description: putative amidohydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-29  103.4   0.0    1.5e-29  103.2   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   8.2e-34   1.5e-29      15     261 .]      15     242 ..       5     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 8.2e-34
                                       HHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEEEEEEECCTTE CS
                      CN_hydrolase  15 eanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvigliereltngk 91 
                                       e+ ++ +++li++  + g++L +lPE+f +    ++  +    +   et++++++++r+++++v++ ++ +  t+  
  gi|488600950|ref|YP_007907421.1|  15 EKSFESAKKLIDGGIEAGVELFLLPEYFSYTP--SNFNM----ERSEETIEFIKKVSREHDCIVAGNVLIK--TDEG 83 
                                       6778999******9***************844..33334....44559********************999..6665 PP

                                       EEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEEEEGGGGGSHHHHHHHHH CS
                      CN_hydrolase  92 lqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGaaiCyeigfpellralal 167
                                       +   n+   + ++g lvg++ K+h        pt+ e+el    ++  +vfd+++ ++Ga+iC +i +pe++r++al
  gi|488600950|ref|YP_007907421.1|  84 Y--MNSLH-IFDSGDLVGIQEKIH--------PTSSEKELGIIAGKeAKVFDVRGFRLGALICADILYPEICRVMAL 149
                                       5..55555.5588999********........9*******99855559***************************** PP

                                       TT-SEEEE..BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEECCSS CS
                      CN_hydrolase 168 kgaeilvn..lserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilaglgee 242
                                       k+aei++n  +s  +++   ++++ +++l  +r+++n + ++ a  +g+ + l+ ++ g S i  p G+ +   +e+
  gi|488600950|ref|YP_007907421.1| 150 KNAEIILNpvVS--FKKNSLPAKELRHCLYFTRSFDNAYAIVKAGGTGI-TFLGSETAGRSLISTPFGIEAIYSNED 223
                                       ********8755..8888899****************************.*************************** PP

                                       STEEEEEEEEHHHHHHHHH CS
                      CN_hydrolase 243 eegvliaeidladvratrr 261
                                       +e+++  +id +++r +r+
  gi|488600950|ref|YP_007907421.1| 224 SEELVSSKIDISMLRDYRK 242
                                       ***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1772.30
//
Query:       gi|488600951|ref|YP_007907422.1|  [L=335]
Description: hypothetical protein Asulf_01442 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   31.6   0.0    3.4e-07   29.9   0.0    2.0  1  Amidohydro_1  Amidohydrolase family
     0.0015   18.2   0.0     0.0024   17.5   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.09   12.3   0.0       0.15   11.6   0.0    1.2  1  Peripla_BP_4  Periplasmic binding protein domain
      0.095   11.9   0.0       0.17   11.1   0.0    1.4  1  Ribosomal_S2  Ribosomal protein S2


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 !   29.9   0.0   7.7e-11   3.4e-07       1     178 [.      45     211 ..      45     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 7.7e-11
                                       EEEE-EEEEEEECETTECSSS...GHHHHH...........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga...tledwl...........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       +++P + ++H+Hl +s  +++    le+++           + ++ +  a++  i+ a++ Gtt++ ++++ + +g+
  gi|488600951|ref|YP_007907422.1|  45 VIIPSFYNSHIHLGDSIAMDPppmELEELVgpggykfrileAEKSRVPSAIKDSIEYAVRYGTTSMTEFREGDLEGL 121
                                       689*****************9999999999*********999999999***********************999999 PP

                                       HHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHH CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealke 140
                                       +++++ +e l+     ++       g ++  ++s+ek+++g+              +++ ++     ++ l+++ ++
  gi|488600951|ref|YP_007907422.1| 122 SLIRDGFEVLA-----IF-------GRPS-TLESAEKMLEGV-------------RGFGMSSVRDHDYAFLEDLRDL 172
                                       99999999852.....22.......3334.466888888888.............566666777777788999**** PP

                                       HHHHTTEEEEEE.TSSCHHHHHHHHHHTTTEEEETTTTS CS
                      Amidohydro_1 141 akkrdlpvaiHa.letkgevedaeaafgetiehgthlev 178
                                       a+k+d ++ iHa   ++ +ve a+a  ++ i h+   + 
  gi|488600951|ref|YP_007907422.1| 173 ARKKDRMFGIHAgEKDSLDVEKAIALQPDFIVHMNMADK 211
                                       ************655666788888887777777776665 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.3e-07    0.0024      42      96 ..     182     240 ..     158     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.3e-07
                                       -BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS.....HH CS
                      Peripla_BP_2  42 vevgadgeidvEklaalkPDlvilskglgltdedeellksgiptvivessntg.....es 96 
                                       + +g  +++dvEk +al+PD ++  ++  + +++ee  ++gip +    sn++     ++
  gi|488600951|ref|YP_007907422.1| 182 IHAGEKDSLDVEKAIALQPDFIVHMNMA-DKKSIEECMDAGIPIISCMRSNFFfglenRK 240
                                       5678899*********************.**************99987777776765544 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 ?   11.6   0.0   3.3e-05      0.15      48     105 ..     192     258 ..     187     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                                       HHHHHHTT-SEEE.E--SSHHHHHHHHHHHHHTT-EEEE..........ESTT....GCTTT-CEEEEEC-HH CS
                      Peripla_BP_4  48 iedaiakgvdgii.vapvdstalapalkkakaaGIpVva..........fdsd....dapsgerlayvgfdne 105
                                       +e+aia ++d i+ ++++d     + ++++++aGIp+++                   + ++ + +++g+dn 
  gi|488600951|ref|YP_007907422.1| 192 VEKAIALQPDFIVhMNMADK----KSIEECMDAGIPIIScmrsnfffglE--NrknyRIFEEYDRWCIGTDNV 258
                                       799*******9998999996....99************966666654431..023444556666667777775 PP

>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.8e-05      0.17     136     181 ..     187     231 ..     156     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                      Ribosomal_S2 136 eknlggikkmkklPdlvvvldpkkekiavkEakklgipviaivDtn 181
                                       + +l+  k  +  Pd++v +++ + k  ++E+  +gip+i+++ +n
  gi|488600951|ref|YP_007907422.1| 187 KDSLDVEKAIALQPDFIVHMNMAD-KKSIEECMDAGIPIISCMRSN 231
                                       4556666777999*****999876.5689************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2235.41
//
Query:       gi|488600952|ref|YP_007907423.1|  [L=462]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-18   64.5   0.1    1.9e-17   63.6   0.1    1.4  1  OrfB_IS605      Probable transposase
     0.0027   17.6   0.0      0.011   15.6   0.0    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.031   14.3   0.2        3.4    7.7   0.0    2.4  2  TBPIP_N         TBP-interacting protein N-terminus
      0.033   14.6   0.0        0.2   12.1   0.0    2.0  2  RuvX            Holliday junction resolvase
      0.056   13.9   0.4       0.13   12.7   0.1    1.8  2  SUKH_6          SMI1-KNR4 cell-wall
      0.081   12.3   0.7       0.14   11.5   0.7    1.3  1  Viral_env_E26   Virus envelope protein E26


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 !   63.6   0.1   6.3e-21   1.9e-17       2     117 ..     178     298 ..     177     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 6.3e-21
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkkskn....ykka 73 
                                       i++  +++++++ +++  giDl+  n+a+ v+e+  + ++++gr l s ++++ k+ia+lqs+++  kn    y ++
  gi|488600952|ref|YP_007907423.1| 178 IVYSKPEQSEVEGKERLMGIDLNKANFAVIVVENHPTaYIIDGRGLMSLLRKYLKKIAKLQSLKDNLKNkglpYNRV 254
                                       678888888888899999***********999997666*************************************** PP

                        OrfB_IS605  74 srklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                        +++a+l++++++ ++++ hk+++ ++    ++ v +++vgn +
  gi|488600952|ref|YP_007907423.1| 255 DERIAKLWKRVRNLLRDFSHKASNLIAGLARKLKVTKIIVGNIY 298
                                       *****************************************986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.6   7.9e+03       6      24 ..     238     256 ..     237     257 .. 0.81
   2 !   15.6   0.0   3.8e-06     0.011      13      69 .]     332     389 ..     320     389 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                    OrfB_Zn_ribbon   6 eqleykakeyGikveevnp 24 
                                       + l++  k++G ++  v++
  gi|488600952|ref|YP_007907423.1| 238 QSLKDNLKNKGLPYNRVDE 256
                                       5688889999999999987 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.8e-06
                    OrfB_Zn_ribbon  13 keyGikveevnpayTS.ktCseCgsknke.....alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                            +v+e++++yTS  ++ ++ + +++     ++ +r +  +     +++DvnAa+Ni+k+
  gi|488600952|ref|YP_007907423.1| 332 G----EVVEIDERYTSgVDSVKHEYPSEDnyepwRRIKRSLFKS-VIGLINADVNAARNIIKK 389
                                       4....89*******662667777777777855554444444444.34449**********996 PP

>> TBPIP_N  TBP-interacting protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.013        40      60      91 ..     200     233 ..     141     244 .. 0.71
   2 ?    7.7   0.0    0.0012       3.4       1      54 [.     251     306 ..     251     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.013
                                       --SSEEEEEES-TT-EEEETTE..EEEEGGGHHH CS
                           TBPIP_N  60 evnnlmvvvvpdkevfyvknga..fvlalkylka 91 
                                       + +n+ v+vv ++ + y+ +g   + l  kylk 
  gi|488600952|ref|YP_007907423.1| 200 NKANFAVIVVENHPTAYIIDGRglMSLLRKYLKK 233
                                       457899************9876114556699984 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                                       HHTS-HHHHHHHHHHTT-.TTEEEEEETTEEEEEETTT--EEEE..EE-SSHHHHHH CS
                           TBPIP_N   1 yeelsekikkvytkvrtl.ddyhweiedslitgihkksnlklvi..dvakskeeadk 54 
                                       y+ ++e+i k++ +vr l  d+  +   +li g+ +k ++   i  ++  sk+e ++
  gi|488600952|ref|YP_007907423.1| 251 YNRVDERIAKLWKRVRNLlRDFS-HKASNLIAGLARKLKVTKIIvgNIYSSKNEEND 306
                                       678899**********8625665.66789******9988864442367777766555 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.52   1.5e+03      72      97 ..     235     258 ..     199     276 .. 0.78
   2 ?   12.1   0.0   6.6e-05       0.2      33      99 ..     270     343 ..     258     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.52
                                       STTHHHHHHHHHT..T-EEEEE--S- CS
                              RuvX  72 kkvrkfaeeLakrlkklpvelvDErl 97 
                                       +k +++ ++L+++  +lp   vDEr+
  gi|488600952|ref|YP_007907423.1| 235 AKLQSLKDNLKNK--GLPYNRVDERI 258
                                       4455556666666..69999999986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.6e-05
                                       ---HHHHHHHHHHHHHHTT--EEEEE------SSS---SSTTHHHHHHHHHT.........T-.EEEEE--S--- CS
                              RuvX  33 rkskekdleelkelvkeeeveeiVvGlPlnldgsegesakkvrkfaeeLakrl.......kkl.pvelvDErltt 99 
                                       r+ ++k+ + ++ l+++ +v++i+vG  ++ +++e++  + v+++ + L +         k + +v+ +DEr+t+
  gi|488600952|ref|YP_007907423.1| 270 RDFSHKASNLIAGLARKLKVTKIIVGNIYSSKNEENDLPDLVNQMFSLLPHGKvvdhlryK-FgEVVEIDERYTS 343
                                       5545677888999********************************9999776556665533.359*********9 PP

>> SUKH_6  SMI1-KNR4 cell-wall
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.7   8.1e+03      26      58 ..      23      55 ..      21      87 .. 0.56
   2 ?   12.7   0.1   4.4e-05      0.13       9      59 ..     121     171 ..     116     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                            SUKH_6 26 ynggefggnefigsseesivndaleilldegke 58
                                      yn+g++ +   +  ++   + + ++ +++  ++
  gi|488600952|ref|YP_007907423.1| 23 YNAGKMWNAANYLLMNGKASFNVFDLYNKLKDD 55
                                      555555555555555555555555444444333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.4e-05
                            SUKH_6   9 kelgvkLPedYkeflkeynggefggnefigsseesivndaleilldegkee 59 
                                       ++l++++P++++e+lkey+  + +  + +g++ +++  ++++i   +++++
  gi|488600952|ref|YP_007907423.1| 121 TKLRLSIPKQLREYLKEYGYSKKYLWIDTGIDLTRYDVRNVQITPLKYSGR 171
                                       689*******************99999999999999999999988887765 PP

>> Viral_env_E26  Virus envelope protein E26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7   4.7e-05      0.14      21     106 ..     202     290 ..     197     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
                     Viral_env_E26  21 rqlavpvgsvnslthtitsttvtsvipknyqekrqkichiisslrnthlnfnkiqsvhkkklrhlqnllr....kkn 93 
                                        ++av v      ++ i    + s++ ++y +k  k+  +   l+n  l +n+++    k  + ++nllr    k  
  gi|488600952|ref|YP_007907423.1| 202 ANFAVIVVENHPTAYIIDGRGLMSLL-RKYLKKIAKLQSLKDNLKNKGLPYNRVDERIAKLWKRVRNLLRdfshKAS 277
                                       55666666655566666666677766.5599999*********************9999999999999985555678 PP

                     Viral_env_E26  94 eiiaelvrklesa 106
                                       ++ia l rkl+ +
  gi|488600952|ref|YP_007907423.1| 278 NLIAGLARKLKVT 290
                                       99*******9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2748.45
//
Query:       gi|488600953|ref|YP_007907424.1|  [L=467]
Description: aspartate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  183.6   0.9    7.2e-54  182.9   0.1    1.7  2  AA_kinase  Amino acid kinase family
      1e-18   66.8   4.2    6.2e-10   38.7   0.0    3.0  3  ACT        ACT domain
    1.4e-18   66.4   2.4    9.4e-10   38.2   0.0    2.7  2  ACT_7      ACT domain
  ------ inclusion threshold ------
      0.022   14.7   0.2        7.5    6.6   0.1    2.6  2  ACT_6      ACT domain
       0.14   12.4   0.0       0.38   11.1   0.0    1.8  1  DUF5601    Domain of unknown function (DUF5601)


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 !  182.9   0.1     2e-57   7.2e-54       1     241 []       1     289 [.       1     289 [. 0.87
   2 ?   -1.4   0.1      0.39   1.4e+03      14      45 ..     303     331 ..     297     425 .. 0.66

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 2e-57
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH....TCCCCCHHHC.......... CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal....ksglssgelaa......... 64 
                                       +rvV+K+GG+s++d+e   + ++a+ i+++ e+ +k+vvV++  ++td l+++    +++ ss+++++         
  gi|488600953|ref|YP_007907424.1|   1 MRVVMKFGGTSVKDGES--ILHVANLIKKF-EDYEKVVVVSAMAGVTDSLIEAakkcYKEPSSSFIKLfiaeltkkh 74 
                                       79*************99..***********.999998888888**********666544444444444766665555 PP

                                       ....E..HHHHHHHHH.......................................HHHHHHHHHHHHHHHHTTHGEE CS
                         AA_kinase  65 .glrstleeagevatr.......................................dalaslgerlvaallaaglpav 101
                                        +  st                                                 d+++s+gerlva +l++++ + 
  gi|488600953|ref|YP_007907424.1|  75 yEAIST---------AvkdpqyqnkafevvdklldelekvlmgigylgeltrrseDYIVSFGERLVAPILSSAILSL 142
                                       533333.........14444444558888888999***************************************999 PP

                                       EE-GGGTCEECCCE.........HHHTTTCEEECCHHHHHHHT.T-EEEEESEEEEETTTE...EEEE-HHHHHHHH CS
                         AA_kinase 102 glsaaaldateagr.......degsdgnvesvdaeaieellea.gvvpvltgfigldeege...lgrgssDtiaall 167
                                       g+++ al+  +ag+       + + + +v+++  + +  ll   +  pv+tgfig++++g    lgrg+sD +a+l+
  gi|488600953|ref|YP_007907424.1| 143 GVDSVALTGGDAGIitdnnfgRAKPKPEVYNLINSRLDPLLRIkKTTPVITGFIGVTDDGSittLGRGGSDLTATLI 219
                                       9999999999999999987876666667777778888888855259******************************* PP

                                       HHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 168 AealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                                       A al+Ad+++++++VdGV++ dpk+vp arl+peis++ea+e    l+ +G+k++hp+a+++++r++ipv+I+n
  gi|488600953|ref|YP_007907424.1| 220 ASALNADEVWLWKEVDGVLTTDPKIVPEARLIPEISYQEAME----LSHFGAKILHPRAIEPVMRKEIPVRIKN 289
                                       ******************************************....**************************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.39
                                       CTCCHHHHHHHHHHHHHHHHTTEEEEEE--H.H CS
                         AA_kinase  14 dkeeaslrrlaeqiaalkesgnklvvVhGgg.s 45 
                                        +++   +++++ ++ +  ++  +v V+G+g  
  gi|488600953|ref|YP_007907424.1| 303 GADT--TKDIVKALSLI--EKVAIVNVSGAGfD 331
                                       5555..77777777777..55667777777642 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       2.3   8.4e+03      54      65 ..      94     105 ..      93     106 .. 0.83
   2 !   28.7   0.2   2.3e-10   8.2e-07      12      66 ..     334     382 ..     322     383 .. 0.82
   3 !   38.7   0.0   1.7e-13   6.2e-10       5      58 ..     402     449 ..     398     458 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHTT CS
                               ACT  54 dleevlealkkl 65 
                                       +++++l++l+k+
  gi|488600953|ref|YP_007907424.1|  94 VVDKLLDELEKV 105
                                       7889999*9997 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 2.3e-10
                                       THHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  12 GlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                        ++++vf+ la+  +N++++ q+ss      + ++ ivvde+d+e +  alk le
  gi|488600953|ref|YP_007907424.1| 334 EIMSDVFSRLAKEKVNVIMVAQSSS------ELNLSIVVDESDIEVAYSALKPLE 382
                                       589**********************......677777777777777777777554 PP

  == domain 3  score: 38.7 bits;  conditional E-value: 1.7e-13
                                       EEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHH CS
                               ACT   5 vgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleev 58 
                                        g+++ PG+++r+f+al+++giN+++i+q+ se+      +v ++v+ ++ +e+
  gi|488600953|ref|YP_007907424.1| 402 AGMAGTPGVAGRIFSALGKNGINVIMISQSCSEY------NVSFTVSKNEGKEA 449
                                       58999***************************65......44444444444444 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.7     7e-10   2.5e-06       4      64 ..     318     379 ..     315     380 .. 0.92
   2 !   38.2   0.0   2.6e-13   9.4e-10       5      65 .]     393     455 ..     391     455 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 7e-10
                                       EEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   4 dgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                                       + ++ ++v+g+g+  d   i++ ++s La++++++ +++   ++   +i+V+e+d+e A++aL+
  gi|488600953|ref|YP_007907424.1| 318 EKVAIVNVSGAGF--DFAEIMSDVFSRLAKEKVNVIMVAqssSELNLSIVVDESDIEVAYSALK 379
                                       5678999999988..66********************99989********************96 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 2.6e-13
                                       EEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
                             ACT_7   5 gwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                                       +++++s vg+g+++ ++G++ +++s+L ++gI++ +iS   +++  ++ V +++ ++Av++Lh+
  gi|488600953|ref|YP_007907424.1| 393 DIAVVSAVGAGMAG-TPGVAGRIFSALGKNGINVIMISqscSEYNVSFTVSKNEGKEAVRVLHR 455
                                       799*********99.***********************************************96 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0021       7.5       6      46 ..     324     366 ..     320     397 .. 0.78
   2 ?    5.5   0.0    0.0046        16      12      44 ..     407     439 ..     393     442 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                             ACT_6   6 tvtGp..drpGltasLtsvlaefgvnilDieqavihgrlsLgl 46 
                                       +v+G+  d + + ++++s+la+ +vn++ + q+  + +ls+++
  gi|488600953|ref|YP_007907424.1| 324 NVSGAgfDFAEIMSDVFSRLAKEKVNVIMVAQSSSELNLSIVV 366
                                       55544338899*********************98777777654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0046
                             ACT_6  12 rpGltasLtsvlaefgvnilDieqavihgrlsL 44 
                                        pG+  +++s+l ++g+n++ i q+  + ++s+
  gi|488600953|ref|YP_007907424.1| 407 TPGVAGRIFSALGKNGINVIMISQSCSEYNVSF 439
                                       59**********************977766665 PP

>> DUF5601  Domain of unknown function (DUF5601)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.38      37      62 ..      83     108 ..      67     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                           DUF5601  37 ktplyktvsseavedlldeiEkyimt 62 
                                       k+p y++ + e v++llde+Ek +m 
  gi|488600953|ref|YP_007907424.1|  83 KDPQYQNKAFEVVDKLLDELEKVLMG 108
                                       678*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3062.49
//
Query:       gi|488600954|ref|YP_007907425.1|  [L=693]
Description: Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-08   32.0   0.5    4.5e-07   29.8   0.3    2.2  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    2.5e-07   30.9   0.3    8.4e-07   29.2   0.3    1.9  1  S1               S1 RNA binding domain
    1.6e-06   28.4  10.4    1.6e-06   28.4  10.4    2.4  2  DnaJ_CXXCXGXG    DnaJ central domain
    0.00048   20.3   0.2    0.00093   19.4   0.2    1.4  1  DHH              DHH family
  ------ inclusion threshold ------
      0.064   13.2   0.1      0.064   13.2   0.1    3.6  3  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
       0.14   11.8   0.1       0.28   10.8   0.1    1.4  1  tRNA_anti-like   tRNA_anti-like
        2.6    5.8   5.8        4.3    5.1   5.8    1.4  1  PolC_DP2         DNA polymerase II large subunit DP2
        7.4    6.6   8.5       0.77    9.8   1.1    2.8  3  DUF2089          Protein of unknown function (DUF2089)
        9.4    6.5  16.1         14    5.9   0.8    2.4  2  PHF5             PHF5-like protein


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.1   2.1e+03      44      59 ..     151     167 ..     134     179 .. 0.80
   2 !   29.8   0.3   2.2e-10   4.5e-07       1      75 [.     207     277 ..     207     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                                       TTS-TTSEEEEE.EEEE CS
                   tRNA_anti-codon  44 enlkeGdvvrvt.Grvk 59 
                                        +l eGd v v+ G ++
  gi|488600954|ref|YP_007907425.1| 151 HTLNEGDTVTVKiGGIR 167
                                       46899****99988765 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 2.2e-10
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                       V ++G vt +  r +g+   + + D tg  ++v+f  + ++ + +++++dvvr+ G v+rr    +e+ + e+e 
  gi|488600954|ref|YP_007907425.1| 207 VEIRGLVTHV--RLTGGPTIFSVIDTTGVCKAVAFE-SGERAYPEIDVDDVVRIAGFVRRRGSI-FEIEILEMEK 277
                                       789*******..************************.************************999.9999998886 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.3   4.2e-10   8.4e-07       5      63 ..     116     166 ..     112     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.2e-10
                                       TCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEE CS
                                S1   5 gevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkv 63 
                                       + v+ G+V+ vt+ G+fV+l    +g++++++l+++        +l +Gd+v vk+ ++
  gi|488600954|ref|YP_007907425.1| 116 NRVYVGTVSVVTDLGVFVDLNKRLRGLIHRKNLHNH--------TLNEGDTVTVKIGGI 166
                                       67999*****************************98........9*********99766 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4  10.4   7.8e-10   1.6e-06       1      67 []       3      73 ..       3      73 .. 0.73
   2 !   10.5  16.1   0.00031      0.62       1      60 [.      51     108 ..      51     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.8e-10
                     DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGvvree.....qkt..lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67
                                      C++C+G+g  +  +++C  C+GsG+ ++      + +   +++++  +  C +C+GtG    + + C+ CkG+g
  gi|488600954|ref|YP_007907425.1|  3 CDNCDGRGVVEI-ERKCVICNGSGKAKSFdpkltE-EltSEQIQMFLKGICGACRGTGVQK-RMEVCPVCKGTG 73
                                      ********8433.667********75444344432.2323346777788*********965.5669******86 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00031
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkC 60 
                                       C  C+G+g  +++++ C+ CkG+G+ ++ +   g++++     C++C+ + + +  k+ C
  gi|488600954|ref|YP_007907425.1|  51 CGACRGTGV-QKRMEVCPVCKGTGKSSKCK-ICGTTIKGDYDLCQKCSKKPHAYLLKNSC 108
                                       99******8.456889********643333.26777778889999999877666555555 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   4.7e-07   0.00093       2      73 ..     336     461 ..     335     471 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.7e-07
                                       EEEE-ECSSSHHHHHHHHHHHH....................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                               DHH   2 ilivghknpDtDsigSaialan....................................................... 23 
                                       i+i   ++ D+D+i+  +al+                                                        
  gi|488600954|ref|YP_007907425.1| 336 III--RHHWDADGICGGVALETaltnlvdettsdpdakyylvkrkvsrapfyeledvvkdlddsledmvrhgdkipl 410
                                       444..7899*******9999998888888888888888888888888888887777777777777777777777777 PP

                                       .CECS--T..CGGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS- CS
                                       .xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  24 .llvDhne..ksqavegeakeeaedviiiDHHrlgeefetlapilflnepvgs 73 
                                        +lvD+++  ++  ++++++  + dvi iDHH + ee++++  +l++ +p+ +
  gi|488600954|ref|YP_007907425.1| 411 lVLVDNGSgyEDIPAIQQFITFGADVITIDHHFPDEEVDRY--LLYHINPYKA 461
                                       77****982245556778****************9888888..5666566655 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 ?    2.3   0.3     0.085   1.7e+02      12      22 ..       2      12 ..       1      15 [. 0.53
   2 ?   13.2   0.1   3.2e-05     0.064       7      28 ..      12      33 ..       8      37 .. 0.88
   3 ?    2.7   5.9     0.064   1.3e+02      12      40 ..      50      73 ..      46      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.085
                                      E-TTTTTTSEE CS
                         Anti-TRAP 12 kCdaCngsGki 22
                                      kCd+C+g G +
  gi|488600954|ref|YP_007907425.1|  2 KCDNCDGRGVV 12
                                      45666555544 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.2e-05
                                      HHCEEE-TTTTTTSEETTE... CS
                         Anti-TRAP  7 peLEtkCdaCngsGkiepeepr 28
                                       e+E kC  CngsGk+++ +p+
  gi|488600954|ref|YP_007907425.1| 12 VEIERKCVICNGSGKAKSFDPK 33
                                      599*************998875 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.064
                                      E-TTTTTTSEETTE......E-TTTTTSS CS
                         Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkg 40
                                       C aC g+G  +         CP C+G g
  gi|488600954|ref|YP_007907425.1| 50 ICGACRGTGVQKRM-----EVCPVCKGTG 73
                                      69999999988776.....3699999987 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00014      0.28      82     145 ..     200     259 ..     197     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                       HHHTT-EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGHHHHHH--TTSEEEEEE CS
                    tRNA_anti-like  82 kkYkGkiieVeGvvsdikkieassvvvlardddgltnVrclledeateasaakiskGqkvtivG 145
                                       +kY Gki+e++G+v+ ++ +++ +++ ++ d   ++ +   +e+ +      +i   ++v i+G
  gi|488600954|ref|YP_007907425.1| 200 SKYVGKIVEIRGLVTHVR-LTGGPTIFSVID-TTGVCKAVAFESGE--RAYPEIDVDDVVRIAG 259
                                       69***************5.599999887777.33344444444444..3344555555555555 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 ?    5.1   5.8    0.0022       4.3     614     655 ..      59     101 ..       2     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0022
                          PolC_DP2 614 veiarrkCkkCgketlearCeeCgekteekl.vCkkceeevee 655
                                       v+   + C+ C+ ++ +++C+ Cg++++  +  C+kc+++ ++
  gi|488600954|ref|YP_007907425.1|  59 VQKRMEVCPVCKGTGKSSKCKICGTTIKGDYdLCQKCSKKPHA 101
                                       4445566777777777777777777777655357777776543 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       4.3   8.6e+03      12      41 ..      15      45 ..       3      50 .. 0.61
   2 ?    9.8   1.1   0.00038      0.77       1      32 [.      66      95 ..      66     104 .. 0.86
   3 ?    0.4   0.1      0.32   6.3e+02      36      56 ..     251     271 ..     238     328 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.3
                           DUF2089 12 rlkcescettieg.eFelsefarLskeqlef 41
                                      + kc  c+ + ++ +F+ +  ++L++eq+++
  gi|488600954|ref|YP_007907425.1| 15 ERKCVICNGSGKAkSFDPKLTEELTSEQIQM 45
                                      5567777665544258888888888888764 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                           DUF2089  1 CPvcgeelvvtrlkcescettiegeFelsefa 32
                                      CPvc+++ +  + kc+ c+tti+g+++l++ +
  gi|488600954|ref|YP_007907425.1| 66 CPVCKGTGK--SSKCKICGTTIKGDYDLCQKC 95
                                      9***99876..56899************9866 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.32
                           DUF2089  36 keqlefvelfikarGnlkeve 56 
                                        ++   +  f++ rG++ e+e
  gi|488600954|ref|YP_007907425.1| 251 VDDVVRIAGFVRRRGSIFEIE 271
                                       566666778999999887765 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.8    0.0072        14      46      70 ..       3      30 ..       1      42 [. 0.76
   2 ?    5.1   8.5     0.013        26      28      78 ..      49      98 ..      38     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0072
                              PHF5 46 cdecs...fgkleekciicgskgvsday 70
                                      cd+c+   + + e+kc+ic+ +g+ +++
  gi|488600954|ref|YP_007907425.1|  3 CDNCDgrgVVEIERKCVICNGSGKAKSF 30
                                      6666422267889*******99988776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
                              PHF5 28 gkcpicdslvkpatkvricdecsfgkleekciicgskgvsdayyclecvrl 78
                                      g c  c  +   ++++++c  c+ + +++kc icg++ + d   c++c++ 
  gi|488600954|ref|YP_007907425.1| 49 GICGACRGT-GVQKRMEVCPVCKGTGKSSKCKICGTTIKGDYDLCQKCSKK 98
                                      566677654.5567899*******************9999999*****875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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):               9  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 3815.45
//
Query:       gi|488600955|ref|YP_007907426.1|  [L=49]
Description: hypothetical protein Asulf_01450 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 339.00
//
Query:       gi|488600956|ref|YP_007907427.1|  [L=45]
Description: hypothetical protein Asulf_01451 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.0   0.1        0.1   12.4   0.1    1.4  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 ?   12.4   0.1   5.8e-06       0.1      51      67 .]       2      18 ..       1      18 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.8e-06
                             rve_3 51 edYNteRPHssLgykTP 67
                                      ++ N+++PH+sL++  P
  gi|488600956|ref|YP_007907427.1|  2 RWHNEVKPHKSLDWNEP 18
                                      799**********9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 332.81
//
Query:       gi|488600957|ref|YP_007907428.1|  [L=65]
Description: hypothetical protein Asulf_01452 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00016   21.8   0.0    0.00017   21.8   0.0    1.0  1  rve         Integrase core domain
  ------ inclusion threshold ------
       0.19    9.9   0.0       0.22    9.6   0.0    1.0  1  Mesothelin  Pre-pro-megakaryocyte potentiating factor precurs


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 !   21.8   0.0   1.9e-08   0.00017      30      89 ..       1      57 [.       1      64 [. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-08
                               rve 30 vddfsrlilaealsdemdastvlalleravarfggvepervlsDngseytskafreflad 89
                                      +dd+srl++++ + de+++++++++l++ ++ +g   p+++ +D   +++ ++ r+ +++
  gi|488600957|ref|YP_007907428.1|  1 MDDASRLVTCYGVFDEATSENAIKVLREGFREYGI--PDEIFTDLE-QFVPSRNRDGAKH 57
                                      69*********************************..9******66.8888877777766 PP

>> Mesothelin  Pre-pro-megakaryocyte potentiating factor precursor (Mesothelin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   2.5e-05      0.22     209     240 ..       6      37 ..       4      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 2.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Mesothelin 209 rlagcpGpldqdqqeavravlqgggtpyGpps 240
                                       rl++c G +d+   e + +vl+ g  +yG p 
  gi|488600957|ref|YP_007907428.1|   6 RLVTCYGVFDEATSENAIKVLREGFREYGIPD 37 
                                       9****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 423.56
//
Query:       gi|488600958|ref|YP_007907429.1|  [L=219]
Description: hypothetical protein Asulf_01453 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   10.2   4.4        1.5    9.8   0.5    2.6  3  Lipocalin_4  Lipocalin-like domain


Domain annotation for each model (and alignments):
>> Lipocalin_4  Lipocalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.097   1.7e+03      55      82 ..      32      59 ..      24      73 .. 0.74
   2 ?   -0.2   0.4      0.12   2.1e+03      54      76 ..      89     112 ..      50     119 .. 0.62
   3 ?    9.8   0.5   8.6e-05       1.5       2      45 ..     122     166 ..     122     176 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.097
                                      EEEEEEETT..TTEEEET-S--EEEEEEEE CS
                       Lipocalin_4 55 sgtytisgn..kltitvtdgesketeiiel 82
                                      +g++t++++  ++ + v+    ++++ii++
  gi|488600958|ref|YP_007907429.1| 32 EGKFTVKNSppEVDLVVSKN--EQMYIIKV 59
                                      78999999988666666544..45777765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
                                       EEEEEEEETT.TTEEEET-S--EE CS
                       Lipocalin_4  54 esgtytisgn.kltitvtdgeske 76 
                                       e+  ++++gn +  + v+   s+e
  gi|488600958|ref|YP_007907429.1|  89 EHERWEVDGNlDKIVRVNQSISSE 112
                                       455677777753335555555544 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 8.6e-05
                                       SSEEE--SS--...STT-.--E.....EEE-SS..S-EEE----. CS
                       Lipocalin_4   2 vGtWklteitydgepetl.decekgsyitfnantttfesyttydg 45 
                                       +GtWk+++  ydge   + d+     y ++++++  ++++ t+d 
  gi|488600958|ref|YP_007907429.1| 122 EGTWKVVAKVYDGETFAVeDQTIVVKYSSTSDDKLDTNKVATTDT 166
                                       6**********9997556433334445555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1475.15
//
Query:       gi|488600959|ref|YP_007907430.1|  [L=343]
Description: hypothetical protein Asulf_01454 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        0.1   11.7   0.1       0.18   10.8   0.1    1.4  1  CTV_P33          Citrus tristeza virus P33 protein
        4.1    7.2   6.1        1.3    8.8   0.6    2.6  2  Trehalase_Ca-bi  Neutral trehalase Ca2+ binding domain


Domain annotation for each model (and alignments):
>> CTV_P33  Citrus tristeza virus P33 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1     2e-05      0.18      66     109 ..     227     270 ..     210     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2e-05
                           CTV_P33  66 vgplaasivvsppvsgthkirahvdnqpnregnvtyvktvdksr 109
                                         p    i ++   +g hki+a+ d q    gn   v+tv  s 
  gi|488600959|ref|YP_007907430.1| 227 TTPNDHNIDITTVSNGQHKIQAKTDAQWSSGGNNVNVNTVSESP 270
                                       55666778888899**************************9885 PP

>> Trehalase_Ca-bi  Neutral trehalase Ca2+ binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.6   0.00014       1.3       3      17 ..      52      66 ..      50      66 .. 0.90
   2 ?   -0.2   0.6     0.095   8.5e+02       9      15 ..     194     200 ..     193     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00014
                   Trehalase_Ca-bi  3 qLLeqEDTDgnfQIT 17
                                      +LLe E TD n Q T
  gi|488600959|ref|YP_007907430.1| 52 LLLEDENTDANNQMT 66
                                      7************77 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.095
                   Trehalase_Ca-bi   9 DTDgnfQ 15 
                                       DTD+ +Q
  gi|488600959|ref|YP_007907430.1| 194 DTDNEMQ 200
                                       9*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2115.09
//
Query:       gi|488600960|ref|YP_007907431.1|  [L=398]
Description: hypothetical protein Asulf_01455 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0035   16.9   0.9     0.0065   16.0   0.9    1.4  1  Stevor           Subtelomeric Variable Open Reading frame
  ------ inclusion threshold ------
      0.033   13.7   0.1      0.055   13.0   0.1    1.3  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
      0.034   13.7   1.4       0.17   11.4   0.0    2.5  3  ZirS_C           Zinc-regulated secreted antivirulence protei
      0.077   13.0   1.5         14    5.8   0.1    3.0  3  BsuPI            Intracellular proteinase inhibitor
       0.19   11.9   0.1       0.34   11.1   0.1    1.4  1  DUF4381          Domain of unknown function (DUF4381)
       0.47   11.4   0.1       0.47   11.4   0.1    2.5  2  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai
        1.2    8.6   6.0        4.6    6.7   6.0    2.0  1  SKG6             Transmembrane alpha-helix domain
        1.6    9.2   5.6       0.14   12.5   0.7    1.8  2  BatA             Aerotolerance regulator N-terminal


Domain annotation for each model (and alignments):
>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.9   2.9e-06    0.0065     201     263 ..     305     362 ..     299     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                            Stevor 201 sesslesalkaavsaaaasdlagtaasaassafepygiaalvllilavvliiLYiwlyrRRKn 263
                                       +++ +++     ++++  ++l+ ++a+    a+    ia+ +llilav+li+L   l+rRRK+
  gi|488600960|ref|YP_007907431.1| 305 QAKVISNG--VVYAISPKKELEVSVAKPIEKAISGVVIAIALLLILAVLLILL---LFRRRKR 362
                                       55555543..344455566778888999999********************98...7899987 PP

>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.4e-05     0.055     145     189 ..     337     381 ..     312     388 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                   LPG_synthase_TM 145 vllllalallllavlalllllllrrrlarlarvlkrlarllarfa 189
                                        ++++ ++ll+lavl++lll+++r+r++ l  +  +l r l++ +
  gi|488600960|ref|YP_007907431.1| 337 GVVIAIALLLILAVLLILLLFRRRKREKILEEIYGNLKRSLETSR 381
                                       667778888888999999999999999999999999988887665 PP

>> ZirS_C  Zinc-regulated secreted antivirulence protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.1   2.4e+03     105     117 ..     103     116 ..      96     133 .. 0.70
   2 ?   11.4   0.0   7.8e-05      0.17      57     119 ..     137     197 ..     122     209 .. 0.79
   3 ?   -1.3   0.1      0.65   1.4e+03      68     127 ..     258     274 ..     245     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                                       -SSSSEEE.EEEEE CS
                            ZirS_C 105 evvpgkyt.qvity 117
                                       ++vpg+yt +vi+ 
  gi|488600960|ref|YP_007907431.1| 103 DAVPGNYTvKVIAI 116
                                       67999999445544 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.8e-05
                                       --B-TT-EEEEEEE-BBTTS-B------B--EE-S-SSSEEEE---EE-SSSSEEEEEEEEES CS
                            ZirS_C  57 avlspgesatittlvkdvdgnpvnevminkavarenlkglwdigplkkevvpgkytqvitylg 119
                                        v   ge a +  +  d  gn + ev + k   +en +    +g l k v+pg+yt v   l 
  gi|488600960|ref|YP_007907431.1| 137 DVTVTGEKAFVEVVAVDPVGN-IAEVALIK-LFKENYEIASAYGKLEKRVTPGNYTAVAYLLN 197
                                       466678888888888888887.67777655.5799*********************9865544 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.65
                                       EEE-BBTTS-B------B--EE-S-SSSEEEE---EE-SSSSEEEEEEEEESS---EEEE CS
                            ZirS_C  68 ttlvkdvdgnpvnevminkavarenlkglwdigplkkevvpgkytqvitylgnsserldv 127
                                       t                                           t v+   gn++e++++
  gi|488600960|ref|YP_007907431.1| 258 T-------------------------------------------TIVLHVTGNTNETIEI 274
                                       3...........................................4455555666666655 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0062        14      68      96 ..      86     116 ..      81     120 .. 0.87
   2 ?    4.9   0.0     0.012        27      80      99 ..     180     199 ..     163     200 .. 0.76
   3 ?   -2.2   0.0         2   4.4e+03      82      97 ..     295     310 ..     283     312 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0062
                                       E-TT-EEEEEEEE...S---SEEEEEEEEE- CS
                             BsuPI  68 lepgesatyeetwd..edlepGeYtleaelv 96 
                                       l+p+e+  +  +++  ed  pG+Yt++++ +
  gi|488600960|ref|YP_007907431.1|  86 LNPNEYRKVYVELKadEDAVPGNYTVKVIAI 116
                                       899999999999998789*********9865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                                       E.S---SEEEEEEEEE--EE CS
                             BsuPI  80 wdedlepGeYtleaelvaee 99 
                                       ++++++pG+Yt++a+l +ee
  gi|488600960|ref|YP_007907431.1| 180 LEKRVTPGNYTAVAYLLNEE 199
                                       33699**********98876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                                       S---SEEEEEEEEE-- CS
                             BsuPI  82 edlepGeYtleaelva 97 
                                       + ++ G+Y ++a +++
  gi|488600960|ref|YP_007907431.1| 295 GGWKDGKYIFQAKVIS 310
                                       567899**99998765 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00015      0.34      22      55 ..     338     369 ..     331     398 .] 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                           DUF4381  22 wlllaalllllllvlalwllrrrkrnrreAlreL 55 
                                        ++++alll+l ++l+l+l+rrrkr  ++ l+e+
  gi|488600960|ref|YP_007907431.1| 338 VVIAIALLLILAVLLILLLFRRRKR--EKILEEI 369
                                       4566566666666666666666665..3333333 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 ?   -1.1   1.5       1.6   3.5e+03      46      64 ..      87     103 ..       5     106 .. 0.54
   2 ?   11.4   0.1   0.00021      0.47       4      31 ..     338     364 ..     335     397 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.6
                          EphA2_TM  46 ensgkkglktYvDPhtYED 64 
                                       + +++   k+Yv++++ ED
  gi|488600960|ref|YP_007907431.1|  87 NPNEY--RKVYVELKADED 103
                                       22333..677777776666 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00021
                          EphA2_TM   4 aavaglvllvilvilvlvlvrrrsknrk 31 
                                       +++a ++ll+++v+l+l+l+ rr+k++k
  gi|488600960|ref|YP_007907431.1| 338 VVIAIALLLILAVLLILLLF-RRRKREK 364
                                       33333333333344444444.4444444 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.0    0.0021       4.6      14      37 ..     338     361 ..     335     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0021
                              SKG6  14 vaVaVPVaViiivLlailifvrRR 37 
                                       v +a+ +  i++vLl++l+f rR+
  gi|488600960|ref|YP_007907431.1| 338 VVIAIALLLILAVLLILLLFRRRK 361
                                       456777788888888888877776 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4         6   1.4e+04      10      15 ..      14      19 ..       6      24 .. 0.48
   2 ?   12.5   0.7   6.4e-05      0.14      10      33 ..     342     364 ..     338     381 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6
                              BatA 10 Llalll 15
                                      Ll +++
  gi|488600960|ref|YP_007907431.1| 14 LLIMAI 19
                                      222222 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.4e-05
                              BatA  10 Llallllplpiillyllkrrpqev 33 
                                        ++ll+l++ +++l+l++rr++e+
  gi|488600960|ref|YP_007907431.1| 342 IALLLILAV-LLILLLFRRRKREK 364
                                       577888888.55566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      910  (0.0507558); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 2215.22
//
Query:       gi|488600961|ref|YP_007907432.1|  [L=66]
Description: hypothetical protein Asulf_01456 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0015   18.8  10.6       0.15   12.3   4.4    2.1  2  TSC22            TSC-22/dip/bun family
     0.0073   16.7   8.7      0.038   14.4   3.3    2.3  2  FlaC_arch        Flagella accessory protein C (FlaC)
  ------ inclusion threshold ------
      0.012   16.1   2.9      0.021   15.3   2.9    1.4  1  Spectrin         Spectrin repeat
      0.012   15.8   4.4      0.012   15.8   4.4    2.0  2  JIP_LZII         JNK-interacting protein  leucine zipper II
      0.015   15.5   0.7      0.018   15.2   0.7    1.1  1  COG5             Golgi transport complex subunit 5
      0.022   14.8   4.1      0.051   13.6   4.1    1.5  1  Laminin_II       Laminin Domain II
      0.023   14.0   2.7      0.025   13.8   2.7    1.0  1  Dynein_C         Dynein heavy chain C-terminal domain
      0.023   15.0   3.6      0.043   14.1   3.6    1.5  1  KxDL             Uncharacterized conserved protein
      0.024   14.6   3.6        1.4    9.0   0.9    2.1  2  Bcr-Abl_Oligo    Bcr-Abl oncoprotein oligomerisation domain
      0.024   13.5   5.6      0.025   13.5   5.6    1.0  1  Spc7             Spc7 kinetochore protein
      0.025   14.9   5.0       0.03   14.6   5.0    1.2  1  Tup_N            Tup N-terminal
      0.027   14.5   6.9      0.035   14.1   0.6    2.1  2  DUF1192          Protein of unknown function (DUF1192)
      0.029   14.4   3.0      0.093   12.8   3.0    1.7  1  Med9             RNA polymerase II transcription mediator com
      0.034   14.3   5.0        0.4   10.8   1.1    2.1  2  Uds1             Up-regulated During Septation
      0.039   14.0   0.4        7.3    6.8   0.2    2.1  2  TolA_bind_tri    TolA binding protein trimerisation
      0.042   13.9   3.8      0.099   12.7   3.8    1.6  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.047   13.0   1.8      0.052   12.8   1.8    1.0  1  DUF3450          Protein of unknown function (DUF3450)
      0.056   12.7   3.5      0.058   12.6   3.5    1.0  1  TMPIT            TMPIT-like protein
      0.058   13.5   6.1      0.067   13.3   6.1    1.1  1  BRE1             BRE1 E3 ubiquitin ligase
       0.06   13.8   5.7      0.073   13.5   5.7    1.1  1  Snapin_Pallidin  Snapin/Pallidin
      0.065   12.3   1.3      0.072   12.2   1.3    1.0  1  PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subuni
      0.065   13.7   3.4      0.094   13.2   3.4    1.3  1  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.068   13.2   4.8       0.23   11.5   1.2    1.7  1  DUF1664          Protein of unknown function (DUF1664)
      0.068   12.9   5.8        1.2    8.9   0.8    2.1  2  DivIC            Septum formation initiator
       0.07   12.7   3.5      0.091   12.3   3.5    1.2  1  Fzo_mitofusin    fzo-like conserved region
       0.07   13.3   6.1      0.099   12.8   6.1    1.3  1  Cnn_1N           Centrosomin N-terminal motif 1
      0.074   13.4   5.4       0.66   10.3   0.6    1.9  2  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.074   13.6   4.5       0.14   12.7   0.5    2.1  2  DUF1843          Domain of unknown function (DUF1843)
      0.086   12.7   5.5       0.16   11.9   2.1    2.6  2  Pox_A_type_inc   Viral A-type inclusion protein repeat
      0.087   13.1   7.3       0.23   11.7   0.8    2.0  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.092   13.0   2.9       0.12   12.7   2.9    1.2  1  DUF948           Bacterial protein of unknown function (DUF94
        0.1   12.5   2.9       0.76    9.7   0.3    2.2  2  MerR_2           MerR HTH family regulatory protein
        0.1   13.3   1.8       0.18   12.4   1.4    1.6  2  SlyX             SlyX
       0.14   11.6   4.1       0.16   11.4   4.1    1.1  1  DUF4349          Domain of unknown function (DUF4349)
       0.15   12.2   4.9        4.2    7.5   0.1    2.1  2  bZIP_2           Basic region leucine zipper
       0.16   11.9   3.1       0.26   11.2   2.7    1.5  1  DUF4446          Protein of unknown function (DUF4446)
       0.21   11.7   5.5       0.79    9.8   0.7    2.0  2  DivIVA           DivIVA protein
       0.27   11.4   7.7        3.5    7.8   2.1    2.1  2  bZIP_1           bZIP transcription factor
       0.38   11.3   4.4          1    9.9   4.4    1.6  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.47   10.6   4.4       0.91    9.7   4.4    1.5  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.48   10.4   7.0        1.6    8.7   0.5    2.7  2  Ribosomal_L29    Ribosomal L29 protein
       0.54   10.9   4.4        0.7   10.6   4.4    1.3  1  YabA             Initiation control protein YabA
        1.3    8.3   5.8        1.3    8.3   5.8    1.1  1  FAM76            FAM76 protein


Domain annotation for each model (and alignments):
>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.4    0.0012       0.5      23      45 ..      11      33 ..       3      37 .. 0.77
   2 !   12.3   4.4   0.00037      0.15       1      28 [.      38      65 ..      38      66 .] 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                             TSC22 23 IkeLeernseleeENslLkalas 45
                                       k+L++ +  l++E ++Lk+++s
  gi|488600961|ref|YP_007907432.1| 11 AKDLLKSVDDLKTEIKILKENVS 33
                                      57888888888888888888887 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00037
                             TSC22  1 MDLVKsHLmfAVrEeVevLkekIkeLee 28
                                      M L K H m AV+ e e+ k+kI +L +
  gi|488600961|ref|YP_007907432.1| 38 MVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      7799**********************75 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 ?    6.1   2.0     0.035        15      21      40 ..      16      35 ..       1      43 [. 0.59
   2 !   14.4   3.3   9.2e-05     0.038       9      35 ..      32      65 ..      28      66 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.035
                         FlaC_arch 21 keneelsksveelkenVkdl 40
                                      k+ ++l+++++ lkenV ++
  gi|488600961|ref|YP_007907432.1| 16 KSVDDLKTEIKILKENVSRV 35
                                      34555666666666666544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.2e-05
                         FlaC_arch  9 lsklst.......eletvkkeneelsksveelke 35
                                      +s++++       e++ vk+e+ee+++++e+lk+
  gi|488600961|ref|YP_007907432.1| 32 VSRVESmvltklhEMDAVKRELEEIKNKIEDLKK 65
                                      5555554555555999**************9997 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.9   5.1e-05     0.021      33      94 ..       8      65 ..       2      66 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.1e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHTTHTTHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin 33 leevqallkkhkaleaelaaqqervkalnela.eklldeghsaseeieerleelnerWeeLke 94
                                      le +++llk  ++l+ e++  +e+v +++ +  +kl     +++++++  lee+ ++ e+Lk+
  gi|488600961|ref|YP_007907432.1|  8 LEVAKDLLKSVDDLKTEIKILKENVSRVESMVlTKL-----HEMDAVKRELEEIKNKIEDLKK 65
                                      78899***********************95541444.....5567777777777777777665 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 ?   15.8   4.4   2.8e-05     0.012      22      56 ..       6      39 ..       1      53 [. 0.76
   2 ?    3.7   1.4      0.17        71      47      68 ..      44      65 ..      34      66 .] 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-05
                          JIP_LZII 22 naLnvvkddLIarvdeLtsereiLreEleslqkak 56
                                      ++L+v+k dL++ vd+L++e +iL+e +++++++ 
  gi|488600961|ref|YP_007907432.1|  6 EVLEVAK-DLLKSVDDLKTEIKILKENVSRVESMV 39
                                      6777775.8******************99998653 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.17
                          JIP_LZII 47 eEleslqkakerlesrikelEe 68
                                      +E+++++ ++e+++++i++l +
  gi|488600961|ref|YP_007907432.1| 44 HEMDAVKRELEEIKNKIEDLKK 65
                                      5666666666666666666655 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.7   4.2e-05     0.018      70     114 ..      14      58 ..       4      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHH CS
                              COG5  70 lssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhq 114
                                       l +++++lk++++ L++ ++r++s vl++  e++ ++++l+ + +
  gi|488600961|ref|YP_007907432.1|  14 LLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKN 58 
                                       4567899*********************************99876 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.1   0.00012     0.051       5      66 ..       4      65 ..       2      66 .] 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                        Laminin_II  5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLek 66
                                      ++e++e ak  l+ + +l+++++ +ke++s++++ v    +++++ ++ +++ ++++ +L+k
  gi|488600961|ref|YP_007907432.1|  4 IEEVLEVAKDLLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      66777777777777777777777777777777777655555566666666666666666655 PP

>> Dynein_C  Dynein heavy chain C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.7   5.9e-05     0.025      31      91 ..       5      65 ..       2      66 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-05
                                      H--------------..----...........-HHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                          Dynein_C 31 ekvlelaadileklpelfdle.eaekkpteyeeplntvllqElerfnkLleeirrsLkelqk 91
                                      e+vle+a+d+l+++ + +++e +  k+++++ e++    l+E++ +++ leei++++++l+k
  gi|488600961|ref|YP_007907432.1|  5 EEVLEVAKDLLKSVDD-LKTEiKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      6899**********97.34442233337999*****************************97 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.6    0.0001     0.043      25      76 ..      14      65 ..       3      66 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.0001
                              KxDL 25 lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslka 76
                                      l k+   L++ +++++e ++++++ +  + + +  vk++Le i+ ki+ lk+
  gi|488600961|ref|YP_007907432.1| 14 LLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      5566678999999*************************************98 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 ?    7.2   0.1     0.012         5      21      46 ..      13      38 ..       5      42 .. 0.82
   2 ?    9.0   0.9    0.0033       1.4      22      46 ..      42      66 .]      36      66 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                     Bcr-Abl_Oligo 21 meLdsvedieqeLerCkaslrrLeke 46
                                        L+sv+d++ e++  k+++ r+e  
  gi|488600961|ref|YP_007907432.1| 13 DLLKSVDDLKTEIKILKENVSRVESM 38
                                      55899999999999999999998865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0033
                     Bcr-Abl_Oligo 22 eLdsvedieqeLerCkaslrrLeke 46
                                      +L+ ++++++eLe+ k+++  L+ke
  gi|488600961|ref|YP_007907432.1| 42 KLHEMDAVKRELEEIKNKIEDLKKE 66
                                      68899****************9986 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.6   5.9e-05     0.025     163     220 ..       5      65 ..       1      66 [] 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-05
                              Spc7 163 eeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkk 220
                                       ee+ e+ ++l +  ++l+ e++ l+e +  +es    +  e+ ++++el+e+k++ie +kk
  gi|488600961|ref|YP_007907432.1|   5 EEVLEVAKDLLKSVDDLKTEIKILKENVSRVESmvlTKLHEMDAVKRELEEIKNKIEDLKK 65 
                                       5666777777777888888888888877777774333345555667777777777777665 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   5.0   7.3e-05      0.03       2      60 ..       4      65 ..       3      66 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.3e-05
                             Tup_N  2 lnelLdavk...qEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikq 60
                                      ++e+L++ k   +  d l++e+++lk++   +e+++ +++ E+++++++l e++++ +++k+
  gi|488600961|ref|YP_007907432.1|  4 IEEVLEVAKdllKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      677777766333567899*************************************9999987 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.6   8.5e-05     0.035      16      52 ..      13      48 ..       3      51 .. 0.81
   2 ?    4.2   1.0      0.11        46      23      35 ..      54      66 .]      52      66 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.5e-05
                           DUF1192 16 DLslLSveELeerIalLeaEIaRleaaiakkkasraA 52
                                      DL   Sv++L++ I+ L++ + R+e  + +k    +A
  gi|488600961|ref|YP_007907432.1| 13 DLL-KSVDDLKTEIKILKENVSRVESMVLTKLHEMDA 48
                                      553.3********************999888776666 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                           DUF1192 23 eELeerIalLeaE 35
                                      eE+++ I++L++E
  gi|488600961|ref|YP_007907432.1| 54 EEIKNKIEDLKKE 66
                                      8**********99 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 ?   12.8   3.0   0.00022     0.093      19      64 ..       9      65 ..       2      66 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                              Med9 19 lsskdletktgelrhkLkkarelirelpg...........idrsveeqeaeieelee 64
                                        +kdl +++++l++ +k  +e ++ ++            + r  ee +++ie+l++
  gi|488600961|ref|YP_007907432.1|  9 EVAKDLLKSVDDLKTEIKILKENVSRVESmvltklhemdaVKRELEEIKNKIEDLKK 65
                                      568999999999999999999999999997777777777788888888888888876 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.025        10      95     120 ..      15      40 ..       3      43 .. 0.67
   2 ?   10.8   1.1   0.00097       0.4      19      42 ..      42      65 ..      36      66 .] 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.025
                              Uds1  95 erkvdelaselekleeraaevrrrLL 120
                                        ++vd+l++e++ l+e+  +v+  +L
  gi|488600961|ref|YP_007907432.1|  15 LKSVDDLKTEIKILKENVSRVESMVL 40 
                                       56677777777777777666666555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00097
                              Uds1 19 sleeVeelkkelkaLeerlealrk 42
                                      +l+e++++k+el+ +++++e l+k
  gi|488600961|ref|YP_007907432.1| 42 KLHEMDAVKRELEEIKNKIEDLKK 65
                                      789******************997 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.021       8.7      19      39 ..      10      30 ..       1      38 [. 0.77
   2 ?    6.8   0.2     0.017       7.3      25      45 ..      44      64 ..      28      66 .] 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.021
                     TolA_bind_tri 19 lllelqqqlealqqelreLRG 39
                                      +  +l++ +++l++e++ L+ 
  gi|488600961|ref|YP_007907432.1| 10 VAKDLLKSVDDLKTEIKILKE 30
                                      456899999999999999985 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                     TolA_bind_tri 25 qqlealqqelreLRGqiEelq 45
                                       +++a ++el e++ +iE+l+
  gi|488600961|ref|YP_007907432.1| 44 HEMDAVKRELEEIKNKIEDLK 64
                                      467888888888888888775 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 ?   12.7   3.8   0.00024     0.099      64     117 ..       9      65 ..       1      66 [] 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00024
                        TPR_MLP1_2  64 eelnelkaeiaelkaeaesakaeleeseesweeqk...eelekelselekriedlne 117
                                       e +++l + + +lk+e + +k+++++ e+   ++    ++ ++el+e++++iedl++
  gi|488600961|ref|YP_007907432.1|   9 EVAKDLLKSVDDLKTEIKILKENVSRVESMVLTKLhemDAVKRELEEIKNKIEDLKK 65 
                                       344444555555555555566555555555554430004456788888888888876 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.8   0.00013     0.052      38      93 ..       3      58 ..       2      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                           DUF3450 38 kidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93
                                      ki+++ + +++ll+ + +lk+e++ l+   +++e++v +  +e++ +++++eei++
  gi|488600961|ref|YP_007907432.1|  3 KIEEVLEVAKDLLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKN 58
                                      67777888999******************************************997 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.5   0.00014     0.058      24      87 ..       3      65 ..       1      66 [] 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                             TMPIT 24 kleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87
                                      k+ee+ +  +++ k+++  k ++k lk++++++++ v   + +e++ +k+el+e+k+ ++++++
  gi|488600961|ref|YP_007907432.1|  3 KIEEVLEVAKDLLKSVDDLKTEIKILKENVSRVESMV-LTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      78999999*************************9986.688999999*********99999875 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   6.1   0.00016     0.067      12      66 ..      11      65 ..       2      66 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00016
                              BRE1 12 feelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnk 66
                                       ++l ++++++++e++il+e+++r+e++      +  a++r+ + ++n++  L+k
  gi|488600961|ref|YP_007907432.1| 11 AKDLLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      68999*******************************************9999986 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.7   0.00018     0.073      21      84 ..       3      65 ..       2      66 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00018
                   Snapin_Pallidin 21 klkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkk 84
                                      k++e+ +  ++Ll+++d l++++k l+e+ +  v + + + +  + ++k+++++++++++ lkk
  gi|488600961|ref|YP_007907432.1|  3 KIEEVLEVAKDLLKSVDDLKTEIKILKENVS-RVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      689999999**************98888887.5556666678899***************9997 PP

>> PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.3   0.00017     0.072     257     314 .]       5      64 ..       1      64 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                   PHA_synth_III_E 257 eeyakiygrlvnaqmalkaemqrlveevl..ealnlPtRsEldtlhkriqelrrevrrlk 314
                                       ee +++  +l+ +  +lk e ++l e+v   e++ l    E+d++ +++ e + ++  lk
  gi|488600961|ref|YP_007907432.1|   5 EEVLEVAKDLLKSVDDLKTEIKILKENVSrvESMVLTKLHEMDAVKRELEEIKNKIEDLK 64 
                                       8999999*******************99622677778889*************9998876 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.4   0.00022     0.094      16      61 ..      14      63 ..       3      65 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00022
                           NPV_P10 16 vddkVdalqqqvddvqenlpdvteln....ekLdaqsaqLaeletkvenI 61
                                      + + Vd l+++++ ++en+  v+ +     +++da   +L+e+++k+e+ 
  gi|488600961|ref|YP_007907432.1| 14 LLKSVDDLKTEIKILKENVSRVESMVltklHEMDAVKRELEEIKNKIEDL 63
                                      44556666666666666666666543211245799999999999999986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.2   0.00054      0.23      74     112 ..       3      41 ..       1      49 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00054
                           DUF1664  74 kldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                       k++e+ e++k++ + v++++ +++ ++e+v+ v+++v +
  gi|488600961|ref|YP_007907432.1|   3 KIEEVLEVAKDLLKSVDDLKTEIKILKENVSRVESMVLT 41 
                                       799*********************************975 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3    0.0086       3.6      35      58 ..      13      36 ..       2      44 .. 0.67
   2 ?    8.9   0.8     0.003       1.2      25      46 ..      45      66 .]      38      66 .] 0.61

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0086
                                      HHHHHHHHHHHHHCC-XXXXXXXX CS
                             DivIC 35 klkaeneeLeaevkdLksdedyie 58
                                       l +  ++L+ e+k Lk + +++e
  gi|488600961|ref|YP_007907432.1| 13 DLLKSVDDLKTEIKILKENVSRVE 36
                                      455566777777777766666666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.003
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC 25 eiaalqaelaklkaeneeLeae 46
                                      e++a ++el+++k+++e+L++e
  gi|488600961|ref|YP_007907432.1| 45 EMDAVKRELEEIKNKIEDLKKE 66
                                      5556666666666666666655 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.5   0.00022     0.091      94     151 ..       9      66 .]       4      66 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                     Fzo_mitofusin  94 qvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkasllese 151
                                        v ++l + ++ l+++++  ++++++  + + ++++++++v+++++ ++nk + l++e
  gi|488600961|ref|YP_007907432.1|   9 EVAKDLLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKKE 66 
                                       688999999999999999999999999999999******************9999876 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   6.1   0.00024     0.099      10      58 ..      12      66 .]       4      66 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00024
                            Cnn_1N 10 dkLkKENFdLKLriyfLeerleklse......eqkeellkenielkveveslqke 58
                                      ++L K   dLK +i+ L+e++ + ++       +++++ +e+ e+k ++e+l+ke
  gi|488600961|ref|YP_007907432.1| 12 KDLLKSVDDLKTEIKILKENVSRVESmvltklHEMDAVKRELEEIKNKIEDLKKE 66
                                      667777779********************************************98 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6    0.0016      0.66      58      87 ..       9      38 ..       1      41 [. 0.73
   2 ?    5.8   0.5      0.04        17      51      71 ..      44      64 ..      38      66 .] 0.44

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0016
                           BLOC1_2 58 eelqpylqqidqiekqvteLeeavseLDey 87
                                      e  + +l+++d+++++++ L+e+vs+++++
  gi|488600961|ref|YP_007907432.1|  9 EVAKDLLKSVDDLKTEIKILKENVSRVESM 38
                                      445678888889999999998888888876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.04
                           BLOC1_2 51 eklnekyeelqpylqqidqie 71
                                      +++++ + el++ +++i++++
  gi|488600961|ref|YP_007907432.1| 44 HEMDAVKRELEEIKNKIEDLK 64
                                      344444444444444444443 PP

>> DUF1843  Domain of unknown function (DUF1843)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   0.00033      0.14      19      52 .]       4      37 ..       1      37 [. 0.90
   2 ?    2.9   0.3      0.37   1.6e+02      16      37 ..      43      64 ..      40      66 .] 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00033
                           DUF1843 19 MKalaaqaeqqLaeygdiasaleqLkaEIAKlEr 52
                                        +++  a+  L++ +d++++++ Lk  +++ E+
  gi|488600961|ref|YP_007907432.1|  4 IEEVLEVAKDLLKSVDDLKTEIKILKENVSRVES 37
                                      5689999**********************99995 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.37
                           DUF1843 16 LakMKalaaqaeqqLaeygdia 37
                                      L +M+a+  + e+  ++ +d++
  gi|488600961|ref|YP_007907432.1| 43 LHEMDAVKRELEEIKNKIEDLK 64
                                      6667776666666666655554 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.85   3.5e+02       2      10 ..      17      25 ..      16      30 .. 0.81
   2 ?   11.9   2.1   0.00038      0.16       1      16 [.      51      66 .]      51      66 .] 0.95

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.85
                    Pox_A_type_inc  2 EmsrlRsRI 10
                                      +++ l+++I
  gi|488600961|ref|YP_007907432.1| 17 SVDDLKTEI 25
                                      688999999 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00038
                    Pox_A_type_inc  1 rEmsrlRsRIsDLErq 16
                                      rE+++ +++I+DL+++
  gi|488600961|ref|YP_007907432.1| 51 RELEEIKNKIEDLKKE 66
                                      8*************97 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 ?   11.7   0.8   0.00055      0.23      67     101 ..       9      43 ..       1      46 [. 0.83
   2 ?    6.3   1.3     0.027        11      68      88 ..      45      65 ..      39      66 .] 0.52

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00055
                                       S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  67 edaeeliaevkelkeelkaleaelkeleaelekll 101
                                       e a++l+++v++lk+e+k l+++++ +e+ + ++l
  gi|488600961|ref|YP_007907432.1|   9 EVAKDLLKSVDDLKTEIKILKENVSRVESMVLTKL 43 
                                       78999*********************998777666 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.027
                                      -TCCCCCCCHHHHHHHHHHHH CS
                      Seryl_tRNA_N 68 daeeliaevkelkeelkalea 88
                                      + ++++ e +e+k+++++l++
  gi|488600961|ref|YP_007907432.1| 45 EMDAVKRELEEIKNKIEDLKK 65
                                      445555555555555555554 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 ?   12.7   2.9   0.00028      0.12      29      88 ..       5      64 ..       2      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00028
                            DUF948 29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88
                                      +e+ +  ++l k vd + +e++ l ++v ++ + v  kl ++d++  +++++ +++++l+
  gi|488600961|ref|YP_007907432.1|  5 EEVLEVAKDLLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLK 64
                                      67778889999********************************************99986 PP

>> MerR_2  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0018      0.76      62      83 ..       8      29 ..       4      30 .. 0.92
   2 ?    3.6   0.1      0.14        60      14      83 ..      37      57 ..      31      65 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                            MerR_2 62 iavildLLdrieqLqrelesLr 83
                                      ++v+ dLL+ ++ L+ e++ L+
  gi|488600961|ref|YP_007907432.1|  8 LEVAKDLLKSVDDLKTEIKILK 29
                                      6899***************998 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                            MerR_2 14 eeflieLvelgliepeieeeewyfdesqlarlekavRLqrDLeinleGiavildLLdrieqLqrelesLr 83
                                      + +l++                                                 L ++++ +rele+++
  gi|488600961|ref|YP_007907432.1| 37 SMVLTK-------------------------------------------------LHEMDAVKRELEEIK 57
                                      444444.................................................555555555555544 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.094        39      28      52 ..      13      37 ..       3      40 .. 0.77
   2 ?   12.4   1.4   0.00043      0.18       4      52 ..      17      65 ..      14      66 .] 0.93

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.094
                                      HHHHHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX 28 eqqqqidrlqrqlrllaerlkelee 52
                                      +  + +d l+++++ l+e+++ +e+
  gi|488600961|ref|YP_007907432.1| 13 DLLKSVDDLKTEIKILKENVSRVES 37
                                      5567899***********9988775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00043
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX  4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52
                                       +++L +++  + + + +   +v    +++d+ +r+l+++++++++l++
  gi|488600961|ref|YP_007907432.1| 17 SVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      578999999************************************9986 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.1    0.0004      0.16      75     137 ..       5      65 ..       2      66 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                           DUF4349  75 tsrstsaeDVTeqyvDleaRlkaleasedrllallekaksvedlleiereLsevqaeiesleg 137
                                       +++ + a+D+ +++ Dl++ +k l++ + r++++    +++ ++ +++reL+e++  ie l++
  gi|488600961|ref|YP_007907432.1|   5 EEVLEVAKDLLKSVDDLKTEIKILKENVSRVESMV--LTKLHEMDAVKRELEEIKNKIEDLKK 65 
                                       5556678999999*********************9..789*******************9986 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1      0.01       4.2      28      52 ..      12      36 ..       7      37 .. 0.88
   2 ?    6.3   1.4     0.024        10      32      54 .]      44      66 .]      42      66 .] 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.01
                                      HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 28 eeleervkeLeeeNaqLrqkveqLe 52
                                      ++l + v +L++e+  L+++v+ +e
  gi|488600961|ref|YP_007907432.1| 12 KDLLKSVDDLKTEIKILKENVSRVE 36
                                      678899**************99876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.024
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 32 ervkeLeeeNaqLrqkveqLeke 54
                                      +++  +++e +++++k+e L+ke
  gi|488600961|ref|YP_007907432.1| 44 HEMDAVKRELEEIKNKIEDLKKE 66
                                      67788999999999999999998 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.7   0.00063      0.26      24      73 ..      18      65 ..       7      66 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00063
                           DUF4446 24 lkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieelee 73
                                      +  lk+++k l   ++ + +e+++ +kl+e++++k+e ee++++ie+l++
  gi|488600961|ref|YP_007907432.1| 18 VDDLKTEIKILK--ENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65
                                      556666666654..588999**************************9987 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7    0.0019      0.79      28      61 ..       5      38 ..       3      46 .. 0.89
   2 ?    4.9   0.7     0.063        26      34     121 ..      46      65 ..      36      66 .] 0.54

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
                                      HHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXX CS
                            DivIVA 28 dqvakdyeallkeneelkekvkeleeklkeykel 61
                                      ++v +  ++llk +++lk+++k l+e++++ +++
  gi|488600961|ref|YP_007907432.1|  5 EEVLEVAKDLLKSVDDLKTEIKILKENVSRVESM 38
                                      789999999******************9998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.063
                                       HHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  34 yeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeak 110
                                       + a+                                                                    ++e++
  gi|488600961|ref|YP_007907432.1|  46 MDAV--------------------------------------------------------------------KRELE 54 
                                       3333....................................................................44444 PP

                                       XXXXXXXXXXX CS
                            DivIVA 111 kiaeeieelkr 121
                                       +i+++ie+lk+
  gi|488600961|ref|YP_007907432.1|  55 EIKNKIEDLKK 65 
                                       44444444444 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.8     0.011       4.5      29      55 ..      12      38 ..       3      45 .. 0.58
   2 ?    7.8   2.1    0.0083       3.5      41      62 ..      45      66 .]      36      66 .] 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 29 eeLerrvkaLekeNksLkseleelkke 55
                                      + L + v+ L++e k Lk+ +++ + +
  gi|488600961|ref|YP_007907432.1| 12 KDLLKSVDDLKTEIKILKENVSRVESM 38
                                      444455555555555555555555555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0083
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 41 eNksLkseleelkkevekLksk 62
                                      e+ + k elee+k+++e Lk++
  gi|488600961|ref|YP_007907432.1| 45 EMDAVKRELEEIKNKIEDLKKE 66
                                      7889999999999999999985 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.4    0.0025         1      37      99 .]       5      64 ..       2      66 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0025
                      Syntaxin-6_N 37 eeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafveevreevkemk 99
                                      ee+ e  ++L k++++++++++ L+e v+ ve+    +  +  e++  ++ +ee++++++++k
  gi|488600961|ref|YP_007907432.1|  5 EEVLEVAKDLLKSVDDLKTEIKILKENVSRVES---MVLTKLHEMDAVKRELEEIKNKIEDLK 64
                                      566677777777777777777777777766665...355666777777777777777777665 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.4    0.0022      0.91      80     123 ..      22      65 ..       1      66 [] 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  80 kksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeq 123
                                       k   k l+e+++r++  + ++ +++ + +  le+ ++ki++L++
  gi|488600961|ref|YP_007907432.1|  22 KTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDLKK 65 
                                       33345677788899999999999999999999999999999997 PP

>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.5    0.0039       1.6       6      46 ..      16      52 ..      11      53 .. 0.62
   2 ?    3.2   2.6      0.21        87       9      21 ..      54      66 .]      50      66 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0039
                                      S-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHH CS
                     Ribosomal_L29  6 lsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkd 46
                                      +s+++Lk ++k lk++  +         l++++++ +v+++
  gi|488600961|ref|YP_007907432.1| 16 KSVDDLKTEIKILKENVSRVESM----VLTKLHEMDAVKRE 52
                                      67777777777777765544333....44567777777775 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.21
                                      HHHHHHHHHHHHH CS
                     Ribosomal_L29  9 eeLkeklkelkke 21
                                      ee+k+k+++lkke
  gi|488600961|ref|YP_007907432.1| 54 EEIKNKIEDLKKE 66
                                      899********98 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.4    0.0017       0.7       4      55 ..      12      63 ..       3      66 .] 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0017
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXX CS
                              YabA  4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleee 55
                                      k+l++++++l+++++ l+e+++++++ + + l+e ++++ e e++++++e+ 
  gi|488600961|ref|YP_007907432.1| 12 KDLLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIEDL 63
                                      78999***************************************99998654 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.8    0.0032       1.3     213     264 ..      10      61 ..       2      66 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0032
                             FAM76 213 nssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelr 264
                                          d l  v +Lk+ei+ lk ++++ ++++l+k +++ ++k el+e +++++
  gi|488600961|ref|YP_007907432.1|  10 VAKDLLKSVDDLKTEIKILKENVSRVESMVLTKLHEMDAVKRELEEIKNKIE 61 
                                       5578888899999999999999999999999999999998888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1893  (0.105583); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                       169  (0.00942607); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 447.72
//
Query:       gi|488600962|ref|YP_007907433.1|  [L=150]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-15   56.1   1.3      4e-15   55.1   0.8    1.8  2  HTH_24           Winged helix-turn-helix DNA-binding
    1.1e-11   44.4   1.5    1.6e-11   43.8   1.5    1.3  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.2e-08   34.7   0.5      2e-08   34.1   0.1    1.6  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    2.4e-07   30.4   0.4    4.2e-07   29.7   0.4    1.3  1  HTH_IclR         IclR helix-turn-helix domain
    5.9e-05   22.9   0.4     0.0029   17.4   0.1    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00011   22.6   1.2    0.00023   21.6   0.3    1.8  2  HTH_27           Winged helix DNA-binding domain
    0.00016   21.5   0.5    0.00042   20.1   0.3    1.7  2  MarR_2           MarR family
    0.00028   20.8   0.1    0.00051   19.9   0.1    1.5  1  HTH_11           HTH domain
    0.00077   19.3   0.9     0.0013   18.6   0.2    1.6  2  MarR             MarR family
      0.001   19.0   0.0     0.0019   18.2   0.0    1.5  1  HTH_Mga          M protein trans-acting positive regulator (M
     0.0011   19.4   0.3     0.0018   18.7   0.3    1.5  1  HTH_40           Helix-turn-helix domain
     0.0077   16.8   0.2      0.055   14.1   0.0    2.3  3  ACT_4            ACT domain
      0.009   16.0   0.1        0.1   12.6   0.1    2.1  2  HTH_Crp_2        Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.021   14.7   0.1    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
      0.014   14.9   0.2      0.032   13.8   0.2    1.5  1  Sigma70_r4       Sigma-70, region 4
      0.019   15.0   0.5      0.035   14.2   0.2    1.5  1  HTH_20           Helix-turn-helix domain
      0.021   14.6   0.2       0.04   13.7   0.2    1.5  1  HTH_10           HTH DNA binding domain
      0.033   14.3   0.1       0.34   11.1   0.0    2.1  2  AsnC_trans_reg2  AsnC-like ligand binding domain
      0.034   14.3   0.2      0.083   13.0   0.0    1.7  2  SpoIIID          Stage III sporulation protein D
      0.044   13.2   0.1      0.062   12.7   0.1    1.3  1  RepL             Firmicute plasmid replication protein (RepL)
      0.051   13.7   0.1        0.1   12.7   0.1    1.5  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
      0.075   13.1   0.0       0.15   12.1   0.0    1.5  1  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein
      0.076   13.5   0.0       0.14   12.6   0.0    1.5  1  HTH_26           Cro/C1-type HTH DNA-binding domain
        0.1   12.8   0.0       0.19   11.9   0.0    1.5  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
       0.11   13.0   0.4          6    7.4   0.0    2.2  2  PCI              PCI domain
       0.16   11.5   1.5          4    7.0   0.1    2.0  2  DDRGK            DDRGK domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.8   5.8e-18     4e-15       1      48 []       3      50 ..       3      50 .. 0.98
   2 ?   -2.0   0.0       3.9   2.7e+03       5      14 ..      77      86 ..      74      89 .. 0.70

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 5.8e-18
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lde+d+ +L++L +++r++ reLAe++gl +st++ r+ +L++eG+I+
  gi|488600962|ref|YP_007907433.1|  3 LDEIDILVLRVLAEDARTTLRELAEKTGLAVSTIHSRITKLISEGVIE 50
                                      79*********************************************7 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                            HTH_24  5 drkILelLqk 14
                                      +r++Le+L k
  gi|488600962|ref|YP_007907433.1| 77 TRDVLEELVK 86
                                      6788888765 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 !   43.8   1.5   2.3e-14   1.6e-11       1      41 [.       3      43 ..       3      44 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.3e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      LDeiD+  L+ L edaR++ +eLAe++Gl+ st++ R+ +L
  gi|488600962|ref|YP_007907433.1|  3 LDEIDILVLRVLAEDARTTLRELAEKTGLAVSTIHSRITKL 43
                                      8*************************************998 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   2.9e-11     2e-08       3      71 ..      70     134 ..      68     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.9e-11
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71 
                                       + ++  +   ++++ e+l + +  +e+y   G ++++lkv+v+d eal++f++e +++++gv ++e ++
  gi|488600962|ref|YP_007907433.1|  70 LDVDTAK---TRDVLEELVKKECLLEVYESLGKFNIVLKVRVKDFEALRNFINE-ISEIDGVMEFEWFL 134
                                       5666555...89999999999999******************************.*******9988665 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 !   29.7   0.4   6.1e-10   4.2e-07       8      49 ..      10      50 ..       8      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.1e-10
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +L+ lae ++  tl+elA++tgl+ St h  +  L+ +G +e
  gi|488600962|ref|YP_007907433.1| 10 VLRVLAEDART-TLRELAEKTGLAVSTIHSRITKLISEGVIE 50
                                      8*********8.***************************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 !   17.4   0.1   4.2e-06    0.0029       6      54 ..       3      51 ..       1      64 [. 0.93
   2 ?    3.6   0.0     0.088        61      32      51 ..      70      89 ..      69     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.2e-06
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      L e ++ v  +L +  + t +e+ae++g+  s++ + + +L++ G++e+
  gi|488600962|ref|YP_007907433.1|  3 LDEIDILVLRVLAEDARTTLRELAEKTGLAVSTIHSRITKLISEGVIEK 51
                                      7799999****************************************98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.088
                                      TTSSCHCHHHHHHHHHHCTS CS
                              TrmB 32 lgvprskvYevLrsLedkGl 51
                                      l+v+ +k  +vL++L++k  
  gi|488600962|ref|YP_007907433.1| 70 LDVDTAKTRDVLEELVKKEC 89
                                      6899999*********9975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   3.3e-07   0.00023       4      50 ..       6      51 ..       3      54 .. 0.94
   2 ?   -1.1   0.0         4   2.8e+03      28      46 ..      70      88 ..      68      92 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.3e-07
                            HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                       ++lvL++++ +++r +l++l++++ +  s+i++ + kL+  G++e+
  gi|488600962|ref|YP_007907433.1|  6 IDILVLRVLA-EDARTTLRELAEKTGLAVSTIHSRITKLISEGVIEK 51
                                      6899******.**********************************87 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4
                            HTH_27 28 lnvedshisyslkkLtekG 46
                                      l+v+ + +  +l++L++k+
  gi|488600962|ref|YP_007907433.1| 70 LDVDTAKTRDVLEELVKKE 88
                                      5667777778899999886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.3   6.1e-07   0.00042       8      53 ..       8      51 ..       3      54 .. 0.92
   2 ?   -1.7   0.0         4   2.8e+03       7      47 ..      77      86 ..      70      97 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.1e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                        vL +L+   +   t +ela+++gl  s+++ ++ +L + G +e+
  gi|488600962|ref|YP_007907433.1|  8 ILVLRVLAEDAR--TTLRELAEKTGLAVSTIHSRITKLISEGVIEK 51
                                      568999999987..8*****************************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLva 47
                                       ++vL +                               Lv+
  gi|488600962|ref|YP_007907433.1| 77 TRDVLEE-------------------------------LVK 86
                                      4455555...............................444 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   7.4e-07   0.00051       6      55 .]      11      64 ..       5      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.4e-07
                            HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgr.GYr 55
                                      l+ L +++   +  eLAe++++  +t++ +I +L + g    + ++ +p + GY+
  gi|488600962|ref|YP_007907433.1| 11 LRVL-AEDARTTLRELAEKTGLAVSTIHSRITKLISEGviekFAVVIDPEKfGYI 64
                                      3334.555569***************************99999999999998995 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.9e-06    0.0013       6      49 ..       8      51 ..       5      54 .. 0.95
   2 ?   -2.3   0.0       6.4   4.4e+03      29      45 ..      72      88 ..      69      90 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +++Lr l+e    ++ eLa+k g+  st+   +++L+ +G ie+
  gi|488600962|ref|YP_007907433.1|  8 ILVLRVLAEDARTTLRELAEKTGLAVSTIHSRITKLISEGVIEK 51
                                      579***************************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.4
                                      S-HHHHHHHHHHHHHTT CS
                              MarR 29 vskstvtrvldrLekkG 45
                                      v+++ +  vl +L+kk+
  gi|488600962|ref|YP_007907433.1| 72 VDTAKTRDVLEELVKKE 88
                                      66677777888898887 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.7e-06    0.0019      10      56 ..      10      56 ..       1      60 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                           HTH_Mga 10 LlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsivi 56
                                       l  L e + ++tl ela+++gl  +t+ s+i++L ++ ++e++ +vi
  gi|488600962|ref|YP_007907433.1| 10 VLRVLAE-DARTTLRELAEKTGLAVSTIHSRITKLISEgVIEKFAVVI 56
                                      3445666.99************************98888888887777 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   2.6e-06    0.0018      13      62 ..      20      69 ..      14     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-06
                            HTH_40 13 lsieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaie 62
                                       ++ e A++ gl++sTI + +++li eg   ++  ++++e++  I++ i 
  gi|488600962|ref|YP_007907433.1| 20 TTLRELAEKTGLAVSTIHSRITKLISEGVIEKFAVVIDPEKFGYITSFIL 69
                                      5899***********************95222333355566655555443 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.3   1.6e+03       9      25 ..      11      27 ..       9      49 .. 0.72
   2 ?   -1.0   0.0         4   2.7e+03      21      40 ..      38      57 ..      27      86 .. 0.66
   3 !   14.1   0.0     8e-05     0.055      46      77 ..      98     129 ..      91     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.3
                             ACT_4  9 leveaedrkglLaditq 25
                                      l+v aed +  L+++++
  gi|488600962|ref|YP_007907433.1| 11 LRVLAEDARTTLRELAE 27
                                      67778888887777765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4
                             ACT_4 21 aditqviseekanivsvnak 40
                                      ++it++ise  +   +v ++
  gi|488600962|ref|YP_007907433.1| 38 SRITKLISEGVIEKFAVVID 57
                                      67788887765554444444 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 8e-05
                             ACT_4  46 glaeikitveVkdvehLsrviakLraipgVis 77 
                                       g ++i ++v Vkd e L++ i+ + +i+gV++
  gi|488600962|ref|YP_007907433.1|  98 GKFNIVLKVRVKDFEALRNFINEISEIDGVME 129
                                       5699**************************86 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00014       0.1      21      61 ..      19      57 ..       8      61 .. 0.83
   2 ?    1.1   0.0      0.59   4.1e+02      57      67 ..     106     116 ..      91     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES- CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririld 61
                                      + t +elA+  Gl  +t+   +++L  eg+i++    ++ d
  gi|488600962|ref|YP_007907433.1| 19 RTTLRELAEKTGLAVSTIHSRITKLISEGVIEKF--AVVID 57
                                      56889**************************954..34445 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.59
                                       EEES-HHHHHH CS
                         HTH_Crp_2  57 irildleaLra 67 
                                       +r++d eaLr+
  gi|488600962|ref|YP_007907433.1| 106 VRVKDFEALRN 116
                                       89*******98 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.1e-05     0.021       6      47 .]       9      51 ..       4      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                       +L+ Lae   ++  elae++gl  st+     kL  +G++ek
  gi|488600962|ref|YP_007907433.1|  9 LVLRVLAEdARTTLRELAEKTGLAVSTIHSRITKLISEGVIEK 51
                                      68999***777******************99999999999986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.6e-05     0.032      11      43 ..       7      42 ..       3      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                                      HHHHHHH...TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 11 evlelrf...geglTleEIgerlgiSrerVrqiekr 43
                                      ++l+lr    +   Tl E++e+ g+  +++++++++
  gi|488600962|ref|YP_007907433.1|  7 DILVLRVlaeDARTTLRELAEKTGLAVSTIHSRITK 42
                                      799****9999999*******************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   5.1e-05     0.035      15      55 ..      10      50 ..       8      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +lr La+++  t+ elae  +l+ +t++ ++ +L + g +e
  gi|488600962|ref|YP_007907433.1| 10 VLRVLAEDARTTLRELAEKTGLAVSTIHSRITKLISEGVIE 50
                                      799********************************999998 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   5.9e-05      0.04      21      47 ..      17      43 ..      14      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                            HTH_10 21 PRrvtlkeLAkelGIskstlsehLrka 47
                                      + r+tl+eLA++ G++ st++ ++ k 
  gi|488600962|ref|YP_007907433.1| 17 DARTTLRELAEKTGLAVSTIHSRITKL 43
                                      5799*****************999875 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 ?    1.1   0.0      0.63   4.4e+02      54      72 ..      16      33 ..      10      45 .. 0.80
   2 ?   11.1   0.0   0.00049      0.34       1      82 []      60     140 ..      60     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.63
                   AsnC_trans_reg2 54 eeveevlaeiaaatgledy 72
                                      e+ +++l+e+a++tgl  +
  gi|488600962|ref|YP_007907433.1| 16 EDARTTLRELAEKTGLA-V 33
                                      6788999*******997.3 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00049
                   AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLps 77 
                                       k+G+  ++ + ++v+ +++ +v e + + +    +Ye   ++n+   v +++ e+++++++ei++  g+ ++e + +
  gi|488600962|ref|YP_007907433.1|  60 KFGYI-TSFILLDVDTAKTRDVLEELVKKECLLEVYESLGKFNIVLKVRVKDFEALRNFINEISEIDGVMEFEWFLT 135
                                       67888.88999999999999999999999999999999999************************************ PP

                   AsnC_trans_reg2  78 trefK 82 
                                       t+ +K
  gi|488600962|ref|YP_007907433.1| 136 TKRYK 140
                                       ****9 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.083      17      45 ..      17      45 ..       5      60 .. 0.86
   2 ?   -1.7   0.0       4.5   3.1e+03      39      56 ..      92     109 ..      64     113 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                           SpoIIID 17 eskatvRkaakvfgvskstvhkDvterLk 45
                                      + ++t+R+ a++ g++ st+h  +t+ ++
  gi|488600962|ref|YP_007907433.1| 17 DARTTLRELAEKTGLAVSTIHSRITKLIS 45
                                      5689*******************998764 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.5
                           SpoIIID  39 DvterLkkinkklakqvk 56 
                                       +v e L k n  l  +vk
  gi|488600962|ref|YP_007907433.1|  92 EVYESLGKFNIVLKVRVK 109
                                       344556666666666665 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   0.1   9.1e-05     0.062      76     118 ..      20      59 ..      12      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.1e-05
                              RepL  76 atnRelaeetgislktvsetlkileeanilkkkanGvlvinPd 118
                                       +t Relae+tg+++ t++  +  l   +++ k a   +vi+P+
  gi|488600962|ref|YP_007907433.1|  20 TTLRELAEKTGLAVSTIHSRITKLISEGVIEKFA---VVIDPE 59 
                                       589****************999999999999988...788886 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 ?   12.7   0.1   0.00015       0.1      18      52 ..      10      44 ..       3      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                      HHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHH CS
                             HTH_9 18 VvetLlrkgrltlrelvkktkLsldqVkksLvvLi 52
                                      V ++L + +r tlrel++kt+L  + +++    Li
  gi|488600962|ref|YP_007907433.1| 10 VLRVLAEDARTTLRELAEKTGLAVSTIHSRITKLI 44
                                      78999*********************998776666 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.15      18      50 ..      19      51 ..       2      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                    Sulfolobus_pRN 18 catleeleektGiekeellvyltrlykrGlisr 50
                                        tl el ektG+   ++   +t+l   G+i +
  gi|488600962|ref|YP_007907433.1| 19 RTTLRELAEKTGLAVSTIHSRITKLISEGVIEK 51
                                      479***************************975 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0002      0.14       2      45 ..      11      51 ..      10      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdk 45
                                      Lr+l+ d + t  eLa++tg+  +t++   ++    +s ++++k
  gi|488600962|ref|YP_007907433.1| 11 LRVLAEDARTTLRELAEKTGLAVSTIHSRITK---LISEGVIEK 51
                                      99************************976665...355555555 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027      0.19      21      54 ..      22      55 ..      20      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                    B-block_TFIIIC 21 qsdLakeskqdprslfyrlksLekkgLIvkqsii 54
                                       ++La  ++  ++ +++r+ +L + g I+k +++
  gi|488600962|ref|YP_007907433.1| 22 LRELAEKTGLAVSTIHSRITKLISEGVIEKFAVV 55
                                      57899999999********************996 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0087         6      61      91 ..      20      50 ..       9      60 .. 0.84
   2 ?    3.8   0.1      0.12        84      30      57 ..      69     102 ..      63     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0087
                                      EEHHHHHHHHTSSHHHHHHHHHHHHHTTSSS CS
                               PCI 61 islerlaklldlsvdevEkilvklIrdgeir 91
                                       +l +la++ +l v+ +++ + klI++g i+
  gi|488600962|ref|YP_007907433.1| 20 TTLRELAEKTGLAVSTIHSRITKLISEGVIE 50
                                      58899**********************9986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                                       HHHTTHHHHHHHHHHHHHHHHHHHHHH......C CS
                               PCI  30 laddglaqllesLekkvrerllrqvsk......i 57 
                                       l d+++a+  + Le+ v++++l +v++      i
  gi|488600962|ref|YP_007907433.1|  69 LLDVDTAKTRDVLEELVKKECLLEVYEslgkfnI 102
                                       678889999999***********99995544444 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0058         4     114     157 ..      20      65 ..      10      67 .. 0.79
   2 ?    4.7   0.6     0.029        20     103     170 ..      51     120 ..      48     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0058
                                       E-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-..EEE-TT--EEE-- CS
                             DDRGK 114 vlleelavkfklktqevierikeLeeqgslt..GvlDdrGkyiyit 157
                                       ++l ela k +l  + + +ri +L ++g ++   v+ d  k+ yit
  gi|488600962|ref|YP_007907433.1|  20 TTLRELAEKTGLAVSTIHSRITKLISEGVIEkfAVVIDPEKFGYIT 65 
                                       6899************************995224444455666665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.029
                                       HHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--E...EE---XXXXXXXXXXXX CS
                             DDRGK 103 efinyikekKvvlleelavkfklktqevierikeLeeqgsltGvlDdrGky...iyitdeEleavakyikk 170
                                       +f   i  +K   ++   + ++++t + ++ ++eL +++ l  v    Gk+   + ++ +++ea+ ++i++
  gi|488600962|ref|YP_007907433.1|  51 KFAVVIDPEKFGYITSF-ILLDVDTAKTRDVLEELVKKECLLEVYESLGKFnivLKVRVKDFEALRNFINE 120
                                       55555666666666655.568999**************************96545678899********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 963.08
//
Query:       gi|488600963|ref|YP_007907434.1|  [L=105]
Description: hypothetical protein Asulf_01458 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   7.1     0.0026   17.5   7.1    1.3  1  DUF2157       Predicted membrane protein (DUF2157)
  ------ inclusion threshold ------
      0.038   13.7   3.8      0.045   13.5   3.8    1.0  1  7tm_3         7 transmembrane sweet-taste receptor of 3 GCPR
      0.098   12.2   0.1      0.098   12.2   0.1    2.5  3  Uroplakin_II  Uroplakin II
       0.18   10.5   4.6       0.19   10.4   4.6    1.0  1  Presenilin    Presenilin
        3.2    7.1   7.3        0.2   11.0   1.4    1.7  2  TssN          Type VI secretion system, TssN


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 !   17.5   7.1   7.4e-07    0.0026      35     113 ..      21      99 ..       3     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.4e-07
                           DUF2157  35 leallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllgavlwrdrrvpprlgeallllaalllgaaia 111
                                       +  ll+l+ lllg +li+ ++  + ++++   +ll ++ ++l++++++    ++ + ++ g+a+l+++ l+ +++i+
  gi|488600963|ref|YP_007907434.1|  21 IVSLLTLALLLLGSALIIYIYDAYRKINQNYLLLLSVGFFVLVIGGALPGMHKTIGLSVDGDAVLIMSLLMQMIGII 97 
                                       6789****************************************999777777789999999999999999999999 PP

                           DUF2157 112 lv 113
                                       l+
  gi|488600963|ref|YP_007907434.1|  98 LI 99 
                                       87 PP

>> 7tm_3  7 transmembrane sweet-taste receptor of 3 GCPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.8   1.3e-05     0.045     150     230 ..      20     100 ..       8     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                             7tm_3 150 llllgykglllllgtflafktrkvpsnfneakfitlsilnvlliwlvfiplylllns.kpdaafavlafaillsatv 225
                                       +++ + ++ llllg  l + + ++ +++n++ ++ ls+ +++l++   +p ++ +   ++d   avl++++l+   +
  gi|488600963|ref|YP_007907434.1|  20 VIVSLLTLALLLLGSALIIYIYDAYRKINQNYLLLLSVGFFVLVIGGALPGMHKTIGlSVDGD-AVLIMSLLMQMIG 95 
                                       344444788888999998889999999**************************8888877777.8899999998888 PP

                             7tm_3 226 lllli 230
                                       ++l+ 
  gi|488600963|ref|YP_007907434.1|  96 IILIF 100
                                       88765 PP

>> Uroplakin_II  Uroplakin II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.7e-05     0.098     142     173 ..       9      40 ..       4      46 .. 0.83
   2 ?    1.4   0.8     0.054   1.9e+02     156     168 ..      53      65 ..      50      75 .. 0.86
   3 ?   -1.2   0.2      0.34   1.2e+03     146     170 ..      72      97 ..      66     104 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                      Uroplakin_II 142 glgmartggmvvitvllsvamfllvvglival 173
                                         g   tgg +vi  ll++a++ll   li+ +
  gi|488600963|ref|YP_007907434.1|   9 QGGHLETGGGIVIVSLLTLALLLLGSALIIYI 40 
                                       557789********************999866 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.054
                      Uroplakin_II 156 vllsvamfllvvg 168
                                       +llsv +f+lv+g
  gi|488600963|ref|YP_007907434.1|  53 LLLSVGFFVLVIG 65 
                                       699********98 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.34
                      Uroplakin_II 146 artggmvvi.tvllsvamfllvvgli 170
                                        +t g+ v    +l +++++ ++g+i
  gi|488600963|ref|YP_007907434.1|  72 HKTIGLSVDgDAVLIMSLLMQMIGII 97 
                                       44444444212233333333444444 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.6   5.3e-05      0.19      68     144 ..      19     102 ..       3     105 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.3e-05
                        Presenilin  68 ilvivvvtfll......vlLykyrcy.kvikgwlilsslllLflvsglllaevlkaynipldyitlllllwnfgvvG 137
                                       i+++ ++t+ l      +++y y+ y k+ +++l+l s+   +lv g  l  + k++ + +d  ++l++ + + ++G
  gi|488600963|ref|YP_007907434.1|  19 IVIVSLLTLALlllgsaLIIYIYDAYrKINQNYLLLLSVGFFVLVIGGALPGMHKTIGLSVDGDAVLIMSLLMQMIG 95 
                                       33333333333001222234666655156679**99999999999999999************************** PP

                        Presenilin 138 viaifwk 144
                                       +i if++
  gi|488600963|ref|YP_007907434.1|  96 IILIFYS 102
                                       *****96 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.4   5.7e-05       0.2      93     138 ..      19      64 ..       3      68 .. 0.86
   2 ?    2.8   7.9     0.018        63      98     138 ..      24      64 ..      21     105 .] 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.7e-05
                              TssN  93 ilfeilltlivillglvlfvlvfnllselqygvwaatsllvfiipl 138
                                       i++  lltl  +llg++l +++++  ++++  ++ + s+ +f++++
  gi|488600963|ref|YP_007907434.1|  19 IVIVSLLTLALLLLGSALIIYIYDAYRKINQNYLLLLSVGFFVLVI 64 
                                       788899************************9999999999988765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.018
                              TssN  98 lltlivillglvlfvlvfnllselqygvwaatsllvfiipl 138
                                       lltl  +llg++l +++++  ++++  ++ + s+ +f++++
  gi|488600963|ref|YP_007907434.1|  24 LLTLALLLLGSALIIYIYDAYRKINQNYLLLLSVGFFVLVI 64 
                                       67777777777777777777777777776666666666553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 655.34
//
Query:       gi|488600964|ref|YP_007907435.1|  [L=134]
Description: hypothetical protein Asulf_01459 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       360  (0.0200792); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 847.51
//
Query:       gi|488600965|ref|YP_007907436.1|  [L=172]
Description: archaeal flagellin N-terminal-like domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-25   87.7   0.5    1.5e-24   86.7   0.2    1.6  2  Pilin_N   Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.21   11.6   0.0    1.3  1  BsuPI     Intracellular proteinase inhibitor


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.2   1.7e-28   1.5e-24       1      80 [.      13      96 ..      13      97 .. 0.90
   2 ?   -1.8   0.0      0.71   6.4e+03      47      73 ..     143     170 ..     124     172 .] 0.57

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 1.7e-28
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievk..idssastgkna.vslehkgGdsidtkdlkiv 75
                                      +AVSpViGviLmvaitvIla+via+fv+g+ ++  ++ap+a++  +  +d+ +stg+++ +++ h+gGd+++ kdl+i+
  gi|488600965|ref|YP_007907436.1| 13 KAVSPVIGVILMVAITVILAGVIASFVFGFgQKMGTAAPNAQLVLSdaVDELTSTGNENiFYMDHNGGDALPCKDLRIL 91
                                      69****************************9999*********76667777777776667******************* PP

                           Pilin_N 76 lnseg 80
                                      ++ ++
  gi|488600965|ref|YP_007907436.1| 92 VYYKQ 96
                                      98765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.71
                           Pilin_N  47 dssastgknavsleh.kgGdsidtkdlk 73 
                                       d++ ++g+++v++ h  +G+ i t d++
  gi|488600965|ref|YP_007907436.1| 143 DTNWGAGTYTVKVLHiPSGNFIFTGDVT 170
                                       3333334444544442577777776666 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    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      63      94 ..     125     156 ..      99     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                                       -EEEEE-TT-EEEEEEEE.S---SEEEEEEEE CS
                             BsuPI  63 lssetlepgesatyeetwdedlepGeYtleae 94 
                                        s++ +epge +t++e  d ++ +G+Yt+++ 
  gi|488600965|ref|YP_007907436.1| 125 GSNDLFEPGERITFTEDGDTNWGAGTYTVKVL 156
                                       566779************99*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1228.44
//
Query:       gi|488600966|ref|YP_007907437.1|  [L=214]
Description: hypothetical protein Asulf_01461 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   32.1   4.5    2.3e-07   30.9   4.5    1.7  1  Dockerin_1  Dockerin type I domain
  ------ inclusion threshold ------
       0.12   12.0   0.7        2.8    7.7   0.0    2.6  2  EF-hand_1   EF hand


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 !   30.9   4.5   2.5e-11   2.3e-07       1      57 [.     161     212 ..     161     213 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.5e-11
                                       TTETTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHHH CS
                        Dockerin_1   1 agDVNgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvinyL 57 
                                       +gD+N D +++  D+ ++ + ++      +++++ + D+N+DG+vn lD+ ++i+ L
  gi|488600966|ref|YP_007907437.1| 161 YGDINMDDEIDVKDLIRLEKIIL-----MKEKRTVTSDINNDGEVNILDLVRLIRVL 212
                                       79*********************.....99************************966 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.022     2e+02       7      24 ..     160     177 ..     156     178 .. 0.83
   2 ?    7.7   0.0   0.00031       2.8      10      27 ..     193     210 ..     191     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.022
                                       HHHTTTSSSEEEHHHHHH CS
                         EF-hand_1   7 refDkDgdGkIdfeEfke 24 
                                       r  D + d  Id +++++
  gi|488600966|ref|YP_007907437.1| 160 RYGDINMDDEIDVKDLIR 177
                                       56699*********9986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00031
                                       TTTSSSEEEHHHHHHHHH CS
                         EF-hand_1  10 DkDgdGkIdfeEfkellk 27 
                                       D ++dG +++ ++++l++
  gi|488600966|ref|YP_007907437.1| 193 DINNDGEVNILDLVRLIR 210
                                       99***********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1458.95
//
Query:       gi|488600967|ref|YP_007907438.1|  [L=187]
Description: hypothetical protein Asulf_01462 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0098   14.8   0.6      0.086   11.6   0.1    2.0  2  BatD      Oxygen tolerance
  ------ inclusion threshold ------
       0.11   12.8   0.6       0.16   12.2   0.0    1.6  2  DUF4625   Domain of unknown function (DUF4625)
          1    9.5  10.4        2.1    8.5  10.4    1.5  1  UPF0370   Uncharacterised protein family (UPF0370)


Domain annotation for each model (and alignments):
>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   1.4e-05     0.086      17      95 ..      14      91 ..       6     104 .. 0.79
   2 ?    1.7   0.0     0.015        91     418     447 ..     152     186 ..     124     187 .] 0.51

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                              BatD 17 dknevevgetfrLtftvngasg....epdfsapslekdfevlsgsqssstqiinGkssssssktwtytLapkkeGtltI 91
                                      ++ +++vge+f+ ++tv++a++    + d+s ++l + ++v +g+  ++++i+ +++ ss++    + +++ k G+ +I
  gi|488600967|ref|YP_007907438.1| 14 SQGQINVGEEFNASITVTDANDlaafQIDLSYSNL-EIVKVSRGNAIKNWSIFDFDTISSNK----IRVIAAKFGEESI 87
                                      6789****************853344566666666.666666779999*********99665....7777888888888 PP

                              BatD 92 paat 95
                                      ++ +
  gi|488600967|ref|YP_007907438.1| 88 GEGE 91
                                      7655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.015
                              BatD 418 slkkkgs...ff..lfwlllllplllfvvllllwr 447
                                       + +++++    +  ++w +++l+l+ + + ++ wr
  gi|488600967|ref|YP_007907438.1| 152 KGSQPNEvveHWivGYWYVIVLILIGVGIGVWKWR 186
                                       22333331233345777665555555555555554 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.6e-05      0.16      27      58 ..      13      44 ..       3      80 .. 0.81
   2 ?   -3.6   0.1         2   1.2e+04      11      23 ..     139     151 ..     134     161 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                           DUF4625 27 eeeevlkiGetlhfeaklsdnealasykvdih 58
                                      +++ ++++Ge+++  ++++d ++la++++d+ 
  gi|488600967|ref|YP_007907438.1| 13 TSQGQINVGEEFNASITVTDANDLAAFQIDLS 44
                                      5667899***********************94 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2
                           DUF4625  11 dtekPvidllevs 23 
                                       + ++P+i+ ++ +
  gi|488600967|ref|YP_007907438.1| 139 TYTQPIITPVMEE 151
                                       4578888877333 PP

>> UPF0370  Uncharacterised protein family (UPF0370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  10.4   0.00035       2.1       2      24 ..     162     184 ..     161     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00035
                           UPF0370   2 eWLadYWWvillllvGillngik 24 
                                       +W+  YW+vi+l+l+G+ + + k
  gi|488600967|ref|YP_007907438.1| 162 HWIVGYWYVIVLILIGVGIGVWK 184
                                       7***************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1225.53
//
Query:       gi|488600968|ref|YP_007907439.1|  [L=78]
Description: hypothetical protein Asulf_01463 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   23.2   0.1    6.5e-05   22.7   0.1    1.2  1  AAA_lid_3  AAA+ lid domain
  ------ inclusion threshold ------
      0.062   13.3   0.2         12    6.0   0.1    2.3  2  FliMN_C    Type III flagellar switch regulator (C-ring) FliN 


Domain annotation for each model (and alignments):
>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   7.2e-09   6.5e-05       3      29 ..      48      74 ..      47      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.2e-09
                         AAA_lid_3  3 dlkeLAerTeGySGADlaalcreAall 29
                                      d+ eLA ++eGy+G D++a+ r++a++
  gi|488600968|ref|YP_007907439.1| 48 DVIELADLMEGYVGVDIEAIYRASARR 74
                                      889*******************99975 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 ?    6.0   0.1    0.0014        12      24      34 ..      22      32 ..      21      39 .. 0.91
   2 ?    5.4   0.0    0.0021        19      27      49 ..      44      66 ..      42      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0014
                                      HHHHHTTSEEE CS
                           FliMN_C 24 llnLkvGdvip 34
                                      +l+L+vGdvi+
  gi|488600968|ref|YP_007907439.1| 22 MLKLQVGDVIK 32
                                      69*******95 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0021
                                      HHTTSEEE--TTGGGCEEEEETT CS
                           FliMN_C 27 LkvGdvipLdkpadepvevyvng 49
                                      + +Gdvi+L   ++  v v ++ 
  gi|488600968|ref|YP_007907439.1| 44 MPAGDVIELADLMEGYVGVDIEA 66
                                      568******88877777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 572.94
//
Query:       gi|488600969|ref|YP_007907440.1|  [L=181]
Description: hypothetical protein Asulf_01464 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1290.11
//
Query:       gi|488600970|ref|YP_007907441.1|  [L=195]
Description: hypothetical protein Asulf_01465 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   13.7   0.1      0.084   12.8   0.1    1.5  1  CdiI_3    CDI immunity proteins


Domain annotation for each model (and alignments):
>> CdiI_3  CDI immunity proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.7e-06     0.084      36      77 ..      22      60 ..       9      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-06
                            CdiI_3 36 DlrllirQeiglellvplAlevLkedpLaegdlYeGdLLeav 77
                                       ++l i+Q i l  l + A +v+ e+ L   ++Y Gd L ++
  gi|488600970|ref|YP_007907441.1| 22 LVMLYISQAIPLTPLTSSAANVMVENTL---EMYAGDVLNTL 60
                                      57788***********************...********887 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:                      396  (0.0220871); 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: 00:00:00.41
# Mc/sec: 1441.81
//
Query:       gi|488600971|ref|YP_007907442.1|  [L=159]
Description: hypothetical protein Asulf_01466 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.7   0.6      0.073   12.6   0.6    1.5  1  Baculo_11_kDa  Baculovirus 11 kDa family
       0.15   11.9   0.0        0.2   11.5   0.0    1.1  1  Ntox27         Bacterial toxin 27


Domain annotation for each model (and alignments):
>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   8.2e-06     0.073      37      61 ..       6      30 ..       3      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.2e-06
                     Baculo_11_kDa 37 vLvicglvvfvvivlfilLlvvilk 61
                                      +++++g++++v +v fi+L+ +++ 
  gi|488600971|ref|YP_007907442.1|  6 LMILSGFLILVGMVAFIILVNNMIY 30
                                      89*****************987654 PP

>> Ntox27  Bacterial toxin 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.3e-05       0.2      22     105 ..      26     114 ..      20     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                            Ntox27  22 nnddyainlpkamGleer.Pvwtvg..veravedrkvrls..vtldGvpgasdidealqallkrGetiekldednir 93 
                                       nn  y +n p+ + + er  +   +  +++aved   + s  v   Gv ++ +++e l++  k  + + +  e+ + 
  gi|488600971|ref|YP_007907442.1|  26 NNMIYVLNSPAMVDVSERnSIESLEylIHKAVEDAVANASytVLTQGVNNSAKAEEILENETKTFKRFFNIIEEYYG 102
                                       889999999******9998887665337899999755554116679***************9999998888888887 PP

                            Ntox27  94 gqGfGtawemsk 105
                                         G      + k
  gi|488600971|ref|YP_007907442.1| 103 MDGKAINISILK 114
                                       777666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1148.39
//
Query:       gi|488600972|ref|YP_007907443.1|  [L=136]
Description: hypothetical protein Asulf_01467 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 910.16
//
Query:       gi|488600973|ref|YP_007907444.1|  [L=230]
Description: hypothetical protein Asulf_01468 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   12.6   0.1       0.13   11.7   0.1    1.5  1  SieB      Super-infection exclusion protein B
          1   10.3   6.3        2.6    9.0   3.2    2.6  3  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.5e-05      0.13      35      81 ..      14      60 ..      10      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.5e-05
                              SieB 35 iglvflisiayllaqvvskllaeikekikkkreqkkvekklknLtee 81
                                      +g+v+l+si+++ + vv+ +++ i++ + +   q++v+ +++ + e+
  gi|488600973|ref|YP_007907444.1| 14 VGMVLLLSISIVAIGVVYMGIGPIIDTYVESSHQREVIYVFELMRES 60
                                      799**********************************9999999775 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.2   0.00029       2.6       2      29 ..       9      36 ..       8      54 .. 0.85
   2 ?    0.8   0.0       0.1   9.4e+02      34      78 ..      94     137 ..      86     140 .. 0.62
   3 ?   -1.2   0.0      0.45     4e+03      56      77 ..     157     181 ..     134     184 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                           Pilin_N  2 AVSpViGviLmvaitvIlaAviaafvlg 29
                                      +VS  +G++L+++i +++++v+   ++ 
  gi|488600973|ref|YP_007907444.1|  9 GVSVQVGMVLLLSISIVAIGVVYMGIGP 36
                                      89*******************9877765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.1
                           Pilin_N  34 eekapqasievkidssastgknavslehkgGdsidtkdlkivlns 78 
                                       +++ p  s+  k d++ s  +n   +++ gG+s+  ++  i+ ++
  gi|488600973|ref|YP_007907444.1|  94 NTTVPIYSVIYKGDEEIS-LENGAIFRKAGGNSFMVEKPLIIHSN 137
                                       556666666333333333.344488999****9988776666554 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.45
                           Pilin_N  56 a...vslehkgGdsidtkdlkivln 77 
                                           +++++ g d  +  + +iv+ 
  gi|488600973|ref|YP_007907444.1| 157 GivrIVFTNLGCDYRTITNNTIVVH 181
                                       1234777777777666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1509.95
//
Query:       gi|488600974|ref|YP_007907445.1|  [L=446]
Description: hypothetical protein Asulf_01469 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.9   0.3        1.7    8.8   0.3    2.2  1  DUF478    Protein of unknown function (DUF478)


Domain annotation for each model (and alignments):
>> DUF478  Protein of unknown function (DUF478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   9.3e-05       1.7      16      42 ..     370     395 ..     341     405 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 9.3e-05
                            DUF478  16 GvfevrGtskGvGviltrffwvfsgre 42 
                                       G fe +G  kG+G i+  +fwv++ + 
  gi|488600974|ref|YP_007907445.1| 370 GEFE-KGDIKGLGDIVQHYFWVIATKS 395
                                       5565.7999*************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2666.75
//
Query:       gi|488600975|ref|YP_007907446.1|  [L=640]
Description: hypothetical protein Asulf_01470 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-39  135.1   4.0    1.1e-20   73.9   1.1    3.9  5  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   3.4      0.26   4.6e+03      99     124 ..      48      73 ..      44      74 .. 0.81
   2 ?   -3.9   1.5      0.68   1.2e+04     106     123 ..      96     113 ..      90     115 .. 0.62
   3 !   70.5   0.1   6.6e-24   1.2e-19       2     124 ..     143     271 ..     142     272 .. 0.95
   4 ?   -8.7   5.2         1   1.8e+04     108     122 ..     289     303 ..     284     305 .. 0.46
   5 !   73.9   1.1   5.9e-25   1.1e-20       1     123 [.     436     561 ..     436     562 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.26
                                       HHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  99 laallepllllvvallvllillaill 124
                                       ++a++  l++++++++v++il  +l+
  gi|488600975|ref|YP_007907446.1|  48 ATAKMVSLIFAIFGAIVGSILAYFLI 73 
                                       56677789999999999999998886 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.68
                                       XXXXXXXXXXXXXXXXXX CS
                             T2SSF 106 llllvvallvllillail 123
                                       + l++ +++v+l+ ++++
  gi|488600975|ref|YP_007907446.1|  96 KSLVFSGVVVILMTIIFY 113
                                       556666666666666665 PP

  == domain 3  score: 70.5 bits;  conditional E-value: 6.6e-24
                                       HHHHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.....SHHHHHCT-TT.TS-HHHHHHHHHHH CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.....slsealertpssefpelvvqlirage 72 
                                       ++ +++l+ +G+ + +++ +la+ +e +g++++e++ri+r+++  g     +ls+a+e +ps+ f+e++  li++++
  gi|488600975|ref|YP_007907446.1| 143 ITFMYSLSLGGMDVIRIFNSLASYKEiYGEVSKEISRIIRDIELLGkdlrtALSDAVEFSPSENFKEFLHGLITIID 219
                                       677999999**********************************9999777777888889999*************** PP

                                       HHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                             T2SSF  73 eggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                       +gg+++ +Le  a+++ e++++ +k+++ +l+ +++ +++++v+++l++i++
  gi|488600975|ref|YP_007907446.1| 220 SGGDITRYLEERADFYLEKARQNQKNFLDFLGLMAESYITAFVAGPLFLIII 271
                                       *************************************************996 PP

  == domain 4  score: -8.7 bits;  conditional E-value: 1
                                       XXXXXXXXXXXXXXX CS
                             T2SSF 108 llvvallvllillai 122
                                       ++++++ ++++++ai
  gi|488600975|ref|YP_007907446.1| 289 VIYIIIPFASFMFAI 303
                                       444444444444444 PP

  == domain 5  score: 73.9 bits;  conditional E-value: 5.9e-25
                                       HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHCT-TT.....TS-HHHHHHHHHHHH CS
                             T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslsealertps....sefpelvvqliragee 73 
                                       fl+ +a + ++Gvp+++a+ ++a+++   pl+ee+++i+++l++G+sls+al r+ +     e++++v+ l ++ ++
  gi|488600975|ref|YP_007907446.1| 436 FLNRVAAANESGVPIYKAIAMIAKTD-TSPLKEEIQKIKADLDWGMSLSDALIRFANrlriFELSRTVTLLNESLKS 511
                                       88999*********************.**************************55555555899************* PP

                                       HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       +g+++evL+  a++  + + lrr++l+++l +++++++ ++v++ ++ i+
  gi|488600975|ref|YP_007907446.1| 512 TGKVTEVLMISAKDASNAELLRRERLSSMLMYVIIIYISFFVFIGIVYIV 561
                                       *********************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1312  (0.0731775); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.53
# Mc/sec: 3652.07
//
Query:       gi|488600976|ref|YP_007907447.1|  [L=559]
Description: Type IV secretory pathway, VirB11 component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-55  186.4   0.0    8.1e-55  185.8   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.024   14.4   0.0      0.057   13.2   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
      0.062   12.8   0.0       0.11   11.9   0.0    1.4  1  AAA_7     P-loop containing dynein motor region
       0.92   10.0   6.7        1.3    9.4   0.0    2.7  2  AAA_23    AAA domain
        7.7    6.7   7.3        0.4   10.8   1.4    1.9  2  RapH_N    response regulator aspartate phosphatase H, N termi


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 !  185.8   0.0   2.3e-58   8.1e-55       6     247 ..     184     429 ..     180     449 .. 0.94

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 2.3e-58
                             T2SSE   6 eallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlr 81 
                                       ++l+ d++  di  + +++ v+v +  +  ++++  + ++++l  l+ ++a+ ++++is  +p++da+lp +g r++
  gi|488600976|ref|YP_007907447.1| 184 TPLMMDRSLEDISCNGYDKpVFV-FHRNYANIETNLRFNERELDTLVVKLAQQSGKHISIAEPMIDATLP-DGSRIQ 258
                                       567789999**************.999999****************************************.****** PP

                             T2SSE  82 vvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                       + l   v +   +++iRk + + +t  dl++ ++++ ++ + l   ++++++++++GgT sGKtt+++a+  +i+ +
  gi|488600976|ref|YP_007907447.1| 259 MTLGREVSDhgSTFTIRKFRDEPVTPIDLIVWKTFSSEQMAYLWLCIENKKSLIFAGGTASGKTTSMNAISLFIPRK 335
                                       **99888877789***************************************************************9 PP

                             T2SSE 157 derivtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgsl 228
                                         +ivt+ED++E+ l ++n + l+++     k+ +++ dllraaLR+rP  i+vGE+R+ke+l++ +A+ TGH    
  gi|488600976|ref|YP_007907447.1| 336 -AKIVTIEDTRELMLPHENWIPLVTReafgeKGVIDMYDLLRAALRQRPEYIIVGEVRGKEALTLFQAMATGHTT-Y 410
                                       .*****************************9999*****************************************.* PP

                             T2SSE 229 sTlHansaagalerLeqlg 247
                                       sTlHa+s+ ga++rLe   
  gi|488600976|ref|YP_007907447.1| 411 STLHADSVNGAIHRLESPP 429
                                       ***************9755 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.057       4      48 ..     285     333 ..     282     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                            AAA_29   4 lqlvNWgtfdghtie.....idlkgatlltGpsGsGKSTllDAiqalLvp 48 
                                       ++l+ W tf+ +++      i+ k + +++G + sGK+T + Ai+ l++p
  gi|488600976|ref|YP_007907447.1| 285 IDLIVWKTFSSEQMAylwlcIENKKSLIFAGGTASGKTTSMNAIS-LFIP 333
                                       78999****9966542222266666999*************9986.4555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.11      11      58 ..     287     333 ..     277     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                             AAA_7  11 eilVptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkld 58 
                                        i+ +t  + ++ y l l+++nkk++++ G t +GKt+ ++ +   ++
  gi|488600976|ref|YP_007907447.1| 287 LIVWKTFSSEQMAY-LWLCIENKKSLIFAGGTASGKTTSMNAISLFIP 333
                                       45555555555555.5689********************998665555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   4.9      0.51   1.8e+03     148     183 ..      11      46 ..       3      58 .. 0.68
   2 ?    9.4   0.0   0.00038       1.3      17      41 ..     301     330 ..     274     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.51
                            AAA_23 148 lkdkkerleelekeleeledekkllekleqekekek 183
                                       + d +e +ee+e++  e  +e+k+lek+ +   ++k
  gi|488600976|ref|YP_007907447.1|  11 EDDAEESIEEYERQAMESIEEAKKLEKVFKSRRRKK 46 
                                       345566888999998888888888888865544444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00038
                            AAA_23  17 F.....skgltlItGpNGaGKTTildAikl 41 
                                       +     +k+  ++ G + +GKTT ++Ai l
  gi|488600976|ref|YP_007907447.1| 301 LwlcieNKKSLIFAGGTASGKTTSMNAISL 330
                                       15555567778999**************86 PP

>> RapH_N  response regulator aspartate phosphatase H, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.5       3.9   1.4e+04      36      44 ..      25      33 ..       8      37 .. 0.52
   2 ?   10.8   1.4   0.00011       0.4      27      53 ..     144     170 ..     138     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.9
                                      HHCTS---H CS
                            RapH_N 36 eleemeedq 44
                                      ++e++ee +
  gi|488600976|ref|YP_007907447.1| 25 AMESIEEAK 33
                                      344444433 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHCTS---HHHHHHHHHH CS
                            RapH_N  27 eelkeeikqeleemeedqdvllYYsLl 53 
                                       e+lk+ i++++e+m  + dv  YY+ l
  gi|488600976|ref|YP_007907447.1| 144 EILKNAIDSLIEDMRINLDVKSYYKIL 170
                                       79**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3557.28
//
Query:       gi|488600977|ref|YP_007907448.1|  [L=235]
Description: hypothetical protein Asulf_01472 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       442  (0.0246528); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1448.05
//
Query:       gi|488600978|ref|YP_007907449.1|  [L=230]
Description: RecA-superfamily ATPases implicated in signal transduction [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-09   35.7   0.0    7.8e-09   35.2   0.0    1.2  1  ATPase    KaiC


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   4.3e-13   7.8e-09       1     226 [.       5     223 ..       5     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 4.3e-13
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdle.k 76 
                                       ++tgI+ lD+ l+gG+peg+ v ++ +p +    + + Fl++ a+   +++ +  +  p+e +++n+ ++G d + +
  gi|488600978|ref|YP_007907449.1|   5 IPTGIHLLDRRLDGGLPEGSLVCVYANPMS----MPEAFLYQFASV--RKTYYFNTSRPSEYIKQNMLAMGFDPDvE 75 
                                       69**************************87....999999999988..99*********************997645 PP

                            ATPase  77 leeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvl.. 151
                                       + +  + ++++ + + + + + +dke  + + ++l++++++ k+ +v+ Ds + +    k +v R     l++ l  
  gi|488600978|ref|YP_007907449.1|  76 FIDVFSQYYLNEYGHFIIEDRYRDKEIFDFIEHQLNNILQDGKEYNVIFDSMSFF---LKLDVSRGLKEWLLNKLyi 149
                                       666656666777777666666699999****************************...5555555555555555553 PP

                            ATPase 152 kklgvTailvsekss.seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikv 226
                                       + +++ +++   + +  +     y v   i+d ++ +d ++i +++   l+i k+R ++ + +++ f I+e gi++
  gi|488600978|ref|YP_007907449.1| 150 ASKQTGNLFYIYVLKnVHPIDLVYTVMD-ICDVILDIDSERIGDKILSRLSIPKIRNKQPMLETFRFYISE-GIEI 223
                                       555555677666655245566789****.****************************************86.6776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1497.72
//
Query:       gi|488600979|ref|YP_007907450.1|  [L=219]
Description: hypothetical protein Asulf_01474 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-41  139.8   0.0    9.3e-41  139.6   0.0    1.0  1  EMG1      EMG1/NEP1 methyltransferase
  ------ inclusion threshold ------
       0.06   13.5   0.1       0.12   12.6   0.1    1.4  1  DUF3258   Protein of unknown function DUF3258


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.0     1e-44   9.3e-41       2     194 .]       6     214 ..       5     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 1e-44
                                       EEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT. CS
                              EMG1   2 vLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagl 62 
                                       v+ e+sLe+++++                k se +L+ ++h+ ++k+l +++k++RpDIvH+cLl++ldsp+ k+  
  gi|488600979|ref|YP_007907450.1|   6 VFLESSLEVIPEEisshpvikkeerkrgkKASEIILDDSKHHIAMKSLPNREKRGRPDIVHFCLLSVLDSPISKKA- 81 
                                       78899*******99**************999*****************************************9965. PP

                                       EEEEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC...SEEEEE-TTS CS
                              EMG1  63 lqvyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp..gskiillsesa 137
                                        ++y+ht ++++I++++ +R+Pr+++rF+gLm++L++++ i++++   +L+++++ +++ ++++  g k il++e++
  gi|488600979|ref|YP_007907450.1|  82 -EIYVHTINDEVIKFENFVRLPRNYNRFVGLMEKLFRDGVIESNGR--VLIQILDIDFEGLIDKlsGRKFILFTEKG 155
                                       .9***************************************99765..7**************99999********* PP

                                       EE-.............EEEE-SSSS....---HH.......EEESSSS---HHHHHHHHHHHCH CS
                              EMG1 138 ekklvdleefvvkpvvfvigamskgsvkidykee.......eisisnypLsaavvcskiltafE 194
                                       +k + d      +  +++iga+++g+ ++ + e        ++s+ +++ s+ +v++k ++ +E
  gi|488600979|ref|YP_007907450.1| 156 RKIMPD-----MRGSTIFIGAFPHGDFDAGIMEVlmessieMVSLGDESYSSNYVTNKAICFLE 214
                                       *55433.....34668*********5444333313334455****************9988765 PP

>> DUF3258  Protein of unknown function DUF3258
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.3e-05      0.12       6      57 ..      81     132 ..      78     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                                       TEEEEEE-SCEEEEEEEEEECCCTEEEEEEEEEEE-TTS-EEEEEEEEEEHH CS
                           DUF3258   6 selykklLdhkvikegLrvklqkdYkRfliaWvevdkDkkieeykvkdieif 57 
                                       +e+y + ++ +vik++  v+l ++Y+Rf     ++ +D+ ie   +  i+i 
  gi|488600979|ref|YP_007907450.1|  81 AEIYVHTINDEVIKFENFVRLPRNYNRFVGLMEKLFRDGVIESNGRVLIQIL 132
                                       588999999*********************************9988877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1528.68
//
Query:       gi|488600980|ref|YP_007907451.1|  [L=298]
Description: thiamine-phosphate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   63.6   0.0    3.5e-17   62.8   0.0    1.4  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0     2e-21   3.5e-17       1      93 [.      28     136 ..      28     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2e-21
                                       SSSEE........EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHH CS
                              AIRS   1 dDaav........vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp.....wle 56 
                                       dD+av        v++ d     +l e+ +f        iG+ +vavn sDla  G +P +++  ++l       +e
  gi|488600980|ref|YP_007907451.1|  28 DDCAViklndrylVLSSD-----MLHEQSDFpkimtpfeIGWMSVAVNFSDLAGSGVKPEYFIFDICLRegiedSFE 99 
                                       8***55555555599***.....999****9*****************************9999999988******* PP

                                       HHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEE CS
                              AIRS  57 evvrglaeaaeelgvplvgGdtsfsneptisvtavGl 93 
                                       e+++g+++ ++++++++vgGd+ f++e++i+ +a+G 
  gi|488600980|ref|YP_007907451.1| 100 EILKGVKALCDRYDAEVVGGDVDFGDELFIVGFALGF 136
                                       **********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1797.23
//
Query:       gi|488600981|ref|YP_007907452.1|  [L=174]
Description: putative phosphatase-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-33  114.9   0.4      3e-33  114.4   0.4    1.2  1  Macro     Macro domain
  ------ inclusion threshold ------
      0.086   13.1   0.1       0.15   12.3   0.1    1.4  1  DUF362    Domain of unknown function (DUF362)


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 !  114.4   0.4   3.3e-37     3e-33       1     118 []      26     136 ..      26     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 3.3e-37
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeel 77 
                                       VnAaN++l +gggvagai+ra+g ++++e+ +     g++++Geav t+a++l+akyviht  p+++  + k++e++
  gi|488600981|ref|YP_007907452.1|  26 VNAANTKLVMGGGVAGAIKRAGGVEIEKEAVAK----GPIKIGEAVETTAGRLKAKYVIHT--PTME-LDFKTDENK 95 
                                       9******************************99....************************..***7.8******** PP

                                       HHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  78 lakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       ++ a+k al++a+e +i+s+afPa++tG++g+++ eaa+++
  gi|488600981|ref|YP_007907452.1|  96 IRLAMKAALNKAKELDIRSIAFPALGTGVGGFSKAEAAKIM 136
                                       **************************************997 PP

>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.7e-05      0.15     102     147 ..      20      89 ..       4     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxx...................xxxxxxxx.x.xx RF
                            DUF362 102 leaDviInlpklKgHalagvtgalKnlfGc......isgsg...................kaeiHskr.d.se 147
                                       le+D+i+n +  K  + +gv ga+K + G+      +                       k  iH+ + + + 
  gi|488600981|ref|YP_007907452.1|  20 LEVDAIVNAANTKLVMGGGVAGAIKRAGGVeiekeaV---AkgpikigeavettagrlkaKYVIHTPTmElDF 89 
                                       59*************************9996555440...044455555555555566556666764433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1212.94
//
Query:       gi|488600982|ref|YP_007907453.1|  [L=155]
Description: cyclic pyranopterin monophosphate synthase subunit MoaC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-50  168.7   4.6    8.2e-50  168.4   4.6    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 !  168.4   4.6   4.6e-54   8.2e-50       1     135 [.      14     152 ..      14     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 4.6e-54
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       mvd+sek+++ r+AvAeg++kl+eet+++i e++++kG+vla+a +ag++a+Kkt+elip+cHp+plt+ve+++e++
  gi|488600982|ref|YP_007907453.1|  14 MVDISEKKDVLRIAVAEGKIKLKEETIHAIVENRVAKGNVLATAIVAGTLAVKKTPELIPMCHPIPLTQVEIDFEID 90 
                                       9*************************************************************************987 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEES CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsg 135
                                          ++++  ++vk +gktGvemEALt+v++a+lt++DmvK+++k+       + i+++r+v+K++
  gi|488600982|ref|YP_007907453.1|  91 ---DHIKAICRVKSRGKTGVEMEALTGVTTALLTIWDMVKSMEKDesgnypeTAIHDIRVVSKEK 152
                                       ...89***************************************99*****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 923.79
//
Query:       gi|488600983|ref|YP_007907454.1|  [L=452]
Description: FAD/FMN-containing dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-51  174.6   0.0    4.3e-51  174.0   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    1.8e-38  131.4   1.5    3.8e-38  130.4   1.5    1.6  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
       0.19   11.1   0.0       0.52    9.6   0.0    1.7  2  Cytokin-bind   Cytokinin dehydrogenase 1, FAD and cytokinin b


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 !  174.0   0.0   7.2e-55   4.3e-51       7     250 .]     218     447 ..     214     447 .. 0.96

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 7.2e-55
                                       EEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHHHH CS
                     FAD-oxidase_C   7 valvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeeleal 83 
                                       +++v+f  +e+a++ v++i+ +   p+ale ++ +a+  +e+ +g+  ++p++ +a l+v ++gd+++ + +++e  
  gi|488600983|ref|YP_007907454.1| 218 TLAVPFRCVEDAIRIVPKIMIE-SMPLALEYIEGEAITYGEKASGK--RWPPRDKANLMVILDGDSKDDLMRKAE-R 290
                                       7899******************.99*********************..9999999********************.* PP

                                       HHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEE CS
                     FAD-oxidase_C  84 veaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglev 160
                                       v++i+e   a dv+va+  +e + l+++R  +++      + ++  +++ D+svPv+++++++r+ ++ ++k g++v
  gi|488600983|ref|YP_007907454.1| 291 VAEICERSNAVDVFVATGREE-KDLLAVRSLIYE------GIKNDLIEILDVSVPVAKIPEYIRKCNDVAEKMGFKV 360
                                       ************888888888.89**********......99*********************************** PP

                                       EEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHH CS
                     FAD-oxidase_C 161 vlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKa 237
                                       +++gHagdgn+h  ++ ++  e+++e ++  + e+   a++lgG+i+gEHG+G  kk+ l+ + +e+++ +m+++K+
  gi|488600983|ref|YP_007907454.1| 361 INYGHAGDGNIHQHPMKRVGWEKDYEGLRMRFFEI---ASDLGGTITGEHGIGALKKDHLKHFISEREYRIMQEMKR 434
                                       *******************9999999888888888...*************************************** PP

                                       HH-TT--BSTT-- CS
                     FAD-oxidase_C 238 alDPkgiLNPgkv 250
                                        +DPkgiLNPgkv
  gi|488600983|ref|YP_007907454.1| 435 IFDPKGILNPGKV 447
                                       ************8 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   1.5   6.3e-42   3.8e-38       3     138 ..      41     175 ..      40     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 6.3e-42
                                       EEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEE.STTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHH CS
                     FAD_binding_4   3 avvrpeseeevaaalrlaneaglpvlvrGgGssll.gqavatggvvldlsrlnrileideeegtatveaGvtlgdlv 78 
                                       +vv+p+++eeva+++r+a e+++pv vrGgG++l+ g++ ++ g+vl+++r++r +e+d+e+  a+  aGvtlg+l 
  gi|488600983|ref|YP_007907454.1|  41 IVVKPRNTEEVARVMRIAYEHNIPVFVRGGGTGLScGAVPTKTGIVLSTERMKR-IEVDAENLCAVCSAGVTLGELI 116
                                       59*********************************777659*************.8********************* PP

                                       HHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  79 ealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       +a++ kgl ++++pgs +++tv+G++atnagG ++ kyG +r++v gl++vladGev+ l
  gi|488600983|ref|YP_007907454.1| 117 NAAESKGLSFPPHPGS-ESATVAGMVATNAGGVRAMKYGVMRNYVIGLKAVLADGEVLSL 175
                                       ****************.578*************************************987 PP

>> Cytokin-bind  Cytokinin dehydrogenase 1, FAD and cytokinin binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.56   3.4e+03      29      50 ..     241     262 ..     234     296 .. 0.72
   2 ?    9.6   0.0   8.8e-05      0.52     249     278 ..     415     446 ..     410     448 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.56
                                       CCTS-SEEEEEEEECCGCCCCH CS
                      Cytokin-bind  29 eeekvdYvEGfvllneellegw 50 
                                       +  +++Y+EG  ++  e ++g 
  gi|488600983|ref|YP_007907454.1| 241 MPLALEYIEGEAITYGEKASGK 262
                                       5667899999988765555544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 8.8e-05
                                       HHHHHHG..HHHHHHHHHHHHH-TT--B-GGG CS
                      Cytokin-bind 249 eWkkhfG..akWerfverKakyDPkaiLspGq 278
                                       +  khf   ++++ ++e+K+ +DPk iL pG+
  gi|488600983|ref|YP_007907454.1| 415 DHLKHFIseREYRIMQEMKRIFDPKGILNPGK 446
                                       566888644569999****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2666.09
//
Query:       gi|488600984|ref|YP_007907455.1|  [L=444]
Description: DNA repair helicase RAD25 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-27   95.0   0.3    1.5e-25   90.2   0.0    2.3  2  ResIII         Type III restriction enzyme, res subunit
    1.6e-21   76.7   1.6    2.4e-21   76.1   1.6    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    5.2e-19   68.6   0.9    1.1e-18   67.6   0.4    1.8  2  Helicase_C     Helicase conserved C-terminal domain
      1e-18   66.9   0.1    3.1e-18   65.4   0.1    1.9  1  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
    2.3e-07   30.7   0.0    1.5e-06   28.1   0.0    2.1  1  DEAD           DEAD/DEAH box helicase
    0.00023   20.0   4.1      0.019   13.7   0.7    3.4  2  SNF2_N         SNF2 family N-terminal domain
     0.0017   18.6   0.0       0.13   12.5   0.0    3.0  3  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.055   13.6   0.1         16    5.6   0.0    2.9  2  AAA_33         AAA domain
      0.065   13.7   0.0       0.26   11.7   0.0    2.0  1  AAA            ATPase family associated with various cellular


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 !   90.2   0.0   7.4e-29   1.5e-25       1     171 []      69     206 ..      69     206 .. 0.95
   2 ?    2.3   0.5     0.074   1.5e+02      62     118 ..     283     340 ..     252     375 .. 0.58

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 7.4e-29
                                       --EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII   1 klelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkf 77 
                                       ++elr+yQeea+++++       d+rg+++++TG+GKT+va+++i++l        +l++vp+++l++q++ +++ f
  gi|488600984|ref|YP_007907455.1|  69 EFELRDYQEEAVQKWM------VDRRGVVVLPTGAGKTYVAMEIIRELNV-----PTLIVVPTLDLIDQWMAKLSIF 134
                                       689************7......689***********************99.....8******************999 PP

                                       TGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHH CS
                            ResIII  78 lseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreil 154
                                        +       +++sg+kk++       k i+++t++s++ +         e l ++f++i++DE+H+l + +s+r i+
  gi|488600984|ref|YP_007907455.1| 135 GEI------GEFSGRKKEI-------KAITISTYDSAYINA--------ETLGNKFLLIVFDEVHHLPS-ESYRVIA 189
                                       974......5789999999.......9**************........99******************.******* PP

                                       HT---SEEEEEESS-S- CS
                            ResIII 155 ekfkeavllglTATper 171
                                       e+  + ++lglTAT+er
  gi|488600984|ref|YP_007907455.1| 190 EMSCAPYRLGLTATMER 206
                                       **************985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.074
                                       SSHHHHHHHHHHGGGGTGG......GEEEESSS-B--............-SEEEEEHHHHHHTH CS
                            ResIII  62 prkslleqtleefkkflseayke..igkkvsgdkkka.....kekdstnkkilvttiqsldads 118
                                        r+   +q++e++k++ +  + +   ++k+      +      ++++++k i++t ++ l  ++
  gi|488600984|ref|YP_007907455.1| 283 MRTGFDKQAYEALKSWEEARKIAynSKNKL------KvlknlLQRHRKDKIIIFTRYNDLVYRI 340
                                       445555555555555554443223222222......1223333577777888888877765544 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 !   76.1   1.6   1.2e-24   2.4e-21      33     185 ..     299     441 ..     282     444 .] 0.86

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.2e-24
                     ERCC3_RAD25_C  33 kkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvnt 109
                                       ++ ++++    nk+++++ L++ h  r+Dkii+f+     + ++++ +  p i+ +t+++er++il++f++   +++
  gi|488600984|ref|YP_007907455.1| 299 EEARKIAYNSKNKLKVLKNLLQRH--RKDKIIIFTRYNDLVYRISRLFLIPAITYKTDQSERKEILRNFRRG-IYRV 372
                                       445566667789*********988..89******8666666677888999*******************987.799* PP

                     ERCC3_RAD25_C 110 iflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrqqfl 185
                                       i+ s+v D+ +D+P+an+ i   s  gs r   qrlGriLr+  k      +a  Y +vs++t+e   s++r++ l
  gi|488600984|ref|YP_007907455.1| 373 IVSSQVLDEGVDVPDANIGII-MSGSGSAREYIQRLGRILRPSGK------KAILYEIVSSETSEERVSRRRRRKL 441
                                       *****************9995.5668999*************887......8*******************99866 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 ?   -2.4   0.0         3   5.9e+03      18      35 ..     113     134 ..     103     163 .. 0.59
   2 !   67.6   0.4   5.6e-22   1.1e-18       2     109 ..     311     412 ..     310     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3
                                       EEEEEESSHHHHHH....HHHH CS
                        Helicase_C  18 kilifvntidrlek....vkll 35 
                                        +li+v+t d +++    ++++
  gi|488600984|ref|YP_007907455.1| 113 PTLIVVPTLDLIDQwmakLSIF 134
                                       5788888888777554332333 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 5.6e-22
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       kl+ l++ll ++++++ki+if+++ d +++++ l     + + +++ ++ q+er+eil++f++g ++v+++++v+ +
  gi|488600984|ref|YP_007907455.1| 311 KLKVLKNLL-QRHRKDKIIIFTRYNDLVYRISRL-----FLIPAITYKTDQSERKEILRNFRRGIYRVIVSSQVLDE 381
                                       89999***9.9***************99743333.....5566688889**************************** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       G+d+p++n  i+++   + ++yiqr GR+ R
  gi|488600984|ref|YP_007907455.1| 382 GVDVPDANIGIIMSGSGSAREYIQRLGRILR 412
                                       *****************************99 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 !   65.4   0.1   1.5e-21   3.1e-18       1      57 []       5      57 ..       5      57 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1.5e-21
                                      EEEETTEEEECSSSTT...-CT.EEETTTTEEEEEGGGHHHHHHHHHCTT--EEEES CS
                           XPB_DRD  1 LrYdrGTllidgdprgkaslpfvewDeRvekyRapAlrYrdlveaLraagiefeDrv 57
                                      L+YdrGT++++gd +    +pf  +DeRv++yR++A++Yrdlve+L  +gie+e++v
  gi|488600984|ref|YP_007907455.1|  5 LSYDRGTIIAKGDVH----IPFGSFDERVGCYRVLAYKYRDLVEYLNLSGIEYEEEV 57
                                      89*************....***********************************998 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   7.5e-10   1.5e-06       2     169 ..      74     204 ..      73     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.5e-10
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       d+Q+ea++  + ++  +v  +TG+GKT +++  +++++       +  +liv+Pt  L+ q + +l+ f++ i+   
  gi|488600984|ref|YP_007907455.1|  74 DYQEEAVQKWMVDRRGVVVLPTGAGKTYVAME-IIREL-------NVPTLIVVPTLDLIDQWMAKLSIFGE-IG--- 138
                                       89*********9****************9654.44344.......5678********************99.33... PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                          ++g ++  ++++      i+++t +      +t     +++ ++V+DE++ l +++++   +   +        
  gi|488600984|ref|YP_007907455.1| 139 --EFSGRKK--EIKA------ITISTYDSAYINAETL---GNKFLLIVFDEVHHLPSESYRVIAEMSCAPY------ 196
                                       ..2344443..3333......4555555555433322...2567799********9997765554422222...... PP

                                       STTTSEEEEEESSB CS
                                       xxxxxxxxxxxxxx RF
                              DEAD 156 gklqrqvivlSATl 169
                                              + l+AT+
  gi|488600984|ref|YP_007907455.1| 197 ------RLGLTATM 204
                                       ......56666666 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 !   13.7   0.7   9.4e-06     0.019      93     116 ..     108     132 ..      75     204 .. 0.77
   2 !    5.3   0.0    0.0035         7     256     318 ..     210     268 ..     174     309 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-06
                                       ....S-EEEE--H.HHHHHHHHHHH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxx RF
                            SNF2_N  93 dtlagptLivvPa.slldqWeneie 116
                                       ++l +ptLivvP+ +l+dqW+ ++ 
  gi|488600984|ref|YP_007907455.1| 108 RELNVPTLIVVPTlDLIDQWMAKLS 132
                                       67899****************8876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0035
                                       HHHHHHTT-STTEE---GGGT--S---EEEEEEEEE--HHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 256 grsrLlqllqrlmlrrakkdveknlPpkteeiiflklskverksYnrllevlrkkalakllkr 318
                                         s L +l+   +   + +++++ l+p t + i ++ls++e+ +Y +l     kk++  l+k+
  gi|488600984|ref|YP_007907455.1| 210 LHSLLPKLVGGKVYEVTHDQISEHLAPFTIKRIKVPLSEKEKGAYDQLS----KKFRDYLKKK 268
                                       223333444455566667777999**********************433....3333333333 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   6.7e-05      0.13       9     109 ..      90     185 ..      85     193 .. 0.74
   2 ?    2.2   0.0     0.099     2e+02      63     117 ..     241     300 ..     202     318 .. 0.73
   3 ?   -1.7   0.0       1.6   3.2e+03      45      71 ..     392     426 ..     375     443 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.....sskdllrellralglelkaerlsseell. 79 
                                       vv+ ++G+GKT+++ ++ ++l         +++++ v ++ +         +++ e+ ++ g++++ +  + + +  
  gi|488600984|ref|YP_007907455.1|  90 VVVLPTGAGKTYVAMEIIREL---------NVPTLIVVPTLDLidqwmAKLSIFGEIGEFSGRKKEIKAITISTYDs 157
                                       66669****************.........77777555554444444788899999999999888886666666665 PP

                            AAA_22  80 ealeqalraravielliiDEaqhlrseeal 109
                                       ++++      +   l++ DE++hl + e +
  gi|488600984|ref|YP_007907455.1| 158 AYINAETLGNKF-LLIVFDEVHHL-PSESY 185
                                       666666666666.9**********.76655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.099
                            AAA_22  63 alglelka.erlsseellealeqalraravielliiDEaqhlr..s...eealeeLrslln 117
                                        ++++l++ e +  ++l ++++++l+++++ +l   D++ ++   +   ++a+e L+s+ +
  gi|488600984|ref|YP_007907455.1| 241 RIKVPLSEkEKGAYDQLSKKFRDYLKKKGM-KLTSMDDFRKIVmrTgfdKQAYEALKSWEE 300
                                       55555555444556677799**********.********9976562566888888888755 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.6
                            AAA_22  45 vtlpsstsskdllrellralglelka........e 71 
                                       + +++s+s ++  ++l r+l  ++k+        +
  gi|488600984|ref|YP_007907455.1| 392 IIMSGSGSAREYIQRLGRILRPSGKKailyeivsS 426
                                       55566777777777777777766666666555543 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.008        16       7      32 ..      94     120 ..      90     191 .. 0.84
   2 ?    5.1   0.1     0.012        24      80     121 ..     399     439 ..     261     444 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.008
                            AAA_33   7 lpGsGKstlaerllkklg.avllssdt 32 
                                       + G+GK+++a +++++l   +l+  +t
  gi|488600984|ref|YP_007907455.1|  94 PTGAGKTYVAMEIIRELNvPTLIVVPT 120
                                       67**************99855555554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                            AAA_33  80 lsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaan 121
                                         r+  +r+ +++r  g + +i++  ++ et +eR+ +R ++
  gi|488600984|ref|YP_007907455.1| 399 SAREYIQRLGRILRPSG-KKAILYEIVSSETSEERVSRRRRR 439
                                       44566688889999999.999****************99986 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   0.00013      0.26       6      72 ..      94     182 ..      90     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       STTSSHHHHHHHHHHHHTHE.EEEEETTTCSSS.............STTHHHHHHHHHHHHHHHTS.........TS CS
                               AAA   6 ppGtGKTllakavakelgve.fleisgsellsk.............yvgesekkirelfkeakeka.........kp 59 
                                       p G GKT++a  +++el+v+ ++ +   +l+++             + + ++k+i+++  +   +a         k 
  gi|488600984|ref|YP_007907455.1|  94 PTGAGKTYVAMEIIRELNVPtLIVVPTLDLIDQwmaklsifgeigeF-SGRKKEIKAITISTYDSAyinaetlgnKF 169
                                       89****************87347777777776666667766655532.33333344433333333344456677444 PP

                                       EEEEEETGGGHHH CS
                               AAA  60 silfiDEidalak 72 
                                         +++DE++ l +
  gi|488600984|ref|YP_007907455.1| 170 LLIVFDEVHHLPS 182
                                       8888888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2540.85
//
Query:       gi|488600985|ref|YP_007907456.1|  [L=451]
Description: hypothetical protein Asulf_01480 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-113  379.3   5.2     2e-113  379.0   5.2    1.0  1  DUF790           Protein of unknown function (DUF790)
  ------ inclusion threshold ------
       0.95   10.2   4.2        2.1    9.1   0.9    2.9  2  Antimicrobial20  Aurein-like antibiotic peptide


Domain annotation for each model (and alignments):
>> DUF790  Protein of unknown function (DUF790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.0   5.2  2.3e-117    2e-113       1     386 [.       1     366 [.       1     367 [. 0.98

  Alignments for each domain:
  == domain 1  score: 379.0 bits;  conditional E-value: 2.3e-117
                            DUF790   1 MLpsdllrvrrrggkivpkflkeenlelaaelielfeehvGekrgeleeelkeleeeatdyklvrGLakllereaef 77 
                                       MLp+++l vr+ +gki+p+f++ e+ ++a+++i+++ +++G+k ++ ++e+k++e+ +++yk +r++a+++ere++f
  gi|488600985|ref|YP_007907456.1|   1 MLPKEYLDVRKIKGKIYPRFVDFEWFDIAKKVISIYAKNTGNKLKKARNEVKKIED-SENYKKIRAFARIVEREIDF 76 
                                       ********************************************************.67****************** PP

                            DUF790  78 etespldpeelReevFeaaaeavvseeereevleevaeelgvspeeveealyadleenkiLtefeeitpeeLlkrYN 154
                                       +++++l+p e+R+ +F++++  v++ +ere+v+eeva+++gv+++e+e ++++d+ee++i+  + +++pe+Ll +YN
  gi|488600985|ref|YP_007907456.1|  77 KSPTTLNPLEVRKLLFSKGP--VTTASEREKVIEEVARRFGVDKREIELSMFGDMEEDSIIDGV-KVDPETLLMKYN 150
                                       ********************..*************************************99998.8*********** PP

                            DUF790 155 lslvqtlLfkatelrirvsdaeykelfravkllgLmyeieedaeegleitvdGPaslfkaterYGlalAkllpallk 231
                                       lsl+qt+L++a+ +r+rv+d ++k++f+ +k+lgLmyeie++      ++++GPas++k+t++YG+a+Akl+pa+++
  gi|488600985|ref|YP_007907456.1| 151 LSLLQTTLMNAIAVRFRVED-NHKKVFSGIKRLGLMYEIEDEF-----VRLTGPASILKQTKKYGTAFAKLIPAIVN 221
                                       ********************.9******************998.....99*************************** PP

                            DUF790 232 vekWeleAeikdrdkkkrelrfeldsedsglvshyeeekefdssveeefaerfeklktdwelerepellkiggsvmi 308
                                       ++ W ++Aei d d   r++r++++sed +++ + + + +fdss+eee+++r+    +d e++rep l+ +gg ++i
  gi|488600985|ref|YP_007907456.1| 222 SRLWVIHAEILDYD---RIYRMSISSEDGVMFYREKLSMDFDSSLEEELYSRLICSRRDLEIVREPSLVSVGGFAFI 295
                                       *************9...************************************999********************* PP

                            DUF790 309 PDFaleekdgrrvyleIvGfwtpeylkkKleklrkaerkelivavserlklekagvkakdlrvilfkdklrvkdVle 385
                                       PDF++ ++++r++y+eI+Gfwt++y+kkK+ek+++a+  +l+v+++e+++ +      k+ +vi fk+kl++ ++l+
  gi|488600985|ref|YP_007907456.1| 296 PDFRI-RRGDREIYIEIAGFWTEDYVKKKVEKIERAN-IPLLVVAREEIAEK---L--KSRHVIRFKNKLPYLKILK 365
                                       *****.9*****************************9.**********9654...3..4557************998 PP

                            DUF790 386 v 386
                                       +
  gi|488600985|ref|YP_007907456.1| 366 F 366
                                       6 PP

>> Antimicrobial20  Aurein-like antibiotic peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.9   0.00023       2.1       3      11 ..      26      34 ..      26      35 .. 0.91
   2 ?    0.6   0.1      0.13   1.2e+03       7      13 .]     173     179 ..     173     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00023
                   Antimicrobial20  3 fDiaKKVvg 11
                                      fDiaKKV++
  gi|488600985|ref|YP_007907456.1| 26 FDIAKKVIS 34
                                      9******97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                   Antimicrobial20   7 KKVvggi 13 
                                       KKV++gi
  gi|488600985|ref|YP_007907456.1| 173 KKVFSGI 179
                                       9****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2899.64
//
Query:       gi|488600986|ref|YP_007907457.1|  [L=168]
Description: Ferritin-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-45  152.0   1.8    1.1e-44  151.8   1.8    1.0  1  Ferritin      Ferritin-like domain
     0.0011   19.4   1.3     0.0024   18.3   1.2    1.6  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
       0.08   13.2   0.4        2.5    8.4   0.1    2.2  2  NusB          NusB family


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 !  151.8   1.8   1.8e-48   1.1e-44       1     141 [.       7     143 ..       7     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 1.8e-48
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS CS
                          Ferritin   1 ikaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke 77 
                                       +kaLn+q+++e+++ay+yl+ma y++++ l+g+a++++ qa+ee+ ha+kl++++ ++Gg     r++l  ie+p++
  gi|488600986|ref|YP_007907457.1|   7 LKALNRQINAEFYSAYLYLSMATYFESISLKGFANWMRVQAKEELMHAMKLFDFVVERGG-----RVKLDGIEKPPS 78 
                                       589*********************************************************.....************ PP

                                       .CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  78 .fgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekler 141
                                        ++s+++++ea++ he kvt++++el++la ee+D+a++ fl++++ eq+e+e+  +++++kl++
  gi|488600986|ref|YP_007907457.1|  79 eWKSPLDAFEAVYRHEVKVTSMINELVDLALEEKDHASYAFLQWYVMEQVEEEASADEIVQKLKL 143
                                       **************************************************************997 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.2   4.1e-07    0.0024       2     127 ..       9     127 ..       8     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.1e-07
                                       HHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   2 iLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                        L++ i +E+    lY ++a  ++  +++  a+ ++  A+eE  Ha +l++++ ++ +  +l       +  +++ +
  gi|488600986|ref|YP_007907457.1|   9 ALNRQINAEFYSAYLYLSMATYFEsISLKGFANWMRVQAKEELMHAMKLFDFVVERGGRVKL------DGIEKPPSE 79 
                                       689999******************999****************************9999993......334445556 PP

                                       TGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEk 127
                                       +++  +  e+++ + + + + m+ ++ +la +e++  a   f ++  +E+
  gi|488600986|ref|YP_007907457.1|  80 WKSPLDAFEAVY-RHEVKVTSMINELVDLALEEKDH-ASYAFLQWYVMEQ 127
                                       655555666555.55555667889999999988777.7888888888886 PP

>> NusB  NusB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00041       2.5      91     124 ..      86     119 ..      84     121 .. 0.93
   2 ?    4.1   0.0    0.0086        52      91     124 ..     119     152 ..     117     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00041
                                       HHHHTTS-SSHHHHHHH.HHHHHHHHS-HHHHHH CS
                              NusB  91 vyellylddvPakvaineavelakkygdeksakF 124
                                       ++e  y+ +v    +ine v+la + +d+ s++F
  gi|488600986|ref|YP_007907457.1|  86 AFEAVYRHEVKVTSMINELVDLALEEKDHASYAF 119
                                       6899*********************999999988 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0086
                                       HHHHTTS-SSHHHHHHH.HHHHHHHHS-HHHHHH CS
                              NusB  91 vyellylddvPakvaineavelakkygdeksakF 124
                                       + +   +++v ++++ +e+v+  k  gdeks  F
  gi|488600986|ref|YP_007907457.1| 119 FLQWYVMEQVEEEASADEIVQKLKLVGDEKSGLF 152
                                       66778899*********************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1009.97
//
Query:       gi|488600987|ref|YP_007907458.1|  [L=205]
Description: hypothetical protein Asulf_01482 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1137.64
//
Query:       gi|488600988|ref|YP_007907459.1|  [L=99]
Description: hypothetical protein Asulf_01483 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 675.87
//
Query:       gi|488600989|ref|YP_007907460.1|  [L=104]
Description: hypothetical protein Asulf_01484 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.048   13.8   0.8      0.059   13.5   0.8    1.1  1  AAA_lid_10  AAA lid domain
      0.066   13.6   0.3       0.14   12.6   0.3    1.7  1  Eaf7        Chromatin modification-related protein EAF7
       0.15   11.2   0.1       0.16   11.2   0.1    1.1  1  RtcB        tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   9.9e-06     0.059      12      78 ..      18      84 ..      10      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.9e-06
                                      ------------------------------------.---HHHHHHHHHHT-TTTTHHHHHHHHHHHH CS
                        AAA_lid_10 12 fyvnektgsailieaeeekkqklPenvkkvrlkisd.daieiasrkvAsvsgdarrAlkiCkrAvEia 78
                                       +v++k  +  + +a+  + +++P+ + +++ +i++ +  e+++r+vA + +    A +i kr +Ei 
  gi|488600989|ref|YP_007907460.1| 18 VVVDKKIREYEVDNARVIEIDRIPKRI-EIESTIEErELAEMITRNVAWMVEKGYNAKQIVKRIAEIY 84
                                      5788888888888888888999**986.688888752789**************************95 PP

>> Eaf7  Chromatin modification-related protein EAF7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   2.3e-05      0.14      41      76 ..      62      97 ..      17     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                              Eaf7 41 kekpksgkhtsiediwekLktlYdLkaldeleneke 76
                                      + +   +k  ++++i +++ ++Y++++ d++e +++
  gi|488600989|ref|YP_007907460.1| 62 NVAWMVEKGYNAKQIVKRIAEIYGMDEHDAMEFYRY 97
                                      45556778899*********************8765 PP

>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.6e-05      0.16      76     131 ..      38      91 ..      14      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.6e-05
                                       HHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  76 kavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadl 131
                                       +++p  ++ ++  +++++el e+++++++w+ve+g+++++ +++i e   ++e d+
  gi|488600989|ref|YP_007907460.1|  38 DRIPKRIEIES--TIEERELAEMITRNVAWMVEKGYNAKQIVKRIAEIYGMDEHDA 91 
                                       45666665444..445899*********************9999998877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 720.24
//
Query:       gi|488600990|ref|YP_007907461.1|  [L=49]
Description: hypothetical protein Asulf_01485 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 316.91
//
Query:       gi|488600991|ref|YP_007907462.1|  [L=81]
Description: hypothetical protein Asulf_01486 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 519.04
//
Query:       gi|488600992|ref|YP_007907463.1|  [L=97]
Description: hypothetical protein Asulf_01487 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   18.9   0.3      0.012   15.5   0.0    2.3  2  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.059   13.2   0.0      0.092   12.6   0.0    1.4  1  OHA       OST-HTH Associated domain
       0.15   10.9   0.0       0.16   10.8   0.0    1.0  1  PPV_E1_C  Papillomavirus helicase


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     2e-06     0.012       1      38 [.      19      57 ..      19      58 .. 0.96
   2 ?    1.1   0.1     0.068   4.1e+02       8      24 ..      68      85 ..      67      89 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      r+si+++  l+++L e+ + ++  + Se++  A++e++ 
  gi|488600992|ref|YP_007907463.1| 19 RLSISISPYLKKKLKEMEKSGEfANISEIVNLAIAEFIG 57
                                      89********************************99975 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.068
                                      HHHHHHHHHHHHHHT.SS CS
                             RHH_1  8 eellerLdelarrrg.rS 24
                                      ++ +e++ e ++ ++ + 
  gi|488600992|ref|YP_007907463.1| 68 RKSAEEIAEEIEQEKhKP 85
                                      577788888877776555 PP

>> OHA  OST-HTH Associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05     0.092      33      75 ..      41      84 ..      25      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                               OHA 33 LGelchiVqlainkkiliyenn.slipveasekaanssqsadnk 75
                                       + +  iV+lai + i  ye +  l+p+++ e +a++++++ +k
  gi|488600992|ref|YP_007907463.1| 41 FANISEIVNLAIAEFIGKYEAQgKLKPRKSAEEIAEEIEQEKHK 84
                                      67899*************887779************99988766 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.7e-05      0.16     206     246 ..      16      56 ..       2      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.7e-05
                          PPV_E1_C 206 raemkkmsmsewikkrlkevedegdWkeivkflryqgveli 246
                                       + e  ++s+s ++kk+lke+e++g++ +i++ ++    e+i
  gi|488600992|ref|YP_007907463.1|  16 KKERLSISISPYLKKKLKEMEKSGEFANISEIVNLAIAEFI 56 
                                       5677789***********************99987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1150  (0.0641419); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 689.94
//
Query:       gi|488600993|ref|YP_007907464.1|  [L=78]
Description: hypothetical protein Asulf_01488 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-05   25.1   0.0    1.6e-05   24.6   0.0    1.2  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     9e-10   1.6e-05       1      38 [.      16      55 ..      16      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 9e-10
                                      EEEEEEEHHHHHHHHHHHHHHT..SSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg..rSrSelIReAlreyle 38
                                      rvs++l  ++l+ +d+ ++++g  +SrS++IR ++r +++
  gi|488600993|ref|YP_007907464.1| 16 RVSVYLTTDELKDFDKAVKKSGrfVSRSDAIRYLIRKFID 55
                                      9*********************999***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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 0.32s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 463.57
//
Query:       gi|488600994|ref|YP_007907465.1|  [L=104]
Description: hypothetical protein Asulf_01489 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.5   0.3        0.1   12.2   0.3    1.3  1  MRP-S25          Mitochondrial ribosomal protein S25
      0.093   12.9   0.0       0.14   12.3   0.0    1.3  1  hGDE_N           N-terminal domain from the human glycogen de
       0.48   10.6   1.6       0.53   10.4   0.3    1.7  2  FbpC_C_terminal  FbpC C-terminal regulatory nucleotide bindin


Domain annotation for each model (and alignments):
>> MRP-S25  Mitochondrial ribosomal protein S25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   1.7e-05       0.1      38     109 ..      29     104 .]      12     104 .] 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                           MRP-S25  38 Pstkltrkpklredpskkkrkktlkkksekk....klektreskkekkkkakklfkppklkyleDklRkqFykdHP 109
                                       P+t++t + +++++++ +++++t++k  e k    + +k ++  + + + + + f ++k+ky++ klRk F +d P
  gi|488600994|ref|YP_007907465.1|  29 PKTNVTVNLPTQPSQTIRHEHHTMPKPPEIKvtltRGQKGSYGWEITYNGTDSEFIISKIKYIDEKLRKLFLEDEP 104
                                       66666666666665555555555555555444432233334444445555666799***************99987 PP

>> hGDE_N  N-terminal domain from the human glycogen debranching enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.4e-05      0.14       3      70 ..      19      82 ..      18     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                                      EEE-TT-GGGTT-EEEE-S-SSSS---TT--EEEE----SSS-EEEEEEE-S-CEEEEEEEEE-TTSS CS
                            hGDE_N  3 fviegasligrkgslwtNyPeegkeFeRdkfrelklkssfekdiyidipitkaGaFafyftydeeeel 70
                                      + i+++s  + k ++ +N P++ ++  R+++++++  ++    i++++   + G++ + +ty+ ++++
  gi|488600994|ref|YP_007907465.1| 19 LKIDDTSADSPKTNVTVNLPTQPSQTIRHEHHTMPKPPE----IKVTLTRGQKGSYGWEITYNGTDSE 82
                                      67899999999*******************999887765....5588888999*********987665 PP

>> FbpC_C_terminal  FbpC C-terminal regulatory nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   8.9e-05      0.53       8      34 ..      15      41 ..      12      47 .. 0.92
   2 ?   -2.2   0.0      0.77   4.6e+03       8      23 ..      51      66 ..      49      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.9e-05
                                      EEE-SSSEEEEEEETTEEEEEEESS-- CS
                   FbpC_C_terminal  8 TtPkaRhvEiSlraGqtVlTlnLpsAP 34
                                      T Pk ++ + S+++ +t +T nLp  P
  gi|488600994|ref|YP_007907465.1| 15 TKPKLKIDDTSADSPKTNVTVNLPTQP 41
                                      889*********************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.77
                                      EEE-SSSEEEEEEETT CS
                   FbpC_C_terminal  8 TtPkaRhvEiSlraGq 23
                                      T Pk   + + l  Gq
  gi|488600994|ref|YP_007907465.1| 51 TMPKPPEIKVTLTRGQ 66
                                      7788888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 674.45
//
Query:       gi|488600995|ref|YP_007907466.1|  [L=45]
Description: hypothetical protein Asulf_01490 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       440  (0.0245412); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 309.67
//
Query:       gi|488600996|ref|YP_007907467.1|  [L=128]
Description: hypothetical protein Asulf_01491 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0018   17.9   1.9      0.047   13.4   0.2    2.7  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
     0.0089   16.4   1.6          1   10.0   0.0    3.0  2  zf-C2H2          Zinc finger, C2H2 type
     0.0097   15.6   1.6       0.55   10.0   0.7    2.4  2  Ribosomal_S27e   Ribosomal protein S27
  ------ inclusion threshold ------
       0.04   14.0   0.4        6.1    7.0   0.0    2.5  2  zf-BED           BED zinc finger
      0.094   12.3   3.9        3.5    7.3   0.1    2.4  2  zf_C2H2_13       Zinc finger domain
       0.15   12.6  10.9        1.3    9.6   0.5    2.5  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.48   10.9   5.5        4.2    7.9   0.1    2.8  3  E6               Early Protein (E6)
        5.5    8.1   0.0        5.5    8.1   0.0    3.8  4  zf-C2H2_4        C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.033        75       3       8 ..       5      10 ..       2      19 .. 0.64
   2 !   13.4   0.2   2.1e-05     0.047      11      27 ..      62      78 ..      58      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.033
                                      -SSS-- CS
                    DNA_RNApol_7kD  3 CgeCga 8 
                                      Cg Cg+
  gi|488600996|ref|YP_007907467.1|  5 CGICGK 10
                                      555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.1e-05
                                      ---SSS----SSS---- CS
                    DNA_RNApol_7kD 11 slkkgdpiRCkeCGhRi 27
                                       + ++  +RCk+CG  +
  gi|488600996|ref|YP_007907467.1| 62 PILQEGEVRCKNCGRPV 78
                                      6667778*******655 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00045         1       2      17 ..       4      19 ..       3      20 .. 0.88
   2 ?    4.6   0.3     0.023        52       2       9 ..      70      77 ..      69      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00045
                                      EETTTTEEESSHHHHH CS
                           zf-C2H2  2 kCpdCgksFkrksnLk 17
                                      +C++Cgk+ +++++ +
  gi|488600996|ref|YP_007907467.1|  4 RCGICGKPLSNPDSVR 19
                                      7**********99866 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.023
                                      EETTTTEE CS
                           zf-C2H2  2 kCpdCgks 9 
                                      +C+ Cg++
  gi|488600996|ref|YP_007907467.1| 70 RCKNCGRP 77
                                      7*****76 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.7   0.00024      0.55      26      41 ..       2      17 ..       1      30 [. 0.80
   2 ?    4.2   0.0     0.016        36      27      36 ..      69      78 ..      65      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                                      -EEESSSTCEEEEECS CS
                    Ribosomal_S27e 26 vvkCisCgkvLvePtG 41
                                       v C +Cgk+L +P  
  gi|488600996|ref|YP_007907467.1|  2 TVRCGICGKPLSNPDS 17
                                      599**********965 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.016
                                      EEESSSTCEE CS
                    Ribosomal_S27e 27 vkCisCgkvL 36
                                      v C  Cg+++
  gi|488600996|ref|YP_007907467.1| 69 VRCKNCGRPV 78
                                      7888888876 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0027       6.1      17      28 ..       3      14 ..       2      23 .. 0.88
   2 ?    4.8   0.1     0.013        28      12      24 ..      64      76 ..      54      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0027
                                      -EETTTTEE--- CS
                            zf-BED 17 avCryCgkilsr 28
                                      ++C +Cgk ls+
  gi|488600996|ref|YP_007907467.1|  3 VRCGICGKPLSN 14
                                      89******9997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
                                      GGSS--EETTTTE CS
                            zf-BED 12 lkeqkavCryCgk 24
                                      l+e+ ++C+ Cg+
  gi|488600996|ref|YP_007907467.1| 64 LQEGEVRCKNCGR 76
                                      6799*******97 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.8     0.006        13      20      28 ..       5      13 ..       4      16 .. 0.91
   2 ?    7.3   0.1    0.0016       3.5      20      27 ..      71      78 ..      68      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.006
                        zf_C2H2_13 20 CnkCGkPis 28
                                      C  CGkP+s
  gi|488600996|ref|YP_007907467.1|  5 CGICGKPLS 13
                                      899****98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                        zf_C2H2_13 20 CnkCGkPi 27
                                      C++CG+P+
  gi|488600996|ref|YP_007907467.1| 71 CKNCGRPV 78
                                      *******8 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 ?    9.6   0.5   0.00059       1.3       6      17 ..       3      14 ..       2      39 .. 0.80
   2 ?    7.3   4.0    0.0031       6.9       6      21 ..      69      84 ..      64     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00059
                   Zn_ribbon_recom  6 lrCgeCGspmtr 17
                                      +rCg CG+p+++
  gi|488600996|ref|YP_007907467.1|  3 VRCGICGKPLSN 14
                                      79*******987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0031
                   Zn_ribbon_recom  6 lrCgeCGspmtrrkrk 21
                                      +rC++CG+p +++   
  gi|488600996|ref|YP_007907467.1| 69 VRCKNCGRPVYYHPDD 84
                                      8**********99765 PP

>> E6  Early Protein (E6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0094        21      71      85 ..       2      16 ..       1      21 [. 0.86
   2 ?    7.9   0.1    0.0019       4.2      32      81 ..      21      78 ..      15      86 .. 0.65
   3 ?   -2.0   0.6       2.1   4.8e+03      33      39 ..      91      97 ..      82     124 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0094
                                      EEEETTT--B--HHH CS
                                E6 71 eiRCvvClklLskee 85
                                      ++RC  C+k+Ls+ +
  gi|488600996|ref|YP_007907467.1|  2 TVRCGICGKPLSNPD 16
                                      79*********9876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0019
                                      BXXHHHHHHHHHHHHHHHEEEEEEHHHHH..HHHTST......GGGSEEEETTT--B- CS
                                E6 32 gvCkkClevlallelllhlerslkakele..elvgks......lsdleiRCvvClklL 81
                                      g+  kC++ l + ++  ++e+ ++  +l+  ++++k+      l++ e+RC +C++++
  gi|488600996|ref|YP_007907467.1| 21 GIGPKCAQKLRSADFRSQMEERIQKLRLKahREYNKNlkkypiLQEGEVRCKNCGRPV 78
                                      6667788888777877777777776665411345555111122455689*****9975 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.1
                                      XXHHHHH CS
                                E6 33 vCkkCle 39
                                      +C+ C+ 
  gi|488600996|ref|YP_007907467.1| 91 CCSPCCP 97
                                      5555553 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0025       5.5       2      17 ..       4      19 ..       3      20 .. 0.87
   2 ?   -3.2   0.0         8   1.8e+04      15      20 ..      47      52 ..      43      53 .. 0.66
   3 ?    1.3   0.3      0.37   8.3e+02       2       9 ..      70      77 ..      69      81 .. 0.84
   4 ?   -5.1   7.0         8   1.8e+04       1       6 [.      90      95 ..      85     105 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                         zf-C2H2_4  2 kCpiCgksFsskkaLl 17
                                      +C iCgk+ s++++++
  gi|488600996|ref|YP_007907467.1|  4 RCGICGKPLSNPDSVR 19
                                      7*********999876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8
                         zf-C2H2_4 15 aLlrHl 20
                                      +L+ H 
  gi|488600996|ref|YP_007907467.1| 47 RLKAHR 52
                                      477775 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.37
                         zf-C2H2_4  2 kCpiCgks 9 
                                      +C+ Cg++
  gi|488600996|ref|YP_007907467.1| 70 RCKNCGRP 77
                                      7****986 PP

  == domain 4  score: -5.1 bits;  conditional E-value: 8
                         zf-C2H2_4  1 fkCpiC 6 
                                      f+C+ C
  gi|488600996|ref|YP_007907467.1| 90 FCCSPC 95
                                      566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 908.62
//
Query:       gi|488600997|ref|YP_007907468.1|  [L=55]
Description: hypothetical protein Asulf_01492 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); 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: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 369.43
//
Query:       gi|488600998|ref|YP_007907469.1|  [L=214]
Description: hypothetical protein Asulf_01493 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   11.4   0.0       0.14   11.0   0.0    1.2  1  HTS       Homoserine O-succinyltransferase


Domain annotation for each model (and alignments):
>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     8e-06      0.14     185     270 ..     120     200 ..      99     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-06
                                       EEEEEEEEEEE--HHHHTT-TTEEEEEEETTTEEEEEEESSSSEEEE-S-TT--TTHHHHHHHHHHHTT------BT CS
                               HTS 185 eflvphsRytevkeedieekkelevLaeseeaGvsllaskdkrevfvlgHpEYdaetLkkEyeRDlekgleielPkn 261
                                       ++++p s+  ++ +   e+    e++ ++ eaG+ l ++++++ + v+ H+E++a     + +RD +k + +++ + 
  gi|488600998|ref|YP_007907469.1| 120 KITLPLSKVRKLYDLMPEKFGVKELFEKAGEAGLALSKQAAGHLIRVFSHVEFNA-----DVRRDGNKLVAVKIEEG 191
                                       556666666666655555555556788899**********************986.....589************** PP

                                       TSGGG-TTS CS
                               HTS 262 Yfpeddpkk 270
                                       Y++e++ +k
  gi|488600998|ref|YP_007907469.1| 192 YLREENRRK 200
                                       **9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1651.86
//
Query:       gi|488600999|ref|YP_007907470.1|  [L=100]
Description: hypothetical protein Asulf_01494 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 741.26
//
Query:       gi|488601000|ref|YP_007907471.1|  [L=109]
Description: hypothetical protein Asulf_01495 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   5.1     0.0064   16.8   5.2    1.7  2  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
     0.0062   17.3   8.2       0.36   11.8   2.0    2.4  2  zf-C2H2_4      C2H2-type zinc finger
  ------ inclusion threshold ------
      0.043   13.6   1.4      0.073   12.9   0.1    1.9  2  Rad50_zn_hook  Rad50 zinc hook motif
      0.064   12.8   0.1       0.08   12.5   0.1    1.1  1  NPC1_N         Niemann-Pick C1 N terminus
      0.081   13.6   0.6       0.14   12.8   0.6    1.4  1  FOXP-CC        FOXP coiled-coil domain
       0.17   12.0   3.0        2.7    8.1   0.3    2.2  2  zf-C2H2_aberr  Aberrant zinc-finger
       0.43   11.1   8.7        2.3    8.8   2.5    2.4  2  zf-C2H2        Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   5.2   2.5e-06    0.0064       4      51 ..       3      49 ..       1      52 [. 0.78
   2 !    6.7   0.7    0.0035       8.9       4      24 ..      32      50 ..      30      58 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
                           zf-Di19  4 tCPy..Cgk.eltvkeLveHvedeHrveskevvCPvCaekvtkdlvaHltl 51
                                      +CPy  C+  + t  +L++Hv + H+ +   + CP C  + + ++++H+ +
  gi|488601000|ref|YP_007907471.1|  3 KCPYhgCKFkSKTLMRLIRHVRVRHPLN---GKCPACGREFK-EVMCHIAH 49
                                      8***667654577788899****99976...56****99887.88889876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0035
                           zf-Di19  4 tCPyCgkeltvkeLveHvede 24
                                      +CP Cg+e+++   ++H+  e
  gi|488601000|ref|YP_007907471.1| 32 KCPACGREFKE--VMCHIAHE 50
                                      69999988865..46776655 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 !   11.8   2.0   0.00014      0.36       2      24 .]       3      27 ..       2      27 .. 0.89
   2 !    9.1   0.5     0.001       2.6       2      19 ..      32      49 ..      32      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                         zf-C2H2_4  2 kCpiCgksFsskka..LlrHlkthH 24
                                      kCp+ g  F+sk+   L rH++  H
  gi|488601000|ref|YP_007907471.1|  3 KCPYHGCKFKSKTLmrLIRHVRVRH 27
                                      8***777**9999999*****9888 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                         zf-C2H2_4  2 kCpiCgksFsskkaLlrH 19
                                      kCp Cg+ F+       H
  gi|488601000|ref|YP_007907471.1| 32 KCPACGREFKEVMCHIAH 49
                                      7********988876666 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.56   1.4e+03      22      42 ..       4      24 ..       3      27 .. 0.72
   2 ?   12.9   0.1   2.8e-05     0.073      19      31 ..      30      42 ..      29      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.56
                                      -TTT--EE-HHHHHHHHHHHH CS
                     Rad50_zn_hook 22 CPlCgReldeehrseLikelq 42
                                      CP  g ++ ++  ++Li++ +
  gi|488601000|ref|YP_007907471.1|  4 CPYHGCKFKSKTLMRLIRHVR 24
                                      555556788888999999876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.8e-05
                                      SEE-TTT--EE-H CS
                     Rad50_zn_hook 19 kgcCPlCgRelde 31
                                      +g+CP CgRe+ e
  gi|488601000|ref|YP_007907471.1| 30 NGKCPACGREFKE 42
                                      46*********87 PP

>> NPC1_N  Niemann-Pick C1 N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.1e-05      0.08      58      92 ..      14      48 ..       6      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                            NPC1_N 58 eqletLkknlklaeellsrCpaClknflnlfCeft 92
                                      + l +L ++++  ++l  +CpaC ++f +++C+++
  gi|488601000|ref|YP_007907471.1| 14 KTLMRLIRHVRVRHPLNGKCPACGREFKEVMCHIA 48
                                      56778888999999999***************985 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   5.5e-05      0.14       7      55 ..       4      52 ..       2      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-05
                           FOXP-CC  7 CkWPgCekvledveeflkhlnseHalddkstaqlrvqmqvvqqlekqlv 55
                                      C   gC+   ++++++++h++  H l+ k+ a  r  ++v+ ++ ++++
  gi|488601000|ref|YP_007907471.1|  4 CPYHGCKFKSKTLMRLIRHVRVRHPLNGKCPACGREFKEVMCHIAHEVR 52
                                      8888***************************999999999998887765 PP

>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0011       2.7       2      24 ..       3      25 ..       2      31 .. 0.89
   2 ?    4.5   0.2     0.013        34     145     161 ..      33      49 ..      26      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                     zf-C2H2_aberr  2 kClykaCdlkyssvlglrrhlve 24
                                      kC+y+ C+ k ++ + l rh++ 
  gi|488601000|ref|YP_007907471.1|  3 KCPYHGCKFKSKTLMRLIRHVRV 25
                                      9*******************974 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                     zf-C2H2_aberr 145 ipGCgkrfkslmaYkYh 161
                                        p Cg++fk++m +  h
  gi|488601000|ref|YP_007907471.1|  33 CPACGREFKEVMCHIAH 49 
                                       689*********98777 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.5   0.00091       2.3       2      23 .]       3      27 ..       2      27 .. 0.95
   2 ?    5.7   0.4    0.0091        23       2      11 ..      32      41 ..      32      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00091
                                      EET..TTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2  2 kCp..dCgksFkrksnLkrHirt.H 23
                                      kCp  +C+ + k+   L rH r+ H
  gi|488601000|ref|YP_007907471.1|  3 KCPyhGCKFKSKTLMRLIRHVRVrH 27
                                      89999*****************999 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0091
                                      EETTTTEEES CS
                           zf-C2H2  2 kCpdCgksFk 11
                                      kCp Cg+ Fk
  gi|488601000|ref|YP_007907471.1| 32 KCPACGREFK 41
                                      7********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 720.06
//
Query:       gi|488601001|ref|YP_007907472.1|  [L=33]
Description: hypothetical protein Asulf_01496 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.037   13.9   0.4      0.037   13.9   0.4    1.1  1  WSN            Domain of unknown function
       0.07   13.0   0.4      0.074   12.9   0.4    1.0  1  HTH_25         Helix-turn-helix domain
       0.11   12.3   0.3       0.11   12.2   0.3    1.2  1  Soyouz_module  N-terminal region of Paramyxovirinae phosphopr
       0.38   10.4   4.7          7    6.4   0.2    2.5  3  EF-hand_1      EF hand


Domain annotation for each model (and alignments):
>> WSN  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   8.2e-06     0.037      36      61 ..       7      32 ..       1      33 [] 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.2e-06
                               WSN 36 isELLnlgsvklseivkldvdklkel 61
                                      + EL++l ++ ++ei+k+d d+l++ 
  gi|488601001|ref|YP_007907472.1|  7 LDELFRLADAVIEEIEKIDFDELEDV 32
                                      78********************9986 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   1.7e-05     0.074      14      40 ..       5      31 ..       3      33 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                      HHHHHHSS--HHHHHHHHCT--TTSS- CS
                            HTH_25 14 eevaketkIrkdylealEeddfdalpe 40
                                      +e+ +  +++ +++e++E+ dfd+l++
  gi|488601001|ref|YP_007907472.1|  5 DELDELFRLADAVIEEIEKIDFDELED 31
                                      7889999*****************986 PP

>> Soyouz_module  N-terminal region of Paramyxovirinae phosphoprotein (P)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   2.5e-05      0.11       1      25 [.       1      23 [.       1      31 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                     Soyouz_module  1 MdsfsdaeIaeLlelgldvIesiqk 25
                                      M+ f  +e++eL+ l  +vIe+i k
  gi|488601001|ref|YP_007907472.1|  1 MNEF--DELDELFRLADAVIEEIEK 23
                                      6666..9***************976 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.87   3.9e+03       6      10 ..       1       5 [.       1       5 [. 0.70
   2 ?    6.1   0.1    0.0021       9.3       1      10 [.       6      15 ..       6      16 .. 0.91
   3 ?    6.4   0.2    0.0016         7      16      25 ..      23      32 ..      22      33 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.87
                                      HHHHT CS
                         EF-hand_1  6 FrefD 10
                                      ++efD
  gi|488601001|ref|YP_007907472.1|  1 MNEFD 5 
                                      57887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0021
                                      HHHHHHHHHT CS
                         EF-hand_1  1 elkeiFrefD 10
                                      el+e+Fr++D
  gi|488601001|ref|YP_007907472.1|  6 ELDELFRLAD 15
                                      89*******9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0016
                                      EEEHHHHHHH CS
                         EF-hand_1 16 kIdfeEfkel 25
                                      kIdf+E+ ++
  gi|488601001|ref|YP_007907472.1| 23 KIDFDELEDV 32
                                      8******886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 241.60
//
Query:       gi|488601002|ref|YP_007907473.1|  [L=189]
Description: hypothetical protein Asulf_01497 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       449  (0.0250432); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1321.68
//
Query:       gi|488601003|ref|YP_007907474.1|  [L=37]
Description: hypothetical protein Asulf_01498 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.46   10.3   3.7       0.46   10.3   3.7    1.1  1  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.7   2.6e-05      0.46      23      41 ..       6      24 ..       2      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.6e-05
                          LapA_dom 23 llvafgiGallgwllslws 41
                                      l+++fg+G++ g+++++w+
  gi|488601003|ref|YP_007907474.1|  6 LALVFGFGFFCGFIACMWF 24
                                      8999*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 271.99
//
Query:       gi|488601004|ref|YP_007907475.1|  [L=246]
Description: monomeric archaeal DNA polymerase sliding clamp [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-14   52.1   1.4      1e-11   44.6   0.4    2.1  2  PCNA_N         Proliferating cell nuclear antigen, N-terminal
    1.7e-07   31.5   0.0    5.9e-07   29.7   0.0    1.9  1  PCNA_C         Proliferating cell nuclear antigen, C-terminal
  ------ inclusion threshold ------
      0.096   12.8   0.2       0.68   10.1   0.1    2.3  2  DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal do


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.4   1.7e-15     1e-11       8      98 ..       8      99 ..       2     111 .. 0.92
   2 !    6.5   0.0    0.0011       6.4       8      92 ..     135     216 ..     128     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.7e-15
                                      SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS.-EEEEEEHHHHHHHHTTSTTT CS
                            PCNA_N  8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDr.nlalgvnlnslskilkcanne 85
                                      q  ++k ++ ++  l++ea f   ++G++++a+D + va+v + + +++fe y  D  ++++gv++n +   +k  +n 
  gi|488601004|ref|YP_007907475.1|  8 QVDVVKVVFKGLNALITEARFRFREDGLKIRAVDPANVAMVLVDIPDDSFEAYSIDEdEVVVGVDVNRVYDFVKGIKNG 86
                                      56789**************************************************9736899***************** PP

                                      SEEEEEEETTSSE CS
                            PCNA_N 86 dsvtlkaedeadt 98
                                      +++ +  +de  +
  gi|488601004|ref|YP_007907475.1| 87 EMIDIAVDDERLV 99
                                      *****99998654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0011
                                       SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTT CS
                            PCNA_N   8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcann 84 
                                       +a  lkk ++      +++ f +d++G+ + a  +  v   +le+ +    ++   +  ++  +l+ l   +k+a +
  gi|488601004|ref|YP_007907475.1| 135 DAEELKKFVNLADKFADHVVFRADEDGFYIEA--EGDVDGLKLEMGDADLVEFNQQKAKSM-FSLEYLKEFVKIASK 208
                                       5667999999999999*************998..566888999999999999999999888.799999999999999 PP

                                       TSEEEEEE CS
                            PCNA_N  85 edsvtlka 92 
                                        d +t++ 
  gi|488601004|ref|YP_007907475.1| 209 GDLLTIRL 216
                                       99999985 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   9.9e-11   5.9e-07       2     127 ..     123     241 ..     122     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 9.9e-11
                                       ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EE CS
                            PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvt 78 
                                       +p+++  a + + + e ++ +    ++ d vv  +  +g    a+Gd+   ++ + +          v+ + ++  +
  gi|488601004|ref|YP_007907475.1| 123 VPQIDLPARIVMDAEELKKFVNLADKFADHVVFRADEDGFYIEAEGDVDGLKLEMGDAD-------LVEFN-QQKAK 191
                                       789999999************9999***********************87644433333.......33333.55677 PP

                                       EEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEE.EEEE-B CS
                            PCNA_C  79 ltfalkYlaeftkatsLservtlslssevPlvveykikdvgll.ayllak 127
                                         f+l+Yl ef+k +s  +  t++l  + P+ + +++ ++  +  y la+
  gi|488601004|ref|YP_007907475.1| 192 SMFSLEYLKEFVKIASKGDLLTIRLGTDYPVWLAFELCEGKCKvEYILAP 241
                                       89**********************************98876541566665 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 ?   -0.4   0.0      0.19   1.2e+03      87     113 ..      11      36 ..       7      40 .. 0.86
   2 ?   10.1   0.1   0.00011      0.68      63     115 ..      64     115 ..      30     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.19
                                       EEEEEEETTEEEEEEETTEEEEEE-BE CS
                     DNA_pol3_beta  87 kvkisvneqklliiksgssrfslstls 113
                                        vk+++++ ++li+ + + rf + +l+
  gi|488601004|ref|YP_007907475.1|  11 VVKVVFKGLNALIT-EARFRFREDGLK 36 
                                       58999999999999.999999999886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00011
                                       EE-EEEEEEHHHHHHHHHHSSTTSEEEEEEETTEEEEEEETTEEEEEE-BEGG CS
                     DNA_pol3_beta  63 eeegkvlvparllldivkaLpndkkvkisvneqklliiksgssrfslstlsae 115
                                       e e  v v    ++d vk + n++ ++i v++++l ++   s  ++ls ++ +
  gi|488601004|ref|YP_007907475.1|  64 EDEVVVGVDVNRVYDFVKGIKNGEMIDIAVDDERLVLT-NRSVSYELSLIAPD 115
                                       555667788899**********************9999.77778888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1919.17
//
Query:       gi|488601005|ref|YP_007907476.1|  [L=82]
Description: hypothetical protein Asulf_01500 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.023   14.7   0.1    1.3  1  DUF4974        Domain of unknown function (DUF4974)
       0.04   13.6   0.1      0.056   13.1   0.1    1.4  1  Choline_kin_N  Choline kinase N terminus
      0.085   13.0   0.0       0.12   12.6   0.0    1.2  1  DUF3861        Domain of Unknown Function with PDB structure 


Domain annotation for each model (and alignments):
>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.9e-06     0.023      24      56 ..      22      54 ..      19      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-06
                                      EEE-TTS----EEEEEES-.-.HHHHHHHHHHH CS
                           DUF4974 24 ivieneelknyrftgtfsrnesleevLelLekt 56
                                       ++e +  +++++t++ +++e++ e+L++L+k 
  gi|488601005|ref|YP_007907476.1| 22 AKLEGNGTAKITITIKAEKKEDIKEILKTLKKG 54
                                      56676667999*******************985 PP

>> Choline_kin_N  Choline kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.3e-06     0.056      17      41 ..      24      54 ..       8      54 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-06
                     Choline_kin_N 17 LDnskpsdy.......FKeeilrLlhtLalkg 41
                                      L+++ ++ +        Ke+i+++l+tL+ kg
  gi|488601005|ref|YP_007907476.1| 24 LEGNGTAKItitikaeKKEDIKEILKTLK-KG 54
                                      555555555555555559***********.86 PP

>> DUF3861  Domain of Unknown Function with PDB structure (DUF3861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05      0.12      12      47 ..      22      58 ..      15      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                           DUF3861 12 da.dgeeseekpleFeaenhdDilkiverlkkkedld 47
                                       + +g+ + + +++++ae+++Di +i+++lkk   ++
  gi|488601005|ref|YP_007907476.1| 22 AKlEGNGTAKITITIKAEKKEDIKEILKTLKKGAVFE 58
                                      55355555555********************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1349  (0.0752412); expected 358.6 (0.02)
Passed bias filter:                      968  (0.0539907); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 617.31
//
Query:       gi|488601006|ref|YP_007907477.1|  [L=50]
Description: hypothetical protein Asulf_01501 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 00:00:00.43
# Mc/sec: 348.61
//
Query:       gi|488601007|ref|YP_007907478.1|  [L=74]
Description: hypothetical protein Asulf_01502 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0069   16.4   1.2     0.0076   16.3   0.4    1.6  2  Med26     TFIIS helical bundle-like domain


Domain annotation for each model (and alignments):
>> Med26  TFIIS helical bundle-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   4.2e-07    0.0076      17      40 ..      30      53 ..      18      61 .. 0.85
   2 ?   -1.8   0.0      0.18   3.3e+03      15      20 ..      68      73 ..      56      74 .] 0.57

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.2e-07
                                      HHHSHHHHHHHHHH-TTS-HHHHH CS
                             Med26 17 kstgIGkvVnalrkhkhetaevkt 40
                                      ++t+I kvVn++r +++++ +vk+
  gi|488601007|ref|YP_007907478.1| 30 TMTQISKVVNKIRENTPCNGQVKS 53
                                      689******************996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.18
                                      HHHHHS CS
                             Med26 15 tLkstg 20
                                      +Lk+t+
  gi|488601007|ref|YP_007907478.1| 68 LLKTTK 73
                                      466666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 518.02
//
Query:       gi|488601008|ref|YP_007907479.1|  [L=174]
Description: hypothetical protein Asulf_01503 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   15.3   0.3      0.014   15.3   0.3    1.8  2  CLTH            CTLH/CRA C-terminal to LisH motif domain
      0.079   13.2   0.1       0.21   11.8   0.1    1.7  1  RyR             RyR domain
       0.11   12.5   2.7       0.13   12.2   2.6    1.3  1  Pox_RNA_Pol_19  Poxvirus DNA-directed RNA polymerase 19 kDa s


Domain annotation for each model (and alignments):
>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   2.3e-06     0.014      24      75 ..      63     122 ..      57     133 .. 0.74
   2 ?   -2.6   0.1      0.75   4.5e+03      38      52 ..     150     164 ..     140     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                              CLTH  24 inenkpelles..nsnLeFkLkllqfielirg..ktkdieealeyarenl.efend...e 75 
                                       i e k++  ++  n++LeF L+++ f+e i    + +di+ a e++ ++l +++++   +
  gi|488601008|ref|YP_007907479.1|  63 IDEIKKRYQRRsfNDTLEFLLNCYDFLEGIAIryNLGDIKSATEFIENHLpKSQAEvihQ 122
                                       55555555555668**************9997664499************5555555441 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.75
                              CLTH  38 LeFkLkllqfielir 52 
                                       ++ kL++ + ie +r
  gi|488601008|ref|YP_007907479.1| 150 ILVKLRRKRAIEVLR 164
                                       678999999999887 PP

>> RyR  RyR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.5e-05      0.21      43      83 ..      43      83 ..      31      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                                      E-SS-BTTTTEETT-S-GGGS-HHHHHHHHHHHHHHHHHHH CS
                               RyR 43 ygeerdekkkthplLvpydaLsekekekdrekaqetlktll 83
                                        ++ +++k +   L  +++++e +k+++r++ ++tl +ll
  gi|488601008|ref|YP_007907479.1| 43 TKSGSSKSKLQRVDLNTFRRIDEIKKRYQRRSFNDTLEFLL 83
                                      33444688889999*************************98 PP

>> Pox_RNA_Pol_19  Poxvirus DNA-directed RNA polymerase 19 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.6   2.2e-05      0.13      22      78 ..      17      73 ..       3     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                    Pox_RNA_Pol_19 22 eeedeeeesslessdvsslkeseykv.ekvssnveeeessskqvsekisaikkrytrr 78
                                      +e+d++e ++  s++v+++k  + k+  k  s+  + +++  ++  +i +ikkry rr
  gi|488601008|ref|YP_007907479.1| 17 NEKDQNEVNNILSDSVNKTKFVN-KMlTKSGSSKSKLQRVDLNTFRRIDEIKKRYQRR 73
                                      33344444567788888888877.5525555566667777889999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1225.61
//
Query:       gi|488601009|ref|YP_007907480.1|  [L=100]
Description: hypothetical protein Asulf_01504 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 746.31
//
Query:       gi|488601010|ref|YP_007907481.1|  [L=141]
Description: hypothetical protein Asulf_01505 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0057   16.8   0.1     0.0057   16.8   0.1    1.7  2  XhlA      Haemolysin XhlA
  ------ inclusion threshold ------
      0.044   14.3   0.1        0.7   10.4   0.0    2.1  2  DUF3899   Domain of unknown function (DUF3899)


Domain annotation for each model (and alignments):
>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.37   3.3e+03      19      27 ..      46      54 ..      31      63 .. 0.44
   2 !   16.8   0.1   6.3e-07    0.0057      19      65 ..      89     136 ..      77     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.37
                              XhlA 19 rvdkleeka 27
                                      ++ + +ek 
  gi|488601010|ref|YP_007907481.1| 46 TIREWKEKI 54
                                      222222222 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.3e-07
                              XhlA  19 rvdkleekaaeaeekiknleedlkklesnqkWlirt.iiGalisaviy 65 
                                       + d +++k  e    i+  ++dl+++ s +kW++ + +iG +++++++
  gi|488601010|ref|YP_007907481.1|  89 DADAVKRKILELAGMIQARHDDLNRIRSINKWTVPLsVIGLILTVIFG 136
                                       56899999999999*******************976256655555554 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.034     3e+02      31      62 ..      20      52 ..      17      76 .. 0.56
   2 ?   10.4   0.0   7.8e-05       0.7      60      78 ..     113     134 ..      86     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.034
                           DUF3899 31 ygfrklkklflkk..skkddsyyeykekkkessk 62
                                      yg  kl + fl +  skk+d+ ++++  + e++ 
  gi|488601010|ref|YP_007907481.1| 20 YGLSKLLREFLVEviSKKVDRSLDDETIR-EWKE 52
                                      66667777766667744444444443321.1222 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 7.8e-05
                           DUF3899  60 s...skkstrplliiGlllivl 78 
                                       +   ++k+t+pl +iGl+l v+
  gi|488601010|ref|YP_007907481.1| 113 RirsINKWTVPLSVIGLILTVI 134
                                       24459**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1029.62
//
Query:       gi|488601011|ref|YP_007907482.1|  [L=129]
Description: hypothetical protein Asulf_01506 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   15.0   0.5      0.041   14.3   0.5    1.4  1  eIF3_N    eIF3 subunit 6 N terminal domain


Domain annotation for each model (and alignments):
>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   2.3e-06     0.041      48     102 ..      36      87 ..      13     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-06
                            eIF3_N  48 dyaadlykelegeeevpeelekkreevleeleeleeeaekvlelledeevvsnlr 102
                                       +++ +  +e ++    ++ +e+ +++v++ele+l +++++++e+l ++e +++ r
  gi|488601011|ref|YP_007907482.1|  36 NFVGEAIEEYYR---SQKVFEEAKKKVIDELEALDTTVARAYEILHSNEAEKKPR 87 
                                       667777777765...4568999***********************9999888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); 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: 00:00:00.41
# Mc/sec: 936.61
//
Query:       gi|488601012|ref|YP_007907483.1|  [L=440]
Description: hypothetical protein Asulf_01507 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.3    5.4e-13   49.1   0.3    1.3  1  Terminase_6    Terminase-like family
    5.1e-13   49.4   0.0    2.2e-12   47.4   0.0    1.9  2  Terminase_6C   Terminase RNaseH-like domain
    4.2e-05   22.3   0.0       0.12   10.9   0.0    2.2  2  Terminase_1    Phage Terminase
    7.9e-05   22.3   0.1    0.00022   20.8   0.0    1.7  2  Terminase_3    Phage terminase large subunit
     0.0017   18.2   0.0      0.003   17.4   0.0    1.3  1  Helicase_RecD  Helicase
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.16   11.7   0.0    1.3  1  AAA_30         AAA domain


Domain annotation for each model (and alignments):
>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.3   1.8e-16   5.4e-13       2     214 ..      51     256 ..      50     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.8e-16
                                       EEE-SSS-HHHHHHHHHHHHHHSSSS.-EEEEEESSHHHHHHHHH.....HHHHHHHTS-TTTS--EEEE-SSEEEE CS
                       Terminase_6   2 ilggrqsGKTfagarellrhalgrgprnqvflsasktqareeggq.....fekgigelakeildiefeesaknlvvl 73 
                                       i++gr+ GKT a+a+   ++a+  +   q++l++s++qa   + +      ++ +  l +  +++ f+      +++
  gi|488601012|ref|YP_007907483.1|  51 IVAGRRFGKTKAMAFSTIHYAITHPGSIQFILAPSYNQANIMFWEittllSKSILVHLVERVYKTPFS-----KIIF 122
                                       789***********9999998887777888888*******9655576666556666666666777777.....5555 PP

                                       TTS-EEEEES....SHHHHHTS--SEEEEESGGGSTTHHHHHHHHHHHHC.STT--EEEEEE---SSSHHHHHHHHH CS
                       Terminase_6  74 snGaslhflslesetaggiqGaqidliyfDElteipksqelekvtrlrat.kgtdtktfattpptpdhgvydfvtgw 149
                                       +nG+++h +s+ +  ++  +G +++ +++DE++ ip++  ++ v    a+  g ++   + tp+ + h++ +  +g+
  gi|488601012|ref|YP_007907483.1| 123 KNGSEIHARSTTK--PEYLRGHKAHRVILDEAAYIPDDVISQVVEPMLADyNGSWI--KIGTPFGKNHFYDTYLKGQ 195
                                       **********999..89*************************99877664155566..******************* PP

                                       HCTSS-EEEEE-GGGSGB-TTSBB-TTHHHHHHHHHTS-HHH..HHHHHS---TTCTCESSXCHHHC CS
                       Terminase_6 150 ldeegpqsvtkiqavvevtiedakklgedlieeleaeysvee..rarllrGewidtsgsiFqrsele 214
                                        + +  + ++  ++       ++++ + ++ie+ ++ey ++   ++ +++ e+i++  ++F+  +++
  gi|488601012|ref|YP_007907483.1| 196 SEGF--PDYSSYRFP----STANPHISHEFIEKKKREYGENSiiFRTEYLAEFIEDQNAVFKWADIQ 256
                                       *888..555555554....5699**************************************988776 PP

>> Terminase_6C  Terminase RNaseH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.54   1.6e+03      70     105 ..      39      74 ..      16      95 .. 0.68
   2 !   47.4   0.0   7.2e-16   2.2e-12       1     151 [.     276     420 ..     276     422 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.54
                                       HHHHHCCT--S-SCEESSH..HHHHHHHHHHHHHH.H CS
                      Terminase_6C  70 aellkrdlesealavkpepaskdkatrvskvkdli.e 105
                                        + l+++++ +   v   ++ k+ka+ +s+++++i +
  gi|488601012|ref|YP_007907483.1|  39 KQILRDRHQFK-TIVAGRRFGKTKAMAFSTIHYAItH 74 
                                       45566666522.3344444459999999999999944 PP

  == domain 2  score: 47.4 bits;  conditional E-value: 7.2e-16
                                       EEEE--SSCTTBEEEEEEEETTTTCEEEEEEEEESSS-CCCHHHHHHHHHHCTTCEEEEECCSCHHHHHHHHHHCCT CS
                      Terminase_6C   1 igvDpaegrggDyaalvvidvkddkfellavlherglspalqaaaikklaerynviyvyieitsaGesvaellkrdl 77 
                                       igvD+a  +  Dy+++vv+dv++ +++l+  ++++++  a++  +ik l +r+n ++v i+  ++G  v e l+  +
  gi|488601012|ref|YP_007907483.1| 276 IGVDLA--KYMDYTVIVVLDVTEKPYRLIYFERYNRRPYAETIFRIKDLHKRFNLARVLIDSSGVGDPVLEDLQGIG 350
                                       79****..******************************************************************999 PP

                                       --S-SCEESSH..HHHHHHHHHHHHHHHTTSEEEETHHCECCCCCCHCC-EEHCC....HHCHCSGCCTCHHHHHHH CS
                      Terminase_6C  78 esealavkpepaskdkatrvskvkdliesgrlkvdkgaecaksfealegfhtdlg....aerstsaehdDlvdAlsy 150
                                            ++++++  k+k+ +++++ +++e+g +k++ +   ++++++l  f + l       + ++  +dD+v Al  
  gi|488601012|ref|YP_007907483.1| 351 A---EGYVFTS--KSKVQLINRLVAAMENGEVKYPYI---EDLIKELQFFEYQLTrtgiKMGARQGFNDDCVIALAL 419
                                       7...8*****9..***********************7...6666666555555554447777888888888888776 PP

                                       H CS
                      Terminase_6C 151 a 151
                                       a
  gi|488601012|ref|YP_007907483.1| 420 A 420
                                       6 PP

>> Terminase_1  Phage Terminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   3.9e-05      0.12      28     152 ..      53     172 ..      42     190 .. 0.80
   2 !    9.2   0.0   0.00013      0.38     254     306 ..     247     306 ..     215     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.9e-05
                       Terminase_1  28 vgrkngKsllvavialiellldpkansqifvaattkdqAekilkkvkrqvklskekikvkdekilksrkkeieislv 104
                                        gr+ gK+   a  ++   +   ++ s  f+ a  ++qA+ ++ ++   +   k+      e++ k+    i     
  gi|488601012|ref|YP_007907483.1|  53 AGRRFGKTKAMAFSTIHYAI--THPGSIQFILAPSYNQANIMFWEITTLLS--KSILVHLVERVYKTPFSKIIFKNG 125
                                       46777777655555544444..56678999**************9998765..555555678999999999999999 PP

                       Terminase_1 105 dsvikplssneDavDGkdpslvilDElaafkddelletikeglikrkn 152
                                       + + +  +  ++ + G +   vilDE a ++dd ++++++e + +  n
  gi|488601012|ref|YP_007907483.1| 126 SEIHARSTTKPEYLRGHKAHRVILDEAAYIPDD-VISQVVEPMLADYN 172
                                       99999999*************************.9******9998555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00013
                       Terminase_1 254 dsllskeswdq....vlvpprdlsGrdvyiGvDlSrkdDvtavvva.fpedg..kvylka 306
                                       +++++  ++++    + +  + +sGr   iGvDl++  D t +vv  + e    ++y+  
  gi|488601012|ref|YP_007907483.1| 247 NAVFKWADIQKniagIQLIDKGISGRRYVIGVDLAKYMDYTVIVVLdVTEKPyrLIYFER 306
                                       55555555555443322334679******************9988513333344566655 PP

>> Terminase_3  Phage terminase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.62   1.9e+03     113     142 ..      10      39 ..       3      43 .. 0.84
   2 !   20.8   0.0   7.4e-08   0.00022       2     199 ..      46     239 ..      45     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.62
                       Terminase_3 113 edidelvetlrapeqekqiilsfNPvsesn 142
                                       +d ++l + +r p ++ qi+l   P + ++
  gi|488601012|ref|YP_007907483.1|  10 KDRKKLKQAIRDPVLFTQIFLNHEPHEAQK 39 
                                       567899999**99********999988765 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 7.4e-08
                       Terminase_3   2 keikvlvggrgssKsysialkivlkklkekrkalvlRkvkntlkdSvfaeikellselgltklf.kilkskiei.el 76 
                                       +++k +v+gr  +K++ +a   +  ++ ++ +  ++   +    + +f ei+ lls+  l +l+ ++ k++     +
  gi|488601012|ref|YP_007907483.1|  46 HQFKTIVAGRRFGKTKAMAFSTIHYAITHPGSIQFILAPSYNQANIMFWEITTLLSKSILVHLVeRVYKTPFSKiIF 122
                                       7899999**************************9988888888999************99999946889998656** PP

                       Terminase_3  77 engskflFkglddpaklkSiknlsdlwlEEasevseedidelvetlrapeqekqiilsfNPvsesnwvykrffkdde 153
                                       +ngs++  +   +p+ l+  k+ + + l+Ea+ +  + i+++ve + a+ +++ i + + P ++++  y +++k  +
  gi|488601012|ref|YP_007907483.1| 123 KNGSEIHARSTTKPEYLRGHKA-HRVILDEAAYIPDDVISQVVEPMLADYNGSWIKIGT-PFGKNH-FYDTYLKGQS 196
                                       ******************9765.67789*******************888777776655.999987.5899996655 PP

                       Terminase_3 154 kekdekddvlihkstyrdnefLdeedvkkleelkkenpdkyrivvl 199
                                        e    +d+ + +     n+++++e ++k +  + en   +r ++l
  gi|488601012|ref|YP_007907483.1| 197 -EG--FPDYSSYRFPSTANPHISHEFIEKKKREYGENSIIFRTEYL 239
                                       .33..47888888888889999999999999999999999999886 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     1e-06     0.003       2     112 ..      51     165 ..      50     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-06
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaa.liaegksnilvtapskenvktlfeflakglealglke..eekkkkaekaelrvrkqr 75 
                                       + A+R  GK+ a++  + + +i +  s  ++ aps+++++ +f  +++ l++  l +  e+  k++ ++ + +++++
  gi|488601012|ref|YP_007907483.1|  51 IVAGRRFGKTKAMAFSTIHyAITHPGSIQFILAPSYNQANIMFWEITTLLSKSILVHlvERVYKTPFSKIIFKNGSE 127
                                       7899999******99766515555557779****************9999988777787677777777777777555 PP

                     Helicase_RecD  76 ieyiapde.llklkeqadllvvDEAAaiplpllkklle 112
                                       i+  + ++    + ++a+ ++ DEAA ip +++++++e
  gi|488601012|ref|YP_007907483.1| 128 IHARSTTKpEYLRGHKAHRVILDEAAYIPDDVISQVVE 165
                                       5543332202233456799**************99984 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.3e-05      0.16       2     110 ..      30     165 ..      29     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
                            AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkal..reaweaaggrviglAptgkaAkvLa............. 63 
                                       ln+e ++a +++l +++++++++++   GKt a++      a+++ g   ++lAp+ ++A+ +              
  gi|488601012|ref|YP_007907483.1|  30 LNHEPHEAQKQILRDRHQFKTIVAGRRFGKTKAMAFStiHYAITHPGSIQFILAPSYNQANIMFweittllsksilv 106
                                       567778999*****************99***999866115555555666679**********994333333333333 PP

                            AAA_30  64 .....eelgieastiakllkrlk.......................grarlepgtllivDEagmvdtkqlaallk 110
                                                                                     +  r ++++ +i DEa+ +  + + ++++
  gi|488601012|ref|YP_007907483.1| 107 hlverV----------------YktpfskiifkngseiharsttkpEYLRGHKAHRVILDEAAYIPDDVISQVVE 165
                                       333220................1466666666666666666666664455567799******9998888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2859.56
//
Query:       gi|488601013|ref|YP_007907484.1|  [L=220]
Description: hypothetical protein Asulf_01508 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.8   0.2      0.039   13.8   0.2    3.0  3  DUF2975   Protein of unknown function (DUF2975)
        2.4    6.3  22.3          3    6.0  22.3    1.1  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.3e-06     0.039      71     123 ..      32      84 ..      22      91 .. 0.79
   2 ?   -1.0   1.8      0.16   1.5e+03      71      86 ..     105     120 ..      88     151 .. 0.47
   3 ?   -3.6   5.0         1   9.2e+03      67      85 ..     159     178 ..     128     216 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-06
                           DUF2975  71 lllaagivalallaelelapgvvllllgvafaslvigllvlvlaellaeAvkl 123
                                       + +a+ +  + l++++  +  ++++++ v+ + l++ l ++v+++++  ++kl
  gi|488601013|ref|YP_007907484.1|  32 VFAALSMYLFKLSRDMNGDERIYIGFGAVSSLYLFLYLAITVISRIFSSGIKL 84 
                                       33444455555555599999******************************997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.16
                           DUF2975  71 lllaagivalallael 86 
                                        l+a ++  + +la +
  gi|488601013|ref|YP_007907484.1| 105 SLFAYMLSSFIFLAIF 120
                                       2222222222222222 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1
                           DUF2975  67 iaa.alllaagivalallae 85 
                                       +++ a ++++ +++++ + +
  gi|488601013|ref|YP_007907484.1| 159 LISlATIFLTSYLVVYNIPS 178
                                       33333333333333333333 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  22.3   0.00034         3      18     178 ..      26     209 ..      11     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00034
                           DUF2070  18 llliillalligllaflssk........lfgillfglpalvaflltlpvlrilggr..ltykrs..lflallteliv 82 
                                       +l ++ + ++++++ f  s         ++g+ ++   +l+  l+ + + ri+++   l +kr    fl + +eli+
  gi|488601013|ref|YP_007907484.1|  26 MLTLVGVFAALSMYLFKLSRdmngderiYIGFGAVSSLYLFLYLAITVISRIFSSGikLWWKREveDFLTFSAELIL 102
                                       45555555555555555555799999986666666555666555555666666555458888888999999999999 PP

                           DUF2070  83 viisllaillsall...qalvllalvlslalvfalrllvlv.avsdesllkavlpaliqpllailllvly....... 148
                                       ++ +++ +l s+++    ++ l ++v ++++  ++ +l+++ +v+  + + +++ ali +++++l+++l+       
  gi|488601013|ref|YP_007907484.1| 103 IVSLFAYMLSSFIFlaiFEFPLESTVYAIFFNHIIGILLFFkFVMPIRRKSISISALISLATIFLTSYLVvynipsk 179
                                       99777777777777888888888888888888888777666255666666666776666666666666667776666 PP

                           DUF2070 149 fspesfllllllslifalavylfivvvdrp 178
                                       f + +++ +++  +i +++ +++i ++  p
  gi|488601013|ref|YP_007907484.1| 180 FLQIFTATTIVEPVIRGIGGAAIIALLATP 209
                                       555555555555555566666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1451.61
//
Query:       gi|488601014|ref|YP_007907485.1|  [L=404]
Description: hypothetical protein Asulf_01509 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-26   93.6   1.2    1.6e-26   93.2   1.2    1.1  1  Phage_portal    Phage portal protein
    9.4e-09   34.5   0.9    1.6e-08   33.7   0.9    1.5  1  DUF1073         Protein of unknown function (DUF1073)
    2.6e-05   23.5   1.4      0.012   14.7   0.0    2.2  2  Phage_prot_Gp6  Phage portal protein, SPP1 Gp6-like
     0.0032   16.7   0.0      0.005   16.0   0.0    1.4  1  Phage_portal_2  Phage portal protein, lambda family
  ------ inclusion threshold ------
      0.063   13.3   1.4        1.5    8.9   0.2    3.0  3  SLT_beta        Shiga-like toxin beta subunit
      0.065   13.0   0.0       0.16   11.7   0.0    1.6  1  UPF0175         Uncharacterised protein family (UPF0175)


Domain annotation for each model (and alignments):
>> Phage_portal  Phage portal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   1.2   5.4e-30   1.6e-26      56     313 ..     102     393 ..      93     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 5.4e-30
                      Phage_portal  56 vanlllygnayalivrdgr.rvvelyplppdrvt.........grleydytddggg......vlpaddvlhirglpl 116
                                       v + l+ gnay +iv d++     l++++p+rv+           ++y+y+ +++g       +++++vlh+r++ +
  gi|488601014|ref|YP_007907485.1| 102 VLTHLIFGNAYNFIVADDNdFGFTLQVVHPKRVKivtdkygkiEYYWYNYDATFTGepkeneKFEPENVLHFRFRQF 178
                                       5566888********9866633459***************977666777777666699999977*********9888 PP

                      Phage_portal 117 .d.lkGlspleaareaielalaaeeyaakffkngarpsgilkikap.gk..lsee...........qrek.lkeefe 176
                                        d ++Gls l  + + + l ++ e++aa++  + a+  +  k++   ++  ++++           + +  l  + +
  gi|488601014|ref|YP_007907485.1| 179 aDnVYGLSLLHNVYNKLSLKNKIEATAAAMAHRDAHRLLWAKVEVSpEEeaINPKtgkayaqekidAVNAlLANRVK 255
                                       789**********************************9999888774113455555554443333322444555555 PP

                      Phage_portal 177 eaysgasnagkvavleggldykplslspkdaqflesrkfaaeeIarafgvpphllgdlgkstysnieeanlafyent 253
                                       ++  g+    + +v ++ +++k ls s + a + ++ +  ++++ ra+ vp+ +lg+ + s+ + +++++++f+   
  gi|488601014|ref|YP_007907485.1| 256 DNQDGTFTVSNNLVFDQSVELKDLSASHDFAGIAKILEHLQRQVDRALKVPKVFLGEAEGSNRATSYNQRRTFM-LF 331
                                       555555533449*************99999*****************************************999.77 PP

                      Phage_portal 254 lepllkrieqelnrkLl..kkglylefdldgllrgdtktraeayaklvqagiltpNEvRell 313
                                       +e + +++e e+nrkL+    +  +++++++ +r+d ++ +e + kl+qagi +  E+Re+ 
  gi|488601014|ref|YP_007907485.1| 332 IESIQRKFETEINRKLIpqITDADVKIKFNSPMREDYSDWVEQAVKLYQAGIVSTVEAREWV 393
                                       *******************5567888888999****************************96 PP

>> DUF1073  Protein of unknown function (DUF1073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.9   5.4e-12   1.6e-08     117     335 ..     136     362 ..      46     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 5.4e-12
                           DUF1073 117 plspdygkpetYevkske....dgtaavkvHkSRlirfigkelpdmlkpaenfwGeSvlqslldavkrfdraaasva 189
                                       +++++ygk+e+Y+ + ++    + +++ k  +  +++f+ ++       a+n+ G S+l ++++++    +++a +a
  gi|488601014|ref|YP_007907485.1| 136 IVTDKYGKIEYYWYNYDAtftgEPKENEKFEPENVLHFRFRQF------ADNVYGLSLLHNVYNKLSLKNKIEATAA 206
                                       56679**********999999988999************8866......9*************************** PP

                           DUF1073 190 qlleranllviktdgla....dalaagdee...........deleerleliklarsne.gmlvi......dkeeele 244
                                       ++ +r  ++ +  +  +    +a+ +++++           +       l++++++n+ g++ +      d+  el+
  gi|488601014|ref|YP_007907485.1| 207 AMAHRDAHRLLWAKVEVspeeEAINPKTGKayaqekidavnA------LLANRVKDNQdGTFTVsnnlvfDQSVELK 277
                                       ****97666665553333666677777777888875544443......44444554431333333333337776666 PP

                           DUF1073 245 qkst..slsglkdllaqfqeklaaaskiPltrLfGqspaGlnatGegDlrnYydrikalQeaelrpvLerllellll 319
                                       + s+  +++g+ ++l+  q ++  a k+P++  +G++++   at+ + +r++  +i+++Q++  +++ ++l++ +  
  gi|488601014|ref|YP_007907485.1| 278 DLSAshDFAGIAKILEHLQRQVDRALKVPKV-FLGEAEGSNRATSYNQRRTFMLFIESIQRKFETEINRKLIPQITD 353
                                       655422799********************97.6799766666*******************9888888899996665 PP

                           DUF1073 320 selgerpddlsfeFnp 335
                                        +       ++++Fn+
  gi|488601014|ref|YP_007907485.1| 354 AD-------VKIKFNS 362
                                       55.......8888886 PP

>> 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 !    7.7   0.2   0.00056       1.7      58     169 ..      67     175 ..      59     195 .. 0.81
   2 !   14.7   0.0   4.1e-06     0.012     347     397 ..     344     393 ..     319     402 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00056
                    Phage_prot_Gp6  58 ylfgepitltvdddddereeildvlennnfdkkdeellkdasiyGrayelvyvdeeg.eikvkvvdpedafpvydds 133
                                       +++g ++++++d   +e  + +++ +   + +++e+ +   +i+G ay ++  d+++  +  +vv p+++ +v d  
  gi|488601014|ref|YP_007907485.1|  67 LVIGAGFQFIGDPRGVE--KCEEFAKLVGLHDILENDVLTHLIFGNAYNFIVADDNDfGFTLQVVHPKRVKIVTDK- 140
                                       67888899999999999..999999999999999999999***************77778***************9. PP

                    Phage_prot_Gp6 134 ierellavvryykdkdektitkvevYtdkevykfek 169
                                        ++ +++   y+  +  ++ +  e + +++v +f++
  gi|488601014|ref|YP_007907485.1| 141 YGKIEYYWYNYD-ATFTGEPKENEKFEPENVLHFRF 175
                                       455555555555.66666666666666666666665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.1e-06
                    Phage_prot_Gp6 347 naldekdgddvedikvkftrnipkndaekadilqklveagivskktllskl 397
                                       n++   + +d+ d+k+kf+ ++ ++ +++++ + kl +agivs+  +++++
  gi|488601014|ref|YP_007907485.1| 344 NRKLIPQITDA-DVKIKFNSPMREDYSDWVEQAVKLYQAGIVSTVEAREWV 393
                                       33333333333.9******************************99998876 PP

>> Phage_portal_2  Phage portal protein, lambda family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-06     0.005     133     331 ..     119     306 ..      77     330 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                    Phage_portal_2 133 l..vplqlqllepdrldtdknvleegnrirqGvefdadgrpvaYwiyrehpgdalsaasseewvrvpaeevlhlfep 207
                                       +  +++ lq+++p+r+    +           +  d++g+   Yw       da+ + + +e ++ + e+vlh   +
  gi|488601014|ref|YP_007907485.1| 119 DndFGFTLQVVHPKRV----K-----------IVTDKYGKIEYYWYNY----DATFTGEPKENEKFEPENVLHFRFR 176
                                       2558999999999999....4...........789*****99999844....677777799**************** PP

                    Phage_portal_2 208 erpgQvRGvpwlapvlerlrdldeyedaelvaakvaAlfaafikseepseeaeealgdpagaaaeeedeeg.kade. 282
                                       + ++ v G ++l+ v ++l   ++ e +    a   A   ++ k e  +ee++ +++  +g+a+ +e+ ++ +a   
  gi|488601014|ref|YP_007907485.1| 177 QFADNVYGLSLLHNVYNKLSLKNKIEATAAAMAHRDAHRLLWAKVEVSPEEEAINPK--TGKAYAQEKIDAvNALLa 251
                                       ********************9999999999999999999999988866555543333..444444443333333333 PP

                    Phage_portal_2 283 reiel.epGtive.....LapGedvkfanparpganfeaFvkallraiAaglgvp 331
                                       ++++  + Gt+         +  ++k +++++  a+ ++  ++l+r++ ++l vp
  gi|488601014|ref|YP_007907485.1| 252 NRVKDnQDGTFTVsnnlvFDQSVELKDLSASHDFAGIAKILEHLQRQVDRALKVP 306
                                       3333225566665555444444555555666666666666666666666666666 PP

>> SLT_beta  Shiga-like toxin beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2    0.0005       1.5       8      31 ..     142     165 ..     136     172 .. 0.84
   2 ?    1.5   0.0       0.1   3.1e+02      13      46 ..     254     285 ..     245     293 .. 0.71
   3 ?   -1.3   0.0      0.75   2.2e+03      42      56 ..     347     361 ..     315     364 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0005
                          SLT_beta   8 GkveytkyndddtftvkvGdkelf 31 
                                       Gk+ey  yn d tft    + e f
  gi|488601014|ref|YP_007907485.1| 142 GKIEYYWYNYDATFTGEPKENEKF 165
                                       9**************876666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                          SLT_beta  13 tkyndddtftvkvGdkelftnrwnlqslllsaqi 46 
                                        k n+d tftv   +  +f +  +l+ l  s + 
  gi|488601014|ref|YP_007907485.1| 254 VKDNQDGTFTVS--NNLVFDQSVELKDLSASHDF 285
                                       68899****985..55566666666666655555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.75
                          SLT_beta  42 lsaqitGmtvtiktn 56 
                                       l  qit   v ik n
  gi|488601014|ref|YP_007907485.1| 347 LIPQITDADVKIKFN 361
                                       456888888888877 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.4e-05      0.16      24      46 ..     374     396 ..     364     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                           UPF0175  24 lAvklYeegrlSlgkAaelagls 46 
                                        AvklY+ g++S  +A+e+++l+
  gi|488601014|ref|YP_007907485.1| 374 QAVKLYQAGIVSTVEAREWVDLP 396
                                       59*****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.36s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2257.68
//
Query:       gi|488601015|ref|YP_007907486.1|  [L=245]
Description: phage putative head morphogenesis protein, SPP1 gp7 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   64.7   0.2    1.9e-17   64.0   0.2    1.3  1  Phage_Mu_F  Phage Mu protein F like protein
  ------ inclusion threshold ------
      0.028   13.4   0.5       0.38    9.7   0.0    2.1  2  SDH_sah     Serine dehydrogenase proteinase
      0.069   13.1   0.1       0.15   12.0   0.1    1.6  1  NPM1-C      Nucleophosmin C-terminal domain
      0.085   13.4   0.3       0.22   12.0   0.0    1.8  2  FliG_N      FliG N-terminal domain


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 !   64.0   0.2   4.3e-21   1.9e-17       1     112 []     135     239 ..     135     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 4.3e-21
                        Phage_Mu_F   1 kkirdavtqaiarGegeeelakelkkrgqlssrsrlrtiartetlraynaarlaqeaaskevkkekwryvavkdsrt 77 
                                       kki+ +++++ + Ge++ +l+ ++ +  ++  ++r+++iarte+ r+ n a  +++    +v+ +kwr+ a++d+rt
  gi|488601015|ref|YP_007907486.1| 135 KKIAYELREGWMLGESIPKLKNRIINVAEM-GKRRAEMIARTESTRVFNRAAFERYS---AVNIKKWRWLAAMDERT 207
                                       589999*********************999.666*******************6655...677789*********** PP

                        Phage_Mu_F  78 rpeHaaldGkvfkvddpfwqtgappedvnCRCrvi 112
                                       +p +   +Gk f+ + + +     + +vnCRC++i
  gi|488601015|ref|YP_007907486.1| 208 CPVCMSKHGKTFSGASQLPP---HGSHVNCRCTII 239
                                       ************99988753...4689*****985 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   8.4e-05      0.38     199     245 ..      54     100 ..      33     106 .. 0.80
   2 ?    1.9   0.1      0.02        90     186     225 ..     107     145 ..     101     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 8.4e-05
                           SDH_sah 199 efvyellkdkydeekakeiakklteGrwthdypltveelkelGlevn 245
                                       e + +++  +++ ekak i +++te  w      +  +lk+lG+ ++
  gi|488601015|ref|YP_007907486.1|  54 EQIKNIIELEMGPEKAKPIVEEFTERFWKDGGDYASRQLKKLGITLE 100
                                       3445566779******************99999999*******9864 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.02
                           SDH_sah 186 ladiakkaikqveefvyellkdkydeekakeiakklteGr 225
                                       la + +  ++q++ + ++l+k ++ ee  k+ia +l eG 
  gi|488601015|ref|YP_007907486.1| 107 LAIVDREILEQIKGLQLDLVK-GLSEEIKKKIAYELREGW 145
                                       5666788899********998.57888889******9995 PP

>> NPM1-C  Nucleophosmin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.4e-05      0.15       1      27 [.     131     157 ..     131     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                            NPM1-C   1 edIKaKmqasieKGvsLPkveaKFiny 27 
                                       e+IK+K+  + ++G++L ++ +K+ n 
  gi|488601015|ref|YP_007907486.1| 131 EEIKKKIAYELREGWMLGESIPKLKNR 157
                                       8****************9999999885 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     5e-05      0.22      35      97 ..      20      78 ..      15      82 .. 0.86
   2 ?   -3.0   0.0       2.4   1.1e+04      31      31 ..     125     125 ..     106     143 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                                      HHHHHHCHTTXXHHHHHHHHHHHHHHHHCCCCHHCHHHHHHHHHHHHHHSHHHHHHHCHHHHX CS
                            FliG_N 35 ltkeiaslksvskeeveaVleefleeleaqeylseggeeyarelLekalgeekaeellerlta 97
                                      +++ + +l++++ +++ +Vl+ fle++   + +    +e++++++e  +g+eka+ ++e++t+
  gi|488601015|ref|YP_007907486.1| 20 VIEYMRKLGKLPVSMKRKVLD-FLETI---DRIDDAEIEQIKNIIELEMGPEKAKPIVEEFTE 78
                                      678899999999999999996.66666...56788899********************99875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                                       H CS
                            FliG_N  31 e 31 
                                        
  gi|488601015|ref|YP_007907486.1| 125 L 125
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1389.18
//
Query:       gi|488601016|ref|YP_007907487.1|  [L=262]
Description: hypothetical protein Asulf_01511 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   13.4   1.1       0.17   12.1   1.1    1.6  1  DUF1430   Protein of unknown function (DUF1430)


Domain annotation for each model (and alignments):
>> DUF1430  Protein of unknown function (DUF1430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.1   9.6e-06      0.17      42      92 ..      13      63 ..       6      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.6e-06
                           DUF1430 42 eyliiqlivllillvlifiltkekiillvvlvlllielllillvqekiekk 92
                                       ++++++i+ l++ ++++ ++ ++i ++++ vll+  +l++ l+q k  k 
  gi|488601016|ref|YP_007907487.1| 13 LVFLLLFIITLLGSIFMYPSKVDQIPAFISSVLLVGIVLVQALLQRKQTKI 63
                                      4566666677777777777777**********************9766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); 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: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1437.00
//
Query:       gi|488601017|ref|YP_007907488.1|  [L=460]
Description: Phage head maturation protease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-10   40.5   0.0    6.3e-10   39.5   0.0    1.5  1  Peptidase_S78    Caudovirus prohead serine protease
    0.00022   21.7  13.7     0.0006   20.3  13.7    1.7  1  APG6_N           Apg6 coiled-coil region
    0.00052   19.8   1.4    0.00052   19.8   1.4    2.0  1  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
    0.00054   19.9   9.0     0.0013   18.7   9.0    1.7  1  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
    0.00073   19.7  13.6     0.0013   18.9  13.6    1.3  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.001   19.5  18.7     0.0095   16.4  18.7    2.5  1  ZapB             Cell division protein ZapB
      0.001   19.6   7.7     0.0025   18.4   7.7    1.7  1  YabA             Initiation control protein YabA
     0.0011   18.4  15.7     0.0019   17.6  15.7    1.3  1  GAS              Growth-arrest specific micro-tubule binding
     0.0015   18.5  14.0     0.0015   18.5  14.0    1.8  1  Ax_dynein_light  Axonemal dynein light chain
     0.0019   17.4   4.6     0.0028   16.8   4.6    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0021   17.9   5.9     0.0095   15.8   5.9    2.1  1  Shugoshin_N      Shugoshin N-terminal coiled-coil region
     0.0028   17.7   4.0     0.0049   16.9   4.0    1.4  1  TolA_bind_tri    TolA binding protein trimerisation
     0.0031   17.6  19.7      0.008   16.3   5.2    3.2  3  bZIP_1           bZIP transcription factor
     0.0032   17.3  11.5     0.0063   16.4  11.5    1.5  1  DUF724           Protein of unknown function (DUF724)
     0.0033   16.4   6.2     0.0048   15.9   6.2    1.2  1  DUF812           Protein of unknown function (DUF812)
     0.0038   17.1  15.0     0.0068   16.3  15.0    1.3  1  ERM              Ezrin/radixin/moesin family
     0.0051   16.4   6.5     0.0051   16.4   6.5    1.5  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
     0.0065   16.3  13.5      0.014   15.2  13.5    1.5  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
     0.0084   15.4   9.3      0.013   14.8   9.3    1.2  1  TMPIT            TMPIT-like protein
  ------ inclusion threshold ------
      0.013   15.3  16.7      0.021   14.6   5.5    3.7  3  DivIC            Septum formation initiator
      0.017   15.4   4.3      0.017   15.4   4.3    2.4  2  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.017   14.5   6.3      0.085   12.2   5.7    2.1  2  CASP_C           CASP C terminal
      0.019   13.8   3.6      0.028   13.3   3.6    1.1  1  Mgr1             Mgr1-like, i-AAA protease complex subunit
      0.027   13.4  11.1      0.037   12.9  11.1    1.1  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
      0.034   14.6   9.3       0.09   13.2   9.3    1.8  1  CENP-H           Centromere protein H (CENP-H)
      0.034   14.4  16.1      0.038   14.2  13.8    2.1  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.037   14.1  10.8        0.1   12.7  10.8    1.7  1  ADIP             Afadin- and alpha -actinin-Binding
      0.043   12.2  14.4      0.069   11.5  14.4    1.3  1  MAD              Mitotic checkpoint protein
      0.058   13.8   0.9      0.058   13.8   0.9    2.0  1  LPP              Lipoprotein leucine-zipper
      0.077   12.7   1.4       0.16   11.7   1.4    1.6  1  Lectin_N         Hepatic lectin, N-terminal domain
      0.091   12.1   3.1       0.15   11.4   3.1    1.3  1  DUF4407          Domain of unknown function (DUF4407)
       0.11   13.1   5.4       0.36   11.4   5.4    1.9  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.12   12.4   0.9       0.28   11.3   0.1    2.0  1  Peptidase_S78_2  Putative phage serine protease XkdF
       0.15   12.2  24.7      0.043   13.9   4.7    3.6  3  bZIP_2           Basic region leucine zipper
       0.18   12.5   8.3       0.52   11.0   8.0    1.9  1  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.19    9.7   3.0       0.27    9.1   3.0    1.1  1  Prominin         Prominin
       0.26   11.7   8.1      0.079   13.4   3.0    2.3  2  Snapin_Pallidin  Snapin/Pallidin
       0.26   11.2   7.4       0.43   10.5   7.4    1.3  1  STAT_alpha       STAT protein, all-alpha domain
       0.34   10.8   5.1       0.61   10.0   5.1    1.4  1  Sec34            Sec34-like family
       0.37   11.1  14.6       0.14   12.5   5.6    3.1  2  TSC22            TSC-22/dip/bun family
        0.4   10.9  13.9        1.3    9.2  13.9    1.8  1  ATG16            Autophagy protein 16 (ATG16)
       0.43   10.6  20.4        0.1   12.6  14.2    2.6  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.45   10.8   4.7       0.35   11.2   0.5    2.4  2  BORCS7           BLOC-1-related complex sub-unit 7
        0.5    8.2   6.6       0.67    7.8   6.6    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.51    9.9   3.3        1.1    8.8   2.5    1.8  2  Exonuc_VII_L     Exonuclease VII, large subunit
       0.57    9.3  18.3          2    7.5   9.2    2.2  2  Taxilin          Myosin-like coiled-coil protein
       0.58    9.4   9.5        1.5    8.1   7.0    2.3  2  DUF3450          Protein of unknown function (DUF3450)
       0.64   10.7   6.3        1.8    9.2   6.3    1.9  1  SlyX             SlyX
       0.69   10.2  12.5      0.064   13.5   5.1    2.5  2  XhlA             Haemolysin XhlA
       0.77    9.3   8.5        1.6    8.3   8.5    1.5  1  NRBF2            Nuclear receptor-binding factor 2, autophagy
       0.87    9.1  14.3          2    7.9  14.3    1.6  1  TMCO5            TMCO5 family
        1.2    9.8   4.9         25    5.5   0.1    3.3  3  MerR-DNA-bind    MerR, DNA binding
        1.2    9.2   6.2        5.5    7.0   6.1    2.1  1  DUF1664          Protein of unknown function (DUF1664)
        1.5    8.8   5.9          1    9.4   3.6    1.9  1  FlxA             FlxA-like protein
        1.6    9.1  11.9       0.78   10.1   9.3    1.7  1  OmpH             Outer membrane protein (OmpH-like)
        1.7    9.2  11.5       0.56   10.7   5.4    2.4  2  DUF16            Protein of unknown function DUF16
        1.9    8.6  13.9         10    6.3  13.7    2.3  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
        2.2    8.1   4.0        3.6    7.5   0.5    2.9  3  DASH_Dam1        DASH complex subunit Dam1
        2.7    8.3   5.9      1e+02    3.2   5.9    2.4  1  DUF948           Bacterial protein of unknown function (DUF94
        2.8    8.1  11.7        1.2    9.2   2.9    3.5  3  DUF1192          Protein of unknown function (DUF1192)
        2.8    8.1   9.1        0.6   10.3   1.1    1.9  2  Fib_alpha        Fibrinogen alpha/beta chain family
        3.1    7.9  11.5        2.1    8.5   5.8    2.4  2  Rab_bind         Rab binding domain
        3.4    7.0   7.4        5.7    6.2   7.4    1.3  1  FAM76            FAM76 protein
        3.5    7.8  14.2        9.1    6.5  11.0    3.1  1  DMPK_coil        DMPK coiled coil domain like
        3.6    6.4  16.7         10    4.9  16.7    1.6  1  Spc7             Spc7 kinetochore protein
          4    7.7  19.9         17    5.7  19.9    2.2  1  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        4.6    7.3  13.1        4.3    7.4   7.0    3.2  2  DUF2205          Short coiled-coil protein
        4.8    6.7   8.9        1.5    8.4   3.4    2.2  2  Fzo_mitofusin    fzo-like conserved region
        6.7    7.0  11.4          2    8.7   1.3    3.2  3  HALZ             Homeobox associated leucine zipper
        7.2    6.9  11.8         14    5.9  11.8    1.4  1  zf-C4H2          Zinc finger-containing protein
        7.4    7.0  17.9         21    5.6  12.4    3.3  1  FlaC_arch        Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> Peptidase_S78  Caudovirus prohead serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   2.5e-12   6.3e-10       2     155 ..       8     160 ..       7     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 2.5e-12
                     Peptidase_S78   2 elevrsseegeetisGYasv.fnevsellggfkeviapgafeetlke.kd............vralfnHdtskvlGr 64 
                                       +le+r++e++   ++GYas  ++  +       e i+ +a++++ ke  +            +++  n + + ++Gr
  gi|488601017|ref|YP_007907488.1|   8 SLETREDEKNVF-VEGYASAaVEDLDG------EIISEEALQKVAKElTEepynkvfldhapMKFNANFEEKLPIGR 77 
                                       688999997775.9***9862555554......555555555555554334555566666345555566777799** PP

                     Peptidase_S78  65 tksgtLelseDekGlrfelkl.pdttvardlyellkrgdldglSfgFrvvedeweereekvvvrtikkveLlEvSvV 140
                                       +     +  e +  l+++l l + +++ + +y+++k+g l+  S+gF+v++     r    + r i+ +++lEvS V
  gi|488601017|ref|YP_007907488.1|  78 IIEAEAKEVEGKLKLWMKLVLnKAHPYFEVVYKSIKEGFLNAFSIGFQVLQ-----R----KGRVITDLKVLEVSLV 145
                                       98776677777777888888888899************************3.....2....3579************ PP

                     Peptidase_S78 141 tvPAyddtsvevsar 155
                                        +PA++++ ve + +
  gi|488601017|ref|YP_007907488.1| 146 GIPANPEAVVEEVYE 160
                                       ********8885544 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3  13.7   2.4e-06    0.0006      44     114 ..     327     403 ..     307     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.4e-06
                            APG6_N  44 k......qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelle 114
                                       +      ++e+++e e+++++le++ +el e+ kele++ +ele+e a l+ee e+l +e ++++++ ++  +e+++
  gi|488601017|ref|YP_007907488.1| 327 AlkslnySKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKAELIEKIK 403
                                       0334445678999****************************************************999886555544 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.4   2.1e-06   0.00052      22      65 ..     335     378 ..     333     379 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.1e-06
                            GIT_CC  22 KkalaaseakiqqLlkvNtslsdelrlLQskvqkLqaeNaqlrd 65 
                                       K+++   e +i++L + N +ls+++++L  k+ +L++eNa l++
  gi|488601017|ref|YP_007907488.1| 335 KENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKE 378
                                       67777889*********************************986 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   9.0   5.1e-06    0.0013       4      70 ..     338     403 ..     335     440 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTHHHH-..-- CS
                      Phage_Mu_Gam   4 anwalrkiaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYaeankdeLfkdgk 70 
                                       +++  ++i+el++   e+ ++++e  a+i e le+e+++lk+e e l +++kqY+e +k+eL ++ k
  gi|488601017|ref|YP_007907488.1| 338 MDEFEKRIKELEATNRELSEKVKELEAKISE-LESENARLKEENERLGNEVKQYVEREKAELIEKIK 403
                                       6677789****************99999976.99****************************95444 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 !   18.9  13.6   5.2e-06    0.0013      70     179 ..     321     434 ..     297     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.2e-06
                           UPF0242  70 leekeaklteld...eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeq 143
                                        +++++ l++l+   e++++ e+ ++el++ ++eL e++++ e ++ +l+ en+ L+e+ e   ++++++    +++
  gi|488601017|ref|YP_007907488.1| 321 AATEHSALKSLNyskENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKAE 397
                                       3444445555557779***************************************************9998776666 PP

                           UPF0242 144 Laek.qellqeyqetieeqrsvlekrqdqieqLeskV 179
                                       L ek + l +e +e+  + + v++ ++ +   Le++V
  gi|488601017|ref|YP_007907488.1| 398 LIEKiKVLTDEVNEEELKVKDVVDLKEYYLTLLETRV 434
                                       65552889999999999*****************998 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  18.7   3.8e-05    0.0095       3      61 ..     335     393 ..     333     424 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-05
                              ZapB   3 lelLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqer 61 
                                        e++++ E++i+++  t ++L+++++eL+++ +el++en++l+eene+l +e ++  er
  gi|488601017|ref|YP_007907488.1| 335 KENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVER 393
                                       5999**********************************************887777666 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   7.7     1e-05    0.0025       4      62 ..     339     397 ..     336     430 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXX CS
                              YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekek 62 
                                       +e+ ++++ele + +el+e+++el+++++el  ena+L+ ene+l +++++  ++ek++
  gi|488601017|ref|YP_007907488.1| 339 DEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKAE 397
                                       567789****************************************9995554444433 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6  15.7   7.6e-06    0.0019      75     170 ..     326     421 ..     317     432 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.6e-06
                               GAS  75 kqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekkl 151
                                        +lk  +  k+ +++ ++r+kele   ++l+++ + le +++++e+e  +l+++ e+  +ev+q ++ ++  L  k+
  gi|488601017|ref|YP_007907488.1| 326 SALKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKAELIEKI 402
                                       56788888999****************************************************************** PP

                               GAS 152 kalqeelEkkeaqleevla 170
                                       k l++e+++ e ++++v+ 
  gi|488601017|ref|YP_007907488.1| 403 KVLTDEVNEEELKVKDVVD 421
                                       ***********99998875 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5  14.0   6.1e-06    0.0015     109     185 ..     325     402 ..     318     404 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.1e-06
                   Ax_dynein_light 109 Fgmrkal.qaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkksnqqlkeq 184
                                       +   k+l  ++++++e+ek+ikeLe++++el ++v+el+ak+++le+++++ ++e+e+  +e  +++++++ +l e+
  gi|488601017|ref|YP_007907488.1| 325 HSALKSLnYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKAELIEK 401
                                       55567774466899****************************************9999999999******9999887 PP

                   Ax_dynein_light 185 l 185
                                       +
  gi|488601017|ref|YP_007907488.1| 402 I 402
                                       6 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 !   16.8   4.6   1.1e-05    0.0028      57     147 ..     319     409 ..     298     434 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                             Atg14  57 qledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqi 133
                                       ++++ + +  ++l+  k  + + ++r++el+++ ++l ++++e  +k+++l +++++ +++ e l ne++++ +++ 
  gi|488601017|ref|YP_007907488.1| 319 SDAATEHSALKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREK 395
                                       5556666677788889999999999**************************************************** PP

                             Atg14 134 aklqdaikrieqkl 147
                                       a+l ++ik  ++  
  gi|488601017|ref|YP_007907488.1| 396 AELIEKIKVLTDEV 409
                                       **999999655543 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   5.9   3.8e-05    0.0095      15      44 ..     351     380 ..     340     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.8e-05
                       Shugoshin_N  15 sNsalslkirelekevseLlsENlnLReli 44 
                                       +N  ls k++ele+++seL sEN  L+e++
  gi|488601017|ref|YP_007907488.1| 351 TNRELSEKVKELEAKISELESENARLKEEN 380
                                       6888999********************986 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   4.0   1.9e-05    0.0049       2      57 ..     341     396 ..     340     406 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.9e-05
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrd 57 
                                       +e+r+++LE      s+   el  ++++l++e ++L+ ++E+l ++++q  er + 
  gi|488601017|ref|YP_007907488.1| 341 FEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKA 396
                                       699**************************************************986 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   6.6   6.6e-05     0.017      25      63 ..     335     373 ..     325     374 .. 0.93
   2 !   16.3   5.2   3.2e-05     0.008      26      58 ..     357     389 ..     356     392 .. 0.93
   3 ?    2.9   4.2      0.47   1.2e+02      23      58 ..     375     411 ..     374     417 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       ++ ++e e+r k+Le+ N +L+++++el+ ++++L+s++
  gi|488601017|ref|YP_007907488.1| 335 KENMDEFEKRIKELEATNRELSEKVKELEAKISELESEN 373
                                       7899********************************998 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevek 58 
                                       ++++eLe + ++Le+eN+ Lk+e+e+l +ev++
  gi|488601017|ref|YP_007907488.1| 357 EKVKELEAKISELESENARLKEENERLGNEVKQ 389
                                       689*************************99986 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  23 RKqaeieeLerrvka.LekeNksLkseleelkkevek 58 
                                       R ++e e+L ++vk+  e e ++L+++++ l++ev++
  gi|488601017|ref|YP_007907488.1| 375 RLKEENERLGNEVKQyVEREKAELIEKIKVLTDEVNE 411
                                       55899999999999845678889******99999975 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  11.5   2.5e-05    0.0063     105     175 ..     332     410 ..     325     421 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.5e-05
                            DUF724 105 tklleerkklekkieeeesekrkleeeidelekkilelerqlallk........ekkeaadkeiarlkseaekleee 173
                                       +  +e++ ++ek+i+e e+ +r+l+e+++ele ki+ele ++a+lk        e k+  ++e a+l  + + l +e
  gi|488601017|ref|YP_007907488.1| 332 NYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKeenerlgnEVKQYVEREKAELIEKIKVLTDE 408
                                       566889999*************************************4444444444444444444444444444444 PP

                            DUF724 174 le 175
                                       ++
  gi|488601017|ref|YP_007907488.1| 409 VN 410
                                       44 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   6.2   1.9e-05    0.0048     328     391 ..     334     399 ..     278     432 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-05
                            DUF812 328 reeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevk..lkkktlell 391
                                        +e+++e +++i+ele++  el+e++k+le++i+++e+e  ++keene+l +evk  +++  +el+
  gi|488601017|ref|YP_007907488.1| 334 SKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKqyVEREKAELI 399
                                       345789999999999999999999999999999999999999999999988887732344444554 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  15.0   2.7e-05    0.0068      24     104 ..     334     415 ..     328     438 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.7e-05
                               ERM  24 aqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaek.eeeekeklerklreaeleaarleeese 99 
                                        +e++ e e+++++L+  +r++ e+ ++Le+k +e+e e++rlke++e+  +e k+ +er+ +e  ++++ l++e++
  gi|488601017|ref|YP_007907488.1| 334 SKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERlGNEVKQYVEREKAELIEKIKVLTDEVN 410
                                       67999999************************************9999956788999***************99998 PP

                               ERM 100 rkeee 104
                                       + e +
  gi|488601017|ref|YP_007907488.1| 411 EEELK 415
                                       86544 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   6.5     2e-05    0.0051      52     151 ..     309     409 ..     285     422 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-05
                      HAUS-augmin3  52 aLktie.psdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakk 127
                                        Lk i+ + +++  +++++ ++l+  +e+  ++e+ ++eL+ +++ + ++ ++L++ +++l++e+ +l+ee++   +
  gi|488601017|ref|YP_007907488.1| 309 FLKAIGpDVKSDAATEHSALKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGN 385
                                       47888843333446666667788888999*********************************************999 PP

                      HAUS-augmin3 128 klkeaqeelraenaetnavLqqlt 151
                                       ++k+  e  +ae  e  +vL++ +
  gi|488601017|ref|YP_007907488.1| 386 EVKQYVEREKAELIEKIKVLTDEV 409
                                       999988887777777777776554 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2  13.5   5.7e-05     0.014       9      77 ..     344     417 ..     336     431 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.7e-05
                          KASH_CCD   9 tvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklks.....tQqalqkaklleeEleelkalvk 77 
                                        +++L++ N+ L+e+++ L +++   e +na+L ee+e L + +k         +++k k+l +E++e    vk
  gi|488601017|ref|YP_007907488.1| 344 RIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQyvereKAELIEKIKVLTDEVNEEELKVK 417
                                       699*************************************9988751111134567788888888876555444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   9.3   5.1e-05     0.013       2      88 ..     336     422 ..     335     437 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-05
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       e+++e+ek++kele+t++e+ +k++el++ +s++ +e ++ k++ ++l +++k++ ++ k+e  e+++ l++e++e+
  gi|488601017|ref|YP_007907488.1| 336 ENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKAELIEKIKVLTDEVNEE 412
                                       7899******************************************************99999************** PP

                             TMPIT  79 kkvlkevesl 88 
                                       +  +k+v +l
  gi|488601017|ref|YP_007907488.1| 413 ELKVKDVVDL 422
                                       9999988665 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   5.5   8.1e-05     0.021      12      57 ..     331     376 ..     326     378 .. 0.89
   2 ?   14.5   3.3   8.9e-05     0.023      19      50 ..     359     390 ..     358     392 .. 0.93
   3 ?    1.8   2.5      0.81     2e+02      22      51 ..     391     420 ..     389     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.1e-05
                                       XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXX CS
                             DivIC  12 gkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyi 57 
                                       ++++  ++ + ++ i++l+a++ +l+++ +eLea++++L+s+ +++
  gi|488601017|ref|YP_007907488.1| 331 LNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARL 376
                                       678899999******************************8766665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.9e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkdL 50 
                                       +k+l+++i +l+ e+a+lk+ene+L  evk++
  gi|488601017|ref|YP_007907488.1| 359 VKELEAKISELESENARLKEENERLGNEVKQY 390
                                       5799*************************986 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.81
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                       +++e a+l ++++ l++e +e e +vkd  
  gi|488601017|ref|YP_007907488.1| 391 VEREKAELIEKIKVLTDEVNEEELKVKDVV 420
                                       689***********************9974 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 ?   15.4   4.3   6.6e-05     0.017      40      93 ..     318     371 ..     315     374 .. 0.87
   2 ?    1.5   0.3       1.5   3.8e+02       5      40 ..     385     420 ..     381     429 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.6e-05
                           BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       k+ aa  ++ l+ ln  +e+++++ ++i+++e++ +eL e v+eL++ ++eLE+
  gi|488601017|ref|YP_007907488.1| 318 KSDAATEHSALKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELES 371
                                       556677788899999999999999999999999999999999999999999997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.5
                           BLOC1_2   5 ekvskyleaeleatvedyklLeklNeaasekykklk 40 
                                       ++v++y+e e +   e++k+L+   ++ + k+k++ 
  gi|488601017|ref|YP_007907488.1| 385 NEVKQYVEREKAELIEKIKVLTDEVNEEELKVKDVV 420
                                       678999999999999999999999999898888875 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.5   3.7e+02     133     215 ..      15      99 ..      14     103 .. 0.69
   2 ?   12.2   5.7   0.00034     0.085      94     133 ..     339     378 ..     327     418 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                            CASP_C 133 EkvRYlqsYnrgskas....tksssessssasalganpnassveagaeldkYrkaYEeslnPfaaFrgrEseraykr 205
                                       Ek  +++ Y +++ ++      s+++ ++ a++  ++++ ++v ++++  k+++++Ee+l P+ +  + E++    +
  gi|488601017|ref|YP_007907488.1|  15 EKNVFVEGYASAAVEDldgeIISEEALQKVAKE-LTEEPYNKVFLDHAPMKFNANFEEKL-PIGRIIEAEAKEVEGK 89 
                                       566677888877766654432222233333333.3455556666799999*********9.9999999999999999 PP

                            CASP_C 206 Lsllerlvls 215
                                       L+l+ +lvl+
  gi|488601017|ref|YP_007907488.1|  90 LKLWMKLVLN 99 
                                       9999998887 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00034
                            CASP_C  94 DRFrkrnaeLEeelrkqeetvsslraeiaslqkDNlkLYE 133
                                       D F kr++eLE+  r+  e+v++l a+i++l+++N  L E
  gi|488601017|ref|YP_007907488.1| 339 DEFEKRIKELEATNRELSEKVKELEAKISELESENARLKE 378
                                       7799********************************9987 PP

>> Mgr1  Mgr1-like, i-AAA protease complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.6   0.00011     0.028     236     365 ..     296     426 ..     286     432 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                              Mgr1 236 valvraqaeaenpiikWfGP.leykPmsfseyLdrleyhLdmlellqek.rkskeaskellekikhteeeleeliek 310
                                        a+ +a    e++++k  GP ++    +    L  l+y  + ++ ++++ ++ +++++el ek+k+ e++++el ++
  gi|488601017|ref|YP_007907488.1| 296 GAVLKALHIDEEVFLKAIGPdVKSDAATEHSALKSLNYSKENMDEFEKRiKELEATNRELSEKVKELEAKISELESE 372
                                       5777777778888888899845555555566799****9998888887636789999******************** PP

                              Mgr1 311 nkenrekilkklsvekektkekklplsskrkeasrgiildedvkspediDleeiw 365
                                       n++ +e+ ++  + +k+  +++k +l +k k      + +e+ k ++ +Dl+e +
  gi|488601017|ref|YP_007907488.1| 373 NARLKEENERLGNEVKQYVEREKAELIEKIKV-LTDEVNEEELKVKDVVDLKEYY 426
                                       ******99999998899999999988776644.4555778999999999999975 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  11.1   0.00015     0.037      73     156 ..     336     420 ..     315     452 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                          CALCOCO1  73 rerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleakeesearir.ELEeDiktltqralek 148
                                       ++  e+e+r++el++  +e+ ekv+ele+k  ele+ ++ l+ee+++l ++ ++ + r + EL e ik lt+ + e 
  gi|488601017|ref|YP_007907488.1| 336 ENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKaELIEKIKVLTDEVNEE 412
                                       45678899999999999999999999999999999999999999999988888877776558999999999999888 PP

                          CALCOCO1 149 EteLeRlk 156
                                       E +++ + 
  gi|488601017|ref|YP_007907488.1| 413 ELKVKDVV 420
                                       88766554 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   9.3   0.00036      0.09       6      78 ..     343     412 ..     325     421 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00036
                            CENP-H   6 eqrdelssellklsqelrelqeeltevekenlrlkrknrelaael.lelakekesekeklkeelekleaelkks 78 
                                       +++ el  +  +ls++++el+++++e+e en rlk++n+ l +e+ +  ++ek++    l e+++ l  e++++
  gi|488601017|ref|YP_007907488.1| 343 KRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVkQYVEREKAE----LIEKIKVLTDEVNEE 412
                                       5678899999999********************************3333333333....344555555555444 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2  13.8   0.00015     0.038      81     155 ..     328     403 ..     316     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00015
                     Jnk-SapK_ap_N  81 eeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklhe.retellkklkelverqr 155
                                       ++  +  +e+  e+++++++le  nrel+ k+k+++ ++s+le+++a lk+e+++l +  ++ + ++ +el+e+++
  gi|488601017|ref|YP_007907488.1| 328 LKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNeVKQYVEREKAELIEKIK 403
                                       55555667888999***************99999999999999999999999999988433334455567777766 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  10.8   0.00041       0.1      53     113 ..     350     411 ..     321     421 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00041
                              ADIP  53 eqreslnetirkleaeierlqskierlktqleqlerela.lvqakerqlekklktleqklkn 113
                                       +++ +l+e++++lea i+ l+s+  rlk+++e+l +e++  v++++++l  k+k l++ +++
  gi|488601017|ref|YP_007907488.1| 350 ATNRELSEKVKELEAKISELESENARLKEENERLGNEVKqYVEREKAELIEKIKVLTDEVNE 411
                                       23445556666666666666666666666666666666644555555555555555544444 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  14.4   0.00027     0.069     139     234 ..     329     423 ..     316     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                               MAD 139 erldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddslivknsksel.aripe.lekelerlreen 213
                                       + l+  k+++ e+e++i++le+ ++el+   +++keLe +i++ e++++ +k+ +++l   + + +e+e+++l e++
  gi|488601017|ref|YP_007907488.1| 329 KSLNYSKENMDEFEKRIKELEATNRELS---EKVKELEAKISELESENARLKEENERLgNEVKQyVEREKAELIEKI 402
                                       46778899*************9998886...589************************978865489********** PP

                               MAD 214 kklnelkenkelLkEevedlk 234
                                       k l +  ++ el   +v dlk
  gi|488601017|ref|YP_007907488.1| 403 KVLTDEVNEEELKVKDVVDLK 423
                                       ***999988888777777776 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   0.00023     0.058       2      51 ..     338     390 ..     337     391 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00023
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaakeEAaR...ANqRlDNiaqsY 51 
                                       +de  + +++L++   +ls++v++++a + +   E aR    N+Rl N +++Y
  gi|488601017|ref|YP_007907488.1| 338 MDEFEKRIKELEATNRELSEKVKELEAKISELESENARlkeENERLGNEVKQY 390
                                       6666666777777777777777777777777777777733349******9999 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00064      0.16      70     119 ..     340     392 ..     319     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00064
                          Lectin_N  70 stlaeiqalssqggslsekvtsleak...lekkqqdlkadhselllhvkqlvk 119
                                       + +  i++l++ +++lsekv+ leak   le +++ lk++   l   vkq+v+
  gi|488601017|ref|YP_007907488.1| 340 EFEKRIKELEATNRELSEKVKELEAKiseLESENARLKEENERLGNEVKQYVE 392
                                       467789******************873336788899********999999975 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.1    0.0006      0.15     106     191 ..     311     398 ..     297     434 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0006
                           DUF4407 106 keIdaelaeeqqeeakelkeqlaaa.....ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttg 177
                                       k+I   +++ ++ e ++lk+   ++     ++++++elea +++l+++++++ea++++l+ e ++  + +   g + 
  gi|488601017|ref|YP_007907488.1| 311 KAIGPDVKSDAATEHSALKSLNYSKenmdeFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNE- 386
                                       5555555555555555553322222455678888888888888888888888888888888777665544322211. PP

                           DUF4407 178 vaGkgpaakekkaq 191
                                       v  k  + +ek + 
  gi|488601017|ref|YP_007907488.1| 387 V--KQYVEREKAEL 398
                                       1..12222333333 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.4    0.0014      0.36      16      77 ..     323     386 ..     313     415 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0014
                      Syntaxin-6_N  16 kaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfkid 77 
                                       + +s +++ +  +e+ ++  ++ +el+ t++eL ++++++e ++++Le   + +++++++ + +
  gi|488601017|ref|YP_007907488.1| 323 TEHSALKSLNYSKENMDEfeKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNE 386
                                       4444444443322222222235555566666666666666666666655554444444443333 PP

>> Peptidase_S78_2  Putative phage serine protease XkdF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0011      0.28       7     113 ..      11     123 ..       5     126 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0011
                   Peptidase_S78_2   7 kkdddkqlvygvvlepd.veDaqgDiltaeeiekaaheflkey.revdkqHe...fera.gegvvvesyiaptdeev 77 
                                       +  +d++ v++  + +  veD +g+i+++e ++k+a e  +e  ++v  +H    f+ + +e  ++  +i  +++ev
  gi|488601017|ref|YP_007907488.1|  11 TR-EDEKNVFVEGYASAaVEDLDGEIISEEALQKVAKELTEEPyNKVFLDHApmkFNANfEEKLPIGRIIEAEAKEV 86 
                                       44.4566666655554449*******************998755888888842112222122444555555555555 PP

                   Peptidase_S78_2  78 geeeikkGtWvvlv.kvad...devwekikkgeitgySia 113
                                       ++   k   W+ lv ++a+   + v+++ik+g ++++Si+
  gi|488601017|ref|YP_007907488.1|  87 EG---KLKLWMKLVlNKAHpyfEVVYKSIKEGFLNAFSIG 123
                                       54...23348654414444666667888999999999985 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.7   0.00017     0.043      23      53 ..     334     364 ..     326     365 .. 0.90
   2 ?   10.7   3.2    0.0017      0.42      26      50 ..     365     389 ..     363     392 .. 0.81
   3 ?    0.7   0.2       2.3   5.8e+02      35      54 .]     389     408 ..     388     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  23 kkakeeeleervkeLeeeNaqLrqkveqLek 53 
                                        k+++ e e+r+keLe+ N +L +kv++Le+
  gi|488601017|ref|YP_007907488.1| 334 SKENMDEFEKRIKELEATNRELSEKVKELEA 364
                                       6999*************************96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  26 keeeleervkeLeeeNaqLrqkveq 50 
                                       k  ele+++ +L+eeN++L ++v+q
  gi|488601017|ref|YP_007907488.1| 365 KISELESENARLKEENERLGNEVKQ 389
                                       6678999999999999999888887 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  35 keLeeeNaqLrqkveqLeke 54 
                                       +++e+e+a+L +k++ L+ e
  gi|488601017|ref|YP_007907488.1| 389 QYVEREKAELIEKIKVLTDE 408
                                       678999****9999988876 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   8.0     0.002      0.52      13      79 ..     353     419 ..     330     431 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.002
                           DUF2203  13 pllkelleelralrkeleeleeeleeakaeaekse.......aaeleaeleeleaeieelveeieelGvevkdl 79 
                                        +l+e+++el a+ +ele+  ++l+e+       +       +++ e+e +el ++i+ l++e++e   +vkd+
  gi|488601017|ref|YP_007907488.1| 353 RELSEKVKELEAKISELESENARLKEE-------NerlgnevKQYVEREKAELIEKIKVLTDEVNEEELKVKDV 419
                                       223333333333333333333333333.......255556679******************************8 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.0    0.0011      0.27     653     727 ..     325     402 ..     301     428 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                          Prominin 653 neaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaa...veraenflkkngseiinneskklldr 726
                                       ++a +  ++ +e +++ e+ +k+l+ + ++l+e+ ++l+++i++l ++   +++ ++ l ++++++++ e+++l + 
  gi|488601017|ref|YP_007907488.1| 325 HSALKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESEnarLKEENERLGNEVKQYVEREKAELIEK 401
                                       34444444555555555555555555555555555555555555544311133333445555555555555555544 PP

                          Prominin 727 i 727
                                       i
  gi|488601017|ref|YP_007907488.1| 402 I 402
                                       4 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.0   0.00031     0.079      11      65 ..     334     383 ..     329     393 .. 0.80
   2 ?    6.0   4.2     0.062        16      14      64 ..     358     408 ..     358     444 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00031
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKL 65 
                                        +  +de+++++kel+++ +eL+e++++l +k+ ele ++      +lke  ++L
  gi|488601017|ref|YP_007907488.1| 334 SKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENA-----RLKEENERL 383
                                       677899999**********************9999998776.....555555555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.062
                   Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakK 64 
                                       k++el++k++el+ +   L+e+ +rl +++k++ e ++ae+++++k   + 
  gi|488601017|ref|YP_007907488.1| 358 KVKELEAKISELESENARLKEENERLGNEVKQYVEREKAELIEKIKVLTDE 408
                                       689**********************************99999999876655 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.4    0.0017      0.43       7      87 ..     330     410 ..     325     419 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0017
                        STAT_alpha   7 rleelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlna.LdqkRkelvdklkel 82 
                                       +l+ +++++ e e+ i++Le +  e++ +++el+ +  ++ ese+++lk+++e l + +++ + ++++el++k+k l
  gi|488601017|ref|YP_007907488.1| 330 SLNYSKENMDEFEKRIKELEATNRELSEKVKELEAK-ISELESENARLKEENERLGNEVKQyVEREKAELIEKIKVL 405
                                       688899999999*********999999999999998.67888888889999999999999999***********999 PP

                        STAT_alpha  83 lnlle 87 
                                        ++++
  gi|488601017|ref|YP_007907488.1| 406 TDEVN 410
                                       88776 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.1    0.0024      0.61      17      76 ..     336     395 ..     325     418 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0024
                             Sec34  17 eqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldp 76 
                                       e++de ++ ++ele   ++ sek ++l+++  +l +e+ rl+e +e + +++k + e ++
  gi|488601017|ref|YP_007907488.1| 336 ENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREK 395
                                       566777777777777777777777777777777777777777777777777777776665 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.9      0.17        42      13      34 ..     335     356 ..     333     358 .. 0.82
   2 ?   12.5   5.6   0.00055      0.14      14      38 ..     357     381 ..     353     394 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.17
                             TSC22  13 rEeVevLkekIkeLeernsele 34 
                                       +E  ++  ++IkeLe++n+el 
  gi|488601017|ref|YP_007907488.1| 335 KENMDEFEKRIKELEATNRELS 356
                                       5777888899999999999986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00055
                             TSC22  14 EeVevLkekIkeLeernseleeENs 38 
                                       E V +L  kI eLe++n++l+eEN+
  gi|488601017|ref|YP_007907488.1| 357 EKVKELEAKISELESENARLKEENE 381
                                       4455555555555555555555555 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  13.9    0.0053       1.3     114     173 ..     334     393 ..     317     417 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0053
                             ATG16 114 leeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEek 173
                                        +e++ e e+r++elea++++l++k+k++e+++ e+e  +  l++E + L  +++q  e+
  gi|488601017|ref|YP_007907488.1| 334 SKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVER 393
                                       445555556666666666666666666666666666666666666666665555554333 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  14.2   0.00041       0.1      22      66 ..     346     390 ..     329     397 .. 0.62
   2 ?   -0.2   1.8       3.9   9.9e+02      43      65 ..     396     418 ..     382     426 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00041
                        TMF_DNA_bd  22 ekLskkelklnntikkLrkknkelekeikelkkkleklekeleel 66 
                                       ++L++++++l++++k+L +k++ele+e ++lk+++e+l  e+++ 
  gi|488601017|ref|YP_007907488.1| 346 KELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQY 390
                                       355666666666666666666666666666666666666666655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.9
                        TMF_DNA_bd  43 kelekeikelkkkleklekelee 65 
                                       +el ++ik l+++++++e +++ 
  gi|488601017|ref|YP_007907488.1| 396 AELIEKIKVLTDEVNEEELKVKD 418
                                       45556666666666666666655 PP

>> BORCS7  BLOC-1-related complex sub-unit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5    0.0014      0.35      50      99 ..     326     375 ..     308     379 .. 0.86
   2 ?    0.5   0.1       2.8   7.2e+02      67      89 ..     397     419 ..     381     425 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0014
                            BORCS7  50 kaaksfaqqedaienteesLkkmsllttelnyqveaisksikqleevqeq 99 
                                       +a ks+ ++ +++++ e+ +k+++++ +el+++v++++ +i++le+ +  
  gi|488601017|ref|YP_007907488.1| 326 SALKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENAR 375
                                       5789*************************************999986665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.8
                            BORCS7  67 esLkkmsllttelnyqveaisks 89 
                                       e ++k+++lt+e+n+++ ++++ 
  gi|488601017|ref|YP_007907488.1| 397 ELIEKIKVLTDEVNEEELKVKDV 419
                                       56888888888888888777655 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.6    0.0027      0.67      64     134 ..     331     401 ..     304     438 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0027
                        V_ATPase_I  64 eapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeeeeeseeeeee 134
                                        + +++++de e+++++le+  +el+e+ ++l+++ +el+ ++a l++ +e l +e ++  e+e+ e  e+
  gi|488601017|ref|YP_007907488.1| 331 LNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKAELIEK 401
                                       33445556666666666666666666666666666666666666666655555544222222222222111 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 ?   -0.9   0.0       3.8   9.7e+02     242     286 ..      98     140 ..      16     143 .. 0.60
   2 ?    8.8   2.5    0.0043       1.1     163     232 ..     330     398 ..     298     441 .. 0.43

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.8
                      Exonuc_VII_L 242 leekkerleeleeklealsplkvLkrGyaivrkedgkvvtsakdl 286
                                       l++++  +e + ++++  + l++ + G+ ++++ +g+v+t+ k l
  gi|488601017|ref|YP_007907488.1|  98 LNKAHPYFEVVYKSIK-EGFLNAFSIGFQVLQR-KGRVITDLKVL 140
                                       4444444554444444.3677888889999997.69999988765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0043
                      Exonuc_VII_L 163 lleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k...ekleekkerl 232
                                        l+ +k++++++++r+k+ e+  ++ +++++ele+++++     l+++++rl+e +erl +   + +e++k++l
  gi|488601017|ref|YP_007907488.1| 330 SLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISE-----LESENARLKEENERLgNevkQYVEREKAEL 398
                                       233333333333333333322222223333333333222.....122222222222222111111111111111 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   9.2    0.0079         2      15      64 ..     333     382 ..     320     392 .. 0.41
   2 ?    7.1   2.6      0.01       2.6     126     176 ..     388     438 ..     384     445 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0079
                           Taxilin  15 speekleaLvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaelsk 64 
                                        ++e +++  k+++el + +++l++++k+l+ k ++l  e+ +l++e+++
  gi|488601017|ref|YP_007907488.1| 333 YSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENER 382
                                       33333333333333333333333333333333333333333333333333 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.01
                           Taxilin 126 neklreenaelteKlkslieqyelreehfekllktkelelqlaeaKlqqad 176
                                       ++ +++e+ael eK+k l ++++  e++++ ++  ke  l l e+++ +a+
  gi|488601017|ref|YP_007907488.1| 388 KQYVEREKAELIEKIKVLTDEVNEEELKVKDVVDLKEYYLTLLETRVIKAK 438
                                       556789999*************************************97776 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.81     2e+02     205     229 ..     196     220 ..     181     229 .. 0.82
   2 ?    8.1   7.0    0.0059       1.5      19      83 ..     325     389 ..     308     411 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.81
                           DUF3450 205 etkqWqaldssyrseirkairiark 229
                                       ++ +W++ld++ +++i+  ++ a k
  gi|488601017|ref|YP_007907488.1| 196 TSSSWEELDDEEKKNIAGHFAYAPK 220
                                       4679************988887766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0059
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeias 83 
                                       ++alk  + + ++  + +k+i++l+   +el++++++l++++++le +n++l++  + + +e+++
  gi|488601017|ref|YP_007907488.1| 325 HSALKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQ 389
                                       33444444444444444444444444444444444444444444444444444444444444443 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.3    0.0071       1.8       2      54 ..     342     394 ..     335     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0071
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54 
                                       e+r++eLE     + + ++eL + + e + + +rl+++ ++l +++k+  e++
  gi|488601017|ref|YP_007907488.1| 342 EKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVERE 394
                                       77888888888888888888888888888888888888888888887766655 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.1   0.00026     0.064       5      48 ..     330     373 ..     327     374 .. 0.91
   2 ?    0.4   0.8       3.1   7.9e+02      21      42 ..     389     410 ..     374     414 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00026
                              XhlA   5 rlerietkldnleervdkleekaaeaeekiknleedlkklesnq 48 
                                        l+  +++ d+ e+r+++le  ++e  ek+k+le ++++les +
  gi|488601017|ref|YP_007907488.1| 330 SLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESEN 373
                                       67777899999******************************965 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 3.1
                              XhlA  21 dkleekaaeaeekiknleedlk 42 
                                       + +e+ +ae  ekik l+++++
  gi|488601017|ref|YP_007907488.1| 389 QYVEREKAELIEKIKVLTDEVN 410
                                       3588999999999999998877 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 ?    8.3   8.5    0.0064       1.6      83     117 ..     354     388 ..     323     418 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0064
                             NRBF2  83 eqatkiadLkrlvelLlaenerLrkenkqLkaeka 117
                                       e   k+++L+  +  L  en rL++en++L  e  
  gi|488601017|ref|YP_007907488.1| 354 ELSEKVKELEAKISELESENARLKEENERLGNEVK 388
                                       33345555555555555555555555555544432 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  14.3    0.0081         2      64     135 ..     336     406 ..     316     439 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0081
                             TMCO5  64 dalkeLeletaklekkneiLlkevveLqkkisrkeskqddleketlkqkleelkvklqkseescaeqekela 135
                                       + + e e+    le +n  L+++v eL+ kis++es++ +l++ + ++  +e+k  +++ ++ + e+ k l 
  gi|488601017|ref|YP_007907488.1| 336 ENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKE-ENERLGNEVKQYVEREKAELIEKIKVLT 406
                                       4455566666666666666666666666666666655555544.3344444444444444444333333332 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.099        25      39      63 ..     332     356 ..     316     357 .. 0.79
   2 ?    5.4   0.7      0.11        27      41      63 ..     355     377 ..     349     379 .. 0.83
   3 ?    1.2   0.2       2.1   5.3e+02      30      56 ..     380     406 ..     374     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.099
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  39 allarklaeleeriaeLqalraeLa 63 
                                       + +++ ++e e+ri+eL+a+ +eL 
  gi|488601017|ref|YP_007907488.1| 332 NYSKENMDEFEKRIKELEATNRELS 356
                                       67888899***************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  41 larklaeleeriaeLqalraeLa 63 
                                       l +k++ele++i eL++  a+L+
  gi|488601017|ref|YP_007907488.1| 355 LSEKVKELEAKISELESENARLK 377
                                       789************98777775 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2.1
                                       TTTBHHHHHHHHHHHHHHHHHHHHHHH CS
                     MerR-DNA-bind  30 rappcqdvrallarklaeleeriaeLq 56 
                                       +++   +v++ ++r  ael e+i+ L+
  gi|488601017|ref|YP_007907488.1| 380 NERLGNEVKQYVEREKAELIEKIKVLT 406
                                       566667999**************9887 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.1     0.022       5.5      42      98 ..     341     389 ..     321     420 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.022
                           DUF1664  42 avesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlse 98 
                                       + +          ++l+at r+Ls++++++++k+ e +   + +kee +++ +++++
  gi|488601017|ref|YP_007907488.1| 341 FEK--------RIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQ 389
                                       222........2233344444444444444444444444444444443333333333 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.6    0.0041         1      25      81 ..     337     389 ..     318     414 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0041
                              FlxA  25 QiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqq 81 
                                        +++ +k +kel    e t+ e +++ ++++a+I+ l+++ a+l++++++  +e +q
  gi|488601017|ref|YP_007907488.1| 337 NMDEFEKRIKEL----EATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQ 389
                                       333344444444....44566677899999999999999999999888764444333 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   9.3    0.0031      0.78      18     101 ..     335     405 ..     323     433 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS...-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  18 kaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e.keekeqelqkkeqelqqkqqqkaqelqkkqqellk 92 
                                       k+ ++    +f+k+ +elea ++el ++++el++k ++l + +++ ++e +++ +e++q+       ++++++el++
  gi|488601017|ref|YP_007907488.1| 335 KENMD----EFEKRIKELEATNRELSEKVKELEAKISELeSeNARLKEENERLGNEVKQY-------VEREKAELIE 400
                                       44444....456666777777777777777776444443222111222233333333333.......3333333333 PP

                                       HHHHHHHHH CS
                              OmpH  93 pildkinka 101
                                       +    i+  
  gi|488601017|ref|YP_007907488.1| 401 K----IKVL 405
                                       2....2222 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.4    0.0022      0.56      32      83 ..     334     385 ..     316     394 .. 0.75
   2 ?    0.7   2.1       2.9   7.4e+02      44      66 ..     396     418 ..     374     432 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0022
                                       BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....... CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvde 83 
                                        k+++ ++e++++ l+    +l +kv+++++ki+el+ e    +ee +++++
  gi|488601017|ref|YP_007907488.1| 334 SKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGN 385
                                       4678888999999999999999999999999999998888877776655444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.9
                                       H...HHHHHHHHHHHHHHHHHHH CS
                             DUF16  44 dklgeqinkleqkvekqgekike 66 
                                       + l e+i++l+++v++ + k+k+
  gi|488601017|ref|YP_007907488.1| 396 AELIEKIKVLTDEVNEEELKVKD 418
                                       24445555555555555555543 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  13.7     0.042        10       1      58 [.     348     406 ..     348     415 .. 0.77
   2 ?   -0.9   0.5       6.9   1.7e+03       2      28 ..     392     418 ..     391     431 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.042
                       Cep57_CLD_2   1 LeaevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgv.AyeelneLkaevealr 58 
                                       Lea++ +L ++ + l+ k+++ e+e++rL  E+++  +   +   +e  eL ++  +l 
  gi|488601017|ref|YP_007907488.1| 348 LEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQyVEREKAELIEKIKVLT 406
                                       89*******************************99766666644445555555555555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 6.9
                       Cep57_CLD_2   2 eaevktLqnrLdsltrklqvheeelkr 28 
                                       e+e+ +L ++ + lt ++ + e   k+
  gi|488601017|ref|YP_007907488.1| 392 EREKAELIEKIKVLTDEVNEEELKVKD 418
                                       788888888888888888777755555 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.58   1.5e+02       9      30 ..     335     356 ..     327     357 .. 0.83
   2 ?    7.5   0.5     0.014       3.6       6      36 ..     353     383 ..     348     385 .. 0.88
   3 ?   -0.8   0.0       5.2   1.3e+03       2      25 ..     399     422 ..     398     425 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.58
                         DASH_Dam1   9 aDsletLdknledLqqihesLs 30 
                                       ++++++++k++++L+ ++ +Ls
  gi|488601017|ref|YP_007907488.1| 335 KENMDEFEKRIKELEATNRELS 356
                                       5789999999999999998887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.014
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLsdfNeSF 36 
                                       +eL++++++L++++++L++ + +L++ Ne +
  gi|488601017|ref|YP_007907488.1| 353 RELSEKVKELEAKISELESENARLKEENERL 383
                                       79********************999999966 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 5.2
                         DASH_Dam1   2 epafaeLaDsletLdknledLqqi 25 
                                        ++++ L+D++++ + +++d  ++
  gi|488601017|ref|YP_007907488.1| 399 IEKIKVLTDEVNEEELKVKDVVDL 422
                                       68999******9988777776666 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   5.9      0.41     1e+02      23      57 ..     354     388 ..     326     422 .. 0.45

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.41
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvn 57 
                                       +l++ ++e++a i ele++   + +e e+l ++v+
  gi|488601017|ref|YP_007907488.1| 354 ELSEKVKELEAKISELESENARLKEENERLGNEVK 388
                                       23333344444444444333333333333333333 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.74   1.9e+02      21      34 ..     337     350 ..     320     351 .. 0.87
   2 ?    9.2   2.9    0.0047       1.2      22      45 ..     359     382 ..     353     387 .. 0.90
   3 ?   -0.1   0.3       3.9   9.8e+02      23      37 ..     396     410 ..     395     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.74
                           DUF1192  21 SveELeerIalLea 34 
                                       +++E e+rI++Lea
  gi|488601017|ref|YP_007907488.1| 337 NMDEFEKRIKELEA 350
                                       579*********97 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0047
                           DUF1192  22 veELeerIalLeaEIaRleaaiak 45 
                                       v+ELe+ I++Le+E aRl+++ ++
  gi|488601017|ref|YP_007907488.1| 359 VKELEAKISELESENARLKEENER 382
                                       89*****************99765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 3.9
                           DUF1192  23 eELeerIalLeaEIa 37 
                                       +EL e I+ L++E+ 
  gi|488601017|ref|YP_007907488.1| 396 AELIEKIKVLTDEVN 410
                                       6999*********96 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   1.1    0.0024       0.6      86     130 ..     328     371 ..     316     374 .. 0.84
   2 ?    5.9   9.1     0.053        13      26     107 ..     348     405 ..     329     439 .. 0.39

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0024
                                       HHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  86 leeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                       l+   ++ ke++d+ e++i++L  + +++++k+++Le +i+++e+
  gi|488601017|ref|YP_007907488.1| 328 LK-SLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELES 371
                                       45.677889999999999999999999999999999999998875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.053
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqes 102
                                       l+ +++++++++++le +++e++++                 + + k++n+++ +++++ +e+e ++l e+i+    
  gi|488601017|ref|YP_007907488.1| 348 LEATNRELSEKVKELEAKISELESE-----------------NARLKEENERLGNEVKQYVEREKAELIEKIKV--- 404
                                       2223333333333333333333333.................33333334444444444444444444333322... PP

                                       HHHHH CS
                         Fib_alpha 103 nirvL 107
                                           L
  gi|488601017|ref|YP_007907488.1| 405 ----L 405
                                       ....1 PP

>> Rab_bind  Rab binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.8    0.0082       2.1      16      64 ..     328     376 ..     318     384 .. 0.89
   2 ?    2.3   0.3       0.7   1.8e+02      37      54 ..     392     409 ..     381     415 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0082
                          Rab_bind  16 iqkLstttksvdhlngLLreteatnavLmeqikLLksevrrLernqere 64 
                                       ++ L+ +   +d ++  ++e eatn  L e++k L + +  Le    r 
  gi|488601017|ref|YP_007907488.1| 328 LKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARL 376
                                       56788889999*******************************9887775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.7
                          Rab_bind  37 eatnavLmeqikLLksev 54 
                                       e   a L+e+ik+L +ev
  gi|488601017|ref|YP_007907488.1| 392 EREKAELIEKIKVLTDEV 409
                                       445566777777777776 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   7.4     0.022       5.7     221     293 ..     338     410 ..     304     418 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.022
                             FAM76 221 vtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirellkeva 293
                                       + +++++i++l+ + ++  +++ e + ki+el +e+ + ++e+++  +e+++ ++++  +l +ki+ l+ ev 
  gi|488601017|ref|YP_007907488.1| 338 MDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVEREKAELIEKIKVLTDEVN 410
                                       3344444444444444444445555667888888888888888777788888888888888888888877765 PP

>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  11.0     0.036       9.1      29      60 ..     340     371 ..     325     386 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.036
                         DMPK_coil  29 afeskLkeaEkknreLeeeleqLkkemEelra 60 
                                       +fe ++ke E+ nreL e++++L  ++ el +
  gi|488601017|ref|YP_007907488.1| 340 EFEKRIKELEATNRELSEKVKELEAKISELES 371
                                       56667777777777777777666666655543 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  16.7      0.04        10     208     271 ..     331     394 ..     310     439 .. 0.45

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.04
                              Spc7 208 laelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrl 271
                                       l+  k++++e++k+++el++   el+ek++el++++sele+e a+ ++  e+  +  ++ v+r 
  gi|488601017|ref|YP_007907488.1| 331 LNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVERE 394
                                       3333333333344444444444444444444444444433333322222222111111111111 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  19.9     0.068        17      12     112 ..     336     430 ..     318     432 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.068
                       TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellG 88 
                                       + +++++++i++lE+  ++l e++++lea+ +e+++e ++l +ene+l ++ k++   e+e +el    e++  l  
  gi|488601017|ref|YP_007907488.1| 336 ENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYV--EREKAEL---IEKIKVLTD 407
                                       44555556666666666666666666666666666666666666666655555443..3333343...344556677 PP

                       TMF_TATA_bd  89 eksEeveELr.aDvaDlKemykeqv 112
                                       e +E  eEL+ +Dv+DlKe y ++ 
  gi|488601017|ref|YP_007907488.1| 408 EVNE--EELKvKDVVDLKEYYLTLL 430
                                       7777..5777569*****9997765 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.0     0.017       4.3       8      57 ..     336     384 ..     329     392 .. 0.59
   2 ?    2.3   1.3      0.65   1.6e+02       4      30 ..     381     407 ..     375     421 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.017
                           DUF2205   8 edveklerearerLqqqakeLqssLqaLaervdeVkeehdKLesenrfLq 57 
                                       e+++++e+ ++ +L++   eL +  ++L +++ e  +e+ +L+ en+ L+
  gi|488601017|ref|YP_007907488.1| 336 ENMDEFEKRIK-ELEATNRELSEKVKELEAKISELESENARLKEENERLG 384
                                       34444444443.35556666666666666666666677777777776665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.65
                           DUF2205   4 rrnsedveklerearerLqqqakeLqs 30 
                                       +r  ++v++  + ++++L++++k L +
  gi|488601017|ref|YP_007907488.1| 381 ERLGNEVKQYVEREKAELIEKIKVLTD 407
                                       334455555555556666666655543 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.4    0.0059       1.5      92     152 ..     330     387 ..     320     392 .. 0.71
   2 ?    1.6   0.7      0.69   1.7e+02     104     133 ..     385     414 ..     378     439 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0059
                     Fzo_mitofusin  92 shqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseL 152
                                       s    +e    f++  ++ + t++el+e++kele++i++le+ + ++   +++ ++l +e+
  gi|488601017|ref|YP_007907488.1| 330 SLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARL---KEENERLGNEV 387
                                       4455555556677777788999******************9877665...45555555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.69
                     Fzo_mitofusin 104 arlcqqvdetekeleeeikelekeieklee 133
                                       ++++q v++ ++el e+ik l+ e+++ e 
  gi|488601017|ref|YP_007907488.1| 385 NEVKQYVEREKAELIEKIKVLTDEVNEEEL 414
                                       567899999999999999999999987554 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.5      0.42   1.1e+02      20      41 ..     344     365 ..     335     367 .. 0.81
   2 ?    8.7   1.3    0.0078         2      17      37 ..     369     389 ..     367     395 .. 0.90
   3 ?   -1.0   0.1       8.5   2.2e+03      24      41 ..     391     408 ..     389     410 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.42
                              HALZ  20 dydsLkkenekLkaelqeLkek 41 
                                       +   L++ n++L  +++eL +k
  gi|488601017|ref|YP_007907488.1| 344 RIKELEATNRELSEKVKELEAK 365
                                       56689999************99 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0078
                              HALZ  17 LksdydsLkkenekLkaelqe 37 
                                       L s++  Lk+ene+L +e+++
  gi|488601017|ref|YP_007907488.1| 369 LESENARLKEENERLGNEVKQ 389
                                       89999*************985 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 8.5
                              HALZ  24 LkkenekLkaelqeLkek 41 
                                       +++e+ +L  +++ L++ 
  gi|488601017|ref|YP_007907488.1| 391 VEREKAELIEKIKVLTDE 408
                                       579*********999875 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  11.8     0.055        14      21     123 ..     326     434 ..     316     454 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.055
                           zf-C4H2  21 kevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakkly.eeykklkeev 96 
                                       +++++l+ +++ + e++k +++Le   ++ +e+++ ++a i++lEs   + +ee+e+  +++k+ + +e ++l e++
  gi|488601017|ref|YP_007907488.1| 326 SALKSLNYSKENMDEFEKRIKELEATNRELSEKVKELEAKISELESENARLKEENERLGNEVKQYVeREKAELIEKI 402
                                       567788889999*********************************************99999987634555666666 PP

                           zf-C4H2  97 nelrse.....lglekledleeeeeellkeei 123
                                         l  e     l ++ + dl+e   +ll++++
  gi|488601017|ref|YP_007907488.1| 403 KVLTDEvneeeLKVKDVVDLKEYYLTLLETRV 434
                                       55555500004444444444444444444444 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 ?    5.6  12.4     0.084        21       1      32 [.     358     389 ..     329     410 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.084
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksvee 32 
                                       +++elE k+s+l++e + +k+ene l ++v++
  gi|488601017|ref|YP_007907488.1| 358 KVKELEAKISELESENARLKEENERLGNEVKQ 389
                                       78899999999999999999999999888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2017  (0.112499); expected 358.6 (0.02)
Passed bias filter:                      968  (0.0539907); expected 358.6 (0.02)
Passed Vit filter:                       249  (0.0138881); expected 17.9 (0.001)
Passed Fwd filter:                        81  (0.00451782); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              71  [number of targets reported over threshold]
# CPU time: 1.05u 0.41s 00:00:01.46 Elapsed: 00:00:00.57
# Mc/sec: 2423.98
//
Query:       gi|488601018|ref|YP_007907489.1|  [L=299]
Description: phage major capsid protein, HK97 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-15   56.7   1.9    2.9e-15   56.3   1.9    1.1  1  Phage_capsid  Phage capsid family
    5.2e-12   45.4   0.2    3.1e-10   39.6   0.2    2.0  1  Phage_cap_P2  Phage major capsid protein, P2 family
  ------ inclusion threshold ------
      0.078   12.8   0.1       0.16   11.8   0.1    1.4  1  Longin_2      Yeast longin domain
      0.097   13.1   2.8       0.11   12.9   0.9    2.1  2  GP67          Gene product 67


Domain annotation for each model (and alignments):
>> Phage_capsid  Phage capsid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   1.9   6.4e-19   2.9e-15       4     276 ..      12     291 ..       9     293 .. 0.78

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 6.4e-19
                      Phage_capsid   4 lvpeelsteiiellrerspirqlatvtr.tsasgtvkilvqtgeaeaawvgeteaipetdsptfgqitlsvkklaal 79 
                                       ++++++++++i++++e+ ++++ ++v +    +g+++ +   ++  ++  + +e++++ +s t+g + +++ k++ +
  gi|488601018|ref|YP_007907489.1|  12 VMNRQQANRFIQMVQEQAVLLKKCRVLPvNHPKGQIDKIGVASRILRSPAE-GETVTSEASVTIGSVNYDTVKVMLK 87 
                                       7899************************87778888887777744444433.3565555555*************** PP

                      Phage_capsid  80 vpvsnelLddsavd..leayiadelaeafarkedeaflnGdGdgng.qpkGilas.........tgavatgtaaavt 144
                                         ++ne+++d+     l+++ia+ +a+ f   +++  +n d++ +  +p+    +         ++++atgt++   
  gi|488601018|ref|YP_007907489.1|  88 YGITNEAIEDNIERenLANTIAKIMAQQFSVDLEDLAINADTATDAaNPD----YdflkiddgwIKQGATGTHTYDH 160
                                       ***********97555************************9988877886....24555788886667776665544 PP

                      Phage_capsid 145 ..atntaddlidliyslkaayrana.sfvmnpstlaalrklk....dadGnylwqpglqagqp.tLlGrpvveseam 213
                                         at++ d  ++li  l+++yr+ + +++m+p+ l+a++       +a G +l+     ++++ +  G+pv++ +  
  gi|488601018|ref|YP_007907489.1| 161 ggATINKDLFSQLIRTLPNKYRRPGlVWIMSPDQLEAFKDYLtnraTAAGDALL----ISDKEvMPRGFPVITPPKW 233
                                       66778888888999*********7769******998888665233344444444....455667************* PP

                      Phage_capsid 214 pdagaksageilfGDfsayiivdregveikvlrdp...ysafekd.qvafratervdgavvdpeAfk 276
                                       pd      +++ +   ++ i+v ++++++ +++ +   +   +kd + ++  t+rvd+ + +++A++
  gi|488601018|ref|YP_007907489.1| 234 PD------DQVWLTIPQNLIVVIQRNITVRKTTSSdevI---DKDlYAKYAMTARVDFIIEEKDAIA 291
                                       64......5677777799999999999887777764444...56625667779*********99996 PP

>> Phage_cap_P2  Phage major capsid protein, P2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.2     7e-14   3.1e-10      29     321 ..      16     291 ..      12     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 7e-14
                      Phage_cap_P2  29 sveqkLeekiqessefLkkInvvgVdeqkGekvglgvsgliasrtdtskkeRktkdvtkldsnkYelektnsdtaik 105
                                       +++++  + +qe++ +Lkk  v++V++ kG+  ++gv + i    +  ++  + ++  ++ s +Y   k+   + i+
  gi|488601018|ref|YP_007907489.1|  16 QQANRFIQMVQEQAVLLKKCRVLPVNHPKGQIDKIGVASRILRSPAE-GETVTSEASVTIGSVNYDTVKVMLKYGIT 91 
                                       567889999**********************9999999888766665.555566666666***************** PP

                      Phage_cap_P2 106 YakldawakfkdfqkrlreaiakrialdrimiGfnGtsvaattdraanpllqDVnkGWlqklreeapervltegkke 182
                                        + ++   + +++++++++++a++++ d      n  ++ +  +++    l  +  GW+++     +++        
  gi|488601018|ref|YP_007907489.1|  92 NEAIEDNIERENLANTIAKIMAQQFSVDLEDLAINADTATDAANPDY-DFL-KIDDGWIKQGA--TGTHTY------ 158
                                       ********************************999888777777765.333.4789**97643..333434...... PP

                      Phage_cap_P2 183 skivigeggdyknLDalvfdavnslideeyredtdLVvlvGrdLladkkfkllnktntekeklaaqliisqkri..g 257
                                            ++gg   n D l ++++ ++++++yr+ ++LV +++ d l++ k  l n++ ++ ++    l+is k++   
  gi|488601018|ref|YP_007907489.1| 159 -----DHGGATINKD-LFSQLI-RTLPNKYRR-PGLVWIMSPDQLEAFKDYLTNRATAAGDA----LLISDKEVmpR 223
                                       .....4455555555.678889.99*****98.**********9999999998855544433....34444555226 PP

                      Phage_cap_P2 258 glpavrvPffPakallvTsldNLsiYtqegsrrrkiednp...krdrienyess.negYvvedyelaa 321
                                       g p++++P  P+++++ T  +NL + +q++ + rk ++ +   ++d +++y +    ++++e+ +++a
  gi|488601018|ref|YP_007907489.1| 224 GFPVITPPKWPDDQVWLTIPQNLIVVIQRNITVRKTTSSDeviDKDLYAKYAMTaRVDFIIEEKDAIA 291
                                       99***************************977776644431236888999887515699999998887 PP

>> Longin_2  Yeast longin 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      0.16      97     155 ..     225     285 ..     218     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                          Longin_2  97 lpvit.eaWsqiskwldeiQkiilsllkkellkekekeldallpldlrvk..fpkevdkiiq 155
                                       +pvit + W + + wl+  Q++i+ + +++++ +k++++d++  +dl +k  +++ vd ii+
  gi|488601018|ref|YP_007907489.1| 225 FPVITpPKWPDDQVWLTIPQNLIVVI-QRNITVRKTTSSDEVIDKDLYAKyaMTARVDFIIE 285
                                       56776269**************9998.66666677888899988887665225677888875 PP

>> GP67  Gene product 67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   7.2e+03      27      58 ..      72     103 ..      67     114 .. 0.70
   2 ?   12.9   0.9   2.5e-05      0.11       9      45 ..     260     296 ..     254     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                              GP67  27 rtidlikeekiaiarnfliegeepedededed 58 
                                        ti  +  + + +  ++ i  e  ed+ e e+
  gi|488601018|ref|YP_007907489.1|  72 VTIGSVNYDTVKVMLKYGITNEAIEDNIEREN 103
                                       56666666667777777777777777776664 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.5e-05
                              GP67   9 ksndlvaarklfae.amaartidlikeekiaiarnfli 45 
                                        s d v  + l+a+ am+ar +d+i eek aiar + i
  gi|488601018|ref|YP_007907489.1| 260 TSSDEVIDKDLYAKyAMTAR-VDFIIEEKDAIARAINI 296
                                       58899999****97578887.8************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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 0.35s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1723.18
//
Query:       gi|488601019|ref|YP_007907490.1|  [L=66]
Description: hypothetical protein Asulf_01514 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.30s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 450.06
//
Query:       gi|488601020|ref|YP_007907491.1|  [L=50]
Description: hypothetical protein Asulf_01515 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 399.41
//
Query:       gi|488601021|ref|YP_007907492.1|  [L=144]
Description: hypothetical protein Asulf_01516 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.35   10.7   0.0    1.7  1  HTH_30    PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.9e-05      0.35      30      45 ..      31      46 ..      30      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHHHHHS--TT CS
                            HTH_30 30 ryRLrrieellgldld 45
                                        R+ +i+el+g+d++
  gi|488601021|ref|YP_007907492.1| 31 DRRIAQIKELTGRDFT 46
                                      67************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 1038.44
//
Query:       gi|488601022|ref|YP_007907493.1|  [L=95]
Description: hypothetical protein Asulf_01517 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.4   0.3     0.0036   17.0   0.3    1.1  1  HD_4           HD domain
     0.0035   17.2   0.5     0.0043   16.9   0.5    1.1  1  Sec20          Sec20
     0.0036   16.8   3.5     0.0044   16.5   3.5    1.1  1  Cluap1         Clusterin-associated protein-1
      0.006   16.8   3.3     0.0078   16.4   3.3    1.1  1  Cortex-I_coil  Cortexillin I, coiled coil
  ------ inclusion threshold ------
      0.011   15.0   0.9      0.012   14.9   0.9    1.0  1  TMPIT          TMPIT-like protein
      0.015   15.4   2.5      0.017   15.1   2.5    1.1  1  Rootletin      Ciliary rootlet component, centrosome cohesion
      0.019   15.0   5.7      0.036   14.1   5.7    1.5  1  TMF_DNA_bd     TATA element modulatory factor 1 DNA binding
      0.021   15.1   2.5      0.024   14.9   1.1    1.7  2  KxDL           Uncharacterized conserved protein
      0.024   14.9   1.6      0.029   14.7   1.6    1.2  1  DUF5093        Domain of unknown function (DUF5093)
      0.024   14.5   0.3      0.027   14.4   0.3    1.1  1  ACCA           Acetyl co-enzyme A carboxylase carboxyltransfe
      0.025   14.3   2.2       0.03   14.0   2.2    1.2  1  CCDC85         CCDC85 family
      0.026   14.2   1.3      0.031   14.0   1.3    1.1  1  Med4           Vitamin-D-receptor interacting Mediator subuni
      0.028   14.7   0.3      0.028   14.7   0.3    1.7  2  UPF0122        Putative helix-turn-helix protein, YlxM / p13 
      0.053   12.9   0.0      0.061   12.7   0.0    1.1  1  DUF5305        Family of unknown function (DUF5305)
      0.064   12.9   0.7        0.1   12.1   0.8    1.4  1  SseC           Secretion system effector C (SseC) like family
      0.064   13.6   2.2      0.091   13.1   2.2    1.2  1  GAT            GAT domain
      0.075   13.3   2.3       0.11   12.7   2.3    1.3  1  Rx_N           Rx N-terminal domain
        3.8    7.8  10.5        2.4    8.4   3.6    2.6  2  XhlA           Haemolysin XhlA


Domain annotation for each model (and alignments):
>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   3.6e-06    0.0036      87     138 ..      12      64 ..       3      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-06
                              HD_4  87 deaeekaeqvenlRkmLlAmveDirvvliklAdrlqtlrslaaa.keekrrdv 138
                                       d+ +e ++q e+  kmLl+ ++Di+ +  kl +  +tl+ +++  k+ ++++v
  gi|488601022|ref|YP_007907493.1|  12 DMLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHEKRlKKVEKVQV 64 
                                       5667889**********************************766333344444 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   4.3e-06    0.0043      13      84 ..      10      83 ..       4      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.3e-06
                             Sec20 13 isqllsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkklerrd..ktdkllvflalglflacv 84
                                      i+ +l++  qq ee  + l + + ++++++ ++ ++ d+l+  +k +kk+e+ +  ++ +++++ a++ f+a++
  gi|488601022|ref|YP_007907493.1| 10 IEDMLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHEKRLKKVEKVQvrHSTYFKIMGAISGFIATI 83
                                      6778999999*****************************************97622678999********9987 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.5   4.4e-06    0.0044     168     223 ..       8      63 ..       3      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.4e-06
                            Cluap1 168 kalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqsvr 223
                                       + +++ +k+++++ e+ +k+l +l+sd +++++k++ +   le ++krL+++++v+
  gi|488601022|ref|YP_007907493.1|   8 RLIEDMLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHEKRLKKVEKVQ 63 
                                       5688999**********************************************986 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.3   7.8e-06    0.0078      42      94 ..      10      62 ..       5      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.8e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Cortex-I_coil 42 lesllasleseaaerekrlreleakldealknleleklarlelesrlsktekd 94
                                      +e++l+ l+++++e+ k+l  l + ++ + k+l+    +  + e rl k+ek 
  gi|488601022|ref|YP_007907493.1| 10 IEDMLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHEKRLKKVEKV 62
                                      6889******************************99999999*********95 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9   1.2e-05     0.012       2      87 ..       4      92 ..       3      95 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                             TMPIT  2 eeweeleke.fkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelke 77
                                      e+w++l ++ +kel+++++e ++ l +ls+ ++++ k+++++   l++ +++lkk++k +   + + +++  ++  +++
  gi|488601022|ref|YP_007907493.1|  4 EDWARLIEDmLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHEKRLKKVEKVQVrhSTYFKIMGAISGFIAT 82
                                      5777765541689999999999999999999999999999999999999999999988643234555566666666666 PP

                             TMPIT 78 rkkvlkeves 87
                                      + + ++ ++s
  gi|488601022|ref|YP_007907493.1| 83 IATLFAAIKS 92
                                      6666666655 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.5   1.7e-05     0.017      90     137 ..      14      61 ..       4      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                         Rootletin  90 nslLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeee 137
                                        + Lr+q+ee+++   +L++d++ + k++++  + le+ ek++++ e+
  gi|488601022|ref|YP_007907493.1|  14 LKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHEKRLKKVEK 61 
                                       5679***************************************99876 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   5.7   3.6e-05     0.036      35      74 .]      14      53 ..      10      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                        TMF_DNA_bd 35 ikkLrkknkelekeikelkkkleklekeleeleerlkeae 74
                                      +k+Lr++n+e++k + +l++ +++  k+l+++ + l+ +e
  gi|488601022|ref|YP_007907493.1| 14 LKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHE 53
                                      89*****************999999999988888887776 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.1   2.4e-05     0.024      39      73 ..      10      44 ..       5      53 .. 0.89
   2 ?   -0.2   0.0       1.3   1.3e+03      29      35 ..      53      59 ..      42      74 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                              KxDL 39 sqerlaklrarfkqgtkllkevkkdLesifkkirs 73
                                       +  l++lr++ +++tk+l ++ +d++si+kk++s
  gi|488601022|ref|YP_007907493.1| 10 IEDMLKELRQQNEEQTKMLLSLSSDIKSIHKKLNS 44
                                      67789***************************987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.3
                              KxDL 29 nreLlel 35
                                      +++L+++
  gi|488601022|ref|YP_007907493.1| 53 EKRLKKV 59
                                      2222221 PP

>> DUF5093  Domain of unknown function (DUF5093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.6   2.9e-05     0.029      87     122 ..      30      64 ..      10      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                           DUF5093  87 eseltdvkelekeldeameeyektekskkkkkKklv 122
                                       +  ++d+k+++k+l+   +++e +ek++kk  K +v
  gi|488601022|ref|YP_007907493.1|  30 S-LSSDIKSIHKKLNSHCDTLEDHEKRLKKVEKVQV 64 
                                       3.348*************************999988 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   2.7e-05     0.027       8      73 ..      10      77 ..       3      90 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                              ACCA  8 iaeleekieelkklaeesevdlseeieklekkleklkkeiy...knltpwqkvqlaRhpeRpktldyie 73
                                      i+++ +++++ ++ +++  ++ls++i++++kkl++  +++    k+l++++kvq+ Rh++  k++  i+
  gi|488601022|ref|YP_007907493.1| 10 IEDMLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEdheKRLKKVEKVQV-RHSTYFKIMGAIS 77
                                      3334444444333344444557888888888888777655422277999999997.8887776665555 PP

>> CCDC85  CCDC85 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.2     3e-05      0.03      18      56 ..      11      49 ..       3      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
                            CCDC85 18 eelvrrLRraeaekvsllvergrlikevnrrLqqhLlei 56
                                      e++++ LR++++e++++l+  ++ ik + ++L+ h   +
  gi|488601022|ref|YP_007907493.1| 11 EDMLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTL 49
                                      899********************************7654 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.3   3.1e-05     0.031      28      79 ..      11      60 ..       7      79 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                              Med4 28 earilqLraeveslDekikeivksLkeyekeLkavpdqenskldtasiklae 79
                                      e+ +++Lr++ e+  + + ++ + +k+++k+L++ + +  ++   +  k+ e
  gi|488601022|ref|YP_007907493.1| 11 EDMLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHC-DTLEDH-EKRLKKVE 60
                                      455666666666666666666666666666666666.222221.12222222 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.4   1.4e+03      83      95 ..      12      24 ..       4      37 .. 0.53
   2 ?   14.7   0.3   2.8e-05     0.028      48      87 ..      36      75 ..      30      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                           UPF0122 83 kikdkllkqkele 95
                                      ++ ++l +q+e++
  gi|488601022|ref|YP_007907493.1| 12 DMLKELRQQNEEQ 24
                                      3333333333222 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.8e-05
                           UPF0122 48 qavydnikrtekllekyEekLkllekykkreellekikdk 87
                                      ++++ +++  ++ le++E++Lk +ek ++r++ + ki+ +
  gi|488601022|ref|YP_007907493.1| 36 KSIHKKLNSHCDTLEDHEKRLKKVEKVQVRHSTYFKIMGA 75
                                      589*****************************99999765 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.1e-05     0.061      68     138 ..      17      93 ..       8      95 .] 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                           DUF5305  68 esieesktsrlpiplteqtyeikkdetd......eengeitetvtvkespslaegilliilgllaliglvvlirrii 138
                                        ++++++++++ ++l++++ +i k++++      + ++++++ ++v++ +s+   i+++i g++a+i+  +++   +
  gi|488601022|ref|YP_007907493.1|  17 LRQQNEEQTKMLLSLSSDIKSIHKKLNShcdtleDHEKRLKKVEKVQVRHSTYFKIMGAISGFIATIATLFAAIKSF 93 
                                       567899999***************99998444423333344444444444444488888888888888877776655 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8    0.0001       0.1       4      83 ..      13      93 ..      10      95 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                              SseC  4 klreLtskaaedsleskqkllkelq.ekqeklrqeqveeireqikkaeekakkaGiigkIfGwilaivsvvagalkvga 81
                                      +l eL+ +++e+++ +   + ++ +  k+ +++ + +e+ ++ +kk e+ +   ++  kI+G+i++ ++++a  +++++
  gi|488601022|ref|YP_007907493.1| 13 MLKELRQQNEEQTKMLLSLSSDIKSiHKKLNSHCDTLEDHEKRLKKVEKVQVRHSTYFKIMGAISGFIATIATLFAAIK 91
                                      5666777776666654444433332134566799999**********99999**************************9 PP

                              SseC 82 sl 83
                                      s+
  gi|488601022|ref|YP_007907493.1| 92 SF 93
                                      97 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.2   9.1e-05     0.091       4      53 ..       7      55 ..       5      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.1e-05
                               GAT  4 aklLsemLsstepdeellenellkeLyetckamqpriqklieetadeedl 53
                                      a+l ++mL+++ ++ + ++  +l  L + +k++++++   +++++d e+ 
  gi|488601022|ref|YP_007907493.1|  7 ARLIEDMLKELRQQ-NEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHEKR 55
                                      7899*******977.778999***********************998864 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.3   0.00011      0.11       5      55 ..      13      63 ..       7      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                              Rx_N  5 llqkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerqikdeavk 55
                                      +l+ L +  +e+ k+l ++ +++++++++L+s    Led+e+r  k e v+
  gi|488601022|ref|YP_007907493.1| 13 MLKELRQQNEEQTKMLLSLSSDIKSIHKKLNSHCDTLEDHEKRLKKVEKVQ 63
                                      5666666677778*****************************766555443 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.4     0.022        22      17      46 ..      11      40 ..       8      43 .. 0.85
   2 ?    8.4   3.6    0.0024       2.4       2      33 ..      38      69 ..      37      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                              XhlA 17 eervdkleekaaeaeekiknleedlkkles 46
                                      e+ +++l + ++e+ + + +l  d+k++ +
  gi|488601022|ref|YP_007907493.1| 11 EDMLKELRQQNEEQTKMLLSLSSDIKSIHK 40
                                      5667788899*****************976 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0024
                              XhlA  2 ikerlerietkldnleervdkleekaaeaeek 33
                                      i ++l+ +   l+++e+r++k+e+ + ++ + 
  gi|488601022|ref|YP_007907493.1| 38 IHKKLNSHCDTLEDHEKRLKKVEKVQVRHSTY 69
                                      889*********************99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2516  (0.140331); expected 358.6 (0.02)
Passed bias filter:                     1265  (0.0705561); expected 358.6 (0.02)
Passed Vit filter:                       210  (0.0117129); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 561.91
//
Query:       gi|488601023|ref|YP_007907494.1|  [L=82]
Description: hypothetical protein Asulf_01518 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 528.89
//
Query:       gi|488601024|ref|YP_007907495.1|  [L=159]
Description: hypothetical protein Asulf_01524 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   27.0   1.9     0.0014   18.1   0.1    3.2  3  HTH_24           Winged helix-turn-helix DNA-binding
    0.00014   21.6   0.0      0.035   13.7   0.0    2.1  2  DDRGK            DDRGK domain
    0.00027   20.9   0.5      0.011   15.7   0.2    2.1  2  DUF977           Bacterial protein of unknown function (DUF97
     0.0013   19.1   0.2        1.7    9.0   0.0    2.5  2  Penicillinase_R  Penicillinase repressor
     0.0016   18.3   0.1       0.72    9.8   0.0    3.1  3  MarR_2           MarR family
      0.002   18.3   0.1       0.34   11.1   0.1    2.7  2  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
     0.0024   18.3   0.9        7.8    7.1   0.0    3.2  3  HTH_27           Winged helix DNA-binding domain
     0.0026   17.6   3.5       0.22   11.5   0.0    3.2  3  MarR             MarR family
     0.0036   17.1   0.0       0.44   10.4   0.0    2.7  2  FtsK_gamma       Ftsk gamma domain
     0.0041   16.9   0.5      0.067   13.0   0.2    2.8  2  LexA_DNA_bind    LexA DNA binding domain
  ------ inclusion threshold ------
      0.039   14.0   0.1       0.27   11.3   0.0    2.4  3  HTH_45           Winged helix-turn-helix
       0.05   12.8   0.6       0.16   11.1   0.3    1.8  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
      0.067   13.3   0.0        0.4   10.8   0.0    2.1  2  FeoC             FeoC like transcriptional regulator
      0.083   12.8   0.2        1.4    8.9   0.0    2.5  3  RuvB_C           RuvB C-terminal winged helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.24     3e+02       4      23 ..       3      22 ..       2      31 .. 0.82
   2 ?    5.4   0.2      0.01        13      36      47 ..      38      49 ..      38      50 .. 0.91
   3 !   18.1   0.1   1.1e-06    0.0014       3      47 ..      99     143 ..      97     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.24
                            HTH_24  4 tdrkILelLqknprisqreL 23
                                      t+ ++Le++++++    ++L
  gi|488601024|ref|YP_007907495.1|  3 TQEEVLEAIKQKGYADLKDL 22
                                      78899******999888887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
                            HTH_24 36 rrlkrLeeeGlI 47
                                      +rl+ Le++GlI
  gi|488601024|ref|YP_007907495.1| 38 QRLRALERKGLI 49
                                      59*********9 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.1e-06
                            HTH_24   3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       e   k+L+ +++n   ++r + +  g    t+++++++L+++G++
  gi|488601024|ref|YP_007907495.1|  99 ESITKLLNFIRENKIVTIRWIQRNMGWDWRTTTKYINKLVRDGIV 143
                                       56679**************************************98 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0068       8.7     102     143 ..       5      49 ..       2      52 .. 0.79
   2 !   13.7   0.0   2.7e-05     0.035      87     143 ..      87     143 ..      82     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0068
                                       HHHHHHHHH-SEE-HHHHHHHH-S-HHH...HHHHHHHHHHHSSS CS
                             DDRGK 102 eefinyikekKvvlleelavkfklktqe...vierikeLeeqgsl 143
                                       ee+++ ik+k +  l++l  +f+l+ q      +r+++Le +g +
  gi|488601024|ref|YP_007907495.1|   5 EEVLEAIKQKGYADLKDLKRHFGLEYQGsswLPQRLRALERKGLI 49 
                                       6889999***************99977522256888888888876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.7e-05
                                       XXXXXXXXXXXXXHHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS CS
                             DDRGK  87 egtekesaeeeeklleefinyikekKvvlleelavkfklktqevierikeLeeqgsl 143
                                        g  k s +++e+ +++++n+i+e+K+v++  +  +++ +     + i++L  +g +
  gi|488601024|ref|YP_007907495.1|  87 RGRPKGSIQYREESITKLLNFIRENKIVTIRWIQRNMGWDWRTTTKYINKLVRDGIV 143
                                       56667777888889************************9999999999999888866 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.038        49      15      89 ..       5      84 ..       1      89 [. 0.73
   2 !   15.7   0.2   8.6e-06     0.011       8      66 ..      95     155 ..      87     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.038
                            DUF977 15 eriiGlvkkneritisdleritGvgrtsvrky..lvdvlerGdli...rpGkyGvfrdervvrvwrkaaekatdqtlir 88
                                      e ++  +k+++   ++dl+r +G +++          +ler +li   r G + v+  +     w +a     +  lir
  gi|488601024|ref|YP_007907495.1|  5 EEVLEAIKQKGYADLKDLKRHFGLEYQGSSWLpqRLRALERKGLIvsmRSGNISVYLANDFDCCWDEAKRILLELGLIR 83
                                      5666778889999999999999999876654311345899999973335677778988888888988888888888888 PP

                            DUF977 89 k 89
                                      k
  gi|488601024|ref|YP_007907495.1| 84 K 84
                                      7 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 8.6e-06
                            DUF977   8 eereelkeriiGlvkkneritisdleritGvgrtsvrkylvdvlerGdl..irpGkyGvfr 66 
                                       + ree   +++ ++++n+ +ti  ++r +G ++++  ky+   +  G +  ir+G+  +f+
  gi|488601024|ref|YP_007907495.1|  95 QYREESITKLLNFIRENKIVTIRWIQRNMGWDWRTTTKYINKLVRDGIVfeIRNGRLRLFT 155
                                       458999999*******************************998888876345788888776 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0013       1.7       5      64 ..       4      62 ..       2      64 .. 0.87
   2 !    7.6   0.1    0.0038       4.8       9      62 ..     105     154 ..      98     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                                      -SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE- CS
                   Penicillinase_R  5 EaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsp 64
                                      ++ev+e++ +kg a  k++  ++  e+    s     lr L++Kgl+ + ++g+  +Y +
  gi|488601024|ref|YP_007907495.1|  4 QEEVLEAIKQKGYADLKDLKRHFGLEY-QGSSWLPQRLRALERKGLIVSMRSGNISVYLA 62
                                      789****************99999883.345567789*********************87 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0038
                                       HHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEE CS
                   Penicillinase_R   9 meilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiY 62 
                                       ++ ++e++ +t+++++  +     +   T++  +++Lv+ g++ + ++gr  ++
  gi|488601024|ref|YP_007907495.1| 105 LNFIRENKIVTIRWIQRNM----GWDWRTTTKYINKLVRDGIVFEIRNGRLRLF 154
                                       5667777777777776655....566788889***************9997766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.026        33      25      53 ..      20      51 ..       2      56 .. 0.65
   2 ?   -0.4   0.1      0.86   1.1e+03      45      55 ..      76      86 ..      74      90 .. 0.79
   3 !    9.8   0.0   0.00056      0.72       9      55 ..     103     147 ..      99     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.026
                                      HHHHHHHTSSHHHHH...HHHHHHHHTTSEEE CS
                            MarR_2 25 gelarrlglsksavs...rilkrLvaaGLver 53
                                      ++l r++gl+ +  s   ++l+ L+++GL++ 
  gi|488601024|ref|YP_007907495.1| 20 KDLKRHFGLEYQGSSwlpQRLRALERKGLIVS 51
                                      555555555555544444899********975 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.86
                                      HHHTTSEEEEE CS
                            MarR_2 45 LvaaGLverrp 55
                                      L + GL+++r+
  gi|488601024|ref|YP_007907495.1| 76 LLELGLIRKRK 86
                                      67899**9984 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00056
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                        +L++++ +    +t++ + r +g +  ++++ +++Lv+ G v + +
  gi|488601024|ref|YP_007907495.1| 103 KLLNFIRENKI--VTIRWIQRNMGWDWRTTTKYINKLVRDGIVFEIR 147
                                       58999*99997..8***************************996655 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00026      0.34       7      39 ..      10      50 ..       5      55 .. 0.87
   2 ?    4.5   0.0      0.03        39      26      44 ..     131     149 ..     102     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                           AbiEi_4  7 asrqvGlfttrelea.aGispsa.......lrrLvrkGwLv 39
                                      a +q+G++  ++l++  G+ ++        lr L rkG++v
  gi|488601024|ref|YP_007907495.1| 10 AIKQKGYADLKDLKRhFGLEYQGsswlpqrLRALERKGLIV 50
                                      45999****************447***************98 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.03
                           AbiEi_4  26 psalrrLvrkGwLvrlrrG 44 
                                       ++++++Lvr G +  +r G
  gi|488601024|ref|YP_007907495.1| 131 TKYINKLVRDGIVFEIRNG 149
                                       245********99888866 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 !    7.1   0.0    0.0061       7.8      30      53 ..      30      54 ..       3      57 .. 0.73
   2 ?    2.5   0.1      0.16     2e+02      42      63 ..      76      97 ..      73      98 .. 0.87
   3 ?    5.8   0.0     0.015        19       8      58 ..     104     150 ..      99     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0061
                            HTH_27 30 vedshis.yslkkLtekGLvertgd 53
                                      ++ s+     l++L++kGL++++++
  gi|488601024|ref|YP_007907495.1| 30 YQGSSWLpQRLRALERKGLIVSMRS 54
                                      4555666678**********88876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                            HTH_27 42 LtekGLvertgdeadrrekrvr 63
                                      L e GL+ + +  +++++ ++r
  gi|488601024|ref|YP_007907495.1| 76 LLELGLIRKRKRGRPKGSIQYR 97
                                      899****999999999998886 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.015
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58 
                                       +L+ ir ++  ++++ + + +  +  ++ + ++kL++ G v +    +++r
  gi|488601024|ref|YP_007907495.1| 104 LLNFIR-ENKIVTIRWIQRNMGWDWRTTTKYINKLVRDGIVFEI---RNGR 150
                                       589999.999999**************************99665...4444 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00017      0.22       4      52 ..       3      54 ..       2      56 .. 0.90
   2 ?   -2.0   0.4       2.8   3.6e+03      40      51 ..      75      86 ..      74      87 .. 0.81
   3 ?    5.5   0.0     0.013        16       9      47 ..     105     143 ..     100     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-...HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvs...kstvtrvldrLekkGlieRsks 52
                                      tq ++L+ ++++g + +++L +++g++   +s +   l++Le+kGli +++s
  gi|488601024|ref|YP_007907495.1|  3 TQEEVLEAIKQKGYADLKDLKRHFGLEyqgSSWLPQRLRALERKGLIVSMRS 54
                                      6778999*******************9777789999***********99987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                      HHHHTTSEEEEE CS
                              MarR 40 rLekkGlieRsk 51
                                       L + Gli+++k
  gi|488601024|ref|YP_007907495.1| 75 ILLELGLIRKRK 86
                                      58899***9987 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.013
                                       HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR   9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47 
                                       L  ++e+   ++  +++ +g +  t+t+ + +L+++G +
  gi|488601024|ref|YP_007907495.1| 105 LNFIRENKIVTIRWIQRNMGWDWRTTTKYINKLVRDGIV 143
                                       556777777888889999999999************987 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.039        50       8      39 ..       5      36 ..       2      57 .. 0.78
   2 !   10.4   0.0   0.00035      0.44       4      51 ..      98     145 ..      95     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.039
                        FtsK_gamma  8 eeavelvveegkaStSllQRrlriGYnRAarl 39
                                      ee++e + ++g a    l+R++ + Y+ ++ l
  gi|488601024|ref|YP_007907495.1|  5 EEVLEAIKQKGYADLKDLKRHFGLEYQGSSWL 36
                                      79999999***************999876655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                        FtsK_gamma   4 DelfeeavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgp 51 
                                       +e +++ ++++ e++ + + ++QR++   +   ++ i++L ++GiV +
  gi|488601024|ref|YP_007907495.1|  98 EESITKLLNFIRENKIVTIRWIQRNMGWDWRTTTKYINKLVRDGIVFE 145
                                       566788899************************************965 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 !   13.0   0.2   5.2e-05     0.067       8      57 ..       4      50 ..       1      55 [. 0.78
   2 ?   -0.7   0.0      0.97   1.2e+03      27      55 ..     115     142 ..     102     152 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                                      HHHHHHHHHHHHHHHSS---HHHHHHHHTS-...HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind  8 QrevldlikasieetgypPsireiaralglk..SpsaveehLkaLerKGyie 57
                                      Q+evl+     i+++gy+   +++ r++gl+   +s   ++L+aLerKG+i 
  gi|488601024|ref|YP_007907495.1|  4 QEEVLEA----IKQKGYA-DLKDLKRHFGLEyqGSSWLPQRLRALERKGLIV 50
                                      6666654....5678998.68999999999632677899**********995 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.97
                                       -HHHHHHHHTS-.HHHHHHHHHHHHHTTS CS
                     LexA_DNA_bind  27 sireiaralglkSpsaveehLkaLerKGy 55 
                                       +ir i r++g    ++  +  ++L r G+
  gi|488601024|ref|YP_007907495.1| 115 TIRWIQRNMGWD-WRTTTKYINKLVRDGI 142
                                       556666666655.4555555555555555 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.95   1.2e+03      37      49 ..      37      49 ..       5      60 .. 0.58
   2 ?   -3.1   0.0       6.4   8.3e+03      42      53 ..      75      86 ..      74      88 .. 0.76
   3 ?   11.3   0.0   0.00021      0.27       8      49 ..     101     143 ..      96     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.95
                            HTH_45 37 nkYLdmLvekgli 49
                                       + L  L  kgli
  gi|488601024|ref|YP_007907495.1| 37 PQRLRALERKGLI 49
                                      3456667777776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.4
                            HTH_45 42 mLvekglikksk 53
                                      +L+e gli+k+k
  gi|488601024|ref|YP_007907495.1| 75 ILLELGLIRKRK 86
                                      588999998765 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00021
                            HTH_45   8 iadILeais.egeakkTkimykanLsykllnkYLdmLvekgli 49 
                                       i  +L+ i+ ++  +  +i  +   +++++ kY+++Lv  g++
  gi|488601024|ref|YP_007907495.1| 101 ITKLLNFIReNKIVTIRWIQRNMGWDWRTTTKYINKLVRDGIV 143
                                       56677777645556666788888999***************98 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.55     7e+02     219     233 ..       3      17 ..       2      32 .. 0.79
   2 ?   11.1   0.3   0.00012      0.16      84     117 ..     104     137 ..      94     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.55
                                       -HHHHHHHHHHTTEE CS
                    NNMT_PNMT_TEMT 219 ekeevlealkkaglk 233
                                       ++eevlea+k+ g++
  gi|488601024|ref|YP_007907495.1|   3 TQEEVLEAIKQKGYA 17 
                                       5899*******9986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00012
                                       EEESSHHHHHHHHHHHTT-TS--THHHHHHHHHH CS
                    NNMT_PNMT_TEMT  84 lsDyldqNrdeLekWlkkeeafdWspvvkvicel 117
                                       l  ++ +N+ + ++W++ +  +dW ++ k+i++l
  gi|488601024|ref|YP_007907495.1| 104 LLNFIRENKIVTIRWIQRNMGWDWRTTTKYINKL 137
                                       5579999************************986 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00032       0.4       4      51 ..       6      56 ..       4      76 .. 0.77
   2 ?   -0.2   0.0      0.85   1.1e+03       3      44 ..     102     143 ..     100     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                              FeoC  4 elkeyleergrvslkeLsrhfkaspea...leamLeqwvrkGrvekvaata 51
                                      e+ e+++++g ++lk+L rhf  + +    l + L  ++rkG +     ++
  gi|488601024|ref|YP_007907495.1|  6 EVLEAIKQKGYADLKDLKRHFGLEYQGsswLPQRLRALERKGLIVSMRSGN 56
                                      677999***************998654222777799999999887766665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.85
                              FeoC   3 telkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrv 44 
                                       t+l ++++e++ v ++ + r +  +  +  + ++ +vr G v
  gi|488601024|ref|YP_007907495.1| 102 TKLLNFIRENKIVTIRWIQRNMGWDWRTTTKYINKLVRDGIV 143
                                       677889999999999999888888877777777777777755 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.1   3.9e+03      10      33 ..       6      26 ..       3      31 .. 0.65
   2 ?    8.9   0.0    0.0011       1.4      41      61 ..      69      89 ..      40      93 .. 0.82
   3 ?    1.2   0.0      0.28   3.5e+02      10      54 ..     103     143 ..      98     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                                      HHHHHHHHT.TT--B-HHHHHHHT CS
                            RuvB_C 10 kyLkllkekfkggpvglktlaail 33
                                      ++L+++k   ++g++ lk l  + 
  gi|488601024|ref|YP_007907495.1|  6 EVLEAIK---QKGYADLKDLKRHF 26
                                      6777887...56777777766655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0011
                                      HHTTHHHHHHTTSEEEETTEE CS
                            RuvB_C 41 edviEPyLlkeglIertsrGR 61
                                       d+   +Ll+ glI++ +rGR
  gi|488601024|ref|YP_007907495.1| 69 WDEAKRILLELGLIRKRKRGR 89
                                      5666789************** PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.28
                                       HHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSE CS
                            RuvB_C  10 kyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglI 54 
                                       k+L+++    +++ v ++ +   +g +  t ++ i   L++ g +
  gi|488601024|ref|YP_007907495.1| 103 KLLNFIR---ENKIVTIRWIQRNMGWDWRTTTKYIN-KLVRDGIV 143
                                       6777787...78999999999999999888776664.45555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 976.20
//
Query:       gi|488601025|ref|YP_007907496.1|  [L=71]
Description: hypothetical protein Asulf_01525 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 473.43
//
Query:       gi|488601026|ref|YP_007907497.1|  [L=502]
Description: hypothetical protein Asulf_01526 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-25   89.3  13.0    6.7e-25   88.6  13.0    1.4  1  AAA_15    AAA ATPase domain
    1.5e-20   74.2   7.4    4.4e-18   66.1   7.4    2.4  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0028   17.1   1.0      0.038   13.4   0.1    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.011   16.3   9.4       0.45   11.0   8.9    2.9  1  AAA_23    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 !   88.6  13.0   1.5e-28   6.7e-25       6     369 .]       3     405 ..       1     405 [. 0.59

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1.5e-28
                            AAA_15   6 ikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn............................ 54 
                                       ++++N +s+k+ +++l++ ltv+iG+Nn+GK+ +++++  + +                                  
  gi|488601026|ref|YP_007907497.1|   3 VEVENLGSIKKGKVELKP-LTVFIGPNNTGKTYLAYLISGLCEDF---Lfrkyifspvrgkrkpvytlservvsdil 75 
                                       89****************.*******************7766633...12445567****99888877544443333 PP

                            AAA_15  55 .kkvikiekedleifeniseskdikIdvef..............................aekekakeyektlkske 100
                                        k           +  +i+ + +  ++ +f                              +    +ke ++ lk + 
  gi|488601026|ref|YP_007907497.1|  76 eK----------GYA-EIKINLKDILAENFeytasifrklserpilvqkfvesfwkflggD----KKEMFSNLKATV 137
                                       31..........222.222222222222334455555555666666555555554333321....222222222221 PP

                            AAA_15 101 kkkadlllkkkesdlkktikdkklklkknelsdekisvekkks...................kkelpkekeekleke 158
                                       k  +    +++e+                                                 + +++k k++  + +
  gi|488601026|ref|YP_007907497.1| 138 KIPNIDSRNEFEEIV---------------------------YnrsghiithmfyeenimlrAISFKKPKSYQMDVR 187
                                       111111111112222...........................12222222222222223333222222233333333 PP

                            AAA_15 159 keelkid..kedlkklikkleeslkkee.......elknvlksaiiklllisakRnvsdedsekkssllgklkekil 226
                                          ++ +  +ed++++ + +++++ +         ++k +l+  +  + +++a+Rn+ + d  k s + +++ e+i 
  gi|488601026|ref|YP_007907497.1| 188 LRLIERKifSEDKQEINDAISKQIDQFLsriilflLMKIILQPILSNVFIFPAQRNALTLDFIK-SAINIATREEIP 263
                                       33333333344455555544444444445558888999999****************9977666.444444444444 PP

                            AAA_15 227 eealqekl......eeelteklkeiqeklkeidkklaeelkkilkkkidkik.kfnykgkkneeieik....ddeel 292
                                       +e     l      ++ + + + +++  ++ i++++++e+  ++ + ++++     + ++++ e ei+     + +l
  gi|488601026|ref|YP_007907497.1| 264 DE----DLivsnpeRLIKSKPILKFLRMVDLISEDIESEYY-DIGQRLEEVLgGHLIISESKGEEEIRfiinGEKSL 335
                                       43....23344344222444555666666666666655555.344444444423334444445555555667***** PP

                            AAA_15 293 plnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                       +l   +s vq+l +l+l + +  k        ++ +i+EPE +LHp+aq+ + + ++e++n +   viitTHSp+i+
  gi|488601026|ref|YP_007907497.1| 336 KLITTSSMVQQLSSLALYLKHQAKS------GDLMVIDEPESNLHPEAQTRITEVIAEMVNGGL-WVIITTHSPFIL 405
                                       *********************9999......9*******************************7.**********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 !   66.1   7.4   9.9e-22   4.4e-18       1     303 []      21     406 ..      21     406 .. 0.65

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 9.9e-22
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarl......drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvr 71 
                                       l+v+iGpN++GK++L +++++l+        + +  +++ ++  + ++r+++  l  ++ ei++++ +++ ++ +  
  gi|488601026|ref|YP_007907497.1|  21 LTVFIGPNNTGKTYLAYLISGLCEDflfrkyIFSPVRGKRKPVYTLSERVVSDILEKGYAEIKINLKDILAENFEYT 97 
                                       79********************9877777776666666667766777777777777777777777777744444444 PP

                            AAA_21  72 yryglrlersqv.................eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkels 131
                                        + + +l ++ +                 +e++s+++ + +++ ++ +   ee++   + +  ++  + ++     +
  gi|488601026|ref|YP_007907497.1|  98 ASIFRKLSERPIlvqkfvesfwkflggdkKEMFSNLKATVKIPNIDSRNEFEEIVYNRSGHIITHMFYEENIMLRAI 174
                                       44444444444444444333333333333333333333333333333333333333333333333333333333333 PP

                            AAA_21 132 vsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeel 208
                                         +  + +++++++++++r+ ++++ +                     ++++ +++ +++++ + i   ++++  + 
  gi|488601026|ref|YP_007907497.1| 175 SFKKPKSYQMDVRLRLIERKIFSEDKQ---------------------EINDAISKQIDQFLSRIILFLLMKIILQP 230
                                       333333333333333333333333333.....................33444444444444444444444444444 PP

                            AAA_21 209 iasvderlrer.................................................................. 219
                                       i s+ +  +                                                                    
  gi|488601026|ref|YP_007907497.1| 231 ILSNVFIFPAQrnaltldfiksainiatreeipdedlivsnperlikskpilkflrmvdlisedieseyydigqrle 307
                                       44333333333666666666666777777777788888888999999999999************************ PP

                            AAA_21 220 ...............gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllel 281
                                                        + +  ++ + l +   S+ +++l  l+++l  ++k+g+l +iDEpE++LHP++++r+ e+
  gi|488601026|ref|YP_007907497.1| 308 evlgghliiseskgeEEIRFIINGEKSLKLITTSSMVQQLSSLALYLKHQAKSGDLMVIDEPESNLHPEAQTRITEV 384
                                       ***************666666666666666666888***************************************** PP

                            AAA_21 282 lkelsrngaQviltTHSpllld 303
                                       + e  ++g  vi+tTHSp++l+
  gi|488601026|ref|YP_007907497.1| 385 IAEMVNGGLWVIITTHSPFILE 406
                                       *******************985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.02        89       6      41 ..       4      36 ..       2      42 .. 0.78
   2 !   13.4   0.1   8.5e-06     0.038     142     214 ..     345     417 ..     116     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.02
                                      EEESETTEECEEEEEETTSSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  6 eienFksyagktvilpfsksftaivGpNGSGKsnll 41
                                      e+en  s+  k+ ++++++ +t+ +GpN  GK+ l 
  gi|488601026|ref|YP_007907497.1|  4 EVENLGSI--KKGKVELKP-LTVFIGPNNTGKTYLA 36
                                      67788888..466666777.899*********9765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.5e-06
                                       HHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 142 ktLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvtkv 214
                                       ++L++laL +  +++k   l+++De +++L  +  +++ e++ e  +    +i+++++  +le+ ++l++ + v
  gi|488601026|ref|YP_007907497.1| 345 QQLSSLALYLK-HQAKSGDLMVIDEPESNLHPEAQTRITEVIAEMVNGgLWVIITTHSPFILEHINNLMKAYVV 417
                                       78999999986.66777889***********************9998768999999999999*99*99998875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   8.9    0.0001      0.45       3     161 ..       4     194 ..       3     359 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                            AAA_23   3 kienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks......grgfeksdveiese..gkv 71 
                                       ++en++s+++ +++++ +lt+++GpN +GKT +   i   +  +  r    s      +  +  s+ ++ s+  +k+
  gi|488601026|ref|YP_007907497.1|   4 EVENLGSIKKGKVELK-PLTVFIGPNNTGKTYLAYLISGLCEDFLFRKYIFSpvrgkrKPVYTLSE-RVVSDilEKG 78 
                                       79*************9.**************99988886654433222111132332221122222.2222223455 PP

                            AAA_23  72 kayveltfenkdgry.............................................................. 86 
                                        a ++++++++  ++                                                              
  gi|488601026|ref|YP_007907497.1|  79 YAEIKINLKDILAENfeytasifrklserpilvqkfvesfwkflggdkkemfsnlkatvkipnidsrnefeeivynr 155
                                       55566665554443344444443444444444322222222222222222222222222222222222223333333 PP

                            AAA_23  87 ...............trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefel 148
                                                                                                                 ++ 
  gi|488601026|ref|YP_007907497.1| 156 sghiithmfyeenimL--------------------------------------------------------RAISF 176
                                       3333333333322221........................................................22222 PP

                            AAA_23 149 kdkke.....rleeleke 161
                                       k++k+     rl+ +e++
  gi|488601026|ref|YP_007907497.1| 177 KKPKSyqmdvRLRLIERK 194
                                       222223333322222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3769.61
//
Query:       gi|488601027|ref|YP_007907498.1|  [L=171]
Description: hypothetical protein Asulf_01527 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   15.0   0.2      0.041   14.4   0.2    1.3  1  eRF1_3    eRF1 domain 3
      0.094   13.1   0.0       0.13   12.6   0.0    1.3  1  Smr       Smr domain


Domain annotation for each model (and alignments):
>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   4.6e-06     0.041       5      80 ..      73     153 ..      69     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS......-HHH-HHHHHH.HHHH CS
                            eRF1_3   5 kklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv......ketgeelelve.liee 73 
                                       +k++e+f e + +++ k++  +++ +k++++g ++ LLv+    +s++  lk+++           e+e+++  +ee
  gi|488601027|ref|YP_007907498.1|  73 AKAIEQFEETITNEKFKYILNIHNCRKCNNYGCIKLLLVVHGRGISSNNdLKDRIykkykfI---LETEELNcDLEE 146
                                       689**************************************999999888888875443320...333334455666 PP

                                       HHHHHHH CS
                            eRF1_3  74 lvenvee 80 
                                       +++++++
  gi|488601027|ref|YP_007907498.1| 147 IINKYKN 153
                                       6666665 PP

>> Smr  Smr domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05      0.13       1      47 [.      65     129 ..      65     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                                       EE-TT--HHHHHHHHHHHHHH...............HHHTT-SEEEEE--STTSTT...HCHHHH CS
                               Smr   1 lDLhglrraealnvletflda...............asakglrsvevihGkGahag...vgvLrp 47 
                                       + L+g + a+a+++ e+ + +                 +  ++ ++v+hG+G +++   + ++ +
  gi|488601027|ref|YP_007907498.1|  65 IELKGINLAKAIEQFEETITNekfkyilnihncrkcNNYGCIKLLLVVHGRGISSNndlKDRIYK 129
                                       57899999999999999999988888888887666433334999********9755455444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1218.10
//
Query:       gi|488601028|ref|YP_007907499.1|  [L=59]
Description: hypothetical protein Asulf_01528 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 372.06
//
Query:       gi|488601029|ref|YP_007907500.1|  [L=199]
Description: hypothetical protein Asulf_01529 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       281  (0.0156729); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1245.07
//
Query:       gi|488601030|ref|YP_007907501.1|  [L=106]
Description: hypothetical protein Asulf_01530 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.078   13.4   0.1       0.22   11.9   0.1    1.9  2  Gifsy-2   ATP-binding sugar transporter from pro-phage


Domain annotation for each model (and alignments):
>> Gifsy-2  ATP-binding sugar transporter from pro-phage
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.21   3.8e+03      78      89 ..       9      20 ..       4      30 .. 0.68
   2 ?   11.9   0.1   1.2e-05      0.22      59      97 ..      63     101 ..      18     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.21
                                      ETTEEEEEEEEE CS
                           Gifsy-2 78 vegkkflvksyd 89
                                      ++gk+ ++k++ 
  gi|488601030|ref|YP_007907501.1|  9 KRGKDITLKRIA 20
                                      567777777764 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.2e-05
                                       EEEE--SS--.--TT-EEEETTEEEEEEEEEEETTEEEE CS
                           Gifsy-2  59 kltvfrgsgykPrlgdrvvvegkkflvksydevdglivl 97 
                                       k++v+ + g+    gd  v +g++f ++++ + d  i l
  gi|488601030|ref|YP_007907501.1|  63 KVVVYVSTGVDVSQGDSLVIDGSEFKIERISRTDAYIKL 101
                                       7999******99********************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 795.89
//
Query:       gi|488601031|ref|YP_007907502.1|  [L=125]
Description: hypothetical protein Asulf_01531 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-07   30.5   0.1    8.9e-07   29.8   0.1    1.4  1  HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-compon
     0.0011   19.0   0.1     0.0012   18.8   0.1    1.1  1  Minor_capsid_2  Minor capsid protein


Domain annotation for each model (and alignments):
>> HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1     1e-10   8.9e-07       7      81 .]      13      79 ..       8      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1e-10
                    HK97-gp10_like  7 leklserevekaikkalkkaAkevldkakkrtpsvdtggdLrdsitvqgkvkkkggeyrvevgnnaeyArlvEfG 81
                                      lekl+ +++ + +k + +    ++++++k+++p vdt g++r+ ++       + ++++  + nn +yA+++ +G
  gi|488601031|ref|YP_007907502.1| 13 LEKLDVKNIADPLKNIFRDEVLRLEAEIKETAP-VDT-GRYRSAWHS------EISDLEAQIANNVKYAKYLIYG 79
                                      77777767888888888888899**********.***.*********......7777***************998 PP

>> Minor_capsid_2  Minor capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.4e-07    0.0012       1      96 [.       3      97 ..       3     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-07
                    Minor_capsid_2  1 ikvkvdlskikrkvsekal.krgqlalanqvl...adinryVPkkegsLrds..aevesdgskiiydtpYAkaqyeGgf 73
                                      ik++v++ ++ +k+  k++    +   +++vl   a+i++  P+++g  r +  +e+++ + +i  + +YAk+  +G  
  gi|488601031|ref|YP_007907502.1|  3 IKIEVNIDGALEKLDVKNIaDPLKNIFRDEVLrleAEIKETAPVDTGRYRSAwhSEISDLEAQIANNVKYAKYLIYG-- 79
                                      79*****************44456667898863336999*********99862266788888***************.. PP

                    Minor_capsid_2 74 aekkgkvkftkyttPgtgkeWdk 96
                                      ++k     f++ ++P + k+ d 
  gi|488601031|ref|YP_007907502.1| 80 TKK-----FRRVKEPHKYKKADL 97
                                      444.....777777776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 801.33
//
Query:       gi|488601032|ref|YP_007907503.1|  [L=129]
Description: hypothetical protein Asulf_01532 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-06   26.1   0.0    9.4e-06   25.8   0.0    1.1  1  DUF3168   Protein of unknown function (DUF3168)
  ------ inclusion threshold ------
      0.088   12.6   0.0       0.11   12.3   0.0    1.2  1  IL31      Interleukin 31


Domain annotation for each model (and alignments):
>> DUF3168  Protein of unknown function (DUF3168)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.1e-09   9.4e-06      17      94 ..      21      97 ..      15     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.1e-09
                           DUF3168 17 ggrvyd.rapqgaalPyivlgpvqsrdasalcgdgaevrvqldvwarepgraeakalaaavraaL..ddaala.lpggr 91
                                       g+vy+ ++ + a++P++ l  v+   +++l+ +   + v+++v+a  ++r e ++l++ v+ a   ++++la     +
  gi|488601032|ref|YP_007907503.1| 21 SGKVYSaYPKKSAEFPCACLDMVSMAGDNTLGAEIHSYLVRISVFA--DDRLELDQLVDKVMNAFvgHADELAsC---H 94
                                      5779**99999***********************************..****************95555555532...3 PP

                           DUF3168 92 las 94
                                        +
  gi|488601032|ref|YP_007907503.1| 95 YNG 97
                                      333 PP

>> IL31  Interleukin 31
   #    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      28      92 ..      24      82 ..       1      94 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                              IL31 28 lledyekkekGvsesesyqlpcltsdreapnninssailaylkaikplldnksdideiieqLkkl 92
                                      ++  y k      +s ++   cl + + a +n   + i++yl  i  ++d++ ++d+++++  + 
  gi|488601032|ref|YP_007907503.1| 24 VYSAYPK------KSAEFPCACLDMVSMAGDNTLGAEIHSYLVRISVFADDRLELDQLVDKVMNA 82
                                      3333332......45666666677777888999999**********************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 865.11
//
Query:       gi|488601033|ref|YP_007907504.1|  [L=297]
Description: hypothetical protein Asulf_01533 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1909.99
//
Query:       gi|488601034|ref|YP_007907505.1|  [L=137]
Description: hypothetical protein Asulf_01534 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.2   0.1       0.24   11.7   0.1    1.2  1  DUF755         Domain of unknown function (DUF755)
       0.17   12.3   2.0         12    6.3   0.1    2.1  2  Microtub_bind  Kinesin-associated microtubule-binding


Domain annotation for each model (and alignments):
>> DUF755  Domain of unknown function (DUF755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.7e-05      0.24      22      62 ..      26      65 ..      22      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                            DUF755 22 kqkkqkqssttgttdgalLqkqLlkEcqktsqLiqlsqqlq 62
                                       q++ + ++  +t++++lL+k +lkE +k ++ i+++++++
  gi|488601034|ref|YP_007907505.1| 26 RQRN-RIIMYLLTEAKDLLEKGVLKENMKLEEAIEVVSKMK 65
                                      4555.7788889999**********************9993 PP

>> Microtub_bind  Kinesin-associated microtubule-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0013        12      26      67 ..      14      55 ..      12      67 .. 0.71
   2 ?    6.2   0.3    0.0014        12      29      59 ..      65     102 ..      60     118 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0013
                     Microtub_bind 26 tepreellerfrqeqeeldaaltieeeeevsqdsleeeesie 67
                                      +ep++ +++++r++++ + + l +e ++ +++ +l+e+  +e
  gi|488601034|ref|YP_007907505.1| 14 SEPKHGVVRELRRQRNRIIMYLLTEAKDLLEKGVLKENMKLE 55
                                      79999************9999999555666666665555555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0014
                     Microtub_bind  29 reellerfrqeqeeldaalti...ee....eeevsqds 59 
                                       + +ll +f q qee++ ++ti   ++    +ee+++ s
  gi|488601034|ref|YP_007907505.1|  65 KPDLLSEFTQMQEEFEYMATIslaTNrvwtTEELDELS 102
                                       5689**************99976633223333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 808.44
//
Query:       gi|488601035|ref|YP_007907506.1|  [L=149]
Description: hypothetical protein Asulf_01535 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1063.96
//
Query:       gi|488601036|ref|YP_007907507.1|  [L=382]
Description: putative Zn peptidase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-15   56.4   0.0    5.8e-15   55.3   0.0    1.6  1  Peptidase_M78  IrrE N-terminal-like domain
      8e-06   25.6   0.1    2.4e-05   24.1   0.1    1.8  1  HTH_25         Helix-turn-helix domain
    1.2e-05   25.2   0.1    0.00031   20.7   0.0    3.2  4  HTH_19         Helix-turn-helix domain
    1.6e-05   25.1   0.0    3.4e-05   24.1   0.0    1.4  1  HTH_31         Helix-turn-helix domain
    0.00051   20.3   1.0     0.0015   18.7   0.4    2.1  2  DUF365         Domain of unknown function (DUF365)
    0.00054   20.0   2.4     0.0027   17.7   0.1    2.9  3  HTH_3          Helix-turn-helix
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.036   13.7   0.0    1.6  1  DUF4344        Putative metallopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   2.3e-18   5.8e-15       2     121 ..     177     300 ..     176     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.3e-18
                     Peptidase_M78   2 erlgidvlaldlgakdldgfrfdnsetkvivlnsnhsptrqrftlaHElgHlllhherdkfreegdskaqerlerea 78 
                                       e+l+i v+   + +kd +gf  ++  + +i +ns +    + ftl+HE+gH+ll+++ +  ++    +++ + er +
  gi|488601036|ref|YP_007907507.1| 177 EELNIFVFQYGMPVKDARGFTLTDDFPIIITVNSKDLYKPRIFTLMHEFGHVLLGESVVDIPN-IAIPTTNIVERWC 252
                                       78999999999*************97777889999999********************87555.55667789***** PP

                     Peptidase_M78  79 nafAaelllPeeaflalaatqrkdlee.....rlaeyfgVSkeavavr 121
                                       n+fAa +llP++   +++ + r+ l++     rl+ +++VSk ++ + 
  gi|488601036|ref|YP_007907507.1| 253 NEFAASFLLPKDVAIKVFGENRSSLTSkrtlgRLSGRYKVSKHMLLYT 300
                                       ********************************************9875 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   9.2e-09   2.4e-05       2      35 ..      21      54 ..      20      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.2e-09
                                      HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                            HTH_25  2 LraaRearglsleevaketkIrkdylealEeddf 35
                                      L+  Re  g+s+eeva+++kI ++ le +Ee+++
  gi|488601036|ref|YP_007907507.1| 21 LKWLREISGYSIEEVAEKLKIEVEKLELIEEGKL 54
                                      7889***************************975 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.2e-07   0.00031       4      60 ..      21      76 ..      19      80 .. 0.94
   2 ?   -0.5   0.0      0.52   1.3e+03       5      16 ..     118     129 ..     116     146 .. 0.91
   3 ?   -1.6   0.0       1.1   2.9e+03       6      14 ..     147     155 ..     144     161 .. 0.78
   4 ?   -3.3   0.0       3.7   9.4e+03      42      53 ..     371     382 .]     357     382 .] 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.2e-07
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                      Lk +Re  g+++ee+ae+l+i   k+  iE gk   p+  l++++++++++++ +++
  gi|488601036|ref|YP_007907507.1| 21 LKWLREISGYSIEEVAEKLKIEVEKLELIEEGKL-GPTFTLIRDLSKIYKVPVAAFF 76
                                      7789****************************99.*****************98776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.52
                            HTH_19   5 keaReelgltqe 16 
                                       ke++e+lg+t+e
  gi|488601036|ref|YP_007907507.1| 118 KELIENLGYTIE 129
                                       7999*****997 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.1
                            HTH_19   6 eaReelglt 14 
                                       ++Ree+glt
  gi|488601036|ref|YP_007907507.1| 147 KYREEFGLT 155
                                       678888887 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 3.7
                            HTH_19  42 aelllkiaealg 53 
                                        ++++k++e +g
  gi|488601036|ref|YP_007907507.1| 371 TRTFNKLLEQVG 382
                                       788999999876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.3e-08   3.4e-05       5      59 ..      20      73 ..      19      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.3e-08
                            HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpa 59
                                       L++lRe +G s eevAe l + + +l  +E G+ g p+   ++ l  ++ +++a
  gi|488601036|ref|YP_007907507.1| 20 VLKWLREISGYSIEEVAEKLKIEVEKLELIEEGKLG-PTFTLIRDLSKIYKVPVA 73
                                      79*********************************9.***************987 PP

>> DUF365  Domain of unknown function (DUF365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.4     6e-07    0.0015      10      52 ..     122     164 ..     115     184 .. 0.83
   2 ?   -2.2   0.0       2.1   5.3e+03      71      86 ..     308     323 ..     300     329 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6e-07
                                       TT-B--EEEEEEEEEEES-THHHHHHTSTTBSS-HHHHHHHHH CS
                            DUF365  10 edtGfvGeaeikrvvlsedpleifekygdrvfltkeelkkyvk 52 
                                       e+ G+  e +i+rv l+++p++i eky+++  lt+e   ++  
  gi|488601036|ref|YP_007907507.1| 122 ENLGYTIEPHIERVSLKDKPEKIAEKYREEFGLTEELQAEFKD 164
                                       899*******************************876555554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                                       EEEEEEE--S-B--SS CS
                            DUF365  71 eledikkydkvvkPkr 86 
                                        l++ ++++k  kP+ 
  gi|488601036|ref|YP_007907507.1| 308 SLKEYEEFKKRFKPSS 323
                                       4555555555555554 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.1e-06    0.0027       1      53 [.      21      73 ..      21      75 .. 0.96
   2 ?   -2.9   0.0         3   7.7e+03      40      52 ..     116     128 ..     114     129 .. 0.60
   3 ?    0.9   0.1      0.19   4.8e+02       3      17 ..     147     160 ..     146     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53
                                      lk lR+  g+s+ee+Aekl + +  +  iE G+  P+ + +  l+k ++v+ +
  gi|488601036|ref|YP_007907507.1| 21 LKWLREISGYSIEEVAEKLKIEVEKLELIEEGKLGPTFTLIRDLSKIYKVPVA 73
                                      799***********************************************976 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                                       HHHHHHHHHTSEH CS
                             HTH_3  40 tlkklakaLgvsl 52 
                                       ++k+l + Lg+++
  gi|488601036|ref|YP_007907507.1| 116 VAKELIENLGYTI 128
                                       5666666666665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.19
                                       HHHHHTTHHHHHHHH CS
                             HTH_3   3 elRkqlglsqeeLAe 17 
                                       ++R++ gl+ eeL++
  gi|488601036|ref|YP_007907507.1| 147 KYREEFGLT-EELQA 160
                                       89*******.78876 PP

>> DUF4344  Putative metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.4e-05     0.036      23     130 ..     142     261 ..     129     277 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                           DUF4344  23 eklaeklnellklprdltivfaeCgeanafydpeekeit.iCyelveeieelfakankeee.......eeaeeavlg 91 
                                       ek+aek +e + l+++l+  f+   +a a+++  +++i+ +   ++++   +  +++ + +       + +++++++
  gi|488601036|ref|YP_007907507.1| 142 EKIAEKYREEFGLTEELQAEFK---DASAMFKYLRQKIEeLNIFVFQYGMPVKDARGFTLTddfpiiiTVNSKDLYK 215
                                       7788888888888888888888...566666666666641333333333333334444444557777777889999* PP

                           DUF4344  92 allfvllHElgHalidl.......lelPilGreEDavDqlaailLl 130
                                       + +f+l+HE+gH l+ +         +P++   E    ++aa +Ll
  gi|488601036|ref|YP_007907507.1| 216 PRIFTLMHEFGHVLLGEsvvdipnIAIPTTNIVERWCNEFAASFLL 261
                                       *************975411111113455566666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
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 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2355.76
//
Query:       gi|488601037|ref|YP_007907508.1|  [L=167]
Description: hypothetical protein Asulf_01537 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-25   89.5   0.2    3.3e-25   88.9   0.2    1.3  1  DUF4411        Domain of unknown function (DUF4411)
  ------ inclusion threshold ------
      0.014   15.9   0.1      0.019   15.5   0.1    1.2  1  Aspzincin_M35  Lysine-specific metallo-endopeptidase


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 !   88.9   0.2   3.6e-29   3.3e-25       1     162 []       5     167 .]       5     167 .] 0.83

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 3.6e-29
                           DUF4411   1 YllDtnvfieakrryYsfdifpsfWewleeeveegkllsikeVkrElergedelskWakenesieklesaedlavve 77 
                                       Y++D++++i  k +  ++di  s W++l e+  e++l+s  eV+ Ele ++del++Wake++++  +++  ++ +++
  gi|488601037|ref|YP_007907508.1|   5 YIIDSSSLIDLK-DRNPLDIYLSVWNKLMELHLENRLYSHIEVYLELEGRDDELKEWAKEQKNE--YPDFFKKYTPD 78 
                                       9********995.55678******************************************9994..55555556666 PP

                           DUF4411  78 evgkvakwvivesekyskaakkeflsvaDpfliAaAlakna..........tvVTkEvkkpnkkknkvkIPdvceal 144
                                       + + va + + + e + k++ +  ++ aDp+l+A+Al+ +           ++ T+Ev     k n+vkIP v++++
  gi|488601037|ref|YP_007907508.1|  79 QQKYVADI-LSKFESFVKIN-DGTTKDADPWLVALALEMRSqptifgpikpIILTEEVL----KGNRVKIPYVAKHY 149
                                       66666666.34456666654.455699**********9776566677777789999999....6668********** PP

                           DUF4411 145 gikcidlfellrelgltf 162
                                       +ikc+++f+++r++g++f
  gi|488601037|ref|YP_007907508.1| 150 RIKCVKIFDMFRQEGWKF 167
                                       ****************98 PP

>> Aspzincin_M35  Lysine-specific metallo-endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   2.2e-06     0.019       2      45 ..      58     100 ..      57     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-06
                     Aspzincin_M35   2 aaaaksdtarfktwFgttdqstrskvaavfskiakeckslnsgs 45 
                                       +++ak++++ +  +F++++ +++++va+++sk+++   ++n g+
  gi|488601037|ref|YP_007907508.1|  58 KEWAKEQKNEYPDFFKKYTPDQQKYVADILSKFESFV-KINDGT 100
                                       67899****************************9964.344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1332.11
//
Query:       gi|488601038|ref|YP_007907509.1|  [L=189]
Description: hypothetical protein Asulf_01538 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-17   64.0   0.5    2.5e-17   63.0   0.0    1.7  2  bPH_3         Bacterial PH domain
    3.7e-10   39.2   8.3    9.1e-10   38.0   8.3    1.7  1  SHOCT         Short C-terminal domain
     0.0065   17.3   5.6      0.012   16.4   5.6    1.5  1  DMAP_binding  DMAP1-binding Domain
  ------ inclusion threshold ------
      0.018   15.2   0.1      0.037   14.1   0.1    1.7  1  bPH_1         Bacterial PH domain
      0.018   15.0   1.6      0.033   14.2   1.6    1.4  1  GvpG          Gas vesicle protein G


Domain annotation for each model (and alignments):
>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0     7e-21   2.5e-17       1      94 [.      12     104 ..      12     105 .. 0.97
   2 ?   -1.4   0.1       0.9   3.2e+03      55      77 ..     116     138 ..     110     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 7e-21
                             bPH_3   1 LkkdEkilyltkgqinakldkpglivvTnkRiifldpkmfggkdfeeipYksIksvdlkkgllgakitlet.sgkti 76 
                                       L ++Eki y +k+     l+kp +++vT++R+i++d+k +g++d  ++pY++++ v+++kg +ga+++l    gk++
  gi|488601038|ref|YP_007907509.1|  12 LYPGEKIVYSVKKLKS--LEKPMYLIVTDRRVIYFDQKLLGRYDLVDFPYEKLELVSYTKGKIGAEFSLVReDGKKV 86 
                                       7899*********999..9****************************************************99**** PP

                             bPH_3  77 tidnidksevrkiveair 94 
                                        i +++k+e ++++ air
  gi|488601038|ref|YP_007907509.1|  87 IIPWMEKDESQQAIIAIR 104
                                       ************999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.9
                             bPH_3  55 svdlkkgllgakitletsgktit 77 
                                       s+d kkgl++   tl+ +++ it
  gi|488601038|ref|YP_007907509.1| 116 SIDKKKGLMKESWTLKKPKEVIT 138
                                       56667788887777777665544 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   8.3   2.5e-13   9.1e-10       1      28 []     159     186 ..     159     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.5e-13
                             SHOCT   1 daLekLkeLyarGeIteEEFeakKakLL 28 
                                       ++L+kLkeLy++G++teEE+e+k+++LL
  gi|488601038|ref|YP_007907509.1| 159 EKLKKLKELYDMGLLTEEEYETKRKELL 186
                                       68*************************8 PP

>> DMAP_binding  DMAP1-binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   5.6   3.5e-06     0.012      11      40 ..     159     188 ..     152     189 .] 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                      DMAP_binding  11 erLaeLeldlseGdiTeKgyekkklkLLre 40 
                                       e+L++L + ++ G +Te++ye+k+++LL++
  gi|488601038|ref|YP_007907509.1| 159 EKLKKLKELYDMGLLTEEEYETKRKELLEK 188
                                       69**************************86 PP

>> bPH_1  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     1e-05     0.037      17      85 ..       3      73 ..       1     111 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                                      CCHHHHGCGCGCT--EEEEEE-TS.....EEEEEESSEEEEEE---SSS--EEEEEEETTTEEEEEEEEESTTS CS
                             bPH_1 17 klekelgellidgEkilfafklir.....DevvFTnkrlilvdkqgvtgkKkeyksipyssIsevsiEtagtfD 85
                                      +l+++++e l +gEki+   k  +      +++ T++r+i +d q + g++ ++  +py++++ vs  t g + 
  gi|488601038|ref|YP_007907509.1|  3 DLPEQVSENLYPGEKIVYSVKKLKslekpMYLIVTDRRVIYFD-QKLLGRY-DLVDFPYEKLELVSY-TKGKIG 73
                                      578999999*******9998877633333589***********.7899977.56779***9998886.556554 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.6   9.1e-06     0.033      27      65 ..     151     189 .]     142     189 .] 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.1e-06
                              GvpG  27 lddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrL 65 
                                        + +e+   +L +L+   d+G  +eee++ +  elL++L
  gi|488601038|ref|YP_007907509.1| 151 KEVKEDPIEKLKKLKELYDMGLLTEEEYETKRKELLEKL 189
                                       45555556789999999*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1103.40
//
Query:       gi|488601039|ref|YP_007907510.1|  [L=988]
Description: phage tail tape measure protein, TP901 family, core region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  136.7  40.7      9e-40  136.6  10.4    6.4  7  PhageMin_Tail  Phage-related minor tail protein
      0.004   15.4  64.7       0.17   10.1   0.0    5.8  6  EzrA           Septation ring formation regulator, EzrA
     0.0042   17.1  74.0      0.024   14.7  24.1    5.0  4  TPR_MLP1_2     TPR/MLP1/MLP2-like protein
     0.0081   16.6  64.8       0.74   10.2  25.7    4.2  4  Fez1           Fez1
  ------ inclusion threshold ------
       0.18   11.3  51.3      0.023   14.3  16.5    4.0  3  MscS_porin     Mechanosensitive ion channel porin domain
       0.22   11.6   5.2        0.2   11.7   1.2    2.9  3  DUF413         Protein of unknown function, DUF
       0.27   11.7   0.0       0.27   11.7   0.0    7.7  7  NPV_P10        Nucleopolyhedrovirus P10 protein
       0.59    9.0  72.3       0.73    8.7  19.7    4.7  4  Spc7           Spc7 kinetochore protein
        1.2    8.9  51.6        2.2    8.0  30.6    4.7  5  SH3BP5         SH3 domain-binding protein 5 (SH3BP5)
        4.6    5.8  53.9       0.79    8.3  29.4    3.7  3  AAA_13         AAA domain
        5.1    6.5   5.7        4.3    6.8   0.3    2.9  2  DUF1129        Protein of unknown function (DUF1129)
        5.6    7.2   5.6        7.5    6.8   0.0    3.7  4  PI_PP_I        Phosphoinositide phosphatase insertion domain
          6    6.2  88.1        1.2    8.4   0.2    5.0  4  Tropomyosin    Tropomyosin
        6.8    4.5  33.0       0.94    7.3  18.3    3.2  4  Prominin       Prominin


Domain annotation for each model (and alignments):
>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.7     0.021        27      89     145 ..      28      85 ..      12      96 .. 0.53
   2 !  136.6  10.4   7.1e-43     9e-40       4     180 ..      99     277 ..      96     290 .. 0.96
   3 ?   -2.3   0.0       2.7   3.4e+03      88     111 ..     352     375 ..     302     412 .. 0.58
   4 ?    1.5   0.1      0.18   2.3e+02     100     128 ..     443     471 ..     434     563 .. 0.75
   5 !    5.7   1.1    0.0095        12     129     188 ..     603     675 ..     588     683 .. 0.74
   6 ?    4.8   1.1     0.017        22     132     189 ..     753     810 ..     743     820 .. 0.79
   7 ?   -0.6   0.0      0.79     1e+03     124     189 ..     822     925 ..     819     932 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.021
                     PhageMin_Tail  89 gatsvedlaealkevgavakaaGlsfeetaaalallaaag.ikgseAgtalknllsrl 145
                                       +++ v+d+++ l+ vg   + aG ++  + a +al       +g+e  +a+kn+ s +
  gi|488601039|ref|YP_007907510.1|  28 AKSQVKDFGKRLQDVGKDLAVAGAKMGAAIAPVALALGHAvRTGAEFEQAMKNVQSVM 85 
                                       4455555565555555555555555555555555555533355555555555544333 PP

  == domain 2  score: 136.6 bits;  conditional E-value: 7.1e-43
                     PhageMin_Tail   4 akelgektkysatelaealeelasaGvsteeilnllegaaklataggaddleeaaeilstalnafglsaadaeeaaD 80 
                                       ak+lge+t +sa+++ae+l+ lasaG++ +e+++++e ++++a+a++ +dl++a+e ++++lnaf ++a++a ++a+
  gi|488601039|ref|YP_007907510.1|  99 AKRLGETTVFSASQAAEGLYFLASAGYKVDEAISAMEPILQFAAATQ-SDLASATELVVSTLNAFEMDASEASRVAN 174
                                       99*********************************************.55******************99******* PP

                     PhageMin_Tail  81 vlaaaanngatsvedlaealkevgavakaaGlsfeetaaalallaaagikgseAgtalknllsrl...tkeaaealk 154
                                       v+aaa +n++ ++e la a++++++ ak++G+s+eet+a+++ll ++gi ++ Ag  l++ l +l   t++a+e l+
  gi|488601039|ref|YP_007907510.1| 175 VFAAAISNSQLTMERLAVAMPYISGLAKSLGISLEETTATIGLLVSSGIRAESAGRLLASSLGSLmnpTDKAQEVLE 251
                                       ***************************************************************************** PP

                     PhageMin_Tail 155 klGistkdaqgkmksldeiledlsea 180
                                       k+G++ +d++ km sl e  + l+e+
  gi|488601039|ref|YP_007907510.1| 252 KYGLTLDDVNPKMHSLAELVDILKEK 277
                                       ******************99999995 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.7
                     PhageMin_Tail  88 ngatsvedlaealkevgavakaaG 111
                                       + +++++ l  a+k ++++ k + 
  gi|488601039|ref|YP_007907510.1| 352 ELKNDLTRLVRAFKDALPTIKEFA 375
                                       233333444444444444444444 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.18
                     PhageMin_Tail 100 lkevgavakaaGlsfeetaaalallaaag 128
                                        + +g+ a+  G+sf  ++a+ al +a +
  gi|488601039|ref|YP_007907510.1| 443 VSFAGSLAGLTGISFSTATALTALRTALT 471
                                       45566666666666666666666666644 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0095
                     PhageMin_Tail 129 ikgseAgtalknllsrl..........tkeaaealkkl...Gistkdaqgkmksldeiledlsealkkltdaq 188
                                       ++ ++A++ +k++  +l          tk+ +ea ++l    +++k+aq   k++++ led +e+l k ++++
  gi|488601039|ref|YP_007907510.1| 603 LELEQATNKVKEAEEELaeakerllnyTKDLQEAEEDLlktRLDFKSAQLSVKDAEDDLEDAKERLRKAQEKA 675
                                       5667888888888888877766668887755555555555599999999999999999999999888884443 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.017
                     PhageMin_Tail 132 seAgtalknllsrltkeaaealkklGistkdaqgkmksldeiledlsealkkltda.qr 189
                                       s+A    k +l++l  e +e ++kl ++++  q k   ++e l+++++++k+l+d+ + 
  gi|488601039|ref|YP_007907510.1| 753 SKALEEQKRILREL-SELEENMEKLKLEVEVEQEKYDRAEELLNKVKNKVKELEDQtAD 810
                                       55666667788888.8999*******9997788888*****************999433 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 0.79
                     PhageMin_Tail 124 laaag.ikgseAgtalknllsrltkeaaealkklGist....................................... 160
                                       +a+++ +++ +  +++ +++s+l    +e+ ++lGi                                         
  gi|488601039|ref|YP_007907510.1| 822 MAETTeKSSKRMVDSIDTVISKL----EELEEELGIYSktsfgsspsrkyienarptqttpppakakpeepsqprkp 894
                                       56655466667777777777777....77777777554456666667777777777777777777777777777777 PP

                     PhageMin_Tail 161 .kdaqgkmksldeiledlsealkkltda.qr 189
                                        +d++  +   + +++ + +++k l+++  r
  gi|488601039|ref|YP_007907510.1| 895 fYDVDRSIYAVKSAIQSVTSSVKALSNQiGR 925
                                       7777777777777777777777777666555 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00013      0.17     119     186 ..      13      80 ..       7      98 .. 0.94
   2 ?   -2.1   0.0      0.63   8.1e+02     454     487 ..     244     277 ..     237     283 .. 0.79
   3 ?   -1.5   0.0      0.42   5.3e+02     393     432 ..     305     344 ..     302     369 .. 0.88
   4 ?   -2.3  32.2      0.71   9.1e+02      84     262 ..     551     725 ..     532     731 .. 0.73
   5 !    6.1  29.9    0.0021       2.7      49     208 ..     690     846 ..     688     858 .. 0.70
   6 ?   -1.1   0.0       0.3   3.9e+02      97     152 ..     896     951 ..     891     957 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                                       HHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH------------- CS
                              EzrA 119 kileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeelten 186
                                       ki+++l++l es ek ++++++  ++ +++ k+l    ++ g a++++ + l +  +  +efe++++n
  gi|488601039|ref|YP_007907510.1|  13 KIKADLAQLEESLEKAKSQVKDFGKRLQDVGKDLAVAGAKMGAAIAPVALALGHAVRTGAEFEQAMKN 80 
                                       7999**************************************************************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.63
                                       HHHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHH CS
                              EzrA 454 eelakeLekkpinikevnkrldeardlveklyek 487
                                       ++ ++ Lek  +++++vn +++   +lv+ l+ek
  gi|488601039|ref|YP_007907510.1| 244 DKAQEVLEKYGLTLDDVNPKMHSLAELVDILKEK 277
                                       5667788888888888888888888888888776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS CS
                              EzrA 393 ekqeeileslkslrkdEkrAreqldeikkelkeikrkiek 432
                                       ek  e+++s+++  k  + A  qld ++  ++ +k+++e 
  gi|488601039|ref|YP_007907510.1| 305 EKIREMEQSITGTSKATEMAAIQLDSFQGLIRLVKSELEG 344
                                       6778999999999999999999999999999999999885 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.71
                                       -GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHH CS
                              EzrA  84 lfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsyg 160
                                       + +++ + +  ++ ++++++ae e el+++++++ + + el+e+++  +k++ e e++ +k +e +++l + ++ + 
  gi|488601039|ref|YP_007907510.1| 551 VLNIDTASKASEIEEYNQRIAESERELADAKQRLIEKQRELDEVMDEYHKKQLELEQATNKVKEAEEELAEAKERLL 627
                                       45566777777777888888888888888888888888888888888888888888888888888888888888888 PP

                                       HHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHH CS
                              EzrA 161 ealeelekqleniekefsefeeltengdyveakeilkkleeeideleevieeiPelleelkkelpkqleelkegyke 237
                                       + ++ l++  e++ k   +f+ +  +   ++a++ l++++e++ + +e+ +   e + + + e+ k l+e+++  + 
  gi|488601039|ref|YP_007907510.1| 628 NYTKDLQEAEEDLLKTRLDFKSA--QLSVKDAEDDLEDAKERLRKAQEKARVALERYGRNSREYAKALKEVEKAERN 702
                                       88777777777777777777765..4457778888888888888888888888888888888888888888888888 PP

                                       STTS--SGGGSSSSSHHHHHHHHHH CS
                              EzrA 238 mkeegYaleelniekeieelekkie 262
                                        ++++  le+  +  ++++le++i 
  gi|488601039|ref|YP_007907510.1| 703 VEKAEIRLERARL--RVKDLEEAIT 725
                                       8888877777555..5566666555 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.0021
                                       SS-S---TTTHHHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHT..THHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA  49 vkklnltgeseekfeewkkkwdeiktkklpeieellfeaeelldkykfkka..kkklaeleeeldeveekikkilee 123
                                       +k+l+ +++ e ++e+ + + +  +  +++++ee ++e e+ + k +  k   ++++++++++ +++ e+ k+il e
  gi|488601039|ref|YP_007907510.1| 690 AKALKEVEKAERNVEKAEIRLERARL-RVKDLEEAITEKEKEVIKVRNSKEerTRAVEKAQKKYSKALEEQKRILRE 765
                                       46677777777777777777777776.77888888888887777766655411456778888888888888888888 PP

                                       HTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH----------------HHHHHHHHHHH CS
                              EzrA 124 lkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeeltengdyveakeilkkle 200
                                       l+el e+ ek + e+e  +ekY++ ++ l++ +++ +e +++  +   +i+++f+++ e+te++     k+++++++
  gi|488601039|ref|YP_007907510.1| 766 LSELEENMEKLKLEVEVEQEKYDRAEELLNKVKNKVKELEDQTADSSGKIKDKFDDMAETTEKSS----KRMVDSID 838
                                       88888888888888888888888888888888888888888888888888888888888887754....45555555 PP

                                       HHHHHHHH CS
                              EzrA 201 eeidelee 208
                                       + i++lee
  gi|488601039|ref|YP_007907510.1| 839 TVISKLEE 846
                                       55555554 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 0.3
                                       HHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT- CS
                              EzrA  97 kkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkl 152
                                        ++ +++ ++++ +++v +++k++ +++  +++     +  ++ +    ++++k++
  gi|488601039|ref|YP_007907510.1| 896 YDVDRSIYAVKSAIQSVTSSVKALSNQIGRIQSVTAAPSVTVTPVIPVHETVQKSV 951
                                       55667777788888888888888888888888888877777777777777777776 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.092   1.2e+02      72      88 ..      17      33 ..      11      52 .. 0.46
   2 ?    5.3  21.9     0.015        19       5      89 ..     558     642 ..     555     651 .. 0.93
   3 !    7.5  17.1    0.0032       4.1      11      97 ..     648     734 ..     642     741 .. 0.81
   4 !   14.7  24.1   1.9e-05     0.024       5     117 ..     712     824 ..     709     827 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.092
                        TPR_MLP1_2 72 eiaelkaeaesakaele 88
                                      ++a+l++++e+ak++++
  gi|488601039|ref|YP_007907510.1| 17 DLAQLEESLEKAKSQVK 33
                                      33333333333333222 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                       s  +ei++++++++e+e++l+ +++ l ++++++ e  + Y++  ++ ++++++++++ eel+e+k+++ + +++++
  gi|488601039|ref|YP_007907510.1| 558 SKASEIEEYNQRIAESERELADAKQRLIEKQRELDEVMDEYHKKQLELEQATNKVKEAEEELAEAKERLLNYTKDLQ 634
                                       56789************************************************************************ PP

                        TPR_MLP1_2  82 sakaelee 89 
                                       +a+++l +
  gi|488601039|ref|YP_007907510.1| 635 EAEEDLLK 642
                                       ***99876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0032
                        TPR_MLP1_2  11 kslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakael 87 
                                       ks++ + ++ae++l+ ++e l+k +e a+ a ++Y r   + a+++ke++++   +++++ +++ ++ +++++++++
  gi|488601039|ref|YP_007907510.1| 648 KSAQLSVKDAEDDLEDAKERLRKAQEKARVALERYGRNSREYAKALKEVEKAERNVEKAEIRLERARLRVKDLEEAI 724
                                       66777888899999999999999999999999999999999999999999999999999999999999999999888 PP

                        TPR_MLP1_2  88 eeseesweeq 97 
                                        e+e++  + 
  gi|488601039|ref|YP_007907510.1| 725 TEKEKEVIKV 734
                                       8888876554 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 1.9e-05
                        TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                       +++  +k+l+e ++e e+++ k+++  e+ ++ +++aq+kY++ l +++  ++el++l e +++lk e++  +++ +
  gi|488601039|ref|YP_007907510.1| 712 RARLRVKDLEEAITEKEKEVIKVRNSKEERTRAVEKAQKKYSKALEEQKRILRELSELEENMEKLKLEVEVEQEKYD 788
                                       56667899********************************************************************* PP

                        TPR_MLP1_2  82 sakaeleeseesweeqkeelekelselekriedlne 117
                                       +a++ l++ +++ +e +++  +   +++ + +d+ e
  gi|488601039|ref|YP_007907510.1| 789 RAEELLNKVKNKVKELEDQTADSSGKIKDKFDDMAE 824
                                       ******************************999875 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.093   1.2e+02      33     101 ..      11      97 ..       6     191 .. 0.74
   2 ?   -2.6   0.0       4.9   6.2e+03      82     108 ..     300     326 ..     241     376 .. 0.51
   3 !    8.6  28.4    0.0019       2.4      19     145 ..     537     680 ..     535     716 .. 0.64
   4 !   10.2  25.7   0.00058      0.74      19     144 ..     717     851 ..     705     858 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.093
                              Fez1  33 ivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk..................kseaellrekvek 91 
                                       ++++ka+l +l+++le+  +++k++ ++l++  ++l v  +++  +                  ++  ++++  +++
  gi|488601039|ref|YP_007907510.1|  11 VIKIKADLAQLEESLEKAKSQVKDFGKRLQDVGKDLAVAGAKMGAAiapvalalghavrtgaefEQAMKNVQSVMGA 87 
                                       67899999999999999999999999999999999888888777775555555555555554444444444444455 PP

                              Fez1  92 leeelkelre 101
                                        ee++k+l e
  gi|488601039|ref|YP_007907510.1|  88 SEEDFKRLTE 97 
                                       5555554444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.9
                              Fez1  82 aellrekvekleeelkelreelselsl 108
                                         +  ek++++e+ ++++ ++ ++++ 
  gi|488601039|ref|YP_007907510.1| 300 IPMGGEKIREMEQSITGTSKATEMAAI 326
                                       445555566666666555554443333 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0019
                              Fez1  19 Lkdsqaevtqklseival....k.aqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekve 90 
                                       L d+   v ++l+e++++    k +++ e ++++ e+e+e+ +++++l ek++el+++ +e ++k+ e e   +kv+
  gi|488601039|ref|YP_007907510.1| 537 LNDTLGSVGERLKEVLNIdtasKaSEIEEYNQRIAESERELADAKQRLIEKQRELDEVMDEYHKKQLELEQATNKVK 613
                                       667777788888888877222222467799999******************************************** PP

                              Fez1  91 kleeelkelreelselsleeeeaa..........................lesdeakaqrqeaeeleelkreverlr 141
                                       ++eeel+e +e+l + +++ +ea+                          +               e+l++  e+ r
  gi|488601039|ref|YP_007907510.1| 614 EAEEELAEAKERLLNYTKDLQEAEedllktrldfksaqlsvkdaeddledA--------------KERLRKAQEKAR 676
                                       ***********9998777766666566665555444433333333332221..............222222222222 PP

                              Fez1 142 aeLk 145
                                        +L+
  gi|488601039|ref|YP_007907510.1| 677 VALE 680
                                       2222 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00058
                              Fez1  19 Lkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleee 95 
                                        kd    +t+k +e+++++++  e + ++e+ +++ +++ e+ +   +el ++e+++++ k e+e+ +ek +++ee 
  gi|488601039|ref|YP_007907510.1| 717 VKDLEEAITEKEKEVIKVRNSKEERTRAVEKAQKKYSKALEEQKRILRELSELEENMEKLKLEVEVEQEKYDRAEEL 793
                                       5899999*******************************99999999******************************* PP

                              Fez1  96 lkelreelselsleeeeaa.........lesdeakaqrqeaeeleelkreverlraeL 144
                                       l++++++++el+ ++++++         ++ ++ k  ++  +++++  +++e+l++eL
  gi|488601039|ref|YP_007907510.1| 794 LNKVKNKVKELEDQTADSSgkikdkfddMAETTEKSSKRMVDSIDTVISKLEELEEEL 851
                                       ******9999888877777667766666333333444445566666666666666666 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.012        15      79     136 ..      17      46 ..      12      82 .. 0.66
   2 ?   14.3  16.5   1.8e-05     0.023      77     168 ..     567     655 ..     546     658 .. 0.85
   3 ?   -2.3  24.5       2.1   2.7e+03      16     174 ..     655     808 ..     653     816 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                        MscS_porin  79 sleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrL 136
                                        l++Le  l++++sq+ +  ++l++  ++                            L
  gi|488601039|ref|YP_007907510.1|  17 DLAQLEESLEKAKSQVKDFGKRLQDVGKD----------------------------L 46 
                                       45555555555555555555555555444............................4 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                        MscS_porin  77 klsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrta 153
                                       ++ ++e e++l++++++l e q++l +  ++  + q  +e+a ++  ea ++l+e   rL +    +++l++a+ ++
  gi|488601039|ref|YP_007907510.1| 567 NQRIAESERELADAKQRLIEKQRELDEVMDEYHKKQLELEQATNKVKEAEEELAEAKERLLNY---TKDLQEAEEDL 640
                                       5567777999**********************************************9999666...469******** PP

                        MscS_porin 154 lqaelaaleaqieel 168
                                       l+++l + +aq++  
  gi|488601039|ref|YP_007907510.1| 641 LKTRLDFKSAQLSVK 655
                                       *****9999998765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.1
                        MscS_porin  16 kallqdLeqalnlLdkidk.skkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqts 91 
                                       k++ +dLe+a + L k+++  +  +e + ++ +++ k l+e+++   +    ++++ + + a+l  ++Le  +++ +
  gi|488601039|ref|YP_007907510.1| 655 KDAEDDLEDAKERLRKAQEkARVALERYGRNSREYAKALKEVEKAERNV---EKAEIRLERARLRVKDLEEAITEKE 728
                                       56779*********99976167799******************999999...9************************ PP

                        MscS_porin  92 sqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaage.alsqaqrtalqaelaaleaqiee 167
                                        ++ ++++   +    + ++q   ++a +++    ++l+e++ + +++    + +++ +q    +ae+ + + +++ 
  gi|488601039|ref|YP_007907510.1| 729 KEVIKVRNSKEERTRAVEKAQKKYSKALEEQKRILRELSELEENMEKL----KlEVEVEQEKYDRAEELLNKVKNKV 801
                                       *******************************************99888....3366667777778888887777777 PP

                        MscS_porin 168 leqells 174
                                        e+e ++
  gi|488601039|ref|YP_007907510.1| 802 KELEDQT 808
                                       7777555 PP

>> DUF413  Protein of unknown function, DUF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.4   1.7e+03      21      53 ..     245     272 ..     242     300 .. 0.65
   2 ?   11.7   1.2   0.00015       0.2      42      83 ..     722     763 ..     713     769 .. 0.90
   3 ?   -3.7   0.1       9.7   1.2e+04      23      61 ..     791     829 ..     789     833 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.4
                            DUF413  21 keaelLeqyGkalkaLeegelePeteeekqfve 53 
                                       k +e+Le+yG +l ++     +P+ ++ +++v+
  gi|488601039|ref|YP_007907510.1| 245 KAQEVLEKYGLTLDDV-----NPKMHSLAELVD 272
                                       5678899999887654.....444444445555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                            DUF413  42 ePeteeekqfvevvkgekaaetelekvWlkYlklirrkkrfh 83 
                                       e+ te+ek+ ++v +++++ + ++ek+  kY k+++++kr+ 
  gi|488601039|ref|YP_007907510.1| 722 EAITEKEKEVIKVRNSKEERTRAVEKAQKKYSKALEEQKRIL 763
                                       6789********************************999875 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9.7
                            DUF413  23 aelLeqyGkalkaLeegelePeteeekqfvevvkgekaa 61 
                                       +elL+++ + +k+Le+ +   + +  ++f +++++ ++ 
  gi|488601039|ref|YP_007907510.1| 791 EELLNKVKNKVKELEDQTADSSGKIKDKFDDMAETTEKS 829
                                       577888888889999888888888888887777766665 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   0.1     0.094   1.2e+02       5      37 ..      10      42 ..       8      51 .. 0.89
   2 ?   11.7   0.0   0.00021      0.27       9      65 ..     498     555 ..     492     565 .. 0.84
   3 ?   -0.4   1.3       1.3   1.7e+03      27      53 ..     609     635 ..     560     663 .. 0.63
   4 ?   -1.4   0.0       2.6   3.3e+03      26      60 ..     692     726 ..     690     734 .. 0.84
   5 ?   -1.2   0.3       2.2   2.9e+03      44      56 ..     756     768 ..     710     796 .. 0.57
   6 ?    2.8   2.7      0.13   1.7e+02      15      64 ..     796     840 ..     760     852 .. 0.60
   7 ?    3.9   0.1     0.057        73       9      64 ..     905     929 ..     897     943 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.094
                           NPV_P10  5 iLlvIradikavddkVdalqqqvddvqenlpdv 37
                                      i + I+ad +++++ ++  ++qv+d  + l+dv
  gi|488601039|ref|YP_007907510.1| 10 IVIKIKADLAQLEESLEKAKSQVKDFGKRLQDV 42
                                      78899999999*999999999999999999997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00021
                           NPV_P10   9 Iradik.avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                       Ir+ ++ av   Vd l++ vd +++ +p v  l++ +da++++L ++ + ++++ +i 
  gi|488601039|ref|YP_007907510.1| 498 IRDVVNsAVGWVVDRLSDLVDWMANTIPGVRTLTDFFDALNDTLGSVGERLKEVLNID 555
                                       6666643677789***********************************9998887775 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.3
                           NPV_P10  27 vddvqenlpdvtelnekLdaqsaqLae 53 
                                        ++v+e  +++ e +e+L + ++ L+e
  gi|488601039|ref|YP_007907510.1| 609 TNKVKEAEEELAEAKERLLNYTKDLQE 635
                                       333333333333333333333333333 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.6
                           NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       ++++v++  ++v++ + +L++    +++le+++++
  gi|488601039|ref|YP_007907510.1| 692 ALKEVEKAERNVEKAEIRLERARLRVKDLEEAITE 726
                                       57788888889999999999999999999998875 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 2.2
                           NPV_P10  44 LdaqsaqLaelet 56 
                                       L++q   L el++
  gi|488601039|ref|YP_007907510.1| 756 LEEQKRILRELSE 768
                                       3333333333332 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.13
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvt.elnekLdaqsaqLaelet.kvenIqdi 64 
                                       +v       +++v++++++  d + ++++k+d+++++ ++ ++  v++I+ +
  gi|488601039|ref|YP_007907510.1| 796 KV-------KNKVKELEDQTADSSgKIKDKFDDMAETTEKSSKrMVDSIDTV 840
                                       23.......3444444444443322455566666666554433255555555 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.057
                           NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                       ++++i+ v + V+al++q+                                 Iq++
  gi|488601039|ref|YP_007907510.1| 905 VKSAIQSVTSSVKALSNQI-------------------------------GRIQSV 929
                                       3445555555555555555...............................444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.028        35     198     283 ..      22     107 ..      10     123 .. 0.56
   2 ?    8.7  19.7   0.00057      0.73     165     261 ..     548     644 ..     527     652 .. 0.77
   3 ?    5.8  21.0    0.0041       5.3     145     250 ..     655     759 ..     645     766 .. 0.84
   4 ?    3.0  13.8      0.03        38     200     281 ..     765     847 ..     758     857 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.028
                              Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkee 274
                                       +e+Le++++++++  + ++   k+la   +++ +  + ++ +     ++ +e ++a + ++   g se++ +rl+e 
  gi|488601039|ref|YP_007907510.1|  22 EESLEKAKSQVKDFGKRLQDVGKDLAVAGAKMGAAIAPVALALGHAVRTGAEFEQAMKNVQSVMGASEEDFKRLTEF 98 
                                       24455555555555555555555555555555555555555555555666666666666666666666666666666 PP

                              Spc7 275 vkaleeltg 283
                                        k+l e+t 
  gi|488601039|ref|YP_007907510.1|  99 AKRLGETTV 107
                                       666666665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00057
                              Spc7 165 ldellp.eleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelk 240
                                       l+e+l+ ++ ++ +e+ee  +++ e ++el++  k++L e ++el+e++ e+++k+ el++ +++++e ee+++e+k
  gi|488601039|ref|YP_007907510.1| 548 LKEVLNiDTASKASEIEEYNQRIAESERELADA-KQRLIEKQRELDEVMDEYHKKQLELEQATNKVKEAEEELAEAK 623
                                       444443245566667777777777777777765.5556666778999999999999999999999999999999999 PP

                              Spc7 241 eqkseleeeiaeaervleeck 261
                                       e+  ++ ++++eae+ l +++
  gi|488601039|ref|YP_007907510.1| 624 ERLLNYTKDLQEAEEDLLKTR 644
                                       999999999999998877766 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0041
                              Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                       ++  ++le+ ke+L k +e++  +l+++ ++  e  + l++ ++a++++e+  + +Le +r ++++l++ i ek+ke
  gi|488601039|ref|YP_007907510.1| 655 KDAEDDLEDAKERLRKAQEKARVALERYGRNSREYAKALKEVEKAERNVEK-AEIRLERARLRVKDLEEAITEKEKE 730
                                       555678899999999999999999999999999999999999999988877.6788999999999999999999999 PP

                              Spc7 222 laelqeqleeleekieelkeqkseleeei 250
                                       + ++++ +ee + ++e++++++s++ ee 
  gi|488601039|ref|YP_007907510.1| 731 VIKVRNSKEERTRAVEKAQKKYSKALEEQ 759
                                       99999999999999999988877766654 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.03
                              Spc7 200 eLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaea.ervleeckgwsesevsrlkeev 275
                                       eL el e++++lk e+e  ++++++ +e l+++++k++el++q ++   +i+ + +++ e ++++s+  v+++ +  
  gi|488601039|ref|YP_007907510.1| 765 ELSELEENMEKLKLEVEVEQEKYDRAEELLNKVKNKVKELEDQTADSSGKIKDKfDDMAETTEKSSKRMVDSIDTVI 841
                                       78888888888888888888888888888888888888888888888888876524555555666666666666655 PP

                              Spc7 276 kaleel 281
                                       ++leel
  gi|488601039|ref|YP_007907510.1| 842 SKLEEL 847
                                       555543 PP

>> SH3BP5  SH3 domain-binding protein 5 (SH3BP5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.55   7.1e+02      22      57 ..      19      57 ..      13      60 .. 0.62
   2 ?   -3.9   0.1       7.8   9.9e+03     112     146 ..     139     173 ..     122     190 .. 0.64
   3 ?    7.3  11.7    0.0028       3.5      87     164 ..     573     648 ..     555     655 .. 0.77
   4 ?    8.0  30.6    0.0017       2.2      14     191 ..     605     780 ..     604     787 .. 0.57
   5 ?    5.7   2.2     0.009        12      68     122 ..     771     824 ..     766     851 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.55
                            SH3BP5 22 NklEveLeearak...frellaesseklkalakklgksv 57
                                       +lE +Le+a+++   f + l+++ ++l     k+g ++
  gi|488601039|ref|YP_007907510.1| 19 AQLEESLEKAKSQvkdFGKRLQDVGKDLAVAGAKMGAAI 57
                                      567777777776522244556666667776666666665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.8
                            SH3BP5 112 tldkawqemLnhatqkVneaeeekkeaeeehqrkt 146
                                       ++ +a q  L  at+ V+ + +  +  ++e  r++
  gi|488601039|ref|YP_007907510.1| 139 QFAAATQSDLASATELVVSTLNAFEMDASEASRVA 173
                                       56777788888888888776655444444444444 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0028
                            SH3BP5  87 ansahaaAketvalaeqslleeeertldkawqemLnhatqkVneaeeekkeaeeehqrktkkleeaekkvqqlekkl 163
                                       ++  +a Ak+++   +++l   e ++  ++ q  L++at kV+eaeee +ea+e   + tk+l+eae+++ + + ++
  gi|488601039|ref|YP_007907510.1| 573 SERELADAKQRLIEKQRELD--EVMDEYHKKQLELEQATNKVKEAEEELAEAKERLLNYTKDLQEAEEDLLKTRLDF 647
                                       44556777777777777777..555555666778*********************************9998877666 PP

                            SH3BP5 164 k 164
                                       k
  gi|488601039|ref|YP_007907510.1| 648 K 648
                                       6 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0017
                            SH3BP5  14 LNeatdeINklEveLeearak...frellaesseklkalakklg...ksvekarpYye.arekakeaqkeaqkaaek 83 
                                       L +at+++ ++E eL+ea+++   + + l+e++e+l +++   +    sv++a    e a+e+ ++aq++a+ a e+
  gi|488601039|ref|YP_007907510.1| 605 LEQATNKVKEAEEELAEAKERllnYTKDLQEAEEDLLKTRLDFKsaqLSVKDAEDDLEdAKERLRKAQEKARVALER 681
                                       67788888888888888887522255556666777766654333112467777765533788888888888888888 PP

                            SH3BP5  84 feransahaaAketvalaeqslleeeertldkawqemLnhatqkVneaeeekkeaeeehqrktkkleeaekkvqqle 160
                                       + r +  +a+A  +v++ae++++         +    L+ a  +V++ ee  +e e+e  ++ ++ ee ++ v++ +
  gi|488601039|ref|YP_007907510.1| 682 YGRNSREYAKALKEVEKAERNVE---------KAEIRLERARLRVKDLEEAITEKEKEVIKVRNSKEERTRAVEKAQ 749
                                       88888888888888888888887.........223344455555555555555555555554445555555555555 PP

                            SH3BP5 161 kklkrsikkskpYfelkaklnkqleeqkekv 191
                                       kk+ ++++  k+   + ++l++++e++k +v
  gi|488601039|ref|YP_007907510.1| 750 KKYSKALEEQKRILRELSELEENMEKLKLEV 780
                                       5555555554444444455555555554444 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.009
                            SH3BP5  68 ekakeaqkeaqkaaekferansahaaAketvalaeqslleeeertldkawqemLn 122
                                       e  ++++ e+    ek++ra++++++ k++v+ +e++++ +++ +++ ++ +m +
  gi|488601039|ref|YP_007907510.1| 771 ENMEKLKLEVEVEQEKYDRAEELLNKVKNKVKELEDQTA-DSSGKIKDKFDDMAE 824
                                       566677778888888888888888888888888888888.555555555555433 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.3   3.9e+02     441     472 ..      13      44 ..       6      84 .. 0.81
   2 ?    8.3  29.4   0.00062      0.79     287     461 ..     529     732 ..     522     738 .. 0.77
   3 ?   -0.1  18.7      0.21   2.8e+02     364     460 ..     721     815 ..     706     826 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.3
                            AAA_13 441 kleeeikeLekqlrdekpaaeeinkeLkafGl 472
                                       k++++ ++Le++l++ k  ++++ k L+++G+
  gi|488601039|ref|YP_007907510.1|  13 KIKADLAQLEESLEKAKSQVKDFGKRLQDVGK 44 
                                       66777777777777777777777777777764 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00062
                            AAA_13 287 rLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksve.lesvka 362
                                       +L +  + ++ +  ++ e+lk+v + +++    ++++ee+++++ + e +L  ++++l +K  e+ + ++ +++ + 
  gi|488601039|ref|YP_007907510.1| 529 TLTDFFDALNDTLGSVGERLKEVLNIDTA--SKASEIEEYNQRIAESERELADAKQRLIEKQRELDEVMDeYHKKQL 603
                                       56666666666666677778888877765..4577899999999999999999999999999999998876899999 PP

                            AAA_13 363 kiesikklvaeineliakhNekvanleeekeeakkklelhlv...........................eeleseld 412
                                       ++e+++++v+e++e  a+  e+  n++++ +ea+++l + ++                           e+++ +l+
  gi|488601039|ref|YP_007907510.1| 604 ELEQATNKVKEAEEELAEAKERLLNYTKDLQEAEEDLLKTRLdfksaqlsvkdaeddledakerlrkaqEKARVALE 680
                                       99999999999999999999999999999999999999988888888888877777777777666666655555555 PP

                            AAA_13 413 eyk...kkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaae 461
                                       +y    ++y+k+ k++ek+e++++++e +l+ ++ ++k+Le+ ++++++ + 
  gi|488601039|ref|YP_007907510.1| 681 RYGrnsREYAKALKEVEKAERNVEKAEIRLERARLRVKDLEEAITEKEKEVI 732
                                       5544556777777778888888888888888888888888888887777665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.21
                            AAA_13 364 iesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelk 440
                                        e+i+++ +e+ ++ ++  e++  +e+++++  k+le    +++  el+e++++++kl+ ++e  +++ + +e+ l+
  gi|488601039|ref|YP_007907510.1| 721 EEAITEKEKEVIKVRNSKEERTRAVEKAQKKYSKALEE--QKRILRELSELEENMEKLKLEVEVEQEKYDRAEELLN 795
                                       23444444444444455556777777777777777776..688899999**************************** PP

                            AAA_13 441 kleeeikeLekqlrdekpaa 460
                                       k+++++keLe q+ d    +
  gi|488601039|ref|YP_007907510.1| 796 KVKNKVKELEDQTADSSGKI 815
                                       ************99977655 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3    0.0034       4.3      17      74 ..     647     705 ..     640     717 .. 0.80
   2 ?    0.5   1.0      0.28   3.6e+02      27      74 ..     769     816 ..     745     843 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0034
                           DUF1129  17 LkkkglsdeekeeileevlpelleaQkkGktArqLyg.tptekaeellekkkkakkesk 74 
                                       +k+++ls +++e+ le+  ++l +aQ+k ++A + yg   +e+a++l+e +k++ + +k
  gi|488601039|ref|YP_007907510.1| 647 FKSAQLSVKDAEDDLEDAKERLRKAQEKARVALERYGrNSREYAKALKEVEKAERNVEK 705
                                       48899999*****************************6667777777766666665555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.28
                           DUF1129  27 keeileevlpelleaQkkGktArqLygtptekaeellekkkkakkesk 74 
                                        ee +e++  e+  +Q+k   A++L++ +++k++el ++ ++ + + k
  gi|488601039|ref|YP_007907510.1| 769 LEENMEKLKLEVEVEQEKYDRAEELLNKVKNKVKELEDQTADSSGKIK 816
                                       4555566666777899999*****************999988776666 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.5     7e+03      28      57 ..      13      42 ..       9      46 .. 0.68
   2 ?    6.8   0.0    0.0058       7.5      59      86 ..     391     418 ..     340     428 .. 0.77
   3 ?    0.1   0.3      0.73   9.3e+02       6      63 ..     589     618 ..     561     659 .. 0.55
   4 ?   -1.1   0.2       1.7   2.2e+03      12      84 ..     749     768 ..     691     809 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.5
                                      HHHHHHHHHHHHHHHHHHH-SSHHHHHHHH CS
                           PI_PP_I 28 klkqdlnqfllkWeeikktslsLeedLnki 57
                                      k+k dl q+  + e+ k++  ++ + L+++
  gi|488601039|ref|YP_007907510.1| 13 KIKADLAQLEESLEKAKSQVKDFGKRLQDV 42
                                      677777777777777777777776666665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0058
                                       CT-SS--HHHHTS-HHHHHHHHHHT.T. CS
                           PI_PP_I  59 nnktplPsWfnelskaqqellrvlaeak 86 
                                       +  +++ +Wfn+l+++ ++ + vl+  +
  gi|488601039|ref|YP_007907510.1| 391 KAGKDFMQWFNSLNPHVKNAIAVLMGFT 418
                                       4556899***************998654 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.73
                                       HCS-HHHHHHHHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS CS
                           PI_PP_I   6 rkLeeyqqaYflnleskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannktp 63 
                                       r+L+e++ +Y  +                            +l+Le+  nk+++ ++ 
  gi|488601039|ref|YP_007907510.1| 589 RELDEVMDEYHKK----------------------------QLELEQATNKVKEAEEE 618
                                       4444444444443............................33333333333332222 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.7
                                       HHHHHHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-HHHHHHHHHHT. CS
                           PI_PP_I  12 qqaYflnleskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnelskaqqellrvlae 84 
                                       q+ Y   le ++                                                       lr l+e
  gi|488601039|ref|YP_007907510.1| 749 QKKYSKALEEQKRI-----------------------------------------------------LRELSE 768
                                       44444443333332.....................................................222222 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00094       1.2      20      99 ..      14      97 ..       6     171 .. 0.81
   2 ?   -0.7   0.0       0.6   7.7e+02      92     133 ..     305     346 ..     302     377 .. 0.61
   3 ?    5.0   8.9      0.01        13      16      85 ..     540     607 ..     527     614 .. 0.52
   4 ?    0.5  65.5      0.25   3.2e+02       2     234 ..     611     847 ..     610     851 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00094
                       Tropomyosin 20 akkkleeaekkaekaeaEvaalnrriqlleeelerteerleeale....kLeeaekaadeserarKvlEnrelkdeekl 94
                                      +k+ l++ e+  eka++ v  + +r+q + ++l  +  ++  a +     L +a ++  e e+a+K + +   ++ee  
  gi|488601039|ref|YP_007907510.1| 14 IKADLAQLEESLEKAKSQVKDFGKRLQDVGKDLAVAGAKMGAAIApvalALGHAVRTGAEFEQAMKNVQSVMGASEEDF 92
                                      6677888888888888888888888888888888888887777662222355556666677888888877777777777 PP

                       Tropomyosin 95 eelea 99
                                      ++l +
  gi|488601039|ref|YP_007907510.1| 93 KRLTE 97
                                      76655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.6
                       Tropomyosin  92 ekleeleaqlkeakeiaeeadrkyeEvarklvvvesdLerae 133
                                       ek++e+e++++   + +e a+ +++  +  + +v+s+Le +e
  gi|488601039|ref|YP_007907510.1| 305 EKIREMEQSITGTSKATEMAAIQLDSFQGLIRLVKSELEGIE 346
                                       667777777777777777777777777777777777776655 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.01
                       Tropomyosin  16 rlekakkkleea.ekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaadeserarKvlEn 85 
                                        l ++ ++l+e  +   ++  +E +  n+ri   e el  +++rl e++++L+e+    de ++    lE+
  gi|488601039|ref|YP_007907510.1| 540 TLGSVGERLKEVlNIDTASKASEIEEYNQRIAESERELADAKQRLIEKQRELDEVM---DEYHKKQLELEQ 607
                                       55555555555412334455566666677777777777777776666666655543...333333333333 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.25
                       Tropomyosin   2 klkqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealek....Leeaekaad 74 
                                       k+k++eeel ea+erl + +k l+eae+   k+  +  + + +++  e++le ++erl +a+ek    Le   +++ 
  gi|488601039|ref|YP_007907510.1| 611 KVKEAEEELAEAKERLLNYTKDLQEAEEDLLKTRLDFKSAQLSVKDAEDDLEDAKERLRKAQEKarvaLERYGRNSR 687
                                       899***********************************************************995555677778888 PP

                       Tropomyosin  75 eserarKvlEnrelkdeekleeleaqlkeakeiaeeadrkyeEvar...klvvvesdLeraeeraeaaeskiveLee 148
                                       e  +a+K +E+ e++ e    +le++    k ++e   +k +Ev +        ++ +e+a+++  +a ++ + +  
  gi|488601039|ref|YP_007907510.1| 688 EYAKALKEVEKAERNVEKAEIRLERARLRVKDLEEAITEKEKEVIKvrnSKEERTRAVEKAQKKYSKALEEQKRILR 764
                                       99999999999999998888888888888888888888888887531112233445667777777777777778889 PP

                       Tropomyosin 149 eLkvvgnnlksLevseekaseredeyeeeirtLeekLkeaeeRaeeAErsvqkLekevdrledeleaekek.ykais 224
                                       eL    +n+ +L+ + e   e+ d+ ee + ++++k ke e+   ++     k++ + d++ + +e+  ++  ++i+
  gi|488601039|ref|YP_007907510.1| 765 ELSELEENMEKLKLEVEVEQEKYDRAEELLNKVKNKVKELEDQTADSS---GKIKDKFDDMAETTEKSSKRmVDSID 838
                                       9**************************************998776654...45666777777766654433033333 PP

                       Tropomyosin 225 eeLdqtlaeL 234
                                         + + l+eL
  gi|488601039|ref|YP_007907510.1| 839 TVI-SKLEEL 847
                                       333.555555 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.74   9.4e+02     665     699 ..      10      44 ..       8      60 .. 0.71
   2 ?   -2.2   0.0      0.55   7.1e+02     326     380 ..     322     376 ..     297     434 .. 0.55
   3 ?   -0.8   6.7      0.21   2.6e+02     621     698 ..     551     634 ..     544     642 .. 0.67
   4 ?    7.3  18.3   0.00074      0.94     235     407 ..     690     857 ..     651     869 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.74
                          Prominin 665 lvlplessvkklkksvkkldeensdlqesikklla 699
                                       +v+++++ +++l++s++k +++ +d++++++++ +
  gi|488601039|ref|YP_007907510.1|  10 IVIKIKADLAQLEESLEKAKSQVKDFGKRLQDVGK 44 
                                       56677777777777777777777777777766655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.55
                          Prominin 326 aleevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklak 380
                                       ++  +  ++++ +++   ++l+ i+  v +++++ ++ l +a +++  +ik++a 
  gi|488601039|ref|YP_007907510.1| 322 EMAAIQLDSFQGLIRLVKSELEGIEIAVFDELKNDLTRLVRAFKDALPTIKEFAI 376
                                       3333444444444444444444444444444444444444444444444433333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.21
                          Prominin 621 ltkvnletlaekleelanelsngk...knlkqslkneaqdlraiqqelvlp...lessvkklkksvkkldeensdlq 691
                                       + +++  + a+++ee  +++ +++   +++kq+l +++++l+++ +e++++   le++++k+k+  ++l e ++ l 
  gi|488601039|ref|YP_007907510.1| 551 VLNIDTASKASEIEEYNQRIAESErelADAKQRLIEKQRELDEVMDEYHKKqleLEQATNKVKEAEEELAEAKERLL 627
                                       55566666777777777777777777778888888888888877766665533367777777777777777666666 PP

                          Prominin 692 esikkll 698
                                       + +k+l 
  gi|488601039|ref|YP_007907510.1| 628 NYTKDLQ 634
                                       5555554 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.00074
                          Prominin 235 lpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldts 311
                                        +aL+e+e+  +n+++a+  Le  +   k+L +  ++ ++ + +v+++ ++       ++  +k+++++++  l+ +
  gi|488601039|ref|YP_007907510.1| 690 AKALKEVEKAERNVEKAEIRLERARLRVKDLEEAITEKEKEVIKVRNSKEER------TRAVEKAQKKYSK-ALEEQ 759
                                       4455555555555555555555555555555555555555555555544443......3556677777776.45555 PP

                          Prominin 312 kcl.dqlpnvdevlealeevletnlssivkeglarlneipekvk...nqtaevvpdlkkalakgreqikklakkipr 384
                                       k + ++l++++e +e+l+  +e + +++  ++ + ln++++kvk   +qta+   ++k + ++  e+ +k +k++  
  gi|488601039|ref|YP_007907510.1| 760 KRIlRELSELEENMEKLKLEVEVE-QEKYDRAEELLNKVKNKVKeleDQTADSSGKIKDKFDDMAETTEKSSKRM-V 834
                                       555488888888888888655444.34455777777888877762226999999999999999999999999999.9 PP

                          Prominin 385 ealdavisdlenterssktfddv 407
                                       + +d+vis+le++e+++  ++++
  gi|488601039|ref|YP_007907510.1| 835 DSIDTVISKLEELEEELGIYSKT 857
                                       99999999999999988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (988 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3326  (0.18551); expected 358.6 (0.02)
Passed bias filter:                      785  (0.0437838); expected 358.6 (0.02)
Passed Vit filter:                       236  (0.013163); expected 17.9 (0.001)
Passed Fwd filter:                       132  (0.00736237); 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: 2.63u 0.44s 00:00:03.07 Elapsed: 00:00:00.78
# Mc/sec: 3811.53
//
Query:       gi|488601040|ref|YP_007907511.1|  [L=617]
Description: hypothetical protein Asulf_01540 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3980.53
//
Query:       gi|488601041|ref|YP_007907512.1|  [L=1104]
Description: hypothetical protein Asulf_01541 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-06   26.9   0.7       0.85    9.2   0.0    4.7  4  TcfC       E-set like domain
    1.3e-05   25.3   7.6       0.35   11.0   0.2    5.4  4  DUF5010_C  DUF5010 C-terminal domain


Domain annotation for each model (and alignments):
>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0     0.094   8.5e+02      41      51 ..     146     156 ..     143     156 .. 0.91
   2 !    6.0   0.0   0.00094       8.4      39      56 ..     227     244 ..     226     247 .. 0.90
   3 !    9.2   0.0   9.4e-05      0.85      40      61 ..     617     638 ..     612     643 .. 0.89
   4 !    5.4   0.0    0.0014        13      32      61 ..     803     832 ..     797     837 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.094
                              TcfC  41 LPsGiYeveir 51 
                                       LP G Y+v+++
  gi|488601041|ref|YP_007907512.1| 146 LPVGAYNVKLK 156
                                       9*******996 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.00094
                              TcfC  39 ssLPsGiYeveirvyeng 56 
                                       s+ P+G+Y++ +rv++++
  gi|488601041|ref|YP_007907512.1| 227 SDIPKGTYKIVLRVRDDN 244
                                       679************987 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 9.4e-05
                              TcfC  40 sLPsGiYeveirvyengqvvrt 61 
                                       +++ G+Y+v++r+ +++ v r+
  gi|488601041|ref|YP_007907512.1| 617 KFAGGTYQVDVRINSTNAVARD 638
                                       699*************999987 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0014
                              TcfC  32 GnqeidtssLPsGiYeveirvyengqvvrt 61 
                                       G+ +++  ++ +G+Yev+ ++ +++ v r+
  gi|488601041|ref|YP_007907512.1| 803 GILQLNSLKFGTGSYEVRAKITNSDPVGRE 832
                                       7777888899*************9988765 PP

>> DUF5010_C  DUF5010 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.1    0.0044        40      23      98 ..     214     293 ..     205     310 .. 0.71
   2 ?   -1.2   0.0      0.24   2.1e+03      38      74 ..     301     338 ..     284     364 .. 0.69
   3 !   11.0   0.2   3.9e-05      0.35      12      54 ..     593     637 ..     584     710 .. 0.77
   4 !    8.2   0.1    0.0003       2.7      53     107 ..     833     900 ..     784     904 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0044
                         DUF5010_C  23 eaGewlewk...eipfkaGavtlkvryattkeaakvrfvidgtagpsv..elpaTgglqewetvdagtlkieakgyh 94 
                                       ++Ge  +w      ++  G++++ +r+   + a  +++++ g    ++  e  +Tgg   ++t++  +++  ++   
  gi|488601041|ref|YP_007907512.1| 214 AQGEYAQWTvgiGSDIPKGTYKIVLRVRDDNVADDIKITVSGSVSGTIltETLSTGG-TSFVTLETSEFNALTEETL 289
                                       678888886322357788**********************88776665336678999.8999999888776555544 PP

                         DUF5010_C  95 tvkl 98 
                                       t+k+
  gi|488601041|ref|YP_007907512.1| 290 TIKV 293
                                       4444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.24
                         DUF5010_C  38 Gavtlkvryattkeaakvrfvidgt.agpsvelpaTgg 74 
                                         ++l  +y  ++  a++ f++d+     +v++ +T g
  gi|488601041|ref|YP_007907512.1| 301 NVIELDYCYIEPTYIARLAFDVDQEyDVGEVKVYDTMG 338
                                       55677888999999999999998761456777777766 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 3.9e-05
                         DUF5010_C  12 Dv.nggwnvt.steaGewlewkeipfkaGavtlkvryattkeaak 54 
                                       D+ ng+  ++ +te+ e l+ k++ f+ G++++ vr+ +t++ a+
  gi|488601041|ref|YP_007907512.1| 593 DTaNGELDAYsDTESTELLRLKSLKFAGGTYQVDVRINSTNAVAR 637
                                       5546666665269999*********************99876544 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0003
                         DUF5010_C  53 akvrfvi.............dgtagpsvelpaTgglqewetvdagtlkieakgyhtvkleive..Gnidl 107
                                       a + f i             d   g++v     gg  +w++++a+  +i+ + + ++k+++++  G+id+
  gi|488601041|ref|YP_007907512.1| 833 AGILFCIsdtnnmylaniylDSSIGKVVLWKRVGG--TWSQLAAAARTINLGEFYKLKVNFDSstGQIDV 900
                                       44445545555555555555999999999999***..************************852266665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.52
# Mc/sec: 6374.37
//
Query:       gi|488601042|ref|YP_007907513.1|  [L=166]
Description: hypothetical protein Asulf_01542 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1206.48
//
Query:       gi|488601043|ref|YP_007907514.1|  [L=285]
Description: hypothetical protein Asulf_01543 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00023   21.4   0.7       0.15   12.3   0.2    2.4  2  FliJ             Flagellar FliJ protein
  ------ inclusion threshold ------
      0.016   14.7   0.6       0.12   11.8   0.2    2.1  2  DUF4618          Domain of unknown function (DUF4618)
      0.019   14.6   0.1      0.046   13.4   0.1    1.7  1  Fungal_KA1       Fungal kinase associated-1 domain
      0.044   14.2   2.3        1.3    9.4   0.1    2.7  3  DUF3510          Domain of unknown function (DUF3510)
       0.16   12.7   2.7        2.3    8.9   0.1    2.8  3  Vir_act_alpha_C  Virulence activator alpha C-term
       0.19   12.0   0.0        1.1    9.6   0.0    2.0  2  WXG100           Proteins of 100 residues with WXG
       0.49   10.2   2.7          5    6.9   0.2    2.8  2  Dna2             DNA replication factor Dna2
       0.92    8.0   4.8        3.4    6.2   0.7    2.1  2  FapA             Flagellar Assembly Protein A
          1   10.0   5.6        2.4    8.8   0.6    2.9  2  Com_YlbF         Control of competence regulator ComK, YlbF/Y
        1.5    9.4   5.7        7.5    7.2   2.0    2.6  2  FeoB_Cyto        FeoB cytosolic helical domain
          3    7.6   7.4        2.4    7.9   0.1    2.5  3  KASH_CCD         Coiled-coil region of CCDC155 or KASH


Domain annotation for each model (and alignments):
>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0038       6.1      16      68 ..     132     184 ..     123     189 .. 0.83
   2 !   12.3   0.2     9e-05      0.15      13      55 ..     243     284 ..     233     285 .] 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0038
                              FliJ  16 qaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqel 68 
                                       ++ +k+ el q+++ey+++l+   + + +  +  ++ f + + e+  + +q++
  gi|488601043|ref|YP_007907514.1| 132 KHISKIRELSQEFDEYRNRLEVLLKEIVPVVFSEFRDFCEEIIEEYRKSEQSI 184
                                       67789***************999988888888888888888877777776665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9e-05
                              FliJ  13 elqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafis 55 
                                        +++  + +++le++++++ k++++e+ gl+a e+r+yq +is
  gi|488601043|ref|YP_007907514.1| 243 IKEELINTINKLEEEINNLFKEWRNEY-GLTALEMRQYQGYIS 284
                                       567888999******************.*************97 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.17   2.7e+02      78     103 ..     132     157 ..     105     180 .. 0.69
   2 ?   11.8   0.2   7.3e-05      0.12     175     224 ..     217     266 ..     211     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
                           DUF4618  78 keekklekLeqqleqlnakvqklqee 103
                                       k  +k+++L q+ ++  +++++l +e
  gi|488601043|ref|YP_007907514.1| 132 KHISKIRELSQEFDEYRNRLEVLLKE 157
                                       33344455555555555554444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.3e-05
                           DUF4618 175 katqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqae 224
                                       +++++ +l  +l+  +l+++i++f ++ eel + i++L++e+++L ++ +
  gi|488601043|ref|YP_007907514.1| 217 EKYRTKMLSWILQDPSLREKIDRFNKIKEELINTINKLEEEINNLFKEWR 266
                                       5677788888999999****************************988765 PP

>> Fungal_KA1  Fungal kinase associated-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.8e-05     0.046      26      56 ..     252     283 ..     215     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                        Fungal_KA1  26 kelrqelaklLreWkk.yGlkdvksdkesnti 56 
                                       ++l +e+++l++eW++ yGl+ ++  + +  i
  gi|488601043|ref|YP_007907514.1| 252 NKLEEEINNLFKEWRNeYGLTALEMRQYQGYI 283
                                       6899***********99******998877655 PP

>> DUF3510  Domain of unknown function (DUF3510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.7   4.3e+03      41      69 ..      39      67 ..      30      78 .. 0.55
   2 ?    9.4   0.1   0.00082       1.3      56      96 ..     148     188 ..     120     193 .. 0.76
   3 ?    3.7   0.1     0.046        75      67      97 ..     233     263 ..     210     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                           DUF3510 41 kplktfkkesekklseevleewlaevlee 69
                                      k +k f+ke ++++  e+ +++++ +l++
  gi|488601043|ref|YP_007907514.1| 39 KYVKLFEKERKRRVIGEIARSIFSPILTS 67
                                      55556655555556666666666666654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00082
                           DUF3510  56 eevleewlaevleevtsrYletisevlssvkkteesLkrlk 96 
                                        + le +l+e++  v+s++ + ++e++++ +k e+s+k  k
  gi|488601043|ref|YP_007907514.1| 148 RNRLEVLLKEIVPVVFSEFRDFCEEIIEEYRKSEQSIKIEK 188
                                       23367799****************************98655 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.046
                           DUF3510  67 leevtsrYletisevlssvkkteesLkrlkk 97 
                                       l+e ++r+ ++ +e++++++k ee +++l k
  gi|488601043|ref|YP_007907514.1| 233 LREKIDRFNKIKEELINTINKLEEEINNLFK 263
                                       567788999999*************998855 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.5     4e+03      21      36 ..     137     152 ..     126     159 .. 0.49
   2 ?    8.9   0.1    0.0014       2.3      20      53 ..     159     196 ..     151     202 .. 0.81
   3 ?    2.9   0.1      0.11   1.7e+02      13      52 ..     226     269 ..     223     284 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.5
                   Vir_act_alpha_C  21 ieeLerrreeheekLa 36 
                                       i+eL +  +e++ +L+
  gi|488601043|ref|YP_007907514.1| 137 IRELSQEFDEYRNRLE 152
                                       2333333333334444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                   Vir_act_alpha_C  20 lieeLerrreeheekLaeyeeieerl....eeargqyl 53 
                                       +   + ++r+ +ee ++ey+++e+++    +++ ++ l
  gi|488601043|ref|YP_007907514.1| 159 VPVVFSEFRDFCEEIIEEYRKSEQSIkiekDDDYYRLL 196
                                       5567899*******************998655766655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.11
                   Vir_act_alpha_C  13 avldpealieeLerrreeheekLaeyeeieerl....eeargqy 52 
                                       + l+ + l+e++ r+ +  ee ++++ ++ee++    +e r  y
  gi|488601043|ref|YP_007907514.1| 226 WILQDPSLREKIDRFNKIKEELINTINKLEEEInnlfKEWRNEY 269
                                       66778889999999999999999999999999877774444333 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.3   2.1e+03      15      30 ..     136     151 ..     125     158 .. 0.47
   2 ?    9.6   0.0   0.00066       1.1       9      42 ..     233     266 ..     229     273 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHH CS
                            WXG100  15 rfqkqaeeledelqrl 30 
                                       ++++ ++e  +  +rl
  gi|488601043|ref|YP_007907514.1| 136 KIRELSQEFDEYRNRL 151
                                       3333333333333332 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00066
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCT CS
                            WXG100   9 lrqaaarfqkqaeeledelqrlkaevdalqsgWs 42 
                                       lr+++ rf+k++eel + +++l+ e+++l   W+
  gi|488601043|ref|YP_007907514.1| 233 LREKIDRFNKIKEELINTINKLEEEINNLFKEWR 266
                                       8999*************************99997 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0031         5      77     146 ..      42     158 ..      37     193 .. 0.60
   2 ?   -0.6   0.2       0.6   9.7e+02     120     145 ..     235     260 ..     210     277 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0031
                              Dna2  77 kvsgesskamliGtilHelfqkalleee...............................................ld 106
                                       k ++++ k  +iG+i  ++f  +l++ +                                               ++
  gi|488601043|ref|YP_007907514.1|  42 KLFEKERKRRVIGEIARSIFSPILTSLSiskeylekgyfiilrqdkvrldllsspnyylkekvnihtqnrysgvyCS 118
                                       55566666666666666666666655442333444444444444445555555555555555555555555555577 PP

                              Dna2 107 kekleelldklleknleelyalglteeeakeeikekleei 146
                                       +e+l +  d++l+k+++++ +l ++ +e +++++  l+ei
  gi|488601043|ref|YP_007907514.1| 119 AEYLLSFSDEILDKHISKIRELSQEFDEYRNRLEVLLKEI 158
                                       7888888888888888888888888777777666555444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.6
                              Dna2 120 knleelyalglteeeakeeikeklee 145
                                       ++++++ +++++  ++ ++++e++++
  gi|488601043|ref|YP_007907514.1| 235 EKIDRFNKIKEELINTINKLEEEINN 260
                                       33333444444444444444444422 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.011        18     340     399 ..     131     189 ..     114     199 .. 0.79
   2 ?    6.2   0.7    0.0021       3.4     330     366 ..     228     264 ..     199     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                              FapA 340 keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleelee 399
                                       ++   +++el +e ++++++++ l k ++ + + se+++  ++++e++ k +++++  ++
  gi|488601043|ref|YP_007907514.1| 131 DKHISKIRELSQEFDEYRNRLEVLLK-EIVPVVFSEFRDFCEEIIEEYRKSEQSIKIEKD 189
                                       55666777888999999999999999.788889999999999999999999998876655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0021
                              FapA 330 ldepelkeklkeleeeleeleeeleklkkkikklpkl 366
                                       l+ p+l+ek++++++  eel + ++kl+++i+ l k+
  gi|488601043|ref|YP_007907514.1| 228 LQDPSLREKIDRFNKIKEELINTINKLEEEINNLFKE 264
                                       4559999999999999999999999999999888773 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4      0.17   2.8e+02      32      90 ..     128     152 ..     119     187 .. 0.63
   2 ?    8.8   0.6    0.0015       2.4      28      72 ..     227     264 ..     218     280 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHH CS
                          Com_YlbF  32 eelqklikefkklqkelqekqmkgeelkeeekkelqelkeeldknplvkeyleaeqeln 90 
                                       e l k i ++++l +e+ e +++                                   +
  gi|488601043|ref|YP_007907514.1| 128 EILDKHISKIRELSQEFDEYRNRL----------------------------------E 152
                                       555566666666666665554443..................................3 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                                       HHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHH CS
                          Com_YlbF  28 leedeelqklikefkklqkelqekqmkgeelkeeekkelqelkee 72 
                                       + +d+ l+++i++f+k+++el +       +++ e+ e+++l +e
  gi|488601043|ref|YP_007907514.1| 227 ILQDPSLREKIDRFNKIKEELINT------INKLEE-EINNLFKE 264
                                       679****************99773......333344.44444444 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3     0.058        95      37      88 ..     126     176 ..      82     179 .. 0.69
   2 ?    7.2   2.0    0.0046       7.5      32      68 ..     224     260 ..     147     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.058
                         FeoB_Cyto  37 gDeelleelkedpelraeveearkeleaelgedledvIvdarykfiegilre 88 
                                        De l +++++  el++e +e r++le  l +++  v+ ++  +f e+i++e
  gi|488601043|ref|YP_007907514.1| 126 SDEILDKHISKIRELSQEFDEYRNRLEVLL-KEIVPVVFSEFRDFCEEIIEE 176
                                       466666677776677777777777777654.345566666666777777665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0046
                         FeoB_Cyto  32 lklLegDeelleelkedpelraeveearkeleaelge 68 
                                       l  + +D++l+e++   +++++e+ +++++le+e+++
  gi|488601043|ref|YP_007907514.1| 224 LSWILQDPSLREKIDRFNKIKEELINTINKLEEEINN 260
                                       666779**********99***************9876 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0015       2.4     140     181 ..     117     158 ..     101     160 .. 0.91
   2 ?   -3.7   0.3       5.6   9.1e+03     166     181 ..     173     188 ..     170     189 .. 0.71
   3 ?    4.1   0.2     0.022        36     163     190 ..     233     260 ..     219     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                          KASH_CCD 140 heleellaekealleektkqieeLkltieEyssiieeLraek 181
                                       +++e ll+  +++l ++  +i eL +  +Ey+   e L +e+
  gi|488601043|ref|YP_007907514.1| 117 CSAEYLLSFSDEILDKHISKIRELSQEFDEYRNRLEVLLKEI 158
                                       678999999************************999988876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.6
                          KASH_CCD 166 tieEyssiieeLraek 181
                                       +ieEy++  + ++ ek
  gi|488601043|ref|YP_007907514.1| 173 IIEEYRKSEQSIKIEK 188
                                       5778888777777776 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.022
                          KASH_CCD 163 LkltieEyssiieeLraeksrLeeqlqq 190
                                       L+  i+ +++i eeL   +++Lee++++
  gi|488601043|ref|YP_007907514.1| 233 LREKIDRFNKIKEELINTINKLEEEINN 260
                                       4455555556666666666666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1629  (0.0908584); expected 358.6 (0.02)
Passed bias filter:                      918  (0.051202); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2002.64
//
Query:       gi|488601044|ref|YP_007907515.1|  [L=267]
Description: hypothetical protein Asulf_01544 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-12   46.2   1.9      7e-12   45.5   0.5    2.0  2  Phage_integrase  Phage integrase family
      0.003   18.0   0.6       0.61   10.6   0.1    2.6  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.049   13.6   2.6      0.078   12.9   0.8    2.3  2  Phage_integr_3   Archaeal phage integrase


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 ?   -0.7   0.0      0.18   1.1e+03      78     117 ..      17      57 ..       6      63 .. 0.65
   2 !   45.5   0.5   1.2e-15     7e-12       7     102 ..      90     191 ..      85     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                                       HHHHHHHHHH.CHCCTTTSBSSBETTSSB--HHHHHHHHHH CS
                   Phage_integrase  78 ellkellska.leeaeksellfaskrgkplsrqtvrkafkr 117
                                       + l++ l+ + ++ ++++ ++ +++ +k+   +tvrk + +
  gi|488601044|ref|YP_007907515.1|  17 SRLTRFLEACsYQIDDDRIIIYINELKKQFEPETVRKHITT 57 
                                       55566666665555666666666667777777777776655 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 1.2e-15
                                       HHHHHHHCCGC.....HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHH CS
                   Phage_integrase   7 everllaalee.....slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseeale 78 
                                        v++l++ +++     +l +r k+++ l+  +GlR+ E+ +L ++d+d++n++++v ++  K   er+  ++eea +
  gi|488601044|ref|YP_007907515.1|  90 HVRNLIHEIDQkvryePLRLRAKAAVLLATTSGLRAMEVYKLMIDDIDVRNRTVFVRAEIAKDYEERITFFNEEAKQ 166
                                       68889999998899999************************************************************ PP

                                       HHHHHHHHHCHCCTTTSBSSBET......T CS
                   Phage_integrase  79 llkellskaleeaeksellfask......r 102
                                       +l+++l+++     +s+ lf++        
  gi|488601044|ref|YP_007907515.1| 167 ALEDYLATN-----PSSNLFYNLrdafekI 191
                                       *********.....7777888774444432 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 !    8.6   0.1   0.00043       2.6      10      66 ..       3      53 ..       1      54 [. 0.81
   2 !   10.6   0.1    0.0001      0.61      13      38 ..      45      70 ..      43      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00043
                   Phage_int_SAM_4 10 rlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqkn 66
                                      rl+++se+ i+  +s ++rfl+ +      +++++ i+ Y+n L   ++  + t++ 
  gi|488601044|ref|YP_007907515.1|  3 RLSNISEEEINKNMSRLTRFLEACS----YQIDDDRIIIYINELK--KQFEPETVRK 53
                                      6677777777777888888888888....**************99..7778999876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                   Phage_int_SAM_4 13 glserTiksYlsaikrflrflkkkap 38
                                      ++ ++T++ ++++ikrfl+f++  ++
  gi|488601044|ref|YP_007907515.1| 45 QFEPETVRKHITTIKRFLKFINYPSV 70
                                      6789*****************94444 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.39   2.3e+03      96     115 ..      38      57 ..      16      63 .. 0.65
   2 ?   12.9   0.8   1.3e-05     0.078      23     146 ..     111     234 ..      92     259 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.39
                                       HHHHHT-T--GHHHHHHHHH CS
                    Phage_integr_3  96 kefeakkkvkakyiRkwvat 115
                                         +e kk+++ +++Rk+++t
  gi|488601044|ref|YP_007907515.1|  38 YINELKKQFEPETVRKHITT 57 
                                       34455666888888887765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHH---HHHHHHHHHS...GGG-..EEETTEEE.EE..EE.E-SSS-EEEEEEESS---....--B--H CS
                    Phage_integr_3  23 velvykllvfsGiRLkevlklLre.yDpekl..iveddiar.Yp..ia.lekgeKkafyiylptelakelerlelse 92 
                                       ++   +l+  sG+R  ev kl+ +  D  +    v  +ia+ Y+  i+  +   K+a   yl t+ + +     l +
  gi|488601044|ref|YP_007907515.1| 111 AKAAVLLATTSGLRAMEVYKLMIDdIDVRNRtvFVRAEIAKdYEerITfFNEEAKQALEDYLATNPSSN-----LFY 182
                                       556667888899999999998766255443333333344332332233344444444444444444422.....222 PP

                                       HHHHHHHHT-T..--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTSCHHCHH CS
                    Phage_integr_3  93 eavkefeakkk..vkakyiRkwvatklaelgvpeevidFiqGrkpssvlekhYlnl 146
                                       +  + fe+  +  +++k++Rk++++   +lg+p+ +   ++G+    v+++ Y++l
  gi|488601044|ref|YP_007907515.1| 183 NLRDAFEKI-DskLRMKHMRKFFSQQSDRLGMPTAIKKILMGHV---VGNEEYVAL 234
                                       222233222.13499***************************96...666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1171  (0.0653132); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1745.86
//
Query:       gi|488601045|ref|YP_007907516.1|  [L=303]
Description: TIGR00269 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-14   53.3   0.0    4.5e-14   52.6   0.0    1.4  1  ATP_bind_3      PP-loop family
    8.8e-07   28.9   0.0    1.2e-06   28.4   0.0    1.2  1  Asn_synthase    Asparagine synthase
    1.1e-06   27.8   0.0    1.6e-06   27.2   0.0    1.2  1  tRNA_Me_trans   tRNA methyl transferase
    0.00013   21.4   0.6    0.00013   21.4   0.6    2.4  3  zn-ribbon_14    Zinc-ribbon
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.023   14.7   0.0    1.3  1  PAPS_reduct     Phosphoadenosine phosphosulfate reductase fam
      0.028   13.9   1.4       0.14   11.6   0.0    2.6  3  QueC            Queuosine biosynthesis protein QueC
       0.35   10.7   6.6        3.7    7.4   0.0    3.7  3  Ribosomal_S14   Ribosomal protein S14p/S29e
        2.2    8.3  11.3        6.1    6.9   0.0    3.6  4  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        2.6    8.2   4.7         14    5.8   0.1    3.3  3  YyzF            YyzF-like protein


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   2.3e-17   4.5e-14       2     180 ..      51     239 ..      50     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.3e-17
                                       EEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv......... 68 
                                       +++A+SgG DS+aL+ +l+kl  k    +++ai+vd g+        e+ k++ ++l+i+++i +++          
  gi|488601045|ref|YP_007907516.1|  51 IAIALSGGKDSTALTFVLKKLYGKRRDlEFFAITVDEGIAGYRPPTVEIAKKVTEMLEIPHYIISFKEefgmdldem 127
                                       78******************98765545**************************************99999988643 PP

                                       HHCT.TSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CC CS
                        ATP_bind_3  69 akkk.gknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPl 144
                                         k  +k+       +R  +l++++++ +++ l+++h+ dD + t+ll++ +g   +    i+++ + + +  + P+
  gi|488601045|ref|YP_007907516.1| 128 V-KIgNKKPCSYCGVFRKYLLNRTARELNATKLATGHNLDDETQTILLNFMQGDIERLARLIPQRVQENLVVRIKPF 203
                                       1.2213333456678999**********************************99987766677666555577788** PP

                                       CT--HHHHHHHHHHTT---B--CGGGCTTSHHHHHH CS
                        ATP_bind_3 145 LkvskeeleeylkekkikwveDesNadekyeRnriR 180
                                        +++ +e+  y+  ++i+    e  +++  +R  iR
  gi|488601045|ref|YP_007907516.1| 204 REIYEKEVMLYCILNGIEVDMNECPYSRFPVRAVIR 239
                                       ********9999999988776666666655566665 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     6e-10   1.2e-06      15     117 ..      46     154 ..      31     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6e-10
                      Asn_synthase  15 radvpvGalLSGGlDSSliaalaarqsk..splktFsigfee....kgsdeakyakevaehlgtehtelvlteeell 85 
                                       +   ++++ LSGG DS+++++++++     ++l  F+i+ +e     + + ++ ak+v e l+++h+ + ++ee ++
  gi|488601045|ref|YP_007907516.1|  46 QKNDRIAIALSGGKDSTALTFVLKKLYGkrRDLEFFAITVDEgiagYRPPTVEIAKKVTEMLEIPHYIISFKEEFGM 122
                                       55667899*****************988889*********76786788899***********************999 PP

                      Asn_synthase  86 dalpdviyhlee.pfadrsaiplyllsrlakrk 117
                                       d l++++++  + p      + +yll r a++ 
  gi|488601045|ref|YP_007907516.1| 123 D-LDEMVKIGNKkPCSYCGVFRKYLLNRTAREL 154
                                       9.9****99999887777777888888888765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   7.9e-10   1.6e-06       2     125 ..      50     164 ..      49     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 7.9e-10
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklwee.edeegkeccaeedlkdaervaeklgiplevvdfekeykek 77 
                                       ++++alSgG DS+   ++lk+ + + + + +  ++  e+    +      ++ a++v e l+ip+++++f++e+  +
  gi|488601045|ref|YP_007907516.1|  50 RIAIALSGGKDSTALTFVLKKLYGKRRDLEFFAITVdEGI---AGYRPPTVEIAKKVTEMLEIPHYIISFKEEFGMD 123
                                       899*****************99988888765555541333...4567778999*********************998 PP

                     tRNA_Me_trans  78 vfeefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHY 125
                                       + +e+++    G+  +P+  C    K+  ll++  +el+a +latGH 
  gi|488601045|ref|YP_007907516.1| 124 L-DEMVK---IGN-KKPCSYCGVFRKY--LLNRTARELNATKLATGHN 164
                                       5.44443...444.48*****988886..45555556**********5 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.8       1.1   2.1e+03       2       7 ..       3       8 ..       2       9 .. 0.85
   2 ?   -2.5   0.2         2   3.9e+03       3       8 ..     136     141 ..     135     142 .. 0.84
   3 !   21.4   0.6   6.5e-08   0.00013       1      23 [.     277     299 ..     277     301 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                      zn-ribbon_14 2 kCerCG 7
                                      C+ CG
  gi|488601045|ref|YP_007907516.1| 3 SCSVCG 8
                                     6****9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                      zn-ribbon_14   3 CerCGy 8  
                                       C+ CG 
  gi|488601045|ref|YP_007907516.1| 136 CSYCGV 141
                                       999*96 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 6.5e-08
                      zn-ribbon_14   1 gkCerCGylSSqkiCkACvLLeg 23 
                                       ++Ce CG  +  +iC+ACvL ++
  gi|488601045|ref|YP_007907516.1| 277 NRCEICGEPTPKQICQACVLRKE 299
                                       69*****************9655 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.2e-05     0.023       2     155 ..      51     222 ..      50     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-E.EEEEE-SCHHHHHHHH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglr.lkvyepeeevaekina 70 
                                       ++++ sgGkds++l   + k   ++       + vd g     p t+e  ++++e +++   ++  +ee + +  ++
  gi|488601045|ref|YP_007907516.1|  51 IAIALSGGKDSTALTFVLKKLYGKRrdlefFAITVDEGIAgyRPPTVEIAKKVTEMLEIPhYIISFKEEFGMDLDEM 127
                                       78999********99888888877567766788999987533689**************988888888888888899 PP

                                       HH-S-THHHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S...........CEEE-CC CS
                       PAPS_reduct  71 ekhgsslyeeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek...........slrvfPl 136
                                        k+g ++  + ++ + + + l+++ ++l+++ l tG   d++ +   l++++ d +  +           ++r+ P 
  gi|488601045|ref|YP_007907516.1| 128 VKIGNKKPCS-YCGVFRKYLLNRTARELNATKLATGHNLDDETQTILLNFMQGDIERLArlipqrvqenlVVRIKPF 203
                                       9999999888.9**********************************999999988766689999************* PP

                                       CT--HHHHHHHHHHCT--B CS
                       PAPS_reduct 137 lnWteedvwqyilrenipy 155
                                        +  e++v  y   ++i++
  gi|488601045|ref|YP_007907516.1| 204 REIYEKEVMLYCILNGIEV 222
                                       ***********99999976 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   2.3e+03     132     150 ..      23      41 ..      19      47 .. 0.84
   2 ?   11.6   0.0     7e-05      0.14       4      61 ..      53     116 ..      50     132 .. 0.79
   3 ?   -0.8   0.7      0.46   9.1e+02     194     204 ..     289     299 ..     259     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                                       GSHHHHHHHHHHHHHHHTS CS
                              QueC 132 crdefvkalnkalnlgedk 150
                                       cr++f+  ++k ++++ +k
  gi|488601045|ref|YP_007907516.1|  23 CRKHFIYDFEKRVKYAVKK 41 
                                       99*********99999544 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7e-05
                                       EE--SSHHHHHHHHHHHHH-.....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE- CS
                              QueC   4 vllSGGlDSttvlalakkeg.....kevealtfdYgqr..hkkeleaakkiakelgveehkildl 61 
                                       + lSGG DSt+++++ kk +      e  a+t+d g    +  ++e+akk+++ l++  h i++ 
  gi|488601045|ref|YP_007907516.1|  53 IALSGGKDSTALTFVLKKLYgkrrdLEFFAITVDEGIAgyRPPTVEIAKKVTEMLEI-PHYIISF 116
                                       679************999884444356788888888776566789999999999999.8888765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.46
                                       SSSHHHHHHHH CS
                              QueC 194 geCdaCalRkk 204
                                       + C+aC+lRk+
  gi|488601045|ref|YP_007907516.1| 289 QICQACVLRKE 299
                                       45999999985 PP

>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.3      0.07   1.4e+02      17      35 ..       3      24 ..       1      27 [. 0.68
   2 ?    1.0   0.0      0.18   3.6e+02      26      36 ..     140     150 ..     134     158 .. 0.84
   3 ?    7.4   0.0    0.0018       3.7      11      24 ..     272     285 ..     262     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.07
                                      --SSS--SSSEE-GG...G-EH CS
                     Ribosomal_S14 17 rCrvtGrprGvirkf...gLsR 35
                                       C v+G++  ++++    +L+R
  gi|488601045|ref|YP_007907516.1|  3 SCSVCGKRAVYFQRHsnrHLCR 24
                                      7******999996542224566 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                                       SEE-GGG-EHH CS
                     Ribosomal_S14  26 GvirkfgLsRi 36 
                                       Gv+rk+ L+R 
  gi|488601045|ref|YP_007907516.1| 140 GVFRKYLLNRT 150
                                       899***99997 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0018
                                       .CTTT---SSS--S CS
                     Ribosomal_S14  11 ptrirnrCrvtGrp 24 
                                       p +  nrC+++G p
  gi|488601045|ref|YP_007907516.1| 272 PQKDLNRCEICGEP 285
                                       67888*******98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.2    0.0056        11      29      50 ..       2      24 ..       2      30 .. 0.87
   2 ?   -0.2   0.1      0.47   9.4e+02       3      17 ..      30      44 ..      28      47 .. 0.89
   3 ?    6.9   0.0    0.0031       6.1       7      51 ..     112     158 ..     108     167 .. 0.80
   4 ?   -2.2   0.8         2     4e+03      30      38 ..     278     286 ..     273     297 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0056
                    OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCp 50
                                      k+Cs+Cg++  + +++++++ C+
  gi|488601045|ref|YP_007907516.1|  2 KSCSVCGKRAVYfQRHSNRHLCR 24
                                      78**********98899888887 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.47
                    OrfB_Zn_ribbon  3 klkeqleykakeyGi 17
                                       ++++++y  k+yG+
  gi|488601045|ref|YP_007907516.1| 30 DFEKRVKYAVKKYGM 44
                                      6999**********7 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0031
                    OrfB_Zn_ribbon   7 qleykakeyGikveevnpayTSktCseCgsknke..alsgrtfkCpn 51 
                                       ++    +e+G+ + e+ +    k Cs Cg   k+  +++ r+++ ++
  gi|488601045|ref|YP_007907516.1| 112 YIISFKEEFGMDLDEMVKIGNKKPCSYCGVFRKYllNRTARELNATK 158
                                       66677799*********************999997777777766665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2
                    OrfB_Zn_ribbon  30 tCseCgskn 38 
                                       +C  Cg+  
  gi|488601045|ref|YP_007907516.1| 278 RCEICGEPT 286
                                       577777654 PP

>> YyzF  YyzF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0072        14      34      45 ..       2      13 ..       1      14 [. 0.92
   2 ?    1.3   0.0      0.18   3.6e+02      31      41 ..     131     141 ..     122     147 .. 0.71
   3 ?    0.7   0.3      0.27   5.3e+02      32      42 ..     275     285 ..     263     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0072
                              YyzF 34 ktCefCekpAtY 45
                                      k+C++C k+A+Y
  gi|488601045|ref|YP_007907516.1|  2 KSCSVCGKRAVY 13
                                      79*********9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.18
                              YyzF  31 klsktCefCek 41 
                                         +k C++C  
  gi|488601045|ref|YP_007907516.1| 131 GNKKPCSYCGV 141
                                       46789****75 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.27
                              YyzF  32 lsktCefCekp 42 
                                         ++Ce C +p
  gi|488601045|ref|YP_007907516.1| 275 DLNRCEICGEP 285
                                       5579****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2006.19
//
Query:       gi|488601046|ref|YP_007907517.1|  [L=282]
Description: RIO-like serine/threonine protein kinase fused to N-terminal HTH domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-39  134.0   0.1    6.8e-39  133.4   0.1    1.3  1  RIO1      RIO1 family
    1.2e-12   47.8   0.1    2.2e-12   47.0   0.1    1.4  1  Rio2_N    Rio2, N-terminal
    8.2e-06   25.4   0.2    1.6e-05   24.5   0.2    1.4  1  Pkinase   Protein kinase domain
     0.0006   19.8   0.0     0.0013   18.7   0.0    1.5  2  APH       Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.021   14.2   0.1       0.23   10.8   0.1    2.2  2  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.4   0.1   1.9e-42   6.8e-39       2     182 ..     107     269 ..     106     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 1.9e-42
                                       EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpiel 78 
                                       Vy+++se+  e++iK++k+++ +F+k+++++++           +   l+  +a+kE+++Lkrl  + ++vP++ ++
  gi|488601046|ref|YP_007907517.1| 107 VYNCYSEKYGECVIKFHKLGA-HFRKIREKRDYGDL--------HLSVLTVRSAKKEYSALKRLFGI-INVPEAFAW 173
                                       9******************96.79**9999999888........456788899**************.********* PP

                                       ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEET CS
                              RIO1  79 krhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQavel 155
                                       + ++++me+i+  g ++ +++  +     e++++ +le  +k++ +ag++H+DLS+yN+lv++d ++iID++Q v+l
  gi|488601046|ref|YP_007907517.1| 174 EGNAVMMELID--GKELFRVRLEN----PEDALDIILEDTKKMF-RAGIIHGDLSQYNILVSDD-LYIIDFPQHVDL 242
                                       ***********..99999998877....7788999****99**9.***************9988.************ PP

                                       TSTTHHHHHHHHHHHHHHHHHTTC--- CS
                              RIO1 156 dhpnalefLerDveniikfFrrkgvek 182
                                       dh+n+ ++L++D+en+  +F++ +  +
  gi|488601046|ref|YP_007907517.1| 243 DHENWPDILKKDIENVLSYFKKAYGIE 269
                                       **********************87654 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.1   6.1e-16   2.2e-12       2      82 .]       9      89 ..       8      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 6.1e-16
                            Rio2_N  2 ryLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlv 80
                                      ++L k d+rv++ +   m ++++Vp++li ++s++ke+e++k l+rl + +l+  ++++y G  Lt+ G    +L+ lv
  gi|488601046|ref|YP_007907517.1|  9 KSLRKIDWRVIEIIFKKMWDYKYVPSDLILKLSGIKESELNKILRRLSDDGLLDNRSQPYFGSSLTFLGMSLYSLRKLV 87
                                      7899************************************************************************999 PP

                            Rio2_N 81 kr 82
                                       r
  gi|488601046|ref|YP_007907517.1| 88 TR 89
                                      87 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2   4.3e-09   1.6e-05       4     142 ..      96     236 ..      94     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.3e-09
                                       EEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH...............HHHHHHHHHHHHHSCTTB--EEE CS
                           Pkinase   4 leklGeGsfGkVykaveketgkivAvKkikkekakkkke...............kkvlrEikilkklkhpnivrlye 65 
                                        +k+GeG+ ++Vy++++ e+  + ++K  k      k +               +++ +E + lk+l    i+++ e
  gi|488601046|ref|YP_007907517.1|  96 GKKMGEGKESVVYNCYS-EKYGECVIKFHKLGAHFRKIRekrdygdlhlsvltvRSAKKEYSALKRLF--GIINVPE 169
                                       689*************6.56666778887764433332223458889999999999999999999985..79***** PP

                                       EEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SG CS
                           Pkinase  66 vfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDF 142
                                       +f  + + + ++e+++g+el+++         e+ ++ +  ile  + ++++giiH Dl + NiL++  ++l i+DF
  gi|488601046|ref|YP_007907517.1| 170 AFAWEGNAV-MMELIDGKELFRVRL-------ENPEDALDIILEDTKKMFRAGIIHGDLSQYNILVS--DDLYIIDF 236
                                       ***999987.79********99875.......3445566668888899*******************..88999999 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.4   1.4e+03      43      84 ..     154     190 ..      97     205 .. 0.47
   2 !   18.7   0.0   3.7e-07    0.0013     149     193 ..     197     236 ..     166     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.4
                                       HHHHHHHTT-...B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                               APH  43 llrlLakagv...pvPevlagdtddeeigllfalieyvpgrsllr 84 
                                       ++ +L ++ +    vPe++a       +g  ++++e ++g+ l r
  gi|488601046|ref|YP_007907517.1| 154 EYSALKRL-FgiiNVPEAFA------WEG-NAVMMELIDGKELFR 190
                                       22222222.11235666665......233.456666666666666 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.7e-07
                                       HHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE--- CS
                               APH 149 eeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDf 193
                                       e+ +l+ +++   + ++++++HgDl+  N+lv   d+    +iDf
  gi|488601046|ref|YP_007907517.1| 197 ED-ALDIILEDTKKMFRAGIIHGDLSQYNILVS--DDLY--IIDF 236
                                       44.44444444444599****************..7886..***9 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.068   2.4e+02     162     205 ..     118     160 ..     103     179 .. 0.66
   2 ?   10.8   0.1   6.3e-05      0.23     131     178 ..     207     247 ..     192     278 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.068
                               Kdo 162 wliDldkarlrlradrwrekdLarLkrsflkielteadweallr 205
                                       ++i ++k      ++  +++d   L+ s+l++   ++++ al+r
  gi|488601046|ref|YP_007907517.1| 118 CVIKFHKLGAHF-RKIREKRDYGDLHLSVLTVRSAKKEYSALKR 160
                                       555666655555.4444455666666666666666666665554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.3e-05
                               Kdo 131 iaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrw 178
                                        +k+ rag+ H+dl   nil+  +      +++iD+ +       + w
  gi|488601046|ref|YP_007907517.1| 207 TKKMFRAGIIHGDLSQYNILVSDD------LYIIDFPQHVDLD-HENW 247
                                       589******************988......5999997655544.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1939.34
//
Query:       gi|488601047|ref|YP_007907518.1|  [L=627]
Description: hypothetical protein Asulf_01548 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-50  168.5   0.2    1.5e-49  167.3   0.2    1.6  1  DUF460           Protein of unknown function (DUF460)
     0.0045   17.3   4.0     0.0045   17.3   4.0    3.3  2  Csm1_N           Csm1 N-terminal domain
  ------ inclusion threshold ------
      0.017   15.4   0.0        0.1   12.9   0.0    2.3  2  PK_C             Pyruvate kinase, alpha/beta domain
      0.017   15.4   0.0      0.049   13.9   0.0    1.7  1  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
      0.038   14.2   0.0        8.3    6.7   0.0    3.5  3  BtrH_N           Butirosin biosynthesis protein H, N-terminal
       0.11   13.0  11.0       0.82   10.2   0.7    2.9  2  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
       0.18   12.2  11.0        2.1    8.8   0.0    4.1  4  Snapin_Pallidin  Snapin/Pallidin
       0.21   11.7  22.8      0.055   13.6   3.7    3.7  2  bZIP_1           bZIP transcription factor
        0.7   10.6   4.7        4.4    8.0   1.9    2.9  2  SlyX             SlyX
       0.87    9.5  15.9        3.4    7.7   0.5    4.5  3  Pox_A_type_inc   Viral A-type inclusion protein repeat
       0.88    9.4  15.2        2.3    8.0   5.9    3.4  2  DivIC            Septum formation initiator
        1.2    8.3   7.1          2    7.6   7.1    1.3  1  TMPIT            TMPIT-like protein
        1.7    8.8   0.0        1.7    8.8   0.0    4.0  4  CREPT            Cell-cycle alteration and expression-elevate
        1.8    8.1   7.7        5.2    6.6   7.7    1.8  1  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
          3    7.3   8.6        6.8    6.2   8.7    1.6  1  Exonuc_VII_L     Exonuclease VII, large subunit
        3.3    7.5  23.9       0.81    9.5   4.1    2.9  3  DUF724           Protein of unknown function (DUF724)
        3.9    7.7  18.5       0.12   12.5   3.4    3.6  3  JIP_LZII         JNK-interacting protein  leucine zipper II
        4.6    7.4  15.4        2.9    8.0   3.9    3.8  3  DUF5595          Domain of unknown function (DUF5595)
        5.2    4.9   7.7          2    6.2   5.3    1.6  2  V_ATPase_I       V-type ATPase 116kDa subunit family
        6.9    6.8   7.7       0.85    9.7   1.2    2.4  2  APC_N_CC         Coiled-coil N-terminus of APC, dimerisation 
        7.2    6.2  14.2          2    8.0   7.1    2.4  2  NRBF2            Nuclear receptor-binding factor 2, autophagy


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 !  167.3   0.2   1.8e-52   1.5e-49       2     141 .]     207     339 ..     206     339 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 1.8e-52
                            DUF460   2 vkskdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpv 78 
                                       +k+k+v+v+ve++e+dkie+ pl kkr ++livGiDPG t+g+avldldg+vl ++s+++++ +evie+i ++Gkpv
  gi|488601047|ref|YP_007907518.1| 207 FKTKNVQVRVEAIERDKIEYIPL-KKRVRHLIVGIDPGSTVGVAVLDLDGKVLGVRSKKGWSFSEVIEYILSFGKPV 282
                                       6899*******************.9**************************************************** PP

                            DUF460  79 ivAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                       ivAtD+s++pe+v+k++++++a++y+P++d+sve K++l++       +k+ +dHeRDal++A
  gi|488601047|ref|YP_007907518.1| 283 IVATDKSNAPEYVSKVRSAFNAIIYTPRDDMSVERKIQLTRG------YKVFNDHERDALSSA 339
                                       ******************************************......8889********998 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   4.0   5.3e-06    0.0045      18      58 ..     406     446 ..     398     454 .. 0.86
   2 ?    6.3   1.6     0.015        13      22      54 ..     455     487 ..     452     491 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.3e-06
                            Csm1_N  18 AdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvk 58 
                                        d l++ l +EN++L+++++   +eiesLk+++ ++  + +
  gi|488601047|ref|YP_007907518.1| 406 KDRLIEELYEENRILKEEIKELRREIESLKQRIVSISREEH 446
                                       599******************************99876654 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                            Csm1_N  22 vsklvhENsvLsqkletkdqeiesLkeqlaele 54 
                                       ++ l  EN  L+ +l+ k+ +i +L+ +la ++
  gi|488601047|ref|YP_007907518.1| 455 IKTLEAENKRLRMELSEKNSKIDELESKLAVIK 487
                                       566778*********************999887 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 ?   12.9   0.0   0.00012       0.1      18      77 ..     281     339 ..     279     373 .. 0.77
   2 ?   -2.0   0.0       4.9   4.2e+03      51      70 ..     489     508 ..     433     559 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                       EEEEE-SSSHHHHHHHHT-TSSEEEEEES..HHHHHHHHHHCTTEEHHH.HHHHH...TTSH CS
                              PK_C  18 aIvvltesGetArliskyrpkvpiiavtp..neltarqlalyrGvypvlvekaktaestdel 77 
                                        ++v+t + +++  +sk r+  + i++tp  + +++r+++l rG+  +  + +   + ++++
  gi|488601047|ref|YP_007907518.1| 281 PVIVATDKSNAPEYVSKVRSAFNAIIYTPrdDMSVERKIQLTRGYKVFN-DHE--RDALSSA 339
                                       589*************************9555666*********99886.332..2222222 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                                       HHHHHHCTTEEHHH.HHHHH CS
                              PK_C  51 arqlalyrGvypvlvekakt 70 
                                        r l l+ G   v+v k+ t
  gi|488601047|ref|YP_007907518.1| 489 MRYLELFEGWKWVKVLKKFT 508
                                       56666666666555543333 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.7e-05     0.049      38      67 ..     142     171 ..     133     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-05
                           acVLRF1  38 aaGGwSqqRfaRrrenqadalleavaeaaa 67 
                                        +GGw q+R+ Rr+ ++++  +++++e ++
  gi|488601047|ref|YP_007907518.1| 142 GKGGWHQNRYRRRVHDEVRMIFNEIKEILK 171
                                       69****************999999888765 PP

>> BtrH_N  Butirosin biosynthesis protein H, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.38   3.2e+02      54      82 ..      87     115 ..      71     117 .. 0.81
   2 ?    6.7   0.0    0.0097       8.3       7      66 ..     166     225 ..     164     251 .. 0.83
   3 ?    0.6   0.0      0.71     6e+02      85     105 ..     275     296 ..     261     313 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.38
                            BtrH_N  54 dlekrlakrlglkvevketkdpeeawkal 82 
                                       +    +a+r+g+++++++ +d+++a + l
  gi|488601047|ref|YP_007907518.1|  87 ESLHAIARRYGIRMNIRSPADEARACAYL 115
                                       557889****************9998776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0097
                            BtrH_N   7 ladllahaglelsEplvFglGgglgfvYlpakklnplpllagrtkpgdlekrlakrlglk 66 
                                       ++++l+++g+e+sE + Fg Gg  + + l  ++ +++p+ +++tk+ ++  ++ +r +++
  gi|488601047|ref|YP_007907518.1| 166 IKEILKNKGFEFSEDVRFGYGGISRGTLLVNAERSEVPINSFKTKNVQVRVEAIERDKIE 225
                                       67899*****************99999999999999********9888877777766655 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.71
                            BtrH_N  85 eLdaGrpvivqvdvyyLp.Ylp 105
                                        L  G+pviv++d  + p Y++
  gi|488601047|ref|YP_007907518.1| 275 ILSFGKPVIVATDKSNAPeYVS 296
                                       4678*********887762444 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.7      0.02        17      15      53 ..     408     446 ..     401     450 .. 0.90
   2 ?   10.2   0.7   0.00096      0.82      17      50 ..     455     488 ..     453     493 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                       Cep57_MT_bd  15 evlkeLedEfehlklelqelaaqynaldpslgkrkRkdL 53 
                                       ++++eL +E + lk e +el++++++l +++ + +R++ 
  gi|488601047|ref|YP_007907518.1| 408 RLIEELYEENRILKEEIKELRREIESLKQRIVSISREEH 446
                                       6899************************99999888875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00096
                       Cep57_MT_bd  17 lkeLedEfehlklelqelaaqynaldpslgkrkR 50 
                                       +k+Le E + l++el+e ++++ +l++ l   kR
  gi|488601047|ref|YP_007907518.1| 455 IKTLEAENKRLRMELSEKNSKIDELESKLAVIKR 488
                                       8*************************99998888 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       7.3   6.2e+03       8      39 ..      44      74 ..      42      90 .. 0.75
   2 ?    8.8   0.0    0.0025       2.1      47      72 ..     332     357 ..     318     360 .. 0.77
   3 ?    3.9   1.2     0.083        71      15      48 ..     403     436 ..     400     451 .. 0.81
   4 ?    3.3   0.5      0.13   1.1e+02      19      51 ..     452     484 ..     448     494 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.3
                   Snapin_Pallidin  8 lellepkldeldeklkelrqsQeeLleqldrl 39
                                      ++ l+p++ ++d +++el  s +eL + l+ l
  gi|488601047|ref|YP_007907518.1| 44 VRELKPDIVAFD-SIQELFSSKRELVDFLKVL 74
                                      677888888887.5899888888887766655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                   Snapin_Pallidin  47 eeaqeaevlpdlkeyakKLvnikkrm 72 
                                       e+++ +++++ +++y++KL+ni+krm
  gi|488601047|ref|YP_007907518.1| 332 ERDALSSAIEAFNSYKNKLMNIEKRM 357
                                       44444789999**************9 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.083
                   Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkelee 48 
                                       +++ d  ++el ++ + L+e++++l++++++l++
  gi|488601047|ref|YP_007907518.1| 403 IKRKDRLIEELYEENRILKEEIKELRREIESLKQ 436
                                       6677778899999999999999999999988876 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.13
                   Snapin_Pallidin  19 deklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                       d+ +k l+++ + L+ +l++ n+k++ele    
  gi|488601047|ref|YP_007907518.1| 452 DNYIKTLEAENKRLRMELSEKNSKIDELESKLA 484
                                       678999999999999999999999999987665 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.7   6.5e-05     0.055      26      62 ..     401     437 ..     399     439 .. 0.86
   2 ?   10.6   1.6   0.00054      0.46      35      63 ..     455     483 ..     448     484 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekLksk 62 
                                       +ei++  r  ++L +eN  Lk+e++el+ e+e+Lk+ 
  gi|488601047|ref|YP_007907518.1| 401 EEIKRKDRLIEELYEENRILKEEIKELRREIESLKQR 437
                                       6777778889999999999999999999999999986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00054
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  35 vkaLekeNksLkseleelkkevekLkskv 63 
                                        k+Le+eNk L+ el+e + ++++L+sk+
  gi|488601047|ref|YP_007907518.1| 455 IKTLEAENKRLRMELSEKNSKIDELESKL 483
                                       589**********************9986 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.9    0.0051       4.4      15      55 ..     406     446 ..     401     463 .. 0.85
   2 ?    1.5   0.0      0.55   4.7e+02       3      15 ..     474     486 ..     472     489 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  15 qedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                        +++ieeL ++     ++i++l+r+++ l++r+ +++ ++ 
  gi|488601047|ref|YP_007907518.1| 406 KDRLIEELYEENRILKEEIKELRREIESLKQRIVSISREEH 446
                                       58999999999999******************977776654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHHHH CS
                              SlyX   3 erleeLEiklafq 15 
                                       ++++eLE+kla  
  gi|488601047|ref|YP_007907518.1| 474 SKIDELESKLAVI 486
                                       689*******975 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.63   5.4e+02       4      12 ..     149     157 ..     149     157 .. 0.90
   2 ?    6.2   4.2     0.012        10       1      16 [.     422     437 ..     422     441 .. 0.93
   3 ?    7.7   0.5     0.004       3.4       2      18 ..     468     484 ..     467     485 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.63
                    Pox_A_type_inc   4 srlRsRIsD 12 
                                       +r+R+R+ D
  gi|488601047|ref|YP_007907518.1| 149 NRYRRRVHD 157
                                       7*****987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                    Pox_A_type_inc   1 rEmsrlRsRIsDLErq 16 
                                       +E+ +lR++I++L+++
  gi|488601047|ref|YP_007907518.1| 422 EEIKELRREIESLKQR 437
                                       79***********986 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.004
                    Pox_A_type_inc   2 EmsrlRsRIsDLErqLs 18 
                                       E+s++ s+I +LE++L+
  gi|488601047|ref|YP_007907518.1| 468 ELSEKNSKIDELESKLA 484
                                       89999***********7 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.9    0.0027       2.3      25      53 ..     402     430 ..     396     449 .. 0.54
   2 ?    4.2   2.6     0.042        36      17      59 ..     446     487 ..     437     493 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                             DivIC  25 eiaalqaelaklkaeneeLeaevkdLksd 53 
                                       ei+++ + +++l +en+ L++e+k+L+ +
  gi|488601047|ref|YP_007907518.1| 402 EIKRKDRLIEELYEENRILKEEIKELRRE 430
                                       55555555555555555555555555432 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.042
                                       XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                             DivIC  17 laykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                       + + + ++ i++l+ae+++l+ e  e ++++++L+ ++ ++ +
  gi|488601047|ref|YP_007907518.1| 446 HERIRRDNYIKTLEAENKRLRMELSEKNSKIDELE-SKLAVIK 487
                                       66778889999999999999999999999999994.5555544 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   7.1    0.0023         2      21     114 ..     406     509 ..     384     520 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0023
                             TMPIT  21 ykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.........eeeeeeveelkeelkerkkvlkevesl 88 
                                         + +eel + +  +++eik+ ++++++lk+++ +++++ +         +  e e ++l+ el+e+++ ++e+es 
  gi|488601047|ref|YP_007907518.1| 406 KDRLIEELYEENRILKEEIKELRREIESLKQRIVSISREEHerirrdnyiKTLEAENKRLRMELSEKNSKIDELESK 482
                                       334567777777777788888888888888888887777556777777777777888999999************** PP

                             TMPIT  89 lpkk.nglylklvlGnvnvsllnkqdk 114
                                       l    + +yl+l+ G   v++l+k  k
  gi|488601047|ref|YP_007907518.1| 483 LAVIkRMRYLELFEGWKWVKVLKKFTK 509
                                       99876999******9999998887655 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 ?    8.8   0.0     0.002       1.7      41     111 ..     286     355 ..     281     358 .. 0.93
   2 ?    2.7   3.3      0.15   1.3e+02      69     115 ..     401     447 ..     396     449 .. 0.88
   3 ?    3.9   2.2     0.064        55      70     113 ..     447     490 ..     442     494 .. 0.88
   4 ?   -2.0   1.0       4.1   3.5e+03      78     108 ..     596     626 ..     586     627 .] 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
                             CREPT  41 kdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvks 111
                                       +dk++a +++++v++a +++  Y+ r +  +e   +l++  + f  + +++l+ a e  +++k+kl ++++
  gi|488601047|ref|YP_007907518.1| 286 TDKSNAPEYVSKVRSAFNAI-IYTPRDDMSVERKIQLTRGYKVFNDHERDALSSAIEAFNSYKNKLMNIEK 355
                                       69999999********9998.5********************************************99986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
                             CREPT  69 aeleeRkklakmledfleaqkellakaeekleelkeklekvksvrke 115
                                       +e++   +l + l +  +++ke++++ ++++e+lk+++  ++ +++e
  gi|488601047|ref|YP_007907518.1| 401 EEIKRKDRLIEELYEENRILKEEIKELRREIESLKQRIVSISREEHE 447
                                       78999999999999999999999999999999999999999887765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.064
                             CREPT  70 eleeRkklakmledfleaqkellakaeekleelkeklekvksvr 113
                                       e   R +  k+le+  + ++++l+++++k++el++kl+ +k +r
  gi|488601047|ref|YP_007907518.1| 447 ERIRRDNYIKTLEAENKRLRMELSEKNSKIDELESKLAVIKRMR 490
                                       5567999999***************************9998765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.1
                             CREPT  78 akmledfleaqkellakaeekleelkeklek 108
                                       +++le+  ++ k +l+  ee ++e++ k ++
  gi|488601047|ref|YP_007907518.1| 596 ERYLEEKRKMEKRKLDLLEELIQEYRLKRKN 626
                                       5678888888889999999999999888765 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 ?    6.6   7.7     0.006       5.2     161     223 ..     401     478 ..     381     487 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.006
                           HAUS6_N 161 rekaaadrarqkyqenaqllekkerelraeleelqaelkae................keaakkekkeasedaeeeki 221
                                       +e++++dr+++++ e+ + l+++++elr+e+e l++++  +                  +a++++++++ ++++ ki
  gi|488601047|ref|YP_007907518.1| 401 EEIKRKDRLIEELYEENRILKEEIKELRREIESLKQRIV-SisreeherirrdnyikTLEAENKRLRMELSEKNSKI 476
                                       7889999*****************************985.4467666666666665433333344444444444455 PP

                           HAUS6_N 222 kk 223
                                       ++
  gi|488601047|ref|YP_007907518.1| 477 DE 478
                                       55 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.7     0.008       6.8     170     266 ..     390     493 ..     289     518 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.008
                      Exonuc_VII_L 170 rleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k......ekleekk..erlkklke 237
                                       + +++ s++   +e ++rk + ++el e+ +  lk+++k+ r+++e+lk+r+ +      e++++ +  ++l++ ++
  gi|488601047|ref|YP_007907518.1| 390 EKKTVPSKV--DREEIKRKDRLIEELYEENRI-LKEEIKELRREIESLKQRIvSisreehERIRRDNyiKTLEAENK 463
                                       111121111..233444444444443333333.45555555555555555554343332222222212244455555 PP

                      Exonuc_VII_L 238 rle.lleekkerleeleeklealsplkvLk 266
                                       rl+ +l+ek+++++ele+kl+ ++ ++ L+
  gi|488601047|ref|YP_007907518.1| 464 RLRmELSEKNSKIDELESKLAVIKRMRYLE 493
                                       5556799*************9999888876 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.1    0.0012         1      66     172 ..     339     443 ..     325     452 .. 0.80
   2 ?    9.5   4.1   0.00095      0.81     108     181 ..     445     519 ..     440     522 .. 0.80
   3 ?   -2.7   0.9         5   4.3e+03     111     133 ..     591     611 ..     575     625 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                            DUF724  66 srseleslkeslaeLekh...GFdVkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekki 139
                                         + ++s+k++l ++ek    G+d  a+++ + k + lk+   + ++e+kk ekk+   + +     eei+ +++ i
  gi|488601047|ref|YP_007907518.1| 339 AIEAFNSYKNKLMNIEKRmpaGYDLDAVKAGVIKGIPLKTILGEERREEKK-EKKTVPSKVD----REEIKRKDRLI 410
                                       6788999********995555***********9999999888777777777.4444433333....4589999**** PP

                            DUF724 140 lelerqlallkekkeaadkeiarlkseaeklee 172
                                        el +++  lke+ ++  +ei +lk+   ++++
  gi|488601047|ref|YP_007907518.1| 411 EELYEENRILKEEIKELRREIESLKQRIVSISR 443
                                       **************9******999998877765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00095
                            DUF724 108 leerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiar.lkseaekleeeledveqeF 181
                                       ++er + ++ i++ e+e+++l  e++e+++ki ele +la++k+++  +  e ++ +k+ ++  +ee+e+ve+eF
  gi|488601047|ref|YP_007907518.1| 445 EHERIRRDNYIKTLEAENKRLRMELSEKNSKIDELESKLAVIKRMRYLELFEGWKwVKVLKKFTKEEIERVEKEF 519
                                       5566666888999999***************************88776666655525666666778888888888 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5
                            DUF724 111 rkklekkieeeesekrkleeeid 133
                                       +kk+e++  ee+ +++k   ++d
  gi|488601047|ref|YP_007907518.1| 591 SKKFEERYLEEKRKMEK--RKLD 611
                                       34444444444444442..3333 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 ?   -2.7   0.1       8.2     7e+03      43      65 ..     378     400 ..     377     406 .. 0.80
   2 ?   12.5   3.4   0.00014      0.12      35      66 ..     410     441 ..     403     445 .. 0.90
   3 ?    5.0   0.6     0.032        27      43      70 ..     456     483 ..     452     486 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.2
                          JIP_LZII  43 eiLreEleslqkakerlesrike 65 
                                       +iL eE ++ +k+k+++ s++  
  gi|488601047|ref|YP_007907518.1| 378 TILGEERREEKKEKKTVPSKVDR 400
                                       68889999999999999888865 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                          JIP_LZII  35 vdeLtsereiLreEleslqkakerlesrikel 66 
                                       ++eL +e+ iL+eE+++l+ + e+l++ri  +
  gi|488601047|ref|YP_007907518.1| 410 IEELYEENRILKEEIKELRREIESLKQRIVSI 441
                                       79**************************9765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.032
                          JIP_LZII  43 eiLreEleslqkakerlesrikelEeel 70 
                                       ++L+ E+++l++++++ +s+i elE +l
  gi|488601047|ref|YP_007907518.1| 456 KTLEAENKRLRMELSEKNSKIDELESKL 483
                                       5677788888888888888888888765 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.9    0.0034       2.9      49      73 .]     406     430 ..     389     430 .. 0.88
   2 ?    4.9   0.3     0.033        28      51      69 ..     453     471 ..     449     475 .. 0.87
   3 ?    0.1   0.2      0.99   8.5e+02      60      73 .]     505     518 ..     500     518 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0034
                           DUF5595  49 deaqlesleeeekrLeeEierleke 73 
                                        ++ +e+l ee+++L+eEi++l +e
  gi|488601047|ref|YP_007907518.1| 406 KDRLIEELYEENRILKEEIKELRRE 430
                                       6789*****************9987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.033
                           DUF5595  51 aqlesleeeekrLeeEier 69 
                                       + +++le+e+krL  E+++
  gi|488601047|ref|YP_007907518.1| 453 NYIKTLEAENKRLRMELSE 471
                                       679*************986 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.99
                           DUF5595  60 ekrLeeEierleke 73 
                                       +k  +eEier+eke
  gi|488601047|ref|YP_007907518.1| 505 KKFTKEEIERVEKE 518
                                       57789********8 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 ?   -3.4   0.0       1.9   1.6e+03     211     245 ..     283     317 ..     280     353 .. 0.65
   2 ?    6.2   5.3    0.0024         2      30     108 ..     408     492 ..     382     566 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                        V_ATPase_I 211 iiffqgeqlkekikkicesfgaklyelpeseeere 245
                                       i+ +  ++  e ++k+ ++f+a +y+ +++ +  +
  gi|488601047|ref|YP_007907518.1| 283 IVATDKSNAPEYVSKVRSAFNAIIYTPRDDMSVER 317
                                       66667777788888888888888888666554322 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0024
                        V_ATPase_I  30 rrcdemerklrfleeeieklekavikeeea......eesleapeekeldeleeelekleeelkelnenleklkkeln 100
                                       r ++e+ ++ r+l+eei++l+ ++ + ++       ee+++ ++++++++le+e ++l  el+e n++ ++l+++l 
  gi|488601047|ref|YP_007907518.1| 408 RLIEELYEENRILKEEIKELRREIESLKQRivsisrEEHERIRRDNYIKTLEAENKRLRMELSEKNSKIDELESKLA 484
                                       33677777778888888876666655555577777788888888999999999999999999999999999999888 PP

                        V_ATPase_I 101 elvelkav 108
                                        ++ ++++
  gi|488601047|ref|YP_007907518.1| 485 VIKRMRYL 492
                                       77776654 PP

>> APC_N_CC  Coiled-coil N-terminus of APC, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.7       1.3   1.1e+03      13      23 ..     420     430 ..     408     447 .. 0.64
   2 ?    9.7   1.2   0.00099      0.85      12      42 ..     457     487 ..     454     490 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                          APC_N_CC  13 LkkenthlrrE 23 
                                       Lk e  +lrrE
  gi|488601047|ref|YP_007907518.1| 420 LKEEIKELRRE 430
                                       55555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00099
                          APC_N_CC  12 aLkkenthlrrELedNSshLskLEtetsgmK 42 
                                        L +en  lr EL++  s++  LE+    +K
  gi|488601047|ref|YP_007907518.1| 457 TLEAENKRLRMELSEKNSKIDELESKLAVIK 487
                                       6999********************9766555 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 ?    4.4   4.2     0.028        24      86     121 ..     401     436 ..     382     441 .. 0.83
   2 ?    8.0   7.1    0.0023         2      79     131 ..     422     477 ..     421     482 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.028
                             NRBF2  86 tkiadLkrlvelLlaenerLrkenkqLkaekaRLqk 121
                                        +i+   rl+e L +en  L++e k+L+ e   L++
  gi|488601047|ref|YP_007907518.1| 401 EEIKRKDRLIEELYEENRILKEEIKELRREIESLKQ 436
                                       4688889**********************9888876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0023
                             NRBF2  79 tkleeqatkiadLkrlv.elLlaenerLrken..kqLkaekaRLqkeplekeldvd 131
                                         + e + +i+ Lk+ +  +  +e er+r++n  k L ae+ RL+ e  ek+  +d
  gi|488601047|ref|YP_007907518.1| 422 EEIKELRREIESLKQRIvSISREEHERIRRDNyiKTLEAENKRLRMELSEKNSKID 477
                                       578888999****976515556889*******8889***********999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1996  (0.111328); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.93u 0.32s 00:00:01.25 Elapsed: 00:00:00.56
# Mc/sec: 3387.09
//
Query:       gi|488601048|ref|YP_007907519.1|  [L=129]
Description: hypothetical protein Asulf_01549 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-39  134.5   0.5    1.7e-39  134.3   0.5    1.0  1  DUF473    Protein of unknown function (DUF473)
  ------ inclusion threshold ------
      0.023   14.6   0.1       0.03   14.3   0.1    1.3  1  DUF5402   Family of unknown function (DUF5402)


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 !  134.3   0.5   1.9e-43   1.7e-39       1     116 [.       1     116 [.       1     118 [. 0.99

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 1.9e-43
                            DUF473   1 MkvvaLtGiseevieeLkknklrtielrsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveistkrvv 77 
                                       M+++++tGis+ +ie+++k+ ++tielrsahNv+t+lk++vg++vFlT ++l+Dl++G++G++aev+++e+++++++
  gi|488601048|ref|YP_007907519.1|   1 MRCFVFTGISRVIIEDVIKGMVKTIELRSAHNVATALKANVGNCVFLTPTRLYDLSRGVSGLVAEVTGKEVISHSIF 77 
                                       9**************************************************************************** PP

                            DUF473  78 essesfieErEttvarvqlkllglgrvrevkeeellkpt 116
                                        s++ f++E+E+tv++++lk++++gr+ +v ++++l++t
  gi|488601048|ref|YP_007907519.1|  78 LSTDRFMDESEMTVVKLRLKPKCIGRILNVLNAGILDST 116
                                       **********************************99987 PP

>> DUF5402  Family of unknown function (DUF5402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.3e-06      0.03       6      76 ..      27      99 ..      21     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-06
                           DUF5402  6 lkdreklekklqnllgkevfvsevdifalrcGcvGilievrGlevddveif..kekileklkelakdleikad 76
                                      l+ ++++   l+  +g+ vf++ + ++ l+ G +G+++ev G ev   +if   ++ +++ +    +l +k++
  gi|488601048|ref|YP_007907519.1| 27 LRSAHNVATALKANVGNCVFLTPTRLYDLSRGVSGLVAEVTGKEVISHSIFlsTDRFMDESEMTVVKLRLKPK 99
                                      45688899999**********************************9999994345666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 931.52
//
Query:       gi|488601049|ref|YP_007907520.1|  [L=241]
Description: TIGR00161 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  142.6   0.1      2e-41  142.4   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 !  142.4   0.1   1.1e-45     2e-41       1     213 []      18     221 ..      18     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 1.1e-45
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEE.TTT.SEEEEEEEE- CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyak.dsgsrdllvlqgre 76 
                                       Li+ fpgiG+Vg++a+ ++i + ++e+ g i sd  +p     pv+++ eg   +p+r+y + +   ++ +++++  
  gi|488601049|ref|YP_007907520.1|  18 LIASFPGIGLVGTIATAHIITESKLEHKGVISSDL-FP-----PVAMLMEGIISPPIRIYESlE---HNAVLIHSDI 85 
                                       899*******************************9.**.....*****************7755...9*******88 PP

                                       HSCHHH..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT....-CEEEEHHH CS
                              PAC2  77 pilqye..efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees....eyggivgit 147
                                       pi+      ++++++++a++++ k+++ L+g+++ e        +++v+gaat++ell+e++e+    + g+i+g++
  gi|488601049|ref|YP_007907520.1|  86 PIGVEIssILSREIIKFAKSINAKRIYSLAGVATFEG-------KHRVFGAATTKELLDEIKEHvevfNSGTISGLA 155
                                       8887767678999*******************96644.......34***************87778899******** PP

                                       HHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHHH CS
                              PAC2 148 glLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleela 213
                                       g++l+++  r++p+++ll+e++   pdP+a+a ++++l++++g e++ ++L+++ae +e+++++la
  gi|488601049|ref|YP_007907520.1| 156 GSILNECVYRNFPGLALLGETSSFNPDPRASAQIIQVLNRIFGWEINIDRLIQEAEYIEAHMQKLA 221
                                       ***************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1582.63
//
Query:       gi|488601050|ref|YP_007907521.1|  [L=297]
Description: ribose-phosphate pyrophosphokinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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    3.4e-21   75.4   0.0    2.4  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
      2e-12   47.6   1.6    4.3e-12   46.5   1.6    1.6  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    2.6e-12   46.5   1.9    1.3e-11   44.3   0.7    2.2  2  Pribosyltran    Phosphoribosyl transferase domain
      1e-05   25.1   0.1    1.7e-05   24.4   0.1    1.3  1  UPRTase         Uracil phosphoribosyltransferase
    3.9e-05   23.2   0.1    8.5e-05   22.1   0.1    1.5  1  PRTase_2        Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   9.3e-25   3.4e-21      10     116 .]      11     117 ..       3     117 .. 0.95
   2 !    8.4   0.1   0.00053       1.9      13      87 ..     174     244 ..     162     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 9.3e-25
                    Pribosyltran_N  10 keLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakritaVi 86 
                                         La +i+kr+g++l  a++++f+dgE +v+++e v+g+dvfi++s+++ +++ ++e +++id ++   a++++ + 
  gi|488601050|ref|YP_007907521.1|  11 GILAYEISKRTGITLSYAELEKFPDGEKYVRVSEAVKGSDVFIVNSFHHMPDEMIIETIFLIDIFKSVGANEVVGIF 87 
                                       5699************************************************************************* PP

                    Pribosyltran_N  87 PylgysrqdrkksrepisaklvaklLeaaG 116
                                       Py++ysr +r    e+   k + kl+++aG
  gi|488601050|ref|YP_007907521.1|  88 PYFPYSRFRRFIGGEANRLKTISKLFRTAG 117
                                       **********99999999999999999998 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00053
                    Pribosyltran_N  13 aekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakritaViP 87 
                                       a+ ++++lg+    ++  r   +++ ++   +v ++dv+++ ++ +        ++  i+alr++ akri aV  
  gi|488601050|ref|YP_007907521.1| 174 ARIVSEKLGTDYKLMRKIRIDAENVIIDSVPDVSNRDVVLVDDIISTGG----TVVQAIKALRHSGAKRIYAVCT 244
                                       5668888999999999999999999999999999999999999998844....456689*************975 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   1.6   1.2e-15   4.3e-12      75     172 ..     200     289 ..     183     297 .] 0.87

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.2e-15
                                       --EES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHH CS
                    Pribosyl_synth  75 ltvvGdvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqk 151
                                       +  v dv+ r  ++vdd+i    ++v+a + l++ Ga +iy+++th lls++a +l+  + id +v t+t+   i  
  gi|488601050|ref|YP_007907521.1| 200 IDSVPDVSNRDVVLVDDIISTGGTVVQAIKALRHSGAKRIYAVCTHPLLSNEALKLIYRAGIDGIVGTDTVLSPI-- 274
                                       66799*****************************************************************97666.. PP

                                       HT-TTEEEE--HHHHHHHHHH CS
                    Pribosyl_synth 152 lrcskiktvdislllaeairr 172
                                               v ++ +++e ir+
  gi|488601050|ref|YP_007907521.1| 275 ------SHVSVAEIISEEIRK 289
                                       ......556666666666665 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.078   2.8e+02      43      93 ..      13      54 ..       3      56 .. 0.77
   2 !   44.3   0.7   3.6e-15   1.3e-11      19     124 ..     148     245 ..     131     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.078
                                      HHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE CS
                      Pribosyltran 43 fakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliV 93
                                      +a++++++ ++ l y + +k+ ++ + +           +e ++g+ V+iV
  gi|488601050|ref|YP_007907521.1| 13 LAYEISKRTGITLSYAELEKFPDGEKYVR---------VSEAVKGSDVFIV 54
                                      68888888888888888888766666665.........6888999999998 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 3.6e-15
                                       TEEEEEE.--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE- CS
                      Pribosyltran  19 aaeilee.yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVD 94 
                                       +a++++  ++ +  vvvg +  +  +a i++ +L+  +  +rk + ++++               +d+ ++ V++VD
  gi|488601050|ref|YP_007907521.1| 148 LADYVKRnFELEDAVVVGADEVAEFWARIVSEKLGTDYKLMRKIRIDAENVIID---------SVPDVSNRDVVLVD 215
                                       55555554667778*********************8888888888877666555.........689*********** PP

                                       SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
                      Pribosyltran  95 DildtGgTllaalelLkekgpeevriavlv 124
                                       Di++tGgT+  a+++L+  g++++ +++ +
  gi|488601050|ref|YP_007907521.1| 216 DIISTGGTVVQAIKALRHSGAKRIYAVCTH 245
                                       **********************99988876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   4.7e-09   1.7e-05     116     158 ..     204     243 ..     186     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.7e-09
                           UPRTase 116 PkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvls 158
                                       P ++++r v+l+D +i+TGg++++ai+ L+  g+  ++I  ++
  gi|488601050|ref|YP_007907521.1| 204 P-DVSNRDVVLVDDIISTGGTVVQAIKALRHSGA--KRIYAVC 243
                                       4.468999***********************776..5666554 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.4e-08   8.5e-05     120     157 ..     207     244 ..     198     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.4e-08
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvvvs 157
                                       +++ +vLvDD istG t+++ i+al+++  ++ y+v++
  gi|488601050|ref|YP_007907521.1| 207 SNRDVVLVDDIISTGGTVVQAIKALRHSGAKRIYAVCT 244
                                       5689***********************99999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 2316.23
//
Query:       gi|488601051|ref|YP_007907522.1|  [L=352]
Description: S-adenosylhomocysteine hydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-26   92.1   0.1    5.5e-26   91.6   0.1    1.2  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
    7.3e-10   38.5   0.1    2.4e-09   36.8   0.1    1.8  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    1.7e-05   24.2   0.0    5.3e-05   22.6   0.0    1.7  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      8e-05   22.3   0.0    0.00026   20.6   0.0    1.8  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    0.00014   22.1   0.3    0.00083   19.6   0.2    2.4  2  TrkA_N           TrkA-N domain
    0.00027   21.4   0.0     0.0006   20.2   0.0    1.6  1  NAD_binding_7    Putative NAD(P)-binding
     0.0016   18.5   0.0     0.0034   17.5   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0025   18.0   0.0      0.008   16.4   0.0    1.8  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0037   16.3   0.0     0.0074   15.3   0.0    1.5  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
      0.008   16.1   0.0      0.015   15.2   0.0    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.095   12.0   0.0       0.22   10.8   0.0    1.6  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.096   11.9   0.0       0.24   10.6   0.0    1.5  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
       0.11   13.0   0.0       0.34   11.4   0.0    1.8  2  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
       0.15   12.5   0.0       0.27   11.8   0.0    1.4  1  XdhC_C           XdhC Rossmann domain


Domain annotation for each model (and alignments):
>> 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 !   91.6   0.1   4.3e-29   5.5e-26       5     161 ..     147     296 ..     143     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 4.3e-29
                                       HCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SE CS
                     AdoHcyase_NAD   5 creslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadi 81 
                                       +   l+d++ r  ++ +  k a v+G+G vG Gca+ l++lG+ v v ++d i    a   G++v+ l+e ++++di
  gi|488601051|ref|YP_007907522.1| 147 TAFGLLDALVRL-NLYFPEKDAFVIGFGRVGEGCAEILRKLGCNVSVYDIDEIKCAIAEYSGYRVKDLQEGLSSSDI 222
                                       555678888885.578899**********************************9999******************** PP

                                       EEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHH CS
                     AdoHcyase_NAD  82 vvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlg 158
                                       +vt+tG + +i+  +++++k+ ai+cn+G    eidv  l+ +  +k++++ ++ ++  +  +   +l++   +nl+
  gi|488601051|ref|YP_007907522.1| 223 IVTATGRDSVIS--DFSTIKNGAILCNMGAGRYEIDVRRLKDY--RKITINEHITKY--ERDNYFYVLCDSMSVNLT 293
                                       *********996..79*************************99..666776666655..555677888888888888 PP

                                       TS- CS
                     AdoHcyase_NAD 159 cat 161
                                        a+
  gi|488601051|ref|YP_007907522.1| 294 MAN 296
                                       776 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 !   36.8   0.1   1.9e-12   2.4e-09      37     129 ..     165     251 ..     159     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.9e-12
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHH CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaee 113
                                       k   +iG+Gr+G+  a++l+++g++v +yd  + k + +e  g+++ +l+e l++sDi++ ++        +i  + 
  gi|488601051|ref|YP_007907522.1| 165 KDAFVIGFGRVGEGCAEILRKLGCNVSVYDIDEIKCAIAEYSGYRVKDLQEGLSSSDIIVTATGR----DSVI--SD 235
                                       56679***************************999998899999***************976552....2333..46 PP

                                       HHCSTTTEEEEESS-G CS
                      2-Hacid_dh_C 114 lakmkkgailiNtaRG 129
                                       ++ +k+gail N++ G
  gi|488601051|ref|YP_007907522.1| 236 FSTIKNGAILCNMGAG 251
                                       8999999999998877 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 !   22.6   0.0   4.1e-08   5.3e-05      18     112 ..     146     253 ..     137     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.1e-08
                                       HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHC.............TT-EEEEE-TTSCCHHHHHCCSS CS
                     THF_DHG_CYH_C  18 ctpkgvvellketgielegkkvvvvGrsnivgkplallLle.............knatVtvchsktkdlaeitread 81 
                                        t+ g ++ l + +    +k+++v+G ++ vg+  a +L +             k a+  +   + kdl+e ++++d
  gi|488601051|ref|YP_007907522.1| 146 GTAFGLLDALVRLNLYFPEKDAFVIGFGR-VGEGCAEILRKlgcnvsvydideiKCAIAEYSGYRVKDLQEGLSSSD 221
                                       5889999999999999999*******986.89999*999993433333333222233344444556*********** PP

                                       EEEE-SS-TT-B-G.GGS-TT-EEEE---EEC CS
                     THF_DHG_CYH_C  82 ivvvavGkpelika.emvkegavviDvGinrv 112
                                       i+v+a+G+ ++i+  + +k+ga++ ++G  r 
  gi|488601051|ref|YP_007907522.1| 222 IIVTATGRDSVISDfSTIKNGAILCNMGAGRY 253
                                       ************86589**********98776 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.8   3.5e+03      18      60 ..      18      62 ..      16      78 .. 0.61
   2 !   20.6   0.0     2e-07   0.00026       4      67 ..     164     226 ..     161     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.8
                                      HHHHHHHHTT--EEEEE-TT-H..HHHHHHHTT-EEEEHHHHHHT CS
                              IlvN 18 aqalnlrdsgldvvvglregsk..svkkAkeegfevltvaeavkk 60
                                      a ++ +rd+++ ++  l+ +++   ++  k   ++v++ +e ++k
  gi|488601051|ref|YP_007907522.1| 18 AVGNSIRDAKVSICFPLEYKTAvlAYELSKFCELRVTKFDEYTTK 62
                                      556677777777777776655423455555555556555555554 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2e-07
                                       TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE- CS
                              IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmil 67 
                                       +k   viG+G  G+  a+ lr  g++v v   ++  +++ A+ +g++v++++e  +++d++++ 
  gi|488601051|ref|YP_007907522.1| 164 EKDAFVIGFGRVGEGCAEILRKLGCNVSVYDIDEI-KCAIAEYSGYRVKDLQEGLSSSDIIVTA 226
                                       67778**********************99877766.8999********************9875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.2     8e+03      29      47 ..      61      79 ..      60      81 .. 0.81
   2 !   19.6   0.2   6.5e-07   0.00083       2      44 ..     168     210 ..     167     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.2
                                      SSHHHHHHHHHTTSEEEES CS
                            TrkA_N 29 kdeerveelreeglevvvg 47
                                      +++++ve l+++g+e++  
  gi|488601051|ref|YP_007907522.1| 61 TKPSAVEWLKDKGVEILSK 79
                                      5688999999999998765 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 6.5e-07
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEE CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglev 44 
                                        +iG+GrvG+  ae L++ g+ +v+v d de +++ ++  g++v
  gi|488601051|ref|YP_007907522.1| 168 FVIGFGRVGEGCAEILRKlGC-NVSVYDIDEIKCAIAEYSGYRV 210
                                       59****************999.5***********9999999876 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 !   20.2   0.0   4.7e-07    0.0006       5      90 ..     162     247 ..     158     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.7e-07
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele....elvklaeeelekdlegadlviaatddrelner 77 
                                       + +k   v+G G+v++  ++ l + g++v v++ +   e++    e   ++ ++l++ l+  d++++at ++++ + 
  gi|488601051|ref|YP_007907522.1| 162 FPEKDAFVIGFGRVGEGCAEILRKLGCNVSVYDID---EIKcaiaEYSGYRVKDLQEGLSSSDIIVTATGRDSVISD 235
                                       668999***************************99...66632323333778888999999********99998777 PP

                     NAD_binding_7  78 iaeaakarrilvn 90 
                                             +  il+n
  gi|488601051|ref|YP_007907522.1| 236 FSTIK-NGAILCN 247
                                       65443.3666666 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.6e-06    0.0034      12      96 ..     164     240 ..     155     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseep 88 
                                       ek + +iG G+++e  a+ L + g++ v v    ++  k    e++g+     ++++l+e l+++d++++at+  ++
  gi|488601051|ref|YP_007907522.1| 164 EKDAFVIGFGRVGEGCAEILRKLGCN-VSVYD--IDEIKCAIAEYSGY-----RVKDLQEGLSSSDIIVTATGRDSV 232
                                       78899********************9.77775..44444444555555.....9*******************9999 PP

                                       SB-HHHHH CS
                      Shikimate_DH  89 ilekeeve 96 
                                       i + + ++
  gi|488601051|ref|YP_007907522.1| 233 ISDFSTIK 240
                                       87766665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.6   3.3e+03      28      62 ..      59      95 ..      51     116 .. 0.76
   2 !   16.4   0.0   6.2e-06     0.008       4     103 ..     169     262 ..     166     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
                                      E-SSHHHHHHHHHTTEEE-SSHHHHHHHC..SEEEE- CS
                     NAD_binding_2 28 ynrtkekveelvaegakaaesieelvasl..dvvitm 62
                                      y  ++++ve l ++g++++++ e l+a+   d+v ++
  gi|488601051|ref|YP_007907522.1| 59 YTTKPSAVEWLKDKGVEILSKDECLTADYymDCVAML 95
                                      5677888999999999999998888877766666554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.2e-06
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglleal 80 
                                       +iG G  G+  a+ l k g++v+vy+ ++ k+  +  +    +++++e ++s d+++t        d+vi++ ++++
  gi|488601051|ref|YP_007907522.1| 169 VIGFGRVGEGCAEILRKLGCNVSVYDIDEIKCAIAEYS-GYRVKDLQEGLSSSDIIVTATGR----DSVISD-FSTI 239
                                       8***************************9888766555.55788999999999***998877....566666.5667 PP

                                       -TT-EEEE-S---HHHHHHHHHH CS
                     NAD_binding_2  81 kkgdilidgstsspedtrelake 103
                                       k+g+il +++   +e   ++ k+
  gi|488601051|ref|YP_007907522.1| 240 KNGAILCNMGAGRYEIDVRRLKD 262
                                       77777777777777766666655 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 !   15.3   0.0   5.8e-06    0.0074     184     227 ..     210     253 ..     165     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.8e-06
                                       ECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--ST CS
                   OCD_Mu_crystall 184 ckseeeavegadivvtvTaakapilkaewvkpGahinavgadap 227
                                       +k+ +e  +  di+vt+T  ++ i   + +k+Ga ++ +ga++ 
  gi|488601051|ref|YP_007907522.1| 210 VKDLQEGLSSSDIIVTATGRDSVISDFSTIKNGAILCNMGAGRY 253
                                       6899999**********************************986 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   1.1e-05     0.015       4      36 ..     169     201 ..     166     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHH CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseeale 36 
                                       viG G +G+g a+++ + g++V ++di+e + +
  gi|488601051|ref|YP_007907522.1| 169 VIGFGRVGEGCAEILRKLGCNVSVYDIDEIKCA 201
                                       9**************************986654 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.22      31      73 ..     167     209 ..     162     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTC CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgak 73 
                                        +viG G +G   +++ ++lg +V v+D+++ +    e  g +
  gi|488601051|ref|YP_007907522.1| 167 AFVIGFGRVGEGCAEILRKLGCNVSVYDIDEIKCAIAEYSGYR 209
                                       69***************************98877766665555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.24     113     175 ..     134     196 ..     127     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                       BCTCTTC.TTBEECCS.ECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSS CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 113 dlgipGvaenvgklvr.tldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveard 175
                                       d +i+G++en +      ld   +l+l   +k++ v+G G +G  +A  l+klg++v + ++ d
  gi|488601051|ref|YP_007907522.1| 134 DSNIKGLGENRHGTAFgLLDALVRLNLYFPEKDAFVIGFGRVGEGCAEILRKLGCNVSV-YDID 196
                                       6688888666655543045555677777777**************************95.4444 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         4   5.2e+03      33      57 ..      53      77 ..      36      99 .. 0.54
   2 ?   11.4   0.0   0.00026      0.34      23      88 ..     180     240 ..     177     262 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4
                                      EEEE-SSTHHCCCCHHGGBTCCEEE CS
                    UDPG_MGDP_dh_C 33 vkiyDPkvkeeaveaeleekgvevv 57
                                      v+ +D ++++  + + l++kgve++
  gi|488601051|ref|YP_007907522.1| 53 VTKFDEYTTKPSAVEWLKDKGVEIL 77
                                      4444444444444444444555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                                       HHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHH CS
                    UDPG_MGDP_dh_C  23 ieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklk 88 
                                       +e L++ g++v++yD    + a+++    ++   v++l+e l+++d+iv +t  d   + d++++k
  gi|488601051|ref|YP_007907522.1| 180 AEILRKLGCNVSVYDIDEIKCAIAE----YSGYRVKDLQEGLSSSDIIVTATGRDSVIS-DFSTIK 240
                                       6789999********9766666665....56667789***************9876655.555444 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.27       2      35 ..     168     206 ..     167     260 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-G.GGG....- CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpre.efa....t 35 
                                       +++G g v++ +a+++++lg++v+v+d +e + a    +
  gi|488601051|ref|YP_007907522.1| 168 FVIGFGRVGEGCAEILRKLGCNVSVYDIDEiKCAiaeyS 206
                                       589************************999555444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2616.71
//
Query:       gi|488601052|ref|YP_007907523.1|  [L=480]
Description: yjeF C-terminal region, hydroxyethylthiazole kinase-related/yjeF N-terminal region [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-43  146.8   0.1      1e-42  146.3   0.1    1.2  1  Carb_kinase  Carbohydrate kinase
      2e-42  145.0   0.1    2.4e-40  138.2   0.0    2.5  3  YjeF_N       YjeF-related protein N-terminus
    9.4e-05   21.9   0.0     0.0034   16.8   0.0    2.2  2  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 !  146.3   0.1   1.7e-46     1e-42       1     243 [.     236     470 ..     236     471 .. 0.90

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 1.7e-46
                                       EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT.....HTTTS....--SSS-SEE CS
                       Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll.....edeqa.kileklerldav 71 
                                       vl++gG  +ytGA+ laalaal++ga++v+ a+ +  +  +   +p++iv  l+     e ++  +i e+ ++ d++
  gi|488601052|ref|YP_007907523.1| 236 VLIVGG-GEYTGAPALAALAALHSGADIVTLAVPESIKDIVAGFSPNLIVRGLKgsrisE-SNIqEIDELIKKHDVL 310
                                       567777.9**********************************************999954.44459999******** PP

                                       EE-TT-SSSHCHHHHCHHHCCCCS-.EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHH CS
                       Carb_kinase  72 viGpGLgrdekikklleevlekdep.lviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlela 147
                                       v+G+G g ++   ++ ee+l+  +   v+DA+++++         ++ + i+TPh +Efkr ++   ++ed+    +
  gi|488601052|ref|YP_007907523.1| 311 VMGMGIGDKDF-VEISEEILKGSVRrAVLDAEAITKDVP------ENVKCIITPHFGEFKRVFGRTPENEDE----V 376
                                       *******9988.78999999988888*******976444......47899*****************55444....6 PP

                                       HHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHH CS
                       Carb_kinase 148 relaqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasde 224
                                       + +a+k + ++llk +kd+i + ++++  n+ g+s++++GG+GDvLaG++gal++ +  ++ +a a+a+++g a+d 
  gi|488601052|ref|YP_007907523.1| 377 KSFAKKHGITILLKSKKDIISD-GEKIRVNESGNSGMTVGGTGDVLAGIVGALFCHAD-PLWSASASAFINGLAGDI 451
                                       78999************98877.99***************************998766.999999************ PP

                                       HCCCT-TS-HCHHHHHHHC CS
                       Carb_kinase 225 aaekkgvgmlatelskiip 243
                                        +e+ g+ ++a +++++ip
  gi|488601052|ref|YP_007907523.1| 452 CFEEFGYNYTALDMLRKIP 470
                                       *******999999999887 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 !  138.2   0.0   4.1e-44   2.4e-40       3     171 .]      29     187 ..      27     187 .. 0.89
   2 !    3.7   0.3    0.0083        50      26      58 ..     233     265 ..     207     276 .. 0.75
   3 ?   -1.1   0.0      0.26   1.5e+03      88     127 ..     265     305 ..     256     308 .. 0.71

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 4.1e-44
                            YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeee.kldedaeralell 78 
                                       +Lmenagr++ae +r+      ++kk+l++ G gnnGgd+++a rhL  +g+++tv+ll +e+   ++ a+r+++l 
  gi|488601052|ref|YP_007907523.1|  29 QLMENAGRGLAEEIRKFG----KDKKILIFSGLGNNGGDAFVAVRHL--RGFDITVFLLGKESeIKTDIAKRNFQLI 99 
                                       8*****************....9************************..8999999666666527777788999999 PP

                            YjeF_N  79 kkaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgt 155
                                       kk+       +p+ +l+     + d+++DA+lG+g++g lre++ +++e +nss+++v+avD+P Gl++dtG+++ +
  gi|488601052|ref|YP_007907523.1| 100 KKVCRIKEIRNPDIELD----DEFDIIVDAMLGTGVKGRLREPYSTAVELINSSDSFVVAVDVPTGLNPDTGEYD-I 171
                                       88655555566666665....579***************************************************.9 PP

                            YjeF_N 156 avkadvtvtfgapkrg 171
                                       +v advt+tf+  k+g
  gi|488601052|ref|YP_007907523.1| 172 CVIADVTITFHKYKPG 187
                                       999*********9997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0083
                            YjeF_N  26 ekkvlvlvGsgnnGgdglaaArhLaqegak.Vtv 58 
                                         +vl++ G+  +G+ +laa + L+  ga+ Vt+
  gi|488601052|ref|YP_007907523.1| 233 HGRVLIVGGGEYTGAPALAALAALH-SGADiVTL 265
                                       55788888888*************5.55552544 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.26
                            YjeF_N  88 ekpeedleekls.apvdlviDAllGiglrgelreelaelie 127
                                          +e+ ++     +++l++ +l G+ ++++  +e+ eli+
  gi|488601052|ref|YP_007907523.1| 265 LAVPESIKDIVAgFSPNLIVRGLKGSRISESNIQEIDELIK 305
                                       44455444333367799**********99888888999987 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.012        69      18      66 ..     274     323 ..     268     339 .. 0.83
   2 !   16.8   0.0   5.7e-07    0.0034     143     208 ..     375     438 ..     367     458 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.012
                                       TTHHHHHHHHH.HHT-EEEE--STTTHHHHHHTSSEEEEE-TT--HHHHH CS
                                HK  18 VaqnfsANvll.AlgaSPimseaeeEvselakianaLllNiGtleekaie 66 
                                       +++ fs N ++  l +S i   + +E++el k  + L++ +G+ ++  +e
  gi|488601052|ref|YP_007907523.1| 274 IVAGFSPNLIVrGLKGSRISESNIQEIDELIKKHDVLVMGMGIGDKDFVE 323
                                       677888887764699999999*******************9997776555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5.7e-07
                                       HHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHH CS
                                HK 143 avqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaa 208
                                        v++ A+k ++++++  + D++sdg+k+ + ++G++ ++ + ++G +l+ +v+a      d+l +a
  gi|488601052|ref|YP_007907523.1| 375 EVKSFAKKHGITILLKSKKDIISDGEKIRVNESGNSGMT-VGGTGDVLAGIVGALFCH-ADPLWSA 438
                                       68999********************************97.9***********997654.4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 3171.19
//
Query:       gi|488601053|ref|YP_007907524.1|  [L=171]
Description: Conserved protein/domain typically associated with flavoprotein oxygenase, DIM6/NTAB family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-22   78.2   0.0    8.5e-22   77.9   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   4.7e-26   8.5e-22       9     142 ..      11     143 ..       4     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 4.7e-26
                                       EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCCCC CS
                     Flavin_Reduct   9 avvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprtddk 85 
                                       +++++    ++p+ +t+ ++++ls++P l++++++++++t + + e++efv+ +   +  + ++  ++ sg  ++dk
  gi|488601053|ref|YP_007907524.1|  11 YLIVA--GVEKPNVMTADWVVPLSFNPKLLGVAIGNQRYTKKLIDENKEFVVAVPTIELLKDVWTAGTVSG-ANKDK 84 
                                       66666..4688999****************************************99988887777777788.999** PP

                                       CCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTT.ECTT CS
                     Flavin_Reduct  86 sifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgdd.adee 142
                                       s++  lt  +s ++  p ++++ a+leC+vv+ v+ gdh+ ++ge+++++ gd+ ad++
  gi|488601053|ref|YP_007907524.1|  85 SELLSLTFVKSeKVSTPSIKECQANLECRVVDAVQTGDHTFYVGEILHASEGDGfADGK 143
                                       ****999999989999***********************************99977755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1223.55
//
Query:       gi|488601054|ref|YP_007907525.1|  [L=123]
Description: putative proteins of PilT N-term/Vapc superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-24   85.1   0.1    4.8e-24   84.9   0.1    1.0  1  PIN_9     PIN like domain
    1.5e-07   31.7   1.3    0.00052   20.3   0.5    2.1  2  PIN_4     PIN domain
    2.9e-06   27.8   0.7      1e-05   26.0   0.7    1.7  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.02   14.7   0.1      0.025   14.3   0.1    1.1  1  DUF4895   Domain of unknown function (DUF4895)
      0.032   14.5   0.1        6.5    7.0   0.1    2.1  2  PIN_2     PIN domain
      0.062   13.8   0.6      0.098   13.1   0.5    1.3  1  PIN_12    PIN domain
       0.11   12.6   0.1       0.18   12.0   0.1    1.2  1  HSR       HSR domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.1   1.9e-27   4.8e-24       2     115 ..       4     114 ..       3     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.9e-27
                             PIN_9   2 ilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaDd 78 
                                       +lDtn+L+  v+ ++d +e l+   g + +++p++vl+ELe+l+++ +gke+  ak+al++a+r e+v+++ +++D+
  gi|488601054|ref|YP_007907525.1|   4 CLDTNFLIYCVKQKIDFVELLRDN-GFNSIIIPESVLHELEKLVSELRGKEKVFAKIALEMAKRFEVVDTK-SSGDE 78 
                                       79**************99888888.**********************************************.***** PP

                             PIN_9  79 ailelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                       a++e+  + d++ + TnDr L +++++ gi++ ++R+
  gi|488601054|ref|YP_007907525.1|  79 ALIEVCLKRDCHLF-TNDRRLIRKARDLGIKTGYVRG 114
                                       **************.****************999996 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.5     2e-07   0.00052       3      42 ..       5      50 ..       3      72 .. 0.84
   2 !   11.2   0.0   0.00013      0.34      84     127 ..      73     109 ..      47     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2e-07
                             PIN_4  3 lDTnvlLhdpealksf......keehdvviPitVleELdklKkgss 42
                                      lDTn+l+++++    f      ++ + ++iP  Vl+EL+kl ++ +
  gi|488601054|ref|YP_007907525.1|  5 LDTNFLIYCVKQKIDFvellrdNGFNSIIIPESVLHELEKLVSELR 50
                                      9*********9877789999*999***************9977665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                             PIN_4  84 seknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                       +++ D++ ++v+l       +r++ L+++D+ l  kA+ lgi++
  gi|488601054|ref|YP_007907525.1|  73 KSSGDEALIEVCL-------KRDCHLFTNDRRLIRKARDLGIKT 109
                                       4455666666665.......456679****************87 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.7   4.1e-09     1e-05       2     107 ..       4     108 ..       3     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.1e-09
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN   2 vlDTsvliallrgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidae 76 
                                       +lDT++li+ ++ + +    ++ll +   + +++++ vl El   ++   ++ +++   + +l+ +++++++++ ++
  gi|488601054|ref|YP_007907525.1|   4 CLDTNFLIYCVKQKIDF---VELLRDNgfNSIIIPESVLHELEKLVSE--LRGKEKVFAKIALEMAKRFEVVDTKSS 75 
                                       9**********999999...555555557*******************..777777777777777********9999 PP

                                       HHHHHHHHHHHHH..SBHHHHHHHHHHHHHT-E CS
                               PIN  77 iaeeaaeialkyg..llpnDaliaAtAkehgik 107
                                         e   e+ lk++  l +nD  ++  A+  gik
  gi|488601054|ref|YP_007907525.1|  76 GDEALIEVCLKRDchLFTNDRRLIRKARDLGIK 108
                                       9999999999999999*****999999999887 PP

>> DUF4895  Domain of unknown function (DUF4895)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   9.9e-06     0.025     136     192 ..      14      68 ..       7      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.9e-06
                           DUF4895 136 nekklkiari.llsdegvnvlvipesvdeefrsLlaEivrvlrkkyGaanlskakyfa 192
                                        ++k+++  + ll+d+g n ++ipesv +e  +L++E+    +    +  l+ ak+f 
  gi|488601054|ref|YP_007907525.1|  14 VKQKIDF--VeLLRDNGFNSIIIPESVLHELEKLVSELRGKEKVFA-KIALEMAKRFE 68 
                                       5789999..449*************************976443333.33688899996 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0025       6.5       2      61 ..       5      64 ..       4      75 .. 0.73
   2 ?    6.4   0.0    0.0038       9.7      92     117 ..      75     100 ..      58     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                             PIN_2  2 vdaNivvsallksrikkrli.lvekaleliapeeaveeiekhkealvkksklseeeleell 61
                                      +d+N ++ ++ + +i   ++   + + ++i+pe +++e+ek +++l  k+k+ ++ + e++
  gi|488601054|ref|YP_007907525.1|  5 LDTNFLIYCVKQ-KIDFVELlRDNGFNSIIIPESVLHELEKLVSELRGKEKVFAKIALEMA 64
                                      689999988664.55544440455678899***********99999988887766665554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0038
                             PIN_2  92 pdDtpfvAlaLlleapiWTeDkdlig 117
                                       + D   + + L+ ++ + T+D+ li 
  gi|488601054|ref|YP_007907525.1|  75 SGDEALIEVCLKRDCHLFTNDRRLIR 100
                                       4577888999*************994 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   3.8e-05     0.098       2      60 ..       4      57 ..       4      88 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                            PIN_12  2 fiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkieeskkle 60
                                      ++DTn+++    + + +  + +l  l ++g  ++i+p+ vl+E++k +++   + k + 
  gi|488601054|ref|YP_007907525.1|  4 CLDTNFLIY-CVKQKID--FVEL--LRDNGFNSIIIPESVLHELEKLVSELRGKEKVFA 57
                                      79******4.6665555..5555..7888889*************99877777663333 PP

>> HSR  HSR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.9e-05      0.18      18      70 ..      12      68 ..       9      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                               HSR 18 saikkpfpflegLrDksl....itekmykesleacrnlvpvqkvvYnvLseLektfs 70
                                      +++k+   f+e LrD+ +    i+e +++e ++  ++l + +kv+ ++  e+ k+f+
  gi|488601054|ref|YP_007907525.1| 12 YCVKQKIDFVELLRDNGFnsiiIPESVLHELEKLVSELRGKEKVFAKIALEMAKRFE 68
                                      799************98555559*********************9999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 844.94
//
Query:       gi|488601055|ref|YP_007907526.1|  [L=407]
Description: translation initiation factor 2 subunit gamma (aeIF-2g) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  109.8   0.9    1.5e-31  108.4   0.9    1.8  1  eIF2_C        Initiation factor eIF2 gamma, C terminal
      3e-27   95.4   2.3    3.2e-26   92.1   2.3    2.1  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.7e-09   38.0   0.4    5.9e-09   36.2   0.4    2.0  1  GTP_EFTU_D2   Elongation factor Tu domain 2
     0.0014   18.7   0.0     0.0031   17.6   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0015   18.4   0.5      0.022   14.7   0.2    2.2  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.038   13.7   0.5        7.3    6.3   0.0    2.7  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.065   11.1   0.0      0.095   10.6   0.0    1.1  1  PolC_DP2      DNA polymerase II large subunit DP2
      0.093   12.8   0.1       0.19   11.8   0.1    1.4  1  Nop10p        Nucleolar RNA-binding protein, Nop10p family
       0.12   12.4   0.1       0.29   11.1   0.1    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.42   10.1   3.2         20    4.7   0.0    3.1  3  FeoB_N        Ferrous iron transport protein B


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 !  108.4   0.9   8.6e-35   1.5e-31       3      86 .]     323     406 ..     321     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 8.6e-35
                                       EEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEE CS
                            eIF2_C   3 leieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWr 79 
                                       +++e++lle++vg++ee  vek+k +E+Lml++G+a+t gvvts+++d+++vkLk+Pvcae+g ++a+sRr+++rWr
  gi|488601055|ref|YP_007907526.1| 323 FTMEVKLLEKVVGTEEEIVVEKIKMNEPLMLSVGTATTLGVVTSARDDVIEVKLKRPVCAEEGWNVAVSRRIGSRWR 399
                                       79*************************************************************************** PP

                                       EEEEEEE CS
                            eIF2_C  80 LiGwGei 86 
                                       LiG G+i
  gi|488601055|ref|YP_007907526.1| 400 LIGAGTI 406
                                       *****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 !   92.1   2.3   1.8e-29   3.2e-26       4     193 ..      12     200 ..      10     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 1.8e-29
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig++ghvDhGKtTL+ +L                   +D+++eE +rgi+i    + +                 
  gi|488601055|ref|YP_007907526.1|  12 VNIGMVGHVDHGKTTLVAALSG---------------VWTDRHSEELKRGISIRLGYADTTfrrcpedgeytvervc 73 
                                       79******************82...............2478888999999999998888877899999999999999 PP

                                       .....TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGS CS
                          GTP_EFTU  65 .....ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDr 134
                                            +++  ++++++D+PGH+  + ++  g++ +Dgavlv++a+e  + pqt+e+l  ++  gv  i+++ NK+  
  gi|488601055|ref|YP_007907526.1|  74 pkhnvETEILRTVSFVDSPGHETLMATMLSGAALMDGAVLVIAANEKcPRPQTKEHLMALNIIGVDkIVIAQNKIEI 150
                                       987655677799*********************************9879****************999********* PP

                                       T.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 135 l.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       + k+++ e  +e++ ++      ++  +++   + p++++Sa +  +++ l+ea+ e +p
  gi|488601055|ref|YP_007907526.1| 151 VsKERVLENYREIQ-EF------IKGTVAE---DAPIIPISAQQRVNIDVLIEAIEERIP 200
                                       *9999999999999.66......5555544...57********************99887 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.4   3.3e-12   5.9e-09       1      73 [.     232     310 ..     232     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.3e-12
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE...EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS...GSSTT CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke...ivtrissletfhededeavaganaGvivaikgled...aiivG 70 
                                       G+v +g++ +G++++Gde+++++  ++++ +    +++++s+ ++ ++++ea +g+ +G+ +++++  +   a + G
  gi|488601055|ref|YP_007907526.1| 232 GGVLGGSLARGKIRVGDEIEVRPgIKDDRGNwnpVTSEVTSIMASGKNVEEATPGGLVGISTRLDPRLTksdA-LSG 307
                                       8899*******************88776666*********************************998776644.777 PP

                                       CEE CS
                       GTP_EFTU_D2  71 dtl 73 
                                       ++l
  gi|488601055|ref|YP_007907526.1| 308 NVL 310
                                       766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.7e-06    0.0031       1      98 [.      13     130 ..      13     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..ETTEE.........................EE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..lkgke.........................ie 49 
                                       +++ vG+   GK+tL+ al+g  + + s++    + i+ g  +  ++  +                         + 
  gi|488601055|ref|YP_007907526.1|  13 NIGMVGHVDHGKTTLVAALSGVwTDRHSEELKRGISIRLGYADttFR--RcpedgeytvervcpkhnveteilrtVS 87 
                                       5899****************965555555555555555554442222..12233444455555566666666666** PP

                                       EEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHH CS
                          MMR_HSR1  50 lvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeele 98 
                                       +vD pG  e       l  ++l+    +d ++lv+ a+e+  +p+ +e  
  gi|488601055|ref|YP_007907526.1|  88 FVDSPG-HE------TLMATMLSGAAlMDGAVLVIAANEKCPRPQTKEHL 130
                                       ******.54......78888888666579999999988444444444433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.12   2.2e+02     104     137 ..      16      46 ..       9      49 .. 0.80
   2 !   14.7   0.2   1.2e-05     0.022      13     101 ..     105     199 ..      79     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                                       EECSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrG 137
                                       +vG+   GK+tL+ al +     t   se+l+rG
  gi|488601055|ref|YP_007907526.1|  16 MVGHVDHGKTTLVAALSGV---WTDRHSEELKRG 46 
                                       7899999*********986...666666666666 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.2e-05
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllv 82 
                                       +a +d +++v++++ +++   + +  L++++  g+ ++vi+ nKi+++++e+      e++e+ + + a + +++ +
  gi|488601055|ref|YP_007907526.1| 105 AALMDGAVLVIAAN-EKCPRPQTKEHLMALNIIGVdKIVIAQNKIEIVSKERvlenyrEIQEFIKGTVAEDAPIIPI 180
                                       8899**********.666666677778888888887999************999988888888888999999***** PP

                                       -TTTHTTHHHHHHHCTTSE CS
                       RsgA_GTPase  83 saktkegleelkellkdkt 101
                                       sa+++ +++ l e++++++
  gi|488601055|ref|YP_007907526.1| 181 SAQQRVNIDVLIEAIEERI 199
                                       ********99999998765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0041       7.3       4      23 ..      14      33 ..      12      45 .. 0.87
   2 ?    4.5   0.4     0.015        27      40     141 ..      88     195 ..      79     197 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0041
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      i ++G+v+ GKttL  al+g
  gi|488601055|ref|YP_007907526.1| 14 IGMVGHVDHGKTTLVAALSG 33
                                      5589*************997 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                         PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGiitkidlaedeenieaveelLk 116
                                       ++D+PG    +++l+ ++ + +a  d  +lv +a +e++  p++  ++++ ++iG+  ki +a+++ +i   e+ L+
  gi|488601055|ref|YP_007907526.1|  88 FVDSPG----HETLMATMLSGAALMDGAVLVIAA-NEKCPRPQTKEHLMALNIIGV-DKIVIAQNKIEIVSKERVLE 158
                                       567777....455666666666667766666655.456788999999999999995.45555544444433333333 PP

                         PduV-EutP 117 s..........aGa..ekifevsavekegieellkyl 141
                                       +            a  + i+ +sa ++++i+ l++ +
  gi|488601055|ref|YP_007907526.1| 159 NyreiqefikgTVAedAPIIPISAQQRVNIDVLIEAI 195
                                       2000000010022211335666666666666666655 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 ?   10.6   0.0   5.3e-05     0.095     615     757 ..      55     197 ..      37     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.3e-05
                          PolC_DP2 615 eiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklgeree 691
                                       + + r+C++ g+ t+e+ C++ + +te   + + +++  +e  +  + + a  ++   + + +  +    + +e + 
  gi|488601055|ref|YP_007907526.1|  55 DTTFRRCPEDGEYTVERVCPKHNVETEILRTVSFVDSPGHETLMATMLSGAALMDGAVLVIAANEKCPRPQTKE-HL 130
                                       66789******************9**999999999888876666665555555555555555554444555555.44 PP

                          PolC_DP2 692 kleelkgvkgltskekipEpleKg.ilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklre 757
                                          ++ gv++++  ++ +E + K  +l + +++  f  gtv  D+  +p+++ +  +i+v +e ++e
  gi|488601055|ref|YP_007907526.1| 131 MALNIIGVDKIVIAQNKIEIVSKErVLENYREIQEFIKGTVAEDAPIIPISAQQRVNIDVLIEAIEE 197
                                       667889****9999999999998549**********************************9998765 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 ?   11.8   0.1    0.0001      0.19       5      28 ..      58      81 ..      55      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                      -EE-TTT--EESSSB-TTT-SB-B CS
                            Nop10p  5 lrkcgkcrvYTLkkvcpecggptk 28
                                       r+c+++++YT + vcp+ + +t+
  gi|488601055|ref|YP_007907526.1| 58 FRRCPEDGEYTVERVCPKHNVETE 81
                                      699**************9888886 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 ?   11.1   0.1   0.00016      0.29      58     100 ..     141     195 ..     135     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                      MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                        +++ NKi  +s+e + e +re              +++iSa++++n+d L e+i
  gi|488601055|ref|YP_007907526.1| 141 IVIAQNKIEIVSKERVLENYREiqefikgtvaedAPIIPISAQQRVNIDVLIEAI 195
                                       567889999999988877777667788888887668999*************998 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 ?    4.7   0.0     0.011        20       2      23 ..      13      34 ..      12      37 .. 0.90
   2 ?    4.6   0.4     0.012        21     106     156 .]     139     195 ..      67     195 .. 0.85
   3 ?   -1.7   0.0         1   1.8e+03      23      43 ..     256     276 ..     252     283 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                                      EEEEEESTTSSHHHHHHHHHTT CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                      ++ +vG  + Gkttl+ al+g+
  gi|488601055|ref|YP_007907526.1| 13 NIGMVGHVDHGKTTLVAALSGV 34
                                      6889***************996 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.012
                                       SSEEEEEETHHHHHHTTEEE-HHHHHHHH......TS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekL......gvpvvktsakkkegieellkai 156
                                        ++v+a n+i+ ++k+++  + ++++e +      + p++++sa+++ +i+ l++ai
  gi|488601055|ref|YP_007907526.1| 139 DKIVIAQNKIEIVSKERVLENYREIQEFIkgtvaeDAPIIPISAQQRVNIDVLIEAI 195
                                       3689999**********9999999999884333334899***********9999876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1
                                       TSEEEEESTTSSSEEEEEEEE CS
                            FeoB_N  23 akqkvgNwpGvtvekkegklk 43 
                                        k + gNw  vt e ++   +
  gi|488601055|ref|YP_007907526.1| 256 IKDDRGNWNPVTSEVTSIMAS 276
                                       566779******998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2713.54
//
Query:       gi|488601056|ref|YP_007907527.1|  [L=304]
Description: thioredoxin reductase (NADPH) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-54  184.3   3.1    3.5e-54  184.0   3.1    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.7e-26   91.5   5.5    1.1e-23   84.0   0.6    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    5.3e-19   68.5   2.9    2.4e-16   60.0   0.2    2.8  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.3e-10   39.2   3.7    0.00097   18.3   0.1    4.0  4  FAD_binding_2   FAD binding domain
    1.6e-09   37.0   1.7      0.004   15.9   0.0    3.1  3  HI0933_like     HI0933-like protein
    4.1e-09   36.0   1.6    0.00016   20.9   0.1    3.3  3  GIDA            Glucose inhibited division protein A
    1.7e-07   31.2   5.0       0.12   11.9   0.1    3.3  3  DAO             FAD dependent oxidoreductase
    9.9e-07   28.9   0.1     0.0011   19.2   0.0    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.9e-06   27.4   0.1      0.012   14.8   0.0    2.4  2  FAD_binding_3   FAD binding domain
    1.3e-05   24.6   2.4     0.0002   20.7   0.0    2.7  2  Thi4            Thi4 family
    1.5e-05   24.3   0.1     0.0049   16.1   0.0    2.4  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    2.4e-05   24.7   0.9    0.00013   22.3   0.1    2.4  2  NAD_binding_7   Putative NAD(P)-binding
    3.3e-05   23.4   1.8    0.00068   19.1   0.2    2.4  3  FAD_oxidored    FAD dependent oxidoreductase
    8.6e-05   21.7   1.1       0.22   10.6   0.0    3.0  3  Lycopene_cycl   Lycopene cyclase protein
    0.00023   20.8   0.0    0.00045   19.8   0.0    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0021   17.4   0.3       0.66    9.2   0.1    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0022   17.5   0.0       0.13   11.6   0.0    2.3  2  PALP            Pyridoxal-phosphate dependent enzyme
     0.0054   17.2   0.0       0.99    9.9   0.0    2.5  2  XdhC_C          XdhC Rossmann domain
     0.0056   15.6   0.6        0.8    8.5   0.1    2.3  2  Trp_halogenase  Tryptophan halogenase
     0.0086   15.4   0.1       0.31   10.4   0.0    2.2  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.016   15.2   0.2      0.079   13.0   0.0    2.1  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.018   13.8   0.0      0.025   13.3   0.0    1.2  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
       0.03   14.3   0.2        1.9    8.5   0.0    2.6  2  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.0   3.1   4.5e-57   3.5e-54       1     294 []       4     289 ..       4     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 184.0 bits;  conditional E-value: 4.5e-57
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHC...C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx...x RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllg...e 73 
                                       +d++++G+GpAG +aa++ a++g+kv+ +  e   +  +  l+++++++++++    e v+k++++ i++ ++   e
  gi|488601056|ref|YP_007907527.1|   4 YDLIIVGAGPAGSTAAIYGARYGLKVAFF--ESVDPVSQLTLTPVIENFPGFEGNGFELVQKIKEQaIRFGAEhkyE 78 
                                       689**************************..777799**************99877788999988867777776656 PP

                                       TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGg 150
                                       +v +i++ + ++ +   + + e+++ ++++++AtG++ + lgipG++e vg++v++++++++     ++  +vv+Gg
  gi|488601056|ref|YP_007907527.1|  79 NVDSIEKRENRFIV---R-SGENEYSAKAVIIATGGRHKELGIPGEKEFVGRGVSYCATCDGNFFRGKK--VVVIGG 149
                                       67777788888888...3.45689**************************************9988887..****** PP

                                       SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx. RF
                       Pyr_redox_2 151 GyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgee. 225
                                       G+++   A++l+++g++v +v++rd+l       + +a ++++ k+G+ v +++ +++i+g++  +e  +l ++ e 
  gi|488601056|ref|YP_007907527.1| 150 GNTAATEAIYLKEIGCDVSIVHRRDELR------ADKAHQNEIFKRGIPVIWNSIPVRIEGKDV-VErIILYNKVEd 219
                                       ***************************7......899999***********************9.555444444444 PP

                                       ....EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 226 ....idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                           +d++ v++a+G+ p t+++  +lg+e+d+rg+i v+++++t+v+g++a+GD++   + +++a +A   G
  gi|488601056|ref|YP_007907527.1| 220 refaVDVSAVFIAIGINPATQIV-ANLGVEMDSRGYIIVNKNQETSVQGVFAAGDCC--NNPLKQAITAAGDG 289
                                       5688*******************.*********************************..88888998887765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.4   0.00048      0.37       1      35 [.       7      40 ..       7      69 .. 0.75
   2 !   84.0   0.6   1.4e-26   1.1e-23      99     305 .]      75     272 ..      73     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00048
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnigns 35
                                      iI+GaGPaG +aai   + gl ++   E    +  
  gi|488601056|ref|YP_007907527.1|  7 IIVGAGPAGSTAAIYGARYGL-KVAFFESVDPVSQ 40
                                      8*************9999999.5777776655555 PP

  == domain 2  score: 84.0 bits;  conditional E-value: 1.4e-26
                       Pyr_redox_3  99 klfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvvViGg 172
                                       +++e+V s++k ++ f+v++ +++y+Ak viiAtG   + + l+ipGe++     + y    + + ++g+kvvViGg
  gi|488601056|ref|YP_007907527.1|  75 HKYENVDSIEKRENRFIVRSGENEYSAKAVIIATGG--RHKELGIPGEKEfvgRGVSYCATCDGNFFRGKKVVVIGG 149
                                       5789*******************************8..88999*****98544456666667888899********* PP

                       Pyr_redox_3 173 knSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvkt 249
                                       +n+a+  A+ l + g++V++v+r++e+++++++ +     + +  +  ++++  ++++ +  v++i   ++   v  
  gi|488601056|ref|YP_007907527.1| 150 GNTAATEAIYLKEIGCDVSIVHRRDELRADKAHQN----EIFKRGIPVIWNSIPVRIEGKDVVERIILYNK---V-- 217
                                       **************************999864444....34444444444443488999999999986532...3.. PP

                       Pyr_redox_3 250 edgkkvev.kddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       ed +++ v  + v++a+G +p ++++++ ++e d+ g++ ++++ +et v+g+f aG
  gi|488601056|ref|YP_007907527.1| 218 ED-REFAVdVSAVFIAIGINPATQIVANLGVEMDSRGYIIVNKN-QETSVQGVFAAG 272
                                       33.3444413566777*************************987.6788******99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0     0.006       4.7       2      31 ..       6      35 ..       5      43 .. 0.89
   2 ?   -1.7   0.0       5.8   4.5e+03      46      71 ..      60      85 ..      57      93 .. 0.75
   3 !   60.0   0.2   3.1e-19   2.4e-16       1      78 [.     143     213 ..     143     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.006
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      +++vG+G  g  +A + a++g kV  +e  
  gi|488601056|ref|YP_007907527.1|  6 LIIVGAGPAGSTAAIYGARYGLKVAFFESV 35
                                      68**********************988865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.8
                                      HHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox 46 lqeklekngievllntkveeiegsed 71
                                      l +k++++ i++  ++k e+++  e+
  gi|488601056|ref|YP_007907527.1| 60 LVQKIKEQAIRFGAEHKYENVDSIEK 85
                                      56788888899988888888875554 PP

  == domain 3  score: 60.0 bits;  conditional E-value: 3.1e-19
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       kvvv+GgG+++  +A +l+e+g++V++v+r+d+l+      a k+ q+++ k+gi v++n+ +++ieg++  ve++ 
  gi|488601056|ref|YP_007907527.1| 143 KVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELR------ADKAHQNEIFKRGIPVIWNSIPVRIEGKDV-VERII 212
                                       79*********************************......**************************9998.88887 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       l
  gi|488601056|ref|YP_007907527.1| 213 L 213
                                       7 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.2e-06   0.00097       1      33 [.       5      37 ..       5      43 .. 0.92
   2 !    7.5   0.0    0.0024       1.9     156     204 ..      69     113 ..      54     140 .. 0.62
   3 ?    3.6   0.2     0.036        28       2      35 ..     144     177 ..     143     182 .. 0.89
   4 !    8.4   0.0    0.0013      0.98     344     405 ..     206     278 ..     182     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      D+i++G+G AG +AA+  a+ Glkva  e +++
  gi|488601056|ref|YP_007907527.1|  5 DLIIVGAGPAGSTAAIYGARYGLKVAFFESVDP 37
                                      89************************9998877 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0024
                                       EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 156 vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ++f ++++ +++   ++r +  +v+    ++e ++ akav++atgG ++
  gi|488601056|ref|YP_007907527.1|  69 IRFGAEHKYENVDSIEKRENRFIVR----SGENEYSAKAVIIATGGRHK 113
                                       5555555555553333333333333....677899***********997 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.036
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                       v+ViG+G    + A+ ++e G +v +v   +e +
  gi|488601056|ref|YP_007907527.1| 144 VVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELR 177
                                       9************************998877755 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0013
                                       .....S-TTTS.EEE...............EEEEE.EEES-EEEBETTSBE..STTEEESSBTEEE-STCEESS CS
                     FAD_binding_2 344 dfgrgidpadr.pip........gpfyavkvvpaq.hytmgGvetdengrv..ldadgqpipGLYAaGevaagg 405
                                       d  + i  +++            + f+a+ + pa+      Gve d +g     +++++ ++G +AaG + +  
  gi|488601056|ref|YP_007907527.1| 206 DVVERIILYNKvE-DrefavdvsAVFIAIGINPATqIVANLGVEMDSRGYIivNKNQETSVQGVFAAGDCCNNP 278
                                       5555555555530.133334444668999999987688889********9877999999*********998655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.1e-06     0.004       2      32 ..       5      35 ..       4      42 .. 0.91
   2 !   14.9   0.1   1.1e-05    0.0083     115     165 ..      60     111 ..      59     116 .. 0.79
   3 ?    4.0   0.1     0.021        17       2      33 ..     143     174 ..     142     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                      d+i++G+G+AG  aAi  a+ g +V+ +e+ 
  gi|488601056|ref|YP_007907527.1|  5 DLIIVGAGPAGSTAAIYGARYGLKVAFFESV 35
                                      89*************************9976 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHT-EEE-S--EEEE..ECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 115 llkelkeagvklrletevksv..ekeedgkfrvktkseeeleadklvlAtGGl 165
                                       l++++ke+ +++  e++ ++v   ++++++f v+  +e+e++a+++++AtGG 
  gi|488601056|ref|YP_007907527.1|  60 LVQKIKEQAIRFGAEHKYENVdsIEKRENRFIVRS-GENEYSAKAVIIATGGR 111
                                       78999999999999998777732233444477777.9**************96 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.021
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                       +v+viGgG      Ai +++ g++V ++ + +
  gi|488601056|ref|YP_007907527.1| 143 KVVVIGGGNTAATEAIYLKEIGCDVSIVHRRD 174
                                       89***********************9997765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1     2e-07   0.00016       1      39 [.       5      42 ..       5      66 .. 0.82
   2 !    7.1   0.0    0.0032       2.5     118     158 ..      80     117 ..      73     134 .. 0.70
   3 !    5.6   0.0    0.0089         7       1      32 [.     143     173 ..     143     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--S CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaels 39
                                      d+i++G+G AG+ AA+  ar G+kv+ + +++d + +l 
  gi|488601056|ref|YP_007907527.1|  5 DLIIVGAGPAGSTAAIYGARYGLKVAFF-ESVDPVSQLT 42
                                      689***********************99.6666655554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0032
                                       EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEE CS
                              GIDA 118 veeliveekkvkgvvtedgetikakavviatGtflkgkihi 158
                                       v+++  e+++ + +v + +++++akav+iatG   + +  i
  gi|488601056|ref|YP_007907527.1|  80 VDSI--EKRENRFIVRSGENEYSAKAVIIATGG-RHKELGI 117
                                       4555..4477778999****************9.4444444 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0089
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkl 32 
                                       +v+ViGgG      A+ +++ G++v ++ h+ 
  gi|488601056|ref|YP_007907527.1| 143 KVVVIGGGNTAATEAIYLKEIGCDVSIV-HRR 173
                                       69*******999999**********998.443 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00015      0.12       1      30 [.       5      36 ..       5      42 .. 0.89
   2 !   11.9   0.0   0.00016      0.12     145     203 ..      57     111 ..      52     132 .. 0.80
   3 !    8.2   0.2    0.0021       1.6       1      33 [.     143     177 ..     143     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                      d++i+G+G +G+++A + ar g  V+ +e+ d
  gi|488601056|ref|YP_007907527.1|  5 DLIIVGAGPAGSTAAIYGARYGlkVAFFESVD 36
                                      789****************9999999999765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGG CS
                               DAO 145 pakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGaw 203
                                        ++l++ + ++a + G+e  ++ +v ++e+++++   v    +gen  +a+av++a+G  
  gi|488601056|ref|YP_007907527.1|  57 GFELVQKIKEQAIRFGAEHKYE-NVDSIEKRENR-FIV--R-SGENeYSAKAVIIATGGR 111
                                       5689999**********99998.*****888766.666..2.26665678********76 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0021
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       +vv+iGGG + ++ A +L + g  V ++ ++d++ 
  gi|488601056|ref|YP_007907527.1| 143 KVVVIGGGNTAATEAIYLKEIGcdVSIVHRRDELR 177
                                       59****************66699*******98865 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 !   19.2   0.0   1.4e-06    0.0011       1      27 [.       8      34 ..       8      48 .. 0.94
   2 !    7.3   0.0    0.0071       5.5       1      31 [.     146     176 ..     146     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                      IvGaG +G++aA + a++g++v  +e+
  gi|488601056|ref|YP_007907527.1|  8 IVGAGPAGSTAAIYGARYGLKVAFFES 34
                                      9************************97 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0071
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       ++G+G ++++ A +L++ g+dv ++ +rd l
  gi|488601056|ref|YP_007907527.1| 146 VIGGGNTAATEAIYLKEIGCDVSIVHRRDEL 176
                                       8***********************9999987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.6e-05     0.012       2      33 ..       4      35 ..       3      47 .. 0.86
   2 !   10.1   0.0   0.00044      0.34       3      35 ..     143     175 ..     142     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +d +IVGaGpaG ++a   +++G +v   e  
  gi|488601056|ref|YP_007907527.1|  4 YDLIIVGAGPAGSTAAIYGARYGLKVAFFESV 35
                                      6889*******************999877765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00044
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       +V+++G+G + ++ a  L+e G +v +v +r++
  gi|488601056|ref|YP_007907527.1| 143 KVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDE 175
                                       69***************************9876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.5e-07    0.0002      17      49 ..       3      34 ..       1      39 [. 0.93
   2 ?    2.7   0.7     0.079        62      19      50 ..     143     173 ..     133     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.5e-07
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                      e D++ivGaG++G taa y a+  +lkva +e+
  gi|488601056|ref|YP_007907527.1|  3 EYDLIIVGAGPAGSTAAIYGARY-GLKVAFFES 34
                                      78*******************99.******996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.079
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailers 50 
                                        vv++G+G +  t a yl +  +  v i+ r+
  gi|488601056|ref|YP_007907527.1| 143 KVVVIGGGNTAATEAIYLKEI-GCDVSIVHRR 173
                                       699999999999999999887.7777776654 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0076         6       2      35 ..       3      34 ..       2      39 .. 0.80
   2 !   16.1   0.0   6.3e-06    0.0049     117     230 ..      78     178 ..      60     192 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0076
                       K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalfler 35
                                       +Dli++G+Gp+  + ai  +     lk+ f+e 
  gi|488601056|ref|YP_007907527.1|  3 EYDLIIVGAGPAGSTAAIYGARYG--LKVAFFES 34
                                      69*********9977666666555..99999996 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 6.3e-06
                       K_oxygenase 117 eeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepk...iPevleklegkervvHsseylerkeella 190
                                       e+v+++e +e    +++ v+s      e+e++a+++++++G++ k   iP   e +     v   ++   +     +
  gi|488601056|ref|YP_007907527.1|  78 ENVDSIEKRE----NRFIVRS-----GENEYSAKAVIIATGGRHKelgIPGEKEFVG--RGVSYCATCDGN---FFR 140
                                       2344444444....5799998.....4799***********7664233776665444..344444444444...589 PP

                       K_oxygenase 191 kkriaVvGsGqSaaeifedllrrqkkvelklvtrsealep 230
                                       +k+++V+G+G +aa  +  l   +   ++++v r+++l++
  gi|488601056|ref|YP_007907527.1| 141 GKKVVVIGGGNTAATEAIYLK--EIGCDVSIVHRRDELRA 178
                                       9************96555544..34468888888888764 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.1   8.4e+02       9      35 ..       5      31 ..       1     113 [. 0.69
   2 !   22.3   0.1   1.7e-07   0.00013       5      46 ..     139     206 ..     138     269 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.1
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtv 35
                                        ++vG+G+ + + +   +++g kv  
  gi|488601056|ref|YP_007907527.1|  5 DLIIVGAGPAGSTAAIYGARYGLKVAF 31
                                      568999999998877777777777765 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.7e-07
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele..........................e 46 
                                       ++gkkv+v+GgG+ Aa+ +  l e g++v +v  + +  ++                          +
  gi|488601056|ref|YP_007907527.1| 139 FRGKKVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELRADkahqneifkrgipviwnsipvriegkD 206
                                       689*****************************999422222333333444444444433333333331 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   8.7e-07   0.00068       1      29 [.       5      33 ..       5      39 .. 0.93
   2 ?   -3.0   0.0       4.4   3.4e+03      98     144 ..      65     109 ..      51     109 .. 0.70
   3 ?    3.3   0.1     0.056        43       2      34 ..     144     176 ..     143     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.7e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLve 29
                                      D+++vG+gpaG +AAi  ar G kv+  e
  gi|488601056|ref|YP_007907527.1|  5 DLIIVGAGPAGSTAAIYGARYGLKVAFFE 33
                                      99***********************9776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.4
                      FAD_oxidored  98 aeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                       +e+ ++   ++++++v+  +kr +  +v+  +g+ +++Ak +i ATg
  gi|488601056|ref|YP_007907527.1|  65 KEQAIRFGAEHKYENVDSIEKRENRFIVR--SGENEYSAKAVIIATG 109
                                       55566666666677777655566666664..4788899998888886 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.056
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvl 34 
                                       vvV+GGg    + Ai  ++ G  v +v++r+ l
  gi|488601056|ref|YP_007907527.1| 144 VVVIGGGNTAATEAIYLKEIGCDVSIVHRRDEL 176
                                       9***************************99865 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00028      0.22       1      32 [.       5      34 ..       5      42 .. 0.87
   2 ?    5.0   0.0     0.014        11      92     146 ..      63     114 ..      58     132 .. 0.77
   3 ?    3.7   0.1     0.034        27       2     128 ..     144     261 ..     143     284 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      D++++GaGpAg   A     a++glkv   e+
  gi|488601056|ref|YP_007907527.1|  5 DLIIVGAGPAGSTAAIYG--ARYGLKVAFFES 34
                                      9**********9999888..9******98876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                     Lycopene_cycl  92 ellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslkk 146
                                       +++e+ +  g++     v+s+e+ e+  + +v +g+++  a++v+ a+g ++ k+
  gi|488601056|ref|YP_007907527.1|  63 KIKEQAIRFGAEHKYENVDSIEKREN--RFIVRSGENEYSAKAVIIATG-GRHKE 114
                                       55666666677777778999999998..9********************.77664 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.034
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleecvehsWsgtivylddgkkillg 78 
                                       vvviG+G      A  l  ++ g  v ++   ++l ++       +++++  +++ +   W+   v+++++  ++  
  gi|488601056|ref|YP_007907527.1| 144 VVVIGGGNTAATEAIYL--KEIGCDVSIVHRRDEL-RAD----KAHQNEI--FKRGIPVIWNSIPVRIEGKDVVERI 211
                                       89999999999999999..9999999999777777.332....2333333..46778899***********999999 PP

                     Lycopene_cycl  79 raYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggr 128
                                         Y++v+ ++++  +   ++  g++     v++   e +++ +++++ ++
  gi|488601056|ref|YP_007907527.1| 212 ILYNKVEDREFAVDVSAVFIAIGINPATQIVANLGVEMDSRGYIIVNKNQ 261
                                       99******999999988888666666666666655555555555555555 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.7e-07   0.00045       3      47 ..     140     184 ..     138     193 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.7e-07
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHT CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkee 47 
                                       +gkk++viG G+ + ++a  l++ g+dv +  r+++  ++kA+++
  gi|488601056|ref|YP_007907527.1| 140 RGKKVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELRADKAHQN 184
                                       79**********************************999999886 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 !    6.3   0.0    0.0068       5.3      31      59 ..       6      34 ..       2      48 .. 0.89
   2 !    9.2   0.1   0.00085      0.66      28      64 ..     141     177 ..     120     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0068
                                      EEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDv 59
                                       +++G+G aG  A+   ++ g kV  ++ 
  gi|488601056|ref|YP_007907527.1|  6 LIIVGAGPAGSTAAIYGARYGLKVAFFES 34
                                      589*********************99875 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00085
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparl 64 
                                         kv+viGgG      +   k++g +V ++  r + +
  gi|488601056|ref|YP_007907527.1| 141 GKKVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELR 177
                                       569*******76666666789********99887654 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.033        26      58      84 ..       6      32 ..       1     110 [. 0.85
   2 !   11.6   0.0   0.00017      0.13      53      90 ..     139     176 ..     123     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.033
                                      EEEEBSSHHHHHHHHHHHHHT-EEEEE CS
                              PALP 58 vveassGNhgralAaaaallGlkvtiv 84
                                      ++  ++G +g  +A+++a++Glkv  +
  gi|488601056|ref|YP_007907527.1|  6 LIIVGAGPAGSTAAIYGARYGLKVAFF 32
                                      78889999***************9866 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00017
                                       TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS- CS
                              PALP  53 tgaktvveassGNhgralAaaaallGlkvtivvpadas 90 
                                        ++k vv+ ++GN+++  A++ + +G++v iv  +d  
  gi|488601056|ref|YP_007907527.1| 139 FRGKKVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDEL 176
                                       6899****************************887765 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.044        34       1      35 [.       6      46 ..       6     117 .. 0.64
   2 !    9.9   0.0    0.0013      0.99       1      38 [.     144     180 ..     144     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.044
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG......- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa......t 35
                                      l+i+Gag+ +   a ++a+ g++v  +++ + +        
  gi|488601056|ref|YP_007907527.1|  6 LIIVGAGPAGSTAAIYGARYGLKVAFFESVDPVSqltltpV 46
                                      79**********************99988775553445551 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatker 38 
                                       +v++G+g+ a+  a +++++g++v++v  r+e+++  +
  gi|488601056|ref|YP_007907527.1| 144 VVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELRAD-K 180
                                       689****************************86532.2 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1     0.001       0.8       2      31 ..       6      32 ..       5      38 .. 0.82
   2 !    5.3   0.1    0.0093       7.2       1      32 [.     143     171 ..     143     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEE CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlv 31
                                      ++ivG+G+aG++aA++ a+++   l+v   
  gi|488601056|ref|YP_007907527.1|  6 LIIVGAGPAGSTAAIYGARYG---LKVAFF 32
                                      79*************999988...556555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0093
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlve 32 
                                       k+v++GGG  + + A++l++ +   ++v++v 
  gi|488601056|ref|YP_007907527.1| 143 KVVVIGGGNTAATEAIYLKEIG---CDVSIVH 171
                                       79*****************999...7787775 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.08        63      38      68 ..       5      35 ..       1      47 [. 0.85
   2 !   10.4   0.0    0.0004      0.31      31      73 ..     136     178 ..     121     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.08
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrs 68
                                       + i+G+G  G+++a + +  g+kv +++  
  gi|488601056|ref|YP_007907527.1|  5 DLIIVGAGPAGSTAAIYGARYGLKVAFFESV 35
                                      578**********************998765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0004
                                       BS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                                       g+  +gk+v +iG G+ + + a +lk++g++v ++ r+ + ++
  gi|488601056|ref|YP_007907527.1| 136 GNFFRGKKVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELRA 178
                                       66689***************************99999866433 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0         2   1.5e+03      13      28 ..       4      19 ..       1      28 [. 0.80
   2 ?   13.0   0.0    0.0001     0.079      10      51 ..     139     180 ..     132     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2
                                      -EEEEES-SHHHHHHH CS
                      Shikimate_DH 13 kkvlliGaGemaelva 28
                                         +++GaG  ++ +a
  gi|488601056|ref|YP_007907527.1|  4 YDLIIVGAGPAGSTAA 19
                                      56799****9988776 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
                                       .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHH CS
                      Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerake 51 
                                       +++kkv++iG G++a   a +L + g++  +v  R+  ra++
  gi|488601056|ref|YP_007907527.1| 139 FRGKKVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELRADK 180
                                       5789************************66666666667765 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.025     269     322 ..     138     195 ..     131     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                       HHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT..... CS
                    Oxidored_nitro 269 ylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleeg....e 322
                                        ++gk+v+++g++ ++   a +lke+G++v  ++ +++ r+d++  +++++ g     
  gi|488601056|ref|YP_007907527.1| 138 FFRGKKVVVIGGGNTAATEAIYLKEIGCDVSIVHRRDELRADKAHQNEIFKRGipviW 195
                                       589****************************************977777777632220 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       0.1        80       2      14 ..       8      20 ..       7      40 .. 0.84
   2 ?    8.5   0.0    0.0024       1.9     115     154 ..      71     109 ..      59     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                     NAD_binding_9  2 ivGaGprGlavle 14
                                      ivGaGp+G +++ 
  gi|488601056|ref|YP_007907527.1|  8 IVGAGPAGSTAAI 20
                                      9*******99875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0024
                     NAD_binding_9 115 vtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       +  e+  ++v ++e+r++++ ++ ++++++ a+aV++A+G
  gi|488601056|ref|YP_007907527.1|  71 FGAEHKYENVDSIEKRENRF-IVRSGENEYSAKAVIIATG 109
                                       45567788899999998886.7789999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2040.80
//
Query:       gi|488601057|ref|YP_007907528.1|  [L=49]
Description: hypothetical protein Asulf_01558 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 348.89
//
Query:       gi|488601058|ref|YP_007907529.1|  [L=127]
Description: hypothetical protein Asulf_01559 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   33.5   0.0     0.0033   17.3   0.0    2.1  2  DrsE_2    DsrE/DsrF/DrsH-like family
     0.0028   18.0   0.0     0.0052   17.1   0.0    1.4  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.2e-06      0.02       7      55 ..       4      53 ..       2      61 .. 0.80
   2 !   17.3   0.0   3.7e-07    0.0033      84     135 ..      59     112 ..      52     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-06
                                      EEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGG.GGB-GGG---T CS
                            DrsE_2  7 iifskgtldkalaalilAsgAaalglevtiFftFwGLn.ilrkeekkkvk 55
                                      ii+ +g+ d+ + a+ +As+  + ++ev +  t+w L  ++   +++ vk
  gi|488601058|ref|YP_007907529.1|  4 IIIHSGDWDRIYHAFNIASVYGSSDQEVVVLLTYWALRtAIESAKEVGVK 53
                                      6777888889**************************97245555555555 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.7e-07
                                       HHHHHHHHHCT---HHHHHHHHHHTT.-EEEEEHHHHHHHT--GGGB-TT-.EE CS
                            DrsE_2  84 kmmkkvmkekgvasleeLleaakeag.vklvaCqmtmdlmglkkeelidgv.ei 135
                                       +++++ +    +++le++++ ak  g v++  C +++ l+g+++++l d v e+
  gi|488601058|ref|YP_007907529.1|  59 EILRNGISRGVIKRLEDMIKLAKSTGnVRIGVCPVSLSLLGYEEKDLPDWVdEV 112
                                       5666777777899**********9866*******************98877444 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.8e-07    0.0052      16      92 ..      13     105 ..       3     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.8e-07
                                       HHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS................---TGGGTS---GGGGGGCGGGT.-EEE CS
                              DrsE  16 aarealelalaaaalghevsvffygdGvllllk................gqtanpadeknlaellkalkeyg.vkly 75 
                                       + + a+++a +  + ++ev+v ++  + + + +                 +       k l +++k +k  g v++ 
  gi|488601058|ref|YP_007907529.1|  13 RIYHAFNIASVYGSSDQEVVVLLTYWALRTAIEsakevgvkdgekeeilRNGISRGVIKRLEDMIKLAKSTGnVRIG 89 
                                       4488999999999999*******99999999999999999965555555444444455556999999999888**** PP

                                       EEHHHHHHTT--GGGE- CS
                              DrsE  76 vCgqaakargldededl 92 
                                       vC  ++   g++e++ l
  gi|488601058|ref|YP_007907529.1|  90 VCPVSLSLLGYEEKD-L 105
                                       ************875.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 851.91
//
Query:       gi|488601059|ref|YP_007907530.1|  [L=906]
Description: alanyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-137  457.7   0.0   8.2e-137  457.0   0.0    1.3  1  tRNA-synt_2c  tRNA synthetases class II (A)
    4.8e-16   59.4   1.0    1.2e-15   58.2   1.0    1.7  1  DHHA1         DHHA1 domain
    2.6e-15   56.2   2.5    5.8e-15   55.1   2.5    1.6  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.0   0.0  1.4e-140  8.2e-137       1     552 []      64     591 ..      64     591 .. 0.96

  Alignments for each domain:
  == domain 1  score: 457.0 bits;  conditional E-value: 1.4e-140
                                       HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVG 77 
                                       ++re +l+fFek++H+++++++v++++++++++++A++a+f+p++++++  p+++++++sQ+ciR++    Dl++VG
  gi|488601059|ref|YP_007907530.1|  64 DMREYYLSFFEKRDHERIERYPVIARWRDDIYLTIASIADFQPFVTSGVVPPPANPLTISQPCIRMD----DLDSVG 136
                                       59*****************************************************************....****** PP

                                       TSSS--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGE CS
                      tRNA-synt_2c  78 ktarHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeeri 147
                                       +t+rH+T+FeM+++++f+     +Y+k+e++e+++ell  elg+++e+++++++++++  +a+++ e +vg+ e ++
  gi|488601059|ref|YP_007907530.1| 137 RTGRHLTLFEMMAHHAFNnpeqeIYWKSETVEYCTELLE-ELGVNREDIIYKEEPWAGggNAGPCLEGIVGGLEVAT 212
                                       **************************************9.*****************999***************** PP

                                       EEE-HHHHEEESSSS........EEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEEST....TS CS
                      tRNA-synt_2c 148 lrfgekdnfwemgdt........gpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnree....dg 212
                                       l+f   +n ++++d         ++++p++++++++g e+++++++++++++d+++ e++++++++ n+++    ++
  gi|488601059|ref|YP_007907530.1| 213 LVF---MNLETHPDGdieikgekYRKMPNYIVDTGYGLERFTWASQGTPTVYDAIFPEVLEMIVSNSNVRHftddEE 286
                                       ***...99999999999999999*********************************************999888789 PP

                                       HEEEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT CS
                      tRNA-synt_2c 213 tlkpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladG 289
                                       + +++ ++s+++G+      + L ++r+++++++++ v+++++ + +          e+++++aDH+ra+ f+l+dG
  gi|488601059|ref|YP_007907530.1| 287 VARIVGESSKVAGVLGTLRGEALIQLRKSVAEKIGIDVEKLEKIVKP---------LENVYALADHTRAILFMLGDG 354
                                       999**************************************999999.........789****************** PP

                                       --SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHH CS
                      tRNA-synt_2c 290 vvpsnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGl 366
                                       +vpsn+g+gY+ R+++Rr++r a++L+++ + l +lv+++ ++l ++   +    e+++ei+e E  r++ T+++G 
  gi|488601059|ref|YP_007907530.1| 355 LVPSNAGAGYLGRLMIRRSLRIAEELEFELS-LFDLVEMHRKILREF--SFPTPLETIQEILELEMDRYSVTISKGI 428
                                       *******************************.999**********86..67899*********************** PP

                                       HHHHHHHHHCCCCSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXX CS
                      tRNA-synt_2c 367 klleelikklkkkkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdve 443
                                        l+e++i++   kk++++ed++++yd+ G+P++l   ia+ekg++v++++ ++a+ ++r++  ++kke++       
  gi|488601059|ref|YP_007907530.1| 429 GLVERTIAR---KKKIEKEDLIEFYDSNGVPPELAVRIAKEKGVEVEMPEDFYAELAERHSRAEKKKESE------- 495
                                       ********7...789*****************************************99998755444444....... PP

                                       XTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEE CS
                      tRNA-synt_2c 444 alkelkkteeflgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdv 520
                                          ++++te+ l+y++     k+l      ef++ev  +e ++v+LdrT+fY+esGGq++D+G+i +e++e++v+dv
  gi|488601059|ref|YP_007907530.1| 496 LKLDYPQTEK-LYYNS-----KLL------EFESEVIGVEGDYVILDRTAFYPESGGQDNDTGVILTEKGELKVVDV 560
                                       5566777777.99999.....555......9********************************************** PP

                                       EEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
                      tRNA-synt_2c 521 qkakgvvlhkgkleegklkvgdkvkaevdeer 552
                                        +++g++lhk++ +  + + g+kvk+ +d++r
  gi|488601059|ref|YP_007907530.1| 561 IDQNGIILHKVEGN-FRPEPGMKVKGIIDRDR 591
                                       ************96.99************875 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   1.0   1.9e-19   1.2e-15       2     132 ..     769     895 ..     768     901 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.9e-19
                                       HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEE CS
                             DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvake 78 
                                       +++ +e+ke +ke+e+l  ++aklka+ llekaee++  +v++  + e++d   +  +   l +  k +v ++++k+
  gi|488601059|ref|YP_007907530.1| 769 KRFFDEWKEQKKEIERLTSEIAKLKAQLLLEKAEEYDSIPVIAEIF-EDMDHQEMVKLGFALAE--KGAVGCLISKK 842
                                       78899*****************************************.99999999999999999..44666666665 PP

                                       ECTEEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHH CS
                             DHHA1  79 egdkvkvsarskkdgvdagelakeaaaklgggGGGH.dlAaGagipaekleeale 132
                                       +  kvkv+  s kd+++a +l++e+ + + ggGGG+ +lA+Gag  a + +++++
  gi|488601059|ref|YP_007907530.1| 843 D--KVKVITFSGKDDINAVDLIREIGKYIKGGGGGKrNLAQGAGQIAPSRDDLVK 895
                                       5..9********99****************************9985555577766 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 !   55.1   2.5   9.7e-19   5.8e-15       1      44 []     690     732 ..     690     732 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 9.7e-19
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +rvv++Gd +v++CgGtH++ TgeIg++ki++ esi++g+ RI+
  gi|488601059|ref|YP_007907530.1| 690 IRVVRVGD-DVQACGGTHCDTTGEIGLIKIMKIESIQDGVIRIE 732
                                       7******9.**********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (906 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 5505.68
//
Query:       gi|488601060|ref|YP_007907531.1|  [L=255]
Description: coenzyme F420-0 gamma-glutamyl ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-65  221.3   0.8    1.6e-65  220.9   0.8    1.1  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 !  220.9   0.8   8.8e-70   1.6e-65       4     244 .]      12     221 ..      11     221 .. 0.99

  Alignments for each domain:
  == domain 1  score: 220.9 bits;  conditional E-value: 8.8e-70
                                       -----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H........ CS
                       F420_ligase   4 tplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfs 80 
                                       +pli+ gdd+a+i++++++     ledgD+vv++++vv+k+eg++ +led kps+kA +ia+k+ ++ p        
  gi|488601060|ref|YP_007907531.1|  12 IPLIRVGDDIADIIADRFE-----LEDGDVVVICSTVVSKSEGRVRKLEDYKPSSKAVKIAKKI-GKTP-------- 74 
                                       79***************99.....****************************************.****........ PP

                                       ..........HHHHHHHHTEEEEEE-..S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHH CS
                       F420_ligase  81 liLkalakatrkvevvlsepsdevgn..qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeik 155
                                                 ++v++v++e+++++ +  +l+++        k+G +++nagid+snve+g+++l P +pdksae+i 
  gi|488601060|ref|YP_007907531.1|  75 ----------EFVQAVMEESEEILIDspFLLVKA-------KFGNICVNAGIDASNVEKGYIILPPLNPDKSAEKIM 134
                                       ..........***************999999999.......************************************ PP

                                       HHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-S CS
                       F420_ligase 156 kklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGs 232
                                       k+l+e+tgk+v+V+i  +D++gr+++ + ++v+ig+s++ al+d+ gkkdl+g+el++t++av+de++ +a+L++G+
  gi|488601060|ref|YP_007907531.1| 135 KRLREITGKRVGVII--TDTNGRCFRYGVVGVSIGLSNVIALKDWVGKKDLFGNELEVTVEAVADEIAGMANLIMGE 209
                                       ***************..************************************************************ PP

                                       SSS---EEEEES CS
                       F420_ligase 233 adegtPvvlvrg 244
                                       + +g+Pvv+vrg
  gi|488601060|ref|YP_007907531.1| 210 GGDGIPVVVVRG 221
                                       ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 1523.92
//
Query:       gi|488601061|ref|YP_007907532.1|  [L=353]
Description: putative ATP-dependent carboligase related to biotin carboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-35  122.9   0.0    1.7e-35  122.4   0.0    1.2  1  ATP-grasp_3      ATP-grasp domain
    9.2e-07   28.4   0.2    0.00058   19.2   0.0    2.9  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    3.1e-06   26.6   0.1    0.00069   18.9   0.0    2.8  3  ATPgrasp_YheCD   YheC/D like ATP-grasp
    7.1e-06   25.7   0.1    0.00034   20.2   0.0    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    9.8e-06   25.2   0.0    8.9e-05   22.1   0.0    2.1  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.1e-05   24.3   0.0    6.3e-05   22.7   0.0    1.9  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    0.00066   19.3   0.1      0.002   17.7   0.0    1.9  2  RimK             RimK-like ATP-grasp domain
     0.0015   18.1   0.0      0.012   15.2   0.0    2.1  2  ATP-grasp_4      ATP-grasp domain
  ------ inclusion threshold ------
      0.012   14.7   0.0       0.17   11.0   0.0    2.2  2  TTL              Tubulin-tyrosine ligase family


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 !  122.4   0.0   8.7e-39   1.7e-35       2     161 .]      96     249 ..      95     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 8.7e-39
                                       TSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEE CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvs 78 
                                        dKlk+y+kL+ ag+++P     e  +e++ +++vKp++G+gge + + e++     ++ ++ l+qe+ieG p+S+s
  gi|488601061|ref|YP_007907532.1|  96 VDKLKFYRKLESAGLPFP-----ELKSEVDGRVIVKPIRGGGGEDIKLLENE-----ICGKDFLIQEYIEGFPCSAS 162
                                       59****************.....67778899********************9.....445677************** PP

                                       EEE.SSSEEEEEEEEEEEET.......TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEEESS..SE CS
                       ATP-grasp_3  79 llsdgekvlvlavnrqliekaeke...fvyaGnvtpietel..keevvelaeevvekleglaGyvGvDlvlkd.eep 149
                                       l++ g+++ v+++nr l ++ e++   f+y+Gn+tp ++++  ++++ +la e++e + +l+G+vGvD+v+    +p
  gi|488601061|ref|YP_007907532.1| 163 LIV-GKDAEVISLNRILAGWSEMNadgFRYSGNTTPLDVKQelRKKLSRLAVELCELF-ELKGSVGVDFVVDRnMNP 237
                                       ***.89*************99999999*********98776669**************.***********988789* PP

                                       EEEEEESS--GG CS
                       ATP-grasp_3 150 yviEvNPRltts 161
                                       y+iE NPR+++s
  gi|488601061|ref|YP_007907532.1| 238 YIIEMNPRFQGS 249
                                       **********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 !    5.7   0.1    0.0038       7.7      55      80 ..     115     140 ..      88     152 .. 0.71
   2 !   19.2   0.0   2.9e-07   0.00058     227     267 ..     207     248 ..     204     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0038
                       ATPgrasp_ST  55 fvkeleeg.vviKpakgsgGkGilvit 80 
                                       + +e+ +g v++Kp++g gG++i  + 
  gi|488601061|ref|YP_007907532.1| 115 LKSEV-DGrVIVKPIRGGGGEDIKLLE 140
                                       44555.334999********9998774 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.9e-07
                       ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNar.pg 267
                                       ++  la+++ e +   g +G+D+v+d++ +p+++E+N r +g
  gi|488601061|ref|YP_007907532.1| 207 KLSRLAVELCELFELKGSVGVDFVVDRNMNPYIIEMNPRfQG 248
                                       56678999999777889********************99654 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 ?   -1.6   0.0      0.66   1.3e+03     155     202 ..      17      66 ..      12      70 .. 0.77
   2 ?    4.3   0.0      0.01        20      49      69 ..     121     141 ..     116     157 .. 0.82
   3 !   18.9   0.0   3.5e-07   0.00069     181     227 ..     199     245 ..     179     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.66
                    ATPgrasp_YheCD 155 tnlsrGGtalpleellkkafg..eekaekileeleelalelaealeesfg 202
                                       + +++G +++ l +++ + +   ++k+  i+ee +e++le a+ l e+++
  gi|488601061|ref|YP_007907532.1|  17 SAFKSGFEVYALTKFVDSDLAlfSKKVYLIEEESREWVLERANELAERYN 66 
                                       66777788888888888887777778888999999999998888888776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.01
                    ATPgrasp_YheCD  49 ksvylKpanGskGkgilriek 69 
                                       ++v++Kp++G +G++i  +e+
  gi|488601061|ref|YP_007907532.1| 121 GRVIVKPIRGGGGEDIKLLEN 141
                                       789************998887 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 3.5e-07
                    ATPgrasp_YheCD 181 kileeleelalelaealeesfgrlgElGlDlgidkegkvWllEvNsk 227
                                       ++++el++   +la  l e f+  g +G+D+ +d++ + +++E+N +
  gi|488601061|ref|YP_007907532.1| 199 DVKQELRKKLSRLAVELCELFELKGSVGVDFVVDRNMNPYIIEMNPR 245
                                       44555555555555555555556788*******************87 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 ?    2.9   0.1     0.033        66      61     109 ..      55     100 ..      46     106 .. 0.80
   2 !   20.2   0.0   1.7e-07   0.00034     125     174 ..     195     244 ..     146     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.033
                                       HHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE-SSS CS
                   Dala_Dala_lig_C  61 lkeaieeafkydekvlvEeaiegreievavlgneklevsevgeivvkkg 109
                                       l++a e a +y+++v+   + e  e++  vlg e  +++    +v k +
  gi|488601061|ref|YP_007907532.1|  55 LERANELAERYNARVVLASGYEDIEVKADVLGCEPSKIHD---VVDKLK 100
                                       7889999*************************66655554...444555 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.7e-07
                                       ESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 125 evpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       + p ++++e ++k++ la++  ++ +l+G++ vDf+++++ ++++ E+N+
  gi|488601061|ref|YP_007907532.1| 195 TTPLDVKQELRKKLSRLAVELCELFELKGSVGVDFVVDRNMNPYIIEMNP 244
                                       468899*******************************************6 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.17   3.5e+02      40      60 ..     122     142 ..     114     187 .. 0.79
   2 !   22.1   0.0   4.5e-08   8.9e-05     134     183 ..     201     249 ..     197     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                                       SEEEEETTCCTTTTEEEESSH CS
                       CPSase_L_D2  40 PviikaafglGGkGmrvarne 60 
                                        vi+k+  g+GG+  ++ +ne
  gi|488601061|ref|YP_007907532.1| 122 RVIVKPIRGGGGEDIKLLENE 142
                                       59**********999998875 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4.5e-08
                                       -HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CC CS
                       CPSase_L_D2 134 tdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsve 183
                                       ++e r++l + av++++  +++g   v+f++d+ +++ y+iE+N+R + +
  gi|488601061|ref|YP_007907532.1| 201 KQELRKKLSRLAVELCELFELKGSVGVDFVVDR-NMNPYIIEMNPRFQGS 249
                                       67899***************************7.99**********9965 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 ?   -3.9   0.0       5.5   1.1e+04      46      63 ..      51      68 ..      47      71 .. 0.74
   2 !   22.7   0.0   3.2e-08   6.3e-05      44     110 ..     203     271 ..     145     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.5
                      ATPgrasp_Ter 46 deelielaerlaeefgld 63
                                      +e ++e a++lae++++ 
  gi|488601061|ref|YP_007907532.1| 51 REWVLERANELAERYNAR 68
                                      566788899999988876 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 3.2e-08
                      ATPgrasp_Ter  44 ekdeelielaerlaeefgldglvnvQvrededg.pkLLEiNpRasGGlgysala.Gvnlpylalklllg 110
                                       e +++l  la +l e f+l+g v+v +  d++  p+++E+NpR++G l+    +  v l +l   ++ g
  gi|488601061|ref|YP_007907532.1| 203 ELRKKLSRLAVELCELFELKGSVGVDFVVDRNMnPYIIEMNPRFQGSLDAIEWSmDVSLFRLHYLAVEG 271
                                       45678999************************99************99875554456555555555555 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.1   2.2e+03      91     105 ..       3      17 ..       2      23 .. 0.77
   2 !   17.7   0.0     1e-06     0.002      73     167 ..     145     246 ..      67     261 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                       EEEEETTEEEEEEEE CS
                              RimK  91 Rvlvvddevvaalrr 105
                                       R+lvv+++v   ++ 
  gi|488601061|ref|YP_007907532.1|   3 RILVVGNNVRNVVQS 17 
                                       9******99776665 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1e-06
                                       GG--EEEEE--SS-S.......EEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHC CS
                              RimK  73 keailvqeyieeaen.......ediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakam 142
                                        +  l+qeyie           +d  v+ ++  + a+   +  +  FR   +      k +l +++ +lA++  ++ 
  gi|488601061|ref|YP_007907532.1| 145 GKDFLIQEYIEGFPCsaslivgKDAEVISLN-RILAGWSEMNAD-GFRYSGNTTPLDVKQELRKKLSRLAVELCELF 219
                                       345599****976552234444555555553.456666666555.58888777778888999999999********* PP

                                       T-S.EEEEE.EEEETTEEEEEEEESS- CS
                              RimK 143 elv.vaGvD.llrakrgllvlEvnssp 167
                                       el   +GvD +++ + +++++E+n   
  gi|488601061|ref|YP_007907532.1| 220 ELKgSVGVDfVVDRNMNPYIIEMNPRF 246
                                       **8469***99************9754 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.28   5.7e+02      91     138 ..      36      83 ..      23      88 .. 0.78
   2 !   15.2   0.0   5.9e-06     0.012      49     155 ..     142     248 ..     134     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.28
                       ATP-grasp_4  91 eedvsdrlyvtsakvieetlealeellkevnallglknfpvHiElrvs 138
                                        + +s+++y++ ++  e  le+ +el ++ na++ l  +   iE++ +
  gi|488601061|ref|YP_007907532.1|  36 LALFSKKVYLIEEESREWVLERANELAERYNARVVLASGYEDIEVKAD 83 
                                       455788888888888888888889999999999999988888888865 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.9e-06
                       ATP-grasp_4  49 vveeesflvEeyieGeEfavdayfdeeGepvil.nilkkefaseed.vsdrlyvtsakvieetlealeellkevnal 123
                                        + +++fl+ eyieG+  +  + + ++ e + l  il     +++d ++    +t+ +v +e  ++l++l  e+ +l
  gi|488601061|ref|YP_007907532.1| 142 EICGKDFLIQEYIEGFPCSASLIVGKDAEVISLnRILAGWSEMNADgFRYSGNTTPLDVKQELRKKLSRLAVELCEL 218
                                       566899******************9997665441577766655555599999************************* PP

                       ATP-grasp_4 124 lglknfpvHiElrvsedgkiipiEvnplrfag 155
                                       ++lk + v + + v+ + + + iE+np rf g
  gi|488601061|ref|YP_007907532.1| 219 FELK-GSVGVDFVVDRNMNPYIIEMNP-RFQG 248
                                       ***7.7899******************.6655 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     0.088   1.8e+02      69     110 ..     123     155 ..      93     156 .. 0.74
   2 ?   11.0   0.0   8.3e-05      0.17     240     258 ..     225     243 ..     199     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.088
                                       ---SS---XX------BSSTHHHHHHHH..SSS-EEEEB--S CS
                               TTL  69 wIvKpsasarGkgirvfnkledikkivsqsqkeplvvqkYie 110
                                       +IvKp  +  G++i + ++             +++++q+Yie
  gi|488601061|ref|YP_007907532.1| 123 VIVKPIRGGGGEDIKLLENEI---------CGKDFLIQEYIE 155
                                       566666666666666665544.........45699*****97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.3e-05
                                       XXXXXXXXXXXXXXXXXXX CS
                               TTL 240 yGvDilidenlkpwLlEvN 258
                                        GvD+++d+n++p+++E N
  gi|488601061|ref|YP_007907532.1| 225 VGVDFVVDRNMNPYIIEMN 243
                                       69***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 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:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 2391.54
//
Query:       gi|488601062|ref|YP_007907533.1|  [L=110]
Description: hypothetical protein Asulf_01563 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   92.0   0.2    2.2e-26   91.8   0.2    1.0  1  Thioredoxin    Thioredoxin
    1.2e-06   28.8   1.6    0.00011   22.5   0.0    2.4  3  Thioredoxin_8  Thioredoxin-like
    1.9e-06   28.3   1.4    1.3e-05   25.6   1.4    1.9  1  Thioredoxin_2  Thioredoxin-like domain
      3e-06   27.2   0.0    3.5e-06   26.9   0.0    1.1  1  HyaE           Hydrogenase-1 expression protein HyaE
    4.9e-05   23.2   0.2    6.8e-05   22.8   0.2    1.3  1  AhpC-TSA       AhpC/TSA family
    0.00022   21.2   1.3      0.055   13.4   0.1    1.7  2  Thioredoxin_6  Thioredoxin-like domain
    0.00027   21.1   0.1    0.00041   20.5   0.1    1.3  1  Thioredoxin_7  Thioredoxin-like
    0.00066   19.4   0.1    0.00082   19.1   0.1    1.1  1  Redoxin        Redoxin
     0.0022   17.7   0.4       0.57    9.8   0.3    2.1  2  Thioredoxin_5  Thioredoxin
     0.0023   17.7   0.0     0.0027   17.5   0.0    1.1  1  DIM1           Mitosis protein DIM1
     0.0034   16.8   0.0     0.0041   16.5   0.0    1.2  1  OST3_OST6      OST3 / OST6 family, transporter family
      0.007   16.2   0.0     0.0087   15.9   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0071   16.5   0.4      0.011   15.9   0.4    1.2  1  Glutaredoxin   Glutaredoxin
     0.0073   15.9   0.7      0.011   15.3   0.7    1.7  1  DUF953         Eukaryotic protein of unknown function (DUF953
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.014   15.2   0.0    1.2  1  Thioredoxin_9  Thioredoxin
      0.064   12.2   0.0      0.075   12.0   0.0    1.1  1  Phosducin      Phosducin
      0.077   12.7   0.0      0.077   12.7   0.0    1.1  1  SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system
      0.092   13.2   0.0       0.11   12.9   0.0    1.2  1  DUF836         Glutaredoxin-like domain (DUF836)


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 !   91.8   0.2   2.2e-29   2.2e-26       2     102 ..       6     104 ..       5     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 2.2e-29
                                       EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                       Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlkl 78 
                                       + +l+k+n++e v +    v+v+FyA+wC++C +++P le+lae++k+kvk++k +v+e +++++ky+++ +Pt+++
  gi|488601062|ref|YP_007907533.1|   6 IFKLNKNNWREIVGS--GVVVVDFYADWCPPCFKIEPILEELAEAFKNKVKVCKFNVEEDDEIPTKYGIQVLPTIYV 80 
                                       57899********99..************************************************************ PP

                                       EETTEEEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  79 fkngkevkkyegarekeklaaflk 102
                                       fkng++ + +eg ++ke++ + ++
  gi|488601062|ref|YP_007907533.1|  81 FKNGDTYSGVEGLAKKESIFKLVE 104
                                       ******************999876 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       9.3   9.3e+03      51      61 ..       4      14 ..       2      17 .. 0.70
   2 !   22.5   0.0   1.1e-07   0.00011       3      43 ..      22      60 ..      19      65 .. 0.86
   3 !    8.3   0.1    0.0028       2.8      62      91 ..      54      83 ..      50      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.3
                                      HHHGGGS-TTS CS
                     Thioredoxin_8 51 ekylkknkkpw 61
                                      ek +k nk++w
  gi|488601062|ref|YP_007907533.1|  4 EKIFKLNKNNW 14
                                      67788887788 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.1e-07
                                      EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE- CS
                     Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl 43
                                      vv++ f+a+wcppc ++ p l el e +k  +kv++   ++
  gi|488601062|ref|YP_007907533.1| 22 VVVVDFYADWCPPCFKIEPILEELAEAFK--NKVKVCKFNV 60
                                      89**************************9..7887766555 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0028
                                      EE.EE-TT-HHHHTT-S--TT-SEEEEE-T CS
                     Thioredoxin_8 62 lsvpfddkkrnklkkkynvkaiPtlvvldk 91
                                        + f+ ++ +++  ky+++ +Pt++v ++
  gi|488601062|ref|YP_007907533.1| 54 KVCKFNVEEDDEIPTKYGIQVLPTIYVFKN 83
                                      567899999*****************9874 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   1.4   1.3e-08   1.3e-05       8     107 ..      23     101 ..      19     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.3e-08
                     Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt. 83 
                                       v+v+f++++Cp C k++  l+el    +      +k++++   +++  ++e +              kyg++ +Pt 
  gi|488601062|ref|YP_007907533.1|  23 VVVDFYADWCPPCFKIEPILEEL---AEA-----FKNKVKVCKFNVEEDDEIP-------------TKYGIQVLPTi 78 
                                       89****************99999...444.....8888888888888888888.............89********5 PP

                     Thioredoxin_2  84 ivfldgkeivarlpGyvpaeelea 107
                                        vf +g+  +  ++G+ ++e + +
  gi|488601062|ref|YP_007907533.1|  79 YVFKNGD-TYSGVEGLAKKESIFK 101
                                       5599999.8889999998877655 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.5e-09   3.5e-06      26     103 ..      18      94 ..       8      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.5e-09
                                       HSEEEEEESS-SS-SSSSS-HCHHHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEESS CS
                              HyaE  26 agdavlllagDpkrfpEvsDvaVvlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvlaki 102
                                        g +v+++   +   p +     +l El +aF+n  +   ++  e+++++  ++g+++ P++ ++++g++ + ++++
  gi|488601062|ref|YP_007907533.1|  18 VGSGVVVVDFYADWCPPCFKIEPILEELAEAFKNKVKVCKFN-VEEDDEIPTKYGIQVLPTIYVFKNGDTYSGVEGL 93 
                                       566666666667777778888889************999999.999*************************999997 PP

                                       S CS
                              HyaE 103 r 103
                                        
  gi|488601062|ref|YP_007907533.1|  94 A 94 
                                       5 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   6.8e-08   6.8e-05      23      71 ..      17      64 ..       5      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.8e-08
                                      HTT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH CS
                          AhpC-TSA 23 ykg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe 71
                                      + g  +vv+ fy+  wcp+C +  p l++l+e+fk ++v+v   +v++ +
  gi|488601062|ref|YP_007907533.1| 17 IVGsGVVVVDFYAD-WCPPCFKIEPILEELAEAFK-NKVKVCKFNVEEDD 64
                                      54433889999999.********************.67999888887665 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   7.8e-05     0.078      82     159 ..       9      82 ..       2      87 .. 0.54
   2 !   13.4   0.1   5.5e-05     0.055       9      71 ..      42     103 ..      37     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.8e-05
                                       -SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEE CS
                     Thioredoxin_6  82 ltpenaeelfeeglppllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPviviv 158
                                       l+++n  e+  +g  ++++ f+        k++ ++e++a++fk+k++++  ++++  ++   +g++   lP+i ++
  gi|488601062|ref|YP_007907533.1|   9 LNKNNWREIVGSG--VVVVDFYADWCPPCFKIEPILEELAEAFKNKVKVCKFNVEEDDEIPTKYGIQ--VLPTIYVF 81 
                                       5666666666666..4566666433334445555666666666666666666666444444455555..55555554 PP

                                       E CS
                     Thioredoxin_6 159 d 159
                                       +
  gi|488601062|ref|YP_007907533.1|  82 K 82 
                                       4 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHTTT-T.TSEEEEE--HHHHHHTT--S.SEEEEEETTTTEEEEEETHT--HHHHHHHH CS
                     Thioredoxin_6   9 seiFekvakelkgdvrfgvtkskevadklgvke.pavllfrkfdeekvkydgekitvddlkkfi 71 
                                        e++ +++k+  + + f v  ++e+ +k+g++  p++++f++ d+    ++g   +++++ k +
  gi|488601062|ref|YP_007907533.1|  42 LEELAEAFKNKVKVCKFNVEEDDEIPTKYGIQVlPTIYVFKNGDTY-SGVEGL-AKKESIFKLV 103
                                       345555555555559**************************97764.445554.4666666555 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   4.2e-07   0.00041      20      81 ..      23      81 ..      21      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.2e-07
                                      EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---...SSEEEEE CS
                     Thioredoxin_7 20 vlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqg...vPvvafl 81
                                      v v+f a+wc++C ++e  +++    ++a+++k+ +++++v+e d+ i   +++g   +P++ ++
  gi|488601062|ref|YP_007907533.1| 23 VVVDFYADWCPPCFKIEPILEEL---AEAFKNKVKVCKFNVEEDDE-I-P-TKYGiqvLPTIYVF 81
                                      679**************999876...566****************8.4.3.33334449999988 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   8.2e-07   0.00082      25      73 ..      16      63 ..       8      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.2e-07
                                      H.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSS CS
                           Redoxin 25 e.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadnd 73
                                      e +  ++vvv f++  +cP+C +  p le+lae +k+k v+v   ++ +d
  gi|488601062|ref|YP_007907533.1| 16 EiVGSGVVVVDFYAD-WCPPCFKIEPILEELAEAFKNK-VKVCKFNVEED 63
                                      545567789999999.*******999*****9997777.77776666666 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.3   0.00057      0.57       7      31 ..      31      55 ..      26      61 .. 0.88
   2 !    6.9   0.0    0.0045       4.4     142     172 ..      59      89 ..      53     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00057
                     Thioredoxin_5  7 lcseCweiEpelkklkveygekikl 31
                                      +c+ C++iEp+l  l +  ++k+k+
  gi|488601062|ref|YP_007907533.1| 31 WCPPCFKIEPILEELAEAFKNKVKV 55
                                      8*****************9999975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0045
                     Thioredoxin_5 142 afqcDlklakemgvtevPtlvffneneeeeg 172
                                       + ++D ++ + +g++ +Pt+++f + ++ +g
  gi|488601062|ref|YP_007907533.1|  59 NVEEDDEIPTKYGIQVLPTIYVFKNGDTYSG 89 
                                       5678999****************95444444 PP

>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.7e-06    0.0027      22      83 ..      22      83 ..      16     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-06
                                      EEEEEEE-TT-HHHHHHHHHHHHHHHHTTTTEEEEEEETTT--TTSCCCTT-SSSEEEEEET CS
                              DIM1 22 lvviRFGrdedaeClklDelLakiaeklknfaviylvdidevpdfnkmyeledpvtilffyr 83
                                      +vv+ F  d+ + C k++ +L++ ae+ kn +++   +++e  +  + y ++   ti +f +
  gi|488601062|ref|YP_007907533.1| 22 VVVVDFYADWCPPCFKIEPILEELAEAFKNKVKVCKFNVEEDDEIPTKYGIQVLPTIYVFKN 83
                                      8***************************************************9999999944 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.1e-06    0.0041      11     106 ..       4      85 ..       1     107 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.1e-06
                         OST3_OST6  11 ngviklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdv 87 
                                       +++ kln++n++e++      s vv+ +       C +C ++ep +e +a++++++       +  +k +++e  ++
  gi|488601062|ref|YP_007907533.1|   4 EKIFKLNKNNWREIVG-----SGVVVVDFY--ADWCPPCFKIEPILEELAEAFKNK-------VKVCKFNVEEDDEI 66 
                                       5789999999999996.....444444444..247*****************9988.......77999********* PP

                         OST3_OST6  88 FqklglnsaPhlllfppkk 106
                                         k+g++ +P +++f+  +
  gi|488601062|ref|YP_007907533.1|  67 PTKYGIQVLPTIYVFKNGD 85 
                                       ***************9843 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.8e-06    0.0087     136     202 ..      27      84 ..      15      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.8e-06
                              TraF 136 FyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpk 202
                                       Fy+  cp c +  pil+++a+ ++ +v++ + + + ++e+p          ++g++  P++++++  
  gi|488601062|ref|YP_007907533.1|  27 FYADWCPPCFKIEPILEELAEAFKNKVKVCKFNVEEDDEIPT---------KYGIQVLPTIYVFKNG 84 
                                       9****************************************9.........***********99876 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   1.1e-05     0.011       6      55 ..      29      80 ..      22      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                      STSSHHHHHHHHHHHHTTGGE.EEEEGCCSH.HHHHHHHHHHTSSSSSEEEE CS
                      Glutaredoxin  6 kptCpyCkkakrlLkelgvkf.eeidvdkde.eireelkelsgvrtvPqvfi 55
                                        +Cp C k+  +L+el  +f   + v k   e+ +e+  + g++ +P++++
  gi|488601062|ref|YP_007907533.1| 29 ADWCPPCFKIEPILEELAEAFkNKVKVCKFNvEEDDEIPTKYGIQVLPTIYV 80
                                      489**************9666666666666666679999999********98 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.7   1.2e-05     0.011      36      67 ..      30      61 ..       8     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                      BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE-- CS
                            DUF953 36 sWCPdCvkaepvieealkeapedvklvrvdvG 67
                                       WCP C k ep++ee  + + + vk+ + +v 
  gi|488601062|ref|YP_007907533.1| 30 DWCPPCFKIEPILEELAEAFKNKVKVCKFNVE 61
                                      6*************999999999998887775 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.4e-05     0.014      45      90 ..      24      70 ..       2      91 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                      EEEE--TT-HHHHHHHHHHHHHHHH-.TTEEEEEE-HHHHHHHTTTT CS
                     Thioredoxin_9 45 ilvltedwCgDaavnvPvlakiaeln.pnievkillrdenlelmdqy 90
                                      ++ + +dwC+ +  + P+l+++ae+  ++++v  +  +e+ e+  +y
  gi|488601062|ref|YP_007907533.1| 24 VVDFYADWCPPCFKIEPILEELAEAFkNKVKVCKFNVEEDDEIPTKY 70
                                      455789*****************975145666666666666666555 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.5e-05     0.075     147     212 ..      21      88 ..      12      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.5e-05
                                       -EEEEEEE-TTSTTHHHHHHHHHHHHHH-.TTSEEEEEEHHHH.--TTSS-TTT-SEEEEEETTEEEE CS
                         Phosducin 147 tlivvhiyedgvkgtealnssliclaaey.ptvkfckvkasvi.gasdrfsrdvlpallvykagells 212
                                        ++vv  y d  + +  ++  l  la  +   vk ck +         ++  +vlp++ v+k g+  s
  gi|488601062|ref|YP_007907533.1|  21 GVVVVDFYADWCPPCFKIEPILEELAEAFkNKVKVCKFNVEEDdEIPTKYGIQVLPTIYVFKNGDTYS 88 
                                       6899*********************9777268*****99876516789****************8765 PP

>> SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.7e-05     0.077     138     171 ..      34      67 ..       3     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-05
                                       HHHHHHHHHHHHHHTTTSEEEEEE-SSHHHHHHH CS
                     SpoIISA_toxin 138 yieglkkllksyadkfeisvsivpfevkeekdel 171
                                          +++ +l+++a+ f+ +v++++f+v+e+++  
  gi|488601062|ref|YP_007907533.1|  34 PCFKIEPILEELAEAFKNKVKVCKFNVEEDDEIP 67 
                                       5568999*********************998754 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011      0.11      10      50 ..      32      74 ..      27     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      -HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCTTT CS
                            DUF836 10 ChlCeqakekLkelkleeg..leleviDIakdeeleakYglei 50
                                      C+ C +++ +L+el+++ +  +++ + ++++d+e  +kYg ++
  gi|488601062|ref|YP_007907533.1| 32 CPPCFKIEPILEELAEAFKnkVKVCKFNVEEDDEIPTKYGIQV 74
                                      99**********9776655559*****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 837.26
//
Query:       gi|488601063|ref|YP_007907534.1|  [L=195]
Description: hypothetical protein Asulf_01564 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-52  177.6   0.0    2.5e-52  177.3   0.0    1.0  1  ThiI           Thiamine biosynthesis protein (ThiI)
    2.1e-08   33.9   0.0    7.1e-05   22.4   0.0    2.7  1  QueC           Queuosine biosynthesis protein QueC
     0.0018   17.2   0.0     0.0026   16.6   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
     0.0078   16.3   0.0     0.0098   15.9   0.0    1.1  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


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 !  177.3   0.0   5.7e-56   2.5e-52       6     188 ..       3     178 ..       1     184 [. 0.90

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 5.7e-56
                              ThiI   6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilek 82 
                                        l+LlSgGiDSpV+ayl+lkRG++v+++h+      s + ++ v  + +l   ++   + +l+v ++ +++ ei++k
  gi|488601063|ref|YP_007907534.1|   3 LLSLLSGGIDSPVSAYLMLKRGFEVDFLHFY----YSRDFEKIVDIISRLKDLFN--YSPRLFVAPHSRIV-EITRK 72 
                                       699***************************4....55555555554554444555..578******99876.7**** PP

                              ThiI  83 vkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiiklAkei 159
                                        + + t+v +k +ml+ Aek+ae+ +a+ l+ G+sLgqVaSqt++Nl v + +v++++lrPLigldK eii++ ++ 
  gi|488601063|ref|YP_007907534.1|  73 YERRFTCVYCKISMLKCAEKLAEKINAQGLLMGDSLGQVASQTIQNLFVEDRAVKIPVLRPLIGLDKVEIIDISRKA 149
                                       ***************************************************************************** PP

                              ThiI 160 gtyeisiekedkCsvlakhPttkakleev 188
                                       g yeisi+k+  C++++++P t   ++++
  gi|488601063|ref|YP_007907534.1| 150 GLYEISIRKTVPCPAVPEKPATSVSIDRI 178
                                       *********************99887766 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.6e-08   7.1e-05       3      49 ..       4      50 ..       2     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.6e-08
                                      EEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHH CS
                              QueC  3 vvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiak 49
                                      + llSGG+DS + ++l++k+g ev  l+f Y +  +k +++ +++ +
  gi|488601063|ref|YP_007907534.1|  4 LSLLSGGIDSPVSAYLMLKRGFEVDFLHFYYSRDFEKIVDIISRLKD 50
                                      789****************************9877666666665555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.7e-07    0.0026       2      33 ..       2      33 ..       1      51 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-07
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflk 33
                                      +++ +lSgG+DS v+a+l+ ++g+ev  +++ 
  gi|488601063|ref|YP_007907534.1|  2 RLLSLLSGGIDSPVSAYLMLKRGFEVDFLHFY 33
                                      67789********************9877665 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.2e-06    0.0098       4     145 ..       5     143 ..       2     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-06
                                       EE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC CS
                       PAPS_reduct   4 vsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee 80 
                                        + sgG+ds V   L+lk   +v +++    + f+++++ + +l++ ++    +++ +++  + ++  ++ ++ ++ 
  gi|488601063|ref|YP_007907534.1|   5 SLLSGGIDSPVSAYLMLKRGFEVDFLHFYYSRDFEKIVDIISRLKDLFNYSPRLFVAPHS--RIVEITRKYERRFTC 79 
                                       578*******************************************99998666666666..222222222356666 PP

                                       HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-.CCCT--HHHHH CS
                       PAPS_reduct  81 aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvf.PllnWteedvw 145
                                        +++i  ++ ++k  ek++++ ll+G    + +s+  ++++ +d++ +  + v+ Pl+  ++ ++ 
  gi|488601063|ref|YP_007907534.1|  80 VYCKISMLKCAEKLAEKINAQGLLMGDSLGQVASQTIQNLFVEDRAVK--IPVLrPLIGLDKVEII 143
                                       788888887788878888888888888888888888888888888865..6666688877777776 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:                      495  (0.0276089); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1422.71
//
Query:       gi|488601064|ref|YP_007907535.1|  [L=169]
Description: Conserved protein/domain typically associated with flavoprotein oxygenase, DIM6/NTAB family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-23   82.0   0.0    5.2e-23   81.8   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain
  ------ inclusion threshold ------
       0.29   10.6   1.8        2.3    7.7   0.2    2.0  2  GTP_EFTU       Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   5.8e-27   5.2e-23       4     146 ..       9     147 ..       6     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 5.8e-27
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHH.HHHHTCS... CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqea.ladafsqksg 79 
                                       +  + +vv +  ++++ ++ +++++++++ +P  va+++++++ t+++++ +g f +++l+++     +  f+ +sg
  gi|488601064|ref|YP_007907535.1|   9 ISYGLYVVAS-MKDGRFNAQIANTVFQVTSQPVKVAVCINKQNLTHEFIEHSGLFSVSILKKETPMkFIGTFGFRSG 84 
                                       6678888888.899************************************************88766********** PP

                                       SCCCCCCCCCCCEEECTCCCSEEE.TTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTTBEEC CS
                     Flavin_Reduct  80 prtddksifagltweesptgapal.lgalasleCqvvgsvelgdhelfigeVvavkvgddadeepLly 146
                                        r+ dk  f+g+++ +++ g p++ ++++a++e++vv+s+++g+h+lf+geV ++++ dd  +e + y
  gi|488601064|ref|YP_007907535.1|  85 -RDIDK--FEGVNYITGKKGTPIVvDNSVAYIEAEVVNSLDVGSHTLFVGEVIDAEIFDD--GEVMTY 147
                                       .*****..*********999998879*****************************99997..344444 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2   0.00025       2.3      98     135 ..      13      52 ..       4     114 .. 0.84
   2 ?    2.8   0.2    0.0083        74      68     114 ..     114     164 ..      98     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00025
                                       EEEE.ETTTB.STHHHHHHHHHHHHTTTEEEEEEESCGST CS
                          GTP_EFTU  98 vlvv.daveG.vepqteevlrlalkegvpiivfiNKmDrl 135
                                       + vv + ++G  ++q  + + ++ ++ v++ v+iNK   +
  gi|488601064|ref|YP_007907535.1|  13 LYVVaSMKDGrFNAQIANTVFQVTSQPVKVAVCINKQNLT 52 
                                       4555055566899***********************7665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0083
                                       SSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETT....TBSTHHHHHH CS
                          GTP_EFTU  68 kkylinliDtPGHvdFskevirglrvlDgavlvvdav....eGvepqteev 114
                                       +   +n +D   H  F+ evi +    Dg v+  d      +G +p+t +v
  gi|488601064|ref|YP_007907535.1| 114 EAEVVNSLDVGSHTLFVGEVIDAEIFDDGEVMTYDYYhsikKGKTPKTATV 164
                                       567899999999***********9999999999986533337777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.33s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 1157.37
//
Query:       gi|488601065|ref|YP_007907536.1|  [L=266]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-97  324.5  23.0      1e-96  324.4  23.0    1.0  1  DUF63     Membrane protein of unknown function DUF63
  ------ inclusion threshold ------
        1.6    8.6   5.1       0.68    9.8   1.4    2.3  2  CoatB     Bacteriophage coat protein B
        8.4    6.5   5.5        2.3    8.3   1.5    2.2  2  NVEALA    NVEALA protein


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.4  23.0  1.7e-100     1e-96       1     270 [.       3     264 ..       3     266 .] 0.99

  Alignments for each domain:
  == domain 1  score: 324.4 bits;  conditional E-value: 1.7e-100
                             DUF63   1 iseFiykyYidpivykegYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllk 77 
                                       i eFi+kyYid++vyk+gYnivntlt+aiiLi+av++iyk+l+k +ik+dekfv+a+ipy++lgss+RvveDa++lk
  gi|488601065|ref|YP_007907536.1|   3 IYEFIKKYYIDSLVYKQGYNIVNTLTFAIILILAVVAIYKYLSK-RIKFDEKFVIANIPYILLGSSVRVVEDAEFLK 78 
                                       78*****************************************9.******************************** PP

                             DUF63  78 pplsyllitPliyflvflitlavlliskklekklkkdykklyaavGvvlvlvvlllLllteevvnlevlllvlllaa 154
                                       pp+sy+++tP+iy+++fli++++l+is +     k+dy+k+yaavGv+l+++vl++L+++ ev++ +++ ++l++a+
  gi|488601065|ref|YP_007907536.1|  79 PPISYFFMTPFIYIVIFLIAFPTLVISLRK----KEDYWKYYAAVGVFLSAAVLAMLFSSLEVIHGWLIPVTLTAAF 151
                                       ****************************98....9****************************************** PP

                             DUF63 155 vltalvllllrklklellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlipv 231
                                       +++a++++l+rk++   +++ l+ l++++h++D+ atf+gi++lgY+E Hv+p+fLid++G a+vm+p k++v+++v
  gi|488601065|ref|YP_007907536.1| 152 LFAAAYHFLTRKFY-PKMHNGLSDLVFFSHMVDGFATFLGIQFLGYWELHVLPRFLIDTFG-AWVMVPSKIIVFLAV 226
                                       *************9.999*******************************************.*************** PP

                             DUF63 232 lyildkevkeeeelrnlvklailvlGlaPgiRnllrmvl 270
                                       lyild++ ++ + ++n++k++++vlGlaPg+R++lrm++
  gi|488601065|ref|YP_007907536.1| 227 LYILDTSEDDIH-FVNFIKFVLVVLGLAPGMRDALRMCF 264
                                       ********9999.************************98 PP

>> CoatB  Bacteriophage coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.4   0.00011      0.68      27      44 ..      29      46 ..      23      48 .. 0.85
   2 ?   -1.5   0.1      0.38   2.3e+03      36      44 ..     154     162 ..     149     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                             CoatB 27 aaVLvvlVgvavfkWvRR 44
                                       a++ +l++va++k++ +
  gi|488601065|ref|YP_007907536.1| 29 FAIILILAVVAIYKYLSK 46
                                      69*************866 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.38
                             CoatB  36 vavfkWvRR 44 
                                       +a++ +++R
  gi|488601065|ref|YP_007907536.1| 154 AAAYHFLTR 162
                                       89*****99 PP

>> NVEALA  NVEALA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.5   0.00038       2.3       2      38 ..      22      59 ..      21      59 .. 0.89
   2 ?   -2.6   0.1      0.95   5.7e+03       8      20 ..     147     159 ..     143     165 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00038
                            NVEALA  2 kifkilfvlvfavlagtgiyksnkkevslsd.LalaNv 38
                                      +i++ l+++++ +la ++iyk   k +++++  + aN+
  gi|488601065|ref|YP_007907536.1| 22 NIVNTLTFAIILILAVVAIYKYLSKRIKFDEkFVIANI 59
                                      68999******************999999887777776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.95
                            NVEALA   8 fvlvfavlagtgi 20 
                                       + ++f ++a + +
  gi|488601065|ref|YP_007907536.1| 147 LTAAFLFAAAYHF 159
                                       4566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1225  (0.0683251); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.47u 0.55s 00:00:01.02 Elapsed: 00:00:00.75
# Mc/sec: 1069.75
//
Query:       gi|488601066|ref|YP_007907537.1|  [L=254]
Description: DNA end-binding protein Ku [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-39  133.7   0.0    9.7e-39  133.2   0.0    1.2  1  Ku            Ku70/Ku80 beta-barrel domain
     0.0092   14.6   0.5      0.011   14.3   0.5    1.1  1  CCDC154       Coiled-coil domain-containing protein 154
  ------ inclusion threshold ------
       0.04   13.5   0.1       0.14   11.8   0.2    1.8  2  zf_C2H2_13    Zinc finger domain
      0.054   13.0   0.2       0.12   11.9   0.2    1.6  1  TF_Zn_Ribbon  TFIIB zinc-binding


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 !  133.2   0.0   2.2e-42   9.7e-39       2     203 ..      11     190 ..      10     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 2.2e-42
                                Ku   2 gggvsipVklykateeakkpkfkkldketnepvkvetkyvcsdtge.vdeedivkgyey.Ggevvpltkeelekiks 76 
                                       +g+v++p+kly+ t   k++ fk l++e++   +v++k+vc+++g+ + ++divkgye+  +e+v+lt+e++eki+ 
  gi|488601066|ref|YP_007907537.1|  11 FGLVNVPIKLYTSTLP-KDVEFKLLHREDGG--RVRYKRVCEKCGKeLGKNDIVKGYEIsKDEYVLLTDEDFEKIPL 84 
                                       799************9.**************..***********777************9889***********999 PP

                                Ku  77 fdskglkllgFvplseilkeylsikssyfiyPddkdekgstkafsaLveamleskkvaivrfvlrskskprlvaLvP 153
                                        ++k++++ +F + +e+   ++  +  y+i P    ekgs++a+ +L++am+e++ ++i ++++r+k++  lva++P
  gi|488601066|ref|YP_007907537.1|  85 KTTKTIQIRQFFSPEELGVVFY--NGFYYISP----EKGSERAYYLLRRAMEETNSIGIGKVTMRNKEN--LVAVRP 153
                                       66**************777777..67******....899999***************************..****** PP

                                Ku 154 qeeelsseeekeglvlvtLpfaddiRslkfpsldeeeeekknkpteeqld 203
                                       +       +  +gl+lv+L+f ++iR++   ++   +  k++ +tee+++
  gi|488601066|ref|YP_007907537.1| 154 Y-------D--GGLILVQLHFLEEIRNPMEVPF---WG-KEEDITEEEIE 190
                                       *.......3..4**************8777777...32.55688888886 PP

>> CCDC154  Coiled-coil domain-containing protein 154
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.5   2.5e-06     0.011     254     324 ..     182     252 ..     164     254 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-06
                           CCDC154 254 kqiqqEeaklleqcrkldeAvvqLtkfvrqnqvslnrvllaeqkarkakvtleesraeelasylqesleav 324
                                       + i++Ee +l ++     +   ++++fv + ++ l  +++a+++ r++kv+ e ++++ l+  l+esle +
  gi|488601066|ref|YP_007907537.1| 182 EDITEEEIELAKKLILAMKKPLRIEEFVDEYKNALLELINAKIEGREVKVSEELEEVKSLIEALKESLEVI 252
                                       567777777777776666667899********************************************965 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2     3e-05      0.14      18      33 ..      46      61 ..      39      65 .. 0.83
   2 ?   -2.5   0.0      0.89     4e+03      25      34 ..     201     210 ..     201     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                        zf_C2H2_13 18 RvCnkCGkPisleaiv 33
                                      RvC+kCGk +  + iv
  gi|488601066|ref|YP_007907537.1| 46 RVCEKCGKELGKNDIV 61
                                      9*******88777666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.89
                        zf_C2H2_13  25 kPisleaivd 34 
                                       kP+ +e  vd
  gi|488601066|ref|YP_007907537.1| 201 KPLRIEEFVD 210
                                       8999999998 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   0.2   2.7e-05      0.12      19      39 ..      45      65 ..      42      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                      CEEESSSSBEEEECCCCCCCH CS
                      TF_Zn_Ribbon 19 elvCtdCGlVlednsidegpe 39
                                        vC++CG  l  n+i++g e
  gi|488601066|ref|YP_007907537.1| 45 KRVCEKCGKELGKNDIVKGYE 65
                                      569**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1212  (0.0676); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1803.45
//
Query:       gi|488601067|ref|YP_007907538.1|  [L=331]
Description: DNA polymerase LigD, ligase domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   0.1    1.5e-30  106.4   0.1    1.2  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    1.6e-17   63.9   0.0    2.5e-17   63.3   0.0    1.3  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    0.00044   20.1   0.2      0.036   13.9   0.0    2.9  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 !  106.4   0.1   2.5e-34   1.5e-30      17     204 .]      27     203 ..      18     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 2.5e-34
                                       TTTSEEEEEEEESSEE..EEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBE CS
                    DNA_ligase_A_M  17 leekafivEiKyDGeR..aqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketgeil 91 
                                       +++++ ++EiK+DG+R  a v+ ++++ +l  Rr  di +++pe   + +e+f k   sv+lDGE+v++ + +  ++
  gi|488601067|ref|YP_007907538.1|  27 FSSSDYLYEIKWDGTRciAFVDVDENRLRLQNRRFLDIKYRYPEF--RFHEQFSK---SVVLDGEIVVLHNGRSDFR 98 
                                       4466778**********999999*********************9..77788887...59********988877777 PP

                                       HHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHH CS
                    DNA_ligase_A_M  92 pfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveele 168
                                         qk  + + ++ k++ + + ++++++vFDiL  dge ++d+pl eR+k+L+e++    +++ +++ + ++     +
  gi|488601067|ref|YP_007907538.1|  99 LLQKREQIE-NRAKIRILSSMYPAVYVVFDIL-WDGEWIMDLPLIERKKILSELT-DTAENLMISDYILGEG----T 168
                                       777766665.44458888899***********.8*********************.7777777888887766....8 PP

                                       HHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 169 elleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                       e++++ai+ g EG+++K+ +s+Y  g++ + w+K+K
  gi|488601067|ref|YP_007907538.1| 169 EFYKKAIELGFEGIMAKKLESPYILGRS-DYWIKIK 203
                                       9*************************98.******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 !   63.3   0.0   4.3e-21   2.5e-17       2      99 .]     223     318 ..     222     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 4.3e-21
                                       GGSEEEEEEEEEETTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCE..SS---HHHHTTEEE-TT-EEEEEESE CS
                    DNA_ligase_A_C   2 gglvgslllgvyddgkleyvgkvgtGfsdaeleelrkklkelerkkppf..aekvpeeekrdvWvePelvveVkfae 76 
                                       ++++gslllg+yd+ +l y+g+vgtGf+ + le ++k++k+l  ++ ++   e+ +  ++    ++P +v+eV+f e
  gi|488601067|ref|YP_007907538.1| 223 EQHFGSLLLGLYDGSDLIYIGRVGTGFDSEFLEYFAKRIKKLVVDRLSIknFEEIEMVRRDVGLIKPYYVAEVEFLE 299
                                       689*************************************777777666424555555444478************* PP

                                       EECTSSSTTEECT-EEEEE-TTS CS
                    DNA_ligase_A_C  77 itasgkykaslRfPrfkrlReDk 99 
                                       +t++     +lR P+fkrlR Dk
  gi|488601067|ref|YP_007907538.1| 300 VTNEL----KLRAPVFKRLRLDK 318
                                       *****....************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 !   13.9   0.0   6.1e-06     0.036      15      84 ..      29      92 ..      23     102 .. 0.79
   2 ?    2.5   0.0     0.019   1.1e+02      92     119 ..     122     148 ..     112     164 .. 0.82
   3 ?   -1.2   0.0      0.25   1.5e+03     168     195 .]     176     203 ..     167     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-06
                                      HS-EEEEEEESSEEEEEEEEECTEEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEEEEEEEC CS
                   mRNA_cap_enzyme 15 qkkYvvseKaDGiRylmllteeeegvylidRenevyrvenlrfprekdkeklekvldetllDgElvidkv 84
                                        +Y    K DG+R++ +++ +e+   l +R  ++  ++  r+p+ +     e++ ++ +lDgE+v+ ++
  gi|488601067|ref|YP_007907538.1| 29 SSDYLYEIKWDGTRCIAFVDVDENRLRLQNR--RFLDIK-YRYPEFRF---HEQFSKSVVLDGEIVVLHN 92
                                      67889999**************987888777..567777.88888884...456888999******9655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.019
                                       EEEEEEEEEETTEEGTTSBHHHHHHHHH CS
                   mRNA_cap_enzyme  92 ryliyDivaingvtvaeeplskRleilk 119
                                        y+++Di+  +g  +++ pl +R +il 
  gi|488601067|ref|YP_007907538.1| 122 VYVVFDIL-WDGEWIMDLPLIERKKILS 148
                                       69****98.69************99885 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.25
                                       TSTEEEEEEEESSSB--SEEEEEEEEE- CS
                   mRNA_cap_enzyme 168 shesDGLIfqpvkepyvagrdsdllKwK 195
                                       +    G++ +  ++py+ gr +  +K K
  gi|488601067|ref|YP_007907538.1| 176 ELGFEGIMAKKLESPYILGRSDYWIKIK 203
                                       5556788999999*******99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2484.32
//
Query:       gi|488601068|ref|YP_007907539.1|  [L=205]
Description: Zn-dependent hydrolase, including glyoxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-27   94.9   0.0    7.6e-27   94.6   0.0    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    8.7e-07   28.6   0.0      1e-06   28.4   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.015   14.5   0.0       0.02   14.0   0.0    1.1  1  PDEase_II      cAMP phosphodiesterases class-II
      0.074   12.5   0.0       0.16   11.4   0.0    1.5  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 !   94.6   0.0   1.7e-30   7.6e-27       5     197 .]      10     192 ..       6     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.7e-30
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       ++n+yl+     ++LiDtGts++ ++++     + + ++++d +i+TH+HlDHiG +g l ++ +++v+a++++ p+
  gi|488601068|ref|YP_007907539.1|  10 GCNVYLL----NNYLIDTGTSNSGEMIL-----KQISDEKIDGIIITHAHLDHIGSAGFLQRELGCKVYAHELDIPY 77 
                                       6899999....79**************9.....8******************************************* PP

                                       CHCHHHHHHHHHCCHH........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECT CS
                       Lactamase_B  82 lfmeeaddaasrkgll........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGD 150
                                        +++ + +++++ g+l        + ++++    +d+  + +++g+   + +   +++gh++g++++  +k l++GD
  gi|488601068|ref|YP_007907539.1|  78 ILGDKKLRYSGFLGILvrfgerlfKWEPPEEVEKIDKILDVFEVGESTHTDIAALHTPGHTPGSICLIYDKNLICGD 154
                                       ********************88884444455555555555566666666666777778888888888889******* PP

                                       TTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 151 allagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       +l  g+    ++          sd+e+yl+s++ + +l+ e+++ gH
  gi|488601068|ref|YP_007907539.1| 155 LLRDGKLSNKSF---------CSDYEQYLHSVRAIMDLDFELVYSGH 192
                                       ***999999999.........*************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.3e-10     1e-06       2      63 ..      18      71 ..      17     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.3e-10
                                      EEEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEEEE CS
                     Lactamase_B_2  2 riLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre..lrpkklplyap 63
                                      ++LiD+g++  +   l++       de  +id++++thaH DH+  + +l++  +     ++ya+
  gi|488601068|ref|YP_007907539.1| 18 NYLIDTGTSNSGEmILKQI-----SDE--KIDGIIITHAHLDHIGSAGFLQRelG----CKVYAH 71
                                      89*******7777333333.....556..***************66666666432....457776 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-06      0.02      67      97 ..      27      57 ..       6      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-06
                                      HS-HHHHHHHHHHTEEEEE-S---GGGTHHH CS
                         PDEase_II 67 sereikktyeiknniksylItHsHLDHvsgl 97
                                      +  e+   + + ++i    ItH+HLDH++++
  gi|488601068|ref|YP_007907539.1| 27 NSGEMILKQISDEKIDGIIITHAHLDHIGSA 57
                                      44556667888999**************985 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.5e-05      0.16      10      71 ..      20      70 ..      16      73 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                     Lactamase_B_6 10 LlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvya 71
                                      L+D G+++s    e +lk++++  +++d i+++ha l+h+G+  +l  +      l ++vya
  gi|488601068|ref|YP_007907539.1| 20 LIDTGTSNS---GEMILKQISD--EKIDGIIITHAHLDHIGSAGFLQRE------LGCKVYA 70
                                      788888875...2345665554..79***************85444432......3456665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1603.14
//
Query:       gi|488601069|ref|YP_007907540.1|  [L=127]
Description: translation initiation factor 5A precursor (eIF-5A) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   20.7   0.0    0.00055   19.9   0.0    1.4  1  EFP_N     Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> 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 !   19.9   0.0   3.1e-08   0.00055       3      33 ..       8      38 ..       6      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.1e-08
                                      GG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                             EFP_N  3 selkkGlvieidgklyvVlefehvkpGkGqa 33
                                       +lk G  + id++++ +l++  +kpGk +a
  gi|488601069|ref|YP_007907540.1|  8 RQLKEGGYVVIDDEPCEILSISVSKPGKHGA 38
                                      589*************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 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:                        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 0.21s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 984.60
//
Query:       gi|488601070|ref|YP_007907541.1|  [L=280]
Description: agmatinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-61  208.7   0.0    1.4e-61  208.5   0.0    1.0  1  Arginase   Arginase family
  ------ inclusion threshold ------
      0.068   13.7   0.0       0.11   13.0   0.0    1.3  1  TetR_C_18  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.5   0.0   1.6e-65   1.4e-61       2     277 ..      18     272 ..      17     274 .. 0.87

  Alignments for each domain:
  == domain 1  score: 208.5 bits;  conditional E-value: 1.6e-65
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHH CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeava 77 
                                       +++++G+P+d++ s++pG+rf+P+aireas++le+   y+l ++  l+ +k++d+g+v+++  +    ++ +e+a +
  gi|488601070|ref|YP_007907541.1|  18 EFIIFGIPYDGTQSFKPGSRFAPNAIREASWNLES---YSLFRNLdLSLVKVFDAGNVNTDG-SF---TQILERASE 87 
                                       689*******************************8...7777777799**********8863.44...444444444 PP

                                       HHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEE CS
                          Arginase  78 eilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvq 154
                                        + k + +pi++GG+H+i+ ++++ +++k   +++ + fDAH+Dlr++  +++ ++h++ +rr+  e+     k+vq
  gi|488601070|ref|YP_007907541.1|  88 FLSKLKGFPIAIGGEHTISCSCMEFVRKK---NACYLVFDAHFDLRDEF-DDNPFNHACTVRRIF-EK---VGKVVQ 156
                                       4444588*****************99987...68*************88.9**************.33...358*** PP

                                       EEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-H CS
                          Arginase 155 iGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltl 231
                                       +Girs  +ee+++a+  gi+v+   +i +  + + ++e+ +++ ++ d +y+S+D+D +Dpa+aPG++tpep G+ +
  gi|488601070|ref|YP_007907541.1| 157 FGIRSGIAEERRFAEGNGIEVFYSWDILDDPK-KKISELIRVL-DQFDRIYVSLDMDSFDPAFAPGVSTPEPFGIHP 231
                                       ***************************88766.5566666777.4789***************************** PP

                                       HHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 232 rellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                         +++++ e+++  +++g+D+vEv P+    ++ t  laa+l+ el
  gi|488601070|ref|YP_007907541.1| 232 IHFMKIISEISD--RIIGFDLVEVVPDG---NKVTQTLAAKLIVEL 272
                                       **********77..9***********93...348999******995 PP

>> TetR_C_18  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05      0.11      46      84 ..     241     279 ..     236     280 .] 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                         TetR_C_18  46 agdrvfqvfmkevlpsaaeasraragelivttlstvGka 84 
                                       ++dr+++  + ev+p+ ++ ++++a++liv+ +s++G +
  gi|488601070|ref|YP_007907541.1| 241 ISDRIIGFDLVEVVPDGNKVTQTLAAKLIVELISSIGSN 279
                                       79**********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 2059.52
//
Query:       gi|488601071|ref|YP_007907542.1|  [L=166]
Description: Rubrerythrin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-26   92.0  14.8    2.9e-25   89.3  14.8    1.9  1  Rubrerythrin     Rubrerythrin
    0.00048   20.1   5.6     0.0013   18.6   5.6    1.7  1  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
      0.032   14.3   1.6      0.075   13.2   1.6    1.6  1  Zn-ribbon_8      Zinc ribbon domain
       0.04   13.9   0.2      0.062   13.3   0.2    1.3  1  DZR              Double zinc ribbon
      0.067   13.1   0.1        0.1   12.5   0.1    1.2  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
       0.19   11.4   1.5        1.8    8.3   0.1    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.57   10.5   4.5       0.63   10.4   0.3    2.3  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
        1.8    8.3   6.2          1    9.1   0.9    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        2.7    8.1   5.5        4.7    7.3   0.8    2.3  2  Rubredoxin       Rubredoxin
        3.5    7.4   5.0        6.7    6.5   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 !   89.3  14.8   1.6e-28   2.9e-25       1     136 [.       5     119 ..       5     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 1.6e-28
                                       HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS------- CS
                      Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakp 76 
                                       ++Le+A+agEs+a r+Y ++aeka+ eg++++a++F+  Ae E  Ha ++ k+++ ++++le               
  gi|488601071|ref|YP_007907542.1|   5 KNLEAAFAGESMANRRYLAFAEKAEkEGFKNVARIFRTAAESETIHAINHLKVMGGIKETLE--------------- 66 
                                       69************************************************************............... PP

                                       TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  77 kflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                              nL+ a eg+++e eemy+++ e+a+kegn++a+++f +++eaEk H+e+++++
  gi|488601071|ref|YP_007907542.1|  67 -------NLKVAFEGETYEKEEMYPKFIEEAKKEGNKQAERTFTWAIEAEKVHAELYKRA 119
                                       .......**************************************************986 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   5.6   7.5e-07    0.0013       2     117 ..       5     134 ..       4     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.5e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH....... CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee....... 71 
                                       k L++++a e  a   yla+a  ++ +g++++a  f++ ae e+ ha   ++ +  + +t         +       
  gi|488601071|ref|YP_007907542.1|   5 KNLEAAFAGESMANRRYLAFAEKAEKEGFKNVARIFRTAAESETIHAINHLKVMGGIKETLENL-----Kvafeget 76 
                                       7899999****************************************76666665555533333.....13344477 PP

                                       ...........C-SSSS.CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                          Ferritin  72 ...........ieapke.fgsveevleaalehekkvteslrelielaeeegDpatadf 117
                                                  +ea+ke  + +e  +  a+e+ek   e ++++i+ +e+ +D    d+
  gi|488601071|ref|YP_007907542.1|  77 yekeemypkfiEEAKKEgNKQAERTFTWAIEAEKVHAELYKRAIAAVEQGKDVEVGDL 134
                                       77788999996556666556********************************887776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.6   4.2e-05     0.075       6      38 ..     135     161 ..     134     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsevrr 38 
                                       Y Ce Cg + e  +      +++CP Cg+++ +
  gi|488601071|ref|YP_007907542.1| 135 YICEVCGFTVEGEV------PEKCPVCGAKADK 161
                                       89*****7777444......456*****98765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.5e-05     0.062      14      40 ..     136     161 ..     128     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                               DZR  14 fCseCgtklkavaaedrCpsCgekvdp 40 
                                        C+ Cg +++  + +++Cp Cg+k+d+
  gi|488601071|ref|YP_007907542.1| 136 ICEVCGFTVE-GEVPEKCPVCGAKADK 161
                                       7********7.4459********9986 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.7e-05       0.1      23      49 ..     134     161 ..     129     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                                       EEE-HHHHHHHHH.TT-B-TTT--B--E CS
                        zf-C3HC4_3  23 lvlCeeCaekllk.rkkkCpiCrrpiek 49 
                                       l++Ce C  +++    +kCp+C ++ +k
  gi|488601071|ref|YP_007907542.1| 134 LYICEVCGFTVEGeVPEKCPVCGAKADK 161
                                       789********8789*******998765 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.11     2e+02       6      11 ..     136     141 ..     135     143 .. 0.89
   2 ?    8.3   0.1   0.00098       1.8       5      16 ..     150     163 ..     148     166 .] 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                           zf-RRN7   6 pCgvCg 11 
                                       +C+vCg
  gi|488601071|ref|YP_007907542.1| 136 ICEVCG 141
                                       69***8 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00098
                           zf-RRN7   5 ppCgvCgc..rsft 16 
                                       + C+vCg+  + f+
  gi|488601071|ref|YP_007907542.1| 150 EKCPVCGAkaDKFR 163
                                       68******776776 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 ?    1.8   0.4      0.17     3e+02      26      33 ..     135     141 ..     127     149 .. 0.78
   2 ?   10.4   0.3   0.00035      0.63       5      16 ..     151     163 ..     147     166 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                                       EEETTTTB CS
                    Prim_Zn_Ribbon  26 wfCrqCgg 33 
                                       ++C +C g
  gi|488601071|ref|YP_007907542.1| 135 YICEVC-G 141
                                       689999.5 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                                       --TTTT-T.TTEE CS
                    Prim_Zn_Ribbon   5 pCPvCGGr.DrFr 16 
                                        CPvCG++ D+Fr
  gi|488601071|ref|YP_007907542.1| 151 KCPVCGAKaDKFR 163
                                       5*****9879998 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.9   0.00056         1       2      17 ..     130     145 ..     129     148 .. 0.88
   2 ?    1.6   0.4      0.12   2.1e+02       8      13 ..     151     156 ..     150     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00056
                                       -TT-EEE-TTT--EEE CS
                   Desulfoferrod_N   2 eklevYkCevCGniVe 17 
                                       e ++ Y CevCG  Ve
  gi|488601071|ref|YP_007907542.1| 130 EVGDLYICEVCGFTVE 145
                                       57899*******8886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                                       E-TTT- CS
                   Desulfoferrod_N   8 kCevCG 13 
                                       kC vCG
  gi|488601071|ref|YP_007907542.1| 151 KCPVCG 156
                                       9****9 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.054        96       2      10 ..     135     143 ..     134     150 .. 0.86
   2 ?    7.3   0.8    0.0026       4.7      36      47 .]     151     162 ..     144     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.054
                                       EEETTT-BE CS
                        Rubredoxin   2 yeCkvCgyv 10 
                                       y C+vCg+ 
  gi|488601071|ref|YP_007907542.1| 135 YICEVCGFT 143
                                       89*****96 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                                       BBTTTB-BGGGE CS
                        Rubredoxin  36 vCPdCgvekeqF 47 
                                       +CP+Cg++ ++F
  gi|488601071|ref|YP_007907542.1| 151 KCPVCGAKADKF 162
                                       6*******9998 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3    0.0038       6.7       1       9 [.     135     143 ..     135     146 .. 0.92
   2 ?    2.7   0.6     0.058     1e+02      16      22 ..     151     157 ..     151     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0038
                      Rubredoxin_2   1 YvCsqCGfe 9  
                                       Y+C+ CGf+
  gi|488601071|ref|YP_007907542.1| 135 YICEVCGFT 143
                                       9*******8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.058
                      Rubredoxin_2  16 rCpsCgs 22 
                                       +Cp Cg+
  gi|488601071|ref|YP_007907542.1| 151 KCPVCGA 157
                                       7****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      835  (0.0465726); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 1059.39
//
Query:       gi|488601072|ref|YP_007907543.1|  [L=446]
Description: putative acyl-CoA transferases/carnitine dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-96  324.3   0.0    1.2e-96  324.1   0.0    1.0  1  CoA_transf_3  CoA-transferase family III


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.1   0.0  6.6e-101   1.2e-96       1     368 []      38     422 ..      38     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: 324.1 bits;  conditional E-value: 6.6e-101
                      CoA_transf_3   1 LaGvrVldlsq.vlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpsee..kgesayflavnrnKrsvalDlksee 74 
                                       L++v V d+s+  +aG +a+slLA++GA+VI++Epp +gD aRk++p+    k++++++ ++ rnK++++l++++ee
  gi|488601072|ref|YP_007907543.1|  38 LEDVVVFDMSYgSFAGLYASSLLAEYGAKVIRIEPP-GGDIARKMTPFGLkiKDTGLAYIVEGRNKYHITLNIETEE 113
                                       899********99***********************.**********99999************************* PP

                      CoA_transf_3  75 grellkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakr..pgyDlvaqaasGlmslt 149
                                       gr+llk+ ++kADV+ie + pg+l++lg+gy++l++inP Liy+++s yG++Gpka++  p yD+v qa+sG++++t
  gi|488601072|ref|YP_007907543.1| 114 GRDLLKKFIKKADVLIETYAPGYLDSLGIGYRQLSKINPGLIYCAISPYGHFGPKANSkkPDYDVVDQAMSGMCWTT 190
                                       *****************************************************8776666***************** PP

                      CoA_transf_3 150 gepdgp.........PvkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgev 217
                                       g p++          P+k g+++g++v+g +aa++ilaall r++tGkGq idv  +ea +++ ++ +++y+++++v
  gi|488601072|ref|YP_007907543.1| 191 GIPEEYkefpehtrvPTKLGPWMGWYVGGGFAAFGILAALLFRKSTGKGQFIDVVPAEAQAKVNNYYIQYYHTKKRV 267
                                       *98888889999999************************************************************** PP

                      CoA_transf_3 218 perqgnrdpaaapygvyrtkdgwvaiaaatdkqwaalckalgrpelaedprfatnasrlenr..aeldaelaewlae 292
                                         r  n dpa+  y++ r+kdg  ++a ++d ++ al ++++rp+l  ++++ t ++rl  +   e+ ae+++w ++
  gi|488601072|ref|YP_007907543.1| 268 VGRIANFDPAVFVYTLVRAKDGMAFMAGFSDVNFYALTTIINRPDL--REKYPTIKERLSPEtwPECLAEIEKWSKN 342
                                       **9******************************************9..7788888888777777************* PP

                      CoA_transf_3 293 rtaaewlellaaag....vpaapvntleevlddpqlaarglvvevddpdygevpvvglpvrlsetparvkraaPklG 365
                                       +t++e+ ++  ++     ++a++v ++ + ++++ +  rg +++++dp+ygev v+g+++++++tp+r+k+ + ++G
  gi|488601072|ref|YP_007907543.1| 343 KTVKEIIQATLDYTgdgtCVAGEVLKPIDSFKQENWWLRGGLRKINDPNYGEVSVQGVVAKFEKTPGRIKWICREVG 419
                                       ******999888866778*****************************************************998888 PP

                      CoA_transf_3 366 edt 368
                                       +d+
  gi|488601072|ref|YP_007907543.1| 420 ADN 422
                                       886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 2900.94
//
Query:       gi|488601073|ref|YP_007907544.1|  [L=451]
Description: putative acyl-CoA transferases/carnitine dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-115  383.6   0.0   1.1e-114  383.4   0.0    1.0  1  CoA_transf_3  CoA-transferase family III
  ------ inclusion threshold ------
      0.029   15.0   0.0         13    6.5   0.0    2.4  2  PGM_PMM_II    Phosphoglucomutase/phosphomannomutase, alpha/be
       0.16   11.9   0.0       0.23   11.3   0.0    1.2  1  Colicin       Colicin pore forming domain


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.4   0.0  1.8e-118  1.1e-114       1     367 [.      33     401 ..      33     402 .. 0.96

  Alignments for each domain:
  == domain 1  score: 383.4 bits;  conditional E-value: 1.8e-118
                      CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpsee..kgesayflavnrnKrsvalDlkseeg 75 
                                       L+G+rVld++++++Gp+++++LA++GAeVI+vE p++gD++R + p+++  k+ +a f+a n +K+++a+D++++eg
  gi|488601073|ref|YP_007907544.1|  33 LKGIRVLDIGTLIFGPMVATYLAEFGAEVIHVEMPGRGDTMRPLAPFADfhKNLAAGFEATNNSKYHIAIDMRTPEG 109
                                       89************************************************9************************** PP

                      CoA_transf_3  76 rellkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgep 152
                                       +el+ rLv+++DV++eN+rpg+ +r+glgy+++r+inPr+iy+s+sg+Gq Gp+  rp+yD+vaqa sGl+  tg p
  gi|488601073|ref|YP_007907544.1| 110 KELIYRLVKRSDVLVENYRPGTTDRWGLGYRQIRKINPRIIYISMSGFGQWGPWTFRPSYDAVAQATSGLIESTGFP 186
                                       ***************************************************************************** PP

                      CoA_transf_3 153 dgpPvkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaa 229
                                       dg P+k+g ++gD++++l++a+a+l al++re+tG+Gq id  ++e+ l+ +++++++   tg+ +er gnrd a+ 
  gi|488601073|ref|YP_007907544.1| 187 DGLPLKAGAWIGDFYGALMGAFAVLVALYYREKTGEGQYIDHPQAENLLRNMDWTWIYIGLTGKNRERYGNRDVAIV 263
                                       ***************************************************************************** PP

                      CoA_transf_3 230 pygvyrtkdgwvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaag 306
                                       p+++ r+kdg+vaiaa++dk+++ lc+a+gr +l e+    +++ + en+  + ++l ew++e+t++e+++l ++ g
  gi|488601073|ref|YP_007907544.1| 264 PSDIVRCKDGFVAIAAFKDKEFKGLCEAMGRIDLYEKYSDPDERLKEENQTVIYQALHEWAKEKTVKELEDLGEEFG 340
                                       *********************************955555555555555556668*********************** PP

                      CoA_transf_3 307 vpaapvntleevlddpqlaarglvvevddpdygevpvvglpvrlsetparvkraa.PklGed 367
                                       ++  +v + e+ +++++++ar+ +  +ddp yg +  v+ ++++se p+r+k+ a P  G d
  gi|488601073|ref|YP_007907544.1| 341 FASNKVFSSEDQYNNEHWRARKAIWIYDDPIYGSLAEVAPVPKMSESPGRIKWTArPN-GID 401
                                       *******************************************************998.665 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 ?    6.0   0.0     0.003        18       3      87 ..      13     102 ..      12     104 .. 0.85
   2 ?    6.5   0.0    0.0021        13       7      46 ..     298     338 ..     295     363 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.003
                                       HHHHGGGTS-..HHHHHHHT-E..EEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TT.SS----TT-TTTTH CS
                        PGM_PMM_II   3 Yiealkekvd..seaikksglk..vvidplhGaggeilkellkelgvdvvelnaepdpdfpt.kapnpeekealkll 74 
                                       Y+e +ke++d  +  +k ++lk   v+d +    g ++ + l e+g++v+ ++    +d +   ap  + +++l++ 
  gi|488601073|ref|YP_007907544.1|  13 YTEYIKEIMDpeKIFEKPEPLKgiRVLDIGTLIFGPMVATYLAEFGAEVIHVEMPGRGDTMRpLAPFADFHKNLAAG 89 
                                       889999999965555666678876788999999999***************999888888887888888899***** PP

                                       HHHGGGGG-SEEE CS
                        PGM_PMM_II  75 ielvkkegadlgl 87 
                                       +e+ +++++++++
  gi|488601073|ref|YP_007907544.1|  90 FEATNNSKYHIAI 102
                                       ******9999876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0021
                                       GGGTS-.HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-E CS
                        PGM_PMM_II   7 lkekvd.seaikksglkvvidplhGaggeilkellkelgvd 46 
                                       +++  d  e++k+++ +v++ +lh  ++e + + l++lg +
  gi|488601073|ref|YP_007907544.1| 298 YEKYSDpDERLKEENQTVIYQALHEWAKEKTVKELEDLGEE 338
                                       5556667899**************************99983 PP

>> Colicin  Colicin pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.9e-05      0.23      45     113 ..     283     354 ..     275     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                           Colicin  45 kkirslsda...lksfekikrnlnkkikakdrvaiakalesvdkkilaenleklskglGvv.gkaidaekLle 113
                                       k+ + l +a   +  +ek+ + +++++k +++++i +al++  k+   ++le l+  +G+  +k+ + e+ ++
  gi|488601073|ref|YP_007907544.1| 283 KEFKGLCEAmgrIDLYEKYSD-PDERLKEENQTVIYQALHEWAKEKTVKELEDLGEEFGFAsNKVFSSEDQYN 354
                                       555566666222567899975.899**********************************86378888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2919.02
//
Query:       gi|488601074|ref|YP_007907545.1|  [L=330]
Description: putative Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-12   46.7   0.1    8.8e-12   45.4   0.1    1.8  1  SPASM        Iron-sulfur cluster-binding domain
      2e-11   44.6   0.0    4.3e-11   43.5   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
     0.0011   19.1   0.0      0.004   17.3   0.0    2.0  2  Fer4_14      4Fe-4S single cluster domain
     0.0041   17.4   0.0     0.0094   16.2   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.1     2e-15   8.8e-12       3      67 ..     230     324 ..     227     325 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2e-15
                             SPASM   3 apsrslfInsdGdVvpCcvd.............kktyveelklGnireesleeIwnseeyqefr.....ksk..... 56 
                                        p ++++ +++G+V+pC++              +k   e+ ++Gni+e++leeIwn+ ey++fr     +       
  gi|488601074|ref|YP_007907545.1| 230 FPDSAVVFSAEGEVYPCVYLnlpfekiqrifrgRKFLIEKPSFGNITEMDLEEIWNQREYKDFRdvfrrR-Gtkifs 305
                                       47788999*********65578888887777787777777**********************99655441.144556 PP

                             SPASM  57 ........kfplielCrnC 67 
                                                 +++e+C+ C
  gi|488601074|ref|YP_007907545.1| 306 lkrilgleSVNMPEYCKGC 324
                                       7777887777788899999 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   9.6e-15   4.3e-11       1     165 [.       8     160 ..       8     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.6e-15
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEE.ESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevil.gggepllypdfvellerlaklavp 76 
                                       ++vtr Cn+ C  C+        + + +    ei e +  + ++k ++ ++l g gepll++++ e ++ ++     
  gi|488601074|ref|YP_007907545.1|   8 IEVTRKCNMSCLMCPHAV---FPKESLIHMDFEIFERISTY-FDK-TELIHLqGWGEPLLHSRIGEMIAIAKDS--- 76 
                                       689**************8...45555555555899999999.999.666655167**********999999997... PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr..vvdrivg 151
                                       + ++ ++tng+l+ ++++e+ll+  +d++++++  +      kl+ rg++f++++e++++l e+++     ++++++
  gi|488601074|ref|YP_007907545.1|  77 KASVGLTTNGVLI-KKFVEELLN--LDYIAISVGGIERH---KLL-RGNDFQKLVENIRLLSELRGSAnpKINITYL 146
                                       *************.*********..88******999997...999.99****************9887887788888 PP

                                       BTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleelle 165
                                       +   n++el e+++
  gi|488601074|ref|YP_007907545.1| 147 MTIDNFKELPEVIR 160
                                       88888888888776 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.9e-07     0.004       5      95 ..      11      92 ..       8     109 .. 0.71
   2 ?   -2.8   0.0       1.5   6.8e+03      68      84 ..     127     144 ..     115     167 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.9e-07
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeypekk 82
                                      + +Cn+sC +C +    k++l +  + e+ e+i + ++k+e     + l G GePL++   + + +++   k+++   +
  gi|488601074|ref|YP_007907545.1| 11 TRKCNMSCLMCPHAVFPKESLIHM-DFEIFERISTYFDKTEL----IHLQGwGEPLLH---SRIGEMIAIAKDSK--AS 79
                                      579*********999555555555.55555577756666665....78********99...55556666556666..77 PP

                           Fer4_14 83 iwletngtleiel 95
                                      + l tng+l +++
  gi|488601074|ref|YP_007907545.1| 80 VGLTTNGVLIKKF 92
                                      7999999887555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
                           Fer4_14  68 lklvkrlkeey.pekkiw 84 
                                       ++l+++l+ +  p+++i+
  gi|488601074|ref|YP_007907545.1| 127 IRLLSELRGSAnPKINIT 144
                                       445555555553334433 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 !   16.2   0.0   2.1e-06    0.0094      13     117 ..      12     108 ..       4     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-06
                           Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllG.GEPllpenaeallelvkevkeekpekdi 88 
                                         Cn+sC  C   ++   +s   +++e+ e+i + +  ++ e + l G GEPll++   +++ ++k  k+       
  gi|488601074|ref|YP_007907545.1|  12 RKCNMSCLMCP-HAVFPKESLIHMDFEIFERISTYF--DKTELIHLQGwGEPLLHSRIGEMIAIAKDSKASVG---- 81 
                                       67*******97.4455555566789***********..777888999999****8888999999998888877.... PP

                           Fer4_12  89 wlytgytleelskkekeellkeidvlvdG 117
                                       + ++g+ ++++ ++     l++i + v G
  gi|488601074|ref|YP_007907545.1|  82 LTTNGVLIKKFVEE--LLNLDYIAISVGG 108
                                       78999999999753..2224444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2175.07
//
Query:       gi|488601075|ref|YP_007907546.1|  [L=221]
Description: ACT domain-containing protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-71  237.3   2.5    4.3e-71  237.3   2.5    1.5  2  DUF5612       Domain of unknown function (DUF5612)
    9.5e-08   31.7   0.1    2.3e-06   27.3   0.0    2.6  2  ACT           ACT domain
     0.0028   18.2   0.5     0.0091   16.6   0.5    2.0  1  ACT_4         ACT domain
  ------ inclusion threshold ------
      0.057   13.0   0.2        0.1   12.2   0.0    1.5  2  Peripla_BP_4  Periplasmic binding protein domain
      0.086   12.2   0.0       0.12   11.7   0.0    1.1  1  HEM4          Uroporphyrinogen-III synthase HemD


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 ?   -3.8   0.0       2.8     1e+04      58      73 ..       3      18 ..       2      21 .. 0.75
   2 !  237.3   2.5   1.2e-74   4.3e-71       2     142 ..      80     219 ..      79     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
                                      HHHHGGGSTTEEEEEE CS
                           DUF5612 58 aveavsrlprvkvlvl 73
                                      +v+a++ + r k+ vl
  gi|488601075|ref|YP_007907546.1|  3 SVRAIQMIVRNKIGVL 18
                                      6888888888887776 PP

  == domain 2  score: 237.3 bits;  conditional E-value: 1.2e-74
                                       --HHHHT-EEEEEEE-HHHHHHHHHHHHHHHHHHHCTSS-EEEEEEE--SHHHHHHHHHHGGGSTTEEEEEEESSB- CS
                           DUF5612   2 kslkeifGkrviilGGGaqvaqvalGaiseadrhnirGerisvdtiplvGeeelaeaveavsrlprvkvlvlaGslm 78 
                                       k+++++fGkrv+i+GGGa v+qvalGaiseadrhn+rGerisvdt+p++Geeelaeav+avsrl+r+++lvlaG+lm
  gi|488601075|ref|YP_007907546.1|  80 KPFEQVFGKRVLIFGGGALVSQVALGAISEADRHNLRGERISVDTMPIIGEEELAEAVRAVSRLHRAEILVLAGGLM 156
                                       6899************************************************************************* PP

                                       -THHHHHHHHHHHT.T-EEEEES-BSSHHHHSSEEESSHHHHHHHHHHHH-TTS---GGGCSS- CS
                           DUF5612  79 GGkiteavkklkeekdiivislnmaGsvtevadlvvtdpvqaGvlavmavadtavfdiervkgk 142
                                       GG+ite+vkkl++  +i+vislnm+G+v+ vad+vv+dpv+aG+lavm+++d+a+fdiervkgk
  gi|488601075|ref|YP_007907546.1| 157 GGQITEEVKKLRKA-GIPVISLNMFGTVPRVADVVVSDPVMAGTLAVMHISDKAKFDIERVKGK 219
                                       *************9.***********************************************97 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   6.4e-10   2.3e-06       3      64 ..       7      69 ..       5      72 .. 0.94
   2 ?    1.6   0.0     0.068   2.4e+02      43      63 ..     121     141 ..     105     145 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.4e-10
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT.ECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk.vagivfvvivvdeedleevlealkk 64
                                      + + v+++ G+L ++++++ad++ Ni  ++++  +++ +ag + + ++++  d e++++++ k
  gi|488601075|ref|YP_007907546.1|  7 IQMIVRNKIGVLRDITRIVADNQGNISYAQTFLIKYGeYAGNALIYLEIEGGDFEKIKDEISK 69
                                      7789*****************************************************999977 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.068
                                       EEEEEEEEEHHHHHHHHHHHH CS
                               ACT  43 ivfvvivvdeedleevlealk 63 
                                        v+++ +++ee+l+e+++a+ 
  gi|488601075|ref|YP_007907546.1| 121 SVDTMPIIGEEELAEAVRAVS 141
                                       344455555555555555544 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5   2.5e-06    0.0091       9      39 ..       7      37 ..       5      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-06
                             ACT_4  9 leveaedrkglLaditqviseekanivsvna 39
                                      ++++++++ g+L+dit++++++++ni+  ++
  gi|488601075|ref|YP_007907546.1|  7 IQMIVRNKIGVLRDITRIVADNQGNISYAQT 37
                                      89************************87666 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.5   5.3e+03      13      34 ..      32      53 ..      24      75 .. 0.53
   2 ?   12.2   0.0   2.9e-05       0.1      68     119 ..     159     209 ..     150     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                                      HHHHHHHHHHHHHHTTCEEEEE CS
                      Peripla_BP_4 13 fsaaregleeaakelgaevtvv 34
                                      +s+a+  l ++ + +g+  ++ 
  gi|488601075|ref|YP_007907546.1| 32 ISYAQTFLIKYGEYAGNALIYL 53
                                      4556666666666666655555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHTT-EEEEESTTGCTTT-CEEEEEC-HHHHHHHHHHHHHHHC CS
                      Peripla_BP_4  68 alapalkkakaaGIpVvafdsddapsgerlayvgfdneaaGelqaeylaekl 119
                                       ++++ +kk+++aGIpV++ + +     +++ +v  d   aG+l+   + +k 
  gi|488601075|ref|YP_007907546.1| 159 QITEEVKKLRKAGIPVISLNMF-GTVPRVADVVVSDPVMAGTLAVMHISDKA 209
                                       566779****************.555555669999***99999987777765 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.3e-05      0.12      72     156 ..     100     187 ..      95     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                                       HHCSEEESSHHHHHHHHHTT---SEE-..SSSHHHHGGGS-...---EEEEEE-SS.S--HHHH...HHHHHTTEEE CS
                              HEM4  72 aslkvaavGpaTaraLeelglrvdlvpseegtaegLaeelae..slagkrvlllrgeiarddla...egLeergaev 143
                                       +++++ a+ +a +  L+  ++ vd +p   g  e+Lae++++  +l    +l+l+g      +    ++L+++g+ v
  gi|488601075|ref|YP_007907546.1| 100 SQVALGAISEADRHNLRGERISVDTMPI-IGE-EELAEAVRAvsRLHRAEILVLAGGLMGGQITeevKKLRKAGIPV 174
                                       567889999999999************9.999.9****999754444445***999999999985556788****** PP

                                       EEE-SEEEEE-HH CS
                              HEM4 144 devevYetvpaee 156
                                         ++++ tvp++ 
  gi|488601075|ref|YP_007907546.1| 175 ISLNMFGTVPRVA 187
                                       ********66654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1487.97
//
Query:       gi|488601076|ref|YP_007907547.1|  [L=77]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-18   66.9   0.2    1.3e-18   66.7   0.2    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.076   13.1   0.3        0.2   11.7   0.3    1.6  1  NapD            NapD protein
      0.089   13.3   0.7       0.14   12.7   0.7    1.5  1  NusG            Transcription termination factor nusG
       0.11   12.3   0.0       0.14   12.0   0.0    1.1  1  Peptidase_C41   Hepatitis E cysteine protease


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 !   66.7   0.2     3e-22   1.3e-18       1      70 [.       6      72 ..       6      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 3e-22
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartets 70
                                      vlv+++p++    +e+ e+lael+e++e+y + G+yd+++k+vvrd e+l++++++k++sl+gv +t+t+
  gi|488601076|ref|YP_007907547.1|  6 VLVKISPKK---EKEVYEKLAELEEIEELYPLFGEYDLIAKIVVRDFEELSDVVVNKIRSLDGVIETKTL 72
                                      799***999...********************************************************97 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   4.4e-05       0.2       6      67 ..       6      69 ..       4      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.4e-05
                              NapD  6 lvVqarperlaavkaalaalpgvE.vhasdeegklVvviEaesedeladti.eaiealpgVlsa 67
                                      ++V++ p++ ++v ++la+l+++E ++   +e  l+  i   + +el d + ++i++l+gV+ +
  gi|488601076|ref|YP_007907547.1|  6 VLVKISPKKEKEVYEKLAELEEIEeLYPLFGEYDLIAKIVVRDFEELSDVVvNKIRSLDGVIET 69
                                      68********************974666666699999999999999999752669999999987 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   3.1e-05      0.14       5      32 ..       7      34 ..       5      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                                      EEEE-TTTHHHHHHHHHHHCT-EEE-SC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              NusG  5 vlqvepgkekkvkenLleeeglevivPa 32
                                      ++++ p+kek+v e+L+e+e++e + P+
  gi|488601076|ref|YP_007907547.1|  7 LVKISPKKEKEVYEKLAELEEIEELYPL 34
                                      57899*****************999998 PP

>> Peptidase_C41  Hepatitis E cysteine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.1e-05      0.14      97     139 ..      31      76 ..      26      77 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                     Peptidase_C41  97 lqplyqaldlpaeivaragrltatv...kvsqvdgridcetllgnk 139
                                       l pl+   dl a+iv r     + v   k+  +dg i+ +tl g k
  gi|488601076|ref|YP_007907547.1|  31 LYPLFGEYDLIAKIVVRDFEELSDVvvnKIRSLDGVIETKTLTGAK 76 
                                       78***************8654444313477889**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 543.73
//
Query:       gi|488601077|ref|YP_007907548.1|  [L=274]
Description: spermidine synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  181.0   0.3    2.4e-53  180.3   0.3    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    6.5e-17   61.2   0.5    1.4e-16   60.1   0.5    1.6  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
    8.6e-05   23.2   0.0    0.00018   22.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    0.00016   21.0   0.2    0.00028   20.2   0.2    1.3  1  DUF43            Branched-chain polyamine synthase A C-termin
  ------ inclusion threshold ------
      0.011   16.4   0.1       0.02   15.6   0.1    1.4  1  Methyltransf_12  Methyltransferase domain
      0.088   12.3   0.0       0.12   11.8   0.0    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3   0.3   8.1e-57   2.4e-53       2     181 ..      56     229 ..      55     236 .. 0.97

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 8.1e-57
                                       HHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEE CS
                    Spermine_synth   2 faykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklv 78 
                                        +y+em++hvpl+   +pk++L+iGGgDGg++rev+khn + ++++v+iD  vi+ ++k+++   +  ++d+rv+++
  gi|488601077|ref|YP_007907548.1|  56 SFYHEMLVHVPLFMVDEPKKILVIGGGDGGTVREVLKHN-PDEVVMVEIDDTVINACRKYIGIDGGA-LEDERVTVL 130
                                       68*************************************.**********************98887.********* PP

                                       ESTCHHHHCTCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSS CS
                    Spermine_synth  79 lgdgfkflkayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfa 155
                                       ++dg+++++++++ fdvvivd +dp   +e+l +++ff+++k++ +   ++ +qa++p+++ke++i++ ks+k++f 
  gi|488601077|ref|YP_007907548.1| 131 IEDGMEYVENCKERFDVVIVDGTDPNPVSESLVKEDFFNNCKRISN---IFATQAQSPFIQKEYFIEIYKSIKKAFE 204
                                       ********************************************99...***************************9 PP

                                       CEEEEEEEETTTSCSCEEEEEEEESS CS
                    Spermine_synth 156 lqvepsavlvPtylsgminfvveskk 181
                                        + + ++  vPty+ g+++++++sk+
  gi|488601077|ref|YP_007907548.1| 205 -NYRIYINFVPTYPLGLWSYMIASKN 229
                                       .***********************99 PP

>> Spermine_synt_N  Spermidine synthase tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.5   4.6e-20   1.4e-16       2      53 .]       3      52 ..       2      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 4.6e-20
                                      EEEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
                   Spermine_synt_N  2 WfteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                      Wf+e++d   al +kV+++L+e k+  Q+i+ife++ fGk+LvLDg++qltE
  gi|488601077|ref|YP_007907548.1|  3 WFIEYYD-DSALMIKVKETLFESKG-IQHIQIFETAGFGKMLVLDGKIQLTE 52
                                      *******.9****************.*************************9 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   5.9e-08   0.00018       1      73 [.      76     153 ..      76     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.9e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.....TEEEEESBCCG.BSSSTTTEEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.....nvefvqgdaed.lpfedgsfDlvvss 71 
                                       +L +G G G ++++++k+    +v++v+i+++ ++a+r+ +  +g      +v+++  d  + ++  +++fD+v++ 
  gi|488601077|ref|YP_007907548.1|  76 ILVIGGGDGGTVREVLKHN-PDEVVMVEIDDTVINACRKYIGIDGGaledeRVTVLIEDGMEyVENCKERFDVVIVD 151
                                       799***************5.7******************998755567888****99999663778999*****995 PP

                                       ST CS
                   Methyltransf_25  72 ga 73 
                                       g+
  gi|488601077|ref|YP_007907548.1| 152 GT 153
                                       54 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 !   20.2   0.2   9.4e-08   0.00028      45     120 ..      73     152 ..      68     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.4e-08
                                       T-EEEEES-TT-HHHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--EE..EE---TTS..---TTTSS-BSEEE CS
                             DUF43  45 gkeilvlGdDDLtslalaLtglpkkvvvvDiDeRlikfiervakelglkie..aivyDlrk..plpeelkekFdvfi 117
                                        k+ilv+G  D  ++   L + p++vv+v+iD+ +i+   + +   g  +e   ++  + +   + e++ke+Fdv+i
  gi|488601077|ref|YP_007907548.1|  73 PKKILVIGGGDGGTVREVLKHNPDEVVMVEIDDTVINACRKYIGIDGGALEdeRVTVLIEDgmEYVENCKERFDVVI 149
                                       589**************************************9876664433114444444312689**********9 PP

                                       E-- CS
                             DUF43 118 tDP 120
                                        D 
  gi|488601077|ref|YP_007907548.1| 150 VDG 152
                                       764 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   6.8e-06      0.02       1      72 [.      77     150 ..      77     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.8e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.....ssfDlvva 72 
                                       L iG+G+G ++r++l++  + e++ v+i+  +i +a +k   +++   +  ++++l   d  +      + fD+v++
  gi|488601077|ref|YP_007907548.1|  77 LVIGGGDGGTVREVLKH-NPDEVVMVEIDDTVI-NACRKYIGIDGGALEDERVTVLIE-DGMEYvenckERFDVVIV 150
                                       569**************.888************.999999888888777777776653.333336779999999985 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 ?   11.8   0.0   4.2e-05      0.12      54     149 ..      71     173 ..      46     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.2e-05
                   Methyltransf_PK  54 revkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelae.....ekkkvgkvyvvglqeftPeegrYdl 125
                                        e k +l +G G G   +++L +   +v +ve  ++++++ +++++      e ++v+ +++ g++     ++r+d+
  gi|488601077|ref|YP_007907548.1|  71 DEPKKILVIGGGDGGTVREVLKHNPDEVVMVEIDDTVINACRKYIGIdggalEDERVTVLIEDGMEYVENCKERFDV 147
                                       566789999************************************9888889999**********999999****** PP

                   Methyltransf_PK 126 iWiqWcvghLtDedlv..aflkrckk 149
                                       + +     + + e lv  +f++ ck+
  gi|488601077|ref|YP_007907548.1| 148 VIVDGTDPNPVSESLVkeDFFNNCKR 173
                                       *9998888888888884458888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1791.11
//
Query:       gi|488601078|ref|YP_007907549.1|  [L=386]
Description: hypothetical protein Asulf_01579 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   50.7   0.0    5.4e-13   49.9   0.0    1.4  1  CAP       Cysteine-rich secretory protein family


Domain annotation for each model (and alignments):
>> CAP  Cysteine-rich secretory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0     3e-17   5.4e-13       1     115 [.     152     270 ..     152     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3e-17
                                       HHHHHHHHHHTT----EE-HHHHHHHHHHHHHHHHH.T---S-GGG--HHHHHHTT-T...............EEEE CS
                               CAP   1 leahNeyRaaaglppLkwdatLekaAqdhardcaashsdsssspeggdllkyaenagk...............enia 62 
                                       l+ +N  R +agl+p kw++   ++A++h++d+ +++++ ++speg d++++ +++g                ++ +
  gi|488601078|ref|YP_007907549.1| 152 LRFVNHEREKAGLKPYKWNDWVRAVAYNHSKDMGERNYFAHTSPEGKDHYDRLKESGMffivsgevlsyqtglGPKD 228
                                       6789*****************************************************************99988*** PP

                                       EES--CCCHHHHHHTSHH.............HHHHHT-..SS--EEEEEEEEBTT CS
                               CAP  63 aaseaaedavdsWysepgtynkgketegsighftnllw..pkstkvGcavatcgn 115
                                       ++ ++a++av++W+++pg             h++ +l+  + ++  G++++  +n
  gi|488601078|ref|YP_007907549.1| 229 NETSIARAAVEGWLESPG-------------HRSIILDidNLFSDAGVGAYCEEN 270
                                       ******************.............**9998611445566666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2657.72
//
Query:       gi|488601079|ref|YP_007907550.1|  [L=405]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-27   95.1   0.3    3.2e-27   95.1   0.3    2.2  2  OrfB_IS605      Probable transposase
    1.3e-22   79.4   0.7    3.4e-22   78.1   0.7    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      1e-10   40.9   0.6    2.3e-10   39.8   0.6    1.7  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0016   18.2   0.9     0.0039   17.0   0.3    2.0  3  Cys_rich_CPCC   Cysteine-rich CPCC
  ------ inclusion threshold ------
      0.021   14.9   0.3      0.052   13.6   0.3    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.12   12.3   0.0       0.32   10.9   0.0    1.6  1  Thioredox_DsbH  Protein of unknown function, DUF255
        1.2    9.5   3.8          3    8.2   3.8    1.6  1  ESM4            Enhancer of split M4 family
        7.4    6.5   9.6         16    5.4   1.4    2.4  2  NOG1_N          NOG1 N-terminal helical 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 ?   -0.3   1.5      0.53   1.2e+03      50      89 ..      42      79 ..      26      98 .. 0.68
   2 !   95.1   0.3   1.4e-30   3.2e-27       5     117 ..     170     278 ..     164     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.53
                        OrfB_IS605 50 ykylakeiaelqsklkksknykkasrklarlhrkrsrrrk 89
                                      ++  + ++   qs++ + k  ++ + +l++++ k+ + ++
  gi|488601079|ref|YP_007907550.1| 42 KEGRRIRREDTQSLIVRIK--REEKPELSKVYSKVLQMVN 79
                                      3333444555666666666..8999999999999877665 PP

  == domain 2  score: 95.1 bits;  conditional E-value: 1.4e-30
                        OrfB_IS605   5 evevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                       ev++ +p p++++a+giD+Gi ++++ ++++   ++ +++ l++++++ +k +++l++k+k+skn++k++  la+l+
  gi|488601079|ref|YP_007907550.1| 170 EVDK-QPLPPTGRAIGIDVGITHFCVDSDGN---YFEHPKYLDRTLEKIKKVQKQLSRKQKGSKNREKVRIGLAKLY 242
                                       4444.999***********************...******************************************* PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                       +k+ ++r+++lhkl+++ +++++ ++ve+Lnv++m+
  gi|488601079|ref|YP_007907550.1| 243 EKLENQRNDFLHKLSRYYVNNYDIMVVEDLNVKEMA 278
                                       ***********************************8 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.7   1.5e-25   3.4e-22       1      68 [.     295     363 ..     295     364 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.5e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       ++k+ + l +ka+++ ++v++vnp +TSk+C+ Cg+++++ +l++rtf+Cp Cg eadrD+nA++Nil+
  gi|488601079|ref|YP_007907550.1| 295 WSKFVRLLCEKAERAARTVVKVNPKNTSKRCAMCGYIVNNlKLHDRTFTCPICGWEADRDYNASLNILD 363
                                       99*****************************************************************85 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 !   39.8   0.6     1e-13   2.3e-10       1      46 [.       1      45 [.       1      46 [. 0.96

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1e-13
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeeg 46
                                      M l +y++r+yP ++ ++kl++ ++ +R+ YN+ L+e ++a +e++
  gi|488601079|ref|YP_007907550.1|  1 M-LISYRFRIYPSKTVQAKLNEQLELCRWLYNRLLSEVNKARKEGR 45
                                      8.99*************************************99975 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         5   1.1e+04      22      31 ..      24      33 ..      20      42 .. 0.72
   2 ?   -3.3   0.0       3.8   8.6e+03      35      56 ..      77      98 ..      74     107 .. 0.74
   3 !   17.0   0.3   1.7e-06    0.0039       2      30 ..     324     353 ..     323     366 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5
                     Cys_rich_CPCC 22 pvCfWedDlv 31
                                      ++C W ++ +
  gi|488601079|ref|YP_007907550.1| 24 ELCRWLYNRL 33
                                      5799988765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                     Cys_rich_CPCC 35 apdleggaNkvsLreArknfkk 56
                                      + +++  +N  sL+e rk   k
  gi|488601079|ref|YP_007907550.1| 77 MVNYQLRSNISSLNELRKKGVK 98
                                      5567788899999998876555 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1.7e-06
                     Cys_rich_CPCC   2 qCpcCgyltleeee.gsydiCpvCfWedDl 30 
                                       +C  Cgy++ + +    +  Cp+C We D 
  gi|488601079|ref|YP_007907550.1| 324 RCAMCGYIVNNLKLhDRTFTCPICGWEADR 353
                                       6*******997776566779*******995 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 ?   13.6   0.3   2.3e-05     0.052      48      94 ..     299     349 ..     272     357 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                       HHHHHCC.T.TTT-EEEEEEE--EEEETTTS-EEECHH..H.HHS-TTTSS CS
                              HypA  48 fellaegtv.legaeLeieevpvkvrCreCgkefelee..k.alrCpkCgs 94 
                                        +ll+e+   +++++++++ ++ + rC  Cg+ ++  +  + +++Cp Cg 
  gi|488601079|ref|YP_007907550.1| 299 VRLLCEKAErAARTVVKVNPKNTSKRCAMCGYIVNNLKlhDrTFTCPICGW 349
                                       344445555489999******************99555454689*****95 PP

>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00014      0.32      74      99 ..      55      80 ..      49      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                    Thioredox_DsbH 74 vsvkvDreerPdldkiymeavqaltg 99
                                      + v++ ree+P+l k+y +++q+++ 
  gi|488601079|ref|YP_007907550.1| 55 LIVRIKREEKPELSKVYSKVLQMVNY 80
                                      5799*******************985 PP

>> ESM4  Enhancer of split M4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.8    0.0013         3      25     103 ..     209     287 ..     196     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                              ESM4  25 kavrrlkkvlkpLrrllkkggkgrkt.eltlahpnnvdlentqqqqqqqqeeldednssnaeLeqqlveeevek.sa 99 
                                       ++  ++kkv k L r++k g k+r++ ++ la+   + len++++  ++++ +  +n     +e   v+e+ e+ s+
  gi|488601079|ref|YP_007907550.1| 209 RTLEKIKKVQKQLSRKQK-GSKNREKvRIGLAKL-YEKLENQRNDFLHKLSRYYVNNYDIMVVEDLNVKEMAENgSS 283
                                       67789**********665.555555536666655.889999888899999999999999999999999999777655 PP

                              ESM4 100 qsca 103
                                         ++
  gi|488601079|ref|YP_007907550.1| 284 TTLN 287
                                       5544 PP

>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.4    0.0072        16      87     152 ..      30      95 ..      27      99 .. 0.78
   2 ?    5.3   1.5    0.0076        17      13      98 ..     206     284 ..     202     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0072
                            NOG1_N  87 lkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvl.kkvdkaldfLedvrkk 152
                                       +++ L++v++ark  r i++e +++l    + +e k    + + +v + +  + + ++  L+++rkk
  gi|488601079|ref|YP_007907550.1|  30 YNRLLSEVNKARKEGRRIRREDTQSLIVRIKREE-KPELSKVYSKVLQMVnYQLRSNISSLNELRKK 95 
                                       6678*****************9999886555444.44445566777766646899999999999987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0076
                            NOG1_N  13 lidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldvlvdkdelkk 89 
                                        +d+ l++ k+ +k+ ++k++  ++  n   +kvr     l++kLe+  ++f  l++l  +y +  d++v  d   k
  gi|488601079|ref|YP_007907550.1| 206 YLDRTLEKIKKVQKQLSRKQKG-SK--N--REKVRIGLAKLYEKLENQRNDF--LHKLSRYYVNNYDIMVVEDLNVK 275
                                       5899999999999999998655.33..3..3456666667899999999999..9999*****99999998874444 PP

                            NOG1_N  90 sLaqvkwar 98 
                                        +a+  ++ 
  gi|488601079|ref|YP_007907550.1| 276 EMAENGSST 284
                                       444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1632  (0.0910257); expected 358.6 (0.02)
Passed bias filter:                      887  (0.0494729); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
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 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2972.94
//
Query:       gi|488601080|ref|YP_007907551.1|  [L=388]
Description: hypothetical protein Asulf_01581 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  103.4  18.6    1.7e-12   47.5   2.2    4.2  4  CBS              CBS domain
  ------ inclusion threshold ------
      0.039   14.7   3.4      0.041   14.7   0.4    2.4  2  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma


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 !   23.1   0.4   8.1e-09   7.3e-05       2      53 ..       7      60 ..       6      64 .. 0.86
   2 ?   -0.7   0.0      0.23   2.1e+03      17      55 ..      88     124 ..      84     126 .. 0.68
   3 !   47.5   2.2   1.9e-16   1.7e-12       1      55 [.     133     187 ..     133     189 .. 0.94
   4 !   41.7   1.5   1.3e-14   1.1e-10       1      56 [.     211     265 ..     211     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.1e-09
                                      HHHSBSSCEEEETTSBHHHHHHHHHHHT...SSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  2 gdimtrdvvtvppdttleealelmrekg...vsrlPVVdedgklvGivtlrDllr 53
                                      ++i ++d+ ++  d+t+++++  + +++    ++++V+d  +k++G++ +rDllr
  gi|488601080|ref|YP_007907551.1|  7 REIIREDYEVIEADETISKVIPHLSRYEpdgAHAIMVMD-GKKVLGVIRERDLLR 60
                                      6889999*****************775566669**9995.557***********8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.23
                                       BHHHHHHHHHHHTSSEEE.E.EETTTBEEEEEEHHHHHHHH CS
                               CBS  17 tleealelmrekgvsrlP.V.VdedgklvGivtlrDllral 55 
                                       + e+++++++e   ++ P V V  +g   G++   D l+++
  gi|488601080|ref|YP_007907551.1|  88 SYEKVARRFVE---DSTPfViVQLNG-KYGLIYINDFLKLI 124
                                       56788888877...455435367778.47888888888877 PP

  == domain 3  score: 47.5 bits;  conditional E-value: 1.9e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       ++d+m+++v+tv+  +t ++al +mr++g++r+ VVde +++ Gi+t +D+++ +
  gi|488601080|ref|YP_007907551.1| 133 ARDVMNPEVITVRTFDTAAKALATMRNNGIDRVVVVDEKNRVRGIITVKDIVDRI 187
                                       58***********************9999****889***************9876 PP

  == domain 4  score: 41.7 bits;  conditional E-value: 1.3e-14
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+++m+++v++++ +++++ +++lm+e+++s++ V+ +d+ + Gi+ ++D+l++ll
  gi|488601080|ref|YP_007907551.1| 211 VESVMSEPVISADANDSVSSIIDLMIENRISSI-VITKDDMPEGIIIKKDILEYLL 265
                                       789******************************.8778888*************97 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.24   2.1e+03      40      72 ..     205     237 ..     162     243 .. 0.73
   2 ?   14.7   0.4   4.5e-06     0.041       2      83 ..     276     371 ..     275     373 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                                       EEEEEEEEEC.TTEEEEEEEEESSHHHHHHHHHH CS
                   Ribosomal_S30AE  40 kkvevtirla.kgkviraeeesedlyaaidlavd 72 
                                       k+  + ++ + + +vi+a++ ++++ + idl+++
  gi|488601080|ref|YP_007907551.1| 205 KTLSIMVESVmSEPVISADA-NDSVSSIIDLMIE 237
                                       56666776667888899855.6999999999886 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.5e-06
                                       EEEECTS---HHHHHHHHHHHCCGGGG.......-EEEEEEE.EE........EEEEEEEEECTTEEEEEEEEESSH CS
                   Ribosomal_S30AE   2 eitgrnievtdalkeyvekkleklekyf......ieadVtls.kk........kkvevtirlakgkviraeeesedl 63 
                                       +it   +e++d  k+   + ++k+ + f      + + V+++ +k          v +++ ++++k+++++ es  +
  gi|488601080|ref|YP_007907551.1| 276 QITTSELELDDFDKDALMEDIDKFMRKFkefftnALFSVYIKkHKetfrglplIFVRIKL-ITDKKTFFVSGESWGV 351
                                       667777777776666666666666644333347777788888855778888666677777.6678888888899*** PP

                                       HHHHHHHHHHHHHHHHHCHH CS
                   Ribosomal_S30AE  64 yaaidlavdklerqlrkyke 83 
                                       + a++ a++kler + k ke
  gi|488601080|ref|YP_007907551.1| 352 EFAVHTALKKLEREVLKEKE 371
                                       ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2617.79
//
Query:       gi|488601081|ref|YP_007907552.1|  [L=369]
Description: Xaa-Pro aminopeptidase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-39  136.1   0.1    1.6e-39  135.7   0.1    1.1  1  Peptidase_M24  Metallopeptidase family M24
    1.8e-05   25.4   0.0      4e-05   24.3   0.0    1.6  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 !  135.7   0.1   1.8e-43   1.6e-39       1     208 [.     146     350 ..     146     351 .. 0.91

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 1.8e-43
                                       HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEE CS
                     Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlv 77 
                                       e+ir+ +++  +a++ +l+ i++  + +el ++ie + +k +g+  la ++iv+sg+ +a +hy+    ++  +d +
  gi|488601081|ref|YP_007907552.1| 146 EKIRQTSKAILEAMDFTLKIIRKVSSCEELRNKIEVFLFK-KGF--LAENTIVSSGTLSADPHYIGM-GEI--EDHL 216
                                       689999999999***99999998888*********88555.454..55689*************996.555..679* PP

                                       EEEEEEEET..TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTB....... CS
                     Peptidase_M24  78 lidagaeyd..gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesagl....... 145
                                       ++d+ ++ +   y sD trTvl+  +++e +e++eav ea ++ai+ +  Gv +sei++ +++vle +g+       
  gi|488601081|ref|YP_007907552.1| 217 IVDIFPRSRenLYFSDFTRTVLLN-DNAEIAEMLEAVIEAKNKAISIIHDGVLASEIHNLVCDVLEGKGYgtlrkks 292
                                       ******999889*********884.6779999**********************************8899999*999 PP

                                       CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 146 akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       ++ f h++GHg+Glevh+e p+++   n ++++++Gmvft+Epg+y     ggvr+edtv+v+
  gi|488601081|ref|YP_007907552.1| 293 VEGFLHSTGHGIGLEVHEE-PRIY--MN-DEVIRKGMVFTVEPGLY-YRKIGGVRVEDTVVVK 350
                                       9999**************9.**98..45.9****************.77889**********8 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 !   24.3   0.0   4.5e-09     4e-05       8      97 ..       5     108 ..       2     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.5e-09
                                       HHHHTT-SEEEEECC...HHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST.... CS
                      Creatinase_N   8 lmeekgldallvtsp...enlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveydd.... 76 
                                       +++e+++ +++  ++   +n++Y tGf       ++ +++  dg+ ll+v +++  +a +es +v+e+ + +d    
  gi|488601081|ref|YP_007907552.1|   5 ILREHNAQFFVMYDSsrnANFYYSTGF---QIPDPAFYMIGDDGTdLLVVSEMEKRRAERES-KVKEIASLNDigfy 77 
                                       688888888888877777*********...6666666669**********************.******99999988 PP

                                       ............HSSHHHHHHHHHHHHT-EEEE CS
                      Creatinase_N  77 ............pvealadllkellesekrvgv 97 
                                                    +++l++l++ ++   k++ v
  gi|488601081|ref|YP_007907552.1|  78 eiykelkdphiaLAQTLYELIRTHGG--KKILV 108
                                       88888888666666666666666644..66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 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:                        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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 2935.90
//
Query:       gi|488601082|ref|YP_007907553.1|  [L=229]
Description: hypothetical protein Asulf_01583 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1797.04
//
Query:       gi|488601083|ref|YP_007907554.1|  [L=525]
Description: ABC-type dipeptide transport system, periplasmic component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  313.3   8.0    2.6e-93  313.0   8.0    1.1  1  SBP_bac_5    Bacterial extracellular solute-binding proteins,
  ------ inclusion threshold ------
      0.039   14.3   0.0        0.4   11.1   0.0    2.1  2  SDH_beta     Serine dehydratase beta chain
      0.096   12.7   0.0        0.2   11.6   0.0    1.5  1  Dzip-like_N  Iguana/Dzip1-like DAZ-interacting protein N-term


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 !  313.0   8.0   4.3e-97   2.6e-93       2     375 ..      83     445 ..      82     447 .. 0.95

  Alignments for each domain:
  == domain 1  score: 313.0 bits;  conditional E-value: 4.3e-97
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                       ++p LAes +ev d+gk+y+f+LRk++kF+DGtp  AeDvv s +r+++  + +++  + +    +++v+avddytv
  gi|488601083|ref|YP_007907554.1|  83 LEPYLAES-YEVQDNGKVYIFHLRKDLKFADGTPCKAEDVVRSVKRVMNIAGDPSWLVTDF----VEDVVAVDDYTV 154
                                       689*****.8**********************************************99995....************ PP

                                       EEEESSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEE CS
                         SBP_bac_5  79 rftlkkpnalfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldri 155
                                       +f+lkkp ++fl+l+a +p+ +++   +++++++ d+++   g GPYk+++++++q+++le n++++ g+kpk dr+
  gi|488601083|ref|YP_007907554.1| 155 KFVLKKPISYFLALVATPPYFPVH---PNYKADEIDPDQTAGGVGPYKIVKWVRDQELILETNENFF-GDKPKTDRV 227
                                       ***********************5...6666666677777777***********************9.********* PP

                                       EEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT...STGGGSHHHHHHHH CS
                         SBP_bac_5 156 efkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtk...kppfddkrvRqAls 228
                                       ++ +++d+++ ++a+++Ge+d++   ++p die+lk++ +l+v  e+pg+ + yl++N +    +p ++k vRqA++
  gi|488601083|ref|YP_007907554.1| 228 VVMFYKDATTLRLAVEKGEVDIAwRTLTPVDIESLKKNANLQV-LEAPGAAIRYLVLNGNestEYPTKNKLVRQAIA 303
                                       *****9999999999*****9987889999*************.****************99999************ PP

                                       HHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEET CS
                         SBP_bac_5 229 yAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllas 305
                                        AiDr+eiv++v+++++t+ +sl+p +++++ + +k++y + ++e AkklL eaGy  +++ +l     +l  + + 
  gi|488601083|ref|YP_007907554.1| 304 AAIDRDEIVQVVYRNTYTQLYSLIPIGMWSYEDVFKQKYGDKNLELAKKLLQEAGYSEDNKLKL-----ELWWTPTH 375
                                       ***********************************************************98765.....78888888 PP

                                       TSHHHHHHHHHHHHHHHHTT.EEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTCT CS
                         SBP_bac_5 306 gspaekaiaeliqqqlkkiG.ikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsssga 375
                                       ++ +ek++a+++++ql++ + i+ve+k+ +w +ty++++++  + ++l+gw++dy+dpd+++ pfl+s+++
  gi|488601083|ref|YP_007907554.1| 376 YGDTEKDLAQILKSQLEATNmIEVELKSAEW-STYTDYARKSAMMLSLFGWYPDYIDPDDYTTPFLKSGAN 445
                                       888899*************************.**********************************99876 PP

>> SDH_beta  Serine dehydratase beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.12   7.1e+02      62     106 ..      67     112 ..      59     130 .. 0.84
   2 ?   11.1   0.0   6.6e-05       0.4      34      95 ..     388     449 ..     367     486 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
                                       HHHHHHHTT--TTTS-GGGHHHHHHHHHHHTEEEETT.TEEEE--H CS
                          SDH_beta  62 eAvllGLegeepetvdpdavesrleeieeekklklag.ekeiefde 106
                                       + ++ GL+  +p t d + + ++  e+++++k+ + + +k+++f  
  gi|488601083|ref|YP_007907554.1|  67 NNIMGGLMRYKPGTTDLEPYLAESYEVQDNGKVYIFHlRKDLKFAD 112
                                       67899*************9999999999999999888778888865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.6e-05
                                       TT-TTT--EEEEEEEHHHHHS-TTSSHHHHHHHHHTT--TTTS-GGGHHHHHHHHHHHTEEE CS
                          SDH_beta  34 kelleevarirveLyGsLaatgkghgtdeAvllGLegeepetvdpdavesrleeieeekklk 95 
                                       k++le+++ i+veL  +   t ++++ ++A++l L g+ p+ +dpd++++ + +  +++ l 
  gi|488601083|ref|YP_007907554.1| 388 KSQLEATNMIEVELKSAEWSTYTDYARKSAMMLSLFGWYPDYIDPDDYTTPFLKSGANRWLG 449
                                       456788999************************************99888776666666555 PP

>> Dzip-like_N  Iguana/Dzip1-like DAZ-interacting protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.4e-05       0.2       6      57 ..     245     297 ..     241     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                       Dzip-like_N   6 rsekldwrklasvDvdrvakeldvdtLqenienitFcnlereeaak.lvdpel 57 
                                       ++  + wr l+ vD++ + k+ ++++L+   + i +  l+ +e ++ +++++l
  gi|488601083|ref|YP_007907554.1| 245 GEVDIAWRTLTPVDIESLKKNANLQVLEAPGAAIRYLVLNGNESTEyPTKNKL 297
                                       566799**********************9999999999988776664555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 3616.14
//
Query:       gi|488601084|ref|YP_007907555.1|  [L=336]
Description: ABC-type dipeptide/oligopeptide/nickel transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-47  159.5  14.4    7.2e-47  159.5  14.4    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.0     0.023   4.1e+02      22      44 ..       8      37 ..       5      92 .. 0.71
   2 !  159.5  14.4     4e-51   7.2e-47       1     185 []     117     336 .]     114     336 .] 0.99

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.023
                      BPD_transp_1 22 pliivllslPsfvlaillvlvf.......v 44
                                      +++ +ll +P++ +++ lv+++        
  gi|488601084|ref|YP_007907555.1|  8 IVTRALLVIPTIFILLTLVFFIlrilpgdP 37
                                      567788899999988887754455555541 PP

  == domain 2  score: 159.5 bits;  conditional E-value: 4e-51
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................. 43 
                                       g+++G+++a++r++k+d  +r+++iv ++l + ++++ll+++f                                  
  gi|488601084|ref|YP_007907555.1| 117 GVITGSISAFRRGSKIDTSMRVYSIVAYTLFIPWFGMLLQMIFgvyfqifpiggritpgmspdritglyvfdslvtl 193
                                       789999*********************************************************************** PP

                      BPD_transp_1  44 ...vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglila 117
                                          ++ ++l hl+lp+i+l+++ +++y+rl+r++ +++l++d++ a+ra+G+++++ + k++++na++p++t+++l+
  gi|488601084|ref|YP_007907555.1| 194 nfsALYDALSHLALPAITLGIVLSGAYTRLLRNNLIDVLSQDFITAYRARGVRERK-VIKHAMKNAFIPVVTLMGLQ 269
                                       ***999**************************************************.778***************** PP

                      BPD_transp_1 118 fggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                       f++ll gavl+e ++swpG+gt+lle i+++dy++ + g++++++ +v++++lv+di+++lldpr+r+
  gi|488601084|ref|YP_007907555.1| 270 FAILLAGAVLTESTFSWPGMGTFLLERIEYRDYTSVQ-GAIVFYAMFVAIISLVVDIIYALLDPRIRY 336
                                       *************************************.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); 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 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2193.25
//
Query:       gi|488601085|ref|YP_007907556.1|  [L=285]
Description: ABC-type dipeptide/oligopeptide/nickel transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-23   83.1  12.0      2e-23   83.1  12.0    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
    2.9e-06   27.2   3.4    2.9e-06   27.2   3.4    4.0  4  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
        6.7    7.3  27.3       0.37   11.3   3.8    3.7  3  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 ?   -4.7   6.6       2.8   1.7e+04      20      44 ..      24      73 ..       9      99 .. 0.53
   2 !   83.1  12.0   3.3e-27     2e-23       1     175 [.     100     271 ..     100     285 .] 0.90

  Alignments for each domain:
  == domain 1  score: -4.7 bits;  conditional E-value: 2.8
                      BPD_transp_1 20 lrpliivllslPsfvlaillvlvf.........................v 44
                                      ++++ ivll l + v+a+++                              
  gi|488601085|ref|YP_007907556.1| 24 ISGMLIVLLVLFMAVFAPVIAPYDpikaskdilqppsakhimgtdnlgrD 73
                                      45555555555555555555444455555555555555555555554443 PP

  == domain 2  score: 83.1 bits;  conditional E-value: 3.3e-27
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g++lG++++ ++++kld+ l+ l++ ++++Ps++lai +        +lg +++  vi++++++ + y+r+ir ++l
  gi|488601085|ref|YP_007907556.1| 100 GVPLGLISG-YFGGKLDRSLSMLMDSMYAFPSLILAIAIA------AVLGPSVMNaVIAISVVYVPTYFRMIRGQVL 169
                                       89*******.******************************......99**777777********************* PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       +   + +veaa+a+Ga++ +i+ k+++Pn++p+++  + l+++ ++   + l+flg    +     ++ +g+ ++++
  gi|488601085|ref|YP_007907556.1| 170 SLKTRLFVEAAKAMGAKDARIMAKYIFPNIIPTLVVVFSLSVADAILTEAGLSFLG----FIVSAPTPDWGFELASG 242
                                       ********************************************************....99999999999999999 PP

                      BPD_transp_1 154 s.......nggvlalviavlllnlvadil 175
                                               ++++ + +++v+ll+l + ++
  gi|488601085|ref|YP_007907556.1| 243 RpylpagyWWMITFPGLMVMLLSLGFALI 271
                                       99999999666666666666666554444 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 !   27.2   3.4   4.8e-10   2.9e-06      18      51 .]      25      59 ..      21      59 .. 0.78
   2 ?   -1.6   1.6      0.46   2.7e+03      21      33 ..      84      96 ..      79     108 .. 0.68
   3 ?    1.0   1.2     0.072   4.3e+02      23      36 ..     132     145 ..     130     160 .. 0.83
   4 ?   -1.0   0.1       0.3   1.8e+03      19      37 ..     258     276 ..     258     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.8e-10
                            OppC_N 18 vglvilllllliaifaPliaPydp....qdliqnllpP 51
                                       g+ i+ll+l++a+faP+iaPydp        + l+pP
  gi|488601085|ref|YP_007907556.1| 25 SGMLIVLLVLFMAVFAPVIAPYDPikasK---DILQPP 59
                                      58888888888*************64422...34***9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.46
                            OppC_N 21 villlllliaifa 33
                                      v+l++++++++f 
  gi|488601085|ref|YP_007907556.1| 84 VVLVVVFVASLFS 96
                                      4566666666664 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.072
                            OppC_N  23 lllllliaifaPli 36 
                                       +l+++++a+++P +
  gi|488601085|ref|YP_007907556.1| 132 ILAIAIAAVLGPSV 145
                                       78899999999987 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.3
                            OppC_N  19 glvilllllliaifaPlia 37 
                                       gl + ll l +a++++ ++
  gi|488601085|ref|YP_007907556.1| 258 GLMVMLLSLGFALIGEGLS 276
                                       6778888888999998874 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.5     0.058   3.4e+02      72      88 ..      24      40 ..      10      48 .. 0.59
   2 ?    3.4   9.0     0.018   1.1e+02      18      88 ..      86     159 ..      80     164 .. 0.58
   3 ?   11.3   3.8   6.1e-05      0.37       7      85 ..     180     267 ..     175     272 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.058
                              FtsX 72 iivlllllallagllsi 88
                                      i ++l++l++l++++ +
  gi|488601085|ref|YP_007907556.1| 24 ISGMLIVLLVLFMAVFA 40
                                      34444444444444333 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.018
                              FtsX  18 lllllteillitlvalviGlglgllaaql..lsdvllssvfs.selkisidlitvliiivlllllallagllsi 88 
                                       l ++++ +l+  +++ ++Gl+ g++  +l  + ++l  s+ + ++l + i + +vl   v+  ++a+ ++++++
  gi|488601085|ref|YP_007907556.1|  86 LVVVFVASLFSMVIGVPLGLISGYFGGKLdrSLSMLMDSMYAfPSLILAIAIAAVLGPSVMNAVIAISVVYVPT 159
                                       34445555555555555556666666665663333333333347777777777777777777777777766665 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 6.1e-05
                              FtsX   7 lralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs.........selkisidlitvliiiv 74 
                                        +a+G+k+++++  ++  +++ tlv  ++  ++ ++++++  ++l+ +v++          +  ++++   ++ i +
  gi|488601085|ref|YP_007907556.1| 180 AKAMGAKDARIMAKYIFPNIIPTLVVVFSLSVADAILTEAGLSFLGFIVSAptpdwgfelASGRPYLPAGYWWMITF 256
                                       69**************************9999967777776666666666444444444566666666666666666 PP

                              FtsX  75 lllllallagl 85 
                                        +l+++ll++ 
  gi|488601085|ref|YP_007907556.1| 257 PGLMVMLLSLG 267
                                       66665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1808.44
//
Query:       gi|488601086|ref|YP_007907557.1|  [L=313]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  105.2   0.0      5e-30  104.8   0.0    1.2  1  ABC_tran      ABC transporter
    1.3e-18   67.2   0.0    2.3e-18   66.5   0.0    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    4.7e-06   26.2   0.8    3.3e-05   23.4   0.8    1.9  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00018   21.4   0.1     0.0068   16.2   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0032   17.9   0.1     0.0049   17.3   0.1    1.6  1  AAA_16        AAA ATPase domain
     0.0057   15.9   0.0      0.013   14.7   0.0    1.5  1  NB-ARC        NB-ARC domain
     0.0073   16.6   0.6      0.078   13.3   0.6    2.1  1  AAA_22        AAA domain
     0.0095   15.5   0.0      0.024   14.2   0.0    1.6  1  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.024   14.4   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.012   15.3   0.1       0.99    9.0   0.0    2.1  2  AAA_15        AAA ATPase domain
      0.014   15.8   0.0      0.027   14.8   0.0    1.5  1  RNA_helicase  RNA helicase
      0.023   15.2   0.0      0.041   14.4   0.0    1.3  1  AAA_23        AAA domain
      0.027   14.9   0.1      0.061   13.7   0.1    1.9  1  AAA           ATPase family associated with various cellular 
      0.054   13.4   0.0       0.12   12.2   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.072   13.0   0.0       0.15   12.0   0.0    1.6  1  NACHT         NACHT domain
       0.11   11.3   0.3        1.7    7.4   0.0    2.0  2  ABC_ATPase    Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.0   4.4e-33     5e-30       2     136 ..      23     178 ..      22     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 4.4e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..x RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe..p 68 
                                       +nv+l++ +ge v ivGe+G+GKStL+  ++++ +       Gei +dg+d+ +    + +    keig+++q+  +
  gi|488601086|ref|YP_007907557.1|  23 ENVDLSVDKGEFVSIVGESGCGKSTLAYSVIRMISYpgeiVGGEIIFDGRDVLKlneeELRALRGKEIGMVFQDpmT 99 
                                       79************************9988888877688789999*******99888555566679********988 PP

                                       -S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       xxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  69 qlfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       +l+p  +++++            ++e ++ a + l+ ++l++++v++ p++LSgGq+qrv++a+a+  +pkll++DE
  gi|488601086|ref|YP_007907557.1| 100 SLDPLEKIGDQitetilehmdvSKKEALQIAGEMLEKVGLPADRVNYYPHQLSGGQRQRVMIAMAVSLNPKLLIADE 176
                                       99999999999*******99875556667777777777788899********************************* PP

                                       TT CS
                                       xx RF
                          ABC_tran 135 pt 136
                                       pt
  gi|488601086|ref|YP_007907557.1| 177 PT 178
                                       *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 !   66.5   0.0     2e-21   2.3e-18       1      65 []     229     292 ..     229     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 2e-21
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE g+++++ +eplHPY+k+L++svp++   k+ ++ ++g +p+l + +eGC+F+pRCpfa++eC
  gi|488601086|ref|YP_007907557.1| 229 VELGSAKEIAHEPLHPYSKGLIDSVPDVWIDKE-VKPLPGFPPDLINPPEGCRFRPRCPFAKQEC 292
                                       8***************************99999.******************************* 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 !   23.4   0.8   2.9e-08   3.3e-05      24     205 ..      32     216 ..      18     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.9e-08
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--.BTTCSSTTEEEEEEEEEETTEE....SSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxxxxxxxxxxxxxxxxxx....xxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk.skekasvkkaeveitfdnedkk....lki 92 
                                        +f +ivG+ G+GKs l  ++  +++    + +  e +   +d+++  ++e +++   e+ ++f+++  +    +ki
  gi|488601086|ref|YP_007907557.1|  32 GEFVSIVGESGCGKSTLAYSVIRMISY-PGEIVGGEIIfdgRDVLKLnEEELRALRGKEIGMVFQDPMTSldplEKI 107
                                       3699*****************999986.4435555543333556665466677777889*****8888886665444 PP

                                       SSSC.EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  93 ekee.vsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                        ++   +i  ++  +++   +i g+  +k  v     +++ ++++LSgG+++ v++a+ ++++   p+ l + De  
  gi|488601086|ref|YP_007907557.1| 108 GDQItETILEHMDVSKKEALQIAGEMLEK--VGLPADRVNYYPHQLSGGQRQRVMIAMAVSLN---PK-LLIADEPT 178
                                       33332456667777777888888887766..5556689999999*************998765...44.8899**** PP

                                       TTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N 169 aaLDeknvkkvaellkekskn.aQfivislreemleka 205
                                        aLD    +k+ +ll+  +k+   ++ i+++  + ++ 
  gi|488601086|ref|YP_007907557.1| 179 TALDVIVQEKIMDLLDDMRKEgRAIMLITHDFALASER 216
                                       ****************9998835556788876665554 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 ?    2.8   0.0     0.074        83       3      16 ..      36      49 ..      34      73 .. 0.87
   2 !   16.2   0.0   6.1e-06    0.0068     233     298 ..     147     209 ..     140     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.074
                            AAA_21  3 vliGpNgsGKSnLL 16
                                       ++G  g+GKS+L 
  gi|488601086|ref|YP_007907557.1| 36 SIVGESGCGKSTLA 49
                                      69**********95 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.1e-06
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        +++lS G+++   ++++  ++++  +ll+ DEp + L+  +++++++ll++ +++g  ++l TH+
  gi|488601086|ref|YP_007907557.1| 147 YPHQLSGGQRQR-VMIAMAVSLNP--KLLIADEPTTALDVIVQEKIMDLLDDMRKEGRAIMLITHD 209
                                       578999999999.77777887777..79999**********************************8 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   0.1   4.3e-06    0.0049       2      51 ..      12      59 ..      11     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.3e-06
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                      ++ R+  +++++++  +v +g  e v ++GesG+GKs+l+ ++ r ++  
  gi|488601086|ref|YP_007907557.1| 12 FYTRRGVVKAVENVDLSVDKG--EFVSIVGESGCGKSTLAYSVIRMISYP 59
                                      566666666666654456666..79**************98888766665 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   1.2e-05     0.013      18      42 ..      31      54 ..      16      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                      SCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlakqiln 42
                                       +  +v++vG  G+GK+tla ++++
  gi|488601086|ref|YP_007907557.1| 31 KG-EFVSIVGESGCGKSTLAYSVIR 54
                                      33.49***************99987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.6   6.9e-05     0.078       5      27 ..      32      54 ..      29     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlle 27
                                        ++ ++GesG+GK+tl+  + +
  gi|488601086|ref|YP_007907557.1| 32 GEFVSIVGESGCGKSTLAYSVIR 54
                                      56899************977766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.1e-05     0.024      30      58 ..      29      57 ..      21      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava 58
                                      + +ge++ ++G +g+GK+tla+++   ++
  gi|488601086|ref|YP_007907557.1| 29 VDKGEFVSIVGESGCGKSTLAYSVIRMIS 57
                                      579*******************9877666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.2e-05     0.024      15      38 ..      25      48 ..      20      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTl 38
                                       ++++d  +++ ++G+sG GKSTl
  gi|488601086|ref|YP_007907557.1| 25 VDLSVDKGEFVSIVGESGCGKSTL 48
                                      56777855599************9 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00088      0.99      14      46 ..      22      55 ..      20      86 .. 0.78
   2 ?    4.6   0.0      0.02        22     254     365 ..     105     209 ..      70     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00088
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlF 46
                                       ++v++++++  +  ++G+ ++GKS++++    +
  gi|488601086|ref|YP_007907557.1| 22 VENVDLSVDKGeFVSIVGESGCGKSTLAYSVIRM 55
                                      5677777777689*************99876555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                            AAA_15 254 kklaeelkkilkkkidkikkfnykgkkneeieik...ddeelplnknGsGvqrllllillileaekkdekeeknvil 327
                                       +k+++++++++ + +d +kk+  +++ + + ++    d ++ + ++ + G+++ + +++    + k          l
  gi|488601086|ref|YP_007907557.1| 105 EKIGDQITETILEHMDVSKKEALQIAGEMLEKVGlpaDRVNYYPHQLSGGQRQRVMIAMAVSLNPKL---------L 172
                                       3456666788888888888888888888888888999******************999987665555.........9 PP

                            AAA_15 328 liEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       + +EP + L    q+ +++ll ++ ++++  +++ TH 
  gi|488601086|ref|YP_007907557.1| 173 IADEPTTALDVIVQEKIMDLLDDMRKEGR-AIMLITHD 209
                                       99********************9999999.99999996 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.4e-05     0.027       2      23 ..      36      57 ..      35      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                                       ++G+sg+GKStla+++++ ++
  gi|488601086|ref|YP_007907557.1| 36 SIVGESGCGKSTLAYSVIRMIS 57
                                      589*************999887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.7e-05     0.041       2      36 ..       3      49 ..       3      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                            AAA_23  2 Lkienfrsf...........rdqeidF..sk.gltlItGpNGaGKTTil 36
                                      L i+n+r +           +  ++d+  +k  ++ I+G+ G+GK+T+ 
  gi|488601086|ref|YP_007907557.1|  3 LDIKNLRTYfytrrgvvkavE--NVDLsvDKgEFVSIVGESGCGKSTLA 49
                                      579999999999877774323..3666765526889***********95 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.5e-05     0.061       3      35 ..      37      83 ..      35     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                                      EESSTTSSHHHHHHHHHHHHTHE..............EEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgve..............fleisgsell 35
                                      ++G  G+GK++la +v++ ++ +              +l+++  el+
  gi|488601086|ref|YP_007907557.1| 37 IVGESGCGKSTLAYSVIRMISYPgeivggeiifdgrdVLKLNEEELR 83
                                      79*****************8544222222222222225555555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.12      90     117 ..      22      50 ..       7      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHH CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLin 117
                                       +e++   +++ +++ +vG+SG GKStL  
  gi|488601086|ref|YP_007907557.1|  22 VENVDLSVDKgEFVSIVGESGCGKSTLAY 50 
                                       555555565559999***********975 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   0.00013      0.15       3      23 ..      35      55 ..      33      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklala 23
                                      v + Ge+G+GK+tL+ ++++ 
  gi|488601086|ref|YP_007907557.1| 35 VSIVGESGCGKSTLAYSVIRM 55
                                      6799***********999875 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 ?    2.0   0.1     0.065        72     241     302 ..      28      90 ..      22      99 .. 0.68
   2 ?    7.4   0.0    0.0015       1.7     322     371 ..     150     199 ..     139     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.065
                                       EE-SS.EEEEEE-TTSSHHHHHHHHHHCCSEE-TTSS-TTEEE-TT-EEE---TT--EEEE-- CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAlekGvynhvpgDGRefvvtdktavkiraEdgrsvkgvDi 302
                                        + kG  + IvG    GKsTL  ++ + +       G e++   ++++k++ E+ r+++g +i
  gi|488601086|ref|YP_007907557.1|  28 SVDKGeFVSIVGESGCGKSTLAYSVIRMISYPGEIVGGEIIFDGRDVLKLNEEELRALRGKEI 90 
                                       567777788************987766554332333556666666666666666666666666 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                                       S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG- CS
                        ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskeke 371
                                       + SG   q + i+ a+ ++ kll+ DE t+A   +++ + m+ l   +ke
  gi|488601086|ref|YP_007907557.1| 150 QLSGGQRQRVMIAMAVSLNPKLLIADEPTTALDVIVQEKIMDLLDDMRKE 199
                                       5699999**********************************988655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2120.59
//
Query:       gi|488601087|ref|YP_007907558.1|  [L=323]
Description: oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  119.2   0.0    2.4e-34  118.8   0.0    1.2  1  ABC_tran     ABC transporter
    1.9e-17   63.5   0.1    3.2e-17   62.8   0.1    1.4  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    8.2e-05   22.6   0.0    0.00016   21.6   0.0    1.4  1  Rad17        Rad17 P-loop domain
     0.0013   19.0   0.9       0.02   15.1   0.9    2.1  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.054   13.4   0.0      0.088   12.7   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.12   12.2   0.3         10    5.9   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.0   7.9e-38   2.4e-34       2     136 ..      33     184 ..      32     185 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 7.9e-38
                                       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  ++l gl++p  G+il++gkd+++   +e + lrk+i++++q+  ++l+p+
  gi|488601087|ref|YP_007907558.1|  33 DDVSFEIRKGEVLSLVGESGCGKTTTGRILVGLETPSDGKILFKGKDVTTlskEEYRALRKNIQMVFQDpyASLNPR 109
                                       89***********************************************999999**************999***** PP

                                       SBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++++e+              e++e + k+l+++gl+   ++  ++ p++LSgGq+qrva+ara++ kp+++++DEp 
  gi|488601087|ref|YP_007907558.1| 110 MKIGEHledplivhgvaegdEAKEMAMKMLDRVGLPA--EQFYNRMPYQLSGGQRQRVAIARAMILKPDFVVADEPV 184
                                       ****************977766777888888888877..66666777*****************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1   1.1e-20   3.2e-17       1      65 []     236     299 ..     236     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.1e-20
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+g+++++++ p+HPYT+aLl+svp++ r+ +  ++i g+ +++ + ++GC++++RCpfa+++C
  gi|488601087|ref|YP_007907558.1| 236 VEIGDTREVIHYPKHPYTAALLSSVPSFVRREQ-RVEIIGDIANPIDVPSGCRYHTRCPFAKQKC 299
                                       8***************************99999.99999************************** PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.5e-08   0.00016      11      66 ..       8      63 ..       4      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.5e-08
                             Rad17 11 ekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                       ky P ++  + v  +k +e  ++++  + e rk ++L + G sGCgk+t+ ++L 
  gi|488601087|ref|YP_007907558.1|  8 KKYFPVQKSAIEVFFSKKKEFIKAVDDVSFEIRKGEVLSLVGESGCGKTTTGRILV 63
                                      79*************************************************99885 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.9   6.9e-06      0.02       5     128 ..      42     213 ..      39     222 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.9e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelka...... 70 
                                         +l ++GesG+GKTt+ r l+   +        +++ +      vt  s+++ + l++++   ++++  +      
  gi|488601087|ref|YP_007907558.1|  42 GEVLSLVGESGCGKTTTGRILVGLETP-------SDGKIlfkgkDVTTLSKEEYRALRKNIQMVFQDPYASlnprmk 111
                                       66899**************99988642.......3333323444444444445555555555555555555555555 PP

                            AAA_22  71 ..............................erlsseellealeqalrarav............ielliiDEaqhlr. 104
                                                                      +l  e++++++  +l+  ++            + +++ DE   ++ 
  gi|488601087|ref|YP_007907558.1| 112 igehledplivhgvaegdeakemamkmldrVGLPAEQFYNRMPYQLSGGQRqrvaiaramilkPDFVVADEPVSMId 188
                                       55555555555555555555555555544423333333322222222222223333333366667777777777555 PP

                            AAA_22 105 ...seealeeLrsllnlsrkgvqliLv 128
                                          ++ +l+ L s+ +  +++++++++
  gi|488601087|ref|YP_007907558.1| 189 vslRASILNLLMSFKD--EYSLSMLFI 213
                                       6444777777777777..777777665 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   2.9e-05     0.088      76     121 ..      17      64 ..       4      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                                       TSEEEE--TTTH.TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  76 gyevllvsaktk.egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        +ev++ ++k+  +++++++ ++++ ++  lvG+SG GK+t    l++
  gi|488601087|ref|YP_007907558.1|  17 AIEVFFSKKKEFiKAVDDVSFEIRKgEVLSLVGESGCGKTTTGRILVG 64 
                                       46677766665458899999999998**************97776665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0065        20       4      22 ..      47      65 ..      44      96 .. 0.85
   2 ?    5.9   0.0    0.0033        10     222     300 ..     142     218 ..      68     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0065
                            AAA_21  4 liGpNgsGKSnLLdaldll 22
                                      l+G  g+GK++  ++l +l
  gi|488601087|ref|YP_007907558.1| 47 LVGESGCGKTTTGRILVGL 65
                                      9***************988 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0033
                            AAA_21 222 vflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsrngaQvilt 295
                                       v l  ++ +++ +++lS G+++  a++ a++  +   ++++ DEp + ++ +l +++l ll   k++ +     ++ 
  gi|488601087|ref|YP_007907558.1| 142 VGLPAEQFYNRMPYQLSGGQRQRVAIARAMILKP---DFVVADEPVSMIDVSLRASILNLLmsfKDEYS--LSMLFI 213
                                       5556666677778999999999977777777766...9********************99976655555..889999 PP

                            AAA_21 296 THSpl 300
                                       TH+ +
  gi|488601087|ref|YP_007907558.1| 214 THDLS 218
                                       99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 2509.64
//
Query:       gi|488601088|ref|YP_007907559.1|  [L=44]
Description: hypothetical protein Asulf_01589 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   37.8   0.0      2e-09   37.6   0.0    1.1  1  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.025   15.0   0.0    1.1  1  GST_N_3        Glutathione S-transferase, N-terminal domain
      0.052   13.8   0.1      0.069   13.4   0.1    1.3  1  zinc_ribbon_9  zinc-ribbon
       0.11   12.6   0.0       0.12   12.5   0.0    1.1  1  Thioredoxin_7  Thioredoxin-like


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 !   37.6   0.0   4.4e-13     2e-09       4      35 ..       6      37 ..       4      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 4.4e-13
                                      EESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH CS
                      Glutaredoxin  4 ftkptCpyCkkakrlLkelgvkfeeidvdkde 35
                                      ++ +tCp+Ck++k++L+e++v+f++i +d+ e
  gi|488601088|ref|YP_007907559.1|  6 YGLTTCPHCKRVKDFLEEHNVNFRTIWLDELE 37
                                      8889*************************976 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 ?   15.0   0.0   5.6e-06     0.025       2      30 ..       6      34 ..       6      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.6e-06
                                      ES-TTSHHHHHHHHHHHHHT--EEEE--- CS
                           GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevt 30
                                      yg +++p+++rv+ +L+e ++ +++ +++
  gi|488601088|ref|YP_007907559.1|  6 YGLTTCPHCKRVKDFLEEHNVNFRTIWLD 34
                                      8999********************99986 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.5e-05     0.069      22      34 ..       9      23 ..       2      24 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                     zinc_ribbon_9 22 vlCPhCg..ggFVEe 34
                                      ++CPhC+   +F+Ee
  gi|488601088|ref|YP_007907559.1|  9 TTCPHCKrvKDFLEE 23
                                      58****8556****8 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05      0.12      25      45 ..       7      27 ..       4      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                      --TT-HHHHHHHHHHHH-HHH CS
                     Thioredoxin_7 25 gaswcftCqalerdflsdeev 45
                                      g ++c++C++++++++++ ++
  gi|488601088|ref|YP_007907559.1|  7 GLTTCPHCKRVKDFLEEHNVN 27
                                      789*************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.27u 0.22s 00:00:00.49 Elapsed: 00:00:00.35
# Mc/sec: 376.46
//
Query:       gi|488601089|ref|YP_007907560.1|  [L=431]
Description: aspartyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-92  310.1   0.1    1.7e-92  309.9   0.1    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    2.7e-15   56.1   0.1    4.5e-15   55.4   0.1    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00071   19.1   0.6       0.23   10.9   0.0    3.0  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.9   0.1   2.9e-96   1.7e-92       3     313 ..     117     425 ..     115     426 .. 0.95

  Alignments for each domain:
  == domain 1  score: 309.9 bits;  conditional E-value: 2.9e-96
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                       ++rl+ r+ldlr++++++++r+r++++++vr++l+++gfie++tP +++++te+g +lF +       ++f    +L
  gi|488601089|ref|YP_007907560.1| 117 DTRLDARFLDLRKPRIQAIFRIRHQMLQSVRDFLTSEGFIEVNTPKIVSTATEGGTELFPI-------SYFereaFL 186
                                       799**********************************************************.......44444445* PP

                                       -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                       +qspqly+++l+ ag+++vf+i++ FRaE+++t rhl+E ++i++e sf+++e +m+vle+li+++ ++v+e+++k 
  gi|488601089|ref|YP_007907560.1| 187 NQSPQLYKQVLMGAGFEKVFEIGPIFRAEEHNTVRHLNEAISIDIEQSFTDHEGVMKVLERLINRVYTDVVEKCEKY 263
                                       **************************************************************************777 PP

                                       CCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 153 iefvirrnskdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeed 223
                                       ++    +  + ++ pf+r+ty+ea+e++++       g+d +++ +++l + e  + ++++d+P e+kpFya   e+
  gi|488601089|ref|YP_007907560.1| 264 LNWAGVKL-EIPEIPFQRVTYDEAVEIIKKRgeeiswGEDFSTPALKLLAE-EFDSHYYIVDWPTEIKPFYAMPYEN 338
                                       76666554.456667************999999****9************9.888999******************* PP

                                       STTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 224 dkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllg 300
                                       ++++++ +Dl+   +El++G++Ri+ p++le+++ +kgl+   +e+f++yl a++yG+pph+G+glG dRl+m +l+
  gi|488601089|ref|YP_007907560.1| 339 EPEISKTFDLMAGSLELASGAQRIHLPDLLEKMISQKGLN---PESFEFYLSAFRYGMPPHAGWGLGADRLLMSILK 412
                                       ************999*************************...********************************** PP

                                       -SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxx RF
                       tRNA-synt_2 301 sesIrdviaFPkl 313
                                       +++Ir++++FP+ 
  gi|488601089|ref|YP_007907560.1| 413 LKNIREAVIFPRD 425
                                       ***********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 !   55.4   0.1   7.5e-19   4.5e-15       1      76 []      19      97 ..      19      97 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 7.5e-19
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET...HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr...eeatklaenlkeGdvvrvtGrvkrr...pggelelkveei 73
                                      V + G+v+ +  r+ g+v+f+ lrD++g+iq+++ +    e tk a ++++++vvrv G+vk+    pgg +e+  +e+
  gi|488601089|ref|YP_007907560.1| 19 VLLYGWVHEV--RDLGGVVFVLLRDREGIIQLTCPKkrnPEITKRARKVRRESVVRVVGEVKEEpkaPGG-YEVLPDEF 94
                                      5678******..****************************************************999999.****9999 PP

                                      EEE CS
                   tRNA_anti-codon 74 ell 76
                                      e+l
  gi|488601089|ref|YP_007907560.1| 95 EVL 97
                                      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 ?    0.8   0.0     0.047   2.8e+02      17      45 ..     137     165 ..     125     169 .. 0.83
   2 !    3.6   0.1    0.0067        40     103     148 ..     204     245 ..     193     265 .. 0.79
   3 !   10.9   0.0   3.8e-05      0.23     212     233 ..     397     418 ..     387     425 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.047
                                       SHHHHHHHHHHHHHHCTTCEESSTTSEEE CS
                      tRNA-synt_2d  17 hpltkvleeikeiflelgfeevegpeves 45 
                                       ++ +++l+ +++++++ gf ev+ p++ s
  gi|488601089|ref|YP_007907560.1| 137 RIRHQMLQSVRDFLTSEGFIEVNTPKIVS 165
                                       5667999****************999865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0067
                                       EEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHH CS
                      tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleel 148
                                       k++ ig +fR ++    h  + h  e + +d + s++d  gv++ l
  gi|488601089|ref|YP_007907560.1| 204 KVFEIGPIFRAEE----HNTVRHLNEAISIDIEQSFTDHEGVMKVL 245
                                       899*********9....77777888888888888888887776654 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 3.8e-05
                                       EEEEEEHHHHHHHHHT-SSGHH CS
                      tRNA-synt_2d 212 fafGlGveRlamlkygieDiRe 233
                                       +++GlG +Rl m  +++++iRe
  gi|488601089|ref|YP_007907560.1| 397 AGWGLGADRLLMSILKLKNIRE 418
                                       68*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); 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:                         3  (0.000167327); expected 0.2 (1e-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: 3083.91
//
Query:       gi|488601090|ref|YP_007907561.1|  [L=418]
Description: histidinol dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.5e-149  498.5   0.8   1.9e-149  498.1   0.8    1.1  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 !  498.1   0.8  1.1e-153  1.9e-149       5     409 .]      14     407 ..      11     407 .. 0.96

  Alignments for each domain:
  == domain 1  score: 498.1 bits;  conditional E-value: 1.1e-153
                                       ----HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHC CS
                     Histidinol_dh   5 eedseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfhea 81 
                                       +++ e+v + v+ei+++v+++Gd+alle+t++ D+v+ l+ +rv+eee+++a++ +++ + +ale a+eni++fh+ 
  gi|488601090|ref|YP_007907561.1|  14 KKSLEDVFQVVREIIDRVKRDGDKALLEITNEIDGVD-LKYIRVPEEEFDKAYDVVEDPVIDALELAKENISNFHSI 89 
                                       5678899***************************885.689***********************************9 PP

                                       C----EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHH CS
                     Histidinol_dh  82 qkeseeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaa 157
                                       +  + + ++ + + ++lg+k++pi+++G+Y+PgG+a+ypSt+lm ++pAk+Agvk++v++tPp+ +g+vn  +l+a+
  gi|488601090|ref|YP_007907561.1|  90 TSVD-RDIRLDFDHMILGKKYTPINSAGIYIPGGRASYPSTALMAGIPAKIAGVKRLVACTPPNkEGRVNALTLVAC 165
                                       9975.5577899***************************************************************** PP

                                       HHCT-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHH CS
                     Histidinol_dh 158 klagvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvA 234
                                       ++++ de+y+vGGaqAi+alAyGte+i++vdki GPGn+yV+aAK lv+++v+iDm+aGPsE+lviaDeta++ef+A
  gi|488601090|ref|YP_007907561.1| 166 DIVEFDEVYAVGGAQAISALAYGTETIERVDKIAGPGNKYVTAAKLLVQNDVAIDMPAGPSEILVIADETANTEFIA 242
                                       ***************************************************************************** PP

                                       HHHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEE CS
                     Histidinol_dh 235 aDLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHle 311
                                       +D+ +q EHd+++ av+++t+e+la+++e++v          ++a++ +++   +++v d+++ai+++n++ApEHl+
  gi|488601090|ref|YP_007907561.1| 243 YDVCAQLEHDPSSIAVVLCTTEKLAKEIETRVG---------DLANEQMSS-NFYTCVADIDTAIAISNSFAPEHLT 309
                                       ****************************99994.........445556666.6788999****************** PP

                                       EESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHH CS
                     Histidinol_dh 312 lqvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaea 388
                                       +  e +e+ +++i+naG++f+G++sp++ gDYa+Gtnh+LPTsg+A+++sglsve+Flk+i++q +++e+lk +++a
  gi|488601090|ref|YP_007907561.1| 310 MVFEGAEDRIDEIENAGSVFIGNHSPVASGDYASGTNHILPTSGYAKIYSGLSVETFLKHITYQMIKPEGLKMIGHA 386
                                       ***************************************************************************** PP

                                       HHHHHHHTT-HHHHHHHHHHH CS
                     Histidinol_dh 389 vetlAeaEgLeaHaeavkvRl 409
                                       +++lAeaEgL+ H+++vkvRl
  gi|488601090|ref|YP_007907561.1| 387 IMKLAEAEGLPFHKKSVKVRL 407
                                       *******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2729.75
//
Query:       gi|488601091|ref|YP_007907562.1|  [L=252]
Description: pantothenate synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-71  237.7   2.6    7.4e-71  237.3   2.6    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.3   2.6   4.1e-75   7.4e-71       1     175 [.      66     238 ..      66     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 237.3 bits;  conditional E-value: 4.1e-75
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseR 77 
                                       +ll+++pvisvNGNtaaLv++ei+eL+e+l+a levN+f+ +eeRv++i+e++++ g + +  l  da++++l+s+R
  gi|488601091|ref|YP_007907562.1|  66 MLLSRHPVISVNGNTAALVPKEIIELSEVLSAVLEVNIFHFSEERVRNIKEYIESFGGKILADL--DAELKGLTSAR 140
                                       699******************************************************9888555..78********* PP

                            PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                       ++vs++Gi+ aD+v+vplEDGDR+e+L+++gKk i+iDLNPlsRt+r+a+itivdn++Ra+pn++++++elk+  k+
  gi|488601091|ref|YP_007907562.1| 141 RMVSSKGILIADTVMVPLEDGDRCEILKTNGKKTITIDLNPLSRTSRMADITIVDNIIRAIPNMIKIAEELKDYPKK 217
                                       ***************************************************************************** PP

                            PPS_PS 155 eleeivkefdnkkvlkealke 175
                                       eleei++++dnkk+l++++ +
  gi|488601091|ref|YP_007907562.1| 218 ELEEILARYDNKKILNRSIIA 238
                                       ****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1427.96
//
Query:       gi|488601092|ref|YP_007907563.1|  [L=67]
Description: hypothetical protein Asulf_01594 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 402.67
//
Query:       gi|488601093|ref|YP_007907564.1|  [L=35]
Description: hypothetical protein Asulf_01595 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 238.14
//
Query:       gi|488601094|ref|YP_007907565.1|  [L=92]
Description: hypothetical protein Asulf_01596 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   21.6   0.0    0.00026   21.0   0.0    1.3  1  HTH_28         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.038   14.4   0.2      0.044   14.2   0.2    1.1  1  Lipocalin_8    Lipocalin-like domain
      0.051   13.1   0.2      0.057   13.0   0.2    1.1  1  Fzo_mitofusin  fzo-like conserved region
      0.086   12.3   0.0       0.28   10.6   0.0    1.8  2  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
       0.11   12.3   0.0       0.17   11.7   0.0    1.4  1  HTH_23         Homeodomain-like domain
        0.3   11.6   1.6       0.62   10.6   1.5    1.9  1  STPPase_N      Serine-threonine protein phosphatase N-termina


Domain annotation for each model (and alignments):
>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   8.8e-08   0.00026       5      50 ..      11      56 ..       6      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.8e-08
                            HTH_28  5 iikllaaGhsvreaArelgisrrtvyrWikryee.gGiagLvprrrr 50
                                      ii++ ++G + + +A++ +i+++++ +  k+y e gGi  L++ ++r
  gi|488601094|ref|YP_007907565.1| 11 IIREKKKGTPTKLIAKIENITPQRINQIYKQYKEtGGILKLKK-PGR 56
                                      688888999*************************888844444.333 PP

>> Lipocalin_8  Lipocalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.5e-05     0.044      52     116 ..      27      91 ..      18      92 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                       Lipocalin_8  52 vaekqgngetgktlgrfeykgdeltlkdpyvndreegdkkvddtveeLepyGinsl.eetFevekl 116
                                       +++ + ++  ++++ +++++g+ l lk+p ++++e +++++++ ++ ++++G  ++ +++F+++++
  gi|488601094|ref|YP_007907565.1|  27 IENIT-PQRINQIYKQYKETGGILKLKKPGRSKKELSNNEIKAIKKHTKNIGAMQQfSKQFRKKAI 91 
                                       44444.78899*****************************************76655999999876 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   0.2   1.9e-05     0.057      92     146 ..      35      91 ..      17      92 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                     Fzo_mitofusin  92 shqvqqelsstfarlc.qqvdetekel.eeeikelekeiekleevqkkakllrnkas 146
                                        +q+ ++ ++t   l+ ++  +++kel ++eik+++k+ +++ ++q+ +k++r+ka 
  gi|488601094|ref|YP_007907565.1|  35 INQIYKQYKETGGILKlKKPGRSKKELsNNEIKAIKKHTKNIGAMQQFSKQFRKKAI 91 
                                       5677777777766665234567788883579************************95 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.4e-05      0.28      17      51 ..       8      42 ..       5      43 .. 0.91
   2 ?   -0.9   0.0      0.37   1.1e+03      10      21 ..      80      91 ..      76      92 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.4e-05
                      HTH_Tnp_ISL3 17 eayilelllesrsvkavArqlgvSwtTVwrildry 51
                                        +i+++ +++ + k +A++ ++++ +++ i+++y
  gi|488601094|ref|YP_007907565.1|  8 IKWIIREKKKGTPTKLIAKIENITPQRINQIYKQY 42
                                      579999988899********************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.37
                      HTH_Tnp_ISL3 10 sriTlrleayil 21
                                      +++++ ++ +++
  gi|488601094|ref|YP_007907565.1| 80 QQFSKQFRKKAI 91
                                      799999999886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-05      0.17      10      45 ..      11      47 ..       2      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryre.eG 45
                                      i++  ++G +++ IA++ +++++ + ++ k y+e +G
  gi|488601094|ref|YP_007907565.1| 11 IIREKKKGTPTKLIAKIENITPQRINQIYKQYKEtGG 47
                                      6777777888888*******************99555 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.5   0.00021      0.62      13      37 ..      47      76 ..       7      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                         STPPase_N 13 g.....kpggkkvqLseaEIrqlCakarei 37
                                      g     kpg++k  Ls++EI+++ ++ + i
  gi|488601094|ref|YP_007907565.1| 47 GilklkKPGRSKKELSNNEIKAIKKHTKNI 76
                                      35555589999999********97777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 587.34
//
Query:       gi|488601095|ref|YP_007907566.1|  [L=285]
Description: putative hydrolase of the metallo-beta-lactamase superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   26.5   0.0    5.3e-06   26.1   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
      2e-05   24.6   0.0    2.8e-05   24.1   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0052   16.8   0.3      0.014   15.4   0.2    1.7  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.069   13.4   1.4       0.37   11.1   0.1    2.3  2  DHH            DHH family


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 !   26.1   0.0   1.2e-09   5.3e-06      24     200 ..      59     234 ..      26     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.2e-09
                                       SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEE.EEE-TTSEEEE CS
                     Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvylaleeepavnv.heldwgesfel 98 
                                        ++ ++  d++++th HyDH +  +   e + +k++ l  p++++   ++n  + +l e  + nv  e++ g+sfe+
  gi|488601095|ref|YP_007907566.1|  59 IKEAVRMSDLIIITHYHYDHHN--PNEPEiFDGKRVLLKHPEEMINRSQRNRARYFLSELRKFNVdYEFADGKSFEF 133
                                       45677888*************4..33333466666666677777777777766666666635555247889****** PP

                                       CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE...CTTEEEEEESS-S.---.HHHHHHHCT.-SEEEEE-S-SST CS
                     Lactamase_B_2  99 gdggleitatparhksgrrldrnagdtlGlrie...gggkrvyyigDtg.yip.eeigerlgg.adllllditayed 169
                                       gd++++i   p+ h+  +         lG++i+   ++ ++++++ D++  i+ ++++ ++++ +d+ ++d+ ++  
  gi|488601095|ref|YP_007907566.1| 134 GDVEIKISN-PVFHGVDE--------KLGYVIQvliSESENFVFSSDVEgPIHrDQAKFLIENdPDVCIIDGPMTYM 201
                                       *76655554.55565555........9******99999**********9444478899999988******9764443 PP

                                       THHHH...HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 170 demir...hmgHltpeeaveaaadlgakrlvliH 200
                                         + r   + + +++++  e+++++g+k lv  H
  gi|488601095|ref|YP_007907566.1| 202 LGY-RfsnRSFESSISNLKEIVEKTGVKHLVIDH 234
                                       332.235578888888888888888888777766 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   6.3e-09   2.8e-05       9     123 ..      17     181 ..      13     204 .. 0.62

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.3e-09
                     Lactamase_B_3   9 sflletagarilvDPfka..nlgyeppa...................eeaDlvlisqaledHahletlkqlaenvkv 64 
                                       + ++et++ +i +DP  a   + y+ p+                   +  Dl++i++ + dH ++++ +  + +  +
  gi|488601095|ref|YP_007907566.1|  17 CTMIETKDLTITIDPSVAlgPKRYGLPPhpieiqrmaelwdkikeavRMSDLIIITHYHYDHHNPNEPEIFDGKRVL 93 
                                       999************95444555555557788888889999999999****************99987775444444 PP

                     Lactamase_B_3  65 lee...............................geslevggleiravatshdavggsergenngflleq...dglt 107
                                       l++                               g+s+e+g++ei+     + + + +  +e  g+++++   +  +
  gi|488601095|ref|YP_007907566.1|  94 LKHpeeminrsqrnraryflselrkfnvdyefadGKSFEFGDVEIK-----ISNPVFHGVDEKLGYVIQVlisESEN 165
                                       4444444444444444444444555544444444444555555554.....33333333444455555544435555 PP

                     Lactamase_B_3 108 iyhlGhlahelsseel 123
                                       +++  ++  +++ ++ 
  gi|488601095|ref|YP_007907566.1| 166 FVFSSDVEGPIHRDQA 181
                                       5555555555555555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   3.1e-06     0.014       7      57 ..      16      78 ..      12      79 .. 0.82
   2 ?   -2.3   0.0      0.81   3.7e+03      59      92 ..     216     249 ..     215     275 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-06
                                      EEEEEEETTCEEEES--SCHHHHHHHH............HHHHHTSGGGGEEEEE-SBSSHHH CS
                       Lactamase_B  7 nsyliegdggviLiDtGtsteaaraal............elaalglkpkdvdavilTHlHlDH 57
                                       ++ ie+++ +i iD+ +    +r  l            +  +++   +  d +i+TH+H+DH
  gi|488601095|ref|YP_007907566.1| 16 MCTMIETKDLTITIDPSVALGPKRYGLpphpieiqrmaeLWDKIKEAVRMSDLIIITHYHYDH 78
                                      6788888888888888888888888888888888888877888999999999*********** PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.81
                                       TTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHH CS
                       Lactamase_B  59 Gglgglveatdvpvgavaeeapalfmeeaddaas 92 
                                       ++l+++ve+t+v++ +  +++   ++     +++
  gi|488601095|ref|YP_007907566.1| 216 SNLKEIVEKTGVKHLVIDHHLTRDINYRSRMSEV 249
                                       5678888888888887777766555555555554 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.11   5.1e+02      49      57 ..      76      86 ..      56     117 .. 0.71
   2 ?   11.1   0.1   8.2e-05      0.37      39      81 ..     222     266 ..     177     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                                      EE-S---S..S CS
                                      xxxxxxxx..x RF
                               DHH 49 iDHHrlge..e 57
                                       DHH+++e   
  gi|488601095|ref|YP_007907566.1| 76 YDHHNPNEpeI 86
                                      59999986540 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.2e-05
                                       HCCCSEEEEEEE-S---S..S---SS--EEEE-SSS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  39 akeeaedviiiDHHrlge..efetlapilflnepvgstaeivael 81 
                                       +++++++ ++iDHH   +    +++++++   e++g+ ae + e+
  gi|488601095|ref|YP_007907566.1| 222 VEKTGVKHLVIDHHLTRDinYRSRMSEVYAFAESAGAKAETAREF 266
                                       5789999*********97765556667777888888888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1630.95
//
Query:       gi|488601096|ref|YP_007907567.1|  [L=124]
Description: formylmethanofuran dehydrogenase, subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-19   70.6   0.0    1.3e-19   70.3   0.0    1.1  1  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.053   13.7   0.0      0.093   12.9   0.0    1.4  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      0.096   12.6   0.0       0.63   10.0   0.0    2.3  3  TOBE_3           TOBE-like domain
      0.097   12.9   0.1       0.14   12.4   0.1    1.4  1  FeoA             FeoA domain
       0.13   12.4   0.1       0.25   11.5   0.0    1.5  1  Rad9_Rad53_bind  Fungal Rad9-like Rad53-binding


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 !   70.3   0.0   3.6e-23   1.3e-19       3     110 ..       7     103 ..       5     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 3.6e-23
                                       EEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESS CS
                   Molydop_binding   3 LitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfg 79 
                                       Li+gr+ldq  ++ ++ ++++ ++++  ++e+++ed +alG+++Gd+V+v++++G+v+v a++++++ +G++f+p+g
  gi|488601096|ref|YP_007907567.1|   7 LISGRTLDQGATVEEKLTDEYFKAVS--YCELSEEDFKALGLSEGDRVKVKTEFGEVVVFAVLNKDLDRGMAFIPMG 81 
                                       9******************9999988..9************************************************ PP

                                       HCC.....S-GHCTS--SCSTTT--CSTT-E CS
                   Molydop_binding  80 wweagekggnaNaltddatdplsgtpefksv 110
                                        ++        N+++ d+ ++ +g+p+fk+v
  gi|488601096|ref|YP_007907567.1|  82 PYA--------NMVI-DPNTDGTGMPQFKGV 103
                                       *77........****.77777899***9986 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 ?   12.9   0.0   2.6e-05     0.093      19      62 ..      36      80 ..      30      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                                      E-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE CS
                           CDC48_N 19 idpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrm 62
                                      +++ed+++lgl++gd v+++    + v++++ +++ d+g   I m
  gi|488601096|ref|YP_007907567.1| 36 LSEEDFKALGLSEGDRVKVKTeFGEVVVFAVLNKDLDRGMAFIPM 80
                                      799******************888899999999999998888877 PP

>> TOBE_3  TOBE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.59   2.1e+03      22      34 ..       4      18 ..       2      30 .. 0.52
   2 ?   10.0   0.0   0.00018      0.63      38      57 ..      35      54 ..      33      57 .. 0.92
   3 ?   -1.9   0.0      0.91   3.3e+03      15      28 ..      78      91 ..      76      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.59
                            TOBE_3 22 RlELerl..gdtgel 34
                                       +EL+ +   d+g +
  gi|488601096|ref|YP_007907567.1|  4 EVELISGrtLDQGAT 18
                                      344444333333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00018
                            TOBE_3 38 elprdrfeelglaeGetvyl 57
                                      el+++ f+ lgl+eG++v +
  gi|488601096|ref|YP_007907567.1| 35 ELSEEDFKALGLSEGDRVKV 54
                                      89***************966 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.91
                            TOBE_3 15 rpvGpivRlELerl 28
                                      +p+Gp++   ++++
  gi|488601096|ref|YP_007907567.1| 78 IPMGPYANMVIDPN 91
                                      79999998777776 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.9e-05      0.14      26      67 ..      39      76 ..       2      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                                      HHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHH CS
                              FeoA 26 rrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeA 67
                                        ++++Gl +G r++v     fg  +v +v ++  +L+r++A
  gi|488601096|ref|YP_007907567.1| 39 EDFKALGLSEGDRVKVKT--EFGEVVVFAVLNK--DLDRGMA 76
                                      5689************95..699******9988..9999998 PP

>> Rad9_Rad53_bind  Fungal Rad9-like Rad53-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     7e-05      0.25      43      82 ..      27      67 ..       4      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7e-05
                   Rad9_Rad53_bind 43 kfeega.vevkkedvkyLdlriGdkvkvdmktyvvrglekk 82
                                      +f+  +  e ++ed k L l  Gd+vkv+++  +v+ ++  
  gi|488601096|ref|YP_007907567.1| 27 YFKAVSyCELSEEDFKALGLSEGDRVKVKTEFGEVVVFAVL 67
                                      577766689*********************96666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 766.76
//
Query:       gi|488601097|ref|YP_007907568.1|  [L=422]
Description: formylmethanofuran dehydrogenase, subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   47.2   0.0    1.1e-11   44.4   0.0    2.2  1  Molybdopterin  Molybdopterin oxidoreductase
  ------ inclusion threshold ------
      0.034   13.6   1.3      0.063   12.8   1.3    1.4  1  TF_Zn_Ribbon   TFIIB zinc-binding
       0.19   11.3   0.0        0.3   10.6   0.0    1.2  1  DUF4464        Domain of unknown function (DUF4464)


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 !   44.4   0.0   1.8e-15   1.1e-11       1     415 [.      45     401 ..      45     410 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.8e-15
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEE.EEBTSSCSHHHHHHHHHHHHHTT-EEE-B CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvag.fssgplmsmeslaslkkllsllggknlsf 76 
                                       R+k Pm+          ++vs +eA e  a+ l++    + p    + ++  + + +e++ ++  l +++gg     
  gi|488601097|ref|YP_007907568.1|  45 RIKSPMID---G-----KEVSYEEAIEKAAEILVN---AKRP----LlYGWASTV-NEAIRLGVILTEKVGG----I 101
                                       88888888...3.....569999999999999999...7788....324443444.7888888888888888....9 PP

                                       EECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG.-SEEEEESS-HHHHSHHHHHHHHHHHHTTC........-EE CS
                     Molybdopterin  77 ydwyadlppasaqqtigsdsrsnyessnpledlen.sdliilwGsNvreerpilnarirkaalkkk........akv 144
                                       yd++a +++a     +   +  ++  s  l+++ n +d+++ wGsN+ e +p     +r++++ k+         kv
  gi|488601097|ref|YP_007907568.1| 102 YDQCASVCHAPGT--LALIEEGVPGGS--LGEIKNrADMVVFWGSNPLEAHPRH--PMRYSVRAKGllikdrkdRKV 172
                                       *********9874..333333334444..67777669***************99..4555555555666667789** PP

                                       EEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCH CS
                     Molybdopterin 145 ivigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevva 221
                                       +v++ r++++++ ad+ ++ikpg d +++ a++ +i++    + ++                        +  +v +
  gi|488601097|ref|YP_007907568.1| 173 VVVDVRKTKSANMADLFIKIKPGYDYPIISALR-AIIKGEESAVPS------------------------EVGGVKK 224
                                       ****************************66666.555555555522........................2334555 PP

                                       HHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTC CS
                     Molybdopterin 222 riarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvl 298
                                       +  +ela+ + +++   ++++G g+++++  d +++ +i+L +l++   +       ++G +++ g a +v a    
  gi|488601097|ref|YP_007907568.1| 225 ELLKELADMMVNAKY-GAVLYGLGVTQSRGRDRNIENAIKLIQLLNRKTRW--IIWPMRGHYNVVG-AGEVPAWEAG 297
                                       678889999988888.9**************************99977762..3445567666666.5555555333 PP

                                       CCCCCCTTHHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESC CS
                     Molybdopterin 299 lsvkslkeekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgr 375
                                                 + +++  +g   + ++ +f+ ++++l++++ ++  ++ ++p+ + + ++       k+  v+ +d +
  gi|488601097|ref|YP_007907568.1| 298 ---------YTYAIDFSRGYPRF-SPGEFS-ANEVLQRKDCDAALIIASDPVAHFPRASVA---HLKKIPVIQIDPF 360
                                       .........33334444555555.555554.589999999*99999996666666665555...67*********** PP

                                       SSHHHHTSSEEEEBE-C.CGSEEEEE-TTSEEEEEEESSS- CS
                     Molybdopterin 376 ltstalyaDiiLPaatw.yEkedlytndegrfqhlkqavsp 415
                                        + t l ++++ P+a   +E e++   ++g   + k++v++
  gi|488601097|ref|YP_007907568.1| 361 PNMTTLVSNVVIPSAVAgIEAEGTAYRMDGIPFRVKKVVET 401
                                       *************996538************9999999987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.3   1.1e-05     0.063      19      41 ..       7      29 ..       3      31 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                      CEEESSSSBEEEECCCCCCCHHH CS
                      TF_Zn_Ribbon 19 elvCtdCGlVlednsidegpewr 41
                                      +++Ct+CG+V +d   d +  + 
  gi|488601097|ref|YP_007907568.1|  7 NVICTFCGSVCDDVLFDVENYKG 29
                                      789*************9988775 PP

>> DUF4464  Domain of unknown function (DUF4464)
   #    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     173     198 ..     159     184 ..     153     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5e-05
                           DUF4464 173 ekgLlfkhkrDrkvinvdpkaekpgd 198
                                       +kgLl+k ++Drkv+ vd +++k  +
  gi|488601097|ref|YP_007907568.1| 159 AKGLLIKDRKDRKVVVVDVRKTKSAN 184
                                       78****************99955443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2509.69
//
Query:       gi|488601098|ref|YP_007907569.1|  [L=563]
Description: formylmethanofuran dehydrogenase, subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-91  307.0   0.0    4.6e-91  306.6   0.0    1.1  1  Amidohydro_3    Amidohydrolase family
    3.5e-11   43.0   0.2    4.6e-05   22.9   0.0    2.5  2  Amidohydro_1    Amidohydrolase family
  ------ inclusion threshold ------
      0.071   13.9   0.0       0.15   12.8   0.0    1.5  1  DUF3349         Protein of unknown function (DUF3349)
       0.14   11.9   0.0       0.29   10.9   0.0    1.4  1  Heme_oxygenase  Heme oxygenase
       0.28   11.6   1.6       0.63   10.5   1.6    1.5  1  G5              G5 domain


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 !  306.6   0.0   1.3e-94   4.6e-91       1     472 [.      45     500 ..      45     501 .. 0.97

  Alignments for each domain:
  == domain 1  score: 306.6 bits;  conditional E-value: 1.3e-94
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwi.vgeGwdeaqfaeer 75 
                                       ++iDa+++lv++G+ D+H+H+ag ++n+ r++r+++         +++vr  ag+      + +  G      ++ +
  gi|488601098|ref|YP_007907569.1|  45 KTIDASNKLVVAGGFDMHAHIAGSKINVgREMRPEE---------MRTVRLIAGK------FrASIGRVLLTSPAIG 106
                                       68**********************************.........5556666666......335556699******* PP

                      Amidohydro_3  76 fpyalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlap 152
                                       + ya++++++++e+a+++++al+tH++++ ++++d+            +++ +++n+++++ +++e+          
  gi|488601098|ref|YP_007907569.1| 107 YEYAKMGYTTAFEAAQPPVGALHTHEELDAIPMIDK------------AALPVFGNWHFVLKYVAEK---------- 161
                                       ************************************............9******************.......... PP

                      Amidohydro_3 153 lareaeaaavaaalaalasyGitsv.......eagggnvsslddleplfeltaeeklplrviikelldaaerlglpl 222
                                        + e+++a++a+al++++++G+++v       ++ ggn  sldd +p f++t++e      ii+ l++  e+l l++
  gi|488601098|ref|YP_007907569.1| 162 -DFEKLRAFIAWALERTKGFGVKVVnpggveaWMYGGNCKSLDDEVPGFGVTPRE------IITALIQETENLNLCH 231
                                       .******************************************************......**************** PP

                      Amidohydro_3 223 s..........pgseeltigavklfad.gvlgsrtalltepyf.....tgwpdfedea..laelvaaadergldvai 281
                                       s          pg++e+ti+++kl+ +  ++ ++++++t+++f     ++w+d+ ++a  +a++v+ +d+ ++d+++
  gi|488601098|ref|YP_007907569.1| 232 SvhlhcnnlgtPGNYETTIESMKLASKfSNEKRQVLHVTHVQFnsyagSSWRDVASGAaeVAKYVNSVDNITIDMGQ 308
                                       ***************************7778999******************************************* PP

                      Amidohydro_3 282 haigdaavd..dvldafeaa...aekngnqdrrrlehaegv...tesqiervaalqvaagvqpvfnfedelldsrlg 350
                                        ++g+a+++  d++ +f+ +   +++++n+d+ ++e + g+    + ++++v+alq+a+g++               
  gi|488601098|ref|YP_007907569.1| 309 PIFGHATAMtgDAPFQFTLHkltGARWSNKDS-EIEGGAGIvpiAYLPKNPVHALQWAIGLE--------------- 369
                                       ********************************.*****************************............... PP

                      Amidohydro_3 351 perargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrgg.............evlrpdeelsleea 413
                                                +++l + + kv+l++D +++gpf+++p+++a++m+k++r++             +++ +d e +l+e+
  gi|488601098|ref|YP_007907569.1| 370 ---------LGLLVDSD-KVVLSTDyPNGGPFTEYPYVMAMLMSKKMREKelervspyvqkatNLPSIDVEKTLYEV 436
                                       .........78887777.*********************************************************** PP

                      Amidohydro_3 414 lalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear......vrltvvdGrvv 472
                                       ++++++ pA+++g++ + G+L+vGadAD++++d +pl+vdp++++e++      +++t+++G+++
  gi|488601098|ref|YP_007907569.1| 437 IHMTRSLPARVMGMDSK-GHLGVGADADIAIYDLNPLEVDPSNDFETVykafktAVYTIKGGEII 500
                                       ****************8.*********************************************97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   4.4e-07    0.0016       1     160 [.      53     247 ..      53     272 .. 0.72
   2 !   22.9   0.0   1.3e-08   4.6e-05     281     341 ..     432     496 ..     370     500 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.4e-07
                                       EEEE-EEEEEEECETTECSSS....GHHHHH..................STTHHHHHHHHHHHHHHHHTTEEEEEEE CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..................vppetaaealesgiktalksGtttvadm 55 
                                       +v++G+ D+H H+ +s +  +    + e+++                  ++p + +e+++ g +ta+++   +v + 
  gi|488601098|ref|YP_007907569.1|  53 LVVAGGFDMHAHIAGSKIN-VgremRPEEMRtvrliagkfrasigrvllTSPAIGYEYAKMGYTTAFEAAQPPVGAL 128
                                       589**********988763.3469977777788899***************************************** PP

                                       EHSSTH.HHHHHHHHHHTSSSEEEEEEESSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSH CS
                      Amidohydro_1  56 gattst.giealleaaeelplglrilggkvsldr.gsaetskasreklkagaaetikgkadgvvkvalapheapafs 130
                                       +++++  +i+ + +aa  ++ + ++++++v  +  ++   ++a++ +  +g+   +k+ ++g+v+++++   + ++ 
  gi|488601098|ref|YP_007907569.1| 129 HTHEELdAIPMIDKAALPVFGNWHFVLKYVAEKDfEKLRAFIAWALERTKGF--GVKVVNPGGVEAWMYGGNCKSLD 203
                                       **6555888888889999*9********333322555555555555555555..44444555555555555555555 PP

                                       HH..........HHHHHHHHHHHHTTEEEEEE....TSSCHHHH CS
                      Amidohydro_1 131 de..........elkealkeakkrdlpvaiHa....letkgeve 160
                                       de           + ++++e +  +l  ++H+    l+t+g +e
  gi|488601098|ref|YP_007907569.1| 204 DEvpgfgvtpreIITALIQETENLNLCHSVHLhcnnLGTPGNYE 247
                                       55777777777666667777777776444444325555555555 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.....CTCGGGTTTCTSEEEEEEEETT CS
                      Amidohydro_1 281 slkealrmaTingAkalglddkvGsievGkdADlvvvdl.....dilaafvglkkdgnvkkvivkG 341
                                       +l+e++ m+   +A+++g+d  +G + vG dAD+++ dl     d+ ++f+ + k+++++   +kG
  gi|488601098|ref|YP_007907569.1| 432 TLYEVIHMTRSLPARVMGMD-SKGHLGVGADADIAIYDLnplevDPSNDFETVYKAFKTAVYTIKG 496
                                       789999999999*******6.******************766666699999998888887666555 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.2e-05      0.15      10      51 ..     381     423 ..     378     446 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                                       HHHH-TT-B-HHHHHHHHHHHCTT.--HHHHHHHHHHHHHH-- CS
                           DUF3349  10 LragYPegvPeqdyvpLlalLrrr.Lsdeevkevaeelvaeaa 51 
                                       L + YP+g P ++y  ++a+L ++ + ++e+++v   + + ++
  gi|488601098|ref|YP_007907569.1| 381 LSTDYPNGGPFTEYPYVMAMLMSKkMREKELERVSPYVQKATN 423
                                       7889**************9876544*********988877773 PP

>> Heme_oxygenase  Heme oxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     8e-05      0.29      81     123 ..     273     315 ..     266     321 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8e-05
                                       HHHHHHSTTHHHHS---HHHHHHHHHHHHHHHH-GGGHHHHHH CS
                    Heme_oxygenase  81 dlaylygsdwrkdieispavqkyverlekiaaeepellvAhaY 123
                                        ++ ++gs wr+     ++v kyv+ +++i    ++ +++ha 
  gi|488601098|ref|YP_007907569.1| 273 QFNSYAGSSWRDVASGAAEVAKYVNSVDNITIDMGQPIFGHAT 315
                                       5899*************************************85 PP

>> G5  G5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.6   0.00017      0.63      30      73 ..      13      57 ..       9      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                      EE--B-EEEEEEEEEEEETTEEEEE---EEEEEE.--B-EEEEE- CS
                                G5 30 vqeGknGvkevtyrvtyenGkevsrevvseevvk.epvpevvkvG 73
                                      v  +knGv  ++  + ++nGk+v++ +vs ev +  + ++ v+ G
  gi|488601098|ref|YP_007907569.1| 13 VIDPKNGVNAEKMDIFVKNGKIVEESEVSGEVKTiDASNKLVVAG 57
                                      55689**********999************997779999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 3714.14
//
Query:       gi|488601099|ref|YP_007907570.1|  [L=235]
Description: formylmethanofuran dehydrogenase, subunit C [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-11   43.7  26.6    1.4e-08   34.6   4.3    3.0  3  GXGXG            GXGXG motif
     0.0049   16.7   0.4      0.014   15.2   0.3    1.9  1  DUF2807          Putative auto-transporter adhesin, head GIN 
  ------ inclusion threshold ------
       0.13   12.6   2.3        5.5    7.4   0.0    3.2  3  Arc_trans_TRASH  Archaeal TRASH domain


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 !   34.6   4.3   2.3e-12   1.4e-08     115     166 ..      72     124 ..      66     131 .. 0.90
   2 !    3.2   6.2    0.0094        56     136     159 ..     139     162 ..     118     163 .. 0.61
   3 !   16.2   2.8     1e-06    0.0062      34      79 ..     163     206 ..     162     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.3e-12
                                       TTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE-SS CS
                             GXGXG 115 avrnsgatavvegv.gdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvlded 166
                                       + r+   ++vv+g+ gdh++ YmtGG++vv g+  + ++a m+gG + v  + 
  gi|488601099|ref|YP_007907570.1|  72 GTRMDEGEIVVKGNiGDHCGAYMTGGKIVVEGNALDWLGAEMKGGEIIVKGNA 124
                                       7899999******99********************************997554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0094
                                       -EEEEEEE-S-B-SSBTTT--EEE CS
                             GXGXG 136 mtGGvvvvLgktgrnfaaGmsgGi 159
                                       m GG++ v g++g+++++ m gG 
  gi|488601099|ref|YP_007907570.1| 139 MSGGKITVDGNVGNYIGEKMGGGE 162
                                       556666666666666666666654 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1e-06
                                       EEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--T CS
                             GXGXG  34 iklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpsk 79 
                                       i++kGsaG+ +g+ + +G+ + ++Gd+  +vG  ++gG+i ik++ 
  gi|488601099|ref|YP_007907570.1| 163 IEIKGSAGDFIGTEMKDGV-IVIHGDCG-FVGGDMKGGTIKIKGNF 206
                                       89*************9997.679****8.68889********9875 PP

>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   2.4e-06     0.014      16     127 ..      52     172 ..      39     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-06
                                       EE-SS-EEEEEEEHHHHCCEEEEEETTEEEEEE-....TTTTSSB.EEEEEEES--SEEEEE.CCEEEEE-S-EEEE CS
                           DUF2807  16 tqgdeqsvviegdenllekvevevedgtLkirle....kefestktlkvtvtvpnleelels.gsgsievegtlkad 87 
                                       ++gde+++v+egd   ++ v + +++g+++++ +     +  +t   k+ v+ + l  l ++  +g+i v+g+++ +
  gi|488601099|ref|YP_007907570.1|  52 KEGDEAKLVLEGDFSKVKWVGTRMDEGEIVVKGNigdhCGAYMTG-GKIVVEGNALDWLGAEmKGGEIIVKGNARNY 127
                                       57*****************************99999774555555.68**********999746789*****44433 PP

                                       EEEEEE.......ECSEEEEEEEEEEEEEEEEECCEEEEEEEEEEEE CS
                           DUF2807  88 klelni.......agsgditlkldaeelsveasgsgdielsGtadrl 127
                                          + +        ++g+it++ ++ +   e  g+g+ie++G+a+++
  gi|488601099|ref|YP_007907570.1| 128 VG-C-AyygdmtgMSGGKITVDGNVGNYIGEKMGGGEIEIKGSAGDF 172
                                       32.2.13577777899***************************9975 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.021   1.3e+02       2      16 ..      88     102 ..      87     104 .. 0.91
   2 ?    7.4   0.0   0.00091       5.5       2      25 ..     107     130 ..     107     132 .. 0.92
   3 ?   -1.2   0.0      0.45   2.7e+03       2      16 ..     171     185 ..     171     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.021
                   Arc_trans_TRASH   2 DYCGkeivgePivyk 16 
                                       D CG  ++g  iv++
  gi|488601099|ref|YP_007907570.1|  88 DHCGAYMTGGKIVVE 102
                                       99*******999986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00091
                   Arc_trans_TRASH   2 DYCGkeivgePivyklknkvYyvC 25 
                                       D+ G e++g  i++k   + Y+ C
  gi|488601099|ref|YP_007907570.1| 107 DWLGAEMKGGEIIVKGNARNYVGC 130
                                       6669******************99 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.45
                   Arc_trans_TRASH   2 DYCGkeivgePivyk 16 
                                       D+ G e+++  iv++
  gi|488601099|ref|YP_007907570.1| 171 DFIGTEMKDGVIVIH 185
                                       7789*****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1500.94
//
Query:       gi|488601100|ref|YP_007907571.1|  [L=92]
Description: putative transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.003   17.5   0.3     0.0041   17.1   0.3    1.2  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
  ------ inclusion threshold ------
       0.06   13.5   0.3       0.09   12.9   0.3    1.2  1  zf-UDP          Zinc-binding RING-finger
      0.069   12.6   1.8        2.4    7.7   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.075   13.0   3.7       0.11   12.4   0.6    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        0.1   12.6   1.2      0.096   12.7   1.2    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.15   12.0   0.1       0.21   11.5   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.15   12.2   0.1       0.26   11.4   0.1    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
       0.16   12.0   1.3       0.53   10.4   1.3    1.8  1  FeoC            FeoC like transcriptional regulator
       0.19   11.5   4.1       0.31   10.8   4.1    1.3  1  zinc_ribbon_2   zinc-ribbon domain
       0.35   10.8   1.8         10    6.1   0.0    2.1  2  HalOD2          Halobacterial output domain 2
        1.7    8.5   3.6          7    6.6   0.4    2.2  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> 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 !   17.1   0.3   2.5e-06    0.0041      13      47 ..      54      86 ..      50      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-06
                          zf-C2HC5 13 LleaapnClnCGkiiCakeglskpCsfCgspllss 47
                                      Ll a p C +CG ++ +  +  ++C+ C+s+ +s+
  gi|488601100|ref|YP_007907571.1| 54 LLVAYPECRKCGFVLKNIGA--SKCPKCKSEWISE 86
                                      67789*********955544..6*******98886 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   5.5e-05      0.09      33      60 ..      56      83 ..      52      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                            zf-UDP 33 cafpvcrpcyeyerkdgnqsCPqCktry 60
                                      +a+p cr+c    +  g+  CP+Ck+++
  gi|488601100|ref|YP_007907571.1| 56 VAYPECRKCGFVLKNIGASKCPKCKSEW 83
                                      89*******9999999*********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 ?    4.2   0.1     0.019        31      19      26 .]      61      68 ..      60      68 .. 0.90
   2 ?    7.7   0.1    0.0014       2.4      15      23 ..      72      80 ..      70      85 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.019
                       zf-ribbon_3 19 CpyCGtkl 26
                                      C +CG +l
  gi|488601100|ref|YP_007907571.1| 61 CRKCGFVL 68
                                      9****987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                       zf-ribbon_3 15 ddnvCpyCG 23
                                      ++++Cp+C 
  gi|488601100|ref|YP_007907571.1| 72 GASKCPKCK 80
                                      677777776 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.24   3.8e+02       2       9 ..      58      65 ..      55      65 .. 0.81
   2 ?   12.4   0.6   6.9e-05      0.11       3      11 ..      74      82 ..      69      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.24
                    PhnA_Zn_Ribbon  2 lpkCplCa 9 
                                      +p C +C+
  gi|488601100|ref|YP_007907571.1| 58 YPECRKCG 65
                                      59999995 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.9e-05
                    PhnA_Zn_Ribbon  3 pkCplCaSe 11
                                      +kCp+C+Se
  gi|488601100|ref|YP_007907571.1| 74 SKCPKCKSE 82
                                      788888888 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 ?   12.7   1.2   5.9e-05     0.096      71      95 ..      59      82 ..       2      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                                      EEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 71 vrCreCgkefeleekalrCpkCgsa 95
                                       +Cr+Cg   +    a +CpkC+s+
  gi|488601100|ref|YP_007907571.1| 59 PECRKCGFVLKNI-GASKCPKCKSE 82
                                      58*****666643.2579*****97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013      0.21      16      57 ..       9      51 ..       4      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                      HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                       Ll  + ++ta+++ +el+++     +vL+  e++G V ++kg
  gi|488601100|ref|YP_007907571.1|  9 DLLiDRRSLTASDVIRELKLDPKMRKDVLNAFEKAGRVLKKKG 51
                                      5666999******************************999886 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00016      0.26      13      44 ..       2      33 ..       2      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      THHHHHHHHHHHHSSBEHHHHHHHHSSTHHHH CS
                             HTH_9 13 evvakVvetLlrkgrltlrelvkktkLsldqV 44
                                      ++v+k +++L+++  lt+++ ++++kL+++  
  gi|488601100|ref|YP_007907571.1|  2 TLVEKLIDLLIDRRSLTASDVIRELKLDPKMR 33
                                      589************************99865 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00033      0.53       5      61 ..       7      65 ..       3      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                              FeoC  5 lkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaatacc..sgsCkkCg 61
                                      l ++l  r++   ++  r++k +p++ ++ L+  ++ Grv k++          C kCg
  gi|488601100|ref|YP_007907571.1|  7 LIDLLIDRRSLTASDVIRELKLDPKMRKDVLNAFEKAGRVLKKKGFRLLvaYPECRKCG 65
                                      5577888999999***************************9998766657778888887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.1   0.00019      0.31       2      19 ..      61      79 ..      60      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                     zinc_ribbon_2  2 CpnCGaelqd.nakFCpyC 19
                                      C +CG  l++ +a  Cp+C
  gi|488601100|ref|YP_007907571.1| 61 CRKCGFVLKNiGASKCPKC 79
                                      *********99******** PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0064        10      17      47 ..      44      74 ..      40      75 .. 0.77
   2 ?    4.4   1.2     0.021        34       3      12 ..      74      83 ..      72      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0064
                            HalOD2 17 GdglGe.GyrqLGayvWkCtrCGevqaaAdpS 47
                                      G+ l + G+r L ay   C +CG v++   +S
  gi|488601100|ref|YP_007907571.1| 44 GRVLKKkGFRLLVAYP-ECRKCGFVLKNIGAS 74
                                      6666666899898885.8*******9876666 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.021
                            HalOD2  3 ekCseCsldW 12
                                       kC++C+ +W
  gi|488601100|ref|YP_007907571.1| 74 SKCPKCKSEW 83
                                      59******** 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 ?    2.9   0.2      0.06        97      14      22 ..      59      67 ..      52      68 .. 0.82
   2 ?    6.6   0.4    0.0043         7       9      20 ..      69      80 ..      68      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.06
                         zf-C2H2_3 14 sqCkeCgMv 22
                                      ++C +Cg v
  gi|488601100|ref|YP_007907571.1| 59 PECRKCGFV 67
                                      56*****75 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0043
                         zf-C2H2_3  9 ksfgasqCkeCg 20
                                      k++gas+C++C+
  gi|488601100|ref|YP_007907571.1| 69 KNIGASKCPKCK 80
                                      68899******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 641.35
//
Query:       gi|488601101|ref|YP_007907572.1|  [L=334]
Description: ketol-acid reductoisomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-77  257.4   1.1    5.3e-77  257.0   1.1    1.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    5.4e-67  224.6   1.8    6.9e-67  224.2   0.8    1.7  2  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    4.4e-09   36.7   0.1    8.8e-09   35.7   0.1    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.3e-08   35.3   0.2    3.8e-08   33.8   0.1    1.8  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    1.7e-08   34.0   0.0      3e-08   33.2   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    8.3e-07   29.2   0.0    1.9e-06   28.1   0.0    1.6  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
      0.002   16.9   0.3     0.0099   14.6   0.0    2.1  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
     0.0021   17.8   0.1       0.19   11.4   0.1    2.3  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
     0.0027   16.2   0.0      0.012   14.0   0.0    1.8  2  FMO-like        Flavin-binding monooxygenase-like
     0.0044   17.4   0.1      0.011   16.2   0.1    1.6  1  NAD_binding_7   Putative NAD(P)-binding
     0.0094   16.7   0.2       0.21   12.4   0.1    2.4  2  GARS_N          Phosphoribosylglycinamide synthetase, N domai
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.043   13.9   0.0    1.6  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.035   14.1   0.3        2.8    7.9   0.2    2.7  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.045   13.6   0.0       0.12   12.2   0.0    1.8  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.047   12.9   0.0       0.07   12.4   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.077   12.6   0.0       0.13   11.9   0.0    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA
        0.1   13.0   0.2       0.24   11.7   0.2    1.6  1  Mur_ligase      Mur ligase family, catalytic domain
        0.1   12.9   0.2       0.29   11.5   0.2    1.8  1  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor
       0.14   12.5   0.2       0.29   11.4   0.2    1.6  1  TrkA_N          TrkA-N domain
       0.15   12.6   0.1       0.53   10.8   0.0    1.9  2  CoA_binding_2   CoA binding domain


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 !  257.0   1.1   5.9e-80   5.3e-77       1     165 []      14     178 ..      14     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 257.0 bits;  conditional E-value: 5.9e-80
                                       HHHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHH CS
                              IlvN   1 llkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevy 77 
                                       +lkgk+ia+iGyGsqGha+a+nlrdsgldvvv+ ++g+++++kA e+gfev++vaeavk+++v+m+l+PD++q +v+
  gi|488601101|ref|YP_007907572.1|  14 VLKGKRIAIIGYGSQGHAHAQNLRDSGLDVVVADKKGTRNWDKAVEDGFEVKEVAEAVKESEVIMVLVPDNIQPAVF 90 
                                       599************************************************************************** PP

                                       HHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHH CS
                              IlvN  78 eeeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelala 154
                                        e+i++nlkeg++l+fahGfnih+++i ppk vdv++vAPkgpGh+vr++++eg Gvpal+av+qd+sgka ++ala
  gi|488601101|ref|YP_007907572.1|  91 YESINDNLKEGDMLMFAHGFNIHYNQIIPPKFVDVTMVAPKGPGHIVRRMFTEGIGVPALVAVYQDYSGKALDKALA 167
                                       ***************************************************************************** PP

                                       HHHHTTHHHH- CS
                              IlvN 155 yakgiGatraG 165
                                       yakgiGat+aG
  gi|488601101|ref|YP_007907572.1| 168 YAKGIGATKAG 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 ?   -2.1   0.0       4.9   4.4e+03     105     114 ..      64      73 ..      48     105 .. 0.54
   2 !  224.2   0.8   7.7e-70   6.9e-67       1     144 []     184     327 ..     184     327 .. 1.00

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.9
                                       HHHHHHHHHT CS
                              IlvC 105 akevieenka 114
                                       +kev e+ k+
  gi|488601101|ref|YP_007907572.1|  64 VKEVAEAVKE 73 
                                       3333333222 PP

  == domain 2  score: 224.2 bits;  conditional E-value: 7.7e-70
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       FkeEtetDlfgEq+ LcGgv+e+++a F++lveaGy+pe+Ayfe+lhelklivdliyegGi++m++s+Sdta+yg++
  gi|488601101|ref|YP_007907572.1| 184 FKEETETDLFGEQVDLCGGVAEMIKASFDVLVEAGYQPEIAYFEVLHELKLIVDLIYEGGIYAMWYSVSDTAKYGGM 260
                                       9**************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                       t+g+r+ite+++eem++il+eiq+Gefa+e+i+en+a+rp ++kl + e++h+iekvgk+lr++mpw
  gi|488601101|ref|YP_007907572.1| 261 TRGKRIITEQTREEMRKILKEIQTGEFAREWILENQANRPVFNKLLEMEKNHPIEKVGKELRKMMPW 327
                                       *****************************************************************98 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 !   35.7   0.1   9.8e-12   8.8e-09       1      87 [.      19     105 ..      19     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 9.8e-12
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SS.HHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrt.kekveelvaegakaaesieelvasldvvitmvkagkavdeviegl 76 
                                       +i++iG G  G+  a+nl ++g +v+v + + + + +++v++g++ +++++e+v++ +v++++v+++ +   ++e++
  gi|488601101|ref|YP_007907572.1|  19 RIAIIGYGSQGHAHAQNLRDSGLDVVVADKKgTRNWDKAVEDGFE-VKEVAEAVKESEVIMVLVPDNIQPAVFYESI 94 
                                       59***************************7637899****99995.677899************************* PP

                                       CCC--TT-EEE CS
                     NAD_binding_2  77 lealkkgdili 87 
                                        ++lk+gd+l+
  gi|488601101|ref|YP_007907572.1|  95 NDNLKEGDMLM 105
                                       ********986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   4.2e-11   3.8e-08       1      86 [.      19      98 ..      19     104 .. 0.86
   2 ?   -2.5   0.0       9.1   8.1e+03      28      47 ..     266     283 ..     259     292 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.2e-11
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      +i+iiG+G++g+a a++l  +g    ++vva   +++  + + ++++ + + ++ +ea++e++v+ + v+ +  ++v  
  gi|488601101|ref|YP_007907572.1| 19 RIAIIGYGSQGHAHAQNLRDSG---LDVVVA---DKKGTRNWDKAVEDGFEVKEVAEAVKESEVIMVLVPDNIQPAVFY 91
                                      79********************...****99...77777888888888888888****************999999888 PP

                                      HCGHHHH CS
                     F420_oxidored 80 elakdal 86
                                      e  +d+l
  gi|488601101|ref|YP_007907572.1| 92 ESINDNL 98
                                      7755554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.1
                                       EEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored  28 ivvansrnpekaeelaeelg 47 
                                       i+  ++++ e+++++ +e++
  gi|488601101|ref|YP_007907572.1| 266 II--TEQTREEMRKILKEIQ 283
                                       44..5788888888877765 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 !   33.2   0.0   3.4e-11     3e-08      32     102 ..      13      84 ..       5      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.4e-11
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlplt 102
                                         l+gk+++iiG+G+ G+a a+ l+  g++v++ d++ +++  ++ e g+e+ ++ e+++es+++++ +p +
  gi|488601101|ref|YP_007907572.1|  13 DVLKGKRIAIIGYGSQGHAHAQNLRDSGLDVVVADKKGTRNWdKAVEDGFEVKEVAEAVKESEVIMVLVPDN 84 
                                       5699*********************************99776788899********************9965 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 !   28.1   0.0   2.1e-09   1.9e-06      20      84 ..      14      79 ..       9     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.1e-09
                                      --TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHH.HHHCTT-EE--HHHCTTT-SEEEE CS
                     AdoHcyase_NAD 20 llaGkvavvaGyGdvGkGcaaslkglGarvivtevdPical.qaameGfevvtleevvkkadivvt 84
                                      +l Gk + ++GyG  G   a+ l+  G  v+v++        +a+ +Gfev+++ e+vk++++++ 
  gi|488601101|ref|YP_007907572.1| 14 VLKGKRIAIIGYGSQGHAHAQNLRDSGLDVVVADKKGTRNWdKAVEDGFEVKEVAEAVKESEVIMV 79
                                      578******************************98877554278899**************99864 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 !   14.6   0.0   1.1e-05    0.0099     268     315 ..      13      59 ..       2     116 .. 0.77
   2 ?   -0.4   0.0      0.42   3.7e+02     286     348 ..     136     202 ..     123     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                       HHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHH CS
                    Oxidored_nitro 268 eylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlk 315
                                       ++l+gkr+ai+g++++ +a a+ l++ G +vv+a  + ++r++++ ++
  gi|488601101|ref|YP_007907572.1|  13 DVLKGKRIAIIGYGSQGHAHAQNLRDSGLDVVVADKK-GTRNWDKAVE 59 
                                       579****************************998433.3344443333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.42
                                       HHHHHHH.HHT-EEEEEEESSS-HHHHHHHHHHS.TT....SEEEES.CHHHHHHHHHHHT-SEEEE CS
                    Oxidored_nitro 286 alarllk.elGmevvaagtetahrddeerlkaeleeg...epeviddadleeleelikelkpdlllg 348
                                        + r+++  +G+   +a++++ + +  +++ a +++    +  vi++   ee+e  +  +++dl+ g
  gi|488601101|ref|YP_007907572.1| 136 IVRRMFTeGIGVPALVAVYQDYSGKALDKALAYAKGIgatKAGVIETTFKEETETDLFGEQVDLCGG 202
                                       5556666358888888999988888888888888887888778888888899999999999998644 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 !   11.4   0.1   0.00021      0.19      26      89 ..      11      77 ..       4     111 .. 0.83
   2 ?    4.0   0.0     0.038        34      96     145 ..     193     242 ..     152     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                      TTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEE....ETTEE-HHHHHHHHHCSSSS CS
                     ELFV_dehydrog 26 kldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviy....dpeGldieellelkeerksv 89
                                      +ld l+gkr+ai G+G  g++ a+ l + g  vv v D++G+       ++G++++e++e  +e + +
  gi|488601101|ref|YP_007907572.1| 11 NLDVLKGKRIAIIGYGSQGHAHAQNLRDSGLDVV-VADKKGTRNwdkaVEDGFEVKEVAEAVKESEVI 77
                                      67789*********************99998887.89****976555478999999999997777665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.038
                                       STSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-S CS
                     ELFV_dehydrog  96 sekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEg 145
                                         ++++   + +e+ +  +d+lv ++ q ei   ++ + +k  v+l+ Eg
  gi|488601101|ref|YP_007907572.1| 193 FGEQVDLCGGVAEMIKASFDVLVEAGYQPEIAYFEVLHELKLIVDLIYEG 242
                                       34466777777788999*******************99***99****998 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.4e-05     0.012     179     266 ..      13     101 ..       5     118 .. 0.87
   2 ?   -0.5   0.0      0.35   3.1e+02     406     499 ..     180     280 ..     164     293 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                          FMO-like 179 evfkgkrvlviGlGnsggdiavelsrtaeqvllstrsGswvlsrvsdsGypwdmllv.trfksllknilptalsnwl 254
                                       +v+kgkr+ +iG G  g   a +l  +  +v+++ ++G+   ++ +++G+ ++ +    + ++++   +p ++  ++
  gi|488601101|ref|YP_007907572.1|  13 DVLKGKRIAIIGYGSQGHAHAQNLRDSGLDVVVADKKGTRNWDKAVEDGFEVKEVAEaVKESEVIMVLVPDNIQPAV 89 
                                       789***********************************************987776515667788888999999999 PP

                          FMO-like 255 vekklnkrfnhe 266
                                         + +n+ ++  
  gi|488601101|ref|YP_007907572.1|  90 FYESINDNLKEG 101
                                       999999988765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                          FMO-like 406 eeitekkekkakrfgesk.sktiqtdyiayldelaaligakpnllsl.llkdpklalkvff.GpcspyqyrlvGpGk 479
                                        e t k+e ++++fge+       ++ i+   ++    g +p++ ++ +l++ kl +++++ G   ++ y +    k
  gi|488601101|ref|YP_007907572.1| 180 IETTFKEETETDLFGEQVdLCGGVAEMIKASFDVLVEAGYQPEIAYFeVLHELKLIVDLIYeGGIYAMWYSVSDTAK 256
                                       56666777777777754303334567788888888999999999987578999999997664888999999999999 PP

                          FMO-like 480 weGar..kailtqwdr..ilkplk 499
                                       + G    k i+t+  r  ++k lk
  gi|488601101|ref|YP_007907572.1| 257 YGGMTrgKRIITEQTReeMRKILK 280
                                       999751346888766522344444 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.2e-05     0.011       5      72 ..      15      84 ..      14     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                     NAD_binding_7  5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk..laeeelekdlegadlviaatddr 72
                                      lkgk++ ++G G+ +   +++l ++g +v+v +++ +++ ++ v+  ++ +e+ + +++ +++++ ++d+
  gi|488601101|ref|YP_007907572.1| 15 LKGKRIAIIGYGSQGHAHAQNLRDSGLDVVVADKKGTRNWDKAVEdgFEVKEVAEAVKESEVIMVLVPDN 84
                                      789********************************77777776665566667777788888888877776 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   0.00023      0.21       2      71 ..      19      98 ..      18     109 .. 0.70
   2 ?    2.0   0.0       0.4   3.6e+02      33      73 ..     171     209 ..     121     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                                      EEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG..........TTHHHHHHHHHHCTESEEEE-SH...HHHHTTH CS
                            GARS_N  2 kvLvvGsGGRehalawklaqspkvekvyvapgNagt..........edlealvefakeekidlvvvGpe...apLvaGv 67
                                      ++ ++G G++ ha a++l++s  ++ v+va +  gt           ++++++e +ke ++ +v+v  +   a   + +
  gi|488601101|ref|YP_007907572.1| 19 RIAIIGYGSQGHAHAQNLRDSG-LD-VVVADKK-GTrnwdkavedgFEVKEVAEAVKESEVIMVLVPDNiqpAVFYESI 94
                                      689***************9994.44.6666655.554788777655445689**9***999999886542223455666 PP

                                      HHHH CS
                            GARS_N 68 adal 71
                                       d+l
  gi|488601101|ref|YP_007907572.1| 95 NDNL 98
                                      6666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.4
                                       --CGGTTHHHHHHHHHHCTESEEEE-SHHHHHTTHHHHHHH CS
                            GARS_N  33 gNagtedlealvefakeekidlvvvGpeapLvaGvadalee 73 
                                       g ++t   + ++e+  +e+ +  + G +  L+ Gva+++++
  gi|488601101|ref|YP_007907572.1| 171 GIGAT--KAGVIETTFKEETETDLFGEQVDLCGGVAEMIKA 209
                                       33333..256888888999999999***********99944 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.8e-05     0.043       7      80 ..      12      78 ..       8     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                                      HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEE CS
                      Shikimate_DH  7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvi 80
                                      l+ lk+k++ +iG G  ++  a++L ++g++ vvva    +r ++ a e         +++e+ e+++e++v++
  gi|488601101|ref|YP_007907572.1| 12 LDVLKGKRIAIIGYGSQGHAHAQNLRDSGLD-VVVADKKGTRNWDKAVED------GFEVKEVAEAVKESEVIM 78
                                      67899*************************9.****99998888765554......235677777777777776 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0032       2.8       2      29 ..      20      47 ..      19     119 .. 0.61
   2 ?   -2.5   0.0       4.9   4.4e+03      97     124 ..     163     190 ..     146     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0032
                                      EEEE--SHHHHHHHHHHHTTT--EEEE- CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwv 29
                                      ia++G Gs G a A+ l + g +v++  
  gi|488601101|ref|YP_007907572.1| 20 IAIIGYGSQGHAHAQNLRDSGLDVVVAD 47
                                      8899999999999999999885554432 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.9
                                       -EEEE---SEET.TTEEHHHHHHHHH-S CS
                    NAD_Gly3P_dh_N  97 ailvsliKGieegtlkllsevieeelke 124
                                        +++  +KGi + +  ++++  +ee+++
  gi|488601101|ref|YP_007907572.1| 163 DKALAYAKGIGATKAGVIETTFKEETET 190
                                       4567788999777777777777777665 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.12       2      33 ..      20      51 ..      19      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      +a+iG G  G+  a+ +  +gl+Vv+ d +  
  gi|488601101|ref|YP_007907572.1| 20 IAIIGYGSQGHAHAQNLRDSGLDVVVADKKGT 51
                                      8**************************98543 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.8e-05      0.07       1      58 [.      18      88 ..      18     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.....HCHHHHHHHHHHHHH........H CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxx........x RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.....skallgvaedaeias........e 58
                                      k++++iG G  G+a a++l+ +g++v++ +++gt  +++ +      ++++++v+e + i+          
  gi|488601101|ref|YP_007907572.1| 18 KRIAIIGYGSQGHAHAQNLRDSGLDVVVADKKGTRNWDKAVEdgfevKEVAEAVKESEVIMVlvpdniqpA 88
                                      589**************************766665555444443333444444444443333555555550 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.13       1      47 [.      20      68 ..      20      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH..HHHHHHHHCEEEEETT CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr..rlealkknGlrltseg 47
                                      iai+G G++G   a +L   g dv++ +++     ++ +++G++++++ 
  gi|488601101|ref|YP_007907572.1| 20 IAIIGYGSQGHAHAQNLRDSGLDVVVADKKGtrNWDKAVEDGFEVKEVA 68
                                      89***************99*******99988733445888888888776 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00027      0.24      19      81 ..      20      72 ..      17      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                                      HHHTTSEEEEEESSHCHHHTT-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTEEEEEHHHHHH CS
                        Mur_ligase 19 lalkGykvdGsdfieslialGaaavvghdaanivvssiskdnpeleaakepgipvesraeaLa 81
                                      +a+ Gy  +G+ ++++l+++G  +vv+++++               +a e g +v+++aea+ 
  gi|488601101|ref|YP_007907572.1| 20 IAIIGYGSQGHAHAQNLRDSGLDVVVADKKG----------TRNWDKAVEDGFEVKEVAEAVK 72
                                      5788**************************9..........7778888888888888888765 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 ?   11.5   0.2   0.00032      0.29      40      89 ..      26      76 ..       9      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                                      SCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES.-SSBHHHH CS
                     Nitro_FeMo-Co 40 gggggklaqllaeegvdvvivgkiGpralakleaagievykg.aggtveea 89
                                      g++g ++aq l ++g dvv++ k G r + k  + g ev ++ ++ + +e+
  gi|488601101|ref|YP_007907572.1| 26 GSQGHAHAQNLRDSGLDVVVADKKGTRNWDKAVEDGFEVKEVaEAVKESEV 76
                                      678999**********************************96555444455 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00032      0.29       1      44 [.      20      64 ..      20      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHH.HHHHHHTTSEE CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeer.veelreeglev 44
                                      i+iiG+G  G + a++L+++g dvvv dk+  r  +++ e+g+ev
  gi|488601101|ref|YP_007907572.1| 20 IAIIGYGSQGHAHAQNLRDSGLDVVVADKKGTRnWDKAVEDGFEV 64
                                      79*****************6657*****98865466666666665 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00059      0.53       1      74 [.      18      92 ..      18     104 .. 0.83
   2 ?   -2.5   0.0       7.7   6.9e+03      66      96 ..     273     303 ..     271     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00059
                                      --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-.....SEETTEES----T....T--EEEE-S-HHHHGGGHHH CS
                     CoA_binding_2  1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpke.....eeilgekvyaslaedpepvdlvdvftppeatpeivke 74
                                      ++ia++G     g+ g+  +++l+++gl+vv+   k+     ++++   +++++ae++++ +++ v++p +++p++  e
  gi|488601101|ref|YP_007907572.1| 18 KRIAIIG----YGSQGHAHAQNLRDSGLDVVVADKKGtrnwdKAVEDGFEVKEVAEAVKESEVIMVLVPDNIQPAVFYE 92
                                      6899999....6778****************9999996555555555559999998789999********999998766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.7
                                       HHHGGGHHHHHHH--SEEEE-TT---HHHHH CS
                     CoA_binding_2  66 eatpeivkealalgakavwlqpgsedeeaae 96 
                                       e++ +i+ke+++ + ++ w+ ++  ++ + +
  gi|488601101|ref|YP_007907572.1| 273 EEMRKILKEIQTGEFAREWILENQANRPVFN 303
                                       6677889999888888888888877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 1861.99
//
Query:       gi|488601102|ref|YP_007907573.1|  [L=221]
Description: DNA-(apurinic or apyrimidinic site) lyase /endonuclease III [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   86.4   0.1    4.1e-24   85.1   0.0    1.6  2  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
      2e-10   40.0   0.4      1e-09   37.8   0.0    2.4  3  HHH            Helix-hairpin-helix motif
    6.7e-06   26.3   6.2      1e-05   25.7   6.2    1.3  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
    4.9e-05   23.8   0.1      0.076   13.6   0.0    2.5  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.015   14.5   0.1       0.02   14.1   0.1    1.1  1  DUF763         Protein of unknown function (DUF763)
       0.08   12.9   0.1       0.43   10.6   0.0    1.9  2  DUF2400        Protein of unknown function (DUF2400)
       0.11   12.8   0.0       0.33   11.3   0.0    1.8  1  HHH_8          Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.9   4.9e+03      36      56 ..      10      29 ..       3      32 .. 0.77
   2 !   85.1   0.0   1.6e-27   4.1e-24       3     107 ..      47     179 ..      45     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                                      SHHHHHHHHHTTSTTHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD 36 adeekLrelirelGfyrrKak 56
                                      +d + L e++++ Gf  rKa+
  gi|488601102|ref|YP_007907573.1| 10 IDWDRLLEAMESEGFK-RKAP 29
                                      6677888888999999.8986 PP

  == domain 2  score: 85.1 bits;  conditional E-value: 1.6e-27
                                       HHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                           HhH-GPD   3 ailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............. 66 
                                       +ils++t+de +++++e+lf+ +   tp+dla+++ ++++ li+++Gfyr+Kak++k++A+ lv             
  gi|488601102|ref|YP_007907573.1|  47 TILSARTRDEQTAKAVENLFKVVS--TPKDLAKLEISEIERLIKSTGFYRNKAKNLKAMAEVLVreynskvpddfde 121
                                       8*********************86..*************************************************** PP

                                       ..................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                       ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ..................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                         +++ ++i vD+hv+ri +rl+++++  +++ +e +l+++++
  gi|488601102|ref|YP_007907573.1| 122 llklpgvgrktanvvlasAFNRNTIGVDTHVHRISNRLGLVNT-SKPEDTEIELKKIVP 179
                                       ******************666689*****************99.5*********99886 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   4.5e+03       9      17 ..      71      79 ..      69      79 .. 0.86
   2 !   37.8   0.0   3.9e-13     1e-09       2      29 ..     111     138 ..     110     139 .. 0.94
   3 ?   -2.2   0.0       1.9   4.8e+03       7      16 ..     168     177 ..     166     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                                      SHHHHHTST CS
                               HHH  9 sreeLlalP 17
                                      ++++L++l+
  gi|488601102|ref|YP_007907573.1| 71 TPKDLAKLE 79
                                      889***996 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 3.9e-13
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIls 29 
                                       +++ +p++++eLl+lPGVG+ktA+++l+
  gi|488601102|ref|YP_007907573.1| 111 YNSKVPDDFDELLKLPGVGRKTANVVLA 138
                                       8999**********************97 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.9
                                       TSSHHHHHTS CS
                               HHH   7 pasreeLlal 16 
                                       ++++ eL+++
  gi|488601102|ref|YP_007907573.1| 168 EDTEIELKKI 177
                                       5899999994 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   6.2   4.1e-09     1e-05       1      17 []     198     214 ..     198     214 .. 0.99

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 4.1e-09
                     EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                       C++ kP Ce+CP++D+C
  gi|488601102|ref|YP_007907573.1| 198 CKPVKPLCEECPINDIC 214
                                       ***************** PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0024       6.1      13      52 ..      60     101 ..      57     105 .. 0.79
   2 !   13.6   0.0     3e-05     0.076       1      18 [.     119     136 ..     117     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                                       HHHHHHHTTT--SHHHHHHS...-HHHHHTSTTS-HHHHHHHH CS
                             HHH_5  13 ktAlallsaGiesvedlaaa...dveeLakipGiGkktAerii 52 
                                       k + +l +  ++++ dla++   ++e+L k +G+   +A++++
  gi|488601102|ref|YP_007907573.1|  60 KAVENLFKV-VSTPKDLAKLeisEIERLIKSTGFYRNKAKNLK 101
                                       677788899.99*******944457889999999888888875 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3e-05
                                       -HHHHTSTT--HHHHHHH CS
                             HHH_5   1 feeLlsvsGiGpktAlal 18 
                                       f+eLl+++G+G+ktA  +
  gi|488601102|ref|YP_007907573.1| 119 FDELLKLPGVGRKTANVV 136
                                       566666666666666544 PP

>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   7.8e-06      0.02     199     275 ..      55     133 ..      25     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-06
                            DUF763 199 skeseearkaildlvkekpekllkelkelkallkgekkl..klpakhevlekvl.ekayelqpedfeellllkgvGp 272
                                       ++++++a + + ++v+  ++  + e++e+++l+k++     k  ++ + + +vl ++ +++ p+df+ell l+gvG+
  gi|488601102|ref|YP_007907573.1|  55 DEQTAKAVENLFKVVSTPKDLAKLEISEIERLIKSTGFYrnK-AKNLKAMAEVLvREYNSKVPDDFDELLKLPGVGR 130
                                       445555556666677666666666777777666655444322.33334455555156666789************** PP

                            DUF763 273 ktl 275
                                       kt 
  gi|488601102|ref|YP_007907573.1| 131 KTA 133
                                       996 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.29   7.4e+02      94     116 ..      62      84 ..      13     118 .. 0.52
   2 ?   10.6   0.0   0.00017      0.43     173     193 ..     146     166 ..     142     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.29
                           DUF2400  94 Leeaflkaeeeeeeleealeafr 116
                                       +e++f+  ++ ++  + ++++++
  gi|488601102|ref|YP_007907573.1|  62 VENLFKVVSTPKDLAKLEISEIE 84 
                                       33333222222222222222222 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                           DUF2400 173 iPlDvHvarvarklgllkrkq 193
                                       i +D+Hv+r++++lgl+++++
  gi|488601102|ref|YP_007907573.1| 146 IGVDTHVHRISNRLGLVNTSK 166
                                       679*************98665 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.33      28      63 ..      93     136 ..      90     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                       HHHHHCCCCC-SS.-HHHH.TT......HCTTSTT--HHHHHHH CS
                             HHH_8  28 YrrAaraiealpe.eitsl.ee......eltklpgiGkkiaaki 63 
                                       Yr+ a++++a+ e  ++++  +      el klpg+G k+a+++
  gi|488601102|ref|YP_007907573.1|  93 YRNKAKNLKAMAEvLVREYnSKvpddfdELLKLPGVGRKTANVV 136
                                       666677777777744555542245556779***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1495.14
//
Query:       gi|488601103|ref|YP_007907574.1|  [L=399]
Description: Acetyl-CoA acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   62.8   0.0    7.3e-17   61.6   0.0    1.6  1  Thiolase_N       Thiolase, N-terminal domain
    1.4e-11   44.1   0.0    5.5e-11   42.2   0.0    2.0  2  Thiolase_C       Thiolase, C-terminal domain
    2.3e-08   33.9   1.4    9.1e-08   32.0   1.4    2.0  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
     0.0039   17.2   0.0      0.088   12.8   0.0    2.4  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   1.6e-20   7.3e-17       1     259 [.       6     232 ..       6     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.6e-20
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TT CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipee 75 
                                       v++ +  +t++g     + d + ++L aea  ++ ++ +++ ++++ ++ Gn + +  +g++ ++  +a ++g+ + 
  gi|488601103|ref|YP_007907574.1|   6 VAVLGVGMTKFGY----HPDKTLVDLFAEAFYEAFDESNIELKDIEALYYGNFVGEmTDGSAnLSGFIADEIGL-RG 77 
                                       6778888999998....99*********************************999978888779999*******.** PP

                                       SEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSS.SEEEEEHHHHHHTEETTT CS
                        Thiolase_N  76 vpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklg.dekakdllipdgladafn 151
                                       +pa + + +c+S+  a  +a  ++a g +d+vv+gG E++ na ta  t++ + +  g +e   +l+ p        
  gi|488601103|ref|YP_007907574.1|  78 IPARRYEAACASSSVAFREAYLAVAHGVYDCVVVGGSERLYNAGTAIGTRALATAVDGlHEMTAGLTFPG------- 147
                                       *********************************************9998887666655144555666666....... PP

                                       TSEHHHHHHHHHHHHT--HHHHHH....HHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HH CS
                        Thiolase_N 152 eehmGltaenlakkykisReeqde....fAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtae 224
                                           +l+a+ + kky+i+ ee+ e    + +k+h+ +a ++ka+ F ++          g+  ++ ++ i+s+v   
  gi|488601103|ref|YP_007907574.1| 148 --VFALAARLYSKKYEIPMEELHEkmalVSIKNHKYGAINPKAQ-FYNKF---------GD--LKVEDVINSKVICS 210
                                       ..789*************9886543333789*************.88856.........33..789*********** PP

                                       HHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 225 kLaklkpaFkkeGtvtAgnasqisDGaaavllmse 259
                                       +L                ++++++DG +av+++s+
  gi|488601103|ref|YP_007907574.1| 211 PLTLF-------------DCCPMTDGGSAVIIASA 232
                                       *****.............**************987 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.6   7.4e+03      41      60 ..     161     180 ..     152     187 .. 0.75
   2 !   42.2   0.0   1.2e-14   5.5e-11      26     100 ..     271     363 ..     258     379 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.6
                                       GESEEEE--SBHHHHHHHHH CS
                        Thiolase_C  41 didlfEinEAFaaqaLavak 60 
                                       +i + E++E  a + ++++k
  gi|488601103|ref|YP_007907574.1| 161 EIPMEELHEKMALVSIKNHK 180
                                       56677888888888877766 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 1.2e-14
                                       HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTT CS
                        Thiolase_C  26 yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGa 84 
                                        a++++ k+ag+t +d+d++Ei++ F+   + +++a+++ +                    vN  GG i  GHP+Ga
  gi|488601103|ref|YP_007907574.1| 271 IASEMAYKEAGITPKDVDFVEIHDCFTIAEIIATEAMGFFEygkgadavaegvtsidgdLPVNPDGGLIGKGHPVGA 347
                                       688999********************************9999***************9889**************** PP

                                       HHHHHHHHHHHHHHHC CS
                        Thiolase_C  85 sGaRivvtllselkke 100
                                       +G+ ++ +++++l+ e
  gi|488601103|ref|YP_007907574.1| 348 TGTSQIYSVVKQLRGE 363
                                       ***********99865 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 !   32.0   1.4     2e-11   9.1e-08     151     218 ..      62     130 ..       6     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2e-11
                                       TTHHHHHHHHHHT--S.SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT CS
                     ketoacyl-synt 151 anviagrisyalglrG.psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag 218
                                       ++ ++g i+ + glrG p+   ++AC+Ss va   a+ ++ +g  d++++GG+e l ++++ +g  a++
  gi|488601103|ref|YP_007907574.1|  62 SANLSGFIADEIGLRGiPARRYEAACASSSVAFREAYLAVAHGVYDCVVVGGSERLYNAGTAIGTRALA 130
                                       45689***********78899*************************************99999988776 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 !   12.8   0.0     2e-05     0.088      29      52 ..     272     295 ..     247     301 .. 0.86
   2 ?    1.3   0.0     0.072   3.2e+02      88     107 ..     342     361 ..     340     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHT--GGGEEEEE-SS- CS
                   Ketoacyl-synt_C  29 aiekalaeagvdpedvdyveahgt 52 
                                       a e a++eag++p+dvd ve h+ 
  gi|488601103|ref|YP_007907574.1| 272 ASEMAYKEAGITPKDVDFVEIHDC 295
                                       5789******************86 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.072
                                       -B-GGGHHHHHHHHHHHHHH CS
                   Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalk 107
                                       GH  +A G+ ++  vv++l+
  gi|488601103|ref|YP_007907574.1| 342 GHPVGATGTSQIYSVVKQLR 361
                                       9***************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2643.32
//
Query:       gi|488601104|ref|YP_007907575.1|  [L=137]
Description: putative nucleic-acid-binding protein containing a Zn-ribbon [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-17   63.3   0.4    2.3e-17   62.8   0.4    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    1.7e-12   47.0   0.9    2.4e-12   46.5   0.9    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.014   15.5   1.0      0.021   15.0   1.0    1.2  1  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like
      0.048   13.3   0.2       0.06   13.0   0.2    1.1  1  TackOD1        Thaumarchaeal output domain 1
      0.084   12.9   0.7       0.12   12.3   0.7    1.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.26   11.3   1.3        2.8    8.0   1.2    2.3  1  CpXC           CpXC protein
          1    9.5   6.4        6.2    7.0   6.4    2.1  1  Zn-ribbon_8    Zinc ribbon domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.4   8.8e-21   2.3e-17       2      62 ..      48     111 ..      47     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 8.8e-21
                                       EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES.....TT-B-EE CS
                     OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevr...iGmrVra 62 
                                       v+lsg+G++ +ft+++ ap g+++e+Py+v++VeL+eg++i++rl+ + +dev    iG +V++
  gi|488601104|ref|YP_007907575.1|  48 VQLSGKGVIRTFTTTYIAPAGYDKEVPYTVAMVELEEGPWIVGRLDFDKADEVGqglIGEEVEV 111
                                       89********************************************999999666669999996 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 !   46.5   0.9   9.3e-16   2.4e-12       1      37 []      10      46 ..      10      46 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 9.3e-16
                           DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgsddle 37
                                      +da+ eg+L+g +C+dCG++  PP avC  Cgs++le
  gi|488601104|ref|YP_007907575.1| 10 FDALLEGKLLGLKCKDCGAYTCPPKAVCDSCGSRNLE 46
                                      69*********************************98 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 ?   15.0   1.0   8.1e-06     0.021       8      40 ..      20      51 ..      15      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.1e-06
                      NOB1_Zn_bind  8 vlrChaCfkvtkdmtkkFCpkCGnktLkrvavs 40
                                       l+C  C   t    k  C++CG+++L++v++s
  gi|488601104|ref|YP_007907575.1| 20 GLKCKDCGAYT-CPPKAVCDSCGSRNLEKVQLS 51
                                      58999998865.568999************987 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.3e-05      0.06      75     102 ..      22      49 ..      12      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                           TackOD1  75 lCpsCksghlnvrevCpkCkSidieeqe 102
                                        C+ C  +    + vC +C+S ++e+ +
  gi|488601104|ref|YP_007907575.1|  22 KCKDCGAYTCPPKAVCDSCGSRNLEKVQ 49 
                                       6***********************9866 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   0.7   4.9e-05      0.12      71     101 ..      21      49 ..      11      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.9e-05
                                       EEETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
                              HypA  71 vrCreCgkefeleekalrCpkCgsadveivs 101
                                       ++C++Cg+ +     ++ C +Cgs+++e v+
  gi|488601104|ref|YP_007907575.1|  21 LKCKDCGAYTCPP--KAVCDSCGSRNLEKVQ 49 
                                       79*****777655..357*******998765 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.2    0.0011       2.8      26      47 ..       9      30 ..       4      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                              CpXC 26 lkeklldgslfeatCpkCgata 47
                                      + ++ll+g+l+  +C +Cga +
  gi|488601104|ref|YP_007907575.1|  9 YFDALLEGKLLGLKCKDCGAYT 30
                                      56899**************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 ?    7.0   6.4    0.0024       6.2       7      39 ..      22      48 ..      20      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.evrrv 39
                                      +C++Cg  ++       +p+ +C +Cgs ++++v
  gi|488601104|ref|YP_007907575.1| 22 KCKDCG-AYT------CPPKAVCDSCGSrNLEKV 48
                                      799999.444......456667*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 897.81
//
Query:       gi|488601105|ref|YP_007907576.1|  [L=383]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-52  175.3   0.2    1.2e-51  174.9   0.2    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      1e-30  106.7   0.1    1.6e-30  106.0   0.1    1.4  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
      1e-24   87.3   0.0    1.5e-24   86.8   0.0    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    6.8e-24   83.9   0.1    1.1e-23   83.3   0.1    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.9   0.2   2.7e-55   1.2e-51       1     149 [.     229     377 ..     229     378 .. 0.99

  Alignments for each domain:
  == domain 1  score: 174.9 bits;  conditional E-value: 2.7e-55
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       ++Gf++ m+ +n +R+ ++a  lg+a  a+e+al+ya++rkafgkpli+hq++++kla+m + +e+a+ll+++aa++
  gi|488601105|ref|YP_007907576.1| 229 NRGFYQLMRFFNESRIKIGALHLGIAIGAYERALQYAKERKAFGKPLIEHQAIQFKLADMFTAIESAKLLIFKAAYL 305
                                       79*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +d+g+p++a +s+aKl+ase+a +v+ +a+q++Gg+G+++ey ver+yrdarv +i+eGtse qr +i+r l
  gi|488601105|ref|YP_007907576.1| 306 VDKGEPNPALSSAAKLYASETAIKVTYEAVQVFGGYGFSKEYDVERYYRDARVGTIYEGTSEAQRIVIGRTL 377
                                       ********************************************************************9976 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.1   3.7e-34   1.6e-30       1     113 []       6     117 ..       6     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 3.7e-34
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       +e+q++l+d+vrefae+e+ p+ +e+de++e+p +++kk+a+lG++g ++peey Gag++ +++ai+  e+ rad++
  gi|488601105|ref|YP_007907576.1|   6 NEDQKMLQDAVREFAEKEIMPYGREYDEKAEYPMDIYKKAAKLGFIGASIPEEYNGAGMGCVDEAIISMEFCRADSS 82 
                                       699************************************************************************** PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkrryLpklasge 113
                                       +++++ + + l++p++  fG+eeqk+ ++ k+ +ge
  gi|488601105|ref|YP_007907576.1|  83 IGSAIDLAT-LGVPMLRYFGSEEQKENFMAKVPKGE 117
                                       *****9976.7779****************998887 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.0   3.3e-28   1.5e-24       3     133 ..     246     366 ..     244     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 3.3e-28
                                       HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHH CS
                     Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtved 79 
                                       i+a  lG+A +a++ ++++a+er+   +g++l +++a+q++la++ +++++A++l+ +aa+     +++g+++    
  gi|488601105|ref|YP_007907576.1| 246 IGALHLGIAIGAYERALQYAKERKA--FGKPLIEHQAIQFKLADMFTAIESAKLLIFKAAYL----VDKGEPN---- 312
                                       78999********************..***********************************....******8.... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  80 raearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                        a +++a+++a+e+ai+++ ++++++Gg++  ke+ ++R++RDa++++++++++
  gi|488601105|ref|YP_007907576.1| 313 PALSSAAKLYASETAIKVTYEAVQVFGGYGFSKEYDVERYYRDARVGTIYEGTS 366
                                       8999**********************************************9987 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.1   2.4e-27   1.1e-23       1      97 []     121     217 ..     121     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 2.4e-27
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS-------EEEEEEE..GGGEE CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpdrarglslflvprdapgvs 74 
                                       a+a+TEp+ G+dva+++t  a+ dg+e+vlnG+K++itn++   +++vla+   +++p  ++g+s flv++d++g +
  gi|488601105|ref|YP_007907576.1| 121 AIAITEPDCGTDVAAMRT-RAQLDGDEWVLNGTKQFITNGKVGIYTVVLAKtdvNASP-PHKGISAFLVETDREGYK 195
                                       78****************.66667777************************7555555.5***************** PP

                                       E-----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  75 vrrieeklGlrglptgelvfedv 97 
                                        ++i +k+G++ ++t+e+v+++v
  gi|488601105|ref|YP_007907576.1| 196 ANPI-HKMGMNCHDTSEVVLNNV 217
                                       ****.69*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2230.89
//
Query:       gi|488601106|ref|YP_007907577.1|  [L=285]
Description: 3-hydroxyacyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  226.6   2.2    2.6e-67  226.2   2.2    1.1  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    1.1e-33  115.7   0.0    1.2e-32  112.4   0.0    2.2  2  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    0.00033   20.8   3.5    0.00084   19.5   3.5    1.6  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.016   15.2   6.3       0.19   11.8   0.5    2.3  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.025   14.9   0.2        4.6    7.6   0.0    2.4  2  DsrD            Dissimilatory sulfite reductase D (DsrD)
      0.028   14.5   2.1      0.047   13.8   2.1    1.5  1  DUF2120         Uncharacterized protein conserved in archaea 
      0.089   13.4   2.0       0.34   11.5   2.0    2.1  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.095   12.7   0.6       0.21   11.5   0.6    1.8  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.097   12.0   1.7       0.13   11.6   0.2    1.8  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.11   12.0   1.5       0.21   11.2   1.5    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.22   11.6   2.6       0.39   10.8   2.6    1.4  1  Cauli_DNA-bind  Caulimovirus DNA-binding protein
       0.28   11.4   4.3        1.6    9.0   1.9    2.9  2  SRP54_N         SRP54-type protein, helical bundle domain


Domain annotation for each model (and alignments):
>> 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 !  226.2   2.2   1.8e-70   2.6e-67       2     179 ..       9     187 ..       8     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 226.2 bits;  conditional E-value: 1.8e-70
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavd 78 
                                       v+v+GaGtmG+gi +v+a ag+eV + di++++l++++++i+ksl+k+v+kgk++e+e++a+l+ri++t d++++ +
  gi|488601106|ref|YP_007907577.1|   9 VGVLGAGTMGNGIVQVCAMAGYEVIMRDIEQSFLDRGMNAIKKSLSKFVSKGKMTEDEMNAVLDRIKPTLDMKDLES 85 
                                       9**************************************************************************** PP

                                       -SEEEE-S-SSHHHHHHHHHHHHCCS.-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT CS
                           3HCDH_N  79 adlviEavvEnlelKrkvfaelekia.kpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgek 154
                                       adlviEavvE++++K++vf+el++i+ ++dai+asnTS+lsi+e+++++++pe+++g+HF+nP+plmk vE+vrg  
  gi|488601106|ref|YP_007907577.1|  86 ADLVIEAVVEKMDVKKAVFKELNEIVkNQDAIFASNTSTLSITEMSAVTRKPENFVGIHFMNPVPLMKGVEIVRGLL 162
                                       *************************94589*********************************************** PP

                                       --HHHHHHHHHHHHHTT-EEEEECS CS
                           3HCDH_N 155 Tseetvatvvelakkigktpvvvkd 179
                                       Ts+et++ +ve++kkigk+pvv+kd
  gi|488601106|ref|YP_007907577.1| 163 TSDETLNFAVEFVKKIGKEPVVCKD 187
                                       ***********************99 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 ?    0.6   0.0      0.59   8.8e+02      55      92 ..      30      68 ..      12      73 .. 0.75
   2 !  112.4   0.0     8e-36   1.2e-32       1      97 []     190     285 .]     190     285 .] 0.99

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.59
                                      HHHHHHHHHHHTTTH.GGHH-HHHHHHHHTT--BGGGTB CS
                             3HCDH 55 akkilevlaeelger.ayapsplleklveagrlgrktgk 92
                                       + i++ +++ + +r ++a ++ l+k+v++g++ + +  
  gi|488601106|ref|YP_007907577.1| 30 YEVIMRDIEQSFLDRgMNAIKKSLSKFVSKGKMTEDEMN 68
                                      455677888888888888888999999999999877665 PP

  == domain 2  score: 112.4 bits;  conditional E-value: 8e-36
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+ nR+l+p++ne + ++ eg+a+ e+iD+ mrl +++pmGp+el+dl+gld++++++e+l++elg++ y+p+pll
  gi|488601106|ref|YP_007907577.1| 190 GFISNRILMPWINEGIYVLYEGIATKEEIDKGMRLFTNVPMGPLELADLIGLDICLAAIETLHRELGDK-YRPCPLL 265
                                       9******************************************************************99.999**** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       +++v+ag lgrktg+gfy+y
  gi|488601106|ref|YP_007907577.1| 266 KQMVSAGLLGRKTGRGFYEY 285
                                       ******************98 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 !   19.5   3.5   5.6e-07   0.00084       2      98 ..       9     129 ..       8     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.6e-07
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelva 54 
                                       +g++G G+MG+ +++ ++ agy+v++ + +++ +++ +++                         +k++ ++++l +
  gi|488601106|ref|YP_007907577.1|   9 VGVLGAGTMGNGIVQVCAMAGYEVIMRDIEQSFLDRGMNAIkkslskfvskgkmtedemnavldrIKPTLDMKDL-E 84 
                                       79****************************976666666544566666666677777776666666666665553.5 PP

                                       HCSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE-S---HHHHH CS
                     NAD_binding_2  55 sldvvitmvkagkavdevieg.llealkkgdilidgstsspedtr 98 
                                       s+d+vi  v ++ +v++ +++ l e +k++d +  + ts  + t+
  gi|488601106|ref|YP_007907577.1|  85 SADLVIEAVVEKMDVKKAVFKeLNEIVKNQDAIFASNTSTLSITE 129
                                       55*******999999998888688888888877766655554443 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6    0.0078        12      13      39 ..       7      33 ..       2      41 .. 0.80
   2 ?   11.8   0.5   0.00013      0.19      51      99 ..      92     137 ..      81     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0078
                                      -EEEEES-SHHHHHHHHHHHCCT-CEE CS
                      Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkv 39
                                      k v ++GaG m++ +++  + +g++ +
  gi|488601106|ref|YP_007907577.1|  7 KVVGVLGAGTMGNGIVQVCAMAGYEVI 33
                                      5578*************9999888833 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                                       HHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCH CS
                      Shikimate_DH  51 elaeelkgeeiealkleelkellaeadvvisataseepilekeeveeal 99 
                                       +++e++   +++   ++el+e++++ d ++++  s+  i e ++v++  
  gi|488601106|ref|YP_007907577.1|  92 AVVEKM---DVKKAVFKELNEIVKNQDAIFASNTSTLSITEMSAVTRKP 137
                                       444455...566899*************************999998766 PP

>> DsrD  Dissimilatory sulfite reductase D (DsrD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0031       4.6      20      48 ..      34      62 ..      21      63 .. 0.92
   2 ?    4.9   0.0     0.021        31      16      56 ..      76     124 ..      67     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
                                      HHHHHHH-TTS-HHHHHHHHHHHHHTTSE CS
                              DsrD 20 fkDlekalPdakpreiKkvvneLVnegkL 48
                                      ++D+e+ + d  +  iKk +++ V+ gk+
  gi|488601106|ref|YP_007907577.1| 34 MRDIEQSFLDRGMNAIKKSLSKFVSKGKM 62
                                      689****99******************98 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                                       S-EEHHHHHHH....-TTS-HHHHHHHH....HHHHHTTSEEEEEETTE CS
                              DsrD  16 skfYfkDleka....lPdakpreiKkvv....neLVnegkLeywSsGST 56 
                                       + + +kDle+a       + ++++Kk+v    ne+V+++  ++ S  ST
  gi|488601106|ref|YP_007907577.1|  76 PTLDMKDLESAdlviEAVVEKMDVKKAVfkelNEIVKNQDAIFASNTST 124
                                       55566777776665422356778888754444999***99999999888 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.1   3.1e-05     0.047      31      88 ..      57     117 ..      50     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                           DUF2120  31 vsrkkeeleeleskleellekldaeevdleseeakklieklde...sireveeieeevdaf 88 
                                       vs++k++ +e++ +l+++   ld ++++ ++  +++++ek+d     ++e +ei +++da+
  gi|488601106|ref|YP_007907577.1|  57 VSKGKMTEDEMNAVLDRIKPTLDMKDLESADLVIEAVVEKMDVkkaVFKELNEIVKNQDAI 117
                                       899***************************************7566566667777666665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.0   0.00023      0.34       2      34 ..       9      35 ..       8     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEES CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansr 34
                                      +g++GaG mg ++++ ++ ag   +e++    r
  gi|488601106|ref|YP_007907577.1|  9 VGVLGAGTMGNGIVQVCAMAG---YEVI-M--R 35
                                      89*******************...9999.3..4 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 ?   11.5   0.6   0.00014      0.21       2      95 ..       9     113 ..       8     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H...........HHHHHHHHHSSBTTTBTT...----TTEEEES-HH CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree...........elieeineehenvkyLpg...iklpenlvattdla 64 
                                       ++vlGaG  G  + +v+a +g ev +   e+           + + ++      +  + +    ++ + ++ t d++
  gi|488601106|ref|YP_007907577.1|   9 VGVLGAGTMGNGIVQVCAMAGYEVIMRDIEQsfldrgmnaikKSLSKFV----SKGKMTEdemNAVLDRIKPTLDMK 81 
                                       89************************99999777655543321111111....111121101122334566666666 PP

                                       HHHTT--EEEE---HHH..HHHHHHHHCCC--T CS
                    NAD_Gly3P_dh_N  65 ealkgadiivlvvPsqa..lrevlkklkgllkk 95 
                                       + l+ ad+++ +v  ++   + v+k+l++++k+
  gi|488601106|ref|YP_007907577.1|  82 D-LESADLVIEAVVEKMdvKKAVFKELNEIVKN 113
                                       5.5667888777765532145677777777644 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   8.6e-05      0.13      37      70 ..       7      40 ..       4      62 .. 0.84
   2 ?   -1.3   0.1       0.8   1.2e+03      75      97 ..      97     119 ..      82     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-05
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                      k vG++G+G +G+ + ++++  g +vi+ d  ++
  gi|488601106|ref|YP_007907577.1|  7 KVVGVLGAGTMGNGIVQVCAMAGYEVIMRDIEQS 40
                                      78**************************998865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.8
                                       HHHHTCEECSHHHHHHH-SEEEE CS
                      2-Hacid_dh_C  75 eeelgvelvsleellaesDivsl 97 
                                       ++ +++ + +l+e++++ D ++ 
  gi|488601106|ref|YP_007907577.1|  97 MDVKKAVFKELNEIVKNQDAIFA 119
                                       45556678899999999999875 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.5   0.00014      0.21       3      85 ..       9      94 ..       7     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                      EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHH....HHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDideekvd....klnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77
                                      + v+G+G +G     v a +g evi+ Di+++  d    +++++ ++++ +g ++  + ++  +r++ t+d++  +e+a
  gi|488601106|ref|YP_007907577.1|  9 VGVLGAGTMGNGIVQVCAMAGYEVIMRDIEQSFLDrgmnAIKKSLSKFVSKGKMTEDEMNAVLDRIKPTLDMKD-LESA 86
                                      78****************************98655222278999999999998766666666699999999998.9999 PP

                                      SEEEE--- CS
                    UDPG_MGDP_dh_N 78 dvifiaVg 85
                                      d+++ aV 
  gi|488601106|ref|YP_007907577.1| 87 DLVIEAVV 94
                                      99998884 PP

>> Cauli_DNA-bind  Caulimovirus DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.6   0.00026      0.39       1      73 [.      46     115 ..      46     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHHHHHT-T.THHHHHHHHTXXXXX CS
                    Cauli_DNA-bind   1 laaiaseieevlsdqkkieaeikaileklgstkpekesleevaakiikdltkkidece.cnkeiveildkkqdk 73 
                                       ++ai++ +++ +s+ k +e e++a+l+++  t +  ++le+ a  +i+ + +k+d  +   ke+ ei++++  +
  gi|488601106|ref|YP_007907577.1|  46 MNAIKKSLSKFVSKGKMTEDEMNAVLDRIKPTLD-MKDLES-ADLVIEAVVEKMDVKKaVFKELNEIVKNQ--D 115
                                       799*******************************.678987.56799999999996551679999999873..3 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 ?    9.0   1.9    0.0011       1.6       5      40 ..      49      84 ..      46     114 .. 0.73
   2 ?    0.8   0.0      0.38   5.6e+02      29      53 ..     156     180 ..     155     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                                      HHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT-- CS
                           SRP54_N  5 lnsalkklsgkskideedleealkeleeaLleaDVg 40
                                      +++ l+k+ +k+k +e+ ++++l+ ++ +L ++D+ 
  gi|488601106|ref|YP_007907577.1| 49 IKKSLSKFVSKGKMTEDEMNAVLDRIKPTLDMKDLE 84
                                      78889999999*******************999974 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.38
                                       HHHHHHHHTT--HHHHHHHHHHHHH CS
                           SRP54_N  29 eleeaLleaDVgvkvvkklienvkk 53 
                                       e+ + Ll++D  ++ + ++++++ k
  gi|488601106|ref|YP_007907577.1| 156 EIVRGLLTSDETLNFAVEFVKKIGK 180
                                       578889****9999*****999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1977.48
//
Query:       gi|488601107|ref|YP_007907578.1|  [L=117]
Description: hypothetical protein Asulf_01609 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 732.34
//
Query:       gi|488601108|ref|YP_007907579.1|  [L=334]
Description: hypothetical protein Asulf_01610 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-49  167.0   0.1    6.9e-49  166.5   0.1    1.2  1  RmuC             RmuC family
      0.002   18.3   1.7       0.53   10.6   0.0    2.7  2  DUF948           Bacterial protein of unknown function (DUF94
      0.003   17.6   0.6      0.003   17.6   0.6    2.4  2  Laminin_II       Laminin Domain II
      0.003   17.6   1.7      0.003   17.6   1.7    2.0  2  ADIP             Afadin- and alpha -actinin-Binding
     0.0036   16.8   1.6     0.0087   15.5   0.1    2.0  2  FliD_C           Flagellar hook-associated protein 2 C-termin
     0.0045   16.8   0.5        2.1    8.3   0.1    3.0  3  HxlR             HxlR-like helix-turn-helix
     0.0064   16.1   1.3      0.014   15.0   0.3    2.0  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.008   16.2   1.7      0.008   16.2   1.7    2.0  2  DHR10            Designed helical repeat protein 10 domain
  ------ inclusion threshold ------
       0.01   15.8   0.8       0.01   15.8   0.8    2.0  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.011   14.6   0.6      0.023   13.6   0.6    1.4  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.012   15.9   0.3      0.088   13.2   0.1    2.4  2  EF-hand_14       EF-hand domain
      0.019   15.1   5.5      0.075   13.2   2.5    2.9  2  XhlA             Haemolysin XhlA
      0.029   13.7   0.1      0.065   12.5   0.1    1.5  1  DUF3450          Protein of unknown function (DUF3450)
      0.032   14.5   0.6       0.38   11.0   0.2    2.4  2  DUF2316          Uncharacterized protein conserved in bacteri
      0.039   13.8   0.7      0.096   12.5   0.7    1.6  1  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
      0.041   13.9   4.2       0.05   13.6   0.4    2.6  3  P4Ha_N           Prolyl 4-Hydroxylase alpha-subunit, N-termin
      0.044   13.9   4.5       0.17   12.0   0.4    2.5  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.047   14.0   5.1       0.12   12.7   0.1    3.4  4  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.052   14.0   0.4        0.3   11.5   0.1    2.3  2  MitMem_reg       Maintenance of mitochondrial structure and f
      0.052   12.9   4.1      0.077   12.4   0.9    2.2  2  Tropomyosin      Tropomyosin
      0.072   12.5   0.5       0.18   11.2   0.5    1.6  1  HBM              Helical bimodular sensor domain
      0.076   13.0   2.5        0.4   10.7   0.7    2.7  2  Prefoldin_2      Prefoldin subunit
       0.11   12.9   0.4       0.11   12.9   0.4    2.8  3  Syntaxin_2       Syntaxin-like protein
       0.19   12.2   1.3        2.8    8.4   0.2    2.6  2  YgaB             YgaB-like protein
       0.24   10.3   3.1        0.1   11.6   0.4    1.7  2  IFT57            Intra-flagellar transport protein 57
       0.25   11.0   5.4      0.069   12.8   1.2    2.1  2  YkyA             Putative cell-wall binding lipoprotein
       0.32   11.5   3.0       0.79   10.2   0.1    2.7  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.33   10.6   7.3        2.3    7.9   0.1    3.0  3  DUF713           Protein of unknown function (DUF713)
       0.34   11.2   4.3        7.7    6.8   1.3    2.5  2  DUF5082          Domain of unknown function (DUF5082)
        0.4   10.7   3.4        2.5    8.1   0.1    2.5  2  DUF1664          Protein of unknown function (DUF1664)
       0.49    9.5   4.4       0.43    9.7   1.3    2.1  2  DLP_helical      Dynamin-like helical domain
        0.6   10.7   5.0        1.2    9.8   1.2    2.8  3  DUF5344          Family of unknown function (DUF5344)
       0.93    9.1   3.7       0.73    9.4   0.4    2.3  2  DUF4795          Domain of unknown function (DUF4795)
          1    9.8   4.3        2.1    8.8   2.2    2.5  2  Snapin_Pallidin  Snapin/Pallidin
        1.1    9.2   9.8          3    7.8   1.3    3.1  3  DUF4446          Protein of unknown function (DUF4446)
        1.1    9.5   4.0         11    6.4   0.5    3.4  3  KxDL             Uncharacterized conserved protein
        2.2    6.3  13.0       0.64    8.1   2.3    2.5  3  EzrA             Septation ring formation regulator, EzrA
          3    7.9   8.4         31    4.6   0.3    3.3  3  BLOC1S3          Biogenesis of lysosome-related organelles co
        5.8    7.1  10.8          1    9.5   1.2    3.3  4  Fib_alpha        Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.5   0.1   1.5e-51   6.9e-49      35     278 ..      74     327 ..      28     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 1.5e-51
                              RmuC  35 l..............keqlkelqelneqlgdeaenLtkaLknsktrGnwGEvqLerilessgleegeeyetqvslkd 97 
                                       +              +e + +++e +++l++ +++L++++  +  r ++GE+qLe il+++ ++++   + q+s+ d
  gi|488601108|ref|YP_007907579.1|  74 VikgafatslkelgiQEDIARIREASSDLKSVTTDLKNIFDVKLRRAKFGEFQLEMILKELFPSHR--LRFQYSIPD 148
                                       2444445555555559**************************************************..666999878 PP

                              RmuC  98 eegelrpDvvvklpggkklviDsKvpleaYerlveaeddeereealkahaksvkkhikeLseKdYeele.sldyvlm 173
                                       + g+  pD+ + + +gk+l+iDsK+ple+++r++eae+ +e++++ k+++k+v +hi +++eK Y   + +  +++m
  gi|488601108|ref|YP_007907579.1| 149 A-GT--PDACIMVEKGKWLCIDSKFPLENFRRYLEAEN-AEKDRYWKEFIKDVSRHIVSIREK-YVGKDaTESFAFM 220
                                       7.76..******************************99.79**********************.999976999**** PP

                              RmuC 174 FiPiEsayaealeadpeLleealrkkVvlasPttLlalLrtvamlwrqeaqeknaeeiaellgelydkfekfgedle 250
                                       F+P++++y  + +  +++l ea ++ V+l+sP+t+ a+L +++  +r e+++++ae+i+e++  l  k++ ++ +l+
  gi|488601108|ref|YP_007907579.1| 221 FVPSDAIYYHLATDAQGVLVEASKNGVILTSPSTMPAYLSLISAKIRAEEISERAEKIQEKIDGLSLKLRDLERNLD 297
                                       ***************************************************************************** PP

                              RmuC 251 klgkklekaqksydkavkkle..gnilrka 278
                                       ++ k++++a +s++k+ ++ +  +n ++++
  gi|488601108|ref|YP_007907579.1| 298 TTTKHINNAYRSMQKLNNSYQdlRNYFERI 327
                                       ***************766665555555544 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 ?    5.8   0.7     0.034        16       8      63 ..       7      63 ..       4     112 .. 0.67
   2 !   10.6   0.0    0.0012      0.53      23      80 ..     263     320 ..     256     331 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.034
                            DUF948  8 iAFvvLviflivvllklkktldeaaatieelekqvdpilk.evedllakvnelledv 63
                                      iA+++++++l +++ +  k+ ++++++ eel + + +i++ +++++l+++  +le+v
  gi|488601108|ref|YP_007907579.1|  7 IAVLFIIVILLYTIYRNLKLERSMNNRFEELINSIPQIVEsNLTKTLTQSSSILENV 63
                                      555555566666655555555555555555555554444324555555555544444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0012
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                       ++k  ++e++++ e++++++d+++ +++dl ++  ++++ +n+   ++++l ++ +dl
  gi|488601108|ref|YP_007907579.1| 263 SAKIRAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDL 320
                                       5555667777777777777777777777777777777777777444444444433333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2       1.7   7.9e+02      54      69 ..      95     110 ..      45     135 .. 0.65
   2 !   17.6   0.6   6.6e-06     0.003      20      78 ..     269     327 ..     261     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.7
                                       XXXXXXXXXXX--TTT CS
                        Laminin_II  54 irdArrsvkkLeklap 69 
                                       ir+A++  k ++  + 
  gi|488601108|ref|YP_007907579.1|  95 IREASSDLKSVTTDLK 110
                                       2222222222222222 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.6e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II  20 aplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       +++s++ e+++ek+ ++  +++  + +++  +k i+ A rs++kL++  ++L + ++++
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYFERI 327
                                       68888999999999999999999999999999999999999999999999888777776 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3       2.4   1.1e+03      40      72 ..      12      44 ..       6     103 .. 0.75
   2 !   17.6   1.7   6.6e-06     0.003      74     132 ..     266     324 ..     260     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.4
                              ADIP 40 viysLlqardrdleqreslnetirkleaeierl 72
                                      +i+ Ll    r+l+ + s+n + ++l ++i + 
  gi|488601108|ref|YP_007907579.1| 12 IIVILLYTIYRNLKLERSMNNRFEELINSIPQI 44
                                      677788888888888888888888777776653 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.6e-06
                              ADIP  74 skierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqy 132
                                        + e  +++ e+ + +++ +  k+r+le++l t++++++n  +++q+l+n  q++++ +
  gi|488601108|ref|YP_007907579.1| 266 IRAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYF 324
                                       56778899**********************************************99866 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 ?    0.5   0.2      0.71   3.3e+02     139     179 ..      46      85 ..      29     128 .. 0.68
   2 !   15.5   0.1   1.9e-05    0.0087     170     239 ..     244     318 ..     190     319 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.71
                                       HHHHHHHHHHHHHHHHHHHTTTSS.......SXSHHHHHHH CS
                            FliD_C 139 eekLkkalkenpssveelFsgstsqektvtsdsglatrlen 179
                                       e+ L+k l+++ s +e++Fs ++  +++v  +  +at+l++
  gi|488601108|ref|YP_007907579.1|  46 ESNLTKTLTQSSSILENVFSSAMIRNAEV-IKGAFATSLKE 85 
                                       67777888888888888888754444443.45556665444 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.9e-05
                                       SXSHHHHHHHHHHHHH.....STT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHH CS
                            FliD_C 170 dsglatrlenllksyv.....kssngtlqtasknltkqikdldkkiedldkrletleerlkkqfaalekavskln 239
                                       ++g++ +  + +  y+     k + + + ++ ++++++i+ l+ k  dl+++l+t+++ +++ + +++k+ ++++
  gi|488601108|ref|YP_007907579.1| 244 KNGVILTSPSTMPAYLslisaKIRAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQ 318
                                       555555545555555544445555568889*****************************************9998 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0045       2.1      18      42 ..      31      55 ..      20      70 .. 0.87
   2 ?   -1.2   0.0         4   1.9e+03      48      82 ..     129     163 ..     116     165 .. 0.74
   3 ?    5.0   0.1     0.046        21      13      46 ..     260     295 ..     255     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0045
                                      -EEHHHHHHHSTTS-HHHHHHHHHH CS
                              HxlR 18 kkRfselkralpkisqkmLaqrLre 42
                                      ++Rf+el + +p+i ++ L+++L +
  gi|488601108|ref|YP_007907579.1| 31 NNRFEELINSIPQIVESNLTKTLTQ 55
                                      68******************99965 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4
                                       SEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHH CS
                              HxlR  48 lierevypevPpkveYsltekGrslepvlqelkkw 82 
                                       +i +e  p+   + +Ys+ ++G+  + ++ e  kw
  gi|488601108|ref|YP_007907579.1| 129 MILKELFPSHRLRFQYSIPDAGTPDACIMVEKGKW 163
                                       55567788888899999999998666666655555 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.046
                                       HHTTS-EEHHHHHHHSTTS-HHH..HHHHHHHHHHT CS
                              HxlR  13 ellkgkkRfselkralpkisqkm..LaqrLreLeqd 46 
                                       +l++ k R +e++++  ki +k+  L+ +Lr Le++
  gi|488601108|ref|YP_007907579.1| 260 SLISAKIRAEEISERAEKIQEKIdgLSLKLRDLERN 295
                                       5788899***************9889*******986 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.6   2.1e+03     118     132 ..      23      37 ..      19      44 .. 0.74
   2 !   15.0   0.3     3e-05     0.014      84     137 ..     269     322 ..     234     327 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.6
                     PI3K_P85_iSH2 118 ereleReinalkpel 132
                                       +++leR++n+   el
  gi|488601108|ref|YP_007907579.1|  23 NLKLERSMNNRFEEL 37 
                                       678888888766665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3e-05
                     PI3K_P85_iSH2  84 eklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqk 137
                                       e+++e  e+++++++ l  + ++Le +l +++++  +  R++++l+   + L++
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRN 322
                                       78999*********************************************9986 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.6   1.7e+03      45      64 ..      88     107 ..      81     112 .. 0.75
   2 !   16.2   1.7   1.7e-05     0.008      51     105 ..     267     321 ..     262     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.6
                             DHR10  45 ieaelakleeakkklkelrd 64 
                                       i++++a+ +ea+++lk+   
  gi|488601108|ref|YP_007907579.1|  88 IQEDIARIREASSDLKSVTT 107
                                       77888888888888887655 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.7e-05
                             DHR10  51 kleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekr 105
                                       + ee ++++++ +++++ ++ +lr+ler+ +  ++ ++na + +++l ++ ++ r
  gi|488601108|ref|YP_007907579.1| 267 RAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLR 321
                                       5689999****************************************99877655 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 ?   -0.9   0.1       3.4   1.6e+03      59      59 ..      90      90 ..      29     116 .. 0.57
   2 ?   15.8   0.8   2.2e-05      0.01      43     100 ..     264     321 ..     260     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.4
                    CENP-F_leu_zip 59 e 59
                                      e
  gi|488601108|ref|YP_007907579.1| 90 E 90
                                      2 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.2e-05
                    CENP-F_leu_zip  43 vileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLe 100
                                       +++ aE+  + +e+++e+i+ l+ +lr+le +L+++++  ++  +++qk ++  ++L 
  gi|488601108|ref|YP_007907579.1| 264 AKIRAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLR 321
                                       5667889999999999999999999999999999999999999999999888877775 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   4.9e-05     0.023     176     240 ..     264     324 ..     250     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-05
                        Fmp27_WPPW 176 leeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkese 240
                                       ++ R+ee++e+ ek++ek++ l+lk +     l++++++++k+i+++ ++++ l++ ++dl++  
  gi|488601108|ref|YP_007907579.1| 264 AKIRAEEISERAEKIQEKIDGLSLKLRD----LERNLDTTTKHINNAYRSMQKLNNSYQDLRNYF 324
                                       6779999999999999999999999999....999999999999999999999999999998755 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.17        80      36      86 ..      32      82 ..      22      83 .. 0.90
   2 ?   13.2   0.1   0.00019     0.088      14      70 ..      71     124 ..      58     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.17
                        EF-hand_14 36 pRLkellkklkkvekekseaeesetleldretFkkcveenivLiakaLknq 86
                                       R++el++ + ++ +++ +++ +++ ++  ++F + +  n+ +i+ a+   
  gi|488601108|ref|YP_007907579.1| 32 NRFEELINSIPQIVESNLTKTLTQSSSILENVFSSAMIRNAEVIKGAFATS 82
                                      6999************9999999999999*******9999999*9998765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00019
                        EF-hand_14  14 tdklsvakllkaLaetGirkdDpRLkellkklkkvekekseaeesetleldretFkk 70 
                                       + ++    + ++L+e Gi++d  R++e  + lk+v  +    +++ +++l r +F +
  gi|488601108|ref|YP_007907579.1|  71 NAEVIKGAFATSLKELGIQEDIARIREASSDLKSVTTDL---KNIFDVKLRRAKFGE 124
                                       56778889***************************9996...778889999999976 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.89   4.1e+02      28      44 ..      96     112 ..      87     117 .. 0.74
   2 ?   13.2   2.5   0.00016     0.075       1      46 [.     270     315 ..     270     318 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.89
                              XhlA  28 aeaeekiknleedlkkl 44 
                                       +ea + +k+++ dlk++
  gi|488601108|ref|YP_007907579.1|  96 REASSDLKSVTTDLKNI 112
                                       56777778888888777 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00016
                              XhlA   1 eikerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                       ei er e+i++k+d l+ ++ +le++ +++ + i n+   + kl +
  gi|488601108|ref|YP_007907579.1| 270 EISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNN 315
                                       7999*********************************999999865 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00014     0.065      21      83 ..     264     326 ..     247     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                           DUF3450  21 alkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeias 83 
                                       a+  ae++ + a+++q+kid l+ + ++l++++ + ++ ++++    ++l+++ +++++ +++
  gi|488601108|ref|YP_007907579.1| 264 AKIRAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYFER 326
                                       555677777788888888888888888888888888888888777777777777777665554 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 ?    0.9   0.0       1.2   5.5e+02      26      50 ..      95     119 ..      82     134 .. 0.85
   2 ?   11.0   0.2   0.00084      0.38       6      63 ..     269     326 ..     265     332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.2
                           DUF2316  26 veevaedLnlttekvekvLelkasr 50 
                                       + e+ +dL+  t+++++++++k +r
  gi|488601108|ref|YP_007907579.1|  95 IREASSDLKSVTTDLKNIFDVKLRR 119
                                       5678899************998655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00084
                           DUF2316   6 eerkaTkkeLqanfelsgltveevaedLnlttekvekvLelkasrledvWilrdyLee 63 
                                       ee  + ++++q++     l++ ++ ++L++tt+++++     ++  +   +lr+y e+
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYFER 326
                                       677788899******************************99999999999*****975 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   0.00021     0.096      31      61 ..     265     295 ..     263     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                     TRAF_BIRC3_bd  31 sttieaverqrrldqekieaLekKvrqLert 61 
                                       ++ +e++++  ++ qeki++L+ K+r+Ler 
  gi|488601108|ref|YP_007907579.1| 265 KIRAEEISERAEKIQEKIDGLSLKLRDLERN 295
                                       56789999999******************97 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         8   3.7e+03       9      28 ..      24      43 ..      19      67 .. 0.63
   2 ?    0.4   0.0       1.3     6e+02      16      46 ..     172     203 ..     169     220 .. 0.72
   3 ?   13.6   0.4   0.00011      0.05      23      81 ..     268     326 ..     263     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8
                            P4Ha_N  9 lklErelveeLesyieeeek 28
                                      lklEr + +++e+ i+ + +
  gi|488601108|ref|YP_007907579.1| 24 LKLERSMNNRFEELINSIPQ 43
                                      56666666666666665544 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                            P4Ha_N  16 veeLesyieeeekklekl.krfleeleeehes 46 
                                       +e++++y+e+e+++ ++  k+f+++++++ +s
  gi|488601108|ref|YP_007907579.1| 172 LENFRRYLEAENAEKDRYwKEFIKDVSRHIVS 203
                                       57899999999877666438899999888755 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00011
                            P4Ha_N  23 ieeeekkleklkrfleeleeehesakedkeeylsnPlnaFklikRltsdWeelekllee 81 
                                       +ee+ ++ ek+++ ++ l+ + ++ +++ +  +++  na++ +++l++ +++l +++e 
  gi|488601108|ref|YP_007907579.1| 268 AEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYFER 326
                                       5778889999999999999999888899999************************9986 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 ?    3.2   0.4      0.19        88      25      52 ..      24      51 ..      16     134 .. 0.80
   2 ?   12.0   0.4   0.00037      0.17      12      87 ..     249     327 ..     247     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                             Mod_r 25 lpevkqlkeekeellaeneslaeknlsl 52
                                      l+  ++++++ eel++++ ++ e+nl +
  gi|488601108|ref|YP_007907579.1| 24 LKLERSMNNRFEELINSIPQIVESNLTK 51
                                      5555788899999999999999999987 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00037
                             Mod_r  12 ledeeklealvk..tl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeld 85 
                                       l++++ + a+++  ++  + +++ e+ e++ +++  l  k  +le  l+   +++++++ ++++l+++++++ ++ +
  gi|488601108|ref|YP_007907579.1| 249 LTSPSTMPAYLSliSAkIRAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYFE 325
                                       5566666666652222234788999999998888888888888899**************************99887 PP

                             Mod_r  86 el 87 
                                       ++
  gi|488601108|ref|YP_007907579.1| 326 RI 327
                                       76 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       3.8   1.8e+03      29      44 ..      31      46 ..      20      66 .. 0.52
   2 ?   -0.5   0.2       3.3   1.5e+03      64      64 ..      83      83 ..      35     114 .. 0.53
   3 ?    2.2   0.1       0.5   2.3e+02      31      59 ..     270     295 ..     263     306 .. 0.54
   4 ?   12.7   0.1   0.00026      0.12      37      71 ..     297     331 ..     292     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.8
                           BLOC1_2 29 Neaasekykklkdvaa 44
                                      N++ +e ++++ ++++
  gi|488601108|ref|YP_007907579.1| 31 NNRFEELINSIPQIVE 46
                                      3333333333333333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.3
                           BLOC1_2 64 l 64
                                      l
  gi|488601108|ref|YP_007907579.1| 83 L 83
                                      1 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.5
                           BLOC1_2  31 aasekykklkdvaaslekkleklnekyee 59 
                                       + se+ +k+++++++l+ kl +l++   +
  gi|488601108|ref|YP_007907579.1| 270 EISERAEKIQEKIDGLSLKLRDLER---N 295
                                       3445555555555555555555554...2 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00026
                           BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqie 71 
                                       +  ++ ++++ ++++kln+ y+ l++y+++i +i+
  gi|488601108|ref|YP_007907579.1| 297 DTTTKHINNAYRSMQKLNNSYQDLRNYFERISDID 331
                                       56677889999***********************8 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       3.2   1.5e+03      66      92 ..      35      60 ..      23      80 .. 0.65
   2 ?   11.5   0.1   0.00066       0.3      11      51 ..     289     328 ..     267     333 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.2
                        MitMem_reg 66 qkllnllPhleteelekefnvetnDvl 92
                                       +l+n++P++ +++l+k + ++    l
  gi|488601108|ref|YP_007907579.1| 35 EELINSIPQIVESNLTKTL-TQSSSIL 60
                                      4567777777776666666.3333344 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00066
                        MitMem_reg  11 lkpsiqdas.stlstglnrqyyslkilqerldlikdYlkkve 51 
                                       l+ + + ++  t+++++n+ y s+++l++  +++++Y +++ 
  gi|488601108|ref|YP_007907579.1| 289 LR-DLE-RNlDTTTKHINNAYRSMQKLNNSYQDLRNYFERIS 328
                                       44.443.235799*************************9987 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.46   2.1e+02     154     188 ..      80     112 ..      65     134 .. 0.73
   2 ?   12.4   0.9   0.00017     0.077     152     210 ..     261     321 ..     256     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.46
                       Tropomyosin 154 gnnlksLevseekaseredeyeeeirtLeekLkea 188
                                       +++lk+L ++e+ a  re +    ++++++ Lk+ 
  gi|488601108|ref|YP_007907579.1|  80 ATSLKELGIQEDIARIREAS--SDLKSVTTDLKNI 112
                                       67899999999988888765..5677777777764 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00017
                       Tropomyosin 152 vvgnnlksLevse..ekaseredeyeeeirtLeekLkeaeeRaeeAErsvqkLekevdrle 210
                                        ++++++  e+se  ek  e+ d    ++r+Le +L ++ +  ++A rs+qkL+++  +l 
  gi|488601108|ref|YP_007907579.1| 261 LISAKIRAEEISEraEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLR 321
                                       5566677777765447888888888899999999999999999999999999999988876 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00039      0.18      41      97 ..     273     327 ..     266     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM  41 ataaavqkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelraayesr 97 
                                       + a+++q+k+d l+ +l +l++++ +  + ++++++  ++q++ +s+++lr+ +e+ 
  gi|488601108|ref|YP_007907579.1| 273 ERAEKIQEKIDGLSLKLRDLERNLDT--TTKHINNAYRSMQKLNNSYQDLRNYFERI 327
                                       56777*****************9865..789*********************99976 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.5   6.9e+02      12      35 ..      93     116 ..      87     119 .. 0.75
   2 ?   10.7   0.7   0.00086       0.4      65     103 ..     269     307 ..     265     310 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  12 qqlqqlaqqikqletqlkelelvl 35 
                                       +++++  +++k++ t+lk++ +v+
  gi|488601108|ref|YP_007907579.1|  93 ARIREASSDLKSVTTDLKNIFDVK 116
                                       467777788888888888887775 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00086
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                                       ee  er+e+++++i+ l+ +l++le++l+   +++++++
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAY 307
                                       67899****************************999875 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3       1.6   7.3e+02      48      82 ..      33      67 ..      25     101 .. 0.51
   2 ?    0.7   0.1       1.5   6.8e+02      18      46 ..      82     110 ..      77     121 .. 0.73
   3 ?   12.9   0.4   0.00024      0.11      13      89 ..     253     327 ..     247     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.6
                        Syntaxin_2 48 ktnellkklsqldnsssdsqqklqkekLkkdfkea 82
                                      + +el++++ q+ +s+++++   + + L + f++a
  gi|488601108|ref|YP_007907579.1| 33 RFEELINSIPQIVESNLTKTLTQSSSILENVFSSA 67
                                      34444444555555444432222333333333333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.5
                        Syntaxin_2  18 lvkqLgtkkdteelreklhelieeineli 46 
                                        +k Lg + d  ++re   +l + +++l 
  gi|488601108|ref|YP_007907579.1|  82 SLKELGIQEDIARIREASSDLKSVTTDLK 110
                                       56778888888888888888877777764 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00024
                        Syntaxin_2  13 stleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeFqki 89 
                                       st+  +++ ++ k   ee+ e++++++e+i  l+ k  +l ++l++ +++ +  + + + +kL+++++++ + F++i
  gi|488601108|ref|YP_007907579.1| 253 STMPAYLSLISAKIRAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHIN--NAYRSMQKLNNSYQDLRNYFERI 327
                                       6777888889999889999999999999999999999999999999888886..4566889********99999987 PP

>> YgaB  YgaB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.68   3.1e+02      31      59 ..      84     112 ..      80     118 .. 0.68
   2 ?    8.4   0.2    0.0061       2.8      32      77 .]     265     310 ..     260     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.68
                              YgaB  31 keLlklekeaklesiqeeikrkkkeLkei 59 
                                       keL  +e  a+++++ +++k    +Lk+i
  gi|488601108|ref|YP_007907579.1|  84 KELGIQEDIARIREASSDLKSVTTDLKNI 112
                                       56666666677777777777777777766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0061
                              YgaB  32 eLlklekeaklesiqeeikrkkkeLkeiqkvFekQteevirsYqss 77 
                                       ++++ e   ++e+iqe+i+ +  +L+++++  ++ t+ + ++Y+s+
  gi|488601108|ref|YP_007907579.1| 265 KIRAEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSM 310
                                       56666777789********************************985 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         5   2.3e+03     311     318 ..      89      96 ..      32     117 .. 0.56
   2 ?   11.6   0.4   0.00022       0.1     258     317 ..     268     327 ..     247     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5
                             IFT57 311 seelekvk 318
                                       +e++ ++ 
  gi|488601108|ref|YP_007907579.1|  89 QEDIARIR 96 
                                       33333333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00022
                             IFT57 258 lekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekv 317
                                        e+i++r + ++++++ l  ++r+++++l++++++++++ +++++l++ ++++ + +e++
  gi|488601108|ref|YP_007907579.1| 268 AEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYFERI 327
                                       588999999999999999999999999999999999999999999999999998887776 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       2.6   1.2e+03     111     111 ..      61      61 ..      24     119 .. 0.53
   2 ?   12.8   1.2   0.00015     0.069      78     127 ..     269     320 ..     261     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.6
                              YkyA 111 e 111
                                       e
  gi|488601108|ref|YP_007907579.1|  61 E 61 
                                       2 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                              YkyA  78 eeakeefekikeeieei..edeelkkeaeelieameeryeaydklykaYkea 127
                                       ee  e  eki+e+i+ +  +  +l+ ++++  + +++ y +++kl+++Y+++
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLslKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDL 320
                                       556677788888888877777899*************************986 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.9   8.9e+02      24      60 ..      89     111 ..      80     118 .. 0.53
   2 ?   10.2   0.1    0.0017      0.79      14      64 ..     276     330 ..     259     334 .] 0.59

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.9
                           NPV_P10  24 qqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                       q+ +++++e + d++ +++ L              +n
  gi|488601108|ref|YP_007907579.1|  89 QEDIARIREASSDLKSVTTDL--------------KN 111
                                       444444444444444443333..............33 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0017
                           NPV_P10  14 kavddkVdalqqqvddvqenlpdvt.elne...kLdaqsaqLaeletkvenIqdi 64 
                                       +++++k+d l+ ++ d++ nl ++t ++n+    +++++++ ++l +  e I+di
  gi|488601108|ref|YP_007907579.1| 276 EKIQEKIDGLSLKLRDLERNLDTTTkHINNayrSMQKLNNSYQDLRNYFERISDI 330
                                       5567777777777777777776644123331113555555555555566666555 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3       2.8   1.3e+03     145     161 ..      34      50 ..      10     114 .. 0.60
   2 ?    7.9   0.1     0.005       2.3      27      51 ..     184     208 ..     178     216 .. 0.91
   3 ?    5.9   0.2     0.021       9.6      66     110 ..     276     319 ..     258     330 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.8
                            DUF713 145 leelrelfskldpsdIp 161
                                       +eel +++ ++  s+  
  gi|488601108|ref|YP_007907579.1|  34 FEELINSIPQIVESNLT 50 
                                       44444444444333332 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.005
                            DUF713  27 eekEqewsdwlkklrepivklknrf 51 
                                        ek+  w++++k++ ++iv++ +++
  gi|488601108|ref|YP_007907579.1| 184 AEKDRYWKEFIKDVSRHIVSIREKY 208
                                       5899*****************9998 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.021
                            DUF713  66 kklekedleelqselsnLakkvlsaynkLeeafeklkelsekfed 110
                                       +k++ e+ + l   l+ L++ + ++ + +++a+ ++++l+++++d
  gi|488601108|ref|YP_007907579.1| 276 EKIQ-EKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQD 319
                                       3333.4667777777888888888888888888888888888877 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.081        37      21      45 ..      87     111 ..      83     114 .. 0.90
   2 ?    6.8   1.3     0.017       7.7      13      58 ..     269     318 ..     263     328 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.081
                           DUF5082  21 aleekIerLkeaktklsdekeslkq 45 
                                       +++e+I+r +ea++ l+++   lk+
  gi|488601108|ref|YP_007907579.1|  87 GIQEDIARIREASSDLKSVTTDLKN 111
                                       589**************99988876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                           DUF5082  13 aelrseiaaleekIerLk....eaktklsdekeslkqkkkklekplnsse 58 
                                       +e ++++++++ekI  L        + l+++ +++ ++ ++++k  ns++
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSlklrDLERNLDTTTKHINNAYRSMQKLNNSYQ 318
                                       44444455555555433332334445555555555555555555555544 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4      0.28   1.3e+02      37     114 ..      28     110 ..      24     116 .. 0.58
   2 ?    8.1   0.1    0.0055       2.5      55     109 ..     269     323 ..     254     331 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.28
                           DUF1664  37 rslsdavesvskqleqvs.eslaatkrhLssridrvdkk..ldeqkeiskeikeevte..vredlseigedvesvke 108
                                       rs+++  e++ +++ q+  ++l++t  + ss +++v ++  + + + i+ + +  ++e  ++ed+++i+e ++ +k+
  gi|488601108|ref|YP_007907579.1|  28 RSMNNRFEELINSIPQIVeSNLTKTLTQSSSILENVFSSamIRNAEVIKGAFATSLKElgIQEDIARIREASSDLKS 104
                                       67777777777777665414577777777777777643211344444444555555542257777777777777776 PP

                           DUF1664 109 avegle 114
                                       + ++l+
  gi|488601108|ref|YP_007907579.1| 105 VTTDLK 110
                                       666665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0055
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       e++++  ++++++id +  kl + ++    ++++++++ + ++++++  + +++ 
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNY 323
                                       4455555555555555555555555555555555555555555555555555444 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.76   3.5e+02     160     304 ..      30      54 ..       4     111 .. 0.52
   2 ?    9.7   1.3   0.00092      0.43      77     126 ..     269     318 ..     264     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.76
                       DLP_helical 160 leneferqlekiseeiskvessfkskvehfndsssklgkqgikylkksklvkinntsilaardgvvsaakilgldlg 236
                                       ++n+fe+ +++i +    ves++                                                      
  gi|488601108|ref|YP_007907579.1|  30 MNNRFEELINSIPQI---VESNLT----------------------------------------------------- 50 
                                       222222222222221...122222..................................................... PP

                       DLP_helical 237 lKFKPWgAvkLAknlnkalaiiGavlelalevwdslkqskkekelkelkeelveklkdqrkeilelln 304
                                                                                                       ++l 
  gi|488601108|ref|YP_007907579.1|  51 ----------------------------------------------------------------KTLT 54 
                                       ................................................................2222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00092
                       DLP_helical  77 peaeerleelekevekleesakriekelaelkkeieearielreelkayf 126
                                       +e+ er+e+++++++ l+ +++++e +l ++ k+i++a + +++  ++y 
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQ 318
                                       7899************************************9998888875 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       3.6   1.6e+03      48      70 ..      30      52 ..      25      61 .. 0.81
   2 ?    0.0   0.0       2.9   1.3e+03      42      63 ..      92     113 ..      72     120 .. 0.76
   3 ?    9.8   1.2    0.0026       1.2       5      62 ..     265     320 ..     264     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.6
                           DUF5344 48 leeeleellkaYktlllknvedt 70
                                      ++  +eel+++  +++++n+++t
  gi|488601108|ref|YP_007907579.1| 30 MNNRFEELINSIPQIVESNLTKT 52
                                      78888999999888888888766 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.9
                           DUF5344  42 vekineleeeleellkaYktll 63 
                                       + +i e +++l+++++++k+++
  gi|488601108|ref|YP_007907579.1|  92 IARIREASSDLKSVTTDLKNIF 113
                                       4567777778888888877776 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0026
                           DUF5344   5 klnqaeVeqkLselktaaeelktsipetisgknsldvvekineleeeleellkaYktl 62 
                                       k+ ++e+ +  +++++++++l  s++    ++n   +++ in   +++++l ++Y++l
  gi|488601108|ref|YP_007907579.1| 265 KIRAEEISERAEKIQEKIDGL--SLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDL 320
                                       788999999999*******99..66666688899999999***************987 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       1.5   6.8e+02     133     133 ..      74      74 ..      24     134 .. 0.50
   2 ?    9.4   0.4    0.0016      0.73      10      60 ..     269     319 ..     257     329 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                           DUF4795 133 p 133
                                        
  gi|488601108|ref|YP_007907579.1|  74 V 74 
                                       1 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                           DUF4795  10 kklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkad 60 
                                       +++ e  ek+qe+++ l+ k ++le +l ++ k+++  + ++++l+++ +d
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQD 319
                                       567788899999999999999999999999999999999999999987665 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         6   2.7e+03      62      82 ..      92     112 ..      83     130 .. 0.59
   2 ?    8.8   2.2    0.0046       2.1      21      84 ..     267     322 ..     259     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6
                   Snapin_Pallidin  62 akKLvnikkrmsslnerlqkl 82 
                                       +++++++  +++s+ + l+++
  gi|488601108|ref|YP_007907579.1|  92 IARIREASSDLKSVTTDLKNI 112
                                       444444444444444444443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0046
                   Snapin_Pallidin  21 klkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkk 84 
                                       + +e+ +  e+ +e++d l+ kL++le++ +        +  k ++n+ + m++ln++ q l+ 
  gi|488601108|ref|YP_007907579.1| 267 RAEEISERAEKIQEKIDGLSLKLRDLERNLD--------TTTKHINNAYRSMQKLNNSYQDLRN 322
                                       6788888999999999999999998877666........6677788888888888888777764 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.3    0.0065         3       2      83 ..       5      87 ..       4      90 .. 0.64
   2 ?   -1.4   0.0       4.5   2.1e+03     103     115 ..     239     251 ..     238     255 .. 0.87
   3 ?    5.2   0.8     0.041        19      23      82 ..     267     310 ..     252     328 .. 0.40

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0065
                           DUF4446  2 iilvlavlvvillillivllvklkklkkkykklmkgkdgksleellkekleeveelkees..eelekeieeleeklkks 78
                                      +++++++++vill ++  +l   +++++++++l++ +  + +e+ l ++l++  ++ e++  +++ ++ e ++  +++s
  gi|488601108|ref|YP_007907579.1|  5 VVIAVLFIIVILLYTIYRNLKLERSMNNRFEELIN-SIPQIVESNLTKTLTQSSSILENVfsSAMIRNAEVIKGAFATS 82
                                      56666666666666666666666789999999998.4566777777777777777666653244556666666666666 PP

                           DUF4446 79 lqkvg 83
                                      l+++g
  gi|488601108|ref|YP_007907579.1| 83 LKELG 87
                                      66655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.5
                           DUF4446 103 lLdeennGvvlns 115
                                       l+++++nGv+l+s
  gi|488601108|ref|YP_007907579.1| 239 LVEASKNGVILTS 251
                                       778999*****98 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.041
                           DUF4446  23 klkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslqkv 82 
                                       + ++++++ +k+++                +++ l+ + ++le+++++ +++++++++ +
  gi|488601108|ref|YP_007907579.1| 267 RAEEISERAEKIQE----------------KIDGLSLKLRDLERNLDTTTKHINNAYRSM 310
                                       33333333333333................333333333333333333333333332222 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.98   4.5e+02      49      68 ..      94     113 ..      87     119 .. 0.73
   2 ?    6.4   0.5     0.024        11      37      73 ..     269     305 ..     267     312 .. 0.90
   3 ?    0.1   0.0       2.2   9.9e+02      54      74 ..     310     330 ..     306     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.98
                              KxDL  49 rfkqgtkllkevkkdLesif 68 
                                       r+++   +lk+v  dL++if
  gi|488601108|ref|YP_007907579.1|  94 RIREASSDLKSVTTDLKNIF 113
                                       55666677777888887777 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                              KxDL  37 alsqerlaklrarfkqgtkllkevkkdLesifkkirs 73 
                                       ++ +er +k+++++      l+++ ++L++++k+i++
  gi|488601108|ref|YP_007907579.1| 269 EEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINN 305
                                       5778999***************************975 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.2
                              KxDL  54 tkllkevkkdLesifkkirsl 74 
                                       ++ l++  +dL++ f++i+ +
  gi|488601108|ref|YP_007907579.1| 310 MQKLNNSYQDLRNYFERISDI 330
                                       566666677888888888776 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.5     0.018       8.4       2      49 ..       9      56 ..       5      66 .. 0.83
   2 ?   -2.1   0.0       1.7   7.8e+02     315     334 ..      92     111 ..      82     127 .. 0.49
   3 ?    8.1   2.3    0.0014      0.64      96     149 ..     268     321 ..     259     330 .. 0.41

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                                      XXXXXXXXXXXXXXXXXXXX-THHHHHHHHHHHHHHHHHHHHHTTTSS CS
                              EzrA  2 iiaiiviiivlyliglllrkkikkeideLeerkneiknlpvqeelskv 49
                                      ++ iivi++ ++  +l+l + ++++ +eL ++  +i+++++++ l + 
  gi|488601108|ref|YP_007907579.1|  9 VLFIIVILLYTIYRNLKLERSMNNRFEELINSIPQIVESNLTKTLTQS 56
                                      456677777777778999********************9999998765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                                       HHT--HHHHTTGGG-TTTS- CS
                              EzrA 315 lehlekqnkelkeeldrlkq 334
                                       + ++++ +++lk+ +++lk+
  gi|488601108|ref|YP_007907579.1|  92 IARIREASSDLKSVTTDLKN 111
                                       22222222222222222222 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0014
                                       HHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHH CS
                              EzrA  96 fkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelr 149
                                         ++ ++ ++++e++d +  k++++   l+  t++ ++    ++kl++ Y++lr
  gi|488601108|ref|YP_007907579.1| 268 AEEISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLR 321
                                       333333333333333333333333333333333333333333333333333333 PP

>> BLOC1S3  Biogenesis of lysosome-related organelles complex 1 subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.067        31     101     144 ..      22      66 ..      21      76 .. 0.88
   2 ?    3.6   0.1      0.14        65     136     166 ..      86     116 ..      80     118 .. 0.87
   3 ?    2.4   0.2      0.33   1.5e+02     121     162 ..     286     327 ..     273     331 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.067
                           BLOC1S3 101 sNarLrkdvkeavsqvysaaskeles.vtsqLnksqsaiqnashs 144
                                       +N +L+ +++++ ++++++  + +es +t+ L++s s+++n+ +s
  gi|488601108|ref|YP_007907579.1|  22 RNLKLERSMNNRFEELINSIPQIVESnLTKTLTQSSSILENVFSS 66 
                                       799*******************9975389************9766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                           BLOC1S3 136 saiqnashsirlilddlkavsekldiitscs 166
                                       ++iq+  + ir ++ dlk+v   l+ i++ +
  gi|488601108|ref|YP_007907579.1|  86 LGIQEDIARIREASSDLKSVTTDLKNIFDVK 116
                                       578888899***************9999866 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.33
                           BLOC1S3 121 skelesvtsqLnksqsaiqnashsirlilddlkavsekldii 162
                                       s +l++++++L ++   i na  s++++++  +++ +  + i
  gi|488601108|ref|YP_007907579.1| 286 SLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYFERI 327
                                       567788888888888888888888888777777766665555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.9       1.5   6.8e+02      48      75 ..      28      55 ..      17     111 .. 0.52
   2 ?    0.8   0.0       1.1     5e+02      40      72 ..      88     120 ..      74     134 .. 0.80
   3 ?   -0.9   0.0       3.6   1.7e+03      71      96 ..     182     207 ..     173     214 .. 0.76
   4 ?    9.5   1.2    0.0022         1      26      83 ..     271     328 ..     267     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.5
                                      CCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 48 snstkeaeelvkeikdslrekqkskkdn 75
                                      +++++  eel+++i ++++++ +++  +
  gi|488601108|ref|YP_007907579.1| 28 RSMNNRFEELINSIPQIVESNLTKTLTQ 55
                                      3344444444444444444444333322 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.1
                                       CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  40 leneleeisnstkeaeelvkeikdslrekqksk 72 
                                       +++++++i++ +++ +++++++k++   k + +
  gi|488601108|ref|YP_007907579.1|  88 IQEDIARIREASSDLKSVTTDLKNIFDVKLRRA 120
                                       578899999999999999999999888777665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHHHHHHCCCHHHHH CS
                         Fib_alpha  71 skkdndnvikksskeleeeilrlket 96 
                                       +++++d++ k++ k++ ++i+ ++e+
  gi|488601108|ref|YP_007907579.1| 182 ENAEKDRYWKEFIKDVSRHIVSIREK 207
                                       34456899999999999999988876 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0022
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkss 83 
                                       +++  ++++++++ l  +l++++++  ++ +++++ + s+++ ++s++d  n+++++s
  gi|488601108|ref|YP_007907579.1| 271 ISERAEKIQEKIDGLSLKLRDLERNLDTTTKHINNAYRSMQKLNNSYQDLRNYFERIS 328
                                       6777889999999999999999999999999999999999999999999899888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2009  (0.112053); expected 358.6 (0.02)
Passed bias filter:                     1360  (0.0758548); expected 358.6 (0.02)
Passed Vit filter:                       227  (0.0126611); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.48
# Mc/sec: 2099.17
//
Query:       gi|488601109|ref|YP_007907580.1|  [L=212]
Description: hypothetical protein Asulf_01611 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   13.8   0.0      0.056   13.2   0.0    1.3  1  AMP_N     Aminopeptidase P, N-terminal domain


Domain annotation for each model (and alignments):
>> AMP_N  Aminopeptidase P, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-06     0.056      61     115 ..     108     164 ..      92     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-06
                                       SEEEE....EEEE----HHHHHHH----HHHHHHHH..HT-SEEEEGGGHHHHHHHHH CS
                             AMP_N  61 edkkeh.kstLfvprkdpekelWdGarlgleeakel..fgvdeaepidelesalakll 115
                                       + ++++  s Lfv++  +  +lW+G   gl+e+++   ++vd+ e++ ++e+  +k++
  gi|488601109|ref|YP_007907580.1| 108 S-PESYiSSSLFVREMREFGALWHGLSWGLHEIVDEnsIDVDDYEWLVDVEDLKPKVI 164
                                       3.33344899***********************9984456677787777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1383.74
//
Query:       gi|488601110|ref|YP_007907581.1|  [L=112]
Description: hypothetical protein Asulf_01612 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   30.8   0.5    3.6e-07   30.1   0.5    1.3  1  HTH_45    Winged helix-turn-helix
    0.00028   21.3   0.0    0.00047   20.6   0.0    1.4  1  HTH_27    Winged helix DNA-binding domain
    0.00038   20.3   0.2    0.00056   19.7   0.2    1.3  1  HxlR      HxlR-like helix-turn-helix
     0.0017   18.1   0.1     0.0021   17.9   0.1    1.2  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.014   15.6   0.1    1.3  1  HTH_34    Winged helix DNA-binding domain
      0.016   15.2   0.9      0.096   12.7   0.1    2.4  3  PadR      Transcriptional regulator PadR-like family
      0.045   13.6   0.3      0.056   13.3   0.3    1.2  1  DUF4393   Domain of unknown function (DUF4393)
      0.071   12.9   0.1       0.15   11.9   0.0    1.6  2  Imm27     Immunity protein 27
      0.078   12.8   0.0       0.15   11.9   0.0    1.5  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.095   12.3   2.2        1.2    8.8   0.1    2.7  2  HTH_24    Winged helix-turn-helix DNA-binding
       0.11   12.6   0.0        4.4    7.5   0.0    2.2  2  zf-SAP30  SAP30 zinc-finger


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 !   30.1   0.5   2.2e-10   3.6e-07      11      75 ..      19      89 ..      14      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.2e-10
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli......kkskekYvlTekGlelleklkeleel 75
                                      IL+++++++   T++m+++  s   ++  +++L++  l+      +k+   Y+lT+ G+++le l+e+e++
  gi|488601110|ref|YP_007907581.1| 19 ILKNLKNKKLIYTELMKNSLVSSGAFSTRINQLINLRLVkveydqEKRRPFYSLTDTGKRILELLEEIERV 89
                                      9*************************************9999987778889*****************987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.9e-07   0.00047       6      68 .]      17      76 ..      12      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.9e-07
                            HTH_27  6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++L +++  + + + ++l++   v++ ++s  +++L++  Lv + ++++++r+ +++lTd G
  gi|488601110|ref|YP_007907581.1| 17 VWILKNLK--NKKLIYTELMKNSLVSSGAFSTRINQLINLRLV-KVEYDQEKRRPFYSLTDTG 76
                                      78888888..666666***************************.777779***********88 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   3.4e-07   0.00056       8      81 ..      17      88 ..      13      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.4e-07
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHH CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkk 81
                                      + il +l ++k  ++el ++   +s    ++r+ +L + +l++ ++y++   +  Yslt++G+ + ++l+e++ 
  gi|488601110|ref|YP_007907581.1| 17 VWILKNLKNKKLIYTELMKNS-LVSSGAFSTRINQLINLRLVK-VEYDQEKRRPFYSLTDTGKRILELLEEIER 88
                                      6799*************9987.8******************97.56888899999**************99876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.3e-06    0.0021      17      75 ..      25      85 ..      17     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                           DUF4364 17 tnsqlseiileneytnYfdlqqalseLvesglieee..ekenktlykiTekGketlelfen 75
                                      +++ ++  +++n +++   ++  +++L++  l+++e  +++ + +y++T+ Gk++lel+e+
  gi|488601110|ref|YP_007907581.1| 25 NKKLIYTELMKNSLVSSGAFSTRINQLINLRLVKVEydQEKRRPFYSLTDTGKRILELLEE 85
                                      45556777889999999999**************9986668999*************9985 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 ?   15.6   0.1   8.6e-06     0.014       9      67 ..      20      78 ..      15      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.6e-06
                            HTH_34  9 Las..vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67
                                      L    +++  ++el +   +++g+ s+ ++ L + + ++v+ + +++  r  +++T++G+ 
  gi|488601110|ref|YP_007907581.1| 20 LKNlkNKKLIYTELMKNSLVSSGAFSTRINQLINLRLVKVEYDQEKR--RPFYSLTDTGKR 78
                                      54444778888899888899*******************99888877..558999*99986 PP

>> PadR  Transcriptional regulator PadR-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   5.9e+02      37      51 ..      19      33 ..      14      43 .. 0.81
   2 ?   12.7   0.1   5.9e-05     0.096      41      74 ..      51      81 ..      31      82 .. 0.73
   3 ?   -1.0   0.0       1.1   1.8e+03      32      43 ..      96     106 ..      79     107 .. 0.50

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.36
                                      HHHHHHHTTSEEEEE CS
                              PadR 37 aLkrLekeglvesew 51
                                      +Lk L++++l+ +e 
  gi|488601110|ref|YP_007907581.1| 19 ILKNLKNKKLIYTEL 33
                                      689999999998775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.9e-05
                                      HHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR 41 LekeglveseweesgegpprkyYrlTdaGrrela 74
                                      L + +lv+ e +   ++++r +Y lTd+G+r l+
  gi|488601110|ref|YP_007907581.1| 51 LINLRLVKVEYD---QEKRRPFYSLTDTGKRILE 81
                                      555555555555...569************9775 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHH CS
                              PadR  32 GslYpaLkrLek 43 
                                       G+ Y+ Lk++ek
  gi|488601110|ref|YP_007907581.1|  96 GE-YRELKEMEK 106
                                       33.677777776 PP

>> DUF4393  Domain of unknown function (DUF4393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   3.4e-05     0.056     115     166 ..      39      89 ..       7     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                           DUF4393 115 enpekvkasldnLerlgLiklsekqklteekvyeelenskiieelkeelkkv 166
                                        +   ++  ++ L+ l+L+k++++q+ ++ ++y+   + k i el ee+++v
  gi|488601110|ref|YP_007907581.1|  39 VSSGAFSTRINQLINLRLVKVEYDQE-KRRPFYSLTDTGKRILELLEEIERV 89 
                                       233345999*****************.9999*******99999998888433 PP

>> Imm27  Immunity protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       4.1   6.6e+03      12      17 ..      17      22 ..      11      30 .. 0.51
   2 ?   11.9   0.0   9.1e-05      0.15       5      39 ..      38      72 ..      34      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.1
                             Imm27 12 lariks 17
                                      + + k 
  gi|488601110|ref|YP_007907581.1| 17 VWILKN 22
                                      333344 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.1e-05
                             Imm27  5 kvikddalariksliknkLkelksdedgwetlYkd 39
                                       v   + + ri++li+ +L +++ d+++++ +Y  
  gi|488601110|ref|YP_007907581.1| 38 LVSSGAFSTRINQLINLRLVKVEYDQEKRRPFYSL 72
                                      566667789************************75 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 ?   11.9   0.0   9.2e-05      0.15      58      89 ..      50      82 ..      35      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-05
                           DUF1495 58 sLielGLveeeeeseglk.lYklteeGieivev 89
                                       Li+l Lv+ e ++e  + +Y+lt++G++i e 
  gi|488601110|ref|YP_007907581.1| 50 QLINLRLVKVEYDQEKRRpFYSLTDTGKRILEL 82
                                      699*****87666555557**********9885 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00073       1.2      20      47 ..      30      57 ..      19      58 .. 0.87
   2 ?    2.6   0.2     0.063     1e+02       2      14 ..      73      85 ..      72      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00073
                            HTH_24 20 qreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++eL + + +S+++ ++r+++L++  l+
  gi|488601110|ref|YP_007907581.1| 30 YTELMKNSLVSSGAFSTRINQLINLRLV 57
                                      6899999***************997666 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.063
                            HTH_24  2 detdrkILelLqk 14
                                       +t ++ILelL++
  gi|488601110|ref|YP_007907581.1| 73 TDTGKRILELLEE 85
                                      68899*****986 PP

>> zf-SAP30  SAP30 zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0027       4.4      21      46 ..      41      66 ..      34      81 .. 0.88
   2 ?    3.4   0.0     0.053        86       7      25 ..      81      99 ..      75     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0027
                          zf-SAP30 21 nasyskriqktvaqkklkleiDssar 46
                                      ++++s ri + ++ + +k+e D++ r
  gi|488601110|ref|YP_007907581.1| 41 SGAFSTRINQLINLRLVKVEYDQEKR 66
                                      689*******************9877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.053
                          zf-SAP30  7 cLvddgeRCkrkaGnasys 25
                                       L+++ eR +rk G + y 
  gi|488601110|ref|YP_007907581.1| 81 ELLEEIERVHRKVGLGEYR 99
                                      699***********99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 708.68
//
Query:       gi|488601111|ref|YP_007907582.1|  [L=48]
Description: hypothetical protein Asulf_01613 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 310.34
//
Query:       gi|488601112|ref|YP_007907583.1|  [L=106]
Description: hypothetical protein Asulf_01614 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.5   0.0     0.0029   17.2   0.0    1.2  1  AHJR-like       REase_AHJR-like
     0.0066   16.6   0.0     0.0094   16.1   0.0    1.1  1  Tn7_Tnp_TnsA_N  TnsA endonuclease N terminal


Domain annotation for each model (and alignments):
>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.2e-07    0.0029       7      70 ..      12      78 ..       7     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-07
                         AHJR-like  7 elererleslaeqyrekGye..vllhPnredlPdfLksYrpDliar.kdeeaviiEvksrrssaseq 70
                                      + ++e++++la+ yr +  +  v+++ +    P  ++s+rpD+i+  ++  + iiE+ ++ +   e+
  gi|488601112|ref|YP_007907583.1| 12 TEHDEAVKKLASRYRRQHPSatVYADASGFLKPRMIGSHRPDIIVVfRNGRGRIIEIETEDTINTEH 78
                                      568999*********99765115556666677**********99753888999****9988744333 PP

>> Tn7_Tnp_TnsA_N  TnsA endonuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     1e-06    0.0094       5      86 ..      24     100 ..      22     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-06
                    Tn7_Tnp_TnsA_N   5 direQ.PltlqiakelgikhpkvrevpsvmtpDfLvtlkdstgeellavevKyseeleeertrekleiereyweekg 80 
                                        +r Q P    +a+ +g+ +p   ++   + pD++v ++++   +  ++e+ +++ ++ e  r + +  r y++ kg
  gi|488601112|ref|YP_007907583.1|  24 RYRRQhPSATVYADASGFLKP---RMIGSHRPDIIVVFRNG---RGRIIEIETEDTINTEHARAQARSFRGYANLKG 94 
                                       5899*****************...88899***********9...556****************************** PP

                    Tn7_Tnp_TnsA_N  81 ipfrii 86 
                                       ++f ++
  gi|488601112|ref|YP_007907583.1|  95 FRFDVF 100
                                       **9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 723.08
//
Query:       gi|488601113|ref|YP_007907584.1|  [L=78]
Description: hypothetical protein Asulf_01615 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-27   93.4   0.0    6.9e-27   93.1   0.0    1.1  1  DUF433    Protein of unknown function (DUF433)
  ------ inclusion threshold ------
      0.058   13.8   0.0       0.14   12.6   0.0    1.7  1  DUF4258   Domain of unknown function (DUF4258)


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 !   93.1   0.0   7.7e-31   6.9e-27       1      56 []       3      58 ..       3      58 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 7.7e-31
                                      EEE-TTSGGGS-EETTT--BTHHHHHHHHTT--HHHHHHHH.TS-HHHHHHHHT.. CS
                            DUF433  1 ItidpeilgGkPvIrgtRipVetilellaaGesieeiledyPdLtlediqaalaYA 56
                                      ++i+pei gGkPvI+gtRi+Ve+ilella+G+s eeile+yP+L++edi +a++YA
  gi|488601113|ref|YP_007907584.1|  3 VEINPEISGGKPVIKGTRITVEFILELLANGWSYEEILENYPQLKKEDILEAISYA 58
                                      689****************************************************8 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05      0.14      13      45 ..      20      52 ..      16      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                           DUF4258 13 gIseedieevlenG....eiieeys.lvlgktsegrpl 45
                                      +I+ e i+e+l+nG    ei e+y+ l     ++++ l
  gi|488601113|ref|YP_007907584.1| 20 RITVEFILELLANGwsyeEILENYPqL-----KKEDIL 52
                                      699**************88******63.....333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 521.78
//
Query:       gi|488601114|ref|YP_007907585.1|  [L=87]
Description: hypothetical protein Asulf_01616 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-07   31.0   0.0    2.1e-07   30.6   0.0    1.3  1  DUF5615   Domain of unknown function (DUF5615)


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 !   30.6   0.0   1.2e-11   2.1e-07      45      76 ..       9      41 ..       2      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.2e-11
                           DUF5615 45 keedriivTkDkDFgel.lllggpppgvillrl 76
                                      + e+++i+T+DkDFg+l ++++ +p gvillr 
  gi|488601114|ref|YP_007907585.1|  9 RGEKAVIITFDKDFGDLiFRKSLKPFGVILLRV 41
                                      5689*************999999999*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 645.29
//
Query:       gi|488601115|ref|YP_007907586.1|  [L=46]
Description: hypothetical protein Asulf_01617 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 315.28
//
Query:       gi|488601116|ref|YP_007907587.1|  [L=116]
Description: hypothetical protein Asulf_01618 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.034   14.2   0.0      0.047   13.7   0.0    1.2  1  TFIIB_C_1  Transcription factor IIB C-terminal module 1


Domain annotation for each model (and alignments):
>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-06     0.047       7      56 ..      11      61 ..       5      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-06
                         TFIIB_C_1  7 nalevllklsrr.deavleealelakrfvGkrrergervekqeevaaaclm 56
                                      n+ +  ++l+ + ++ v + a++  k  + +rr+r++r+ +qe     c  
  gi|488601116|ref|YP_007907587.1| 11 NINKKTCDLIWNlPDVVSRPAMDYPKLIIPHRRDRDQRISEQEARFVYCSV 61
                                      55566677777669**************************99987776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 00:00:00.39
# Mc/sec: 892.33
//
Query:       gi|488601117|ref|YP_007907588.1|  [L=86]
Description: hypothetical protein Asulf_01619 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0016   18.6   0.0     0.0024   18.0   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 !   18.0   0.0   1.3e-07    0.0024      11      62 ..      28      79 ..      20      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-07
                   HicB_lk_antitox 11 saygvvvPdlpGcfsagdtleeaianakeaielhlegliedgeeipepssie 62
                                      + +   +P l+G++  +d+lee  ++ +e++e ++   + +  +ipe+  ++
  gi|488601117|ref|YP_007907588.1| 28 QVFYGEIPGLNGVYAYADSLEECKKELEEVLEEWILIRVSRSFQIPEVDGVK 79
                                      5556679****************************99999999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 551.60
//
Query:       gi|488601118|ref|YP_007907589.1|  [L=88]
Description: hypothetical protein Asulf_01620 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 517.02
//
Query:       gi|488601119|ref|YP_007907590.1|  [L=244]
Description: monomeric archaeal DNA polymerase sliding clamp [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   50.2   0.5    3.3e-11   43.0   0.2    2.1  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    5.4e-10   39.5   0.9    4.6e-09   36.5   0.1    2.5  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
  ------ inclusion threshold ------
      0.039   13.5   1.4       0.16   11.6   0.8    2.0  2  Pox_TAP   Viral Trans-Activator Protein


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.2   5.5e-15   3.3e-11       8      96 ..       7      95 ..       1     106 [. 0.93
   2 !    5.6   0.0     0.002        12       9     104 ..     134     225 ..     126     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5.5e-15
                                      SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTS CS
                            PCNA_N  8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcanned 86
                                      ++ +lk +  a+  lv+ea f  +++G++ +a+D + va+v + + s++f ky  + + + gv++n +  i k  +n+d
  gi|488601119|ref|YP_007907590.1|  7 NGEILKTVSKAMVSLVSEARFHFKEEGLHSRAVDPANVAMVIVDVPSSSFIKYESEGDFVAGVDVNRIFDISKSIKNDD 85
                                      689**************************************************************************** PP

                                      EEEEEEETTS CS
                            PCNA_N 87 svtlkaedea 96
                                      +v +  ++e+
  gi|488601119|ref|YP_007907590.1| 86 VVEMTINEES 95
                                      **99988766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.002
                                       HHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTT CS
                            PCNA_N   9 asllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcanne 85 
                                       a  +kk + a   + +++ f ++++G+ + a  +  v  ++++l +    ++      ++  +l+ l   +k+a   
  gi|488601119|ref|YP_007907590.1| 134 AGEFKKAIVAADKISDHVVFRTNEEGFFIEA--EGDVDRITFSLSDAELAEFNRQEAKSM-FSLEYLKEFVKIASSG 207
                                       5668898889999999999999999999998..556888899999999999987777776.799999999****999 PP

                                       SEEEEEEETTSSEEEEEEE CS
                            PCNA_N  86 dsvtlkaedeadtlalvfe 104
                                       d++t++  ++   + +vfe
  gi|488601119|ref|YP_007907590.1| 208 DVLTIRLGNDYP-VRMVFE 225
                                       999999776543.445665 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.11   6.6e+02      39      75 ..      55      93 ..      43     116 .. 0.60
   2 !   36.5   0.1   7.7e-13   4.6e-09       2     126 ..     121     238 ..     120     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                                      TEEEEEEEETTEEEEEE...E--BEESSSGGGCBEEEESS CS
                            PCNA_C 39 egvkfsasGdiGsasiv...lkqvkdvdkeeeavklelke 75
                                        +k+ ++Gd  ++ +    + + +++ k+++ v++ ++e
  gi|488601119|ref|YP_007907590.1| 55 SFIKYESEGDFVAG-VDvnrIFDISKSIKNDDVVEMTINE 93
                                      45788888887666.4300134455555566666666654 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 7.7e-13
                                       ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EE CS
                            PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvt 78 
                                       ip+++  a + + + ef++ +    ++sd vv     eg    a+Gd+   +  l++ +         + +  +  +
  gi|488601119|ref|YP_007907590.1| 121 IPQIDLPAKIVMDAGEFKKAIVAADKISDHVVFRTNEEGFFIEAEGDVDRITFSLSDAE-------LAEFNR-QEAK 189
                                       999*********************************************98855554443.......334444.4456 PP

                                       EEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEE.EEEE- CS
                            PCNA_C  79 ltfalkYlaeftkatsLservtlslssevPlvveykikdvgll.aylla 126
                                         f+l+Yl ef+k +s  +  t++l ++ P+ + ++++ + ++  y la
  gi|488601119|ref|YP_007907590.1| 190 SMFSLEYLKEFVKIASSGDVLTIRLGNDYPVRMVFEVAGGKVRvEYILA 238
                                       78**********************************9988775145555 PP

>> Pox_TAP  Viral Trans-Activator Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   2.6e-05      0.16      51     108 ..      51     109 ..      38     155 .. 0.85
   2 ?   -0.1   0.0     0.096   5.7e+02     146     175 ..     188     217 ..     167     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                           Pox_TAP  51 vplssnvfydgdenkvfnlpvlkvksclcsfhndavvsleadleddvvklss.ehvvsv 108
                                       vp ss + y+ + ++v  + v ++ +   s++nd vv+++ + e  +vk+ s ++ vs+
  gi|488601119|ref|YP_007907590.1|  51 VPSSSFIKYESEGDFVAGVDVNRIFDISKSIKNDDVVEMTINEESFIVKFGSvKYSVSL 109
                                       78899999**********************************99999*99662566664 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.096
                           Pox_TAP 146 artvvsldlllgfikcisqyqyltvafkdk 175
                                       a++++sl+ l  f+k  s  + lt+ + ++
  gi|488601119|ref|YP_007907590.1| 188 AKSMFSLEYLKEFVKIASSGDVLTIRLGND 217
                                       678899999999999999999999987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1532.72
//
Query:       gi|488601120|ref|YP_007907591.1|  [L=344]
Description: cell division protein pelota [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-30  105.8   3.2    2.3e-30  105.2   3.2    1.3  1  eRF1_1    eRF1 domain 1
    5.7e-24   84.8   1.8    7.1e-24   84.5   0.2    2.0  2  eRF1_3    eRF1 domain 3
    1.9e-05   25.0   0.1    0.00026   21.3   0.1    2.3  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 !  105.2   3.2   3.9e-34   2.3e-30       1     128 [.       1     123 [.       1     124 [. 0.94

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 3.9e-34
                                       HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT CS
                            eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd 77 
                                       mk+++++++++ +g ++Lipe+ +dlwhl  +i+pgd v a t+r   ++s +  +++e++++++ i+vekv+f+k 
  gi|488601120|ref|YP_007907591.1|   1 MKVVEENIKGE-KGEIKLIPENLDDLWHLKFIIEPGDIVFALTKRVS-ESSDKLRSDKEKITVRIGIEVEKVEFQKF 75 
                                       9*******965.9*******************************976.447777788******************** PP

                                       SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  78 agvlrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                       +++lr+sGk++ + e      +ht+++ ++++++iike+w++ ++er+k+a
  gi|488601120|ref|YP_007907591.1|  76 SNRLRVSGKIVAGVE---DSGHHTINISVNKEISIIKERWKKEQIERIKKA 123
                                       **************9...699****************************98 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.51   3.1e+03      85      85 ..      96      96 ..      45     144 .. 0.54
   2 !   84.5   0.2   1.2e-27   7.1e-24       4     113 .]     250     343 ..     247     343 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.51
                                      E CS
                            eRF1_3 85 v 85
                                       
  gi|488601120|ref|YP_007907591.1| 96 T 96
                                      2 PP

  == domain 2  score: 84.5 bits;  conditional E-value: 1.2e-27
                                       HHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHH CS
                            eRF1_3   4 ekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenvee 80 
                                       e++++e++l e+++d gkavYG++ev+ka+++gAve LL+++++  ++   +e+++           ++ l++ ve+
  gi|488601120|ref|YP_007907591.1| 250 EAEYMERLLAEISRD-GKAVYGKDEVEKAMNYGAVEVLLIVDDYMLKE---RENWD-----------VDGLMRAVED 311
                                       889************.***************************99986...55533...........899******* PP

                                       TT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  81 sgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       sg+kv+i+sse+e G+ql  ++gGiaa+LR+++
  gi|488601120|ref|YP_007907591.1| 312 SGGKVVILSSEFEPGKQL-VSLGGIAALLRFQI 343
                                       ******************.9***********96 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   4.4e-08   0.00026      74     126 ..     183     235 ..     131     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.4e-08
                                       TTTESEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC CS
                            eRF1_2  74 kdklkgiilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek 126
                                       + + +  ++agpgf+k++fl+ +  ++ + +kv++ +d+s+ g  g+ evl+ 
  gi|488601120|ref|YP_007907591.1| 183 NIEFRYGVVAGPGFTKDDFLKFLKDREPEIAKVMVKADASSIGVRGFIEVLRR 235
                                       44566669***************999************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2137.36
//
Query:       gi|488601121|ref|YP_007907592.1|  [L=487]
Description: prolyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  104.3   0.2    3.8e-29  101.9   0.0    1.9  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    5.9e-20   71.2   0.1    1.2e-19   70.2   0.1    1.6  1  HGTP_anticodon  Anticodon binding domain
    1.6e-05   25.0   0.8    9.4e-05   22.5   0.4    2.4  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
      0.071   12.7   0.1        4.2    7.0   0.0    2.6  2  LEDGF           Lens epithelium-derived growth factor (LEDGF)


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 !  101.9   0.0   8.4e-33   3.8e-29       2     178 ..      99     279 ..      98     280 .. 0.93
   2 ?    0.0   0.0      0.16   7.2e+02      81     110 ..     309     369 ..     303     465 .. 0.70

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 8.4e-33
                                       EEE....ETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEE.EEEEEEES CS
                                       xxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                      tRNA-synt_2b   2 kle....drndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhq.kdgyvfha 72 
                                       ++     d+ d +++L+Pt+e++++ +++ + +rs  ++Pl++yqi   +R+E++ +r+L+R+re++  k+++  h 
  gi|488601121|ref|YP_007907592.1|  99 WVThgglDELDVKLALRPTSETAMYPMFKLW-IRShTDMPLRVYQIVNTFRYETKHTRPLIRLREITSfKEAHTAHR 174
                                       5555565888999****************88.***777*****************9**********8659******* PP

                                       .GGGHHHHHHHHHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  73 .easlddslrdlikaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlga 147
                                         ++++++++d +k++++++  l +++ +i++  ++ k + + ++  f+ +++  +++++igt++ lg+++++++++
  gi|488601121|ref|YP_007907592.1| 175 nFEEAEEQVKDAVKLYKEFYDFLAIPYMVIRRPeWD-KFPGAVYTIAFDTIMP-DGRTLQIGTVHHLGNNFAKTFDI 249
                                       6699**********************9999999666.5599************.9********************** PP

                                       EEECTTSSEEEEEEEEEEEEHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 148 tvldennreksvimicaaigveRllsaileq 178
                                       ++   ++ ++ v+ +c++i+ eR ++a++++
  gi|488601121|ref|YP_007907592.1| 250 KYETPDGDHEYVHQTCYGIS-ERCVAALISV 279
                                       ********************.******9875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHT.T.SCEEEEEEGTTSC...............................B CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...............................x RF
                      tRNA-synt_2b  81 rdlikaisriferl.glefraiielmsaks...............................a 110
                                       ++++++++++f++l gl +r ++ + +++                                 
  gi|488601121|ref|YP_007907592.1| 309 EEVMEVAEKVFNKLkGLGYRTVLDS-GDERpgakyykwelkgatirieigpkevekgeivvS 369
                                       6788899999999977776655555.333334444445444444444444444444444443 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.1   2.8e-23   1.2e-19       1      90 [.     296     387 ..     296     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 2.8e-23
                                       SEEEEESSSS..HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETT CS
                    HGTP_anticodon   1 qvvviplnek..aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrd 75 
                                       q+v+ip+  k  +ee++e+a+k+ ++L+  g+r++ld  +e++g k+ +++l+g  +++++G+ke+ekg++ v+ rd
  gi|488601121|ref|YP_007907592.1| 296 QFVIIPVLYKgkEEEVMEVAEKVFNKLKGLGYRTVLDSGDERPGAKYYKWELKGATIRIEIGPKEVEKGEIVVSFRD 372
                                       789***999999999************************************************************** PP

                                       TCEEEEEETTHHHHH CS
                    HGTP_anticodon  76 treqervsldelvek 90 
                                       +r++ ++s+del ++
  gi|488601121|ref|YP_007907592.1| 373 ERKKFSMSMDELTDE 387
                                       ***********9875 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.48   2.2e+03      21      32 ..     176     187 ..     168     206 .. 0.82
   2 !   22.5   0.4   2.1e-08   9.4e-05       4      58 ..     421     477 ..     418     487 .] 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.48
                                       GHHHHHHHHHHH CS
                         ProRS-C_1  21 eeecEekIkeet 32 
                                        ee+Ee++k+ +
  gi|488601121|ref|YP_007907592.1| 176 FEEAEEQVKDAV 187
                                       5899****9976 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.1e-08
                                       HHHHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB...-SSCCCSB-TTT-SB CS
                         ProRS-C_1   4 fkealekkgfvlapWcgeeecEekIkeetgakslcipfdq...epseegtkCivcgkp 58 
                                       +   + + g++++++c +eec e I+++++a +l+   +      ++ + kCivcg++
  gi|488601121|ref|YP_007907592.1| 421 LRGWIRT-GVAIVHFCMSEECAEVIEKDVSAGILGKFEEAgewCDKDITGKCIVCGRE 477
                                       5555554.799************************955547786678899******98 PP

>> LEDGF  Lens epithelium-derived growth factor (LEDGF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.021        95      62      98 ..     163     198 ..     129     212 .. 0.78
   2 ?    7.0   0.0   0.00093       4.2      74      96 ..     303     325 ..     295     334 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.021
                             LEDGF  62 leewklteeekvefkekakeirkkAeeiYnkfkslfl 98 
                                       ++++k+ +  + +f+e  +++++ A ++Y+ f ++++
  gi|488601121|ref|YP_007907592.1| 163 ITSFKEAHTAHRNFEEAEEQVKD-AVKLYKEFYDFLA 198
                                       45667778888999999999975.999***9988776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00093
                             LEDGF  74 efkekakeirkkAeeiYnkfksl 96 
                                        +k k +e+++ Ae+++nk+k l
  gi|488601121|ref|YP_007907592.1| 303 LYKGKEEEVMEVAEKVFNKLKGL 325
                                       589999**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3180.82
//
Query:       gi|488601122|ref|YP_007907593.1|  [L=57]
Description: hypothetical protein Asulf_01625 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   59.0  12.2    5.3e-10   38.7   2.4    2.1  2  Fer4             4Fe-4S binding domain
      3e-13   49.2  12.4      4e-09   36.2   2.7    2.1  2  Fer4_6           4Fe-4S binding domain
      6e-10   39.1   9.6    7.6e-10   38.8   9.6    1.2  1  Fer4_21          4Fe-4S dicluster domain
    2.6e-09   36.6  10.8    3.5e-05   23.6   2.3    2.1  2  Fer4_2           4Fe-4S binding domain
    3.6e-09   37.1  25.1    4.4e-07   30.4  14.6    2.0  2  Fer4_7           4Fe-4S dicluster domain
    8.1e-09   35.5   8.8    1.5e-05   25.0   1.4    2.0  2  Fer4_10          4Fe-4S dicluster domain
    1.9e-07   31.1  12.1    4.3e-07   30.0  12.1    1.5  1  Fer4_9           4Fe-4S dicluster domain
      1e-05   26.4  13.3     0.0023   18.8   2.8    2.1  2  Fer4_16          4Fe-4S double cluster binding domain
    1.9e-05   24.8  14.8    0.00064   20.0   3.3    2.2  2  Fer4_4           4Fe-4S binding domain
    3.1e-05   24.6  11.7      0.023   15.4   3.8    2.7  3  Fer4_15          4Fe-4S single cluster domain
    0.00041   20.8  14.3      0.015   15.9   3.8    2.1  2  Fer4_17          4Fe-4S dicluster domain
    0.00047   20.5  15.0     0.0064   16.9   3.4    2.1  2  Fer4_8           4Fe-4S dicluster domain
    0.00058   20.3  11.4      0.019   15.5   2.3    2.1  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
     0.0022   18.8  18.8      0.028   15.3   6.2    2.2  2  Fer4_3           4Fe-4S binding domain
     0.0022   18.2   2.1     0.0022   18.2   2.1    2.0  2  Fer4_18          4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.37   10.5  10.1       0.12   12.0   1.7    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        8.6    6.2  10.2         12    5.8   1.1    2.2  2  zf-C2H2_11       zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   2.4   4.7e-09   4.9e-06       2      22 ..       3      23 ..       2      23 .. 0.95
   2 !   38.7   2.4     5e-13   5.3e-10       1      24 []      31      54 ..      31      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.7e-09
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                      vid  kC +CGaC++vC ++A
  gi|488601122|ref|YP_007907593.1|  3 VIDRYKCAYCGACISVCKFNA 23
                                      89*****************98 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 5e-13
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      v +deekC+ C+ Cv vCP gAI+
  gi|488601122|ref|YP_007907593.1| 31 VRVDEEKCTLCKMCVRVCPMGAIS 54
                                      579*******************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 !   19.0   2.3     1e-06    0.0011       3      23 ..       3      23 ..       1      24 [. 0.93
   2 !   36.2   2.7   3.8e-12     4e-09       1      24 []      30      53 ..      30      53 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                            Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                      +id+ kC  Cg+C++vC ++a
  gi|488601122|ref|YP_007907593.1|  3 VIDRYKCAYCGACISVCKFNA 23
                                      89****************998 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 3.8e-12
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +v++d++kC+ C  CvrvCP+gai
  gi|488601122|ref|YP_007907593.1| 30 FVRVDEEKCTLCKMCVRVCPMGAI 53
                                      699********************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 !   38.8   9.6   7.2e-13   7.6e-10       2      58 ..       3      54 ..       2      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.2e-13
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      +id+ kC  Cg C+ +C+ ++ + +e    t ++v e++C+ C++C+ vCP+ ++i+
  gi|488601122|ref|YP_007907593.1|  3 VIDRYKCAYCGACISVCKFNANELVE----TFVRVDEEKCTLCKMCVRVCPM-GAIS 54
                                      69****************98888886....5799*****************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 !   18.4   1.5   1.6e-06    0.0017       4      20 ..       3      19 ..       1      21 [. 0.91
   2 !   23.6   2.3   3.3e-08   3.5e-05       4      21 ..      32      49 ..      30      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaC 20
                                      v+d+ +C  CgaC+s+C
  gi|488601122|ref|YP_007907593.1|  3 VIDRYKCAYCGACISVC 19
                                      799************** PP

  == domain 2  score: 23.6 bits;  conditional E-value: 3.3e-08
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                       vd+++C+ C+ Cv +CP
  gi|488601122|ref|YP_007907593.1| 32 RVDEEKCTLCKMCVRVCP 49
                                      69**************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.7   4.3e-06    0.0046      33      52 .]       4      23 ..       2      23 .. 0.89
   2 !   30.4  14.6   4.2e-10   4.4e-07       1      52 []       8      52 ..       8      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.3e-06
                            Fer4_7 33 idpekClgCgaCvavCPtga 52
                                      id  kC +CgaC++vC ++a
  gi|488601122|ref|YP_007907593.1|  4 IDRYKCAYCGACISVCKFNA 23
                                      67889***********9987 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 4.2e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C  CgaC ++C+ +a el e         v++d+ekC+ C++Cv+vCP ga
  gi|488601122|ref|YP_007907593.1|  8 KCAYCGACISVCKFNANELVET-------FVRVDEEKCTLCKMCVRVCPMGA 52
                                      7******************987.......489*****************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 !   15.5   1.1   1.3e-05     0.014       2      19 ..       2      19 ..       1      29 [. 0.77
   2 !   25.0   1.4   1.4e-08   1.5e-05       2      23 ..      31      52 ..      30      57 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                           Fer4_10  2 vvidddtCirCgkCvkaC 19
                                      +vid+ +C  Cg+C ++C
  gi|488601122|ref|YP_007907593.1|  2 LVIDRYKCAYCGACISVC 19
                                      578888888888888888 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.4e-08
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      v++d+++C+ C+ Cv++CP+ +
  gi|488601122|ref|YP_007907593.1| 31 VRVDEEKCTLCKMCVRVCPMGA 52
                                      6899****************44 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0  12.1   4.1e-10   4.3e-07       1      51 []       8      53 ..       8      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.1e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC+ CgaC+++C++++++   +e+++r+++   e+C+ C+ Cv +Cp gai
  gi|488601122|ref|YP_007907593.1|  8 KCAYCGACISVCKFNANE--LVETFVRVDE---EKCTLCKMCVRVCPMGAI 53
                                      7*************9976..5666777655...48*************997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   5.8   0.00067      0.71       1      20 [.       8      27 ..       8      38 .. 0.72
   2 !   18.8   2.8   2.2e-06    0.0023       1      20 [.      37      56 ..      37      57 .] 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C  Cg+C++vC  na +  
  gi|488601122|ref|YP_007907593.1|  8 KCAYCGACISVCKFNANELV 27
                                      59999999999988885544 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.2e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C+ C+ C+ vCP +ai+ +
  gi|488601122|ref|YP_007907593.1| 37 KCTLCKMCVRVCPMGAISVE 56
                                      5****************865 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   3.7   0.00066       0.7       3      17 .]       8      22 ..       6      22 .. 0.87
   2 !   20.0   3.3   6.1e-07   0.00064       2      17 .]      36      51 ..      35      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C  Cg+C+++C+++
  gi|488601122|ref|YP_007907593.1|  8 KCAYCGACISVCKFN 22
                                      6888********975 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6.1e-07
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      e+C+ C+ Cv++CP+g
  gi|488601122|ref|YP_007907593.1| 36 EKCTLCKMCVRVCPMG 51
                                      89************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 !   13.4   0.7   9.1e-05     0.096       2      19 ..       3      20 ..       2      28 .. 0.88
   2 !   15.4   3.8   2.2e-05     0.023       1      19 [.      31      49 ..      31      52 .. 0.95
   3 ?    5.8   0.1     0.022        23      57      66 .]      46      55 ..      45      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-05
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      v+Dr +C  cg+C+ +++
  gi|488601122|ref|YP_007907593.1|  3 VIDRYKCAYCGACISVCK 20
                                      79*************996 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.2e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      V+vD+++C+ c +Cv+++p
  gi|488601122|ref|YP_007907593.1| 31 VRVDEEKCTLCKMCVRVCP 49
                                      89****************8 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.022
                           Fer4_15 57 raCPvdAIrv 66
                                      r+CP +AI+v
  gi|488601122|ref|YP_007907593.1| 46 RVCPMGAISV 55
                                      89******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 !   11.3   2.7   0.00037      0.39       1      17 [.       8      24 ..       8      35 .. 0.85
   2 !   15.9   3.8   1.4e-05     0.015      44      59 ..      36      51 ..      32      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                           Fer4_17  1 rCiqCgyClpeCpsyea 17
                                      +C+ Cg+C+ +C ++++
  gi|488601122|ref|YP_007907593.1|  8 KCAYCGACISVCKFNAN 24
                                      6***********99876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.4e-05
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C+ C++C+r+CP+g
  gi|488601122|ref|YP_007907593.1| 36 EKCTLCKMCVRVCPMG 51
                                      5899999999999997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   2.8   0.00033      0.35       3      17 ..       7      21 ..       5      36 .. 0.73
   2 !   16.9   3.4   6.1e-06    0.0064      49      64 ..      36      51 ..      25      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      +kC  CgaC s C +
  gi|488601122|ref|YP_007907593.1|  7 YKCAYCGACISVCKF 21
                                      578888888888864 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.1e-06
                            Fer4_8 49 wsCttcgaCtevCpvg 64
                                      ++Ct c++C++vCp+g
  gi|488601122|ref|YP_007907593.1| 36 EKCTLCKMCVRVCPMG 51
                                      68************87 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   1.9   0.00075      0.79       1      16 [.       4      19 ..       4      24 .. 0.95
   2 !   15.5   2.3   1.8e-05     0.019       1      17 [.      33      49 ..      33      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00075
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      +Dr +C  cgaC +++
  gi|488601122|ref|YP_007907593.1|  4 IDRYKCAYCGACISVC 19
                                      89************99 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.8e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VD+++C+ c+ Cv ++P
  gi|488601122|ref|YP_007907593.1| 33 VDEEKCTLCKMCVRVCP 49
                                      9**************** PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   4.6    0.0019         2       1      15 []       9      23 ..       9      23 .. 0.87
   2 !   15.3   6.2   2.7e-05     0.028       1      15 []      38      52 ..      38      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C  CgaC  vC  +A
  gi|488601122|ref|YP_007907593.1|  9 CAYCGACISVCKFNA 23
                                      556********9987 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.7e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      Ct C  Cv+vCP gA
  gi|488601122|ref|YP_007907593.1| 38 CTLCKMCVRVCPMGA 52
                                      ****99******998 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.7      0.02        22      60      72 ..       8      20 ..       4      24 .. 0.71
   2 !   18.2   2.1   2.1e-06    0.0022      54      74 ..      31      51 ..      20      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.02
                           Fer4_18 60 dcidcescvkvcP 72
                                      +c  c++c++vc 
  gi|488601122|ref|YP_007907593.1|  8 KCAYCGACISVCK 20
                                      5777777777775 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.1e-06
                           Fer4_18 54 kekgagdcidcescvkvcPtg 74
                                       + ++ +c+ c++cv+vcP+g
  gi|488601122|ref|YP_007907593.1| 31 VRVDEEKCTLCKMCVRVCPMG 51
                                      5567889************98 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.7   0.00011      0.12       5      27 ..       5      27 ..       3      27 .. 0.82
   2 ?    3.5   1.5     0.053        56       8      22 ..      37      51 ..      33      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      -EEE-TTT--EEEECC--SS-EE CS
                   Desulfoferrod_N  5 evYkCevCGniVeVleaGgGeLV 27
                                      + YkC  CG  + V +  + eLV
  gi|488601122|ref|YP_007907593.1|  5 DRYKCAYCGACISVCKFNANELV 27
                                      67*********999877666666 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.053
                                      E-TTT--EEEECC-- CS
                   Desulfoferrod_N  8 kCevCGniVeVleaG 22
                                      kC++C   V V   G
  gi|488601122|ref|YP_007907593.1| 37 KCTLCKMCVRVCPMG 51
                                      9****9999998777 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 ?    5.8   1.1     0.011        12       5      13 ..       7      15 ..       6      18 .. 0.87
   2 ?    5.2   2.3     0.017        18       6      13 ..      37      44 ..      36      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                        zf-C2H2_11  5 cqCleCGlc 13
                                      ++C  CG c
  gi|488601122|ref|YP_007907593.1|  7 YKCAYCGAC 15
                                      69******* PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                        zf-C2H2_11  6 qCleCGlc 13
                                      +C++C++c
  gi|488601122|ref|YP_007907593.1| 37 KCTLCKMC 44
                                      8******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 410.79
//
Query:       gi|488601123|ref|YP_007907594.1|  [L=391]
Description: 2,3-di-O-geranylgeranylglyceryl phosphate reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   75.9   3.2    6.5e-20   71.7   3.2    2.3  1  FAD_binding_3   FAD binding domain
    1.9e-12   47.3   0.6    3.2e-12   46.5   0.6    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    2.1e-08   33.7   1.1    3.6e-08   32.9   0.4    1.7  2  FAD_binding_2   FAD binding domain
    5.8e-08   31.8   1.3    1.2e-07   30.9   0.2    1.9  2  HI0933_like     HI0933-like protein
    9.1e-08   31.4   2.1       0.01   14.7   0.2    3.0  2  Trp_halogenase  Tryptophan halogenase
    1.7e-07   31.2   1.9     0.0031   17.1   0.3    2.3  2  DAO             FAD dependent oxidoreductase
    2.2e-07   30.3   0.0    4.7e-05   22.6   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    2.2e-06   27.8   0.0    4.9e-06   26.7   0.0    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    6.6e-06   25.6   5.1    2.2e-05   23.9   3.4    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.2e-05   22.5   1.2    0.00019   20.7   1.4    1.9  2  GIDA            Glucose inhibited division protein A
    0.00021   20.6   0.1    0.00065   19.0   0.1    1.8  1  Thi4            Thi4 family
    0.00041   20.9   0.8      0.026   15.1   0.2    2.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0097   14.4   0.1      0.016   13.6   0.1    1.4  1  FMO-like        Flavin-binding monooxygenase-like
  ------ inclusion threshold ------
      0.011   15.6   0.3      0.031   14.1   0.0    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.037   13.3   1.3      0.043   13.1   0.4    1.5  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.24   11.4   0.7        4.5    7.2   0.1    2.2  2  NAD_binding_9   FAD-NAD(P)-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 !   71.7   3.2   5.8e-23   6.5e-20       2     312 ..       5     298 ..       4     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 5.8e-23
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS.--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr.adglnqrtmellrqlGledrilaegapnelmgealy 77 
                                       +dV+++GaGp G m+a+  +e G +v+lvekr++     r a+g++++ +e + +  ++++ +a+     ++g + y
  gi|488601123|ref|YP_007907594.1|   5 YDVVVIGAGPGGSMAAKTCAEEGLNVLLVEKRQEIGAPVRcAEGISKEGLERFFE--IDRKWIARE----VSGAIIY 75 
                                       79******************************998777754999***99997654..678887776....8889999 PP

                                       EECCCCCEEEEEHHCH.HCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlele.sspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetv 153
                                        +       +++l+ e ++ e   v+  + ++r+L+  a+++g++v  kt  +++e++++g   ++r k+ ge+++v
  gi|488601123|ref|YP_007907594.1|  76 SP----DGTELKLSSEmAGNEVGFVLERKIFDRDLARMASKAGAEVIVKTTATGMEREKDG--LRIRLKRMGEDYEV 146
                                       99....3344555544266677778899999******************************..57888999****** PP

                                       EEEEEEE--GTT-HHHHHHTGGEEEE....EEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEEEEEECCETEEEE CS
                     FAD_binding_3 154 rakYlvGaDGgrStvrktlgiefege....etvyeagvldvlfdadlsdiveplvlilsaesrgvmviPlentlerf 226
                                       +ak +vGaDG+ S+v k +gi+ + +    e+ ++  + ++ fd d+      +++i+++  +g            +
  gi|488601123|ref|YP_007907594.1| 147 TAKIVVGADGVESRVGKWAGIDTTVKlgeiESCVQYLMTNIEFDPDFC-----HFWIGQKYAPGG-----------Y 207
                                       *********************977652112445566777888888888.....9*****999984...........3 PP

                                       EEEEECCE-GGGS....CCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEE.EESSSEETTEEE-GGGTEEE-S CS
                     FAD_binding_3 227 yvqvearaekeer....sekfteeevkarlreivgektldveieevsawtvaqr.vaekyrkgrvflaGDAaHihpP 298
                                       +++++ +++ ++      + +t++ +k  l++ v+e+  d +i e+ + +v      ++  +++v+l+GDAa    P
  gi|488601123|ref|YP_007907594.1| 208 VWLFPKGESSANVgigiLPTMTKKTAKWWLDRFVQEYYPDGKIVEFVVGGVPVTgPIDTAVSDNVMLVGDAARHADP 284
                                       444444444443333346778888999999999999999999999998888654257888899************** PP

                                       TTSHHHHHHHHHHH CS
                     FAD_binding_3 299 tgGqGlNtaiqDav 312
                                        +G G+  ai+  +
  gi|488601123|ref|YP_007907594.1| 285 ITGGGIANAIKGGY 298
                                       *****999987665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.6   2.9e-15   3.2e-12       1     158 [.       6     171 ..       6     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.9e-15
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee...qvvtgiareflerlrq.rgga 73 
                                       DvvV+G+gp+G +AA ++a++G +vlLve+r+ +G  +  + + + +g +  +      + iare+  ++    +g 
  gi|488601123|ref|YP_007907594.1|   6 DVVVIGAGPGGSMAAKTCAEEGLNVLLVEKRQEIGAPVRCAEGISKEGLE--RffeIDRKWIAREVSGAIIYsPDGT 80 
                                       9**********************************777666666666644..2232223347777777776653333 PP

                      FAD_oxidored  74 ..rlkkrskwn....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                         +l+++++ n    + e +++ + l  m ++ag +v+ +t+++++e+e+ +   +++++  ++++++Ak+++ A g
  gi|488601123|ref|YP_007907594.1|  81 elKLSSEMAGNevgfVLERKIFDRDLARMASKAGAEVIVKTTATGMEREK-DGLRIRLKRMGEDYEVTAKIVVGADG 156
                                       2322222222245669********************************95.567788865556**********9977 PP

                      FAD_oxidored 145 .dGdlaalaGvpyrv 158
                                        +  ++ +aG+ ++v
  gi|488601123|ref|YP_007907594.1| 157 vESRVGKWAGIDTTV 171
                                       678888888888776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.4   3.2e-11   3.6e-08       1      43 [.       6      48 ..       6      51 .. 0.94
   2 ?   -1.8   0.0       1.1   1.2e+03      78     117 ..     103     141 ..      66     169 .. 0.61

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.2e-11
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                      Dv+ViG+G +G +AA ++ae+Gl+v++vek qe g    +++G
  gi|488601123|ref|YP_007907594.1|  6 DVVVIGAGPGGSMAAKTCAEEGLNVLLVEKRQEIGAPVRCAEG 48
                                      9********************************9998888888 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                       -HHHHHHHHHTHHHHHHHHHHTT----BCCTS.SB-EEE-T CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeelgvpfsrtedg.pvdvrelG 117
                                       d++l+++  +a++e +   +++g+   +  dg +++++++G
  gi|488601123|ref|YP_007907594.1| 103 DRDLARMASKAGAEVIVKTTATGMEREK--DGlRIRLKRMG 141
                                       4444455555555555444444444444..33444444444 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   0.2     1e-10   1.2e-07       1      40 [.       5      44 ..       5      48 .. 0.93
   2 ?   -1.4   0.0      0.64   7.2e+02     115     163 ..     106     156 ..     103     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1e-10
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                      +dv+viG+G+ G maA ++a++g +Vll+ek +++g  ++
  gi|488601123|ref|YP_007907594.1|  5 YDVVVIGAGPGGSMAAKTCAEEGLNVLLVEKRQEIGAPVR 44
                                      59*********************************98766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.64
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE--- CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktk...seeeleadklvlAtG 163
                                       l + +++ag ++ ++t+ +++e+e+dg +r+++k   ++ e++a+ +v A G
  gi|488601123|ref|YP_007907594.1| 106 LARMASKAGAEVIVKTTATGMEREKDG-LRIRLKrmgEDYEVTAKIVVGADG 156
                                       556678899999999999999999999.888884232344555555555555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   9.2e-06      0.01       1      37 [.       6      40 ..       6      73 .. 0.72
   2 !   13.5   0.1   2.1e-05     0.024     145     372 ..      91     326 ..      76     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.2e-06
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS.S- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee.ig 37
                                      ++v++G+G+ G++aA ++a+ +   l+v+lve+ + ig
  gi|488601123|ref|YP_007907594.1|  6 DVVVIGAGPGGSMAAKTCAEEG---LNVLLVEKRQeIG 40
                                      69*****************999...9******965144 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.1e-05
                                       S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEE.EEE-TTS.-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT- CS
                    Trp_halogenase 145 lsyAyhldaalyakfLrrvaearGvtrvegkvve.vqldedg.rveslrledgreveadlfiDcsGfrgllieqaLk 219
                                        + ++ l+++ +++ L r+a ++G +++  + ++ ++ ++dg r+   r+ ++ ev a +++ + G ++++ + a  
  gi|488601123|ref|YP_007907594.1|  91 NEVGFVLERKIFDRDLARMASKAGAEVIVKTTATgMEREKDGlRIRLKRMGEDYEVTAKIVVGADGVESRVGKWAGI 167
                                       5678999******************99876666515555577467777888899****************9888855 PP

                                       --EEE-TTT----EEEEEEEE--H.---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT- CS
                    Trp_halogenase 220 tgfedwsdvLltdrAlavqvesee.lvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldg 294
                                        ++ +  ++  + + l +++e+++   + + +      G +W  P  ++  n G+     ++ + +A   l + ++ 
  gi|488601123|ref|YP_007907594.1| 168 DTTVKLGEIESCVQYLMTNIEFDPdFCHFWIGQKYAPGGYVWLFPKGESSANvGIGILPTMT-KKTAKWWLDRFVQ- 242
                                       55566666666667778888888756666677888899999999999999998888888776.6677666666665. PP

                                       -TTTS-EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHHHHHHHH CS
                    Trp_halogenase 295 kleaeprkirfttGr......rkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepaaiaefnr 365
                                       +   + + ++f +G         +a + nv+++G+a+   +P+ + +i+ + ++ +   ++  + +d++   +ef r
  gi|488601123|ref|YP_007907594.1| 243 EYYPDGKIVEFVVGGvpvtgpIDTAVSDNVMLVGDAARHADPITGGGIANAIKGGYFAGKVAKEAVDAENYSKEFLR 319
                                       4455558899998888888889999***********************99999999998888888888899999999 PP

                                       HHHHHHH CS
                    Trp_halogenase 366 evarele 372
                                       +++++++
  gi|488601123|ref|YP_007907594.1| 320 RYDEMWK 326
                                       9988886 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   2.8e-06    0.0031       1      33 [.       6      40 ..       6      52 .. 0.93
   2 !   13.5   0.1   3.6e-05      0.04     150     318 ..     104     264 ..      44     294 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.8e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dvv+iG+G  G+ +A   a++g  V+l+ek+ ++g
  gi|488601123|ref|YP_007907594.1|  6 DVVVIGAGPGGSMAAKTCAEEGlnVLLVEKRQEIG 40
                                      9******************************8887 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEE.E.EEEEEEE--GGGHH..HHHTTCTTT..SEEE CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgve.rttp.gen.d.aadavVnaaGawsd..llgllkeld..lpis 218
                                       + lar a ++G+e++ +t++tg e+e     g++ r ++ ge  + +a+ vV a G+ s+  ++     +d  +++ 
  gi|488601123|ref|YP_007907594.1| 104 RDLARMASKAGAEVIVKTTATGMERE---KDGLRiRLKRmGEDyEvTAKIVVGADGVESRvgKW---AGIDttVKLG 174
                                       459*******************9875...34555577777887433445599999999986555...3333112333 PP

                                       E..EEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEE..TTSEEEEEESSEEETTCSS......TSCSHHHH CS
                               DAO 219 p..vrgqvlvlkplseklvspaailpvpetdddgrgvyvtpr..kdgrvlvGgtadeesgddd......pevdeedi 285
                                             q+l++ +++               d d+ ++ + +   ++g v++ + +  es+ ++      + +   + 
  gi|488601123|ref|YP_007907594.1| 175 EieSCVQYLMT-NIEF--------------DPDFCHFWIGQKyaPGGYVWLFPKG--ESSANVgigilpTMTKKTAK 234
                                       31123333333.3322..............2222222222222234444444444..22222233433133334444 PP

                                       HHHHHHHHHHSGGGCGEEEEEEEEEEETTSSEE CS
                               DAO 286 dellealrklfPqlgdvlrkwaGlrplpdglpl 318
                                        +l + +++++P+ g++++  +G  p   ++p+
  gi|488601123|ref|YP_007907594.1| 235 WWLDRFVQEYYPD-GKIVEFVVGGVP--VTGPI 264
                                       4488888888888.777766666666..33344 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   4.2e-08   4.7e-05       1     145 [.       6     161 ..       6     192 .. 0.73
   2 !    5.6   0.0     0.006       6.7     237     306 ..     252     327 ..     239     358 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.2e-08
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleec..vehsW.....sgtivyld 70 
                                       DvvviGaGp g   A+    a+ gl+v+l+e  +++   +  v + e+   ++le++  ++ +W     sg+i+y +
  gi|488601123|ref|YP_007907594.1|   6 DVVVIGAGPGGSMAAKTC--AEEGLNVLLVEKRQEI---GAPVRCAEGISKEGLERFfeIDRKWiarevSGAIIYSP 77 
                                       9********997766666..9*************99...55566777666666777633556774444467889999 PP

                     Lycopene_cycl  71 dgkkillg.....raYg.rvsskrlkeellerlvengvk.lleakvesveeeeageslvvleggr..kirarlvvda 138
                                       dg + +l+      + g  +++k + + l++   ++g++  ++ +++ +e e++g +      g+  ++ a++vv a
  gi|488601123|ref|YP_007907594.1|  78 DGTELKLSsemagNEVGfVLERKIFDRDLARMASKAGAEvIVKTTATGMEREKDGLRIRLKRMGEdyEVTAKIVVGA 154
                                       99988877675553334135788888888888887776625788899999999977666555555569********* PP

                     Lycopene_cycl 139 rglaslk 145
                                        g+ s+ 
  gi|488601123|ref|YP_007907594.1| 155 DGVESRV 161
                                       **77765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.006
                     Lycopene_cycl 237 eeEqgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres........slsarawa 305
                                       e   g +Pv  g+   ++  +v+ +G aa    P TG  +a++++    +a  +a+ +            ++++ w+
  gi|488601123|ref|YP_007907594.1| 252 EFVVGGVPV-TGPIDTAVSDNVMLVGDAARHADPITGGGIANAIKGGY-FAGKVAKEAVDAenyskeflRRYDEMWK 326
                                       555677999.44445556667**********************98765.6666666555443334444444444444 PP

                     Lycopene_cycl 306 t 306
                                       +
  gi|488601123|ref|YP_007907594.1| 327 N 327
                                       4 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   4.4e-09   4.9e-06       1      36 [.       9      44 ..       9      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.4e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      ++GaG +G+ aA ++a++g++vll+ekr+ +G  ++
  gi|488601123|ref|YP_007907594.1|  9 VIGAGPGGSMAAKTCAEEGLNVLLVEKRQEIGAPVR 44
                                      8*******************************6544 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 !   23.9   3.4     2e-08   2.2e-05       1     119 [.       5     167 ..       5     182 .. 0.62
   2 ?   -2.7   0.0       2.3   2.6e+03     269     279 ..     270     282 ..     256     337 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2e-08
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHH................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve.legtclnggcllskallgvaedaeias................... 57 
                                       +dvvviG+Gp+G  aa+t a+ g++v+lve +++    ++c      +g +++ ei +                   
  gi|488601123|ref|YP_007907594.1|   5 YDVVVIGAGPGGSMAAKTCAEEGLNVLLVEkRQEIGAPVRCAEGISKEGLERFFEIDRkwiarevsgaiiyspdgte 81 
                                       69***************************854444445556665555555555555557777777777777788777 PP

                                       ..........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE--- CS
                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ..........................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtG 108
                                                                 +  +k   g e++ ++++++++++k  + ++ k+ g+  +++++ +v A G
  gi|488601123|ref|YP_007907594.1|  82 lklssemagnevgfvlerkifdrdlaRMASKA--GAEVIVKTTATGMEREKDGLRIRLKRMGEDYEVTAKIVVGADG 156
                                       76666666666666666666655544222222..3333333335555555555555444447777777777777777 PP

                                       EEE-BCTCTTC CS
                                       xxxxxxxxxxx RF
                       Pyr_redox_2 109 ssprdlgipGv 119
                                        ++r  +  G 
  gi|488601123|ref|YP_007907594.1| 157 VESRVGKWAGI 167
                                       76666555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                                       TTEEE-GGGC..T CS
                                       xxxxxxxxxx..x RF
                       Pyr_redox_2 269 pgiyaiGDva..g 279
                                       +++ ++GD a   
  gi|488601123|ref|YP_007907594.1| 270 DNVMLVGDAArhA 282
                                       5666666666330 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.4   1.7e-07   0.00019       1      41 [.       6      46 ..       6     152 .. 0.85
   2 ?   -1.4   0.0      0.87   9.7e+02     282     317 ..     144     179 ..      98     188 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.7e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSS CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCn 41
                                      dv+ViG+G  G+ AA ++a+ G++vlL+ ++ +  a + C 
  gi|488601123|ref|YP_007907594.1|  6 DVVVIGAGPGGSMAAKTCAEEGLNVLLVEKRQEIGAPVRCA 46
                                      79**************************5544444445555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.87
                                       T-S--EEEEEESSTT--EEEEET----S-HHHHHHH CS
                              GIDA 282 dkeshqvfLepegleteliylvgfstslpeevqkev 317
                                        +  + + +  +g+e++     g+ t+ ++++ +  
  gi|488601123|ref|YP_007907594.1| 144 YEVTAKIVVGADGVESRVGKWAGIDTTVKLGEIESC 179
                                       444566777777777777777777777777666555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   5.8e-07   0.00065      18      54 ..       5      40 ..       2      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.8e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                       Dvv++GaG+ G  aa++ a++ +l+v+++e++  +G
  gi|488601123|ref|YP_007907594.1|  5 YDVVVIGAGPGGSMAAKTCAEE-GLNVLLVEKRQEIG 40
                                      6*********************.********998877 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   2.4e-05     0.026       2      43 ..       7      42 ..       6      60 .. 0.84
   2 ?    3.0   0.0      0.14   1.5e+02      46      78 ..     106     137 ..      93     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeas 43
                                      vvv+G+G  g ++A++ ae g +V +ve + ++       a 
  gi|488601123|ref|YP_007907594.1|  7 VVVIGAGPGGSMAAKTCAEEGLNVLLVEKRQEIG------AP 42
                                      8*******************************98......44 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                                       HHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  46 lqeklekngievllntkveeiegsedgvesvkl 78 
                                       l++  +k g ev+ +t+++ +e ++dg++ ++l
  gi|488601123|ref|YP_007907594.1| 106 LARMASKAGAEVIVKTTATGMEREKDGLR-IRL 137
                                       56677899**************9999954.665 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.5e-05     0.016       4      50 ..       7      54 ..       4      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                          FMO-like  4 vaviGaGvsGlasikccleegleptcfersddiGGlwrfken.veeGr 50
                                      v viGaG  G ++ k+c eegl+    e+ ++iG   r  e  ++eG 
  gi|488601123|ref|YP_007907594.1|  7 VVVIGAGPGGSMAAKTCAEEGLNVLLVEKRQEIGAPVRCAEGiSKEGL 54
                                      89********************************98888775256665 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05     0.031       2      34 ..       7      39 ..       6      70 .. 0.85
   2 ?   -2.6   0.0         4   4.5e+03      14      51 ..     106     142 ..     104     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      v viGaG  G+  a+ +a++gl+V lv+ ++e+
  gi|488601123|ref|YP_007907594.1|  7 VVVIGAGPGGSMAAKTCAEEGLNVLLVEKRQEI 39
                                      89**************************99875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4
                                       HHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N  14 iaavfasagleVvlvdiseealekalekieksleklve 51 
                                       +a ++ +ag eV +  + +  +e+ ++ ++ +l+++ e
  gi|488601123|ref|YP_007907594.1| 106 LARMASKAGAEVIVKTT-ATGMEREKDGLRIRLKRMGE 142
                                       56777778888865544.44566666666666666555 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   0.4   3.9e-05     0.043       1      33 [.       8      40 ..       8      45 .. 0.89
   2 ?   -2.9   0.0       2.9   3.2e+03     180     211 ..     107     138 ..     103     157 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                      ++iGaGP G  aa ++ + gl ++l +Ek  +ig
  gi|488601123|ref|YP_007907594.1|  8 VVIGAGPGGSMAAKTCAEEGL-NVLLVEKRqEIG 40
                                      79*******************.79****985666 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                       Pyr_redox_3 180 AlelvrkgaeVtvvtrgseiekeesdpsyslk 211
                                       A    ++gaeV v t  + +e+e++   ++lk
  gi|488601123|ref|YP_007907594.1| 107 ARMASKAGAEVIVKTTATGMEREKDGLRIRLK 138
                                       44455566666666666655555544444443 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 ?    7.2   0.1    0.0041       4.5       1      37 [.       8      40 ..       8      48 .. 0.81
   2 ?    2.4   0.0      0.13   1.4e+02     107     152 ..     105     154 ..      97     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0041
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepg 37
                                      +++GaGp G ++++  +++      l++ l+++ +e+g
  gi|488601123|ref|YP_007907594.1|  8 VVIGAGPGGSMAAKTCAEE-----GLNVLLVEKrQEIG 40
                                      69********999988877.....69999999944445 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                     NAD_binding_9 107 llarlpegvtvev.hraevvdleeradgqavll.adgas..laadaVvLA 152
                                        lar+ ++   ev ++++++ +e+++dg +++l + g+   ++a+ Vv A
  gi|488601123|ref|YP_007907594.1| 105 DLARMASKAGAEViVKTTATGMEREKDGLRIRLkRMGEDyeVTAKIVVGA 154
                                       44555444444441699***********9999843444322677777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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 0.30s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 2433.02
//
Query:       gi|488601124|ref|YP_007907595.1|  [L=156]
Description: arginine decarboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-52  176.8   0.2      3e-52  176.7   0.2    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.7   0.2   1.7e-56     3e-52       1     162 []       4     155 ..       4     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.7 bits;  conditional E-value: 1.7e-56
                          PvlArgDC   1 vPkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepg 77 
                                       vPkkvfl++G+g+++++l sF+lAL+dAgIe+fNLv+vSSilPp++eiv +eeglk+l+pG+iv++vmar +sn+ g
  gi|488601124|ref|YP_007907595.1|   4 VPKKVFLVSGKGSHSDALVSFELALRDAGIEKFNLVTVSSILPPNCEIVDKEEGLKHLSPGEIVFTVMARYTSNQAG 80 
                                       7**************************************************************************** PP

                          PvlArgDC  78 rliaaavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrglleekiietkeievaaveakvekygt 154
                                       + i a++g+a+p++   +Gy++Eysg + +++ +e++ae++a+ m+++ +g   + +++++ +e    +a+v++++t
  gi|488601124|ref|YP_007907595.1|  81 KKIFASIGLARPEK--GHGYLTEYSG-EWDKSVDEKHAEKMAELMVES-MGS--KATFKKTVFE----VAEVREFTT 147
                                       **********9966..**********.66******************8.554..3555544444....34689**** PP

                          PvlArgDC 155 vlaaavfv 162
                                       v++aavfv
  gi|488601124|ref|YP_007907595.1| 148 VVSAAVFV 155
                                       ******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1077.32
//
Query:       gi|488601125|ref|YP_007907596.1|  [L=538]
Description: amino acid:proton symporter, ABT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-30  105.5  43.0    3.8e-30  105.1  43.0    1.2  1  AA_permease_2    Amino acid permease
    1.1e-19   70.4  39.1    1.5e-19   69.9  39.1    1.3  1  AA_permease      Amino acid permease
    5.1e-10   39.5   0.1    5.1e-10   39.5   0.1    1.6  2  NTP_transf_2     Nucleotidyltransferase domain
    5.7e-07   29.5   0.2    5.7e-07   29.5   0.2    2.1  2  Polbeta          Polymerase beta, Nucleotidyltransferase
     0.0009   18.2  15.2     0.0009   18.2  15.2    2.2  2  Spore_permease   Spore germination protein
  ------ inclusion threshold ------
      0.022   13.8  22.8       0.04   13.0  22.8    1.4  1  Trp_Tyr_perm     Tryptophan/tyrosine permease family
      0.027   14.2   6.9       0.81    9.5   0.5    2.7  2  SP_C-Propep      Surfactant protein C, N terminal propeptide
        1.5    8.5   6.7       0.26   10.9   1.5    2.4  2  RhodobacterPufX  Intrinsic membrane protein PufX
        2.6    8.2  12.4       0.11   12.7   0.8    3.1  3  DUF3302          Protein of unknown function (DUF3302)


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 !  105.1  43.0   1.9e-33   3.8e-30       1     420 [.       5     403 ..       5     409 .. 0.81

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 1.9e-33
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       ++++ af + +g +ig gif++   ++     a+ + +++a li  la ++ ya ls ++p++gG + +  +a+g  
  gi|488601125|ref|YP_007907596.1|   5 IGFWEAFSIGVGGMIGGGIFAVLglSIQLSKSAAPVAFLLAGLIA-LATAYSYARLSVRFPSEGGTIEFIVRAYGT- 79 
                                       89*******************977555445555555555555555.9**********99***************84. PP

                     AA_permease_2  76 vaflsawfn...wfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgi 149
                                        + +s+ +n   + +y+++l++++++++sy +n+lg ++++   +  l++ ++++l++++n++g  +s+k    l++
  gi|488601125|ref|YP_007907596.1|  80 -GLFSGTLNvllLASYIVMLSLYAYAFGSYGANMLG-FINP-ILAKHLLITLVIVLFTVVNALGAVISGKTEDLLVV 153
                                       .666666664447889999999***********997.5544.3466888999************************* PP

                     AA_permease_2 150 lkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk.kdvpkaifi 225
                                       lk+  +l+i+  +g+++v  +++        + +++  ++v++g+  +++++ Gfe +an  + v+    +pka   
  gi|488601125|ref|YP_007907596.1| 154 LKLA-ILLIVAGAGMAFV--DTARL----SPSNWADPVSIVAGGMI-IFLAYEGFELIANTGSDVEDpSILPKAFYA 222
                                       ***6.5444444666666..55542....23556666667777765.9*******************556******* PP

                     AA_permease_2 226 gllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvleal 302
                                       ++l+v+v+y+ v+++ +g +p d i + ++   ++a+ ++ + g ++++++ +++  s   ain+ ++g+ r  + +
  gi|488601125|ref|YP_007907596.1| 223 AVLLVVVVYVMVAVVTVGNLPYDMIIKARDY--ALAAAAKPSLGEAGFWLITLAALASTSSAINATLYGTVRASYMV 297
                                       *************************998983..456666666679******************************** PP

                     AA_permease_2 303 ardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrph 378
                                       a+ g lP+   k   k+   + ++ ++ ++sli+      a++a++ f+++++s g+++++l++ i+al+lr++ + 
  gi|488601125|ref|YP_007907596.1| 298 AKYGQLPEAVEKPLwKQ--AYEGLLIISLLSLIF------ANTASLEFISTAGSGGFLLIFLFVNIAALKLRDCVKL 366
                                       *******9999998677..666777677777554......56889*****************************554 PP

                     AA_permease_2 379 lkrpgkilvaiigalfllfllvalffppkgpatqssliytii 420
                                             +++ ++g++++l +lv+l++  ++ ++ + + + ++
  gi|488601125|ref|YP_007907596.1| 367 N-----PVIPAVGTVLTLAALVVLIYRMAETDVRNLTVFVCL 403
                                       3.....334566777777777777777777777666555544 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9  39.1   7.7e-23   1.5e-19       3     400 ..      11     370 ..       9     412 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 7.7e-23
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfvi 78 
                                       + i +gg+iG g+f  lg  ++     +a +a+llag++ +++++s + +++ +p+ gg+  ++ r  g   ++++ 
  gi|488601125|ref|YP_007907596.1|  11 FSIGVGGMIGGGIFAVLGLSIQLSKS-AAPVAFLLAGLIALATAYSYARLSVRFPSEGGTIEFIVRAYGTgLFSGTL 86 
                                       6799**************99976555.99**************************************9997899999 PP

                       AA_permease  79 Glnylfswitvlaleltaa.siliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafi 154
                                       + ++l s+i+ l l   a  s+  ++++++  ++ ++  +++++v+++++n +g+  +g++e +l ++k+ +++++ 
  gi|488601125|ref|YP_007907596.1|  87 NVLLLASYIVMLSLYAYAFgSYGANMLGFINPILAKHLLITLVIVLFTVVNALGAVISGKTEDLLVVLKLAILLIVA 163
                                       999999999999886666515557888888888889999******************************98777666 PP

                       AA_permease 155 ivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeks 231
                                         g+ ++  +++++     ++ d++s                    ++++ +i+++a+ G+el+a+++++v+dP+  
  gi|488601125|ref|YP_007907596.1| 164 GAGMAFVDTARLSPS----NWADPVS--------------------IVAGGMIIFLAYEGFELIANTGSDVEDPS-I 215
                                       666888888888888....9999999....................555569999*******************7.7 PP

                       AA_permease 232 iPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssanssl 308
                                       +Pka+  +v++++++Yv+++++ +  +p+++     d a    +   + k s   +   li+++ l+++ s++n+ l
  gi|488601125|ref|YP_007907596.1| 216 LPKAFYAAVLLVVVVYVMVAVVTVGNLPYDMIIKARDYA----LA-AAAKPSLGEAGFWLITLAALASTSSAINATL 287
                                       9******************************66555555....44.555555555556799**************** PP

                       AA_permease 309 ysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwllii 384
                                       y + R+ y  ak g +P +v k +  ++  + ++l+ +++sl++   + ++l+      f++++    +l+++l+++
  gi|488601125|ref|YP_007907596.1| 288 YGTVRASYMVAKYGQLPeAVEKPL--WKQAYEGLLIISLLSLIFA--NTASLE------FISTAGSGGFLLIFLFVN 354
                                       *****************5555555..5556999999999999998..666666......7777777788999***** PP

                       AA_permease 385 lsylrfRkalkyqgrs 400
                                       ++ l++R   k++   
  gi|488601125|ref|YP_007907596.1| 355 IAALKLRDCVKLNPVI 370
                                       ******9998888773 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       7.1   1.4e+04      18      24 ..     103     109 ..     102     111 .. 0.82
   2 !   39.5   0.1   2.5e-13   5.1e-10      11      81 ..     454     521 ..     446     535 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.1
                                       EEEHHHH CS
                      NTP_transf_2  18 vlfGSya 24 
                                       ++fGSy 
  gi|488601125|ref|YP_007907596.1| 103 YAFGSYG 109
                                       79***96 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 2.5e-13
                                       HTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC CS
                      NTP_transf_2  11 lepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled 81 
                                        + +a+v+l+GS arG+ +k  D+Dll+++++  s   k+++++   +  ++ ++ l++ vd+++ +k ++
  gi|488601125|ref|YP_007907596.1| 454 TFEDAEVYLVGSIARGDIKKANDVDLLIFTNNLPS---KDREKDIVRKLKQKAKLTLQHSVDIHFANKQRK 521
                                       3449*****************************98...78888899999999999999******8877665 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       1.1   2.1e+03      15      24 ..     101     110 ..     100     114 .. 0.81
   2 !   29.5   0.2   2.9e-10   5.7e-07      16      75 ..     460     522 ..     448     537 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                                       STTEEEEEE- CS
                           Polbeta  15 laylFGSrak 24 
                                        ay FGS+  
  gi|488601125|ref|YP_007907596.1| 101 YAYAFGSYGA 110
                                       58*****975 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 2.9e-10
                                       TTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH....SSSEEEEEETTTS-HH CS
                           Polbeta  16 aylFGSrakgkareeSDiDlavllkekldleeelelaaeledi...klgkkvDlvdlneappl 75 
                                       +yl GS+a+g++++  D+Dl +++++  ++++e ++  +l++     l+++vD+ + n+++++
  gi|488601125|ref|YP_007907596.1| 460 VYLVGSIARGDIKKANDVDLLIFTNNLPSKDREKDIVRKLKQKaklTLQHSVDIHFANKQRKE 522
                                       8**************************99999999999999888888999****999955443 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2  15.2   4.5e-07    0.0009       3     237 ..       6     245 ..       4     251 .. 0.83
   2 ?    0.1   2.6      0.14   2.8e+02      83     137 ..     346     398 ..     320     424 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.5e-07
                    Spore_permease   3 stkqlfvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpek.tliellkkilg.kwL 77 
                                        + ++f++ v  ++G gi  +++  ++ ++  + ++ llag+i+l  ++ + +l+ +fp++   ie++    g  + 
  gi|488601125|ref|YP_007907596.1|   6 GFWEAFSIGVGGMIGGGIFAVLGLSIQLSKSAAPVAFLLAGLIALATAYSYARLSVRFPSEgGTIEFIVRAYGtGLF 82 
                                       566789999999***************99889**************************9752689999888884677 PP

                    Spore_permease  78 GsllsilfilyFlllaafelRefseliqvflledtplwi.iilllllvilYlvvkGieslar..eflfiivilliil 151
                                       + +l++l+++ ++++++  +  f+     +l    p+ +  +l+ l+++l++vv+ +  ++      +++v  l+il
  gi|488601125|ref|YP_007907596.1|  83 SGTLNVLLLASYIVMLSLYAYAFGSYGANMLGFINPILAkHLLITLVIVLFTVVNALGAVISgkTEDLLVVLKLAIL 159
                                       99********9999999988888764333332223333312334445556677777777776534556777789999 PP

                    Spore_permease 152 llillfslklaeiknlrPvlgngikpvlkslkttslsflgveillllvpflkdkkkvkkaallgvlistllyllttl 228
                                       l++    + +++   l P      ++++ +   + l++ g+e++      ++d+    ka   +vl+++++y+++ +
  gi|488601125|ref|YP_007907596.1| 160 LIVAGAGMAFVDTARLSPSNWADPVSIVAGGMIIFLAYEGFELIANTGSDVEDPSILPKAFYAAVLLVVVVYVMVAV 236
                                       999****************99999***************************************************** PP

                    Spore_permease 229 ivilvlsve 237
                                       ++++ l  +
  gi|488601125|ref|YP_007907596.1| 237 VTVGNLPYD 245
                                       *99887655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                    Spore_permease  83 ilfilyFlllaafelRefseliqvflledtplwiiilllllvilYlvvkGiesla 137
                                       +l+i  F+ +aa +lR+ ++l    +++ + +++ ++ l+++i+ ++   +++l+
  gi|488601125|ref|YP_007907596.1| 346 FLLIFLFVNIAALKLRDCVKLNP--VIPAVGTVLTLAALVVLIYRMAETDVRNLT 398
                                       44555555555555555555533..344444444444444444444445555555 PP

>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  22.8     2e-05      0.04       4     258 ..       6     255 ..       3     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                      Trp_Tyr_perm   4 sllggvlliagtviGaGmlalPvatagagfipsllllilswvlmlasgllllEvllaake.....easfttlakkll 75 
                                        ++ + ++  g +iG+G++a+   +++     + ++++l+ +++la+++ ++ +++  ++     e  +    + l+
  gi|488601125|ref|YP_007907596.1|   6 GFWEAFSIGVGGMIGGGIFAVLGLSIQLSKSAAPVAFLLAGLIALATAYSYARLSVRFPSeggtiEFIVRAYGTGLF 82 
                                       6888999999***********************************************99954444444445556778 PP

                      Trp_Tyr_perm  76 GkkgniivalvllfllyiLlvAyisggGsilselleeasgialsarlavliftlvlgalvvlstkavdrinrvllfl 152
                                         + n++  ++++++l    +A+ s g ++l   ++        ++l + ++++++ ++  l++ +  ++  +l++l
  gi|488601125|ref|YP_007907596.1|  83 SGTLNVLLLASYIVMLSLYAYAFGSYGANMLGF-INPIL----AKHLLITLVIVLFTVVNALGAVISGKTEDLLVVL 154
                                       888888888888888887788888888887765.56555....35666666666666666666666678889999** PP

                      Trp_Tyr_perm 153 klvafvlllalllskvksdvLlsaksdtskvslvlsalPvlllsf.GFhgivpslvkyldknvkkvkkailiGtlia 228
                                       kl  + ++   ++  v+++ L    s+ ++   ++    +++l++ GF  i  +   + d   + + ka+    l+ 
  gi|488601125|ref|YP_007907596.1| 155 KLAILLIVAGAGMAFVDTARLSP--SNWADPVSIVAGGMIIFLAYeGFELIANTGSDVED--PSILPKAFYAAVLLV 227
                                       *********************99..45556556666666777777799988888777766..667999********* PP

                      Trp_Tyr_perm 229 LvlyllWelivlGnlpreelariiakggnl 258
                                        v+y++  ++++Gnlp   ++++ + +  l
  gi|488601125|ref|YP_007907596.1| 228 VVVYVMVAVVTVGNLPYDMIIKARDYA--L 255
                                       ****************99887765544..4 PP

>> SP_C-Propep  Surfactant protein C, N terminal propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5   0.00041      0.81      32      60 ..     117     145 ..      96     182 .. 0.87
   2 ?    7.0   1.1    0.0025         5      39      58 ..     224     243 ..     217     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00041
                       SP_C-Propep  32 cplnlkrllivvvvvvlvvvvvlgallmg 60 
                                        p+  k lli +v+v++ vv  lga++ g
  gi|488601125|ref|YP_007907596.1| 117 NPILAKHLLITLVIVLFTVVNALGAVISG 145
                                       58899********************9987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0025
                       SP_C-Propep  39 llivvvvvvlvvvvvlgall 58 
                                       +l+vvvv v+v vv +g l 
  gi|488601125|ref|YP_007907596.1| 224 VLLVVVVYVMVAVVTVGNLP 243
                                       689999999*******9985 PP

>> RhodobacterPufX  Intrinsic membrane protein PufX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3       2.2   4.4e+03      21      31 ..     158     168 ..     153     171 .. 0.77
   2 ?   10.9   1.5   0.00013      0.26      28      51 ..     219     242 ..     215     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
                   RhodobacterPufX  21 lllMlkGAgyA 31 
                                       +ll + GAg A
  gi|488601125|ref|YP_007907596.1| 158 ILLIVAGAGMA 168
                                       56889999998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                   RhodobacterPufX  28 AgyAavfvlvllfllvalaliGrl 51 
                                       A+yAav ++v+++++va+  +G+l
  gi|488601125|ref|YP_007907596.1| 219 AFYAAVLLVVVVYVMVAVVTVGNL 242
                                       9********************974 PP

>> DUF3302  Protein of unknown function (DUF3302)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.1       0.1   2.1e+02       3      25 ..     119     141 ..     118     145 .. 0.87
   2 ?   -3.1   0.1       4.3   8.7e+03      15      22 ..     156     163 ..     150     195 .. 0.46
   3 ?   12.7   0.8   5.5e-05      0.11       6      41 ..     222     258 ..     219     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.1
                           DUF3302   3 ylalivlivvvlvlvygiivlhd 25 
                                       +la  +li++v+vl+ ++ +l+ 
  gi|488601125|ref|YP_007907596.1| 119 ILAKHLLITLVIVLFTVVNALGA 141
                                       68999**********99988876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.3
                           DUF3302  15 vlvygiiv 22 
                                         +++i++
  gi|488601125|ref|YP_007907596.1| 156 LAILLIVA 163
                                       22333222 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 5.5e-05
                           DUF3302   6 livlivvvlvlvygiivlhdiPye.iakrRnhPhada 41 
                                        +vl+vvv+ +++ ++ ++++Py  i k R++  a a
  gi|488601125|ref|YP_007907596.1| 222 AAVLLVVVVYVMVAVVTVGNLPYDmIIKARDYALAAA 258
                                       35666666677778899******74788898776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1327  (0.0740142); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3547.02
//
Query:       gi|488601126|ref|YP_007907597.1|  [L=213]
Description: protein-L-isoaspartate(D-aspartate) O-methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  253.1   0.0    2.3e-75  253.0   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.9e-12   47.2   0.0    2.7e-12   46.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      1e-07   31.3   0.1    9.6e-07   28.1   0.0    2.1  2  RrnaAD           Ribosomal RNA adenine dimethylase
    9.2e-07   29.5   0.0    1.5e-06   28.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    9.5e-07   28.2   0.0    1.8e-06   27.3   0.0    1.4  1  Methyltransf_3   O-methyltransferase
      5e-05   22.5   0.1    6.5e-05   22.1   0.1    1.2  1  Fibrillarin      Fibrillarin
    5.1e-05   23.0   0.0    0.00015   21.5   0.0    1.7  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00019   21.2   0.0    0.00028   20.7   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00047   19.5   0.0    0.00053   19.4   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
      0.002   17.5   0.0     0.0026   17.2   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0069   17.0   0.0      0.015   15.9   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0076   16.3   0.0      0.012   15.6   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0098   15.7   0.0      0.014   15.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   16.4   0.0      0.022   15.8   0.0    1.3  1  Methyltransf_24  Methyltransferase domain
      0.047   13.2   0.0      0.092   12.2   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
      0.051   13.1   0.0       0.11   12.0   0.0    1.5  2  MTS              Methyltransferase small domain
      0.059   13.1   0.0      0.082   12.7   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
      0.083   13.0   0.0       0.15   12.3   0.0    1.4  1  RraA-like        Aldolase/RraA


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 !  253.0   0.0   2.3e-78   2.3e-75       3     207 ..       9     209 ..       7     212 .. 0.97

  Alignments for each domain:
  == domain 1  score: 253.0 bits;  conditional E-value: 2.3e-78
                                       HHHHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEE CS
                              PCMT   3 kealieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLe 79 
                                       ++++ ++lk++  + sd+v++a+++v+R+ fvp +++++aY d+pl+ig ++tiSaphmva+++ell+l++g +vLe
  gi|488601126|ref|YP_007907597.1|   9 RKKMADRLKEEL-NLSDRVYNAMLKVPRHLFVPYNYRDSAYLDTPLPIGKGQTISAPHMVAIMCELLDLREGHKVLE 84 
                                       577888888776.9*************************************************************** PP

                                       ES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS-- CS
                              PCMT  80 vGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiP 156
                                       +G+G Gy++a++a++vg++g+v++ier++el+e+ak++l  l+++nv+v+vgDG kGye++aPYd+i+ +a+ap+iP
  gi|488601126|ref|YP_007907597.1|  85 IGTGRGYHSAIVAEIVGKSGKVITIERVPELAEHAKQTLSSLGYDNVVVIVGDGSKGYEAEAPYDRIYATASAPKIP 161
                                       ***************************************************************************** PP

                                       HHHHHTEEEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BC CS
                              PCMT 157 ealidQLkeGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltd 207
                                       e+lidQLk+GG+lv+Pvg ++ Q+l +v+k++  ++++k   +vrfvpl +
  gi|488601126|ref|YP_007907597.1| 162 EPLIDQLKKGGKLVIPVG-NYMQELIVVEKND--EIKTKVWGAVRFVPLFG 209
                                       ******************.***********99..9*************976 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   2.7e-15   2.7e-12       3     119 ..      78     186 ..      76     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 2.7e-15
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDli 78 
                                       +g +vl++G+G G+ +   ae +g+ ++v+ i++ +e  e+A++ +++lg+dnv + +gd  +  e   e +++D i
  gi|488601126|ref|YP_007907597.1|  78 EGHKVLEIGTGRGYHSAIVAEIVGKSGKVITIERVPELAEHAKQTLSSLGYDNVVVIVGDGSKgYE--AE-APYDRI 151
                                       6789***********************************************************888..44.99***6 PP

                   Methyltransf_31  79 lsnevlnaladpdkileeiervlkpggilliedprllaelp 119
                                        +      +a+ +ki e +++ lk+gg l+i   + ++el+
  gi|488601126|ref|YP_007907597.1| 152 YA------TASAPKIPEPLIDQLKKGGKLVIPVGNYMQELI 186
                                       65......8999*******************9999888887 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.15   1.5e+02      57      78 ..       5      26 ..       2      48 .. 0.85
   2 !   28.1   0.0   9.6e-10   9.6e-07      24      87 ..      72     140 ..      60     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.15
                                      EE-S-HHHHHHHHCHTTTCCCE CS
                            RrnaAD 57 vlElderLakllqkklskdekl 78
                                       +E+++++a +l+++l+++ ++
  gi|488601126|ref|YP_007907597.1|  5 EFEKRKKMADRLKEELNLSDRV 26
                                      689***********99976665 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 9.6e-10
                                       HHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCG CS
                            RrnaAD  24 dklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDflk 87 
                                       + l+l+e  +vleig+G G  ++++a+++    +v  +E  ++La++ +++ls   + ++ v+  D+ k
  gi|488601126|ref|YP_007907597.1|  72 ELLDLREGHKVLEIGTGRGYHSAIVAEIVgksGKVITIERVPELAEHAKQTLSslGYDNVVVIVGDGSK 140
                                       55899************************97778******************999999**999999744 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.5e-09   1.5e-06       1      75 [.      82     158 ..      82     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.5e-09
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       vL++G+G+G +++ +a+ +g ++kv+ ++  +e+ e+a++ +++ g+ nv +++gd ++  ++++ +D ++++ +  
  gi|488601126|ref|YP_007907597.1|  82 VLEIGTGRGYHSAIVAEIVGkSGKVITIERVPELAEHAKQTLSSLGYdNVVVIVGDGSKGYEAEAPYDRIYATASAP 158
                                       9*****************9669**********************999************999999******964444 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.8e-09   1.8e-06      42     172 ..      73     195 ..      60     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.8e-09
                                       HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTS CS
                    Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkd 118
                                       L++l +  +vleiG+ +Gy    +a  + + Gk+++i+  +e +e a++ +   g+++ + +i+gd+ k  e    +
  gi|488601126|ref|YP_007907597.1|  73 LLDLREGHKVLEIGTGRGYHSAIVAEIVGKSGKVITIERVPELAEHAKQTLSSLGYDN-VVVIVGDGSKGYEA---E 145
                                       8999999************************************************987.56899999987653...3 PP

                                       SS---EEEEEE-S-GGGHHHHHHHHHHTEEEEE..EEEEE-TTGGGGGG-SS--SH CS
                    Methyltransf_3 119 kklpefDfifvDaDkssyvnyyeklleLvkvGg..liaiDntLWeGkvveeddeea 172
                                          + +D i++ a   s ++  e l++ +k+Gg  +i + n + e  vve++de +
  gi|488601126|ref|YP_007907597.1| 146 ---APYDRIYATA---SAPKIPEPLIDQLKKGGklVIPVGNYMQELIVVEKNDEIK 195
                                       ...3588888877...5567778888888888833344578888888888866654 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   6.5e-08   6.5e-05      65     133 ..      73     143 ..      63     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.5e-08
                                       --S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHT..TSTTEEEEES-TTSGGG CS
                       Fibrillarin  65 elpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievak..kRknivPileDArkPek 133
                                        l +++g+kvL +G++ G   + v++ivg++g+v ++e  p    +  +  +     n+v i++D +k ++
  gi|488601126|ref|YP_007907597.1|  73 LLDLREGHKVLEIGTGRGYHSAIVAEIVGKSGKVITIERVPELAEHAKQTLSslGYDNVVVIVGDGSKGYE 143
                                       46799*********************************9998877665544311579*******9987544 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.5e-07   0.00015       3      84 ..      73     152 ..      71     160 .. 0.92
   2 ?   -1.8   0.0         2     2e+03     124     135 ..     164     175 ..     156     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.5e-07
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggel 79 
                                       lL+++e+ ++l++ ++ G   + +ae++ ++g+v+ +++  e +++ +++l+ Lg  n+ v+ +D++k   + +++ 
  gi|488601126|ref|YP_007907597.1|  73 LLDLREGHKVLEIGTGRGYHSAIVAEIVGKSGKVITIERVPELAEHAKQTLSSLGYDNVVVIVGDGSKG--YEAEAP 147
                                       7999***************************************************************98..555556 PP

                                       EEEEE CS
                   Methyltr_RsmB-F  80 fDriL 84 
                                       +Dri 
  gi|488601126|ref|YP_007907597.1| 148 YDRIY 152
                                       99985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                                       HCCCEEEEEEEE CS
                   Methyltr_RsmB-F 124 aidllkkgGvlv 135
                                       +id+lkkgG lv
  gi|488601126|ref|YP_007907597.1| 164 LIDQLKKGGKLV 175
                                       799******998 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.8e-07   0.00028      29      95 ..      67     133 ..      56     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.8e-07
                             GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvt 95 
                                       ++++   L+l++G +v+e GtG g  s  +a  v+  G++ t+e   + ae+a++ + + + +++v 
  gi|488601126|ref|YP_007907597.1|  67 VAIMCELLDLREGHKVLEIGTGRGYHSAIVAEIVGKSGKVITIERVPELAEHAKQTLSSLGYDNVVV 133
                                       56777889********************************************999998888776554 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.3e-07   0.00053      51     131 ..      67     151 ..       7     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.3e-07
                                       HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--..EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-- CS
                              CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydv..kvvglTlSkeqaklakkrvdeldlerkvevklldyedld 125
                                       + +++e l+l++G+++L+iG+G G+     +e  +   kv+ +    e a++ak+++ +l+ ++ v +   + +  +
  gi|488601126|ref|YP_007907597.1|  67 VAIMCELLDLREGHKVLEIGTGRGYHSAIVAEIVGKsgKVITIERVPELAEHAKQTLSSLGYDNVVVIVGDGSKGYE 143
                                       56899*******************87777666655411666666677999*********998888777655444433 PP

                                       -..--SEE CS
                              CMAS 126 e..kvdrv 131
                                          ++dr+
  gi|488601126|ref|YP_007907597.1| 144 AeaPYDRI 151
                                       33377776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.6e-06    0.0026      44     118 ..      75     149 ..      65     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.6e-06
                                       -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EE CS
                   Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfD 118
                                         ++g+kvl++ +G g  ++ +++ vg++gkv+ ++  +++ + +++ l   g+ n+  +++++ +  + +  +D
  gi|488601126|ref|YP_007907597.1|  75 DLREGHKVLEIGTGRGYHSAIVAEIVGKSGKVITIERVPELAEHAKQTLSSLGYDNVVVIVGDGSKGYEAEAPYD 149
                                       5689**********************************************************9988766666655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.5e-05     0.015       1      69 [.      83     155 ..      83     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvsse 69 
                                       L++G+G+G++++ +a+ +   ++v++++  +e+ + ak+  s  g  +v ++v+d +k   +++ +D ++++ 
  gi|488601126|ref|YP_007907597.1|  83 LEIGTGRGYHSAIVAEIVgksGKVITIERVPELAEHAKQTLSSLGYdNVVVIVGDGSKGYEAEAPYDRIYATA 155
                                       89*************7777889*********************99999999****998444456777777665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05     0.012      15      78 ..      69     128 ..      60     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                   Methyltransf_32  15 kllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78 
                                        +++   + ++  +v+++G G+gY s ++a   + ++ kv+ i+   el+e+a++  + lg  +
  gi|488601126|ref|YP_007907597.1|  69 IMCEL-LDLREGHKVLEIGTGRGYHSAIVAE-IVGKSGKVITIERVPELAEHAKQTLSSLG--Y 128
                                       33443.34467789****************9.55689******************999998..6 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.4e-05     0.014      16      96 ..      73     161 ..      63     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevl.rengf..svtgvDlspeaveiae............kakkaqkdqfdeqeaa 77 
                                       ll+ lr+g +vL+iG+G G+ + +  +  g+  +v+ ++  pe+ e a+                 + d     +  
  gi|488601126|ref|YP_007907597.1|  73 LLD-LREGHKVLEIGTGRGYHSAIVaEIVGKsgKVITIERVPELAEHAKqtlsslgydnvvV---IVGDGS---KGY 142
                                       444.78999**********666666155688899*******999998876666665553331...222222...333 PP

                   Methyltransf_23  78 epqgkfdlIvlrevlehvp 96 
                                       e ++ +d I+++ +   +p
  gi|488601126|ref|YP_007907597.1| 143 EAEAPYDRIYATASAPKIP 161
                                       5555777777766655555 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   2.2e-05     0.022       1      54 [.      83     135 ..      83     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-05
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrli 54 
                                       +EiG+  G+ ++++++ + + g+  +++++  p+ ae+a++ + ++g+d++v ++
  gi|488601126|ref|YP_007907597.1|  83 LEIGTGRGYHSAIVAEIVGKSGK--VITIERVPElAEHAKQTLSSLGYDNVVVIV 135
                                       7******************9995..********7667777777779998876554 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.2e-05     0.092       4      60 ..      81     138 ..      78     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-05
                                       EEEEET-TTSHHHHHHHHHSTTS.EEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdk.nflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                        vleiG+G+G +    A+   +  +++ iE   ++ +++ ++   l++ N+ ++ gd 
  gi|488601126|ref|YP_007907597.1|  81 KVLEIGTGRGYHSAIVAEIVGKSgKVITIERVPELAEHAKQTLSSLGYDNVVVIVGDG 138
                                       589***************9876538*****************************9997 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.11      22     101 ..      69     151 ..      66     154 .. 0.85
   2 ?   -3.1   0.0       4.9   4.9e+03     128     137 ..     167     176 ..     165     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.T CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleeve.e 95 
                                       ++ e l+ ++ +kvl +G+G G+ +a +a+   +   v  ++   +  e ak++l++ + + v v+  d+ +  e e
  gi|488601126|ref|YP_007907597.1|  69 IMCELLDLREGHKVLEIGTGRGYHSAIVAEIVGKSGkVITIERVPELAEHAKQTLSSLGYDnVVVIVGDGSKGYEaE 145
                                       67788999999******************99887655999999999999********99999999999998888745 PP

                                       S-EEEE CS
                               MTS  96 kkfdli 101
                                       + +d i
  gi|488601126|ref|YP_007907597.1| 146 APYDRI 151
                                       566655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.9
                                       HEEEEEEEEE CS
                               MTS 128 aLkegGeLli 137
                                       +Lk+gG+L+i
  gi|488601126|ref|YP_007907597.1| 167 QLKKGGKLVI 176
                                       7999***988 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.3e-05     0.082      25      77 ..      78     131 ..      63     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                            DUF938  25 ttervLEiasGtGqHAvffApalpn.lkwqpsdqdeelresiaawadelalsnl 77 
                                       ++++vLEi++G G H +  A+ + +  k ++ +  +el e  ++++++l+ +n+
  gi|488601126|ref|YP_007907597.1|  78 EGHKVLEIGTGRGYHSAIVAEIVGKsGKVITIERVPELAEHAKQTLSSLGYDNV 131
                                       4569****************9986515889999999999999999999999997 PP

>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.15      15      63 ..      89     140 ..      70     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                       STB.TT..EES...EEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.S CS
                         RraA-like  15 sggirp.lers...fvGpavTvkvveadnslvkealeeagpgdvlVvdgggde 63 
                                       +g ++  + ++    +G+++T++ v++  ++ k++l++ g ++v+V+ g+g++
  gi|488601126|ref|YP_007907597.1|  89 RG-YHSaIVAEivgKSGKVITIERVPELAEHAKQTLSSLGYDNVVVIVGDGSK 140
                                       33.3333555446788**********98899****************888743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1259.42
//
Query:       gi|488601127|ref|YP_007907598.1|  [L=136]
Description: putative redox protein, regulator of disulfide bond formation [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-17   61.3   0.0    1.3e-16   60.9   0.0    1.1  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   7.1e-21   1.3e-16       1      97 [.      42     132 ..      42     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 7.1e-21
                                       TTXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHH CS
                              OsmC   1 gdgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkkl 77 
                                       g+++g+ P+elll ++a+C+++t+ ++++ kg+++++le+++e +r ++g +   e+++kv +  +g   e+  +++
  gi|488601127|ref|YP_007907598.1|  42 GENTGFKPTELLLISVAGCLGTTIVSMCESKGVDVKGLEIDIEFDRGDDGIW---EAKIKVGL--DGVN-EDVKEEI 112
                                       7899*****************************************9999655...66666666..5545.79***** PP

                                       HHHHHHHSHHHHHHCT-SSS CS
                              OsmC  78 lekaekrCpvsntlkngvkv 97 
                                       ++ a++ C +sn l+ g+++
  gi|488601127|ref|YP_007907598.1| 113 VKSADHLCKISNILRDGCRI 132
                                       ***************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 922.59
//
Query:       gi|488601128|ref|YP_007907599.1|  [L=380]
Description: acetylornithine aminotransferase apoenzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-113  379.9   0.0   1.6e-113  379.5   0.0    1.1  1  Aminotran_3      Aminotransferase class-III
    4.5e-05   22.8   0.0    7.4e-05   22.1   0.0    1.3  2  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.018   14.4   0.0       0.03   13.6   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  379.5   0.0  2.6e-117  1.6e-113      10     406 .]      22     380 .]      18     380 .] 0.97

  Alignments for each domain:
  == domain 1  score: 379.5 bits;  conditional E-value: 2.6e-117
                                       CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                       Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                       ++  ++++G++l+d +gk+ylDl+++ia v +Gh+hP+ +  v eq+ +l+hvs +++ +ep+++laekl ++ +  
  gi|488601128|ref|YP_007907599.1|  22 PVTFKRGKGCWLYDFNGKKYLDLIAGIACVSIGHSHPEFISRVYEQMRELMHVS-NLFYTEPQIRLAEKLKEISGF- 96 
                                       57899*************************************************.******************999. PP

                                       .SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TT CS
                       Aminotran_3  87 ldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkyp 163
                                        dk+f++nsG+eAve+AlK+ark       t k+k++a++++fHGrt+gals+t++ +k ++ f+p++ ev + k++
  gi|488601128|ref|YP_007907599.1|  97 -DKFFFCNSGTEAVEAALKIARK------VTGKKKFLALENSFHGRTMGALSITWK-EKFRKPFEPLIQEVEFCKFN 165
                                       .**********************......9**************************.******************** PP

                                       BGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTT CS
                       Aminotran_3 164 deevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGr 240
                                       d                 + +   + + +++Avi+Epiqge+Gv+ +s+ef+ ++ e  ++++ l+i+DEvqtGf r
  gi|488601128|ref|YP_007907599.1| 166 D-----------------VDDFLGRVNADICAVILEPIQGEAGVYEVSKEFMDAVFEEKERYGYLVIFDEVQTGFCR 225
                                       9.................7777778899************************************************* PP

                                       TSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHH CS
                       Aminotran_3 241 TGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllena 317
                                       TG++fA +h+g spD+mt+aKa+++G+p+  v++t+ev++ ++ ++hgsTfgGnplac ++la++ei+++e+l+en 
  gi|488601128|ref|YP_007907599.1| 226 TGEWFAKDHFGCSPDIMTMAKAMASGFPIGGVAVTNEVANKIEISEHGSTFGGNPLACTASLATIEIMQKENLAENS 302
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHH CS
                       Aminotran_3 318 qelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdee 394
                                       +++g +++++L el        e RgkGl+i++++ +++      ++ k++ekGv+  ++ d++ir++ppl+it++e
  gi|488601128|ref|YP_007907599.1| 303 RDMGGYFRKRLAELGF------EARGKGLLIGFDVGDAKA-----LVSKLLEKGVVANNTSDTTIRFAPPLVITKDE 368
                                       ***************4......56*********9988887.....9******************************* PP

                                       HHHHHHHHHHHH CS
                       Aminotran_3 395 idelleilkkal 406
                                       id ++++l+++l
  gi|488601128|ref|YP_007907599.1| 369 IDFAVDALEECL 380
                                       ********9986 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 ?   -3.3   0.0      0.64   3.8e+03      77     156 ..     106     130 ..      86     136 .. 0.58
   2 !   22.1   0.0   1.2e-08   7.4e-05     166     362 ..     196     375 ..     156     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEE CS
                     Aminotran_1_2  77 agaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvil 153
                                       +                                                       ea+e+alk a +   k+k+++
  gi|488601128|ref|YP_007907599.1| 106 T-------------------------------------------------------EAVEAALKIARKVTGKKKFLA 127
                                       3.......................................................344444444333333444444 PP

                                       EES CS
                     Aminotran_1_2 154 ves 156
                                       +e+
  gi|488601128|ref|YP_007907599.1| 128 LEN 130
                                       444 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.2e-08
                                       -HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHH CS
                     Aminotran_1_2 166 tleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsq 242
                                       ++e   ++ + +++y+ l+++De+  gf+ + + +++ +++ ++++      +++Ka++  G+ +G ++++ +v++ 
  gi|488601128|ref|YP_007907599.1| 196 SKEFMDAVFEEKERYGYLVIFDEVQTGFCRTGEWFAKDHFGCSPDIM-----TMAKAMA-SGFPIGGVAVTNEVANK 266
                                       667778889999*******************9988888******988.....******7.59*************** PP

                                       HHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHH CS
                     Aminotran_1_2 243 lrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetake 319
                                       +++   + ++    + a++a+l + + +  + e+ ++   ++  ++r++Laelg++  ++ + ++ + +++a+   +
  gi|488601128|ref|YP_007907599.1| 267 IEISEHGSTF-GGNPLACTASLATIEIM--QKENLAENSRDMGGYFRKRLAELGFEARGK-GLLIGFDVGDAK---A 336
                                       9877766555.55566677777776655..66777888889999*************997.777778888877...* PP

                                       HHHHHHHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHHHHHH CS
                     Aminotran_1_2 320 lskkLleevgvyvtpgtsftvpgrlRitv.Aglteeeleelvea 362
                                       l  kLle+ gv+       t  + +R+ +    t++e++ +v+a
  gi|488601128|ref|YP_007907599.1| 337 LVSKLLEK-GVVANN----TSDTTIRFAPpLVITKDEIDFAVDA 375
                                       ********.999888....4455677777556677777666665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.1e-06      0.03      36     213 ..      85     263 ..      63     357 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-06
                                       HHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEE.EE-..EBTTTB CS
                   Beta_elim_lyase  36 rLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklr.dlk..nkeaGk 108
                                       rL+++++e+ g+++ +f+ +Gt A + +lki   + g+++++  ++ +h ++ ga++     k+r +++  ++e   
  gi|488601128|ref|YP_007907599.1|  85 RLAEKLKEISGFDKFFFCNSGTEAVEAALKIARkVTGKKKFLALENSFHGRTMGALSITWKEKFRkPFEplIQEVEF 161
                                       899**************************999988999999999999********9988444443133322444478 PP

                                       E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHH CS
                   Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkem 185
                                        +++++ + + +v+a   +i +++l+     ag   vs e +++v +  ++yg+ +++D       + + +  +k+ 
  gi|488601128|ref|YP_007907599.1| 162 CKFNDVDDFLGRVNA---DICAVILEPIQGEAGVYEVSKEFMDAVFEEKERYGYLVIFDEVQT-GFCRTGEWFAKDH 234
                                       888999999988666...888888888888888888999999999999999999999997653.4567777778888 PP

                                       H.TTSSEEEEESSSTT--SS-EEEEE-HH CS
                   Beta_elim_lyase 186 f.syvDsvtmslkKdllanvGgvlafrdd 213
                                       f    D++tm      ++++Ggv ++++ 
  gi|488601128|ref|YP_007907599.1| 235 FgCSPDIMTMAKAMASGFPIGGVAVTNEV 263
                                       84447888888888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2096.12
//
Query:       gi|488601129|ref|YP_007907600.1|  [L=334]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   60.8   0.0    1.7e-09   37.7   0.0    2.4  2  PAS       PAS fold
      1e-14   54.6   0.0    1.4e-09   38.2   0.0    2.4  2  PAS_9     PAS domain
    2.9e-10   39.9   0.1    8.1e-05   22.5   0.0    2.9  3  PAS_8     PAS domain
    5.5e-10   39.5   0.0     0.0013   18.9   0.0    2.8  3  PAS_4     PAS fold
    2.5e-09   37.3   0.1      4e-08   33.4   0.0    2.6  3  PAS_3     PAS fold
    0.00038   20.4   0.9    0.00082   19.4   0.5    1.8  1  HisKA     His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   9.8e-08   0.00029       3      51 ..      18      66 ..      16      77 .. 0.89
   2 !   37.7   0.0   5.5e-13   1.7e-09       5      98 ..     142     236 ..     138     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9.8e-08
                                      HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBS CS
                               PAS  3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldlih 51
                                      l+++++ lp  +++vDe +ril+vN+a+e+ ++l+ ee+ gk    lih
  gi|488601129|ref|YP_007907600.1| 18 LKEFIDFLPFYVILVDEEHRILLVNTAFEQEFNLRLEEARGKFCPQLIH 66
                                      67788889999******************************98777777 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 5.5e-13
                                       HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHH..HHHHHHTT-ECCCCEE CS
                               PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaell..eqlleqgeesrageis 78 
                                        i+e++ +++++v e  ri+++N+++ el G+s ee+ gk   +l++++dd  +  e++  +++++ +e +r +ei+
  gi|488601129|ref|YP_007907600.1| 142 LIFENTGNATILV-EGDRIVLANKKFVELSGYSKEEIEGKLEWRLFVHKDDLdK-MEKFnrLRYENPKEAPREFEIK 216
                                       6999*********.999*********************************9953.4444113567889999****** PP

                                       EECTTSSEEEEEEEEEEEEE CS
                               PAS  79 fklrdgrpihlevraspvrd 98 
                                       f  r+gr++h++v a ++  
  gi|488601129|ref|YP_007907600.1| 217 FVDRKGRIRHVLVSAGSISK 236
                                       *************9988765 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.3e-05     0.038       4      41 ..      29      68 ..      26     125 .. 0.77
   2 !   38.2   0.0   4.6e-13   1.4e-09       5     104 .]     152     251 ..     148     251 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                             PAS_9  4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf..v 41
                                      ++++++++ril +N+a+++ +    ee  gk + +l+  v
  gi|488601129|ref|YP_007907600.1| 29 VILVDEEHRILLVNTAFEQEFNLRLEEARGKFCPQLIhgV 68
                                      45588*******************************9430 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 4.6e-13
                             PAS_9   5 lidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk....kerevevvlirkngetfw 77 
                                       +++ +  ri+ aN+++ +l Gys+ee+ gk  + lf  ++++ ++++++ +   +     +re+e+ +++++g+  +
  gi|488601129|ref|YP_007907600.1| 152 ILV-EGDRIVLANKKFVELSGYSKEEIEGKLEWRLF-VHKDDLDKMEKFNRLRYEnpkeAPREFEIKFVDRKGRIRH 226
                                       444.3347****************************.44444444444444444455569***************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       vl++a  +  +d     i++ l+D+te
  gi|488601129|ref|YP_007907600.1| 227 VLVSAGSISKKD--PSTIVLSLTDLTE 251
                                       ********5444..3336699***998 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.3e-05     0.038       2      51 ..      17      67 ..      16      80 .. 0.80
   2 !   22.5   0.0   2.7e-08   8.1e-05       5      57 ..     142     193 ..     135     203 .. 0.77
   3 ?   -1.9   0.0       1.2   3.6e+03       6      17 ..     276     287 ..     271     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                             PAS_8  2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51
                                       l+ +++ +p  +++vd+  ri+ vN a+++ + ++ ++ +g+ + ql+++
  gi|488601129|ref|YP_007907600.1| 17 LLKEFIDFLPFYVILVDEEHRILLVNTAFEQEFNLRlEEARGKFCPQLIHG 67
                                      678899999999*****6669************999777777666555554 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.7e-08
                             PAS_8   5 alfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle 57 
                                        +fe+  ++ ++v +++ iv +N+++ el Gys +++ g+l  ++l v+++ l+
  gi|488601129|ref|YP_007907600.1| 142 LIFENTGNATILVEGDR-IVLANKKFVELSGYSkEEIEGKLE-WRLFVHKDDLD 193
                                       58999999999998555.***************777777666.66666666655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                             PAS_8   6 lfesspdgiavv 17 
                                       l++++++++a++
  gi|488601129|ref|YP_007907600.1| 276 LVDHIRNPLAII 287
                                       799999999986 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.5e-07    0.0013       4      46 ..      25      67 ..      22     128 .. 0.71
   2 !   17.8   0.0     1e-06     0.003      16     109 ..     158     253 ..     144     254 .. 0.78
   3 ?   -3.3   0.0       3.7   1.1e+04      48      63 ..     306     321 ..     299     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.5e-07
                             PAS_4  4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpe 46
                                      lp++++ +d++ r+l +N+a+++ f ++ ee++Gk + +l   
  gi|488601129|ref|YP_007907600.1| 25 LPFYVILVDEEHRILLVNTAFEQEFNLRLEEARGKFCPQLIHG 67
                                      899**********************************987665 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1e-06
                             PAS_4  16 rvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvl...egeepiefleelll.pgeerhyelrllPl 88 
                                       r++ aN+ + el g++ ee+ Gk  + l+ + d  + ++  +r+      e+p ef++  ++  g+ rh+++++  +
  gi|488601129|ref|YP_007907600.1| 158 RIVLANKKFVELSGYSKEEIEGKLEWRLFVHKDDLDKMEKFNRLRyenPKEAPREFEIKFVDrKGRIRHVLVSAGSI 234
                                       899************************999995555555555544111456788888877778***********999 PP

                             PAS_4  89 rdesGevigvlvisrDiTerr 109
                                         ++ ++  +++ ++D+Ter+
  gi|488601129|ref|YP_007907600.1| 235 --SKKDPSTIVLSLTDLTERK 253
                                       ..56889999*********97 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.7
                             PAS_4  48 daarleralrrvlege 63 
                                       + +r+e+++rr+ eg+
  gi|488601129|ref|YP_007907600.1| 306 QIDRIESIVRRLDEGW 321
                                       5688999999998886 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.33   9.9e+02       3      33 ..      40      68 ..      38      71 .. 0.86
   2 ?   -1.6   0.0       1.2   3.5e+03      62      85 ..      93     117 ..      92     120 .. 0.81
   3 !   33.4   0.0   1.3e-11     4e-08       2      77 ..     160     236 ..     159     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.33
                             PAS_3  3 yvserveeilGyspeellgkveswldlvhpe 33
                                       v+ ++e+ + ++ ee +gk  ++ +l+h  
  gi|488601129|ref|YP_007907600.1| 40 LVNTAFEQEFNLRLEEARGK--FCPQLIHGV 68
                                      689999**************..999999965 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                             PAS_3  62 dGeyrwveararvi.rdengkpvrv 85 
                                       d +  wv++ ++++ +  ngk +++
  gi|488601129|ref|YP_007907600.1|  93 DRSEKWVKSAVYPTnYIYNGKRIFI 117
                                       67889**999999988888887765 PP

  == domain 3  score: 33.4 bits;  conditional E-value: 1.3e-11
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqeal..kkge.pyegeyRirrkdGeyrwveararvi 75 
                                       + +++++ e+ Gys+ee++gk  +w+ +vh +D++++++ ++++   + +e p e+e++++ + G +r+v  +a  i
  gi|488601129|ref|YP_007907600.1| 160 VLANKKFVELSGYSKEEIEGK-LEWRLFVHKDDLDKMEK-FNRLRyeNPKEaPREFEIKFVDRKGRIRHVLVSAGSI 234
                                       66899****************.78**********99876.55444546666789****************9999888 PP

                             PAS_3  76 rd 77 
                                         
  gi|488601129|ref|YP_007907600.1| 235 SK 236
                                       44 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 !   19.4   0.5   2.7e-07   0.00082       6      66 ..     273     324 ..     268     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.7e-07
                                       HHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   6 lagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       +a +   +r+PL+ i+g ae+  +            ++i ++++r++++v +l d ++i++
  gi|488601129|ref|YP_007907600.1| 273 FAILVDHIRNPLAIIQGIAEMRLE------G--MERDIILKQIDRIESIVRRL-DEGWIQS 324
                                       7888999**************333......2..3358***************8.9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2041.69
//
Query:       gi|488601130|ref|YP_007907601.1|  [L=339]
Description: glyceraldehyde 3-phosphate dehydrogenase (NAD(P)+) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  105.6   0.1    2.8e-30  105.0   0.1    1.3  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
    5.2e-11   42.7   1.2    8.7e-11   42.0   0.6    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    4.3e-07   30.2   0.3    3.2e-06   27.4   0.3    2.4  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
    0.00015   22.0   0.1    0.00047   20.4   0.1    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.001   19.7   0.2     0.0029   18.2   0.2    1.9  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
     0.0041   17.5   0.3      0.021   15.2   0.1    2.2  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0054   16.1   0.4      0.075   12.4   0.3    2.4  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.012   15.8   0.1       0.04   14.2   0.1    1.9  1  TrkA_N           TrkA-N domain
      0.015   16.1   0.0      0.033   15.0   0.0    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.1   1.4e-33   2.8e-30       1     157 [.     146     298 ..     146     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1.4e-33
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldgl 75 
                                       L++l++ ++++f ikk+++t++++++++         k+ +++ +++  +n+i+ +++++++v+++lp  ++++ + 
  gi|488601130|ref|YP_007907601.1| 146 LTRLIYTIKKNFPIKKVRATMIRRVVDP---------KEDKKGLVNGiqPNPIKLPSHHGPDVQSILP--DVNIITA 211
                                       789*************************.........999******999*******************..69***** PP

                                       EEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS.SEEEEGGGCEEE CS
                           Gp_dh_C  76 AvrVPtpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph.ssifdaketivv 147
                                       A++VPt+ ++v+++ +e+ek+ + e++++a+ e+++    ++++g++s+++ +++++Dl+ + + +++ +++ +i v
  gi|488601130|ref|YP_007907601.1| 212 AFKVPTTIMHVHSVAIEMEKDISEEDIKSAFAEEPRimlfNSEDGFTSTAKIIEFARDLRLRYDlYENAVWEDSIGV 288
                                       *************************************************************9999************ PP

                                       TTTEEEEEEE CS
                           Gp_dh_C 148 eenlvkvvaw 157
                                        + +v+v+++
  gi|488601130|ref|YP_007907601.1| 289 VDGEVYVTQA 298
                                       *******997 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.6   4.4e-14   8.7e-11       1     106 [.       3     113 ..       3     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 4.4e-14
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH............HHSSSS--S-BEBSSHHHHH CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag............ellglgklgvavtddleevl 65 
                                       +kvav+G+ G++Gk+v++a++ ++d+e+v++ ++k+ ++++k a             ++  +++ g++v+ ++e++l
  gi|488601130|ref|YP_007907601.1|   3 VKVAVNGY-GTIGKRVADAISLQKDMEVVGVTKTKP-DFDAKMAIkkgyrlyaaipdRVKVFESAGLEVEGTIEDLL 77 
                                       69******.**************************9.6666655567799****9955555559************* PP

                                       HH-SEEEE-S-HHHHHHHHHHHHHTT-EEEE--SS--HHHH CS
                            DapB_N  66 ekadvliDFTtpeavlenlklalekgvklViGTTGlseeel 106
                                       +++d+++D +  +   en kl+ + gvk+++     +  e+
  gi|488601130|ref|YP_007907601.1|  78 KEVDIVVDCSPNKIGAENKKLYEKLGVKAIF-----QGGEK 113
                                       **********555556665555555**9998.....33333 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 !   27.4   0.3   1.6e-09   3.2e-06       1      68 [.       3      72 ..       3      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.6e-09
                                      CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEE.TTEEEETTE CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaind.ltdletlayllkyDsvhgrfkgeveae.eealvvngk 68
                                      vkva+nG+G IG+ v+ a+  +k++evv + +   d +  + + k    +  ++ +v++  ++ l+v+g+
  gi|488601130|ref|YP_007907601.1|  3 VKVAVNGYGTIGKRVADAISLQKDMEVVGVTKtKPDFDAKMAIKKGYRLYAAIPDRVKVFeSAGLEVEGT 72
                                      69******************************44555555555555566777788887762455888774 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.4e-07   0.00047       3      80 ..       7      90 ..       5     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.4e-07
                                      EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH........TTTCEEEEE--TTTHHHHHHHHHTTSSEE CS
                   Sacchrp_dh_NADP  3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka........lgvrfeaialdaenyeavLaallkegdlv 73
                                      + G+G +G+ va+ ++ ++d+  e++ ++++k   +a  a +           r++  +    ++e +++ llke d+v
  gi|488601130|ref|YP_007907601.1|  7 VNGYGTIGKRVADAISLQKDM--EVVGVTKTKPDFDAKMAIKkgyrlyaaIPDRVKVFESAGLEVEGTIEDLLKEVDIV 83
                                      66*******************..9999999999999998877677777765556666666667788899********** PP

                                      EE-SSGG CS
                   Sacchrp_dh_NADP 74 vnlsppi 80
                                      v++sp+ 
  gi|488601130|ref|YP_007907601.1| 84 VDCSPNK 90
                                      *****96 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.5e-06    0.0029       1      71 [.       9      91 ..       9     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                                      --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT................HHHHHT--CB---HHHHHHHHS-EE CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd................rkallasealtldlddliahldpdv 62
                                      G+G+iG++v++++  q++   +e+v+v++ + +  +k                 +  + a  ++   ++dl++  ++d+
  gi|488601130|ref|YP_007907601.1|  9 GYGTIGKRVADAISLQKD---MEVVGVTKTKpDFDAKMaikkgyrlyaaipdrvKVFESAGLEVEGTIEDLLK--EVDI 82
                                      99***************6...8*********555555599999999999988764445566677788999999..**** PP

                                      EEE-S--HH CS
                     NAD_binding_3 63 vVEcassea 71
                                      vV+c + + 
  gi|488601130|ref|YP_007907601.1| 83 VVDCSPNKI 91
                                      ****98765 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.1e-05     0.021       1      94 [.       4     107 ..       4     110 .. 0.84
   2 ?   -0.9   0.0       1.1   2.1e+03      90     118 ..     260     304 ..     217     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT..TTTSBHHHHSG.........GGTTTECEBEEEGGGGGCTT CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssr..saGkklaeavk.........aleegkdlkvedvdeeelke 66 
                                       kva+ G  G +G++++  ++ ++++e+v ++ ++   +a  ++++ ++         ++ e + l+ve + e+ lke
  gi|488601130|ref|YP_007907601.1|   4 KVAVNG-YGTIGKRVADAISLQKDMEVVGVTKTKPdfDAKMAIKKGYRlyaaipdrvKVFESAGLEVEGTIEDLLKE 79 
                                       677888.899999******99********9999995545555555555888888988888889999999999999** PP

                                       -SEEEE-SCHHHHHHHHHHHHHTTSEEE CS
                    Semialdhyde_dh  67 vdivflalpagvskelapklaeagvkvi 94 
                                       vdiv+ + p+++ +e  + + + gvk i
  gi|488601130|ref|YP_007907601.1|  80 VDIVVDCSPNKIGAENKKLYEKLGVKAI 107
                                       **************99999999998766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                                       TSEEEESSSTTTTST................TSEBE-HHHHGGGG CS
                    Semialdhyde_dh  90 gvkviDlssdfRlkd................davyvlpevnreai 118
                                        +k+i  + d+Rl+                   vyv   +n+e i
  gi|488601130|ref|YP_007907601.1| 260 TAKIIEFARDLRLRYdlyenavwedsigvvdGEVYVTQAINQESI 304
                                       467888888888887677777777666666656677777777665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.3   3.8e-05     0.075      38      71 ..       4      38 ..       2     102 .. 0.89
   2 ?   -1.7   0.0       0.8   1.6e+03      46     106 ..      90     148 ..      89     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                                      EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrskkk 71
                                      +v++ G+G IG++va+ ++ + +m+v+++ ++k +
  gi|488601130|ref|YP_007907601.1|  4 KVAVNGYGTIGKRVADAISlQKDMEVVGVTKTKPD 38
                                      7999**************999********999663 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.8
                                       HHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEEEE-S--STTTT CS
                      2-Hacid_dh_C  46 rIGqavakrlkafgmkviaydrskkkeeeeeelgv.elvsleellaesDivslhlpltpetr 106
                                       +IG +  k+ +++g+k i+    kk+ +   e+ +   ++ ee++ +  + ++ ++ t  tr
  gi|488601130|ref|YP_007907601.1|  90 KIGAENKKLYEKLGVKAIFQGGEKKDVA---EVSFnAIANYEEAVGKQFVRVVSCNTTGLTR 148
                                       5899999999999999999888877444...3333245677777777666666666666655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     2e-05      0.04       1      61 [.       5      68 ..       5      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHH..HHHHHHTTSEEEES-TTSHHHHHHTTGG CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeer..veelreeglevvvgdatdeevLeeagie 61
                                      +++ G+G++G+++a+ +s  + ++vv++ k +    ++ + ++g++ + + + + +v e+ag+e
  gi|488601130|ref|YP_007907601.1|  5 VAVNGYGTIGKRVADAISLqKDMEVVGVTKTKPDfdAKMAIKKGYRLYAAIPDRVKVFESAGLE 68
                                      5799*************9955577****9988654678888999******99999999999986 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 ?   15.0   0.0   1.6e-05     0.033       2      78 ..       4      95 ..       3     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                      EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS..................HHHHHTCTT CS
                      GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd..................leelladpe 62
                                      +va+ G+G ig++ + ++  + ++ evv++ ++++    ++a + g   y+                   +e+ll+  e
  gi|488601130|ref|YP_007907601.1|  4 KVAVNGYGTIGKRVADAISLQ-KDMEVVGVTKTKPDFDAKMAIKKGYRLYAAipdrvkvfesaglevegtIEDLLK--E 79
                                      89*************666666.*************999999999999988888889999999****999999***9..9 PP

                                      ESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA 63 idavivatpngtheel 78
                                      +d+v+ ++pn+ ++e 
  gi|488601130|ref|YP_007907601.1| 80 VDIVVDCSPNKIGAEN 95
                                      **********766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2225.94
//
Query:       gi|488601131|ref|YP_007907602.1|  [L=61]
Description: putative RNA-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   77.7   6.8    6.3e-22   77.6   6.8    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 !   77.6   6.8   3.5e-26   6.3e-22       1      61 []       1      60 [.       1      60 [. 0.99

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 3.5e-26
                              CooT  1 MCeanvyllkngkeeelvmedVdkiepeedgvvltdifGeekevegkIkeidLvehkiile 61
                                      MCe++v +lk+gke e++medV++ie+e+d+v l +++Ge +ev+gkIk +d+ +hki+le
  gi|488601131|ref|YP_007907602.1|  1 MCESKVAILKDGKE-EIIMEDVVRIEVEGDTVKLFGLLGEMTEVKGKIKLMDMKNHKILLE 60
                                      ************99.********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 404.85
//
Query:       gi|488601132|ref|YP_007907603.1|  [L=269]
Description: hypothetical protein Asulf_01635 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-20   73.4   0.2    4.7e-20   73.0   0.2    1.1  1  Metallophos    Calcineurin-like phosphoesterase
    0.00025   21.3   0.0    0.00039   20.7   0.0    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
       0.11   12.5   2.9       0.23   11.6   2.9    1.5  1  DSS1_SEM1      DSS1/SEM1 family


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.2   7.8e-24   4.7e-20       4     201 ..      32     215 ..      30     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 7.8e-24
                                       EEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS..HHHHHHHHHHHHHHHHTSEEEEEC-TTS... CS
                       Metallophos   4 lvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg..dlekellellaalvkypipvylllGNHe... 75 
                                       +v+gD+H     ++ ++l++++    ++ k++++l  GD+ drg  ++e+ + e l+ + +    v++l+GNHe   
  gi|488601132|ref|YP_007907603.1|  32 IVVGDIH-----ADVETLREII---SKDAKCYIFL--GDYADRGeyPVET-YFEILRLMNE--SYVVMLRGNHEsgn 95 
                                       69*****.....8888888888...5556******..*******888888.5555677777..368********988 PP

                                       ....CHHHHHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC CS
                       Metallophos  76 ....gfeeellnkygylgif.sepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg 147
                                                  +   y+g+f  e+ ++ +e  + lp+++      +++++hGg p                     g
  gi|488601132|ref|YP_007907603.1|  96 vyphD---LPYHIKSYFGEFaEEILEKISELWSKLPVCA-CRE--DYFFVHGGIPTM-------------------G 147
                                       54331...455555555566566666668888*******.555..7*******3222...................2 PP

                                       ....HHHHHHHHHHTTCSEEEEEESSESS..........CSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                       Metallophos 148 ....dewlkdlekrekadwvivlgHsply..........rgsgylfgdealedllkkygvdlvisGHt 201
                                           +e+ ++  k  ++d v+ + +  ++          rg +y fg + ++ +l++ + +++++GH+
  gi|488601132|ref|YP_007907603.1| 148 rkyfEEFSEEMIKNPDDDAVMEMLWNDPWekdenglnyqRGRYYFFGMRTTRAFLDQLEFKVIVRGHE 215
                                       222222222244448999999999999999*************************************8 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.5e-08   0.00039       4     100 ..      32     142 ..      30     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.5e-08
                     Metallophos_2   4 aiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellela......pvlaVrGNnD.........e 63 
                                       +++ D+H+ ++ l++++++ +++     i++GD+    +e   +e+ +e++       v++ rGN++         +
  gi|488601132|ref|YP_007907603.1|  32 IVVGDIHADVETLREIISKDAKC----YIFLGDYadR-GEY-PVETYFEILrlmnesYVVMLRGNHEsgnvyphdlP 102
                                       79*****************9999....99****9633.333.45555555556688899999*****8666555442 PP

                     Metallophos_2  64 evveedvlreaaelgtdlpeeaelel....agekvlliHgd 100
                                       +++++ +++ a+e+ +++ +e + +l     +e+ +++Hg 
  gi|488601132|ref|YP_007907603.1| 103 YHIKSYFGEFAEEILEKI-SELWSKLpvcaCREDYFFVHGG 142
                                       223333333333333333.2222222223233346777765 PP

>> DSS1_SEM1  DSS1/SEM1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.9   3.8e-05      0.23      15      45 ..     151     180 ..     149     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                                       TTHHHHH----------..---BESSTTTSC CS
                         DSS1_SEM1  15 FEeFpvedwdeeeeeakeekklWednWDDdd 45 
                                       FEeF +e  ++ +++a   + lW+d W+ d+
  gi|488601132|ref|YP_007907603.1| 151 FEEFSEEMIKNPDDDAV-MEMLWNDPWEKDE 180
                                       ******99988877765.9*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1843.06
//
Query:       gi|488601133|ref|YP_007907604.1|  [L=564]
Description: DNA ligase I, ATP-dependent (dnl1) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-58  196.2   0.1      1e-57  195.1   0.1    1.6  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    4.8e-38  131.2   2.2    9.5e-36  123.7   0.7    3.0  3  DNA_ligase_A_N  DNA ligase N terminus
    6.1e-21   74.9   0.1    2.4e-20   73.0   0.0    2.0  2  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
    9.1e-06   26.1   0.3    2.4e-05   24.7   0.1    1.8  2  RNA_ligase      RNA ligase


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.1   0.1   2.2e-61     1e-57       2     204 .]     229     428 ..     228     428 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 2.2e-61
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEE CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDG 78 
                                       mLA+ ++s+e+a+ ++ ++ + vE+K+DG+R+q+h  +++++++SRrl+++t+a+p++v+++k+ +k     vilDG
  gi|488601133|ref|YP_007907604.1| 229 MLAQVAESVESAVMEM-GRVA-VEWKFDGTRVQIHYADGRITIYSRRLENVTKALPDVVEMVKKSVKSG---VILDG 300
                                       9**************9.6666.9******************************************9985...9**** PP

                                       EEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEH....TTSCHHHHHHHHHHHB--BTT CS
                    DNA_ligase_A_M  79 ElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesl....tdeplkeRrklLeeilkesed 151
                                       E++a+  ++g++lpfq + +r+++k++++++++++++ + vFDiLy+d+e +    +d+pl+eRrk+Le+++k + +
  gi|488601133|ref|YP_007907604.1| 301 EAIAI--KDGKPLPFQNILRRFRRKHRISQAVEKIPITVQVFDILYCDNEIYsgetIDLPLHERRKILENVVKDDGN 375
                                       ****7..889**************************************99888888********************* PP

                                       TEEE--EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 152 rvelaeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                        ++la++  ++dv+ + e+++eai++g+EG+++K pds Y pgkr+knwlK+K
  gi|488601133|ref|YP_007907604.1| 376 GLKLARQEITSDVRRVHEIFDEAIAAGHEGVMLKRPDSLYIPGKRGKNWLKIK 428
                                       ****************************************************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 !  123.7   0.7   2.1e-39   9.5e-36       2     173 .]       6     180 ..       5     180 .. 0.94
   2 !   15.2   0.0   4.6e-06      0.02      57     102 ..     168     213 ..     168     250 .. 0.81
   3 ?   -0.1   0.0      0.23     1e+03     104     131 ..     420     447 ..     377     464 .. 0.75

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 2.1e-39
                                       CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT- CS
                    DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealgl 74 
                                       F e++e+++++e+  ++ +e ++ +anf+r++e  +++d+y ++ +    ++P +d+re gig  l+++al  ++gl
  gi|488601133|ref|YP_007907604.1|   6 FLEFSEFCDELEK-ISSTIELSSKIANFLRNIE--SDDDIYNIALFltgrIYPPWDEREVGIGVGLVYEALRLTTGL 79 
                                       8899999999999.5666899**********88..466899988888****************************** PP

                                       -HHHHHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHH CS
                    DNA_ligase_A_N  75 skkkikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEak 149
                                       +k++i++  +++gDlg + e+vls++ ++    ++lti+ + e +d +++  g++s+++k+++l +l+++asp Eak
  gi|488601133|ref|YP_007907604.1|  80 KKREIEEIVKETGDLGLASEKVLSRKLQTiLFREELTIAYLREVFDAMSSLkGEKSQKKKVRMLMDLFSSASPIEAK 156
                                       ***********************9999999******************97799************************ PP

                                       HHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 150 yliriilkdlriglsektvldala 173
                                       y++r++l+++r+g++e+ ++da+a
  gi|488601133|ref|YP_007907604.1| 157 YITRLLLGEMRLGVGEGILRDAIA 180
                                       *********************997 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.6e-06
                                       ----HHHHHHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCHHH CS
                    DNA_ligase_A_N  57 ygigesllakalaealglskkkikdalakvgDlgevaeevlskrst 102
                                       +g+ge +l+ a+a+a++ls + ++ a+  ++D+g+va  ++++  +
  gi|488601133|ref|YP_007907604.1| 168 LGVGEGILRDAIAKAFNLSADIVERAYMITNDFGKVAVTAKKEGEE 213
                                       69*******************999999889******9888876655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.23
                                       ------BHHHHHHHHHHHHH-STTHHHH CS
                    DNA_ligase_A_N 104 akkspltieevnelLdklaaagkgsede 131
                                       + k+ l i+ev e+Ld +  ag+  e +
  gi|488601133|ref|YP_007907604.1| 420 RGKNWLKIKEVMETLDLVVVAGEWGEGK 447
                                       56788999*******9998775544433 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 ?   -2.3   0.0       1.6     7e+03      23      42 ..      74      93 ..      69     106 .. 0.77
   2 !   73.0   0.0   5.3e-24   2.4e-20       2      99 .]     449     539 ..     448     539 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                      EE-SS--HHHHHHHHHHHGG CS
                    DNA_ligase_A_C 23 kvgtGfsdaeleelrkklke 42
                                      +  tG++++e+ee+ k+  +
  gi|488601133|ref|YP_007907604.1| 74 RLTTGLKKREIEEIVKETGD 93
                                      5679999***9999998765 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 5.3e-24
                                       GGSEEEEEEEEEE.TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEE CS
                    DNA_ligase_A_C   2 gglvgslllgvyd.dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaei 77 
                                       ++ ++s+ l++   +g+l  vgkv+tGf++++leel++ +k    ++ ++      ee ++v ++P++v+eV+++ei
  gi|488601133|ref|YP_007907604.1| 449 SHFISSFELACVAeNGDLLPVGKVATGFTEDDLEELTELFK----NEIEY------EEGKKVVFKPKYVFEVAYQEI 515
                                       6789******9999**************************4....44555......11122569************* PP

                                       ECTSSSTT..EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  78 tasgkyka..slRfPrfkrlReDk 99 
                                       ++s+ky++  +lRfPrf+rlReDk
  gi|488601133|ref|YP_007907604.1| 516 QKSPKYESgyALRFPRFVRLREDK 539
                                       ***********************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   5.4e-09   2.4e-05       2     161 .]     246     428 ..     245     428 .. 0.66
   2 ?   -2.1   0.0      0.94   4.2e+03      66      76 ..     486     496 ..     433     546 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.4e-09
                                       EEEEEEE-SSEEEEEEEETT.EEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES........ CS
                        RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqilpfgeekfkefkrwaaalrkklkeklaneelilyGElig........ 69 
                                       +v v+ K DGt+++i++ ++ +++ sR+ +           ++   +  + +k+  +   +il GE i         
  gi|488601133|ref|YP_007907604.1| 246 RVAVEWKFDGTRVQIHYADGrITIYSRRLEN---------VTKALPDVVEMVKKSVK-SGVILDGEAIAikdgkplp 312
                                       578999***********95569999999888.........34444555556677777.45*********76665555 PP

                                       ..SS..TTSS.................EEEEEEEEEEECTT....BECE--HHHHHHHHH........CCTB..EEE CS
                        RNA_ligase  70 .hsikygglpk................efyvFdifdirdke....eqrylspdevealak........glgtvpvly 117
                                        ++i +                        vFdi+  + +e    e   l+  e++++++        g    +++ 
  gi|488601133|ref|YP_007907604.1| 313 fQNILR----RfrrkhrisqavekipiTVQVFDILYCD-NEiysgETIDLPLHERRKILEnvvkddgnG---LKLA- 380
                                       533322....133334777778888888899****998.223455888999999966666244333321...2222. PP

                                       EE.SS.HHHHHCCC...HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                        RNA_ligase 118 egkfl.aaeellel..llskgnkrEGlVikpeselyk.nkg.raifKvk 161
                                       + +++ + + + e+  +       EG+ +k +++ly   k+ ++++K+k
  gi|488601133|ref|YP_007907604.1| 381 RQEITsDVRRVHEIfdE-AIAAGHEGVMLKRPDSLYIpGKRgKNWLKIK 428
                                       22222233334444431.234589**************9999*****97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.94
                                       EEES.SS..TT CS
                        RNA_ligase  66 Elighsikygg 76 
                                       El+ + i+y++
  gi|488601133|ref|YP_007907604.1| 486 ELFKNEIEYEE 496
                                       44444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 3265.12
//
Query:       gi|488601134|ref|YP_007907605.1|  [L=369]
Description: hypothetical protein Asulf_01637 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  110.9   5.4    7.7e-11   42.1   0.0    5.2  5  TPR_12        Tetratricopeptide repeat
      1e-18   66.5   3.0    3.3e-05   23.6   0.0    6.3  6  TPR_10        Tetratricopeptide repeat
    1.4e-15   56.3  11.9    0.00024   20.8   0.0    5.6  6  TPR_1         Tetratricopeptide repeat
    1.7e-15   55.8  13.0    0.00044   20.1   0.1    6.4  6  TPR_2         Tetratricopeptide repeat
    4.9e-13   48.2  18.9    0.00047   20.1   0.1    6.5  7  TPR_8         Tetratricopeptide repeat
    2.7e-10   39.5   2.4     0.0073   16.3   0.0    6.3  6  TPR_7         Tetratricopeptide repeat
    9.1e-06   25.3   0.0    4.6e-05   23.0   0.0    1.9  2  TPR_MalT      MalT-like TPR region
    8.2e-05   22.7   2.0       0.51   10.8   0.0    4.7  5  TPR_17        Tetratricopeptide repeat
    0.00066   20.3   3.7         45    5.3   0.0    5.8  5  TPR_14        Tetratricopeptide repeat
    0.00085   19.8   7.4       0.19   12.3   0.2    4.9  5  TPR_19        Tetratricopeptide repeat
     0.0088   16.7   4.2      0.047   14.3   0.0    3.6  2  TPR_16        Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.021   14.5   0.3        3.5    7.4   0.0    3.3  3  TPR_11        TPR repeat
      0.064   13.2   0.1       0.15   12.0   0.1    1.6  1  RHD_DNA_bind  Rel homology DNA-binding domain
      0.065   13.3   0.1      0.065   13.3   0.1    3.7  4  MIT           MIT (microtubule interacting and transport) dom
      0.076   13.7  10.7         37    5.2   0.0    6.3  5  TPR_6         Tetratricopeptide repeat
       0.34   11.0   8.0        1.1    9.4   0.8    3.9  3  ANAPC5        Anaphase-promoting complex subunit 5
       0.36   11.2   6.9       0.72   10.2   1.0    3.3  4  RPN6_N        26S proteasome regulatory subunit RPN6 N-termin
       0.59   10.3  12.5       0.57   10.3   3.3    3.2  3  DUF4363       Domain of unknown function (DUF4363)
       0.89    9.2  12.8        3.4    7.4   4.8    2.8  3  DUF2225       Uncharacterized protein conserved in bacteria (
        9.6    6.4   9.2       0.49   10.5   2.0    2.6  3  DUF4110       Domain of unknown function (DUF4110)


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 !   11.1   0.4   0.00042      0.38      30      75 ..      92     135 ..      88     137 .. 0.84
   2 !   33.4   0.0   4.6e-11   4.1e-08       7      77 .]     153     224 ..     148     224 .. 0.90
   3 !   42.1   0.0   8.6e-14   7.7e-11       3      77 .]     192     269 ..     190     269 .. 0.93
   4 !   34.8   0.1   1.7e-11   1.5e-08       1      75 [.     235     312 ..     235     314 .. 0.86
   5 !   22.6   0.3   1.1e-07   9.5e-05       4      76 ..     283     358 ..     280     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                            TPR_12  30 leiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                         +ar+   + ++l+a+tl n + ++++++  + A++++ ea +i+
  gi|488601134|ref|YP_007907605.1|  92 AKLARKF--GLKELEAITLSNSAKALSMMNMADRAERAYAEADRIF 135
                                       5667666..56789**************************996665 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 4.6e-11
                            TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdh.pltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                       n  ++++ + +r+deA+++l +a++++++  +  + + +a +l nLg l  ++++++eA e++ +a +i++k
  gi|488601134|ref|YP_007907605.1| 153 NDFGSFCIEHERFDEAEKYLMEAHDLVNKNRELFSdDMLAHILSNLGSLKTEQKKFDEAMEFYSKAEEIFRK 224
                                       45788888889****************88877777789*******************************986 PP

  == domain 3  score: 42.1 bits;  conditional E-value: 8.6e-14
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdh...pltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       a +l+nl+++ ++++++deA e++ ka ei+r++ ++d+    ++a++l n g +yr+++++ +A+e ++ea +i+e
  gi|488601134|ref|YP_007907605.1| 192 AHILSNLGSLKTEQKKFDEAMEFYSKAEEIFRKVVEKDKskeIDLAIVLSNFGAMYREMKDFSKAEEKFNEAKEIFE 268
                                       8899******************************88877567899****************************9998 PP

                            TPR_12  77 k 77 
                                       +
  gi|488601134|ref|YP_007907605.1| 269 E 269
                                       5 PP

  == domain 4  score: 34.8 bits;  conditional E-value: 1.7e-11
                            TPR_12   1 dvatalnnlaavlrrlgrydeAlellekaleiarrllGpd...hpltattlrnLgrlyralgryeeAlelleealai 74 
                                       d+a++l+n +a++r+++++ +A+e +++a ei+++l   +   + ++  +l nLg++y ++gr++eA+e++ + l+i
  gi|488601134|ref|YP_007907605.1| 235 DLAIVLSNFGAMYREMKDFSKAEEKFNEAKEIFEELAKRNlfyRSYLGDALTNLGIIYKKTGRLKEAEEAFLKDLEI 311
                                       5799*****************************99955542223578899********************9887777 PP

                            TPR_12  75 a 75 
                                       +
  gi|488601134|ref|YP_007907605.1| 312 K 312
                                       6 PP

  == domain 5  score: 22.6 bits;  conditional E-value: 1.1e-07
                            TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpl....tattlrnLgrlyralgryeeAlelleealaiae 76 
                                        al+nl+ ++ + gr+ eA+e + k lei + l  + +p+    +a +l n+++ y + g+ ++A+++ eea +i+e
  gi|488601134|ref|YP_007907605.1| 283 DALTNLGIIYKKTGRLKEAEEAFLKDLEIKKDL-MERNPAylksYAHSLDNIADFYKEVGNEKKARKYKEEANRIYE 358
                                       5889**************************877.455554122268899***********************98886 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3       2.4   2.2e+03       5      28 ..     108     131 ..     105     137 .. 0.62
   2 ?    3.8   0.0     0.063        56      15      28 ..     162     175 ..     150     179 .. 0.77
   3 !   16.4   0.0   6.9e-06    0.0061       1      38 [.     191     228 ..     191     229 .. 0.89
   4 !    9.2   0.0    0.0012       1.1       2      31 ..     237     266 ..     236     274 .. 0.79
   5 !   23.6   0.0   3.7e-08   3.3e-05       3      40 ..     283     320 ..     281     322 .. 0.93
   6 !    7.7   0.1    0.0038       3.4       2      32 ..     327     357 ..     327     361 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.4
                            TPR_10   5 lnNLanalrqrgrydeAealleea 28 
                                       l+N a al+ ++  d+Ae+ + ea
  gi|488601134|ref|YP_007907605.1| 108 LSNSAKALSMMNMADRAERAYAEA 131
                                       555566666666666677666665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.063
                            TPR_10  15 rgrydeAealleea 28 
                                         r+deAe++l ea
  gi|488601134|ref|YP_007907605.1| 162 HERFDEAEKYLMEA 175
                                       579*******9998 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 6.9e-06
                            TPR_10   1 tAsslnNLanalrqrgrydeAealleealairrrllGp 38 
                                       +A +l+NL+ + ++++++deA++++ +a +i r++++ 
  gi|488601134|ref|YP_007907605.1| 191 LAHILSNLGSLKTEQKKFDEAMEFYSKAEEIFRKVVEK 228
                                       5899*********************9998888888775 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0012
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                                       A  l+N ++++r+++++ +Ae+ + ea +i
  gi|488601134|ref|YP_007907605.1| 237 AIVLSNFGAMYREMKDFSKAEEKFNEAKEI 266
                                       5679*****************866666555 PP

  == domain 5  score: 23.6 bits;  conditional E-value: 3.7e-08
                            TPR_10   3 sslnNLanalrqrgrydeAealleealairrrllGpdH 40 
                                        +l+NL++++ ++gr++eAe+ + + l+i + l ++++
  gi|488601134|ref|YP_007907605.1| 283 DALTNLGIIYKKTGRLKEAEEAFLKDLEIKKDLMERNP 320
                                       589****************************9999875 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0038
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealair 32 
                                       A sl N+a  + ++g+ ++A+++ eea +i+
  gi|488601134|ref|YP_007907605.1| 327 AHSLDNIADFYKEVGNEKKARKYKEEANRIY 357
                                       789*******************988876666 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.6   5.4e+02       2      27 ..     106     131 ..     105     131 .. 0.87
   2 ?    4.1   0.0     0.049        44      15      29 ..     163     177 ..     156     180 .. 0.85
   3 !   20.8   0.0   2.7e-07   0.00024       3      30 ..     194     221 ..     192     224 .. 0.91
   4 !   13.7   0.1   4.7e-05     0.042       3      31 ..     239     267 ..     237     270 .. 0.86
   5 !   20.8   0.1   2.7e-07   0.00024       2      26 ..     283     307 ..     282     314 .. 0.91
   6 ?   -2.3   0.1       5.4   4.8e+03       6      23 ..     332     349 ..     332     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekA 27 
                                        +l n + a+  +++ d A+ +y +A
  gi|488601134|ref|YP_007907605.1| 106 ITLSNSAKALSMMNMADRAERAYAEA 131
                                       57888999999***********9877 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.049
                                       T-HHHHHHHHHHHHH CS
                             TPR_1  15 gkydeAleyyekALe 29 
                                       +++deA++y  +A  
  gi|488601134|ref|YP_007907605.1| 163 ERFDEAEKYLMEAHD 177
                                       79********99976 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2.7e-07
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                       +l nlG +  +++k+deA e+y+kA e+
  gi|488601134|ref|YP_007907605.1| 194 ILSNLGSLKTEQKKFDEAMEFYSKAEEI 221
                                       689**********************887 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 4.7e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                       +l n G++y++++++ +A+e +++A e+ 
  gi|488601134|ref|YP_007907605.1| 239 VLSNFGAMYREMKDFSKAEEKFNEAKEIF 267
                                       5666699******************9986 PP

  == domain 5  score: 20.8 bits;  conditional E-value: 2.7e-07
                                       HHHHHHHHHHHHTT-HHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyek 26 
                                       +al nlG +y k g+++eA+e++ k
  gi|488601134|ref|YP_007907605.1| 283 DALTNLGIIYKKTGRLKEAEEAFLK 307
                                       79********************977 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 5.4
                                       HHHHHHHHTT-HHHHHHH CS
                             TPR_1   6 nlGnayfklgkydeAley 23 
                                       n++  y + g+ ++A +y
  gi|488601134|ref|YP_007907605.1| 332 NIADFYKEVGNEKKARKY 349
                                       677789999999999876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.33   2.9e+02       3      27 ..     107     131 ..     105     131 .. 0.87
   2 ?    6.6   0.0      0.01       9.3      11      31 ..     159     179 ..     152     182 .. 0.83
   3 !   13.2   0.0   8.1e-05     0.072       2      31 ..     193     222 ..     192     225 .. 0.89
   4 !   14.6   0.0   2.9e-05     0.026       1      32 [.     237     268 ..     237     270 .. 0.89
   5 !   20.1   0.1     5e-07   0.00044       2      32 ..     283     313 ..     282     315 .. 0.91
   6 ?    3.1   0.3      0.14   1.3e+02       3      27 ..     329     353 ..     327     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.33
                             TPR_2   3 alynlGlayyklgdyeeAleafekA 27 
                                        l n ++a+  ++  ++A++a+ +A
  gi|488601134|ref|YP_007907605.1| 107 TLSNSAKALSMMNMADRAERAYAEA 131
                                       678889999999**********998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                             TPR_2  11 yyklgdyeeAleafekAleld 31 
                                       +++  +++eA++++ +A  l 
  gi|488601134|ref|YP_007907605.1| 159 CIEHERFDEAEKYLMEAHDLV 179
                                       67789************9886 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 8.1e-05
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                        +l nlG +  ++++++eA e++ kA e+ 
  gi|488601134|ref|YP_007907605.1| 193 HILSNLGSLKTEQKKFDEAMEFYSKAEEIF 222
                                       57899*********************9886 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 2.9e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       a +l n G  y++++d+ +A+e f++A e+ +
  gi|488601134|ref|YP_007907605.1| 237 AIVLSNFGAMYREMKDFSKAEEKFNEAKEIFE 268
                                       5678899********************99875 PP

  == domain 5  score: 20.1 bits;  conditional E-value: 5e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                       +al nlG +y k g+++eA+eaf k le+  
  gi|488601134|ref|YP_007907605.1| 283 DALTNLGIIYKKTGRLKEAEEAFLKDLEIKK 313
                                       6899*********************999865 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.14
                             TPR_2   3 alynlGlayyklgdyeeAleafekA 27 
                                        l n+++ y + g+ ++A+++ e+A
  gi|488601134|ref|YP_007907605.1| 329 SLDNIADFYKEVGNEKKARKYKEEA 353
                                       5789999*************96666 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       5.4   4.9e+03      11      30 ..     115     134 ..     108     137 .. 0.69
   2 ?    5.7   0.0     0.023        21       7      27 ..     155     175 ..     150     178 .. 0.84
   3 !   17.0   0.1   5.5e-06    0.0049       1      31 [.     192     222 ..     192     225 .. 0.90
   4 ?    5.7   0.4     0.023        20       6      30 ..     242     266 ..     237     270 .. 0.82
   5 ?    3.7   0.2       0.1        91      14      30 ..     257     273 ..     253     275 .. 0.83
   6 !   20.1   0.1   5.3e-07   0.00047       2      33 ..     283     314 ..     282     315 .. 0.92
   7 !    8.7   0.3    0.0025       2.3       1      30 [.     327     356 ..     327     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.4
                                       HHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  11 ylklgdyeeAkeyyekalel 30 
                                       ++ ++  + A+ +y +a ++
  gi|488601134|ref|YP_007907605.1| 115 LSMMNMADRAERAYAEADRI 134
                                       55566778888888888665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.023
                                       HHHHHHHTT-HHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyeka 27 
                                        gs +++ ++++eA++y+++a
  gi|488601134|ref|YP_007907605.1| 155 FGSFCIEHERFDEAEKYLMEA 175
                                       677888889**********98 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 5.5e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       a+++ nlgs+  ++++++eA+e+y ka e+ 
  gi|488601134|ref|YP_007907605.1| 192 AHILSNLGSLKTEQKKFDEAMEFYSKAEEIF 222
                                       56788**********************9985 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.023
                                       HHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekalel 30 
                                       n g  y++++d+ +A+e +++a e+
  gi|488601134|ref|YP_007907605.1| 242 NFGAMYREMKDFSKAEEKFNEAKEI 266
                                       6677899999999999999999887 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.1
                                       TT-HHHHHHHHHHHHHH CS
                             TPR_8  14 lgdyeeAkeyyekalel 30 
                                        ++++eAke +e+  + 
  gi|488601134|ref|YP_007907605.1| 257 EEKFNEAKEIFEELAKR 273
                                       5789********98775 PP

  == domain 6  score: 20.1 bits;  conditional E-value: 5.3e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +a+ nlg iy+k+g+++eA+e++ k le+++d
  gi|488601134|ref|YP_007907605.1| 283 DALTNLGIIYKKTGRLKEAEEAFLKDLEIKKD 314
                                       6899*********************9998875 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0025
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a+++ n+++ y++ g+ ++A +y e+a ++
  gi|488601134|ref|YP_007907605.1| 327 AHSLDNIADFYKEVGNEKKARKYKEEANRI 356
                                       56788******************8888666 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       2.1   1.9e+03      14      29 ..     127     141 ..     107     145 .. 0.56
   2 ?   -2.3   0.0       6.8   6.1e+03      13      22 ..     163     172 ..     156     173 .. 0.79
   3 !    8.0   0.0    0.0034       3.1       2      24 ..     195     217 ..     194     234 .. 0.91
   4 ?    4.2   0.0     0.057        51       2      24 ..     240     262 ..     239     273 .. 0.85
   5 !   16.3   0.0   8.1e-06    0.0073       1      31 [.     284     314 ..     284     318 .. 0.94
   6 ?    4.1   0.0     0.062        56       1      21 [.     329     349 ..     329     360 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                             TPR_7  14 dyeeAielyeqsLalt 29 
                                        y+eA +++++ L++t
  gi|488601134|ref|YP_007907605.1| 127 AYAEADRIFRE-LEMT 141
                                       35555555555.6655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.8
                             TPR_7  13 GdyeeAiely 22 
                                        +++eA++++
  gi|488601134|ref|YP_007907605.1| 163 ERFDEAEKYL 172
                                       5899**9985 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0034
                             TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                       L+nL++l  ++ +++eA e+y +
  gi|488601134|ref|YP_007907605.1| 195 LSNLGSLKTEQKKFDEAMEFYSK 217
                                       89******************966 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.057
                             TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                       L+n + +y+++ d+++A+e + +
  gi|488601134|ref|YP_007907605.1| 240 LSNFGAMYREMKDFSKAEEKFNE 262
                                       6778999***********98865 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 8.1e-06
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                       aL nL+ +y + G+ +eA+e + + L++ kd
  gi|488601134|ref|YP_007907605.1| 284 ALTNLGIIYKKTGRLKEAEEAFLKDLEIKKD 314
                                       799*********************9999987 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.062
                             TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                       +L+n+a+ y ++G+ ++A ++
  gi|488601134|ref|YP_007907605.1| 329 SLDNIADFYKEVGNEKKARKY 349
                                       799***********9999777 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   5.1e-08   4.6e-05      12     183 ..     119     304 ..     111     310 .. 0.76
   2 ?    1.8   0.0      0.14   1.2e+02      43     155 ..     285     315 ..     281     359 .. 0.50

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.1e-08
                          TPR_MalT  12 iasgdaeralelArqALallpeddllariaatav..lGeasllqGdleaAlqalqeaeklarqadslhv..allall 84 
                                        +  +aera + A ++   l+  d   r+ ++ +   G      +++++A++ l+ea +l  +   l    +l ++l
  gi|488601134|ref|YP_007907605.1| 119 NMADRAERAYAEADRIFRELEMTDEILRGFVSNLndFGSFCIEHERFDEAEKYLMEAHDLVNKNRELFSddMLAHIL 195
                                       5667899999999999999999999999888666234666666779*************986555553334888888 PP

                          TPR_MalT  85 .qqaeilvaqGrLheAletyeqa...lqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.e 156
                                         ++ + ++q +++eA+e y +a   ++ + e++ ++     ++l   +  ++E+ d+ +Ae+  +e+ e+ e+l +
  gi|488601134|ref|YP_007907605.1| 196 sNLGSLKTEQKKFDEAMEFYSKAeeiFRKVVEKDKSKEIDLAIVLSNFGAMYREMKDFSKAEEKFNEAKEIFEELaK 272
                                       68999***************7652226666667766666666777889**************************978 PP

                          TPR_MalT 157 peaaldayvllar.....ialaqGdleeAetl 183
                                       ++ ++++y+  a      i+   G+l+eAe++
  gi|488601134|ref|YP_007907605.1| 273 RNLFYRSYLGDALtnlgiIYKKTGRLKEAEEA 304
                                       89999888754431111144556666666665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.14
                          TPR_MalT  43 tavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlp 119
                                       + +lG ++  +G+l++A++a+                                                        
  gi|488601134|ref|YP_007907605.1| 285 LTNLGIIYKKTGRLKEAEEAF-------------------------------------------------------- 305
                                       445555555555555555555........................................................ PP

                          TPR_MalT 120 lvgfllvlladllyEwndLeeAeqhlqeGielleql 155
                                                                 ++ +e+ ++l
  gi|488601134|ref|YP_007907605.1| 306 --------------------------LKDLEIKKDL 315
                                       ..........................4444444443 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.6   5.9e+03      18      33 ..     110     125 ..     105     126 .. 0.75
   2 ?    0.4   0.0       1.2   1.1e+03      18      33 ..     190     205 ..     190     211 .. 0.79
   3 ?    1.3   0.0      0.64   5.8e+02       2      34 .]     222     258 ..     221     258 .. 0.78
   4 !   10.8   0.0   0.00057      0.51      14      34 .]     283     303 ..     269     303 .. 0.94
   5 ?    4.9   0.1     0.045        40       7      34 .]     317     348 ..     313     348 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.6
                            TPR_17  18 nLAelllknGdlmtAr 33 
                                       n A++l++ +  ++A+
  gi|488601134|ref|YP_007907605.1| 110 NSAKALSMMNMADRAE 125
                                       5588888888888886 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                            TPR_17  18 nLAelllknGdlmtAr 33 
                                       +LA +l+++G l+t +
  gi|488601134|ref|YP_007907605.1| 190 MLAHILSNLGSLKTEQ 205
                                       5999999999777654 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.64
                            TPR_17   2 ylkaleldPnn....adaynnLAelllknGdlmtArq 34 
                                       ++k++e+d++     a ++ n +  +++ +d+ +A++
  gi|488601134|ref|YP_007907605.1| 222 FRKVVEKDKSKeidlAIVLSNFGAMYREMKDFSKAEE 258
                                       56677777666666699999*******9999999985 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00057
                            TPR_17  14 daynnLAelllknGdlmtArq 34 
                                       da++nL+ +++k G+l++A++
  gi|488601134|ref|YP_007907605.1| 283 DALTNLGIIYKKTGRLKEAEE 303
                                       89*****************96 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.045
                            TPR_17   7 eldPnn....adaynnLAelllknGdlmtArq 34 
                                       e++P +    a ++ n A ++++ G+ ++Ar+
  gi|488601134|ref|YP_007907605.1| 317 ERNPAYlksyAHSLDNIADFYKEVGNEKKARK 348
                                       566555555599999**************996 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.98   8.8e+02       9      29 ..     113     133 ..     111     142 .. 0.74
   2 ?    4.6   0.0     0.082        73       8      35 ..     156     183 ..     152     194 .. 0.82
   3 ?    5.3   0.0      0.05        45       7      31 ..     198     222 ..     189     229 .. 0.79
   4 ?    0.1   0.0       2.3     2e+03      11      27 ..     247     263 ..     235     275 .. 0.57
   5 ?    3.2   0.0      0.23   2.1e+02       6      24 ..     287     305 ..     283     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.98
                            TPR_14   9 eallalGdpdeAiallrrala 29 
                                       +al      d+A++++ +a +
  gi|488601134|ref|YP_007907605.1| 113 KALSMMNMADRAERAYAEADR 133
                                       566666778899999988865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.082
                            TPR_14   8 aeallalGdpdeAiallrralalaPdda 35 
                                       ++++ + +++deA+++l +a +l  +++
  gi|488601134|ref|YP_007907605.1| 156 GSFCIEHERFDEAEKYLMEAHDLVNKNR 183
                                       57788899*********99988766655 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.05
                            TPR_14   7 laeallalGdpdeAiallrralala 31 
                                       l+++  ++ ++deA++ + +a + +
  gi|488601134|ref|YP_007907605.1| 198 LGSLKTEQKKFDEAMEFYSKAEEIF 222
                                       5666777888*******99998866 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.3
                            TPR_14  11 llalGdpdeAiallrra 27 
                                       +++  d+ +A++ +++a
  gi|488601134|ref|YP_007907605.1| 247 YREMKDFSKAEEKFNEA 263
                                       44455555555555554 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.23
                            TPR_14   6 alaeallalGdpdeAiall 24 
                                        l+ ++   G+++eA++++
  gi|488601134|ref|YP_007907605.1| 287 NLGIIYKKTGRLKEAEEAF 305
                                       58999***********998 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.8   3.4e+03      32      50 ..     112     130 ..     106     140 .. 0.60
   2 ?    3.6   0.0       0.1        94       3      39 ..     161     199 ..     159     203 .. 0.79
   3 ?    5.1   0.1     0.037        34       3      21 ..     204     230 ..     202     274 .. 0.52
   4 !   12.3   0.2   0.00021      0.19       3      50 ..     256     307 ..     254     324 .. 0.80
   5 ?   -0.8   0.0       2.6   2.3e+03      30      46 ..     332     348 ..     309     349 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.8
                            TPR_19  32 AeallalgqldeAealLda 50 
                                       A+al  ++  d Ae++ ++
  gi|488601134|ref|YP_007907605.1| 112 AKALSMMNMADRAERAYAE 130
                                       4555555555555554444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                            TPR_19   3 aegdyaeAlalleqalqedpknaearl..lLAeallalg 39 
                                       + ++++eA ++l +a +  +kn e+     LA +l +lg
  gi|488601134|ref|YP_007907605.1| 161 EHERFDEAEKYLMEAHDLVNKNRELFSddMLAHILSNLG 199
                                       567899999999999999999999888766777777776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.037
                            TPR_19   3 aegdyaeAlalleqalqe........d 21 
                                       ++++++eA++++++a +         +
  gi|488601134|ref|YP_007907605.1| 204 EQKKFDEAMEFYSKAEEIfrkvvekdK 230
                                       688899998888887544333333222 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00021
                            TPR_19   3 aegdyaeAlalleqalqe....dpknaearllLAeallalgqldeAealLda 50 
                                       ae+++ eA +++e++ +         ++a+ +L +++ ++g+l+eAe++  +
  gi|488601134|ref|YP_007907605.1| 256 AEEKFNEAKEIFEELAKRnlfyRSYLGDALTNLGIIYKKTGRLKEAEEAFLK 307
                                       67899999999999755566644447888889***************98755 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 2.6
                            TPR_19  30 lLAeallalgqldeAea 46 
                                       + A+ + + g+ ++A++
  gi|488601134|ref|YP_007907605.1| 332 NIADFYKEVGNEKKARK 348
                                       45899999999999986 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      0.42   3.8e+02      33      60 ..     191     218 ..     160     224 .. 0.70
   2 !   14.3   0.0   5.3e-05     0.047      11      58 ..     258     306 ..     247     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.42
                            TPR_16  33 aaeAllllgdaalrqgrlaeAaalyraa 60 
                                        a+ l +lg +  +q+ ++eA ++y +a
  gi|488601134|ref|YP_007907605.1| 191 LAHILSNLGSLKTEQKKFDEAMEFYSKA 218
                                       5666667777777888888888888877 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.3e-05
                            TPR_16  11 gdyddAaaaleaalkrdpssPd....aaeAllllgdaalrqgrlaeAaalyr 58 
                                        ++ +A + +e++ kr+    +      +Al +lg ++ + grl+eA+++++
  gi|488601134|ref|YP_007907605.1| 258 EKFNEAKEIFEELAKRN---LFyrsyLGDALTNLGIIYKKTGRLKEAEEAFL 306
                                       47999999999999999...8888999*********************6665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0039       3.5       1      23 [.     199     221 ..     199     222 .. 0.88
   2 ?   -0.6   0.0       1.2   1.1e+03       1      20 [.     244     263 ..     244     270 .. 0.86
   3 ?    2.8   0.0       0.1        92      30      42 .]     284     296 ..     283     315 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0039
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                       G + +eq k++eA+e Y+kA ++
  gi|488601134|ref|YP_007907605.1| 199 GSLKTEQKKFDEAMEFYSKAEEI 221
                                       566789**************886 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                            TPR_11   1 GdayyeqGkyeeAieaYkkA 20 
                                       G +y+e  ++ +A e++++A
  gi|488601134|ref|YP_007907605.1| 244 GAMYREMKDFSKAEEKFNEA 263
                                       66899********9999999 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.1
                            TPR_11  30 ayynLGlayykqG 42 
                                       a+ nLG +y k G
  gi|488601134|ref|YP_007907605.1| 284 ALTNLGIIYKKTG 296
                                       6677777777776 PP

>> RHD_DNA_bind  Rel homology DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00016      0.15      67     150 ..     175     250 ..     155     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                       SSEEESTTEETTEEEEEE-TT.TSEEE-SSEEEEE--CGGHHHHHHHHHHCT--TTS-TCGGCTSGGGS-TTEEEEE CS
                      RHD_DNA_bind  67 ahslvgkdckdgvcevelkpe.dmvasfqnlGIlcvkkkeveealkerielkekeknvekeakeeakeidlnvvrlc 142
                                       ah+lv k       + el ++    ++++nlG l++++k+ +ea++   +++e  ++ +  +k++ keidl +v   
  gi|488601134|ref|YP_007907605.1| 175 AHDLVNK-------NRELFSDdMLAHILSNLGSLKTEQKKFDEAMEFYSKAEEI-FR-KVVEKDKSKEIDLAIVLSN 242
                                       5666666.......23344441567999*****************965555443.33.4566777889******999 PP

                                       EEEEE-CS CS
                      RHD_DNA_bind 143 Fqaflpds 150
                                       F a++++ 
  gi|488601134|ref|YP_007907605.1| 243 FGAMYREM 250
                                       99998544 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 ?   -2.7   0.0       7.3   6.5e+03      29      40 ..     167     178 ..     163     187 .. 0.57
   2 ?   13.3   0.1   7.2e-05     0.065      16      47 ..     204     233 ..     192     243 .. 0.84
   3 ?   -0.8   0.0       1.8   1.6e+03      18      39 ..     251     272 ..     234     276 .. 0.75
   4 ?    2.4   0.4      0.18   1.6e+02      24      54 ..     323     354 ..     312     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.3
                               MIT  29 ealelLlqalke 40 
                                       ea ++L++a   
  gi|488601134|ref|YP_007907605.1| 167 EAEKYLMEAHDL 178
                                       555666666653 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.2e-05
                               MIT  16 nagnyeeAlelYkealelLlqalkekneerre 47 
                                       ++++++eA+e Y++a e++ +++  k+ +++e
  gi|488601134|ref|YP_007907605.1| 204 EQKKFDEAMEFYSKAEEIFRKVVE-KD-KSKE 233
                                       689********************7.33.4443 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.8
                               MIT  18 gnyeeAlelYkealelLlqalk 39 
                                       +++++A e++ ea e++ ++ k
  gi|488601134|ref|YP_007907605.1| 251 KDFSKAEEKFNEAKEIFEELAK 272
                                       7788888888888888877766 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.18
                               MIT  24 lelYkealelLlqalke.kneerrellrekie 54 
                                       l+ Y ++l+ +    ke  ne++  +++e+++
  gi|488601134|ref|YP_007907605.1| 323 LKSYAHSLDNIADFYKEvGNEKKARKYKEEAN 354
                                       688*************9988888888888776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.96   8.6e+02       9      25 ..     114     130 ..     108     138 .. 0.54
   2 ?    3.1   0.1       0.2   1.8e+02       8      26 ..     200     218 ..     195     229 .. 0.64
   3 ?    4.7   0.2     0.062        56      11      29 ..     254     273 ..     244     274 .. 0.59
   4 ?    5.2   0.0     0.041        37       1      23 [.     283     305 ..     283     307 .. 0.92
   5 ?    0.2   0.0       1.7   1.5e+03       3      22 ..     330     349 ..     328     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.96
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6   9 syrklgdtdkAlealer 25 
                                       ++ +++ +d+A +a+ +
  gi|488601134|ref|YP_007907605.1| 114 ALSMMNMADRAERAYAE 130
                                       44445555555555543 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerl 26 
                                        +  ++++ d+A+e + + 
  gi|488601134|ref|YP_007907605.1| 200 SLKTEQKKFDEAMEFYSKA 218
                                       5555667777777777654 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.062
                                       HH.HHHHHHHHHHHHHHHHH CS
                             TPR_6  11 rk.lgdtdkAlealerlike 29 
                                        k   +  +A+e++e+l k+
  gi|488601134|ref|YP_007907605.1| 254 SKaEEKFNEAKEIFEELAKR 273
                                       33224677888888888776 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAleal 23 
                                       dAl +l+  y+k+g+  +A ea+
  gi|488601134|ref|YP_007907605.1| 283 DALTNLGIIYKKTGRLKEAEEAF 305
                                       7999********99*****9998 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAlea 22 
                                       l ++a  y++ g+  kA+++
  gi|488601134|ref|YP_007907605.1| 330 LDNIADFYKEVGNEKKARKY 349
                                       56788889995588899875 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0       0.2   1.8e+02      38      58 ..      82     102 ..      64     124 .. 0.75
   2 ?    9.4   0.8    0.0012       1.1       8      68 ..     159     219 ..     156     241 .. 0.86
   3 ?    1.2   0.2      0.42   3.8e+02      37      67 ..     323     353 ..     221     358 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                            ANAPC5  38 ksyqyalLnlaslhadfghne 58 
                                        s+ +a Ln+a l  +fg +e
  gi|488601134|ref|YP_007907605.1|  82 ASWSVASLNSAKLARKFGLKE 102
                                       56889************9776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                            ANAPC5   8 alrakdYqqaldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeai 68 
                                       +++++++++a  +L++  D v++++e  +  ++   l nl sl+++  + +eA++  + a 
  gi|488601134|ref|YP_007907605.1| 159 CIEHERFDEAEKYLMEAHDLVNKNRELFSDDMLAHILSNLGSLKTEQKKFDEAMEFYSKAE 219
                                       68999**************************************999999999987665554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.42
                            ANAPC5  37 kksyqyalLnlaslhadfghneeAvkaleea 67 
                                        ksy  +l n a +  + g++++A k  eea
  gi|488601134|ref|YP_007907605.1| 323 LKSYAHSLDNIADFYKEVGNEKKARKYKEEA 353
                                       2455555666666666666666666655555 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 ?    2.0   0.1      0.28   2.5e+02      37      67 ..     194     224 ..     162     230 .. 0.74
   2 ?   10.2   1.0    0.0008      0.72       9      70 ..     215     272 ..     202     274 .. 0.85
   3 ?    0.2   0.1         1   9.2e+02      37      56 ..     284     303 ..     282     315 .. 0.83
   4 ?    1.9   0.3      0.31   2.8e+02       8      55 ..     297     347 ..     291     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.28
                            RPN6_N  37 alleLgelyrdqkkaeeLaelikesrsflss 67 
                                        l +Lg+l ++qkk +e +e+ ++ ++++ +
  gi|488601134|ref|YP_007907605.1| 194 ILSNLGSLKTEQKKFDEAMEFYSKAEEIFRK 224
                                       4778888888888888888888888887765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0008
                            RPN6_N   9 pkeaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrsflssiaK 70 
                                       +++aee+++++++k+++++     +    l + g +yr+ k+ ++  e ++e +++++++aK
  gi|488601134|ref|YP_007907605.1| 215 YSKAEEIFRKVVEKDKSKEI----DLAIVLSNFGAMYREMKDFSKAEEKFNEAKEIFEELAK 272
                                       68899999999998884444....5567899*****************************99 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1
                            RPN6_N  37 alleLgelyrdqkkaeeLae 56 
                                       al++Lg +y+++++ +e  e
  gi|488601134|ref|YP_007907605.1| 284 ALTNLGIIYKKTGRLKEAEE 303
                                       999*******9998887655 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.31
                            RPN6_N   8 dpkeaeelykeilskks...kedeealreqeqalleLgelyrdqkkaeeLa 55 
                                       + keaee++ + l+ k+   +++ + l+++ ++l ++++ y++ +++++ +
  gi|488601134|ref|YP_007907605.1| 297 RLKEAEEAFLKDLEIKKdlmERNPAYLKSYAHSLDNIADFYKEVGNEKKAR 347
                                       67888888777666655445666699****************999888765 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.5     0.015        14      49      82 ..     154     187 ..     103     206 .. 0.77
   2 ?   10.3   3.3   0.00063      0.57      30     101 ..     201     275 ..     187     278 .. 0.89
   3 ?   -2.2   0.1       4.8   4.3e+03      14      40 ..     330     353 ..     321     365 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                           DUF4363  49 kklsifiehdeldeietslaklkayietedkeea 82 
                                       ++ s+ ieh+++de e  l +++++++++ +  +
  gi|488601134|ref|YP_007907605.1| 154 DFGSFCIEHERFDEAEKYLMEAHDLVNKNRELFS 187
                                       5667889999999999999999998887765444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00063
                           DUF4363  30 weeakekleelekeWekkkkklsifiehdeldeietslaklk...ayietedkeealaelaelkfllehikekek 101
                                        ++ ++k++e+ + ++k ++++  ++e d+ +ei+ +++  +    y e++d + a ++ +e+k+++e++++ + 
  gi|488601134|ref|YP_007907605.1| 201 LKTEQKKFDEAMEFYSKAEEIFRKVVEKDKSKEIDLAIVLSNfgaMYREMKDFSKAEEKFNEAKEIFEELAKRNL 275
                                       567789********************************999733358899********************99876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.8
                           DUF4363  14 lsekleeleeaienedweeakekleel 40 
                                       l++  +  +   e +++++a +  ee+
  gi|488601134|ref|YP_007907605.1| 330 LDNIADFYK---EVGNEKKARKYKEEA 353
                                       333333333...223333444443333 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       4.4   3.9e+03     171     194 ..      91     114 ..      77     130 .. 0.67
   2 ?    5.3   2.7     0.016        14     129     184 ..     203     256 ..     127     275 .. 0.57
   3 ?    7.4   4.8    0.0037       3.4      61     157 ..     258     366 ..     252     369 .] 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.4
                           DUF2225 171 iaeLerrlgnkeealrwlskvigs 194
                                       +a+L+r++g ke    +ls+ +++
  gi|488601134|ref|YP_007907605.1|  91 SAKLARKFGLKELEAITLSNSAKA 114
                                       688888888888665566554443 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                           DUF2225 129 rdkedeekeklflkkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeea 184
                                        ++++ ++  +f+ kA e++++++ek+++  ++id a vl   + + r +++  +a
  gi|488601134|ref|YP_007907605.1| 203 TEQKKFDEAMEFYSKAEEIFRKVVEKDKS--KEIDLAIVLSNFGAMYREMKDFSKA 256
                                       33444444455555555555555555544..3444444433333333333333322 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0037
                           DUF2225  61 kdfeklskeekeklkekiskkwksr........dfskertldeaiesYkLallc.yelkkekks...kkAklalrlA 125
                                       ++f++ ++  +e+ k+++  +             ++k   l+ea e+++  l+   +l++ + +   + A  + ++A
  gi|488601134|ref|YP_007907605.1| 258 EKFNEAKEIFEELAKRNLFYRSYLGdaltnlgiIYKKTGRLKEAEEAFLKDLEIkKDLMERNPAylkSYAHSLDNIA 334
                                       5555555555555555533222222355666667888889999999999999885677777777888999******* PP

                           DUF2225 126 WlyrdkedeekeklflkkAlelykeayekesf 157
                                        +y++ ++e+k  ++ ++A ++y+  + ke+ 
  gi|488601134|ref|YP_007907605.1| 335 DFYKEVGNEKKARKYKEEANRIYEGLMRKEKG 366
                                       ***************************99986 PP

>> DUF4110  Domain of unknown function (DUF4110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       7.9   7.1e+03      54      72 ..     122     140 ..     104     143 .. 0.70
   2 ?   -2.5   0.1       6.1   5.4e+03      57      73 ..     162     178 ..     157     185 .. 0.64
   3 ?   10.5   2.0   0.00054      0.49      11      72 ..     206     272 ..     197     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.9
                           DUF4110  54 elAeerywelrpvLeelra 72 
                                       + Ae+ y e+ +++ el+ 
  gi|488601134|ref|YP_007907605.1| 122 DRAERAYAEADRIFRELEM 140
                                       6677778887777777665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.1
                           DUF4110  57 eerywelrpvLeelral 73 
                                       +er+ e+++ L e + l
  gi|488601134|ref|YP_007907605.1| 162 HERFDEAEKYLMEAHDL 178
                                       68899988777665554 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00054
                           DUF4110  11 rpgEslrdFfaRTseeWqelaieslkekgaek........kseKelkkeafelAeerywelrpvLeelra 72 
                                       +++    +F+++ +e + +++ + +++ + +         +  +e+k   f+ Aee+++e+++++eel++
  gi|488601134|ref|YP_007907605.1| 206 KKFDEAMEFYSKAEEIFRKVVEKDKSK-EIDLaivlsnfgAMYREMK--DFSKAEEKFNEAKEIFEELAK 272
                                       56777889*****99999887776665.4554589855555555554..5999**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2153.55
//
Query:       gi|488601135|ref|YP_007907606.1|  [L=219]
Description: hypothetical protein Asulf_01638 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1586.27
//
Query:       gi|488601136|ref|YP_007907607.1|  [L=378]
Description: Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-36  122.5   4.3    3.7e-20   71.9   0.1    2.7  3  CCG       Cysteine-rich domain
    8.4e-09   35.8   6.3    8.4e-09   35.8   6.3    3.2  4  Fer4_17   4Fe-4S dicluster domain
    9.9e-07   29.1   5.4    9.9e-07   29.1   5.4    2.7  3  Fer4_8    4Fe-4S dicluster domain
    7.4e-06   26.5   7.9      1e-05   26.0   6.2    2.2  2  Fer4_7    4Fe-4S dicluster domain
     0.0006   19.5   1.3     0.0006   19.5   1.3    2.9  2  Fer4      4Fe-4S binding domain
     0.0013   19.7   6.1     0.0013   19.7   6.1    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0013   18.8   9.4     0.0013   18.8   9.4    2.8  3  Fer4_9    4Fe-4S dicluster domain
     0.0038   17.3   8.8     0.0038   17.3   8.8    2.8  3  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.15   12.1   5.0        4.4    7.4   0.1    3.6  4  CpXC      CpXC protein
        0.2   11.8   8.7       0.36   11.0   0.5    3.1  3  Fer4_21   4Fe-4S dicluster domain
       0.49   10.6  18.3       0.37   11.0   2.0    3.1  3  Fer4_2    4Fe-4S binding domain
        1.7    8.8   7.9        1.4    9.2   0.6    2.6  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         6   8.9e+03      74      81 ..      67      74 ..      42      76 .. 0.60
   2 !   51.8   0.1   4.6e-17   6.9e-14       3      84 ..     140     221 ..     138     222 .. 0.97
   3 !   71.9   0.1   2.5e-23   3.7e-20       1      85 []     266     353 ..     266     353 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6
                               CCG 74 vtacpgCl 81
                                      +t+c+ C 
  gi|488601136|ref|YP_007907607.1| 67 CTTCGLCE 74
                                      56666665 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 4.6e-17
                               CCG   3 yfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacp 78 
                                       +f gC  +  + +   +   +ll+   +e+ +l ++e CCG+  +r+g+ +  e++ ++n++ +e++g++ i+t c+
  gi|488601136|ref|YP_007907607.1| 140 FFAGC-TASFKERSIAEGSVRLLNHFDIEFSHLgRDELCCGSTLFRTGQRKAGEKMFEKNLKIFEKMGVERIITSCA 215
                                       9****.99999****************************************************************** PP

                               CCG  79 gCllql 84 
                                       gC+ ++
  gi|488601136|ref|YP_007907607.1| 216 GCFRTF 221
                                       **9876 PP

  == domain 3  score: 71.9 bits;  conditional E-value: 2.5e-23
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                       v+y+d+Chl+r++  y+e+r+++k++ + ++ve+e+  e+++CCGaggg + + + l+ ++a++++++a +tga+++
  gi|488601136|ref|YP_007907607.1| 266 VTYHDPCHLGRHSgvYDEPREIIKAI-GFELVEMEHSrENSMCCGAGGGLRAQFKdLSINIARMRLKEAIDTGAKYL 341
                                       89************************.********************998888666********************* PP

                               CCG  74 vtacpgCllqlk 85 
                                       +t cp+C+ +l+
  gi|488601136|ref|YP_007907607.1| 342 ITSCPFCKRHLR 353
                                       *******99885 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   6.3   5.6e-12   8.4e-09       1      60 [.      16      81 ..      16      82 .. 0.83
   2 ?    0.2   0.1      0.76   1.1e+03      30      49 ..     198     217 ..     177     245 .. 0.77
   3 ?   -1.3   0.0       2.2   3.3e+03      20      48 ..     282     309 ..     270     312 .. 0.64
   4 ?   -2.1   0.0       3.9   5.9e+03      11      19 ..     344     352 ..     336     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 5.6e-12
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraakl......glleeaeke..ekaslCieCgeCerkCPqgl 60
                                      +C+qC yC+  Cp y++ ++e  +++ +++l      ++le  +++  + + +C++Cg+Ce +C  ++
  gi|488601136|ref|YP_007907607.1| 16 ACAQCNYCRV-CPAYQIDGWESVSPRGKLYLmkaflkNKLEM-NTNvlKDFFKCTTCGLCENVCQTDI 81
                                      6*********.*********9999999988887666444443.4446789**************9887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.76
                           Fer4_17  30 klglleeaekeekaslCieC 49 
                                       +l+++e++  e+ + +C++C
  gi|488601136|ref|YP_007907607.1| 198 NLKIFEKMGVERIITSCAGC 217
                                       44566666666788888888 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.2
                           Fer4_17  20 nepkkllraaklglleeaekeekaslCie 48 
                                       +ep+++++a+ ++l+e  e +++ s C++
  gi|488601136|ref|YP_007907607.1| 282 DEPREIIKAIGFELVEM-EHSRENSMCCG 309
                                       46888888888877766.55666677766 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.9
                           Fer4_17  11 eCpsyeayd 19 
                                       +Cp+++++ 
  gi|488601136|ref|YP_007907607.1| 344 SCPFCKRHL 352
                                       588777765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   5.4   6.6e-10   9.9e-07       2      65 .]      14      81 ..      13      81 .. 0.82
   2 ?   -0.6   0.1       1.3   1.9e+03      44      55 ..     201     218 ..     163     219 .. 0.65
   3 ?   -1.8   0.0       3.1   4.6e+03      14      22 ..     344     352 ..     324     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.6e-10
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                      + +C +C +C+  Cp+++  + ++ ++rg+        ++  e++++  + +++Cttcg C++vC ++i
  gi|488601136|ref|YP_007907607.1| 14 VLACAQCNYCRV-CPAYQIDGWESVSPRGKLYLmkaflKNKLEMNTNVLKDFFKCTTCGLCENVCQTDI 81
                                      679********9.********999******9987777633333333337899*************9876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                            Fer4_8  44 e......eealwsCttcg 55 
                                              e+++ sC +c 
  gi|488601136|ref|YP_007907607.1| 201 IfekmgvERIITSCAGCF 218
                                       033344577788888885 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.1
                            Fer4_8  14 aCpvlrrtk 22 
                                       +Cp+++r  
  gi|488601136|ref|YP_007907607.1| 344 SCPFCKRHL 352
                                       577777655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   6.2   6.8e-09     1e-05       1      52 []      16      81 ..      16      81 .. 0.74
   2 ?   -2.2   0.0       4.4   6.6e+03      34      41 ..     210     217 ..     182     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.8e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt...............ekveidpekClgCgaCvavCPtga 52
                                      +C +C++C ++Cp++ i+ +e+ +++g+                 v  d  kC++Cg C++vC t++
  gi|488601136|ref|YP_007907607.1| 16 ACAQCNYC-RVCPAYQIDGWESVSPRGKlylmkaflknklemnTNVLKDFFKCTTCGLCENVCQTDI 81
                                      5*******.69**********9999965555444444333322444567789***********9975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.4
                            Fer4_7  34 dpekClgC 41 
                                         ++C gC
  gi|488601136|ref|YP_007907607.1| 210 IITSCAGC 217
                                       45567776 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   3.6       2.3   3.5e+03       8      14 ..      20      26 ..      16      28 .. 0.72
   2 !   19.5   1.3     4e-07    0.0006       4      22 ..      63      81 ..      60      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.3
                                      SSS-THH CS
                              Fer4  8 CigCGaC 14
                                      C +C  C
  gi|488601136|ref|YP_007907607.1| 20 CNYCRVC 26
                                      7777777 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4e-07
                                      ETTTSSS-THHHHHSTTTE CS
                              Fer4  4 deekCigCGaCvevCPvgA 22
                                      d  kC+ CG+C++vC ++ 
  gi|488601136|ref|YP_007907607.1| 63 DFFKCTTCGLCENVCQTDI 81
                                      7779***********9985 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 !   19.7   6.1   8.5e-07    0.0013       2      65 ..      17      78 ..      16      80 .. 0.83
   2 ?   -2.2   0.0       5.6   8.3e+03      52      60 ..     209     217 ..     185     220 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.5e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisy.ntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      C +C+ C  vCP+  i++   +++ +r +    +   k++l+ +++  k   ++t C+ C++vC 
  gi|488601136|ref|YP_007907607.1| 17 CAQCNYCR-VCPAYQIDGW--ESVSPRGKLYLmKAFLKNKLEMNTNVLKDFFKCTTCGLCENVCQ 78
                                      *******5.9*********..677766665556667788888888888888*************6 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.6
                           Fer4_16  52 eaitgCdiC 60 
                                         it C+ C
  gi|488601136|ref|YP_007907607.1| 209 RIITSCAGC 217
                                       333677766 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   9.4   8.8e-07    0.0013       1      49 [.      16      80 ..      16      81 .. 0.78
   2 ?   -1.3   0.1       1.7   2.6e+03      34      39 ..     212     217 ..     178     219 .. 0.63
   3 ?   -2.5   0.0       3.9   5.9e+03      33      40 ..     338     349 ..     320     350 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.8e-07
                            Fer4_9  1 kCtgCgaCveaCpagvv.vedaaerkarlraase................eaCigCgaCveaCpkg 49
                                      +C++C++C   Cpa  +   +++    +l   ++                 +C++Cg C+++C+++
  gi|488601136|ref|YP_007907607.1| 16 ACAQCNYCRV-CPAYQIdGWESVSPRGKLYLMKAflknklemntnvlkdfFKCTTCGLCENVCQTD 80
                                      6*******98.*8877745555555555555555788889999999999999************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                            Fer4_9  34 eaCigC 39 
                                       ++C gC
  gi|488601136|ref|YP_007907607.1| 212 TSCAGC 217
                                       556666 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.9
                            Fer4_9  33 e....eaCigCg 40 
                                       +    ++C +C+
  gi|488601136|ref|YP_007907607.1| 338 AkyliTSCPFCK 349
                                       044456677775 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   8.8   2.6e-06    0.0038       2      55 ..      10      77 ..       9      78 .. 0.87
   2 ?   -1.7   0.0       2.2   3.3e+03      38      49 ..     207     218 ..     192     220 .. 0.67
   3 ?   -1.6   0.0         2     3e+03      41      48 ..     341     348 ..     325     354 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.6e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl...............tsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                      ++ +   C +C+ C+ +CPa+                 +   k++ + +  v k+  kCt+cg C  +C
  gi|488601136|ref|YP_007907607.1| 10 IINEVLACAQCNYCR-VCPAYQidgwesvsprgklylMKAFLKNKLEMNTNVLKDFFKCTTCGLCENVC 77
                                      5666778*******7.6***99*************99777777777788888889************** PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                           Fer4_10  38 vrkkvekCtgcg 49 
                                       v+  + +C gc+
  gi|488601136|ref|YP_007907607.1| 207 VERIITSCAGCF 218
                                       555667777775 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                           Fer4_10  41 kvekCtgc 48 
                                        + +C++c
  gi|488601136|ref|YP_007907607.1| 341 LITSCPFC 348
                                       56677777 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.066        98      23      44 ..       3      24 ..       1      31 [. 0.88
   2 ?    7.4   0.1    0.0029       4.4      22      65 ..      52      95 ..      47     121 .. 0.88
   3 ?   -2.8   0.0       4.3   6.4e+03       2      16 ..     213     227 ..     212     236 .. 0.61
   4 ?    1.5   0.0      0.19   2.8e+02      19      52 ..     324     357 ..     313     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.066
                              CpXC 23 dpelkeklldgslfeatCpkCg 44
                                      d+ +  k++++ l  a+C +C 
  gi|488601136|ref|YP_007907607.1|  3 DSRIDSKIINEVLACAQCNYCR 24
                                      677899***************5 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0029
                              CpXC 22 edpelkeklldgslfeatCpkCgatakleapllyhdpekellil 65
                                      ++ e+  ++l++ +  +tC  C++  + ++pll  ++e ++ i+
  gi|488601136|ref|YP_007907607.1| 52 NKLEMNTNVLKDFFKCTTCGLCENVCQTDIPLLKLWEEMRTNIV 95
                                      56789999*************************99988877665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.3
                              CpXC   2 tCpaCgkefeaeiwt 16 
                                       +C  C  +f+++  +
  gi|488601136|ref|YP_007907607.1| 213 SCAGCFRTFSIDYRK 227
                                       466666666665544 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.19
                              CpXC  19 dadedpelkeklldg.slfeatCpkCgatakleap 52 
                                       +++ +  lke++ +g +++ + Cp C +  + + +
  gi|488601136|ref|YP_007907607.1| 324 NIA-RMRLKEAIDTGaKYLITSCPFCKRHLRSSNS 357
                                       555.678899997773577778**99998877665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.8     0.026        38      40      53 ..      16      28 ..       3      33 .. 0.75
   2 ?   11.0   0.5   0.00024      0.36      38      52 ..      62      78 ..      46      82 .. 0.76
   3 ?   -2.3   0.0       3.4   5.1e+03      39      44 ..     212     217 ..     199     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.026
                           Fer4_21 40 eCvGCnlCssvCPv 53
                                       C  Cn C  vCP 
  gi|488601136|ref|YP_007907607.1| 16 ACAQCNYC-RVCPA 28
                                      58888888.58885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                           Fer4_21 38 ed..eCvGCnlCssvCP 52
                                      +d  +C+ C lC +vC 
  gi|488601136|ref|YP_007907607.1| 62 KDffKCTTCGLCENVCQ 78
                                      44448***********5 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.4
                           Fer4_21  39 deCvGC 44 
                                        +C GC
  gi|488601136|ref|YP_007907607.1| 212 TSCAGC 217
                                       567777 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.9   0.00076       1.1       7      22 .]      14      28 ..       9      28 .. 0.87
   2 ?   11.0   2.0   0.00024      0.37       9      20 ..      66      77 ..      57      79 .. 0.86
   3 ?   -3.3   0.3       8.5   1.3e+04       9      13 ..     213     217 ..     212     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00076
                            Fer4_2  7 tdrCigCgaCvsaCPa 22
                                        +C +C+ C  +CPa
  gi|488601136|ref|YP_007907607.1| 14 VLACAQCNYC-RVCPA 28
                                      568*******.****8 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                            Fer4_2  9 rCigCgaCvsaC 20
                                      +C+ Cg C ++C
  gi|488601136|ref|YP_007907607.1| 66 KCTTCGLCENVC 77
                                      8*********** PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.5
                            Fer4_2   9 rCigC 13 
                                       +C gC
  gi|488601136|ref|YP_007907607.1| 213 SCAGC 217
                                       58888 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.5     0.096   1.4e+02      53      73 ..       9      28 ..       2      38 .. 0.74
   2 ?    9.2   0.6   0.00092       1.4      51      76 ..      57      82 ..      37      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.096
                           Fer4_18 53 rkekgagdcidcescvkvcPt 73
                                      +  +++  c +c++c +vcP 
  gi|488601136|ref|YP_007907607.1|  9 KIINEVLACAQCNYC-RVCPA 28
                                      455667789999999.79996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00092
                           Fer4_18 51 eerkekgagdcidcescvkvcPtgid 76
                                      +++  k+  +c++c+ c +vc t+i 
  gi|488601136|ref|YP_007907607.1| 57 NTNVLKDFFKCTTCGLCENVCQTDIP 82
                                      3444567789************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2322.38
//
Query:       gi|488601137|ref|YP_007907608.1|  [L=430]
Description: FAD/FMN-containing dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-32  110.5   0.0    7.7e-32  109.9   0.0    1.2  1  FAD_binding_4  FAD binding domain
      3e-05   23.8   0.0    0.00011   21.9   0.0    2.0  2  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.072   13.2   0.1    1.9  1  BBE            Berberine and berberine like


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.0   1.3e-35   7.7e-32       2     133 ..      48     179 ..      47     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 1.3e-35
                                       EEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHH CS
                     FAD_binding_4   2 aavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdl 77 
                                       +a+v+p+s+eev ++l+l ++++ p+++rG+ +s  g+++ ++gg+v+d+sr+ +  ei+e+e+t  +e+G+++ d+
  gi|488601137|ref|YP_007907608.1|  48 EAIVQPQSVEEVLEILKLSKKYSKPIVPRGSATSGYGGVIpYFGGIVVDFSRMYK-FEINEDEKTFIAEPGAVWWDV 123
                                       79**************************************9**************.8******************** PP

                                       HHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTS CS
                     FAD_binding_4  78 vealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladG 133
                                       ++++++kgl l+++p+s  ++tvGG+ia++++G gs + G i+d+v++l+v + +G
  gi|488601137|ref|YP_007907608.1| 124 EKRANKKGLSLRVYPTSALSSTVGGWIAQGGVGIGSMMFGGIKDCVERLQVADFNG 179
                                       ***************************************************99887 PP

>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.3   1.8e+03     124     152 ..      21      50 ..       9      57 .. 0.73
   2 !   21.9   0.0   1.9e-08   0.00011     105     250 .]     275     413 ..     207     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.3
                                       HCTTEEEEEEEEEEEHHHHHHH.HHHHHHH CS
                     FAD-oxidase_C 124 lkagvavlseDtsvPvsrladl.vrdikal 152
                                         ++  v+s+D+sv ++ + ++ +rd++a+
  gi|488601137|ref|YP_007907608.1|  21 DYHERKVYSHDISVLPEYIEKIaCRDAEAI 50 
                                       56778899******9998877436666665 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.9e-08
                                       .ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHH....EEEEEEEEEETTEEEEEEEE CS
                     FAD-oxidase_C 105 aealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyg....levvlfgHagdgnlhlyilf 177
                                       a+ +w+ R + ++     ++++ + ++++++  P+++l ++++ i + l+  +    ++++  g    gn+++ ++ 
  gi|488601137|ref|YP_007907608.1| 275 AKDFWEERFYPMR-----VKRKWPSIVMTEILMPLENLENYCKIIGKELKGRDfgiqIHFCKEGGRILGNVIIILAS 346
                                       3589*********.....99999**************************9999654444444444449********* PP

                                       EEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 178 dladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaalDPkgiLNPgkv 250
                                       d++d+   + ++k ++ + ++ ++l G  + +   G+  ++  +++ +  +++ + r K+  DP+++LNPgk+
  gi|488601137|ref|YP_007907608.1| 347 DENDRRFTKDWRKSMKLL-KMGLKLSGKPYST---GMFLSHLSKKYLK--DYEELLRFKKSVDPDNLLNPGKI 413
                                       ****99999998877666.99*********97...5555555777774..499999***************96 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.2e-05     0.072      19      38 ..     388     407 ..     381     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                       HGGGHHHHHHHHHHH-TT-- CS
                               BBE  19 FggNferLvkvKtkyDPdNv 38 
                                       + +++e L + K+++DPdN+
  gi|488601137|ref|YP_007907608.1| 388 YLKDYEELLRFKKSVDPDNL 407
                                       899****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2450.03
//
Query:       gi|488601138|ref|YP_007907609.1|  [L=425]
Description: hydroxymethylpyrimidine synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-186  619.3   0.0   3.4e-186  619.1   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 !  619.1   0.0  1.9e-190  3.4e-186       1     417 [.       3     420 ..       3     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 619.1 bits;  conditional E-value: 1.9e-190
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkek.pvaiGkglrtkvnaniGtsadasdiee 76 
                                       t +e ar+++  e ++eva++e+v+ +f+ + +a+G++v+p+n++++++ p aiG+ ++tkvnan+Gts+d+++  e
  gi|488601138|ref|YP_007907609.1|   3 TLMELARNSKHPEWLKEVARDERVDLDFLLKLIAKGEVVVPRNIRRENSrPKAIGRFMKTKVNANVGTSDDYVNEGE 79 
                                       789*******************************************7766*************************** PP

                      ThiC_Rad_SAM  77 EveKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvd 153
                                       Ev+K+ +a+k+gad++mdLstggd+d+ir+kil++ +vp+gtvpiYqa++ + +kv++++e++++ v+e+qa+dGvd
  gi|488601138|ref|YP_007907609.1|  80 EVKKAVIAEKYGADAIMDLSTGGDLDRIRKKILDAISVPFGTVPIYQAAR-SCRKVVDMDEDDFFGVVEKQARDGVD 155
                                       *************************************************8.66899********************* PP

                      ThiC_Rad_SAM 154 fltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaD 230
                                       f+tiHagv+ +++e+lk++kRl+g+vSrgG++++ wml+n+kenp+ye+fd+lleilkeydvt+Slgd++RpG+i+D
  gi|488601138|ref|YP_007907609.1| 156 FMTIHAGVNWNSVERLKRSKRLLGVVSRGGAITIGWMLHNQKENPYYENFDYLLEILKEYDVTISLGDAFRPGCIHD 232
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 231 atdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsai 307
                                       a+d+++++e+i lgelv+++reagvq mveGPGHvpldeie++v+++k+++k+aP+y+lGplvtDi++gYDhi+sai
  gi|488601138|ref|YP_007907609.1| 233 ASDRVKFTEFILLGELVEKCREAGVQSMVEGPGHVPLDEIETSVRAMKHVTKNAPLYLLGPLVTDISAGYDHISSAI 309
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 308 GaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakg..lkkarerdkalskaRkeldwekqfel 382
                                       Gaa+a+++Gad++Cyvtp+EHl+lP++edv+eGviaakiaaha dl+k   +++ar+rd ++s aRk+ldwekqfel
  gi|488601138|ref|YP_007907609.1| 310 GAAIAGMHGADFICYVTPSEHLALPTVEDVREGVIAAKIAAHAVDLVKDgqREHARKRDYEMSLARKNLDWEKQFEL 386
                                       ************************************************7557899********************** PP

                      ThiC_Rad_SAM 383 aldpekareireeklpeeeeaCsmCgekCavkive 417
                                       ++dpekar++ e+++ ++++aCsmCge Ca+kiv+
  gi|488601138|ref|YP_007907609.1| 387 SIDPEKARAVWERRK-SKSDACSMCGELCAIKIVK 420
                                       ***********9987.599*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3186.10
//
Query:       gi|488601139|ref|YP_007907610.1|  [L=349]
Description: translation initiation factor 2B subunit I family (IF-2BI) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-87  291.4   0.0    7.6e-87  291.1   0.0    1.1  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.1   0.0   4.2e-91   7.6e-87       2     281 ..      42     330 ..      41     331 .. 0.96

  Alignments for each domain:
  == domain 1  score: 291.1 bits;  conditional E-value: 4.2e-91
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       +rG+pa+  a+ ++++ +  + + +  +++ +++++++++L +arPtav+l+  ++r+l+   ++k  s+ +ea+k 
  gi|488601139|ref|YP_007907610.1|  42 IRGAPALEAAGGYGVALACIEREFDSFEDFLKYVSERASSLANARPTAVNLSVGVERVLR---KVKAASSIEEARKL 115
                                       89**********************************************************...7899********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG 147
                                       ++++++++++e++  ++++g ++a+li+dgd ilTicn+++        +l+v+r+a+ e+k+++V+++E+rP +qG
  gi|488601139|ref|YP_007907610.1| 116 AVQEAEKIAEEDVFRNRLMGSFGAKLIEDGDSILTICNTGSlatvewgtALGVIRSAKLEGKNIRVFACETRPLNQG 192
                                       ***************************************************************************** PP

                                       .HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGB CS
                             IF-2B 148 .rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkf 222
                                        rlt +eL ++gi+vtlitds++++vm++ +vdkvivGAdri+++G ++nkiGT++lAvlAke+ ip++v+a++++f
  gi|488601139|ref|YP_007907610.1| 193 sRLTTWELINDGIDVTLITDSMAGIVMQKgMVDKVIVGADRIVSDG-VFNKIGTYTLAVLAKEHGIPFFVAAPLTTF 268
                                       **********************************************.****************************** PP

                                       ESTSSSGGGSSXXBEXTHHHHEE....TTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEX CS
                             IF-2B 223 servqldedifieerdpeellni....tgeriaeeelkvvnpafDvtPpelItliITevGvlp 281
                                       +++ ++d+ ++ieerd++el ++    ++ ria+e++kv+npafD tP ++++++ITe+Gv+ 
  gi|488601139|ref|YP_007907610.1| 269 DWEKKMDD-VVIEERDADELRYChvkcKNCRIAPENVKVYNPAFDSTPLSYVSALITEKGVIF 330
                                       ***87777.777********876111156789999*************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 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:                        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: 00:00:00.41
# Mc/sec: 2563.10
//
Query:       gi|488601140|ref|YP_007907611.1|  [L=307]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  104.9   0.0    4.6e-30  104.5   0.0    1.1  1  LysR_substrate  LysR substrate binding domain
    3.2e-16   59.0   0.0    6.8e-16   58.0   0.0    1.6  1  HTH_1           Bacterial regulatory helix-turn-helix protein
  ------ inclusion threshold ------
       0.06   13.3   0.1        6.5    6.8   0.0    2.6  2  RWP-RK          RWP-RK domain
      0.083   12.9   0.2       0.21   11.6   0.2    1.8  1  DUF2089         Protein of unknown function (DUF2089)


Domain annotation for each model (and alignments):
>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0     1e-33   4.6e-30      13     206 ..      94     290 ..      85     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 1e-33
                                       ECCCHHHHHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSS...CCTTEEEEEEEEEEEEEEEET CS
                    LysR_substrate  13 pptlaryllppllarfraryPevelelvegdseelldllaegelDlairagpp...edsglearpLaeeplvlvasp 86 
                                       +  ++  ++ +l   ++a+yP +++e+v    +e+l+ll++ge+D+ i+++     +ds + +++++++ lvl++s+
  gi|488601140|ref|YP_007907611.1|  94 SGMVGLNIVFQLQTLLKAKYPSLQVEIVLRGAHECLKLLNRGEVDFTIVGDYSddvDDSKFLIEKIGKDWLVLIVSR 170
                                       345688999999999*************************************9************************ PP

                                       TSGGGGSSSECGGGGCTSEEEEESTTSTHHHHHHHHHHCTTEECEEEEEESSHHHHHHHHHTTS-BEEEEGGGHHCC CS
                    LysR_substrate  87 dhpLargepvsledLadeplilleegsglrdlledalreaglkprvalevnsleallalvaaGlGiallprsavrde 163
                                       +hpLa+ ++v+le++ ++p+i+l++++g+  + ++al+ +g +++++l v ++   ++ va++lG+a+ +  a++++
  gi|488601140|ref|YP_007907611.1| 171 NHPLAKADEVTLEEVVNYPMIFLTDDYGITSSTRKALKMSGYDVKPSLVVGDFFLKINSVANNLGVAITSMIAASKA 247
                                       ***************************************************************************** PP

                                       CHTTTEEEEEESSTTCEEEEEEEEETTCCCHHHHHHHHHHHHH CS
                    LysR_substrate 164 ladgrlvalplpepplprelylvyrkgrelspavrafidflre 206
                                        + g + + p++++  +r++y++  k ++  ++++   +fl++
  gi|488601140|ref|YP_007907611.1| 248 YETGMVTIKPIKDFYDERDIYMISSKLSQDCKRMKEYHEFLLK 290
                                       *************6666**********9999999999999876 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   1.5e-19   6.8e-16       3      59 ..       5      61 ..       3      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.5e-19
                                      HHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHH CS
                             HTH_1  3 qlrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaG 59
                                       +++f++v+e gs+  AA+eLg+s +++s qi++LEe  g++L++R+  g++LTe+G
  gi|488601140|ref|YP_007907611.1|  5 FMKTFLKVVEKGSLKSAAKELGMSISSISFQINSLEEFYGAKLLNRKVSGVTLTEEG 61
                                      699*******************************************999*******9 PP

>> RWP-RK  RWP-RK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0014       6.5      12      28 ..      15      31 ..       5      33 .. 0.86
   2 ?    3.7   0.0     0.014        62      11      29 ..     223     241 ..     219     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0014
                            RWP-RK 12 slplkeAAksLgvsktt 28
                                      +++lk AAk+Lg+s ++
  gi|488601140|ref|YP_007907611.1| 15 KGSLKSAAKELGMSISS 31
                                      589*********99875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.014
                            RWP-RK  11 FslplkeAAksLgvskttL 29 
                                       F l+++ +A++Lgv  t++
  gi|488601140|ref|YP_007907611.1| 223 FFLKINSVANNLGVAITSM 241
                                       8899**********99986 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   4.7e-05      0.21      39      97 ..       3      83 ..       1      99 [. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                           DUF2089 39 lefvelfika..rGnlkevekelgisYpTvrnrldeileaLgyeeeeeeeee....................eeerkei 95
                                      l+f+++f+k+  +G+lk+ +kelg+s   +  +++++ e  g +  +++ +                      ee k++
  gi|488601140|ref|YP_007907611.1|  3 LDFMKTFLKVveKGSLKSAAKELGMSISSISFQINSLEEFYGAKLLNRKVSGvtlteegiiamknmetvlglIEEAKKL 81
                                      78*****995449*****************9999999887777766552221334444555555555555554455555 PP

                           DUF2089 96 le 97
                                      ++
  gi|488601140|ref|YP_007907611.1| 82 IA 83
                                      55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1842.44
//
Query:       gi|488601141|ref|YP_007907612.1|  [L=121]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.1     0.0007   19.4   0.0    1.7  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0032   17.3   0.0     0.0082   16.0   0.0    1.7  2  MarR_2       MarR family
      0.009   15.9   5.2      0.011   15.6   4.9    1.3  1  TFIIE_alpha  TFIIE alpha subunit
  ------ inclusion threshold ------
      0.026   14.1   0.1      0.057   13.0   0.0    1.6  1  SMC_ScpB     Segregation and condensation complex subunit Scp
      0.027   14.4   0.1      0.046   13.7   0.1    1.6  1  PadR         Transcriptional regulator PadR-like family
      0.047   13.9   0.0      0.085   13.0   0.0    1.5  1  HTH_34       Winged helix DNA-binding domain
       0.35   11.3   5.1       0.14   12.5   1.9    1.9  2  DUF2870      Protein of unknown function (DUF2870)


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 !   19.4   0.0   2.7e-07    0.0007       1      58 [.      16      73 ..      16      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.7e-07
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      L++ GL+ + akv + L k g+a  ++i +++++ ++ v  ++++L++ G+++ ++ +
  gi|488601141|ref|YP_007907612.1| 16 LSEAGLNRNIAKVVVFLSKTGEAISRDIERAANLRQPEVSLAMKELKEWGWIKERELK 73
                                      677899999999999999**********************************999855 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.27   6.8e+02      41      50 ..      12      21 ..      11      21 .. 0.91
   2 !   16.0   0.0   3.2e-06    0.0082       2      55 ..      20      71 ..      19      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.27
                                      HHHHHHHTTS CS
                            MarR_2 41 ilkrLvaaGL 50
                                      i+k L++aGL
  gi|488601141|ref|YP_007907612.1| 12 IVKLLSEAGL 21
                                      9********8 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.2e-06
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      gl++ +a v  +L   ++     ++++r+ +l ++ vs + k+L + G++ +r+
  gi|488601141|ref|YP_007907612.1| 20 GLNRNIAKVVVFLSKTGE--AISRDIERAANLRQPEVSLAMKELKEWGWIKERE 71
                                      899999999999999999..999***************************9985 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   4.9   4.3e-06     0.011      13     101 ..      23     113 ..      10     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECC...CHCCCHH CS
                       TFIIE_alpha  13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinye...klvdvvk 86 
                                        + ++v+  L + ge    d+++  ++ ++e+  ++ +L+e + +k +  +  +k+     ++++y+    + + vk
  gi|488601141|ref|YP_007907612.1|  23 RNIAKVVVFLSKTGEAISRDIERAANLRQPEVSLAMKELKEWGWIKERELKKKGKGRPLKSYKLTYDikdIVSELVK 99 
                                       68899*******************************************99998887766666666642114566666 PP

                                       HHHHHHHHHHHHHHC CS
                       TFIIE_alpha  87 rkleevvkkLeekle 101
                                       +k ee+ kk e++le
  gi|488601141|ref|YP_007907612.1| 100 KKREEI-KKAEKDLE 113
                                       666554.56666665 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 ?   13.0   0.0   2.2e-05     0.057     104     143 ..      47      88 ..       3      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                          SMC_ScpB 104 eeiRGvnsdsvvrtLlerglieekgrkee.pgrpil.YgtTe 143
                                       +++R  +++ ++++L e g+i+e++ k++ +grp+  Y++T 
  gi|488601141|ref|YP_007907612.1|  47 ANLRQPEVSLAMKELKEWGWIKERELKKKgKGRPLKsYKLTY 88 
                                       36899999***************99666559**987699886 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.8e-05     0.046      36      67 ..      56      88 ..      28     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                      HHHHHHHHTTSEEEEEE-S.TSSS-EEEEEESH CS
                              PadR 36 paLkrLekeglvesewees.gegpprkyYrlTd 67
                                       a+k+L++ g++++++ ++ g+g+p k Y+lT 
  gi|488601141|ref|YP_007907612.1| 56 LAMKELKEWGWIKERELKKkGKGRPLKSYKLTY 88
                                      4899**********9999989**********95 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.3e-05     0.085       4      63 ..      27      88 ..      26     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.3e-05
                            HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievd..kefkgkkprtllriTp 63
                                      +v+ +L+++ ea  +++  a ++ + + s  +k L++ g+i+ +  k++ +++p  ++++T 
  gi|488601141|ref|YP_007907612.1| 27 KVVVFLSKTGEAISRDIERAANLRQPEVSLAMKELKEWGWIKERelKKKGKGRPLKSYKLTY 88
                                      58899************************************854223333446999999996 PP

>> DUF2870  Protein of unknown function (DUF2870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.71   1.8e+03      26      38 ..      26      38 ..       5      63 .. 0.64
   2 ?   12.5   1.9   5.7e-05      0.14      32      73 ..      72     113 ..      69     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.71
                           DUF2870 26 tkiivklqkkgsg 38
                                       k++v l+k+g++
  gi|488601141|ref|YP_007907612.1| 26 AKVVVFLSKTGEA 38
                                      5666666666654 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.7e-05
                           DUF2870  32 lqkkgsgaParepvvseeeqkalmaaayrkqeelkkleeddd 73 
                                       l+kkg+g P +   ++++ ++ + + + +k+ee+kk e+d +
  gi|488601141|ref|YP_007907612.1|  72 LKKKGKGRPLKSYKLTYDIKDIVSELVKKKREEIKKAEKDLE 113
                                       89**********************************988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1739  (0.0969937); expected 358.6 (0.02)
Passed bias filter:                      786  (0.0438396); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 814.52
//
Query:       gi|488601142|ref|YP_007907613.1|  [L=378]
Description: hypothetical protein Asulf_01646 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  164.2  54.1    1.5e-32  112.9  24.0    2.0  2  MFS_1       Major Facilitator Superfamily
    1.9e-20   73.1  23.0    1.1e-11   44.3   5.8    2.1  2  MFS_1_like  MFS_1 like family
    1.3e-08   33.7  17.0    4.2e-07   28.7   0.6    2.2  2  MFS_3       Transmembrane secretion effector
      3e-08   32.9  11.5      3e-08   32.9  11.5    4.1  4  Sugar_tr    Sugar (and other) transporter
    5.5e-06   25.4  29.9     0.0033   16.2  12.0    3.3  2  LacY_symp   LacY proton/sugar symporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9  24.0   4.3e-36   1.5e-32       2     235 ..      10     224 ..       9     226 .. 0.90
   2 !   61.2  28.8   2.3e-20   8.1e-17       2     172 ..     202     374 ..     201     378 .] 0.89

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 4.3e-36
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.ll 77 
                                       +l+af+++l+++i++p+lp + a+dlg+s+  ig ++++y++  +v+ ++ G lsdr+Grrr++llgl+l+++  +l
  gi|488601142|ref|YP_007907613.1|  10 SLSAFIVMLGMGIITPLLP-IFAQDLGASGIWIGVIFSAYSFSRLVFLPISGMLSDRYGRRRTILLGLFLYSSVtFL 85 
                                       799****************.9*****************************************************444 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       ++l  s  +  l ++r+l G+++++++p+++a + d++ k + g+ ig ++ +  lG++ gp++gg+l + lg  ++
  gi|488601142|ref|YP_007907613.1|  86 YIL--SKTPeQLSFVRMLHGITSAMIIPVAMASVGDISIKGKEGFFIGKFNQSLFLGMASGPIVGGVLNDILGMKLT 160
                                       444..99999******************************************************************* PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltll 230
                                       f+ l +++++ ++++++ +pe+ ++rk k+                   ++++  lwi++i  +++++g  ++l++l
  gi|488601142|ref|YP_007907613.1| 161 FMSLSFFGFFTLLVVFISFPETVTTRKEKK------------------PVFRNSKLWIAFIFRFINSMGRGSILSFL 219
                                       ***********7764444444444444442..................367788899889999999999999***** PP

                             MFS_1 231 plylq 235
                                       p+yl 
  gi|488601142|ref|YP_007907613.1| 220 PIYLG 224
                                       ***75 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 2.3e-20
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       ++  f+++++r+ ++++lp ++   l++s ++ig l++l  + +a+ ++ +Grlsdr+G r  +++++l+ a   l+
  gi|488601142|ref|YP_007907613.1| 202 FIFRFINSMGRGSILSFLP-IYLGFLNYSTTVIGSLVSLNLFISALIQPSFGRLSDRVGVRYPVIMSALAGAGI-LF 276
                                       7888***************.66689*************************************666666666666.45 PP

                             MFS_1  79 llfa.sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.... 149
                                       +l +  s+   l++l vl G+++++++pa++a++a   +k   g+ +g+lsa+ slG ++gp+++g++ + +g    
  gi|488601142|ref|YP_007907613.1| 277 AL-PrVSSLdSLIFLSVLLGITSAMSIPAVGAIVAVEGKKGGMGQLMGILSASKSLGRVVGPVVSGVIFDVFGggiy 352
                                       55.23444559**********************************************************99999*99 PP

                             MFS_1 150 .Wravfyilaivsllafvlfllll 172
                                         r +f ++ ++s+ ++++  +++
  gi|488601142|ref|YP_007907613.1| 353 gVRMAFTLASLLSVSSAII--FWI 374
                                       9***************997..443 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 !   35.0   9.2     2e-12   7.3e-09     227     384 ..       6     162 ..       1     163 [. 0.95
   2 !   44.3   5.8     3e-15   1.1e-11     215     378 ..     186     348 ..     163     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2e-12
                        MFS_1_like 227 viifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilr 303
                                       ++++ l a+i+   +gii   l ++ ++lgas++ +G++     ++ ++++ ++  l +++G ++ ++++l++y   
  gi|488601142|ref|YP_007907613.1|   6 LFGISLSAFIVMLGMGIITPLLPIFAQDLGASGIWIGVIFSAYSFSRLVFLPISGMLSDRYGRRRTILLGLFLYSSV 82 
                                       566778899999999************************************************************** PP

                        MFS_1_like 304 fllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksai 380
                                        +ly + + +  + ++ +Lhgi+ +++  +a+  v +i  k+ e++ +g ++   f lG a+G ++GG+l d+ + +
  gi|488601142|ref|YP_007907613.1|  83 TFLYILSKTPEQLSFVRMLHGITSAMIIPVAMASVGDISIKGKEGFFIGKFNQSLF-LGMASGPIVGGVLNDILGMK 158
                                       ***************************************************99877.9**************99999 PP

                        MFS_1_like 381 flFr 384
                                        +F+
  gi|488601142|ref|YP_007907613.1| 159 LTFM 162
                                       9996 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 3e-15
                        MFS_1_like 215 lqvllnilknpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvk 291
                                       +++ + +++n +++i +++ +i  m  g i +Fl +YL  l++s+t++Gslv l  + +  +     +l +++G++ 
  gi|488601142|ref|YP_007907613.1| 186 RKEKKPVFRNSKLWIAFIFRFINSMGRGSILSFLPIYLGFLNYSTTVIGSLVSLNLFISALIQPSFGRLSDRVGVRY 262
                                       3556789*********************************************************************9 PP

                        MFS_1_like 292 lliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsl 368
                                        +i++ la +  ++ +  ++++  ++++ vL gi+ ++   a+   v+    k+  ++++g+ls+   +lGr +G +
  gi|488601142|ref|YP_007907613.1| 263 PVIMSALAGAGILFALPRVSSLDSLIFLSVLLGITSAMSIPAVGAIVAVEGKKGGMGQLMGILSAS-KSLGRVVGPV 338
                                       8888888888888888899999999999***********999999999999************975.8********* PP

                        MFS_1_like 369 iGGllwdlks 378
                                       ++G+++d ++
  gi|488601142|ref|YP_007907613.1| 339 VSGVIFDVFG 348
                                       ******9886 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.6   1.2e-10   4.2e-07      39     196 ..      33     186 ..      27     196 .. 0.82
   2 !   10.1   9.4   5.4e-05      0.19      86     170 ..     269     351 ..     189     375 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.2e-10
                             MFS_3  39 disasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligi 115
                                       d+ as + + ++  a +   +++  ++G l+D + rR+ +l +  l   + ++l +l+     +p  l  + +l gi
  gi|488601142|ref|YP_007907613.1|  33 DLGASGIWIGVIFSAYSFSRLVFLPISGMLSDRYGRRRTILLGLFLYS-SVTFLYILSK----TPEQLSFVRMLHGI 104
                                       56777788888888888888888889**************99976554.5556666654....57888888999*** PP

                             MFS_3 116 GaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafa.vnalsylalivallrwkr 191
                                        +a+  P   Asvg++  + +    +      + +  + GP +gGvl  ++G  l+f  +  + +++l+v+++    
  gi|488601142|ref|YP_007907613.1| 105 TSAMIIPVAMASVGDISIKGKEGFFIGKFNQSLFLGMASGPIVGGVLNDILGMKLTFMsLSFFGFFTLLVVFISFPE 181
                                       ****************999988888888888888999*******************972566789999999888877 PP

                             MFS_3 192 evrks 196
                                       +v+++
  gi|488601142|ref|YP_007907613.1| 182 TVTTR 186
                                       77655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.4e-05
                             MFS_3  86 alvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvl 162
                                       ++++   +++a+  + s  +l+ l++l+gi +a+  Pa  A+v    k+  + + + + s    + R vGP ++Gv+
  gi|488601142|ref|YP_007907613.1| 269 LAGA--GILFALPRVSSLDSLIFLSVLLGITSAMSIPAVGAIVAVEGKKGGMGQLMGILSASKSLGRVVGPVVSGVI 343
                                       2333..3345556667778899******************************************************* PP

                             MFS_3 163 vaavGaal 170
                                         ++G  +
  gi|488601142|ref|YP_007907613.1| 344 FDVFGGGI 351
                                       *9998532 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9  11.5   8.5e-12     3e-08      44     194 ..      37     182 ..      28     194 .. 0.92
   2 !    3.3   7.4    0.0087        31      55     128 ..     137     224 ..     136     242 .. 0.78
   3 ?    1.5   2.2      0.03   1.1e+02      44     115 ..     229     297 ..     224     310 .. 0.78
   4 ?    0.7   4.0     0.052   1.9e+02      47      91 ..     321     370 ..     309     376 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 8.5e-12
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       s +++g+i+s++++ +++   ++g+l+dr+GR+ ++l + +l++  ++l +++k   + e+l + R+l Gi   ++ 
  gi|488601142|ref|YP_007907613.1|  37 SGIWIGVIFSAYSFSRLVFLPISGMLSDRYGRRRTILLGLFLYSSVTFLYILSK---TPEQLSFVRMLHGITSAMII 110
                                       6789**************************************************...9******************* PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG.GGS--- CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill.lflPES 194
                                        ++   ++ i+ k + g++++ ++ ++ +G+  + i+g +ln++ +   +++++ + +++  + l+++ + +PE+
  gi|488601142|ref|YP_007907613.1| 111 PVAMASVGDISIKGKEGFFIGKFNQSLFLGMASGPIVGGVLNDILG---MKLTFMSLSFFGFFTLLVVfISFPET 182
                                       **********************************************...99999999999965555542446777 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0087
                                       HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..............SS-TGGGGGHHHHHHHHH CS
                          Sugar_tr  55 flvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..............nsvevlivgRvlvGigvG 117
                                       +++G + G +++g l d++G k +++  +++ +   ++ +++  +              +++++ ++ R++  +g G
  gi|488601142|ref|YP_007907613.1| 137 LFLGMASGPIVGGVLNDILGMKLTFMSLSFFGFFTLLVVFISFPEtvttrkekkpvfrnSKLWIAFIFRFINSMGRG 213
                                       6799999***************999975544333322222222223557779******99***************** PP

                                       HHHHHHHHHHH CS
                          Sugar_tr 118 lasvlvPmyis 128
                                        +  + P+y++
  gi|488601142|ref|YP_007907613.1| 214 SILSFLPIYLG 224
                                       *********85 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.03
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGig 115
                                       s++ +g +vs+ l+++++ +  +g l+dr+G ++  +++a+   +ga + +a +  +s+  li+  vl+Gi 
  gi|488601142|ref|YP_007907613.1| 229 STTVIGSLVSLNLFISALIQPSFGRLSDRVGVRYPVIMSAL---AGAGILFALPRVSSLDSLIFLSVLLGIT 297
                                       5667788888888888888888999********99999865...6666666666667888888888888886 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.052
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTT.....HHHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfG.....Rkkslliaavlfvigav 91 
                                       l+g++ ++ ++G+++G +++g + d+fG      + ++  a++l+v +a+
  gi|488601142|ref|YP_007907613.1| 321 LMGILSASKSLGRVVGPVVSGVIFDVFGggiygVRMAFTLASLLSVSSAI 370
                                       7999********************98762221156666666666555544 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  12.0   9.3e-07    0.0033      10     190 ..       7     181 ..       1     188 [. 0.69
   2 !   12.7   9.9   1.1e-05      0.04       4     116 ..     193     296 ..     189     377 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.3e-07
                         LacY_symp  10 ylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvl 86 
                                       +  +l+ f+ ++ m+++ pl+p++ ++ lg s+  +G++fs+ s+  ++f p+ G++sd+ G ++ +l     l++ 
  gi|488601142|ref|YP_007907613.1|   7 FGISLSAFIVMLGMGIITPLLPIFAQD-LGASGIWIGVIFSAYSFSRLVFLPISGMLSDRYGRRRTILLG---LFLY 79 
                                       4444555666666**********9776.799**********************************98864...4455 PP

                         LacY_symp  87 fapfliyvfepllqlnilvGalvGgvflGlvysagagaieayiekvsraskfeyGkarvfGclGyalcaslaGilfs 163
                                        +  ++y+ +   +   +v +l G     ++  a a++ +     +  +  f  Gk   +  lG a +  + G+l  
  gi|488601142|ref|YP_007907613.1|  80 SSVTFLYILSKTPEQLSFVRMLHGITSAMIIPVAMASVGDIS---IKGKEGFFIGKFNQSLFLGMASGPIVGGVLND 153
                                       566677777655443333333333333333333333333332...34567788888888888888888888888887 PP

                         LacY_symp 164 i.dpslvfwlasgfalilllllllskpd 190
                                       i   +l+f   s f+   ll++++s p+
  gi|488601142|ref|YP_007907613.1| 154 IlGMKLTFMSLSFFGFFTLLVVFISFPE 181
                                       7346788888888887777777666655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.1e-05
                         LacY_symp   4 lkntnfylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwv. 79 
                                       ++n++ ++  +f f+  +  + + +++p++l + l+ s t +G + s + ++s l qp fG +sd++G++ +++ + 
  gi|488601142|ref|YP_007907613.1| 193 FRNSKLWIAFIFRFINSMGRGSILSFLPIYL-GFLNYSTTVIGSLVSLNLFISALIQPSFGRLSDRVGVRYPVIMSa 268
                                       5677777655555555555889********9.5788999********************************998642 PP

                         LacY_symp  80 islllvlfapfliyvfepllqlnilvGalvGgvflGl 116
                                       ++   +lfa   +   + l+ l          v lG+
  gi|488601142|ref|YP_007907613.1| 269 LAGAGILFALPRVSSLDSLIFLS---------VLLGI 296
                                       55555666544444444444333.........33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 2268.89
//
Query:       gi|488601143|ref|YP_007907614.1|  [L=204]
Description: hypothetical protein Asulf_01647 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-48  165.1  14.3    1.6e-48  164.8  14.3    1.0  1  Lys_export  Lysine exporter LysO
     0.0017   18.2   5.4     0.0017   18.2   5.4    2.0  3  Asp-Al_Ex   Predicted Permease Membrane Region


Domain annotation for each model (and alignments):
>> Lys_export  Lysine exporter LysO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8  14.3   1.7e-52   1.6e-48       2     189 ..       8     200 ..       7     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 1.7e-52
                        Lys_export   2 laliaGillGlllllea........elleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsl 70 
                                       l+l+ Gi++G++ +  +        +++++e+++++L++++fl+G+++g  ++ +ek+k+  + + l+++ t++gsl
  gi|488601143|ref|YP_007907614.1|   8 LILASGITTGYVREYIMpesiyttiDFFSSEIVQIVLIAFIFLIGLDMGLMESRMEKIKRSWKLGGLVAVGTVTGSL 84 
                                       67888999999544333334676778899999*******************9999********************** PP

                        Lys_export  71 lggllaalllglslkeslavasGfGwYSLsgilitelkgaelGtiallanllREllalllipllakrfgklaaisva 147
                                       ++gl+++l+l+++l+ +l+v++G+GwYSL+g+++++++ga +G++++ an+lRE+l+++ +p +     k++ais++
  gi|488601143|ref|YP_007907614.1|  85 IAGLVIHLILKVPLSIALSVCAGMGWYSLTGPFLSKTLGAFAGALGFGANFLREVLTFISYPKFRD---KTSAISIG 158
                                       **************************************************************9965...6889**** PP

                        Lys_export 148 GatsmDttLPiitkssgkevvvlaivhGvilsllvPilvslf 189
                                       Gat+mDttLP+i+k+s++e +++a++hG+ ++++vP+l+s++
  gi|488601143|ref|YP_007907614.1| 159 GATTMDTTLPLIAKFSDSERALIAFIHGFFITIIVPVLLSIL 200
                                       ***************************************986 PP

>> Asp-Al_Ex  Predicted Permease Membrane Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   5.4   1.9e-07    0.0017      30     122 ..      10     107 ..       3     109 .. 0.75
   2 ?   -2.1   0.1      0.32   2.9e+03     115     124 ..     120     129 ..     105     165 .. 0.79
   3 ?   -1.5   0.0      0.22   1.9e+03     122     147 ..     159     183 ..     132     202 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-07
                         Asp-Al_Ex  30 LivglllGqlgktgpiv.....ldis.alsllrelgLllFlaavGlsaGpgffsslkkd..Glklvllallvtvvpl 98 
                                       L  g+  G +++   i+     ++i  ++s + ++ L+ F++ +Gl++G    s ++k   ++kl +l ++ tv++ 
  gi|488601143|ref|YP_007907614.1|  10 LASGITTGYVREY--IMpesiyTTIDfFSSEIVQIVLIAFIFLIGLDMGLM-ESRMEKIkrSWKLGGLVAVGTVTGS 83 
                                       5566777777543..22223233332146788999**************64.4444432249*************** PP

                         Asp-Al_Ex  99 llalvlaklvlkldlallaGllaG 122
                                       l+a ++++l+lk+ l +++ ++aG
  gi|488601143|ref|YP_007907614.1|  84 LIAGLVIHLILKVPLSIALSVCAG 107
                                       *****************9999998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.32
                         Asp-Al_Ex 115 llaGllaGal 124
                                        ++G++aGal
  gi|488601143|ref|YP_007907614.1| 120 KTLGAFAGAL 129
                                       4566666665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.22
                         Asp-Al_Ex 122 GalTstpalgaandalaeldlpavgy 147
                                       Ga+T    l ++    ++++ + +++
  gi|488601143|ref|YP_007907614.1| 159 GATTMDTTLPLIAKF-SDSERALIAF 183
                                       455544444444444.3333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1496.01
//
Query:       gi|488601144|ref|YP_007907615.1|  [L=87]
Description: hypothetical protein Asulf_01648 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-07   30.4   1.6      3e-07   30.2   1.6    1.0  1  Lys_export       Lysine exporter LysO
    0.00013   21.4   1.8    0.00014   21.3   1.8    1.0  1  KdgT             2-keto-3-deoxygluconate permease
     0.0005   19.0   2.9    0.00056   18.8   2.9    1.0  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
    0.00078   18.8   1.7    0.00083   18.7   1.7    1.0  1  Sbt_1            Na+-dependent bicarbonate transporter superf
     0.0027   17.5   2.5     0.0031   17.4   2.5    1.0  1  Asp-Al_Ex        Predicted Permease Membrane Region
  ------ inclusion threshold ------
      0.014   14.1   0.1      0.016   13.9   0.1    1.1  1  Ammonium_transp  Ammonium Transporter Family
       0.26   11.4   4.3       0.24   11.5   1.6    2.0  2  DUF1029          Protein of unknown function (DUF1029)


Domain annotation for each model (and alignments):
>> Lys_export  Lysine exporter LysO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   1.6   1.2e-10     3e-07       2      73 ..       6      80 ..       5      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.2e-10
                        Lys_export  2 laliaGillGlllllea....elleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsllgg 73
                                      +a+iaG++lG++++ ++    + + +++ +++L+lL+f+ G+++gss ++ e+ +++++  +++++ t++ s + +
  gi|488601144|ref|YP_007907615.1|  6 VAVIAGFALGVFIEKREskisKDFISKALTVCLFLLIFFLGYDIGSSLNVEEM-SRVGKLSVVFAITTMFFSYAIS 80
                                      799********999988666656777779******************996555.7777777777777766666554 PP

>> KdgT  2-keto-3-deoxygluconate permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.8   5.4e-08   0.00014     162     237 ..       3      83 ..       1      87 [] 0.72

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.4e-08
                              KdgT 162 qslvaviiPlivGiilGnldeel.rkflkkgvki....lipflafalGaginlktivkaglsGilLgvivvvvtgil 233
                                       + lvavi  + +G+++   ++++ ++f++k+ ++    li+fl++ +G+++n++++ ++g   ++ ++++++++  +
  gi|488601144|ref|YP_007907615.1|   3 EYLVAVIAGFALGVFIEKRESKIsKDFISKALTVclflLIFFLGYDIGSSLNVEEMSRVGKLSVVFAITTMFFSYAI 79 
                                       56888888888888888877776355777776652222788899999999999999999998888888888877666 PP

                              KdgT 234 lylv 237
                                         ++
  gi|488601144|ref|YP_007907615.1|  80 SKVL 83 
                                       5444 PP

>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.9   2.2e-07   0.00056      24      94 ..       5      80 ..       2      87 .] 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-07
                                      HHHHHHHHHHTTTTTS..........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 24 vgliiaGlllGpsglg...lieps..eedlevlselglilllFlaGleldlrelrknlksilllallgvlitvvli 94
                                      ++++iaG  lG ++ +    i+++     l+v + l++++l +++G +l+ +e+ +++k ++++a++ ++++ +++
  gi|488601144|ref|YP_007907615.1|  5 LVAVIAGFALGVFIEKresKISKDfiSKALTVCLFLLIFFLGYDIGSSLNVEEMSRVGKLSVVFAITTMFFSYAIS 80
                                      68899********99955434444766667777777777777999***************************9985 PP

>> Sbt_1  Na+-dependent bicarbonate transporter superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.7   3.3e-07   0.00083     165     237 ..       5      79 ..       2      87 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.3e-07
                             Sbt_1 165 vvlLlggliiGlltgekgleklepffedlFkgvLalfLLemGlvaar..rlkelrkvglflilfailaplvnall 237
                                       +v++++g+++G+++++++ +  + f+ ++ +  L l+++ +G   ++  +++e+++vg   ++fai++ +++ ++
  gi|488601144|ref|YP_007907615.1|   5 LVAVIAGFALGVFIEKRESKISKDFISKALTVCLFLLIFFLGYDIGSslNVEEMSRVGKLSVVFAITTMFFSYAI 79 
                                       68899**************************99998888888776661156799************998876555 PP

>> Asp-Al_Ex  Predicted Permease Membrane Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.5   1.2e-06    0.0031      29     107 ..       7      86 ..       4      87 .] 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                         Asp-Al_Ex  29 vLivglllGqlgktgpivldisalsllrelgLllFlaavGlsaGpgf.fsslkkdGlklvllallvtvvplllalvl 104
                                       + i+g  lG + ++++  ++  + s++ ++ L l ++ +G+++G+++ ++++++ G   v++a++ ++++ ++  vl
  gi|488601144|ref|YP_007907615.1|   7 AVIAGFALGVFIEKRESKISKDFISKALTVCLFLLIFFLGYDIGSSLnVEEMSRVGKLSVVFAITTMFFSYAISKVL 83 
                                       57999******99999999999999999******************967899999************9999998888 PP

                         Asp-Al_Ex 105 akl 107
                                        ++
  gi|488601144|ref|YP_007907615.1|  84 LRY 86 
                                       775 PP

>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.4e-06     0.016     159     231 ..       6      73 ..       2      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-06
                                       HHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.....HHHHHHHHH CS
                   Ammonium_transp 159 vggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrara....raavtTllAa 231
                                       v+ +ag+a+ +++ kre++       i    ++ a+  +l+L ++++g+  Gs+l++++ +r     +  v++++ +
  gi|488601144|ref|YP_007907615.1|   6 VAVIAGFALGVFIEKRESK-------ISKDFISKALTVCLFLLIFFLGYDIGSSLNVEEMSRVgklsV--VFAITTM 73 
                                       5667777777777777765.......56666677777799*******************999877543..3333322 PP

>> DUF1029  Protein of unknown function (DUF1029)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.8       0.3   7.6e+02      25      48 ..      20      43 ..       4      48 .. 0.57
   2 ?   11.5   1.6   9.3e-05      0.24      19      44 ..      52      78 ..      39      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.3
                           DUF1029 25 srktKldiiFvlqsilFlWfifHf 48
                                       r++K++  F+ +++    f++ f
  gi|488601144|ref|YP_007907615.1| 20 KRESKISKDFISKALTVCLFLLIF 43
                                      567788777776665555555544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.3e-05
                           DUF1029 19 laNf.vlsrktKldiiFvlqsilFlWf 44
                                       +N+  +sr  Kl+++F++ +++F++ 
  gi|488601144|ref|YP_007907615.1| 52 SLNVeEMSRVGKLSVVFAITTMFFSYA 78
                                      4454269*****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 600.74
//
Query:       gi|488601145|ref|YP_007907616.1|  [L=176]
Description: signal peptidase I, archaeal type [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-05   25.2   2.3      3e-05   23.9   1.5    1.9  2  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   1.5   1.7e-09     3e-05       2      54 ..      40     113 ..      39     125 .. 0.84
   2 ?    0.8   0.0     0.027   4.8e+02      25      65 ..     107     147 ..     105     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.7e-09
                                       XXSSTTCCTXXTTXEEEEE.CTS................---TTSEEEEEETTCE..-EEEEEEE..EETTEEE CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVd.kfs................epkrGdivvfrlpgee..eayiKrvi..glpgdrv 54 
                                       ++++SMep ++ Gd+++   +++                  + Gd++v + +g++  +  i+rvi   ++g+++
  gi|488601145|ref|YP_007907616.1|  40 IESGSMEPHMHVGDVVILMsPDRvgittyvegveknykaFGDYGDVIVYHPNGDRskTPVIHRVIayVEKGEHI 113
                                       89************99887355599****************************************554555554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.027
                                       --TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SST.TSTEE CS
                     Peptidase_S24  25 pkrGdivvfrlpgeeeayiKrviglpgdrvllasnn.eyppl 65 
                                       +++G+ + +++ ++  ++ K v  + g + +  +nn +++p+
  gi|488601145|ref|YP_007907616.1| 107 VEKGEHIPVKIGNKL-YLSKYVADHSGYVTQGDHNNaPDQPI 147
                                       578888889998996.88888888888888888888447665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1178.56
//
Query:       gi|488601146|ref|YP_007907617.1|  [L=747]
Description: ribonucleoside-diphosphate reductase class II [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-172  573.6   0.0   2.6e-170  567.4   0.0    2.1  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    5.1e-27   93.7   0.1    1.1e-26   92.7   0.1    1.6  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    2.1e-11   43.9   0.4    1.5e-10   41.1   0.3    2.4  2  TSCPD            TSCPD domain
  ------ inclusion threshold ------
      0.052   13.5   0.5       0.27   11.2   0.0    2.4  3  NTase_sub_bind   Nucleotidyltransferase substrate binding pro
       0.45   10.8   4.4          1    9.6   4.4    1.6  1  IBR              IBR domain, a half RING-finger domain
        1.4    8.9   5.6        3.7    7.5   5.6    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        2.8    7.5   8.6        6.7    6.3   8.6    1.7  1  TF_Zn_Ribbon     TFIIB zinc-binding
        3.1    7.8   6.3        6.5    6.7   6.3    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


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 !  567.4   0.0  1.1e-173  2.6e-170       1     524 []      84     550 ..      84     550 .. 0.97

  Alignments for each domain:
  == domain 1  score: 567.4 bits;  conditional E-value: 1.1e-173
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       s+Cfv+ v+ds+e+I++++ ++a++ k+ggG+G+++s+lR+kg++vk+t g asGpvsfmk++d+ ++ +kqgG+Rr
  gi|488601146|ref|YP_007907617.1|  84 SACFVIPVDDSIEGIFKALADMAKVQKSGGGTGFSFSRLRPKGDIVKSTMGVASGPVSFMKIFDSATEQIKQGGRRR 160
                                       79*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeee 154
                                       GA+m++l+v+HpDie+fi+aK +    ee +l+n+nisv v+d+Fm+av edk+++ ++Prt+ +            
  gi|488601146|ref|YP_007907617.1| 161 GANMGILNVHHPDIEEFITAK-R----EEGVLRNFNISVAVTDKFMKAVIEDKEYEQINPRTK-E------------ 219
                                       *********************.4....689*******************************31.1............ PP

                                       .............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 155 yeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCn 231
                                                   ++v+a+++f+ i+  aw++gePg++f+D++N+ n++   + g+I++tN+CgE+pll+yes   Cn
  gi|488601146|ref|YP_007907617.1| 220 ----------VVRRVPARKIFDMIIDGAWRNGEPGMVFIDAVNKFNPT--PHIGEIESTNPCGEQPLLPYES---CN 281
                                       ..........2349**********************************..999*******************...** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 232 LasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgip 308
                                       L+sinLakfv     ++ ++dwd+lk+ ++++vr+Ld+vidvn+yp+peie+ tk +R+iGlGvmg+ad+l++lgip
  gi|488601146|ref|YP_007907617.1| 282 LGSINLAKFV-----KDGDIDWDSLKEIVHIAVRFLDDVIDVNDYPIPEIEEMTKGNRKIGLGVMGWADMLFMLGIP 353
                                       **********.....358*********************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 309 ydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyGlrnam 385
                                       yds+eal++a++++++++ ++ kaS +lA+erg+fp++++s ++k       ++                  +rna+
  gi|488601146|ref|YP_007907617.1| 354 YDSREALELAERVMSFIQEESHKASQDLAEERGVFPNWKESVWEKRG-----IR------------------IRNAT 407
                                       *****************************************999883.....32..................8**** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                   Ribonuc_red_lgC 386 vtalaPTgsiSliagtssgiePifalvykksvtv..geflevnpvfeeeLkklglwseellkki..lesvqgleeip 458
                                       +t++aPTg+iS+iag+ssgieP+fal+yk+ ++   +ef+e+npv+e++L+++gl+s+e+l+ki   ++ +g++eip
  gi|488601146|ref|YP_007907617.1| 408 TTTIAPTGTISIIAGCSSGIEPVFALAYKRMNILdgEEFFEINPVLERTLRENGLYSDEILSKIveNGTLEGVDEIP 484
                                       ******************************99987778**************************65555******** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 459 eeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                       e +krvfk+al+i++e+h+++qaa qk+ d+++Sktinlpn+at +dv++++llA++lG+Kg+t+Y
  gi|488601146|ref|YP_007907617.1| 485 ESMKRVFKCALEISPEWHVRMQAAFQKYTDNAVSKTINLPNSATRKDVERAFLLAYELGCKGITVY 550
                                       *****************************************************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.1   4.7e-30   1.1e-26       3      82 ..       3      80 ..       1      81 [. 0.93

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 4.7e-30
                   Ribonuc_red_lgN  3 ltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmnaGte 81
                                      l+  a  vl++rYllkde+g+++E+p++m++RvA+a+a ae++y    + +++a++f++ + +q+f+p+sPtlmnaGt 
  gi|488601146|ref|YP_007907617.1|  3 LSRTAEVVLRKRYLLKDEHGNVIETPEEMCWRVARAIAKAEENY--NGDSEKWAKRFFEIIYNQQFMPNSPTLMNAGTS 79
                                      6667889***********************************88..68999**************************98 PP

                   Ribonuc_red_lgN 82 l 82
                                      l
  gi|488601146|ref|YP_007907617.1| 80 L 80
                                      6 PP

>> TSCPD  TSCPD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.68   1.5e+03      22      40 ..     416     434 ..     403     446 .. 0.82
   2 !   41.1   0.3   6.9e-14   1.5e-10       2      73 ..     598     687 ..     597     688 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.68
                             TSCPD  22 nvkfvgGCngnlkgiskLv 40 
                                       +++++ GC++ ++ + +L 
  gi|488601146|ref|YP_007907617.1| 416 TISIIAGCSSGIEPVFALA 434
                                       68999***99999888886 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 6.9e-14
                             TSCPD   2 ktkgvCs.reieievddk....liknvkfvgGC.ngnlkgiskLv.....egmkveevikklkGikC.......gnk 60 
                                       +tk++C+  +++i+ d++    ++ ++ + gGC ++++++i++L+     +  ++e +i++lkGi+C       ++ 
  gi|488601146|ref|YP_007907617.1| 598 ETKTGCGsLYVTINEDEHgiaeVFVQLGKSGGCaASQTEAIGRLIsialrSWVSPEAIIRQLKGIRCpsigfeeNEI 674
                                       5899998689*****955588889999******99**********999988899****************9997778 PP

                             TSCPD  61 eTSCpDqlakAlk 73 
                                        TSC+D +ak l+
  gi|488601146|ref|YP_007907617.1| 675 ITSCADGVAKILE 687
                                       8********9886 PP

>> NTase_sub_bind  Nucleotidyltransferase substrate binding protein like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.4   5.4e+03      42      57 ..      30      45 ..      26      57 .. 0.72
   2 ?   11.2   0.0   0.00012      0.27      30      76 ..     183     229 ..     167     239 .. 0.85
   3 ?   -2.9   0.0       2.8   6.4e+03      97     116 ..     354     372 ..     351     383 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                                      HHHHHHHHHHHHHHTS CS
                    NTase_sub_bind 42 Elawkllkryleeegi 57
                                      E++w++ + + + e++
  gi|488601146|ref|YP_007907617.1| 30 EMCWRVARAIAKAEEN 45
                                      8999999998887554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCTTT..HHHHHHHHHTTS CS
                    NTase_sub_bind  30 rdgvIqrFEftyElawkllkryleeegisaeavsp..rdliReaaeagl 76 
                                       ++gv  +F++++ +  k++k ++e++++  e+++p  ++++R+   +++
  gi|488601146|ref|YP_007907617.1| 183 EEGVLRNFNISVAVTDKFMKAVIEDKEY--EQINPrtKEVVRRVPARKI 229
                                       68***********************999..6777768999998665555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.8
                                       TSHHHHHHHHHTHH.HHHHH CS
                    NTase_sub_bind  97 Ydeetaeevveaiaeeylpe 116
                                       Yd+  a e++e++  ++++e
  gi|488601146|ref|YP_007907617.1| 354 YDSREALELAERVM-SFIQE 372
                                       88888888888888.77664 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 ?    9.6   4.4   0.00046         1      20      49 ..     721     746 ..     707     747 .] 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                               IBR  20 wCprpdCeaiieksegcksvtCskCgfefC 49 
                                        Cp  dC++++e segc  +tC+ Cg+  C
  gi|488601146|ref|YP_007907617.1| 721 ACP--DCGGVLEYSEGC--MTCKGCGYTKC 746
                                       6*9..***********8..56******988 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.6    0.0017       3.7      21      55 ..     712     744 ..     708     746 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
                    OrfB_Zn_ribbon  21 evnpayTSktCseCgsknkealsgrtfkCpnCgfe 55 
                                       + +   T   C+ Cg ++++  s+  ++C+ Cg++
  gi|488601146|ref|YP_007907617.1| 712 KKSTKITGDACPDCGGVLEY--SEGCMTCKGCGYT 744
                                       556667999***********..***********97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.6     0.003       6.7       3      27 ..     722     743 ..     721     744 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.003
                                       ETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCGl 27 
                                       CP+Cg+   v+++++g ++C+ CG+
  gi|488601146|ref|YP_007907617.1| 722 CPDCGG---VLEYSEGCMTCKGCGY 743
                                       ******...8**************6 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.3    0.0029       6.5       4      30 ..     722     744 ..     722     745 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0029
                                       ESTTTSBEEEEECSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgYe 30 
                                       Cp+Cg  L++ e+  +    C  CgY 
  gi|488601146|ref|YP_007907617.1| 722 CPDCGGVLEYSEGCMT----CKGCGYT 744
                                       ****************....******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (747 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4772.45
//
Query:       gi|488601147|ref|YP_007907618.1|  [L=364]
Description: hypothetical protein Asulf_01651 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-119  397.6   0.0     4e-119  397.4   0.0    1.0  1  DUF763    Protein of unknown function (DUF763)
  ------ inclusion threshold ------
      0.071   13.3   0.7       0.15   12.3   0.7    1.5  1  Rtt102p   Rtt102p-like transcription regulator protein
      0.085   12.8   0.0       0.19   11.7   0.0    1.6  1  HHH       Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.4   0.0  6.7e-123    4e-119       3     312 .]       6     321 ..       4     321 .. 0.94

  Alignments for each domain:
  == domain 1  score: 397.4 bits;  conditional E-value: 6.7e-123
                            DUF763   3 adLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkeal. 78 
                                       ++LpLh+gk+P wll+rmkkLsk+i+e+i++e+g++e++er+s+P++Fqs++nvlG+dW+sSG Ttv++g+lk++l 
  gi|488601147|ref|YP_007907618.1|   6 ISLPLHYGKAPYWLLNRMKKLSKQIIEIIINEFGEKEFFERISNPIFFQSFSNVLGFDWNSSGATTVMTGVLKSVLn 82 
                                       58**************************************************************************8 PP

                            DUF763  79 kseelgilvaGGkGkksrktpeeleklaeklgldeek.lvkasrlvakvdnaalqdgyqlYlhalivsekgkwaviq 154
                                       +see+ i+vaGGkG ++r+tpe+++kl++ l+ +e + l+ +srl+a++dn+alqdgy+lY+ha+i+se+  w+viq
  gi|488601147|ref|YP_007907618.1|  83 SSEEIAIRVAGGKGLNARQTPEHIMKLGSFLDESEIDlLIANSRLSARIDNNALQDGYDLYHHAIIFSEN-YWTVIQ 158
                                       899*************************99887776689*****************************98.8***** PP

                            DUF763 155 QGmneeerlARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelk.al 230
                                       QGmne+ r+ARRYh+  ++ e++  e++++i++++ke+e++nl+sk+s+e+rk+ild++++++ +l+++++ ++ + 
  gi|488601147|ref|YP_007907618.1| 159 QGMNEKLRTARRYHFKPRKFERIEVESQKEIISDRKENEIINLTSKHSRENRKTILDIIRDSR-SLKRDIEFISiKQ 234
                                       ************************************************************976.6777776654133 PP

                            DUF763 231 lkgekkl.....klpakhevlekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkDPvkysfav 302
                                       ++g+k++     +     +v++k++e ay+lqp++fe+lll++g+G+ t+raLal+a+liy+++++ +DP+kysfav
  gi|488601147|ref|YP_007907618.1| 235 IRGQKTIdgriiEYAVPRKVNWKAIEVAYSLQPDNFEDLLLIEGMGKGTIRALALIADLIYNSEYDRQDPAKYSFAV 311
                                       455666588888555566779******************************************************** PP

                            DUF763 303 GgKdgvPypv 312
                                       GgKdgvP+pv
  gi|488601147|ref|YP_007907618.1| 312 GGKDGVPFPV 321
                                       *********8 PP

>> Rtt102p  Rtt102p-like transcription regulator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   2.5e-05      0.15      44     120 ..     161     237 ..     124     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                       ---------B-S--EEEEEE-STT-.---------.----TTCCB--XXXXX..XXXXXXXXXXXXX..XXXXXXXX CS
                           Rtt102p  44 esneeneeekysfkyktWlksdeaeqkdieeeneeldlldlskydrtkkske..lkvtnaksaneeaegdsLtvddI 118
                                        +++     +y fk +++ +++ ++qk+i ++ +e ++++l++   ++++k+      +++s  ++   + +++  I
  gi|488601147|ref|YP_007907618.1| 161 MNEKLRTARRYHFKPRKFERIEVESQKEIISDRKENEIINLTSKHSRENRKTilDIIRDSRSLKRDI--EFISIKQI 235
                                       4555567789*****************999999999*****87666666666443344444444443..67777777 PP

                                       XX CS
                           Rtt102p 119 Rg 120
                                       Rg
  gi|488601147|ref|YP_007907618.1| 236 RG 237
                                       77 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.2e-05      0.19       5      28 ..     265     288 ..     264     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
                                       HHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH   5 lipasreeLlalPGVGpktAeaIl 28 
                                       l p+++e+Ll ++G G+ t +a +
  gi|488601147|ref|YP_007907618.1| 265 LQPDNFEDLLLIEGMGKGTIRALA 288
                                       78*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2282.75
//
Query:       gi|488601148|ref|YP_007907619.1|  [L=242]
Description: Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-26   92.6   0.2      3e-26   92.3   0.2    1.1  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.2   1.7e-30     3e-26      73     241 ..      54     213 ..      16     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 1.7e-30
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHT CS
                             IF-2B  73 keakksliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrl 149
                                       +++ ++ +e i+ + + i+ +++k +++ +e + +g+++ Ti++s  v e l++a+k      V+v+Es P  +Grl
  gi|488601148|ref|YP_007907619.1|  54 NKVAERGVEGIEAVERYIKDSNQKTSRNLREIV-EGKVVTTISRSHIVSEGLKSAKK------VFVLESNPGGEGRL 123
                                       4455557777887778899999**999998877.9********************99......************** PP

                                       HHHHHHHTTXE.EEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBEST CS
                             IF-2B 150 takeLvqagip.vtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfser 225
                                       +a eL+  g++ v +++d+ ++y   e  d+vi GAd+i + G  +nk+GT+ lA++A++ ++p++ +++s+kfs +
  gi|488601148|ref|YP_007907619.1| 124 LADELELVGVEyVEVVPDAFMGYAVAE-SDYVISGADSISKHG-FVNKVGTLPLALVARHYEVPFILAVPSYKFSSN 198
                                       **********9678*************.9**************.78******************************* PP

                                       SSSGGGSSXXBEXTHH CS
                             IF-2B 226 vqldedifieerdpee 241
                                       + ++++if e+   + 
  gi|488601148|ref|YP_007907619.1| 199 LVVQNKIF-EFVSMKY 213
                                       99988777.7766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1527.90
//
Query:       gi|488601149|ref|YP_007907620.1|  [L=119]
Description: hypothetical protein Asulf_01653 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  134.6   0.1    1.3e-39  134.4   0.1    1.0  1  DUF190    Uncharacterized ACR, COG1993
  ------ inclusion threshold ------
      0.092   11.9   0.1        0.1   11.8   0.1    1.1  1  DUF815    Protein of unknown function (DUF815)


Domain annotation for each model (and alignments):
>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   0.1   1.5e-43   1.3e-39       2      97 .]       9     104 ..       8     104 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 1.5e-43
                                       EEEEEEETT-EETTEEHHHHHHHHHHHTT-S--EEEE-S---------------------EEEEEEEE-HHHHHHHH CS
                            DUF190   2 lLrIyigesdrlegkplyeaivelareeglagatvlrGieGfgassrihtakllelsedlPvvieivdteekieafl 78 
                                       lLrIyig sdr+ gkply+ ++e++r+eg+agatvlrGi Gfg++s ihta++l+ls+dlP+vieivd+ ekie++l
  gi|488601149|ref|YP_007907620.1|   9 LLRIYIGDSDRYMGKPLYKFLLEFFRKEGFAGATVLRGISGFGKTSIIHTASILRLSTDLPIVIEIVDKIEKIEKVL 85 
                                       79*************************************************************************** PP

                                       HHHHT----SEEEEEEEE- CS
                            DUF190  79 pelkelvkeglvtlekvev 97 
                                       p+lk++vkegl+t+ekv v
  gi|488601149|ref|YP_007907620.1|  86 PVLKDVVKEGLITIEKVGV 104
                                       ****************976 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.1e-05       0.1      47     112 ..      33      98 ..      23     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                            DUF815  47 fleglpannvLLwGarGtGKSslvkallneyaeegLr.lievekedlkelpklvellrerperfilf 112
                                       f +   a   +L G  G GK s+++++     ++ L  +ie+  +++++++k++ +l+++ ++ ++ 
  gi|488601149|ref|YP_007907620.1|  33 FRKEGFAGATVLRGISGFGKTSIIHTASILRLSTDLPiVIEIV-DKIEKIEKVLPVLKDVVKEGLIT 98 
                                       555566788899************9887766666665156775.67999999999999887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 865.66
//
Query:       gi|488601150|ref|YP_007907621.1|  [L=125]
Description: camphor resistance protein CrcB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-23   82.8   6.9    1.9e-23   82.5   6.9    1.0  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)
  ------ inclusion threshold ------
      0.024   14.3   8.7       0.76    9.4   2.6    2.1  2  DUF4203   Domain of unknown function (DUF4203)
       0.47   10.2   2.9       0.66    9.8   2.9    1.2  1  SPC25     Microsomal signal peptidase 25 kDa subunit (SPC25)
        3.5    8.0  10.0         12    6.3  10.0    1.8  1  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   6.9   4.3e-27   1.9e-23       2      94 ..       6     115 ..       5     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 4.3e-27
                                       HHHHHHHHHHHHHHHH.HHHHBE...BHHHHHHHHHHHHHHHHHHH..............HHTTTHHHHHS-SHHHH CS
                              CRCB   2 lvalggalGallRyllssllnkr...plgtlavNvlGsfllgllla..............llttGflGglTTfStfv 61 
                                       +v++gg++Ga+lRy+l++l++ +   plgtl vNv+Gsfl+ l+++              +lt+G++ ++TT+Stf+
  gi|488601150|ref|YP_007907621.1|   6 IVGIGGFIGAILRYILAGLIQDNlefPLGTLSVNVIGSFLISLVMHlseleglfsaetrlFLTVGVIASFTTMSTFS 82 
                                       799*************8888777**989***************999888877777777777**************** PP

                                       HHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHH CS
                              CRCB  62 lelvslleegellaallyvllsvvlgllavvlg 94 
                                       +el++l+ee+e++ +++y+l +++++++av+lg
  gi|488601150|ref|YP_007907621.1|  83 YELFKLFEEKETFLMIMYLLGNILVSFFAVYLG 115
                                       *********9********************997 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4   0.00029       1.3     145     195 ..       4      50 ..       4      53 .. 0.85
   2 ?    9.4   2.6   0.00017      0.76      84     129 ..      67     114 ..      59     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00029
                           DUF4203 145 avvlgiDyfvgaglkefllnlfpratvalltypltrgdwvllalwivlalv 195
                                       ++++gi+ f+ga l ++l+ l++++     ++pl ++++ +++++++ +++
  gi|488601150|ref|YP_007907621.1|   4 IFIVGIGGFIGAILRYILAGLIQDNL----EFPLGTLSVNVIGSFLISLVM 50 
                                       589****************9998666....599999998888888887766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00017
                           DUF4203  84 algGlllallilsllegglitslpskaif..lvivvlgllgavlslkl 129
                                       + +G++ +++++s +++ l++ +++k  f  ++++   +l+++++++l
  gi|488601150|ref|YP_007907621.1|  67 LTVGVIASFTTMSTFSYELFKLFEEKETFlmIMYLLGNILVSFFAVYL 114
                                       579**************************5444444444444444444 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.9   0.00015      0.66      30      87 ..      67     121 ..      58     125 .] 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                             SPC25  30 LalGylavaiaavaflydykveFeeskpvlaiavvlYfilsgiltlystfvekntifv 87 
                                       L +G++a++ ++ +f y+ ++ Fee+ +   +++++Y + ++++ +++ ++ + t++v
  gi|488601150|ref|YP_007907621.1|  67 LTVGVIASFTTMSTFSYELFKLFEEKET---FLMIMYLLGNILVSFFAVYLGRITVLV 121
                                       6689*********************987...566789999999999999999998887 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  10.0    0.0027        12      16      98 ..      43     125 .]       3     125 .] 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHTTSS-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.......CTSHHHHHHHHHHHHHHHHHH. CS
                              MgtE  16 asristalhlgelekklkkvllkelrvvlllgvilgllifllalllgw......slllalvvglalvlvllaaall. 85 
                                       +  is  +hl+el      ++  e+r++l++gvi ++  ++    ++       + + ++++ + l+ ++l++ ++ 
  gi|488601150|ref|YP_007907621.1|  43 SFLISLVMHLSEL----EGLFSAETRLFLTVGVIASFTTMST---FSYelfklfEEKETFLMIMYLLGNILVSFFAv 112
                                       4456667778888....5667888888888888877776655...11122334533334445566777788888889 PP

                                       ..HHHHHHHHHHT CS
                              MgtE  86 ilgvllplllwkl 98 
                                       +lg +++l+ w++
  gi|488601150|ref|YP_007907621.1| 113 YLGRITVLVVWRR 125
                                       99*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 915.03
//
Query:       gi|488601151|ref|YP_007907622.1|  [L=279]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-09   36.4   0.0    0.00029   20.5   0.0    4.9  6  Prenyltrans    Prenyltransferase and squalene oxidase repeat
     0.0039   15.8   0.1      0.032   12.8   0.0    2.0  2  Ribophorin_II  Oligosaccharyltransferase subunit Ribophorin I


Domain annotation for each model (and alignments):
>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.79   7.1e+03       4      16 ..      16      28 ..      16      30 .. 0.74
   2 ?   -3.1   0.0      0.78     7e+03      33      44 .]      44      55 ..      43      55 .. 0.78
   3 ?    0.1   0.0     0.078     7e+02       2      12 ..      60      70 ..      59      71 .. 0.88
   4 ?    0.8   0.0     0.048   4.3e+02      15      32 ..     162     179 ..     157     181 .. 0.71
   5 !    7.7   0.0   0.00034         3      17      41 ..     200     225 ..     185     227 .. 0.91
   6 !   20.5   0.0   3.3e-08   0.00029       4      42 ..     235     274 ..     232     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.79
                                      HHHHHHHHHHSHT CS
                       Prenyltrans  4 ekavefLlscQne 16
                                      +k+++++ s+  e
  gi|488601151|ref|YP_007907622.1| 16 KKIIRYVQSRRVE 28
                                      699***9777655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.78
                                      HHHHHHHHHHCT CS
                       Prenyltrans 33 tywalaaLallG 44
                                      ty+ l++L  lG
  gi|488601151|ref|YP_007907622.1| 44 TYYSLSILTSLG 55
                                      888899887665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.078
                                      HHHHHHHHHHH CS
                       Prenyltrans  2 dvekavefLls 12
                                      d++k+v fLl+
  gi|488601151|ref|YP_007907622.1| 60 DKNKIVKFLLN 70
                                      89*******96 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.048
                                       HTTS-BBSSTTSSBBHHH CS
                       Prenyltrans  15 nedGGwggrpgsesdtyy 32 
                                       + +GG+g+      dt+y
  gi|488601151|ref|YP_007907622.1| 162 RSQGGFGLKFPNLRDTFY 179
                                       579****98766666666 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.00034
                                       TS-BBSSTTS.SBBHHHHHHHHHHHH CS
                       Prenyltrans  17 dGGwggrpgs.esdtyytywalaaLa 41 
                                       +GG++ +p s ++ +  ty+a+++L+
  gi|488601151|ref|YP_007907622.1| 200 EGGFAKSPKSyPPYLEETYYAISSLY 225
                                       7**********99**********996 PP

  == domain 6  score: 20.5 bits;  conditional E-value: 3.3e-08
                                       HHHHHHHHHHSHTTS-BBSSTTS.SBBHHHHHHHHHHHHH CS
                       Prenyltrans   4 ekavefLlscQnedGGwggrpgs.esdtyytywalaaLal 42 
                                       ek ++f+l+ Qn+dGG++ +     s++ +t++a+ +L +
  gi|488601151|ref|YP_007907622.1| 235 EKTRNFILTLQNPDGGFRRSIYCgISTLENTFYAVKSLEM 274
                                       899**************98876569999999999988855 PP

>> Ribophorin_II  Oligosaccharyltransferase subunit Ribophorin II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.5e-06     0.032      22      93 ..      20      90 ..       5     108 .. 0.73
   2 ?    0.8   0.0     0.015   1.4e+02      42      68 ..     214     242 ..     184     276 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-06
                     Ribophorin_II 22 sasdrsrlkevfe.sgesssdleeayyalaglevlgekvskea..Ckfvvkllsssklssleslfyalsankalk 93
                                            r+++ f   +  + +l+e+yy+l+ l++lg k+++++   kf+   l+s+k +++ slfy l++ ++l+
  gi|488601151|ref|YP_007907622.1| 20 RYVQSRRVENGFAfCKPLPPSLAETYYSLSILTSLGLKIDDKNkiVKFL---LNSVK-KEPYSLFYTLQSLRLLG 90
                                      5555566666666333334899****************98875444444...77777.99*********999998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.015
                     Ribophorin_II  42 leeayyalaglevlgek..vskeaCkfvv 68 
                                       lee+yya++ l +l+ +   ++++ +f+ 
  gi|488601151|ref|YP_007907622.1| 214 LEETYYAISSLYKLNYTldAPEKTRNFIL 242
                                       55666666666666655332222233332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2197.56
//
Query:       gi|488601152|ref|YP_007907623.1|  [L=521]
Description: translation elongation factor 1A GTP binding domain family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-37  126.7   0.1    1.2e-36  126.1   0.1    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.4e-12   47.9   1.7    3.8e-12   46.4   0.3    2.6  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    2.1e-08   34.5   0.1    5.8e-08   33.0   0.1    1.8  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    3.6e-06   27.3   0.3      8e-06   26.2   0.3    1.6  1  AlbA_2       Putative DNA-binding domain
     0.0004   20.3   0.4      0.025   14.5   0.1    2.3  2  RsgA_GTPase  RsgA GTPase
     0.0096   15.7   0.1       0.21   11.3   0.0    2.3  2  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.067   13.3   0.0       0.31   11.1   0.0    2.1  1  MMR_HSR1     50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.1   4.7e-40   1.2e-36       1     190 [.     112     331 ..     112     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 4.7e-40
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE............. CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle............. 64 
                                       k+++ +g++ghvDhGK+TL+++L+  + ++ + ++    + +lDtlk+E erg++ + + + l+             
  gi|488601152|ref|YP_007907623.1| 112 KEHIIVGTAGHVDHGKSTLVGCLISGNPDDGSGAT----SIYLDTLKHEIERGLSADLSYAVLSfqnegaikmknpl 184
                                       5899********************88888777333....457***************999888888*********** PP

                                       ........TTCSSEEEEEEEESSSGGGHHHHHHH..HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEES CS
                          GTP_EFTU  65 ........ketkkylinliDtPGHvdFskevirg..lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNK 131
                                                e++++ +++iDt GH+ + +++irg   +++D+ +lvv+a++Gv+  t+e+l +++++++p+i++i+K
  gi|488601152|ref|YP_007907623.1| 185 nkneralmVEKADKIVSFIDTVGHEPWLRTTIRGllGQKIDYGLLVVAANDGVMRTTKEHLGILIAMDLPVIIAITK 261
                                       ****9985499***********************7779*************************************** PP

                                       CGST.HHHHHHHHHHHHHHHHHH............HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 132 mDrl.kaelkeiveevkqklsrk............eeklekygekgekevpvvfgSalkgegvktllealve 190
                                       +D++ +++++e+++e++++l+++             +++  +  ++  +vp++ +Sa++ +g++ +le l  
  gi|488601152|ref|YP_007907623.1| 262 ADMVgEERVEEVINEISKTLRSVgripylvkekedARRVARILSRD-IIVPIIETSAITLKGYD-ILEELLY 331
                                       ****9999************66677777776655434444444444.79************999.5555444 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 ?   -1.7   0.1       1.6     4e+03      21      21 ..      76      76 ..      47     118 .. 0.55
   2 ?   -3.6   0.0       5.9   1.5e+04      30      44 ..     209     225 ..     197     237 .. 0.63
   3 !   46.4   0.3   1.5e-15   3.8e-12       1      74 []     357     428 ..     357     428 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                                      E CS
                       GTP_EFTU_D2 21 i 21
                                      i
  gi|488601152|ref|YP_007907623.1| 76 I 76
                                      2 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.9
                                       E..EEEEEEEEEEETEE CS
                       GTP_EFTU_D2  30 e..ivtrissletfhed 44 
                                       e   +t+i++l+  + d
  gi|488601152|ref|YP_007907623.1| 209 EpwLRTTIRGLLGQKID 225
                                       34678899988876655 PP

  == domain 3  score: 46.4 bits;  conditional E-value: 1.5e-15
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       Gtv+ g++ sG+++ G+ev+i++  d  +++ ++r++s+e++  + + a +g+ +G+ +++   ++ +++G++lt
  gi|488601152|ref|YP_007907623.1| 357 GTVVSGTIKSGEIRAGEEVYIGPfHD--GSFRKVRVQSIEMHYYRIERACDGDIVGLAIKGARFDE-LRRGMVLT 428
                                       9**********************654..67788*********************************.9*****96 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 !   33.0   0.1   2.3e-11   5.8e-08       2      99 ..     432     508 ..     431     520 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.3e-11
                                       -EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEEC. CS
                       GTP_EFTU_D3   2 ikphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnviveveli. 77 
                                       i+p+ +f A+vyi+++  +t i  gY+pvl++ t ++t+ +++++++              +++ G++ +v+++ + 
  gi|488601152|ref|YP_007907623.1| 432 IHPVYEFLAEVYIFNH--PTRIKRGYEPVLHLETISETVVFEDIEKE--------------YMMAGERGKVRMKFKy 492
                                       78999***********..*********************99999443..............4555555555555432 PP

                                       CEEEE--TTTHCCCCEEEEECT CS
                       GTP_EFTU_D3  78 kpialekgseypqlGrFaiReg 99 
                                       +p  + kg+      +F  Reg
  gi|488601152|ref|YP_007907623.1| 493 HPYYICKGQ------KFIFREG 508
                                       455555555......5555554 PP

>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.3   3.1e-09     8e-06       1     101 [.      12     113 ..      12     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.1e-09
                            AlbA_2   1 EdellEfKeslgnklkkrersiakticAfaNse.....g.GtlliGVeDdgkvvGvecsdqeedqlrlelksiikrf 71 
                                       E+e++EfKe+l +++ ++  +  +t+++ +N +     g  + ++G++D+g+++G+  +++  ++  ++lk+i++++
  gi|488601152|ref|YP_007907623.1|  12 EKENIEFKEFLTDYHLRD--DRFQTLACQMNHRilmgrGkAVYVVGISDSGELKGI--THERFNKTLQILKKIASEI 84 
                                       899***********9964..489********855554477999*************..8888888888888899999 PP

                            AlbA_2  72 kpkvlpdiervelkgkkvlvvkvekskkkp 101
                                       + +v+  +e+++++g  v +v++ k++ k 
  gi|488601152|ref|YP_007907623.1|  85 DAEVRS-VEKYKINGGIVGIVEISKTRPKE 113
                                       999885.9999************9987665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.019        49      98     122 ..     110     137 ..      66     178 .. 0.65
   2 !   14.5   0.1   9.6e-06     0.025      16     101 ..     224     308 ..     213     313 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.019
                                       TTSEEEEECSTT...SSHHHHHHHHCTT CS
                       RsgA_GTPase  98 kdktsvlvGqSG...vGKStLinallpe 122
                                       + k  ++vG  G    GKStL+  l++ 
  gi|488601152|ref|YP_007907623.1| 110 RPKEHIIVGTAGhvdHGKSTLVGCLISG 137
                                       3366778888884336******999884 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 9.6e-06
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH...HHHHHHHHHHHTTSEEEE--TTTHTT CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee...eleelkeelealgyevllvsaktkeg 89 
                                       +d  l+vv+++  +  +++ +  L ++ + +++++i+++K+D++ ee+    ++e++++l+++g  ++lv++k  e+
  gi|488601152|ref|YP_007907623.1| 224 IDYGLLVVAAN--DGVMRTTKEHLGILIAMDLPVIIAITKADMVGEERveeVINEISKTLRSVGRIPYLVKEK--ED 296
                                       78889999999..555677889999999*****************9997777888889999999888877554..77 PP

                                       HHHHHHHCTTSE CS
                       RsgA_GTPase  90 leelkellkdkt 101
                                       ++++++ l+ ++
  gi|488601152|ref|YP_007907623.1| 297 ARRVARILSRDI 308
                                       777777776655 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 ?    1.9   0.0     0.065   1.7e+02       2      34 ..     120     152 ..     116     166 .. 0.79
   2 !   11.3   0.0   8.2e-05      0.21     149     234 ..     245     329 ..     235     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.065
                        ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDP 34 
                                       +G++  GK+t+vg l++  ++ g     + LD+
  gi|488601152|ref|YP_007907623.1| 120 AGHVDHGKSTLVGCLISGNPDDGSGATSIYLDT 152
                                       344447**********99999999999998887 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.2e-05
                        ATP_bind_1 149 lsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekee..ekykklaeaiaelleefalvlrflplsse 223
                                       l +++ ++lP +++++k+D++ e+  +  e+++++ +  +         k k+ a+ +a++l+   +v  ++  s+ 
  gi|488601152|ref|YP_007907623.1| 245 LGILIAMDLPVIIAITKADMVGEE--RVEEVINEISKTLRSVGRIPylVKEKEDARRVARILSRDIIV-PIIETSAI 318
                                       66899***************9954..344444444443333333336777789999999999999888.88888888 PP

                        ATP_bind_1 224 keesiedllsl 234
                                       + ++++ l +l
  gi|488601152|ref|YP_007907623.1| 319 TLKGYDILEEL 329
                                       88877777655 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   0.00012      0.31       2     114 .]     117     261 ..     116     261 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       EEEEESTTSSHHHHHHHHHT....STEEESSSTTSSSSEEEEE.EEETTEE.......................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg....ekaivsdkpgtTrdinegr.vklkgke.......................... 47 
                                       v+ +G+   GKStL+  l+     + + ++++   T++ + +r ++    +                          
  gi|488601152|ref|YP_007907623.1| 117 VGTAGHVDHGKSTLVGCLISgnpdDGSGATSIYLDTLKHEIERgLSA---Dlsyavlsfqnegaikmknplnknera 190
                                       678999************96333312333333344444333321221...122334444444555566666777777 PP

                                       .........EEEEECGGCSSHHHHHHHHHHHHHH..HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  48 .........ielvDtpGliegaseekglgkafla..leeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                                + ++Dt+G  e     + l+ +++    ++ d  llvv a+ +++ +  +e   +l   + p+i++++
  gi|488601152|ref|YP_007907623.1| 191 lmvekadkiVSFIDTVG-HE----PW-LRTTIRGllGQKIDYGLLVVAAN-DGVMRTTKEHLGILIAMDLPVIIAIT 260
                                       888888888********.44....77.55555442145699999999877.66777777777777778888888887 PP

                                       S CS
                          MMR_HSR1 114 k 114
                                       k
  gi|488601152|ref|YP_007907623.1| 261 K 261
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); 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: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3178.27
//
Query:       gi|488601153|ref|YP_007907624.1|  [L=222]
Description: metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-77  258.2   1.4    5.8e-77  258.1   1.4    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 !  258.1   1.4   3.3e-81   5.8e-77       1     218 [.       1     217 [.       1     218 [. 0.98

  Alignments for each domain:
  == domain 1  score: 258.1 bits;  conditional E-value: 3.3e-81
                   Diphthami_syn_2   1 mkvavlysGGkDsilaLykalkesevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedL 77 
                                       m+ a l+sGGkDs la + a +e e++ Lvsv+s n++symfh++n+hlv+++a ++ +pl k  t Geee ev+dL
  gi|488601153|ref|YP_007907624.1|   1 MRLASLVSGGKDSLLATHLASEENEIDCLVSVVSSNPDSYMFHTPNIHLVDATAIAMDLPLFKIFTRGEEELEVKDL 77 
                                       899************************************************************************** PP

                   Diphthami_syn_2  78 kgtlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGr 154
                                        + l++ldv+++viG+i+s yqk+r+e vC+elGlk++aPLW+k+  e +++   ek++ i+v v+a+gl e+++Gr
  gi|488601153|ref|YP_007907624.1|  78 IKGLRNLDVDGIVIGGIASSYQKKRFELVCEELGLKLIAPLWGKSD-EEVMKLAMEKMDFIIVKVSAMGLSEKWVGR 153
                                       *********************************************9.7777888899******************** PP

                   Diphthami_syn_2 155 ridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldierak 218
                                       ++d k + elkk+ ekygi+ agegGe+etlvl+aP+fkkr+e+ e +   d+   ++ ++r++
  gi|488601153|ref|YP_007907624.1| 154 KMDEKALSELKKIKEKYGINLAGEGGEFETLVLNAPMFKKRIEILESHVVSDNMSAVMVVDRYR 217
                                       **************************************************99999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1535.30
//
Query:       gi|488601154|ref|YP_007907625.1|  [L=319]
Description: L-alanine dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-113  377.6   0.1   4.2e-113  377.5   0.1    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.026   14.6   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.12   12.2   1.7        1.4    8.9   0.0    2.6  2  Myosin_N         Myosin N-terminal SH3-like domain


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 !  377.5   0.1    7e-117  4.2e-113       2     317 ..       2     310 ..       1     311 [. 0.98

  Alignments for each domain:
  == domain 1  score: 377.5 bits;  conditional E-value: 7e-117
                                       -EEEE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTC CS
                   OCD_Mu_crystall   2 ekavltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenk 78 
                                       e+ +lt+++++ +l +dd +kave+af+   + +v++p +++le+++  g+l++mpayl g  ++gvK+vnshp+n 
  gi|488601154|ref|YP_007907625.1|   2 ETIILTKEDIMDILTMDDTLKAVEHAFEMHGKNEVQMPAKIYLEFEK--GDLRAMPAYLDG--KAGVKWVNSHPHNS 74 
                                       6889*************************9999**************..************..************** PP

                                       CCTSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--S CS
                   OCD_Mu_crystall  79 ksglptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldik 155
                                       + glptv+al++ ndpetG+pla+mdat++t++RT+A++++a kyLarkd++ +++iG+Gvqa+tql a  +++d++
  gi|488601154|ref|YP_007907625.1|  75 EVGLPTVMALLIYNDPETGFPLAVMDATHITNMRTGAAGGIASKYLARKDSKIIGFIGCGVQAYTQLSAHLKLFDVE 151
                                       ***************************************************************************** PP

                                       EEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB CS
                   OCD_Mu_crystall 156 evriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteL 232
                                       +vr yd++e+ a+kf++++++   ++ a     e + ++di+vt+T++++p+++aewv  G+hina+gadapgk+eL
  gi|488601154|ref|YP_007907625.1| 152 KVRCYDLSESHAKKFVDYCSK--QNIDAEFARIEKACDCDILVTITPSRKPVVMAEWVADGTHINAIGADAPGKQEL 226
                                       ********************7..789999999999****************************************** PP

                                       -HHHHHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHH CS
                   OCD_Mu_crystall 233 dddilkradifvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaakl 309
                                       d++ilk++++fvd+++qa ++Ge++v+++kg+++e+++  ++gevi Gk++GR  d eit+fds+Gla++D+++a +
  gi|488601154|ref|YP_007907625.1| 227 DPEILKKSRVFVDDKEQAFHSGEVNVPLSKGIISENDIAGTIGEVIVGKVKGRIGD-EITVFDSTGLAIQDISTASI 302
                                       *****************************************************986.7******************* PP

                                       HHHHHCCC CS
                   OCD_Mu_crystall 310 vyeraeek 317
                                       +y ra ek
  gi|488601154|ref|YP_007907625.1| 303 IYSRAIEK 310
                                       ****9987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.3e-06     0.026       3      99 ..     116     211 ..     114     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-06
                                       HHHHHS..TT-EEEEES-SHHH.HHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SE CS
                      Shikimate_DH   3 akkkleslkekkvlliGaGema.elvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadv 78 
                                       a+k l + ++k +  iG G  a +++  hL    v+kv     + ++ak++++ +++++i   ++  ++++  ++d+
  gi|488601154|ref|YP_007907625.1| 116 ASKYLARKDSKIIGFIGCGVQAyTQLSAHLKLFDVEKVRCYDLSESHAKKFVDYCSKQNI-DAEFARIEKA-CDCDI 190
                                       566666677788899****7662677889**************************88855.5689999966.579** PP

                                       EEE-SSSSS-SB-HHHHHCCH CS
                      Shikimate_DH  79 visataseepilekeeveeal 99 
                                       +++ t s++p++ +e+v +  
  gi|488601154|ref|YP_007907625.1| 191 LVTITPSRKPVVMAEWVADGT 211
                                       ****************98876 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00023       1.4       1      18 [.     233     250 ..     233     252 .. 0.95
   2 ?    1.1   0.9     0.059   3.5e+02      15      28 ..     273     286 ..     272     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                                       SEEEEETTSTTS-EEEEE CS
                          Myosin_N   1 KklVWVpDpkegyvkGeI 18 
                                       K++V+V D+++++  Ge+
  gi|488601154|ref|YP_007907625.1| 233 KSRVFVDDKEQAFHSGEV 250
                                       99**************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.059
                                       EEEEEEEESSEEEE CS
                          Myosin_N  15 kGeIkeeeGdkvtV 28 
                                        G++k + Gd++tV
  gi|488601154|ref|YP_007907625.1| 273 VGKVKGRIGDEITV 286
                                       599**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1820.30
//
Query:       gi|488601155|ref|YP_007907626.1|  [L=211]
Description: proteasome endopeptidase complex, beta component , Threonine peptidase, MEROPS family T01A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-55  187.8   0.7    1.6e-55  187.5   0.7    1.1  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 !  187.5   0.7   9.1e-60   1.6e-55       2     190 .]       6     188 ..       5     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 187.5 bits;  conditional E-value: 9.1e-60
                                       HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                        Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                        kGtt+vG+ +kdg+v++++krat+g+ ++s++ ++Ki++i d+i++++aG+++Da+ l r++++e +ly++r +r+
  gi|488601155|ref|YP_007907626.1|   6 YKGTTTVGLICKDGIVMGTEKRATMGNFIASRR-AKKIYQIADRIALTTAGSVGDAQFLYRIIKVETSLYEIRKERR 81 
                                       68***************************8888.7****************************************** PP

                                       TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHS CS
                        Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyk 155
                                       ++++    +va+++++ + + +  p+ v+lli+gvde+g p +y+idp+G  ieekd+va+Gsgs  a+++le+++ 
  gi|488601155|ref|YP_007907626.1|  82 PTIR----SVATMVSNLLNQTRYFPYFVQLLIGGVDERG-PTVYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFY 153
                                       ****....999999999999999*************998.************************************* PP

                                       TTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 156 edltleeavelavkalkealerdklsgknievavi 190
                                       e +  +eave++++a++ a++rd++sg++++v+ i
  gi|488601155|ref|YP_007907626.1| 154 EGMPTDEAVEVVIRAIHTAMKRDSASGDGMDVVKI 188
                                       *******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1392.18
//
Query:       gi|488601156|ref|YP_007907627.1|  [L=634]
Description: arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-27   93.9   4.4    7.2e-25   86.7   0.3    2.9  3  KH_7           KH domain
    1.1e-26   93.3   0.0    4.9e-26   91.2   0.0    2.1  2  Beta-Casp      Beta-Casp domain
    2.2e-17   62.7   0.0    7.2e-17   61.1   0.0    2.0  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.9e-15   57.4   0.0    3.6e-12   46.7   0.0    2.5  2  Lactamase_B    Metallo-beta-lactamase superfamily
    8.2e-12   44.9   0.0    1.4e-11   44.2   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
      3e-10   40.0   0.0    5.9e-10   39.0   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.3e-06   28.1   0.5    7.9e-05   22.4   0.2    2.8  2  KH_2           KH domain
    3.5e-05   23.8   0.0    7.9e-05   22.6   0.0    1.5  1  Lactamase_B_3  Beta-lactamase superfamily domain
    0.00065   19.5   0.2     0.0021   17.9   0.2    1.9  1  KH_4           KH domain
  ------ inclusion threshold ------
      0.018   14.8   0.7       0.23   11.3   0.7    2.7  2  KH_1           KH domain
       0.17   11.7   0.0        0.4   10.5   0.0    1.5  1  RRM_9          RNA recognition motif


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 !   86.7   0.3   4.4e-28   7.2e-25       1      68 []       4      70 ..       4      70 .. 0.96
   2 !    7.7   0.3    0.0021       3.4       5      53 ..      74     125 ..      72     127 .. 0.79
   3 ?   -3.3   0.0       5.7   9.2e+03      45      66 ..     584     605 ..     581     605 .. 0.83

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 4.4e-28
                              KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      +e+l+elk+k+  +lP  v++++veFEGP lViY++np+++ae+gd+i+klAk+lrkRi iRpDp+ l
  gi|488601156|ref|YP_007907627.1|  4 DEYLSELKRKVAASLP-SVRVKNVEFEGPVLVIYVENPQELAESGDVIKKLAKDLRKRILIRPDPKSL 70
                                      5899************.67**********************************************976 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
                              KH_7   5 eelkekieeklPkevkitdveF..EGPelViYtknpklfa.engdlirklAk 53 
                                       ee ke i + +P+++++t+  F  E  e++i ++ p +++ ++g ++r++ k
  gi|488601156|ref|YP_007907627.1|  74 EEAKEIIRQIVPEDAQVTSFFFdhENGEVIIEAEKPGIVIgKQGVMLREIMK 125
                                       689***************9755448889999888888887566666676655 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.7
                              KH_7  45 gdlirklAkelrkRiviRpDps 66 
                                        +++r l++   k i++  D+s
  gi|488601156|ref|YP_007907627.1| 584 MNYVRALSSRPEKVITVHGDES 605
                                       5789999999999999999875 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.7   4.4e+03      16      36 ..     283     301 ..     269     307 .. 0.65
   2 !   91.2   0.0     3e-29   4.9e-26       2     110 .]     420     544 ..     419     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                                       .TTS-S-EEEEE-HHHHHHHH CS
                         Beta-Casp  16 kledlklpiyldsplaskate 36 
                                       ++e    p+++ s+l+++a++
  gi|488601156|ref|YP_007907627.1| 283 AREGN--PVVYESNLVREALK 301
                                       33244..99999999999987 PP

  == domain 2  score: 91.2 bits;  conditional E-value: 3e-29
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.......................E-SHH....HHH CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.......................veakslewmesk 55 
                                       qe+++ Lee+++ kkl    l +yld+ ++++at+++++y+e                       ++  s    +sk
  gi|488601156|ref|YP_007907627.1| 420 QEVMIALEEAIRTKKL--EGLTVYLDG-MIYEATAIHTAYPEylnthlrdmifhhglnpfisesfTQVDS----SSK 489
                                       9**********99774..2369*****.*******************************87666533333....334 PP

                                       H..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  56 keelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       + ++ ++++p+vila+sgml+gG++ e++++l++d++nt+++vgyqaegTlgr++
  gi|488601156|ref|YP_007907627.1| 490 RADVIDEAEPSVILATSGMLNGGPVMEYFRHLAGDEKNTIVFVGYQAEGTLGRRI 544
                                       43566789*********************************************97 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   4.4e-20   7.2e-17       2      62 .]     562     625 ..     561     625 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 4.4e-20
                             RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                       ++vk+ +e++d fSgH+d+++l++++r l+ r+  vi vHG+e ++++la+ + + ++i++ +P
  gi|488601156|ref|YP_007907627.1| 562 VEVKMNVETVDgFSGHSDRRQLMNYVRALSSRPekVITVHGDESKCLDLASSIYKTYKIETRAP 625
                                       79***************************999999******************99999998877 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   2.2e-15   3.6e-12       4      64 ..     191     252 ..     188     256 .. 0.90
   2 !    8.0   0.0    0.0016       2.6     126     163 ..     326     377 ..     312     430 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 2.2e-15
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH.HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGC CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal.elaalglkpkdvdavilTHlHlDHiGglggl 64 
                                       ++ ++yl++++++ iLiD+G+  ++ ++   ++  +  +++ +dav++TH+HlDH+G ++ l
  gi|488601156|ref|YP_007907627.1| 191 VGRSCYLLQTPESKILIDCGVNVSNIQQSPyLYVPELQPLDSIDAVVITHAHLDHCGLVPIL 252
                                       6789************************99777778888888***************99877 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                                       ECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC............... CS
                       Lactamase_B 126 tggpghghghgvveygggkvlftGDallagetgridl..............t 163
                                        ++ g++  h++++ g  +++f+GD+ +++ ++ +                t
  gi|488601156|ref|YP_007907627.1| 326 GHILGSSIAHFHIGEGLYNIAFSGDFKFERTRLFDKAetnfprlealimeaT 377
                                       688899999*******************988887777666666655555542 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 !   44.2   0.0   8.3e-15   1.4e-11       1     174 [.     197     363 ..     197     374 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 8.3e-15
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekv..iptvdliLLshatlehlGayallyakfksklllnipvyatlpv 75 
                                       lL+  + kiL+D+G++ s+++ +  l ++ +   ++++d+++++ha l+h G  ++ly     k++ + p+y t p+
  gi|488601156|ref|YP_007907627.1| 197 LLQTPESKILIDCGVNVSNIQQSPYL-YVPELqpLDSIDAVVITHAHLDHCGLVPILY-----KYGYRGPIYLTPPT 267
                                       6788899*********9999765555.444432489****************655555.....46889********* PP

                     Lactamase_B_6  76 vkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..Wkis 150
                                         L  ++ ld ++    +g+      e + ++ea ++ +t+ Y   ++++    ++ +t ynaGh lG +i  ++i 
  gi|488601156|ref|YP_007907627.1| 268 RDLMVLLQLDFIEVGAREGNPV--VYESNLVREALKHTITIDYGVVTDISP---DIRLTFYNAGHILGSSIahFHIG 339
                                       ****999999998876666443..3455679*************9999985...8**************99668888 PP

                     Lactamase_B_6 151 kesekivYavdwnhakeshLngaa 174
                                       +++ +i +  d+  ++ ++ ++a+
  gi|488601156|ref|YP_007907627.1| 340 EGLYNIAFSGDFKFERTRLFDKAE 363
                                       999999999999888888877765 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 !   39.0   0.0   3.6e-13   5.9e-10       2     165 ..     204     377 ..     203     387 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.6e-13
                                       EEEES--TT..HHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH....... CS
                     Lactamase_B_2   2 riLiDagpd..lrqqalral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla....... 68 
                                        iLiD+g +    qq +++l  P   ++ l++idaV++thaH DH+ gl  +   ++ + p+y ++ +++       
  gi|488601156|ref|YP_007907627.1| 204 KILIDCGVNvsNIQQ-SPYLyVP--ELQPLDSIDAVVITHAHLDHC-GLVPILYKYGYRGPIYLTPPTRDlmvllql 276
                                       59*******765566.9999666..4677779**************.666555545555799999999888887777 PP

                                       .............HCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEEC CS
                     Lactamase_B_2  69 .............vleanfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrieg 132
                                                    v e+n+v++a       ++ ++d g  +++  +++++t+  a h  g         ++ + i++
  gi|488601156|ref|YP_007907627.1| 277 dfievgaregnpvVYESNLVREA-----LKHTITIDYGVVTDIS-PDIRLTFYNAGHILGS-------SIAHFHIGE 340
                                       77776554444444444444444.....4445888899999997.6999999999999999.......999999999 PP

                                       TTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S CS
                     Lactamase_B_2 133 ggkrvyyigDtgyip....eeigerlggadlllldit 165
                                       g  +++++gD ++      +++++ +  ++ l++++t
  gi|488601156|ref|YP_007907627.1| 341 GLYNIAFSGDFKFERtrlfDKAETNFPRLEALIMEAT 377
                                       9999******994334455566667777777777766 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.062     1e+02      44      58 ..      47      61 ..      10      67 .. 0.89
   2 !   22.4   0.2   4.8e-08   7.9e-05      25      74 ..      98     148 ..      75     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.062
                                      GHHHHHHHHHHHHHH CS
                              KH_2 44 Gsnikkigkelrkdi 58
                                      G  ikk+ k+lrk+i
  gi|488601156|ref|YP_007907627.1| 47 GDVIKKLAKDLRKRI 61
                                      899**********99 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 4.8e-08
                                       CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEE.EET CS
                              KH_2  25 nrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklniv.kVk 74 
                                       +  +++i +++pgivIGk+G ++++i k+++   ++++  ++k + v +V+
  gi|488601156|ref|YP_007907627.1|  98 ENGEVIIEAEKPGIVIGKQGVMLREIMKAVGWSPKVMRTPPIKSKTVdNVR 148
                                       5567999**********************9988888888888877666665 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 !   22.6   0.0   4.8e-08   7.9e-05       5      52 ..     191     248 ..     189     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.8e-08
                     Lactamase_B_3   5 lghnsflletagarilvDPf........kanlgyeppa..........eeaDlvlisqaledHahl 52 
                                       +g +++ll+t++ +il+D +        +        +          +++D+v+i++a+ dH+ l
  gi|488601156|ref|YP_007907627.1| 191 VGRSCYLLQTPESKILIDCGvnvsniqqS--------PylyvpelqplDSIDAVVITHAHLDHCGL 248
                                       589***************99555554431........24455556666***************976 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.3e-06    0.0021       4      52 ..      76     121 ..      73     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                              KH_4   4 vedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtld 52 
                                       +++i++++v  pe+ +vt     ++++ e+ +e e+ G+vIGk+G +l+
  gi|488601156|ref|YP_007907627.1|  76 AKEIIRQIV--PEDAQVTSF-FFDHENGEVIIEAEKPGIVIGKQGVMLR 121
                                       6899****9..99*****99.34567778888899**********9985 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   0.00014      0.23       4      28 ..     102     126 ..     100     165 .. 0.80
   2 ?   -0.7   0.0      0.79   1.3e+03      44      57 ..     594     608 ..     577     613 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       EEEGGGHHHHHHTGGGHHHHHHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIree 28 
                                       +++ +++ g +IGk+G +++eI++ 
  gi|488601156|ref|YP_007907627.1| 102 VIIEAEKPGIVIGKQGVMLREIMKA 126
                                       677788889**************94 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.79
                                       T.-EEEEEE.SHHHH CS
                              KH_1  44 derevtisG.speav 57 
                                       +e+++t+ G + ++ 
  gi|488601156|ref|YP_007907627.1| 594 PEKVITVHGdESKCL 608
                                       699******555544 PP

>> RRM_9  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025       0.4      25      48 ..      20      43 ..       7      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                             RRM_9 25 rvalqnasveggvlvgyVktkkda 48
                                       v+++n+++eg+vlv+yV+++++ 
  gi|488601156|ref|YP_007907627.1| 20 SVRVKNVEFEGPVLVIYVENPQEL 43
                                      5899*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3947.38
//
Query:       gi|488601157|ref|YP_007907628.1|  [L=159]
Description: molybdopterin-guanine dinucleotide biosynthesis protein MobB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-32  111.2   0.0      4e-32  110.9   0.0    1.1  1  MobB            Molybdopterin guanine dinucleotide synthesis 
    6.6e-06   26.1   0.0      9e-06   25.6   0.0    1.3  1  AAA_26          AAA domain
     0.0036   16.9   0.1      0.006   16.2   0.1    1.6  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
     0.0041   17.2   0.0     0.0049   16.9   0.0    1.3  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0045   17.1   0.1     0.0095   16.0   0.0    1.6  2  MMR_HSR1        50S ribosome-binding GTPase
     0.0067   15.4   0.0     0.0095   14.9   0.0    1.3  1  DUF463          YcjX-like family, DUF463
     0.0082   16.1   0.2     0.0086   16.0   0.2    1.5  1  ATPase_2        ATPase domain predominantly from Archaea
     0.0082   15.1   0.1      0.015   14.3   0.1    1.4  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
  ------ inclusion threshold ------
      0.015   14.4   0.1      0.021   14.0   0.1    1.2  1  LpxK            Tetraacyldisaccharide-1-P 4'-kinase
      0.015   14.7   0.0      0.021   14.3   0.0    1.2  1  KTI12           Chromatin associated protein KTI12
      0.024   14.7   0.0      0.031   14.3   0.0    1.1  1  Glyco_transf_4  Glycosyltransferase Family 4
      0.036   14.3   0.0      0.051   13.8   0.0    1.3  1  AAA_22          AAA domain
       0.04   13.3   0.0      0.061   12.8   0.0    1.4  1  SRPRB           Signal recognition particle receptor beta sub
      0.076   12.6   0.0        0.1   12.1   0.0    1.2  1  NLBH            Neuraminyllactose-binding hemagglutinin precu
      0.088   13.0   0.1       0.13   12.5   0.1    1.3  1  Roc             Ras of Complex, Roc, domain of DAPkinase
      0.094   12.4   0.0       0.13   12.0   0.0    1.3  1  PRK             Phosphoribulokinase / Uridine kinase family
        0.1   12.5   0.0       0.17   11.8   0.0    1.4  1  APS_kinase      Adenylylsulphate kinase
       0.11   12.1   0.1       0.18   11.4   0.1    1.3  1  SRP54           SRP54-type protein, GTPase domain
       0.11   12.4   0.2       0.43   10.5   0.0    1.9  2  NTPase_1        NTPase
       0.13   12.0   0.1       0.26   11.1   0.1    1.4  1  ATP_bind_1      Conserved hypothetical ATP binding protein
       0.14   12.7   0.1        0.2   12.2   0.1    1.6  1  AAA_18          AAA domain
       0.16   10.7   0.0        0.3    9.9   0.0    1.3  1  AAA_35          AAA-like domain
        0.2   11.4   0.0       0.28   10.9   0.0    1.4  1  AAA_30          AAA domain


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   5.1e-35     4e-32       1     125 [.       3     123 ..       3     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 5.1e-35
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleea 77 
                                       v++i+g+s+sGKT+L+++l++ l+++g+rvg++Kh+ +++d+dk+gkDs+r+ kAG   v+v s+ ++a   +   +
  gi|488601157|ref|YP_007907628.1|   3 VISIIGFSNSGKTSLITQLVELLTNQGYRVGVVKHSDKKVDLDKEGKDSWRIFKAGY-DVAVLSPVKFAYRAR---R 75 
                                       799*****************************************************6.589999****99887...4 PP

                              MobB  78 elsleellarlsevDlvlvEGfkkealpkievlraelgkeellllede 125
                                       elsl e+l++++++D v+vEGfk+   + i v+r++ + +ell++ d+
  gi|488601157|ref|YP_007907628.1|  76 ELSLIEILRYFEDYDYVFVEGFKSDIRNGIAVVRSHEELDELLKQIDQ 123
                                       79*********************************9888888776655 PP

>> AAA_26  AAA 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     9e-06      10     109 ..      10      99 ..       2     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-08
                            AAA_26  10 tgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaarqegedi 86 
                                        ++GKT++++ Lv+ l+++g++vg++K   ++   d++ ++  +++++  +   ++p+ ++ +      ar+e    
  gi|488601157|ref|YP_007907628.1|  10 SNSGKTSLITQLVELLTNQGYRVGVVKHSDKKVDLDKEGKDSWRIFKAGYDVAVLSPVKFAYR------ARREL--- 77 
                                       489*****************************999***********************99855......34333... PP

                            AAA_26  87 dlekivkelekdadivvVEGagg 109
                                        l +i  +  +d+d v+VEG+++
  gi|488601157|ref|YP_007907628.1|  78 SLIEI-LRYFEDYDYVFVEGFKS 99 
                                       33333.3557999******9986 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 !   16.2   0.1   7.7e-06     0.006       2      44 ..       3      47 ..       2      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                                      EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCC CS
                              cobW  2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDae 44
                                      v+ + Gf  sGKT+L+++l+    ++g+++ v+    ++v++D+e
  gi|488601157|ref|YP_007907628.1|  3 VISIIGFSNSGKTSLITQLVelLTNQGYRVGVVKHSDKKVDLDKE 47
                                      67899***************99889********988888888876 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 !   16.9   0.0   6.3e-06    0.0049       8      38 ..      10      41 ..       3     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.3e-06
                                      TTSSHHHHHHHHHHHHHHTT--EEEEE.EEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                              CbiA  8 GGvGKTtlaanLaralarrglrVllvD.aDpq 38
                                      +++GKT+l + L  +l ++g+rV +v+  D  
  gi|488601157|ref|YP_007907628.1| 10 SNSGKTSLITQLVELLTNQGYRVGVVKhSDKK 41
                                      89***********************9966655 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   0.0   1.2e-05    0.0095       2      21 ..       4      23 ..       3      53 .. 0.80
   2 ?   -2.3   0.0       5.7   4.4e+03      82      96 ..     107     120 ..      87     135 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      + i+G +N+GK++Li +l++
  gi|488601157|ref|YP_007907628.1|  4 ISIIGFSNSGKTSLITQLVE 23
                                      78****************86 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                                       EEETTTTCSHHHHHH CS
                          MMR_HSR1  82 vvdaseeklkpldee 96 
                                       vv+++ e+l++l ++
  gi|488601157|ref|YP_007907628.1| 107 VVRSH-EELDELLKQ 120
                                       33322.223333222 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.2e-05    0.0095       3      32 ..       4      31 ..       3      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                            DUF463  3 lavTGLsraGKtvfitsLvnqLlaaekkar 32
                                      +++ G+s +GKt +it Lv+ L+++  + r
  gi|488601157|ref|YP_007907628.1|  4 ISIIGFSNSGKTSLITQLVELLTNQ--GYR 31
                                      6799****************99844..444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.1e-05    0.0086      22      51 ..       3      32 ..       1     156 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                          ATPase_2 22 iyfiYGpegsGKtaLlkeiienledkdkyv 51
                                      ++ i G  +sGKt+L+ +++e l +++++v
  gi|488601157|ref|YP_007907628.1|  3 VISIIGFSNSGKTSLITQLVELLTNQGYRV 32
                                      67899******************9999865 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 !   14.3   0.1     2e-05     0.015      30      63 ..       2      35 ..       1      39 [. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                      +v+ + G+  +Gk  l+ +l++ l+++G+rv+v+
  gi|488601157|ref|YP_007907628.1|  2 KVISIIGFSNSGKTSLITQLVELLTNQGYRVGVV 35
                                      58999***************************98 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.6e-05     0.021      47      71 ..      11      35 ..       1      38 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                      -HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 47 GtGKTPlvialvkllqarglkvgvl 71
                                       +GKT+l+ +lv+ll+++g++vgv+
  gi|488601157|ref|YP_007907628.1| 11 NSGKTSLITQLVELLTNQGYRVGVV 35
                                      58**********************8 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.7e-05     0.021       1      39 [.       1      39 [.       1      54 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                      E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THH CS
                             KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvviddes 39
                                      M  + + G+  sGK+++  +L + l++++++v v++   
  gi|488601157|ref|YP_007907628.1|  1 MKVISIIGFSNSGKTSLITQLVELLTNQGYRVGVVKHSD 39
                                      777899*************************99987443 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     4e-05     0.031       7      92 ..      17     108 ..      12     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4e-05
                    Glyco_transf_4   7 hvleLaraLarrGheVtvvtpgddgpleeev.....elvvrvprvplpllkrllrslaflrrlrrllkre.kpDvvH 77 
                                        + +L++ L  +G++V vv ++d++   +++     + ++++  v  +++ ++ ++ +  ++l ++l+ + ++D v 
  gi|488601157|ref|YP_007907628.1|  17 LITQLVELLTNQGYRVGVVKHSDKKVDLDKEgkdswRIFKAGYDVAVLSPVKFAYRARRELSLIEILRYFeDYDYVF 93 
                                       578999*************8888888888888999866666666777777788888888889999999999****** PP

                    Glyco_transf_4  78 ahspaalgaallalr 92 
                                       + ++ + +  ++a  
  gi|488601157|ref|YP_007907628.1|  94 VEGFKSDIRNGIAVV 108
                                       **9999988888766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.6e-05     0.051       7      56 ..       3      55 ..       1      94 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsst..sskdl 56
                                      ++ ++G s +GKT l+ +l+e l+++ +    r++vv     +v+l +++  s++ +
  gi|488601157|ref|YP_007907628.1|  3 VISIIGFSNSGKTSLITQLVELLTNQGY----RVGVVkhsdkKVDLDKEGkdSWRIF 55
                                      789********************87766....5555555555555555554477766 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.8e-05     0.061       6      26 ..       4      24 ..       1      53 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                                      EEEE-STTSSHHHHHHHHHHS CS
                             SRPRB  6 vllvGlsdsGKTslftrLttd 26
                                      + ++G s+sGKTsl+t+L + 
  gi|488601157|ref|YP_007907628.1|  4 ISIIGFSNSGKTSLITQLVEL 24
                                      669*************99765 PP

>> NLBH  Neuraminyllactose-binding hemagglutinin precursor (NLBH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013       0.1      79     140 ..      11      74 ..       5      83 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHCTT-EEEEE..SSCC.CS-HHHHHH-SEEEEEEEEEEEEEEEEEE--ST CS
                              NLBH  79 dkFqnalvkqvqeilekkGYkvirl..kdaq.eltaeqKkkiylvlklkGevgileDvkintdkp 140
                                       +  + +l+ q+ e+l ++GY+v  +  +d++ +l + + k+ + + k    v++l  vk    ++
  gi|488601157|ref|YP_007907628.1|  11 NSGKTSLITQLVELLTNQGYRVGVVkhSDKKvDLDK-EGKDSWRIFKAGYDVAVLSPVKFAYRAR 74 
                                       555789***************988853444313333.4457899999999999998887766655 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 ?   12.5   0.1   0.00017      0.13       2      29 ..       4      31 ..       2      62 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekek 29
                                      + ++G s++GKtsl++++ve   ++ ++
  gi|488601157|ref|YP_007907628.1|  4 ISIIGFSNSGKTSLITQLVELLTNQGYR 31
                                      5699**************9866665543 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   0.00017      0.13       1      42 [.       3      40 ..       3      72 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrld 42
                                      vI++ g S +Gkt++  +l++++ +++ +     g++ ++ +
  gi|488601157|ref|YP_007907628.1|  3 VISIIGFSNSGKTSLITQLVELLTNQGYR----VGVVKHSDK 40
                                      8**********************988777....333344433 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.17       4      38 ..       3      37 ..       1      50 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEH CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdG 38
                                      v+ + G+s+sGK+++ ++l + L+++g++v ++  
  gi|488601157|ref|YP_007907628.1|  3 VISIIGFSNSGKTSLITQLVELLTNQGYRVGVVKH 37
                                      78899***********************9987765 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   0.1   0.00023      0.18       2      35 ..       2      35 ..       1      39 [. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      +vi ++G+  +GKT+ +++L +ll+++g++v +v
  gi|488601157|ref|YP_007907628.1|  2 KVISIIGFSNSGKTSLITQLVELLTNQGYRVGVV 35
                                      68999*************************9987 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   0.00055      0.43       3      31 ..       5      33 ..       3      57 .. 0.87
   2 ?   -0.2   0.0         1   8.2e+02      68     105 ..     100     136 ..      79     149 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00055
                                      EEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvg 31
                                       i G + +GKt l+ +++ell ++g++vg
  gi|488601157|ref|YP_007907628.1|  5 SIIGFSNSGKTSLITQLVELLTNQGYRVG 33
                                      57788899*******************97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                                       SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---S CS
                          NTPase_1  68 eprvgkyvvdvesfeelalealrkalseadviviDEiG 105
                                        +r+g  vv+ ++  +  l++++++ + a+++  DE G
  gi|488601157|ref|YP_007907628.1| 100 DIRNGIAVVRSHEELDELLKQIDQS-RLAGIYFRDEMG 136
                                       5555555554443222234444432.445555555554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00033      0.26       1      30 [.       6      35 ..       6      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavv 30
                                      ++G   sGKt+++ +l+e+l+++g++v vv
  gi|488601157|ref|YP_007907628.1|  6 IIGFSNSGKTSLITQLVELLTNQGYRVGVV 35
                                      79999*********************9998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00026       0.2       1      37 [.       4      50 ..       4     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf..........gvnlrdvakengl 37
                                      I + G + +GKt+l   L ++l +          +++  d+ ke+  
  gi|488601157|ref|YP_007907628.1|  4 ISIIGFSNSGKTSLITQLVELLTNqgyrvgvvkhSDKKVDLDKEGKD 50
                                      6799*****************95555565544444444444444433 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00038       0.3      33      65 ..       3      35 ..       2      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00038
                            AAA_35 33 lirikapkkmGKtSLlarilakakqqgyktvsl 65
                                      +i i + ++ GKtSL++++++  ++qgy++ ++
  gi|488601157|ref|YP_007907628.1|  3 VISIIGFSNSGKTSLITQLVELLTNQGYRVGVV 35
                                      78999999********************98665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.28      22      56 ..       5      39 ..       1      70 [. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggrviglAptg 56
                                       + G   +GKt ++++l+e+++++g+rv ++ ++ 
  gi|488601157|ref|YP_007907628.1|  5 SIIGFSNSGKTSLITQLVELLTNQGYRVGVVKHSD 39
                                      57788889*******************98876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1041.88
//
Query:       gi|488601158|ref|YP_007907629.1|  [L=254]
Description: hypothetical protein Asulf_01663 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-22   79.2   1.5    3.4e-22   78.8   0.2    1.9  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
    3.1e-11   43.6  10.0    3.1e-11   43.6  10.0    2.0  2  Peptidase_A24  Type IV leader peptidase family


Domain annotation for each model (and alignments):
>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1         1   9.1e+03      63      79 ..     129     145 ..     127     146 .. 0.78
   2 !   78.8   0.2   3.8e-26   3.4e-22       2      92 .]     159     244 ..     158     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                       Arc_PepC_II  63 ieetvWvtygvPflipi 79 
                                       ++++v v++++  + +i
  gi|488601158|ref|YP_007907629.1| 129 LSNSVIVSPALLIITFI 145
                                       67889999998777776 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 3.8e-26
                       Arc_PepC_II   2 kllymligyrvkvkellkkflflleefeekdgkikrkfisvekeldeelrkelkkykkkglieetvWvtygvPflip 78 
                                       ++ly+++g+rvk +++  +f+ +le +++  gki r  ++++ e+de++rk+l k  ++g+i+ +vWvt+++Pfl++
  gi|488601158|ref|YP_007907629.1| 159 NFLYYFVGKRVKANSI-PEFHSVLEFVDD-SGKIVR--VRRGIEVDEKVRKKLMKAYDEGIID-RVWVTPNLPFLLF 230
                                       689*************.9*******9998.666888..889999****************666.9************ PP

                       Arc_PepC_II  79 itaGfiialvlGDl 92 
                                       itaGfii++v+GD+
  gi|488601158|ref|YP_007907629.1| 231 ITAGFIISVVIGDI 244
                                       *************7 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6  10.0   3.5e-15   3.1e-11       2      93 ..      19     112 ..      18     144 .. 0.85
   2 ?   -2.1   0.5      0.59   5.3e+03      52      62 ..     230     240 ..     219     252 .. 0.53

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.5e-15
                     Peptidase_A24   2 vlltillvlsviDldtrtlpdeltlpllllgvlfa....qllllglpnlaqavlgalvgalvlllislvdeqamGgG 74 
                                       +++++ll+++v Dl++r++p++l+ +++ +   +       ++  l ++  +v+++++++++ +l  l+ ++  Gg+
  gi|488601158|ref|YP_007907629.1|  19 LAMIFLLYACVLDLRYRIVPNRLWKYMVAVLTPILvlefVTAKYSLSTIIFSVMQFVMMFVFSYL--LYSLGTYGGA 93 
                                       6799**********************999999988888844567999999999999********9..********** PP

                     Peptidase_A24  75 Dvklaavlgaflgwerlll 93 
                                       D+k ++v++++++++  ++
  gi|488601158|ref|YP_007907629.1|  94 DAKAFIVMAYIFPVYPAVM 112
                                       *************988733 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.59
                     Peptidase_A24  52 galvgalvlll 62 
                                        + +g+++ ++
  gi|488601158|ref|YP_007907629.1| 230 FITAGFIISVV 240
                                       33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); 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:                         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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1667.18
//
Query:       gi|488601159|ref|YP_007907630.1|  [L=326]
Description: homoserine dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-55  185.7   0.6    8.5e-55  185.3   0.6    1.2  1  Homoserine_dh    Homoserine dehydrogenase
    5.6e-11   43.1   0.0    1.3e-10   42.0   0.0    1.6  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    2.4e-05   24.2   0.2      5e-05   23.1   0.2    1.6  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    0.00015   22.1   0.3    0.00046   20.4   0.3    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.017   15.8   2.0      0.077   13.6   0.7    2.6  3  PglD_N           PglD N-terminal domain
       0.03   14.7   0.7       0.42   10.9   0.1    2.5  3  DUF3010          Protein of unknown function (DUF3010)
       0.04   14.5   0.2       0.13   12.9   0.2    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.074   13.3   0.6       0.25   11.6   0.2    2.0  2  TrkA_N           TrkA-N domain
       0.11   13.3   0.1        1.3    9.8   0.1    2.6  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
       0.17   11.8   1.2       0.51   10.2   1.2    1.9  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
        1.1    8.5   4.3          3    7.2   1.1    2.7  3  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


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 !  185.3   0.6   5.2e-58   8.5e-55       1     173 []     148     322 ..     148     322 .. 0.98

  Alignments for each domain:
  == domain 1  score: 185.3 bits;  conditional E-value: 5.2e-58
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       P+ik +k  l+g+ i+ i+G+lngt+nyilt+me+e++++++vl+eaqel +aea+p  Dv+G+D+a+Kl+ila+ +
  gi|488601159|ref|YP_007907630.1| 148 PLIKLVKYNLAGNSIEFIKGVLNGTCNYILTRMEQEKMTYQQVLAEAQELNIAEANPDYDVKGFDSAAKLLILANAL 224
                                       99*************************************************************************** PP

                                       CTTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE...CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEE CS
                     Homoserine_dh  78 fgleveledvevegiskltaedikeakeegkvlklvasa...vearVkpelvpkshplasvkgsenavlvetdrlge 151
                                       +g++v+l+dve+ gi+++t+e ++ ak+++++++l+a++     + V p+lvp +hpla ++g++na l++td +g+
  gi|488601159|ref|YP_007907630.1| 225 MGMDVKLSDVEIVGITDITPEAFDVAKSKNYTIRLIAEVnkkGYIGVTPRLVPIEHPLA-IHGTMNAALIKTDLAGD 300
                                       **************************************7655369**************.***************** PP

                                       EEEEES-SSHHHHHHHHHHHHH CS
                     Homoserine_dh 152 lviqGpgaGaepTAsavlsDll 173
                                       +v+ G+gaG+++TAsa++sDl+
  gi|488601159|ref|YP_007907630.1| 301 VVVMGRGAGKYETASAIISDLI 322
                                       ********************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 !   42.0   0.0   7.7e-14   1.3e-10       1     117 []       8     140 ..       8     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 7.7e-14
                                       --SHHHHHHHHHHHH---S.....SEEEEEEEEESS.EEE-TT.......HHHHHT--CB---HHHHHHHHS-EEEE CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqse.....ielelvavadrd.sllskd.......rkallasealtldlddliahldpdvvV 64 
                                       G+Ga+G++v+e+l+r ++e      ++ lvav+d++ s ++++       ++++ +     ++  ++i+ +d dv +
  gi|488601159|ref|YP_007907630.1|   8 GFGAVGQGVAEILLRRKEElekkiGKFSLVAVTDSRgSIVDENgidiikaIERKKKGRFDGKSTMEVIEGVDFDVMI 84 
                                       99****************************************9****7664444444444455555566669***** PP

                                       E-..S--HHHH...TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  65 Ec..asseava...elvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                       Ec  +  +  +    ++ k+L++g +++t nkg l+  a ++ +  +ae++g k+++e
  gi|488601159|ref|YP_007907630.1|  85 ECsvTNIDDGEpglTHIMKCLEKGAHIITSNKGPLV--ADFHGINRLAEKKGLKFMFE 140
                                       **5444433323337*********************..**************999986 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 !   23.1   0.2   3.1e-08     5e-05      34      88 ..       3      66 ..       2     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.1e-08
                                      EEEEE--SHHHHHHHHHHHHCT-....E.....EEEEEESSEEEEETTEE-HHHHHHHHHCSSS CS
                     ELFV_dehydrog 34 rvaisGsGnvgsyaallltelga....k.....vvavsDssGviydpeGldieellelkeerks 88
                                      ++ai G+G vg+ +a++l ++ +    k      vav Ds+G i+d++G+di + +e k++ + 
  gi|488601159|ref|YP_007907630.1|  3 KIAIIGFGAVGQGVAEILLRRKEelekKigkfsLVAVTDSRGSIVDENGIDIIKAIERKKKGRF 66
                                      68999**********9997765422222233336******************999998887764 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   2.8e-07   0.00046       1      98 [.       4     113 ..       4     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.8e-07
                                       EEEE--SHHHHHHHHHHHCTCCT-G....EEEEEESSHHHHHHHHCHHTTTCEE.EEE--TT...THHHHHHHHHTT CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvda....eitvadrskeklealaakalgvrfe.aialdae...nyeavLaallke 69 
                                       + iiG+G+vGq+vae l+r+++  +    ++ ++  ++++   ++++ +g++++ ai+  ++   + ++ + +++++
  gi|488601159|ref|YP_007907630.1|   4 IAIIGFGAVGQGVAEILLRRKEELEkkigKFSLVAVTDSRG-SIVDE-NGIDIIkAIERKKKgrfDGKS-TMEVIEG 77 
                                       789*****************999888888888888888884.55555.444433033333322225566.7777888 PP

                                       S..SEEEE-SSGG.....GHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  70 g..dlvvnlsppi.....ssldvlkaCietgvhyvd 98 
                                          d+ + +s+        +l+ +  C+e+g+h ++
  gi|488601159|ref|YP_007907630.1|  78 VdfDVMIECSVTNiddgePGLTHIMKCLEKGAHIIT 113
                                       888999999998878776677888889999999997 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   4.7e-05     0.077       1      49 [.       3      59 ..       3      75 .. 0.80
   2 ?   -0.3   0.0         1   1.7e+03      16      31 ..     198     213 ..     197     250 .. 0.64
   3 ?   -2.5   0.0       5.1   8.3e+03      24      35 ..     234     245 ..     229     267 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.7e-05
                            PglD_N  1 kivIiGaGGhgkvvadii........eangeyeiigflDdnkk.tevegypvlgkaie 49
                                      ki+IiG G  g+ va+i+        +++g++++++++D++ +   ++g+ +++ + e
  gi|488601159|ref|YP_007907630.1|  3 KIAIIGFGAVGQGVAEILlrrkeeleKKIGKFSLVAVTDSRGSiVDENGIDIIKAI-E 59
                                      79****************6655555556789999******9764678999999864.3 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1
                            PglD_N  16 diieangeyeiigflD 31 
                                       +i+ean +y+++gf  
  gi|488601159|ref|YP_007907630.1| 198 NIAEANPDYDVKGFDS 213
                                       6888899999988843 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.1
                            PglD_N  24 yeiigflDdnkk 35 
                                        ei+g++D +++
  gi|488601159|ref|YP_007907630.1| 234 VEIVGITDITPE 245
                                       577777776654 PP

>> DUF3010  Protein of unknown function (DUF3010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00026      0.42      54      98 ..      44      89 ..      17      96 .. 0.79
   2 ?    1.1   0.0      0.27   4.4e+02      13      56 ..     175     218 ..     165     225 .. 0.84
   3 ?   -2.1   0.0       2.7   4.4e+03       4      35 ..     225     257 ..     223     265 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                           DUF3010 54 aklmedykvdkvvikkRakkGkfAggavsFklEaa.iqliedveve 98
                                       + ++++++d +   +R+kkG+f g ++   +E++ + ++ +++v+
  gi|488601159|ref|YP_007907630.1| 44 GSIVDENGIDIIKAIERKKKGRFDGKSTMEVIEGVdFDVMIECSVT 89
                                      57899********************999999999866677777666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.27
                           DUF3010  13 aiicllslekelfelpdvrtkklslkdnesteeireFqktfakl 56 
                                        i+  ++ ek +++ +  +++ l++ +++   +++ F ++ + l
  gi|488601159|ref|YP_007907630.1| 175 YILTRMEQEKMTYQQVLAEAQELNIAEANPDYDVKGFDSAAKLL 218
                                       577788899999999999*******************9887655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.7
                           DUF3010   4 cGvelkgneaiiclls.lekelfelpdvrtkkl 35 
                                        G+++k +++ i+ ++ ++ e f++ + +   +
  gi|488601159|ref|YP_007907630.1| 225 MGMDVKLSDVEIVGITdITPEAFDVAKSKNYTI 257
                                       577888888877655447888888887776555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   7.8e-05      0.13       1      25 [.       3      28 ..       3      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.8e-05
                                      EEEEETTSHHHHHHHHHHHHTTS.-G CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaaga.qp 25
                                      ki+iiG+G +g+++a+ ll++ +  +
  gi|488601159|ref|YP_007907630.1|  3 KIAIIGFGAVGQGVAEILLRRKEeLE 28
                                      7*****************99986544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00016      0.25       1      35 [.       4      45 ..       4      62 .. 0.70
   2 ?   -1.7   0.0       2.1   3.3e+03      82     102 ..     249     269 ..     245     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                      EEEES-SHHHHHHHHHHHHTT........EEEEEEESSHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLsegg........kdvvvidkdeerve 35
                                      i+iiG+G vG+ +ae L +++        k ++++   ++r  
  gi|488601159|ref|YP_007907630.1|  4 IAIIGFGAVGQGVAEILLRRKeelekkigK-FSLVAVTDSRGS 45
                                      79****************965477777753.555555544444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                                       HHHHHTSSSEEEEEESSGGGH CS
                            TrkA_N  82 lakelnpkkkiiaraqdpeha 102
                                       +ak+ n +++ ia+++++ ++
  gi|488601159|ref|YP_007907630.1| 249 VAKSKNYTIRLIAEVNKKGYI 269
                                       689999999999999998775 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 ?    9.8   0.1   0.00083       1.3       1     110 [.       2     131 ..       2     140 .. 0.69
   2 ?    0.1   0.0      0.85   1.4e+03      26      50 ..     234     259 ..     221     298 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00083
                                       EEEEEETTSHHHHHHHHHHHHTTTTE.......EEEEEECSSHHHHHHH.........HHHTTHEEESSHHHHHTCT CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrle.......evvalldpdaeraeav.........aesfgveaysdleelladp 61 
                                       +++aiiG+G +g+  ++ l ++++++        +va+ d++ +  ++          +++ g    ++  e+ +  
  gi|488601159|ref|YP_007907630.1|   2 IKIAIIGFGAVGQGVAEILLRRKEELekkigkfSLVAVTDSRGSIVDENgidiikaieRKKKGRFDGKSTMEVIEGV 78 
                                       689********999996666664444999999999999999887666555555554444444444445577777777 PP

                                       TESEEEE-S-G.....GGHHHHHHHHHHTT-EEEEES..SS-SSHHHHHHHHHHHH CS
                      GFO_IDH_MocA  62 eidavivatpn.....gtheelakaaleagkhvllEK..Plattveeakelvelae 110
                                       + d+ i ++ +     + +  +++++le+g h++     Pl+   ++   + +lae
  gi|488601159|ref|YP_007907630.1|  79 DFDVMIECSVTniddgEPGLTHIMKCLEKGAHIITSNkgPLV---ADFHGINRLAE 131
                                       888888888887888777999999999999999974325774...44444444444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.85
                                       EEEEEEECSSHHHHHHH.HHHTTHEE CS
                      GFO_IDH_MocA  26 eevvalldpdaeraeav.aesfgvea 50 
                                        e+v++ d+ +e+ + + ++++ +  
  gi|488601159|ref|YP_007907630.1| 234 VEIVGITDITPEAFDVAkSKNYTIRL 259
                                       57788888887777665444444444 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.2   0.00031      0.51       1     101 [.       3     102 ..       3     154 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                                       EEEEE--SCCHHHHHHHHHHT..T-EEEEE-S-HHHHHHHHHHHHH........HHHCCTTTTSS-HHHHCCCHHCE CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasa..gleVvlvdiseealekalekiek........sleklvekgklkeeeveaalari 67 
                                       k+a+iG G +G+g+a++++++  +le ++   s  a+++++ +i +         +e+ ++kg+++           
  gi|488601159|ref|YP_007907630.1|   3 KIAIIGFGAVGQGVAEILLRRkeELEKKIGKFSLVAVTDSRGSIVDengidiikAIER-KKKGRFD----------G 68 
                                       69****************9983344444444444555555544444211111102222.2223332..........2 PP

                                       EEES-HHHHHC-SEEEE-S-SSHHHHHHHHHHHH CS
                           3HCDH_N  68 sfttdleeavdadlviEavvEnlelKrkvfaele 101
                                       + t ++ e vd d++iE+ v n++  +  ++++ 
  gi|488601159|ref|YP_007907630.1|  69 KSTMEVIEGVDFDVMIECSVTNIDDGEPGLTHIM 102
                                       3333333344555555555555555555555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.1    0.0018         3      38      55 ..       3      20 ..       2      27 .. 0.90
   2 ?    1.0   0.0      0.15   2.4e+02     125     145 ..      40      62 ..      24      67 .. 0.80
   3 ?   -2.1   0.0       1.2     2e+03      27      62 ..     222     257 ..     215     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0018
                                      EEEEES-SHHHHHHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrl 55
                                      +++iiG+G++Gq va++l
  gi|488601159|ref|YP_007907630.1|  3 KIAIIGFGAVGQGVAEIL 20
                                      689************997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                                       ESS-GGGB-HH..HHHHHHHTTS CS
                      2-Hacid_dh_C 125 NtaRGglvdee..aLleaLksgk 145
                                         +RG++vde+  ++++a++++k
  gi|488601159|ref|YP_007907630.1|  40 TDSRGSIVDENgiDIIKAIERKK 62 
                                       559*******9667899988876 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.2
                                       CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EE CS
                      2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkv 62 
                                       +al+g +++ + v i+G+ +I  ++ +++k+ +  +
  gi|488601159|ref|YP_007907630.1| 222 NALMGMDVKLSDVEIVGITDITPEAFDVAKSKNYTI 257
                                       567888888999999999999888888887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2021.68
//
Query:       gi|488601160|ref|YP_007907631.1|  [L=170]
Description: ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-08   33.8   0.2    2.9e-07   30.1   0.1    2.2  2  ACT       ACT domain
  ------ inclusion threshold ------
       0.01   16.4   1.4       0.05   14.2   0.1    2.1  2  ACT_4     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 !   30.1   0.1   3.3e-11   2.9e-07       2      65 ..       5      68 ..       4      71 .. 0.81
   2 ?    1.3   0.0     0.033     3e+02      41      66 ..     129     154 ..     123     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.3e-11
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65
                                      ++ v+++D+PG L + +  +++ g Ni si + +++ +   +v v i  d+++le + + +++l
  gi|488601160|ref|YP_007907631.1|  5 SIVVELEDKPGQLLKALEPISREGGNILSIIHQRDKKTPLQRVPVEISFDAKNLEIANRIIEAL 68
                                      6899**********************************66666666666666666666666555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.033
                                       CEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  41 agivfvvivvdeedleevlealkkle 66 
                                        + ++++  ++ ++lee++e  ++++
  gi|488601160|ref|YP_007907631.1| 129 STAMITISATGKDELEEAVEIMRNVC 154
                                       467899999999*******9999886 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.6e-06      0.05       8      71 ..       5      70 ..       3      74 .. 0.93
   2 ?    1.1   0.2     0.068   6.1e+02      20      71 ..     100     152 ..      85     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-06
                             ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkk..dglaeikitveVkdvehLsrviakLra 71
                                      ++ ve ed++g L + ++ is e++ni s+  + +kk   + + ++i++  k++e  +r+i++L++
  gi|488601160|ref|YP_007907631.1|  5 SIVVELEDKPGQLLKALEPISREGGNILSIIHQRDKKtpLQRVPVEISFDAKNLEIANRIIEALKE 70
                                      699***************************999999888779999*****************9986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.068
                             ACT_4  20 Laditqvisee.kanivsvnaktrkkdglaeikitveVkdvehLsrviakLra 71 
                                       L+d ++ i ++  a +v++++   + ++  +  it++    ++L++ ++ +r+
  gi|488601160|ref|YP_007907631.1| 100 LSDTINRIDSTgFAEVVDLQINMPEVNKPSTAMITISATGKDELEEAVEIMRN 152
                                       66666777777667788888887777899999999999999999888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1151.27
//
Query:       gi|488601161|ref|YP_007907632.1|  [L=289]
Description: branched chain amino acid aminotransferase apoenzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-58  197.2   0.0      4e-58  196.9   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 !  196.9   0.0   2.2e-62     4e-58       1     222 [.      30     255 ..      30     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 2.2e-62
                       Aminotran_4   1 glfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg...aat 74 
                                       g+fE++r+yng++f+l+eH++RL  sa+ + le+p+++ee+++++ e+l++nn +n+++r++v+rg g+lg     +
  gi|488601161|ref|YP_007907632.1|  30 GVFEGIRAYNGRVFRLKEHIDRLYDSAKVICLEIPISKEEFMELILETLRKNNLKNAYIRPIVTRGIGDLGldpRKC 106
                                       8**************************9999*****************************************77777 PP

                       Aminotran_4  75 sepsvavyvsalppgpeseke..lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnvtE 149
                                       s+p+++++ +++     + +e  l++vt + +r       p++K+lnyl+n+l + ea+e+g de++++d++g+++E
  gi|488601161|ref|YP_007907632.1| 107 SKPNIIIITKEWDRLYGDLYEkgLKAVTVAIRRNAIDALPPNIKSLNYLNNILGKIEANEKGGDEAIFLDSNGYISE 183
                                       77777777777777777777799999999978888889999************************************ PP

                       Aminotran_4 150 gstsNvfivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvrs 222
                                       gs  N+fivk+g+++tPp+ +  L+Gitr++++e+ ++lg++++e ++ + dl  ade+f+t+t++++ p++ 
  gi|488601161|ref|YP_007907632.1| 184 GSGDNIFIVKNGRVYTPPILN-NLRGITREVVIEIIEKLGIPFKEMNLGIYDLYSADEIFVTGTAAEIAPITV 255
                                       *******************99.7************************************************86 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:                      373  (0.0208043); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1844.46
//
Query:       gi|488601162|ref|YP_007907633.1|  [L=353]
Description: putative peptide-modifying radical SAM enzyme, AF0577 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   62.2   0.1    1.6e-16   61.1   0.1    1.6  1  Radical_SAM  Radical SAM superfamily
    2.5e-08   34.3   0.5    1.3e-07   32.0   0.0    2.1  2  Fer4_12      4Fe-4S single cluster domain
    3.7e-05   23.8   1.1    8.1e-05   22.7   0.0    2.1  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 !   61.1   0.1   2.7e-20   1.6e-16       2     149 ..       6     142 ..       5     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 2.7e-20
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       + t  Cnl+Cs+C  + ++r  + + s ++ee+ e + + +       + + ggepll+ d+++++ + ++      
  gi|488601162|ref|YP_007907633.1|   6 ILTGKCNLNCSYCGGSIDERIMPAEISYPLEELYEFLNRDS----DLSIAFYGGEPLLRIDLIKDIMENVEA----K 74 
                                       67889***********8766666666666666666666665....89***************9999999996....8 PP

                                       EEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdri 149
                                       ++ + tng+l+ ++ +++l++ + + ++ ++++ + +  v ++  rg+t+e+v++++e+++++   + + r+
  gi|488601162|ref|YP_007907633.1|  75 HFILQTNGLLL-DRLIDELDDINeFSTILVSIDGVKE--VNDYY-RGKTYERVMRNVEIIKKHYKGELIARM 142
                                       ***********.*************************..9****.9****************9766555555 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.2e-11   1.3e-07       8     120 ..       4     110 ..       2     130 .. 0.79
   2 ?   -0.5   0.3      0.23   1.4e+03      12      45 ..     284     320 ..     276     330 .. 0.61

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.2e-11
                           Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp 84 
                                       ++++++ Cnl+C++C   ++ +     e++ +l ee+ e l+ +s+  + + GGEPll    + + +++++v+++ +
  gi|488601162|ref|YP_007907633.1|   4 IIILTGKCNLNCSYCG-GSIDERIMPAEISYPL-EELYEFLNRDSDLSIAFYGGEPLL--RIDLIKDIMENVEAKHF 76 
                                       5678999********9.6666666666666665.68999*******************..99999999999999999 PP

                           Fer4_12  85 ekdiwlytgytleelskk..ekeellkeidvlvdGkfe 120
                                          i+ ++g  l+ l ++  + +e  + i v +dG  e
  gi|488601162|ref|YP_007907633.1|  77 ---ILQTNGLLLDRLIDEldDINE-FSTILVSIDGVKE 110
                                       ...9***********987633333.5666677777544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.23
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkef...tkelleeii 45 
                                       +s C  +C ++  + +ws ++ + +   tk+l+ +i 
  gi|488601162|ref|YP_007907633.1| 284 FSVCGGRCLFFNRERLWSENKMNAVcdaTKNLISRIE 320
                                       4556667777555566766655555443566666665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.4e-08   8.1e-05       3     116 ..       6     106 ..       4     108 .. 0.68
   2 ?   -2.9   0.4       1.2   7.1e+03      12      23 ..     249     259 ..     246     301 .. 0.50
   3 ?   -2.2   0.2      0.75   4.5e+03       6      14 ..     285     308 ..     275     339 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-08
                           Fer4_14   3 vrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79 
                                       + +++Cnl+C  C  +   +++  + + +  le+   ++ +++++ + + + GGePL+       ++l+k + e+++
  gi|488601162|ref|YP_007907633.1|   6 ILTGKCNLNCSYCGGSI--DERIMPAEISYPLEELY-EFLNRDSDLS-IAFYGGEPLLR------IDLIKDIMENVE 72 
                                       6689*********9554..44444444444443333.4445555556.89*******66......9**********9 PP

                           Fer4_14  80 ekkiwletngtleielektpdlkeklealskidllvd 116
                                        k+  l+tng+l   l   +   + ++  s i +++d
  gi|488601162|ref|YP_007907633.1|  73 AKHFILQTNGLLLDRLI--D-ELDDINEFSTILVSID 106
                                       9*********9873322..3.3355555666666666 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                           Fer4_14  12 CkgCdnketwks 23 
                                       C+ C + e w+ 
  gi|488601162|ref|YP_007907633.1| 249 CPICADLE-WNL 259
                                       66665554.443 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.75
                           Fer4_14   6 sgCnlsCk...............g 14 
                                       s C   C                 
  gi|488601162|ref|YP_007907633.1| 285 SVCGGRCLffnrerlwsenkmnaV 308
                                       344444443333333333333333 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:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2327.97
//
Query:       gi|488601163|ref|YP_007907634.1|  [L=61]
Description: hypothetical protein Asulf_01668 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   0.4      0.028   14.5   0.4    1.0  1  MetOD2    Metanogen output domain 2
       0.05   13.6   0.1      0.071   13.1   0.1    1.2  1  DUF2767   Protein of unknown function (DUF2767)
      0.094   12.7   2.3       0.51   10.3   0.5    2.5  2  RHH_1     Ribbon-helix-helix protein, copG family
       0.12   12.9   0.0       0.12   12.9   0.0    1.1  1  HPPK      7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase


Domain annotation for each model (and alignments):
>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   6.2e-06     0.028      32      83 ..       6      57 ..       3      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.2e-06
                            MetOD2 32 vevnkrllslLsqtydidddkaevseeieaalknlekkleaqeerlkqikke 83
                                       ++ k l++ L +  ++d++ ++ se+i+ a++ + ++l +  +r+ ++k++
  gi|488601163|ref|YP_007907634.1|  6 LDIPKELYDDLMEHVGEDKKFVNLSEAIRTAIRKMLDQLDEIDRRHGRLKEK 57
                                      5777889998999999*********************************987 PP

>> DUF2767  Protein of unknown function (DUF2767)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.6e-05     0.071      25      56 ..      17      48 ..      15      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                           DUF2767 25 laelGqetkriviadvlrTrlarkkdqrdale 56
                                      +   G + k + +++ +rT++ +  dq d+ +
  gi|488601163|ref|YP_007907634.1| 17 MEHVGEDKKFVNLSEAIRTAIRKMLDQLDEID 48
                                      7889***********************99765 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 ?   10.3   0.5   0.00011      0.51       5      39 .]       7      43 ..       3      43 .. 0.70
   2 ?    4.7   0.2    0.0071        32       9      23 ..      39      53 ..      38      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                                      EEEHHHHHHHHHHHHHHT..SSHHHHHHHHHHHHHHH CS
                             RHH_1  5 rldeellerLdelarrrg..rSrSelIReAlreyler 39
                                       +++el++ L e++ + +  ++ Se+IR A+r  l++
  gi|488601163|ref|YP_007907634.1|  7 DIPKELYDDLMEHVGEDKkfVNLSEAIRTAIRKMLDQ 43
                                      56666666666666444447899*********98876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0071
                                      HHHHHHHHHHHHHTS CS
                             RHH_1  9 ellerLdelarrrgr 23
                                      ++l++Lde+ rr gr
  gi|488601163|ref|YP_007907634.1| 39 KMLDQLDEIDRRHGR 53
                                      89*******999875 PP

>> HPPK  7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05      0.12      39      75 ..      22      56 ..       6      61 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                                      SS-GEEEEEEEEEESS-HHHHHHHHHHHHHHTT--CS CS
                              HPPK 39 dqpdFlNavvevetelspeellealkeiEkelgrerr 75
                                      ++++F+N   +++t+   +++l++l ei++++gr ++
  gi|488601163|ref|YP_007907634.1| 22 EDKKFVNLSEAIRTA--IRKMLDQLDEIDRRHGRLKE 56
                                      4678********996..67***************863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      766  (0.0427241); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 383.62
//
Query:       gi|488601164|ref|YP_007907635.1|  [L=239]
Description: conserved hypothetical integral membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-55  187.3  14.5      2e-55  187.3  14.5    1.9  2  Vut_1     Putative vitamin uptake transporter
  ------ inclusion threshold ------
        1.1    8.5   4.0       0.67    9.3   0.1    2.3  2  DUF4407   Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.7       0.2   1.8e+03      10      40 ..      16      47 ..       4      59 .. 0.58
   2 !  187.3  14.5   2.2e-59     2e-55       1     149 [.      65     226 ..      65     227 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                             Vut_1 10 tflitdiisevyGkkaarkvvl.lgflanlla 40
                                      ++++  iise +G + a  +   l+++an++a
  gi|488601164|ref|YP_007907635.1| 16 IVTTIAIISERFGVEIAIGIYAsLTVIANIIA 47
                                      45556667777776666655431344444444 PP

  == domain 2  score: 187.3 bits;  conditional E-value: 2.2e-59
                             Vut_1   1 taGvllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa.........ealesvfgltprivla 68 
                                       +aGv+++++tflitdiise+yGk+ a+k+v++gf+an++a++ +++a+++ +         ++++++f++tpr+v+a
  gi|488601164|ref|YP_007907635.1|  65 PAGVIVYASTFLITDIISEIYGKEIAKKTVITGFFANIVAVASIMIAVIWSPapfmpenllKSFDTIFSMTPRVVIA 141
                                       69**************************************87777776666559999999999************** PP

                             Vut_1  69 sliaylvsqlldvyvfhrlkkltkgkklwlrnigStlvsqlvdtlifvtiaflg....eqlleiilsqylikllial 141
                                       s+iayl+sq++dvy++h++k +tk+++lwlrn++St+vsql+dt++f+t+af+g    ++ll++i +qyl+kl+ial
  gi|488601164|ref|YP_007907635.1| 142 SIIAYLISQTHDVYAYHFWKAKTKERFLWLRNNASTMVSQLIDTIVFITLAFYGvfdlNVLLAMITGQYLLKLTIAL 218
                                       ****************************************************99*********************** PP

                             Vut_1 142 ldtplvyl 149
                                       +dtp++y+
  gi|488601164|ref|YP_007907635.1| 219 VDTPFMYI 226
                                       *******8 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   7.5e-05      0.67      73      98 ..     126     151 ..      84     158 .. 0.84
   2 ?   -0.3   0.7     0.063   5.6e+02      27      50 ..     185     208 ..     175     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7.5e-05
                           DUF4407  73 kkrrelalalpRlllAvligvvisep 98 
                                       k+  ++++++pR+++A +i+ +is++
  gi|488601164|ref|YP_007907635.1| 126 KSFDTIFSMTPRVVIASIIAYLISQT 151
                                       56778999****************86 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.063
                           DUF4407  27 AalsgayAlytvlksplllallvG 50 
                                         ++ ++A+y v++ ++lla++ G
  gi|488601164|ref|YP_007907635.1| 185 TIVFITLAFYGVFDLNVLLAMITG 208
                                       5678999***********999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1529.44
//
Query:       gi|488601165|ref|YP_007907636.1|  [L=106]
Description: Sec-independent protein translocase TatA [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   69.6   1.1    1.6e-19   68.9   0.9    1.5  2  MttA_Hcf106     mttA/Hcf106 family
  ------ inclusion threshold ------
      0.019   14.6   0.8      0.021   14.4   0.8    1.1  1  Relaxase        Relaxase/Mobilisation nuclease domain
      0.026   14.8   0.1      0.046   14.0   0.1    1.3  1  KxDL            Uncharacterized conserved protein
      0.036   13.9   0.5        1.7    8.4   0.2    2.0  2  PhageMin_Tail   Phage-related minor tail protein
      0.087   13.5   1.4       0.17   12.5   0.6    1.7  2  DUF4404         Domain of unknown function (DUF4404)
        0.1   13.1   1.3        7.6    7.1   0.1    2.2  2  YflT            Heat induced stress protein YflT
        0.1   12.4   0.1       0.42   10.5   0.0    2.0  2  HTH_10          HTH DNA binding domain
       0.16   12.7   0.8       0.79   10.5   0.2    2.0  2  PTS_IIB         PTS system, Lactose/Cellobiose specific IIB s
       0.17   10.6   0.1       0.17   10.6   0.1    1.1  1  Prismane        Prismane/CO dehydrogenase family
       0.19   11.8   2.0        1.1    9.3   0.5    2.0  2  DUF2089         Protein of unknown function (DUF2089)
       0.81    9.5   4.3       0.28   11.0   1.5    1.7  2  Arm-DNA-bind_4  Arm DNA-binding domain


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.9     1e-22   1.6e-19       1      53 []       4      56 ..       4      77 .. 0.93
   2 ?   -2.5   0.0       2.1   3.4e+03      21      30 ..      70      79 ..      67      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1e-22
                                      S-HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH---XXXXX CS
                       MttA_Hcf106  1 lgapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleeenekeaad 53
                                      +g+ ell Il++a+llFG++kLPE+ar+LGk++ eFkka+ke+e e ++ ++d
  gi|488601165|ref|YP_007907636.1|  4 IGPNELLAILLIAFLLFGASKLPELARSLGKSMGEFKKAQKEAEIELRRFEKD 56
                                      799*****************************************997776654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                                      THHHHHHHHH CS
                       MttA_Hcf106 21 kLPEvaraLG 30
                                      kL  +a+ LG
  gi|488601165|ref|YP_007907636.1| 70 KLEKIAKDLG 79
                                      7778899998 PP

>> Relaxase  Relaxase/Mobilisation nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   1.3e-05     0.021     180     231 ..      31      79 ..      23      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                          Relaxase 180 alenasdfedlkealkekglelrrktgkkltykltdenqkkvrgsklgkdyq 231
                                       +    +++ ++k+a ke ++elrr+ +     k+t ++ k+++ +k++kd++
  gi|488601165|ref|YP_007907636.1|  31 S--LGKSMGEFKKAQKEAEIELRRFEKDLEEGKYTPQD-KRAKLEKIAKDLG 79 
                                       3..4599****************888888888888888.**********975 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.8e-05     0.046      25      71 ..      32      78 ..      27      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                              KxDL 25 lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkki 71
                                      l k+  e ++ +++++ +l ++++++++g+ + ++ ++ Le+i k +
  gi|488601165|ref|YP_007907636.1| 32 LGKSMGEFKKAQKEAEIELRRFEKDLEEGKYTPQDKRAKLEKIAKDL 78
                                      66788899***********************************9975 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 ?    4.0   0.0     0.025        41      49      75 ..      20      46 ..      16      50 .. 0.82
   2 ?    8.4   0.2    0.0011       1.7     148     186 ..      70     103 ..      49     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.025
                     PhageMin_Tail 49 ggaddleeaaeilstalnafglsaada 75
                                      +ga++l e+a++l++ ++ f++++++a
  gi|488601165|ref|YP_007907636.1| 20 FGASKLPELARSLGKSMGEFKKAQKEA 46
                                      677778999999999999999996655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                     PhageMin_Tail 148 eaaealkklGistkdaqgkmksldeiledlsealkkltd 186
                                       + ++ +k+lGi+t     + ks deile++++al k ++
  gi|488601165|ref|YP_007907636.1|  70 KLEKIAKDLGIDT-----EGKSDDEILEEINKALPKTEK 103
                                       456788999*998.....78************9988754 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.66   1.1e+03      25      48 ..      24      47 ..      22      55 .. 0.71
   2 ?   12.5   0.6   0.00011      0.17       4      65 ..      49     106 .]      47     106 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.66
                           DUF4404 25 lLeslaedieellaeedaaaeeee 48
                                      +L +la+ + + + e ++a++e+e
  gi|488601165|ref|YP_007907636.1| 24 KLPELARSLGKSMGEFKKAQKEAE 47
                                      677888888888888888887765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                           DUF4404   4 lLekLheeLeqnesldeetralLeslaedieellaeedaaaeeeelaerlneaverFeeeHP 65 
                                       +L++ ++ Le+ + + +++ra+Le++a+d+   +++e++ ++e  + e++n+a+ + e+  P
  gi|488601165|ref|YP_007907636.1|  49 ELRRFEKDLEEGKYTPQDKRAKLEKIAKDLG--IDTEGKSDDE--ILEEINKALPKTEKAEP 106
                                       6888999***********************9..8999988888..89999999988777665 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.017        27      82      97 ..      47      62 ..      27      63 .. 0.90
   2 ?    7.1   0.1    0.0047       7.6      33      69 ..      67     103 ..      65     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                              YflT 82 edeaeeyeeeldeGki 97
                                      e e++++e++l+eGk+
  gi|488601165|ref|YP_007907636.1| 47 EIELRRFEKDLEEGKY 62
                                      56899*********98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0047
                              YflT  33 dkdrlerlaentdaetettseeglwdsiknlfrskgd 69 
                                       ++++le++a++ +++te++s+  ++++i +++ ++++
  gi|488601165|ref|YP_007907636.1|  67 KRAKLEKIAKDLGIDTEGKSDDEILEEINKALPKTEK 103
                                       56789***********************999988765 PP

>> HTH_10  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      0.69   1.1e+03      26      39 ..      25      38 ..      22      56 .. 0.68
   2 ?   10.5   0.0   0.00026      0.42      21      36 ..      66      81 ..      62     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.69
                            HTH_10 26 lkeLAkelGIskst 39
                                      l eLA  lG s   
  gi|488601165|ref|YP_007907636.1| 25 LPELARSLGKSMGE 38
                                      66788888855544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                            HTH_10 21 PRrvtlkeLAkelGIs 36
                                      ++r++l+++Ak+lGI 
  gi|488601165|ref|YP_007907636.1| 66 DKRAKLEKIAKDLGID 81
                                      79*************5 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.55   8.9e+02      20      37 ..      39      56 ..      22      66 .. 0.72
   2 ?   10.5   0.2   0.00048      0.79      19      40 ..      70      91 ..      68      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.55
                                      HHHHHHHCTEEEEETTEE CS
                           PTS_IIB 20 lekaakelgieaegeagv 37
                                       +ka ke++ie +  + +
  gi|488601165|ref|YP_007907636.1| 39 FKKAQKEAEIELRRFEKD 56
                                      467777777777666555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00048
                                      HHHHHHHHCTEEEEETTEEGGG CS
                           PTS_IIB 19 klekaakelgieaegeagvele 40
                                      klek+ak+lgi++eg++ +e+ 
  gi|488601165|ref|YP_007907636.1| 70 KLEKIAKDLGIDTEGKSDDEIL 91
                                      9***************999333 PP

>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0001      0.17      65     102 ..      61      98 ..      14     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                                       TTTB-SHHHHHHHHHHHHCHHHCCSSHHHHHHHHCCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane  65 tnvnfddekklkrlaealgieeelkdieelaakvaeva 102
                                       + +  d+++kl+++a++lgi++e+k+++e+ ++++++ 
  gi|488601165|ref|YP_007907636.1|  61 KYTPQDKRAKLEKIAKDLGIDTEGKSDDEILEEINKAL 98 
                                       355678899***********************999754 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.077   1.2e+02      68     106 ..      23      64 ..      21      67 .. 0.64
   2 ?    9.3   0.5   0.00067       1.1      67     109 ..      68     104 ..      50     106 .] 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.077
                           DUF2089  68 nrldeileaLgyeeeeeee.ee..eeerkeileklekgeisv 106
                                       ++l e++++Lg ++ e ++ ++  e e ++  ++le+g+ + 
  gi|488601165|ref|YP_007907636.1|  23 SKLPELARSLGKSMGEFKKaQKeaEIELRRFEKDLEEGKYTP 64 
                                       578888888888888664433223445566667777777665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00067
                           DUF2089  67 rnrldeileaLgyeeeeeeeeeeeerkeileklekgeisveeA 109
                                       r++l++i+++Lg+++e +      + +eile+++k   ++e+A
  gi|488601165|ref|YP_007907636.1|  68 RAKLEKIAKDLGIDTEGK------SDDEILEEINKALPKTEKA 104
                                       89************9955......4789999998877776666 PP

>> Arm-DNA-bind_4  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.5   0.00017      0.28      27      45 ..      43      61 ..      39      62 .. 0.90
   2 ?   -3.2   0.1       4.4   7.2e+03      36      43 ..      89      96 ..      88      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                    Arm-DNA-bind_4 27 KkEAekaeaeflkkinkgl 45
                                      +kEAe ++++f+k++++g+
  gi|488601165|ref|YP_007907636.1| 43 QKEAEIELRRFEKDLEEGK 61
                                      8***************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                    Arm-DNA-bind_4 36 eflkkink 43
                                      e+l++ink
  gi|488601165|ref|YP_007907636.1| 89 EILEEINK 96
                                      89999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 693.61
//
Query:       gi|488601166|ref|YP_007907637.1|  [L=703]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  178.4   4.2    3.2e-16   59.5   0.0    4.6  4  PAS_9        PAS domain
    2.1e-44  150.1   0.0    1.5e-15   57.1   0.0    4.4  4  PAS          PAS fold
    4.6e-43  146.0   0.0    2.1e-15   56.9   0.0    4.3  4  PAS_4        PAS fold
    1.9e-32  111.4   0.0    3.3e-10   40.1   0.0    3.8  4  PAS_3        PAS fold
    2.9e-22   78.2   0.0    6.9e-06   26.0   0.0    4.6  4  PAS_8        PAS domain
    7.7e-20   71.5   2.5    1.8e-19   70.3   0.2    2.6  3  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.5e-07   30.9   0.4      0.047   13.9   0.0    5.5  5  PAS_7        PAS fold
    1.2e-06   28.6   0.0     0.0073   16.4   0.0    3.6  3  PAS_11       PAS domain
    3.1e-06   26.8   2.3      6e-06   25.9   0.5    2.5  2  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain
    0.00048   20.0   0.0     0.0014   18.5   0.0    1.8  1  HATPase_c_5  GHKL domain
    0.00069   19.5   0.0      0.095   12.6   0.0    3.1  2  MEKHLA       MEKHLA domain
    0.00096   18.8   0.1        1.5    8.4   0.0    3.3  3  PAS_12       UPF0242 C-terminal PAS-like domain
     0.0012   18.8   0.2      0.032   14.2   0.0    2.4  2  UvrC_HhH_N   UvrC Helix-hairpin-helix N-terminal
     0.0031   17.1   0.0     0.0058   16.2   0.0    1.3  1  HisKA_4TM    Archaeal 4TM region of histidine kinase
  ------ inclusion threshold ------
      0.027   14.5   0.2      0.027   14.5   0.2    2.8  2  HisKA        His Kinase A (phospho-acceptor) domain
      0.058   13.5   1.2        6.3    7.0   0.2    2.9  2  HisKA_2      Histidine kinase
       0.13   12.4   2.9         13    6.0   0.6    2.8  2  DMPK_coil    DMPK coiled coil domain like
       0.14   12.2   0.0       0.31   11.2   0.0    1.5  1  MLTR_LBD     MmyB-like transcription regulator ligand binding
        1.8    8.8   5.8         15    5.8   0.1    4.0  4  HAS-barrel   HAS barrel domain


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-07   0.00016       6     104 .]      26     114 ..      22     114 .. 0.71
   2 !   55.7   0.1   4.9e-18   4.6e-15       3     104 .]     139     237 ..     137     237 .. 0.86
   3 !   39.6   0.0   5.3e-13     5e-10       2     104 .]     261     361 ..     260     361 .. 0.94
   4 !   59.5   0.0   3.4e-19   3.2e-16       3     104 .]     386     487 ..     384     487 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                             PAS_9   6 idnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                       ++++d++il +N+  +rl+G     v gk+++++f  +++p + + + ++l+ g+    e+e  ++       w ++
  gi|488601166|ref|YP_007907637.1|  26 LIDEDFNILTINREIERLFG----NVTGKKCFEVFhsANAPPDYCAILNLLKGGS---GEEEFYEQSI---GRWLKV 92 
                                       456***************99....8**********55555555555555555555...3333333333...349999 PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       +as++  +d ++++   + +D+te
  gi|488601166|ref|YP_007907637.1|  93 RASRLNIGDSTVFL--HLAEDVTE 114
                                       99999655545555..99999997 PP

  == domain 2  score: 55.7 bits;  conditional E-value: 4.9e-18
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvl 79 
                                        i +  p+g+il++N+a + + Gys+ee++gk++ d+f t+ +++++++++ + +++ + + ev+ + k+g+ +  +
  gi|488601166|ref|YP_007907637.1| 139 IIYLLSPEGKILDVNPAIKSI-GYSKEEIIGKYVYDIF-TPNSRKKFFDKLDNLMKEGFLRHEVEVVSKDGRIISME 213
                                       566777***************.****************.66666666666666666699****************** PP

                             PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                       + as ++d+ g + +ii+i rDite
  gi|488601166|ref|YP_007907637.1| 214 CVASIIRDN-GDVSSIISIHRDITE 237
                                       ******986.678889********8 PP

  == domain 3  score: 39.6 bits;  conditional E-value: 5.3e-13
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirknget 75 
                                       d++ + +pdg  l++N+ +++l+ y++ee+   +  dl+  +p+++er+r+++++  +    +++    +i+k+get
  gi|488601166|ref|YP_007907637.1| 261 DAVYLLTPDG-FLFVNDRVCDLTRYTKEELYRIDPLDLI--HPDDRERIREYIRRRFSgekAPESHISKIITKDGET 334
                                       5677767***.****************************..*****************9*999999999******** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                        ++++++ ++   ++++++  + +rDite
  gi|488601166|ref|YP_007907637.1| 335 RYCEFSVKAITYMGQTVIL--GSVRDITE 361
                                       **********888999999..*******8 PP

  == domain 4  score: 59.5 bits;  conditional E-value: 3.4e-19
                             PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwv 78 
                                        ++  +++gr +y N+++ +++Gys+++++gk+++ ++  +++ +++++++ + ++  k   +ev+li kng++++v
  gi|488601166|ref|YP_007907637.1| 386 IVFALDTEGRFTYLNKKFDEITGYSSKDLIGKHFRLVL-APEYVDSTIEKFKRGLSGeKIPLYEVELIGKNGRRIFV 461
                                       455577********************************.99999999999999999999****************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       +l+++ +k  dg+++g +++ rDite
  gi|488601166|ref|YP_007907637.1| 462 ELNVTNMKGRDGKVIGRLGVARDITE 487
                                       ********99***************8 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0     0.007       6.6       6      35 ..      16      45 ..      12      97 .. 0.81
   2 !   40.6   0.0   2.2e-13     2e-10       2     113 .]     128     235 ..     127     235 .. 0.93
   3 !   40.3   0.0   2.7e-13   2.5e-10       1     113 []     250     359 ..     250     359 .. 0.93
   4 !   57.1   0.0   1.6e-18   1.5e-15       1     113 []     374     485 ..     374     485 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.007
                                      HHHHSSSEEEEEETTSBEEEECHHHHHHHS CS
                               PAS  6 ileslpdpifvvDedgrilyvNaaaeellG 35
                                      +l++l+    ++Ded +il +N+++e+l+G
  gi|488601166|ref|YP_007907637.1| 16 VLDQLDLLAALIDEDFNILTINREIERLFG 45
                                      56677777789******************9 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 2.2e-13
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++++++es+ d i ++   g+il vN+a+ ++ G+s ee++gk ++d + ++++ ++ ++l +l+++g  ++ +e+ 
  gi|488601166|ref|YP_007907637.1| 128 KFKSLFESAVDIIYLLSPEGKILDVNPAIKSI-GYSKEEIIGKYVYDIFTPNSRKKFFDKLDNLMKEGFLRHEVEV- 202
                                       57899**********************99887.*******************999***********9999999999. PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                          +dgr+i +e+ as +rd g+ +  ++ ++rdi
  gi|488601166|ref|YP_007907637.1| 203 -VSKDGRIISMECVASIIRDNGD-VSSIISIHRDI 235
                                       .3359****************87.78********8 PP

  == domain 3  score: 40.3 bits;  conditional E-value: 2.7e-13
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r+++e ++d++ ++  dg +l+vN+  ++l+ ++ ee+ +   ldlih++d++  +e ++++ +  + +++   
  gi|488601166|ref|YP_007907637.1| 250 EKYRTLVEKTHDAVYLLTPDG-FLFVNDRVCDLTRYTKEELYRIDPLDLIHPDDRERIREYIRRRFSGEKAPESHIS 325
                                       579**************9999.69*****************************999999999999999998888888 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       ++ ++dg+++++e  ++ ++ +g++   +lg +rdi
  gi|488601166|ref|YP_007907637.1| 326 KIITKDGETRYCEFSVKAITYMGQT--VILGSVRDI 359
                                       88889******************97..9****9998 PP

  == domain 4  score: 57.1 bits;  conditional E-value: 1.6e-18
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r+++e++ d +f++D  gr++y N+++ e++G+s ++++gk++  ++ +e+   + + +e+  +  + +++   
  gi|488601166|ref|YP_007907637.1| 374 EKYRTLVETINDIVFALDTEGRFTYLNKKFDEITGYSSKDLIGKHFRLVLAPEY---VDSTIEKFKRGLSGEKIPLY 447
                                       579********************************************9999986...66666666666666666555 PP

                                       EEEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++l  ++gr i +e++++ +  ++g+++g lgv+rdi
  gi|488601166|ref|YP_007907637.1| 448 EVELigKNGRRIFVELNVTNMKGRDGKVIGRLGVARDI 485
                                       5555669******************************8 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   3.9e-06    0.0036       1     109 [.      17     116 ..      17     117 .. 0.87
   2 !   45.8   0.0   6.2e-15   5.9e-12       1     110 []     133     240 ..     133     240 .. 0.98
   3 !   20.7   0.0   3.9e-07   0.00037       2     109 ..     257     363 ..     256     364 .. 0.91
   4 !   56.9   0.0   2.2e-18   2.1e-15       2     109 ..     381     489 ..     380     490 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.9e-06
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ld+l  + a +d+d+++l +N+++++     +  ++Gk+++e++    a++  +a+  +l+g+   e+  e      
  gi|488601166|ref|YP_007907637.1|  17 LDQLDLLAALIDEDFNILTINREIER----LFGNVTGKKCFEVFHSANAPPDYCAILNLLKGGSGEEEFYEQSI--- 86 
                                       68999999999************999....999*********99999777777777788889877776666666... PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +r++ +r+++l    G+   +l ++ D+Ter+
  gi|488601166|ref|YP_007907637.1|  87 GRWLKVRASRL--NIGDSTVFLHLAEDVTERK 116
                                       9*********9..56999999999******98 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 6.2e-15
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++s  d+++ l+p+g++l++N+a+ + +g++ ee++Gk +++++++ ++  + + l+ +++++   +++e++  +g+
  gi|488601166|ref|YP_007907637.1| 133 FESAVDIIYLLSPEGKILDVNPAIKS-IGYSKEEIIGKYVYDIFTPNSRKKFFDKLDNLMKEGFLRHEVEVVSKDGR 208
                                       78999********************9.************************************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                          +e+ ++ +rd +G+v  ++ i rDiTer++
  gi|488601166|ref|YP_007907637.1| 209 IISMECVASIIRD-NGDVSSIISIHRDITERKQ 240
                                       ***********98.*****************85 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 3.9e-07
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pg 76 
                                       +++ da++ l pdg +l++N + ++l +++ eel+   + +l  ++d++r+++++rr  +ge++ e+++      +g
  gi|488601166|ref|YP_007907637.1| 257 EKTHDAVYLLTPDG-FLFVNDRVCDLTRYTKEELYRIDPLDLIHPDDRERIREYIRRRFSGEKAPESHISKIItkDG 332
                                       67789999999999.79******************99999*99999******************99999988899** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       e+r++e+++  +    G+   +l+ +rDiTe +
  gi|488601166|ref|YP_007907637.1| 333 ETRYCEFSVKAIT-YMGQ-TVILGSVRDITEKK 363
                                       *********9995.5666.68999******975 PP

  == domain 4  score: 56.9 bits;  conditional E-value: 2.2e-18
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegee.piefleelllpge 77 
                                       + ++d++++ld++gr++y+N+ + e+ g++ ++l+Gk+++ +l +e  +   +  +r l+ge+ p++++e    +g+
  gi|488601166|ref|YP_007907637.1| 381 ETINDIVFALDTEGRFTYLNKKFDEITGYSSKDLIGKHFRLVLAPEYVDSTIEKFKRGLSGEKiPLYEVELIGKNGR 457
                                       7899************************************999999***************9956777777777*** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       + ++el+++ ++ ++G+vig l+++rDiTer+
  gi|488601166|ref|YP_007907637.1| 458 RIFVELNVTNMKGRDGKVIGRLGVARDITERK 489
                                       *******************************8 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.6   6.2e+03       3      50 ..      35      76 ..      33      85 .. 0.68
   2 !   37.6   0.0   2.1e-12     2e-09       2      89 .]     150     232 ..     149     232 .. 0.94
   3 !   40.1   0.0   3.5e-13   3.3e-10       2      81 ..     272     349 ..     271     356 .. 0.91
   4 !   29.1   0.0   9.4e-10   8.9e-07       2      89 .]     397     482 ..     396     482 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.6
                             PAS_3  3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge 50
                                      ++++++e+++G     ++gk  ++ ++ h    +  + a+ ++lk+g+
  gi|488601166|ref|YP_007907637.1| 35 TINREIERLFGN----VTGK--KCFEVFHSANAPPDYCAILNLLKGGS 76
                                      667777777775....4566..77777777777777777777777776 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 2.1e-12
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + v+++++ i Gys+ee++gk   ++d+  p  r++++++l++++k+g  + +e+ ++ kdG ++ +e+ a++i  +
  gi|488601166|ref|YP_007907637.1| 150 LDVNPAIKSI-GYSKEEIIGK--YVYDIFTPNSRKKFFDKLDNLMKEGF-LRHEVEVVSKDGRIISMECVASII-RD 221
                                       67999**999.**********..99********************8887.9***********************.99 PP

                             PAS_3  79 ngkpvrvigva 89 
                                       ng +  +i+++
  gi|488601166|ref|YP_007907637.1| 222 NGDVSSIISIH 232
                                       99999999875 PP

  == domain 3  score: 40.1 bits;  conditional E-value: 3.5e-13
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       ++v++rv++++ y++eel+    + ldl+hp+Drer+re + + +++ + p ++  +i++kdGe+r+ e ++++i  
  gi|488601166|ref|YP_007907637.1| 272 LFVNDRVCDLTRYTKEELYRI--DPLDLIHPDDRERIREYIRRRFSGEKaPESHISKIITKDGETRYCEFSVKAI-T 345
                                       79*******************..**********************9999888999**************999999.5 PP

                             PAS_3  78 engk 81 
                                         g+
  gi|488601166|ref|YP_007907637.1| 346 YMGQ 349
                                       5555 PP

  == domain 4  score: 29.1 bits;  conditional E-value: 9.4e-10
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvird 77 
                                       +y+++++ ei+Gys+ +l+gk  +++ ++ pe  + + e++++ l++ + p   e+ ++ k+G  + ve  ++ ++ 
  gi|488601166|ref|YP_007907637.1| 397 TYLNKKFDEITGYSSKDLIGK--HFRLVLAPEYVDSTIEKFKRGLSGEKiP-LYEVELIGKNGRRIFVELNVTNMKG 470
                                       699******************..**********************888844.5999********************* PP

                             PAS_3  78 engkpvrvigva 89 
                                       ++gk++  +gva
  gi|488601166|ref|YP_007907637.1| 471 RDGKVIGRLGVA 482
                                       ******999985 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0059       5.6       3      48 ..      13      55 ..      12      88 .. 0.80
   2 !   16.2   0.0   8.6e-06    0.0081       2      50 ..     128     176 ..     127     194 .. 0.78
   3 !   23.2   0.0   5.5e-08   5.1e-05       1      57 [.     250     303 ..     250     314 .. 0.76
   4 !   26.0   0.0   7.4e-09   6.9e-06       1      46 [.     374     420 ..     374     440 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0059
                             PAS_8  3 lralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgql 48
                                      l+ ++++++   a++d++ +i+ +N+  ++l+G +  + g+++ ++
  gi|488601166|ref|YP_007907637.1| 13 LEDVLDQLDLLAALIDEDFNILTINREIERLFG-N--VTGKKCFEV 55
                                      57789999998899995456*************.6..666666544 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 8.6e-06
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllp 50 
                                       ++++lfes+ d i ++  +g+ i+dvN+a   + Gys ++++g+ + ++++
  gi|488601166|ref|YP_007907637.1| 128 KFKSLFESAVDIIYLLSpEGK-ILDVNPAIKSI-GYSkEEIIGKYVYDIFT 176
                                       89************9996666.***********.***99999998863333 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 5.5e-08
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellg.qllpvlrplle 57 
                                       e++r+l+e  +d++ ++  ++ +++vN++ ++l+ y+   k+el + + l+ ++p  +
  gi|488601166|ref|YP_007907637.1| 250 EKYRTLVEKTHDAVYLLTPDG-FLFVNDRVCDLTRYT---KEELYRiDPLDLIHPDDR 303
                                       79**************9999*.*************99...445554444444444444 PP

  == domain 4  score: 26.0 bits;  conditional E-value: 7.4e-09
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46 
                                       e++r+l+e+++d ++ +d+ +r+++ N+++ e++Gys +dl+g+ ++
  gi|488601166|ref|YP_007907637.1| 374 EKYRTLVETINDIVFALDTEGRFTYLNKKFDEITGYSsKDLIGKHFR 420
                                       79****************5567***************8888887765 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 ?   -0.9   0.1       2.5   2.3e+03      14      47 ..     187     224 ..     181     254 .. 0.63
   2 ?   -2.2   0.0       6.2   5.8e+03      45      94 ..     315     371 ..     298     390 .. 0.67
   3 !   70.3   0.2   1.9e-22   1.8e-19       7     110 ..     601     698 ..     597     700 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.5
                                       HHHHHHHHSTTTEEEEEEEEEE.....TEEEEEEEESSS CS
                         HATPase_c  14 vdNavkfatkageieveikase.....ddlvisveDnGi 47 
                                       +dN++k+    +e+ev  k        + +   ++DnG 
  gi|488601166|ref|YP_007907637.1| 187 LDNLMKEGFLRHEVEVVSKD-GriismECVASIIRDNGD 224
                                       78888885577778776552.123332344445888883 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                                       SSSSSTTHHHTGTCSTTCH.....HCSTCHTSTSSSHHHHHHHHHHH..HTTTEEEE CS
                         HATPase_c  45 nGiGipkedlkklfekfsq.....ddstkrggggtGlGlsivkklve..lmgGeiwv 94 
                                       +G   p++++ k+ +k  +      + +++++ g  + l  v+ ++e  lm+ +++ 
  gi|488601166|ref|YP_007907637.1| 315 SGEKAPESHISKIITKDGEtryceFSVKAITYMGQTVILGSVRDITEkkLMEDKLRE 371
                                       566666666776666444445666667777788888888888886664445555544 PP

  == domain 3  score: 70.3 bits;  conditional E-value: 1.9e-22
                                       HHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHHH CS
                         HATPase_c   7 rqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsivk 82 
                                         +i+n+v Na+ + +k+++i+++ik +++  +i++ D G+G+p e+ +k+fe  f +      ++g tGlGl+ivk
  gi|488601166|ref|YP_007907637.1| 601 GSVIDNIVNNAIVH-GKTDRIDITIK-HNGFCEIRIADYGKGVPDEIKEKIFEeGFFS-----GDTGHTGLGLYIVK 670
                                       579***********.***********.5569**********************99999.....5689********** PP

                                       HHHHHTTTEEEEEEETTTEEEEEEEEES CS
                         HATPase_c  83 klvelmgGeiwvesepgrGttftftlpl 110
                                       k+ve+++Ge+wve+++ +G  f+++l+ 
  gi|488601166|ref|YP_007907637.1| 671 KVVERYDGEVWVEDNEPKGAVFVIKLKT 698
                                       ************************9985 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.74     7e+02       9      29 ..      25      45 ..      17      50 .. 0.89
   2 ?    3.4   0.0     0.085        80      80     114 ..      82     119 ..      58     120 .. 0.76
   3 !   13.9   0.0     5e-05     0.047      27     115 .]     149     243 ..     145     243 .. 0.80
   4 ?   -0.2   0.1       1.2   1.1e+03      57      86 ..     304     333 ..     267     367 .. 0.56
   5 ?    4.8   0.0     0.033        31       2      46 ..     381     424 ..     380     493 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.74
                             PAS_7  9 svfDadlrLvawNrrylelld 29
                                      +++D+d +++++Nr++ +l++
  gi|488601166|ref|YP_007907637.1| 25 ALIDEDFNILTINREIERLFG 45
                                      589**************9996 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.085
                             PAS_7  80 rerpdgrvievrgnpl...pdgGfVttytDiTerrrae 114
                                        e++ gr+++vr+++l   +   f+   +D+Ter++ e
  gi|488601166|ref|YP_007907637.1|  82 YEQSIGRWLKVRASRLnigDSTVFLHLAEDVTERKKME 119
                                       45678**********9554455677888******9876 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 5e-05
                             PAS_7  27 lldlpeelvqvgvpleellrynaergefgagdveaeverrlaaara.gkphsfererpdgrvievrgnpl......p 96 
                                       +ld+ + +  +g + ee++        f+++++++++++  + +++ + +h +e+  +dgr+i++++ +       +
  gi|488601166|ref|YP_007907637.1| 149 ILDVNPAIKSIGYSKEEIIGKY-VYDIFTPNSRKKFFDKLDNLMKEgFLRHEVEVVSKDGRIISMECVASiirdngD 224
                                       6777777777788888888766.45678889999999999999998789***************9998765655444 PP

                             PAS_7  97 dgGfVttytDiTerrraee 115
                                          +++++ DiTer++ ee
  gi|488601166|ref|YP_007907637.1| 225 VSSIISIHRDITERKQMEE 243
                                       5668899********9885 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.2
                             PAS_7  57 gdveaeverrlaaaragkphsfererpdgr 86 
                                       ++++++++rr++  +a ++h  +  ++dg+
  gi|488601166|ref|YP_007907637.1| 304 ERIREYIRRRFSGEKAPESHISKIITKDGE 333
                                       345566777776666666666666666654 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.033
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleellr 46 
                                       e +++ +  +D ++r +  N+++ e+ +++++ + +g++++ +l+
  gi|488601166|ref|YP_007907637.1| 381 ETINDIVFALDTEGRFTYLNKKFDEITGYSSKDL-IGKHFRLVLA 424
                                       5666667889*******************99998.8888887765 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.7e-06    0.0073       8     106 ..     143     233 ..     139     240 .. 0.84
   2 ?    5.8   0.0     0.016        15      29      78 ..     283     332 ..     271     346 .. 0.83
   3 ?    1.6   0.0       0.3   2.8e+02       5      56 ..     387     435 ..     367     448 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.7e-06
                            PAS_11   8 ldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvk 84 
                                       l+++gkI++v++    a  s g++kee++g+++yd++ p+ +++  ++l + + ++g      +   +++++++++ 
  gi|488601166|ref|YP_007907637.1| 143 LSPEGKILDVNP----AIKSIGYSKEEIIGKYVYDIFTPNSRKKFFDKLDNLM-KEGF-LRHEVEVVSKDGRIISME 213
                                       6889********....667889*******************************.5554.555567778899999999 PP

                            PAS_11  85 tksklfknqksneqdfimatht 106
                                       +++ + +  ++ ++ +i+++h 
  gi|488601166|ref|YP_007907637.1| 214 CVASIIR--DNGDVSSIISIHR 233
                                       9999998..7888888988885 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                            PAS_11  29 glekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqd 78 
                                        ++keel ++   dL+hp+d++++++  r  +s +++ +s + +++++++
  gi|488601166|ref|YP_007907637.1| 283 RYTKEELYRIDPLDLIHPDDRERIREYIRRRFSGEKAPESHISKIITKDG 332
                                       799*******************9999999888777777777777766665 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.3
                            PAS_11   5 ttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshl 56 
                                        + ld++g+++ +++   +    +g+++++l+g+ +   + p+ + ++ +++
  gi|488601166|ref|YP_007907637.1| 387 VFALDTEGRFTYLNK---KFDEITGYSSKDLIGKHFRLVLAPEYVDSTIEKF 435
                                       566788888888888...7777777877788887777666666666666665 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 !   25.9   0.5   6.3e-09     6e-06       4      55 ..     493     545 ..     490     551 .. 0.89
   2 ?   -3.1   0.0       7.2   6.8e+03      42      56 ..     570     584 ..     558     585 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.3e-09
                            SPOB_a   4 eeikelkeliklL.rsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelke 55 
                                       +++ el+e +kl+ + +RHD lN+L vIs  l+++k +  ee+i+++ k++++
  gi|488601166|ref|YP_007907637.1| 493 KKLVELNETLKLInKILRHDLLNDLTVISYALEMYKETGDEEIIDRAFKAIER 545
                                       4566999999999888*********************************9987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.2
                            SPOB_a  42 aeeyieevvkelkee 56 
                                       +++++e+v++ ++e+
  gi|488601166|ref|YP_007907637.1| 570 VRKVVEDVTEKYQEI 584
                                       788889998888775 PP

>> HATPase_c_5  GHKL 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    0.0014      10      91 ..     600     686 ..     596     696 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                       HATPase_c_5  10 lgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg.....ekkkless...kskkeehGiGlksireiv 78 
                                       +g ++dN ++ +    + +  I++t++ ++++  i+i  + +g     + +k++++   + ++++ G+Gl  ++++v
  gi|488601166|ref|YP_007907637.1| 600 FGSVIDNIVNNAIVHGK-TDRIDITIK-HNGFCEIRIADYGKGvpdeiK-EKIFEEgffSGDTGHTGLGLYIVKKVV 673
                                       67777777777666664.677999885.678999999999888555331.3444223447899************** PP

                       HATPase_c_5  79 kkykgnlsieaed 91 
                                       ++y+g++++e ++
  gi|488601166|ref|YP_007907637.1| 674 ERYDGEVWVEDNE 686
                                       ********98775 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.082        77      62     117 ..     159     213 ..     153     228 .. 0.81
   2 !   12.6   0.0    0.0001     0.095       6     117 ..     351     462 ..     348     478 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.082
                            MEKHLA  62 lettweeltdlpsrksaepeekeeRealLekvaeqgfvenysGvrisstGrrfsie 117
                                         ++ ee++   +  ++ p+++++   +L++++++gf+++ +   +s++Gr +s+e
  gi|488601166|ref|YP_007907637.1| 159 IGYSKEEIIGKYVYDIFTPNSRKKFFDKLDNLMKEGFLRH-EVEVVSKDGRIISME 213
                                       56667777777788899999999999***********985.556699****99887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0001
                            MEKHLA   6 lllqSYrrltgkeLles.sesaeelakaLfe.apfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaep 80 
                                       ++l S r +t+k+L+e+  +++ee+ ++L e  +++v++ +++    f+y N++  ++  ++ ++l+  + r+++ p
  gi|488601166|ref|YP_007907637.1| 351 VILGSVRDITEKKLMEDkLRESEEKYRTLVEtINDIVFALDTE--GRFTYLNKKFDEITGYSSKDLIGKHFRLVLAP 425
                                       7999*************76678999999999688999998877..89*****************************9 PP

                            MEKHLA  81 eekeeRealLekvaeqgfvenysGvrisstGrrfsie 117
                                       e  ++  +++++    + + +y+   i ++Grr+ +e
  gi|488601166|ref|YP_007907637.1| 426 EYVDSTIEKFKRGLSGEKIPLYEVELIGKNGRRIFVE 462
                                       9988889**************************9987 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 !    6.0   0.1    0.0092       8.7      50     139 ..     131     220 ..     108     232 .. 0.77
   2 ?   -1.0   0.0       1.3   1.2e+03      62      88 ..     264     290 ..     257     300 .. 0.83
   3 !    8.4   0.0    0.0016       1.5      55      95 ..     382     422 ..     367     463 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0092
                            PAS_12  50 sLrsEnlgailvysqkenkllfaNaqirallGwssdkflqdf.seivqe.gleeWkralaklsskteskirlvlKtK 124
                                       sL +     i + s  e k+l +N  i++ +G+s+++++ ++  +i ++ + +++  +l++l ++   + ++++ +K
  gi|488601166|ref|YP_007907637.1| 131 SLFESAVDIIYLLS-PEGKILDVNPAIKS-IGYSKEEIIGKYvYDIFTPnSRKKFFDKLDNLMKEGFLRHEVEVVSK 205
                                       55544444444444.489*********98.6******9987626887752678899999999999999999999999 PP

                            PAS_12 125 agqevllncllgiip 139
                                        g  + ++c   ii 
  gi|488601166|ref|YP_007907637.1| 206 DGRIISMECVASIIR 220
                                       999999999999885 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                            PAS_12  62 ysqkenkllfaNaqirallGwssdkfl 88 
                                       y    +  lf+N+++ +l+ + ++++ 
  gi|488601166|ref|YP_007907637.1| 264 YLLTPDGFLFVNDRVCDLTRYTKEELY 290
                                       55556668**************99986 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0016
                            PAS_12  55 nlgailvysqkenkllfaNaqirallGwssdkflqdfseiv 95 
                                       +   i++    e +  + N+++ +++G+ss +++ + + +v
  gi|488601166|ref|YP_007907637.1| 382 TINDIVFALDTEGRFTYLNKKFDEITGYSSKDLIGKHFRLV 422
                                       5556666667899****************999886544332 PP

>> 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 ?    2.1   0.0      0.17   1.6e+02      84     143 ..     205     267 ..     124     268 .. 0.81
   2 !   14.2   0.0   3.4e-05     0.032      53     123 ..     299     370 ..     279     405 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.17
                                       ESSSHHHHHHHHHHHHHTT----EEEEES..............SSSEE.EE--TT-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx.xxxxxxxxxxxxxx RF
                        UvrC_HhH_N  84 iDGGkgqlnaakevleelglkipvvglaKdkkrktraka..eereeev.lelkkssealkllq 143
                                        DG    ++ + +++++ g    ++++ +d +++++ ++  +e+ee+    ++k+++a++ll+
  gi|488601166|ref|YP_007907637.1| 205 KDGRIISMECVASIIRDNGDVSSIISIHRDITERKQMEEklKESEEKYrTLVEKTHDAVYLLT 267
                                       588889999999999999977789*****9888777776665555555677888899998885 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.4e-05
                                       S--HHHHHHHHHHHHHTTS.....---SEEEESSSHHHHHHHHHHHHHTT----EEEEES............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                        UvrC_HhH_N  53 egdDyaamrevlrRrfkrllkefsklPdLiliDGGkgqlnaakevleelglkipvvglaKdkkrktraka..e 123
                                       ++dD + +re +rRrf+  ++ +s+   +i  DG     +  +++++ +g ++ ++g ++d ++k+  +   +
  gi|488601166|ref|YP_007907637.1| 299 HPDDRERIREYIRRRFSGEKAPESHISKIITKDGETRYCEFSVKAITYMGQTV-ILGSVRDITEKKLMEDklR 370
                                       49*********************************************999555.5555554433333322342 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.1e-06    0.0058     130     156 ..     495     521 ..     455     528 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.1e-06
                         HisKA_4TM 130 akrisdalafvndlirhdlrndlvvir 156
                                            ++l ++n+++rhdl ndl+vi 
  gi|488601166|ref|YP_007907637.1| 495 LVELNETLKLINKILRHDLLNDLTVIS 521
                                       335689*******************96 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 ?   -2.6   0.1       6.2   5.9e+03      42      58 ..     367     383 ..     352     387 .. 0.54
   2 ?   14.5   0.2   2.9e-05     0.027       9      62 ..     509     557 ..     502     561 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.2
                                       HHHHHHHHHHHHHHHHH CS
                             HisKA  42 etiesearrldhlvedl 58 
                                       ++++++++  + lve++
  gi|488601166|ref|YP_007907637.1| 367 DKLRESEEKYRTLVETI 383
                                       33444444444444443 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                             HisKA   9 vaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdls 62 
                                       + H+L + L++i+ ++e+ k+        +e ++++ + ++r  +l+  +++l+
  gi|488601166|ref|YP_007907637.1| 509 LRHDLLNDLTVISYALEMYKE-----TGDEEIIDRAFKAIERGIKLIRKMRELE 557
                                       79*****************99.....7889999999999999999999998885 PP

>> HisKA_2  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.046        43      13      43 ..     225     255 ..     206     267 .. 0.88
   2 ?    7.0   0.2    0.0067       6.3       4      72 ..     511     581 ..     509     584 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.046
                           HisKA_2  13 isslLslqarkakdeevkealresqnRvlsi 43 
                                       +ss++s++ + ++ ++++e l+es+++ +++
  gi|488601166|ref|YP_007907637.1| 225 VSSIISIHRDITERKQMEEKLKESEEKYRTL 255
                                       799*********************9987775 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0067
                           HisKA_2   4 HRvkNnLqvisslLslqarkakdeevkealresqnRvlsialihe..eLyksedletvdfseylekLvenl 72 
                                       H   N L+vis  L++ +++ ++e + +a++ +++ ++ i  + e   L + ++l+++++++++e+++e+ 
  gi|488601166|ref|YP_007907637.1| 511 HDLLNDLTVISYALEMYKETGDEEIIDRAFKAIERGIKLIRKMREleGLTNLSELRKISVRKVVEDVTEKY 581
                                       6677********************************99999998622699999************999986 PP

>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6     0.013        13      29      47 ..     240     258 ..     234     261 .. 0.87
   2 ?    5.3   0.1     0.022        21      30      49 ..     365     384 ..     355     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                         DMPK_coil  29 afeskLkeaEkknreLeee 47 
                                       ++e kLke+E k r L e+
  gi|488601166|ref|YP_007907637.1| 240 QMEEKLKESEEKYRTLVEK 258
                                       789***********99875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.022
                         DMPK_coil  30 feskLkeaEkknreLeeele 49 
                                       +e kL+e+E k r L e ++
  gi|488601166|ref|YP_007907637.1| 365 MEDKLRESEEKYRTLVETIN 384
                                       689************99887 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 ?   11.2   0.0   0.00033      0.31       4      40 ..      12      50 ..       9      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                          MLTR_LBD  4 alrrlLdalepvPAlVldrrwdvlaaNraaraLlgd...p 40
                                       l+ +Ld+l +  A+ +d ++++l  Nr  ++L+g     
  gi|488601166|ref|YP_007907637.1| 12 NLEDVLDQL-DLLAALIDEDFNILTINREIERLFGNvtgK 50
                                      6899*****.8999999******************95540 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0       0.2   1.8e+02      24      81 ..      85     147 ..      45     170 .. 0.85
   2 ?    0.2   0.1      0.93   8.8e+02      50      80 ..     224     259 ..     200     266 .. 0.76
   3 ?    5.8   0.1     0.016        15      35      80 ..     348     393 ..     334     412 .. 0.76
   4 ?   -1.8   0.1       3.8   3.6e+03      39      58 ..     478     503 ..     471     536 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                        HAS-barrel  24 kvGeyVeielp.....dgeivlGmvtdirrgnselsndlalvlsleeleeangddevalated 81 
                                       ++G +++++       d +++l + +d+ ++++ + +  ++++ ++ l+e+  d+ ++l +e+
  gi|488601166|ref|YP_007907637.1|  85 SIGRWLKVRASrlnigDSTVFLHLAEDVTERKKMEMDLIERERKFKSLFESAVDIIYLLSPEG 147
                                       678888888888888888889999999999999999999*****************9999885 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.93
                        HAS-barrel  50 n.....selsndlalvlsleeleeangddevalate 80 
                                       +     s++++++++ + +e+l+e+++ + +++ ++
  gi|488601166|ref|YP_007907637.1| 224 DvssiiSIHRDITERKQMEEKLKESEEKYRTLVEKT 259
                                       033344688899999999999999999888887765 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.016
                        HAS-barrel  35 dgeivlGmvtdirrgnselsndlalvlsleeleeangddevalate 80 
                                       + +++lG v+di +++  + + ++ ++  ++l e ++d+++al te
  gi|488601166|ref|YP_007907637.1| 348 GQTVILGSVRDITEKKLMEDKLRESEEKYRTLVETINDIVFALDTE 393
                                       4589**********99444455666666666666666777776666 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.8
                        HAS-barrel  39 vlGmvtdirrgn......selsndla 58 
                                       +lG+ +di +++       el   l+
  gi|488601166|ref|YP_007907637.1| 478 RLGVARDITERKkmekklVELNETLK 503
                                       57888888886555333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4495.00
//
Query:       gi|488601167|ref|YP_007907638.1|  [L=694]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-54  180.8   0.0      1e-17   64.4   0.0    4.3  4  PAS_4     PAS fold
    2.3e-49  166.0   2.8      1e-13   51.4   0.0    4.6  5  PAS_9     PAS domain
    3.8e-47  159.0   0.0    8.5e-15   54.7   0.0    5.0  5  PAS       PAS fold
    1.4e-42  143.9   0.1    1.8e-13   50.6   0.0    3.9  3  PAS_3     PAS fold
    1.2e-32  111.4   0.0    6.4e-09   35.6   0.0    4.6  4  PAS_8     PAS domain
    3.2e-15   56.2   0.0    7.2e-05   22.9   0.0    4.3  4  PAS_11    PAS domain
    4.2e-09   36.9   0.5      0.095   13.3   0.0    4.1  4  PAS_10    PAS domain
      3e-07   30.4   0.0      0.031   14.2   0.0    3.5  3  MEKHLA    MEKHLA domain
    5.9e-07   29.4   0.0    2.3e-06   27.5   0.0    2.2  1  HisKA     His Kinase A (phospho-acceptor) domain
    2.3e-05   24.5   0.1      0.073   13.2   0.0    3.5  3  PAS_7     PAS fold
    3.8e-05   24.3   0.0        2.1    9.0   0.0    4.2  4  PAS_2     PAS fold
    7.7e-05   23.0   0.0     0.0012   19.2   0.0    2.8  3  GAF_2     GAF domain
     0.0052   17.1   0.0      0.011   16.1   0.0    1.6  1  GAF_3     GAF domain
  ------ inclusion threshold ------
       0.02   15.5   0.0      0.051   14.2   0.0    1.7  1  GAF       GAF domain
       0.13   12.5   0.4        2.9    8.1   0.1    3.2  3  DUF3369   Domain of unknown function (DUF3369)


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 !   43.9   0.0     2e-14   2.3e-11       1     109 [.       9     116 ..       9     117 .. 0.96
   2 !   24.1   0.0   2.7e-08   3.2e-05      13     110 .]     144     241 ..     138     241 .. 0.90
   3 !   64.4   0.0   8.4e-21     1e-17       2     108 ..     254     359 ..     253     361 .. 0.97
   4 !   43.2   0.0   3.3e-14   3.9e-11       1     107 [.     377     474 ..     377     476 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++++ +a++++d+dgr+  +N+ + e++g+++eel+G+t + l+ ++d + l  +  + + g+++ +++ +   +g+
  gi|488601167|ref|YP_007907638.1|   9 FEKSEEAFFIIDSDGRFAEVNRKYVEMLGYSREELIGHTARKLVHPDDLEVLKKNFLEIINGKATRFECRVIAKDGR 85 
                                       789999************************************99999****************************** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                         ++e+   P++ e+ +v g+ +i+rDiT ++
  gi|488601167|ref|YP_007907638.1|  86 VMYVEIVEWPIF-EENRVSGAEGILRDITKEK 116
                                       ***********9.6***************876 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.7e-08
                             PAS_4  13 pdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pgeerhyelrllP 87 
                                        dg++ y+N+  ael g++ +el+Gk++ ++  +e ++ ++ +l+  ++g+  ++         +ge r+ e++ ++
  gi|488601167|ref|YP_007907638.1| 144 QDGVFKYVNPKLAELWGYDVDELIGKSPLQFIHPEYRELVDKNLKLRIDGKVKAINYKLQIIrkDGEVRTNEVFGSR 220
                                       59****************************99999***************977766554444679************ PP

                             PAS_4  88 lrdesGevigvlvisrDiTerrr 110
                                       +  + G+  +++++++DiTe +r
  gi|488601167|ref|YP_007907638.1| 221 V--TYGGRPAIIGTLIDITESER 241
                                       *..67999************875 PP

  == domain 3  score: 64.4 bits;  conditional E-value: 8.4e-21
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       ++ +d++++ld +gr+l++N+ +ae++g+++eel+G+t + l+ ++    ++++ r+v++g+++ +++     +g+e
  gi|488601167|ref|YP_007907638.1| 254 ENAQDLFFILDNNGRFLDVNPKYAEMLGYSREELIGHTARKLVHPDEVSMVRENFRKVMQGKTVRYEAKAIAKDGRE 330
                                       7899*************************************99999*************************99**** PP

                             PAS_4  79 rhyelrllPlrdesGevigvlvisrDiTer 108
                                        ++e+ l P++ e+G+v+g+ +i+rDi+e 
  gi|488601167|ref|YP_007907638.1| 331 YVMEVILWPVF-ENGRVVGAEGILRDISEK 359
                                       **********9.6**************996 PP

  == domain 4  score: 43.2 bits;  conditional E-value: 3.3e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++++p ++a++++d+ ++ aN+a   +++  +   +Gk+l e+lpe +a r + +++r+ + ++p++f +e +    
  gi|488601167|ref|YP_007907638.1| 377 FEKSPNLIAIINRDFAFIEANPA---MVKNLGTNPIGKRLSEVLPENVANRMMKYIKRMFKRNKPLKFRDESNG--- 447
                                       799********************...777999**************************************5555... PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTe 107
                                        r++  +l+P++ ++G+   +lvis D+T+
  gi|488601167|ref|YP_007907638.1| 448 -RYFINTLVPIDLPDGK--YCLVISKDVTD 474
                                       .****************..*********96 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1   3.6e-14   4.2e-11       2     104 .]      14     114 ..      13     114 .. 0.93
   2 !   39.4   0.0   4.7e-13   5.6e-10       3     104 .]     139     238 ..     137     238 .. 0.86
   3 !   51.4   0.0   8.5e-17     1e-13       2     104 .]     258     358 ..     257     358 .. 0.90
   4 !   29.2   0.0   7.2e-10   8.6e-07       1     104 []     381     474 ..     381     474 .. 0.92
   5 ?   -2.6   0.0       5.6   6.7e+03      79      79 ..     530     530 ..     490     588 .. 0.55

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 3.6e-14
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       ++++i+++dgr   +N++  ++lGys+ee++g+  + l+ ++++ +  ++++le +  k+ ++e   i k+g+ ++v
  gi|488601167|ref|YP_007907638.1|  14 EAFFIIDSDGRFAEVNRKYVEMLGYSREELIGHTARKLV-HPDDLEVLKKNFLEIINGKATRFECRVIAKDGRVMYV 89 
                                       7899999********************************.999999999999999999******************* PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       ++   p++++ +++ g+ +ilrDit+
  gi|488601167|ref|YP_007907638.1|  90 EIVEWPIFEE-NRVSGAEGILRDITK 114
                                       *******976.5667778******95 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 4.7e-13
                             PAS_9   3 gilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirknget 75 
                                       gi ++  dg +  y+N+++++l Gy+ +e++gks  +++  +pe +e +++ l+   +   k+ ++ +++irk+ge 
  gi|488601167|ref|YP_007907638.1| 139 GIYLI-QDG-VFkYVNPKLAELWGYDVDELIGKSPLQFI--HPEYRELVDKNLKLRIDgkvKAINYKLQIIRKDGEV 211
                                       67766.899.999**************************..77777777777777777789**************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                         +++  s+v  +++   +ii++l+Dite
  gi|488601167|ref|YP_007907638.1| 212 RTNEVFGSRVTYGGRP--AIIGTLIDITE 238
                                       **********765544..466*******8 PP

  == domain 3  score: 51.4 bits;  conditional E-value: 8.5e-17
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d ++i +++gr l++N++ +++lGys+ee++g+  + l+  +p++ + +r+ ++   + k  ++e   i k+g+++ 
  gi|488601167|ref|YP_007907638.1| 258 DLFFILDNNGRFLDVNPKYAEMLGYSREELIGHTARKLV--HPDEVSMVRENFRKVMQgKTVRYEAKAIAKDGREYV 332
                                       5689989********************************..66666666666666666699**************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                        ++ + pv++ +g++vg+ +ilrDi+e
  gi|488601167|ref|YP_007907638.1| 333 MEVILWPVFE-NGRVVGAEGILRDISE 358
                                       ********96.6899999*******98 PP

  == domain 4  score: 29.2 bits;  conditional E-value: 7.2e-10
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       p+ i+i+n d+  + aN+a+ + lG++    +gk++++++  +++ ++r+ ++++++    r++++ ++++++++++
  gi|488601167|ref|YP_007907638.1| 381 PNLIAIINRDFAFIEANPAMVKNLGTN---PIGKRLSEVL--PENVANRMMKYIKRMF--KRNKPLKFRDESNGRYF 450
                                       56789999*****************88...789*******..****************..***********999999 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       ++ t++p+   dg++++  vi++D+t+
  gi|488601167|ref|YP_007907638.1| 451 IN-TLVPIDLPDGKYCL--VISKDVTD 474
                                       66.467**888******..******96 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 5.6
                             PAS_9  79 l 79 
                                        
  gi|488601167|ref|YP_007907638.1| 530 A 530
                                       1 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   6.9e-16   8.3e-13       2     113 .]       4     112 ..       3     112 .. 0.83
   2 !   36.3   0.0   3.8e-12   4.6e-09       2     113 .]     128     236 ..     127     236 .. 0.92
   3 !   54.7   0.0   7.1e-18   8.5e-15       1     113 []     247     356 ..     247     356 .. 0.85
   4 !   12.8   0.0   7.4e-05     0.089       2      67 ..     372     430 ..     371     471 .. 0.85
   5 ?   -0.6   0.0         1   1.3e+03      58      88 ..     498     528 ..     486     530 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 6.9e-16
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++ ++e + ++ f++D dgr+ +vN+++ e+lG+sree++g +   l+h++d + l++ +++ + +g+  r +++ 
  gi|488601167|ref|YP_007907638.1|   4 RYKDFFEKSEEAFFIIDSDGRFAEVNRKYVEMLGYSREELIGHTARKLVHPDDLEVLKKNFLE-IINGKATRFECRV 79 
                                       6778889999***************************************99865444444444.4445555555665 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + + dgr+ ++e+   p++++  ++ g+ g+lrdi
  gi|488601167|ref|YP_007907638.1|  80 IAK-DGRVMYVEIVEWPIFEE-NRVSGAEGILRDI 112
                                       666.***************99.6788999999998 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 3.8e-12
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++a+ e + ++i ++  dg++ yvN++ +el G++ +e++gks l +ih+e+++ + + l+ ++  + ++ +++  
  gi|488601167|ref|YP_007907638.1| 128 MFEALAEKSLVGIYLI-QDGVFKYVNPKLAELWGYDVDELIGKSPLQFIHPEYRELVDKNLKLRIDGKVKAINYKLQ 203
                                       7889999999999999.9**********************************9988888888888888899999999 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       + ++dg+++  ev  s v+ +g     ++g+l di
  gi|488601167|ref|YP_007907638.1| 204 IIRKDGEVRTNEVFGSRVTYGGRP--AIIGTLIDI 236
                                       999*****************9765..9*****998 PP

  == domain 3  score: 54.7 bits;  conditional E-value: 7.1e-18
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r++ e++ d  f++D +gr+l vN++++e+lG+sree++g +   l+h+++ + ++e ++++++ ++ +   + 
  gi|488601167|ref|YP_007907638.1| 247 EEYRRFYENAQDLFFILDNNGRFLDVNPKYAEMLGYSREELIGHTARKLVHPDEVSMVRENFRKVMQGKTVRYEAK- 322
                                       68*************************************************9955566666666665555554444. PP

                                       EEEC..TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfkl..rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                             +dgr++ +ev   pv++  g++ g+ g+lrdi
  gi|488601167|ref|YP_007907638.1| 323 ---AiaKDGREYVMEVILWPVFEN-GRVVGAEGILRDI 356
                                       ...3446*****************.5677*******98 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHH CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlle 67 
                                       ++r i+e +p+ i ++++d  ++++N+a+ + lG ++   +gk l+++++e+    +a ++ ++++
  gi|488601167|ref|YP_007907638.1| 372 KFRKIFEKSPNLIAIINRDFAFIEANPAMVKNLGTNP---IGKRLSEVLPEN----VANRMMKYIK 430
                                       7899******************************875...999999999999....8888877776 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1
                                       HHHHHHHHHHHTT-ECCCCEEEECTTSSEEE CS
                               PAS  58 laelleqlleqgeesrageisfklrdgrpih 88 
                                        + +l++++e+ ++ +++  ++ + dg+++ 
  gi|488601167|ref|YP_007907638.1| 498 EQNILRKACEELNSLEGFSATILTIDGKKVS 528
                                       7899********************9999876 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   1.5e-16   1.8e-13       3      83 ..      27     103 ..      25     109 .. 0.88
   2 !   40.9   0.0   1.6e-13   1.9e-10       3      82 ..     150     227 ..     148     233 .. 0.88
   3 !   48.0   0.0   9.6e-16   1.1e-12       2      88 ..     270     352 ..     269     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.5e-16
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                        v++++ e+lGys+eel+g+  + ++lvhp+D+e +++++ e++ +g++  +e R++ kdG +++ve    +i  e+
  gi|488601167|ref|YP_007907638.1|  27 EVNRKYVEMLGYSREELIGH--TARKLVHPDDLEVLKKNFLEII-NGKATRFECRVIAKDGRVMYVEIVEWPI-FEE 99 
                                       6899****************..**********************.5555899***************999998.555 PP

                             PAS_3  80 gkpv 83 
                                       +++ 
  gi|488601167|ref|YP_007907638.1| 100 NRVS 103
                                       5555 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 1.6e-13
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       yv+++  e++Gy+ +el+gk  s l+++hpe re v ++l+  ++++  +++   +i+rkdGe+r  e  ++ +   
  gi|488601167|ref|YP_007907638.1| 150 YVNPKLAELWGYDVDELIGK--SPLQFIHPEYRELVDKNLKLRIDGKVkAINYKLQIIRKDGEVRTNEVFGSRV-TY 223
                                       99******************..**********************8888899**************988887776.55 PP

                             PAS_3  79 ngkp 82 
                                        g+p
  gi|488601167|ref|YP_007907638.1| 224 GGRP 227
                                       5555 PP

  == domain 3  score: 48.0 bits;  conditional E-value: 9.6e-16
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + v++++ e+lGys+eel+g+  + ++lvhp++ + vre++ +++++++ +  e + + kdG  + +e    ++  e
  gi|488601167|ref|YP_007907638.1| 270 LDVNPKYAEMLGYSREELIGH--TARKLVHPDEVSMVRENFRKVMQGKT-VRYEAKAIAKDGREYVMEVILWPV-FE 342
                                       679******************..**********************6666.888*********************.** PP

                             PAS_3  79 ngkpvrvigv 88 
                                       ng++v   g+
  gi|488601167|ref|YP_007907638.1| 343 NGRVVGAEGI 352
                                       *****99887 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   9.4e-11   1.1e-07       2      51 ..       4      54 ..       3      69 .. 0.85
   2 !   22.3   0.0     8e-08   9.5e-05       3      55 ..     129     181 ..     127     192 .. 0.82
   3 !   35.6   0.0   5.3e-12   6.4e-09       3      51 ..     249     298 ..     247     315 .. 0.83
   4 !   15.8   0.0   8.7e-06      0.01       1      35 [.     371     405 ..     371     430 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 9.4e-11
                             PAS_8  2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51
                                      r++ +fe s ++ +++d ++r+ +vN+++ e+lGys ++l+g + ++l++ 
  gi|488601167|ref|YP_007907638.1|  4 RYKDFFEKSEEAFFIIDSDGRFAEVNRKYVEMLGYSrEELIGHTARKLVHP 54
                                      9****************8888***************999999998755443 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 8e-08
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrpl 55 
                                       ++al e s +gi ++ +g  + +vN++ +el+Gy+ ++l+g+   q+++  + +
  gi|488601167|ref|YP_007907638.1| 129 FEALAEKSLVGIYLIQDGV-FKYVNPKLAELWGYDvDELIGKSPLQFIHPEYRE 181
                                       899**********987666.***************9998888777666655555 PP

  == domain 3  score: 35.6 bits;  conditional E-value: 5.3e-12
                             PAS_8   3 lralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpv 51 
                                       +r ++e+++d  +++d+++r++dvN++++e+lGys ++l+g + ++l++ 
  gi|488601167|ref|YP_007907638.1| 249 YRRFYENAQDLFFILDNNGRFLDVNPKYAEMLGYSrEELIGHTARKLVHP 298
                                       9***************6667***************999999888766654 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 8.7e-06
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellG 35 
                                       e++r +fe sp+ ia+++++  ++++N+a+ + lG
  gi|488601167|ref|YP_007907638.1| 371 EKFRKIFEKSPNLIAIINRDFAFIEANPAMVKNLG 405
                                       79***************96557*******987666 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     6e-08   7.2e-05       3      84 ..      14      90 ..      12     103 .. 0.91
   2 ?    5.7   0.0     0.013        15      29      78 ..     160     208 ..     155     214 .. 0.86
   3 !   20.9   0.0   2.4e-07   0.00029       5      62 ..     260     313 ..     256     322 .. 0.91
   4 ?    0.5   0.0      0.55   6.5e+02      13      37 ..     518     542 ..     508     549 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6e-08
                            PAS_11  3 qfttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfv 81
                                      +  +++d dg++ +v++   +    lg+++eel+g  + +L+hp+dl+ lk+ + e+i  ng+at    R +++++++ 
  gi|488601167|ref|YP_007907638.1| 14 EAFFIIDSDGRFAEVNR---KYVEMLGYSREELIGHTARKLVHPDDLEVLKKNFLEII--NGKATRFECRVIAKDGRVM 87
                                      566789999******99...99999*********************************..9999999999999999998 PP

                            PAS_11 82 kvk 84
                                      +v 
  gi|488601167|ref|YP_007907638.1| 88 YVE 90
                                      886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                            PAS_11  29 glekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrl.sqd 78 
                                       g+  +el+g+s  +++hp+ ++ +++ l+  i   g+ +   y+L++ ++d
  gi|488601167|ref|YP_007907638.1| 160 GYDVDELIGKSPLQFIHPEYRELVDKNLKLRI--DGKVKAINYKLQIiRKD 208
                                       67889************************999..78888888888885544 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 2.4e-07
                            PAS_11   5 ttrldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlreviss 62 
                                        ++ld +g++++v++   +    lg+++eel+g  + +L+hp+++s +++ +r+v+ +
  gi|488601167|ref|YP_007907638.1| 260 FFILDNNGRFLDVNP---KYAEMLGYSREELIGHTARKLVHPDEVSMVRENFRKVM-Q 313
                                       5789***********...9999*********************************9.3 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.55
                            PAS_11  13 kIisvDtsaLrasfslglekeelvg 37 
                                        I+++D   ++  +++ + k+e+++
  gi|488601167|ref|YP_007907638.1| 518 TILTIDGKKVSVAYKNEFLKQEWID 542
                                       699******************9986 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    0.0025         3      12     106 .]      16     113 ..       6     113 .. 0.82
   2 !   13.3   0.0     8e-05     0.095      14     105 ..     262     356 ..     251     357 .. 0.78
   3 !   10.4   0.0   0.00065      0.78      21      95 ..     391     464 ..     385     473 .. 0.89
   4 ?   -1.9   0.0       4.3   5.1e+03      36      62 ..     653     678 ..     645     688 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0025
                            PAS_10  12 ltflDdnlqirrFtpaa.kklfklipadvGrpladihpkkavknveeviealrtgekdevevvv.pkngkwvlvryl 86 
                                          +D++ ++   ++++ ++l   +++ +G +  ++++++ ++ +++ + ++++g+  + e  v +k+g++++v++ 
  gi|488601167|ref|YP_007907638.1|  16 FFIIDSDGRFAEVNRKYvEMLGYSREELIGHTARKLVHPDDLEVLKKNFLEIINGKATRFECRViAKDGRVMYVEIV 92 
                                       56689999999999986367777788889****************************999988857********998 PP

                            PAS_10  87 ..pyrdedgeiaGvvetfvDit 106
                                         p+  e++++ G+  ++ Dit
  gi|488601167|ref|YP_007907638.1|  93 ewPIF-EENRVSGAEGILRDIT 113
                                       33444.7888999888888886 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8e-05
                            PAS_10  14 flDdnlqirrFtpa.akklfklipadvGrpladihpkkavknveeviealrtgekdevevvv.pkngkwvlvryl.. 86 
                                        lD+n +++  +p+ a++l   +++ +G +  +++++++v+ v+e + ++ +g++++ e +  +k+g+ +++++   
  gi|488601167|ref|YP_007907638.1| 262 ILDNNGRFLDVNPKyAEMLGYSREELIGHTARKLVHPDEVSMVRENFRKVMQGKTVRYEAKAiAKDGREYVMEVIlw 338
                                       58***********83567777778889****************************7666555378888777665322 PP

                            PAS_10  87 pyrdedgeiaGvvetfvDi 105
                                       p+  e+g++ G+  ++ Di
  gi|488601167|ref|YP_007907638.1| 339 PVF-ENGRVVGAEGILRDI 356
                                       554.788888877777776 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00065
                            PAS_10  21 irrFtpaakklfklipadvGrpladihpkkavknveeviealrtgekdevevvvpkngkwvlvrylpyrdedgei 95 
                                       + +   + +++ +l  + +G +l+++ p++  +++ + i+++ +++k   ++  ++ng++++ +  p+   dg++
  gi|488601167|ref|YP_007907638.1| 391 FAFIEANPAMVKNLGTNPIGKRLSEVLPENVANRMMKYIKRMFKRNKP-LKFRDESNGRYFINTLVPIDLPDGKY 464
                                       55566678999*****************************99988876.678999*************9999988 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.3
                            PAS_10  36 padvGrpladihpkkavknveevieal 62 
                                       + ++ ++la+i++++ ++++ +++e+l
  gi|488601167|ref|YP_007907638.1| 653 EMEMDDKLAKIVTEQ-IDRILKIVEKL 678
                                       556667777775543.34444455555 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0016       1.9      51     128 ..      25     100 ..      17     110 .. 0.81
   2 ?    3.6   0.0     0.047        57      37      90 ..     134     187 ..     108     232 .. 0.80
   3 !   14.2   0.0   2.6e-05     0.031      59     128 ..     277     344 ..     256     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                            MEKHLA  51 fnyaNqaaldllettweeltdlpsrksaepee.keeRealLekvaeqgfvenysGvrisstGrrfsienavvWkvld 126
                                       f   N++  ++l ++ eel+  + rk ++p++ +   ++ + ++  +g ++ ++   i+++Gr +++ + v W +++
  gi|488601167|ref|YP_007907638.1|  25 FAEVNRKYVEMLGYSREELIGHTARKLVHPDDlEVL-KKNFLEII-NGKATRFECRVIAKDGR-VMYVEIVEWPIFE 98 
                                       555699999**********************95555.55555554.588899**********7.6677789999998 PP

                            MEKHLA 127 ee 128
                                       e+
  gi|488601167|ref|YP_007907638.1|  99 EN 100
                                       87 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.047
                            MEKHLA  37 pfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealL 90 
                                       ++ ++   l +d vf y N +  +l+ ++++el+  +  + ++pe +e  ++ L
  gi|488601167|ref|YP_007907638.1| 134 EKSLVGIYLIQDGVFKYVNPKLAELWGYDVDELIGKSPLQFIHPEYRELVDKNL 187
                                       5566666677899*******************9987766666666666655555 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.6e-05
                            MEKHLA  59 ldllettweeltdlpsrksaepeekeeRealLekvaeqgfvenysGvrisstGrrfsienavvWkvldee 128
                                        ++l ++ eel+  + rk ++p+e +  ++ ++kv++      y++  i+++Gr++ + ++++W v+++ 
  gi|488601167|ref|YP_007907638.1| 277 AEMLGYSREELIGHTARKLVHPDEVSMVRENFRKVMQGKT-VRYEAKAIAKDGREYVM-EVILWPVFENG 344
                                       589*********************888899*****97665.56***********9876.5899*999764 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 !   27.5   0.0     2e-09   2.3e-06       5      66 ..     633     685 ..     629     686 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   5 flagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                        +a +  ++r+PLs+i+g ae+        e+  ++ +++ ++++r++++ve l d +++e+
  gi|488601167|ref|YP_007907638.1| 633 QFAILVDQIRNPLSVIYGLAEM--------EMDDKLAKIVTEQIDRILKIVEKL-DRGWLES 685
                                       6899999***************........45578999***************8.8888876 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.1e-05     0.073       3      44 ..      11      51 ..       9     119 .. 0.88
   2 ?   -2.7   0.0       5.5   6.6e+03      83     112 ..     209     241 ..     181     243 .. 0.66
   3 !    7.3   0.0    0.0041       4.9       8      45 ..     260     296 ..     254     351 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                             PAS_7  3 nmsqGisvfDadlrLvawNrrylelldlpeelvqvgvpleel 44
                                      + ++++ ++D+d+r   +Nr+y+e+l++++e + +g + ++l
  gi|488601167|ref|YP_007907638.1| 11 KSEEAFFIIDSDGRFAEVNRKYVEMLGYSREEL-IGHTARKL 51
                                      5578899*********************99877.66666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.5
                             PAS_7  83 pdgrvievrgnplpdgG...fVttytDiTerrr 112
                                        + r+ ev g+++  gG   ++ t  DiTe+ r
  gi|488601167|ref|YP_007907638.1| 209 GEVRTNEVFGSRVTYGGrpaIIGTLIDITESER 241
                                       333556777777777764445778888888765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0041
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleell 45 
                                       + ++D+++r + +N +y e+l++++e + +g + ++l+
  gi|488601167|ref|YP_007907638.1| 260 FFILDNNGRFLDVNPKYAEMLGYSREEL-IGHTARKLV 296
                                       6799********************9988.777777666 PP

>> PAS_2  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0018       2.1      35      67 ..      32      64 ..      18      90 .. 0.84
   2 !    9.0   0.0    0.0018       2.2      33      69 ..     274     310 ..     259     333 .. 0.84
   3 ?   -0.7   0.0         2   2.3e+03      18      70 ..     383     432 ..     370     457 .. 0.63
   4 ?   -1.4   0.0       3.1   3.7e+03      59      95 ..     603     640 ..     580     647 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                                      HHHHCSS-CCCCTTTCCCCCSECTTHHHHCCHS CS
                             PAS_2 35 aaemLglteekllgtdlralltassaalLekal 67
                                        emLg + e+l+g ++r+l+++  ++ L+k +
  gi|488601167|ref|YP_007907638.1| 32 YVEMLGYSREELIGHTARKLVHPDDLEVLKKNF 64
                                      679**************************9976 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                                       TTHHHHCSS-CCCCTTTCCCCCSECTTHHHHCCHS-C CS
                             PAS_2  33 eNaaemLglteekllgtdlralltassaalLekalsa 69 
                                          aemLg + e+l+g ++r+l+++ +++ +++ +++
  gi|488601167|ref|YP_007907638.1| 274 PKYAEMLGYSREELIGHTARKLVHPDEVSMVRENFRK 310
                                       55789***********************999988765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2
                                       EEEEETTTTEEEEEETTHHHHCSS-CCCCTTTCCCCCSECTTHHHHCCHS-CC CS
                             PAS_2  18 llavdekslrvlqvSeNaaemLglteekllgtdlralltassaalLekalsar 70 
                                       l+a+ ++++  +++   + + Lg   ++ +g+ l+++l ++ a  + k +++ 
  gi|488601167|ref|YP_007907638.1| 383 LIAIINRDFAFIEANPAMVKNLG---TNPIGKRLSEVLPENVANRMMKYIKRM 432
                                       44444444444444444444444...456999999999998888887776654 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.1
                                       THHHHCCHS-CCCHCCCCCEEEE.EEECCCEEEEEEEE CS
                             PAS_2  59 saalLekalsareisllnpilih.srtsgkpfyailhr 95 
                                        a+ L +al+a+e++ l++  +  + ++ ++f +++ +
  gi|488601167|ref|YP_007907638.1| 603 LASNLASALKATELERLKRKALIqIDRNIEQFAILVDQ 640
                                       36678888888888777654433266677777766655 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.5   8.9e+03      15      48 ..     132     168 ..     128     172 .. 0.70
   2 ?   -2.2   0.0       3.9   4.7e+03      94     106 ..     336     348 ..     262     349 .. 0.80
   3 !   19.2   0.0   9.8e-07    0.0012       3     137 ..     497     611 ..     495     612 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.5
                                       HHHSS..EEEEEEE-TTS-EEEE......EEEES-TTSTT CS
                             GAF_2  15 lvelgaalgyillvdddgglrla......awgeaeeefga 48 
                                       l+e  + +g++l+ d  g ++++       wg++ +e+ +
  gi|488601167|ref|YP_007907638.1| 132 LAE-KSLVGIYLIQD--GVFKYVnpklaeLWGYDVDELIG 168
                                       444.46688888866..87777777777899999888765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                       EEEEE-TTS---E CS
                             GAF_2  94 lavPlisegrvvG 106
                                       +  P++++grvvG
  gi|488601167|ref|YP_007907638.1| 336 ILWPVFENGRVVG 348
                                       6779999999998 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 9.8e-07
                                       HHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG-S CS
                             GAF_2   3 dleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleedp 78 
                                       +++ +l+ +++el  l g+++  il +d+++     + ++  e++ ++  +     +vge+lr +r++    + +  
  gi|488601167|ref|YP_007907638.1| 497 TEQNILRKACEELNSLeGFSA-TILTIDGKKV----SVAYKNEFLKQEWID----EIVGESLRYRRAIR-KMFTD-- 561
                                       678899999999999988663.6666674443....444444555444423....35777777766555.12222.. PP

                                       -HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  79 dkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                               + +   +l++P+i e +v G ++l +++++ +++++  l+++la+ +a a+
  gi|488601167|ref|YP_007907638.1| 562 -------HEGKKIKILSFPMIVEREVKGLIVL-HTNRY-LSRDEFKLINTLASNLASAL 611
                                       .......23444457*******99*******9.55555.7*****************98 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.3e-06     0.011      80     127 ..     566     611 ..     497     613 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.3e-06
                             GAF_3  80 draalavPLvagrqviGvlalastkprafdaedlelleslArqiatai 127
                                       + ++l  P++++r+v G+++l++++  ++++++  l+++lA+ +a+a+
  gi|488601167|ref|YP_007907638.1| 566 KIKILSFPMIVEREVKGLIVLHTNR--YLSRDEFKLINTLASNLASAL 611
                                       578999*****************87..78******************8 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.3e-05     0.051      81     133 .]     559     611 ..     539     611 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                                       HHHHTTES.EEEEEEEEETTEEEEEEEEEESSSCSHHHHHHHHHHHHHHHHHHH CS
                               GAF  81 llenmgir.sslvvPlvndgelwGllvlhnpsppftreelellqvladqvaval 133
                                       + ++ g +   l+ P+++++e+ Gl+vlh  +   +r+e  l+ +la+ +a al
  gi|488601167|ref|YP_007907638.1| 559 FTDHEGKKiKILSFPMIVEREVKGLIVLHTNRY-LSRDEFKLINTLASNLASAL 611
                                       455555556799******************888.8**************99986 PP

>> DUF3369  Domain of unknown function (DUF3369)
   #    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      68      94 ..      11      37 ..       4      53 .. 0.72
   2 ?   -2.0   0.0         3   3.6e+03      84     118 ..     286     324 ..     283     332 .. 0.74
   3 ?    8.1   0.1    0.0024       2.9      99     161 ..     552     613 ..     499     618 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                           DUF3369 68 aaskelkvlaatgkfesligkpleela 94
                                      ++++ + ++ + g+f++ ++k +e l+
  gi|488601167|ref|YP_007907638.1| 11 KSEEAFFIIDSDGRFAEVNRKYVEMLG 37
                                      344449***********9999887764 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                           DUF3369  84 sligkpleela.deel...relleraleskkslfeddfv 118
                                       +lig+   +l  ++e+   re+++++++ k+  +e +++
  gi|488601167|ref|YP_007907638.1| 286 ELIGHTARKLVhPDEVsmvRENFRKVMQGKTVRYEAKAI 324
                                       566666666555555566699**********99998765 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0024
                           DUF3369  99 relleraleskkslfeddfvvlyfktkegsegvlylettrplseldrkLlevFannvavafeN 161
                                       r+++++++++++    +  +   +  +++ +g+++l+t+r ls ++ kL++ +a+n+a a++ 
  gi|488601167|ref|YP_007907638.1| 552 RRAIRKMFTDHEGKKIKILSF-PMIVEREVKGLIVLHTNRYLSRDEFKLINTLASNLASALKA 613
                                       556666666655554433333.444556799****************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); 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:                        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: 0.76u 0.35s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 3811.13
//
Query:       gi|488601168|ref|YP_007907639.1|  [L=272]
Description: fumarase, class I alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-94  314.2   0.1    8.5e-94  314.0   0.1    1.0  1  Fumerase  Fumarate hydratase (Fumerase)
  ------ inclusion threshold ------
      0.037   14.5   0.1        5.3    7.6   0.0    2.6  2  PP2C_C    Protein serine/threonine phosphatase 2C, C-terminal


Domain annotation for each model (and alignments):
>> Fumerase  Fumarate hydratase (Fumerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.0   0.1   9.4e-98   8.5e-94       2     267 ..       8     267 ..       7     269 .. 0.97

  Alignments for each domain:
  == domain 1  score: 314.0 bits;  conditional E-value: 9.4e-98
                          Fumerase   2 eaveealkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeevevetg 78 
                                       eav+e++ +a+t l edv+e ++ka+ekE++e+a++ l+++l+N++ A++ k+p+CqDTGi++vf+++g+e+  ++ 
  gi|488601168|ref|YP_007907639.1|   8 EAVYELFLKAETDLGEDVVEVIRKAYEKETNETARNNLSAILRNIDSARKLKVPMCQDTGIPIVFAEVGRELC-IDF 83 
                                       7899********************************************************************6.999 PP

                          Fumerase  79 dleeaineGvreaykegplRksvvadplerkntgd....nlPavihielvpgdeleitvlakGgGsenksklkmlnp 151
                                       dl++ai +Gv++a++e p+R+++v +pl+r+n g+    ++P +i+i+lv+gd+l++ v++kG+Gsen s+l+ml p
  gi|488601168|ref|YP_007907639.1|  84 DLKQAIIDGVKKATSEIPMRPNAV-HPLSRENPGNnvgfHVP-QINIDLVDGDTLKLAVMPKGAGSENVSALRMLLP 158
                                       ************************.**********999999*.********************************** PP

                          Fumerase 152 sdglegvkkfvletvkeagtnaCpPlvlgvgiGgtseeaallakkallrelgeenpdeelaeleeellekinklgiG 228
                                       s+ ++++ kf+++ vk+a +++CpP++lgvgiG t++ +a+lakkallr+ ++      ++++e++++e++n+lgiG
  gi|488601168|ref|YP_007907639.1| 159 SQ-IKEIPKFIIDVVKNAMGKPCPPVFLGVGIGSTFDGCAKLAKKALLRDARK------MTDVEQKITEMANRLGIG 228
                                       87.********************************************998743......679*************** PP

                          Fumerase 229 pqGlGGkttvldvkierlprhiAslpvavnvsCsadRra 267
                                       p+GlGG+ttvl+++ie +++h+Aslpvavnv+C+a+Rra
  gi|488601168|ref|YP_007907639.1| 229 PMGLGGDTTVLGTFIEIGYCHTASLPVAVNVQCWANRRA 267
                                       *************************************98 PP

>> PP2C_C  Protein serine/threonine phosphatase 2C, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1    0.0075        67      18      59 ..      15      57 ..       8      64 .. 0.77
   2 ?    7.6   0.0   0.00059       5.3       6      37 ..     192     223 ..     191     228 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0075
                            PP2C_C 18 vkkEkeldekleervkeiie.keekkeeldlekvlkvLasedi 59
                                      +k+E++l e + e ++ ++e +++++ + +l+ +l+++ s++ 
  gi|488601168|ref|YP_007907639.1| 15 LKAETDLGEDVVEVIRKAYEkETNETARNNLSAILRNIDSARK 57
                                      5778888888888888888877788888899999999887655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00059
                            PP2C_C   6 afpgaPkvseeavkkEkeldekleervkeiie 37 
                                       +f+g+ k+ ++a+ ++++  + +e++++e+ +
  gi|488601168|ref|YP_007907639.1| 192 TFDGCAKLAKKALLRDARKMTDVEQKITEMAN 223
                                       7****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1659.52
//
Query:       gi|488601169|ref|YP_007907640.1|  [L=202]
Description: fumarase, class I beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-48  162.9   0.2    7.3e-48  162.6   0.2    1.1  1  Fumerase_C  Fumarase C-terminus
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.23   11.4   0.0    1.4  1  SH3_9       Variant SH3 domain


Domain annotation for each model (and alignments):
>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.2   8.1e-52   7.3e-48      34     205 ..       7     179 ..       2     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 8.1e-52
                        Fumerase_C  34 qketeeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPv..ktpedeavgsaGPT 108
                                       +++ ++e+ k+++g+ + +sG++++aRD aH r  e +++g+elp  v++++ v+Y++GP   k  ++++  saGPT
  gi|488601169|ref|YP_007907640.1|   7 TPIKKDEILKLRAGDIVYVSGEIFTARDEAHMRAIEYMDEGKELP--VNFDGAVVYHCGPLmkKVGGEWKAVSAGPT 81 
                                       5677899**************************************..8888*********975556788999***** PP

                        Fumerase_C 109 TatRmdkyvekllkktgllimlaKgnrskkvleaikkhggvYLgaiGGaAilakkaikkvevvefeelGm.EAiyei 184
                                       T+ Rm++ + k+l+k  ++++++Kg++s++v++a+k  +gvY+   GGa  la++aikkv+ v + +lGm EA++ +
  gi|488601169|ref|YP_007907640.1|  82 TSARMNSLAPKILEKVEVMGIIGKGGMSSEVVNALK-GKGVYFAYTGGAGALASHAIKKVKGVYWDDLGMpEAVWVF 157
                                       **********************************97.589************************************* PP

                        Fumerase_C 185 evedf.pafvvvddkGndlfke 205
                                       eve+f p +v +d++Gn+l+++
  gi|488601169|ref|YP_007907640.1| 158 EVENFgPLIVGIDSHGNSLYAR 179
                                       *****778888*********86 PP

>> SH3_9  Variant SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.5e-05      0.23       9      26 ..      10      28 ..       7      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.5e-05
                             SH3_9  9 edde.LsLqrGDvitviee 26
                                      ++de L L++GD+++v++e
  gi|488601169|ref|YP_007907640.1| 10 KKDEiLKLRAGDIVYVSGE 28
                                      57777***********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1295.16
//
Query:       gi|488601170|ref|YP_007907641.1|  [L=533]
Description: Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-85  284.7   0.2    1.2e-84  284.4   0.2    1.1  1  AMP-binding    AMP-binding enzyme
    2.6e-20   73.2   0.0    7.2e-20   71.7   0.0    1.8  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.4   0.2   1.4e-88   1.2e-84       7     422 ..      20     434 ..      14     435 .. 0.87

  Alignments for each domain:
  == domain 1  score: 284.4 bits;  conditional E-value: 1.4e-88
                                       HSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                       AMP-binding   7 ktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                         p++  +++  + +++ Y++++erv++lA++L+slGvk+g++Va+l + s++++  ++ai ++Gav+ ++n +l++
  gi|488601170|ref|YP_007907641.1|  20 YAPNQEIVYR--DLHRYKYKDMYERVKKLANVLESLGVKEGTKVAVLDWDSHRYLECYYAIPMVGAVLHTVNVRLSP 94 
                                       5577777766..8999************************************************************* PP

                                       HHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS..-TSCCCS-BT CS
                       AMP-binding  84 eelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae..kpeeeeelkp 158
                                       e++ y ++++e +v++  v ++ l+ ++ +++kl++vk+ +v+ +d++++++  + e es  k +   + + +  ++
  gi|488601170|ref|YP_007907641.1|  95 EDILYTMQHAEDEVVF--VFKDFLPLIETIKDKLDTVKHYVVMTDDGMPETSLTDMEYESLLK-DadSNYDFPDFDE 168
                                       ****************..766678889999999*************99988544433333322.13445577889** PP

                                       TSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH...HHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                       AMP-binding 159 ddlayiiYTSGTTGkPKGVmlshrnlvanvaslk...letr..fklkeddvvlsilplahifglilelllallsGat 230
                                       +++a++ YT GTTG+PKGV  +hr+lv  + +++   l +    +l++++v++   p++h+ ++    +++ + G +
  gi|488601170|ref|YP_007907641.1| 169 NTMATMAYTTGTTGRPKGVWFTHRQLVLHTLAVAvsvLGRSsaIRLSDREVYMPLTPMFHVHAW-GIPYVSTMLGYK 244
                                       *************************9777666664553333445566799**************.************ PP

                                       EEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHH CS
                       AMP-binding 231 vvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffral 306
                                        v++ + +   p+++++li  ++vt+ ++vP++l+++++  ++        +++ +++v lgg++l + l+ ++r++
  gi|488601170|ref|YP_007907641.1| 245 QVYPGRYE---PQMIAKLIFSERVTFSHCVPTILQMIVDnLPEGV------KFNNWKVV-LGGSKLTKGLALRAREK 311
                                       ***88665...567899**********************554333......7899**96.7**************** PP

                                       HTCEEEEEEEEGGGSSECEE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEEEET CS
                       AMP-binding 307 fgeevlegYGlTEttgvvtv.........lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.Gellvrgp 372
                                       ++   + gYG++Et++v+t          l +ee+ ++  ++G+p+p v +++v+e+ +e v+ dg+e Ge++ r p
  gi|488601170|ref|YP_007907641.1| 312 GII-TMAGYGMSETCPVLTLgflrpevrdLSEEEQIEYMIKTGFPIPLVYIRVVNEN-MEDVKnDGKEmGEIVARAP 386
                                       998.89************999999***99787888888899***************9.66665388889******** PP

                                       TS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 373 gvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       ++++ Ylk++e+t+e +   g+wl+TGD++++de Gy+ iv+R+kd++k+
  gi|488601170|ref|YP_007907641.1| 387 WLTQSYLKNEEKTKELWE--GGWLHTGDIAVVDELGYITIVDRLKDVVKS 434
                                       ***************986..67**************************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 !   71.7   0.0   8.1e-24   7.2e-20       2      76 .]     444     522 ..     443     522 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 8.1e-24
                                       HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHH.....HT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrk.....elgpyavpkkvvfvdelpktr 73 
                                       +E+ l+ hp+V+e+aV+G+pde++Ge+++a++++  g+++++eeLk+++ k     ++ ++avp++ +fvde+pkt 
  gi|488601170|ref|YP_007907641.1| 444 LENLLSMHPKVREVAVIGIPDEKWGERPLAIITPM-GEKPTPEELKEFLMKfveegKITKWAVPDRYEFVDEIPKTS 519
                                       79********************************6.75567788888884444445********************* PP

                                       TS- CS
                     AMP-binding_C  74 sGK 76 
                                        GK
  gi|488601170|ref|YP_007907641.1| 520 VGK 522
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3396.36
//
Query:       gi|488601171|ref|YP_007907642.1|  [L=95]
Description: hypothetical protein Asulf_01676 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   0.0        0.2   11.6   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 ?   11.6   0.0   1.1e-05       0.2      19      66 ..      37      86 ..      27      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                               VHL 19 prvvkplWidfeGePqsYeelk..PgtgrrmttyvgHpWlFRDAetddpl 66
                                      +++v  ++++ +G+ + Y+++   P+t  ++  y     lF DA + d l
  gi|488601171|ref|YP_007907642.1| 37 TYIVLEVYLQNNGNKTIYQRMTslPQTVMKILCYDHMIHLFEDAYQIDDL 86
                                      578999**************97669999****************987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 715.57
//
Query:       gi|488601172|ref|YP_007907643.1|  [L=51]
Description: hypothetical protein Asulf_01678 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 375.09
//
Query:       gi|488601173|ref|YP_007907644.1|  [L=156]
Description: putative nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-20   72.3   0.2    5.6e-20   71.6   0.2    1.3  1  PIN_6           PIN domain of ribonuclease
     0.0014   19.0   1.0     0.0067   16.7   1.0    1.9  1  PIN_4           PIN domain
     0.0023   18.7   0.6     0.0028   18.4   0.6    1.5  1  zinc_ribbon_15  zinc-ribbon family
     0.0077   16.4   0.6      0.015   15.4   0.6    1.5  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
     0.0079   15.6   0.7      0.023   14.1   0.2    1.9  2  PIN_5           PINc domain ribonuclease
  ------ inclusion threshold ------
      0.036   14.1   0.1      0.092   12.8   0.1    1.7  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.042   13.6   0.8      0.067   12.9   0.8    1.3  1  zinc_ribbon_2   zinc-ribbon domain
      0.058   13.4   1.6       0.14   12.2   1.6    1.7  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.067   13.1   0.1       0.29   11.0   0.1    2.1  2  Rad50_zn_hook   Rad50 zinc hook motif
      0.073   13.1   0.1        0.1   12.6   0.1    1.2  1  DZR             Double zinc ribbon
      0.081   12.9   1.0       0.14   12.1   1.0    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
        0.3   11.2   2.1       0.45   10.7   2.1    1.3  1  UPF0547         Uncharacterised protein family UPF0547


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 !   71.6   0.2   3.8e-23   5.6e-20       2      89 .]       5      85 ..       4      85 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 3.8e-23
                             PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDi 80
                                      V+D++a+i +     + + +k++t+peVv+E++d+++ + l++   +lev eP+++++k ++++a+ktGD+  LS+tDi
  gi|488601173|ref|YP_007907644.1|  5 VIDTSAIIFK-----KGFYKKMVTVPEVVEEVKDSNSSSYLSI--IDLEVIEPDRKYIKNIERVARKTGDIYRLSETDI 76
                                      99******88.....899************************9..69******************************** PP

                             PIN_6 81 evlALtyeL 89
                                      ++lAL+ eL
  gi|488601173|ref|YP_007907644.1| 77 KLLALASEL 85
                                      ******987 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.0   4.5e-06    0.0067       1     129 [.       4     113 ..       4     114 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                             PIN_4   1 fVlDTnvlLhdpealksfkeehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsaeel 77 
                                       +V+DT+ ++ +  + k++     v +P + +eE+   K ++s    ++l    +++++   +  +   +v +++ ++
  gi|488601173|ref|YP_007907644.1|   4 YVIDTSAIIFKKGFYKKM-----VTVPEV-VEEV---KDSNS---SSYLSIIDLEVIEPDRKYIKNIERVARKTGDI 68 
                                       677777777666555555.....777754.4666...44444...33343344455555554445555555556566 PP

                             PIN_4  78 peeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgieaed 129
                                        +     +++D + la a el+e++   +vvLv++D   ++ A+  g+++ +
  gi|488601173|ref|YP_007907644.1|  69 YR----LSETDIKLLALASELSEKE---EVVLVTDDYSIQNVARKIGFKTDS 113
                                       65....3489*************97...9******************99875 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.6   1.9e-06    0.0028      64      86 .]     116     147 ..      33     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                    zinc_ribbon_15  64 e.........kkeCknCgkeveeefkyCpkCg 86 
                                       +         +++C+ C+++++++++ Cp Cg
  gi|488601173|ref|YP_007907644.1| 116 QkgisseykwVRKCRGCKRVIKDDVDRCPVCG 147
                                       03333346679********************9 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 !   15.4   0.6     1e-05     0.015       5      32 ..     123     149 ..     119     156 .] 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                      NOB1_Zn_bind   5 kswvlrChaCfkvtkdmtkkFCpkCGnk 32 
                                        +wv +C++C +v+kd     Cp CG++
  gi|488601173|ref|YP_007907644.1| 123 YKWVRKCRGCKRVIKDDVD-RCPVCGSE 149
                                       68************99544.4*****95 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.35   5.3e+02       2      13 ..       4      15 ..       3      49 .. 0.69
   2 !   14.1   0.2   1.6e-05     0.023     156     190 ..      72     110 ..      29     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.35
                             PIN_5  2 fvlDTsaltdpe 13
                                      +v+DTsa++ ++
  gi|488601173|ref|YP_007907644.1|  4 YVIDTSAIIFKK 15
                                      899999987544 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.6e-05
                             PIN_5 156 saeDldvllLAkEL....daavvssDeGikkwaeklGlr 190
                                       s+ D+ +l LA EL    + ++v++D  i+++a+k+G +
  gi|488601173|ref|YP_007907644.1|  72 SETDIKLLALASELsekeEVVLVTDDYSIQNVARKIGFK 110
                                       899***********54444689***************87 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.1e-05     0.092       1       9 [.     142     150 ..     142     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                    DNA_ligase_ZBD   1 hCPvCGsav 9  
                                       +CPvCGs++
  gi|488601173|ref|YP_007907644.1| 142 RCPVCGSEL 150
                                       5******98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   4.5e-05     0.067       1      23 []     128     150 ..     128     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-05
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                       +C  C + ++d++  Cp CG++l
  gi|488601173|ref|YP_007907644.1| 128 KCRGCKRVIKDDVDRCPVCGSEL 150
                                       7999****************997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.6   9.2e-05      0.14      63      95 ..     101     149 ..      39     155 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-05
                                       E..................EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  63 e..................ieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                       +                   +e + + +Cr C++ ++ + +  rCp Cgs+
  gi|488601173|ref|YP_007907644.1| 101 QnvarkigfktdsiiqkgiSSEYKWVRKCRGCKRVIKDDVD--RCPVCGSE 149
                                       2444444455555555554456677889*****99997766..9*****96 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.3   6.5e+03      34      48 ..     100     114 ..      96     116 .. 0.76
   2 ?   11.0   0.1   0.00019      0.29      17      29 ..     138     150 ..     134     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.3
                                       HHHHHHHHHHHHHHH CS
                     Rad50_zn_hook  34 rseLikelqsklerl 48 
                                        +++++++  k++++
  gi|488601173|ref|YP_007907644.1| 100 IQNVARKIGFKTDSI 114
                                       688889998888875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00019
                                       T-SEE-TTT--EE CS
                     Rad50_zn_hook  17 eakgcCPlCgRel 29 
                                       +  ++CP+Cg+el
  gi|488601173|ref|YP_007907644.1| 138 DDVDRCPVCGSEL 150
                                       45569******98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.8e-05       0.1       1      20 [.     129     148 ..     102     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.8e-05
                               DZR   1 CpqCgeelppdarfCseCgt 20 
                                       C  C++ +++d   C+ Cg+
  gi|488601173|ref|YP_007907644.1| 129 CRGCKRVIKDDVDRCPVCGS 148
                                       55555555555555555555 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   9.3e-05      0.14       5      28 ..     127     148 ..     123     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-05
                       Prok-RING_1   5 kkCpvCgkelkeedDiVvCpeCgt 28 
                                        kC  C++ +k++  +  Cp+Cg+
  gi|488601173|ref|YP_007907644.1| 127 RKCRGCKRVIKDD--VDRCPVCGS 148
                                       59********866..779****96 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.1    0.0003      0.45       1      21 [.     127     147 ..     127     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                           UPF0547   1 KvCPeCeakvPvaaqfCphCG 21 
                                       ++C +C + ++ ++ +Cp CG
  gi|488601173|ref|YP_007907644.1| 127 RKCRGCKRVIKDDVDRCPVCG 147
                                       59******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1028.52
//
Query:       gi|488601174|ref|YP_007907645.1|  [L=403]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-31  108.6   0.1    1.1e-15   57.6   0.0    2.5  2  PAS_3            PAS fold
    2.1e-30  105.0   0.0    2.2e-15   56.6   0.0    2.3  2  PAS              PAS fold
      2e-29  101.9   0.3      1e-14   54.7   0.1    2.6  2  PAS_9            PAS domain
      1e-25   90.1   0.0    1.4e-14   54.3   0.0    2.3  2  PAS_4            PAS fold
    1.5e-18   66.3   0.0    1.8e-09   37.4   0.0    2.7  2  PAS_8            PAS domain
    5.5e-10   39.4   0.0    0.00092   19.3   0.0    2.3  2  PAS_11           PAS domain
    5.8e-08   32.7   1.2    2.7e-07   30.5   0.0    2.6  3  HisKA            His Kinase A (phospho-acceptor) domain
    0.00043   20.2   0.0          1    9.2   0.0    2.8  3  MEKHLA           MEKHLA domain
  ------ inclusion threshold ------
      0.038   13.6   0.0       0.97    9.1   0.0    2.3  2  PAS_12           UPF0242 C-terminal PAS-like domain
      0.041   14.5   0.0       0.71   10.5   0.0    2.9  3  PAS_10           PAS domain
       0.15   11.3   0.0        0.3   10.3   0.0    1.4  1  Chordopox_A33R   Chordopoxvirus A33R protein
       0.33   11.7   5.7         16    6.2   0.0    3.7  3  Vir_act_alpha_C  Virulence activator alpha C-term


Domain annotation for each model (and alignments):
>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   7.6e-19   1.1e-15       2      85 ..      76     156 ..      75     159 .. 0.94
   2 !   48.6   0.0     5e-16   7.5e-13       3      88 ..     204     286 ..     202     287 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 7.6e-19
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       i v++++ e+lGy peel+g+  + + + hpeD+e ++e ++++lk+++    e+R + kdG ++w+e    +++d 
  gi|488601174|ref|YP_007907645.1|  76 IDVNPKFAEMLGYAPEELIGH--TSKRITHPEDLEGLKELFKRVLKGNT-GRYEFRGVSKDGRIIWFEVIEWPVFDG 149
                                       899******************..**********************8888.456************************ PP

                             PAS_3  79 ngkpvrv 85 
                                       +g++ +v
  gi|488601174|ref|YP_007907645.1| 150 EGEVKEV 156
                                       **99876 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 5e-16
                             PAS_3   3 yvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwveararvirde 78 
                                       yv++++ ei+Gy+ +el+g+  s l+++hp+D e vr++l++ +++   +++   R++rkdGe r+ e  ++ i   
  gi|488601174|ref|YP_007907645.1| 204 YVNPKMAEIWGYETDELIGR--SPLEFIHPDDKETVRKNLERRIAGEIeSINYCLRMIRKDGEKRYNEVFGSRI-VY 277
                                       9*******************..**********************9999899999***********999999988.88 PP

                             PAS_3  79 ngkpvrvigv 88 
                                       +gkp  +ig+
  gi|488601174|ref|YP_007907645.1| 278 KGKPA-IIGT 286
                                       88887.6665 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   1.5e-18   2.2e-15       2     105 ..      54     155 ..      53     166 .. 0.80
   2 !   46.4   0.0   2.3e-15   3.4e-12       1     113 []     181     290 ..     181     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.5e-18
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       +++++ e+++d  f++D++gr++ vN++++e+lG+++ee++g +  +  h+e d e  ++l ++ + g+ +r     
  gi|488601174|ref|YP_007907645.1|  54 RYERFYENARDIFFILDKNGRFIDVNPKFAEMLGYAPEELIGHTSKRITHPE-DLEGLKELFKRVLKGNTGRY---E 126
                                       89****************************************9988655555.44455555555555544444...3 PP

                                       EEC..TTSSEEEEEEEEEEEEETTEEEEE CS
                               PAS  79 fkl..rdgrpihlevraspvrdaggeilg 105
                                       f+   +dgr+i++ev   pv+d++ge+++
  gi|488601174|ref|YP_007907645.1| 127 FRGvsKDGRIIWFEVIEWPVFDGEGEVKE 155
                                       444446*******************9875 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 2.3e-15
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r++ e + ++i ++  dg++ yvN++++e+ G++ +e++g+s l++ih++d +++++ le++++   es +++ 
  gi|488601174|ref|YP_007907645.1| 181 EMFRTLAEKSLVGIYLI-QDGVFKYVNPKMAEIWGYETDELIGRSPLEFIHPDDKETVRKNLERRIAGEIESINYCL 256
                                       57889999999999999.9**********************************988999999999998888888888 PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +  ++dg++++ ev  s ++ +g+    ++g+l di
  gi|488601174|ref|YP_007907645.1| 257 RMIRKDGEKRYNEVFGSRIVYKGKP--AIIGTLIDI 290
                                       8888******************987..9*****998 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   6.7e-18     1e-14       2     104 .]      64     168 ..      63     168 .. 0.95
   2 !   44.9   0.0   7.3e-15   1.1e-11       3     104 .]     193     292 ..     191     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 6.7e-18
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfw 77 
                                       d ++i +++gr +++N++++++lGy pee++g+  + +   +pe+ e l++++++  k +  ++e   + k+g+ +w
  gi|488601174|ref|YP_007907645.1|  64 DIFFILDKNGRFIDVNPKFAEMLGYAPEELIGHTSKRIT--HPEDLEGLKELFKRVLKgNTGRYEFRGVSKDGRIIW 138
                                       6799999***************************99999..999999999999999999****************** PP

                             PAS_9  78 vlltaspvkdddgelvg...iivilrDite 104
                                       +++   pv+d++ge++    i +i+rDite
  gi|488601174|ref|YP_007907645.1| 139 FEVIEWPVFDGEGEVKEvkeIEGIVRDITE 168
                                       *****************77666*******8 PP

  == domain 2  score: 44.9 bits;  conditional E-value: 7.3e-15
                             PAS_9   3 gilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirknget 75 
                                       gi ++  dg +  y+N++++++ Gy  +e++g+s  +++  +p+++e++r+ le+      +  ++ + +irk+ge+
  gi|488601174|ref|YP_007907645.1| 193 GIYLI-QDG-VFkYVNPKMAEIWGYETDELIGRSPLEFI--HPDDKETVRKNLERRIAgeiESINYCLRMIRKDGEK 265
                                       67766.89*.999**************************..555555555555555555999*************** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                        ++++  s++  +++  +   ++l+Dite
  gi|488601174|ref|YP_007907645.1| 266 RYNEVFGSRIVYKGKPAII--GTLIDITE 292
                                       **********988766666..*******8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   9.3e-18   1.4e-14       2     109 ..      60     170 ..      59     171 .. 0.92
   2 !   33.7   0.0   2.4e-11   3.5e-08      13     108 ..     198     293 ..     192     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 9.3e-18
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgee 78 
                                       ++  d++++ld++gr++++N+ +ae++g++peel+G+t   +  +ed ++l +  +rvl+g++  ++   +  +g+ 
  gi|488601174|ref|YP_007907645.1|  60 ENARDIFFILDKNGRFIDVNPKFAEMLGYAPEELIGHTSKRITHPEDLEGLKELFKRVLKGNTGRYEFRGVSKDGRI 136
                                       78899*************************************************************9999999**** PP

                             PAS_4  79 rhyelrllPlrdesGevigv...lvisrDiTerr 109
                                        ++e+   P++d +Gev  v    +i+rDiTer+
  gi|488601174|ref|YP_007907645.1| 137 IWFEVIEWPVFDGEGEVKEVkeiEGIVRDITERK 170
                                       ***************97665111679******98 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 2.4e-11
                             PAS_4  13 pdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlege.epiefleelll.pgeerhyelrllP 87 
                                        dg++ y+N+ +ae+ g++ +el+G+++ e+  ++d++ ++ +l+r ++ge e+i  +  + + +ge r+ e++ ++
  gi|488601174|ref|YP_007907645.1| 198 QDGVFKYVNPKMAEIWGYETDELIGRSPLEFIHPDDKETVRKNLERRIAGEiESINYCLRMIRkDGEKRYNEVFGSR 274
                                       59****************************99999**************98566666666666************** PP

                             PAS_4  88 lrdesGevigvlvisrDiTer 108
                                       +   +G+  +++++++DiTer
  gi|488601174|ref|YP_007907645.1| 275 I-VYKGK-PAIIGTLIDITER 293
                                       9.57999.9***********9 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.2e-12   1.8e-09       2      57 ..      54     112 ..      53     122 .. 0.80
   2 !   26.1   0.0   4.1e-09   6.1e-06       1      48 [.     181     228 ..     181     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.2e-12
                             PAS_8   2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellg..qllpvlrplle 57 
                                       r++ ++e+++d  +++d +g+ ++dvN++++e+lGy  ++l+g +    + +++l++l+e
  gi|488601174|ref|YP_007907645.1|  54 RYERFYENARDIFFILDkNGR-FIDVNPKFAEMLGYApEELIGHTSKriTHPEDLEGLKE 112
                                       9****************5555.***************99999999955566666666655 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 4.1e-09
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgql 48 
                                       e +r+l e s +gi ++ +g  + +vN++++e++Gy+ ++l+g    ++
  gi|488601174|ref|YP_007907645.1| 181 EMFRTLAEKSLVGIYLIQDGV-FKYVNPKMAEIWGYEtDELIGRSPLEF 228
                                       579************987666.***************888888665444 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.1e-07   0.00092       6      82 ..      67     138 ..      63     149 .. 0.88
   2 !   17.7   0.0     2e-06     0.003      29      77 ..     214     262 ..     205     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.1e-07
                            PAS_11   6 trldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvk 82 
                                       ++ld +g++i+v++   +    lg+  eel+g   +++ hp+dl+ lk+ ++ v+  +g+++   +R  ++++++++
  gi|488601174|ref|YP_007907645.1|  67 FILDKNGRFIDVNP---KFAEMLGYAPEELIGHTSKRITHPEDLEGLKELFKRVL--KGNTGRYEFRGVSKDGRIIW 138
                                       7899**********...999999********************************..77777777777777777776 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2e-06
                            PAS_11  29 glekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsq 77 
                                       g+e++el+grs  +++hp+d +t+++ l+  i  + e+   + R++ ++
  gi|488601174|ref|YP_007907645.1| 214 GYETDELIGRSPLEFIHPDDKETVRKNLERRIAGEIESINYCLRMIRKD 262
                                       89**************************998844444555555555554 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 ?   -1.7   0.2         2     3e+03      32      46 ..      40      54 ..      28      65 .. 0.74
   2 ?   -1.9   0.0       2.5   3.7e+03      46      65 ..     154     173 ..     153     175 .. 0.82
   3 !   30.5   0.0   1.8e-10   2.7e-07       9      66 ..     317     371 ..     314     372 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                                      T-HSSCHHHHHHHHH CS
                             HisKA 32 klteelkeyleties 46
                                      k  ee k++le++++
  gi|488601174|ref|YP_007907645.1| 40 KRKEERKRMLERLKR 54
                                      445888888888765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHHHCCHH CS
                             HisKA  46 searrldhlvedlLdlsrie 65 
                                       +e++ ++ +v d+ +  +ie
  gi|488601174|ref|YP_007907645.1| 154 KEVKEIEGIVRDITERKKIE 173
                                       57889999****98888887 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 1.8e-10
                                       HHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                             HisKA   9 vaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsriea 66 
                                       +  ++r+PL++i+g +e++ +    + el+e+ e+i + ++r++++v+ l d +++e+
  gi|488601174|ref|YP_007907645.1| 317 LVDQIRNPLTVISGITEVMLD--GKDGELRELKEIIMDAVKRIEDVVSKL-DRGWLES 371
                                       6789***************99..579***********************8.8888876 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.2   1.8e+03      81      98 ..      40      57 ..      32      76 .. 0.80
   2 !    9.2   0.0    0.0007         1      58     130 ..      82     152 ..      69     155 .. 0.84
   3 !    7.5   0.0    0.0024       3.5      27      92 ..     176     243 ..     163     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                            MEKHLA 81 eekeeRealLekvaeqgf 98
                                      ++keeR+++Le++++ + 
  gi|488601174|ref|YP_007907645.1| 40 KRKEERKRMLERLKRYER 57
                                      45899*****99998764 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0007
                            MEKHLA  58 aldllettweeltdlpsrksaepeekeeRealLekvaeqgfvenysGvrisstGrrfsienavvWkvldeegk 130
                                         ++l +  eel+  +s+++ +pe+ e  ++l+++v + g +  y+   +s++Gr +++e ++ W v+d eg+
  gi|488601174|ref|YP_007907645.1|  82 FAEMLGYAPEELIGHTSKRITHPEDLEGLKELFKRVLK-GNTGRYEFRGVSKDGRIIWFE-VIEWPVFDGEGE 152
                                       56899999**************9998777888888876.56677999999*******997.789****99886 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0024
                            MEKHLA  27 eelakaLfe..apfavlshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLek 92 
                                        + ++++f+  a++ ++   l +d vf y N +  +++ ++ +el+  +  + ++p++ke  ++ Le+
  gi|488601174|ref|YP_007907645.1| 176 LKDSEEMFRtlAEKSLVGIYLIQDGVFKYVNPKMAEIWGYETDELIGRSPLEFIHPDDKETVRKNLER 243
                                       45556666666778888888999**********************98777677777777776676765 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 ?    9.1   0.0   0.00065      0.97      54      95 ..      60     101 ..      44     118 .. 0.89
   2 ?    2.0   0.0       0.1   1.5e+02      57      89 ..     190     222 ..     178     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00065
                            PAS_12  54 EnlgailvysqkenkllfaNaqirallGwssdkflqdfseiv 95 
                                       En+  i++   k+ + + +N ++ ++lG+++++++ + s+ +
  gi|488601174|ref|YP_007907645.1|  60 ENARDIFFILDKNGRFIDVNPKFAEMLGYAPEELIGHTSKRI 101
                                       8888999999************************99877655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.1
                            PAS_12  57 gailvysqkenkllfaNaqirallGwssdkflq 89 
                                       +++ +y  ++    ++N ++ ++ G+++d+++ 
  gi|488601174|ref|YP_007907645.1| 190 SLVGIYLIQDGVFKYVNPKMAEIWGYETDELIG 222
                                       666677777777889**************9985 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00047      0.71      14      84 ..      68     140 ..      56     167 .. 0.81
   2 ?   -1.3   0.0       2.2   3.2e+03      22      63 ..     203     245 ..     186     291 .. 0.64
   3 ?   -0.2   0.0         1   1.5e+03      59     104 ..     291     337 ..     265     338 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
                            PAS_10  14 flDdnlqirrFtpa.akklfklipadvGrpladihpkkavknveeviealrtgekdevevvv.pkngkwvlvr 84 
                                        lD+n +++  +p+ a++l    ++ +G + + i++++ ++ ++e+++++ +g++ + e+   +k+g+++  +
  gi|488601174|ref|YP_007907645.1|  68 ILDKNGRFIDVNPKfAEMLGYAPEELIGHTSKRITHPEDLEGLKELFKRVLKGNTGRYEFRGvSKDGRIIWFE 140
                                       58***********85678888888889****************************999987636999876544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                            PAS_10  22 rrFtpaakklfkli.padvGr.pladihpkkavknveeviealr 63 
                                       ++ +p+ +++  +  ++ +Gr pl+ ihp+  ++ v++ +e+ +
  gi|488601174|ref|YP_007907645.1| 203 KYVNPKMAEIWGYEtDELIGRsPLEFIHPD-DKETVRKNLERRI 245
                                       555555555554430344677345555555.3444444444444 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1
                            PAS_10  59 iealrtgekdevevvv.pkngkwvlvrylpyrdedgeiaGvvetfvD 104
                                       +e+l  ++ + + +++ +kn + + + +  +r    +i G+ e+++D
  gi|488601174|ref|YP_007907645.1| 291 TERLELEKAKLKAFEQiEKNIENYAILVDQIRNPLTVISGITEVMLD 337
                                       55555555544444442688888888889999999999999999988 PP

>> Chordopox_A33R  Chordopoxvirus A33R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002       0.3      55     163 ..     286     391 ..     280     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                    Chordopox_A33R  55 sllaiattlalqyskckavkesihneqslnsyelvtpdkldnivklkeckGivfdsacyrlvkepktfseaskdcak 131
                                       +l+ i+  l l  +k ka  +   +e+ +++y  +  +  ++   +++   ++ d++  +l++ +    +a+k   +
  gi|488601174|ref|YP_007907645.1| 286 TLIDITERLELEKAKLKAFEQ---IEKNIENYAILVDQIRNPLTVISGITEVMLDGKDGELRELKEIIMDAVKRIED 359
                                       689999999999999999887...999******6555555566666******************************* PP

                    Chordopox_A33R 132 kkaslPakdlkkkwlsdylegtwGeeGyGlsk 163
                                         ++l    l ++ + d+l g  G + +G  k
  gi|488601174|ref|YP_007907645.1| 360 VVSKLDRGWLESERIRDFLRGKLGGKRKGWKK 391
                                       **********************9998888665 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.27     4e+02      28      45 ..      42      62 ..      31      82 .. 0.66
   2 ?    6.2   0.0     0.011        16      10      51 ..     227     268 ..     225     280 .. 0.82
   3 ?    3.9   0.4     0.057        85      24      46 ..     290     318 ..     284     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.27
                   Vir_act_alpha_C 28 reehe...ekLaeyeeieerl 45
                                      +ee++   e+L++ye+ +e+ 
  gi|488601174|ref|YP_007907645.1| 42 KEERKrmlERLKRYERFYENA 62
                                      444442226666666666654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                   Vir_act_alpha_C  10 faaavldpealieeLerrreeheekLaeyeeieerleeargq 51 
                                        +++  d+e++++ Lerr +   e ++ ++++ ++++e+r+ 
  gi|488601174|ref|YP_007907645.1| 227 EFIHPDDKETVRKNLERRIAGEIESINYCLRMIRKDGEKRYN 268
                                       589999***************999999999999999555554 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.057
                   Vir_act_alpha_C  24 LerrreeheekLaeyeeieerl......e 46 
                                       +++r+e+ ++kL+ +e+ie+++       
  gi|488601174|ref|YP_007907645.1| 290 ITERLELEKAKLKAFEQIEKNIenyailV 318
                                       7899999*************995444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1191  (0.0664287); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); 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):              12  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 2336.51
//
Query:       gi|488601175|ref|YP_007907646.1|  [L=328]
Description: NMD protein affecting ribosome stability and mRNA decay [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-48  164.9   0.9    2.8e-48  164.5   0.9    1.2  1  NMD3           NMD3 family
  ------ inclusion threshold ------
      0.054   13.9   0.0        0.1   13.1   0.0    1.3  1  CENP-H         Centromere protein H (CENP-H)
       0.12   12.7   0.1         18    5.7   0.1    2.7  2  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
       0.14   12.6   3.1        2.2    8.8   0.2    2.6  2  zf-C4pol       C4-type zinc-finger of DNA polymerase delta
       0.89    9.9   0.0       0.89    9.9   0.0    2.8  3  zinc_ribbon_9  zinc-ribbon
        1.5    8.9   6.2        1.9    8.5   3.2    2.4  2  DZR            Double zinc ribbon
        2.2    7.9   8.0        8.3    6.1   2.0    3.2  3  RecR           RecR protein
        8.6    5.9   7.2        4.6    6.8   0.1    3.2  3  zf-ribbon_3    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 !  164.5   0.9   1.2e-51   2.8e-48       1     243 []       4     225 ..       4     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 1.2e-51
                              NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvse 77 
                                       C  CGke+e    ++C++C++++++i ++++ ++++ C++Cgr++ + kW+++      +l++ l++ + ++++++ 
  gi|488601175|ref|YP_007907646.1|   4 CALCGKETE---YEICPECYIERNEIYDIEPYLQIKTCPKCGRFFVE-KWTDV------DLSRALHHSALRSFRYDP 70 
                                       9*******7...58*******************************98.9*555......666666666566677555 PP

                              NMD3  78 eveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk 154
                                       e++  ++e+       +e +  ++++ ++++g++rg     ++++  +e++ kr++C+rCsr++ggy+eai+Q+R++
  gi|488601175|ref|YP_007907646.1|  71 EFKIDSFEI-------SEIG--ENRCVLHIEGSFRG---LRIERDHYLEFRQKREVCDRCSRYYGGYFEAIIQLRAE 135
                                       444444443.......2332..446799******88...5678********************************** PP

                              NMD3 155 .relteeehkrtfelleqli..lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedk 228
                                        rel+++e + +++l+ + i  + ++  af+ski+e +eG+Dfy+gs++ Ark v+++++e+gg ++es+k++++ k
  gi|488601175|ref|YP_007907646.1| 136 nRELEKDEVELAKKLILKEIekEVDNPGAFVSKIEELEEGIDFYIGSRNIARKAVRRMENEIGGVITESQKIAGR-K 211
                                       ***************9999954445699***********************************************.8 PP

                              NMD3 229 ksgkevyrltysvrl 243
                                       + g++ +r+tys+rl
  gi|488601175|ref|YP_007907646.1| 212 D-GRDIFRTTYSIRL 225
                                       8.***********97 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.4e-05       0.1      27      96 ..     127     204 ..     119     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                            CENP-H  27 eeltevekenlrlkrknrelaael.l.elakekesek......eklkeelekleaelkksrqrwrvvknvasaiivg 95 
                                       e++ ++++en++l++ ++ela++l l e +ke ++        e+l+e ++      + +r+ +r + n + ++i++
  gi|488601175|ref|YP_007907646.1| 127 EAIIQLRAENRELEKDEVELAKKLiLkEIEKEVDNPGafvskiEELEEGIDFYIGSRNIARKAVRRMENEIGGVITE 203
                                       578899******************55455555555558888877788888888888889999999999999999998 PP

                            CENP-H  96 S 96 
                                       S
  gi|488601175|ref|YP_007907646.1| 204 S 204
                                       8 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.008        18      38      60 ..      28      50 ..      13      62 .. 0.85
   2 ?    4.1   0.0     0.025        55      41      57 ..     108     124 ..      90     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.008
                                      --SSTCCCTB-TTT--B--CTTT CS
                              Rpr2 38 rlppsvkrtvCkkCgsvlipgvt 60
                                       ++p ++ ++C kCg ++++ +t
  gi|488601175|ref|YP_007907646.1| 28 DIEPYLQIKTCPKCGRFFVEKWT 50
                                      678889999**********9987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.025
                                       STCCCTB-TTT--B--C CS
                              Rpr2  41 psvkrtvCkkCgsvlip 57 
                                          kr+vC +C+ ++  
  gi|488601175|ref|YP_007907646.1| 108 FRQKREVCDRCSRYYGG 124
                                       5679*******987655 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 ?    8.8   0.2   0.00097       2.2       1      21 [.       4      24 ..       4      37 .. 0.82
   2 ?    3.8   0.0     0.036        81      10      38 ..     112     139 ..      97     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00097
                          zf-C4pol  1 ClvCkeklkkalCkkCrsdkq 21
                                      C  C+++++ ++C +C  +++
  gi|488601175|ref|YP_007907646.1|  4 CALCGKETEYEICPECYIERN 24
                                      9***************74443 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.036
                          zf-C4pol  10 kalCkkCrsdkqesllkllsrlkelekkl 38 
                                       +++C++C+ +    +++ + +l++ +++l
  gi|488601175|ref|YP_007907646.1| 112 REVCDRCS-RYYGGYFEAIIQLRAENREL 139
                                       67899995.44444555555555555444 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.6      0.29   6.6e+02      20      27 ..      12      19 ..       3      21 .. 0.73
   2 ?    9.9   0.0    0.0004      0.89      22      33 ..      36      47 ..      27      49 .. 0.83
   3 ?   -3.4   0.2       5.5   1.2e+04      21      27 ..     113     118 ..     109     121 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.29
                     zinc_ribbon_9 20 sdvlCPhC 27
                                      +  +CP+C
  gi|488601175|ref|YP_007907646.1| 12 EYEICPEC 19
                                      4446**** PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0004
                     zinc_ribbon_9 22 vlCPhCgggFVE 33
                                      ++CP Cg  FVE
  gi|488601175|ref|YP_007907646.1| 36 KTCPKCGRFFVE 47
                                      58*********9 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 5.5
                     zinc_ribbon_9  21 dvlCPhC 27 
                                       +v C +C
  gi|488601175|ref|YP_007907646.1| 113 EV-CDRC 118
                                       55.6666 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.2   0.00087       1.9       1      36 [.       4      43 ..       2      50 .. 0.75
   2 ?   -0.1   0.1      0.44   9.8e+02      29      34 ..     113     118 ..     100     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00087
                               DZR  1 CpqCgeelppdarfCseCgtklkavaa......edrCpsCge 36
                                      C+ Cg+e   + + C+eC  + ++  +       ++Cp+Cg+
  gi|488601175|ref|YP_007907646.1|  4 CALCGKE--TEYEICPECYIERNEIYDiepylqIKTCPKCGR 43
                                      7788887..67889999999955444455555599*****97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.44
                               DZR  29 drCpsC 34 
                                       ++C++C
  gi|488601175|ref|YP_007907646.1| 113 EVCDRC 118
                                       344444 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.0    0.0037       8.3      17      34 ..       2      19 ..       1      23 [. 0.91
   2 ?    3.4   0.0     0.026        59      15      25 ..      34      44 ..      33      54 .. 0.85
   3 ?   -0.3   0.1      0.36   8.1e+02      28      35 ..     112     119 ..     107     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0037
                                      EE-TTT--EESSSS-CCC CS
                              RecR 17 rhCsrCgnlteedlCaIC 34
                                      r C  Cg  te ++C+ C
  gi|488601175|ref|YP_007907646.1|  2 RKCALCGKETEYEICPEC 19
                                      89**************99 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.026
                                      H-EE-TTT--E CS
                              RecR 15 kvrhCsrCgnl 25
                                      +++ C++Cg +
  gi|488601175|ref|YP_007907646.1| 34 QIKTCPKCGRF 44
                                      69******965 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.36
                                       SSS-CCCC CS
                              RecR  28 edlCaICs 35 
                                       +++C+ Cs
  gi|488601175|ref|YP_007907646.1| 112 REVCDRCS 119
                                       57888886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.18     4e+02      17      24 ..       2       9 ..       1      11 [. 0.78
   2 ?    0.3   0.5      0.23   5.1e+02       4       8 ..      15      19 ..      12      19 .. 0.63
   3 ?    6.8   0.1     0.002       4.6       3      10 ..      36      43 ..      34      48 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                       zf-ribbon_3 17 nvCpyCGt 24
                                      ++C+ CG+
  gi|488601175|ref|YP_007907646.1|  2 RKCALCGK 9 
                                      78999997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.23
                       zf-ribbon_3  4 rCPnC 8 
                                       CP+C
  gi|488601175|ref|YP_007907646.1| 15 ICPEC 19
                                      56666 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.002
                       zf-ribbon_3  3 vrCPnCGa 10
                                      ++CP+CG 
  gi|488601175|ref|YP_007907646.1| 36 KTCPKCGR 43
                                      46777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      791  (0.0441185); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2247.12
//
Query:       gi|488601176|ref|YP_007907647.1|  [L=334]
Description: methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-67  225.9   0.1    8.6e-67  224.7   0.1    1.5  2  Met_10           Met-10+ like-protein
      4e-14   52.2   0.1      1e-13   50.9   0.1    1.7  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    8.2e-05   22.6   0.0    0.00022   21.2   0.0    1.7  2  Methyltransf_18  Methyltransferase domain
     0.0014   18.2   0.0     0.0023   17.6   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0043   16.6   0.0     0.0072   15.9   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0097   15.3   0.0      0.017   14.5   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
       0.01   14.8   0.0      0.016   14.2   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.012   15.1   0.0      0.024   14.1   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
      0.081   12.1   0.0        0.1   11.8   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
        0.1   13.3   0.0       0.23   12.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.1   3.7e+03      75      94 ..      50      69 ..      42      73 .. 0.72
   2 !  224.7   0.1   4.8e-70   8.6e-67       2     197 ..      88     281 ..      87     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.1
                                      EEETTTS---GGGHHHHHHH CS
                            Met_10 75 klDvskvyfsskleaErerl 94
                                       +D+  vy  s l+a ++rl
  gi|488601176|ref|YP_007907647.1| 50 YFDYEVVYADSPLSARHRRL 69
                                      57788888888888888777 PP

  == domain 2  score: 224.7 bits;  conditional E-value: 4.8e-70
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEE.S-.SEEEEEETTEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaG.sdstetihkEngcrfkl 76 
                                       ++++iG+++++++ +el+ y+k ige +l  + ++k+v+r+ ++ e ++R+++le laG +  tet++ Engc fkl
  gi|488601176|ref|YP_007907647.1|  88 SYKMIGEIILVKIADELEAYRKAIGECLLRLHpNCKSVWRDLGK-EDMLRKPRLEFLAGdESYTETVKLENGCYFKL 163
                                       79******************************************.**************76679************* PP

                                       ETTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCE CS
                            Met_10  77 DvskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvv 153
                                       Dv+kv++s ++++E++r+a+lve+ge+Vvd+fAGiG+f+ipiak+s+akr+++i++nPes++yl eni+lN+v++v+
  gi|488601176|ref|YP_007907647.1| 164 DVKKVMYSVGNQHEKMRIARLVEDGEIVVDMFAGIGYFSIPIAKHSNAKRIYSIEINPESYHYLLENIRLNEVDNVI 240
                                       ****************************************************************************9 PP

                                       EEEES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEE CS
                            Met_10 154 kpileDgrevireqladrvvmnlpksaieFldkvlaalkdggvi 197
                                        pil+D+  v+ + +adr++m+++ +++eFl++++ a+ +g ++
  gi|488601176|ref|YP_007907647.1| 241 -PILGDSMFVT-PPKADRIIMGHI-YCHEFLKTAFLAVDEGYIH 281
                                       .******9997.889*********.9*********999877655 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   5.6e-17     1e-13       1      46 [.       5      50 ..       5      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 5.6e-17
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--HHH CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepegy 46
                                      ++kVpk+++EkvRkk  + g+ d+n+ I+sd++++yIP+   +e y
  gi|488601176|ref|YP_007907647.1|  5 ALKVPKRDAEKVRKKAESIGAKDKNRLIRSDGEFVYIPILTGFERY 50
                                      79*************************************9888765 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.7   6.6e+03      48      74 ..      10      36 ..       4      39 .. 0.57
   2 !   21.2   0.0   1.2e-07   0.00022       7      87 ..     180     258 ..     177     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.7
                   Methyltransf_18 48 egplekakeniekagledkievrlsdG 74
                                      +   ek ++++e+ g +dk +++ sdG
  gi|488601176|ref|YP_007907647.1| 10 KRDAEKVRKKAESIGAKDKNRLIRSDG 36
                                      344455555666666666666555555 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.2e-07
                   Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeev 83 
                                       +ia+lve+g++v+D  +  gy +i ++k+++ak+++ ++in+++++   eni+ ++++ ++  +l+d + +  + ++
  gi|488601176|ref|YP_007907647.1| 180 RIARLVEDGEIVVDMFAGIGYFSIPIAKHSNAKRIYSIEINPESYHYLLENIRLNEVD-NVIPILGDSMFVTPP-KA 254
                                       699***************************************************9995.677889999877754.47 PP

                   Methyltransf_18  84 dtvv 87 
                                       d ++
  gi|488601176|ref|YP_007907647.1| 255 DRII 258
                                       7776 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0023       2      59 ..     189     247 ..     188     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvf 59 
                                       ++++D+f+G G  +i +a++   +++++iein+e      +N ++ +v+ ++ ++lgd +
  gi|488601176|ref|YP_007907647.1| 189 EIVVDMFAGIGYFSIPIAKHsnAKRIYSIEINPESYHYLLENIRLNEVD-NVIPILGDSM 247
                                       689***************987789*********************9885.5778888865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     4e-06    0.0072      32     102 ..     188     258 ..     178     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4e-06
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdliv 102
                                        + v+D+ +G+G+ ++ +ak+s+  ++  ++++ ++ +   en++ n+++  + ++  +++ + +  k d i+
  gi|488601176|ref|YP_007907647.1| 188 GEIVVDMFAGIGYFSIPIAKHSNAKRIYSIEINPESYHYLLENIRLNEVDnvIPILGDSMFVTPP--KADRII 258
                                       4459*********************************************9755555555554444..666666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   9.4e-06     0.017     157     216 ..     183     243 ..     178     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.4e-06
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaak.LgakkvvavDiDevAvkvakeNaelNkveakleva 216
                                       +lv+ ge v+D+ +G G  +i  ak  +ak+++ + i++ + +   eN++lN+v++ + + 
  gi|488601176|ref|YP_007907647.1| 183 RLVEDGEIVVDMFAGIGYFSIPIAKhSNAKRIYSIEINPESYHYLLENIRLNEVDNVIPIL 243
                                       78999****************87762689**************************988663 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 ?   14.2   0.0   9.2e-06     0.016     205     251 ..     191     239 ..     177     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.2e-06
                   tRNA_U5-meth_tr 205 llelycGnGnfslalar..nfekvlateiakssveaaqyniaankidnv 251
                                       +++++ G G fs+++a+  n +++ + ei   s +  + ni  n++dnv
  gi|488601176|ref|YP_007907647.1| 191 VVDMFAGIGYFSIPIAKhsNAKRIYSIEINPESYHYLLENIRLNEVDNV 239
                                       6789***********9733678**************************8 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.024       3      61 ..     189     247 ..     187     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                       EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CC CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdal 61 
                                        +v+++  G G f + +Ak+   k +  iEi+ ++ +++l++i+ +e+ N+  + gd +
  gi|488601176|ref|YP_007907647.1| 189 EIVVDMFAGIGYFSIPIAKHSNAKRIYSIEINPESYHYLLENIRLNEVDNVIPILGDSM 247
                                       6899999********************************************99999875 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.7e-05       0.1      52     109 ..     190     245 ..      96     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                                       EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S- CS
                               TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvinedd 109
                                        v+d +++ G  +i  a+  +++k+++  +i+++ ++ + eN++lnev++++ i  +d
  gi|488601176|ref|YP_007907647.1| 190 IVVDMFAGIGYFSIPIAKH-SNAKRIYSIEINPESYHYLLENIRLNEVDNVIPIL-GD 245
                                       5899**************9.9****************************955443.35 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.23       1      70 [.     191     259 ..     191     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       v+d+ +G G +++ +ak+ ++++++ ++i++e   +  e+++ +++ nv  + gd   +  +  + D +++
  gi|488601176|ref|YP_007907647.1| 191 VVDMFAGIGYFSIPIAKHSNAKRIYSIEINPESYHYLLENIRLNEVdNVIPILGDSMFVTPP--KADRIIM 259
                                       899***************889********************999999998888887665544..3555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); 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:                        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 0.31s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2170.03
//
Query:       gi|488601177|ref|YP_007907648.1|  [L=140]
Description: transcriptional regulator, CopG family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   97.5   2.6    4.9e-28   97.1   2.6    1.2  1  NikR_C           NikR C terminal nickel binding domain
      2e-11   43.4   0.2    5.3e-11   42.1   0.2    1.7  1  RHH_1            Ribbon-helix-helix protein, copG family
     0.0014   18.7   0.1      0.011   15.9   0.0    2.1  2  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 !   97.1   2.6   8.2e-32   4.9e-28       1      76 [.      58     133 ..      58     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 8.2e-32
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                       +Gv++++ydh+ r+++++++++qh++ d++++++h+h+d++ncLe+i +kG++++ik+++ +l+al+gV +vk+ +
  gi|488601177|ref|YP_007907648.1|  58 IGVVSVIYDHKYRGVTDTIISLQHDFGDVVTTTMHIHIDEENCLEMITVKGDMSKIKKMVGRLSALRGVTSVKFIT 133
                                       69***********************************************************************876 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 !   42.1   0.2   8.8e-15   5.3e-11       1      38 [.       7      45 ..       7      46 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 8.8e-15
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      r+ ++l+++ll+++d ++r rg +SrSe+IR+A+r+y+ 
  gi|488601177|ref|YP_007907648.1|  7 RIGVSLPKNLLAEFDSIIRSRGySSRSEAIRDAIRMYIN 45
                                      899**********************************86 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 !   15.9   0.0   1.8e-06     0.011      86     120 ..       2      37 ..       1      40 [. 0.87
   2 ?    2.0   0.0     0.036   2.2e+02      37      82 ..      36      81 ..      34     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-06
                   HicB_lk_antitox  86 dgkaeriNitlpervlkriDaavkaag.esRSgfla 120
                                       d+  +ri ++lp+++l++ D++++++g +sRS  + 
  gi|488601177|ref|YP_007907648.1|   2 DEAIVRIGVSLPKNLLAEFDSIIRSRGySSRSEAIR 37 
                                       56779**********************679**8775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.036
                   HicB_lk_antitox 37 akeaielhlegliedgeeipepssieellanpeyaggiwalvdvdl 82
                                      +++ai +++++    ++e  e+  + +++ ++ y+g++ ++++++ 
  gi|488601177|ref|YP_007907648.1| 36 IRDAIRMYINEYKWLEKESGEVIGVVSVIYDHKYRGVTDTIISLQH 81
                                      6889999999988888888888888888888888888887777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1014.12
//
Query:       gi|488601178|ref|YP_007907649.1|  [L=169]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  147.7   0.0    1.7e-43  147.3   0.0    1.2  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56


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 !  147.3   0.0   9.7e-48   1.7e-43       1     119 []      54     166 ..      54     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 9.7e-48
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnq 77 
                                       wGg+f +e +++++k+++ef+   g +vhltmyG++++e ++ i+k+e+ +lvvvG+ekvp evye++d+n+s+gnq
  gi|488601178|ref|YP_007907649.1|  54 WGGDFLIE-SVEWRKFLREFD---GLKVHLTMYGIPLTEKLDVIRKSER-VLVVVGSEKVPPEVYEMCDMNISIGNQ 125
                                       *******9.679*********...*********************9977.*************************** PP

                                       ---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                             Trm56  78 PhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                       Phsevaala+fldrll+ k+++++f+dak++viP+e+gkkvv
  gi|488601178|ref|YP_007907649.1| 126 PHSEVAALAVFLDRLLD-KTFRMKFDDAKIEVIPCEKGKKVV 166
                                       ***************97.89********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1217.94
//
Query:       gi|488601179|ref|YP_007907650.1|  [L=366]
Description: hypothetical protein Asulf_01685 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   50.3   7.8    5.3e-08   32.4   0.2    2.5  2  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   2.9   1.7e-08   0.00031       2     107 ..     135     212 ..     134     232 .. 0.86
   2 !   32.4   0.2   2.9e-12   5.3e-08     186     230 ..     246     290 ..     228     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.7e-08
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp....LGGyVkmageepeeelsee 74 
                                       f +++++++  HE+GH+++Ak++g+k                  +++Y+i++      LG++++ +g  p+++    
  gi|488601179|ref|YP_007907650.1| 135 FSFAIMFVLGSHEMGHYIIAKRWGMKT-----------------SLPYFIPFPTivgtLGAIIRHKGAIPNRK---- 190
                                       78999*********************9.................67888888888888999999999998888.... PP

                                       ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  75 eakaflkkspwqrllivlAGplanfilailvfv 107
                                                  + + + ++Gpl+++  +i++ +
  gi|488601179|ref|YP_007907650.1| 191 -----------ALFDVGVSGPLVGIFASIIITA 212
                                       ...........7888888888888888888766 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 2.9e-12
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 186 aglssflqllalisvnLgilNLlPipvLDGghllfalleairrkp 230
                                       + ++++++++ ++++ ++++NL+P  +LDGgh+l+a+l + + + 
  gi|488601179|ref|YP_007907650.1| 246 SEVIHPIAFAGWVGMLVTFFNLIPAGQLDGGHILRAMLGKKADRI 290
                                       5677999******************************99877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2298.51
//
Query:       gi|488601180|ref|YP_007907651.1|  [L=143]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-12   46.7   0.6    3.5e-12   45.7   0.6    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.7e-12   47.1   0.0    2.5e-12   46.6   0.0    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    5.3e-12   45.4   0.0    9.3e-12   44.6   0.0    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    3.8e-08   33.1   0.5    6.5e-08   32.4   0.5    1.4  1  HTH_11          HTH domain
    0.00026   20.7   0.1    0.00041   20.0   0.1    1.3  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    0.00037   20.5   0.0    0.00068   19.6   0.0    1.4  1  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0005   19.9   0.1     0.0014   18.5   0.1    1.8  2  MarR            MarR family
    0.00087   19.3   0.0     0.0013   18.7   0.0    1.3  1  HTH_20          Helix-turn-helix domain
     0.0015   18.4   0.0     0.0026   17.6   0.0    1.4  1  MarR_2          MarR family
     0.0018   18.1   2.0     0.0049   16.7   0.8    2.0  2  TFIIE_alpha     TFIIE alpha subunit
     0.0023   18.0   0.1     0.0035   17.4   0.1    1.3  1  HTH_28          Helix-turn-helix domain
     0.0049   16.8   2.0      0.011   15.7   1.0    2.1  2  HTH_12          Ribonuclease R winged-helix domain
     0.0052   16.4   0.0      0.011   15.3   0.0    1.5  1  HTH_50          Helix-turn-helix domain
     0.0065   16.5   0.2      0.066   13.2   0.1    2.4  2  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
  ------ inclusion threshold ------
      0.016   15.0   0.1      0.022   14.5   0.1    1.3  1  HTH_39          Helix-turn-helix domain
      0.016   15.1   0.1       0.03   14.3   0.1    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.018   14.9   0.1      0.034   14.0   0.1    1.6  2  HxlR            HxlR-like helix-turn-helix
      0.022   14.9   0.1      0.032   14.4   0.1    1.4  1  HTH_34          Winged helix DNA-binding domain
      0.025   14.5   0.1      0.042   13.8   0.1    1.2  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.029   14.3   0.0       0.06   13.3   0.0    1.5  1  HTH_6           Helix-turn-helix domain, rpiR family
      0.031   13.8   0.1      0.086   12.4   0.1    1.8  2  HTH_CodY        CodY helix-turn-helix domain
      0.043   13.6   0.1      0.079   12.8   0.1    1.3  1  HTH_23          Homeodomain-like domain
      0.045   13.6   0.1      0.099   12.5   0.1    1.6  1  HTH_10          HTH DNA binding domain
      0.046   13.7   0.1        0.1   12.6   0.1    1.7  1  HTH_36          Helix-turn-helix domain
      0.051   13.7   0.2      0.098   12.8   0.2    1.5  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.061   13.7   0.0       0.17   12.2   0.1    1.7  2  Rrf2            Transcriptional regulator
      0.069   13.0   0.1       0.12   12.2   0.1    1.4  1  HTH_8           Bacterial regulatory protein, Fis family
      0.095   12.6   0.0       0.18   11.7   0.0    1.5  1  P22_Cro         DNA-binding transcriptional regulator Cro
       0.12   12.3   0.2        0.2   11.6   0.2    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.13   12.2   0.1       0.26   11.2   0.0    1.5  2  DUF4859         Domain of unknown function (DUF4859)


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.6   5.9e-15   3.5e-12       2      48 .]       5      51 ..       4      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 5.9e-15
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      de+d+kI+  L +++r s++  A++lg++ +++++r+k+Le  G+I+
  gi|488601180|ref|YP_007907651.1|  5 DEKDKKIIGMLAEDSRVSYTKMAKELGITEAAIRKRVKNLEARGIIR 51
                                      9*********************************************7 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   4.2e-15   2.5e-12       2      74 ..      71     140 ..      67     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 4.2e-15
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       +v +ep++   + +++++l++ +  +++y +tGd+ ++++++++d ++l ++++ek++++pgv+++   i+le
  gi|488601180|ref|YP_007907651.1|  71 GVDTEPEK---FLDVAKKLKDEEFTRSVYITTGDHMIMAEIWAKDGDELTKIISEKIGKIPGVKKICPAIILE 140
                                       56777777...***********************************************************998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.6e-14   9.3e-12       1      42 []       4      45 ..       4      45 .. 0.98

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.6e-14
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +De D+kI+  L ed+R sy+++A+++G++e+++++Rv+ Le
  gi|488601180|ref|YP_007907651.1|  4 IDEKDKKIIGMLAEDSRVSYTKMAKELGITEAAIRKRVKNLE 45
                                      6***************************************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.5   1.1e-10   6.5e-08       3      54 ..       9      64 ..       7      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.1e-10
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgr.GY 54
                                      ++i+ +L ++++ +s  ++A+eL+++++++r+++k Le+ g    + Ie ++ + GY
  gi|488601180|ref|YP_007907651.1|  9 KKIIGML-AEDSRVSYTKMAKELGITEAAIRKRVKNLEARGiirkYTIEVDSTKlGY 64
                                      68999**.99999********************************777777766688 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   6.8e-07   0.00041       3      46 ..       9      52 ..       7      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.8e-07
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      ++i+ +l+++  +s ++ + +lg++ea iR+  ++Le+ g++++
  gi|488601180|ref|YP_007907651.1|  9 KKIIGMLAEDSRVSYTKMAKELGITEAAIRKRVKNLEARGIIRK 52
                                      79***************************************987 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.1e-06   0.00068       5      45 ..       6      45 ..       4      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                           HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      + + k++  L e +++ ++++ akeLg++e ++++++ +L 
  gi|488601180|ref|YP_007907651.1|  6 EKDKKIIGMLAE-DSRVSYTKMAKELGITEAAIRKRVKNLE 45
                                      567899******.*************************996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.3e-06    0.0014      12      55 ..      15      58 ..       5      59 .. 0.87
   2 ?   -2.5   0.0       8.6   5.1e+03       2      22 ..      98     118 ..      97     121 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-06
                                      HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTS CS
                              MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeD 55
                                      l+e    s +++ak lg++ +++ + ++ Le +G i+++  + D
  gi|488601180|ref|YP_007907651.1| 15 LAEDSRVSYTKMAKELGITEAAIRKRVKNLEARGIIRKYTIEVD 58
                                      5566667889****************************988766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.6
                                       -HHHHHHHHHHHHSTTEEHHH CS
                              MarR   2 tltqfviLrilyeqgplsvse 22 
                                       t   ++i++ ++ +++  +++
  gi|488601180|ref|YP_007907651.1|  98 TTGDHMIMAEIWAKDGDELTK 118
                                       556678888888877655555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.2e-06    0.0013      13      56 ..       9      52 ..       3      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       +i  +La++  ++ +  a++l+++ + ++++++ Le  g+++ 
  gi|488601180|ref|YP_007907651.1|  9 KKIIGMLAEDSRVSYTKMAKELGITEAAIRKRVKNLEARGIIRK 52
                                      57999************************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.4e-06    0.0026      22      53 ..      21      52 ..       9      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                                      EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLver 53
                                      ++ +  a++lg++ +a+ +++k L+a+G +++
  gi|488601180|ref|YP_007907651.1| 21 VSYTKMAKELGITEAAIRKRVKNLEARGIIRK 52
                                      6667789***********************97 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.8   8.2e-06    0.0049      11      67 ..       4      61 ..       1      94 [. 0.80
   2 ?    0.9   0.1      0.67     4e+02      65      91 ..     100     126 ..      75     134 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.2e-06
                                      S-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSE.EEEEEEETTT CS
                       TFIIE_alpha 11 ygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlv.kykrrrdeek 67
                                       +e+ ++++ +L+e++ v+   +akel+i    +rk + +L   +++ ky  ++d  k
  gi|488601180|ref|YP_007907651.1|  4 IDEKDKKIIGMLAEDSRVSYTKMAKELGITEAAIRKRVKNLEARGIIrKYTIEVDSTK 61
                                      678999************************************9999855666666544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.67
                                       TTTEEEEEEEEEECCCHCCCHHHHHHH CS
                       TFIIE_alpha  65 eekswykyywrinyeklvdvvkrklee 91 
                                        +  ++   w  + ++l++++++k+ +
  gi|488601180|ref|YP_007907651.1| 100 GDHMIMAEIWAKDGDELTKIISEKIGK 126
                                       444555666667777777777777655 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   5.9e-06    0.0035       4      41 ..      10      49 ..       9      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.9e-06
                            HTH_28  4 eiikllaaG.h.svreaArelgisrrtvyrWikryeegGi 41
                                      +ii  la+  + s++  A+elgi++  +++ +k +e+ Gi
  gi|488601180|ref|YP_007907651.1| 10 KIIGMLAEDsRvSYTKMAKELGITEAAIRKRVKNLEARGI 49
                                      799999953245**************************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 !   15.7   1.0   1.8e-05     0.011       3      51 ..      11      53 ..       9      63 .. 0.86
   2 ?   -2.7   0.0       9.7   5.8e+03      40      50 ..      84      94 ..      83      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                            HTH_12  3 ILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrv 51
                                      I+ +lae ++ ++  ++a+eL      i e a+R r + le rg++r+ 
  gi|488601180|ref|YP_007907651.1| 11 IIGMLAEDSR-VSYTKMAKELG-----ITEAAIRKRVKNLEARGIIRKY 53
                                      7778888888.89999999885.....778889**************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.7
                            HTH_12 40 rkleergltrr 50
                                      +kl ++++tr 
  gi|488601180|ref|YP_007907651.1| 84 KKLKDEEFTRS 94
                                      67888888885 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.8e-05     0.011       9      45 ..       5      42 ..       2      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                            HTH_50  9 eefErelikkayek.YpStRklAkrLGvShtaianklr 45
                                      +e ++++i+ + e    S  k+Ak LG++ +ai ++++
  gi|488601180|ref|YP_007907651.1|  5 DEKDKKIIGMLAEDsRVSYTKMAKELGITEAAIRKRVK 42
                                      56677777777664145899****************98 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   0.00011     0.066      25      46 ..      18      39 ..      10      39 .. 0.88
   2 ?    0.2   0.0       1.3     8e+02      24      40 ..     115     131 ..     110     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                      --EE-HHHHHHHCTS-HHHHHH CS
                    Put_DNA-bind_N 25 veriSSteLaealgvtaaqvRK 46
                                       +r+S t++a++lg+t+a +RK
  gi|488601180|ref|YP_007907651.1| 18 DSRVSYTKMAKELGITEAAIRK 39
                                      589******************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                                       T--EE-HHHHHHHCTS- CS
                    Put_DNA-bind_N  24 gveriSSteLaealgvt 40 
                                       + ++i S+++++  gv+
  gi|488601180|ref|YP_007907651.1| 115 ELTKIISEKIGKIPGVK 131
                                       567899****9987775 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.7e-05     0.022       3      42 ..       8      49 ..       6      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
                            HTH_39  3 carilaaLrqhgsittleamrelditr..laaRIkeLrekGy 42
                                      +++i+ +L ++++++  +  +el+it+   ++R+k+L+++G+
  gi|488601180|ref|YP_007907651.1|  8 DKKIIGMLAEDSRVSYTKMAKELGITEaaIRKRVKNLEARGI 49
                                      5899999********************555799********6 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     5e-05      0.03      20      59 ..      19      57 ..       3      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrgrriri 59
                                       +++ + +A  lG+t   + +  + L+ +g+i++ + i++
  gi|488601180|ref|YP_007907651.1| 19 SRVSYTKMAKELGITEAAIRKRVKNLEARGIIRKYT-IEV 57
                                      579999***************************876.887 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.7e-05     0.034       6      65 ..       8      66 ..       3      95 .. 0.80
   2 ?   -1.6   0.0       4.1   2.5e+03      50      76 ..      92     120 ..      76     126 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-05
                                      THHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE CS
                              HxlR  6 WkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsl 65
                                       k +i +   + +  +++++++l +i++  + +r ++Le+ g+i + +++   +k  Y++
  gi|488601180|ref|YP_007907651.1|  8 DKKIIGMLAEDSRVSYTKMAKEL-GITEAAIRKRVKNLEARGIIRKYTIEVDSTKLGYNV 66
                                      55555555555666788999999.9*******************************9975 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.1
                                       EEEEESSSS-EEEEE..E-TCGGGGHHHH CS
                              HxlR  50 erevypevPpkveYs..ltekGrslepvl 76 
                                        r+vy +++ ++      ++ G +l++++
  gi|488601180|ref|YP_007907651.1|  92 TRSVYITTGDHMIMAeiWAKDGDELTKII 120
                                       56666666655543211355566666665 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 ?   14.4   0.1   5.4e-05     0.032       5      45 ..      11      51 ..       9      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-05
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      ++ +La++++++++++ ++l++t++++ + +k Le+ g i 
  gi|488601180|ref|YP_007907651.1| 11 IIGMLAEDSRVSYTKMAKELGITEAAIRKRVKNLEARGIIR 51
                                      7889********************************99884 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.1e-05     0.042      15      39 ..      22      46 ..      16      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.1e-05
                                      SHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 15 sftrAAeeLglsqpavsrqikrLEe 39
                                      s t+ A+eLg++ +a+ +++k+LE+
  gi|488601180|ref|YP_007907651.1| 22 SYTKMAKELGITEAAIRKRVKNLEA 46
                                      78889*******************7 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0    0.0001      0.06      18      62 ..       8      48 ..       2      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHHHH---S-SS CS
                             HTH_6 18 ekkiaeyilaspdkaielsikalAkaaavSeativrfakkLGfkG 62
                                      +kki+ ++ ++    +++s  ++Ak++++ ea+i +  k L ++G
  gi|488601180|ref|YP_007907651.1|  8 DKKIIGMLAED----SRVSYTKMAKELGITEAAIRKRVKNLEARG 48
                                      56666555444....578999*******************99998 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 ?   12.4   0.1   0.00014     0.086       4      36 ..      20      52 ..      17      65 .. 0.85
   2 ?   -2.6   0.0       7.2   4.3e+03      16      21 ..      91      96 ..      79      99 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                          HTH_CodY  4 rLtaskiaDriGitrsvivnaLrkLesaGiies 36
                                      r+   k+a ++Git + i   ++ Le+ Gii  
  gi|488601180|ref|YP_007907651.1| 20 RVSYTKMAKELGITEAAIRKRVKNLEARGIIRK 52
                                      6667899***********************976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.2
                          HTH_CodY 16 itrsvi 21
                                       trsv 
  gi|488601180|ref|YP_007907651.1| 91 FTRSVY 96
                                      688886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013     0.079      10      46 ..      11      49 ..       8      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      i+ +lae  + s+++ A+eLg+++  +++ +k  ++ G+
  gi|488601180|ref|YP_007907651.1| 11 IIGMLAEdsRVSYTKMAKELGITEAAIRKRVKNLEARGI 49
                                      888999999*******************99998766775 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00016     0.099      22      48 ..      19      45 ..      13      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrkae 48
                                       rv+  ++AkelGI+++++ +++++ e
  gi|488601180|ref|YP_007907651.1| 19 SRVSYTKMAKELGITEAAIRKRVKNLE 45
                                      58999****************999877 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017       0.1      27      55 .]      22      50 ..       6      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s+  +ak lg+ +  +++ +k+Le  G+i
  gi|488601180|ref|YP_007907651.1| 22 SYTKMAKELGITEAAIRKRVKNLEARGII 50
                                      899************************98 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00016     0.098       8      56 ..       7      54 ..       1      61 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                           DUF2250  8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      +++  +   ++   v Y k +akel i    +r+ +k+Le  G++ +++
  gi|488601180|ref|YP_007907651.1|  7 KDKKIIGMLAEDSRVSYTK-MAKELGITEAAIRKRVKNLEARGIIRKYT 54
                                      4444444456678899998.699***********************998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00029      0.17      20      56 ..      15      51 ..      10      54 .. 0.87
   2 ?   -2.3   0.0       9.9   5.9e+03      37      58 ..      74      95 ..      70      96 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00029
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                       +e++ vs +++a++ +i +  ++k +++L+  g+++
  gi|488601180|ref|YP_007907651.1| 15 LAEDSRVSYTKMAKELGITEAAIRKRVKNLEARGIIR 51
                                      455666*****************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.9
                                      S-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 37 ispsylekilakLrkaglvksv 58
                                      ++p+    + +kL+ +++ +sv
  gi|488601180|ref|YP_007907651.1| 74 TEPEKFLDVAKKLKDEEFTRSV 95
                                      5666666788899988888875 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00019      0.12       7      40 ..       9      42 ..       4      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                      HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHH CS
                             HTH_8  7 kelIeaALertgGnkskAArlLGisRrtLyrKLk 40
                                      k++I    e ++   +k+A++LGi+   ++++ k
  gi|488601180|ref|YP_007907651.1|  9 KKIIGMLAEDSRVSYTKMAKELGITEAAIRKRVK 42
                                      667777778888889***********99999977 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 ?   11.7   0.0    0.0003      0.18      13      32 ..      24      43 ..      22      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                                      HHHHHHHTS-HHHHHHHHTC CS
                           P22_Cro 13 ekvAkalgvtksAVsqWgee 32
                                      +k+Ak lg+t++A++++ ++
  gi|488601180|ref|YP_007907651.1| 24 TKMAKELGITEAAIRKRVKN 43
                                      89*************99654 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00033       0.2      17      56 ..      15      54 ..       4      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      L +  + + ++ a+elg+ ++ + + +++Le +G++++  
  gi|488601180|ref|YP_007907651.1| 15 LAEDSRVSYTKMAKELGITEAAIRKRVKNLEARGIIRKYT 54
                                      667777788899************************9865 PP

>> DUF4859  Domain of unknown function (DUF4859)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00043      0.26      10      49 ..      22      61 ..      16      76 .. 0.88
   2 ?   -2.6   0.0       7.8   4.7e+03      27      39 ..      93     105 ..      81     128 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00043
                           DUF4859 10 daakiakaLgltteelvtalkaeeagskvklytvesdgtl 49
                                      + +k+ak+Lg+t++ + +++k+ ea + +  yt+e d+t+
  gi|488601180|ref|YP_007907651.1| 22 SYTKMAKELGITEAAIRKRVKNLEARGIIRKYTIEVDSTK 61
                                      6789*********************************995 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.8
                           DUF4859  27 talkaeeagskvk 39 
                                         +    ++  ++
  gi|488601180|ref|YP_007907651.1|  93 RSVYITTGDHMIM 105
                                       4433333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1021.65
//
Query:       gi|488601181|ref|YP_007907652.1|  [L=229]
Description: aspartate racemase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-62  210.5   0.0    3.1e-62  210.4   0.0    1.0  1  Asp_Glu_race     Asp/Glu/Hydantoin racemase
     0.0024   17.3   0.5      0.012   15.0   0.2    2.0  2  Pantoate_transf  Ketopantoate hydroxymethyltransferase
     0.0025   17.3   0.1     0.0064   16.0   0.0    1.6  2  PEP_mutase       Phosphoenolpyruvate phosphomutase
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.031   14.3   0.0    1.5  2  PA               PA domain


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.4   0.0   6.8e-66   3.1e-62       1     223 [.       7     223 ..       7     224 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 6.8e-66
                                       EEECSCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CCS-TCHHHHHCH.T..THHHHHHHHHHHHCTTESEEEE-- CS
                      Asp_Glu_race   1 IGgmgpeatlsvlrklveatpaesdqehlplivlndsaipdrteaieeesgddpvlklleaakkLekagadaiviaC 77 
                                       +Ggm++e+t++++r ++e+ + + +  h++ i+l++ +++++ e++++e+++     l+e a++Le+agad+++i+ 
  gi|488601181|ref|YP_007907652.1|   7 LGGMSWESTAEYYRIINEMISSKLGNLHSAKILLYSFDFEEIVEKQKTEDWKALGDILAERAAALENAGADMVLICT 83 
                                       7***************************************************9999********************* PP

                                       CHHHHHHHHHHHH-SSEEEECHHHHHHHHHHHSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCC CS
                      Asp_Glu_race  78 nTahavadelqkkikiPvlgiveataealkatgvkkvglLgTrgtlksglyqkeleanqgievvvpseelqssvnqa 154
                                       nT+h vad++q+ i+iP+++i++atae++ ++g+kkvglLgT +t+++++y++ l++ +gi+vvvp++++++ v+ +
  gi|488601181|ref|YP_007907652.1|  84 NTMHKVADDVQSRINIPLVSIIDATAEEIVKNGIKKVGLLGTLFTMEDDFYRDGLKK-YGIDVVVPDKKERKFVHDV 159
                                       *********************************************************.5****************** PP

                                       HCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHHHH CS
                      Asp_Glu_race 155 iyeelkaGevteearrailkllerlaergadaviLGCTelplllekaealekeksvpvidptdilaret 223
                                       i  el++G++++e+++++l+++++l e+g+++++LGCTe+pll +++     + ++p++d+t+i+ar++
  gi|488601181|ref|YP_007907652.1| 160 IFGELCKGIIKKESKSRFLEIISKLVENGVEGIVLGCTEIPLLVKQE-----DVDIPIFDTTEIHARKA 223
                                       ***********************************************.....458************97 PP

>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   2.7e-06     0.012     162     202 ..      63     104 ..      49     117 .. 0.86
   2 ?    0.2   0.0      0.09     4e+02     112     183 ..     170     197 ..     162     212 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-06
                   Pantoate_transf 162 klledakaleeaGafalvl.EavpaelakeiteklsiptIGI 202
                                        l e+a ale+aGa ++++   + +++a+ ++++++ip ++I
  gi|488601181|ref|YP_007907652.1|  63 ILAERAAALENAGADMVLIcTNTMHKVADDVQSRINIPLVSI 104
                                       47899*********9976537899***************998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.09
                   Pantoate_transf 112 KleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEav 183
                                       K                                            +e++++ le   +l e+G+  +vl ++
  gi|488601181|ref|YP_007907652.1| 170 K--------------------------------------------KESKSRFLEIISKLVENGVEGIVLGCT 197
                                       3............................................445555555566666666666666655 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06    0.0064     160     218 ..      66     121 ..      57     137 .. 0.87
   2 ?   -2.0   0.0      0.43   1.9e+03      86     104 ..     176     194 ..     171     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                        PEP_mutase 160 eRaraYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgtlsvaelaelGvaris 218
                                       eRa a  +AGAd+v+++  +  +   ++ +++++pl+ +    + + +e+ + G++ + 
  gi|488601181|ref|YP_007907652.1|  66 ERAAALENAGADMVLICTNTMHKVADDVQSRINIPLVSII---DATAEEIVKNGIKKVG 121
                                       8****************9988888889999999**99999...7899999999988775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.43
                        PEP_mutase  86 evaetvrrliaaGvvgvni 104
                                       ++ e + +l++ Gv g+++
  gi|488601181|ref|YP_007907652.1| 176 RFLEIISKLVENGVEGIVL 194
                                       5667888999999999887 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.8e-06     0.031      27      88 ..      37     111 ..      17     112 .. 0.78
   2 ?   -3.3   0.0       2.1   9.4e+03      38      53 ..     180     195 ..     168     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.8e-06
                                PA  27 kivLvqrtf.....................aeKarnAqaaGAagviivndgelgaatgasgnegepdgitiPavgvs 82 
                                       ki+L   +f                     ae+a++ ++aGA  v+i +++           ++ +++i+iP v++ 
  gi|488601181|ref|YP_007907652.1|  37 KILLY--SFdfeeivekqktedwkalgdilAERAAALENAGADMVLICTNTM------HKVADDVQSRINIPLVSII 105
                                       67777..556677777777778888888899*****************7665......3333334667******998 PP

                                PA  83 redgea 88 
                                        +++e+
  gi|488601181|ref|YP_007907652.1| 106 DATAEE 111
                                       887776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                                PA  38 KarnAqaaGAagviiv 53 
                                        +    ++G +g+++ 
  gi|488601181|ref|YP_007907652.1| 180 IISKLVENGVEGIVLG 195
                                       5555566677776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1501.51
//
Query:       gi|488601182|ref|YP_007907653.1|  [L=653]
Description: Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-37  125.1   0.1    1.2e-17   63.9   0.0    2.4  2  CCG              Cysteine-rich domain
      4e-12   46.4   4.1    8.2e-12   45.4   4.1    1.5  1  Fer4_8           4Fe-4S dicluster domain
      1e-07   32.0   6.5    1.5e-07   31.4   4.5    2.2  2  Fer4_9           4Fe-4S dicluster domain
    1.2e-07   31.8  22.2    1.1e-06   28.7  11.9    2.5  2  Fer4_10          4Fe-4S dicluster domain
    6.8e-07   29.8   6.7    2.4e-06   28.0   6.7    2.0  1  Fer4_7           4Fe-4S dicluster domain
    1.8e-06   27.7   7.3    3.3e-06   26.8   7.3    1.4  1  Nitrate_red_gam  Nitrate reductase gamma subunit
    1.9e-05   24.5  11.1    0.00047   20.1   1.6    2.6  2  Fer4_2           4Fe-4S binding domain
    1.9e-05   25.5   8.3    8.5e-05   23.4   8.1    2.2  2  Fer4_16          4Fe-4S double cluster binding domain
    0.00066   19.9   1.2        1.1    9.5   0.2    2.5  2  Fer4_18          4Fe-4S dicluster domain
    0.00099   19.6  14.8      0.011   16.3  13.9    2.6  3  Fer4_17          4Fe-4S dicluster domain
     0.0034   17.5   7.8       0.12   12.5   0.7    2.8  3  Fer4_21          4Fe-4S dicluster domain
     0.0042   17.5  11.8      0.021   15.3   0.5    3.0  3  Fer4_4           4Fe-4S binding domain
     0.0066   16.2  20.4      0.014   15.2   2.5    2.8  3  Fer4             4Fe-4S binding domain
     0.0084   16.9   6.3      0.051   14.4   0.2    3.0  2  Fer4_22          4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.37   11.0  14.3       0.67   10.1   2.7    2.7  2  Fer4_6           4Fe-4S binding domain
       0.39   10.2   2.6       0.84    9.1   2.6    1.5  1  DUF1129          Protein of unknown function (DUF1129)
        1.5    9.9  22.0       0.36   11.9   5.1    2.8  2  Fer4_3           4Fe-4S binding domain
        3.8    8.3   6.7        6.9    7.5   0.3    2.5  2  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 !   59.0   0.0   4.1e-19   4.1e-16       2      84 ..     417     501 ..     416     502 .. 0.96
   2 !   63.9   0.0   1.2e-20   1.2e-17       1      84 [.     536     623 ..     536     624 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 4.1e-19
                               CCG   2 ayfdgCh.llraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivta 76 
                                       ++++gC    +++++ v k+l ++l+a g  + +l ++e CCG+  +r g+e l++ l+++n +t+e++g++ iv++
  gi|488601182|ref|YP_007907653.1| 417 LWWVGCGhSFDNRNKIVSKKLVEILNAIGFSYAILgREEGCCGNDVRRVGEEGLFQLLMEENTATFEKYGVERIVAT 493
                                       79****7799999**************************************************************** PP

                               CCG  77 cpgCllql 84 
                                       +p+C++ +
  gi|488601182|ref|YP_007907653.1| 494 SPHCYNAF 501
                                       *****987 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 1.2e-20
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                       v+++d+C+l+r++  y+ +r++lk +++ ++ve++++ e++ CCGaggg+ ++e     + ++ ++++a  tga+++
  gi|488601182|ref|YP_007907653.1| 536 VTFHDPCYLGRYNgmYELPREILKTIPGIELVEMPRNrERSFCCGAGGGNLVREYpGEDRPNNIRAKEAAGTGAEIL 612
                                       89*****************************************************7777****************** PP

                               CCG  74 vtacpgCllql 84 
                                       ++acp+C ++l
  gi|488601182|ref|YP_007907653.1| 613 AVACPFCMIML 623
                                       ********998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   4.1   8.2e-15   8.2e-12       3      64 ..     276     352 ..     274     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 8.2e-15
                            Fer4_8   3 ekCieCgaCqsaCp...............vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                        +C++Cg+Cq+aCp                lr+t  +++d  g+ +e+ +  + + + +a+w+Cttc+aC e Cpv 
  gi|488601182|ref|YP_007907653.1| 276 LACMRCGRCQDACPafnsgttlspmylmqNLRKTLSDSHDFLGRPKEETVLLDSVLDMDAVWACTTCRACMEMCPVY 352
                                       58***********9555555555555444444466777777777777666666666689****************85 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   4.5   1.5e-10   1.5e-07       1      48 [.     277     351 ..     277     353 .. 0.87
   2 ?   -1.0   0.0       2.1   2.1e+03      11      23 ..     615     627 ..     592     635 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.5e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...........................eaCigCgaCveaCpk 48 
                                       +C++Cg+C++aCpa       ++ +  ++ ++                            +aC++C+aC+e Cp 
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACPAFNSGTTLSPMYLMQNLRKTlsdshdflgrpkeetvlldsvldmdavWACTTCRACMEMCPV 351
                                       6***********8888777777777776666667888888889******************************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                            Fer4_9  11 aCpagvvvedaae 23 
                                       aCp+++++ +++ 
  gi|488601182|ref|YP_007907653.1| 615 ACPFCMIMLEDGV 627
                                       5777666666655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7  11.9   1.1e-09   1.1e-06       8      56 .]     277     350 ..     271     350 .. 0.81
   2 !   17.3   2.6   3.8e-06    0.0038       8      27 ..     338     357 ..     330     378 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-09
                           Fer4_10   8 tCirCgkCvkaCPadl.........................tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                        C+rCg+C++aCPa +                             +++    +++ +  +v++Ct+c aC+e CP
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACPAFNsgttlspmylmqnlrktlsdshdflG-RPKEETVLLDSVLDMdAVWACTTCRACMEMCP 350
                                       7*************88********************998742.333333334444444599*************9 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.8e-06
                           Fer4_10   8 tCirCgkCvkaCPadltsvg 27 
                                        C+ C++C+++CP+++++++
  gi|488601182|ref|YP_007907653.1| 338 ACTTCRACMEMCPVYIEHME 357
                                       48888888888888774444 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   6.7   2.5e-09   2.4e-06       1      50 [.     277     351 ..     277     353 .. 0.54

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.5e-09
                            Fer4_7   1 rCigCgaCvaaCp..vkaield.........eeenek...........gtekv.........eid.pekClgCgaCv 45 
                                       +C+ Cg+C++aCp  ++  +l          +                +             ++d  + C++C+aC+
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACPafNSGTTLSpmylmqnlrK----TlsdshdflgrpK---EetvlldsvlDMDaVWACTTCRACM 346
                                       5***********85433333332222222220....1222233443221...12234555336664568******** PP

                            Fer4_7  46 avCPt 50 
                                       + CP+
  gi|488601182|ref|YP_007907653.1| 347 EMCPV 351
                                       ****8 PP

>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   7.3   3.4e-09   3.3e-06      46     215 ..      82     248 ..      72     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.4e-09
                   Nitrate_red_gam  46 lgsplFHvGilvvllgHlvGlliPksvtealgvseelyqllalvaGliagvlalvGlllLllRRltnkrvraa.... 118
                                       +   l  +G++v+ +g ++ l i +++ +++  + ++y + + +a  +ag+++++Gl++  l R   k  r a    
  gi|488601182|ref|YP_007907653.1|  82 VMHLLMLWGLIVLTIGTVI-LTIADHFESSF-FRGTFYLIHE-AAMDLAGLALIAGLVIAALNRYIIKPSRFAkkwe 155
                                       5556666888888888776.55555555555.5666666654.455689**********999887666555441111 PP

                   Nitrate_red_gam 119 tsasDkvvlllLllqillGllttlvsaldygseretispwlrsll.tlqpd.aellaevplifklHvllglllfalf 193
                                         + D +vl+ L++ ++lG+l+  +         + + p+   +   ++ + +  l+    ++ +H l+++l +al+
  gi|488601182|ref|YP_007907653.1| 156 HAKDDGLVLFGLIAITVLGFLVESIRLA------SGMPPYTAIIGgAISSTlPFNLEAYRALWSIHSLFAMLFVALI 226
                                       3467899999999999999988777644......445555555531222333677899999**************** PP

                   Nitrate_red_gam 194 PFtrLvHvlsapleYllrpyqv 215
                                       PFt+L Hv++apl+ l+r+  v
  gi|488601182|ref|YP_007907653.1| 227 PFTKLAHVIAAPLNILTRTERV 248
                                       ******************8665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.6   4.7e-07   0.00047       8      22 .]     276     290 ..     269     290 .. 0.88
   2 !    8.9   2.4    0.0018       1.8       9      21 ..     338     350 ..     330     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.7e-07
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                        +C++Cg C++aCPa
  gi|488601182|ref|YP_007907653.1| 276 LACMRCGRCQDACPA 290
                                       68************8 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0018
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                       +C+ C+aC   CP
  gi|488601182|ref|YP_007907653.1| 338 ACTTCRACMEMCP 350
                                       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 !   23.4   8.1   8.6e-08   8.5e-05       2      66 ..     278     351 ..     277     352 .. 0.75
   2 !   11.9   3.5   0.00033      0.33       2      16 ..     339     353 ..     338     423 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.6e-08
                           Fer4_16   2 CgtCgkCaevCPtnaikek...kekeiearecisy......ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C +Cg+C ++CP+    ++    + + + r++ s       + +e+  l ++   ++  +a+t C++C+++CP+
  gi|488601182|ref|YP_007907653.1| 278 CMRCGRCQDACPAFNSGTTlspMYLMQNLRKTLSDshdflgRPKEETVLLDSVLDMDAVWACTTCRACMEMCPV 351
                                       ************96644441114444466666666889997777777777778888889**************7 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00033
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C+tC++C+e+CP+  
  gi|488601182|ref|YP_007907653.1| 339 CTTCRACMEMCPVYI 353
                                       ************965 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0023       2.3      70      96 ..     262     289 ..     227     298 .. 0.82
   2 !    9.5   0.2    0.0011       1.1      56      76 ..     334     354 ..     317     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
                           Fer4_18  70 vcPtgidirkGl.qleciscllcidacd 96 
                                       + P ++  r+ l  l c+ c++c dac 
  gi|488601182|ref|YP_007907653.1| 262 IEPKDLQWRDMLsSLACMRCGRCQDACP 289
                                       5577777777763589**********96 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                           Fer4_18  56 kgagdcidcescvkvcPtgid 76 
                                       +++  c++c++c+++cP+ i+
  gi|488601182|ref|YP_007907653.1| 334 DAVWACTTCRACMEMCPVYIE 354
                                       55668************9986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   3.0    0.0008       0.8      24      58 ..     257     290 ..     247     291 .. 0.68
   2 !   16.3  13.9   1.1e-05     0.011       1      58 [.     277     351 ..     277     354 .. 0.79
   3 !   12.8   3.7   0.00013      0.13       1      19 [.     338     356 ..     338     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0008
                           Fer4_17  24 kllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       +++ a+++++l+   ++     C+ Cg+C+ +CP+
  gi|488601182|ref|YP_007907653.1| 257 EYMGAIEPKDLQW-RDMLSSLACMRCGRCQDACPA 290
                                       5566666654443.344577789999999999995 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.1e-05
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydnepkkllraakl................glleeaekeekaslCieCgeCerkCPq 58 
                                       +C++Cg C ++Cp ++  +   p+ l+++++                  ll+ + +++++  C++C+ C + CP 
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACPAFNSgTTLSPMYLMQNLRKtlsdshdflgrpkeetVLLDSVLDMDAVWACTTCRACMEMCPV 351
                                       5************999877778888888776656677777776666543566677889****************5 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00013
                           Fer4_17   1 rCiqCgyClpeCpsyeayd 19 
                                       +C+ C++C+++Cp y+++ 
  gi|488601182|ref|YP_007907653.1| 338 ACTTCRACMEMCPVYIEHM 356
                                       5*************99864 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.3    0.0027       2.7       7      19 ..     277     289 ..     263     296 .. 0.81
   2 !   12.5   0.7   0.00012      0.12      40      56 ..     338     352 ..     322     357 .. 0.87
   3 ?   -2.2   0.0       4.8   4.8e+03       9      17 ..     614     622 ..     599     630 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0027
                           Fer4_21   7 kCigCgkCliaCe 19 
                                        C+ Cg+C  aC+
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACP 289
                                       5888888888886 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                           Fer4_21  40 eCvGCnlCssvCPvedc 56 
                                        C+ C  C+++CPv  +
  gi|488601182|ref|YP_007907653.1| 338 ACTTCRACMEMCPV--Y 352
                                       6************9..4 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.8
                           Fer4_21   9 igCgkClia 17 
                                       + C  C+i+
  gi|488601182|ref|YP_007907653.1| 614 VACPFCMIM 622
                                       344444444 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5   2.1e-05     0.021       3      15 ..     277     289 ..     271     303 .. 0.91
   2 !    8.5   1.2    0.0031       3.1       4      16 ..     339     351 ..     333     357 .. 0.92
   3 ?   -2.0   0.1       7.2   7.2e+03       6      11 ..     615     620 ..     613     621 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                        C +Cg+C +aCP
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACP 289
                                       5************ PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0031
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C+ C++C+  CP+
  gi|488601182|ref|YP_007907653.1| 339 CTTCRACMEMCPV 351
                                       ***********96 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.2
                            Fer4_4   6 gCgsCv 11 
                                        C+ C+
  gi|488601182|ref|YP_007907653.1| 615 ACPFCM 620
                                       588885 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.5   1.4e-05     0.014       7      19 ..     277     289 ..     274     290 .. 0.92
   2 !   11.0   4.8   0.00029      0.29       8      20 ..     339     351 ..     338     353 .. 0.92
   3 ?   -3.3   0.2       9.8   9.8e+03      16      20 ..     614     618 ..     613     618 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                       TSSS-THHHHHST CS
                              Fer4   7 kCigCGaCvevCP 19 
                                        C++CG+C ++CP
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACP 289
                                       6************ PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00029
                                       SSS-THHHHHSTT CS
                              Fer4   8 CigCGaCvevCPv 20 
                                       C+ C aC+e+CPv
  gi|488601182|ref|YP_007907653.1| 339 CTTCRACMEMCPV 351
                                       ************8 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.8
                                       HHSTT CS
                              Fer4  16 evCPv 20 
                                        +CP+
  gi|488601182|ref|YP_007907653.1| 614 VACPF 618
                                       69**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 !   14.4   0.2   5.2e-05     0.051      61      94 ..     257     290 ..     242     291 .. 0.80
   2 ?    4.6   0.4     0.061        60      81      95 ..     338     352 ..     323     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-05
                           Fer4_22  61 rlrqrllhklsefkekfgesgCvGCgRCieacpv 94 
                                        +   +  k  ++++  ++ +C+ CgRC++acp+
  gi|488601182|ref|YP_007907653.1| 257 EYMGAIEPKDLQWRDMLSSLACMRCGRCQDACPA 290
                                       55556666778899999***************96 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.061
                           Fer4_22  81 gCvGCgRCieacpvk 95 
                                       +C+ C  C+e+cpv 
  gi|488601182|ref|YP_007907653.1| 338 ACTTCRACMEMCPVY 352
                                       677777777777765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.7   0.00067      0.67       8      21 ..     277     290 ..     276     293 .. 0.91
   2 ?    5.4   4.0     0.021        21       8      22 ..     338     352 ..     338     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00067
                            Fer4_6   8 kCigCgdCvrvCPe 21 
                                       +C  Cg+C ++CP+
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACPA 290
                                       6999*********7 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                            Fer4_6   8 kCigCgdCvrvCPeg 22 
                                       +C+ C++C+  CP +
  gi|488601182|ref|YP_007907653.1| 338 ACTTCRACMEMCPVY 352
                                       6************75 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.6   0.00084      0.84      85     191 ..      90     199 ..      74     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00084
                           DUF1129  85 sLlllalfallfgilalfskkkqtas.....iGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllillll 156
                                       +L++l + +++  i   f+++    +        + l+ +al++Gl++  ++r++ +  +  k+ +  k   ++l+ 
  gi|488601182|ref|YP_007907653.1|  90 GLIVLTIGTVILTIADHFESSFFRGTfylihEAAMDLAGLALIAGLVIAALNRYIIKPSRFAKKWEHAKDDGLVLFG 166
                                       6788888888888888888876666555555566678899***************998999999999********** PP

                           DUF1129 157 lvvwlvlftlvallpaviNpvLpplvliiigviaf 191
                                       l++++vl +lv+++   +   +pp+  ii g+i+ 
  gi|488601182|ref|YP_007907653.1| 167 LIAITVLGFLVESIR--LASGMPPYTAIIGGAISS 199
                                       ***********9985..7899**********9986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.9     0.006         6       1      12 [.     278     289 ..     278     293 .. 0.92
   2 ?   11.9   5.1   0.00036      0.36       1      13 [.     339     351 ..     339     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.006
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ Cg+C ++CP
  gi|488601182|ref|YP_007907653.1| 278 CMRCGRCQDACP 289
                                       999********* PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00036
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       Ct C+aC+e CPv
  gi|488601182|ref|YP_007907653.1| 339 CTTCRACMEMCPV 351
                                       ************8 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.6      0.19   1.9e+02       7      21 ..     277     291 ..     275     295 .. 0.89
   2 ?    7.5   0.3     0.007       6.9       6      24 ..     337     355 ..     331     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.19
                           Fer4_15   7 aCigcglCvaeapev 21 
                                       aC+ cg+C +++p +
  gi|488601182|ref|YP_007907653.1| 277 ACMRCGRCQDACPAF 291
                                       7***********965 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.007
                           Fer4_15   6 daCigcglCvaeapevfel 24 
                                       +aC+ c +C++ +p ++e 
  gi|488601182|ref|YP_007907653.1| 337 WACTTCRACMEMCPVYIEH 355
                                       58************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (653 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.72u 0.26s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 3825.40
//
Query:       gi|488601183|ref|YP_007907654.1|  [L=555]
Description: acetolactate synthase, large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-59  199.5   0.1    6.5e-58  195.1   0.1    2.1  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    4.7e-54  181.9   0.0    8.4e-54  181.0   0.0    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    3.1e-51  173.2   0.4    7.6e-50  168.7   0.0    2.7  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.067   12.9   1.9       0.07   12.9   0.5    1.7  2  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 !  195.1   0.1   1.5e-61   6.5e-58       1     164 [.       1     162 [.       1     168 [. 0.98
   2 ?    2.0   0.0     0.031   1.4e+02     137     161 ..     507     531 ..     491     536 .. 0.84

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 1.5e-61
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       m++a+a+v+aL+++gv+++fg+pG+ i +++dal ++q i+++l+rhEq+a++aAdgyara+gk gv+++tsgpGat
  gi|488601183|ref|YP_007907654.1|   1 MRGADAIVKALEEEGVKTIFGIPGGAIIEVYDALYDSQ-ITHILTRHEQAAVHAADGYARASGKTGVAFTTSGPGAT 76 
                                       789**********************************7.************************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       na+t+la+A+ d++P++vl+g++p+sl+g +++q e d++++  p+tk+++ +++peel + +++A+ +a +grpgP
  gi|488601183|ref|YP_007907654.1|  77 NAVTGLATAYMDSSPIVVLTGQVPRSLIGYDAFQ-EADITGITMPITKHNYIIHKPEELLPSIKEAFYIASTGRPGP 152
                                       **********************************.****************************************** PP

                                       EEEEEEHHHC CS
                      TPP_enzyme_N 155 vylelpkdvl 164
                                       v++++pkd+ 
  gi|488601183|ref|YP_007907654.1| 153 VLIDVPKDIT 162
                                       ********96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHSSS--EEEEEEEH CS
                      TPP_enzyme_N 137 pealrrAirtalsgrpgPvylelpk 161
                                       p+++++A+++a + r +Pv++++  
  gi|488601183|ref|YP_007907654.1| 507 PSEVDEALKEAFEIRDRPVVIDFRV 531
                                       678889999999999******9876 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 !  181.0   0.0   1.9e-57   8.4e-54       1     137 []     190     325 ..     190     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 1.9e-57
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       i++aa+l+ +++rp+il+Gggv+ s+as+el++lae++ + vvttlmgkg+ipe+hpl+lg++g+hgsk+an al e
  gi|488601183|ref|YP_007907654.1| 190 IKRAAQLIMESERPIILAGGGVILSNASDELVKLAETIPAHVVTTLMGKGSIPETHPLCLGFVGMHGSKYANYALTE 266
                                       79*************************************************************************** PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                       +Dlv+a+G+rf+d rttg+ + fap akiihid+dpaeigkn++vd++ivgd+k++l++L
  gi|488601183|ref|YP_007907654.1| 267 CDLVIAVGTRFSD-RTTGNVESFAPYAKIIHIDVDPAEIGKNVRVDVPIVGDAKNVLSSL 325
                                       *************.******************************************9876 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.7   7.5e+03      48      77 ..      64      94 ..      50      97 .. 0.56
   2 ?    1.8   0.0     0.042   1.9e+02     127     153 .]     128     157 ..     106     157 .. 0.85
   3 !  168.7   0.0   1.7e-53   7.6e-50       2     153 .]     380     529 ..     379     529 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.7
                                      EEEEEEEHHHHHHT.GGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C 48 evvaivGDGgflmi.lqelatavrrnlpitv 77
                                      + va++  G  + + ++ lata     pi+v
  gi|488601183|ref|YP_007907654.1| 64 TGVAFTTSGPGATNaVTGLATAYMDSSPIVV 94
                                      4455555555555556666666666666665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.042
                                       ESSH.HHHHHHHHHHHH.....CSSSEEEEEE CS
                      TPP_enzyme_C 127 vekadveeleealkeal.....ekkgpaliev 153
                                       ++k+  eel + +kea+      + gp+li+v
  gi|488601183|ref|YP_007907654.1| 128 IHKP--EELLPSIKEAFyiastGRPGPVLIDV 157
                                       4455..**********999999999*****97 PP

  == domain 3  score: 168.7 bits;  conditional E-value: 1.7e-53
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvv 78 
                                       +G++++waa+++k k pr++++sgglgtmG+g+paAiGa++a p+++vv ++GDG+flm++qelat+v  n+p+++ 
  gi|488601183|ref|YP_007907654.1| 380 VGQNQMWAAQYFKTKYPRQFISSGGLGTMGFGFPAAIGAQMAFPEKNVVDVAGDGSFLMNIQELATCVDFNIPVKIA 456
                                       9**************************************************************************** PP

                                       EEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH.CSSSEEEEEE CS
                      TPP_enzyme_C  79 vlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkeal.ekkgpaliev 153
                                       ++nN+ +gm++++qe f+++r+s++     k+++f k+ae++G  g++ve++  +e++ealkea+  +++p++i++
  gi|488601183|ref|YP_007907654.1| 457 IMNNQFLGMVRQWQELFYKERYSATC-LRCKEMRFDKIAEGFGGVGIVVERP--SEVDEALKEAFeIRDRPVVIDF 529
                                       ***********************988.468899***************99**..***********8899*****95 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 ?   12.9   0.5   1.6e-05      0.07      37      94 ..      38      97 ..      23     103 .. 0.78
   2 ?   -3.6   0.0       1.7   7.7e+03     180     216 ..     347     383 ..     331     394 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                                      E.EEEE-SSHHHHHHHHHH.HHCTT-EEEEE.EECCHHHHCCCCHHHHHHTT--EEEEEE CS
                             POR_N 37 dvevvqmesEigaisaviG.AaaaGaraaTa.TSgqGllLmienlglaageelPvvivvv 94
                                      +++ + +  E +a+ a+ G A a+G  ++ + TSg+G   ++  l  a ++  P+v+   
  gi|488601183|ref|YP_007907654.1| 38 QITHILTRHEQAAVHAADGyARASGKTGVAFtTSGPGATNAVTGLATAYMDSSPIVVLTG 97
                                      456788899**********56667776655438***********************9765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                                       SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSX CS
                             POR_N 180 kleeyerkeyaldpekpiargtaanpdtglehrekgn 216
                                       k++ + rk+ +l+p+  i r     pdt ++ +  +n
  gi|488601183|ref|YP_007907654.1| 347 KYPLRYRKDDKLRPQYIIERIFEIEPDTIVTTEVGQN 383
                                       4444445555555555555555555555554443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.71u 0.39s 00:00:01.10 Elapsed: 00:00:00.60
# Mc/sec: 2783.91
//
Query:       gi|488601184|ref|YP_007907655.1|  [L=171]
Description: acetolactate synthase, small subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-32  110.4   5.7    5.8e-32  109.7   1.5    2.3  2  ALS_ss_C         Small subunit of acetolactate synthase
    1.2e-18   66.5   0.1    2.5e-18   65.5   0.1    1.5  1  ACT              ACT domain
    3.1e-18   65.4   1.1    8.6e-18   63.9   1.1    1.8  1  ACT_5            ACT domain
    8.9e-08   32.6   2.1    1.7e-07   31.8   2.1    1.5  1  ACT_4            ACT domain
    0.00096   19.5   0.8          1    9.8   0.2    2.4  2  Acylphosphatase  Acylphosphatase
     0.0037   17.1   0.2        3.5    7.5   0.0    2.5  2  NIL              NIL domain
     0.0059   17.0   0.2      0.011   16.2   0.2    1.5  1  Saccharop_dh_N   LOR/SDH bifunctional enzyme conserved region
  ------ inclusion threshold ------
      0.016   14.3   0.3      0.017   14.3   0.3    1.1  1  APG17            Autophagy protein Apg17
      0.054   13.5   0.1      0.054   13.5   0.1    2.5  2  DUF2187          Uncharacterized protein conserved in bacteri
      0.057   13.4   0.2        0.2   11.6   0.1    2.0  2  ACT_6            ACT 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 ?    2.6   0.1     0.087   1.6e+02      37      63 ..      53      80 ..      36      87 .. 0.76
   2 !  109.7   1.5   3.2e-35   5.8e-32       1      74 []      90     163 ..      90     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.087
                                      EEEEEEE-HHHHHHHHHHS-.GGGEEEE CS
                          ALS_ss_C 37 liieltgteekidaliellk.pfgilev 63
                                      ++i + g+++ ++++++ l+  ++i++v
  gi|488601184|ref|YP_007907655.1| 53 MTIVVNGDTKMVEQVMKQLNkLIEIIKV 80
                                      6778888888888888888624446655 PP

  == domain 2  score: 109.7 bits;  conditional E-value: 3.2e-35
                                       EEEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                          ALS_ss_C   1 RElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                       REl+LiKVka++e+r ei e+a+ifr+++vdvs+dsliieltg+e+ki a+++l+++fgi e++RtG+vA++RG
  gi|488601184|ref|YP_007907655.1|  90 RELVLIKVKATSETRGEIVELANIFRGRVVDVSKDSLIIELTGDEDKIRAFVNLMRQFGIRELARTGKVAMQRG 163
                                       9************************************************************************8 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.1   1.4e-21   2.5e-18       1      66 [.      10      75 ..      10      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.4e-21
                                      EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                      ++++v+v+++PG+Larv++++ +r++Ni+s+++++++++  +++++v+ +d++ +e+v+++l+kl+
  gi|488601184|ref|YP_007907655.1| 10 YTISVLVENKPGVLARVSSLFRRRNFNIESLTVGTTDREDISRMTIVVNGDTKMVEQVMKQLNKLI 75
                                      79**************************************************************97 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   1.1   4.8e-21   8.6e-18       2      62 .]      19      80 ..      18      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 4.8e-21
                             ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                                      +pgvL Rv +++rrr F+++sl++ tt++++ +r++++V++  ++ve++++Ql+KLi+++kV
  gi|488601184|ref|YP_007907655.1| 19 KPGVLARVSSLFRRRNFNIESLTVGTTDREDISRMTIVVNGdTKMVEQVMKQLNKLIEIIKV 80
                                      7**********************************************************998 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   2.1   9.3e-11   1.7e-07       6      78 ..       9      80 ..       4      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 9.3e-11
                             ACT_4  6 tvrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78
                                      + +++v +e+++g+La++++++   + ni+s+++ t++++ + +++i v+  d++ +++v+++L+++ ++i+V
  gi|488601184|ref|YP_007907655.1|  9 KYTISVLVENKPGVLARVSSLFRRRNFNIESLTVGTTDREDISRMTIVVN-GDTKMVEQVMKQLNKLIEIIKV 80
                                      679*********************************98888998888888.89******************99 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2   0.00056         1      32      75 ..      46      89 ..      33      93 .. 0.84
   2 !    8.0   0.0    0.0021       3.8      28      66 ..     115     155 ..     110     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
                   Acylphosphatase 32 rNlsdgsVeivaegeeekvekfleelksgppkarvdeveveele 75
                                       +++  +  iv+ g+++ ve+++++l++  + ++v++v+ + +e
  gi|488601184|ref|YP_007907655.1| 46 DREDISRMTIVVNGDTKMVEQVMKQLNKLIEIIKVSDVTENSVE 89
                                      555556889*******************9999999999887766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                   Acylphosphatase  28 kGyvrNlsdgsVeivaegeeekvekfleelks.gppk.arv 66 
                                       +G v   s++s+ i+++g+e+k+++f++ +++ g  + ar 
  gi|488601184|ref|YP_007907655.1| 115 RGRVVDVSKDSLIIELTGDEDKIRAFVNLMRQfGIRElART 155
                                       68899999999*****************9998655444555 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0025       4.4      19      66 ..      25      73 ..      16      80 .. 0.83
   2 !    7.5   0.0     0.002       3.5      45      69 ..     125     149 ..     110     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                                      HHHHHH.T-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHH CS
                               NIL 19 hlvrql.glevnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrk 66
                                      ++++ +   ++nI +  v++ + + + +++i + g+ + ++++++ l+k
  gi|488601184|ref|YP_007907655.1| 25 RVSSLFrRRNFNIESLTVGTTDREDISRMTIVVNGDTKMVEQVMKQLNK 73
                                      5555555567888888999999**********************99987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                                       EEEEEEES-HHHHHHHHHHHHHTT- CS
                               NIL  45 qlvielsgsqesiaaalqylrkrnv 69 
                                       +l+iel+g++++i a ++ +r+ ++
  gi|488601184|ref|YP_007907655.1| 125 SLIIELTGDEDKIRAFVNLMRQFGI 149
                                       79***************99998776 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 !   16.2   0.2     6e-06     0.011      29      87 ..      34      91 ..      22     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
                                      EEEEEEEEXXSS.TTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEEEECESSCT CS
                    Saccharop_dh_N 29 sfevlefevGkk.kkdtSyaelevsaedeevLeeileeltelgaelveeedvklekaekd 87
                                      +f++++++vG++ ++d S  ++ v++++ + +e+++++l++l   + +++dv+ +++e++
  gi|488601184|ref|YP_007907655.1| 34 NFNIESLTVGTTdREDISRMTIVVNGDT-KMVEQVMKQLNKLIEII-KVSDVTENSVERE 91
                                      7*********863688999999999876.789********995443.4456655555554 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   9.3e-06     0.017     220     278 ..      36     110 ..       6     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.3e-06
                                       .........S-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 220 e........lseeereelleVlekDaaeledVvkelqerleem........ekakkllsekkeeiekllsalkka 278
                                       +         + e+   +  V+  D++ +e+V+k+l++ +e++        + + +l+  k +++ ++  +++++
  gi|488601184|ref|YP_007907655.1|  36 NiesltvgtTDREDISRMTIVVNGDTKMVEQVMKQLNKLIEIIkvsdvtenSVERELVLIKVKATSETRGEIVEL 110
                                       344555555677889999*************************88776655444445555555555555555554 PP

>> DUF2187  Uncharacterized protein conserved in bacteria (DUF2187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.96   1.7e+03      21      30 ..      79      88 ..      58      95 .. 0.73
   2 ?   13.5   0.1     3e-05     0.054       4      38 ..     103     134 ..     100     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.96
                           DUF2187 21 iVekvnenSV 30
                                      +V  v enSV
  gi|488601184|ref|YP_007907655.1| 79 KVSDVTENSV 88
                                      4666777777 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3e-05
                           DUF2187   4 kvGdiieFkkgdlkltGiVekvnenSViVdltimd 38 
                                       + G+i+e  +    ++G+V+ v ++S i++lt  +
  gi|488601184|ref|YP_007907655.1| 103 TRGEIVELANI---FRGRVVDVSKDSLIIELTGDE 134
                                       57999999999...******************333 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00011       0.2       5      65 ..      12      74 ..      11      81 .. 0.85
   2 ?   -3.1   0.0       4.4   7.9e+03       3      10 ..     126     133 ..     125     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                             ACT_6  5 itvtGpdrpGltasLtsvlaefgvni..lDieqavihgrlsLgllvsgpedalarlekaLlfl 65
                                      i+v+ +++pG++a+++s+  + + ni  l+++    ++    +++v g+ + +++++k+L +l
  gi|488601184|ref|YP_007907655.1| 12 ISVLVENKPGVLARVSSLFRRRNFNIesLTVGTTDREDISRMTIVVNGDTKMVEQVMKQLNKL 74
                                      7788899************998888833567777777779999999999*********99886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.4
                             ACT_6   3 llitvtGp 10 
                                       l+i +tG+
  gi|488601184|ref|YP_007907655.1| 126 LIIELTGD 133
                                       56666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); 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:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1093.84
//
Query:       gi|488601185|ref|YP_007907656.1|  [L=78]
Description: hypothetical protein Asulf_01691 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 549.00
//
Query:       gi|488601186|ref|YP_007907657.1|  [L=624]
Description: Lon-B peptidase, Serine peptidase, MEROPS family S16 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  117.7   0.1    4.2e-23   81.9   0.0    3.1  3  AAA_32           AAA domain
    1.8e-31  109.3   2.4    3.2e-31  108.5   2.4    1.4  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    7.2e-17   61.5   0.1    1.6e-10   40.7   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.7e-14   53.9   0.0    2.3e-07   30.7   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
    2.8e-10   40.1   0.7      7e-10   38.8   0.7    1.7  1  ChlI             Subunit ChlI of Mg-chelatase
    6.5e-10   39.1   0.0      8e-05   22.7   0.0    2.9  2  AAA_5            AAA domain (dynein-related subfamily)
    1.5e-08   34.0   0.0     0.0012   18.0   0.0    2.4  2  MCM              MCM P-loop domain
    1.1e-06   29.1   0.0      0.003   18.0   0.0    3.3  3  AAA              ATPase family associated with various cellul
    2.3e-05   24.7   0.0     0.0005   20.3   0.0    2.7  2  AAA_22           AAA domain
      3e-05   24.4   0.0      0.019   15.3   0.0    2.5  2  AAA_19           AAA domain
    4.3e-05   23.3   0.0      0.023   14.5   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00016   21.0   0.0       0.17   11.1   0.0    2.5  2  TIP49            TIP49 P-loop domain
    0.00019   21.3   0.0       0.81    9.6   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00038   20.0   0.0     0.0013   18.3   0.0    1.8  2  AAA_7            P-loop containing dynein motor region
    0.00061   19.3   0.0     0.0031   17.0   0.0    2.1  2  PhoH             PhoH-like protein
    0.00076   19.2   0.1      0.014   15.1   0.0    2.7  3  AAA_30           AAA domain
     0.0019   18.3   0.0       0.32   11.1   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0037   16.2   0.1        1.9    7.3   0.0    2.4  2  AAA_PrkA         PrkA AAA domain
     0.0046   17.1   0.0       0.82    9.7   0.0    2.6  2  DUF87            Helicase HerA, central domain
     0.0055   17.1   0.0      0.022   15.1   0.0    2.1  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.047   14.2   0.0    2.0  2  ABC_tran         ABC transporter
      0.011   14.9   0.0      0.027   13.6   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
      0.012   15.3   0.0      0.031   14.0   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.014   15.8   0.8      0.052   14.0   0.2    2.2  2  MCM_lid          MCM AAA-lid domain
      0.024   15.0   0.0      0.048   14.1   0.0    1.5  1  RNA_helicase     RNA helicase
      0.027   14.6   0.0      0.079   13.1   0.0    1.8  1  AAA_33           AAA domain
      0.035   14.0   0.0      0.071   13.0   0.0    1.6  1  NACHT            NACHT domain
      0.036   13.1   0.0      0.064   12.3   0.0    1.2  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.038   14.5   0.0       0.15   12.6   0.0    2.1  1  AAA_18           AAA domain
      0.039   12.9   0.0      0.071   12.0   0.0    1.4  1  AAA_10           AAA-like domain
      0.055   13.3   0.9       0.16   11.8   0.4    1.9  2  DUF4118          Domain of unknown function (DUF4118)
      0.066   13.2   0.0       0.33   10.9   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
      0.076   11.5   1.4       0.93    7.9   0.0    2.3  2  Aldedh           Aldehyde dehydrogenase family
      0.078   12.9   0.0       0.77    9.6   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
      0.086   13.1   0.0       0.36   11.1   0.0    2.1  1  AAA_28           AAA domain
       0.13   11.9   0.0       0.26   11.0   0.0    1.5  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.5e-10   1.3e-07       7      93 ..      35     116 ..      29     127 .. 0.84
   2 !   81.9   0.0   8.5e-26   4.2e-23     281     508 ..     175     401 ..     170     406 .. 0.89
   3 ?    0.7   0.0      0.36   1.8e+02     456     481 ..     598     623 ..     590     624 .] 0.88

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.5e-10
                            AAA_32   7 leeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpa 83 
                                       ++++igq+ Avea++ +     ++ ++ ++G++gtG+++l+k + e   k  +  +D++   n ++p++P++  +pa
  gi|488601186|ref|YP_007907657.1|  35 VDQVIGQDDAVEAIKKAAV---QKRHVMLIGSPGTGKSMLAKAMAELLPK--EELEDILVYPNLEDPNQPRIRTVPA 106
                                       4899***********9864...4459**************9999987644..4467888889*************** PP

                            AAA_32  84 GkGkelkkdm 93 
                                       GkGke  ++ 
  gi|488601186|ref|YP_007907657.1| 107 GKGKEIVDSY 116
                                       ****987665 PP

  == domain 2  score: 81.9 bits;  conditional E-value: 8.5e-26
                            AAA_32 281 nvlvdnsetegaPVvvednptyanLfGkieyesemg.alvt.dftlIkaGaLhkAnGGyLildaedlLeeplaWeaL 355
                                       ++lv+n+++e aP    +  +   LfG + ++  +   l t  +++++aGa+h+A+ G+L +d  + L+ + + +++
  gi|488601186|ref|YP_007907657.1| 175 KLLVNNKDKETAPYEDATGAHAGALFGDVRHDPFQSgGLETpPHERVEAGAIHRAHKGVLFIDETNTLTIE-SQQKI 250
                                       79***********99999************99754436665279************************866.56778 PP

                            AAA_32 356 kraLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteene 432
                                         a+++k+  i       + +s    + ep+p+d   +  G+ +    ++ +     + +  +  ++d+m+ t en 
  gi|488601186|ref|YP_007907657.1| 251 LTAMQEKKFPITGQ---SERSSGAMVRTEPVPCDFILVAAGNLDALTGMHPALRSRIEGYGYEIYMNDTMKDTVENR 324
                                       889********953...446788999********9888888887766666666666678999*************** PP

                            AAA_32 433 kkyarfias.ivkkekllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekAl 508
                                       +k++rf+a+ ++k+ k+++fdr+ava++i+++ r a+++++l++r++e+  l+r A  +ak+e++++v+ ehV +A 
  gi|488601186|ref|YP_007907657.1| 325 RKLVRFVAQeVIKDGKIPHFDRNAVAEIIKEAKRRAGRRNHLTLRLRELGGLVRTAGDIAKSENSDLVRVEHVLRAK 401
                                       *******863789999*********************************************************9995 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.36
                            AAA_32 456 varlieyssrlaedqeklstrfseia 481
                                       + +++eys r  ed+++l  r++e++
  gi|488601186|ref|YP_007907657.1| 598 IDEVLEYSLRDGEDKDRLLDRLRELM 623
                                       679***************99998886 PP

>> 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 !  108.5   2.4   6.4e-34   3.2e-31       7     203 ..     412     606 ..     406     608 .. 0.85

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 6.4e-34
                                       THHHH-S-SS--SSSSS--BSSEEEEEEE.ETTEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHHHHHHT CS
                             Lon_C   7 leellGkkrfrseeaekedqvGvvtGlaw.tevGGdlltieavllp....gkgklkltGklgdvmkesaqaalsyvr 78 
                                        ++++ ++r     + + ++vG v Gla   e+ G +l i a ++p     +g+++ tG+l ++ +e+++   ++++
  gi|488601186|ref|YP_007907657.1| 412 ADKYIERRRDYRLFITEGEEVGRVNGLAViGETAGVVLPIMAEVTPslskEEGRVIATGRLQEIAREAVMNVSAIIK 488
                                       55666655555555667899*******9735899******9988763333689**************9998887777 PP

                                       SS-GGGSS-SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHH CS
                             Lon_C  79 sraeelgidkevfekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekl 155
                                       +   +      + ++kd+hi +       +G sa +++ata++s++ +++v + vamtG ++++G+vlp+GG+ +k+
  gi|488601186|ref|YP_007907657.1| 489 KYIGK------NISEKDVHIQFVGTYEGVEGDSASISIATAVISAIENIPVYQSVAMTGSLSVKGEVLPVGGVTQKI 559
                                       55433......356789*****9999999************************************************ PP

                                       HHHHHTT-SBEEEEGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB CS
                             Lon_C 156 laakragikkvilPkenekdlediPeevreeleiilveevdevlkaal 203
                                        aa +ag+k+vi+Pk+n +d+  +  e    +eii+v+++devl+  l
  gi|488601186|ref|YP_007907657.1| 560 EAAIQAGMKRVIIPKDNLDDVL-LDAESSGRIEIIPVSRIDEVLEYSL 606
                                       ******************9985.67888999*************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 !   40.7   0.0   3.2e-13   1.6e-10       3      55 ..      36      88 ..      35      95 .. 0.93
   2 !   18.2   0.0   2.5e-06    0.0013      96     158 ..     220     290 ..     211     314 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.2e-13
                      Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                       +v+Gq++a +a++ aa  + +++l+G+pG+GK+mlak++++llp+ + e++l
  gi|488601186|ref|YP_007907657.1| 36 DQVIGQDDAVEAIKKAAVQKRHVMLIGSPGTGKSMLAKAMAELLPKEELEDIL 88
                                      589******************************************98887766 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.5e-06
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtis....rakakv....efparfqlvaamNp 158
                                       +++ G+i +ah+GvLf+DE+  ++ +  + + + +++++  i+    r++  +      p++f lvaa N+
  gi|488601186|ref|YP_007907657.1| 220 RVEAGAIHRAHKGVLFIDETNTLTIESQQKILTAMQEKKFPITgqseRSSGAMvrtePVPCDFILVAAGNL 290
                                       6789***************9988887777777777777776652111332222111247888888888885 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   7.3e-07   0.00036      10      49 ..      43      82 ..      36      95 .. 0.87
   2 !   30.7   0.0   4.6e-10   2.3e-07      85     130 ..     222     267 ..     214     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.3e-07
                                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTT CS
                   Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrk 49
                                      +++e ikk+a ++ +v++ G  GtGK++la+a+ e  +++
  gi|488601186|ref|YP_007907657.1| 43 DAVEAIKKAAVQKRHVMLIGSPGTGKSMLAKAMAELLPKE 82
                                      67899****************************9866554 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 4.6e-10
                                       BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       ++G++++a++G+lf+De ++l++e Q+k+l+++qe+++   G+s+ 
  gi|488601186|ref|YP_007907657.1| 222 EAGAIHRAHKGVLFIDETNTLTIESQQKILTAMQEKKFPITGQSER 267
                                       57************************************99998765 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.7   1.4e-12     7e-10      12     121 .]     466     576 ..     455     576 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.4e-12
                              ChlI  12 ftivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGe 87 
                                       +  +G +++  +e+   v +++k+ +g ++ +k + +         eG + +++iA ++++a+e+i++ +++ + G 
  gi|488601186|ref|YP_007907657.1| 466 VIATGRLQEIAREAVMNVSAIIKKyIGKNISEKDVHIQFVGTYEGVEGDSASISIATAVISAIENIPVYQSVAMTGS 542
                                       55678889999***********99899************************************************** PP

                              ChlI  88 LsldGslrpvkgvlpialaakkegikkvivpken 121
                                       Ls +G++ pv gv++ + aa ++g+k+vi+pk+n
  gi|488601186|ref|YP_007907657.1| 543 LSVKGEVLPVGGVTQKIEAAIQAGMKRVIIPKDN 576
                                       ********************************98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.6e-07     8e-05       1      37 [.      57      94 ..      57     130 .. 0.77
   2 !   13.3   0.0   0.00012     0.061      60     137 ..     221     303 ..     196     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.6e-07
                                      EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-- CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtt 37
                                      +v+L+G pGtgKs+la+ +a++l + e+e ++ + +++
  gi|488601186|ref|YP_007907657.1| 57 HVMLIGSPGTGKSMLAKAMAELLpKEELEDILVYPNLE 94
                                      79*********************888888777766665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                                       -----....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS--.-TT CS
                             AAA_5  60 vraar....egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller....frviatanpldrsln 128
                                       v+a+     ++ +l++DE +++  e +++ l+ + e+++++    e+ + +   ++e+    f ++a++n     l 
  gi|488601186|ref|YP_007907657.1| 221 VEAGAihraHKGVLFIDETNTLTIESQQKILTAMQEKKFPITGQSERSSGAMV-RTEPvpcdFILVAAGNLDA--LT 294
                                       555556666899***********99999999*********8777777777663.344489**********988..99 PP

                                       -TTHHHHTT CS
                             AAA_5 129 elspalrsR 137
                                        + palrsR
  gi|488601186|ref|YP_007907657.1| 295 GMHPALRSR 303
                                       999*****9 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.6e-05     0.028      47      83 ..      45      81 ..       2      86 .. 0.73
   2 !   18.0   0.0   2.4e-06    0.0012     111     152 ..     220     261 ..     179     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                      BBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                               MCM 47 kledktklrgdinvllvgdpgtaKsqlLkyveklapr 83
                                       +  k+    + +v+l+g pgt+Ks l k++++l+p+
  gi|488601186|ref|YP_007907657.1| 45 VEAIKKAAVQKRHVMLIGSPGTGKSMLAKAMAELLPK 81
                                      333345577889********************99997 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.4e-06
                                       EEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEE CS
                               MCM 111 vleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisi 152
                                        +eaGa+  a+kGv+ iDe +  + e +++++ am +++  i
  gi|488601186|ref|YP_007907657.1| 220 RVEAGAIHRAHKGVLFIDETNTLTIESQQKILTAMQEKKFPI 261
                                       589********************************9887655 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 !   18.0   0.0   6.1e-06     0.003       1      22 [.      58      79 ..      58     132 .. 0.71
   2 ?    7.1   0.0     0.014       6.9      58     125 ..     230     305 ..     218     309 .. 0.82
   3 ?   -1.4   0.1       5.9     3e+03      47      81 ..     350     390 ..     325     489 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.1e-06
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      v+l+G pGtGK++laka+a+ l
  gi|488601186|ref|YP_007907657.1| 58 VMLIGSPGTGKSMLAKAMAELL 79
                                      68*****************986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.014
                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..GGG CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..pdk 114
                                       ++ +lfiDE   l+ ++           ++++lt++++ k                      ++i+++a+n      
  gi|488601186|ref|YP_007907657.1| 230 HKGVLFIDETNTLTIES-----------QQKILTAMQEKKFPitgqserssgamvrtepvPCDFILVAAGNLdaLTG 295
                                       359**********9999...........8899999988888888889999999999999966699999999988888 PP

                                       STHHHHSTTSS CS
                               AAA 115 ldpallrgRfd 125
                                       + pal+ +R++
  gi|488601186|ref|YP_007907657.1| 296 MHPALR-SRIE 305
                                       999999.8876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.9
                                       HHHHHHHHHTS...TSEEEEEETGGGHHHHH...TTCCCHH CS
                               AAA  47 relfkeakeka...kpsilfiDEidalaksr...sgsesee 81 
                                       +e++keak+ a   ++  l + E+  l+++     +se+++
  gi|488601186|ref|YP_007907657.1| 350 AEIIKEAKRRAgrrNHLTLRLRELGGLVRTAgdiAKSENSD 390
                                       55555555555554445555555555555553332222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     1e-06    0.0005       4      38 ..      54      94 ..      50     126 .. 0.77
   2 ?    0.7   0.0       1.2     6e+02      85     110 ..     225     248 ..     199     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee......e 38
                                      ++++++++G +GtGK++l++ ++e l++e+  +       e
  gi|488601186|ref|YP_007907657.1| 54 QKRHVMLIGSPGTGKSMLAKAMAELLPKEELEDIlvypnlE 94
                                      6899**********************987665445555552 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.2
                            AAA_22  85 alraravielliiDEaqhlrseeale 110
                                       a++++++ ++l iDE   l + e  +
  gi|488601186|ref|YP_007907657.1| 225 AIHRAHK-GVLFIDETNTL-TIESQQ 248
                                       4566666.9******9999.433333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.7e-05     0.019       4      38 ..      47      83 ..      44      93 .. 0.80
   2 ?    6.3   0.0     0.022        11     102     128 ..     229     257 ..     173     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-05
                            AAA_19  4 av.e.alkekvllvtaGpGtGKTrvlkhivallvelg 38
                                      a+ + a++++++++++ pGtGK+ + k++ +ll +++
  gi|488601186|ref|YP_007907657.1| 47 AIkKaAVQKRHVMLIGSPGTGKSMLAKAMAELLPKEE 83
                                      66346899***************99998888876665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.022
                            AAA_19 102 eee.llivDEfqdvd.elqyrLlkallge 128
                                       +++ +l++DE+  ++ e q+++l a+ ++
  gi|488601186|ref|YP_007907657.1| 229 AHKgVLFIDETNTLTiESQQKILTAMQEK 257
                                       44569********************9944 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 !   14.5   0.0   4.5e-05     0.023      22      56 ..      44      78 ..      31      87 .. 0.83
   2 ?    5.9   0.0      0.02        10      84     121 ..     230     267 ..     221     305 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-05
                            RuvB_N 22 fieaakkreealdhvllyGpPGlGkttlakiiake 56
                                      ++ea kk   +  hv+l+G+PG Gk+ lak +a+ 
  gi|488601186|ref|YP_007907657.1| 44 AVEAIKKAAVQKRHVMLIGSPGTGKSMLAKAMAEL 78
                                      4677777788889*****************99975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigkGp 121
                                       +k vlfide   l+ + ++ + +am++ ++ i+ ++ +
  gi|488601186|ref|YP_007907657.1| 230 HKGVLFIDETNTLTIESQQKILTAMQEKKFPITGQSER 267
                                       578***********************999988744333 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00034      0.17      32      75 ..      44      80 ..      19      87 .. 0.82
   2 !    7.1   0.0    0.0055       2.7     279     309 ..     231     261 ..     220     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 32 areaagvivelikekklaGravLlaGpsgtGktalaiaiskelg 75
                                      a       ve ik+  +  r v+l G +gtGk+ la a+++ l 
  gi|488601186|ref|YP_007907657.1| 44 A-------VEAIKKAAVQKRHVMLIGSPGTGKSMLAKAMAELLP 80
                                      4.......56699999999*******************998775 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0055
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhmlDiecfsylnraleselaPi 309
                                       +GvlfiDe++ l ie+   +  a+ ++  Pi
  gi|488601186|ref|YP_007907657.1| 231 KGVLFIDETNTLTIESQQKILTAMQEKKFPI 261
                                       7***************999988988887776 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 !    9.6   0.0    0.0016      0.81       1      24 [.      57      80 ..      57      94 .. 0.86
   2 !    9.1   0.0    0.0023       1.2      63      98 ..     231     266 ..     218     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                             AAA_3  1 hvllegvPGlaktllvkalakald 24
                                      hv+l g PG++k +l+ka+a+ l 
  gi|488601186|ref|YP_007907657.1| 57 HVMLIGSPGTGKSMLAKAMAELLP 80
                                      9*******************9885 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                             AAA_3  63 anllladeinrappktqsalleameerqvtvegeth 98 
                                       + +l+ de n  +  +q  +l am+e++  ++g++ 
  gi|488601186|ref|YP_007907657.1| 231 KGVLFIDETNTLTIESQQKILTAMQEKKFPITGQSE 266
                                       46899***********************99988765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.6e-06    0.0013      27      63 ..      49      85 ..      44      91 .. 0.88
   2 ?   -3.0   0.0       8.6   4.3e+03     100     115 ..     230     245 ..     228     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.6e-06
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkekyl 63
                                      ++   +k++v+l+G+ GtGK++++k + + l+ke++ 
  gi|488601186|ref|YP_007907657.1| 49 KKAAVQKRHVMLIGSPGTGKSMLAKAMAELLPKEELE 85
                                      6677899**********************99999875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.6
                             AAA_7 100 kklvvFvDDlnmpake 115
                                       +k v+F+D+ n  + e
  gi|488601186|ref|YP_007907657.1| 230 HKGVLFIDETNTLTIE 245
                                       57799****9987766 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.2e-06    0.0031       8      54 ..      40      89 ..      35     118 .. 0.84
   2 ?   -1.9   0.0       3.8   1.9e+03     122     148 ..     233     258 ..     230     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.2e-06
                                      HHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEE CS
                              PhoH  8 eQkeylealk....kndivfaiGpaGtGKtylavalavealkkkkvkriil 54
                                      +Q++++ea+k    ++  v+ iG+ GtGK++la a+a e+l k++++ i++
  gi|488601186|ref|YP_007907657.1| 40 GQDDAVEAIKkaavQKRHVMLIGSPGTGKSMLAKAMA-ELLPKEELEDILV 89
                                      699999999977777779*****************98.6777777777654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                                       EEEE-SGGG--HHHHHHHHTTB-TT-E CS
                              PhoH 122 fvilDEAQnttkeqmkmfltRlGensk 148
                                       ++++DE   +t e+ + +lt + e+ k
  gi|488601186|ref|YP_007907657.1| 233 VLFIDETNTLTIESQQKILTAMQEK-K 258
                                       6789999999999999999988553.4 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.8e-05     0.014       8      46 ..      46      83 ..      40      93 .. 0.78
   2 ?   -0.2   0.0       1.4   6.9e+02      87     115 ..     229     257 ..     191     263 .. 0.83
   3 ?   -1.3   0.1         3   1.5e+03      81     123 ..     411     470 ..     377     473 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-05
                            AAA_30  8 aavealltsgdrvavltGpAGtGKttalkalreaweaag 46
                                      +a+++++ ++ r ++l G +GtGK+++ ka++e++ +++
  gi|488601186|ref|YP_007907657.1| 46 EAIKKAAVQK-RHVMLIGSPGTGKSMLAKAMAELLPKEE 83
                                      5666666666.59999*****************998774 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                            AAA_30  87 epgtllivDEagmvdtkqlaallkaaeka 115
                                       +++ +l +DE+  + +++ +++l+a++++
  gi|488601186|ref|YP_007907657.1| 229 AHKGVLFIDETNTLTIESQQKILTAMQEK 257
                                       4558999*************999999885 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3
                            AAA_30  81 k.................grarlepg.tllivDEagmvdtkqlaallkaaekagakvilvG 123
                                                         g +++ +   l ++ E++ v    +a+++ +++k++ +vi  G
  gi|488601186|ref|YP_007907657.1| 411 LadkyierrrdyrlfiteG-EEVGRVnGLAVIGETAGVVLPIMAEVTPSLSKEEGRVIATG 470
                                       2333344444444444432.34444446777777777777777777777777777777666 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 !   11.1   0.0   0.00065      0.32      13      43 ..      47      77 ..      43     100 .. 0.88
   2 ?    4.4   0.0     0.074        37      64      96 ..     225     257 ..     200     294 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00065
                                      HHHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
                   Sigma54_activ_2 13 rLeqaaqsklpvfltGekGsgkelvArlLhk 43
                                       +++aa +k  v l+G +G+gk++ A+++++
  gi|488601186|ref|YP_007907657.1| 47 AIKKAAVQKRHVMLIGSPGTGKSMLAKAMAE 77
                                      6899***********************9987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.074
                                       HHHHTTTSEEEEEE-TT--HHHHHHHHHHHHHH CS
                   Sigma54_activ_2  64 lleqakggtLylkdiadlskaeqkeLlellaka 96 
                                        + +a+ g+L++ + + l  + q+++l +++++
  gi|488601186|ref|YP_007907657.1| 225 AIHRAHKGVLFIDETNTLTIESQQKILTAMQEK 257
                                       455699********************9999984 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0038       1.9      79     129 ..      46      96 ..      32     117 .. 0.82
   2 !    6.3   0.0    0.0075       3.7     226     267 ..     223     264 ..     214     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0038
                          AAA_PrkA  79 aaaqrleerkqilyllGPvggGksslverlkklleaapiyalegsPvfeeP 129
                                       +a ++  ++k+ ++l+G  g+Gks l++++ +ll ++ +  +   P  e+P
  gi|488601186|ref|YP_007907657.1|  46 EAIKKAAVQKRHVMLIGSPGTGKSMLAKAMAELLPKEELEDILVYPNLEDP 96 
                                       5778888999********************999988876666666666665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0075
                          AAA_PrkA 226 sGalnranrGllefvemfkadikvlhplltatqegnykstek 267
                                        Ga+ ra +G+l   e     i+   ++lta qe++++ t++
  gi|488601186|ref|YP_007907657.1| 223 AGAIHRAHKGVLFIDETNTLTIESQQKILTAMQEKKFPITGQ 264
                                       599*********999**********************99886 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0016      0.82      23      48 ..      55      80 ..      38      90 .. 0.82
   2 ?    4.5   0.0     0.067        33     168     213 ..     555     600 ..     552     606 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                             DUF87 23 trHlAilgsTGsGKSntvavLleell 48
                                      +rH+  +gs G+GKS +++ + e l 
  gi|488601186|ref|YP_007907657.1| 55 KRHVMLIGSPGTGKSMLAKAMAELLP 80
                                      79******************998876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.067
                             DUF87 168 lldkledllrkggsfsnsstdliallleklekegkitiidlsgvde 213
                                       + +k+e  ++ g ++   ++d+++++l ++e++g+i ii++s +de
  gi|488601186|ref|YP_007907657.1| 555 VTQKIEAAIQAGMKRVIIPKDNLDDVLLDAESSGRIEIIPVSRIDE 600
                                       667788888888888999*************************998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.5e-05     0.022       7      51 ..      43      82 ..      37     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.5e-05
                            AAA_16  7 eeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                      + +e+++ a       + + v+l+G +G+GKs l+++ ++ l k+
  gi|488601186|ref|YP_007907657.1| 43 DAVEAIKKAA-----VQKRHVMLIGSPGTGKSMLAKAMAELLPKE 82
                                      4444443322.....23489*****************99888776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.4e-05     0.047      11      39 ..      55      83 ..      46     119 .. 0.87
   2 ?   -1.8   0.0         8     4e+03      48      74 ..     315     341 ..     290     416 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.4e-05
                                      TSEEEEEESTTSSHHHHHHHHTTSS--SE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllkpte 39
                                       + v ++G+ G+GKS L+k++a+ll ++e
  gi|488601186|ref|YP_007907657.1| 55 KRHVMLIGSPGTGKSMLAKAMAELLPKEE 83
                                      67899*****************9987654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8
                                       EGGGB-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  48 dlkeqeleslrkeigvlpqepqlfpel 74 
                                       d+ +++ e  rk ++++ qe   + ++
  gi|488601186|ref|YP_007907657.1| 315 DTMKDTVENRRKLVRFVAQEVIKDGKI 341
                                       333457777777777777773322222 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   0.0   5.4e-05     0.027      53      83 ..      55      85 ..      32      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                            DUF815 53 annvLLwGarGtGKSslvkallneyaeegLr 83
                                       ++v+L+G+ GtGKS l ka+ + + +e+L 
  gi|488601186|ref|YP_007907657.1| 55 KRHVMLIGSPGTGKSMLAKAMAELLPKEELE 85
                                      579******************9988888775 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 ?   14.0   0.0   6.3e-05     0.031      46      69 ..      54      77 ..      15      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-05
                         IstB_IS21 46 kkenivllGpsGvGKshlaialgv 69
                                      +k  ++l+G +G+GKs la a++ 
  gi|488601186|ref|YP_007907657.1| 54 QKRHVMLIGSPGTGKSMLAKAMAE 77
                                      456799****************86 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2    0.0001     0.052      37      85 ..     360     406 ..     337     408 .. 0.83
   2 ?   -0.5   0.0       3.4   1.7e+03      18      37 ..     403     422 ..     402     428 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                                       HTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHHHH CS
                           MCM_lid  37 eedskrksipitvRqLesliRLseAlAklrlsevvteedveeairllke 85 
                                       + + +r++++   R+L  l+R +  +Ak + s+ v+ e+v +a ++ k+
  gi|488601186|ref|YP_007907657.1| 360 A-G-RRNHLTLRLRELGGLVRTAGDIAKSENSDLVRVEHVLRAKKIAKT 406
                                       2.2.47889999*******************************999875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.4
                                       ETCHHHHHHHHHHHHHHHHH CS
                           MCM_lid  18 lseeakeklseaYvelRkee 37 
                                       + ++ +e+l++ Y+e R++ 
  gi|488601186|ref|YP_007907657.1| 403 IAKTIEEQLADKYIERRRDY 422
                                       6678899*********9965 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.6e-05     0.048       1      50 [.      58     119 ..      58     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.6e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..........klkkkdsvys..rnpeddfwdgYtgq 50 
                                       ++l G++g+GKS+lak +a+ l k+           ++++++++ +   ++ ++++d+Y+++
  gi|488601186|ref|YP_007907657.1|  58 VMLIGSPGTGKSMLAKAMAELLPKEEledilvypnlEDPNQPRIRTvpAGKGKEIVDSYKQE 119
                                       6899*************887777665788899999966666666664578889999999976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00016     0.079       2      24 ..      58      80 ..      58     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                            AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                      v+l+G pG+GKs la+ +++ l+
  gi|488601186|ref|YP_007907657.1| 58 VMLIGSPGTGKSMLAKAMAELLP 80
                                      89**************9997665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.071       1      30 [.      56      85 ..      56     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                      SCEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklp 30
                                      r v+l G +G GK++L++ +a+++ +++l+
  gi|488601186|ref|YP_007907657.1| 56 RHVMLIGSPGTGKSMLAKAMAELLPKEELE 85
                                      5689******************99988876 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.064     107     139 ..      48      80 ..      44      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                         Parvo_NS1 107 lskqlgkrntvwfyGpantGktnlaeaIakavp 139
                                       ++k  +++  v+++G++ tGk++la+a+a+ +p
  gi|488601186|ref|YP_007907657.1|  48 IKKAAVQKRHVMLIGSPGTGKSMLAKAMAELLP 80 
                                       5677888999*******************9988 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0003      0.15       1      44 [.      58     100 ..      58     129 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0003
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       ++l G pG+GK+ lak+ +++l   ++l d++   +l+++++p 
  gi|488601186|ref|YP_007907657.1|  58 VMLIGSPGTGKSMLAKAMAELL-PKEELEDILVYPNLEDPNQPR 100
                                       789***************9995.256666666666666666665 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014     0.071      12      43 ..      46      77 ..      41     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                            AAA_10 12 qevkgsktnasasliiGdlGnGKSvlakllvl 43
                                      +++k +  +  ++++iG++G GKS+lak +  
  gi|488601186|ref|YP_007907657.1| 46 EAIKKAAVQKRHVMLIGSPGTGKSMLAKAMAE 77
                                      67888888999*****************9865 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00032      0.16      27      62 ..     131     166 ..     121     169 .. 0.91
   2 ?   -2.0   0.0         6     3e+03      61      80 ..     234     253 ..     233     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                           DUF4118  27 ivllfllavllvallgglgpgllaallsvllfnyff 62 
                                       +++lf++ +  +a++g +++g++aa++ +l+  y f
  gi|488601186|ref|YP_007907657.1| 131 LFTLFIFIIGYSAIRGEIIWGIIAAAMLFLVSRYIF 166
                                       5789******************************99 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6
                           DUF4118  61 fftpPyftltiadpeylltl 80 
                                       +f+  + tlti++++ +lt 
  gi|488601186|ref|YP_007907657.1| 234 LFIDETNTLTIESQQKILTA 253
                                       6999999*********9985 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00067      0.33       8      58 ..      41      88 ..      38     135 .. 0.81
   2 ?   -1.5   0.0       4.5   2.3e+03     130     159 ..     228     256 ..     198     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58
                                      Q +a+e+++++    +++++++    GtGK+++a k++++ll k++ e +l
  gi|488601186|ref|YP_007907657.1| 41 QDDAVEAIKKAA--VQKRHVMLIGSPGTGKSMLA-KAMAELLPKEELEDIL 88
                                      889999999887..5999************9876.5556666555554544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.5
                                       TTT-SEEEEETGGGTTS.TTTHHHHHT--- CS
                            ResIII 130 rdrfdviiiDEaHrlgakkswreilekfke 159
                                       r ++ v++iDE   l+  +s ++il +++e
  gi|488601186|ref|YP_007907657.1| 228 RAHKGVLFIDETNTLTI-ESQQKILTAMQE 256
                                       45666888998888888.777777776665 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0019      0.93     173     229 ..      22      78 ..      11      85 .. 0.79
   2 ?    2.0   0.2      0.11        57      21      87 ..     339     407 ..     319     430 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0019
                                       HHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTT CS
                            Aldedh 173 aelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknl 229
                                       ++  +e+++P+ ++  v g+++ v +   ++ + ++v+++Gs  +g+ ++++a ++l
  gi|488601186|ref|YP_007907657.1|  22 FKTTAEIEIPERLVDQVIGQDDAVEAIKKAAVQKRHVMLIGSPGTGKSMLAKAMAEL 78 
                                       6778999************6665555555788999*************999976544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                                       EEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHH..HHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHH CS
                            Aldedh  21 akvpaataedvdaavaaAkeafkawaklpaeeR..aeiLrkaadlleerkeelaeletletGkplaear 87 
                                       +k+p+ +++ v +++++Ak+   + ++l+++ R  + ++r+a d+ ++++ +l+++e     k +a++ 
  gi|488601186|ref|YP_007907657.1| 339 GKIPHFDRNAVAEIIKEAKRRAGRRNHLTLRLRelGGLVRTAGDIAKSENSDLVRVEHVLRAKKIAKTI 407
                                       689999**************888666666655522789****************999887777777664 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0015      0.77      86     120 ..      41      76 ..      23      87 .. 0.79
   2 ?   -0.4   0.0       1.9   9.7e+02      32      56 ..     158     182 ..     148     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                                       THTTHHHHHHH.CTTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  86 tkegleelkel.lkdktsvlvGqSGvGKStLinall 120
                                       + +++e++k++ ++++ ++l+G+ G GKS L +a++
  gi|488601186|ref|YP_007907657.1|  41 QDDAVEAIKKAaVQKRHVMLIGSPGTGKSMLAKAMA 76 
                                       557788888751566999*************98875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHTT-EEEEEEE-G CS
                       RsgA_GTPase  32 lnlldrfLvlaeekgiepvivlnKi 56 
                                       l l++r+++  eek+i+ ++v nK 
  gi|488601186|ref|YP_007907657.1| 158 LFLVSRYIFPKEEKNIPKLLVNNKD 182
                                       6789*************99999985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00072      0.36       2      21 ..      58      77 ..      57      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00072
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      ++++G ++tGK+ l++a+a+
  gi|488601186|ref|YP_007907657.1| 58 VMLIGSPGTGKSMLAKAMAE 77
                                      789**************997 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   0.00053      0.26       2      22 ..      55      75 ..      54      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                            AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                      k+ ++++G++g+GK++lak +
  gi|488601186|ref|YP_007907657.1| 55 KRHVMLIGSPGTGKSMLAKAM 75
                                      6789***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); 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):              36  [number of targets reported over threshold]
# CPU time: 0.85u 0.37s 00:00:01.22 Elapsed: 00:00:00.57
# Mc/sec: 3319.34
//
Query:       gi|488601187|ref|YP_007907658.1|  [L=425]
Description: putative Zn-dependent protease and their inactivated-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-52  179.4   0.0      2e-52  178.8   0.0    1.3  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 !  178.8   0.0   1.1e-56     2e-52       3     279 .]       5     283 ..       3     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 1.1e-56
                                       EEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE....ESSHHHHHHHHHHHHHHCCS---TT-... CS
                         PmbA_TldD   3 evrleesestsvrfengevetnsssedsglgvrvikggrlgfastl.dtsdealeeaveraveiaklapedpea... 75 
                                       ++r +++es+++ +eng+ve  ++++ +g g+rv+k+  +g+ s l d s  +  +++er +  a   + d  +   
  gi|488601187|ref|YP_007907658.1|   5 DIRDVRTESLTILLENGSVEKPKFERFHGKGFRVFKN-GWGYYSGLvDDS--EGIKLAERNIIRADTEGIDATSfsg 78 
                                       788899*****************************97.5***77775666..5556666655555444444444888 PP

                                       ..........GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEE CS
                         PmbA_TldD  76 ..........eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvsl 142
                                                 ++vs+eeki+ll+e+ek l++            i+++++ + ++k + ++ nS G +ve+  +rv++
  gi|488601187|ref|YP_007907658.1|  79 kyefmqkenvDDVSVEEKIQLLREIEKELKD--S--------FIVNTRVGYIENKRRFHYRNSSGEEVEYFVPRVGV 145
                                       88999*********************88544..3........6788999999999********************** PP

                                       EEEEEE...S.TCS..ETEEEEEEEE....SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHH CS
                         PmbA_TldD 143 slsvia.d.d.ggs..gdgmgggsgy....edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllh 210
                                       s++++a d + +    + ++ + +g+    +     ++ e+a e++ek++++ +a p+p+g++pV+++p+  g+++h
  gi|488601187|ref|YP_007907658.1| 146 SIQAVAkDgSlQ-FlsK-RLFRVGGFevltD-----EVFEMAIELREKLKDLVNALPPPSGRMPVLMDPSLGGVFIH 215
                                       ******553341.1332.2222333322444.....5555************************************* PP

                                       GHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 211 eavghaleadavlegrSflkdklGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLkny 279
                                       ea+gha+ead++l+g S+lk k G +v++e l ++ddp+  ++g++p+DdEG +++++++Ie Gv+k +
  gi|488601187|ref|YP_007907658.1| 216 EAFGHAVEADHLLKGASILK-KTGIRVGPEELYVYDDPLMPEFGFFPYDDEGYKAEKKTIIESGVFKEF 283
                                       *******************4.7****************879**************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2653.00
//
Query:       gi|488601188|ref|YP_007907659.1|  [L=424]
Description: putative Zn-dependent protease and their inactivated-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-50  173.0   1.9    1.5e-50  172.7   1.9    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 !  172.7   1.9   8.1e-55   1.5e-50       2     279 .]      24     301 ..      23     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 172.7 bits;  conditional E-value: 8.1e-55
                                       EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-... CS
                         PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea... 75 
                                       +e++ e +    +++e+++++++    ++g++vrvi + ++gfa+t+d++  ++ +a e av+i++++++  +    
  gi|488601188|ref|YP_007907659.1|  24 WEIFHEIEYQKVLKIEKNRLSSLIDDVEEGIAVRVINDSKVGFAYTTDPD--SIISACEMAVKISRVSEDRLSDfpe 98 
                                       799999999999*********************************88888..*************988777777999 PP

                                       ......GGS-HHHHHHHHHHHH......HH.CHCSTTEEEEE.EEEEE......EEE.EEEEEEETTSEEEEEEEEE CS
                         PmbA_TldD  76 ......eevsaeekielleele......kalrsadpkiensk.garisgvsaslsaskeeklianSeGldveqtrtr 139
                                             + ++ e+ +e +++ e      k       + +  + + +++ +++ ++ s ++++i+nS+G++ve ++t 
  gi|488601188|ref|YP_007907659.1|  99 ggaamvDGIFSEKVVETIKQPEwlyetgK-------RMTAIAdEEKVNLTEGVIELSASKTRILNSTGTEVEKEETA 168
                                       99999977777777777777764433331.......22222235588899999999999****************** PP

                                       EEEEEEEEE.STCSETEEEEEEEE.....SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHG CS
                         PmbA_TldD 140 vslslsviaddggsgdgmgggsgy.....edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllhe 211
                                       vs++++++ +         +gs+y     +dl+  d+e++++      ++    +++ +g+y+Vv+sp av +ll +
  gi|488601188|ref|YP_007907659.1| 169 VSVFVECVSE---------SGSAYdvaysRDLD-LDVENVVRNSSLFSKQTD--EKIDSGEYNVVFSPLAVHQLLNY 233
                                       *********3.........24444333342333.355556666655555555..779******************** PP

                                       HHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 212 avghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                       a+ +a+ ad+vl+grS+lkdklGek++s+ ++i+dd+t    l s+pfDdEGv ++r ++I++GvL+++
  gi|488601188|ref|YP_007907659.1| 234 ALYPAFFADNVLKGRSMLKDKLGEKIFSD-ISIIDDGTAdSLLMSSPFDDEGVESRRSYIIKDGVLEGF 301
                                       ******************99********9.9*******8899*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2842.93
//
Query:       gi|488601189|ref|YP_007907660.1|  [L=64]
Description: Uncharacterized protein containing a Zn-ribbon [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-23   80.9   1.9    5.2e-23   80.8   1.9    1.0  1  DUF2116      Uncharacterized protein containing a Zn-ribbon (
    0.00024   21.2   0.0    0.00028   21.0   0.0    1.1  1  DUF2615      Protein of unknown function (DUF2615)
  ------ inclusion threshold ------
      0.019   14.4   2.2      0.027   13.9   2.2    1.3  1  zf-ribbon_3  zinc-ribbon domain
      0.019   14.9   0.1      0.023   14.6   0.1    1.0  1  T2SSF        Type II secretion system (T2SS), protein F
       0.02   15.2   0.0      0.022   15.1   0.0    1.1  1  Orf78        Orf78 (ac78)
      0.072   13.2   0.0      0.076   13.1   0.0    1.2  1  ETRAMP       Malarial early transcribed membrane protein (ETR
       0.63   10.2   3.9        3.3    7.9   0.1    2.2  2  DUF2256      Uncharacterized protein conserved in bacteria (D


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 !   80.8   1.9     2e-26   5.2e-23       2      55 ..       6      58 ..       5      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 2e-26
                           DUF2116  2 pHkHCivCGkaIpldesfCsekCqeeyekkrkkvarsqqilfgililllavvlv 55
                                      pH+HC++CGkaI+++e++Cs++C+e ++k++k++++s++++++++++ l+++l+
  gi|488601189|ref|YP_007907660.1|  6 PHRHCVICGKAIEPEEITCSDECEETLQKEKKRQRNSMILMLVAFLA-LIIMLF 58
                                      9****************************************999999.445544 PP

>> DUF2615  Protein of unknown function (DUF2615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.1e-07   0.00028      36      77 ..      23      64 .]      18      64 .] 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                           DUF2615 36 eCldeselpgpeaskeggsslfliallwlvvaavlfllrPss 77
                                       C de e + ++++k++ +s++l+++++l+++++lf++ P+s
  gi|488601189|ref|YP_007907660.1| 23 TCSDECEETLQKEKKRQRNSMILMLVAFLALIIMLFVFAPKS 64
                                      566666633456888999*********************985 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   2.2     1e-05     0.027       2      20 ..       7      25 ..       6      29 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                       zf-ribbon_3  2 tvrCPnCGa.plssddnvCp 20
                                      +++C  CG+ + +++ ++C 
  gi|488601189|ref|YP_007907660.1|  7 HRHCVICGKaI-EPEEITCS 25
                                      79*******66.*******6 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.2e-06     0.023      84     121 ..      24      61 ..      22      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.2e-06
                                       HHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                             T2SSF  84 laeyleeerelrrkllaallepllllvvallvllilla 121
                                       ++++ ee ++ ++k++ +++  +l++++al+++l+++a
  gi|488601189|ref|YP_007907660.1|  24 CSDECEETLQKEKKRQRNSMILMLVAFLALIIMLFVFA 61 
                                       68999***************9************99985 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   8.6e-06     0.022      55      82 ..      31      59 ..      14      61 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
                             Orf78 55 n.aaekaqalnillisllavvcvlvllyv 82
                                      + ++ek+ + n ++++l+a+++++++l+v
  gi|488601189|ref|YP_007907660.1| 31 TlQKEKKRQRNSMILMLVAFLALIIMLFV 59
                                      134678888899999************98 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05     0.076      40      71 ..      26      57 ..       5      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                            ETRAMP 40 kkiddkiekkkkkkKliiistiatalallvas 71
                                      ++ +++++k kk++++ +i ++++ lal + +
  gi|488601189|ref|YP_007907660.1| 26 DECEETLQKEKKRQRNSMILMLVAFLALIIML 57
                                      5678899*********************9865 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 ?    7.9   0.1    0.0013       3.3       5      17 ..       5      17 ..       3      21 .. 0.87
   2 ?    3.7   0.6     0.027        70      32      38 ..      23      29 ..      19      31 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                           DUF2256  5 lpsKiCavCgrpf 17
                                      +p++ C++Cg+ +
  gi|488601189|ref|YP_007907660.1|  5 IPHRHCVICGKAI 17
                                      699*******986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.027
                           DUF2256 32 yCSerCr 38
                                      +CS++C 
  gi|488601189|ref|YP_007907660.1| 23 TCSDECE 29
                                      7*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1958  (0.109209); expected 358.6 (0.02)
Passed bias filter:                     1170  (0.0652574); expected 358.6 (0.02)
Passed Vit filter:                       156  (0.00870099); expected 17.9 (0.001)
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 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 417.27
//
Query:       gi|488601190|ref|YP_007907661.1|  [L=645]
Description: Chlor_Arch_YYY domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-69  234.5  38.9    3.2e-69  234.0  38.9    1.2  1  DUF2298   Uncharacterized membrane protein (DUF2298)


Domain annotation for each model (and alignments):
>> DUF2298  Uncharacterized membrane protein (DUF2298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0  38.9   1.8e-73   3.2e-69      29     497 .]      55     463 ..      22     463 .. 0.86

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 1.8e-73
                           DUF2298  29 laalgllalvrkrkalaaaerlrailevellFlaaFlflvllRalnPdlwhpagEkpmdfgfLnailrsptlPPeDp 105
                                       +a+++++  +r  ++      ++  +++e++Fla+Fl+++ lR+l P++++  +Ek md++fLn++lr++ + P Dp
  gi|488601190|ref|YP_007907661.1|  55 FAIFLISGIYRAYRD-----GFNFEFRYEAVFLAVFLYFLFLRFLIPQAYG--AEKIMDYAFLNSVLRADMFHPPDP 124
                                       333333333333222.....57778899***********************..************************ PP

                           DUF2298 106 WfAggsin.YYYfGyllvallakltgtapevaYnLalatlfAllvtaafglaynlaaargrkesralvaGvlaallv 181
                                       +fAgg in YYYfGy++ a+++  + ++ + ++n+a+a++ A+ +++ + l++++ + +g   ++++ ++v+a++++
  gi|488601190|ref|YP_007907661.1| 125 FFAGGVINfYYYFGYVFGAAVTLSSLLSLSKGFNVAIAVVPAYFAMLSYYLIRRICDCNG--GRSRI-YSVIALIFA 198
                                       ************************************************************..66666.9******** PP

                           DUF2298 182 llagnlatavrlllasllaglssalasaaalteeraWfwdasRvi.kse.detInEFPlFsfllgDlHaHvialpll 256
                                       ++ gn  +++++l +     + + l           ++w+a+R+i +s+  +tInEFP+Fsf+ +D HaH +alp+ 
  gi|488601190|ref|YP_007907661.1| 199 VFSGNFYAFYEFLKDIIRGTKPGYL-----------FYWNATRIIdDSTyGKTINEFPYFSFIHADFHAHFVALPVK 264
                                       *************999988888654...........678******87778*************************** PP

                           DUF2298 257 llalalllallrrpaskrrrrrsllllllalvlGalaatNtWdfptyllllllalllaaarpatllpsrvlallkrl 333
                                       +la+++l+ ++++ ++        ++ l++ +  +l+a+N+Wd p++l +++l++l++ ++             +r 
  gi|488601190|ref|YP_007907661.1| 265 VLAIIILYDYFKKGKN--------WVYLIP-LNFILFAVNSWDAPIFLFITFLTALYRFYS-------------TRD 319
                                       **********997766........344444.4557899*******************5544.............478 PP

                           DUF2298 334 llallaavavlvlalllalPFllsfaasvggiallpersslselllvhGlflvlllaylvllrvsrlsarralalla 410
                                       ++ + ++++vl+l+++ +l  + ++++++++  l+ er+sl+++ l +G++++l ++yl+ +   ++ ++++la+l 
  gi|488601190|ref|YP_007907661.1| 320 VAEIKKGAIVLALSAISILTLYSTMETPSAKPFLTGERTSLTQFFLYFGIIFILSYIYLY-D---EIVKSKRLAMLS 392
                                       8889*******************************************************9.3...456666666666 PP

                           DUF2298 411 allllagvllalalalaalllllpllllalallrrslaaeagfalvlalaglglvllvElvylrdaleeseRmNTvF 487
                                       +l+ +++ ++      +++ +++pl++l++  + r       +  +l++ + ++vl++E+v ++       RmNT F
  gi|488601190|ref|YP_007907661.1| 393 VLAGILAYPFI-----PIFPVIFPLTILSARKFLR-----GDYLSMLIFSATLIVLACEFVAVE------SRMNTFF 453
                                       66666665644.....3455888999999886665.....68999****************885......699**** PP

                           DUF2298 488 KfyyqaWvLl 497
                                       Kfy+ aWvLl
  gi|488601190|ref|YP_007907661.1| 454 KFYLAAWVLL 463
                                       ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1067  (0.0595125); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4513.14
//
Query:       gi|488601191|ref|YP_007907662.1|  [L=533]
Description: hypothetical protein Asulf_01697 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-38  132.2  25.8    4.1e-38  131.6  25.8    1.2  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
    5.1e-28   98.0   0.2    8.6e-28   97.3   0.2    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.4e-07   31.7   0.0    1.9e-07   31.2   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.3e-05   23.1   0.2    8.7e-05   22.1   0.2    1.5  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
      0.004   17.7   0.5     0.0077   16.7   0.1    1.7  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.43   10.6   0.0       0.43   10.6   0.0    2.2  2  PsbL             PsbL protein
       0.73    9.2   6.3       0.18   11.2   3.0    1.7  2  Ceramidase       Ceramidase


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 !  131.6  25.8   1.6e-41   4.1e-38       3     301 .]     246     518 ..     243     518 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 1.6e-41
                   LPG_synthase_TM   3 lglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglf 79 
                                       +++ +++l+l+ +   ++++++a+++ ++d   ++la  ++++s+++r++r+ ++++ lg+  +l  ++  ++i++ 
  gi|488601191|ref|YP_007907662.1| 246 VSISIALLILFAIAGYIGFGSVANTIGKADIKAIILASSIYAGSFIVRGWRYSYIMSILGYDAPLIFSTESIAISQT 322
                                       33344455555558889************************************************************ PP

                   LPG_synthase_TM  80 vnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallll 156
                                       +n +tP+++ G++ ray+ k  ++v++s++++++ ver++dl+++++l + ++lll++  ++      l+a all++
  gi|488601191|ref|YP_007907662.1| 323 LNVITPVRI-GDLGRAYVFKL-QDVPYSTSFSALAVERVFDLISVIILSFTSILLLSAIELAK---TPLYATALLVV 394
                                       *********.***********.**********************************9988664...45555555555 PP

                   LPG_synthase_TM 157 avlalllllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealtlylllralg 233
                                        v+al+++++++     + r   r++r                     ++ ++++l sl+ w++++ ++y++lr++ 
  gi|488601191|ref|YP_007907662.1| 395 IVIALYFASRIQNIIGDIVRDANRVMRT--------------------KKAPVILLVSLFLWMIDIIVCYIILRSFS 451
                                       5666666776666666666666666554....................3489************************* PP

                   LPG_synthase_TM 234 vdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                           ++l +l++ + ++  +lp++PgG+G++Ea+++ +l++  vs++ a a++l++++i  +++++lG
  gi|488601191|ref|YP_007907662.1| 452 SGDLFLLTVLAVSIGNITKVLPITPGGIGTYEAVMTGILSHS-VSSSIAFAVSLIDHAIKNIITVVLG 518
                                       *99999999*********************************.*********************9998 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 !   97.3   0.2   3.4e-31   8.6e-28       1     166 [.       5     169 ..       5     173 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 3.4e-31
                                       EEEEEESS-TTTHHHHHHHHHHH....GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq....dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalna 73 
                                       ++v p+yNe++ l+ ++e +++        +d+eii++ DgStD+t  i+++la+++++v  ++ +e+ G ++al +
  gi|488601191|ref|YP_007907662.1|   5 TIVLPAYNEADKLEIAVEEVRKEmskyFSEEDYEIIIAEDGSTDGTDVIARNLAERYDNVFHVHSDERLGRGKALLN 81 
                                       69************************99************************************************* PP

                                       HHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  74 glraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgn 150
                                       ++r+++gd++++lD D+  d  +l++l++  ++  +d v g+r  +++et +  ++    + +++y++  +  l  +
  gi|488601191|ref|YP_007907662.1|  82 AFRQSSGDVLVYLDVDLSTDISHLKELIDLTQN--YDFVTGSRLLKDSETERPFKRD---FASKGYNFLVRLLLRSK 153
                                       *****************************9999..777*****************98...59*************** PP

                                       STTCSTCCCEEEEHHH CS
                   Glycos_transf_2 151 lsfeigsaallrreal 166
                                       l +  +++ ++rr+a+
  gi|488601191|ref|YP_007907662.1| 154 LKDHQCGFKAFRRKAF 169
                                       **************98 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   7.4e-11   1.9e-07       4     130 ..       4     128 ..       2     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7.4e-11
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqe..y.pr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk 75 
                                       ++++ p++ne+d+l+  +e++ + +  y ++  +e+++  d+s+++t   a+ la+++++v  + v+ +++lg +gk
  gi|488601191|ref|YP_007907662.1|   4 ITIVLPAYNEADKLEIAVEEVRKEMskYfSEedYEIIIAEDGSTDGTDVIARNLAERYDNV-FH-VHSDERLG-RGK 77 
                                       899*********999999999987656783346*************************996.45.67777799.588 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrs 130
                                         al +a+r+ ++d+++ +D D  ++   lk l  +  t+++++v+++++l+  +
  gi|488601191|ref|YP_007907662.1|  78 --ALLNAFRQSSGDVLVYLDVDLSTDISHLKELIDL--TQNYDFVTGSRLLKDSE 128
                                       ..67******************99999999997777..69999999999887544 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 !   22.1   0.2   3.4e-08   8.7e-05       1     106 [.       5     112 ..       5     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.4e-08
                   Glyco_tranf_2_2   1 svviplraseerhyi.eerv.lqkakyy.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarN 74 
                                       ++v+p +++ ++  i  e v ++  ky+ +e+ e+i+ +dgS++ +    +++ +   +v+  +  d+  + ++a  
  gi|488601191|ref|YP_007907662.1|   5 TIVLPAYNEADKLEIaVEEVrKEMSKYFsEEDYEIIIAEDGSTDGTDVIARNLAERYDNVFHVHS-DERLGRGKALL 80 
                                       57888887766543314677245566779999*************77667777777777786676.7789******9 PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekilkli 106
                                         + ++ +d++++lD+D      +++ ++ l 
  gi|488601191|ref|YP_007907662.1|  81 NAFRQSSGDVLVYLDVDLSTDISHLKELIDLT 112
                                       *****************877666666666655 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 !   16.7   0.1     3e-06    0.0077      21      81 ..      38      97 ..      12     109 .. 0.79
   2 ?   -3.1   0.0       4.6   1.2e+04      58      74 ..     165     181 ..     151     212 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                   Glyco_tranf_2_4 21 rilvydndstDgtrailke....lpevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                                      +i++++++stDgt+ i ++    +++v ++h+d+      r+ +ll+a+ ++   +d ++++D+D
  gi|488601191|ref|YP_007907662.1| 38 EIIIAEDGSTDGTDVIARNlaerYDNVFHVHSDERL---GRGKALLNAFRQS--SGDVLVYLDVD 97
                                      59***********88887721114445566555555...5889999999877..59999999998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.6
                   Glyco_tranf_2_4  58 qvellkallaryaeadw 74 
                                        +++  ++ +++++++w
  gi|488601191|ref|YP_007907662.1| 165 RRKAFFKVVEHVKDNHW 181
                                       44444444445555555 PP

>> PsbL  PsbL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   1.0         6   1.5e+04      23      33 ..     362     372 ..     362     373 .. 0.86
   2 ?   10.6   0.0   0.00017      0.43      10      33 ..     379     403 ..     377     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6
                              PsbL  23 LvfvlalLFss 33 
                                       L+ v++l F+s
  gi|488601191|ref|YP_007907662.1| 362 LISVIILSFTS 372
                                       78899999998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                              PsbL  10 vELNRtSLYl.GLLLvfvlalLFss 33 
                                       +EL +t LY   LL v+v+al F+s
  gi|488601191|ref|YP_007907662.1| 379 IELAKTPLYAtALLVVIVIALYFAS 403
                                       8********73688899******98 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       1.8   4.7e+03     107     126 ..     239     258 ..     219     287 .. 0.56
   2 ?   11.2   3.0   6.9e-05      0.18     110     200 ..     358     448 ..     338     463 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.8
                        Ceramidase 107 strvllgvlltalavvvtll 126
                                        +r++l+v +++  +++ ++
  gi|488601191|ref|YP_007907662.1| 239 GERKFLAVSISIALLILFAI 258
                                       35555555554444443333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.9e-05
                        Ceramidase 110 vllgvlltalavvvtllylvlkepvlhqvafalltvlvllrsiyliekkvdksdeaakkevkklall..gliifllg 184
                                       +++ ++ +++  ++++l  ++     +  ++a++ ++v++ ++y   +++++   ++ +++++++ +  + +i+l+ 
  gi|488601191|ref|YP_007907662.1| 358 RVFDLISVIILSFTSILL-LSAIELAKTPLYATALLVVIVIALYFA-SRIQNIIGDIVRDANRVMRTkkAPVILLVS 432
                                       444444444444444443.334445566677777777777777766.56666666777777777766114578999* PP

                        Ceramidase 185 fliWnlDnlfCstltr 200
                                       +++W++D ++C  + r
  gi|488601191|ref|YP_007907662.1| 433 LFLWMIDIIVCYIILR 448
                                       ***********98744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3523.35
//
Query:       gi|488601192|ref|YP_007907663.1|  [L=321]
Description: hypothetical protein Asulf_01698 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-34  118.9  22.7    3.3e-34  118.8  22.7    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
        0.1   11.3  16.4      0.025   13.3  13.2    1.6  2  EMP70            Endomembrane protein 70


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 !  118.8  22.7   3.7e-38   3.3e-34       2     294 ..      11     296 ..      10     302 .. 0.94

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 3.7e-38
                   LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayligl 78 
                                       l+ l++++++l++++++v+++   ++++++d+  +++a l+++  +ll + r ++l++++g+ i ++++l+  + g+
  gi|488601192|ref|YP_007907663.1|  11 LVQLLIGLIILYVIYSRVNFS--LTSIKKVDVAGIVFASLCYMTLNLLLSFRLKVLVNGMGCSIDYSKALQSHFGGM 85 
                                       688999999999999997776..689*****9999*****999999******************************* PP

                   LPG_synthase_TM  79 fvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalalll 155
                                       +++ +tPg++ G +   +++k+  g +l   +a ++v + ++ l+ ++  +lalll++++ + + +++++ a++ll+
  gi|488601192|ref|YP_007907663.1|  86 LLSEFTPGRS-GYLSTPFFIKKLGGCNLNVGMAGILVPQAVEFLIKIFGSILALLLIFHHTEKFKELVAVSAISLLF 161
                                       **********.**************************************************9999999999999999 PP

                   LPG_synthase_TM 156 lavlalllllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealtlylllral 232
                                       ++v+ ++lll++ + +   + +l++ +r++a f  +        +++ + +++ ++   ll w+++ l  y++ ++l
  gi|488601192|ref|YP_007907663.1| 162 IFVISVILLLASWYNRGPSRIRLPKRLRFMANFLLRYSE----HSAKTKDMFWFILVTGLLGWVITSLQWYFVGKSL 234
                                       999998888888888888888899999999998887775....679999999999999******************* PP

                   LPG_synthase_TM 233 gvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitl 294
                                        +d++++++lli+++++ ++ lp++P+GlG++E+++++++ llGv+a++al+++ll+r + +
  gi|488601192|ref|YP_007907663.1| 235 ALDLNFYVYLLIQPLISSLMFLPITPAGLGLMEGGAVTAFYLLGVDASTALLYSLLVRTTNI 296
                                       *********************************************************98765 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4     0.099   8.9e+02     423     460 ..      13      51 ..       6      68 .. 0.62
   2 ?   13.3  13.2   2.8e-06     0.025     304     462 ..      86     254 ..      43     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.099
                             EMP70 423 vllgGilpFgaifielyfilsslwlekiY.ylfgfLflv 460
                                        ll G++   +i+  + f l+s+ +  +  ++f  L+ +
  gi|488601192|ref|YP_007907663.1|  13 QLLIGLIILYVIYSRVNFSLTSIKKVDVAgIVFASLCYM 51 
                                       567788888888888888888886555322333333333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.8e-06
                             EMP70 304 llyvllgliaGYvsarly.ktfgge..kwkkntlltalllpgllflvffllnlilwakessgalpfgtlvlllllwf 377
                                       ll  ++   +GY+s+ ++ k +gg   ++    +l++ ++ +l+ ++  +l l+l+++++ +   +  + ++ ll++
  gi|488601192|ref|YP_007907663.1|  86 LLSEFTPGRSGYLSTPFFiKKLGGCnlNVGMAGILVPQAVEFLIKIFGSILALLLIFHHTEKFKELVAVSAISLLFI 162
                                       55556667799*99987526666541244444566677777777888888**************************9 PP

                             EMP70 378 lisvPlvliGsllgfkkkaiehpvrtnqiprqipk....qpwylkpllsvllgGilpFgaifielyfilsslwlek. 449
                                       ++   + l+ s++ +  ++i+ p r   +++ + +    ++     +  +l++G+l +++  ++ yf+ +sl l+  
  gi|488601192|ref|YP_007907663.1| 163 FVISVILLLASWYNRGPSRIRLPKRLRFMANFLLRysehSAKTKDMFWFILVTGLLGWVITSLQWYFVGKSLALDLn 239
                                       9999999******99977778888887777644432221445555678899***********************962 PP

                             EMP70 450 ..iYylfgfLflvfl 462
                                         +Y l++ L+ +++
  gi|488601192|ref|YP_007907663.1| 240 fyVYLLIQPLISSLM 254
                                       222333344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 1726.24
//
Query:       gi|488601193|ref|YP_007907664.1|  [L=236]
Description: Glycosyltransferases involved in cell wall biogenesis [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-31  107.0   0.9    1.2e-30  106.5   0.3    1.5  2  Glycos_transf_2  Glycosyl transferase family 2
    1.8e-10   41.1   0.0    2.2e-10   40.8   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.5e-07   29.6   0.3    1.1e-06   28.4   0.2    1.6  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00072   20.0   0.7     0.0022   18.5   0.1    2.1  3  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 !  106.5   0.3   2.7e-34   1.2e-30       1     166 [.      10     174 ..      10     178 .. 0.97
   2 ?   -2.2   0.0      0.68     3e+03     111     141 ..     193     221 ..     187     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 2.7e-34
                                       EEEEEESS-TTTHHHHHHHHHHH....GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq....dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalna 73 
                                       ++v p+yNe++ l+ ++e +++        +d+eii++ DgStD+t  i+++la+++++v  ++ +e+ Gk++a+ +
  gi|488601193|ref|YP_007907664.1|  10 TIVLPAYNEADKLEIAVEEVRKEmskyFSEEDYEIIIAEDGSTDGTDVIARNLAERYDNVFHVHSDERLGKGRAILN 86 
                                       69************************99************************************************* PP

                                       HHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCC CS
                   Glycos_transf_2  74 glraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgn 150
                                       ++r+++gd+++f+D D+  d  +l++l++  ++  +d v g+r  +++et +  ++    + +++y++  +  l  +
  gi|488601193|ref|YP_007907664.1|  87 AFRQSKGDVLVFMDVDLSTDISHLKELIDLTQN--YDFVTGSRLLKDSETERPFKRD---FASKGYNFLVRLLLRSK 158
                                       *****************************9999..777*****************98...59*************** PP

                                       STTCSTCCCEEEEHHH CS
                   Glycos_transf_2 151 lsfeigsaallrreal 166
                                       l +  +++ ++rr+a+
  gi|488601193|ref|YP_007907664.1| 159 LKDHQCGFKAFRRKAF 174
                                       **************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.68
                                       EEEEEEEEEECCCCCCCHC-SSEEEECCHCC CS
                   Glycos_transf_2 111 vvlgqrprifgetdeiernkrvgenerlyfk 141
                                       ++l+qr+ +++++++ +++++  e+++++f+
  gi|488601193|ref|YP_007907664.1| 193 MILAQRMGYRVKEFPVRWRQG--ERSKVRFR 221
                                       578888999999999888887..44444443 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 !   40.8   0.0   4.8e-14   2.2e-10       2     131 ..       8     134 ..       7     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 4.8e-14
                   Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqe..y.pr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgst 73 
                                       r ++++ p++ne+d+l+  +e++ + +  y ++  +e+++  d+s+++t   a+ la+++++v  + v+ +++l   
  gi|488601193|ref|YP_007907664.1|   8 R-ITIVLPAYNEADKLEIAVEEVRKEMskYfSEedYEIIIAEDGSTDGTDVIARNLAERYDNV-FH-VHSDERL--- 78 
                                       3.89**********999999999987656783346*************************996.45.5665545... PP

                   Glyco_tranf_2_3  74 gksralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrst 131
                                       gk ra+ +a+r+ k+d+++++D D  ++   lk l  +  t+++++v+++++l+  +t
  gi|488601193|ref|YP_007907664.1|  79 GKGRAILNAFRQSKGDVLVFMDVDLSTDISHLKELIDL--TQNYDFVTGSRLLKDSET 134
                                       5999*********************9999999998877..6999****9999875443 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 !   28.4   0.2   2.4e-10   1.1e-06       1     106 [.      10     117 ..      10     125 .. 0.77
   2 ?   -1.1   0.0      0.24   1.1e+03     137     171 ..     119     152 ..     109     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.4e-10
                   Glyco_tranf_2_2   1 svviplraseerhyi.eerv.lqkakyy.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarN 74 
                                       ++v+p +++ ++  i  e v ++  ky+ +e+ e+i+ +dgS++ +    +++ +   +v+  +  d+  ++++a  
  gi|488601193|ref|YP_007907664.1|  10 TIVLPAYNEADKLEIaVEEVrKEMSKYFsEEDYEIIIAEDGSTDGTDVIARNLAERYDNVFHVHS-DERLGKGRAIL 85 
                                       57888888766543315677245566779999*************77667777777777786666.7889******* PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekilkli 106
                                         + ++++d+++F+D+D      +++ ++ l 
  gi|488601193|ref|YP_007907664.1|  86 NAFRQSKGDVLVFMDVDLSTDISHLKELIDLT 117
                                       *****************877777777666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.24
                   Glyco_tranf_2_2 137 vedltassrvledllaakstlvkffapssssilin 171
                                         d ++ sr+l+d  +   ++ ++fa ++ ++l++
  gi|488601193|ref|YP_007907664.1| 119 NYDFVTGSRLLKDSET-ERPFKRDFASKGYNFLVR 152
                                       4455566777777777.788888888888888876 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   4.8e-07    0.0022      21      81 ..      43     102 ..      17     114 .. 0.79
   2 ?   -1.7   0.0      0.98   4.4e+03      50      74 ..     164     186 ..     148     196 .. 0.66
   3 ?   -1.3   0.1      0.74   3.3e+03      35      54 ..     193     212 ..     164     226 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.8e-07
                   Glyco_tranf_2_4  21 rilvydndstDgtrailke....lpevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81 
                                       +i++++++stDgt+ i ++    +++v ++h+d+       ++++l+a+ ++  ++d ++++D+D
  gi|488601193|ref|YP_007907664.1|  43 EIIIAEDGSTDGTDVIARNlaerYDNVFHVHSDERLG---KGRAILNAFRQS--KGDVLVFMDVD 102
                                       59***********888877222145566666666654...689999999877..59999999998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.98
                   Glyco_tranf_2_4  50 ksyederrqvellkallaryaeadw 74 
                                       + +  +++ +++  ++ +++++++w
  gi|488601193|ref|YP_007907664.1| 164 CGF--KAFRRKAFFKVVEHVKDNHW 186
                                       333..35566666666666667666 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.74
                   Glyco_tranf_2_4  35 ailkelpevkllhvdksyed 54 
                                        il++   +++ +++  +++
  gi|488601193|ref|YP_007907664.1| 193 MILAQRMGYRVKEFPVRWRQ 212
                                       34444455555555555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1330.34
//
Query:       gi|488601194|ref|YP_007907665.1|  [L=325]
Description: putative ATP-utilizing enzyme (ATP-grasp superfamily) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-36  126.1   0.0      2e-36  125.5   0.0    1.3  1  ATP-grasp_3     ATP-grasp domain
    1.4e-14   54.1   0.0    2.7e-14   53.2   0.0    1.5  1  preATP-grasp_3  pre ATP-grasp 3 domain
     0.0017   17.6   0.0      0.053   12.8   0.0    2.3  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.047   13.2   0.0      0.094   12.2   0.0    1.5  1  CPSase_L_D2     Carbamoyl-phosphate synthase L chain, ATP bin


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 !  125.5   0.0   4.5e-40     2e-36       2     161 .]     112     256 ..     111     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 4.5e-40
                                       TSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEE CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvs 78 
                                       s+K+ ty +Lk++ v++P     ++ e+ + ++v+Kp +++gg ++ +          ++   ++qef+eGk+lSvs
  gi|488601194|ref|YP_007907665.1| 112 SSKWLTYLRLKDR-VNMP----LTSKEPLDVSYVIKPERSCGGAGIDFGSGT------VPDGFVAQEFVEGKNLSVS 177
                                       89***********.****....55556667789*************999887......333459************* PP

                                       EEE.SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEE CS
                       ATP-grasp_3  79 llsdgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekleglaGyvGvDlvlkdeepyviE 153
                                       +++ g ++ +l+vn ql+++    f+y+G ++p++  +  ++ vve+a e+v +++gl GyvGvD+vl+d  py+iE
  gi|488601194|ref|YP_007907665.1| 178 FIV-GDEITPLSVNSQLLDH----FKYSGALVPANIGKkeEKMVVEEATEAVGCIKGLHGYVGVDVVLSD-SPYIIE 248
                                       ***.88*************9....**********98873355689*************************.****** PP

                                       EESS--GG CS
                       ATP-grasp_3 154 vNPRltts 161
                                       +N+Rltt+
  gi|488601194|ref|YP_007907665.1| 249 INARLTTP 256
                                       ******96 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 !   53.2   0.0     6e-18   2.7e-14      20      77 .]      52     108 ..      41     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 6e-18
                    preATP-grasp_3  20 evlvvdseedvdetfrrlaaeaDaVlvIAPEtdgiLarltrlveaagkrlLGssskAi 77 
                                       + + +++ +++ e fr+++++aD+ l+IAPE +giL++lt+++e+  + +LGssskAi
  gi|488601194|ref|YP_007907665.1|  52 TMYNIPPVRNFEEDFRECCENADYALIIAPEDEGILETLTKIAEKR-CENLGSSSKAI 108
                                       667899999***********************************99.9*********9 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.016        70      59      80 ..     135     156 ..     106     173 .. 0.82
   2 !   12.8   0.0   1.2e-05     0.053     242     270 ..     231     260 ..     207     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.016
                       ATPgrasp_ST  59 leegvviKpakgsgGkGilvit 80 
                                       l+  +viKp ++ gG Gi + +
  gi|488601194|ref|YP_007907665.1| 135 LDVSYVIKPERSCGGAGIDFGS 156
                                       45569************97655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.2e-05
                       ATPgrasp_ST 242 lgylGwDivldeekgplllElNar...pglai 270
                                       +gy+G+D+vl ++  p+++E+Nar   p++a+
  gi|488601194|ref|YP_007907665.1| 231 HGYVGVDVVLSDS--PYIIEINARlttPSIAF 260
                                       69********875..7******9854455555 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05     0.094     133     201 ..     208     274 ..     190     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                                       --HHHHHHHHHHHHHHHHHH.T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHH CS
                       CPSase_L_D2 133 Ltdeerqalreaavkvvrev.gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaak 201
                                       + ++e +++ e+a ++v ++ g+ g   v+ +l+    + y+iE+N+Rl   s   e++ G++l++   k
  gi|488601194|ref|YP_007907665.1| 208 IGKKEEKMVVEEATEAVGCIkGLHGYVGVDVVLSD---SPYIIEINARLTTPSIAFEQVYGFNLAELIYK 274
                                       55677888889999998888457888899999885...789***********************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 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:                        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: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1894.11
//
Query:       gi|488601195|ref|YP_007907666.1|  [L=55]
Description: hypothetical protein Asulf_01702 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.017   14.9   0.0    1.2  1  Cys_rich_KTR  Cysteine-rich KTR
      0.064   12.8   0.1      0.094   12.3   0.1    1.4  1  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.9e-06     0.017      28      42 ..       1      15 [.       1      23 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-06
                      Cys_rich_KTR 28 LfCPKCkqetlinvk 42
                                      ++CP C++e li+v 
  gi|488601195|ref|YP_007907666.1|  1 MYCPNCQNEELIDVD 15
                                      8***********995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     1e-05     0.094       1      12 [.       1      24 [.       1      30 [. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                                      EEETTTTCEE.C...........H CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.l...........v 12
                                      + CPnC +++ +           +
  gi|488601195|ref|YP_007907666.1|  1 MYCPNCQNEElIdvdlyeelvkgL 24
                                      78******9955555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 358.65
//
Query:       gi|488601196|ref|YP_007907667.1|  [L=72]
Description: looped-hinge helix DNA binding domain, AbrB family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-11   43.2   0.1    4.7e-11   42.3   0.1    1.5  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    6.3e-06   26.5   0.2    8.1e-06   26.2   0.2    1.3  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin


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 !   42.3   0.1   5.2e-15   4.7e-11       3      36 ..       4      39 ..       2      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 5.2e-15
                                      ETTEEEEEE-CCCHHHCCEECTCEEEEEECTT..CC CS
                    MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgd..ki 36
                                      v+++++++iPk vr+el+i++Gdev+++  +d  ki
  gi|488601196|ref|YP_007907667.1|  4 VTRKYQITIPKRVREELNIKAGDEVVFIKTEDgyKI 39
                                      89*************************988875544 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2     9e-10   8.1e-06       4      40 ..       4      39 ..       2      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9e-10
                    PrlF_antitoxin  4 ltergqttiPasvRkaLklkkgrdkiaytilddgkvv 40
                                      +t+++q tiP+ vR+ L++k   d++++   +dg  +
  gi|488601196|ref|YP_007907667.1|  4 VTRKYQITIPKRVREELNIKA-GDEVVFIKTEDGYKI 39
                                      8*******************9.779999887777543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); 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: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 431.37
//
Query:       gi|488601197|ref|YP_007907668.1|  [L=131]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-10   39.5   0.0    1.4e-09   38.5   0.0    1.6  1  PIN              PIN domain
  ------ inclusion threshold ------
      0.089   13.2   0.0       0.22   12.0   0.0    1.7  2  Acylphosphatase  Acylphosphatase


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 !   38.5   0.0   1.6e-13   1.4e-09       1     113 [.       3     108 ..       3     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.6e-13
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidae 76 
                                       ivlDT+v+     ++     + ++l +   +  +s +++ Elly + +  +k +  +e+v+++l++  ++++p+d e
  gi|488601197|ref|YP_007907668.1|   3 IVLDTNVFQ----NRR----FCEWLKKGnHDARISTITYTELLYHYLK--KKGKDGREFVDAFLDALKVQVMPFDRE 69 
                                       678888887....333....34566666699*****************..9************************** PP

                                       HHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESS CS
                               PIN  77 iaeeaaeialkyg...llpnDaliaAtAkehgikliatfD 113
                                        a++a+  a  ++   +++ D +i ++A + +++ i t++
  gi|488601197|ref|YP_007907668.1|  70 CARIASNAAIGRWdfrKKVRDYMIGSLAVKLRCPMI-TYN 108
                                       ************************************.986 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.22      42      74 ..       4      36 ..       1      47 [. 0.82
   2 ?   -2.3   0.0       0.7   6.3e+03       8      22 ..      60      74 ..      49      80 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                   Acylphosphatase 42 vaegeeekvekfleelksgppkarvdeveveel 74
                                      v+  +  + ++f+e+lk+g+  ar++ ++++el
  gi|488601197|ref|YP_007907668.1|  4 VLDTNVFQNRRFCEWLKKGNHDARISTITYTEL 36
                                      55555667789*******************986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.7
                   Acylphosphatase  8 rVQgvgFRkfvrrlA 22
                                      +VQ + F + + r+A
  gi|488601197|ref|YP_007907668.1| 60 KVQVMPFDRECARIA 74
                                      355555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 911.54
//
Query:       gi|488601198|ref|YP_007907669.1|  [L=45]
Description: hypothetical protein Asulf_01705 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 314.25
//
Query:       gi|488601199|ref|YP_007907670.1|  [L=159]
Description: hypothetical protein Asulf_01706 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   31.2  12.0    9.9e-05   22.3   1.1    2.0  2  VIT1             VIT family
     0.0027   17.6   7.0     0.0033   17.3   7.0    1.1  1  DUF975           Protein of unknown function (DUF975)
  ------ inclusion threshold ------
       0.12   12.4   0.4       0.12   12.4   0.4    2.5  3  DUF5510          Family of unknown function (DUF5510)
       0.96    8.7   4.4        1.3    8.3   4.4    1.2  1  DUF3810          Protein of unknown function (DUF3810)
        2.4    8.4  12.2        0.2   11.9   5.3    2.2  2  DUF1516          Protein of unknown function (DUF1516)
        7.1    6.7   7.9       0.74    9.9   1.1    2.3  2  Phage_holin_2_1  Bacteriophage P21 holin S


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   1.1   3.3e-08   9.9e-05       6      66 ..      12      71 ..       8      73 .. 0.81
   2 !   16.0   3.2   2.8e-06    0.0083     133     214 ..      71     151 ..      67     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.3e-08
                              VIT1  6 lGanDGLvspfalvaGlsaaslgssktvllaGl.aellAGaiSMgiGeYlsvkserdlekae 66
                                      +G+   ++++++l++Gl   s   sk+v+++G+   ++A+a+S ++G  +s ++e++++++e
  gi|488601199|ref|YP_007907670.1| 12 FGLTSAVITTLGLMVGLH--SGTHSKIVVIGGIlTIAIADAFSDALGIHVSEEAENKHTTKE 71
                                      566666778899999999..434789999999836679******************999876 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.8e-06
                              VIT1 133 splkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaa 209
                                       + +++ +s++ls ++++l  ++p l+++  ++a++vs++  l  l +f +  a+  ++++++ + + l+i ++  ++
  gi|488601199|ref|YP_007907670.1|  71 EIWESTISTFLSKFVFALTFVVPLLLFQ-LSTAIIVSVIWGLSLLGIFSFQIAKEQKTKPWKVVTEHLVIALIVIVI 146
                                       4599*********************999.99******77777777777777777779999*************9999 PP

                              VIT1 210 aylig 214
                                       +  +g
  gi|488601199|ref|YP_007907670.1| 147 THYVG 151
                                       98876 PP

>> DUF975  Protein of unknown function (DUF975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   7.0   1.1e-06    0.0033      56     165 ..      35     149 ..       6     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                            DUF975  56 ivlllgtlltlsavfvv.....iklvkrkekvelkeslasfkeknfiklLvllllkelflllwsliallglliiiis 127
                                        ++++g++lt+ +  ++     i++ ++ e+ +  + +      +f++++v +l++ ++lll+ l  ++++++i   
  gi|488601199|ref|YP_007907670.1|  35 KIVVIGGILTIAIADAFsdalgIHVSEEAENKHTTKEIWESTISTFLSKFVFALTFVVPLLLFQLSTAIIVSVIWGL 111
                                       344455555554433322222378888855555555555554799******************99999888887666 PP

                            DUF975 128 lslallsseieenlvvvllvlliilllivlilaiivey 165
                                       + l + s +i +++    + ++   l+i+li+++i +y
  gi|488601199|ref|YP_007907670.1| 112 SLLGIFSFQIAKEQKTKPWKVVTEHLVIALIVIVITHY 149
                                       66656677777777777777777777777777766655 PP

>> DUF5510  Family of unknown function (DUF5510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   3.9e-05      0.12      14      44 ..      18      48 ..       5      54 .. 0.89
   2 ?   -1.3   0.7      0.73   2.2e+03      32      32 ..     102     102 ..      78     121 .. 0.56
   3 ?   -2.5   0.4       1.7   5.1e+03      18      24 ..     140     146 ..     133     149 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                           DUF5510 14 iviilGivilifspakfriiviGtilGlaca 44
                                      ++  lG+++ + s +  +i+viG il +a a
  gi|488601199|ref|YP_007907670.1| 18 VITTLGLMVGLHSGTHSKIVVIGGILTIAIA 48
                                      45679**********************9987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.73
                           DUF5510  32 i 32 
                                        
  gi|488601199|ref|YP_007907670.1| 102 A 102
                                       2 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.7
                           DUF5510  18 lGivili 24 
                                         ivi+i
  gi|488601199|ref|YP_007907670.1| 140 ALIVIVI 146
                                       2344444 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.4   0.00044       1.3       8      74 ..      72     147 ..      66     153 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00044
                           DUF3810   8 viskilsrlsglfpFSvgellivllillvilylvlai.........klkkrkkkkkrllkvllrvllvllvvyflf 74 
                                       ++ +++s++++ f F++  ++ +ll+ l ++++v +i          ++  k++k++ +kv+++ l+++l+v+++ 
  gi|488601199|ref|YP_007907670.1|  72 IWESTISTFLSKFVFALTFVVPLLLFQLSTAIIVSVIwglsllgifSFQIAKEQKTKPWKVVTEHLVIALIVIVIT 147
                                       6777777777777777766666555555555555555566788888444455555666666666666666666554 PP

>> DUF1516  Protein of unknown function (DUF1516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.9      0.24   7.2e+02      47      77 ..      20      48 ..      14      85 .. 0.60
   2 ?   11.9   5.3   6.5e-05       0.2      58     106 ..      98     146 ..      74     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.24
                           DUF1516 47 tglvllirtfknspllyilKvllgllvIglm 77
                                      t l l++  +  s +   + v+ g+l+I++ 
  gi|488601199|ref|YP_007907670.1| 20 TTLGLMVGLH--SGTHSKIVVIGGILTIAIA 48
                                      4444555443..3333333445555555554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.5e-05
                           DUF1516  58 nspllyilKvllgllvIglmEmalarkkkkksssgllilfivvlvlvil 106
                                       + ++ +i+ v+ gl ++g++ + +a+++k k+ + +   ++++l+++++
  gi|488601199|ref|YP_007907670.1|  98 QLSTAIIVSVIWGLSLLGIFSFQIAKEQKTKPWKVVTEHLVIALIVIVI 146
                                       667899***********************88877766555555444432 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.1   0.00025      0.74       5      44 ..       8      45 ..       5      51 .. 0.85
   2 ?    0.2   0.9      0.26   7.7e+02      22      49 ..     120     149 ..     101     153 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                   Phage_holin_2_1  5 tgvsYgaSggsigywlkqlldklspeeWsaigvlgglvig 44
                                      tg s+g   + i    ++l+ +l++   s i v+gg++ +
  gi|488601199|ref|YP_007907670.1|  8 TGFSFGLTSAVI--TTLGLMVGLHSGTHSKIVVIGGILTI 45
                                      899999887777..5679******************9876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.26
                   Phage_holin_2_1  22 qlldklspeeWsaig..vlgglvigllTyl 49 
                                       q+ ++   + W+++   ++  l+++++T  
  gi|488601199|ref|YP_007907670.1| 120 QIAKEQKTKPWKVVTehLVIALIVIVITHY 149
                                       555555666787775556667777788765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1259  (0.0702214); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 995.38
//
Query:       gi|488601200|ref|YP_007907671.1|  [L=312]
Description: Collagenase-related protease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  136.0   0.0    1.8e-39  135.3   0.0    1.3  1  Peptidase_U32  Peptidase family U32
  ------ inclusion threshold ------
      0.025   14.9   0.0       0.08   13.3   0.0    1.9  2  Radical_SAM    Radical SAM superfamily


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 !  135.3   0.0     2e-43   1.8e-39       2     220 ..      74     292 ..      73     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 2e-43
                     Peptidase_U32   2 eklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikai 78 
                                       + +r+ l++l+++gvda+i++D g+++++++++p++ + +S  +ni n+e++ f+++ Ga  vv+   l+++e+++i
  gi|488601200|ref|YP_007907671.1|  74 DMFRERLDFLYSAGVDAIILNDAGLMRVVSDTYPDIDIVASIGCNILNYEEALFYRKAGAGMVVADCKLTIDEMREI 150
                                       678999*********************************************************************** PP

                     Peptidase_U32  79 kekvpdvelEvfvhGalcvaysGrcllssylsgrs............an.rgecaqpcrldyrlieekekgeeepie 142
                                       k+k+ +v +Ev+vh ++ + y G+c +ssy   ++            +n  g c++pc ++++l+ ++       ++
  gi|488601200|ref|YP_007907671.1| 151 KDKA-GVGIEVLVHANTDFTYLGKCWMSSYKALKYeelngksyyigsPNrGGVCFRPCLMRWSLLGDDVYA----RD 222
                                       ****.*************************8888899**********99889***********88776422....22 PP

                     Peptidase_U32 143 edekgtyllspkdlclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagreevkeelkeeleklan 219
                                             + l +  + l+ee+p lle  vd+lKI+GR++s   ++++vr Yr+ ++a+  g+    + +k++l ++a+
  gi|488601200|ref|YP_007907671.1| 223 ------FNLPNSMFLLLEEIPSLLEV-VDCLKIQGREYSVGLIKEIVRFYRDFVEACSGGE-VDFAVWKKKLMDIAS 291
                                       ......5666777899*********8.*****************************99998.777899999999987 PP

                     Peptidase_U32 220 r 220
                                       r
  gi|488601200|ref|YP_007907671.1| 292 R 292
                                       7 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.9e-06      0.08      84     166 ..       6      82 ..       1      83 [. 0.72
   2 ?   -2.1   0.0      0.48   4.3e+03      26      62 ..     250     284 ..     247     305 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.9e-06
                                       ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend.ee 159
                                       ++g+    e++++  e+g d v++g++ ++ +  l+      + +e++e+++++++ g+k     i  +p  ++ ++
  gi|488601200|ref|YP_007907671.1|   6 APGGN--AEMVKAVFEAGADSVYVGVKGWSRR-ALR---YEMSDSEIVEVVKIAHDFGGKL-RAAINAMPKPSEiDM 75 
                                       55666..6999********************9.444...446789*************994.444333333332255 PP

                                       HHHHHHH CS
                                       xxxxxxx RF
                       Radical_SAM 160 leellel 166
                                       ++e l++
  gi|488601200|ref|YP_007907671.1|  76 FRERLDF 82 
                                       6666655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  26 grslsveeileevkelkaekgvkevilgggepllypd 62 
                                       gr+ sv  i+e+v+ ++ +  v+ +  g  +  ++++
  gi|488601200|ref|YP_007907671.1| 250 GREYSVGLIKEIVRFYR-DF-VEACSGGEVDFAVWKK 284
                                       56777888888888775.33.5544444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2260.96
//
Query:       gi|488601201|ref|YP_007907672.1|  [L=293]
Description: Collagenase-related protease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-34  117.9   0.0    4.9e-34  117.5   0.0    1.1  1  Peptidase_U32  Peptidase family U32


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.0   2.7e-38   4.9e-34       2     231 ..      73     283 ..      72     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 2.7e-38
                     Peptidase_U32   2 eklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikai 78 
                                       +++ ++++ +a+l+vda+    +gv+ ++++e  +l++h+   +ni++s++v++lk+ G++rv  a El le+i+ i
  gi|488601201|ref|YP_007907672.1|  73 PEVFRLIDLVADLEVDAIESTNFGVISYVKRE-YDLRVHAGGLTNIYTSATVELLKSIGVERVMPAYELPLEDIAGI 148
                                       677889999***********************.8******************************************* PP

                     Peptidase_U32  79 kekvpdvelEvfvhGalcvaysGrcllssylsgrsan.rgecaqpcrldyrlieekekgeeepieedekgtyllspk 154
                                       k++   ve+Ev vhG++ + +s +c+l ++    + n   ec + c+++  + + +   ++        g  +ls k
  gi|488601201|ref|YP_007907672.1| 149 KAAG--VEVEVVVHGKIPLGISHECFLLEF----EKNvGVECPHICKREMVFRSGDLVLKP-------FGHATLSGK 212
                                       *976..************************....56746689999*999774444444444.......47799**** PP

                     Peptidase_U32 155 dlclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagreevkeelkeeleklanrgltsgfllgrk 231
                                       d+c++e+++el + Gvd+l++e  + +  y ++v ++Yr+++++  +++        e+l ++a+ g+ +gf+++++
  gi|488601201|ref|YP_007907672.1| 213 DVCMYEHIDELRKVGVDALRVETISERIGYREKVGNIYRNLLERGFDRN------DFEKLMEIAKYGICNGFYFNKA 283
                                       *******************************************976555......67899999999*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 2010.10
//
Query:       gi|488601202|ref|YP_007907673.1|  [L=230]
Description: hypothetical protein Asulf_01709 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   0.0    2.1e-19   69.6   0.0    1.3  1  Peptidase_U32    Peptidase family U32
     0.0057   16.2   0.1      0.023   14.2   0.1    1.8  1  Glycos_transf_1  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.29   11.2   0.0    1.7  1  PDZ_1            PDZ-like domain


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 !   69.6   0.0   3.5e-23   2.1e-19       2     135 ..      54     183 ..      53     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 3.5e-23
                     Peptidase_U32   2 eklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikai 78 
                                       + +++ +e +++l+  +vi++D g++  ++ +  + ++  S+  n  n   ++flk+ Ga+ vv++ El+ +    i
  gi|488601202|ref|YP_007907673.1|  54 DPVAEVVEVIERLKCKGVILNDAGLIWKVSVMKNKKKIVSSVGLNPLNELDIEFLKSIGADVVVIPPELNSD----I 126
                                       56788999999**********************************************************965....6 PP

                     Peptidase_U32  79 kekvpdvelEvfvhGalcvaysGrcllssylsgrsan.rgecaqpcrldyrlieekek 135
                                         k  dve+E+f +  + ++y G+c++ssy++g s   +g c+++c ++++++ e+++
  gi|488601202|ref|YP_007907673.1| 127 SIKK-DVEIEAFGFALIEMFYKGKCMISSYFNGISTKkSGLCTKKCCRRWKVVFEDKE 183
                                       6666.78****************************999*************7766543 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 !   14.2   0.1   3.9e-06     0.023      10     126 ..      36     158 ..      29     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-06
                                       TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHS CS
                   Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsr 83 
                                       ++ ++k++++ ++r++    v+ +++++++lk    + v l  aG   +++  k+ kk + + +l    + l e+  
  gi|488601202|ref|YP_007907673.1|  36 ELSKDKNVFVALNRIRGLDPVAEVVEVIERLK---CKGVILNDAGliwKVSVMKNKKKIVSSVGL----NPLNEL-- 103
                                       55667777777777777777777777777665...345555556666666666666666666666....233344.. PP

                                       SSHHHHHHC.ESEEEEEESS............BSS-HHHHHHHHTT--EEEETTTT CS
                   Glycos_transf_1  84 edleellkn.adifvlpsis............EgfGivllEAmaaglpviasnagg 126
                                        d+e l+++ ad++v+p +             E+fG +l+E ++ g++ i+s   g
  gi|488601202|ref|YP_007907673.1| 104 -DIEFLKSIgADVVVIPPELnsdisikkdveiEAFGFALIEMFYKGKCMISSYFNG 158
                                       .57777777**********9******************************998555 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.8e-05      0.29      28      66 ..      66     104 ..      56     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.8e-05
                             PDZ_1  28 ipvkgvyvseasgsfklsskekkgviitsinnqptpnLd 66 
                                       +++kgv++++a++ +k+s  ++k+ i++s+   p  +Ld
  gi|488601202|ref|YP_007907673.1|  66 LKCKGVILNDAGLIWKVSVMKNKKKIVSSVGLNPLNELD 104
                                       799*******************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1493.00
//
Query:       gi|488601203|ref|YP_007907674.1|  [L=51]
Description: hypothetical protein Asulf_01710 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 358.43
//
Query:       gi|488601204|ref|YP_007907675.1|  [L=523]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.1    1.2e-10   41.4   0.0    2.6  2  PAS           PAS fold
    2.3e-18   66.7   0.2    4.6e-18   65.8   0.2    1.5  1  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    6.6e-14   51.5   0.0    5.6e-07   29.4   0.0    2.5  2  PAS_8         PAS domain
    1.2e-11   44.8   2.6    1.1e-07   32.1   0.1    2.8  2  PAS_9         PAS domain
    1.8e-08   34.6   0.0      0.028   14.7   0.0    3.6  3  PAS_4         PAS fold
    7.3e-06   26.0   0.0    1.3e-05   25.1   0.0    1.4  1  HATPase_c_2   Histidine kinase-like ATPase domain
    0.00013   21.6   1.6    0.00019   21.1   0.2    2.1  2  SPOB_a        Sensor_kinase_SpoOB-type, alpha-helical domain
    0.00048   20.4   0.0     0.0014   18.9   0.0    1.8  1  PAS_3         PAS fold
     0.0012   18.7   0.1     0.0052   16.7   0.1    2.1  1  HATPase_c_5   GHKL domain
     0.0018   17.9   0.1     0.0032   17.0   0.1    1.3  1  HisKA_4TM     Archaeal 4TM region of histidine kinase
     0.0043   17.2   0.1        4.1    7.6   0.0    3.1  2  PAS_7         PAS fold
  ------ inclusion threshold ------
       0.06   13.2   0.2       0.12   12.2   0.2    1.5  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
       0.49   10.5   2.6        1.2    9.2   0.4    2.7  3  HisKA         His Kinase A (phospho-acceptor) domain
        4.2    7.7   5.9        2.1    8.7   0.2    3.1  3  Ribosomal_S6  Ribosomal protein S6


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 !   25.0   0.0   1.1e-08   1.4e-05       1      35 [.     109     143 ..     109     148 .. 0.96
   2 !   41.4   0.0   9.5e-14   1.2e-10       2      69 ..     197     263 ..     196     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHS CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellG 35 
                                       e++r i+e++ d i++v+ dg+++++N aae+ lG
  gi|488601204|ref|YP_007907675.1| 109 ERYRKIVENIKDIIILVNNDGVVVEANNAAEKVLG 143
                                       68*******************************99 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 9.5e-14
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHT CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqg 69 
                                       +++ i+e++ + i+++De+gri+ +N++ ee++G++reevlgk+ +d +++  + ++ +++++ le g
  gi|488601204|ref|YP_007907675.1| 197 FVEKIIETANSLIVGLDEKGRIVMFNRKCEEITGYAREEVLGKNWFDIFVPRVE-YTLKIFKKTLEIG 263
                                       7899*****************************************987776432.5666666666655 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 !   65.8   0.2   3.6e-21   4.6e-18       6     109 ..     417     515 ..     413     517 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 3.6e-21
                                       HHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHH CS
                         HATPase_c   6 LrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsiv 81 
                                       +  +++n++ Nav + +k+++i++++k++++  ++++ D G+Gip e+ kk+f+  fs       +++gtGlGl+++
  gi|488601204|ref|YP_007907675.1| 417 ISSLFDNIIRNAVIH-GKTNRIDIKVKRKNGVCEVRIADYGRGIPNEIKKKIFDeGFSH-----GETKGTGLGLYVA 487
                                       567899999999999.99*********77799*********************99****.....6689********* PP

                                       HHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                         HATPase_c  82 kklvelmgGeiwvesepgrGttftftlp 109
                                       kk++e++gG+i++e++  +G  f+++++
  gi|488601204|ref|YP_007907675.1| 488 KKVMERYGGSISIEDNNPKGAVFVLRFK 515
                                       ***********************99876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.3e-10   5.6e-07       1      51 [.     109     157 ..     109     166 .. 0.88
   2 !   19.5   0.0   5.6e-07   0.00071       2      57 ..     197     250 ..     196     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.3e-10
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellg.qllpv 51 
                                       er+r ++e++ d i++v++++ +v++N+aa++ lG +  ++g++l+ ++ ++
  gi|488601204|ref|YP_007907675.1| 109 ERYRKIVENIKDIIILVNNDGVVVEANNAAEKVLG-K--IIGKKLDkKWYDG 157
                                       7*****************8888*************.8..9999997666555 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 5.6e-07
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpvlrplle 57 
                                       + + ++e+++  i+ +d+ +riv+ N++ +e++Gy     + l  ++++ + p  e
  gi|488601204|ref|YP_007907675.1| 197 FVEKIIETANSLIVGLDEKGRIVMFNRKCEEITGYA--REEVLGKNWFDIFVPRVE 250
                                       667899999999999**5557*************99..444444588887777655 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00016       0.2       2      36 ..     120     150 ..     119     162 .. 0.84
   2 !   32.1   0.1   8.4e-11   1.1e-07       5     104 .]     209     304 ..     205     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksi 36 
                                       d i+++n+dg ++ aN+aa+++lG     ++gk++
  gi|488601204|ref|YP_007907675.1| 120 DIIILVNNDGVVVEANNAAEKVLG----KIIGKKL 150
                                       5678899***666**********9....6777775 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 8.4e-11
                             PAS_9   5 li.dnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                       ++  +++gri+ +N++ ++++Gy +eevlgk+++d+f   p+ + +l+ + ++++ + ++  ++ ir + ++  +  
  gi|488601204|ref|YP_007907675.1| 209 IVgLDEKGRIVMFNRKCEEITGYAREEVLGKNWFDIF--VPRVEYTLKIFKKTLE-IGWNSYIHPIRAKTGEKIISW 282
                                       44588********************************..8888888888888888.888888888888888888788 PP

                             PAS_9  81 taspvkdddgelvgiivilrDite 104
                                       + + v  ++++++   +i +Dit+
  gi|488601204|ref|YP_007907675.1| 283 SNTVVEREGERIIV--AIGNDITD 304
                                       88888666656655..99999995 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   9.1e-05      0.12       1      29 [.     115     143 ..     115     161 .. 0.83
   2 ?    3.3   0.0     0.077        99      77     109 ..     162     189 ..     154     190 .. 0.88
   3 !   14.7   0.0   2.2e-05     0.028       6      47 ..     207     248 ..     202     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.1e-05
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfg 29 
                                       ++++ d+++ ++ dg+v+ aN+aa++++g
  gi|488601204|ref|YP_007907675.1| 115 VENIKDIIILVNNDGVVVEANNAAEKVLG 143
                                       6899*******************999544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.077
                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       e+r+y+ +++ l+d     +g +vi+ DiTe +
  gi|488601204|ref|YP_007907675.1| 162 EGRFYSSSIYNLKD-----VGKVVIVSDITEKV 189
                                       789*********99.....888********975 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.2e-05
                             PAS_4   6 dalavldpdgrvlyaNaaaaelfgappeellGktlaellpee 47 
                                        +++ ld+ gr++  N+  +e+ g+++ee+lGk +++++ ++
  gi|488601204|ref|YP_007907675.1| 207 SLIVGLDEKGRIVMFNRKCEEITGYAREEVLGKNWFDIFVPR 248
                                       566678*******************************99874 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     1e-08   1.3e-05      39     120 ..     424     509 ..     405     514 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1e-08
                       HATPase_c_2  39 actNavehayleapegpvevrlesdeealtvevaDsGpg.fdpetlpdpteeepkeslkegGrGlalikglvDev.. 112
                                       ++ Nav+h++      ++ ++++++++ ++v++aD G+g  +  +++  +e  + ++ k  G+Gl++ k++++ +  
  gi|488601204|ref|YP_007907675.1| 424 IIRNAVIHGKT----NRIDIKVKRKNGVCEVRIADYGRGiPNEIKKKIFDEGFSHGETKGTGLGLYVAKKVMERYgg 496
                                       45677777775....8999********************8888888888888889*****************99876 PP

                       HATPase_c_2 113 ey.....dgegnv 120
                                       ++     +++g v
  gi|488601204|ref|YP_007907675.1| 497 SIsiednNPKGAV 509
                                       4444555555555 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1         5   6.4e+03      39      53 ..     191     205 ..     190     207 .. 0.73
   2 !   21.1   0.2   1.5e-07   0.00019       5      54 ..     311     361 ..     307     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5
                            SPOB_a  39 ydkaeeyieevvkel 53 
                                       ++k +e++e++++ +
  gi|488601204|ref|YP_007907675.1| 191 LEKEKEFVEKIIETA 205
                                       678888888888766 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.5e-07
                            SPOB_a   5 eikelkeliklL.rsqRHDflNhLQvIsGylqLgkydkaeeyieevvkelk 54 
                                       + +el+el  ++ +  RHD lN+L ++ G l+L++ +k + +ie+++k++ 
  gi|488601204|ref|YP_007907675.1| 311 RAEELSELFRVInKIMRHDILNDLSIVVGALELYMENKDVFLIEKAIKAAY 361
                                       5678888888887789******************************99875 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-06    0.0014       2      69 ..     219     282 ..     218     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwve 69 
                                       +  ++++eei+Gy +ee+lgk  +w d+  p   e++ + +++ l+ g  +y   + ir k Ge +  +
  gi|488601204|ref|YP_007907675.1| 219 VMFNRKCEEITGYAREEVLGK--NWFDIFVPRV-EYTLKIFKKTLEIGWnSY--IHPIRAKTGEKIISW 282
                                       567999***************..********97.999999999998888444..444555555544333 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.1e-06    0.0052       4      91 ..     415     504 ..     412     512 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                       HATPase_c_5   4 ldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ek.kkle....sskskkeehGiGlk 72 
                                         +++++ n++ NA+   +     +  I+++v++k++   ++i  + +g   e+ kk++    s   +++  G+Gl 
  gi|488601204|ref|YP_007907675.1| 415 EAISSLFDNIIRNAVIHGK-----TNRIDIKVKRKNGVCEVRIADYGRGipnEIkKKIFdegfS-HGETKGTGLGLY 485
                                       5678888899988885544.....456***********99999999776555333333333313.44577889999* PP

                       HATPase_c_5  73 sireivkkykgnlsieaed 91 
                                         ++++++y+g++sie ++
  gi|488601204|ref|YP_007907675.1| 486 VAKKVMERYGGSISIEDNN 504
                                       ***************9887 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.5e-06    0.0032     126     158 ..     308     340 ..     295     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                         HisKA_4TM 126 dasrakrisdalafvndlirhdlrndlvvirgy 158
                                         +ra+  s+ +  +n+++rhd+ ndl ++ g 
  gi|488601204|ref|YP_007907675.1| 308 ARRRAEELSELFRVINKIMRHDILNDLSIVVGA 340
                                       4589***********************999775 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0095        12      83     114 ..     161     192 ..     117     193 .. 0.87
   2 !    7.6   0.0    0.0032       4.1       8      39 ..     209     239 ..     202     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0095
                             PAS_7  83 pdgrvievrgnplpdgGfVttytDiTerrrae 114
                                       ++gr+ +     l d G V++ +DiTe+++ e
  gi|488601204|ref|YP_007907675.1| 161 HEGRFYSSSIYNLKDVGKVVIVSDITEKVKLE 192
                                       5788888888899**************99876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0032
                             PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgv 39 
                                       i+ +D+++r+v++Nr++ e+ ++ +e v  g+
  gi|488601204|ref|YP_007907675.1| 209 IVGLDEKGRIVMFNRKCEEITGYAREEV-LGK 239
                                       6779******************999877.555 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   9.2e-05      0.12      10      64 ..     424     478 ..     416     503 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-05
                       HATPase_c_3  10 lvdNsld.AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeak 64 
                                       +++N++  ++ ++++i+v++++  + e++i D G G+++e  k+ +  + s+ e+k
  gi|488601204|ref|YP_007907675.1| 424 IIRNAVIhGKTNRIDIKVKRKN-GVCEVRIADYGRGIPNEIKKKIFDEGFSHGETK 478
                                       7999964399999*******86.69************9986667888777777753 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       2.2   2.8e+03      40      60 ..     100     120 ..      83     121 .. 0.59
   2 ?   -1.7   0.0       2.3     3e+03      35      51 ..     192     208 ..     184     213 .. 0.84
   3 ?    9.2   0.4   0.00092       1.2       9      63 ..     326     375 ..     309     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             HisKA  40 yletiesearrldhlvedlLd 60 
                                        le +    +r +++ve++ d
  gi|488601204|ref|YP_007907675.1| 100 VLECLLLADERYRKIVENIKD 120
                                       444444444577777777655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                                       SSCHHHHHHHHHHHHHH CS
                             HisKA  35 eelkeyletiesearrl 51 
                                       e+ ke++e+i++ a+ l
  gi|488601204|ref|YP_007907675.1| 192 EKEKEFVEKIIETANSL 208
                                       78899*****9999876 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00092
                                       HHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                             HisKA   9 vaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsr 63 
                                       + H++ + Ls + g++e+ ++      +   ++e++++ a    +l++++++l++
  gi|488601204|ref|YP_007907675.1| 326 MRHDILNDLSIVVGALELYME-----NKDVFLIEKAIKAAYKSINLIKEIRQLES 375
                                       89****************877.....56666888888888888888888888876 PP

>> Ribosomal_S6  Ribosomal protein S6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0016       2.1      13      58 ..     107     165 ..     104     177 .. 0.81
   2 ?   -1.0   0.1       1.7   2.2e+03      13      42 ..     187     216 ..     178     223 .. 0.61
   3 ?   -0.9   0.2       1.6     2e+03      70      89 ..     312     331 ..     306     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                                       -HHHHHHHHHHHHHHHH..HTTEEEEEEEEEEEEEEEEEETTE...........EEEEE CS
                      Ribosomal_S6  13 seeevkelvekvgklil..enggvvrkveswGkrkLaypikkk...........teGyy 58 
                                        +e+ +++ve+++++i   +n gvv++ ++  ++ L ++i kk           +eG +
  gi|488601204|ref|YP_007907675.1| 107 ADERYRKIVENIKDIIIlvNNDGVVVEANNAAEKVLGKIIGKKldkkwydgfitHEGRF 165
                                       678999********985449********************9997777766655555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                                       -HHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                      Ribosomal_S6  13 seeevkelvekvgklilenggvvrkveswG 42 
                                       ++ ++++  e v+k+i+ ++  ++ +++ G
  gi|488601204|ref|YP_007907675.1| 187 EKVKLEKEKEFVEKIIETANSLIVGLDEKG 216
                                       444666666666777776666666666655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.6
                                       HHHHHHHHHCSTTEEEEEEE CS
                      Ribosomal_S6  70 ikelertlrldervlRyliv 89 
                                        +el++ +r  ++++R+ i+
  gi|488601204|ref|YP_007907675.1| 312 AEELSELFRVINKIMRHDIL 331
                                       6899999*********9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3235.30
//
Query:       gi|488601205|ref|YP_007907676.1|  [L=242]
Description: Deacetylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-38  131.5   0.1      8e-25   87.9   0.0    3.0  3  Hist_deacetyl  Histone deacetylase domain
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.34   11.0   0.0    1.6  2  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 !   13.7   0.0   3.6e-06     0.032       4      56 ..      20      64 ..      16      69 .. 0.86
   2 !   87.9   0.0   8.9e-29     8e-25      86     180 ..      64     155 ..      61     162 .. 0.93
   3 !   28.0   0.0   1.6e-10   1.5e-06     232     305 ..     167     239 ..     162     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-06
                                      GTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  4 npkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsn 56
                                      +p Rl+ i+e+l++  +       +++ps+a+++++l vH++++le+++++++
  gi|488601205|ref|YP_007907676.1| 20 SPGRLECIVEELRDY-E-------FVEPSPASESDILLVHTPSHLEFVKTMQS 64
                                      789999999999995.5.......4689********************98875 PP

  == domain 2  score: 87.9 bits;  conditional E-value: 8.9e-29
                                       TCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  86 ktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDvH 162
                                       ++++ + l++g++++a +   ++    af l+rPpgHHa ++   GFC++Nn+ai +++l  ++++++ +i+D+D+H
  gi|488601205|ref|YP_007907676.1|  64 SVYEISCLSAGSAIRASEIAFEE---PAFSLARPPGHHASPNSSWGFCYFNNIAISVRRLIVNSKIEKAVIVDFDLH 137
                                       678888999*******9999966...9***********************************999************ PP

                                       --HHHHHHCTT-TTEEEE CS
                                       xxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 163 hGnGteeafysdpdvltl 180
                                       +G+Gt + f++d +v + 
  gi|488601205|ref|YP_007907676.1| 138 YGDGTANTFEDDGRVKYY 155
                                       ************999775 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 1.6e-10
                                       HHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G.EEEEE-S---HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 232 pvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.kkvvllleGGYnlealaravtavls 305
                                       + le+ + d+i vsaGfD + +d  +   l +e+y e+ k ++e+++++ ++  ++leGGY+++ l ++v+a+++
  gi|488601205|ref|YP_007907676.1| 167 EFLEKSEYDIIAVSAGFDKHVDDWGSY--LMTEDYREIGKIIREFSERCdGRRYAVLEGGYSTKVLGKNVKAFIR 239
                                       677888889***********9997654..56789*************9956****************99998765 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.88   7.9e+03      28      50 ..       9      34 ..       4      36 .. 0.75
   2 ?   11.0   0.0   3.8e-05      0.34      23      91 ..     145     227 ..     141     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.88
                       B12-binding 28 gfeVqllganven...edivaairae 50
                                       ++V+  +  +++   e iv+++r+ 
  gi|488601205|ref|YP_007907676.1|  9 FYDVYTHDPAASPgrlECIVEELRDY 34
                                      57888889888888888888888775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.8e-05
                       B12-binding  23 alrdagfeVqllganven.edivaairaekpdvvglSal............ltsqleavkelvel..lkrirprvkv 84 
                                        ++d+g +V+++ +  ++ + iv+ +++ ++d++++Sa             +t  ++++ +++++  ++  ++r  v
  gi|488601205|ref|YP_007907676.1| 145 TFEDDG-RVKYYHMPKDDiDGIVEFLEKSEYDIIAVSAGfdkhvddwgsylMTEDYREIGKIIREfsERCDGRRYAV 220
                                       566655.77888777777899***************88877777777777799999999999999998888889999 PP

                       B12-binding  85 vvGGahp 91 
                                       + GG   
  gi|488601205|ref|YP_007907676.1| 221 LEGGYST 227
                                       9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 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:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1364.77
//
Query:       gi|488601206|ref|YP_007907677.1|  [L=260]
Description: putative amidohydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-58  197.7   0.0    2.5e-58  197.5   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase
  ------ inclusion threshold ------
       0.13   12.5   0.1         11    6.4   0.0    2.3  2  DUF2209       Uncharacterized protein conserved in archaea (D


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 !  197.5   0.0   2.8e-62   2.5e-58       3     261 .]       9     244 ..       8     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 2.8e-62
                                       EEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS.SSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEE CS
                      CN_hydrolase   3 AvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy.keeahfleaAeaglgetlallaalarkngiav 78 
                                       A+ Ql++ + d++ nl k+l+li++A + +a+L+vlPElf+tg+   + + +e        +++l+ +l+++ +i++
  gi|488601206|ref|YP_007907677.1|   9 AIGQLRI-SPDRDVNLMKALSLIKRAIQVNAKLVVLPELFNTGFyPKNYELVE---DNIEDEIDLILKLSERRDITI 81 
                                       8899999.79********************************99444444444...44459**************** PP

                                       EEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGG CS
                      CN_hydrolase  79 vigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCye 155
                                       v+ ++e+  +ngkl  yn+av++ + g+++gkyrK+hLf      p + er++f+ g++++v+dtpvgkiG++iCye
  gi|488601206|ref|YP_007907677.1|  82 VGSVAEK--ENGKL--YNSAVVI-HRGEILGKYRKTHLF------PLTEERKYFSTGNELKVVDTPVGKIGLMICYE 147
                                       *******..9****..*******.677778*********......8999**************************** PP

                                       GGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TT CS
                      CN_hydrolase 156 igfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpd 232
                                        +fpe++r l +kgaeil      a++pk +   +w +l +ara+en+cfv  an + g       + g+S+i+dp+
  gi|488601206|ref|YP_007907677.1| 148 VRFPEIARYLVRKGAEILAI-P--AEFPKERI-NHWKILLKARAIENQCFVFGANCAEG----EDAYPGSSMIVDPW 216
                                       ******************88.4..67887776.566***********************....77899********* PP

                                       S-EEEECCSSSTEEEEEEEEHHHHHHHHH CS
                      CN_hydrolase 233 Grilaglgeeeegvliaeidladvratrr 261
                                       G++l++ g  +e +++aeid ++v++trr
  gi|488601206|ref|YP_007907677.1| 217 GNVLVEGGDRQE-IIMAEIDIGEVEKTRR 244
                                       ***********7.************9986 PP

>> DUF2209  Uncharacterized protein conserved in archaea (DUF2209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0012        11      35     110 ..       7      83 ..       2      90 .. 0.81
   2 ?    4.8   0.0    0.0039        35      58     107 ..      85     134 ..      79     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0012
                           DUF2209  35 veqvkilvvaseeepkledvvklieeaveelkeegtivaE..kGelynepewlveailkkefkyqeslgEreaielA 109
                                       ++ +  l +  +++++l + ++li++a++  + + +++ E  +  +y ++ +lve  ++ e+     l+Er+ i + 
  gi|488601206|ref|YP_007907677.1|   7 ISAIGQLRISPDRDVNLMKALSLIKRAIQV-NAKLVVLPElfNTGFYPKNYELVEDNIEDEIDLILKLSERRDITIV 82 
                                       444444456678899999*********975.57888888855577***************************99986 PP

                           DUF2209 110 H 110
                                        
  gi|488601206|ref|YP_007907677.1|  83 G 83 
                                       5 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0039
                           DUF2209  58 ieeaveelkeegtivaEkGelynepewlveailkkefkyqeslgEreaie 107
                                       ++e  ++   + ++v+ +Ge+  + +++    l++e ky  +  E+++++
  gi|488601206|ref|YP_007907677.1|  85 VAEKENGKLYNSAVVIHRGEILGKYRKTHLFPLTEERKYFSTGNELKVVD 134
                                       4444444447889*****************************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1401.35
//
Query:       gi|488601207|ref|YP_007907678.1|  [L=93]
Description: hypothetical protein Asulf_01714 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   36.4   0.0    4.7e-09   36.2   0.0    1.1  1  HTH_20          Helix-turn-helix domain
    2.2e-07   30.6   0.5    4.3e-07   29.7   0.5    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    4.8e-07   29.2   0.0    7.1e-07   28.7   0.0    1.2  1  GerE            Bacterial regulatory proteins, luxR family
    0.00028   20.5   0.0    0.00041   20.0   0.0    1.2  1  Sigma70_r4_2    Sigma-70, region 4
     0.0007   19.3   0.1     0.0012   18.5   0.1    1.5  1  HTH_23          Homeodomain-like domain
    0.00071   19.5   0.3     0.0011   18.9   0.3    1.2  1  HTH_45          Winged helix-turn-helix
     0.0012   18.9   0.0     0.0016   18.4   0.0    1.3  1  HTH_29          Winged helix-turn helix
     0.0024   17.4   0.5     0.0053   16.3   0.5    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0033   17.2   0.0     0.0049   16.6   0.0    1.4  1  HTH_38          Helix-turn-helix domain
     0.0063   16.6   0.0     0.0094   16.1   0.0    1.2  1  HTH_28          Helix-turn-helix domain
     0.0072   16.1   0.1      0.017   14.9   0.1    1.6  1  HTH_10          HTH DNA binding domain
  ------ inclusion threshold ------
      0.046   13.8   0.0      0.072   13.1   0.0    1.3  1  KorB            KorB domain
      0.066   13.4   0.1      0.083   13.1   0.1    1.1  1  TetR_C_5        QacR-like protein, C-terminal region
       0.09   12.9   0.1       0.18   12.0   0.1    1.6  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.092   12.7   0.5      0.092   12.7   0.5    1.6  2  HTH_12          Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0     4e-12   4.7e-09       3      53 ..      24      71 ..      22      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 4e-12
                                      HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTT CS
                            HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagL 53
                                      ++ A+++P Rr+il+++  aeg    e+a+ l+ls ++l+yHL++L e+g+
  gi|488601207|ref|YP_007907678.1| 24 YHIAVSSPLRRKILKLI--AEGKNKQEIAKSLGLSEKNLDYHLKIL-EHGF 71
                                      66699************..***************************.6665 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 !   29.7   0.5   3.6e-10   4.3e-07       1      40 [.      30      68 ..      30      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.6e-10
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHH CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLr 40
                                      +p R+kILkl aeg+ +  e+a+ lgls+ ++++HLk+L+
  gi|488601207|ref|YP_007907678.1| 30 SPLRRKILKLIAEGKNK-QEIAKSLGLSEKNLDYHLKILE 68
                                      599**********9876.8********************7 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   5.9e-10   7.1e-07       8      39 ..      34      65 ..      30      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5.9e-10
                                      HHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHH CS
                              GerE  8 revLrllaeGksnkeIAeelniSekTVkvhks 39
                                      r++L+l+aeGk  +eIA++l++Sek+  +h++
  gi|488601207|ref|YP_007907678.1| 34 RKILKLIAEGKNKQEIAKSLGLSEKNLDYHLK 65
                                      78**************************9986 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 !   20.0   0.0   3.5e-07   0.00041      12      47 ..      30      64 ..      30      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.5e-07
                                      -HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 12 perqreifllryleglsykEIAellgisegtVksrl 47
                                      ++ +r+i+ l+  eg+  +EIA+ lg+se++ +++l
  gi|488601207|ref|YP_007907678.1| 30 SPLRRKILKLI-AEGKNKQEIAKSLGLSEKNLDYHL 64
                                      6899******8.6*******************9998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     1e-06    0.0012       7      31 ..      33      57 ..      28      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1e-06
                            HTH_23  7 RlrillllaeGlsvreIAreLgvsr 31
                                      R +il+l aeG++++eIA+ Lg s+
  gi|488601207|ref|YP_007907678.1| 33 RRKILKLIAEGKNKQEIAKSLGLSE 57
                                      889********************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 !   18.9   0.3     9e-07    0.0011      10      65 ..      35      89 ..      31      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9e-07
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlel 65
                                       IL+ i  ++++k +i ++  Ls k+l+  L++L +   ik +++  +lT++G+ +
  gi|488601207|ref|YP_007907678.1| 35 KILKLI-AEGKNKQEIAKSLGLSEKNLDYHLKILEHGFCIKINGDRISLTKEGEII 89
                                      69****.9999***********************99888**************865 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0016       1      28 [.      33      59 ..      33      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrt 28
                                      R ++l l+aeG  + ++iAk lgls++ 
  gi|488601207|ref|YP_007907678.1| 33 RRKILKLIAEGK-NKQEIAKSLGLSEKN 59
                                      889********9.9***********985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   4.5e-06    0.0053       4      42 ..      32      68 ..      30      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.5e-06
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLe 42
                                      ++rkIL+l+ +  + + +e+A+ lglS  ++ ++lk Le
  gi|488601207|ref|YP_007907678.1| 32 LRRKILKLIAE--GKNKQEIAKSLGLSEKNLDYHLKILE 68
                                      689********..**********************9887 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.1e-06    0.0049      10      33 ..      33      56 ..      27      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.1e-06
                            HTH_38 10 ReeIerllaeGlslreIArrLgrs 33
                                      R++I +l+aeG++  eIA+ Lg s
  gi|488601207|ref|YP_007907678.1| 33 RRKILKLIAEGKNKQEIAKSLGLS 56
                                      9********************977 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.9e-06    0.0094       2      38 ..      33      69 ..      32      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.9e-06
                            HTH_28  2 RleiikllaaGhsvreaArelgisrrtvyrWikryee 38
                                      R++i+kl+a+G++  e+A+ lg+s+  +   +k +e+
  gi|488601207|ref|YP_007907678.1| 33 RRKILKLIAEGKNKQEIAKSLGLSEKNLDYHLKILEH 69
                                      99***********************999888888777 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.4e-05     0.017      26      46 ..      46      66 ..      43      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                            HTH_10 26 lkeLAkelGIskstlsehLrk 46
                                       +e+Ak lG+s+ +l +hL+ 
  gi|488601207|ref|YP_007907678.1| 46 KQEIAKSLGLSEKNLDYHLKI 66
                                      589****************86 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     6e-05     0.072       2      34 ..      42      74 ..      41      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-05
                              KorB  2 kgvkqadIAkaLGksksfvslylklldvpdylr 34
                                      +g ++++IAk LG s++ +  +lk+l+   +++
  gi|488601207|ref|YP_007907678.1| 42 EGKNKQEIAKSLGLSEKNLDYHLKILEHGFCIK 74
                                      699**********************99877776 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 ?   13.1   0.1   6.9e-05     0.083      14      78 ..       8      71 ..       4      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-05
                          TetR_C_5 14 kkyktateklYalaelsleeyktPlsnaieelaseqvksksilekllkLerkslkayekileeGi 78
                                      k+y+t+ ek   + +     +  Pl + i  l +e   +++i  k l+L++k+l+ + kile G 
  gi|488601207|ref|YP_007907678.1|  8 KEYSTSLEKSKEYHRRYHIAVSSPLRRKILKLIAEGKNKQEIA-KSLGLSEKNLDYHLKILEHGF 71
                                      7899999999988765556799***********9987777766.5679**************995 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 ?   12.0   0.1   0.00015      0.18       3      51 ..      32      75 ..      30      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                    B-block_TFIIIC  3 dqfklLelIassRysGitqsdLakeskqdprslfyrlksLekkgLIvkq 51
                                      +++k+L lIa     G + +++ak+++ + ++l y+lk Le+ g++ k+
  gi|488601207|ref|YP_007907678.1| 32 LRRKILKLIAE----GKNKQEIAKSLGLSEKNLDYHLKILEH-GFCIKI 75
                                      56788888875....7788*********************99.888776 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 ?   -2.9   0.1       5.7   6.8e+03      27      38 ..      19      25 ..       8      27 .. 0.51
   2 ?   12.7   0.5   7.7e-05     0.092       2      47 ..      35      71 ..      34      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.7
                            HTH_12 27 gydigeravRyr 38
                                      +y       Ry+
  gi|488601207|ref|YP_007907678.1| 19 EYHR-----RYH 25
                                      3332.....555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.7e-05
                            HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergl 47
                                      +ILk++ae ++   ++eia++L + + ++      y+L++le  g+
  gi|488601207|ref|YP_007907678.1| 35 KILKLIAEGKN---KQEIAKSLGLSEKNL-----DYHLKILEH-GF 71
                                      699*****999...9*******9888777.....9******96.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 604.84
//
Query:       gi|488601208|ref|YP_007907679.1|  [L=165]
Description: ATP:cob(I)alamin adenosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-31  108.9   0.2    3.7e-31  108.5   0.2    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.2     2e-35   3.7e-31      10     161 ..       7     151 ..       4     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 2e-35
                                       XXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HH CS
                   Cob_adeno_trans  10 tTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkkitee 86 
                                       +T+l++ + v+Kd+  ++ +Gt+De+n++igla+ +++  +e +k+ Le+iq  +f++g el       ++ +++e+
  gi|488601208|ref|YP_007907679.1|   7 KTHLLDRSLVDKDSELIKGLGTLDEANAFIGLAKVFAR--DELVKKYLEKIQMMIFKAGLELI------SDYRMSEK 75 
                                       8*********************************7775..568*******************7......45789999 PP

                                       HHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHHHHHHHHHH CS
                   Cob_adeno_trans  87 eveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRLSDlLfvla 161
                                       e +el + i+e+e+ +++ ++fil ++++++a l+vaRtv+RraER++v l+++  v+  ++++lN+LS l++++ 
  gi|488601208|ref|YP_007907679.1|  76 EYDELLNIIQEFESIVKKPRNFILLEKNESSAFLSVARTVVRRAEREIVGLEKAGkVSLLLVEWLNKLSYLIYLMN 151
                                       9**************************************************98768889999***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 994.53
//
Query:       gi|488601209|ref|YP_007907680.1|  [L=345]
Description: LAO/AO transport system ATPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  368.5   1.2   1.6e-110  368.3   1.2    1.1  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
    1.3e-08   34.9   0.6    0.00011   22.1   0.1    2.5  2  ATP_bind_1      Conserved hypothetical ATP binding protein
    2.3e-05   24.1   2.1      0.036   13.6   0.1    3.0  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
      8e-05   22.3   0.4     0.0012   18.6   0.1    2.2  2  SRP54           SRP54-type protein, GTPase domain
     0.0002   21.3   0.9    0.00061   19.7   0.9    1.8  1  NTPase_1        NTPase
    0.00049   20.6   1.1     0.0071   16.9   0.1    2.3  2  AAA_18          AAA domain
    0.00078   19.4   0.1       0.16   11.9   0.0    2.9  3  RsgA_GTPase     RsgA GTPase
    0.00098   18.7   0.3     0.0024   17.4   0.1    1.7  2  KTI12           Chromatin associated protein KTI12
     0.0014   18.6   0.0     0.0023   18.0   0.0    1.5  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0019   18.6   0.4     0.0072   16.7   0.1    2.0  2  AAA_16          AAA ATPase domain
     0.0022   18.0   0.8     0.0056   16.8   0.8    2.1  1  MMR_HSR1        50S ribosome-binding GTPase
     0.0023   17.8   0.4     0.0091   15.9   0.1    2.1  2  MobB            Molybdopterin guanine dinucleotide synthesis 
     0.0033   17.2   0.1     0.0077   16.0   0.1    1.5  1  AAA_30          AAA domain
     0.0058   17.2   0.1      0.087   13.3   0.1    2.3  2  ABC_tran        ABC transporter
      0.006   16.1   0.0      0.012   15.1   0.0    1.4  1  ParA            NUBPL iron-transfer P-loop NTPase
     0.0063   16.8   0.1      0.017   15.4   0.0    1.7  2  AAA_22          AAA domain
     0.0064   15.7   3.5      0.026   13.7   0.2    2.3  2  NB-ARC          NB-ARC domain
     0.0079   15.8   0.3      0.073   12.6   0.3    2.2  1  GTP_EFTU        Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.013   15.0   1.0        2.5    7.6   0.1    2.5  2  FeoB_N          Ferrous iron transport protein B
      0.022   14.0   0.0       0.04   13.2   0.0    1.8  1  KAP_NTPase      KAP family P-loop domain
       0.03   14.1   0.4      0.085   12.6   0.4    1.8  1  PRK             Phosphoribulokinase / Uridine kinase family
      0.039   14.1   0.0      0.043   14.0   0.0    1.4  1  MnmE_helical    MnmE helical domain
      0.044   13.1   0.1      0.095   12.0   0.1    1.5  1  Zeta_toxin      Zeta toxin
      0.069   12.9   0.6        0.3   10.8   0.1    2.0  2  DUF1131         Protein of unknown function (DUF1131)
      0.084   11.8   0.1       0.19   10.6   0.1    1.5  1  TrwB_AAD_bind   Type IV secretion-system coupling protein DNA
      0.093   12.6   0.0       0.24   11.3   0.0    1.6  1  Ploopntkinase3  P-loop Nucleotide Kinase3
       0.19   12.2   1.0        1.2    9.5   0.1    2.4  2  AAA             ATPase family associated with various cellula
       0.19   12.1   2.4       0.23   11.9   0.1    2.2  3  AAA_17          AAA domain
       0.24   11.5   4.7        1.8    8.6   0.4    2.6  3  DUF87           Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.3   1.2  2.6e-113  1.6e-110       1     262 [.      18     310 ..      18     315 .. 0.98

  Alignments for each domain:
  == domain 1  score: 368.3 bits;  conditional E-value: 2.6e-113
                                       HHHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------ CS
                              MeaB   1 LaraitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsil 77 
                                       Larait+ve+++pe ke+l+r+ +k+G a+v+G+tG+PG+Gkst+v++l++e+r rGk v+++avDP+spftGG++l
  gi|488601209|ref|YP_007907680.1|  18 LARAITYVENDYPEGKEILKRIYPKTGSAHVIGITGFPGVGKSTIVSKLTQEFRTRGKTVGIVAVDPGSPFTGGALL 94 
                                       8**************************************************************************** PP

                                       ------HCCC......TSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEE CS
                              MeaB  78 GDklRleela......vdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvv 148
                                       GD+lR++ l+      vd+gvf+Rs++srG++GGl+akt++v++l++a+GfDv+ +etvG+Gqsevd++ev+dt++v
  gi|488601209|ref|YP_007907680.1|  95 GDRLRMDGLDtnrqlwVDPGVFFRSMSSRGRAGGLSAKTGDVIRLMDAFGFDVIFVETVGAGQSEVDIIEVADTSIV 171
                                       *********9999999************************************************************* PP

                                       EEESSTTTTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCST.........................TB CS
                              MeaB 149 lllpeaGDelqgikkGileiaDiivvnkaDkkeaekaarelraaleleee.........................ke 200
                                        l+pe GD++q +k+Gilei+Di+vvnkaD+ +aek++r+++a+l +++e                         ++
  gi|488601209|ref|YP_007907680.1| 172 ALMPEMGDDIQINKAGILEIGDIYVVNKADLGGAEKTERWIKAMLMMDQEaveilsktthadealvqsgqiyekiRR 248
                                       ************************************************************************9888* PP

                                       TTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              MeaB 201 keWrpkvlktsavegeGidelvdaieehrevlkktGllekrrrerakeelrelvedellkrv 262
                                       +eW p+v+kt+a +geGid+l+daie+h+++lkk+G+l + r++r  +e+ e+  +e+ + +
  gi|488601209|ref|YP_007907680.1| 249 SEWIPPVIKTVAEKGEGIDQLADAIEDHFDYLKKSGRLIETRKKRLSREMVEILVNEIRNYL 310
                                       ****************************************************9999987765 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 !   22.1   0.1   1.8e-07   0.00011       1      36 [.      51      86 ..      51      89 .. 0.95
   2 !   10.8   0.0   0.00051      0.32     155     240 ..     189     278 ..     181     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-07
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                      ++G +G+GK+t+v++l++ +++rg++v +v  DP++
  gi|488601209|ref|YP_007907680.1| 51 ITGFPGVGKSTIVSKLTQEFRTRGKTVGIVAVDPGS 86
                                      68********************************86 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00051
                        ATP_bind_1 155 lelPhvvvlnkfDllkek.lekelef..fedvealslllekee.ekykklaeaiaelleefalvlrflplssekees 227
                                       le+  + v+nk+Dl   + +e+ ++   + d ea++ l ++++ +    +  +i e +   + ++ ++   +ek+e+
  gi|488601209|ref|YP_007907680.1| 189 LEIGDIYVVNKADLGGAEkTERWIKAmlMMDQEAVEILSKTTHaDEALVQSGQIYEKIRRSEWIPPVIKTVAEKGEG 265
                                       5677899******9776665555554115567777777777777666777889************************ PP

                        ATP_bind_1 228 iedllslidealq 240
                                       i++l ++i+++++
  gi|488601209|ref|YP_007907680.1| 266 IDQLADAIEDHFD 278
                                       *********9987 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   5.9e-05     0.036       2      32 ..      48      80 ..      47      89 .. 0.78
   2 !    8.4   0.3    0.0025       1.5      82     168 ..     144     217 ..     129     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                                      EEEEEESTTCCHHHHHHHHH..CT--SS-EEEE CS
                              cobW  2 vtvltGflGsGKTtLlnhll..enraglklavi 32
                                      v+++tGf+G GK+t++++l+   +++g+ + ++
  gi|488601209|ref|YP_007907680.1| 48 VIGITGFPGVGKSTIVSKLTqeFRTRGKTVGIV 80
                                      789****************95434555666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                                       T-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC.. CS
                              cobW  82 rldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeal 158
                                        +dvi++Et+G  +                +d+ ++ +      + +++i+ +    l+  d+ v+nK+Dl  +e++
  gi|488601209|ref|YP_007907680.1| 144 GFDVIFVETVGAGQSEVD--------IIEVADTSIVALMP----EMGDDIQINKAGILEIGDIYVVNKADLGGAEKT 208
                                       588999999997665544........12334444444444....57889998889999*************999966 PP

                                       HHHHHHHHHH CS
                              cobW 159 lekleerlrq 168
                                        e+  + +  
  gi|488601209|ref|YP_007907680.1| 209 -ERWIKAMLM 217
                                       .665555544 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.9e-06    0.0012       3      38 ..      48      83 ..      46      86 .. 0.94
   2 ?    1.4   0.0      0.34   2.1e+02     154     187 ..     131     167 ..     129     175 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      vi + G+ G+GK t ++KL + ++++gk+v +va+D
  gi|488601209|ref|YP_007907680.1| 48 VIGITGFPGVGKSTIVSKLTQEFRTRGKTVGIVAVD 83
                                      77899*****************************99 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.34
                                       SSTTHHHHHHHHHTS-EEE...EE-SSSTTGEEE--H CS
                             SRP54 154 akgGaalsiaaelklPikf...igvGekiedleefdp 187
                                       ak G ++ ++++++  ++f   +g G++  d+ e+  
  gi|488601209|ref|YP_007907680.1| 131 AKTGDVIRLMDAFGFDVIFvetVGAGQSEVDIIEVAD 167
                                       5666666666666665555222355666555555554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.9   9.8e-07   0.00061       2      31 ..      49      78 ..      48      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.8e-07
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                      + iTG pGvGK+T+v+k++++ + +g +vg
  gi|488601209|ref|YP_007907680.1| 49 IGITGFPGVGKSTIVSKLTQEFRTRGKTVG 78
                                      78********************99998875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.2e-05    0.0071       1      22 [.      49      70 ..      49     110 .. 0.77
   2 ?    2.3   0.1      0.38   2.4e+02      26      69 ..     274     315 ..     255     343 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                      I++tG pGvGK+t+   L ++ 
  gi|488601209|ref|YP_007907680.1| 49 IGITGFPGVGKSTIVSKLTQEF 70
                                      89***************97764 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.38
                            AAA_18  26 vnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                       + + d++k++g l+e  ++  + s++++e  ++++ + le+ s+
  gi|488601209|ref|YP_007907680.1| 274 EDHFDYLKKSGRLIETRKK--RLSREMVEILVNEIRNYLEKDSK 315
                                       5568999999999999999..99999999999999999999876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00026      0.16      90     126 ..      36      73 ..       8      81 .. 0.70
   2 ?    2.9   0.1      0.15        93      50      93 ..     194     236 ..     183     244 .. 0.81
   3 ?    2.4   0.1      0.21   1.3e+02      50     101 ..     223     277 ..     207     284 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       l+++ ++  + +++ + G  GvGKSt++ +l++e +++
  gi|488601209|ref|YP_007907680.1|  36 LKRIYPKTGSaHVIGITGFPGVGKSTIVSKLTQEFRTR 73 
                                       34444444444777899999***********9986555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                                       EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHH CS
                       RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvsaktkegleel 93 
                                       + v+nK+Dl   e+ +e++ +++  ++ e + + +kt+++ e+l
  gi|488601209|ref|YP_007907680.1| 194 IYVVNKADLGGAEK-TERWIKAMLMMDQEAVEILSKTTHADEAL 236
                                       6799*******999.99999999999999888877776666665 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.21
                                       EEEEE-GGG--HHH.HHHHHHHHHH..HTTSEEEE--TTTHTTHHHHHHHCTTSE CS
                       RsgA_GTPase  50 vivlnKiDlleeee.eleelkeele..algyevllvsaktkegleelkellkdkt 101
                                       v +l+K+  ++e+  +  ++ e+++  ++  +v+++ a+++eg+++l+++++d++
  gi|488601209|ref|YP_007907680.1| 223 VEILSKTTHADEALvQSGQIYEKIRrsEWIPPVIKTVAEKGEGIDQLADAIEDHF 277
                                       44566666666655433344443331155579999999***********999976 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.9e-06    0.0024       5      36 ..      50      81 ..      47      85 .. 0.91
   2 ?   -1.9   0.0       2.9   1.8e+03     129     129 ..     298     298 ..     219     341 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-06
                                      EEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekrsvvvid 36
                                       +tG+P +GKst++++L ++++ ++++v ++ 
  gi|488601209|ref|YP_007907680.1| 50 GITGFPGVGKSTIVSKLTQEFRTRGKTVGIVA 81
                                      59************************999875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                                       H CS
                             KTI12 129 l 129
                                       +
  gi|488601209|ref|YP_007907680.1| 298 M 298
                                       1 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.8e-06    0.0023       9      55 ..      56     265 ..      48     332 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.8e-06
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       GvGK+t++ +L + +  rg+ V  v +Dp ++ +     l +d+ +                               
  gi|488601209|ref|YP_007907680.1|  56 GVGKSTIVSKLTQEFRTRGKTVGIVAVDPGSPFTG--GALLGDRLRmdgldtnrqlwvdpgvffrsmssrgraggls 130
                                       9*****************************99987..3333333334556666677777777777777777777777 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|488601209|ref|YP_007907680.1| 131 aktgdvirlmdafgfdvifvetvgagqsevdiievadtsivalmpemgddiqinkagileigdiyvvnkadlggaek 207
                                       77777777777777777777777777777766666666666666666666666666666666666666666666666 PP

                                       .........................................................C CS
                                       .........................................................x RF
                              CbiA  55 .........................................................d 55 
                                                                                                +
  gi|488601209|ref|YP_007907680.1| 208 terwikamlmmdqeaveilsktthadealvqsgqiyekirrsewippviktvaekgeG 265
                                       6666666666666655555555555555555555555555555555555555555552 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.2e-05    0.0072      20      52 ..      42      74 ..      33      96 .. 0.83
   2 ?   -1.4   0.0       4.3   2.6e+03     117     134 ..     267     284 ..     218     320 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdg 52
                                      ++g+ +++ ++G +GvGKs++v +l ++++++g
  gi|488601209|ref|YP_007907680.1| 42 KTGSAHVIGITGFPGVGKSTIVSKLTQEFRTRG 74
                                      567778999*****************9999883 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.3
                            AAA_16 117 srllellkrllallsrde 134
                                        +l++++ +++++l++ +
  gi|488601209|ref|YP_007907680.1| 267 DQLADAIEDHFDYLKKSG 284
                                       555555555555555433 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.8     9e-06    0.0056       2      23 ..      49      71 ..      48     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9e-06
                                      EEEEESTTSSHHHHHHHHHTS.T CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.k 23
                                      ++i G p vGKSt++++lt+e +
  gi|488601209|ref|YP_007907680.1| 49 IGITGFPGVGKSTIVSKLTQEfR 71
                                      89*****************9632 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.5e-05    0.0091       1      33 [.      48      80 ..      48      85 .. 0.95
   2 ?   -2.4   0.0       6.7   4.2e+03      85     110 ..     137     166 ..     130     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvgti 33
                                      v+gi+g+ g GK t+++kl +e++ rg +vg++
  gi|488601209|ref|YP_007907680.1| 48 VIGITGFPGVGKSTIVSKLTQEFRTRGKTVGIV 80
                                      799***************************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.7
                              MobB  85 larlse..vDlvlvE..Gfkkealpkievl 110
                                       ++ +++   D+++vE  G  +++++ iev 
  gi|488601209|ref|YP_007907680.1| 137 IRLMDAfgFDVIFVEtvGAGQSEVDIIEVA 166
                                       555555557888888555555555566655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.2e-05    0.0077      17      53 ..      45      81 ..      37      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrviglA 53
                                      ++ v  +tG +G GK+t++++l++ ++++g++v ++A
  gi|488601209|ref|YP_007907680.1| 45 SAHVIGITGFPGVGKSTIVSKLTQEFRTRGKTVGIVA 81
                                      456899**************************99888 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00014     0.087      11      39 ..      46      77 ..      36     110 .. 0.80
   2 ?    1.6   0.0      0.59   3.6e+02      51     110 ..     204     295 ..     169     338 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                                      TSEEEEEESTTSSHHHHHHHHTTSS--...SE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx...xx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllkp...te 39
                                       ++++i+G  G GKSt+++ l+++ +    t 
  gi|488601209|ref|YP_007907680.1| 46 AHVIGITGFPGVGKSTIVSKLTQEFRTrgkTV 77
                                      5789*******************998633344 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.59
                                       G.B-HHHCCHCEEEE-SS.--S-TTSBHHHH..............................HHHTCHHHHHHHSTTG CS
                                       x.xxxxxxxxxxxxxxxx.xxxxxxxxxxxx..............................xxxxxxxxxxxxxxxx RF
                          ABC_tran  51 e.qeleslrkeigvlpqe.pqlfpeltvren..............................esdeeiekalsklglk 95 
                                         +++e++ k + ++ qe  ++ +++t +++                                d+ ++++ ++++  
  gi|488601209|ref|YP_007907680.1| 204 GaEKTERWIKAMLMMDQEaVEILSKTTHADEalvqsgqiyekirrsewippviktvaekgeGIDQLADAIEDHFDYL 280
                                       35666777777777777765555555544434776667766665555555555555433331122233334444444 PP

                                       GTTCBGESTTSGGS- CS
                                       xxxxxxxxxxxxxxx RF
                          ABC_tran  96 elkdtvvksspssLS 110
                                       ++  + ++++++ LS
  gi|488601209|ref|YP_007907680.1| 281 KKSGRLIETRKKRLS 295
                                       444444444444444 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05     0.012      11      41 ..      53      83 ..      45      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                              ParA 11 gKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                      g  GVGKSt+ ++l+ +++++g++vg++ +D
  gi|488601209|ref|YP_007907680.1| 53 GFPGVGKSTIVSKLTQEFRTRGKTVGIVAVD 83
                                      556************************9988 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.8e-05     0.017       5      56 ..      46      93 ..      42     127 .. 0.79
   2 ?   -2.3   0.0         8     5e+03      70      78 ..     283     294 ..     237     321 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                      a ++ +tG +G+GK+t + +l++++  +     + +++v v++ s+ +   l
  gi|488601209|ref|YP_007907680.1| 46 AHVIGITGFPGVGKSTIVSKLTQEFRTRG----KTVGIVAVDPGSPFTGGAL 93
                                      667889******************95432....4666667777776665555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8
                            AAA_22  70 a...erlsseel 78 
                                       +    + ++++l
  gi|488601209|ref|YP_007907680.1| 283 SgrlIETRKKRL 294
                                       333322222222 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   4.2e-05     0.026      17      46 ..      44      72 ..      32      81 .. 0.78
   2 ?    2.5   0.2      0.11        69     135     191 ..     286     344 ..     266     345 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                      TSCSEEEEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqilnksde 46
                                      ++   v+++ G +GvGK+t++++  +++ +
  gi|488601209|ref|YP_007907680.1| 44 GSA-HVIGITGFPGVGKSTIVSKLTQEFRT 72
                                      333.69*****************9998765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                                       EEEESBCCCCCCS-S-EEEEEESS--HHHHHHH..HHHCCTS-GGCHH..CHHHHHHHH CS
                            NB-ARC 135 llTTRdeevanavsatsekievelLekdeawel..lenkvfekkleekesleevakeiv 191
                                       l+ TR++ ++ ++ +       + Lekd   ++  l +kv +++l+ ++ +e++++ei 
  gi|488601209|ref|YP_007907680.1| 286 LIETRKKRLSREMVEILVNEIRNYLEKDSKVKFdeLVEKVSKNDLDPHTAIENLLEEIL 344
                                       6779999999999998666667899999987764477899********99***999986 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 !   12.6   0.3   0.00012     0.073      68     192 ..     133     277 ..      45     279 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                       SSEEEEEEEESS.SGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHH..HHHHHHTTTEEEEEEESCGST...... CS
                          GTP_EFTU  68 kkylinliDtPG.HvdFskevirglrvlDgavlvvdaveGvepqteev..lrlalkegvpiivfiNKmDrl...... 135
                                       +   i l+D+ G +v F+++v +g + +D+  +   +    +p       ++ a  +++  i ++NK+D        
  gi|488601209|ref|YP_007907680.1| 133 TGDVIRLMDAFGfDVIFVETVGAGQSEVDIIEVADTSIVALMPEMGDDiqINKAGILEIGDIYVVNKADLGgaekte 209
                                       55556666666633446666666655555433333333334444433300344555666689********9877766 PP

                                       ..HHHHHHHHHHHHHHHHHH.........HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                          GTP_EFTU 136 ..kaelkeiveevkqklsrk.........eeklekygekgekevpvvfgSalkgegvktllealvell 192
                                         ++ + ++ +e+ + ls++          +++ ++  ++e + pv+ + a kgeg+++l +a+ +++
  gi|488601209|ref|YP_007907680.1| 210 rwIKAMLMMDQEAVEILSKTthadealvqSGQIYEKIRRSEWIPPVIKTVAEKGEGIDQLADAIEDHF 277
                                       664444555555554554445666666554444444444447899*******************9986 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 ?    6.0   0.1     0.013       7.9       3      23 ..      49      69 ..      47      82 .. 0.85
   2 ?    7.6   0.1    0.0041       2.5     113     156 .]     230     273 ..     157     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                                      EEEEESTTSSHHHHHHHHHTT CS
                            FeoB_N  3 valvGnpnvGkttlfnaltga 23
                                      + + G p vGk+t++ +lt+ 
  gi|488601209|ref|YP_007907680.1| 49 IGITGFPGVGKSTIVSKLTQE 69
                                      6789**************986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0041
                                       ETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 113 nmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                          dea  +  +i +k  +++   pv+kt+a+k+egi++l +ai
  gi|488601209|ref|YP_007907680.1| 230 THADEALVQSGQIYEKIRRSEWIPPVIKTVAEKGEGIDQLADAI 273
                                       4456666677777777777777789***************9986 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 ?   13.2   0.0   6.4e-05      0.04      18      59 ..      44      83 ..      33     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                        KAP_NTPase 18 atpivvgLygkWGsGKssllnkledelkefakpvrflfaefn 59
                                      +   v+g++g  G+GKs+++ kl +e +++   +++ ++ ++
  gi|488601209|ref|YP_007907680.1| 44 GSAHVIGITGFPGVGKSTIVSKLTQEFRTR--GKTVGIVAVD 83
                                      56779***********************99..4455555444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   0.00014     0.085       1      29 [.      48      76 ..      48      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvk 29
                                      vIg++g  G Gk+t+  kl++ f+  +++
  gi|488601209|ref|YP_007907680.1| 48 VIGITGFPGVGKSTIVSKLTQEFRTRGKT 76
                                      8**********************987766 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     7e-05     0.043     107     169 ..     252     314 ..       6     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                      MnmE_helical 107 eeevlkiSaktgegieeLeeaike.le.leeieeeplltnaRhkealekaleal.eeakealeagl 169
                                         +v+k+ a++gegi++L +ai++ +  l   +++  l+++R+k + ++++e l +e+++ le++ 
  gi|488601209|ref|YP_007907680.1| 252 IPPVIKTVAEKGEGIDQLADAIEDhFDyL---KKSGRLIETRKKRLSREMVEILvNEIRNYLEKDS 314
                                       33455999**************9966644...3568899999999999999999655555566553 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015     0.095       6      49 ..      37      79 ..      32      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                        Zeta_toxin  6 kdkkypsqerPklillgGqpGAGKselaellkdelerqgnvvrl 49
                                      k++ yp+  +  +i + G pG GKs++ ++l++e++++g+ v +
  gi|488601209|ref|YP_007907680.1| 37 KRI-YPKTGSAHVIGITGFPGVGKSTIVSKLTQEFRTRGKTVGI 79
                                      544.677788889999********************88888766 PP

>> DUF1131  Protein of unknown function (DUF1131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00048       0.3      50      95 ..     127     172 ..     120     183 .. 0.91
   2 ?    0.0   0.1      0.99   6.1e+02      15      97 ..     179     260 ..     174     284 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00048
                           DUF1131  50 sGmetenGkivsifqalkddkvklvisGqekgkveridvldkeikt 95 
                                       +G++++ G+++++++a+  d + ++  G+ +++v+ i+v+d++i +
  gi|488601209|ref|YP_007907680.1| 127 GGLSAKTGDVIRLMDAFGFDVIFVETVGAGQSEVDIIEVADTSIVA 172
                                       6899*************************************99865 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.99
                           DUF1131  15 sslevseqGvgeitastalteeaieealdgdyrlrsGmetenGkivsifqalkddkvklvisGqekgkveridvldk 91 
                                       + ++++++G+ ei     +++  +  a +++ r  + m + + + v+i+    + + +lv sGq   k++r +   +
  gi|488601209|ref|YP_007907680.1| 179 DDIQINKAGILEIGDIYVVNKADLGGA-EKTERWIKAMLMMDQEAVEILSKTTHADEALVQSGQIYEKIRRSEWIPP 254
                                       566777777777777666666666544.4444566677777888888888888888888888888888888777777 PP

                           DUF1131  92 eiktew 97 
                                        ikt +
  gi|488601209|ref|YP_007907680.1| 255 VIKTVA 260
                                       777654 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0003      0.19      16      53 ..      47      86 ..      39      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                     TrwB_AAD_bind 16 qhilivGttGsGKtqalekllrairargdra..ivlDltG 53
                                      + i i+G  G GK++ ++kl ++ r rg+++  + +D++ 
  gi|488601209|ref|YP_007907680.1| 47 HVIGITGFPGVGKSTIVSKLTQEFRTRGKTVgiVAVDPGS 86
                                      4468************************875214456665 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00038      0.24       5      29 ..      48      72 ..      45      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                    Ploopntkinase3  5 liylvGqPGaGkstlmaeltkgfdr 29
                                      +i + G PG Gkst++++lt+ f  
  gi|488601209|ref|YP_007907680.1| 48 VIGITGFPGVGKSTIVSKLTQEFRT 72
                                      68899****************9965 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1     0.002       1.2       3      23 ..      51      71 ..      49     104 .. 0.85
   2 ?    0.7   0.1       1.1   6.6e+02      21      46 ..     293     318 ..     228     338 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.002
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      ++G pG+GK+++++ + +e+ 
  gi|488601209|ref|YP_007907680.1| 51 ITGFPGVGKSTIVSKLTQEFR 71
                                      6899*************9975 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                                       HHTHEEEEEETTTCSSSSTTHHHHHH CS
                               AAA  21 elgvefleisgsellskyvgesekki 46 
                                        l++e++ei + e+++ + ++s+ k+
  gi|488601209|ref|YP_007907680.1| 293 RLSREMVEILVNEIRNYLEKDSKVKF 318
                                       23344444444444444444444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00037      0.23       1      19 [.      52      70 ..      52      87 .. 0.87
   2 ?   -1.8   0.1       6.1   3.8e+03      81      81 ..     255     255 ..     188     307 .. 0.58
   3 ?   -1.5   0.1       4.9     3e+03      92     106 ..     294     308 ..     257     337 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                                      EE-TTSSHHHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklveky 19
                                      +G PG+GK+t+++kl +++
  gi|488601209|ref|YP_007907680.1| 52 TGFPGVGKSTIVSKLTQEF 70
                                      69*************9987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.1
                                       E CS
                            AAA_17  81 r 81 
                                       +
  gi|488601209|ref|YP_007907680.1| 255 V 255
                                       1 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.9
                                       SHHHHHHHH..SEEE CS
                            AAA_17  92 lpkevleelkpdaii 106
                                       l +e++e l  ++  
  gi|488601209|ref|YP_007907680.1| 294 LSREMVEILVNEIRN 308
                                       222222333222223 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4    0.0029       1.8      26      60 ..      49      84 ..      42      96 .. 0.85
   2 ?    3.5   0.1       0.1        63     133     200 ..     233     305 ..     208     310 .. 0.80
   3 ?    1.8   0.2      0.35   2.2e+02     117     151 ..     295     330 ..     273     344 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                             DUF87 26 lAilgsTGsGKSntvavLleelle.kkgatililDp 60
                                      ++i g  G+GKS+ v+ L +e     k + i+ +Dp
  gi|488601209|ref|YP_007907680.1| 49 IGITGFPGVGKSTIVSKLTQEFRTrGKTVGIVAVDP 84
                                      57888889*************997666678888887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                             DUF87 133 ekeklssdepveklleelk.....kekeelrklknqaiarlldkledllrkggsfsnsstdlialllekleke 200
                                       ++  ++s ++ ek++ + +     k+++e  +  +q++ +++d++++l+++g+++ + +++l ++++e+l +e
  gi|488601209|ref|YP_007907680.1| 233 DEALVQSGQIYEKIRRSEWippviKTVAEKGEGIDQLADAIEDHFDYLKKSGRLIETRKKRLSREMVEILVNE 305
                                       4555666777777777777888888888999999*********************999999998888887665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.35
                             DUF87 117 qrsvleealdqaka.keekeklssdepveklleelk 151
                                       +r+++e +++++++  e++ k+++de+vek+ ++  
  gi|488601209|ref|YP_007907680.1| 295 SREMVEILVNEIRNyLEKDSKVKFDELVEKVSKNDL 330
                                       344444444444445589999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 2181.39
//
Query:       gi|488601210|ref|YP_007907681.1|  [L=139]
Description: methylmalonyl-CoA mutase C-terminal domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   80.2   0.6    1.4e-22   80.0   0.6    1.1  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.018   14.1   0.0      0.023   13.7   0.0    1.1  1  IMPDH        IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.6   1.6e-26   1.4e-22       1     114 [.       5     118 ..       5     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.6e-26
                       B12-binding   1 ikvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkr 77 
                                       i+vl+a+vg d h++G++v+a++lrdagfeV++ g+  ++e+++ a+ +e++dv+g+S++++++++ v ++++ +k+
  gi|488601210|ref|YP_007907681.1|   5 IRVLVAKVGLDGHDRGAKVVARFLRDAGFEVIYSGLHRTPEEVAMAAVQEDVDVIGISLHSGAHMTLVPKVLNYIKE 81 
                                       589*****************************************************************999999666 PP

                       B12-binding  78 ir...prvkvvvGGahpsldpeetleaklgiddvvvgege 114
                                       ++   +++ v+vGG++p+   ++ l+a lg +d v+  g+
  gi|488601210|ref|YP_007907681.1|  82 YGgdpSEMVVLVGGIIPEDEFDD-LKA-LG-VDGVFIPGT 118
                                       6522269***********99999.655.**.777999887 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-06     0.023     104     170 ..      43     113 ..      31     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-06
                                       THHHHHHHHHHTT-SEEEEE-STS.SSHHHHHHHHHHHHHTT...TSEEEEEEE-SHHHHHHHHHTT-SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 104 dalervkalveagvdvlvvdsahg.hsekvleavkeikkkve...eveviaGnvataegakaLieagadav 170
                                         +e + a v+++vdv+ +    g h + v +++++ik+      e+ v++G +  ++ + +L + g+d+v
  gi|488601210|ref|YP_007907681.1|  43 TPEEVAMAAVQEDVDVIGISLHSGaHMTLVPKVLNYIKEYGGdpsEMVVLVGGIIPEDEFDDLKALGVDGV 113
                                       556778899**********98777255666677788887654322577889******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 884.00
//
Query:       gi|488601211|ref|YP_007907682.1|  [L=565]
Description: methylmalonyl-CoA mutase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-222  739.2   0.0   2.4e-222  739.1   0.0    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  739.1   0.0  1.3e-226  2.4e-222       5     513 .]      41     557 ..      37     557 .. 0.98

  Alignments for each domain:
  == domain 1  score: 739.1 bits;  conditional E-value: 1.3e-226
                     MM_CoA_mutase   5 gievkplYtaedl....eekklgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsv 77 
                                        ie++++Y ++d+       +    +PGefP+tRGv++tmyrgr Wt+rq+ gf++ae+tn+r k+lL++Gqtgls+
  gi|488601211|ref|YP_007907682.1|  41 WIEINRVYDPSDIehldF--ERDIGYPGEFPYTRGVYPTMYRGRLWTMRQFSGFGSAEDTNQRWKMLLKEGQTGLST 115
                                       689**********75431..44446**************************************************** PP

                     MM_CoA_mutase  78 afdlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdlekl 154
                                       afd ptl+g+Dsd+p + gevGk+Gvaid+l+d+e+l++gi+ld+vs+s+tin +a ++lamy+a+ ++qgv++++l
  gi|488601211|ref|YP_007907682.1| 116 AFDFPTLMGLDSDDPLSDGEVGKVGVAIDTLKDFEILFEGIPLDRVSTSFTINPPAGIILAMYTAIGDAQGVPRDQL 192
                                       ***************************************************************************** PP

                     MM_CoA_mutase 155 sgtiqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvra 231
                                       +gtiqnD+Lke+ a++t+++ppeps+++i+di+e+  ++vpkfn is+sgyhireaG+tavqElAft+adG++Yv+a
  gi|488601211|ref|YP_007907682.1| 193 RGTIQNDMLKEFHAQNTLVLPPEPSVKIITDIFEWGVENVPKFNLISISGYHIREAGSTAVQELAFTIADGMAYVEA 269
                                       ***************************************************************************** PP

                     MM_CoA_mutase 232 lleaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNi 308
                                       ++e+G+d+d+ ap+lsFff+ ++dffeeiAk+RAaRr+Wa+i+++++gak+++s++l++h+qT+g+sltaq+p +Ni
  gi|488601211|ref|YP_007907682.1| 270 AIERGIDIDKLAPQLSFFFNSHNDFFEEIAKFRAARRMWAKIMRDEYGAKNPRSWWLKFHTQTAGCSLTAQQPLNNI 346
                                       ***************************************************************************** PP

                     MM_CoA_mutase 309 lRttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawk 385
                                       +Rtt++a+aAvlggtqslhtnsfDea+alP+e+++r+A++tq+i+a+Esg+ +++DPl+GSyyvE+LTd++++ aw+
  gi|488601211|ref|YP_007907682.1| 347 VRTTIQAMAAVLGGTQSLHTNSFDEAWALPSEEAVRVALRTQQIIAYESGIPNTIDPLAGSYYVEWLTDKMEKLAWD 423
                                       ***************************************************************************** PP

                     MM_CoA_mutase 386 lfqeieeaG......GmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqa 456
                                       ++++i+++G      G+l+ ie+G++ +ei ++aa+ q+++e++k+vivGvNk++  +e+ ++++lk+d+ev++rq+
  gi|488601211|ref|YP_007907682.1| 424 YIERIRKMGegsmlrGVLAGIENGFFVKEITNAAAKFQREVEEGKRVIVGVNKYA-IDEKLKIPILKVDPEVQRRQI 499
                                       ******************************************************5.555689*************** PP

                     MM_CoA_mutase 457 erlealraerdeaavkaaLaalgeaarse.nllaraveaaralatlGeisdaleevfg 513
                                       erl+++++erd+ avk+aL+ l++aa+++ n++++++ea++a+a++Gei+++l++v+g
  gi|488601211|ref|YP_007907682.1| 500 ERLKKIKSERDNVAVKEALEWLRNAAENNeNVMPAILEAVKAYASVGEIMSVLKQVYG 557
                                       ***************************889*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3610.05
//
Query:       gi|488601212|ref|YP_007907683.1|  [L=109]
Description: hypothetical protein Asulf_01719 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   36.9   1.2    3.1e-09   36.7   1.2    1.1  1  Thioredoxin    Thioredoxin
    4.4e-05   23.4   1.5    5.9e-05   23.0   1.5    1.2  1  Thioredoxin_3  Thioredoxin domain
    5.4e-05   23.6   1.6    0.00059   20.3   1.6    2.0  1  Thioredoxin_2  Thioredoxin-like domain
    6.8e-05   23.1   0.3       0.13   12.6   0.1    2.2  2  Thioredoxin_8  Thioredoxin-like
    0.00023   21.0   1.6       0.19   11.5   0.0    2.1  2  DSBA           DSBA-like thioredoxin domain
     0.0025   18.0   0.8     0.0038   17.4   0.8    1.3  1  Glutaredoxin   Glutaredoxin
     0.0047   16.6   0.9       0.15   11.8   0.6    1.9  2  Thioredoxin_5  Thioredoxin
  ------ inclusion threshold ------
      0.025   14.5   0.1       0.05   13.6   0.1    1.5  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
      0.045   13.6   0.1      0.063   13.1   0.1    1.2  1  TraF           F plasmid transfer operon protein
      0.058   12.6   0.0      0.059   12.6   0.0    1.2  1  NAD_kinase     ATP-NAD kinase
      0.091   12.9   0.1       0.16   12.2   0.0    1.4  2  ZoocinA_TRD    Target recognition domain of lytic exoenzyme
        0.1   12.7   1.5       0.58   10.3   0.5    2.0  2  Thioredoxin_4  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   1.2   2.1e-12   3.1e-09      25      98 ..      32     104 ..      15     109 .] 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.1e-12
                                       EE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEE..TTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHH CS
                       Thioredoxin  25 FyApwCghCkalaPeleklaeelkdkvklakvd..vdenedlakkyevegiPtlklfkngkevkkyegarekekla 98 
                                       F++p C+hCk+++P + +++++++  + +++v+  +d+++++a+k++ +g+Pt ++++++k v  y+g+ + ++l+
  gi|488601212|ref|YP_007907683.1|  32 FFSPNCPHCKNVEPYVINASKKVE--INFCQVEnlTDTCKEIAEKIKLRGVPTAVVVEKDK-VYVYSGETKVKNLM 104
                                       99*********************9..9999999445999***************9988887.77888887766665 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.5   3.9e-08   5.9e-05       6      72 ..      33     105 ..      28     109 .] 0.80

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.9e-08
                                       ESSSSTTCHHHHHHHHHHCHCCTCEC.EEECC.TTHHHH.HHCT-SSSSEE.ECT.TCE.EEESS---CCHHH CS
                     Thioredoxin_3   6 lgpgCakCpklekavkeaaaekgika.evekv.tdfeei.ekygVmsvPal.vid.gkv.vvsGkvpseeeir 72 
                                       ++p+C++C+++e  v  a ++ +i++ +ve+   + +ei ek + + vP+  v++ +kv v+sG+++ ++ + 
  gi|488601212|ref|YP_007907683.1|  33 FSPNCPHCKNVEPYVINASKKVEINFcQVENLtDTCKEIaEKIKLRGVPTAvVVEkDKVyVYSGETKVKNLML 105
                                       69***********************99*****5667999**********994555644427788666555555 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.6   3.9e-07   0.00059       9     102 ..      29     100 ..      22     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.9e-07
                     Thioredoxin_2   9 lvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                       +++f +p+Cp Ck  +  +                ++++++ +++ + ++        ++ +e a+k ++rg+Pt v
  gi|488601212|ref|YP_007907683.1|  29 IYFFFSPNCPHCKNVEPYVI---------------NASKKVEINFCQVENLT------DTCKEIAEKIKLRGVPTAV 84 
                                       7999*********9666444...............44788888898888884......88899************** PP

                     Thioredoxin_2  86 fldgkeivarlpGyvpa 102
                                       + +++ +v+++ G ++ 
  gi|488601212|ref|YP_007907683.1|  85 VVEKD-KVYVYSGETKV 100
                                       **999.88999998765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   8.6e-05      0.13       6      31 ..      30      55 ..      27      65 .. 0.87
   2 !    9.0   0.0    0.0011       1.7      69      93 ..      66      90 ..      56      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.6e-05
                                      EEE--SSSHHHHHHHHHHHHHHHHHH CS
                     Thioredoxin_8  6 Lyfgaswcppckaftpklkelyeklk 31
                                       +f++ +cp+ck++ p +++ ++k++
  gi|488601212|ref|YP_007907683.1| 30 YFFFSPNCPHCKNVEPYVINASKKVE 55
                                      69*******************99986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                                      T-HHHHTT-S--TT-SEEEEE-TT- CS
                     Thioredoxin_8 69 kkrnklkkkynvkaiPtlvvldkng 93
                                      + ++++++k ++ ++Pt vv+ k++
  gi|488601212|ref|YP_007907683.1| 66 DTCKEIAEKIKLRGVPTAVVVEKDK 90
                                      56899*****************986 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.9   0.00081       1.2       2      24 ..      29      51 ..      28      63 .. 0.73
   2 !   11.5   0.0   0.00012      0.19     149     188 ..      61     103 ..      56     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00081
                                      EEEEEBTTBHHHHHHHHHHHHHH CS
                              DSBA  2 vdeffDvlCPyCylgkerlekla 24
                                      + +ff+ +CP+C+ +++ +  + 
  gi|488601212|ref|YP_007907683.1| 29 IYFFFSPNCPHCKNVEPYVINAS 51
                                      779**********9986554444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHTT-SSSSEEEE...TTC.EEEESSSSHHHH CS
                              DSBA 149 vkeavrentaaaqslgvtGvPtvvv...dgk.rmvfGadrldtl 188
                                       v++  ++  + a++++++GvPt vv   d k ++ +G +++++l
  gi|488601212|ref|YP_007907683.1|  61 VENLTDTCKEIAEKIKLRGVPTAVVvekD-KvYVYSGETKVKNL 103
                                       56677777889**************8743.46999999998887 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.8   2.6e-06    0.0038       4      55 ..      32      85 ..      29      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.6e-06
                                      EESTSSHHHHHHHHHH..HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEE CS
                      Glutaredoxin  4 ftkptCpyCkkakrlL..kelgvkfeeidvdkdeeireelkelsgvrtvPqvfi 55
                                      f +p+Cp+Ck++  +    +++v++ + +v++  +  +e+ e+ + r vP+ ++
  gi|488601212|ref|YP_007907683.1| 32 FFSPNCPHCKNVEPYVinASKKVEINFCQVENLTDTCKEIAEKIKLRGVPTAVV 85
                                      667*************88888899999999999999999999999999997655 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.6   9.7e-05      0.15       1      44 [.      30      69 ..      30      74 .. 0.81
   2 ?    4.5   0.0     0.017        25     148     167 ..      70      89 ..      61     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.7e-05
                     Thioredoxin_5  1 YlFidPlcseCweiEpelkklkveygekiklrfilllnlktlnk 44
                                      Y F+ P c++C ++Ep ++    ++++k++++f  + nl+++ k
  gi|488601212|ref|YP_007907683.1| 30 YFFFSPNCPHCKNVEPYVI----NASKKVEINFCQVENLTDTCK 69
                                      99**************886....567788888888888877655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.017
                     Thioredoxin_5 148 klakemgvtevPtlvffnen 167
                                       ++a+ ++ + vPt+v+++++
  gi|488601212|ref|YP_007907683.1|  70 EIAEKIKLRGVPTAVVVEKD 89 
                                       69999***********9954 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.4e-05      0.05      19      35 ..      35      51 ..      28      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-05
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktr 35
                                      + CPhC++ ++y i++ 
  gi|488601212|ref|YP_007907683.1| 35 PNCPHCKNVEPYVINAS 51
                                      78**********99874 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.2e-05     0.063     133     203 ..      29      90 ..      24     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-05
                              TraF 133 LlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpks 203
                                       + fF++++cp c+   p + +  +k ++    V       +e+++         +++++ +P+ v+v++++
  gi|488601212|ref|YP_007907683.1|  29 IYFFFSPNCPHCKNVEPYVINASKKVEINFCQVENLTDTCKEIAE---------KIKLRGVPTAVVVEKDK 90 
                                       569***********************9999999877777766666.........9**********999984 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     4e-05     0.059     227     255 ..      31      59 ..      22     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                                       EEEEEESESSS----EEE-TT-EEEEEE- CS
                        NAD_kinase 227 ilivpicPhslssrpiVvssssklrirva 255
                                       +  +p+cPh +  +p V++ s+k++i + 
  gi|488601212|ref|YP_007907683.1|  31 FFFSPNCPHCKNVEPYVINASKKVEINFC 59 
                                       5679*********************9865 PP

>> ZoocinA_TRD  Target recognition domain of lytic exoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.16      48      92 ..      18      62 ..      13      75 .. 0.87
   2 ?   -3.1   0.0       5.8   8.6e+03      67      82 ..      83      98 ..      80     104 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                       ZoocinA_TRD 48 nliadqvlkvGdyfvfnPksvlsveepiygvaGltfakvkfaege 92
                                      + + dqv+k   yf f P++ +  + + y ++  +  +++f + e
  gi|488601212|ref|YP_007907683.1| 18 EKTEDQVVKGDIYFFFSPNCPHCKNVEPYVINASKKVEINFCQVE 62
                                      5788*****999*********999999999999999999998765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.8
                       ZoocinA_TRD 67 svlsveepiygvaGlt 82
                                      +v + ++++y  +G t
  gi|488601212|ref|YP_007907683.1| 83 AVVVEKDKVYVYSGET 98
                                      5555555556666554 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   0.00039      0.58      17      35 ..      29      47 ..      19      57 .. 0.82
   2 ?    1.5   0.0       0.2     3e+02     128     148 ..      67      87 ..      56     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                                      EEEEE-TT-HHHHHHHHHH CS
                     Thioredoxin_4 17 vieyedlrCphCakfeeev 35
                                      ++ + + +CphC++ e  v
  gi|488601212|ref|YP_007907683.1| 29 IYFFFSPNCPHCKNVEPYV 47
                                      6789*********998766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                                       HHHHHHHHHT--SS-EEEETT CS
                     Thioredoxin_4 128 aeskeakkagiestPtfiing 148
                                       + ++ a+k ++ ++Pt ++ +
  gi|488601212|ref|YP_007907683.1|  67 TCKEIAEKIKLRGVPTAVVVE 87 
                                       556778999999***998833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 722.74
//
Query:       gi|488601213|ref|YP_007907684.1|  [L=112]
Description: hypothetical protein Asulf_01720 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00016   21.9   9.4    0.00025   21.2   9.4    1.2  1  VKOR      Vitamin K epoxide reductase family


Domain annotation for each model (and alignments):
>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   9.4   1.4e-08   0.00025       5     121 ..       7     105 ..       4     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHHHHHHHHH...HT---SS-SSSS..HHHHHCSTTSEETTEEHHHHHHHHHHHHHHHHHS-.HHHHHH CS
                              VKOR   5 vlalvGllvsiyltleklglktsssaalCdissvsCdkvlnSpyasilgvplsllGllayalvlllalapllwllll 81 
                                       +l  +Gll s+yl++  +   t   + +C +s+  C++ l+    +   +p +l+Gl++++l  +l        +l 
  gi|488601213|ref|YP_007907684.1|   7 MLISLGLLDSGYLLISTY---T---PDFCPTSG--CSTNLTMYGLN---IP-ALFGLMWFLLYGFLKG-----KMLS 66 
                                       67789***********99...4...447****9..***99864444...44.7*********999954.....5679 PP

                                       HHHHHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHHH CS
                              VKOR  82 lgslagvvfslyLiylslfvigalCpyClvsavlsllllv 121
                                       ++ ++gv++++ L  + +     +CpyC+ +++l l+l+v
  gi|488601213|ref|YP_007907684.1|  67 IWKILGVAGIGSLGSYAILN-SYFCPYCFFAYFLGLSLIV 105
                                       9***************9977.9************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 751.73
//
Query:       gi|488601214|ref|YP_007907685.1|  [L=102]
Description: hypothetical protein Asulf_01721 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 638.16
//
Query:       gi|488601215|ref|YP_007907686.1|  [L=163]
Description: hypothetical protein Asulf_01722 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.8   0.7       0.01   16.5   0.2    2.0  2  CoA_binding      CoA binding domain
     0.0054   16.9   0.2        1.7    8.8   0.0    2.2  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.025   14.3   0.3      0.058   13.2   0.3    1.7  1  Synaptonemal_3   Synaptonemal complex central element protein
       0.03   14.2   0.0      0.044   13.7   0.0    1.2  1  YjeF_N           YjeF-related protein N-terminus
      0.045   13.9   0.6        7.2    6.8   0.0    2.3  2  Tubulin          Tubulin/FtsZ family, GTPase domain
      0.046   14.3   0.3      0.097   13.3   0.3    1.6  1  PglD_N           PglD N-terminal domain
      0.053   14.3   0.1       0.25   12.1   0.1    2.0  2  GARS_N           Phosphoribosylglycinamide synthetase, N doma
      0.058   13.0   0.0       0.08   12.6   0.0    1.3  1  Urocanase        Urocanase Rossmann-like domain
       0.12   12.6   0.3        4.5    7.5   0.0    2.1  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   5.2e-06      0.01       4      69 ..       2      67 ..       1      96 [. 0.90
   2 ?   -0.9   0.0       1.4   2.8e+03      50      63 ..     119     133 ..     105     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.2e-06
                                      EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC.TTTEEEEE CS
                       CoA_binding  4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt.evdvavit 69
                                      + ++v+G gg g+ ++  fk++ +y+++ ++ vn++k  + v+  + + ++d+l++ + e d  ++t
  gi|488601215|ref|YP_007907686.1|  2 KTIAVVGSGGAGQNIVNIFKRESEYENVDIYVVNGEKWVDCVEFYKFK-QLDKLIKVLsEYDHVILT 67
                                      679***********************************9999999988.999999999768888887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                                       EESCHHHHHHHC.TT CS
                       CoA_binding  50 vyksvdeleekt.ev 63 
                                       v k++del+ek+ ++
  gi|488601215|ref|YP_007907686.1| 119 VLKNLDELIEKMpDI 133
                                       667888888887543 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00087       1.7       3      57 ..       4      55 ..       2      65 .. 0.81
   2 !    6.7   0.1    0.0039       7.7       3      72 ..      65     135 ..      63     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00087
                                      EEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BE CS
                            DapB_N  3 vavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvav 57
                                      +avvG  G  G+++v+  ++++++e v  +  ++++    d  e+ ++++l+  +
  gi|488601215|ref|YP_007907686.1|  4 IAVVGS-GGAGQNIVNIFKRESEYENVDIYVVNGEK--WVDCVEFYKFKQLDKLI 55
                                      99***8.889******************99999964..45888888888777655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0039
                                       EEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC.STTTTTBHHHHSSSS--S-BEBSSHHHHHHH.-SEEE CS
                            DapB_N   3 vavvGasGrmGkevvkaveeaedlelvaavdrke.selegkdagellglgklgvavtddleevlek.advli 72 
                                       ++ +G  Gr G ++vk+++e +++    + +  + ++ + + a e ++l k++v + ++l+e++ek  d++i
  gi|488601215|ref|YP_007907686.1|  65 ILTAGLGGRGGDALVKLANELDNIAGIVVCKPFRiERSRVERAEEQIKLLKSNVVL-KNLDELIEKmPDIAI 135
                                       5679****************988887777777664444555555666665666555.578888877788877 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 ?   13.2   0.3   2.9e-05     0.058      20      48 ..     118     146 ..     100     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                    Synaptonemal_3  20 qlnkdleklteqmedvsvkltwmaydmvv 48 
                                        + k+l+ l+e+m d++++   m+ dm +
  gi|488601215|ref|YP_007907686.1| 118 VVLKNLDELIEKMPDIAIHDGLMTLDMEL 146
                                       45599**********************65 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 ?   13.7   0.0   2.2e-05     0.044      25     113 ..      60     143 ..      46     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                            YjeF_N  25 aekkvlvlvGsgnnGgdgla.aArhLaqegakVtvllleeeekldedaeralellkkaggkvveekpeedleeklsa 100
                                       +  +v++ +G g  Ggd+l+ +A +L +    V   ++++ +  ++ +era e+ k ++ +vv ++ +e  e k   
  gi|488601215|ref|YP_007907686.1|  60 EYDHVILTAGLGGRGGDALVkLANELDNIAGIV---VCKPFRIERSRVERAEEQIKLLKSNVVLKNLDELIE-K--- 129
                                       5678999************96788884433333...468999999999999999999999999777776554.3... PP

                            YjeF_N 101 pvdlvi.DAllGig 113
                                       ++d+ i D+l+ + 
  gi|488601215|ref|YP_007907686.1| 130 MPDIAIhDGLMTLD 143
                                       47777667877654 PP

>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.011        23       2      20 ..       4      22 ..       3      30 .. 0.82
   2 ?    6.8   0.0    0.0036       7.2     103     175 ..      51     112 ..      44     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                                      EEEEEEHHHHHHHHHHHHH CS
                           Tubulin  2 iivigvGqcGnqignelwe 20
                                      i v+g G++G +i+n + +
  gi|488601215|ref|YP_007907686.1|  4 IAVVGSGGAGQNIVNIFKR 22
                                      899***********98876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0036
                                       HHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G-HHHHHHHHHHHH CS
                           Tubulin 103 leeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefsevvvepynailalk 175
                                       l+++ k +++ d+   +++ta+lgG  G      ++++++e   +++   vv  P++++    + + a++ +k
  gi|488601215|ref|YP_007907686.1|  51 LDKLIKVLSEYDH---VILTAGLGGRGG----DALVKLANEL--DNIAGIVVCKPFRIE--RSRVERAEEQIK 112
                                       5666677777777...********9977....5566777777..777778888888773..344444444444 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.9e-05     0.097       2      31 ..       4      33 ..       3      72 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                            PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflD 31
                                      i+++G GG g+ + +i +++ eye + ++ 
  gi|488601215|ref|YP_007907686.1|  4 IAVVGSGGAGQNIVNIFKRESEYENVDIYV 33
                                      99*********************9765443 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00013      0.25       3      45 ..       4      56 ..       1      93 [. 0.75
   2 ?    0.8   0.0      0.44   8.7e+02       3      31 ..      65      94 ..      63     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      EEEEESSHHHHHHHHHHTTSTTES..EEEEEE--CGG........TTHHHHHH CS
                            GARS_N  3 vLvvGsGGRehalawklaqspkve..kvyvapgNagt........edlealve 45
                                      + vvGsGG  + ++  +++++++e  ++yv+ g + +        ++l++l++
  gi|488601215|ref|YP_007907686.1|  4 IAVVGSGGAGQNIVNIFKRESEYEnvDIYVVNGEKWVdcvefykfKQLDKLIK 56
                                      88******************999944467777777776666655433334444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.44
                                      EEEEESSHHHHHHHHHHTTS.TTESEEEEE CS
                            GARS_N  3 vLvvGsGGRehalawklaqs.pkvekvyva 31
                                      +L  G GGR      kla++ +++  ++v+
  gi|488601215|ref|YP_007907686.1| 65 ILTAGLGGRGGDALVKLANElDNIAGIVVC 94
                                      566677777654444444432455555444 PP

>> Urocanase  Urocanase Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     4e-05      0.08      28      88 ..      62     131 ..      47     161 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                                       T-EEEEE--STTGGGH..HHHHHHTT-EEEEE....ES-HHHHHHHHHTTS-...SEEES-HHHHHHHHH CS
                         Urocanase  28 gklvvtaGlGgMsgaQ..plAatiagavalvv....evdesriekrleqgyv...devaddldealalik 88 
                                        ++++taGlGg +g     lA ++ +++++vv     +++sr+e+  eq  +   + v ++lde+++++ 
  gi|488601215|ref|YP_007907686.1|  62 DHVILTAGLGGRGGDAlvKLANELDNIAGIVVckpfRIERSRVERAEEQIKLlksNVVLKNLDELIEKMP 131
                                       689**********975336899999999998833334666666665555443121335667777766654 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 ?    7.5   0.0    0.0023       4.5       1      31 [.       4      35 ..       4      39 .. 0.90
   2 ?    3.3   0.0     0.048        95       2      70 ..      66     130 ..      65     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                                      EEEE--SHHHHHHHHHHHCTCCT-G.EEEEEE CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvda.eitvad 31
                                      + ++G+G+ Gq ++   +r++++++ +i v+ 
  gi|488601215|ref|YP_007907686.1|  4 IAVVGSGGAGQNIVNIFKRESEYENvDIYVVN 35
                                      689********************989998875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.048
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg 70 
                                       l  G G+ G  ++ +la++ d  a i+v+ + + +  ++  ++ ++++ +  +  +n ++++++     
  gi|488601215|ref|YP_007907686.1|  66 LTAGLGGRGGDALVKLANELDNIAGIVVCKPFRIERSRVERAEEQIKLLKSNVVLKNLDELIEK----M 130
                                       6669988888888888888888789999999999988888888888888888888887774444....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); 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: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 960.32
//
Query:       gi|488601216|ref|YP_007907687.1|  [L=183]
Description: hypothetical protein Asulf_01723 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1340.68
//
Query:       gi|488601217|ref|YP_007907688.1|  [L=159]
Description: hypothetical protein Asulf_01724 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1073.76
//
Query:       gi|488601218|ref|YP_007907689.1|  [L=239]
Description: Sec-independent protein translocase TatC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-42  145.6  18.1    2.1e-42  145.3  18.1    1.1  1  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3  18.1   1.2e-46   2.1e-42       1     204 [.      13     217 ..      13     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 1.2e-46
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCCHHHHC.CTTS-EE--SSS-HHHHHHHHHHHHHHHHSHHHHH CS
                              TatC   1 ehLeeLrkrlirallavaiafiitfvfaeeliafllepleeaeeevelivlspleafllklkvslvaglvlasPvil 77 
                                       ehL+eL+kr ir+ ++++i++ii++ +++eli+ +++ + ++  + ++++++p+e ++++l  s+v+ ++++ P+i+
  gi|488601218|ref|YP_007907689.1|  13 EHLAELKKRTIRISIVILIGIIIVYPYSPELIDSFWQGIFNK--KLDMVIYTPTEWIVTRLIFSFVFVFFFSYPYIV 87 
                                       8********************************888888774..5689***************************** PP

                                       HHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT..TTTSSTTEEHHHHHHHHHHHHHHHH CS
                              TatC  78 yqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll..seevepllslseylsfvlllllafg 152
                                       yql++f +pgL +her++v++f+++s +lfl+G ++ay vv+p ++++ +    ++ep ls+++ +  ++++++afg
  gi|488601218|ref|YP_007907689.1|  88 YQLYQFAKPGLFEHERKFVKTFIPFSYILFLIGTLLAYEVVIPRLYNWAVvpYFGAEPHLSVKKTIYGAFKIFMAFG 164
                                       ***********************************************999553335999****************** PP

                                       HHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHH CS
                              TatC 153 iaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqlll 204
                                       ++F++P++ +++++lg++++++l+ kr +++++++++a  +t   + +sql++
  gi|488601218|ref|YP_007907689.1| 165 LSFQIPVLALIAVKLGMIDSDWLKGKRVIVYILVFILATNITFdISGMSQLIV 217
                                       ******************************************99999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1733.15
//
Query:       gi|488601219|ref|YP_007907690.1|  [L=438]
Description: K+ transport systems, NAD-binding component [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-47  159.3   2.4    2.5e-23   82.5   0.7    2.4  2  TrkA_N           TrkA-N domain
    3.8e-34  116.3   2.2      2e-16   59.6   0.5    3.0  3  TrkA_C           TrkA-C domain
      2e-10   41.0   2.4    7.9e-05   23.0   0.0    2.5  2  NAD_binding_7    Putative NAD(P)-binding
      1e-07   32.3   1.5      0.017   15.4   0.0    2.4  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    2.5e-06   27.6   0.5      0.035   14.2   0.4    2.6  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    5.5e-06   26.5   0.1      0.031   14.2   0.0    2.9  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    3.2e-05   23.3   2.1        0.1   11.9   0.0    2.3  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    3.9e-05   24.1   5.9       0.14   12.7   0.0    3.6  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00032   20.6   0.3       0.14   12.0   0.0    2.4  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00043   19.6   0.5      0.032   13.4   0.0    2.3  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00066   19.3   3.6       0.01   15.4   0.5    2.9  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0009   19.8   0.2        2.8    8.6   0.0    2.6  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00097   18.8   0.1        0.8    9.3   0.0    2.4  2  ApbA             Ketopantoate reductase PanE/ApbA
     0.0021   17.0   0.0       0.36    9.6   0.0    2.2  2  Trp_halogenase   Tryptophan halogenase
     0.0041   17.3   0.6       0.19   11.9   0.3    2.2  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
  ------ inclusion threshold ------
      0.014   15.0   2.1      0.047   13.2   1.5    2.0  2  NmrA             NmrA-like family
      0.016   14.5   0.0        1.5    8.0   0.0    2.2  2  FAD_binding_3    FAD binding domain
      0.022   15.2   0.0       0.27   11.7   0.0    2.3  2  XdhC_C           XdhC Rossmann domain
      0.023   14.9   0.0       0.29   11.4   0.0    2.2  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
      0.042   13.4   0.0        3.1    7.3   0.0    2.3  2  DAO              FAD dependent oxidoreductase
       0.11   11.1   0.1       0.65    8.6   0.0    2.0  2  HI0933_like      HI0933-like protein


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 !   82.5   0.7     3e-26   2.5e-23       1     116 []       3     120 ..       3     120 .. 0.91
   2 !   76.2   0.0   2.7e-24   2.3e-21       1     116 []     225     341 ..     225     341 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 3e-26
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeani 77 
                                       i+++G+G+vG+++a+ L +++ dv vi+kde++++e+ + ++ev+ g+a++ +vL +a+++kad+++ +tg de+n+
  gi|488601219|ref|YP_007907690.1|   3 IVVAGAGEVGYNVAKALCDNH-DVFVIEKDEKKIDEIYKLNVEVIEGNAANINVLSKAKVSKADIFLGVTGVDEVNL 78 
                                       89*******************.7****************************************************** PP

                                       HHHHHHHHHTSSSEEEEEESSGGG..HHHHHH..HTTSEEEEH CS
                            TrkA_N  78 lavllakelnpkkkiiaraqdpeh..aellkk..lgadvvisp 116
                                       l   +ak++   kk+i+r+ +pe+    l+k+  lg+d vi p
  gi|488601219|ref|YP_007907690.1|  79 LSGIAAKKMGA-KKTIVRVGNPEYvdRPLVKNhpLGFDLVICP 120
                                       ******98655.89**********5444455566788888765 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 2.7e-24
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg..levvvgdatdeevLeeagiekadaviaatgddea 75 
                                       ++i G G+vG+ la+ L +++ ++ +i+k+ee +e+l      ++vv+gd+td ++L e ++ + d+v  ++++de+
  gi|488601219|ref|YP_007907690.1| 225 VVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELCENLCSAYnrVRVVIGDPTDLDLLYEEDVGRSDVVASCLENDEK 301
                                       79*****************6646**************55554699******************************** PP

                                       HHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  76 nilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       n+l++ll k+l   +k ia++++  + +l++k+g+dvv+sp
  gi|488601219|ref|YP_007907690.1| 302 NLLVSLLSKNLGT-RKAIAQVSKGNYMKLFEKVGIDVVLSP 341
                                       ********97666.89**********************998 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.5   2.3e-19     2e-16       1      70 []     150     218 ..     150     218 .. 0.97
   2 ?   -1.9   0.0       3.6   3.1e+03      54      67 ..     270     283 ..     270     284 .. 0.89
   3 !   55.1   0.0   5.6e-18   4.8e-15       5      70 .]     375     438 .]     371     438 .] 0.94

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 2.3e-19
                                       CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                            TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrellg 70 
                                       l+e++v+++s l++k++ +l l++ +v++ ai R+gel++p+g t+  +GD++ +vg+++dl ++++++g
  gi|488601219|ref|YP_007907690.1| 150 LIEIVVDENSVLANKKIEDLHLPE-NVIITAIYRDGELLVPRGQTKVLPGDKVAIVGKSQDLITIQDIFG 218
                                       689*********************.***************************************999986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                                       EEEEEHHHHHHHHH CS
                            TrkA_C  54 lvvgspsdlaelre 67 
                                       +v+g+p dl+ l+e
  gi|488601219|ref|YP_007907690.1| 270 VVIGDPTDLDLLYE 283
                                       69********9987 PP

  == domain 3  score: 55.1 bits;  conditional E-value: 5.6e-18
                                       EEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                            TrkA_C   5 tvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrellg 70 
                                       ++ ++ +l Gk+++el++++ ++l+ +i Rg++++ip g+t++ +GD+ll++++ s+++e+++++g
  gi|488601219|ref|YP_007907690.1| 375 EL-ENEKLSGKKISELKIPE-RALIGGILRGDDCLIPKGETQILKGDRLLIFTPWSEVEEIEDYFG 438
                                       55.5999*************.*****************************************9997 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.8   6.7e-06    0.0057       9      75 ..       2      77 ..       1     103 [. 0.73
   2 !   23.0   0.0   9.2e-08   7.9e-05       6      84 ..     221     311 ..     216     324 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.7e-06
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekd...........legadlviaatddreln 75
                                      +++v+G+Gev+++ ++ l+++  +v v+ ++ +++++e++kl+ e +e++           +++ad+ + +t  +e+n
  gi|488601219|ref|YP_007907690.1|  2 HIVVAGAGEVGYNVAKALCDN-HDVFVIEKD-EKKIDEIYKLNVEVIEGNaaninvlskakVSKADIFLGVTGVDEVN 77
                                      89******************9.*********.7778888888776665543444444444477788877777777776 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 9.2e-08
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee.............lekdlegadlviaat 69 
                                       +++kv+++GgG+v+   +r l +++ +++++ ++ +e +e+l+++ ++              +e+d+ + d+v  + 
  gi|488601219|ref|YP_007907690.1| 221 TTRKVVIFGGGTVGSYLARVLDSSNLNIKLIEKN-EELCENLCSAYNRVrvvigdptdldllYEEDVGRSDVVASCL 296
                                       579*******************************.8999988776655556666677788777************** PP

                     NAD_binding_7  70 ddrelneriaeaaka 84 
                                       +++e n  +  + k+
  gi|488601219|ref|YP_007907690.1| 297 ENDEKNLLVSLLSKN 311
                                       ***999777666665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.7   2.1e-05     0.018       1      76 [.       3      70 ..       3      78 .. 0.89
   2 !   15.4   0.0     2e-05     0.017       1      76 [.     225     295 ..     225     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE- CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnl 76
                                      +++ GaG vG  va+ l +++dv     v++++++k +++     + ++e i+ +a+n+   L+++ ++++d+++ +
  gi|488601219|ref|YP_007907690.1|  3 IVVAGAGEVGYNVAKALCDNHDV----FVIEKDEKKIDEI----YKLNVEVIEGNAANINV-LSKAkVSKADIFLGV 70
                                      7999*****************87....8********8887....799************98.777669999998765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE- CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnl 76 
                                       v+i+G+G vG+ +a++l  ++ +  +i ++++++e +e+l+++    r+  +  d+ + + + ++ +   d+v ++
  gi|488601219|ref|YP_007907690.1| 225 VVIFGGGTVGSYLARVLDSSN-L--NIKLIEKNEELCENLCSAY--NRVRVVIGDPTDLDLLYEEDVGRSDVVASC 295
                                       89***************9986.5..8***************855..555555556666555334445555666666 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.4   4.1e-05     0.035      14      96 ..       2      84 ..       1     110 [. 0.72
   2 !   11.1   0.0   0.00035       0.3       4      84 ..     214     297 ..     212     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHH.HHHT-SEEEE-SSSSS-SB CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelke.llaeadvvisataseepil 90
                                      ++++ GaGe++  vak+L+++  ++v+v+  + ++ +e+ +   +  e +a +++ l++  +++ad+ +  t+  e+ l
  gi|488601219|ref|YP_007907690.1|  2 HIVVAGAGEVGYNVAKALCDN--HDVFVIEKDEKKIDEIYKLNvEVIEGNAANINVLSKaKVSKADIFLGVTGVDEVNL 78
                                      58999**************55..579**********9997743255566677777775415999999999998877666 PP

                                      -HHHHH CS
                      Shikimate_DH 91 ekeeve 96
                                       ++   
  gi|488601219|ref|YP_007907690.1| 79 LSGIAA 84
                                      555444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00035
                                       HHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHH....HHHHT- CS
                      Shikimate_DH   4 kkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelk....ellaea 76 
                                       +++++s +++kv++ G G +++ +a+ L +++++ +  +  + e  ++l++ ++ +++ + + ++l+    e + ++
  gi|488601219|ref|YP_007907690.1| 214 QDIFGSDTTRKVVIFGGGTVGSYLARVLDSSNLN-IKLIEKNEELCENLCSAYNRVRVVIGDPTDLDllyeEDVGRS 289
                                       678898899***********************99.******************999888777666651111445566 PP

                                       SEEEE-SS CS
                      Shikimate_DH  77 dvvisata 84 
                                       dvv s+  
  gi|488601219|ref|YP_007907690.1| 290 DVVASCLE 297
                                       77766655 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0015       1.3       2      41 ..       3      41 ..       2      65 .. 0.79
   2 !   14.2   0.0   3.6e-05     0.031       1      51 [.     224     274 ..     224     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeinee 41
                                      i v GaG  G  +Ak+l +n  +v ++ ++e+ i+ei + 
  gi|488601219|ref|YP_007907690.1|  3 IVVAGAGEVGYNVAKALCDNH-DVFVIEKDEKKIDEIYKL 41
                                      8899**************996.9********999998654 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.6e-05
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT- CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgi 51 
                                       k+ ++G+G  G+ lA+vl + + +++l+ ++eel+e++ ++ + v+ + g 
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELCENLCSAYNRVRVVIGD 274
                                       799*********************************998887777766555 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 !    8.6   2.6    0.0012         1      30      98 ..       2      70 ..       1      97 [. 0.84
   2 !   11.9   0.0   0.00012       0.1      29      95 ..     223     292 ..     214     312 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHH.HHHH-SEEEE- CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellae.avkeadvvigt 98
                                      +++v G+G +G + ++ a   + +V v++++++++ ++ +l+ +++e  +++ + l++ +v++ad+  g 
  gi|488601219|ref|YP_007907690.1|  2 HIVVAGAGEVGYNVAK-ALCDNHDVFVIEKDEKKIDEIYKLNVEVIEGNAANINVLSKaKVSKADIFLGV 70
                                      689*********9776.556689*********************999999998877652799***99874 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE....HCHHHHHHHHHHHH-SEE CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev....lksqeellaeavkeadvv 95 
                                        kv+++GgG++G   +++  + + ++++++++++  e+l s  ++ v+v     +    l++e v ++dvv
  gi|488601219|ref|YP_007907690.1| 223 RKVVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELCENLCSAYNR-VRVvigdPTDLDLLYEEDVGRSDVV 292
                                       59*************************************998777.7763444223333445555555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.6   0.00074      0.63       1      67 [.       2      65 ..       2      81 .. 0.87
   2 !   12.7   0.0   0.00016      0.14       1      35 [.     224     258 ..     224     266 .. 0.92
   3 ?   -0.3   0.0       1.9   1.6e+03      54      78 ..     352     376 ..     334     380 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00074
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT..TEEEECSEEEEEEE CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn..gievllntkveeie 67
                                      ++vv G+G +g  +A+al +  ++V v+e  +k      +e+ k+  e +e n  +i+vl ++kv + +
  gi|488601219|ref|YP_007907690.1|  2 HIVVAGAGEVGYNVAKALCDN-HDVFVIEKDEKKI----DEIYKLNVEVIEGNaaNINVLSKAKVSKAD 65
                                      79****************995.59******99999....899999999999888899999999998765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00016
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       kvv+ GgG++g  lA +l   + +++++e +++l+
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELC 258
                                       79******************************998 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.9
                                       TEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  54 gievllntkveeiegsedgvesvkl 78 
                                       + ++l+ ++++eieg e  v +++l
  gi|488601219|ref|YP_007907690.1| 352 HLRLLTLETLAEIEGGEAVVLEIEL 376
                                       6789999*******98874544555 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 !    6.3   0.2    0.0094         8       2      42 ..       3      42 ..       2      74 .. 0.79
   2 !   12.0   0.0   0.00016      0.14       1      38 [.     224     261 ..     224     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0094
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42
                                      + v GaG +G  +a++++  +++V +++ +e+++++  +  
  gi|488601219|ref|YP_007907690.1|  3 IVVAGAGEVGYNVAKALC-DNHDVFVIEKDEKKIDEIYKLN 42
                                      7899**********9876.579*********9999877654 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealeka 38 
                                       kv + G Gt+G+ +a v+ s++l+++l++ +ee  e+ 
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELCENL 261
                                       699*****************************988875 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.018        15       2      32 ..       2      32 ..       1     118 [. 0.70
   2 !   13.4   0.0   3.8e-05     0.032       2      45 ..     224     267 ..     146     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.018
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE.TT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.le 32
                                      ++vv G+G  G+++a+ l   +++v ++e +e
  gi|488601219|ref|YP_007907690.1|  2 HIVVAGAGEVGYNVAKALCD-NHDVFVIEkDE 32
                                      56777777777777777766.67777776422 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.8e-05
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllska 45 
                                       +vv+ GgG  G  +a+ l  +++++ l+e+++++  + c+ ++ 
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELCENLCSAYNR 267
                                       45555555555555555555555555555444444444555444 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 !   15.4   0.5   1.2e-05      0.01       1      52 [.       1      51 [.       1      68 [. 0.88
   2 ?    3.8   0.0     0.044        38       2      39 ..     224     261 ..     223     295 .. 0.86
   3 ?   -3.1   0.0       5.7   4.9e+03     158     174 ..     382     398 ..     359     400 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLe 52
                                      m+i+v G+G vG   a +l    h+v ++ +de+k+d++ + +++++e + +
  gi|488601219|ref|YP_007907690.1|  1 MHIVVAGAGEVGYNVAKALCD-NHDVFVIEKDEKKIDEIYKLNVEVIEGNAA 51
                                      78**************99986.59******************9999997655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.044
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdkl 39 
                                       k++++G G vG   a vl +   ++ ++ ++ee  ++l
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELCENL 261
                                       899*************************9999877665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.7
                                       TTSHHHHHHS-S-EEEE CS
                    UDPG_MGDP_dh_N 158 egsavkdllnpdrvviG 174
                                        g+ + +l  p+r +iG
  gi|488601219|ref|YP_007907690.1| 382 SGKKISELKIPERALIG 398
                                       36666666677776666 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 !    8.4   0.5    0.0037       3.2       2      55 ..       3      50 ..       2      99 .. 0.64
   2 !    8.6   0.0    0.0033       2.8       1      50 [.     224     270 ..     224     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0037
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdn 55
                                      i + GaG++g  +a+ l  +    h++ v+ +++++k++e+ + l+v+v+++++
  gi|488601219|ref|YP_007907690.1|  3 IVVAGAGEVGYNVAKALCDN----HDVFVI-EKDEKKIDEIYK-LNVEVIEGNA 50
                                      5566***********99888....9***89.*******99954.4555554333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0033
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.-EE CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.vkv 50 
                                       k+ i G+G +g+ la+ l +++    +i ++ ++n+e  e l ++++ v+v
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSN---LNIKLI-EKNEELCENLCSAYNrVRV 270
                                       67889*************9999...999988.***********99986444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0042       3.6       1      58 [.       3      61 ..       3      79 .. 0.80
   2 !    9.3   0.0   0.00094       0.8       1      39 [.     225     264 ..     225     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0042
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppeal 58
                                      i+++GaG +G  +a  L   ++dv +i +++ +++++ k ++++ + +  + +++ ++++
  gi|488601219|ref|YP_007907690.1|  3 IVVAGAGEVGYNVAKALCD-NHDVFVIEKDEkKIDEIYKLNVEVIEGNaANINVLSKAKV 61
                                      89***************77.99*********99*99888777776666455555555444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00094
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkkn 39 
                                       ++i G G +Gs+la  L   + ++ li +++  +e+l ++
  gi|488601219|ref|YP_007907690.1| 225 VVIFGGGTVGSYLARVLDSSNLNIKLIEKNEeLCENLCSA 264
                                       689**************************99888887655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0     0.009       7.7       2      35 ..       3      32 ..       2      38 .. 0.88
   2 !    9.6   0.0   0.00042      0.36       1      35 [.     224     255 ..     224     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.009
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      iv++G+G  G+ +A al   +    +v ++e++e
  gi|488601219|ref|YP_007907690.1|  3 IVVAGAGEVGYNVAKALCDNH----DVFVIEKDE 32
                                      9*************9998777....899999976 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00042
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35 
                                       k+vi GGGt G+  A +l       l+++l+e++e
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSN---LNIKLIEKNE 255
                                       79*********98888888777...9******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 !   11.9   0.3   0.00023      0.19       2      96 ..       3     103 ..       2     110 .. 0.81
   2 ?    3.5   0.0     0.083        71       3      66 ..     226     299 ..     224     328 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHC.......SEEEE-SSSHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasl.......dvvitmvkagkavde 71 
                                       i + G G+ G n a+ l + +++v v++ +++k++e+ + +++++e  ++ ++ l         +++ v+  ++v+ 
  gi|488601219|ref|YP_007907690.1|   3 IVVAGAGEVGYNVAKALCD-NHDVFVIEKDEKKIDEIYKLNVEVIEGNAANINVLskakvskADIFLGVTGVDEVNL 78 
                                       6789***********9987.599*****************9666665554444444447776779999999999987 PP

                                       HHHSHCCC--TT-EEEE-S---HHH CS
                     NAD_binding_2  72 viegllealkkgdilidgstssped 96 
                                       +    ++++ + ++++ +++ ++ d
  gi|488601219|ref|YP_007907690.1|  79 LSGIAAKKMGAKKTIVRVGNPEYVD 103
                                       7777999999999999999988765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.083
                                       EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..........EEE-SSHHHHHHHCSEEEE-SSSH CS
                     NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..........akaaesieelvasldvvitmvkag 66 
                                        + G G+ Gs +a+ l +++ ++ +++ ++e +e+l ++            ++    ee v + dvv  +++++
  gi|488601219|ref|YP_007907690.1| 226 VIFGGGTVGSYLARVLDSSNLNIKLIEKNEELCENLCSAYnrvrvvigdpTDLDLLYEEDVGRSDVVASCLEND 299
                                       567999**************************999998865555433333222222223333336666666655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.5   5.5e-05     0.047       3      83 ..       4      82 ..       3      95 .. 0.83
   2 ?   -0.8   0.0       1.1   9.4e+02       3      33 ..     226     256 ..     225     321 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.5e-05
                                      ESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE---GGS-HHH CS
                              NmrA  3 viGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtgfyskeie 80
                                      v+ ++G+ G  v++al  ++h+v+++ +d  +++++++ +  ve+++g++ + ++l++a ++++d +  vtg+ + ++ 
  gi|488601219|ref|YP_007907690.1|  4 VVAGAGEVGYNVAKALC-DNHDVFVIEKD--EKKIDEIYKLNVEVIEGNAANINVLSKAkVSKADIFLGVTGVDEVNLL 79
                                      78899*******99987.58****99666..6789*********************999899****9999997666666 PP

                                      HHH CS
                              NmrA 81 dgk 83
                                       g 
  gi|488601219|ref|YP_007907690.1| 80 SGI 82
                                      554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                       ESSTTSHHHHHHHHHHHHHT-EEEEEES-S- CS
                              NmrA   3 viGaTGrqGksvvrallkaghkvralvRdtk 33 
                                       vi + G  G++++r+l +++ +++ + ++++
  gi|488601219|ref|YP_007907690.1| 226 VIFGGGTVGSYLARVLDSSNLNIKLIEKNEE 256
                                       4445688888888888888888877766653 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.023        19       4      38 ..       3      36 ..       1      40 [. 0.91
   2 ?    8.0   0.0    0.0018       1.5       3      37 ..     224     258 ..     222     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.023
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvv 38
                                      +++ GaG +G   a+ L+    +v ++ek +++++
  gi|488601219|ref|YP_007907690.1|  3 IVVAGAGEVGYNVAKALCDN-HDVFVIEKDEKKID 36
                                      6899****************.9********99876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0018
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37 
                                       +V+I G+G +G  la++L +   +  l+ek ++  
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELC 258
                                       79******************999999999998765 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.63   5.3e+02       2      31 ..       4      32 ..       3     100 .. 0.78
   2 ?   11.7   0.0   0.00032      0.27       1      34 [.     225     258 ..     225     325 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.63
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-G CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpre 31
                                      v+ Gag+v+  +a+ +   + +v v++++e
  gi|488601219|ref|YP_007907690.1|  4 VVAGAGEVGYNVAKALCD-NHDVFVIEKDE 32
                                      899*********998876.45666666666 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00032
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa 34 
                                       +vifG+g v+  lar++ + ++++ +++++ee+ 
  gi|488601219|ref|YP_007907690.1| 225 VVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELC 258
                                       69***************************99865 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 ?    0.8   0.0      0.68   5.8e+02       2      28 ..       6      31 ..       5      33 .. 0.86
   2 ?   11.4   0.0   0.00034      0.29       1      32 [.     227     258 ..     227     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.68
                                      E--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekr 28
                                       GaG  G   A +L + ++dv ++ek 
  gi|488601219|ref|YP_007907690.1|  6 AGAGEVGYNVAKALCD-NHDVFVIEKD 31
                                      6999999999999998.59*****997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00034
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32 
                                       I G+G  G+++A+ L   ++++ l+ek++ l+
  gi|488601219|ref|YP_007907690.1| 227 IFGGGTVGSYLARVLDSSNLNIKLIEKNEELC 258
                                       67*************************99886 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.04        34       1      29 [.       2      31 ..       2      34 .. 0.90
   2 ?    7.3   0.0    0.0037       3.1       1      33 [.     224     258 ..     224     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.04
                                      EEEEECTSHHHHHHHHHHHHTT.EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekg 29
                                      ++v+ G+G +G  +A +L   + V ++ek+
  gi|488601219|ref|YP_007907690.1|  2 HIVVAGAGEVGYNVAKALCDNHdVFVIEKD 31
                                      79****************86657******8 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0037
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       +vvi GGG +G+  A+ L   +  + l+ek+++++
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSNlnIKLIEKNEELC 258
                                       59****************665588******98766 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.44   3.7e+02       2      34 ..       2      33 ..       1      38 [. 0.84
   2 ?    8.6   0.0   0.00076      0.65       2      37 ..     224     259 ..     223     264 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.44
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      +++v G+G  G   A ++   +++V ++ek +k
  gi|488601219|ref|YP_007907690.1|  2 HIVVAGAGEVGYNVAKAL-CDNHDVFVIEKDEK 33
                                      68999******9888776.78899*****9876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00076
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                       +v++ GgG  G + A  + + + ++ l+ek+++l +
  gi|488601219|ref|YP_007907690.1| 224 KVVIFGGGTVGSYLARVLDSSNLNIKLIEKNEELCE 259
                                       79*****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2861.51
//
Query:       gi|488601220|ref|YP_007907691.1|  [L=475]
Description: potassium uptake protein, TrkH family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-71  238.8  19.2    2.7e-38  131.7   5.5    2.2  2  TrkH      Cation transport protein


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   5.5   1.5e-42   2.7e-38      11     273 ..      44     283 ..      37     290 .. 0.89
   2 !  113.1   5.7   6.5e-37   1.2e-32     315     491 ..     292     467 ..     284     473 .. 0.95

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.5e-42
                              TrkH  11 itialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivvees 87 
                                       ++++++  l++  k ++  ++ k++f iv   +  +s +g+++        +f+da+fe++sg+tttg++ ++  e 
  gi|488601220|ref|YP_007907691.1|  44 VNLIISLILYSV-KPKSEVFRYKEGFAIVGLGWFLISLIGAIPYC--MIGTGFIDAIFESMSGFTTTGATIFDRIEV 117
                                       444444444444.44556899**********************87..678899************************ PP

                              TrkH  88 lprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvl 164
                                       lp+s+l +r+ ++++Gg+g++vl ++++p + +++++l ++e+++  ++++ +++l++++  l+ +y+++++l ++l
  gi|488601220|ref|YP_007907691.1| 118 LPKSILLWRSLTEWVGGMGIIVLFVAVFPSIAKKGYALFQAEVPGITVSKV-TPRLKDTALRLWEIYLLFTVLEVAL 193
                                       *******************************************99998876.79*********************** PP

                              TrkH 165 lvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFpillrvi 241
                                       l         y +++      +l++a++hs+++++++Gfs++ +S+a++++ ++i+ +++if+i+ +++F++++  +
  gi|488601220|ref|YP_007907691.1| 194 L---------YLAGL------NLFDAINHSFTTMSTGGFSTHTESIAYYRS-PLIETIITIFMIVAGVNFSLHYYWL 254
                                       *.........****9......******************************.*********************9765 PP

                              TrkH 242 iaikkkilrdlkqikeslsflldlprrcftLl 273
                                        + + +ilrd +++k  +s+l  +++ c+t+l
  gi|488601220|ref|YP_007907691.1| 255 -KGDARILRD-PEFKAYISLL-AIAIACLTIL 283
                                       .678899998.8999888876.4666666665 PP

  == domain 2  score: 113.1 bits;  conditional E-value: 6.5e-37
                              TrkH 315 rvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavs 390
                                       +++ ++F +vs+ t+ G+++ d++ + ++ k++++  m+igg++gStaggI+ +++y + + ++++i +e +p++ +
  gi|488601220|ref|YP_007907691.1| 292 SFRYSAFNAVSLMTTtGYASYDFDRWMDSSKLIILTLMFIGGCSGSTAGGIKVIRIYLLEKYSIHQILKEADPRTAR 368
                                       567789*****99999**********************************************************999 PP

                              TrkH 391 kksidgkhlerqllvdlwslflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGa.knaslsaqltt 466
                                        +++  + l+++++ d+ ++f+++++i+ +++ ++s  +   ++++ +  +vv+++ +vG++lGa   +++   l +
  gi|488601220|ref|YP_007907691.1| 369 VIKMNDRILKKEIIDDITAFFVLYVLIFAVSSVVISLFG---MDLLSAVSAVVATMSNVGPGLGAvGATESYSALHP 442
                                       99999**************************99999999...9*********************8899999999*** PP

                              TrkH 467 isklvlialmirGrlrglpvlldra 491
                                       + kl+l ++m+ Grl+ ++vl +++
  gi|488601220|ref|YP_007907691.1| 443 VVKLILFFNMWAGRLELFTVLSLFI 467
                                       ********************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3215.12
//
Query:       gi|488601221|ref|YP_007907692.1|  [L=491]
Description: DNA polymerase II small subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.2   0.0    1.8e-14   53.6   0.0    1.3  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    4.3e-14   53.5   0.2    6.9e-14   52.8   0.2    1.3  1  Metallophos      Calcineurin-like phosphoesterase
    6.1e-08   33.0   0.0    2.3e-07   31.2   0.0    1.9  2  Metallophos_2    Calcineurin-like phosphoesterase superfamily
    0.00015   21.7   2.0    0.00021   21.2   0.2    2.2  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.018   14.8   0.1      0.046   13.4   0.1    1.7  1  HIN              HIN-200/IF120x domain
      0.068   12.9   0.1       0.13   12.0   0.1    1.4  1  CDC24_OB3        Cell division control protein 24, OB domain 
      0.075   12.7   0.4       0.12   11.9   0.4    1.3  1  tRNA_anti-like   tRNA_anti-like


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 !   53.6   0.0     7e-18   1.8e-14       2     203 ..     233     434 ..     232     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 7e-18
                                       EEEES--S-TT---...-HHHHHHHHHHH.......HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHH CS
                       DNA_pol_E_B   2 vivsglnldndnrs...leaLrkiLqgya......peesppdvlilaGnfvdaahkaiasskvstdekkenfdalal 69 
                                       v++s++++ ++ +     +a+ k+L+         + ++++  l +aG  vd      +++k    e  +     ++
  gi|488601221|ref|YP_007907692.1| 233 VFISDIHFGSNTFLeksWNAFVKWLNCEVgneymqEIAEKVRYLFIAGDVVDGVGIYPGQEKE--LEIFDIYGQYEE 307
                                       667777777444335557777777777777777766677777778888888754444443332..344555555667 PP

                                       THHHHTTS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH-- CS
                       DNA_pol_E_B  70 llsilesllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlk 146
                                         + le++ + ++++l Pg  D++ + + Pq++lp+ + +   r+   +k v NP +++ ++v+v+++ +  ++d+ 
  gi|488601221|ref|YP_007907692.1| 308 AGEQLEKIPKRIKIILSPGNHDAVRQ-AEPQPALPKEFADLFPRN---VKHVGNPAWVDADGVKVLIYHGRSIDDMI 380
                                       778888999*****************.*****************8...99*************************** PP

                                       -EEESHHHHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE-- CS
                       DNA_pol_E_B 147 reslkesntdverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlp 203
                                        ++ + +    +  + +++ +l+ rhl+P++    p   +k d lv++++Pd++  +
  gi|488601221|ref|YP_007907692.1| 381 MKIPRLDY---SDPSGVIEEMLKRRHLCPIYGGRTPLAPEKEDLLVIDEVPDIVHTG 434
                                       ****9999...699***************************************9776 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.2   2.7e-17   6.9e-14       4     204 .]     233     439 ..     230     439 .. 0.74

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.7e-17
                                       EEEESBTB...TTCCTHHHHHHHHH.....HHHHHH......TTESEEEEESTSSSSS................HHH CS
                       Metallophos   4 lvigDlHl...algggqlddllkll.....ddllre......ekpdlvllaGDlvdrg................dle 50 
                                       ++i+D+H+      + ++++++k+l     +    e      ek+ ++++aGD+vd+                 +  
  gi|488601221|ref|YP_007907692.1| 233 VFISDIHFgsnTFLEKSWNAFVKWLncevgN----EymqeiaEKVRYLFIAGDVVDGVgiypgqekeleifdiyGQY 305
                                       79*****998866668888888888444441....033334468888888*******87998888888888666333 PP

                                       HHHHHHHHHHHHHTSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEE CS
                       Metallophos  51 kellellaalvkypipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspel 127
                                       +e  e+l++  k +i+++l +GNH+      +++ +  ++f++++ ++++ ++n+  ++  +   kvl++hG s+++
  gi|488601221|ref|YP_007907692.1| 306 EEAGEQLEKIPK-RIKIILSPGNHD-AVRQAEPQPALPKEFADLFPRNVKHVGNPAWVDADGV--KVLIYHGRSIDD 378
                                       336666555555.6999********.55677788888888999*****9999*******8888..********7777 PP

                                       THHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTT.ESEEEEESSSS CS
                       Metallophos 128 lvsldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkyg.vdlvisGHtHv 203
                                          ++k+ +l++ +++    +e+lk+             +  p+y  +g +   ++ edll + + +d+v  GH+H+
  gi|488601221|ref|YP_007907692.1| 379 --MIMKIPRLDYSDPSGVI-EEMLKR------------RHLCPIY--GGRTPLAPEKEDLLVIDEvPDIVHTGHVHT 438
                                       ..66777777766665555.999999............5555666..6667777777777666663777777****8 PP

                                       E CS
                       Metallophos 204 y 204
                                       y
  gi|488601221|ref|YP_007907692.1| 439 Y 439
                                       7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.6   6.6e+03      51      62 ..      38      55 ..      25      85 .. 0.67
   2 !   31.2   0.0     9e-11   2.3e-07       4     143 ..     233     452 ..     231     464 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                     Metallophos_2 51 la......pvlaVrGNnD 62
                                      ++      +++ V GN+ 
  gi|488601221|ref|YP_007907692.1| 38 RNfenaidEICKVLGNCV 55
                                      444445568888888885 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 9e-11
                     Metallophos_2   4 aiiSDlH..snldaleav...............lealkevgvdaiihaGD....................l..eeee 41 
                                       ++iSD+H  sn ++ + +               +++++e  v +++ aGD                    +  +ee+
  gi|488601221|ref|YP_007907692.1| 233 VFISDIHfgSNTFLEKSWnafvkwlncevgneyMQEIAEK-VRYLFIAGDvvdgvgiypgqekeleifdiYgqYEEA 308
                                       689******6666666667777777888887777777777.8********999988888888888876643555666 PP

                     Metallophos_2  42 pevleellelapvlaVrGNnD.......eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl........ 102
                                        e le++ ++ +++  +GN+D       +   + +++++ + +  +++ + a+++++g+kvl++Hg           
  gi|488601221|ref|YP_007907692.1| 309 GEQLEKIPKRIKIILSPGNHDavrqaepQ-PaLPKEFADLFPRNVKHVGNPAWVDADGVKVLIYHGRSIddmimkip 384
                                       6788888888899999*****99877533.358888899999999999******************977******** PP

                     Metallophos_2 103 ............................gvkdalaellke...aeegsdvvvcGHtHvpevekeggvlvvnP 143
                                                                        la+  ++    +e+ d+v  GH H+ +++  +g+l +n 
  gi|488601221|ref|YP_007907692.1| 385 rldysdpsgvieemlkrrhlcpiyggrtP----LAPEKEDllvIDEVPDIVHTGHVHTYGARYYRGILALNS 452
                                       ************************66541....4444444443468888******************99995 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.9     5e+03      64      73 ..      83     101 ..      68     104 .. 0.55
   2 !   21.2   0.2   8.1e-08   0.00021       1      57 [.     149     203 ..     149     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                                       S.........SEEEEEEEE CS
                   tRNA_anti-codon  64 g.........elelkveei 73 
                                                 ++elkv +i
  gi|488601221|ref|YP_007907692.1|  83 VktkvekiveKFELKVRDI 101
                                       2333334455677777776 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 8.1e-08
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGr 57 
                                       V++ G vt+++   +++   i+++D+tg+i v ++  + +++a++l  + v+ v+G 
  gi|488601221|ref|YP_007907692.1| 149 VSIIGIVTDVR-ETSKGNYIIEIEDKTGKISVLATA-KLREVASELLGDEVIAVSGS 203
                                       89********8.88899*******************.*****************996 PP

>> HIN  HIN-200/IF120x domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.8e-05     0.046      99     156 ..     134     191 ..     117     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                       S---HHHHTTSSTT.EEEEEEEEEEEEEEESS.EEEEEEEETTEEEEEEEECSCTGCC-T CS
                               HIN  99 etpkikklkkqasg.tivnGlfkvqkktvkkk.niiyeikDntgkmevvvsgkltkikce 156
                                       +++ i +lkk +++   + G+  v+  ++++k n+i ei+D+tgk+ v+ + kl+++  e
  gi|488601221|ref|YP_007907692.1| 134 NSIPIASLKKVNQKeVSIIGI--VTDVRETSKgNYIIEIEDKTGKISVLATAKLREVASE 191
                                       566777887765541334454..5555555554999******************999876 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 ?   12.0   0.1     5e-05      0.13       8      49 ..     148     183 ..     143     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                         CDC24_OB3   8 nvtLlGrvvaifreknsekkkmdryslrieDttGaidatlwe 49 
                                       +v+++G v+++ re+++      +y+++ieD+tG+i ++   
  gi|488601221|ref|YP_007907692.1| 148 EVSIIGIVTDV-RETSK-----GNYIIEIEDKTGKISVLATA 183
                                       799********.33333.....368***********995544 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   4.8e-05      0.12      86     148 ..     146     205 ..     137     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.8e-05
                                       T-EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGHHHHHH--TTSEEEEEEE-- CS
                    tRNA_anti-like  86 GkiieVeGvvsdikkieassvvvlardddgltnVrclledeateasaakiskGqkvtivGqvn 148
                                        k + + G+v+d+++  + ++++ ++d+ g+  V ++ + ++    a ++   ++++++G + 
  gi|488601221|ref|YP_007907692.1| 146 QKEVSIIGIVTDVRETSKGNYIIEIEDKTGKISVLATAKLRE---VASELLGDEVIAVSGSFR 205
                                       57899**********************999999999988888...555678888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2849.37
//
Query:       gi|488601222|ref|YP_007907693.1|  [L=64]
Description: hypothetical protein Asulf_01729 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 409.25
//
Query:       gi|488601223|ref|YP_007907694.1|  [L=259]
Description: Enoyl-CoA hydratase/carnithine racemase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-78  261.9   0.5    5.7e-78  261.7   0.5    1.0  1  ECH_1           Enoyl-CoA hydratase/isomerase
    3.5e-44  151.7   0.2    8.9e-38  130.6   0.1    2.0  2  ECH_2           Enoyl-CoA hydratase/isomerase
    0.00058   18.9   0.1     0.0012   17.9   0.0    1.5  2  SDH_sah         Serine dehydrogenase proteinase
    0.00092   19.2   0.1       0.26   11.2   0.0    2.4  2  Peptidase_S49   Peptidase family S49
  ------ inclusion threshold ------
      0.039   12.6   0.2      0.056   12.1   0.2    1.2  1  Carboxyl_trans  Carboxyl transferase domain


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.7   0.5   1.6e-81   5.7e-78       2     250 ..       8     256 ..       7     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: 261.7 bits;  conditional E-value: 1.6e-81
                                       EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHH CS
                             ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevl 78 
                                       +++g++  +lnrP+a Nal++e+++ l + + k++++k +rav++tG+++aF+aGad+k  ++ e+ ++ ++ e + 
  gi|488601223|ref|YP_007907694.1|   8 KSDGILIARLNRPNAFNALNEEVVDGLEELIRKVRTEKDIRAVIITGSGRAFSAGADIKMFLRSETFQARDIIERLG 84 
                                       6789999*********************************************************9999999****** PP

                                       HHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHH CS
                             ECH_1  79 elwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilll 155
                                         +++  ++++p+iaa+nG+a+gGG+ela+acD++ia++na+fg++e+++G+ipgaggtq+lar +G +kA+e +l+
  gi|488601223|ref|YP_007907694.1|  85 RVLEEFEDLDVPIIAAINGFALGGGCELAMACDMIIASENAVFGQPEINIGIIPGAGGTQRLARLIGWKKAMEYCLT 161
                                       ***************************************************************************** PP

                                       T-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHH CS
                             ECH_1 156 gkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskdd 232
                                       g+kisa+ea+k Glv+kvv +e+l++ a+ela+ +aeksp+a+  +k+a+n+ +++ l+ +l+ e++lf   fs++d
  gi|488601223|ref|YP_007907694.1| 162 GEKISAKEAEKLGLVNKVVKAEELEKAAMELARTIAEKSPTAVMLVKQAVNRGYKMSLKDGLAYERDLFALAFSSED 238
                                       ***************************************************************************** PP

                                       HHHHHHHHHTCSH----- CS
                             ECH_1 233 ikeGlqaflEkrkpefed 250
                                        keG  af+Ekr p+f++
  gi|488601223|ref|YP_007907694.1| 239 AKEGFSAFVEKRMPNFKK 256
                                       ****************97 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.1   2.5e-41   8.9e-38       3     186 ..      14     194 ..      12     195 .. 0.96
   2 !   22.8   0.0   1.6e-08   5.7e-05     247     320 ..     187     257 ..     185     259 .] 0.89

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 2.5e-41
                                       EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHH CS
                             ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYkl 79 
                                       ++ Lnrp+a+NaL+ e+v+ l+e ++++++++++++v+++g+g +af+AG D++++ ++++ ++   ++++++  ++
  gi|488601223|ref|YP_007907694.1|  14 IARLNRPNAFNALNEEVVDGLEELIRKVRTEKDIRAVIITGSG-RAFSAGADIKMFLRSETFQA---RDIIERLGRV 86 
                                       689**************************************88.**************999966...469******* PP

                                       HHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH-- CS
                             ECH_2  80 nyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGa 155
                                           +++  p++a ++G+++GgG+ l++ + + +++e++vf  PE++IG++P  Gg+  L+rl g + ++  +lTG+
  gi|488601223|ref|YP_007907694.1|  87 LEEFEDLDVPIIAAINGFALGGGCELAMACDMIIASENAVFGQPEINIGIIPGAGGTQRLARLIGwKKAMEYCLTGE 163
                                       ***************************************************************887999999***** PP

                                       -B-HHHHHHTTS--EE--GGGHHHHHHHHHT CS
                             ECH_2 156 rlkgadalaaglathyvpseklealeeaLae 186
                                       ++++++a ++gl +++v++e+le+ + +La+
  gi|488601223|ref|YP_007907694.1| 164 KISAKEAEKLGLVNKVVKAEELEKAAMELAR 194
                                       ***********************99998876 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------SSS CS
                             ECH_2 247 ewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWkpa 320
                                       + a + ++t++++sPt++ ++ ++++rg k+s l++ l+ E +l + +++++D  eG  a  v+k + P++k +
  gi|488601223|ref|YP_007907694.1| 187 KAAMELARTIAEKSPTAVMLVKQAVNRGYKMS-LKDGLAYERDLFALAFSSEDAKEGFSAF-VEK-RMPNFKKK 257
                                       5678899************************5.************************9986.566.67888766 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.57   2.1e+03      79     122 ..      35      76 ..      30      86 .. 0.58
   2 !   17.9   0.0   3.3e-07    0.0012     124     223 ..      99     198 ..      83     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.57
                           SDH_sah  79 eevlrairltpkdkpidliihtpGGlvlaa.tqiakalkehkakt 122
                                       ee++r +r    +k i  +i t  G +++a  +i   l++   ++
  gi|488601223|ref|YP_007907694.1|  35 EELIRKVR---TEKDIRAVIITGSGRAFSAgADIKMFLRSETFQA 76 
                                       45555554...4566766777776666544155666666555555 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.3e-07
                           SDH_sah 124 vivphyamsGGtlialaadeiildenavlGpvdpqlgqypaasilkvvek.keakdiddktliladiakkaikqvee 199
                                         +  +a+ GG+ +a+a d ii  enav+G  + ++g +p a   + + +  + k++ +  l    i+ k  +++  
  gi|488601223|ref|YP_007907694.1|  99 AAINGFALGGGCELAMACDMIIASENAVFGQPEINIGIIPGAGGTQRLARlIGWKKAMEYCLTGEKISAKEAEKL-G 174
                                       457789**********************************98877766652577888888888888888887776.4 PP

                           SDH_sah 200 fvyellkdkydeekakeiakklte 223
                                       +v +++k +  e+ a e+a++++e
  gi|488601223|ref|YP_007907694.1| 175 LVNKVVKAEELEKAAMELARTIAE 198
                                       566666766666666677766665 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   7.2e-05      0.26       4      40 ..      92     128 ..      89     138 .. 0.90
   2 !    5.5   0.2    0.0043        16     119     151 ..     161     193 ..     152     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-05
                                       HTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49   4 kakkPvvasaenvaaSggYylasaadkivanpstivg 40 
                                       +   P++a +++ a  gg  la+a+d i+a+ +++ g
  gi|488601223|ref|YP_007907694.1|  92 DLDVPIIAAINGFALGGGCELAMACDMIIASENAVFG 128
                                       5568*****************************9987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0043
                                       CCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHC CS
                     Peptidase_S49 119 egrvltgqqAlklgLvdelgtvddavaeleela 151
                                       +g+  ++++A klgLv ++   +++ + ++ela
  gi|488601223|ref|YP_007907694.1| 161 TGEKISAKEAEKLGLVNKVVKAEELEKAAMELA 193
                                       56778999*******************999987 PP

>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.6e-05     0.056     342     436 ..      68     178 ..      63     218 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                                       E--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-T.EEEHHHHHTTTGG..GSTTTTEEETTT-EEESS-HHHHHH CS
                    Carboxyl_trans 342 flvGqrqeyggilkhGaklvdalaeakvPkitvilr.kayGGayvvmdsk..ingadlvaawptariaVlgpegave 415
                                       fl ++   + +i+ +   +++++ +++vP+i  i + ++ GG  ++m     i ++++v+++p+  i++++++g  +
  gi|488601223|ref|YP_007907694.1|  68 FLRSETFQARDIIERLGRVLEEFEDLDVPIIAAINGfALGGGCELAMACDmiIASENAVFGQPEINIGIIPGAGGTQ 144
                                       666666677899999999******************88889999999876225566777*************99777 PP

                                       HHSHHHHHHHHHHH........HHHHHH.........H CS
                    Carboxyl_trans 416 ilfrkekaaaemer........kdlaae.........r 436
                                        l r    +++me         +    +         +
  gi|488601223|ref|YP_007907694.1| 145 RLARLIGWKKAMEYcltgekisA----KeaeklglvnK 178
                                       66666666666555444454431....11223455443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1613.65
//
Query:       gi|488601224|ref|YP_007907695.1|  [L=207]
Description: hypothetical protein Asulf_01731 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.3   0.4      0.035   13.8   0.4    1.3  1  DUF835    Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   1.9e-06     0.035      42     136 .]      55     149 ..      19     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-06
                            DUF835  42 vkviwltkveeentvsPtnlekltetivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilv 118
                                        +v+ l +++++++v+ +nl+++   ++k  +  e+ vvl+  +  L+l +g e+++ fl ++   + +++  +i  
  gi|488601224|ref|YP_007907695.1|  55 IHVLSLIQSRKYKSVNVNNLSEIGILLSKISEGMEDFVVLMTAIPELLLIHGLERTYVFLMNVIGKTTNQGRKFIGG 131
                                       56777888889************99999999999999**************************************** PP

                            DUF835 119 idkealeekelalLkref 136
                                       i k+a ++++  ++ r f
  gi|488601224|ref|YP_007907695.1| 132 ITKDAQNKRDEIMISRLF 149
                                       ***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1256.78
//
Query:       gi|488601225|ref|YP_007907696.1|  [L=75]
Description: hypothetical protein Asulf_01732 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   40.6   0.4    2.6e-10   40.4   0.4    1.2  1  DUF5371        Family of unknown function (DUF5371)
  ------ inclusion threshold ------
      0.044   14.6   0.1      0.048   14.4   0.1    1.0  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola
      0.065   13.4   0.0      0.079   13.1   0.0    1.4  1  rve_2          Integrase core domain


Domain annotation for each model (and alignments):
>> DUF5371  Family of unknown function (DUF5371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.4   4.3e-14   2.6e-10       2      46 ..       2      46 ..       1      59 [. 0.86

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.3e-14
                           DUF5371  2 vKivHAqtvLaeeeLeeLKkKtnesstkdAlsiAveHYleCeYtd 46
                                       K    qt L+++ L +LK+ t++ + k+Al  Av HY+eC  ++
  gi|488601225|ref|YP_007907696.1|  2 EKYLIVQTRLPKNMLDDLKEATGKKTVKEALYQAVIHYIECHNIE 46
                                      566778***********************************9887 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1     8e-06     0.048      10      62 ..      13      66 ..       4      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                     ATC_hydrolase 10 valyealkkeigkeeakeiirkalerlg.kergkklaekakakkdkadvekfla 62
                                      + +++ lk+++gk ++ke++++a+ +++ + + ++++e  k++k+   ++  la
  gi|488601225|ref|YP_007907696.1| 13 KNMLDDLKEATGKKTVKEALYQAVIHYIeCHNIERIREIHKVNKKRGRFPVHLA 66
                                      77999*******************99999************9999998887665 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05     0.079      21      41 ..      30      50 ..      19      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                             rve_2 21 eeleaaiedYIewYNnkRlkg 41
                                      e l++a+  YIe+ N +R+++
  gi|488601225|ref|YP_007907696.1| 30 EALYQAVIHYIECHNIERIRE 50
                                      5689**************743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 460.60
//
Query:       gi|488601226|ref|YP_007907697.1|  [L=472]
Description: Aromatic ring hydroxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-82  277.9   0.1    1.3e-82  277.5   0.1    1.1  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina
    1.1e-50  171.6   0.0    1.4e-50  171.2   0.0    1.2  1  HpaB           4-hydroxyphenylacetate 3-hydroxylase C termina
  ------ inclusion threshold ------
      0.033   14.4   0.0      0.086   13.0   0.0    1.7  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      0.065   13.4   0.1       0.13   12.4   0.1    1.6  1  Fer4_14        4Fe-4S single cluster domain
       0.16   11.8   0.0       0.38   10.6   0.0    1.6  1  STN            Secretin and TonB N terminus short domain


Domain annotation for each model (and alignments):
>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.5   0.1   3.7e-86   1.3e-82       2     272 .]       5     268 ..       4     268 .. 0.96

  Alignments for each domain:
  == domain 1  score: 277.5 bits;  conditional E-value: 3.7e-86
                                       HHHHHHHHHHS---EEETTEE-S-TTTSTTTHHHHHHHHHHHHHTTSTTTHHHHEEEE..TTEEEEGGG----SHHH CS
                            HpaB_N   2 geeYlesLrdkgrevYvdGekVedvtthpafrpavrsvarlYdlahdpeykdlltatspetgekvnrffhiprskeD 78 
                                       g++Y+e+L   +re+Yv+GekVed+t+hp ++p+v+s+a +Y+la ++   d    +s++ ++kvnr++ +++++eD
  gi|488601226|ref|YP_007907697.1|   5 GDKYVERLSGYEREIYVRGEKVEDFTNHPNIKPVVKSIALTYELAGKK---DEYSPYSKLVDDKVNRLNYVNENAED 78 
                                       789*******9999******************************9986...578899******************** PP

                                       HHHHHHHHHHHHHHTTT--S--THHHHHHHHHHHHTG.GGGG.G....GHHHHHHHHHHHHHHT--EEEEES--SS- CS
                            HpaB_N  79 llkkrkairelarktggclgRcpdydalnalalvaaa.dvfekegtkeyaenfrkyleyvqendlvlthaitdpkgd 154
                                       l+++ + +rel+++ g+c +Rc+++da+n l+ ++++ d  e+ gt+ y+++f + l+++q++d+++t a+td kgd
  gi|488601226|ref|YP_007907697.1|  79 LIARYDFQRELSMRLGTCNYRCTGCDAINSLYPATKEmD--ERLGTD-YHKRFLELLKEIQRKDYACTAALTDTKGD 152
                                       *************************************99..989999.***************************** PP

                                       TTS-GGGSSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE- CS
                            HpaB_N 155 RskrpseqedpdvyvrvveetddGivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklicr 231
                                       Rskrp+e   +d+yv+vve+++dGivV+Gak++++ga++ad ++vlpt++  ke+++++a+afav+ + +G+k+i++
  gi|488601226|ref|YP_007907697.1| 153 RSKRPKE--AKDMYVHVVEKREDGIVVSGAKIHQSGAFAADINFVLPTQTF-KEGEEEFAIAFAVKPEDEGVKYILQ 226
                                       *******..999************************************777.************************* PP

                                       -----.-.S..-TTT-TTTTT----EEEEEEEEEEEEGGGEEE CS
                            HpaB_N 232 esfed.k.leesefdyplssrfdendalvvfDdVfVPwerVfl 272
                                       ++  + k +e+ ef+ ++    d+ +++v+fD+Vf+PwerVf+
  gi|488601226|ref|YP_007907697.1| 227 NTGYQaKfREGGEFEIGNP-YGDRITCTVIFDNVFIPWERVFV 268
                                       *988877666*********.889*******************6 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.0     4e-54   1.4e-50       2     201 ..     276     468 ..     275     469 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 4e-54
                                       HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-TT CS
                              HpaB   2 gklveefaalhrqsyqgvirkavkldfliGlaalaaeanGiekfshvqeklgelialrellyalliaaeaeaekdps 78 
                                       ++l ++fa  hr+   +  +ka+++d ++G+a+l++++nG+++ +  ++k+ge++ ++e+ +a+++ +++++ ++ +
  gi|488601226|ref|YP_007907697.1| 276 RNLLTNFAISHRCVGAS--CKAGFIDSMTGAASLMLKVNGLDRVPVLRQKIGEMVGVSEAAHAIAVGSATKGFES-Y 349
                                       678999*********99..********************************************************.* PP

                                       S-EE--HHHHHHHHHHHHHHHHHHHHHHHHHHGGGGT----HHHHHST.THHHHHHHT-BTT.B-HHHHHHHHHHHH CS
                              HpaB  79 GvylPdlllanaarvlvtrlypriveilqdiaGGglitlPseadfknpeigpllekylrgsegvsaeeRvkllklaw 155
                                       G++lP++l+an ++v+  + + +++  l +iaGG+++t+Pse d+k++e+g+++ekyl +++++saeeR+k++k+++
  gi|488601226|ref|YP_007907697.1| 350 GTWLPNMLMANSGKVIGVEGFNKVIMNLAEIAGGIPVTAPSEFDLKSEEVGKYVEKYLVANPEFSAEERMKVIKFVE 426
                                       ***************************************************************************** PP

                                       HHHTSHHHHHHHHHHHHTT--HHHHHHHHHHHS--HHHHHHHHHHC CS
                              HpaB 156 dltgsefggrhelyerhgaGspeaqriaiyrqydleekkelvkkll 201
                                        ++ s+    h+l  +hg+Gsp+a  + ++  +d++e++e+v++++
  gi|488601226|ref|YP_007907697.1| 427 FWITSS----HLLGAVHGGGSPAAAVVFLQILADMKEREEAVRDII 468
                                       *****5....5888*****************************997 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.086      14      74 ..     161     222 ..     152     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                       GG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---..----EEEEEEE..GGGEE CS
                     Acyl-CoA_dh_M  14 asvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd..rarglslflvprdapgvs 74 
                                       +++   ++e+ ++++v++G+Ki  ++a  a++ +vl  ++ ++  ++  +  f+v+  ++gv+
  gi|488601226|ref|YP_007907697.1| 161 KDMYVHVVEKREDGIVVSGAKIHQSGAFAADINFVLPTQTFKEgeEEFAI-AFAVKPEDEGVK 222
                                       56666678999999**********************99455554346666.889998899887 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.6e-05      0.13       3      46 ..      91     140 ..      89     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                           Fer4_14   3 vrlsgCnlsCkgCd.......nketwkselgkpqteelleqilkdlkksei 46 
                                       +rl+ Cn  C+gCd        +++ +++lg+ + ++ l + lk+ + +++
  gi|488601226|ref|YP_007907697.1|  91 MRLGTCNYRCTGCDainslypATKEMDERLGTDYHKRFL-ELLKEIQRKDY 140
                                       799***********9999998666688899998888887.55555554444 PP

>> STN  Secretin and TonB N terminus short domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.38      26      45 ..     218     237 ..     215     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                               STN  26 deaLdeLLkgtgLqykitgn 45 
                                       de+ + +L++tg+q+k++++
  gi|488601226|ref|YP_007907697.1| 218 DEGVKYILQNTGYQAKFREG 237
                                       89999************544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3121.90
//
Query:       gi|488601227|ref|YP_007907698.1|  [L=271]
Description: hypothetical protein Asulf_01734 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.9e-05   23.7   0.0    0.00064   20.3   0.0    2.1  2  TIR_2        TIR domain
  ------ inclusion threshold ------
      0.045   14.1   0.1        0.2   11.9   0.1    2.0  1  DUF1863      MTH538 TIR-like domain (DUF1863)
       0.26   11.5   1.5          1    9.6   0.2    2.6  3  CRISPR_Cas2  CRISPR associated protein Cas2


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 ?    1.3   0.0     0.087   5.2e+02      66     105 ..      63     106 ..       9     117 .. 0.64
   2 !   20.3   0.0   1.1e-07   0.00064       1     114 [.     128     250 ..     128     254 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.087
                             TIR_2  66 ewcreeleaale.aaeegkkrlipvlle...p.ekpplaslqyid 105
                                       +++ +e+ea le +++   +r+ p+l e     ++p  + l y  
  gi|488601227|ref|YP_007907698.1|  63 QKVLAEIEALLEgEDKAITERIRPILSEakqWaDHP-TNPLGYAE 106
                                       346778888887566666666777777754312223.34555544 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.1e-07
                             TIR_2   1 VFiSyss..edkewaeklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspayles.......ewc 68 
                                       +Fi y+   ed++ a k+ +  e +g++++  +    + ed+ +++++ i++s+ v+++++++   +       +w 
  gi|488601227|ref|YP_007907698.1| 128 IFIGYRYtaEDEKLANKFIQLFELEGFKCVSGK--TAKAEDIDKKVKKLIDQSEGVIIIFTREKELKdggwttsRWL 202
                                       6777765448******************97555..47899*******************999965333544444666 PP

                             TIR_2  69 reeleaaleaaeegkkrlipvlle....p.ekppl.aslqyidlskk.deeal 114
                                        +e  +a+     g+++ + +++e    + e +++ ++l y+ ++++  +ea+
  gi|488601227|ref|YP_007907698.1| 203 TDEKAYAM-----GRGKPVLLFFEnciaQtERKGIhGELEYVEFNREhLDEAF 250
                                       66666666.....577766666664543122233479999**99976644455 PP

>> DUF1863  MTH538 TIR-like domain (DUF1863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.4e-05       0.2      14     104 ..     140     218 ..     126     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                           DUF1863  14 erlnklkkllaesyrkiagkraglgeasgnalepirdrdedsaaedikeairdaldrssvliVLvgsetat...... 84 
                                       +++nk+ +l+  +                  ++ ++ + +  +aedi +++++ +d+s+ +i++  +e         
  gi|488601227|ref|YP_007907698.1| 140 KLANKFIQLFELE-----------------GFKCVSGKTA--KAEDIDKKVKKLIDQSEGVIIIFTREKELkdggwt 197
                                       3444444444442.................2333444444..599********************999866678888 PP

                           DUF1863  85 .srWvdwEIaaslkkgkrllg 104
                                        srW   E a+++ +gk++l 
  gi|488601227|ref|YP_007907698.1| 198 tSRWLTDEKAYAMGRGKPVLL 218
                                       9*****999999999999985 PP

>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.32   1.9e+03      43      59 ..       6      22 ..       3      39 .. 0.68
   2 ?   -3.0   0.0       1.5   8.8e+03      45      61 ..      62      77 ..      59      95 .. 0.57
   3 ?    9.6   0.2   0.00017         1      38      67 ..     156     186 ..     134     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.32
                                      HHHHHHHHHHHHHSHTT CS
                       CRISPR_Cas2 43 aqleklkkrlkkiidpe 59
                                      +qlekl++++++++ + 
  gi|488601227|ref|YP_007907698.1|  6 KQLEKLARKIQELLGEY 22
                                      46777777777766543 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                                      HHHHHHHHHHHSHTTTC CS
                       CRISPR_Cas2 45 leklkkrlkkiidpeed 61
                                      ++k+ ++++ +++ e d
  gi|488601227|ref|YP_007907698.1| 62 VQKVLAEIEALLEGE-D 77
                                      566666777666655.4 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00017
                                       E.EESHHHHHHHHHHHHHHSHTTTCEEEEEE CS
                       CRISPR_Cas2  38 g.elseaqleklkkrlkkiidpeedsiriyk 67 
                                       +   + a++e++ k++kk+id++e+ i+i++
  gi|488601227|ref|YP_007907698.1| 156 CvSGKTAKAEDIDKKVKKLIDQSEGVIIIFT 186
                                       54556788***************99888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1624.71
//
Query:       gi|488601228|ref|YP_007907699.1|  [L=233]
Description: hypothetical protein Asulf_01735 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0071   16.5   0.2      0.011   15.9   0.2    1.2  1  GramPos_pilinD1  Gram-positive pilin subunit D1, N-terminal d


Domain annotation for each model (and alignments):
>> GramPos_pilinD1  Gram-positive pilin subunit D1, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2     6e-07     0.011      31      88 ..      42     104 ..      28     122 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6e-07
                   GramPos_pilinD1  31 teedgnkit.........gksskelaGVtFavydvtdeydgvetedldsndeeatkklkeaakakag 88 
                                       t + g +it           +++el+GV+F+vy  ++++    +e+l+++d + + +++ + k++ +
  gi|488601228|ref|YP_007907699.1|  42 TAQLGSEITihlieeikkRLDGEELNGVKFDVYTYKKKK----EEKLTGADLAGVLEIEVNGKKTSK 104
                                       444444444555556667889************887644....666666665555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1484.76
//
Query:       gi|488601229|ref|YP_007907700.1|  [L=136]
Description: hypothetical protein Asulf_01736 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00097   19.5   0.0     0.0011   19.3   0.0    1.2  1  GyrI-like  GyrI-like small molecule binding domain


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 !   19.3   0.0     6e-08    0.0011       2      60 ..      21      85 ..      20     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6e-08
                                      CEEEEEE--EEEEEEEEEEEHCCCHH...HHHHHHHHHHHHHHHHCTT...--SSEEEEEEEEE- CS
                         GyrI-like  2 eveivelpafrvvgirhrgdyneegg...ipklweelyawaseiklsn...avspligvssdepe 60
                                      ++eive+++ +++ i+++g++   ++   +++l++ +y+ +   k +    +v++l+g+++ e +
  gi|488601229|ref|YP_007907700.1| 21 TPEIVEIEEGQFLTIEGKGSPDGDEFqakVSALYSLAYGVKNICKREGkdfVVPKLEGLWWVESD 85
                                      69*********************9988999999999998888777766999*********97754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1003.20
//
Query:       gi|488601230|ref|YP_007907701.1|  [L=290]
Description: DNA repair photolyase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   37.1   0.4    3.9e-08   33.9   0.1    2.2  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.018   15.3   0.1       0.17   12.2   0.0    2.5  2  TcdB_N       TcdB toxin N-terminal helical 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 !   33.9   0.1   4.3e-12   3.9e-08       2     163 ..      28     213 ..      27     217 .. 0.78
   2 !    4.3   0.1    0.0051        46      87     120 ..     209     246 ..     202     284 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.3e-12
                                       EEESEESS--TTTSCCTT.........HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE.SSTGGGSTTHHHHH CS
                                       xxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet.........vrregrgrslsveeileevkelkaekg.vkevilg.ggepllypdfvell 67 
                                       ++++ C ++C++C+++ +               +++  +  +++e+ +  a+k   +++ l+   ep +y ++  ++
  gi|488601230|ref|YP_007907701.1|  28 NPYQLCEFNCVYCYIRGSkygentkhgL----AVKINAPTLLEKELYKR-ARKKeYGFIALSsATEPWMYIEEKYKV 99 
                                       56788***************88643332....33333333333333333.3333255555554899****9999999 PP

                                       HHHHHTC..CCTEEEEEEECSSCHG...............HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSH CS
                                       xxxxxxx..xxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       Radical_SAM  68 erlakla..vpgiritvetngtlpd...............eeklerllelgvdrvslgleaaddekvlklmn.rght 126
                                        r + +     ++ +++ t  +l+                +e l+  l++g   ++++l ++d+  v k ++   + 
  gi|488601230|ref|YP_007907701.1| 100 TRKCLEViaRFKFPVHCLTKSPLILrdvdlldeidkhavlPEDLKNKLNRG-VLITVSLSTLDES-VAKVFEpNSPK 174
                                       999988899677777777777777677999999999999999999999999.*************.******999** PP

                                       HHHHHHHHHHHHHTTSETEEEEEEEBTTTSH..HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivglpGend..eeleel 163
                                       + e+l+al+ l ++g+   + ++++lp  +d  eelee+
  gi|488601230|ref|YP_007907701.1| 175 PRERLNALKELIDNGFYAGIAFMPVLPFISDsnEELEEM 213
                                       ***************************999955555555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0051
                                       SCHGHHHHHHHHHTT-SEEEEEEBSSSHH......HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxx RF
                       Radical_SAM  87 tlpdeeklerllelgvdrvslgleaadde......kvlkl 120
                                        l  ee++++ +el v +v+++  + +d       kvl++
  gi|488601230|ref|YP_007907701.1| 209 EL--EEMVKTARELDVRHVYFSPLTMHDAgrelyfKVLEK 246
                                       22..566666666667777777777666655544433333 PP

>> TcdB_N  TcdB toxin N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.23     2e+03      32      48 ..     129     145 ..     128     149 .. 0.78
   2 ?   12.2   0.0   1.9e-05      0.17       8      38 ..     158     188 ..     156     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHSTT-TT CS
                            TcdB_N  32 lkkeidnYnnlykkekn 48 
                                       l +eid + +l +  kn
  gi|488601230|ref|YP_007907701.1| 129 LLDEIDKHAVLPEDLKN 145
                                       78999999999776666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHTTTTS-HHHHHHHHHHHHHHHHH CS
                            TcdB_N   8 enleeklnklseeqskkkyellkklkkeidn 38 
                                       ++l+e ++k  e++s+k++e l+ lk++idn
  gi|488601230|ref|YP_007907701.1| 158 STLDESVAKVFEPNSPKPRERLNALKELIDN 188
                                       7899*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 1971.21
//
Query:       gi|488601231|ref|YP_007907702.1|  [L=229]
Description: putative DNA alkylation repair enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  137.0   5.2    8.3e-40  136.8   5.2    1.1  1  DNA_alkylation  DNA alkylation repair enzyme
  ------ inclusion threshold ------
      0.039   14.6   0.1      0.087   13.5   0.1    1.6  1  CHASE6_C        C-terminal domain of two-partite extracellula
      0.072   13.6   2.0      0.083   13.4   1.2    1.6  2  TFIIS_M         Transcription factor S-II (TFIIS), central do


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 !  136.8   5.2   1.4e-43   8.3e-40       1     211 [.       6     213 ..       6     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 1.4e-43
                    DNA_alkylation   1 ikaeLealadpekaeemqryfk.egdeflGvkvpelrklakeffkelkleeelqelaeeLwksperEerllAldllt 76 
                                       i++eLe+l+++++ e mqr++  +  + lGv+ pelr++ak++ k+       qel  eLw+s+++E+r+lA+++++
  gi|488601231|ref|YP_007907702.1|   6 IIKELESLGSKKNVEGMQRFGItSRAKILGVSKPELREIAKKIGKN-------QELSIELWESGIHEARILACMIAD 75 
                                       689******************98999****************9999.......6799*******************7 PP

                    DNA_alkylation  77 qakkklaeadlelyeklvetinnWdlvDslaskivgalladkperrdllkeWaksenlWerRaAivatlklikk... 150
                                       +  +k +++   l+ ++v +i+nWdl+D+ a++++ +     +++ +++  W +s+ ++++Ra++ ++ kl+     
  gi|488601231|ref|YP_007907702.1|  76 P--EKFTDD---LMDRWVSEIDNWDLCDQCAMNLFWKT----KHAYKKAMVWCQSDCEFTKRAGFALMAKLAISdkk 143
                                       7..777766...9***********************99....45679999******************999877789 PP

                    DNA_alkylation 151 ...tdlellleiaeelladkedfiqkAiGwaLrelsktdpdlveeFlek......hakrmprlslreAie 211
                                           ++e+ + i+++ ++d+++ ++kA+ waLr+++k++pdl ++++e+       ++r +++   +Ai+
  gi|488601231|ref|YP_007907702.1| 144 addRKFEQFFPIIKREASDNRNYVKKAVSWALRQIGKRNPDLNKKAIETakeiqkINSRSAKWIASDAIR 213
                                       999*********************************************9666665444566666666666 PP

>> CHASE6_C  C-terminal domain of two-partite extracellular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.4e-05     0.087      14      50 ..     163     200 ..     160     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                          CHASE6_C  14 drevvekaaelllerilkYrpeLaekleqakqkill.k 50 
                                       +r+ v+ka++++l++i k +p+L++k  +  ++i+  +
  gi|488601231|ref|YP_007907702.1| 163 NRNYVKKAVSWALRQIGKRNPDLNKKAIETAKEIQKiN 200
                                       6899********************99877777774321 PP

>> TFIIS_M  Transcription factor S-II (TFIIS), central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.5   8.7e+03      56      70 ..      42      54 ..      28      71 .. 0.60
   2 ?   13.4   1.2   1.4e-05     0.083      42     110 ..     157     225 ..     107     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
                                      HHHHHHHS-TT-HHH CS
                           TFIIS_M 56 rslvfNLkdkkNpeL 70
                                      r++   +   kN+eL
  gi|488601231|ref|YP_007907702.1| 42 REIAKKIG--KNQEL 54
                                      33333332..45555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.4e-05
                                       HT------HHHHHHHHHHHHHS-TT-HHHHHTSSSS--STTTTS---TTTSS-HHHHHHHHHHHHHHHH CS
                           TFIIS_M  42 kekkstdkkykqkvrslvfNLkdkkNpeLrrrvlsgeispeklvkmspeElaseelkeereklekeale 110
                                       k + s +++y +k  s  +    k+Np+L ++ ++ + +++k+ + s++  as+ ++e++ ++ +e ++
  gi|488601231|ref|YP_007907702.1| 157 KREASDNRNYVKKAVSWALRQIGKRNPDLNKKAIETAKEIQKINSRSAKWIASDAIRELTSEAVQERFK 225
                                       34456678899999999998889***************************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1376.65
//
Query:       gi|488601232|ref|YP_007907703.1|  [L=288]
Description: Triphosphoribosyl-dephospho-CoA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-60  204.5   0.0    2.9e-60  204.3   0.0    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.3   0.0   1.6e-64   2.9e-60       3     281 .]      11     281 ..       9     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 204.3 bits;  conditional E-value: 1.6e-64
                                       XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH CS
                              CitG   3 lavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaa 79 
                                        av+A++lEvs +pK G+Vdr++++  +D+++e+F+aSa+++ p+f+ aa          +++ s+Gel+ +a+ ++
  gi|488601232|ref|YP_007907703.1|  11 SAVMAMILEVSGNPKAGNVDRDHNF--PDLKYEHFIASAVSSFPVFRMAA----------KKELSCGELILRAVEDS 75 
                                       699**********************..***********************..........8999************* PP

                                       ...------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--.......... CS
                              CitG  80 ...tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv.......... 142
                                          ++  N h+Ga++ll++l+a +  +    ++a+++el+    + l+++t++d++++ +a+r+ ++          
  gi|488601232|ref|YP_007907703.1|  76 skwHKAKNVHFGAFLLLIPLLANWDAE----NSAKAGELS---LQYLKNTTYKDSLHVlNAFRISSArvmgskkldl 145
                                       *************************66....455555665...899*********************9999865544 PP

                                       .---.HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS--H CS
                              CitG 143 .eel.kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelpDt 217
                                        + + +++ +++++++l+++++++ + + i++e+ + + ++++     l e+ ++ +dln+a+v ++  +l++l D 
  gi|488601232|ref|YP_007907703.1| 146 rD-DdTERFITEERVNLYKWMSMAPKDNIIAKEIINSYTISVKQSR-KLIEWYKELDDLNHAIVLCYHDMLSRLIDP 220
                                       32.13444444799*****************************555.678888777********************* PP

                                       HHHHHHHHHHHHHHHHHHH..........H-SHHHHHHHHHHHHHHT---HHHHHHHHHHHHHH CS
                              CitG 218 nilrrgGaegaeevqeeArallaaggvaaeaglealeeldrelvernisPGgsADllaatlfla 281
                                       +i++++G+++a ev+++A ++++     +++ l++++e+d+el+e++i+PG++ADl+++t++la
  gi|488601232|ref|YP_007907703.1| 221 LIISKFGRDAALEVSKKAGEIMNL---PEKQRLDKIKEFDEELIEKGINPGSVADLTISTIYLA 281
                                       ***********************9...55669*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1661.14
//
Query:       gi|488601233|ref|YP_007907704.1|  [L=188]
Description: hypothetical protein Asulf_01740 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-37  126.9   0.1    8.2e-37  126.7   0.1    1.0  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.7   0.1   4.6e-41   8.2e-37       1     176 []      13     184 ..      13     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 4.6e-41
                                       EEEEEEEE-TT-EEEEEEEEEESSSE...EEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEE CS
                            DUF447   1 yEvivtTksekrpnaaPiGvivkgdk...vvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdse 74 
                                       +E+i  T +e+  n aP+G+iv++ +     +rl++ ++T eN+++n++l +nv++D++lfa a ++dl+e+ f+s 
  gi|488601233|ref|YP_007907704.1|  13 NEIIGITVGEW-INTAPLGIIVDNPDsrfARVRLYS-NHTRENIKRNDRLWVNVVNDAVLFALASFEDLSEDFFESL 87 
                                       68999999999.**********665555699*****.6**********************************99999 PP

                                       TTTCTT.EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCC....SHHHH CS
                            DUF447  75 tkpakiavlksaeawveveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldi....edkek 147
                                       ++p    +l ++ aw+ ++++      +   +ele+++ e++++ v+++nRg++a+iEa+V+atRl      +++ +
  gi|488601233|ref|YP_007907704.1|  88 NPP----ILINSLAWCGMRAKL-----KGAFAELELLSGEVIRKDVRAVNRGFNAIIEALVHATRLVAfkdpSKRVE 155
                                       985....9***********994.....46789**********************************99998889999 PP

                                       HHHHHHHHHHHHHHH--HHHHHHHHHHHH CS
                            DUF447 148 lleeieylssvikktggerekealellke 176
                                       l+e++ey+  +++k+ggere+ea+++++e
  gi|488601233|ref|YP_007907704.1| 156 LKERVEYYLALAEKCGGEREIEAAKIIRE 184
                                       **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1252.23
//
Query:       gi|488601234|ref|YP_007907705.1|  [L=348]
Description: Coenzyme F420-reducing hydrogenase, beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-36  123.6   0.4    1.2e-35  122.6   0.4    1.5  1  FrhB_FdhB_C    Coenzyme F420 hydrogenase/dehydrogenase, beta 
    8.5e-11   41.9   0.0    2.3e-10   40.5   0.0    1.7  2  FrhB_FdhB_N    Coenzyme F420 hydrogenase/dehydrogenase, beta 
    1.2e-05   24.9  20.3     0.0018   18.0   4.4    3.2  3  Fer4           4Fe-4S binding domain
    1.6e-05   24.9  13.2    1.9e-05   24.7  10.8    2.4  3  Fer4_10        4Fe-4S dicluster domain
    2.1e-05   24.6  11.1    2.1e-05   24.6  11.1    2.4  3  Fer4_9         4Fe-4S dicluster domain
    2.9e-05   24.0  19.9     0.0014   18.6   3.3    2.9  3  Fer4_6         4Fe-4S binding domain
    4.2e-05   24.4   8.9       0.12   13.4   1.2    3.4  3  Fer4_16        4Fe-4S double cluster binding domain
     0.0001   22.4  15.0    0.00012   22.1  11.8    2.6  2  Fer4_21        4Fe-4S dicluster domain
    0.00013   22.4   4.2      0.075   13.5   0.2    2.6  2  Fer4_8         4Fe-4S dicluster domain
    0.00017   21.5  18.1      0.003   17.5   3.4    3.3  3  Fer4_2         4Fe-4S binding domain
    0.00033   20.9  19.6      0.033   14.7   5.3    3.4  3  Fer4_4         4Fe-4S binding domain
     0.0087   16.6  19.1      0.019   15.5  15.8    2.7  2  Fer4_7         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.023   15.5   6.6       0.21   12.5   0.2    3.0  3  Fer4_22        4Fe-4S dicluster domain
       0.15   13.1  23.1        0.2   12.7   4.7    3.3  2  Fer4_3         4Fe-4S binding domain
       0.55   10.8  15.1       0.93   10.1   2.8    2.9  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
        2.9    8.5  18.6       0.98   10.0   2.6    2.9  4  Fer4_17        4Fe-4S dicluster domain
        4.7    7.5  12.1        9.3    6.6   0.9    3.0  3  Gamma-thionin  Gamma-thionin family
        5.2    7.3  16.6        1.1    9.4   3.9    2.8  2  Fer4_18        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.4   1.2e-38   1.2e-35       3     149 ..     175     316 ..     173     320 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 1.2e-38
                       FrhB_FdhB_C   3 kvavvGtPCqiaalrklqk..kklkekilltiglfCggnfspealrklleelgvdpedvkklefrgkgkfrvelkd. 76 
                                        v+vvGtPC++ ++rklq+  + ++ek++l++glfC++nf++++l+++l e+gvd +++ k ++ +kgkf+++++d 
  gi|488601234|ref|YP_007907705.1| 175 GVGVVGTPCMVSGIRKLQSeiNLFREKVKLICGLFCTENFYHHQLHAYLIEKGVDFSKLIKTDI-TKGKFIATMTDs 250
                                       699****************9999*****************************************.9**********9 PP

                       FrhB_FdhB_C  77 ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveagelel 149
                                       ++++++kel+e+++++C+vC d+ta  +D+svG+v      g +d g stv+vrte+++++le ++e+++ ++
  gi|488601234|ref|YP_007907705.1| 251 VVSFPVKELNEIVPHGCEVCIDFTAVESDFSVGSV------G-SDAGFSTVVVRTETAKSVLEFIKENDYADF 316
                                       99*********************************......9.********************9999998765 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.5   9.5e+03      30      51 ..      62      82 ..      62      83 .. 0.74
   2 !   40.5   0.0   2.3e-13   2.3e-10       4      75 ..      95     163 ..      92     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.5
                       FrhB_FdhB_N 30 eegiidgvivvapskdpwrpkp 51
                                      ee  +d+  +v+    +w ++p
  gi|488601234|ref|YP_007907705.1| 62 EERCVDCSACVRVC-PRWNYEP 82
                                      56789999999987.4677666 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 2.3e-13
                       FrhB_FdhB_N   4 ArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeella..aaGskYtlspnlk 75 
                                       Ars+    r k+q+G ++t+ ++++Le g+id  + v ++ ++wr+k + ++++++l +    G+kY+ +++l 
  gi|488601234|ref|YP_007907705.1|  95 ARSK----RFKGQDGAMATEFMASALEMGLIDRTLFVGRD-EEWRTKVYHIRSVDQLKDtkLTGTKYSFASVLP 163
                                       4444....99******************************.79**************986689*****887765 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   2.7   1.1e-05     0.011       2      23 ..      28      49 ..      27      50 .. 0.88
   2 !   18.0   4.4   1.8e-06    0.0018       5      19 ..      62      76 ..      59      77 .. 0.93
   3 ?    0.2   0.2      0.77   7.6e+02      10      16 ..     266     272 ..     265     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      vi   +C +C +C+ +CPv+ I
  gi|488601234|ref|YP_007907705.1| 28 VIERGLCSHCSTCAAICPVEGI 49
                                      677899************9866 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.8e-06
                                      TTTSSS-THHHHHST CS
                              Fer4  5 eekCigCGaCvevCP 19
                                      ee+C+ C aCv vCP
  gi|488601234|ref|YP_007907705.1| 62 EERCVDCSACVRVCP 76
                                      89************* PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.77
                                       S-THHHH CS
                              Fer4  10 gCGaCve 16 
                                       gC  C++
  gi|488601234|ref|YP_007907705.1| 266 GCEVCID 272
                                       9****87 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7  10.8   1.9e-08   1.9e-05       3      56 .]      28      76 ..      26      76 .. 0.81
   2 !   13.1   3.8   7.8e-05     0.078       7      24 ..      63      85 ..      60     109 .. 0.70
   3 ?   -2.0   0.0       3.9   3.9e+03      39      46 ..     264     271 ..     250     275 .. 0.62

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.9e-08
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk..kvekCtgcgaCveaCP 56
                                      vi++  C +C +C + CP+       +g++s++++++     e+C +c aCv++CP
  gi|488601234|ref|YP_007907705.1| 28 VIERGLCSHCSTCAAICPV-------EGIISGDQEIDFpdWEERCVDCSACVRVCP 76
                                      788999*************.......666666666666214568***********9 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.8e-05
                           Fer4_10  7 dtCirCgkCvkaCPadl.....t 24
                                      ++C+ C +Cv++CP ++     +
  gi|488601234|ref|YP_007907705.1| 63 ERCVDCSACVRVCPRWNyepkcD 85
                                      78999999999999966655540 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.9
                           Fer4_10  39 rkkvekCt 46 
                                        +++e C+
  gi|488601234|ref|YP_007907705.1| 264 PHGCEVCI 271
                                       44455554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   2.2   0.00024      0.24      34      49 ..      32      47 ..      18      50 .. 0.74
   2 !   24.6  11.1   2.1e-08   2.1e-05       2      48 ..      34      77 ..      33      81 .. 0.87
   3 ?   -2.9   0.2       7.9   7.9e+03      38      43 ..     266     271 ..     265     273 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                            Fer4_9 34 eaCigCgaCveaCpkg 49
                                        C +C +C+++Cp +
  gi|488601234|ref|YP_007907705.1| 32 GLCSHCSTCAAICPVE 47
                                      36***********984 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 2.1e-08
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48
                                      C  C +C + Cp + ++  ++e       ++e +C++C aCv +Cp+
  gi|488601234|ref|YP_007907705.1| 34 CSHCSTCAAICPVEGIISGDQEIDFPD--WEE-RCVDCSACVRVCPR 77
                                      **************9998888877775..554.8************8 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.9
                            Fer4_9  38 gCgaCv 43 
                                       gC+ C+
  gi|488601234|ref|YP_007907705.1| 266 GCEVCI 271
                                       566665 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   2.3   8.6e-06    0.0086       3      23 ..      28      49 ..      28      50 .. 0.84
   2 !   18.6   3.3   1.4e-06    0.0014       6      20 ..      62      76 ..      62      81 .. 0.92
   3 ?   -3.0   0.5       9.5   9.4e+03      11      16 ..     266     271 ..     265     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.6e-06
                            Fer4_6  3 eidpdkCigCgdCvrvCP.ega 23
                                      +i + +C +C  C+++CP eg+
  gi|488601234|ref|YP_007907705.1| 28 VIERGLCSHCSTCAAICPvEGI 49
                                      57899*************4466 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.4e-06
                            Fer4_6  6 pdkCigCgdCvrvCP 20
                                      +++C++C +CvrvCP
  gi|488601234|ref|YP_007907705.1| 62 EERCVDCSACVRVCP 76
                                      589************ PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.5
                            Fer4_6  11 gCgdCv 16 
                                       gC+ C+
  gi|488601234|ref|YP_007907705.1| 266 GCEVCI 271
                                       799996 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   0.7   0.00013      0.13       2      26 ..      34      57 ..      33      63 .. 0.78
   2 !   13.4   1.2   0.00012      0.12       1      19 [.      64      82 ..      64     111 .. 0.76
   3 ?    0.0   0.0       1.7   1.7e+03      54      62 ..     263     272 ..     232     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeie 26
                                      C  C  Ca +CP++ i +  ++ei+
  gi|488601234|ref|YP_007907705.1| 34 CSHCSTCAAICPVEGIISG-DQEID 57
                                      9***********9776655.35555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00012
                           Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                      rC++C +C+ vCP    + 
  gi|488601234|ref|YP_007907705.1| 64 RCVDCSACVRVCPRWNYEP 82
                                      6************876555 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.7
                           Fer4_16  54 i.tgCdiCqd 62 
                                       + +gC +C d
  gi|488601234|ref|YP_007907705.1| 263 VpHGCEVCID 272
                                       2489999965 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1  11.8   1.2e-07   0.00012       2      52 ..      28      76 ..      27      80 .. 0.91
   2 ?   -0.6   0.1       1.5   1.5e+03      43      49 ..     266     272 ..     251     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52
                                      +i++  C +C  C+  C+      i++d++  ++  e++Cv C  C+ vCP
  gi|488601234|ref|YP_007907705.1| 28 VIERGLCSHCSTCAAICPV--EGIISGDQEIDFPDWEERCVDCSACVRVCP 76
                                      588899************5..56789999999******************* PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                           Fer4_21  43 GCnlCss 49 
                                       GC++C++
  gi|488601234|ref|YP_007907705.1| 266 GCEVCID 272
                                       8999986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.6    0.0013       1.3      50      63 ..      33      46 ..      20      49 .. 0.80
   2 !   13.5   0.2   7.5e-05     0.075       4      19 ..      64      79 ..      62     140 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                            Fer4_8 50 sCttcgaCtevCpv 63
                                       C++c  C+  Cpv
  gi|488601234|ref|YP_007907705.1| 33 LCSHCSTCAAICPV 46
                                      68888888888886 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.5e-05
                            Fer4_8  4 kCieCgaCqsaCpvlr 19
                                      +C+ C+aC   Cp ++
  gi|488601234|ref|YP_007907705.1| 64 RCVDCSACVRVCPRWN 79
                                      7888888888888333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   2.4   0.00016      0.16       4      21 ..      28      45 ..      25      46 .. 0.87
   2 !   17.5   3.4     3e-06     0.003       7      21 ..      62      76 ..      58      77 .. 0.93
   3 ?   -1.2   0.1       2.7   2.7e+03      12      18 ..     266     272 ..     266     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v+++  C +C++C   CP
  gi|488601234|ref|YP_007907705.1| 28 VIERGLCSHCSTCAAICP 45
                                      678889*******999** PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3e-06
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                      ++rC+ C+aCv +CP
  gi|488601234|ref|YP_007907705.1| 62 EERCVDCSACVRVCP 76
                                      68************* PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.7
                            Fer4_2  12 gCgaCvs 18 
                                       gC+ C++
  gi|488601234|ref|YP_007907705.1| 266 GCEVCID 272
                                       7999975 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.4   0.00011      0.11       4      16 ..      34      46 ..      25      51 .. 0.89
   2 !   14.7   5.3   3.3e-05     0.033       2      15 ..      63      76 ..      62      88 .. 0.93
   3 ?    1.5   0.2      0.57   5.7e+02       6      13 ..     266     273 ..     265     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C +C  C a+CP+
  gi|488601234|ref|YP_007907705.1| 34 CSHCSTCAAICPV 46
                                      ************7 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.3e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      erC++C +Cv++CP
  gi|488601234|ref|YP_007907705.1| 63 ERCVDCSACVRVCP 76
                                      8************* PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.57
                            Fer4_4   6 gCgsCvaa 13 
                                       gC +C+++
  gi|488601234|ref|YP_007907705.1| 266 GCEVCIDF 273
                                       8****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 !   12.0   2.8   0.00025      0.25      32      50 ..      28      46 ..       8      48 .. 0.77
   2 !   15.5  15.8   1.9e-05     0.019       2      49 ..      34      76 ..      33      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                            Fer4_7 32 eidpekClgCgaCvavCPt 50
                                      +i+   C++C  C+a CP+
  gi|488601234|ref|YP_007907705.1| 28 VIERGLCSHCSTCAAICPV 46
                                      5667789999999999998 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.9e-05
                            Fer4_7  2 CigCgaCvaaCp.vkaieldeeenekgtekveidpekClgCgaCvavCP 49
                                      C +C  C+a Cp  + i+ d+e     ++++   +e+C++C aCv+vCP
  gi|488601234|ref|YP_007907705.1| 34 CSHCSTCAAICPvEGIISGDQEI---DFPDW---EERCVDCSACVRVCP 76
                                      ************55566666653...23444...59************* PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.1     0.049        49       2      13 ..      34      45 ..      24      51 .. 0.84
   2 ?   12.5   0.2   0.00021      0.21       1      50 [.      64     116 ..      64     149 .. 0.78
   3 ?   -2.3   0.0       8.5   8.4e+03      75      91 ..     257     273 ..     239     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.049
                           Fer4_22  2 ClsCgaCtlvCp 13
                                      C +C++C+++Cp
  gi|488601234|ref|YP_007907705.1| 34 CSHCSTCAAICP 45
                                      888888888888 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00021
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedet...keeskegervrvwdsClleeftkvag 50 
                                       rC++C+aC  vCp        d     + ++++++r++ +d  + +ef + a 
  gi|488601234|ref|YP_007907705.1|  64 RCVDCSACVRVCPRWNYEPKCDIGeyiELTAARSKRFKGQDGAMATEFMASAL 116
                                       7************8765544444444467788999999999999999987765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.5
                           Fer4_22  75 ekfgesgCvGCgRCiea 91 
                                       ++ +e +  GC  Ci+ 
  gi|488601234|ref|YP_007907705.1| 257 KELNEIVPHGCEVCIDF 273
                                       45566777789888875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.3   0.00087      0.86       1      13 [.      34      46 ..      34      49 .. 0.90
   2 ?   12.7   4.7    0.0002       0.2       1      12 [.      65      76 ..      65      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00087
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C +C++C   CPv
  gi|488601234|ref|YP_007907705.1| 34 CSHCSTCAAICPV 46
                                      9***********7 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0002
                            Fer4_3  1 CtgCgaCvevCP 12
                                      C+ C+aCv+vCP
  gi|488601234|ref|YP_007907705.1| 65 CVDCSACVRVCP 76
                                      999********* 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 ?    6.8   2.9      0.01        10       1      17 [.      29      45 ..      29      46 .. 0.92
   2 ?   10.1   2.8   0.00093      0.93       3      18 ..      62      77 ..      60      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.01
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      ++r  C+ c +C++++P
  gi|488601234|ref|YP_007907705.1| 29 IERGLCSHCSTCAAICP 45
                                      67889***********9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00093
                           Fer4_13  3 rdtCiacgaCvelaPd 18
                                      +++C++c aCv ++P 
  gi|488601234|ref|YP_007907705.1| 62 EERCVDCSACVRVCPR 77
                                      489************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 ?    7.4   3.2    0.0065       6.5      44      57 ..      32      45 ..      11      48 .. 0.78
   2 ?    7.1   3.1    0.0082       8.2       2      15 ..      34      47 ..      33      58 .. 0.70
   3 ?   10.0   2.6   0.00098      0.98      44      57 ..      63      76 ..      49      78 .. 0.79
   4 ?    7.5   4.3     0.006         6       1      14 [.      64      77 ..      64     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0065
                           Fer4_17 44 slCieCgeCerkCP 57
                                      +lC++C  C++ CP
  gi|488601234|ref|YP_007907705.1| 32 GLCSHCSTCAAICP 45
                                      57888888888887 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0082
                           Fer4_17  2 CiqCgyClpeCpsy 15
                                      C++C+ C++ Cp  
  gi|488601234|ref|YP_007907705.1| 34 CSHCSTCAAICPVE 47
                                      77777777777764 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00098
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++C+ C  C+r+CP
  gi|488601234|ref|YP_007907705.1| 63 ERCVDCSACVRVCP 76
                                      68999999999998 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.006
                           Fer4_17  1 rCiqCgyClpeCps 14
                                      rC  C++C+++Cp+
  gi|488601234|ref|YP_007907705.1| 64 RCVDCSACVRVCPR 77
                                      46666666666665 PP

>> Gamma-thionin  Gamma-thionin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.9    0.0093       9.3      12      32 ..      32      52 ..      31      56 .. 0.91
   2 ?    5.3   3.0     0.024        24      10      29 ..      61      80 ..      59      86 .. 0.89
   3 ?   -1.3   0.0       2.7   2.7e+03       4      12 ..      94     102 ..      91     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0093
                                      S---THHHHHHHHHHTTSSEE CS
                     Gamma-thionin 12 gpClsdsnCasvCknegfsdG 32
                                      g+C   s Ca +C  eg  +G
  gi|488601234|ref|YP_007907705.1| 32 GLCSHCSTCAAICPVEGIISG 52
                                      99**************99888 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.024
                                      --S---THHHHHHHHHHTTS CS
                     Gamma-thionin 10 fkgpClsdsnCasvCknegf 29
                                      ++ +C+  s C +vC ++++
  gi|488601234|ref|YP_007907705.1| 61 WEERCVDCSACVRVCPRWNY 80
                                      8999***********99986 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.7
                                       EEE-SS--S CS
                     Gamma-thionin   4 eskSerfkg 12 
                                        ++S+rfkg
  gi|488601234|ref|YP_007907705.1|  94 AARSKRFKG 102
                                       689*****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 ?    5.9   1.8     0.015        15      55      74 ..      28      47 ..      17      58 .. 0.82
   2 ?    9.4   3.9    0.0011       1.1      58      72 ..      62      76 ..      48      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                        + g c +c++c ++cP++
  gi|488601234|ref|YP_007907705.1| 28 VIERGLCSHCSTCAAICPVE 47
                                      556789************86 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                           Fer4_18 58 agdcidcescvkvcP 72
                                      +  c+dc++cv+vcP
  gi|488601234|ref|YP_007907705.1| 62 EERCVDCSACVRVCP 76
                                      567************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2248.04
//
Query:       gi|488601235|ref|YP_007907706.1|  [L=241]
Description: Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   81.6  34.6    1.6e-08   34.0   3.0    4.3  4  Fer4             4Fe-4S binding domain
      1e-20   74.1  26.6    1.1e-11   45.2  10.3    2.9  3  Fer4_7           4Fe-4S dicluster domain
    7.3e-19   67.0  32.4      2e-07   30.8   1.8    4.3  4  Fer4_6           4Fe-4S binding domain
    8.3e-19   67.5  24.8    4.3e-10   39.6  10.2    2.4  2  Fer4_9           4Fe-4S dicluster domain
    8.8e-16   57.8  29.7    9.3e-09   35.3  13.1    2.7  3  Fer4_21          4Fe-4S dicluster domain
    9.1e-16   57.7  52.0    9.1e-07   28.9  15.3    3.6  4  Fer4_10          4Fe-4S dicluster domain
    6.7e-15   55.8  26.1     0.0013   19.6   0.7    4.3  4  Fer4_16          4Fe-4S double cluster binding domain
    1.3e-12   47.0  36.2    2.1e-05   24.3   2.4    4.3  4  Fer4_2           4Fe-4S binding domain
      3e-10   40.4  25.0    2.4e-05   24.7   5.8    3.6  3  Fer4_8           4Fe-4S dicluster domain
    3.1e-08   34.0  26.0       0.11   13.1   0.2    4.2  5  Fer4_17          4Fe-4S dicluster domain
    1.4e-05   25.2  37.4      0.028   14.9   4.8    4.5  4  Fer4_4           4Fe-4S binding domain
    7.8e-05   23.3  25.9     0.0033   18.1   2.6    4.7  4  Fer4_15          4Fe-4S single cluster domain
    7.9e-05   23.1  29.5      0.037   14.6   3.4    4.5  4  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
     0.0016   19.2  38.9       0.38   11.8   3.8    4.3  4  Fer4_3           4Fe-4S binding domain
     0.0053   17.6  29.1      0.063   14.1   2.8    4.2  4  Fer4_22          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   15.2   0.2      0.015   15.2   0.2    3.5  4  Enterotoxin_HS1  Heat stable E.coli enterotoxin 1
       0.02   15.1  30.1        1.3    9.3   3.2    4.1  3  Fer4_18          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.3   1.3e-06    0.0014       4      24 .]      57      77 ..      54      77 .. 0.92
   2 !   28.7   1.7   6.9e-10   7.3e-07       2      24 .]      89     111 ..      88     111 .. 0.93
   3 !   18.2   6.1   1.5e-06    0.0016       4      24 .]     184     204 ..     182     204 .. 0.94
   4 !   34.0   3.0   1.5e-11   1.6e-08       2      23 ..     215     236 ..     214     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                                      ETTTSSS-THHHHHSTTTEEE CS
                              Fer4  4 deekCigCGaCvevCPvgAIt 24
                                       +e Ci C +C  +CP +AIt
  gi|488601235|ref|YP_007907706.1| 57 QPENCISCFRCSFICPANAIT 77
                                      69******************7 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 6.9e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        id+ kCi+C  Cv+ CP +A++
  gi|488601235|ref|YP_007907706.1|  89 SIDYAKCIFCHFCVDSCPGNALK 111
                                       69*******************85 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.5e-06
                                       ETTTSSS-THHHHHSTTTEEE CS
                              Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                       d+  C +C +Cv+ CP +AI+
  gi|488601235|ref|YP_007907706.1| 184 DPKSCLACRICVNSCPSEAIE 204
                                       999*****************6 PP

  == domain 4  score: 34.0 bits;  conditional E-value: 1.5e-11
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                        id++kC+gCG+Cv+ CPv  +
  gi|488601235|ref|YP_007907706.1| 215 RIDKDKCTGCGICVKECPVQIL 236
                                       69*****************876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   8.3   3.8e-11     4e-08       2      52 .]      61     109 ..      60     109 .. 0.91
   2 !   18.6   2.3     2e-06    0.0021       1      25 [.      94     118 ..      94     144 .. 0.71
   3 !   45.2  10.3     1e-14   1.1e-11       1      52 []     187     235 ..     187     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.8e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       Ci C +C   Cp++ai+++ ++n++   ++ id+ kC++C+ Cv+ CP +a
  gi|488601235|ref|YP_007907706.1|  61 CISCFRCSFICPANAITMELAKNNRY--YPSIDYAKCIFCHFCVDSCPGNA 109
                                       ******************98876655..8899****************876 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeene 25 
                                       +Ci C++Cv+ Cp +a++ ++ ++ 
  gi|488601235|ref|YP_007907706.1|  94 KCIFCHFCVDSCPGNALKPTKIHDV 118
                                       7****************98864332 PP

  == domain 3  score: 45.2 bits;  conditional E-value: 1e-14
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C  C+ Cv+ Cp++aie++ee   +g+++++id +kC+gCg Cv++CP+++
  gi|488601235|ref|YP_007907706.1| 187 SCLACRICVNSCPSEAIEVKEE---EGKRTLRIDKDKCTGCGICVKECPVQI 235
                                       5******************998...57788*******************985 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   2.1   5.6e-09   5.9e-06       3      24 .]      55      76 ..      53      76 .. 0.94
   2 !   11.1   2.2   0.00031      0.33       2      24 .]      88     110 ..      87     110 .. 0.91
   3 !   16.6   3.7   5.5e-06    0.0058       5      24 .]     184     203 ..     183     203 .. 0.95
   4 !   30.8   1.8   1.9e-10     2e-07       3      24 .]     215     236 ..     213     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.6e-09
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                       ++p++Ci+C +C  +CP++ai
  gi|488601235|ref|YP_007907706.1| 55 LFQPENCISCFRCSFICPANAI 76
                                      69*******************8 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00031
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + id+ kCi C  Cv+ CP +a+
  gi|488601235|ref|YP_007907706.1|  88 PSIDYAKCIFCHFCVDSCPGNAL 110
                                       679****************7775 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 5.5e-06
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       dp +C+ C+ Cv+ CP  ai
  gi|488601235|ref|YP_007907706.1| 184 DPKSCLACRICVNSCPSEAI 203
                                       899*************9998 PP

  == domain 4  score: 30.8 bits;  conditional E-value: 1.9e-10
                            Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                       +id+dkC+gCg Cv+ CP +++
  gi|488601235|ref|YP_007907706.1| 215 RIDKDKCTGCGICVKECPVQIL 236
                                       79*****************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 !   33.8   6.6   2.7e-11   2.8e-08       1      50 [.      60     109 ..      60     110 .. 0.95
   2 !   39.6  10.2   4.1e-13   4.3e-10       2      50 ..     188     235 ..     187     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.7e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +C++C +C   Cpa++++++ a++ + +   ++ +Ci+C+ Cv+ Cp +a
  gi|488601235|ref|YP_007907706.1|  60 NCISCFRCSFICPANAITMELAKNNRYYPSIDYAKCIFCHFCVDSCPGNA 109
                                       6***************************99999**************876 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 4.1e-13
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C  C+ Cv++Cp+++++ ++ e+k+ lr++++ +C+gCg Cv+ Cp ++
  gi|488601235|ref|YP_007907706.1| 188 CLACRICVNSCPSEAIEVKEEEGKRTLRIDKD-KCTGCGICVKECPVQI 235
                                       ***************************99998.9************984 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   8.3   1.7e-09   1.8e-06       4      52 ..      57     106 ..      54     112 .. 0.83
   2 !   14.5   1.4   2.7e-05     0.029       2      28 ..      89     115 ..      88     132 .. 0.75
   3 !   35.3  13.1   8.8e-12   9.3e-09       4      55 ..     184     234 ..     182     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.7e-09
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCP 52 
                                       ++++Ci+C +C   C+ ++++    +++++++ +   +C+ C+ C++ CP
  gi|488601235|ref|YP_007907706.1|  57 QPENCISCFRCSFICPANAITMELAKNNRYYPSIdYAKCIFCHFCVDSCP 106
                                       689*************877766667788888887369************* PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.7e-05
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaiei 28 
                                        id +kCi C  C+ +C+ ++ +  +i
  gi|488601235|ref|YP_007907706.1|  89 SIDYAKCIFCHFCVDSCPGNALKPTKI 115
                                       59999************9888765544 PP

  == domain 3  score: 35.3 bits;  conditional E-value: 8.8e-12
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55 
                                       d+++C+ C  C+ +C+ ++++  e ++k++l++ +d+C+GC +C++ CPv +
  gi|488601235|ref|YP_007907706.1| 184 DPKSCLACRICVNSCPSEAIEVKEEEGKRTLRIDKDKCTGCGICVKECPV-Q 234
                                       6789************877777788889999******************9.4 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   9.3   2.1e-09   2.2e-06       3      56 .]      55     106 ..      53     106 .. 0.92
   2 !   17.7   1.0   2.8e-06     0.003       3      24 ..      89     116 ..      87     139 .. 0.68
   3 !   28.9  15.3   8.6e-10   9.1e-07       4      56 .]     183     232 ..     181     232 .. 0.93
   4 !   21.5   3.4   1.7e-07   0.00018       3      21 ..     215     233 ..     213     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.1e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        ++++ Ci C +C   CPa  ++   + ++++    ++++ kC++c  Cv++CP
  gi|488601235|ref|YP_007907706.1|  55 LFQPENCISCFRCSFICPA--NAITMELAKNNRYYPSIDYAKCIFCHFCVDSCP 106
                                       57899**************..88888899999999999***************9 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.8e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPadl......t 24 
                                        id  +Ci C  Cv++CP ++      +
  gi|488601235|ref|YP_007907706.1|  89 SIDYAKCIFCHFCVDSCPGNAlkptkiH 116
                                       68999*************9666666431 PP

  == domain 3  score: 28.9 bits;  conditional E-value: 8.6e-10
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d+++C+ C+ Cv++CP+   +    +e++++ + r++ +kCtgcg Cv++CP
  gi|488601235|ref|YP_007907706.1| 183 KDPKSCLACRICVNSCPS---EAIEVKEEEGKRTLRIDKDKCTGCGICVKECP 232
                                       589***************...8888889999999999***************9 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 1.7e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPa 21 
                                       +id+d+C++Cg Cvk CP+
  gi|488601235|ref|YP_007907706.1| 215 RIDKDKCTGCGICVKECPV 233
                                       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 !   19.6   0.7   1.2e-06    0.0013       1      22 [.      60      81 ..      60      93 .. 0.81
   2 !   18.8   0.3   2.2e-06    0.0023       1      40 [.      94     133 ..      94     151 .. 0.70
   3 !   17.3   2.1   6.7e-06    0.0071       2      22 ..     188     208 ..     187     219 .. 0.83
   4 !   14.3   3.3   5.5e-05     0.058       1      19 [.     220     238 ..     220     241 .] 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                                      +C++C +C  +CP+nai+++ +
  gi|488601235|ref|YP_007907706.1| 60 NCISCFRCSFICPANAITMELA 81
                                      6*****************9833 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.2e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkd 40 
                                       +C+ C+ C+++CP na+k +k   + +++ ++ +++ ++ 
  gi|488601235|ref|YP_007907706.1|  94 KCIFCHFCVDSCPGNALKPTKIHDVVYKDMEEMTVKAEEM 133
                                       5*****************9977777766655553333333 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 6.7e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                       C  C+ C+++CP++ai+ k+e
  gi|488601235|ref|YP_007907706.1| 188 CLACRICVNSCPSEAIEVKEE 208
                                       99***************9944 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 5.5e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                       +C++Cg C++ CP++ ++ 
  gi|488601235|ref|YP_007907706.1| 220 KCTGCGICVKECPVQILEL 238
                                       5999999999999999875 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.0   1.6e-05     0.017       3      22 .]      54      73 ..      52      73 .. 0.88
   2 !   12.5   2.4   0.00012      0.13       2      21 ..      87     106 ..      86     106 .. 0.93
   3 !   12.1   8.0   0.00016      0.17       6      21 ..     184     199 ..     182     200 .. 0.92
   4 !   24.3   2.4     2e-08   2.1e-05       5      21 ..     216     232 ..     212     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      + + +++Ci+C  C   CPa
  gi|488601235|ref|YP_007907706.1| 54 ILFQPENCISCFRCSFICPA 73
                                      667799*************8 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++ +d ++Ci C  Cv++CP
  gi|488601235|ref|YP_007907706.1|  87 YPSIDYAKCIFCHFCVDSCP 106
                                       6789***************9 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00016
                            Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                       d+ +C++C++Cv++CP
  gi|488601235|ref|YP_007907706.1| 184 DPKSCLACRICVNSCP 199
                                       8999************ PP

  == domain 4  score: 24.3 bits;  conditional E-value: 2e-08
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       +d d+C+gCg+Cv+ CP
  gi|488601235|ref|YP_007907706.1| 216 IDKDKCTGCGICVKECP 232
                                       89*************** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   1.0   0.00013      0.14       3      19 ..      59      75 ..      57      90 .. 0.73
   2 !   24.7   5.8   2.2e-08   2.4e-05       3      63 ..      93     200 ..      91     203 .. 0.79
   3 !   13.0  13.4   9.8e-05       0.1       4      65 .]     187     235 ..     185     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                            Fer4_8  3 ekCieCgaCqsaCpvlr 19
                                      e+Ci C++C   Cp+  
  gi|488601235|ref|YP_007907706.1| 59 ENCISCFRCSFICPANA 75
                                      68***********9544 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.2e-08
                            Fer4_8   3 ekCieCgaCqsaCp............vlrrtkkhlldargeaae............dvqeeqvlee........... 44 
                                        kCi C +C ++Cp            v++++ ++  +a+++++e            +                    
  gi|488601235|ref|YP_007907706.1|  93 AKCIFCHFCVDSCPgnalkptkihdvVYKDMEEMTVKAEEMVKEpkivredeftveY--------Vfeddiemvkvk 161
                                       69***********99988888888888888888888888888888766555555552........044555555777 PP

                            Fer4_8  45 ....................eealwsCttcgaCtevCpv 63 
                                                            +  +sC++c+ C++ Cp 
  gi|488601235|ref|YP_007907706.1| 162 grdylvpeirpfekireyssCKDPKSCLACRICVNSCPS 200
                                       888888899999999998888899**************7 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 9.8e-05
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       +C  C  C ++Cp+   + k+    +g+++    + ++       ++Ct+cg C+++Cpv+i
  gi|488601235|ref|YP_007907706.1| 187 SCLACRICVNSCPSEAIEVKEE---EGKRTL---RIDK-------DKCTGCGICVKECPVQI 235
                                       7************766665543...344333...2334.......67************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 !   10.9   0.2    0.0005      0.53      44      59 ..      59      74 ..      36      76 .. 0.86
   2 !   13.1   0.2    0.0001      0.11       1      28 [.      94     121 ..      94     143 .. 0.75
   3 !    9.3   4.3    0.0016       1.7      41      59 ..     183     201 ..     162     203 .. 0.75
   4 !   10.7   2.4   0.00059      0.62       2      17 ..     188     203 ..     187     218 .. 0.69
   5 !   12.0   3.5   0.00023      0.24       1      14 [.     220     233 ..     220     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++Ci+C +C+  CP++
  gi|488601235|ref|YP_007907706.1| 59 ENCISCFRCSFICPAN 74
                                      78************86 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0001
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllra 28 
                                       +Ci C +C+++Cp ++  +++ + ++++
  gi|488601235|ref|YP_007907706.1|  94 KCIFCHFCVDSCPGNALKPTKIHDVVYK 121
                                       6************999988887777776 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0016
                           Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                       +  ++C+ C+ C+ +CP++
  gi|488601235|ref|YP_007907706.1| 183 KDPKSCLACRICVNSCPSE 201
                                       4668899999999999975 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00059
                           Fer4_17   2 CiqCgyClpeCpsyea 17 
                                       C  C+ C+++Cps ++
  gi|488601235|ref|YP_007907706.1| 188 CLACRICVNSCPSEAI 203
                                       8889999999988666 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00023
                           Fer4_17   1 rCiqCgyClpeCps 14 
                                       +C++Cg C++eCp 
  gi|488601235|ref|YP_007907706.1| 220 KCTGCGICVKECPV 233
                                       58888888888886 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.4     0.088        93       1      16 [.      58      73 ..      58      77 .. 0.88
   2 !   11.9   0.9   0.00024      0.25       3      15 ..      94     106 ..      92     121 .. 0.89
   3 !   14.2   3.7   4.4e-05     0.047       1      16 [.     185     200 ..     185     202 .. 0.91
   4 !   14.9   4.8   2.6e-05     0.028       1      17 []     218     234 ..     218     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.088
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+Ci C +C  +CP 
  gi|488601235|ref|YP_007907706.1| 58 PENCISCFRCSFICPA 73
                                      699****999999996 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00024
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       +Ci C  Cv++CP
  gi|488601235|ref|YP_007907706.1|  94 KCIFCHFCVDSCP 106
                                       8999********* PP

  == domain 3  score: 14.2 bits;  conditional E-value: 4.4e-05
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +++C+ C+ Cv++CP+
  gi|488601235|ref|YP_007907706.1| 185 PKSCLACRICVNSCPS 200
                                       589************7 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 2.6e-05
                            Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                       +++C+gCg Cv  CP++
  gi|488601235|ref|YP_007907706.1| 218 KDKCTGCGICVKECPVQ 234
                                       69*************85 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.6     0.021        22       5      19 ..      58      72 ..      54      79 .. 0.83
   2 !   10.5   1.2   0.00078      0.82       3      46 ..      90     130 ..      89     156 .. 0.71
   3 ?    4.1   1.1     0.075        79       5      30 ..     185     212 ..     184     216 .. 0.59
   4 !   18.1   2.6   3.1e-06    0.0033       2      19 ..     215     232 ..     214     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                           Fer4_15  5 rdaCigcglCvaeap 19
                                       ++Ci+c++C   +p
  gi|488601235|ref|YP_007907706.1| 58 PENCISCFRCSFICP 72
                                      589*******98887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00078
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpd 46 
                                       +D  +Ci c  Cv+ +p    l+   +++v+ +d e  e +v+ 
  gi|488601235|ref|YP_007907706.1|  90 IDYAKCIFCHFCVDSCPGN-ALKPTKIHDVVYKDME--EMTVKA 130
                                       89**************854.3444455555544333..344444 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.075
                           Fer4_15   5 rdaCigcglCvaea..pevfeldedgla 30 
                                        + C  c  Cv  +  + + +++e+g+ 
  gi|488601235|ref|YP_007907706.1| 185 PKSCLACRICVNSCpsEAIEVKEEEGKR 212
                                       5678888888888853334444445665 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 3.1e-06
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       ++D+d+C+gcg Cv+e+p
  gi|488601235|ref|YP_007907706.1| 215 RIDKDKCTGCGICVKECP 232
                                       69***************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 ?    6.1   2.5     0.016        17       4      18 ..      59      73 ..      57      74 .. 0.91
   2 !    8.7   0.6    0.0024       2.6       1      17 [.      90     106 ..      90     126 .. 0.95
   3 !    9.7   1.6    0.0012       1.3       2      18 ..     184     200 ..     184     210 .. 0.91
   4 !   14.6   3.4   3.5e-05     0.037       1      17 [.     216     232 ..     216     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      ++Ci+c  C  ++P 
  gi|488601235|ref|YP_007907706.1| 59 ENCISCFRCSFICPA 73
                                      79************6 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0024
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D  +Ci c+ Cv+ +P
  gi|488601235|ref|YP_007907706.1|  90 IDYAKCIFCHFCVDSCP 106
                                       7889************9 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0012
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D ++C ac +Cv+ +P 
  gi|488601235|ref|YP_007907706.1| 184 DPKSCLACRICVNSCPS 200
                                       6789***********95 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.5e-05
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D+d+C++cg+Cv+ +P
  gi|488601235|ref|YP_007907706.1| 216 IDKDKCTGCGICVKECP 232
                                       8***************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 ?    6.9   2.5     0.013        14       1      15 []      61      75 ..      61      75 .. 0.95
   2 !   11.8   3.8   0.00036      0.38       1      15 []      95     109 ..      95     109 .. 0.96
   3 !    7.7   4.2    0.0071       7.5       1      15 []     188     202 ..     188     202 .. 0.90
   4 !   11.3   4.9   0.00052      0.55       1      13 [.     221     233 ..     221     235 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C +C   CP +A
  gi|488601235|ref|YP_007907706.1| 61 CISCFRCSFICPANA 75
                                      ************987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00036
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C  Cv++CP +A
  gi|488601235|ref|YP_007907706.1|  95 CIFCHFCVDSCPGNA 109
                                       ****99*******98 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0071
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C+ Cv++CP+ A
  gi|488601235|ref|YP_007907706.1| 188 CLACRICVNSCPSEA 202
                                       999*99******876 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00052
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       CtgCg Cv+ CPv
  gi|488601235|ref|YP_007907706.1| 221 CTGCGICVKECPV 233
                                       ************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 ?    6.3   2.7     0.016        17       1      14 [.      60      73 ..      60      79 .. 0.84
   2 ?    6.3   0.5     0.016        17      68      94 ..      81     107 ..      73     109 .. 0.83
   3 ?    2.4  10.3      0.27   2.8e+02       1      95 [.      94     201 ..      94     203 .. 0.61
   4 !   14.1   2.8     6e-05     0.063      76      96 .]     215     235 ..     202     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C+sC +C+++Cp+
  gi|488601235|ref|YP_007907706.1| 60 NCISCFRCSFICPA 73
                                      59999999999996 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                           Fer4_22  68 hklsefkekfgesgCvGCgRCieacpv 94 
                                        k + +  +++  +C+ C  C+++cp 
  gi|488601235|ref|YP_007907706.1|  81 AKNNRYYPSIDYAKCIFCHFCVDSCPG 107
                                       56777888899999**********996 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.27
                           Fer4_22   1 rClsCgaCtlvCptCs..Cfdvedet.....keeskegervrvwdsClleeftkvagge......nvrkekkerlrq 64 
                                       +C+ C  C   Cp      ++++d++     + + k+ e v+  +    +eft     e      +v+ +     + 
  gi|488601235|ref|YP_007907706.1|  94 KCIFCHFCVDSCPGNAlkPTKIHDVVykdmeEMTVKAEEMVKEPKIVREDEFTVEYVFEddiemvKVKGRDYLVPEI 170
                                       69999999999997541146666766776653333444444544555555555544444111000333333334455 PP

                           Fer4_22  65 rllhklsefkekfgesgCvGCgRCieacpvk 95 
                                       r ++k++e+ +  + ++C  C  C+++cp++
  gi|488601235|ref|YP_007907706.1| 171 RPFEKIREYSSCKDPKSCLACRICVNSCPSE 201
                                       6678888888889***************975 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 6e-05
                           Fer4_22  76 kfgesgCvGCgRCieacpvki 96 
                                       ++++ +C+GCg C++ cpv+i
  gi|488601235|ref|YP_007907706.1| 215 RIDKDKCTGCGICVKECPVQI 235
                                       67999*************997 PP

>> Enterotoxin_HS1  Heat stable E.coli enterotoxin 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.3         2   2.1e+03      12      22 ..      61      71 ..      58      74 .. 0.79
   2 ?   15.2   0.2   1.4e-05     0.015       8      33 ..      88     113 ..      85     115 .. 0.90
   3 ?    0.2   4.0      0.74   7.8e+02      11      24 ..     187     200 ..     177     202 .. 0.80
   4 ?   -3.0   1.1       7.2   7.6e+03      12      22 ..     221     231 ..     219     232 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2
                   Enterotoxin_HS1 12 yASCIWCvTAC 22
                                      + SC  C   C
  gi|488601235|ref|YP_007907706.1| 61 CISCFRCSFIC 71
                                      88999998777 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                   Enterotoxin_HS1   8 PASSyASCIWCvTACaSshGRTTKPS 33 
                                       P   yA CI C     S++G   KP 
  gi|488601235|ref|YP_007907706.1|  88 PSIDYAKCIFCHFCVDSCPGNALKPT 113
                                       6667********************96 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.74
                   Enterotoxin_HS1  11 SyASCIWCvTACaS 24 
                                       S+  C  Cv  C S
  gi|488601235|ref|YP_007907706.1| 187 SCLACRICVNSCPS 200
                                       78888889999977 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 7.2
                   Enterotoxin_HS1  12 yASCIWCvTAC 22 
                                       +  C  Cv  C
  gi|488601235|ref|YP_007907706.1| 221 CTGCGICVKEC 231
                                       55566666555 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   9.1     0.038        40      59      95 ..      59     105 ..      54     107 .. 0.67
   2 ?    9.0   3.0    0.0014       1.5      49      74 ..     176     201 ..     157     209 .. 0.80
   3 ?    9.3   3.2    0.0012       1.3      55      75 ..     215     235 ..     201     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.038
                           Fer4_18  59 gdcidcescvkvcPtg...idirkGlql.......eciscllcidac 95 
                                        +ci+c  c  +cP +   +++ k  ++       +ci c  c+d+c
  gi|488601235|ref|YP_007907706.1|  59 ENCISCFRCSFICPANaitMELAKNNRYypsidyaKCIFCHFCVDSC 105
                                       57999999999999752224555544322222334799999999999 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                           Fer4_18  49 ekeerkekgagdcidcescvkvcPtg 74 
                                        +e  + k+   c++c+ cv+ cP +
  gi|488601235|ref|YP_007907706.1| 176 IREYSSCKDPKSCLACRICVNSCPSE 201
                                       556667778889************74 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0012
                           Fer4_18  55 ekgagdcidcescvkvcPtgi 75 
                                       + ++ +c+ c+ cvk cP++i
  gi|488601235|ref|YP_007907706.1| 215 RIDKDKCTGCGICVKECPVQI 235
                                       446789************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); 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:                        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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1454.80
//
Query:       gi|488601236|ref|YP_007907707.1|  [L=359]
Description: NADH dehydrogenase subunit H [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-82  275.3  29.2    8.2e-82  274.9  29.2    1.1  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 !  274.9  29.2   4.6e-86   8.2e-82       8     297 ..      54     352 ..      46     354 .. 0.94

  Alignments for each domain:
  == domain 1  score: 274.9 bits;  conditional E-value: 4.6e-86
                                       HHHHHHHHHHHHHHHHHHHHHTTS--S-SST.TT.TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCT CS
                            NADHdh   8 vvlllvvalltlleRkvlAriqdRlGPnrvG.pl.GllqplaDalKlllKediipkkadkllfllapvlalilalla 82 
                                       v+ll+v+++++++eRk++Ariq+R GP ++  p+ G++qplaD+++++++e i++++a++ +fl  p+l++i++ll 
  gi|488601236|ref|YP_007907707.1|  54 VTLLIVLLFIIWFERKLTARIQWRRGPLEIArPVgGIIQPLADGMRYFFQEVIVHRDAHRPYFLQFPILIFIPVLLP 130
                                       34566666*********************985446****************************************** PP

                                       TTTS-SSS.SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS- CS
                            NADHdh  83 faviPfge.vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagsls 158
                                       +++iP g+ v ++  ++l +++a++sl +++++  Gwasns++a++G++R+a ++ +yEv++++s+++++l++g+ +
  gi|488601236|ref|YP_007907707.1| 131 LVMIPAGTiVGIKTPYALPIAVAIISLIPVFVVAIGWASNSRFAYIGTVREAFMYFAYEVPFIISVISMILIYGTAD 207
                                       ******9656677788************************************************************* PP

                                       HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh 159 lseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsala 235
                                       l eiv++q+ i  i+l+++a+++f+ia+++ t+r PF++pea++E++ G+++EYsg+ f+l++   y +m+++++l+
  gi|488601236|ref|YP_007907707.1| 208 LIEIVNKQA-IPGIILNPVAAFVFFIAMVMATSRLPFEIPEADQEIAFGPFVEYSGIMFGLVMTIAYEKMYVMALLF 283
                                       ********7.5559999************************************************************ PP

                                       HHHCT.SS-HCCS.......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                            NADHdh 236 vllFlgGwllpfs.......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                       ++lFlgG ++  +       +++w+++K++++++ + ++r++++R+R+dq++k++w++++ l+l++ll+
  gi|488601236|ref|YP_007907707.1| 284 SVLFLGGGNGFNIailgdlsPTVWLFIKTMVIMVALSFLRSIYARIRLDQALKFSWSMMMKLSLLSLLI 352
                                       *******9875447889999**********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2073.06
//
Query:       gi|488601237|ref|YP_007907708.1|  [L=413]
Description: NADH dehydrogenase subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-87  291.9   0.0    5.3e-87  291.4   0.0    1.1  1  Complex1_49kDa   Respiratory-chain NADH dehydrogenase, 49 Kd 
     0.0052   16.3   0.1     0.0079   15.8   0.1    1.2  1  Nitrate_red_gam  Nitrate reductase gamma subunit
  ------ inclusion threshold ------
       0.01   14.7   0.0      0.034   13.0   0.0    1.8  2  NiFeSe_Hases     Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.4   0.0   8.8e-91   5.3e-87       2     271 .]     147     413 .]     147     413 .] 0.96

  Alignments for each domain:
  == domain 1  score: 291.4 bits;  conditional E-value: 8.8e-91
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkk 78 
                                       lG++t f++ f+ Re i+++l++++G+R+tasyi++GGv+rD++ ++le i++++  +e++l+++e++++kn+++++
  gi|488601237|ref|YP_007907708.1| 147 LGHTTGFMWPFALREPIIEALTKISGTRITASYIIPGGVRRDVDLRTLEFIRKVTFVIERRLKSFERIFIKNPTVIT 223
                                       69*************************************************************************** PP

                                       HHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  79 RtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                       R+++vg+lskeea+++g++Gp+lRasGv+yD+R +epYeaYd+++fd+pv++egD+y+R+lvrveE+ qS++Ii+qa
  gi|488601237|ref|YP_007907708.1| 224 RLRDVGILSKEEAIKYGVVGPFLRASGVEYDVRVVEPYEAYDSVNFDIPVADEGDSYSRFLVRVEEISQSFSIIRQA 300
                                       ***************************************************************************** PP

                                       HHT-...-.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS.-S CS
                    Complex1_49kDa 156 lekl...pegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgssk.py 228
                                       +++l   +eg++l+++     p+k++v   + ++         ++ +p+ge++a +Ea++G l + ++sdg+s+ py
  gi|488601237|ref|YP_007907708.1| 301 INELrkmKEGNILSDQLAEFEPSKSDVRGYFYRIF-------GDLILPRGEFTALTEASRGSLLYSIISDGESNvPY 370
                                       66552227799999999999999888888777665.......7899**************************999** PP

                                       EEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 229 rlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       r++i +p++++l+ ++e l+ge++aD++ai+gs+ ++ +e+DR
  gi|488601237|ref|YP_007907708.1| 371 RVRIVTPGWYYLKGFMESLRGERVADLQAIYGSFGYFPPEADR 413
                                       ******************************************9 PP

>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.3e-06    0.0079      44      76 ..     131     163 ..     119     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                   Nitrate_red_gam  44 LrlgsplFHvGilvvllgHlvGlliPksvteal 76 
                                        r+g  l+  Gil+v+lgH++G++ P ++ e +
  gi|488601237|ref|YP_007907708.1| 131 GRIGTHLYDAGILAVFLGHTTGFMWPFALREPI 163
                                       589***********************8877655 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.7e-06     0.034      31      65 ..     101     135 ..      71     139 .. 0.75
   2 ?   -1.8   0.0      0.18   1.1e+03     169     219 ..     170     219 ..     154     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-06
                                       HHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases  31 alasvravedAlgikipknarlirnliaaalllhd 65 
                                       +l  vra+e+Al+i++p+ a++ir ++a    +  
  gi|488601237|ref|YP_007907708.1| 101 TLGYVRAIEQALDIEVPERAKYIRMIVAELGRIGT 135
                                       56679********************9987666555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.18
                                       HHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHHHHHTHHHHH CS
                      NiFeSe_Hases 169 ifggknPhpqslvvGGvtcaidllnaerlaevkslikevkefveevylpDv 219
                                       i g +   ++ ++ GGv   +dl + e +++v+ +i++  +  e+++++  
  gi|488601237|ref|YP_007907708.1| 170 ISGTRIT-ASYIIPGGVRRDVDLRTLEFIRKVTFVIERRLKSFERIFIKNP 219
                                       4444444.4459999*99999999999999999998877666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2474.81
//
Query:       gi|488601238|ref|YP_007907709.1|  [L=353]
Description: NADH dehydrogenase subunit B /NADH dehydrogenase subunit C [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-21   76.9   0.1    3.2e-21   76.2   0.1    1.3  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    1.1e-19   70.5   0.0      2e-19   69.7   0.0    1.4  1  Oxidored_q6     NADH ubiquinone oxidoreductase, 20 Kd subunit
  ------ inclusion threshold ------
      0.057   13.5   0.1       0.28   11.3   0.0    2.0  2  bZIP_1          bZIP transcription factor


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.1   5.3e-25   3.2e-21      10     118 ..     235     345 ..     226     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 5.3e-25
                                       HHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.....-EEEEEE....-S-BEE--TTT-STHHHHH CS
                    Complex1_30kDa  10 evakflkdeeelgfdvlsdltavDek.eerfevvyhllslekn....erirvkvevdeeepevpSvtdlfpgadwyE 81 
                                       ++a+ l      +fd++ ++  +D + e++f v y+++s++ +    + + + +++++++p++pS+ +++++ad++E
  gi|488601238|ref|YP_007907709.1| 235 AIASKLCS----KFDHVKNVNVIDLPhENSFIVEYQVSSYSVRdlmpVVVNIFARIPRDNPRFPSLRSFWESADYME 307
                                       45555554....7***********77799**********9655566666667777799******************* PP

                                       HHHHHHSHHBCTTSSTS.S-SSSSTTSSS-TTSTTS-- CS
                    Complex1_30kDa  82 REayDmfGivfeghpdl.rrillpedfeghPLRkdfpl 118
                                       RE++++fG++feg+p + +r+ll  d   +PLRkd ++
  gi|488601238|ref|YP_007907709.1| 308 REMHEFFGVWFEGNPAMgERFLLAPDTPDYPLRKDRKV 345
                                       ***************9967****999999******876 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 !   69.7   0.0   3.3e-23     2e-19      44     130 ..      60     140 ..      34     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 3.3e-23
                                       TTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS-- CS
                       Oxidored_q6  44 keadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevvpvdinipGCPph 120
                                       ++ ++++veGa++rk++  l++++e+++++k+vi +G+C   GG++  +n ++++    + ++vvpvd++ipGCPp+
  gi|488601238|ref|YP_007907709.1|  60 RQTNLIIVEGAISRKMARVLKITYEQMPDPKFVIVMGACGLKGGLF--WNGYHMV----RPSDVVPVDFFIPGCPPT 130
                                       47889*****************************************..7766776....45789************* PP

                                       HHHHHHHHHH CS
                       Oxidored_q6 121 peailetlla 130
                                       pe +l+++ +
  gi|488601238|ref|YP_007907709.1| 131 PESLLRAIRE 140
                                       ******9986 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.35   2.1e+03      43      56 ..     203     216 ..     199     217 .. 0.77
   2 ?   11.3   0.0   4.7e-05      0.28      12      42 ..     221     251 ..     219     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHH CS
                            bZIP_1  43 ksLkseleelkkev 56 
                                       ++L+sel+ l +++
  gi|488601238|ref|YP_007907709.1| 203 EELRSELDGLYDQI 216
                                       67999999988876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.7e-05
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  12 kNReaArrsRqRKqaeieeLerrvkaLekeN 42 
                                       kNR+a r +R+R  a  ++L ++++  ++ N
  gi|488601238|ref|YP_007907709.1| 221 KNRIAIRTCRRRISAIASKLCSKFDHVKNVN 251
                                       8***********************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2430.18
//
Query:       gi|488601239|ref|YP_007907710.1|  [L=121]
Description: NADH dehydrogenase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-07   30.8   0.9    3.5e-07   30.3   0.9    1.2  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
      0.093   12.5   5.8       0.11   12.3   5.8    1.0  1  DUF443       Protein of unknown function (DUF443)


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 !   30.3   0.9   3.9e-11   3.5e-07       3      90 ..      21     107 ..      19     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.9e-11
                                       HHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHH CS
                       Oxidored_q4   3 lllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemll 79 
                                       ++l+l+++l + + ++ k+s YE+G  p++e ++r++++++ ++ +F+ ++  +v+++  +++ + +++f+++ + +
  gi|488601239|ref|YP_007907710.1|  21 AILVLAKILPKYNLTEIKTSRYEAGNIPIREPKKRLPMQYFGYMYMFMALEPVLVIVLLLSIKPT-ISFFAILGISV 96 
                                       57889999987778888******************************998877766666666433.45555544444 PP

                                       HHHHHHHHHHH CS
                       Oxidored_q4  80 FllillvglvY 90 
                                        l+i ++ + Y
  gi|488601239|ref|YP_007907710.1|  97 ILFIPAIYFGY 107
                                       44444444444 PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.8   1.2e-05      0.11      91     187 ..       3     100 ..       1     107 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                            DUF443  91 sklvnliillivlllvlvlriyiskkl.kkklynevelekkskekiilipkslknfllllfaylfflglvilalval 166
                                       ++++++  ++++ llv    +++ k l k +l++ +++++++   i ++ ++ +  +++  +  +f++l  +++++l
  gi|488601239|ref|YP_007907710.1|   3 DNVIVIGAVIVISLLVDAAILVLAKILpKYNLTE-IKTSRYEAGNIPIREPKKRLPMQYFGYMYMFMALEPVLVIVL 78 
                                       5677777777777777666666665551456666.5789**********9677777777777778899987777666 PP

                            DUF443 167 i.etqniiilivlllllfllfl 187
                                       + +++ +i ++++l++ ++lf+
  gi|488601239|ref|YP_007907710.1|  79 LlSIKPTISFFAILGISVILFI 100
                                       66*************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 728.95
//
Query:       gi|488601240|ref|YP_007907711.1|  [L=409]
Description: NADH dehydrogenase subunit N [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-17   63.9  30.5    1.3e-17   63.9  30.5    3.4  2  Proton_antipo_M  Proton-conducting membrane transporter
    5.4e-05   23.3  26.3    5.4e-05   23.3  26.3    3.3  2  HisKA_7TM        N-terminal 7TM region of histidine kinase


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   4.8      0.31   2.8e+03     129     213 ..      30     105 ..       7     129 .. 0.62
   2 !   63.9  30.5   1.5e-21   1.3e-17       3     293 .]      92     353 ..      90     353 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.31
                   Proton_antipo_M 129 vlllirlllllavssneisqlllilaiismllgslvalaqtdiKrl.lAySsishlGymlialavatqygveaaiih 204
                                       +l+l++ +l   + s++++ + +++ +i++l   ++ +++++iK +  A S i  ++ +l+ + +          ++
  gi|488601240|ref|YP_007907711.1|  30 ILALVAAML---TLSPDVYFYGVLIFAIAILNLITLYITKNQIKGVdYALSAIMAVATLLVIMTN-D------FATL 96 
                                       333333333...34455555555555555555556667777777765677777777777776666.2......3344 PP

                   Proton_antipo_M 205 llthalfka 213
                                       + t++l+++
  gi|488601240|ref|YP_007907711.1|  97 MATFVLVSV 105
                                       444444444 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 1.5e-21
                   Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgil.llynltgtlefeelskalelglns 78 
                                       d ++l   + lv++p+y+L+ l   ++ ++  ++k++    l+ +++++g +  +y++++     + +         
  gi|488601240|ref|YP_007907711.1|  92 DFATLMATFVLVSVPTYVLVMLG--DEPKVDLGIKYITFMVLATILFIIGAFiTVYSYQS-----NPA--------- 152
                                       55666667778999999999887..44578889999999999998888887768898888.....333......... PP

                   Proton_antipo_M  79 lelllllllllvgllvKsaqvplhlWlpdayvea.PtpvsallAatlvkagvlllirllllla.vssneisqlllil 153
                                          +l++++l++gl++ ++++plh W+pd++  a P+p+s++  +++  +  ++ +++l   a  + ++i+ + ++l
  gi|488601240|ref|YP_007907711.1| 153 -LYVLGYVMLILGLALEVGVAPLHEWVPDVFASAdPIPISIIA-SIAKFVPFIVAFKILISTAnPALETITMFSALL 227
                                       .458999***********************977669****886.8776666666665555555889999******** PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektr 230
                                       a++sm++g+++al+  +  r+l+yS+++ +Gy+l  +++   + v++ +i+l    ++ all l+a+s+     k  
  gi|488601240|ref|YP_007907711.1| 228 AVVSMFVGNIGALTSKEHGRVLGYSTVANMGYVLATFVA---I-VNLNYIYLA---ISGALLQLMANSA----GKIG 293
                                       **********************************99999...3.466666664...4556777777666....3344 PP

                   Proton_antipo_M 231 dirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvlt 293
                                        ++a+    kk+ + + v + l++s +G+Pp+ gF+sk+ i  ++v+ + ++l+++ v+ s+++
  gi|488601240|ref|YP_007907711.1| 294 FFTAI----KKNEVGSPVTFALAFSFVGMPPFMGFWSKLFIVLSIVNTGYLWLAILlVINSAIS 353
                                       44444....455566666677899*****************99999999999999989999885 PP

>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3  26.3   6.1e-09   5.4e-05      46     214 ..      33     207 ..       3     212 .. 0.75
   2 ?  -12.4  19.3         2   1.8e+04      27      94 ..     222     285 ..     199     405 .. 0.39

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.1e-09
                         HisKA_7TM  46 llattleakllw.aklqylgivfipvlwllfaleytgkrrwltrrrlallllvpvltlilvltnplhhlfy....vs 117
                                       l+    +a+l +  ++ + g+ ++++++l +++ y+ k   ++   +al +++ v+tl++++tn++  l+     vs
  gi|488601240|ref|YP_007907711.1|  33 LV----AAMLTLsPDVYFYGVLIFAIAILNLITLYITK-NQIKGVDYALSAIMAVATLLVIMTNDFATLMAtfvlVS 104
                                       22....333333256788899999**999999999985.567776778888899************99973345666 PP

                         HisKA_7TM 118 agsfvvlef......ehGplfwvhlaysyllliagvvlliralirssglyrrqalllligllvPwlanllyllglsp 188
                                       + ++v++        + G+ ++++++ + +l+i+g+++ + ++ +++ ly   +++l++gl++ + +  l+   +  
  gi|488601240|ref|YP_007907711.1| 105 VPTYVLVMLgdepkvDLGIKYITFMVLATILFIIGAFITVYSYQSNPALYVLGYVMLILGLALEVGVAPLHEW-VPD 180
                                       666666555899999******99***************************************99977777764.334 PP

                         HisKA_7TM 189 lp.gidltplafaltglllaiaifryr 214
                                       ++ + d++p++++ + + +   i+ ++
  gi|488601240|ref|YP_007907711.1| 181 VFaSADPIPISIIASIAKFVPFIVAFK 207
                                       4559*******9999887766666655 PP

  == domain 2  score: -12.4 bits;  conditional E-value: 2
                         HisKA_7TM  27 aflllllavalwslgyalellattleakllwaklqylgivfipvlwllfaleytg.krrwltrrrlall 94 
                                        f++ll+ v++  +g + +l++ +    l ++++  +g v ++++  ++ l+y++     ++  +l l+
  gi|488601240|ref|YP_007907711.1| 222 MFSALLAVVSM-FVGNIGALTSKEHGRVLGYSTVANMGYV-LATFVAIVNLNYIYlA---ISGALLQLM 285
                                       44444444444.5555555554443333333333333222.1223333333333322...222111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); 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:                         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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2774.45
//
Query:       gi|488601241|ref|YP_007907712.1|  [L=636]
Description: NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-40  137.5  38.8    5.4e-38  130.8  30.4    3.2  3  Proton_antipo_M  Proton-conducting membrane transporter
    3.9e-07   30.0   3.7    3.9e-07   30.0   3.7    3.9  5  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 !   11.0   0.0   1.9e-05      0.17       1      29 [.     132     160 ..     132     164 .. 0.92
   2 !  130.8  30.4   6.1e-42   5.4e-38      40     279 ..     191     442 ..     183     467 .. 0.89
   3 ?   -2.0   0.7      0.18   1.6e+03     175     192 ..     488     505 ..     483     557 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.9e-05
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkp 29 
                                       +++L++l +g+E+ ++++  Lig w+++ 
  gi|488601241|ref|YP_007907712.1| 132 SDNLFTLLIGWEGLGIASWGLIGHWFRDD 160
                                       79***********************9986 PP

  == domain 2  score: 130.8 bits;  conditional E-value: 6.1e-42
                   Proton_antipo_M  40 lltllgsliLLlgilllynltgtlefeelskal.elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtp 115
                                        + ++g+++++++i+++y+ltgtl+++ +        +++ +++ll++++++g  +Ksaq+p++ Wl  a + +Pt 
  gi|488601241|ref|YP_007907712.1| 191 STIRFGDMPMFFAIAAIYALTGTLDIHSIPWHSmFEKIGYAGTVLLFIMFMMGPFTKSAQLPFSEWLMTA-MTGPTT 266
                                       5679************************9876557889999*****************************.****** PP

                   Proton_antipo_M 116 vsall.Aatlvkagvlllirllllla......vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGy 185
                                       vsall +at+v+ag +l++r++  ++       + ++i+ ++l+l++is+l+g++val  ++ K llA S++s lG+
  gi|488601241|ref|YP_007907712.1| 267 VSALLhSATMVAAGTYLFMRISWYIQpwtmelPAIEAIYLFILFLGLISALYGATVALGLRERKVLLAASTMSSLGL 343
                                       *********************998877765667889999************************************** PP

                   Proton_antipo_M 186 mlialav...atqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGl 259
                                       m+  +++    +q+++  a+ +l++ha+ ka+lFl+ag +i+++ + r      ++akkm + +lv +++++ laG+
  gi|488601241|ref|YP_007907712.1| 344 MFASASAsywLGQIALIVAFWYLIVHAFAKASLFLVAGHLIHAT-HDRFCSGNLKFAKKMKVAFLVTIIATVFLAGI 419
                                       **9999866679999**************************999.7788888889********************** PP

                   Proton_antipo_M 260 PptagFlskfl...iLeaavavs 279
                                       Pp++ ++ k +   ++e +++ +
  gi|488601241|ref|YP_007907712.1| 420 PPFTAYWVKSAmdgLMEHLMEEH 442
                                       ***99998854111455555555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.18
                   Proton_antipo_M 175 lAySsishlGymlialav 192
                                       lAyS +  + ++l+a+++
  gi|488601241|ref|YP_007907712.1| 488 LAYSIMVSMQFVLLAVIL 505
                                       455555555555555554 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 ?   -4.0   0.3       1.8   1.6e+04      28      37 ..      43      52 ..      40      53 .. 0.72
   2 !   30.0   3.7   4.3e-11   3.9e-07       3      54 ..      67     116 ..      65     123 .. 0.84
   3 ?   -0.4   0.5      0.14   1.3e+03      16      29 ..     117     130 ..     110     132 .. 0.89
   4 ?   -3.9   0.3       1.7   1.5e+04      26      40 ..     358     372 ..     357     373 .. 0.78
   5 ?   -2.0   0.2      0.45   4.1e+03      14      31 ..     517     534 ..     514     538 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.8
                   Proton_antipo_N 28 vvtfvsllvh 37
                                      +  fvsll+ 
  gi|488601241|ref|YP_007907712.1| 43 LGLFVSLLIT 52
                                      5578999986 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 4.3e-11
                   Proton_antipo_N   3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFf 54 
                                        W++  +++i++ f +D ls  m ++  f+++l+ +Y ++YM+dd +   + 
  gi|488601241|ref|YP_007907712.1|  67 PWIE--SFNINFVFVVDYLSKYMGALTAFIAFLIGVYGLEYMKDDYRLGWYW 116
                                       6776..789***********************************97644333 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.14
                   Proton_antipo_N  16 fllDklsalmllvv 29 
                                       f++++++a ml+vv
  gi|488601241|ref|YP_007907712.1| 117 FFFNTFTASMLMVV 130
                                       889999*****998 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 1.7
                   Proton_antipo_N  26 llvvtfvsllvhlYS 40 
                                       +l+v f  l+vh ++
  gi|488601241|ref|YP_007907712.1| 358 ALIVAFWYLIVHAFA 372
                                       578888888999886 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 0.45
                   Proton_antipo_N  14 igfllDklsalmllvvtf 31 
                                        gf++ ++s+  l++v  
  gi|488601241|ref|YP_007907712.1| 517 EGFMVASMSVGALVTVAY 534
                                       588999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4300.64
//
Query:       gi|488601242|ref|YP_007907713.1|  [L=479]
Description: Formate hydrogenlyase subunit 3/Multisubunit Na+/H+ antiporter, MnhD subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  171.9  27.1    1.6e-49  168.7  22.2    2.4  2  Proton_antipo_M  Proton-conducting membrane transporter
    2.7e-05   24.2   0.8    0.00035   20.6   0.8    3.0  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
        6.5    6.2  18.2        0.1   12.1   3.5    3.1  3  DUF1129          Protein of unknown function (DUF1129)


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 !  168.7  22.2   2.6e-53   1.6e-49       1     278 [.     129     394 ..     129     399 .. 0.95
   2 !    6.2   0.2   0.00086       5.1      39      73 ..     395     433 ..     392     460 .. 0.79

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 2.6e-53
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       +++ +lly++lE+ l+ ++lLi l+++ +++   ++ +f+ t ++ ++ L+g+++    +++  ++++s +      
  gi|488601242|ref|YP_007907713.1| 129 SGNFVLLYIFLEISLITSFLLIYLYGYGNRRWV-AVLYFIWTNVAGVLTLIGFIIAGLDNSSFAIKDISFI------ 198
                                       6799**********************9966665.57788999999999999*9998888889999999999...... PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllila 154
                                           + + ll+++g+l+K++ +  h Wlp a+ eaPtpvsall+ ++v +++++l+r+ l+   +  +++ ++l+ a
  gi|488601242|ref|YP_007907713.1| 199 ---SFTAWLLIFIGMLIKLPGLGPHIWLPWAHAEAPTPVSALLSPLTVGLAGYILLRVYLIDPSFISTYRDIILVYA 272
                                       ...88999*******************************************************9************* PP

                   Proton_antipo_M 155 iismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrd 231
                                       iis ++++++  +qtd+KrllAyS++s++Gy+li+l + + yg+ +++i+ ++ha+ k+ lF+ ag++i   +  rd
  gi|488601242|ref|YP_007907713.1| 273 IISSIYAGFAVFKQTDYKRLLAYSTVSQMGYILIGLCL-GTYGLIGVVIQYMSHAFGKSILFMGAGGIIAVYHGLRD 348
                                       **************************************.999*********************************** PP

                   Proton_antipo_M 232 irayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavav 278
                                       +r++ggL +++P ++ + l++++ l+G+ +t g +++f iL ++v+v
  gi|488601242|ref|YP_007907713.1| 349 LRKMGGLHEYVPSISNATLMGFMNLGGI-LTIGMFGEFFILRGIVDV 394
                                       ****************************.99**********999875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00086
                   Proton_antipo_M  39 flltllgsliLLlgilllynltgtlefeelskal....e 73 
                                       f  +l++ l+L+++++ ++ l+g+ +f +l++++    +
  gi|488601242|ref|YP_007907713.1| 395 FGSNLMSELPLIVAVVFIFILSGWYSFYTLKRVFyglpK 433
                                       567999************************998755441 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 !   20.6   0.8   5.9e-08   0.00035      14      47 ..      65      98 ..      63     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.9e-08
                   Proton_antipo_N 14 igfllDklsalmllvvtfvsllvhlYSigYMadd 47
                                      + +l+D++s    l+v++vs++v  YS+ YM + 
  gi|488601242|ref|YP_007907713.1| 65 FYLLIDPISNAIGLTVCLVSAMVGYYSLPYMLHR 98
                                      6789***************************542 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.1     0.006        36     108     165 ..      73     130 ..      43     161 .. 0.67
   2 ?   -2.5   0.3      0.51     3e+03     113     129 ..     269     285 ..     255     322 .. 0.62
   3 ?   12.1   3.5   1.7e-05       0.1      88     175 ..     381     469 ..     366     478 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.006
                           DUF1129 108 tasiGlitlllvalvgGlamvlvyrlltre..kkkkkrpplwkrllilllllvvwlvlft 165
                                       +++iGl++ l++a+vg + + ++ + +++    +++ r+ ++ +  + ++  ++wlv   
  gi|488601242|ref|YP_007907713.1|  73 SNAIGLTVCLVSAMVGYYSLPYMLHRFEEMgyGESEYRKYII-IYGFYAV-SMLWLVYSG 130
                                       4457999999999999999*******9987643333333333.2222222.334444433 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.51
                           DUF1129 113 litlllvalvgGlamvl 129
                                       l++ +++++ +G+a + 
  gi|488601242|ref|YP_007907713.1| 269 LVYAIISSIYAGFAVFK 285
                                       33444444444444333 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 1.7e-05
                           DUF1129  88 llalfallfgilalfskkkqtasiGlitlllvalvgGla.mvlvyrlltrekkkkkrpplwkrllilllllvvwlvl 163
                                       +++ f +l gi+ +f+++ +++   +++++++ +++G++ ++++ r+++  +k+ +rp++ ++l + l ++ ++ +l
  gi|488601242|ref|YP_007907713.1| 381 MFGEFFILRGIVDVFGSNLMSELPLIVAVVFIFILSGWYsFYTLKRVFYGLPKEMSRPKVSRYLDVPLYMIGILSIL 457
                                       4566899*************9998888999999999*973777788888879999*******999999998888888 PP

                           DUF1129 164 ftlvallpaviN 175
                                       f++  l++  +N
  gi|488601242|ref|YP_007907713.1| 458 FIFPPLVTVLLN 469
                                       887666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2945.91
//
Query:       gi|488601243|ref|YP_007907714.1|  [L=103]
Description: hypothetical protein Asulf_01750 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   21.9  11.3    0.00019   21.0  11.3    1.4  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 !   21.0  11.3   1.1e-08   0.00019       2     103 ..       7      96 ..       6      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHH.. CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivi.. 76 
                                       +l++++l+ ++G  + + +++l++ li+le++  av+l+l+ + + +              +++ + ++L +i++  
  gi|488601243|ref|YP_007907714.1|   7 VLITSVLVLMVGYTMAISSKDLIRLLISLEMMFGAVFLALIPLFSIK--------------SLISESFMLAVITVft 69 
                                       6899***********999***********************997765..............7888888888887655 PP

                                       HHHHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  77 gaaetavgLallvrlyreygtddvqel 103
                                       + +e+ ++++ +v+l r ++ ++v+++
  gi|488601243|ref|YP_007907714.1|  70 SSSELLILIGAIVKLDRIKKDISVDSI 96 
                                       778999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 660.11
//
Query:       gi|488601244|ref|YP_007907715.1|  [L=152]
Description: hypothetical protein Asulf_01751 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   23.9  19.6    0.00011   22.0  19.6    1.9  1  Oxidored_q3     NADH-ubiquinone/plastoquinone oxidoreductase 
  ------ inclusion threshold ------
       0.79    9.3  23.6        1.6    8.3  23.6    1.6  1  Virul_fac_BrkB  Virulence factor BrkB
        2.4    7.8  15.6       0.27   10.9  10.0    1.9  2  NrsF            Negative regulator of sigma F
        9.2    6.0  10.9       0.57   10.0   4.7    1.9  2  Trp_oprn_chp    Tryptophan-associated transmembrane protein (


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0  19.6   2.4e-08   0.00011       1     136 [.      18     138 ..      18     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.4e-08
                                       HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHH CS
                       Oxidored_q3   1 gallvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslal 77 
                                       ++l+++++k  +ysal+++l+++++a+++ + + + + +l + ++vGAi ++ +   +     + + +++ls+++ +
  gi|488601244|ref|YP_007907715.1|  18 SSLGALLTKDNFYSALYMALTMISIATIYAMADVQEVFVLIVFIFVGAIGIVTVALAAV---YKFKPKTQLSKAWLI 91 
                                       579999*******************************************9999888888...566777788888877 PP

                                       HHHHHHHHHHHHHTT--......--------TT-HHHHHHHHTTTTHHH.HHHHHHHHHH CS
                       Oxidored_q3  78 aalligllllalllllllessssavdaqvadvsnieaigsllftkyllp.felasllLLv 136
                                        +++++++l ++++                +v ++++   +l ++y+ +   l+sl++L+
  gi|488601244|ref|YP_007907715.1|  92 PSAVTAAVLGYVFYSNS-------------EVVSLSKPDLALGSEYVTViAALISLMILL 138
                                       77777777777754441.............122233333333332222202222222222 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  23.6   0.00036       1.6     135     244 ..      20     145 ..       1     149 [. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00036
                    Virul_fac_BrkB 135 flqslllasa.................pllglglelsell.llqllrwlvallllvlafallYrvlpnvkvrlraal 193
                                       ++  l    +                 + + +  +++e++ l+ ++ +  a++++++a+a++Y++ p+++ +  +++
  gi|488601244|ref|YP_007907715.1|  20 LGALL----TkdnfysalymaltmisiATIYAMADVQEVFvLIVFIFV-GAIGIVTVALAAVYKFKPKTQLSKAWLI 91 
                                       11112....122235555666666667444555578888866666666.5888999********************* PP

                    Virul_fac_BrkB 194 pGallaall.wllvkilfslylsnfa.synaiYG.slgaliilllWlylsalil 244
                                       p a+ aa+l +++ ++  ++ ls+   + ++ Y   ++ali l++ l ls +++
  gi|488601244|ref|YP_007907715.1|  92 PSAVTAAVLgYVFYSNSEVVSLSKPDlALGSEYVtVIAALISLMILLMLSVMLV 145
                                       ****99876245555555566666544556666558999999999999999876 PP

>> NrsF  Negative regulator of sigma F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.6     0.075   3.4e+02      58      94 ..       8      40 ..       1      53 [. 0.32
   2 ?   10.9  10.0     6e-05      0.27      43     140 ..      48     144 ..      28     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.075
                              NrsF 58 alllalaallaalrlarPgae.arrawlllalpvlllw 94
                                      +l+la++a+l        ga  ++  +  ++ ++l+++
  gi|488601244|ref|YP_007907715.1|  8 LLALAAIAFLS-----SLGALlTKDNFYSALYMALTMI 40
                                      22222222222.....2222212222333333333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6e-05
                              NrsF  43 aealatpvfwlklalalllalaallaalrla.rPgaearrawlllalpvlllwlaalvellaappaerlalllgetw 118
                                       ++ +++ ++++ ++++ +++++++++a+     P+ + ++awl+  ++ ++++  ++++  ++ + + ++l lg++ 
  gi|488601244|ref|YP_007907715.1|  48 MADVQEVFVLIVFIFVGAIGIVTVALAAVYKfKPKTQLSKAWLIPSAVTAAVLGYVFYSNSEVVSLSKPDLALGSEY 124
                                       3456777777778888888887776666655269999***************************************9 PP

                              NrsF 119 rvCllaivllslpllaallwal 140
                                          ++  +l+sl++l++l ++l
  gi|488601244|ref|YP_007907715.1| 125 V--TVIAALISLMILLMLSVML 144
                                       6..7788888999888887776 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 ?   -0.3   0.4      0.18   8.1e+02      73      88 ..       8      22 ..       5      32 .. 0.46
   2 ?   10.0   4.7   0.00013      0.57      42     139 ..      31     147 ..      25     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.18
                      Trp_oprn_chp 73 llalagagaavaalsl 88
                                      llala a+a +++l +
  gi|488601244|ref|YP_007907715.1|  8 LLALA-AIAFLSSLGA 22
                                      33333.3333333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00013
                      Trp_oprn_chp  42 apaltalAlvllAaavAvlavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaave.lta 117
                                       +++ +al ++ +A + A++ v+ ++  +v + + ++g+++++ a+    +p+++  +a    ++v++a+  +  +++
  gi|488601244|ref|YP_007907715.1|  31 SALYMALTMISIATIYAMADVQEVFVLIVFIFVGAIGIVTVALAAVYKFKPKTQLSKAWLIPSAVTAAVLGYVfYSN 107
                                       67789*******************************99999999999899888888888554555455444445333 PP

                      Trp_oprn_chp 118 ..................wpvlalaggvllllagvllllr 139
                                                          +++al+  ++ll+ +v+l+ r
  gi|488601244|ref|YP_007907715.1| 108 sevvslskpdlalgseyvTVIAALISLMILLMLSVMLVSR 147
                                       4566667677888855544444555555555556665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1352  (0.0754086); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1071.70
//
Query:       gi|488601245|ref|YP_007907716.1|  [L=155]
Description: hypothetical protein Asulf_01752 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   23.4   8.0       0.45   10.0   0.1    4.3  4  zf-ribbon_3      zinc-ribbon domain
    0.00043   20.3   5.7       0.19   11.9   0.1    3.5  3  Zn-ribbon_8      Zinc ribbon domain
     0.0013   18.3  10.2       0.11   12.2   0.3    4.3  4  zinc_ribbon_2    zinc-ribbon domain
     0.0019   18.3   0.8       0.61   10.3   0.4    2.5  2  FYVE             FYVE zinc finger
     0.0043   17.3   3.2        1.5    9.2   0.1    3.7  3  RNA_pol_N        RNA polymerases N / 8 kDa subunit
     0.0053   16.8   9.4       0.65   10.1   3.3    3.1  2  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.011   15.5   4.9       0.77    9.7   0.2    3.3  3  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.019   14.8   0.1        1.9    8.4   0.0    2.6  2  Rad50_zn_hook    Rad50 zinc hook motif
      0.037   13.8   2.4       0.89    9.4   0.1    2.6  2  zf-RING_4        RING/Ubox like zinc-binding domain
      0.047   13.2  10.6       0.35   10.4   0.8    2.9  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.079   12.8   7.5       0.58   10.1   0.4    3.3  3  Prok-RING_4      Prokaryotic RING finger family 4
      0.082   12.9  14.5       0.73    9.8   2.4    3.2  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.083   12.9  16.1       0.84    9.7   0.3    4.9  5  YhfH             YhfH-like protein
       0.21   11.4   7.3      0.066   13.0   3.0    2.4  2  zinc_ribbon_5    zinc-ribbon domain
       0.23   11.4   6.1          4    7.5   0.8    3.3  3  zf-RING_5        zinc-RING finger domain
       0.25   11.3   8.7        3.7    7.5   1.6    3.8  3  C1_1             Phorbol esters/diacylglycerol binding domain
       0.62    9.7   8.9         35    4.1   0.0    4.2  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.75    9.8   9.9        5.2    7.1   0.9    3.1  2  zinc-ribbons_6   zinc-ribbons
       0.86    9.7  10.6        2.5    8.2   0.5    3.8  4  zf-BED           BED zinc finger
        1.1    9.1   8.2        5.9    6.8   0.0    3.9  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        1.3    9.0   9.6        4.2    7.3   0.9    3.2  3  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)
        1.3    9.2   0.1        1.3    9.2   0.1    3.4  3  UPF0547          Uncharacterised protein family UPF0547
        2.3    8.6   9.8        1.7    9.0   0.5    3.2  3  C1_2             C1 domain
        2.3    9.0   8.5          8    7.3   1.9    2.7  2  zinc_ribbon_15   zinc-ribbon family
        2.6    7.7  11.9        7.1    6.3   4.1    3.6  3  RecR             RecR protein
          3    8.0  12.4        5.8    7.1   0.2    3.3  3  zf-UDP           Zinc-binding RING-finger
          5    7.1   8.0         28    4.7   2.1    3.1  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        6.5    6.9   9.4       0.35   11.0   0.8    2.8  2  Elf1             Transcription elongation factor Elf1 like
        7.4    6.3   9.5         17    5.2   0.1    4.0  4  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        9.2    6.3  11.7         17    5.4   0.8    4.0  4  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
        9.4    6.6   9.1         12    6.2   0.3    3.6  3  zf-LITAF-like    LITAF-like zinc ribbon domain
        9.5    6.2  14.8         16    5.4   0.3    4.7  5  VATC             Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.079        44      17      26 .]       3      12 ..       2      12 .. 0.81
   2 !    7.2   0.0    0.0059       3.3       4      13 ..      22      31 ..      20      32 .. 0.76
   3 !   10.0   0.1   0.00081      0.45       3      11 ..     111     120 ..     106     123 .. 0.77
   4 ?    4.7   0.1     0.037        21       2      13 ..     135     146 ..     134     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.079
                       zf-ribbon_3 17 nvCpyCGtkl 26
                                      + C+ CG+++
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEI 12
                                      57*****875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0059
                       zf-ribbon_3  4 rCPnCGapls 13
                                      +CP CG +l+
  gi|488601245|ref|YP_007907716.1| 22 TCPICGDILD 31
                                      7999998766 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00081
                       zf-ribbon_3   3 vrCPnCGa.p 11 
                                       ++CP+CGa  
  gi|488601245|ref|YP_007907716.1| 111 KTCPACGAdF 120
                                       6888888855 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.037
                       zf-ribbon_3   2 tvrCPnCGapls 13 
                                       +v+C  CG+++s
  gi|488601245|ref|YP_007907716.1| 135 KVYCGTCGKLIS 146
                                       689999**9776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.7    0.0073       4.1       8      33 ..       5      27 ..       3      32 .. 0.78
   2 !   11.9   0.1   0.00034      0.19      18      39 ..     105     123 ..     101     124 .. 0.71
   3 ?    1.1   0.0      0.78   4.4e+02      28      34 ..     137     143 ..     126     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0073
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCg 33
                                      C+ Cg   e+++  + ++ ++CP Cg
  gi|488601245|ref|YP_007907716.1|  5 CKICG---EEIVGGKFEDYETCPICG 27
                                      99999...7777777445677****9 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00034
                       Zn-ribbon_8  18 lqsisdapltaCPeCgsevrrv 39 
                                       +    +++ ++CP+Cg++ +r+
  gi|488601245|ref|YP_007907716.1| 105 II---KENYKTCPACGADFTRQ 123
                                       33...345677******99996 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.78
                       Zn-ribbon_8  28 aCPeCgs 34 
                                        C +Cg+
  gi|488601245|ref|YP_007907716.1| 137 YCGTCGK 143
                                       3777776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.092        52       2       9 ..       5      12 ..       2      15 .. 0.70
   2 ?    3.6   0.0       0.1        58       2       7 ..      23      28 ..      18      37 .. 0.69
   3 !   12.2   0.3    0.0002      0.11       9      22 ..     106     119 ..     103     120 .. 0.86
   4 ?    3.0   0.2      0.16        87       1       9 [.     137     145 ..     136     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.092
                     zinc_ribbon_2  2 CpnCGael 9 
                                      C+ CG+e+
  gi|488601245|ref|YP_007907716.1|  5 CKICGEEI 12
                                      66677766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp CG 
  gi|488601245|ref|YP_007907716.1| 23 CPICGD 28
                                      666665 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.0002
                     zinc_ribbon_2   9 lqdnakFCpyCGtp 22 
                                       +++n k Cp CG+ 
  gi|488601245|ref|YP_007907716.1| 106 IKENYKTCPACGAD 119
                                       699*********96 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.16
                     zinc_ribbon_2   1 fCpnCGael 9  
                                       +C  CG+ +
  gi|488601245|ref|YP_007907716.1| 137 YCGTCGKLI 145
                                       577777655 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.018       9.9       9      40 ..       2      46 ..       1      88 [. 0.78
   2 !   10.3   0.4    0.0011      0.61       7      37 ..     108     147 ..     101     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
                                      -SB-TTT--B-..-SSS--EE-TTT--EE-...........STTS CS
                              FYVE  9 vkkCeiCakkF..sllrrrhhCrlCGkvvC...........ekCs 40
                                      vk C+iC ++     ++    C +CG+++             kC 
  gi|488601245|ref|YP_007907716.1|  2 VKLCKICGEEIvgGKFEDYETCPICGDILDdiiakylemvaMKCA 46
                                      678999999985445788999999999986555555555555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                                       .--SB-TTT--B--.........SSS--EE-TTT--EE-S CS
                              FYVE   7 sevkkCeiCakkFs.........llrrrhhCrlCGkvvCe 37 
                                       ++ k+C++C + F+             + +C +CGk++ +
  gi|488601245|ref|YP_007907716.1| 108 ENYKTCPACGADFTrqcldiekdGDWVKVYCGTCGKLISK 147
                                       6789*********8455444443146799******99876 PP

>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       1.2   6.8e+02       7      22 ..       5      21 ..       2      24 .. 0.78
   2 ?    5.7   0.0     0.032        18       7      29 ..      23      63 ..      21     101 .. 0.63
   3 !    9.2   0.1    0.0026       1.5       5      20 ..     136     151 ..     134     155 .] 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                                      -TTT--.B-STHHHHHH CS
                         RNA_pol_N  7 CFtCGk.vigekweeyl 22
                                      C  CG+ ++g k+e+y+
  gi|488601245|ref|YP_007907716.1|  5 CKICGEeIVGGKFEDYE 21
                                      88999636789999997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.032
                                      -TTT--B-STHHHHHHHHHHTT..................- CS
                         RNA_pol_N  7 CFtCGkvigekweeylellekg..................e 29
                                      C  CG ++ +   +yle++  +                   
  gi|488601245|ref|YP_007907716.1| 23 CPICGDILDDIIAKYLEMVAMKcaqqefdgitlnmiikylD 63
                                      889*************9997765555555555555554440 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0026
                                       SS-TTT--B-STHHHH CS
                         RNA_pol_N   5 VrCFtCGkvigekwee 20 
                                       V C tCGk+i++++  
  gi|488601245|ref|YP_007907716.1| 136 VYCGTCGKLISKHYAP 151
                                       88**********9975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.4    0.0036         2      14      38 ..       4      30 ..       2      48 .. 0.72
   2 !   10.1   3.3    0.0012      0.65       8      36 ..     106     143 ..     101     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
                               DZR 14 fCseCgtklkavaa....edrCpsCgekv 38
                                       C+ Cg+++          ++Cp Cg  +
  gi|488601245|ref|YP_007907716.1|  4 LCKICGEEIVG--GkfedYETCPICGDIL 30
                                      68888888752..2346678888887765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                               DZR   8 lppdarfCseCgtklkavaa...........edrCpsCge 36 
                                       ++++ ++C++Cg++  +  +           +  C  Cg+
  gi|488601245|ref|YP_007907716.1| 106 IKENYKTCPACGADFTR--QcldiekdgdwvKVYCGTCGK 143
                                       678899********872..223555566666666666665 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2    0.0014      0.77      25      45 ..       4      28 ..       2      33 .. 0.85
   2 ?    5.9   0.1     0.021        12      33      47 ..     105     120 ..     102     123 .. 0.74
   3 ?    0.1   0.1       1.4   7.6e+02      24      33 ..     136     145 ..     124     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                                      E-HHHHHHHHH....TT-B-TTT-- CS
                        zf-C3HC4_3 25 lCeeCaekllk....rkkkCpiCrr 45
                                      lC+ C e++        ++CpiC  
  gi|488601245|ref|YP_007907716.1|  4 LCKICGEEIVGgkfeDYETCPICGD 28
                                      7********87889999******75 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                                       HHH.TT-B-TTT--B- CS
                        zf-C3HC4_3  33 llk.rkkkCpiCrrpi 47 
                                       + k + k+Cp C ++ 
  gi|488601245|ref|YP_007907716.1| 105 IIKeNYKTCPACGADF 120
                                       445589******9876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                                       EE-HHHHHHH CS
                        zf-C3HC4_3  24 vlCeeCaekl 33 
                                       v+C +C + +
  gi|488601245|ref|YP_007907716.1| 136 VYCGTCGKLI 145
                                       4566666555 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0       0.1        58      19      30 ..      21      31 ..      16      33 .. 0.76
   2 ?    8.4   0.0    0.0034       1.9      15      31 ..     106     122 ..     101     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
                                      SEE-TTT--EE- CS
                     Rad50_zn_hook 19 kgcCPlCgReld 30
                                      +  CP Cg  ld
  gi|488601245|ref|YP_007907716.1| 21 E-TCPICGDILD 31
                                      4.8****97666 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0034
                                       HTT-SEE-TTT--EE-H CS
                     Rad50_zn_hook  15 lkeakgcCPlCgRelde 31 
                                       +ke+   CP Cg ++++
  gi|488601245|ref|YP_007907716.1| 106 IKENYKTCPACGADFTR 122
                                       566667*********86 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4      0.11        62      23      43 ..       3      26 ..       2      31 .. 0.81
   2 ?    9.4   0.1    0.0016      0.89      28      47 ..     101     120 ..      98     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                         zf-RING_4 23 qiClfCyhrile...eeegrCPaC 43
                                      ++C  C ++i+    e  + CP C
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEIVGgkfEDYETCPIC 26
                                      679999999998666668999999 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                         zf-RING_4  28 CyhrileeeegrCPaCreeY 47 
                                        +++i++e+ + CPaC  ++
  gi|488601245|ref|YP_007907716.1| 101 WFEKIIKENYKTCPACGADF 120
                                       47999999********7765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.1     0.012       6.8       3      34 ..       5      35 ..       4      38 .. 0.80
   2 ?   10.4   0.8   0.00063      0.35       2      33 ..     112     149 ..     111     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                                      ETTTTCEEC....HEETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon  3 CPnCgstnl....veDpergelvCtdCGlVlednsi 34
                                      C++Cg + +     eD+e    +C+ CG +l+d ++
  gi|488601245|ref|YP_007907716.1|  5 CKICGEE-IvggkFEDYE----TCPICGDILDDIIA 35
                                      9999976.5588888888....9*****99998765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00063
                                       EETTTTCEEC......HEETSTTCEEESSSSBEEEECC CS
                      TF_Zn_Ribbon   2 kCPnCgstnl......veDpergelvCtdCGlVledns 33 
                                       +CP Cg +++      + D +   ++C+ CG ++  ++
  gi|488601245|ref|YP_007907716.1| 112 TCPACGADFTrqcldiEKDGDWVKVYCGTCGKLISKHY 149
                                       6******997799999999999999******9987765 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 ?   10.1   0.4     0.001      0.58      28      41 ..      18      31 ..       2      35 .. 0.67
   2 ?    5.2   0.4     0.034        19      28      41 ..     108     121 ..     104     127 .. 0.82
   3 ?   -0.6   0.1       2.2   1.2e+03      24      42 ..     124     147 ..     120     150 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.001
                       Prok-RING_4 28 kdlssCPlCqrris 41
                                      +d+++CP+C   ++
  gi|488601245|ref|YP_007907716.1| 18 EDYETCPICGDILD 31
                                      3888*****98876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.034
                       Prok-RING_4  28 kdlssCPlCqrris 41 
                                       +++++CP C   + 
  gi|488601245|ref|YP_007907716.1| 108 ENYKTCPACGADFT 121
                                       7999*****87765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.2
                       Prok-RING_4  24 Cfdskdls.....sCPlCqrrisk 42 
                                       C+d ++        C  C + isk
  gi|488601245|ref|YP_007907716.1| 124 CLDIEKDGdwvkvYCGTCGKLISK 147
                                       555553333444456667666665 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.4    0.0013      0.73       5      27 ..       3      27 ..       1      29 [. 0.92
   2 ?    9.2   0.7    0.0021       1.2      22      35 ..     112     125 ..     107     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                       Prok-RING_1  5 kkCpvCgkelkee..dDiVvCpeCg 27
                                      k C++Cg+e+  +  +D  +Cp Cg
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEIVGGkfEDYETCPICG 27
                                      57*********99899********9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                       Prok-RING_1  22 vCpeCgtpyHraCy 35 
                                       +Cp+Cg+ + r+C 
  gi|488601245|ref|YP_007907716.1| 112 TCPACGADFTRQCL 125
                                       6***********96 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.7     0.059        33      14      23 ..       3      12 ..       2      14 .. 0.91
   2 ?    3.6   0.1      0.12        67      15      26 ..      22      33 ..      19      40 .. 0.81
   3 ?   -0.3   0.0         2   1.1e+03       5      12 ..      69      76 ..      67      77 .. 0.84
   4 ?    9.7   0.3    0.0015      0.84      13      27 ..     110     124 ..     107     125 .. 0.88
   5 ?    2.4   0.2      0.27   1.5e+02      15      24 ..     137     146 ..     135     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.059
                              YhfH 14 KkCteCGkei 23
                                      K C  CG+ei
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEI 12
                                      89******98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                              YhfH 15 kCteCGkeieEq 26
                                      +C+ CG+ ++++
  gi|488601245|ref|YP_007907716.1| 22 TCPICGDILDDI 33
                                      7*****998876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2
                              YhfH  5 veFfrnLP 12
                                      veFf+ L+
  gi|488601245|ref|YP_007907716.1| 69 VEFFEDLE 76
                                      8***9996 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0015
                              YhfH  13 kKkCteCGkeieEqa 27 
                                        K+C+ CG ++  q+
  gi|488601245|ref|YP_007907716.1| 110 YKTCPACGADFTRQC 124
                                       6********998886 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.27
                              YhfH  15 kCteCGkeie 24 
                                        C +CGk i 
  gi|488601245|ref|YP_007907716.1| 137 YCGTCGKLIS 146
                                       59****9885 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         5   2.8e+03       5       9 ..      23      27 ..      22      30 .. 0.76
   2 ?   13.0   3.0   0.00012     0.066       5      33 ..     113     143 ..     111     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5
                     zinc_ribbon_5  5 CpdCd 9 
                                      Cp C+
  gi|488601245|ref|YP_007907716.1| 23 CPICG 27
                                      88886 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                     zinc_ribbon_5   5 CpdCdtkFklvdsklKksgkkVr..CakCae 33 
                                       Cp+C+  F      + k g +V+  C+ C++
  gi|488601245|ref|YP_007907716.1| 113 CPACGADFTRQCLDIEKDGDWVKvyCGTCGK 143
                                       ********99999999***998888****96 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.8    0.0071         4      25      43 ..       5      27 ..       4      28 .. 0.71
   2 ?    4.6   0.0     0.058        32      34      43 ..     108     117 ..      92     118 .. 0.80
   3 ?    0.1   0.1       1.4     8e+02      37      43 ..     136     142 ..     122     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0071
                         zf-RING_5 25 CekClkkll....ekeavCpiCr 43
                                      C+ C  +      e + +CpiC+
  gi|488601245|ref|YP_007907716.1|  5 CKICGEEIVggkfEDYETCPICG 27
                                      55555555555599********7 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.058
                         zf-RING_5  34 ekeavCpiCr 43 
                                       e++++Cp+C+
  gi|488601245|ref|YP_007907716.1| 108 ENYKTCPACG 117
                                       5689*****7 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                         zf-RING_5  37 avCpiCr 43 
                                       ++C +C+
  gi|488601245|ref|YP_007907716.1| 136 VYCGTCG 142
                                       4555554 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.6    0.0066       3.7      13      36 ..       4      28 ..       1      47 [. 0.65
   2 ?    0.8   0.1      0.85   4.8e+02      30      43 ..     112     125 ..     101     131 .. 0.70
   3 ?    3.9   0.1     0.091        51      12      23 ..     136     147 ..     133     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                                      B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1 13 fCkhCgeflwg.kekqglkCswCkl 36
                                       Ck Cge + g k+    +C  C+ 
  gi|488601245|ref|YP_007907716.1|  4 LCKICGEEIVGgKFEDYETCPICGD 28
                                      5777777776667766667766653 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.85
                                       EETTT--EE-CCCC CS
                              C1_1  30 kCswCkllvHkkCh 43 
                                       +C +C+  +  +C+
  gi|488601245|ref|YP_007907716.1| 112 TCPACGADFTRQCL 125
                                       57777777666665 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.091
                                       -B-TTT-SB--S CS
                              C1_1  12 tfCkhCgeflwg 23 
                                        +C +Cg+++++
  gi|488601245|ref|YP_007907716.1| 136 VYCGTCGKLISK 147
                                       69*******943 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.16        88       4      12 ..       4      12 ..       3      17 .. 0.89
   2 ?    2.4   0.1      0.21   1.2e+02       2      10 ..      20      28 ..      19      32 .. 0.80
   3 ?    3.2   0.1      0.12        68       2      11 ..     110     119 ..     109     123 .. 0.81
   4 ?    4.1   0.0     0.063        35       4      15 ..     137     148 ..     135     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                            zf_UBZ  4 lCerCgkei 12
                                      lC+ Cg+ei
  gi|488601245|ref|YP_007907716.1|  4 LCKICGEEI 12
                                      7******98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.21
                            zf_UBZ  2 tylCerCgk 10
                                      + +C+ Cg 
  gi|488601245|ref|YP_007907716.1| 20 YETCPICGD 28
                                      679****96 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.12
                            zf_UBZ   2 tylCerCgke 11 
                                       + +C+ Cg+ 
  gi|488601245|ref|YP_007907716.1| 110 YKTCPACGAD 119
                                       579****985 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.063
                            zf_UBZ   4 lCerCgkeipes 15 
                                        C  Cgk i+ +
  gi|488601245|ref|YP_007907716.1| 137 YCGTCGKLISKH 148
                                       6********976 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.9    0.0094       5.2      19      40 ..       5      31 ..       2      49 .. 0.73
   2 ?    5.4   2.5     0.032        18      31      61 ..     112     147 ..     103     151 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0094
                                      -TTT--.....EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6 19 CeaCqe.....dlkkealCpeCeqele 40
                                      C+ C e     +++   +Cp C++ l+
  gi|488601245|ref|YP_007907716.1|  5 CKICGEeivggKFEDYETCPICGDILD 31
                                      777776666666777777777776655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.032
                                       E-SSS-.....S---EEEETTEEEE--TTTT----T CS
                    zinc-ribbons_6  31 lCpeCe.....qelevlkaCgavdyfCnkcneLiSk 61 
                                       +Cp C+     q l++ k    v+ +C +c +LiSk
  gi|488601245|ref|YP_007907716.1| 112 TCPACGadftrQCLDIEKDGDWVKVYCGTCGKLISK 147
                                       455554111112233333444456666667777776 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.071        40      19      29 ..       5      15 ..       3      22 .. 0.89
   2 ?    0.3   0.0       1.3   7.3e+02      18      27 ..      22      31 ..      18      33 .. 0.87
   3 ?    0.8   0.2       0.9     5e+02      13      28 ..     107     122 ..      98     126 .. 0.79
   4 ?    8.2   0.5    0.0044       2.5      12      29 ..     131     148 ..     124     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.071
                                      ETTTTEE---- CS
                            zf-BED 19 CryCgkilsrg 29
                                      C++Cg+++ +g
  gi|488601245|ref|YP_007907716.1|  5 CKICGEEIVGG 15
                                      *******9987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                                      EETTTTEE-- CS
                            zf-BED 18 vCryCgkils 27
                                      +C +Cg il+
  gi|488601245|ref|YP_007907716.1| 22 TCPICGDILD 31
                                      6*****9986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.9
                                       GSS--EETTTTEE--- CS
                            zf-BED  13 keqkavCryCgkilsr 28 
                                       ke+  +C  Cg+ ++r
  gi|488601245|ref|YP_007907716.1| 107 KENYKTCPACGADFTR 122
                                       788889*****99988 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0044
                                       GGSS--EETTTTEE---- CS
                            zf-BED  12 lkeqkavCryCgkilsrg 29 
                                        ++ k++C  Cgk +s +
  gi|488601245|ref|YP_007907716.1| 131 GDWVKVYCGTCGKLISKH 148
                                       6899*********99986 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 ?   -0.1   0.3       1.4     8e+02       2      12 ..       3      13 ..       2      15 .. 0.85
   2 ?    3.5   0.0      0.11        61       2       9 ..      21      28 ..      20      36 .. 0.87
   3 ?    6.8   0.0      0.01       5.9       3      10 ..     112     119 ..     110     123 .. 0.82
   4 ?    0.7   0.1      0.83   4.6e+02       2      13 ..     136     147 ..     135     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                                      EE-SSS--EEE CS
                    zf-C4_Topoisom  2 ekCPkCggdLv 12
                                      + C  Cg+++v
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEIV 13
                                      57999**9997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                                      EE-SSS-- CS
                    zf-C4_Topoisom  2 ekCPkCgg 9 
                                      e+CP Cg+
  gi|488601245|ref|YP_007907716.1| 21 ETCPICGD 28
                                      79****96 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.01
                                       E-SSS--E CS
                    zf-C4_Topoisom   3 kCPkCggd 10 
                                       +CP+Cg+d
  gi|488601245|ref|YP_007907716.1| 112 TCPACGAD 119
                                       8*****98 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.83
                                       EE-SSS--EEEE CS
                    zf-C4_Topoisom   2 ekCPkCggdLvl 13 
                                       + C  Cg+ + +
  gi|488601245|ref|YP_007907716.1| 136 VYCGTCGKLISK 147
                                       679999987765 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 ?    7.3   0.9    0.0074       4.2      21      41 .]       4      26 ..       3      26 .. 0.92
   2 ?    6.1   0.2     0.018       9.9      27      41 .]     103     116 ..     101     116 .. 0.87
   3 ?   -1.7   0.1         5   2.8e+03      21      26 ..     137     142 ..     135     150 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0074
                                      B-CHHHHHHHHC..TSSB--TTT CS
                          zf-C3HC4 21 fCskCirkilks..rkkvkCPlC 41
                                      +C+ C ++i+    + +++CP+C
  gi|488601245|ref|YP_007907716.1|  4 LCKICGEEIVGGkfEDYETCPIC 26
                                      8*********99999999***** PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.018
                                       HHHHHCTSSB--TTT CS
                          zf-C3HC4  27 rkilksrkkvkCPlC 41 
                                       +ki+k +++++CP C
  gi|488601245|ref|YP_007907716.1| 103 EKIIK-ENYKTCPAC 116
                                       57889.9999***** PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5
                                       B-CHHH CS
                          zf-C3HC4  21 fCskCi 26 
                                       +C +C 
  gi|488601245|ref|YP_007907716.1| 137 YCGTCG 142
                                       566664 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3       2.1   1.2e+03       1      10 [.       3      12 ..       3      13 .. 0.70
   2 ?    2.4   0.1      0.31   1.7e+02      16      21 ..      22      27 ..      18      30 .. 0.72
   3 ?    9.2   0.1    0.0023       1.3       8      21 ..     104     117 ..     103     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.1
                           UPF0547  1 KvCPeCeakv 10
                                      K C+ C +++
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEI 12
                                      5588887776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.31
                           UPF0547 16 fCphCG 21
                                       Cp CG
  gi|488601245|ref|YP_007907716.1| 22 TCPICG 27
                                      577776 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0023
                           UPF0547   8 akvPvaaqfCphCG 21 
                                        +++++ + Cp CG
  gi|488601245|ref|YP_007907716.1| 104 KIIKENYKTCPACG 117
                                       68999999999999 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5     0.003       1.7      19      42 ..       3      30 ..       1      33 [. 0.73
   2 ?    2.5   0.4      0.33   1.8e+02      15      27 ..     107     119 ..      93     126 .. 0.74
   3 ?    2.1   0.1      0.45   2.5e+02      19      29 ..     136     146 ..     125     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.003
                              C1_2 19 fnCsaCgrk..idgff..Y.sCseCdfsl 42
                                      + C++Cg++  + g+f  Y +C++C  +l
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEivG-GKFedYeTCPICGDIL 30
                                      57*******853.44459945*9996555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.33
                              C1_2  15 ssesfnCsaCgrk 27 
                                       +++ ++C aCg +
  gi|488601245|ref|YP_007907716.1| 107 KENYKTCPACGAD 119
                                       4566889999876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.45
                              C1_2  19 fnCsaCgrkid 29 
                                         C +Cg+ i+
  gi|488601245|ref|YP_007907716.1| 136 VYCGTCGKLIS 146
                                       67*****9974 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.089        50      67      86 .]       4      27 ..       2      47 .. 0.77
   2 ?    7.3   1.9     0.014         8      34      79 ..     107     149 ..      99     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.089
                    zinc_ribbon_15 67 eCknCgkeve....eefkyCpkCg 86
                                       Ck Cg+e+     e+++ Cp Cg
  gi|488601245|ref|YP_007907716.1|  4 LCKICGEEIVggkfEDYETCPICG 27
                                      677787777533334677788887 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.014
                    zinc_ribbon_15  34 kkpylacskCkslleaskelgkeiekkessekkeCknCgkeveeef 79 
                                       k+ y +c  C++ ++ +     +iek  +  k +C  Cgk +++++
  gi|488601245|ref|YP_007907716.1| 107 KENYKTCPACGADFTRQC---LDIEKDGDWVKVYCGTCGKLISKHY 149
                                       378899999999999997...7788888888999999999998765 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.1     0.013       7.1      16      36 ..       2      28 ..       1      32 [. 0.74
   2 ?    3.6   0.1     0.086        48      13      23 ..     107     117 ..     105     123 .. 0.90
   3 ?   -0.7   0.1         2   1.1e+03      18      25 ..     137     144 ..     136     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                                      -EE-TTT--E......ESSSS-CCCCS CS
                              RecR 16 vrhCsrCgnl......teedlCaICsd 36
                                      v+ C++Cg         + + C+IC d
  gi|488601245|ref|YP_007907716.1|  2 VKLCKICGEEivggkfEDYETCPICGD 28
                                      78999997532333339999*****87 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.086
                                       HHH-EE-TTT- CS
                              RecR  13 kekvrhCsrCg 23 
                                       ke+ + C+ Cg
  gi|488601245|ref|YP_007907716.1| 107 KENYKTCPACG 117
                                       8999******8 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2
                                       E-TTT--E CS
                              RecR  18 hCsrCgnl 25 
                                       +C  Cg l
  gi|488601245|ref|YP_007907716.1| 137 YCGTCGKL 144
                                       89999965 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4     0.035        20       9      18 ..       3      12 ..       1      21 [. 0.83
   2 ?    3.1   0.4      0.18     1e+02       9      25 ..      21      37 ..      15      49 .. 0.69
   3 ?    7.1   0.2      0.01       5.8      44      72 ..     104     130 ..      96     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.035
                            zf-UDP  9 qiCqiCgddv 18
                                      ++C+iCg+++
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEI 12
                                      79******98 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.18
                            zf-UDP  9 qiCqiCgddvgltedge 25
                                      + C iCgd ++    + 
  gi|488601245|ref|YP_007907716.1| 21 ETCPICGDILDDIIAKY 37
                                      68*****9776655555 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.01
                            zf-UDP  44 yerkdgnqsCPqCktrykrlkgsprvegd 72 
                                          k+  ++CP C + ++r   +  +e d
  gi|488601245|ref|YP_007907716.1| 104 KIIKENYKTCPACGADFTR--QCLDIEKD 130
                                       556888899****999999..66666666 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 ?    2.6   0.5      0.24   1.3e+02      30      35 ..      22      27 ..       3      31 .. 0.49
   2 ?    4.0   0.0     0.087        49      30      41 ..      22      37 ..      19      51 .. 0.70
   3 ?    4.7   2.1      0.05        28      29      53 ..     111     142 ..     106     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.24
                    OrfB_Zn_ribbon 30 tCseCg 35
                                      tC+ Cg
  gi|488601245|ref|YP_007907716.1| 22 TCPICG 27
                                      455555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.087
                    OrfB_Zn_ribbon 30 tCseCgsknke....a 41
                                      tC+ Cg ++++     
  gi|488601245|ref|YP_007907716.1| 22 TCPICGDILDDiiakY 37
                                      8*****9988764443 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.05
                    OrfB_Zn_ribbon  29 ktCseCgsknke.......alsgrtfkCpnCg 53 
                                       ktC+ Cg+  ++       + ++ +++C  Cg
  gi|488601245|ref|YP_007907716.1| 111 KTCPACGADFTRqcldiekDGDWVKVYCGTCG 142
                                       79999999988888887666666677787777 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   2.3       2.4   1.4e+03      24      28 ..      23      27 ..       3      77 .. 0.53
   2 ?   11.0   0.8   0.00062      0.35      23      54 ..     112     144 ..     102     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.4
                              Elf1 24 CpfCn 28
                                      Cp C+
  gi|488601245|ref|YP_007907716.1| 23 CPICG 27
                                      33333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00062
                              Elf1  23 dCpfCnheksvev.kldkkekiaevsCkvCges 54 
                                       +Cp C+++ + ++ +++k  +  +v C++Cg+ 
  gi|488601245|ref|YP_007907716.1| 112 TCPACGADFTRQClDIEKDGDWVKVYCGTCGKL 144
                                       7*******9999868999999*********975 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.66   3.7e+02       5      12 ..       3      10 ..       1      14 [. 0.76
   2 ?    2.4   0.1      0.22   1.2e+02       5      11 ..      21      27 ..      18      31 .. 0.89
   3 ?    5.2   0.1      0.03        17       6      14 ..     112     119 ..     111     122 .. 0.76
   4 ?    0.6   0.2      0.82   4.6e+02      23      28 ..     137     142 ..     135     145 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.66
                           zf-RRN7  5 ppCgvCgc 12
                                      + C +Cg 
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGE 10
                                      6699**97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                           zf-RRN7  5 ppCgvCg 11
                                      + C++Cg
  gi|488601245|ref|YP_007907716.1| 21 ETCPICG 27
                                      67****9 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.03
                           zf-RRN7   6 pCgvCgcrs 14 
                                        C++Cg+ +
  gi|488601245|ref|YP_007907716.1| 112 TCPACGA-D 119
                                       7*****9.4 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.82
                           zf-RRN7  23 yCrrCh 28 
                                       yC  C+
  gi|488601245|ref|YP_007907716.1| 137 YCGTCG 142
                                       555554 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.8     0.031        17       6      13 ..       5      12 ..       2      16 .. 0.89
   2 ?    2.6   0.4      0.23   1.3e+02       2      11 ..      19      28 ..      18      30 .. 0.89
   3 ?    2.9   0.1      0.19   1.1e+02       3      11 ..     110     118 ..     108     123 .. 0.83
   4 ?   -0.4   0.0         2   1.1e+03       6      14 ..     138     146 ..     135     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.031
                      zf-dskA_traR  6 CeeCGEpI 13
                                      C  CGE+I
  gi|488601245|ref|YP_007907716.1|  5 CKICGEEI 12
                                      *******9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.23
                      zf-dskA_traR  2 iygsCeeCGE 11
                                      +y++C  CG+
  gi|488601245|ref|YP_007907716.1| 19 DYETCPICGD 28
                                      6999*****7 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.19
                      zf-dskA_traR   3 ygsCeeCGE 11 
                                       y +C  CG 
  gi|488601245|ref|YP_007907716.1| 110 YKTCPACGA 118
                                       889****96 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2
                      zf-dskA_traR   6 CeeCGEpIp 14 
                                       C +CG+ I 
  gi|488601245|ref|YP_007907716.1| 138 CGTCGKLIS 146
                                       778999886 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.0       1.2   6.7e+02      58      63 ..      22      27 ..       2      34 .. 0.68
   2 ?    2.9   0.0      0.23   1.3e+02      54      64 ..     108     118 ..     102     123 .. 0.73
   3 ?    6.2   0.3     0.022        12      55      68 ..     134     147 ..     124     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.2
                     zf-LITAF-like 58 yCpnCg 63
                                      +Cp Cg
  gi|488601245|ref|YP_007907716.1| 22 TCPICG 27
                                      455554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.23
                     zf-LITAF-like  54 dvehyCpnCga 64 
                                       + + +Cp Cga
  gi|488601245|ref|YP_007907716.1| 108 ENYKTCPACGA 118
                                       55677888886 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.022
                     zf-LITAF-like  55 vehyCpnCgallgt 68 
                                       v+ yC+ Cg+l+ +
  gi|488601245|ref|YP_007907716.1| 134 VKVYCGTCGKLISK 147
                                       789********986 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.085        48       4      15 ..       3      14 ..       1      18 [. 0.82
   2 ?    3.8   0.1     0.093        52       2      16 ..      19      33 ..      18      48 .. 0.80
   3 ?    0.0   0.1       1.4   7.9e+02      16      23 ..      82      89 ..      60      91 .. 0.75
   4 ?    5.4   0.3     0.029        16       1      14 [.     108     121 ..     108     129 .. 0.90
   5 ?   -0.7   0.1       2.4   1.4e+03      25      29 ..     136     140 ..     133     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.085
                              VATC  4 lrCsiCgesleg 15
                                      + C iCge+++g
  gi|488601245|ref|YP_007907716.1|  3 KLCKICGEEIVG 14
                                      56******9987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.093
                              VATC  2 nvlrCsiCgeslegk 16
                                      ++ +C iCg  l  +
  gi|488601245|ref|YP_007907716.1| 19 DYETCPICGDILDDI 33
                                      899******988765 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.4
                              VATC 16 kvyFekfd 23
                                       +y+e+f 
  gi|488601245|ref|YP_007907716.1| 82 AKYYERFR 89
                                      679*9996 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.029
                              VATC   1 knvlrCsiCgesle 14 
                                       +n+++C +Cg+++ 
  gi|488601245|ref|YP_007907716.1| 108 ENYKTCPACGADFT 121
                                       69********9985 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 2.4
                              VATC  25 rYCst 29 
                                       +YC+t
  gi|488601245|ref|YP_007907716.1| 136 VYCGT 140
                                       78887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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):              32  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 814.72
//
Query:       gi|488601246|ref|YP_007907717.1|  [L=141]
Description: hypothetical protein Asulf_01753 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-34  117.8   0.1    3.5e-34  116.7   0.0    1.6  2  DUF22     Domain of unknown function DUF22
  ------ inclusion threshold ------
       0.61   10.0   3.2        2.1    8.3   0.2    2.3  2  Myosin_N  Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.0   3.9e-38   3.5e-34       1     106 []       3     110 ..       3     110 .. 0.98
   2 ?   -1.5   0.0      0.23     2e+03      77      92 ..     126     141 .]     122     141 .] 0.82

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 3.9e-38
                             DUF22   1 evkivyrkd..geivrekvevepfgytrstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalg 75 
                                       ev+ivyr++  ge++ e v++e +++t++t+++w++liAdedve+k+Gevk ++i++  lp+++iv ++ ++rha+g
  gi|488601246|ref|YP_007907717.1|   3 EVRIVYRDEktGELKAEIVDTEDYEFTIATRGSWKMLIADEDVEFKAGEVKPVRIRRTPLPRESIVLRCPVTRHAFG 79 
                                       689****99888***************************************************************** PP

                             DUF22  76 tvldvvekgkpkkveeereiteavflpvedG 106
                                       +v++++++g+p+++ee+re+++++f ++++G
  gi|488601246|ref|YP_007907717.1|  80 YVASLGRRGEPQPIEEDRELNYVIFKALDNG 110
                                       ***************************9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.23
                             DUF22  77 vldvvekgkpkkveee 92 
                                       v++v + +kpkkv ee
  gi|488601246|ref|YP_007907717.1| 126 VMMVRRAKKPKKVREE 141
                                       7888999999999886 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2   0.00023       2.1       7      30 ..       9      32 ..       7      35 .. 0.88
   2 ?    1.8   0.2     0.025   2.2e+02       7      19 ..      41      53 ..      40      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00023
                                      TTSTTS-EEEEEEEEESSEEEEEE CS
                          Myosin_N  7 pDpkegyvkGeIkeeeGdkvtVet 30
                                      +D+k g +k+eI+++e+ ++t+ t
  gi|488601246|ref|YP_007907717.1|  9 RDEKTGELKAEIVDTEDYEFTIAT 32
                                      6999999************99988 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.025
                                      TTSTTS-EEEEEE CS
                          Myosin_N  7 pDpkegyvkGeIk 19
                                       D+++++ +Ge+k
  gi|488601246|ref|YP_007907717.1| 41 ADEDVEFKAGEVK 53
                                      69**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 938.43
//
Query:       gi|488601247|ref|YP_007907718.1|  [L=360]
Description: Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase-related flavin-dependent oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-68  230.9   0.0    2.6e-68  230.7   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.7   0.0   1.5e-72   2.6e-68       1     314 []       1     329 [.       1     329 [. 0.96

  Alignments for each domain:
  == domain 1  score: 230.7 bits;  conditional E-value: 1.5e-72
                    Bac_luciferase   1 mefgvflptrqggalgaasaslrylvelaraaEelGfdavwvaehhggpgga..................ldaftll 59 
                                       m+fg+++pt           ++ ++ + a+++Ee G+ ++w+a+h++g++ +                   daf+ +
  gi|488601247|ref|YP_007907718.1|   1 MRFGTVAPTFP---------PISEVSKTAKRLEEKGYSSLWFADHLMGWYPHdlwketvfamkypschmfYDAFCAI 68 
                                       78888888888.........9******************************************************** PP

                    Bac_luciferase  60 aalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlr 136
                                       ++++  Teri lgt+vt +++rhPavl qqa+t dh ++GRf+lg+g+g++++    +G+++   + rl+E++e+++
  gi|488601247|ref|YP_007907718.1|  69 CYASTSTERINLGTGVTEVFRRHPAVLLQQAVTADHATNGRFILGIGAGEAENT-VPYGIEFKNHVSRLEEALELMK 144
                                       ******************************************************.********************** PP

                    Bac_luciferase 137 rlwrg...eevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlraga 210
                                        ++++   e+++feG+f++ ++a    +p  + +P++++a+++++l+l+a+++dg+l++  ppee+a+++e+l++  
  gi|488601247|ref|YP_007907718.1| 145 IMLETdygETINFEGRFYRFRNAVFDLKPIRK-VPIWIGAHGDRMLKLTAKYGDGWLPTTIPPEEYARKAEKLDQ-- 218
                                       ***55675888*********999999999999.*****************************************8.. PP

                    Bac_luciferase 211 aeagrdpadirvgisltvivadteeeAraearaliagld..........fyaldsegagreaeaaeiqeeedanlwa 277
                                         ag    +i+ ++ ++++++++e+ ++  +r+ i +++          +  +++++ ++++ +++i+  +++++  
  gi|488601247|ref|YP_007907718.1| 219 -YAGD--KTIEKALFVSLVIDESEKGVENILRQPIMKVHalllpseyyrQLGYEHPLGKFYGLLDYIPTNYNKEEIL 292
                                       .4444..59**********************999988889999999998889999********************** PP

                    Bac_luciferase 278 gaadavpdelvaatalvGtpeqvaerlaayaeagvde 314
                                       +  + +pde+v+ ++++Gt e+v++++++ya+agv++
  gi|488601247|ref|YP_007907718.1| 293 SLVEKIPDEVVRLAYVAGTLEEVIQKFDEYARAGVEH 329
                                       ***********************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 00:00:00.41
# Mc/sec: 2657.50
//
Query:       gi|488601248|ref|YP_007907719.1|  [L=382]
Description: tungsten-dependent benzoyl-CoA reductase-related protein bamD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-35  121.4   0.1    2.9e-17   62.6   0.0    2.4  2  CCG         Cysteine-rich domain
    5.4e-08   33.2   3.8    1.4e-07   31.8   3.8    1.8  1  Fer4_8      4Fe-4S dicluster domain
      7e-08   32.9   6.8    1.8e-07   31.6   4.7    2.4  2  Fer4_17     4Fe-4S dicluster domain
    1.2e-07   31.8   8.0    2.6e-07   30.7   6.5    2.4  2  Fer4_9      4Fe-4S dicluster domain
    5.1e-05   24.1   5.6       0.11   13.4   0.2    2.8  2  Fer4_16     4Fe-4S double cluster binding domain
    0.00012   22.1  11.2     0.0074   16.4  11.1    2.9  3  Fer4_10     4Fe-4S dicluster domain
    0.00013   22.4   5.6    0.00013   22.4   5.6    2.2  1  Fer4_7      4Fe-4S dicluster domain
    0.00064   19.4  14.0      0.019   14.8   0.5    3.0  3  Fer4        4Fe-4S binding domain
     0.0028   17.8   7.5       0.35   11.0   0.3    2.8  3  Fer4_21     4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   15.9  15.3      0.066   13.3   1.5    2.8  2  Fer4_2      4Fe-4S binding domain
       0.02   15.4  16.7       0.14   12.7   1.4    3.1  3  Fer4_4      4Fe-4S binding domain
      0.081   13.1   1.5        5.9    7.1   0.1    2.6  2  Fer4_18     4Fe-4S dicluster domain
          8    7.4  14.5          8    7.4   2.7    3.7  3  Fer4_22     4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   2.1e-20   2.9e-17       2      85 .]     148     233 ..     147     233 .. 0.97
   2 !   56.6   0.0   1.6e-18   2.2e-15       1      84 [.     267     354 ..     267     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.1e-20
                               CCG   2 ayfdgCh.llraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivta 76 
                                       ++f+gC+   ++++ ev+k+l+++l+  gv++ +l ++e CCG+  +r+g+e l+e l+++n++t++++g++ ++t+
  gi|488601248|ref|YP_007907719.1| 148 LWFVGCAhSFDNRNIEVTKKLARILNDIGVNFAILgREEGCCGNDVRRAGEEGLFELLMDENAKTFDKYGVERLFTH 224
                                       79****8799999**************************************************************** PP

                               CCG  77 cpgCllqlk 85 
                                       +p+C++ +k
  gi|488601248|ref|YP_007907719.1| 225 SPHCFNAFK 233
                                       *****9875 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 1.6e-18
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkeelae.alakrnvetaeetgadai 73 
                                       v+y+d+C l+r++  y+ +r++l+ ++++++ve++ + e + CCG g+g+ + + + e + a+ ++ +a e ga+++
  gi|488601248|ref|YP_007907719.1| 267 VTYHDSCFLGRYNkiYDLPREILQMIPGVELVEMKSNrEMSLCCGGGAGNIVGDYEGEiQPARVRAIEAAESGAEIL 343
                                       89**********************************************9999887444466665555555669**** PP

                               CCG  74 vtacpgCllql 84 
                                       ++acp+Cll+l
  gi|488601248|ref|YP_007907719.1| 344 AVACPFCLLML 354
                                       *********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 !   31.8   3.8     1e-10   1.4e-07       3      63 ..      21      79 ..      19      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1e-10
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                       kC +Cg C+  Cpv  + ++++       +     e++l ++  +w C++c+ Cte Cp 
  gi|488601248|ref|YP_007907719.1| 21 LKCYQCGTCTGICPVSTTDQNFPRRFVLYSQL--GIEEKLLDAPEAWLCLSCKLCTEFCPR 79
                                      69************998877776666555444..222233446779**************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 !   31.6   4.7   1.3e-10   1.8e-07       1      59 [.      22      80 ..      22      82 .. 0.94
   2 ?    0.3   0.0      0.74     1e+03      22      48 ..     285     311 ..     270     314 .. 0.61

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.3e-10
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      +C qCg C+  Cp     +n p++++   +lg+ e+  + ++a lC++C++C++ CP +
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPVSTTDQNFPRRFVLYSQLGIEEKLLDAPEAWLCLSCKLCTEFCPRD 80
                                      6****************999999988888***99**99*******************86 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.74
                           Fer4_17  22 pkkllraaklglleeaekeekaslCie 48 
                                       p+++l+ +   +l e++ ++++slC++
  gi|488601248|ref|YP_007907719.1| 285 PREILQMIPGVELVEMKSNREMSLCCG 311
                                       55555555554566778889*****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 !   30.7   6.5   1.9e-10   2.6e-07       1      50 [.      22      81 ..      22      82 .. 0.92
   2 ?   -1.5   0.0       2.1   2.9e+03      11      25 ..     346     360 ..     339     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.9e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkga 50
                                      kC++Cg+C+  Cp  ++ +   +r++ + + +           + C++C+ C+e Cp++a
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPVSTTDQNFPRRFVLYSQLGIeeklldapeaWLCLSCKLCTEFCPRDA 81
                                      7*************9999999999998877666999**********************86 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                            Fer4_9  11 aCpagvvvedaaerk 25 
                                       aCp+++ + +++ ++
  gi|488601248|ref|YP_007907719.1| 346 ACPFCLLMLEDGVKM 360
                                       799998887776655 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 !   13.4   0.2   8.3e-05      0.11       1      20 [.      22      41 ..      19      59 .. 0.83
   2 !   12.1   1.2   0.00021      0.29       2      20 ..      67      85 ..      66     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.3e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C +Cg C+ +CP++  +++
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPVSTTDQN 41
                                      59999999999999877665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00021
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C +C+ C+e CP +a  ++
  gi|488601248|ref|YP_007907719.1| 67 CLSCKLCTEFCPRDAQPSE 85
                                      99***********997666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  11.1   5.3e-06    0.0074       8      56 .]      22      78 ..      17      78 .. 0.77
   2 !   13.4   1.0   4.6e-05     0.063       8      37 ..      66      95 ..      59     102 .. 0.74
   3 ?   -1.3   0.0       1.8   2.5e+03      18      23 ..     346     351 ..     327     372 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.3e-06
                           Fer4_10  8 tCirCgkCvkaCPadl......tsvgakgeaseeeavrk..kvekCtgcgaCveaCP 56
                                      +C +Cg+C+  CP++       ++ + + +  +ee+  +    + C  c  C+e CP
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPVSTtdqnfpRRFVLYSQLGIEEKLLDapEAWLCLSCKLCTEFCP 78
                                      8*************99*****955555554444444444257899***********9 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.6e-05
                           Fer4_10  8 tCirCgkCvkaCPadltsvgakgeaseeea 37
                                       C+ C+ C+++CP d++ +++  ++++ ++
  gi|488601248|ref|YP_007907719.1| 66 LCLSCKLCTEFCPRDAQPSEVMLAIKRMAV 95
                                      5************97766655555555544 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
                           Fer4_10  18 aCPadl 23 
                                       aCP++l
  gi|488601248|ref|YP_007907719.1| 346 ACPFCL 351
                                       466654 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   5.6   9.7e-08   0.00013       1      52 []      22      81 ..      22      81 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.7e-08
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.....gtekv...eidpekClgCgaCvavCPtga 52
                                      +C +Cg C+  Cpv++ + +   +       g+e+    + +++ Cl+C+ C + CP +a
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPVSTTDQNFPRRFVlysqlGIEEKlldAPEAWLCLSCKLCTEFCPRDA 81
                                      7************99999997633333333322222333445678************987 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.2   6.7e-05     0.092       7      20 ..      22      35 ..      19      37 .. 0.93
   2 !   14.8   0.5   1.4e-05     0.019       7      22 ..      66      81 ..      66      82 .. 0.94
   3 ?   -2.5   0.2         4   5.5e+03      16      20 ..     345     349 ..     344     349 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                                      TSSS-THHHHHSTT CS
                              Fer4  7 kCigCGaCvevCPv 20
                                      kC  CG+C  +CPv
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPV 35
                                      8************8 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                                      TSSS-THHHHHSTTTE CS
                              Fer4  7 kCigCGaCvevCPvgA 22
                                      +C  C++C e CP +A
  gi|488601248|ref|YP_007907719.1| 66 LCLSCKLCTEFCPRDA 81
                                      6*************99 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4
                                       HHSTT CS
                              Fer4  16 evCPv 20 
                                        +CP+
  gi|488601248|ref|YP_007907719.1| 345 VACPF 349
                                       69**6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.6   0.00053      0.74      40      54 ..      22      36 ..       9      43 .. 0.82
   2 !   11.0   0.3   0.00025      0.35      40      52 ..      66      78 ..      47      82 .. 0.85
   3 ?   -2.9   0.0       5.6   7.7e+03      42      47 ..     345     350 ..     332     358 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00053
                           Fer4_21 40 eCvGCnlCssvCPve 54
                                      +C  C  C+ +CPv+
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPVS 36
                                      788899999999984 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00025
                           Fer4_21 40 eCvGCnlCssvCP 52
                                       C  C+lC++ CP
  gi|488601248|ref|YP_007907719.1| 66 LCLSCKLCTEFCP 78
                                      5999********9 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.6
                           Fer4_21  42 vGCnlC 47 
                                       v+C  C
  gi|488601248|ref|YP_007907719.1| 345 VACPFC 350
                                       333333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.5   4.8e-05     0.066       8      21 ..      21      34 ..      13      35 .. 0.88
   2 ?   11.7   1.7   0.00016      0.22       9      21 ..      66      78 ..      60      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                            Fer4_2  8 drCigCgaCvsaCP 21
                                       +C +Cg+C+  CP
  gi|488601248|ref|YP_007907719.1| 21 LKCYQCGTCTGICP 34
                                      59************ PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00016
                            Fer4_2  9 rCigCgaCvsaCP 21
                                       C++C+ C+  CP
  gi|488601248|ref|YP_007907719.1| 66 LCLSCKLCTEFCP 78
                                      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 ?   11.6   2.5   0.00023      0.32       3      16 ..      22      35 ..      20      41 .. 0.89
   2 ?   12.7   1.4    0.0001      0.14       4      16 ..      67      79 ..      62      86 .. 0.91
   3 ?   -2.4   0.3       7.2   9.9e+03       6      10 ..     346     350 ..     345     351 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +C +Cg C+ +CP+
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPV 35
                                      699**********5 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C+ C+ C+ +CP 
  gi|488601248|ref|YP_007907719.1| 67 CLSCKLCTEFCPR 79
                                      ************5 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.2
                            Fer4_4   6 gCgsC 10 
                                        C+ C
  gi|488601248|ref|YP_007907719.1| 346 ACPFC 350
                                       46666 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0042       5.9      55      74 ..      17      36 ..       5      52 .. 0.78
   2 ?    4.4   0.2      0.03        41      61      73 ..      67      79 ..      53      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0042
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                      ++++ +c +c++c  +cP+ 
  gi|488601248|ref|YP_007907719.1| 17 AESSLKCYQCGTCTGICPVS 36
                                      45667899999999999875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.03
                           Fer4_18 61 cidcescvkvcPt 73
                                      c++c+ c + cP 
  gi|488601248|ref|YP_007907719.1| 67 CLSCKLCTEFCPR 79
                                      9999999999996 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.7    0.0058         8       1      15 [.      22      36 ..      22      44 .. 0.88
   2 ?    4.4   1.3      0.05        69       2      13 ..      67      78 ..      64      84 .. 0.91
   3 ?    0.9   0.1      0.61   8.4e+02      30      49 ..     263     282 ..     249     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0058
                           Fer4_22  1 rClsCgaCtlvCptC 15
                                      +C +Cg+Ct +Cp  
  gi|488601248|ref|YP_007907719.1| 22 KCYQCGTCTGICPVS 36
                                      7***********975 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.05
                           Fer4_22  2 ClsCgaCtlvCp 13
                                      ClsC  Ct  Cp
  gi|488601248|ref|YP_007907719.1| 67 CLSCKLCTEFCP 78
                                      999999999998 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.61
                           Fer4_22  30 egervrvwdsClleeftkva 49 
                                         ++v  +dsC+l +++k+ 
  gi|488601248|ref|YP_007907719.1| 263 INKKVTYHDSCFLGRYNKIY 282
                                       56788899999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2290.32
//
Query:       gi|488601249|ref|YP_007907720.1|  [L=146]
Description: TIGR00725 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-44  149.1   6.1    8.3e-44  148.9   6.1    1.0  1  LDcluster4       SLOG cluster4 family
    2.6e-11   43.7   0.1    2.6e-11   43.7   0.1    1.8  3  Lysine_decarbox  Possible lysine decarboxylase
    3.8e-06   26.3   2.4    0.00066   19.0   0.5    2.1  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 !  148.9   6.1   1.4e-47   8.3e-44       2     129 ..       2     125 ..       1     145 [. 0.91

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 1.4e-47
                        LDcluster4   2 lkigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdi 78 
                                        +igV+G+++  ++ e +e+a+e+GrliA++g++l++Gg +Gvmea++kGa ++gGl++G++p  s+k+ +n+y++ 
  gi|488601249|ref|YP_007907720.1|   2 KQIGVIGASR--CDAEIYEIAYEVGRLIARRGYILINGGLGGVMEASAKGAMDEGGLVIGVIPY-SDKNLANEYCTA 75 
                                       69********..****************************************************.777778999*** PP

                        LDcluster4  79 iiyTGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgt 129
                                       +i+T++g+a Rn+i+v+ssd++ia++g++GT+sE+a+al+egk v+++k +
  gi|488601249|ref|YP_007907720.1|  76 VIATNMGHA-RNMIIVHSSDALIAVDGGYGTVSEMAIALKEGKRVVAIKPK 125
                                       ********9.**************************************944 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       1.2     7e+03      54      64 ..      30      40 ..      28      42 .. 0.83
   2 !   43.7   0.1   4.3e-15   2.6e-11       1      74 [.      43     114 ..      43     131 .. 0.88
   3 ?   -1.2   0.0      0.34     2e+03       8      26 ..     112     130 ..     110     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                      SEEEE-S-SHH CS
                   Lysine_decarbox 54 dafvilPGGiG 64
                                       +++++ GG+G
  gi|488601249|ref|YP_007907720.1| 30 RGYILINGGLG 40
                                      5889999**99 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 4.3e-15
                                       HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHHHH CS
                   Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleElleilt 74 
                                       mea akga++ gg viG+ip +   ++ +ne+ + ++ ++  + R++ +v+ +da++++ GG+GT+ E+  +l 
  gi|488601249|ref|YP_007907720.1|  43 MEASAKGAMDEGGLVIGVIPYSD--KNLANEYCTAVIATNMGHARNMIIVHSSDALIAVDGGYGTVSEMAIALK 114
                                       9*****************88765..57779**************************************977665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.34
                                       HHHTTS-EEEEEECCHHHH CS
                   Lysine_decarbox   8 aleaggrviGiipkillae 26 
                                       al+ g+rv++i+pk +l  
  gi|488601249|ref|YP_007907720.1| 112 ALKEGKRVVAIKPKVILDG 130
                                       5678899999999888764 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 !   19.0   0.5   1.1e-07   0.00066      43     105 ..       2      64 ..       1      81 [. 0.93
   2 !    7.5   0.1   0.00037       2.2     144     188 ..      83     125 ..      71     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-07
                    DNA_processg_A  43 ravaiVGtRkaseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgtg 105
                                       ++++++G+ ++ ++  e+a ++ + +a++g++ + G+  G+ +a+ ++a+++gg  ++v++ +
  gi|488601249|ref|YP_007907720.1|   2 KQIGVIGASRCDAEIYEIAYEVGRLIARRGYILINGGLGGVMEASAKGAMDEGGLVIGVIPYS 64 
                                       689********************************************************9865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00037
                    DNA_processg_A 144 peRnriiaglseavlvveaaekSGalitaelAlelgrevfavpgd 188
                                        +Rn ii+  s+a++ v  +   G++  + +Al++g+ v+a++ +
  gi|488601249|ref|YP_007907720.1|  83 HARNMIIVHSSDALIAVDGGY--GTVSEMAIALKEGKRVVAIKPK 125
                                       58*************999875..9****************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 935.15
//
Query:       gi|488601250|ref|YP_007907721.1|  [L=167]
Description: Flavodoxin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0059   16.8   0.0       0.48   10.7   0.0    2.1  2  Flavodoxin_5  Flavodoxin domain
  ------ inclusion threshold ------
      0.021   14.5   0.0       0.21   11.3   0.0    2.0  2  Flavodoxin_3  Flavodoxin domain
      0.076   12.7   0.0       0.37   10.5   0.0    1.9  2  Flavodoxin_4  Flavodoxin
       0.13   12.1   0.0       0.21   11.4   0.0    1.3  1  DUF2016       Domain of unknown function (DUF2016)


Domain annotation for each model (and alignments):
>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00011      0.48       3      34 ..       6      37 ..       5      54 .. 0.87
   2 !    4.4   0.0    0.0094        42      45      95 ..      69     114 ..      59     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                      Flavodoxin_5  3 lYsSrdGqTkkiaeriaeelreegelvdvedv 34
                                      +Y+S  G T+k+ ++i++ l+++g +v+ +++
  gi|488601250|ref|YP_007907721.1|  6 IYFSWSGRTAKVFSYIEKFLKDRGYDVSKKEI 37
                                      8**********************999887776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0094
                      Flavodoxin_5  45 davvigasvyygkllpelakFvekhreaLstkpvalfsvsltarkpeksyv 95 
                                       d + +g++  + + +p +++F++k++  Ls k++ ++++     ++e+ y+
  gi|488601250|ref|YP_007907721.1|  69 DIIFLGSPKWTLNCPP-VTEFIKKYD--LSGKEIFIVLTYGG-FDEER-YL 114
                                       7788999999999999.******865..99999988775443.44444.44 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.06   2.7e+02       2      24 ..       5      27 ..       4      45 .. 0.81
   2 ?   11.3   0.0   4.6e-05      0.21      40      94 ..      67     122 ..      58     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.06
                      Flavodoxin_3  2 ilysSltGNTkkvAeaikealee 24
                                      ++y S +G T kv + i++ l++
  gi|488601250|ref|YP_007907721.1|  5 LIYFSWSGRTAKVFSYIEKFLKD 27
                                      5899***********99999987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.6e-05
                      Flavodoxin_3  40 eadvvfvGf..wvdkgtadeealkfle..tlknkkillfgTlGagkdseyakkilekvk 94 
                                       ++d++f+G   w+    +   +++f++  +l++k+i+++ T G  +++ y +++ +k+ 
  gi|488601250|ref|YP_007907721.1|  67 NSDIIFLGSpkWTLNCPP---VTEFIKkyDLSGKEIFIVLTYGGFDEERYLESLKQKIM 122
                                       567777775334444444...3445542269********************99998875 PP

>> Flavodoxin_4  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.13     6e+02       1      26 [.       2      30 ..       2      44 .. 0.61
   2 ?   10.5   0.0   8.2e-05      0.37      75     115 ..      69     108 ..      62     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                                      -EEEEE--SSSHHHHH...HHHHHHHHT- CS
                      Flavodoxin_4  1 kilvayfscsgvtkav...aeklaaitga 26
                                      ki + yfs sg t  v    ek+    g 
  gi|488601250|ref|YP_007907721.1|  2 KIDLIYFSWSGRTAKVfsyIEKFLKDRGY 30
                                      67788999999987762223444444444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.2e-05
                                       SEEEEEEE-BTTB--HHHHHHHHTS--TT-EEEEEEE-SS- CS
                      Flavodoxin_4  75 evlfvgfpvwwyiaptiintflesydfagkivvpfatsggs 115
                                       +++f+g p w   +p +   f++ yd++gk +  + t gg 
  gi|488601250|ref|YP_007907721.1|  69 DIIFLGSPKWTLNCPPV-TEFIKKYDLSGKEIFIVLTYGGF 108
                                       789******99999986.67**********99999998885 PP

>> DUF2016  Domain of unknown function (DUF2016)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.7e-05      0.21      35      57 ..     141     163 ..     135     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                           DUF2016  35 nGlflevrrpWLkviqklaaqkk 57 
                                        G f+ev+ pWLk i ++ ++++
  gi|488601250|ref|YP_007907721.1| 141 SGGFVEVVEPWLKEISRINFEQR 163
                                       578***************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1134.74
//
Query:       gi|488601251|ref|YP_007907722.1|  [L=66]
Description: hypothetical protein Asulf_01758 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.4   0.0     0.0029   16.3   0.0    1.0  1  Terminase_GpA    Phage terminase large subunit (GpA)
  ------ inclusion threshold ------
      0.012   16.0   0.2      0.014   15.7   0.2    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.015   14.8   1.8      0.062   12.8   0.1    2.0  2  Mu-like_Com      Mu-like prophage protein Com
      0.022   14.9   0.8      0.053   13.6   0.8    1.6  1  Zn-ribbon_8      Zinc ribbon domain
      0.052   13.5   0.8      0.084   12.8   0.8    1.3  1  zf-DNL           DNL zinc finger
      0.058   13.3   0.8         10    6.1   0.1    2.2  2  zinc_ribbon_4    zinc-ribbon domain
      0.063   13.3   0.5       0.23   11.5   0.6    1.6  1  CpXC             CpXC protein
      0.069   13.0   0.3      0.088   12.7   0.3    1.1  1  zf-ZPR1          ZPR1 zinc-finger domain
      0.071   13.2   4.0        3.4    7.8   0.3    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.073   12.8   1.1        1.2    8.9   0.2    2.2  2  Ribosomal_S27e   Ribosomal protein S27
      0.073   12.8   0.1      0.082   12.6   0.1    1.0  1  zf-DNA_Pol       DNA Polymerase alpha zinc finger
      0.089   13.3   1.1       0.58   10.7   0.1    2.0  2  Ribosomal_L44    Ribosomal protein L44
       0.13   12.7   3.7        8.3    7.0   2.3    2.3  2  zf-H2C2_2        Zinc-finger double domain
       0.36   10.8   3.0         11    6.1   0.5    2.2  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in


Domain annotation for each model (and alignments):
>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.2e-06    0.0029     191     236 ..       4      49 ..       1      51 [. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-06
                     Terminase_GpA 191 esdqrryyvpCphCgelqelsferlkwpegeaeekaryvCphcgsl 236
                                        sd ++y  +Cp+Cg+  + + + l   ege+    ++ C++c+s+
  gi|488601251|ref|YP_007907722.1|   4 GSDSEYYLFECPKCGDVNKHKGKVLDKAEGENIIVLKVKCEDCNSV 49 
                                       69*******************9999999**9************986 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.2   1.1e-05     0.014       5      36 ..      13      48 ..      10      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigq....cvyCadCga 36
                                       CP Cg  ++++   + +ae++      v C+dC+ 
  gi|488601251|ref|YP_007907722.1| 13 ECPKCGDVNKHKGKVLDKAEGENiivlKVKCEDCNS 48
                                      7*********9999999998888***********98 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 ?   12.8   0.1   4.9e-05     0.062      26      43 ..      13      30 ..      10      37 .. 0.84
   2 ?    2.4   0.1     0.083   1.1e+02      18      32 ..      34      48 ..      30      57 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                       Mu-like_Com 26 KCPRCGtLnHlkaeslda 43
                                       CP+CG +n  k++ ld 
  gi|488601251|ref|YP_007907722.1| 13 ECPKCGDVNKHKGKVLDK 30
                                      6************99983 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.083
                       Mu-like_Com 18 eAlDeltiKCPRCGt 32
                                      e +  l++KC  C  
  gi|488601251|ref|YP_007907722.1| 34 ENIIVLKVKCEDCNS 48
                                      555568889988865 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   0.8   4.1e-05     0.053       4      36 ..      10      51 ..       9      55 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                       Zn-ribbon_8  4 YeYrCeeCghefe....vlqsisdap.......lta.CPeCgs.ev 36
                                      Y ++C +Cg +      vl +    +       l++ C +C+s  +
  gi|488601251|ref|YP_007907722.1| 10 YLFECPKCGDVNKhkgkVLDK----AegeniivLKVkCEDCNSvGL 51
                                      88*******777755555554....334468996666****98665 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   6.5e-05     0.084       3      40 ..      11      52 ..       9      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.5e-05
                            zf-DNL  3 tftCkaCetrsske...iskkaYekGvVi.vqCpgCknrHli 40
                                       f C +C+  ++++   + k   e+ +V+ v+C++C++  li
  gi|488601251|ref|YP_007907722.1| 11 LFECPKCGDVNKHKgkvLDKAEGENIIVLkVKCEDCNSVGLI 52
                                      69******99988644355666677777789******98777 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.011        14       4      32 ..      13      18 ..      11      20 .. 0.54
   2 ?    6.1   0.1    0.0079        10       2      10 ..      40      48 ..      38      53 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                     zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCg 32
                                      +Cp+C                       g
  gi|488601251|ref|YP_007907722.1| 13 ECPKC-----------------------G 18
                                      55555.......................4 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0079
                     zinc_ribbon_4  2 kitCpsCka 10
                                      k+ C+ C++
  gi|488601251|ref|YP_007907722.1| 40 KVKCEDCNS 48
                                      345555554 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   0.00018      0.23      34      68 ..       8      42 ..       5      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                              CpXC 34 slfeatCpkCgatakleapllyhdpekellillvp 68
                                      ++  ++CpkCg  +k + ++l + + +++++l v 
  gi|488601251|ref|YP_007907722.1|  8 EYYLFECPKCGDVNKHKGKVLDKAEGENIIVLKVK 42
                                      67789***********9999988877776666554 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   6.9e-05     0.088       2      37 ..      13      47 ..      12      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                           zf-ZPR1  2 lCpsCgkengetrllltkiPyfkeviimsfeCehCg 37
                                      +Cp+Cg +  +++ ++++    +++i+  ++Ce+C+
  gi|488601251|ref|YP_007907722.1| 13 ECPKCG-DVNKHKGKVLDKAEGENIIVLKVKCEDCN 47
                                      6****7.778888888899****************7 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0027       3.4       3      12 ..      13      22 ..      12      24 .. 0.77
   2 ?    6.8   0.4    0.0056       7.1       2       9 ..      41      48 ..      41      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0027
                            zf-ACC  3 KCpsCgemly 12
                                       Cp+Cg +  
  gi|488601251|ref|YP_007907722.1| 13 ECPKCGDVNK 22
                                      6*****9866 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0056
                            zf-ACC  2 tKCpsCge 9 
                                      +KC+ C++
  gi|488601251|ref|YP_007907722.1| 41 VKCEDCNS 48
                                      7*****98 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.072        93       9      15 ..      13      19 ..       6      31 .. 0.76
   2 ?    8.9   0.2    0.0009       1.2       6      15 ..      39      48 ..      35      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.072
                                      E-TTTS- CS
                    Ribosomal_S27e  9 kCpdCen 15
                                       Cp+C++
  gi|488601251|ref|YP_007907722.1| 13 ECPKCGD 19
                                      5777764 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0009
                                      EEEE-TTTS- CS
                    Ribosomal_S27e  6 ldvkCpdCen 15
                                      l+vkC dC+ 
  gi|488601251|ref|YP_007907722.1| 39 LKVKCEDCNS 48
                                      89******96 PP

>> zf-DNA_Pol  DNA Polymerase alpha zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.4e-05     0.082      11      54 ..       6      48 ..       5      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
                                      T---EEEE-TTT--EEEE-.SSS--S.SEEEETTEEEET..TT-- CS
                        zf-DNA_Pol 11 dceplelrCpsCkeefefe.gvfesaeeekvtasglrCsnesCka 54
                                      d+e   ++Cp+C+  ++ + +v ++ae+e++    ++C+  +C++
  gi|488601251|ref|YP_007907722.1|  6 DSEYYLFECPKCGDVNKHKgKVLDKAEGENIIVLKVKCE--DCNS 48
                                      6788899*********9993477777999*********8..6876 PP

>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2      0.19   2.4e+02      54      68 ..      12      26 ..      10      32 .. 0.77
   2 ?   10.7   0.1   0.00046      0.58      49      75 ..      36      62 ..      22      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                                      EEETTT--EEE---- CS
                     Ribosomal_L44 54 leCteCkkkrlkalk 68
                                      +eC +C+     ++k
  gi|488601251|ref|YP_007907722.1| 12 FECPKCGDVNKHKGK 26
                                      79****998877766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00046
                                      B--EEEEETTT--EEE----BBS--EE CS
                     Ribosomal_L44 49 KivlrleCteCkkkrlkalkRakkfel 75
                                       ivl+++C++C++  l ++ + +++e+
  gi|488601251|ref|YP_007907722.1| 36 IIVLKVKCEDCNSVGLIKILKPGNIEI 62
                                      59***********99999988888776 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 ?    7.0   2.3    0.0065       8.3      15      22 ..      12      19 ..       5      23 .. 0.84
   2 ?    5.5   0.0     0.019        25       5      22 ..      23      48 ..      19      50 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0065
                         zf-H2C2_2 15 yeCplCdk 22
                                      +eCp+C++
  gi|488601251|ref|YP_007907722.1| 12 FECPKCGD 19
                                      8*****97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                         zf-H2C2_2  5 HirkHt....gekp....yeCplCdk 22
                                      H  k      ge++    ++C+ C+ 
  gi|488601251|ref|YP_007907722.1| 23 HKGKVLdkaeGENIivlkVKCEDCNS 48
                                      4444445555777533337*****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 ?    6.1   0.5    0.0085        11      31      39 ..      12      20 ..       2      39 .. 0.72
   2 ?    5.7   0.1     0.011        14       9      23 ..      39      53 ..      35      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0085
                                      .E-TTTTTS CS
                         Anti-TRAP 31 leCPkCsGk 39
                                      +eCPkC+ +
  gi|488601251|ref|YP_007907722.1| 12 FECPKCGDV 20
                                      69****854 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                                      CEEE-TTTTTTSEET CS
                         Anti-TRAP  9 LEtkCdaCngsGkie 23
                                      L +kC+ Cn  G i+
  gi|488601251|ref|YP_007907722.1| 39 LKVKCEDCNSVGLIK 53
                                      7799****9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 490.50
//
Query:       gi|488601252|ref|YP_007907723.1|  [L=453]
Description: seryl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  138.3   0.0    1.3e-39  136.0   0.0    1.9  2  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    1.8e-22   79.6  13.6    3.2e-22   78.8  13.6    1.3  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
     0.0064   16.7   4.3      0.011   15.9   4.3    1.3  1  CREPT         Cell-cycle alteration and expression-elevated p
     0.0086   16.5   0.1       0.02   15.3   0.1    1.6  1  ANAPC15       Anaphase-promoting complex subunit 15
  ------ inclusion threshold ------
      0.073   13.5  14.0       0.14   12.5  14.0    1.4  1  DUF4200       Domain of unknown function (DUF4200)
        0.1   11.3   2.6       0.55    8.9   1.2    2.4  2  Dor1          Dor1-like family
       0.26   10.1   4.4       0.47    9.3   4.4    1.3  1  FemAB         FemAB family
       0.57    8.7   6.5       0.86    8.1   6.5    1.2  1  FapA          Flagellar Assembly Protein A
       0.65    9.2   4.4          1    8.6   4.4    1.2  1  TMPIT         TMPIT-like protein
       0.79   10.2   8.8        1.9    9.0   8.8    1.6  1  APG6_N        Apg6 coiled-coil region
        0.8    9.0   5.2        1.2    8.3   5.2    1.2  1  DUF3450       Protein of unknown function (DUF3450)
        2.6    7.8   9.5          5    6.9   9.5    1.4  1  DUF724        Protein of unknown function (DUF724)
        6.2    6.7   8.8         16    5.4   8.8    1.7  1  DivIC         Septum formation initiator
        6.3    7.1   8.7         17    5.7   2.1    2.5  2  Spc24         Spc24 subunit of Ndc80


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 ?   -0.1   0.0      0.59   7.6e+02      49      91 ..      59     100 ..      44     212 .. 0.78
   2 !  136.0   0.0     1e-42   1.3e-39       1     178 [.     235     416 ..     234     417 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.59
                                       TTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  49 EksdsrGLlRvreFhqkdgyvfha.easlddslrdlikaisrif 91 
                                       E ++++G  R re  +k +  + +  +s + +l++l+++ ++++
  gi|488601252|ref|YP_007907723.1|  59 EMKNLKG--REREKAMKKAKEIASmVKSKEKELKELENELNEVL 100
                                       3337888..99998888888777756777777888887777765 PP

  == domain 2  score: 136.0 bits;  conditional E-value: 1e-42
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhae 73 
                                       Yk+ed+   +++L++t+e+++++++ devl +k+LPl ++ +++++R+E+     d++G++Rv++F++ ++++f+++
  gi|488601252|ref|YP_007907723.1| 235 YKVEDE---DLYLIATSEHPIAAMHMDEVLEEKELPLLYAGVSPCFRKEAGahgkDTKGIFRVHQFNKVEQFIFCLP 308
                                       566665...8******************99********************77899********************** PP

                                       GGHHHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  74 aslddslrdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvl 150
                                       ++++d  ++l++ ++++++ l +++r +  +++++ + +++k+++e++++s++k++e+++++++ + +s rl+++++
  gi|488601252|ref|YP_007907723.1| 309 EQSWDWHEKLLENVEDLWQGLEIPYRIVNICTGDIGIVAAKKYDLEVWMPSQGKYREMVSCSNCTDWQSYRLNIRFA 385
                                       ************************9988888********************************************** PP

                                       CTTS..SEEEEEEEEEE.EEHHHHHHHHHHH CS
                                       xxxx..xxxxxxxxxxx.xxxxxxxxxxxxx RF
                      tRNA-synt_2b 151 denn..reksvimicaa.igveRllsaileq 178
                                       +e +   + +v++++ + i+++R + ai+e+
  gi|488601252|ref|YP_007907723.1| 386 EERGkpTKGFVHTLNSTaIATTRAITAIIEN 416
                                       **99445679*****999***********98 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8  13.6   2.5e-25   3.2e-22       4     107 ..       5     106 ..       5     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.5e-25
                                       HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHH CS
                      Seryl_tRNA_N   4 iklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelk 80 
                                       +k +renp+ + +++kkR +d + v++ +eld+k+re++ +l++l++erN++s+e++++k +  ++e+ ++++ke+ 
  gi|488601252|ref|YP_007907723.1|   5 LKSLRENPKILIDSQKKRDGDLEIVERAIELDKKWREMRYQLDKLRHERNKISREMKNLKGR--EREKAMKKAKEIA 79 
                                       589*********************************************************86..79*********** PP

                                       HHHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  81 eelkaleaelkeleaeleklllaiPNi 107
                                         +k +e+elkele+el+++ll+iPNi
  gi|488601252|ref|YP_007907723.1|  80 SMVKSKEKELKELENELNEVLLSIPNI 106
                                       **************************9 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 !   15.9   4.3     9e-06     0.011      50     126 ..      26     106 ..      11     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9e-06
                             CREPT  50 lkqveealella...eYnkrLeaeleeRkklakmledfleaqkellakaeek.leelkeklekvksvrkelkshiqs 122
                                       l+ ve a+el +   e   +L++  +eR+k+++ +++++   +e++ k++++ ++ +k+k +++k+ ++el++ + s
  gi|488601252|ref|YP_007907723.1|  26 LEIVERAIELDKkwrEMRYQLDKLRHERNKISREMKNLKGREREKAMKKAKEiASMVKSKEKELKELENELNEVLLS 102
                                       555666665544000344578888899************999988766555505678******************** PP

                             CREPT 123 LPdL 126
                                       +P++
  gi|488601252|ref|YP_007907723.1| 103 IPNI 106
                                       **97 PP

>> ANAPC15  Anaphase-promoting complex subunit 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.5e-05      0.02      23      59 ..      83     119 ..      78     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                           ANAPC15  23 cddEteLaqlEqehqewlqsIaekdnnlvpiGKpase 59 
                                       ++ E eL++lE+e +e l sI +   + vpiG+  se
  gi|488601252|ref|YP_007907723.1|  83 KSKEKELKELENELNEVLLSIPNILHDSVPIGRDDSE 119
                                       6789******************************999 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5  14.0   0.00011      0.14      21      91 ..      27      98 ..      18     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                           DUF4200 21 eiqrleealkqreeelekkeqeleedllkfdkflkend.akraralkkaeeerklkkekeaeikklkaeiet 91
                                      ei ++  +l+++++e++ +  +l+ + +k  + +k  + ++r++a+kka+e + + k+ke+e+k+l++e+++
  gi|488601252|ref|YP_007907723.1| 27 EIVERAIELDKKWREMRYQLDKLRHERNKISREMKNLKgREREKAMKKAKEIASMVKSKEKELKELENELNE 98
                                      678888899**************************9875899***************************987 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.2   0.00043      0.55       8      76 ..      38     110 ..      29     124 .. 0.63
   2 ?    0.7   0.0      0.13   1.7e+02     229     250 ..     292     312 ..     279     341 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00043
                              Dor1   8 pleelekepelLaeeaeeilaqiqdLarknyktlidaaealeair....qelediraqledLvlklpkLteec 76 
                                       +  e++ +  +L+ e+++i +++++L+   +   +++a+++ ++     +el++++++l++++l++p++ +  
  gi|488601252|ref|YP_007907723.1|  38 KWREMRYQLDKLRHERNKISREMKNLKGREREKAMKKAKEIASMVkskeKELKELENELNEVLLSIPNILHDS 110
                                       4556666777777777777777777777777777777766665541111456666666666666666655444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.13
                              Dor1 229 vrvnlfdvllqYraifpdegst 250
                                        rv+ f++++q+   +p e+s 
  gi|488601252|ref|YP_007907723.1| 292 FRVHQFNKVEQFIFCLP-EQSW 312
                                       56666666666655555.4333 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.4   0.00037      0.47     238     297 ..      33      95 ..      23     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00037
                             FemAB 238 lnlaeylkelqekleklekklakleekleknpe...kkkkkklkelekqlaslekelkeaeef 297
                                       ++l+++  e++ +l+kl+++++k+ +++++ +    +k++kk ke+ + ++s ekelke+e+ 
  gi|488601252|ref|YP_007907723.1|  33 IELDKKWREMRYQLDKLRHERNKISREMKNLKGrerEKAMKKAKEIASMVKSKEKELKELENE 95 
                                       7788888888889999999988888876555446789**********************9974 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.5   0.00067      0.86     334     411 ..      34      99 ..      19     122 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00067
                              FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                       el++k +e++ +l +l+ e +k+ +++k l+              + +k+ ++ +++ + +++ e+elkel++el++
  gi|488601252|ref|YP_007907723.1|  34 ELDKKWREMRYQLDKLRHERNKISREMKNLKG------------REREKAMKKAKEIASMVKSKEKELKELENELNE 98 
                                       45555556666666666666666666555555............566777777777777777777777777777776 PP

                              FapA 411 k 411
                                        
  gi|488601252|ref|YP_007907723.1|  99 V 99 
                                       5 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.4   0.00078         1      21      90 ..      28      97 ..      11     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00078
                             TMPIT 21 ykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllp 90
                                      + ++  el k   +++ +++k +++ +++++++k+lk + +e+  ++++e+++++k+++k lke+e+ l 
  gi|488601252|ref|YP_007907723.1| 28 IVERAIELDKKWREMRYQLDKLRHERNKISREMKNLKGREREKAMKKAKEIASMVKSKEKELKELENELN 97
                                      4556667778888888999999999999999999999998899999999999999999999999998875 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.8    0.0015       1.9      54     122 ..      30      99 ..       4     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                            APG6_N  54 eeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne.lqlelleleeeldsl 122
                                       e+  +l+k+ +e+  +L++l +er ++ +e+++l+  ++++  ++++++ +  + ++ el+ele+el+ +
  gi|488601252|ref|YP_007907723.1|  30 ERAIELDKKWREMRYQLDKLRHERNKISREMKNLKGREREKAMKKAKEIASMVKsKEKELKELENELNEV 99 
                                       3445688889999999999999999999999999988888888888888777666999999999999877 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.2   0.00096       1.2      34      91 ..      41      99 ..      27     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00096
                           DUF3450 34 qsqkkidklddekqellaeyralk.eeleslevyneqlerlvasqeqeiasleeqieei 91
                                      ++  + dkl  e++++++e+++lk +e e++ ++ ++ +++v+s e+e+++le++++e+
  gi|488601252|ref|YP_007907723.1| 41 EMRYQLDKLRHERNKISREMKNLKgREREKAMKKAKEIASMVKSKEKELKELENELNEV 99
                                      5566789****************96788999999*********************9986 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.5    0.0039         5     103     176 ..      24      94 ..      15     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                            DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeled 176
                                          ++ e+  +l+kk +e +++  kl +e +++++++++l+ ++   +ek ++++keia++ +++ek  +ele+
  gi|488601252|ref|YP_007907723.1|  24 GDLEIVERAIELDKKWREMRYQLDKLRHERNKISREMKNLKGRE---REKAMKKAKEIASMVKSKEKELKELEN 94 
                                       556778888899*************************9999988...688889999999987766655555554 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   8.8     0.012        16      20      72 ..      33      86 ..      29      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX.XXXXXXXXXXXXXXXXXXXX CS
                             DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLks.dedyieerARselglvkpgE 72
                                       +l+++  +   +l+kl+ e+++  +e k+Lk  +++   ++A++   +vk+ E
  gi|488601252|ref|YP_007907723.1| 33 IELDKKWREMRYQLDKLRHERNKISREMKNLKGrEREKAMKKAKEIASMVKSKE 86
                                      67888999999********************76777888999********9988 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.0     0.018        23       8      44 ..      27      68 ..      20      78 .. 0.66
   2 ?    5.7   2.1     0.013        17       8      43 ..      70     105 ..      65     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
                             Spc24  8 riakelsdleselesleselaelkeeleeleeesee.....k 44
                                      +i++ + +l+++  +++ +l++l++e +++++e ++     +
  gi|488601252|ref|YP_007907723.1| 27 EIVERAIELDKKWREMRYQLDKLRHERNKISREMKNlkgreR 68
                                      566677777788888888888888888888888777643322 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                             Spc24   8 riakelsdleselesleselaelkeeleeleeesee 43 
                                       ++ k+++++ s ++s e+el+el++el+e+  +  +
  gi|488601252|ref|YP_007907723.1|  70 KAMKKAKEIASMVKSKEKELKELENELNEVLLSIPN 105
                                       678999**********************98776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1775  (0.0990016); expected 358.6 (0.02)
Passed bias filter:                      888  (0.0495287); expected 358.6 (0.02)
Passed Vit filter:                       154  (0.00858944); 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: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 2916.00
//
Query:       gi|488601253|ref|YP_007907724.1|  [L=379]
Description: hypothetical protein Asulf_01760 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00014   22.0   0.0    0.00029   21.0   0.0    1.4  1  DUF4157   Domain of unknown function (DUF4157)


Domain annotation for each model (and alignments):
>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.6e-08   0.00029      40      76 ..     112     148 ..     104     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-08
                           DUF4157  40 AfTlgndivfaageyqpesaagrellaHELtHvvqqr 76 
                                       Af   + +++ +++++p s++g+e laHEL H +q r
  gi|488601253|ref|YP_007907724.1| 112 AFYWKDAVYVVRENFDPYSNSGKEALAHELEHAIQDR 148
                                       6666788999999**********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2179.64
//
Query:       gi|488601254|ref|YP_007907725.1|  [L=72]
Description: hypothetical protein Asulf_01761 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.2   0.0     0.0083   15.7   0.0    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.017   15.1   0.1    1.1  1  Peptidase_M16  Insulinase (Peptidase family M16)
       0.03   14.4   0.0      0.037   14.1   0.0    1.1  1  Sigma70_r3     Sigma-70 region 3
        0.1   13.0   0.0       0.22   11.9   0.0    1.7  1  FaeA           FaeA-like 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 !   15.7   0.0   1.8e-06    0.0083      19      47 ..      39      67 ..      39      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-06
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      s++e+Ae  +++++  + ++ +Le+eG +
  gi|488601254|ref|YP_007907725.1| 39 SISEVAESMNMTVTEFLSYVGKLEKEGKL 67
                                      789************************76 PP

>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   3.7e-06     0.017      32      75 ..      14      57 ..      10      68 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-06
                                      THHHHHHHHTTSBBSSSCHHHHHHHHHHTTCEEEEEEESSEEEE CS
                     Peptidase_M16 32 GlAHllehmafkgTkkypsnklaeeleklGgslnAttsrentvY 75
                                      G+A ++eh+ +k+Tk+++++kl +   ++ +++   t +e  +Y
  gi|488601254|ref|YP_007907725.1| 14 GMAEICEHFTLKNTKQRKEKKLRSGSISEVAESMNMTVTEFLSY 57
                                      9*****************98876655444444444455555555 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.2e-06     0.037       7      37 ..      25      54 ..      23      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.2e-06
                                      HHHHHHHHHHHSSXXXHHHHHHHHTXXHHHH CS
                        Sigma70_r3  7 kraqreLeqelgrePtpeEiAeeLglseekV 37
                                      k+++ + e +l r+ ++ E+Ae++++++ + 
  gi|488601254|ref|YP_007907725.1| 25 KNTKQRKEKKL-RSGSISEVAESMNMTVTEF 54
                                      66777778888.***************9875 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.9e-05      0.22      16      46 ..      38      68 ..       5      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.9e-05
                                      --HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA 16 ckTreiAdalglsaYQaRyYLeqLekegkik 46
                                      +  +e+A+ + ++     +Y  +Lekegk+k
  gi|488601254|ref|YP_007907725.1| 38 GSISEVAESMNMTVTEFLSYVGKLEKEGKLK 68
                                      5679*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 428.40
//
Query:       gi|488601255|ref|YP_007907726.1|  [L=375]
Description: hypothetical protein Asulf_01762 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   50.6   0.0    6.3e-13   49.5   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    1.5e-06   28.6   1.2    2.7e-06   27.8   0.2    2.0  2  SPASM        Iron-sulfur cluster-binding domain
    6.9e-06   26.2   0.0    1.7e-05   25.0   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
    0.00047   20.4   0.0    0.00095   19.4   0.0    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 !   49.5   0.0   1.4e-16   6.3e-13       1     137 [.       4     113 ..       4     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.4e-16
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       ++vt  CnlrCs+C r+        gr++++e i++++++       ++v+ g gepll++++++++ rl  +    
  gi|488601255|ref|YP_007907726.1|   4 IEVTSSCNLRCSYCFRK------NNGRDIDLEIIEKIADSD-----DEFVLYGYGEPLLNKNLEKIVSRLNGK---- 65 
                                       68999************......69*************999.....69*************999999999887.... PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealekl 137
                                         it+ tngt +        +e + dr+ ++ ++++   +l++m rg ++e++ ++l+k+
  gi|488601255|ref|YP_007907726.1|  66 --ITINTNGTID--------AEIPADRIGFSMDSLNRY-YLQKM-RGVEPEKIERNLKKA 113
                                       ..*********9........67777*************.*****.9************98 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.1         4   1.8e+04       7      16 ..      65      74 ..      63      75 .. 0.80
   2 !   27.8   0.2   5.9e-10   2.7e-06       5      67 ..     268     339 ..     265     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 4
                             SPASM  7 slfInsdGdV 16
                                       ++In +G++
  gi|488601255|ref|YP_007907726.1| 65 KITINTNGTI 74
                                      5789999985 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 5.9e-10
                             SPASM   5 srslfInsdGdVvpCcvd........kktyvee..lklGnireesleeIwnse.eyqefrkskkfplielCrnC 67 
                                       + slf++sdG+V+ C++         ++++++   +++G+++ ++++++ +s   ++ +r + + +++++C++C
  gi|488601255|ref|YP_007907726.1| 268 RDSLFVRSDGKVSSCMILsrshreflNNHWRDVpeFIVGDLNSQDIDDVRESLaSFESIR-A-NMRNFPWCADC 339
                                       5789***********66689987777555544478**************99998999999.3.3333557**** 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 !   25.0   0.0   3.7e-09   1.7e-05       5      96 ..       7      79 ..       4      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.7e-09
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeypekk 82
                                      +s+Cnl C  C++k+      g   + e++e+i   ++++e      vl G GePL+    k+l k+v+rl       k
  gi|488601255|ref|YP_007907726.1|  7 TSSCNLRCSYCFRKN-----NGRDIDLEIIEKIA--DSDDE-----FVLYGyGEPLLN---KNLEKIVSRLNG-----K 65
                                      79**********999.....66667777776776..44444.....59********54...677788888765.....5 PP

                           Fer4_14 83 iwletngtleiele 96
                                      i+++tngt++ e+ 
  gi|488601255|ref|YP_007907726.1| 66 ITINTNGTIDAEIP 79
                                      6********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 !   19.4   0.0   2.1e-07   0.00095      13      82 ..       8      65 ..       4      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.1e-07
                           Fer4_12 13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllG.GEPllpenaeallelvkevkee 82
                                      s Cnl+C++Cf     + ++g++++ e++e+i      +s+++++l G GEPll   ++ l ++v ++  +
  gi|488601255|ref|YP_007907726.1|  8 SSCNLRCSYCF-----RKNNGRDIDLEIIEKIA-----DSDDEFVLYGyGEPLL---NKNLEKIVSRLNGK 65
                                      78*********.....7899*****99999986.....56899999999*****...66677777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2224.73
//
Query:       gi|488601256|ref|YP_007907727.1|  [L=234]
Description: preQ(0) biosynthesis protein QueC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-67  227.4   0.0    1.5e-67  227.2   0.0    1.0  1  QueC             Queuosine biosynthesis protein QueC
    0.00012   21.8   0.0    0.00023   20.8   0.0    1.6  2  ThiI             Thiamine biosynthesis protein (ThiI)
    0.00012   21.9   0.1    0.00019   21.2   0.1    1.2  1  Asn_synthase     Asparagine synthase
    0.00026   19.9   0.0     0.0004   19.3   0.0    1.3  1  tRNA_Me_trans    tRNA methyl transferase
     0.0005   19.5   0.2     0.0012   18.2   0.1    1.7  2  Arginosuc_synth  Arginosuccinate synthase
    0.00058   19.1   0.0     0.0011   18.1   0.0    1.5  2  NAD_synthase     NAD synthase
     0.0018   18.0   0.0     0.0061   16.3   0.0    1.8  2  ATP_bind_3       PP-loop family


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.2   0.0   5.9e-71   1.5e-67       2     208 ..       3     207 ..       2     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 227.2 bits;  conditional E-value: 5.9e-71
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG------ CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeie 78 
                                       av+++SGG+DStt+l++  ++g+ev+altf Ygq+h++e++a kkiak lg+ +hk++d++ ++el +   +++ +e
  gi|488601256|ref|YP_007907727.1|   3 AVLIFSGGVDSTTLLYYLISKGYEVHALTFIYGQKHAREVDASKKIAKLLGI-KHKVVDITSIHELISRGSLTGGEE 78 
                                       9***************************************************.**********99886655555568 PP

                                       -----...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH.HTS--EE CS
                              QueC  79 vpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg.edkkiei 154
                                       vpk  ++ee+ + t+Vp+RN+i+l++a +ya + ++++++++++++d+s YPDcr+efvk +++al l+  ++++e+
  gi|488601256|ref|YP_007907727.1|  79 VPKDFYTEETQKLTIVPNRNMILLAIAGGYAVKENIREVYYAAHKSDYSIYPDCRKEFVKVMDAALYLAnLWTPVEL 155
                                       *********************************************************************7789**** PP

                                       E-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHH CS
                              QueC 155 eaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfee 208
                                       +aP++d++K+eiv lg +lgvp+e+t+sCYeg+e+  +C +C +C  R+++f +
  gi|488601256|ref|YP_007907727.1| 156 KAPFVDIEKSEIVGLGLKLGVPYELTWSCYEGKER--PCLSCGTCLERTEAFLM 207
                                       ********************************555..**************976 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   8.8e-08   0.00023       6      57 ..       3      53 ..       1     116 [. 0.80
   2 ?   -3.0   0.0       1.8   4.6e+03     142     160 ..     157     175 ..     152     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.8e-08
                              ThiI  6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaella 57
                                      ++++ SgG+DS    y l+++G +v++++++ +  + +++ +  +k+a+ll 
  gi|488601256|ref|YP_007907727.1|  3 AVLIFSGGVDSTTLLYYLISKGYEVHALTFI-YGQKHAREVDASKKIAKLLG 53
                                      68899*************************8.44444555566677777664 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                              ThiI 142 rPLigldKeeiiklAkeig 160
                                        P + ++K ei+ l  ++g
  gi|488601256|ref|YP_007907727.1| 157 APFVDIEKSEIVGLGLKLG 175
                                       5899999999998887776 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   7.6e-08   0.00019      23      80 ..       6      62 ..       3      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.6e-08
                      Asn_synthase 23 lLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlt 80
                                       +SGG+DS+++ +++  +   ++++ +  + +k+  e+++ k++a+ lg++h  + +t
  gi|488601256|ref|YP_007907727.1|  6 IFSGGVDSTTLLYYLISKGY-EVHALTFIYGQKHAREVDASKKIAKLLGIKHKVVDIT 62
                                      58***********9999985.9********99********************999887 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.6e-07    0.0004       4      72 ..       4      63 ..       1      67 [. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-07
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                      v  +SgGVDS+  ++ l ++gyev ++++   ++         + +++   +++a+ lgi+++vvd+++
  gi|488601256|ref|YP_007907727.1|  4 VLIFSGGVDSTTLLYYLISKGYEVHALTFIYGQK---------HAREVDASKKIAKLLGIKHKVVDITS 63
                                      6678*********************998766544.........346778899*************9875 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   4.8e-07    0.0012       1      60 [.       4      62 ..       4      68 .. 0.86
   2 ?   -2.8   0.0       1.1   2.9e+03      46      65 ..     121     138 ..      99     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                   Arginosuc_synth  1 vLaysGGlDtsviikllkeklgeeviavavdvGqee.edldevkekalklgavksvvvDak 60
                                      vL +sGG+D +  + +l  k+ +ev a++   Gq++  ++d+ k+ a+ lg  k+ vvD+ 
  gi|488601256|ref|YP_007907727.1|  4 VLIFSGGVDSTTLLYYLISKG-YEVHALTFIYGQKHaREVDASKKIAKLLGI-KHKVVDIT 62
                                      799****************99.************972577777777777776.99999975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                   Arginosuc_synth  46 alklgavksvvvDakeefve 65 
                                       a+k     s+  D+++efv+
  gi|488601256|ref|YP_007907727.1| 121 AHKSDY--SIYPDCRKEFVK 138
                                       433332..556688888886 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.4e-07    0.0011      21      90 ..       3      70 ..       1     106 [. 0.83
   2 ?   -2.6   0.0      0.92   2.4e+03     149     172 ..     157     180 ..     156     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.4e-07
                                      EEEEE-SSHHHHHH.HHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHH CS
                      NAD_synthase 21 vvlGlSGGvDSslv.aalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafeq 90
                                      +vl  SGGvDS++   +l  k     +v+al +   +++ ++v +++++a+ lgi+ k++di++i + ++ 
  gi|488601256|ref|YP_007907727.1|  3 AVLIFSGGVDSTTLlYYLISKGY---EVHALTFIYGQKHAREVDASKKIAKLLGIKHKVVDITSIHELISR 70
                                      68889******875145666655...899999999999999***********************9988776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.92
                                       ETTTTS-HHHHHHHHHHTT--HHH CS
                      NAD_synthase 149 apiaellKtevkeLakelnvPerv 172
                                       ap  ++ K+e+  L  +l+vP ++
  gi|488601256|ref|YP_007907727.1| 157 APFVDIEKSEIVGLGLKLGVPYEL 180
                                       588899999999999999999775 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.4e-06    0.0061       3      67 ..       4      62 ..       2      82 .. 0.76
   2 ?   -1.3   0.0       0.6   1.5e+03     129     153 ..     144     168 ..     107     179 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-06
                                      EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE-- CS
                        ATP_bind_3  3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvd 67
                                      ++ +SgG+DS++Ll+ l ++      ++ a+++ +g +   ++e ++ k+++k l+ik+++ +++
  gi|488601256|ref|YP_007907727.1|  4 VLIFSGGVDSTTLLYYLISKG----YEVHALTFIYGQK--HAREVDASKKIAKLLGIKHKVVDIT 62
                                      6779*************9984....4777887777755..4556666678888888888777766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.6
                                       S-SEEEETTCCEE-CCCT--HHHHH CS
                        ATP_bind_3 129 ikeaseiasirlvRPlLkvskeele 153
                                       +  a+  + ++l  P+++++k+e+ 
  gi|488601256|ref|YP_007907727.1| 144 LYLANLWTPVELKAPFVDIEKSEIV 168
                                       3333333446777788888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1307.88
//
Query:       gi|488601257|ref|YP_007907728.1|  [L=328]
Description: phosphoribosylformylglycinamidine cyclo-ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-22   80.0   0.0    7.9e-22   78.1   0.0    2.0  2  AIRS_C    AIR synthase related protein, C-terminal domain
    1.4e-18   67.3   0.6    4.1e-18   65.8   0.6    1.8  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 ?   -1.6   0.0      0.29   2.6e+03      47      74 ..      26      56 ..       5      70 .. 0.73
   2 !   78.1   0.0   8.9e-26   7.9e-22       1     153 [.     168     322 ..     168     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.29
                                      HHHHHHHHHHH...HTTECEEEE--TTHHHH CS
                            AIRS_C 47 liyvkralaal...kglvkaahDvTgGGLlg 74
                                      +i+ +r+   +   +g+  ++ D++++G++ 
  gi|488601257|ref|YP_007907728.1| 26 KIKFVREGFGRpilTGHYAGVVDLGDFGIAI 56
                                      5555555555556677888888999999875 PP

  == domain 2  score: 78.1 bits;  conditional E-value: 8.9e-26
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT....TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds....avqlgdvlleptliyvkralaalkglvkaahDvTgGGLl 73 
                                       ++Gd++i+++s+G++++g+ l+rk +e++g  ++    ++ +g++ll+pt+iy  +    +k ++++++++Tg GLl
  gi|488601257|ref|YP_007907728.1| 168 QDGDLIIGLPSSGIHSNGLTLARKAVESAGYSYFdefeGKTIGEELLTPTRIYSELVGLWDKYEIHGMAHITGSGLL 244
                                       58****************************9998***7777*************98888889**************9 PP

                                       HHHHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEE CS
                            AIRS_C  74 galaemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIG 143
                                         l ++ +    + +id +    +if  ++     s+ em++++n+G ++ ++++e+   +++i++e    +++++G
  gi|488601257|ref|YP_007907728.1| 245 K-LRRLKE---MKYVIDNPlpPQKIFRFIQkagnvSEREMYRTFNMGMGFAVIASEDV--AKDIAKEL---DCRIVG 312
                                       5.555533...3467777777667777777778*************************..99999984...79**** PP

                                       EEEESSSEEE CS
                            AIRS_C 144 evtakeelsv 153
                                       +v+++++  v
  gi|488601257|ref|YP_007907728.1| 313 RVEEGNGIFV 322
                                       ****997665 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 !   65.8   0.6   4.6e-22   4.1e-18       2      94 .]      51     156 ..      44     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 4.6e-22
                                       SSEEEEEEEEEE.EECC....TCCCC..HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHH CS
                              AIRS   2 Daavvvttdshnrpvlv....epvhf..iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaae 67 
                                       D ++++ttd+++++++v       +f  +G  +va+n++Dl+a GA+Pla+++++a++     ++ee++ gl+e+++
  gi|488601257|ref|YP_007907728.1|  51 DFGIAITTDGVGSKIIVaekiR--KFdtVGIDCVAMNVNDLIAIGAEPLAFVDYIAIQkpdpeIMEEIAIGLEEGCR 125
                                       55689**********9954333..3366************************************************* PP

                                       HTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  68 elgvplvgGdtsfsne....ptisvtavGlv 94 
                                        +++ lvgG+t+  +e    + ++ ta+G+v
  gi|488601257|ref|YP_007907728.1| 126 IANITLVGGETATLPEiingFDLAGTAIGWV 156
                                       ************9999999999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1922.40
//
Query:       gi|488601258|ref|YP_007907729.1|  [L=406]
Description: TIGR00300 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-37  125.8   0.0    1.5e-36  124.8   0.0    1.5  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
  ------ inclusion threshold ------
      0.013   15.3   0.4       0.13   12.0   0.0    2.3  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
      0.017   15.0   0.2        1.6    8.7   0.1    2.7  2  DUF1236         Protein of unknown function (DUF1236)
      0.059   12.6   0.2        2.1    7.5   0.0    2.4  3  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 !  124.8   0.0   3.3e-40   1.5e-36       2     100 .]       5     103 ..       4     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 3.3e-40
                                       EEEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCE CS
                    Saccharop_dh_N   2 reveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeed 78 
                                       +e+e+eGhliDs+i++kvld+il+++g+fe+lef++Gkkk+dtSya+++v+++d  +L++il+el++lga+++++e+
  gi|488601258|ref|YP_007907729.1|   5 KELEFEGHLIDSMIFPKVLDTILDLDGEFEILEFRIGKKKTDTSYARIMVMGKDPGHLQRILQELHKLGAKIPDAEE 81 
                                       5789************************************************************************* PP

                                       EEECESSCTTB--TTB----SS CS
                    Saccharop_dh_N  79 vklekaekdgvlpedFYsttnh 100
                                       v++++a++d+vlpe+FY+ttnh
  gi|488601258|ref|YP_007907729.1|  82 VEVAPAPDDKVLPENFYVTTNH 103
                                       *********************8 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.072   3.2e+02      12      37 ..     199     224 ..     184     256 .. 0.73
   2 ?   12.0   0.0     3e-05      0.13      67     135 ..     326     395 ..     308     397 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.072
                                       SSEEEEE-CHHCHTTGHHHHHHHHHH CS
                      TPP_enzyme_M  12 krpvilvGggvarsgaseelrelaek 37 
                                        ++++++G  v+  ga+++l+ +++ 
  gi|488601258|ref|YP_007907729.1| 199 GKIAVVAGPAVDHTGARDALAGMIRD 224
                                       4899***************9877765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3e-05
                                       SCHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC....--SEEEECTHHHHHH CS
                      TPP_enzyme_M  67 gskaanealeeaDlvlalGarfddirttgsepefapea.kiihididpaeigkny....qvdlaivgdvketle 135
                                       ++k+ ++al+    vl+l + ++ i +++  p     + k i +di+pa++ k        +++iv dv+ ++ 
  gi|488601258|ref|YP_007907729.1| 326 AKKEIKKALRGINMVLMLSTMLHSIAVGNLLP----STvKTICVDINPATVTKLIdrgtAQAIGIVTDVGLFVP 395
                                       5788999*****************98876544....34489*********999984443356999999998875 PP

>> DUF1236  Protein of unknown function (DUF1236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00035       1.6      19      52 ..      72     107 ..      62     108 .. 0.88
   2 ?    3.4   0.0     0.016        73      15      28 ..     348     361 ..     340     376 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00035
                           DUF1236  19 vGaalPet..VelrpvPdevvipeyrYvvvndrtvi 52 
                                        Ga++P+   Ve+ p Pd+ v+pe  Yv  n  t+i
  gi|488601258|ref|YP_007907729.1|  72 LGAKIPDAeeVEVAPAPDDKVLPENFYVTTNHPTYI 107
                                       79****9999*********7789*****99988877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.016
                           DUF1236  15 eevsvGaalPetVe 28 
                                        +++vG  lP+tV+
  gi|488601258|ref|YP_007907729.1| 348 HSIAVGNLLPSTVK 361
                                       689*********97 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00046       2.1      42      77 ..     209     244 ..     180     258 .. 0.78
   2 ?    2.3   0.0     0.018        81     134     164 ..     270     305 ..     260     316 .. 0.73
   3 ?   -3.7   0.0       1.2   5.3e+03     268     285 ..     381     398 ..     375     400 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00046
                                DS  42 lissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       +  +G r+ +a +++++++d++ +  +   +D+  +
  gi|488601258|ref|YP_007907729.1| 209 VDHTGARDALAGMIRDGYIDLLLSGNALAVHDIEIS 244
                                       4469***********************999998544 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.018
                                DS 134 spselikelG..kein...deeSilywAykndipvf 164
                                       ++s++i+  G  k+++    +++i+y + kn++p  
  gi|488601258|ref|YP_007907729.1| 270 TISKIISLGGirKAVEsgvLKDGIMYECIKNNVPFI 305
                                       6677766555545555555679************65 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.2
                                DS 268 aksvkvyaDaTivlPLlv 285
                                       a+ + +++D+ +++PLl+
  gi|488601258|ref|YP_007907729.1| 381 AQAIGIVTDVGLFVPLLY 398
                                       67788999*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2532.77
//
Query:       gi|488601259|ref|YP_007907730.1|  [L=534]
Description: hypothetical protein Asulf_01766 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-34  117.5   0.0    7.9e-34  116.8   0.0    1.3  1  CHASE4       CHASE4 domain
    8.5e-19   68.1   0.1      3e-18   66.3   0.0    1.9  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.7e-05   24.1   0.0    4.8e-05   23.3   0.0    1.4  1  HATPase_c_2  Histidine kinase-like ATPase domain
     0.0002   21.6   0.5     0.0013   19.1   0.4    2.3  3  HAMP         HAMP domain
      0.001   18.7   0.2     0.0031   17.2   0.2    1.9  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain
     0.0021   18.0   0.0     0.0062   16.4   0.0    1.9  1  HATPase_c_5  GHKL domain
     0.0058   16.2   0.0      0.018   14.6   0.1    1.7  2  HisKA_4TM    Archaeal 4TM region of histidine kinase
  ------ inclusion threshold ------
      0.046   13.1   0.5       0.12   11.8   0.0    1.7  2  Ceramidase   Ceramidase


Domain annotation for each model (and alignments):
>> CHASE4  CHASE4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   0.0   3.5e-37   7.9e-34       2     126 ..      63     196 ..      62     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 3.5e-37
                            CHASE4   2 lqaeldqlerllkdwavWDdtyafvqdrdpdyiesnlgdetletlgldlvlfldadgklvy....dqengq...... 68 
                                       l+++++ lerl++dwa+WDdty+f++++++dyiesnl +et+  ++l+l++f+++++++vy    d+e+++      
  gi|488601259|ref|YP_007907730.1|  63 LDSQIGYLERLNTDWAYWDDTYYFIENKSKDYIESNLVNETFIEQKLNLIVFINRNKSIVYakafDFEKNRvipvpe 139
                                       7899*********************************************************7766666655766544 PP

                            CHASE4  69 .ekllseaeee......sgrsgllkldggpalvaaapIltsegegpsrGtlvfgryldeallsrl 126
                                        +               ++ sg+lk+dg+++++++  I +s+g+g++rG+lv+gr++++++ ++l
  gi|488601259|ref|YP_007907730.1| 140 lS--------PyldylaNESSGFLKIDGEVLMFSSKRIIKSDGSGDPRGWLVMGRFVNDSFFRAL 196
                                       31........0233333389****************************************99887 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.9   6.6e+03      28      55 ..     203     229 ..     197     251 .. 0.67
   2 !   66.3   0.0   1.4e-21     3e-18       5     108 ..     432     530 ..     429     533 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.9
                                       EEEEEEEETEEEEEEEESSSSSTTHHHT CS
                         HATPase_c  28 eveikaseddlvisveDnGiGipkedlk 55 
                                        + i++s+ + +is++D G+ i+   +k
  gi|488601259|ref|YP_007907730.1| 203 NIYIDRSDHNQTISIQD-GKLITYRPIK 229
                                       55566556788999998.7766665555 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 1.4e-21
                                       HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHH CS
                         HATPase_c   5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsi 80 
                                        ++ +++nl+ Na+++ +k++++++++++ ++  +++v D G Gip e+ +++fe  f        ++ gtGlG++i
  gi|488601259|ref|YP_007907730.1| 432 AIYSVFDNLIRNAIQH-GKTDRVDITCRKLNGFCEVRVADYGTGIPDEIKNMIFEeGFKY-----GEKAGTGLGMYI 502
                                       67899***********.***********64589*********************997766.....4489******** PP

                                       HHHHHHHTTTEEEEEEETTTEEEEEEEE CS
                         HATPase_c  81 vkklvelmgGeiwvesepgrGttftftl 108
                                       vkkl+e++gG++ ve+++ +Gttf++++
  gi|488601259|ref|YP_007907730.1| 503 VKKLMERYGGSVAVEDNKPKGTTFVLKF 530
                                       ************************9976 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 !   23.3   0.0   2.1e-08   4.8e-05      40     123 ..     441     528 ..     427     530 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.1e-08
                       HATPase_c_2  40 ctNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep.keslkegGrGlalikglvDev..e 113
                                       + Na++h++     ++v ++++  ++ ++v+vaD G g + e +++  ee+   +++   G+G++++k+l++ +  +
  gi|488601259|ref|YP_007907730.1| 441 IRNAIQHGKT----DRVDITCRKLNGFCEVRVADYGTGIPDEIKNMIFEEGFkYGEKAGTGLGMYIVKKLMERYggS 513
                                       4567777765....9***********************5555555555555447888899************98775 PP

                       HATPase_c_2 114 y.....dgegnvvtm 123
                                       +     +++g++ ++
  gi|488601259|ref|YP_007907730.1| 514 VavednKPKGTTFVL 528
                                       555655666776655 PP

>> HAMP  HAMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   5.6e-07    0.0013       6      51 ..     280     326 ..     278     328 .. 0.91
   2 ?   -3.3   0.0       5.7   1.3e+04      35      45 ..     385     395 ..     382     395 .. 0.83
   3 ?   -1.3   0.0       1.4   3.1e+03      13      28 ..     404     420 ..     403     423 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.6e-07
                                       THHHHHHHHHHHHHHT.TTBTSSTCCTTSSSHHHHHHHHHHHHHHHH CS
                              HAMP   6 ilrPLrrLaraarria.aGdldtrlpvsgrDEiGeLarafNaMldrL 51 
                                       i  ++ rL r  +++a +Gd++ r++v+g D i+eLar++N  l+++
  gi|488601259|ref|YP_007907730.1| 280 INERIIRLNRELDELAkKGDISGRVTVDGEDGIAELARNINLVLESV 326
                                       778999**********55***********************999986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.7
                                       SHHHHHHHHHH CS
                              HAMP  35 DEiGeLarafN 45 
                                       DE++++ +++N
  gi|488601259|ref|YP_007907730.1| 385 DEMRDMEQSVN 395
                                       89999999887 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.4
                                       HHHHHHHHTTT.BTSST CS
                              HAMP  13 LaraarriaaG.dldtr 28 
                                       L++++++ia+G d+++ 
  gi|488601259|ref|YP_007907730.1| 404 LKDVIESIASGyDIEVN 420
                                       88999******987765 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 !   17.2   0.2   1.4e-06    0.0031       6      43 ..     333     371 ..     328     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                            SPOB_a   6 ikelkeliklL.rsqRHDflNhLQvIsGylqLgkydkae 43 
                                       i+++++++ +  + +RHD lN+L v++G+ +L + d++e
  gi|488601259|ref|YP_007907730.1| 333 IENARDILATSnKILRHDMLNNLTVLRGLFELIEDDRRE 371
                                       566666666555678*****************9999975 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.8e-06    0.0062       5      91 ..     432     520 ..     428     529 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.8e-06
                       HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg...ekkkle....sskskkeehGiGlksi 74 
                                        +++++ nl+ NAi+  ++       +++t+r+ +++  +++  + +g   e+k++      +  +k   G+G+  +
  gi|488601259|ref|YP_007907730.1| 432 AIYSVFDNLIRNAIQHGKT-----DRVDITCRKLNGFCEVRVADYGTGipdEIKNMIfeegFKYGEKAGTGLGMYIV 503
                                       689***********97665.....35999999999999999999977755533222222222245678999****** PP

                       HATPase_c_5  75 reivkkykgnlsieaed 91 
                                       ++++++y+g++++e ++
  gi|488601259|ref|YP_007907730.1| 504 KKLMERYGGSVAVEDNK 520
                                       ***********998765 PP

>> HisKA_4TM  Archaeal 4TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   3.4e+03      45      69 ..     161     186 ..     155     209 .. 0.72
   2 !   14.6   0.1   7.9e-06     0.018     131     163 ..     334     366 ..     324     367 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                         HisKA_4TM  45 glvyagyrlastdlpaeqe.wtvlvw 69 
                                       +l++++ r+ ++d +++ + w v+  
  gi|488601259|ref|YP_007907730.1| 161 VLMFSSKRIIKSDGSGDPRgWLVMGR 186
                                       68999999999999988544777655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.9e-06
                         HisKA_4TM 131 krisdalafvndlirhdlrndlvvirgyaeaie 163
                                       +++ d la  n+++rhd+ n+l+v+rg  e ie
  gi|488601259|ref|YP_007907730.1| 334 ENARDILATSNKILRHDMLNNLTVLRGLFELIE 366
                                       677899*********************999886 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.65   1.5e+03     131     159 ..      12      40 ..       3      62 .. 0.64
   2 ?   11.8   0.0   5.3e-05      0.12      32      77 ..     235     281 ..     232     295 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.65
                        Ceramidase 131 kepvlhqvafalltvlvllrsiyliekkv 159
                                       k   ++  +f+l+ ++++l+s+y  ++ v
  gi|488601259|ref|YP_007907730.1|  12 KTIRIKTWIFGLIFLTIILSSMYAFHSYV 40 
                                       44455666677777777777777765555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.3e-05
                        Ceramidase  32 nllfillallgiynaakkkle.krfllaylglalvGlgSalFHaTLk 77 
                                       nl+f+++  +   + +k + +    ++ ++g+a+ G+gSa++H +++
  gi|488601259|ref|YP_007907730.1| 235 NLFFLVFEKKSNLEERKAEFHeYFSAVFFIGIAFLGIGSAIYHISIN 281
                                       66777777666666665554426778899**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      717  (0.0399911); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 3782.72
//
Query:       gi|488601260|ref|YP_007907731.1|  [L=419]
Description: diaminopimelate decarboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-57  193.1   0.0    6.2e-57  192.8   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    2.9e-26   91.5   0.0    3.3e-26   91.4   0.0    1.2  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
    2.8e-09   37.0   0.0    6.5e-09   35.8   0.0    1.5  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 !  192.8   0.0     1e-60   6.2e-57       3     247 .]      34     281 ..      32     281 .. 0.95

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 1e-60
                                       HHHHHHHHHHHHCTCCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHH CS
                     Orn_Arg_deC_N   3 sierklkrwkkalprikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelrya 79 
                                       ++ ++l+++k+a+p+ ++ YavKan +la+l++++++G g d+ S +El+l+l ag++pe+i f ++ k+ ee+ + 
  gi|488601260|ref|YP_007907731.1|  34 KLMENLRAYKSAFPNQRLLYAVKANYNLAILKIIQKEGFGADVFSMGELYLALLAGFKPESILFNGNSKSDEEILAG 110
                                       678999*********************************************************************** PP

                                       HHCTHTEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTE CS
                     Orn_Arg_deC_N  80 lekgvkvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaaleeavealleaakeenl 152
                                          gvk + vd+ +el+ ++++a +     ++  R+++dvs +t++ i+tg ++sKFG+  e++vea++ a +  n+
  gi|488601260|ref|YP_007907731.1| 111 IRAGVK-FSVDSLDELYTISDMAIKegkeVEIAFRVNPDVSPETHPKIATGLKKSKFGIPWEQTVEAYRIAYELPNV 186
                                       *****9.9*************99887888999********************************************* PP

                                       EEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHHH CS
                     Orn_Arg_deC_N 153 qlvGvsfHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeeaf 229
                                          G+++H+GS++  +++f +a+++++ +  e++++G++l+++d+GGG+g++ye+ +  l+ e+  ++i    e+  
  gi|488601260|ref|YP_007907731.1| 187 IPKGIHCHIGSQILSASPFIEAINRLFDVSAEIQKIGIELEFMDIGGGLGIDYEG-TGSLSKEDFSKEILSVFEKRR 262
                                       ******************************************************6.555555999999998888887 PP

                                       H.TSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 230 p.gdkevtiiaEpGRalva 247
                                           +e+++++EpGR++v+
  gi|488601260|ref|YP_007907731.1| 263 DeINPELELWLEPGRSIVG 281
                                       767899**********995 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 !   91.4   0.0   5.5e-30   3.3e-26       5      98 .]     182     370 ..      27     370 .. 0.69

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 5.5e-30
                                       E............................................................................ CS
                                       x............................................................................ RF
                   Orn_DAP_Arg_deC   5 d............................................................................ 5  
                                       +                                                                            
  gi|488601260|ref|YP_007907731.1| 182 Elpnvipkgihchigsqilsaspfieainrlfdvsaeiqkigielefmdiggglgidyegtgslskedfskeilsvf 258
                                       05555555555555555555555555555555555666666666666666666666666666666666666666666 PP

                                       .......................GGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-EESBTT-SCEEC. CS
                                       .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   6 .......................eagvLvtrViavkesekkkfvivdaGmndllrpalygsfheipvkeeeaekeee 59 
                                                              ++ vL+trV++vk+  k +fv vdaG+n+l+rpa+y+++h+++v +   + +++
  gi|488601260|ref|YP_007907731.1| 259 ekrrdeinpelelwlepgrsivgDTTVLITRVNSVKRAYK-NFVAVDAGFNTLIRPAMYNAYHRVSVAN---KLNRK 331
                                       66666666666666666666666899**********8865.9***********************5542...23334 PP

                                       EEEEEEEE-SSSSTT-EEEEEEEEEE--TT-EEEESS-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  60 eeeevdvvGptCesgDvlakdrelpelevGdllafedaG 98 
                                       +ee ++++Gp+CesgD+la+dr+lp +e Gdl+a+ daG
  gi|488601260|ref|YP_007907731.1| 332 NEEVYTIAGPICESGDILAEDRKLPVVEKGDLIAVYDAG 370
                                       5678*********************************98 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 !   35.8   0.0   1.1e-12   6.5e-09       4     159 ..      33     198 ..      30     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.1e-12
                                       HHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC..ST CS
                    Ala_racemase_N   4 dalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg..fs 78 
                                        +l +Nlr+ ++++ p+++l+  vKa  y++ ++++ +  +  gad f +  l        ag++ + ++++g   s
  gi|488601260|ref|YP_007907731.1|  33 GKLMENLRAYKSAF-PNQRLLYAVKA-NYNLAILKIIQ-KEGFGADVFSMGELY---LALLAGFKPESILFNGnsKS 103
                                       67899*********.9999*******.9**********.554689966666555...44456676777788887669 PP

                                       GGGHHHHHHTTEEEEESSHHHHHHHHHHHHH............TTS-EEEEEEBESSSS..SSSBSCHHHHHHHHHH CS
                    Ala_racemase_N  79 peelaalaeydltvtvdsleqlealaaaare............agkplrvhlkidtgmg..RlGftpeeleelleal 141
                                        ee+ a ++++++  vdsl++l  +++ a +             +   + h ki tg+   + G+++e+  e+++ +
  gi|488601260|ref|YP_007907731.1| 104 DEEILAGIRAGVKFSVDSLDELYTISDMAIKegkeveiafrvnPDVSPETHPKIATGLKksKFGIPWEQTVEAYRIA 180
                                       999999999**********************777777777777777777788888888899**************** PP

                                       HHTTTEEEEEEE-S-SST CS
                    Ala_racemase_N 142 aalpglrleglmtHfasa 159
                                        +lp++ ++g+  H +s 
  gi|488601260|ref|YP_007907731.1| 181 YELPNVIPKGIHCHIGSQ 198
                                       **************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2480.83
//
Query:       gi|488601261|ref|YP_007907732.1|  [L=389]
Description: LL-diaminopimelate aminotransferase apoenzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-61  208.0   0.0    2.5e-61  207.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
        0.2   10.1   0.0       0.28    9.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   0.0   2.8e-65   2.5e-61       2     363 .]      35     384 ..      34     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 2.8e-65
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi++g+++++      t+++++ a  e  + ++++ +y+ ++g  +++ea+a+++ r++++kl++e++vv + G++
  gi|488601261|ref|YP_007907732.1|  35 DVIDFGVGDPDLP----TPDHIVNALCE-SARKEENQKYPSYEGMLSFREAVAEYYMRRKGVKLDPEKEVVSLIGSK 106
                                       89**********9....***********.9*********************************************** PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++i+ l+ ++ +n+gd  lvpdp y+ y+ +  l++g+ + + l++e +f+ d++++ e++ +        k+++++
  gi|488601261|ref|YP_007907732.1| 107 EGIAHLPLAF-VNRGDYTLVPDPGYPVYHGATLLADGKPYHMILEEERGFTPDFDKIPEDVVR------NAKIMFLN 176
                                       **********.9***********************************************9999......669***** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                        p+NPt +v+++e ++  +d+++ +n++l  D aY + +f++  + +  ++++ + + ++  +slsK ++++G+R+G
  gi|488601261|ref|YP_007907732.1| 177 YPNNPTSAVCDKEFIKSAIDFCYDNNIILAHDAAYTDIYFEER-PLS-FLEIDSAFDvVVEFNSLSKTYNMTGWRIG 251
                                       *****************************************54.333.66667777789999*************** PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                       +++gn+  ++ l k+++++ s    ++q+a  aal  ++++   +e + + + +rr++l+++L+++glkv+ +++++
  gi|488601261|ref|YP_007907732.1| 252 FAVGNETALQGLLKVKTNVDSgvFQAVQEAGIAALLGSDDV---IERNNEIYRERRDKLVNGLEKAGLKVFVPKATF 325
                                       ***************************************86...8999***************************** PP

                                       EEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 307 flltdlsae.takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       +++  ++     ++++kkLl+  g++vtpg  f+   +g++R+ + + + + +e++ve+l
  gi|488601261|ref|YP_007907732.1| 326 YVWCKVPDGyGSMDFAKKLLNDAGILVTPGIGFGEggEGFVRFAL-TRNVSVIEKAVERL 384
                                       ***887766699*********************************.************97 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   3.1e-05      0.28      86     187 ..     115     223 ..     102     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.1e-05
                                       TTS-TTEEEEEES...TSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----...H CS
                   Cys_Met_Meta_PP  86 allkaGdeivvsd...dlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvD...i 156
                                       a+++ Gd  +v d    +Y g+  l +    ++ +e +   t d++++ + +  n k+++l  p np+  v+D   i
  gi|488601261|ref|YP_007907732.1| 115 AFVNRGDYTLVPDpgyPVYHGATLLADGKPYHMILEEERGFTPDFDKIPEDVVRNAKIMFLNYPNNPTSAVCDkefI 191
                                       5666666666655222466676666666666666777777778999999************************7767 PP

                                       HHHHHHHHHTT-EEEEEGTTTHTTT.S-GGGG CS
                   Cys_Met_Meta_PP 157 ekiaklakkagvlvvvDntfaspll.qrplkl 187
                                       ++ ++++ ++++++  D++++  ++  rpl++
  gi|488601261|ref|YP_007907732.1| 192 KSAIDFCYDNNIILAHDAAYTDIYFeERPLSF 223
                                       77788888999999999988776552456654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2341.41
//
Query:       gi|488601262|ref|YP_007907733.1|  [L=372]
Description: citrate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-125  417.8   0.0   3.9e-125  417.7   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.7   0.0  2.2e-129  3.9e-125       1     361 []       3     354 ..       3     354 .. 0.95

  Alignments for each domain:
  == domain 1  score: 417.7 bits;  conditional E-value: 2.2e-129
                                       GGTTEEEEEESSEEEETTTTE..EEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekge..lrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvl 75 
                                       gl++v+a+et+i+++  e+ +  l YRGydi+eLa ++ss+eeva+lLl+g+lP+k+e+++fkeela +r+lp +++
  gi|488601262|ref|YP_007907733.1|   3 GLEDVVACETSICRIAVEEDRgvLEYRGYDIHELA-KNSSYEEVAFLLLFGDLPSKSEFESFKEELAMKRELPPQII 78 
                                       799************65554445************.8**************************************** PP

                                       HHHHCSSTTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHH CS
                      Citrate_synt  76 ealealpkdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsya 152
                                         l +lp  +hpm vlr+a+s l++ d++++ k  s+e+ ++++++liAk+pti+a+++r+r+g++ ++p+++ls+a
  gi|488601262|ref|YP_007907733.1|  79 GLLTHLPPFTHPMVVLRTAISYLGSMDKHIQYK--SHERSIEKSISLIAKFPTIVAYFHRIRTGQNLIHPREDLSHA 153
                                       *******999****************9754444..45889************************86669**99**** PP

                                       HHHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHH CS
                      Citrate_synt 153 enflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmle 229
                                       enflyml+g++p+e +ak ldl ++lha+HelnaSTfaar++aStlad+y++i+a+ g+l Gplhgga+++v++ml+
  gi|488601262|ref|YP_007907733.1| 154 ENFLYMLHGEEPTETMAKSLDLDFILHAEHELNASTFAARIAASTLADMYACIVAATGTLLGPLHGGASQKVMEMLR 230
                                       ***************************************************************************** PP

                                       HHSSGG.GHHHHHHHHHHTTTS--TTBC-SSSS.S--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCH CS
                      Citrate_synt 230 eigsaeveveeylekvlakekerlpGfGHrvyk.ksDpRakilkelaeelaeekgkdpllklaeeleevapevlkek 305
                                       e+  +  ++e+y++++l++ +er++GfGHrvy+ + DpR+  lk la++la+e ++ ++++++e++ee++ +     
  gi|488601262|ref|YP_007907733.1| 231 EVAVPW-RAESYVREKLEN-GERIMGFGHRVYRkVMDPRTIELKILAKKLADE-KNPKWYQISEAIEEAVYK----- 299
                                       **8887.***********7.5***********8468***************97.6667**************..... PP

                                       HGCT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------E CS
                      Citrate_synt 306 eeknlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRPr 361
                                         k+l pNvDfys+ +y  lgip++lf  +fai+R+ Gw+Ah++eq+++n++iRPr
  gi|488601262|ref|YP_007907733.1| 300 Y-KGLLPNVDFYSASVYANLGIPDDLFVNIFAIGRISGWCAHVIEQYENNRLIRPR 354
                                       4.9****************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 2151.67
//
Query:       gi|488601263|ref|YP_007907734.1|  [L=507]
Description: AMP phosphorylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-15   55.9   0.4    7.3e-15   54.4   0.4    1.9  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    1.9e-12   46.8   0.3    4.5e-12   45.6   0.1    1.7  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    2.9e-11   43.4   0.3    3.4e-10   39.9   0.3    2.2  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    0.00057   19.9   0.1     0.0012   18.9   0.1    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.029   13.2   0.1      0.047   12.5   0.1    1.2  1  DUF2254          Predicted membrane protein (DUF2254)
      0.097   12.5   1.5        1.2    9.0   0.1    3.1  2  Biotin_lipoyl    Biotin-requiring enzyme


Domain annotation for each model (and alignments):
>> 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 !   54.4   0.4   2.5e-18   7.3e-15       2      69 ..     423     483 ..     422     489 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.5e-18
                                       EEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHH CS
                            PYNP_C   2 vseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklk 69 
                                       v+e+ +++i ++a+++GA       p d+++G++lhkk G+ Vk G+p++tiYa+ke+kl++a++ + 
  gi|488601263|ref|YP_007907734.1| 423 VEEVYNKNIVKIARTAGA-------PKDKGAGVYLHKKRGEVVKVGDPIITIYAEKEWKLDNAIDVAL 483
                                       789999************.......**************************************99775 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 !   45.6   0.1   1.5e-15   4.5e-12       3      63 .]      91     151 ..      90     151 .. 0.98
   2 ?   -4.1   0.0       5.1   1.5e+04      13      21 ..     216     224 ..     213     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.5e-15
                                       HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       +i+k++ g++Lt++ei+++i++ ++g+++++++ Af ++  l+ ++ +Ei  +++Am+e g
  gi|488601263|ref|YP_007907734.1|  91 YIRKKIFGHKLTKDEIYAIIKDTVDGSLNEVELTAFVASNMLRSMDFDEIEWMTRAMIETG 151
                                       9********************************************************9976 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 5.1
                                       --HHHHHHH CS
                   Glycos_trans_3N  13 Ltaeeirfa 21 
                                       Lt +ei+++
  gi|488601263|ref|YP_007907734.1| 216 LTVDEIKEI 224
                                       677777654 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.3   1.1e-13   3.4e-10       3     253 .]     160     386 ..     158     386 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.1e-13
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                        +vD+++ GG+  n   i++   ++vA+ G+ ++k   r+++s  G+aD+ e l  +++lt +e++++ e+vg ++ 
  gi|488601263|ref|YP_007907734.1| 160 IVVDKHSIGGVPGNK--ITLLIVPIVASSGLLIPKTASRAITSATGTADTFEVL-ADVNLTVDEIKEITERVGRVIA 233
                                       68************9..9**********************************99.47778889999**999997765 PP

                                       ..EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHH CS
                   Glycos_transf_3  80 ..fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGlde 154
                                         +a+e  +a + ++ v   l i            p    + l +v++k+   ++ +v+ +++v+++  v+g  +++
  gi|488601263|ref|YP_007907734.1| 234 wgGATEIAPADDIIIRVEHPLSI-----------DP--KPQLLASVMAKKGSVGAKHVVIDIPVGKGSKVPG--VEK 295
                                       22567777777777777666666...........34..2244559999*9999*****************99..9** PP

                                       HHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHT CS
                   Glycos_transf_3 155 vsllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvla 230
                                        ++la+  v      g     +l+   ++++ra + ale    ke++++l++  +g +s    +  l +ag +l ++
  gi|488601263|ref|YP_007907734.1| 296 GRELANDFVELGRrLGLNVRCALSYGGQPVGRAIGPALEA---KEALKTLEER-KGSSSL--IEKSLGLAGILLEMS 366
                                       *********9999999999*******************99...9999999998.777776..577788888888888 PP

                                       TSSSSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 231 gkadslkegvakaeevidsGkAl 253
                                       g   +  +g + a+e+ +sGkA+
  gi|488601263|ref|YP_007907734.1| 367 G---KTSNGYEYAKEIFNSGKAY 386
                                       8...567899999*******995 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     4e-07    0.0012      31      66 ..      16      51 ..      10      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4e-07
                                      EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEE CS
                   Molydop_binding 31 vveinpedAaalGikdGdlVevesrrGsvevrakvt 66
                                       + i+++dA++ G++ Gd+V+v+  r +v +++kv 
  gi|488601263|ref|YP_007907734.1| 16 IIAISENDAKEIGVRGGDRVRVSCGRKRVIAEVKVI 51
                                      799****************************99875 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.6e-05     0.047     186     255 ..     406     476 ..     376     489 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                           DUF2254 186 eseeeeatpiraersGylqaidveaLvklae......ehdlvielevrpGdfvvkgeplakvwgeeddeelaeklr 255
                                        +  ++ ++++a++ G + +++ +++vk+a+      ++++ ++l+++ G+ v  g+p+++++ e++      kl 
  gi|488601263|ref|YP_007907734.1| 406 VPIGDKVYTLKATKEGAVEEVYNKNIVKIARtagapkDKGAGVYLHKKRGEVVKVGDPIITIYAEKE-----WKLD 476
                                       45567788999*******************822222245689*********************8882.....2232 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.16   4.9e+02      39      59 ..     410     429 ..     382     436 .. 0.71
   2 ?    9.0   0.1    0.0004       1.2      15      40 ..     445     471 ..     437     472 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.16
                                       TTEEEEEEBSSSEEEEEESST CS
                     Biotin_lipoyl  39 mKmemeieapkaGvvkeilvk 59 
                                       +K+  +++a k+G v+e++ k
  gi|488601263|ref|YP_007907734.1| 410 DKV-YTLKATKEGAVEEVYNK 429
                                       554.57899999999999877 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0004
                                       ..ECSESSSTTCEE-TTSEEEEEECTT CS
                     Biotin_lipoyl  15 g.vvevlvkvGdkVkagqvlaeveamK 40 
                                       g  v  ++k G+ Vk g++++++ a K
  gi|488601263|ref|YP_007907734.1| 445 GaGVYLHKKRGEVVKVGDPIITIYAEK 471
                                       445567788888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3389.31
//
Query:       gi|488601264|ref|YP_007907735.1|  [L=508]
Description: AMP phosphorylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   53.9   0.4    2.6e-14   52.6   0.4    1.7  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    5.2e-12   45.4   0.1    1.6e-11   43.8   0.0    2.0  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    1.4e-11   44.5   0.7    4.2e-11   42.9   0.7    1.7  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    0.00077   19.3   0.4     0.0031   17.4   0.4    2.1  1  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
     0.0082   16.2   0.1      0.049   13.6   0.0    2.0  2  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
      0.041   12.7   0.1      0.069   12.0   0.1    1.3  1  DUF2254          Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> 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 !   52.6   0.4   8.8e-18   2.6e-14       2      69 ..     429     489 ..     428     495 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 8.8e-18
                                       EEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHH CS
                            PYNP_C   2 vseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklk 69 
                                       v+ + ++ i ++a+++GA       p d+++G++lhkk G+ Vk G+p++tiYa+ke+kl++a++ + 
  gi|488601264|ref|YP_007907735.1| 429 VTHVRNDVIVKIARTAGA-------PKDKGAGVYLHKKRGEVVKVGDPIITIYAEKEWKLDNAIDVAL 489
                                       7888999999********.......**************************************99775 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 !   43.8   0.0   5.5e-15   1.6e-11       3      63 .]      97     157 ..      95     157 .. 0.98
   2 ?   -4.2   0.0       5.6   1.7e+04      13      21 ..     222     230 ..     220     232 .. 0.63

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 5.5e-15
                                       HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       +i+k+++g +L+ +eir +i++ ++g+++ +++ Af  + +++G++ +Ei  +++Am+e g
  gi|488601264|ref|YP_007907735.1|  97 YIRKKMEGYKLSLDEIRSIINDTVSGSLSNIELTAFILSNFVNGMDFDEIEWMTRAMIETG 157
                                       8********************************************************9976 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 5.6
                                       --HHHHHHH CS
                   Glycos_trans_3N  13 Ltaeeirfa 21 
                                       Lt +ei+++
  gi|488601264|ref|YP_007907735.1| 222 LTVDEIKEI 230
                                       667777654 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.7   1.4e-14   4.2e-11       3     253 .]     166     392 ..     164     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.4e-14
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                        +vD+++ GG+  n     + + ++vA+ G+ ++k   r+++s  G+aD+ e l  +++lt +e++++ e+vg ++ 
  gi|488601264|ref|YP_007907735.1| 166 IVVDKHSIGGVPGNK--TALLLVPIVASSGLLIPKTASRAITSATGTADTFEVL-ADVNLTVDEIKEITERVGGVIA 239
                                       68********95555..4999*******************************99.477888999******9986665 PP

                                       .EHHSSSSHHHH.HHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHH CS
                   Glycos_transf_3  80 .fapeyhkamkh.vapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGlde 154
                                         a+ ++++++   ++++ +l+i           +p  + + + +++s + a ++ +v+ +++v++ + v++  ld 
  gi|488601264|ref|YP_007907735.1| 240 wSASANLAPADDrLIEIQYNLQI-----------SP--IPHFITSIMSRKSAVGAKHVVVDIPVGEYAKVTS--LDV 301
                                       15566666655404455555555...........55..568899****************************..999 PP

                                       HHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHT CS
                   Glycos_transf_3 155 vsllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvla 230
                                        ++la+         g   + +++ + ++++ra + ale    ke++++l++  +g +s    +  l +ag +l ++
  gi|488601264|ref|YP_007907735.1| 302 GKELAHKFSELGRrFGLNVTSVITNARQPVGRAIGPALEA---KEALKTLEER-KGSSSL--IEKSLGLAGILLEMS 372
                                       99999999888888999999*******************9...*******998.777777..577788899999998 PP

                                       TSSSSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 231 gkadslkegvakaeevidsGkAl 253
                                       g   +  +g + a+e+ +sGkA+
  gi|488601264|ref|YP_007907735.1| 373 G---KTSNGYEYAKEIFNSGKAY 392
                                       8...5678*************96 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 !   17.4   0.4     1e-06    0.0031      10      42 ..      67     100 ..      63     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-06
                                       EE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCH CS
                    MazE_antitoxin  10 riPkevrfelgireGdevelevdgd.kiilrplk 42 
                                        iPke+++  g+  Gde+e+++++   ++++  k
  gi|488601264|ref|YP_007907735.1|  67 LIPKELADLIGVVDGDEIEIYPVKKpESVIYIRK 100
                                       59**********************9966665544 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.7e-05     0.049      30      78 ..      21      70 ..      11      76 .. 0.89
   2 ?    1.5   0.0     0.097   2.9e+02      32      53 ..      66      87 ..      62      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                      -EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS.B-TTEEEEES CS
                   Molydop_binding 30 evveinpedAaalGikdGdlVevesrrGsvevrakvter.vrpGvvfmpf 78
                                      + v +n +d  +lG+ +Gd++++   +  +++++ +t + v+ G + +p 
  gi|488601264|ref|YP_007907735.1| 21 KAVIMNKDDSYELGLIEGDRIRLCKGKSVCVAEVNITSGmVASGEILIPK 70
                                      4899******************************8888779999999987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.097
                                      EEEEHHHHHHHT--TT-EEEEE CS
                   Molydop_binding 32 veinpedAaalGikdGdlVeve 53
                                      ++i  e A   G+ dGd++e++
  gi|488601264|ref|YP_007907735.1| 66 ILIPKELADLIGVVDGDEIEIY 87
                                      6777889999**********96 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.3e-05     0.069     186     255 ..     412     482 ..     382     495 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                           DUF2254 186 eseeeeatpiraersGylqaidveaLvklae......ehdlvielevrpGdfvvkgeplakvwgeeddeelaeklr 255
                                        +  ++ ++++a++ G ++++  + +vk+a+      ++++ ++l+++ G+ v  g+p+++++ e++      kl 
  gi|488601264|ref|YP_007907735.1| 412 VPIGDKVYTLKATKEGAVTHVRNDVIVKIARtagapkDKGAGVYLHKKRGEVVKVGDPIITIYAEKE-----WKLD 482
                                       45567788999*******************822222245689*********************8882.....2232 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3382.21
//
Query:       gi|488601265|ref|YP_007907736.1|  [L=80]
Description: phosphoribosylformylglycinamidine synthase, purS protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  104.2   0.2    3.3e-30  104.1   0.2    1.0  1  PurS       Phosphoribosylformylglycinamidine (FGAM) synthase
  ------ inclusion threshold ------
      0.048   13.6   0.3      0.078   12.9   0.3    1.3  1  DpnD-PcfM  DpnD/PcfM-like protein


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 !  104.1   0.2   3.6e-34   3.3e-30       2      77 .]       3      78 ..       2      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 3.6e-34
                                      EEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEEE CS
                              PurS  2 akveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeiel 77
                                      a v+++lK+gv Dp+G+  kkalk lg+++v++v++ k++++e++a+++eeae+e+++mceklLaNpvi+ y+i++
  gi|488601265|ref|YP_007907736.1|  3 ADVYIELKEGVADPEGESTKKALKLLGFDNVKNVSTRKVFRIEIDAKSREEAEKEIKQMCEKLLANPVIQRYSINW 78
                                      78***********************************************************************976 PP

>> DpnD-PcfM  DpnD/PcfM-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   8.7e-06     0.078      13      30 ..      44      61 ..      41      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-06
                         DpnD-PcfM 13 VeVeAeseeeAerlVeek 30
                                      +e++A+s+eeAe+ ++++
  gi|488601265|ref|YP_007907736.1| 44 IEIDAKSREEAEKEIKQM 61
                                      79***********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1333  (0.0743488); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 578.54
//
Query:       gi|488601266|ref|YP_007907737.1|  [L=778]
Description: phosphoribosylformylglycinamidine synthase subunit II [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-58  194.7   1.0    5.9e-34  117.4   0.2    2.3  2  AIRS_C          AIR synthase related protein, C-terminal doma
    1.2e-34  118.8   0.1    2.3e-20   73.0   0.1    2.4  2  AIRS            AIR synthase related protein, N-terminal doma
    2.4e-18   66.4   0.0    4.9e-18   65.4   0.0    1.6  1  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 !  117.4   0.2     1e-37   5.9e-34       4     155 ..     239     392 ..     236     393 .. 0.92
   2 !   75.8   0.0   6.4e-25   3.8e-21       1     148 [.     611     747 ..     611     751 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 1e-37
                                       EEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHH CS
                            AIRS_C   4 dvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlga 75 
                                       d  il g+    +G++g++ ++++++ e+++++ + avqlg+++ ++ li ++++ +++ +l+++++D++gGGL++a
  gi|488601266|ref|YP_007907737.1| 239 DIFILAGGltgrDGIHGVT-FASAELKETSEEESRgAVQLGNPIIKEPLIHACLEVIEK-KLITGMKDLGGGGLSCA 313
                                       555555556666*******.7778899999988779**********************7.***************** PP

                                       HHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEE CS
                            AIRS_C  76 laemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeels 152
                                       + ema a+g+ga++ ld+vp+ ++ + p+e+++se+++r++++++pe  d+vl ++e++++p a+v+Gev a++ l+
  gi|488601266|ref|YP_007907737.1| 314 VGEMALAAGFGARVFLDRVPLKEPDMAPWEIWVSESQERMMITAKPEMVDEVLYVFEKWDVP-ATVVGEVKAEKTLE 389
                                       *************************************************************7.**********9988 PP

                                       EEE CS
                            AIRS_C 153 viv 155
                                       v++
  gi|488601266|ref|YP_007907737.1| 390 VYY 392
                                       875 PP

  == domain 2  score: 75.8 bits;  conditional E-value: 6.4e-25
                                       STTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHH CS
                            AIRS_C   1 kpGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlga 75 
                                       ++G  ++l+g+    +gg+++s++  ++++       v+++ +++++t  +++++   + ++v a+hD++gGGL+ a
  gi|488601266|ref|YP_007907737.1| 611 RVGSSIVLVGEteAEFGGSVYSAVT-GQKSYL-----VPRTSPERLKTYSDAMLESFKE-FKVLACHDISGGGLAIA 680
                                       6899********9999999966655.554444.....56*******************8.***************** PP

                                       HHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
                            AIRS_C  76 laemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                                       +aem+++ g+gaeidl  +   +++      l+se+  r +v +p+e+a+ ++a l e+g+  a +IG v ++
  gi|488601266|ref|YP_007907737.1| 681 IAEMCFGKGLGAEIDLRGIAGDAHV-----KLFSESNTRWIVELPEEDAQGFIAFLMERGC-RAFEIGCVSKD 747
                                       *****************88888877.....8******************************.7*****99876 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 !   73.0   0.1   3.8e-24   2.3e-20       2      94 .]     111     224 ..     101     224 .. 0.93
   2 !   43.4   0.0   6.9e-15   4.1e-11       5      94 .]     494     598 ..     480     598 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 3.8e-24
                                       SSEEEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC..................HHHHHHH CS
                              AIRS   2 DaavvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp..................wleevvr 60 
                                       D a vv+ +shn+p+++ep+ + +a++++++l+D+++mGA+P+al++ l ++                   l++vv+
  gi|488601266|ref|YP_007907737.1| 111 DHAYVVAFESHNHPSAIEPYGG-AATGIGGILRDVVCMGAKPVALIDPLFFGkpdfphsvlpkgtkhplyLLSGVVA 186
                                       44459*****************.****************************************************** PP

                                       HHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  61 glaeaaeelgvplvgGdtsfsne....ptisvtavGlv 94 
                                       g++++++++g+p+v+G + f+n+    ++++v+++G++
  gi|488601266|ref|YP_007907737.1| 187 GIRDYGNRVGIPTVSGMIFFDNSyltnCLVNVGCIGIA 224
                                       *********************999*9**********85 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 6.9e-15
                                       EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvp 72 
                                       +++t+d ++  + ++p+ + +a +  + +++l+a++ +P  ++++l+++         ++ e v+ ++ +a+ ++ p
  gi|488601266|ref|YP_007907737.1| 494 LAITADVNPWMTKIDPFWG-TASSFDEMIRNLIAVNSKPHSFVDCLNFGnpekpermgEFVESVKAMGWMARGINLP 569
                                       59*****************.***********************************999999999999999******* PP

                                       EEEEEEEEESS.......EEEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne.......ptisvtavGlv 94 
                                        v+G++sf+ne       pt+++  +G++
  gi|488601266|ref|YP_007907737.1| 570 CVSGNVSFYNEtphsavaPTPTLLGIGII 598
                                       **********99****9999999999975 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 !   65.4   0.0   8.2e-22   4.9e-18       1      50 []      28      77 ..      28      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 8.2e-22
                    FGAR-AT_linker  1 LeeankelglaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                      L++++ elgl+Ls +E+++++e+f + grnP d+El+ ++q+wSEHC++K
  gi|488601266|ref|YP_007907737.1| 28 LKAISDELGLSLSVDEMRRIKEYFIAKGRNPYDIELQALGQAWSEHCCYK 77
                                      7899********************999**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (778 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 5337.14
//
Query:       gi|488601267|ref|YP_007907738.1|  [L=271]
Description: phosphoribosylformylglycinamidine synthase subunit I [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-71  240.0   0.0    2.5e-71  239.8   0.0    1.0  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    9.7e-08   32.0   0.0    1.4e-07   31.5   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    2.9e-05   23.7   0.0    4.5e-05   23.1   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00025   20.9   0.0    0.00067   19.5   0.0    1.7  1  DJ-1_PfpI      DJ-1/PfpI family
     0.0013   18.6   0.0     0.0021   17.8   0.0    1.4  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.039   13.8   0.0      0.075   12.9   0.0    1.5  1  SNO            SNO glutamine amidotransferase family


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 !  239.8   0.0   8.4e-75   2.5e-71       2     260 .]       3     268 ..       2     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 239.8 bits;  conditional E-value: 8.4e-75
                          GATase_5   2 pkvailreeGvngeyemaaafekaGfeavdvhmsdllegrv......slddfqilalpGGfsygDelgsgkgwaksl 72 
                                       p++a+lr eG+n+e e+ +a+++aG+ a+ vh+++  ++ +      ++ d+ ++++pGGfs+gD   +g+++++++
  gi|488601267|ref|YP_007907738.1|   3 PRIAVLRIEGTNCEDETVKALKAAGAFAEAVHLKQFYSDMIkesekrKITDYTGIVIPGGFSAGDYVRAGAIFSARM 79 
                                       9*******************************8876544333333459**************************999 PP

                          GATase_5  73 llneklrealekflnredtlaLGiCnGfqlLvklglvpggeiee.aeksptltrNksgrfesrlvsvvvsekspsvf 148
                                       +  + l+++le+f+n+ d  +LGiCnGfq+Lv+lg++pg e++  ++ ++ l+ N+s+rfe+r+++++ ++  +++f
  gi|488601267|ref|YP_007907738.1|  80 K--SVLKRDLEEFINN-DFPILGICNGFQVLVELGALPGFEDKLsEKPEIVLAINNSNRFECRMSYLRHENRGKCMF 153
                                       9..9************.**********************9999878999******************999******* PP

                          GATase_5 149 lkgme..glslpvahGeGrfvf...kseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvl 220
                                       +kg++  ++  pvah+eG++vf    +   +++l++n q+++rYvde+g+    yp+NPNgS ++iagi++++G vl
  gi|488601267|ref|YP_007907738.1| 154 TKGLDnrVVVYPVAHAEGKVVFpkgMEGIYIDRLVENDQIVFRYVDENGDY-AGYPWNPNGSIYNIAGICNAKGNVL 229
                                       ****76688888**********4333345689***************9998.57*********************** PP

                          GATase_5 221 almpHpervveavqksiipeeeeeevspwlrlFenavkyv 260
                                       +lmpHperv+++++   ++ + e +++++  +F+n+v+y+
  gi|488601267|ref|YP_007907738.1| 230 GLMPHPERVMHEWSYLDCEWSPE-GHGDGWIIFKNMVDYI 268
                                       ************99876643333.479999*******995 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   4.7e-11   1.4e-07       7      91 ..      17     125 ..      13     240 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.7e-11
                                       TSTHHHHHHHHHHTT-EEEEEETTSH.HHHHHH.THHSTSEEEEEEESSCTT.........TTTHHHHHHHHCT... CS
                            GATase   7 dsvtenlvhalvelgvkvevvpidas.aeeile.llknpdgilvsgGpgspg.........vegkieaikeare... 69 
                                       d  +++l+ a++ ++  v+++++ ++ ++e+++ + ++++gi+++gG+ +           +  + +++k+ +e   
  gi|488601267|ref|YP_007907738.1|  17 DETVKALKAAGAFAE-AVHLKQFYSDmIKESEKrKITDYTGIVIPGGFSAGDyvragaifsA-RMKSVLKRDLEefi 91 
                                       555566666655444.344444444303333345799***********99888888888852.33333332222255 PP

                                       .STS-EEEETHHHHHHHHHTTT...........E CS
                            GATase  70 .nkiPiLGICLGmQllaiefgr...........k 91 
                                        n+ PiLGIC G+Q+l++  +            +
  gi|488601267|ref|YP_007907738.1|  92 nNDFPILGICNGFQVLVELGALpgfedklsekpE 125
                                       5***************987666555555555541 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 !   23.1   0.0   1.5e-08   4.5e-05      30      90 ..      46     109 ..      20     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                          GATase_3  30 vplkdeslgedadlvilpGgkdtiqdl......allresgldeaikeaaeaggpvlgiCGGlqmLGe 90 
                                       +  +++++ +d+  +++pGg++  +         +  +s l+++++e+++++ p+lgiC G+q+L e
  gi|488601267|ref|YP_007907738.1|  46 S--EKRKI-TDYTGIVIPGGFSAGDYVragaifSARMKSVLKRDLEEFINNDFPILGICNGFQVLVE 109
                                       3..46667.56999*****9975433200011133446889***********************976 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 !   19.5   0.0   2.2e-07   0.00067      58     115 ..      50     115 ..      18     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.2e-07
                                       TCCG-SEEEE--BHHHHHHHHTSH....HHHHHHH....HHHHTT-EEEEETTTHHHHHHTTTTTT CS
                         DJ-1_PfpI  58 kaaeyDalvlpGGragperlrene....kvvelvk....efaekgklvaaICagpqlLaaagvlkg 115
                                       k  +y  +v+pGG +  +++r+ +    ++ +++k    ef +++ ++  IC g q+L++ g l+g
  gi|488601267|ref|YP_007907738.1|  50 KITDYTGIVIPGGFSAGDYVRAGAifsaRMKSVLKrdleEFINNDFPILGICNGFQVLVELGALPG 115
                                       456899*************998762222334444322226788999**************999986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   7.2e-07    0.0021      98     123 ..      87     111 ..       6     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.2e-07
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnvalG 123
                                       +++ +++++PilgiC G+q+l v lG
  gi|488601267|ref|YP_007907738.1|  87 LEEFINNDFPILGICNGFQVL-VELG 111
                                       567899**************9.7776 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.5e-05     0.075       5      81 ..      26     107 ..       7     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                                       SSSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HH.......HHHHHHHHTT-HHHHHHHHHTT.--EEEE CS
                               SNO   5 qGaveehveaikkclaenktvkrkedlaevdaliiPGGest.......amskliertglyedllefvknsekvvlGt 74 
                                        Ga+ e v ++k+   +  +  +k ++ +  +++iPGG s+       a+     +  l  dl ef++n   ++lG 
  gi|488601267|ref|YP_007907738.1|  26 AGAFAEAV-HLKQFYSDMIKESEKRKITDYTGIVIPGGFSAgdyvragAIFSARMKSVLKRDLEEFINND-FPILGI 100
                                       35555543.4555555556666677788999*******98633332224444455677899******998.****** PP

                                       THHHHHH CS
                               SNO  75 CaGlill 81 
                                       C G+ +l
  gi|488601267|ref|YP_007907738.1| 101 CNGFQVL 107
                                       ***8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1935.98
//
Query:       gi|488601268|ref|YP_007907739.1|  [L=274]
Description: putative permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-38  130.5  30.7    8.7e-38  130.3  30.7    1.0  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 !  130.3  30.7   4.9e-42   8.7e-38       3     235 ..      11     267 ..       8     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 4.9e-42
                              TauE   3 lagllaGfvagllGiGggliavPlLll.l.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGa 77 
                                       l+++l++ + + +G+ g+++++P+ +  l ++ +++  t+++++++   sg+++++r+g++  +l+l++++g+l+G+
  gi|488601268|ref|YP_007907739.1|  11 LFAFLISSFTSQAGVSGAFLILPFQISvLgFSSPAVSSTNFVYNIVAIPSGVYRYIREGRFLKPLALVIAFGTLPGI 87 
                                       7789999*******************966889999**************************9*************** PP

                              TauE  78 llGallll.llpse.llkllfgvlllllallmllrkkr...................srak..grerrptaillvli 131
                                       ++Gal+   +lp++  +kl++gv+ll+l+l++l++kk+                      +  +r++  + + ++li
  gi|488601268|ref|YP_007907739.1|  88 FIGALIRVtYLPDPkNFKLFVGVVLLYLGLRLLYTKKSerrevrvarivkvsirevvY--EfsNRTYSFSVLKVFLI 162
                                       ******77788877689****************9777767888888777776655542..0558899********** PP

                              TauE 132 gglvGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyal.agavdwpllllllpgallGal 207
                                       ++l+G+++G  G+GgG++++p+l++++glp+ ++++++l++++++s+ag++ y + + + +w  +l +++g+++G++
  gi|488601268|ref|YP_007907739.1| 163 AFLIGIVGGAYGVGGGAMIAPILVSVFGLPIYTTAGATLFATFISSIAGVAYYSIlGYSPNWIQGLSIGIGGFFGMY 239
                                       999*************************************************955266667888888********** PP

                              TauE 208 lGarlarrlsertlrrlfallllvlgvk 235
                                       +Ga + + ++er++r+ + +l++vl++k
  gi|488601268|ref|YP_007907739.1| 240 VGAGMQKFMPERVIRIGLSVLIIVLAIK 267
                                       **************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2049.47
//
Query:       gi|488601269|ref|YP_007907740.1|  [L=381]
Description: Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase-related deacylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   91.0   0.5    1.9e-25   89.8   0.5    1.6  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.8e-10   40.7   0.0    4.1e-10   39.5   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
       0.07   12.1   0.0         12    4.8   0.0    2.6  3  Peptidase_M42  M42 glutamyl aminopeptidase
      0.088   12.5   0.0       0.15   11.8   0.0    1.4  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.5   4.3e-29   1.9e-25       1     206 [.      68     375 ..      68     376 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 4.3e-29
                                       EEEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT. CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Peptidase_M20   1 llgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr. 75 
                                       +l  H+D+Vp ++          + + dGklyGrG++d kg  + +++a+ + k++       ++l+f++dEE+g+ 
  gi|488601269|ref|YP_007907740.1|  68 MLTTHMDTVPsHDAL------LNPVIVDGKLYGRGSCDAKGCMAVYIHAALNSKAD-----VGLKLAFTCDEEVGGi 133
                                       6889******44433......5677888*********************9665555.....69**********9889 PP

                                       THHHHHHHHHHTTTCESEEEEEEEESSSBTCHST.ETEEEE.................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.................................... RF
                     Peptidase_M20  76 gGakallegleerekvdavfelhieepgileagk.laigvv.................................... 115
                                       +G ++++e    +e++d+v+   ++ep + ++ + l++ vv                                    
  gi|488601269|ref|YP_007907740.1| 134 NGLGYVFE----KERADFVL---VGEPFGADRVGaLQASVVsaditikgesghtaskdsrkgaiyraseyiiettkk 203
                                       9*******....99****66...*******9444455555599999******************************* PP

                                       ............................................................................E CS
                                       ............................................................................x RF
                     Peptidase_M20 116 ............................................................................k 116
                                                                                                                   +
  gi|488601269|ref|YP_007907740.1| 204 isslkgdyanfesffkglgfefevrgishaifnpavikggvkrnvvapectisadirfapwigrdeirdaiysehaE 280
                                       *************************************************************************9663 PP

                                       EEEEEE.....EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSGGCTTST CS
                                       xxxxxx.....xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 117 vevell.....eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgsglaHsp 185
                                       +++  +          + ++ d ++ k+l+++++++ g ++  ++s  g  d+r++   g+p++ ++gp + + Hs 
  gi|488601269|ref|YP_007907740.1| 281 FRINGVlqpfgILIDGTNTEkDIEFLKILRDSIKDF-GMRPVAVCSL-GVGDTRHVrkYGVPAF-YYGPRGYGLHSD 354
                                       333333333243334555558999***********5.*777777777.********88888877.7**88899**** PP

                                       TTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 186 nEyvdledlekgikvlarlle 206
                                       nE v +e+l+++ kv++r++e
  gi|488601269|ref|YP_007907740.1| 355 NECVVIEELYTCSKVIERIIE 375
                                       ******************997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   9.1e-14   4.1e-10       6      97 ..     166     274 ..     163     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 9.1e-14
                                       EEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC......................TCCTCCCCCEECCE CS
                         M20_dimer   6 laggkitvkgkagHsgapgagaNAieklarllaeledeegdia.................eerslprttlnvtgieg 65 
                                       ++++ it+kg++gH + ++    Ai+ +++ + e  ++ ++ +                 e r +++  +n+++i+g
  gi|488601269|ref|YP_007907740.1| 166 VVSADITIKGESGHTASKDSRKGAIYRASEYIIETTKKISSLKgdyanfesffkglgfefEVRGISHAIFNPAVIKG 242
                                       7899**********************999999988888666668888****************************** PP

                                       -CCCCEESSEEEEEEEEEHHHHHHHHHHHHHH CS
                         M20_dimer  66 GsaknvipdeaeakidiRllpgedpeevleei 97 
                                       G ++nv+++e++ + diR+ p   ++e++++i
  gi|488601269|ref|YP_007907740.1| 243 GVKRNVVAPECTISADIRFAPWIGRDEIRDAI 274
                                       *********************98888888877 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0027        12       2      25 ..      55      76 ..      54      78 .. 0.87
   2 ?    4.3   0.0    0.0037        17     136     170 ..     101     132 ..      84     153 .. 0.66
   3 ?   -2.2   0.0      0.37   1.7e+03     256     291 ..     333     368 ..     328     369 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0027
                                      -EEEEEESSTTSSEEEEEEE--B- CS
                     Peptidase_M42  2 nliakkkgkekepkvmiaAHmDei 25
                                      nli++++    ep+ m+++HmD++
  gi|488601269|ref|YP_007907740.1| 55 NLIVEIQR--GEPEFMLTTHMDTV 76
                                      67787777..89**********98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTS CS
                     Peptidase_M42 136 ragvavllellkelkeeeleatvylvatvqEEvGl 170
                                       + ++av ++++    +++ ++ + l++t+ EEvG 
  gi|488601269|ref|YP_007907740.1| 101 KGCMAVYIHAAL---NSKADVGLKLAFTCDEEVGG 132
                                       444444444433...334579************83 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.37
                                       HTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHH CS
                     Peptidase_M42 256 hltgegvptalisiptryiHspvevahlddleatvk 291
                                       h+ + gvp+   ++    +Hs +e + ++ l  + k
  gi|488601269|ref|YP_007907740.1| 333 HVRKYGVPAFYYGPRGYGLHSDNECVVIEELYTCSK 368
                                       788999999999999999******999999988876 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05      0.15       1      82 [.      55     140 ..      55     217 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                                       EEEEEESTTCESEEEEEEEE--B-TTT.........TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEE CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg.........rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflf 67 
                                       N+i++++ ++    ++l+ H+D+v+ +         +g+    G  D A g++a+ ++  +l++   + + g++++f
  gi|488601269|ref|YP_007907740.1|  55 NLIVEIQRGE--PEFMLTTHMDTVPSHdallnpvivDGKlYGRGSCD-AKGCMAV-YIHAALNS---KADVGLKLAF 124
                                       8899998887..468**********9999988887755544456666.7787776.45556665...68******** PP

                                       ESSCSG.SSHHHHHHH CS
                     Peptidase_M28  68 fdaEEa.gllGSkafa 82 
                                       +  EE  g+ G  + +
  gi|488601269|ref|YP_007907740.1| 125 TCDEEVgGINGLGYVF 140
                                       *****94444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2413.72
//
Query:       gi|488601270|ref|YP_007907741.1|  [L=241]
Description: hypothetical protein Asulf_01777 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1464.87
//
Query:       gi|488601271|ref|YP_007907742.1|  [L=63]
Description: hypothetical protein Asulf_01778 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 477.86
//
Query:       gi|488601272|ref|YP_007907743.1|  [L=587]
Description: hypothetical protein Asulf_01779 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1299  (0.0724525); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4080.89
//
Query:       gi|488601273|ref|YP_007907744.1|  [L=404]
Description: hypothetical protein Asulf_01780 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2711.22
//
Query:       gi|488601274|ref|YP_007907745.1|  [L=329]
Description: Zn-dependent hydrolase, including glyoxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-21   75.1   1.8    1.1e-20   74.5   1.8    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.8e-05   23.7   0.0    4.6e-05   23.0   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.026   14.0   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
       0.16   11.3   0.0       0.89    8.9   0.0    2.0  2  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,


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 !   74.5   1.8   2.4e-24   1.1e-20       6     197 .]      47     238 ..      44     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 2.4e-24
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       +++++   +++++L+D Gt+   +++++  a+++l+ +dv+ ++lTH H+DH+Gglg + e +++++++v+++++++
  gi|488601274|ref|YP_007907745.1|  47 ISTWVFKSNKKAFLVDVGTTKTVKLLVE--ALKYLGVEDVEFILLTHIHIDHAGGLGSFLEYYPNAKVVVHDKGKKH 121
                                       6789999********************5..9999******************************************* PP

                                       HCHHHHHHHHHCCHH...TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHH CS
                       Lactamase_B  83 fmeeaddaasrkgll...lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallage 156
                                       + + +  +++  + l   ++ +  +kp++ +++++ ++ + ++++v ++ ++gh + + +y  ++++f+G a+ ++ 
  gi|488601274|ref|YP_007907745.1| 122 LINPERLWEGSLKVLgdiARMYGGIKPVPEKNIYE-GDVEFEGTEVEVIATPGHAPHHNCYIYDRYIFVGEAIGVHH 197
                                       9999999999999999*555555555555555555.5566778999999************************9998 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        +++   +  +++++   +e +++s++k+ ++ + + ++gH
  gi|488601274|ref|YP_007907745.1| 198 YLKTWDFYLRPATPPKFVYEVARESIEKIHDSGNFTACFGH 238
                                       88888866666677777777777777777777766666666 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 !   23.0   0.0     1e-08   4.6e-05      27      70 ..      80     122 ..      58     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1e-08
                                       -..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHC CS
                     Lactamase_B_2  27 elppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavl 70 
                                        +++++++llth H+DH  gl ++ e +p +++++++++  ++l
  gi|488601274|ref|YP_007907745.1|  80 GVEDVEFILLTHIHIDHAGGLGSFLEYYP-NAKVVVHDKGKKHL 122
                                       5789**********************666.68999999888887 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-06     0.026       8      58 ..      58     106 ..      52     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                     Lactamase_B_6   8 kiLlDvGwdeskvslesalkelekv.iptvdliLLshatlehlGayallyak 58 
                                        +L+DvG++++       ++ l+   +++v+ iLL+h  ++h G++  ++ +
  gi|488601274|ref|YP_007907745.1|  58 AFLVDVGTTKTVKL---LVEALKYLgVEDVEFILLTHIHIDHAGGLGSFLEY 106
                                       68*******98433...4444444349*****************99766655 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.12   5.3e+02      99     112 ..      55      68 ..      41      94 .. 0.68
   2 ?    8.9   0.0    0.0002      0.89      75     128 ..     105     166 ..      90     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                                       -TT-EEEE---EEC CS
                     THF_DHG_CYH_C  99 kegavviDvGinrv 112
                                       +++a+++DvG++++
  gi|488601274|ref|YP_007907745.1|  55 NKKAFLVDVGTTKT 68 
                                       46799*****9987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0002
                                       HHHCCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC........-TTEEE-SB-HHHHCT CS
                     THF_DHG_CYH_C  75 eitreadivvvavGkpelikaemvkegavviDvGinrv........ekgklvGDvdfeevke 128
                                       e+  +a +vv   Gk++li+ e + eg+  +   i r+        ek+   GDv+fe  + 
  gi|488601274|ref|YP_007907745.1| 105 EYYPNAKVVVHDKGKKHLINPERLWEGSLKVLGDIARMyggikpvpEKNIYEGDVEFEGTEV 166
                                       56679**********************9766555555556777778888899****997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2379.70
//
Query:       gi|488601275|ref|YP_007907746.1|  [L=49]
Description: LSU ribosomal protein L40E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   26.7   4.4    4.3e-06   26.5   4.4    1.2  1  Ribosomal_L40e  Ribosomal L40e family
    0.00016   21.3   3.4    0.00023   20.8   3.4    1.2  1  zinc_ribbon_2   zinc-ribbon domain
    0.00035   20.5   0.7    0.00035   20.5   0.7    1.1  1  DZR             Double zinc ribbon
    0.00096   18.8   4.0     0.0016   18.1   4.0    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
     0.0077   15.6   2.7       0.01   15.2   2.7    1.2  1  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.033   13.5   3.0      0.048   13.0   3.0    1.3  1  zf-RanBP        Zn-finger in Ran binding protein and others
       0.19   11.6   4.1       0.76    9.7   0.6    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


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 !   26.5   4.4   1.7e-09   4.3e-06      16      48 ..      14      43 ..       7      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.7e-09
                    Ribosomal_L40e 16 KmiCrkCYArlpprAtnCrkkkCghsnnlrpKK 48
                                       +iC kC Ar p++At Cr  kCg  + lrpK 
  gi|488601275|ref|YP_007907746.1| 14 VKICMKCNARNPIKATTCR--KCGY-KGLRPKS 43
                                      58*****************..9**7.5678775 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   3.4   8.9e-08   0.00023       2      22 ..      17      37 ..      16      38 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.9e-08
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C +C a ++ +a+ C +CG++
  gi|488601275|ref|YP_007907746.1| 17 CMKCNARNPIKATTCRKCGYK 37
                                      *******************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.7   1.4e-07   0.00035      28      49 .]      14      35 ..       2      45 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.4e-07
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                       + C++C++ ++ +a++C +CG
  gi|488601275|ref|YP_007907746.1| 14 VKICMKCNARNPIKATTCRKCG 35
                                      5667777777777777777776 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 !   18.1   4.0   6.3e-07    0.0016       2      26 ..      16      37 ..      16      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.3e-07
                                      B-SSS--B----SSS----SSS--- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGhR 26
                                      iC++C+a++ +k++    C++CG++
  gi|488601275|ref|YP_007907746.1| 16 ICMKCNARNPIKAT---TCRKCGYK 37
                                      8*************...9*****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 !   15.2   2.7   3.9e-06      0.01       3      25 ..      15      37 ..      13      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.9e-06
                       zf-ribbon_3  3 vrCPnCGa.plssddnvCpyCGtk 25
                                      + C +C+a +    +++C +CG+k
  gi|488601275|ref|YP_007907746.1| 15 KICMKCNArN-PIKATTCRKCGYK 37
                                      6799******.***********97 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.0   1.9e-05     0.048       6      25 ..      16      35 ..      16      37 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                                      E-SSS--EEESSSSB-TTT- CS
                          zf-RanBP  6 dCskClvqNfawstkCvaCq 25
                                      +C kC+++N+ ++t+C  C+
  gi|488601275|ref|YP_007907746.1| 16 ICMKCNARNPIKATTCRKCG 35
                                      59**************9996 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 ?    4.5   0.1     0.013        32      24      33 ..      17      26 ..       7      29 .. 0.75
   2 ?    9.7   0.6    0.0003      0.76      23      30 ..      30      37 ..      24      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.013
                                      ESSSS-EEES CS
                    RNA_POL_M_15KD 24 CrqCgYeepa 33
                                      C +C +  p+
  gi|488601275|ref|YP_007907746.1| 17 CMKCNARNPI 26
                                      8888888887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0003
                                      EESSSS-E CS
                    RNA_POL_M_15KD 23 eCrqCgYe 30
                                       Cr+CgY+
  gi|488601275|ref|YP_007907746.1| 30 TCRKCGYK 37
                                      3******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 380.09
//
Query:       gi|488601276|ref|YP_007907747.1|  [L=351]
Description: amino acid/amide ABC transporter membrane protein 2, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-52  178.4  40.8    1.7e-52  178.2  40.8    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.02   14.7   0.8      0.056   13.2   0.3    2.2  3  Coa1          Cytochrome oxidase complex assembly protein 1
       0.31   10.9   3.4       0.47   10.3   0.2    2.7  3  Cortexin      Cortexin of kidney
        3.7    6.8   6.3          2    7.6   3.3    1.9  2  CorA          CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.2  40.8   3.9e-56   1.7e-52       2     268 .]       7     318 ..       6     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 3.9e-56
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl........................ 54 
                                       iln++ ++++++i++l+l++ +g++G++n+g + ++++Ga++++ ++++ l+                         
  gi|488601276|ref|YP_007907747.1|   7 ILNIIIWIGLYLIVGLSLNIEYGFGGIPNFGRALAVLIGAIAVGGVVNRILMVilgvsgqiidasgvvktafndiia 83 
                                       89*************************************************************************** PP

                      BPD_transp_2  55 .........lllallvallvgaavglllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgf 122
                                                l ++l++a  +ga+ g++++l++++l +d+l+itll+ls+ ++l+ +++  i++g++g++ ++ l ++
  gi|488601276|ref|YP_007907747.1|  84 qnpavgiaiLVFSLILAGFLGAVTGAIFILPSAKLSEDYLAITLLALSESAFLISYYHPDIIGGYYGVTFPNVLNFI 160
                                       *********999***************************************************************** PP

                      BPD_transp_2 123 agallsflsavivllalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallal 199
                                       +g+ + f++a+i +l+++lv++++ +++ +++Gr l+a++ene +++  G++++ ++++t+++++++A+laGal+++
  gi|488601276|ref|YP_007907747.1| 161 PGEQRLFAFAFIIILIAILVYILVSRMLASPYGRLLKAMRENEAVVETYGKDIMMLRIKTVAVGSGIAALAGALYSM 237
                                       ***************************************************************************** PP

                      BPD_transp_2 200 llgsipp..nigvglgfnaiaavvlGgagsllgtviGaliigvvksllltllgi..........ptelarvllgall 264
                                       +++++ +  + +v+++f++i++ +lGg+g+ +g++iG   ++++ ++l+t++            p +l+++l+g ++
  gi|488601276|ref|YP_007907747.1| 238 FSVNVIAtnFSRVEWTFYPILMILLGGLGNTRGVFIGVASFVIARIFLITYKFEivstlglpfdPVWLEYILFGFVM 314
                                       *99999999999***************************************97799999999999************ PP

                      BPD_transp_2 265 ilvl 268
                                       +++l
  gi|488601276|ref|YP_007907747.1| 315 LVIL 318
                                       *987 PP

>> Coa1  Cytochrome oxidase complex assembly protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   4.9e+03       8      39 ..     102     133 ..      96     136 .. 0.71
   2 ?   13.2   0.3   1.3e-05     0.056       4      51 ..     167     214 ..     164     245 .. 0.86
   3 ?   -3.3   0.0       1.6   7.2e+03       6      43 ..     309     346 ..     307     350 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                              Coa1   8 vvgvvvalayifnyektsssivrsvlyqlrrs 39 
                                       ++g+v+  ++i+ + k+s +++  +l +l +s
  gi|488601276|ref|YP_007907747.1| 102 FLGAVTGAIFILPSAKLSEDYLAITLLALSES 133
                                       45566666778888888888888888887766 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
                              Coa1   4 f.avfvvgvvvalayifnyektsssivrsvlyqlrrspevrelLGeeip 51 
                                       f  +f+++++++l+yi+ ++++ s++    l+++r+++ v+e  G++i 
  gi|488601276|ref|YP_007907747.1| 167 FaFAFIIILIAILVYILVSRMLASPY-GRLLKAMRENEAVVETYGKDIM 214
                                       43578899999999999999998875.678***************9885 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.6
                              Coa1   6 vfvvgvvvalayifnyektsssivrsvlyqlrrspevr 43 
                                       +f  ++ v+l+y  +   ++ +i+++ ++++ ++ +++
  gi|488601276|ref|YP_007907747.1| 309 LFGFVMLVILVYRPEGILKEKPILTEPIKKVVKKRNIK 346
                                       56666777777777777777777777777776666655 PP

>> Cortexin  Cortexin of kidney
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2    0.0001      0.47      21      54 ..     163     195 ..     158     204 .. 0.81
   2 ?   -3.8   0.0       2.7   1.2e+04      26      37 ..     252     263 ..     248     265 .. 0.73
   3 ?   -0.3   0.1      0.22   9.8e+02      28      43 ..     307     322 ..     304     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                          Cortexin  21 eqkt.vfafvilLlifLglLivrCfriLLDPYssm 54 
                                       eq+  +faf+i+L+ +L+ ++v   r+L  PY ++
  gi|488601276|ref|YP_007907747.1| 163 EQRLfAFAFIIILIAILVYILV--SRMLASPYGRL 195
                                       6664389999999999998887..58999999875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.7
                          Cortexin  26 fafvilLlifLg 37 
                                       ++f  +L+i+Lg
  gi|488601276|ref|YP_007907747.1| 252 WTFYPILMILLG 263
                                       678888899887 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.22
                          Cortexin  28 fvilLlifLglLivrC 43 
                                       ++++ +++L++L+ r 
  gi|488601276|ref|YP_007907747.1| 307 YILFGFVMLVILVYRP 322
                                       5667788899998875 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.18   8.2e+02     249     286 ..      98     138 ..      88     141 .. 0.75
   2 ?    7.6   3.3   0.00045         2     248     287 ..     143     184 ..     137     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.18
                              CorA 249 litGiyGmNfkg...lPelewsygypfvlllglmallaill 286
                                       +++G++G  ++    lP ++ s  y++++ll+l+  +++++
  gi|488601276|ref|YP_007907747.1|  98 ILAGFLGAVTGAifiLPSAKLSEDYLAITLLALSESAFLIS 138
                                       68888888777777799999999999998888875555555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00045
                              CorA 248 TlitGiyGmNfkg....lPelewsygypfvlllglmallailll 287
                                        +i+G+yG  f++    +P+ +  +  +f+++++l+a+l+ +l+
  gi|488601276|ref|YP_007907747.1| 143 DIIGGYYGVTFPNvlnfIPGEQRLF--AFAFIIILIAILVYILV 184
                                       69**********999999*999999..66555666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2199.00
//
Query:       gi|488601277|ref|YP_007907748.1|  [L=306]
Description: amino acid/amide ABC transporter membrane protein 1, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  147.7  43.3    4.2e-43  147.5  43.3    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5  43.3   2.3e-47   4.2e-43       4     268 .]       6     283 ..       3     286 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 2.3e-47
                      BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrl 80 
                                         + ++ +l+++++Gl+++++ + v+n+++g+f+++G+yva++l  l++ ++++++++ +++g+++gl++++ vl+ 
  gi|488601277|ref|YP_007907748.1|   6 GAIIYSNLLVLLSIGLTMTYITTAVPNFAQGSFAVFGSYVALTLFRLYGIHPYASIPITFVAGGLLGLVIYIGVLKP 82 
                                       5678899********************************************************************** PP

                      BPD_transp_2  81 kvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.........llalllvlavlll 148
                                        +++ + +++l+++ +++ l+ll+ i   +     +++ ++++  + ++ ++  +         ++++l+++ ++ll
  gi|488601277|ref|YP_007907748.1|  83 LIRRGAEVVILMIATLAVDLILLGVIGAYSDYLGVITKKSAKKFIFTPYDFSIGSmsgiffvsiAVIALILFGLYLL 159
                                       ************************9999999999888888888888888777777888889998888888999999* PP

                      BPD_transp_2 149 lrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGga 225
                                       l +t+fG+a+ra +en+++a+ +G+nv+ ++l+++++s+alA laGall ++++++p  +g  ++ +++a+ ++Gg+
  gi|488601277|ref|YP_007907748.1| 160 LFKTKFGVAMRASMENPSLAEIMGVNVETTRLTSWILSAALASLAGALLPFRQEIVP-MTGGIIIVSIFASSIVGGL 235
                                       ******************************************************999.9****************** PP

                      BPD_transp_2 226 gsllgtviGaliigvvksllltllgi.....ptelarvllgallilvl 268
                                       gs++g++iG++++g+++s+ ++ l+         ++rv++ ++li++l
  gi|488601277|ref|YP_007907748.1| 236 GSIFGALIGGYVVGMSESFVTFELSKvfgtgVLVYSRVVSLIVLIIML 283
                                       ******************666666557776658888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2373.75
//
Query:       gi|488601278|ref|YP_007907749.1|  [L=433]
Description: amino acid/amide ABC transporter substrate-binding protein, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-35  120.8   0.5    1.5e-34  120.2   0.5    1.3  1  Peripla_BP_6  Periplasmic binding protein
    3.5e-27   95.5   0.0    5.2e-27   94.9   0.0    1.1  1  ANF_receptor  Receptor family ligand binding region
     0.0001   21.3   0.0    0.00015   20.7   0.0    1.2  1  LppC          LppC putative lipoprotein
  ------ inclusion threshold ------
      0.015   14.3   0.0       0.06   12.3   0.0    1.9  2  Peripla_BP_5  Periplasmic binding protein domain


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 !  120.2   0.5   3.3e-38   1.5e-34       1     314 [.      47     379 ..      47     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 3.3e-38
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTE..EEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGinGr..kielverDdaydpdraaeaarrlvdqdgvdalvg 75 
                                       +i iG+l++lsGp+ ++g++  a ++ a +eiN+    +G+  ++++ ++D+  dp++a+++++ l   +gv++++g
  gi|488601278|ref|YP_007907749.1|  47 EIPIGVLVDLSGPLTTYGEDIKATVEIAKDEINKYFEEKGKpyRVKVYVEDTRVDPKVALDKVQALHG-KGVRLIIG 122
                                       589*******************************99999997789999******************88.******** PP

                                       -BSHHHHHHHHHHHHHHT-EEEESS........-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEES CS
                      Peripla_BP_6  76 plssavaaavaevlakdgvpvigpa........gltgekcspyvfslgpsysaqasalveylakelggkkvalvyad 144
                                       p++s+ ++ +a++++++++++i+p+        g t  + +  +f++ + +  q++a+++  ++elg+k v++ y+ 
  gi|488601278|ref|YP_007907749.1| 123 PMGSGEVKNIADYVTANKIIIISPSstaipqllGITKPEEKKFIFRFVAPDTFQTKAIAKE-VQELGIKGVVITYVG 198
                                       ***********************99555555555667899********************9.9************** PP

                                       SHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTH.HHHHHHHHHHHTTT-S..........EEEEESSHHHHHHHHHHH CS
                      Peripla_BP_6 145 yafgregiaalkaaakaaGgevvgeepvplgt.tdfsaqvlqikaagad..........avllagtgadlaallkaa 210
                                       +a+g+ +++a+k +++++G+ev   +++p +  +dfs ++++i++ g +          + ++a+  + + ++l ++
  gi|488601278|ref|YP_007907749.1| 199 NAWGKGLADAAKPLFEEYGIEVAKVVEYPDPPpADFSQYINAIED-GIKnladkygtekIAVVAFSYEETYTMLSQI 274
                                       **********************99999996555************.444466688888845556667779******* PP

                                       HHTT-SSSCEEEECCC..-CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHH CS
                      Peripla_BP_6 211 aeaGldakrillvsws..gseedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyia 285
                                        e  +  k + ++ ++  ++   +  +     + v ++++ f++  ++  +++ + y+ +yg++  + q+++ +y+a
  gi|488601278|ref|YP_007907749.1| 275 PEDSILLKVMWIG-CDgnAYSRKITEMCD-RVNAVKMYSTLFES-KGDSYEQLNKTYYGKYGRT--TYQYGLDAYDA 346
                                       9999998744443.332355555666654.57777777777765.79****************8..9999******* PP

                                       HHHHHHHHHCC....THCCHHHHHHHHHHS-BE CS
                      Peripla_BP_6 286 adlllealkaa....gsltreavraaleslgfd 314
                                       a++l+    ++    g+++++av++ + +++ +
  gi|488601278|ref|YP_007907749.1| 347 AWVLALSFAQVydkeGKFDPDAVAEVIPKVTEE 379
                                       *9998888888777799******9988777644 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 !   94.9   0.0   1.2e-30   5.2e-27       5     350 ..      70     412 ..      67     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 1.2e-30
                                       HHHHHHHHHHT-TTSSTTE.EEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEES CS
                      ANF_receptor   5 AmklAveeinsdpnllpgi.klgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvisy 80 
                                       +++ A +ein+  +  ++  ++ ++++dt  d++ al +++ ++ + v  +iGp +s++++ +a + +++ki++is+
  gi|488601278|ref|YP_007907749.1|  70 TVEIAKDEINKYFEEKGKPyRVKVYVEDTRVDPKVALDKVQALHGKGVRLIIGPMGSGEVKNIADYVTANKIIIISP 146
                                       68889999999977776666************************977****************************** PP

                                       S---G..G..GG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEE CS
                      ANF_receptor  81 gstsp..e..lsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqaleeeleergicvalk 153
                                       +st+      +++ ++ ++++r v +dt+q +Ai++ ++++g k v++ y  +++g+++++a +  +ee+gi+va +
  gi|488601278|ref|YP_007907749.1| 147 SSTAIpqLlgITKPEEKKFIFRFVAPDTFQTKAIAKEVQELGIKGVVITYVGNAWGKGLADAAKPLFEEYGIEVAKV 223
                                       **653113245777787888********************************************************* PP

                                       EEEST..CHHHCHHHHHH....HHHHTT..T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS- CS
                      ANF_receptor 154 ekipe..ssnddevvrkl....lkeiks..karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldk 222
                                        ++p   + ++++ ++++    ++ +++  ++++ v+ +s e+ +  l ++ +  +  +  +wi+ d+ ++s ++  
  gi|488601278|ref|YP_007907749.1| 224 VEYPDppPADFSQYINAIedgiKNLADKygTEKIAVVAFSYEETYTMLSQIPEDSILLK-VMWIGCDGNAYSRKIT- 298
                                       ****99*55555555555444344445588889*****************999999996.****999988887777. PP

                                       CC..HHHHHTT-EEEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSS CS
                      ANF_receptor 223 peltgleaaegvlgfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkp 299
                                             e+ + v  ++++++  ++  + +      + +k+ y ++g++ ++y + + Yda ++la  + +++ k+++
  gi|488601278|ref|YP_007907749.1| 299 ------EMCDRVNAVKMYSTLFESKGDSY-----EQLNKTYYGKYGRTTYQYGLDA-YDAAWVLALSFAQVYDKEGK 363
                                       ......57888888888888888888888.....3446899*************88.***************76655 PP

                                       SHCCB-HHHHCCHHHHHHHHHHHT-EEE..ETTSCEEB-TTSBBE.-EEEEEEE CS
                      ANF_receptor 300 gralscntlkpweggqkllrylrnvnfe..GltGdvkfdengdrv.ptydilnl 350
                                       +   +       e   k++++  +  +    ++G +k++e +dr+ ++y i+ +
  gi|488601278|ref|YP_007907749.1| 364 FDPDA-----VAEVIPKVTEEYSKGAYGvtPVSGFIKLNEWNDRAsGNYAIWGV 412
                                       55222.....2333333343333433323377********************87 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.4e-08   0.00015     192     382 ..      22     227 ..      12     283 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.4e-08
                                       HHHSTTSHHHHS--HHHHHHHT--------EEEEE--SSTTHHHHHHHHHHHHHHH...........TT--S-EEEE CS
                              LppC 192 kaeyPehpaakllPkaltdllnlqqtkltkvalLLPlsGklakvaetirdGFlaak........daetqsnaqvkvf 260
                                       +ae P  + a+++P+a ++   ++ +++  +++L  lsG l + +e i++  + ak        ++ + ++++v v 
  gi|488601278|ref|YP_007907749.1|  22 QAEKPVPTPAEKTPTAENT-PEVKEVEI-PIGVLVDLSGPLTTYGEDIKATVEIAKdeinkyfeEKGKPYRVKVYVE 96 
                                       5778888899999999888.55555554.59*************************988886433444466667777 PP

                                       ETTTS...-HHHHHHHHHHTT--EEE---SHHHHHHHHHSGG.GTTSEEEES---T.....T-.--BTTEEE----H CS
                              LppC 261 Dtaae...slediyaqakaagidlvVGPLlkqnvdkllaqeqlvqsidvLaLNssd.....ns.raiaqlcyfgLsp 328
                                       Dt +    +l+++ + ++ +g++l++GP+  ++v+++++      +i +++  s+      ++ +  ++ + f   +
  gi|488601278|ref|YP_007907749.1|  97 DTRVDpkvALDKV-QALHGKGVRLIIGPMGSGEVKNIADYVTA-NKIIIISPSSTAipqllGItKPEEKKFIFRFVA 171
                                       9*99965444444.56789*****************9876665.444444333332111114423345566666555 PP

                                       HH..HHHHHHHHHHHTT-SSEEEEEESSHHHHHHHHHHHHHHHHHHSS--EEEEES CS
                              LppC 329 Ed..eaesaAsklwadgvRnplvlvpqndlGrRvveAFnerwqqlagtdaaielvd 382
                                        d  +++++A+++ + g++ +++    n++G+  ++A +  + +++ ++a +  + 
  gi|488601278|ref|YP_007907749.1| 172 PDtfQTKAIAKEVQELGIKGVVITYVGNAWGKGLADAAKPLFEEYGIEVAKVVEYP 227
                                       55234667788888888888888888888888888888888888887776655444 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 ?   12.3   0.0   1.3e-05      0.06       1      92 [.      48     140 ..      48     148 .. 0.85
   2 ?   -1.2   0.0      0.18   7.9e+02     273     320 ..     339     386 ..     286     397 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                      Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlg..rkieavvvdpasdwelfaekaeklieedkvevvfGc 75 
                                       i +GvL  lsG +++  + +k ++ +a +ein+    +g   +++  v+d + d+++  +k ++l   ++v+ ++G 
  gi|488601278|ref|YP_007907749.1|  48 IPIGVLVDLSGPLTTYGEDIKATVEIAKDEINKYFEEKGkpYRVKVYVEDTRVDPKVALDKVQALHG-KGVRLIIGP 123
                                       679*****************************97655552268999**********99999988765.99******9 PP

                      Peripla_BP_5  76 wtSasRkavlpvveeln 92 
                                         S   k++ + v +++
  gi|488601278|ref|YP_007907749.1| 124 MGSGEVKNIADYVTANK 140
                                       99998888888776655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.18
                      Peripla_BP_5 273 vtndpmeaayiqvklwaqAvekagstdvekvreallgqelkapeGevk 320
                                          d   aa++    +aq + k g+ d+++v e + +++ +  +G+  
  gi|488601278|ref|YP_007907749.1| 339 YGLDAYDAAWVLALSFAQVYDKEGKFDPDAVAEVIPKVTEEYSKGAYG 386
                                       333566777777777888888888888888888887777666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2709.95
//
Query:       gi|488601279|ref|YP_007907750.1|  [L=258]
Description: amino acid/amide ABC transporter ATP-binding protein 1, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   94.1   0.0    1.3e-26   93.8   0.0    1.1  1  ABC_tran      ABC transporter
    2.2e-10   40.8   0.9    0.00017   21.5   0.3    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.1e-06   27.5   0.1    3.6e-06   26.8   0.1    1.4  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    2.2e-05   24.0   0.0     0.0031   17.0   0.2    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    2.4e-05   25.0   1.0    3.7e-05   24.3   1.0    1.3  1  AAA_23        AAA domain
    3.2e-05   23.6   0.1    6.4e-05   22.6   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
    5.7e-05   23.0   0.0    0.00028   20.7   0.0    1.9  2  AAA_15        AAA ATPase domain
    0.00095   18.9   0.0     0.0027   17.4   0.0    1.7  2  AAA_30        AAA domain
     0.0041   17.5   0.0     0.0062   16.9   0.0    1.6  1  AAA_16        AAA ATPase domain
     0.0062   15.6   0.0       0.01   15.0   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
     0.0062   16.8   0.0     0.0098   16.2   0.0    1.6  1  AAA_22        AAA domain
     0.0082   16.0   0.1      0.014   15.2   0.1    1.3  1  ATP_bind_1    Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.018   15.0   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
      0.012   15.2   0.0      0.037   13.6   0.0    1.8  2  SRP54         SRP54-type protein, GTPase domain
      0.016   14.9   0.0      0.037   13.7   0.0    1.6  1  AAA_24        AAA domain
      0.023   14.6   0.0      0.044   13.7   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.027   14.8   0.1      0.052   13.9   0.1    1.7  1  AAA_19        AAA domain
      0.049   13.5   0.0       0.22   11.4   0.0    1.9  2  Rad17         Rad17 P-loop domain
      0.055   13.6   0.1       0.16   12.2   0.0    1.7  2  AAA_33        AAA domain
      0.075   12.6   0.0       0.11   12.0   0.0    1.2  1  AAA_27        AAA domain
      0.078   12.9   0.0       0.17   11.8   0.0    1.6  1  NACHT         NACHT domain
      0.081   12.4   0.0       0.13   11.8   0.0    1.2  1  AAA_7         P-loop containing dynein motor region
      0.085   12.4   0.1       0.14   11.7   0.1    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.087   12.9   0.0       0.33   11.0   0.0    2.0  2  AAA_14        AAA domain
       0.16   10.5   0.1       0.21   10.2   0.1    1.1  1  AAA_13        AAA domain
       0.17   11.2   0.0       0.33   10.3   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.18   10.9   0.0       0.18   10.9   0.0    1.1  1  G-alpha       G-protein alpha subunit
       0.21    9.0   0.2       0.29    8.6   0.2    1.0  1  DUF3584       Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0     2e-29   1.3e-26       1     137 []      24     182 ..      24     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 2e-29
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+ v++ +k ++++ i+G+nG+GK+t++++++g +k +eG++ ++g ++++  ++e++++ i   +q pq  ++ltv
  gi|488601279|ref|YP_007907750.1|  24 LNGVNIRVKDNRVTLIIGPNGSGKTTFINTVSGFYKADEGHVYFEGLEITNkPPHEIYQNGIVRTFQIPQPLKKLTV 100
                                       789*********************************************999899*********************** PP

                                       HHH.........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSS CS
                                       xxx.........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpk 128
                                        en                         +  e++ ++l+ l++++l d+ +    ++LSgGq + +++ ra+++++k
  gi|488601279|ref|YP_007907750.1| 101 LENlliadynpgesvvgsllpgwkkyeeDLVERAFDVLKFLKIDHLWDNLA----YQLSGGQLKLLEIGRAMMTDAK 173
                                       **********************88655444444888888899999888888....********************** PP

                                       EEEEESTTT CS
                                       xxxxxxxxx RF
                          ABC_tran 129 llllDEpta 137
                                       l+++DEp a
  gi|488601279|ref|YP_007907750.1| 174 LIIMDEPVA 182
                                       *******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 !   21.5   0.3   2.6e-07   0.00017       1      25 [.      36      60 ..      36      88 .. 0.79
   2 !   18.1   0.0   2.8e-06    0.0018     220     294 ..     137     208 ..      72     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.6e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      ++++iGpNgsGK++++ + +++  +
  gi|488601279|ref|YP_007907750.1| 36 VTLIIGPNGSGKTTFINTVSGFYKA 60
                                      69**************999888654 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.8e-06
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                        + fl+ ++  +  a++lS G+++ll +  a+  ++   +l++ DEp +g +P l +++l+ +kel+++g  +++
  gi|488601279|ref|YP_007907750.1| 137 VLKFLKIDHLWDNLAYQLSGGQLKLLEIGRAMMTDA---KLIIMDEPVAGVNPVLAKSILDRIKELKARGYTFLI 208
                                       4555555555555689*********99999999999...9**************************999988876 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 !   26.8   0.1   5.6e-09   3.6e-06       2      23 .]     231     252 ..     230     252 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.6e-09
                      BCA_ABC_TP_C   2 vIAeGtPaEvrndPrVieAYLG 23 
                                       vIAeG  ++++++ +Vie+YLG
  gi|488601279|ref|YP_007907750.1| 231 VIAEGVEEDIMSNREVIEVYLG 252
                                       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 !   17.0   0.2   4.9e-06    0.0031      23      44 ..      33      54 ..      19      64 .. 0.87
   2 ?    5.3   0.0     0.018        12     135     200 ..     134     214 ..      57     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-06
                                      TSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlldAi 44
                                      ++++t i+GpNGSGK+ +++ +
  gi|488601279|ref|YP_007907750.1| 33 DNRVTLIIGPNGSGKTTFINTV 54
                                      5789*************99877 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                                       T..................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEE CS
                                       x..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                             SMC_N 135 e..................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQf 192
                                                          +LSgG+ +L+ +       ++  a l ++De  a       k + +++ke + +   f
  gi|488601279|ref|YP_007907750.1| 134 AfdvlkflkidhlwdnlayQLSGGQLKLLEIG----RAMMTDAKLIIMDEPVAGVNPVLAKSILDRIKELKARgYTF 206
                                       05555555555555555558********8875....45788999999999999999999999999999988765788 PP

                                       EEE-SSHH CS
                                       xxxxxxxx RF
                             SMC_N 193 ivislree 200
                                       +++ +r +
  gi|488601279|ref|YP_007907750.1| 207 LIVEHRLD 214
                                       88888765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   1.0   5.8e-08   3.7e-05      11      37 ..      25      52 ..       9      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.8e-08
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTild 37
                                      ++++i   ++ +tlI+GpNG+GKTT+++
  gi|488601279|ref|YP_007907750.1| 25 NGVNIRVkDNRVTLIIGPNGSGKTTFIN 52
                                      55667777889***************97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   9.9e-08   6.4e-05      13      40 ..      25      52 ..      22      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.9e-08
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllD 40
                                      +g  i+++ + +tl++Gp+GsGK+T++ 
  gi|488601279|ref|YP_007907750.1| 25 NGVNIRVKDNRVTLIIGPNGSGKTTFIN 52
                                      56778888777***************96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.4e-07   0.00028      17      50 ..      27      61 ..      23     113 .. 0.78
   2 ?    0.0   0.0      0.84   5.4e+02     322     351 ..     170     199 ..     120     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.4e-07
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      v i ++++ +t++iG+N+sGK+++++    F + +
  gi|488601279|ref|YP_007907750.1| 27 VNIRVKDNrVTLIIGPNGSGKTTFINTVSGFYKAD 61
                                      667788888****************9877777655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.84
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkel 351
                                       ++ ++++++EP a   p + k++ + +kel
  gi|488601279|ref|YP_007907750.1| 170 TDAKLIIMDEPVAGVNPVLAKSILDRIKEL 199
                                       456789999999999999999998888887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.3e-06    0.0027      15      49 ..      31      65 ..      26     100 .. 0.89
   2 ?   -1.3   0.0       2.4   1.5e+03      81      96 ..     155     179 ..     126     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.3e-06
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                       +++rv+++ Gp G+GKtt ++++   ++a++g+v
  gi|488601279|ref|YP_007907750.1| 31 VKDNRVTLIIGPNGSGKTTFINTVSGFYKADEGHV 65
                                      56788***********************9996666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                            AAA_30  81 k.........grarlepgtllivDE 96 
                                                 gra +++++l+i DE
  gi|488601279|ref|YP_007907750.1| 155 SggqlklleiGRAMMTDAKLIIMDE 179
                                       1555556666667788889999999 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   0.0   9.7e-06    0.0062      21      56 ..      33      67 ..      21     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.7e-06
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif.l 56
                                      ++  +++l++G+ G+GK++ ++++   +++d+g++ +
  gi|488601279|ref|YP_007907750.1| 33 DN--RVTLIIGPNGSGKTTFINTVSGFYKADEGHVyF 67
                                      33..799******************999999665533 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.6e-05      0.01     126     159 ..      31      64 ..      15      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                             T2SSE 126 vrerglilvsGgTgsGKttllyallkeinksder 159
                                       v+ + + l+ G+ gsGKtt+++++  + ++++ +
  gi|488601279|ref|YP_007907750.1|  31 VKDNRVTLIIGPNGSGKTTFINTVSGFYKADEGH 64 
                                       6677888999**************9998888655 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   1.5e-05    0.0098       4      34 ..      33      63 ..      29     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeak 34
                                      + ++++++G+ G+GKTt ++++   +++++ 
  gi|488601279|ref|YP_007907750.1| 33 DNRVTLIIGPNGSGKTTFINTVSGFYKADEG 63
                                      67899***************99888865544 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 !   15.2   0.1   2.2e-05     0.014       1      26 [.      39      64 ..      39      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrs 26
                                      ++Gp GsGKttf++++s ++++ + +
  gi|488601279|ref|YP_007907750.1| 39 IIGPNGSGKTTFINTVSGFYKADEGH 64
                                      79***************999887555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.8e-05     0.018       1      56 [.      17      69 ..      17      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-05
                          ATPase_2  1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyia 56
                                      Ffd  ++l+ ++  ++   n++ +i Gp gsGKt++++ +     + d+ ++y+  
  gi|488601279|ref|YP_007907750.1| 17 FFDGLTALNGVNIRVKD--NRVTLIIGPNGSGKTTFINTVSGFY-KADEGHVYFEG 69
                                      66666666666666655..99****************9865554.44666666655 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   5.8e-05     0.037       2      31 ..      35      64 ..      34      71 .. 0.85
   2 ?   -2.1   0.0       3.8   2.5e+03      71      94 ..     231     257 ..     225     258 .] 0.63

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.8e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkk 31
                                      +v+l++G++G+GKTt +  ++  +k+++ +
  gi|488601279|ref|YP_007907750.1| 35 RVTLIIGPNGSGKTTFINTVSGFYKADEGH 64
                                      589***************999999887655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.8
                                       HHHHHHHHHHHTT...SSEEEEEE--S CS
                             SRP54  71 vakeavekakeek...idvvlvDTaGr 94 
                                       v++e+ve+   ++   i+v l DT Gr
  gi|488601279|ref|YP_007907750.1| 231 VIAEGVEEDIMSNrevIEVYLGDTGGR 257
                                       556666655444412277779999999 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.8e-05     0.037       3      22 ..      35      54 ..      33      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                      +  li+Gp+g+GKTt++++ 
  gi|488601279|ref|YP_007907750.1| 35 RVTLIIGPNGSGKTTFINTV 54
                                      5689*************987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.8e-05     0.044      97     122 ..      31      57 ..      18      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.8e-05
                                       CTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinallpe 122
                                       +kd ++++++G+ G GK+t+in++ + 
  gi|488601279|ref|YP_007907750.1|  31 VKDnRVTLIIGPNGSGKTTFINTVSGF 57 
                                       55559*****************99875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.1e-05     0.052       9      38 ..      33      62 ..      27     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-05
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelg 38
                                       ++v l++++ G+GKT+ ++++   +++ +
  gi|488601279|ref|YP_007907750.1| 33 DNRVTLIIGPNGSGKTTFINTVSGFYKADE 62
                                      67899***************9987777655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00034      0.22      35      66 ..      24      55 ..      16      80 .. 0.85
   2 ?   -0.6   0.0       1.7   1.1e+03     119     140 ..     159     179 ..     144     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                      l+   +  + +r+ Li GP G gk+t ++ +s
  gi|488601279|ref|YP_007907750.1| 24 LNGVNIRVKDNRVTLIIGPNGSGKTTFINTVS 55
                                      555556667889***************99887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                             Rad17 119 ylklqklGddlrtdkklilved 140
                                         kl   G  + td kli++++
  gi|488601279|ref|YP_007907750.1| 159 L-KLLEIGRAMMTDAKLIIMDE 179
                                       3.56669999999****99997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00024      0.16       1      18 [.      36      53 ..      36      64 .. 0.89
   2 ?   -2.2   0.0       6.8   4.3e+03      50      77 ..     145     172 ..     130     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                            AAA_33  1 lvllvGlpGsGKstlaer 18
                                      ++l++G++GsGK+t++  
  gi|488601279|ref|YP_007907750.1| 36 VTLIIGPNGSGKTTFINT 53
                                      6799***********876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.8
                            AAA_33  50 rvldrlyqilnelarkalsagrnvilda 77 
                                       +++d+l ++l++   k l+ gr++++da
  gi|488601279|ref|YP_007907750.1| 145 HLWDNLAYQLSGGQLKLLEIGRAMMTDA 172
                                       4555655555555558999999999987 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.11      20      47 ..      28      55 ..      19      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                            AAA_27 20 dfsaeeadlhliyGpNEAGKstalrAis 47
                                      +++ ++++++li+GpN +GK+t ++ +s
  gi|488601279|ref|YP_007907750.1| 28 NIRVKDNRVTLIIGPNGSGKTTFINTVS 55
                                      56678999**************999876 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       1      20 [.      35      54 ..      35      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                      SCEEEEC-TTTCHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqkl 20
                                      r+ ++ G++GsGKTt++  +
  gi|488601279|ref|YP_007907750.1| 35 RVTLIIGPNGSGKTTFINTV 54
                                      6899************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 ?   11.8   0.0    0.0002      0.13      29      54 ..      30      55 ..      24      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                             AAA_7 29 llknkkpvllvGptGtGKtviikdll 54
                                       +k ++ +l++Gp G+GKt+ i+++ 
  gi|488601279|ref|YP_007907750.1| 30 RVKDNRVTLIIGPNGSGKTTFINTVS 55
                                      5788999***************9875 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 ?   11.7   0.1   0.00022      0.14       2      21 ..      36      55 ..      35      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      vt++ G+ GsGKTt++n++ 
  gi|488601279|ref|YP_007907750.1| 36 VTLIIGPNGSGKTTFINTVS 55
                                      799**************975 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   0.00051      0.33       2      37 ..      34      68 ..      33     103 .. 0.78
   2 ?   -1.3   0.0       3.3   2.1e+03      78     105 ..     133     162 ..     124     182 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyin 37
                                      +++ +i G+  +GKTt+++++   +   +e  +y++
  gi|488601279|ref|YP_007907750.1| 34 NRVTLIIGPNGSGKTTFINTVSGFYK-ADEGHVYFE 68
                                      7899**************98864444.556666665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                            AAA_14  78 ewekalkslvdeg..knldvivtGSnskll 105
                                       +++++lk l  ++  +nl + ++G ++kll
  gi|488601279|ref|YP_007907750.1| 133 RAFDVLKFLKIDHlwDNLAYQLSGGQLKLL 162
                                       555555555555545555555555555555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00033      0.21      16      58 ..      34      75 ..      25     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00033
                            AAA_13 16 kriNliYGwNGaGKTtLSrllrslelgetepkfangsieitng 58
                                      +r+ li G NG+GKTt+ +  + + +    + +  + +eitn+
  gi|488601279|ref|YP_007907750.1| 34 NRVTLIIGPNGSGKTTFINTVSGFYKADEGHVY-FEGLEITNK 75
                                      57789************9999998554333222.333344443 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00052      0.33      42      58 ..      37      53 ..      17      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00052
                                      EEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE 42 llvaGatgsGKStalnt 58
                                      +l++G  gsGK+t++nt
  gi|488601279|ref|YP_007907750.1| 37 TLIIGPNGSGKTTFINT 53
                                      79**************8 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.18      26      69 ..      37      87 ..      23     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                      EEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHC.CHHHHHHH.HHH CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkg.....fseeelat.wraviqln.ivr 69
                                       l++G ++SGK+T+++ +  +yk       f+  e+ +     i++n ivr
  gi|488601279|ref|YP_007907750.1| 37 TLIIGPNGSGKTTFINTVSGFYKADeghvyFEGLEITNkPPHEIYQNgIVR 87
                                      5899***************99976667777666666332333444441444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00045      0.29       8      41 ..      25      58 ..      21      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00045
                           DUF3584  8 kGrvaeldldghtnieGtNaaGKTtLlrLiPlFY 41
                                       G+ ++++ +  t i G N++GKTt + ++  FY
  gi|488601279|ref|YP_007907750.1| 25 NGVNIRVKDNRVTLIIGPNGSGKTTFINTVSGFY 58
                                      5666677777789***************999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1597.00
//
Query:       gi|488601280|ref|YP_007907751.1|  [L=236]
Description: amino acid/amide ABC transporter ATP-binding protein 2, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-32  112.1   0.0    4.1e-32  111.6   0.0    1.3  1  ABC_tran     ABC transporter
    7.8e-14   52.2   2.6    2.1e-06   27.8   0.5    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      2e-08   33.9   0.6    1.7e-07   30.9   0.6    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
    2.8e-06   27.3   2.9    7.5e-05   22.6   0.3    2.1  2  AAA_15       AAA ATPase domain
    2.4e-05   24.6   0.2     0.0001   22.6   0.2    1.9  1  AAA_22       AAA domain
    3.1e-05   24.6   1.0    4.2e-05   24.1   1.0    1.7  1  AAA_23       AAA domain
    6.3e-05   22.6   0.1    0.00015   21.4   0.1    1.6  1  AAA_29       P-loop containing region of AAA domain
    0.00061   19.7   0.0     0.0011   18.9   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0012   18.9   0.3     0.0015   18.5   0.3    1.5  1  ATPase_2     ATPase domain predominantly from Archaea
     0.0018   17.3   0.2      0.005   15.8   0.1    1.6  2  AAA_10       AAA-like domain
     0.0018   18.3   0.3     0.0077   16.3   0.3    2.1  1  AAA_14       AAA domain
     0.0026   16.6   0.4      0.054   12.3   0.2    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
     0.0031   17.7   0.0       0.04   14.1   0.0    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.006   17.0   0.1      0.012   16.0   0.1    1.7  1  AAA_16       AAA ATPase domain
     0.0084   15.2   0.1      0.018   14.1   0.0    1.5  2  T2SSE        Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.016   15.0   0.0       0.04   13.6   0.0    1.6  2  AAA_30       AAA domain
      0.021   14.4   0.4      0.037   13.6   0.1    1.5  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.022   14.9   0.2      0.027   14.6   0.2    1.4  1  AAA_33       AAA domain
       0.03   14.3   0.0      0.059   13.3   0.0    1.5  1  Rad17        Rad17 P-loop domain
      0.034   13.9   0.0       0.08   12.7   0.0    1.5  2  VirE         Virulence-associated protein E
      0.035   13.7   0.0      0.055   13.0   0.0    1.3  1  AAA_27       AAA domain
      0.067   13.1   0.3       0.24   11.3   0.2    1.9  2  NACHT        NACHT domain
      0.075   13.1   0.0       0.17   12.0   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
       0.08   12.1   0.1       0.26   10.4   0.0    1.8  2  NB-ARC       NB-ARC domain
       0.09   12.0   0.0       0.14   11.4   0.0    1.2  1  Septin       Septin
      0.097   13.2   0.1       0.17   12.4   0.1    1.8  1  AAA_18       AAA domain
       0.11   12.0   0.0       0.17   11.3   0.0    1.4  1  PhoH         PhoH-like protein
       0.11   11.3   0.0       0.16   10.7   0.0    1.3  1  Adeno_IVa2   Adenovirus IVa2 protein
       0.15   11.8   0.1       0.28   10.9   0.1    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 !  111.6   0.0   6.6e-35   4.1e-32       3     137 .]      19     162 ..      17     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 6.6e-35
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                       +++ ++k+++++ ivG+nG+GKStLlk+l gl++  +G++ ++++d+++  ++ +++  i++lpq +++f +ltv+e
  gi|488601280|ref|YP_007907751.1|  19 DINAEVKKNQITTIVGPNGSGKSTLLKTLFGLTNIYSGKVIYKDDDITYtPPHDRTKLGIAYLPQVDNVFTNLTVEE 95 
                                       7999*********************************************889999999******************* PP

                                       H...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n           e++e+ e al+ +   +   + +++++ +LSgG++q +a+a al++k++ll+lDEpta
  gi|488601280|ref|YP_007907751.1|  96 NlkiagytlddgEYEERREIALNAFPELK---DYLNRKAGTLSGGERQFLAIATALIRKSELLMLDEPTA 162
                                       ***********999999999999987433...4555555*****************************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 !   27.8   0.5   3.4e-09   2.1e-06       1      41 [.      29      59 ..      29      96 .. 0.78
   2 !   24.5   0.1   3.3e-08     2e-05     227     282 ..     124     177 ..     105     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.4e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsgggg 41
                                      ++ ++GpNgsGKS+LL++l +l            + sg++ 
  gi|488601280|ref|YP_007907751.1| 29 ITTIVGPNGSGKSTLLKTLFGLTN----------IYSGKVI 59
                                      799****************88854..........3333333 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 3.3e-08
                            AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ell 282
                                       +d+ ++ a  lS G +++la++tal+r      ll +DEp + L Pk+ + ++ ++l
  gi|488601280|ref|YP_007907751.1| 124 KDYLNRKAGTLSGGERQFLAIATALIRKS---ELLMLDEPTAQLSPKFAEIIFnKIL 177
                                       5677788899****************988...9****************99996655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.6   2.7e-10   1.7e-07      23     202 ..      26     194 ..      11     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.7e-10
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeev 97 
                                       ++++t ivGpNGSGKs ll  + F L   +  + +    +d i++   +++ ++  a++  + dn   +  + +e++
  gi|488601280|ref|YP_007907751.1|  26 KNQITTIVGPNGSGKSTLLKTL-FGLT--NIYSGKVIYKDDDITYtpPHDRTKLGIAYLPQV-DNVFTN-LTVEENL 97 
                                       5679******************.7666..444455555555555524445555555544432.333333.3344667 PP

                                       EEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                       +i      +ge  y+ +++e+  +   el    + +  +LSgGe++ +a+a    +  ++++ l +lDe  a+L  k
  gi|488601280|ref|YP_007907751.1|  98 KIAGYTLDDGE--YE-ERREIALNAFPELKDYLNRKAGTLSGGERQFLAIA----TALIRKSELLMLDEPTAQLSPK 167
                                       77777777777..33.55555556555555555667789********9986....45689999************** PP

                                       HHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellkeksknaQfivislreeml 202
                                         +++ + + e ++++ + +  l e+ +
  gi|488601280|ref|YP_007907751.1| 168 FAEIIFNKILELRDDFRLTIA-LVEQNV 194
                                       *********999988876554.444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.3   1.2e-07   7.5e-05      19      48 ..      22      52 ..      10      79 .. 0.67
   2 ?    5.1   0.2     0.025        15     298     354 ..     135     182 ..      81     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-07
                            AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFln 48
                                       +++++ +t+++G+N+sGKS++l+ l  + n
  gi|488601280|ref|YP_007907751.1| 22 AEVKKNqITTIVGPNGSGKSTLLKTLFGLTN 52
                                      3334447*****************9943333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.025
                            AAA_15 298 GsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkeland 354
                                       + G +++l +++ ++++++          l+++EP a L p++ ++++++++el +d
  gi|488601280|ref|YP_007907751.1| 135 SGGERQFLAIATALIRKSEL---------LMLDEPTAQLSPKFAEIIFNKILELRDD 182
                                       55666777777666666665.........**********************999765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   1.7e-07    0.0001       4      56 ..      26      78 ..      22     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.7e-07
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                      + +i++++G+ G+GK+tll++l+   ++++     +++ +++t+p++ +   +
  gi|488601280|ref|YP_007907751.1| 26 KNQITTIVGPNGSGKSTLLKTLFGLTNIYSGKVIYKDDDITYTPPHDRTKLGI 78
                                      789*********************99766444446666678888887765555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   1.0   6.8e-08   4.2e-05      11      39 ..      12      47 ..       9     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.8e-08
                            AAA_23 11 rdqeidF.......skgltlItGpNGaGKTTildAi 39
                                      +++++ F       ++ +t I+GpNG+GK+T+l  +
  gi|488601280|ref|YP_007907751.1| 12 KEVQVLFdinaevkKNQITTIVGPNGSGKSTLLKTL 47
                                      55555555566777889***************9865 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   0.1   2.5e-07   0.00015      17      39 ..      22      44 ..      16      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      +e++ +++t ++Gp+GsGKSTll
  gi|488601280|ref|YP_007907751.1| 22 AEVKKNQITTIVGPNGSGKSTLL 44
                                      46676679**************8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.7e-06    0.0011      90     130 ..      17      58 ..       4      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       l ++++++k+ +++++vG+ G GKStL+++l + +++  g+v
  gi|488601280|ref|YP_007907751.1|  17 LFDINAEVKKnQITTIVGPNGSGKSTLLKTLFGLTNIYSGKV 58 
                                       55677777777********************98777666665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   2.5e-06    0.0015      15      67 ..      22      74 ..      12     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.5e-06
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesisklde 67
                                      +e ++n+i  i Gp gsGK++Llk +    + ++ +viy ++  ++   + ++
  gi|488601280|ref|YP_007907751.1| 22 AEVKKNQITTIVGPNGSGKSTLLKTLFGLTNIYSGKVIYKDDDITYTPPHDRT 74
                                      567789*********************99999999999988876666655555 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   8.1e-06     0.005      15      56 ..      21      62 ..      16      69 .. 0.89
   2 ?   -1.7   0.0       1.7   1.1e+03     102     140 ..     165     203 ..     154     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.1e-06
                            AAA_10 15 kgsktnasasliiGdlGnGKSvlakllvlyisllggkaliiD 56
                                      + +++++  + i+G+ G GKS l k+l+    +  gk+++ D
  gi|488601280|ref|YP_007907751.1| 21 NAEVKKNQITTIVGPNGSGKSTLLKTLFGLTNIYSGKVIYKD 62
                                      5567788889****************************9977 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                            AAA_10 102 aeslaedilelllgvkkkesekkaalseaveavlegkqr 140
                                       + ++ae i++ +l+++++     a++++ v++ le  ++
  gi|488601280|ref|YP_007907751.1| 165 SPKFAEIIFNKILELRDDFRLTIALVEQNVKRALEISEK 203
                                       557888899999999999888888899989888875444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   1.2e-05    0.0077       2      45 ..      27      77 ..      26     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikell.......vkkesilyinldderdkk 45
                                      ++i +i+G+  +GK+tllk+l+            k+++i y    d ++  
  gi|488601280|ref|YP_007907751.1| 27 NQITTIVGPNGSGKSTLLKTLFGLTNiysgkviYKDDDITYTPPHDRTKLG 77
                                      7899*****************965554555555555566665555555544 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 !   12.3   0.2   8.7e-05     0.054     244     264 ..      26      47 ..      22      53 .. 0.87
   2 ?    2.1   0.0       0.1        64     309     351 ..     120     162 ..     114     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.7e-05
                                       SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAl 264
                                       k  +t+IvG++  GKsTLL+ l
  gi|488601280|ref|YP_007907751.1|  26 KNqITTIVGPNGSGKSTLLKTL 47 
                                       444****************987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                                       -CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 309 LPegkdttkfstedASGStsqAanimealeagakllLiDEDts 351
                                        Pe kd  +    + SG   q  +i+ al ++++ll++DE t+
  gi|488601280|ref|YP_007907751.1| 120 FPELKDYLNRKAGTLSGGERQFLAIATALIRKSELLMLDEPTA 162
                                       56666666667777899999********************875 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   6.5e-05      0.04      25      82 ..     126     170 ..     108     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.5e-05
                           SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesia 82 
                                        l+r++gtlSGGe+qfla   +a a   l++++       +l++LDE  ++l++++++
  gi|488601280|ref|YP_007907751.1| 126 YLNRKAGTLSGGERQFLA---IATA---LIRKS-------ELLMLDEPTAQLSPKFAE 170
                                       4899**********8764...3322...33442.......578888888877777766 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   0.1   1.9e-05     0.012      19      46 ..      24      49 ..      10     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-05
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellr 46
                                      v+++  +++ ++G+ G+GKs+l+++l+ 
  gi|488601280|ref|YP_007907751.1| 24 VKKN--QITTIVGPNGSGKSTLLKTLFG 49
                                      4444..6899***************993 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.9e-05     0.018     122     173 ..      20      71 ..       6      96 .. 0.86
   2 ?   -2.2   0.0       2.8   1.7e+03     115     136 ..     191     210 ..     142     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                             T2SSE 122 lrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleg 173
                                       +++ v+++++  + G+ gsGK+tll +l    n ++ +++   D + + + +
  gi|488601280|ref|YP_007907751.1|  20 INAEVKKNQITTIVGPNGSGKSTLLKTLFGLTNIYSGKVIYKDDDITYTPPH 71 
                                       67788889999999***************99999999999888877776655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                             T2SSE 115 kekiaevlrkavrerglilvsG 136
                                       +++++++l+ +  e+  +l+sG
  gi|488601280|ref|YP_007907751.1| 191 EQNVKRALEIS--EKAYLLISG 210
                                       24555555544..556666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.5e-05      0.04      16      45 ..      25      54 ..      18      61 .. 0.79
   2 ?   -2.1   0.0       4.2   2.6e+03      81      97 ..     138     160 ..      92     172 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa 45
                                      +++++++++Gp G+GK+t+lk+l  + +  
  gi|488601280|ref|YP_007907751.1| 25 KKNQITTIVGPNGSGKSTLLKTLFGLTNIY 54
                                      45679****************987666555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.2
                            AAA_30  81 k......grarlepgtllivDEa 97 
                                       +      ++a +++++ll+ DE 
  gi|488601280|ref|YP_007907751.1| 138 ErqflaiATALIRKSELLMLDEP 160
                                       03444554455666688888885 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     6e-05     0.037       2      32 ..      29      59 ..      28      66 .. 0.80
   2 ?   -2.9   0.0       7.3   4.5e+03     147     150 ..     173     176 ..     138     204 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                                      EEEEEESTTCCHHHHHHHHHCT--SS-EEEE CS
                              cobW  2 vtvltGflGsGKTtLlnhllenraglklavi 32
                                      +t ++G+ GsGK+tLl++l   ++ ++  vi
  gi|488601280|ref|YP_007907751.1| 29 ITTIVGPNGSGKSTLLKTLFGLTNIYSGKVI 59
                                      689***************9866666666665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.3
                                       EE-H CS
                              cobW 147 lnKt 150
                                       +nK+
  gi|488601280|ref|YP_007907751.1| 173 FNKI 176
                                       2222 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   4.4e-05     0.027       3      32 ..      31      63 ..      29     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklg...avllssdt 32
                                       +vG++GsGKstl++ l   +    + ++ +d+
  gi|488601280|ref|YP_007907751.1| 31 TIVGPNGSGKSTLLKTLFGLTNiysGKVIYKDD 63
                                      579************998544465655555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-05     0.059      41      65 ..      23      47 ..      11      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                             Rad17 41 esrkkriLLisGPsGCgkstvvkvL 65
                                      e +k++i  i GP G gkst +k L
  gi|488601280|ref|YP_007907751.1| 23 EVKKNQITTIVGPNGSGKSTLLKTL 47
                                      667889*****************97 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013      0.08      47      85 ..      22      62 ..      14      70 .. 0.79
   2 ?   -2.5   0.0       5.6   3.4e+03     157     165 ..     136     144 ..      83     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                              VirE 47 PgiKfDfvlvLvGkqgsgKstflekl.gee.wftdslksve 85
                                        +K  +++++vG+ gsgKst+l++l g    ++ ++  ++
  gi|488601280|ref|YP_007907751.1| 22 AEVKKNQITTIVGPNGSGKSTLLKTLfGLTnIYSGKVIYKD 62
                                      578999********************864337776665555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                              VirE 157 tGeRRflpv 165
                                        GeR fl +
  gi|488601280|ref|YP_007907751.1| 136 GGERQFLAI 144
                                       255666655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     9e-05     0.055      23      47 ..      24      48 ..      14      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-05
                            AAA_27 23 aeeadlhliyGpNEAGKstalrAis 47
                                       ++++++ i+GpN +GKst+l+ + 
  gi|488601280|ref|YP_007907751.1| 24 VKKNQITTIVGPNGSGKSTLLKTLF 48
                                      4688999*************99764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00038      0.24       3      20 ..      30      47 ..      28      52 .. 0.88
   2 ?   -0.7   0.0       1.9   1.2e+03      52      84 ..     166     198 ..     118     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                                      EEEEC-TTTCHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkl 20
                                        + G++GsGK+tLl+ l
  gi|488601280|ref|YP_007907751.1| 30 TTIVGPNGSGKSTLLKTL 47
                                      5799***********988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                                       .-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEE CS
                             NACHT  52 rsladllfsqlpepaapvsevwavllelperlL 84 
                                       + +a+++f + +e+ ++ +  +a++ ++ +r+L
  gi|488601280|ref|YP_007907751.1| 166 PKFAEIIFNKILELRDDFRLTIALVEQNVKRAL 198
                                       567778888888888777776666666666666 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00028      0.17       3      22 ..      31      50 ..      29      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                                      EEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                       ivG   +GKStL+++l+g 
  gi|488601280|ref|YP_007907751.1| 31 TIVGPNGSGKSTLLKTLFGL 50
                                      59***************984 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   0.00042      0.26      20      41 ..      27      48 ..      12      55 .. 0.81
   2 ?   -1.6   0.0         2   1.2e+03      94     110 ..     142     158 ..     122     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                                      SEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 20 slvvalvGmgGvGKttlakqil 41
                                        + ++vG  G+GK+tl+k  +
  gi|488601280|ref|YP_007907751.1| 27 NQITTIVGPNGSGKSTLLKTLF 48
                                      34889************99876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                                       HHHHHHCCCTTEEEEEE CS
                            NB-ARC  94 rklvrlLltkrfllvlD 110
                                         +  +L++k  ll+lD
  gi|488601280|ref|YP_007907751.1| 142 LAIATALIRKSELLMLD 158
                                       568999*********99 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.14       9      31 ..      32      54 ..      26      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                      EEEBTTSSCCCCCCTTSSSS--- CS
                            Septin  9 vvGesglGkttlintlfetdlie 31
                                      +vG +g Gk+tl++tlf  + i 
  gi|488601280|ref|YP_007907751.1| 32 IVGPNGSGKSTLLKTLFGLTNIY 54
                                      89***************754443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00028      0.17       3      44 ..      32      71 ..      31     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00028
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                      + G+ G+GK+tl k L  ++   + +++v+++++  ++  p+
  gi|488601280|ref|YP_007907751.1| 32 IVGPNGSGKSTLLKTLFGLT--NIYSGKVIYKDDDITYTPPH 71
                                      89**************6666..55566666655544444444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.17      15      47 ..      23      56 ..      15      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                                      HHHH-SEEEEE--TTSST.THHHHHHHHHHHHTT CS
                              PhoH 15 alkkndivfaiGpaGtGK.tylavalavealkkk 47
                                       +kkn+i++++Gp G+GK t+l +  +++ + ++
  gi|488601280|ref|YP_007907751.1| 23 EVKKNQITTIVGPNGSGKsTLLKTLFGLTNIYSG 56
                                      5789**************5566677777666555 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026      0.16      85     109 ..      25      49 ..       5      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                        Adeno_IVa2  85 lqPviGviyGPtGsGksqllrnlis 109
                                       ++  i  i GP GsGks ll++l  
  gi|488601280|ref|YP_007907751.1|  25 KKNQITTIVGPNGSGKSTLLKTLFG 49 
                                       4556899**************9975 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00045      0.28       4      22 ..      29      47 ..      26      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00045
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                         i+Gp+g+GK+tl+k+l
  gi|488601280|ref|YP_007907751.1| 29 ITTIVGPNGSGKSTLLKTL 47
                                      5689*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1550.38
//
Query:       gi|488601281|ref|YP_007907752.1|  [L=221]
Description: hypothetical protein Asulf_01788 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1325.37
//
Query:       gi|488601282|ref|YP_007907753.1|  [L=101]
Description: hypothetical protein Asulf_01789 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-44  148.6   0.2    4.8e-44  148.4   0.2    1.0  1  NitrOD5   Nitrosopumilus output domain 5


Domain annotation for each model (and alignments):
>> NitrOD5  Nitrosopumilus output domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   0.2   2.7e-48   4.8e-44       1      94 []       5      98 ..       5      98 .. 0.99

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 2.7e-48
                           NitrOD5  1 snprdllikavkealkkvdPallkiLevhLkakankglelayedPkkFkeaveeLFGeysarllellliselkellglk 79
                                      s+prdl+i+avk+a+kk+dP+llkiLevhL+++++kgl++aye+P+kF++++++LFGeys+r++ellli+e+kel+g+k
  gi|488601282|ref|YP_007907753.1|  5 SSPRDLVITAVKNAIKKTDPTLLKILEVHLESREGKGLDMAYENPEKFVDSMRDLFGEYSGRFFELLLIQEVKELVGFK 83
                                      689**************************************************************************** PP

                           NitrOD5 80 edvnsleevveilkk 94
                                      e++nsl+e++eilk+
  gi|488601282|ref|YP_007907753.1| 84 EQPNSLKEAIEILKT 98
                                      *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.44
# Mc/sec: 682.78
//
Query:       gi|488601283|ref|YP_007907754.1|  [L=443]
Description: RecA-superfamily ATPases implicated in signal transduction [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-87  293.0   6.0    1.1e-43  149.2   0.3    2.0  2  ATPase           KaiC
    1.1e-19   70.8   0.0    1.5e-08   34.5   0.0    2.3  2  AAA_25           AAA domain
    5.2e-14   52.2   0.0    3.2e-06   26.7   0.0    2.2  2  DnaB_C           DnaB-like helicase C terminal domain
    5.3e-12   45.7   0.0    8.5e-05   22.1   0.0    2.5  2  RecA             recA bacterial DNA recombination protein
    1.7e-10   40.9   0.0    2.3e-05   24.2   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
    6.3e-10   38.7   0.4    3.4e-07   29.8   0.0    2.5  2  Rad51            Rad51
    8.8e-10   39.0   0.0     0.0018   18.6   0.0    2.3  2  AAA_22           AAA domain
    1.3e-08   34.8   2.9     0.0012   18.6   0.1    2.6  2  AAA_24           AAA domain
    1.8e-08   33.5   3.1    1.3e-07   30.6   0.4    3.0  2  GvpD             GvpD gas vesicle protein
    5.5e-08   33.4   0.0     0.0006   20.3   0.0    2.4  2  ABC_tran         ABC transporter
    1.7e-07   31.8   7.0    4.2e-06   27.2   0.2    3.3  2  AAA              ATPase family associated with various cellul
    3.9e-07   29.7   0.0    0.00016   21.0   0.0    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    5.2e-07   29.8   2.0     0.0081   16.2   0.3    2.7  2  AAA_14           AAA domain
    1.1e-06   29.2   0.0      0.002   18.5   0.0    2.7  2  AAA_16           AAA ATPase domain
    5.4e-06   26.4   0.0     0.0038   17.2   0.0    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
      7e-06   25.7   0.2      0.022   14.3   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
    9.9e-06   25.3   0.0     0.0098   15.5   0.0    2.8  3  SRP54            SRP54-type protein, GTPase domain
    2.2e-05   24.5   2.1       0.33   10.9   0.6    3.1  3  ResIII           Type III restriction enzyme, res subunit
    2.4e-05   23.9   0.1      0.068   12.6   0.0    2.3  2  PhoH             PhoH-like protein
    2.4e-05   24.3   0.1      0.015   15.2   0.0    3.1  2  NACHT            NACHT domain
    0.00024   20.9   0.1      0.041   13.6   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    0.00024   21.3   0.2        0.5   10.6   0.0    2.4  2  Roc              Ras of Complex, Roc, domain of DAPkinase
    0.00029   20.0   0.2       0.26   10.3   0.0    2.3  2  T2SSE            Type II/IV secretion system protein
     0.0003   21.2   0.5       0.03   14.7   0.0    2.5  2  AAA_19           AAA domain
    0.00052   19.1   0.2       0.24   10.3   0.0    2.2  2  AAA_10           AAA-like domain
    0.00076   19.5   2.7      0.057   13.3   0.5    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00094   19.5   0.6       0.15   12.4   0.0    2.7  2  RNA_helicase     RNA helicase
    0.00098   18.9   0.1       0.11   12.2   0.0    2.4  2  AAA_30           AAA domain
     0.0012   17.8   0.0       0.02   13.7   0.0    2.3  2  AAA_35           AAA-like domain
     0.0013   19.0   0.1          2    8.7   0.0    2.3  2  CobA_CobO_BtuR   ATP:corrinoid adenosyltransferase BtuR/CobO/
     0.0015   18.1   0.2      0.074   12.5   0.1    2.1  2  Elong_Iki1       Elongator subunit Iki1
     0.0038   16.4   0.0       0.31   10.2   0.0    2.3  2  ArsA_ATPase      Anion-transporting ATPase
     0.0042   17.1   0.3        1.8    8.6   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.005   17.4   4.4      0.025   15.1   0.2    2.7  2  AAA_18           AAA domain
     0.0054   16.4   2.2        2.7    7.8   0.4    2.7  2  AAA_29           P-loop containing region of AAA domain
     0.0055   16.2   0.0        1.9    7.8   0.0    3.1  3  ELP6             Elongation complex protein 6
     0.0063   16.3   0.3          2    8.1   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0069   16.0   0.4       0.29   10.7   0.0    2.2  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0072   15.6   0.0      0.012   14.9   0.0    1.4  1  KAP_NTPase       KAP family P-loop domain
     0.0073   16.2   2.2      0.019   14.9   0.3    2.4  2  Mistic           Membrane-integrating protein Mistic
     0.0086   16.0   0.3        1.5    8.7   0.1    2.4  2  RsgA_GTPase      RsgA GTPase
     0.0089   15.8   0.0       0.16   11.7   0.0    2.3  2  AAA_11           AAA domain
     0.0097   15.1   1.0      0.033   13.4   0.0    2.0  2  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.012   15.4   0.5        5.1    6.8   0.0    3.1  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.012   14.8   0.0      0.064   12.5   0.0    2.0  2  TIP49            TIP49 P-loop domain
      0.015   15.3   0.0        3.7    7.4   0.0    2.4  2  AAA_31           AAA domain
      0.016   15.4   0.0        5.5    7.1   0.0    2.3  2  AAA_33           AAA domain
      0.018   15.1   1.1        2.9    8.0   0.0    2.5  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.025   14.1   0.1          2    7.8   0.0    2.8  2  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.025   14.4   0.7       0.12   12.2   0.1    2.1  2  Bac_DnaA         Bacterial dnaA  protein
      0.034   14.4   0.0        3.3    7.9   0.0    2.5  2  AAA_28           AAA domain
      0.052   13.2   0.0        1.7    8.2   0.0    2.2  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.057   13.2   0.0        5.2    6.8   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
      0.062   13.4   0.1        3.5    7.7   0.0    2.6  2  MMR_HSR1         50S ribosome-binding GTPase
      0.067   12.3   0.1       0.22   10.6   0.0    1.8  2  PAXNEB           PAXNEB protein
      0.076   12.3   0.2       0.64    9.2   0.0    2.1  2  Septin           Septin
      0.089   12.1   0.1       0.26   10.6   0.0    1.8  1  Zeta_toxin       Zeta toxin
        0.1   11.6   0.2       0.21   10.5   0.0    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.13   12.2   2.7        0.3   11.0   0.1    2.6  2  NTPase_1         NTPase
       0.15   12.0   1.7        1.4    8.8   0.1    2.5  2  MobB             Molybdopterin guanine dinucleotide synthesis
        1.2    9.5  10.5        2.1    8.8   1.3    2.7  2  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   1.0   2.3e-45   6.7e-43      10     227 ..       9     213 ..       5     217 .. 0.92
   2 !  149.2   0.3   3.7e-46   1.1e-43       1     227 [.     229     442 ..     229     443 .] 0.97

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 2.3e-45
                            ATPase  10 eilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaii 86 
                                       +i++g +peg+++ i+GepGtGKti++   + + +++ g++++fv+++e+++d+ +  k+lG +le   +e ++ ++
  gi|488601283|ref|YP_007907754.1|   9 KIIEGDFPEGSIIMIAGEPGTGKTILVSSIAHEEIKE-GKKVLFVSFNETKQDFFKYTKKLGFELE---NE-NFRYM 80 
                                       6889*********************************.*************************875...44.799** PP

                            ATPase  87 dasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrq.lvrvlkklgvTailvs 162
                                       d+++ +        ++ ++  ++ + + i++++ + +viDsit++     ++ +R+ l++ l r++kk+g Ta +++
  gi|488601283|ref|YP_007907754.1|  81 DLFTAG--------RDVVDTQLSFIFSEIEKFNPNIIVIDSITAILSVLAKENIRTFLHTsLGRFVKKKGATAFIIA 149
                                       ****97........5688899999999******************888899999*99987366777*********** PP

                            ATPase 163 ekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvl 227
                                       ek+ ++e++ gygveef+vdg i+L++ + +e+ +R+le+ kmRg k++k +++++It++gi  +
  gi|488601283|ref|YP_007907754.1| 150 EKPIGSEEF-GYGVEEFVVDGLIILRYLKHDEHYRRILEVPKMRGLKIKKPQYEYTITDKGIFFF 213
                                       ****97665.7**************************************************9765 PP

  == domain 2  score: 149.2 bits;  conditional E-value: 3.7e-46
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekl 77 
                                       v+tgI++lDe++ gG+++g+++   G++GtGKt+f+l+F+++ a + g++ +f+t+ee++e++ + +++ G+d  ++
  gi|488601283|ref|YP_007907754.1| 229 VSTGIKELDELVGGGFYRGSITVFIGNTGTGKTTFGLHFTYNNALN-GKKALFITFEESEENILRAMRNYGMDYSAV 304
                                       78********************************************.****************************** PP

                            ATPase  78 eeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkkl 154
                                       +e+  ++i d+  +a         +++  + +++ + i+++k + + iDs ++l++ ++e ++ + +r +  ++k l
  gi|488601283|ref|YP_007907754.1| 305 KEN--MIIKDMIPEA---------YSPVTFFARIYDLIESFKPEVLFIDSFSSLNEHMEEVELSKMVRYIQLTVKRL 370
                                       ***..9999999984.........7899**************************8888899999************* PP

                            ATPase 155 gvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvl 227
                                       g+T   + + + + +++ + g++  ++d+++ L ++++++++ R l i+k R+t+hs+k+h +eIt++gi+++
  gi|488601283|ref|YP_007907754.1| 371 GITLCTTLNLEGNLRKIPQTGLST-LSDNIVLLWYELENDSVHRKLLILKSRSTDHSRKIHSYEITDDGIRII 442
                                       **********99************.**********************************************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0     5e-11   1.5e-08      23     160 ..       8     125 ..       7     149 .. 0.78
   2 !   33.9   0.0   7.5e-11   2.2e-08       6     160 ..     220     353 ..     216     377 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5e-11
                            AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealr 98 
                                       +++++g  p+g+++++aG pgtGKt l++++a++   +Gk           kVl+vs+ ++ +++ +  +++g +l 
  gi|488601283|ref|YP_007907754.1|   8 NKIIEGDFPEGSIIMIAGEPGTGKTILVSSIAHEEIkEGK-----------KVLFVSFNETKQDFFKYTKKLGFEL- 72 
                                       689*******************************995555...........9***********************9. PP

                            AAA_25  99 ddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg..den 160
                                         +++ + +      ++Lf+++r+   ++ ++  +  +ie+  ++  +viD+++++l+    en
  gi|488601283|ref|YP_007907754.1|  73 --ENENFRY------MDLFTAGRDV--VDTQLSFIFSEIEK-FNPNIIVIDSITAILSVlaKEN 125
                                       ..4555544......2456655555..5555666*******.67***********998854444 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 7.5e-11
                            AAA_25   6 elsavsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEd 81 
                                       ++ ++s++++ + +++++ lv+g   +g++++++G +gtGKtt+ l+  +  a  Gk           k l++ +E+
  gi|488601283|ref|YP_007907754.1| 220 RIGEASFERVSTGIKELDELVGGGFYRGSITVFIGNTGTGKTTFGLHFTYNNAlNGK-----------KALFITFEE 285
                                       5666789999999*********8888***************************5555...........89******* PP

                            AAA_25  82 sedelrrRlravgealrd.darllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg 157
                                       se+++ r +r  g ++++ +++  + d   +       +++ +++   +++++ + ie+  +++++ iD++s++ ++
  gi|488601283|ref|YP_007907754.1| 286 SEENILRAMRNYGMDYSAvKENMIIKD---M------IPEAYSPV--TFFARIYDLIES-FKPEVLFIDSFSSLNEH 350
                                       **9999999999999955144444444...2......23344444..78999*******.67************999 PP

                            AAA_25 158 den 160
                                        e+
  gi|488601283|ref|YP_007907754.1| 351 MEE 353
                                       554 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 !   23.5   0.0     1e-07     3e-05      16      81 ..      15      79 ..       2     137 .. 0.69
   2 !   26.7   0.0   1.1e-08   3.2e-06       2     113 ..     229     348 ..     228     411 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1e-07
                                      BXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 16 lqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrt 81
                                      + +g +i+iA+ p++Gkt l+ +ia++  + e ++v+++s++ ++++ ++       e++++++r 
  gi|488601283|ref|YP_007907754.1| 15 FPEGSIIMIAGEPGTGKTILVSSIAHEEIK-EGKKVLFVSFNETKQDFFKYTKKLGFELENENFRY 79
                                      78999********************98775.6779*******999998766555555566555544 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.1e-08
                                       BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHH..HHHHHH.HHHTX CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.xxxxx RF
                            DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeql..vqRlls.seaei 74 
                                       +stg k+LD+l++ G+ +g +++  +  ++Gkt++ l++  n a +  ++ +++ +e s+e++  ++R      + +
  gi|488601283|ref|YP_007907754.1| 229 VSTGIKELDELVGgGFYRGSITVFIGNTGTGKTTFGLHFTYNNALNG-KKALFITFEESEENIlrAMRNYGmDYSAV 304
                                       79********99637***************************99855.5899999****999933344443223344 PP

                                       XHHHHHHTTSXH.....HHHHHHHHHHHHHHHSEEEEEEXSSXC CS
                                       xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  75 dskklrtgklke.....edweklteaieelseaklfiddtpalt 113
                                       +++ + +  + e     + ++++ + ie+++   lfid  ++l+
  gi|488601283|ref|YP_007907754.1| 305 KENMIIKDMIPEayspvTFFARIYDLIESFKPEVLFIDSFSSLN 348
                                       44444333322222222456777777788888888888766553 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.6e-07   0.00019      48     144 ..      13     118 ..       6     128 .. 0.77
   2 !   22.1   0.0   2.9e-07   8.5e-05      29      94 ..     224     288 ..     215     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.6e-07
                                       SSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS--.--.HHHHHHTT--GGG.......-EEE--SS CS
                              RecA  48 GGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaeha.ld.pkyakklGvdide.......llvsqpdt 115
                                       G +p+G ii i G   +Gkt l  ++  e  k+g+ + f+  + +  d  ky+kklG ++++       l+ +  d 
  gi|488601283|ref|YP_007907754.1|  13 GDFPEGSIIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNETkQDfFKYTKKLGFELENenfrymdLFTAGRDV 89 
                                       88********************99999999**********97555155359********997333333345555555 PP

                                       HHHHHHHHHHHHTTT--SEEEEE-TTT-- CS
                              RecA 116 Geqaleiadalvrsgaidlivvdsvaalv 144
                                        +  l  + + ++    ++iv+ds++a+ 
  gi|488601283|ref|YP_007907754.1|  90 VDTQLSFIFSEIEKFNPNIIVIDSITAIL 118
                                       55556555556666778999****99975 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.9e-07
                                       ----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS---- CS
                              RecA  29 lkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehald 94 
                                        + e +s+G   ld  +G GG+ +G i+   G   +Gktt+ lh   +   +g+ a fi  e + +
  gi|488601283|ref|YP_007907754.1| 224 ASFERVSTGIKELDELVG-GGFYRGSITVFIGNTGTGKTTFGLHFTYNNALNGKKALFITFEESEE 288
                                       56799*************.****************************************9987755 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 !   24.2   0.0   7.8e-08   2.3e-05      49      86 ..      20      57 ..       8      83 .. 0.84
   2 !   14.0   0.0   0.00011     0.032      33      93 ..     234     293 ..     216     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.8e-08
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrvedL 86
                                       i++ G +G+GK+ l  ++++e +++g++vlfv+ ++ 
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNET 57
                                      5899*****************************98765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00011
                         IstB_IS21  33 rkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkra 93 
                                       ++++eL+++ f +     v++G +G+GK+ +   + ++ + +g++ lf++ e+  e++ ra
  gi|488601283|ref|YP_007907754.1| 234 KELDELVGGGFYR-GSITVFIGNTGTGKTTFGLHFTYNNALNGKKALFITFEESEENILRA 293
                                       5566777777754.4567899*****************************99877766555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.013       3.8      28      58 ..       9      39 ..       6     120 .. 0.82
   2 !   29.8   0.0   1.2e-09   3.4e-07      18     109 ..     228     311 ..     196     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                                      HHHTSSEESSSEEEEEESTTSSHHHHHHHHH CS
                             Rad51 28 elLgGGietgsiteifGefrsGktqlchtlc 58
                                      ++++G ++ gsi  i Ge ++Gkt l  +++
  gi|488601283|ref|YP_007907754.1|  9 KIIEGDFPEGSIIMIAGEPGTGKTILVSSIA 39
                                      7899********************9987765 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.2e-09
                                       EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHH CS
                             Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaer 94 
                                       +++tG k+lDel+gGG+  gsit  +G+ ++Gkt +   ++    l+       +ka++i  e +   e +++    
  gi|488601283|ref|YP_007907754.1| 228 RVSTGIKELDELVGGGFYRGSITVFIGNTGTGKTTFGLHFTYNNALN------GKKALFITFEES--EENILRAMRN 296
                                       699*******************************9998877665554......589999998875..5678888899 PP

                                       TT--HHHHGGGEEEE CS
                             Rad51  95 ykldkeevlenvaya 109
                                       y++d ++v en+ + 
  gi|488601283|ref|YP_007907754.1| 297 YGMDYSAVKENMIIK 311
                                       999999998887653 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     6e-06    0.0018       5     105 ..      18     119 ..      16     150 .. 0.70
   2 !   18.1   0.0   8.4e-06    0.0025       5     112 ..     247     354 ..     245     384 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellea 81 
                                        +i+++ Ge+GtGKT l+  ++++  +      e+++v+fv  ++ +   + + +  ++lg el++e+ +  +l++a
  gi|488601283|ref|YP_007907754.1|  18 GSIIMIAGEPGTGKTILVSSIAHEEIK------EGKKVLFVSFNETK---QDFFKYTKKLGFELENENFRYMDLFTA 85 
                                       589********************9733......37777777665555...333455555555555566778888899 PP

                            AAA_22  82 leqalrarav..........ielliiDEaqh.lrs 105
                                        ++ ++++            + +++iD +   l s
  gi|488601283|ref|YP_007907754.1|  86 GRDVVDTQLSfifseiekfnPNIIVIDSITAiL-S 119
                                       988888888877777777777788887776644.4 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.4e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka........er 72 
                                        +i+v +G +GtGKTt    +++++        ++++ +f+t  +s+ +    +r+   ++   +++        e 
  gi|488601283|ref|YP_007907754.1| 247 GSITVFIGNTGTGKTTFGLHFTYNNAL------NGKKALFITFEESEeNILRAMRNYGMDYSAVKENmiikdmipEA 317
                                       6899*******************9843......48888888888888666666777777777777779999999999 PP

                            AAA_22  73 lsseellealeqalraravielliiDEaqhlr.seealeeL 112
                                        s   +++++++ +++ +  e+l iD +  l+ +   +ee+
  gi|488601283|ref|YP_007907754.1| 318 YSPVTFFARIYDLIESFKP-EVLFIDSFSSLNeH---MEEV 354
                                       9999999************.***********543...3333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   4.1e-06    0.0012       5      81 ..      21     121 ..      17     128 .. 0.69
   2 !   15.7   0.4   3.2e-05    0.0093       6      39 ..     251     291 ..     247     355 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.1e-06
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfi.......dtekGlksldadkfpdie...............swedf 52 
                                       i+i G++g+GKT l++++       g+k+lf+       d++k +           +                +++ 
  gi|488601283|ref|YP_007907754.1|  21 IMIAGEPGTGKTILVSSIaheeikeGKKVLFVsfnetkqDFFKYT-----------KklgfelenenfrymdLFTAG 86 
                                       89******************************4444444333333...........222333333334444456666 PP

                            AAA_24  53 ldevvel......aaeladyktlviDtideleelc 81 
                                       +d v++       + e+ + +++viD+i+ + +  
  gi|488601283|ref|YP_007907754.1|  87 RDVVDTQlsfifsEIEKFNPNIIVIDSITAILSVL 121
                                       66666558889986666677999999999987755 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.2e-05
                            AAA_24   6 liyGpsgiGKTtlakel.......gpkplfidtekGlksld 39 
                                       + +G  g+GKTt+ +++       g+k+lfi +e++  ++ 
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFGLHFtynnalnGKKALFITFEESEENIL 291
                                       668********************************866553 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.4   4.6e-10   1.3e-07      10     261 ..      18     250 ..       8     253 .. 0.72
   2 ?    1.4   0.2      0.32        95      16      31 ..     253     268 ..     250     318 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.6e-10
                              GvpD  10 GktllikGaPGtGktlftlr.gldvlrresdvlyvstrvddetvseayfsgeaeld..ktalldllkdpleldldvd 83 
                                       G  ++i G+PGtGkt++      + +++ ++vl+vs   +++  +    +   el+  +  ++dl+  +  + +d +
  gi|488601283|ref|YP_007907754.1|  18 GSIIMIAGEPGTGKTILVSSiAHEEIKEGKKVLFVSFNETKQDFFKYTKKLGFELEneNFRYMDLFTAGRDV-VDTQ 93 
                                       78899**********9876514678***********999888877654333334543377899999887654.2333 PP

                              GvpD  84 vPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaans 160
                                       + +       +++ ++      +  ii +ds   ++  la++ ++      ++  l  + +++g+   +++e    s
  gi|488601283|ref|YP_007907754.1|  94 LSF-------IFSEIE----KFNPNIIVIDSITAILSVLAKE-NIRTF---LHTSLGRFVKKKGATAFIIAEKPIGS 155
                                       333.......333333....44567999***99999999976.44444...45566666699999999999986554 PP

                              GvpD 161 r.l.....eyivdGvvtl.nvkeddrgrlrrdlrleklrGvrignrlqPftladGkfksitrvelvtidtvtdeaky 230
                                       + +     e++vdG++ l  +k+d     rr l + k+rG++i++  + +t++d         el       +ea +
  gi|488601283|ref|YP_007907754.1| 156 EeFgygveEFVVDGLIILrYLKHD--EHYRRILEVPKMRGLKIKKPQYEYTITDKGIFFFDIPELNR----IGEASF 226
                                       3222333389********778988..5789***************9999*99984433333344443....455666 PP

                              GvpD 231 ePlandkakfsvglrdldkllseGtdrGsvv 261
                                       e       + s+g+++ld+l+ +G+ rGs+ 
  gi|488601283|ref|YP_007907754.1| 227 E-------RVSTGIKELDELVGGGFYRGSIT 250
                                       6.......789******************96 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.32
                              GvpD  16 kGaPGtGktlftlrgl 31 
                                        G+ GtGkt+f l++ 
  gi|488601283|ref|YP_007907754.1| 253 IGNTGTGKTTFGLHFT 268
                                       5999********9985 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     2e-06    0.0006       5      48 ..      12      76 ..       9     151 .. 0.69
   2 !   10.8   0.0    0.0018      0.52       7      27 ..     243     263 ..     239     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2e-06
                                      EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.....................EETTCE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxx RF
                          ABC_tran  5 slklkegekvaivGenGaGKStLlkllagllkpteGei.....................lldgkd 48
                                      + ++ eg+++ i Ge G+GK+ L++ +a+++ ++  ++                     +l++++
  gi|488601283|ref|YP_007907754.1| 12 EGDFPEGSIIMIAGEPGTGKTILVSSIAHEEIKEGKKVlfvsfnetkqdffkytkklgfELENEN 76
                                      66899**************************9988888555555444444444444444444444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0018
                                       EEETTSEEEEEESTTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStL 27 
                                        +++g++++++G++G+GK+t+
  gi|488601283|ref|YP_007907754.1| 243 GFYRGSITVFIGNTGTGKTTF 263
                                       5789****************7 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   1.4e-08   4.2e-06       2      86 ..      22     127 ..      21     151 .. 0.69
   2 ?    4.7   2.1      0.13        38       2      21 ..     251     270 ..     250     386 .. 0.49

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.4e-08
                                       EEESSTTSSHHHHHHHHHHH.....HTHEEEEEETTTCSSS.........................STTHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavake.....lgvefleisgsellsk.........................yvgesekkire 48 
                                       ++ G pGtGKT+l++++a+e        ++l +s  e  ++                                +++ 
  gi|488601283|ref|YP_007907754.1|  22 MIAGEPGTGKTILVSSIAHEeikegK--KVLFVSFNETKQDffkytkklgfelenenfrymdlftaGRDVVDTQLSF 96 
                                       789*****************655440..333333333333334455556666666677777777778999999**** PP

                                       HHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHH CS
                               AAA  49 lfkeakekakpsilfiDEidalaksrsgseseeeervv 86 
                                       +f+e+++ + p i++iD i a+ +         +e++ 
  gi|488601283|ref|YP_007907754.1|  97 IFSEIEKFN-PNIIVIDSITAILSVL------AKENIR 127
                                       ******999.***********98766......444444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.13
                                       EEESSTTSSHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavake 21 
                                       +++G+ GtGKT++      +
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFGLHFTYN 270
                                       58999999999986555444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.5e-07   0.00016       2      48 ..      19      63 ..      18      93 .. 0.84
   2 ?    6.6   0.0     0.014         4       7      48 ..     253     292 ..     248     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.5e-07
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlr 48
                                      +++++ G++GtGKt++ +++++e    +e++++ ++s N+  ++  +
  gi|488601283|ref|YP_007907754.1| 19 SIIMIAGEPGTGKTILVSSIAHEE--IKEGKKVLFVSFNETKQDFFK 63
                                      5899*******************8..9************99998554 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                           DUF2075   7 tGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlr 48 
                                        G++GtGKt  +l++ ++     ++++a +++  +++ ++lr
  gi|488601283|ref|YP_007907754.1| 253 IGNTGTGKTTFGLHFTYNN--ALNGKKALFITFEESEENILR 292
                                       59*************9998..667777777777776666666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.8e-05    0.0081       3     111 ..      19     144 ..      17     149 .. 0.63
   2 !   12.2   0.1   0.00046      0.14       4      88 ..     249     329 ..     246     370 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd............kkladpe.kllelileklke.... 62 
                                        i++i G   +GKT l+  +++e++ + +++l++++++ ++             +++  + ++++l+     +    
  gi|488601283|ref|YP_007907754.1|  19 SIIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNETKQdffkytkklgfeLENE--NfRYMDLFT----Agrdv 89 
                                       68999********************999********998775665544433221111..123333333....13334 PP

                            AAA_14  63 .ekktylflDEiqev......pewekalkslvdegknldvivtGSnskllskeiat 111
                                        + +  +++ Ei +        +  +a+ s++ ++ n++ ++  S+  + +k+ at
  gi|488601283|ref|YP_007907754.1|  90 vDTQLSFIFSEIEKFnpniivIDSITAILSVLAKE-NIRTFLHTSLGRFVKKKGAT 144
                                       44566677777777754444433444444444444.67777777777776666665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00046
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                       i v  G   +GKTt+  ++ +++  + ++ l+i++++ ++  l+      ++ ++  ++ k+++++ D i e+ +  
  gi|488601283|ref|YP_007907754.1| 249 ITVFIGNTGTGKTTFGLHFTYNNALNGKKALFITFEESEENILRAM---RNYGMDY-SAVKENMIIKDMIPEAYSPV 321
                                       778889999**********999999************888655533...3444443.33355666666666665555 PP

                            AAA_14  81 kalkslvd 88 
                                       ++  +++d
  gi|488601283|ref|YP_007907754.1| 322 TFFARIYD 329
                                       55555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.9e-06     0.002      23      63 ..      17      59 ..       7      95 .. 0.79
   2 ?    7.8   0.0     0.014         4      23      60 ..     246     285 ..     233     370 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.9e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd..ggiflrgkcdql 63
                                      +++++++ Ge+G+GK+ lv +++++  k+  +++f++ + ++ 
  gi|488601283|ref|YP_007907754.1| 17 EGSIIMIAGEPGTGKTILVSSIAHEEIKEgkKVLFVSFNETKQ 59
                                      3489*****************9986666633477766655544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.014
                            AAA_16  23 rpelvllsGesGvGKsslvrell..ralekdggiflrgkc 60 
                                       r+++++++G+ G+GK++   ++   +al++++++f++ + 
  gi|488601283|ref|YP_007907754.1| 246 RGSITVFIGNTGTGKTTFGLHFTynNALNGKKALFITFEE 285
                                       34899************88666632466666777755444 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   1.3e-05    0.0038       2      75 ..      21     115 ..      20     129 .. 0.78
   2 ?    7.0   0.0     0.018       5.4       3      74 ..     251     344 ..     249     358 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-05
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--...........--------......... CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik..ngttslvdsplvraar......... 64 
                                       +++ G+pGtgK+ l+ ++a+     +++v+ v +++ t+++ +k+  ++    +++ ++   l +a+r         
  gi|488601283|ref|YP_007907754.1|  21 IMIAGEPGTGKTILVSSIAHEEikeGKKVLFVSFNE-TKQDFFKYTKKLGfeLENENFRYMDLFTAGRdvvdtqlsf 96 
                                       5789***************98889999999999998.66666666666658889999999***********966666 PP

                                       ........G-SEEEEESGG CS
                             AAA_5  65 ........egeilvlDEve 75 
                                               ++ i+v+D ++
  gi|488601283|ref|YP_007907754.1|  97 ifseiekfNPNIIVIDSIT 115
                                       6666666666666666655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                                       EEE--SSSSHHHHHHHGGG..GB.S--EEEEE--TT--HHHHH--B--.........--------............ CS
                             AAA_5   3 lLvGppGtgKselaerlaa..al.nreveyvqltrdtteedlkgrreikngttslvdsplvraar............ 64 
                                       + +G++GtgK+++  ++    al +++ + + + +  +e+ l+  r++ ++  + +++ + + +             
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFGLHFTYnnALnGKKALFITF-EESEENILRAMRNYGMDYSAVKENMIIKDMIpeayspvtffar 326
                                       679*********999876511554444444444.4466666666666665555555555555555666666666666 PP

                                       ........G-SEEEEESG CS
                             AAA_5  65 ........egeilvlDEv 74 
                                               ++e+l++D +
  gi|488601283|ref|YP_007907754.1| 327 iydliesfKPEVLFIDSF 344
                                       666666666666666655 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 !   14.3   0.0   7.5e-05     0.022      34      72 ..      19      57 ..       7      61 .. 0.87
   2 !    9.1   0.1    0.0029      0.86      36      70 ..     250     284 ..     243     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.5e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                        +++ G+ GtGKt++++++ ++  ke  ++l+++f+ +
  gi|488601283|ref|YP_007907754.1| 19 SIIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNET 57
                                      5689***************888888899999**999975 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0029
                             AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfs 70 
                                       ++++G+tGtGKt+   +++ +   +  + l+i+f 
  gi|488601283|ref|YP_007907754.1| 250 TVFIGNTGTGKTTFGLHFTYNNALNGKKALFITFE 284
                                       689**********9888555544455555566554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.3e-05    0.0098       2      37 ..      19      54 ..      18     113 .. 0.91
   2 ?   -0.2   0.0       2.3   6.7e+02      79     124 ..      72     114 ..      52     148 .. 0.62
   3 ?    6.7   0.0     0.017         5       3      36 ..     249     282 ..     247     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.3e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEE CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaa 37
                                      ++i+++G  G+GKT  ++ +a+   kegkkvl+v+ 
  gi|488601283|ref|YP_007907754.1| 19 SIIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSF 54
                                      589******************************986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.3
                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETT CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldat 124
                                        ++e++ ++ + TaGr   d++l    ++i+k+     +++v+d++
  gi|488601283|ref|YP_007907754.1|  72 LENENFRYMDLFTAGRDVVDTQLSFIFSEIEKFN---PNIIVIDSI 114
                                       5555555555569999999999865555555544...223333333 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.017
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllva 36 
                                       +++++G +G+GKTt           +gkk+l+++
  gi|488601283|ref|YP_007907754.1| 249 ITVFIGNTGTGKTTFGLHFTYNNALNGKKALFIT 282
                                       789***********98888877777788887776 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0011      0.34      27      63 ..      21      55 ..       6     113 .. 0.76
   2 ?    0.1   0.0       2.4   6.9e+02      59     118 ..     165     222 ..     164     245 .. 0.72
   3 !   10.9   0.6    0.0011      0.33      27      64 ..     250     285 ..     224     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0011
                                      EEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESS CS
                            ResIII 27 glikmaTGtGKTlvaaklierllkkgkeekflflvpr 63
                                      ++i+ + GtGKT++  +++ +  k+gk  k+lf+  +
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAHEEIKEGK--KVLFVSFN 55
                                      6789999*****************987..9**99654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.4
                                       EEESSHHHHHHHH..HHGGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                            ResIII  59 flvprkslleqtl..eefkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldads 118
                                       f+v+++++l  ++  e+++++l+ +++  g k+++ +++     +t+k i+++ i +l+++ 
  gi|488601283|ref|YP_007907754.1| 165 FVVDGLIILRYLKhdEHYRRILEVPKM-RGLKIKKPQYEY---TITDKGIFFFDIPELNRIG 222
                                       788888888877777788888888866.444444444444...6899999999999999876 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0011
                                       EEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH CS
                            ResIII  27 glikmaTGtGKTlvaaklierllkkgkeekflflvprk 64 
                                        ++   TGtGKT   ++++++ + +gk  k+lf+  ++
  gi|488601283|ref|YP_007907754.1| 250 TVFIGNTGTGKTTFGLHFTYNNALNGK--KALFITFEE 285
                                       578889*************99999988..788876544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00023     0.068      19      54 ..      18      53 ..       8      97 .. 0.79
   2 !    8.9   0.1    0.0031      0.92      20      48 ..     248     276 ..     238     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                                      -SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEE CS
                              PhoH 19 ndivfaiGpaGtGKtylavalavealkkkkvkriil 54
                                       +i++++G+ GtGKt l  ++a e +k++k   ++ 
  gi|488601283|ref|YP_007907754.1| 18 GSIIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVS 53
                                      5699*********************99987655554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0031
                                       SEEEEE--TTSSTTHHHHHHHHHHHHTTS CS
                              PhoH  20 divfaiGpaGtGKtylavalavealkkkk 48 
                                       +i++ iG++GtGKt + +    +   ++k
  gi|488601283|ref|YP_007907754.1| 248 SITVFIGNTGTGKTTFGLHFTYNNALNGK 276
                                       6999**********998887766665555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.1e-05     0.015       2      28 ..      20      47 ..      19      64 .. 0.75
   2 ?    5.5   0.0     0.049        14       3      99 ..     250     353 ..     248     382 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-05
                                      CEEEEC-TTTCHHHHHHHHHHH.HCTS- CS
                             NACHT  2 lvilqGeaGsGKTtLlqklala.waegk 28
                                      ++++ Ge+G GKT+L+ ++a++ ++egk
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEeIKEGK 47
                                      689****************975144443 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.049
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....-HCHHHCCCCTS--SSS-C...... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..rsladllfsqlpepaapvse...... 71 
                                        +  G  G GKTt+  ++    a +  ++    l++ ++ +e +   ++  +++++  +++   +++ ++e      
  gi|488601283|ref|YP_007907754.1| 250 TVFIGNTGTGKTTFGLHFTYNNALNGKKA----LFITFEESEENILRAMrnYGMDYSAVKENMIIKDMIPEayspvt 322
                                       5789*********9877777666555332....22222222222222224456666555555555555555555555 PP

                                       ...CHHHHCCSCCCEEEEEE-STT-SS-TCH CS
                             NACHT  72 ...vwavllelperlLlilDglDelvtdlgq 99 
                                           +  l+e ++  +l +D++  l +++++
  gi|488601283|ref|YP_007907754.1| 323 ffaRIYDLIESFKPEVLFIDSFSSLNEHMEE 353
                                       5553333333344444445666666666555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00014     0.041      23      57 ..      19      55 ..       8      64 .. 0.74
   2 ?    4.6   0.0     0.081        24      25      56 ..     250     283 ..     228     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00014
                                      S-EEEECSTTSSHHHHHHHH.HHHSTT.TTS-EEEEE CS
                   Sigma54_activat 23 lsvlitGesGtGKellarai.heaskr.kekpfvavn 57
                                      + ++i Ge GtGK++l ++i he+ k+ k+  fv++n
  gi|488601283|ref|YP_007907754.1| 19 SIIMIAGEPGTGKTILVSSIaHEEIKEgKKVLFVSFN 55
                                      569***********99888736655541444678877 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.081
                                       EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEE CS
                   Sigma54_activat  25 vlitGesGtGKellaraihe..askrkekpfvav 56 
                                       ++  G++GtGK+++  +     a + k++ f+++
  gi|488601283|ref|YP_007907754.1| 250 TVFIGNTGTGKTTFGLHFTYnnALNGKKALFITF 283
                                       4557********9986554312233344455555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0017       0.5       2      37 ..      21      55 ..      20     103 .. 0.80
   2 !    8.4   0.0     0.008       2.3       3      28 ..     251     276 ..     250     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0017
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfl 37
                                      +++ G+ g+GKt l++++ +++++e +k  + v+f 
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAHEEIKEGKKV-LFVSFN 55
                                      7999****************999877543.344444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.008
                                       EEESSTTSSHHHHHHCHCT-CCC-EE CS
                               Roc   3 vlvGdsgvGKtsllkrfvedkfseke 28 
                                       v++G++g+GKt++  +f+ ++  + +
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFGLHFTYNNALNGK 276
                                       79***************998875544 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 !    7.5   0.0    0.0066       1.9     129     160 ..      18      49 ..       7      53 .. 0.72
   2 !   10.3   0.0   0.00089      0.26     132     180 ..     250     300 ..     217     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                             T2SSE 129 rglilvsGgTgsGKttllyallk.einksderi 160
                                         +i+++G  g+GKt+l+ ++ + ei++  +++
  gi|488601283|ref|YP_007907754.1|  18 GSIIMIAGEPGTGKTILVSSIAHeEIKEG-KKV 49 
                                       5689*************977665155554.444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00089
                             T2SSE 132 ilvsGgTgsGKttll..yallkeinksderivtvEDpvEiqleganqvqln 180
                                        ++ G Tg+GKtt+    +  + +n ++  ++t E + E  l++     + 
  gi|488601283|ref|YP_007907754.1| 250 TVFIGNTGTGKTTFGlhFTYNNALNGKKALFITFEESEENILRAMRNYGMD 300
                                       4667*********9656888999999999********99888877666555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0    0.0001      0.03       5      51 ..      11      55 ..       7      71 .. 0.76
   2 ?    4.1   0.3      0.18        52      11      31 ..     248     268 ..     244     364 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.0001
                            AAA_19  5 ve.alkekvllvtaG.pGtGKTrvlkhivallvelggvkpeeillvaft 51
                                      +e +++e+ ++++aG pGtGKT ++  i ++ +++g    +++l v+f+
  gi|488601283|ref|YP_007907754.1| 11 IEgDFPEGSIIMIAGePGTGKTILVSSIAHEEIKEG----KKVLFVSFN 55
                                      5555555555555544*******9999999988888....678888886 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.18
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                       ++ + ++  GtGKT+   h  
  gi|488601283|ref|YP_007907754.1| 248 SITVFIGNTGTGKTTFGLHFT 268
                                       56788999******9866654 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0082       2.4      11      68 ..       8      65 ..       3     142 .. 0.80
   2 !   10.3   0.0   0.00081      0.24      16      70 ..     242     296 ..     236     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0082
                            AAA_10 11 nqevkgsktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketl 68
                                      n+ ++g   + s  +i G++G GK +l+  + +     g+k+l++   + ++ f +  
  gi|488601283|ref|YP_007907754.1|  8 NKIIEGDFPEGSIIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNETKQDFFKYT 65
                                      566777777777789*****************************98777766654443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00081
                            AAA_10  16 gsktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe 70 
                                       g  ++ s +++iG++G GK  +     ++ +l g+kal+i   + +e+  +++++
  gi|488601283|ref|YP_007907754.1| 242 GGFYRGSITVFIGNTGTGKTTFGLHFTYNNALNGKKALFITFEESEENILRAMRN 296
                                       5556677789******************************888877887777755 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.5    0.0002     0.057      20     116 ..      18     104 ..       9     151 .. 0.59
   2 ?    6.1   0.1     0.031       9.1       8      64 ..     233     290 ..     226     376 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0002
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialre.esiskldefie...eeeekkklekalgiavpkaele 92 
                                        +i++i G  g GKt L+  i+ +  + +k+v++++  ++ ++  k++++++   e+e+ +++              
  gi|488601283|ref|YP_007907754.1|  18 GSIIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNETkQDFFKYTKKLGfelENENFRYM-------------- 80 
                                       5799*********************999******96443303334444444442222222222.............. PP

                          ATPase_2  93 eilkeksklvfkaielllekikkk 116
                                        ++   +  v+ +++ ++ +i+k 
  gi|488601283|ref|YP_007907754.1|  81 DLFTAGRDVVDTQLSFIFSEIEKF 104
                                       222233333444444444444443 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.031
                          ATPase_2   8 lkeleeilere..pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesisk 64 
                                       +kel e++  +  + +i +  G  g GKt++  ++  n    +k+ ++++ ++e++++ 
  gi|488601283|ref|YP_007907754.1| 233 IKELDELVGGGfyRGSITVFIGNTGTGKTTFGLHFTYNNALNGKKALFIT-FEESEENI 290
                                       777777777662245799999**************999988898888875.33333333 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   0.00052      0.15       1      47 [.      21      64 ..      21      70 .. 0.76
   2 ?    4.6   0.1      0.14        41       2      21 ..     251     270 ..     250     341 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00052
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys.rnpeddfwdgY 47
                                      i++ G++g+GK+ l+ ++a++     k+ kk  ++s +++++df+ +Y
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAHEEI---KEGKKVLFVSfNETKQDFF-KY 64
                                      7899*************777655...7778888888566666665.44 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.14
                      RNA_helicase   2 wlyGpsgeGKStlakeLaka 21 
                                       ++ G++g+GK+t+  +++ +
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFGLHFTYN 270
                                       689*********98775543 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   0.00038      0.11      20      54 ..      20      54 ..      15      71 .. 0.87
   2 ?    4.1   0.1      0.12        34      20      34 ..     249     263 ..     244     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00038
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAp 54
                                      + ++ G +GtGKt +++++++   ++g++v+ ++ 
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSF 54
                                      67899**************9999999999998765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.12
                            AAA_30  20 vavltGpAGtGKtta 34 
                                       ++v  G  GtGKtt 
  gi|488601283|ref|YP_007907754.1| 249 ITVFIGNTGTGKTTF 263
                                       78999********96 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   6.9e-05      0.02      30      81 ..      17      68 ..       6      96 .. 0.92
   2 ?    1.5   0.0      0.35     1e+02      40      81 ..     256     297 ..     245     368 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-05
                            AAA_35 30 pGalirikapkkmGKtSLlarilakakqqgyktvsldlqladkeilsdldkf 81
                                      +G++i i +   +GKt L++ i ++  ++g+k++ ++++++++++++  +k+
  gi|488601283|ref|YP_007907754.1| 17 EGSIIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNETKQDFFKYTKKL 68
                                      699******************************************9988775 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.35
                            AAA_35  40 kkmGKtSLlarilakakqqgyktvsldlqladkeilsdldkf 81 
                                         +GKt +  +   + + +g+k++ + +++ +++il+ + ++
  gi|488601283|ref|YP_007907754.1| 256 TGTGKTTFGLHFTYNNALNGKKALFITFEESEENILRAMRNY 297
                                       56899999999999999999999*******999999988765 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0067         2       5     123 ..      20     130 ..      17     138 .. 0.80
   2 !    8.2   0.0    0.0092       2.7       2      64 ..     246     307 ..     245     372 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0067
                    CobA_CobO_BtuR   5 ihvytGd.GKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaalkkleielerlgkegfvkmeeeekeedaaa 80 
                                       i++  G+ G GKt     +a   + +g+kvl+v F  ++   +  + +kkl++ele+ +   f +m+    ++ ++ 
  gi|488601283|ref|YP_007907754.1|  20 IIMIAGEpGTGKTILVSSIAHEEIKEGKKVLFVSFNETK--QDFFKYTKKLGFELENEN---FRYMDL--FTAGRDV 89 
                                       5555564499*************************9994..677899999999888655...443444..5678899 PP

                    CobA_CobO_BtuR  81 akealekakealaseeydlvvlDEinyalklglldeeevlell 123
                                       ++++l+ + +++++ + +++v+D i++ l+  +l++e++ ++l
  gi|488601283|ref|YP_007907754.1|  90 VDTQLSFIFSEIEKFNPNIIVIDSITAILS--VLAKENIRTFL 130
                                       9999999999999999********999875..56677666666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0092
                    CobA_CobO_BtuR   2 kglihvytGd.GKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaalkkl...eielerlgke 64 
                                       +g i v+ G+ G GKtt  l      + +g+k l++ F  +     E+++l+++   ++++  ++++
  gi|488601283|ref|YP_007907754.1| 246 RGSITVFIGNtGTGKTTFGLHFTYNNALNGKKALFITFEES-----EENILRAMrnyGMDYSAVKEN 307
                                       5899*****769*************************9655.....667776665435777666643 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00025     0.074      28     117 ..      33     131 ..      20     145 .. 0.75
   2 ?    3.7   0.0      0.13        37      90     120 ..     326     364 ..     265     409 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                        Elong_Iki1  28 plleelirrakssktkvifvsfetlkk.................pkgvdvfieaterskklkelakeiksalspkss 87 
                                        l+++++++  ++ +kv+fvsf+ +k+                  +++d f    ++   +++  + i s++++   
  gi|488601283|ref|YP_007907754.1|  33 ILVSSIAHEEIKEGKKVLFVSFNETKQdffkytkklgfelenenFRYMDLFTAGRDV---VDTQLSFIFSEIEKF-- 104
                                       6888999999999**********8888899998889988866665566655555333...344444444444222.. PP

                        Elong_Iki1  88 ekkkkalviiDslnplaslikeeslaafls 117
                                          + ++++iDs+++++s   +e++ +fl 
  gi|488601283|ref|YP_007907754.1| 105 ---NPNIIVIDSITAILSVLAKENIRTFLH 131
                                       ...578********9999778888888886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                        Elong_Iki1  90 k........kkalviiDslnplaslikeeslaaflssll 120
                                       +        k  +++iDs+++l ++ +e +l+++++ + 
  gi|488601283|ref|YP_007907754.1| 326 RiydliesfKPEVLFIDSFSSLNEHMEEVELSKMVRYIQ 364
                                       1334555567889*********99888988888887664 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0011      0.31       3      37 ..      20      54 ..      18      84 .. 0.91
   2 ?    4.1   0.0     0.074        22       5      64 ..     251     310 ..     248     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE- CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllist 37
                                      +i+++G  G GKt + +++a +  ++gkkvl +s 
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSF 54
                                      89*******************************96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.074
                                       EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT.THHHHHHTS--BSS-EEETSSEEE CS
                       ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvllistDPA.hslsDsfdqklgkeptkvkeNLsa 64 
                                       ++ G  G GKtt    + ++ + +gkk l i+      ++  ++ +  g +  +vkeN+ +
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFGLHFTYNNALNGKKALFITFEESeENILRAMRN-YGMDYSAVKENMII 310
                                       678999***********************99976441345544443.66666666666665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0061       1.8      19      42 ..      18      41 ..       4      60 .. 0.82
   2 ?    5.9   0.1     0.042        12      19      36 ..     247     264 ..     223     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0061
                                      TEEEEEEESTTSSHHHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglaka 42
                                      g++i++ G+ G+GKT lv ++a++
  gi|488601283|ref|YP_007907754.1| 18 GSIIMIAGEPGTGKTILVSSIAHE 41
                                      6789***************99976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.042
                                       TEEEEEEESTTSSHHHHH CS
                              TsaE  19 gdvilLeGdLGaGKTtlv 36 
                                       g++ ++ G+ G+GKTt+ 
  gi|488601283|ref|YP_007907754.1| 247 GSITVFIGNTGTGKTTFG 264
                                       667999**********95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   8.5e-05     0.025       1      89 [.      21     121 ..      21     193 .. 0.80
   2 ?    3.2   0.6      0.42   1.2e+02       4      18 ..     253     267 ..     251     370 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..............gvnlrdvakenglllevdpe....aldeskrldedkldk 59 
                                       I+++G pG+GKt l   ++ + ++               +   ++ k+ g +le++++     +   + +++ +l  
  gi|488601283|ref|YP_007907754.1|  21 IMIAGEPGTGKTILVSSIAHE-EIkegkkvlfvsfnetKQDFFKYTKKLGFELENENFrymdLFTAGRDVVDTQLSF 96 
                                       99****************777.4666888899999988888889999999999999996666555666666666666 PP

                            AAA_18  60 lldaleenssaleegknlvidghlaelese 89 
                                       +++++e+ +     ++ +vid++ a l   
  gi|488601283|ref|YP_007907754.1|  97 IFSEIEKFN-----PNIIVIDSITAILSVL 121
                                       666666666.....5999****99987655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.42
                            AAA_18   4 tGtpGvGKttlakeL 18 
                                        G  G+GKtt++ + 
  gi|488601283|ref|YP_007907754.1| 253 IGNTGTGKTTFGLHF 267
                                       6889******99877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.014       4.2      10      40 ..       4      36 ..       2      40 .. 0.73
   2 !    7.8   0.4    0.0091       2.7      23      38 ..     247     263 ..     243     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
                            AAA_29 10 gtfdghtieid.lkg.atlltGpsGsGKSTllD 40
                                      g+f+++ ie d ++g +++++G+ G+GK+ l+ 
  gi|488601283|ref|YP_007907754.1|  4 GYFKNKIIEGDfPEGsIIMIAGEPGTGKTILVS 36
                                      566666666552355799**********99885 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0091
                            AAA_29  23 g.atlltGpsGsGKSTl 38 
                                       g +t+++G++G+GK+T+
  gi|488601283|ref|YP_007907754.1| 247 GsITVFIGNTGTGKTTF 263
                                       5589***********96 PP

>> ELP6  Elongation complex protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0066       1.9      15      85 ..      15      86 ..       9      96 .. 0.76
   2 ?    3.3   0.0      0.16        46     133     171 ..      99     136 ..      88     179 .. 0.75
   3 ?    1.4   0.0       0.6   1.8e+02     136     172 ..     332     367 ..     281     432 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0066
                              ELP6 15 leqgelilladsq.aDgsFLiHHflsfylkagckvvfvalvqsfsHysivaqkLGvsLtqakekgqlvFleG 85
                                      +++g++i++a +  +  + L+       +k g kv+fv++ ++ + +   ++kLG +L + + + +  F  G
  gi|488601283|ref|YP_007907754.1| 15 FPEGSIIMIAGEPgTGKTILVSSIAHEEIKEGKKVLFVSFNETKQDFFKYTKKLGFELENENFRYMDLFTAG 86
                                      667777777764414445666666666799****************************98877766666666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.16
                              ELP6 133 dgeeewkppvllvDdlsvLlslgvsaaavldFihyCrat 171
                                       +  e+ +p ++++D++  +ls+ ++++++ +F+h    +
  gi|488601283|ref|YP_007907754.1|  99 SEIEKFNPNIIVIDSITAILSV-LAKENIRTFLHTSLGR 136
                                       44578899*************8.5667899999976555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.6
                              ELP6 136 eewkppvllvDdlsvLlslgvsaaavldFihyCratv 172
                                       e+ kp vl +D+ s L +  ++ +++++ ++y + tv
  gi|488601283|ref|YP_007907754.1| 332 ESFKPEVLFIDSFSSL-NEHMEEVELSKMVRYIQLTV 367
                                       6778999999999986.55788889999999987774 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0069         2       3      28 ..      20      45 ..      18      60 .. 0.84
   2 ?    5.7   0.0     0.038        11       4      20 ..     250     266 ..     248     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0069
                         PduV-EutP  3 killiGkvgsGKttLtqalkgeelkY 28
                                       i++ G+ g+GKt L  ++ +ee+k 
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEEIKE 45
                                      6999*******************985 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.038
                         PduV-EutP   4 illiGkvgsGKttLtqa 20 
                                        ++iG++g+GKtt   +
  gi|488601283|ref|YP_007907754.1| 250 TVFIGNTGTGKTTFGLH 266
                                       589**********8654 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   0.0   0.00098      0.29       2      42 ..      20      60 ..      19      74 .. 0.82
   2 ?    3.4   0.1      0.18        52       2      22 ..     249     271 ..     248     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00098
                                      EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCC CS
                              cobW  2 vtvltGflGsGKTtLlnhllenraglklavivNefgevsiD 42
                                      +++++G +G+GKT L++++ +++ ++   v+   f e++ D
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNETKQD 60
                                      6899****************777777777777777777766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.18
                                       EEEEEESTTCCHHHHHHHHH..C CS
                              cobW   2 vtvltGflGsGKTtLlnhll..e 22 
                                       +tv+ G  G+GKTt+  h +  +
  gi|488601283|ref|YP_007907754.1| 249 ITVFIGNTGTGKTTFGLHFTynN 271
                                       68999*********987777532 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 !   14.9   0.0     4e-05     0.012      15      63 ..      13      59 ..       6     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-05
                        KAP_NTPase 15 ptlatpivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsf 63
                                       +  +++++++ g+ G+GK+ l+ ++ +e  ++   +++lf++fn  ++
  gi|488601283|ref|YP_007907754.1| 13 GDFPEGSIIMIAGEPGTGKTILVSSIAHEEIKE--GKKVLFVSFNETKQ 59
                                      4567899**********************9999..899*****998665 PP

>> Mistic  Membrane-integrating protein Mistic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1         3   8.7e+02       8      29 ..      39      60 ..      36     107 .. 0.65
   2 !   14.9   0.3   6.6e-05     0.019      23      67 ..     269     314 ..     266     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 3
                                      HHHTTTHHHHHHHHH--SSS-S CS
                            Mistic  8 AiDkmnegldafieLYNeseed 29
                                      A  +++eg  ++   +Ne ++d
  gi|488601283|ref|YP_007907754.1| 39 AHEEIKEGKKVLFVSFNETKQD 60
                                      5567889999999999998887 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.6e-05
                                       --SSS-SS-..SS-SHHHHHHHHHHHHHHTSSSS-HHHHHHHHHHHH CS
                            Mistic  23 YNeseedkp..liefeeevleaiekAkekYGeevvnkKiNtivkevL 67 
                                       YN++ + k+  +i f ee +e+i +A + YG ++   K N i+k+++
  gi|488601283|ref|YP_007907754.1| 269 YNNALNGKKalFITF-EESEENILRAMRNYGMDYSAVKENMIIKDMI 314
                                       788766655114555.67899***********************996 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.076        22      99     123 ..      18      42 ..      11      55 .. 0.84
   2 !    8.7   0.1    0.0052       1.5      97     115 ..     245     263 ..     218     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.076
                                       TSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                       +++++++G+ G GK+ L+ +++ e+
  gi|488601283|ref|YP_007907754.1|  18 GSIIMIAGEPGTGKTILVSSIAHEE 42 
                                       57899***************99875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0052
                                       CTTSEEEEECSTTSSHHHH CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStL 115
                                        +++++v++G++G GK+t+
  gi|488601283|ref|YP_007907754.1| 245 YRGSITVFIGNTGTGKTTF 263
                                       46799************97 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00055      0.16      16      44 ..      17      45 ..       7     112 .. 0.83
   2 ?    1.7   0.0      0.62   1.8e+02      17      37 ..     247     267 ..     235     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00055
                            AAA_11 16 eseitliqGPPGtgKTktivellsqllsr 44
                                      e +i +i G PGtgKT  + ++ ++ +++
  gi|488601283|ref|YP_007907754.1| 17 EGSIIMIAGEPGTGKTILVSSIAHEEIKE 45
                                      55689****************99998744 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.62
                            AAA_11  17 seitliqGPPGtgKTktivel 37 
                                        +it++ G  GtgKT++ +++
  gi|488601283|ref|YP_007907754.1| 247 GSITVFIGNTGTGKTTFGLHF 267
                                       4579999********976655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00011     0.033       9      43 ..       7      41 ..       3      67 .. 0.86
   2 ?   -0.3   0.2       1.7   4.9e+02      22      36 ..     249     263 ..     234     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                      HHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  9 iekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                      ++k  e d ++  ++ + G +G GKt+l+++i ++
  gi|488601283|ref|YP_007907754.1|  7 KNKIIEGDFPEGSIIMIAGEPGTGKTILVSSIAHE 41
                                      5777877888889*******************998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                                       EEEEEESTTSSHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttl 36 
                                       +  + G  G GKtt 
  gi|488601283|ref|YP_007907754.1| 249 ITVFIGNTGTGKTTF 263
                                       44568********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 ?    6.8   0.0     0.017       5.1      36      56 ..      21      41 ..      17      74 .. 0.87
   2 ?   -1.7   0.0       7.4   2.2e+03      37      50 ..     251     264 ..     248     274 .. 0.85
   3 ?    5.1   0.1     0.059        17      84     110 ..     335     361 ..     323     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.017
                            RuvB_N 36 vllyGpPGlGkttlakiiake 56
                                      ++++G PG Gkt l + ia+e
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAHE 41
                                      7899**********9999987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.4
                            RuvB_N  37 llyGpPGlGkttla 50 
                                       +++G  G Gktt+ 
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFG 264
                                       6899*******975 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.059
                            RuvB_N  84 ekdvlfideihrlsraveevlysamed 110
                                       + +vlfid    l++++eev  s m  
  gi|488601283|ref|YP_007907754.1| 335 KPEVLFIDSFSSLNEHMEEVELSKMVR 361
                                       458****************98877755 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022     0.064      49      86 ..      17      57 ..       5      78 .. 0.80
   2 ?   -0.9   0.0       2.4   7.1e+02      50      83 ..     247     283 ..     236     289 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                                      XXXXXXXXXXXXXXXXXXXXXXXXX.X..XXXXXXXXXXXX CS
                             TIP49 49 aGravLlaGpsgtGktalaiaiske.l..gedvpfvalsgs 86
                                       G  +++aG++gtGkt l  +i++e +  g++v fv+++ +
  gi|488601283|ref|YP_007907754.1| 17 EGSIIMIAGEPGTGKTILVSSIAHEeIkeGKKVLFVSFNET 57
                                      5889******************9753533588999998865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.4
                                       XXXXXXXXXXXXXXXXXXXXXX..XXXX.XXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiais..kelg.edvpfval 83 
                                       G   ++ G++gtGkt   +  +  ++l+ ++  f+++
  gi|488601283|ref|YP_007907754.1| 247 GSITVFIGNTGTGKTTFGLHFTynNALNgKKALFITF 283
                                       5566789********9876543114454455556555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.013       3.7      11      39 ..      27      55 ..      19     126 .. 0.79
   2 ?    5.6   0.0     0.045        13      11      40 ..     256     285 ..     248     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.013
                            AAA_31 11 GGvGKTTtsvnlaaalaklgkkvLlvDlD 39
                                       G GKT  +  +a    k+gkkvL v + 
  gi|488601283|ref|YP_007907754.1| 27 PGTGKTILVSSIAHEEIKEGKKVLFVSFN 55
                                      599**********************9875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.045
                            AAA_31  11 GGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                        G GKTT  + + +  a +gkk L + +  
  gi|488601283|ref|YP_007907754.1| 256 TGTGKTTFGLHFTYNNALNGKKALFITFEE 285
                                       599*********************998764 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.019       5.5       2      21 ..      21      40 ..      20      78 .. 0.87
   2 ?    6.1   0.0     0.041        12       2      15 ..     250     263 ..     249     298 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.019
                            AAA_33  2 vllvGlpGsGKstlaerllk 21
                                      +++ G pG+GK+ l+ +++ 
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAH 40
                                      8999**********998865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.041
                            AAA_33   2 vllvGlpGsGKstl 15 
                                       ++++G  G+GK+t+
  gi|488601283|ref|YP_007907754.1| 250 TVFIGNTGTGKTTF 263
                                       689**********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 ?    8.0   0.0    0.0097       2.9       1      33 [.      20      52 ..      20     147 .. 0.88
   2 ?    5.8   0.4     0.047        14       1      32 [.     249     280 ..     249     373 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0097
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllv 33
                                      i+++++  G+GKT l+ ++a    ++g++Vl v
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFV 52
                                      56778888**********************987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.047
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVll 32 
                                       i++  +  G+GKTt+ +++    a +g++ l 
  gi|488601283|ref|YP_007907754.1| 249 ITVFIGNTGTGKTTFGLHFTYNNALNGKKALF 280
                                       56778899*******99999999998888775 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0067         2       8      58 ..      22      75 ..      19     127 .. 0.62
   2 ?    3.0   0.1      0.21        60       2      50 ..     246     293 ..     245     385 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0067
                              KdpD  8 flGaapGvGktyamLeeaqelkeegvdvv.iglvethgr..ketealleglevi 58
                                       +   pG Gkt+ + + a+e+ +eg++v+ +++ et+++  k t++l  +le  
  gi|488601283|ref|YP_007907754.1| 22 MIAGEPGTGKTILVSSIAHEEIKEGKKVLfVSFNETKQDffKYTKKLGFELENE 75
                                      566679*********************973555565554334555555555544 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.21
                              KdpD   2 rGrlkiflGaapGvGktyamLeeaqelkeegvdvviglvethgrketea 50 
                                       rG++++f+G   G Gkt   L+   +++ +g++ +  + e+ +++  +a
  gi|488601283|ref|YP_007907754.1| 246 RGSITVFIGN-TGTGKTTFGLHFTYNNALNGKKALFITFEESEENILRA 293
                                       6777888885.58888877777777777777665544444444333333 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00042      0.12      37     101 ..      21      83 ..      16     141 .. 0.90
   2 ?    0.1   0.1       2.1   6.2e+02      39      95 ..     252     308 ..     249     314 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00042
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEE CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvL 101
                                       ++i ge G Gkt L+ +i++e +  ++ ++v++++ +e  +++ k  ++   e   e++r +D+ 
  gi|488601283|ref|YP_007907754.1|  21 IMIAGEPGTGKTILVSSIAHEEI--KEGKKVLFVSFNETKQDFFKYTKKLGFELENENFRYMDLF 83 
                                       5799***************9765..5789****************99998888888899999975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.1
                                       EE-SSSSSHHHH.HHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHT..T-HHHHHHHH CS
                          Bac_DnaA  39 iygevGlGktHL.lkaignevlenapelrvvYltaeeFlnelvkalrd..kkaeefkekl 95 
                                       + g++G Gkt   l+   n++l   + ++ +++t ee  +++++a+r+   + ++ ke++
  gi|488601283|ref|YP_007907754.1| 252 FIGNTGTGKTTFgLHFTYNNAL---NGKKALFITFEESEENILRAMRNygMDYSAVKENM 308
                                       4589999998753555555544...56677777777777788888877444455566555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.011       3.3       2      23 ..      21      42 ..      20      86 .. 0.81
   2 ?    4.0   0.0      0.18        52       3      15 ..     251     263 ..     249     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.011
                            AAA_28  2 ivitGgestGKTtlleaLaarg 23
                                      i+i G ++tGKT l++ +a ++
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAHEE 42
                                      7899*************99663 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.18
                            AAA_28   3 vitGgestGKTtl 15 
                                       v++G  +tGKTt 
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTF 263
                                       89**********6 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0058       1.7      13      58 ..      17      63 ..      11      88 .. 0.83
   2 ?    2.6   0.0       0.3        88       1      31 [.     232     264 ..     232     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0058
                                      TT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEEESEEHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 13 qGqrtlipgafgvGktvisqslskqsnsdd.aiiyvgiGergnevae 58
                                      +G  ++i g+ g+Gkt +++s++++  ++   + +v   e +++  +
  gi|488601283|ref|YP_007907754.1| 17 EGSIIMIAGEPGTGKTILVSSIAHEEIKEGkKVLFVSFNETKQDFFK 63
                                      688899*****************997666458888888877776655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.3
                                       SSHHHHHHS-..EBTT-EEEEEESTTSSHHHHH CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfp..ivqGqrtlipgafgvGktvis 31 
                                       Gi+ lD l+   + +G  t+ +g+ g+Gkt+  
  gi|488601283|ref|YP_007907754.1| 232 GIKELDELVGggFYRGSITVFIGNTGTGKTTFG 264
                                       677788887533789***************965 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.018       5.2      13      54 ..      17      53 ..       8     132 .. 0.80
   2 ?    4.3   0.0      0.11        32      18      48 ..     251     309 ..     238     386 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.018
                                      TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalive 54
                                      +g  +++a+e G+GKT   +  + +++     k+g+k+l+v+
  gi|488601283|ref|YP_007907754.1| 17 EGSIIMIAGEPGTGKTILVSSIAHEEI-----KEGKKVLFVS 53
                                      456678999*********999999888.....6666666664 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                                       EEEESTTSSHHHHHHHHHHHHHHHSTTSTS..............................- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............................x RF
                              DEAD  18 lvaaeTGsGKTlaflipvlqivyetkgktg..............................p 48 
                                       +  ++TG+GKT+  l   +++ ++  gk++                               
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFGLHFTYNNALN--GKKAlfitfeeseenilramrnygmdysavkenmI 309
                                       56789******9987777766654..33333333333333444444444444444444440 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     0.012       3.5       2      31 ..      21      51 ..      20     150 .. 0.68
   2 ?    3.2   0.0       0.3        87       3      28 ..     251     276 ..     249     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.012
                                      EEEEESTTSSHHHHHHHHHTSTEEE.SSSTT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaiv.sdkpg 31
                                      ++i+G p +GK+ L++++  e+ +  ++  +
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAHEEIKEgKKVLF 51
                                      79****************9874433133333 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.3
                                       EEEESTTSSHHHHHHHHHTSTEEESS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltgekaivsd 28 
                                       +++G++ +GK+t+    t ++a  ++
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTFGLHFTYNNALNGK 276
                                       79**********97777766655444 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.2   1.2e+03      28      82 ..       9      62 ..       8      66 .. 0.81
   2 ?   10.6   0.0   0.00075      0.22      19      41 ..     229     251 ..     225     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.2
                            PAXNEB 28 klLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewl 82
                                      k++ G +p Gsi++i  +   + +++L+   + e + ++++vl++s+++++++++
  gi|488601283|ref|YP_007907754.1|  9 KIIEGDFPEGSIIMIAGE-PGTGKTILVSSIAHEEIKEGKKVLFVSFNETKQDFF 62
                                      577888999999999855.344478999999999999999999999999888876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00075
                            PAXNEB  19 tStGtpsLDklLgGGLplGsill 41 
                                       +StG+++LD+l+gGG+  Gsi +
  gi|488601283|ref|YP_007907754.1| 229 VSTGIKELDELVGGGFYRGSITV 251
                                       8****************999965 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0022      0.64       7      37 ..      21      51 ..      18      93 .. 0.78
   2 ?    0.6   0.0      0.94   2.8e+02       9      25 ..     252     268 ..     247     309 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                                      EEEEEBTTSSCCCCCCTTSSSS--------- CS
                            Septin  7 lmvvGesglGkttlintlfetdlieeeklee 37
                                      +m++Ge g+Gkt l+ ++ +++++e +k+  
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAHEEIKEGKKVLF 51
                                      8*******************99999865543 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.94
                                       EEEBTTSSCCCCCCTTS CS
                            Septin   9 vvGesglGkttlintlf 25 
                                        +G+ g+Gktt+   + 
  gi|488601283|ref|YP_007907754.1| 252 FIGNTGTGKTTFGLHFT 268
                                       57*********955544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00088      0.26      17      53 ..      19      56 ..       5      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00088
                        Zeta_toxin 17 klillgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                       +i+++G pG GK+ l + ++ e   ++++v+ ++  +
  gi|488601283|ref|YP_007907754.1| 19 SIIMIAGEPGTGKTILVSSIAHEEIkEGKKVLFVSFNE 56
                                      5899**********998877765442666666665555 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   0.00072      0.21      31      63 ..      20      52 ..      13      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00072
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                       + + G PG+Gk  lv+ ++ e +++Gk+v  +
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFV 52
                                      57799************************9766 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     0.001       0.3       2      39 ..      21      58 ..      20      76 .. 0.78
   2 ?   -0.4   0.7       3.3   9.7e+02       6      15 ..     254     263 ..     250     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.001
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                      ++i G+pG+GKt lv+ ++++  ++g kv  +  +e +
  gi|488601283|ref|YP_007907754.1| 21 IMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFNETK 58
                                      79***************998877888887666655555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.3
                                       --TTSSHHHH CS
                          NTPase_1   6 GppGvGKtTl 15 
                                       G+ G+GKtT+
  gi|488601283|ref|YP_007907754.1| 254 GNTGTGKTTF 263
                                       99*******8 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0049       1.4       1      36 [.      20      55 ..      20      67 .. 0.85
   2 ?    1.9   0.2      0.67     2e+02       3      15 ..     251     263 ..     249     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0049
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvgtiKha 36
                                      ++ i+g  g+GKT L++ + +e  ++g +v  +  +
  gi|488601283|ref|YP_007907754.1| 20 IIMIAGEPGTGKTILVSSIAHEEIKEGKKVLFVSFN 55
                                      689*******************99999999877655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.67
                              MobB   3 givgksgsGKTtL 15 
                                        ++g+ g+GKTt+
  gi|488601283|ref|YP_007907754.1| 251 VFIGNTGTGKTTF 263
                                       689*********8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.1       0.1        31       7      39 ..       3      38 ..       1     108 [. 0.92
   2 ?    8.8   1.3    0.0072       2.1      20      35 ..     248     263 ..     236     280 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.1
                            AAA_23  7 frsfrdqei..dF.skgltlItGpNGaGKTTildAi 39
                                      f+ f+++ i  dF +  +  I G+ G+GKT ++  i
  gi|488601283|ref|YP_007907754.1|  3 FGYFKNKIIegDFpEGSIIMIAGEPGTGKTILVSSI 38
                                      77888888777888888*************998776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0072
                            AAA_23  20 gltlItGpNGaGKTTi 35 
                                        +t+++G++G+GKTT+
  gi|488601283|ref|YP_007907754.1| 248 SITVFIGNTGTGKTTF 263
                                       59*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        61  (0.00340231); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              61  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 2889.82
//
Query:       gi|488601284|ref|YP_007907755.1|  [L=453]
Description: amidophosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-20   73.9   0.0    1.5e-20   73.3   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
    1.8e-19   70.3   0.0      3e-19   69.6   0.0    1.3  1  GATase_6      Glutamine amidotransferase domain
    1.5e-07   30.6   0.0    1.3e-06   27.6   0.0    2.4  2  GATase_4      Glutamine amidotransferases class-II
    8.7e-07   28.6   0.0    1.9e-06   27.5   0.0    1.6  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
       0.45   10.4   1.6        1.3    9.0   1.6    1.8  1  VPDSG-CTERM   VPDSG-CTERM motif


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   4.1e-24   1.5e-20       7     122 ..      80     201 ..      72     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 4.1e-24
                          GATase_7   7 idseagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerl 74 
                                       +   ++aQP++  s+ g++++++nG ++Ny+elr+eLe  g  f+t+sDtev++ ll++          +  + ++l
  gi|488601284|ref|YP_007907755.1|  80 QSRIENAQPLAVkSRYGSIAVAHNGNLVNYRELRKELEIDGKVFHTDSDTEVIVYLLSSylldndleTALSMLTKKL 156
                                       5566899***998999*****************************************99****999777788889** PP

                          GATase_7  75 nGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                        G+f + ++ ++   ++  RD++G+kPL +ge +  ++++aSe  a+ 
  gi|488601284|ref|YP_007907755.1| 157 MGSFTLTLLLNDM--VVGYRDPMGFKPLCVGEGE-FGYIIASESCAID 201
                                       *********9999..******************7.68******99985 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   8.2e-23     3e-19       4     134 .]      58     196 ..      56     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 8.2e-23
                          GATase_6   4 sglaslvedevalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevll 78 
                                       ++++s+ +++  ++HvR +++g ++ e aqP+  +s++g ++++hNG   ny+elr+el+  +g  f ++sDtev++
  gi|488601284|ref|YP_007907755.1|  58 NKILSMLKGNSSIGHVRYSTTGQSRIENAQPLavKSRYGSIAVAHNGNLVNYRELRKELEI-DGKVFHTDSDTEVIV 133
                                       567889999999***********966666***999**************************.*************** PP

                          GATase_6  79 all........eelGeevl.erlrGmfafaiwdkrentlila.rdrlgvkplyyavdesglafase 134
                                        ll         e++  +l ++l G f+  +     n +++  rd +g kpl++++ e g ++ase
  gi|488601284|ref|YP_007907755.1| 134 YLLssylldndLETALSMLtKKLMGSFTLTL---LLNDMVVGyRDPMGFKPLCVGEGEFGYIIASE 196
                                       *996655443323333333356666555543...456666666*************9999999998 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.6e-10   1.3e-06       1     176 [.       1     166 [.       1     175 [. 0.62
   2 ?   -1.2   0.0      0.21   7.7e+02     234     256 ..     205     227 ..     187     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.6e-10
                          GATase_4   1 mceLLgmssn.vptdis...fsftgfaarggl.tdahadGwGiafyegka..arvfkdpepsaesplaelvreypik 70 
                                       mc ++g+ +n v + +    + + ++++rg++ ++ + +G G+  y++ +   +vf         ++  +     +k
  gi|488601284|ref|YP_007907755.1|   1 MCGIVGVFCNdVDLTPHityYALFSLQHRGQEsAGMAVSGVGVNLYKDMGlvSEVFS-------NKILSM-----LK 65 
                                       666666665522333330013445667776542566777888888875440023332.......223333.....56 PP

                          GATase_4  71 sknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl..egrfePvGsTDsElaf.Celleelasr 144
                                        +  + H+R  t+G+ + en++p + +    ++  AHnG+l +y++ +   +    v +TDs++    +ll+    +
  gi|488601284|ref|YP_007907755.1|  66 GNSSIGHVRYSTTGQSRIENAQPLAVKSRYGSIAVAHNGNLVNYRELRkeLEIDGKVFHTDSDTEViVYLLS----S 138
                                       7899*********************999999**********9998877333444578889998643033333....2 PP

                          GATase_4 145 fekaepsaeeleralaelakeiaelGvfnlll 176
                                       +       ++le+al+ l+k++    +++lll
  gi|488601284|ref|YP_007907755.1| 139 Y----LLDNDLETALSMLTKKLMGSFTLTLLL 166
                                       2....234556666666666665555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                          GATase_4 234 detWkklepGellvfrdGalvat 256
                                       +e  ++++pGe ++++dG+l+  
  gi|488601284|ref|YP_007907755.1| 205 AELIRDVRPGEAVIIEDGDLRFE 227
                                       56678899999999999998765 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   5.4e-10   1.9e-06      79     120 ..     324     373 ..     262     375 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 5.4e-10
                                       .........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran  79 s........rlledpagkkVliVDDildtGgTllaalelLkekgpeevri 120
                                                 l  ++ gk+Vl++DD +  G+T ++++el++++g++e+++
  gi|488601284|ref|YP_007907755.1| 324 ElsvklkmnVLRDNVNGKRVLLIDDSIVRGTTSRKIVELVRKAGAKEIHF 373
                                       045555555678899*********************************86 PP

>> VPDSG-CTERM  VPDSG-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.6   0.00035       1.3       1       9 [.     281     289 ..     281     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00035
                       VPDSG-CTERM   1 sVPDsGSTl 9  
                                       +VPDsG+T 
  gi|488601284|ref|YP_007907755.1| 281 PVPDSGTTS 289
                                       7*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3090.68
//
Query:       gi|488601285|ref|YP_007907756.1|  [L=59]
Description: LSU ribosomal protein L37E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-22   79.4  13.2    1.8e-22   79.2  13.2    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
    0.00016   21.5   2.8    0.00023   20.9   2.8    1.3  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
        1.4    8.4   6.9       0.29   10.7   3.3    1.7  2  DUF2688         Protein of unknown function (DUF2688)


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 !   79.2  13.2     3e-26   1.8e-22       1      54 []       2      56 ..       2      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 3e-26
                    Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKak 54
                                      +kGt+s+Gkr +k +Hi+CrrCgk s+h +k +CascG+ +s++lr+y+W +K+k
  gi|488601285|ref|YP_007907756.1|  2 SKGTASMGKRGRKIVHIKCRRCGKVSFHRRKGYCASCGFgRSKRLRSYSWVRKKK 56
                                      69*************************************************9986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   2.8   3.9e-08   0.00023      13      32 ..      19      39 ..      14      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.9e-08
                           DUF35_N 13 rCpdCGtvqfPPr.avCphCg 32
                                      +C+ CG+v f +r  +C  Cg
  gi|488601285|ref|YP_007907756.1| 19 KCRRCGKVSFHRRkGYCASCG 39
                                      8*******************5 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.3   4.8e-05      0.29       4      15 ..      14      25 ..      11      35 .. 0.85
   2 ?   -1.0   0.3      0.21   1.2e+03      10      18 ..      35      43 ..      26      50 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.8e-05
                           DUF2688  4 eiVtTqCrRCGk 15
                                      +iV  +CrRCGk
  gi|488601285|ref|YP_007907756.1| 14 KIVHIKCRRCGK 25
                                      79*********9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.21
                           DUF2688 10 CrRCGksls 18
                                      C  CG   s
  gi|488601285|ref|YP_007907756.1| 35 CASCGFGRS 43
                                      777775555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 415.75
//
Query:       gi|488601286|ref|YP_007907757.1|  [L=77]
Description: Small nuclear ribonucleoprotein, LSM family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-22   78.3   0.4    2.9e-22   78.1   0.4    1.0  1  LSM       LSM domain
      0.001   19.1   0.0     0.0012   19.0   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.4   3.2e-26   2.9e-22       2      67 .]       8      72 ..       7      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 3.2e-26
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                       l+k+++  v+v+lk+gre+rG+L g+D +mNlvL d+ee++ ++  +rklg v+iRG+++v++s+
  gi|488601286|ref|YP_007907757.1|  8 VLNKSLQTSVIVRLKGGREFRGILDGYDIHMNLVLMDAEEIQGGE-IVRKLGSVVIRGDTVVFVSP 72
                                      699***************************************999.*****************986 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.3e-07    0.0012      14      51 ..      15      50 ..       3      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-07
                                      SEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                            SM-ATX 14 kevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                      ++v v++k G  ++Gi+++++    +++vL  a +++ 
  gi|488601286|ref|YP_007907757.1| 15 TSVIVRLKGGREFRGILDGYDI--HMNLVLMDAEEIQG 50
                                      689*******************..*********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 464.33
//
Query:       gi|488601287|ref|YP_007907758.1|  [L=157]
Description: RNA-binding protein, containing PUA domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-19   69.2   1.2    4.5e-19   68.2   1.2    1.5  1  PUA       PUA domain
      3e-18   65.9   0.9    9.3e-18   64.3   1.1    1.7  2  DUF1947   Domain of unknown function (DUF1947)
      1e-05   26.1   0.8    0.00053   20.6   0.8    2.4  1  Pre-PUA   Pre-PUA-like domain
    0.00014   22.0   0.3    0.00031   20.9   0.3    1.5  1  UPF0113   UPF0113 PUA domain
  ------ inclusion threshold ------
      0.062   13.3   0.0      0.096   12.7   0.0    1.2  1  NLPC_P60  NlpC/P60 family


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 !   68.2   1.2   1.3e-22   4.5e-19       2      74 .]      72     144 ..      71     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1.3e-22
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveiervl 74 
                                       +vvvd+gA  ++++ga+++ pG+v +++++ +gd V +  e+ + ++avG+a+++++e+    +gk+v+++++l
  gi|488601287|ref|YP_007907758.1|  72 KVVVDNGALPFVMNGADIMKPGIVYADEEINKGDFVFVTVEGkDSPIAVGIALVDGKEMIGK-KGKAVKNIHHL 144
                                       89***************************************769***************665.67777777765 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   1.1   2.6e-21   9.3e-18       2      65 ..       3      65 ..       2      66 .. 0.96
   2 ?   -2.6   0.0         2   7.1e+03      38      52 ..      70      84 ..      67      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.6e-21
                                      -EE--HHHHHHHHHHHHTTT---TT--..-EEEE-SS-EEEEETTEEEEEE.SSSEEE-HHHHHH CS
                           DUF1947  2 RHfLSkKeakeileklkekyisislesdkiEieeekkeklYlingvpilfe.eekliPtLklLlk 65
                                      R  L+kK+ak+i++ ++eky si++e+d i++ e +++k+Yl+n+ p+lfe +++++Pt+ +Llk
  gi|488601287|ref|YP_007907758.1|  3 RQRLRKKKAKRIKNLIAEKY-SIEIEGD-IDLVEIDGRKVYLVNDDPLLFEhDGEIYPTILALLK 65
                                      5569****************.******9.**********************************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                                      S-EEEEETTEEEEEE CS
                           DUF1947 38 keklYlingvpilfe 52
                                      ++k+ ++ng + ++ 
  gi|488601287|ref|YP_007907758.1| 70 GRKVVVDNGALPFVM 84
                                      678889999887776 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.8   1.5e-07   0.00053      49      85 ..      32      65 ..       1      66 [. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                           Pre-PUA 49 vvklqgehvelyvvdgeplffqdregellPtlytlwk 85
                                      +v +     ++y+v+++pl+f++ +ge++Pt+ +l k
  gi|488601287|ref|YP_007907758.1| 32 LVEID--GRKVYLVNDDPLLFEH-DGEIYPTILALLK 65
                                      44444..5689************.********99976 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   8.7e-08   0.00031       2      67 ..      73     141 ..      72     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.7e-08
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvV.lnengeplGiGkirkdt.k.aspgkivvknl 67 
                                       vvv+  a   ++ G d++k +i++ +e+++++++v+V +  ++ p+++G++  d+ +   ++++ vkn+
  gi|488601287|ref|YP_007907758.1|  73 VVVDNGALPFVMNGADIMKPGIVYADEEINKGDFVFVtVEGKDSPIAVGIALVDGkEmIGKKGKAVKNI 141
                                       66665455555679***********************889999***********986788999999997 PP

>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-05     0.096      49      99 ..      98     152 ..      87     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                                       GGG--TTEEEEESG..TGGESEEEEEE.ETTEEEEEETTEEE.EEETTSTTBHSC CS
                          NLPC_P60  49 kselkrGDLvffkt..kkgisHvgiYl.gngkmlhassekvs.vsslsekywkkr 99 
                                       ++e+++GD+vf+++  k+ +  vgi l ++++m+ ++++ v+ +++l+ ++w++ 
  gi|488601287|ref|YP_007907758.1|  98 DEEINKGDFVFVTVegKDSPIAVGIALvDGKEMIGKKGKAVKnIHHLKDRIWNTF 152
                                       6899**********88888889999765888999999887765888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 1022.26
//
Query:       gi|488601288|ref|YP_007907759.1|  [L=102]
Description: RNase P subunit RPR2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   33.6   1.1    5.9e-08   32.9   1.1    1.4  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
     0.0092   15.9   0.0       0.02   14.9   0.0    1.5  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.017   15.2   0.2      0.023   14.7   0.2    1.2  1  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   1.1   9.8e-12   5.9e-08      15      90 .]      27      89 ..      16      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 9.8e-12
                                      HH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
                              Rpr2 15 easpalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90
                                      +  ++lsr++++ + ++s k+++r+p++++ t+C+kC + + +  ++++r+ +  k          +  ++Cl Cg
  gi|488601288|ref|YP_007907759.1| 27 TDDSDLSRRYVELAMKISSKYRVRIPKEYRNTFCRKCYTPF-KSENVKIRLLRGVK----------T--IECLVCG 89
                                      67899*********************************998.55677777754222..........2..8888886 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.3e-06      0.02       2      17 ..      42      57 ..      41      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-06
                                      EETTEEEEEE-CCCHH CS
                    MazE_antitoxin  2 kvGnsgavriPkevrf 17
                                      k++++++vriPke r 
  gi|488601288|ref|YP_007907759.1| 42 KISSKYRVRIPKEYRN 57
                                      899**********995 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   3.8e-06     0.023      11      37 ..      56      91 ..      48      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-06
                               DZR 11 darfCseCgtklkavaa.........edrCpsCgek 37
                                      ++ fC +C t+ k+++           + C  Cg+k
  gi|488601288|ref|YP_007907759.1| 56 RNTFCRKCYTPFKSENVkirllrgvkTIECLVCGYK 91
                                      566*********9655599***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:01.02
# Mc/sec: 302.08
//
Query:       gi|488601289|ref|YP_007907760.1|  [L=368]
Description: nucleoside-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-82  275.2   0.0    5.9e-82  275.0   0.0    1.0  1  Bmp       ABC transporter substrate-binding protein PnrA-like


Domain annotation for each model (and alignments):
>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.0   0.0   3.3e-86   5.9e-82       2     298 ..      36     331 ..      35     335 .. 0.95

  Alignments for each domain:
  == domain 1  score: 275.0 bits;  conditional E-value: 3.3e-86
                                       EEEEEECSS-TTTSCHHHHHHHHHHHHHHHCTTEEEEEEEEC.GGGHHHHHHHHHHCTT-SEEEEESCCHHHHHHHH CS
                               Bmp   2 vkvavlvegtidDksfnessyeGirrlkkeqnieliskesslltdedyiadlknlkeegsdlivatgfalqdalqev 78 
                                        kva++++++i D+++++ ++ G++ +++ + +e++++e++     d ++++++ +e+g+d+i++t+f ++d +++v
  gi|488601289|ref|YP_007907760.1|  36 LKVAFVYVSPIGDAGWSYAHDLGRKFIEEHYPVETKYSEAVP-EGPDAERVIREYAEQGYDIIFTTSFGYMDPTITV 111
                                       689***************************************.5********************************* PP

                                       HHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEECSS-SCCCHHCHHHHHHHHHHH-T CS
                               Bmp  79 ssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvgGveipvvksfingFeaGikyvnp 155
                                       ++dfp++ F++++++++++  nv ++++r++++++L+G++a+ m+ktnkig+v++ +ip+v + in+F++G+k+vnp
  gi|488601289|ref|YP_007907760.1| 112 AKDFPNTVFMHCSGYKTAK--NVGTYFGRMYQARYLSGLVAGSMTKTNKIGYVAAHPIPEVIRGINAFALGVKKVNP 186
                                       *******************..******************************************************** PP

                                       T-EEEEEE-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--CGCSTTCCEEEEE CS
                               Bmp 156 dievvvkvagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsnyvIgvdkdqsylapenvitsii 232
                                       d++v v ++gt++D++k+k++A sl ++g+dvi++  +++++g ++aa+e+g++  +Ig+++d+s++ap++++t  i
  gi|488601289|ref|YP_007907760.1| 187 DAKVIVVWTGTWYDPAKEKEAAISLLDQGCDVIAQ--HQDSPGPQQAAEERGVY--SIGYNSDMSKFAPNAHLTAPI 259
                                       ***********************************..*****************..********************* PP

                                       EEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-........S--TCCHHHHCHHHHHHHHHHHCCCCHH CS
                               Bmp 233 knvedlvvsiiekvakgevlaggevitlglkegvvgld........eesdvledekvkeqlkkenkkiikeisv 298
                                       +n++ ++++++e+v+ g+  +++e i++g+++gvv l         ++ +++e+ek k++  + ++++++++++
  gi|488601289|ref|YP_007907760.1| 260 WNWSVIYSYVVENVMAGT--WKSEEIWWGIDKGVVDLApfnkvvpeDVRKIVEQEKEKYLKGEVPEQYPFVGPI 331
                                       ******************..******************666777766677777777777777777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2215.70
//
Query:       gi|488601290|ref|YP_007907761.1|  [L=170]
Description: Acetyltransferase, including N-acetylase of ribosomal protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-20   74.1   0.0    1.3e-20   73.8   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    9.2e-13   49.1   0.0    1.1e-12   48.8   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    4.4e-12   46.0   0.0    5.9e-12   45.6   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.4e-11   44.7   0.0    2.1e-11   44.1   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.8e-08   34.7   0.1    2.4e-08   34.3   0.1    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00022   21.3   0.0     0.0075   16.4   0.0    2.6  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0026   17.7   0.0     0.0047   16.9   0.0    1.4  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.085   12.5   0.0       0.23   11.2   0.0    1.7  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
        0.1   12.8   0.0       0.16   12.2   0.0    1.3  1  PK_C             Pyruvate kinase, alpha/beta domain
       0.13   11.7   0.0       0.17   11.3   0.0    1.3  1  GNAT_acetyltr_2  GNAT acetyltransferase 2


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 !   73.8   0.0   7.2e-24   1.3e-20      14     117 .]      40     144 ..      18     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 7.2e-24
                                       HHHHHHHHHHHHHHHHSTTCEEEE.EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHH CS
                    Acetyltransf_1  14 ppnedaseeefeesfsleaegllv.aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeera 89 
                                       p +e+ + ++ +  +sle + ++v +  dg+++G ++l+k + +k  +++  ++aV+p+y++kG+G+aLl+++ee+a
  gi|488601290|ref|YP_007907761.1|  40 PKRERMEKDRIRFLASLESNLTVVaVTNDGKVVGQCQLFKSDSPKLSHVAKVGIAVAPSYWRKGIGTALLRKIEEIA 116
                                       33333344444445777888556659999**************988899999************************* PP

                                       HHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  90 reegikkivlaveedndaairlYeklGF 117
                                       ++egi ki+++v ++n+aa +l++k G+
  gi|488601290|ref|YP_007907761.1| 117 KSEGIIKIEAEVIAPNTAALNLFKKNGY 144
                                       ***********************88997 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   6.1e-16   1.1e-12       4     137 ..      14     144 ..       7     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 6.1e-16
                    Acetyltransf_3   4 LrplteeDlealfelrsdpevmry.lpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeede 79 
                                       L  +tee +e +++++s+  v  y + +p+ + +++++++ ++a+   e++++ + v++d++v+G + l++ +    
  gi|488601290|ref|YP_007907761.1|  14 LEDYTEEKYEFIYNWMSQ--VADYlYFTPKRERMEKDRIR-FLAS--LESNLTVVAVTNDGKVVGQCQLFKSDSPKL 85 
                                       566777777888899995..77886555677777777777.5554..3455554444688878*******9888776 PP

                    Acetyltransf_3  80 e..aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                       +  a +g+ +aps+w+kG++t  +r + e+a + +g+ +++a++ + N+a  ++++k G+
  gi|488601290|ref|YP_007907761.1|  86 ShvAKVGIAVAPSYWRKGIGTALLRKIEEIA-KSEGIIKIEAEVIAPNTAALNLFKKNGY 144
                                       699****************************.7777999*******************97 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   3.3e-15   5.9e-12       3     112 ..      15     150 ..      13     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.3e-15
                   Acetyltransf_10   3 adyseegi...............etf.kefispealreri.eegealllvaeeggkivGviel.rdgs....hisll 57 
                                       +dy+ee++                t  +e ++++++r     e++ ++++++++gk+vG ++l +++s    h++ +
  gi|488601290|ref|YP_007907761.1|  15 EDYTEEKYefiynwmsqvadylyFTPkRERMEKDRIRFLAsLESNLTVVAVTNDGKVVGQCQLfKSDSpklsHVAKV 91 
                                       567777777777777766666665566788888888888844999999***************99988977777665 PP

                   Acetyltransf_10  58 ..fVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgee 112
                                         +V+p+y ++Gig+aLl ++ee a+ +gi + e +v a + +a ++++k G+++ g+ 
  gi|488601290|ref|YP_007907761.1|  92 giAVAPSYWRKGIGTALLRKIEEIAKSEGIIKiEAEVIAPNtAALNLFKKNGYHQEGRR 150
                                       88***************************999*********99************9764 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.2e-14   2.1e-11       5      75 ..      62     145 ..      56     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.2e-14
                                       EEEEEETTEEEEEEEEEEES......TCTEE..EEE-GGGTTSSHHHHHHHH.TT....SEEEEE.EEEE...THHH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld......aeitr..laVdpeyrgkGiGraLlea.ae....kgiile.qlel...naek 64 
                                       v  + +dgk+vG++ l  +d          +  +aV+p+y +kGiG+aLl+  +e    +gii + ++e+   n ++
  gi|488601290|ref|YP_007907761.1|  62 VVAVTNDGKVVGQCQLFKSDspklshVA--KvgIAVAPSYWRKGIGTALLRKiEEiaksEGII-KiEAEViapN-TA 134
                                       4556788*******99999998874333..367*****************9641245678855.3445554333.39 PP

                                       HHHHHHHTTEE CS
                    Acetyltransf_7  65 aikfYeklGFe 75 
                                       a+++++k+G++
  gi|488601290|ref|YP_007907761.1| 135 ALNLFKKNGYH 145
                                       9********97 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   1.3e-11   2.4e-08      38     153 ..      50     163 ..       9     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.3e-11
                    Acetyltransf_4  38 ekflealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienl 114
                                        +fl++l   +  v  v +++++vG+++l + ++   ++ a + + +a      +g+g +l+  +e+++k  +i ++
  gi|488601290|ref|YP_007907761.1|  50 IRFLASL-ESNLTVVAVTNDGKVVGQCQLFKSDSPKLSHVAKVGIAVA-PSYWRKGIGTALLRKIEEIAKSEGIIKI 124
                                       2777777.66677778888***********999988899999999998.7899************************ PP

                    Acetyltransf_4 115 laeiaspnensiqfhkalGFelvgifkkcikkngrwiDm 153
                                       +ae+++pn+++ +++k+ G+  +g+  k ++ +g   D+
  gi|488601290|ref|YP_007907761.1| 125 EAEVIAPNTAALNLFKKNGYHQEGRRLKKFNFKGSLVDE 163
                                       ***********************9998888888877776 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.11     2e+02      96     120 ..      11      35 ..       8      39 .. 0.84
   2 !   16.4   0.0   4.2e-06    0.0075      30     107 ..      48     121 ..      33     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                                       HHHHHHHHHTT--EEEE--SSHHHH CS
                    Acetyltransf_9  96 araleemreegqplsllfPssipiY 120
                                       +++le++ ee++++++ + s+++ Y
  gi|488601290|ref|YP_007907761.1|  11 KASLEDYTEEKYEFIYNWMSQVADY 35 
                                       6799*************98887666 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.2e-06
                                       HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT CS
                    Acetyltransf_9  30 eireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreeg 106
                                       ++ +++  l ++  v+ + ++g++vgq++l++ +       l   + +g+avap + ++g+ ++Ll++  e +++eg
  gi|488601290|ref|YP_007907761.1|  48 DRIRFLASLESNLTVVAVTNDGKVVGQCQLFKSDSPK----LSHVAKVGIAVAPSYWRKGIGTALLRKIEEIAKSEG 120
                                       44455566666667888888**********9988654....444444689**********************99997 PP

                                       - CS
                    Acetyltransf_9 107 q 107
                                       +
  gi|488601290|ref|YP_007907761.1| 121 I 121
                                       5 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.6e-06    0.0047      27      79 ..      93     146 ..      86     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                                       EEE-GGG-SSSHHHHHHHHHHHHHHH.S-S.-EEEEEETT-HHHHHHHHHHT-EE CS
                              FR47  27 lqvlpehrrrGlgsrlvkalakeiae.rgk.tvllvvvasNtpsirlyeklGfek 79 
                                       + v p+  r+G g+ l +++ +eia+ +g+ ++ + v a Nt++ +l++k G+ +
  gi|488601290|ref|YP_007907761.1|  93 IAVAPSYWRKGIGTALLRKI-EEIAKsEGIiKIEAEVIAPNTAALNLFKKNGYHQ 146
                                       7899***************8.56777588625679999**************986 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.23      50     141 ..      66     148 ..      18     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                       EETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-H CS
                    Acetyltransf_8  50 lldgepvgyfeiYwakedelaeyydaepgdrGiHlligeaeargkglttallralvhylfadprtrrvvvEPdvrNe 126
                                       + dg+ vg  +++  k d      +   +   + ++++ +++ +kg++tallr++ + + +++++ ++ +E  + N+
  gi|488601290|ref|YP_007907761.1|  66 TNDGKVVGQCQLF--KSD-----SPKLSHVAKVGIAVA-PSYWRKGIGTALLRKIEEIA-KSEGIIKIEAEVIAPNT 133
                                       5556666666665..333.....344555566667888.56778*********986655.555************** PP

                                       HHHHHHHHTT-EEEE CS
                    Acetyltransf_8 127 rairllekaGfekek 141
                                       +a++l++k G+++e+
  gi|488601290|ref|YP_007907761.1| 134 AALNLFKKNGYHQEG 148
                                       ***********9876 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 ?   12.2   0.0   8.7e-05      0.16      31      99 ..      52     130 ..      48     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
                                       HHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH............TTS.HHHHHHHHHHHTTSS-STSEE CS
                              PK_C  31 liskyrpkvpiiavtpneltarqlalyrGvypvlvekakt.........aestde.llreavkvakeaglvkkgdev 97 
                                        ++ + +++ ++avt++ ++  q++l++  +p l   ak           + + + llr++ ++ak++g++k + ev
  gi|488601290|ref|YP_007907761.1|  52 FLASLESNLTVVAVTNDGKVVGQCQLFKSDSPKLSHVAKVgiavapsywRKGIGTaLLRKIEEIAKSEGIIKIEAEV 128
                                       567788899********************99999777666999998888666655589999**************** PP

                                       EE CS
                              PK_C  98 vv 99 
                                       ++
  gi|488601290|ref|YP_007907761.1| 129 IA 130
                                       97 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.3e-05      0.17      86     131 ..      78     123 ..      54     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.3e-05
                   GNAT_acetyltr_2  86 qdeefaslsGaRivRiAvhpelqkmGYGsralellekyyegklssl 131
                                        +++ ++ls +  v iAv p++ ++G G++ l+++e+  + +   +
  gi|488601290|ref|YP_007907761.1|  78 FKSDSPKLSHVAKVGIAVAPSYWRKGIGTALLRKIEEIAKSEGIIK 123
                                       4567789999999**********************99887665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1067.18
//
Query:       gi|488601291|ref|YP_007907762.1|  [L=271]
Description: putative metal-dependent hydrolase of the TIM-barrel fold protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-48  166.6   0.0    1.2e-48  166.3   0.0    1.0  1  Amidohydro_2  Amidohydrolase
    7.2e-08   32.1   0.0    9.4e-07   28.5   0.0    2.1  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
        0.1   11.2   0.1       0.13   10.8   0.1    1.1  1  GvpD          GvpD gas vesicle protein


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 !  166.3   0.0   2.1e-52   1.2e-48       1     288 [.       3     267 ..       3     267 .. 0.93

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 2.1e-52
                                       EEEEEEE..SHHHCCCCCCGGCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHHH......HHHHH CS
                      Amidohydro_2   1 iDvHaHllppeaairddgepngfdpeerlafmkragvdpqlaspeallvlnaaagiaravivaalc......rgann 71 
                                       +D+Ha+l+         +e +++ p +++  + r + +++ +s+e +l+ ++ ag+++av+v   +      +  n+
  gi|488601291|ref|YP_007907762.1|   3 VDTHAQLWT--------REVIESLPRSMVDSYSRVFGKDFSISVEKMLADMDEAGVEKAVVVGVDAettysyKVSND 71 
                                       7*******9........88****************************************665544400011155566 PP

                                       HHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE CS
                      Amidohydro_2  72 rvlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdih 148
                                        v     +  +r++++a v+p+ ++ a++e+ r v +l fkG+++ ph ++ +++++  + +i++a++++glp+ +h
  gi|488601291|ref|YP_007907762.1|  72 AVYRAYEESGGRLIPFAGVDPHKGKVALKEIDRIV-KLNFKGLKFMPHLHELNPNDPKMY-EIYRAANDYGLPLLFH 146
                                       6888888899*************************.*********************999.**************** PP

                                       ....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEEC CS
                      Amidohydro_2 149 tGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfds 225
                                       tG     +  + + ++ +  pl+l++va++fP+lki++aH+G+p  ++++al+ ++r +nvy+ + g        +s
  gi|488601291|ref|YP_007907762.1| 147 TG-----TQFHKGSKIKYCRPLYLDDVAVDFPDLKIIIAHFGYP--WYEEALAVVRRNENVYFNIAG--------WS 208
                                       99.....8899999******************************..*******************99........9* PP

                                       CHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHH CS
                      Amidohydro_2 226 pladppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarl 288
                                       p+++p+++ r  + +  d++lfG+DyP  ++++ +e+l++l l    ++   ek+++ NA r+
  gi|488601291|ref|YP_007907762.1| 209 PKYIPEVVIRQMNSILSDKVLFGTDYPLMNYKRVVEELKQLNL----KETTYEKMFYRNAKRI 267
                                       ******************************************9....*************995 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.6e-10   9.4e-07      11     215 ..      33     241 ..       3     266 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.6e-10
                                       CCTTTHHHHHHHHHHTTEEEEEEE-SSG.......GGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHH CS
                        TatD_DNase  11 efeedreeileraeeagvaavvvvgtss.......kdskavlelakkypnkvyavlGiHPnevdeasedlleelkel 80 
                                       +f+ + e+ l+ ++eagv++ vvvg++        ++++av +  +++ +++++ +G+ P++ +        +lke+
  gi|488601291|ref|YP_007907762.1|  33 DFSISVEKMLADMDEAGVEKAVVVGVDAettysykVSNDAVYRAYEESGGRLIPFAGVDPHKGKV-------ALKEI 102
                                       34445899999*****************999998447779********************87773.......33444 PP

                                       HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HH...........HHHHHHHHCG CS
                        TatD_DNase  81 anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaee...........dlleilkeaa 146
                                            +++v +   GL ++++ ++      +++ e  r+A +++lpl  H++  +             l +++ +  
  gi|488601291|ref|YP_007907762.1| 103 -----DRIVKLNFKGLKFMPHLHELNPNDPKMY-EIYRAANDYGLPLLFHTGTQFHkgskikycrplYLDDVAVD-- 171
                                       .....3444445568999777766666666665.678****************4442433433333222233333.. PP

                                       GCCS....EEEETT--S-HHHHHHHHHT..TEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCT CS
                        TatD_DNase 147 eaka....kvvlHsfsgsaeeakkflkl..gyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyr 215
                                          +     ++ H     +eea +++ +  ++y+ ++g++++   + +++ + ++ +d++L +TD+P ++   +r
  gi|488601291|ref|YP_007907762.1| 172 ---FpdlkIIIAHFGYPWYEEALAVVRRneNVYFNIAGWSPKYIPEVVIRQMNSILSDKVLFGTDYPLMNY--KR 241
                                       ...144535666776677788888885456***********9999999999*****************998..33 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   2.2e-05      0.13     334     409 ..       5      82 ..       1      91 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.2e-05
                              GvpD 334 slaekylenaittskddaidP.drltgsdyvisleggrlk.ydiyiaivervreesegPllyvismdtayeafetrl 408
                                        +a+ ++  +i + +  ++d   r+ g+d+ is+e+     ++  ++++ +v  ++e  + y +s d +y+a+e   
  gi|488601291|ref|YP_007907762.1|   5 THAQLWTREVIESLPRSMVDSySRVFGKDFSISVEKMLADmDEAGVEKAVVVGVDAETTYSYKVSNDAVYRAYEESG 81 
                                       566777777788888888887579**********98755425677888889999*******************9754 PP

                              GvpD 409 g 409
                                       g
  gi|488601291|ref|YP_007907762.1|  82 G 82 
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1900.68
//
Query:       gi|488601292|ref|YP_007907763.1|  [L=117]
Description: NADH:ubiquinone oxidoreductase subunit 3 (chain A) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  109.2   8.7    1.1e-31  108.9   8.7    1.2  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
     0.0026   17.6   1.8     0.0029   17.4   1.8    1.0  1  DUF443       Protein of unknown function (DUF443)
  ------ inclusion threshold ------
       0.02   14.6   2.1      0.024   14.3   2.1    1.2  1  TMEM72       Transmembrane protein family 72
       0.33   10.9   4.1       0.25   11.2   1.1    1.8  2  DUF2721      Protein of unknown function (DUF2721)
       0.42   11.1   3.4       0.46   10.9   1.2    1.9  2  MerC         MerC mercury resistance protein


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   8.7   3.1e-35   1.1e-31       2      99 .]      19     114 ..       6     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 3.1e-35
                                       HHHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHH CS
                       Oxidored_q4   2 llllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfglieml 78 
                                       +l++++s+ll+p+k +kek ++YEcG ep+  a+ ++s+++y++a+lF+iFDve++fl+pwa+++k  ++  +++ +
  gi|488601292|ref|YP_007907763.1|  19 FLAYIVSRLLRPEKLEKEKYTTYECGEEPITPAWYQYSLQYYMYAILFVIFDVEILFLYPWALQMK--NTEIFVAGM 93 
                                       57889**********************************************************998..5567899** PP

                                       HHHHHHHHHHHHHHHH-S-XX CS
                       Oxidored_q4  79 lFllillvglvYewkkgaLeW 99 
                                       +Fl+i++vglvYew+kg+LeW
  gi|488601292|ref|YP_007907763.1|  94 IFLFIVFVGLVYEWSKGILEW 114
                                       ********************* PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.8   8.1e-07    0.0029      94     188 ..       5     102 ..       1     110 [. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.1e-07
                            DUF443  94 vnliillivlllvlvlriyiskklkkklynevelekkskekiilipkslknfllllfaylfflglvilalvali... 167
                                       + +++  +++++  +l  ++s+ l+ +  ++ +++ ++  +  ++p   ++ l++ ++ ++f+ + +  l ++    
  gi|488601292|ref|YP_007907763.1|   5 LTVMVYSVTVIAFAFLAYIVSRLLRPEKLEKEKYTTYECGEEPITPAWYQYSLQYYMYAILFVIFDVEILFLYPwal 81 
                                       4445555555555555555666666555666688999999999***999************9999988877775667 PP

                            DUF443 168 etqniiilivlllllfllfll 188
                                       +++n+ i+++ +++lf++f++
  gi|488601292|ref|YP_007907763.1|  82 QMKNTEIFVAGMIFLFIVFVG 102
                                       ******************986 PP

>> TMEM72  Transmembrane protein family 72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.1   6.7e-06     0.024      45     110 ..       9      74 ..       3     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.7e-06
                            TMEM72  45 llsgvavsvlEisyfvalllevclrckeesllfelwkkvrrlggfqkfllYvllsvacflhpvlvw 110
                                       + s +++ +  ++y+v+ ll+     ke+ +++e+ ++      +q +l Y + ++++ ++ v++ 
  gi|488601292|ref|YP_007907763.1|   9 VYSVTVIAFAFLAYIVSRLLRPEKLEKEKYTTYECGEEPITPAWYQYSLQYYMYAILFVIFDVEIL 74 
                                       445667889999*********************************************999998875 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.18   6.3e+02      69      88 ..       7      26 ..       2      33 .. 0.54
   2 ?   11.2   1.1     7e-05      0.25      63     121 ..      53     108 ..      51     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.18
                           DUF2721 69 llvlsallvvlvvlllflsa 88
                                      ++v s+++++++ l++++s 
  gi|488601292|ref|YP_007907763.1|  7 VMVYSVTVIAFAFLAYIVSR 26
                                      44445555555555555544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7e-05
                           DUF2721  63 irrailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslllflrEir 121
                                        ++++  ++ ++l+v++ v +lfl   + + l++  + +fv+++++l++  + +++E++
  gi|488601292|ref|YP_007907763.1|  53 YQYSLQYYMYAILFVIFDVEILFL---YPWALQMKNTEIFVAGMIFLFIVFVGLVYEWS 108
                                       6778889999**************...8889999******************9999975 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2       0.1   3.8e+02      65      84 ..      11      30 ..       3      74 .. 0.52
   2 ?   10.9   1.2   0.00013      0.46      41      84 ..      63     106 ..      46     117 .] 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.1
                              MerC 65 svlvlgalGllillvalflg 84
                                      sv+v++ + l+ ++  l+ +
  gi|488601292|ref|YP_007907763.1| 11 SVTVIAFAFLAYIVSRLLRP 30
                                      44445444444444444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                              MerC  41 vllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflg 84 
                                        +l+++  + +l l++ + + ++t ++v g++ l+i++v+l+++
  gi|488601292|ref|YP_007907763.1|  63 AILFVIFDVEILFLYPWALQMKNTEIFVAGMIFLFIVFVGLVYE 106
                                       444555567889999999**********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 800.96
//
Query:       gi|488601293|ref|YP_007907764.1|  [L=167]
Description: NADH dehydrogenase subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-26   91.8   0.1    4.2e-26   91.3   0.1    1.2  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 !   91.3   0.1   2.3e-30   4.2e-26       3     131 .]      38     148 ..      37     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 2.3e-30
                                       HHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEE CS
                       Oxidored_q6   3 GcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviav 79 
                                       +c i+l+a+  + +d      +r+++   a+++         +adv++v+G vt+k+++ +++l+e+++++k+via+
  gi|488601293|ref|YP_007907764.1|  38 CCAIELMAMGAPRFDG----VERFGMLARATPR---------QADVMIVSGWVTNKMAPVVRRLYEQMPEPKYVIAM 101
                                       4999998888888888....4788777778888.........9********************************** PP

                                       SHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHHH CS
                       Oxidored_q6  80 GtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetllal 131
                                       G+CA++GG +   ++++ +  v ++++ +pvd+++pGCPp+pea+l+++++l
  gi|488601293|ref|YP_007907764.1| 102 GECAISGGPW--FDSYN-V--VDGVDRIIPVDVYVPGCPPRPEALLDGIVKL 148
                                       *********9..34223.4..469***********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1089.69
//
Query:       gi|488601294|ref|YP_007907765.1|  [L=155]
Description: NADH (or F420H2) dehydrogenase, subunit C [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-43  145.8   0.1    1.1e-42  145.5   0.1    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.1   5.9e-47   1.1e-42       2     121 ..      37     152 ..      36     153 .. 0.97

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 5.9e-47
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STHH CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllsleknerirvkvevdeeepevpSvtdlfpgad 78 
                                       ++++++l+e+++f+kd   lgfd+ls+++++D+ ++ +evvyh  s+ +++ i+ +v++++++p+++Svtd++ +ad
  gi|488601294|ref|YP_007907765.1|  37 EIDRDSLHEFCRFIKD---LGFDHLSCIVGIDR-KDYLEVVYHAWSYIHRVMISARVKLPADDPVIDSVTDIWGSAD 109
                                       799*************...*************7.6****************************************** PP

                                       HHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS----- CS
                    Complex1_30kDa  79 wyEREayDmfGivfeghpdlrrillpedfeghPLRkdfplsge 121
                                       w+EREa+DmfG+ f++hp+l+rillpedf+g+PLRk+f+l+++
  gi|488601294|ref|YP_007907765.1| 110 WHEREAFDMFGVIFSNHPKLKRILLPEDFKGFPLRKEFQLKER 152
                                       ***************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 895.61
//
Query:       gi|488601295|ref|YP_007907766.1|  [L=367]
Description: NADH dehydrogenase subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-93  312.6   0.1    3.2e-90  301.9   0.1    2.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    4.1e-06   26.0   0.0    5.7e-05   22.2   0.0    2.0  2  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.9   0.1   3.6e-94   3.2e-90       5     271 .]     126     367 .]     121     367 .] 0.97

  Alignments for each domain:
  == domain 1  score: 301.9 bits;  conditional E-value: 3.6e-94
                                       HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHS CS
                    Complex1_49kDa   5 ltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtk 81 
                                       +t+++y+freRekild++e++tGaRl ++y+riGGv+ Dlp g+++ +++fl+ele +++++e+l+ +n+if++Rt+
  gi|488601295|ref|YP_007907766.1| 126 FTLMMYTFREREKILDMFEMLTGARLGYNYMRIGGVSDDLPLGFTDYVRTFLEELEVRMEDYERLVYDNEIFIARTE 202
                                       7**************************************************************************** PP

                                       SSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT CS
                    Complex1_49kDa  82 gvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqalek 158
                                       g+gvls ++a++lg+tGpvlR+sGv+ D+Rk+epY++Y+eld+++++g++gD+++R+ v +eEm+ S++I+eq+l++
  gi|488601295|ref|YP_007907766.1| 203 GIGVLSPDKAINLGATGPVLRGSGVRRDVRKDEPYSIYHELDWKIITGKRGDCLSRVSVWIEEMKMSAEIVEQLLDS 279
                                       ***************************************************************************** PP

                                       --.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-H CS
                    Complex1_49kDa 159 lpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirap 235
                                       +p+g++ a+ +kv+                         + ++gevy+++E+p+Gelgv+lvsdgs +pyrlkir+p
  gi|488601295|ref|YP_007907766.1| 280 IPAGSIRAKVPKVI-------------------------RPKEGEVYSRIESPRGELGVHLVSDGSARPYRLKIRSP 331
                                       *****999777664.........................4568********************************** PP

                                       HHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 236 sfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       +f+nl++l++++k+ llaD+++i+gsld+v+gevDR
  gi|488601295|ref|YP_007907766.1| 332 AFCNLSILPHISKDVLLADLIVIIGSLDPVFGEVDR 367
                                       ***********************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.4e-09   5.7e-05       1      68 [.      46     113 ..      46     116 .. 0.98
   2 ?    1.6   0.0     0.011     1e+02     386     438 ..     266     314 ..     241     328 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.4e-09
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhiv 68 
                                       RG+E+i ++r+  +   l+++   +  ++  +a v+ave+ +gi++p  a++ir ++   + + +h++
  gi|488601295|ref|YP_007907766.1|  46 RGFEKIAENRNYIQIIPLTDKLDYIASMANNMAYVKAVEELMGIEVPLRAEYIRVMVLELQRIASHLL 113
                                       9*****************************************************************87 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEE CS
                      NiFeSe_Hases 386 aellkewldelvenikkgdtetaneekldkkevpkeakGvglveapRGaLsHw 438
                                       +++  e +++l ++i +g  +    +k+ k   pke + +  +e pRG L+ +
  gi|488601295|ref|YP_007907766.1| 266 MKMSAEIVEQLLDSIPAGSIR----AKVPKVIRPKEGEVYSRIESPRGELGVH 314
                                       566778899999999998333....334556667899*************843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        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 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2324.12
//
Query:       gi|488601296|ref|YP_007907767.1|  [L=324]
Description: NADH:ubiquinone oxidoreductase subunit 1 (chain H) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-115  386.0  17.3   1.3e-115  385.8  17.3    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 !  385.8  17.3  7.2e-120  1.3e-115       3     297 ..      19     315 ..      17     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: 385.8 bits;  conditional E-value: 7.2e-120
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHH CS
                            NADHdh   3 lllllvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalila 79 
                                       +l+++ ++ + v++l+++eRk++Ar+q+R+GPnr+G++G+lq++aD+lKl+lKedi+p+++d++ + lapvl+++la
  gi|488601296|ref|YP_007907767.1|  19 ALIVVGMISVSVLILIWAERKIIARLQHRYGPNRAGKFGILQTIADGLKLFLKEDITPAGVDRITYSLAPVLCFALA 95 
                                       5788889999999**************************************************************** PP

                                       HCTTTTS-SSS..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh  80 llafaviPfge..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvlla 154
                                       ++ f++iP+g+  ++adln+g+l+ila++sl+v+ +++aGw++n+kY llG+lR aa misyE++ gl+++++++ +
  gi|488601296|ref|YP_007907767.1|  96 MIPFIAIPVGRnyIVADLNAGILFILAVASLSVIPVMMAGWSANNKYNLLGGLRGAALMISYEIPAGLAIIGILVQS 172
                                       **********668**************************************************************** PP

                                       -SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHH CS
                            NADHdh 155 gslslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlv 231
                                       gsl l +iveaq+++wfil q+l+f +fli++++e  r PFDl eaesE+v+G++tEY+g+kfal++++ey++ vl 
  gi|488601296|ref|YP_007907767.1| 173 GSLRLADIVEAQRDGWFILPQFLGFAAFLISAFMESARPPFDLLEAESEIVQGWTTEYGGVKFALLMFGEYTHSVLS 249
                                       *****************999********************************************************* PP

                                       HHHHHHHCT.SS-HCCSHHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                            NADHdh 232 salavllFlgGwllpfsgllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                       ++l+++l+lgGwl+pf + lw+++K+ll++++++w+ra+++R+R+dq++++gwkvl+p+al+n+++
  gi|488601296|ref|YP_007907767.1| 250 AMLIAILYLGGWLGPFDSSLWLIIKALLVMIFLMWVRASVARIRIDQMLNFGWKVLIPIALLNIVI 315
                                       ****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1971.72
//
Query:       gi|488601297|ref|YP_007907768.1|  [L=126]
Description: Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-11   42.6  15.4    6.1e-06   25.8   3.4    2.2  2  Fer4      4Fe-4S binding domain
    1.2e-09   38.6  14.2      2e-09   37.9  14.2    1.3  1  Fer4_7    4Fe-4S dicluster domain
    1.3e-07   31.6  12.9    2.1e-07   31.0  12.9    1.3  1  Fer4_9    4Fe-4S dicluster domain
    1.6e-07   31.6   5.1     0.0043   17.5   1.1    2.2  2  Fer4_8    4Fe-4S dicluster domain
    2.3e-07   30.5  10.1     0.0016   18.4   1.9    2.4  2  Fer4_2    4Fe-4S binding domain
      2e-06   27.8  13.9    3.7e-06   27.0  13.9    1.5  1  Fer4_10   4Fe-4S dicluster domain
    1.5e-05   25.8  15.1     0.0017   19.3   1.2    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00012   22.1  14.8     0.0023   18.0  15.5    2.0  2  Fer4_21   4Fe-4S dicluster domain
    0.00025   21.5  13.3       0.11   13.1   2.3    2.3  2  Fer4_17   4Fe-4S dicluster domain
     0.0035   17.4  17.9      0.072   13.2   2.8    2.5  2  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.033   15.0   9.6       0.28   12.1   0.5    2.2  2  Fer4_22   4Fe-4S dicluster domain
      0.034   14.4   2.5      0.034   14.4   2.5    2.2  2  Fer4_18   4Fe-4S dicluster domain
      0.038   14.9   4.8      0.038   14.9   4.8    2.3  2  Fer4_3    4Fe-4S binding domain
      0.059   13.9  15.7        1.2    9.8   2.1    2.4  2  Fer4_4    4Fe-4S binding domain
          2    9.0  15.2        2.7    8.6   2.3    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        5.9    7.7  11.6        0.7   10.7   0.3    2.6  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   4.3   5.3e-08   5.9e-05       3      24 .]      38      59 ..      36      59 .. 0.90
   2 !   25.8   3.4   5.4e-09   6.1e-06       4      20 ..      77      93 ..      74      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.3e-08
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                      +  +kC++C  C+  CP+++I+
  gi|488601297|ref|YP_007907768.1| 38 YYVDKCTACLSCERNCPNNCIR 59
                                      6679****************96 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.4e-09
                                      ETTTSSS-THHHHHSTT CS
                              Fer4  4 deekCigCGaCvevCPv 20
                                         +C++CG+CvevCP+
  gi|488601297|ref|YP_007907768.1| 77 FAGRCMFCGICVEVCPT 93
                                      5689************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 !   37.9  14.2   1.8e-12     2e-09       1      51 [.      42      94 ..      42      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.8e-12
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt..ekveidpekClgCgaCvavCPtg 51
                                      +C+ C  C+++Cp+++i+++ ++++k++  e++ + + +C++Cg Cv+vCPt+
  gi|488601297|ref|YP_007907768.1| 42 KCTACLSCERNCPNNCIRIKTRKENKKRivEEYIYFAGRCMFCGICVEVCPTK 94
                                      7******************9886666544566667799*************95 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0  12.9   1.9e-10   2.1e-07       1      49 [.      42      94 ..      42      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.9e-10
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkg 49
                                      kCt C +C++ Cp++ ++ +  ++  +  + +e      +C++Cg Cve+Cp++
  gi|488601297|ref|YP_007907768.1| 42 KCTACLSCERNCPNNCIRIKTRKENKKR-IVEEyiyfaGRCMFCGICVEVCPTK 94
                                      7***************988776665554.33444889999************85 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.1   3.8e-06    0.0043      45      64 ..      37      56 ..       8      57 .. 0.78
   2 !   16.4   0.2   8.4e-06    0.0095      38      64 ..      72      94 ..      58     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
                            Fer4_8 45 eealwsCttcgaCtevCpvg 64
                                       +++++Ct+c +C+++Cp++
  gi|488601297|ref|YP_007907768.1| 37 VYYVDKCTACLSCERNCPNN 56
                                      46899*************87 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.4e-06
                            Fer4_8 38 eeqvleeeealwsCttcgaCtevCpvg 64
                                      ee      + +++C+ cg C+evCp++
  gi|488601297|ref|YP_007907768.1| 72 EEY----IYFAGRCMFCGICVEVCPTK 94
                                      333....46789999999999999985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.9   1.4e-06    0.0016       4      22 .]      37      55 ..      34      55 .. 0.88
   2 !   16.7   1.3   5.1e-06    0.0058       8      22 .]      79      93 ..      72      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                      v+  d+C++C +C  +CP+
  gi|488601297|ref|YP_007907768.1| 37 VYYVDKCTACLSCERNCPN 55
                                      67789*************5 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.1e-06
                            Fer4_2  8 drCigCgaCvsaCPa 22
                                       rC+ Cg+Cv +CP+
  gi|488601297|ref|YP_007907768.1| 79 GRCMFCGICVEVCPT 93
                                      58999*********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 !   27.0  13.9   3.3e-09   3.7e-06       4      56 .]      38      92 ..      35      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.3e-09
                           Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrk..kvekCtgcgaCveaCP 56
                                      +  d+C+ C  C + CP +  + ++++e+++  +++     ++C++cg Cve+CP
  gi|488601297|ref|YP_007907768.1| 38 YYVDKCTACLSCERNCPNNCIRIKTRKENKKRIVEEYiyFAGRCMFCGICVEVCP 92
                                      5679**************9988888888888888887557899***********9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7  16.3   9.2e-06      0.01       1      66 [.      42      93 ..      42      94 .. 0.78
   2 !   19.3   1.2   1.5e-06    0.0017       1      30 [.      80     111 ..      80     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.2e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                      +C+ C  C   CP n+i+ k      +r+      ++kk++ e++      +++++C+iC++vCP 
  gi|488601297|ref|YP_007907768.1| 42 KCTACLSCERNCPNNCIRIK------TRK------ENKKRIVEEYIYFA--GRCMFCGICVEVCPT 93
                                      5*****************99......222......23455555565555..99************7 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.5e-06
                           Fer4_16   1 rCgtCgkCaevCPt..naikekkekeiearec 30 
                                       rC  Cg C+evCPt  +ai+++ e+e++++  
  gi|488601297|ref|YP_007907768.1|  80 RCMFCGICVEVCPTkpKAIRMTDEYELASDSR 111
                                       6999*********9777999998888776655 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   5.0    0.0001      0.11      37      58 ..      39      59 ..      27      60 .. 0.87
   2 !   18.0  15.5     2e-06    0.0023       6      59 .]      41     100 ..      39     100 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                           Fer4_21 37 vedeCvGCnlCssvCPvedcie 58
                                        d+C++C  C   CP ++ci+
  gi|488601297|ref|YP_007907768.1| 39 YVDKCTACLSCERNCP-NNCIR 59
                                      469*************.7**97 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2e-06
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidakt..vl......kvvedeCvGCnlCssvCPv.edciem 59 
                                       dkC  C +C   C++   ++i+i++++  +        + + +C+ C +C++vCP+  ++i+m
  gi|488601297|ref|YP_007907768.1|  41 DKCTACLSCERNCPN---NCIRIKTRKenKKriveeyIYFAGRCMFCGICVEVCPTkPKAIRM 100
                                       79************7...6665443321122123321334779************95577776 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   5.3    0.0002      0.22      42      59 ..      39      56 ..      19      58 .. 0.86
   2 !   13.1   2.3   9.6e-05      0.11      41      58 ..      76      93 ..      56      96 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                      ++++C+ C  Cer CP++
  gi|488601297|ref|YP_007907768.1| 39 YVDKCTACLSCERNCPNN 56
                                      6899************97 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.6e-05
                           Fer4_17 41 ekaslCieCgeCerkCPq 58
                                        a++C+ Cg C+++CP 
  gi|488601297|ref|YP_007907768.1| 76 YFAGRCMFCGICVEVCPT 93
                                      478999999999999996 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   7.3   0.00093         1       7      23 ..      41      57 ..      40      59 .. 0.90
   2 !   13.2   2.8   6.4e-05     0.072       9      22 ..      81      94 ..      76      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00093
                            Fer4_6  7 dkCigCgdCvrvCPega 23
                                      dkC+ C  C+r+CP + 
  gi|488601297|ref|YP_007907768.1| 41 DKCTACLSCERNCPNNC 57
                                      8*************765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.4e-05
                            Fer4_6  9 CigCgdCvrvCPeg 22
                                      C  Cg Cv vCP++
  gi|488601297|ref|YP_007907768.1| 81 CMFCGICVEVCPTK 94
                                      555*********93 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.0    0.0085       9.6       1      28 [.      42      68 ..      42      77 .. 0.73
   2 ?   12.1   0.5   0.00025      0.28       1      15 [.      80      94 ..      80     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0085
                           Fer4_22  1 rClsCgaCtlvCptCsCfdvedetkees 28
                                      +C +C +C   Cp   C++++ ++++++
  gi|488601297|ref|YP_007907768.1| 42 KCTACLSCERNCPN-NCIRIKTRKENKK 68
                                      7***********96.5777766664333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00025
                           Fer4_22  1 rClsCgaCtlvCptC 15
                                      rC+ Cg C  vCpt 
  gi|488601297|ref|YP_007907768.1| 80 RCMFCGICVEVCPTK 94
                                      7************94 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   4.1      0.27   3.1e+02      59      74 ..      41      56 ..      37      65 .. 0.79
   2 ?   14.4   2.5     3e-05     0.034      53      74 ..      73      94 ..      57     108 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.27
                           Fer4_18 59 gdcidcescvkvcPtg 74
                                       +c++c sc + cP +
  gi|488601297|ref|YP_007907768.1| 41 DKCTACLSCERNCPNN 56
                                      579**********975 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3e-05
                           Fer4_18 53 rkekgagdcidcescvkvcPtg 74
                                      +    ag c+ c+ cv+vcPt+
  gi|488601297|ref|YP_007907768.1| 73 EYIYFAGRCMFCGICVEVCPTK 94
                                      33456899************96 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   8.4      0.59   6.6e+02       1      14 [.      43      56 ..      43      57 .. 0.90
   2 ?   14.9   4.8   3.4e-05     0.038       1      14 [.      81      94 ..      81      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.59
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      Ct C  C++ CP++
  gi|488601297|ref|YP_007907768.1| 43 CTACLSCERNCPNN 56
                                      999*88******97 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.4e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ Cg CvevCP++
  gi|488601297|ref|YP_007907768.1| 81 CMFCGICVEVCPTK 94
                                      99**********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 ?    9.2   5.9    0.0017       1.9       2      16 ..      41      55 ..      41      63 .. 0.92
   2 ?    9.8   2.1    0.0011       1.2       3      16 ..      80      93 ..      78     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++C+ C sC++ CP 
  gi|488601297|ref|YP_007907768.1| 41 DKCTACLSCERNCPN 55
                                      79************5 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      rC  Cg Cv +CP+
  gi|488601297|ref|YP_007907768.1| 80 RCMFCGICVEVCPT 93
                                      8999*********7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.3      0.02        23       4      18 ..      41      55 ..      40      60 .. 0.91
   2 ?    8.6   2.3    0.0025       2.7       5      18 ..      80      93 ..      78      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.02
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      d+C+ac +C   +P+
  gi|488601297|ref|YP_007907768.1| 41 DKCTACLSCERNCPN 55
                                      59************7 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0025
                           Fer4_13  5 tCiacgaCvelaPd 18
                                      +C+ cg+Cve++P 
  gi|488601297|ref|YP_007907768.1| 80 RCMFCGICVEVCPT 93
                                      7************5 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   5.5       1.3   1.4e+03       8      64 ..      43      58 ..      40      70 .. 0.66
   2 ?   10.7   0.3   0.00063       0.7       7      19 ..      80      95 ..      78     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.3
                           Fer4_15  8 CigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                      C+ c  C +++                                         P  +I
  gi|488601297|ref|YP_007907768.1| 43 CTACLSCERNC-----------------------------------------PNNCI 58
                                      55555555555.........................................55555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00063
                           Fer4_15  7 aCigcglCvaea...p 19
                                      +C+ cg Cv+++   p
  gi|488601297|ref|YP_007907768.1| 80 RCMFCGICVEVCptkP 95
                                      8***********5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 810.81
//
Query:       gi|488601298|ref|YP_007907769.1|  [L=159]
Description: NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-28   98.0  16.3    5.1e-28   97.6  16.3    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
     0.0022   18.1  14.0     0.0022   18.1  14.0    2.4  3  DUF4040      Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
        3.8    7.3   5.7       0.98    9.2   0.4    2.6  3  Spore_YhaL   Sporulation protein YhaL


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6  16.3   8.5e-32   5.1e-28       1     144 []      16     155 ..      16     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 8.5e-32
                                       HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----.TTCHHHHH CS
                       Oxidored_q3   1 gallvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeep.eslsrsla 76 
                                       +a++v+ ++ ++ sal+++l+f+++aglfill+aeF+a++q l+Y+GA++v++lF+iml++++e + + ++  + l 
  gi|488601298|ref|YP_007907769.1|  16 SAIMVVHAREVFNSALYMALLFIATAGLFILLDAEFVAVVQTLIYAGAVTVILLFAIMLTKREEGKDMlRTDINPLK 92 
                                       69*********************************************************844333333033333344 PP

                                       HHHHHHHHHHHHHHTT--......--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHC CS
                       Oxidored_q3  77 laalligllllalllllllessssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaivl 144
                                       ++++++++l ++ l+ +     s+    ++  ++++  i+s lf++y+l fel+++lLLv+li +++l
  gi|488601298|ref|YP_007907769.1|  93 VISIILFALAIIPLAGT-----SKILLIKKGIYGSPYIIASELFERYVLHFELIAILLLVTLISSVYL 155
                                       44344444444443333.....444556677899*****************************99986 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  14.0   3.7e-07    0.0022       2      66 ..      12      76 ..      11      77 .. 0.96
   2 ?   -0.4   0.1      0.22   1.3e+03      52      62 ..      93     103 ..      90     106 .. 0.82
   3 ?   -2.1   0.3      0.74   4.4e+03      57      59 ..     145     147 ..     137     156 .. 0.46

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-07
                           DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlp 66
                                      +++ +a+++v ar++++++++++++ +++a lf+ll+A  vA  q ++ +g +tv+ll+a+  ++
  gi|488601298|ref|YP_007907769.1| 12 IILFSAIMVVHAREVFNSALYMALLFIATAGLFILLDAEFVAVVQTLIYAGAVTVILLFAIMLTK 76
                                      7999********************************************************98876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.22
                           DUF4040  52 glttvllllal 62 
                                       +++++l++la+
  gi|488601298|ref|YP_007907769.1|  93 VISIILFALAI 103
                                       78999999986 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.74
                           DUF4040  57 lll 59 
                                       ll+
  gi|488601298|ref|YP_007907769.1| 145 LLV 147
                                       111 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   0.00016      0.98       8      22 ..       9      23 ..       7      26 .. 0.84
   2 ?   -0.6   0.0      0.18   1.1e+03       9      21 ..      64      76 ..      59      83 .. 0.69
   3 ?   -3.0   0.1       1.1   6.3e+03       8      19 ..     145     156 ..     142     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00016
                        Spore_YhaL  8 viagIlfSgymavkt 22
                                      + a IlfS++m+v++
  gi|488601298|ref|YP_007907769.1|  9 LWAIILFSAIMVVHA 23
                                      5689*********98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.18
                        Spore_YhaL  9 iagIlfSgymavk 21
                                      +  Il+ ++m+ k
  gi|488601298|ref|YP_007907769.1| 64 VTVILLFAIMLTK 76
                                      5567888888755 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.1
                        Spore_YhaL   8 viagIlfSgyma 19 
                                       + + ++ S+y+a
  gi|488601298|ref|YP_007907769.1| 145 LLVTLISSVYLA 156
                                       456677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1174.79
//
Query:       gi|488601299|ref|YP_007907770.1|  [L=100]
Description: NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-19   67.4   8.7    8.4e-19   67.2   8.7    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.047   13.7   0.2      0.059   13.4   0.2    1.2  1  BMC          BMC domain


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   8.7   9.4e-23   8.4e-19       2     102 ..       7      94 ..       6      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 9.4e-23
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaiviga 78 
                                       + ll+++l liG+ygv+++rn++++l+++e++++++n++l++++++               d+ +q+lv + ++i+ 
  gi|488601299|ref|YP_007907770.1|   7 YILLSTTLLLIGAYGVIVSRNVIRILMCIEIMMSSANVNLIAFSNYL-------------SDISGQILVTFSLAIAG 70 
                                       67999*****************************************9.............***************** PP

                                       HHHHHHHHHHHHHHHHSSS-BCCG CS
                       Oxidored_q2  79 aetavgLallvrlyreygtddvqe 102
                                       ae+++g ++++ ++r+y++++ + 
  gi|488601299|ref|YP_007907770.1|  71 AEASIGFGIILLIFRTYHSTEASL 94 
                                       ******************998765 PP

>> BMC  BMC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.5e-06     0.059       1      38 [.      19      59 ..      19      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-06
                                      EEEEEEEESHHHHHHHHHHHHHHSSEEEEEEEECTTT...C CS
                               BMC  1 AlGlietrglaaaieaaDaalKaAnVelvgvekvggg...k 38
                                      A G+i +r++  +++++  ++ +AnV+l+ +++  +    +
  gi|488601299|ref|YP_007907770.1| 19 AYGVIVSRNVIRILMCIEIMMSSANVNLIAFSNYLSDisgQ 59
                                      89***************************998877633553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 647.23
//
Query:       gi|488601300|ref|YP_007907771.1|  [L=483]
Description: multisubunit sodium/proton antiporter, MrpD subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-58  196.5  31.2    5.3e-58  196.5  31.2    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
    7.1e-05   22.8   0.2    7.1e-05   22.8   0.2    3.3  3  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 ?   -2.8   0.2      0.31   2.8e+03     229     259 ..      98     129 ..      82     130 .. 0.65
   2 !  196.5  31.2   5.9e-62   5.3e-58       1     291 [.     132     421 ..     132     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.31
                   Proton_antipo_M 229 trdirayggLak.kmPilalvllvlllslaGl 259
                                         +i ++++L++ ++  ++++++++l +++G+
  gi|488601300|ref|YP_007907771.1|  98 LYSIGYMRSLREhSQTRYFACFAIALSATMGI 129
                                       45666777777744455777888888888886 PP

  == domain 2  score: 196.5 bits;  conditional E-value: 5.9e-62
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       a++L++lyl++E+  +++ylL+    +++++  A+ k+f++ l +s++ L +i+l y +tgt++f +   +   g  
  gi|488601300|ref|YP_007907771.1| 132 AGNLITLYLFYEILTVSTYLLVVHE-ESVEAFFAGWKYFVYLLGASVMQLSAIVLTYVYTGTTDFSYGGVF---GNI 204
                                       78********************988.788*************************************99999...999 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla...vssneisqll 150
                                       ++e+ +lll+++++  +K+a++p+h Wlp a + aPtpvsall A  +vkagv+ ++r +++++     s +is l+
  gi|488601300|ref|YP_007907771.1| 205 KPEIAILLLIFFIAGYTKAAVMPFHSWLPTA-MIAPTPVSALLhAVAVVKAGVFSILRGVFFIIgyqNLSADISVLF 280
                                       9999999************************.***********9999***********9999887778899****** PP

                   Proton_antipo_M 151 lilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyere 227
                                       +   +i+++++sl al+q ++K  lAyS++s+l y+++++++ t  g+ + i+h+ +ha+ k++lF +ags+ y  +
  gi|488601300|ref|YP_007907771.1| 281 AYFVSITIIVASLFALSQDNLKLRLAYSTVSQLSYIILGALLLTPSGMIGGIFHIASHAFGKITLFFCAGSI-YVSS 356
                                       *********************************************************************999.7788 PP

                   Proton_antipo_M 228 ktrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasv 291
                                         ++i +++g+  kmPi+ + +++++l++ GlPp agF+sk+++  + +++++i l+++ +v+s+
  gi|488601300|ref|YP_007907771.1| 357 GLKNISEMSGIGRKMPITMISFAIATLTMIGLPPGAGFISKWYLALGTIEMHQIPLLIVlLVSSI 421
                                       ****************************************************9988887677765 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 ?   -5.0   1.3         2   1.8e+04      27      36 ..      12      21 ..       9      24 .. 0.49
   2 !   22.8   0.2   7.9e-09   7.1e-05      12      56 ..      72     118 ..      68     120 .. 0.91
   3 ?   -4.1   0.4         2   1.8e+04      25      36 ..     280     288 ..     274     295 .. 0.46

  Alignments for each domain:
  == domain 1  score: -5.0 bits;  conditional E-value: 2
                   Proton_antipo_N 27 lvvtfvsllv 36
                                      ++v++v++l 
  gi|488601300|ref|YP_007907771.1| 12 ILVSMVASLL 21
                                      4555555443 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 7.9e-09
                   Proton_antipo_N  12 ieigfllDklsalmllvvtfvsllvhlYSigYMad..degyqRFfay 56 
                                       +e+++ +D + + ++++ +++  l  lYSigYM++  + +++R+fa+
  gi|488601300|ref|YP_007907771.1|  72 VELKLKVDAFGMFFATTASLLWILNTLYSIGYMRSlrEHSQTRYFAC 118
                                       68999****************************9544999*****97 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 2
                   Proton_antipo_N  25 mllvvtfvsllv 36 
                                       ++ +v   s  +
  gi|488601300|ref|YP_007907771.1| 280 FAYFV---SITI 288
                                       33333...3332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3035.25
//
Query:       gi|488601301|ref|YP_007907772.1|  [L=85]
Description: hypothetical protein Asulf_01808 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   11.2   0.1       0.17   11.0   0.1    1.1  1  ECSIT     Evolutionarily conserved signalling intermediate in


Domain annotation for each model (and alignments):
>> ECSIT  Evolutionarily conserved signalling intermediate in Toll pathway
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.6e-06      0.17      33      74 ..      10      52 ..       2      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.6e-06
                             ECSIT 33 lfekaagekkdkatfleave.vfekrsvrrrghveFiyaAlkk 74
                                      l ek  +++k ++ f  ++  +f +    rr+hveF+++A+  
  gi|488601301|ref|YP_007907772.1| 10 LVEKGENRRKLRRIFYIVLAiTFISDFFIRREHVEFVWQAIPG 52
                                      3344555666677787777625888888***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 580.47
//
Query:       gi|488601302|ref|YP_007907773.1|  [L=592]
Description: multisubunit sodium/proton antiporter, MrpD subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-47  160.6  23.0    4.6e-47  160.6  23.0    2.3  2  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.6     0.071   1.3e+03      37      61 ..      61      86 ..      14     110 .. 0.66
   2 !  160.6  23.0   2.6e-51   4.6e-47       1     288 [.     115     387 ..     115     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.071
                   Proton_antipo_M 37 klflltllgsliLLlgil.llynltg 61
                                      + ++l+++ +l+++++ + ++ +++g
  gi|488601302|ref|YP_007907773.1| 61 YNLVLSRVDDLSMVFAYVfVIMAFAG 86
                                      44555555555555554434444554 PP

  == domain 2  score: 160.6 bits;  conditional E-value: 2.6e-51
                   Proton_antipo_M   1 andLlllylglElvllplylLigl....wkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskale 73 
                                       a+dL++ly+++E++ +++++Li l    w++k+k+l+A++ ++++ ++g +iLL gi+l   +tg++ef++++    
  gi|488601302|ref|YP_007907773.1| 115 AGDLFTLYIFWEIMAVSSVFLIWLnsdpWQEKKKALQAGFRYIMVHAAGGVILLGGIVLYILNTGSIEFDKIIYG-- 189
                                       78********************87333467899****************************************99.. PP

                   Proton_antipo_M  74 lglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqll 150
                                                l+++l+l+++++ +a+ pl+ Wl day ea++ +s+ + a + k +v++l+r ++ ++        +l
  gi|488601302|ref|YP_007907773.1| 190 --------DLASVLILISFMLNAAVPPLSAWLSDAYPEASVTGSVYMTAYTTKTAVYVLLRAFSGVE--------IL 250
                                       ........8999***********************************999**********9998888........9* PP

                   Proton_antipo_M 151 lilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyere 227
                                       ++l++i +++g + a+ ++di+rllAy  is++Gym+ +++++t+++++++  h + h+l kallF+ ag+vi+ + 
  gi|488601302|ref|YP_007907773.1| 251 IWLGAIMAVYGVIYAVLENDIRRLLAYHIISQVGYMVAGAGIGTEMAINGSASHAFCHILYKALLFMGAGAVIHVT- 326
                                       ************************************************************************9988. PP

                   Proton_antipo_M 228 ktrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavv 288
                                         r+++++gg + +mPi+ ++ +++ +s+++ P+++gF+sk ++++a+ + +l l++l+++
  gi|488601302|ref|YP_007907773.1| 327 GRRKLTELGGVYRYMPITLALYMIGGFSISAFPLFSGFVSKSMVISASAESHLPLIWLMLT 387
                                       99***************************************************99999843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 3363.07
//
Query:       gi|488601303|ref|YP_007907774.1|  [L=490]
Description: proton-translocating NADH-quinone oxidoreductase, chain M [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-70  235.5  27.2    7.4e-70  235.5  27.2    2.1  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0008   19.4   2.1     0.0008   19.4   2.1    4.8  5  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
     0.0033   17.5   9.4     0.0033   17.5   9.4    3.5  3  Oxidored_q5_N    NADH-ubiquinone oxidoreductase chain 4, amin
  ------ inclusion threshold ------
      0.042   13.6   0.3      0.042   13.6   0.3    2.8  5  Trp_oprn_chp     Tryptophan-associated transmembrane protein 
       0.67    9.7  10.1        4.9    6.9   1.3    3.5  3  Arteri_Gl        Arterivirus GL envelope glycoprotein


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   2.0      0.27   9.6e+02     142     167 ..      20      45 ..       1      92 [. 0.59
   2 !  235.5  27.2   2.1e-73   7.4e-70       1     289 [.     120     422 ..     120     426 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.27
                   Proton_antipo_M 142 ssneisqlllilaiismllgslvala 167
                                        + e+s +++++++  ++l s++ l 
  gi|488601303|ref|YP_007907774.1|  20 TKREVSRVVALISAFIAFLISVMMLL 45 
                                       33344444444444444444443333 PP

  == domain 2  score: 235.5 bits;  conditional E-value: 2.1e-73
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynl....tgtlefeelskal. 72 
                                       + d +l+y+++E+vl+p++++ig+w+ + ++ ++++k++++t ++s+++L gi+++y++    tg+  f+ l +   
  gi|488601303|ref|YP_007907774.1| 120 SLDFFLFYIFWEIVLIPMFFVIGIWGGE-RKDYSAIKFLIYTHVSSVVMLAGIFAIYHFnwidTGKATFDILTLLKn 195
                                       56899********************999.888999***********************9444457777777766654 PP

                   Proton_antipo_M  73 ..elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssnei 146
                                         +  + +l   +++l+ll+g+lvK+++vp+h+Wlpda+veaPt++s+llA++l+k+g+++l+r+l++++  +s++ 
  gi|488601303|ref|YP_007907774.1| 196 ysSIEIPQLWKDFIFLALLFGFLVKMPAVPFHTWLPDAHVEAPTVGSILLAGVLLKMGGYGLLRFLVPMSsNASEFF 272
                                       45556666667899********************************************************99999** PP

                   Proton_antipo_M 147 sqlllilaiismllgslvalaqtdiKrllAySsishlGymlialav........atqygveaaiihllthalfkall 215
                                         l++i +++s++++ ++al q diKrl+A+Ssi+h+G++ +++a+          + ++++a ++l++h+++++ +
  gi|488601303|ref|YP_007907774.1| 273 VLLIAIFGAVSIIYTPFAALPQKDIKRLIAFSSIGHMGFVSLGMAAalmagdvkYRVLALSGAGFQLFAHGIITSVM 349
                                       ***************************************9988877444232222345789**************** PP

                   Proton_antipo_M 216 FllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavva 289
                                       F  a +vi++ + +r ++++ggL+k+mP ++ ++++++++ +G P++agF+++f++L++a+a +++++++a+ +
  gi|488601303|ref|YP_007907774.1| 350 FGSA-GVIQHHVGSRLFEKLGGLMKSMPKFSFLMVIGFFASMGFPGMAGFVAEFSVLAGALALMPLFAIIALAS 422
                                       ****.6778888*******************************************************9998654 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 ?   -2.6   1.4       1.7   6.2e+03      22      37 ..      25      40 ..      23      44 .. 0.77
   2 !   19.4   2.1   2.2e-07    0.0008       3      41 ..      58      94 ..      56      95 .. 0.86
   3 ?   -1.3   1.6      0.65   2.3e+03      22      38 ..     152     168 ..     149     187 .. 0.72
   4 ?    0.4   0.0       0.2     7e+02       2      22 ..     177     197 ..     176     200 .. 0.84
   5 ?   -2.5   0.3       1.6   5.6e+03      21      41 ..     414     434 ..     406     435 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                   Proton_antipo_N 22 salmllvvtfvsllvh 37
                                      s +++l+  f+++l+ 
  gi|488601303|ref|YP_007907774.1| 25 SRVVALISAFIAFLIS 40
                                      6678888888888885 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.2e-07
                   Proton_antipo_N  3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSi 41
                                      +W+s  +l i+  + +D+ls+ m+l+ tf+sll  +Y++
  gi|488601303|ref|YP_007907774.1| 58 SWVS--SLGISYHVGVDGLSMPMVLLTTFISLLCVIYAW 94
                                      5665..566888999**********************97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.65
                   Proton_antipo_N  22 salmllvvtfvsllvhl 38 
                                       sa+  l+ t vs++v+l
  gi|488601303|ref|YP_007907774.1| 152 SAIKFLIYTHVSSVVML 168
                                       77778888888888874 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.2
                   Proton_antipo_N   2 ftWlsvgglsieigfllDkls 22 
                                       f+W+++g+ +++i  ll ++s
  gi|488601303|ref|YP_007907774.1| 177 FNWIDTGKATFDILTLLKNYS 197
                                       89******9999988887776 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 1.6
                   Proton_antipo_N  21 lsalmllvvtfvsllvhlYSi 41 
                                       l a+ +l    +s + h+Y++
  gi|488601303|ref|YP_007907774.1| 414 LFAIIALASIPLSIIYHIYAL 434
                                       566667777778888999986 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 !   17.5   9.4   9.3e-07    0.0033       6     108 ..       8     115 ..       1     117 [. 0.58
   2 ?   -1.0   1.4      0.53   1.9e+03       5      51 ..     134     180 ..     124     199 .. 0.58
   3 ?   -2.7   0.1       1.8   6.4e+03      95     101 ..     271     277 ..     258     314 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.3e-07
                     Oxidored_q5_N   6 lptlmliplvllskkkllwststlvslllallsll.l......lnlsssfsls...nlsyllglDslSapLilLSlW 72 
                                       l++l+  ++++ +k+++   + ++  ++ +l+s++ l      +n++++ s+     +sy +g+D lS+p++lL+++
  gi|488601303|ref|YP_007907774.1|   8 LVLLIGSLSAFATKREVSRVVALISAFIAFLISVMmLlnmdngFNHEENISWVsslGISYHVGVDGLSMPMVLLTTF 84 
                                       2222233445555555555555555555555566544122433444444444422257999**************** PP

                     Oxidored_q5_N  73 llpLmilASqkhlkkepknrqrlFllllilLlllLi 108
                                       ++ L+++  +     e  ++ + F  l+ilL ++L+
  gi|488601303|ref|YP_007907774.1|  85 ISLLCVIYAW-----EERFKANQFFGLIILLDFALV 115
                                       ****987322.....225556777788888887775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.53
                     Oxidored_q5_N   5 llptlmliplvllskkkllwststlvslllallsllllnlsssfsls 51 
                                       l+p++++i ++   +k +  + +++++ + ++++l  ++  ++f++ 
  gi|488601303|ref|YP_007907774.1| 134 LIPMFFVIGIWGGERKDYSAIKFLIYTHVSSVVMLAGIFAIYHFNWI 180
                                       34444444444444444555555666666666666644444445554 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.8
                     Oxidored_q5_N  95 lFlllli 101
                                       +F+ll++
  gi|488601303|ref|YP_007907774.1| 271 FFVLLIA 277
                                       2222222 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 ?   13.6   0.3   1.2e-05     0.042      45      87 ..       3      45 ..       1      84 [. 0.90
   2 ?   -4.0   0.1         3   1.1e+04      49      59 ..     164     174 ..     161     176 .. 0.64
   3 ?   -3.5   0.1       2.1   7.5e+03     122     138 ..     243     259 ..     234     266 .. 0.69
   4 ?   -3.3   0.2       1.9   6.9e+03      60      68 ..     320     328 ..     303     351 .. 0.56
   5 ?   -2.7   1.4       1.2   4.4e+03      42      60 ..     403     421 ..     388     424 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                      Trp_oprn_chp 45 ltalAlvllAaavAvlavrglgrrvvgvllalagagaavaals 87
                                      + a+ lvll + + ++a+++ + rvv+++ a ++++++v  l 
  gi|488601303|ref|YP_007907774.1|  3 ISAMLLVLLIGSLSAFATKREVSRVVALISAFIAFLISVMMLL 45
                                      57899******************************99987665 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3
                      Trp_oprn_chp  49 AlvllAaavAv 59 
                                       ++v+lA++ A+
  gi|488601303|ref|YP_007907774.1| 164 SVVMLAGIFAI 174
                                       46677777665 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.1
                      Trp_oprn_chp 122 alaggvllllagvllll 138
                                        l++gvll ++g  ll+
  gi|488601303|ref|YP_007907774.1| 243 ILLAGVLLKMGGYGLLR 259
                                       45666776666666655 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.9
                      Trp_oprn_chp  60 lavrglgrr 68 
                                       l+++ +  r
  gi|488601303|ref|YP_007907774.1| 320 LMAGDVKYR 328
                                       223333333 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 1.2
                      Trp_oprn_chp  42 apaltalAlvllAaavAvl 60 
                                       + ++ alAl+ l a++A++
  gi|488601303|ref|YP_007907774.1| 403 SVLAGALALMPLFAIIALA 421
                                       4456677777777777765 PP

>> Arteri_Gl  Arterivirus GL envelope glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.5    0.0027       9.8      68     102 ..       9      44 ..       2      57 .. 0.80
   2 ?    6.9   1.3    0.0014       4.9      64      98 ..     386     420 ..     375     439 .. 0.84
   3 ?   -0.5   0.1      0.26   9.3e+02      81     104 ..     444     467 ..     425     471 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0027
                         Arteri_Gl  68 vaal.sytgyvhvryvlssayaalalvAlvlgvysf 102
                                       v+ + s+ ++  +r v++++ ++ a++A++ +v+ +
  gi|488601303|ref|YP_007907774.1|   9 VLLIgSLSAFATKREVSRVVALISAFIAFLISVMML 44 
                                       344448899999*********************954 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                         Arteri_Gl  64 lflnvaalsytgyvhvryvlssayaalalvAlvlg 98 
                                       +f+++++ +++g+v+  +vl  a+a+++l+A++ +
  gi|488601303|ref|YP_007907774.1| 386 FFASMGFPGMAGFVAEFSVLAGALALMPLFAIIAL 420
                                       5677788899*********************9974 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.26
                         Arteri_Gl  81 yvlssayaalalvAlvlgvysfvv 104
                                         +s ay+   l+ l+++v ++v 
  gi|488601303|ref|YP_007907774.1| 444 KEYSEAYFHELLPLLIWVVATVVL 467
                                       55799999999999***9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3136.03
//
Query:       gi|488601304|ref|YP_007907775.1|  [L=469]
Description: proton-translocating NADH-quinone oxidoreductase, chain N [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-66  222.9  35.1    4.8e-66  222.9  35.1    2.2  2  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
        4.8    6.8  10.4         15    5.2  10.2    1.9  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 ?    0.0   2.5     0.043   3.9e+02     114     163 ..      61     109 ..      35     111 .. 0.80
   2 !  222.9  35.1   5.4e-70   4.8e-66       1     292 [.     110     404 ..     110     405 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.043
                   Proton_antipo_M 114 tpvsallAatlvkagvlllirlllllavssneisqlllilaiismllgsl 163
                                       tp s +++ + +++++++ +  l  ++   ++ +++l++l++ +m++ s+
  gi|488601304|ref|YP_007907775.1|  61 TPFSQFFSLVFLTVALFVCLSSLNSVS-RFEDEYYFLILLSTFGMMVVSM 109
                                       889999999999999999887777777.6677788999999999988776 PP

  == domain 2  score: 222.9 bits;  conditional E-value: 5.4e-70
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       ++d ++l++++E+ ++++y L+g+ k ++ s+eA++k+f+ + ++s +LL+gi+++y+++g++e+  + ++   +  
  gi|488601304|ref|YP_007907775.1| 110 SSDFIMLFIAFEIASIATYALAGFEKGSEFSVEAAFKYFIFGGFSSALLLFGISIVYGYAGSVEIASITRM-AEMEP 185
                                       7899*******************************************************************.77888 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllil 153
                                           +++l+++++g+ +Ksa+vp+h+W pd y ++Ptp+sallA+ + k+g  ++++++ l+a   + e++ l++++
  gi|488601304|ref|YP_007907775.1| 186 TAYSTIGLVMIVAGFGFKSALVPFHMWAPDTYHGSPTPISALLASSAKKMGFAGMFKVMILMAlAIKLEMYVLMAVI 262
                                       88999**********************************************************999999******** PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialavatqygve....aaiihllthalfkallFllagsviye. 225
                                       a+i+m lg+l+al q +iKr+lAySsi+h Gy+ +a+a+  + g++    +a++h+l+ha+ +a  F+ +    y+ 
  gi|488601304|ref|YP_007907775.1| 263 AVITMTLGNLAALMQESIKRMLAYSSIAHAGYISMAFAIFAISGMDmalaGAFLHVLSHAIATACAFVTV---AYAg 336
                                       *********************************9999996666665000055566666666666666555...4443 PP

                   Proton_antipo_M 226 rektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvl 292
                                           ++ ++ ++L  ++P++ + + ++llslaG+Ppt+gF+skf ++ +a++++l++l+l+ ++ s+l
  gi|488601304|ref|YP_007907775.1| 337 GYILDKADSFNSLGRRKPLIGISMSIILLSLAGIPPTLGFYSKFVLFLSAIEAKLLWLALIaLLNSAL 404
                                       5579999999*************************************************998887776 PP

>> GET2  GET complex subunit GET2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  10.2    0.0016        15     209     242 ..      85     132 ..      24     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0016
                              GET2 209 s...............alvralteasvrnFftvFltfEvvllsiyylll 242
                                       s               ++  ++++ s + F+++F++fE++++++y l+ 
  gi|488601304|ref|YP_007907775.1|  85 SvsrfedeyyflillsTFGMMVVSMS-SDFIMLFIAFEIASIATYALAG 132
                                       23334444447777654545555555.7*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2818.80
//
Query:       gi|488601305|ref|YP_007907776.1|  [L=359]
Description: HEAT repeat protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-49  164.4   9.8    1.1e-11   44.9   0.3    5.1  5  HEAT_2         HEAT repeats
    3.9e-37  123.1   0.6     0.0013   18.9   0.0    8.8  9  HEAT           HEAT repeat
    1.5e-22   79.6   1.4    0.00055   20.4   0.0    7.6  8  HEAT_EZ        HEAT-like repeat
    1.4e-18   65.6  14.5    0.00076   19.9   0.1    8.7  8  HEAT_PBS       PBS lyase HEAT-like repeat
    1.3e-13   51.3   7.8     0.0014   18.7   0.3    6.4  7  Cnd1           non-SMC mitotic condensation complex subunit 1
    3.4e-08   34.0   3.1        2.9    8.5   0.0    6.0  5  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
    6.2e-08   33.0   2.6       0.57   10.6   0.0    5.5  6  RasGEF_N_2     Rapamycin-insensitive companion of mTOR RasGEF
    7.8e-07   28.9   0.0      0.024   14.7   0.0    5.5  6  Arm            Armadillo/beta-catenin-like repeat
    1.4e-06   28.5   2.0       0.13   12.6   0.0    5.7  7  Cohesin_HEAT   HEAT repeat associated with sister chromatid c
    3.5e-05   23.5   4.6        2.2    7.8   0.0    5.3  6  CLASP_N        CLASP N terminal
    0.00092   19.3   0.6        5.5    7.0   0.0    4.1  4  Aconitase_B_N  Aconitate B N-terminal domain
     0.0028   17.8   1.3         14    5.9   0.0    4.4  4  RTP1_C1        Required for nuclear transport of RNA pol II C
  ------ inclusion threshold ------
      0.029   13.9   0.2         18    4.7   0.1    3.5  4  Tti2           Tti2 family
       0.04   13.1   0.0       0.93    8.6   0.0    2.8  3  Cnd3           Nuclear condensing complex subunits, C-term do
        1.3    7.7   7.7        6.1    5.5   0.1    4.0  5  API5           Apoptosis inhibitory protein 5 (API5)


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.3   9.4e-15   1.1e-11       2      73 ..      37     106 ..      36     109 .. 0.89
   2 !   34.0   0.0   2.4e-11   2.9e-08       2      75 ..      98     171 ..      97     171 .. 0.96
   3 !   42.2   0.1   6.7e-14     8e-11       3      60 ..     162     220 ..     160     240 .. 0.85
   4 !   40.5   0.1   2.3e-13   2.7e-10       2      59 ..     250     306 ..     249     309 .. 0.92
   5 !   33.3   0.0     4e-11   4.8e-08      10      74 ..     288     355 ..     287     359 .] 0.87

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 9.4e-15
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldd 73 
                                       + L+++l +d+dpevr+ a++aL +++ pe++ aL++ l d++++vR+  a++L ++ ++   ++L +++ d
  gi|488601305|ref|YP_007907776.1|  37 KGLIKLL-EDEDPEVRAGAADALSDFDKPEVISALINTLADKNREVRWRSAKSLERLCRD-KTDVLIQAFID 106
                                       6799*99.9**********************************************99885.67777777765 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 2.4e-11
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldddd 75 
                                       d+L+qa  ++++   + + +  Lgr+g+++a++ L e+ +  d +vRra + aLg+i+d+++l  L ++l+d+d
  gi|488601305|ref|YP_007907776.1|  98 DVLIQAFIDSKSIFQKVTLAYILGRLGDKKAIAPLAEAQNFGDKYVRRASVIALGRIRDERSLYYLIQSLKDPD 171
                                       7899999999999999******************************************************9985 PP

  == domain 3  score: 42.2 bits;  conditional E-value: 6.7e-14
                            HEAT_2   3 aLlqalendpdpevrraairaLgrig..npealpaLvellededpavRraaaeaLgaigd 60 
                                       +L+q l +dpd +vr++a++++grig  n+e+ ++L++ l+de+ +vR+a a+++ ++g+
  gi|488601305|ref|YP_007907776.1| 162 YLIQSL-KDPDADVRKRAVESIGRIGilNDEVKKTLLDSLKDENYEVRKASAKTIERLGL 220
                                       699***.9***************7754489*************************99984 PP

  == domain 4  score: 40.5 bits;  conditional E-value: 2.3e-13
                            HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaig 59 
                                       daL  al +d+d+++++ a +++ +ig ++a+++L +l+eded+ vR++a+ aLg+++
  gi|488601305|ref|YP_007907776.1| 250 DALEIAL-KDEDWNIKKWASEVISDIGGDKAIAILKKLAEDEDWTVRYHAVSALGRLK 306
                                       5666667.9**********************************************986 PP

  == domain 5  score: 33.3 bits;  conditional E-value: 4e-11
                            HEAT_2  10 ndpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgai......gdpealpaLkellddd 74 
                                       +d+d+ vr++a+ aLgr++    +++L++ l+d+dp+vR  a+e++  +      +d++ ++ Lke+l+  
  gi|488601305|ref|YP_007907776.1| 288 EDEDWTVRYHAVSALGRLKQ---IDLLIKHLDDPDPNVRDLAIEYIKDFvkvierKDSKKAEKLKEILQKH 355
                                       79**************9888...9**********************85544455489999******99865 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.1e-06    0.0025       5      27 ..      39      61 ..      36      63 .. 0.92
   2 !   11.2   0.1    0.0003      0.36       2      29 ..      67      94 ..      66      95 .. 0.92
   3 ?   -1.1   0.0       2.7   3.2e+03       5      28 ..     100     124 ..      98     126 .. 0.75
   4 ?    4.0   0.0     0.063        75      15      27 ..     142     154 ..     139     154 .. 0.89
   5 !   18.1   0.0   1.8e-06    0.0022       4      27 ..     162     185 ..     160     186 .. 0.90
   6 !   15.9   0.0   9.4e-06     0.011       4      27 ..     195     218 ..     194     222 .. 0.89
   7 !    7.9   0.0    0.0035       4.2       3      27 ..     250     274 ..     248     276 .. 0.87
   8 !   17.2   0.0   3.6e-06    0.0043       4      27 ..     282     305 ..     280     308 .. 0.86
   9 !   18.9   0.0     1e-06    0.0013       3      30 ..     309     336 ..     308     337 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                                      HHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT  5 llkllsDpspeVReaAakaLgal 27
                                      l+kll+D++peVR+ Aa aL ++
  gi|488601305|ref|YP_007907776.1| 39 LIKLLEDEDPEVRAGAADALSDF 61
                                      89******************986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0003
                                      HHHHHHHHT-SSHHHHHHHHHHHHHHHH CS
                              HEAT  2 lPlllkllsDpspeVReaAakaLgalae 29
                                      + +l++ l D++ eVR  +ak+L +l++
  gi|488601305|ref|YP_007907776.1| 67 ISALINTLADKNREVRWRSAKSLERLCR 94
                                      678999********************96 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.7
                                       HHHHH.T-SSHHHHHHHHHHHHHHH CS
                              HEAT   5 llkll.sDpspeVReaAakaLgala 28 
                                       l+++   ++s ++  + a+ Lg+l 
  gi|488601305|ref|YP_007907776.1| 100 LIQAFiDSKSIFQKVTLAYILGRLG 124
                                       5555437799999999999999985 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.063
                                       HHHHHHHHHHHHH CS
                              HEAT  15 eVReaAakaLgal 27 
                                        VR+a++ aLg++
  gi|488601305|ref|YP_007907776.1| 142 YVRRASVIALGRI 154
                                       6**********97 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 1.8e-06
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                        l++ l+Dp+++VR+ A++++g++
  gi|488601305|ref|YP_007907776.1| 162 YLIQSLKDPDADVRKRAVESIGRI 185
                                       578899****************98 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 9.4e-06
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +ll  l+D++ eVR+a+ak++ +l
  gi|488601305|ref|YP_007907776.1| 195 TLLDSLKDENYEVRKASAKTIERL 218
                                       58999***************9887 PP

  == domain 7  score: 7.9 bits;  conditional E-value: 0.0035
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       ++l  +l+D+++++ + A + + ++
  gi|488601305|ref|YP_007907776.1| 250 DALEIALKDEDWNIKKWASEVISDI 274
                                       5677789************999987 PP

  == domain 8  score: 17.2 bits;  conditional E-value: 3.6e-06
                                       HHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                       +l kl +D+++ VR+ A+ aLg+l
  gi|488601305|ref|YP_007907776.1| 282 ILKKLAEDEDWTVRYHAVSALGRL 305
                                       456777****************98 PP

  == domain 9  score: 18.9 bits;  conditional E-value: 1e-06
                                       HHHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgalaev 30 
                                       +ll+k l Dp+p+VR+ A++ + ++++v
  gi|488601305|ref|YP_007907776.1| 309 DLLIKHLDDPDPNVRDLAIEYIKDFVKV 336
                                       799**********************997 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.6e-07   0.00055      24      53 ..      30      59 ..      20      61 .. 0.83
   2 !   13.8   0.0   5.3e-05     0.064      27      55 .]      64      92 ..      63      92 .. 0.95
   3 ?   -2.2   0.0       5.6   6.7e+03      28      55 .]      99     123 ..      97     123 .. 0.81
   4 ?    5.8   0.0     0.017        21      38      55 .]     137     154 ..     126     154 .. 0.75
   5 !   11.4   0.0   0.00029      0.35      32      55 .]     162     185 ..     157     185 .. 0.93
   6 ?    5.0   0.0     0.029        35      31      55 .]     194     218 ..     190     218 .. 0.85
   7 !    7.7   0.0    0.0042         5      35      55 .]     284     305 ..     279     305 .. 0.79
   8 ?    6.2   0.0     0.013        16      30      49 ..     308     327 ..     306     328 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.6e-07
                           HEAT_EZ 24 plvpeilpaLlalLnddsdeVRaaAagaLg 53
                                      + ++  ++ L++lL+d+++eVRa Aa aL+
  gi|488601305|ref|YP_007907776.1| 30 LRIKGNVKGLIKLLEDEDPEVRAGAADALS 59
                                      55777899*********************8 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.3e-05
                           HEAT_EZ 27 peilpaLlalLnddsdeVRaaAagaLgnl 55
                                      pe++ aL+++L d++ eVR+ +a  L++l
  gi|488601305|ref|YP_007907776.1| 64 PEVISALINTLADKNREVRWRSAKSLERL 92
                                      89***********************9987 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.6
                           HEAT_EZ  28 eilpaLlalLnddsdeV..RaaAagaLgnl 55 
                                       +++ a++     ds+++  + + a+ Lg+l
  gi|488601305|ref|YP_007907776.1|  99 VLIQAFI-----DSKSIfqKVTLAYILGRL 123
                                       6788899.....999888888888888886 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.017
                           HEAT_EZ  38 nddsdeVRaaAagaLgnl 55 
                                       n  ++ VR a+++aLg++
  gi|488601305|ref|YP_007907776.1| 137 NFGDKYVRRASVIALGRI 154
                                       556788**********97 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00029
                           HEAT_EZ  32 aLlalLnddsdeVRaaAagaLgnl 55 
                                       +L++ L+d++++VR+ A+  +g++
  gi|488601305|ref|YP_007907776.1| 162 YLIQSLKDPDADVRKRAVESIGRI 185
                                       799*******************97 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.029
                           HEAT_EZ  31 paLlalLnddsdeVRaaAagaLgnl 55 
                                       + Ll  L+d++ eVR+a+a ++++l
  gi|488601305|ref|YP_007907776.1| 194 KTLLDSLKDENYEVRKASAKTIERL 218
                                       568888999888**********997 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0042
                           HEAT_EZ  35 alLnddsd.eVRaaAagaLgnl 55 
                                       + L  d+d +VR+ A+ aLg+l
  gi|488601305|ref|YP_007907776.1| 284 KKLAEDEDwTVRYHAVSALGRL 305
                                       445567779***********97 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.013
                           HEAT_EZ  30 lpaLlalLnddsdeVRaaAa 49 
                                       +++L++ L d++++VR  A+
  gi|488601305|ref|YP_007907776.1| 308 IDLLIKHLDDPDPNVRDLAI 327
                                       678999**********9996 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 !    9.9   0.0    0.0011       1.3       1      27 []      50      76 ..      50      76 .. 0.95
   2 ?    2.4   0.0      0.29   3.5e+02       1      24 [.      81     103 ..      81     106 .. 0.79
   3 !   12.2   0.1    0.0002      0.24       6      24 ..     117     135 ..     114     137 .. 0.92
   4 !   19.9   0.1   6.4e-07   0.00076       1      27 []     143     169 ..     143     169 .. 0.98
   5 ?    5.0   0.0     0.041        49       1      27 []     174     202 ..     174     202 .. 0.84
   6 ?    3.9   0.2     0.093   1.1e+02       1      27 []     207     258 ..     207     258 .. 0.70
   7 ?    2.5   0.0      0.26   3.1e+02       7      27 .]     269     289 ..     264     289 .. 0.81
   8 !   11.6   0.0   0.00032      0.38       1      27 []     294     317 ..     294     317 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                                      HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                      vR+ Aa aL  +  +e+i aL++ L+d
  gi|488601305|ref|YP_007907776.1| 50 VRAGAADALSDFDKPEVISALINTLAD 76
                                      8*********************98876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHCTSGGGHHHHHHH CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLlea 24 
                                       vR++ ak+L +l   +  ++L++a
  gi|488601305|ref|YP_007907776.1|  81 VRWRSAKSLERLCR-DKTDVLIQA 103
                                       8*********9987.666666666 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.0002
                                       HHHHHHCTSGGGHHHHHHH CS
                          HEAT_PBS   6 akaLgqlgdeeaipaLlea 24 
                                       a+ Lg+lgd+ ai++L ea
  gi|488601305|ref|YP_007907776.1| 117 AYILGRLGDKKAIAPLAEA 135
                                       899*************998 PP

  == domain 4  score: 19.9 bits;  conditional E-value: 6.4e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vRra + aLg+++de+++  L++ L+d
  gi|488601305|ref|YP_007907776.1| 143 VRRASVIALGRIRDERSLYYLIQSLKD 169
                                       9***********************998 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHCTS..GGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgd..eeaipaLleaLqd 27 
                                       vR +A++++g++g   +e+  +Ll  L+d
  gi|488601305|ref|YP_007907776.1| 174 VRKRAVESIGRIGIlnDEVKKTLLDSLKD 202
                                       89***********9888887777777766 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.093
                                       HHHHHHHHHHHCTS.........................GGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgd.........................eeaipaLleaLqd 27 
                                       vR a ak + +lg                          + ai+aL  aL+d
  gi|488601305|ref|YP_007907776.1| 207 VRKASAKTIERLGLkledneelalylsalmrgaelillgDKAIDALEIALKD 258
                                       56666777777776666666666666666666666777779*****999987 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.26
                                       HHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   7 kaLgqlgdeeaipaLleaLqd 27 
                                       + +  +g + ai++L+++ +d
  gi|488601305|ref|YP_007907776.1| 269 EVISDIGGDKAIAILKKLAED 289
                                       556779999********9887 PP

  == domain 8  score: 11.6 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR+ A+ aLg+l+    i++L++ L+d
  gi|488601305|ref|YP_007907776.1| 294 VRYHAVSALGRLKQ---IDLLIKHLDD 317
                                       9*************...*****99998 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 !   10.3   0.0   0.00045      0.53      54      86 ..      30      62 ..      24      65 .. 0.87
   2 ?    4.7   0.1     0.024        28      59     102 ..      66     109 ..      61     117 .. 0.76
   3 ?   -0.3   0.0      0.84     1e+03      33      47 ..     139     153 ..     125     162 .. 0.77
   4 !   18.7   0.3   1.2e-06    0.0014       2      86 ..     143     219 ..     142     230 .. 0.80
   5 !    8.1   0.1    0.0021       2.5      20      49 ..     190     220 ..     188     278 .. 0.78
   6 ?    5.3   0.0     0.016        19      23      82 ..     249     302 ..     228     307 .. 0.56
   7 !   12.4   0.2    0.0001      0.12      23     102 ..     280     353 ..     276     358 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                              Cnd1 54 vkekgflselaklleDenprVvanalaalteis 86
                                       + kg ++ l klleDe+p+V+a a  al++  
  gi|488601305|ref|YP_007907776.1| 30 LRIKGNVKGLIKLLEDEDPEVRAGAADALSDFD 62
                                      567999999****************99999875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                              Cnd1  59 flselaklleDenprVvanalaalteiseksenaiynllpdiis 102
                                       ++s l + l D+n++V+  +  +l+ + + +++ +++ ++d+ s
  gi|488601305|ref|YP_007907776.1|  66 VISALINTLADKNREVRWRSAKSLERLCRDKTDVLIQAFIDSKS 109
                                       67888888888888888888888888888877888888877655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.84
                              Cnd1  33 edpyVRktaaivvak 47 
                                        d yVR+  +i++ +
  gi|488601305|ref|YP_007907776.1| 139 GDKYVRRASVIALGR 153
                                       689*****9999876 PP

  == domain 4  score: 18.7 bits;  conditional E-value: 1.2e-06
                              Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakL.ilndmvkekgflselaklleDenprVvan 77 
                                       +R   +++lg ir +  + yl+    ++LkD+d+ VRk a+  + ++ ilnd vk     ++l++ l+Den +V++ 
  gi|488601305|ref|YP_007907776.1| 143 VRRASVIALGRIRDERSLYYLI----QSLKDPDADVRKRAVESIGRIgILNDEVK-----KTLLDSLKDENYEVRKA 210
                                       6667777777777776666666....5789**********************999.....579999********998 PP

                              Cnd1  78 alaalteis 86 
                                       +   ++ + 
  gi|488601305|ref|YP_007907776.1| 211 SAKTIERLG 219
                                       877776665 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0021
                              Cnd1  20 eylvepLrkrLkDedpyVRktaaivvakL.i 49 
                                       +++ + L  +LkDe+  VRk  a ++ +L +
  gi|488601305|ref|YP_007907776.1| 190 DEVKKTLLDSLKDENYEVRKASAKTIERLgL 220
                                       6677789999*************99999862 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.016
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaal 82 
                                       ++ L+ +LkDed  ++k a  v++ +         + ++ l+kl eDe+ +V+  a++al
  gi|488601305|ref|YP_007907776.1| 249 IDALEIALKDEDWNIKKWASEVISDIGG------DKAIAILKKLAEDEDWTVRYHAVSAL 302
                                       5555555555555555555555544322......12244455555555555555555555 PP

  == domain 7  score: 12.4 bits;  conditional E-value: 0.0001
                              Cnd1  23 vepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek...senaiynl 96 
                                       +  L+k  +Ded +VR +a+ ++ +L         ++++ l k l+D++p+V+++a+  +++  +    ++++  + 
  gi|488601305|ref|YP_007907776.1| 280 IAILKKLAEDEDWTVRYHAVSALGRL---------KQIDLLIKHLDDPDPNVRDLAIEYIKDFVKVierKDSKKAEK 347
                                       55688888999999999999999988.........57889999*************999988776643233444444 PP

                              Cnd1  97 lpdiis 102
                                       l++i++
  gi|488601305|ref|YP_007907776.1| 348 LKEILQ 353
                                       555555 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.067        80      71      89 ..      37      55 ..      30      63 .. 0.81
   2 !    8.5   0.0    0.0024       2.9      27      68 ..      65     106 ..      57     118 .. 0.83
   3 ?    3.2   0.1      0.11   1.3e+02      31      53 ..     162     184 ..     146     218 .. 0.72
   4 ?    5.7   0.0     0.019        22      27      51 ..     278     302 ..     245     308 .. 0.73
   5 !    7.3   0.0    0.0061       7.3      29      66 ..     308     345 ..     304     357 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.067
                     Vac14_Fab1_bd 71 dalvklvaDsdesvksgae 89
                                      ++l+kl+ D+d++v+ ga+
  gi|488601305|ref|YP_007907776.1| 37 KGLIKLLEDEDPEVRAGAA 55
                                      5688999999999998874 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0024
                     Vac14_Fab1_bd  27 eivkpvlkcfsDkdsrvRyyacEslyniakvakgevlkllne 68 
                                       e+++ +++++ Dk+++vR+ ++ sl  +++   + +++ + +
  gi|488601305|ref|YP_007907776.1|  65 EVISALINTLADKNREVRWRSAKSLERLCRDKTDVLIQAFID 106
                                       68999********************99999999999988854 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.11
                     Vac14_Fab1_bd  31 pvlkcfsDkdsrvRyyacEslyn 53 
                                        ++++++D d+ vR  a+Es+  
  gi|488601305|ref|YP_007907776.1| 162 YLIQSLKDPDADVRKRAVESIGR 184
                                       56778888888888888888644 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.019
                     Vac14_Fab1_bd  27 eivkpvlkcfsDkdsrvRyyacEsl 51 
                                       + ++++ k  +D+d  vRy+a+ +l
  gi|488601305|ref|YP_007907776.1| 278 KAIAILKKLAEDEDWTVRYHAVSAL 302
                                       44666667789*********99887 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0061
                     Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEslyniakvakgevlkll 66 
                                       ++ ++k ++D d  vR  a+E++   +kv++ +  k+ 
  gi|488601305|ref|YP_007907776.1| 308 IDLLIKHLDDPDPNVRDLAIEYIKDFVKVIERKDSKKA 345
                                       678999**********************9987655544 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.078        93      10      32 ..      39      61 ..      35      67 .. 0.87
   2 !   10.6   0.0   0.00048      0.57       6      44 ..      66     106 ..      66     123 .. 0.80
   3 ?    1.3   0.0      0.37   4.4e+02       8      29 ..     161     182 ..     159     194 .. 0.86
   4 ?    1.3   0.0      0.36   4.3e+02       9      32 ..     195     218 ..     188     243 .. 0.80
   5 ?   -1.9   0.0       3.6   4.3e+03      24      44 ..     247     268 ..     228     288 .. 0.75
   6 !   10.5   0.0   0.00052      0.62       7      36 ..     308     337 ..     307     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.078
                        RasGEF_N_2 10 lvnqLydqsrevvaaaleiLeea 32
                                      l++ L+d+++ev+a a+++L ++
  gi|488601305|ref|YP_007907776.1| 39 LIKLLEDEDPEVRAGAADALSDF 61
                                      8999****************876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00048
                        RasGEF_N_2   6 giellvnqLydqsrevvaaaleiLeeacddk..eslevlve 44 
                                       +i+ l+n L d++rev+  +++ Le+ c dk    ++++++
  gi|488601305|ref|YP_007907776.1|  66 VISALINTLADKNREVRWRSAKSLERLCRDKtdVLIQAFID 106
                                       5889*************************996444555555 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.37
                        RasGEF_N_2   8 ellvnqLydqsrevvaaaleiL 29 
                                         l+++L+d++ +v++ a+e +
  gi|488601305|ref|YP_007907776.1| 161 YYLIQSLKDPDADVRKRAVESI 182
                                       5699**************9865 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.36
                        RasGEF_N_2   9 llvnqLydqsrevvaaaleiLeea 32 
                                        l+++L+d++ ev++a+++ +e+ 
  gi|488601305|ref|YP_007907776.1| 195 TLLDSLKDENYEVRKASAKTIERL 218
                                       68999************9999887 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 3.6
                        RasGEF_N_2  24 aaleiLeeacddk.eslevlve 44 
                                       +a+++Le a++d+  ++++ ++
  gi|488601305|ref|YP_007907776.1| 247 KAIDALEIALKDEdWNIKKWAS 268
                                       7888888888777677766655 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00052
                        RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLeeacddk 36 
                                       i+ll++ L d++++v++ a+e+++++++  
  gi|488601305|ref|YP_007907776.1| 308 IDLLIKHLDDPDPNVRDLAIEYIKDFVKVI 337
                                       89**********************997644 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     2e-05     0.024       3      37 ..      25      59 ..      23      60 .. 0.87
   2 ?   -0.8   0.0       1.5   1.8e+03      13      29 ..      66      82 ..      63      94 .. 0.79
   3 ?    1.7   0.0      0.25   2.9e+02      17      36 ..     163     182 ..     162     185 .. 0.84
   4 ?    1.2   0.0      0.34   4.1e+02      16      36 ..     195     215 ..     194     218 .. 0.84
   5 ?    0.9   0.0      0.44   5.3e+02       8      39 ..     274     305 ..     268     305 .. 0.76
   6 ?    1.1   0.1      0.38   4.5e+02      14      29 ..     308     323 ..     306     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                      HHHHHHHHTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                               Arm  3 enkdavieaGavppLvrLLssedeevqeeAawALs 37
                                      +n + ++  G v+ L++LL++ed+ev+  Aa ALs
  gi|488601305|ref|YP_007907776.1| 25 QNVESLRIKGNVKGLIKLLEDEDPEVRAGAADALS 59
                                      66666677788999********************8 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                                      HHHHHHHHTTTSSHHHH CS
                               Arm 13 avppLvrLLssedeevq 29
                                      ++ +L++ L +++ ev+
  gi|488601305|ref|YP_007907776.1| 66 VISALINTLADKNREVR 82
                                      79999999999888775 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.25
                                       HHHHTTTSSHHHHHHHHHHH CS
                               Arm  17 LvrLLssedeevqeeAawAL 36 
                                       L++ L+++d +v++ A+  +
  gi|488601305|ref|YP_007907776.1| 163 LIQSLKDPDADVRKRAVESI 182
                                       788899********998665 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.34
                                       HHHHHTTTSSHHHHHHHHHHH CS
                               Arm  16 pLvrLLssedeevqeeAawAL 36 
                                        L++ L++e+ ev++++a ++
  gi|488601305|ref|YP_007907776.1| 195 TLLDSLKDENYEVRKASAKTI 215
                                       5888899*********99887 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.44
                                       HHHTTHHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                               Arm   8 vieaGavppLvrLLssedeevqeeAawALsNL 39 
                                       +    a+ +L +L ++ed +v+  A++AL+ L
  gi|488601305|ref|YP_007907776.1| 274 IGGDKAIAILKKLAEDEDWTVRYHAVSALGRL 305
                                       55566788888888899999999999999865 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.38
                                       HHHHHHHTTTSSHHHH CS
                               Arm  14 vppLvrLLssedeevq 29 
                                       ++ L++ L+++d++v+
  gi|488601305|ref|YP_007907776.1| 308 IDLLIKHLDDPDPNVR 323
                                       789*********9996 PP

>> Cohesin_HEAT  HEAT repeat associated with sister chromatid cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.12   1.5e+02      23      36 ..      39      52 ..      36      58 .. 0.84
   2 ?   -0.0   0.0      0.96   1.1e+03      16      29 ..      63      76 ..      59      82 .. 0.83
   3 ?    2.2   0.1       0.2   2.3e+02      24      41 ..     164     181 ..     162     182 .. 0.82
   4 ?    4.1   0.0     0.051        61      15      38 ..     188     211 ..     185     215 .. 0.88
   5 ?   -3.2   0.0       9.6   1.1e+04      21      38 ..     250     267 ..     249     267 .. 0.77
   6 ?   -2.9   0.0       7.8   9.3e+03      23      41 ..     283     301 ..     281     302 .. 0.76
   7 !   12.6   0.0   0.00011      0.13      21      40 ..     309     328 ..     308     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                      HHHHHHSS-HHHHH CS
                      Cohesin_HEAT 23 iarrltDsspsVRd 36
                                      +++ l+D++p VR+
  gi|488601305|ref|YP_007907776.1| 39 LIKLLEDEDPEVRA 52
                                      56669********7 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.96
                                      SHHHHHHHHHHHHS CS
                      Cohesin_HEAT 16 apevldtiarrltD 29
                                       pev++++++ l D
  gi|488601305|ref|YP_007907776.1| 63 KPEVISALINTLAD 76
                                      699********999 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.2
                                       HHHHHSS-HHHHHHHHHH CS
                      Cohesin_HEAT  24 arrltDsspsVRdAaLel 41 
                                       +  l D+++ VR+ a+e 
  gi|488601305|ref|YP_007907776.1| 164 IQSLKDPDADVRKRAVES 181
                                       44599*******999986 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.051
                                       GSHHHHHHHHHHHHSS-HHHHHHH CS
                      Cohesin_HEAT  15 sapevldtiarrltDsspsVRdAa 38 
                                        ++ev++t+   l D+   VR+A+
  gi|488601305|ref|YP_007907776.1| 188 LNDEVKKTLLDSLKDENYEVRKAS 211
                                       5789******************96 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 9.6
                                       HHHHHHHHSS-HHHHHHH CS
                      Cohesin_HEAT  21 dtiarrltDsspsVRdAa 38 
                                       d+++  l D++  ++++a
  gi|488601305|ref|YP_007907776.1| 250 DALEIALKDEDWNIKKWA 267
                                       788889999987777775 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 7.8
                                       HHHHHHSS-HHHHHHHHHH CS
                      Cohesin_HEAT  23 iarrltDsspsVRdAaLel 41 
                                       +++ ++D++  VR  a++ 
  gi|488601305|ref|YP_007907776.1| 283 LKKLAEDEDWTVRYHAVSA 301
                                       6777889998899888886 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 0.00011
                                       HHHHHHHHSS-HHHHHHHHH CS
                      Cohesin_HEAT  21 dtiarrltDsspsVRdAaLe 40 
                                       d ++++l D++p VRd a+e
  gi|488601305|ref|YP_007907776.1| 309 DLLIKHLDDPDPNVRDLAIE 328
                                       7899**************98 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0052       6.2     178     201 ..      36      59 ..      24      64 .. 0.82
   2 ?    1.5   0.1      0.15   1.8e+02     129     160 ..      64      95 ..      55     118 .. 0.75
   3 ?    0.4   0.0      0.33     4e+02     181     196 ..     163     178 ..     155     184 .. 0.88
   4 ?    3.0   0.1     0.054        65     174     199 ..     189     214 ..     176     222 .. 0.84
   5 ?    0.0   0.0      0.44   5.2e+02     173     197 ..     275     299 ..     252     308 .. 0.77
   6 !    7.8   0.0    0.0018       2.2     179     211 ..     309     341 ..     297     356 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0052
                           CLASP_N 178 ekslkkgleDanptVRetaRstfw 201
                                       +k l+k+leD +p+VR  a +++ 
  gi|488601305|ref|YP_007907776.1|  36 VKGLIKLLEDEDPEVRAGAADALS 59 
                                       6889************99877665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                           CLASP_N 129 prilqvlsvalqdKnvqpReysaiwLkilltr 160
                                       p++++ l + l dKn + R  sa+ L+ l ++
  gi|488601305|ref|YP_007907776.1|  64 PEVISALINTLADKNREVRWRSAKSLERLCRD 95 
                                       66777778888888888888888877777665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.33
                           CLASP_N 181 lkkgleDanptVReta 196
                                       l++ l+D++  VR+ a
  gi|488601305|ref|YP_007907776.1| 163 LIQSLKDPDADVRKRA 178
                                       8899*********976 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.054
                           CLASP_N 174 ldliekslkkgleDanptVRetaRst 199
                                        d+++k+l   l+D n +VR+++ +t
  gi|488601305|ref|YP_007907776.1| 189 NDEVKKTLLDSLKDENYEVRKASAKT 214
                                       38899***************998776 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.44
                           CLASP_N 173 lldliekslkkgleDanptVRetaR 197
                                       + d +  +lkk+ eD + tVR +a 
  gi|488601305|ref|YP_007907776.1| 275 GGDKAIAILKKLAEDEDWTVRYHAV 299
                                       4577788999999999999998875 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0018
                           CLASP_N 179 kslkkgleDanptVRetaRstfweffkvwPsrA 211
                                       ++l+k l D++p+VR+ a + +  f kv   + 
  gi|488601305|ref|YP_007907776.1| 309 DLLIKHLDDPDPNVRDLAIEYIKDFVKVIERKD 341
                                       5799************99999999988876554 PP

>> Aconitase_B_N  Aconitate B N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0046       5.5      95     120 ..      35      60 ..      32      81 .. 0.92
   2 ?   -1.1   0.0       1.5   1.8e+03      96     120 ..      67      91 ..      61     118 .. 0.74
   3 ?    3.2   0.0     0.068        81      84     130 ..     148     194 ..     132     220 .. 0.77
   4 ?    4.0   0.0      0.04        48      81     128 ..     296     340 ..     278     358 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0046
                     Aconitase_B_N  95 nvksLidllkekdeelaeeaaeaLkk 120
                                       nvk Li+ll+++d e+++ aa+aL++
  gi|488601305|ref|YP_007907776.1|  35 NVKGLIKLLEDEDPEVRAGAADALSD 60 
                                       9***********************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                     Aconitase_B_N  96 vksLidllkekdeelaeeaaeaLkk 120
                                       +++Li+ l +k++e++   a+ L++
  gi|488601305|ref|YP_007907776.1|  67 ISALINTLADKNREVRWRSAKSLER 91 
                                       6789999999999999999988876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.068
                     Aconitase_B_N  84 velLgtMlGGynvksLidllkekdeelaeeaaeaLkktllvydafed 130
                                       v  Lg +    +   Li+ lk+ d+++++ a+e + ++ ++ d++++
  gi|488601305|ref|YP_007907776.1| 148 VIALGRIRDERSLYYLIQSLKDPDADVRKRAVESIGRIGILNDEVKK 194
                                       5566777777778899*****9**********999999999998554 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.04
                     Aconitase_B_N  81 eeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLkktllvydaf 128
                                        +Av+ Lg ++    ++ Li+ l++ d ++++ a e +k+ + v +  
  gi|488601305|ref|YP_007907776.1| 296 YHAVSALGRLK---QIDLLIKHLDDPDPNVRDLAIEYIKDFVKVIERK 340
                                       56777777775...7999999999999999999999999999888763 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.14   1.7e+02      26      69 ..      42      94 ..      31     107 .. 0.52
   2 ?    4.8   0.1     0.025        30      35      87 ..     153     204 ..      67     263 .. 0.65
   3 ?   -0.7   0.0       1.3   1.6e+03       8      26 ..     287     305 ..     280     310 .. 0.76
   4 ?    5.9   0.0     0.011        14       5      47 ..     312     354 ..     308     358 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
                           RTP1_C1 26 liekkske.........avldiekilkllleaLkdedsYvYLnaikgLvaLad 69
                                      l+e++++e         +  d++++++ l+++L+d++  v   + k L+ L+ 
  gi|488601305|ref|YP_007907776.1| 42 LLEDEDPEvragaadalSDFDKPEVISALINTLADKNREVRWRSAKSLERLCR 94
                                      44444444444444443444455555555555555555555555555555554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.025
                           RTP1_C1  35 vldiekilkllleaLkdedsYvYLnaikgLvaLadvfpeevlklLleeyeeen 87 
                                       ++  e+ l  l+++Lkd+d  v   a++ +  ++   ++ev k+Ll+  ++en
  gi|488601305|ref|YP_007907776.1| 153 RIRDERSLYYLIQSLKDPDADVRKRAVESIGRIGIL-NDEVKKTLLDSLKDEN 204
                                       455566666777778888877777777777777655.5777777777764333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                           RTP1_C1   8 lqdpllpvrahglvlLrkl 26 
                                        +d+   vr h+++ L +l
  gi|488601305|ref|YP_007907776.1| 287 AEDEDWTVRYHAVSALGRL 305
                                       5678888999999988776 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.011
                           RTP1_C1   5 lkdlqdpllpvrahglvlLrkliekkskeavldiekilkllle 47 
                                       +k+l dp + vr  ++  +++ ++  ++++ +++ek+ ++l++
  gi|488601305|ref|YP_007907776.1| 312 IKHLDDPDPNVRDLAIEYIKDFVKVIERKDSKKAEKLKEILQK 354
                                       789****************998888777777777777777655 PP

>> Tti2  Tti2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.032        39     127     150 ..      38      61 ..      35      65 .. 0.91
   2 ?    0.2   0.0      0.37   4.4e+02     124     152 ..      66      94 ..      62     104 .. 0.85
   3 ?   -2.0   0.0       1.7     2e+03     130     150 ..     285     305 ..     281     307 .. 0.86
   4 ?    4.7   0.1     0.015        18     128     161 ..     311     353 ..     308     358 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.032
                              Tti2 127 piLnllDdtdtsvKlrGlklLqtl 150
                                       ++++ll+d+d++v++ +   L+++
  gi|488601305|ref|YP_007907776.1|  38 GLIKLLEDEDPEVRAGAADALSDF 61 
                                       6899****************9988 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.37
                              Tti2 124 ivPpiLnllDdtdtsvKlrGlklLqtlle 152
                                       ++++++n l d++ +v+ r+ k L++l+ 
  gi|488601305|ref|YP_007907776.1|  66 VISALINTLADKNREVRWRSAKSLERLCR 94 
                                       68999999999999999999999999875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.7
                              Tti2 130 nllDdtdtsvKlrGlklLqtl 150
                                       +l++d+d +v++++++ L +l
  gi|488601305|ref|YP_007907776.1| 285 KLAEDEDWTVRYHAVSALGRL 305
                                       5899***********999876 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.015
                              Tti2 128 iLnllDdtdtsvKlrGlklLqtlleklessk.........llk 161
                                       +++ lDd+d++v+  +++ ++++++ +e+++         +l+
  gi|488601305|ref|YP_007907776.1| 311 LIKHLDDPDPNVRDLAIEYIKDFVKVIERKDskkaeklkeILQ 353
                                       56779**********************9998555555444444 PP

>> Cnd3  Nuclear condensing complex subunits, C-term domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.23   2.7e+02     121     145 ..      36      59 ..      19      92 .. 0.82
   2 ?    8.6   0.0   0.00078      0.93      31      67 ..     163     199 ..     159     216 .. 0.82
   3 ?   -1.4   0.0      0.86     1e+03      43     263 ..     323     327 ..     261     353 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
                                       HHHHHHHHC-TT-HHHHHHHHHHHH CS
                              Cnd3 121 lkllykaLdsednpelqaiaaeglc 145
                                       +k l+k+L++e +pe++a aa +l+
  gi|488601305|ref|YP_007907776.1|  36 VKGLIKLLEDE-DPEVRAGAADALS 59 
                                       56688899766.5999999998875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00078
                                       HHHHHC-SSHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              Cnd3  31 ilpavrskeaairelglkcLglfclldkklakenlkl 67 
                                       ++++++  +a++r++++++ g  ++l+ ++ k+ l+ 
  gi|488601305|ref|YP_007907776.1| 163 LIQSLKDPDADVRKRAVESIGRIGILNDEVKKTLLDS 199
                                       6899999********************9888776654 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.86
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHH-CGGGGGGHH..............H CS
                              Cnd3  43 relglkcLglfclldkklakenlklflqalskgneelkiialkaifDllllhglevldkekkedsdeeeeesessks 119
                                       r                                                                            
  gi|488601305|ref|YP_007907776.1| 323 R---------------------------------------------------------------------------- 323
                                       1............................................................................ PP

                                       HHHHHHHHHC-TT-HHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHH-GGGTT-HHHHHHHHHHHHHHHCC-HHHH CS
                              Cnd3 120 llkllykaLdsednpelqaiaaeglcKLllagiltdselLsrLvllyFnpeteenqrLrQcLsvffpvYafsspknq 196
                                                                                                                    
  gi|488601305|ref|YP_007907776.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHHHHHHHHHCH--...-SHCHHHHHHHHHHHHT-GGGS---------TT.....--HHH CS
                              Cnd3 197 ellaeiflptlrtllnapeesplaeeevspskvleqlvdltdprklvnkteeeesksesekeeelhl 263
                                                                                                      +l++
  gi|488601305|ref|YP_007907776.1| 324 ---------------------------------------------------------------DLAI 327
                                       ...............................................................2222 PP

>> API5  Apoptosis inhibitory protein 5 (API5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.052        62      64     102 ..      39      75 ..      29      76 .. 0.85
   2 ?    5.5   0.1    0.0051       6.1      59      94 ..      65     100 ..      60     107 .. 0.91
   3 ?   -2.7   0.0       1.6   1.9e+03     120     154 ..     148     182 ..     132     196 .. 0.61
   4 ?   -2.2   0.0       1.1   1.3e+03      59      85 ..     191     217 ..     185     225 .. 0.69
   5 ?    2.9   0.3     0.032        38     132     166 ..     308     342 ..     246     357 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.052
                              API5  64 qlDLiedddlgirkqAikdLpslckdtkeyvskiadiLa 102
                                       ++ L+ed+d ++r  A  +L  +  d++e +s +++ La
  gi|488601305|ref|YP_007907776.1|  39 LIKLLEDEDPEVRAGAADALSDF--DKPEVISALINTLA 75 
                                       7899***************9999..77888888877776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0051
                              API5  59 kaidaqlDLiedddlgirkqAikdLpslckdtkeyv 94 
                                       ++i a+++ + d++ ++r    k+L +lc+d+++ +
  gi|488601305|ref|YP_007907776.1|  65 EVISALINTLADKNREVRWRSAKSLERLCRDKTDVL 100
                                       689999**************************9976 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.6
                              API5 120 llsllkldakasltalfkqieteeetvRekvlkfi 154
                                       +++l ++  + sl  l ++++  +  vR+++++ i
  gi|488601305|ref|YP_007907776.1| 148 VIALGRIRDERSLYYLIQSLKDPDADVRKRAVESI 182
                                       55555555555555555555555555555555444 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.1
                              API5  59 kaidaqlDLiedddlgirkqAikdLps 85 
                                       ++  ++lD + d++ ++rk+  k + +
  gi|488601305|ref|YP_007907776.1| 191 EVKKTLLDSLKDENYEVRKASAKTIER 217
                                       445567777778888888777776655 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.032
                              API5 132 ltalfkqieteeetvRekvlkfireklftlkeell 166
                                       ++ l k++   + +vR+ ++++i++ ++ ++ +  
  gi|488601305|ref|YP_007907776.1| 308 IDLLIKHLDDPDPNVRDLAIEYIKDFVKVIERKDS 342
                                       33466777777777777777777777777754444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2258.05
//
Query:       gi|488601306|ref|YP_007907777.1|  [L=415]
Description: peptide-modifying radical SAM enzyme CbpB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-21   76.3   0.0    8.7e-21   75.0   0.0    1.7  1  Radical_SAM  Radical SAM superfamily
    2.4e-09   37.6   2.1    1.3e-08   35.2   1.9    2.3  2  SPASM        Iron-sulfur cluster-binding domain
      1e-05   25.6   0.0    2.4e-05   24.5   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
     0.0001   22.6   0.0    0.00037   20.8   0.0    2.0  2  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   1.9e-24   8.7e-21       1     166 [.      57     212 ..      57     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.9e-24
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       v++t +Cn +C++C++p +     r + +s +e++ +++++ +  g  +v+++g epll++d ++ + +       +
  gi|488601306|ref|YP_007907777.1|  57 VNPTDACNAGCPYCYIPPS--VKSRRKKMSYDELAYIAEKAIEFLGNSVVVFHGTEPLLNKDNIFRIIEDYSD---K 128
                                       6899**************7..9999999999999999999998999*****************9888888887...* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpG 154
                                       +++ + tng+l++ee +e +++l+   v l+l+++++e + + ++++++f+++ e+le++ ++ +    ++++ +  
  gi|488601306|ref|YP_007907777.1| 129 LNFGIQTNGLLLEEEDVEFIKKLE-VNVGLSLDSPHKE-TNDFLRGKGSFDKISELLELFDNYSGL---NVVTTITK 200
                                       ************************.*************.*******************99998666...56666666 PP

                                       TSHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 155 endeeleellel 166
                                       +n  +l++++++
  gi|488601306|ref|YP_007907777.1| 201 YNQNHLKDMVDF 212
                                       677777777776 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.92   4.1e+03      14      22 ..     215     223 ..     210     235 .. 0.73
   2 !   35.2   1.9   2.9e-12   1.3e-08       1      67 [.     290     352 ..     290     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.92
                             SPASM  14 GdVvpCcvd 22 
                                       G+V++C + 
  gi|488601306|ref|YP_007907777.1| 215 GKVSLCLMN 223
                                       9*****665 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 2.9e-12
                             SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefrkskkfplielCrnC 67 
                                       C  ++r + I++dG ++pC    + + +e+  Gni+++++e+I+ns+++ ++  ++k + i+ Cr+C
  gi|488601306|ref|YP_007907777.1| 290 CGGGRRFFSITADGSCYPC---GEFIGTEFCGGNIFRDDFEKIINSKAFAAVT-KRKVEDIPECRDC 352
                                       8789999************...6788888**********************99.556667899**** 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 !   24.5   0.0   5.3e-09   2.4e-05       4      94 ..      59     142 ..      56     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5.3e-09
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80 
                                        +  Cn  C+ C+   + ks+ +k + +el    ++++  +    + +v+ G ePL   nk++++++++ + ++   
  gi|488601306|ref|YP_007907777.1|  59 PTDACNAGCPYCYIPPSVKSRRKKMSYDELA--YIAEKAIEFLGNSVVVFHGTEPL--LNKDNIFRIIEDYSDKL-- 129
                                       5678*********999888888877766655..565777777888899********..9************9998.. PP

                           Fer4_14  81 kkiwletngtleie 94 
                                        +  ++tng+l  e
  gi|488601306|ref|YP_007907777.1| 130 -NFGIQTNGLLLEE 142
                                       .7788888887633 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   8.2e-08   0.00037      12     131 ..      60     171 ..      46     180 .. 0.74
   2 ?   -2.7   0.0       1.5   6.6e+03      71      99 ..     181     209 ..     175     220 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.2e-08
                           Fer4_12  12 vsgCnlsCkgCfnketw.sfksgkeft..kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                       +  Cn  C++C+ +    s +++  ++    ++e++ie l    ++ +++ G EPll  n++ + ++++    +   
  gi|488601306|ref|YP_007907777.1|  60 TDACNAGCPYCYIPPSVkSRRKKMSYDelAYIAEKAIEFL---GNSVVVFHGTEPLL--NKDNIFRIIEDYSDKLN- 130
                                       567********97655505555555554444555555555...8899**********..*********99988876. PP

                           Fer4_12  86 kdiwlytgytleelskkekeellkeidvlvdGkfeesledeslrfr 131
                                          + ++g  lee +     e++k+++v v   ++   ++++  +r
  gi|488601306|ref|YP_007907777.1| 131 -FGIQTNGLLLEEED----VEFIKKLEVNVGLSLDSPHKETNDFLR 171
                                       .46899999999986....689999999888777766666654444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                           Fer4_12  71 allelvkevkeekpekdiwlytgytleel 99 
                                       +llel+++    ++  +i++y+   l+++
  gi|488601306|ref|YP_007907777.1| 181 ELLELFDNYSGLNVVTTITKYNQNHLKDM 209
                                       56667777776666556777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2847.92
//
Query:       gi|488601307|ref|YP_007907778.1|  [L=214]
Description: hypothetical protein Asulf_01814 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); 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):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1277.81
//
Query:       gi|488601308|ref|YP_007907779.1|  [L=303]
Description: Coenzyme F420-reducing hydrogenase, delta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   69.8   0.4    4.6e-19   68.6   0.4    1.7  1  FlpD         Methyl-viologen-reducing hydrogenase, delta subu
      1e-08   34.6   2.2      1e-08   34.6   2.2    3.1  4  Fer4         4Fe-4S binding domain
      1e-06   29.2  11.5    0.00038   21.0   0.3    3.0  2  Fer4_7       4Fe-4S dicluster domain
    1.8e-06   27.7  12.3    1.4e-05   25.0   2.1    2.6  2  Fer4_6       4Fe-4S binding domain
      8e-06   26.7  16.2      0.001   20.0   1.4    3.4  2  Fer4_16      4Fe-4S double cluster binding domain
    1.1e-05   25.2   0.8    1.1e-05   25.2   0.8    3.0  2  Fer4_2       4Fe-4S binding domain
      2e-05   24.6  12.8      2e-05   24.6  12.8    2.1  2  Fer4_21      4Fe-4S dicluster domain
    2.2e-05   24.5   9.7    2.2e-05   24.5   9.7    2.1  2  Fer4_10      4Fe-4S dicluster domain
    5.1e-05   23.4  21.2      0.001   19.2  11.9    2.9  4  Fer4_9       4Fe-4S dicluster domain
     0.0012   18.6   0.4       0.01   15.7   0.1    2.6  2  IF2_N        Translation initiation factor IF-2, N-terminal r
     0.0027   18.2   8.3      0.085   13.4   0.6    3.1  3  Fer4_17      4Fe-4S dicluster domain
      0.003   18.1   2.3      0.003   18.1   2.3    2.5  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.011   16.5   1.4      0.011   16.5   1.4    3.3  3  Fer4_15      4Fe-4S single cluster domain
      0.015   15.4   0.1        0.4   10.8   0.0    2.7  2  HemN_C       HemN C-terminal domain
      0.053   14.0   1.2      0.053   14.0   1.2    3.1  2  Fer4_4       4Fe-4S binding domain
       0.12   12.4   0.0        1.2    9.2   0.1    2.5  3  HTH_Crp_2    Crp-like helix-turn-helix domain
       0.27   11.4   9.2       0.14   12.4   6.4    1.9  2  Fer4_18      4Fe-4S dicluster domain
       0.33   11.4  13.0       0.32   11.5   1.0    2.9  2  Fer4_8       4Fe-4S dicluster domain
        0.4   10.5   9.3          2    8.2   6.5    2.3  2  GF_recep_IV  Growth factor receptor domain IV
        2.8    8.8  10.3        2.6    8.9   1.1    3.0  2  Fer4_22      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.4   5.1e-22   4.6e-19      26     114 ..     103     190 ..      84     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 5.1e-22
                              FlpD  26 pnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerrveklkelleelgiepeRvrleevsa 102
                                       +n  ii ++Csgr+d++++++a+++Ga+g++v+gC+  +C ++ G+++a  +v+ +k++le++g +p R+ +   ++
  gi|488601308|ref|YP_007907779.1| 103 ENAGIISMMCSGRIDMTMMAEAFRRGAWGIIVAGCQ--ECSNKYGSKEAMVKVDVMKKVLEQMGENPGRIMFIYGNP 177
                                       4688*******************************9..9*******************************9977665 PP

                              FlpD 103 a.egekfaevike 114
                                       + e  +f e+++e
  gi|488601308|ref|YP_007907779.1| 178 EeEITRFSEKLNE 190
                                       4144566666555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   2.2   1.1e-11     1e-08       1      23 [.       9      31 ..       9      32 .. 0.94
   2 !    9.7   3.2   0.00084      0.76       3      23 ..      39      59 ..      37      60 .. 0.82
   3 ?   -3.0   0.6       8.9     8e+03      10      15 ..     136     141 ..     136     142 .. 0.76
   4 ?   -2.4   0.0       5.5     5e+03       3       9 ..     294     300 ..     293     301 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.1e-11
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      ++ide kCi CG+Cv+ CP++A+
  gi|488601308|ref|YP_007907779.1|  9 IIIDEKKCISCGICVSLCPHNAL 31
                                      68********************8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00084
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      + + kC  CG+C   C + AI
  gi|488601308|ref|YP_007907779.1| 39 VTTGKCKVCGICSASCVTKAI 59
                                      6789************66666 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.9
                                       S-THHH CS
                              Fer4  10 gCGaCv 15 
                                       gC +C 
  gi|488601308|ref|YP_007907779.1| 136 GCQECS 141
                                       798885 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 5.5
                                       EETTTSS CS
                              Fer4   3 ideekCi 9  
                                        de kC+
  gi|488601308|ref|YP_007907779.1| 294 KDELKCV 300
                                       6899998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   4.3e-07   0.00038       1      19 [.      15      33 ..       4      39 .. 0.79
   2 !   10.6   5.4   0.00076      0.68       1      27 [.      43      80 ..      43     143 .. 0.50

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.3e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaiel 19
                                      +Ci Cg Cv+ Cp++a++l
  gi|488601308|ref|YP_007907779.1| 15 KCISCGICVSLCPHNALSL 33
                                      6888888888888888766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00076
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek...........g 27
                                      +C  Cg C a C +kai+++ ++  +           +
  gi|488601308|ref|YP_007907779.1| 43 KCKVCGICSASCVTKAISMKSKKFTDdgllesfngnlK 80
                                      7*****************98642222233333333330 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   2.1   1.5e-08   1.4e-05       2      24 .]       9      31 ..       8      31 .. 0.93
   2 !    7.6   2.8    0.0046       4.1       8      24 .]      43      59 ..      39      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.5e-08
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + id+ kCi+Cg Cv+ CP++a+
  gi|488601308|ref|YP_007907779.1|  9 IIIDEKKCISCGICVSLCPHNAL 31
                                      569******************97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0046
                            Fer4_6  8 kCigCgdCvrvCPegai 24
                                      kC  Cg C + C ++ai
  gi|488601308|ref|YP_007907779.1| 43 KCKVCGICSASCVTKAI 59
                                      8***********99987 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 !   20.0   1.4   1.1e-06     0.001       1      20 [.      15      34 ..      15      41 .. 0.90
   2 !    8.9   7.5    0.0032       2.9       1      26 [.      43      67 ..      43     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++Cg C++ CP+na++ +
  gi|488601308|ref|YP_007907779.1| 15 KCISCGICVSLCPHNALSLE 34
                                      5****************977 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0032
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeie 26
                                      +C+ Cg C  +C t+ai++k++ ++ 
  gi|488601308|ref|YP_007907779.1| 43 KCKVCGICSASCVTKAISMKSK-KFT 67
                                      5******************954.443 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.8   1.2e-08   1.1e-05       3      22 .]       9      28 ..       7      28 .. 0.92
   2 ?    4.2   4.0      0.06        54       7      20 ..      41      54 ..      37      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      + +d+ +Ci+Cg+Cvs CP+
  gi|488601308|ref|YP_007907779.1|  9 IIIDEKKCISCGICVSLCPH 28
                                      679****************7 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.06
                            Fer4_2  7 tdrCigCgaCvsaC 20
                                      t +C  Cg+C  +C
  gi|488601308|ref|YP_007907779.1| 41 TGKCKVCGICSASC 54
                                      569*******8889 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6  12.8   2.2e-08     2e-05       2      59 .]      10      61 ..       9      61 .. 0.92
   2 ?   -2.3   0.2       5.9   5.3e+03      43      48 ..     136     141 ..     134     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      +ide+kCi+Cg C+  C+   h+a++++  + ++v++ +C  C +Cs+ C  +++i+m
  gi|488601308|ref|YP_007907779.1| 10 IIDEKKCISCGICVSLCP---HNALSLE--NGIPVTTGKCKVCGICSASCV-TKAISM 61
                                      59****************...8999985..789*****************6.599988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.9
                           Fer4_21  43 GCnlCs 48 
                                       GC+ Cs
  gi|488601308|ref|YP_007907779.1| 136 GCQECS 141
                                       788886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   9.7   2.5e-08   2.2e-05       2      55 ..       9      54 ..       8      55 .. 0.95
   2 ?   -1.6   0.1       3.3     3e+03      11      15 ..     136     140 ..     123     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.5e-08
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                      ++id+++Ci Cg Cv+ CP         ++ s e+ + +  +kC  cg C ++C
  gi|488601308|ref|YP_007907779.1|  9 IIIDEKKCISCGICVSLCPH--------NALSLENGIPVTTGKCKVCGICSASC 54
                                      79******************........999999999999************** PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                           Fer4_10  11 rCgkC 15 
                                       +C++C
  gi|488601308|ref|YP_007907779.1| 136 GCQEC 140
                                       34444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.8   5.3e-06    0.0048      33      50 ..      13      30 ..       2      31 .. 0.75
   2 !   19.2  11.9   1.1e-06     0.001       1      51 []      15      59 ..      15      59 .. 0.95
   3 !    6.7   3.8    0.0089       7.9       1      24 [.      43      66 ..      43      73 .. 0.80
   4 ?    0.5   0.0       0.8   7.2e+02       4      10 ..     136     142 ..     105     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.3e-06
                            Fer4_9 33 eeaCigCgaCveaCpkga 50
                                      e++Ci+Cg Cv  Cp++a
  gi|488601308|ref|YP_007907779.1| 13 EKKCISCGICVSLCPHNA 30
                                      258************986 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.1e-06
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC++Cg Cv+ Cp+++ + +++            +C  Cg C + C ++ai
  gi|488601308|ref|YP_007907779.1| 15 KCISCGICVSLCPHNALSLENGIPVTTG------KCKVCGICSASCVTKAI 59
                                      7*********************999998......6***********99987 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0089
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaer 24
                                      kC  Cg C ++C ++++++++++ 
  gi|488601308|ref|YP_007907779.1| 43 KCKVCGICSASCVTKAISMKSKKF 66
                                      699999999999998888877665 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.8
                            Fer4_9   4 gCgaCve 10 
                                       gC++C +
  gi|488601308|ref|YP_007907779.1| 136 GCQECSN 142
                                       5666654 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.4   1.2e+03      22      49 ..     186     206 ..     181     207 .. 0.69
   2 !   15.7   0.1   1.1e-05      0.01       1      24 [.     257     280 ..     257     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                             IF2_N  22 kkLfkelGievkshsssLDeetaeliae 49 
                                       +kL++ lG++       LD+e +++++e
  gi|488601308|ref|YP_007907779.1| 186 EKLNE-LGKP------ELDFEIVKEVVE 206
                                       67844.8877......677777777765 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.1e-05
                             IF2_N   1 mskirVyeLAkeLgvkskevikkL 24 
                                       m+ +++ eLA++ g++s ev+k+ 
  gi|488601308|ref|YP_007907779.1| 257 MDYTSIEELAEKTGMDSREVVKTI 280
                                       899******************975 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.6   9.5e-05     0.085      45      59 ..      15      29 ..       5      35 .. 0.75
   2 !    8.2   0.3    0.0041       3.7       1      17 [.      43      59 ..      43     105 .. 0.75
   3 ?   -1.3   0.0       3.8   3.4e+03      48      53 ..     136     141 ..     134     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.5e-05
                           Fer4_17 45 lCieCgeCerkCPqg 59
                                      +Ci+Cg C++ CP++
  gi|488601308|ref|YP_007907779.1| 15 KCISCGICVSLCPHN 29
                                      566666666666664 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0041
                           Fer4_17  1 rCiqCgyClpeCpsyea 17
                                      +C  Cg C ++C + ++
  gi|488601308|ref|YP_007907779.1| 43 KCKVCGICSASCVTKAI 59
                                      6999********98665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.8
                           Fer4_17  48 eCgeCe 53 
                                       +C+eC+
  gi|488601308|ref|YP_007907779.1| 136 GCQECS 141
                                       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 !   18.1   2.3   3.3e-06     0.003       1      18 [.      11      28 ..      11      29 .. 0.94
   2 ?   -2.5   3.4       8.8   7.9e+03       4      16 ..      42      54 ..      39      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.3e-06
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +D+++Ci+cg+Cv+l+P+
  gi|488601308|ref|YP_007907779.1| 11 IDEKKCISCGICVSLCPH 28
                                      89***************6 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.8
                           Fer4_13  4 dtCiacgaCvela 16
                                       +C  cg+C + +
  gi|488601308|ref|YP_007907779.1| 42 GKCKVCGICSASC 54
                                      58999****9877 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.5   1.4   1.2e-05     0.011       1      31 [.       9      39 ..       9      45 .. 0.83
   2 ?    0.1   2.0       1.5   1.4e+03       7      19 ..      43      56 ..      37      71 .. 0.76
   3 ?    1.2   0.0      0.69   6.2e+02      11      53 ..      86     125 ..      84     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglas 31
                                      + +D+++Ci+cg Cv ++p      e+g+++
  gi|488601308|ref|YP_007907779.1|  9 IIIDEKKCISCGICVSLCPHNALSLENGIPV 39
                                      689***************9877777777764 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
                           Fer4_15  7 aCigcglCvaea.p 19
                                      +C  cg C a + +
  gi|488601308|ref|YP_007907779.1| 43 KCKVCGICSASCvT 56
                                      7*******998853 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.69
                           Fer4_15  11 cglCvaeapevfeldedglasvllddgeiaegevpddeeeaaq 53 
                                       ++ C ++++e++++++   a ++   +   +g+++ +++++a+
  gi|488601308|ref|YP_007907779.1|  86 VFSCRKLVKELIKEKKFENAGII---SMMCSGRIDMTMMAEAF 125
                                       79999********9998888777...45667888888888887 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.47   4.2e+02      42      58 ..      63      79 ..      56      80 .. 0.79
   2 ?   10.8   0.0   0.00044       0.4      15      54 ..     254     292 ..     253     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.47
                            HemN_C 42 leklqeqGLLeldggrl 58
                                       +k++++GLLe  +g+l
  gi|488601308|ref|YP_007907779.1| 63 SKKFTDDGLLESFNGNL 79
                                      699*******9766665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00044
                            HemN_C  15 LRlreGldlaafeqrfgldleellaaaleklqeqGLLeld 54 
                                       LR  +  +++++++++g d +e+  +++ +++++G+++++
  gi|488601308|ref|YP_007907779.1| 254 LRVMDYTSIEELAEKTGMDSREV-VKTILEMRRRGMINFE 292
                                       67778889***********6665.667**********986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.2     6e-05     0.053       2      15 ..      14      27 ..      13      36 .. 0.92
   2 ?   -2.1   0.6       9.1   8.2e+03       6      10 ..     136     140 ..     135     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++Ci Cg Cv+ CP
  gi|488601308|ref|YP_007907779.1| 14 KKCISCGICVSLCP 27
                                      69***********9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.1
                            Fer4_4   6 gCgsC 10 
                                       gC  C
  gi|488601308|ref|YP_007907779.1| 136 GCQEC 140
                                       55555 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.1   5.5e+03      43      54 ..      64      76 ..      59      86 .. 0.74
   2 ?   -0.8   0.0       1.7   1.6e+03      43      57 ..     100     116 ..     100     122 .. 0.72
   3 ?    9.2   0.1    0.0013       1.2      23      52 ..     261     290 ..     248     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.1
                                      HHHHHTTSEE.ET CS
                         HTH_Crp_2 43 seLkreglis.rg 54
                                      +++ ++gl++  +
  gi|488601308|ref|YP_007907779.1| 64 KKFTDDGLLEsFN 76
                                      7899999999533 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                       HHHHHTTSEE.E..TEEE CS
                         HTH_Crp_2  43 seLkreglis.r..grri 57 
                                       ++++++g+is    gr i
  gi|488601308|ref|YP_007907779.1| 100 KKFENAGIISmMcsGR-I 116
                                       689******9633244.5 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0013
                                       HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglis 52 
                                       + eelA+  G+    v +++ e++r+g+i 
  gi|488601308|ref|YP_007907779.1| 261 SIEELAEKTGMDSREVVKTILEMRRRGMIN 290
                                       669**************************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 ?   12.4   6.4   0.00016      0.14      58      97 ..      13      56 ..       3      71 .. 0.78
   2 ?   -2.7   0.0       7.2   6.4e+03      91     104 ..     152     165 ..     133     172 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                           Fer4_18 58 agdcidcescvkvcPtg.idirkGlql...eciscllcidacdk 97
                                      + +ci+c+ cv++cP + + + +G+ +   +c  c+ c  +c +
  gi|488601308|ref|YP_007907779.1| 13 EKKCISCGICVSLCPHNaLSLENGIPVttgKCKVCGICSASCVT 56
                                      578************753899***98733468888888888854 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.2
                           Fer4_18  91 cidacdkvmeklgk 104
                                        +d  +kv+e++g 
  gi|488601308|ref|YP_007907779.1| 152 KVDVMKKVLEQMGE 165
                                       35555555555555 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   1.0   0.00036      0.32       3      17 ..      14      28 ..      12      38 .. 0.82
   2 ?    4.1   5.0     0.074        66       4      20 ..      43      58 ..      40     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      +kCi Cg C s Cp 
  gi|488601308|ref|YP_007907779.1| 14 KKCISCGICVSLCPH 28
                                      589999999999994 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.074
                            Fer4_8  4 kCieCgaCqsaCpvlrr 20
                                      kC  Cg C ++C   ++
  gi|488601308|ref|YP_007907779.1| 43 KCKVCGICSASCV-TKA 58
                                      7999999999994.222 PP

>> GF_recep_IV  Growth factor receptor domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.5    0.0023         2      74     128 ..      15      63 ..       2      67 .. 0.80
   2 ?    2.6   0.0      0.13   1.1e+02       9      40 ..     127     158 ..     121     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                       GF_recep_IV  74 eClkCahfkdgseCvseCPegvkgekelifkyadaeevCekChenctegctgpee 128
                                       +C++C        Cvs CP+++ + ++ i   + + +vC  C + c + + ++++
  gi|488601308|ref|YP_007907779.1|  15 KCISC------GICVSLCPHNALSLENGIPVTTGKCKVCGICSASCVTKAISMKS 63 
                                       45544......46**********999999999999***********766655554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                       GF_recep_IV   9 egCWGpgpeqClsCkkfsrakeCvesCnllkg 40 
                                       +g WG   + C +C++   +ke + + +++k 
  gi|488601308|ref|YP_007907779.1| 127 RGAWGIIVAGCQECSNKYGSKEAMVKVDVMKK 158
                                       789***********998888887777777655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1    0.0029       2.6      81      94 ..      15      28 ..       4      30 .. 0.66
   2 ?    4.6   0.8     0.067        60       1      15 [.      43      57 ..      41      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                           Fer4_22 81 gCvGCgRCieacpv 94
                                      +C+ Cg C++ cp+
  gi|488601308|ref|YP_007907779.1| 15 KCISCGICVSLCPH 28
                                      55666666655554 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.067
                           Fer4_22  1 rClsCgaCtlvCptC 15
                                      +C  Cg C++ C t 
  gi|488601308|ref|YP_007907779.1| 43 KCKVCGICSASCVTK 57
                                      688899999888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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):              20  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1991.53
//
Query:       gi|488601309|ref|YP_007907780.1|  [L=994]
Description: Heterodisulfide reductase, subunit A-related polyferredoxin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-40  139.0   0.0    3.1e-27   95.6   0.0    3.5  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-25   88.0  41.1    1.5e-09   37.3   3.9    4.7  4  Fer4            4Fe-4S binding domain
      2e-20   73.1  29.0      3e-09   37.3  10.5    4.6  4  Fer4_7          4Fe-4S dicluster domain
    2.6e-17   62.8   0.1    2.2e-07   31.0   0.1    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.7e-16   58.7  23.4    1.3e-05   25.2   0.3    4.6  4  Fer4_10         4Fe-4S dicluster domain
    5.9e-16   58.6   5.2    3.8e-08   32.8   0.2    2.8  3  FAD_binding_2   FAD binding domain
    6.1e-16   57.7  55.4    1.5e-06   28.0   3.5    5.5  4  Fer4_6          4Fe-4S binding domain
    2.2e-15   57.3  30.3    5.6e-09   36.8   8.3    4.7  3  Fer4_16         4Fe-4S double cluster binding domain
    4.4e-14   52.7   0.1    8.6e-06   25.3   0.0    2.5  2  FAD_oxidored    FAD dependent oxidoreductase
    3.1e-13   50.0   3.1    0.00022   20.9   0.3    4.0  4  DAO             FAD dependent oxidoreductase
    3.2e-13   48.9  47.2    0.00011   22.1   3.4    5.2  4  Fer4_2          4Fe-4S binding domain
    2.2e-12   46.9  36.7    0.00055   20.0   2.2    5.1  4  Fer4_21         4Fe-4S dicluster domain
    3.6e-12   46.3  38.9    1.7e-07   31.3   7.8    4.5  4  Fer4_9          4Fe-4S dicluster domain
    9.3e-12   44.8   9.1    0.00055   19.3   1.8    4.6  4  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-10   40.8  36.3     0.0033   17.8   2.8    5.2  4  Fer4_4          4Fe-4S binding domain
    1.4e-09   37.7   2.3    9.2e-05   21.8   0.1    2.5  2  FAD_binding_3   FAD binding domain
    3.1e-09   37.3   7.4     0.0015   19.1   0.7    4.2  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.1e-08   34.6   4.8     0.0005   19.3   0.0    3.4  3  GIDA            Glucose inhibited division protein A
      3e-08   32.8   5.2      0.002   16.9   0.2    3.3  4  HI0933_like     HI0933-like protein
    5.8e-08   32.3   0.2     0.0089   15.3   0.0    2.5  2  Thi4            Thi4 family
    2.5e-07   31.3  19.4     0.0096   16.6   0.6    5.0  4  Fer4_15         4Fe-4S single cluster domain
    3.5e-07   30.7  29.1     0.0036   17.8  11.4    4.5  4  Fer4_17         4Fe-4S dicluster domain
    3.8e-07   30.5  30.6      0.006   17.0   0.8    4.2  3  Fer4_8          4Fe-4S dicluster domain
    5.6e-06   27.1  25.1       0.18   12.7   0.7    5.2  4  Fer4_22         4Fe-4S dicluster domain
    6.1e-06   25.8   0.1       0.14   11.4   0.0    3.1  4  Amino_oxidase   Flavin containing amine oxidoreductase
    0.00012   21.4   0.0      0.041   13.2   0.0    2.7  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0004   20.9  34.6        0.3   11.6   3.0    4.8  4  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
     0.0007   20.0   0.6       0.85   10.1   0.1    3.2  2  NAD_binding_7   Putative NAD(P)-binding
     0.0012   17.9   3.0        1.7    7.6   0.3    3.3  4  Lycopene_cycl   Lycopene cyclase protein
     0.0018   18.2   0.5         16    5.5   0.0    4.0  4  NAD_binding_9   FAD-NAD(P)-binding
     0.0046   15.9   1.7        6.6    5.4   0.2    3.1  3  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
       0.14   12.0   1.0        3.5    7.5   0.1    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.43    9.7   3.5        1.8    7.7   0.0    2.9  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
       0.82    9.9  24.7        1.8    8.8   1.3    5.2  5  Fer4_18         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.0     6e-30   3.1e-27       3     291 ..       5     407 ..       3     410 .. 0.81
   2 !   38.1   0.0   1.9e-12     1e-09       2     146 ..     582     726 ..     581     891 .. 0.73

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 6e-30
                                       EEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx........ RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias........ 57 
                                       v+v+GgG+AG++ al+la++g+kv+l+e            ++t+++++c +   s++l +v+++++i+         
  gi|488601309|ref|YP_007907780.1|   5 VLVVGGGIAGMQSALDLAESGFKVYLLEklpaiggrmsqIDKTFPTNDCAMcilSPKLNEVGRHENIEIinnsells 81 
                                       99*************************888888899999*********999888************999******** PP

                                       ....................................HHHHCHHHHCCCCHC........CT.CEEEEESCEEEEETE CS
                                       ....................................xxxxxxxxxxxxxxx........xx.xxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ....................................evvkklnqgielllg........ee.vvkidpgkkkvklek 89 
                                                                           + ++++n+g+ ++          ++ v +id++k ++ +  
  gi|488601309|ref|YP_007907780.1|  82 vegeagdftvrikrnplyvdmdrctgcgecakacpvNAIDEYNEGLSFRSSiyirypqaVPkVYAIDKEK-CIGC-- 155
                                       ************************************999*******999997777777744366666655.3333.. PP

                                       EEC................TCEEEEEESEEEE---EEE-BCTCTTC.........TTBEECCSECHHHHHHCCSS-T CS
                                       xxx................xxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  90 kke................gdeekiaydklvlAtGssprdlgipGv........aenvgklvrtldsaealklkllp 142
                                         +                 +e +++ ++++l  G++  d+   G+          +++++ r l  + +++ + l+
  gi|488601309|ref|YP_007907780.1| 156 --GicenvcvakainynqrPEEIELKVGSIILTLGGKLADPVERGEygygifpnVVTGIQFERLLSATGPFEGHVLR 230
                                       ..0334456999999**997788888899999999888888555666666666644444444566666666666666 PP

                                       ...................SEEEEES-SHHHHHHHHHHHHHT-...E.EEEEESSSSSS..TTS-HHHHHHHHHHHH CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxx...x.xxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 ...................krivvvGgGyiGvElAaalaklgk...e.vtlveardrll..raldkelsaaleeale 194
                                                          +++    +  ++++++ +++k +    e  + ve    ++  r+++k +++++++a e
  gi|488601309|ref|YP_007907780.1| 231 adgkepkriafiqcvcsrdEKT----NPWCSSVCCTYATKHAIiakEhMPDVETHIFVMdlRTFGKGFEEYAKRAEE 303
                                       7777774444444444444444....467777777776444333324488888888888****************** PP

                                       HTTEEEEESCEEEEEEETTEEEE.EEETTSCE..EEESEEEE-S-EEES-HHCS..HCCT-EEEETTEEE--TTS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx..xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2 195 keGvevklgtsvkeidgngekle.vvledgee..idadlvvvavGvrpstelle..eklglelderggivvdefl.. 264
                                       + Gv  k g + + +++ + +l    ++dg++  +++d+vv+++G++p  e ++  e lg+el+e g+ ++d+f   
  gi|488601309|ref|YP_007907780.1| 304 EYGVVYKYGRVSVVMQKPNGNLIlKYEKDGRTfeEEYDMVVLSTGFEPPEEAKKyaEILGIELNEYGFCKTDPFKpl 380
                                       *******9987655555444344367788887889*****************99*******************9777 PP

                                       BESSTTEEE-GGGCTECCSS--HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtnvpgiyaiGDvaggkggpelaqaAv 291
                                       +tn pgi+++G + ++k++pe++  A+
  gi|488601309|ref|YP_007907780.1| 381 ETNKPGIFVAGVFSEPKDIPESVAQAS 407
                                       ***********************9997 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 1.9e-12
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHH..CCCCHCCTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx..xxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.evvkklnqg..ielllgeev 75 
                                       + ++iGgG AG+++al+la++g++ ++ve  ++  +gg l +  ++  ++++++++ e v+k++++  i+++ ++ +
  gi|488601309|ref|YP_007907780.1| 582 KALIIGGGLAGMTCALELAEQGFESYIVE--KEAELGGNLKHLFYTIDGKNPQELLkELVEKVEKEpkITVFRNARI 656
                                       678*************************4..4445555566665555555555555866666666654666666668 PP

                                       EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCT.TC.TTBEECCSECHHHHHHCCSS-TSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gip.Gvaenvgklvrtldsaealklkllpkriv 146
                                        +id   +++  + +++g+ ++++ + +++AtG++  ++   + G +++v++    ++  e l + + p+++v
  gi|488601309|ref|YP_007907780.1| 657 ESIDGFVGNFRSKISVDGEVKEVEHGVVIVATGAEEYKPrEYEyGKNPKVITQ---VELEEMLARGEAPESVV 726
                                       88886668899999999**********************87777887777654...77777777777775554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   3.9   2.8e-12   1.5e-09       2      24 .]      99     121 ..      98     121 .. 0.95
   2 !   22.3   6.1   1.5e-07   7.8e-05       2      18 ..     146     162 ..     145     167 .. 0.92
   3 !   30.4   4.0   4.1e-10   2.2e-07       3      24 .]     916     937 ..     914     937 .. 0.92
   4 !   16.0   3.4   1.5e-05     0.008       2      23 ..     952     973 ..     951     974 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.8e-12
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       ++d+++C+gCG+C+++CPv+AI+
  gi|488601309|ref|YP_007907780.1|  99 YVDMDRCTGCGECAKACPVNAID 121
                                       89*******************95 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.5e-07
                                       EEETTTSSS-THHHHHS CS
                              Fer4   2 videekCigCGaCvevC 18 
                                        id+ekCigCG+C++vC
  gi|488601309|ref|YP_007907780.1| 146 AIDKEKCIGCGICENVC 162
                                       69*************** PP

  == domain 3  score: 30.4 bits;  conditional E-value: 4.1e-10
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       +  e+C +CG+Cv++CPv+AI+
  gi|488601309|ref|YP_007907780.1| 916 VVRERCDACGLCVKACPVNAIE 937
                                       678******************6 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.5e-05
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       +++   C gCG C   CP  AI
  gi|488601309|ref|YP_007907780.1| 952 EVNRAVCLGCGVCHATCPKSAI 973
                                       689999**************99 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   1.8e-08   9.3e-06      31      52 .]      98     119 ..      61     120 .. 0.83
   2 !   21.3   0.1   5.6e-07    0.0003       1      24 [.     151     174 ..     137     202 .. 0.89
   3 ?   -1.2   0.0       5.9   3.1e+03       2      17 ..     730     750 ..     706     788 .. 0.75
   4 !   37.3  10.5   5.7e-12     3e-09       1      52 []     920     972 ..     920     972 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.8e-08
                            Fer4_7  31 veidpekClgCgaCvavCPtga 52 
                                       +++d+++C+gCg+C+++CP++a
  gi|488601309|ref|YP_007907780.1|  98 LYVDMDRCTGCGECAKACPVNA 119
                                       589*****************97 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 5.6e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeen 24 
                                       +CigCg C+++C +kai+++++ +
  gi|488601309|ref|YP_007907780.1| 151 KCIGCGICENVCVAKAINYNQRPE 174
                                       7***************99998754 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.9
                            Fer4_7   2 CigCg.....aCvaaCpvkai 17 
                                       C+g +     +C + C + ai
  gi|488601309|ref|YP_007907780.1| 730 CVGSRnderpYCSRICCQTAI 750
                                       444434444477777765444 PP

  == domain 4  score: 37.3 bits;  conditional E-value: 5.7e-12
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt..ekveidpekClgCgaCvavCPtga 52 
                                       rC  Cg Cv+aCpv+aiel+++ +++g+   k+e++   ClgCg+C a+CP+ a
  gi|488601309|ref|YP_007907780.1| 920 RCDACGLCVKACPVNAIELKQF-ENRGVveLKAEVNRAVCLGCGVCHATCPKSA 972
                                       7******************998.5566633556788889************976 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.9e-09   9.9e-07       1      39 [.       7      45 ..       7      60 .. 0.91
   2 !   31.0   0.1   4.1e-10   2.2e-07       1      36 [.     585     620 ..     585     630 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.9e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39
                                      +vG+G++G+  A  La+ gf+v llek + +GGr++ ++
  gi|488601309|ref|YP_007907780.1|  7 VVGGGIAGMQSALDLAESGFKVYLLEKLPAIGGRMSQID 45
                                      8**********************************9875 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 4.1e-10
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36 
                                       I+G+Gl+G+++A +La++gf+  ++ek   lGG+++
  gi|488601309|ref|YP_007907780.1| 585 IIGGGLAGMTCALELAEQGFESYIVEKEAELGGNLK 620
                                       9********************************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 !   25.2   0.3   2.5e-08   1.3e-05       3      23 ..      99     119 ..      97     139 .. 0.78
   2 !   15.9   0.6     2e-05     0.011       4      33 ..     147     176 ..     144     186 .. 0.71
   3 !   22.5  11.0   1.7e-07   8.8e-05       5      56 .]     917     969 ..     913     969 .. 0.85
   4 !   12.8   2.1   0.00019     0.098       2      23 ..     951     972 ..     950     990 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-08
                           Fer4_10   3 vidddtCirCgkCvkaCPadl 23 
                                       ++d d+C++Cg+C kaCP+++
  gi|488601309|ref|YP_007907780.1|  99 YVDMDRCTGCGECAKACPVNA 119
                                       6799***************44 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2e-05
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeas 33 
                                       id+++Ci+Cg C ++C a++ ++++++e+ 
  gi|488601309|ref|YP_007907780.1| 147 IDKEKCIGCGICENVCVAKAINYNQRPEEI 176
                                       89**************44445555544444 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1.7e-07
                           Fer4_10   5 dddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +++C  Cg CvkaCP+++ + ++ ++    e + +++   C gcg C + CP
  gi|488601309|ref|YP_007907780.1| 917 VRERCDACGLCVKACPVNAiELKQFENRGVVELKAEVNRAVCLGCGVCHATCP 969
                                       5789*************887666677777777788888999***********9 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00019
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                       +++++  C++Cg C + CP ++
  gi|488601309|ref|YP_007907780.1| 951 AEVNRAVCLGCGVCHATCPKSA 972
                                       5678999************944 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.5     5e-09   2.6e-06       2      36 ..       5      39 ..       4      44 .. 0.94
   2 !   32.8   0.2   7.2e-11   3.8e-08       2      38 ..     583     619 ..     582     625 .. 0.93
   3 ?   -1.3   0.0       1.7   8.7e+02     141     204 ..     632     693 ..     624     734 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5e-09
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      v+V+G+G+AG+ +Al +ae G kv ++ek ++ gg
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGFKVYLLEKLPAIGG 39
                                      9******************************9998 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 7.2e-11
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38 
                                       +++iG+GlAG+++Ale+ae+G +  +veke e gg++
  gi|488601309|ref|YP_007907780.1| 583 ALIIGGGLAGMTCALELAEQGFESYIVEKEAELGGNL 619
                                       69********************************975 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 141 hallarlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ++ll+ lve+++k + ++++ +++++++   dg v     + + +g+  +++   v++atg+ + 
  gi|488601309|ref|YP_007907780.1| 632 QELLKELVEKVEKEPkITVFRNARIESI---DGFVGNFRSKISVDGEVKEVEHGVVIVATGAEEY 693
                                       68999999999999899*****999999...6666656666567777777777788888887663 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   3.5   2.8e-09   1.5e-06       4      24 .]     100     120 ..      98     120 .. 0.95
   2 !   20.8   4.9   5.4e-07   0.00028       4      24 .]     147     167 ..     146     167 .. 0.93
   3 !   24.0   4.1   5.1e-08   2.7e-05       2      24 .]     914     936 ..     913     936 .. 0.93
   4 !   17.7   2.6     5e-06    0.0027       1      24 []     950     973 ..     950     973 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.8e-09
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       +d d+C+gCg+C+++CP +ai
  gi|488601309|ref|YP_007907780.1| 100 VDMDRCTGCGECAKACPVNAI 120
                                       8******************98 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 5.4e-07
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       id++kCigCg C++vC ++ai
  gi|488601309|ref|YP_007907780.1| 147 IDKEKCIGCGICENVCVAKAI 167
                                       9***************99987 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 5.1e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       + + +++C+ Cg Cv++CP +ai
  gi|488601309|ref|YP_007907780.1| 914 AFVVRERCDACGLCVKACPVNAI 936
                                       67899****************98 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 5e-06
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       ++e+++  C+gCg C + CP  ai
  gi|488601309|ref|YP_007907780.1| 950 KAEVNRAVCLGCGVCHATCPKSAI 973
                                       689*****************9997 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 !   36.8   8.3   1.1e-11   5.6e-09       1      66 [.     104     164 ..     104     165 .. 0.74
   2 !   21.6   0.8     6e-07   0.00032       1      26 [.     920     942 ..     920     956 .. 0.78
   3 !   12.9   1.0   0.00032      0.17       2      24 ..     958     979 ..     957     991 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.1e-11
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkek.eiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       rC++Cg+Ca++CP+nai+e +e  ++++   i y +a  k +a+d+ekc       gC+iC++vC+a
  gi|488601309|ref|YP_007907780.1| 104 RCTGCGECAKACPVNAIDEYNEGlSFRSSIYIRYPQAVPKVYAIDKEKCI------GCGICENVCVA 164
                                       6******************9433135555555556666666666666665......*********87 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 6e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                       rC  Cg C+++CP+nai+ k   ++e
  gi|488601309|ref|YP_007907780.1| 920 RCDACGLCVKACPVNAIELK---QFE 942
                                       6*****************99...333 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00032
                           Fer4_16   2 CgtCgkCaevCPtnaikekkeke 24 
                                       C +Cg C  +CP +ai  k  ++
  gi|488601309|ref|YP_007907780.1| 958 CLGCGVCHATCPKSAIVVK-GFT 979
                                       99**************987.344 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.2e-08   1.2e-05       2      40 ..       5      43 ..       4      52 .. 0.96
   2 !   25.3   0.0   1.6e-08   8.6e-06       3      67 ..     584     670 ..     583     755 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.2e-08
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                      v+VvGGg+aG+  A+  a++G kv L+e+ + +GG +++
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGFKVYLLEKLPAIGGRMSQ 43
                                      99*********************************9985 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.6e-08
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.......................qvv 56 
                                       +++GGg+aG+++A+  a++G +  +ve++  lGG+l   l  t++g++ +e                       + +
  gi|488601309|ref|YP_007907780.1| 584 LIIGGGLAGMTCALELAEQGFESYIVEKEAELGGNLK-HLFYTIDGKNPQEllkelvekvekepkitvfrnariESI 659
                                       79*********************************96.677888886633344444444444555555555555555 PP

                      FAD_oxidored  57 tgiareflerl 67 
                                        g+++ f++++
  gi|488601309|ref|YP_007907780.1| 660 DGFVGNFRSKI 670
                                       55555555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2     5e-07   0.00026       2      33 ..       5      38 ..       4      43 .. 0.91
   2 ?   -1.6   0.0       2.9   1.5e+03     152     202 ..     297     349 ..     294     362 .. 0.60
   3 !   20.9   0.3   4.2e-07   0.00022       2      35 ..     583     617 ..     582     621 .. 0.92
   4 ?    6.1   0.0     0.014       7.2     135     202 ..     622     690 ..     617     695 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5e-07
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      v+++GGGi+G+  A++La+ g  V llek + +g
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGfkVYLLEKLPAIG 38
                                      89**************************987666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.9
                                       HHHHHHHT.T-EEEESECEEEE.EEEETCEEEEE..EECTEEE.E.EEEEEEE--GG CS
                               DAO 152 laraaeal.Gveilegtevtgl.eeedgkvwgve..rttpgen.d.aadavVnaaGa 202
                                       +a++ae+  Gv   +g +v  + ++++g +       +++g++ + ++d vV+++G 
  gi|488601309|ref|YP_007907780.1| 297 YAKRAEEEyGVVYKYG-RVSVVmQKPNGNL---IlkYEKDGRTfEeEYDMVVLSTGF 349
                                       6788855515666666.6666525565332...12323336554235677*****95 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 4.2e-07
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                        +iiGGG +G+++A+eLa++g    ++ek+ ++g g
  gi|488601309|ref|YP_007907780.1| 583 ALIIGGGLAGMTCALELAEQGfeSYIVEKEAELG-G 617
                                       58****************************9988.5 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.014
                                       EEETTEEEEEHHHHHHHHHHHHHHTT.-EEEESECEEEEEEEETCEEEEE....EECTEEEEEEEE..EEE--GG CS
                               DAO 135 lfypdtgqvdpakltaalaraaealG.veilegtevtgleeedgkvwgve....rttpgendaada..vVnaaGa 202
                                       lfy+ +g  +p++l++ l +++e+   ++++++++++++   dg v++ +    +  +ge++++++  v++a+Ga
  gi|488601309|ref|YP_007907780.1| 622 LFYTIDGK-NPQELLKELVEKVEKEPkITVFRNARIESI---DGFVGNFRskisV--DGEVKEVEHgvVIVATGA 690
                                       77777788.9************88855************...5455555465321..26554445566******8 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   3.4   2.1e-07   0.00011       3      21 ..      98     116 ..      96     117 .. 0.92
   2 !   20.6   2.5   5.9e-07   0.00031       2      20 ..     144     162 ..     142     164 .. 0.91
   3 !   20.9   3.0   4.8e-07   0.00026       3      21 ..     914     932 ..     912     933 .. 0.91
   4 !   14.5   2.5   5.4e-05     0.029       3      21 ..     951     969 ..     949     970 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.1e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                        +vd drC+gCg C +aCP
  gi|488601309|ref|YP_007907780.1|  98 LYVDMDRCTGCGECAKACP 116
                                       789**************** PP

  == domain 2  score: 20.6 bits;  conditional E-value: 5.9e-07
                            Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                       ++++d ++CigCg+C ++C
  gi|488601309|ref|YP_007907780.1| 144 VYAIDKEKCIGCGICENVC 162
                                       489**************** PP

  == domain 3  score: 20.9 bits;  conditional E-value: 4.8e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       ++v+++rC +Cg Cv+aCP
  gi|488601309|ref|YP_007907780.1| 914 AFVVRERCDACGLCVKACP 932
                                       6899*************** PP

  == domain 4  score: 14.5 bits;  conditional E-value: 5.4e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       ++v+++ C+gCg C   CP
  gi|488601309|ref|YP_007907780.1| 951 AEVNRAVCLGCGVCHATCP 969
                                       689***********777*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 !   16.3   3.9   1.5e-05     0.008      34      57 ..      98     120 ..      50     122 .. 0.83
   2 !   16.3   0.8   1.5e-05    0.0079      35      52 ..     146     163 ..     133     174 .. 0.64
   3 !   20.0   2.2     1e-06   0.00055      30      58 ..     910     937 ..     887     938 .. 0.67
   4 !   15.7   1.3   2.3e-05     0.012       1      23 [.     951     973 ..     951     989 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                           Fer4_21  34 lkvvedeCvGCnlCssvCPvedci 57 
                                       l v  d+C+GC  C++ CPv ++i
  gi|488601309|ref|YP_007907780.1|  98 LYVDMDRCTGCGECAKACPV-NAI 120
                                       467889*************9.777 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.5e-05
                           Fer4_21  35 kvvedeCvGCnlCssvCP 52 
                                       ++ +++C+GC +C +vC 
  gi|488601309|ref|YP_007907780.1| 146 AIDKEKCIGCGICENVCV 163
                                       444556666666666663 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 1e-06
                           Fer4_21  30 aktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +++++ vv ++C +C lC++ CPv ++ie
  gi|488601309|ref|YP_007907780.1| 910 DASKAFVVRERCDACGLCVKACPV-NAIE 937
                                       234457899**************9.9987 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 2.3e-05
                           Fer4_21   1 AridedkCigCgkCliaCedtsh 23 
                                       A ++++ C+gCg C+ +C+++++
  gi|488601309|ref|YP_007907780.1| 951 AEVNRAVCLGCGVCHATCPKSAI 973
                                       7899999***********97543 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.3   3.8e-06     0.002      33      51 .]      88     120 ..      51     120 .. 0.67
   2 !   26.7  11.9   8.4e-09   4.4e-06       1      51 []     104     167 ..     104     167 .. 0.93
   3 !    9.9   8.5    0.0015      0.79       1      29 [.     151     179 ..     151     265 .. 0.80
   4 !   31.3   7.8   3.3e-10   1.7e-07       1      51 []     920     973 ..     912     973 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.8e-06
                            Fer4_9  33 e..............eaCigCgaCveaCpkgai 51 
                                       +              ++C+gCg+C++aCp +ai
  gi|488601309|ref|YP_007907780.1|  88 DftvrikrnplyvdmDRCTGCGECAKACPVNAI 120
                                       04444444456777789************9987 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 8.4e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCpkgai 51 
                                       +CtgCg+C +aCp +++ e + +   r  ++               e+CigCg C+++C  +ai
  gi|488601309|ref|YP_007907780.1| 104 RCTGCGECAKACPVNAIDEYNEGLSFRSSIYIRypqavpkvyaidkEKCIGCGICENVCVAKAI 167
                                       6********************9999998887668999**********************98876 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0015
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlr 29 
                                       kC+gCg C+++C a+++++ + +++++l+
  gi|488601309|ref|YP_007907780.1| 151 KCIGCGICENVCVAKAINYNQRPEEIELK 179
                                       7******************9999998875 PP

  == domain 4  score: 31.3 bits;  conditional E-value: 3.3e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...eaCigCgaCveaCpkgai 51 
                                       +C  Cg Cv+aCp ++++ +++e+   ++ + e     C+gCg C + Cpk ai
  gi|488601309|ref|YP_007907780.1| 920 RCDACGLCVKACPVNAIELKQFENRGVVELKAEvnrAVCLGCGVCHATCPKSAI 973
                                       5************************9999988899989*************987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00098      0.52       1      32 [.       6      37 ..       6      52 .. 0.84
   2 ?    1.1   0.0      0.37   1.9e+02      87     121 ..      62      96 ..      58     101 .. 0.86
   3 !   14.0   0.0   4.3e-05     0.023     246     305 .]     327     391 ..     292     391 .. 0.73
   4 !   19.3   1.8     1e-06   0.00055     165     266 ..     581     689 ..     579     698 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00098
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.ni 32
                                      +++G+G aG+++a+ l ++g+ ++  lEk  +i
  gi|488601309|ref|YP_007907780.1|  6 LVVGGGIAGMQSALDLAESGF-KVYLLEKLpAI 37
                                      69*******************.58899996555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.37
                       Pyr_redox_3  87 lrevaksfelpiklfeeVesvkkedegfevetske 121
                                       l+ev ++++++i  ++e  sv+ e++ f+v+ +++
  gi|488601309|ref|YP_007907780.1|  62 LNEVGRHENIEIINNSELLSVEGEAGDFTVRIKRN 96 
                                       56888999999999999999999999999987765 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 4.3e-05
                       Pyr_redox_3 246 kvktedgkkvevkddvvla.tGykpdlsflkk...slfeldedgrpvlte.eteetnvpglflaG 305
                                          ++dg+++e++ d+v++ tG++p  +  k     ++el+e g+ + ++ +  etn pg+f+aG
  gi|488601309|ref|YP_007907780.1| 327 LKYEKDGRTFEEEYDMVVLsTGFEPPEEAKKYaeiLGIELNEYGFCKTDPfKPLETNKPGIFVAG 391
                                       33478999999966666666*****9655443337999************8889**********9 PP

  == domain 4  score: 19.3 bits;  conditional E-value: 1e-06
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienr.leelvke....ekikvlfnaevk 236
                                       +k ++iGg+  ++  Alel+++g e  +v +++e+  + ++  y++   + ++ l+elv++     ki+v  na+++
  gi|488601309|ref|YP_007907780.1| 581 KKALIIGGGLAGMTCALELAEQGFESYIVEKEAELGGNLKHLFYTIDGKNPQElLKELVEKvekePKITVFRNARIE 657
                                       67778888888888888888888888888888888888888888888777555245666666555558888888888 PP

                       Pyr_redox_3 237 eikekeeeykvk.tedgkkvev.kddvvlatG 266
                                       +i+    +++ k + dg+  ev +  v++atG
  gi|488601309|ref|YP_007907780.1| 658 SIDGFVGNFRSKiSVDGEVKEVeHGVVIVATG 689
                                       88877777766623344444442344555577 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   2.8   6.3e-06    0.0033       1      17 []     102     118 ..     102     121 .. 0.93
   2 !   10.5   4.8    0.0014      0.75       1      14 [.     149     162 ..     149     163 .. 0.96
   3 !   12.1   3.8   0.00041      0.22       2      17 .]     919     934 ..     918     934 .. 0.93
   4 !   16.4   1.7   1.8e-05    0.0093       4      15 ..     958     969 ..     954     978 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.3e-06
                            Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                       ++rC+gCg C  aCP++
  gi|488601309|ref|YP_007907780.1| 102 MDRCTGCGECAKACPVN 118
                                       59*************75 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                            Fer4_4   1 qerCigCgsCvaaC 14 
                                       +e+CigCg C+++C
  gi|488601309|ref|YP_007907780.1| 149 KEKCIGCGICENVC 162
                                       69************ PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00041
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       erC  Cg Cv aCP++
  gi|488601309|ref|YP_007907780.1| 919 ERCDACGLCVKACPVN 934
                                       89************75 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 1.8e-05
                            Fer4_4   4 CigCgsCvaaCP 15 
                                       C+gCg+C+a+CP
  gi|488601309|ref|YP_007907780.1| 958 CLGCGVCHATCP 969
                                       ************ PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.5   2.5e-05     0.013       4      33 ..       5      34 ..       3      37 .. 0.95
   2 !   21.8   0.1   1.8e-07   9.2e-05       3      35 ..     582     614 ..     580     620 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      Vl+VG+G aG+ +al L+e G +v l+ek 
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGFKVYLLEKL 34
                                      9***************************97 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.8e-07
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       + lI+G+G+aG++ al+L+e+G ++ +vek ++
  gi|488601309|ref|YP_007907780.1| 582 KALIIGGGLAGMTCALELAEQGFESYIVEKEAE 614
                                       579***************************876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.7   2.8e-06    0.0015       2      77 ..       5      92 ..       4      96 .. 0.76
   2 !   16.7   1.0   1.5e-05     0.008       1      68 [.     582     661 ..     582     674 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.8e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS...TTSSHHHHHH......H....HHHHHHTTEEEECSEEEEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll...rllDeeaski......l....qeklekngievllntkveeie 67
                                      v+vvGgG  g+  A  lae g kV+++e  + +    +++D+++ ++      l     e  ++++ie++ n+++ ++e
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGFKVYLLEKLPAIGgrmSQIDKTFPTNdcamciLspklNEVGRHENIEIINNSELLSVE 83
                                      89*******************************9988899998766422211132221333355699999999999999 PP

                                      EETTSEEEEE CS
                         Pyr_redox 68 gsedgvesvk 77
                                      g++  ++ v+
  gi|488601309|ref|YP_007907780.1| 84 GEAGDFT-VR 92
                                      9997744.55 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.5e-05
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS...TTS........SHHHHHHHHHHHHHT.TEEEECSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll...rll........Deeaskilqeklekn.gievllntkvee 65 
                                       k++++GgG+ g+ +A +lae g + ++ve + +l    + l        ++e+ k+l ek+ek+ +i+v  n+++e+
  gi|488601309|ref|YP_007907780.1| 582 KALIIGGGLAGMTCALELAEQGFESYIVEKEAELGgnlKHLfytidgknPQELLKELVEKVEKEpKITVFRNARIES 658
                                       579*******************9999999999987533211333333337888888999999999***********9 PP

                                       EEE CS
                         Pyr_redox  66 ieg 68 
                                       i+g
  gi|488601309|ref|YP_007907780.1| 659 IDG 661
                                       997 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.4e-07    0.0005       2      29 ..       5      41 ..       4      71 .. 0.78
   2 !   12.3   0.3   0.00012     0.065       3      29 ..     584     610 ..     582     623 .. 0.84
   3 ?    3.3   0.1     0.069        37      99     167 ..     636     702 ..     629     728 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.4e-07
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE.........E CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi.........t 29
                                      v V+GgG AG+  Al +a++G+kv L+          
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGFKVYLLeklpaiggrM 41
                                      89************************95555554441 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                                       EEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLit 29 
                                        +iGgG+AG+ +Al++a+ G++  ++ 
  gi|488601309|ref|YP_007907780.1| 584 LIIGGGLAGMTCALELAEQGFESYIVE 610
                                       69******************9988774 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.069
                                       HHHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS..-EEEECEEEE--TT-BT-EEEETTEEEESSC CS
                              GIDA  99 kevteklenepnleiiee.eveeliveekkvkgvvtedg..etikakavviatGtflkgkihigekelsaGr 167
                                       ke+ ek+e+ep+++++++ ++e+++   ++ +  +  dg  ++++  +v++atG+       ++ +e++ G+
  gi|488601309|ref|YP_007907780.1| 636 KELVEKVEKEPKITVFRNaRIESIDGFVGNFRSKISVDGevKEVEHGVVIVATGA-----EEYKPREYEYGK 702
                                       6788999********98625777755446666655555511456777*******9.....444445555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   5.4e-06    0.0028       3      37 ..       5      39 ..       3      44 .. 0.93
   2 ?   -1.3   0.0       1.2   6.5e+02      99     148 ..      45      94 ..      39     101 .. 0.81
   3 !   16.9   0.2   3.8e-06     0.002       2      37 ..     582     617 ..     581     621 .. 0.91
   4 ?   -2.1   0.0       2.3   1.2e+03     109     164 ..     632     690 ..     624     693 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.4e-06
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                      v+v+GgG AG+  A+ +a+ g +V llek +++g 
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGFKVYLLEKLPAIGG 39
                                      89***************************999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                       TEEEETT.-CHHHHHHHHHHH.HHHT-EEE-S--EEEEECETTE.EEEEE. CS
                       HI0933_like  99 grlFpvsdkaedivdallkel.keagvklrletevksvekeedgkfrvktk 148
                                       ++ Fp++d a  i++  l+e+ +++++++  ++e+ sve e++  f+v++k
  gi|488601309|ref|YP_007907780.1|  45 DKTFPTNDCAMCILSPKLNEVgRHENIEIINNSELLSVEGEAGD-FTVRIK 94 
                                       678***********988888735699************876666.999883 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 3.8e-06
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                       + ++iGgG AG+ +A+++a++g +  ++ek+ +lg 
  gi|488601309|ref|YP_007907780.1| 582 KALIIGGGLAGMTCALELAEQGFESYIVEKEAELGG 617
                                       679****************************99985 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHH.HT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE---- CS
                       HI0933_like 109 edivdallkelke.agvklrletevksvekeedgkfrvkt..k.seeeleadklvlAtGG 164
                                       +++++ l++++++  ++++  + +++s++   ++ fr k+  + + +e+e   +++AtG 
  gi|488601309|ref|YP_007907780.1| 632 QELLKELVEKVEKePKITVFRNARIESIDGFVGN-FRSKIsvDgEVKEVEHGVVIVATGA 690
                                       6677777777765378999999999999654433.544442122667899999999*997 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   3.1e-05     0.016      19      58 ..       4      42 ..       1      55 [. 0.90
   2 !   15.3   0.0   1.7e-05    0.0089      15      58 ..     574     620 ..     563     658 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                       v++vG+G +G+ +a  la++ ++kv +le+  ++GG + 
  gi|488601309|ref|YP_007907780.1|  4 AVLVVGGGIAGMQSALDLAES-GFKVYLLEKLPAIGGRMS 42
                                      589******************.**************9775 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.7e-05
                                       HTEEEE....EEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                              Thi4  15 yaesDv....vivGaGssGLtaayylakkpdlkvailersvspGGGaw 58 
                                       y+e D+    +i+G+G +G+t+a  la++ +++  i+e++  +GG   
  gi|488601309|ref|YP_007907780.1| 574 YVEVDInkkaLIIGGGLAGMTCALELAEQ-GFESYIVEKEAELGGNLK 620
                                       677776555479*****************.************999754 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   1.8e-05    0.0096       2      21 ..      99     117 ..      98     129 .. 0.82
   2 !    9.4   0.4    0.0032       1.7       3      18 ..     147     162 ..     146     179 .. 0.86
   3 !    9.7   0.6    0.0027       1.4       5      19 ..     918     932 ..     915     948 .. 0.85
   4 ?    6.0   0.6     0.037        20       3      20 ..     953     970 ..     951     983 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-05
                           Fer4_15   2 vvDrdaCigcglCvaeapev 21 
                                       +vD d+C+gcg C++++p v
  gi|488601309|ref|YP_007907780.1|  99 YVDMDRCTGCGECAKACP-V 117
                                       79***************8.3 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0032
                           Fer4_15   3 vDrdaCigcglCvaea 18 
                                       +D+++Cigcg C  ++
  gi|488601309|ref|YP_007907780.1| 147 IDKEKCIGCGICENVC 162
                                       9***********8777 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0027
                           Fer4_15   5 rdaCigcglCvaeap 19 
                                       r++C+ cglCv+++p
  gi|488601309|ref|YP_007907780.1| 918 RERCDACGLCVKACP 932
                                       89************7 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.037
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       v+r  C gcg+C a +p+
  gi|488601309|ref|YP_007907780.1| 953 VNRAVCLGCGVCHATCPK 970
                                       88999***********96 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   3.2   5.3e-05     0.028      40      58 ..      96     117 ..      51     121 .. 0.57
   2 !   17.8  11.4   6.9e-06    0.0036       1      57 [.     104     163 ..     104     168 .. 0.73
   3 !   10.5   1.6    0.0013      0.68       1      23 [.     151     174 ..     151     185 .. 0.76
   4 !   12.9   9.9   0.00023      0.12       1      58 [.     920     970 ..     920     973 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.3e-05
                           Fer4_17  40 e...ekaslCieCgeCerkCPq 58 
                                       +     +++C++CgeC+++CP 
  gi|488601309|ref|YP_007907780.1|  96 NplyVDMDRCTGCGECAKACPV 117
                                       3443489**************6 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.9e-06
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepk.kllraaklglleeaeke..ekaslCieCgeCerkCP 57 
                                       rC++Cg C+++Cp +++ + ++  +++  +++   +++ k      ++Ci+Cg Ce +C 
  gi|488601309|ref|YP_007907780.1| 104 RCTGCGECAKACPVNAIDEYNEGlSFRSSIYIRYPQAVPKVyaIDKEKCIGCGICENVCV 163
                                       7*************999664433267777777544454443224669************6 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0013
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydnepk 23 
                                       +Ci+Cg C+++C   ++ y+++p+
  gi|488601309|ref|YP_007907780.1| 151 KCIGCGICENVCVAKAInYNQRPE 174
                                       6***********986653666565 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 0.00023
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       rC  Cg C+++Cp +++  +       ++++  + e ++e +   C++Cg C + CP+
  gi|488601309|ref|YP_007907780.1| 920 RCDACGLCVKACPVNAIELK-------QFENRGVVELKAEVNRAVCLGCGVCHATCPK 970
                                       7*************999655.......333333334445556678************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 !   17.0   0.8   1.1e-05     0.006      45      64 ..      99     118 ..      50     120 .. 0.69
   2 !   13.1   0.1   0.00019     0.099       3      18 ..     150     164 ..     148     210 .. 0.82
   3 !   14.8  10.0   5.7e-05      0.03       3      64 ..     919     971 ..     917     973 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-05
                            Fer4_8  45 eealwsCttcgaCtevCpvg 64 
                                       +  +++Ct+cg+C+++Cpv+
  gi|488601309|ref|YP_007907780.1|  99 YVDMDRCTGCGECAKACPVN 118
                                       56688999999999999986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00019
                            Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                       ekCi+Cg C++ C  +
  gi|488601309|ref|YP_007907780.1| 150 EKCIGCGICENVCV-A 164
                                       79***********4.3 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 5.7e-05
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       e+C  Cg+C +aCpv   + k  +++rg ++  + e  +         C++cg C   Cp++
  gi|488601309|ref|YP_007907780.1| 919 ERCDACGLCVKACPVNAIELKQ-FENRGVVEL-KAEVNR-------AVCLGCGVCHATCPKS 971
                                       68************87777643.556666555.333333.......46************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 !   12.7   0.7   0.00034      0.18      76      95 ..      99     118 ..      86     119 .. 0.80
   2 !   12.0   0.3   0.00057       0.3      76      94 ..     146     164 ..     124     166 .. 0.76
   3 ?    5.0   0.9     0.083        44      78      95 ..     917     934 ..     888     935 .. 0.76
   4 !   12.5   0.7   0.00037       0.2      71      94 ..     947     970 ..     937     972 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00034
                           Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                        +++  C+GCg C +acpv+
  gi|488601309|ref|YP_007907780.1|  99 YVDMDRCTGCGECAKACPVN 118
                                       568899***********986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00057
                           Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                        +++++C+GCg C+++c +
  gi|488601309|ref|YP_007907780.1| 146 AIDKEKCIGCGICENVCVA 164
                                       34899************87 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.083
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                        ++ C  Cg C++acpv+
  gi|488601309|ref|YP_007907780.1| 917 VRERCDACGLCVKACPVN 934
                                       577899999999999975 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00037
                           Fer4_22  71 sefkekfgesgCvGCgRCieacpv 94 
                                        e+k+++++ +C GCg C+++cp+
  gi|488601309|ref|YP_007907780.1| 947 VELKAEVNRAVCLGCGVCHATCPK 970
                                       56788899**************97 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00027      0.14       1      32 [.      12      43 ..      12      47 .. 0.94
   2 ?   -3.7   0.0       9.9   5.2e+03     206     259 ..     291     346 ..     276     349 .. 0.72
   3 !   10.8   0.0    0.0004      0.21       1      30 [.     590     619 ..     590     622 .. 0.95
   4 ?   -2.9   0.0         6   3.2e+03     210     266 ..     636     694 ..     632     703 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                      HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-E CS
                     Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrvGGRirt 32
                                      +aG+  A  L++ Gf+V +lE  + +GGR++ 
  gi|488601309|ref|YP_007907780.1| 12 IAGMQSALDLAESGFKVYLLEKLPAIGGRMSQ 43
                                      89***************************975 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.9
                                       TTHTHHHHHHHHHTTTTEEEETSEEEEEEEEETTC.EEEEET.TSTEE..EESEEEE- CS
                     Amino_oxidase 206 rgGlsqlpealaeelrgldirlntrVkeikregdg.vtvtle.dgevv..eaDaVvvT 259
                                        +G+++ +++ +e + g+  +++ rV+ + + ++g   +++e dg+++  e+D Vv+ 
  gi|488601309|ref|YP_007907780.1| 291 GKGFEEYAKRAEE-EYGVVYKYG-RVSVVMQKPNGnLILKYEkDGRTFeeEYDMVVLS 346
                                       5677777777777.788888888.7777888777764455545999999999999986 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRi 30 
                                       laG+++A +L+++Gf+  ++E +  +GG +
  gi|488601309|ref|YP_007907780.1| 590 LAGMTCALELAEQGFESYIVEKEAELGGNL 619
                                       79**************************86 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 6
                                       HHHHHHHHHTTTTEEEETSEEEEEEEE..ETTCEEEEETTSTEEEESE..EEE-S-HHHHH CS
                     Amino_oxidase 210 sqlpealaeelrgldirlntrVkeikr..egdgvtvtledgevveaDa..VvvTvplgvlk 266
                                       ++l+e +++ +++ ++  n+r  +i+   ++   ++  +dgev e+ +  V+v++     k
  gi|488601309|ref|YP_007907780.1| 636 KELVEKVEK-EPKITVFRNARIESIDGfvGNFRSKIS-VDGEVKEVEHgvVIVATGAEEYK 694
                                       456666666.888899999999999998755555553.49999955555599999877666 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   7.8e-05     0.041      29      63 ..       3      37 ..       1      77 [. 0.85
   2 ?    5.2   0.0     0.021        11      30      68 ..     582     620 ..     575     644 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrpar 63
                                      + vlv+GgG+aG+q++   ++ g kV++l++ pa 
  gi|488601309|ref|YP_007907780.1|  3 GAVLVVGGGIAGMQSALDLAESGFKVYLLEKLPAI 37
                                      68*************************99988775 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqle 68 
                                       k l+iGgG aG+  +   ++ g + ++++++++   +l+
  gi|488601309|ref|YP_007907780.1| 582 KALIIGGGLAGMTCALELAEQGFESYIVEKEAELGGNLK 620
                                       789*********998888888888888887777665555 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   3.0   0.00058       0.3       1      17 [.     100     116 ..     100     124 .. 0.96
   2 !    9.2   4.1    0.0033       1.8       1      16 [.     147     162 ..     147     164 .. 0.95
   3 ?    7.4   2.5     0.012       6.3       3      17 ..     918     932 ..     916     934 .. 0.92
   4 !    9.4   1.9     0.003       1.6       1      18 [.     953     970 ..     953     971 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00058
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD d+C++cg C++++P
  gi|488601309|ref|YP_007907780.1| 100 VDMDRCTGCGECAKACP 116
                                       8***************9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0033
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       +D+++Ci+cg+C +++
  gi|488601309|ref|YP_007907780.1| 147 IDKEKCIGCGICENVC 162
                                       8*************99 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.012
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                       r++C acg+Cv+++P
  gi|488601309|ref|YP_007907780.1| 918 RERCDACGLCVKACP 932
                                       799***********9 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.003
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       V+r  C +cg+C +++P+
  gi|488601309|ref|YP_007907780.1| 953 VNRAVCLGCGVCHATCPK 970
                                       8999*************7 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 ?    6.6   0.0      0.02        10      10      38 ..       5      33 ..       2      79 .. 0.84
   2 !   10.1   0.1    0.0016      0.85       7      87 ..     580     706 ..     577     714 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.02
                     NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvap 38
                                      vlvvGgG  +++ +  l+e+g kv ++ +
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGFKVYLLEK 33
                                      9***********************98765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0016
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev.....keele................elvklaeee........ 54 
                                       +kk l++GgG  +++ +  l+e+g +  +v +e          +                elv+  e+e        
  gi|488601309|ref|YP_007907780.1| 580 NKKALIIGGGLAGMTCALELAEQGFESYIVEKEAelggnL---KhlfytidgknpqellkELVEKVEKEpkitvfrn 653
                                       699*****************************96554440...1444444455555444444443333356666666 PP

                     NAD_binding_7  55 ..................lekdlegad..lviaatddrelneriaeaakarri 87 
                                                         +++++++++  +vi+at  +e + r +e+ k+ ++
  gi|488601309|ref|YP_007907780.1| 654 ariesidgfvgnfrskisVDGEVKEVEhgVVIVATGAEEYKPREYEYGKNPKV 706
                                       66666666666655554445557777778999999999988888887776555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.3    0.0032       1.7       2      34 ..       5      35 ..       4      44 .. 0.90
   2 ?   -3.7   0.0       8.9   4.7e+03      99     145 ..     304     352 ..     295     366 .. 0.65
   3 !    7.5   0.1    0.0034       1.8       3      36 ..     584     615 ..     583     645 .. 0.77
   4 ?    1.0   0.0      0.32   1.7e+02     102     149 ..     649     697 ..     630     712 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0032
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasp 34
                                      v+v+G+G Ag++ A  l  a+ g kv l+e  p
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDL--AESGFKVYLLEKLP 35
                                      89***************..99********8766 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.9
                     Lycopene_cycl  99 engvklleakvesveeeeageslv.vleggrki..rarlvvdarglaslk 145
                                       e gv +  ++v  v+++++g+    + ++gr+   +  +vv ++g ++++
  gi|488601309|ref|YP_007907780.1| 304 EYGVVYKYGRVSVVMQKPNGNLILkYEKDGRTFeeEYDMVVLSTG-FEPP 352
                                       568999999999999999977665144577755114567777777.5444 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0034
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       ++iG+G+Ag+  A +l  a++g +  ++e  ++l
  gi|488601309|ref|YP_007907780.1| 584 LIIGGGLAGMTCALEL--AEQGFESYIVEKEAEL 615
                                       69**************..8899999999887776 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.32
                     Lycopene_cycl 102 vklleakvesveeeea.geslvvleggr.kirarlvvdarglaslkkarr 149
                                         +++a++es+       +s + ++g++ +++  +v++a+g a++ k+r+
  gi|488601309|ref|YP_007907780.1| 649 TVFRNARIESIDGFVGnFRSKISVDGEVkEVEHGVVIVATG-AEEYKPRE 697
                                       468999999999877657899999999889***********.55554444 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.15        79       2      41 ..       7      41 ..       6      51 .. 0.81
   2 ?    5.5   0.0      0.03        16     104     154 ..     294     348 ..     287     350 .. 0.87
   3 ?    4.2   0.1     0.071        38       2      20 ..     585     603 ..     584     619 .. 0.80
   4 ?   -0.6   0.0       2.2   1.2e+03     101     154 ..     632     689 ..     628     691 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrv 41
                                      +vG+G++G+  +  L+++      +++ l ++ ++ g gr+
  gi|488601309|ref|YP_007907780.1|  7 VVGGGIAGMQSALDLAES-----GFKVYLLEKLPAiG-GRM 41
                                      8**************999.....59999999966635.655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.03
                     NAD_binding_9 104 feellarlpegvtvevhraevvdleeradgqavll..adgasl..aadaVvLAlG 154
                                       fee ++r++e+  v +  ++v  + ++++g  +l+  +dg+++  ++d VvL +G
  gi|488601309|ref|YP_007907780.1| 294 FEEYAKRAEEEYGVVYKYGRVSVVMQKPNGNLILKyeKDGRTFeeEYDMVVLSTG 348
                                       789999999999******************8776666899985559********9 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.071
                     NAD_binding_9   2 ivGaGprGlavlerLlara 20 
                                       i+G+G +G++++ +L+++ 
  gi|488601309|ref|YP_007907780.1| 585 IIGGGLAGMTCALELAEQG 603
                                       9**************9984 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.2
                     NAD_binding_9 101 rdlfeellarlpegvtvevh.raevvdleeradgq..avlladg..aslaadaVvLAlG 154
                                       ++l++el+++++++ +++v+ +a++++++   +++  ++   dg  ++++   V++A+G
  gi|488601309|ref|YP_007907780.1| 632 QELLKELVEKVEKEPKITVFrNARIESIDGFVGNFrsKI-SVDGevKEVEHGVVIVATG 689
                                       678999999999999999983559999999877763233.3444235578888999998 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.013       6.6       2      33 ..       5      33 ..       4      43 .. 0.88
   2 ?    3.6   0.0     0.046        24     154     210 ..     292     350 ..     236     357 .. 0.83
   3 ?    4.3   0.1     0.028        15       3      31 ..     584     609 ..     582     614 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.013
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlves 33
                                      +++vGGG+aG  +A  la+ +   ++v l+e+
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESG---FKVYLLEK 33
                                      89****************999...88888886 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.046
                                       HHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE..-SEEEE-SGGG CS
                    Trp_halogenase 154 alyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreve..adlfiDcsGfr 210
                                       + ++++ +r  e+ Gv    g+v  v ++++g+      +dgr++e  +d+++  +Gf+
  gi|488601309|ref|YP_007907780.1| 292 KGFEEYAKRAEEEYGVVYKYGRVSVVMQKPNGNLILKYEKDGRTFEeeYDMVVLSTGFE 350
                                       56888999999999*********999999999998878889999853379999999997 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.028
                                       EEE--SHHHHHHHHHHHHHTTTSSEEEEE CS
                    Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlv 31 
                                       +i+GGG aG + A  la+++   +e  +v
  gi|488601309|ref|YP_007907780.1| 584 LIIGGGLAGMTCALELAEQG---FESYIV 609
                                       8****************998...444444 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 ?    7.5   0.1    0.0066       3.5       2      30 ..       5      33 ..       4      48 .. 0.89
   2 ?    2.8   0.1      0.18        94       4      33 ..     585     614 ..     582     690 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      v v+G G+ G + a  +a++g++V l++ 
  gi|488601309|ref|YP_007907780.1|  5 VLVVGGGIAGMQSALDLAESGFKVYLLEK 33
                                      78***********************9986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.18
                                       EE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdisee 33 
                                       +iG G+ G   a  +a++g+e  +v+ ++e
  gi|488601309|ref|YP_007907780.1| 585 IIGGGLAGMTCALELAEQGFESYIVEKEAE 614
                                       9********************999987655 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 ?   -2.5   0.1         4   2.1e+03     193     213 ..       4      24 ..       2      44 .. 0.83
   2 ?    7.7   0.0    0.0033       1.8     303     341 ..     314     350 ..     293     351 .. 0.78
   3 ?    1.7   0.0      0.21   1.1e+02     140     197 ..     672     728 ..     637     733 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
                       K_oxygenase 193 riaVvGsGqSaaeifedllrr 213
                                        ++VvG+G  + + + dl+++
  gi|488601309|ref|YP_007907780.1|   4 AVLVVGGGIAGMQSALDLAES 24 
                                       699*****9998888888776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0033
                       K_oxygenase 303 vesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                                       v  + ++++   +l l+ e++g+++++e+d+vvl+TG++
  gi|488601309|ref|YP_007907780.1| 314 VSVVMQKPN--GNLILKYEKDGRTFEEEYDMVVLSTGFE 350
                                       555555554..567777888*****************97 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.21
                       K_oxygenase 140 aegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVv 197
                                        +ge +e+e   +++++G e + P  +e  + +++v+ + e+ e  ++ +a+++++ +
  gi|488601309|ref|YP_007907780.1| 672 VDGEVKEVEHGVVIVATGAEEYKPREYEYGK-NPKVITQVELEEMLARGEAPESVVMI 728
                                       4788888899999999999999999999766.59999998888888888888888765 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.033        18      58      74 ..     102     118 ..      86     131 .. 0.80
   2 ?    2.7   1.1      0.26   1.4e+02      58      72 ..     149     163 ..     138     171 .. 0.82
   3 ?   -1.8   0.0       6.7   3.5e+03       9      31 ..     308     330 ..     302     348 .. 0.70
   4 ?    5.6   1.9     0.033        18      57      74 ..     917     934 ..     897     942 .. 0.75
   5 ?    8.8   1.3    0.0034       1.8      49      88 ..     946     985 ..     935     992 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.033
                           Fer4_18  58 agdcidcescvkvcPtg 74 
                                       +  c+ c+ c k cP++
  gi|488601309|ref|YP_007907780.1| 102 MDRCTGCGECAKACPVN 118
                                       567999******99985 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.26
                           Fer4_18  58 agdcidcescvkvcP 72 
                                       + +ci c+ c +vc 
  gi|488601309|ref|YP_007907780.1| 149 KEKCIGCGICENVCV 163
                                       678999999999996 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 6.7
                           Fer4_18   9 vcPyarvqsvlydeetllvvyda 31 
                                       v  y+rv  v++ ++  l+    
  gi|488601309|ref|YP_007907780.1| 308 VYKYGRVSVVMQKPNGNLILKYE 330
                                       6679*******999875544333 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.033
                           Fer4_18  57 gagdcidcescvkvcPtg 74 
                                           c +c+ cvk cP++
  gi|488601309|ref|YP_007907780.1| 917 VRERCDACGLCVKACPVN 934
                                       4567999********985 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0034
                           Fer4_18  49 ekeerkekgagdcidcescvkvcPtgidirkGlqlecisc 88 
                                        +e+++e + + c+ c++c + cP    + kG+ ++ i+ 
  gi|488601309|ref|YP_007907780.1| 946 VVELKAEVNRAVCLGCGVCHATCPKSAIVVKGFTIDQIKA 985
                                       56788889999**********************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (994 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.98u 0.35s 00:00:01.33 Elapsed: 00:00:00.53
# Mc/sec: 5656.11
//
Query:       gi|488601310|ref|YP_007907781.1|  [L=137]
Description: F420-non-reducing hydrogenase subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-54  183.3   0.1    1.6e-54  183.1   0.1    1.0  1  FlpD      Methyl-viologen-reducing hydrogenase, delta subunit


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 !  183.1   0.1   8.9e-59   1.6e-54       1     123 []       8     130 ..       8     130 .. 1.00

  Alignments for each domain:
  == domain 1  score: 183.1 bits;  conditional E-value: 8.9e-59
                              FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerr 77 
                                       il+F+Cnwc+ya+adlag+sr+qy pn+ri+rv+Csg+v+p++il+a++kG+dgV+v+gChpgdChy+ Gn++a++r
  gi|488601310|ref|YP_007907781.1|   8 ILVFACNWCSYAGADLAGTSRIQYTPNIRIVRVMCSGMVNPAMILYAFKKGVDGVVVAGCHPGDCHYNVGNYYAKKR 84 
                                       89*************************************************************************** PP

                              FlpD  78 veklkelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                       + +lkelle +g+++eR+ l ++saaeg+kfae +++f+ekik+LG
  gi|488601310|ref|YP_007907781.1|  85 IVLLKELLEFVGFDSERLMLIWASAAEGKKFAEEMTKFAEKIKQLG 130
                                       *********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 783.51
//
Query:       gi|488601311|ref|YP_007907782.1|  [L=314]
Description: hypothetical protein Asulf_01818 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-09   35.9  14.6    2.1e-07   31.4  13.1    2.5  2  Fer4_17       4Fe-4S dicluster domain
    2.7e-08   33.8  12.0    0.00093   19.3   0.3    3.2  3  Fer4_10       4Fe-4S dicluster domain
    1.5e-05   25.5  20.4     0.0064   17.1   5.9    3.3  3  Fer4_7        4Fe-4S dicluster domain
    2.2e-05   24.8  13.6    2.2e-05   24.8  13.6    2.0  1  Fer4_8        4Fe-4S dicluster domain
    2.6e-05   24.1   8.4    0.00018   21.3   8.4    2.4  1  FrhB_FdhB_C   Coenzyme F420 hydrogenase/dehydrogenase, beta s
     0.0001   22.2  19.5     0.0001   22.1   0.8    3.4  4  Fer4_2        4Fe-4S binding domain
     0.0001   21.9  14.6     0.0011   18.7   3.0    3.6  4  Fer4          4Fe-4S binding domain
    0.00012   22.1  20.7     0.0029   17.8  17.1    3.0  2  Fer4_9        4Fe-4S dicluster domain
    0.00055   20.1   4.8      0.089   13.0   0.0    2.4  2  Fer4_18       4Fe-4S dicluster domain
     0.0014   18.6   4.2     0.0014   18.6   4.2    3.1  3  Fer4_6        4Fe-4S binding domain
  ------ inclusion threshold ------
      0.012   16.1   4.2      0.012   16.1   4.2    3.2  2  Fer4_4        4Fe-4S binding domain
      0.077   13.1  13.9        1.1    9.5   4.2    3.1  3  Fer4_21       4Fe-4S dicluster domain
       0.12   12.0   0.1       0.24   11.1   0.1    1.5  1  DDE_Tnp_ISL3  Transposase
       0.84   10.5  21.1    3.2e+02    2.2  21.1    2.6  1  Fer4_22       4Fe-4S dicluster domain
        2.3    9.3  19.7        5.6    8.1   3.1    3.2  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   5.5   9.1e-06     0.011       4      58 ..     146     209 ..     145     211 .. 0.67
   2 !   31.4  13.1   1.7e-10   2.1e-07       1      61 []     196     279 ..     196     279 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.1e-06
                           Fer4_17   4 qCgyClpeCpsyeaydn...epkkllraakl.glleeaeke.......ekaslCieCgeCerkCPq 58 
                                       +C+yC +  p+  +yd+   e k++ r+++  +++e+ ++e       +++++Ci C  C+++CP+
  gi|488601311|ref|YP_007907782.1| 146 NCKYCDA--PTPVIYDElfgEIKTVERDFSDiEEFEKLSREerweywmKEMEKCIRCYACRSACPM 209
                                       6888888..6655665544566677777755644444333334445659****************8 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.7e-10
                           Fer4_17   1 rCiqCgyClpeCpsyea..............ydnepkkllraaklglleeaeke.........ekaslCieCgeCer 54 
                                       +Ci+C +C+ +Cp++++              + + ++k ++   lg++ +a+++         + a++C+ CgeCer
  gi|488601311|ref|YP_007907782.1| 196 KCIRCYACRSACPMCYCteclvdpvnlavspMTKAEEKAMYPRFLGKTVNASDNlfyhlirviHHAGRCADCGECER 272
                                       6***************955555444443333222344555555555555555556777777789************* PP

                           Fer4_17  55 kCPqgld 61 
                                       +CP++++
  gi|488601311|ref|YP_007907782.1| 273 ACPMDIP 279
                                       ****985 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.6   1.9e+03      38      49 ..     140     151 ..     125     158 .. 0.69
   2 !   17.4   4.6   2.9e-06    0.0035       4      23 ..     192     211 ..     189     246 .. 0.77
   3 !   19.3   0.3   7.8e-07   0.00093       2      24 ..     257     282 ..     256     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                           Fer4_10  38 vrkkvekCtgcg 49 
                                       ++  +++C  c 
  gi|488601311|ref|YP_007907782.1| 140 DDFIYDNCKYCD 151
                                       455666666665 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.9e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadl 23 
                                       ++ ++CirC +C++aCP++ 
  gi|488601311|ref|YP_007907782.1| 192 KEMEKCIRCYACRSACPMCY 211
                                       6789*************965 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 7.8e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl...t 24 
                                       v++ + +C  Cg+C +aCP+d+   +
  gi|488601311|ref|YP_007907782.1| 257 VIHHAGRCADCGECERACPMDIplrK 282
                                       5677889*************765441 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.4       1.1   1.3e+03      35      42 ..     144     151 ..      77     157 .. 0.67
   2 !   17.1   5.9   5.4e-06    0.0064      18      49 ..     177     208 ..     145     211 .. 0.65
   3 !   13.6   5.4   6.3e-05     0.075      31      51 ..     257     277 ..     211     278 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
                            Fer4_7  35 pekClgCg 42 
                                       +++C +C+
  gi|488601311|ref|YP_007907782.1| 144 YDNCKYCD 151
                                       46666665 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.4e-06
                            Fer4_7  18 eldeeenekgtekveidpekClgCgaCvavCP 49 
                                       e+++ ++e++ e++  ++ekC+ C+aC ++CP
  gi|488601311|ref|YP_007907782.1| 177 EFEKLSREERWEYWMKEMEKCIRCYACRSACP 208
                                       3556667778899999**************** PP

  == domain 3  score: 13.6 bits;  conditional E-value: 6.3e-05
                            Fer4_7  31 veidpekClgCgaCvavCPtg 51 
                                       v +++ +C +Cg+C+++CP +
  gi|488601311|ref|YP_007907782.1| 257 VIHHAGRCADCGECERACPMD 277
                                       4567899************87 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8  13.6   1.8e-08   2.2e-05       1      65 []     193     278 ..     193     278 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.8e-08
                            Fer4_8   1 elekCieCgaCqsaCpvlrr.........tkkhlldargeaaedvqeeqvlee....................eeal 48 
                                       e+ekCi+C aC+saCp++ +                     + +++e+ ++                       + +
  gi|488601311|ref|YP_007907782.1| 193 EMEKCIRCYACRSACPMCYCteclvdpvnL-------AVSPMTKAEEKAMY-PrflgktvnasdnlfyhlirvIHHA 261
                                       589*************88773333332221.......22222212222221.134444555566667788999999* PP

                            Fer4_8  49 wsCttcgaCtevCpvgi 65 
                                       ++C  cg+C+++Cp++i
  gi|488601311|ref|YP_007907782.1| 262 GRCADCGECERACPMDI 278
                                       **************987 PP

>> 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 !   21.3   8.4   1.5e-07   0.00018       2     105 ..      71     159 ..      70     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk.kklkekilltiglfCggnfspealrk.lleelgvdpedvkklefrgkgkfrvelkd 76 
                                       +kv+vv+++C+ +a++kl+   k  ++ +++ig+ C g+ +++++ + +  + +++ ++++  +       ++    
  gi|488601311|ref|YP_007907782.1|  71 DKVGVVVKGCDSKAIKKLMMeDKIDRERVYIIGVTCDGVANYRKIVEaVGSDFKIEGDKIVAGDT------VL---- 137
                                       589**************99886788888************9999888777888888777766555......44.... PP

                       FrhB_FdhB_C  77 ekeislkeleefirpsCkvCkdktaelAD 105
                                              ++++fi ++Ck+C+  t+   D
  gi|488601311|ref|YP_007907782.1| 138 -------NIDDFIYDNCKYCDAPTPVIYD 159
                                       .......3456778888888776665544 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   0.1       2.9   3.5e+03      12      16 ..     146     150 ..     142     152 .. 0.61
   2 !   22.1   0.8   8.8e-08    0.0001       7      21 ..     194     208 ..     187     209 .. 0.86
   3 ?   -2.3   0.2       5.1   6.1e+03      10      13 ..     212     215 ..     211     217 .. 0.82
   4 !   11.7   3.0   0.00019      0.22       8      21 ..     262     275 ..     256     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                            Fer4_2  12 gCgaC 16 
                                       +C+ C
  gi|488601311|ref|YP_007907782.1| 146 NCKYC 150
                                       56655 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 8.8e-08
                            Fer4_2   7 tdrCigCgaCvsaCP 21 
                                        ++Ci+C aC+saCP
  gi|488601311|ref|YP_007907782.1| 194 MEKCIRCYACRSACP 208
                                       79************* PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.1
                            Fer4_2  10 CigC 13 
                                       C++C
  gi|488601311|ref|YP_007907782.1| 212 CTEC 215
                                       9999 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00019
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                        rC  Cg C  aCP
  gi|488601311|ref|YP_007907782.1| 262 GRCADCGECERACP 275
                                       69************ PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.4      0.35   4.2e+02       4      12 ..     143     151 ..     141     152 .. 0.80
   2 !   18.7   3.0   9.4e-07    0.0011       5      19 ..     194     208 ..     191     209 .. 0.92
   3 ?   -3.5   0.3       9.3   1.1e+04       8      11 ..     212     215 ..     211     216 .. 0.72
   4 !   16.4   3.8   4.8e-06    0.0058       4      21 ..     260     277 ..     257     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.35
                                       ETTTSSS-T CS
                              Fer4   4 deekCigCG 12 
                                       +++ C +C 
  gi|488601311|ref|YP_007907782.1| 143 IYDNCKYCD 151
                                       7899*9996 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 9.4e-07
                                       TTTSSS-THHHHHST CS
                              Fer4   5 eekCigCGaCvevCP 19 
                                       +ekCi+C aC ++CP
  gi|488601311|ref|YP_007907782.1| 194 MEKCIRCYACRSACP 208
                                       79************* PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.3
                                       SSS- CS
                              Fer4   8 CigC 11 
                                       C+ C
  gi|488601311|ref|YP_007907782.1| 212 CTEC 215
                                       8877 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 4.8e-06
                                       ETTTSSS-THHHHHSTTT CS
                              Fer4   4 deekCigCGaCvevCPvg 21 
                                       +  +C  CG+C+ +CP +
  gi|488601311|ref|YP_007907782.1| 260 HAGRCADCGECERACPMD 277
                                       6789************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 !    8.7  11.2    0.0016       1.9       4      48 ..     146     209 ..     145     212 .. 0.79
   2 !   17.8  17.1   2.4e-06    0.0029       1      49 [.     196     277 ..     196     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                            Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraase.....................eaCigCgaCveaCpk 48 
                                       +C++C +  p+ v+ ++ ++++  ++++                       e+Ci C aC  aCp 
  gi|488601311|ref|YP_007907782.1| 146 NCKYCDA--PTPVIYDELFGEIKTVERDFSdieefeklsreerweywmkemEKCIRCYACRSACPM 209
                                       6888877..7777777777777776554446888888888888888999999************96 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.4e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.................................eaCigCgaCve 44 
                                       kC++C aC +aCp++ ++e  +   +                                         +C +Cg+C+ 
  gi|488601311|ref|YP_007907782.1| 196 KCIRCYACRSACPMCYCTECLVDPVNLAVSPMTkaeekamyprflgktvnasdnlfyhlirvihhaGRCADCGECER 272
                                       7***********999999888888877655444678899999999*********************99********* PP

                            Fer4_9  45 aCpkg 49 
                                       aCp +
  gi|488601311|ref|YP_007907782.1| 273 ACPMD 277
                                       ***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 !    7.4   2.0     0.004       4.8      27      73 ..     156     209 ..     144     217 .. 0.60
   2 !   13.0   0.0   7.4e-05     0.089      56      79 ..     259     282 ..     235     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.004
                           Fer4_18  27 vvydakrGekiagrkk.......ekkalkekeerkekgagdcidcescvkvcPt 73 
                                       v+yd   Ge ++ ++        ek + +e+ e   k++ +ci c +c + cP+
  gi|488601311|ref|YP_007907782.1| 156 VIYDELFGEIKTVERDfsdieefEKLSREERWEYWMKEMEKCIRCYACRSACPM 209
                                       56666666654422220000000111222222334688999************8 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.4e-05
                           Fer4_18  56 kgagdcidcescvkvcPtgidirk 79 
                                       + ag c dc+ c + cP++i +rk
  gi|488601311|ref|YP_007907782.1| 259 HHAGRCADCGECERACPMDIPLRK 282
                                       56899***************9997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.4       8.9   1.1e+04       6      10 ..     144     148 ..     142     151 .. 0.55
   2 ?    3.7  10.7     0.062        74       7      21 ..     195     209 ..     193     216 .. 0.91
   3 !   18.6   4.2   1.2e-06    0.0014       6      22 ..     261     277 ..     257     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.9
                            Fer4_6   6 pdkCi 10 
                                       +d+C 
  gi|488601311|ref|YP_007907782.1| 144 YDNCK 148
                                       56664 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
                            Fer4_6   7 dkCigCgdCvrvCPe 21 
                                       +kCi C++C ++CP+
  gi|488601311|ref|YP_007907782.1| 195 EKCIRCYACRSACPM 209
                                       89************5 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.2e-06
                            Fer4_6   6 pdkCigCgdCvrvCPeg 22 
                                       + +C +Cg+C+r+CP++
  gi|488601311|ref|YP_007907782.1| 261 AGRCADCGECERACPMD 277
                                       569************87 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   7.6   6.4e-05     0.077       2      16 ..     195     209 ..     194     210 .. 0.92
   2 ?   16.1   4.2     1e-05     0.012       3      16 ..     263     276 ..     261     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       e+Ci+C +C++aCP+
  gi|488601311|ref|YP_007907782.1| 195 EKCIRCYACRSACPM 209
                                       99************6 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       rC +Cg C++aCP+
  gi|488601311|ref|YP_007907782.1| 263 RCADCGECERACPM 276
                                       9************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 ?   -1.0   0.0       1.7     2e+03      43      53 ..     146     156 ..     130     158 .. 0.75
   2 ?    9.5   4.2   0.00088       1.1      37      56 ..     193     212 ..     180     225 .. 0.76
   3 ?    8.6   0.6    0.0017       2.1       7      52 ..     263     275 ..     250     280 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                           Fer4_21  43 GCnlCssvCPv 53 
                                        C+ C ++ Pv
  gi|488601311|ref|YP_007907782.1| 146 NCKYCDAPTPV 156
                                       47777777777 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00088
                           Fer4_21  37 vedeCvGCnlCssvCPvedc 56 
                                         ++C+ C  C s CP+  c
  gi|488601311|ref|YP_007907782.1| 193 EMEKCIRCYACRSACPMCYC 212
                                       45788888888888887554 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0017
                           Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       +C +Cg+C  aC                                 P
  gi|488601311|ref|YP_007907782.1| 263 RCADCGECERAC---------------------------------P 275
                                       455555555555.................................5 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.24      15      73 ..      61     119 ..      49     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                      DDE_Tnp_ISL3  15 vtvvvdllvdggrlldilpgRkketlkafleslsek.erekveavvmDmsaayksavkea 73 
                                       +t +++l  ++ ++  +++g +++++k+++++ + + er  +  v++D+ a+y+++v+++
  gi|488601311|ref|YP_007907782.1|  61 ITLMQEL-NKRDKVGVVVKGCDSKAIKKLMMEDKIDrERVYIIGVTCDGVANYRKIVEAV 119
                                       5777777.5559999***************977544477788899***********9976 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2  21.1      0.27   3.2e+02       1      96 []     196     278 ..     196     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.27
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekf 77 
                                       +C++C aC  +Cp C+C+++  +   + + +  ++  +  ++ +f   + +            + ++h ++ ++   
  gi|488601311|ref|YP_007907782.1| 196 KCIRCYACRSACPMCYCTECLVDPV-NLAVSPMTKAEEKAMYPRFLGKTVN---------ASDNLFYHLIRVIH--- 259
                                       7*****************9876663.3556666677777777766543333.........33445555554443... PP

                           Fer4_22  78 gesgCvGCgRCieacpvki 96 
                                       ++  C  Cg C++acp++i
  gi|488601311|ref|YP_007907782.1| 260 HAGRCADCGECERACPMDI 278
                                       3457999999999999876 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   8.8     0.047        56       1      12 [.     197     208 ..     197     217 .. 0.96
   2 ?    8.1   3.1    0.0047       5.6       3      13 ..     266     276 ..     263     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.047
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ C+aC  +CP
  gi|488601311|ref|YP_007907782.1| 197 CIRCYACRSACP 208
                                       ************ PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0047
                            Fer4_3   3 gCgaCvevCPv 13 
                                        Cg C+++CP 
  gi|488601311|ref|YP_007907782.1| 266 DCGECERACPM 276
                                       5*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2041.11
//
Query:       gi|488601312|ref|YP_007907783.1|  [L=319]
Description: hypothetical protein Asulf_01819 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  104.6   6.6    3.9e-30  104.6   6.6    2.1  2  Fer4_22      4Fe-4S dicluster domain
    1.1e-06   28.3  11.7      0.003   17.6   1.7    2.5  2  Fer4_2       4Fe-4S binding domain
    7.1e-06   26.0   8.1     0.0057   16.7   0.5    2.6  2  Fer4_10      4Fe-4S dicluster domain
      2e-05   24.8   1.2       0.02   15.1   0.0    2.5  2  Fer4_18      4Fe-4S dicluster domain
    3.3e-05   23.5  19.5     0.0049   16.6   6.1    2.5  2  Fer4         4Fe-4S binding domain
    3.8e-05   24.2  11.1    0.00036   21.1  11.3    2.3  1  Fer4_7       4Fe-4S dicluster domain
    4.9e-05   23.8   9.6      0.004   17.7  10.7    2.4  2  Fer4_17      4Fe-4S dicluster domain
    5.9e-05   23.2  11.9      0.012   15.8  13.4    2.5  3  Fer4_9       4Fe-4S dicluster domain
    0.00019   22.3  11.5      0.038   14.9   1.0    2.9  2  Fer4_16      4Fe-4S double cluster binding domain
    0.00024   21.5   9.8     0.0014   19.0   9.8    2.2  1  Fer4_8       4Fe-4S dicluster domain
     0.0032   17.6  17.8      0.013   15.6   2.9    2.6  2  Fer4_21      4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   15.8   4.8      0.011   15.8   4.8    2.5  2  Fer4_6       4Fe-4S binding domain
      0.021   14.7   1.7      0.031   14.1   0.3    2.1  2  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
      0.022   15.2   2.0      0.022   15.2   2.0    2.7  2  Fer4_4       4Fe-4S binding domain
      0.028   14.2   0.0      0.068   13.0   0.0    1.6  1  BTRD1        Bacterial tandem repeat domain 1
       0.72   10.4  13.9        1.9    9.1   4.7    2.8  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.2   5.8e+03      27      63 ..     170     206 ..     159     214 .. 0.60
   2 !  104.6   6.6   3.5e-33   3.9e-30       1      95 [.     216     307 ..     216     308 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.2
                           Fer4_22  27 eskegervrvwdsClleeftkvaggenvrkekkerlr 63 
                                       ++++ e++r  ++ + ++f++  + e ++ + ke+++
  gi|488601312|ref|YP_007907783.1| 170 DENDIEKFREKENEVKSTFKRKLNIEGLSGRLKENFE 206
                                       4556677777777777777666665555555555555 PP

  == domain 2  score: 104.6 bits;  conditional E-value: 3.5e-33
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekf 77 
                                       +C++Cg Ct++CptC+Cfd+ de +   keg r+r wdsC++  +t  ++++n+r+ek +rlr+r+++k+ ++ e+ 
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPTCFCFDMLDEGE---KEGFRYRAWDSCQFPLYTLESSSHNPRNEKWQRLRNRFYDKFLYMLENK 289
                                       5*********************995...67*********************************************** PP

                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       ge  CvGCgRCi+ cp++
  gi|488601312|ref|YP_007907783.1| 290 GEIFCVGCGRCISECPAG 307
                                       ***************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 !   17.6   1.7   2.7e-06     0.003       9      22 .]     216     229 ..     209     229 .. 0.91
   2 !   15.4   2.7   1.3e-05     0.015      10      22 .]     294     306 ..     289     306 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                            Fer4_2   9 rCigCgaCvsaCPa 22 
                                       +C+gCg+C+  CP+
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPT 229
                                       6************7 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       C+gCg C+s CPa
  gi|488601312|ref|YP_007907783.1| 294 CVGCGRCISECPA 306
                                       ************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 !   12.2   1.9   0.00013      0.15       8      24 ..     216     237 ..     210     274 .. 0.76
   2 !   16.7   0.5   5.1e-06    0.0057       8      23 ..     293     308 ..     288     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                           Fer4_10   8 tCirCgkCvkaCPadl.....t 24 
                                        C++Cg C+  CP+++     +
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPTCFcfdmlD 237
                                       6************977666551 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.1e-06
                           Fer4_10   8 tCirCgkCvkaCPadl 23 
                                        C++Cg+C + CPa +
  gi|488601312|ref|YP_007907783.1| 293 FCVGCGRCISECPAGV 308
                                       5*************44 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.3     0.003       3.4      55      74 ..     211     230 ..     178     238 .. 0.79
   2 !   15.1   0.0   1.8e-05      0.02      54      79 ..     287     312 ..     257     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.003
                           Fer4_18  55 ekgagdcidcescvkvcPtg 74 
                                       +k + +c+ c+ c  +cPt 
  gi|488601312|ref|YP_007907783.1| 211 KKVSINCVGCGICTFLCPTC 230
                                       566789************95 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.8e-05
                           Fer4_18  54 kekgagdcidcescvkvcPtgidirk 79 
                                       ++kg+  c+ c+ c++ cP g+di +
  gi|488601312|ref|YP_007907783.1| 287 ENKGEIFCVGCGRCISECPAGVDIVE 312
                                       5667777*****************76 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   5.4   0.00011      0.12       8      20 ..     217     229 ..     215     229 .. 0.95
   2 !   16.6   6.1   4.4e-06    0.0049       8      21 ..     294     307 ..     292     308 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                       SSS-THHHHHSTT CS
                              Fer4   8 CigCGaCvevCPv 20 
                                       C+gCG+C   CP+
  gi|488601312|ref|YP_007907783.1| 217 CVGCGICTFLCPT 229
                                       ************7 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.4e-06
                                       SSS-THHHHHSTTT CS
                              Fer4   8 CigCGaCvevCPvg 21 
                                       C+gCG+C++ CP g
  gi|488601312|ref|YP_007907783.1| 294 CVGCGRCISECPAG 307
                                       ************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1  11.3   3.2e-07   0.00036       2      52 .]     217     308 ..     216     308 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.2e-07
                            Fer4_7   2 CigCgaCvaaCp.vkaieldeeenek.....gtekv......................................eid 34 
                                       C+gCg C+  Cp   ++++ +e +++         +                                      +  
  gi|488601312|ref|YP_007907783.1| 217 CVGCGICTFLCPtCFCFDMLDEGEKEgfryrA---WdscqfplytlessshnprnekwqrlrnrfydkflymleNKG 290
                                       ***********854566666655555333330...133333333333333333444447777777777765544444 PP

                            Fer4_7  35 pekClgCgaCvavCPtga 52 
                                       +  C+gCg+C+++CP+g+
  gi|488601312|ref|YP_007907783.1| 291 EIFCVGCGRCISECPAGV 308
                                       555************996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   3.0   0.00076      0.85      30      58 ..     193     229 ..     175     232 .. 0.60
   2 !   17.7  10.7   3.5e-06     0.004       1      61 []     216     309 ..     216     309 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00076
                           Fer4_17  30 kl........glleeaekeekaslCieCgeCerkCPq 58 
                                       ++        + +e    +++  +C++Cg C+  CP 
  gi|488601312|ref|YP_007907783.1| 193 NIeglsgrlkENFESDYWKKVSINCVGCGICTFLCPT 229
                                       4454443222233344445778899999999999995 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.5e-06
                           Fer4_17   1 rCiqCgyClpeCpsyea....ydnepkkllraakl..............................glleeaekeeka 43 
                                       +C +Cg C+  Cp++ +     + e++ ++++a +                               ++ ++ +++  
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPTCFCfdmlDEGEKEGFRYRA-WdscqfplytlessshnprnekwqrlrnrfyDKFLYMLENKGE 291
                                       6************97774443222333344333.2234444455554554443333322222222334446666777 PP

                           Fer4_17  44 slCieCgeCerkCPqgld 61 
                                         C++Cg+C ++CP+g+d
  gi|488601312|ref|YP_007907783.1| 292 IFCVGCGRCISECPAGVD 309
                                       88*************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 !   10.2   3.6   0.00059      0.66      33      48 ..     209     229 ..     177     233 .. 0.72
   2 !   15.8  13.4     1e-05     0.012       1      49 [.     216     307 ..     216     310 .. 0.90
   3 !   15.5   1.4   1.3e-05     0.015       2      18 ..     294     310 ..     293     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00059
                            Fer4_9  33 e.....eaCigCgaCveaCpk 48 
                                       +      +C+gCg C+  Cp+
  gi|488601312|ref|YP_007907783.1| 209 YwkkvsINCVGCGICTFLCPT 229
                                       145566689999999999996 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1e-05
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...........................................e 34 
                                       +C+gCg C+  Cp++ + +   e++ +  ++++                                            
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPTCFCFDMLDEGEKEGFRYRAwdscqfplytlessshnprnekwqrlrnrfydkflymlenkgeI 292
                                       6************99997777777766666666678****************************************8 PP

                            Fer4_9  35 aCigCgaCveaCpkg 49 
                                        C+gCg+C+  Cp g
  gi|488601312|ref|YP_007907783.1| 293 FCVGCGRCISECPAG 307
                                       8************87 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 1.3e-05
                            Fer4_9   2 CtgCgaCveaCpagvvv 18 
                                       C+gCg+C++ Cpagv +
  gi|488601312|ref|YP_007907783.1| 294 CVGCGRCISECPAGVDI 310
                                       99999999999998865 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 !   11.0   3.6   0.00057      0.64      38      65 ..     202     228 ..     165     230 .. 0.64
   2 !   14.9   1.0   3.4e-05     0.038       1      16 [.     293     308 ..     293     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00057
                           Fer4_16  38 kkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       k++++ d+ k+    ++ gC+iC+  CP
  gi|488601312|ref|YP_007907783.1| 202 KENFESDYWKKV-SINCVGCGICTFLCP 228
                                       445555555555.445788888888888 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.4e-05
                           Fer4_16   1 rCgtCgkCaevCPtna 16 
                                       +C++Cg+C++ CP+++
  gi|488601312|ref|YP_007907783.1| 293 FCVGCGRCISECPAGV 308
                                       6************975 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   9.8   1.3e-06    0.0014       4      65 .]     216     308 ..     213     308 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                            Fer4_8   4 kCieCgaCqsaCpvlrrtk.khlldargeaae...................dvqeeqvlee...........eealw 49 
                                       +C++Cg C+  Cp++ +++  +  +++g +                     +++++q+l +           +++  
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPTCFCFDmLDEGEKEGFRYRawdscqfplytlessshnpRNEKWQRLRNrfydkflymleNKGEI 292
                                       8***********98888553333333333333444555555444444444433333333335555688888888899 PP

                            Fer4_8  50 sCttcgaCtevCpvgi 65 
                                        C++cg+C ++Cp g+
  gi|488601312|ref|YP_007907783.1| 293 FCVGCGRCISECPAGV 308
                                       9************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 !   15.6   2.9   1.1e-05     0.013      32      59 .]     208     235 ..     201     235 .. 0.83
   2 !   13.0   0.9   7.4e-05     0.083      41      53 ..     294     306 ..     285     316 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                           Fer4_21  32 tvlkvvedeCvGCnlCssvCPvedciem 59 
                                        ++k v+ +CvGC +C+  CP+  c +m
  gi|488601312|ref|YP_007907783.1| 208 DYWKKVSINCVGCGICTFLCPTCFCFDM 235
                                       567888899************9777666 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.4e-05
                           Fer4_21  41 CvGCnlCssvCPv 53 
                                       CvGC  C+s CP 
  gi|488601312|ref|YP_007907783.1| 294 CVGCGRCISECPA 306
                                       5555555555553 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   9.3     0.044        50       8      21 ..     216     229 ..     216     235 .. 0.94
   2 ?   15.8   4.8   9.7e-06     0.011       9      23 ..     294     308 ..     293     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.044
                            Fer4_6   8 kCigCgdCvrvCPe 21 
                                       +C+gCg C+  CP+
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPT 229
                                       6************6 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.7e-06
                            Fer4_6   9 CigCgdCvrvCPega 23 
                                       C+gCg+C++ CP+g+
  gi|488601312|ref|YP_007907783.1| 294 CVGCGRCISECPAGV 308
                                       ************986 PP

>> 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 ?   14.1   0.3   2.8e-05     0.031       3      85 ..      74     169 ..      72     238 .. 0.73
   2 ?   -1.5   0.1       1.8     2e+03      82     106 ..     286     310 ..     242     311 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                       FrhB_FdhB_C   3 kvavvGtPCqiaalrklqk..........kklkekilltiglfCggnfspealrk.lleelgvdpedvkklefrgkg 68 
                                       k a+v+ PC+++++  l k           k +++  l+i + C +  ++ + ++     ++ + +dv   e+   g
  gi|488601312|ref|YP_007907783.1|  74 KRAIVVSPCDARGITLLDKvfldglvdpyYKARRDNSLVISIACNKAGDYCFCESlGFSPYSSEGSDVFVAEVD--G 148
                                       679**************************7777778***********999999996444445568888888884..7 PP

                       FrhB_FdhB_C  69 kfrvelkd....ekeislkel 85 
                                       k+ +el+d      +i+lke+
  gi|488601312|ref|YP_007907783.1| 149 KYFIELSDkakdILDIELKEA 169
                                       777777776665223333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                       FrhB_FdhB_C  82 lkeleefirpsCkvCkdktaelADi 106
                                       l++  e++  +C +C  + +   Di
  gi|488601312|ref|YP_007907783.1| 286 LENKGEIFCVGCGRCISECPAGVDI 310
                                       2233346666777776666665555 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   7.7       0.3   3.4e+02       3      16 ..     216     229 ..     211     235 .. 0.91
   2 ?   15.2   2.0     2e-05     0.022       4      17 .]     294     307 ..     286     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.3
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +C+gCg C+  CP+
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPT 229
                                       6********99995 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-05
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C+gCg+C++ CP g
  gi|488601312|ref|YP_007907783.1| 294 CVGCGRCISECPAG 307
                                       ************75 PP

>> BTRD1  Bacterial tandem repeat domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     6e-05     0.068      15      38 ..       9      32 ..       5      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-05
                             BTRD1 15 yqakfdklkakGYrpvhvsgYgvg 38
                                      + + fd+lk+kGYr    +gYg  
  gi|488601312|ref|YP_007907783.1|  9 FKSLFDELKSKGYRIYIPDGYGFK 32
                                      7899***********999999864 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 ?    9.1   4.7    0.0017       1.9       5      23 ..     216     234 ..     214     244 .. 0.83
   2 ?    5.5   1.8     0.023        26       6      18 ..     294     306 ..     291     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                           Fer4_13   5 tCiacgaCvelaPdvFeed 23 
                                       +C++cg+C  l+P +F  d
  gi|488601312|ref|YP_007907783.1| 216 NCVGCGICTFLCPTCFCFD 234
                                       6*************99766 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.023
                           Fer4_13   6 CiacgaCvelaPd 18 
                                       C++cg C + +P 
  gi|488601312|ref|YP_007907783.1| 294 CVGCGRCISECPA 306
                                       ************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1845.03
//
Query:       gi|488601313|ref|YP_007907784.1|  [L=278]
Description: 2-polyprenylphenol hydroxylase-related flavodoxin oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   65.6   0.0    8.9e-18   64.9   0.0    1.2  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    7.9e-13   48.0   2.0    1.5e-12   47.1   2.0    1.5  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0023   18.3   0.0     0.0045   17.3   0.0    1.5  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.39   10.8   0.0    2.2  2  NAD_binding_6    Ferric reductase NAD binding domain
      0.084   12.5   0.0       0.19   11.3   0.0    1.6  1  Kelch_1          Kelch motif


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 !   64.9   0.0   2.5e-21   8.9e-18       2     106 ..     120     219 ..     119     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 2.5e-21
                                       EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHH CS
                     NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvq 78 
                                       ++gG G +P+rsv + +++++kd + +++vyG+rt++dl+y++el ++ ++  +   v    + +e+gw++  g+v 
  gi|488601313|ref|YP_007907784.1| 120 VGGGIGQTPLRSVYQYVMDNEKDYGDLTIVYGARTSKDLVYKDELMKMIENGYN---VELSIDMPEEGWKYFVGFVP 193
                                       79**********************************************555444...3333689************* PP

                                       HHHHHHHHHHSSTTEEEEEECSHHHHHH CS
                     NAD_binding_1  79 dalleellslkkeethvyvCGppgMika 106
                                       d+l + l + + e+t +++CGpp Mik 
  gi|488601313|ref|YP_007907784.1| 194 DNL-KRLKP-NPENTIAVICGPPIMIKI 219
                                       ***.77777.79*************985 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   2.0   4.1e-16   1.5e-12       1      41 [.     239     271 ..     239     272 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.1e-16
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e+rM+CG+G C+ C+++         k+vCkdGPvF++de+
  gi|488601313|ref|YP_007907784.1| 239 ERRMKCGIGKCGRCRIEG--------KYVCKDGPVFRYDEL 271
                                       89***************9........89***********97 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 !   17.3   0.0   1.3e-06    0.0045      16      96 ..      34     105 ..      21     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       EEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-TT-EEEEEE CS
                     FAD_binding_6  16 ifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelkigdtleikG 92 
                                       +fr+k++    ++++ +Gq   +++   ge     +t+++s+ ++  +e+ v  ++ Gk++  L+e+ +gd++ ++G
  gi|488601313|ref|YP_007907784.1|  34 TFRLKVE---PRFNYQPGQGCLVSVFGRGE---SWFTIANSP-TRPDIEFSV--LKTGKVTTKLHEMDVGDVVGLRG 101
                                       4444444...56778888888888887777...446755555.455666654..799******************** PP

                                       EE-S CS
                     FAD_binding_6  93 PlGk 96 
                                       P+G+
  gi|488601313|ref|YP_007907784.1| 102 PHGR 105
                                       **97 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.39       3      61 ..     116     170 ..     114     180 .. 0.81
   2 ?    2.4   0.0     0.044   1.6e+02     132     149 ..     202     218 ..     192     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6   3 nvllvagGiGitpfisilkdllkkskkealktkkikliwvvressslewfkdvLnelee 61 
                                       n+l v+gGiG tp+ s+ + ++ ++k    +   ++++   r s++l   +++++ +e+
  gi|488601313|ref|YP_007907784.1| 116 NILTVGGGIGQTPLRSVYQYVMDNEK----DYGDLTIVYGARTSKDLVYKDELMKMIEN 170
                                       899**********************9....88888999999999998777766665554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.044
                                       xxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6 132 hknssvgvfvCGppklvk 149
                                       +++++++ ++CGpp+++k
  gi|488601313|ref|YP_007907784.1| 202 NPENTIA-VICGPPIMIK 218
                                       4555555.57******97 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.3e-05      0.19      14      33 ..     117     136 ..     116     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.3e-05
                                       EEEEEEBCSSSBEEEEEEEE CS
                           Kelch_1  14 iYviGGsdggnalssvevyD 33 
                                       i  +GG+ g+++l+sv+ y 
  gi|488601313|ref|YP_007907784.1| 117 ILTVGGGIGQTPLRSVYQYV 136
                                       789***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1781.34
//
Query:       gi|488601314|ref|YP_007907785.1|  [L=175]
Description: Heterodisulfide reductase, subunit C [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-09   38.2   7.2      3e-09   36.9   7.3    1.6  1  Fer4_9    4Fe-4S dicluster domain
    5.4e-09   36.5   3.0    0.00093   19.7   0.2    2.3  2  Fer4_7    4Fe-4S dicluster domain
    9.5e-09   35.7   5.8      2e-08   34.7   5.8    1.5  1  Fer4_17   4Fe-4S dicluster domain
    4.2e-08   33.5   7.3    9.5e-08   32.4   7.4    1.6  1  Fer4_8    4Fe-4S dicluster domain
    1.5e-06   28.2   9.3    3.9e-06   26.9   9.3    1.7  1  Fer4_10   4Fe-4S dicluster domain
    3.8e-05   23.3  14.8     0.0056   16.4   2.2    2.3  2  Fer4      4Fe-4S binding domain
     0.0035   18.2  14.0      0.085   13.8  13.4    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.019   15.1   2.1       0.38   11.0   0.2    2.2  2  Fer4_18   4Fe-4S dicluster domain
      0.019   15.0  12.0      0.063   13.4   1.9    2.3  2  Fer4_2    4Fe-4S binding domain
      0.021   15.3  11.0        0.5   11.0   2.6    2.3  2  Fer4_4    4Fe-4S binding domain
       0.42   10.8  11.7        2.8    8.1  11.7    2.0  2  Fer4_21   4Fe-4S dicluster domain
       0.58   11.0  13.7        1.5    9.8   2.4    2.3  2  Fer4_22   4Fe-4S dicluster domain
       0.66   10.2  15.1       0.14   12.3   2.4    2.3  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   7.3   2.2e-12     3e-09       1      50 [.      26      86 ..      26      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.2e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase............eaCigCgaCveaCpkga 50
                                      kC++Cg+C++ Cp+gv+ e  + +   + + +             + C++Cg C+e+Cp++a
  gi|488601314|ref|YP_007907785.1| 26 KCYQCGTCIADCPTGVAAEPLSVKRLIH-MIKLglrdklledetpWMCVTCGGCEERCPREA 86
                                      7***************977777666554.444457999*********************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 !   19.7   0.2   6.8e-07   0.00093      32      52 .]      21      41 ..       1      41 [. 0.72
   2 !   17.3   0.3   3.8e-06    0.0052      34      52 .]      68      86 ..      49      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.8e-07
                            Fer4_7 32 eidpekClgCgaCvavCPtga 52
                                       +d  kC++Cg C+a CPtg+
  gi|488601314|ref|YP_007907785.1| 21 GHDLLKCYQCGTCIADCPTGV 41
                                      456789*************96 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.8e-06
                            Fer4_7 34 dpekClgCgaCvavCPtga 52
                                       p++C++Cg C+++CP +a
  gi|488601314|ref|YP_007907785.1| 68 TPWMCVTCGGCEERCPREA 86
                                      5899************876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   5.8   1.4e-11     2e-08       1      59 [.      26      85 ..      26      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.4e-11
                           Fer4_17  1 rCiqCgyClpeCpsyea.ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      +C qCg C++ Cp++ a  +   k+l+  +klgl ++  ++e+   C++Cg+Ce++CP +
  gi|488601314|ref|YP_007907785.1| 26 KCYQCGTCIADCPTGVAaEPLSVKRLIHMIKLGLRDKLLEDETPWMCVTCGGCEERCPRE 85
                                      6*************98856689999*********************************76 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   7.4   6.9e-11   9.5e-08       2      63 ..      24      84 ..      23      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.9e-11
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      l kC +Cg C + Cp+  +    l  +r  ++ +   +++l e+e+ w C+tcg C+e+Cp 
  gi|488601314|ref|YP_007907785.1| 24 LLKCYQCGTCIADCPTGVAAE-PLSVKRLIHMIKLGLRDKLLEDETPWMCVTCGGCEERCPR 84
                                      789************665553.3333334444435666666667789**************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   9.3   2.8e-09   3.9e-06       5      56 .]      23      83 ..      19      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.8e-09
                           Fer4_10  5 dddtCirCgkCvkaCPadl..........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      d  +C +Cg+C + CP+ +           ++ + g +++   +++ ++ C +cg C e CP
  gi|488601314|ref|YP_007907785.1| 23 DLLKCYQCGTCIADCPTGVaaeplsvkrlIHMIKLGLRDKL-LEDETPWMCVTCGGCEERCP 83
                                      6679*************99*******964333333333333.33447**************9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.2   4.1e-06    0.0056       4      22 ..      23      41 ..      22      42 .. 0.89
   2 !   12.3   5.0   8.2e-05      0.11       7      22 ..      71      86 ..      71      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.1e-06
                                      ETTTSSS-THHHHHSTTTE CS
                              Fer4  4 deekCigCGaCvevCPvgA 22
                                      d  kC  CG+C+  CP+g+
  gi|488601314|ref|YP_007907785.1| 23 DLLKCYQCGTCIADCPTGV 41
                                      5669*************96 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.2e-05
                                      TSSS-THHHHHSTTTE CS
                              Fer4  7 kCigCGaCvevCPvgA 22
                                      +C+ CG C+e CP +A
  gi|488601314|ref|YP_007907785.1| 71 MCVTCGGCEERCPREA 86
                                      5************998 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  13.4   6.2e-05     0.085       1      65 [.      26      83 ..      26      85 .. 0.79
   2 !    9.4   3.8    0.0014         2       2      16 ..      72      86 ..      71     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      +C +Cg C+  CPt++  e+   +++  + i      k +l+++  +++  + +  C+ C++ CP
  gi|488601314|ref|YP_007907785.1| 26 KCYQCGTCIADCPTGVAAEP--LSVK--RLIHM---IKLGLRDKLLEDETPWMCVTCGGCEERCP 83
                                      5*******************..4444..44333...246777777777777889*********** PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                           Fer4_16  2 CgtCgkCaevCPtna 16
                                      C+tCg C e CP +a
  gi|488601314|ref|YP_007907785.1| 72 CVTCGGCEERCPREA 86
                                      ************988 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00027      0.38      55      75 ..      21      41 ..       3      46 .. 0.74
   2 ?    3.9   0.1     0.044        61      60      73 ..      71      84 ..      52      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                           Fer4_18 55 ekgagdcidcescvkvcPtgi 75
                                       ++  +c +c++c++ cPtg+
  gi|488601314|ref|YP_007907785.1| 21 GHDLLKCYQCGTCIADCPTGV 41
                                      555668*************98 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.044
                           Fer4_18 60 dcidcescvkvcPt 73
                                       c++c+ c + cP 
  gi|488601314|ref|YP_007907785.1| 71 MCVTCGGCEERCPR 84
                                      59999999999986 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   1.9   4.6e-05     0.063       6      22 .]      23      39 ..      20      39 .. 0.89
   2 ?    6.7   2.7    0.0063       8.7       9      21 ..      71      83 ..      64      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                            Fer4_2  6 dtdrCigCgaCvsaCPa 22
                                      d  +C +Cg+C+  CP+
  gi|488601314|ref|YP_007907785.1| 23 DLLKCYQCGTCIADCPT 39
                                      7789*******999**7 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0063
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      +C+ Cg C   CP
  gi|488601314|ref|YP_007907785.1| 71 MCVTCGGCEERCP 83
                                      8*******999*9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.6   0.00036       0.5       3      17 .]      26      40 ..      24      40 .. 0.92
   2 ?    8.9   1.4    0.0017       2.4       4      16 ..      72      84 ..      67      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C +Cg C+a CP+g
  gi|488601314|ref|YP_007907785.1| 26 KCYQCGTCIADCPTG 40
                                      699**********86 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0017
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C+ Cg C+  CP 
  gi|488601314|ref|YP_007907785.1| 72 CVTCGGCEERCPR 84
                                      *********9995 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  11.7    0.0021       2.8       7      52 ..      26      83 ..      23      86 .. 0.70
   2 ?    6.2   2.7     0.008        11       7      20 ..      71      84 ..      66     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                           Fer4_21  7 kCigCgkCliaCedtshqaieidaktvl.........kvvede....CvGCnlCssvCP 52
                                      kC +Cg C+  C+ t++ a  ++ k+ +         k++ede    Cv C  C + CP
  gi|488601314|ref|YP_007907785.1| 26 KCYQCGTCIADCP-TGVAAEPLSVKRLIhmiklglrdKLLEDEtpwmCVTCGGCEERCP 83
                                      8************.577666444444333456666665555533444************ PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.008
                           Fer4_21  7 kCigCgkCliaCed 20
                                      +C+ Cg C   C+ 
  gi|488601314|ref|YP_007907785.1| 71 MCVTCGGCEERCPR 84
                                      45555555555554 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.8    0.0095        13       1      16 [.      26      41 ..      26      56 .. 0.86
   2 ?    9.8   2.4    0.0011       1.5      78      94 ..      68      84 ..      47      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0095
                           Fer4_22  1 rClsCgaCtlvCptCs 16
                                      +C +Cg+C + Cpt +
  gi|488601314|ref|YP_007907785.1| 26 KCYQCGTCIADCPTGV 41
                                      6999********9965 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                         +Cv Cg C+e+cp 
  gi|488601314|ref|YP_007907785.1| 68 TPWMCVTCGGCEERCPR 84
                                      5579***********97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.4    0.0001      0.14       8      23 ..      26      41 ..      22      42 .. 0.89
   2 ?    3.2   5.1     0.077   1.1e+02       9      21 ..      72      84 ..      71      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            Fer4_6  8 kCigCgdCvrvCPega 23
                                      kC +Cg C++ CP+g+
  gi|488601314|ref|YP_007907785.1| 26 KCYQCGTCIADCPTGV 41
                                      799***********96 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.077
                            Fer4_6  9 CigCgdCvrvCPe 21
                                      C+ Cg C+  CP 
  gi|488601314|ref|YP_007907785.1| 72 CVTCGGCEERCPR 84
                                      ***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1089.63
//
Query:       gi|488601315|ref|YP_007907786.1|  [L=296]
Description: Heterodisulfide reductase, subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-31  107.6   0.2    2.5e-18   66.1   0.1    2.2  2  CCG            Cysteine-rich domain
    0.00021   21.0   0.1      0.024   14.4   0.0    2.5  2  HydF_tetramer  Hydrogen maturase F tetramerization 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 !   39.8   0.0   4.3e-14   3.8e-10       2      85 .]       5      87 ..       4      87 .. 0.93
   2 !   66.1   0.1   2.8e-22   2.5e-18       1      85 []     147     240 ..     147     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 4.3e-14
                               CCG  2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee.laealakrnvetaeetgadaivtacpg 79
                                       ++ gC  + a +p+v+ka+++ l+ lg+++++ e++ CC+a g++ + +e  a+a+++ n+++ae++g+d ++++c++
  gi|488601315|ref|YP_007907786.1|  5 GLYLGC-NMPAIRPDVEKAIRESLTTLGLDIVDIEGAACCPAFGTFYSVDEtSALAVNAWNLAMAERLGVD-LIAQCGS 81
                                      6799**.78999******************************9999999887889****************.8999*** PP

                               CCG 80 Cllqlk 85
                                      C+ +lk
  gi|488601315|ref|YP_007907786.1| 82 CYSTLK 87
                                      **9986 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 2.8e-22
                               CCG   1 vayfdgChllraa......ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeet. 68 
                                       v+++ +Ch+lr++       pe + a+k+++ alg+e++++ ++++CCG +gg+s +++   ++++k+++++++e+ 
  gi|488601315|ref|YP_007907786.1| 147 VVVQNPCHVLRPSkivgfdDPERPMAFKEIVMALGAEIPYYeREKQCCGGAGGFSKRDKkANLEFVKMKFDSMKEEv 223
                                       67899****************************************************995666************88 PP

                               CCG  69 gadaivtacpgCllqlk 85 
                                       ++d iv+ c +Cl++++
  gi|488601315|ref|YP_007907786.1| 224 DPDLIVVSCITCLMHMD 240
                                       **************985 PP

>> HydF_tetramer  Hydrogen maturase F tetramerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0045        40      67      81 ..      72      86 ..      53     104 .. 0.79
   2 !   14.4   0.0   2.6e-06     0.024      46     109 ..     204     269 ..     200     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0045
                                      T-SEEEE-TT----H CS
                     HydF_tetramer 67 eyklvihCggCmitr 81
                                       ++l+ +Cg+C+ t 
  gi|488601315|ref|YP_007907786.1| 72 GVDLIAQCGSCYSTL 86
                                      689********9764 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.6e-06
                                       HH----EEEEE--SS--HHHTT-SEEEE-TT----HHHHHHHHHHH..HHTT--EEEHHHHHHHHT CS
                     HydF_tetramer  46 ktgkelefevaagrefpeeleeyklvihCggCmitrkellaRikel..kekgvpitNyGlllayla 109
                                         +++lef  ++  +++ee++   +v+ C +C+++  ++++ +k++   + ++p+  y  +la + 
  gi|488601315|ref|YP_007907786.1| 204 DKKANLEFVKMKFDSMKEEVDPDLIVVSCITCLMHMDNIQEEMKKAgmIDYQIPVFDYSQILAICL 269
                                       556788888888889999999999*****************99986226789******99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1970.78
//
Query:       gi|488601316|ref|YP_007907787.1|  [L=500]
Description: hypothetical protein Asulf_01823 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-149  495.3   0.2   1.1e-148  494.8   0.2    1.2  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    3.6e-28   97.8   6.1    3.1e-13   50.0   0.4    3.5  3  CBS       CBS 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 !  494.8   0.2  1.2e-152  1.1e-148       1     347 []      23     358 ..      23     358 .. 0.99

  Alignments for each domain:
  == domain 1  score: 494.8 bits;  conditional E-value: 1.2e-152
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio   1 avVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkikiekvwLngvpayaglaavdlylga 77 
                                       avV+taee+k++v+e ge+kaa+evDVVttgTfg+m+ssg++ln+g+++p+ik++++wLn+v+ay+g+aavd+ylg 
  gi|488601316|ref|YP_007907787.1|  23 AVVVTAEEMKEIVEELGEEKAAKEVDVVTTGTFGAMCSSGVFLNFGHSDPPIKMKRIWLNDVEAYTGIAAVDAYLGV 99 
                                       8**************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio  78 taeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNsse 154
                                       t+ s+  k + eyGG+hviedLv+gkevel+ae+++tdcyprkei tei l+dln+a +vnpRnayq+Y+aa+Nss+
  gi|488601316|ref|YP_007907787.1| 100 TQISD--KLGMEYGGAHVIEDLVRGKEVELKAESYGTDCYPRKEIVTEIALEDLNQAEMVNPRNAYQRYKAATNSSN 174
                                       ****9..4456****************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 155 etiytymgelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtL 231
                                       + + tymg+l pn+gn+t++g+Ge+sPl nDpe++tig+Gtri+L+GaeGyvigeGTq+sp           p+gtL
  gi|488601316|ref|YP_007907787.1| 175 RILRTYMGTLLPNYGNVTFAGTGEISPLNNDPEYRTIGLGTRIFLCGAEGYVIGEGTQHSP-----------PFGTL 240
                                       ************************************************************5...........699** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 232 avigdlkeMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael 308
                                       +v+g+lkeM+++y+r+a++ +yG+++++g+gipiPvldee+++ +av+d+die++++D++++rr+r+++ +v+Y+el
  gi|488601316|ref|YP_007907787.1| 241 MVKGNLKEMDKKYMRAAVFPGYGVTMYIGIGIPIPVLDEEMARFTAVRDRDIETEIIDYAIPRRNRPVVRKVNYEEL 317
                                       ***************************************************************************** PP

                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HcyBio 309 ..GkieiegkevktarlsslkrareiaeeLkewiekgeflL 347
                                         Gk+ei+g+ev++++lss++ arei  eLk++iekgef L
  gi|488601316|ref|YP_007907787.1| 318 ksGKVEINGEEVRVSPLSSYSIAREIMIELKKRIEKGEFYL 358
                                       ***************************************87 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.13   1.2e+03      16      38 ..       9      29 ..       3      35 .. 0.70
   2 !   48.4   0.1   1.1e-16   9.8e-13       1      56 [.     382     436 ..     382     437 .. 0.94
   3 !   50.0   0.4   3.4e-17   3.1e-13       1      56 [.     443     498 ..     443     499 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                                      SBHHHHHHHHHHHTSSEEEEE.ET CS
                               CBS 16 ttleealelmrekgvsrlPVV.de 38
                                       ++ee+ +++ ++g s++ VV  e
  gi|488601316|ref|YP_007907787.1|  9 KSIEEINRRI-SEG-SAV-VVtAE 29
                                      5899******.666.688.66333 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 1.1e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+ +m++ + ++p++tt+ ea +++++kgv++lPVVde++ l Givt  D+++a++
  gi|488601316|ref|YP_007907787.1| 382 VRNLMSKAI-SIPENTTIVEASKIIIDKGVNHLPVVDESNTLKGIVTSWDIAKAVA 436
                                       678898877.**************99***************************986 PP

  == domain 3  score: 50.0 bits;  conditional E-value: 3.4e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+++mtr+v+tv+pd+++e a++++r++++s+lPV+d  +k++G+++ +Dl r+++
  gi|488601316|ref|YP_007907787.1| 443 VSEVMTRKVITVYPDDPIELAADKLRKHNISALPVIDAKKKVLGLLSSEDLSRLIV 498
                                       89**********************************99999**********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2937.78
//
Query:       gi|488601317|ref|YP_007907788.1|  [L=129]
Description: hypothetical protein Asulf_01824 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   52.9  14.7    3.5e-07   29.8   4.3    2.3  2  Fer4             4Fe-4S binding domain
    2.2e-13   50.6  22.9    8.1e-10   39.1  12.5    1.7  2  Fer4_7           4Fe-4S dicluster domain
    2.6e-12   46.1  13.6    1.2e-06   28.2   4.3    2.3  2  Fer4_2           4Fe-4S binding domain
    3.6e-11   43.0  19.6    2.1e-08   34.2  10.3    1.7  2  Fer4_9           4Fe-4S dicluster domain
    2.2e-10   40.1  17.4    1.3e-05   25.0   3.6    2.6  2  Fer4_6           4Fe-4S binding domain
    3.3e-10   39.7  13.3    3.5e-05   24.0   2.0    2.2  2  Fer4_4           4Fe-4S binding domain
    4.8e-10   39.4  25.2      2e-07   31.0  14.3    2.3  2  Fer4_10          4Fe-4S dicluster domain
    1.9e-09   37.5  24.3    2.4e-07   30.8  13.0    1.8  2  Fer4_21          4Fe-4S dicluster domain
      7e-09   35.4   0.1    9.1e-09   35.0   0.1    1.2  1  NIL              NIL domain
    1.2e-08   35.7   8.5    0.00053   20.9   0.6    2.6  2  Fer4_16          4Fe-4S double cluster binding domain
    3.7e-06   27.1  10.1     0.0021   18.2   0.8    2.1  2  Fer4_18          4Fe-4S dicluster domain
    1.3e-05   26.0   4.3      0.024   15.5   0.1    2.2  2  Fer4_22          4Fe-4S dicluster domain
    0.00011   22.6  12.4      0.008   16.7   1.9    2.3  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    0.00015   22.1  14.3      0.036   14.5   3.0    2.3  2  Fer4_8           4Fe-4S dicluster domain
    0.00067   20.2  11.6       0.18   12.4   1.8    2.3  2  Fer4_17          4Fe-4S dicluster domain
    0.00089   20.0  20.2      0.045   14.7   5.8    2.2  2  Fer4_3           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.015   16.0  10.9       0.33   11.7   1.4    2.6  3  Fer4_15          4Fe-4S single cluster domain
       0.12   12.8   0.0       0.18   12.3   0.0    1.3  1  Pfk_N            Phosphofructokinase N-terminal domain yeast
       0.12   12.4   0.0       0.18   11.9   0.0    1.3  1  TPK_catalytic    Thiamin pyrophosphokinase, catalytic domain
        0.7    9.7  11.3        3.5    7.5   2.1    2.3  2  zf-C2H2_11       zinc-finger C2H2-type
       0.81   10.1   9.6        1.6    9.1   0.9    2.2  2  Keratin_matx     Keratin, high-sulphur matrix protein
        5.3    6.6   5.9        5.5    6.6   0.5    2.1  2  HCV_NS2          Hepatitis C virus non-structural protein NS2
        8.1    6.7   8.1        2.7    8.3   0.6    2.2  2  c-SKI_SMAD_bind  c-SKI Smad4 binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   4.3   4.5e-10   3.5e-07       2      22 ..      73      93 ..      72      95 .. 0.90
   2 !   28.9   2.7   8.2e-10   6.4e-07       4      23 ..     105     124 ..     102     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.5e-10
                                      EEETTTSSS-THHHHHSTTTE CS
                              Fer4  2 videekCigCGaCvevCPvgA 22
                                      + d ekC++CGaC+++CPv++
  gi|488601317|ref|YP_007907788.1| 73 IKDDEKCVHCGACISICPVEV 93
                                      789****************97 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 8.2e-10
                                       ETTTSSS-THHHHHSTTTEE CS
                              Fer4   4 deekCigCGaCvevCPvgAI 23 
                                       d e+C++CG Cv vCP  A+
  gi|488601317|ref|YP_007907788.1| 105 DSERCVRCGVCVTVCPLKAL 124
                                       89**************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 !   23.4   2.6   8.9e-08   6.9e-05      28      52 .]      69      93 ..      46      93 .. 0.76
   2 !   39.1  12.5     1e-12   8.1e-10       1      52 []      78     123 ..      78     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.9e-08
                            Fer4_7 28 tekveidpekClgCgaCvavCPtga 52
                                       ek+  d ekC++CgaC++ CP+++
  gi|488601317|ref|YP_007907788.1| 69 YEKIIKDDEKCVHCGACISICPVEV 93
                                      36778899**************975 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 1e-12
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C++CgaC + Cpv++++l+++       +v+ d+e+C+ Cg+Cv+vCP +a
  gi|488601317|ref|YP_007907788.1|  78 KCVHCGACISICPVEVFRLEYD------YRVAADSERCVRCGVCVTVCPLKA 123
                                       7******************987......46999****************765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.9   5.5e-08   4.3e-05       3      21 ..      72      90 ..      70      91 .. 0.87
   2 !   28.2   4.3   1.6e-09   1.2e-06       2      21 ..     101     120 ..     100     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.5e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +  d ++C++CgaC+s CP
  gi|488601317|ref|YP_007907788.1| 72 IIKDDEKCVHCGACISICP 90
                                      667899************* PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.6e-09
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       +v++d++rC++Cg Cv++CP
  gi|488601317|ref|YP_007907788.1| 101 RVAADSERCVRCGVCVTVCP 120
                                       6899***************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 !   20.6   1.8   4.9e-07   0.00038      33      49 ..      71      92 ..      45      94 .. 0.72
   2 !   34.2  10.3   2.7e-11   2.1e-08       1      50 [.      78     123 ..      78     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.9e-07
                            Fer4_9 33 e.....eaCigCgaCveaCpkg 49
                                      +     e+C++CgaC+ +Cp +
  gi|488601317|ref|YP_007907788.1| 71 KiikddEKCVHCGACISICPVE 92
                                      13333489************86 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2.7e-11
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       kC+ CgaC++ Cp +v++ +   r a+  +    +C+ Cg Cv +Cp +a
  gi|488601317|ref|YP_007907788.1|  78 KCVHCGACISICPVEVFRLEYDYRVAADSE----RCVRCGVCVTVCPLKA 123
                                       7************************99866....6************876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   3.6   1.7e-08   1.3e-05       5      23 ..      75      93 ..      71      94 .. 0.88
   2 !   23.6   2.9   4.9e-08   3.8e-05       2      20 ..     102     120 ..     101     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                            Fer4_6  5 dpdkCigCgdCvrvCPega 23
                                      d++kC++Cg+C+++CP  +
  gi|488601317|ref|YP_007907788.1| 75 DDEKCVHCGACISICPVEV 93
                                      99**************875 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4.9e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCP 20 
                                       v+ d ++C+ Cg Cv+vCP
  gi|488601317|ref|YP_007907788.1| 102 VAADSERCVRCGVCVTVCP 120
                                       788**************** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   2.0   4.5e-08   3.5e-05       2      16 ..      77      91 ..      76      96 .. 0.93
   2 !   21.1   3.8   3.8e-07    0.0003       1      16 [.     106     121 ..     106     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.5e-08
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e+C++Cg+C+++CP+
  gi|488601317|ref|YP_007907788.1| 77 EKCVHCGACISICPV 91
                                      79************7 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.8e-07
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +erC++Cg+Cv +CP 
  gi|488601317|ref|YP_007907788.1| 106 SERCVRCGVCVTVCPL 121
                                       69*************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 !   31.0  14.3   2.6e-10     2e-07       1      56 []      71     120 ..      71     120 .. 0.85
   2 !   20.4   3.1   5.3e-07   0.00041       3      21 ..     103     121 ..     101     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.6e-10
                           Fer4_10   1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       k+++dd++C++Cg+C + CP+           +++ +v  ++e+C +cg Cv +CP
  gi|488601317|ref|YP_007907788.1|  71 KIIKDDEKCVHCGACISICPV------EVFRLEYDYRVAADSERCVRCGVCVTVCP 120
                                       5899*****************......4444455666677889************9 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.3e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPa 21 
                                         d+++C+rCg Cv++CP 
  gi|488601317|ref|YP_007907788.1| 103 AADSERCVRCGVCVTVCPL 121
                                       6799**************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 !   18.8   3.5   1.7e-06    0.0013      35      54 ..      71      92 ..      46      96 .. 0.70
   2 !   30.8  13.0     3e-10   2.4e-07       4      55 ..      75     122 ..      71     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                           Fer4_21 35 kvv..edeCvGCnlCssvCPve 54
                                      k++  +++Cv C  C+s+CPve
  gi|488601317|ref|YP_007907788.1| 71 KIIkdDEKCVHCGACISICPVE 92
                                      33333789************94 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 3e-10
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55 
                                       d++kC++Cg C+  C+   ++  +++ + +++  +++Cv C +C++vCP+ +
  gi|488601317|ref|YP_007907788.1|  75 DDEKCVHCGACISICP---VEVFRLEYDYRVAADSERCVRCGVCVTVCPL-K 122
                                       789*************...899999999999******************8.4 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1   1.2e-11   9.1e-09       3      72 ..       3      66 ..       1      67 [. 0.94

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.2e-11
                                      EEEEEES-S-SS-HHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHTT-EEE CS
                               NIL  3 irltftgksavePllshlvrqlglevnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkrnvdvE 72
                                      i l+f  k+++eP++s+ + + +  +nI+ +sv    g + G l+ie+  ++ + +++++++++++v+v 
  gi|488601317|ref|YP_007907788.1|  3 ILLQFDSKTVREPVISQTTLEKKTLINIIRASV----GAREGELIIEV--DDSRADEIIEFIESKGVKVT 66
                                      6799*****************************....599********..68899*************95 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 !   20.9   0.6   6.8e-07   0.00053       1      27 [.      78     104 ..      78     107 .. 0.85
   2 !   18.3   1.8   4.3e-06    0.0034       1      20 [.     108     127 ..     108     129 .] 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.8e-07
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiea 27 
                                       +C+ Cg+C+++CP+++++ + +++++a
  gi|488601317|ref|YP_007907788.1|  78 KCVHCGACISICPVEVFRLEYDYRVAA 104
                                       6****************9997776665 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.3e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       rC++Cg C+ vCP +a++  
  gi|488601317|ref|YP_007907788.1| 108 RCVRCGVCVTVCPLKALELS 127
                                       6***************9865 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.8   2.7e-06    0.0021      24      75 ..      41      93 ..      32      98 .. 0.72
   2 !   14.0   2.6   5.5e-05     0.043      51      73 ..      99     121 ..      92     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                           Fer4_18 24 tllvvydakrGekiagrkkek.kalkekeerkekgagdcidcescvkvcPtgi 75
                                       l++  d  r ++i++  ++k +++++  e+  k++ +c++c++c+++cP+++
  gi|488601317|ref|YP_007907788.1| 41 ELIIEVDDSRADEIIEFIESKgVKVTKIYEKIIKDDEKCVHCGACISICPVEV 93
                                      56677788888888765444313334444556888999************986 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.5e-05
                           Fer4_18  51 eerkekgagdcidcescvkvcPt 73 
                                       + r ++++  c+ c++cv+vcP 
  gi|488601317|ref|YP_007907788.1|  99 DYRVAADSERCVRCGVCVTVCPL 121
                                       5666778889************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 !   15.5   0.1     3e-05     0.024      69      95 ..      64      92 ..      43      93 .. 0.75
   2 !   12.0   0.7   0.00036      0.28      77      93 ..     104     120 ..      94     123 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-05
                           Fer4_22 69 klsefkekf..gesgCvGCgRCieacpvk 95
                                      k++++ ek+  + ++Cv Cg Ci+ cpv+
  gi|488601317|ref|YP_007907788.1| 64 KVTKIYEKIikDDEKCVHCGACISICPVE 92
                                      444555554568899***********987 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00036
                           Fer4_22  77 fgesgCvGCgRCieacp 93 
                                        +++ Cv Cg C+++cp
  gi|488601317|ref|YP_007907788.1| 104 ADSERCVRCGVCVTVCP 120
                                       56667777777777776 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.9     1e-05     0.008       2      25 ..      75      99 ..      73     104 .. 0.84
   2 !   11.2   3.1   0.00052      0.41       2      17 ..     105     120 ..     102     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-05
                           Fer4_13  2 DrdtCiacgaCvelaP.dvFeedde 25
                                      D ++C+ cgaC +++P +vF+ + +
  gi|488601317|ref|YP_007907788.1| 75 DDEKCVHCGACISICPvEVFRLEYD 99
                                      669*************889987766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00052
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       D ++C+ cg+Cv ++P
  gi|488601317|ref|YP_007907788.1| 105 DSERCVRCGVCVTVCP 120
                                       889************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 !   14.5   3.0   4.6e-05     0.036       3      17 ..      77      91 ..      75     107 .. 0.80
   2 !   13.3   3.5   0.00011     0.085       3      17 ..     107     121 ..     104     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-05
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      ekC++CgaC s Cpv
  gi|488601317|ref|YP_007907788.1| 77 EKCVHCGACISICPV 91
                                      689999999999994 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00011
                            Fer4_8   3 ekCieCgaCqsaCpv 17 
                                       e+C++Cg C + Cp+
  gi|488601317|ref|YP_007907788.1| 107 ERCVRCGVCVTVCPL 121
                                       688888888888884 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   1.8   0.00023      0.18      44      59 ..      77      92 ..      43      94 .. 0.75
   2 !   10.7  11.9   0.00079      0.62       1      57 [.      78     120 ..      78     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C++Cg C + CP +
  gi|488601317|ref|YP_007907788.1| 77 EKCVHCGACISICPVE 92
                                      6777777777777765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00079
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                       +C +Cg+C+  Cp    + ++  +++++               ++C+ Cg C+++CP
  gi|488601317|ref|YP_007907788.1|  78 KCVHCGACISICPVEVFRLEYDYRVAAD--------------SERCVRCGVCVTVCP 120
                                       6***************999977666666..............479***********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 !   14.7   5.8   5.8e-05     0.045       1      13 [.      79      91 ..      79      93 .. 0.95
   2 !   11.4   6.5   0.00066      0.52       1      15 []     109     123 ..     109     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.8e-05
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C++CgaC   CPv
  gi|488601317|ref|YP_007907788.1| 79 CVHCGACISICPV 91
                                      ************7 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00066
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ Cg Cv vCP +A
  gi|488601317|ref|YP_007907788.1| 109 CVRCGVCVTVCPLKA 123
                                       99**********887 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       9.8   7.7e+03      42      51 ..      40      53 ..      23      57 .. 0.62
   2 ?   10.0   1.1    0.0015       1.2       4      25 ..      75      97 ..      72     101 .. 0.82
   3 ?   11.7   1.4   0.00043      0.33       1      19 [.     102     120 ..     102     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9.8
                           Fer4_15 42 g....evpddeeea 51
                                      g    ev+d + ++
  gi|488601317|ref|YP_007907788.1| 40 GeliiEVDDSRADE 53
                                      23344666666555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0015
                           Fer4_15  4 DrdaCigcglCvaeap.evfeld 25
                                      D ++C  cg+C+  +p evf+l+
  gi|488601317|ref|YP_007907788.1| 75 DDEKCVHCGACISICPvEVFRLE 97
                                      899************74777766 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00043
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V  D ++C  cg+Cv+++p
  gi|488601317|ref|YP_007907788.1| 102 VAADSERCVRCGVCVTVCP 120
                                       56799*************8 PP

>> Pfk_N  Phosphofructokinase N-terminal domain yeast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00023      0.18      12      44 ..      47      79 ..      41      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                             Pfk_N 12 keekyeelikfYkklGfkvvksyskeantksel 44
                                      ++++ +e i+f ++ G+kv+k+y+k  + ++++
  gi|488601317|ref|YP_007907788.1| 47 DDSRADEIIEFIESKGVKVTKIYEKIIKDDEKC 79
                                      6778899******************99988776 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.18      41      74 ..      48      81 ..      42     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                     TPK_catalytic 41 DSirpevkefyeskgteivkkpdqdstDlekaia 74
                                      DS  +e+ ef+eskg++++k  ++   D ek+++
  gi|488601317|ref|YP_007907788.1| 48 DSRADEIIEFIESKGVKVTKIYEKIIKDDEKCVH 81
                                      9999****************************95 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 ?    7.3   2.0    0.0052         4       6      15 ..      78      87 ..      77      90 .. 0.86
   2 ?    7.5   2.1    0.0045       3.5       4      15 ..     106     117 ..     104     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0052
                        zf-C2H2_11  6 qCleCGlcft 15
                                      +C++CG c +
  gi|488601317|ref|YP_007907788.1| 78 KCVHCGACIS 87
                                      8*******66 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0045
                        zf-C2H2_11   4 tcqCleCGlcft 15 
                                       + +C+ CG+c t
  gi|488601317|ref|YP_007907788.1| 106 SERCVRCGVCVT 117
                                       679*******65 PP

>> Keratin_matx  Keratin, high-sulphur matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.9     0.002       1.6      19      42 ..      75      97 ..      59     104 .. 0.80
   2 ?    5.9   2.1     0.021        16      19      38 ..     105     123 ..     100     129 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                      Keratin_matx 19 ssdkscrcGvclpstcpheislle 42
                                        +k+ +cG+c+ s cp e+  le
  gi|488601317|ref|YP_007907788.1| 75 DDEKCVHCGACI-SICPVEVFRLE 97
                                      4567779****8.89***998886 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                      Keratin_matx  19 ssdkscrcGvclpstcphei 38 
                                        s+++ rcGvc+ + cp + 
  gi|488601317|ref|YP_007907788.1| 105 DSERCVRCGVCV-TVCPLKA 123
                                       578999*****8.5798765 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 ?    6.6   0.5    0.0071       5.5     164     192 ..      63      91 ..      59      95 .. 0.90
   2 ?    2.9   0.6     0.097        76     169     194 ..      98     123 ..      93     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0071
                           HCV_NS2 164 vvfspmekkiirwgadtlaCGdivaGlPV 192
                                       v +++   kii++  + + CG +++  PV
  gi|488601317|ref|YP_007907788.1|  63 VKVTKIYEKIIKDDEKCVHCGACISICPV 91 
                                       66788889*******************99 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.097
                           HCV_NS2 169 mekkiirwgadtlaCGdivaGlPVsA 194
                                        + ++  ++ + + CG +v+  P  A
  gi|488601317|ref|YP_007907788.1|  98 YDYRVAADSERCVRCGVCVTVCPLKA 123
                                       688999**************999866 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 ?    8.3   0.6    0.0035       2.7      11      40 ..      59      91 ..      55      99 .. 0.76
   2 ?    2.4   1.7      0.24   1.8e+02      24      37 ..     105     118 ..      97     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0035
                   c-SKI_SMAD_bind 11 kckGlfvpelys...sseakCikCleCkllfsp 40
                                      ++kG+ v+++y+   +++ kC++C  C  +   
  gi|488601317|ref|YP_007907788.1| 59 ESKGVKVTKIYEkiiKDDEKCVHCGACISICPV 91
                                      6789999999973335899********877655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                   c-SKI_SMAD_bind  24 seakCikCleCkll 37 
                                       ++ +C++C  C ++
  gi|488601317|ref|YP_007907788.1| 105 DSERCVRCGVCVTV 118
                                       6779*******765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 707.46
//
Query:       gi|488601318|ref|YP_007907789.1|  [L=246]
Description: hypothetical protein Asulf_01825 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00025   20.7   0.7      0.012   15.2   0.7    2.1  1  ApbE      ApbE family


Domain annotation for each model (and alignments):
>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.7   6.4e-07     0.012     127     202 ..      89     160 ..      81     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.4e-07
                                       HHHHHHHHHHHHHH.TT-EEEEEETTEEEEEC-ECT-EEEEEE-TT...S.SEEEEEEESSS..EEEEEETTSSEEE CS
                              ApbE 127 KGyavdrvaellka.giksalvnlGGdiralGpdgkpwrvgiedPr...a.ellavlslsdd..avaTSGdyeryfe 196
                                        G ++  ++++ k+ g + a+v+ GGdi++ G + +  ++g+   +     e l+  +++d+  +++TS+       
  gi|488601318|ref|YP_007907789.1|  89 AGTIAGYAVNYAKKsGADFAVVDNGGDIAMFG-E-ERLTIGVYAQKlkvGfE-LNPSDMTDSiySICTSS------- 155
                                       58899999************************.3.58888888776433132.22333443445677765....... PP

                                       TEEEES CS
                              ApbE 197 gkryhH 202
                                       g ++ H
  gi|488601318|ref|YP_007907789.1| 156 G-TIGH 160
                                       3.3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); 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: 0.59u 0.39s 00:00:00.98 Elapsed: 00:00:00.58
# Mc/sec: 1274.37
//
Query:       gi|488601319|ref|YP_007907790.1|  [L=144]
Description: hypothetical protein Asulf_01826 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-12   47.4   2.0    3.2e-12   47.0   2.0    1.2  1  CxxCxxCC       Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
       0.05   12.6   0.0      0.062   12.3   0.0    1.1  1  Coatomer_WDAD  Coatomer WD associated region


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 !   47.0   2.0   3.5e-16   3.2e-12       1      84 [.      12     106 ..      12     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 3.5e-16
                          CxxCxxCC   1 eCkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiakadgrCvfldeetklCkiYeeRpkicrlfpas..... 72 
                                       +C +Cg+CC+e++v lt  ++ r+k+ + + ee+ +  ++k +g+C+f+ ++   C+i  ++p +c+lfp++     
  gi|488601319|ref|YP_007907790.1|  12 HCSACGKCCREYRVPLTFGEYLRFKKLGLV-EEKRKFYLRKINGKCPFQIGN--ICSIQDKKPIVCKLFPFTirfrg 85 
                                       6***************************94.44455666679**********..8****************999999 PP

                          CxxCxxCC  73 .........ekeellaraetC 84 
                                                ++e++ +++ +C
  gi|488601319|ref|YP_007907790.1|  86 nddalywygDEEYYVYIDVSC 106
                                       888888887777778888887 PP

>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.9e-06     0.062      14      72 ..      57     115 ..      44     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-06
                                       ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Coatomer_WDAD  14 elkdgellslqlkelgsieiypqslshnpngrfvlVcgdgeyiiytalalrnkaygkgl 72 
                                        ++ g++ s+q k+   ++ +p ++++  n+ +++  gd+ey +y  ++++n  +g+ +
  gi|488601319|ref|YP_007907790.1|  57 PFQIGNICSIQDKKPIVCKLFPFTIRFRGNDDALYWYGDEEYYVYIDVSCKNIVFGSPT 115
                                       378899999*******************************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 903.33
//
Query:       gi|488601320|ref|YP_007907791.1|  [L=61]
Description: hypothetical protein Asulf_01827 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 408.60
//
Query:       gi|488601321|ref|YP_007907792.1|  [L=70]
Description: Sulfur transfer protein involved in thiamine biosynthesis [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   16.9   0.1     0.0083   16.7   0.1    1.1  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.6e-07    0.0083      12      77 .]      14      70 .]       4      70 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.6e-07
                                      T.CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS 12 g.eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                        e+el l+e+st  ++l+  + +       + v ++ +g+ vp    d ++ +g e+ i+ +++GG
  gi|488601321|ref|YP_007907792.1| 14 PkEKELILEENSTYLDILNIFSINP------ESVLILKDGSPVPL---DDVVEEG-EIKIMKVISGG 70
                                      268999*******************......**************...8888887.9*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 378.95
//
Query:       gi|488601322|ref|YP_007907793.1|  [L=118]
Description: hypothetical protein Asulf_01829 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-19   69.4   6.3    3.7e-19   69.3   6.3    1.0  1  Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
  ------ inclusion threshold ------
      0.016   14.4   3.0      0.017   14.3   3.0    1.0  1  DUF4317   Domain of unknown function (DUF4317)
      0.022   14.9   0.5        1.2    9.3   0.0    2.4  2  DUF3567   Protein of unknown function (DUF3567)
      0.049   13.3   2.2      0.065   12.9   1.5    1.6  2  DUF4972   Domain of unknown function (DUF4972)
       0.12   11.1   0.0       0.12   11.1   0.0    1.0  1  SURNod19  Stress up-regulated Nod 19


Domain annotation for each model (and alignments):
>> 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 !   69.3   6.3     1e-22   3.7e-19       3     104 ..       7     107 ..       5     108 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1e-22
                                       HHHHHHHHHHHHSHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHH CS
                          Com_YlbF   3 dkareLaeaIkeseeykeykeaeealeedeelqklikefkklqkelqekqmkgeelkeeekkelqelkeeldknplv 79 
                                       +k+ +L eaI ++eey ++ e ee l++dee qkl+ +f+++q+++ +kqm+g e++++  ++l  l++el++ + +
  gi|488601322|ref|YP_007907793.1|   7 EKVIALSEAITKTEEYVDFLEKEEVLKADEETQKLLLDFQQKQQDFIAKQMSG-EVDQDLLNQLSGLQNELRSRESL 82 
                                       78889************************************************.77777777*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  80 keyleaeqelnellqevnkiiaeai 104
                                        ++l+++ +l +ll ev++ ++e++
  gi|488601322|ref|YP_007907793.1|  83 TNFLDSYSRLLDLLGEVTDLMSEKL 107
                                       *********************9987 PP

>> DUF4317  Domain of unknown function (DUF4317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.0   4.7e-06     0.017      25     116 ..      20     110 ..       3     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-06
                           DUF4317  25 gcYVdk.ekeivlklketflnleeeeqekyleifkkvLsGtigknlleleFpleeeeeggeqelLmelrksklkdee 100
                                         YVd  eke vlk +e+ ++l  + q+k  + + k +sG++++ ll+    l++e    ++e+L++ ++s  +  +
  gi|488601322|ref|YP_007907793.1|  20 EEYVDFlEKEEVLKADEETQKLLLDFQQKQQDFIAKQMSGEVDQDLLNQLSGLQNE--LRSRESLTNFLDSYSRLLD 94 
                                       569**99****************************************987777777..6788999999999999999 PP

                           DUF4317 101 lleefydkiiesydye 116
                                       ll e+ d + e+++++
  gi|488601322|ref|YP_007907793.1|  95 LLGEVTDLMSEKLNVD 110
                                       9999999999988765 PP

>> DUF3567  Protein of unknown function (DUF3567)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.018        66      51      77 ..       2      28 ..       1      38 [. 0.85
   2 ?    9.3   0.0   0.00033       1.2      46      81 ..      57      92 ..      42      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.018
                           DUF3567 51 Aesfrkevkalieeepseeevddflde 77
                                       e++r++v al e   ++ee  dfl++
  gi|488601322|ref|YP_007907793.1|  2 NENLREKVIALSEAITKTEEYVDFLEK 28
                                      5899**********9999999999987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00033
                           DUF3567 46 ldGslAesfrkevkalieeepseeevddfldeyaal 81
                                      + G++ +++ ++++ l++e +s+e++ +fld+y+ l
  gi|488601322|ref|YP_007907793.1| 57 MSGEVDQDLLNQLSGLQNELRSRESLTNFLDSYSRL 92
                                      46899999999**********************987 PP

>> DUF4972  Domain of unknown function (DUF4972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.5   1.8e-05     0.065      80     122 ..      12      54 ..       6      60 .. 0.93
   2 ?   -1.7   0.0      0.61   2.2e+03      45      56 ..      65      76 ..      54      95 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                           DUF4972  80 LedaivklkesiakikegnkaeaeeeadrlikeakkaieeFka 122
                                       L +ai k +e +  ++++++ +a+ee+++l+ + +++ ++F a
  gi|488601322|ref|YP_007907793.1|  12 LSEAITKTEEYVDFLEKEEVLKADEETQKLLLDFQQKQQDFIA 54 
                                       889*************************************977 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.61
                           DUF4972 45 yieqleelinkl 56
                                        +ql+ l+n+l
  gi|488601322|ref|YP_007907793.1| 65 LLNQLSGLQNEL 76
                                      344444444444 PP

>> SURNod19  Stress up-regulated Nod 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.5e-05      0.12      49     123 ..      13      90 ..       4     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                          SURNod19  49 gnpvplhetYlhhwvvekyyakkeakke.seeekkkksdailarnsGvCqkkvlkqyfglgse..trktatavpdpy 122
                                        +++ + e Y+     e+  ++ e++++   + ++k++d+i ++ sG  +++ l+q  gl  e  +r+  t+  d+y
  gi|488601322|ref|YP_007907793.1|  13 SEAITKTEEYVDFLEKEEVLKADEETQKlLLDFQQKQQDFIAKQMSGEVDQDLLNQLSGLQNElrSRESLTNFLDSY 89 
                                       567788888888888777776655554436677888999999999*****************944456667788887 PP

                          SURNod19 123 g 123
                                       +
  gi|488601322|ref|YP_007907793.1|  90 S 90 
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1367  (0.0762452); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 805.15
//
Query:       gi|488601323|ref|YP_007907794.1|  [L=54]
Description: hypothetical protein Asulf_01831 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 313.65
//
Query:       gi|488601324|ref|YP_007907795.1|  [L=127]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-13   51.0   0.8    2.6e-13   50.6   0.8    1.2  1  PIN        PIN domain
  ------ inclusion threshold ------
       0.12   11.8   0.1       0.46    9.9   0.1    1.8  2  adh_short  short chain dehydrogenase


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 !   50.6   0.8   2.9e-17   2.6e-13       1     118 [.       2     115 ..       2     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.9e-17
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidae 76 
                                       ivlDT vli+++ r+++k e+++k le+ ++++t+++ l E++ + +r           ++l ++ + lkil+++++
  gi|488601324|ref|YP_007907795.1|   2 IVLDTDVLIEIFdRNSKKGEEVLKKLEG-YDVATTSINLHEIACGFSR---------IGKLLPEEIRFLKILDFTSK 68 
                                       79*************************9.*******************.........6677777799********** PP

                                       HHHHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTH.HHH CS
                               PIN  77 iaeeaaeialkyg.....llpnDaliaAtAkehgikliatfDed.frr 118
                                       +a+  a++ +k++     ++ +D +iaA ++ +++ +iatf+++ f+r
  gi|488601324|ref|YP_007907795.1|  69 DALLSAKLENKLEkvdnaVGRFDTMIAAICINRNA-AIATFNKKhFER 115
                                       ***********************************.666***996655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.046   4.1e+02      29      47 ..      12      30 ..       4      43 .. 0.75
   2 ?    9.9   0.1   5.1e-05      0.46      59     107 ..      71     119 ..      20     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.046
                                      EEESCHHHHHHHHHHHHHT CS
                         adh_short 29 vvdrseekleevakelkee 47
                                      ++dr+++k eev+k+l+  
  gi|488601324|ref|YP_007907795.1| 12 IFDRNSKKGEEVLKKLEGY 30
                                      589999*******999865 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 5.1e-05
                                       TSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHH CS
                         adh_short  59 tdreevealvekavkklgkldvLvnNAGitgsgpfselseeewerviev 107
                                         ++++e+ +ek+ + +g+ d +++   i+++++++ ++++ +er +e 
  gi|488601324|ref|YP_007907795.1|  71 LLSAKLENKLEKVDNAVGRFDTMIAAICINRNAAIATFNKKHFERFVEF 119
                                       3356789999***********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 833.70
//
Query:       gi|488601325|ref|YP_007907796.1|  [L=121]
Description: Cytochrome c-type biogenesis protein CcmE [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   53.0   1.7      4e-14   52.7   1.7    1.0  1  CcmE      CcmE
  ------ inclusion threshold ------
      0.066   12.9   0.1      0.095   12.3   0.1    1.3  1  CopK      Copper resistance protein K


Domain annotation for each model (and alignments):
>> CcmE  CcmE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   1.7   4.5e-18     4e-14      12     127 ..      10     118 ..       3     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.5e-18
                                       XXXXXXXXXXXXXXXXXXSSSXXBXTTTTTS--S-TTSEEEEEEEE-TTT-EE-TTSSEEEEEEE-T.-EEEEEEES CS
                              CcmE  12 lllvlaavvvlvlsalqenlvyfltpsevlekkaeegrrlrvgGlVkegsvkrdpesleveFvvtdlekelkVeYeg 88 
                                       + +v+++ +++v+++l  nl+ + t+sev+++++  + +++v G ++++s +   ++ +  F +td+++ ++V Yeg
  gi|488601325|ref|YP_007907796.1|  10 FGFVMVISIIFVYYTLITNLSPYKTVSEVVNSGN--QYNIQVNGSIVKNSTRIV-DG-KTIFLLTDGKSVMEVIYEG 82 
                                       3445566778899****************98855..56789*********8664.55.556******9********* PP

                                       ---TT--TTSEEEEEEEE-TTSEEEECCEEESS-XXXX. CS
                              CcmE  89 ilPdlFregqgvvveGrleedgvfeAeevlaKhdekYmp 127
                                          +  +e+  vvv+G +  dg f+A +vl+K+ ++Y +
  gi|488601325|ref|YP_007907796.1|  83 TTHN--QEDVAVVVTGDYI-DGKFYAANVLTKCHTEYVA 118
                                       9876..8***********7.68***************76 PP

>> CopK  Copper resistance protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.1e-05     0.095       5      43 ..      54      93 ..      50     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                                      EEEEEEBTTSEEEEEETTS-EEEEETT.SEEEE--TT-EE CS
                              CopK  5 vkksveLkdGstlyifkDGKmamEdkl.Gravrmkegavm 43
                                      vk+s  + dG t+++  DGK  mE  + G + + ++ av+
  gi|488601325|ref|YP_007907796.1| 54 VKNSTRIVDGKTIFLLTDGKSVMEVIYeGTTHNQEDVAVV 93
                                      7899999*****************8762444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 747.33
//
Query:       gi|488601326|ref|YP_007907797.1|  [L=579]
Description: Cytochrome c biogenesis factor [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-31  107.7  14.7    6.7e-31  107.7  14.7    4.6  4  Cytochrom_C_asm  Cytochrome C assembly protein
    3.3e-11   43.1   0.1    3.3e-11   43.1   0.1    1.8  2  CcmF_C           Cytochrome c-type biogenesis protein CcmF C-


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.1   6.8         2   1.8e+04      85     101 ..       7      23 ..       1      70 [. 0.46
   2 !  107.7  14.7   7.5e-35   6.7e-31       1     208 [.      85     276 ..      85     281 .. 0.82
   3 ?  -11.5  16.7         2   1.8e+04      19      62 ..     308     359 ..     289     449 .. 0.53
   4 ?   -3.3   0.1      0.72   6.5e+03      77      92 ..     554     569 ..     545     574 .. 0.68

  Alignments for each domain:
  == domain 1  score: -5.1 bits;  conditional E-value: 2
                   Cytochrom_C_asm  85 tliigallsialliier 101
                                       + +i +llsi+  i  +
  gi|488601326|ref|YP_007907797.1|   7 LILISFLLSIISSITLY 23 
                                       44444444443332221 PP

  == domain 2  score: 107.7 bits;  conditional E-value: 7.5e-35
                   Cytochrom_C_asm   1 lsnleesllllawilsllgllleylarklnls.llaavaliaalillgfalf....lllaelqesadlnpalqspil 72 
                                       +   e++lll+a+ +sl+ l++   +++  ls l  +++++++++l++++l+       ++  e+  lnp+l++  +
  gi|488601326|ref|YP_007907797.1|  85 WAGKEGALLLWALFVSLMNLFAV--SNGDRLSrLSVSISSFFFAFLTLLLLTtsnpFTRTQAFEGVGLNPLLRTIEM 159
                                       667899************99992..333223202333333333333333333666677777788999********** PP

                   Cytochrom_C_asm  73 miHvplallsYatliigallsialliierqlkkkkklklsanlkllkqldrlsyriiliGfvlltigiilGsvWa.. 147
                                       +iH+pl+++sY++++i ++++ia +                   l +++ + +y + l++++ + +gi++G++Wa  
  gi|488601326|ref|YP_007907797.1| 160 AIHPPLIFMSYSGFLIPFSMAIAGI------------------YLGEKWTKKAYPYLLFSWISISAGIFVGALWAyk 218
                                       *************************..................3445566689**********************99 PP

                   Cytochrom_C_asm 148 eeaWGsywsWDpketaslitWlvfaallhsriekgwrgkkaailailgflllllayfgvrl 208
                                        ++WG++w WDp+e+as+++Wl  +al+h++   + +g+++ +l+ l+f+l++ a ++ r 
  gi|488601326|ref|YP_007907797.1| 219 TLGWGGFWGWDPVENASFFPWLSSTALIHTV---KREGRRTYLLTTLTFVLVVVAGYITRA 276
                                       9******************************...78******************9998886 PP

  == domain 3  score: -11.5 bits;  conditional E-value: 2
                   Cytochrom_C_asm  19 gllleylarklnlsllaavaliaalillgfalf........lllaelqesad 62 
                                       ++l+    rk ++ +   +++++++ l++++lf        +l++ l++ + 
  gi|488601326|ref|YP_007907797.1| 308 YFLFRIEGRKFEFGFNMEGLITLFIYLTVLLLFsilvgsclTLFTNLKPDKN 359
                                       4455555666666666666666666555555555534433333333333222 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 0.72
                   Cytochrom_C_asm  77 plallsYatliigall 92 
                                       +l+++++a+ +ig+++
  gi|488601326|ref|YP_007907797.1| 554 SLLWIGMALTLIGSFY 569
                                       5666777777777665 PP

>> CcmF_C  Cytochrome c-type biogenesis protein CcmF C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.4      0.89   7.9e+03     132     147 ..      34      49 ..       8      60 .. 0.41
   2 !   43.1   0.1   3.7e-15   3.3e-11      79     317 ..     330     568 ..     327     572 .. 0.75

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 0.89
                            CcmF_C 132 lkvlaalglalavwvv 147
                                       +++ ++ + +l++++ 
  gi|488601326|ref|YP_007907797.1|  34 ISIYTVYAYFLTIFLS 49 
                                       2333333333333322 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 3.7e-15
                            CcmF_C  79 vfvplmvplllllgvGpllr.Wkrakl.aellkrllvalvlalvlalllalllgelkvlaalglalavwvvlaalae 153
                                       +f+ l+v+ll+ + vG++l  + + k+ ++  ++l++    a+vl +l  +++++lk+  +   +l v +v+aa++ 
  gi|488601326|ref|YP_007907797.1| 330 LFIYLTVLLLFSILVGSCLTlFTNLKPdKNYYESLMIP-YEAIVLVIL-GFCISRLKIRRYTYYILPV-IVFAAIQF 403
                                       68889999998888888766244444414456666666.333333333.4444445555544444444.44445555 PP

                            CcmF_C 154 laerl..rakakellarlrklprsawGmvlAHlGvavtvlGvalvsayeverdvrlkpgesvevagyefefegveev 228
                                       l+  l  +  ++ ++ ++ +l r+    ++ HlG+ ++ +G + v + +++ + +++ +++++  gye+++ ++++ 
  gi|488601326|ref|YP_007907797.1| 404 LFGNLllSIFSALFVFSAVNL-RKPSHVIIIHLGIMLIFMGSIGVWKASEKYTFTISENQTITADGYELRLIKIDSE 479
                                       555553322223333333333.333446788********************************************** PP

                            CcmF_C 229 eGpNYtaeraelevsrdgkevatlepekRlYtvqemp..mteaaidagllrdlYvalGeeledeawavrlyvkpfvr 303
                                       +       + ++ev +d k+v  +ep    Y+  +m+  ++  +i ++ l+d+Yv+ G   +++ +++ ++++ +++
  gi|488601326|ref|YP_007907797.1| 480 DRRDSFIIKFRFEVLKDRKHVGFVEPRVIEYKIWRMEriVSSVGILNTPLEDIYVSTGI--SKDGIQLEVHINRLAS 554
                                       99999999************************988763268999**************8..6778************ PP

                            CcmF_C 304 wiWlGallmalGGl 317
                                       ++W+G +l  +G++
  gi|488601326|ref|YP_007907797.1| 555 LLWIGMALTLIGSF 568
                                       ********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 3300.31
//
Query:       gi|488601327|ref|YP_007907798.1|  [L=222]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-31  109.3  13.8    2.2e-31  108.8  13.8    1.2  1  PrsW-protease  PrsW family intramembrane metalloprotease
  ------ inclusion threshold ------
       0.36   10.9   5.2      0.095   12.8   1.5    1.9  2  DUF3974        Domain of unknown function (DUF3974)


Domain annotation for each model (and alignments):
>> PrsW-protease  PrsW family intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8  13.8   2.4e-35   2.2e-31       1     191 [.      32     195 ..      32     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 2.4e-35
                     PrsW-protease   1 eplwlllaaflwgalvavllalllntvlqallraelgkfiaeflaaflvaglvEEllKalgvllllllrrrefdepl 77 
                                       ep ++++ +f+ ga+v+v +a++l+++++         f +++l+ +l+++ +EE  Kal++ + +   ++++d+ +
  gi|488601327|ref|YP_007907798.1|  32 EPAKYIAITFFYGAIVSVGIAMFLERLASY-------IFPQAALFIALISASIEEPSKALAIRIPY--DSKQMDGLM 99 
                                       7999***************99999999884.......367889999****************9987..9******** PP

                     PrsW-protease  78 dGivygaavglGFavlEnllYyvqalpsaanegqlgglqllilRillsvagHalftallGiglglaksrrraarrvq 154
                                       dG+vyg+++glGFa++EnllY +             g+q++++Ri+l +++H +++a++G+g+gl ++       v+
  gi|488601327|ref|YP_007907798.1| 100 DGVVYGVTAGLGFAATENLLYGL-----------GFGIQVTLIRIILTPFAHGAWSAIVGVGYGLKAEG-----YVR 160
                                       **********************5...........358****************************9933.....468 PP

                     PrsW-protease 155 illlglllavllHalwNllasl.aelllavvgvllyvp 191
                                        ++  llla+++H+lwN+l  + +++ l   ++ll++ 
  gi|488601327|ref|YP_007907798.1| 161 SIIPFLLLAMFMHFLWNFLIFMsSDNML---YLLLILL 195
                                       99999**************988444433...2222222 PP

>> DUF3974  Domain of unknown function (DUF3974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.46   4.1e+03      14      31 ..       8      26 ..       5      30 .. 0.67
   2 ?   12.8   1.5   1.1e-05     0.095       7      32 ..     189     214 ..     182     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.46
                           DUF3974 14 lllig.ltvvvllvyfgrk 31
                                      l+li+ + +++l+ yf  k
  gi|488601327|ref|YP_007907798.1|  8 LILISyVPAIALVWYFYHK 26
                                      4555514589999999776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.1e-05
                           DUF3974   7 vllligillligltvvvllvyfgrkl 32 
                                        llli +llli + ++++lvy+g k 
  gi|488601327|ref|YP_007907798.1| 189 YLLLILLLLLINIGIIGFLVYLGTKE 214
                                       58999999***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1458.41
//
Query:       gi|488601328|ref|YP_007907799.1|  [L=179]
Description: hypothetical protein Asulf_01836 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   53.1   7.8    5.5e-07   29.7   2.7    2.7  2  DUF445       Protein of unknown function (DUF445)
  ------ inclusion threshold ------
       0.11   12.6   2.6       0.45   10.6   0.1    2.1  2  ECF_trnsprt  ECF transporter, substrate-specific component


Domain annotation for each model (and alignments):
>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   1.6e-09   1.4e-05       2      45 ..      12      57 ..      11      65 .. 0.91
   2 !   29.7   2.7   6.2e-11   5.5e-07     284     364 ..      96     175 ..      56     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.6e-09
                            DUF445  2 eaAliGaladwfAikaLFRhP.....lg.lpiPfttglIPknkeriakkl 45
                                      ++A +G +++  A+  LF+ P     ++ ++i    gl+P + ++i+++ 
  gi|488601328|ref|YP_007907799.1| 12 IGAFVGFITNVVAVELLFH-PkkpinIFgIRIQ---GLVPARSKEIIERF 57
                                      8*****************9.9999**888****...**********9876 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 6.2e-11
                            DUF445 284 klaedpklreklnkflenaaakvlekyrldiskiveetvnafdaeeleelIelivgkeLqaIrinGtlvGgliGlll 360
                                       +++ d+ + +++  ++++ ++k + + ++d+ ++v  + ++ ++ee+e l  + ++keL++I   G ++G++iG+++
  gi|488601328|ref|YP_007907799.1|  96 NFKIDEWVSKTILPWVKDFLTKSISE-NVDVREFVLRKAEEISDEEIEILFKKFAKKELRFIELSGLVLGFVIGIIQ 171
                                       33333444455556777766666665.79***********************************************9 PP

                            DUF445 361 ylvs 364
                                        ++ 
  gi|488601328|ref|YP_007907799.1| 172 SIFF 175
                                       8875 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1     5e-05      0.45      41      62 ..       6      27 ..       4      65 .. 0.75
   2 ?    2.3   0.3     0.017   1.6e+02      44      60 ..     160     176 ..     142     179 .] 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5e-05
                                      HCTTCHHHHHHHHHHHHHHHHC CS
                       ECF_trnsprt 41 llfGpikGailgiitsvlkail 62
                                      l+f p+ Ga++g+it+v++  l
  gi|488601328|ref|YP_007907799.1|  6 LIFPPLIGAFVGFITNVVAVEL 27
                                      79*************9998643 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.017
                                       TCHHHHHHHHHHHHHHH CS
                       ECF_trnsprt  44 GpikGailgiitsvlka 60 
                                       G + G+++gii s++ +
  gi|488601328|ref|YP_007907799.1| 160 GLVLGFVIGIIQSIFFY 176
                                       55556666666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1174.35
//
Query:       gi|488601329|ref|YP_007907800.1|  [L=135]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-43  147.7   1.8    1.9e-43  147.5   1.8    1.0  1  DUF61     Protein of unknown function DUF61


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5   1.8   1.1e-47   1.9e-43       1     127 []       4     130 ..       4     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 1.1e-47
                                       -S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE CS
                             DUF61   1 drilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelge 77 
                                       +r+lak+i+++nkh+Pa+rktLke+L+e++p+i+++dg+e++++k+el++++e+++e  wdk+++PI+lem+  +ge
  gi|488601329|ref|YP_007907800.1|   4 ERALAKMIEAMNKHMPARRKTLKEMLNEDEPSIKARDGNEYIIEKDELKFISEYVDELDWDKFNIPIILEMNDLHGE 80 
                                       589************************************************************************** PP

                                       ..EEEES-HHHHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST...TEE CS
                             DUF61  78 svylvrgkaevkvvskilgkereeedelviykpevrelrrklptatqliF 127
                                        v+++r+k++ ++++k++g +r+ +d ++iy +e+r++rr l+ta+q++F
  gi|488601329|ref|YP_007907800.1|  81 TVVFIRDKLHQEFMRKAFGFDRYVRDVMMIYLYEMRKVRRALRTASQVVF 130
                                       *************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 912.99
//
Query:       gi|488601330|ref|YP_007907801.1|  [L=315]
Description: hypothetical protein Asulf_01839 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1893.22
//
Query:       gi|488601331|ref|YP_007907802.1|  [L=393]
Description: Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-30  103.3   5.8      7e-17   61.4   0.1    2.8  3  CCG       Cysteine-rich domain
    1.5e-07   31.8   8.2    2.2e-07   31.2   7.1    2.0  1  Fer4_8    4Fe-4S dicluster domain
    2.7e-05   24.2   9.2    4.1e-05   23.7   7.5    2.2  2  Fer4_9    4Fe-4S dicluster domain
    7.5e-05   23.2   7.8    7.5e-05   23.2   7.8    2.1  1  Fer4_17   4Fe-4S dicluster domain
    0.00013   22.0   9.3    0.00049   20.1   9.3    2.1  1  Fer4_10   4Fe-4S dicluster domain
     0.0019   18.7  11.0       0.02   15.5  11.6    2.4  2  Fer4_7    4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.03   14.0   0.8        1.9    8.2   0.1    2.8  2  ScdA_N    Domain of Unknown function (DUF542)
       0.47   10.3  12.3        3.8    7.5   2.3    2.7  2  Fer4      4Fe-4S binding domain
        1.9    8.7  14.4       0.85    9.8   9.7    2.6  2  Fer4_21   4Fe-4S dicluster domain
        2.4    8.4  16.9        2.6    8.3   4.1    2.8  2  Fer4_2    4Fe-4S binding domain
        2.9    8.9  12.9        8.4    7.4   3.1    3.3  4  Fer4_16   4Fe-4S double cluster 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 ?   -3.4   0.9         7   1.1e+04      73      81 ..      48      56 ..      35      59 .. 0.65
   2 !   44.5   0.0   8.1e-15   1.3e-11       2      85 .]     166     250 ..     165     250 .. 0.93
   3 !   61.4   0.1   4.3e-20     7e-17       1      84 [.     283     366 ..     283     367 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7
                               CCG 73 ivtacpgCl 81
                                      ++ +c++C+
  gi|488601331|ref|YP_007907802.1| 48 VCMQCGTCS 56
                                      556677776 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 8.1e-15
                               CCG   2 ayfdgChllraa..ypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivta 76 
                                        +f gC +  ++  + ev ++++++++  g+++ + ++e CCG+ +++ g+e l+e l ++n   ++e g++++++ 
  gi|488601331|ref|YP_007907802.1| 166 YWFIGC-VSSYEsrSMEVVEKTARIFKDIGIDFSVDADEGCCGNEAMVLGEEGLFELLKEENEMFFKERGVEKVIAS 241
                                       689***.55555559************************************************************** PP

                               CCG  77 cpgCllqlk 85 
                                       +p+C++ +k
  gi|488601331|ref|YP_007907802.1| 242 SPHCYNAFK 250
                                       *****9875 PP

  == domain 3  score: 61.4 bits;  conditional E-value: 4.3e-20
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaiv 74 
                                       v+y+d+C+l+r++  y+++r+++k + ++++ve+++  e+++CCG g g+  +e    + + ++v++a +t+ad++v
  gi|488601331|ref|YP_007907802.1| 283 VTYHDPCYLGRYNgiYDAPREVIKSVYNVEFVEMQRIrENSYCCGGGSGNFLRE---SRANVQRVREALSTNADILV 356
                                       89***********************************************77777...59999*************** PP

                               CCG  75 tacpgCllql 84 
                                       + cp Cl++l
  gi|488601331|ref|YP_007907802.1| 357 VSCPICLIML 366
                                       ********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 !   31.2   7.1   1.3e-10   2.2e-07       2      65 .]      46     102 ..      45     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.3e-10
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       l+ C++Cg C ++C + ++++ ++l  + + ++ +  ++       +w Cttc  C+++Cp gi
  gi|488601331|ref|YP_007907802.1|  46 LSVCMQCGTCSASCTSRQSFNLRKLILNLNLTG-NDLSDS------IWDCTTCLTCQTRCPRGI 102
                                       577***********9999999666666666677.666666......9**************997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   7.5   2.5e-08   4.1e-05       2      49 ..      49     101 ..      48     102 .. 0.73
   2 ?   -2.0   0.0       2.6   4.3e+03      11      26 ..     358     373 ..     356     377 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.5e-08
                            Fer4_9   2 CtgCgaCveaC.pagvvvedaaerkarlraase....eaCigCgaCveaCpkg 49 
                                       C++Cg+C ++C   + ++ ++     +l+  +     ++C++C +C  +Cp+g
  gi|488601331|ref|YP_007907802.1|  49 CMQCGTCSASCtSRQSFNLRKLILNLNLTGNDLsdsiWDCTTCLTCQTRCPRG 101
                                       ***********633444555555554444433377889*************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                            Fer4_9  11 aCpagvvvedaaerka 26 
                                       +Cp ++++ ++a ++ 
  gi|488601331|ref|YP_007907802.1| 358 SCPICLIMLEDAVKTL 373
                                       7999998888777665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   7.8   4.6e-08   7.5e-05       2      60 ..      49     102 ..      48     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.6e-08
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                       C+qCg C ++C s +  +   +kl+ +++l+   +   ++ + +C++C  C+++CP g+
  gi|488601331|ref|YP_007907802.1|  49 CMQCGTCSASCTSRQSFNL--RKLILNLNLT---GNDLSDSIWDCTTCLTCQTRCPRGI 102
                                       *************999888..6777776664...33457899**************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 !   20.1   9.3     3e-07   0.00049       6      56 .]      46      99 ..      41      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                           Fer4_10  6 ddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       + C++Cg+C ++C +        ++   + +  ++  ++ +++Ct+c  C+  CP
  gi|488601331|ref|YP_007907802.1| 46 LSVCMQCGTCSASC-T-SrqsfnLRKLILNLNLTGNDLSDSIWDCTTCLTCQTRCP 99
                                      578***********.4.4466654444555566677778899*************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 !    7.0   3.6    0.0055       8.9      36      49 ..      47      60 ..      28      63 .. 0.70
   2 !   15.5  11.6   1.2e-05      0.02       2      52 .]      49     102 ..      48     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0055
                            Fer4_7 36 ekClgCgaCvavCP 49
                                      + C++Cg C a C 
  gi|488601331|ref|YP_007907802.1| 47 SVCMQCGTCSASCT 60
                                      55777777777775 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
                            Fer4_7   2 CigCgaCvaaCp.vkaieldeeenek..gtekveidpekClgCgaCvavCPtga 52 
                                       C++Cg C a C   + ++l++   +   +  ++  + ++C++C  C+++CP g+
  gi|488601331|ref|YP_007907802.1|  49 CMQCGTCSASCTsRQSFNLRKLILNLnlTGNDLSDSIWDCTTCLTCQTRCPRGI 102
                                       ***********855666666642221123377888999*************986 PP

>> ScdA_N  Domain of Unknown function (DUF542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0012       1.9      14      26 ..     185     197 ..     182     210 .. 0.80
   2 ?    3.2   0.1     0.044        72      26      31 ..     324     329 ..     323     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                            ScdA_N  14 raakvFrkygIDF 26 
                                       ++a++F++ gIDF
  gi|488601331|ref|YP_007907802.1| 185 KTARIFKDIGIDF 197
                                       79*********** PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.044
                            ScdA_N  26 FCCgGk 31 
                                       +CCgG 
  gi|488601331|ref|YP_007907802.1| 324 YCCGGG 329
                                       9****6 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.3    0.0023       3.8       6      18 ..      47      59 ..      44      60 .. 0.90
   2 ?    7.3   2.6    0.0028       4.5       8      21 ..      88     101 ..      87     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                                      TTSSS-THHHHHS CS
                              Fer4  6 ekCigCGaCvevC 18
                                      + C+ CG+C   C
  gi|488601331|ref|YP_007907802.1| 47 SVCMQCGTCSASC 59
                                      57********999 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0028
                                       SSS-THHHHHSTTT CS
                              Fer4   8 CigCGaCvevCPvg 21 
                                       C+ C +C   CP g
  gi|488601331|ref|YP_007907802.1|  88 CTTCLTCQTRCPRG 101
                                       ************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 ?    9.8   9.7   0.00052      0.85       7      52 ..      48      99 ..      44     103 .. 0.66
   2 ?   -0.4   0.1      0.81   1.3e+03      35      57 ..     343     363 ..     323     376 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                           Fer4_21  7 kCigCgkCliaCedtshqai.........eidaktvlkvved..eCvGCnlCssvCP 52
                                       C++Cg C  +C   s q           +++++    + ++  +C+ C  C + CP
  gi|488601331|ref|YP_007907802.1| 48 VCMQCGTCSASCT--SRQSFnlrklilnlNLTGN---DLSDSiwDCTTCLTCQTRCP 99
                                      7***********9..5666633333222222222...22222449************ PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.81
                           Fer4_21  35 kvvedeCvGCnlCssvCPvedci 57 
                                       +v+e   +  ++ +  CP+  c+
  gi|488601331|ref|YP_007907802.1| 343 RVREALSTNADILVVSCPI--CL 363
                                       5555555555555555665..33 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.1    0.0016       2.6       9      21 ..      48      60 ..      45      61 .. 0.86
   2 ?    4.9   5.0      0.02        33      10      21 ..      88      99 ..      86     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                            Fer4_2  9 rCigCgaCvsaCP 21
                                       C++Cg+C  +C 
  gi|488601331|ref|YP_007907802.1| 48 VCMQCGTCSASCT 60
                                      6*******88895 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                            Fer4_2 10 CigCgaCvsaCP 21
                                      C+ C +C++ CP
  gi|488601331|ref|YP_007907802.1| 88 CTTCLTCQTRCP 99
                                      ***********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 ?    6.1   0.7     0.013        21       2      13 ..      49      60 ..      31      64 .. 0.75
   2 ?    7.4   3.1    0.0052       8.4      50      65 ..      84      99 ..      73     101 .. 0.82
   3 ?    5.0   4.8      0.03        49       2      29 ..      88     113 ..      87     172 .. 0.66
   4 ?   -2.8   0.0         8   1.3e+04      12      49 ..     206     246 ..     205     253 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                           Fer4_16  2 CgtCgkCaevCP 13
                                      C +Cg C  +C 
  gi|488601331|ref|YP_007907802.1| 49 CMQCGTCSASCT 60
                                      667777777664 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0052
                           Fer4_16 50 kqeaitgCdiCqdvCP 65
                                      + +++t C +Cq+ CP
  gi|488601331|ref|YP_007907802.1| 84 SIWDCTTCLTCQTRCP 99
                                      4799999999999999 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.03
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare 29 
                                       C+tC  C   CP +   ++    +++r+
  gi|488601331|ref|YP_007907802.1|  88 CTTCLTCQTRCPRGIPLTE--IIVDSRK 113
                                       9999999999998863333..3333333 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 8
                           Fer4_16  12 CPtnaikekkekeiearecisy...ntaekkdlaedeekck 49 
                                       C  +a+   +e  +e  +++++   ++++ ++++ ++ +c+
  gi|488601331|ref|YP_007907802.1| 206 CGNEAMVLGEEGLFELLKEENEmffKERGVEKVIASSPHCY 246
                                       66677777766777766666665556666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2764.13
//
Query:       gi|488601332|ref|YP_007907803.1|  [L=298]
Description: hypothetical protein Asulf_01841 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       631  (0.0351944); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1933.82
//
Query:       gi|488601333|ref|YP_007907804.1|  [L=411]
Description: ATPases of the AAA+ class [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-38  131.2   0.1    1.1e-37  129.4   0.0    2.0  1  AAA              ATPase family associated with various cellul
    1.9e-10   40.4   0.0    5.3e-10   38.9   0.0    1.8  1  AAA_lid_3        AAA+ lid domain
    4.1e-06   26.8   0.1    1.9e-05   24.7   0.1    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
    4.1e-06   27.4   0.0    1.3e-05   25.7   0.0    2.0  1  AAA_18           AAA domain
    3.8e-05   24.0   0.2     0.0047   17.2   0.2    2.5  1  AAA_22           AAA domain
    0.00011   22.4   0.0    0.00023   21.3   0.0    1.6  1  AAA_33           AAA domain
    0.00014   22.1   0.0    0.00027   21.2   0.0    1.6  1  AAA_28           AAA domain
    0.00067   19.2   0.0      0.006   16.1   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
    0.00067   19.8   0.2     0.0025   18.0   0.0    2.0  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.002   18.5   0.1        0.1   13.0   0.1    2.4  2  AAA_16           AAA ATPase domain
     0.0023   17.7   0.1     0.0088   15.8   0.0    2.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0025   17.6   0.1     0.0067   16.2   0.0    1.7  2  AAA_11           AAA domain
     0.0032   17.9   0.7      0.038   14.4   0.1    2.6  1  AAA_17           AAA domain
     0.0048   17.1   0.0      0.018   15.2   0.0    1.9  2  Cytidylate_kin2  Cytidylate kinase-like family
     0.0088   16.6   0.0      0.021   15.4   0.0    1.7  1  ABC_tran         ABC transporter
     0.0091   15.4   0.0      0.019   14.4   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
       0.01   15.9   0.1      0.037   14.1   0.0    2.0  1  AAA_14           AAA domain
      0.012   15.6   0.0      0.029   14.3   0.0    1.7  1  Rad17            Rad17 P-loop domain
      0.019   14.7   0.1      0.044   13.5   0.1    1.7  1  AAA_24           AAA domain
      0.023   14.8   0.0      0.049   13.7   0.0    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
      0.023   15.1   0.1       0.11   12.9   0.0    2.4  1  RNA_helicase     RNA helicase
      0.028   14.4   0.1        9.4    6.1   0.0    2.3  2  NACHT            NACHT domain
      0.049   13.2   0.0       0.23   11.0   0.0    2.0  2  AAA_25           AAA domain
      0.058   13.7   0.5       0.21   11.9   0.5    1.9  1  AAA_19           AAA domain
      0.059   13.5   0.0       0.12   12.5   0.0    1.5  1  SKI              Shikimate kinase
       0.08   12.1   0.0       0.13   11.4   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
       0.09   12.5   0.0       0.17   11.6   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
        0.1   12.2   0.1       0.27   10.9   0.1    1.7  1  SRP54            SRP54-type protein, GTPase domain
       0.13   12.0   0.0       0.23   11.1   0.0    1.5  1  AAA_30           AAA domain
       0.17   12.0   0.4        2.2    8.4   0.1    2.6  2  ADK              Adenylate kinase
       0.22   11.3   2.4        8.6    6.3   0.1    2.9  2  YycC             YycC-like protein


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 !  129.4   0.0   1.8e-40   1.1e-37       1     131 [.     203     331 ..     203     332 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 1.8e-40
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       ++++GppGtGKT++a+a+ k l+ +++e+++s ++s+y+ge++k+i+++f+ ak+ + p+ilfiDE+d +ak+r+++
  gi|488601333|ref|YP_007907804.1| 203 LMFIGPPGTGKTTTARALSKRLHLPLVEVKLSMITSQYLGETSKNIEKVFEIAKRLS-PCILFIDEFDYVAKTRTSD 278
                                       589*****************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                       e+   +r+vn+Ll+ +d+ +  e+ vi+i+atn+p+ ld a+  +Rfd++ie++
  gi|488601333|ref|YP_007907804.1| 279 EHAAVKRAVNTLLKSIDEINLVEDGVILIAATNHPSLLDTAVW-RRFDKIIEFP 331
                                       *******************************************.7******997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   9.2e-13   5.3e-10       2      32 ..     353     383 ..     352     396 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 9.2e-13
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlr 32 
                                       +d++eL+++T+G++GAD++ ++reA+l+ l 
  gi|488601333|ref|YP_007907804.1| 353 FDIDELVKLTDGFTGADIKLVIREAVLNSLM 383
                                       7*************************99885 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   3.4e-08   1.9e-05       2     138 .]     203     324 ..     202     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.4e-08
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       ++ +GppGtgK++ a+ l+++l  ++++v l+  t+  + +g+++           ++ + a+  +++il++DE++ 
  gi|488601333|ref|YP_007907804.1| 203 LMFIGPPGTGKTTTARALSKRLHLPLVEVKLSMITS--QYLGETS-------KNIEKVFEIAKrlSPCILFIDEFDY 270
                                       789***************************987332..3333333.......3345555566668999999999998 PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                       + +  ++  +    +    l ++  +++  +d+    + +ia++n ++     l+ a+++Rf
  gi|488601333|ref|YP_007907804.1| 271 VAKTRTSDEHAAVKRAVNTLLKSIDEINLVEDG----VILIAATNHPS----LLDTAVWRRF 324
                                       887777777777777777777777777666666....88888888888....8888888887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   2.2e-08   1.3e-05       3      80 ..     205     308 ..     203     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.2e-08
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......aldeskr 51 
                                         G+pG+GKtt a++Lskrl++                      +++ ++ak   +++ + +e        +++++ 
  gi|488601333|ref|YP_007907804.1| 205 FIGPPGTGKTTTARALSKRLHLplvevklsmitsqylgetsknIEKVFEIAKRLSPCILFIDEfdyvaktRTSDEHA 281
                                       68*****************9888988888889988888888887888888888888888888888888777777778 PP

                            AAA_18  52 ldedkldklldaleenssaleegknlvid 80 
                                       +++  ++ ll+ ++e++    e ++++i 
  gi|488601333|ref|YP_007907804.1| 282 AVKRAVNTLLKSIDEINL--VEDGVILIA 308
                                       888888888888888874..566665554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   8.2e-06    0.0047       8      43 ..     203     229 ..     200     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.2e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                       l+ +G++GtGKTt++r l ++l         + ++v
  gi|488601333|ref|YP_007907804.1| 203 LMFIGPPGTGKTTTARALSKRL---------HLPLV 229
                                       6789***************999.........45555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     4e-07   0.00023       2      91 ..     203     327 ..     203     341 .. 0.52

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt..............................lrrrlfgtdqqskt 46 
                                       ++++G+pG+GK+t a+ l k+l+     ++                                 +             
  gi|488601333|ref|YP_007907804.1| 203 LMFIGPPGTGKTTTARALSKRLHlpL--VEVKLsmitsqylgetskniekvfeiakrlspcilF------------I 265
                                       59*******************99553..433332233333455444444444433333333321............0 PP

                            AAA_33  47 ............dytrvldrlyqilnelarkalsagrnvil.dat....nlsrrerarflkl 91 
                                                   d   + +r+ ++l + +++    + +vil  at    +l+ + ++rf+k+
  gi|488601333|ref|YP_007907804.1| 266 defdyvaktrtsDEHAAVKRAVNTLLKSIDEINLVEDGVILiAATnhpsLLDTAVWRRFDKI 327
                                       22222222222233344455555555555555444444444244444445555666666665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.7e-07   0.00027       3      49 ..     204     251 ..     202     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.7e-07
                            AAA_28   3 vitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv 49 
                                       +++G+++tGKTt+++aL++r   p v+    +i+++ l ++ +++++v
  gi|488601333|ref|YP_007907804.1| 204 MFIGPPGTGKTTTARALSKRlHLPLVEVKLSMITSQYLGETSKNIEKV 251
                                       79****************997777776666666666656666555555 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 ?   -0.1   0.0         1   5.8e+02      20      61 ..      17      59 ..       2      79 .. 0.75
   2 !   16.1   0.0     1e-05     0.006      28     109 ..     195     268 ..     183     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1
                             AAA_7 20 vrysyllelllknkkpvllvGptGtGKtviikd.llkkldkek 61
                                       ry+ l+e  + ++   +++G++G ++ +++k  + kk++k+ 
  gi|488601333|ref|YP_007907804.1| 17 NRYEELTEDDIPKEIRKIFYGKSGISRPLVVKMdTAKKVSKNI 59
                                      5777788888888899999999999999999987888877554 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-05
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvv 104
                                         + +  +++++Gp GtGKt++++ l k+l+   ++ +++++  +    ++ + ie+ +e  +           +++
  gi|488601333|ref|YP_007907804.1| 195 IGVLEVGKLMFIGPPGTGKTTTARALSKRLH-LPLVEVKLSMITSQYLGETSKNIEKVFEIAK-------RLSPCIL 263
                                       555566689********************99.4444444444444445677777777666544.......2334666 PP

                             AAA_7 105 FvDDl 109
                                       F+D++
  gi|488601333|ref|YP_007907804.1| 264 FIDEF 268
                                       66665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.1   2.9e+03      50      82 ..       3      57 ..       1      66 [. 0.69
   2 !   18.0   0.0   4.3e-06    0.0025       3     107 ..     200     298 ..     198     312 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.1
                                      THHHHHHHHHTTT-HHHHTTS......................EEEEETGGG--- CS
                             AAA_2 50 ehlvsrligappgyvgaeegG......................ivllDEidKihp 82
                                      e+ v +l+ +++ y+++ee                        +v +D   K+++
  gi|488601333|ref|YP_007907804.1|  3 ETKVIELLLTAEVYNRYEELTeddipkeirkifygksgisrplVVKMDTAKKVSK 57
                                      5567778888888888888777777777777666677777777777776666666 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 4.3e-06
                                       ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG CS
                             AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidK 79 
                                       +++++++gp g+Gkt +a+al++ l++    +l+ +  s ++   +     s+ i +   + ++    i+++DE d 
  gi|488601333|ref|YP_007907804.1| 200 VGKLMFIGPPGTGKTTTARALSKRLHL----PLVEVKLSMITS--QYLGETSKNIEKVFEIAKRLSPCILFIDEFDY 270
                                       6889**********************8....666666666555..33333555555555556666677********* PP

                                       -------------HHHHHHHHHHHH--E CS
                             AAA_2  80 ihpkessgadvSregVqrdLLqileggt 107
                                       ++++++s +    +  ++ LL+ +++ +
  gi|488601333|ref|YP_007907804.1| 271 VAKTRTSDEHAAVKRAVNTLLKSIDEIN 298
                                       ***9777777777777788888777655 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   0.1   0.00017       0.1      27      49 ..     203     225 ..     189     240 .. 0.89
   2 ?    2.8   0.0      0.23   1.3e+02     128     148 ..     253     272 ..     245     300 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                            AAA_16  27 vllsGesGvGKsslvrellrale 49 
                                       ++++G++G+GK++ +r+l ++l 
  gi|488601333|ref|YP_007907804.1| 203 LMFIGPPGTGKTTTARALSKRLH 225
                                       6789**************99875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.23
                            AAA_16 128 allsrderplvlvlDdlqwad 148
                                       + ++r  +p +l++D+++ + 
  gi|488601333|ref|YP_007907804.1| 253 EIAKR-LSPCILFIDEFDYVA 272
                                       55666.668*********433 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.7   3.3e+03       9      35 ..      35      61 ..      28      63 .. 0.81
   2 !   15.8   0.0   1.5e-05    0.0088      35      99 ..     202     274 ..     180     329 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.7
                            RuvB_N  9 yigqekvkeklkifieaakkreealdh 35
                                      + g++ +   l + +++akk ++++d 
  gi|488601333|ref|YP_007907804.1| 35 FYGKSGISRPLVVKMDTAKKVSKNIDS 61
                                      789999999999999999999998886 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.5e-05
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelg.....vklk.itsgPvlekagdlaalltnlee..kdvlfideihrlsra 99 
                                        ++++GpPG Gktt a+ ++k l+     vkl  its    e ++++  ++   ++    +lfide   ++++
  gi|488601333|ref|YP_007907804.1| 202 KLMFIGPPGTGKTTTARALSKRLHlplveVKLSmITSQYLGETSKNIEKVFEIAKRlsPCILFIDEFDYVAKT 274
                                       6899*****************9862221144442355555556666665544333311359999998877665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.4   1.4e+03      75     114 ..     138     176 ..     132     199 .. 0.72
   2 !   16.2   0.0   1.2e-05    0.0067      19      43 ..     202     239 ..     170     285 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.4
                            AAA_11  75 lrglldsegekykpkivRvgneeeriseavksvsleekve 114
                                       + +l ++e   + + +vR++++e +i+ +  s+ l  ++ 
  gi|488601333|ref|YP_007907804.1| 138 IAELEKNEQTAEMLGLVRIYSPE-DIKIDFASIALTDEQI 176
                                       44566677777788999****99.7888888777765544 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.2e-05
                            AAA_11  19 itliqGPPGtgKTktivellsqll.............s 43 
                                         ++ GPPGtgKT+t  +l ++l+             +
  gi|488601333|ref|YP_007907804.1| 202 KLMFIGPPGTGKTTTARALSKRLHlplvevklsmitsQ 239
                                       46889******************877776666444431 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   6.5e-05     0.038       1      47 [.     206     249 ..     206     348 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.5e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr 47 
                                       +G+PG GK+t ++ l ++++++ ++   +  ++++++ l+++ ++++
  gi|488601333|ref|YP_007907804.1| 206 IGPPGTGKTTTARALSKRLHLPLVE---VKLSMITSQYLGETSKNIE 249
                                       69*****************999987...3334444444444444444 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.8   3.9e+03      31      46 ..     132     147 ..     111     185 .. 0.57
   2 !   15.2   0.0     3e-05     0.018       9      80 ..     210     285 ..     207     309 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.8
                   Cytidylate_kin2  31 eiieevakelglseee 46 
                                       e ++ ++ el+ +e++
  gi|488601333|ref|YP_007907804.1| 132 EWLKTIIAELEKNEQT 147
                                       3333333333333333 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3e-05
                   Cytidylate_kin2   9 GsgGetigeaLAekLglpfydreiieevakelglseeeveevde.rsrlssflskllaarvagdtl...dekldde 80 
                                       G+g++t ++aL+++L+lp+++ ++   +++ lg + + +e+v e ++rls  +  +   ++ ++t    ++   ++
  gi|488601333|ref|YP_007907804.1| 210 GTGKTTTARALSKRLHLPLVEVKLSMITSQYLGETSKNIEKVFEiAKRLSPCILFIDEFDYVAKTRtsdEHAAVKR 285
                                       9********************************9999999998876666666655555554444442222222222 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.6e-05     0.021      13      74 ..     202     262 ..     194     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpel 74 
                                       k+ ++G+ G+GK+t +++l++ l+    e++l +  +++  l +++k+i+ +++  ++l p +
  gi|488601333|ref|YP_007907804.1| 202 KLMFIGPPGTGKTTTARALSKRLHLPLVEVKLSMITSQY--LGETSKNIEKVFEIaKRLSPCI 262
                                       6789********************999999999888888..8888899988888755666655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.2e-05     0.019      23      46 ..     201     224 ..     185     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                      Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsll 46 
                                        +l+++GppG+GKt  a++l++ l
  gi|488601333|ref|YP_007907804.1| 201 GKLMFIGPPGTGKTTTARALSKRL 224
                                       579***************998644 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.3e-05     0.037       7      80 ..     205     275 ..     201     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-05
                            AAA_14   7 itGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                         G+  +GKTt ++ l k+l       ++++l   + + l +++k++e ++e +k+    +lf+DE  +v + +
  gi|488601333|ref|YP_007907804.1| 205 FIGPPGTGKTTTARALSKRLH---LPLVEVKLSMITSQYLGETSKNIEKVFEIAKRLSPCILFIDEFDYVAKTR 275
                                       579999**********98888...7888888888888777766677888888766667899*******995443 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.9e-05     0.029      48      79 ..     203     234 ..     168     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                       L+  GP+G gk+t+ + Lsk l   l e   +
  gi|488601333|ref|YP_007907804.1| 203 LMFIGPPGTGKTTTARALSKRLHLPLVEVKLS 234
                                       7889****************998887776544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   7.7e-05     0.044       4      29 ..     202     226 ..     201     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplfi 29 
                                       k++ +Gp+g+GKTt+a+ l  k l +
  gi|488601333|ref|YP_007907804.1| 202 KLMFIGPPGTGKTTTARAL-SKRLHL 226
                                       67899************99.666655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.5e-05     0.049       2      45 ..     203     256 ..     202     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.5e-05
                                       EEEEESTTSSHHHHHHHHHT.........S.TEEESSSTTSSSSEEEEEEEETT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.........e.kaivsdkpgtTrdinegrvklkg 45 
                                        +++G p +GK+t  +al++         +   i+s++ g T + +e+ +++ +
  gi|488601333|ref|YP_007907804.1| 203 LMFIGPPGTGKTTTARALSKrlhlplvevKlSMITSQYLGETSKNIEKVFEIAK 256
                                       689****************8777777755446799*******999999888544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00018      0.11       2      26 ..     204     228 ..     203     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl 26 
                                       ++ Gp+g+GK+t+a+ L+k+l   l
  gi|488601333|ref|YP_007907804.1| 204 MFIGPPGTGKTTTARALSKRLHLPL 228
                                       799***************9998444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.021        12       4      23 ..     204     223 ..     202     231 .. 0.86
   2 ?    6.1   0.0     0.016       9.4      57     119 ..     235     301 ..     232     318 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                                       EEEC-TTTCHHHHHHHHHHH CS
                             NACHT   4 ilqGeaGsGKTtLlqklala 23 
                                       +  G++G GKTt ++ l   
  gi|488601333|ref|YP_007907804.1| 204 MFIGPPGTGKTTTARALSKR 223
                                       568***********999766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                                       HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCTTTTT CS
                             NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirkkllp 119
                                       +++sq++ + ++  e++ +++++     l +D +D++++        + k++v+tlL+++ + +l+ 
  gi|488601333|ref|YP_007907804.1| 235 MITSQYLGETSKNIEKVFEIAKRLSPCILFIDEFDYVAKTRTSdehaAVKRAVNTLLKSIDEINLVE 301
                                       5778887777766666777888888888999*****9987777555566666666666655555555 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   0.00039      0.23      11      53 ..     178     220 ..     171     228 .. 0.85
   2 ?   -0.9   0.0       1.8     1e+03     130     174 ..     248     292 ..     221     308 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                            AAA_25  11 svadlaapppprrwlvk.gllpagelallaGapgtGKttlaldl 53 
                                       +++++++++++r++l + g+l + +  +++G+pgtGKtt a  l
  gi|488601333|ref|YP_007907804.1| 178 EFDKIEVALERRDYLKEiGVL-EVGKLMFIGPPGTGKTTTARAL 220
                                       478889999999999999998.7888899**********98666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                            AAA_25 130 vdaleaaieevegvrlvviDplsralgg.densnsdvgalvealer 174
                                       ++++ + +++   +  + iD ++ +     ++++++v+++v+ l +
  gi|488601333|ref|YP_007907804.1| 248 IEKVFEIAKR-LSPCILFIDEFDYVAKTrTSDEHAAVKRAVNTLLK 292
                                       5666666666.34777888888887777444444445777766544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   0.00036      0.21      11      35 ..     201     225 ..     194     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivallv 35 
                                       + l+ +++pGtGKT++ ++  + l 
  gi|488601333|ref|YP_007907804.1| 201 GKLMFIGPPGTGKTTTARALSKRLH 225
                                       567889**********988776654 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0002      0.12       1      23 [.     209     231 ..     209     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+t++++l+k+l+l+++++
  gi|488601333|ref|YP_007907804.1| 209 PGTGKTTTARALSKRLHLPLVEV 231
                                       69*****************9986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.13      55     121 ..     202     273 ..     169     325 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                            DUF815  55 nvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellr...erperfilfvDDLsFeee 121
                                       +++++G  GtGK ++ +al ++++     ++l  ++ + l e +k +e++    +r   +ilf+D   + ++
  gi|488601333|ref|YP_007907804.1| 202 KLMFIGPPGTGKTTTARALSKRLHLPLveVKLSMITSQYLGETSKNIEKVFeiaKRLSPCILFIDEFDYVAK 273
                                       67899****************998776567777778888877777666655111555669*****9876543 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00029      0.17      49      73 ..     202     226 ..     177     293 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                         IstB_IS21  49 nivllGpsGvGKshlaialgveavr 73 
                                        ++++Gp+G+GK+  a al+++   
  gi|488601333|ref|YP_007907804.1| 202 KLMFIGPPGTGKTTTARALSKRLHL 226
                                       5789***************987655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00046      0.27       4      26 ..     203     225 ..     201     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                                       EEEEESTTSSHHHHHHHHHHHHH CS
                             SRP54   4 illvGlqGaGKTttlaKLaallk 26 
                                       ++++G+ G+GKTtt+  L+++l+
  gi|488601333|ref|YP_007907804.1| 203 LMFIGPPGTGKTTTARALSKRLH 225
                                       79*************99999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0004      0.23      23      40 ..     205     222 ..     197     278 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                            AAA_30  23 ltGpAGtGKttalkalre 40 
                                         Gp+GtGKtt+ +al +
  gi|488601333|ref|YP_007907804.1| 205 FIGPPGTGKTTTARALSK 222
                                       67***********99965 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0037       2.2       2      23 ..     206     227 ..     205     256 .. 0.90
   2 ?    0.9   0.0      0.76   4.4e+02     101     123 ..     322     360 ..     306     408 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0037
                                       EESTTSSHHHHHHHHHHHHTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   2 lGaPgaGKGtqaeklvkkygla 23 
                                       +G+Pg+GK t a+ l k+++l+
  gi|488601333|ref|YP_007907804.1| 206 IGPPGTGKTTTARALSKRLHLP 227
                                       8***************999876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.76
                                       SEESEEEEEE--HHHHHHHHHT................G CS
                                       xxxxxxxxxxxxxxxxxxxxxx................x RF
                               ADK 101 vkldlvleldvpeevlveRltg................D 123
                                        + d ++e+  p e++ +R+ +                 
  gi|488601333|ref|YP_007907804.1| 322 RRFDKIIEFPEPPEIIRRRIFElslsrikgefdidelvK 360
                                       568999999999999999999877777777775544440 PP

>> YycC  YycC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.068        39       2      18 ..      43      59 ..      42      61 .. 0.91
   2 ?    6.3   0.1     0.015       8.6      10      24 ..     216     230 ..     213     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.068
                              YycC  2 rPlQiSpeTAvkLskkL 18
                                      rPl +  +TA+k sk++
  gi|488601333|ref|YP_007907804.1| 43 RPLVVKMDTAKKVSKNI 59
                                      9*************985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                              YycC  10 TAvkLskkLnvPLEh 24 
                                       TA  Lsk+L +PL +
  gi|488601333|ref|YP_007907804.1| 216 TARALSKRLHLPLVE 230
                                       9***********955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 2632.47
//
Query:       gi|488601334|ref|YP_007907805.1|  [L=263]
Description: Metal-dependent hydrolases of the beta-lactamase superfamily I [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-29  101.5   0.0    5.2e-29  101.2   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
      3e-18   66.5   0.0    4.3e-18   66.0   0.0    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    4.6e-08   33.1   0.0      7e-08   32.5   0.0    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.15   11.5   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
       0.21   11.8   1.5       0.34   11.1   0.2    1.9  2  DUF3909        Protein of unknown function (DUF3909)


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 !  101.2   0.0   1.4e-32   5.2e-29       2     201 .]      47     220 ..      46     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 1.4e-32
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                       +iLiD++pdlr q++ra         +++i+aV++th+H+DH+ag+  + + ++ ++++y +k+v++++ + +++l 
  gi|488601334|ref|YP_007907805.1|  47 NILIDTSPDLRMQLMRAN--------VEEIEAVIWTHCHFDHFAGFGEFYRVQD-NVKVYTSKEVHEDIGNYMKFLK 114
                                       9************77776........899**********************765.6****************98875 PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S.---HHHHHHH CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg.yipeeigerl 154
                                         +       e+++ ++fe++  g+++t+  ++h   r       ++ G++ e+ g +++ +gDt+  ++e   e +
  gi|488601334|ref|YP_007907805.1| 115 YRK------IEVEPYKPFEIA--GIKFTLADVNHPPMR-------RAHGVVAEWRGYKIVISGDTNkNLSENTIEVF 176
                                       554......5999*******9..888888888888888.......9*******************9445699999** PP

                                       CT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 155 ggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       +++dl ++d+ a e+ +      H++ e a+++a+++ga+++v++Hi
  gi|488601334|ref|YP_007907805.1| 177 KNPDLFIVDAIAPENFK---LRKHMNAETAMKLADEIGARKTVFTHI 220
                                       *********99888877...468***********************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 !   66.0   0.0   1.2e-21   4.3e-18       6     197 .]      36     222 ..      32     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.2e-21
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                        +s+li+++g++iLiDt  + + +++       + + ++++avi TH H+DH++g g++ +  d+++++ ++e ++ 
  gi|488601334|ref|YP_007907805.1|  36 RFSILIQNKGKNILIDTSPDLRMQLM-------RANVEEIEAVIWTHCHFDHFAGFGEFYRVQDNVKVYTSKEVHED 105
                                       5899*********************9.......79****************************************** PP

                                       HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTTSSHHCC CS
                       Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDallagetg 158
                                       +++++++              +k +v +    ++ag   +l  + +p+    hgvv   +g k++++GD+  + ++ 
  gi|488601334|ref|YP_007907805.1| 106 IGNYMKFLK-----------YRKIEVEPYKPFEIAGIKFTLADVNHPPMRRAHGVVAEwRGYKIVISGDTNKNLSEN 171
                                       *****7654...........456778888888888888889999999999999888777*************99999 PP

                                       CCCC.............TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 159 ridl............tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       +i+              + +++ r++  ae +++ ++++ + k+    +gH
  gi|488601334|ref|YP_007907805.1| 172 TIEVfknpdlfivdaiAPENFKLRKHMNAETAMKLADEIGARKTVFTHIGH 222
                                       999999************************999999999888876665555 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 !   32.5   0.0     2e-11     7e-08       9     158 ..      38     214 ..      37     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2e-11
                     Lactamase_B_3   9 sflletagarilvDPfka..nlgyeppaeeaDlvlisqaledHah.letlkqlaenvkvleeges............ 70 
                                       s+l++ +g++il+D       + ++++ ee+++v+ ++ + dH++   +  ++++nvkv +++e             
  gi|488601334|ref|YP_007907805.1|  38 SILIQNKGKNILIDTSPDlrMQLMRANVEEIEAVIWTHCHFDHFAgFGEFYRVQDNVKVYTSKEVhedignymkflk 114
                                       789***********77555466666777***************983466788899****999544444555555555 PP

                     Lactamase_B_3  71 ......levggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvgg... 138
                                                + +ei +++    +v+ ++ ++  g + e +g++i+  G++  +ls+++++ ++++D++++  +    
  gi|488601334|ref|YP_007907805.1| 115 yrkievEPYKPFEIAGIKFTLADVNHPPMRRAHGVVAEWRGYKIVISGDTNKNLSENTIEVFKNPDLFIVDAIApen 191
                                       555332234688888888888888888888899999999***********************************9** PP

                     Lactamase_B_3 139 ...pltlgqeealelakrLkpkl 158
                                           + +++e+a++la ++ ++ 
  gi|488601334|ref|YP_007907805.1| 192 fklRKHMNAETAMKLADEIGARK 214
                                       *9999***********9998875 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.1e-05      0.15       6      82 ..      45     110 ..      39     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                     Lactamase_B_6   6 nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvk.LGrv 81 
                                       + +iL+D + d         ++ ++  ++++++++ +h   +h +++  +y     ++  n++vy+++ v++ +G+ 
  gi|488601334|ref|YP_007907805.1|  45 GKNILIDTSPDLR-------MQLMRANVEEIEAVIWTHCHFDHFAGFGEFY-----RVQDNVKVYTSKEVHEdIGNY 109
                                       5567777777753.......5668889*******************95444.....5778*******9998535655 PP

                     Lactamase_B_6  82 s 82 
                                       +
  gi|488601334|ref|YP_007907805.1| 110 M 110
                                       5 PP

>> DUF3909  Protein of unknown function (DUF3909)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   9.6e-05      0.34      38      87 ..      84     133 ..      57     141 .. 0.82
   2 ?   -1.3   0.1      0.64   2.3e+03      32      50 ..     237     254 ..     228     261 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.6e-05
                           DUF3909  38 tfeygrdednhyvirtskkmleemefyla.lkydreeidlymhaeidgvcy 87 
                                         e+ r +dn  v  tsk++ e++  y+  lky + e++ y   ei g+ +
  gi|488601334|ref|YP_007907805.1|  84 FGEFYRVQDNVKV-YTSKEVHEDIGNYMKfLKYRKIEVEPYKPFEIAGIKF 133
                                       3478899999765.79********9888549****************9976 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.64
                           DUF3909  32 kydfeptfeygrdednhyv 50 
                                        ydfe tf + r+ d    
  gi|488601334|ref|YP_007907805.1| 237 GYDFE-TFYFDRERDRVVE 254
                                       58998.7888888876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2066.21
//
Query:       gi|488601335|ref|YP_007907806.1|  [L=357]
Description: Zn-dependent protease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-33  112.7   4.6    3.6e-16   59.4   0.2    2.6  2  CBS             CBS domain
    5.7e-13   48.7  12.5    4.4e-08   32.7   0.3    3.4  3  Peptidase_M50   Peptidase family M50
    1.1e-05   25.2   3.2    1.1e-05   25.2   3.2    1.8  1  Peptidase_M50B  Peptidase M50B-like
  ------ inclusion threshold ------
      0.026   14.8   4.6      0.026   14.8   4.6    2.5  3  DUF3267         Putative zincin peptidase


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 !   54.3   0.8     3e-18   1.4e-14       1      55 [.     236     289 ..     236     291 .. 0.92
   2 !   59.4   0.2     8e-20   3.6e-16       1      55 [.     294     347 ..     294     348 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 3e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V++imt+ ++tv+p + ++e+l++m ++++ ++PVVd dg +vGi+tl+D+++a 
  gi|488601335|ref|YP_007907806.1| 236 VREIMTPSPITVTPAMKVSEVLDMMLRYKHLGYPVVD-DGDIVGIITLKDIMNAS 289
                                       89***********************999967*****6.777**********9985 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 8e-20
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+ +m+rdv++++p+++  eal+lm e++++rlPVV e+gklvGiv+++Dl+r l
  gi|488601335|ref|YP_007907806.1| 294 VEKLMSRDVLMISPSANAIEALQLMNERNIGRLPVV-ENGKLVGIVSRTDLIRTL 347
                                       7789*********************8888*******.9**************976 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   4.1   1.7e-07   0.00076       3     107 ..      59     128 ..      57     135 .. 0.84
   2 !   32.7   0.3   9.9e-12   4.4e-08     189     249 ..     138     195 ..     129     199 .. 0.84
   3 ?   -1.2   0.1      0.21   9.6e+02      88     109 ..     194     233 ..     191     320 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                       ++ l++ v++HEl H l+ k++gvkv+                     i+l+ +GG+  +++   e           
  gi|488601335|ref|YP_007907806.1|  59 AISLFLAVLLHELSHSLIGKRMGVKVKG--------------------IILFIFGGVALLEKIP-E----------- 103
                                       578999********************98....................889999**55555544.4........... PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  80 lkkspwqrllivlAGplanfilailvfv 107
                                          +p +++ i++AGpl+ + la + ++
  gi|488601335|ref|YP_007907806.1| 104 ---EPRSEIKIAVAGPLMSIFLASVSLI 128
                                       ...57899**********9999988765 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 9.9e-12
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 189 ssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglallll 249
                                       s+++ ++ + +++L+++NL+P ++LDGg++l+al+    rk+   +++++a  vg +l +l
  gi|488601335|ref|YP_007907806.1| 138 SELFLTFSIYNFALAFFNLIPAFPLDGGRILRALIA---RKTGFLKATKIAAEVGKILAFL 195
                                       4667778899************************76...6678888999999998877765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.21
                                       XXXXXXXXXXXXXXXXXXXXX..................- CS
                                       xxxxxxxxxxxxxxxxxxxxx..................x RF
                     Peptidase_M50  88 llivlAGplanfilailvfvv..................p 109
                                       +li + G ++n +l +++f++                   
  gi|488601335|ref|YP_007907806.1| 194 FLIGILGLFFNPWLILIAFFIymgaseeeksvivenilkN 233
                                       5677788888888888888885554444444444333330 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   3.2   2.4e-09   1.1e-05      21     102 ..      62     147 ..      49     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.4e-09
                    Peptidase_M50B  21 kllvvffHElGHalaalLtGgrvkgielhsdesGvtvtrg..pgglgqiltllaGYlgpallGlllills..asgka 93 
                                         l+v++HEl+H l+ + +G +vkgi l+   +Gv++ +   ++  + i +++aG+l++ +l ++ +++   + +++
  gi|488601335|ref|YP_007907806.1|  62 LFLAVLLHELSHSLIGKRMGVKVKGIILFI-FGGVALLEKipEEPRSEIKIAVAGPLMSIFLASVSLIIYlsKIDII 137
                                       5799**********************9997.68*****999656667899************987665441144555 PP

                    Peptidase_M50B  94 .rlllvllvl 102
                                        +l+l++ + 
  gi|488601335|ref|YP_007907806.1| 138 sELFLTFSIY 147
                                       5666663333 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       1.6   7.4e+03      59      68 ..      22      31 ..      14      50 .. 0.55
   2 ?   14.8   4.6   5.9e-06     0.026       2      95 ..      63     157 ..      62     162 .. 0.79
   3 ?    1.1   0.2      0.11   4.9e+02      63      89 ..     191     217 ..     172     223 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                           DUF3267 59 vllgilllll 68
                                      +++ i++ ++
  gi|488601335|ref|YP_007907806.1| 22 FIVLIIFSYA 31
                                      2222222222 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.9e-06
                           DUF3267   2 lvlvilHEllHglffklfgkkpkkkvkfgiklliayatsseallskkqfiiillaPfvllgilllllalllpsstl. 77 
                                       ++ v+lHEl H l  k++g+k+k  + f ++ ++++   +e++  ++++ i+   P++ + ++ + l+++l +    
  gi|488601335|ref|YP_007907806.1|  63 FLAVLLHELSHSLIGKRMGVKVKGIILFIFGGVALLEKIPEEP--RSEIKIAVAGPLMSIFLASVSLIIYLSKI-Di 136
                                       8899*****************9999999557677777777777..99999999999777666666666665543.14 PP

                           DUF3267  78 ...llllllalnaagsagDll 95 
                                          l+l ++++n+a+++  l+
  gi|488601335|ref|YP_007907806.1| 137 iseLFLTFSIYNFALAFFNLI 157
                                       678999999****99988765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.11
                           DUF3267  63 illlllalllpsstl.llllllalnaag 89 
                                       il +l+++l   +++ +l+l++++  +g
  gi|488601335|ref|YP_007907806.1| 191 ILAFLIGIL-GLFFNpWLILIAFFIYMG 217
                                       444444444.222232445444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 2757.34
//
Query:       gi|488601336|ref|YP_007907807.1|  [L=401]
Description: pheromone shutdown-related protein TraB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-30  104.3   0.1    1.5e-29  103.7   0.1    1.2  1  TraB             TraB family
  ------ inclusion threshold ------
      0.084   13.0   7.3       0.76    9.9   3.1    2.9  2  Phage_holin_4_1  Bacteriophage holin family
        0.3   10.7   4.0       0.38   10.3   0.7    2.6  2  VASP_tetra       VASP tetramerisation domain


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 !  103.7   0.1   2.5e-33   1.5e-29       9     249 ..      11     220 ..       5     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 2.5e-33
                              TraB   9 gttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsdd..tdeatqkelaklkllpdgktlsdllseelyar 83 
                                       +++++L+GT+Hvskks++++++++    ek+d+v++Eld+++      ++++e++  ++++  ++++ ll + l++ 
  gi|488601336|ref|YP_007907807.1|  11 DERIILVGTAHVSKKSIEQVKETILS--EKPDAVAIELDEKRFfaLVHKKAQEISIVDVIK-RGETHLLLFQLLLSY 84 
                                       4559**********************..9***********999887778888888888898.78999********** PP

                              TraB  84 lqkalakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsllsslpd 160
                                       +q+++ + + ++       P  + ++l ++e a k+ g d+ l+Dr++++t+kr + +++++E+v++ +sl+   + 
  gi|488601336|ref|YP_007907807.1|  85 FQRKVGE-KYGV------TP--GEEMLKAIEVA-KEVGADILLIDRDISITFKRFWSSLSFIEKVKLFVSLIV--SL 149
                                       *******.9999......99..99999999985.888999999*****************************3..33 PP

                              TraB 161 eeqlealeetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallkepgsvfv 237
                                        +++e   + l  l+  +d ++ +v               e+e+++p+  ++l++eR+ ++a k+ +  k+ +++++
  gi|488601336|ref|YP_007907807.1| 150 FHKEEIEVDEL--LK--EDIITAMVS--------------EFEKISPNAVNALIKERDTYMAGKLLQFSKRYNKIVA 208
                                       33333333233..33..577899999..............************************************* PP

                              TraB 238 aVGagHlaGedg 249
                                       +VGagH++G++ 
  gi|488601336|ref|YP_007907807.1| 209 VVGAGHVNGIKE 220
                                       *********984 PP

>> Phage_holin_4_1  Bacteriophage holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.1   0.00013      0.76      40     100 ..     236     297 ..     215     305 .. 0.78
   2 ?    3.9   0.2    0.0095        57      13      80 ..     308     380 ..     298     398 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                   Phage_holin_4_1  40 skkglkgiikkvlilllvlvah.llDvllgknletlrtlviifyianeliSIleNagkmGvp 100
                                        k ++  ++k +++ ++ +va+ +++vll  n+e + +++i+++++n ++S l  +   G p
  gi|488601336|ref|YP_007907807.1| 236 VKQSRFNLAKTIGYSIFAFVAIiFISVLLSLNTELILKAFIYWFLINGILSALGALLARGSP 297
                                       56667778899999888888873457777776667****************98776666655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0095
                   Phage_holin_4_1  13 lltallllmviDyltGllaaiv....egk....lsskkglkgii.kkvlilllvlvahllDvllgknletlrtlvii 80 
                                       +lt l  +++  +++G++ a+v    + k    ls +++++ ++  k + +llv+    l  ++g+    +   +++
  gi|488601336|ref|YP_007907807.1| 308 WLTSLNPAIAAGWISGIVEAWVrkptS-KdlekLSEARSIRDLLdNKFFRVLLVAALTNLGSMIGTF---IGIYAVL 380
                                       566666778888999999999966641.144456666666655525777777777777777777753...3333333 PP

>> VASP_tetra  VASP tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.14   8.3e+02       4      14 ..      27      37 ..      25      37 .. 0.88
   2 ?   10.3   0.7   6.4e-05      0.38       6      33 ..     160     187 ..     156     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.14
                        VASP_tetra  4 lErlKqEILeE 14
                                       E++K+ IL+E
  gi|488601336|ref|YP_007907807.1| 27 IEQVKETILSE 37
                                      699******98 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.4e-05
                        VASP_tetra   6 rlKqEILeEvrkELqKvKeEIIeAirqE 33 
                                        lK++I++ ++ E++K+    ++A+++E
  gi|488601336|ref|YP_007907807.1| 160 LLKEDIITAMVSEFEKISPNAVNALIKE 187
                                       5788888888888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2476.32
//
Query:       gi|488601337|ref|YP_007907808.1|  [L=102]
Description: translation initiation factor 1 (eIF-1/SUI1) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   76.2   2.9    2.8e-21   75.8   2.9    1.1  1  SUI1      Translation initiation factor SUI1
    0.00056   20.1   1.0    0.00081   19.6   1.0    1.3  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
  ------ inclusion threshold ------
      0.057   12.8   0.1      0.068   12.5   0.1    1.1  1  DPCD      DPCD protein family
      0.093   12.4   0.6       0.11   12.1   0.6    1.1  1  DTW       DTW domain


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   2.9   6.3e-25   2.8e-21       1      76 [.      24      95 ..      24      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 6.3e-25
                              SUI1  1 akpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                      ++++i i++ +r+ +K vT+++g+++ +i++++lak lk+k+ac+g+v k++  +i++QG++  +v+elL++k g+
  gi|488601337|ref|YP_007907808.1| 24 EQQQIVIKTTKRRYGKEVTVIEGIDTGEINIEELAKYLKSKLACGGTV-KNK--VIELQGNHVGRVRELLIKK-GF 95
                                      589********************************************9.777..9*****************9.87 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.0   1.8e-07   0.00081      14      80 .]      28      95 ..      17      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.8e-07
                              Img2 14 PVYtdvkrggtkkltvirkie.GDia..alredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                       V + +kr+  k++tvi  i+ G+i+  +l++ L++ l+  +  + +++ ie++G++v +v++ L +kgF
  gi|488601337|ref|YP_007907808.1| 28 IVIKTTKRRYGKEVTVIEGIDtGEINieELAKYLKSKLA--CGGTVKNKVIELQGNHVGRVRELLIKKGF 95
                                      577889999999********7587663377777777777..788889999*******************9 PP

>> DPCD  DPCD protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.5e-05     0.068     115     139 ..      21      45 ..      12      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                              DPCD 115 vdeeereivvrTtNkKYyKklsipd 139
                                       v +e+++iv++Tt ++Y K++++ +
  gi|488601337|ref|YP_007907808.1|  21 VAKEQQQIVIKTTKRRYGKEVTVIE 45 
                                       78999**************999754 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   2.5e-05      0.11       2      31 ..       4      30 ..       3      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                               DTW  2 elCerCllpaevclcsslppleklpikvli 31
                                      e+C  C lp+ +c+c+++ + e++  +++i
  gi|488601337|ref|YP_007907808.1|  4 EICSICGLPKDLCVCEEVAK-EQQ--QIVI 30
                                      68*****************9.655..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 641.59
//
Query:       gi|488601338|ref|YP_007907809.1|  [L=283]
Description: hypothetical protein Asulf_01847 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-24   84.9   0.2    9.4e-24   83.3   0.0    1.9  2  DisA_N    DisA bacterial checkpoint controller nucleotide-bin


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.15   2.7e+03      16      46 ..     112     140 ..     107     144 .. 0.58
   2 !   83.3   0.0   5.3e-28   9.4e-24       3     118 ..     148     273 ..     146     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.15
                                       EEEESSSC.CCTTCCTSEEEEEE--HHHHHHH CS
                            DisA_N  16 iviereee.lkeiietgvkldaevskellkei 46 
                                       iv +++++ +++ i    +  +++++e+lk i
  gi|488601338|ref|YP_007907809.1| 112 IVSNQKKSrVNKAI---QECSDRINPEVLKAI 140
                                       44444433134444...566777778887777 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 5.3e-28
                                       HHHHHHHHT--EEEEEESSSC............CCTTCCTSEEEEEE--HHHHHHHTSTTSTTCSSEEEE.ETTEEE CS
                            DisA_N   3 aveelskkkiGaliviereee............lkeiietgvkldaevskellkeifekksplhDGAvii.rdgriv 66 
                                       ++++++++kiG+ +vi++ +e             +    +  ++++++ +e + e+     +++DG +i+ ++g+i+
  gi|488601338|ref|YP_007907809.1| 148 SLKGREGRKIGTAFVIGDVKEvmkrskqmiinpFEGHPVEVRNIKDPYIWESIMEF-----AQLDGVFIVdEEGTII 219
                                       578999***************77766666544422222356688899999999999.....*********99***** PP

                                       EEEEEE--.TT-TTS.ST-SHHHHHHHHHHHHSSSEEEEE-TTTS-EEEEETTE CS
                            DisA_N  67 aagviLpl.senkel.kelGtRHraAlgiseetdalvivVSeetgkislakdgk 118
                                       +ag++L++ ++n +l ++lGtRH a+++is+et+a+ +vVSe+ g i+++kdgk
  gi|488601338|ref|YP_007907809.1| 220 SAGRYLDVsATNLDLrPGLGTRHLACAAISQETEAISVVVSESGGDITIFKDGK 273
                                       ********555999966***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1937.51
//
Query:       gi|488601339|ref|YP_007907810.1|  [L=112]
Description: putative metal-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   0.1    1.4e-22   79.9   0.1    1.0  1  CGGC      CGGC domain


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.1   7.6e-27   1.4e-22       1     106 []       3     109 ..       3     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 7.6e-27
                              CGGC   1 kiaiirCekved...vCpg.vkClkalkerkgaFeeyeeevelvgfvtCggCpgkkvveklkelk...kegvdvihl 70 
                                       k+ ++ C  ++d   +Cpg ++Clka++  +g+F+   e+  +++fv+C+ Cpgk++v ++ + +   + ++dvi++
  gi|488601339|ref|YP_007907810.1|   3 KVFVVGCGAYMDatyGCPGeWRCLKAAALGEGEFD---EPSAIIAFVRCE-CPGKTLVPNIGMAMklsEIKPDVIYM 75 
                                       899*******888999*******************...677*********.*********9988778899******* PP

                              CGGC  71 ssCiktkkakkeCpei..eeikeaieeklgievvegth 106
                                       ssC+    ak+ Cp++  e+ k+aieek+gi+vv+gth
  gi|488601339|ref|YP_007907810.1|  76 SSCM----AKPGCPYMspEDAKKAIEEKTGIKVVMGTH 109
                                       ****....6899****999******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 776.62
//
Query:       gi|488601340|ref|YP_007907811.1|  [L=423]
Description: tryptophanyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  137.9   0.0    6.6e-21   74.9   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
       0.13   11.2   0.0          3    6.6   0.0    2.2  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 !   74.9   0.0   7.4e-25   6.6e-21       2     174 ..      63     228 ..      62     240 .. 0.94
   2 !   61.1   0.0   1.2e-20   1.1e-16     179     293 .]     292     405 ..     275     405 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 7.4e-25
                                       HHS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b   2 kerplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlak 78 
                                       +++p +v+sG++P+g +H G+ + +  +++ qk+g  +f+ iaDl+A +++    + +k ++    ++++   ++a 
  gi|488601340|ref|YP_007907811.1|  63 NKEPWAVMSGFMPSGYPHFGHKMTMDEIIWHQKMGGMAFVGIADLEANVVRGL--SKEKCKEIGLLYVKS---IIAL 134
                                       67899***********************************************9..78999999999*999...**** PP

                                       TCHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.S.C--BHHHHHHHHHHHHHHHHTCHSE CS
                      tRNA-synt_1b  79 gldpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.g.egislgeftYplLqaaDilllkadl 153
                                       gl+  ++ +++qs+ +  ++la  l+  +++ +l+ ++ f   +++l++   + ++++++++p+L  +     k+ +
  gi|488601340|ref|YP_007907811.1| 135 GLEK-ESLIYFQSANQTVKDLAFELSAEVNFSELKAIYGFLP-ETSLAKmFvTCVQASDILHPQLEFYGGP--KPVV 207
                                       **98.6789*******************************99.77777743599***************99..99** PP

                                       EEEEGGGHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 154 vpgGsDQkqnielgrdlarrf 174
                                       vp+G DQ+ +++l+rdla+r+
  gi|488601340|ref|YP_007907811.1| 208 VPVGADQDPHLRLTRDLADRI 228
                                       *******************98 PP

  == domain 2  score: 61.1 bits;  conditional E-value: 1.2e-20
                                       TTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHTHHHCHHHHHHH CS
                      tRNA-synt_1b 179 vfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklktelsnelierlea 253
                                       +f +p++++++++tgl+G+ KmS+S+++s I L +++++++kki +avt  ++  e ++ + +++e++  ++e +++
  gi|488601340|ref|YP_007907811.1| 292 AFIQPSSTYHKFITGLTGG-KMSSSKPESFISLMERPDTAEKKIMRAVTGGRAtaEEQRRYGGRPEICT-VFEFYSY 366
                                       799****************.********************************9999*************.******* PP

                                       HCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 254 vsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                       ++ +++ +e+ e++ e++++++ +g +kk+ a+ ++e+l+
  gi|488601340|ref|YP_007907811.1| 367 HLVEDD-KELAEIESECRNGKILCGSCKKRCAQIVREFLK 405
                                       *****9.******************************995 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00034         3      19      41 ..      61      83 ..      51      96 .. 0.77
   2 ?    2.1   0.0    0.0081        73     261     304 ..     291     335 ..     236     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00034
                      tRNA-synt_1f 19 kaekdevvvesGispSGliHiGn 41
                                       ++k+   v sG  pSG +H G 
  gi|488601340|ref|YP_007907811.1| 61 IKNKEPWAVMSGFMPSGYPHFGH 83
                                      3467999***************5 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.0081
                      tRNA-synt_1f 261 lggeaPekvvYelillkggekmssSkGn.vltledwlevaepevl 304
                                       + + +P +    +i+   g+kmssSk + +++l +  + ae++++
  gi|488601340|ref|YP_007907811.1| 291 FAFIQPSSTYHKFITGLTGGKMSSSKPEsFISLMERPDTAEKKIM 335
                                       778899999999**999999*****97525666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); 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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2453.60
//
Query:       gi|488601341|ref|YP_007907812.1|  [L=315]
Description: tRNA intron endonuclease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   96.6   2.7    8.7e-26   89.8   0.3    3.3  3  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    4.2e-15   55.2   1.3    7.1e-08   32.0   0.1    2.4  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
     0.0034   17.6   0.0     0.0079   16.5   0.0    1.7  1  Sen15            Sen15 protein
  ------ inclusion threshold ------
       0.13   12.4   0.1        3.8    7.8   0.0    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 ?    2.7   0.0     0.029   1.3e+02       4      17 ..      74      87 ..      71     109 .. 0.85
   2 ?    2.4   0.0     0.037   1.7e+02      72      85 .]     125     138 ..     121     138 .. 0.92
   3 !   89.8   0.3   1.9e-29   8.7e-26       1      76 [.     223     300 ..     223     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.029
                                      HHHHHHHHHHTT-E CS
                     tRNA_int_endo  4 kyavyrdLrekGyv 17
                                       + vy dLr++G  
  gi|488601341|ref|YP_007907812.1| 74 YFFVYCDLRDRGRK 87
                                      5779********86 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.037
                                       EEEEEETTTSCEEE CS
                     tRNA_int_endo  72 lilaivdaegdvty 85 
                                       +ila+vd+e ++ty
  gi|488601341|ref|YP_007907812.1| 125 FILAVVDEESEITY 138
                                       89**********98 PP

  == domain 3  score: 89.8 bits;  conditional E-value: 1.9e-29
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE...TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY...qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklil 74 
                                       f+++y vyrdLrekG+vv++G+kFGadFrvY   ++ ++l hs+ylV +vs+d    ++d+s+avrlahsv+Kk+++
  gi|488601341|ref|YP_007907812.1| 223 FLERYEVYRDLREKGLVVKTGFKFGADFRVYeeiEDVSQLPHSKYLVSIVSNDGL-NLQDISRAVRLAHSVRKKMVF 298
                                       789****************************9999999***********988876.7*******************9 PP

                                       EE CS
                     tRNA_int_endo  75 ai 76 
                                        +
  gi|488601341|ref|YP_007907812.1| 299 TF 300
                                       76 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 !   32.0   0.1   1.6e-11   7.1e-08      19      67 .]      16      62 ..      11      62 .. 0.93
   2 !   21.8   0.2   2.4e-08   0.00011       1      55 [.     157     206 ..     157     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.6e-11
                                      HHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHHH CS
                   tRNA_int_endo_N 19 krlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeell 67
                                      ++l++++ +Gk + +++L+L +vE  YLl kG++++++g++++sf e++
  gi|488601341|ref|YP_007907812.1| 16 RKLLRRN-FGK-DVGDKLELHPVEVGYLLLKGIVTLKDGDKTISFAEFI 62
                                      7788888.***.**********************************995 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.4e-08
                                       EEEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE CS
                   tRNA_int_endo_N   1 vegeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv 55 
                                       +eg++ gdrvl  d     +++++ f+G  ++d    Ls++E+lY +e G+l++ 
  gi|488601341|ref|YP_007907812.1| 157 IEGYFAGDRVLTDD----LEIFSRFFFGS-EKDGMVALSILESLYMIEEGILTLN 206
                                       589999*****998....558889*****.**********************986 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-06    0.0079      40      92 ..      99     143 ..      40     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                             Sen15  40 elvlPlelteklslekldkvfkelkeekserkkrivLaivddDsTvvYYkvtd 92 
                                       ++ lP++ ++k+ l++l+++f+e          +++La+vd++s + YY+v++
  gi|488601341|ref|YP_007907812.1|  99 NIYLPVSERKKVFLKDLNEFFDE--------HGAFILAVVDEESEITYYRVYK 143
                                       78899999**************9........568****************986 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 ?    2.3   0.0     0.043   1.9e+02      41      63 ..      22      42 ..      13      50 .. 0.78
   2 ?    7.8   0.0   0.00085       3.8      47      70 ..     182     205 ..     132     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.043
                   tRNA_int_end_N2 41 tmGvsrarrgrlwLlpeEaLYLv 63
                                      ++G+     ++l+L+p E+ YL+
  gi|488601341|ref|YP_007907812.1| 22 NFGKD--VGDKLELHPVEVGYLL 42
                                      56633..6799**********98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00085
                   tRNA_int_end_N2  47 arrgrlwLlpeEaLYLvErGsldi 70 
                                       ++ g + L   E LY++E G l +
  gi|488601341|ref|YP_007907812.1| 182 EKDGMVALSILESLYMIEEGILTL 205
                                       3889999*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2190.17
//
Query:       gi|488601342|ref|YP_007907813.1|  [L=885]
Description: hypothetical protein Asulf_01851 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-269  894.2  23.1   7.7e-269  894.0  23.1    1.0  1  UPF0182      Uncharacterised protein family (UPF0182)
    9.2e-05   22.3   2.2    9.2e-05   22.3   2.2    2.7  3  Tetraspanin  Tetraspanin family
  ------ inclusion threshold ------
      0.081   12.0   1.8        1.3    8.0   0.8    2.4  1  PHO4         Phosphate transporter family


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  894.0  23.1  1.3e-272  7.7e-269       5     758 .]      20     758 ..      16     758 .. 0.96

  Alignments for each domain:
  == domain 1  score: 894.0 bits;  conditional E-value: 1.3e-272
                           UPF0182   5 lavlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvflllalllllnlllaerlelleklerlrea 81 
                                       l+++++l++l ++ + lyte+lwfk+l+  ++f++++++rl lf ++f+l++l++++n + ++++         +e 
  gi|488601342|ref|YP_007907813.1|  20 LLTILILIILSSTGVYLYTEYLWFKSLDLGTYFVKTIIYRLELFGFFFTLSFLIFAINRFAMHKA---------SEE 87 
                                       667788888899*************************************************9999.........567 PP

                           UPF0182  82 lekklkllllaialvlsllvglvassqwekvllflnstsfgvkDpifgkDisFYvFklPflelllslllalvllali 158
                                       +  ++ ++ l i ++lsl++g+v++++w k++ f n+++fg++Dpifg D+sFYvFklPfl+ +l ++la+v+++++
  gi|488601342|ref|YP_007907813.1|  88 FLGEPLKVPLWILFLLSLFIGYVLARDWIKFVFFQNAENFGISDPIFGIDVSFYVFKLPFLKDILYTILAIVIFCFL 164
                                       7888888889999**************************************************************** PP

                           UPF0182 159 avllvyllsgesl.girl..kfaelskaarrhlsvllallllllalsywLdryellyskrgvvtGagYtdvnavlpa 232
                                       +++++y++  +++ +  +   ++ + +   +h+s+l+a++l+++++  ++ r++ll ++ gv++GagYtdv +++p 
  gi|488601342|ref|YP_007907813.1| 165 ISVVYYFFIFRWVkS--FeeFKELFPNLGYIHISALIAVILFIVGIYAYIGRFDLLNAQGGVLSGAGYTDVYVRIPS 239
                                       *******99988833..2444467788899*********************************************** PP

                           UPF0182 233 ktilavialvvavlllvaivlkklklplialallvllaillgvvlpalvqkfiVkPnelekEkpYiernIeaTreAy 309
                                        +++++i+++++++ ++  v+++l+++ + +++++++  +l +v++ ++qk+ V+Pne+++E++Yie++I++Tr Ay
  gi|488601342|ref|YP_007907813.1| 240 LLLISFISFLASIFAIYYGVKRQLEMLPTLFLIVIAIF-FLAMVFAFAFQKVRVEPNEISLEEKYIEYSINFTRMAY 315
                                       *************9999999999976665555544444.599999******************************** PP

                           UPF0182 310 gLdkveveefeaeaeltaedleenaetienirLlDprplletfrqlqqirnYYkFedldvdrYtidgeerqvviaaR 386
                                       gL +v+++ f++ ++lt +d+e+n+  i+nirL+D+rplle++rqlqqir+YY  +d+d+drY i+g+++q++i+aR
  gi|488601342|ref|YP_007907813.1| 316 GL-DVNKKLFPVGKTLTIQDIERNKGIINNIRLWDHRPLLEVYRQLQQIRTYYYINDVDIDRYYINGNYTQIMISAR 391
                                       **.8************************************************************************* PP

                           UPF0182 387 EldysalpeeaktwvnkhlvYTHGyGvvaspvnkvteeGlpeflvkdipseeeeslkieepriYfGeltndyvivgt 463
                                       El+++ l+++a+twvn+hl+YTHGyG++aspvn v+eeG+p+f+v dip+  ++++++++p+iYfGeltndyviv+t
  gi|488601342|ref|YP_007907813.1| 392 ELSTDLLQTNAQTWVNRHLIYTHGYGIIASPVNVVSEEGKPDFIVYDIPP--KGEIEVDRPEIYFGELTNDYVIVKT 466
                                       *************************************************9..9************************ PP

                           UPF0182 464 kvkEfdypsgeenvyntYdGkgGvkigsllrrllfaiklkdlklllsseitseskilfrRnikeRvekvaPfLtlDs 540
                                       k+kEfdypsge+nv +tY+G+gGvki+s+l++llf+i+++d++lll++++t+es+il++Rni +Rv++vaPfL++D+
  gi|488601342|ref|YP_007907813.1| 467 KQKEFDYPSGERNVFTTYNGTGGVKIDSYLKKLLFSIRYGDVNLLLTTYLTPESRILIHRNILDRVQSVAPFLKYDT 543
                                       ***************************************************************************** PP

                           UPF0182 541 dpYlvvadgrlyWivDaYTtsdrYPySepeeatsgeeevnYiRNSVKvvvDAydGtvklYvvdeeDPiikawskiFp 617
                                       dpY+vv+d++lyWivDaYT+ dr+PyS      ++   +nYiRNSVKv +DAy+G++k+Yvvd ++P++k+ +k+Fp
  gi|488601342|ref|YP_007907813.1| 544 DPYIVVIDKKLYWIVDAYTVLDRFPYSAG---FNNYGFFNYIRNSVKVYIDAYNGSLKFYVVD-DEPVVKTLMKAFP 616
                                       ***************************88...3345679************************.78*********** PP

                           UPF0182 618 glfkplsempeeLrshlrYPedlFkvqsellakYHvtdpevFYnredlWevpke...eeeqpvePyYlilklpgeek 691
                                       +lf p sem+ee ++h+rYP dlFk+q+ +++ YH++dp++FYn+ed+W++p+e   + e ++ePyY+++++   ++
  gi|488601342|ref|YP_007907813.1| 617 ELFIPSSEMSEEEKEHMRYPADLFKIQAIIYSIYHMDDPRTFYNKEDVWDIPTEmfdQFEIKMEPYYVMMNIG--NR 691
                                       ******************************************************98777888*********95..88 PP

                           UPF0182 692 eefillspftpssrenliawlaarsdgenygklllyelpkqelvyGpeqiearinqdpeisqqlsLw 758
                                       +efil++pftp++r+n+iaw+a+r+d+enyg++llye+pk +lvyGp+qieari+qdpeis+ ++Lw
  gi|488601342|ref|YP_007907813.1| 692 TEFILMLPFTPKDRNNIIAWMAGRCDKENYGEILLYEFPKGTLVYGPMQIEARIDQDPEISKIFTLW 758
                                       9*****************************************************************9 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.5      0.96   5.7e+03      55      55 ..      62      62 ..      17     111 .. 0.53
   2 ?    0.3   1.7     0.079   4.7e+02      81     104 ..     152     175 ..     150     189 .. 0.81
   3 !   22.3   2.2   1.5e-08   9.2e-05      12     105 ..     196     293 ..     190     351 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.96
                                      X CS
                                      x RF
                       Tetraspanin 55 v 55
                                      +
  gi|488601342|ref|YP_007907813.1| 62 L 62
                                      1 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.079
                                       XXXXXXXXXXXXXXXXXXXXX--H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  81 tfsllllvlfllelaagilgfvfs 104
                                       ++ +l +v+f+++++++ ++f+f+
  gi|488601342|ref|YP_007907813.1| 152 LYTILAIVIFCFLISVVYYFFIFR 175
                                       689999999999999999999987 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.5e-08
                                       XXXXXXXXXXXXXXXXX.....XXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  12 fwligivllavGvwlrl.....khaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfs 83 
                                         li+++l++vG+++ +      +  a+   l+ + ++d  +    l++++++ fl +++ ++  +k++  +l t +
  gi|488601342|ref|YP_007907813.1| 196 SALIAVILFIVGIYAYIgrfdlLN--AQGGVLSGAGYTDVYVRIPSLLLISFISFLASIFAIYYGVKRQLEMLPTLF 270
                                       679************99*986533..33333444444444444447899999*********9887777776666555 PP

                                       XXXXXXXXX.XXXXXXXXX--HH CS
                                       xxxxxxxxx.xxxxxxxxxxxxx RF
                       Tetraspanin  84 llllvlfll.elaagilgfvfsd 105
                                       l+++ +f+l ++ a ++  v  +
  gi|488601342|ref|YP_007907813.1| 271 LIVIAIFFLaMVFAFAFQKVRVE 293
                                       55555555505544445555444 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.8   0.00022       1.3     123     177 ..     241     286 ..     133     651 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00022
                              PHO4 123 vlsPllggiiaallfllvkrlilvk.....eklknalralpvlvlvtiailalsilfkge 177
                                       +l  ++++++              +       +k++l++lp l+l++iai+ l+++f  +
  gi|488601342|ref|YP_007907813.1| 241 LLISFISFLA--------------SifaiyYGVKRQLEMLPTLFLIVIAIFFLAMVFAFA 286
                                       1111111111..............022222356677778888888777777777777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (885 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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):               3  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 5431.09
//
Query:       gi|488601343|ref|YP_007907814.1|  [L=35]
Description: hypothetical protein Asulf_01853 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 260.92
//
Query:       gi|488601344|ref|YP_007907815.1|  [L=92]
Description: hypothetical protein Asulf_01854 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   21.6   0.0    0.00026   21.0   0.0    1.3  1  HTH_28         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.038   14.4   0.2      0.044   14.2   0.2    1.1  1  Lipocalin_8    Lipocalin-like domain
      0.051   13.1   0.2      0.057   13.0   0.2    1.1  1  Fzo_mitofusin  fzo-like conserved region
      0.086   12.3   0.0       0.28   10.6   0.0    1.8  2  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
       0.11   12.3   0.0       0.17   11.7   0.0    1.4  1  HTH_23         Homeodomain-like domain
        0.3   11.6   1.6       0.62   10.6   1.5    1.9  1  STPPase_N      Serine-threonine protein phosphatase N-termina


Domain annotation for each model (and alignments):
>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   8.8e-08   0.00026       5      50 ..      11      56 ..       6      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.8e-08
                            HTH_28  5 iikllaaGhsvreaArelgisrrtvyrWikryee.gGiagLvprrrr 50
                                      ii++ ++G + + +A++ +i+++++ +  k+y e gGi  L++ ++r
  gi|488601344|ref|YP_007907815.1| 11 IIREKKKGTPTKLIAKIENITPQRINQIYKQYKEtGGILKLKK-PGR 56
                                      688888999*************************888844444.333 PP

>> Lipocalin_8  Lipocalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.5e-05     0.044      52     116 ..      27      91 ..      18      92 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                       Lipocalin_8  52 vaekqgngetgktlgrfeykgdeltlkdpyvndreegdkkvddtveeLepyGinsl.eetFevekl 116
                                       +++ + ++  ++++ +++++g+ l lk+p ++++e +++++++ ++ ++++G  ++ +++F+++++
  gi|488601344|ref|YP_007907815.1|  27 IENIT-PQRINQIYKQYKETGGILKLKKPGRSKKELSNNEIKAIKKHTKNIGAMQQfSKQFRKKAI 91 
                                       44444.78899*****************************************76655999999876 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   0.2   1.9e-05     0.057      92     146 ..      35      91 ..      17      92 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                     Fzo_mitofusin  92 shqvqqelsstfarlc.qqvdetekel.eeeikelekeiekleevqkkakllrnkas 146
                                        +q+ ++ ++t   l+ ++  +++kel ++eik+++k+ +++ ++q+ +k++r+ka 
  gi|488601344|ref|YP_007907815.1|  35 INQIYKQYKETGGILKlKKPGRSKKELsNNEIKAIKKHTKNIGAMQQFSKQFRKKAI 91 
                                       5677777777766665234567788883579************************95 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.4e-05      0.28      17      51 ..       8      42 ..       5      43 .. 0.91
   2 ?   -0.9   0.0      0.37   1.1e+03      10      21 ..      80      91 ..      76      92 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.4e-05
                      HTH_Tnp_ISL3 17 eayilelllesrsvkavArqlgvSwtTVwrildry 51
                                        +i+++ +++ + k +A++ ++++ +++ i+++y
  gi|488601344|ref|YP_007907815.1|  8 IKWIIREKKKGTPTKLIAKIENITPQRINQIYKQY 42
                                      579999988899********************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.37
                      HTH_Tnp_ISL3 10 sriTlrleayil 21
                                      +++++ ++ +++
  gi|488601344|ref|YP_007907815.1| 80 QQFSKQFRKKAI 91
                                      799999999886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-05      0.17      10      45 ..      11      47 ..       2      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryre.eG 45
                                      i++  ++G +++ IA++ +++++ + ++ k y+e +G
  gi|488601344|ref|YP_007907815.1| 11 IIREKKKGTPTKLIAKIENITPQRINQIYKQYKEtGG 47
                                      6777777888888*******************99555 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.5   0.00021      0.62      13      37 ..      47      76 ..       7      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                         STPPase_N 13 g.....kpggkkvqLseaEIrqlCakarei 37
                                      g     kpg++k  Ls++EI+++ ++ + i
  gi|488601344|ref|YP_007907815.1| 47 GilklkKPGRSKKELSNNEIKAIKKHTKNI 76
                                      35555589999999********97777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 729.15
//
Query:       gi|488601345|ref|YP_007907816.1|  [L=245]
Description: Sec-independent protein secretion pathway component TatC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  164.5  23.8    3.4e-48  164.2  23.8    1.1  1  TatC         Sec-independent protein translocase protein (Tat
  ------ inclusion threshold ------
          6    6.5   9.3         12    5.5   9.3    1.6  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2  23.8   3.8e-52   3.4e-48       2     207 .]      12     225 ..      11     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 3.8e-52
                                       HHHHHHHHHHHHHHHHHHHHHHHHH.THHHHHHHCCHHHHC.CTTS-EE--SSS-HHHHHHHHHHHHHHHHSHHHHH CS
                              TatC   2 hLeeLrkrlirallavaiafiitfv.faeeliafllepleeaeeevelivlspleafllklkvslvaglvlasPvil 77 
                                       +L  +r+r++r ++++a+++++t++ +a+++i+ + + l    e+++li+++ple+++lklk+sl++g+++  P+++
  gi|488601345|ref|YP_007907816.1|  12 ILLMIRNRFMRLVAIIAVTWALTYMfIADTIISKIKTDLLP--EGANLIYTAPLEGLILKLKISLYIGIIAGTPYLV 86 
                                       68889******************983455566655545443..5789****************************** PP

                                       HHHHCCCTT..TTS--...-STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT....TTTSSTTEEHHHHHHHHH CS
                              TatC  78 yqlwafvap..gLykh...errlvlvfliaslllfllGaafayfvvlplvlkfll....seevepllslseylsfvl 145
                                       y +++ ++    L ++    +  ++++li++++lf lG+a++y+++lp++++fl+    s++v +++sl+e+++f++
  gi|488601345|ref|YP_007907816.1|  87 YLIYKALKTrtELLENinlTKSSAIKYLIVAIMLFTLGIAYGYMIMLPIFMQFLYssaaSQGVLATYSLAEFINFII 163
                                       *9999986511344447778899********************************87777777778*********** PP

                                       HHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S.SHHHHHHHHHH CS
                              TatC 146 llllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltPpdvisqlllavP 207
                                       l+l +fg++F++Pl++++l+ ++lv+++t++++r++++v++++++a +tPpdv++q ++a+P
  gi|488601345|ref|YP_007907816.1| 164 LMLAVFGLVFQMPLIMLFLVGNDLVEYRTITYYRKHFYVAFFIIGAAITPPDVFTQAMVAFP 225
                                       ************************************************************99 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.3    0.0014        12      14     104 ..      79     174 ..      70     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0014
                                       XXXXXXXXXXXXXXX..XXX.....................XXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  14 ligivllavGvwlrl..khaeaalacllsesaedpailaillivvGv....llfllgflGcigalkenkcllltfsl 84 
                                       ++g   l++ ++  l  ++++ ++ +l+++sa +  i+ai+l+ +G+    +++l  f+ ++ +   ++ +l+t+sl
  gi|488601345|ref|YP_007907816.1|  79 IAGTPYLVYLIYKALktRTELLENINLTKSSAIKYLIVAIMLFTLGIaygyMIMLPIFMQFLYSSAASQGVLATYSL 155
                                       444444444444444555555555666677777777888888888887775777777888999************** PP

                                       XXXXXXXXXXXXXXXXX--H CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  85 lllvlfllelaagilgfvfs 104
                                         ++ f++++  +++g+vf+
  gi|488601345|ref|YP_007907816.1| 156 AEFINFIILML-AVFGLVFQ 174
                                       ****9999886.55677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.44
# Mc/sec: 1683.16
//
Query:       gi|488601346|ref|YP_007907817.1|  [L=614]
Description: Aldehyde:ferredoxin oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-97  326.4   0.0      3e-97  326.1   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    7.8e-68  228.3   0.0    1.2e-67  227.7   0.0    1.3  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma
  ------ inclusion threshold ------
      0.031   14.2   0.0        1.8    8.6   0.0    2.6  2  KOW       KOW motif


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.1   0.0    5e-101     3e-97       1     382 []     222     610 ..     222     610 .. 0.90

  Alignments for each domain:
  == domain 1  score: 326.1 bits;  conditional E-value: 5e-101
                                       XHHHHHHHHHHHSH.HHHHHHHH-GGGHHH.HHHHTT---BTTTTB.S--TTGGGGSHHHHHHHTEEEE.E-TT-SS CS
                            AFOR_C   1 elgkkiqkeiksspqvtaelrkyGTaelvn.ianetgalptknfqe.gtfekaekisgealeekylvknegCfsCpi 75 
                                       e++k++++++++s++v+ +l+k G ++    +++e+ +l++knf++ +  e      +  +++ ++ k ++CfsCpi
  gi|488601346|ref|YP_007907817.1| 222 EVAKMWRENLWKSDVVN-ALAKGGLPQSEYkYTKESYLLSAKNFTDvSPPE-----FAVGMSK-FKYKPKACFSCPI 291
                                       5899**********555.*******8876549**************44433.....3367887.9999989****** PP

                                       --EEEEE......ET...EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-H CS
                            AFOR_C  76 aCgrevkveegkkvk...vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkk 149
                                       aC+ ev+++eg++     +     e+l ++ s lg++d+ a+++l el+d+lG++t ++G+tia+++e+ye+G+++k
  gi|488601346|ref|YP_007907817.1| 292 ACSYEVEITEGPYKGfvaTPAGGGENLEGVSSLLGVYDPGATFYLIELADRLGFETSTIGSTIAMLIEAYERGIVSK 368
                                       ************9335553333567999999999******************************************* PP

                                       HHHTS----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHH..... CS
                            AFOR_C 150 edtdglelefgdaeallellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmal..... 220
                                       ed+dg+el++gd++ ++el++k A++eg ig+ll+ G+kr+ae++gae++a+hvkG+ ++ +d+r ++++ l     
  gi|488601346|ref|YP_007907817.1| 369 EDLDGMELKWGDPKLVEELMKKAANKEGfIGYLLSLGPKRAAEAIGAENIAIHVKGTGINLHDWRVTWAILLgqlig 445
                                       ******************************************************************99977777777 PP

                                       .HHHH-TTSS-SGGG-THHHH....S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHH CS
                            AFOR_C 221 .aYatsnrGacHlrayliale....ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsa 292
                                        +Y     G +   a++++++    + +dp++++ k+++v+++q  +++vds+g+C+f+  + ++ +le +a++++a
  gi|488601346|ref|YP_007907817.1| 446 gGYSWPAPGVD---AWATEPDigydSYQDPFDWRLKPKAVRDTQLKKNWVDSIGICWFAD-WGVPSALEFEAMVVEA 518
                                       78888888887...44444444455999********************************.9*************** PP

                                       HHT----HHHHHHHHHHHHHHHHHHHHHHT--HHH...S---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT- CS
                            AFOR_C 293 vtGidvteeellkaGeRiynleRlfnlreGltrkd...dtlperlleeplkegpakgkvledeleemldeyYelrGW 366
                                       +tG++v+++e l +Ge+++nleR++nlr+Gl+++d   d + +r+l ep ++gp k k +++++++m++eyY+l+GW
  gi|488601346|ref|YP_007907817.1| 519 ATGFTVSRDEALIIGEKVINLERIVNLRLGLRPEDdiyD-VGPRFL-EPPPKGPGKDKDVRKHVKWMVREYYRLMGW 593
                                       ********************************9774744.556***.9999*****8887666************** PP

                                       -T.TS---HHHHHHCT- CS
                            AFOR_C 367 de.tGvPtketlkrLgL 382
                                       +e tG P k+tl+rLgL
  gi|488601346|ref|YP_007907817.1| 594 NEkTGEPLKSTLQRLGL 610
                                       ****************8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.7   0.0     2e-71   1.2e-67       1     198 []       7     209 ..       7     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 2e-71
                                       SEEEEEETTTTEEEEEE--.HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelp.eelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvva 76 
                                       gkilrvdLs+ +++ e+lp e+++++++Gg+gl++++l++ +++++ p++p npl+f+tGpltg p+p+ + +++v+
  gi|488601346|ref|YP_007907817.1|   7 GKILRVDLSRDEVWFEPLPdESVLKSFIGGKGLGLWYLFNCLDENISPFDPANPLIFMTGPLTGLPVPCGNNTTAVS 83 
                                       79*****************999******************************************************* PP

                                       E-TTTSS.EEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS.. CS
                            AFOR_N  77 ksPltgt.lgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd.. 150
                                       +   tg   g s+  g+fg++lk+aG+d+i+i+Gkae+pvyl+i+d++ ei++a+++wg+dt+et++ +k+++g+  
  gi|488601346|ref|YP_007907817.1|  84 INADTGYtTGASHTHGYFGPNLKKAGFDGIIITGKAESPVYLWIQDKETEIRNASKFWGKDTHETEDLIKKDVGEdk 160
                                       *****976999************************************************************888888 PP

                                       .EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                            AFOR_N 151 .kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                        +va+iGpaGen++ +A i  d++++++ +G+Ga+mgsKnlkai+v gt
  gi|488601346|ref|YP_007907817.1| 161 aSVAAIGPAGENMCCGAGIWNDKHHSFAHSGMGAIMGSKNLKAIAVYGT 209
                                       8999***************77799999*******************986 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.02   1.2e+02      14      29 ..       4      19 ..       3      20 .. 0.87
   2 ?    8.6   0.0    0.0003       1.8       4      17 ..     296     309 ..     296     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.02
                                      TCEEEEEEEETTTTEE CS
                               KOW 14 GktGkVvkvdqhkvrV 29
                                      G +Gk+++vd  ++ V
  gi|488601346|ref|YP_007907817.1|  4 GYVGKILRVDLSRDEV 19
                                      899*******998665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0003
                                       EEEESSSTTTTCEE CS
                               KOW   4 hVkVvsGphkGktG 17 
                                       +V+++ Gp+kG+++
  gi|488601346|ref|YP_007907817.1| 296 EVEITEGPYKGFVA 309
                                       59**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3802.70
//
Query:       gi|488601347|ref|YP_007907818.1|  [L=444]
Description: amino acid/amide ABC transporter substrate-binding protein, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-64  217.6   0.9    4.6e-64  217.2   0.9    1.1  1  Peripla_BP_6  Periplasmic binding protein
    1.1e-16   60.9   0.0    1.6e-16   60.3   0.0    1.2  1  ANF_receptor  Receptor family ligand binding region
      3e-14   52.8   0.1    1.6e-06   27.3   0.0    2.1  2  Peripla_BP_5  Periplasmic binding protein domain
     0.0015   17.8   0.1      0.012   14.9   0.0    2.0  2  ABC_sub_bind  ABC transporter substrate binding protein
  ------ inclusion threshold ------
      0.034   13.9   1.8        0.2   11.4   0.3    2.7  3  XPC-binding   XPC-binding domain


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 !  217.2   0.9   1.3e-67   4.6e-64       2     341 ..      48     410 ..      47     412 .. 0.92

  Alignments for each domain:
  == domain 1  score: 217.2 bits;  conditional E-value: 1.3e-67
                                       EEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHH.TTEET..TE..EEEEEEEE-TTSHHHHHHHHHHHHHCT--SEE CS
                      Peripla_BP_6   2 ikiGlltplsGpyassgksllagaqaafeeiNa.aGGin..Gr..kielverDdaydpdraaeaarrlvdqdgvdal 73 
                                       i iG   ++sG y+  g+++l+g+qaa++++N+  GG+   G+  k+e+  +Dd+++ +  ++ ++rl+++d++  l
  gi|488601347|ref|YP_007907818.1|  48 ILIGGTLSMSGKYSKEGQMSLWGIQAAIKWVNDvHGGVSvgGKklKLEFKYYDDESKKEAVQSLVERLITSDKANFL 124
                                       88*******************************99**9998886778888*************************** PP

                                       EE-BSHHHHHHHHHHHHHHT-EEEESS-HHC...CTTSTTEEESS--HHHHHHHHHHHHHH.HTTSCEEEEEEESSH CS
                      Peripla_BP_6  74 vgplssavaaavaevlakdgvpvigpagltg...ekcspyvfslgpsysaqasalveylak.elggkkvalvyadya 146
                                       ++p ss+ ++a a++++k+gv++++ +g ++   ++++ yv++++  +s + +a+++ ++  + ++kk+a+vy d+ 
  gi|488601347|ref|YP_007907818.1| 125 LAPYSSGLTLAGAPIADKHGVLYMSHGGASDrifDQGYAYVVQTLSPASEYQTAFIDMIKAiDPDAKKIAMVYEDSE 201
                                       *************************7766643448**********99999999999976555677************ PP

                                       HHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEE CS
                      Peripla_BP_6 147 fgregiaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillv 223
                                       f++++ a++k+ a+++G+evv + ++p++ +d++++++++kaa++d+++++g +ad   l+ ++a+  ldak i ++
  gi|488601347|ref|YP_007907818.1| 202 FSKAVFAGAKKHAEELGFEVVIDKTYPPNPQDLTPLLQEVKAANPDIIIGGGHFADGQLLASQMADLKLDAKAISIL 278
                                       *******************999**************************************************99999 PP

                                       CCC-CHHHHHHHHHHHHTTEEEEESCSTC..............CCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHH CS
                      Peripla_BP_6 224 swsgseedlkalggeaaegvlavtpyfpd..............ldnpavrafvaayeaayggapppsqfaaggyiaa 286
                                          + ++  +alg  +aeg+ ++ ++  +              + +p++++f + + +++g++  ps++aa++ +a+
  gi|488601347|ref|YP_007907818.1| 279 VAPALPAFYEALGN-NAEGICGPGQWEVGvkyspesakeagleYFGPTQDEFLELFHEFAGKDVTPSYHAAEAAAAV 354
                                       99999999999998.9****8888877665555556666666667888***************99************ PP

                                       HHHHHHHHCCTHCCHHHHHHHHHHS-BECCCTCCBEE.CTTSBEE--EEEEEE-TS CS
                      Peripla_BP_6 287 dlllealkaagsltreavraaleslgfdgllgplkft.aedhqasrpvyvvqvdgg 341
                                       +++++a+++a sl+ ++vr+++++l+f +++g++k++ a+  q ++++ ++q++gg
  gi|488601347|ref|YP_007907818.1| 355 LAYVKAIESANSLDTDKVRETMNNLHFMTFFGEWKIDpATGKQIGHKMVIFQWQGG 410
                                       *************************************4456669**********87 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 !   60.3   0.0   4.6e-20   1.6e-16      22     353 ..      91     410 ..      71     411 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 4.6e-20
                                       TEEEEEEEEE-TT-HHHHHHHHHHHCCC.CEEEEEE-SSHHHHHHHHHHHCCTT-EEEESS---GGGG-TTTTTTEE CS
                      ANF_receptor  22 giklgyeiidtccdfslaleaaldflkg.kvvaviGpssssvsdavaslanlfkiPvisygstspelsdknryptfl 97 
                                       + kl+++  d++++ ++++  +  +++  k+  ++ p+ss+ + a a +a++  +   s+g  s+ + d + y +++
  gi|488601347|ref|YP_007907818.1|  91 KLKLEFKYYDDESKKEAVQSLVERLITSdKANFLLAPYSSGLTLAGAPIADKHGVLYMSHGGASDRIFD-QGYAYVV 166
                                       56899999*******************967************************************666.578999* PP

                                       ESS--CHHHHHHHHHHHH..HTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEESTCHHHCHHHHHHHHH CS
                      ANF_receptor  98 rtvpsdtsqaqAivdilk..hfgWkkvaliysdddygesglqaleeeleergicvalkekipessnddevvrkllke 172
                                       +t  +++ + +A++d++k      kk+a++y+d++  + +    ++ +ee g++v+  +++p    + +++++ll+e
  gi|488601347|ref|YP_007907818.1| 167 QTLSPASEYQTAFIDMIKaiDPDAKKIAMVYEDSEFSKAVFAGAKKHAEELGFEVVIDKTYP---PNPQDLTPLLQE 240
                                       ******************4444689*************************************...889********* PP

                                       HTT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEE.......ETCHCCCECTTS-CC...............HH CS
                      ANF_receptor 173 iks.karvivlfcssedarellkaarrlgltgeeyvwi.......asdawtsslvldkpe.............ltgl 228
                                       +k  ++++i+   +  d + l  ++ +l+l+ +    +               ++ + ++             +++ 
  gi|488601347|ref|YP_007907818.1| 241 VKAaNPDIIIGGGHFADGQLLASQMADLKLDAKAISILvapalpaF-------YEALGNNaegicgpgqwevgVKYS 310
                                       ***9****************************99999944333332.......333322222222224444443333 PP

                                       HHHTT-EEEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB- CS
                      ANF_receptor 229 eaaegvlgfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralsc 305
                                          ++  g++++ p++++f e +   +++          +   +sy+aa    aV ++++A++ ++           
  gi|488601347|ref|YP_007907818.1| 311 PESAKEAGLEYFGPTQDEFLELF---HEF--------AGKDVTPSYHAAEAAAAVLAYVKAIESAN----------- 365
                                       33444448888999999999999...333........34455689********************9........... PP

                                       HHHHCCHHHHHHHHHHHT-EEEETTSCEEB-T.TSBBE.-EEEEEEEECT CS
                      ANF_receptor 306 ntlkpweggqkllrylrnvnfeGltGdvkfde.ngdrv.ptydilnlqgs 353
                                              + +k+ +++ n++f  + G+ k+d+  g+ +  ++ i+++qg 
  gi|488601347|ref|YP_007907818.1| 366 -----SLDTDKVRETMNNLHFMTFFGEWKIDPaTGKQIgHKMVIFQWQGG 410
                                       .....678899*******************85278888999999999975 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 !   23.5   0.0   6.7e-09   2.4e-05       3     195 ..      50     251 ..      48     281 .. 0.86
   2 !   27.3   0.0   4.5e-10   1.6e-06     255     359 ..     324     427 ..     316     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.7e-09
                      Peripla_BP_5   3 vGvLhSlsGtmaisekslkdaallaieeina.agGvl..gr..kieavvvdpasdwelfaekaeklieedkvevvfG 74 
                                       +G   S+sG ++   +  + +++ ai+ +n  +gGv+  g+  k+e   +d +s  e+ ++  e+li++dk ++++ 
  gi|488601347|ref|YP_007907818.1|  50 IGGTLSMSGKYSKEGQMSLWGIQAAIKWVNDvHGGVSvgGKklKLEFKYYDDESKKEAVQSLVERLITSDKANFLLA 126
                                       77788************************97468876546622578999**************************** PP

                      Peripla_BP_5  75 cwtSasRkavlpvveelnalLfYpvqYEGeEssknviYtGaa.pnqqaipavdyllselg........akrvflvGs 142
                                        + S    a  p+ +++  l+   + + G  +s+ ++  G a   q + pa +y +            ak++++v  
  gi|488601347|ref|YP_007907818.1| 127 PYSSGLTLAGAPIADKHGVLY---MSHGG--ASDRIFDQGYAyVVQTLSPASEYQTAFIDmikaidpdAKKIAMVYE 198
                                       **************9997664...46666..69******9662679999*****887766677788999******** PP

                      Peripla_BP_5 143 dyvypretnrilkallkakggevvgeeYlplgssdvqkivakikkakpdvvls 195
                                       d  +++ +   +k+  ++ g evv ++  p + +d++ +++++k+a+pd+++ 
  gi|488601347|ref|YP_007907818.1| 199 DSEFSKAVFAGAKKHAEELGFEVVIDKTYPPNPQDLTPLLQEVKAANPDIIIG 251
                                       **********************999999999*******************985 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 4.5e-10
                      Peripla_BP_5 255 penkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvreallgqelkapeGevkidpenhhlskt 331
                                       p+ ++f++ f++++g+d + + ++  a  +v  +++A+e+a+s d++kvre++ + ++ +  Ge kidp++      
  gi|488601347|ref|YP_007907818.1| 324 PTQDEFLELFHEFAGKDVTPSYHAAEAAAAVLAYVKAIESANSLDTDKVRETMNNLHFMTFFGEWKIDPATGKQIGH 400
                                       67899*************9999999999*****************************************99776666 PP

                      Peripla_BP_5 332 vrigkikadGqfeivwetkkpvkpdpys 359
                                        ++    + G+ +ivw  k++ ++dpy 
  gi|488601347|ref|YP_007907818.1| 401 KMVIFQWQGGEKKIVWP-KAAANADPYY 427
                                       665555678*******8.5667788875 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 !   14.9   0.0   3.3e-06     0.012     119     164 ..     178     222 ..     169     242 .. 0.90
   2 ?    0.8   0.0     0.063   2.3e+02      45      81 ..     230     267 ..     221     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-06
                                       HHHHHHHHHSTT--EEEEEE-TT-HHHHHHHHHHHHHHHHTT-EEE CS
                      ABC_sub_bind 119 ktieLikkllPnvkkigilyspgeansvslveelkklakkaglkvv 164
                                       + i++ik++ P++kki ++y  +e  s+++    kk a++ g++vv
  gi|488601347|ref|YP_007907818.1| 178 AFIDMIKAIDPDAKKIAMVYEDSEF-SKAVFAGAKKHAEELGFEVV 222
                                       569********************99.99999*************98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.063
                                       -HHHHHHHHHHHHTT--SEEEEESHHH.HHHHHHH-SS CS
                      ABC_sub_bind  45 dqskvaqiirqlkaekpdlivgiatpa.aqilksatkn 81 
                                       +++++   ++ +ka +pd+i+g++  a  q l+s +++
  gi|488601347|ref|YP_007907818.1| 230 NPQDLTPLLQEVKAANPDIIIGGGHFAdGQLLASQMAD 267
                                       677888889999**********9975426777777666 PP

>> XPC-binding  XPC-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.67   2.4e+03      43      54 ..     173     184 ..     168     185 .. 0.88
   2 ?   11.4   0.3   5.6e-05       0.2      20      38 ..     230     248 ..     225     250 .. 0.93
   3 ?   -0.5   0.1      0.29     1e+03      45      55 ..     325     335 ..     319     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.67
                       XPC-binding  43 qqnqeeFlqlLn 54 
                                       +++q +F+++++
  gi|488601347|ref|YP_007907818.1| 173 SEYQTAFIDMIK 184
                                       5899******96 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.6e-05
                       XPC-binding  20 nPqlLqplLqqlaqsnPql 38 
                                       nPq L plLq++++ nP++
  gi|488601347|ref|YP_007907818.1| 230 NPQDLTPLLQEVKAANPDI 248
                                       9****************97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.29
                       XPC-binding  45 nqeeFlqlLne 55 
                                        q+eFl+l++e
  gi|488601347|ref|YP_007907818.1| 325 TQDEFLELFHE 335
                                       69******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2769.78
//
Query:       gi|488601348|ref|YP_007907819.1|  [L=298]
Description: amino acid/amide ABC transporter membrane protein 1, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-40  137.2  36.3    6.7e-40  136.9  36.3    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.38   11.1  14.5       0.15   12.4   4.1    3.4  3  DUF4396       Domain of unknown function (DUF4396)


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9  36.3   7.5e-44   6.7e-40       2     268 .]      11     285 ..      10     285 .. 0.92

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 7.5e-44
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       ++ ++ l++++++  +Gl+l+fg+++++n ghg f+++Ga++a+++ +l++  ++ +++va+++g+a+g+++ + v+
  gi|488601348|ref|YP_007907819.1|  11 LIYGAILGSVYGLSTMGLSLIFGVLRIVNVGHGPFIMVGAFTAFWMFTLFGLAPIGSIPVAIVLGLALGFVIFYTVI 87 
                                       6788999********************************************************************** PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagal..lsflsavivllalllvlavllllrrtr 153
                                       r  ++ +  ++ll ++++g++l  + + ++g+        + +++  +  +++++   ++  ++++++++l++++t+
  gi|488601348|ref|YP_007907819.1|  88 RRLLNAPELSTLLATFAIGILLEEVAKFIWGPDHRGYSWNIGDVDIGIilIPYSKILAFISSIIIAYLLYLWFQKTK 164
                                       **********************999999999998886666666665550055666666699**************** PP

                      BPD_transp_2 154 fGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsll 229
                                       +G a+rav e+ e a+  Ginv+++ +l+f+i+ al   +G+l++l+  ++   ++g +++++a++++vlGg+gs+ 
  gi|488601348|ref|YP_007907819.1| 165 LGKAVRAVVEDAEGAATCGINVRWIYALSFAIGIALTVASGVLVTLFVPVGINpYMGHEYTLKAFVIAVLGGLGSPW 241
                                       *******************************************99887666555*********************** PP

                      BPD_transp_2 230 gtviGaliigvvksllltllgi.....ptelarvllgallilvl 268
                                       g++++++++g++++ + t+lg      p +l+r++ + ll+++l
  gi|488601348|ref|YP_007907819.1| 242 GAFFAGFLFGLIENGSYTILGLipgvePFSLTRFVAFTLLLVIL 285
                                       **************777776669999999********9999986 PP

>> DUF4396  Domain of unknown function (DUF4396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.1   1.7e-05      0.15      17      64 ..      47      90 ..      40     118 .. 0.75
   2 ?    3.4   0.7      0.01        90      40      77 ..     136     173 ..     100     186 .. 0.75
   3 ?    0.5   0.3     0.079   7.1e+02      43      59 ..     187     203 ..     177     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                           DUF4396 17 aiGdilgmviltslslalglpmaatmilsvvlalllgllletalllre 64
                                      ++G +++ +++t    ++gl+ + ++++++vl+l+lg+++++  ++r 
  gi|488601348|ref|YP_007907819.1| 47 MVGAFTAFWMFT----LFGLAPIGSIPVAIVLGLALGFVIFYTVIRRL 90
                                      578888888888....6799*************************984 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                           DUF4396  40 atmilsvvlalllgllletalllrekglslaealktAl 77 
                                       + ++ s +la++ ++++ ++l l  ++ +l++a+++ +
  gi|488601348|ref|YP_007907819.1| 136 ILIPYSKILAFISSIIIAYLLYLWFQKTKLGKAVRAVV 173
                                       44566779999999999999988888888888887654 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.079
                           DUF4396  43 ilsvvlalllgllleta 59 
                                          ++l++++g++l++a
  gi|488601348|ref|YP_007907819.1| 187 RWIYALSFAIGIALTVA 203
                                       45677777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1773.12
//
Query:       gi|488601349|ref|YP_007907820.1|  [L=329]
Description: amino acid/amide ABC transporter membrane protein 2, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-34  118.9  44.3    3.1e-34  118.4  44.3    1.2  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
        1.9    7.8   3.1       0.68    9.3   0.4    1.5  2  DAG1          Dystroglycan (Dystrophin-associated glycoprotei


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4  44.3   3.5e-38   3.1e-34       8     266 ..      34     302 ..      27     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 3.5e-38
                      BPD_transp_2   8 laailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl......lllallvallvgaavglllgllvl 78 
                                        ++ ++ ++ ++++  g++G +++g  +f+alGay +al+   + s+      ++l+l++a++++ ++ l++g+  l
  gi|488601349|ref|YP_007907820.1|  34 FIMFYITLGQAFNIFLGLTGYVDFGYVAFLALGAYGMALAFDTFASPgmgfgiIILGLILAIIMSSILSLAVGAVAL 110
                                       567788899999***************************************************************** PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv....llalllvlavllllrr 151
                                       rl+  +++i+++++ + ++++    + + + +  + s++    f +++++++s +++    +++++l+++v++++++
  gi|488601349|ref|YP_007907820.1| 111 RLRGAYFAIATIGVNEGFRYFIEGAKLWGGSEGIIISGDMRKMFGREMANYISTFVSdvlvFIIAILAAIVTVMILN 187
                                       ********************9955554444444444444444445555555555555555599999999******** PP

                      BPD_transp_2 152 trfGralravgeneeaaralGinvkrvklltfvisgalAglaGall.alllgsipp..nigvglgfnaiaavvlGga 225
                                        ++G+al+av+e+e+aa+++Ginv+++k+++f++s+ +Agl Ga   +l  + + p   + ++++ +ai++v+lGga
  gi|488601349|ref|YP_007907820.1| 188 RKMGYALMAVREDEDAAKVMGINVTKYKIMAFITSASFAGLIGATAwTLKMTYVFPsdVFLITYTVEAIVIVMLGGA 264
                                       ******************************************985414445555558999***************** PP

                      BPD_transp_2 226 gsllgtviGaliigvvksllltllgiptelarvllgallil 266
                                       g+llg+++G+li+g++k  l+ +l   + ++ ++l  lli+
  gi|488601349|ref|YP_007907820.1| 265 GTLLGPIVGGLIYGILKYYLSIIL---PGFQLLILAPLLIV 302
                                       ******************666666...44555555545444 PP

>> DAG1  Dystroglycan (Dystrophin-associated glycoprotein 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4   7.5e-05      0.68     143     191 ..     159     209 ..     148     213 .. 0.73
   2 ?   -3.3   0.1       0.5   4.4e+03     143     159 ..     245     261 ..     243     267 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX.XXXXXXXXXXX CS
                              DAG1 143 dvylhtvipavvvaailliagiiamicyrkkr.kGkltl.edqatfikkGv 191
                                        +y+ t++  v+v +i ++a+i+ ++ +++k     + + ed+ + +  G+
  gi|488601349|ref|YP_007907820.1| 159 ANYISTFVSDVLVFIIAILAAIVTVMILNRKMgYALMAVrEDEDAAKVMGI 209
                                       57***********99999999998777766540445555766665555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.5
                                       XXXXXXXXXXXXXXXXX CS
                              DAG1 143 dvylhtvipavvvaail 159
                                       dv+l+t+    +v+++l
  gi|488601349|ref|YP_007907820.1| 245 DVFLITYTVEAIVIVML 261
                                       89999987666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2218.26
//
Query:       gi|488601350|ref|YP_007907821.1|  [L=244]
Description: amino acid/amide ABC transporter ATP-binding protein 1, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-28   97.7   0.0    1.5e-27   96.8   0.0    1.4  1  ABC_tran      ABC transporter
    2.7e-06   27.4   1.7      0.003   17.4   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00015   21.3   2.3      0.099   12.1   0.4    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00018   21.8   0.1       0.59   10.4   0.0    2.2  2  AAA_22        AAA domain
    0.00039   19.9   0.9     0.0033   16.8   0.1    2.1  2  TniB          Bacterial TniB protein
    0.00078   20.0   0.2     0.0013   19.3   0.2    1.3  1  AAA_23        AAA domain
     0.0012   18.7   0.0     0.0028   17.5   0.0    1.6  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
     0.0023   17.6   0.0     0.0051   16.5   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0031   17.5   0.0        0.2   11.7   0.0    2.2  2  AAA_14        AAA domain
  ------ inclusion threshold ------
       0.01   16.4   0.1        1.1    9.8   0.1    2.4  2  AAA_18        AAA domain
      0.034   12.9   2.0          2    7.1   0.2    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.036   13.2   0.3       0.39    9.9   0.0    2.2  2  NB-ARC        NB-ARC domain
      0.046   13.3   0.4        7.8    6.0   0.0    2.2  2  AAA_25        AAA domain
      0.054   13.9   0.3        6.3    7.2   0.0    2.3  2  AAA           ATPase family associated with various cellular 
      0.066   12.9   0.1       0.27   10.9   0.1    1.9  1  AAA_30        AAA domain
      0.085   12.6   0.0      0.085   12.6   0.0    1.2  1  AAA_15        AAA ATPase domain
      0.085   12.9   0.2        8.9    6.3   0.0    2.4  2  AAA_5         AAA domain (dynein-related subfamily)
       0.11   10.9   0.7       0.58    8.6   0.2    1.9  2  DUF2114       Uncharacterized protein conserved in archaea (D
       0.12   12.1   0.3        1.5    8.5   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
       0.14   12.0   0.0       0.33   10.8   0.0    1.5  1  EBV-NA1       Epstein Barr virus nuclear antigen-1, DNA-bindi
       0.15   12.5   0.0       0.22   11.9   0.0    1.5  1  AAA_16        AAA ATPase domain
       0.22   10.1   0.0       0.25    9.9   0.0    1.1  1  AAA_13        AAA domain
       0.24   11.2   0.2        0.4   10.5   0.2    1.3  1  Coilin_N      Coilin N-terminus


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   1.9e-30   1.5e-27       2     136 ..      20     166 ..      19     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 1.9e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++vs+++++ge ++ivG+nG+GK+tL +l+ g + p+eG+i ++g+d+++   +++++  i+  +q p+ f+  tvr
  gi|488601350|ref|YP_007907821.1|  20 NKVSFSIEKGEAIGIVGPNGSGKTTLYNLINGVYIPDEGKIFFEGQDITNlPIHTRAHLGIARTFQIPRPFNSATVR 96 
                                       79************************************************8888899999***************** PP

                                       HH...............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx...............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en               e       ++++l+ +gl +++d ++     +L   +k+ +++aral+ kpkllllDE +
  gi|488601350|ref|YP_007907821.1|  97 ENvavgamfgyakasvdE---AlaiADDYLKVVGLYDKRDAPA----GKLTPLEKRLMEVARALAMKPKLLLLDEVM 166
                                       **********98654443...156699999****999999999....****************************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 !   17.4   0.1   3.8e-06     0.003       3      22 ..      33      52 ..      32      76 .. 0.78
   2 !    9.3   0.2    0.0011      0.87     254     285 ..     153     184 ..     145     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.8e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +++GpNgsGK++L  ++ ++
  gi|488601350|ref|YP_007907821.1| 33 GIVGPNGSGKTTLYNLINGV 52
                                      69***********9999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                            AAA_21 254 alkkgsllliDEpEngLHPkllrrllellkel 285
                                       ++ k++lll+DE+ +g++P+ + rl+ llk+ 
  gi|488601350|ref|YP_007907821.1| 153 LAMKPKLLLLDEVMAGMNPSDIDRLINLLKRI 184
                                       456779*************9999999999654 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 !   12.1   0.4   0.00013     0.099      26      42 ..      31      47 ..      17      54 .. 0.77
   2 !    9.1   0.1     0.001      0.82     160     209 ..     158     207 ..     141     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlld 42
                                         ivGpNGSGK+ l +
  gi|488601350|ref|YP_007907821.1| 31 AIGIVGPNGSGKTTLYN 47
                                      457**********9876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                                       SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                                        l llDe+ a +  + + ++ +llk+ +++  + ++s+ e++++   k+ 
  gi|488601350|ref|YP_007907821.1| 158 KLLLLDEVMAGMNPSDIDRLINLLKRIREEEDISIVSMVEHLMHAITKFA 207
                                       3789**********************************999999876654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00075      0.59       7      24 ..      31      48 ..      26      56 .. 0.85
   2 !    9.4   0.0    0.0015       1.2      55     126 ..     120     193 ..      79     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00075
                            AAA_22  7 ilvvtGesGtGKTtllrr 24
                                       + ++G+ G+GKTtl++ 
  gi|488601350|ref|YP_007907821.1| 31 AIGIVGPNGSGKTTLYNL 48
                                      5669***********986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                            AAA_22  55 dllrellralglelkaerlsseellealeqalrarav.ielliiDEaqh.lr.s..eealeeLrsllnlsrkgvqli 126
                                       d + +++  ++ +     +++  l ++l + +ra a+ ++ll++DE+   ++ s  +++++ L+++ +  + +++++
  gi|488601350|ref|YP_007907821.1| 120 DDYLKVVGLYDKRDAP-AGKLTPLEKRLMEVARALAMkPKLLLLDEVMAgMNpSdiDRLINLLKRIRE--EEDISIV 193
                                       4455555555543333.4555555599999999999999**********9987578999999999999..9998887 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.22   1.7e+02      37      52 ..      31      46 ..       7      53 .. 0.86
   2 !   16.8   0.1   4.3e-06    0.0033     104     160 ..     139     195 ..     122     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.22
                              TniB 37 nlllvGdsnnGKtmiv 52
                                       + +vG+   GKt++ 
  gi|488601350|ref|YP_007907821.1| 31 AIGIVGPNGSGKTTLY 46
                                      5679*********986 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.3e-06
                              TniB 104 vskleqqvlrllr..elkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       ++ le++ +++ r  ++k+++L++DE+   +  + ++  +++n+lk++ +e +i+iv +
  gi|488601350|ref|YP_007907821.1| 139 LTPLEKRLMEVARalAMKPKLLLLDEVMAGM--NPSDIDRLINLLKRIREEEDISIVSM 195
                                       44555666666652257899*******8877..899999******************86 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   1.7e-06    0.0013      21      40 ..      31      50 ..       5      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-06
                            AAA_23 21 ltlItGpNGaGKTTildAik 40
                                         I+GpNG+GKTT+ + i 
  gi|488601350|ref|YP_007907821.1| 31 AIGIVGPNGSGKTTLYNLIN 50
                                      567************99885 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.6e-06    0.0028      11      23 .]     227     239 ..     218     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
                      BCA_ABC_TP_C  11 vrndPrVieAYLG 23 
                                       v ndPrV+e+YLG
  gi|488601350|ref|YP_007907821.1| 227 VLNDPRVVEVYLG 239
                                       89**********9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.6e-06    0.0051      15      50 ..      22      57 ..      17      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       +++i+  +a+ ++Gp+GsGK+Tl   i+ + +p++
  gi|488601350|ref|YP_007907821.1| 22 VSFSIEKGEAIGIVGPNGSGKTTLYNLINGVYIPDE 57
                                      667787555999************877777777766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00026       0.2       3      43 ..      30      69 ..      28      91 .. 0.82
   2 ?    3.9   0.0     0.064        50      52      92 ..     142     189 ..     108     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                      +++ i+G+  +GKTtl ++li+  ++++e  ++++ +d ++
  gi|488601350|ref|YP_007907821.1| 30 EAIGIVGPNGSGKTTL-YNLINGVYIPDEGKIFFEGQDITN 69
                                      6899************.788888888999888888887766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.064
                            AAA_14  52 llelileklke..ekktylflDEiqev......pewekalkslvdegkn 92 
                                       l++ ++e +++   k ++l+lDE+         +++ + lk++ +e+ +
  gi|488601350|ref|YP_007907821.1| 142 LEKRLMEVARAlaMKPKLLLLDEVMAGmnpsdiDRLINLLKRIREEE-D 189
                                       444444432223347899*****976555544455666666666555.3 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0014       1.1       1      17 [.      32      48 ..      32      65 .. 0.91
   2 ?    4.3   0.0     0.071        55      28      91 ..     119     174 ..     102     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                            AAA_18  1 IlltGtpGvGKttlake 17
                                      I++ G+ G+GKttl + 
  gi|488601350|ref|YP_007907821.1| 32 IGIVGPNGSGKTTLYNL 48
                                      89***********9765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.071
                            AAA_18  28 lrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaa 91 
                                         d++k  gl++ +d++    ++   e++l+++ +al   +      k l++d ++a + + + 
  gi|488601350|ref|YP_007907821.1| 119 ADDYLKVVGLYDKRDAP--AGKLTPLEKRLMEVARALAMKP------KLLLLDEVMAGMNPSDI 174
                                       56899999999999999..9999999999999999999975......79999999999987765 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0088       6.8     242     276 ..      26      58 ..      21      62 .. 0.78
   2 ?    7.1   0.2    0.0026         2     356     413 ..     160     215 ..     147     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0088
                                       E-SS.EEEEEE-TTSSHHHHHHHHHHCCSEE-TTSS CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAlekGvynhvpgDG 276
                                       i kG  + IvG++  GK+TL + + +Gvy  +p+ G
  gi|488601350|ref|YP_007907821.1|  26 IEKGeAIGIVGPNGSGKTTLYNLI-NGVY--IPDEG 58 
                                       67777778***********98855.6888..55555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0026
                                       H---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEE.SS-GCCTTT-SEEEEEET CS
                        ABC_ATPase 356 mirDermqelvskekepitplvdrvrelykklgvstilvv.ggsgdyldvAdtvilmee 413
                                       ++ De m+ + +     i  l++++++++++ ++s++  v   + + ++ A++vi+m++
  gi|488601350|ref|YP_007907821.1| 160 LLLDEVMAGMNP---SDIDRLINLLKRIREEEDISIVSMVeHLMHAITKFAERVIVMHQ 215
                                       555777777663...34788888888888889999886553778888899999999986 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    0.0005      0.39      22      40 ..      31      49 ..      18      56 .. 0.84
   2 ?    1.3   0.0      0.21   1.6e+02      91     114 ..     144     167 ..     112     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0005
                                      EEEEEESTTSSHHHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlakqi 40
                                       +++vG  G+GKttl + i
  gi|488601350|ref|YP_007907821.1| 31 AIGIVGPNGSGKTTLYNLI 49
                                      689************9876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.21
                                       SHHHHHHHHCCCTTEEEEEEEE-S CS
                            NB-ARC  91 slkrklvrlLltkrfllvlDDVwe 114
                                       ++  ++ r+L  k  ll+lD V  
  gi|488601350|ref|YP_007907821.1| 144 KRLMEVARALAMKPKLLLLDEVMA 167
                                       367788999****9******9975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0      0.01       7.8      30      49 ..      26      45 ..      23      52 .. 0.91
   2 ?    5.3   0.1     0.016        13     122     189 ..     133     199 ..      94     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                            AAA_25 30 lpagelallaGapgtGKttl 49
                                      + +ge + ++G+ g+GKttl
  gi|488601350|ref|YP_007907821.1| 26 IEKGEAIGIVGPNGSGKTTL 45
                                      56899999***********8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                            AAA_25 122 ggtl..ltadvdaleaaieeveg.vrlvviDplsralggdensnsdvgalvealeriarrtgaa.vllvhHv 189
                                       + ++  lt+  ++l++++++ +  ++l+ +D + + ++      sd+++l++ l+ri+++ ++  v +v H+
  gi|488601350|ref|YP_007907821.1| 133 DAPAgkLTPLEKRLMEVARALAMkPKLLLLDEVMAGMN-----PSDIDRLINLLKRIREEEDISiVSMVEHL 199
                                       33333466666677777776644599999998877664.....47899**********99996648888886 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 ?    7.2   0.0    0.0081       6.3       3      18 ..      34      49 ..      32      63 .. 0.89
   2 ?    4.7   0.1     0.049        38      49      80 ..     146     187 ..     135     221 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0081
                                      EESSTTSSHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakav 18
                                      ++Gp G GKT+l + +
  gi|488601350|ref|YP_007907821.1| 34 IVGPNGSGKTTLYNLI 49
                                      68*********98765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.049
                                       HHHHHHHTS.TSEEEEEETGGGHHHHH.........TTCCCH CS
                               AAA  49 lfkeakeka.kpsilfiDEidalaksr.........sgsese 80 
                                       l++ a++ a kp+ l++DE+ a ++ +         ++  +e
  gi|488601350|ref|YP_007907821.1| 146 LMEVARALAmKPKLLLLDEVMAGMNPSdidrlinllKRIREE 187
                                       455577777889*******98866555233333333222333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00035      0.27      20      47 ..      31      75 ..      22     197 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.g................g 47
                                         ++Gp G+GKtt+ + ++ ++  + g                +
  gi|488601350|ref|YP_007907821.1| 31 AIGIVGPNGSGKTTLYNLINGVYIPDeGkiffegqditnlpihtR 75
                                      56799**************99887774566666644444444441 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.085      25      45 ..      31      51 ..      18     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            AAA_15 25 ltvliGkNnsGKSsilealdl 45
                                         ++G+N+sGK+++ ++++ 
  gi|488601350|ref|YP_007907821.1| 31 AIGIVGPNGSGKTTLYNLING 51
                                      7779***********999964 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 ?    6.3   0.0     0.011       8.9       4      21 ..      34      51 ..      32      77 .. 0.86
   2 ?    4.3   0.1     0.049        38      59      93 ..     146     185 ..     128     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                                      EE--SSSSHHHHHHHGGG CS
                             AAA_5  4 LvGppGtgKselaerlaa 21
                                      +vGp G+gK++l   +  
  gi|488601350|ref|YP_007907821.1| 34 IVGPNGSGKTTLYNLING 51
                                      69**********988765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.049
                                       ------....G-SEEEEESGGG--.HHHHHHHHHHHHSSE CS
                             AAA_5  59 lvraar....egeilvlDEverae.sevlnsLlslleerr 93 
                                       l++ ar    ++++l+lDEv     ++ +++L++ll + r
  gi|488601350|ref|YP_007907821.1| 146 LMEVARalamKPKLLLLDEVMAGMnPSDIDRLINLLKRIR 185
                                       5555556668999*******98766999999999998655 PP

>> DUF2114  Uncharacterized protein conserved in archaea (DUF2114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.21   1.6e+02     133     172 ..       4      45 ..       1      55 [. 0.79
   2 ?    8.6   0.2   0.00074      0.58     312     369 ..     165     224 ..     145     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.21
                           DUF2114 133 mskenlpeklrkyslldkvvf...dGavasvvpPkgktgvevv 172
                                       +  en+++++     ++kv f   +G  +++v P+g+ g  + 
  gi|488601350|ref|YP_007907821.1|   4 LKLENVTKRFGGLVAVNKVSFsieKGEAIGIVGPNGS-GKTTL 45 
                                       67789999999999*****995555999999999998.65555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00074
                           DUF2114 312 cdvgengsdlekleeigaeilekeglkvl..lavldevsakivkrlievaveeglveekt 369
                                       +  g n sd+++l ++ ++i e+e+++++  ++ l + ++k+++r+i + + ++l+e +t
  gi|488601350|ref|YP_007907821.1| 165 VMAGMNPSDIDRLINLLKRIREEEDISIVsmVEHLMHAITKFAERVIVMHQGSKLLEGET 224
                                       56799********************9986115668888999******9999999988776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0     0.002       1.5      44      68 ..      26      50 ..      14      82 .. 0.80
   2 ?    1.5   0.0      0.27   2.1e+02     103     146 ..     150     193 ..     137     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      iek e+i ++Gp G GK+ l   + 
  gi|488601350|ref|YP_007907821.1| 26 IEKGEAIGIVGPNGSGKTTLYNLIN 50
                                      8999**************9866555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.27
                         IstB_IS21 103 lkrl.lkvdllilDdlgllpldqaeaellfeviekryerrsiiit 146
                                       +++l +k++ll+lD++ +  ++  +   l +++++  e + i i 
  gi|488601350|ref|YP_007907821.1| 150 ARALaMKPKLLLLDEV-MAGMNPSDIDRLINLLKRIREEEDISIV 193
                                       4444156799999997.3455666666666666666666655555 PP

>> EBV-NA1  Epstein Barr virus nuclear antigen-1, DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00042      0.33      17      64 ..       5      52 ..       2      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                                      HHHHHHHHHHHHHTTS---S--SS--EEEEEEEEES-HHHHHHHHHHH CS
                           EBV-NA1 17 kfeniaeglrlllarshvertteegtwvagvfvyggsktslynlrrgi 64
                                      k+en+++ +  l+a  +v  + e+g+ +  v   g  kt+lynl  g+
  gi|488601350|ref|YP_007907821.1|  5 KLENVTKRFGGLVAVNKVSFSIEKGEAIGIVGPNGSGKTTLYNLINGV 52
                                      89**************************99999***********9997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.22      25      63 ..      30      69 ..      20     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                            AAA_16 25 elvllsGesGvGKsslvrellr.alekdggiflrgkcdql 63
                                      e++ ++G+ G+GK++l + +   ++ ++g if++g+   +
  gi|488601350|ref|YP_007907821.1| 30 EAIGIVGPNGSGKTTLYNLINGvYIPDEGKIFFEGQDITN 69
                                      77889***********999987355555677777777666 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00032      0.25      21      48 ..      34      61 ..      33     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00032
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkf 48
                                      i G NG+GKTtL +l++ +      + f
  gi|488601350|ref|YP_007907821.1| 34 IVGPNGSGKTTLYNLINGVYIPDEGKIF 61
                                      569*************988554444444 PP

>> Coilin_N  Coilin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00051       0.4      27      75 ..     190     236 ..     177     244 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00051
                          Coilin_N  27 ckvvkdLaqhirklFklkrpsillLyldgclLpptEsirvlrdndcirV 75 
                                       +  v  ++++  + +k+ ++  +  +++g  L++ E i+vl+d  +++V
  gi|488601350|ref|YP_007907821.1| 190 ISIVSMVEHLMHAITKFAER--VIVMHQGSKLLEGETIKVLNDPRVVEV 236
                                       5668899999999*****77..*********************999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1500.50
//
Query:       gi|488601351|ref|YP_007907822.1|  [L=237]
Description: amino acid/amide ABC transporter ATP-binding protein 2, HAAT family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  116.8   0.0    1.3e-33  116.4   0.0    1.2  1  ABC_tran     ABC transporter
    1.9e-09   37.8   1.5    0.00025   21.0   0.3    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.8e-05   23.7   0.7     0.0011   18.4   0.7    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00014   21.5   0.0     0.0003   20.4   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
    0.00043   20.1   0.4      0.015   15.1   0.0    2.1  2  AAA_15       AAA ATPase domain
    0.00062   20.0   0.2       0.04   14.2   0.0    2.1  2  AAA_22       AAA domain
     0.0014   19.2   0.4     0.0029   18.1   0.4    1.4  1  AAA_23       AAA domain
     0.0066   16.8   0.4      0.082   13.2   0.4    2.3  1  AAA_19       AAA domain
     0.0094   15.7   0.0      0.031   14.0   0.0    1.8  1  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.049   13.2   0.0    1.8  3  AAA_27       AAA domain
      0.019   14.9   0.0      0.037   13.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.023   15.1   0.1      0.035   14.5   0.1    1.6  1  AAA_16       AAA ATPase domain
      0.028   13.2   0.5       0.51    9.1   0.3    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.031   13.9   0.0      0.043   13.4   0.0    1.2  1  DUF5563      Family of unknown function (DUF5563)
      0.041   13.8   0.3       0.43   10.5   0.1    2.1  2  NACHT        NACHT domain
      0.055   12.4   0.0      0.089   11.7   0.0    1.3  1  AAA_10       AAA-like domain
      0.061   13.6   0.1        0.8   10.0   0.1    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
        0.1   11.4   0.0       0.16   10.7   0.0    1.2  1  Adeno_IVa2   Adenovirus IVa2 protein
       0.11   12.4   0.0       0.22   11.4   0.0    1.6  1  ATPase_2     ATPase domain predominantly from Archaea
       0.14   12.2   0.2       0.77    9.8   0.0    2.3  3  AAA_14       AAA domain
       0.16   12.1   0.0       0.25   11.4   0.0    1.6  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 !  116.4   0.0   1.5e-36   1.3e-33       5     136 ..      24     165 ..      20     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 1.5e-36
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren. 79 
                                       ++++++g+++ ++G+nGaGKStLlk++ gl++p +G+i ++++d++   +++++++ + ++ +  +lfp++tvren 
  gi|488601351|ref|YP_007907822.1|  24 EIEVSKGSITTVLGPNGAGKSTLLKTIFGLVRPWNGKIFFKDEDVTLmPPHKKVENGLTMVLEGRHLFPNMTVRENl 100
                                       6789*************************************99999879**************************** PP

                                       ....HHHTCHHHHHHHSTTGG....TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ....xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ....esdeeiekalsklglke....lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                           +sd+ +ek+ ++l+l++      +++ ++ + +LSgG++q+va+aral+++p+++llDEp+
  gi|488601351|ref|YP_007907822.1| 101 ilgaYSDRAMEKMNESLELIYslfpRLKERSEQLAGTLSGGEQQMVAIARALMTNPEIILLDEPS 165
                                       ***999999**********9977664455555666*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   2.9e-07   0.00025       1      22 [.      32      53 ..      32      82 .. 0.84
   2 !   15.9   0.0     1e-05    0.0086     234     290 ..     135     188 ..     114     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.9e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      ++ + GpNg+GKS+LL+++ +l
  gi|488601351|ref|YP_007907822.1| 32 ITTVLGPNGAGKSTLLKTIFGL 53
                                      6899***************887 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1e-05
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrnga 290
                                       a  lS G +++ a++ al   +    ++l+DEp  gL Pkl+   ++ + +l+++g 
  gi|488601351|ref|YP_007907822.1| 135 AGTLSGGEQQMVAIARALMTNP---EIILLDEPSQGLAPKLVMQMFDTIHKLKDEGL 188
                                       5678*******88888888777...9*************999888887744444455 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   1.3e-06    0.0011      24     187 ..      30     184 ..      22     202 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHC.CCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrsek.lsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                        s+t ++GpNG+GKs ll  i F L    + k+  ++    l+     +++v+++   ++   e+++     +++++
  gi|488601351|ref|YP_007907822.1|  30 GSITTVLGPNGAGKSTLLKTI-FGLVRPWNGKIFFKDeDVTLMP---PHKKVENGLTMVL---EGRH---LFPNMTV 96 
                                       5799*****************.8887654434333330223333...3455555543332...3333...3678888 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiske....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                       + +++ +  s+ ++++ + + + + +l+++ +  +e    +LSgGe+++va+a  +   + +p+ + llDe  + L 
  gi|488601351|ref|YP_007907822.1|  97 RENLILGAYSDRAMEKMNESLELIYSLFPRLKERSEqlagTLSGGEQQMVAIARAL---MTNPE-IILLDEPSQGLA 169
                                       88888888888889888888888888888777666644446899999999888553...33443.556677666666 PP

                                       HHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkeks 187
                                        k v ++ + +++ +
  gi|488601351|ref|YP_007907822.1| 170 PKLVMQMFDTIHKLK 184
                                       666666666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.6e-07    0.0003      16      48 ..      24      56 ..      18      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.6e-07
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvp 48
                                      +ie++  g +t + Gp+G+GKSTll  i  l  p
  gi|488601351|ref|YP_007907822.1| 24 EIEVSK-GsITTVLGPNGAGKSTLLKTIFGLVRP 56
                                      677874.55***************9777666655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.7e-05     0.015      17      44 ..      23      51 ..      20      79 .. 0.79
   2 ?    3.2   0.1     0.069        59     323     354 ..     155     186 ..     142     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsileald 44
                                      +ei++s+  +t++ G+N++GKS++l+ + 
  gi|488601351|ref|YP_007907822.1| 23 AEIEVSKGsITTVLGPNGAGKSTLLKTIF 51
                                      589999989*****************994 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.069
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkeland 354
                                       ++ i+l++EP   L p++ +++++++ +l ++
  gi|488601351|ref|YP_007907822.1| 155 NPEIILLDEPSQGLAPKLVMQMFDTIHKLKDE 186
                                       679***********************998665 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   4.7e-05      0.04       4      26 ..      29      51 ..      25      85 .. 0.87
   2 ?    4.1   0.0     0.061        52      59     128 ..     122     193 ..      99     200 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      + +i++v G+ G+GK+tll++++
  gi|488601351|ref|YP_007907822.1| 29 KGSITTVLGPNGAGKSTLLKTIF 51
                                      6799****************987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.061
                            AAA_22  59 ellralglelkaerlsseellealeqalrarav.ielliiDEaqh.lr.s..eealeeLrsllnlsrkgvqliLv 128
                                        l+  l+++ +   ++++   +++   +ra ++ +e++++DE    l  +  ++++ ++++l +    g++++Lv
  gi|488601351|ref|YP_007907822.1| 122 SLFPRLKERSEQLAGTLSGGEQQMVAIARALMTnPEIILLDEPSQgLApKlvMQMFDTIHKLKD---EGLTILLV 193
                                       444455544444333444444666777777777999******7666975377999999988887...55555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   3.4e-06    0.0029      14      39 ..      24      50 ..      20      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.4e-06
                            AAA_23 14 eidFsk.gltlItGpNGaGKTTildAi 39
                                      ei+ sk  +t + GpNGaGK+T+l  i
  gi|488601351|ref|YP_007907822.1| 24 EIEVSKgSITTVLGPNGAGKSTLLKTI 50
                                      788877359**************9876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.4   9.6e-05     0.082       8      75 ..      28     183 ..      23     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.6e-05
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp...................................eeillva 49 
                                       +k ++  v+++ G GK+++lk+i  l+   +g                                      e+++l a
  gi|488601351|ref|YP_007907822.1|  28 SKGSITTVLGPNGAGKSTLLKTIFGLVRPWNGKIFfkdedvtlmpphkkvengltmvlegrhlfpnmtvrENLILGA 104
                                       6778899****************99988877654488899999999********************9999999999* PP

                            AAA_19  50 ftgrAakelrerlaalgae......................................................atTi 72 
                                       +  rA+++++e+l+ +  +                                                       +Ti
  gi|488601351|ref|YP_007907822.1| 105 YSDRAMEKMNESLELIY-SlfprlkerseqlagtlsggeqqmvaiaralmtnpeiilldepsqglapklvmqmFDTI 180
                                       ***********993332.23556666655555555555555555555555555555555555555555555554555 PP

                            AAA_19  73 Hrl 75 
                                       H+l
  gi|488601351|ref|YP_007907822.1| 181 HKL 183
                                       554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   3.7e-05     0.031      15      68 ..      27     119 ..      15     193 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaa.g......................................grvigl 52 
                                        s+  ++++ Gp G+GK+t+lk++  +++   g                                      +++i+ 
  gi|488601351|ref|YP_007907822.1|  27 VSKGSITTVLGPNGAGKSTLLKTIFGLVRPWnGkiffkdedvtlmpphkkvengltmvlegrhlfpnmtvrENLILG 103
                                       5667799***************9987777664466777766666666666666666666666666665555555555 PP

                            AAA_30  53 AptgkaAkvLaeelgi 68 
                                       A + +a ++++e+l++
  gi|488601351|ref|YP_007907822.1| 104 AYSDRAMEKMNESLEL 119
                                       6666666666655554 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.8e-05     0.049      25      48 ..      29      52 ..      13      55 .. 0.83
   2 ?   -3.2   0.0         6   5.2e+03      70     109 ..     134     175 ..     128     182 .. 0.60
   3 ?   -2.9   0.0       4.8   4.1e+03      57      78 ..     204     225 ..     195     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.8e-05
                            AAA_27 25 eadlhliyGpNEAGKstalrAisd 48
                                      + +++ ++GpN AGKst+l+ i  
  gi|488601351|ref|YP_007907822.1| 29 KGSITTVLGPNGAGKSTLLKTIFG 52
                                      567889*************98865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                            AAA_27  70 igavleeadgeelefaRrkgrkkt..lldaddqalpeevlaa 109
                                       ++++l+  +++ +++aR   ++ +  lld+ +q l+++++ +
  gi|488601351|ref|YP_007907822.1| 134 LAGTLSGGEQQMVAIARALMTNPEiiLLDEPSQGLAPKLVMQ 175
                                       677777777777888877555444114455555555555555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.8
                            AAA_27  57 tkdnflhdakkLrigavleead 78 
                                       ++++++ ++ ++ +g++++e +
  gi|488601351|ref|YP_007907822.1| 204 SDYAYVLNEGRIVLGGTIDEIK 225
                                       7788888888888888886544 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   4.3e-05     0.037      97     121 ..      28      52 ..      20      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                                       CTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                                        k+++++++G+ G+GKStL++++ +
  gi|488601351|ref|YP_007907822.1|  28 SKGSITTVLGPNGAGKSTLLKTIFG 52 
                                       56799***************99865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.1e-05     0.035      22      48 ..      30      54 ..      19     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrellral 48
                                      g  +++ + G+ G GKs+l+++++  +
  gi|488601351|ref|YP_007907822.1| 30 G--SITTVLGPNGAGKSTLLKTIFGLV 54
                                      3..7899***************99544 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 ?    9.1   0.3    0.0006      0.51     242     264 ..      27      50 ..      18      54 .. 0.89
   2 ?    2.4   0.0     0.063        54     310     348 ..     125     163 ..      95     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0006
                                       E-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                       + kG +t++ G++  GKsTLL+ +
  gi|488601351|ref|YP_007907822.1|  27 VSKGsITTVLGPNGAGKSTLLKTI 50 
                                       56888****************987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.063
                                       CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEG CS
                        ABC_ATPase 310 PegkdttkfstedASGStsqAanimealeagakllLiDE 348
                                       P  k+ ++    + SG   q ++i++al  + +++L+DE
  gi|488601351|ref|YP_007907822.1| 125 PRLKERSEQLAGTLSGGEQQMVAIARALMTNPEIILLDE 163
                                       66667777777888************************9 PP

>> DUF5563  Family of unknown function (DUF5563)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     5e-05     0.043      67     101 ..      79     113 ..      63     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5e-05
                           DUF5563  67 ekvkvplkgrpvypnrrereamilssyaGilmnsi 101
                                       + + + l+gr+ +pn   re +il +y+   m+ +
  gi|488601351|ref|YP_007907822.1|  79 NGLTMVLEGRHLFPNMTVRENLILGAYSDRAMEKM 113
                                       457899*********************99888765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0005      0.43       4      23 ..      34      53 ..      31      63 .. 0.83
   2 ?    0.9   0.0      0.46   3.9e+02     111     142 ..      89     120 ..      65     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                      EEEC-TTTCHHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklala 23
                                       + G++G GK+tLl+ +  +
  gi|488601351|ref|YP_007907822.1| 34 TVLGPNGAGKSTLLKTIFGL 53
                                      689************99755 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.46
                                       HHHCTTTTT--EEEEEEECCCHHHHCTTSSCE CS
                             NACHT 111 elirkkllpeasllltvrpralrdleeqleea 142
                                       +l++   ++e+ +l + + ra +++ e+le  
  gi|488601351|ref|YP_007907822.1|  89 HLFPNMTVRENLILGAYSDRAMEKMNESLELI 120
                                       68888899999999999999999999999865 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001     0.089      22      56 ..      31      65 ..      19      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                            AAA_10 22 sasliiGdlGnGKSvlakllvlyisllggkaliiD 56
                                      s + ++G+ G+GKS l k+++  ++  +gk+++ D
  gi|488601351|ref|YP_007907822.1| 31 SITTVLGPNGAGKSTLLKTIFGLVRPWNGKIFFKD 65
                                      556899******************99999998765 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 ?   10.0   0.1   0.00093       0.8      27      88 ..     132     180 ..     125     182 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00093
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       ++ +gtlSGGe+q++   a+a     ++        ++++++LDE  ++l ++ + ++++++
  gi|488601351|ref|YP_007907822.1| 132 EQLAGTLSGGEQQMV---AIA----RALMT------NPEIILLDEPSQGLAPKLVMQMFDTI 180
                                       66789*******543...333....33333......36788888888888777777777766 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00019      0.16      89     136 ..      32      77 ..      24      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                        Adeno_IVa2  89 iGviyGPtGsGksqllrnlissklisPiPetvifitPekdmipPeelk 136
                                       i  + GP G+Gks ll+++    l+ P    ++f   ++ ++pP+ + 
  gi|488601351|ref|YP_007907822.1|  32 ITTVLGPNGAGKSTLLKTIF--GLVRPWNGKIFFKDEDVTLMPPHKKV 77 
                                       67789************997..59********************8765 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   0.00026      0.22      18      52 ..      28      62 ..      23     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyvi 52
                                      ++ +i  + Gp g GK++Llk i    + ++ +++
  gi|488601351|ref|YP_007907822.1| 28 SKGSITTVLGPNGAGKSTLLKTIFGLVRPWNGKIF 62
                                      5678999***************9887777765444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0009      0.77       3      23 ..      31      51 ..      29      86 .. 0.86
   2 ?   -0.8   0.0       1.7   1.4e+03      58      74 ..     150     165 ..     115     200 .. 0.69
   3 ?   -1.7   0.0       3.1   2.7e+03      69      79 ..     220     230 ..     171     233 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0009
                            AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                       i ++ G+  +GK+tllk+++
  gi|488601351|ref|YP_007907822.1| 31 SITTVLGPNGAGKSTLLKTIF 51
                                      6899**************998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                            AAA_14  58 eklkeekktylflDEiq 74 
                                       + l++ + ++++lDE +
  gi|488601351|ref|YP_007907822.1| 150 RALMT-NPEIILLDEPS 165
                                       33344.56778888854 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.1
                            AAA_14  69 flDEiqevpew 79 
                                        +DEi+ ++e+
  gi|488601351|ref|YP_007907822.1| 220 TIDEIKDSEEI 230
                                       47888777665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.25       4      42 ..      35      78 ..      33     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                      EEESTTSSHHHHHHHHHT.....STEEESSSTTSSSSEEEEEEE CS
                          MMR_HSR1  4 ivGrpNvGKStLinaltg.....ekaivsdkpgtTrdinegrvk 42
                                      ++G   +GKStL+++++g     +  i  +   +T+ + +++v+
  gi|488601351|ref|YP_007907822.1| 35 VLGPNGAGKSTLLKTIFGlvrpwNGKIFFKDEDVTLMPPHKKVE 78
                                      78999***********9954433334556666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1550.98
//
Query:       gi|488601352|ref|YP_007907823.1|  [L=396]
Description: putative conserved protein containing a ferredoxin-like domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  116.0   0.9    2.1e-33  115.7   0.9    1.1  1  LUD_dom   LUD domain
    4.4e-10   39.9   3.6    9.6e-10   38.8   3.6    1.6  1  Fer4_8    4Fe-4S dicluster domain
    2.1e-09   37.4   1.5     0.0013   18.8   0.1    2.5  2  Fer4_10   4Fe-4S dicluster domain
    3.9e-08   33.8   4.9    7.4e-08   32.9   4.9    1.5  1  Fer4_7    4Fe-4S dicluster domain
    1.5e-07   31.9   6.2    3.6e-07   30.6   6.2    1.7  1  Fer4_17   4Fe-4S dicluster domain
    1.9e-06   27.9   5.9      5e-06   26.6   5.8    1.8  1  Fer4_9    4Fe-4S dicluster domain
    2.1e-05   24.3   1.0    0.00033   20.4   0.1    2.5  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
    4.8e-05   23.3  14.1     0.0036   17.3   4.8    2.3  2  Fer4_6    4Fe-4S binding domain
    8.6e-05   22.7   7.6      0.036   14.6   0.9    2.3  2  Fer4_4    4Fe-4S binding domain
    0.00011   22.0  10.3     0.0034   17.4   1.8    2.3  2  Fer4_2    4Fe-4S binding domain
     0.0002   21.0  12.7     0.0089   15.8   5.1    2.4  2  Fer4      4Fe-4S binding domain
    0.00063   20.5   5.4       0.36   11.7   0.7    2.4  2  Fer4_22   4Fe-4S dicluster domain
    0.00074   20.4   7.1        0.1   13.5   0.8    2.7  2  Fer4_16   4Fe-4S double cluster binding domain
      0.002   18.3   2.9       0.26   11.5   0.1    2.4  2  Fer4_18   4Fe-4S dicluster domain
     0.0057   16.8   9.7      0.037   14.2   9.9    2.1  1  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   15.9   0.1        5.9    7.3   0.0    2.7  2  ACDC      AP2-coincident C-terminal
       0.33   11.5   8.1        6.5    7.4   8.1    2.5  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        1.2    9.9   4.7        2.1    9.2   0.8    2.6  2  Fer4_15   4Fe-4S single cluster 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 !  115.7   0.9   2.1e-36   2.1e-33       3     189 .]      53     279 ..      51     279 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 2.1e-36
                           LUD_dom   3 efienleangaevyyaktaeealelilellkeksv.....................vseggstdlgeigl....... 51 
                                        +i++l++ng++v++a++  +a e+i++ + ++                       ++e+++td+g++ +       
  gi|488601352|ref|YP_007907823.1|  53 AAIKSLKENGFNVFFAEDSSKAIEIIKKEIGKERLvvksksnitkeinlvkeleadGIEVVETDIGDRLIqllnenp 129
                                       689******************************8889999*************************999999****** PP

                           LUD_dom  52 ....apalhsgreevldlfeekl..........treareelrekfltadvgitganfaiAetGtlvlvdnegnrral 114
                                            pa+h   +++  ++++k            ++  ++++e + ++++gi+gan ai+ +G++ + +negn   +
  gi|488601352|ref|YP_007907823.1| 130 shptGPAVHLSLNQISSILDKKYgvrlngpkeiIKFLLKDVKESIQKSKIGISGAN-AITAEGSILVLHNEGNIFEV 205
                                       ********************************************************.******************** PP

                           LUD_dom 115 tflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsrtadielvlvygvhgpkrihvilv 189
                                          p++ i+v+gi+k +p++e+a++ +k  + +at+ +  ++ +++isg s+tadie +l +g h pk+ +vil+
  gi|488601352|ref|YP_007907823.1| 206 ANRPEKWIIVAGIDKFYPNIEEAINSAKIQTFYATG-NIVPSFIEIISGVSKTADIEKKLIKGIHNPKECTVILI 279
                                       ************************************.************************************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 !   38.8   3.6   9.6e-13   9.6e-10       1      65 []     293     352 ..     293     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 9.6e-13
                            Fer4_8   1 elekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       el++Ci+Cg C  +Cp++r ++++ +  r      +     +e++ +l+ C++c++C+++Cp +i
  gi|488601352|ref|YP_007907823.1| 293 ELFHCIGCGNCVINCPAYRVFGEEFKGGRFALYS-AF----YEGKSNLKLCLSCKRCKKNCPLEI 352
                                       579******************9764444444333.22....233688***************876 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.3e-06    0.0013       6      21 ..     294     309 ..     284     325 .. 0.77
   2 !   17.1   0.2   4.4e-06    0.0044       5      24 ..     334     356 ..     331     374 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
                           Fer4_10   6 ddtCirCgkCvkaCPa 21 
                                          Ci+Cg+Cv  CPa
  gi|488601352|ref|YP_007907823.1| 294 LFHCIGCGNCVINCPA 309
                                       5579999999999998 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.4e-06
                           Fer4_10   5 dddtCirCgkCvkaCPadl...t 24 
                                       + + C+ C++C+k CP  +   +
  gi|488601352|ref|YP_007907823.1| 334 NLKLCLSCKRCKKNCPLEIdipK 356
                                       6789************9664331 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   4.9   7.4e-11   7.4e-08       1      50 [.     296     350 ..     296     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 7.4e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.....gtekveidpekClgCgaCvavCPt 50 
                                       +CigCg+Cv +Cp++ +  +e++  +      + + + +   Cl+C++C + CP 
  gi|488601352|ref|YP_007907823.1| 296 HCIGCGNCVINCPAYRVFGEEFKGGRfalysAFYEGKSNLKLCLSCKRCKKNCPL 350
                                       6*****************999855544444444666888999************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 !   30.6   6.2   3.7e-10   3.6e-07       2      61 .]     297     353 ..     296     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.7e-10
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                       Ci+Cg C+ +Cp y+  ++e k  + a++++  e+   +++ +lC++C++C++ CP ++d
  gi|488601352|ref|YP_007907823.1| 297 CIGCGNCVINCPAYRVFGEEFKGGRFALYSAFYEG---KSNLKLCLSCKRCKKNCPLEID 353
                                       ********************999999988876666...79****************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 !   26.6   5.8     5e-09     5e-06       2      49 ..     297     351 ..     296     353 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5e-09
                            Fer4_9   2 CtgCgaCveaCpagvvvedaae..rkarlraase........eaCigCgaCveaCpkg 49 
                                       C+gCg+Cv  Cpa  v +++++  r+a +    +        + C++C++C + Cp +
  gi|488601352|ref|YP_007907823.1| 297 CIGCGNCVINCPAYRVFGEEFKggRFALYS---AfyegksnlKLCLSCKRCKKNCPLE 351
                                       *************99955555500444544...33469******************75 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.19   1.9e+02      12      38 ..     285     309 ..     278     315 .. 0.78
   2 !   20.4   0.1   3.3e-07   0.00033      22      53 ..     336     365 ..     322     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.19
                                       --HHHHHHHHTT----TT-HHHHCSTT CS
                           Fer4_20  12 lteeealeeAsRClqCkkapcvkgCPv 38 
                                       +  e+  +e   C+ C   +cv +CP+
  gi|488601352|ref|YP_007907823.1| 285 YLIENGYKELFHCIGC--GNCVINCPA 309
                                       555666778889****..68999***7 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.3e-07
                                       TT----TT-HHHHCSTT---HHHHHHHHHTT- CS
                           Fer4_20  22 sRClqCkkapcvkgCPveidipefikkiaegn 53 
                                       + Cl+C  + c+k+CP+eidip++i++ +eg 
  gi|488601352|ref|YP_007907823.1| 336 KLCLSC--KRCKKNCPLEIDIPKMISNAREGS 365
                                       56****..78****************999875 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   4.8   3.6e-06    0.0036       9      22 ..     297     310 ..     297     313 .. 0.92
   2 !   11.0   1.9   0.00036      0.35       8      20 ..     337     349 ..     334     357 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                            Fer4_6   9 CigCgdCvrvCPeg 22 
                                       CigCg+Cv++CP++
  gi|488601352|ref|YP_007907823.1| 297 CIGCGNCVINCPAY 310
                                       ************86 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00036
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                       +C++C +C ++CP
  gi|488601352|ref|YP_007907823.1| 337 LCLSCKRCKKNCP 349
                                       8***********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 !   14.6   0.9   3.6e-05     0.036       4      16 ..     297     309 ..     289     317 .. 0.91
   2 !   11.4   0.9   0.00036      0.36       2      16 ..     336     350 ..     335     360 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       CigCg Cv+ CP 
  gi|488601352|ref|YP_007907823.1| 297 CIGCGNCVINCPA 309
                                       ************4 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00036
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C+ C++C   CP 
  gi|488601352|ref|YP_007907823.1| 336 KLCLSCKRCKKNCPL 350
                                       67************5 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.8   3.4e-06    0.0034       9      22 .]     296     309 ..     290     309 .. 0.92
   2 !    9.3   1.6    0.0013       1.3       8      21 ..     336     349 ..     332     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
                            Fer4_2   9 rCigCgaCvsaCPa 22 
                                       +CigCg Cv +CPa
  gi|488601352|ref|YP_007907823.1| 296 HCIGCGNCVINCPA 309
                                       7************8 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0013
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                         C++C+ C ++CP
  gi|488601352|ref|YP_007907823.1| 336 KLCLSCKRCKKNCP 349
                                       57***********9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   5.1     9e-06    0.0089       8      20 ..     297     309 ..     295     310 .. 0.93
   2 !    9.5   0.8   0.00088      0.88       6      19 ..     336     349 ..     333     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9e-06
                                       SSS-THHHHHSTT CS
                              Fer4   8 CigCGaCvevCPv 20 
                                       CigCG+Cv  CP 
  gi|488601352|ref|YP_007907823.1| 297 CIGCGNCVINCPA 309
                                       ************5 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00088
                                       TTSSS-THHHHHST CS
                              Fer4   6 ekCigCGaCvevCP 19 
                                        +C  C++C + CP
  gi|488601352|ref|YP_007907823.1| 336 KLCLSCKRCKKNCP 349
                                       68************ PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.7   0.00036      0.36      78      94 ..     293     309 ..     269     311 .. 0.76
   2 !   10.7   0.3   0.00076      0.76      73      96 .]     329     352 ..     319     352 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       +  +C+GCg C+ +cp+
  gi|488601352|ref|YP_007907823.1| 293 ELFHCIGCGNCVINCPA 309
                                       56789999999999996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00076
                           Fer4_22  73 fkekfgesgCvGCgRCieacpvki 96 
                                       ++ k + + C  C RC+++cp +i
  gi|488601352|ref|YP_007907823.1| 329 YEGKSNLKLCLSCKRCKKNCPLEI 352
                                       555678899***********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 !   13.5   0.8    0.0001       0.1      39      66 ..     284     309 ..     256     310 .. 0.63
   2 !    9.2   0.7    0.0023       2.3       2      14 ..     338     350 ..     337     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                           Fer4_16  39 kdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       k l+e+  k+    +++gC++C+  CPa
  gi|488601352|ref|YP_007907823.1| 284 KYLIENGYKE--LFHCIGCGNCVINCPA 309
                                       3333333333..4889999999999996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0023
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C +C++C + CP 
  gi|488601352|ref|YP_007907823.1| 338 CLSCKRCKKNCPL 350
                                       999********96 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.3    0.0085       8.4      57      73 ..     293     309 ..     267     313 .. 0.80
   2 !   11.5   0.1   0.00026      0.26      60      79 ..     337     356 ..     327     361 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0085
                           Fer4_18  57 gagdcidcescvkvcPt 73 
                                       +  +ci c+ cv  cP 
  gi|488601352|ref|YP_007907823.1| 293 ELFHCIGCGNCVINCPA 309
                                       55679999999999985 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00026
                           Fer4_18  60 dcidcescvkvcPtgidirk 79 
                                        c++c+ c k cP +idi k
  gi|488601352|ref|YP_007907823.1| 337 LCLSCKRCKKNCPLEIDIPK 356
                                       5*****************76 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   9.9   3.7e-05     0.037       7      54 ..     296     351 ..     292     356 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                           Fer4_21   7 kCigCgkCliaCedtshqai..eidaktvl........kvvedeCvGCnlCssvCPve 54 
                                       +CigCg+C+i C+   +     e+++ + +        k   + C  C+ C + CP+e
  gi|488601352|ref|YP_007907823.1| 296 HCIGCGNCVINCPA--YRVFgeEFKGGRFAlysafyegKSNLKLCLSCKRCKKNCPLE 351
                                       6************5..6655556666664455555655667789************84 PP

>> ACDC  AP2-coincident C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0059       5.9       7      33 ..     159     186 ..     154     240 .. 0.69
   2 ?    6.0   0.1     0.014        14      21      67 ..     347     395 ..     332     396 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0059
                              ACDC   7 kKeaikliLeDLlnncl.pqlasslank 33 
                                        Ke+ik++L+D+++++  +++  s+an+
  gi|488601352|ref|YP_007907823.1| 159 PKEIIKFLLKDVKESIQkSKIGISGANA 186
                                       59************99624566666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                              ACDC  21 nclpql..asslanktsskelkrvieahikyvenakslkelqpylklFs 67 
                                       nc +++  ++++ n+++ +e+++ +  h k +++a  l++l  y ++++
  gi|488601352|ref|YP_007907823.1| 347 NCPLEIdiPKMISNAREGSEIYNFLLSHAKWITRAVYLEFLSLYYQIME 395
                                       5554431144555665559*************************99875 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 ?    7.4   8.1    0.0065       6.5       5      54 ..     296     351 ..     293     352 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0065
                           Fer4_13   5 tCiacgaCvelaPd..vFeeddeggasvvae....qptseeekadaeeAadaCPve 54 
                                        Ci+cg+Cv  +P   vF e+ +gg+++ +     ++++ ++   +++  ++CP e
  gi|488601352|ref|YP_007907823.1| 296 HCIGCGNCVINCPAyrVFGEEFKGGRFALYSafyeGKSNLKLCLSCKRCKKNCPLE 351
                                       6************6559*99999997666543333888999999999999999977 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.8    0.0021       2.1       8      23 ..     297     312 ..     294     320 .. 0.83
   2 ?    1.1   0.2      0.68   6.7e+02       7      19 ..     337     349 ..     334     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                           Fer4_15   8 CigcglCvaeapevfe 23 
                                       Cigcg+Cv ++p + +
  gi|488601352|ref|YP_007907823.1| 297 CIGCGNCVINCPAYRV 312
                                       ***********98755 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.68
                           Fer4_15   7 aCigcglCvaeap 19 
                                       +C +c +C +++p
  gi|488601352|ref|YP_007907823.1| 337 LCLSCKRCKKNCP 349
                                       79********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2297.23
//
Query:       gi|488601353|ref|YP_007907824.1|  [L=127]
Description: putative Zn-finger containing protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-11   43.7   1.1    3.7e-11   43.0   1.1    1.3  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
    0.00012   21.4   2.3    0.00023   20.4   2.3    1.4  1  zf-ribbon_3     zinc-ribbon domain
    0.00026   20.9   0.2      0.016   15.2   0.0    2.3  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
     0.0022   17.9   1.0     0.0035   17.3   1.0    1.3  1  zinc-ribbons_6  zinc-ribbons
     0.0034   17.4   0.3     0.0054   16.7   0.3    1.3  1  DZR             Double zinc ribbon
     0.0046   16.9   0.6     0.0077   16.1   0.6    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
  ------ inclusion threshold ------
      0.011   15.8   3.9       0.68   10.1   2.2    2.8  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.023   14.9   0.2      0.034   14.3   0.2    1.4  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.029   13.9   3.8        3.2    7.3   0.2    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.034   14.1   0.5       0.16   12.0   0.2    2.0  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.042   14.6   2.1      0.066   13.9   2.0    1.4  1  RecG_N          RecG N-terminal helical domain
      0.045   14.1   0.5        1.9    8.9   0.0    2.2  2  GFA             Glutathione-dependent formaldehyde-activating
      0.054   13.4   0.1      0.086   12.8   0.1    1.4  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.067   12.9   5.7       0.19   11.5   5.7    1.8  1  zinc_ribbon_2   zinc-ribbon domain
       0.14   11.9   2.8       0.36   10.6   2.8    1.8  1  A2L_zn_ribbon   A2L zinc ribbon domain
       0.16   12.0   0.8         15    5.6   0.5    2.4  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.44   10.8   3.2         13    6.1   0.4    2.3  2  zf-LITAF-like   LITAF-like zinc ribbon domain
        2.4    8.5   5.0         12    6.3   0.2    2.2  2  zinc_ribbon_9   zinc-ribbon
        2.8    8.5   6.4        6.2    7.4   0.4    2.3  2  zf-H2C2_2       Zinc-finger double domain
        3.5    7.7   6.1         20    5.2   6.1    2.0  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


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 !   43.0   1.1   4.1e-14   3.7e-11       5      39 ..      11      43 ..       7      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.1e-14
                     Auto_anti-p27  5 elLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                      +lL kG++ML  +Cp+C++PL++  k+ k++C+ C
  gi|488601353|ref|YP_007907824.1| 11 KLLYKGAKMLPYHCPECNSPLFK--KDDKMFCPYC 43
                                      79*********************..56799***** PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   2.3   2.6e-07   0.00023       3      24 ..      22      45 ..      22      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.6e-07
                       zf-ribbon_3  3 vrCPnCGa.p.lssddnvCpyCGt 24
                                      ++CP+C++ +  ++d ++CpyC +
  gi|488601353|ref|YP_007907824.1| 22 YHCPECNSpLfKKDDKMFCPYCKK 45
                                      69******665688889*****86 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-05     0.016       1      14 [.      23      36 ..      23      38 .. 0.89
   2 ?    3.6   0.0     0.076        68       2      12 ..      40      50 ..      39      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                    DNA_ligase_ZBD  1 hCPvCGsavvReeg 14
                                      hCP+C+s++ ++++
  gi|488601353|ref|YP_007907824.1| 23 HCPECNSPLFKKDD 36
                                      9********98875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.076
                    DNA_ligase_ZBD  2 CPvCGsavvRe 12
                                      CP C  ++v e
  gi|488601353|ref|YP_007907824.1| 40 CPYCKKEAVFE 50
                                      *****999944 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.0   3.9e-06    0.0035       2      26 ..      23      47 ..      22      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-06
                                      --SSS-S--EE-SSEEE-TTT--EE CS
                    zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqedl 26
                                      +CpeC+++l k++++++C  C+++ 
  gi|488601353|ref|YP_007907824.1| 23 HCPECNSPLFKKDDKMFCPYCKKEA 47
                                      7********************9975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3     6e-06    0.0054      14      35 ..      23      44 ..       6      52 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-06
                               DZR 14 fCseCgtklkavaaedrCpsCg 35
                                       C+eC+++l +  ++ +Cp C+
  gi|488601353|ref|YP_007907824.1| 23 HCPECNSPLFKKDDKMFCPYCK 44
                                      3444444444444444444444 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.6   8.5e-06    0.0077       6      27 ..      23      44 ..      19      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.5e-06
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCg 27
                                      +Cp C+ +l ++dD   Cp C+
  gi|488601353|ref|YP_007907824.1| 23 HCPECNSPLFKKDDKMFCPYCK 44
                                      8********************7 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.2   0.00076      0.68       4      15 ..      24      35 ..      23      43 .. 0.81
   2 ?    4.0   1.2     0.059        53       4      19 ..      40      56 ..      38      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00076
                            zf-ACC  4 CpsCgemlykke 15
                                      Cp+C++ l+kk+
  gi|488601353|ref|YP_007907824.1| 24 CPECNSPLFKKD 35
                                      ***********7 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.059
                            zf-ACC  4 CpsC.gemlykkeLern 19
                                      Cp C +e ++ k++e+ 
  gi|488601353|ref|YP_007907824.1| 40 CPYCkKEAVFEKDVENT 56
                                      77783489******986 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   3.8e-05     0.034       9      34 ..      22      48 ..      15      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                      NOB1_Zn_bind  9 lrChaCfk.vtkdmtkkFCpkCGnktL 34
                                      + C  C + ++k+ +k+FCp C ++ +
  gi|488601353|ref|YP_007907824.1| 22 YHCPECNSpLFKKDDKMFCPYCKKEAV 48
                                      68999*9945599*********98765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4     0.004       3.6       1      12 [.      22      33 ..      22      37 .. 0.77
   2 ?    7.3   0.2    0.0036       3.2       1      17 [.      38      55 ..      38      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.004
                                      EEETTTTCEECH CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlv 12
                                      y CP+C+s+ + 
  gi|488601353|ref|YP_007907824.1| 22 YHCPECNSPLFK 33
                                      56******8665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0036
                                      EEETTTTCEE.CHEETST CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.lveDper 17
                                      + CP+C+ +  ++ D e+
  gi|488601353|ref|YP_007907824.1| 38 MFCPYCKKEAvFEKDVEN 55
                                      68*****99988888665 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 ?   12.0   0.2   0.00018      0.16      58      97 ..       8      48 ..       1      62 [. 0.70
   2 ?    0.4   0.0      0.69   6.2e+02      38      59 ..      85     106 ..      79     120 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                      TT-EEEEEEE-.-EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                              HypA 58 egaeLeieevp.vkvrCreCgkefeleekalrCpkCgsadv 97
                                      e+ +L ++  + + ++C eC++   ++++++ Cp C+++ v
  gi|488601353|ref|YP_007907824.1|  8 ESVKLLYKGAKmLPYHCPECNSPLFKKDDKMFCPYCKKEAV 48
                                      5555555543315689*****98887766788*****9865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.69
                                       T--HHHHHHHHHHHHCC.TTTT CS
                              HypA  38 gvepeaLefafellaegtvleg 59 
                                       ++ +e L++++e +++ +++++
  gi|488601353|ref|YP_007907824.1|  85 SILEEKLNYVLEYMKKAKTIDE 106
                                       4556667777777766655443 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.0   7.4e-05     0.066      40      84 ..      79     124 ..      43     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.4e-05
                                       GGGG-HHHH.HHHHHHHHHHTTSSSS-H.HHHHHHHHHHHHHHHHH CS
                            RecG_N  40 plleneevlkeklskfldYikpiasLpe.eRkikRlknglemiekl 84 
                                         ++++++l+ekl+  l+Y+k+ + ++e eR    + +++++iek 
  gi|488601353|ref|YP_007907824.1|  79 LGMNHKSILEEKLNYVLEYMKKAKTIDEiERLTNLADKLVTLIEKI 124
                                       336899********************755999999999999*9995 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0021       1.9      43      64 ..      15      36 ..       3      38 .. 0.78
   2 ?    5.0   0.1     0.034        31      48      68 ..      36      56 ..      33      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                               GFA 43 sgnkvtrsfCpeCgsplysees 64
                                      +g k+  + CpeC spl+ + +
  gi|488601353|ref|YP_007907824.1| 15 KGAKMLPYHCPECNSPLFKKDD 36
                                      57888889**********8655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                               GFA 48 trsfCpeCgsplyseesaape 68
                                      +++fCp C  + ++e++ +++
  gi|488601353|ref|YP_007907824.1| 36 DKMFCPYCKKEAVFEKDVENT 56
                                      579******999987666554 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 ?   12.8   0.1   9.6e-05     0.086       5      33 ..      22      46 ..      21      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                    Zn_ribbon_SprT  5 YrCtgCgreythhlsirrhnYrCrrCkgt 33
                                      Y+C+ C       ++++  ++ C++Ck +
  gi|488601353|ref|YP_007907824.1| 22 YHCPECN---SPLFKKDD-KMFCPYCKKE 46
                                      9******...*****954.588****976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.7   0.00021      0.19       2      19 ..      24      43 ..      23      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                     zinc_ribbon_2  2 CpnCGael.q.dnakFCpyC 19
                                      Cp+C  +l + d+  FCpyC
  gi|488601353|ref|YP_007907824.1| 24 CPECNSPLfKkDDKMFCPYC 43
                                      *********769******** 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 ?   10.6   2.8   0.00041      0.36       3      27 ..      21      43 ..      19      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00041
                     A2L_zn_ribbon  3 lkvCsvCggngilnseqgylvCieC 27
                                      +++C  C+++ ++ ++++ ++C+ C
  gi|488601353|ref|YP_007907824.1| 21 PYHCPECNSP-LF-KKDDKMFCPYC 43
                                      699******9.68.*********99 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5     0.017        15       1       8 [.      23      30 ..      23      34 .. 0.89
   2 ?    4.3   0.0     0.044        40       2      12 ..      40      50 ..      39      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
                         Ogr_Delta  1 rCPhCgap 8 
                                      +CP+C +p
  gi|488601353|ref|YP_007907824.1| 23 HCPECNSP 30
                                      8*****98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.044
                         Ogr_Delta  2 CPhCgapaaar 12
                                      CP+C+++a+  
  gi|488601353|ref|YP_007907824.1| 40 CPYCKKEAVFE 50
                                      *****999765 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.019        17      48      67 ..      13      32 ..       9      35 .. 0.77
   2 ?    6.1   0.4     0.015        13       5      15 ..      37      47 ..      33      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.019
                     zf-LITAF-like 48 cvdslkdvehyCpnCgallg 67
                                      ++++ k   ++Cp+C++ l 
  gi|488601353|ref|YP_007907824.1| 13 LYKGAKMLPYHCPECNSPLF 32
                                      56777888899999998775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                     zf-LITAF-like  5 qvdCpaCqqrv 15
                                      ++ Cp+C+++ 
  gi|488601353|ref|YP_007907824.1| 37 KMFCPYCKKEA 47
                                      68899998876 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.9      0.07        63      24      29 ..      24      29 ..      16      32 .. 0.86
   2 ?    6.3   0.2     0.013        12      19      29 ..      35      45 ..      30      48 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.07
                     zinc_ribbon_9 24 CPhCgg 29
                                      CP+C++
  gi|488601353|ref|YP_007907824.1| 24 CPECNS 29
                                      ****98 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                     zinc_ribbon_9 19 dsdvlCPhCgg 29
                                      d+  +CP+C+ 
  gi|488601353|ref|YP_007907824.1| 35 DDKMFCPYCKK 45
                                      44459****85 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   0.4    0.0069       6.2      14      21 ..      21      28 ..      14      29 .. 0.85
   2 ?    3.9   1.0     0.093        84      17      23 ..      40      46 ..      32      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0069
                         zf-H2C2_2 14 pyeCplCd 21
                                      py+Cp+C+
  gi|488601353|ref|YP_007907824.1| 21 PYHCPECN 28
                                      8******8 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.093
                         zf-H2C2_2 17 CplCdka 23
                                      Cp+C+k 
  gi|488601353|ref|YP_007907824.1| 40 CPYCKKE 46
                                      *****96 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.1     0.022        20       3      28 ..      21      46 ..      19      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
                    PhnA_Zn_Ribbon  3 p.kCplCaSeytY.edgallvCpeCahE 28
                                      p +Cp+C+S  ++   ++ + Cp C+ E
  gi|488601353|ref|YP_007907824.1| 21 PyHCPECNS--PLfKKDDKMFCPYCKKE 46
                                      668*****9..66688888999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 746.16
//
Query:       gi|488601354|ref|YP_007907825.1|  [L=86]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  107.9   0.9    2.1e-31  107.8   0.9    1.0  1  UPF0147      Uncharacterised protein family (UPF0147)
     0.0026   18.0   0.1        2.1    8.7   0.0    2.2  2  UPF0253      Uncharacterised protein family (UPF0253)
  ------ inclusion threshold ------
      0.094   12.4   0.0       0.11   12.2   0.0    1.0  1  Raco_middle  RACo middle region
       0.11   11.0   0.1       0.13   10.8   0.1    1.0  1  AATase       Alcohol acetyltransferase


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 !  107.8   0.9   4.8e-35   2.1e-31       5      81 .]       6      82 ..       2      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 4.8e-35
                                      HHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                           UPF0147  5 ikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                       +ev+++L++ii d+svPrniR+ a+e+ke+L + +eslavra++ais L+e+++Dpn+P+h+Rtliw+v s+LE+i
  gi|488601354|ref|YP_007907825.1|  6 PQEVLDVLDRIIFDDSVPRNIRKLANEIKEDLIHGEESLAVRASSAISQLEEVASDPNLPMHVRTLIWNVSSQLERI 82
                                      689************************************************************************97 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0012       5.4      30      51 ..       9      30 ..       4      32 .. 0.90
   2 !    8.7   0.0   0.00047       2.1      28      48 ..      49      69 ..      43      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                           UPF0253 30 alktLdevaanealpeevrekA 51
                                      +l +Ld++  ++++p+++r  A
  gi|488601354|ref|YP_007907825.1|  9 VLDVLDRIIFDDSVPRNIRKLA 30
                                      799****************866 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00047
                           UPF0253 28 scalktLdevaanealpeevr 48
                                      s a+  L+eva++ +lp +vr
  gi|488601354|ref|YP_007907825.1| 49 SSAISQLEEVASDPNLPMHVR 69
                                      46899**************99 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.11      40      97 ..      11      68 ..       6      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                       Raco_middle 40 DvlsRiayakeeeegleklqkavveeinelieelleeagiekeeiyevvvagNttMlh 97
                                      Dvl Ri + ++ + +++kl +++ e++ +  e+l+ +a+ + ++++ev+   N  M+ 
  gi|488601354|ref|YP_007907825.1| 11 DVLDRIIFDDSVPRNIRKLANEIKEDLIHGEESLAVRASSAISQLEEVASDPNLPMHV 68
                                      9************************************************999999985 PP

>> AATase  Alcohol acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   2.9e-05      0.13      79     142 ..       7      67 ..       3      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.9e-05
                            AATase  79 eDyvkviekiklddvvlneqpe.ysellekileeykdddekvdeelnellselvipvgdpkkPlw 142
                                       ++ + v+++i +dd v    p   ++l ++i e+  + +e+   + ++++s+l     dp+ P  
  gi|488601354|ref|YP_007907825.1|   7 QEVLDVLDRIIFDDSV----PRnIRKLANEIKEDLIHGEESLAVRASSAISQLEEVASDPNLPMH 67 
                                       567899**********....6559*************************************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 592.58
//
Query:       gi|488601355|ref|YP_007907826.1|  [L=115]
Description: hypothetical protein Asulf_01865 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-27   94.6   0.2    4.5e-27   94.4   0.2    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 !   94.4   0.2   2.5e-31   4.5e-27       1     111 [.       4     111 ..       4     112 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 2.5e-31
                                       EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEE CS
                      Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviil 77 
                                       vlivdDdplvr++l+++l  ++y +v eae+gkea++l+k  k+dl+l+D+ mp+mdG+++ ++i + dp+ ++i +
  gi|488601355|ref|YP_007907826.1|   4 VLIVDDDPLVRSILKSMLS-KEY-KVYEAENGKEAIALYKVYKPDLVLMDVVMPEMDGIKASEMILKIDPNAKIIGV 78 
                                       8*****************9.778.9**************************************************** PP

                                       ESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                      Response_reg  78 tahseeedavealkagaddflsKpfdpeeLlkal 111
                                       ta+++    +e ++aga ++l Kp+++e+L +++
  gi|488601355|ref|YP_007907826.1|  79 TAYAK-GKGKELVNAGALEVLEKPITRERLSERM 111
                                       ***97.8899********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 761.47
//
Query:       gi|488601356|ref|YP_007907827.1|  [L=171]
Description: hypothetical protein Asulf_01868 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.4   0.2        0.1   12.3   0.2    1.5  1  Wza_C           Outer-membrane lipoprotein Wza C-terminal dom
        0.1   13.2  47.9    1.8e+04  -13.2  47.9    3.2  1  KRTAP           Keratin-associated matrix


Domain annotation for each model (and alignments):
>> Wza_C  Outer-membrane lipoprotein Wza C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.2e-05       0.1      10      27 ..     119     136 ..     119     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                             Wza_C  10 IsQLLPTItgvndlteaa 27 
                                       Is LLPT + +ndl++a+
  gi|488601356|ref|YP_007907827.1| 119 ISLLLPTTNALNDLSSAT 136
                                       9**************986 PP

>> KRTAP  Keratin-associated matrix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -13.2  47.9         2   1.8e+04       6      59 ..       5      59 ..       1     127 [. 0.75

  Alignments for each domain:
  == domain 1  score: -13.2 bits;  conditional E-value: 2
                             KRTAP  6 nyyGGlgYGsg.gyGglgcgygcgygsirrlGyGsGggygyGsGYGgyGygcgrp 59
                                       y  G+g Gsg g+G +g+g+g g++ + + G  +G g g+G+G G +G g g +
  gi|488601356|ref|YP_007907827.1|  5 TYRTGVGVGSGvGVGVVGTGVGVGVDVGVGSGVDVGVGVGSGVGVGVVGTGVGVG 59
                                      6778889999888888888888887755444444445555555555333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      123  (0.00686039); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1095.86
//
Query:       gi|488601357|ref|YP_007907828.1|  [L=1168]
Description: hypothetical protein Asulf_01869 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-09   37.0   3.1    4.9e-09   35.9   3.1    1.6  1  PGF-CTERM  PGF-CTERM motif
    2.1e-05   25.5   4.5       0.19   12.8   0.1    4.8  4  CopC       CopC domain
  ------ inclusion threshold ------
      0.016   15.6   1.5       0.22   12.0   0.1    3.6  4  MG2        MG2 domain
      0.017   15.1   3.4      0.075   13.0   0.1    3.7  4  CE2_N      Carbohydrate esterase 2 N-terminal
      0.074   12.8   0.2         31    4.4   0.0    3.3  2  Big_3_4    Domain of unknown function
       0.12   12.0   0.0       0.38   10.4   0.0    1.8  1  EF-hand_1  EF hand
       0.63   10.0  10.3         13    5.7   0.3    5.2  5  FlgD_ig    FlgD Ig-like domain


Domain annotation for each model (and alignments):
>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   3.1   1.9e-12   4.9e-09       1      23 []    1145    1167 ..    1145    1167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.9e-12
                         PGF-CTERM    1 tPGFGavlAlaGLLaaalLaRRr 23  
                                        +PGF +v+A+aGLLa+a+L+RRr
  gi|488601357|ref|YP_007907828.1| 1145 IPGFKIVYAIAGLLAVAYLLRRR 1167
                                        6*********************9 PP

>> CopC  CopC 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      19      38 ..     120     142 ..     115     155 .. 0.69
   2 !   12.8   0.1   7.4e-05      0.19       8      92 .]     279     361 ..     276     361 .. 0.82
   3 !    6.6   0.0    0.0062        16       4      72 ..     694     802 ..     692     812 .. 0.67
   4 ?    3.5   0.1      0.06   1.5e+02      35      91 ..     860     918 ..     836     919 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7
                              CopC  19 peevtLtFsepvel...skvkvt 38 
                                       p  v + F+e+v++   + +++t
  gi|488601357|ref|YP_007907828.1| 120 PILVGIYFKEKVNDgsfTWINIT 142
                                       666889999*9999555444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.4e-05
                              CopC   8 tPaagatvaaapeevtLtFsepvelskvkvtdpdgke.evetvdaktveaelkvplpelaaGtYtVewrvvsaDGHp 83 
                                       +Pa+g+ ++a+ +++++++s  +++s++k+   +++  +  tvd++t   +++ + ++la+G++tV+ + + +D   
  gi|488601357|ref|YP_007907828.1| 279 SPADGSYINANATTISVRYS-LIDPSTIKMFVDGNNVtSSITVDQNT--STITYQATNLAEGAHTVKINGTGTDNSG 352
                                       7******************8.5889*****98776445333555555..66777777899**************999 PP

                              CopC  84 vsGsfsFtv 92 
                                        s ++sFtv
  gi|488601357|ref|YP_007907828.1| 353 HSLTWSFTV 361
                                       898999987 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0062
                              CopC   4 lvsstPaagatvaaapeevtLtFsepvel.skvkvtdpdgke................................... 44 
                                       l + +P+ +++v  a  +v+++F++++++ s+v++ d + ++                                   
  gi|488601357|ref|YP_007907828.1| 694 LANNKPTMDTSV-VAGGKVKISFNQQIKAvSAVAIKDVKYDAavrmditqgllnianitlnyggkalkeiillnkht 769
                                       667889999999.999***********99988888777643345666666666666666666666666666666666 PP

                              CopC  45 .....evetvdaktveaelkvplpelaaGtYtV 72 
                                            e   + a t+++el+ + + l+ GtY+V
  gi|488601357|ref|YP_007907828.1| 770 niwipERMVKAAYTSSNELELDTSGLETGTYRV 802
                                       666653334444455556666666666666666 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.06
                              CopC  35 vkvtdpdgke....evetvdaktveaelkvplpelaaGtYtVewrvvsaDGHpvsGsfsFt 91 
                                       v +t p+g++    ++++  +++ + +++vp++  ++G+YtV+ + +   G   ++s++F+
  gi|488601357|ref|YP_007907828.1| 860 VYLTYPNGTKvsvvDLSNIGKESYSGTFTVPMT--QSGAYTVSAETTDIAGNLATDSIKFS 918
                                       455555555555554444445555667777777..********999999999999999986 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         2   5.1e+03      35      71 ..     302     338 ..     290     361 .. 0.71
   2 ?   -2.0   0.0         2   5.1e+03      13      44 ..     509     540 ..     503     550 .. 0.78
   3 ?   -2.8   0.0       3.7   9.4e+03      71      81 ..     795     805 ..     782     815 .. 0.71
   4 ?   12.0   0.1   8.4e-05      0.22      33      93 ..     855     914 ..     834     916 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2
                                       EEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT- CS
                               MG2  35 plkltirdpdgkevkelplatdetggaesefalpeaa 71 
                                       p ++++  ++++++++ +++++++ +  +  +l e+a
  gi|488601357|ref|YP_007907828.1| 302 PSTIKMFVDGNNVTSSITVDQNTSTITYQATNLAEGA 338
                                       6677777778888888887777776666666665554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                                       TT-EEEEEEEEESTTCSB---EEEEEEEE-TT CS
                               MG2  13 PgetVslkallrdetlqglaklplkltirdpd 44 
                                       Pg + ++++++ +++ +++++ p ++ ++d++
  gi|488601357|ref|YP_007907828.1| 509 PGSKTNYTVYIDNNANKTITSFPSTAIVYDEN 540
                                       78888888888888888888888877777766 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.7
                                       --SEEEEEEEE CS
                               MG2  71 aklGeysvels 81 
                                        ++G+y+v++ 
  gi|488601357|ref|YP_007907828.1| 795 LETGTYRVYVV 805
                                       57999999983 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 8.4e-05
                                       -EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT-EEEEE CS
                               MG2  33 klplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaeeslssgs 93 
                                        + lk++++ p+g +v+  +l +  + +++++f++p ++  G y+v++++ + +++l++ s
  gi|488601357|ref|YP_007907828.1| 855 LDTLKVYLTYPNGTKVSVVDLSNIGKESYSGTFTVPMTQ-SGAYTVSAETTDIAGNLATDS 914
                                       3789******************999***********875.7*******9888888887776 PP

>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.5     9e+03      40      55 ..     200     215 ..     191     231 .. 0.67
   2 ?   13.0   0.1   2.9e-05     0.075      19      82 ..     283     343 ..     280     364 .. 0.80
   3 ?   -0.8   0.0      0.58   1.5e+03      43      61 ..     512     531 ..     502     541 .. 0.77
   4 ?   -2.6   0.0       2.1   5.4e+03      20      48 ..     832     860 ..     827     879 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.5
                                       SSS-EEEEEEETTS-- CS
                             CE2_N  40 dkgknrlaviiDgkrv 55 
                                         +++ ++v+i+g + 
  gi|488601357|ref|YP_007907828.1| 200 GINTTLVKVYINGTEL 215
                                       5666777888888764 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.9e-05
                                       T-EEEEEEEEEEEEEEEEE..SSS-EEEEEEETTS-.-EEEEE-SS-EEEE.EEEEEEEEEEEEEE CS
                             CE2_N  19 GtsvefrftGtslsvrlkdkedkgknrlaviiDgkr.vkdlkldgeektyt.laeglepgehtvrl 82 
                                       G+++ ++ t  s++ +l d      + +++++Dg+  ++++++d++++t+t  a++l++g htv++
  gi|488601357|ref|YP_007907828.1| 283 GSYINANATTISVRYSLID-----PSTIKMFVDGNNvTSSITVDQNTSTITyQATNLAEGAHTVKI 343
                                       7888888888888888888.....99**********5566777666666552589*********99 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.58
                                       -EEEEEEETTS--EEEEE.- CS
                             CE2_N  43 knrlaviiDgkrvkdlkl.d 61 
                                       k+ ++v+iD+++ k+++  +
  gi|488601357|ref|YP_007907828.1| 512 KTNYTVYIDNNANKTITSfP 531
                                       67899******988886544 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.1
                                       -EEEEEEEEEEEEEEEEE..SSS-EEEEE CS
                             CE2_N  20 tsvefrftGtslsvrlkdkedkgknrlav 48 
                                       +++ ++f+G+ + v+ + +++++   l+v
  gi|488601357|ref|YP_007907828.1| 832 VYLDVSFSGNNANVSYSASDTNELDTLKV 860
                                       78889999999999988855555555555 PP

>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.012        31      32      63 ..     796     827 ..     781     852 .. 0.86
   2 ?    4.4   0.0     0.012        31      26      50 ..     887     911 ..     873     914 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                           Big_3_4  32 edGeyvvellaedeaGnqayiakllyvvdien 63 
                                       e G y v ++a+d+     yi +ll +v ++ 
  gi|488601357|ref|YP_007907828.1| 796 ETGTYRVYVVALDNDYKVFYIGELLLTVTTDT 827
                                       6799************************9875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.012
                           Big_3_4  26 vpvPldedGeyvvellaedeaGnqa 50 
                                        +vP+ ++G y v   + d aGn a
  gi|488601357|ref|YP_007907828.1| 887 FTVPMTQSGAYTVSAETTDIAGNLA 911
                                       59*********************76 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.38       6      24 ..     371     389 ..     369     393 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                       HHHHTTTSSSEEEHHHHHH CS
                         EF-hand_1   6 FrefDkDgdGkIdfeEfke 24 
                                       F + D DgdG+I+++E ++
  gi|488601357|ref|YP_007907828.1| 371 FTISDSDGDGFIERNEVLT 389
                                       6777************876 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3    0.0053        13      28      61 ..     317     350 ..     301     357 .. 0.75
   2 ?    5.1   0.0    0.0082        21      12      40 ..     419     447 ..     409     450 .. 0.80
   3 ?   -0.7   0.1      0.52   1.3e+03      18      41 ..     508     531 ..     501     535 .. 0.80
   4 ?   -2.0   0.0       1.4   3.5e+03      64      77 ..     795     808 ..     790     810 .. 0.80
   5 ?    0.7   0.1      0.18   4.7e+02      64      76 ..     892     904 ..     839     907 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0053
                                       EEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS CS
                           FlgD_ig  28 tikDasGevVrtidlgaqsaGvvsftWdGtdndG 61 
                                       +i+ ++++   t ++++ ++G ++++ +Gt+ d 
  gi|488601357|ref|YP_007907828.1| 317 SITVDQNTSTITYQATNLAEGAHTVKINGTGTDN 350
                                       55555555556889999**********9987664 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0082
                                       EEEEEE.ESSSEEEEEEEE-SS--EEEEE CS
                           FlgD_ig  12 aplgvelpeaadevtvtikDasGevVrti 40 
                                       +  +++l++   + +++++D++G+ V++ 
  gi|488601357|ref|YP_007907828.1| 419 STKQFTLDSYGNKIKIRVYDKAGNFVDSA 447
                                       4556779999999*************875 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.52
                                       .ESSSEEEEEEEE-SS--EEEEEE CS
                           FlgD_ig  18 lpeaadevtvtikDasGevVrtid 41 
                                       +p + +++tv i + +++++ +  
  gi|488601357|ref|YP_007907828.1| 508 VPGSKTNYTVYIDNNANKTITSFP 531
                                       67778899**********998765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.4
                                       --SEEEEEEEEEET CS
                           FlgD_ig  64 ladGaYtvkvtats 77 
                                       l+ G+Y+v v+a +
  gi|488601357|ref|YP_007907828.1| 795 LETGTYRVYVVALD 808
                                       789*******9976 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.18
                                       --SEEEEEEEEEE CS
                           FlgD_ig  64 ladGaYtvkvtat 76 
                                        ++GaYtv++++t
  gi|488601357|ref|YP_007907828.1| 892 TQSGAYTVSAETT 904
                                       5789999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 6898.53
//
Query:       gi|488601358|ref|YP_007907829.1|  [L=271]
Description: hypothetical protein Asulf_01870 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.4   0.0        0.1   12.7   0.0    2.1  1  ETRAMP    Malarial early transcribed membrane protein (ETRAMP
      0.074   13.3   9.8        2.3    8.5   9.8    2.7  1  Cohesin   Cohesin domain


Domain annotation for each model (and alignments):
>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    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       1      61 [.       1     199 [.       1     224 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                            ETRAMP   1 MKvtkvllffafLlavnlltpeslcdevnkkk............................................. 32 
                                       M+v k++++++f+l+   l+++s  ++ +k +                                             
  gi|488601358|ref|YP_007907829.1|   1 MNVRKIFYLIFFCLLAVHLVSGSQINVKTKVEnsyvvvgvslenftgklalgsflikydpnhvefveydktlngyiy 77 
                                       9*****99999988888888888888888766789999999999999999999999998888888888888888888 PP

                            ETRAMP  33 ............................................................................. 32 
                                                                                                                    
  gi|488601358|ref|YP_007907829.1|  78 aifdeykevgiikmslynvspqilrnptlfslvfeckegsfsdewvnvtalelrdyngnvistgykyismennitiq 154
                                       88888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                            ETRAMP  33 ................ekakkaikkiddkiekkkkkkKliiisti 61 
                                                         ++ ++    d+ +k+++ +K  + st+
  gi|488601358|ref|YP_007907829.1| 155 knvhpeqsskpkteitVEQNSNFGGYADNTQKNNSENKVTVNSTV 199
                                       888888888888888856666666666666666666666555554 PP

>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   9.8   0.00025       2.3      12      52 ..      32      72 ..      22     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00025
                                      TTSEEEEEEEEESECTTEEEEEEEEEE.TTTEEEEEEEE-T CS
                           Cohesin 12 vGdtvtvpvtvsnvskkvaaaqftikYDpavlevvsvkaGs 52
                                        + v v v+++n ++k+a  +f ikYDp+ +e+v++++  
  gi|488601358|ref|YP_007907829.1| 32 ENSYVVVGVSLENFTGKLALGSFLIKYDPNHVEFVEYDKTL 72
                                      467799*****************************877633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1346  (0.0750739); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1771.02
//
Query:       gi|488601359|ref|YP_007907830.1|  [L=2362]
Description: hypothetical protein Asulf_01871 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  123.4  37.0    8.9e-21   74.1   2.6    6.9  6  CARDB            CARDB
    1.6e-11   44.6  55.6      5e-05   23.8   1.5   11.8 12  VCBS             Repeat domain in Vibrio, Colwellia, Bradyrhi
    5.4e-08   32.2   1.7     0.0011   18.0   0.5    2.3  2  TED_complement   A-macroglobulin TED domain
    0.00066   19.5   0.0     0.0045   16.8   0.0    2.6  1  PEGA             PEGA domain
     0.0068   16.1   1.7       0.32   10.8   0.0    3.4  3  Prenyltrans      Prenyltransferase and squalene oxidase repea
  ------ inclusion threshold ------
      0.019   14.6   0.2      0.049   13.3   0.2    1.6  1  Lysyl_oxidase    Lysyl oxidase
      0.081   12.0   0.0       0.21   10.7   0.0    1.6  2  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
        2.4    8.2   8.6         10    6.2   0.1    4.7  5  PQQ              PQQ enzyme repeat


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 !   74.1   2.6     4e-24   8.9e-21       1      99 [.     715     811 ..     715     814 .. 0.97
   2 !   19.4   2.3   4.1e-07   0.00091      49     102 .]     897     953 ..     862     953 .. 0.85
   3 !   47.2   1.2   9.1e-16     2e-12       1     102 []     959    1056 ..     959    1056 .. 0.95
   4 ?   -3.2   3.6       4.6     1e+04      36      93 ..    1849    1916 ..    1833    1918 .. 0.59
   5 ?    3.0   0.1     0.056   1.2e+02      50      88 ..    1937    1978 ..    1926    1982 .. 0.65
   6 ?   -3.7   0.0       6.5   1.5e+04      36      66 ..    2117    2146 ..    2094    2154 .. 0.51

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 4e-24
                                       S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CE CS
                             CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteatege 77 
                                       +pDLtv ++  ++ ++ +e+++i++tvkN G+a+s +t+++ly++g+ v+t++vp+La++++++ s+++t + +eg 
  gi|488601359|ref|YP_007907830.1| 715 KPDLTV-SIECVDHLNINEQLQINLTVKNIGSANSNSTTLDLYVSGTRVQTFNVPQLAPNAEAKFSYSYTFT-SEGL 789
                                       69****.99999***********************************************************9.**** PP

                                       EEEEEEESTT-SS--SSCCCSE CS
                             CARDB  78 vtltvvvDpdnevaEsnEtNNe 99 
                                       +++++vvDp+n  +E nE NN 
  gi|488601359|ref|YP_007907830.1| 790 HEIKAVVDPGNANDELNELNNF 811
                                       *********************6 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 4.1e-07
                                       EEEEEESEE-CTEEEEEEEEEE-S...-S-CEEEEEEEESTT-SS--SSCCCSEEEE CS
                             CARDB  49 vgtvtvpsLaagesttvsftwtte...ategevtltvvvDpdnevaEsnEtNNeltk 102
                                        g+ +++ L+a++  + s t +++   +  g +t++++vD++n+++E nE NN+ t+
  gi|488601359|ref|YP_007907830.1| 897 IGQEELNDLNADGVLNLSDTAVVDassIDVGCYTFNITVDSNNDIEEINEGNNNATR 953
                                       367778999999999999999998777788***********************9885 PP

  == domain 3  score: 47.2 bits;  conditional E-value: 9.1e-16
                                        S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S- CS
                             CARDB    1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteate 75  
                                        +pDL+   ++ + ++ +  + ++++ v N G+  +++t+++ly++ +lv+t ++p L++ge  ++s+++  +  +
  gi|488601359|ref|YP_007907830.1|  959 QPDLVP--IVLAPDLINPGTANFEIVVVNIGDVWAKQTNASLYINNNLVNTYSIPLLKPGEFWNISVNYNFP--A 1029
                                        589999..77788888888899*************************************************9..9 PP

                                        CEEEEEEEESTT-SS--SSCCCSEEEE CS
                             CARDB   76 gevtltvvvDpdnevaEsnEtNNeltk 102 
                                        g + +t+v+D+d+  aE nE NN++tk
  gi|488601359|ref|YP_007907830.1| 1030 GIHNITLVADSDDVEAELNEGNNTFTK 1056
                                        ************************986 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 4.6
                                        EEEEEEEEETTEEEEEEEE......SEE-C...TEEEEEEEEEE-S.-S-CEEEEEEEESTT-SS--S CS
                             CARDB   36 gatkvalyldgelvgtvtv......psLaa...gesttvsftwtte.ategevtltvvvDpdnevaEs 93  
                                        ga+  +++++ ++ + ++v      +++++   +e+t+++++ +   + +g++ ++v+v+ + +va +
  gi|488601359|ref|YP_007907830.1| 1849 GAVVKDVTVNSTNPKVIIVltpdelNAVNSngtSENTNRRIHTVNVtRVSGDSLVIVSVENEQTVAQT 1916
                                        45555566666665555557775553333310033344444444335788999999999999999876 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.056
                                        EEEEESEE-CTEEEEEEEEEE-S...-S-CEEEEEEEESTT- CS
                             CARDB   50 gtvtvpsLaagesttvsftwtte...ategevtltvvvDpdn 88  
                                        gtv+++s++ +++ + ++  t +    + +++++tv vD +n
  gi|488601359|ref|YP_007907830.1| 1937 GTVKIASMEVQQQNELTILPTLPdnmVEGKSYEVTVRVDNNN 1978
                                        566667777777777776666666633344444777777776 PP

  == domain 6  score: -3.7 bits;  conditional E-value: 6.5
                                        EEEEEEEEETTEEEEEEEESEE-CTEEEEEE CS
                             CARDB   36 gatkvalyldgelvgtvtvpsLaagesttvs 66  
                                        g++k+++  +g +  +++v sL++g+++t s
  gi|488601359|ref|YP_007907830.1| 2117 GSHKIRISKSGYVPVEFDV-SLNPGDNVTYS 2146
                                        3333333333333333333.55555555555 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   1.5   2.2e-08     5e-05       1      61 []     200     266 ..     200     266 .. 0.76
   2 !   21.5   1.4   1.2e-07   0.00026       1      61 []     255     312 ..     255     312 .. 0.81
   3 !    6.8   0.6    0.0047        10       1      19 [.     301     319 ..     301     361 .. 0.72
   4 !   12.4   1.8   8.1e-05      0.18       1      61 []     391     451 ..     391     451 .. 0.81
   5 ?    5.4   0.5     0.013        29       1      27 [.     440     466 ..     440     476 .. 0.71
   6 !    9.3   3.5   0.00073       1.6      16      61 .]     532     587 ..     483     587 .. 0.66
   7 !    9.1   0.7    0.0009         2      41      60 ..     611     630 ..     593     631 .. 0.81
   8 !    6.3   0.0    0.0067        15       1      14 [.     681     697 ..     681     710 .. 0.70
   9 ?   -1.8   0.1       2.2   4.9e+03      26      57 ..     879     911 ..     875     913 .. 0.72
  10 ?   -0.8   0.0       1.1   2.4e+03      12      37 ..    1037    1063 ..    1035    1080 .. 0.67
  11 ?   -1.4   0.2       1.6   3.7e+03      45      54 ..    2265    2274 ..    2215    2279 .. 0.50
  12 ?    2.9   1.2     0.074   1.7e+02      11      54 ..    2276    2323 ..    2268    2325 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.2e-08
                              VCBS   1 DldgDGrlDlvva......ndgg....lrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDllv 61 
                                       Dl+gDG  D+v+a      n +g     +v++n  dG  ++ ++++l+++  + ++++ Dl+gDG  D+++
  gi|488601359|ref|YP_007907830.1| 200 DLNGDGAKDFVFAihtydpN-EGgmvyKVVALNGVDG--SELWNVPLASH-EISHITADDLNGDGLKDIVI 266
                                       9**************87542.3335545555555555..67777777765.7999**************85 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.2e-07
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDllv 61 
                                       Dl+gDG+ D+v++  +++   rn+g+     vt + ++ s  +++  + D+D+DG  +++v
  gi|488601359|ref|YP_007907830.1| 255 DLNGDGLKDIVIFCGDAIFAVRNDGSL---LVTYINSSLSISHWNYGITDVDNDGFKEIIV 312
                                       9************98888888887553...4566666667777778889**********98 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0047
                              VCBS   1 DldgDGrlDlvvan.dgglr 19 
                                       D+d+DG+ +++v+  d+  +
  gi|488601359|ref|YP_007907830.1| 301 DVDNDGFKEIIVGAtDSD-W 319
                                       9***********952332.2 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 8.1e-05
                              VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDllv 61 
                                       D+d++Gr D+++ + +gg +v++  +  +++  ++ +++   + +   v D DgDG +D+lv
  gi|488601359|ref|YP_007907830.1| 391 DFDNNGRKDVLLKYsQGGKYVLEAINGSSGETFWTRTFDYEPNVY-SPVDDKDGDGIEDVLV 451
                                       9***********965899999999877777877777776655444.3489**********98 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.013
                              VCBS   1 DldgDGrlDlvvandgglrvyrnngdG 27 
                                       D dgDG  D++v+ dg+ +v +  g++
  gi|488601359|ref|YP_007907830.1| 440 DKDGDGIEDVLVSLDGPYTVILSGGNN 466
                                       569*********977776666665543 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.00073
                              VCBS  16 gglrvyrnngdGtftdvtktslgg..........sgggtg...vavgDlDgDGdlDllv 61 
                                       g+++ + n+ +G+f+ v     g           s+  +g     vgDl gDG lD++v
  gi|488601359|ref|YP_007907830.1| 532 GNNYDWKNH-TGNFKLVKLEVNGNelwnlsrdyvSN--AGldlFCVGDLTGDGVLDYVV 587
                                       333334443.78888776532222233343343322..3344456************98 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.0009
                              VCBS  41 gggtgvavgDlDgDGdlDll 60 
                                       ++ + + +gD+DgDG+ Dl+
  gi|488601359|ref|YP_007907830.1| 611 NTVFYIFLGDFDGDGKGDLF 630
                                       55566899**********97 PP

  == domain 8  score: 6.3 bits;  conditional E-value: 0.0067
                              VCBS   1 DldgDGrlDlvva...n 14 
                                       D++gDG  Dl+++   +
  gi|488601359|ref|YP_007907830.1| 681 DVNGDGAKDLIAVlnpY 697
                                       9**********987542 PP

  == domain 9  score: -1.8 bits;  conditional E-value: 2.2
                              VCBS  26 dGtftdvtktslggsgggtg.vavgDlDgDGdl 57 
                                       d tf  +++++++++ ++ g   + Dl+ DG l
  gi|488601359|ref|YP_007907830.1| 879 DKTFDLSATYKGHSYSTSIGqEELNDLNADGVL 911
                                       567777777777777766652468899999976 PP

  == domain 10  score: -0.8 bits;  conditional E-value: 1.1
                              VCBS   12 vandgglrvyrnngdGtftdv.tktsl 37  
                                        va+++ ++  +n+g++tft+  t+ +l
  gi|488601359|ref|YP_007907830.1| 1037 VADSDDVEAELNEGNNTFTKMlTAAIL 1063
                                        67778888899*******976233333 PP

  == domain 11  score: -1.4 bits;  conditional E-value: 1.6
                              VCBS   45 gvavgDlDgD 54  
                                        g  +gD+DgD
  gi|488601359|ref|YP_007907830.1| 2265 GRKLGDVDGD 2274
                                        3468999999 PP

  == domain 12  score: 2.9 bits;  conditional E-value: 0.074
                              VCBS   11 vvandgglrvyrnngdGtftdvtkt...slgg.sgggtgvavgDlDgD 54  
                                         v+++++++v+r+n   t+++ + +     ++ ++++ + + gD+DgD
  gi|488601359|ref|YP_007907830.1| 2276 GVTDWDSWVVLRYNYEKTLENMGIQvqrHPDTsYMWSKSSVYGDVDGD 2323
                                        56778889999999999*9988765433223336666689*******9 PP

>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.9e-05     0.042      16      88 ..    1478    1554 ..    1466    1616 .. 0.81
   2 !   18.0   0.5     5e-07    0.0011      43     203 ..    1647    1821 ..    1638    1848 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                        TTHHHHHSSS--SSHHHHGGGTHHHHHHHHHHHHTTGTTTSHHHHHHHHHHHHHHHHHT....CBETTSEBBSSS CS
                    TED_complement   16 penlesLlrlPygcgEqnmvllapnvyvlkYLekteqltkeikkkaleklekgyqrqls....ykkadgsysafg 86  
                                         ++l+ L++ Pygc Eq+ + l   + +  Y ++    +   + ++ + +  g+q+  +     ++++gs+s++g
  gi|488601359|ref|YP_007907830.1| 1478 LRGLDYLVQYPYGCVEQTTSRLLGALHTDWYYRTKGYPDVYDSARVNKSIMMGVQSLAKggvrGQHDNGSWSMWG 1552
                                        568999***************************99999998888888888888888654221167*********9 PP

                                        .. CS
                    TED_complement   87 kd 88  
                                         +
  gi|488601359|ref|YP_007907830.1| 1553 WN 1554
                                        43 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5e-07
                                        HHHH.HHHTTGTTTSHHHHHHHHHHHHHHHHHTCBETTSEBBSSS........SS-BEHHHHHHHHHHHHHCHHH CS
                    TED_complement   43 vlkY.Lekteqltkeikkkaleklekgyqrqlsykkadgsysafg.kd.....ssegstWLtAfvlkvlaqakef 110 
                                        v++Y L +   ++  +k+ a +++ +  +  +s +++dg++  +g kd     s + st L+ + lk +   ++ 
  gi|488601359|ref|YP_007907830.1| 1647 VSHYqLINEGLINSSAKQVANQTMANVTKYLVSVQNSDGGWNQWGaKDdpakpSDAISTALSVWGLKLYGTPSDE 1721
                                        5555344455566778899999999999999999***********844676677788999999999999997777 PP

                                        ST..--HHHHHHHHHHHHTTB-...TTS-B--SS-SS-TTCSSSTHCHHHHHHHHHHHHHHHHTTCS....HHHH CS
                    TED_complement  111 if..ideeeiseslewLlseQk...edGsFkeegsllnrkmkggvekevtLtAyvliaLleakeile....lkkk 176 
                                        +   + e++i++ ++wLl++     +d  ++  ++l    +     ++   tAy++iaL+e++++++      ++
  gi|488601359|ref|YP_007907830.1| 1722 VNrsQIENAIEKGVAWLLNNTYsaaPDKVYWH-HPLA-SPWWDNYGRKSEATAYAIIALNESRSMNNlnftVLDS 1794
                                        765566899*********76540103333332.2222.2344445788999*************99988998999 PP

                                        HHHHHHHHHHHHHHHHHHS---HHHHH CS
                    TED_complement  177 velsiskAleyLeekqaeelesvyalA 203 
                                        ++++i+kA++yL +    + +  y+++
  gi|488601359|ref|YP_007907830.1| 1795 NNATIAKAVNYLVSVYRGHGSFGYTAS 1821
                                        9***********995555555555544 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     2e-06    0.0045      13      67 ..    2099    2150 ..    2097    2153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2e-06
                              PEGA   13 atVyidGkylGkTPvtlsleaGnyslrvekeGYedlektvtvtagetvklnltLe 67  
                                        a+V++dG    kT    ++ +G++++r++k GY ++e +v++++g++v+ ++ L 
  gi|488601359|ref|YP_007907830.1| 2099 ASVTLDG--AAKTSKIQAI-EGSHKIRISKSGYVPVEFDVSLNPGDNVTYSVALY 2150
                                        7888888..5566555555.9**************************99998875 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.5       1.5   3.4e+03      14      40 ..    1542    1569 ..    1542    1569 .. 0.70
   2 !   10.8   0.0   0.00014      0.32       5      42 ..    1672    1714 ..    1669    1716 .. 0.71
   3 ?    2.3   0.0     0.063   1.4e+02       3      21 ..    1799    1817 ..    1797    1817 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                                        SHTTS-BBSSTTS.SBBHHHHHHHHHHH CS
                       Prenyltrans   14 QnedGGwggrpgs.esdtyytywalaaL 40  
                                        Q++ G+w+ + +    d++yt++a+ +L
  gi|488601359|ref|YP_007907830.1| 1542 QHDNGSWSMWGWNpKGDGFYTMYASYGL 1569
                                        7788999887444566888888887765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
                                        HHHHHHHHHSHTTS-BBSSTTS......SBBHHHHHHHHHHHHH CS
                       Prenyltrans    5 kavefLlscQnedGGwggrpgs......esdtyytywalaaLal 42  
                                         ++ +L s Qn dGGw+ + g       +sd+  t+  + +L+l
  gi|488601359|ref|YP_007907830.1| 1672 NVTKYLVSVQNSDGGWNQW-GAkddpakPSDAISTALSVWGLKL 1714
                                        5789************987.445666667777766666666655 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.063
                                        HHHHHHHHHHHSHTTS-BB CS
                       Prenyltrans    3 vekavefLlscQnedGGwg 21  
                                        ++kav++L s  + +G++g
  gi|488601359|ref|YP_007907830.1| 1799 IAKAVNYLVSVYRGHGSFG 1817
                                        89***************98 PP

>> Lysyl_oxidase  Lysyl oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   2.2e-05     0.049     137     191 ..     902     956 ..     884     964 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                     Lysyl_oxidase 137 isvgcadtyradidcqwiditdvkpgeyilkvevnpefkvaEsdfenNavkcelr 191
                                       +    ad   +  d   +d + ++ g y+++++v+ ++ ++E++  nN ++ +l 
  gi|488601359|ref|YP_007907830.1| 902 LNDLNADGVLNLSDTAVVDASSIDVGCYTFNITVDSNNDIEEINEGNNNATRTLC 956
                                       5555567777788999*****************************9999876655 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.2e-05      0.21      40      93 ..    1663    1721 ..    1641    1734 .. 0.76
   2 ?   -3.9   0.0       2.5   5.6e+03      43      71 ..    1795    1823 ..    1789    1828 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.2e-05
                   SQHop_cyclase_N   40 geddeeeeekiakylrsqqredGgWely.....pggpgdlsttveaYlALkllGdspda 93  
                                        ++  ++++++++kyl s q++dGgW+ +     p +p+d   t  +  +Lkl G++ d+
  gi|488601359|ref|YP_007907830.1| 1663 KQVANQTMANVTKYLVSVQNSDGGWNQWgakddPAKPSDAISTALSVWGLKLYGTPSDE 1721
                                        556678999*****************985422224556777777777899999988876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.5
                   SQHop_cyclase_N   43 deeeeekiakylrsqqredGgWelypggp 71  
                                        ++++++k+++yl s  r +G+++     +
  gi|488601359|ref|YP_007907830.1| 1795 NNATIAKAVNYLVSVYRGHGSFGYTASTQ 1823
                                        577889999***********998776555 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.034        77      11      28 ..     226     243 ..     225     249 .. 0.86
   2 ?   -2.0   0.1       1.9   4.2e+03       9      16 ..     326     333 ..     323     341 .. 0.88
   3 ?   -1.1   0.2         1   2.2e+03      10      29 ..     498     516 ..     492     517 .. 0.81
   4 ?    6.2   0.1    0.0047        10      10      29 ..     594     613 ..     592     617 .. 0.91
   5 ?   -3.9   0.0       7.4   1.7e+04      12      25 ..    1841    1854 ..    1836    1859 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.034
                                       EEEEEETTTCCEEEEEES CS
                               PQQ  11 ylyAlDadTGkvlWrfkt 28 
                                       +++Al+  +G +lW +++
  gi|488601359|ref|YP_007907830.1| 226 KVVALNGVDGSELWNVPL 243
                                       699***********8776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                                       TSEEEEEE CS
                               PQQ   9 dGylyAlD 16 
                                       +Gy++A+D
  gi|488601359|ref|YP_007907830.1| 326 NGYVVAID 333
                                       9******9 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                                       SEEEEEETTTCCEEEEEESS CS
                               PQQ  10 GylyAlDadTGkvlWrfktg 29 
                                         +y  D +TG+  W +++g
  gi|488601359|ref|YP_007907830.1| 498 SSVYVRD-NTGNAEWNYELG 516
                                       5799999.*******99987 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0047
                                       SEEEEEETTTCCEEEEEESS CS
                               PQQ  10 GylyAlDadTGkvlWrfktg 29 
                                       Gy +A++ ++G ++W+++t+
  gi|488601359|ref|YP_007907830.1| 594 GYALAVNGADGSIIWEKNTV 613
                                       7899************9986 PP

  == domain 5  score: -3.9 bits;  conditional E-value: 7.4
                                        EEEEETTTCCEEEE CS
                               PQQ   12 lyAlDadTGkvlWr 25  
                                         + +++d+G v+  
  gi|488601359|ref|YP_007907830.1| 1841 TVTINIDNGAVVKD 1854
                                        5679*****99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.20u 0.38s 00:00:01.58 Elapsed: 00:00:00.79
# Mc/sec: 8976.57
//
Query:       gi|488601360|ref|YP_007907831.1|  [L=723]
Description: hypothetical protein Asulf_01872 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  185.2   5.0    4.7e-34  118.0   0.7    2.3  2  Peptidase_S8  Subtilase family
      7e-21   74.2   3.6    1.6e-19   69.7   3.6    2.1  1  Peptidase_M6  Immune inhibitor A peptidase M6
     0.0015   18.7   3.4     0.0045   17.2   3.4    1.9  1  Dockerin_1    Dockerin type I domain
     0.0073   16.3   3.0      0.009   16.0   0.0    2.4  2  Big_1         Bacterial Ig-like domain (group 1)


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 !   68.9   0.3   9.7e-23   4.4e-19       1     130 [.     137     241 ..     137     274 .. 0.85
   2 !  118.0   0.7   1.1e-37   4.7e-34     144     298 .]     498     638 ..     481     638 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 9.7e-23
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanap 77 
                                       g g++vav+DtG+ + h+d+s+       +          ++ +d  + +++ ++d+ g    HGthvAG++a+n  
  gi|488601360|ref|YP_007907831.1| 137 GGGIKVAVVDTGI-YPHKDFSDR------I----------IAWKDFVNNKNYPYDDN-G----HGTHVAGTVAGN-G 190
                                       679**********.88*****22......2..........67788888888888775.8....************.9 PP

                                       SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  78 eegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslg 130
                                        +g++ gvap+a + +vkv+d sg++    + +i+++++a  +++dvi++s g
  gi|488601360|ref|YP_007907831.1| 191 ASGTITGVAPDAYLMGVKVFDSSGSAPV--SRVIEGLQWAYSNGADVISYSGG 241
                                       99**********************9885..9********************99 PP

  == domain 2  score: 118.0 bits;  conditional E-value: 1.1e-37
                                       HHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT..........-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                      Peptidase_S8 144 alainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssd...gklkpdi 217
                                       + a+++ v ++g+ vvi+aGN+g +g       ++++p+ts ++it+ga+++ + ia+fSsrGp+       +kpd 
  gi|488601360|ref|YP_007907831.1| 498 DKAVDAIV-RNGTAVVIAAGNSGSYGF-----RTINSPGTSYSAITIGAIDSSARIADFSSRGPVGFgsnITIKPDF 568
                                       22899999.99************7766.....9*******************************85444499***** PP

                                       EEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 218 vapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfa 294
                                       vapG nivst  +          y +msGTSmA+P+++g++Al+l+ +pkltpe++r +l n+  dlg+a  + ++ 
  gi|488601360|ref|YP_007907831.1| 569 VAPGYNIVSTCLWG---------YCYMSGTSMATPHISGVIALMLQVNPKLTPEEIRNILKNASIDLGDA--GPDNV 634
                                       ******88876665.........589*****************************************888..***** PP

                                       SSTT CS
                                       xxxx RF
                      Peptidase_S8 295 qGaG 298
                                       +G+G
  gi|488601360|ref|YP_007907831.1| 635 YGFG 638
                                       **99 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 !   69.7   3.6   3.6e-23   1.6e-19     344     513 ..     344     489 ..     332     544 .. 0.77

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 3.6e-23
                      Peptidase_M6 344 GetayysgrGddlkntlsraldltkksaaklefkawyeieadyDfvevevsvdGaktlididgeidvspaksdqsdk 420
                                        ++ +ysg+G++l+ntlsr +dl + ++a+l+fk++y+i++ +D+ +vev  + ++ ++    e ++          
  gi|488601360|ref|YP_007907831.1| 344 ENYIWYSGNGNNLDNTLSRDFDLRNITKATLRFKTYYDIDEGWDYGYVEVVCNNTTYVL---AEYTG---------- 407
                                       4799*********************************************9765443332...22222.......... PP

                      Peptidase_M6 421 nalsgkvdawidakydLsayaGkkveLkfdyltDgglamkGfavDdlavtvdGeqvfsDdaegatskftlnGft.kk 496
                                             ++ +++ + +Ls++aG+++ L f+y+tD+++ + G+++Dd+++    e  f Dd e     +++ G+  ++
  gi|488601360|ref|YP_007907831.1| 408 -----YSKPYVE-EINLSKFAGNNITLVFRYVTDSSVVYPGWYIDDIEIP---EIGFYDDVEKGSTGWNASGWSiVE 475
                                       .....2234554.468*******************************996...666*******9********85133 PP

                      Peptidase_M6 497 ggtkekaqyyllelrny 513
                                       +g+     yy+  +  y
  gi|488601360|ref|YP_007907831.1| 476 EGV---IPYYVKVYVGY 489
                                       342...23444444444 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.4     1e-06    0.0045       1      53 [.     652     703 ..     652     708 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-06
                                       TTETTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHH CS
                        Dockerin_1   1 agDVNgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallv 53 
                                       +gD+N Dg+V+  D++ +   l  ++ + + +   + D+N++Gr++  D++ +
  gi|488601360|ref|YP_007907831.1| 652 KGDINLDGNVDIADITNMAYLLV-GKVKADGIHYYNGDLNRNGRIDIGDLAKL 703
                                       59****************98888.9999999999999**********999987 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 !   16.0   0.0     2e-06     0.009       5      34 ..     288     317 ..     286     344 .. 0.83
   2 ?   -0.9   0.9      0.38   1.7e+03      17      51 ..     492     527 ..     490     540 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-06
                             Big_1   5 dtntltatvkDangnpvagatVtfsvsgga 34 
                                       d n l+ t+ D ngn v+g++++++ +++ 
  gi|488601360|ref|YP_007907831.1| 288 DLNNLSFTLYDPNGNEVQGIEINWTQTNDM 317
                                       7799***********************954 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.38
                             Big_1  17 ngnpvagatVtfsvsggals.assgtTdanGkatvt 51 
                                       +g+ +a+++V   v +g+++  + g +++ G  t++
  gi|488601360|ref|YP_007907831.1| 492 DGTSLADKAVDAIVRNGTAVvIAAGNSGSYGFRTIN 527
                                       799999999999999977776889998888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (723 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 4019.54
//
Query:       gi|488601361|ref|YP_007907832.1|  [L=309]
Description: ATP phosphoribosyltransferase (homohexameric) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-30  106.4   0.0    2.2e-30  105.7   0.0    1.3  1  HisG      ATP phosphoribosyltransferase
    0.00063   19.8   0.0     0.0016   18.5   0.0    1.6  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 !  105.7   0.0   2.4e-34   2.2e-30       1     159 [.      54     228 ..      54     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 2.4e-34
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHC.....T...TEEEEEEESESEEEEEEEEETTS..S--SGCGG...TT.-. CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEs.....keeeeveelldLgfgkcklvvavpees..evkslkdl..ved.kg 67 
                                       r++ +p y+++g+ d G+tG+D++e+s     k +e+v+ + +L f  +klvvav+ee+   vk+++dl  v++ k+
  gi|488601361|ref|YP_007907832.1|  54 RPQIMPFYIMRGRGDGGFTGEDILENSmlryeKLNEKVVVVERLPFRPTKLVVAVSEEMypGVKTIEDLkeVAGdKE 130
                                       7999**********************66667777889********************54115666666644333688 PP

                                       EEEEES-HHHHHHHHHHTT-EEEEEE-SS-CTHH..HHTTS-SEEEEEESSSHHHHHTTEEEEEEEEE.EEEEEEEE CS
                              HisG  68 kriaTsypnlakkyfeekglkveiiklsGsvEaa..palglaDaIvDlvetGeTLrangLkaietile.ssavLian 141
                                       +  a+++p lakky+eekgl++ +++  G +Ea+  p+   aD+I++++e G+TLr+ng+++i+ + + + +v+ian
  gi|488601361|ref|YP_007907832.1| 131 LMFASEFPDLAKKYCEEKGLNAIVFDPIGKTEASilPPDPEADLILEITEFGTTLRENGCRIIDVVKDpVYSVFIAN 207
                                       89******************************98778999************************999889******* PP

                                       HHHHHS...HHHHHHHHHHHH CS
                              HisG 142 kkslkk...kekieellerlr 159
                                       k+s+++   ++++e+l+++++
  gi|488601361|ref|YP_007907832.1| 208 KESYSNphkRKLMENLITDIK 228
                                       ****96455559999999987 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.8e-07    0.0016       6      68 ..     238     301 ..     234     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-07
                                       EEEEEEEGGG.HHHHHHH---SS.S-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEE CS
                            HisG_C   6 llmynvpkes.leevlkilPGlr.sPTvspladegwvaVsavveekevaevideLkaaGAsdIlv 68 
                                          +nvp e+ ++++l+ l +    PTvs+la+ g va+++++++++v  + + ++++G++ I  
  gi|488601361|ref|YP_007907832.1| 238 SFLFNVPDENdIPKILEFLTSEGfDPTVSKLAK-GGVAIHIIIDRSKVKFLKPVIREMGGKRIAT 301
                                       5567888654388999987766438******86.89***********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2174.95
//
Query:       gi|488601362|ref|YP_007907833.1|  [L=354]
Description: Acyl-CoA dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-39  135.8   1.4      3e-39  134.6   0.4    1.9  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      1e-19   70.5   0.1    1.6e-19   69.8   0.1    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      3e-18   66.4   0.0    5.6e-18   65.5   0.0    1.5  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    4.6e-12   46.6   0.3    2.1e-11   44.5   0.0    2.1  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.29   1.3e+03      37      71 ..      40      75 ..      28      98 .. 0.66
   2 !  134.6   0.4   6.6e-43     3e-39       1     148 [.     204     353 ..     204     354 .] 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.29
                                      HHTSB-CC.-BGGGSHHHHHHHHHHHHHHHHHHHHH CS
                     Acyl-CoA_dh_1 37 arrrkafg.kplidhqlvreklaemaaeleaarllv 71
                                      a   k+fg + + +  l++e+la++ a ++ +    
  gi|488601362|ref|YP_007907833.1| 40 ALASKDFGlESYSKASLIAEELAKVSAGVAHVTVVH 75
                                      555667777777777788888888877665554433 PP

  == domain 2  score: 134.6 bits;  conditional E-value: 6.6e-43
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       gkG++va+ tl+++R+   a  lg+a+r++e a++ya+ r+afgk+l+d+q ++++la++ a++ea+  l+   a  
  gi|488601362|ref|YP_007907833.1| 204 GKGMKVALATLAVNRIPFSAIGLGIAKRCFELAVKYAKGRDAFGKKLMDFQGMQWMLADIFADIEALDKLIKYSAMV 280
                                       79*****************************************************************7777666654 PP

                                       -------..HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpd..raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                       +d + +   ++  +++Kl+a+e+a ++ad a++++Gg+G++ + pver+yrda++l i+eGtsei++ i++r+
  gi|488601362|ref|YP_007907833.1| 281 ADGEIEGstTVLGAVCKLKAAEVAKRCADVAIEVYGGHGVMSGSPVERAYRDAKILDIAEGTSEIMKVILSRS 353
                                       4444443789*********************************************************999885 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.1   3.7e-23   1.6e-19       2      97 .]     105     192 ..     104     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 3.7e-23
                                       EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE--- CS
                     Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrri 78 
                                       +a+TEp++Gsdvas+kt +ae+ +g+y +nG+K+ itnaa a++++v+a+      +++++ f+v+r + g++ r++
  gi|488601362|ref|YP_007907833.1| 105 IAITEPSGGSDVASMKT-VAEKVEGGYLINGRKTLITNAAFAKIFIVFAK-----VDGKITAFIVDR-DDGITTRKL 174
                                       79***************.9999999*************************.....489********5.779***999 PP

                                       --BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  79 eeklGlrglptgelvfedv 97 
                                        +  G rg   + ++f+dv
  gi|488601362|ref|YP_007907833.1| 175 -NPSGFRGSGLSSVEFKDV 192
                                       .58**************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   1.2e-21   5.6e-18       3     128 ..     221     338 ..     219     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.2e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHH CS
                     Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtved 79 
                                       ++a+ lG+A+++++ +v++a++r    +g+kl d++ +q  la++ a+++A+ +l++  a      a++++e   ++
  gi|488601362|ref|YP_007907833.1| 221 FSAIGLGIAKRCFELAVKYAKGRDA--FGKKLMDFQGMQWMLADIFADIEALDKLIKYSAMV----ADGEIE--GST 289
                                       799*********************9..*****************************999988....555555..799 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCT CS
                     Acyl-CoA_dh_2  80 raearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaa 128
                                       +  +++ ++ a+e a +++d ++e+ Gg+++ + sp++R++RDa+++ +
  gi|488601362|ref|YP_007907833.1| 290 TVLGAVCKLKAAEVAKRCADVAIEVYGGHGVMSGSPVERAYRDAKILDI 338
                                       99******************************************99765 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   4.6e-15   2.1e-11      20     106 ..      12      94 ..       4     101 .. 0.88
   2 ?   -1.3   0.0      0.77   3.5e+03      69      89 ..     301     322 ..     270     329 .. 0.64

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 4.6e-15
                                       HHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHH CS
                     Acyl-CoA_dh_N  20 aphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslvapailrf 96 
                                       +++ ae+d+++e+p+e++k+l e+Gl+     +++g ++ +y  a ++aeela+++ag+a +  vh++ v  a+  f
  gi|488601362|ref|YP_007907833.1|  12 QKRSAEIDAKNEMPEEVLKALFENGLMSALASKDFG-LE-SYSKASLIAEELAKVSAGVAHVTVVHNMAV-DALRLF 85 
                                       45678999999************************5.66.69*****************99999999888.89**** PP

                                       S-HHHHHHHH CS
                     Acyl-CoA_dh_N  97 GteeqkrryL 106
                                       G+e+qk+ y+
  gi|488601362|ref|YP_007907833.1|  86 GSEDQKE-YM 94 
                                       ******8.55 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.77
                                       HHHHHH-HHHHH.HHHHHHHTT CS
                     Acyl-CoA_dh_N  69 eelaradaglal.llgvhsslv 89 
                                        e+a+ +a +a+ ++g h  + 
  gi|488601362|ref|YP_007907833.1| 301 AEVAKRCADVAIeVYGGHGVMS 322
                                       3555556766776666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 00:00:00.44
# Mc/sec: 2415.45
//
Query:       gi|488601363|ref|YP_007907834.1|  [L=603]
Description: putative signal-transduction protein containing cAMP-binding and CBS domains [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-37  128.6   0.0    2.8e-37  127.6   0.0    1.5  1  DUF294        Putative nucleotidyltransferase DUF294
      8e-31  106.8   0.0    1.4e-30  106.0   0.0    1.4  1  DUF294_C      Putative nucleotidyltransferase substrate bindi
      3e-20   72.4   9.9    1.4e-11   44.7   0.9    3.8  4  CBS           CBS domain
    2.5e-18   65.9   0.0    6.6e-18   64.6   0.0    1.8  1  cNMP_binding  Cyclic nucleotide-binding domain


Domain annotation for each model (and alignments):
>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.6   0.0   6.3e-41   2.8e-37       3     135 ..     298     423 ..     296     426 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 6.3e-41
                            DUF294   3 ierlvrallaegvkaealarlvselndallrrlielaeeelgkppvpfallvmGSeGReEqtlktDqDnalvledee 79 
                                       +++ v+al  +g +  +l+r++++++d +++r++ ++e+e++ p  ++ ++ mGS+GR+Eq+++tDqDn ++++   
  gi|488601363|ref|YP_007907834.1| 298 VRKAVAALALKGFHFYELSRMITSVYDSAVHRVLVMTEKEFDLP--DYVWIHMGSSGRKEQIIATDQDNMIIYDG-- 370
                                       5678899999******************************9887..9***************************9.. PP

                            DUF294  80 eeaareyfaelaervneaLaalGyplCpggimasnpewrkslseWkeqfrkwirep 135
                                          +++++ e+a+rvn++L+++G+p+C+ ++masnp+w+++++eWk++f++w+++ 
  gi|488601363|ref|YP_007907834.1| 371 ---DKKEVLEFAKRVNDRLDEIGIPKCTANYMASNPKWNLTIDEWKDNFKRWFNAL 423
                                       ...88999********************************************9875 PP

>> DUF294_C  Putative nucleotidyltransferase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0     3e-34   1.4e-30       3     145 .]     462     598 ..     460     598 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 3e-34
                          DUF294_C   3 flarlarnalrfkpplglfgrlvtersgehkgelDLKkagifplvdlvRllALeag.ieatnTleRlkalaeagvls 78 
                                        +++la +a+ ++pp+g+fg ++  ++g     lD+Kk gi p+ ++vR+lALe+g ++ tnT eR+++l+e +++ 
  gi|488601363|ref|YP_007907834.1| 462 AIRFLALDATTIEPPIGIFG-IKGLDKG-----LDIKKFGIYPIANGVRVLALENGiVKITNTKERIERLSEISAI- 531
                                       6799***************8.6999999.....***********************9999****************. PP

                          DUF294_C  79 aelaedlleayefllrlrlrhqleaieageepdnyvdpeeLsklerdlLkealkvvkrlqellklrf 145
                                        +  +dlleayefl++lrlrhq    +ag e dn ++ +e+ k e   L+ealk+v+++q+++k r+
  gi|488601363|ref|YP_007907834.1| 532 GDRKDDLLEAYEFLQELRLRHQSISFSAGFEGDNIIKIDEIDKIESFVLREALKIVSSFQKFIKGRY 598
                                       6778***********************************************************9887 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.047   2.1e+02      29      54 ..      45      79 ..      38      82 .. 0.75
   2 !   44.7   0.9   3.1e-15   1.4e-11       1      56 [.     153     207 ..     153     208 .. 0.93
   3 !   29.4   0.1   1.8e-10     8e-07       5      55 ..     219     269 ..     215     271 .. 0.91
   4 ?   -3.6   0.0       3.6   1.6e+04      27      38 ..     324     335 ..     317     337 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.047
                                      T.SSEE.EEE........ETTTBEEEEEEHHHHHHH CS
                               CBS 29 g.vsrl.PVV........dedgklvGivtlrDllra 54
                                      g +s + +VV        d+d  l+ +vt+  ++  
  gi|488601363|ref|YP_007907834.1| 45 GkHSKYvYVVfqgsvglyDDDT-LIDVVTRGEIFGI 79
                                      4455443788899999999888.*******999865 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 3.1e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+ + ++d+v+++ dt +e+a+++m++++v+++ VV e+gk+vG++t++Dl ++l+
  gi|488601363|ref|YP_007907834.1| 153 VEKLIRKDPVVCSRDTVVEDAAKTMINNRVGSIVVV-ENGKPVGVLTDSDLKKVLV 207
                                       667899***************************778.9*************99886 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 1.8e-10
                                       SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       m ++ ++++ + ++ ea  ++ +kg+++l VV++d k +G++t +D+l+ l
  gi|488601363|ref|YP_007907834.1| 219 MVSPAIYIDSEKPVFEAYLTLLNKGINHLIVVNKDSKAIGVITSKDILSQL 269
                                       889999**************99*******999****************865 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 3.6
                                       HHTSSEEEEEET CS
                               CBS  27 ekgvsrlPVVde 38 
                                       +++v+r++V+ e
  gi|488601363|ref|YP_007907834.1| 324 DSAVHRVLVMTE 335
                                       566999988643 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0   1.5e-21   6.6e-18       2      89 .]      33     115 ..      32     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1.5e-21
                                       EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEE CS
                      cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalp 78 
                                       + +++gev+f++G++ +++y+v +G+v +y  ++d    +++v+++G++fG ++++tg+p + t++A++d  +++++
  gi|488601363|ref|YP_007907834.1|  33 EAYEKGEVVFKKGKHSKYVYVVFQGSVGLY--DDDT---LIDVVTRGEIFGIISAITGNPLSLTAIAMEDLICYEIK 104
                                       579**************************5..4444...************************************** PP

                                       HHHHHHHHHH- CS
                      cNMP_binding  79 rddflellqqd 89 
                                       +d+f+e+++++
  gi|488601363|ref|YP_007907834.1| 105 KDAFNEIFEKN 115
                                       ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3969.41
//
Query:       gi|488601364|ref|YP_007907835.1|  [L=204]
Description: exonuclease, DNA polymerase III, epsilon subunit family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-27   94.8   0.0    9.6e-27   94.5   0.0    1.1  1  RNase_T         Exonuclease
    7.8e-07   29.2   0.0    2.4e-06   27.6   0.0    1.7  1  DUF5051         3' exoribonuclease, RNase T-like
      0.007   16.1   0.2      0.044   13.5   0.1    2.1  2  DNA_pol_A_exo1  3'-5' exonuclease
  ------ inclusion threshold ------
      0.011   14.9   0.7        8.6    5.4   0.0    3.0  3  CAF1            CAF1 family ribonuclease
      0.025   14.6   0.2        0.1   12.6   0.1    2.0  1  RNase_H_2       RNase_H superfamily


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   2.7e-30   9.6e-27       2     165 .]      10     170 ..       9     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.7e-30
                                       EEEEEESSSTTCTTS-EEEEEEEEEETTCCEEEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHH CS
                           RNase_T   2 viDlEttgldakekdeiieiaaisidggeneigetfhfyvkptelakltdecteftgitqemldeapsfkevleefk 78 
                                       viDlEttgl++ ++dei++ia + ++g +    e+fh+y+kp++    + ++++++gi++ ++++ap+f ev + ++
  gi|488601364|ref|YP_007907835.1|  10 VIDLETTGLNV-KRDEILSIAVVPMQGTKILSSESFHTYIKPKRY---KLKSMRIHGIDPSTIENAPKFSEVSKYLF 82 
                                       8**********.8*****************99999*********7...889************************** PP

                                       HHHHHHTCCCETTTCEEEESSHHHHHHHHHHHHHHHHHCSEHCECHHHHHHHHHC......HHHHHHHHHTTCHSSS CS
                           RNase_T  79 ellrklallvahnaafdvgflraadkrilkkevpkrnqfldtlildkatlkelar......tsldklaeklgleedg 149
                                       +llr ++++v+h +++d +fl++++k    ++++  n+++d +i+ k    +l +       +ld l++++ l++  
  gi|488601364|ref|YP_007907835.1|  83 DLLR-DTIIVGHAVEIDFSFLKKYFKN---ENMNLNNKYIDIAIVEKWLCERLGErkgnmdLTLDVLLKSYNLSGRF 155
                                       ****.*********************5...5677778888888875444433333555999**************99 PP

                                       STSSHHHHHHHHHHHH CS
                           RNase_T 150 raHrAldDaeataklf 165
                                       r H Al Da  ta++f
  gi|488601364|ref|YP_007907835.1| 156 R-HHALTDAFLTAQIF 170
                                       8.***********998 PP

>> DUF5051  3' exoribonuclease, RNase T-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   6.7e-10   2.4e-06       4     163 ..      10     171 ..       7     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.7e-10
                           DUF5051   4 miDiEtlgne.etaelvsIGaVffpetG.......eFyaeidlesd....ee.agidaetieWWlkqskearaellk 67 
                                       +iD+Et+g + ++ e++sI++V  p +G       +F++ i+++      ++  gid +ti                
  gi|488601364|ref|YP_007907835.1|  10 VIDLETTGLNvKRDEILSIAVV--PMQGtkilsseSFHTYIKPKRYklksMRiHGIDPSTI---------------- 68 
                                       79******999***********..888888999999******9666444322122555555................ PP

                           DUF5051  68 dtqeakslkdalqaleeFlekslkvwangasfDlviLraafel......lipwkywndrdvrt.lvalapelekgee 137
                                          +a++++++ + l++ l+ ++ ++++  + D++ L+++f+       +   ky +   v+  l++   e ++  +
  gi|488601364|ref|YP_007907835.1|  69 --ENAPKFSEVSKYLFDLLR-DTIIVGHAVEIDFSFLKKYFKNenmnlnN---KYIDIAIVEKwLCERLGERKGNMD 139
                                       ..469**************5.889******************98775441...444444443312222222222223 PP

                           DUF5051 138 kkreipfe......gvkHnALaDAkhqakavs 163
                                        + ++  +        +H+AL DA   a++++
  gi|488601364|ref|YP_007907835.1| 140 LTLDVLLKsynlsgRFRHHALTDAFLTAQIFQ 171
                                       3333333356677789********99999886 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 !   13.5   0.1   1.2e-05     0.044      25     128 ..      11     149 ..       3     155 .. 0.77
   2 ?   -2.3   0.0      0.87   3.1e+03     157     170 ..     159     172 ..     154     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                       EEEEEE-SSSTTSSEEEEEEEEECSSEEEEEECTTTTTT-............................HGHHHHHHH CS
                    DNA_pol_A_exo1  25 vDtEttsldlisatlvliliqlgekeeayiidplelgddv............................alealkrll 73 
                                       +D Ett+l+   +++++ +i++   +++ i+++ + ++++                            + ++l  ll
  gi|488601364|ref|YP_007907835.1|  11 IDLETTGLNV--KRDEILSIAVVPMQGTKILSSESFHTYIkpkryklksmrihgidpstienapkfseVSKYLFDLL 85 
                                       6889999999..89999999999888888888888888888888888888899999999999999999999****** PP

                                       T-TTSEEEESSHHHHHHHHHHHHTS--SSE....EEH.HHHHHHTTHSTT......SSHHHHHHHH CS
                    DNA_pol_A_exo1  74 edenitkvghnakfDlevlardfgielenl....fdt.mlaayvldyers......hsLdsLaeky 128
                                       +d   ++vgh+ + D  +l++ f+ e  nl    +d   + ++++    +        Ld+L+++y
  gi|488601364|ref|YP_007907835.1|  86 RDT--IIVGHAVEIDFSFLKKYFKNENMNLnnkyIDIaIVEKWLCERLGErkgnmdLTLDVLLKSY 149
                                       *86..8****************88777665111155545555555544446666666677776666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.87
                                       HHHHHHTHHHHHHH CS
                    DNA_pol_A_exo1 157 AaeDadvllrlfkk 170
                                       A +Da +++++f+ 
  gi|488601364|ref|YP_007907835.1| 159 ALTDAFLTAQIFQI 172
                                       77899999999884 PP

>> CAF1  CAF1 family ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0024       8.6      17      33 ..       3      19 ..       1      30 [. 0.78
   2 ?    3.7   0.1    0.0082        29     189     226 ..      68     107 ..      44     116 .. 0.77
   3 ?    3.0   0.0     0.013        48     302     319 .]     153     170 ..     114     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0024
                                      HHH-SEEEEEEEES-SS CS
                                      xxxxxxxxxxxxxxxxx RF
                              CAF1 17 ikeasFvAiDlEftGls 33
                                      +++a F  iDlE tGl+
  gi|488601364|ref|YP_007907835.1|  3 LRSARFSVIDLETTGLN 19
                                      899*************2 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0082
                                       HHHHSBTHHHHHHHH..HC--EEEESSTHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                              CAF1 189 iakqsgfrlvfealv..ksrkpiVgHNgllDllflyqtfy 226
                                       i+++  f++v + l    +  +iVgH + +D+ fl + f 
  gi|488601364|ref|YP_007907835.1|  68 IENAPKFSEVSKYLFdlLRDTIIVGHAVEIDFSFLKKYFK 107
                                       5555566666666662235789*************99885 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.013
                                       ------HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                              CAF1 302 eesaHeAGyDafmTGlvf 319
                                       +   H+A  Daf+T+++f
  gi|488601364|ref|YP_007907835.1| 153 GRFRHHALTDAFLTAQIF 170
                                       3338************99 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.8e-05       0.1       3      94 ..      11     121 ..       9     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                         RNase_H_2   3 fDiEttGlspkknliyliGvldvdekeiek...ltqllaeepeeekail................elf...lellek 57 
                                       +D+EttGl+ k++ i  i+v+ +++ +i +   + +++++++ + k++                 e +   l +l +
  gi|488601364|ref|YP_007907835.1|  11 IDLETTGLNVKRDEILSIAVVPMQGTKILSsesFHTYIKPKRYKLKSMRihgidpstienapkfsE-VskyLFDLLR 86 
                                       7*********************99988744456999999999999999988888887777765541.1444667777 PP

                         RNase_H_2  58 kkalvtfngksFDvpflkrlfkkykldeeefrhiDLl 94 
                                       ++ +v +  +  D++flk+ fk+ +++  +++ iD+ 
  gi|488601364|ref|YP_007907835.1|  87 DTIIVGHAVEI-DFSFLKKYFKNENMNL-NNKYIDIA 121
                                       88888888888.*******998888886.88999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1264.46
//
Query:       gi|488601365|ref|YP_007907836.1|  [L=239]
Description: ABC-type cobalt transport system, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  111.1   0.0      8e-32  110.6   0.0    1.2  1  ABC_tran      ABC transporter
    9.6e-13   48.6   0.4    4.6e-06   26.7   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.4e-07   31.2   0.0    6.8e-07   29.0   0.0    1.8  1  SMC_N         RecF/RecN/SMC N terminal domain
    8.3e-05   22.5   0.0    0.00024   21.0   0.0    1.5  2  AAA_15        AAA ATPase domain
    0.00037   20.4   0.1    0.00086   19.2   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
     0.0036   17.0   0.1     0.0067   16.2   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0039   17.4   0.0      0.069   13.4   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0046   17.0   0.1      0.017   15.1   0.0    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.018   15.0   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.012   15.3   0.0      0.016   14.9   0.0    1.4  1  AAA_30        AAA domain
      0.014   15.7   0.0       0.02   15.3   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.019   15.5   0.0      0.034   14.7   0.0    1.4  1  AAA_23        AAA domain
      0.027   14.7   0.0      0.054   13.7   0.0    1.5  1  AAA_28        AAA domain
      0.033   14.6   0.8        0.3   11.5   0.8    2.3  1  AAA           ATPase family associated with various cellular 
      0.055   13.2   0.1       0.52   10.0   0.0    2.0  2  IstB_IS21     IstB-like ATP binding protein
      0.075   12.6   0.0       0.12   12.0   0.0    1.3  1  AAA_25        AAA domain
      0.098   12.8   0.1       0.29   11.3   0.0    1.7  2  MMR_HSR1      50S ribosome-binding GTPase
        0.1   13.0   0.0       0.19   12.1   0.0    1.5  1  RNA_helicase  RNA helicase
       0.19   11.1   0.1        0.4   10.0   0.1    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.21   11.5   0.3       0.48   10.3   0.1    1.7  2  NACHT         NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   8.9e-35     8e-32       2     137 .]      26     171 ..      25     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 8.9e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltv 76 
                                       k+ s +++ ge+++++G+nG+GKStL++ll+gl+kp+ G+i++ g + ++++ e+lr++igv++q+  ++lf+ + v
  gi|488601365|ref|YP_007907836.1|  26 KDFSAEIRDGERIVLLGPNGCGKSTLIMLLSGLVKPKTGKIRIFGVEPNRNNAEFLRRNIGVVFQNpdDFLFNPT-V 101
                                       78999*************************************************************877888887.7 PP

                                       HHH..........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx..........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren..........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        e+           +de    + + ++k+g+++l +++       LSgG+k++v++++al+ +pk+l+lDEpta
  gi|488601365|ref|YP_007907836.1| 102 LEEllytpsqlniPYDEAvelARTHARKFGIDYLLEKPP----FRLSGGEKKKVSIVCALMLDPKILFLDEPTA 171
                                       7777*9999999944444123555556666666666665....*****************************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 !   20.4   0.4   4.3e-07   0.00038       3      44 ..      39      68 ..      38      97 .. 0.79
   2 !   26.7   0.0   5.1e-09   4.6e-06     220     299 ..     126     199 ..      70     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.3e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44
                                      vl GpNg+GKS+L+ +l++l            +++++g+ir+
  gi|488601365|ref|YP_007907836.1| 39 VLLGPNGCGKSTLIMLLSGL------------VKPKTGKIRI 68
                                      9****************999............4444444444 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 5.1e-09
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                       + + +  ++  e p++ lS G k+   ++ al  ++   ++l++DEp ++ + k  r+++e+l   +++++ +i++T
  gi|488601365|ref|YP_007907836.1| 126 HARKFGIDYLLEKPPFRLSGGEKKKVSIVCALMLDP---KILFLDEPTANVDGKTRRKIVEIL---QKRNSTLIVAT 196
                                       55555556666779999****************999...9********************999...444578***** PP

                            AAA_21 297 HSp 299
                                       H  
  gi|488601365|ref|YP_007907836.1| 197 HEL 199
                                       *75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   7.5e-10   6.8e-07      27     215 ..      38     215 ..      24     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.5e-10
                                       EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEE...SSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkk...lkiekeev 97 
                                        +++GpNG+GKs l+  ++ +    ++ k+r             ++++a+  + ++ ++f+n+d+     ++ +e +
  gi|488601365|ref|YP_007907836.1|  38 IVLLGPNGCGKSTLIMLLSGLVK-PKTGKIRIF-------GvepNRNNAEFLRRNIGVVFQNPDDFlfnPTVLEELL 106
                                       5789**********976633322.222233333.......32245889999999***********955333445557 PP

                                       EEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                       ++  ++    +  +++ +++++k  +  lle+  +    LSgGek+ v++  + A  + +p+ l+ lDe  a+ D k
  gi|488601365|ref|YP_007907836.1| 107 YTPSQLNIPYDEAVELARTHARKFGIDYLLEKPPFR---LSGGEKKKVSI--VCA-LMLDPKILF-LDEPTANVDGK 176
                                       888888888899********************9995...9*****97664..433.578998765.8********** PP

                                       HHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-.SCEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                             SMC_N 175 nvkkvaellkeksknaQfivislreemleka.dklvgvtkve 215
                                        ++k++e+l++++  + +iv +++ +++ k  d+++ + + +
  gi|488601365|ref|YP_007907836.1| 177 TRRKIVEILQKRN--STLIVATHELDIVPKIaDRIILIGM-D 215
                                       *********9998..99*******9998775488777766.4 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.6e-07   0.00024      15      83 ..      26      89 ..      24     155 .. 0.79
   2 ?   -1.5   0.0       1.7   1.5e+03     344     368 ..     177     201 ..     159     202 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.6e-07
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83
                                      kd++ ++ +    vl G+N++GKS+++++l  + + k      + ki    +e ++n++e+ +  I v f
  gi|488601365|ref|YP_007907836.1| 26 KDFSAEIRDGeRIVLLGPNGCGKSTLIMLLSGLVKPK------TGKIRIFGVEPNRNNAEFLRRNIGVVF 89
                                      7778888877789**********************88......678888899999999999999999999 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                            AAA_15 344 likllkelandnktQviitTHSphi 368
                                         +++ e++++ +  +i+ TH   i
  gi|488601365|ref|YP_007907836.1| 177 TRRKIVEILQKRNSTLIVATHELDI 201
                                       4466677777777778888887665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.6e-07   0.00086      90     131 ..      25      67 ..       4      70 .. 0.86
   2 ?   -2.7   0.0       5.5   4.9e+03      21      46 ..     192     217 ..     177     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.6e-07
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       +++ +++++d + +vl+G+ G GKStLi  l +  + ktg+++
  gi|488601365|ref|YP_007907836.1|  25 VKDFSAEIRDgERIVLLGPNGCGKSTLIMLLSGLVKPKTGKIR 67 
                                       5666777887799********************9999999986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.5
                                       EEEESTTTT--HHHHHHHHHHHHHTT CS
                       RsgA_GTPase  21 ivvslkepelslnlldrfLvlaeekg 46 
                                       ++v+++e ++ +++ dr++++  +k+
  gi|488601365|ref|YP_007907836.1| 192 LIVATHELDIVPKIADRIILIGMDKK 217
                                       45555557777777777766655555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.4e-06    0.0067      17      39 ..      30      52 ..      21      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.4e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                      +ei+  g  ++l Gp+G GKSTl+
  gi|488601365|ref|YP_007907836.1| 30 AEIRD-GeRIVLLGPNGCGKSTLI 52
                                      45553.35899************9 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 !   13.4   0.0   7.7e-05     0.069      63      89 ..     160     186 ..     120     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.7e-05
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                       +++++fLDE  +++D++++++++e+l+
  gi|488601365|ref|YP_007907836.1| 160 DPKILFLDEPTANVDGKTRRKIVEILQ 186
                                       4789*******************9987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05     0.017       2      23 ..      38      59 ..      37      81 .. 0.88
   2 ?   -0.9   0.0       1.7   1.5e+03      57      75 ..     152     170 ..     138     217 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                      ++L+Gp G+gKs+l++ l+ ++
  gi|488601365|ref|YP_007907836.1| 38 IVLLGPNGCGKSTLIMLLSGLV 59
                                      68****************9987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                                       --------G-SEEEEESGG CS
                             AAA_5  57 splvraaregeilvlDEve 75 
                                       s++   +  ++il+lDE +
  gi|488601365|ref|YP_007907836.1| 152 SIVCALMLDPKILFLDEPT 170
                                       4445456678888888844 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     2e-05     0.018      46      72 ..      37      62 ..      24     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                             Rad17 46 riLLisGPsGCgkstvvkvLskelgik 72
                                      ri+ + GP GCgkst +  Ls    +k
  gi|488601365|ref|YP_007907836.1| 37 RIV-LLGPNGCGKSTLIMLLSGLVKPK 62
                                      454.56*************99766555 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   1.8e-05     0.016      21      82 ..      38     103 ..      26     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLaeelgieastiakllkrlk..g 82 
                                        vl Gp G GK+t++  l  +++ + g  r++g+ p+ + A+ L++++g+  ++ + +l + +  +
  gi|488601365|ref|YP_007907836.1|  38 IVLLGPNGCGKSTLIMLLSGLVKPKtGkIRIFGVEPNRNNAEFLRRNIGVVFQNPDDFLFNPTvlE 103
                                       6899****************999986568999*****************98888777775555552 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   2.2e-05      0.02      23      51 ..      34      62 ..      24     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                      ++e ++l G+ G+GKs+l+  l   ++ +
  gi|488601365|ref|YP_007907836.1| 34 DGERIVLLGPNGCGKSTLIMLLSGLVKPK 62
                                      346788*************8887544444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.7e-05     0.034      23      39 ..      39      55 ..      27      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                            AAA_23 23 lItGpNGaGKTTildAi 39
                                      ++ GpNG+GK+T++  +
  gi|488601365|ref|YP_007907836.1| 39 VLLGPNGCGKSTLIMLL 55
                                      789**********9765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.1e-05     0.054       1      20 [.      37      56 ..      37      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
                            AAA_28  1 kivitGgestGKTtlleaLa 20
                                      +iv++G+ ++GK+tl+  L+
  gi|488601365|ref|YP_007907836.1| 37 RIVLLGPNGCGKSTLIMLLS 56
                                      79**************9887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   0.00033       0.3       1      23 [.      38      60 ..      38     214 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                                      EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA  1 vllyGppGtGKTllakavakelg 23
                                      ++l Gp G+GK++l+  +   ++
  gi|488601365|ref|YP_007907836.1| 38 IVLLGPNGCGKSTLIMLLSGLVK 60
                                      5799***********99988764 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 ?   10.0   0.0   0.00058      0.52      44      65 ..      32      53 ..      20      63 .. 0.85
   2 ?    0.7   0.0      0.41   3.7e+02     105     139 ..     157     190 ..     145     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00058
                         IstB_IS21 44 iekkenivllGpsGvGKshlai 65
                                      i++ e ivllGp G GKs l +
  gi|488601365|ref|YP_007907836.1| 32 IRDGERIVLLGPNGCGKSTLIM 53
                                      78899*************9865 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.41
                         IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviekrye 139
                                        +l +++l lD+  + ++d + ++++ e+++kr  
  gi|488601365|ref|YP_007907836.1| 157 LMLDPKILFLDEP-TANVDGKTRRKIVEILQKRNS 190
                                       5667789999996.578999999999999999743 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.12      31      54 ..      33      56 ..      25      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                            AAA_25 31 pagelallaGapgtGKttlaldla 54
                                      + ge ++l G+ g+GK+tl + l+
  gi|488601365|ref|YP_007907836.1| 33 RDGERIVLLGPNGCGKSTLIMLLS 56
                                      6799***************99876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.29       1      39 [.      37      76 ..      37      94 .. 0.80
   2 ?   -1.5   0.0       2.9   2.6e+03      26      44 ..     170     188 ..     149     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                      EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEE CS
                          MMR_HSR1  1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdineg 39
                                      +++++G    GKStLi  l+g  k +++++     ++n+ 
  gi|488601365|ref|YP_007907836.1| 37 RIVLLGPNGCGKSTLIMLLSGLvKPKTGKIRIFGVEPNRN 76
                                      689****************997677888776666666655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                                       ESSSTTSSSSEEEEEEEET CS
                          MMR_HSR1  26 vsdkpgtTrdinegrvklk 44 
                                       +++  g+Tr  + + ++++
  gi|488601365|ref|YP_007907836.1| 170 TANVDGKTRRKIVEILQKR 188
                                       4566666666666655533 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   0.00021      0.19       1      19 [.      38      56 ..      38      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                      RNA_helicase  1 iwlyGpsgeGKStlakeLa 19
                                      i+l Gp+g+GKStl+  L+
  gi|488601365|ref|YP_007907836.1| 38 IVLLGPNGCGKSTLIMLLS 56
                                      7899**********99865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00045       0.4      24      50 ..      37      63 ..      29      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00045
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppls 50
                                       ++l+Gp G+GK+ l+  l++l+ p +
  gi|488601365|ref|YP_007907836.1| 37 RIVLLGPNGCGKSTLIMLLSGLVKPKT 63
                                      689****************99987765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00053      0.48       2      20 ..      37      55 ..      36      67 .. 0.83
   2 ?   -2.2   0.0       3.9   3.5e+03      71      85 ..     179     193 ..     164     227 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                       ++l G++G+GK+tL+  l
  gi|488601365|ref|YP_007907836.1| 37 RIVLLGPNGCGKSTLIMLL 55
                                      689************8765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                                       CCHHHHCCSCCCEEE CS
                             NACHT  71 evwavllelperlLl 85 
                                       ++++++l+ ++++L+
  gi|488601365|ref|YP_007907836.1| 179 RKIVEILQKRNSTLI 193
                                       334444444444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1463.75
//
Query:       gi|488601366|ref|YP_007907837.1|  [L=253]
Description: cobalt ABC transporter, permease protein CbiQ [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   96.2  13.5    2.9e-27   95.7  13.5    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 !   95.7  13.5   1.6e-31   2.9e-27       4     209 ..      31     222 ..      28     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.6e-31
                                       CCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE....... CS
                              CbiQ   4 vlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlitteg 80 
                                       +l r+dpr k + +fll+++++    +  ll + +++++l+l+  +  v ++  +  +lf+l++++i++        
  gi|488601366|ref|YP_007907837.1|  31 FLQRVDPRIKIAGIFLLIVLTTTTFDVDKLLAV-FFVVVLFLILSKIEVMLFLKR-VWLFPLFSFIIVMP------H 99 
                                       789***********************9999555.666666666666678999999.9*********9988......4 PP

                                       EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  81 efvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleev 157
                                        f ++g++      +G ++++++++R+l++++ll+ll+lTTp+ +++s++++++ P+ ++ i+ ++yR+i l + e+
  gi|488601366|ref|YP_007907837.1| 100 MFGYSGIN-----WDGFVYAAVFTFRVLIAVALLSLLILTTPFSDIVSAFRSYRLPETFVSIIVVTYRYIHLTFSEL 171
                                       56777777.....899************************************************************* PP

                                       HHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS- CS
                              CbiQ 158 qrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGY 209
                                        ri  A+++R +++  g+ + +r  g +++  f+r+++r+er+ lA +aRG 
  gi|488601366|ref|YP_007907837.1| 172 FRIILARESRRFRK-MGFSEIWRNGGNAMGVFFIRVFERSERLHLASMARGG 222
                                       *************9.9**********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1689.75
//
Query:       gi|488601367|ref|YP_007907838.1|  [L=91]
Description: hypothetical protein Asulf_01879 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-09   35.5   0.1    9.1e-09   35.1   0.1    1.3  1  PDGLE     PDGLE domain
     0.0065   16.2   0.3     0.0077   16.0   0.3    1.1  1  Yip1      Yip1 domain
  ------ inclusion threshold ------
      0.058   13.5   0.0      0.063   13.4   0.0    1.2  1  DUF4235   Protein of unknown function (DUF4235)
       0.31   11.1   3.0       0.74    9.8   3.0    1.6  1  TM_helix  Conserved TM helix


Domain annotation for each model (and alignments):
>> PDGLE  PDGLE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1     2e-12   9.1e-09      44      88 ..      41      84 ..      18      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2e-12
                             PDGLE 44 laeiqektalLpDYsfkgaeekkagtsvAgivGvlltlalaglig 88
                                      ++e q+ + +LpDYs++g +    gt ++g++G+l+tla+a++i+
  gi|488601367|ref|YP_007907838.1| 41 AEEHQDYEGILPDYSVPGLDMF-SGTLISGVIGALITLAVAYGIA 84
                                      33444559*************8.*******************996 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.7e-06    0.0077      21      88 ..       4      88 ..       1      90 [. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                              Yip1 21 apdlallllalltlllgllas........lnlgqtlasg................eevqgltlssllgaiiggylglll 75
                                       ++  l +l++l+ ++++la                 +                  + ++ +l ++ g++i+g++g l+
  gi|488601367|ref|YP_007907838.1|  4 KFWILLGILLFLSPVFAYLADlvnyseplE-------NVaehlgaeehqdyegilPDYSVPGLDMFSGTLISGVIGALI 75
                                      467778888888888888888755544442.......445555555777777776444566677888888888888888 PP

                              Yip1 76 gllllalllhlia 88
                                      +l++  ++ +++a
  gi|488601367|ref|YP_007907838.1| 76 TLAVAYGIAKVVA 88
                                      8888888888765 PP

>> DUF4235  Protein of unknown function (DUF4235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.063      40      74 ..      55      89 ..      29      91 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                           DUF4235 40 dvslrevllfAaisGavlavvrvaadRgtargver 74
                                      +v+  ++   ++isG+++a++ +a+  g a++v+ 
  gi|488601367|ref|YP_007907838.1| 55 SVPGLDMFSGTLISGVIGALITLAVAYGIAKVVAS 89
                                      56677889999********************9986 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.0   0.00016      0.74      17      35 ..      70      88 ..      65      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHHHHHHHHH CS
                          TM_helix 17 LvgAilILlvGwiiAkfvs 35
                                      ++gA++ L+v++ iAk+v+
  gi|488601367|ref|YP_007907838.1| 70 VIGALITLAVAYGIAKVVA 88
                                      69***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 647.40
//
Query:       gi|488601368|ref|YP_007907839.1|  [L=213]
Description: ABC-type Co2+ transport system, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-67  226.6  18.1      3e-67  226.5  18.1    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi
  ------ inclusion threshold ------
      0.018   14.3   9.4      0.015   14.6   4.3    2.0  2  DUF2776   Protein of unknown function (DUF2776)
       0.13   11.2   0.0       0.27   10.2   0.0    1.4  1  TMEM171   Transmembrane protein family 171
       0.47   10.0   4.8        2.9    7.5   0.2    2.2  2  NADH5_C   NADH dehydrogenase subunit 5 C-terminus


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 !  226.5  18.1   6.7e-71     3e-67       1     207 []       2     202 ..       2     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 226.5 bits;  conditional E-value: 6.7e-71
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldearvpllallaafifaaqminipipggtslHllgavlaaiLl 77 
                                       Hipdg+L++++++++y++++++ +++l ++++elde+rvp+++++a++ifaaqm+n+pipggts+H++g++la+++l
  gi|488601368|ref|YP_007907839.1|   2 HIPDGFLDLSIAGVFYVLTGIVFVISLIKAKDELDEKRVPVVGMVASAIFAAQMLNWPIPGGTSAHFVGGALAGVIL 78 
                                       ***************************************************************************** PP

                              CbiM  78 GpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaal 154
                                       Gp+a+fla+a+vl++q+l+f+dGGitaLGaNi+nm+v++v+++y+v++ll     +kk+  laa++a++l+++laa+
  gi|488601368|ref|YP_007907839.1|  79 GPYAGFLAMASVLIIQTLVFADGGITALGANIWNMGVVAVFVGYYVFKLL-----EKKNPYLAAAVAGWLGITLAAI 150
                                       ************************************************98.....6789999*************** PP

                              CbiM 155 lvalelalsgleaslsltaalaamllvhlpvgilEgviTaaivkalkkvrpel 207
                                       ++++e++ls++ +++s+++++++m ++h ++gi+EgviTa +v++++++rp++
  gi|488601368|ref|YP_007907839.1| 151 FAGIEIGLSST-FKYSIAVTVPVMGMWHGILGIIEGVITAGVVAYIYSTRPDI 202
                                       *********88.89*************************************95 PP

>> DUF2776  Protein of unknown function (DUF2776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.015        65      56     108 ..      20      72 ..       5      92 .. 0.72
   2 ?   14.6   4.3   3.3e-06     0.015      16      95 ..     113     189 ..     106     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.015
                           DUF2776  56 taatiirqlikkyntvaklllPilGylvavitiivGlvllaeaetaaelvagh 108
                                       t  + +  lik  ++  +  +P++G ++++i     l     + t+a++v g 
  gi|488601368|ref|YP_007907839.1|  20 TGIVFVISLIKAKDELDEKRVPVVGMVASAIFAAQMLNWPIPGGTSAHFVGGA 72 
                                       55566667788888888888888888888887777777777777777777765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.3e-06
                           DUF2776  16 maliclayGlfvlelgkdserlvagpvvislgaicialfataatiirqlikkyntvaklllPilGylvavitiivGl 92 
                                       m+++ ++ G +v++l ++++ ++a+ v   lg+   a+fa        l ++++ ++ +++P++G   +++ ii G+
  gi|488601368|ref|YP_007907839.1| 113 MGVVAVFVGYYVFKLLEKKNPYLAAAVAGWLGITLAAIFAGI---EIGLSSTFKYSIAVTVPVMGMWHGILGIIEGV 186
                                       9*******************************9999999764...4578899************************9 PP

                           DUF2776  93 vll 95 
                                       + +
  gi|488601368|ref|YP_007907839.1| 187 ITA 189
                                       765 PP

>> TMEM171  Transmembrane protein family 171
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     6e-05      0.27     158     191 ..       6      38 ..       4      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6e-05
                           TMEM171 158 gfLslqilGplivlvGLCffvvahvkkrnnlsvs 191
                                       gfL l i G   vl+G+  fv++ +k +++l+++
  gi|488601368|ref|YP_007907839.1|   6 GFLDLSIAGVFYVLTGIV-FVISLIKAKDELDEK 38 
                                       9***************96.79*******999875 PP

>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2   0.00064       2.9       6      53 ..      15      62 ..      11      99 .. 0.91
   2 ?    4.4   1.0    0.0054        24      15      82 ..     124     192 ..     114     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00064
                           NADH5_C  6 iyyvllgsprfsslspineenptllnpilrLalgsiiaGsllswlifp 53
                                      ++yvl+g + + sl   ++e      p+++++  +i+a  +l+w i+ 
  gi|488601368|ref|YP_007907839.1| 15 VFYVLTGIVFVISLIKAKDELDEKRVPVVGMVASAIFAAQMLNWPIPG 62
                                      79******************************************9986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0054
                           NADH5_C  15 rfsslspineenptllnpilrLalgsiiaGslls.wlifpktpvitlplllKllallvtilGlllglel 82 
                                        f+ l   n      + + l+  l +i+aG+ +  + +f ++  +t+p++  +  +l +i G++++  +
  gi|488601368|ref|YP_007907839.1| 124 VFKLLEKKNPYLAAAVAGWLGITLAAIFAGIEIGlSSTFKYSIAVTVPVMGMWHGILGIIEGVITAGVV 192
                                       5555555555555566677888999*****988515566699999999999999999999998887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 1121.99
//
Query:       gi|488601369|ref|YP_007907840.1|  [L=387]
Description: Aspartate/tyrosine/aromatic aminotransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-61  206.8   0.0    5.9e-61  206.6   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 !  206.6   0.0   3.3e-65   5.9e-61       2     363 .]      34     379 ..      33     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 206.6 bits;  conditional E-value: 3.3e-65
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       dvi Lg++e+++     t+ +++++++   +  +++++y+ + gl el+ ++ak+++ + +l+ +++ ++vv+sG +
  gi|488601369|ref|YP_007907840.1|  34 DVISLGVGEPDFP----TPWRIREEMIY--SLEKGITSYTSNYGLEELRVEIAKYYR-KFGLDANPD-NIVVTSGVS 102
                                       89**********9....*********99..99999**********************.8999*****.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       ++ ++  +++ +npgd +l+p+p+y sy++ + l+gg vv++++   +  +l+ e++ +a +        +k+++++
  gi|488601369|ref|YP_007907840.1| 103 EGFDLSLRAT-VNPGDFVLIPEPSYVSYQPLAILCGGNVVTISIP--PPSRLTYEEITTASRMI-----DPKILILN 171
                                       **********.9*******************************66..6679********88874.....78****** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH.HGGSTTSTT.EEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat.ranveeepn.llivgslsKafGlaGeRv 230
                                        p+NPtG+ ++++ele+++d + +  +++++De+Y+++ ++      t +a+++   + +++++++sK+f+++G+R+
  gi|488601369|ref|YP_007907840.1| 172 YPSNPTGVSYSKKELEEIADAVVEMDMIVISDEIYSELTYK-FP--HTsIAGLNGMEDrVVVLNGFSKSFAMTGLRI 245
                                       ****************************************9.33..4448888887778****************** PP

                                       EEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCS CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsg 305
                                       Gy+++ +++++++ k+++      +   q  + +al++ +    el+emr+++ +rr +++ +L+e  l+  +++++
  gi|488601369|ref|YP_007907840.1| 246 GYVIAPDEILDAVLKIHQYSMLcaPITSQIGAIEALRNGES---ELDEMRAEYMRRRNFFVRKLNE-VLETHMPEGA 318
                                       **************999987776799999999999*99996...9*******************77.67777778** PP

                                       SEEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 306 mflltdlsae..takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       ++ +  ++    + +e+++ Ll e++v+v+pg+ f+   +g +R  + +++ ++l+e+++++
  gi|488601369|ref|YP_007907840.1| 319 FYAFPSIKDTglSSEEFAERLLLEKNVAVVPGNAFGEsgEGYIRCAY-AVSMDKLREAADRI 379
                                       *********9*9********99999************99999****9.************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2349.82
//
Query:       gi|488601370|ref|YP_007907841.1|  [L=165]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   63.1   0.4    3.1e-17   62.3   0.2    1.6  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    2.1e-05   24.0   0.2    4.9e-05   22.8   0.1    1.6  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00013   21.8   0.0    0.00029   20.7   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00024   20.8   0.1    0.00097   18.9   0.0    2.0  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00044   20.0   0.3     0.0021   17.8   0.0    2.4  4  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.026   14.4   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.025   14.1   0.0      0.092   12.3   0.0    1.9  2  Sigma70_r4      Sigma-70, region 4
      0.027   15.1   0.1      0.086   13.5   0.1    1.9  1  HHH_5           Helix-hairpin-helix domain
      0.028   14.4   0.0      0.033   14.2   0.0    1.3  1  DUF1985         Domain of unknown function (DUF1985)
      0.051   13.5   0.0        0.1   12.5   0.0    1.4  1  HTH_15          Helix-turn-helix domain of alkylmercury lyase
      0.067   13.5   0.0       0.12   12.6   0.0    1.4  1  DUF5013         Domain of unknown function (DUF5013)
       0.14   12.4   1.4        0.2   11.9   0.3    1.8  2  UPF0122         Putative helix-turn-helix protein, YlxM / p13


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 ?   -2.3   0.0         3   4.5e+03      48      60 ..      34      45 ..      22      56 .. 0.54
   2 !   62.3   0.2   2.1e-20   3.1e-17       1      74 [.      72     143 ..      70     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3
                                      HHHHHHHHHTTTT CS
                    AsnC_trans_reg 48 ealerflreklas 60
                                      e+ e++++e   +
  gi|488601370|ref|YP_007907841.1| 34 EDVEKIISE-CEN 45
                                      444444444.444 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 2.1e-20
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       v+v+l++++  +++++++++a++peV  +  v+G+yd+ + v+ ++l++ + f++ek+++lp+v++t+t++vl+
  gi|488601370|ref|YP_007907841.1|  72 VRVNLTREK--NYDDIARRIAKFPEVHAVRLVSGEYDFQIVVKGKSLKDVSFFVSEKVSTLPEVRDTNTHFVLK 143
                                       567777666..9*************************************************************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   3.3e-08   4.9e-05       6      44 ..       8      46 ..       4      47 .. 0.91
   2 ?   -3.8   0.0       6.6   9.8e+03      21      27 ..      83      89 ..      81      89 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.3e-08
                            HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeee 44
                                       ++L+lL++n+r s  e+A+ +glS+  v + + ++e+e
  gi|488601370|ref|YP_007907841.1|  8 VEVLKLLEDNARYSVDEIADITGLSREDVEKIISECENE 46
                                      689***********************9999999999986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.6
                            HTH_24 21 reLAerl 27
                                       ++A+r+
  gi|488601370|ref|YP_007907841.1| 83 DDIARRI 89
                                      6788774 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 !   20.7   0.0   1.9e-07   0.00029      21      65 ..      19      61 ..       3      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.9e-07
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririldleaL 65
                                      + + +e+A++ Gl+re v +i+se ++e+ i + +  +i d+e+L
  gi|488601370|ref|YP_007907841.1| 19 RYSVDEIADITGLSREDVEKIISECENEKSILKYK--TIIDWEKL 61
                                      67889**************************9776..89999999 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.5e-07   0.00097       9      34 ..      11      36 ..       8      38 .. 0.93
   2 ?   -1.9   0.0       2.1   3.2e+03      22      38 ..      84      89 ..      81      91 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.5e-07
                     HTH_AsnC-type  9 LeaLqedaRisyaeLAervGlSestv 34
                                      L++L+ +aR s+ e+A+ +GlS++ v
  gi|488601370|ref|YP_007907841.1| 11 LKLLEDNARYSVDEIADITGLSREDV 36
                                      89*********************988 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                     HTH_AsnC-type 22 eLAervGlSestvlrRv 38
                                      ++A+           R+
  gi|488601370|ref|YP_007907841.1| 84 DIAR-----------RI 89
                                      4555...........44 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0021       2      41 ..       2      43 ..       1      49 [. 0.87
   2 ?   -3.6   0.0       7.3   1.1e+04      18      26 ..      80      88 ..      76      89 .. 0.72
   3 ?   -3.0   0.0       4.7     7e+03      38      45 ..     142     149 ..     141     150 .. 0.79
   4 ?   -2.3   0.0       2.8   4.2e+03       2      11 ..     155     164 ..     154     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                            HTH_23  2 asereRlrillllae..GlsvreIAreLgvsrrTvyrwlkry 41
                                       +++++ ++l+ll +  ++sv eIA++ g sr  v ++++  
  gi|488601370|ref|YP_007907841.1|  2 HEADKKVEVLKLLEDnaRYSVDEIADITGLSREDVEKIISEC 43
                                      68899*********99****************9888888776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.3
                            HTH_23 18 lsvreIAre 26
                                      +++ +IAr+
  gi|488601370|ref|YP_007907841.1| 80 KNYDDIARR 88
                                      567788886 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.7
                            HTH_23  38 lkryreeG 45 
                                       lk y+eeG
  gi|488601370|ref|YP_007907841.1| 142 LKSYKEEG 149
                                       78999999 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.8
                            HTH_23   2 asereRlril 11 
                                        +e++Rl i+
  gi|488601370|ref|YP_007907841.1| 155 DEEDRRLAIV 164
                                       6899999986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-05     0.026       3      29 ..       6      33 ..       5      36 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHTT.SSEEHHHHHHHHTS-H CS
                             HTH_5  3 tRlkILklLae.gelcvcelaeelglsq 29
                                      +++++LklL++   ++v e+a+++gls+
  gi|488601370|ref|YP_007907841.1|  6 KKVEVLKLLEDnARYSVDEIADITGLSR 33
                                      799********666************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.2e-05     0.092      18      43 ..      17      42 ..       5      43 .. 0.81
   2 ?   -1.8   0.0       1.6   2.4e+03      18      29 ..      77      88 ..      63      90 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                                      TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 18 geglTleEIgerlgiSrerVrqiekr 43
                                         ++  EI+++ g+Sre V  i+++
  gi|488601370|ref|YP_007907841.1| 17 NARYSVDEIADITGLSREDVEKIISE 42
                                      667899**************999875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                      TTT--HHHHHHH CS
                        Sigma70_r4 18 geglTleEIger 29
                                       ++ ++ +I++r
  gi|488601370|ref|YP_007907841.1| 77 TREKNYDDIARR 88
                                      577888888887 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.7e-05     0.086      27      55 ..      15      43 ..       6      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                                      HHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                             HHH_5 27 edlaaadveeLakipGiGkktAeriilel 55
                                      ed a+ +v+e+a+i+G++ + +e+ii e 
  gi|488601370|ref|YP_007907841.1| 15 EDNARYSVDEIADITGLSREDVEKIISEC 43
                                      4556779*******************996 PP

>> DUF1985  Domain of unknown function (DUF1985)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.2e-05     0.033      14      67 ..      10      68 ..       1     124 [. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                           DUF1985 14 wilvngkplrFglreFaiitGLkCkkdekdflvdkekknklikkk.....lfgekkevt 67
                                      +++  +   r+++ e a itGL  ++ ek + +++++k+ l+ k       +ge+  v 
  gi|488601370|ref|YP_007907841.1| 10 VLKLLEDNARYSVDEIADITGLSREDVEKIISECENEKSILKYKTiidweKLGEEFVVA 68
                                      455566789**************999999887777777766555333333223333333 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.9e-05       0.1      26      57 ..      10      41 ..       6      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                            HTH_15 26 LlrlLakGepVtveeLAaatgrsveevrqaLa 57
                                      +l+lL + +  +v+e+A++tg s e v+++++
  gi|488601370|ref|YP_007907841.1| 10 VLKLLEDNARYSVDEIADITGLSREDVEKIIS 41
                                      7999************************9987 PP

>> DUF5013  Domain of unknown function (DUF5013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.1e-05      0.12      69     120 ..      98     146 ..      95     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-05
                           DUF5013  69 vtLpaGkYelsvtvaeengqnsngtaylvvakgstLPdlenletalaylsyl 120
                                       v L  G+Y++++ v+ ++ ++    +++v  k stLP++ + +t  + +sy+
  gi|488601370|ref|YP_007907841.1|  98 VRLVSGEYDFQIVVKGKSLKDV---SFFVSEKVSTLPEVRDTNTHFVLKSYK 146
                                       77999*********99886655...6***************99998888885 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 ?   11.9   0.3   0.00014       0.2      20      59 ..       5      45 ..       4      61 .. 0.78
   2 ?   -3.2   0.0       6.6   9.9e+03      57      77 ..     138     159 ..     135     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                           UPF0122 20 ekqanylelyya.dDlSlsEiAeefnvsrqavydnikrtek 59
                                      +k++++l+l  +   +S+ EiA+   +sr+ v   i+ +e+
  gi|488601370|ref|YP_007907841.1|  5 DKKVEVLKLLEDnARYSVDEIADITGLSREDVEKIISECEN 45
                                      566777777654146**********************9974 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.6
                           UPF0122  57 teklleky.EekLkllekykkr 77 
                                       t+ +l++y Ee + l+++ + r
  gi|488601370|ref|YP_007907841.1| 138 THFVLKSYkEEGVLLFSDEEDR 159
                                       6667788845556666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 00:00:00.49
# Mc/sec: 1020.48
//
Query:       gi|488601371|ref|YP_007907842.1|  [L=264]
Description: Zn-dependent hydrolase, including glyoxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   53.1   0.1    7.4e-14   52.2   0.1    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.7e-05   23.8   0.0    4.4e-05   23.1   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.41   10.6   0.0    1.6  1  DNA_meth_N     DNA methylase N-terminal domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.1   1.2e-17   7.4e-14      17     163 ..      34     191 ..      30     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.2e-17
                                       EEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHH CS
                       Lactamase_B  17 viLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasr 93 
                                       ++LiD+G+++ a   +       +k +dv+  ++TH+H DH+G+ + l+e    + + ++ +     ++e  d++  
  gi|488601371|ref|YP_007907842.1|  34 NLLIDCGCPNTAREVV-----DLVKNLDVEIALITHYHEDHVGAINNLKEIGIKVYAPEKSISILKSPPEIPDYRK- 104
                                       79*************9.....6**************************9998888888777777777777766554. PP

                                       CCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC........ CS
                       Lactamase_B  94 kglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl........ 162
                                               ++  p++ + e  +  ++ ++++v +  ++gh+  +v++ ++++lf+GD++ + ++    +        
  gi|488601371|ref|YP_007907842.1| 105 -------LVWGQPVAADCEPLDSKMEFGDTVVEVVETPGHTFDHVSILIDDFLFSGDLIISTNQMICLReeefgdti 174
                                       .......5799999999999999************************************988887777744444444 PP

                                       ................. CS
                       Lactamase_B 163 ................t 163
                                                        
  gi|488601371|ref|YP_007907842.1| 175 tslerilkkdfeyyfgG 191
                                       44444444444444444 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 !   23.1   0.0   7.3e-09   4.4e-05       1      98 [.      33     113 ..      33     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.3e-09
                                       SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHH CS
                     Lactamase_B_2   1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyl 77 
                                       r++LiD+g       +r    v l+++  +++  l+th H DH+  +  l+e+    +++yap++ +++l++     
  gi|488601371|ref|YP_007907842.1|  33 RNLLIDCGCPNT---AREV--VDLVKN-LDVEIALITHYHEDHVGAINNLKEI---GIKVYAPEKSISILKSPPE-- 98 
                                       799999998732...2333..233333.478899******************5...389***********99943.. PP

                                       HCHTTTTEEEEEE-TTSEEEE CS
                     Lactamase_B_2  78 aleeepavnvheldwgesfel 98 
                                             + + ++l wg++++ 
  gi|488601371|ref|YP_007907842.1|  99 ------IPDYRKLVWGQPVAA 113
                                       ......334455555555554 PP

>> DNA_meth_N  DNA methylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.9e-05      0.41      19      36 ..     242     259 ..     239     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.9e-05
                        DNA_meth_N  19 LrkvgeseWsretLnRwv 36 
                                        ++v+++eWsre L R +
  gi|488601371|ref|YP_007907842.1| 242 MEAVSQKEWSRENLVRSL 259
                                       579***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1809.89
//
Query:       gi|488601372|ref|YP_007907843.1|  [L=271]
Description: pseudouridylate synthase I [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-27   94.6   0.0    6.7e-21   74.8   0.0    2.2  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.9e-07    0.0034       5      81 ..       9      80 ..       7      95 .. 0.78
   2 !   74.8   0.0   3.7e-25   6.7e-21       4     108 .]     128     227 ..     125     227 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-07
                   PseudoU_synth_1  5 lvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl.favgqgklspedvkel 81
                                      + G ++ g   +q q++ +tv   l  a++e+   +    v++ ++s+++d++V+a+++v  ++v  +k  p ++++ 
  gi|488601372|ref|YP_007907843.1|  9 YFGDNFHG---SQYQPNLRTVEGELFKAFSELGIDA---GVARYRCSSRTDAGVHALGNVFaIDVDAKKYLPRIINSK 80
                                      66666666...6777888888888888888777664...59*******************989998877766665544 PP

  == domain 2  score: 74.8 bits;  conditional E-value: 3.7e-25
                   PseudoU_synth_1   4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvke 80 
                                         +Gthdf++f+k+ +e+++ +rti++++++     ++ +++++++g++F++++VR++  +l  +g+g +++e++k+
  gi|488601372|ref|YP_007907843.1| 128 IIEGTHDFSNFTKRFAESSSNIRTIKSVEVR----LDDRFITIEIEGNAFTWNMVRNLATALEMIGRGVRDVEWMKS 200
                                       579****************************....55569************************************* PP

                   PseudoU_synth_1  81 llnakkrkkiavetapavglvlfhvrYd 108
                                       +l+ ++  +  +e  pa gl l +v+Y+
  gi|488601372|ref|YP_007907843.1| 201 MLDPENYFE-RMEPSPAYGLLLKDVKYS 227
                                       ******888.9****************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1759.54
//
Query:       gi|488601373|ref|YP_007907844.1|  [L=103]
Description: hypothetical protein Asulf_01885 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 631.28
//
Query:       gi|488601374|ref|YP_007907845.1|  [L=187]
Description: Phosphatidylglycerophosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-13   49.1   0.8    7.4e-13   49.1   0.8    2.0  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.8   4.1e-17   7.4e-13       3      66 .]      27      89 ..      25      89 .. 0.92
   2 ?   -0.2   0.1     0.097   1.7e+03      26      27 ..     125     147 ..      95     177 .. 0.51

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.1e-17
                                      HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      Pn +T+++ll ++++++l+ ++  l+l+ +++++++l+D+lDG lAR    ++++G ++Ds+ D
  gi|488601374|ref|YP_007907845.1| 27 PNHLTFIGLLVGFSSAYLI-SIGELILGGIFIILSGLFDMLDGALARNQTLKTDFGGYIDSVSD 89
                                      9***************888.55558************************88888*******998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.097
                                       ....................... CS
                   CDP-OH_P_transf  26 p.....................l 27 
                                                             +
  gi|488601374|ref|YP_007907845.1| 125 AraeniiekcdvgiaergerliI 147
                                       24444444444444444444431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1008.23
//
Query:       gi|488601375|ref|YP_007907846.1|  [L=190]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   59.5   0.5    2.6e-16   58.9   0.5    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.1e-13   50.7   0.0    1.6e-13   50.2   0.0    1.2  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.5e-06   28.0   0.0    2.4e-06   27.4   0.0    1.4  1  MarR_2          MarR family
    9.5e-06   25.4   0.1    2.5e-05   24.0   0.0    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
    1.5e-05   24.8   0.0    2.7e-05   24.0   0.0    1.3  1  MarR            MarR family
     0.0002   21.2   0.0     0.0003   20.7   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00022   21.1   0.0    0.00042   20.2   0.0    1.4  1  HTH_11          HTH domain
    0.00077   19.2   0.0     0.0035   17.1   0.0    2.0  2  HTH_39          Helix-turn-helix domain
     0.0031   17.5   0.0     0.0053   16.8   0.0    1.3  1  HTH_20          Helix-turn-helix domain
     0.0075   16.4   0.0      0.013   15.7   0.0    1.3  1  HTH_28          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.017   15.0   0.1    1.3  1  TFIIE_alpha     TFIIE alpha subunit
      0.012   15.5   0.1      0.041   13.8   0.0    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.014   15.2   0.0      0.022   14.6   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.019   14.9   0.0       0.05   13.5   0.0    1.6  2  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.024   14.8   0.0      0.042   14.1   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.027   14.4   0.0      0.046   13.7   0.0    1.3  1  HTH_36          Helix-turn-helix domain
      0.067   12.7   0.1       0.13   11.8   0.1    1.4  1  Sigma70_r4      Sigma-70, region 4
      0.085   12.9   0.0       0.14   12.2   0.0    1.4  1  HTH_Mga         M protein trans-acting positive regulator (MG
       0.18   11.8   0.0       0.37   10.8   0.0    1.6  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
       0.19   11.5   0.0       0.29   11.0   0.0    1.3  1  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.5   2.9e-19   2.6e-16       1      47 [.       7      53 ..       7      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.9e-19
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      lde+d+ ILe+L++np isq+e+A+++glS++ v +r+k++ e G+I
  gi|488601375|ref|YP_007907846.1|  7 LDEKDKMILEILERNPEISQNEIAKEVGLSQPSVGARIKKMRELGII 53
                                      79********************************************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 !   50.2   0.0   1.8e-16   1.6e-13       1      42 []       7      48 ..       7      48 .. 0.99

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.8e-16
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDe D+ ILe+L++++ is  e+A++vGlS++ v +R+++++
  gi|488601375|ref|YP_007907846.1|  7 LDEKDKMILEILERNPEISQNEIAKEVGLSQPSVGARIKKMR 48
                                      8***************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   2.6e-09   2.4e-06       9      51 ..      13      53 ..      10      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.6e-09
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      ++L  L r+p+  ++++e+a++ gls+++v  ++k++ + G +
  gi|488601375|ref|YP_007907846.1| 13 MILEILERNPE--ISQNEIAKEVGLSQPSVGARIKKMRELGII 53
                                      689999****9..****************************98 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.8e-08   2.5e-05       6      46 ..      13      54 ..       8      55 .. 0.92
   2 ?   -3.1   0.0       8.2   7.3e+03      29      37 ..     116     124 ..     110     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.8e-08
                                      HHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  6 kILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       IL +L++++  +  e+a+e+glsq+ v    kk+re+G+++
  gi|488601375|ref|YP_007907846.1| 13 MILEILERNPeISQNEIAKEVGLSQPSVGARIKKMRELGIIN 54
                                      6999****887999**************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.2
                                       HHHHHHHHH CS
                             HTH_5  29 qstvShHLk 37 
                                       +++v++H +
  gi|488601375|ref|YP_007907846.1| 116 EAIVDQHIR 124
                                       678999975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     3e-08   2.7e-05       7      48 ..      13      54 ..       9      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3e-08
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      +iL+il++++++s+ e+ak +g+s+++v   ++++ + G i+
  gi|488601375|ref|YP_007907846.1| 13 MILEILERNPEISQNEIAKEVGLSQPSVGARIKKMRELGIIN 54
                                      69*********************************9999985 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 !   20.7   0.0   3.4e-07    0.0003      19      61 ..      21      63 ..       4      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.4e-07
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES- CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrgrririld 61
                                      +  ++q e+A  +Gl++ +v   ++++++ g+i   ++i +++
  gi|488601375|ref|YP_007907846.1| 21 NPEISQNEIAKEVGLSQPSVGARIKKMRELGIINHAYGINLKN 63
                                      4579*****************************9653377766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.6e-07   0.00042       5      44 ..      14      52 ..      10      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.6e-07
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ile+L e ++ is +e+A+e ++S   v  +Ik+++elg+
  gi|488601375|ref|YP_007907846.1| 14 ILEIL-ERNPEISQNEIAKEVGLSQPSVGARIKKMRELGI 52
                                      89999.66666****************************4 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.9e-06    0.0035       3      42 ..      11      52 ..       9      70 .. 0.90
   2 ?   -0.7   0.0       1.4   1.2e+03       8      27 ..     104     123 ..     101     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.9e-06
                            HTH_39  3 carilaaLrqhgsittleamrelditrla..aRIkeLrekGy 42
                                      +++il++L++  +i++ e  +e +  +++  aRIk +re G+
  gi|488601375|ref|YP_007907846.1| 11 DKMILEILERNPEISQNEIAKEVGLSQPSvgARIKKMRELGI 52
                                      589************************7444*********96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                            HTH_39   8 aaLrqhgsittleamreldi 27 
                                       +++  ++ ++tlea+ + +i
  gi|488601375|ref|YP_007907846.1| 104 TMMFIGEDLSTLEAIVDQHI 123
                                       66777888999999988776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.9e-06    0.0053      14      55 ..      13      54 ..       8      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-06
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +il  L r+ + + +e+a++++ls+ ++  ++++++e g++ 
  gi|488601375|ref|YP_007907846.1| 13 MILEILERNPEISQNEIAKEVGLSQPSVGARIKKMRELGIIN 54
                                      699999*********************************996 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05     0.013       5      41 ..      13      52 ..      10      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                            HTH_28  5 iikllaaGh...svreaArelgisrrtvyrWikryeegGi 41
                                      +i+++++ +   s++e+A+e+g+s+ +v   ik+ +e Gi
  gi|488601375|ref|YP_007907846.1| 13 MILEILERNpeiSQNEIAKEVGLSQPSVGARIKKMRELGI 52
                                      6777776544479************************997 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.8e-05     0.017      12      58 ..       8      54 ..       1      58 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                      -HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 12 geeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                      +e+ + +l++L ++ e++ +++ake+++ ++ ++  + +++e ++++
  gi|488601375|ref|YP_007907846.1|  8 DEKDKMILEILERNPEISQNEIAKEVGLSQPSVGARIKKMRELGIIN 54
                                      378899***********************************999986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.6e-05     0.041       4      54 ..       5      55 ..       1      68 [. 0.91
   2 ?   -1.1   0.0         2   1.8e+03      24      42 ..     114     132 ..     110     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                                      CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      + L e +  +   L ++ + + +eia+e+g+++++v   ++++ + G+++ 
  gi|488601375|ref|YP_007907846.1|  5 FELDEKDKMILEILERNPEISQNEIAKEVGLSQPSVGARIKKMRELGIINH 55
                                      7899999999999999*******************************9976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                                       HHCHHCCCTTSSCHCHHHH CS
                              TrmB  24 tadeiaeelgvprskvYev 42 
                                       t + i  +  +p ++vY++
  gi|488601375|ref|YP_007907846.1| 114 TLEAIVDQHIRPDPNVYDI 132
                                       6677777778899999986 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   2.4e-05     0.022       7      47 ..      13      52 ..      12      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGy 47
                                      +iL++l++ p+  +  e+A++ gl+ ++v   ++ + elG+
  gi|488601375|ref|YP_007907846.1| 13 MILEILERNPE-ISQNEIAKEVGLSQPSVGARIKKMRELGI 52
                                      69******999.8****************988888888886 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.6e-05      0.05      20      39 ..      30      49 ..      25      51 .. 0.93
   2 ?   -2.3   0.0       4.8   4.3e+03       3      13 ..     111     121 ..     110     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                      HHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEe 39
                                      A+e+glsqp+v ++ik+++e
  gi|488601375|ref|YP_007907846.1| 30 AKEVGLSQPSVGARIKKMRE 49
                                      99****************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHH CS
                             HTH_1   3 qlrlfvavaee 13 
                                       +l +++a++++
  gi|488601375|ref|YP_007907846.1| 111 DLSTLEAIVDQ 121
                                       78899999875 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-05     0.042      12      54 ..      13      55 ..      12      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                       I+++ e +  +++ ++a++ + s +sV   +kk+++ G +++
  gi|488601375|ref|YP_007907846.1| 13 MILEILERNPEISQNEIAKEVGLSQPSVGARIKKMRELGIINH 55
                                      688888989999*************************998776 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.2e-05     0.046      27      55 .]      25      53 ..      18      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      sq  +ak  gls  +v   ik+ ++lG+i
  gi|488601375|ref|YP_007907846.1| 25 SQNEIAKEVGLSQPSVGARIKKMRELGII 53
                                      99*************************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 ?   11.8   0.1   0.00014      0.13       4      42 ..       6      45 ..       4      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                      HS-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4  4 sLpererevlelrf.geglTleEIgerlgiSrerVrqiek 42
                                      +L+e+++++le      + ++ EI+++ g+S+  V  ++k
  gi|488601375|ref|YP_007907846.1|  6 ELDEKDKMILEILErNPEISQNEIAKEVGLSQPSVGARIK 45
                                      799*******98888****************987766666 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 ?   12.2   0.0   0.00016      0.14       8      58 ..      12      63 ..       8      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                           HTH_Mga  8 lkLlelLteneksltldelakeLglseltlqsdiseLnel..Fpeelsivikk 58
                                        +le+L   +++++  e+ake gls  ++  +i +++el   ++ ++i++k+
  gi|488601375|ref|YP_007907846.1| 12 KMILEILER-NPEISQNEIAKEVGLSQPSVGARIKKMRELgiINHAYGINLKN 63
                                      558888877.***************************9987777777777765 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.8   7.9e+03      52      64 ..      12      24 ..       7      26 .. 0.60
   2 ?   10.8   0.0   0.00042      0.37       4      73 ..      72     138 ..      69     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.8
                                      HHHHHTTTTSTTE CS
                    AsnC_trans_reg 52 rflreklaslpgv 64
                                      + + e l ++p++
  gi|488601375|ref|YP_007907846.1| 12 KMILEILERNPEI 24
                                      4556666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
                                       EE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg   4 slepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73 
                                        l+ ++    ++++ ++  +p  +  + v+G  ++ +    +dl  le++++++++  p+v +++  iv 
  gi|488601375|ref|YP_007907846.1|  72 DLKCRQ---PRDLINVFSGCPFFLNGFIVAGNKNLTMMFIGEDLSTLEAIVDQHIRPDPNVYDIDVGIVV 138
                                       555555...77788888888888888999*********************************99998886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00033      0.29       7      45 ..      10      51 ..       6      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                            HTH_23  7 Rlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      + +++l  +e    +s+ eIA+e g s+  v   +k+ re G
  gi|488601375|ref|YP_007907846.1| 10 KDKMILEILErnpEISQNEIAKEVGLSQPSVGARIKKMRELG 51
                                      556777777778889****************96666657766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1045.22
//
Query:       gi|488601376|ref|YP_007907847.1|  [L=93]
Description: hypothetical protein Asulf_01888 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 616.93
//
Query:       gi|488601377|ref|YP_007907848.1|  [L=331]
Description: DNA repair and recombination protein RadA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-93  312.7   0.1    1.9e-93  312.4   0.1    1.1  1  Rad51            Rad51
    9.5e-13   48.2   0.2    1.4e-12   47.6   0.2    1.3  1  RecA             recA bacterial DNA recombination protein
    1.5e-12   48.0   1.5    4.4e-12   46.4   1.5    1.9  1  HHH_5            Helix-hairpin-helix domain
    1.4e-09   37.7   0.1      2e-09   37.1   0.1    1.3  1  ATPase           KaiC
    4.7e-08   32.8   0.0    7.2e-08   32.2   0.0    1.3  1  AAA_25           AAA domain
    1.5e-05   25.1   0.0    7.2e-05   23.0   0.0    2.1  2  Cdd1             Pathogenicity locus
    0.00015   21.5   1.8       0.15   12.0   0.1    2.7  2  HHH              Helix-hairpin-helix motif
    0.00033   20.7   0.1    0.00066   19.7   0.1    1.5  1  RNA_pol_RpbG     DNA-directed RNA polymerase, subunit G
    0.00044   20.3   1.2    0.00077   19.5   0.3    1.9  1  HHH_2            Helix-hairpin-helix motif
     0.0011   18.7   0.0      0.013   15.3   0.0    2.5  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0021   18.6   0.1     0.0083   16.7   0.1    2.0  1  AAA_18           AAA domain
     0.0039   17.4   0.0      0.011   16.0   0.0    1.9  1  IMS_HHH          IMS family HHH motif
     0.0048   17.2   0.4       0.14   12.6   0.1    2.6  2  HHH_8            Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.037   14.3   0.2    1.8  1  AAA_22           AAA domain
       0.02   14.6   0.0      0.035   13.8   0.0    1.4  1  AAA_24           AAA domain
       0.03   14.6   0.1       0.11   12.7   0.0    2.1  2  DUF4332          Domain of unknown function (DUF4332)
      0.041   13.5   0.0      0.097   12.3   0.0    1.8  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.051   12.9   0.0       0.11   11.9   0.0    1.5  1  Coq4             Coenzyme Q (ubiquinone) biosynthesis protein
      0.053   14.0   0.1        0.1   13.1   0.1    1.5  1  ABC_tran         ABC transporter
      0.055   13.4   0.0      0.092   12.6   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
      0.067   13.6   0.4       0.21   12.0   0.1    2.0  2  AAA              ATPase family associated with various cellul
       0.11   12.3   0.1       0.31   10.9   0.1    1.8  1  NACHT            NACHT domain
       0.16   12.0   0.2       0.38   10.8   0.2    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


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 !  312.4   0.1   2.5e-96   1.9e-93       2     254 ..      76     330 ..      75     331 .] 0.96

  Alignments for each domain:
  == domain 1  score: 312.4 bits;  conditional E-value: 2.5e-96
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                       gf s+ ++le+r+++ ++ttGsk+lD+lLgGG+et++ite+fGef+sGktqlch+l+v vqlp+++gG eg +v id
  gi|488601377|ref|YP_007907848.1|  76 GFESGEKILERRKKVGKITTGSKELDKLLGGGVETQAITELFGEFGSGKTQLCHQLAVNVQLPKDQGGLEGCVVVID 152
                                       79999************************************************************************ PP

                                       SSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHH...HTHHHHHHS...-EEEEEEETTTGGGCH-- CS
                             Rad51  79 tegtfrperlveiaerykldkeevlenvayaRaytiehqeellq...qaaallaed...kfallivDsvtalyRtdf 149
                                       te tfrper+v++ae  +l+++evl+n+ +a ay+++hq+ l++   ++a+++++d   +++l+ivDs++a++R+++
  gi|488601377|ref|YP_007907848.1| 153 TENTFRPERIVQMAEAKGLNPDEVLKNIYVAQAYNSNHQMLLVDnakELAQKIKKDegkNVKLIIVDSLMAHFRAEY 229
                                       ******************************************98444567777765222699*************** PP

                                       -----THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STT CS
                             Rad51 150 sgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkge 226
                                        grg la+Rqqkl+++l+ L ++ + f++a+v+tnqv+a++d+    f +dp++P+gG+++ah++t R++lrk kge
  gi|488601377|ref|YP_007907848.1| 230 VGRGTLADRQQKLNRHLHDLMRFGEIFNAAIVVTNQVQAKPDT----FFGDPNRPVGGHIVAHTATFRIYLRKSKGE 302
                                       ******************************************9....99**************************** PP

                                       EEEEEEES-SSS-S-EEEEEEETTEEE- CS
                             Rad51 227 eRivkvvdsPnlpeleavfaigeeGied 254
                                        R+++++dsP+lpe ea+f ++e+Gi+d
  gi|488601377|ref|YP_007907848.1| 303 LRVARLIDSPHLPEGEAIFKVTEKGITD 330
                                       **************************98 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.2   1.8e-15   1.4e-12      27     223 ..      86     300 ..      63     310 .. 0.76

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.8e-15
                                       .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...HTT...--EEEEESS----H.. CS
                              RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...kkg...gvaafidaehaldp.. 95 
                                       +++kv  i++Gs  ld  lG GG+    i+e++G   sGkt l+ ++ +++q    +g   g ++ id+e ++ p  
  gi|488601377|ref|YP_007907848.1|  86 RRKKVGKITTGSKELDKLLG-GGVETQAITELFGEFGSGKTQLCHQLAVNVQlpkDQGgleGCVVVIDTENTFRPer 161
                                       357999**************.**********************99888888744334422257899*******9833 PP

                                       ..HHHHHTT--....GGG-EEE--SSHHH.......HHHHHHHHHTT..T--SEEEEE-TTT---STT-..------ CS
                              RecA  96 ..kyakklGvd....idellvsqpdtGeq.......aleiadalvrs..gaidlivvdsvaalvpkaei..eGemgd 155
                                         + a++ G++    +++++v+q  + ++       a e+a+++ +     + li+vds+ a   +ae    G ++d
  gi|488601377|ref|YP_007907848.1| 162 ivQMAEAKGLNpdevLKNIYVAQAYNSNHqmllvdnAKELAQKIKKDegKNVKLIIVDSLMAHF-RAEYvgRGTLAD 237
                                       33468888998333345678999987653111111155777777664225799*******9976.555512456666 PP

                                       ----HHHHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES CS
                              RecA 156 skvglqarlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrie 223
                                        +  l      + l  l    +  n++++  nq++ k    fg+p+   GG+ +   a+ r+ +r+++
  gi|488601377|ref|YP_007907848.1| 238 RQQKL-----NRHLHDLMRFGEIFNAAIVVTNQVQAKPDTFFGDPNRPVGGHIVAHTATFRIYLRKSK 300
                                       65554.....44455555555667889999***********************************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 !   46.4   1.5   5.6e-15   4.4e-12       3      57 .]      16      70 ..      14      70 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 5.6e-15
                                      HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                      +L +++G+G ++A +l +aGi ++e++a a++ e+++i  +G+ tA +ii ++++
  gi|488601377|ref|YP_007907848.1| 16 DLEDIPGVGSAIAEKLREAGIYTIEAVAVATPGEISSIAEVGESTAVKIISSARK 70
                                      799*************************************************997 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.1   2.6e-12     2e-09       2     200 ..      94     309 ..      93     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.6e-12
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaeky...gepgvfvtveepa....edlrenakslG 71 
                                        tg ++lD++l gG+  ++++ + Ge G+GKt ++ q +++    +   g +g  v ++ ++    e + + a++ G
  gi|488601377|ref|YP_007907848.1|  94 TTGSKELDKLLGGGVETQAITELFGEFGSGKTQLCHQLAVNVQLPKdqgGLEGCVVVIDTENtfrpERIVQMAEAKG 170
                                       799*************************************97654411155566666666655688*********** PP

                            ATPase  72 wdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl..aye.......ekeav 139
                                        + +++ ++  +++ +a++s+++       ++++el++++++  + +++k +++Ds+ ++  a++       +++++
  gi|488601377|ref|YP_007907848.1| 171 LNPDEVLKN--IYVAQAYNSNHQML---LVDNAKELAQKIKKD-EGKNVKLIIVDSLMAHfrAEYvgrgtlaDRQQK 241
                                       *********..99999999987744...6999*******9986.77899*******988742211111111134455 PP

                            ATPase 140 aReilrqlvrvlkklgvTailvsekss........seeaaggygveefivdgvivLdlkeieeelvRtl 200
                                       + + l+ l+r+ +  +   + +++++          ++ +gg+ v++  ++  i L++ + e ++ R +
  gi|488601377|ref|YP_007907848.1| 242 LNRHLHDLMRFGEIFNAAIVVTNQVQAkpdtffgdPNRPVGGHIVAH-TATFRIYLRKSKGELRVARLI 309
                                       55556666665555565555666655566666666556667777777.666666666666665666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   9.2e-11   7.2e-08      11     157 ..      89     227 ..      81     267 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 9.2e-11
                            AAA_25  11 svadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelr 87 
                                       +v+++ +  +++++l++g +  ++++ l+G  g+GKt l+ +la+ v + k   g      g V+++++E++    +
  gi|488601377|ref|YP_007907848.1|  89 KVGKITTGSKELDKLLGGGVETQAITELFGEFGSGKTQLCHQLAVNVQLPKDQGG----LEGCVVVIDTENTF--RP 159
                                       6777888889999****999****************************7665544....589**********8..57 PP

                            AAA_25  88 rRlravgeal..rddarllvldlagveslpLfakdrggtl.ltadvdaleaaieeveg..vrlvviDplsralgg 157
                                       +R+ ++ ea   ++d+ l  +++a+       ++ +++ l ++   ++l+++i++ eg  v+l+++D+l + +++
  gi|488601377|ref|YP_007907848.1| 160 ERIVQMAEAKglNPDEVLKNIYVAQA------YNSNHQMLlVDN-AKELAQKIKKDEGknVKLIIVDSLMAHFRA 227
                                       77777774444488899988888886......444455552555.59********99999*********987765 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   9.2e-08   7.2e-05       3      41 ..      12      50 ..      10      65 .. 0.90
   2 ?   -1.4   0.0       3.6   2.8e+03      33      63 ..     193     223 ..     185     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 9.2e-08
                              Cdd1  3 kalkelqdiPniGkalaedlvelGirsveelkgedpeel 41
                                      +++ +l+diP++G a+ae+l+e Gi+++e ++  +p e+
  gi|488601377|ref|YP_007907848.1| 12 NKIVDLEDIPGVGSAIAEKLREAGIYTIEAVAVATPGEI 50
                                      67889**************************99999876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                              Cdd1  33 lkgedpeelyeklekltgarhDpCvldvfrs 63 
                                       l   +++el +k++k  g+++   ++d +++
  gi|488601377|ref|YP_007907848.1| 193 LLVDNAKELAQKIKKDEGKNVKLIIVDSLMA 223
                                       5567889999999999999999999998886 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00019      0.15       5      29 ..       9      33 ..       5      34 .. 0.81
   2 !    8.4   0.3    0.0027       2.1       2      29 ..      39      66 ..      38      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                      HHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH  5 lipasreeLlalPGVGpktAeaIls 29
                                      + ++ + +L+++PGVG + Ae+ ++
  gi|488601377|ref|YP_007907848.1|  9 EANNKIVDLEDIPGVGSAIAEKLRE 33
                                      55666669*************9875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0027
                                      HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH  2 leglipasreeLlalPGVGpktAeaIls 29
                                      +e++  a++ e+ ++  VG++tA +I+s
  gi|488601377|ref|YP_007907848.1| 39 IEAVAVATPGEISSIAEVGESTAVKIIS 66
                                      688999*****************88876 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   8.5e-07   0.00066      14      93 ..     175     257 ..     161     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.5e-07
                      RNA_pol_RpbG  14 sklkdlkivkikcqne.eielDiiseln.ifkeed..kveviisrekPeyldgkdFcghGylvtekeeenkiitliS 86 
                                       + lk+++++++ + n+  + +D ++el  ++k+++  +v++ii  +   +    +++g+G+l+ ++++ n+ +  + 
  gi|488601377|ref|YP_007907848.1| 175 EVLKNIYVAQAYNSNHqMLLVDNAKELAqKIKKDEgkNVKLIIVDSLMAHFR-AEYVGRGTLADRQQKLNRHLHDLM 250
                                       679*******99999846678*****963566554449***99999999888.8****************9999999 PP

                      RNA_pol_RpbG  87 lfGllvk 93 
                                        fG +++
  gi|488601377|ref|YP_007907848.1| 251 RFGEIFN 257
                                       9999987 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   9.9e-07   0.00077       8      52 ..      20      65 ..      16      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.9e-07
                             HHH_2  8 IrhVGektAklLakrFk.sldaLkkasleeLlevddiGeeiAqsiv 52
                                      I+ VG++ A++L ++   +++a + a+  e++++ ++Ge +A +i+
  gi|488601377|ref|YP_007907848.1| 20 IPGVGSAIAEKLREAGIyTIEAVAVATPGEISSIAEVGESTAVKII 65
                                      99**********998555************************9997 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 !   15.3   0.0   1.7e-05     0.013       4      28 ..      18      42 ..      16      49 .. 0.90
   2 ?    0.3   0.0      0.83   6.5e+02       4      18 ..      51      65 ..      48      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                   DNA_pol_lambd_f  4 tkvyGVGpktAkkwyakGirtledl 28
                                        + GVG+++A+k+ ++Gi t+e +
  gi|488601377|ref|YP_007907848.1| 18 EDIPGVGSAIAEKLREAGIYTIEAV 42
                                      6799******************987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.83
                   DNA_pol_lambd_f  4 tkvyGVGpktAkkwy 18
                                      +++  VG +tA k +
  gi|488601377|ref|YP_007907848.1| 51 SSIAEVGESTAVKII 65
                                      578889999998765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.1e-05    0.0083       3      91 ..     116     230 ..     115     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.......................gvnlrdvakenglllevdpealdeskrldedk 56 
                                       l G  G+GKt+l++ L+   ++                          + ++a  +gl  ++  + +   +  + + 
  gi|488601377|ref|YP_007907848.1| 116 LFGEFGSGKTQLCHQLAVNVQLpkdqgglegcvvvidtentfrpeR--IVQMAEAKGLNPDEVLKNIYVAQAYNSNH 190
                                       67889***********665333555555677799777777777432..33333333333322222345555666666 PP

                            AAA_18  57 ldklldaleenss..aleegknl...vidghlaeleseaa 91 
                                       ++ l+d+ +e ++  + +egkn+   ++d+++a+++ e+ 
  gi|488601377|ref|YP_007907848.1| 191 QMLLVDNAKELAQkiKKDEGKNVkliIVDSLMAHFRAEYV 230
                                       66666666666557744555555556*********99875 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.5e-05     0.011      12      32 .]      16      36 ..      12      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                           IMS_HHH 12 pitkipGiGgklgekLeklGi 32
                                      ++ +ipG+G+  +ekL+  Gi
  gi|488601377|ref|YP_007907848.1| 16 DLEDIPGVGSAIAEKLREAGI 36
                                      899**************9998 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00018      0.14      48      65 ..      16      33 ..       3      34 .. 0.79
   2 ?    1.8   0.0      0.39   3.1e+02      48      63 ..      49      64 ..      37      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                      HCTTSTT--HHHHHHHHH CS
                             HHH_8 48 eltklpgiGkkiaakiee 65
                                      +l+++pg+G +ia+k++e
  gi|488601377|ref|YP_007907848.1| 16 DLEDIPGVGSAIAEKLRE 33
                                      69**************99 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.39
                                      HCTTSTT--HHHHHHH CS
                             HHH_8 48 eltklpgiGkkiaaki 63
                                      e++++  +G+++a ki
  gi|488601377|ref|YP_007907848.1| 49 EISSIAEVGESTAVKI 64
                                      58999*********99 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.8e-05     0.037       4      98 ..     110     219 ..     108     262 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......... 70 
                                       t+ i+ ++Ge G+GKT l+ +l+ + +  +++   +  vv ++  +   ++ + + +++a gl+ ++          
  gi|488601377|ref|YP_007907848.1| 110 TQAITELFGEFGSGKTQLCHQLAVNVQLPKDQGGLEGCVVVIDTENTFRPERIVQ-MAEAKGLNPDEvlkniyvaqa 185
                                       788999****************999865555555555555555555554444433.233333322222222222222 PP

                            AAA_22  71 erlsseell.ealeqalrarav.....ielliiD 98 
                                       ++ + + ll +   + +++ ++     ++l+i+D
  gi|488601377|ref|YP_007907848.1| 186 YNSNHQMLLvDNAKELAQKIKKdegknVKLIIVD 219
                                       2222233333333333333333444444455555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-05     0.035       7      74 ..     116     221 ..     111     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                            AAA_24   7 iyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvel...... 59 
                                       ++G+ g+GKT l+ +l             +  +++idte+ +    + +++++      + +++l+ +         
  gi|488601377|ref|YP_007907848.1| 116 LFGEFGSGKTQLCHQLavnvqlpkdqgglEGCVVVIDTENTF---RPERIVQMAeakglNPDEVLKNIYVAqaynsn 189
                                       79************************999999********66...66666655556688445555555555222222 PP

                            AAA_24  60 .................aaeladyktlviDti 74 
                                                        ++e ++ k +++D++
  gi|488601377|ref|YP_007907848.1| 190 hqmllvdnakelaqkikKDEGKNVKLIIVDSL 221
                                       33333333333455556666666666666665 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014      0.11      52      88 ..      14      50 ..      10      74 .. 0.85
   2 ?   -2.9   0.0       9.9   7.7e+03      82      94 ..     195     207 ..     182     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                           DUF4332 52 lAdLarikgigeeyaeLLeaaGvdsvaeLaqrnpanL 88
                                      ++dL  i+g+g++ ae L +aG+ +++++a  +p ++
  gi|488601377|ref|YP_007907848.1| 14 IVDLEDIPGVGSAIAEKLREAGIYTIEAVAVATPGEI 50
                                      789999*********************9999998765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.9
                           DUF4332  82 qrnpanLhqklkr 94 
                                         n+++L qk+k+
  gi|488601377|ref|YP_007907848.1| 195 VDNAKELAQKIKK 207
                                       4566677777665 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   0.00012     0.097      17     120 ..     114     227 ..      96     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                       EEEEESTTSSHHHHHHHHHHHSSTS......SEEEEEEESEEHHHHHHHHHHCHHSS.....GGGGEEEEEEETTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxx RF
                       ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsd......daiiyvgiGergnevaevleefpegt.....imkrtvlvantsnep 82 
                                       t ++g+fg Gkt+++++l+ + +        + +++v   e++   +++++  + ++     ++k+ + va   n+ 
  gi|488601377|ref|YP_007907848.1| 114 TELFGEFGSGKTQLCHQLAVNVQLPkdqgglEGCVVVIDTENTFRPERIVQMAEAKGlnpdeVLKN-IYVAQAYNS- 188
                                       568**************9998755477898778999988888888888887777744333425444.455555554. PP

                                       HHHHHHHHHHHHHHHHHHHH.TTSEE.EEEEETHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxx RF
                       ATP-synt_ab  83 vaareasiytgitlAEyfrd.qgknv.lliadslsrwaeA 120
                                          +++ +  +  lA   ++ +gknv l+i+dsl  + +A
  gi|488601377|ref|YP_007907848.1| 189 -NHQMLLVDNAKELAQKIKKdEGKNVkLIIVDSLMAHFRA 227
                                       .4578889999999999987799**944567888877766 PP

>> Coq4  Coenzyme Q (ubiquinone) biosynthesis protein Coq4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.11      21      81 ..      41     103 ..      28     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                              Coq4  21 iaalvdpergdlvaalgettglpalerlre..kmlsdeeGrriLkerpritsetldleklkkl 81 
                                        +a++ p +   +a +ge t+++++++ r+  ++   e+G++iL+ r ++ + t   ++l+kl
  gi|488601377|ref|YP_007907848.1|  41 AVAVATPGEISSIAEVGESTAVKIISSARKlaEIGGFESGEKILERRKKVGKITTGSKELDKL 103
                                       468889999999************9998863367889*************9999988888876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00013       0.1       8     102 ..     108     202 ..     102     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvrenesde 83 
                                       ++   ++ ++Ge G+GK+ L+  la +++  +++  l+g  +   +e ++  ++i  + + + l+p+  v +n + +
  gi|488601377|ref|YP_007907848.1| 108 VETQAITELFGEFGSGKTQLCHQLAVNVQLPKDQGGLEGCVVVIdTENTFRPERIVQMAEAKGLNPDE-VLKNIYVA 183
                                       67788999******************999966666667665555356777778888888889999999.99996666 PP

                                       CHHHHHHHSTTGGTTCBGE CS
                                       xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  84 eiekalsklglkelkdtvv 102
                                       ++++  +++ l++ +++ +
  gi|488601377|ref|YP_007907848.1| 184 QAYNSNHQMLLVDNAKELA 202
                                       6666666666666444444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012     0.092      18     127 ..     109     221 ..      97     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienl.edkdk....yviyyialreesiskldefieeeeekkklekalgiavpka 89 
                                       e++ i  ++G  gsGKt+L  +++ n  + kd+      + +i+ ++ +  +    ++e +  +  e  +++++  a
  gi|488601377|ref|YP_007907848.1| 109 ETQAITELFGEFGSGKTQLCHQLAVNVqLPKDQggleGCVVVIDTENTFRPERIVQMAEAKGLNPDE--VLKNIYVA 183
                                       5899999***************999883444447787677777777777766665545544444222..22333333 PP

                          ATPase_2  90 eleeilk.eksklvfkaielllekikkkgkk..iiiiiDel 127
                                       ++   ++ +++ l+  + ++l +kikk+  k    ii+D l
  gi|488601377|ref|YP_007907848.1| 184 QA---YNsNHQMLLVDNAKELAQKIKKDEGKnvKLIIVDSL 221
                                       33...333566677777788888888877776667788876 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 ?   -2.3   0.0       7.2   5.6e+03      24      57 ..      39      72 ..      22      87 .. 0.65
   2 ?   12.0   0.1   0.00026      0.21       3      91 ..     116     223 ..     115     274 .. 0.49

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.2
                                      HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                               AAA 24 vefleisgsellskyvgesekkirelfkeakeka 57
                                      +e + +  +  +s++ + +e+   +++++a++ a
  gi|488601377|ref|YP_007907848.1| 39 IEAVAVATPGEISSIAEVGESTAVKIISSARKLA 72
                                      5566666666666777777777777777777665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00026
                                       EESSTTSSHHHHHHHHHHHHTHE.........EEEEETTTCSSS............................STTHH CS
                               AAA   3 lyGppGtGKTllakavakelgve.........fleisgsellsk............................yvges 42 
                                       l+G  G GKT l++++a +++ +         ++ i+  + +                                   
  gi|488601377|ref|YP_007907848.1| 116 LFGEFGSGKTQLCHQLAVNVQLPkdqgglegcVVVIDTENTFRPerivqmaeakglnpdevlkniyvaqaynS---- 188
                                       799****************876566666667744444444442234444333222222333333333333220.... PP

                                       HHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHH CS
                               AAA  43 ekkirelfkeakekakpsilfiDEidalaksr.sgseseeeervvnqLlt 91 
                                                      ++  l++D++ +la++  +++ ++++  +v+ L++
  gi|488601377|ref|YP_007907848.1| 189 ---------------NHQMLLVDNAKELAQKIkKDEGKNVKLIIVDSLMA 223
                                       ...............34455555555554444222222222223333322 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0004      0.31       6      99 ..     117     207 ..     113     272 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                                       EC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCC CS
                             NACHT   6 qGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelper 82 
                                        Ge GsGKT L ++la+  + +k+++g    v ++    + r++++    ++  ++++ p +  +++ +  + + + 
  gi|488601377|ref|YP_007907848.1| 117 FGEFGSGKTQLCHQLAVNVQLPKDQGGLEGCVVVIDTENTFRPERI---VQMAEAKGLNPDEVLKNIYVAQAYNSNH 190
                                       6999****************99999987566666666665555533...3333445555555444433344444444 PP

                                       EEEEEE-STT-SS-TCH CS
                             NACHT  83 lLlilDglDelvtdlgq 99 
                                        +l++D + el+++ ++
  gi|488601377|ref|YP_007907848.1| 191 QMLLVDNAKELAQKIKK 207
                                       45556666666665555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00049      0.38      19      44 ..     111     136 ..      88     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                                       TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                       +++  L G+ G+GKT+l+++la +++
  gi|488601377|ref|YP_007907848.1| 111 QAITELFGEFGSGKTQLCHQLAVNVQ 136
                                       45688**************9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1830.98
//
Query:       gi|488601378|ref|YP_007907849.1|  [L=287]
Description: RecA-superfamily ATPases implicated in signal transduction [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-36  123.2   0.1      2e-35  122.2   0.1    1.5  1  ATPase     KaiC
    0.00048   19.7   0.0     0.0022   17.6   0.0    1.8  1  AAA_25     AAA domain
  ------ inclusion threshold ------
      0.016   14.5   0.1      0.027   13.8   0.1    1.3  1  Rad51      Rad51
      0.023   14.0   0.0      0.032   13.5   0.0    1.3  1  DnaB_C     DnaB-like helicase C terminal domain
      0.063   13.3   0.0       0.13   12.3   0.0    1.5  1  AAA_14     AAA domain
       0.12   12.1   0.0       0.21   11.3   0.0    1.3  1  IstB_IS21  IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   0.1   6.6e-39     2e-35       1     221 [.       8     218 ..       8     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 6.6e-39
                            ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGw.dlek 76 
                                       + tgI gl e+l+gG+  ++vv + G++G GKtif+ q+l++g+++ g+++++++++ ++ed++++++slGw ++ +
  gi|488601378|ref|YP_007907849.1|   8 IDTGIIGLNELLDGGFLPNSVVAVLGSSGVGKTIFSIQYLLSGVQR-GDRCIYISFDLEKEDIIKQMSSLGWtEIAD 83 
                                       57*****************************************999.*************************78*** PP

                            ATPase  77 leeegklaiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvlk 152
                                       + e+gk+++   ++++         +  + l+   +  ++e ++ +r+viDs t++  ++ + + R+ ++ ++++++
  gi|488601378|ref|YP_007907849.1|  84 YIENGKIYVKSFFAENVS-------FVNNDLL---NILVSEAGIsTRIVIDSFTPM-ISSFNLESRNDIKWFFQRVR 149
                                       ************999764.......4444444...44577888879**********.999999************** PP

                            ATPase 153 klgvTailvsekss.seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte 221
                                       ++  Tai++ e +  ++       +  f++d +i+L++  + e + Rtl+i+k Rg+ h   ++p++I +
  gi|488601378|ref|YP_007907849.1| 150 EIS-TAIITVEEPLdGKIDDPSVSIPIFLSDTAIHLKNIGYGEAFSRTLKIIKHRGSWHAEGIFPYKILK 218
                                       996.88888886663666666677778*****************************************87 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.4e-07    0.0022      22     177 ..      15     153 ..       4     157 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.4e-07
                            AAA_25  22 rrwlvk.gllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg.. 94 
                                       ++ l++ g+lp ++++++ G +g+GKt + ++  l+ + +G+           +++y+s++   +++ + ++ +g  
  gi|488601378|ref|YP_007907849.1|  15 LNELLDgGFLP-NSVVAVLGSSGVGKTIFSIQYLLSGVqRGD-----------RCIYISFDLEKEDIIKQMSSLGwt 79 
                                       56666647886.9999********************994444...........899999999999999999988873 PP

                            AAA_25  95 ..ealrddarllvldlagveslpLfakdrggtlltadvdaleaaieeveg.vrlvviDplsralgg.densnsdvga 167
                                         +++ ++++ +v +          +++ + + ++ d+ +    + e +g    +viD+++ + +  + +s +d++ 
  gi|488601378|ref|YP_007907849.1|  80 eiADYIENGKIYVKSF---------FAE-NVSFVNNDLLN--ILVSE-AGiSTRIVIDSFTPMISSfNLESRNDIKW 143
                                       3333344444444442.........222.33346777533..33444.44467799999999888889999999999 PP

                            AAA_25 168 lvealeriar 177
                                       +++++++i++
  gi|488601378|ref|YP_007907849.1| 144 FFQRVREIST 153
                                       9888888875 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   8.9e-06     0.027      18      57 ..       7      46 ..       3      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.9e-06
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                      ++ tG   l+elL+GG+   s+  ++G ++ Gkt ++ + 
  gi|488601378|ref|YP_007907849.1|  7 RIDTGIIGLNELLDGGFLPNSVVAVLGSSGVGKTIFSIQY 46
                                      699*******************************998774 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.032       3      71 ..       9      77 ..       8     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                      XSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHH CS
                                      xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  3 stgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsse 71
                                      +tg   L++l+ +G+ ++ ++ + + +++Gkt + ++   + ++ +  +++++s++ ++e++++++ s  
  gi|488601378|ref|YP_007907849.1|  9 DTGIIGLNELLdGGFLPNSVVAVLGSSGVGKTIFSIQYLLSGVQ-RGDRCIYISFDLEKEDIIKQMSSLG 77
                                      6888888887735799*********************9988775.5568999***********9997743 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.2e-05      0.13       3      50 ..      27      74 ..      25     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe 50
                                       ++++ G   vGKT +  q++ +   + ++++yi++d e+++ +++ +
  gi|488601378|ref|YP_007907849.1| 27 SVVAVLGSSGVGKTIFSIQYLLSGVQRGDRCIYISFDLEKEDIIKQMS 74
                                      6899************988876655889*********99996665443 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.9e-05      0.21      48      83 ..      27      62 ..      13      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.9e-05
                         IstB_IS21 48 enivllGpsGvGKshlaialgveavraglsvlfvrv 83
                                        +++lG sGvGK+ ++i    ++v++g + ++++ 
  gi|488601378|ref|YP_007907849.1| 27 SVVAVLGSSGVGKTIFSIQYLLSGVQRGDRCIYISF 62
                                      56899**************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1803.99
//
Query:       gi|488601379|ref|YP_007907850.1|  [L=119]
Description: hypothetical protein Asulf_01891 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.086   12.7   0.1       0.12   12.2   0.1    1.3  1  Activator-TraM  Transcriptional activator TraM


Domain annotation for each model (and alignments):
>> Activator-TraM  Transcriptional activator TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.6e-06      0.12       5      91 ..       6      94 ..       3     118 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.6e-06
                    Activator-TraM  5 eeiikeiavkhGiavg...r.ddPililqtinerllqdsakaqqelldqfkeeleaiasrWgddakekaervlnaalaa 79
                                       +i+k+i +  G++++   r d  il  +t      ++  +a   l +q ke l +i+sr  d+a+ k  +++   + a
  gi|488601379|ref|YP_007907850.1|  6 SKILKKILAIDGVIMSalyRiDGEILCAKTNV--SSREVLTALYWLENQIKEMLYQISSRDLDEARFKFGKIVIILFPA 82
                                      56666666666666552222244455554422..2355666667777899***************************** PP

                    Activator-TraM 80 skealvkllqeg 91
                                      sk +++ ++ + 
  gi|488601379|ref|YP_007907850.1| 83 SKTTVIGVMIDE 94
                                      ****99888432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 721.32
//
Query:       gi|488601380|ref|YP_007907851.1|  [L=246]
Description: putative hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-19   71.8   0.0    1.6e-19   71.4   0.0    1.2  1  Abhydrolase_6    Alpha/beta hydrolase family
    6.4e-18   65.3   0.0    8.6e-15   55.1   0.0    2.1  1  Abhydrolase_1    alpha/beta hydrolase fold
    1.5e-16   60.4   0.0    2.8e-16   59.5   0.0    1.4  1  Hydrolase_4      Serine aminopeptidase, S33
    1.8e-07   30.1   0.0    2.8e-07   29.5   0.0    1.2  1  Ndr              Ndr family
    1.8e-05   25.0   0.0    5.2e-05   23.5   0.0    1.8  1  Thioesterase     Thioesterase domain
    4.9e-05   23.2   0.0     0.0011   18.7   0.0    2.1  2  PGAP1            PGAP1-like protein
    9.8e-05   22.2   0.0     0.0068   16.2   0.0    2.2  2  Abhydrolase_5    Alpha/beta hydrolase family
    0.00011   22.1   0.0      0.016   15.1   0.0    2.1  1  Ser_hydrolase    Serine hydrolase
    0.00023   20.9   0.0      0.056   13.1   0.1    2.9  2  FSH1             Serine hydrolase (FSH1)
      0.001   18.9   0.0     0.0016   18.3   0.0    1.5  1  Lipase_3         Lipase (class 3)
     0.0014   18.1   0.0       0.69    9.3   0.1    2.5  2  Peptidase_S9     Prolyl oligopeptidase family
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.032   14.1   0.0    1.6  1  Abhydrolase_3    alpha/beta hydrolase fold
      0.016   14.5   0.0        1.3    8.3   0.0    2.5  2  DUF915           Alpha/beta hydrolase of unknown function (DU
      0.022   13.7   0.0        3.1    6.6   0.0    2.4  2  Chlorophyllase2  Chlorophyllase enzyme
       0.03   14.4   0.0      0.052   13.7   0.0    1.3  1  Abhydrolase_4    TAP-like protein
      0.048   13.2   0.0       0.17   11.4   0.0    1.9  1  DUF676           Putative serine esterase (DUF676)
       0.19   10.8   0.0       0.35    9.9   0.0    1.3  1  DUF2048          Abhydrolase domain containing 18


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.5e-22   1.6e-19       1     218 [.      16     235 ..      16     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.5e-22
                                       EEEE--GC.....G.CHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT...TTSEEEEEETC CS
                     Abhydrolase_6   1 vlllHGagssassW.lvapLaallaagvhvlapDlpGhGrsdpppldledladl.aalldelaa.gggpvvlvGHSl 74 
                                       vl +HG+gs++ +W    +L   + +g   +a+DlpGhG  ++++ + e ++d+ + +l++  + g ++ ++ GHSl
  gi|488601380|ref|YP_007907851.1|  16 VLYIHGSGSNSKIWkN--QL--EAIGG---YAIDLPGHG--ESDDANIETVEDYaRYVLEAMEEkGLDRMFIAGHSL 83 
                                       6789**********55..66..55666...6********..99999999999995445555554556666******* PP

                                       HHHHHHHHHHCC.......EE.EEES-..----TTTS----TTHHHHHHTT-C...CCCHCCH.S-HSCCCCHHHCC CS
                     Abhydrolase_6  75 GGalalaaapla.....lvvg.vlldppptalpagllaaalelllallallrl...lawlsre.plprlfladedad 141
                                       GGa+a++   +      +v g +l+ +   +++++ l+ +le l+   +  ++     ++sr+ +++ ++ +     
  gi|488601380|ref|YP_007907851.1|  84 GGAIAQM---VYlidrsRVMGlILVGT---GARLRVLDEILEGLKNDFDTMAKklvNMLFSRKfSDS-RIKD----- 148
                                       *******...66655667788788888...9999999999999997777666623222222222222.4444..... PP

                                       CCHCHCCCGHH.....HHCCHHCHTTCCHHTT-TTGC...EEEC..TT-C.....HHHHCHHCCCH.STTEEETCE. CS
                     Abhydrolase_6 142 aawrarlarla.....allaglgllpaaawadlpvpl...lvlg..geDp.....lvprllerlla.qagarlpvvl 202
                                       +   + l+ ++     ++ a++ +  +++++   v +   ++ +  g+D+      + +++    +   ga++ +v+
  gi|488601380|ref|YP_007907851.1| 149 EVLKDLLSCGSrithrDFSACDKFDLLSDYKEGKVKVdvpVL-CivGSDDimtpvKYSEFF----RkTIGAEV-KVI 219
                                       333333333332222122222223334455555555554422.333888865544333444....44477999.*** PP

                                       ..SSS-HHHHSHHHHH CS
                     Abhydrolase_6 203 pgaGHlphleepdeva 218
                                       ++aGH++++e+pdev+
  gi|488601380|ref|YP_007907851.1| 220 EDAGHMVMIEKPDEVN 235
                                       **************97 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   8.2e-18   8.6e-15       2     257 .]      15     231 ..      15     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 8.2e-18
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       +++++hG + +s +w +    +a+       +++Dl+G+g+S+ a  +     +  ++a+++  +++  g+d+  + 
  gi|488601380|ref|YP_007907851.1|  15 PVLYIHGSGSNSKIWKN--QLEAIG-----GYAIDLPGHGESDDANIE-----TVEDYARYVLEAMEEKGLDRMFIA 79 
                                       799***********999..666665.....59***********99975.....778899999999************ PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrh 155
                                       GhS+GG+ia ++++   +rV +l+l+g+     +  +  + +++++ + fd++a +      ++l++++   ++   
  gi|488601380|ref|YP_007907851.1|  80 GHSLGGAIAQMVYLIDRSRVMGLILVGT----GARLRVLDEILEGLKNDFDTMAKKLV----NMLFSRKFSDSRIK- 147
                                       ****************************....44445555556666666666655555....55555554444444. PP

                                       HHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHH CS
                     Abhydrolase_1 156 rlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaled 232
                                                ++ k++ s gs++ + + + a   ++  +++ ++k+  +        +p+l i g++D ++p k++e+
  gi|488601380|ref|YP_007907851.1| 148 --------DEVLKDLLSCGSRITHRD-FSACDKFDLLSDYKEGKVKVD--------VPVLCIVGSDDIMTPVKYSEF 207
                                       ........566677888885555554.444456666666666665533........3******************** PP

                                       HHHCHTSEEEEEEETCSSSHHHHSH CS
                     Abhydrolase_1 233 laqllpkkrlvvisdagHlaflegp 257
                                       +++ +   +++vi+dagH++ +e+p
  gi|488601380|ref|YP_007907851.1| 208 FRKTIGA-EVKVIEDAGHMVMIEKP 231
                                       *******.**************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   2.6e-19   2.8e-16      34     238 ..      38     230 ..      16     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.6e-19
                       Hydrolase_4  34 vyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPa 110
                                        ya+D  GhG+s+ +        + v+D a +v ++ ee++  ++f+ GhS+GG+ia+ + l  +++v glil+++ 
  gi|488601380|ref|YP_007907851.1|  38 GYAIDLPGHGESDDANI------ETVEDYARYVLEAMEEKGLDRMFIAGHSLGGAIAQMVYLIDRSRVMGLILVGTG 108
                                       59**********87777......78889999999999999999**************9999888888********** PP

                       Hydrolase_4 111 lkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevvaayeadplv.hgkitvr..lllelldamkrle 184
                                        +++    + ++l+ l + + ++++kl    n++++   +d +  +++ +d l  + +it r   + + +d++++ +
  gi|488601380|ref|YP_007907851.1| 109 ARLRV---LDEILEGLKNDFDTMAKKLV---NMLFSRKFSDSRIKDEVLKDLLScGSRITHRdfSACDKFDLLSDYK 179
                                       99985...56777766666666555544...477888888888888888888887889998833456779******* PP

                       Hydrolase_4 185 eraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                       e + k+++P+l + G++D  ++ + s+ + +++g+   ++k+++ + H+++ E+
  gi|488601380|ref|YP_007907851.1| 180 EGKVKVDVPVLCIVGSDDIMTPVKYSEFFRKTIGA---EVKVIEDAGHMVMIEK 230
                                       **********************9999999999995...*************997 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   2.7e-10   2.8e-07      61     277 ..      41     243 ..      31     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.7e-10
                                       EE-TT-STT-----TT-----HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S-- CS
                               Ndr  61 vdaPGqeegaaslpedyqfpslddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaa 137
                                       +d PG+ e     ++d ++ +++d a  +l+ ++   l+ +   G   G  i     l  ++rv+gl+L+ + ++ +
  gi|488601380|ref|YP_007907851.1|  41 IDLPGHGE-----SDDANIETVEDYARYVLEAMEEKGLDRMFIAGHSLGGAIAQMVYLIDRSRVMGLILVGTGARLR 112
                                       66666655.....35677889**********************************99*************9776655 PP

                                       -HHHHHHHHHH.......TTTS-HHHHHHHHHS-HHHHHH..T-HHHHHHHHHHHT-TTHHHHHHHHHHHHT----- CS
                               Ndr 138 gwvewakeKlsskllkkvgltdllkdlllahkFgkeekse..nsdlvreyrkllkerlnsknlelyleaynkRrdle 212
                                        + + + e l +     + +++ l+++l ++kF+    +    +dl  ++ +++++r+  +      + ++   d +
  gi|488601380|ref|YP_007907851.1| 113 -VLDEILEGLKN---DFDTMAKKLVNMLFSRKFSDSRIKDevLKDLL-SCGSRITHRDF-SA----CDKFDLLSDYK 179
                                       .66666777775...6789***************9998773335565.78888888877.33....45567777888 PP

                                       --TTSSSS-EEEEEETTSTTHHHHHHHHHHS-TTTEEEEE.ETT-TT-HHHH-HHHHHHHHHHHHH CS
                               Ndr 213 ierkklevkvllvvGdkspfvdevvevnskldkkkttllk.vadsgglvleeqPdklaeslklflk 277
                                       + + k++v+vl +vG+      + v+  + + k+  + +k ++d+g +v+ e+Pd +  ++  f+k
  gi|488601380|ref|YP_007907851.1| 180 EGKVKVDVPVLCIVGSDD--IMTPVKYSEFFRKTIGAEVKvIEDAGHMVMIEKPDEVNSTILEFVK 243
                                       8888999********775..556788889999988888873699***************9999987 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.9e-08   5.2e-05      22     187 ..      32     203 ..      17     242 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.9e-08
                                       HCTTCEEEEEEECSTTST.SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEE CS
                      Thioesterase  22 klsdpvvevlavqlpgre.rdepplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArqLesqGlavksl 97 
                                       +l +  +  +a+ lpg++ +d++ +e+ e+ a +++ea+++   +    ++GhSlGg++A+ v   L ++ + v +l
  gi|488601380|ref|YP_007907851.1|  32 QLEA--IGGYAIDLPGHGeSDDANIETVEDYARYVLEAMEEKGLD-RMFIAGHSLGGAIAQMVY--LIDR-SRVMGL 102
                                       4444..7899******************************99999.788***********8762..3333.345566 PP

                                       EEESCCCCCCHHCHHCCCHTTHHT....HHHHHCCTTHH..HCCTTTHCCHHHHHHHH....HHHHHHHHHTCCS-T CS
                      Thioesterase  98 flidssapseteaqeasrraedee....fveeltdlggt..epeelledeellsellp....alradyraleqyslr 164
                                       +l+++ a+ ++  +     + +++    + ++l  ++ +  ++++  +de +l++ll+     +  d+ a  ++ l 
  gi|488601380|ref|YP_007907851.1| 103 ILVGTGARLRVLDE---ILEGLKNdfdtMAKKLVNMLFSrkFSDSRIKDE-VLKDLLScgsrITHRDFSACDKFDLL 175
                                       66665555442222...111111112234444444444443333333333.44444431111455555555555555 PP

                                       TSCSE.....HHCEEEEEEGSS-CTCCC CS
                      Thioesterase 165 peaaq.....klratlfngsddklkdld 187
                                       ++ ++      +++ + +gsdd ++ ++
  gi|488601380|ref|YP_007907851.1| 176 SDYKEgkvkvDVPVLCIVGSDDIMTPVK 203
                                       5555555555555666666666666666 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.092        97       5      21 ..      14      30 ..      11      41 .. 0.83
   2 !   18.7   0.0     1e-06    0.0011      67     152 ..      52     130 ..      44     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.092
                             PGAP1  5 ipVlFvpGnagsykqvr 21
                                       pVl+++G++ + k ++
  gi|488601380|ref|YP_007907851.1| 14 LPVLYIHGSGSNSKIWK 30
                                      6********99988665 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1e-06
                             PGAP1  67 dqaeylndaIkyIlslysssekeptsviliGHSmGGivaraaltlknyikqsvntiltlasPhalpplsfdkdilkl 143
                                         +e ++d  +y+l+ +  +ek   ++++ GHS+GG +a+++   ++   + v  ++ +++   l +l  d+ +  l
  gi|488601380|ref|YP_007907851.1|  52 ANIETVEDYARYVLEAM--EEKGLDRMFIAGHSLGGAIAQMVYLIDR---SRVMGLILVGTGARLRVL--DEILEGL 121
                                       56788999999999999..889999**************99988887...567777777777777666..6666666 PP

                             PGAP1 144 yervnefwk 152
                                        +  +++ k
  gi|488601380|ref|YP_007907851.1| 122 KNDFDTMAK 130
                                       655555555 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.5e-06    0.0068      49      88 ..      67     106 ..      56     112 .. 0.78
   2 ?    3.8   0.0      0.04        43      85     133 ..     173     219 ..     157     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.5e-06
                     Abhydrolase_5  49 iikeapklekfvvgGhslGGvvasrfaa.eeekiegvvfla 88 
                                       +++  ++l++++++GhslGG++a  +   + +++ g+++++
  gi|488601380|ref|YP_007907851.1|  67 AME-EKGLDRMFIAGHSLGGAIAQMVYLiDRSRVMGLILVG 106
                                       444.456899************9876552668999999876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.04
                     Abhydrolase_5  85 vflasYPekdelselskkvlsivgteDgvlnvkslekakkflpkdtkvv 133
                                        +l+ Y e   + +  ++vl ivg++D + +vk  e  +k++  + kv+
  gi|488601380|ref|YP_007907851.1| 173 DLLSDYKE--GKVKVDVPVLCIVGSDDIMTPVKYSEFFRKTIGAEVKVI 219
                                       56667764..3578899********999888887776777776666554 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.5e-05     0.016      39     154 ..      57     226 ..      16     236 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHC-S.TTEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET--SGG..................... CS
                     Ser_hydrolase  39 ledWvaaleaaveaae.ekvvlvAHSlgclavlhaaelqlakkvagalLVapadve..................... 93 
                                       +ed +  + +a+e+    ++ +  HSlg +++  +  l  +++v g +LV   +                       
  gi|488601380|ref|YP_007907851.1|  57 VEDYARYVLEAMEEKGlDRMFIAGHSLGGAIAQMVY-LIDRSRVMGLILVGTGARLrvldeileglkndfdtmakkl 132
                                       555555555555554414577888999987665555.8899999999999876644588899999999999999999 PP

                                       ............................S..TT.GGGCGCTTS-...SSH..HCCHCEEEEETTBTTC-HHHHHHHH CS
                     Ser_hydrolase  94 ............................eeaaklaelaefaplp...rek..lpfpslvvaSenDpyvsfeeaeela 137
                                                                    +++  +++++f+ l+   + k    +p l +  ++D + +++++e + 
  gi|488601380|ref|YP_007907851.1| 133 vnmlfsrkfsdsrikdevlkdllscgsrITHRDFSACDKFDLLSdykEGKvkVDVPVLCIVGSDDIMTPVKYSEFFR 209
                                       9999999999999999999988888887444444455555544411144411445669999999************* PP

                                       HHCT-EEEEETT-TTSS CS
                     Ser_hydrolase 138 eawgaelvdlgeaGHin 154
                                       +++gae+ +++ aGH+ 
  gi|488601380|ref|YP_007907851.1| 210 KTIGAEVKVIEDAGHMV 226
                                       ***************85 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.072        76       5      27 ..      14      36 ..      10      43 .. 0.88
   2 !   13.1   0.1   5.3e-05     0.056      83     202 ..      54     226 ..      45     233 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.072
                              FSH1  5 kkiLcLhGytqsgeiFraktsal 27
                                      + +L +hG +++++i++++++a+
  gi|488601380|ref|YP_007907851.1| 14 LPVLYIHGSGSNSKIWKNQLEAI 36
                                      569****************9886 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.3e-05
                              FSH1  83 yegleesldavkdyikengp.fdGiiGFSqGaalaallaslleellkea............................ 130
                                       +e +e+  ++v ++++e+g     i G S G+a+a+++  l+++ +                               
  gi|488601380|ref|YP_007907851.1|  54 IETVEDYARYVLEAMEEKGLdRMFIAGHSLGGAIAQMVY-LIDRSRVMGlilvgtgarlrvldeileglkndfdtma 129
                                       566666677777777777754556777777777777654.3444333335677777777777777777777776666 PP

                              FSH1 131 .................shpslkfailvsGfkleepk.........yeeyy..eedkiqtptLhvlGelDtvvdeer 179
                                                        +++ lk  +l +G ++++++          +  y   + k+ +p+L ++G++D + + + 
  gi|488601380|ref|YP_007907851.1| 130 kklvnmlfsrkfsdsriKDEVLK-DLLSCGSRITHRDfsacdkfdlLS-DYkeGKVKVDVPVLCIVGSDDIMTPVKY 204
                                       66666666666655553333344.356677888777766666655422.443567788****************999 PP

                              FSH1 180 seaLaeafknsskvlkHpggHfv 202
                                       se + +++  + kv++ + gH+v
  gi|488601380|ref|YP_007907851.1| 205 SEFFRKTIGAEVKVIE-DAGHMV 226
                                       9999988888777766.566776 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.6e-06    0.0016      49      82 ..      58      91 ..      17     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHHHHHHHTT-EEEEEEEETHHHHHHHHH CS
                          Lipase_3 49 eqvlkelkrllekypeysivvtGHSLGgalAlLa 82
                                      e+  + + + +e++   ++ ++GHSLGga+A ++
  gi|488601380|ref|YP_007907851.1| 58 EDYARYVLEAMEEKGLDRMFIAGHSLGGAIAQMV 91
                                      555566677778888889*************986 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00065      0.69      45      88 ..      57      99 ..       7     109 .. 0.77
   2 !    6.5   0.0     0.005       5.3     127     206 ..     171     243 ..     149     246 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00065
                                      HHHHHHHHHHHHHTT.S--GGGEEEEEETHHHHHHHHHHH.H-GGG CS
                      Peptidase_S9 45 fdDfiaaaealakeg.yvdserlaitGgSyGGyltgaaln.qrpdl 88
                                      ++D+   a+++ +       +r++i G+S GG  + ++   +r+++
  gi|488601380|ref|YP_007907851.1| 57 VEDY---ARYVLEAMeEKGLDRMFIAGHSLGGAIAQMVYLiDRSRV 99
                                      4444...44444444455569************9999877666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                                       HHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHH CS
                      Peptidase_S9 127 gykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarlla 203
                                       +++ ls y+   +vk+++p+L+i+G  D  +p++ ++ +     +k   +++++  d+gH v   ++  e   ++l+
  gi|488601380|ref|YP_007907851.1| 171 KFDLLSDYKEG-KVKVDVPVLCIVGSDDIMTPVKYSEFF-----RKTIGAEVKVIEDAGHMVM-IEKPDEVNSTILE 240
                                       44455555553.3469*********99988877665544.....3455678889999999655.3333366667777 PP

                                       HHH CS
                      Peptidase_S9 204 Flk 206
                                       F+k
  gi|488601380|ref|YP_007907851.1| 241 FVK 243
                                       766 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     3e-05     0.032      49     110 ..      54     109 ..      51     227 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                                       HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-S CS
                     Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvt 110
                                       +e + + +r+++e  +e+g   +r+++aG S GG +a  v l  r++    v g++l+  + 
  gi|488601380|ref|YP_007907851.1|  54 IETVEDYARYVLEAMEEKG--LDRMFIAGHSLGGAIAQMVYLIDRSR----VMGLILVGTGA 109
                                       5666677777777754444..6799***************9888886....77777776633 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 ?    3.3   0.0      0.04        42       9      25 ..      11      27 ..       5      37 .. 0.79
   2 ?    8.3   0.0    0.0012       1.3      78     123 ..      50      95 ..      46     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.04
                            DUF915  9 kkeiPtifihGyggtae 25
                                       k  P+++ihG+g++ +
  gi|488601380|ref|YP_007907851.1| 11 DKDLPVLYIHGSGSNSK 27
                                      5778********99876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0012
                            DUF915  78 rdaslkkqakwlkkvlseLkkkYnikkfnavGhSmGgl.altsYlee 123
                                        da++++ + +   vl+ +++k +++++ + GhS Gg  a ++Yl++
  gi|488601380|ref|YP_007907851.1|  50 DDANIETVEDYARYVLEAMEEK-GLDRMFIAGHSLGGAiAQMVYLID 95 
                                       46999999***********998.9***********986155789887 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.003       3.1      74     113 ..      58      97 ..      10     133 .. 0.77
   2 ?    5.1   0.0    0.0089       9.3     173     215 ..     197     238 ..     184     246 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.003
                   Chlorophyllase2  74 akgLesvlpeevepdlsklalsgHSrGgktafalalgkak 113
                                       +++ + vl+   e  l+++ ++gHS Gg +a  + l  ++
  gi|488601380|ref|YP_007907851.1|  58 EDYARYVLEAMEEKGLDRMFIAGHSLGGAIAQMVYLIDRS 97 
                                       44455566666677899************99888776555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0089
                   Chlorophyllase2 173 capkgvnhaefydeckppaihlvvkdyGHldmldddtglvgkl 215
                                       ++++ v+++ef++++  + ++ v++d GH+ m++    + +++
  gi|488601380|ref|YP_007907851.1| 197 DIMTPVKYSEFFRKTIGAEVK-VIEDAGHMVMIEKPDEVNSTI 238
                                       677889*******99988877.689********9875444444 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     5e-05     0.052      15      91 ..     169     242 ..     151     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                     Abhydrolase_4  15 CagwpvspqrprdestakgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYL 91 
                                       C++ +  ++ +  ++  k+++pvL + +  D +TP +  + ++k++g a++ + e++GH +++++ + v++++ +++
  gi|488601380|ref|YP_007907851.1| 169 CDKFDLLSDYKEGKV--KVDVPVLCIVGSDDIMTPVKYSEFFRKTIG-AEVKVIEDAGHMVMIEKPDEVNSTILEFV 242
                                       555555555554444..4489************************99.888888999*****988888888888876 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.17      63      96 ..      60      91 ..      49     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                            DUF676 63 laeevlevvkkkkdknkkiSfvghSlGgliaraa 96
                                       a +vle +++k  +  ++ + ghSlGg ia+++
  gi|488601380|ref|YP_007907851.1| 60 YARYVLEAMEEKGLD--RMFIAGHSLGGAIAQMV 91
                                      578999999999999..9************9876 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00033      0.35     164     193 ..      62      91 ..      55     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                           DUF2048 164 lvllhwlereGyGplgltGlSmGGhmasla 193
                                       + +l+++e++G  ++ ++G S+GG  a+++
  gi|488601380|ref|YP_007907851.1|  62 RYVLEAMEEKGLDRMFIAGHSLGGAIAQMV 91 
                                       568999**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 1428.42
//
Query:       gi|488601381|ref|YP_007907852.1|  [L=97]
Description: uncharacterized protein, MTH1187 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   64.8   0.1    5.8e-18   64.6   0.1    1.0  1  Thiamine_BP    Thiamine-binding protein
    0.00095   18.5   0.1     0.0011   18.3   0.1    1.0  1  Prophage_tail  Prophage endopeptidase tail


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 !   64.6   0.1   6.4e-22   5.8e-18       1      91 [.       3      90 ..       3      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 6.4e-22
                                      EEEEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEES CS
                       Thiamine_BP  1 veisviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrr 78
                                      veisv+P+g+ ges+s+y+a+v++v+k++   ++lt mgT+i+++ + e+ +++  + e+l  ++++R + vik+d+r 
  gi|488601381|ref|YP_007907852.1|  3 VEISVVPIGV-GESLSRYIARVIDVIKKQSKDFKLTDMGTIIKVDsFTELGKLLDLIREEL--KDCPRLYFVIKADERF 78
                                      89********.**************************************************..679************7 PP

                                      SS---HHHHHHHH CS
                       Thiamine_BP 79 dkeqtleeKvksv 91
                                           l+ Kv+sv
  gi|488601381|ref|YP_007907852.1| 79 KD-YDLDYKVESV 90
                                      66.8999999987 PP

>> Prophage_tail  Prophage endopeptidase tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.2e-07    0.0011     203     266 ..      23      83 ..      15      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-07
                                       .....--GGGG-----B.---EE-TT-SS-TTHHHHH------S..-EEEEEE------.---- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Prophage_tail 203 evrledqesidkygkrnylspitddeitdqdaLkeeaknqlkknnePevsltvtaaklekdiel 266
                                       ++ +++++s +++ +++++ +i++d++t   +L++  +++lk+   P++ ++++a++  kd++l
  gi|488601381|ref|YP_007907852.1|  23 VIDVIKKQS-KDFKLTDMGTIIKVDSFTELGKLLDLIREELKDC--PRLYFVIKADERFKDYDL 83 
                                       555666666.9999999***************************..***********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 710.41
//
Query:       gi|488601382|ref|YP_007907853.1|  [L=388]
Description: cell division protein FtsZ [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-37  129.4   1.1    4.8e-37  128.1   1.1    1.7  1  Tubulin          Tubulin/FtsZ family, GTPase domain
    7.3e-35  119.2   2.2      9e-35  118.9   0.6    2.0  2  FtsZ_C           FtsZ family, C-terminal domain
     0.0033   16.8   1.9        2.1    7.7   0.0    3.2  4  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
        0.2   10.8   0.1       0.91    8.7   0.0    1.8  2  Na_H_antiporter  Na+/H+ antiporter family
       0.32   11.3   2.2        1.8    8.8   0.2    2.9  2  TrkA_N           TrkA-N domain
        0.5    9.5  10.9        3.3    6.8   0.3    2.8  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 !  128.1   1.1   1.6e-40   4.8e-37       1     195 [.      33     191 ..      33     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 1.6e-40
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +iiv+g+G++Gn+++++l +      g+             +g v++i    ai+td+q+l +++a+      +++l
  gi|488601382|ref|YP_007907853.1|  33 KIIVVGCGGSGNNTITRLKQ----L-GV-------------EG-VTTI----AINTDKQHLLNTQAD------KRVL 80 
                                       69*****************9....4.88.............66.7777....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       +g + ++++gaggype+g++aae  +  +++ ++++d+   +f++a++gGGTG+G +pv++e++k++  +a+v+++v
  gi|488601382|ref|YP_007907853.1|  81 IGRTLTKGLGAGGYPEIGRKAAELARGTLEELLSGADL---VFVCAGMGGGTGTGSAPVVAEIAKKQ--GAIVIGMV 152
                                       **************************************...**************************..******** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlki 195
                                        +P++   +  ++++a+++l+el++++d+v+v+dN++Ll+ 
  gi|488601382|ref|YP_007907853.1| 153 QTPFRV--ERARIKKAEEGLEELRKQADTVVVLDNNKLLEY 191
                                       ****98..899***************************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 ?   -2.2   0.0       1.7   5.1e+03      54      54 ..     123     123 ..     101     156 .. 0.57
   2 !  118.9   0.6     3e-38     9e-35       1      94 [.     240     333 ..     240     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                                       H CS
                            FtsZ_C  54 v 54 
                                       +
  gi|488601382|ref|YP_007907853.1| 123 A 123
                                       1 PP

  == domain 2  score: 118.9 bits;  conditional E-value: 3e-38
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvA+m vGe++++++a++++++++++pLL+vd++gAkg+l++++gg+dlt+kE+ee++++++ e+d+ anvi+Ga+i
  gi|488601382|ref|YP_007907853.1| 240 GVAVMLVGESRSQNKAKDVVKDCLNHPLLEVDYRGAKGALIHLSGGTDLTIKEAEEIVNNLTFEIDDAANVIWGARI 316
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES- CS
                            FtsZ_C  78 deeledeirvtvvatgl 94 
                                        +e+e+++rv++++tg+
  gi|488601382|ref|YP_007907853.1| 317 SKEMEGCVRVMAIMTGV 333
                                       ****************8 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0007       2.1      11      65 ..       8      61 ..       1      81 [. 0.71
   2 ?    0.1   0.1      0.15   4.4e+02      28      57 ..      78     107 ..      62     113 .. 0.76
   3 ?    0.1   0.0      0.15   4.4e+02      79      98 ..     103     122 ..      87     129 .. 0.65
   4 !    6.1   0.1    0.0021       6.4      50      97 ..     136     182 ..     123     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0007
                                      HHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-E.EEEE CS
                      2-Hacid_dh_C 11 laeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmk.viay 65
                                       ++++ e r++++  ++++ ++e    ++ ++G+G  G++++ rlk++g++ v+ +
  gi|488601382|ref|YP_007907853.1|  8 AQKYYMEERNRRM--SSNFDIEEYGLPKIIVVGCGGSGNNTITRLKQLGVEgVTTI 61
                                      4444555555555..888999999999*********************99513333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                                       CGSBS-GTTSEEEEES-SHHHHHHHHHHHH CS
                      2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlka 57 
                                       ++l+ +   k +G  G+ +IG+++a+++++
  gi|488601382|ref|YP_007907853.1|  78 RVLIGRTLTKGLGAGGYPEIGRKAAELARG 107
                                       4455555567899999**********9986 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.15
                                       TCEECSHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C  79 gvelvsleellaesDivslh 98 
                                       ++   +leell+ +D v+++
  gi|488601382|ref|YP_007907853.1| 103 ELARGTLEELLSGADLVFVC 122
                                       33445677777777777765 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0021
                                       HHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE CS
                      2-Hacid_dh_C  50 avakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivsl 97 
                                        va+++k+ g+ vi++ +++ + e  ++ +   + leel +++D v++
  gi|488601382|ref|YP_007907853.1| 136 VVAEIAKKQGAIVIGMVQTPFRVE-RARIKKAEEGLEELRKQADTVVV 182
                                       599*************99998777.555555678***********997 PP

>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.18   5.3e+02     208     231 ..     123     143 ..     102     148 .. 0.80
   2 ?    8.7   0.0    0.0003      0.91      74     154 ..     174     260 ..     145     264 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.18
                   Na_H_antiporter 208 allvafatGtswgtigIilpiavp 231
                                       a+   +++Gt +g+ +++++ia++
  gi|488601382|ref|YP_007907853.1| 123 AG---MGGGTGTGSAPVVAEIAKK 143
                                       44...78999***********986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0003
                   Na_H_antiporter  74 r.......eleekeltk.lpiavliiltlskmpytgalalvaivkafivalafqntdvatalvvgalaglivatlle 142
                                       r       +l+ ++l++ +p + +   ++s m ++++ ++  i+  +i++  ++n d+a+   v ++ g++v++++e
  gi|488601382|ref|YP_007907853.1| 174 RkqadtvvVLDNNKLLEyVPNLPIE-QAFSVMDQLISETIKGIS-DTITQPSLMNIDFADVRAVMGQGGVAVMLVGE 248
                                       2444444445555444478999988.78889999*****99999.9******************************* PP

                   Na_H_antiporter 143 laslseidklln 154
                                       ++s ++++++++
  gi|488601382|ref|YP_007907853.1| 249 SRSQNKAKDVVK 260
                                       *98888888776 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2   0.00061       1.8       1      36 [.      34      70 ..      34      86 .. 0.74
   2 ?    0.4   0.1      0.25   7.4e+02      14      31 ..     170     187 ..     164     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00061
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeervee 36
                                      ii++G+G  G + + +L++ g + v+ i  + ++ + 
  gi|488601382|ref|YP_007907853.1| 34 IIVVGCGGSGNNTITRLKQlGVEGVTTIAINTDKQHL 70
                                      89*****************777666666666655433 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.25
                                       HHHHHHTTEEEEEEESSH CS
                            TrkA_N  14 aeeLseggkdvvvidkde 31 
                                       +eeL+++ + vvv d+++
  gi|488601382|ref|YP_007907853.1| 170 LEELRKQADTVVVLDNNK 187
                                       688999665577777764 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3    0.0011       3.3       1      23 [.      35      57 ..      35      79 .. 0.82
   2 ?    5.5   5.0    0.0027         8     116     176 ..      90     137 ..      58     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                         Tubulin_2  1 lviGLGGtGgkvlaelrrrlree 23
                                      +v+G+GG+G +++++l+++ +e 
  gi|488601382|ref|YP_007907853.1| 35 IVVGCGGSGNNTITRLKQLGVEG 57
                                      89**************9986665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0027
                         Tubulin_2 116 GAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDv 176
                                       GAG+++ +GR a    +e +r +l+++++ +           vfV+ ++ GGTG G++  v
  gi|488601382|ref|YP_007907853.1|  90 GAGGYPEIGRKA----AELARGTLEELLSGADL---------VFVCAGMGGGTGTGSAPVV 137
                                       677777777754....56666666666666555.........**************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2732.04
//
Query:       gi|488601383|ref|YP_007907854.1|  [L=139]
Description: secondary thiamine-phosphate synthase enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  116.6   0.0    7.1e-34  116.4   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.041   13.8   0.0    1.6  2  DUF4898   Domain of unknown function (DUF4898)


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 !  116.4   0.0   7.9e-38   7.1e-34       1     115 []      21     135 ..      21     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 7.9e-38
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGG.TTS..THHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhn.aegpdnadaHlkss 75 
                                       dit+e++++   +g+keG+v+vf++ +ta++t+ E+ ++++ +D++e++e+++p++ +Y hn + g+ n+++Hl++s
  gi|488601383|ref|YP_007907854.1|  21 DITREIRKV--IEGWKEGFVNVFVQGSTAGVTVMEY-ESGLIKDIREFFEEIIPKNrNYAHNlTWGDANGHSHLRAS 94 
                                       7********..88**********************9.*************************655999********* PP

                                       HH-SEEEEEEETTEE---TTEEEEEEESS.-SSEEEEEEEE CS
                           UPF0047  76 llgssltipvedgklalGtwqsiylveld.gpreRkvvvqv 115
                                       ll++sltip++dgk  lGtwq+++++++d ++r+Rk+++qv
  gi|488601383|ref|YP_007907854.1|  95 LLKPSLTIPFKDGKDFLGTWQQVVVLDFDnKRRKRKIILQV 135
                                       *****************************66699***9986 PP

>> DUF4898  Domain of unknown function (DUF4898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.6e-06     0.041      15      41 ..      50      76 ..      36      78 .. 0.86
   2 ?   -3.3   0.0         1   9.1e+03      42      51 ..     117     126 ..     115     134 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-06
                           DUF4898 15 fvkkislkiIsdyekffnfilPkdkki 41
                                       v  ++  +I+d + ff+ i+Pk++++
  gi|488601383|ref|YP_007907854.1| 50 TVMEYESGLIKDIREFFEEIIPKNRNY 76
                                      5688999*****************877 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                           DUF4898  42 vvvvpsdled 51 
                                       vvv+ +d + 
  gi|488601383|ref|YP_007907854.1| 117 VVVLDFDNKR 126
                                       5666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 00:00:00.42
# Mc/sec: 988.42
//
Query:       gi|488601384|ref|YP_007907855.1|  [L=165]
Description: 3-isopropylmalate dehydratase, small subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-20   72.5   0.0    6.3e-20   71.8   0.0    1.3  1  Aconitase_C    Aconitase C-terminal domain
    4.5e-07   29.7   0.1    2.4e-05   24.1   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 !   71.8   0.0     7e-24   6.3e-20      64     126 ..      42     102 ..      12     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 7e-24
                                       HHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEE CS
                       Aconitase_C  64 daaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLpl 126
                                       d  +  k+e+ +++v++ knfG GSSRehA+   +l G+ avia+SF+rIf++n+i+ gl pl
  gi|488601384|ref|YP_007907855.1|  42 DPDFAKKVEKGDFIVAG-KNFGMGSSREHAPIVIKLAGVSAVIAKSFARIFYRNSINVGL-PL 102
                                       33344467799999988.****************************************95.55 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 !   24.1   0.1   2.7e-09   2.4e-05       7     168 ..      10     154 ..       5     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.7e-09
                                       EEEEEHHHHS-GGGGGGTTSHHHHHCCTT-S-BTTSHHHHHHHHTTSS-EEEEEEEEEES---THHHHHHHHHHSEE CS
                     Aconitase_2_N   7 eGetntDdlsPasdAwsRsDiplHakamlkkkaeeelkaieelkkkgvplayvgdvvGtGssRksavnsvlWtiged 83 
                                         +++tD + P+   + Rs++p  ak +++   ++  k++e    kg  +   g   G GssR  a           
  gi|488601384|ref|YP_007907855.1|  10 GDDISTDHITPGRYYHLRSNLPELAKHVMEDADPDFAKKVE----KGDFI-VAGKNFGMGSSREHA----------- 70 
                                       569*******************9999999999999877775....56555.567789******765........... PP

                                       ETTEEEEEE--EEEEEEE-HHHHHHHHHTT-EEEE---TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHH CS
                     Aconitase_2_N  84 ipyvPnkraggvvlGgkiaPiFfntvedsGalpieadvskletGdvieikpkegkikkeegevvsefklkpetllde 160
                                        p+v      + v+  + a iF+    + G   + ad +k++ Gd +e++  +g i++ ++++ +e k  p+ +l  
  gi|488601384|ref|YP_007907855.1|  71 -PIVIKLAGVSAVIAKSFARIFYRNSINVGLPLLIADTDKIDSGDELEVDLRKGIIRNLTKNIEIEAKPLPDFMLKI 146
                                       .6676666677899999******9888887656679**********************999999999999****999 PP

                                       HHHTSHHH CS
                     Aconitase_2_N 161 vraggrip 168
                                       + +gg + 
  gi|488601384|ref|YP_007907855.1| 147 IDTGGLVH 154
                                       99999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1180.39
//
Query:       gi|488601385|ref|YP_007907856.1|  [L=310]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-100  334.4   0.4     6e-100  334.2   0.4    1.0  1  DUF1152   Protein of unknown function (DUF1152)


Domain annotation for each model (and alignments):
>> DUF1152  Protein of unknown function (DUF1152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.2   0.4  3.4e-104    6e-100       2     293 ..      17     301 ..      16     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 334.2 bits;  conditional E-value: 3.4e-104
                           DUF1152   2 vlgiGGGGDvvsalvlaellkklgveavlgsvvWeRlvvDplPGPisleelegveaineavaivnaesrairgarsv 78 
                                       v+g+GGGGD+v+++ +a+l++++g+e+++g++vW+R+++Dp+PGP+++e+le+ve +n+++ai+++++r     +++
  gi|488601385|ref|YP_007907856.1|  17 VFGMGGGGDIVATVPTANLMREFGFEVLHGTIVWDRYIIDPEPGPRAIEDLENVEIVNDTIAIASEKTR----IGEI 89 
                                       8*******************************************************************8....799* PP

                           DUF1152  79 lpqlarvakvlneevvlldikkgveglaealeelaeklgidliigvDvGGDvLAkGdEegLrSPLaDalslAalskl 155
                                       +p++ar+ ++l+ +vv+ldi+kg+++lae+l++++++ +i + +g+D GGDvLA+G E+g+rSPLaDa+slA+ls +
  gi|488601385|ref|YP_007907856.1|  90 IPTVARAGRCLG-KVVALDITKGPKRLAEGLKAFMDENNIAIAVGIDSGGDVLASGFESGVRSPLADAISLATLSLI 165
                                       ************.9*************************************************************** PP

                           DUF1152 156 eeesvlavaGpGsDGELseeelleriseiakeggllgilgldeedaellekileeveteAskiplaaakGlrGevei 232
                                       e+ s++  +G+GsDGEL+ eell+++s+++ke+++lg +++++ed++ + +++++v+teAs+ipl+a++G+ G +++
  gi|488601385|ref|YP_007907856.1| 166 EN-SFIGFFGFGSDGELRIEELLMKVSSLIKENMFLGSVSMSDEDYREMMELTKNVVTEASSIPLRAYEGELGVLRV 241
                                       *7.************************************************************************** PP

                           DUF1152 233 RkgtrkveltplsalvfyldpkavaelsklaklvagtesleeAeerlnelgiytEldlErd 293
                                       R + r+v+++pls ++fy++++ v++++klak+v + es++ A++rlne+gi+tE+d+E  
  gi|488601385|ref|YP_007907856.1| 242 RAE-RSVPVSPLSIMTFYFKTEGVFKMNKLAKTVLDVESIDVARKRLNEMGIFTEMDFEYL 301
                                       **9.*******************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1925.84
//
Query:       gi|488601386|ref|YP_007907857.1|  [L=172]
Description: hypothetical protein Asulf_01898 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   15.3   0.0      0.057   13.4   0.0    2.0  2  RHH_1     Ribbon-helix-helix protein, copG family
       0.14   12.1   0.1       0.36   10.7   0.0    1.8  2  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


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 ?   13.4   0.0   6.4e-06     0.057       1      32 [.       2      33 ..       2      37 .. 0.92
   2 ?   -2.8   0.0      0.78     7e+03       9      21 ..     147     159 ..     146     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.4e-06
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReA 32
                                      r++i ++ ++ ++L e++ + g+S Se+I ++
  gi|488601386|ref|YP_007907857.1|  2 RITIDIPPDVEKKLLEKCNAAGVSPSEFINAL 33
                                      8***************************9655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.78
                                       HHHHHHHHHHHHH CS
                             RHH_1   9 ellerLdelarrr 21 
                                       e+++ ++e ++++
  gi|488601386|ref|YP_007907857.1| 147 EVYKIVEEEKKKE 159
                                       6678888888876 PP

>> 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 ?   10.7   0.0   4.1e-05      0.36       3      36 ..       2      35 ..       1      40 [. 0.96
   2 ?   -3.0   0.1      0.79   7.1e+03      10      19 ..     163     172 .]     163     172 .] 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.1e-05
                             RHH_5  3 RvnvtLPeelleeLeewAdeegRsvSnlaafLve 36
                                      R+++  P ++ ++L e + + g+s S +++ Lve
  gi|488601386|ref|YP_007907857.1|  2 RITIDIPPDVEKKLLEKCNAAGVSPSEFINALVE 35
                                      99******************************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.79
                             RHH_5  10 eelleeLeew 19 
                                       e++++ L+ w
  gi|488601386|ref|YP_007907857.1| 163 EDVKKLLDNW 172
                                       7999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1133.29
//
Query:       gi|488601387|ref|YP_007907858.1|  [L=332]
Description: Actin-like ATPase involved in cell morphogenesis [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-15   54.9   0.1    6.4e-14   51.5   0.1    1.9  1  MreB_Mbl  MreB/Mbl protein
    5.2e-11   42.9   0.2    1.7e-10   41.3   0.0    1.9  2  ALP_N     Actin like proteins N terminal domain
    1.1e-06   27.6   0.2     0.0014   17.4   0.1    2.1  2  Actin     Actin
     0.0032   17.9   1.1       0.12   12.8   0.2    3.0  2  FtsA      Cell division protein FtsA
  ------ inclusion threshold ------
        0.2    9.5   0.5        2.6    5.8   0.7    2.0  2  SrfB      Virulence factor SrfB


Domain annotation for each model (and alignments):
>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.1   1.8e-17   6.4e-14       3     318 ..       3     300 ..       1     307 [. 0.84

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.8e-17
                                       EEEEEE-SSEEEEEETTTEEEEEEES-EEEETT.......T--EEEESHHHHTTTTS-GTTEEEE-SEETTEESSHH CS
                          MreB_Mbl   3 dlgiDLGtantlvyvkgkgivlnepsvvAikkk.......tkkvlavGeeAkkmlgktpgnikavrPlkdGviadle 72 
                                        +g+D+Gt  t   + gk  vl+ ps+v + ++       ++k + +G+eA +++    +n++++rPl++G +   +
  gi|488601387|ref|YP_007907858.1|   3 PVGLDIGTNYTKTTADGKE-VLTFPSLVVFGEErdwslkaSHKDIYIGDEALTIVQ-NVENVEILRPLHEGRVMHKS 77 
                                       589*********9999986.78999999998777888877778889******9986.6799**********998766 PP

                                       HHHHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHH..HHHHHTT--TTSSS-E CS
                          MreB_Mbl  73 vaeellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevllieepl..aAAiGaglpveepsgn 147
                                       +  el k+ +k +      + + +  ++P +++  er+ v ++ ++    +vll  ep+  +A +G        +  
  gi|488601387|ref|YP_007907858.1|  78 YL-ELAKHALKTLDV----NDAIIATGLPVKSSRKEREDVVKSLETELKAKVLLFPEPVgtMAHMGV-------ETG 142
                                       54.567777777766....5788999*******************99999*******9722333333.......234 PP

                                       EEEEE-SS-EEEEEEETTEEEEEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHHEEEEEE CS
                          MreB_Mbl 148 mvvdiGggttevavislggivtsksvrvaGdeldeaiikyirkkynlliGertaekikieigsavkeeeeekmeikG 224
                                       + +diG gtt+++vis  +  + +++ ++ d+l e++   +r+k  + +  +       e++++ ++e+ e  +i+G
  gi|488601387|ref|YP_007907858.1| 143 VCIDIGFGTTDIVVISHMEYLKGDTLLMGVDRLYENLEVTVRNKAGISLTPE-------EMTMLLMNENFEIGRIRG 212
                                       789*****************************************99988654.......566777888888888888 PP

                                       EETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHS.S. CS
                          MreB_Mbl 225 rdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllseetg.l. 299
                                               k+++vs+ ++ e  ++ + +  e +++  + +   L++ ivd+ i+ltGGg+ l g+ + ++++++ + 
  gi|488601387|ref|YP_007907858.1| 213 G-------KRISVSHGDIIEDYRDLMVSWAERIANRAKMIVEGLSTTIVDN-IILTGGGSALPGVFEEFRKSFEdVg 281
                                       5.......68999999999999999999999999999999999******98.899**********999999986232 PP

                                       -EEE-SSTTTHHHHHHHHT CS
                          MreB_Mbl 300 pvkvaedpltcvakGtgkv 318
                                        +++ +dp+++ a G  ++
  gi|488601387|ref|YP_007907858.1| 282 TISTPKDPMKANALGYYTL 300
                                       4556689999999987665 PP

>> ALP_N  Actin like proteins N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   4.7e-14   1.7e-10       1     121 [.       5     119 ..       5     132 .. 0.88
   2 ?   -1.6   0.1      0.78   2.8e+03       2      12 ..     145     155 ..     144     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 4.7e-14
                                       EEEE-SSEEEEE-GGG-EEEEES-EEEE--..SS-EETTT.EEEBBSSTTSEEEGGG--..SSSEB--SSTT-TTST CS
                             ALP_N   1 GiDiGygntKavsgeletvifPSvvapaeerslssligegdglrvevdgekyfvGelaerqgssasrsldddkaase 77 
                                       G+DiG ++tK++ +  e  +fPS+v  +eer+ s +++ +   ++ +++e   + +++e       r l++ ++ ++
  gi|488601387|ref|YP_007907858.1|   5 GLDIGTNYTKTTADGKEVLTFPSLVVFGEERDWSLKASHK---DIYIGDEALTIVQNVE--NVEILRPLHEGRVMHK 76 
                                       89**********9998999***********7777666555...9999999999999995..3333357********* PP

                                       TTHHHHHHHHHHH---EEEEEEEEE-GGGHHHHHHHHHHHHTTE CS
                             ALP_N  78 dykalllaalallgkeeevvLvtGLPveqykkqkealkkrlkge 121
                                       +y+ l++ al  l + ++  ++tGLPv+  +k++e+  k l+ e
  gi|488601387|ref|YP_007907858.1|  77 SYLELAKHALKTL-DVNDAIIATGLPVKSSRKEREDVVKSLETE 119
                                       ***********99.679999******************999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.78
                                       EEE-SSEEEEE CS
                             ALP_N   2 iDiGygntKav 12 
                                       iDiG+g t +v
  gi|488601387|ref|YP_007907858.1| 145 IDIGFGTTDIV 155
                                       8*****99665 PP

>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.8e-07    0.0014       9     167 ..       6     165 ..       1     204 [. 0.72
   2 !    8.4   0.0    0.0002      0.73     300     342 ..     229     271 ..     191     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.8e-07
                             Actin   9 lDnGssttraGyagedaPkavipslvgkprgrkvea.....klyvgdealt...krpelevrspvedGvvedwdave 77 
                                       lD G+++t+     + +  +++pslv   ++r+ +      ++y+gdealt   +++++e+ +p+++G v     + 
  gi|488601387|ref|YP_007907858.1|   6 LDIGTNYTKT--TADGKEVLTFPSLVVFGEERDWSLkashkDIYIGDEALTivqNVENVEILRPLHEGRVMHKS-YL 79 
                                       6777777776..455555678888887444443322446669******5555447***************9765.55 PP

                             Actin  78 elwehvlkeelkvdpeehpllltepplnppkqrekalEivfEkfkvpalylaksavlsafasgkstglvvDsGasvt 154
                                       el +h+lk  l  d ++  +    p+++++k+re ++   +E+   + + l+ ++v ++   g +tg+ +D+G ++t
  gi|488601387|ref|YP_007907858.1|  80 ELAKHALKT-L--DVNDAIIATGLPVKSSRKEREDVVKS-LETELKAKVLLFPEPVGTMAHMGVETGVCIDIGFGTT 152
                                       677777655.4..44444555556788899999999985.6777777788999************************ PP

                             Actin 155 svvpVldGyvLkk 167
                                        +v +     Lk 
  gi|488601387|ref|YP_007907858.1| 153 DIVVISHMEYLKG 165
                                       **99876666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0002
                             Actin 300 skllgiselivaainacdvdlrpeLlanivvtGGnsllpglte 342
                                       + +++++e i +  +++   l  +++ ni++tGG s lpg+ e
  gi|488601387|ref|YP_007907858.1| 229 DLMVSWAERIANRAKMIVEGLSTTIVDNIILTGGGSALPGVFE 271
                                       56788999999999999999*******************9866 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.41   1.5e+03       1      12 [.       4      15 ..       4      25 .. 0.86
   2 !   12.8   0.2   3.3e-05      0.12       1     102 [.     143     295 ..     143     296 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.41
                                      EEEEE-SSSEEE CS
                                      xxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdv 12
                                      +++DiG++ t+ 
  gi|488601387|ref|YP_007907858.1|  4 VGLDIGTNYTKT 15
                                      689****99875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       EEEEE-SSSEEEEEEETTEEEEEEEES--HHHHHHH......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                              FtsA   1 alvDiGagktdvavaedgalvhlrvigvggngitkd......................................... 36 
                                       +++DiG g+td++v+++ +  + +++ +g + + +                                          
  gi|488601387|ref|YP_007907858.1| 143 VCIDIGFGTTDIVVISHMEYLKGDTLLMGVDRLYENlevtvrnkagisltpeemtmllmnenfeigrirggkrisvs 219
                                       68**************9776665555555555555533333333333333334444444444444444444444444 PP

                                       ....HHHHHT--HHHHHHHHHHH--S--EEEEEHHHHH.....................GGGGSTTHHHHHHHHH.. CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxx.. RF
                              FtsA  37 ....iakalrtaveeAerikikyGsalaekeigrkels.....................ggsalpnleelaeral.. 86 
                                           i+      v+ Aeri+                 +                     ggsalp++ e +++++  
  gi|488601387|ref|YP_007907858.1| 220 hgdiIEDYRDLMVSWAERIA-----------------NrakmiveglsttivdniiltgGGSALPGVFEEFRKSFed 279
                                       55555555555555555555.................0222334555566667777888888888888888888733 PP

                                       .....T-..HHHT-GGGHHHH CS
                                       .....xxxxxxxxxxxxxxxx RF
                              FtsA  87 .....spkleevsdpeyasal 102
                                                   +dp+ a al
  gi|488601387|ref|YP_007907858.1| 280 vgtisT-----PKDPMKANAL 295
                                       333222.....4666666665 PP

>> SrfB  Virulence factor SrfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.7   0.00072       2.6     564     580 ..     144     160 ..     140     181 .. 0.78
   2 ?    1.0   0.0      0.02        72     744     782 ..     237     275 ..     190     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00072
                              SrfB 564 siDiGgGTTDLvitkYe 580
                                       +iDiG GTTD+v+ ++ 
  gi|488601387|ref|YP_007907858.1| 144 CIDIGFGTTDIVVISHM 160
                                       8*********9986643 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.02
                              SrfB 744 eiektlkalaevvslyecDvlLLtGRPsrlpgvqalfre 782
                                       +i +  k + e +s+  +D ++LtG  s lpgv + fr+
  gi|488601387|ref|YP_007907858.1| 237 RIANRAKMIVEGLSTTIVDNIILTGGGSALPGVFEEFRK 275
                                       566666777777888889***************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2038.31
//
Query:       gi|488601388|ref|YP_007907859.1|  [L=442]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   66.9   1.0    2.8e-18   65.6   1.0    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    7.4e-08   32.6   1.5    7.4e-08   32.6   1.5    2.8  2  OrfB_IS605      Probable transposase
     0.0089   15.1   1.1      0.019   14.0   1.1    1.5  1  DUF3987         Protein of unknown function (DUF3987)
  ------ inclusion threshold ------
      0.053   13.6   1.1        0.1   12.7   1.1    1.4  1  DZR             Double zinc ribbon
      0.054   13.5   0.3       0.12   12.4   0.3    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.19   11.3   2.5       0.44   10.1   2.5    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.23   11.2   1.7        8.3    6.1   0.0    2.4  2  EMC3_TMCO1      Integral membrane protein EMC3/TMCO1-like
       0.31   11.0   2.4       0.85    9.6   2.4    1.8  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
          1    9.1   3.9         12    5.8   0.9    2.4  2  zf-C2H2_11      zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   1.0   1.4e-21   2.8e-18       1      68 [.     338     404 ..     338     405 .. 0.99

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.4e-21
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                       fr++ e+l+ k  e     + vn++ + k+CseCgsk++e +++r f+C +Cg+e drDvnAa Nilk
  gi|488601388|ref|YP_007907859.1| 338 FREFAEILKTKLMENNNIAIIVNEWMSTKQCSECGSKKTE-VNDRHFRCLECGYEDDRDVNAAKNILK 404
                                       89**************************************.*************************98 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   4.3     0.079   1.6e+02      45      83 ..      83     121 ..      71     126 .. 0.60
   2 !   32.6   1.5   3.7e-11   7.4e-08       3     103 ..     208     303 ..     202     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.079
                        OrfB_IS605  45 rlksdykylakeiaelqsklkksknykkasrklarlhrk 83 
                                       ++k+  ++++ke  +l++k+++    +k+++ + +l+r 
  gi|488601388|ref|YP_007907859.1|  83 SYKKLHREWQKEVVKLERKIERCMDKHKRKKLEHKLYRL 121
                                       466666666666666666666555555555555555543 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 3.7e-11
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtw...flykgrrlksdykylakeiaelqsklkksknykkasrk 76 
                                       +ve    + ++k+++ +giDlG+++++t ++++g+     l++  ++k+ + ++++ + ++ ++    + + +  r 
  gi|488601388|ref|YP_007907859.1| 208 VVEK---EVVVKPKRLVGIDLGLKRIITAYETNGEEnrvLLFSKEEYKEFFIRMRRLNNRIGKL----Q-RLRKYRI 276
                                       3333...5699**********************9997766666555555555555555554444....3.3566899 PP

                        OrfB_IS605  77 larlhrkrsrrrkhllhklathliktl 103
                                       l++l +kr++  +++ +kla +l+++ 
  gi|488601388|ref|YP_007907859.1| 277 LKKLRHKRRNYARDFRRKLAVELVRQF 303
                                       9**********************9986 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   1.1   9.5e-06     0.019      56     125 ..      62     132 ..      59     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.5e-06
                           DUF3987  56 vlrpleeieaelreeyeeelkeyeaekkaweaelealekkaakak.eakaeealaeleaeepeePklprll 125
                                       ++ +  ++ ++ r++   + k+y++ +++w++e  +le+k++++  + k+++   +l ++++ eP lp ++
  gi|488601388|ref|YP_007907859.1|  62 ITGLPSAFAQACRDKALWMYKSYKKLHREWQKEVVKLERKIERCMdKHKRKKLEHKLYRLKKREPSLPTIM 132
                                       567788899999999999**************************998888888888889999999888776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.1     5e-05       0.1      12      44 ..     365     398 ..     362     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                               DZR  12 arfCseCgtklkavaa.edrCpsCgekvdpearf 44 
                                        + CseCg+k  +v++ + rC +Cg++ d + + 
  gi|488601388|ref|YP_007907859.1| 365 TKQCSECGSKKTEVNDrHFRCLECGYEDDRDVNA 398
                                       589*******887777799*******98877665 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 ?   12.4   0.3   6.2e-05      0.12      47      96 ..     341     392 ..     329     403 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-05
                                       HHHHHHCC.T.TTT-EEEEEEE--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA  47 afellaegtv.legaeLeieevpvkvrCreCgkefeleek.alrCpkCgsad 96 
                                         e+l+ + +  ++  + ++e   + +C+eCg++ ++ ++ ++rC +Cg +d
  gi|488601388|ref|YP_007907859.1| 341 FAEILKTKLMeNNNIAIIVNEWMSTKQCSECGSKKTEVNDrHFRCLECGYED 392
                                       445554443323344455777788899*****88886555599*****9874 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   2.5   0.00022      0.44       2      28 ..     367     391 ..     367     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                       EETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlV 28 
                                       +C +Cgs++++++     ++C +CG+ 
  gi|488601388|ref|YP_007907859.1| 367 QCSECGSKKTEVNDR--HFRCLECGYE 391
                                       7********988866..9*******85 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.6     0.022        43      45      85 ..      82     126 ..      50     164 .. 0.78
   2 ?    6.1   0.0    0.0042       8.3      41     104 ..     248     311 ..     242     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.022
                        EMC3_TMCO1  45 ekeqkrekelqkrarelqk....ngdklklkklekrqeelmedqs 85 
                                       + ++k+ +e qk++ +l++      dk k kkle++  +l++ + 
  gi|488601388|ref|YP_007907859.1|  82 KSYKKLHREWQKEVVKLERkierCMDKHKRKKLEHKLYRLKKREP 126
                                       345666666666666666655559999999999999888887765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0042
                        EMC3_TMCO1  41 kkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsemmmdqmkpmivtmipqil 104
                                       k++ +++  r+++l +r  +lq+ ++   lkkl++++  ++ d +  +   +  ++ + +++i 
  gi|488601388|ref|YP_007907859.1| 248 KEEYKEFFIRMRRLNNRIGKLQRLRKYRILKKLRHKRRNYARDFRRKLAVELVRQFSNCLIFIG 311
                                       677888999********************************99999999888888888888876 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 ?    9.6   2.4   0.00043      0.85      15      45 ..     362     390 ..     360     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00043
                     Zn_Tnp_IS1595  15 WpngfvCPhCgsrkayriktrglfqCkeCrk 45 
                                       W ++  C  Cg +k +++++ + f+C eC++
  gi|488601388|ref|YP_007907859.1| 362 WMSTKQCSECG-SKKTEVND-RHFRCLECGY 390
                                       888889*****.56678998.9*******98 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9    0.0058        12       3      12 ..     364     373 ..     363     376 .. 0.87
   2 ?    3.8   0.1     0.024        48       5      11 ..     383     389 ..     379     391 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0058
                        zf-C2H2_11   3 stcqCleCGl 12 
                                       st qC eCG 
  gi|488601388|ref|YP_007907859.1| 364 STKQCSECGS 373
                                       89*******6 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.024
                        zf-C2H2_11   5 cqCleCG 11 
                                       ++CleCG
  gi|488601388|ref|YP_007907859.1| 383 FRCLECG 389
                                       69****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1194  (0.066596); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2743.53
//
Query:       gi|488601389|ref|YP_007907860.1|  [L=44]
Description: hypothetical protein Asulf_01901 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      786  (0.0438396); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 278.02
//
Query:       gi|488601390|ref|YP_007907861.1|  [L=174]
Description: LSU ribosomal protein L10AE [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  106.4   0.3    1.3e-30  106.1   0.3    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.16   12.3   0.0    1.3  1  UPF0058        Uncharacterised protein family UPF0058


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 !  106.1   0.3   1.5e-34   1.3e-30       4     132 .]      14     162 ..      12     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 1.5e-34
                                       SXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXX CS
                     Ribosomal_L16   4 kkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvf 68 
                                       ++ +K++  y+ g++  + +++++g+        + Lva+e+ q++++aleaari++n+y  k  g+    l++r++
  gi|488601390|ref|YP_007907861.1|  14 RPLTKRQ--YVDGAPgIRVRQFDMGNknaefpiqLTLVAKENVQIRDTALEAARITANKYAAKRLGGsnyYLKLRIY 88 
                                       5789999..***********************9999**************************999999999****** PP

                                       XXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE...TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                     Ribosomal_L16  69 phhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei...kagvneeiakealrraasKlpiktkiv 132
                                       phh+++++     ag+dR+++G+    Gkp g +arv +g+ +++i    +    e+ k+al+ra +Klp++t++v
  gi|488601390|ref|YP_007907861.1|  89 PHHILREHkmavgAGADRISQGMrmayGKPVGNAARVFKGTKVMSIwvrPE--GFEVGKNALKRAGYKLPTPTQVV 162
                                       **********************************************86544..78899***************997 PP

>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05      0.16      31      68 ..      80     114 ..      63     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                                       HHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHH CS
                           UPF0058  31 keYeeLdisPhhihrsKaehkaAifvLgnaiakalsek 68 
                                       + Y +L i Phhi r   ehk A+   +  i++ ++  
  gi|488601390|ref|YP_007907861.1|  80 NYYLKLRIYPHHILR---EHKMAVGAGADRISQGMRMA 114
                                       6799*********99...8*****99999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 00:00:00.44
# Mc/sec: 1179.37
//
Query:       gi|488601391|ref|YP_007907862.1|  [L=186]
Description: hypothetical protein Asulf_01903 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  104.7  15.9    5.4e-30  104.5  15.9    1.0  1  MFS_1       Major Facilitator Superfamily
    2.3e-13   49.8   9.6    2.3e-13   49.8   9.6    1.5  2  Sugar_tr    Sugar (and other) transporter
    2.7e-13   49.6  11.4    3.4e-13   49.2  11.4    1.2  1  MFS_1_like  MFS_1 like family
      4e-12   45.3   4.0    4.9e-12   45.0   4.0    1.0  1  MFS_3       Transmembrane secretion effector
    3.2e-07   29.2   2.4    1.7e-05   23.5   0.2    1.9  2  TRI12       Fungal trichothecene efflux pump (TRI12)
    1.4e-06   27.2  10.7    1.8e-06   26.8  10.7    1.0  1  MFS_2       MFS/sugar transport protein
     0.0011   18.1   4.2      0.002   17.2   3.7    1.7  1  PUCC        PUCC protein
      0.002   16.9  10.2     0.0042   15.9  10.2    1.6  1  LacY_symp   LacY proton/sugar symporter
  ------ inclusion threshold ------
       0.56    8.4   7.5       0.45    8.7   0.1    2.1  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5  15.9   2.7e-33   5.4e-30       2     181 ..       8     185 ..       7     186 .] 0.91

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 2.7e-33
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +++++  +++ ++++++lp++++++lg+ +  +gll+t+ a++ a+ s++lG +sdrfGr++++ll+ +lfa++ +l
  gi|488601391|ref|YP_007907862.1|   8 SFSLLPLMISTGMIYSILPIYISKELGAEEIHVGLLFTTGAVTGAIVSILLGKVSDRFGRKPLILLSQFLFAIT-ML 83 
                                       678889999*****************************************************************.33 PP

                             MFS_1  79 llfa.sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       l  + ++++ + +   +l G++ +++ +++ al+ad +  ++rg a+g+++++++lG ++gpllgg la+ +g+r +
  gi|488601391|ref|YP_007907862.1|  84 LY-StINHYiYAFPIHALEGFAWATASTSAPALVADFSDIKNRGEAMGVYNTAWNLGWVIGPLLGGTLAQVYGFRIM 159
                                       33.22555556677777************************************************************ PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkr 181
                                         +  i+ ++++vl    +++e++++k+
  gi|488601391|ref|YP_007907862.1| 160 LRFSFIMIIFGMVL--TAFTVEEVRSKW 185
                                       **********9888..888888887765 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.39   7.7e+02     114     129 ..      16      31 ..      14      32 .. 0.90
   2 !   49.8   9.6   1.1e-16   2.3e-13      45     190 ..      37     176 ..      26     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHT CS
                          Sugar_tr 114 igvGlasvlvPmyisE 129
                                       i+ G+++ + P+yis+
  gi|488601391|ref|YP_007907862.1|  16 ISTGMIYSILPIYISK 31 
                                       689***********96 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 1.1e-16
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                       ++ +gl++    v ++i s+++g+++drfGRk+ +l + +lf i  +l  +++   ++   +    l G+++ +as+
  gi|488601391|ref|YP_007907862.1|  37 EIHVGLLFTTGAVTGAIVSILLGKVSDRFGRKPLILLSQFLFAITMLLYSTIN---HYIYAFPIHALEGFAWATAST 110
                                       5778888888889999999**********************************...99999999************* PP

                                       HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGG CS
                          Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllf 190
                                        +P +++ ++  k Rg  +++y++a+ +G +++  +g  l+++ +   +ri+l +++++ ++ ++l  f
  gi|488601391|ref|YP_007907862.1| 111 SAPALVADFSDIKNRGEAMGVYNTAWNLGWVIGPLLGGTLAQVYG---FRIMLRFSFIMIIFGMVLTAF 176
                                       *******************************************99...**********99998887765 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 !   49.2  11.4   1.7e-16   3.4e-13     226     384 ..       3     161 ..       1     180 [. 0.96

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.7e-16
                        MFS_1_like 226 eviifllvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayi 301
                                       ++ ++ + +l l +s g+i++ l +Y+ kelga ++ +G l + g+v   ++ ++  k+ +++G   l++++ ++++
  gi|488601391|ref|YP_007907862.1|   3 KIYALSFSLLPLMISTGMIYSILPIYIsKELGAEEIHVGLLFTTGAVTGAIVSILLGKVSDRFGRKPLILLSQFLFA 79 
                                       6778888899999**************************************************************** PP

                        MFS_1_like 302 lrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlks 378
                                       ++ lly++i+    ++pi +L+g++ ++   +a   v+++   + ++  +g+++++ + lG  +G l+GG l + ++
  gi|488601391|ref|YP_007907862.1|  80 ITMLLYSTINHYIYAFPIHALEGFAWATASTSAPALVADFSDIKNRGEAMGVYNTA-WNLGWVIGPLLGGTLAQVYG 155
                                       *****************************************************998.***************99999 PP

                        MFS_1_like 379 aiflFr 384
                                        +++ r
  gi|488601391|ref|YP_007907862.1| 156 FRIMLR 161
                                       887655 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   4.0   2.5e-15   4.9e-12     232     394 ..      16     177 ..       9     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.5e-15
                             MFS_3 232 lsasavlaLLPlvardqldgdalvyGillgalGvGAilgalllsrL...RerlsserlvllaavalAlvllslalas 305
                                       +s+  ++++LP+ + ++l+++ +  G+l++   +GA++ga+++  L    +r++ + l+ll+ + +A+ +l  +  +
  gi|488601391|ref|YP_007907862.1|  16 ISTGMIYSILPIYISKELGAEEIHVGLLFT---TGAVTGAIVSILLgkvSDRFGRKPLILLSQFLFAITMLLYSTIN 89 
                                       5677899********************965...6777777665544111789************************* PP

                             MFS_3 306 slwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaa 382
                                       +   a+++ +l G aW ta ++  + v   +    +g a+ vY t+ + g   G ll G++a+ ++ ++ L  + + 
  gi|488601391|ref|YP_007907862.1|  90 HYIYAFPIHALEGFAWATASTSAPALVADFSDIKNRGEAMGVYNTAWNLGWVIGPLLGGTLAQVYGFRIMLRFSFIM 166
                                       ***********************999999999999*************************************99887 PP

                             MFS_3 383 lllaaaillllk 394
                                       ++ ++++ + + 
  gi|488601391|ref|YP_007907862.1| 167 IIFGMVL-TAFT 177
                                       7666544.4444 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   8.4e-09   1.7e-05      70     158 ..      29     119 ..       8     125 .. 0.80
   2 !    9.2   0.3   0.00018      0.37      61     124 ..     109     173 ..      92     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.4e-09
                             TRI12  70 ilqdvgqsens..slfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgva 144
                                       i +++g  e +   lf+t   tg  vsil +g+++drfgr+p+++l++ l  +  ++  t +++   +   +l g a
  gi|488601391|ref|YP_007907862.1|  29 ISKELGAEEIHvgLLFTTGAVTGAIVSIL-LGKVSDRFGRKPLILLSQFLFAITMLLYSTINHYIYAFPIHALEGFA 104
                                       45667766644214789999999999997.6********************************99999999999999 PP

                             TRI12 145 agpag.asplfvgel 158
                                          a  ++p +v ++
  gi|488601391|ref|YP_007907862.1| 105 WATAStSAPALVADF 119
                                       666541567777665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00018
                             TRI12  61 qasasalpnilqdvg.qsensslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaiv 124
                                        +sa al   + d+  + e  +++ t w +g  +  l+ g l++ +g r ++  + i+ + g ++
  gi|488601391|ref|YP_007907862.1| 109 STSAPALVADFSDIKnRGEAMGVYNTAWNLGWVIGPLLGGTLAQVYGFRIMLRFSFIMIIFGMVL 173
                                       3456667777778752578899***************************9998888888877765 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8  10.7     9e-10   1.8e-06       7     195 ..      12     180 ..       7     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 9e-10
                             MFS_2   7 laanilsvllatylliFytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsii 83 
                                       l+ +i++ ++   l i+ ++ lg + ++vgl++ +  ++ ai+ +++G ++d+     Gr +P++lls+ ++a  ++
  gi|488601391|ref|YP_007907862.1|  12 LPLMISTGMIYSILPIYISKELGAEEIHVGLLFTTGAVTGAIVSILLGKVSDR----FGR-KPLILLSQFLFA-ITM 82 
                                       566788888888999*********************************99996....588.9*******9999.789 PP

                             MFS_2  84 llftppelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvli 160
                                       ll+++++       i+++ +  l   ++++ + +  +lv+   +d + R  +++v +++ +lg v++ +l ++l+++
  gi|488601391|ref|YP_007907862.1|  83 LLYSTIN-----HYIYAFPIHALEGFAWATASTSAPALVADF-SDIKNRGEAMGVYNTAWNLGWVIGPLLGGTLAQV 153
                                       9999999.....799999999999******************.89*****************************988 PP

                             MFS_2 161 lgglkserkgylifaliialLmllgviivvlgtke 195
                                       +g         +i++ +  +++++g++++++++ e
  gi|488601391|ref|YP_007907862.1| 154 YGF--------RIMLRFSFIMIIFGMVLTAFTVEE 180
                                       885........666666666666666666555554 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.7     1e-06     0.002      71     174 ..      71     177 ..      53     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-06
                              PUCC  71 ivlsgkgeae...aaatwaglilaavafllvGlgvslsqTallALladlaeeeerpkvvgllyvmlligivvsaivv 144
                                       i+ls+ + a       t+   i a+ +++l G++  + +T+  AL+ad ++ ++r ++ g+      +g v++ +  
  gi|488601391|ref|YP_007907862.1|  71 ILLSQFLFAItmlLYSTINHYIYAFPIHALEGFAWATASTSAPALVADFSDIKNRGEAMGVYNTAWNLGWVIGPLLG 147
                                       555554444432234567788999999*************************************************9 PP

                              PUCC 145 gallkdytearLirvvqgvalitlvlnvla 174
                                       g+l + y    ++r+   + +  +vl+ + 
  gi|488601391|ref|YP_007907862.1| 148 GTLAQVYGFRIMLRFSFIMIIFGMVLTAFT 177
                                       999999998888888888888888888765 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  10.2   2.1e-06    0.0042      11      95 ..       4      95 ..       2     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                         LacY_symp 11 lfalffffyffi..msayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkell......wvis 81
                                      ++al+f+++ ++   +++++++p+++++ lg  + ++G++f+   ++  +   l+G +sd++G +k+l+      ++i+
  gi|488601391|ref|YP_007907862.1|  4 IYALSFSLLPLMisTGMIYSILPIYISKELGAEEIHVGLLFTTGAVTGAIVSILLGKVSDRFG-RKPLIllsqflFAIT 81
                                      578889888665256789*********************************************.455541111115566 PP

                         LacY_symp 82 lllvlfapfliyvf 95
                                      +ll  +   +iy f
  gi|488601391|ref|YP_007907862.1| 82 MLLYSTINHYIYAF 95
                                      66666666666655 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 ?    1.9   3.8     0.027        54      13      90 ..      14      93 ..       4     100 .. 0.74
   2 ?    8.7   0.1   0.00022      0.45     140     195 ..      99     154 ..      89     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.027
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                              OATP 13 qamvsgyfkstit.tiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgslll.alPhfi 89
                                       +++ g++ s++   i k+ + +  ++gl+ ++  ++ ++++++++ + +r  r  +i ++ +l+a+ +ll+ ++ h+i
  gi|488601391|ref|YP_007907862.1| 14 LMISTGMIYSILPiYISKELGAEEIHVGLLFTTGAVTGAIVSILLGKVSDRFGRKPLILLSQFLFAITMLLYsTINHYI 92
                                      3444444444443257899999999999999999999999999999999998888888999999999999872467777 PP

                                      x RF
                              OATP 90 s 90
                                      +
  gi|488601391|ref|YP_007907862.1| 93 Y 93
                                      7 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00022
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 140 lllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkly 195
                                        l G++ ++  t + + + D+++ kn    +g++ +++ lG+++G llG+ l+++y
  gi|488601391|ref|YP_007907862.1|  99 ALEGFAWATASTSAPALVADFSDIKNRGEAMGVYNTAWNLGWVIGPLLGGTLAQVY 154
                                       5778888888888899999***********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1135.90
//
Query:       gi|488601392|ref|YP_007907863.1|  [L=322]
Description: Methionine synthase II (cobalamin-independent) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0018   17.6   0.0       0.06   12.6   0.0    2.5  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
  ------ inclusion threshold ------
      0.091   12.7   0.0       0.68    9.8   0.0    2.1  2  DUF2480      Protein of unknown function (DUF2480)


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   6.7e-06      0.06     272     315 ..     266     309 ..     145     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-06
                                       S--THHHHHHHHHCHHCTS-STSB-BB-SS-STTS-HHHHHHHH CS
                       Meth_synt_2 272 rvpsmeeiaalikkaldvapkerlwvnPdCGLktrkreearaal 315
                                         +s e+i+++i+ka ++  +   +v PdCGL   +++e   +l
  gi|488601392|ref|YP_007907863.1| 266 ELESPEKIYERIEKAYNIFGELIAYVGPDCGLGGFPTQESAVKL 309
                                       67899*************988899********998887765544 PP

>> DUF2480  Protein of unknown function (DUF2480)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.076   6.8e+02     100     135 ..      17      52 ..      11      75 .. 0.77
   2 ?    9.8   0.0   7.6e-05      0.68      83     147 ..     220     284 ..     213     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.076
                           DUF2480 100 lekelyeealekldveeykdkkvvikGCsdkevpea 135
                                       ++ke++ee+l++ ++ee+ ++  v+k  s  evp+ 
  gi|488601392|ref|YP_007907863.1|  17 ITKEWVEENLSSREFEEMCQRAFVMKVKSGVEVPNY 52 
                                       67788999999999****99*999999999999975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7.6e-05
                           DUF2480  83 sklepvakkvvlgsleelekelyeealekldveeykdkkvvikGCsdkevpeaayvelvkklqpv 147
                                        +le++ k + +g  ++   +l++e  +k +v+++kd+ +++k   + e pe++y ++ k  + +
  gi|488601392|ref|YP_007907863.1| 220 EELESYDKMLRIGISRSDIDALIAEFNTKHNVNAWKDRDLIVKAIDELESPEKIYERIEKAYNIF 284
                                       57888888888888888888899999999**************************9988766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1746.25
//
Query:       gi|488601393|ref|YP_007907864.1|  [L=213]
Description: membrane protein, MarC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  203.6  10.9    2.3e-60  203.4  10.9    1.0  1  MarC      MarC family integral membrane protein
    4.1e-05   23.4   9.2     0.0019   17.9   9.2    2.3  2  TerC      Integral membrane protein TerC family
  ------ inclusion threshold ------
        1.3    9.2   3.3        2.5    8.4   0.3    2.3  2  Sid-5     Sid-5 family


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 !  203.4  10.9   3.9e-64   2.3e-60       2     202 ..       5     204 ..       4     205 .. 0.97

  Alignments for each domain:
  == domain 1  score: 203.4 bits;  conditional E-value: 3.9e-64
                              MarC   2 kaiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgi 78 
                                       +++i +f+++++i++p gn+p+f++++e  +++ r+ri++ka++la+++ll+  ++G +il +f+is+d+lkiaGgi
  gi|488601393|ref|YP_007907864.1|   5 SFFITSFTTIFIIVDPPGNIPMFIAITEMLDEKDRDRISKKAVLLATVLLLLVTVTGGYILYFFKISMDSLKIAGGI 81 
                                       799************************************************************************** PP

                              MarC  79 llfliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaal 155
                                       llf +++d+l ++ +k +++ ++ +es ++d+ av+P+AlPl++GPgait+ +vl+s+a++ v+k++v+l+ill ++
  gi|488601393|ref|YP_007907864.1|  82 LLFAVSVDILMGSRRK-EAYVEKSKESVDVDSLAVFPIALPLYSGPGAITAAIVLYSTAETPVMKLMVILSILLTYA 157
                                       ***************6.7788888889************************************************** PP

                              MarC 156 itllilllsslilrllgktginaleRlmGllLvalavqlivdGikei 202
                                       i+ l++++++ i+r+lgk+g ++++Rlm+++L+a+av+  + G+++ 
  gi|488601393|ref|YP_007907864.1| 158 IVRLTHIYTNQIIRVLGKSGSDIVARLMAIFLAAIAVEYTFSGLEGK 204
                                       *******************************************9986 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   9.2   3.1e-07    0.0019      14      99 ..      23     112 ..      18     194 .. 0.78
   2 ?    0.1   4.4     0.094   5.6e+02      43      80 ..     149     199 ..     130     213 .] 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.1e-07
                              TerC  14 NlvviallvkklpeeqqkkalllGilgAlvlRillillavallelf....dlilligglfLlytavkellekrlenk 86 
                                       N+ +++ +++ l e+ ++++    +l+A vl +l+++++ ++l +f    d ++++gg++L++++v+ l+ +r ++ 
  gi|488601393|ref|YP_007907864.1|  23 NIPMFIAITEMLDEKDRDRISKKAVLLATVLLLLVTVTGGYILYFFkismDSLKIAGGILLFAVSVDILMGSRRKEA 99 
                                       88899999999**********************************77778********************9885555 PP

                              TerC  87 lvkeekkkkkktk 99 
                                       +v++ k++ ++ +
  gi|488601393|ref|YP_007907864.1| 100 YVEKSKESVDVDS 112
                                       5555555444443 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.094
                              TerC  43 vlRillillavallel.............fdlilligglfLlytavkelle 80 
                                       +l ill++++v l ++              d++  + ++fL ++av+  ++
  gi|488601393|ref|YP_007907864.1| 149 ILSILLTYAIVRLTHIytnqiirvlgksgSDIVARLMAIFLAAIAVEYTFS 199
                                       344444444444444466666666665544888888888888888776654 PP

>> Sid-5  Sid-5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2     0.067     4e+02      18      39 ..      47      69 ..      38      91 .. 0.70
   2 ?    8.4   0.3   0.00041       2.5      11      47 ..     138     174 ..     131     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.067
                             Sid-5 18 ilLaisillll.lNilqvvffnR 39
                                      +lLa+++lll+ +  + +++f++
  gi|488601393|ref|YP_007907864.1| 47 VLLATVLLLLVtVTGGYILYFFK 69
                                      55655555444133356777766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00041
                             Sid-5  11 aaeencvilLaisilllllNilqvvffnRakllklyR 47 
                                       +ae   + l++i+ +ll + i+ + +++ +++++++ 
  gi|488601393|ref|YP_007907864.1| 138 TAETPVMKLMVILSILLTYAIVRLTHIYTNQIIRVLG 174
                                       67888899**************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1344.99
//
Query:       gi|488601394|ref|YP_007907865.1|  [L=145]
Description: ADP-ribose pyrophosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-19   70.7   0.0    1.4e-19   70.5   0.0    1.1  1  NUDIX        NUDIX domain
    0.00053   19.5   0.0      0.042   13.4   0.0    2.1  1  DUF4916      Domain of unknown function (DUF4916)
    0.00061   19.8   0.0     0.0012   18.8   0.0    1.5  1  NUDIX_4      NUDIX domain
  ------ inclusion threshold ------
      0.039   13.3   0.0      0.066   12.6   0.0    1.3  1  F420_ligase  F420-0:Gamma-glutamyl ligase


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 !   70.5   0.0   3.1e-23   1.4e-19       4     129 ..      10     133 ..       7     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 3.1e-23
                                       EEEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   4 ravgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpyg 79 
                                       ++vg+v++++  +vLlv+r++ p +g W++PgG v+ gE+++ A++RE++EEtGle e  ++  ++ ++  ++g  +
  gi|488601394|ref|YP_007907865.1|  10 VGVGAVIIQNG-KVLLVKRANEPNKGyWSVPGGLVRVGESLRSALAREVKEETGLEIEIGDVA-CVSEEIIGNGEVR 84 
                                       78999955555.3*******999999****************************977555554.4556666666666 PP

                                       EEEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHH.HHHHTHCTHHHHHH CS
                             NUDIX  80 deheilyvfl.eevegelepndenevsevrwvpleel.lkeklaaesrkllp 129
                                         h++++ f+ e + ge++     +  evrw++++ +   ek +++ +kl++
  gi|488601394|ref|YP_007907865.1|  85 -FHYVIIDFFsEIKGGEPKA--GSDALEVRWFDINSIdSSEKVVDFVKKLMK 133
                                       .5777766663555555444..68889**********988888888888776 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   9.3e-06     0.042      46     152 ..      29     126 ..       5     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.3e-06
                                       -TTS-EEEE-EEEE--TT--HHHHHHHHHHHHH-TT--B---SS---SEEEEEESSTTSSSEE-TT-EEEEEEEEEE CS
                           DUF4916  46 seegelertlvsGrvlyhetvreallrhiekdlGelalpqlPaslqPftvaeyfPtpgvseytdprqhavslayvvp 122
                                       +e ++   ++  G v + e++r al+r+++++ G     ++    +   v+e        +  + r h v + +   
  gi|488601394|ref|YP_007907865.1|  29 NEPNKGYWSVPGGLVRVGESLRSALAREVKEETGL----EIEIGDVA-CVSEEII-----GNGEVRFHYVIIDFFSE 95 
                                       34444445666788999999999999999999884....22222222.3444333.....33467889999999999 PP

                                       B-S.-----TTEEEEEEE-HHHHTSHHHHHT CS
                           DUF4916 123 vaG.dceprqdaleleWltpeealseevlae 152
                                       ++G + ++ +dale+ W++ ++  s+e + +
  gi|488601394|ref|YP_007907865.1|  96 IKGgEPKAGSDALEVRWFDINSIDSSEKVVD 126
                                       9853789999999999999887766554444 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.6e-07    0.0012       3     108 ..      14     132 ..      12     134 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-07
                                       EEEEECTEEEEEE--TTSSSTT-EE-SEEE.-TTS-HHHHHH...HHHHS-EEE.......EEEEEEEEEEETTEEE CS
                           NUDIX_4   3 llirddgrvllekRpekgllggLwefPgge.eegeeleeala...reelgieve.......elepgtvkHvftHfrl 68 
                                       ++i+++g+vll kR ++   +g w++Pgg    ge+l++ala   +ee+g+e+e       +      + +    ++
  gi|488601394|ref|YP_007907865.1|  14 AVIIQNGKVLLVKRANE-PNKGYWSVPGGLvRVGESLRSALArevKEETGLEIEigdvacvS------EEIIGNGEV 83 
                                       578888********997.99*******99988898888888766777888765544332210......233444444 PP

                                       EEE.EEEE....EEE.S..---.....EEEEEEGGGGG.GS---CCCHCCH CS
                           NUDIX_4  69 tlt.vylv....rveegeeapa.....elrwvtpeele.eyalptavrkll 108
                                       + + v+ +    +++ g e++a     e+rw++ ++++  + +   v+kl+
  gi|488601394|ref|YP_007907865.1|  84 RFHyVI-IdffsEIK-GGEPKAgsdalEVRWFDINSIDsSEKVVDFVKKLM 132
                                       444222.24444554.32222245677888888888853566666666665 PP

>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05     0.066       6      47 ..      42      84 ..      38      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                                      ---TT--HHHHHHCCS-......--TT-EEEEEHHHHHHHTT- CS
                       F420_ligase  6 likegddlaeivvesvkka.gleledgDivvvtekvvakaegn 47
                                      l++ g+ l + ++ +vk++ gle+e gD+ +v+e ++++ e +
  gi|488601394|ref|YP_007907865.1| 42 LVRVGESLRSALAREVKEEtGLEIEIGDVACVSEEIIGNGEVR 84
                                      7899*************999*****************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        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 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 913.69
//
Query:       gi|488601395|ref|YP_007907866.1|  [L=230]
Description: rRNA methylase, putative, group 3 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-35  119.8   0.0    1.7e-34  119.0   0.0    1.4  1  SpoU_methylase  SpoU rRNA Methylase family
    1.7e-06   28.2   0.4    4.3e-06   26.9   0.1    1.8  2  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b
  ------ inclusion threshold ------
      0.016   14.6   0.2        1.9    7.8   0.0    2.1  2  ZnuA            Zinc-uptake complex component A periplasmic
       0.16   12.7   0.2       0.53   11.0   0.0    1.9  2  DUF5593         Domain of unknown function (DUF5593)


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 !  119.0   0.0   3.7e-38   1.7e-34       3     142 .]      83     220 ..      81     220 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 3.7e-38
                                       EEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEE CS
                    SpoU_methylase   3 ivvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalv 79 
                                       iv+l++++dp+NlGa++Rta+ f + ++v+ k+rsa  +n++++++++ga +++++   ++  +a+k++k++g++++
  gi|488601395|ref|YP_007907866.1|  83 IVILDGVKDPNNLGAVIRTAEFFSCAGVVIRKRRSA-GINETVAKVSTGAVFHIPI-ARENPVNAVKKIKNAGIEVY 157
                                       79****************************997776.******************5.77899999************ PP

                                       EESTT-SEGCCSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                    SpoU_methylase  80 atslkgkslseidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                       ++++ g+++s++dl+ ++a+v+G+EdkG+s+ +l+ +d ++kI   g+v+SLN+++A++il+y
  gi|488601395|ref|YP_007907866.1| 158 SAENFGEDISQFDLTPPIAFVIGEEDKGVSKPVLKVCDGVLKIRGFGKVNSLNLSNATSILIY 220
                                       *************************************************************98 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 !   26.9   0.1   9.5e-10   4.3e-06       5      47 ..       6      47 ..       6      49 .. 0.94
   2 ?   -3.1   0.0       2.1   9.6e+03      36      49 ..     146     159 ..     140     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 9.5e-10
                     SpoU_sub_bind  5 lhaVleaLksgrriekllvtegradkrleellklakkrgikve 47
                                      +++++eaLk++ r++k++ ++++a +r++e+++l+kkrg++v+
  gi|488601395|ref|YP_007907866.1|  6 INSIIEALKAD-RVNKIYYNPEKASARIKEVISLCKKRGVPVK 47
                                      599*******6.6****************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                     SpoU_sub_bind  36 lklakkrgikvelv 49 
                                       +k++k +gi+v+ +
  gi|488601395|ref|YP_007907866.1| 146 VKKIKNAGIEVYSA 159
                                       67788888888765 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00043       1.9     185     225 ..       4      47 ..       3      69 .. 0.75
   2 ?    5.0   0.0     0.003        14     184     236 ..     114     165 ..      94     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00043
                                       HHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHH...HHT-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                              ZnuA 185 aqiaalieeikeagvkaifveplaspklaetlae...eagvkva 225
                                       ++i+++ie++k+++v+ i+++p   ++ ++++++   + gv v 
  gi|488601395|ref|YP_007907866.1|   4 SDINSIIEALKADRVNKIYYNPEKASARIKEVISlckKRGVPVK 47 
                                       699*******************8877777777765646686663 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHH..HHT-EEEEE-STSSSTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                              ZnuA 184 aaqiaalieeikeagvkaifveplaspklaetlae..eagvkvatlysldslgde 236
                                        ++ a + e++ +  + a+f  p a+++ ++++++  +ag++v   ys +++g++
  gi|488601395|ref|YP_007907866.1| 114 KRRSAGINETVAKVSTGAVFHIPIARENPVNAVKKikNAGIEV---YSAENFGED 165
                                       66778899999999*******************9965556665...666666655 PP

>> DUF5593  Domain of unknown function (DUF5593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.53      34      69 ..      26      61 ..      10      70 .. 0.81
   2 ?   -1.4   0.0      0.85   3.8e+03      25      49 ..     105     129 ..      97     158 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                           DUF5593 34 kaalaavrsaiaevvrsgepvsritpksdrviraep 69
                                      ++a a+++++i+ +++ g pv+++++k++++i+ae+
  gi|488601395|ref|YP_007907866.1| 26 EKASARIKEVISLCKKRGVPVKKSVIKGEHPIKAEV 61
                                      68899**************************66654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.85
                           DUF5593  25 tplasllrrkaalaavrsaiaevvr 49 
                                        + a ++ rk+  a +++ +a+v +
  gi|488601395|ref|YP_007907866.1| 105 FSCAGVVIRKRRSAGINETVAKVST 129
                                       5555555556666666666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1483.19
//
Query:       gi|488601396|ref|YP_007907867.1|  [L=450]
Description: Hydrogenase maturation factor [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-14   54.9   0.5    2.1e-14   53.9   0.5    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.8e-09   38.1   0.6    4.1e-09   37.0   0.6    1.6  1  AIRS      AIR synthase related protein, N-terminal domain
  ------ inclusion threshold ------
       0.28   11.6   2.4        1.4    9.3   0.3    2.6  2  DUF1104   Protein of unknown function (DUF1104)


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 !   53.9   0.5   3.5e-18   2.1e-14       1     154 [.     228     378 ..     228     380 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.5e-18
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH.....HTTECEEEE--TTHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal.....kglvkaahDvTgGGL 72 
                                       + Gdv++lt++ G g ++t ++  + +e               e   i+  +a+  +      g+++++ DvT+GG+
  gi|488601396|ref|YP_007907867.1| 228 RKGDVILLTEGAGGGTVVTTAIYYGMHEVI------------EESLNIDFLLACESIfkenlVGKIHSMSDVTNGGI 292
                                       57**************99999996665433............3333333333333333336779************* PP

                                       HHHHHHHHHTTTEEEEEECG......THHHHHHHH.HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEE CS
                            AIRS_C  73 lgalaemapasgvgaeidld......kvpifdele.splemllsensGrllvavppeeadavlaileeeglpeaavI 142
                                        g++ e+ + s+  +++d++      ++++++ le ++++ + +     l+v++pp+ ad+v++++++    +  ++
  gi|488601396|ref|YP_007907867.1| 293 RGDAEEISAVSKKAIVFDYEkvrkavNPKVLKMLEkLEIDFMGVSID-SLMVICPPDVADEVKKAVRKFV--NIHEV 366
                                       ********************888888888888886555555555555.59******************94..69*** PP

                                       EEEEESSSEEEE CS
                            AIRS_C 143 Gevtakeelsvi 154
                                       G v+++e+  vi
  gi|488601396|ref|YP_007907867.1| 367 GWVEDGEGAFVI 378
                                       *****9987776 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.6   6.9e-13   4.1e-09       1      92 [.     105     216 ..     105     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 6.9e-13
                                       SSSEEEEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHH CS
                              AIRS   1 dDaavvvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wleevvrgla 63 
                                       dDa+ v++ +++  +++++++h         +G  +  ++++D+++mGArPla++  + +       ++ + ++g+ 
  gi|488601396|ref|YP_007907867.1| 105 DDAG-VMKYKDFYISIAIDGIHSrlseypfiAGFHVTRAAMRDVYVMGARPLAVFSDIHVAddgdvsKIFDHIAGIT 180
                                       7999.777777777788888888888888899********************8777777777**9998888999*** PP

                                       HHHHHTT-EEEEEEEEEESS.......EEEEEEEEE CS
                              AIRS  64 eaaeelgvplvgGdtsfsne.......ptisvtavG 92 
                                       + ++ ++vplv+G t +  +       +t  v++vG
  gi|488601396|ref|YP_007907867.1| 181 AVCDLINVPLVSGSTLRIGGdmvigerMTGGVGCVG 216
                                       **************9876444455555666666666 PP

>> DUF1104  Protein of unknown function (DUF1104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       0.1   6.1e+02      57      82 ..     304     329 ..     295     335 .. 0.70
   2 ?    9.3   0.3   0.00024       1.4      48      82 ..     395     429 ..     380     438 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.1
                                       TTS-HHHHHHHHHHHHHHHHHT---- CS
                           DUF1104  57 ekmtvkefeklrkevrkalkkkikkm 82 
                                       +k  v ++ek+rk+v+ ++ k ++k+
  gi|488601396|ref|YP_007907867.1| 304 KKAIVFDYEKVRKAVNPKVLKMLEKL 329
                                       45556688888888887777777665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHTTS-HHHHHHHHHHHHHHHHHT---- CS
                           DUF1104  48 lkeaaeknlekmtvkefeklrkevrkalkkkikkm 82 
                                            +k + + t  +fe++r++v ka++++i+k 
  gi|488601396|ref|YP_007907867.1| 395 AYTPLKKVVGEQTPPDFEEMREKVDKAVEHAINKK 429
                                       334456677778999**************998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2690.01
//
Query:       gi|488601397|ref|YP_007907868.1|  [L=261]
Description: daunorubicin resistance ABC transporter membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-40  138.4  20.0    2.1e-40  138.4  20.0    1.6  2  ABC2_membrane    ABC-2 type transporter
    5.1e-14   52.1  28.5    5.1e-14   52.1  28.5    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
    0.00031   20.1  19.1    0.00071   18.9  19.1    1.7  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
        1.1    9.2  15.4      0.064   13.2   9.7    1.8  2  ABC2_membrane_4  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 !  138.4  20.0   4.6e-44   2.1e-40       3     209 ..      16     225 ..      14     226 .. 0.96
   2 ?   -1.8   0.2      0.39   1.7e+03      54     152 ..     239     251 ..     229     256 .. 0.50

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 4.6e-44
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnr.....pgllffsvlflafsaltsvap 73 
                                       +++l+ r++++++r +s + + +l +p++++ ++g  f +++  s +g+n+     pg++++ +lf++  ++++v++
  gi|488601397|ref|YP_007907868.1|  16 VYTLWLRDLKRYVRARSRI-IGSLGMPVFFLAFLGMGFRRANiPSLEGMNYidflaPGIIAMVILFTG--TFSGVSI 89 
                                       679*************999.********************8876777777788899************..******* PP

                     ABC2_membrane  74 vferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaasslg 148
                                       v++r+ g+l + +vsp+ s+ a+ +++ ++ ++ +++q+l+++++++++ g++++   ++l+l++++l+a+ +++lg
  gi|488601397|ref|YP_007907868.1|  90 VWDRQFGFLREIMVSPI-SRTAISIGRNFGGATTAIIQGLMMFALSLLI-GFRPNiyGIALALVFMFLIAVSFTGLG 164
                                       *****************.******************************8.*****9555****************** PP

                     ABC2_membrane 149 llisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                       ++is+l+++++ ++++++++++p ++lsG+++p+d +p +++ ++y+ Plty+v++lr++l
  gi|488601397|ref|YP_007907868.1| 165 IIISTLMEDIHGFQLVINFFVFPVFFLSGALYPLDELPAYVRLVSYFDPLTYGVDGLRYSL 225
                                       **********************************************************986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.39
                     ABC2_membrane  54 gllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf 130
                                        l++fs++ + f                                                                 
  gi|488601397|ref|YP_007907868.1| 239 VLIAFSIFAILF----------------------------------------------------------------- 250
                                       233333333332................................................................. PP

                     ABC2_membrane 131 flflllllltalaasslgllis 152
                                                            s
  gi|488601397|ref|YP_007907868.1| 251 ---------------------S 251
                                       .....................2 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 !   52.1  28.5   1.1e-17   5.1e-14     156     344 ..      62     252 ..      50     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.1e-17
                   ABC2_membrane_3 156 lsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afg 230
                                        +n+ +fl++ i++++i++t++f  vsiv +++ + +  ++vs++s++++ +++ +g ++ +++q l +++l  ++g
  gi|488601397|ref|YP_007907868.1|  62 GMNYIDFLAPGIIAMVILFTGTFSGVSIVWDRQFGFLREIMVSPISRTAISIGRNFGGATTAIIQGLMMFALslLIG 138
                                       5799******9999999999999************************************************655778 PP

                   ABC2_membrane_3 231 lgipfg..nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiP 305
                                         +  +  ++ l+l++++l + +++ lg  +s+l+ +    q++i ++ ++ ++++g+l+pl+ lp +++ ++++ P
  gi|488601397|ref|YP_007907868.1| 139 --FRPNiyGIALALVFMFLIAVSFTGLGIIISTLMEDIHGFQLVINFFVFPVFFLSGALYPLDELPAYVRLVSYFDP 213
                                       ..666666999999*************************************************************** PP

                   ABC2_membrane_3 306 ffapglgllrlitgdplweillsliilalfavvylllal 344
                                       +++  +gl   +tg + ++ +l+li+l++f+++ +l+++
  gi|488601397|ref|YP_007907868.1| 214 LTYGVDGLRYSLTGFNEFNPALDLIVLIAFSIFAILFSA 252
                                       ********8888655447889************999886 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 !   18.9  19.1   1.6e-07   0.00071      77     286 ..      70     258 ..      17     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-07
                   ABC2_membrane_2  77 vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilal 152
                                        ++i+a++i + ++ f+  +i+ ++  g l+  + +P+sR +i +g   gg++ +++ +++++  ++l+        
  gi|488601397|ref|YP_007907868.1|  70 APGIIAMVILFTGT-FSGVSIVWDRQFGFLREIMVSPISRTAISIGRNFGGATTAIIqGLMMFALSLLI-------- 137
                                       34577777766655.555677789******************************777777777777555........ PP

                   ABC2_membrane_2 153 givlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqei 229
                                       g  +++  + l +v+  l+++   f++lg+ +S+++       +l++ +fv+ +++ +++ly++ el+a   +    
  gi|488601397|ref|YP_007907868.1| 138 GFRPNIYGIALALVFMFLIAV--SFTGLGIIISTLME-DIHGFQLVINFFVFPVFFLSGALYPLDELPA---Y---- 204
                                       555555555444444444444..689***********.999**********************999888...3.... PP

                   ABC2_membrane_2 230 ndflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrk 286
                                          ++l+s++++ +++++ +  +    + +  a  l++l++  +  + +++ +F r 
  gi|488601397|ref|YP_007907868.1| 205 ---VRLVSYFDPLTYGVDGLRYSLTGFNEFNPALDLIVLIAFSIFAILFSAIRFSRT 258
                                       ...577899999999888887776534445555555555555555555566888886 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   9.7   1.4e-05     0.064      19     169 ..      34     188 ..      24     195 .. 0.72
   2 ?   -1.9   0.3      0.63   2.8e+03     101     112 ..     239     250 ..     231     258 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                   ABC2_membrane_4  19 vlaallvpl..lallyfnllgk..tgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsr 91 
                                       ++++l +p+  la+l +   ++  ++l+  ++ ++  +  +++ ++ l +g +++ +i   +q + l+++++ P+sr
  gi|488601397|ref|YP_007907868.1|  34 IIGSLGMPVffLAFLGMGFRRAniPSLEGMNYIDF--LAPGIIAMVILFTGTFSGVSIVWDRQFGFLREIMVSPISR 108
                                       34444555411455555433221144444445444..5556888999999*************************** PP

                   ABC2_membrane_4  92 tklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlp..iialvllkksyv 166
                                       t++ ++  +  + ++++  l+ f++++l++      g+  +lv+ +l  +  +gl++++ +l   i  + l+ + +v
  gi|488601397|ref|YP_007907868.1| 109 TAISIGRNFGGATTAIIQGLMMFALSLLIGFRPNIYGIALALVFMFLIAVSFTGLGIIISTLMedIHGFQLVINFFV 185
                                       ******************99999999999999999999888888877777777777766665432445566666666 PP

                   ABC2_membrane_4 167 lpl 169
                                       +p+
  gi|488601397|ref|YP_007907868.1| 186 FPV 188
                                       666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.63
                   ABC2_membrane_4 101 vllllsvllmlv 112
                                       vl+ +s++ +l+
  gi|488601397|ref|YP_007907868.1| 239 VLIAFSIFAILF 250
                                       333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1615.83
//
Query:       gi|488601398|ref|YP_007907869.1|  [L=320]
Description: daunorubicin resistance ABC transporter ATP-binding subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-36  123.8   0.0      1e-35  123.2   0.0    1.3  1  ABC_tran      ABC transporter
    3.7e-13   50.0   2.1    2.7e-06   27.4   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      5e-07   30.3   0.1      1e-06   29.4   0.1    1.5  1  DUF4162       Domain of unknown function (DUF4162)
      7e-05   22.5   0.0    0.00013   21.6   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00064   20.3   0.0    0.00092   19.8   0.0    1.4  1  AAA_23        AAA domain
    0.00072   20.0   0.9      0.089   13.2   0.4    3.3  2  AAA           ATPase family associated with various cellular 
     0.0018   18.1   0.2      0.052   13.3   0.0    2.2  2  AAA_15        AAA ATPase domain
     0.0078   15.7   0.1       0.11   11.9   0.1    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0089   16.6   0.3      0.059   13.9   0.3    2.2  1  AAA_18        AAA domain
  ------ inclusion threshold ------
       0.02   15.3   0.2      0.053   13.9   0.2    2.0  1  AAA_16        AAA ATPase domain
      0.029   14.3   0.0      0.056   13.4   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.069   12.9   0.0      0.096   12.4   0.0    1.4  1  AAA_30        AAA domain
      0.096   12.1   0.0       0.22   10.9   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.11   11.2   0.0       0.18   10.4   0.0    1.3  1  AAA_13        AAA domain
       0.14   11.8   0.1       0.31   10.6   0.1    1.5  1  SRP54         SRP54-type protein, GTPase domain
       0.15   12.3   0.2       0.65   10.3   0.2    2.2  1  AAA_22        AAA domain
        1.1    9.1   0.0        1.1    9.1   0.0    2.5  3  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 !  123.2   0.0   9.9e-39     1e-35       1     136 [.      20     163 ..      20     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 9.9e-39
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk vs+ +++ge+ +++G+nGaGK+tL+k+l+ llkp eG+  + g ++++ e +++r++ig+++qep+l+ elt+r
  gi|488601398|ref|YP_007907869.1|  20 LKGVSFRVERGEIFGLLGPNGAGKTTLIKILSTLLKPSEGKAFVAGYSITD-EPSRVRQNIGIVFQEPTLDLELTAR 95 
                                       799************************************************.88999******************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en              ++e+i+++ls +gl +++d+ v    +++SgG+++r+++ar l+  p++l+lDEpt
  gi|488601398|ref|YP_007907869.1|  96 ENldfhgriygmdgqLRKERIDEVLSLVGLLDKADELV----KKFSGGMQRRLEIARGLMHSPQVLFLDEPT 163
                                       **********9999888899*****************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 !   22.0   0.3   1.2e-07   0.00012       2      26 ..      33      62 ..      32      91 .. 0.72
   2 !   27.4   0.1   2.6e-09   2.7e-06     238     297 ..     137     191 ..     107     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl.....d 26
                                       +l GpNg+GK++L+++l+ l        +
  gi|488601398|ref|YP_007907869.1| 33 FGLLGPNGAGKTTLIKILSTLLKPsegkaF 62
                                      689***************999654444443 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.6e-09
                            AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       S G++r l ++  l   +    +l++DEp +gL+ +  r ++e +++ ++  + +iltTH
  gi|488601398|ref|YP_007907869.1| 137 SGGMQRRLEIARGLMHSP---QVLFLDEPTLGLDVQTRRNIWEYIESMEN--VTIILTTH 191
                                       555555555555555545...9**************************99..******** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   9.6e-10     1e-06       2      81 .]     216     300 ..     216     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.6e-10
                                       -HHHHHTTS-SSEEEEE.-------..--.-EEE.E-TTS-EEEEE--.-----------.----EEEEEEEE---H CS
                           DUF4162   2 tleeiKrsygknrieve.adaeelleepg.veev.eeeggelelkled.eeaanellkal.tsgveirsFeeeePsL 73 
                                       t+e +++  g++ iev   d e+l +  +   e   +++ ++ +  ++ e+  +++ + + ++gv i+s+++++ sL
  gi|488601398|ref|YP_007907869.1| 216 TVESLRSLVGRDSIEVYtRDGEKLIAALAeYDESvFKTDYGVLISANEgEKLIPKIVTLAnENGVAINSISLKKSSL 292
                                       6899************9877788877766344442444467899998889**********66*************** PP

                                       HHHHHHHH CS
                           DUF4162  74 ndIFiekv 81 
                                       +d+Fi+++
  gi|488601398|ref|YP_007907869.1| 293 EDVFIRLT 300
                                       *****975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.2e-07   0.00013      10      52 ..      18      60 ..      13      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                            AAA_29 10 gtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkv 52
                                      + ++g ++++++ +++ l Gp+G+GK+Tl+  +++lL p++  
  gi|488601398|ref|YP_007907869.1| 18 YALKGVSFRVERGEIFGLLGPNGAGKTTLIKILSTLLKPSEGK 60
                                      66778889999777999**********************9854 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.8e-07   0.00092      19      43 ..      30      54 ..      12     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.8e-07
                            AAA_23 19 kgltlItGpNGaGKTTildAiklaL 43
                                        ++ + GpNGaGKTT++  +   L
  gi|488601398|ref|YP_007907869.1| 30 GEIFGLLGPNGAGKTTLIKILSTLL 54
                                      36999*************9888776 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 !   13.2   0.4   8.4e-05     0.089       3      66 ..      35     161 ..      33     208 .. 0.61
   2 ?    2.8   0.1      0.14   1.4e+02      52     120 ..     205     272 ..     176     280 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.4e-05
                                       EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelgve..fleisgsellsk........................................ 37 
                                       l Gp G GKT+l+k + + l+ +     + g +++++                                        
  gi|488601398|ref|YP_007907869.1|  35 LLGPNGAGKTTLIKILSTLLKPSegKAFVAGYSITDEpsrvrqnigivfqeptldleltarenldfhgriygmdgql 111
                                       78**************9999632231223333333222333334444444455555555555555555555555555 PP

                                       ....................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 ....................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                           +v++ +  ++  ++ a+    +p +lf+DE
  gi|488601398|ref|YP_007907869.1| 112 rkeridevlslvglldkadeLVKKFSGGMQRRLEIARGLMhSPQVLFLDE 161
                                       55666666666665555555666666666666666555556677777777 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                                       HHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..SSTEEEEEEESSGGGSTHHHH CS
                               AAA  52 eakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..eskvivigatnrpdkldpall 120
                                        + +     i+ +D +++l +   +++ e+ +r  ++L+++l +++++  + +  v++ +n+ +kl p+++
  gi|488601398|ref|YP_007907869.1| 205 IIDHG---RIIALDTVESLRSLVGRDSIEVYTRDGEKLIAALAEYDESvfKTDYGVLISANEGEKLIPKIV 272
                                       33222...688888888886666666777777777777777777766666667888888888888888776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   4.9e-05     0.052      28      54 ..      35      61 ..      23     101 .. 0.78
   2 ?    2.5   0.1     0.095     1e+02     323     364 ..     153     191 ..     128     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                            AAA_15 28 liGkNnsGKSsilealdlFlnnkekkn 54
                                      l G+N++GK++++++l  +l+ +e k 
  gi|488601398|ref|YP_007907869.1| 35 LLGPNGAGKTTLIKILSTLLKPSEGKA 61
                                      78*******************995443 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.095
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++ +l+++EP + L  q  + +++++ ++ n +   +i+tTH
  gi|488601398|ref|YP_007907869.1| 153 SPQVLFLDEPTLGLDVQTRRNIWEYIESMENVT---IILTTH 191
                                       56789************************9999...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 !   11.9   0.1   0.00011      0.11      28     200 ..      34     194 ..      18     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                       EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsisrr 102
                                        ++GpNG+GK+ l+  ++ +L  +        + ++ +      +++s  + ++ i+f+++  +      e++ + +
  gi|488601398|ref|YP_007907869.1|  34 GLLGPNGAGKTTLIKILSTLLKPS--------EGKAFVAGysITDEPSRVRQNIGIVFQEPTLD-----LELTAREN 97 
                                       589**********99885555544........44444444333456777778899999988887.....44555555 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                       +  +g+  y ++g+  +k+ + e+l+ +g+  +       +SgG +  + +a      + +p+ l+ lDe    LD 
  gi|488601398|ref|YP_007907869.1|  98 LDFHGR-IYGMDGQ-LRKERIDEVLSLVGLLDKadelvkKFSGGMQRRLEIARG---LMHSPQVLF-LDEPTLGLDV 168
                                       555555.6666664.456666666666666555555555999997776555543...456666655.8999999999 PP

                                       HHHHHHHHHHHHHCTTSEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkeksknaQfivislree 200
                                       + ++++ e++++ + n+ +i +++  e
  gi|488601398|ref|YP_007907869.1| 169 QTRRNIWEYIESME-NVTIILTTHYIE 194
                                       99999999999877.777777776544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   5.6e-05     0.059       3      25 ..      35      76 ..      34     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrl.gf..................g 25
                                      l G+ G+GKttl k Ls +l  +                   
  gi|488601398|ref|YP_007907869.1| 35 LLGPNGAGKTTLIKILSTLLkPSegkafvagysitdepsrvR 76
                                      78**************99973335555555444444444443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     5e-05     0.053      21      63 ..      29      70 ..      17     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                      +g  e+  l G+ G GK++l++ l + l+ + g  f++g     
  gi|488601398|ref|YP_007907869.1| 29 RG--EIFGLLGPNGAGKTTLIKILSTLLKPSeGKAFVAGYSITD 70
                                      33..78889************98888777774123344433333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.3e-05     0.056      43      72 ..      28      57 ..      18      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-05
                             Rad17 43 rkkriLLisGPsGCgkstvvkvLskelgik 72
                                      ++ +i  + GP G gk+t +k+Ls  l ++
  gi|488601398|ref|YP_007907869.1| 28 ERGEIFGLLGPNGAGKTTLIKILSTLLKPS 57
                                      445688899***************988775 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   9.1e-05     0.096      20      53 ..      32      67 ..      24     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.1e-05
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.ggr.viglA 53
                                      +  l Gp G+GKtt++k l  +++ + g+  v+g++
  gi|488601398|ref|YP_007907869.1| 32 IFGLLGPNGAGKTTLIKILSTLLKPSeGKAfVAGYS 67
                                      66789**************99998885533144444 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   0.00021      0.22      27      53 ..      35      61 ..      29      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplseee 53
                                      l+Gp G+GKt l+k l++ll p + + 
  gi|488601398|ref|YP_007907869.1| 35 LLGPNGAGKTTLIKILSTLLKPSEGKA 61
                                      79******************9987665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.18      23      51 ..      37      65 ..      32      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                            AAA_13 23 GwNGaGKTtLSrllrslelgetepkfang 51
                                      G NGaGKTtL ++l+ l + +  ++f +g
  gi|488601398|ref|YP_007907869.1| 37 GPNGAGKTTLIKILSTLLKPSEGKAFVAG 65
                                      99*************99777766666554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0003      0.31       6      33 ..      35      62 ..      31      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvl 33
                                      l+G++GaGKTt +  L+ llk ++ k+ 
  gi|488601398|ref|YP_007907869.1| 35 LLGPNGAGKTTLIKILSTLLKPSEGKAF 62
                                      89************99999998766655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00062      0.65      10      31 ..      35      56 ..      27     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00062
                            AAA_22 10 vtGesGtGKTtllrrlleqlde 31
                                      + G+ G+GKTtl++ l   l+ 
  gi|488601398|ref|YP_007907869.1| 35 LLGPNGAGKTTLIKILSTLLKP 56
                                      78************99988853 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4       1.1   1.2e+03      96     106 ..       2      12 ..       1      13 [. 0.90
   2 ?    9.1   0.0     0.001       1.1       4      26 ..      35      57 ..      32      80 .. 0.83
   3 ?   -2.6   0.0       4.2   4.4e+03      37     102 ..     191     207 ..     169     239 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                                       H-EEEE---ST CS
                          NTPase_1  96 adviviDEiGk 106
                                        d+iv+D iGk
  gi|488601398|ref|YP_007907869.1|   2 DDIIVVDSIGK 12 
                                       59********7 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                                      EE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkss 26
                                      + Gp G GKtTl+k ++ llk s
  gi|488601398|ref|YP_007907869.1| 35 LLGPNGAGKTTLIKILSTLLKPS 57
                                      669***********999999866 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.2
                                       EE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-.EEEE- CS
                          NTPase_1  37 evreggrrigFkivdlasgeegiLarveakreprvgkyvvdvesfeelalealrkalsead.viviD 102
                                        +                                                  +++a + +d v +iD
  gi|488601398|ref|YP_007907869.1| 191 HY--------------------------------------------------IEEAERLCDrVAIID 207
                                       22..................................................233333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 2049.91
//
Query:       gi|488601399|ref|YP_007907870.1|  [L=117]
Description: hypothetical protein Asulf_01911 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0087   16.6   0.2      0.025   15.1   0.2    1.6  2  PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-lik
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.19   11.6   0.0    1.2  1  Utp13       Utp13 specific WD40 associated domain


Domain annotation for each model (and alignments):
>> PepSY_like  Putative beta-lactamase-inhibitor-like, PepSY-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   2.8e-06     0.025      33      81 ..      15      69 ..       5      70 .. 0.91
   2 ?   -1.5   0.0      0.42   3.7e+03      56      73 ..      88     105 ..      82     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-06
                                      GGGS-HHHHHHHHHHTTTEEEEEEEECS..SEEEEEETT....SEEEEEETTS-E CS
                        PepSY_like 33 lsilpkavlkaiknsypdekvtkierkk..keyeielen....eielyfdedGnl 81
                                      +++l ++++  + n+y+ e++ +i+rk+  k++ i +++    +++l+ d +Gnl
  gi|488601399|ref|YP_007907870.1| 15 TTDLANQIMFCLVNKYSIEEIMDITRKNssKNIYIMVSKrnpeKVSLFVDHNGNL 69
                                      5568899999999****************************************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.42
                                       EEECSSEEEEEETTSEEE CS
                        PepSY_like  56 ierkkkeyeieleneiel 73 
                                       +e +k  +ei+l+ +i l
  gi|488601399|ref|YP_007907870.1|  88 LEPDKDYFEITLKANICL 105
                                       566778888888877655 PP

>> Utp13  Utp13 specific WD40 associated domain
   #    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      76     132 ..      10      66 ..       6      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                                       HTSTTTHHHHHHHHHHHHHHS-HHHHHS---HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             Utp13  76 ntnartsevAqrvLnailkslsaeelleleglkellealipYteRHlkRldrlvees 132
                                        t   t ++A+ ++ ++++++s+ee++++   ++  +  i  ++R  ++++ +v+  
  gi|488601399|ref|YP_007907870.1|  10 TTTPETTDLANQIMFCLVNKYSIEEIMDITRKNSSKNIYIMVSKRNPEKVSLFVDHN 66 
                                       6788899**********************9888888888888888888777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 802.89
//
Query:       gi|488601400|ref|YP_007907871.1|  [L=250]
Description: hypothetical protein Asulf_01912 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-09   35.4   0.0      1e-08   35.1   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 !   35.1   0.0   5.8e-13     1e-08      34     200 ..      55     212 ..      16     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 5.8e-13
                         DDE_Tnp_1  34 ygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleekgvdyiirlkk 108
                                        gy + +++++ +  +++v+i++++++ +k+ + ++  l     k k v+aDaG++ +++++   + ++ +i+++k+
  gi|488601400|ref|YP_007907871.1|  55 VGYIVAVLINLSNLSLVDVRIFSKKTSKVKADEMVISNLGTLngKIKAVIADAGFSCYKVYEMSMSYRIIPIVKPKN 131
                                       69*******************************99999987799************9******************** PP

                         DDE_Tnp_1 109 ntklyrk..............gaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaely 171
                                       n k++++              +  +    +   +d n+i++++ ++ n                        +++++
  gi|488601400|ref|YP_007907871.1| 132 NLKKLERvikamlvnfdwlnsR--YSSVFDDLVKDLNEIIKTTLQAIND-----------------------YEDFA 183
                                       *************999998543..4444555666667777777777777.......................67*** PP

                         DDE_Tnp_1 172 rlRwqiErvFkwlkrkfgldrlryrglnr 200
                                         R++iE  Fk  k  fgl  l+ + ++ 
  gi|488601400|ref|YP_007907871.1| 184 EMRAEIEILFKATKALFGLKDLHIYYRDL 212
                                       *******************9999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1478.96
//
Query:       gi|488601401|ref|YP_007907872.1|  [L=62]
Description: hypothetical protein Asulf_01913 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 385.32
//
Query:       gi|488601402|ref|YP_007907873.1|  [L=87]
Description: hypothetical protein Asulf_01914 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0064   16.3   2.1     0.0067   16.2   2.1    1.0  1  DUF975     Protein of unknown function (DUF975)
  ------ inclusion threshold ------
       0.15   12.7   2.5         12    6.6   0.4    2.3  2  OAD_gamma  Oxaloacetate decarboxylase, gamma chain
       0.17   12.3   3.2        2.5    8.6   0.8    2.5  3  ATP19      ATP synthase subunit K
        0.2   11.8   5.0       0.36   11.0   0.9    2.0  2  COX2_TM    Cytochrome C oxidase subunit II, transmembrane dom


Domain annotation for each model (and alignments):
>> DUF975  Protein of unknown function (DUF975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.1   1.5e-06    0.0067      57     125 ..       5      74 ..       1      86 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-06
                            DUF975  57 vlllgtlltlsavfvviklvkrkekvelkeslasfke.knfiklLvllllkelflllwsliallglliii 125
                                       ++l+ ++l l +v++ +k +k  +k+  ++ la+     +f+ + v++++ +++++l ++i+ + +   +
  gi|488601402|ref|YP_007907873.1|   5 MMLIFGVLWLIVVVYDLKTNKFTKKPTPEDILALGTLaTIFLASVVVAITNSIIMFLAAFISRMLITYTA 74 
                                       689*******************9*******999887779**********************999886555 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0033        15      11      27 ..       5      21 ..       3      38 .. 0.74
   2 ?    6.6   0.4    0.0026        12      17      45 ..      57      85 ..      42      87 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0033
                         OAD_gamma 11 mgvVFvvLilLslvisl 27
                                      m  +F vL l+++v+ l
  gi|488601402|ref|YP_007907873.1|  5 MMLIFGVLWLIVVVYDL 21
                                      8899*********9988 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0026
                         OAD_gamma 17 vLilLslvislfskiikkkakkkkkkaka 45
                                      ++++L  +is +    ++++k+kk ++++
  gi|488601402|ref|YP_007907873.1| 57 IIMFLAAFISRMLITYTAYKKEKKHNESN 85
                                      67899999999999999999999988766 PP

>> ATP19  ATP synthase subunit K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.46   2.1e+03      23      40 ..      10      28 ..       6      35 .. 0.46
   2 ?    8.6   0.8   0.00055       2.5      15      31 ..      34      50 ..      29      57 .. 0.78
   3 ?    3.7   0.0     0.018        81      19      42 ..      61      84 ..      52      87 .] 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.46
                                      HHHH--XXXXXXXXXX.XX CS
                             ATP19 23 gttglivylamggskk.kk 40
                                      g + liv++   + +k +k
  gi|488601402|ref|YP_007907873.1| 10 GVLWLIVVVYDLKTNKfTK 28
                                      4444454444444444233 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00055
                                      S-SHHHHHHHHH--XXX CS
                             ATP19 15 hyLAlgtLgttglivyl 31
                                       +LAlgtL+t++l  ++
  gi|488601402|ref|YP_007907873.1| 34 DILALGTLATIFLASVV 50
                                      68*********987654 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.018
                                      HHHHHHHH--XXXXXXXXXXXX.. CS
                             ATP19 19 lgtLgttglivylamggskkkkaa 42
                                      l+ +++ +li+y a  ++kk +++
  gi|488601402|ref|YP_007907873.1| 61 LAAFISRMLITYTAYKKEKKHNES 84
                                      7888999999**999999995544 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   8.1e-05      0.36      35      82 ..       5      53 ..       1      56 [. 0.81
   2 ?    4.4   1.4    0.0095        42      26      58 ..      49      81 ..      40      87 .] 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                           COX2_TM 35 lilVlyilvlilvefrrrknkitakylvhgqe.iEiiWTiiPalilili 82
                                      ++l++++l li+v +  + nk+t+k++ +    + ++ Ti+ a ++++i
  gi|488601402|ref|YP_007907873.1|  5 MMLIFGVLWLIVVVYDLKTNKFTKKPTPEDILaLGTLATIFLASVVVAI 53
                                      45666777777888999********999888779999999999999887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0095
                           COX2_TM 26 yilliltlililVlyilvlilvefrrrknkita 58
                                       ++ i   i+++    + ++l+++++ k++  +
  gi|488601402|ref|YP_007907873.1| 49 VVVAITNSIIMFLAAFISRMLITYTAYKKEKKH 81
                                      555666678888888888888888766655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1284  (0.0716158); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 618.58
//
Query:       gi|488601403|ref|YP_007907874.1|  [L=139]
Description: hypothetical protein Asulf_01915 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.2   7.0      0.019   14.0   7.0    1.0  1  Acyl_transf_3    Acyltransferase family
      0.085   12.2   0.6       0.13   11.6   0.0    1.5  2  DUF4191          Domain of unknown function (DUF4191)
       0.57   10.2   0.1       0.57   10.2   0.1    2.5  2  Phage_holin_2_1  Bacteriophage P21 holin S
        1.2    9.0   3.5         17    5.3   0.2    2.7  3  Synaptobrevin    Synaptobrevin
        2.8    7.4   8.5        4.8    6.7   8.5    1.6  1  5TM-5TMR_LYT     5TMR of 5TMR-LYT


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   7.0   5.4e-06     0.019     166     276 ..       9     114 ..       1     117 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 166 lilllllslvfirhelfgpatsvgllplpsvlallfflfGalladaddrdrnlsrglkislllsllllalillalfg 242
                                       +++l+ l+ +++++   ++at+++++ +p+v++  ff+ G+l +  ++ + +    +k+ l+l++ +l+li + + +
  gi|488601403|ref|YP_007907874.1|   9 FGILFGLVGFTLTLLTMYSATGILDWRFPAVIGTGFFGGGFLGSLMRRLY-KGGEERKANLILLVCALCLIPVIIEN 84 
                                       56778888888888888889999999999999666666555555555555.55566666666666666666666666 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Acyl_transf_3 243 qtdggglvasvliqsaslllvslgimllllllfa 276
                                        +    +v + ++ ++ ++ v+ g++l+  + f+
  gi|488601403|ref|YP_007907874.1|  85 LY----DVFTGNWRTWKAISVVGGVYLICFAIFR 114
                                       66....58899**************999888776 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.62   2.2e+03      55      70 ..       8      23 ..       2      32 .. 0.66
   2 ?   11.6   0.0   3.6e-05      0.13      11      72 ..      54     115 ..      50     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.62
                           DUF4191 55 ilgillgllvalivlt 70
                                       +gil+gl+ ++++l 
  gi|488601403|ref|YP_007907874.1|  8 KFGILFGLVGFTLTLL 23
                                      5677777777776654 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.6e-05
                           DUF4191  11 iaqvfkltrkedkkllwlllaaflvvvvvfvvlglllgslilllilgillgllvalivltrr 72 
                                       +++ +k  ++++ +l+ l++a++l++v++  ++ +++g++ ++  ++++ g+ +  + + r 
  gi|488601403|ref|YP_007907874.1|  54 MRRLYKGGEERKANLILLVCALCLIPVIIENLYDVFTGNWRTWKAISVVGGVYLICFAIFRV 115
                                       67889999999999***********************9*************98888776665 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.4      0.21   7.6e+02      45      50 ..      19      24 ..       7      59 .. 0.59
   2 ?   10.2   0.1   0.00016      0.57      21      44 ..      83     108 ..      73     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.21
                   Phage_holin_2_1 45 llTylt 50
                                       lT+lt
  gi|488601403|ref|YP_007907874.1| 19 TLTLLT 24
                                      333333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                   Phage_holin_2_1  21 kqlldklspe..eWsaigvlgglvig 44 
                                       ++l+d ++++   W+ai+v+gg+ ++
  gi|488601403|ref|YP_007907874.1|  83 ENLYDVFTGNwrTWKAISVVGGVYLI 108
                                       5667777664338*********9876 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.016        56      62      87 ..       3      28 ..       1      30 [. 0.86
   2 ?   -1.1   0.0      0.47   1.7e+03      69      84 ..      67      82 ..      62      84 .. 0.56
   3 ?    5.3   0.2    0.0046        17      63      88 ..      93     118 ..      90     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.016
                                      HHHTXXXXXXXXXXXXXXXXXXXXXX CS
                     Synaptobrevin 62 wwknmkliiililvvlililiiiivi 87
                                      w++++k+ i+++lv + l l+ + ++
  gi|488601403|ref|YP_007907874.1|  3 WLRDIKFGILFGLVGFTLTLLTMYSA 28
                                      99************999998887765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.47
                                      XXXXXXXXXXXXXXXX CS
                     Synaptobrevin 69 iiililvvlililiii 84
                                       +il +++l+li +ii
  gi|488601403|ref|YP_007907874.1| 67 NLILLVCALCLIPVII 82
                                      4555555555555554 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0046
                                       HHTXXXXXXXXXXXXXXXXXXXXXXX CS
                     Synaptobrevin  63 wknmkliiililvvlililiiiivic 88 
                                       w+ +k i ++++v li++ i+ ++ c
  gi|488601403|ref|YP_007907874.1|  93 WRTWKAISVVGGVYLICFAIFRVARC 118
                                       9*****************99987766 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 ?    6.7   8.5    0.0013       4.8      16      65 ..       4      53 ..       1     116 [. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0013
                      5TM-5TMR_LYT 16 ksklllglifglfsilgtytgieiegaiantRaigvvvaGllgGplvGli 65
                                       + +  g++fgl++ ++t+  +  +  i + R   v+  G++gG + G +
  gi|488601403|ref|YP_007907874.1|  4 LRDIKFGILFGLVGFTLTLLTMYSATGILDWRFPAVIGTGFFGGGFLGSL 53
                                      5677899**************************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 903.44
//
Query:       gi|488601404|ref|YP_007907875.1|  [L=264]
Description: DNA repair photolyase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-13   50.2   0.1    1.1e-12   48.7   0.0    1.7  2  Radical_SAM      Radical SAM superfamily
  ------ inclusion threshold ------
      0.033   13.8   0.2      0.046   13.3   0.2    1.1  1  Mit_ribos_Mrp51  Mitochondrial ribosomal protein subunit
       0.05   13.0   0.1      0.082   12.4   0.1    1.4  1  DUF5131          Protein of unknown function (DUF5131)
       0.06   13.5   0.5       0.16   12.1   0.1    1.9  2  Fer4_14          4Fe-4S single cluster domain
       0.16   11.0   0.1       0.23   10.5   0.1    1.2  1  GIDA             Glucose inhibited division protein A
       0.62   10.6   4.6       0.47   11.0   2.3    1.9  2  Cas_Cas6         CRISPR associated protein Cas6
          1    9.1  11.7        3.3    7.3   4.9    3.1  3  DUF1848          Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   4.2e-16   1.1e-12       5     159 ..      28     184 ..      24     191 .. 0.86
   2 ?   -1.1   0.0      0.87   2.2e+03     127     142 ..     223     248 ..     202     259 .. 0.47

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 4.2e-16
                                       SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC....CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla....vp 76 
                                        gC ++C++C+ +++ r++ +g+  s+  ++e +  l ++k+ v++ + ++  +++ +  +e+ +rl ++     ++
  gi|488601404|ref|YP_007907875.1|  28 IGCQHACKYCYAKFMCRWYNHGKWGSWVVVKENMADL-VKKQvVNGSVYMSS-VSDPYQPIEKEFRLTRNVlknmDK 102
                                       59*************9999999999999999999999.78884555444444.444444557777777777789*** PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivgl 152
                                        i++++ t   l+  + ++++++ +   v l+++++    ++k+++    ++++++ea++ lre+g+++  ++ +++
  gi|488601404|ref|YP_007907875.1| 103 RIKLSILTKSDLV-LRDIDLFKKFNDIEVGLTINSFEGA-IKKKVEpFSSSNKRRIEAFKELRENGVRNYAFISPII 177
                                       *************.*************************.*******99**************************** PP

                                       TTTSHHH CS
                                       xxxxxxx RF
                       Radical_SAM 153 pGendee 159
                                       p  +d e
  gi|488601404|ref|YP_007907875.1| 178 PHLTDIE 184
                                       **99943 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.87
                                       H..........HHHHHHHHHHHHTTS CS
                                       x..........xxxxxxxxxxxxxxx RF
                       Radical_SAM 127 f..........eevlealeklreagi 142
                                       +          + v+e++ ++++a i
  gi|488601404|ref|YP_007907875.1| 223 YeilsdktkaeKYVKEVINAIKKAEI 248
                                       14444444444444444444445444 PP

>> Mit_ribos_Mrp51  Mitochondrial ribosomal protein subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.8e-05     0.046      99     206 ..     124     247 ..     121     254 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                   Mit_ribos_Mrp51  99 kfqElgipl..kssekeakakkSvFeeeadvt...sekakekedkrwkfkgPllagmte........gelseylkkk 162
                                       kf+++++ l  +s+e   k+k   F +++       ++ +e+  + + f  P +++ t+        ++++++   +
  gi|488601404|ref|YP_007907875.1| 124 KFNDIEVGLtiNSFEGAIKKKVEPFSSSNKRRieaFKELRENGVRNYAFISPIIPHLTDiehlieetKSFTNFYWFE 200
                                       66655555554555555555555555555333343466677778889999999999999877876664444444433 PP

                   Mit_ribos_Mrp51 163 ...vrkrrkeFkkfLreklaeektaearraalekgeealkekiseee 206
                                          +++  keF+++L+++++e+    + ++++ek  +++ ++i+++e
  gi|488601404|ref|YP_007907875.1| 201 flnLKASGKEFREWLKQNYPESYEILSDKTKAEKYVKEVINAIKKAE 247
                                       77799999************998888888888888777666666655 PP

>> DUF5131  Protein of unknown function (DUF5131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.2e-05     0.082       2     115 ..      15     113 ..      14     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                           DUF5131   2 tkIewtdatwnpvtGCtkvspgCdnCyaerlakrlkaakaekyglkltgkkaervrlseekleeplrwkkprrvfvn 78 
                                       tkI  ++ ++n  +GC++   +C+ Cya+ + + +++ k        +      v ++e+  +   +   +  v+++
  gi|488601404|ref|YP_007907875.1|  15 TKIPGAKWVVNQYIGCQH---ACKYCYAKFMCRWYNHGK-WG----SW------VVVKENMADLVKKQVVNGSVYMS 77 
                                       6777788899******96...7******99876555544.22....23......44555555566666678899999 PP

                           DUF5131  79 slsDlfhekvpdefi..drvfaviaatpqhtflvlTKrp 115
                                       s+sD +++ +++ef+  ++v++ +++  + +  +lTK  
  gi|488601404|ref|YP_007907875.1|  78 SVSDPYQP-IEKEFRltRNVLKNMDK--RIKLSILTKSD 113
                                       99999975.55555411556665554..55667888865 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 ?   12.1   0.1   6.2e-05      0.16       5      78 ..      27     100 ..      23     133 .. 0.64
   2 ?   -1.5   0.0         1   2.6e+03      97     102 ..     229     234 ..     203     253 .. 0.45

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                           Fer4_14   5 lsgCnlsCkgCdnketwks.elgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeey 78 
                                         gC+++Ck C+ k   +  + gk  +  ++++ ++dl k++++   + ++   +P ++ +  + ++l +++ +++
  gi|488601404|ref|YP_007907875.1|  27 YIGCQHACKYCYAKFMCRWyNHGKWGSWVVVKENMADLVKKQVVNGSVYMSSvSDPYQPIE--KEFRLTRNVLKNM 100
                                       559*********7654443355666677777777777777777666666666667765533..3345555555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                           Fer4_14  97 ktpdlk 102
                                       kt++ k
  gi|488601404|ref|YP_007907875.1| 229 KTKAEK 234
                                       222222 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   8.8e-05      0.23     189     266 ..     168     244 ..     138     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.8e-05
                                       EEEEEE--EEEGGGS-TTTSEEE---.SS-B-SSSSSSSTCG----EEEEE--HHHHHHHHCTCCC-T.T----B-- CS
                              GIDA 189 rlktgtppridkesidfskleeqsgd.kegeefsylnkplnkeqvecfltatneathkiikenlkksaklfegciee 264
                                       r +  ++p+i   + d++ l+e+ ++ ++   f++ln + + ++++++l+++ ++  +i+ ++ k +  ++++ i+ 
  gi|488601404|ref|YP_007907875.1| 168 RNYAFISPIIPHLT-DIEHLIEETKSfTNFYWFEFLNLKASGKEFREWLKQNYPESYEILSDKTKAEK-YVKEVINA 242
                                       44444566665554.9999999999999999**********************************866.99999987 PP

                                       S- CS
                              GIDA 265 lg 266
                                       ++
  gi|488601404|ref|YP_007907875.1| 243 IK 244
                                       76 PP

>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1         1   2.7e+03      66      81 ..      93     108 ..      64     154 .. 0.57
   2 ?   11.0   2.3   0.00018      0.47      19     112 ..     155     253 ..     144     258 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHHH CS
                          Cas_Cas6  66 sellkenlkkkykaly 81 
                                       ++++ +n++k++k+  
  gi|488601404|ref|YP_007907875.1|  93 TRNVLKNMDKRIKLSI 108
                                       3555555555544333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00018
                                       EEEE----S--TCEE.EEESS-BBEE....EE.EEETTCCEEEEE.......-TTSTTHHHHHHHHHHHHHHHHHSS CS
                          Cas_Cas6  19 evellkepeitssevvfktlSPivvr....st.kkengkkktyyl.......spddeeFsellkenlkkkykalyge 83 
                                       ++e++ke   + +     ++SPi+ +    ++ + e+ k+ t ++       + + +eF e lk+n  + y+ l ++
  gi|488601404|ref|YP_007907875.1| 155 RIEAFKELREN-GVRNYAFISPIIPHltdiEHlI-EETKSFTNFYwfeflnlKASGKEFREWLKQNYPESYEILSDK 229
                                       55565555543.3334788999999965542242.2333333322234445577********************999 PP

                                       ..SS---EEEEEEEEE......TEEEEEE CS
                          Cas_Cas6  84 ekeeklsikpdkkvkkivvkkketyirGy 112
                                       +k ek   ++++ +kk      e++++G 
  gi|488601404|ref|YP_007907875.1| 230 TKAEKYVKEVINAIKK-----AEIFVKGI 253
                                       9666664445553333.....46777765 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.9    0.0013       3.3     252     265 .]      26      39 ..      23      39 .. 0.91
   2 ?   -1.6   0.0       0.7   1.8e+03     150     179 ..      75     105 ..      58     131 .. 0.62
   3 ?    4.4   0.2      0.01        26      77     108 ..     130     165 ..     110     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0013
                           DUF1848 252 ayntClhgCvYCYA 265
                                       +y  C+h C+YCYA
  gi|488601404|ref|YP_007907875.1|  26 QYIGCQHACKYCYA 39 
                                       7899*********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.7
                           DUF1848 150 vviSfvdlykkvkrnlkk.klelrelseeek 179
                                        + S+ d+y+ ++++++  +  l++++++ k
  gi|488601404|ref|YP_007907875.1|  75 YMSSVSDPYQPIEKEFRLtRNVLKNMDKRIK 105
                                       3456777788888888532234444444444 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.01
                           DUF1848  77 fqfTltdye....kelepnvpsleerietfkelsek 108
                                       + +T++++e    k++ep   s ++rie+fkel e+
  gi|488601404|ref|YP_007907875.1| 130 VGLTINSFEgaikKKVEPFSSSNKRRIEAFKELREN 165
                                       556777665111144555557788899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1265  (0.0705561); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1789.99
//
Query:       gi|488601405|ref|YP_007907876.1|  [L=31]
Description: hypothetical protein Asulf_01917 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.043   13.2   1.3       0.04   13.3   1.3    1.0  1  Helo_like_N  Fungal N-terminal domain of STAND proteins


Domain annotation for each model (and alignments):
>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.3   2.2e-06      0.04      34      57 ..       3      26 ..       1      31 [] 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-06
                       Helo_like_N 34 rdktvreLkeeleaLeevLesLee 57
                                      ++k+++eLkee+e L ++L++L e
  gi|488601405|ref|YP_007907876.1|  3 KKKEIKELKEEIELLDDILSALVE 26
                                      789*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.26s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 232.71
//
Query:       gi|488601406|ref|YP_007907877.1|  [L=690]
Description: Phytoene dehydrogenase-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-21   75.1   0.0    9.1e-21   74.7   0.0    1.2  1  Amino_oxidase  Flavin containing amine oxidoreductase
    5.4e-14   52.2   0.1    1.2e-13   51.1   0.1    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    5.2e-12   46.0   0.5    9.4e-11   41.9   0.5    2.3  1  DAO            FAD dependent oxidoreductase
    1.1e-08   34.6   0.1    3.1e-07   29.8   0.1    2.2  2  FAD_binding_2  FAD binding domain
    1.7e-07   30.8   0.1      4e-07   29.5   0.1    1.6  1  Thi4           Thi4 family
    1.9e-07   30.0   0.3    0.00063   18.4   0.1    2.3  2  GDI            GDP dissociation inhibitor
    1.7e-05   24.3   0.2    2.6e-05   23.7   0.2    1.2  1  FAD_binding_3  FAD binding domain
    0.00011   21.1   0.0    0.00061   18.6   0.1    1.9  2  HI0933_like    HI0933-like protein
    0.00016   21.0   0.1    0.00048   19.5   0.0    1.8  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00024   20.6   0.0     0.0034   16.8   0.0    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
     0.0019   17.5   0.1     0.0036   16.6   0.1    1.4  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0087   15.2   0.4      0.046   12.8   0.1    2.1  2  GIDA           Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.014   15.9   0.9       0.35   11.5   0.2    3.0  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.046   13.2   0.0       0.51    9.8   0.0    2.1  2  SpoIIP         Stage II sporulation protein P (SpoIIP)


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   7.1e-24   9.1e-21       1     451 [.     219     683 ..     219     684 .. 0.75

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 7.1e-24
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET..TTHHHHHHHHHTTCCCCEEEESCCGC CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg..agnpllellkelgledslslpdpgap 75 
                                       +aGL++   L+ +G++V+vlE   +vGG ++++++ +++++ G + ++g     p+  ll+elgl+ ++ +  ++  
  gi|488601406|ref|YP_007907877.1| 219 IAGLTCGALLSKRGYKVLVLEQHYQVGGYCSSFKRRDFVFNAGVSDVSGlwEKGPIAYLLRELGLKREDLFVRNT-- 293
                                       8*********************************************************************99988.. PP

                                       EEEEETTEECCTTEECHHHHHHHHHHHHHHHH.CHHHHHHHHHHHHHHHHH....................HHHCCC CS
                     Amino_oxidase  76 krvlskggrefpgdlspvpaewealleqgals.aellsleeklrlgleall....................qktlde 131
                                        r+++k+++++ ++l+++ +++ ++ ++++ +      + ++ ++++e+                       k+l +
  gi|488601406|ref|YP_007907877.1| 294 IRYVFKDEEVEVQNLEEFMRKLSDMFPEEKENiY---AFFDEAKKAYEECYkdaeaygiplpaelivkvfgAKKLLD 367
                                       8899999999844444443333333332222221...122222222222224445556677777777777799999* PP

                                       CHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTH CS
                     Amino_oxidase 132 ldldskslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgG 208
                                        + +++++ +++++++r+ + +     ++ ++ l + l+ ++g+ + + ++  a+ al ++  +  +  + ++prgG
  gi|488601406|ref|YP_007907877.1| 368 YPKEHPHFYDWMNKTFRQKLDE-----YFKNEDLKTLLGALLGYIGTEADKTPASNALTAVVSYYIH--GGYFPRGG 437
                                       ********************99.....7777778899999999999665555555444444444444..446***** PP

                                       THHHHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEES.CCSHHHHHHH CS
                     Amino_oxidase 209 lsqlpealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsP.plpdekaeai 282
                                        ++ +++l e  e +g++++l+++  +i  ++++v    +  +v++a  Vv  +   +   +l    +l     e +
  gi|488601406|ref|YP_007907877.1| 438 AQRFANSLKEviEGHGGKVLLRHKADKILIGNGKVEGIKVGDKVFRASIVVANANAKTTFLELVGEkHLDARFIEYL 514
                                       ******************************88888886667777788888888888877766666655566777777 PP

                                       HHS.EEEEEEEEEEEESSGGSGCSTSECECECCCEEETTTEEEEECC.ECCCSTTTEEE....EEEEEEC.HHHHHH CS
                     Amino_oxidase 283 rnl.gfgsvnkvilefdrkfwednalgqgvlvseltttlgeafissd.fpsrappgkgl....vllvyvg.gdaane 352
                                       + l  ++s++ v+l +d     +       +   ++++  + +i s+  +s ap+gk       l  y    +++ e
  gi|488601406|ref|YP_007907877.1| 515 KTLkMSPSCFAVFLGVDADL-TEYP-----TIVVDLDDGYYVVINSNaDSSLAPNGKASvtilTLANYHDfPERGTE 585
                                       7778889999*******999.3333.....45555555555555555688889999998333344444443444433 PP

                                       HTTS.-HHHHHHHHHHHHHHHHT...GTSSTCSEEEEEECCT.ETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE CS
                     Amino_oxidase 353 lesl.sdeelvqavlrdLrklfg...eevpepkatlvtrWht.dplargsysyvsvgpghedydplakpegdprlff 424
                                        e l  ++e ++ +++  +k+ +   + +  + a++ + + +  ++++g+   +++ ++ +  +p  k+ ++ +l++
  gi|488601406|ref|YP_007907877.1| 586 -EYLqKKKEFAEMLIKKAEKVIPdlsKRIIVQDAATPKTFERyTSMPEGAI--YAFDQSIDTKRPYFKT-PIRGLYL 658
                                       .44479999999999999999998885555555566666655577887775..6777788888888888.******* PP

                                       .SGGGCTTTTTS.HHHHHHHHHHHHHHH CS
                     Amino_oxidase 425 AGehtsreypgt.vegAilSGlraAari 451
                                       A ++t    pg+ +e  + SG   A++i
  gi|488601406|ref|YP_007907877.1| 659 ASASTF---PGGgIEAVVISGMICANDI 683
                                       ****99...9999*************99 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 !   51.1   0.1   9.4e-17   1.2e-13       1      53 [.     214     266 ..     214     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 9.4e-17
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifh 53 
                                       IvG+G++Gl++ +lL+k+g++vl+le++ ++GG ++s+++ +++++ g++ + 
  gi|488601406|ref|YP_007907877.1| 214 IVGSGIAGLTCGALLSKRGYKVLVLEQHYQVGGYCSSFKRRDFVFNAGVSDVS 266
                                       9********************************************99987655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.5   7.3e-14   9.4e-11       1     311 [.     211     621 ..     211     681 .. 0.52

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 7.3e-14
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSE.EEEESSSSTHHSTH.................. CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrns.gllhsglrylpeas.................. 55 
                                       dv+i+G+Gi+Gl++   L++rg  V++le++ ++g   +S +    ++ +g+++   +                   
  gi|488601406|ref|YP_007907877.1| 211 DVIIVGSGIAGLTCGALLSKRGykVLVLEQHYQVGGyCSSFKRRdFVFNAGVSDVS-GLwekgpiayllrelglkre 286
                                       8******************************9999523333333145566664333.21111222223333333344 PP

                                       .....................HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHHHH........... CS
                               DAO  56 .....................elarlslealeelreleeelgididyrrtGllslaadeeeleald........... 100
                                                                                                        +           
  gi|488601406|ref|YP_007907877.1| 287 dlfvrntiryvfkdeevevqnL-------------------------------------------Eefmrklsdmfp 320
                                       4444444444444433333330...........................................233344444444 PP

                                       ....................................................................HHHHHH... CS
                               DAO 101 ....................................................................kllall... 106
                                                                                                           + +++    
  gi|488601406|ref|YP_007907877.1| 321 eekeniyaffdeakkayeecykdaeaygiplpaelivkvfgakklldypkehphfydwmnktfrqkldEYFKNEdlk 397
                                       44444444444444444444444444444444444444444444444444444444444444444444555554543 PP

                                       .HHTTTTEEEEEHHHHHHHSTT.ST......TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEE CS
                               DAO 107 .leagldaelldaeevrelepa.lp......gllgalfypdtgqvdpakltaalaraaealGveilegtevtgleee 175
                                        l +g+   ++  e  +++ pa  +       +  + ++p +g    ++++++l + +e +G+++l+++++ ++   
  gi|488601406|ref|YP_007907877.1| 398 tL-LGALLGYIGTE--ADKTPAsNAltavvsYYIHGGYFPRGGA---QRFANSLKEVIEGHGGKVLLRHKADKILIG 468
                                       31.22211245553..3555553114456754446667788776...8*************************9888 PP

                                       ETCEEEEEEECTEEEEEEEE..EEE--GGGHHHHHTT..CTT.........TSEEEEEEEEEEEEEECCTHSTGSGC CS
                               DAO 176 dgkvwgverttpgendaada..vVnaaGawsdllgll..kel.........dlpispvrgqvlvlkplseklvspaa 239
                                       +gkv g+++   g ++ ++a  vV  a+a +++l+l+  k l          l++sp   + +++    +  ++   
  gi|488601406|ref|YP_007907877.1| 469 NGKVEGIKV---GDKV-FRAsiVVANANAKTTFLELVgeKHLdarfieylkTLKMSP---SCFAV---FLGVDADLT 535
                                       89*****32...6653.3665366667777776666655555322222211122222...22222...111111113 PP

                                       SEEEEEEEETTTTEEEEEETTSEEEEEESSE...............EETTCSSTSCSHHHHHHHHHHHHHHSGGG.C CS
                               DAO 240 ilpvpetdddgrgvyvtprkdgrvlvGgtad...............eesgdddpevdeedidellealrklfPql.g 300
                                        +p+   +d ++g+yv+   +    + +++                e++++++++   e ++ l+++++k++P+l +
  gi|488601406|ref|YP_007907877.1| 536 EYPTI-VVDLDDGYYVVINSNADSSLAPNGKasvtiltlanyhdfpERGTEEYLQKKKEFAEMLIKKAEKVIPDLsK 611
                                       44444.555566666666544444444444477888888888899555555559999999999***********744 PP

                                       GEEEEEEEEEE CS
                               DAO 301 dvlrkwaGlrp 311
                                       ++  + a  +p
  gi|488601406|ref|YP_007907877.1| 612 RIIVQDA-ATP 621
                                       4443322.344 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   2.4e-10   3.1e-07       1      36 [.     211     246 ..     211     252 .. 0.93
   2 ?    2.6   0.0     0.045        58     147     182 ..     445     480 ..     308     508 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.4e-10
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                       Dvi++GsG+AGL++++ ++++G kv+v+e+  ++gg
  gi|488601406|ref|YP_007907877.1| 211 DVIIVGSGIAGLTCGALLSKRGYKVLVLEQHYQVGG 246
                                       9*******************************9998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.045
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenp 182
                                       l e ++ +g +++ r++ad++++ +g+v G+ v ++
  gi|488601406|ref|YP_007907877.1| 445 LKEVIEGHGGKVLLRHKADKILIGNGKVEGIKVGDK 480
                                       444456677999*******************99865 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   3.2e-10     4e-07      12      55 ..     204     246 ..     198     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.2e-10
                                       HHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4  12 llkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGG 55 
                                       l    e Dv+ivG+G +GLt++  l+k+ + kv++le++  +GG
  gi|488601406|ref|YP_007907877.1| 204 LKGENEYDVIIVGSGIAGLTCGALLSKR-GYKVLVLEQHYQVGG 246
                                       5556799*********************.*************99 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   4.9e-07   0.00063       2      47 ..     207     252 ..     206     260 .. 0.92
   2 !    9.3   0.0   0.00027      0.35     230     283 ..     438     490 ..     377     503 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.9e-07
                                       XXEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE- CS
                               GDI   2 deeydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesaslt 47 
                                       ++eydvi++G+G+       lls  g kvl+l+++   Gg ++s +
  gi|488601406|ref|YP_007907877.1| 207 ENEYDVIIVGSGIAGLTCGALLSKRGYKVLVLEQHYQVGGYCSSFK 252
                                       579*******************************9999*9999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00027
                                       TTHHHHHHHHHHHHTT-EEETS--ECEEEE-TTS-EEEEEETTEEEEECEEEE- CS
                               GDI 230 lGelpqgfarlsaiyGGtymlnkpvdevvldedgkvvGvkseeevakakkvicd 283
                                          + +++  +   +GG  +l ++ d++++  +gkv G+k +++v++a+ v+++
  gi|488601406|ref|YP_007907877.1| 438 AQRFANSLKEVIEGHGGKVLLRHKADKILI-GNGKVEGIKVGDKVFRASIVVAN 490
                                       5555555555566689************99.89*****************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 !   23.7   0.2     2e-08   2.6e-05       1      33 [.     209     241 ..     209     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2e-08
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       e+dV+IVG+G aGl+ + lLs++G +v+++e++
  gi|488601406|ref|YP_007907877.1| 209 EYDVIIVGSGIAGLTCGALLSKRGYKVLVLEQH 241
                                       589****************************98 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   0.1   4.8e-07   0.00061       1      36 [.     210     245 ..     210     247 .. 0.95
   2 ?   -0.1   0.0      0.23   2.9e+02      98     161 ..     429     489 ..     379     494 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.8e-07
                                       -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +dvi++G G AGl + + ++krg +Vl+le+  ++g
  gi|488601406|ref|YP_007907877.1| 210 YDVIIVGSGIAGLTCGALLSKRGYKVLVLEQHYQVG 245
                                       59*****************************98887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.23
                                       TTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE- CS
                       HI0933_like  98 sgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlA 161
                                       +g  Fp+   a++  + l++ ++  g k+ l+++  ++   ++++  +k+ + +++  +++v+A
  gi|488601406|ref|YP_007907877.1| 429 HGGYFPRG-GAQRFANSLKEVIEGHGGKVLLRHKADKILIGNGKVEGIKV-G-DKVFRASIVVA 489
                                       77889999.99***************************999999999999.4.45555566666 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.8e-07   0.00048       1      32 [.     210     245 ..     161     263 .. 0.81
   2 ?   -3.5   0.0       3.7   4.8e+03     175     204 ..     373     402 ..     371     414 .. 0.82
   3 ?   -3.2   0.0       3.1   3.9e+03     183     217 ..     439     473 ..     401     491 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.8e-07
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....le 32 
                                       +dv+++G+G+AGl++   l++ g+kv+++e     +
  gi|488601406|ref|YP_007907877.1| 210 YDVIIVGSGIAGLTCGALLSKRGYKVLVLEqhyqVG 245
                                       588888999999988888888888888885444433 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.7
                                       SSSSTTS-HHHHHHHHHHHHHTTEEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 175 drllraldkelsaaleealekeGvevklgt 204
                                       ++++  ++k +++ l e++++e+ ++ lg+
  gi|488601406|ref|YP_007907877.1| 373 PHFYDWMNKTFRQKLDEYFKNEDLKTLLGA 402
                                       677888999999999999999999988887 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngekle 217
                                       +++++ l+e++e +G +v l++++ +i   + k+e
  gi|488601406|ref|YP_007907877.1| 439 QRFANSLKEVIEGHGGKVLLRHKADKILIGNGKVE 473
                                       45555555555555555555555555432222244 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.6e-06    0.0034       1      40 [.     211     250 ..     211     288 .. 0.93
   2 ?    1.4   0.0      0.13   1.6e+02      89     140 ..     441     488 ..     429     491 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.6e-06
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40 
                                       Dv++vG+g+aG+++     ++G kvl++e++  +GG  +s
  gi|488601406|ref|YP_007907877.1| 211 DVIIVGSGIAGLTCGALLSKRGYKVLVLEQHYQVGGYCSS 250
                                       9***********************************9886 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                      FAD_oxidored  89 akavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfi 140
                                       +++ l+e+++++g +vll ++++++   ++++e+++v    g+k++rA++++
  gi|488601406|ref|YP_007907877.1| 441 FANSLKEVIEGHGGKVLLRHKADKILIGNGKVEGIKV----GDKVFRASIVV 488
                                       567788999******************8889******....57899998876 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 !   16.6   0.1   2.8e-06    0.0036       1      41 [.     213     253 ..     213     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.8e-06
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiyrypk 41 
                                       iI+G G aGl+++  l k g  ++l+lE++ ++g   + + +
  gi|488601406|ref|YP_007907877.1| 213 IIVGSGIAGLTCGALLSKRGY-KVLVLEQHyQVGGYCSSFKR 253
                                       8********************.7******9888877666655 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   3.6e-05     0.046       1      33 [.     211     243 ..     211     252 .. 0.89
   2 ?   -0.5   0.0       0.4   5.1e+02      96     145 ..     440     488 ..     438     512 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkld 33 
                                       dvi++G G AG+ + + ++++G+kvl + ++++
  gi|488601406|ref|YP_007907877.1| 211 DVIIVGSGIAGLTCGALLSKRGYKVLVLEQHYQ 243
                                       7*************************9977765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEE CS
                              GIDA  96 lyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavv 145
                                       +++++++e++e +    +++ +++++++ ++kv+g++  d ++++a++vv
  gi|488601406|ref|YP_007907877.1| 440 RFANSLKEVIEGHGGKVLLRHKADKILIGNGKVEGIKVGD-KVFRASIVV 488
                                       6889999999999999999****************98654.344444444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00027      0.35       2      34 ..     212     244 ..     211     249 .. 0.91
   2 ?   -0.3   0.0       1.2   1.6e+03      34      71 ..     375     412 ..     370     417 .. 0.80
   3 ?    0.2   0.0       0.9   1.1e+03      43      78 ..     442     477 ..     435     480 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34 
                                       v++vG+G  gl +++ l++ g kV v+e + ++
  gi|488601406|ref|YP_007907877.1| 212 VIIVGSGIAGLTCGALLSKRGYKVLVLEQHYQV 244
                                       89************************9987665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                       SSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  34 llrllDeeaskilqeklekngievllntkveeiegsed 71 
                                       +   +++++++ l e+++++  + ll++ +  i +++d
  gi|488601406|ref|YP_007907877.1| 375 FYDWMNKTFRQKLDEYFKNEDLKTLLGALLGYIGTEAD 412
                                       556789999*********99999999987777776666 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.9
                                       HHHHHHHHHHTTEEEECSEEEEEEE.EETTSEEEEEE CS
                         Pyr_redox  43 skilqeklekngievllntkveeie.gsedgvesvkl 78 
                                       ++ l+e +e +g +vll +k+ +i  g+++ ve++k+
  gi|488601406|ref|YP_007907877.1| 442 ANSLKEVIEGHGGKVLLRHKADKILiGNGK-VEGIKV 477
                                       666777788889999999999999844444.888887 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 ?    0.7   0.0      0.22   2.8e+02     100     143 ..     205     253 ..     189     259 .. 0.77
   2 ?    9.8   0.0    0.0004      0.51     194     226 ..     584     616 ..     531     629 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.22
                            SpoIIP 100 stdeeknvveVGeeLa....eeL.ekygisvihdktvhdlesynksYkr 143
                                       ++++e++v+ VG+ +a     +L +k+g++v++ ++ +++  y +s+kr
  gi|488601406|ref|YP_007907877.1| 205 KGENEYDVIIVGSGIAgltcGALlSKRGYKVLVLEQHYQVGGYCSSFKR 253
                                       567889999999988633332455*********9999998888887775 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0004
                            SpoIIP 194 knpnweknlefakklkaklekkYPglsrgillk 226
                                        +++++k +efa+ l +k+ek  P+ls+ i+++
  gi|488601406|ref|YP_007907877.1| 584 TEEYLQKKKEFAEMLIKKAEKVIPDLSKRIIVQ 616
                                       45899*************************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 4399.80
//
Query:       gi|488601407|ref|YP_007907878.1|  [L=157]
Description: hypothetical protein Asulf_01919 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1067.45
//
Query:       gi|488601408|ref|YP_007907879.1|  [L=82]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    5.4e-09   36.1   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 !   36.1   0.0     3e-13   5.4e-09       5      72 ..       8      74 ..       5      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3e-13
                                      EEE-SSHHHHHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1  5 svpfpterlAsialrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvlet 72
                                      ++  ++ ++A+ ++++L+v+       ++ ++ l+g  L ++++A+++ ++R+++n++l+++ ++ e+
  gi|488601408|ref|YP_007907879.1|  8 EFKIENYKKAELIFNALKVEGGRGIR-SEAKIYLKGGSLILKIEAEDLTSFRASLNSWLRLIRICNEI 74
                                      6788999*************666444.899********************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 521.91
//
Query:       gi|488601409|ref|YP_007907880.1|  [L=116]
Description: prefoldin, beta subunit, archaeal [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   91.6  22.1      3e-26   91.4  22.1    1.0  1  Prefoldin_2      Prefoldin subunit
     0.0078   16.6   4.5     0.0078   16.6   4.5    2.9  2  FlaC_arch        Flagella accessory protein C (FlaC)
  ------ inclusion threshold ------
      0.013   15.6   7.7      0.021   15.0   7.7    1.2  1  Uds1             Up-regulated During Septation
      0.022   14.1  20.1      0.041   13.2  20.1    1.3  1  GAS              Growth-arrest specific micro-tubule binding
      0.031   13.9  14.8      0.047   13.3  14.8    1.2  1  PspA_IM30        PspA/IM30 family
      0.031   14.3  17.2      0.092   12.8   1.8    2.1  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.043   14.0   3.8      0.043   14.0   3.8    2.2  2  XhlA             Haemolysin XhlA
      0.046   13.8  15.2        0.5   10.4   2.1    2.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.084   13.0   1.9       0.11   12.7   1.9    1.2  1  DUF2852          Protein of unknown function (DUF2852)
      0.091   12.6   3.0       0.11   12.4   3.0    1.1  1  PhageMin_Tail    Phage-related minor tail protein
        0.1   11.9  15.5       0.39   10.0   3.5    2.0  2  DUF3450          Protein of unknown function (DUF3450)
       0.11   12.0  16.3       0.92    9.0   8.0    2.0  2  Leu_zip          Leucine zipper
       0.11   11.0   1.2       0.13   10.7   1.2    1.0  1  FUSC             Fusaric acid resistance protein family
       0.14   11.5   6.7       0.18   11.1   6.7    1.2  1  DUF4407          Domain of unknown function (DUF4407)
       0.14   12.6  17.7       0.19   12.2   6.5    2.1  2  ZapB             Cell division protein ZapB
       0.14    9.7  12.0       0.16    9.5  12.0    1.0  1  DUF3584          Protein of unknown function (DUF3584)
       0.14   12.7  23.5      0.087   13.3   4.9    2.1  2  APG6_N           Apg6 coiled-coil region
       0.26   11.6  15.3       0.89    9.8   4.4    2.2  2  Spc24            Spc24 subunit of Ndc80
       0.29   11.4   6.0          2    8.7   1.7    2.6  2  WXG100           Proteins of 100 residues with WXG
        0.3   10.8   6.9        3.6    7.3   4.6    2.6  3  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
       0.31   11.1  19.9       0.41   10.7   8.3    2.1  2  DHR10            Designed helical repeat protein 10 domain
       0.31    8.9   7.4       0.43    8.4   7.4    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.35   10.7  11.6        0.2   11.4   2.7    2.1  2  Nsp1_C           Nsp1-like C-terminal region
       0.37   11.3  11.8       0.56   10.7  11.8    1.2  1  AAA_23           AAA domain
       0.39   11.2  12.4       0.17   12.3   4.6    2.6  3  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
       0.43   10.6  11.8       0.81    9.7  11.7    1.5  1  Laminin_II       Laminin Domain II
       0.44   10.8   9.5       0.36   11.1   2.8    2.2  2  KxDL             Uncharacterized conserved protein
       0.73    9.7   2.7        5.8    6.8   0.5    2.4  2  DASH_Dam1        DASH complex subunit Dam1
        1.1    9.4   9.5        2.2    8.4   9.5    1.6  1  Spore_III_AB     Stage III sporulation protein AB (spore_III_
        1.2    8.4   5.6        1.4    8.1   5.6    1.0  1  Peptidase_U57    YabG peptidase U57
        1.3    7.8  18.6        1.8    7.4   3.7    1.7  1  Spc7             Spc7 kinetochore protein
        1.5    7.3  14.5        1.8    7.0  14.5    1.0  1  Macoilin         Macoilin family
          2    8.0  17.0       0.45   10.1   6.8    2.0  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
        2.1    8.7   7.8         10    6.5   7.8    2.0  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
        2.6    8.2  11.9          4    7.6  11.9    1.2  1  Fib_alpha        Fibrinogen alpha/beta chain family
        2.9    6.9  13.1       0.22   10.6   5.9    2.0  2  DUF3086          Protein of unknown function (DUF3086)
        3.3    7.6  11.1         11    5.9   0.8    2.0  2  Cauli_AT         Aphid transmission protein
        3.5    7.7  13.7         11    6.1  13.7    1.9  1  Nup54            Nucleoporin complex subunit 54
        3.6    7.7   6.8         13    5.8   6.8    1.8  1  Cob_adeno_trans  Cobalamin adenosyltransferase
        4.5    7.4  10.6        1.4    9.1   2.5    2.5  2  YojJ             Bacterial membrane-spanning protein N-termin
        5.1    6.3  16.5         27    3.9  16.5    1.8  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
        5.2    7.8  17.6        4.9    7.8   3.4    2.4  2  SlyX             SlyX
        6.5    6.8  17.3        5.2    7.2   5.7    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
        6.9    7.4  14.7        2.5    8.8   2.9    2.2  2  YabA             Initiation control protein YabA
          8    5.7  12.0         10    5.3  12.0    1.2  1  FAM76            FAM76 protein
        9.3    6.3  13.5        5.1    7.2   3.4    2.1  2  DUF1664          Protein of unknown function (DUF1664)
        9.3    6.5  12.6       0.59   10.3   2.4    2.7  2  BRCC36_C         BRCC36 C-terminal helical domain
         10    5.4  17.6       0.75    9.1   8.1    2.0  2  DUF4763          Domain of unknown function (DUF4763)


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 !   91.4  22.1   8.1e-29     3e-26       1     104 [.      10     112 ..      10     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 8.1e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       q++++++qq+qqqlq +++q++q+++ lke+e +leel++ ++ t+vyk vG++lvk++kee+++eLee+ketle +
  gi|488601409|ref|YP_007907880.1|  10 QNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKED-TTVYKTVGNILVKTSKEEMLKELEEKKETLEIR 85 
                                       89*************************************9655.5******************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklq 104
                                       iktl++q+ekl++++ el++++q++l+
  gi|488601409|ref|YP_007907880.1|  86 IKTLQRQEEKLRERFVELQKKIQSMLG 112
                                       ************************997 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.8       1.3   4.7e+02      26      26 ..      26      26 ..       3      63 .. 0.60
   2 !   16.6   4.5   2.1e-05    0.0078       2      41 ..      72     111 ..      71     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.3
                         FlaC_arch 26 l 26
                                      +
  gi|488601409|ref|YP_007907880.1| 26 V 26
                                      2 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.1e-05
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdll 41 
                                       ++elE+k + l+++++t++++ e+l++   el+++++ +l
  gi|488601409|ref|YP_007907880.1|  72 LKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQSML 111
                                       58***********************************998 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   7.7   5.5e-05     0.021      22     119 ..       8     107 ..       5     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.5e-05
                              Uds1  22 eVeelkkelkaLeerlea.lrkkLaletklrdaarsLsrlyssskksak..ssaarsnskssreslakaeeelaese 95 
                                       +V+++  +l++++++l+  + +k ++   l++a ++L++l+ +++  +   + ++   ++s++e l++ ee+ +++e
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVvVAQKAQVDAGLKEAEMALEELK-KKEDTTVykTVGNILVKTSKEEMLKELEEKKETLE 83 
                                       6778888999999999972578899****************.444443466333333455566789999999999** PP

                              Uds1  96 rkvdelaselekleeraaevrrrL 119
                                        +++ l+++ ekl+er  e+++++
  gi|488601409|ref|YP_007907880.1|  84 IRIKTLQRQEEKLRERFVELQKKI 107
                                       *******************99986 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  20.1   0.00011     0.041      34     138 ..       8     109 ..       3     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                               GAS  34 eieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehev 110
                                       +++++ ++ ++ +++l+ + +++ +    Lk+ae  +eeL+k+  +     +   n+  + ++ e+ lk+l++++e 
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTVY--KTVGNILVK-TSKEEMLKELEEKKET 81 
                                       8899*************************************97554443..223333333.2346779999999999 PP

                               GAS 111 leqrfekvekerdelykkfeaaiqevqq 138
                                       le r+++++++ ++l+++f +  +++q 
  gi|488601409|ref|YP_007907880.1|  82 LEIRIKTLQRQEEKLRERFVELQKKIQS 109
                                       9999999999999999999998888875 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  14.8   0.00013     0.047      31     122 ..       8     108 ..       4     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                         PspA_IM30  31 airdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkg.........eeeLArealaeikslek 98 
                                        +++m ++l++ +q+l  v+a++ q+   l+e++  +++l+kk      k          +ee  +e+ +++++le 
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTVYKTvgnilvktsKEEMLKELEEKKETLEI 84 
                                       5899***************************************999999999999********************** PP

                         PspA_IM30  99 qaealetqlaqqrsaveqlrkqle 122
                                        ++ l+ q +++r+   +l+k+++
  gi|488601409|ref|YP_007907880.1|  85 RIKTLQRQEEKLRERFVELQKKIQ 108
                                       **********************98 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.8   0.00025     0.092      57     103 ..       5      51 ..       2      57 .. 0.89
   2 ?    7.0   7.9     0.014       5.4       8      39 ..      68      99 ..      63     111 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00025
                    CENP-F_leu_zip  57 lkeeieelaeelreleldLvalrsekeeLekelqkkqervseLesln 103
                                       l  +++++ ++l++++++L+ +  +k +++  l++     +eL++ +
  gi|488601409|ref|YP_007907880.1|   5 LPPQVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKE 51 
                                       566899************************************99865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                    CENP-F_leu_zip  8 vlekLKeserkadsLkdkvenLerelemseen 39
                                       +e LKe e+k++ L+ +++ L+r+ e + e 
  gi|488601409|ref|YP_007907880.1| 68 KEEMLKELEEKKETLEIRIKTLQRQEEKLRER 99
                                      45556666666666666666666655555443 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4      0.39   1.5e+02      12      46 ..      15      49 ..       8      57 .. 0.70
   2 ?   14.0   3.8   0.00011     0.043       3      44 ..      69     110 ..      67     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.39
                              XhlA 12 kldnleervdkleekaaeaeekiknleedlkkles 46
                                      +l  ++++++ +   +a +++ +k++e  l++l++
  gi|488601409|ref|YP_007907880.1| 15 QLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKK 49
                                      55666667777777777777777777777777765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00011
                              XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                       +e l+++e+k ++le r+++l++ +++ +e+  +l++++ ++
  gi|488601409|ref|YP_007907880.1|  69 EEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQSM 110
                                       789************************************987 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.1    0.0013       0.5      59     100 ..       9      50 ..       6      58 .. 0.75
   2 ?    9.1   5.6    0.0036       1.3      78     117 ..      66     105 ..      62     111 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                        TPR_MLP1_2  59 lqalreelnelkaeiaelkaeaesakaeleeseesweeqkee 100
                                       +q++ ++l++++++++ + a+  ++ a l+e+e ++ee k++
  gi|488601409|ref|YP_007907880.1|   9 VQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKK 50 
                                       566667888888888888888888888888888888877764 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0036
                        TPR_MLP1_2  78 aeaesakaeleeseesweeqkeelekelselekriedlne 117
                                       ++ e+  +elee++e +e + ++l+++ ++l++r  +l++
  gi|488601409|ref|YP_007907880.1|  66 TSKEEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQK 105
                                       4455555556666666666666666666666666665554 PP

>> DUF2852  Protein of unknown function (DUF2852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.9   0.00029      0.11      34     111 ..      20      95 ..       8     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00029
                           DUF2852  34 skrlaaakaakeeveekvkelfskakrereaaraskraaassGNaaFdeyreeeLerLeeeqreFeeflerLrrAkD 110
                                       +++l+ + a+k +v++ +ke+  ++++ ++  ++ ++ +++ GN      +ee+L+ Lee++++ e  +++L+r  +
  gi|488601409|ref|YP_007907880.1|  20 QQQLQVVVAQKAQVDAGLKEAEMALEELKK--KEDTTVYKTVGNILVKTSKEEMLKELEEKKETLEIRIKTLQRQEE 94 
                                       445555556677777777777666666666..778899999**********************99999999987655 PP

                           DUF2852 111 k 111
                                       k
  gi|488601409|ref|YP_007907880.1|  95 K 95 
                                       4 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 ?   12.4   3.0   0.00029      0.11      86     187 ..       9     113 ..       8     116 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00029
                     PhageMin_Tail  86 anngatsvedlaealkevgavakaaGlsfeetaaalallaaagikgseAgtalknllsrl.....tkeaaealkklG 157
                                       ++n  + ++++ + l+ v a+ ++    ++e+  al  l +  ++  ++  ++ n+l +       ke +e+ ++l 
  gi|488601409|ref|YP_007907880.1|   9 VQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKK--KEDTTVYKTVGNILVKTskeemLKELEEKKETLE 83 
                                       5889999**********************************..5566777777777777743333445556666668 PP

                     PhageMin_Tail 158 istkdaqgkmksldeiledlsealkkltda 187
                                       i +k +q +   l e + +l+++++++  +
  gi|488601409|ref|YP_007907880.1|  84 IRIKTLQRQEEKLRERFVELQKKIQSMLGP 113
                                       999999999999999999999999999665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.2    0.0047       1.8      45      89 ..       8      52 ..       4      58 .. 0.90
   2 ?   10.0   3.5     0.001      0.39      48      90 ..      67     109 ..      63     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0047
                           DUF3450 45 ekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqie 89
                                      + q+++a++++++++l+   ++++q+++ ++++e  +++l+++ +
  gi|488601409|ref|YP_007907880.1|  8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKED 52
                                      67999**********************************999765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.001
                           DUF3450  48 ellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       + ++ +++l+e++e le+  + l+r+ +++++++ +l+++i++
  gi|488601409|ref|YP_007907880.1|  67 SKEEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQS 109
                                       5677889999*****************************9987 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.0    0.0025      0.92     206     273 ..       7      78 ..       1      81 [. 0.78
   2 ?    6.6   4.5     0.013       4.8     127     161 ..      78     112 ..      71     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0025
                           Leu_zip 206 ktleektasaksleedlastkhelLkvqeqLelaekeLe..kkfqqtaayknlkemltk..kneqikelRkr 273
                                        ++++  a+ ++++++l+    +  +v + L+ ae  Le  kk ++t+ yk + ++l+k  k e +kel ++
  gi|488601409|ref|YP_007907880.1|   7 PQVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEelKKKEDTTVYKTVGNILVKtsKEEMLKELEEK 78 
                                       5666777788888888888888888899888888887776678899**********965449999***9876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                           Leu_zip 127 gaeLLkkeierLkeenekLkerlkelEkqatsale 161
                                         e L++ i+ L+ + ekL+er+ el k+++s+l 
  gi|488601409|ref|YP_007907880.1|  78 KKETLEIRIKTLQRQEEKLRERFVELQKKIQSMLG 112
                                       467899***********************998875 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.2   0.00035      0.13     227     305 ..       8     105 ..       3     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                              FUSC 227 rmlallallsslarllarlraeeaaavpe...laallaelaal................eaaaaaealeaalaalra 284
                                       ++++++a+l+ ++++l+ + a++a+  +     +  l+el++                 +++++ ++le++ ++l+ 
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGlkeAEMALEELKKKedttvyktvgnilvktSKEEMLKELEEKKETLEI 84 
                                       788999*************999998877755566666666666****************88899************* PP

                              FUSC 285 rlralrraleadadtaallla 305
                                       r++ l+r++e+ +++  +l+ 
  gi|488601409|ref|YP_007907880.1|  85 RIKTLQRQEEKLRERFVELQK 105
                                       *********955555555544 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.7   0.00047      0.18     129     221 ..      17     109 ..       4     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
                           DUF4407 129 aaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkak 205
                                       ++ +++l+   aq a+ +a +++ae +l++l+++ +  +  t g+    +  k++  ke +++ ++++ ++++l+++
  gi|488601409|ref|YP_007907880.1|  17 QQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTVYKTVGNI-LVKTSKEEMLKELEEKKETLEIRIKTLQRQ 92 
                                       3478888888888889999999999999999999999999888654.446677788888888888888888888888 PP

                           DUF4407 206 ld.atarlaalraelae 221
                                        +  ++r+ +l++++++
  gi|488601409|ref|YP_007907880.1|  93 EEkLRERFVELQKKIQS 109
                                       44566777777776665 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.3     0.032        12      12      53 ..       8      49 ..       4      65 .. 0.84
   2 ?   12.2   6.5    0.0005      0.19      27      67 ..      72     112 ..      66     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.032
                              ZapB 12 kiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlke 53
                                      ++q+++ ++++ q++++ + +++++     +e e  +e+lk+
  gi|488601409|ref|YP_007907880.1|  8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKK 49
                                      7999*******************9999999999977766664 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0005
                              ZapB  27 ieeLkeeneelkeenreleeeneqlkeereawqerlkkLLg 67 
                                       ++eL+e++e+l+ +++ l+++ e+l+e   ++q++++++Lg
  gi|488601409|ref|YP_007907880.1|  72 LKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQSMLG 112
                                       57899999999999999999999999999999999999997 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  12.0   0.00043      0.16     604     704 ..      12     111 ..       5     116 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00043
                           DUF3584 604 Lrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaerkq 680
                                       + ++lq+++++lq   a+++q+++ lk+++ +lee+k+++     +   +   ++  ++e+ +e +++++ ++ r +
  gi|488601409|ref|YP_007907880.1|  12 MVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTVYKTVGN-ILVKTSKEEMLKELEEKKETLEIRIK 87 
                                       56789999999999999999999999999999999999887654444333.34566777888888899999999999 PP

                           DUF3584 681 qaeeqlqkldaqlkqleeqqkaal 704
                                       + ++q +kl +    l+++++++l
  gi|488601409|ref|YP_007907880.1|  88 TLQRQEEKLRERFVELQKKIQSML 111
                                       999999999999999999999987 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.9   0.00023     0.087      55     102 ..       8      55 ..       3      63 .. 0.91
   2 ?    5.7  10.6     0.053        20      53      89 ..      69     105 ..      61     111 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00023
                            APG6_N  55 eleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfw 102
                                       +++++ ++ ++ +++L+ + +++++++a l+++e  le+l+++e+  +
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTV 55 
                                       6788889999**********************************9865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.053
                            APG6_N  53 eeeleklekeeeelleeLkelekereeleaelaalee 89 
                                       ee l++le+++e+l+  +k l++++e+l++   +l++
  gi|488601409|ref|YP_007907880.1|  69 EEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQK 105
                                       3335555555555555555555555555555555555 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   7.7      0.26        96       6      56 ..       9      57 ..       4      80 .. 0.71
   2 ?    9.8   4.4    0.0024      0.89       8      43 ..      74     109 ..      66     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.26
                             Spc24  6 kfriakelsdleselesleselaelkeeleeleeesee.keservedetllk 56
                                       ++++ +l++++++l+ + +++a+  + l+e e+  ee k +  +ed+t++k
  gi|488601409|ref|YP_007907880.1|  9 VQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEElK-K--KEDTTVYK 57
                                      5566777778888888888888888888888888777731.2..33666654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0024
                             Spc24   8 riakelsdleselesleselaelkeeleeleeesee 43 
                                       ++ ++ + le  ++ l+ + ++l+e++ el+++ ++
  gi|488601409|ref|YP_007907880.1|  74 ELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQS 109
                                       56778899***********************99875 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 ?    8.7   1.7    0.0054         2      56      85 ..       5      34 ..       1      35 [. 0.82
   2 ?    4.3   0.1      0.12        46       7      37 ..      80     110 ..      68     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0054
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100 56 wkqaaqklvdaLeeisealkqaanafedaD 85
                                      + +++q++v++L++i+++l+ + ++ +++D
  gi|488601409|ref|YP_007907880.1|  5 LPPQVQNMVAQLQQIQQQLQVVVAQKAQVD 34
                                      668999************998877766666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                            WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdal 37 
                                       e l+  ++++q+q+e+l+++  +l+++++++
  gi|488601409|ref|YP_007907880.1|  80 ETLEIRIKTLQRQEEKLRERFVELQKKIQSM 110
                                       4455556677777777777777777777665 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.21        80       2      41 ..       9      48 ..       8      51 .. 0.84
   2 ?    0.8   2.3         1   3.7e+02      26      40 ..      68      82 ..      43      92 .. 0.73
   3 ?    7.3   4.6    0.0095       3.6      15      52 ..      71     108 ..      63     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.21
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-XXXXXX CS
                        Vac_Fusion  2 lkdleerllvlekdfqlvikcckrvnealkRlEnHleTlR 41
                                      +++++ +l +++++ q v+ +  +v+  lk  E  le l 
  gi|488601409|ref|YP_007907880.1|  9 VQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELK 48
                                      6789999999****99999999999999998887777666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1
                                      HHHHHHHHH-XXXXX CS
                        Vac_Fusion 26 vnealkRlEnHleTl 40
                                      ++e+lk lE   eTl
  gi|488601409|ref|YP_007907880.1| 68 KEEMLKELEEKKETL 82
                                      468889999999998 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0095
                                       HHHHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXX CS
                        Vac_Fusion  15 dfqlvikcckrvnealkRlEnHleTlRkamlaLakKID 52 
                                         ++++++  + + ++k l +  e lR   ++L+kKI 
  gi|488601409|ref|YP_007907880.1|  71 MLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQ 108
                                       567788888999999**********************6 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.8     0.025       9.3      22      63 ..      10      51 ..       7      59 .. 0.49
   2 ?   10.7   8.3    0.0011      0.41      62     102 ..      68     108 ..      63     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.025
                             DHR10 22 qakidalqvvekdlrsciklleeieaelakleeakkklkelr 63
                                      q+ ++ lq+++++l+ ++++  ++ a l++ e a ++lk+ +
  gi|488601409|ref|YP_007907880.1| 10 QNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKE 51
                                      444444444444444444444444444444444444444444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0011
                             DHR10  62 lrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                        ++ l+e+e++++ le +++ lqrq e+ +e++  l+++ +
  gi|488601409|ref|YP_007907880.1|  68 KEEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQ 108
                                       567899999999999*****************999999876 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.4    0.0011      0.43      16     105 ..      14     106 ..       6     112 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                        V_ATPase_I  16 edvnafqrkfvkevrr...cdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkeln 89 
                                       ++++++q++    v +   +d   ++ ++  ee++k+e++++ ++  +   ++++e+ l+elee+ e+le ++k+l+
  gi|488601409|ref|YP_007907880.1|  14 AQLQQIQQQLQVVVAQkaqVDAGLKEAEMALEELKKKEDTTVYKTVGNILVKTSKEEMLKELEEKKETLEIRIKTLQ 90 
                                       445555554444443300033333444455566666566666665557777888888999***************** PP

                        V_ATPase_I  90 enleklkkelnelvel 105
                                       +++ekl++++ el+++
  gi|488601409|ref|YP_007907880.1|  91 RQEEKLRERFVELQKK 106
                                       **********999876 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 ?   11.4   2.7   0.00055       0.2      66     108 ..       9      51 ..       3      59 .. 0.84
   2 ?    4.9   1.7     0.058        22      66     107 ..      72     113 ..      60     116 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00055
                            Nsp1_C  66 vleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellskl 108
                                       v +  ++ ++i q+L+++ +q+ + ++ L++ E  leel +k 
  gi|488601409|ref|YP_007907880.1|   9 VQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKE 51 
                                       5555667789****************************99765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.058
                            Nsp1_C  66 vleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsk 107
                                       + e e++++ ++ +++ +++q + L +   ++ k+++++l+ 
  gi|488601409|ref|YP_007907880.1|  72 LKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQSMLGP 113
                                       456788999999999999999999999999999999998865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  11.8    0.0015      0.56     121     195 ..      13     110 ..       5     112 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0015
                            AAA_23 121 isellgskkiilnlilflgqer........feefelkdkke.....................rleelekeleelede 168
                                       + + l++ +++l++++ ++++             +l++ k+                      l+ele+++e+le +
  gi|488601409|ref|YP_007907880.1|  13 VAQ-LQQIQQQLQVVVAQKAQVdaglkeaeM---ALEELKKkedttvyktvgnilvktskeeMLKELEEKKETLEIR 85 
                                       443.455556677777776666888885431...3333333345788888888888886555777777777777777 PP

                            AAA_23 169 kkllekleqekekekeleeleeeleei 195
                                       +k l++  qe++ ++++ el+++++++
  gi|488601409|ref|YP_007907880.1|  86 IKTLQR--QEEKLRERFVELQKKIQSM 110
                                       777775..5567899999999999875 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.8      0.34   1.3e+02      26      66 ..      11      49 ..       4      57 .. 0.50
   2 ?    1.8   0.3      0.87   3.2e+02      58      69 ..      69      80 ..      64      82 .. 0.82
   3 ?   12.3   4.6   0.00047      0.17       5      41 ..      74     110 ..      70     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.34
                       Cep57_MT_bd 26 hlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlEa 66
                                       + ++lq+ ++q++     ++k++ ++  +e e+ +++l +
  gi|488601409|ref|YP_007907880.1| 11 NMVAQLQQIQQQLQVVV--AQKAQVDAGLKEAEMALEELKK 49
                                      44444555555554444..3444444444444444444444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.87
                       Cep57_MT_bd 58 eelvkrlEaKad 69
                                      ee++k+lE+K++
  gi|488601409|ref|YP_007907880.1| 69 EEMLKELEEKKE 80
                                      899999999987 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00047
                       Cep57_MT_bd   5 psqspkeaLaevlkeLedEfehlklelqelaaqynal 41 
                                       +  + ke+L+  +k+L+ + e+l+ ++ el+++++++
  gi|488601409|ref|YP_007907880.1|  74 ELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQSM 110
                                       556789*****************************98 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  11.7    0.0022      0.81       5      93 ..      16     108 ..       9     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0022
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       +++++++++ v +q+a++++ l++ +  l+e++++ + t  k      +  + ++  k+Le++ + L+ ++k+l+ +
  gi|488601409|ref|YP_007907880.1|  16 LQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTVYKTVGNILVKTSKEEMLKELEEKKETLEIRIKTLQRQ 92 
                                       6789999****************************4444433333334444556778******************** PP

                                       HHH.......HHHHHH CS
                        Laminin_II  82 eeasss....lsdnis 93 
                                       ee+       l ++i+
  gi|488601409|ref|YP_007907880.1|  93 EEKLRErfveLQKKIQ 108
                                       *996655666666665 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.6      0.17        62      41      76 ..      14      49 ..       3      58 .. 0.49
   2 ?   11.1   2.8   0.00097      0.36      19      60 ..      69     110 ..      62     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.17
                              KxDL 41 erlaklrarfkqgtkllkevkkdLesifkkirslka 76
                                      ++l++++++++  +    +v + L+     ++ lk+
  gi|488601409|ref|YP_007907880.1| 14 AQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKK 49
                                      334444444444444444444444444444444443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00097
                              KxDL  19 aqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkev 60 
                                       ++++++l++k+++L+  ++ +q++ +klr+rf + +k ++++
  gi|488601409|ref|YP_007907880.1|  69 EEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQSM 110
                                       689*******************************99999887 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.37   1.4e+02      16      30 ..      10      24 ..       7      27 .. 0.80
   2 ?    6.8   0.5     0.015       5.8       3      32 ..      70     100 ..      69     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.37
                         DASH_Dam1 16 dknledLqqihesLs 30
                                      ++ + +Lqqi+++L+
  gi|488601409|ref|YP_007907880.1| 10 QNMVAQLQQIQQQLQ 24
                                      566789999999986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.015
                         DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLsd.f 32 
                                       + ++eL+++ etL+ +++ Lq+ +e+L + f
  gi|488601409|ref|YP_007907880.1|  70 EMLKELEEKKETLEIRIKTLQRQEEKLRErF 100
                                       5799*********************998756 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   9.5    0.0058       2.2      90     149 ..      41      95 ..       4     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0058
                                       HHHHHHHGGGS---HHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spore_III_AB  90 eeavekllkklaLkkedkeilkelgeslgysdregqlkalelaleeleeeieeareeakk 149
                                       e a+e+l      kked  + k++g+ l ++++e+ lk le  +e le +i+ ++++ +k
  gi|488601409|ref|YP_007907880.1|  41 EMALEEL-----KKKEDTTVYKTVGNILVKTSKEEMLKELEEKKETLEIRIKTLQRQEEK 95 
                                       2233332.....36899***********************************99998776 PP

>> Peptidase_U57  YabG peptidase U57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.6    0.0037       1.4      64     152 ..      15     108 ..       4     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0037
                     Peptidase_U57  64 leekveeslkkllkerkeeee.....kkkkkekkekekeeafelpgkvLhlDgdeeYlekclklYkklgleavgvvv 135
                                       + ++++++l+ ++ ++++ ++     ++  +e k+ke+++++++ g++L   + ee l++  +  ++l++++++   
  gi|488601409|ref|YP_007907880.1|  15 QLQQIQQQLQVVVAQKAQVDAglkeaEMALEELKKKEDTTVYKTVGNILVKTSKEEMLKELEEKKETLEIRIKTLQR 91 
                                       4456677777776666666666666577788889999999************************************* PP

                     Peptidase_U57 136 kEkeqpekvkellekvk 152
                                       +E++  e+ +el +k++
  gi|488601409|ref|YP_007907880.1|  92 QEEKLRERFVELQKKIQ 108
                                       *******9999988876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.7    0.0047       1.8     221     268 ..       8      55 ..       3      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0047
                              Spc7 221 elaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesev 268
                                       +++++ +ql++++++++ + +qk+++ + ++eae  lee k+ +++ v
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTV 55 
                                       567778899999999999999999999999999999999998887766 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  14.5    0.0049       1.8     452     556 ..       7     110 ..       3     112 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0049
                          Macoilin 452 tklhelvsakqkdkqtlqqlekrLkeekearaslekqLaeekkrkkeeeetaarav..alaaasrsecteslkskkr 526
                                        +++++v + q+ +q+lq +  +  +     +++e  L+e kk+   e+ t  ++v   l ++s++e+ + l +kk+
  gi|488601409|ref|YP_007907880.1|   7 PQVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKK---EDTTVYKTVgnILVKTSKEEMLKELEEKKE 80 
                                       57899999999999999988766555555556667766655443...334444444116788999************ PP

                          Macoilin 527 eleaeikkLekel.klkeeqirelelkvqel 556
                                        le  ik L+ +  kl+e    el+ k+q++
  gi|488601409|ref|YP_007907880.1|  81 TLEIRIKTLQRQEeKLRER-FVELQKKIQSM 110
                                       *********9865266655.56677788887 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   4.3      0.22        84      91     128 ..      10      47 ..       3      58 .. 0.57
   2 ?   10.1   6.8    0.0012      0.45      66     110 ..      65     109 ..      47     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.22
                      HAUS-augmin3  91 qkekalklkrlnkLqvqaaslqqelrkleeeekeakkk 128
                                       q++ a +++  ++Lqv++a+ +q++  l+e+e + ++ 
  gi|488601409|ref|YP_007907880.1|  10 QNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEEL 47 
                                       34444444444556666666666666666666655443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                      HAUS-augmin3  66 vellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaas 110
                                        ++ e+ l+e+ee++e Le  +++Lq++++ + +r+ +Lq  + s
  gi|488601409|ref|YP_007907880.1|  65 KTSKEEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQS 109
                                       356688999******************************987765 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 ?    6.5   7.8     0.027        10       6      89 ..       6      96 ..       3     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.027
                                      HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHH........HHHHHHHHHHHHHSS--EEEE CS
                   AMP-binding_C_2  6 PsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelea........lekkiakklksklgvsvkvel 76
                                      P q+++++ ++++++++ q+vv ++ + D    + E++ +  ++  e  +        l k+ ++++ ++l  + +   
  gi|488601409|ref|YP_007907880.1|  6 PPQVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKK-EDTTvyktvgniLVKTSKEEMLKELEEKKETLE 83
                                      99***********************99998888888777443432.222212222333445555555555555555555 PP

                                      E-TT-S------- CS
                   AMP-binding_C_2 77 vepgtlprsegKa 89
                                      ++ +tl+r+e+K+
  gi|488601409|ref|YP_007907880.1| 84 IRIKTLQRQEEKL 96
                                      6666777777665 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  11.9     0.011         4      29     126 ..       8     108 ..       2     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                                       CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn......dnvikksskeleeeilrlketida 99 
                                       + +++  +l++++++l+ +  ++ +++   ke +  l+e +k+++ +      + ++k s++e+     +l+e+  +
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTvyktvgNILVKTSKEEML---KELEEKKET 81 
                                       55788899999999999999999999999999888888877777653333344444555554444...334444444 PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 100 qesnirvLqnvlesneqkiqkLeqdid 126
                                        e +i+ Lq   e+++++  +L+++i+
  gi|488601409|ref|YP_007907880.1|  82 LEIRIKTLQRQEEKLRERFVELQKKIQ 108
                                       456666677777777777777776665 PP

>> DUF3086  Protein of unknown function (DUF3086)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.6      0.51   1.9e+02       2      24 ..      10      32 ..       7      59 .. 0.64
   2 ?   10.6   5.9   0.00059      0.22       2      32 ..      69      99 ..      68     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.51
                           DUF3086  2 qealkeleerkqalqieveqLer 24
                                      q+ +++l++ +q+lq+ v q  +
  gi|488601409|ref|YP_007907880.1| 10 QNMVAQLQQIQQQLQVVVAQKAQ 32
                                      55666666666666666655443 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00059
                           DUF3086  2 qealkeleerkqalqieveqLerrkerieke 32
                                      +e lkelee+k++l+i +++L+r++e++++ 
  gi|488601409|ref|YP_007907880.1| 69 EEMLKELEEKKETLEIRIKTLQRQEEKLRER 99
                                      5789************************985 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.8      0.03        11     115     157 ..       8      50 ..       2      60 .. 0.89
   2 ?    5.7   5.6     0.035        13      87     142 ..      54     109 ..      48     112 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                          Cauli_AT 115 eaqnrikkleeetkklaekivtekllkeevkdlderlseirds 157
                                       ++qn + +l++ +++l+  +  ++++++ +k+ +  l+e++++
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKK 50 
                                       578999999999999*9999**************999999865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.035
                          Cauli_AT  87 svfkklkkifkeggedkekktklletLkeaqn.rikkleeetkklaek.ivtekllke 142
                                        v+k++ +i   +  +ke+ +k+le  ke+ + rik l+++ +kl e+ ++ +k++++
  gi|488601409|ref|YP_007907880.1|  54 TVYKTVGNI--LVKTSKEEMLKELEEKKETLEiRIKTLQRQEEKLRERfVELQKKIQS 109
                                       344444444..23344445555555544444489999999999999997777777765 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  13.7      0.03        11      32     125 ..      17     109 ..       6     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SS CS
                             Nup54  32 edLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldae 108
                                       +++++ +++  ++ aq    lke +  leel++k+++++ + + ++  +  + ++ l +l  k e l+ r + l+ +
  gi|488601409|ref|YP_007907880.1|  17 QQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTVYKTVGNILVKTSK-EEMLKELEEKKETLEIRIKTLQRQ 92 
                                       6788888899999999999999999999999999999999999998776554.6668888899999999999***** PP

                                       HHHHHHHHHHHHHHHS- CS
                             Nup54 109 Eeelrarletleaqlnd 125
                                       Ee+lr+r+ +l++++++
  gi|488601409|ref|YP_007907880.1|  93 EEKLRERFVELQKKIQS 109
                                       *************9984 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.8     0.036        13      50     109 ..       9     100 ..       1     112 [. 0.54

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.036
                                       THHHHHHHHHHHHHHHHHHHHHHT..................................-BTCCG-S--HHHHHHHHH CS
                   Cob_adeno_trans  50 eeelkeaLeeiqneLfdlgaelatp.................................ekkkekkkiteeeveelek 93 
                                        +++ ++L++iq++L  + a+ a                                   +k++  k++ ee+ e+le 
  gi|488601409|ref|YP_007907880.1|   9 VQNMVAQLQQIQQQLQVVVAQKAQVdaglkeaemaleelkkkedttvyktvgnilvktSKEEMLKEL-EEKKETLEI 84 
                                       5678899999999999999999844444444433333333333333333444444332222222222.222466777 PP

                                       HHHHHHHHS--EESEE CS
                   Cob_adeno_trans  94 eideleaelpplksfi 109
                                       +i++l+ + ++l++ +
  gi|488601409|ref|YP_007907880.1|  85 RIKTLQRQEEKLRERF 100
                                       7777776666666544 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   1.2      0.31   1.2e+02      14      31 ..      12      29 ..       7      53 .. 0.75
   2 ?    9.1   2.5    0.0037       1.4       7      53 ..      64     110 ..      60     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.31
                              YojJ 14 lkeeLeqiekeleevlka 31
                                      +  +L+qi+++l+ v+++
  gi|488601409|ref|YP_007907880.1| 12 MVAQLQQIQQQLQVVVAQ 29
                                      556777777777776654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0037
                              YojJ   7 eeelkeklkeeLeqiekeleevlkaldeedeClLcelesirekfael 53 
                                        +  ke++ +eLe+ +++le  +k+l+ ++e l   + ++++k++ +
  gi|488601409|ref|YP_007907880.1|  64 VKTSKEEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQSM 110
                                       56779**************************9999898888888876 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  16.5     0.072        27      29     102 ..       8     113 ..       3     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.072
                              HemX  29 qvqeltaevaelqqqlaaleqqlaq................................veaekeqkqeleerlqqlae 73 
                                       qvq++ a+ +++qqql+ + +q+aq                                 ++++e  +elee+ ++l+ 
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQvdaglkeaemaleelkkkedttvyktvgnilvKTSKEEMLKELEEKKETLEI 84 
                                       5667777778888888888877777888888888888888888999*******999655666678899999999999 PP

                              HemX  74 klealekeleqlqkqleelqqqlskvsga 102
                                       ++++l+++ e+l ++  elq++++ + g 
  gi|488601409|ref|YP_007907880.1|  85 RIKTLQRQEEKLRERFVELQKKIQSMLGP 113
                                       9**********************999875 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   6.3     0.072        27      14      53 ..      14      53 ..       8      59 .. 0.86
   2 ?    7.8   3.4     0.013       4.9       2      35 ..      76     109 ..      67     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.072
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX 14 fqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53
                                       q ++i++  +vv++q  q+d+  ++ ++  e+lk+ e++
  gi|488601409|ref|YP_007907880.1| 14 AQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDT 53
                                      5778899999************999999999999988765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidr 35 
                                       ee+ e LEi++  ++++ e+L +  +e q++i+ 
  gi|488601409|ref|YP_007907880.1|  76 EEKKETLEIRIKTLQRQEEKLRERFVELQKKIQS 109
                                       5556677777777777777777777777777765 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.7     0.038        14      77     116 ..      10      49 ..       4      54 .. 0.68
   2 ?    7.2   5.7     0.014       5.2      52      98 ..      62     108 ..      55     112 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.038
                              ADIP  77 erlktqleqlerelalvqakerqlekklktleqklkneke 116
                                       + + +ql+q +++l++v a+++q  + lk++e +l ++k 
  gi|488601409|ref|YP_007907880.1|  10 QNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKK 49 
                                       4555677777777777777777777777777777666653 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                              ADIP  52 leqreslnetirkleaeierlqskierlktqleqlerelalvqaker 98 
                                       + +++s +e +++le  +e l+ +i+ l++q e+l+ +   +q+k +
  gi|488601409|ref|YP_007907880.1|  62 ILVKTSKEEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQ 108
                                       55666666666666666666666666666666666666655555544 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.9    0.0066       2.5      13      62 ..       5      54 ..       2      69 .. 0.76
   2 ?    4.4   4.6      0.16        59      23      56 ..      71     104 ..      52     114 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0066
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXX CS
                              YabA 13 leeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekek 62
                                      l  q+++++++l++++++l+ ++ + a++ +  ++    lee +kke+++
  gi|488601409|ref|YP_007907880.1|  5 LPPQVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTT 54
                                      56789999999999999999999999999988888887775555444443 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXX CS
                              YabA  23 eleelkeelaelleenaeLeleneklrerleeee 56 
                                        l+el+e+ ++l  + ++L+ + eklrer+ e +
  gi|488601409|ref|YP_007907880.1|  71 MLKELEEKKETLEIRIKTLQRQEEKLRERFVELQ 104
                                       3444555555555555566666666666653222 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  12.0     0.028        10     212     296 ..       7      97 ..       2     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.028
                             FAM76 212 snssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekeke......lreklkelekeakekiekle 282
                                       +++++ + +++q++++++    q +q d  l e +  + elk ++ ++  +      +++  +e+ ke +ek e+le
  gi|488601409|ref|YP_007907880.1|   7 PQVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKKKEDTTVYKtvgnilVKTSKEEMLKELEEKKETLE 83 
                                       6788889999*******************************98876553331111113444566778999******* PP

                             FAM76 283 kkirellkevaels 296
                                        +i++l+++  +l 
  gi|488601409|ref|YP_007907880.1|  84 IRIKTLQRQEEKLR 97 
                                       ********988775 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.3     0.094        35      63     101 ..      11      49 ..       2      68 .. 0.50
   2 ?    7.2   3.4     0.014       5.1      49      92 ..      67     110 ..      58     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.094
                           DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                       ++ +++++++++l+ + + ++++++ ++e++  l+e+++
  gi|488601409|ref|YP_007907880.1|  11 NMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELKK 49 
                                       333444444444444444444444444444444444433 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtev 92 
                                       + e++ ++l++ k+ L+ ri++++++ ++  e   e++++++++
  gi|488601409|ref|YP_007907880.1|  67 SKEEMLKELEEKKETLEIRIKTLQRQEEKLRERFVELQKKIQSM 110
                                       55777889999999999999999999999888888888888765 PP

>> BRCC36_C  BRCC36 C-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.1      0.37   1.4e+02      54      73 ..       6      25 ..       1      33 [. 0.73
   2 ?   10.3   2.4    0.0016      0.59      40      81 .]      55      96 ..      34      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.37
                          BRCC36_C 54 vPllqtLesrlkenknrlaa 73
                                       P +q++ ++l++ +++l+ 
  gi|488601409|ref|YP_007907880.1|  6 PPQVQNMVAQLQQIQQQLQV 25
                                      57888888888888888775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0016
                          BRCC36_C 40 vytkslcalseviavPllqtLesrlkenknrlaaLeqekeeL 81
                                      vy      l+ ++   +l+ Le++ +++++r++ L++++e+L
  gi|488601409|ref|YP_007907880.1| 55 VYKTVGNILVKTSKEEMLKELEEKKETLEIRIKTLQRQEEKL 96
                                      554433445666777799*********************998 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   6.2      0.46   1.7e+02     101     141 ..       8      48 ..       2      54 .. 0.56
   2 ?    9.1   8.1     0.002      0.75      51     126 ..      37     110 ..      28     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.46
                           DUF4763 101 eileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqek 141
                                       +++++  + ++++qql+ +  ++ + ++ lke ++ l ++k
  gi|488601409|ref|YP_007907880.1|   8 QVQNMVAQLQQIQQQLQVVVAQKAQVDAGLKEAEMALEELK 48 
                                       45555555555555555555555555555555555554444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.002
                           DUF4763  51 LdeiydelekiKqrvlelrskLalnvpecPeidecvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkas 126
                                       L+e+   le++K++ ++  +k + n+  + + +e+++e +e+++    +  i++Lqr++ kLr +  elq++ +++
  gi|488601409|ref|YP_007907880.1|  37 LKEAEMALEELKKKEDTTVYKTVGNILVKTSKEEMLKELEEKKETL--EIRIKTLQRQEEKLRERFVELQKKIQSM 110
                                       8888889999999999999999989876665555555555555554..67789*****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3424  (0.190976); expected 358.6 (0.02)
Passed bias filter:                      996  (0.0555525); expected 358.6 (0.02)
Passed Vit filter:                       165  (0.00920297); expected 17.9 (0.001)
Passed Fwd filter:                        67  (0.00373696); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 690.56
//
Query:       gi|488601410|ref|YP_007907881.1|  [L=65]
Description: hypothetical protein Asulf_01922 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.053   13.0   4.1      0.056   12.9   4.1    1.1  1  DUF373           Domain of unknown function (DUF373)
       0.21   11.6   2.2       0.27   11.3   2.2    1.0  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        2.6    8.1  14.5        5.1    7.2   0.9    2.3  2  DUF2273          Small integral membrane protein (DUF2273)


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 ?   12.9   4.1   9.4e-06     0.056     162     204 ..      21      63 ..       5      65 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.4e-06
                            DUF373 162 GlllliyalllllglpelalaiillllGlylllrGfgldelle 204
                                        ++l+ ++++ l+ + +l++++i +  Gl+l+++G++l ++l+
  gi|488601410|ref|YP_007907881.1|  21 TIFLIAISIFFLTYPYNLIVSTIGITAGLVLIYKGIKLGKSLK 63 
                                       3456667777777777899*******************99876 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.2   4.5e-05      0.27      42      89 ..       9      57 ..       6      64 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                   Phage_holin_3_6 42 aagvlallalllllvala...lalaalwlaalivaavllvlagvlalvglk 89
                                      +a +l ++++++ ++++a   ++l       liv  + + +++vl++ g+k
  gi|488601410|ref|YP_007907881.1|  9 IAFALFHFGIFSTIFLIAisiFFL--TYPYNLIVSTIGITAGLVLIYKGIK 57
                                      444455555555555554111555..6777899999999999999999998 PP

>> DUF2273  Small integral membrane protein (DUF2273)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.7    0.0032        19      16      36 ..       7      27 ..       7      33 .. 0.89
   2 ?    7.2   0.9   0.00085       5.1       1      26 [.      30      55 ..      30      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0032
                           DUF2273 16 lilaililtiGFwktLliill 36
                                      +i+a+ ++ +G++ t+++i +
  gi|488601410|ref|YP_007907881.1|  7 VIIAFALFHFGIFSTIFLIAI 27
                                      69****************976 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00085
                           DUF2273  1 flkkhrgkiiGaliGlilaililtiG 26
                                      f+ ++++ +i  +iG+  ++ ++  G
  gi|488601410|ref|YP_007907881.1| 30 FFLTYPYNLIVSTIGITAGLVLIYKG 55
                                      6778***************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 442.18
//
Query:       gi|488601411|ref|YP_007907882.1|  [L=52]
Description: hypothetical protein Asulf_01923 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 361.88
//
Query:       gi|488601412|ref|YP_007907883.1|  [L=199]
Description: hypothetical protein Asulf_01924 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.8    8.6   3.9          1    9.3   1.1    2.1  2  UPF0542   Uncharacterised protein family UPF0542


Domain annotation for each model (and alignments):
>> UPF0542  Uncharacterised protein family UPF0542
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.19   3.4e+03       3      19 ..      87     103 ..      85     125 .. 0.73
   2 ?    9.3   1.1   5.7e-05         1      12      41 ..     156     185 ..     149     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.19
                           UPF0542   3 dwlskvalqlvlyvakd 19 
                                        +++ v + lvl +a +
  gi|488601412|ref|YP_007907883.1|  87 YYFAFVIVALVLMAAGS 103
                                       57777778888877755 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 5.7e-05
                           UPF0542  12 lvlyvakdPweFlttvlliltPllllsafl 41 
                                       l+   a  P   + tv++il Pll+lsaf+
  gi|488601412|ref|YP_007907883.1| 156 LATLMAGKPLLPFETVVFILHPLLFLSAFV 185
                                       6667788899999***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1212.10
//
Query:       gi|488601413|ref|YP_007907884.1|  [L=451]
Description: hypothetical protein Asulf_01925 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2559.42
//
Query:       gi|488601414|ref|YP_007907885.1|  [L=182]
Description: adenylylsulfate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-61  206.7   0.0    2.2e-61  206.4   0.0    1.1  1  APS_kinase       Adenylylsulphate kinase
    9.2e-11   42.4   0.0    1.6e-10   41.6   0.0    1.4  1  AAA_18           AAA domain
    2.6e-08   34.1   0.0    3.9e-08   33.6   0.0    1.3  1  AAA_33           AAA domain
    4.1e-06   26.7   0.4      0.014   15.2   0.0    3.2  3  Cytidylate_kin   Cytidylate kinase
    1.1e-05   25.0   0.0    1.2e-05   24.9   0.0    1.2  1  KTI12            Chromatin associated protein KTI12
    6.6e-05   23.5   0.0    0.00016   22.2   0.0    1.7  1  ABC_tran         ABC transporter
    0.00016   21.6   0.1    0.00029   20.8   0.1    1.4  1  NACHT            NACHT domain
    0.00018   21.5   0.0    0.00046   20.1   0.0    1.7  1  NTPase_1         NTPase
    0.00022   21.6   0.1    0.00058   20.3   0.1    1.7  1  AAA              ATPase family associated with various cellul
    0.00039   20.8   0.1     0.0012   19.1   0.0    1.7  1  RNA_helicase     RNA helicase
    0.00049   20.0   0.5       0.75    9.6   0.0    2.5  2  dNK              Deoxynucleoside kinase
    0.00051   19.4   0.0     0.0008   18.7   0.0    1.3  1  Zeta_toxin       Zeta toxin
    0.00074   19.2   0.1     0.0021   17.8   0.1    1.8  1  Thymidylate_kin  Thymidylate kinase
    0.00081   19.5   0.0    0.00099   19.2   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00091   19.2   0.1     0.0039   17.2   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0011   19.4   0.0     0.0013   19.2   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0012   18.6   0.0     0.0017   18.1   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0012   19.1   0.1     0.0021   18.4   0.1    1.5  1  AAA_22           AAA domain
     0.0014   18.9   0.1     0.0035   17.6   0.1    1.6  1  AAA_28           AAA domain
     0.0015   17.7   0.1     0.0025   17.0   0.1    1.2  1  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0023   17.6   0.2     0.0039   16.8   0.0    1.6  1  SRP54            SRP54-type protein, GTPase domain
     0.0025   17.6   0.0     0.0035   17.1   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
     0.0041   16.9   0.0     0.0074   16.0   0.0    1.7  1  AAA_24           AAA domain
     0.0046   17.1   0.4       0.73    9.9   0.1    2.2  2  SKI              Shikimate kinase
     0.0059   16.1   0.0     0.0081   15.6   0.0    1.2  1  ParA             NUBPL iron-transfer P-loop NTPase
      0.008   15.8   0.3      0.026   14.1   0.1    1.8  2  AAA_25           AAA domain
     0.0094   15.9   0.0      0.021   14.8   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
  ------ inclusion threshold ------
      0.013   15.9   0.6      0.026   15.0   0.1    1.9  1  AAA_17           AAA domain
      0.016   14.4   0.0      0.034   13.3   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.021   14.7   0.1       0.17   11.7   0.1    2.1  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.022   14.4   0.0      0.061   12.9   0.0    1.7  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.029   14.1   0.0      0.055   13.2   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.032   14.0   0.0      0.055   13.2   0.0    1.3  1  AAA_30           AAA domain
      0.034   14.3   0.2       0.86    9.7   0.1    2.5  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.036   13.0   0.0      0.067   12.2   0.0    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.036   14.0   0.0      0.064   13.2   0.0    1.7  1  ATPase_2         ATPase domain predominantly from Archaea
      0.043   13.7   0.1        2.8    7.8   0.1    2.6  2  DAHP_snth_FXD    DAHP synthase ferredoxin-like domain
      0.045   13.6   0.1        0.1   12.5   0.0    1.6  1  RsgA_GTPase      RsgA GTPase
      0.046   13.6   0.0      0.077   12.9   0.0    1.4  1  AAA_31           AAA domain
      0.046   12.9   0.5      0.075   12.2   0.0    1.6  2  NB-ARC           NB-ARC domain
      0.046   13.5   0.1      0.085   12.6   0.1    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.049   13.0   0.0      0.071   12.5   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.05   13.5   0.0        0.1   12.5   0.0    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.051   13.0   0.3       0.11   12.0   0.2    1.5  1  PhoH             PhoH-like protein
      0.076   12.2   0.1       0.16   11.1   0.1    1.5  1  ArsA_ATPase      Anion-transporting ATPase
      0.077   12.1   0.0       0.13   11.3   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.078   12.8   0.1       0.18   11.6   0.0    1.6  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.078   13.5   1.4       0.14   12.7   0.0    1.8  2  AAA_23           AAA domain
      0.098   12.7   0.0       0.21   11.6   0.0    1.6  1  AAA_14           AAA domain
        0.1   11.7   0.0       0.12   11.4   0.0    1.2  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   0.0     6e-64   2.2e-61       2     156 ..       2     153 ..       1     155 [. 0.98

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 6e-64
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEE CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivl 78 
                                       ++v+wltG sg+GK+t+a+al++kL+e+g ++++LdGd +R  L+ dLgfs+++R+++ r v+e+aklla++g+i++
  gi|488601414|ref|YP_007907885.1|   2 SFVIWLTGPSGAGKTTLAMALAEKLQEMGCQAEVLDGDGIRSRLYPDLGFSKQEREMHNRVVTEMAKLLAKNGVITI 78 
                                       79*************************************************************************** PP

                                       EE----SHHHHHHHHHHHHCHTEEEEEEEE--HHHHHHHTTTSHHHHHHTTSSSSHTTTSS-----SS-SEEEETTT CS
                        APS_kinase  79 vafisPyreeReaarelleealkfievfvdtplevceerDpkglYkkareGeikeftGidspYeaPenpelvvdtdk 155
                                       v++i+Pyr++Re ar+ +    +f+ev++++plev+ erDpkglY+ka +Ge+ke+tG+d +Ye+Pe+pel++dtd+
  gi|488601414|ref|YP_007907885.1|  79 VSVIAPYRAWREYARKEIG---SFVEVYLRCPLEVRIERDPKGLYAKALKGEVKELTGLDGEYEEPESPELILDTDR 152
                                       ******************9...5***************************************************987 PP

                                       S CS
                        APS_kinase 156 e 156
                                        
  gi|488601414|ref|YP_007907885.1| 153 M 153
                                       5 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   4.4e-13   1.6e-10       1     109 [.       5     114 ..       5     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.4e-13
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                       I+ltG++G+GKttla +L+++l ++     +v+  +g++    p+    + + ++++++++++++ +    l+++++
  gi|488601414|ref|YP_007907885.1|   5 IWLTGPSGAGKTTLAMALAEKLqEM-GCQAEVLDGDGIRSRLYPD--LGFSKQEREMHNRVVTEMAKL---LAKNGV 75 
                                       99*******************8444.5566788899999999999..888888888999999999998...568899 PP

                            AAA_18  77 lvidghlaeleseaakdikk......vvLtaspeelleR 109
                                       + i +++a ++ ++   +k       v+L+++ e+++eR
  gi|488601414|ref|YP_007907885.1|  76 ITIVSVIAPYRAWREYARKEigsfveVYLRCPLEVRIER 114
                                       988888888776655444447779**************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.1e-10   3.9e-08       1      74 [.       4      76 ..       4     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-10
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvi 74
                                      +++l G++G+GK+tla  l++kl+     a++l+ d +r+rl+++   sk++    ++  ++ + e+a+    a+++vi
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQemgcqAEVLDGDGIRSRLYPDLGFSKQE----REMHNRVVTEMAKLL--AKNGVI 76
                                      7999***************************************977766643....334455555555333..333333 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.8e-05     0.014       3      24 ..       7      28 ..       5      37 .. 0.86
   2 ?    2.0   0.0      0.41   1.5e+02      76     111 ..      66     101 ..      44     112 .. 0.79
   3 ?    6.0   0.0     0.024       8.7     189     210 ..     146     167 ..     140     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.8e-05
                                      EE-STTSSHHHHHHHHHHHHT- CS
                    Cytidylate_kin  3 iDGPagsGKssvaralaeklgl 24
                                      + GP+g+GK ++a alaekl+ 
  gi|488601414|ref|YP_007907885.1|  7 LTGPSGAGKTTLAMALAEKLQE 28
                                      78*****************985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.41
                                       -TTGGGSHHHHHHHHHHTTSHHHHHHHHHHHHTT-B CS
                    Cytidylate_kin  76 veeelrsdevekavSavaaipavRailvkklrelvk 111
                                       + + l ++ v ++vS +a ++a R++  k + ++v+
  gi|488601414|ref|YP_007907885.1|  66 MAKLLAKNGVITIVSVIAPYRAWREYARKEIGSFVE 101
                                       455688899999*************99999888776 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.024
                                       EEEETTTS-HHHHHHHHHHHHH CS
                    Cytidylate_kin 189 liidtskltieevvekilelik 210
                                       li+dt+++++ee ve++l++ik
  gi|488601414|ref|YP_007907885.1| 146 LILDTDRMSVEEEVEEVLKKIK 167
                                       79*****************997 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.5e-08   1.2e-05       4     141 ..       5     142 ..       1     177 [. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.5e-08
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSS.S--GGGHHHHHHHHHHHHHHHHTT.SEE.EE-S CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekds.ykdsakekalRsslrsavkrdLskekvV.IvDs 78 
                                       + ltG   +GK+t+a  La++l+e + +  v+d + ++ +  +    s++e+++ +++  ++++ L k+ v+ Iv  
  gi|488601414|ref|YP_007907885.1|   5 IWLTGPSGAGKTTLAMALAEKLQEMGCQAEVLDGDGIRSRLYPdLGFSKQEREMHNRVVTEMAKLLAKNGVItIVSV 81 
                                       45899999***************************99966665699*********************9976427777 PP

                                       ---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S..S-HHH..HHHHHHH---TT CS
                             KTI12  79 lnyikgfRYeLyciakaakttlcvvyvvapldvlvkwneereekeeyekel..ldaLiqRyeePd 141
                                       ++ ++ +R      a++    ++ vy+ +pl+v ++++ +   ++  + e+  l  L   yeeP+
  gi|488601414|ref|YP_007907885.1|  82 IAPYRAWRE----YARKEIGSFVEVYLRCPLEVRIERDPKGLYAKALKGEVkeLTGLDGEYEEPE 142
                                       777777663....5777777777777777777777777555555554444322445555666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.4e-07   0.00016      14     102 ..       5     176 ..       2     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.4e-07
                                       EEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkp..teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren......... 79 
                                       + ++G++GaGK+tL+++la++l+    + e+ ldg+ +++    +l   +g+ +qe ++ +++ v e          
  gi|488601414|ref|YP_007907885.1|   5 IWLTGPSGAGKTTLAMALAEKLQEmgCQAEV-LDGDGIRS----RLYPDLGFSKQEREMHNRV-VTEMakllakngv 75 
                                       6799*****************9974323333.44555555....4444444444444444444.3333344444455 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                          ABC_tran  80 ............................................................................. 79 
                                                                                                                    
  gi|488601414|ref|YP_007907885.1|  76 itivsviapyrawreyarkeigsfvevylrcplevrierdpkglyakalkgevkeltgldgeyeepespelildtdr 152
                                       55566667677766667777777777777777777777777777777777777777777777777777777777666 PP

                                       .HHHTCHHHHHHHSTTGGTTCBGE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .esdeeiekalsklglkelkdtvv 102
                                          +ee+e++l+k+++ +l d++ 
  gi|488601414|ref|YP_007907885.1| 153 mSVEEEVEEVLKKIKDLGLLDQIT 176
                                       655666777777777777666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   8.2e-07   0.00029       2      31 ..       4      33 ..       3      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.2e-07
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpq 31
                                      +++l+G++G GKTtL+  la++++e  +++
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQEMGCQA 33
                                      69**********************988876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.3e-06   0.00046       2      30 ..       5      33 ..       4      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-06
                                      EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      + +TGp+G GKtTl   ++e+l++ g++ 
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQEMGCQA 33
                                      789**********************9975 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.6e-06   0.00058       2      54 ..       6      68 ..       5      80 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.6e-06
                                      EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS.......STTHHHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel...gvefleisgsellsk.......yvgesekkirelfkeak 54
                                       l+Gp G GKT+la a+a++l   g +   ++g  ++s          +e+e++ r + + ak
  gi|488601414|ref|YP_007907885.1|  6 WLTGPSGAGKTTLAMALAEKLqemGCQAEVLDGDGIRSRlypdlgfSKQEREMHNRVVTEMAK 68
                                      599*****************7333466667777777766666675433333333344444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.5e-06    0.0012       1      25 [.       5      29 ..       5      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.5e-06
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      iwl+Gpsg GK+tla  La++l++ 
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQEM 29
                                      8*******************99865 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0021      0.75       2      30 ..       6      35 ..       5      50 .. 0.84
   2 !    8.4   0.1    0.0049       1.8      92     200 ..      67     167 ..      42     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                                      EEEESTTSSHHHHHHHHHCCST.CEEEE-H CS
                               dNK  2 vveGnIgaGKstlvklLskklg.vkvfeEp 30
                                       + G+ gaGK+tl+  L++kl+ + +  E+
  gi|488601414|ref|YP_007907885.1|  6 WLTGPSGAGKTTLAMALAEKLQeMGCQAEV 35
                                      578999************999766666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0049
                                       HHHHHHTTSS-HHH.HHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHH CS
                               dNK  92 akalaekgtlseee.lkiykelldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewl 167
                                       ak+la++g+++ +  ++ y ++++ + +e+    + +YL+++le+  er  k    +  k e + l  L  +yee  
  gi|488601414|ref|YP_007907885.1|  67 AKLLAKNGVITIVSvIAPYRAWREYARKEIG-SFVEVYLRCPLEVRIERDPKGLYAKALKGEVKELTGLDGEYEEP- 141
                                       688889999997762688************9.7789********99999655555555577788888888888864. PP

                                       TSGGCS-EEEEETSS.-TTTHCCHHHHHHHHHH CS
                               dNK 168 kklnevpvlvidveeldlvaeeekredvveevk 200
                                           e+p l++d ++   +  ee+ e+v++++k
  gi|488601414|ref|YP_007907885.1| 142 ----ESPELILDTDR---MSVEEEVEEVLKKIK 167
                                       ....67889999998...677777778888776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.2e-06    0.0008      18      76 ..       4      64 ..       3      76 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                        Zeta_toxin 18 lillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe.lhPeyeeilkadpkkaselt 76
                                      +i l G +GAGK++la +l+++l+ ++ ++ +ld+D +R+ l+P+     +++++++  +t
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQeMGCQAEVLDGDGIRSrLYPDLGFSKQEREMHNRVVT 64
                                      57899*******************88889999*******7256774443334444444444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   5.7e-06    0.0021       3      29 ..       9      36 ..       7      88 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.7e-06
                                      ESTTSSHHHHHHHHHHHHHHTTE..EEE CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik.vvl 29
                                      G  GaGKtt a++l+e+l+e+g +  vl
  gi|488601414|ref|YP_007907885.1|  9 GPSGAGKTTLAMALAEKLQEMGCQaEVL 36
                                      788*******************885554 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 !   19.2   0.0   2.8e-06   0.00099       5      69 ..       8     165 ..       4     182 .] 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.8e-06
                                       ESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                              CbiA   5 stkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                        + +G+GKTtla +La  l++ g +  ++D D  ++ l    g ++++++                           
  gi|488601414|ref|YP_007907885.1|   8 TGPSGAGKTTLAMALAEKLQEMGCQAEVLDGDGIRSRLYPDLGFSKQEREmhnrvvtemakllakngvitivsviap 84 
                                       5779*********************9999999887777665555555444566788888888888877777777777 PP

                                       ..................................................................CCHCCCHHHHH CS
                                       ..................................................................xxxxxxxxxxx RF
                              CbiA  55 ..................................................................dlkrllellea 65 
                                                                                                         d+ +++e +e+
  gi|488601414|ref|YP_007907885.1|  85 yrawreyarkeigsfvevylrcplevrierdpkglyakalkgevkeltgldgeyeepespelildtDRMSVEEEVEE 161
                                       77777777777777777777777777777777777777777777777777777777777777776655555666655 PP

                                       HCHC CS
                                       xxxx RF
                              CbiA  66 lgkk 69 
                                       + kk
  gi|488601414|ref|YP_007907885.1| 162 VLKK 165
                                       5555 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   1.1e-05    0.0039       4      61 ..       7      65 ..       4      83 .. 0.70
   2 ?   -0.3   0.0       2.8   9.9e+02      88     106 ..     147     165 ..     110     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-05
                                      EE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........----- CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvr 61
                                      L Gp+G gK++la+ la+ l +   +   l  d  ++ l   + ++++++++++ ++++
  gi|488601414|ref|YP_007907885.1|  7 LTGPSGAGKTTLAMALAEKLqEMGCQAEVLDGDGIRSRLYPDLGFSKQEREMHNRVVTE 65
                                      99******************755555556666666666666666666666666666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.8
                                       HHHSSEEE..-SSSEEE-- CS
                             AAA_5  88 lleerrllleeggelvkak 106
                                       +l+++r+++ee  e+v +k
  gi|488601414|ref|YP_007907885.1| 147 ILDTDRMSVEEEVEEVLKK 165
                                       7899999999999988776 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   3.6e-06    0.0013      27      55 ..       5      33 ..       3     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.6e-06
                            AAA_16 27 vllsGesGvGKsslvrellralekdggif 55
                                      + l+G+sG GK++l+ +l++ l++ g+ +
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQEMGCQA 33
                                      679*****************999885443 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.7e-06    0.0017      50      76 ..       5      31 ..       2      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.7e-06
                         IstB_IS21 50 ivllGpsGvGKshlaialgveavragl 76
                                      i l+GpsG+GK+ la+al+ +  + g 
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQEMGC 31
                                      679****************99887776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   5.7e-06    0.0021       8      33 ..       5      30 ..       4     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.7e-06
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeea 33
                                      + +tG+sG+GKTtl+  l+e+l+e  
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQEMG 30
                                      669******************98755 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   9.7e-06    0.0035       2      29 ..       5      34 ..       4      38 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.7e-06
                            AAA_28  2 ivitGgestGKTtlleaLaar..gypvvpE 29
                                      i +tG++++GKTtl+ aLa++  ++ + +E
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKlqEMGCQAE 34
                                      789****************87665555555 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 !   17.0   0.1   6.9e-06    0.0025     117     143 ..       5      31 ..       4      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.9e-06
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavplygc 143
                                       +w++Gp   Gkt la+a+a+ ++++gc
  gi|488601414|ref|YP_007907885.1|   5 IWLTGPSGAGKTTLAMALAEKLQEMGC 31 
                                       9*************************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 !   16.8   0.0   1.1e-05    0.0039       2      41 ..       3      42 ..       2      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                       vi l G+ GaGKTt +  La++l+++g ++ +   D  R
  gi|488601414|ref|YP_007907885.1|  3 FVIWLTGPSGAGKTTLAMALAEKLQEMGCQAEVLDGDGIR 42
                                      5899***********************9988888777776 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.6e-06    0.0035       1      55 [.       4      56 ..       4      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.6e-06
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkr 55
                                      vI ++g+SGaGktt+a +l + +++ + +a + +gd + +  r + dl   +++r
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQEMGCQAEVLDGDGIRS--RLYPDLGFSKQER 56
                                      7899********************9999988888876654..4555555555444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-05    0.0074       3      24 ..       3      24 ..       1      92 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakelgp 24
                                        i+++Gpsg+GKTtla  l +
  gi|488601414|ref|YP_007907885.1|  3 FVIWLTGPSGAGKTTLAMALAE 24
                                      579**************98844 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1     0.002      0.73       1      17 [.      11      27 ..      11      41 .. 0.91
   2 ?    5.6   0.0     0.045        16      46     157 ..      50     166 ..      44     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.002
                                      TTSSHHHHHHHHHHHHT CS
                               SKI  1 mGaGKstvGkllAkklg 17
                                      +GaGK+t++ +lA+kl+
  gi|488601414|ref|YP_007907885.1| 11 SGAGKTTLAMALAEKLQ 27
                                      59*************96 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHHHCCCS......SEEEEE-TTGGGSHHHHHHHH...HHSEEEEEE--HHHHHHHHHHTTSSGGGCS CS
                               SKI  46 gFrelEsevlkelleee......glViatGGGavlseenrellk...ekgiviyLdvsleellerlkadkeRPllqe 113
                                       gF ++E+e+ +++++e       + Vi     ++  ++ re+ +    + + +yL+++le+ +e   +d++   +++
  gi|488601414|ref|YP_007907885.1|  50 GFSKQEREMHNRVVTEMakllakNGVITIVSVIAPYRAWREYARkeiGSFVEVYLRCPLEVRIE---RDPKGLYAKA 123
                                       57777777766555555333344666666555666666777777666677789***99998666...5555333333 PP

                                       CHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHHHHH CS
                               SKI 114 kskeeelleelaereplyeeaadvvvdeseeskeevaeeileal 157
                                        + e ++l+ l   e    e+   + d+++ s ee +ee+l+++
  gi|488601414|ref|YP_007907885.1| 124 LKGEVKELTGLD-GEYEEPESPELILDTDRMSVEEEVEEVLKKI 166
                                       333333444444.2222333556777777777788888887776 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.3e-05    0.0081       9      43 ..       7      41 ..       2      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                              ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDiy 43
                                      l g  G GK+t+a+ lA +L+++g +  +lD D +
  gi|488601414|ref|YP_007907885.1|  7 LTGPSGAGKTTLAMALAEKLQEMGCQAEVLDGDGI 41
                                      56778**************************9944 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   7.3e-05     0.026      34      54 ..       3      23 ..       1      32 [. 0.89
   2 ?   -1.3   0.0       3.8   1.4e+03     113     139 ..     143     168 ..     115     173 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.3e-05
                            AAA_25 34 elallaGapgtGKttlaldla 54
                                       ++ l+G++g+GKttla+ la
  gi|488601414|ref|YP_007907885.1|  3 FVIWLTGPSGAGKTTLAMALA 23
                                      5788**************998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.8
                            AAA_25 113 slpLfakdrggtlltadvdaleaaiee 139
                                       s  L+ ++++++ ++++v+++ ++i++
  gi|488601414|ref|YP_007907885.1| 143 SPELILDTDRMS-VEEEVEEVLKKIKD 168
                                       334433333333.35555544444443 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.8e-05     0.021      21      44 ..       4      27 ..       1      35 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.8e-05
                                      EEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE 21 vilLeGdLGaGKTtlvrglakalg 44
                                      vi L+G+ GaGKTtl+ +la++l+
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQ 27
                                      699*****************9985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   7.2e-05     0.026       1      48 [.       8      60 ..       8     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.2e-05
                                      EE-TTSSHHHHHHHHHHHH.....TEEEEEHHHHHHHHHHTT.TSHSSHHHHCT CS
                            AAA_17  1 lGgPGsGKgtqceklveky.....gfthlsaGdllreeakrg.glakardemrk 48
                                      +G+ G+GK+t++  l+ek+     + ++l  Gd +r+   ++ g +k++ em++
  gi|488601414|ref|YP_007907885.1|  8 TGPSGAGKTTLAMALAEKLqemgcQAEVLD-GDGIRSRLYPDlGFSKQEREMHN 60
                                      69**************99876655566777.99999777665466666666643 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-05     0.034      53      76 ..       5      28 ..       2      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 53 vLlaGpsgtGktalaiaiskelge 76
                                      + l+Gpsg+Gkt la+a++++l e
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQE 28
                                      789****************99975 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00047      0.17       3      27 ..       4      28 ..       2     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00047
                                      EEEEEE-TTSSHHHHHHHHHHHSSS CS
                               CPT  3 iilLnGgsssGKsslaralqevlde 27
                                      +i L G s +GK++la al e l+e
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQE 28
                                      799****************998887 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 ?   12.9   0.0   0.00017     0.061       2      25 ..       4      27 ..       3      42 .. 0.75
   2 ?   -2.4   0.0       8.4     3e+03     106     121 ..      66      81 ..      57      96 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                                      EEEEEESTTCCHHHHHHHHHCT-- CS
                              cobW  2 vtvltGflGsGKTtLlnhllenra 25
                                      v+ ltG+ G+GKTtL  +l e+ +
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQ 27
                                      788************999984433 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.4
                                       HHHCCCECEEEEEEET CS
                              cobW 106 lksdltldavvavvDa 121
                                       +++ l  ++v+++v++
  gi|488601414|ref|YP_007907885.1|  66 MAKLLAKNGVITIVSV 81 
                                       4555667788888887 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00015     0.055      36      58 ..       5      27 ..       2      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00015
                            RuvB_N 36 vllyGpPGlGkttlakiiakelg 58
                                      + l+Gp G Gkttla+ +a++l+
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQ 27
                                      5699***************8765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00015     0.055      21      48 ..       5      32 ..       2      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00015
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggr 48
                                        ltGp G+GKtt+  al+e +++ g +
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQEMGCQ 32
                                      579***************9999987744 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0024      0.86       2      34 ..       5      37 ..       4      74 .. 0.71
   2 ?    3.2   0.0      0.23        84      80     130 ..      54     114 ..      34     168 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0024
                   Cytidylate_kin2  2 ITIsreyGsgGetigeaLAekLglpfydreiie 34
                                      I +++  G+g++t++ aLAekL+   +  e+++
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQEMGCQAEVLD 37
                                      6677889***************86555555554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.23
                   Cytidylate_kin2  80 elfeaqervirela...aeesvV..ivGRga......dliLkdrpnvlrvfltapledrvkr 130
                                       + +e++ rv++e+a   a+ ++V  iv   a      ++  k++   + v+l  ple+r++r
  gi|488601414|ref|YP_007907885.1|  54 QEREMHNRVVTEMAkllAK-NGVitIVSVIApyrawrEYARKEIGSFVEVYLRCPLEVRIER 114
                                       5556666666666533222.333123444441111112333445566778888888888865 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 ?   12.2   0.0   0.00019     0.067      31      63 ..       4      36 ..       1      43 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                      v+ ltG  GaGk tl  al+++l++ G +  vl
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQEMGCQAEVL 36
                                      789************************998887 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00018     0.064      21      49 ..       3      31 ..       1     171 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00018
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledkdk 49
                                       ++ ++Gp g GKt+L + ++e+l++ + 
  gi|488601414|ref|YP_007907885.1|  3 FVIWLTGPSGAGKTTLAMALAEKLQEMGC 31
                                      57899*******************98775 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.28     1e+02      17      33 ..      22      38 ..      15      40 .. 0.88
   2 ?    7.8   0.1    0.0079       2.8      10      29 ..     155     174 ..     150     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.28
                     DAHP_snth_FXD 17 vierieelGlkvhvskG 33
                                      + e+++e+G++++v  G
  gi|488601414|ref|YP_007907885.1| 22 LAEKLQEMGCQAEVLDG 38
                                      679**********9998 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0079
                     DAHP_snth_FXD  10 teeqieevierieelGlkvh 29 
                                        ee++eev+++i++lGl  +
  gi|488601414|ref|YP_007907885.1| 155 VEEEVEEVLKKIKDLGLLDQ 174
                                       69**************9655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00029       0.1     102     124 ..       5      27 ..       2      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00029
                                       EEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpele 124
                                       + l G+SG+GK+tL  al+++l+
  gi|488601414|ref|YP_007907885.1|   5 IWLTGPSGAGKTTLAMALAEKLQ 27 
                                       6799************9998754 PP

>> AAA_31  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     0.077      12      41 ..      12      41 ..       6      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00022
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQ 41
                                      G GKTT +++la+ l ++g +  + D D  
  gi|488601414|ref|YP_007907885.1| 12 GAGKTTLAMALAEKLQEMGCQAEVLDGDGI 41
                                      99******************9999999964 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   0.0   0.00021     0.075      20      48 ..       2      30 ..       1      36 [. 0.88
   2 ?   -2.8   0.1       7.7   2.8e+03      92     112 ..     155     175 ..     145     179 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                                      SEEEEEEESTTSSHHHHHHHHCCSHCCCC CS
                            NB-ARC 20 slvvalvGmgGvGKttlakqilnksdeve 48
                                      s+v+ l G  G GKttla    +k++e+ 
  gi|488601414|ref|YP_007907885.1|  2 SFVIWLTGPSGAGKTTLAMALAEKLQEMG 30
                                      58999**************9999988865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.7
                                       HHHHHHHHCCCTTEEEEEEEE CS
                            NB-ARC  92 lkrklvrlLltkrfllvlDDV 112
                                        ++++ ++L++ + l +lD +
  gi|488601414|ref|YP_007907885.1| 155 VEEEVEEVLKKIKDLGLLDQI 175
                                       344555555555555555555 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 ?   12.6   0.1   0.00024     0.085      26      39 ..       6      19 ..       2      26 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00024
                            AAA_29 26 lltGpsGsGKSTll 39
                                       ltGpsG+GK+Tl 
  gi|488601414|ref|YP_007907885.1|  6 WLTGPSGAGKTTLA 19
                                      69**********96 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0002     0.071      25      62 ..       5      43 ..       2      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllppls.eeealevakias 62
                                      + l+Gp+G+GKt la +l++ l ++  ++e+l+   i+s
  gi|488601414|ref|YP_007907885.1|  5 IWLTGPSGAGKTTLAMALAEKLQEMGcQAEVLDGDGIRS 43
                                      6799**************999998852567776666655 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 ?   12.5   0.0   0.00028       0.1       1      31 [.       4      34 ..       4      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvg 31
                                      v+ ++g sg+GKTtL   l ++l++ g++  
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQEMGCQAE 34
                                      57799*******************9998765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00029      0.11      21      43 ..       4      26 ..       2      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                                      EEEEE--TTSSTTHHHHHHHHHH CS
                              PhoH 21 ivfaiGpaGtGKtylavalavea 43
                                      ++  +Gp+G+GKt la+ala ++
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKL 26
                                      56789*************99765 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00044      0.16       3      35 ..       4      36 ..       2      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvlli 35
                                      vi ++G  G GKtt++ a+a kl e+g +  ++
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQEMGCQAEVL 36
                                      6889*********************99876665 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   0.0   0.00036      0.13     131     155 ..       4      28 ..       1      37 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                             T2SSE 131 lilvsGgTgsGKttllyallkeink 155
                                       +i ++G+ g GKttl+ al +++++
  gi|488601414|ref|YP_007907885.1|   4 VIWLTGPSGAGKTTLAMALAEKLQE 28 
                                       6889**************9998876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00049      0.18       2      30 ..       8      36 ..       7      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00049
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavv 30
                                      +Gp G+GKtt+  al+e l++ g + +v+
  gi|488601414|ref|YP_007907885.1|  8 TGPSGAGKTTLAMALAEKLQEMGCQAEVL 36
                                      7********************99988875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00039      0.14      24      39 ..       7      22 ..       4      26 .. 0.90
   2 ?   -0.2   0.3       3.3   1.2e+03     178     192 ..     152     166 ..      48     178 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00039
                            AAA_23 24 ItGpNGaGKTTildAi 39
                                      +tGp GaGKTT+  A+
  gi|488601414|ref|YP_007907885.1|  7 LTGPSGAGKTTLAMAL 22
                                      79**********9998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.3
                            AAA_23 178 ekekekeleeleeel 192
                                       + + e+e ee+ +++
  gi|488601414|ref|YP_007907885.1| 152 RMSVEEEVEEVLKKI 166
                                       222223333333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00059      0.21       4      27 ..       4      27 ..       2      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00059
                            AAA_14  4 ilvitGaRrvGKTtllkqlikell 27
                                      ++ +tG+  +GKTtl+  l+++l 
  gi|488601414|ref|YP_007907885.1|  4 VIWLTGPSGAGKTTLAMALAEKLQ 27
                                      689****************98876 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.12      47      71 ..      12      36 ..       9      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                      -HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK 47 GtGKTPlvialvkllqarglkvgvl 71
                                      G+GKT l++al+++lq+ g+++ vl
  gi|488601414|ref|YP_007907885.1| 12 GAGKTTLAMALAEKLQEMGCQAEVL 36
                                      9*******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); expected 358.6 (0.02)
Passed Vit filter:                       156  (0.00870099); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              50  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 1182.36
//
Query:       gi|488601415|ref|YP_007907886.1|  [L=453]
Description: hypothetical protein Asulf_01927 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  199.0   0.5    1.9e-58  198.8   0.5    1.0  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
     0.0076   15.7   0.0       0.22   10.9   0.0    2.7  3  Sulfatase     Sulfatase


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.8   0.5   2.1e-62   1.9e-58       1     357 []       4     404 ..       4     404 .. 0.93

  Alignments for each domain:
  == domain 1  score: 198.8 bits;  conditional E-value: 2.1e-62
                                       EEEEEETT-BTTHHHHHG.STSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEE CS
                      Phosphodiest   1 vlvislDGlradlldrla.ellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgey 76 
                                       v vi+lD+++++ll++ + ++lpn+++L++++++++ +++ +P++T+p+++ ++TG++Pge G +g  f++rk+++y
  gi|488601415|ref|YP_007907886.1|   4 VFVIGLDSAPPELLFHEFiNDLPNIRKLLENSIYGA-MKSCIPAITIPAWMVMATGKTPGEMGLYG--FRHRKGNSY 77 
                                       689*************9999****************.*****************************..99******9 PP

                                       EEEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC...........TBHHSBTCT....... CS
                      Phosphodiest  77 vvfvtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs..........etppryled....... 136
                                          +++++     +++  +wd +  + g+k+  +++p s++++ + ++lvs          +t p+ l+        
  gi|488601415|ref|YP_007907886.1|  78 SDIWIAHSL---MVKEKAVWDYLGEK-GYKSVLVGVPPSYPPKKINGWLVScfitpdssvsYTYPQNLKAevekvvg 150
                                       999999887...5999**********.******************************99998888888777777777 PP

                                       .CSTTSCHHHHHHHHHHHHHHHCHTHSHHHHHCT...SSESEEEEEECCCHHHHHHH-TT..SHH............ CS
                      Phosphodiest 137 dfnakvpledkvdkavlqtwldaafakvvlekel...ekpdlllvyleetDtvgHkfGpd..spe............ 196
                                       d+  +v ++++  ++v+++  ++ +++ +l ++l   ++++++ ++  ++D+++H f ++  +++            
  gi|488601415|ref|YP_007907886.1| 151 DYIFDVVFRKDERDEVKDKIWEMTEKRFELVRHLietKDWNYFEFVEIGLDRIHHAF-WKyfDENhhlhepdskyrn 226
                                       7777778888777668888888888887888788999********************.97788889999999***** PP

                                       .HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGH................... CS
                      Phosphodiest 197 .vedalrrvDkaigdLlealderglsaetniilvSDHGmadvsddkvielndlleekg................... 253
                                        ++d+++ +Dk ig++l++lde+     t++++vSDHG++ +  ++ + +n++l ++g                   
  gi|488601415|ref|YP_007907886.1| 227 vIPDYYKLLDKEIGKTLKLLDED-----TAVMIVSDHGIKRM--KGCFAVNQWLIDEGllkaeyeygnvkrleelkt 296
                                       ***********************.....**************..********************************* PP

                                       .GEEEEECBHHS.SSEEEEEESTEE.E.CCCTTHHHHHHHHHHTCHHCCHSTHTT..TEEEEEGGGS-GGGCHSTTS CS
                      Phosphodiest 254 .llhlkdegkggakaliainpkare.lnrvaeaeaeevyaelkakleelrkkege..alavylkeaipkrlhykkra 326
                                        +++++++++gg++a+i +n k+re  + ++  e+++ ++e++++++++  ++ge   ++v+++e+i   ++  +  
  gi|488601415|ref|YP_007907886.1| 297 sWSDTIAWAWGGYYARIFLNIKGREkNGVIRLSEYDRFRDEIADMVKSIKGPDGErwDTKVFYPEDIYPVAK--GDK 371
                                       *********************************************9999855999999*******6665666..9** PP

                                       -SEEE.EE-TTEEEESSTTCS.SBS-SEE--SS CS
                      Phosphodiest 327 pdlvl.vadpgwsitskdkpd.eyeikgthGyd 357
                                       pd ++  +d  w+++++ ++d  y ++++ G+d
  gi|488601415|ref|YP_007907886.1| 372 PDMMVyFDDLYWRSAGTVGHDsLYLPENDTGPD 404
                                       *****999999******9999988888888876 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.047   4.2e+02      48     100 ..      47     108 ..      17     111 .. 0.78
   2 !   10.9   0.0   2.5e-05      0.22     209     253 ..     223     262 ..     161     309 .. 0.79
   3 ?    0.4   0.0     0.039   3.5e+02     295     309 .]     429     443 ..     421     443 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.047
                                       SHHHHHHHHHHSS-HHHHTHSSCCSTTT.........HHCTTTS-HHHHHHHHTT-EEEEEE CS
                         Sulfatase  48 lcspsraalltgryphnsgvasntevgg.........gglpqteatLpellkeaGYntaaig 100
                                        + p+   + tg+ p ++g +      g          +l+ +e ++ ++l e+GY++ ++g
  gi|488601415|ref|YP_007907886.1|  47 ITIPAWMVMATGKTPGEMGLYGFRHRKGnsysdiwiaHSLMVKEKAVWDYLGEKGYKSVLVG 108
                                       566677777788888888877766555577888888899999***************99987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCC CS
                         Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasl 253
                                       +++++  +  +  D+ ig+ l+ L     +++t v+++SDhg   
  gi|488601415|ref|YP_007907886.1| 223 KYRNVIPDYYKLLDKEIGKTLKLL-----DEDTAVMIVSDHGIKR 262
                                       445555555566799*********.....*************876 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.039
                                       EGGGHHHHHHHHTTE CS
                         Sulfatase 295 shiDlfptildlagi 309
                                       s  D++pt+l+l+gi
  gi|488601415|ref|YP_007907886.1| 429 SIYDFAPTVLSLFGI 443
                                       678**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3071.18
//
Query:       gi|488601416|ref|YP_007907887.1|  [L=316]
Description: hypothetical protein Asulf_01928 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.0    0.00051   20.2   0.0    1.6  1  DHH       DHH family
  ------ inclusion threshold ------
      0.076   13.2   0.0       0.12   12.5   0.0    1.4  1  RFC1      Replication factor RFC1 C terminal domain
        0.1   13.0   0.2        0.4   11.1   0.1    2.0  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 !   20.2   0.0   8.5e-08   0.00051       7      80 ..       6     111 ..       2     123 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.5e-08
                                       ECSSSHHHHHH.HHHHHH................CECS--TCGGCGCCH............HCCCSEEEEEEE-S-- CS
                                       xxxxxxxxxxx.xxxxxx................xxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxx RF
                               DHH   7 hknpDtDsigS.aialan................llvDhneksqavege............akeeaedviiiDHHrl 54 
                                       +++ DtD+++S a+++++                + +D  +k+ ++++e            +++ + d + iDHH +
  gi|488601416|ref|YP_007907887.1|   6 IHHWDTDGVASaALVVKAldetsdfrnlvppigkFRLDERIKKYMANAEklfildlnlpdeVEALDRDAVFIDHHIQ 82 
                                       6799*******777777777777777777777774555555555555555555555555555678************ PP

                                       -S....S---SS--EEEE-SSS-HHHHHHH CS
                                       xx....xxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  55 ge....efetlapilflnepvgstaeivae 80 
                                       ++    ++++++p+ +  ++  st  +v e
  gi|488601416|ref|YP_007907887.1|  83 PKiknsRIRQINPV-LDGKTSPSTTFVVSE 111
                                       96655433333222.223444455555555 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.12      72     151 ..     100     179 ..      81     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                                       ------HHHHHTTTHHHHHH.HHS---------..HHHHHHTTT--SHHHHHHHHHH-X...XXXXXXXXXXXXXXX CS
                              RFC1  72 ktsaskselrldylpllkkk.lvkpLkeegkdg..veevielmdeysLtkedvdslvelslvkgekkkedplkkidt 145
                                       kts s++ +  +y +l +    +  + + g+++  ++ viel+++ ++t+++ +++vel     ++      +k++ 
  gi|488601416|ref|YP_007907887.1| 100 KTSPSTTFVVSEYYNLWNAWsALGAIGDVGRRAfeIQRVIELLKKEGITRNEAEKIVELIDS--NYI-VMDRNKVED 173
                                       66666666666666666554466666666655567************************655..222.222347788 PP

                                       XXXXXX CS
                              RFC1 146 kvKaaf 151
                                       +vK  +
  gi|488601416|ref|YP_007907887.1| 174 AVKVLL 179
                                       877655 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.66   3.9e+03      45      78 ..      79     111 ..      45     128 .. 0.53
   2 ?   11.1   0.1   6.6e-05       0.4      28     133 ..     196     305 ..     168     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.66
                                       EECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEE CS
                             DHHA1  45 aevgeewdagalgiaadklksklkk.pvivfvake 78 
                                       +++++++++  ++++   l    k  p+ +fv++e
  gi|488601416|ref|YP_007907887.1|  79 HHIQPKIKNSRIRQINPVLDG--KTsPSTTFVVSE 111
                                       444444444444444443333..333444444333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.6e-05
                                       HHHHHTCEEEC......TCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH...SS- CS
                             DHHA1  28 eellekaeevk......gvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdkvkvsarskkd...gvd 95 
                                        e++e++   +       v   +a  +   d +++  +a kl  +l+   +v+v  ++  k+ + +r+++d   +v+
  gi|488601416|ref|YP_007907887.1| 196 LEAIESEI--DnvlsnvVVEDGLALAEFSSDFNIISKVARKLVWELGYNGAVAVNRNFHGKAQLYFRVSPDmaeRVK 270
                                       33333322..123444544444444445778899************99666666666666***************** PP

                                       HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHH CS
                             DHHA1  96 agelakeaaaklgggGGGHdlAaGagipaekleealea 133
                                       + e+++       ++ GG++   G   + ++l+++le 
  gi|488601416|ref|YP_007907887.1| 271 MDEIISS---LKDFNAGGKKDVFGCVCERDRLNDVLEI 305
                                       ****999...4448889998888888888999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1982.41
//
Query:       gi|488601417|ref|YP_007907888.1|  [L=468]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   56.7   0.1    5.1e-15   55.8   0.1    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.011   15.6   0.0       0.04   13.8   0.0    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.14   12.6   0.1        5.5    7.6   0.0    2.8  2  PC_rep          Proteasome/cyclosome repeat
       0.16   11.4   0.0       0.24   10.8   0.0    1.2  1  EH_Signature    EH_Signature domain
       0.28   11.2   3.9         59    3.8   0.0    4.1  4  Sigma70_r1_2    Sigma-70 factor, region 1.2


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 !   55.8   0.1   1.4e-18   5.1e-15       3     116 ..     185     303 ..     183     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.4e-18
                        OrfB_IS605   3 pveveve.lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkkskn...ykkas 74 
                                       ++ ve+e +++p+++   +iD++ +n+a+ v e     ++++gr l s ++++ k+i +lqsk +  +    ++k  
  gi|488601417|ref|YP_007907888.1| 185 VYSVEQEqTQQPEKEMLMSIDFNTSNFAVIVIEGHPVsYIIDGRGLMSLLRKYLKKISRLQSKRDNLNEglpHHKLD 261
                                       566655548888888999***********999987667*************************999988******** PP

                        OrfB_IS605  75 rklarlhrkrsrrrkhllhklathliktlkevgvetLnvgnm 116
                                       +++a+l++++++ ++++ h +++ +++  k+  v  ++vgn 
  gi|488601417|ref|YP_007907888.1| 262 ERIAKLWKRVRNLLRDFSHRVSNLIVELAKKFRVTRIVVGNV 303
                                       ****************************************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 ?   -2.2   0.0       1.1     4e+03       4      29 ..     282     307 ..     280     308 .. 0.84
   2 ?   13.8   0.0   1.1e-05      0.04       5      69 .]     330     395 ..     326     395 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                    OrfB_Zn_ribbon   4 lkeqleykakeyGikveevnpayTSk 29 
                                       + + + + ak++ ++ ++v   ++Sk
  gi|488601417|ref|YP_007907888.1| 282 VSNLIVELAKKFRVTRIVVGNVHSSK 307
                                       56778889999999999999999998 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.1e-05
                    OrfB_Zn_ribbon   5 keqleykakeyGikveevnpay.TSktCseCgsknke.....alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                        + l+yk       ++ev+++y +  ++ ++ + ++e     ++ +r +  +     +++Dvn+a+Nilk+
  gi|488601417|ref|YP_007907888.1| 330 VKHLKYKFG----DIVEVSEEYtSGVDSVKHEYPSREyyeprKRVKRGLFKS-VIGIINADVNSARNILKK 395
                                       555555554....688999999455777788888888988874555555544.57779***********96 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.13   4.6e+02      14      28 ..     227     240 ..     226     244 .. 0.85
   2 ?    7.6   0.0    0.0015       5.5       6      28 ..     379     399 ..     379     400 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.13
                                       TCHHHHHHHHHHHHH CS
                            PC_rep  14 gneeaislLkpylsd 28 
                                       g++ ++slL++yl++
  gi|488601417|ref|YP_007907888.1| 227 GRG-LMSLLRKYLKK 240
                                       677.99*******86 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                                       HHHHCTTSTCHHHHHHHHHHHHH CS
                            PC_rep   6 LGlihaGsgneeaislLkpylsd 28 
                                       +G+i+a   n+ a+++Lk+yl++
  gi|488601417|ref|YP_007907888.1| 379 IGIINAD-VNS-ARNILKKYLYE 399
                                       7******.999.*********95 PP

>> EH_Signature  EH_Signature domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.7e-05      0.24      70     118 ..     229     302 ..     225     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.7e-05
                      EH_Signature  70 vlrsLlrsYfksfdplas..................rkrmrelrnllkrqskelsrsrqellesik.......e 118
                                        l+sLlr Y+k+ ++l+s                  +k+++ +rnll++ s + s   +el+++++       +
  gi|488601417|ref|YP_007907888.1| 229 GLMSLLRKYLKKISRLQSkrdnlneglphhklderiAKLWKRVRNLLRDFSHRVSNLIVELAKKFRvtrivvgN 302
                                       589***************************************************99999999999877666663 PP

>> Sigma70_r1_2  Sigma-70 factor, region 1.2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.016        59      14      24 ..      13      23 ..      11      26 .. 0.85
   2 ?    1.7   0.1     0.073   2.6e+02       3      12 ..     234     243 ..     232     244 .. 0.89
   3 ?   -1.4   0.0      0.69   2.5e+03      22      29 ..     287     294 ..     287     295 .. 0.88
   4 ?    3.5   0.1     0.021        74       2      13 ..     392     403 ..     391     404 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                                      X--THHHHHHH CS
                      Sigma70_r1_2 14 PLLtaeEEveL 24
                                      P Lt+e+E+ +
  gi|488601417|ref|YP_007907888.1| 13 PRLTREQEIVI 23
                                      88******976 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.073
                                       HHHHHHHHHH CS
                      Sigma70_r1_2   3 vrlYLrEIGr 12 
                                       +r YL+ I+r
  gi|488601417|ref|YP_007907888.1| 234 LRKYLKKISR 243
                                       89******98 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.69
                                       HHHHHHHH CS
                      Sigma70_r1_2  22 veLAkrie 29 
                                       veLAk+++
  gi|488601417|ref|YP_007907888.1| 287 VELAKKFR 294
                                       8****986 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHS CS
                      Sigma70_r1_2   2 pvrlYLrEIGri 13 
                                       +++ YL EIG++
  gi|488601417|ref|YP_007907888.1| 392 ILKKYLYEIGQT 403
                                       5899******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2991.12
//
Query:       gi|488601418|ref|YP_007907889.1|  [L=76]
Description: hypothetical protein Asulf_01930 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.011   15.7   1.7       0.18   11.8   0.0    2.8  3  RHH_1         Ribbon-helix-helix protein, copG family
       0.03   14.6   0.7       0.06   13.7   0.7    1.5  1  PG_binding_2  Putative peptidoglycan binding domain
      0.034   14.7   0.2       0.07   13.7   0.2    1.6  2  POTRA         Surface antigen variable number repeat
      0.043   13.5   0.1       0.13   12.0   0.0    1.7  2  CheR_N        CheR methyltransferase, all-alpha domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     4e-05      0.18       2      27 ..       9      35 ..       9      51 .. 0.91
   2 ?    0.6   0.4      0.13     6e+02       8      19 ..      42      53 ..      39      56 .. 0.55
   3 ?    1.0   0.3       0.1   4.5e+02       8      22 ..      59      73 ..      58      75 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSe 27
                                      +++++++ l++++  +++ +g  S+S+
  gi|488601418|ref|YP_007907889.1|  9 TTVSIPKPLYDKIKSRIEGTGfTSVSD 35
                                      69***********************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHH CS
                             RHH_1  8 eellerLdelar 19
                                      +e+l+ L+e  +
  gi|488601418|ref|YP_007907889.1| 42 REVLASLEEEDK 53
                                      556666666544 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.1
                                      HHHHHHHHHHHHHHT CS
                             RHH_1  8 eellerLdelarrrg 22
                                      ee+ e++ e+ r++g
  gi|488601418|ref|YP_007907889.1| 59 EEEEEKVKERLRALG 73
                                      677777777766665 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 ?   13.7   0.7   1.3e-05      0.06       6      30 ..      50      74 ..      44      76 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                      PG_binding_2  6 kpeeervlaedvaeevqaaLsrLGy 30
                                      ++ +e v  e+++e+v++ L++LGy
  gi|488601418|ref|YP_007907889.1| 50 EEDKEEVFSEEEEEKVKERLRALGY 74
                                      456777889999************* PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.16   6.9e+02      42      55 ..      20      33 ..       4      39 .. 0.80
   2 ?   13.7   0.2   1.6e-05      0.07      10      54 ..      29      76 .]      20      76 .] 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                                      HHHHHHHCTT-EE. CS
                             POTRA 42 alksryanlGyfda 55
                                      ++ksr++ +G+ ++
  gi|488601418|ref|YP_007907889.1| 20 KIKSRIEGTGFTSV 33
                                      67889999999875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.6e-05
                                      S....SSS-HHHHHTTT.SSSTT...SBHCHHHHHHHHHHHHHHHHCTT-EE CS
                             POTRA 10 G...nkktkdeelrrel.elkeg...dvynpekleadkealksryanlGyfd 54
                                      G    + + +++lr++l +l e    +v+++e+ e+ ke    r+++lGy+d
  gi|488601418|ref|YP_007907889.1| 29 GftsVSDYVTYVLREVLaSLEEEdkeEVFSEEEEEKVKE----RLRALGYLD 76
                                      243356777889999995354445559************....*******87 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     3e-05      0.13      29      50 ..      20      41 ..      17      43 .. 0.88
   2 ?   -1.5   0.0      0.47   2.1e+03      32      39 ..      67      74 ..      64      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                      HHHHHHHTTT-SSSHHHHHHTS CS
                            CheR_N 29 RlsrRmralglksfeeYldlLr 50
                                       + +R+  +g++s+++Y+ ++ 
  gi|488601418|ref|YP_007907889.1| 20 KIKSRIEGTGFTSVSDYVTYVL 41
                                      5899****************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                                      HHHHTTT- CS
                            CheR_N 32 rRmralgl 39
                                       R+ralg+
  gi|488601418|ref|YP_007907889.1| 67 ERLRALGY 74
                                      58888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1231  (0.0686597); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 506.68
//
Query:       gi|488601419|ref|YP_007907890.1|  [L=211]
Description: hypothetical protein Asulf_01931 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-12   45.9   0.0    6.8e-12   45.3   0.0    1.3  1  DSPc             Dual specificity phosphatase, catalytic doma
    4.1e-05   23.2   0.0    0.00012   21.7   0.0    1.7  1  Y_phosphatase2   Tyrosine phosphatase family
    0.00071   19.2   0.0    0.00098   18.8   0.0    1.2  1  Y_phosphatase    Protein-tyrosine phosphatase
     0.0022   18.1   0.0     0.0047   17.0   0.0    1.5  1  PTPlike_phytase  Inositol hexakisphosphate
     0.0042   16.1   0.5        0.2   10.6   0.1    2.0  2  Dsl1_N           Retrograde transport protein Dsl1 N terminal
      0.005   16.8   0.0     0.0063   16.5   0.0    1.3  1  Y_phosphatase3   Tyrosine phosphatase family
  ------ inclusion threshold ------
      0.063   13.4   0.0       0.62   10.2   0.0    2.1  2  DUF442           Putative phosphatase (DUF442)


Domain annotation for each model (and alignments):
>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   2.7e-15   6.8e-12      13     131 ..      27     139 ..      20     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.7e-15
                                       HHHHHTCSEEEEESSSSSECECCTTTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEESSSSSHHHH CS
                              DSPc  13 llsklgitlvinvtkevpnanalkkseieklripvedehetkiskyleeavefidkakqkgkkvlVHCqaGisRSat 89 
                                       +l+++g++ ++ +t e+p  + ++   +++ +ip+++      ++yl+++ve ++ + +  + v+VHCq G   +++
  gi|488601419|ref|YP_007907890.1|  27 QLKDMGFKGILTLT-EKPL-MYDEIRYFQYHHIPLKN----FKAPYLDQMVEAVEFIDNVDGPVAVHCQFGKGKTGC 97 
                                       67888899999888.5554.33356677777888777....34688999999999999999**************** PP

                                       HHHHHHHHHHTSCHHHHHHHHHHHSTT-SSTHHHHHHHHHHH CS
                              DSPc  90 liiaYlmktknlslneayeflkerrpaispnagfirqLleye 131
                                       +  aYl++++n+ ++e ++ lk   ++  +  ++++ L ++e
  gi|488601419|ref|YP_007907890.1|  98 ILGAYLIYKFNMCTDEVIRRLKAIFNSYIELSEQVEALKDFE 139
                                       *******************99988766666557777777666 PP

>> Y_phosphatase2  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.7e-08   0.00012       6     111 ..       5     101 ..       1     109 [. 0.81

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.7e-08
                                       T-EEEET.TEEEESS--HHHHHHHHHCT-SEEEE-SSS---HHHHHHHHHCT-EEEE-------GGG----HHHHHH CS
                    Y_phosphatase2   6 nFsaves.elyrssyprasnfsflksLkLktiislspeeesqdelqfleeekiklyhiaiesnkeelveiksdllkk 81 
                                       nF ++   +l   + p+ + +  lk +  k i+ l++++  +de  +++ ++i l +++++  ++         +++
  gi|488601419|ref|YP_007907890.1|   5 NFRVIIDgKLAGMGLPDREALIQLKDMGFKGILTLTEKPLMYDEIRYFQYHHIPLKNFKAPYLDQ---------MVE 72 
                                       5555444367777899999999999********************99777777777776665555.........999 PP

                                       HHHHHH-GGG-SEEEE-SSSSSHHHHHHHH CS
                    Y_phosphatase2  82 alklllnkenypvllhckrGkhrtglvigc 111
                                       a++++ n++  pv +hc+ Gk +tg++ g+
  gi|488601419|ref|YP_007907890.1|  73 AVEFIDNVD-GPVAVHCQFGKGKTGCILGA 101
                                       999986665.7****************986 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.8e-07   0.00098     136     195 ..      50     106 ..      36     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-07
                                       EEEEESSS-SSSSG.SCCHHHHHHHHHHHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHH CS
                     Y_phosphatase 136 kqlqytnWpdhgvp.esaksllklirkvekskeaksgpvvVhCsaGvgRtgtfvaldillq 195
                                       + +qy++ p ++ + +  +++++ ++ + +      gpv VhC  G g+tg+++ + ++++
  gi|488601419|ref|YP_007907890.1|  50 RYFQYHHIPLKNFKaPYLDQMVEAVEFIDNVD----GPVAVHCQFGKGKTGCILGAYLIYK 106
                                       55555555544444235777888888888888....****************998776654 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.8e-06    0.0047     100     149 ..      52      99 ..      37     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                                       -EEEEEEE-TTS---HHHHHHHHHHHHTS.-TT-EEEEE-SSSSHHHHHHH CS
                   PTPlike_phytase 100 lrYaRipitdekapeeedfdalvsilkea.pektalvfnCqmGrgRTTtam 149
                                       ++Y+ ip+++ kap    +d++v++++   + + ++ ++Cq G+g+T   +
  gi|488601419|ref|YP_007907890.1|  52 FQYHHIPLKNFKAPY---LDQMVEAVEFIdNVDGPVAVHCQFGKGKTGCIL 99 
                                       79***********95...6666666666633389*************7665 PP

>> Dsl1_N  Retrograde transport protein Dsl1 N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   7.7e-05       0.2     181     210 ..     109     138 ..     102     147 .. 0.90
   2 !    3.8   0.0    0.0091        23     194     232 ..     159     197 ..     155     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            Dsl1_N 181 dlqekvrnkLntilkdyiklnevveklKea 210
                                          ++v  +L+ i+++yi+l+e ve+lK++
  gi|488601419|ref|YP_007907890.1| 109 MCTDEVIRRLKAIFNSYIELSEQVEALKDF 138
                                       56799***********************86 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0091
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXX CS
                            Dsl1_N 194 lkdyiklnevveklKeaifsksvkieyeeekktlklslt 232
                                        +dy  ++e ++++K +++++++++ +++++ ++ ls +
  gi|488601419|ref|YP_007907890.1| 159 KRDYSMFEECIHHFKVCVYEDETEMILKTDSGEIVLSFK 197
                                       579***********************9999988877665 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.4e-06    0.0063     105     151 ..      65     114 ..      40     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.4e-06
                    Y_phosphatase3 105 sakkayrkvfealad.eepvlfHCtaGKDRTGvl..aalllsllGvdeed 151
                                        + +++ +++e + + ++pv +HC  GK  TG +  a+l++++  + +e+
  gi|488601419|ref|YP_007907890.1|  65 PYLDQMVEAVEFIDNvDGPVAVHCQFGKGKTGCIlgAYLIYKFNMCTDEV 114
                                       455778888888888555**************752266666665555555 PP

>> DUF442  Putative phosphatase (DUF442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.22   5.5e+02       8      33 ..      13      38 ..       7      43 .. 0.80
   2 ?   10.2   0.0   0.00024      0.62      59      96 ..      53      91 ..      48      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.22
                            DUF442  8 dlsvspqidlddiaelaeaGfksvin 33
                                      +l+  + +d + +++l++ Gfk++++
  gi|488601419|ref|YP_007907890.1| 13 KLAGMGLPDREALIQLKDMGFKGILT 38
                                      566667789999**********9975 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00024
                            DUF442 59 aylfvPvisge.iteddveafqralaeaegpvlayCrsG 96
                                      +y+++P+ + + +  d++ +  + +++++gpv ++C+ G
  gi|488601419|ref|YP_007907890.1| 53 QYHHIPLKNFKaPYLDQMVEAVEFIDNVDGPVAVHCQFG 91
                                      799***98644144566666667899**********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1155.05
//
Query:       gi|488601420|ref|YP_007907891.1|  [L=77]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-15   54.8   0.0    7.9e-15   54.7   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 !   54.7   0.0   4.4e-19   7.9e-15       6      72 ..       7      73 ..       2      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 4.4e-19
                                      HHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTST CS
                            DUF357  6 leealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgl 72
                                      l++  ek k   +e+ +     e++l+++++Y+ D+ yflekgdlv+A+ ++++a++wL+ g  +g 
  gi|488601420|ref|YP_007907891.1|  7 LRKETEKWKAKIEEKMKNVSGDEDFLRNIRAYILDSTYFLEKGDLVRAFECIVWAWAWLEIGEIVGK 73
                                      5556666664445666666666****************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      862  (0.0480785); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 508.81
//
Query:       gi|488601421|ref|YP_007907892.1|  [L=428]
Description: Nodulation efficiency protein NfeD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-15   57.3   0.8    1.5e-15   57.3   0.8    2.4  2  NfeD          NfeD-like C-terminal, partner-binding
      6e-08   32.8   0.4    1.1e-07   31.9   0.4    1.4  1  CLP_protease  Clp protease


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.35   3.2e+03      60      73 ..      42      55 ..      31      58 .. 0.74
   2 !   57.3   0.8   1.7e-19   1.5e-15       5      84 .]     348     426 ..     342     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.35
                                      -.SSB-TT-EEEEE CS
                              NfeD 60 segeiekgerVrVv 73
                                       +gei++g+ V V 
  gi|488601421|ref|YP_007907892.1| 42 IDGEINEGTVVYVE 55
                                      46778999988885 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 1.7e-19
                                       XXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-B.S-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SSSE CS
                              NfeD   5 vsvlllvllrplllkklkkkekktnaealiGkegvvledi.gtGrvkvdGeeWsarsegeiekgerVrVveveGltl 80 
                                       +++l++++l++l++ ++ kk  k + ealiGk+g+v+e   g+G +k+dGe+W+ +s++e+ +g++V V++++Gl l
  gi|488601421|ref|YP_007907892.1| 348 MGALVTFMLMKLVQLRKEKK--KVGGEALIGKRGKVMEFSdGSGLAKIDGEIWKIESDDELREGDEVIVTGRDGLIL 422
                                       45566666666655544332..378789**********77769********************************** PP

                                       EEEE CS
                              NfeD  81 iVep 84 
                                        V++
  gi|488601421|ref|YP_007907892.1| 423 SVKR 426
                                       **96 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.4   1.2e-11   1.1e-07      43     181 ..      63     196 ..      36     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.2e-11
                                       H-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE..E.EEETHHHHHHHTS-TTGEEEETTEEEEES-TEE CS
                      CLP_protease  43 edpdkdillyinspGGsvtaglaIydtmqyikpdvsticl..G.laaSmgslllaagekgkRfalpnarimihqPlg 116
                                       + + + +l++in+pGG v+++  I  ++ +   +v+t++   G   aS+gs++l++ge +  ++ + + +    P+ 
  gi|488601421|ref|YP_007907892.1|  63 NIQADAVLVVINTPGGLVSSTEKIVSMILTSDIPVITYVYpqGaFSASAGSFILLSGEVS--AMCNGTSVGAATPVT 137
                                       445568999******************************95542478*************..788999999999*99 PP

                                       EEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE-SS CS
                      CLP_protease 117 gaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLideviek 181
                                          g     + e + ++ i +  ++ +a++ g++++  ek ++    l+++eA + G id v ++
  gi|488601421|ref|YP_007907892.1| 138 VGFG-----KVENKTINYIASY-ARSIAEKRGRPADIAEKFVTESLSLTSREAYKKGVIDLVTDS 196
                                       9999.....5566777777765.556688899***99999********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2895.72
//
Query:       gi|488601422|ref|YP_007907893.1|  [L=125]
Description: hypothetical protein Asulf_01934 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 846.54
//
Query:       gi|488601423|ref|YP_007907894.1|  [L=68]
Description: hypothetical protein Asulf_01935 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   6.9    2.2e-12   46.5   6.9    1.9  2  DUF131           Protein of unknown function DUF131
  ------ inclusion threshold ------
       0.97    9.9   4.0        2.8    8.4   4.0    1.7  1  DUF202           Domain of unknown function (DUF202)
        6.9    6.6   6.5         12    5.8   0.8    2.2  2  LapA_dom         Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.7       0.2   1.2e+03      26      31 ..      11      16 ..       7      18 .. 0.86
   2 !   46.5   6.9   3.6e-16   2.2e-12      20      61 ..      24      65 ..      19      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                            DUF131 26 GVvliG 31
                                      G+++iG
  gi|488601423|ref|YP_007907894.1| 11 GLIMIG 16
                                      899999 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 3.6e-16
                            DUF131 20 srvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                      +   +GG++liGPIPI+FGs++++a +a+iL++ +++++++l
  gi|488601423|ref|YP_007907894.1| 24 THANVGGIILIGPIPIVFGSSPESASLALILGLFFFVMMFAL 65
                                      66789**********************************997 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.0   0.00048       2.8      15      53 ..       7      64 ..       2      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00048
                            DUF202 15 Rtslalialglallrffl...................tgepsalgkilglilivlgil 53
                                       ++ +li++gla+l +                     ++e ++l+ ilgl+++v+ ++
  gi|488601423|ref|YP_007907894.1|  7 IFGFGLIMIGLAMLSLSThanvggiiligpipivfgsSPESASLALILGLFFFVMMFA 64
                                      5677888999999987557778888888888888877777777889999998887655 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 ?    5.8   0.8     0.002        12      25      40 ..       6      21 ..       5      27 .. 0.87
   2 ?    4.2   0.5    0.0063        38       8      29 ..      39      60 ..      35      67 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.002
                          LapA_dom 25 vafgiGallgwllslw 40
                                      + fg+G+++++l++l+
  gi|488601423|ref|YP_007907894.1|  6 IIFGFGLIMIGLAMLS 21
                                      68************95 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0063
                          LapA_dom  8 vnflfaqvelpLsllllvafgi 29
                                      + f  +  +++L+l+l ++f++
  gi|488601423|ref|YP_007907894.1| 39 IVFGSSPESASLALILGLFFFV 60
                                      4444444578888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 518.69
//
Query:       gi|488601424|ref|YP_007907895.1|  [L=104]
Description: TIGR00304 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   58.4   0.0      4e-16   58.4   0.0    2.1  2  DUF131       Protein of unknown function DUF131
  ------ inclusion threshold ------
      0.046   12.5   3.7       0.22   10.2   3.7    1.8  1  DUF2207      Predicted membrane protein (DUF2207)
      0.094   13.0   0.6         17    5.8   0.7    2.1  2  DUF3040      Protein of unknown function (DUF3040)
       0.17   11.6   1.8       0.79    9.4   1.8    1.9  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   5.1       0.4   1.8e+03      43      58 ..       4      19 ..       2      23 .. 0.65
   2 !   58.4   0.0   8.9e-20     4e-16      13      61 ..      48      97 ..      30      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.4
                            DUF131 43 laktaiiLaIilmill 58
                                      ++ ++iiL+ il+i++
  gi|488601424|ref|YP_007907895.1|  4 IIAMLIILTGILLIFF 19
                                      5677788876666655 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 8.9e-20
                            DUF131 13 e..eaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                         ++++ +++vk +G+v+iGPIPIiFG d+r+a ++ iLaI +m+l+li 
  gi|488601424|ref|YP_007907895.1| 48 AkkMDTEPRREVKSAGIVMIGPIPIIFG-DSRMALYLAILAIFMMFLFLIT 97
                                      144789999*******************.66899999************96 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.7   4.9e-05      0.22     354     424 ..      28      98 ..       1     104 [] 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.9e-05
                           DUF2207 354 kkalkkwksavkk.....kergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliai 424
                                       ++++++w +++++     +  + +d++++++ k+ +++ +g i +++  + +al+     l +l+i++++l+li i
  gi|488601424|ref|YP_007907895.1|  28 YEEWRDWDEEMEEidyrkVDAKKMDTEPRREVKSAGIVMIGPIPIIFGDSRMALY-----LAILAIFMMFLFLITI 98 
                                       5678999999999999998899999999999999999999999888887776666.....4555555555555544 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.7    0.0037        17      45      63 ..       3      22 ..       1      26 [. 0.80
   2 ?    5.4   0.0    0.0049        22      36      82 ..      50      95 ..      37      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0037
                           DUF3040 45 avlavllfvaGllllvlG.v 63
                                      +++a+l++++G+ll+++G +
  gi|488601424|ref|YP_007907895.1|  3 GIIAMLIILTGILLIFFGlI 22
                                      5788999999********44 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0049
                           DUF3040 36 arrrslrrlavlavllfvaGllllvlGvaaaavvlgvvGfvvmlagv 82
                                      +   ++rr  v ++ ++++G + +++G +  a+ l+++ + +m++ +
  gi|488601424|ref|YP_007907895.1| 50 KMDTEPRR-EVKSAGIVMIGPIPIIFGDSRMALYLAILAIFMMFLFL 95
                                      34444555.7888888888999*****55555799999999998765 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.8   0.00018      0.79       5      29 ..       2      42 ..       1     104 [] 0.58

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00018
                                      XXXXXXXXXXXXXXXXXXXXXXXX................X CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx................x RF
                       Tetraspanin  5 lfffnllfwligivllavGvwlrl................k 29
                                      l ++++l++l+gi+l+++G+  r                 +
  gi|488601424|ref|YP_007907895.1|  2 LGIIAMLIILTGILLIFFGLISRPpdyeewrdwdeemeeiD 42
                                      7899***************7776688777777665543320 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); 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):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 654.44
//
Query:       gi|488601425|ref|YP_007907896.1|  [L=190]
Description: hypothetical protein Asulf_01937 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-14   52.6   0.3    6.8e-14   52.1   0.3    1.2  1  PK_C          Pyruvate kinase, alpha/beta domain
  ------ inclusion threshold ------
      0.029   13.8   0.0      0.062   12.7   0.0    1.7  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.13   12.2   2.9       0.72    9.9   0.5    2.6  2  RHH_1         Ribbon-helix-helix protein, copG family


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 !   52.1   0.3   1.1e-17   6.8e-14       1     117 []      17     166 ..      17     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.1e-17
                                       HHHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TS..SEEEEEES..............HHHH........... CS
                              PK_C   1 eaiakaaveaaeelgakaIvvltesGetArliskyrpk..vpiiavtp..............nelt........... 50 
                                       e++++ av++aeelg+++Ivv++++GetA+++ ++ ++  ++ ++vt+              +  t           
  gi|488601425|ref|YP_007907896.1|  17 ERTLELAVKRAEELGIRYIVVASSTGETALKLIELVEGknIKPVVVTYhrgfyregedsmdkS--Teerirekailv 91 
                                       67899*******************************997755567777699988888887550..255567777887 PP

                                       .........HHHHH.HCTTEEHHH.HHHHH...TTSHHHHHHHHHHH.......TTSS-STSEEEEEE-SSSS..SS CS
                              PK_C  51 .........arqla.lyrGvypvlvekaktaestdellreavkvake.......aglvkkgdevvvtaGtpkgesgt 110
                                                +r+++ +++G ++++++    ae + +l+ +++kv++e       +g ++  +ev++++G  +g    
  gi|488601425|ref|YP_007907896.1|  92 rqshilsglERSISrKLGGASRTEAI----AEALRSLFGHGLKVCVEitimaadSGAIPI-EEVIAVGGRARG---- 159
                                       77777888888888888888888854....455777777779****99988888888885.8***********.... PP

                                       --EEEEE CS
                              PK_C 111 tNtlrVv 117
                                       ++t+ V+
  gi|488601425|ref|YP_007907896.1| 160 ADTAVVI 166
                                       ***9997 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 ?   12.7   0.0     1e-05     0.062      69     111 ..      17      86 ..       6     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHHHTBSEEEEEBCC...........................GBCTTTSGHHHHHHHHHH CS
                      AP_endonuc_2  69 vdalkraielaaaLGapllvlhpGt...........................agagpkgseeeawerlae 111
                                        + l+ a+++a++LG++++v+ ++t                           +  g+++ ++++ er++e
  gi|488601425|ref|YP_007907896.1|  17 ERTLELAVKRAEELGIRYIVVASSTgetalklielvegknikpvvvtyhrgfYREGEDSMDKSTEERIRE 86 
                                       5678999***************999999999999999999999999999888445555555555555555 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.05     3e+02       5      19 ..      75      89 ..      75      94 .. 0.84
   2 ?    9.9   0.5   0.00012      0.72      19      35 ..     106     123 ..     102     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.05
                                      EEEHHHHHHHHHHHH CS
                             RHH_1  5 rldeellerLdelar 19
                                      ++d+++ er++e+a+
  gi|488601425|ref|YP_007907896.1| 75 SMDKSTEERIREKAI 89
                                      579999******996 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00012
                                       HHHT.SSHHHHHHHHHHH CS
                             RHH_1  19 rrrg.rSrSelIReAlre 35 
                                       r++g  Sr e+I eAlr 
  gi|488601425|ref|YP_007907896.1| 106 RKLGgASRTEAIAEALRS 123
                                       66777***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1219.43
//
Query:       gi|488601426|ref|YP_007907897.1|  [L=563]
Description: Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-110  370.3   0.0   1.2e-110  370.0   0.0    1.1  1  AMP-binding      AMP-binding enzyme
    3.1e-22   79.4   1.8    7.2e-22   78.2   1.8    1.7  1  AMP-binding_C    AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.041   13.7   0.0    1.7  1  POTRA_2          POTRA domain, ShlB-type
      0.044   14.1   0.1      0.096   13.0   0.1    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 !  370.0   0.0  2.7e-114  1.2e-110       2     421 ..      45     463 ..      44     465 .. 0.87

  Alignments for each domain:
  == domain 1  score: 370.0 bits;  conditional E-value: 2.7e-114
                                       HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       e +a k+p+ val +   g+ + Yreld+ +nr+A++L + G++k +rV + +pn+p++v+++++ilkaG +vv +n
  gi|488601426|ref|YP_007907897.1|  45 ENSASKYPENVALDF--IGKAIKYRELDDIANRVASFLYENGYEK-SRVILGCPNTPHYVATYYGILKAGSIVVQCN 118
                                       7899*********88..**********************989998.57***************************** PP

                                       TTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT.S...... CS
                       AMP-binding  79 ptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseeka.e...... 148
                                       p +t++el++i e+se+k+++ +  +   ++l++  ++   v++vi+  +d l++  ++  + ++++++ +      
  gi|488601426|ref|YP_007907897.1| 119 PMYTERELRHIAENSESKIMF-AF-EPMFPRLKALLDEGLLVDVVICKIEDYLKFPLNFLYSLKKQKVSiDrkvmyw 193
                                       *********************.22.2225556666655555555555444444444333333334433331566778 PP

                                       ........-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHH CS
                       AMP-binding 149 ........kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifgl 217
                                               ++++++ + ++d+a+++YT+GTTG PK+Vml+h nlvan+++l +e   +++e+dv++  lp++h++g+
  gi|488601426|ref|YP_007907897.1| 194 kdvmkyppTDKRVNVNPKEDVAVFQYTGGTTGLPKAVMLTHFNLVANIYQL-MEWLPEVNENDVIMGALPYFHSYGM 269
                                       889999984445556778********************************8.554578999**************** PP

                                       HHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS- CS
                       AMP-binding 218 ilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggep 294
                                       +++++l++++Ga++vl+p    +d k++le i+k++vt+ +gvP++++a+ + ++ +    ++dlss+r +++g++p
  gi|488601426|ref|YP_007907897.1| 270 TTSMNLPIAVGAKIVLIPDP--RDLKRVLESIQKHRVTLYCGVPTMYNAINNYPEVN----KYDLSSIRACVSGAAP 340
                                       *****************944..5677999*********************9998777....67************** PP

                                       EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEE CS
                       AMP-binding 295 lspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrg 371
                                       l+ e+ r+f++l+g++++egYGl+Et++v++ +++ +  +k gs+G p+p++ + +vD e g+ +p ge+Gel ++g
  gi|488601426|ref|YP_007907897.1| 341 LPLEVKRKFEELTGGKLVEGYGLSETSPVTH-ANPINGVNKEGSIGLPIPDTIAVVVDSE-GNILPIGETGELAIKG 415
                                       ******************************8.777888899*****************99.**************** PP

                                       TTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                       AMP-binding 372 pgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlik 421
                                       p+vmkgY+k +e+t+ +++ + +wl TGD++++dedGy++iv+Rkkd+i+
  gi|488601426|ref|YP_007907897.1| 416 PQVMKGYYKMEEETKNTLI-N-GWLLTGDIAKIDEDGYFYIVDRKKDMII 463
                                       *******************.5.7**************************8 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   1.8   1.6e-25   7.2e-22       1      76 []     473     548 ..     473     548 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 1.6e-25
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                       evE++l +hp++ eaaV+Gvpd+++Ge+++afVvl++g + ++e++++++r++l++y+vp+ ++f +elpk   GK
  gi|488601426|ref|YP_007907897.1| 473 EVEEVLYEHPDIVEAAVIGVPDPKRGETVKAFVVLREGANVTAEDIEKFCRQHLAAYKVPRIIEFKKELPKSNVGK 548
                                       8**********************************98865589*****************************9998 PP

>> POTRA_2  POTRA domain, ShlB-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.2e-06     0.041      21      59 ..      54      92 ..      45      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.2e-06
                                      HHHCCCSSSEEEHHHHHHHHHHHHHHHHHTT-TT-EEEE CS
                           POTRA_2 21 allqpylgkclgladlnqlakeltnayiekGYvtsrvll 59
                                      +++ +++gk ++  +l  +a+++  +++e+GY  srv l
  gi|488601426|ref|YP_007907897.1| 54 NVALDFIGKAIKYRELDDIANRVASFLYENGYEKSRVIL 92
                                      5666899******************************98 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.1e-05     0.096       1      55 [.     466     520 ..     466     556 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHH CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelea 55 
                                       G n++P ++eevl e +++ +   i v ++++ ++++  v ++eg++ + ++ e+
  gi|488601426|ref|YP_007907897.1| 466 GYNIYPREVEEVLYEHPDIVEAAVIGVPDPKRGETVKAFVVLREGANVTAEDIEK 520
                                       89**************************999999999999999987655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3539.59
//
Query:       gi|488601427|ref|YP_007907898.1|  [L=624]
Description: DNA gyrase subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-56  190.5   0.8    2.6e-56  189.9   0.8    1.4  1  DNA_gyraseB    DNA gyrase B
    1.8e-30  104.9   0.2    4.6e-30  103.6   0.2    1.6  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    4.3e-23   82.0   0.0    1.1e-22   80.7   0.0    1.7  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    4.6e-19   68.6   0.0    1.3e-18   67.1   0.0    1.8  1  Toprim         Toprim domain
    1.7e-05   24.7   0.0    4.2e-05   23.4   0.0    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.9   0.8   7.1e-60   2.6e-56       1     173 [.     219     384 ..     219     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 189.9 bits;  conditional E-value: 7.1e-60
                       DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktln 77 
                                       G+++++  +nk+k+++++ v+++e+ek  e+ i++e+a+q+t+++ enil F+Nni+t eGGtHv gf+s+lt+++n
  gi|488601427|ref|YP_007907898.1| 219 GISEYIAIINKNKHPIHD-VIYFETEK--EN-IQIEIAIQFTNTDFENILAFANNIHTIEGGTHVIGFRSGLTRAIN 291
                                       9***********888887.********..88.********************************************* PP

                       DNA_gyraseB  78 eyakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakki 154
                                       ey k  +++kk +  +sg+direglta++svki epqFeGQTK+kL+nsevk++ve++v+ e+ ++lee+++ a++i
  gi|488601427|ref|YP_007907898.1| 292 EYGK--RFVKKYQ-PLSGQDIREGLTAIISVKILEPQFEGQTKTKLTNSEVKTAVESAVYSEMLRWLEEHPNSANAI 365
                                       ***9..6888987.*************************************************************** PP

                       DNA_gyraseB 155 lekaveaakareaarkare 173
                                       +ek++ a kar+aa++are
  gi|488601427|ref|YP_007907898.1| 366 IEKCLLALKARQAAKRARE 384
                                       *****************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 !  103.6   0.2   1.3e-33   4.6e-30       3      62 ..     553     612 ..     552     613 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.3e-33
                     DNA_gyraseB_C   3 kveiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefi 62 
                                       ++e+qR+KGLGEmnpeqLweTTm+p+tR Llqvtie+a +a+elfs+LmG++ve+Rr+fi
  gi|488601427|ref|YP_007907898.1| 553 NAEVQRYKGLGEMNPEQLWETTMNPKTRILLQVTIEEALQAEELFSILMGEDVEARRQFI 612
                                       679********************************************************9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.0     3e-26   1.1e-22       4     111 ..      34     173 ..      32     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 3e-26
                                       HHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT.............GTCSTTCHHC CS
                         HATPase_c   4 krLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk.............klfekfsqdd 65 
                                       ++L+++++++vdN++++  a+++++i+v+++    d + sveD+G+Gip e +              + ++kf++ +
  gi|488601427|ref|YP_007907898.1|  34 RGLHHLLWEIVDNSIDEalAGYCKNIKVTLH--T-DGSASVEDDGRGIPTERHSsgktalelvltklHAGGKFDK-K 106
                                       78***************7667**********..5.9*****************************555555****.* PP

                                       STCHTSTSSSHHHHHHHHHHHHTTTEEEE.......................EEETTTEEEEEEEEESS CS
                         HATPase_c  66 stkrggggtGlGlsivkklvelmgGeiwv.......................esepgrGttftftlple 111
                                       ++k++gg +G+Gls+v++l+e ++  +wv                        +++  Gtt++f++++e
  gi|488601427|ref|YP_007907898.1| 107 AYKVSGGLHGVGLSVVNALSEWLE--VWVkrngrifyqryrrgvpegdveviGETDSSGTTIRFKPDEE 173
                                       *********************644..44444555555666655555555556333356********987 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   3.6e-22   1.3e-18       1     102 [.     412     523 ..     412     524 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3.6e-22
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEE CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiila 69 
                                       el+ivEg+s+ +++++a++++fqa+++++G+il++e+  ++++++  ei+ + ++++a     ++  + r+++ii++
  gi|488601427|ref|YP_007907898.1| 412 ELYIVEGESAGGSAKQARDRTFQAILPLRGKILNVEKaGLSKALKneEIRAIASAIGAgigsdFDITKARYKRIIIM 488
                                       69***********************************8677777678888888888889999*************** PP

                                       CSSSHHHHHHHHHHHHHHT....HHHTTTEEEEEESS CS
                            Toprim  70 tDpDreGeaiawellevlk....ellenkigrvefse 102
                                       tD+D++G++i+++ll++++    +l+en  g++++++
  gi|488601427|ref|YP_007907898.1| 489 TDADVDGSHIRTLLLTFFYrhmrPLIEN--GYLYIAQ 523
                                       *******************988888888..8888775 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.2e-08   4.2e-05       7      50 ..      40      83 ..      35     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.2e-08
                       HATPase_c_3  7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGmseeel 50
                                      l e+vdNs+d    + ++n+k++++++    g+ ++eDdG G++ e  
  gi|488601427|ref|YP_007907898.1| 40 LWEIVDNSIDealaGYCKNIKVTLHTD----GSASVEDDGRGIPTERH 83
                                      78********988677899*******7....69**********98854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.31s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3858.94
//
Query:       gi|488601428|ref|YP_007907899.1|  [L=777]
Description: DNA gyrase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-166  554.2   0.7   4.8e-166  552.9   1.2    1.4  2  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    2.3e-61  203.0   7.9    1.5e-13   50.0   0.1    6.7  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  552.9   1.2  5.4e-170  4.8e-166       1     426 []      26     460 ..      26     460 .. 0.99
   2 ?   -3.7   0.0      0.47   4.2e+03     164     196 ..     575     605 ..     571     624 .. 0.68

  Alignments for each domain:
  == domain 1  score: 552.9 bits;  conditional E-value: 5.4e-170
                     DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGn 76 
                                       RaiP+vrDGlKPvqRriLyam+++ l+++++++K+a++vG+vlgkYhPHGd+++yda+vr+aqdf++++pl+d+qGn
  gi|488601428|ref|YP_007907899.1|  26 RAIPDVRDGLKPVQRRILYAMYEMnLTSNRPHRKSARIVGDVLGKYHPHGDSAVYDALVRMAQDFSMRYPLIDGQGN 102
                                       9**************************************************************************** PP

                     DNA_topoisoIV  77 fGsildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipp 153
                                       fGsi dgd +Aa+RY+e+rL+kia+ell++idk+tvd+++n+D + +EP  lp++iPnlL+nG++GIavGmat++pp
  gi|488601428|ref|YP_007907899.1| 103 FGSI-DGDVPAAMRYTEARLTKIAEELLEDIDKDTVDFVPNFDSTLEEPSALPAKIPNLLINGSSGIAVGMATNMPP 178
                                       ****.************************************************************************ PP

                     DNA_topoisoIV 154 hnlkeiidaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveieektivitElPig 227
                                       hn++ei++a+ia+++++ +   +l+++v+gPdfptgg+i+gk++ik+ yetg+Gk+ vr++ve+e+++i+i+E+P++
  gi|488601428|ref|YP_007907899.1| 179 HNISEICRAIIAYIENPLIsikDLMKIVKGPDFPTGGIIVGKDGIKDVYETGKGKLIVRGRVEFEGNAIIIKEIPYQ 255
                                       *****************8899******************************************999*********** PP

                     DNA_topoisoIV 228 vntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkkpky 302
                                       vn++kl+eki+elv+++k++ ++ +rdesdr g+r+viel+rg + ++v++kly++t+L++++ v nl++++++pk+
  gi|488601428|ref|YP_007907899.1| 256 VNKAKLVEKIAELVRDGKLEeVKFVRDESDReGIRVVIELRRG-DFDTVVNKLYAYTQLQTTFGVINLAIVNGTPKI 331
                                       ****************************9999*********98.77788888************************* PP

                     DNA_topoisoIV 303 lslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeqa 377
                                       l+lke+++ef+++r++v+ rr++yll+k+eer++ilegl++al +idevi++i++s++ ++akk+L+e+  lse qa
  gi|488601428|ref|YP_007907899.1| 332 LNLKELISEFVNHRRNVIYRRTQYLLKKAEERYHILEGLMIALRNIDEVISIIKSSESPDTAKKSLMERfeLSEVQA 408
                                       *********************************************************************99****** PP

                     DNA_topoisoIV 378 eyllemrlrrLtkeeveklekeieelekeikelekllak...lkklikeeld 426
                                       +++l+mrl+rLt++e+e l++e++el+++ik++++++++   + ++i++el+
  gi|488601428|ref|YP_007907899.1| 409 NSILQMRLQRLTALEMETLTREYSELKDKIKDFKDIISSerrIDDIIIKELK 460
                                       **************************************99999999999985 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.47
                     DNA_topoisoIV 164 iallkgeeaellelvlgPdfptgggiigkeeik 196
                                       i+l +ge+  ++++v  Pdf +  +i+++++  
  gi|488601428|ref|YP_007907899.1| 575 ISLSEGEK--VVSVVSVPDFDGEVVILTEDGYI 605
                                       55555664..48889999999998888666633 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 !   41.2   0.4   9.4e-15   8.4e-11       1      39 [.     491     529 ..     491     530 .. 0.97
   2 !   27.6   0.0   1.6e-10   1.4e-06      11      48 .]     550     590 ..     541     590 .. 0.90
   3 !   25.3   0.0   8.4e-10   7.5e-06       2      31 ..     595     622 ..     594     630 .. 0.94
   4 !   29.0   0.1   5.8e-11   5.2e-07       1      44 [.     634     677 ..     634     681 .. 0.94
   5 !   50.0   0.1   1.7e-17   1.5e-13       2      47 ..     685     731 ..     684     732 .. 0.95
   6 !   28.3   0.0   9.7e-11   8.7e-07       1      32 [.     735     766 ..     735     769 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 9.4e-15
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTS CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegd 39 
                                       d++++iTs Gyvkr+++++++ q+Rg+ Gv+g+ l+ +d
  gi|488601428|ref|YP_007907899.1| 491 DNIIVITSEGYVKRMDIETFRTQRRGGVGVIGVSLRQND 529
                                       89**********************************998 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 1.6e-10
                                       EEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEEEES CS
                     DNA_gyraseA_C  11 yvkrfplselpeqgRgakGvkgi...klkegdklvsvlvvs 48 
                                       ++++++++e+p q R++kG+++     l+eg+k+vsv+ v+
  gi|488601428|ref|YP_007907899.1| 550 KAYWINAYEIPKQDRNGKGIHLKnfiSLSEGEKVVSVVSVP 590
                                       89***********************************9885 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 8.4e-10
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvk 31 
                                       e+++ T+ Gy+kr++lse+ + +Rg  Gv 
  gi|488601428|ref|YP_007907899.1| 595 EVVILTEDGYIKRTKLSEFENAKRG--GVS 622
                                       79***********************..885 PP

  == domain 4  score: 29.0 bits;  conditional E-value: 5.8e-11
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsv 44 
                                       d++l+ T+ G   ++p+s +p+ +R+akGv++i++ +gd++ ++
  gi|488601428|ref|YP_007907899.1| 634 DIILISTKMGLTAKIPVSNVPRYSRTAKGVRAINMQKGDSIAGL 677
                                       7899999999*******************************987 PP

  == domain 5  score: 50.0 bits;  conditional E-value: 1.7e-17
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvlvv 47 
                                       +ll+ T++G++kr+p++e++ ++RgakGv+ i+++ + +++v ++ v
  gi|488601428|ref|YP_007907899.1| 685 YLLTLTEKGFGKRTPVEEYRLTRRGAKGVRNIRITSKnGHVVFAEFV 731
                                       8*****************************************99866 PP

  == domain 6  score: 28.3 bits;  conditional E-value: 9.7e-11
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEG CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkg 32 
                                       +ell++++ Gy+++++++e+p+ +R++ Gv +
  gi|488601428|ref|YP_007907899.1| 735 EELLTMSEDGYAIKISVDEIPVYSRNSAGVSV 766
                                       58****************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (777 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 4915.01
//
Query:       gi|488601429|ref|YP_007907900.1|  [L=271]
Description: Zn-dependent hydrolase, including glyoxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-11   42.3   1.7    1.5e-10   41.4   1.7    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.026   14.4   0.0    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 !   41.4   1.7   1.7e-14   1.5e-10       6     162 ..      21     163 ..      18     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.7e-14
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       +n+++i  d ++ LiDtG + e  ++            ++d v+++H+H DHi +++ ++ + +v+    ++++ + 
  gi|488601429|ref|YP_007907900.1|  21 CNCVYI-KDRKTCLIDTGAGDEVIKL------------KPDFVLNSHWHEDHITNNHLFRAKIGVHELDAEAVESYE 84 
                                       8*****.8*****************7............7********************999888765333333333 PP

                                       HCHHHHHHHHHCCHH..TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHC CS
                       Lactamase_B  83 fmeeaddaasrkgll..lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallaget 157
                                       +   +++ + +       + + + k+d++  ++d+  +g+ +++v+++pgh++gh ++ + +g +++ GD  l+   
  gi|488601429|ref|YP_007907900.1|  85 EFKKRYGLSDKL--VkiFINFEFTKVDFTFRVGDVLNFGDTEVEVIHTPGHSAGHCCFLI-DGEMIYLGDIDLTSFG 158
                                       333333333333..2347788888888888888888888888888888888888888766.6789999999998888 PP

                                       CCCCC CS
                       Lactamase_B 158 gridl 162
                                       ++ ++
  gi|488601429|ref|YP_007907900.1| 159 PWYGC 163
                                       88777 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 ?   14.4   0.0   2.9e-06     0.026      17     101 ..      30     142 ..      19     157 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-06
                     Lactamase_B_3  17 arilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql...............................aenv 62 
                                       ++ l+D +    g e  + ++D vl s+ +edH + + l ++                               +   
  gi|488601429|ref|YP_007907900.1|  30 KTCLIDTGA---GDEVIKLKPDFVLNSHWHEDHITNNHLFRAkigvheldaeavesyeefkkryglsdklvkiF--- 100
                                       566777554...889999*********************99855555444444444444444444443333332... PP

                     Lactamase_B_3  63 kvlee.............geslevggleiravatshdavggsergenngfll 101
                                                         g+ l++g++e++ ++t      g+  g  ++fl+
  gi|488601429|ref|YP_007907900.1| 101 ----InfeftkvdftfrvGDVLNFGDTEVEVIHTP-----GHSAG-HCCFLI 142
                                       ....0333333333333334444444444444443.....33333.355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1583.23
//
Query:       gi|488601430|ref|YP_007907901.1|  [L=295]
Description: hypothetical protein Asulf_01942 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-09   38.3   0.0      2e-09   37.5   0.0    1.4  1  Peptidase_M23    Peptidase family M23
     0.0023   18.1   3.0     0.0054   16.9   3.0    1.6  1  Dockerin_1       Dockerin type I domain
     0.0068   15.9   0.8        1.3    8.7   0.0    2.6  2  EF-hand_1        EF hand
  ------ inclusion threshold ------
      0.012   15.5   0.3        4.1    7.6   0.0    2.5  2  EF-hand_6        EF-hand domain
       0.13   12.7   0.1          4    8.0   0.0    2.3  2  EF-hand_7        EF-hand domain pair
        0.2   11.5   0.4       0.44   10.4   0.4    1.5  1  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   6.7e-13     2e-09       5      74 ..      72     151 ..      68     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 6.7e-13
                                       SEEEEETTT-EEEESSSEEE.EEEEEET.......TTEEEEEEEECTCEEEEEEEESEES..S-TTEEE-TTCEEEE CS
                     Peptidase_M23   5 GidiaapkgtpVlAaadGtV.vfagkke.......gyGnvviidhgdgystlyahlskis..vkegqkVkaGqvIGt 71 
                                       +i +a    +p++A+++GtV +f  ++        g G  ++i+ g++y   y h+ ++   ++eg+ Vk+G+vIG+
  gi|488601430|ref|YP_007907901.1|  72 AIFFANRSRDPIYAPCNGTVtYFLPWEYfenasepGKGGEIWIRYGENYAVAYRHIVTVGlnLSEGDIVKQGDVIGY 148
                                       5778888899**********63333322345666688******************999664588************* PP

                                       EBS CS
                     Peptidase_M23  72 vgs 74 
                                       v +
  gi|488601430|ref|YP_007907901.1| 149 VAD 151
                                       986 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.0   1.8e-06    0.0054       1      52 [.     238     284 ..     238     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                                       TTETTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHH CS
                        Dockerin_1   1 agDVNgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDall 52 
                                       +gD N++gkV+  Da+ +   +      ++ ++   aD N++Gr++  D++ 
  gi|488601430|ref|YP_007907901.1| 238 KGDFNDNGKVDFEDAMHVAGMVM-----KKVKPDLSADFNNNGRIDVGDLAK 284
                                       59*********************.....999***************999876 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.2     0.006        18      10      23 ..     240     253 ..     238     258 .. 0.85
   2 !    8.7   0.0   0.00045       1.3       9      27 ..     269     287 ..     268     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.006
                                       TTTSSSEEEHHHHH CS
                         EF-hand_1  10 DkDgdGkIdfeEfk 23 
                                       D + +Gk+dfe+ +
  gi|488601430|ref|YP_007907901.1| 240 DFNDNGKVDFEDAM 253
                                       899********865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00045
                                       HTTTSSSEEEHHHHHHHHH CS
                         EF-hand_1   9 fDkDgdGkIdfeEfkellk 27 
                                       +D +++G+Id  ++ +++ 
  gi|488601430|ref|YP_007907901.1| 269 ADFNNNGRIDVGDLAKIVY 287
                                       79***********999876 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0071        21      10      24 ..     240     254 ..     238     260 .. 0.87
   2 ?    7.6   0.0    0.0014       4.1      10      25 ..     270     285 ..     268     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0071
                         EF-hand_6  10 DkdgdGkidaeElrk 24 
                                       D++++Gk+d+e+ ++
  gi|488601430|ref|YP_007907901.1| 240 DFNDNGKVDFEDAMH 254
                                       99********99665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0014
                         EF-hand_6  10 DkdgdGkidaeElrka 25 
                                       D++++G id  +l k+
  gi|488601430|ref|YP_007907901.1| 270 DFNNNGRIDVGDLAKI 285
                                       9************886 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.074   2.2e+02      54      65 ..     240     251 ..     221     258 .. 0.79
   2 ?    8.0   0.0    0.0013         4      11      30 ..     269     288 ..     267     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.074
                         EF-hand_7  54 DtdkdGvisfdE 65 
                                       D +++G+++f++
  gi|488601430|ref|YP_007907901.1| 240 DFNDNGKVDFED 251
                                       777777777776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
                         EF-hand_7  11 lDtdgdgyldkeellrllrk 30 
                                        D +++g++d+ +l +++ +
  gi|488601430|ref|YP_007907901.1| 269 ADFNNNGRIDVGDLAKIVYH 288
                                       7************9986654 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00015      0.44      16      30 ..     132     146 ..     130     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                   Biotin_lipoyl_2  16 lnVkdGqrVkaGdvL 30 
                                       ln  +G+ Vk+Gdv+
  gi|488601430|ref|YP_007907901.1| 132 LNLSEGDIVKQGDVI 146
                                       7889**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 1547.91
//
Query:       gi|488601431|ref|YP_007907902.1|  [L=163]
Description: hypothetical protein Asulf_01943 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   58.1   0.0    1.1e-15   57.7   0.0    1.1  1  DUF1850   Domain of unknown function (DUF1850)


Domain annotation for each model (and alignments):
>> DUF1850  Domain of unknown function (DUF1850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0     6e-20   1.1e-15       2      86 .]      48     135 ..      47     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 6e-20
                           DUF1850   2 tlswtHSVektpveEdyrvegggLvleetrfksfGaGlpspaeagerv...edgwfvlrinrpleelrlrvggiadh 75 
                                       ++s++HSVe t+  ++yrveg++++l +t  k+ G+Glps++++ + +    ++wf++ri r l+++++   + +++
  gi|488601431|ref|YP_007907902.1|  48 SISFIHSVELTREIDFYRVEGNSFILFKTLTKTAGWGLPSTEKNFSITtykGEEWFEYRIIRYLKAIEILGYPLNKY 124
                                       79*****************************************999889999************************* PP

                           DUF1850  76 rlcvdgreypL 86 
                                       +l +++ +++L
  gi|488601431|ref|YP_007907902.1| 125 SLETENYSINL 135
                                       ****9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 914.09
//
Query:       gi|488601432|ref|YP_007907903.1|  [L=680]
Description: TRAP transporter, 4TM/12TM fusion protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-118  393.7  41.5   8.9e-118  393.7  41.5    1.8  2  DctM      Tripartite ATP-independent periplasmic transporter,


Domain annotation for each model (and alignments):
>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.7  41.5    5e-122  8.9e-118       1     412 [.     132     601 ..     132     603 .. 0.97
   2 ?   -5.1   3.0      0.56     1e+04      18      72 ..     622     675 ..     606     677 .. 0.39

  Alignments for each domain:
  == domain 1  score: 393.7 bits;  conditional E-value: 5e-122
                              DctM   1 lvsllvllalgvpvaislalasl..lllallgelllgv......pleqilaqrvve.......glssfallaipfFv 62 
                                       l++++vl+a++++v+++l++++l  +++a +g+ l+gv      +++++l++ +++       +l++++ +++  Fv
  gi|488601432|ref|YP_007907903.1| 132 LAVIFVLEATRRVVNPALVVIALvfIFYAKYGANLPGVlshpeyTWKEVLEHLYFTkegifgtPLAVSSSFVVL-FV 207
                                       5789*****************999999999999999999*******************999999*********9.** PP

                              DctM  63 laGivlersGlakrlidlaaalvGrvrGGlakvsvvgsalfgaiSGsavAnvaavGsitipamkrsGykrefaaavi 139
                                       ++G++le+sG++k++idla+a++G++ GG+ak++vv+sal+g+iSGs+vAn++++G++tip+mk+ Gyk+efa+av+
  gi|488601432|ref|YP_007907903.1| 208 IFGAFLEKSGAGKFFIDLAYAFTGWMVGGPAKAAVVSSALMGTISGSSVANTVTTGAFTIPLMKKVGYKPEFAGAVE 284
                                       ***************************************************************************** PP

                              DctM 140 aasstlgqiiPPslglivfama.vlgvsigdlfaaaiipglllavglllavaiaakkenlrsktkaelkrlgqalke 215
                                        a+st+gqi+PP++g+++f+ma ++g++++ +++aaiip++l+++g++ av+++a+kenlr+ ++ elk+ +q+lke
  gi|488601432|ref|YP_007907903.1| 285 PAASTGGQIMPPIMGAAAFVMAeFVGIPYIHIVYAAIIPAFLYFFGVFSAVDFEARKENLRGIPRSELKSPLQVLKE 361
                                       ***************************************************************************** PP

                              DctM 216 aipalllpliiligillgiftpteagavavvyalviallv..................yrrltleevaaallstakt 274
                                       ++  +l+pl+i+i++l+ ++tp+ a++++++ +++i +l                     r  ++++++al++++++
  gi|488601432|ref|YP_007907903.1| 362 GW-FYLVPLFIIIYMLVNGYTPILAAVYSIFSVIAIIILEpiirnkrapegekltgneILRNIIKTILSALEHGGRS 437
                                       **.9999********************************9999*99999988776654445556667777******* PP

                              DctM 275 taavlfilaaagifaglltltgvplklselllslsggk.llfLilvnllvlvlGmfldttaaiiilvpilaPaaakl 350
                                       +++v++++a+agi++g++tltg+++kl++ ++s+s+g  l++L++++ ++l+lGm+++tta++ii+++i+aPa++++
  gi|488601432|ref|YP_007907903.1| 438 AVTVAMACASAGIIVGVVTLTGLGFKLASSAISVSQGYiLIILVITMFVSLILGMGVPTTANYIITSTIAAPAIITF 514
                                       *************************************9888999999****************************** PP

                              DctM 351 gidp................ihfgvvivlnlsiglitPPvGlalfvassia.........kvsveeivkalvPflvv 402
                                       + +                 + ++++++++++ +++tPPv+la++++s+ia         +++ ++i+k+lvP+l++
  gi|488601432|ref|YP_007907903.1| 515 MAHGygmsvrdfltaypelvLPAHMFVFYFGVAADLTPPVALAAYAGSAIAksdpwktgiNAVKIGIGKYLVPYLFI 591
                                       ************************************************************9**************** PP

                              DctM 403 lvvalvlitl 412
                                       +++a++li +
  gi|488601432|ref|YP_007907903.1| 592 FSPAILLIGV 601
                                       *******975 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 0.56
                              DctM  18 lalasllllallgelllgvpleqilaqrvveglssfallaipfFvlaGivlersG 72 
                                       +a+++ ++  l+++l   ++l  +l++ ++  + +  + +i+f ++ +i+l++ G
  gi|488601432|ref|YP_007907903.1| 622 MAINATTIGCLIKKLSREMRLA-MLIAGILLLIPNGYTKIIGFLIFTAIFLNQYG 675
                                       2222222222222221111232.33333333456666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.83u 0.40s 00:00:01.23 Elapsed: 00:00:00.57
# Mc/sec: 3605.63
//
Query:       gi|488601433|ref|YP_007907904.1|  [L=336]
Description: TRAP transporter solute receptor, TAXI family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-96  322.2   6.6    3.5e-96  322.0   6.6    1.0  1  NMT1_3          NMT1-like family
    1.3e-09   38.3   0.6    3.1e-09   37.1   0.5    1.6  1  NMT1            NMT1/THI5 like
    1.3e-06   28.2   0.8      2e-06   27.6   0.7    1.5  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.074   12.4   0.1       0.12   11.7   0.1    1.3  1  DctP            Bacterial extracellular solute-binding protei


Domain annotation for each model (and alignments):
>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.0   6.6  7.9e-100   3.5e-96       1     289 []      49     333 ..      49     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 322.0 bits;  conditional E-value: 7.9e-100
                            NMT1_3   1 igTastgGtyYpvGvaiatliseklakdqkvkasaqssaGsveNiqllkkgeadlailqsdvayeAyeGegefegkk 77 
                                       i T++ +GtyYp+G+a+a++i++     ++vka+a +s++sv N + + + ea++++lq+dvay+Ay+G + f++ +
  gi|488601433|ref|YP_007907904.1|  49 IVTGGSAGTYYPIGGAMAQAINQY---AKGVKATAVTSGASVVNARKIGNLEAEFGLLQNDVAYYAYNGLEMFKD-A 121
                                       78******************9644...368********************************************9.8 PP

                            NMT1_3  78 plknlraitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesad 154
                                       +++++r +++ly+e +q+v+ k+ +i++i dlkgkrv+vG++gsGt + a++il+a+g++e+++++ ++l+++e  d
  gi|488601433|ref|YP_007907904.1| 122 KIDKIRGVATLYPEIIQIVTLKENNIKTIYDLKGKRVAVGAPGSGTAVDAMQILKAAGIDESNTDI-RYLNFKEVSD 197
                                       ***************************************************************996.9********* PP

                            NMT1_3 155 alkdgqldgaalvaGvPvsavtqlaasedikliplddeqldkllkeypvftkyvipagtypq.dedikTiavpnflv 230
                                       alkd+ +d+ ++vaGvP+savt+++a +d+ ++++ de  +kl+++yp++ + +ipagty++ d+d+kT++v ++l+
  gi|488601433|ref|YP_007907904.1| 198 ALKDKTIDAGFIVAGVPTSAVTDISAVRDVAIVEVPDEIYEKLKADYPFYVQVTIPAGTYKGvDQDVKTVSVLAMLA 274
                                       *************************************************************98************** PP

                            NMT1_3 231 vradldeelvYeitkaifenldelnsihkaakeislekalaglpvplHpGAerYYkEqG 289
                                       ++ad++e++vYe+tkaife+ d l+++hk a++i+le+al+g+p+plHpGAe+YYkE+G
  gi|488601433|ref|YP_007907904.1| 275 TNADVSEDVVYEVTKAIFEHKDVLEAAHKRAEDITLETALDGMPIPLHPGAEKYYKEKG 333
                                       **********************************************************9 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.5   6.9e-13   3.1e-09      58     149 ..     121     211 ..      98     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 6.9e-13
                                       HTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HH CS
                              NMT1  58 akglpvvsvaallqeplsglivlkdsgikspkDLkGkrigyvg.spfekallkallakdggdpsdvtlvnvggtsla 133
                                       ak  +++ va+l+  +  ++++lk+++ik++ DLkGkr+++   ++ +     ++l+++g+d+s   +   ++ +++
  gi|488601433|ref|YP_007907904.1| 121 AKIDKIRGVATLY-PEIIQIVTLKENNIKTIYDLKGKRVAVGApGSGTAVDAMQILKAAGIDESNTDIRYLNFKEVS 196
                                       4555799999999.678899*******************9665133344445678*************99999**** PP

                                       HHHHCTSSSEEECEET CS
                              NMT1 134 kalltgkvDaaiggye 149
                                       +al ++++Da++ ++ 
  gi|488601433|ref|YP_007907904.1| 197 DALKDKTIDAGF-IVA 211
                                       **********99.554 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 !   27.6   0.7   4.5e-10     2e-06      88     172 ..     138     218 ..      64     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.5e-10
                                       EEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HH.HHSSEEEE--HHHHHHHHHTTSSSEEEE CS
                    Phosphonate-bd  88 viivradsdiqsledLkgktiafvspsStsGylvpaalLvkeagldpe.ddfsevfsgshdaavlavlsgdadaaav 163
                                       +i++ ++++i+++ dLkgk++a+++p S  G+ v a++++k ag+d + +d+++    +  ++ +a+ ++++da+++
  gi|488601433|ref|YP_007907904.1| 138 QIVTLKENNIKTIYDLKGKRVAVGAPGS--GTAVDAMQILKAAGIDESnTDIRYL---NFKEVSDALKDKTIDAGFI 209
                                       699***********************96..999***9999******883466665...4557888888888888884 PP

                                       EHHHHHHHH CS
                    Phosphonate-bd 164 sadaledlv 172
                                        a++ ++ v
  gi|488601433|ref|YP_007907904.1| 210 VAGVPTSAV 218
                                       444433333 PP

>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.8e-05      0.12      98     177 ..     116     206 ..      62     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHTEEEEEEEEEEEEEEEE.SSS--SSGGGGTT..EEEEETSSHHHHHHHHHHTSEEEE........-TG CS
                              DctP  98 kllkslekkglkvLafwenGfrqfts.nkkpinspeDlkg..lklRvpessvllevfkalGanptp........ipf 163
                                       +++k+ + + ++++a+ +  + q+++  +  i+++ Dlkg   +   p s+++++++++l a+ ++        ++f
  gi|488601433|ref|YP_007907904.1| 116 EMFKDAKIDKIRGVATLYPEIIQIVTlKENNIKTIYDLKGkrVAVGAPGSGTAVDAMQILKAAGIDesntdiryLNF 192
                                       467777777889999988888888887999**********666677799***********99765522222222779 PP

                                       GGHHHHHHTTSSSE CS
                              DctP 164 gevytaLqtgvvDG 177
                                        ev +aL+++++D+
  gi|488601433|ref|YP_007907904.1| 193 KEVSDALKDKTIDA 206
                                       9999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); 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: 0.61u 0.38s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1885.75
//
Query:       gi|488601434|ref|YP_007907905.1|  [L=65]
Description: hypothetical protein Asulf_01946 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 379.00
//
Query:       gi|488601435|ref|YP_007907906.1|  [L=75]
Description: hypothetical protein Asulf_01947 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   17.8   3.4      0.003   17.5   3.4    1.0  1  Colicin_V  Colicin V production protein


Domain annotation for each model (and alignments):
>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.4   1.7e-07     0.003      24      88 ..       7      72 ..       5      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.7e-07
                         Colicin_V 24 evlsllgwvvafvvasllypslaellae.lilspalaaiiaflllfllvllivsllgallsklvsk 88
                                       v+   +w+++++ a++ y++++e++ +  +ls+   a +a    fll+++++ +l+  l  l+s 
  gi|488601435|ref|YP_007907906.1|  7 KVIWATSWICVWLTAFYHYKTVGEYFVSeNMLSKIPLAYVAVESWFLLTVIVLMWLSWKLIELISD 72
                                      5777889*********************86678888888888889999999999999999888865 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:                      245  (0.013665); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 443.22
//
Query:       gi|488601436|ref|YP_007907907.1|  [L=236]
Description: hypothetical protein Asulf_01948 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
          2    8.0  10.8        2.9    7.5  10.8    1.2  1  Chorion_3  Chorion family 3


Domain annotation for each model (and alignments):
>> Chorion_3  Chorion family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  10.8   0.00016       2.9      11      79 ..     133     201 ..     127     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00016
                         Chorion_3  11 aaaplasasYGsagggGGkGsgdlgagasagleelvnaaaGGaassgGaiegadaeivaspeeagrlss 79 
                                       aaa++asa+ G+ +ggG +G++  g+g++a   +   a aGG  + +G++ + ++ + +++++++ +++
  gi|488601436|ref|YP_007907907.1| 133 AAATIASAGGGAGAGGGAGGGTTSGTGTTASTPNPTTAGAGGGTTESGTGATGESIVSPTAKPTAPAKP 201
                                       788899998555544444455566788888888999998888888777888888888888877766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1321.43
//
Query:       gi|488601437|ref|YP_007907908.1|  [L=634]
Description: hypothetical protein Asulf_01949 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-11   43.3   0.0    0.00048   20.3   0.0    2.5  2  bMG10            Bacterial Alpha-2-macroglobulin MG10 domain
    5.8e-08   32.9  11.4     0.0048   17.1   2.0    4.5  3  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    6.3e-08   32.8   2.5      0.012   15.9   0.2    2.9  2  DUF11            Domain of unknown function DUF11
    0.00023   21.9  28.3     0.0004   21.1   1.0    5.7  4  Big_7            Bacterial Ig domain
    0.00069   19.8   0.1        2.2    8.5   0.0    2.6  2  LRR_adjacent     LRR adjacent
    0.00075   19.9   0.1        2.9    8.4   0.0    2.8  2  MG2              MG2 domain
     0.0018   18.8   0.1        4.6    7.9   0.0    2.8  2  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
     0.0029   18.0   3.4         43    4.5   0.0    5.5  6  LTD              Lamin Tail Domain
     0.0067   16.5   0.0        9.4    6.4   0.0    3.1  2  Fn3-like         Fibronectin type III-like domain
  ------ inclusion threshold ------
      0.016   14.9   1.9        4.7    7.0   0.1    2.8  2  Lysis_col        Lysis protein
      0.016   15.8   0.1         14    6.2   0.0    3.0  2  LEA_2            Late embryogenesis abundant protein
       0.16   12.1   3.2         49    4.1   0.0    3.7  3  GBS_Bsp-like     GBS Bsp-like repeat
        1.4    9.2  10.0         94    3.3   0.1    4.7  4  He_PIG           Putative Ig domain


Domain annotation for each model (and alignments):
>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.5e-07   0.00048      22     107 ..      33     109 ..      18     117 .. 0.79
   2 !   20.3   0.0   3.6e-07    0.0005      22     107 ..     156     232 ..     131     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-07
                             bMG10  22 klkvGdkvrvrltvttprdleyvaledplPAGlepvnpslgtesesaeeyewleeltefsyreirddrvvffadylp 98 
                                       +l+ G++ +v+ltvt++   ++ a+++ lPAG+e+v+   g++ + +  +       +++ ++  d  +++ ++ +p
  gi|488601437|ref|YP_007907908.1|  33 SLAPGSTATVTLTVTVDG-ADFYAIDEVLPAGWEIVDAGGGNTADPGHIK-------WIALQNAEDTTYTYQVR-VP 100
                                       7999***********997.599******************9999988877.......67777777777777776.66 PP

                             bMG10  99 kgtytfeyl 107
                                       +g+ + +y+
  gi|488601437|ref|YP_007907908.1| 101 EGAAEGTYT 109
                                       666655554 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3.6e-07
                             bMG10  22 klkvGdkvrvrltvttprdleyvaledplPAGlepvnpslgtesesaeeyewleeltefsyreirddrvvffadylp 98 
                                       +l+ G++ +v+ltvt++   ++ a+++ lPAG+e+v+   g++ + +  +       +++ ++  d  +++ ++ +p
  gi|488601437|ref|YP_007907908.1| 156 SLAPGSTATVTLTVTVDG-ADFYAIDEVLPAGWEIVDAGGGNTADPGHIK-------WIALQNAEDTTYTYQVR-VP 223
                                       7999***********997.599******************9999988877.......67777777777777776.66 PP

                             bMG10  99 kgtytfeyl 107
                                       +g+ + +y+
  gi|488601437|ref|YP_007907908.1| 224 EGAAEGTYT 232
                                       666655554 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 !   17.0   2.2   3.9e-06    0.0054       2      73 ..      35     111 ..      34     117 .. 0.81
   2 ?    4.9   0.1     0.023        32      46      61 ..     156     171 ..     150     179 .. 0.78
   3 !   17.1   2.0   3.5e-06    0.0048       2      73 ..     158     234 ..     157     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.9e-06
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWt......vvevspasaa..slapGetveatvkVtppagaaaGdy 70 
                                        pG+t t+tltvt dg +      ++  lP+GW+        +++p  ++  +l+  e ++ t +V++p+gaa G+y
  gi|488601437|ref|YP_007907908.1|  35 APGSTATVTLTVTVDGADFY---AIDEVLPAGWEivdaggGNTADPGHIKwiALQNAEDTTYTYQVRVPEGAAEGTY 108
                                       69************998754...688889*****6333322455666666999************************ PP

                       NPCBM_assoc  71 evt 73 
                                       +  
  gi|488601437|ref|YP_007907908.1| 109 TFS 111
                                       865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.023
                       NPCBM_assoc  46 slapGetveatvkVtp 61 
                                       slapG t+++t++Vt+
  gi|488601437|ref|YP_007907908.1| 156 SLAPGSTATVTLTVTV 171
                                       6788888888888876 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 3.5e-06
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWt......vvevspasaa..slapGetveatvkVtppagaaaGdy 70 
                                        pG+t t+tltvt dg +      ++  lP+GW+        +++p  ++  +l+  e ++ t +V++p+gaa G+y
  gi|488601437|ref|YP_007907908.1| 158 APGSTATVTLTVTVDGADFY---AIDEVLPAGWEivdaggGNTADPGHIKwiALQNAEDTTYTYQVRVPEGAAEGTY 231
                                       69************998754...688889*****6333322455666666999************************ PP

                       NPCBM_assoc  71 evt 73 
                                       +  
  gi|488601437|ref|YP_007907908.1| 232 TFS 234
                                       865 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   8.9e-06     0.012       9      85 ..      33     106 ..      19     110 .. 0.84
   2 !   15.7   0.2   9.7e-06     0.013      10      85 ..     157     229 ..     137     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.9e-06
                             DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrvtrtaas 84 
                                        ++pG t t+tltvt  g++      +  +lPag ++v +  + +ta+        L++ e +t +++vrv+  aa+
  gi|488601437|ref|YP_007907908.1|  33 SLAPGSTATVTLTVTVDGADFY---AIDEVLPAGWEIVDAGGG-NTADPGHIKwIALQNAEDTTYTYQVRVPEGAAE 105
                                       578************9999877...9**********9998888.444443333799***************999987 PP

                             DUF11  85 g 85 
                                       g
  gi|488601437|ref|YP_007907908.1| 106 G 106
                                       6 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 9.7e-06
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv.gsLeagesatlsftvrvtrtaasg 85 
                                       ++pG t t+tltvt  g++      +  +lPag ++v +  + +ta+        L++ e +t +++vrv+  aa+g
  gi|488601437|ref|YP_007907908.1| 157 LAPGSTATVTLTVTVDGADFY---AIDEVLPAGWEIVDAGGG-NTADPGHIKwIALQNAEDTTYTYQVRVPEGAAEG 229
                                       78************9999877...9**********9998888.444443333799***************9999876 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.4      0.12   1.6e+02      19      68 ..      44     110 ..      31     111 .. 0.56
   2 ?    2.9   2.7      0.14   1.9e+02      19      68 ..     167     233 ..     153     234 .. 0.57
   3 !    8.5   0.8    0.0024       3.3      43      69 ..     307     342 ..     260     343 .. 0.61
   4 !   21.1   1.0   2.9e-07    0.0004       2      69 ..     366     440 ..     365     441 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                                       EEEEEEEE-SS-EEEEEEEETTEE........................EEEE-SSSEEEEEE--....SEEEEE CS
                             Big_7  19 vtisasAsddggvskVefyvdgtl.g......................lgtdtsapysltwttta.ltagthtl 68 
                                       +t++++  d  ++++V       l +                      l++  +++y++++  +  +++gt+t 
  gi|488601437|ref|YP_007907908.1|  44 LTVTVDGADFYAIDEV-------LpAgweivdagggntadpghikwiaLQNAEDTTYTYQVRVPEgAAEGTYTF 110
                                       2222222222444444.......222334444333334567888888888888889999999888899999985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                                       EEEEEEEE-SS-EEEEEEEETTEE........................EEEE-SSSEEEEEE--....SEEEEE CS
                             Big_7  19 vtisasAsddggvskVefyvdgtl.g......................lgtdtsapysltwttta.ltagthtl 68 
                                       +t++++  d  ++++V       l +                      l++  +++y++++  +  +++gt+t 
  gi|488601437|ref|YP_007907908.1| 167 LTVTVDGADFYAIDEV-------LpAgweivdagggntadpghikwiaLQNAEDTTYTYQVRVPEgAAEGTYTF 233
                                       2222222222444444.......222334444333334567888888888888888999999888899999985 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0024
                                       ........EEEE-S..SSEEEEEE--...SEEEEEE CS
                             Big_7  43 g.......lgtdts..apysltwtttaltagthtlt 69 
                                       +       +++dt+  +++s++w+t ++++g + ++
  gi|488601437|ref|YP_007907908.1| 307 NdgagwveIYNDTNgdDGWSAEWDTVTVPDGCYIIR 342
                                       13445588999999778*************988765 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 2.9e-07
                                       EEEEEE--TT--EBTSEEEEEEEEE-S...S-EEEE.EEE...ETTEE..EEEE-S..SSEEEEEE--...SEEEEE CS
                             Big_7   2 tvtitsPangatvsggtvtisasAsdd...ggvskV.efy...vdgtlg.lgtdts..apysltwtttaltagthtl 68 
                                         +i +P +ga+v  gt+ti+a   d+   + v++V e y   +d+t++ +g+dt+  +++s+ w+++ +++g++ +
  gi|488601437|ref|YP_007907908.1| 366 EPSIPNPGDGASVA-GTITIEAV-DDSgqnDVVKSVfE-YapaADTTWTlIGEDTDgsDGWSVDWNASGVEDGEYLI 439
                                       55899*********.99999863.33346555566633.42436666646666555449***************988 PP

                                       E CS
                             Big_7  69 t 69 
                                       +
  gi|488601437|ref|YP_007907908.1| 440 R 440
                                       6 PP

>> LRR_adjacent  LRR adjacent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0016       2.2      18      50 ..      78     112 ..      66     115 .. 0.78
   2 !    8.5   0.0    0.0016       2.2      18      50 ..     201     235 ..     189     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                                       TEEEEE-SST-SEEEEEEEEEEEET..TEEEEEEE CS
                      LRR_adjacent  18 pnitWnlesttsevsYtFsqkitig..kitatfsG 50 
                                       ++i+W   +  + + Yt++  ++ g  ++t tfsG
  gi|488601437|ref|YP_007907908.1|  78 GHIKWIALQNAEDTTYTYQVRVPEGaaEGTYTFSG 112
                                       68***888999999*********994344555666 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                                       TEEEEE-SST-SEEEEEEEEEEEET..TEEEEEEE CS
                      LRR_adjacent  18 pnitWnlesttsevsYtFsqkitig..kitatfsG 50 
                                       ++i+W   +  + + Yt++  ++ g  ++t tfsG
  gi|488601437|ref|YP_007907908.1| 201 GHIKWIALQNAEDTTYTYQVRVPEGaaEGTYTFSG 235
                                       68***888999999*********994344555666 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0021       2.9      17      80 ..      42     112 ..      34     124 .. 0.69
   2 !    8.4   0.0    0.0021         3      17      79 ..     165     234 ..     157     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                                       EEEEEEEESTTCSB---.EEEEEEEE-TTSSEEE...EEEE...EE-CTTEEEEEEE--TT--SEEEEEEE CS
                               MG2  17 Vslkallrdetlqglak.lplkltirdpdgkevk...elpl...atdetggaesefalpeaaklGeysvel 80 
                                       V l++ +  +++ ++ + lp+  +i+d++g+++    + ++   ++ e+ ++ +++++pe+a  G+y+ + 
  gi|488601437|ref|YP_007907908.1|  42 VTLTVTVDGADFYAIDEvLPAGWEIVDAGGGNTAdpgHIKWialQNAEDTTYTYQVRVPEGAAEGTYTFSG 112
                                       444444444666666667777777777777766522233335558889999****************9875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0021
                                       EEEEEEEESTTCSB---.EEEEEEEE-TTSSEEE...EEEE...EE-CTTEEEEEEE--TT--SEEEEEE CS
                               MG2  17 Vslkallrdetlqglak.lplkltirdpdgkevk...elpl...atdetggaesefalpeaaklGeysve 79 
                                       V l++ +  +++ ++ + lp+  +i+d++g+++    + ++   ++ e+ ++ +++++pe+a  G+y+ +
  gi|488601437|ref|YP_007907908.1| 165 VTLTVTVDGADFYAIDEvLPAGWEIVDAGGGNTAdpgHIKWialQNAEDTTYTYQVRVPEGAAEGTYTFS 234
                                       444444444666666667777777777777766522233335558889999****************987 PP

>> 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 !    7.7   0.0    0.0038       5.2      70      92 ..      88     110 ..      33     112 .. 0.76
   2 !    7.9   0.0    0.0033       4.6      60      92 ..     202     233 ..     134     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0038
                   Pur_ac_phosph_N  70 epgttYyYrvgddeggwSevysf 92 
                                       +++ttY Y+v+  eg+   +y+f
  gi|488601437|ref|YP_007907908.1|  88 AEDTTYTYQVRVPEGAAEGTYTF 110
                                       689*******9999888888887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0033
                   Pur_ac_phosph_N  60 yshkatltgLepgttYyYrvgddeggwSevysf 92 
                                       ++ ++ l++ +++ttY Y+v+  eg+   +y+f
  gi|488601437|ref|YP_007907908.1| 202 HIKWIALQN-AEDTTYTYQVRVPEGAAEGTYTF 233
                                       555555555.689*******9999888888887 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.5     2e+03      52      70 ..      29      45 ..      15      57 .. 0.75
   2 ?    4.5   0.0     0.031        43      12      36 ..      65      93 ..      64     178 .. 0.70
   3 ?    3.6   0.0     0.062        85      12      35 ..     188     215 ..     187     217 .. 0.86
   4 ?    4.5   0.0     0.031        43      17      35 ..     304     322 ..     294     361 .. 0.79
   5 ?   -2.6   0.1         5     7e+03       3      20 ..     377     394 ..     375     402 .. 0.74
   6 ?   -1.4   0.0       2.1   2.8e+03      84     111 ..     562     589 ..     549     590 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                               LTD 52 fpngtgtlaageyvvvwsg 70
                                      +p+g  +la+g++++v+  
  gi|488601437|ref|YP_007907908.1| 29 LPDG--SLAPGSTATVTLT 45
                                      4555..5*******99865 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.031
                               LTD 12 evmedgagnnan....efvelyNtsskav 36
                                      e++++g+gn a+    +++ l N+ +++ 
  gi|488601437|ref|YP_007907908.1| 65 EIVDAGGGNTADpghiKWIALQNAEDTTY 93
                                      77888877777799*********999875 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.062
                               LTD  12 evmedgagnnan....efvelyNtsska 35 
                                       e++++g+gn a+    +++ l N+ +++
  gi|488601437|ref|YP_007907908.1| 188 EIVDAGGGNTADpghiKWIALQNAEDTT 215
                                       7888887887779***********9986 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.031
                               LTD  17 gagnnanefvelyNtsska 35 
                                       g++n+++ +ve+yN ++ +
  gi|488601437|ref|YP_007907908.1| 304 GKANDGAGWVEIYNDTNGD 322
                                       44444449*******9875 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 5
                               LTD   3 aaagdvvIsevmedgagn 20 
                                       + ag++ I+ v++ g+++
  gi|488601437|ref|YP_007907908.1| 377 SVAGTITIEAVDDSGQND 394
                                       678999999999988443 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 2.1
                               LTD  84 ssavwnnggdavaLydasgevvdsvgyg 111
                                       + + ++++ d+++  +a+ ++ d +gy+
  gi|488601437|ref|YP_007907908.1| 562 TLFMIDESYDRIWVWNAEEQTHDLYGYN 589
                                       4555666888899999999999988885 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0068       9.4      29      48 ..      34      53 ..      32      68 .. 0.81
   2 !    6.4   0.0    0.0068       9.4      29      48 ..     157     176 ..     155     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0068
                                      E-TT-EEEEEEEEECGGG-E CS
                          Fn3-like 29 LapGesktvtftldrkdlsv 48
                                      LapG ++tvt+t++++   +
  gi|488601437|ref|YP_007907908.1| 34 LAPGSTATVTLTVTVDGADF 53
                                      9************9865544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0068
                                       E-TT-EEEEEEEEECGGG-E CS
                          Fn3-like  29 LapGesktvtftldrkdlsv 48 
                                       LapG ++tvt+t++++   +
  gi|488601437|ref|YP_007907908.1| 157 LAPGSTATVTLTVTVDGADF 176
                                       9************9865544 PP

>> Lysis_col  Lysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0047       6.5      23      44 ..      22      43 ..       1      48 [. 0.72
   2 ?    7.0   0.1    0.0034       4.7      25      44 ..     147     166 ..     145     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0047
                         Lysis_col 23 QvNyvRDvqGGtVaPSSsselT 44
                                           RD   G+ aP S++ +T
  gi|488601437|ref|YP_007907908.1| 22 AQDVCRDLPDGSLAPGSTATVT 43
                                      34557*************9998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0034
                         Lysis_col  25 NyvRDvqGGtVaPSSsselT 44 
                                       N  RD   G+ aP S++ +T
  gi|488601437|ref|YP_007907908.1| 147 NVCRDLPDGSLAPGSTATVT 166
                                       889*************9998 PP

>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0      0.01        14      36      68 ..      31      63 ..      27     116 .. 0.69
   2 ?    6.2   0.0      0.01        14      36      68 ..     154     186 ..     150     239 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                                      -EEESSSCEEEEEEEEEEEHHHHHHHHHHHH... CS
                             LEA_2 36 gfsqpargtttlevpvsvsaddlarelrall.ag 68
                                       +s+++++t t++++v+v+++d + +++ +l ag
  gi|488601437|ref|YP_007907908.1| 31 DGSLAPGSTATVTLTVTVDGAD-FYAIDEVLpAG 63
                                      68899****************9.55555554333 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.01
                                       -EEESSSCEEEEEEEEEEEHHHHHHHHHHHH... CS
                             LEA_2  36 gfsqpargtttlevpvsvsaddlarelrall.ag 68 
                                        +s+++++t t++++v+v+++d + +++ +l ag
  gi|488601437|ref|YP_007907908.1| 154 DGSLAPGSTATVTLTVTVDGAD-FYAIDEVLpAG 186
                                       68899****************9.55555554333 PP

>> GBS_Bsp-like  GBS Bsp-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.035        49      41      72 ..      79     109 ..      39     115 .. 0.87
   2 ?    4.1   0.0     0.036        49      41      72 ..     202     232 ..     162     237 .. 0.87
   3 ?    1.9   0.2      0.18   2.5e+02      26      81 ..     393     447 ..     376     458 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.035
                      GBS_Bsp-like  41 dlkWytatkqsdgtykvtvniknhkneaGkYn 72 
                                        +kW   ++ +d ty+ +v + +    +G+Y+
  gi|488601437|ref|YP_007907908.1|  79 HIKWIALQNAEDTTYTYQVRVPEGA-AEGTYT 109
                                       699*****************99877.788887 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.036
                      GBS_Bsp-like  41 dlkWytatkqsdgtykvtvniknhkneaGkYn 72 
                                        +kW   ++ +d ty+ +v + +    +G+Y+
  gi|488601437|ref|YP_007907908.1| 202 HIKWIALQNAEDTTYTYQVRVPEGA-AEGTYT 232
                                       699*****************99877.788887 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.18
                      GBS_Bsp-like  26 ksVqvpvWseadgqddlkWytatkqsdgtykvtvniknhkneaGkYnvhvYvtdkn 81 
                                       + V   v+  a   +d +W    +++dg+   +v+ +    e G+Y + + ++d+ 
  gi|488601437|ref|YP_007907908.1| 393 NDVVKSVFEYAP-AADTTWTLIGEDTDGSDGWSVDWNASGVEDGEYLIRATMYDTC 447
                                       555555666665.67899999999999999999***************99999874 PP

>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.5      0.14   1.9e+02      29      46 ..      30      48 ..      28      51 .. 0.70
   2 ?    3.3   0.1     0.068        94      18      40 ..      85     110 ..      60     111 .. 0.85
   3 ?    2.9   0.1     0.091   1.3e+02      29      46 ..     153     171 ..     143     174 .. 0.74
   4 ?    3.3   0.1     0.068        94      18      40 ..     208     233 ..     183     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                            He_PIG 29 pdqtvapG.sytftVtatd 46
                                      pd + apG + t+t+t+t 
  gi|488601437|ref|YP_007907908.1| 30 PDGSLAPGsTATVTLTVTV 48
                                      6667777777778888774 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.068
                            He_PIG  18 L...dsstGtitGtpdqtvapGsytf 40 
                                       L   + +t t+++ +  + a G+ytf
  gi|488601437|ref|YP_007907908.1|  85 LqnaEDTTYTYQVRVPEGAAEGTYTF 110
                                       455578899999999999999****9 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.091
                            He_PIG  29 pdqtvapG.sytftVtatd 46 
                                       pd + apG + t+t+t+t 
  gi|488601437|ref|YP_007907908.1| 153 PDGSLAPGsTATVTLTVTV 171
                                       6667777777777777774 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.068
                            He_PIG  18 L...dsstGtitGtpdqtvapGsytf 40 
                                       L   + +t t+++ +  + a G+ytf
  gi|488601437|ref|YP_007907908.1| 208 LqnaEDTTYTYQVRVPEGAAEGTYTF 233
                                       455578899999999999999****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 3617.32
//
Query:       gi|488601438|ref|YP_007907909.1|  [L=873]
Description: conserved repeat domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-11   41.9   3.7    4.5e-10   39.2   0.1    3.0  3  PKD         PKD domain
    8.8e-05   22.7   1.7    0.00013   22.2   0.5    1.9  2  DUF11       Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.095   12.9   0.1       0.23   11.6   0.1    1.7  1  Ig_GlcNase  Exo-beta-D-glucosaminidase Ig-fold domain


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.024   1.4e+02       7      63 ..      43     102 ..      39     105 .. 0.77
   2 !   39.2   0.1   7.6e-14   4.5e-10       9      69 ..     155     218 ..     152     220 .. 0.89
   3 ?   -2.0   0.0      0.54   3.2e+03      29      36 ..     425     438 ..     414     455 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.024
                                       --BSSEEEEEEEES..-SS-SEEEEE--SS..--EEEEETTEEEEEE-SSEEEEEEEEEE CS
                               PKD   7 vlvpgatvaftaav.pdganvtysWdfgdg..svvqvlseptvthtYlspGeYeVtvtas 63 
                                       v  +g tv+ t +v  + ++++++ d+ d+   +++vl e   t+ + +  +Y ++ +++
  gi|488601438|ref|YP_007907909.1|  43 VYKIGDTVNYTMTVtNPSEDYSFTLDVFDDlpNATTVLLENDLTLLPGESKTYYISYVVN 102
                                       667888999999998889999999999998888888888888888887777777776665 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 7.6e-14
                                       BSSEEEEEEEES...-SS-SEEEEE--SS--EEEEETTEEE.EEE-SSEEEEEEEEEE-SS-EE CS
                               PKD   9 vpgatvaftaav..pdganvtysWdfgdgsvvqvlseptvt.htYlspGeYeVtvtasnavgsa 69 
                                       +++ tv+f ++   pdg++v+ +Wdfgdg + +++  p ++ h ++++G+Y+Vt+   +++g+ 
  gi|488601438|ref|YP_007907909.1| 155 ECNLTVRFVGVGidPDGSIVNHTWDFGDGPTITDSGAPGAMlHQFPAEGTYTVTLSGCDNDGLC 218
                                       69***************************777777777766599****************9985 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.54
                                       EEE--SS......- CS
                               PKD  29 sWdfgdg......s 36 
                                       sW+ gdg      +
  gi|488601438|ref|YP_007907909.1| 425 SWTAGDGidsfdaD 438
                                       6*****86655440 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.5   2.2e-08   0.00013      10      78 ..      44     101 ..      33     115 .. 0.79
   2 ?   -4.0   0.0         3   1.8e+04      14      22 ..     201     209 ..     195     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78 
                                        + Gdtv+yt tvtN++ + + ++ v D lP +++                  +L +ges+t  ++  v
  gi|488601438|ref|YP_007907909.1|  44 YKIGDTVNYTMTVTNPSEDYSFTLDVFDDLPNATTVLLENDL-----------TLLPGESKTYYISYVV 101
                                       679****************************88886555544...........5777777766555555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3
                             DUF11  14 dtvtytltv 22 
                                       ++ tyt+t+
  gi|488601438|ref|YP_007907909.1| 201 AEGTYTVTL 209
                                       577999997 PP

>> Ig_GlcNase  Exo-beta-D-glucosaminidase Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.9e-05      0.23      30     104 ..      47     122 ..      23     123 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.9e-05
                        Ig_GlcNase  30 keetkvtvtLenkssvpAffvrlnlvdaageevlPvlwsDNyvtLlPgEsltltvey...paaalkgkkp..kvevs 101
                                        ++ ++t+t++n+s+  +f +  ++ d+  +  + ++  +N +tLlPgEs+t  ++y    a+ ++g++   +++v+
  gi|488601438|ref|YP_007907909.1|  47 GDTVNYTMTVTNPSEDYSFTL--DVFDDLPN--ATTVLLENDLTLLPGESKTYYISYvvnAADITDGNHIwnTLRVE 119
                                       458899999999999999875..56666522..3345579************9999944222222333334578888 PP

                        Ig_GlcNase 102 GwN 104
                                       G+N
  gi|488601438|ref|YP_007907909.1| 120 GYN 122
                                       888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (873 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.35s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 4845.54
//
Query:       gi|488601439|ref|YP_007907910.1|  [L=30]
Description: hypothetical protein Asulf_01951 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 190.41
//
Query:       gi|488601440|ref|YP_007907911.1|  [L=84]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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   1.9    1.1e-21   76.6   1.9    1.0  1  HTH_45    Winged helix-turn-helix
      0.003   17.3   0.2     0.0034   17.1   0.2    1.1  1  DUF4364   Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   1.9   1.2e-25   1.1e-21       1      74 [.       2      80 ..       2      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.2e-25
                            HTH_45  1 rRskleIiadILeais.egeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkelee 74
                                      rR++++I++dI +++  +g+ +kTki+y anL++k+++kYL +Lv+ +++     + k++Y+ TekG++l++k+ e+ e
  gi|488601440|ref|YP_007907911.1|  2 RRTRFDIVIDIIKVVTqNGRCNKTKIVYGANLNFKIAEKYLVYLVDLEYLelelINGKTTYRATEKGKDLVRKFSEISE 80
                                      8************99879999****************************8777689*******************9986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   3.8e-07    0.0034      31      75 ..      33      77 ..      16      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-07
                           DUF4364 31 tnYfdlqqalseLvesglieeeekenktlykiTekGketlelfen 75
                                      +n+   +++l  Lv+ +++e e  ++kt+y+ TekGk+ ++ f +
  gi|488601440|ref|YP_007907911.1| 33 LNFKIAEKYLVYLVDLEYLELELINGKTTYRATEKGKDLVRKFSE 77
                                      67778899********************************99963 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 477.72
//
Query:       gi|488601441|ref|YP_007907912.1|  [L=31]
Description: hypothetical protein Asulf_01953 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.53
# Mc/sec: 174.63
//
Query:       gi|488601442|ref|YP_007907913.1|  [L=162]
Description: hypothetical protein Asulf_01954 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.6   0.0        0.1   12.5   0.0    1.5  1  DUF3285   Protein of unknown function (DUF3285)


Domain annotation for each model (and alignments):
>> DUF3285  Protein of unknown function (DUF3285)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.7e-06       0.1       7      23 ..      61      77 ..      57      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-06
                           DUF3285  7 vKLAMRNMVrKggkSLk 23
                                      vKLA  N V Kg++S++
  gi|488601442|ref|YP_007907913.1| 61 VKLALHNLVVKGRRSIW 77
                                      9**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 919.38
//
Query:       gi|488601443|ref|YP_007907914.1|  [L=185]
Description: putative regulator of amino acid metabolism, contains ACT domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-06   26.6   1.1    7.8e-06   25.6   0.1    2.1  3  ACT       ACT domain
      0.007   16.9   0.3        2.1    9.0   0.1    2.5  2  ACT_4     ACT domain
     0.0087   15.8   0.0       0.02   14.7   0.0    1.6  1  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8   1.1e+04      22      29 ..      43      50 ..      39      51 .. 0.76
   2 ?   -1.2   0.0      0.31   1.9e+03      43      60 ..      75      92 ..      58      98 .. 0.61
   3 !   25.6   0.1   1.3e-09   7.8e-06       2      65 ..     114     176 ..     113     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                                      HHTTSEEE CS
                               ACT 22 adrgiNid 29
                                       ++gi+i+
  gi|488601443|ref|YP_007907914.1| 43 LRLGISIR 50
                                      57899997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.31
                                      EEEEEEEEEHHHHHHHHH CS
                               ACT 43 ivfvvivvdeedleevle 60
                                       v+v  + + e++ee+ +
  gi|488601443|ref|YP_007907914.1| 75 KVVVSAIQNIEGDEELRK 92
                                      445555555555555554 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 1.3e-09
                                       EEEEEEESS.TTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   2 vlrvgvpDr.PGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                       vl+++++ +  G+ + ++++l++ gi+i+ i     e     ++ +++v+d++ +  +++++ ++
  gi|488601443|ref|YP_007907914.1| 114 VLEIYAESKkIGIVSGITSILTREGISIRYILAEDPEL--SVESKLTVVTDTKIPGRLVDEFLDV 176
                                       67888887779***************************..7***************999998765 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0033        20      55      80 .]      83     108 ..      67     108 .. 0.87
   2 !    9.0   0.1   0.00035       2.1      10      78 ..     116     182 ..     113     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0033
                             ACT_4  55 eVkdvehLsrviakLraipgVisVeR 80 
                                       +++  e+L++v  +L+ + ++ +V R
  gi|488601443|ref|YP_007907914.1|  83 NIEGDEELRKVFSSLKPVANIADVAR 108
                                       5777899*****************99 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00035
                             ACT_4  10 evea.edrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78 
                                       e++a + + g+++ it++++ e+++i+ + a++   +  +e k+tv V d++   r+++    ++gV++V
  gi|488601443|ref|YP_007907914.1| 116 EIYAeSKKIGIVSGITSILTREGISIRYILAED--PELSVESKLTV-VTDTKIPGRLVDEFLDVDGVEKV 182
                                       5555345679**********************9..68899999998.78888888888888888888877 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.4e-06      0.02      20      41 ..     123     144 ..     111     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-06
                                       S--HHHHHHHHHHTTT---EEE CS
                             ACT_7  20 vtGivaklaspLaeagIsifqi 41 
                                        +Giv++++s L+++gIsi +i
  gi|488601443|ref|YP_007907914.1| 123 KIGIVSGITSILTREGISIRYI 144
                                       68*****************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1131.86
//
Query:       gi|488601444|ref|YP_007907915.1|  [L=389]
Description: Cell division GTPase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-26   92.3   0.0    8.8e-26   91.3   0.0    1.5  1  Tubulin    Tubulin/FtsZ family, GTPase domain
      0.003   16.8   0.1     0.0048   16.1   0.1    1.3  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 !   91.3   0.0   9.8e-30   8.8e-26       4     192 ..       5     172 ..       2     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 9.8e-30
                                       EEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--C CS
                           Tubulin   4 vigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgk 80 
                                        ig+Gq+G++i++ +++   k+ g+              g ++ +   +ai+  +++l  ++      +++++l+g+
  gi|488601444|ref|YP_007907915.1|   5 AIGFGQAGSKILDLFVD-NEKQRGA--------------GIKHNV---LAINSARTDLLGLRHI---DHKDRILIGQ 60 
                                       79***************.3333344..............444444...6999866666655544...466******* PP

                                       CCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE...SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEE CS
                           Tubulin  81 egagnngaggypevgkeaaeeileeirkevekcds..lqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvv 155
                                       +  +++g+g ++++g+++a+e  e i  ++++  +  +++f+i+a+lgGGTGSG +pv++++l+e+y   +v++v +
  gi|488601444|ref|YP_007907915.1|  61 TLVKGHGVGTDNKLGAKVAQEDIETILSAIDERGThdVDAFLIIAGLGGGTGSGGAPVLARYLSEMY-AEPVYAVGI 136
                                       *******************************6555459****************************9.668****** PP

                                       E--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHH CS
                           Tubulin 156 lPsefsevvvepynailalkelieesdavividNdaL 192
                                       lP  + e+++++ na+ ++ +l +++d +i++dN a+
  gi|488601444|ref|YP_007907915.1| 137 LPAPE-EGKLYSLNAARSMITLLKYVDNLILVDNGAW 172
                                       ***88.9***************************987 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.4e-07    0.0048     136     222 ..      80     155 ..      70     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.4e-07
                         Tubulin_2 136 realrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdvfplnkegger 212
                                       +e +++ ++++ ++ g++++  + ++ +L GGTGSG +  +a +l +++ e       +g++++P+        g+ 
  gi|488601444|ref|YP_007907915.1|  80 QEDIETILSAIDER-GTHDVDAFLIIAGLGGGTGSGGAPVLARYLSEMYAEPVY---AVGILPAPEE-------GKL 145
                                       55666666666663.4466667899************************99887...5677777765.......677 PP

                         Tubulin_2 213 vkaNayaaLk 222
                                       + +Na++++ 
  gi|488601444|ref|YP_007907915.1| 146 YSLNAARSMI 155
                                       7777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2203.72
//
Query:       gi|488601445|ref|YP_007907916.1|  [L=294]
Description: Sugar kinase, ribokinase family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-51  173.7   0.0      7e-51  173.3   0.0    1.1  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.3   0.0   3.9e-55     7e-51      11     297 ..       9     279 ..       1     284 [. 0.88

  Alignments for each domain:
  == domain 1  score: 173.3 bits;  conditional E-value: 3.9e-55
                                       EEEEEEECSSH.TTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEE CS
                              PfkB  11 lidliavsekl.egelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkid 85 
                                       l+d     +k  ++  +  v+++e+ aGGa+ Nv ++l++lg + +f + +G D+ ++f+l+e++++gv++ y++  
  gi|488601445|ref|YP_007907916.1|   9 LVDYTHLIDKYpPAGGHaIVRKTERFAGGAAGNVIFGLSKLGLRCRFYTTLGEDDDSRFYLSEMRSAGVEVVYTI-- 83 
                                       555555555556455566999**************************************************7777.. PP

                                       SSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE.. CS
                              PfkB  86 edtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt.. 160
                                        +   g++ i vd  gert+ ++++ a  +  +    + ++++e d++y++ +  + + e +l  +++a+k++ +  
  gi|488601445|ref|YP_007907916.1|  84 SHRYAGKCDIYVDPSGERTFFVHPNSAGIINLD---VSSEDFKEIDYVYLDPFPAEMSFEFHLSVAKKARKENCCvm 157
                                       888**********************99988886...68**************6666666***************765 PP

                                       EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEET CS
                              PfkB 161 fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvek 237
                                         p +   +     ++l+ell ++d+++++++Elea+  ++     + l+++        + +vvt+GkeG+ ++++
  gi|488601445|ref|YP_007907916.1| 158 INPGFPYISLG--FKRLKELLKYCDIVFMSRDELEAIDAST----GDFLEYV--------EILVVTMGKEGSSAYTR 220
                                       55555555554..677*******************876666....5778885........56*************** PP

                                       TEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSST CS
                              PfkB 238 dgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaia 297
                                       d+ ++  a ++vk vDttGAGD+f++gf++a+++g +le++l+ +n+vA+++vqk ga++
  gi|488601445|ref|YP_007907916.1| 221 DKRFFERA-FEVKTVDTTGAGDAFAAGFIYAYTKGYDLEKCLKTGNYVASVNVQKVGARN 279
                                       ***99999.89***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1575.14
//
Query:       gi|488601446|ref|YP_007907917.1|  [L=552]
Description: thermosome subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-184  614.6  24.6   1.3e-184  614.4  24.6    1.0  1  Cpn60_TCP1     TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.17   12.4   1.3        3.1    8.3   0.1    3.1  3  CoA_binding_2  CoA binding domain


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 !  614.4  24.6  1.5e-188  1.3e-184       1     490 [.      35     525 ..      35     526 .. 0.98

  Alignments for each domain:
  == domain 1  score: 614.4 bits;  conditional E-value: 1.5e-188
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a++v++tlGP+GmdKmlv++ g+vv+TnDG+tilke+++ehPaak+++e+a++q++evGDGTtt+v+Lage l++a
  gi|488601446|ref|YP_007907917.1|  35 IAEAVRSTLGPRGMDKMLVDSLGDVVITNDGVTILKEMDVEHPAAKMIIEVAKTQEDEVGDGTTTAVVLAGEFLKKA 111
                                       799************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e+l+++++h   i +gy+ a eka+e+L+e   +i+++++d+e+L+k+a t++++k  +   ++l++++v+Av ++ 
  gi|488601446|ref|YP_007907917.1| 112 EELLEQDIHSAIISSGYRLASEKAMEILNEL--AIPVSKDDDEMLKKIAMTAMTGKGAEVALDKLAEIAVRAVkSVA 186
                                       *******************************..8888889*********************************5555 PP

                                       CCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 154 eene..keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       ee +   e+d++ ik++k +ggs++++el++G+vldk+v++p+mpkk+++ak+ll++  Le ++tet+++++++d+e
  gi|488601446|ref|YP_007907917.1| 187 EEVNgeVEVDAEYIKIEKRQGGSIDETELIDGVVLDKEVVHPSMPKKVKDAKILLINSALEVKETETDAKIRITDPE 263
                                       5555777778888**************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                        l+k+ ++eek+l+++++ki+++g+nvv+cqkgiddla+ +lak+g+la+rrvkk+d+e+l+katGa+++++l d++
  gi|488601446|ref|YP_007907917.1| 264 MLQKFIEQEEKMLKDMVDKIVNAGANVVICQKGIDDLAQYYLAKAGVLAVRRVKKSDIEKLSKATGAKVLTELRDVK 340
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       pe+lG a+ vee+kig+ek+++i+++k++k++til+rg t++v++ei r iedA++vv++a+ed+kv++GGGa e+ 
  gi|488601446|ref|YP_007907917.1| 341 PEDLGAAELVEERKIGDEKMVFITGCKNPKAVTILIRGGTEHVVEEIARGIEDAIRVVECALEDGKVLAGGGAPEID 417
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       ++ klke+a ++ g+eqla+eafakA+e+ipktLaeNaGldpi+vl +l++ah+kg+k +g++ve+g+++d++e+gv
  gi|488601446|ref|YP_007907917.1| 418 VSLKLKEWAPTLGGREQLAVEAFAKAMEIIPKTLAENAGLDPIDVLVELKSAHEKGNKYAGVNVETGKVEDMKENGV 494
                                       ***************************************************************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiikak 490
                                       v+pl+vk+qa+ sAte+a +iLrid++i ak
  gi|488601446|ref|YP_007907917.1| 495 VEPLRVKTQAIASATEVAVMILRIDDVIAAK 525
                                       ****************************998 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.054   4.8e+02      71     106 ..     110     147 ..      76     150 .. 0.83
   2 ?    8.3   0.1   0.00034       3.1      66     101 ..     274     309 ..     220     318 .. 0.77
   3 ?   -2.3   0.0      0.67     6e+03      88     102 ..     365     379 ..     322     402 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.054
                                       GHHHHHHH--SEEEE-TT..---HHHHHHHHHTT-EEE CS
                     CoA_binding_2  71 ivkealalgakavwlqpg..sedeeaaelaeeagirvv 106
                                        ++e+l++++ ++++ +g    +e+a+e+++e +i+v 
  gi|488601446|ref|YP_007907917.1| 110 KAEELLEQDIHSAIISSGyrLASEKAMEILNELAIPVS 147
                                       46788888999999999999999999999999988876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00034
                                       HHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHT CS
                     CoA_binding_2  66 eatpeivkealalgakavwlqpgsedeeaaelaeea 101
                                       + + ++v++++ +ga++v++q g+ d + + la++ 
  gi|488601446|ref|YP_007907917.1| 274 KMLKDMVDKIVNAGANVVICQKGIDDLAQYYLAKAG 309
                                       457899*****************9998888777764 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.67
                                       T---HHHHHHHHHTT CS
                     CoA_binding_2  88 gsedeeaaelaeeag 102
                                       g  +++a+ ++ + g
  gi|488601446|ref|YP_007907917.1| 365 GCKNPKAVTILIRGG 379
                                       333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 3235.11
//
Query:       gi|488601447|ref|YP_007907918.1|  [L=501]
Description: sodium/proton antiporter, CPA1 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-73  247.6  43.4      2e-73  247.4  43.4    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.4  43.4   1.1e-77     2e-73       3     380 ..      12     387 ..      10     388 .. 0.94

  Alignments for each domain:
  == domain 1  score: 247.4 bits;  conditional E-value: 1.1e-77
                                       HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHH CS
                    Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksi 79 
                                       +l+++++ v ++++ ++lp++++l+++Gll+G+       + ++  ++++ l l++llF+ +l++dl elr+n+k+i
  gi|488601447|ref|YP_007907918.1|  12 ALLMISVAVAIVVKYVRLPYTIALVVVGLLVGLANIF--PEIKLSEDLIFLLILPPLLFEGALNTDLGELRSNFKPI 86 
                                       455544444446********************99776..3335888899**************************** PP

                                       HHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCC CS
                    Na_H_Exchanger  80 lllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavav 156
                                       l+la++gvl++vv++G+l+++  +l ipl+ allfga++++tdpv vla++ +e + p+rl t+++ges+lnD+++v
  gi|488601447|ref|YP_007907918.1|  87 LCLAIVGVLVSVVVTGFLVRW--LLSIPLSIALLFGAMITPTDPVSVLATF-RELKAPKRLSTIIEGESILNDGTGV 160
                                       ********************9..799*************************.99999******************** PP

                                       CCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTS CS
                    Na_H_Exchanger 157 vllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaell 233
                                       v++ ++l+++   ++g++sl+++ ++f +v vgg+++g+ +g+ + +i+r++ dd  +e+ ++++la++++l+ae++
  gi|488601447|ref|YP_007907918.1| 161 VIFGLILEMV---RTGHFSLVSGMVEFGFVTVGGIVVGFSFGYTAYRILRYI-DDHLIEITITIILAYSTYLFAESV 233
                                       **********...**************************************8.************************ PP

                                       XXXHHHHHHHHHHHHHHHHHHTTHHHH....HHHHHH...HHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 234 gvsgilgaflaGlvlseyefsnklsek....lesfre...glfnplfFvlvGlsldlkvlnnhlsvlilvllilvai 303
                                       +vsg+++++ aGl++++y++  ++s +    l  f+    +++n ++F+l+G+ +  + ++  ++    +l+i v+i
  gi|488601447|ref|YP_007907918.1| 234 HVSGVIAVVTAGLIIGNYGRLFSMSPStriaLTDFWAlfvFIVNSIVFLLIGIDVSGEKIF--VYSMETLLAIPVVI 308
                                       *******************999999999999*************************77775..77777777777777 PP

                                       HTHHHHHHHHHTTTX.....SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHHHHHHHH CS
                    Na_H_Exchanger 304 llgrilavflllrll.....glslrealiigfgglqrgavalalaalgpalgllarel.yallivvvlftvlvqGls 374
                                        +gr+lav++ll l+     +++ r+++i+++ggl  g++ +ala+++ +   + r++  +++++vvlf+++vqGls
  gi|488601447|ref|YP_007907918.1| 309 -AGRALAVYPLLTLTdkiseRIPARWKHIVFWGGL-HGTIPVALALSLSDI--PHRDMiASMTFGVVLFSLIVQGLS 381
                                       .9*****************99**************.***********9995..************************ PP

                                       HHHHHH CS
                    Na_H_Exchanger 375 lkpllk 380
                                       l  ++k
  gi|488601447|ref|YP_007907918.1| 382 LEYIVK 387
                                       *99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1113  (0.0620782); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3143.05
//
Query:       gi|488601448|ref|YP_007907919.1|  [L=425]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   79.1   0.4    1.5e-21   76.1   0.1    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.7e-19   70.2   0.2    3.8e-19   69.1   0.2    1.6  1  OrfB_IS605      Probable transposase
     0.0015   18.0   0.6     0.0015   18.0   0.6    1.9  2  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.0   0.2      0.028   13.8   0.2    1.6  1  Vps36-NZF-N     Vacuolar protein sorting 36 NZF-N zinc-finger
        0.1   12.4   0.2        0.2   11.4   0.2    1.4  1  AAA_lid_11      Dynein heavy chain AAA lid domain
       0.11   12.9   0.2        0.6   10.4   0.1    2.2  2  zf-C2H2_8       C2H2-type zinc ribbon
       0.12   13.0   1.7       0.18   12.4   0.3    2.0  2  RPA_interact_C  Replication protein A interacting C-terminal
       0.23   11.1   3.2       0.19   11.4   1.2    1.8  2  TackOD1         Thaumarchaeal output domain 1
       0.62   10.2   4.2       0.36   10.9   1.8    1.9  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres


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 ?    0.0   0.0      0.41   8.1e+02      13      29 ..     232     248 ..     221     263 .. 0.64
   2 !   76.1   0.1   7.5e-25   1.5e-21       1      67 [.     312     377 ..     312     379 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.41
                    OrfB_Zn_ribbon  13 keyGikveevnpayTSk 29 
                                        +   ++++vn  +TSk
  gi|488601448|ref|YP_007907919.1| 232 ARCQSHLKQVNNKNTSK 248
                                       33444455666666665 PP

  == domain 2  score: 76.1 bits;  conditional E-value: 7.5e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       f+ ++e+l+  a+++Gikv+ v++ayTS++C+ C skn + +++r+fkC nCg++a+rDv++++Ni+
  gi|488601448|ref|YP_007907919.1| 312 FGYIMERLRTTAENFGIKVKPVDEAYTSSECPWCHSKNVK-KHKRLFKCLNCGVKAHRDVVGVLNIA 377
                                       78899***********************************.*************************8 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.2   1.9e-22   3.8e-19       4     119 ..     179     292 ..     176     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.9e-22
                        OrfB_IS605   4 vevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrklar 79 
                                       vev  e ++++++k+a  DlG+ n++t   e +++ + ++g++l +d  y++k+ia++qs lk+ +n k +s++l+r
  gi|488601448|ref|YP_007907919.1| 179 VEV--EVEEVRSTKRAYADLGVINIITACIEGERQpIAFSGKPLLADWWYWSKKIARCQSHLKQVNN-KNTSKRLKR 252
                                       444..468999**********9988876666655559****************************99.********* PP

                        OrfB_IS605  80 lhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                       l+rkr+rr +h ++ ++ + ++ ++++ v+++++g+ + i
  gi|488601448|ref|YP_007907919.1| 253 LYRKRKRRFRHNINTIVYRFVRLCHAKSVGEIVIGDITHI 292
                                       ***********************************98865 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 !   18.0   0.6   7.5e-07    0.0015       1      33 [.       3      36 ..       1      45 [. 0.92
   2 ?   -3.7   0.2       4.3   8.6e+03      29      44 ..     225     240 ..     225     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.5e-07
                    HTH_OrfB_IS605  1 M.vlkaykyrlyPTpeQeeklartfGcvRfVYNk 33
                                      M v++  k+rl PT++Qe  l   ++++ + +N+
  gi|488601448|ref|YP_007907919.1|  3 MkVRRVNKFRLRPTKKQEKVLFSLCEMSAVLWNR 36
                                      6889999**************************7 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.3
                    HTH_OrfB_IS605  29 fVYNkaLaerkeayee 44 
                                       + + k +a+++ + ++
  gi|488601448|ref|YP_007907919.1| 225 WYWSKKIARCQSHLKQ 240
                                       5688889999988776 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.4e-05     0.028      19      48 ..     349     371 ..     337     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                       Vps36-NZF-N  19 NevpsnfdpnastplPpClaCGvkpdleli 48 
                                       N       +++++ l +Cl+CGvk+ ++++
  gi|488601448|ref|YP_007907919.1| 349 N-------VKKHKRLFKCLNCGVKAHRDVV 371
                                       3.......25689999*********99976 PP

>> AAA_lid_11  Dynein heavy chain AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2    0.0001       0.2      23      78 ..      15      78 ..       3      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                      ....HHHHHHHHHHHHHHHHHGGGGTT........TS-SS-----HHHHHHHHHHHHHHHHHCS CS
                        AAA_lid_11 23 keeefkkllfsLcffHavvqeRrkFgp........lGwnipYeFnesdleisvevlkmyldeye 78
                                       +++ +k+lfsLc + av+ +R +++         + wn   e+ne    +   + ++++++++
  gi|488601448|ref|YP_007907919.1| 15 PTKKQEKVLFSLCEMSAVLWNRVNYKRrqsffageIDWNTEEEYNEFKRILGSATTQQIIRKND 78
                                      456789*******************996666655569*******99888877777777776655 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.1   2.3e+03      72      90 ..      86     104 ..      66     107 .. 0.81
   2 ?   10.4   0.1    0.0003       0.6      36      82 ..     326     370 ..     314     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                         zf-C2H2_8  72 cllrfrthrslfkhlhvcs 90 
                                        llr++ +  l kh+h +s
  gi|488601448|ref|YP_007907919.1|  86 KLLRLKQQDKLPKHVHKVS 104
                                       5899999999****99765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0003
                         zf-C2H2_8  36 frcstascaetfpsmqelvahtklhykpnryfkcencllrfrthrsl 82 
                                       f    + + e++ s +   +h+k   k +r fkc nc +  ++hr +
  gi|488601448|ref|YP_007907919.1| 326 FGIKVKPVDEAYTSSECPWCHSKNVKKHKRLFKCLNCGV--KAHRDV 370
                                       55566667788999999999*****************76..466665 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 ?   -2.5   0.1         4   7.9e+03      21      40 ..     234     253 ..     230     268 .. 0.63
   2 ?   12.4   0.3   9.3e-05      0.18       2      27 ..     342     368 ..     341     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
                    RPA_interact_C  21 Cglrletseesltleelkrr 40 
                                       C+ +l++ +++ t ++lkr+
  gi|488601448|ref|YP_007907919.1| 234 CQSHLKQVNNKNTSKRLKRL 253
                                       55666665555555555544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.3e-05
                    RPA_interact_C   2 CPvCkkrklketsevifCe.Cglrlet 27 
                                       CP C+++++k+++++  C  Cg++ ++
  gi|488601448|ref|YP_007907919.1| 342 CPWCHSKNVKKHKRLFKCLnCGVKAHR 368
                                       ******************88**98766 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.3   6.6e+03       9      66 ..      18      75 ..      14      80 .. 0.63
   2 ?   11.4   1.2   9.3e-05      0.19      88     112 ..     340     365 ..     333     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.3
                           TackOD1  9 teekllayllsrdeeklepvldpkskelysypllealskeke.eseelleelvkrglle 66
                                      ++ek+l  l + +   l +++++k ++ +    ++  ++e+  e +++l + +++++++
  gi|488601448|ref|YP_007907919.1| 18 KQEKVLFSLCEMS-AVLWNRVNYKRRQSFFAGEIDWNTEEEYnEFKRILGSATTQQIIR 75
                                      5566666666666.677777777777766666666655555556777777777777766 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.3e-05
                           TackOD1  88 evCpkCkSidieeqe.lihhftCgnv 112
                                        +Cp C+S ++++++ l+++ +Cg  
  gi|488601448|ref|YP_007907919.1| 340 SECPWCHSKNVKKHKrLFKCLNCGVK 365
                                       68*********9865288******75 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.4   1.3e+04      45      52 ..     236     243 ..     232     244 .. 0.75
   2 ?   10.9   1.8   0.00018      0.36       2      27 ..     342     367 ..     341     370 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.4
                          zf-Mss51  45 dtLrqvne 52 
                                       + L+qvn+
  gi|488601448|ref|YP_007907919.1| 236 SHLKQVNN 243
                                       57999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00018
                          zf-Mss51   2 CPvpkhkqtapkhvdfeCpdCGipty 27 
                                       CP +++k+ ++++  f+C +CG+  +
  gi|488601448|ref|YP_007907919.1| 342 CPWCHSKNVKKHKRLFKCLNCGVKAH 367
                                       ********9999999*******9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); 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: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2405.64
//
Query:       gi|488601449|ref|YP_007907920.1|  [L=402]
Description: arsenite efflux ATP-binding protein ArsA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-95  318.8   0.0      4e-95  318.5   0.0    1.0  1  ArsA_ATPase  Anion-transporting ATPase
    1.9e-17   62.5   0.0    3.9e-17   61.5   0.0    1.6  1  ArsA_HSP20   HSP20-like domain found in ArsA
    2.6e-12   47.0   0.0    5.6e-12   45.9   0.0    1.5  1  AAA_31       AAA domain
    5.2e-10   39.5   0.0    7.5e-09   35.7   0.0    2.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.3e-05   24.8   0.4    4.5e-05   23.0   0.4    1.9  2  ParA         NUBPL iron-transfer P-loop NTPase
    0.00026   20.5   0.1    0.00065   19.2   0.0    1.7  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00029   20.8   0.0    0.00059   19.8   0.0    1.5  1  DUF2100      Uncharacterized protein conserved in archaea (DU
    0.00034   20.1   0.0    0.00067   19.2   0.0    1.4  1  PhoH         PhoH-like protein
     0.0017   17.7   0.3     0.0039   16.6   0.1    1.7  2  ATPase       KaiC
     0.0023   17.6   1.1     0.0046   16.6   1.1    1.5  1  SRP54        SRP54-type protein, GTPase domain
     0.0067   15.9   0.0      0.012   15.1   0.0    1.5  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0092   15.2   0.3      0.019   14.1   0.3    1.5  1  NB-ARC       NB-ARC domain
       0.01   14.9   0.2      0.018   14.0   0.2    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.018   14.8   0.0    1.4  1  AAA_24       AAA domain
      0.023   14.3   0.3      0.042   13.4   0.3    1.3  1  AAA_25       AAA domain
      0.035   14.5   0.1      0.084   13.3   0.1    1.6  1  AAA_16       AAA ATPase domain
      0.093   13.1   0.0       0.28   11.6   0.0    1.9  1  AAA          ATPase family associated with various cellular a
       0.15   12.0   0.1       0.24   11.3   0.1    1.3  1  APS_kinase   Adenylylsulphate kinase


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 !  318.5   0.0     4e-98     4e-95       1     304 [.      22     319 ..      22     320 .. 0.96

  Alignments for each domain:
  == domain 1  score: 318.5 bits;  conditional E-value: 4e-98
                                       -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHH CS
                       ArsA_ATPase   1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeak 77 
                                       +++il++GKGGVGKttv++ata+k s+ gkk+l+istDPAhslsDsf  +lg eptkv++NL+a+E+++e ele+ +
  gi|488601449|ref|YP_007907920.1|  22 TRIILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTDPAHSLSDSFGIELGPEPTKVRDNLFAMEVNIEYELEKHW 98 
                                       699************************************************************************** PP

                                       CCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHH CS
                       ArsA_ATPase  78 qevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevlekllek 154
                                       +  +++ + ++++++ +dv+aeela++PG de++s+ +ll+ +++ +y+v++lD aPTG+tlrlls+pe+ ++++++
  gi|488601449|ref|YP_007907920.1|  99 ETIKEYLKIFFQSQGIDDVVAEELAIFPGFDELASLLHLLDNYEKGTYEVIILDCAPTGETLRLLSVPEIAKWYMNR 175
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHCCCSHCHHHHHH..HHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHH CS
                       ArsA_ATPase 155 lvklkeklsplakqlvkllglggvsie..ealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaike 229
                                       ++ +++ l +++k++ +   + +v ++  e+l+++++ + +i +++eil+ p+ ts+r+V++pEk++++E+eRa+++
  gi|488601449|ref|YP_007907920.1| 176 FFGIERRLLKIVKPIAEP--VLDVPLPseEVLDKIQDLYMRIGRLKEILESPQ-TSVRIVMNPEKMVIRESERAFTY 249
                                       ***************886..555555555********************9986.7********************** PP

                                       HHHTT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHHC CS
                       ArsA_ATPase 230 LkkygikvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklselly 304
                                       L+++g +vdavi+Nk++pee  +   +++++ +iqk+ylkei+e f +++ + l++ +eEvvG   l+++++ ly
  gi|488601449|ref|YP_007907920.1| 250 LNLFGYRVDAVIINKYIPEEAGD---YFKKWIEIQKEYLKEIYERF-PVKKFMLKFKSEEVVGS-LLDEIADELY 319
                                       ********************995...********************.788999**********5.7999999888 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 !   61.5   0.0   3.9e-20   3.9e-17       2      63 .]     340     401 ..     339     401 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 3.9e-20
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkignfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       +++ l+++ Pfv+ke+i+l ++g+eL++ +g+++R i LP++la ke++sAkf+ g+ +I+F
  gi|488601449|ref|YP_007907920.1| 340 GDFYLSIKAPFVKKEDIKLLKRGEELIVVAGQWKRIIYLPQSLALKEPVSAKFMSGEIRIKF 401
                                       7889********************************************************99 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   5.6e-15   5.6e-12       4     129 ..      24     157 ..      22     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 5.6e-15
                            AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne....iektlyevli.eeknikeaiik 75 
                                       I +   KGGvGKTT + + a   +klgkk+L++  Dp  +++ ++gie       +  +l+ + +  e+++++    
  gi|488601449|ref|YP_007907920.1|  24 IILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTDPAHSLSDSFGIELGPeptkVRDNLFAMEVnIEYELEKHWE- 99 
                                       445678**************************************99986662222455555554334444444444. PP

                            AAA_31  76 tkvenldlipssid...Laeaeielvelekkeeilkellekvkde.YDyiiiDcpPsL 129
                                       t  e l++   s     +++ e  ++   ++   l +ll++ ++  Y +ii+Dc P+ 
  gi|488601449|ref|YP_007907920.1| 100 TIKEYLKIFFQSQGiddVVAEELAIFPGFDELASLLHLLDNYEKGtYEVIILDCAPTG 157
                                       3344456655544400244445555555556667888898887644**********85 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   7.6e-12   7.5e-09       1     109 [.      24     285 ..      24     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 7.6e-12
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i++  +kGGvGKTt+a + a+  ++ g+++l + +Dp  +++   +g e   ep                       
  gi|488601449|ref|YP_007907920.1|  24 IILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTDPAHSLSD-SFGIELGPEPtkvrdnlfamevnieyelekhwe 99 
                                       56788***********************************999.88888888888888******************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|488601449|ref|YP_007907920.1| 100 tikeylkiffqsqgiddvvaeelaifpgfdelasllhlldnyekgtyeviildcaptgetlrllsvpeiakwymnrf 176
                                       ****************************************************9999999999999999999999999 PP

                                       .................................................................CCHCCCHHHHHH CS
                                       .................................................................xxxxxxxxxxxx RF
                              CbiA  55 .................................................................dlkrllelleal 66 
                                                                                                                 e  
  gi|488601449|ref|YP_007907920.1| 177 fgierrllkivkpiaepvldvplpseevldkiqdlymrigrlkeilespqtsvrivmnpekmvirES-------E-- 244
                                       9999999999999999999999999999999999999888777777777755555443332222211.......2.. PP

                                       CHCHHHH...........EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EE CS
                                       xxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  67 gkkkall.........lkiagvvlnrvdgeneetllkealeelkqrygvpvl 109
                                                        ++  v++n++ +e++    k+ +e +k     + l
  gi|488601449|ref|YP_007907920.1| 245 ------RaftylnlfgYRVDAVIINKYIPEEAGDYFKKWIEIQK-----EYL 285
                                       ......13444444478888999999999988888888887754.....333 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.4   4.5e-08   4.5e-05       3      52 ..      21      69 ..      19     162 .. 0.78
   2 ?   -1.6   0.0       1.5   1.5e+03     136     173 ..     226     263 ..     218     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-08
                              ParA  3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllg 52
                                      k+ i+   gKGGVGK+tva+  A++ +k g+k+ ++ +D   +s+ + +g
  gi|488601449|ref|YP_007907920.1| 21 KTRIILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTDP-AHSLSDSFG 69
                                      5678899**************************9999884.355555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                              ParA 136 lagaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                        + + iV  p+++ + + ++a++ ++    +v +v+ N
  gi|488601449|ref|YP_007907920.1| 226 QTSVRIVMNPEKMVIRESERAFTYLNLFGYRVDAVIIN 263
                                       566679999*********99999999999999888877 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 !   19.2   0.0   6.5e-07   0.00065       2      40 ..      24      62 ..      23      94 .. 0.90
   2 ?   -3.2   0.0       4.4   4.3e+03     222     259 ..     296     333 ..     284     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.5e-07
                         Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                       i + GkGG+Gk+t ++ +++  ++ gkk li+  DP +
  gi|488601449|ref|YP_007907920.1| 24 IILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTDPAH 62
                                      67789********************************86 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                         Fer4_NifH 222 ktvieyapeseqakeyrelarkilenkklviPkplsed 259
                                       k + ++++e+ ++    e+a+++++ +   + ++++  
  gi|488601449|ref|YP_007907920.1| 296 KFMLKFKSEEVVGSLLDEIADELYDSDPSQVFTEMKPM 333
                                       56677888888889999999999998877777776655 PP

>> DUF2100  Uncharacterized protein conserved in archaea (DUF2100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.9e-07   0.00059     145     208 ..     258     321 ..     253     336 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.9e-07
                                       HHHTT..XXXSTTTTTSHHHHHHHHHHHHHHHHHHXXSXEEEEXS..SHHHHHHHHHHHHHHXX CS
                           DUF2100 145 DmkeiNPkipekalkgieKkveivkeeieklikklkpekvvvvveeddkadellakrAeelyna 208
                                       D  +iN  ipe+a    +K +ei ke ++++ +++  +k ++  + ++ ++ ll + A+ely+ 
  gi|488601449|ref|YP_007907920.1| 258 DAVIINKYIPEEAGDYFKKWIEIQKEYLKEIYERFPVKKFMLKFKSEEVVGSLLDEIADELYDS 321
                                       6679*******************************99*************************98 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   6.7e-07   0.00067      18      80 ..      21      83 ..      10     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.7e-07
                                      H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTT CS
                              PhoH 18 kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdleekvdpyl 80
                                      k  i+  +G+ G GKt +a a+a++  k +k + ii t pa +  ++ G+  g + +kv+  l
  gi|488601449|ref|YP_007907920.1| 21 KTRIILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTDPAHSLSDSFGIELGPEPTKVRDNL 83
                                      5679999***********************************997777766666666665444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.9e-06    0.0039      17      80 ..      20      82 ..      13     119 .. 0.76
   2 ?   -2.7   0.0         3     3e+03     166     203 ..     239     281 ..     215     283 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.9e-06
                            ATPase 17 pegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGwdlekleee 80
                                      p+ r++l tG+ G GKt++a   +ik  +k g+++++++++  a++l  ++  +lG + +k++++
  gi|488601449|ref|YP_007907920.1| 20 PKTRIILFTGKGGVGKTTVASATAIKT-SKLGKKTLIISTDP-AHSLSDSFGiELGPEPTKVRDN 82
                                      789************************.556********984.4555555544555555555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3
                            ATPase 166 s...seeaaggygveefivdgvivLdlkeiee..elvRtleiv 203
                                       +   se+a++  ++  + vd vi+ ++  +e    +++ +ei 
  gi|488601449|ref|YP_007907920.1| 239 VireSERAFTYLNLFGYRVDAVIINKYIPEEAgdYFKKWIEIQ 281
                                       1444778888888888888888876654333344566666665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.1   4.6e-06    0.0046       2      38 ..      23      59 ..      22      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-06
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      ++il+ G  G+GKTt ++  a + +k gkk+l++++D
  gi|488601449|ref|YP_007907920.1| 23 RIILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTD 59
                                      589********************************99 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.012       6      55 ..      27      75 ..      22     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                          CBP_BcsQ  6 lqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqr 55
                                      ++G +GGvG+t++++a a+   +lg++ l+i + p+  L  +F +++  +
  gi|488601449|ref|YP_007907920.1| 27 FTG-KGGVGKTTVASATAIKTSKLGKKTLIISTDPAHSLSDSFGIELGPE 75
                                      444.8**********************************99998876554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.3     2e-05     0.019      12      46 ..      14      48 ..       6      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                                      HHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC 12 LlekdelqslvvalvGmgGvGKttlakqilnksde 46
                                       + kd++++ ++ + G+gGvGKtt+a+    k ++
  gi|488601449|ref|YP_007907920.1| 14 SDSKDKPKTRIILFTGKGGVGKTTVASATAIKTSK 48
                                      5668899999***************9976655555 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 !   14.0   0.2   1.8e-05     0.018      28      70 ..      21      63 ..      15      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      +++ + +tG  G+Gk t+ +a +++  + Gk+  +++ DP+ +
  gi|488601449|ref|YP_007907920.1| 21 KTRIILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTDPAHS 63
                                      5677889*********************************865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.8e-05     0.018       5      38 ..      25      64 ..      21     156 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                            AAA_24  5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksl 38
                                      il +G+ g+GKTt+a+         g+k+l+i t+  ++sl
  gi|488601449|ref|YP_007907920.1| 25 ILFTGKGGVGKTTVASATaiktsklGKKTLIISTDP-AHSL 64
                                      7889************999***************97.3333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   4.2e-05     0.042      31      63 ..      20      53 ..      17      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                            AAA_25 31 pagelallaGapgtGKttlaldlalava.tGkpw 63
                                      p+  ++l++G +g+GKtt+a+  a++++ +Gk+ 
  gi|488601449|ref|YP_007907920.1| 20 PKTRIILFTGKGGVGKTTVASATAIKTSkLGKKT 53
                                      6678899******************999888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.4e-05     0.084      22      44 ..      20      42 ..      12      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrel 44
                                      + ++++l++G  GvGK++++ + 
  gi|488601449|ref|YP_007907920.1| 20 PKTRIILFTGKGGVGKTTVASAT 42
                                      4459***************9654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.28       1      22 [.      25      46 ..      25     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      +l++G  G+GKT++a+a a ++
  gi|488601449|ref|YP_007907920.1| 25 ILFTGKGGVGKTTVASATAIKT 46
                                      699**************99775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00024      0.24       3      39 ..      23      59 ..      21      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                       ++++tG  g GK+t+a a + k  + g+++ ++  d
  gi|488601449|ref|YP_007907920.1| 23 RIILFTGKGGVGKTTVASATAIKTSKLGKKTLIISTD 59
                                      689*****************99999999998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 2253.70
//
Query:       gi|488601450|ref|YP_007907921.1|  [L=65]
Description: hypothetical protein Asulf_01962 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.4   0.0      0.051   13.2   0.0    1.2  1  Prok_Ub   Prokaryotic Ubiquitin
       0.15   13.1   0.8       0.19   12.7   0.8    1.3  1  PdaC      Deacetylase PdaC


Domain annotation for each model (and alignments):
>> Prok_Ub  Prokaryotic Ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.7e-06     0.051      13      50 ..       3      41 ..       1      55 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-06
                           Prok_Ub 13 girLaDp.npklspeeVrdfYaatYPeLttAevegpevk 50
                                      +i+++ p   +  peeV+++  + Y eL+ A  +g e+k
  gi|488601450|ref|YP_007907921.1|  3 EIKIKVPdIDEILPEEVMKHLLQSYKELLMAFKKGIEYK 41
                                      5555555337899****************9977776666 PP

>> PdaC  Deacetylase PdaC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   2.1e-05      0.19       9      58 ..       3      53 ..       1      65 [] 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                      EEEEEEEEE-S-S-HHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHTT-- CS
                              PdaC  9 eikikyPvisglknkevqdkinkkiekdadkflkeyekeake.....eakkndfp 58
                                      eikik+P i ++  +ev +++ +++++ +++f k +e++ +      e    ++ 
  gi|488601450|ref|YP_007907921.1|  3 EIKIKVPDIDEILPEEVMKHLLQSYKELLMAFKKGIEYKIERidrieE----KMT 53
                                      69***********************99999999999777666754431....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1267  (0.0706676); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 386.13
//
Query:       gi|488601451|ref|YP_007907922.1|  [L=309]
Description: hypothetical protein Asulf_01963 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   27.4   0.0    5.9e-06   26.1   0.0    1.7  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    0.00011   21.8   0.0     0.0006   19.4   0.0    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.044   13.8   1.1        2.4    8.1   1.6    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
      0.073   13.0   0.0       0.17   11.8   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.3e-09   5.9e-06       7      43 ..     248     284 ..     242     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-09
                             RMMBL   7 rieeidfSgHadknellelirklkprnvilvHGeeea 43 
                                       ri  i  S H d+n+l+++i++ +p++vi+ HG + +
  gi|488601451|ref|YP_007907922.1| 248 RIPRIVISDHLDFNGLIDMIEHCNPEHVIFYHGKPSE 284
                                       566677899************************9865 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.3e-07    0.0006      35     170 ..      54     159 ..      50     173 .. 0.89
   2 ?   -0.4   0.0      0.15   6.8e+02     178     200 ..     257     279 ..     242     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-07
                                       E-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE- CS
                     Lactamase_B_2  35 llthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatpar 111
                                       l+thaH DH+ g   l    p   + +a++++++ l+      + ++        +++g++++l+  gl+i++ p +
  gi|488601451|ref|YP_007907922.1|  54 LITHAHSDHY-GQYNLDN--P---NAIASQETARMLSVLNGKRFIGRT-------FEIGKEIKLN--GLRIKTYPTE 115
                                       89********.8788888..4...579************888887777.......*********9..89******** PP

                                       EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTT CS
                     Lactamase_B_2 112 hksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayedd 170
                                       h  g           +++ie ++ r++ +gD++ +      +l  +d+l+ ++t+ ++d
  gi|488601451|ref|YP_007907922.1| 116 HIFGS---------SAFLIE-SESRILITGDVKDYR-----KLPRCDVLITEATYGKPD 159
                                       ****9.........99****.99**********555.....788999999999987776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.15
                                       ---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 178 HltpeeaveaaadlgakrlvliH 200
                                       Hl+ ++ ++++++++++ +++ H
  gi|488601451|ref|YP_007907922.1| 257 HLDFNGLIDMIEHCNPEHVIFYH 279
                                       77777777777777777777777 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.6   0.00054       2.4      49      59 ..      54      64 ..      54      66 .. 0.93
   2 ?    2.7   0.0     0.024   1.1e+02     107     162 ..      93     148 ..      77     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00054
                                      E-SBSSHHHHT CS
                       Lactamase_B 49 ilTHlHlDHiG 59
                                      ++TH+H+DH+G
  gi|488601451|ref|YP_007907922.1| 54 LITHAHSDHYG 64
                                      69********9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.024
                                       EEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 107 dvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                       +++ e++ ++ + +++ +++++    ++++ +   + ++l+tGD+   ++ +r d 
  gi|488601451|ref|YP_007907922.1|  93 GRTFEIGKEIKLNGLRIKTYPTEHIFGSSAFLIESESRILITGDVKDYRKLPRCDV 148
                                       67778888999999999999999999999999999*********876666666665 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 ?   11.8   0.0   3.7e-05      0.17      39      85 ..      52     116 ..      35     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                     Lactamase_B_3  39 lvlisqaledHahletlkql........aenvkvlee.................geslevggleiravatsh 85 
                                       + li++a++dH+   +l +         a       +                 g++++++gl+i++ +t+h
  gi|488601451|ref|YP_007907922.1|  52 INLITHAHSDHYGQYNLDNPnaiasqetA-------RmlsvlngkrfigrtfeiGKEIKLNGLRIKTYPTEH 116
                                       559**********9999984444554443.......044445558888777777788999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.32s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1705.74
//
Query:       gi|488601452|ref|YP_007907923.1|  [L=257]
Description: NAD-dependent protein deacetylase, SIR2 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-55  187.8   0.0      2e-55  187.4   0.0    1.1  1  SIR2          Sir2 family
     0.0009   19.0   0.0       0.38   10.5   0.0    2.3  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.4   0.0   2.2e-59     2e-55       1     177 []      27     204 ..      27     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 2.2e-59
                                       -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEE CS
                              SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllr 77 
                                       GAGiS+esGip+fR+k+Gl++k+++eela+pea+++++ lv+e +y ++++l+  + epn aH+a++kle++g  ++
  gi|488601452|ref|YP_007907923.1|  27 GAGISAESGIPTFRGKDGLWNKYRPEELATPEAFRRNPALVWE-WYAWRMNLVF-SREPNYAHRAIAKLEDTGYIKH 101
                                       9******************************************.****999998.79******************** PP

                                       EEES-SSSHHHHTT-SSEEETTEEEEEEEETT.TSBEEECCGGHCHHH.CCTT.B-TTTCCBEEEEE--CTSB-S.H CS
                              SIR2  78 liTQNiDgLekkaGskkvvelHGslakakcvk.cekkldkeelqeeie.aekvpecekcgkllkpdvvfFGealp.d 151
                                       +iTQN+D+L+++aGs++v++lHG+l+++kc + c ++   ++l +  +  e++p+c++c +ll+p vv+FGe l+ d
  gi|488601452|ref|YP_007907923.1| 102 VITQNVDDLHERAGSRNVTHLHGKLKEVKCWNgCIQIALPSDLVDLSRiPEELPKCPECSGLLRPAVVWFGERLDpD 178
                                       ******************************86477776667777666647889**********************9* PP

                                       HHHHHHHHHHH-SEEEEES--STSTT CS
                              SIR2 152 klkkliekveeadlllviGtSlkVap 177
                                        l + ++ +e+ dl+lv+GtS+ V+p
  gi|488601452|ref|YP_007907923.1| 179 VLMRSFDLAEKSDLILVVGTSAVVQP 204
                                       ************************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 !    6.2   0.0   0.00091       8.1       2      25 ..      10      33 ..       9      40 .. 0.88
   2 !   10.5   0.0   4.3e-05      0.38      74     114 ..     186     227 ..     182     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00091
                                      HHHHHHHHH-SSEEEEE-CHHCHT CS
                      TPP_enzyme_M  2 ekaaellkaakrpvilvGggvars 25
                                      ++++++lk++k  ++l G g++ +
  gi|488601452|ref|YP_007907923.1| 10 NEVVDMLKESKHAIVLTGAGISAE 33
                                      689*****************9865 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4.3e-05
                                       HHHH-SEEEEES-SSSTCCCTTTTT.TTTTT-.EEEEEESSCC CS
                      TPP_enzyme_M  74 aleeaDlvlalGarfddirttgsep.efapea.kiihididpa 114
                                       ++e++Dl+l++G+     + ++s p   ++ + kii+i++d++
  gi|488601452|ref|YP_007907923.1| 186 LAEKSDLILVVGTSAVV-QPAASVPmMTKRSGgKIIEINPDET 227
                                       5799********98644.566678855555568******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1562.73
//
Query:       gi|488601453|ref|YP_007907924.1|  [L=134]
Description: hypothetical protein Asulf_01965 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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    6.4  14.2        3.9    6.1  14.2    1.0  1  Presenilin    Presenilin
        3.2    5.9  17.5        3.6    5.7  17.5    1.0  1  DUF2070       Predicted membrane protein (DUF2070)
        5.7    6.8   4.7          1    9.2   1.0    1.7  2  Myc_target_1  Myc target protein 1


Domain annotation for each model (and alignments):
>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  14.2   0.00066       3.9      70     168 ..      17     126 ..       7     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00066
                        Presenilin  70 vivvvtfllvlLykyrcykvikg...wlilsslllLflvsglllaevlkaynipldyitl..llllwnfg......v 135
                                       ++ +++ ++++++ y  y+++++   ++ ls +ll f +++++++++l++  + + y+ +  +ll   f+      v
  gi|488601453|ref|YP_007907924.1|  17 ALSLLSGFIIFFWGYGLYEILTTfqiYFRLSYILLAFTIAFIFFTAFLEHRGVEIPYLFVssALLASLFTfiglciV 93 
                                       566778889999999999998652228999******************99955555543311333233331112235 PP

                        Presenilin 136 vGviaifwkgplllqqaYlilisalmAlvfiky 168
                                        Gvi+i+ + p + +   + +is+++ ++fik+
  gi|488601453|ref|YP_007907924.1|  94 NGVISIYKSFPPIDNFLIMFSISIIVGFIFIKM 126
                                       699********9988777888999******995 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  17.5   0.00061       3.6      20     119 ..      14     128 ..       3     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00061
                           DUF2070  20 liillalligllaflssk...........lfgillfglpalvaflltlpvlrilggr...ltykrslflallteliv 82 
                                       + i l+ll g++ f  +            +f++ +++l + +af++++ +l+  g     l ++ +l+ +l+t + +
  gi|488601453|ref|YP_007907924.1|  14 INIALSLLSGFIIFFWGYglyeilttfqiYFRLSYILLAFTIAFIFFTAFLEHRGVEipyLFVSSALLASLFTFIGL 90 
                                       444444444444444444555588899999***********************999975555555577788888888 PP

                           DUF2070  83 viisllaillsall.qalvllalvlslalvfalrllvl 119
                                       +i+  + +++  +   + +l ++ +s+++ f++  +v+
  gi|488601453|ref|YP_007907924.1|  91 CIVNGVISIYKSFPpIDNFLIMFSISIIVGFIFIKMVF 128
                                       88777777777655877777777777777777776665 PP

>> Myc_target_1  Myc target protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       1.4   8.7e+03      25      40 ..      12      27 ..       7      30 .. 0.66
   2 ?    9.2   1.0   0.00017         1      18      41 ..     106     129 ..      93     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.4
                      Myc_target_1 25 FcvSmvvGLllgaliy 40
                                      F + +++ Ll g +i+
  gi|488601453|ref|YP_007907924.1| 12 FYINIALSLLSGFIIF 27
                                      6666666666666665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00017
                      Myc_target_1  18 ledlilaFcvSmvvGLllgaliyv 41 
                                       +++ ++ F++S++vG++   ++++
  gi|488601453|ref|YP_007907924.1| 106 IDNFLIMFSISIIVGFIFIKMVFT 129
                                       78999***************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 744.72
//
Query:       gi|488601454|ref|YP_007907925.1|  [L=314]
Description: methenyltetrahydromethanopterin cyclohydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-139  463.2   0.1   4.7e-139  463.0   0.1    1.0  1  MCH       Cyclohydrolase (MCH)


Domain annotation for each model (and alignments):
>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.0   0.1  2.6e-143  4.7e-139       1     311 []       3     310 ..       3     310 .. 1.00

  Alignments for each domain:
  == domain 1  score: 463.0 bits;  conditional E-value: 2.6e-143
                                       -HHHHHHHHHHHHHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEEEEEETTEEEEEEE CS
                               MCH   1 SvnelalelveellekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevslelsevkgaklpave 77 
                                       S+ne+a+++ve++l+++eelrie+++lengatviD+Gv+++Gg+eAG+l+++ic+ggLae+++ +++++++++++++
  gi|488601454|ref|YP_007907925.1|   3 SINEMAMDIVEDMLDFEEELRIESKKLENGATVIDCGVNVPGGYEAGILYTQICMGGLAEIEIVTDTINDVPFAFIT 79 
                                       8**************************************************************************** PP

                                       EEESSHHHHHTTTTS--EEEEETTEEEEEESTTHHHHTS.HHHHHHHT-----S-EEEEEESSS---HHHHHHHHHH CS
                               MCH  78 vstdhPvlacLasqkAgWelsaekffalgsGPaRalaak.eelfeelgyedeadaavlvlesdklPdeevvekvaee 153
                                        +tdhP++acL+sqkAgW++s++k+fa+gsGPaRala k ++++e+++y+d+++ av++le++klP+eev+e +a+e
  gi|488601454|ref|YP_007907925.1|  80 EYTDHPAVACLGSQKAGWAISVGKYFAMGSGPARALALKpKKTYEKIEYQDDSEYAVIALEASKLPNEEVMEFIAKE 156
                                       ***************************************************************************** PP

                                       HTS-GGGEEEEEE-SSSHHHHHHHHTTHHHHHHHHHHHTT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH- CS
                               MCH 154 cgvepenvtllvaptaSlaGsvqvaaRvvevalhkleelgfdlekivsavgtaPiapvakdelkamgrtndailYgg 230
                                       c+v+penv+++vaptaS++Gsvq+++R+ve+a++k++e+g+d++ ivs++g++Piap+ +d+lkamg+tnd+++Y+g
  gi|488601454|ref|YP_007907925.1| 157 CDVDPENVYAVVAPTASIVGSVQISGRIVETAIYKMTEIGYDPKLIVSGAGRCPIAPIVGDDLKAMGSTNDSMMYYG 233
                                       ***************************************************************************** PP

                                       EEEEEES...TTHHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---HHHH CS
                               MCH 231 rvhltveaedeeaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelneell 307
                                       +v ltv+    e+++++k++ps++skdygkpF+eifk+a++dfykid++lF+pA++ vndl+tgkt+++G+ln+e+l
  gi|488601454|ref|YP_007907925.1| 234 SVFLTVK----EYDEILKNVPSNTSKDYGKPFYEIFKDANFDFYKIDPNLFAPAQIAVNDLSTGKTYVHGKLNAEVL 306
                                       *******....9***************************************************************** PP

                                       HHHT CS
                               MCH 308 aesf 311
                                        +s+
  gi|488601454|ref|YP_007907925.1| 307 FKSY 310
                                       *997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1775.22
//
Query:       gi|488601455|ref|YP_007907926.1|  [L=232]
Description: Metal-dependent hydrolases of the beta-lactamase superfamily III [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-12   46.8   0.0    3.1e-12   46.4   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.1e-07   32.1   0.0    1.4e-07   31.7   0.0    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0085   16.0   0.2        0.1   12.5   0.0    2.2  2  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.034   13.3   0.5       0.22   10.6   0.1    2.0  2  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 !   46.4   0.0     7e-16   3.1e-12      29     201 .]      44     201 ..      26     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 7e-16
                                       .SEEEEE-SS--HHHHGGGGCCCC......C--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-.TTSEEEE CS
                     Lactamase_B_2  29 ppidaVllthaHyDHlaglltlre......lrpkklplyapkgvlavleanfvylaleeepavnvheld.wgesfel 98 
                                       + + a+llth+H DH  ++l + +      + +++ ++++p+g++ ++e+ f      ++ +++++ ++  +e+fe+
  gi|488601455|ref|YP_007907926.1|  44 NNLSAILLTHNHLDHNGDVLAILKsrwlsgI-EERPKIIGPAGTINHIESLFESYPYLRK-KLSFELMEvENEKFEV 118
                                       5899******************999887642.2235699*************99999999.7777777755899*** PP

                                       CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHH CS
                     Lactamase_B_2  99 gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirh 175
                                       +  g+e++a++ +h+ +           +++i+     v+ +gDt  ++e +g   + +++l++++ +    +    
  gi|488601455|ref|YP_007907926.1| 119 D--GFEVEAIATKHSIKS---------TAYLID---SEVLISGDTRAMKEVVG---RECKVLIHEMSLPFGFK---A 175
                                       8..899********9999.........9*****...8**************99...77779999988766656...6 PP

                                       HT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 176 mgHltpeeaveaaadlgakrlvliHi 201
                                         H tpe+  e+++ + a++ +l+Hi
  gi|488601455|ref|YP_007907926.1| 176 VDHTTPENFKEVLDSCTAEKILLTHI 201
                                       78***********************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 !   31.7   0.0   3.2e-11   1.4e-07      35     154 ..      36     152 ..       6     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.2e-11
                                       HHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEET CS
                       Lactamase_B  35 laalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdee 111
                                       l ++g+  ++++a++lTH HlDH G++  + + ++   ++++ +   + +     ++ +++   +++ ++k  + + 
  gi|488601455|ref|YP_007907926.1|  36 LLRIGKLTNNLSAILLTHNHLDHNGDVLAILKSRWLSGIEERPKIIGPAGTINHIESLFES---YPYLRKKLSFELM 109
                                       55677777899******************************************99999987...89999999***** PP

                                       TTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSS CS
                       Lactamase_B 112 eldgnaggrralyvtggpghghghgvveygggkvlftGDalla 154
                                       e + + +++ +++v  + + +++    ++ +  vl++GD+   
  gi|488601455|ref|YP_007907926.1| 110 EVENEKFEVDGFEVEAIATKHSIKSTAYLIDSEVLISGDTRAM 152
                                       ***************************************9765 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 !   12.5   0.0   2.3e-05       0.1      18      86 ..      26     131 ..      18     166 .. 0.74
   2 ?    1.2   0.0     0.066     3e+02      35      68 ..     186     219 ..     170     232 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                     Lactamase_B_3  18 rilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkql...........................aenvkvle 66 
                                       ri+vD + +  l  ++ + +  ++l+++++ dH+    l+ l                           +e +++l+
  gi|488601455|ref|YP_007907926.1|  26 RIAVDVGIGsLLRIGKLTNNLSAILLTHNHLDHNGDV-LAILksrwlsgieerpkiigpagtinhieslFESYPYLR 101
                                       6677766444455666678999***********8643.555567799999777777777666666666655555555 PP

                     Lactamase_B_3  67 e..........geslevggleiravatshd 86 
                                       +           e++ev+g+e++a+at+h 
  gi|488601455|ref|YP_007907926.1| 102 KklsfelmeveNEKFEVDGFEVEAIATKHS 131
                                       58888777777788************9994 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.066
                     Lactamase_B_3  35 eeaDlvlisqaledHahletlkqlaenvkvleeg 68 
                                       e  D  +  + l +H ++++++q++++ ++l+++
  gi|488601455|ref|YP_007907926.1| 186 EVLDSCTAEKILLTHIYPNAMEQIDTILEYLDDE 219
                                       6667777778889999999999997777777653 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   4.9e-05      0.22      76     125 ..      41      91 ..      34      97 .. 0.73
   2 ?    0.7   0.0     0.049   2.2e+02     190     208 ..     125     143 ..      92     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.9e-05
                                       HHHHTEEEEE-S---GGGTHHH..HHHGGGGGS-S.--EEEEE-HHHHHHHH CS
                         PDEase_II  76 eiknniksylItHsHLDHvsgl..vinSaefykaqlkkktivGlpytInalq 125
                                       ++ nn+   l+tH HLDH + +  ++ S      + ++k i+G   tIn ++
  gi|488601455|ref|YP_007907926.1|  41 KLTNNLSAILLTHNHLDHNGDVlaILKSRWLSGIEERPK-IIGPAGTINHIE 91 
                                       5789**************988633566665555443444.568888888775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.049
                                       -TTT--EEEEEEEEEEETT CS
                         PDEase_II 190 likknsevlSsaflftdev 208
                                        i ++  ++S+a+l+  ev
  gi|488601455|ref|YP_007907926.1| 125 AIATKHSIKSTAYLIDSEV 143
                                       5667778999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1275.31
//
Query:       gi|488601456|ref|YP_007907927.1|  [L=388]
Description: 2,3-di-O-geranylgeranylglyceryl phosphate reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   27.0   0.1    9.4e-06   25.1   0.0    1.9  2  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.012   16.2   0.0      0.034   14.8   0.0    1.8  2  TPR_6          Tetratricopeptide repeat


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 ?   -1.2   0.0       0.1   9.3e+02       3      34 ..       7      36 ..       5      40 .. 0.85
   2 !   25.1   0.0     1e-09   9.4e-06     151     308 ..     139     292 ..     101     308 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.1
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      dV++ G G aG+ l + L+    +v+ ++kr+
  gi|488601456|ref|YP_007907927.1|  7 DVCVAGVGIAGAFLLRSLKDL--DVIGIDKRQ 36
                                      8***********999999887..888888876 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1e-09
                                       EEEEEEEEEE--GTT-HHHHHHTGG.EEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEE..EEEECCETEE CS
                     FAD_binding_3 151 etvrakYlvGaDGgrStvrktlgie.fegeetvyeagvldvlfdadlsdiveplvlilsaesrgv..mviPlentle 224
                                       ++++a+ ++G+DG++S++ ++lg++ f+ + +     + +v  d+d+       ++++++  +g    +iP  ++l 
  gi|488601456|ref|YP_007907927.1| 139 KRIKAEVVAGCDGANSRISSALGFKrFTVPAKQ--YVMEGVECDEDVV-----YMYVGKRICPGGyaWIIPKGDGLA 208
                                       59***********************99999988..4555777778666.....444444433333348999999555 PP

                                       EE.EEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STT CS
                     FAD_binding_3 225 rf.yvqvearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtg 300
                                       ++ + +v+a+ ek++ + k   e+ +++++ +++  +    ++e+ a+   +   ek  +gr  l GDAa ++    
  gi|488601456|ref|YP_007907927.1| 209 NVgVGFVRAKGEKGD-NAKKALERFVREYPHSSKFLRNSKVVSEIGAVVPVDLPLEKAVHGRTILLGDAAGMVISHV 284
                                       440444445444444.5555555555556655555555556666666666778899999****************** PP

                                       SHHHHHHH CS
                     FAD_binding_3 301 GqGlNtai 308
                                       G G+ t++
  gi|488601456|ref|YP_007907927.1| 285 GAGIPTSM 292
                                       ****9998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.8e-06     0.034      11      33 .]     217     239 ..     210     239 .. 0.83
   2 ?   -3.1   0.1       1.9   1.7e+04       3      12 ..     320     329 ..     320     332 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-06
                                       HHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6  11 rklgdtdkAlealerlikeYPdS 33 
                                        k+ + d+A++aler+++eYP S
  gi|488601456|ref|YP_007907927.1| 217 AKGEKGDNAKKALERFVREYPHS 239
                                       5555779**************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHH CS
                             TPR_6   3 lyklalsyrk 12 
                                       ++k+a++  +
  gi|488601456|ref|YP_007907927.1| 320 MWKMAMLKAM 329
                                       6899988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2156.10
//
Query:       gi|488601457|ref|YP_007907928.1|  [L=101]
Description: hypothetical protein Asulf_01969 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.0   1.4       0.65    9.8   0.2    1.9  2  DIM1      Mitosis protein DIM1


Domain annotation for each model (and alignments):
>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   3.6e-05      0.65      34      89 ..       3      64 ..       1      67 [. 0.81
   2 ?    1.5   0.1     0.013   2.3e+02      26      45 ..      69      88 ..      65      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.6e-05
                                      HHHHHHHHHHHHHHHTTTT....EEEEEEETTT--TTSCCCTT-..SSSEEEEEETTEEEEE CS
                              DIM1 34 eClklDelLakiaeklknf....aviylvdidevpdfnkmyele..dpvtilffyrnkhmkv 89
                                      +Cl   e+L+ki+++ +++     +  +++  +v  f+  y l+  ++  i ++y+n  + +
  gi|488601457|ref|YP_007907928.1|  3 DCLDRKEMLKKIMDSFEHIkkalREKSVCEGRKVIIFDPPYTLHlmKDEYIALYYENEELAC 64
                                      7**********9977655411014568**************99988999999999*998876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.013
                                      EEE-TT-HHHHHHHHHHHHH CS
                              DIM1 26 RFGrdedaeClklDelLaki 45
                                      RF   +d +C  +D  L+  
  gi|488601457|ref|YP_007907928.1| 69 RFSFCDDVACQIMDSWLKTL 88
                                      888899********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); 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: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 558.45
//
Query:       gi|488601458|ref|YP_007907929.1|  [L=93]
Description: hypothetical protein Asulf_01970 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0094   15.2   0.0     0.0099   15.2   0.0    1.0  1  DUF5410   Family of unknown function (DUF5410)


Domain annotation for each model (and alignments):
>> DUF5410  Family of unknown function (DUF5410)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.5e-07    0.0099     126     202 ..       3      80 ..       1      90 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-07
                           DUF5410 126 vkditseildlykllqekfylkrdskdeldsriaqsinfllyae.lfresdiyeklglksaelerelqdpngkyakl 201
                                       +k i   + ++ + l+++ y     +++ +  ++q + f+l+    +  s i++klgl s+ l+ +++   gk +k+
  gi|488601458|ref|YP_007907929.1|   3 IKTIEFTVDEFGEWLKDRGYQNLMGEENFEIFLSQGLAFMLFTSsNLLMSFIFNKLGLPSERLNERIRLEVGKRVKE 79 
                                       77788888888999***************************97523445669****************999*99997 PP

                           DUF5410 202 l 202
                                       +
  gi|488601458|ref|YP_007907929.1|  80 I 80 
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 544.05
//
Query:       gi|488601459|ref|YP_007907930.1|  [L=563]
Description: Mismatch repair ATPase (MutS family) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-09   36.2   0.0    1.1e-08   35.4   0.0    1.3  1  MutS_V    MutS domain V
    0.00036   20.6   0.2     0.0016   18.4   0.0    2.3  2  AAA_14    AAA domain
     0.0049   17.1   0.4       0.04   14.2   0.0    2.5  2  AAA_28    AAA domain
  ------ inclusion threshold ------
      0.014   15.2   0.1      0.014   15.2   0.1    2.4  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      0.024   14.4   9.6        0.9    9.2   0.0    3.0  3  AAA_15    AAA ATPase domain
      0.082   13.4   0.1      0.082   13.4   0.1    3.3  2  AAA_23    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 !   35.4   0.0   3.6e-12   1.1e-08       2     119 ..     380     493 ..     379     508 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.6e-12
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TT CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatek 78 
                                       ++tG+n +Gk ++l  +  i++laq+G  vpae+a ++++d+if     + + + g  +F + ++ + + lk   + 
  gi|488601459|ref|YP_007907930.1| 380 VLTGANSGGKTSLLMLIVQIQVLAQMGFPVPAEQAVVNVLDEIFFF--KKKKSVYGAGAFETALKSLINALKGKGR- 453
                                       89******************************************75..47788899999******99999998765. PP

                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatH 119
                                        l++lDE    t    G+ i  a+++   e ++ +t+   H
  gi|488601459|ref|YP_007907930.1| 454 KLILLDEFEAITEPGAGVKILSALLKVAYE-KRFYTVVVSH 493
                                       6*******9999999999999999887666.5666666666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.6   4.7e+03      34      47 ..     270     283 ..     244     307 .. 0.59
   2 !   18.4   0.0   5.4e-07    0.0016       3      84 ..     377     472 ..     375     526 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                            AAA_14  34 lyinldderdkkla 47 
                                        +in+d+ +  k++
  gi|488601459|ref|YP_007907930.1| 270 PEINFDELERVKQE 283
                                       45666665554433 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 5.4e-07
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.......vkkesilyinldderdkkladpe.......kllelileklkeekk 65 
                                        ++v+tGa   GKT ll  +++ +        v++e+ +   ld+  + k++++        + l+ + + lk++++
  gi|488601459|ref|YP_007907930.1| 377 GVVVLTGANSGGKTSLLMLIVQIQVlaqmgfpVPAEQAVVNVLDEIFFFKKKKSVygagafeTALKSLINALKGKGR 453
                                       689****************9988889999**99999999999999988766644344552224444444445559** PP

                            AAA_14  66 tylflDEiqevpewekalk 84 
                                       ++++lDE   ++e    +k
  gi|488601459|ref|YP_007907930.1| 454 KLILLDEFEAITEPGAGVK 472
                                       ********99955444333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2       0.3     9e+02      51     125 ..     191     276 ..     132     305 .. 0.54
   2 !   14.2   0.0   1.3e-05      0.04       2      32 ..     379     415 ..     378     459 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.3
                            AAA_28  51 dllafaervleeqleeeaaa.aankvlfcDrglldtlaYaraygge.aeae.lea.......aarekrydl.vfllp 116
                                       ++ +f ++ l e +e  +++ +++k++++ r++l+ +    ++     e + +e+       +a++   ++ +f+ +
  gi|488601459|ref|YP_007907930.1| 191 EFEEFVHKKLGEIKESIEKRlEKEKIVLSGRDILEFMQKGSFDVFSiIEDAiFEEvlkaeqeIAEKFGFRAeFFVRK 267
                                       45555555454444444444467777777777666554433333322111111111111222333444444355555 PP

                            AAA_28 117 papeidddg 125
                                       ++pei  d+
  gi|488601459|ref|YP_007907930.1| 268 VMPEINFDE 276
                                       566664343 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.3e-05
                            AAA_28   2 ivitGgestGKTtll......eaLaargypvvpEaar 32 
                                       +v+tG+ s+GKT+ll      + La++g+pv +E a 
  gi|488601459|ref|YP_007907930.1| 379 VVLTGANSGGKTSLLmlivqiQVLAQMGFPVPAEQAV 415
                                       8*************97777777777889999866554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       1.1   3.2e+03      53      53 ..     236     236 ..     171     322 .. 0.62
   2 ?   15.2   0.1   4.6e-06     0.014       1      51 [.     378     428 ..     378     446 .. 0.74
   3 ?   -2.3   0.0         1     3e+03     258     267 ..     451     462 ..     439     463 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                            AAA_21  53 d 53 
                                       +
  gi|488601459|ref|YP_007907930.1| 236 S 236
                                       2 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.6e-06
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldl 51 
                                       + vl+G+N+ GK++LL ++  ++ l++++++   e+   + +++i ++   
  gi|488601459|ref|YP_007907930.1| 378 VVVLTGANSGGKTSLLMLIVQIQVLAQMGFPVPAEQAVVNVLDEIFFFKKK 428
                                       579****************99987777777766666666666666555555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1
                            AAA_21 258 g..sllliDEpE 267
                                          +l+l+DE+E
  gi|488601459|ref|YP_007907930.1| 451 KgrKLILLDEFE 462
                                       2469*******9 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.14   4.2e+02     222     283 ..      22      80 ..       6     115 .. 0.65
   2 ?    7.8   2.5   0.00079       2.4     170     272 ..     186     311 ..     116     344 .. 0.72
   3 ?    9.2   0.0    0.0003       0.9      14      43 ..     367     396 ..     363     431 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                            AAA_15 222 kekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkknee 283
                                       ++ il+e ++++l+ e  +++ ++ + + +++++l  + ++ +kk+++ki++++  +++  +
  gi|488601459|ref|YP_007907930.1|  22 YRAILSE-IRDRLIFEESRDFLSLFKPVADKNEIL--KRQNYFKKIFEKINSVELHKFDPLN 80 
                                       4444444.555566566666666666666666666..4446677777777766666665544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00079
                            AAA_15 170 kklikkleeslkkee.elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl........... 234
                                       ++ ik++ee + k+  e+k+++++ ++k ++  + R++ +   + + ++++ + + i+ee l+ ++           
  gi|488601459|ref|YP_007907930.1| 186 ENRIKEFEEFVHKKLgEIKESIEKRLEKEKIVLSGRDILEFMQKGSFDVFSIIEDAIFEEVLKAEQeiaekfgfrae 262
                                       3345556666655559*********************************************99999999*******9 PP

                            AAA_15 235 ....eeelteklkeiqeklkeidkklaeelk.......kilkkkidkik 272
                                           + + + +++e++   +e++ +l+ e         +++k ++ k+k
  gi|488601459|ref|YP_007907930.1| 263 ffvrKVMPEINFDELERVKQELERELTVERYmlardimRKIKHILPKLK 311
                                       9999555555555555555555555544443333333333333333332 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0003
                            AAA_15  14 lkdveidlseeltvliGkNnsGKSsileal 43 
                                       +++++ dl + + vl G+N+ GK+s+l+++
  gi|488601459|ref|YP_007907930.1| 367 IENFSEDLAKGVVVLTGANSGGKTSLLMLI 396
                                       55666677788*****************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -10.2  16.4         6   1.8e+04     102     170 ..     188     292 ..       6     321 .. 0.59
   2 ?   13.4   0.1   2.7e-05     0.082       6      39 ..     363     396 ..     360     399 .. 0.85

  Alignments for each domain:
  == domain 1  score: -10.2 bits;  conditional E-value: 6
                            AAA_23 102 kttkkaklelleideleqfisellgskki..............ilnlilflgqerfeefelkdkke........... 153
                                       + + ++++   +  e ++ i++ l+++ki              ++++++++ +  fee ++++++            
  gi|488601459|ref|YP_007907930.1| 188 RIKEFEEFVHKKLGEIKESIEKRLEKEKIvlsgrdilefmqkgSFDVFSIIEDAIFEEVLKAEQEIaekfgfraeff 264
                                       22222222222222223333333333333333222233333333333333333333333332222233444544444 PP

                            AAA_23 154 ...........rleelekeleeledekk 170
                                                  +le +++ele + ++++
  gi|488601459|ref|YP_007907930.1| 265 vrkvmpeinfdELERVKQELERELTVER 292
                                       4444444444455555555555444444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.7e-05
                            AAA_23   6 nfrsfrdqeidFskgltlItGpNGaGKTTildAi 39 
                                       +f  +++++ d+ kg++++tG N  GKT++l  i
  gi|488601459|ref|YP_007907930.1| 363 GFDTIENFSEDLAKGVVVLTGANSGGKTSLLMLI 396
                                       556667888899******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.72u 0.36s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 3117.55
//
Query:       gi|488601460|ref|YP_007907931.1|  [L=403]
Description: hypothetical protein Asulf_01972 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.4     0.0078   16.3   0.0    3.3  4  Wzt_C         Wzt C-terminal domain
     0.0049   16.8   0.8        1.4    8.9   0.0    3.3  3  DUF3324       Protein of unknown function C-terminal (DUF3324
     0.0081   16.3   0.8      0.086   13.0   0.2    2.7  2  DUF2012       Protein of unknown function (DUF2012)
  ------ inclusion threshold ------
       0.02   14.9   1.1         11    6.1   0.0    3.4  4  Y_Y_Y         Y_Y_Y domain
      0.034   14.4   0.4       0.63   10.3   0.0    2.7  2  DUF5625       Domain of unknown function (DUF5625)
       0.11   12.7   2.5          4    7.6   0.1    3.1  2  Cupredoxin_1  Cupredoxin-like domain
        2.9    8.4   5.5          3    8.4   1.2    2.9  3  DUF4369       Domain of unknown function (DUF4369)


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 ?   -0.1   0.0      0.34   8.7e+02      26      47 ..      27      48 ..      22      76 .. 0.66
   2 ?   -2.3   0.0       1.7   4.3e+03      91     106 ..      67      83 ..      36      88 .. 0.63
   3 ?   -1.0   0.0      0.62   1.6e+03      21      42 ..     182     203 ..     162     212 .. 0.75
   4 !   16.3   0.0   3.1e-06    0.0078      86     130 ..     229     274 ..     207     286 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.34
                             Wzt_C 26 stfesgeevtlrikvkahedve 47
                                       +f +ge++tl+i+   +++++
  gi|488601460|ref|YP_007907931.1| 27 YEFLQGENITLKIYTSGNASLS 48
                                      569999*****99985555543 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                             Wzt_C  91 ef.klpLapGeYlltva 106
                                       e+ + +L pG Y l +a
  gi|488601460|ref|YP_007907931.1|  67 EIpTSKLSPGIYKLYIA 83 
                                       33323688999988765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.62
                             Wzt_C  21 egeetstfesgeevtlrikvka 42 
                                       + +  s++ +ge++t+ ik +a
  gi|488601460|ref|YP_007907931.1| 182 SVKAPSEIYVGEPITIIIKTNA 203
                                       4456677999999999998854 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 3.1e-06
                             Wzt_C  86 vevefefklpLapGeYlltvaledrdgeene...iydwlddalsfeVv 130
                                       +e+ef+  l L+pG+Y++++a+++++++ ++   ++++ ++ l ++V+
  gi|488601460|ref|YP_007907931.1| 229 GEIEFDD-LWLKPGDYSISIAVNNSKNS-DYlklPLEVQKSFLDVKVE 274
                                       4555555.6*************777665.4467777777777777766 PP

>> DUF3324  Protein of unknown function C-terminal (DUF3324)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.014        35      56     130 ..      29      97 ..      11     114 .. 0.75
   2 ?   -0.9   0.0      0.58   1.5e+03     116     129 ..     155     181 ..     117     187 .. 0.50
   3 !    8.9   0.0   0.00055       1.4      86     121 ..     222     257 ..     197     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
                           DUF3324  56 ilnklkveakvtkkgskkvlyksekenlqmAPnSnfnfpislkgeelkaGtYtlkvtakskkkkwefekeFtIte 130
                                       +l+  +++ k++  g+ +  + ++++ l+m  + + +++i++   +l +G Y+l +     +++ ef k+++I++
  gi|488601460|ref|YP_007907931.1|  29 FLQGENITLKIYTSGNASLSIVNDTTVLSMNIEKSKTLEIPT--SKLSPGIYKLYIA----DRTSEFLKDIKIKS 97 
                                       666667889999999999999999999999999888999987..77*******9886....33444444444443 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
                           DUF3324 116 k.............kkkwefekeFtIt 129
                                       +             +++  + ++F+I+
  gi|488601460|ref|YP_007907931.1| 155 GiynlkvifgslvlNETKVYVEKFKIE 181
                                       222222222223444444444444444 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00055
                           DUF3324  86 APnSnfnfpislkgeelkaGtYtlkvtakskkkkwe 121
                                       A  S+++ +i++++  lk+G+Y++++ ++++k++  
  gi|488601460|ref|YP_007907931.1| 222 ARFSSLTGEIEFDDLWLKPGDYSISIAVNNSKNSDY 257
                                       556888999*******************99987655 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.26   6.6e+02      36      62 ..      72      97 ..      69     139 .. 0.66
   2 !   13.0   0.2   3.4e-05     0.086      27      88 ..     141     204 ..     119     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.26
                           DUF2012 36 dlpegsYlLevespeyvFepyrVdvkd 62
                                      +l++g Y L +  ++ +F +  +++k+
  gi|488601460|ref|YP_007907931.1| 72 KLSPGIYKLYIADRTSEFLK-DIKIKS 97
                                      6899********99999977.455553 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.4e-05
                           DUF2012  27 rrDGsFifr.dlpegsYlLevespeyvFepyrVdvk...dkgkakasklrivetaevnvvdesgne 88 
                                        +DG+F ++ d+peg Y+L+v    +v ++ +V v     +  + +s++++ e+ +++   ++++e
  gi|488601460|ref|YP_007907931.1| 141 VNDGKFEVSfDVPEGIYNLKVIFGSLVLNETKVYVEkfkIESVKAPSEIYVGEPITIII--KTNAE 204
                                       47****9977*************************977544444556666666666654..44444 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.5   3.8e+03      42      65 ..      36      60 ..      34      61 .. 0.81
   2 ?    6.1   0.0    0.0043        11      29      59 ..      65      96 ..      57     101 .. 0.75
   3 ?   -2.2   0.0       1.6   4.2e+03      36      45 ..     152     161 ..     122     161 .. 0.65
   4 ?    5.5   0.0    0.0063        16      36      56 ..     238     256 ..     231     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                                      EEEEEEEETTS-B-SS-.EEEEEEE CS
                             Y_Y_Y 42 tlkVkakdndgqwnydi.tslsfti 65
                                      tlk++++ n + +  ++ t ls +i
  gi|488601460|ref|YP_007907931.1| 36 TLKIYTSGNASLSIVNDtTVLSMNI 60
                                      7999999999999999977776665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0043
                                      ..EEEEES--SEEEEEEEEEEETTS-B-SS-E CS
                             Y_Y_Y 29 q.easytnlppGdYtlkVkakdndgqwnydit 59
                                      + e+  + l+pG Y+l+++ + +++ ++ +i+
  gi|488601460|ref|YP_007907931.1| 65 TlEIPTSKLSPGIYKLYIADRTSEFLKDIKIK 96
                                      45777789**********99988877766655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.6
                                       --SEEEEEEE CS
                             Y_Y_Y  36 lppGdYtlkV 45 
                                        p+G Y lkV
  gi|488601460|ref|YP_007907931.1| 152 VPEGIYNLKV 161
                                       4777777776 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0063
                                       --SEEEEEEEEEEETTS-B-S CS
                             Y_Y_Y  36 lppGdYtlkVkakdndgqwny 56 
                                       l+pGdY + +++ +  +++++
  gi|488601460|ref|YP_007907931.1| 238 LKPGDYSISIAVNN--SKNSD 256
                                       89**********55..44443 PP

>> DUF5625  Domain of unknown function (DUF5625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.26   6.5e+02      73     110 ..      49      82 ..      33      93 .. 0.62
   2 ?   10.3   0.0   0.00024      0.63      27     110 ..     146     247 ..     115     252 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.26
                                       EEEEEEEEE-S--SSTTE...EEEEEEEE-SEEEEEEE CS
                           DUF5625  73 vildkkinakglgsgaateyereIktlsLkkGkYsiri 110
                                       ++ d ++  ++ + +  +    eI t +L++G Y++ i
  gi|488601460|ref|YP_007907931.1|  49 IVNDTTVLSMNIEKS--KT--LEIPTSKLSPGIYKLYI 82 
                                       333444444444333..32..3699*********9876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00024
                                       EEEEE----CCCCTTHHHHHH-....................TT--T...---EEEEEEEEE.-TTS-EEEEEEEEE CS
                           DUF5625  27 laLlfavndqkeemervekllG....................stdkd...gvivpvklkivk.nkkndkkvildkki 79 
                                       +++ f+v++    + +++ ++G                             v  p+ + i    +  +  v+ ++ +
  gi|488601460|ref|YP_007907931.1| 146 FEVSFDVPEG---IYNLKVIFGslvlnetkvyvekfkiesvkA---PseiYVGEPITIIIKTnAEFFTRVVLQNESY 216
                                       4444444444...333444444555555555555554432221...1434566678877777444456666778899 PP

                                       EE-S--SSTTE...EEEEEEEE-SEEEEEEE CS
                           DUF5625  80 nakglgsgaateyereIktlsLkkGkYsiri 110
                                       + ++++  ++   e e ++l Lk+G Ysi+i
  gi|488601460|ref|YP_007907931.1| 217 MLEKTARFSSLTGEIEFDDLWLKPGDYSISI 247
                                       99999999999999***************99 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0016         4      28      91 ..      18      81 ..      12      89 .. 0.87
   2 ?    3.3   0.5     0.033        85      23      82 ..     137     201 ..      99     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0016
                      Cupredoxin_1 28 kdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeft 91
                                      +   +e +k e  +ge+++lki   ++ + +++ +    + ++++ kt +i  ++l+pG Y+++
  gi|488601460|ref|YP_007907931.1| 18 NAVIVELNKYEFLQGENITLKIYTSGNASLSIVNDTTVLSMNIEKSKTLEIPTSKLSPGIYKLY 81
                                      55556677788889**********************99999********************975 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.033
                      Cupredoxin_1  23 veitvkdggfePskievkage.kvklk.....iknkdktpeefesedlgeekvlapgktttitiap 82 
                                        e++v+dg+fe s  +v++g  ++k+      ++ ++  +e+f++e+++   ++  g+  ti i++
  gi|488601460|ref|YP_007907931.1| 137 KEVEVNDGKFEVS-FDVPEGIyNLKVIfgslvLNETKVYVEKFKIESVKAPSEIYVGEPITIIIKT 201
                                       5788999999875.7888886233333111103333333588888888888889999988888876 PP

>> DUF4369  Domain of unknown function (DUF4369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.22   5.6e+02      26      84 ..      49     112 ..      10     115 .. 0.62
   2 ?    8.4   1.2    0.0012         3       7      71 ..     110     181 ..     104     200 .. 0.69
   3 ?   -1.7   0.0       1.7   4.5e+03      63      79 ..     236     252 ..     198     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                           DUF4369  26 vklDsavv.....knGkFtfkgkvdeprlaylliddkggalpfflengtititiddgss..akvtG 84 
                                        + D++v+     k  + ++ ++  +p ++ l+i d+++   f  + +  +++++ + s  +k++G
  gi|488601460|ref|YP_007907931.1|  49 IVNDTTVLsmnieKSKTLEIPTSKLSPGIYKLYIADRTS--EFLKDIKIKSFKAHADVSikSKISG 112
                                       444555555555444446666666667777777777766..5554444444555544445566665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                           DUF4369   7 ikgladgkkvylsydd.........ngvvklDsavvknGkFtfkgkvdeprlaylliddkgg...alpfflengtit 71 
                                       i+    gk+v+l +++         + + +   ++v++GkF+ + +v+e  ++ l +  ++    ++ +++e+ +i+
  gi|488601460|ref|YP_007907931.1| 110 IS----GKVVVLGETNipngyklkiRLNSVEKEVEVNDGKFEVSFDVPE-GIYNLKVIFGSLvlnETKVYVEKFKIE 181
                                       44....355555555556666333311222235777*************.888888877777778888888887775 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.7
                           DUF4369  63 fflengtititiddgss 79 
                                       ++l++g+++i+i+ ++s
  gi|488601460|ref|YP_007907931.1| 236 LWLKPGDYSISIAVNNS 252
                                       56777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2335.87
//
Query:       gi|488601461|ref|YP_007907932.1|  [L=249]
Description: SPFH domain, Band 7 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-37  127.0   3.3      1e-36  126.6   3.3    1.1  1  Band_7    SPFH domain / Band 7 family
    2.7e-06   27.3   1.2      8e-06   25.7   1.1    1.9  1  Band_7_1  SPFH domain-Band 7 family
  ------ inclusion threshold ------
       0.09   13.2   0.0       0.16   12.4   0.0    1.4  1  DUF4228   Domain of unknown function (DUF4228)
        0.1   13.0   0.0       0.26   11.7   0.0    1.6  2  RTBV_P12  Rice tungro bacilliform virus P12 protein


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 !  126.6   3.3   2.2e-40     1e-36       2     177 ..      23     192 ..      22     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 2.2e-40
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       +++e e+gv++r G+l + ++pGl f++P+++ + +v++r+ t+dv+  ++v+t+D++ v+++++v+yrv  d+ k+
  gi|488601461|ref|YP_007907932.1|  23 VVREYERGVIFRLGRLIGARGPGLFFVIPILENMMLVDLRTYTYDVPS-QEVVTRDNVTVKVNAVVYYRV-LDPEKA 97 
                                       799*********************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       v++v     +++   +++++ +lr+vi++ +l++llsnre+l+ +l++ + e+ + +G+ v  v i+d+++p+e ++
  gi|488601461|ref|YP_007907932.1|  98 VTEV----FDYRFATSQIAQTTLRSVIGQAELDDLLSNREKLNVQLQRIIDEATNPWGIKVSAVEIKDVELPKEMQR 170
                                       ****....888888999999********************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraeae 177
                                       a+a+ ++ae+e++a+i ra +e
  gi|488601461|ref|YP_007907932.1| 171 AMAMQAEAERERRAKIIRADGE 192
                                       *****************99776 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 !   25.7   1.1   1.8e-09     8e-06      99     209 ..      79     178 ..      52     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.8e-09
                          Band_7_1  99 vrvrafGtyslrvvdpakllreivGtdgefdteeise.qlkslivtrlsdvlaeskipvldlaakseelaeklkeal 174
                                       v v+ +  +  rv dp+k ++e+   d +f t++i++ +l+s+i        ++++  + dl ++ e+l  +l+  +
  gi|488601461|ref|YP_007907932.1|  79 VTVKVNAVVYYRVLDPEKAVTEVF--DYRFATSQIAQtTLRSVI--------GQAE--LDDLLSNREKLNVQLQRII 143
                                       556666667778999999999986..778888888651355554........4444..469999************* PP

                          Band_7_1 175 keelaeyGlelekleienislpeevekaldkrasm 209
                                       +e+ +  G++++++ei++++lp+e+++a+  +a++
  gi|488601461|ref|YP_007907932.1| 144 DEATNPWGIKVSAVEIKDVELPKEMQRAMAMQAEA 178
                                       *****************************998875 PP

>> DUF4228  Domain of unknown function (DUF4228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.5e-05      0.16      10      48 ..     175     213 ..     168     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                           DUF4228  10 aaaassakvvkvvhpdGeveelsrpvtAaevmaenPghf 48 
                                        a+a++++ +k++ +dGe + +++   Aa+vm+e  g +
  gi|488601461|ref|YP_007907932.1| 175 QAEAERERRAKIIRADGEFQAAKKLKEAADVMMESKGAM 213
                                       344557789************************987754 PP

>> RTBV_P12  Rice tungro bacilliform virus P12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.4   1.1e+04      11      37 ..      85     111 ..      77     121 .. 0.69
   2 ?   11.7   0.0   5.8e-05      0.26      35      70 ..     197     232 ..     191     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                          RTBV_P12  11 alekfknlesdtagkdkfnwvftleni 37 
                                       a+  ++ l+ + a  + f++ f+  +i
  gi|488601461|ref|YP_007907932.1|  85 AVVYYRVLDPEKAVTEVFDYRFATSQI 111
                                       555666777777777777777776665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.8e-05
                          RTBV_P12  35 eniksaadvnlaskglvqlyalqeidkkinnlttqv 70 
                                       +++k aadv + skg + l  lq i    n+ +t++
  gi|488601461|ref|YP_007907932.1| 197 KKLKEAADVMMESKGAMMLRILQTISETTNDPATKI 232
                                       5789***********************999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); 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: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1398.45
//
Query:       gi|488601462|ref|YP_007907933.1|  [L=136]
Description: protein tyrosine phosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-25   87.7   0.0    1.1e-24   87.5   0.0    1.1  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 !   87.5   0.0   5.9e-29   1.1e-24       1     140 [.       8     129 ..       8     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 5.9e-29
                                       EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHH CS
                             LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelae 77 
                                       vlf C+ N++RS+mAe l+r++     +++++ev+SaG++    k+++p+av+v++e gi++s+++++ +++    +
  gi|488601462|ref|YP_007907933.1|   8 VLFLCTENSARSQMAEGLLRAL-----YGDRFEVYSAGIK---PKTVNPNAVKVMREIGIDISSQKSKSVEEFRGMK 76 
                                       89********************.....7889*********...899******************************* PP

                                       SSEEEESSHHHHHHHHHHCCTTGGGGEEEGGGGSSTSS---HTTSS.HHHHHHHHHHHHHHHHH CS
                             LMWPc  78 lDlilamdeenkreleslapekekakvkllgeyteqldieDPyyge.ieafeevldeieeavkk 140
                                       +Dl++++++++k e +++ p+k+            ++   DP++++  +af++v+dei + + +
  gi|488601462|ref|YP_007907933.1|  77 FDLVVTVCDDAK-ENCPFFPGKK----------IVHKSFTDPAKSNnLDAFRKVRDEIRKWIIE 129
                                       ***********9.99******33..........368999****76659**********987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 724.93
//
Query:       gi|488601463|ref|YP_007907934.1|  [L=191]
Description: TIGR00288 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   87.5   0.1    1.7e-24   87.0   0.1    1.2  1  NYN       NYN domain
  ------ inclusion threshold ------
      0.066   13.3   0.2       0.16   12.1   0.0    1.7  2  FliH      Flagellar assembly protein FliH


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 !   87.0   0.1   1.8e-28   1.7e-24       1     145 [.      28     158 ..      28     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.8e-28
                               NYN   1 rvavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrggsgk 76 
                                       +v+++iDg n+    k+ +++++++++ i+++g++++ar+++n++++   k+ +a++++g+ ++ +           
  gi|488601463|ref|YP_007907934.1|  28 KVGLLIDGPNMLR--KEFNINLHEIRQIIEEYGNIKVARVFLNQYAG--DKLVEAIENQGFePIIT----------S 90 
                                       699**********..6668************************6555..6999********99954..........4 PP

                               NYN  77 kavDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefis 145
                                       ++vDv++av+a+el+y++++d + Lv++D+DF  +++k++e gk++++++ae +  s +L+++ad  i 
  gi|488601463|ref|YP_007907934.1|  91 GDVDVRMAVEAMELIYNDSIDALALVTRDADFKAVLKKAMEMGKETIIIGAE-PGFSAALKNSADIAII 158
                                       89************************************************65.99*********97665 PP

>> FliH  Flagellar assembly protein FliH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.45     4e+03      56      75 ..      50      68 ..      38      97 .. 0.62
   2 ?   12.1   0.0   1.8e-05      0.16      38      94 ..     123     181 ..     111     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.45
                                      HHHHHTTSCHHHS-EEEEE- CS
                              FliH 56 vrealaklpvdekkitlrvn 75
                                      +r+++ +++   k +++++n
  gi|488601463|ref|YP_007907934.1| 50 IRQII-EEYGNIKVARVFLN 68
                                      44444.44444444444444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.8e-05
                                       HHHHHHS--S-HHHHHHHHHHHHTTSCHHHS-EEEEE-HHHHHHHHHHHH..HHHHHCT CS
                              FliH  38 rkvikkelsvdpekilalvrealaklpvdekkitlrvnpdDlelvrehlg..eelsarg 94 
                                       ++v+kk+++  +e i+   +  +++ +  + +i +++n+dD++ v+e  +  +e+++++
  gi|488601463|ref|YP_007907934.1| 123 KAVLKKAMEMGKETIIIGAEPGFSAALKNSADIAIILNQDDFDEVEEDNNysKEIEHKN 181
                                       789*******************************************9766446666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1153.66
//
Query:       gi|488601464|ref|YP_007907935.1|  [L=163]
Description: molybdopterin guanine dinucleotide biosynthesis accessory protein MobB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-29  100.0   0.0    1.1e-28   99.8   0.0    1.1  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
     0.0015   17.6   0.0     0.0025   16.9   0.0    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.002   17.7   0.0     0.0024   17.4   0.0    1.2  1  KTI12         Chromatin associated protein KTI12
     0.0084   15.8   0.0      0.015   15.0   0.0    1.4  1  SRP54         SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.014   14.9   0.0       0.12   11.9   0.0    2.1  2  FeoB_N        Ferrous iron transport protein B
      0.036   14.0   0.0      0.071   13.0   0.0    1.5  1  NTPase_1      NTPase
      0.038   14.1   0.0      0.074   13.1   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.043   13.3   0.1      0.076   12.5   0.1    1.5  1  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.044   13.8   0.1      0.072   13.1   0.1    1.7  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      0.047   13.3   0.0      0.074   12.6   0.0    1.3  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.065   13.6   0.0       0.12   12.7   0.0    1.6  1  RNA_helicase  RNA helicase
       0.12   12.6   0.0       0.13   12.5   0.0    1.5  1  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.0   7.3e-32   1.1e-28       1     132 [.       2     131 ..       2     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 7.3e-32
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahh.gfdvdkpgkDsyrhrkAGAkevlvaskerlalikelee 76 
                                       +++ivg  +sGKTtL+ek+   + +rgl+++++Kh++h +f++dk+gkDs+++ + GA+ v++++k+++a+i ++++
  gi|488601464|ref|YP_007907935.1|   2 IISIVGSPDSGKTTLIEKMAGYFLERGLKICVVKHHSHgDFEFDKEGKDSWNFYQKGAD-VAISAKNEFAIIGKINQ 77 
                                       799*******************************997746*****************97.89*************99 PP

                              MobB  77 aelsleellarl.sevDlvlvEGfkkealpkievlraelgkeelllledekliavvs 132
                                       ++ +l+  ++++ s++Dl+l+EGf     ++++vl ++ + e+    ++ +++avv+
  gi|488601464|ref|YP_007907935.1|  78 EKYNLDYFCDKYlSDYDLILTEGFNIYGKDRVVVLNENDDLERF---KKGRVLAVVC 131
                                       9********999899********************998555333...4668888886 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 !   16.9   0.0   1.7e-06    0.0025      32      63 ..       3      34 ..       1      39 [. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                                      EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavl 63
                                      + + G+P +Gk tl+e+++  + +rG ++ v+
  gi|488601464|ref|YP_007907935.1|  3 ISIVGSPDSGKTTLIEKMAGYFLERGLKICVV 34
                                      7899*************************998 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-06    0.0024       3      41 ..       2      40 ..       1      77 [. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                      EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                      ++ + G P sGK+t+ +++a ++ e++ ++ v++  s g
  gi|488601464|ref|YP_007907935.1|  2 IISIVGSPDSGKTTLIEKMAGYFLERGLKICVVKHHSHG 40
                                      57799****************************998876 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   0.0   9.9e-06     0.015       3      35 ..       2      34 ..       1      38 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.9e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      +i +vG   +GKTt + K+a ++ ++g k+++v
  gi|488601464|ref|YP_007907935.1|  2 IISIVGSPDSGKTTLIEKMAGYFLERGLKICVV 34
                                      67899************************9987 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.1e-05      0.12       3      23 ..       3      23 ..       1      45 [. 0.91
   2 ?    0.7   0.0      0.23   3.4e+02      95     120 ..      95     120 ..      86     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                                      EEEEESTTSSHHHHHHHHHTT CS
                            FeoB_N  3 valvGnpnvGkttlfnaltga 23
                                      + +vG p++Gkttl+++++g 
  gi|488601464|ref|YP_007907935.1|  3 ISIVGSPDSGKTTLIEKMAGY 23
                                      789**************9985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.23
                                       HHHHHHHHHTTSSEEEEEETHHHHHH CS
                            FeoB_N  95 LyLtlqllelgvpvvlalnmideaek 120
                                       L+Lt      g++ v++ln  d +e+
  gi|488601464|ref|YP_007907935.1|  95 LILTEGFNIYGKDRVVVLNENDDLER 120
                                       67777777789999*******99886 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.7e-05     0.071       2      31 ..       3      32 ..       2      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                      + i G+p +GKtTl++k++    ++g+k++
  gi|488601464|ref|YP_007907935.1|  3 ISIVGSPDSGKTTLIEKMAGYFLERGLKIC 32
                                      6789****************9999999986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     5e-05     0.074       2      21 ..       3      22 ..       2      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      + ivG p +GK+tLi ++ g
  gi|488601464|ref|YP_007907935.1|  3 ISIVGSPDSGKTTLIEKMAG 22
                                      78**************9987 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   0.1   5.1e-05     0.076       5      24 ..       2      21 ..       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                                      EEEEEESTTSSHHHHHHHHH CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLl 24
                                       i+i+g  D+GKtTL++++ 
  gi|488601464|ref|YP_007907935.1|  2 IISIVGSPDSGKTTLIEKMA 21
                                      589**************986 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.8e-05     0.072       9      34 ..      10      35 ..       2     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                                      TSSHHHHHHHHHHHHHHTT--EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVllvD 34
                                      ++GKTtl  ++a ++ +rgl++ +v+
  gi|488601464|ref|YP_007907935.1| 10 DSGKTTLIEKMAGYFLERGLKICVVK 35
                                      79**********************99 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 ?   12.6   0.0     5e-05     0.074       2      33 ..       2      35 ..       1      50 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-05
                                      EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEE CS
                              cobW  2 vtvltGflGsGKTtLlnhll..enraglklaviv 33
                                      ++ ++G++ sGKTtL++++     ++glk+ v+ 
  gi|488601464|ref|YP_007907935.1|  2 IISIVGSPDSGKTTLIEKMAgyFLERGLKICVVK 35
                                      57799**************988777899999886 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.2e-05      0.12       2      53 ..       4      62 ..       3      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl......klkkkdsvysrnpeddfwdgYt.gqevv 53
                                       ++G++  GK+tl++++a  +l++       k ++++++ + +  +d w+ Y+ g +v 
  gi|488601464|ref|YP_007907935.1|  4 SIVGSPDSGKTTLIEKMAGYFLERGlkicvvKHHSHGDFEFDKEGKDSWNFYQkGADVA 62
                                      689******************98878889999999999999999999999999565554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.7e-05      0.13       2      25 ..       3      30 ..       2     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.7e-05
                            AAA_28  2 ivitGgestGKTtlleaLa....argyp 25
                                      i i+G + +GKTtl+e++a    +rg +
  gi|488601464|ref|YP_007907935.1|  3 ISIVGSPDSGKTTLIEKMAgyflERGLK 30
                                      779***************9666666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 910.99
//
Query:       gi|488601465|ref|YP_007907936.1|  [L=578]
Description: glutamine--fructose-6-phosphate transaminase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-49  167.7   0.8    1.6e-25   89.5   0.0    2.4  2  SIS       SIS domain
    2.8e-24   85.8   0.1    6.5e-24   84.6   0.1    1.6  1  GATase_6  Glutamine amidotransferase domain
    4.3e-22   78.3   0.0    4.5e-21   75.0   0.0    2.3  2  GATase_7  Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.014   14.3   0.1      0.031   13.2   0.1    1.5  2  GATase_4  Glutamine amidotransferases class-II
      0.084   13.2   0.0       0.24   11.7   0.0    1.8  1  AlkA_N    AlkA N-terminal 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 !   76.5   0.3   4.5e-25   1.6e-21       8     129 ..     276     394 ..     273     396 .. 0.96
   2 !   89.5   0.0   4.4e-29   1.6e-25       2     128 ..     431     558 ..     430     561 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 4.5e-25
                                       EEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEE CS
                               SIS   8 iyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakii 84 
                                        +++++Gtsy++++ +++ +e++++ +v ve ase+ +    +  e+   i+i++sget+d+++a +lak+ g +++
  gi|488601465|ref|YP_007907936.1| 276 FVFVACGTSYHAGLIAKHVIEKVAKLPVRVEIASEFNYH---PPPERATYIAITQSGETADTLEAMRLAKKLGNRVV 349
                                       589********************************9999...66688899*************************** PP

                                       EEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                               SIS  85 aITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                       +I++  gs++ r ad++l ++a+pe+ va+tks+ +ql+++++la
  gi|488601465|ref|YP_007907936.1| 350 TIANVLGSTATRIADETLFTRAGPEISVAATKSFISQLIVIYVLA 394
                                       ******************************************998 PP

  == domain 2  score: 89.5 bits;  conditional E-value: 4.4e-29
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lak 77 
                                       L+k +++ ++G+G  y++a+e+alk++ei++i++e+++a+elkhg+ al+ +d++vi+   ++et +  +++  + k
  gi|488601465|ref|YP_007907936.1| 431 LSKYRNLMYVGRGIAYPTAMEGALKMKEISYIHAEAYPAGELKHGPFALLGKDMPVIACVVRDETYEIMLNNIkEIK 507
                                       88999**************************************************************9999888*** PP

                                       HTTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                               SIS  78 ergakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                       +rg  ++aI d+++  + ++ d+++ ++a++  l ++t s+ +ql+a++++
  gi|488601465|ref|YP_007907936.1| 508 ARGSFVLAISDENDEEIEKYVDHVVKLPAVNPLLTPITQSVALQLLAYYTA 558
                                       ***********************************************9875 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.1   1.8e-27   6.5e-24      10     134 .]      60     188 ..      44     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 1.8e-27
                          GATase_6  10 vedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllalleelG. 85 
                                         +++a++H+R+a++g++++  a+P +  ++ +++vhNG i n++el+e l a k++ f+s++Dtevl++l+ee+  
  gi|488601465|ref|YP_007907936.1|  60 SNGRMAIGHTRWATHGEPNDVNAHPHTDCSEAIAVVHNGIITNFQELKEVLTA-KNHVFKSETDTEVLAHLIEEFYd 135
                                       46789*************77777***9999***********************.******************55433 PP

                          GATase_6  86 .......eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                              e++l++++G +a+a++ + e+++++ar   +++pl+ +v ++ l +as+
  gi|488601465|ref|YP_007907936.1| 136 gdlkeavEKALSAVKGSYAIAVIHANEDKIVVAR---NKSPLILGVGDDELFVASD 188
                                       456566699************************5...569*******999999996 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   1.3e-24   4.5e-21      13     122 ..      82     193 ..      68     194 .. 0.92
   2 ?    0.4   0.0      0.16   5.6e+02      73      96 ..     507     530 ..     481     537 .. 0.74

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.3e-24
                          GATase_7  13 aQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.......ewgeealerlnGmfAfai 82 
                                       a P + + ++ +++v+nG i+N++el+e L+ak+h f++++Dtevl++l+e+       e +e+al+ ++G++A+a+
  gi|488601465|ref|YP_007907936.1|  82 AHPHT-DCSEAIAVVHNGIITNFQELKEVLTAKNHVFKSETDTEVLAHLIEEfydgdlkEAVEKALSAVKGSYAIAV 157
                                       55666.467889***************************************************************** PP

                          GATase_7  83 wdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       ++++e+++++aR+   + PL++g  + d+l++aS   a+l
  gi|488601465|ref|YP_007907936.1| 158 IHANEDKIVVARN---KSPLILGVGD-DELFVASDTPAIL 193
                                       *************...6********6.7*******99987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.16
                          GATase_7  73 rlnGmfAfaiwdeeekrlllaRDr 96 
                                       + +G+f +ai de+++++    D+
  gi|488601465|ref|YP_007907936.1| 507 KARGSFVLAISDENDEEIEKYVDH 530
                                       568*********999887666665 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.6e-06     0.031      70     139 ..      61     131 ..      26     172 .. 0.71
   2 ?   -3.6   0.0       1.1     4e+03     157     179 ..     497     519 ..     491     521 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-06
                          GATase_4  70 ksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelle 139
                                       + ++++ H R at+Ge ++ n+hp +     + +   HnG ++++++      ++++    +TD+E+ + +l+e
  gi|488601465|ref|YP_007907936.1|  61 NGRMAIGHTRWATHGEPNDVNAHPHTD--CSEAIAVVHNGIITNFQELKevltAKNHVFKSETDTEV-LAHLIE 131
                                       46889*******************986..46778889***999987655444533333336788874.444444 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.1
                          GATase_4 157 ralaelakeiaelGvfnlllsdg 179
                                       +++ + +kei+++G f l +sd 
  gi|488601465|ref|YP_007907936.1| 497 EIMLNNIKEIKARGSFVLAISDE 519
                                       55666789999****99999986 PP

>> AlkA_N  AlkA N-terminal domain
   #    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      59     115 ..     395     450 ..     385     451 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
                            AlkA_N  59 lkvrlslsdlraleaviarvrrllDLdadpeaieaaLdpllapevaarpGlRvPgav 115
                                       +k++ ++++l++le++  +vr++lD   d+e +++ L  + ++++    G+  P a+
  gi|488601465|ref|YP_007907936.1| 395 FKLSNRIDLLNELEKISGEVRKILDNKEDIEDVAEIL-SKYRNLMYVGRGIAYPTAM 450
                                       677778899****************************.7788888888899888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 3320.37
//
Query:       gi|488601466|ref|YP_007907937.1|  [L=386]
Description: UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-34  118.2   0.0    5.7e-34  117.8   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
      2e-21   74.8  31.2    4.3e-08   32.6   0.9    5.2  6  Hexapep          Bacterial transferase hexapeptide (six repea
      3e-12   46.1  26.3    7.7e-06   25.6   0.6    5.1  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    4.8e-12   46.5   0.0    8.4e-12   45.7   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
    5.5e-05   23.0   0.0    0.00012   22.0   0.0    1.5  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0041   16.1   0.9       0.66    8.8   0.9    2.8  1  Fucokinase       L-fucokinase
     0.0064   16.4   0.2      0.031   14.2   0.0    2.1  3  CTP_transf_3     Cytidylyltransferase
  ------ inclusion threshold ------
      0.072   13.3   0.9       0.31   11.2   0.1    2.5  3  CDC48_N          Cell division protein 48 (CDC48), N-terminal
       0.26    9.4  15.1       0.26    9.4   7.4    2.4  2  DUF4954          Domain of unknown function (DUF4954)
        2.7    8.3  11.8        0.5   10.7   4.1    2.4  2  Bactofilin       Polymer-forming cytoskeletal


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0   3.2e-37   5.7e-34       2     232 ..       3     206 ..       2     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 3.2e-37
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       avILa G+G+RL+P t + +k+++ + gk +++++ ++++ ++gi++i++v+  ++++++ +++++g +f+v+++++
  gi|488601466|ref|YP_007907937.1|   3 AVILAAGEGQRLRPFTAKKPKPMIEISGK-PILEHLIEEVRKAGIRDIVLVV-GYRRERIMDYFGSGRDFDVDIEYV 77 
                                       8****************************.*****************66665.5899999***************** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                       +++++ gtA+A++ a+ l+e+e+     +v+ggD +i+    e++k+ +++      +++ +  e+ ++yG i++++
  gi|488601466|ref|YP_007907937.1|  78 IQEQQLGTANALKSAESLVENEF-----IVIGGDNIID---HETIKNVKKRCF----SIAYSISEDCSKYGAITFKN 142
                                       ********************888.....9*********...566777666655....78889999**********98 PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEX CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDv 232
                                        g v+++vEKP+e+  s+++++G+Y   ++v+ ++         +e ++ ++++ ++++g++  a+ ++    W+D+
  gi|488601466|ref|YP_007907937.1| 143 -GFVKEIVEKPEEKL-SYTVNTGLYCLSTDVFRYI--------DEERDLVNVINSMISDGYEFKAIEARL---WQDI 206
                                       .79*********977.*******************........467788999999999998887755555...9998 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       2.3   4.1e+03       2      12 ..     101     111 ..     100     114 .. 0.72
   2 !   20.8   2.1   1.2e-07   0.00022      10      36 .]     230     256 ..     225     256 .. 0.92
   3 !   32.6   0.9   2.4e-11   4.3e-08       2      34 ..     258     290 ..     257     292 .. 0.92
   4 !   28.2   2.3   5.6e-10     1e-06       2      35 ..     276     308 ..     275     309 .. 0.94
   5 !   15.5   1.2   5.9e-06     0.011       2      24 ..     293     314 ..     292     324 .. 0.68
   6 !   24.4   1.1   9.1e-09   1.6e-05       1      31 [.     342     372 ..     342     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                                       EEEETTEEE-T CS
                           Hexapep   2 tvIGsnvlIgp 12 
                                       +vIG +++I++
  gi|488601466|ref|YP_007907937.1| 101 IVIGGDNIIDH 111
                                       57888888775 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.2e-07
                                       E-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + +++++ gnV+IG++++I ag++i g
  gi|488601466|ref|YP_007907937.1| 230 VEKNVTVKGNVIIGEGSIIKAGTYIEG 256
                                       678*********************976 PP

  == domain 3  score: 32.6 bits;  conditional E-value: 2.4e-11
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       ++IG+n+ Igp++v+ + ++IGdnv I+a + i
  gi|488601466|ref|YP_007907937.1| 258 VIIGENCEIGPNTVLKPYTTIGDNVSIEALTII 290
                                       79**************************97776 PP

  == domain 4  score: 28.2 bits;  conditional E-value: 5.6e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       t+IG+nv I + ++i +n +IGdn+ Ig+g+ i+
  gi|488601466|ref|YP_007907937.1| 276 TTIGDNVSIEALTII-SNSIIGDNCMIGSGANIK 308
                                       89*************.9999***********996 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 5.9e-06
                                       EEEETTEEE-TTEEEETTEEE-T CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGd 24 
                                       ++IG+n++Ig++a i + V I +
  gi|488601466|ref|YP_007907937.1| 293 SIIGDNCMIGSGANIKDSV-IDR 314
                                       6788888888888884444.555 PP

  == domain 6  score: 24.4 bits;  conditional E-value: 9.1e-09
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETT CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgag 31 
                                       +++IG+n+ Ig++ v+ + ++IG+ + I+  
  gi|488601466|ref|YP_007907937.1| 342 GAFIGENCRIGNNIVVKPLTVIGNECMIEDM 372
                                       68**************************975 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.5   0.00017       0.3      13      32 ..     233     254 ..     231     255 .. 0.86
   2 !   25.6   0.6   4.3e-09   7.7e-06       1      28 [.     257     286 ..     257     290 .. 0.95
   3 !   12.9   1.6   3.9e-05     0.071       3      16 ..     294     307 ..     292     321 .. 0.87
   4 !   11.4   0.7   0.00011       0.2      20      32 ..     345     357 ..     338     359 .. 0.86
   5 !    9.8   3.5   0.00037      0.67       4      26 ..     345     369 ..     343     370 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                       T-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2  13 nagi.G.vslGdncvvgaGvvi 32 
                                       n ++ G v++G+++++ aG +i
  gi|488601466|ref|YP_007907937.1| 233 NVTVkGnVIIGEGSIIKAGTYI 254
                                       5666777**************9 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 4.3e-09
                                       .EEE-TT-EE-TT-EE.S.EEE-TT-EE-T CS
                         Hexapep_2   1 pviIGdnCliGanagi.G.vslGdncvvga 28 
                                       pviIG+nC iG+n +  + +++Gdn+ ++a
  gi|488601466|ref|YP_007907937.1| 257 PVIIGENCEIGPNTVLkPyTTIGDNVSIEA 286
                                       8**************9888*******9998 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 3.9e-05
                                       EE-TT-EE-TT-EE CS
                         Hexapep_2   3 iIGdnCliGanagi 16 
                                       iIGdnC+iG+ a i
  gi|488601466|ref|YP_007907937.1| 294 IIGDNCMIGSGANI 307
                                       8*********9866 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00011
                                       E-TT-EE-TT-EE CS
                         Hexapep_2  20 lGdncvvgaGvvi 32 
                                       +G+nc +g+++v+
  gi|488601466|ref|YP_007907937.1| 345 IGENCRIGNNIVV 357
                                       99*********99 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00037
                                       E-TT-EE-TT-EE.S.EEE-TT-EE CS
                         Hexapep_2   4 IGdnCliGanagi.G.vslGdncvv 26 
                                       IG+nC iG n ++ + + +G++c +
  gi|488601466|ref|YP_007907937.1| 345 IGENCRIGNNIVVkPlTVIGNECMI 369
                                       7777777777665566777777766 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 !   45.7   0.0   4.7e-15   8.4e-12       1     107 [.       3     117 ..       3     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 4.7e-15
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTC..TS-EEE- CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd..eevlaal...arl..gvrvved 65 
                                       aviLA+G+++R+     +++K+++++ gkp+le++++ +r+ag++++v+v+g+  e + +++   +++  ++++v +
  gi|488601466|ref|YP_007907937.1|   3 AVILAAGEGQRLrpftaKKPKPMIEISGKPILEHLIEEVRKAGIRDIVLVVGYrrERIMDYFgsgRDFdvDIEYVIQ 79 
                                       79**********4444335*******************************999544566555332333334666777 PP

                                       TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHH CS
                      NTP_transf_3  66 edpgkgplaslaaalraaadadavlvlacDmPlltpelverl 107
                                       e ++ g++ +l++a + +  +  ++v+ +D + ++ e+++ +
  gi|488601466|ref|YP_007907937.1|  80 E-QQLGTANALKSAESLV--ENEFIVIGGDNI-IDHETIKNV 117
                                       6.4789999998888755..577788888874.577777665 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 !   22.0   0.0   6.4e-08   0.00012       1      58 [.       1      59 [.       1      77 [. 0.80

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.4e-08
                                      EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHH CS
                              IspD  1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddtee 58
                                      + +vi AAG+G+R++   a +pK  +e++g+++leh ++ + +   +  iv+vv   + e+
  gi|488601466|ref|YP_007907937.1|  1 MQAVILAAGEGQRLRpftAKKPKPMIEISGKPILEHLIEEVRK-AGIRDIVLVVGYRR-ER 59
                                      579**********8544489*******************9998.56777777765444.44 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.9   0.00037      0.66     281     318 ..     260     298 ..     145     378 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00037
                        Fucokinase 281 lessvsvgegsvie.hsslkgnvsigsnsivsgleless 318
                                       + +++++g+++v++ + ++++nvsi++ +i+s+  +  +
  gi|488601466|ref|YP_007907937.1| 260 IGENCEIGPNTVLKpYTTIGDNVSIEALTIISNSIIGDN 298
                                       445555555555555666666666666666666555543 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.7e-05     0.031      15      43 ..      22      50 ..      20      62 .. 0.89
   2 ?   -1.6   0.0       1.2   2.2e+03     172     200 ..     105     133 ..      68     157 .. 0.63
   3 ?   -2.5   0.0       2.3   4.1e+03      16      28 ..     358     370 ..     355     371 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                      TGGGSEETTEEHHHHHHHHHHHTTTTSEE CS
                      CTP_transf_3 15 gKnlldlggkpliayvleaalkskafekv 43
                                       K++++++gkp++++++e+++k++  + v
  gi|488601466|ref|YP_007907937.1| 22 PKPMIEISGKPILEHLIEEVRKAGIRDIV 50
                                      5*********************9986655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                       TTTSEEEEEEEEEEHHHHHHHHHHSHHHH CS
                      CTP_transf_3 172 rrlylshagiytfrkeqplkelvidtpts 200
                                        ++++ h++i   +k+ + + ++i  ++s
  gi|488601466|ref|YP_007907937.1| 105 GDNIIDHETIKNVKKRCFSIAYSISEDCS 133
                                       34455555555555555555555555555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.3
                                       GGGSEETTEEHHH CS
                      CTP_transf_3  16 Knlldlggkplia 28 
                                       K+l  +g++++i+
  gi|488601466|ref|YP_007907937.1| 358 KPLTVIGNECMIE 370
                                       9**********96 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.7   6.7e+03      36      61 ..     113     139 ..     109     142 .. 0.76
   2 ?   -2.1   0.0       2.6   4.6e+03      73      82 ..     277     286 ..     276     289 .. 0.82
   3 ?   11.2   0.1   0.00017      0.31      56      79 ..     327     350 ..     321     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.7
                                       EEEC.CCCEEEEEEEBSTTSTTTTEEE CS
                           CDC48_N  36 eieg.krkTvaivwpaepedegkgiIr 61 
                                       +i++ k++   i++++ ++ ++ g I 
  gi|488601466|ref|YP_007907937.1| 113 TIKNvKKRCFSIAYSISEDCSKYGAIT 139
                                       688877779999999999888777776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                                       -TTEEEEEEE CS
                           CDC48_N  73 siGdkVtVrk 82 
                                       +iGd V+++ 
  gi|488601466|ref|YP_007907937.1| 277 TIGDNVSIEA 286
                                       69*****987 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00017
                                       TTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  56 gkgiIrmdgvtRknagvsiGdkVt 79 
                                       g+giI +dg++ +nag+ iG+  +
  gi|488601466|ref|YP_007907937.1| 327 GEGIIEIDGILKANAGAFIGENCR 350
                                       68******************9765 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.7    0.0034       6.1     222     256 ..     232     268 ..     214     273 .. 0.80
   2 ?    9.4   7.4   0.00015      0.26     172     272 ..     274     370 ..     268     379 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0034
                           DUF4954 222 egVile.dfiissGskikdgavisr.cfvGqavklkk 256
                                       ++V+++ ++ii +Gs ik g+ i+  +++G++++++ 
  gi|488601466|ref|YP_007907937.1| 232 KNVTVKgNVIIGEGSIIKAGTYIEGpVIIGENCEIGP 268
                                       566654489999*********99853899****9975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00015
                           DUF4954 172 evGeigekvkilnaglikNvkigdyatiegasklengtinSskeapveiGeg..ViledfiissGskikdgavisrc 246
                                        + +ig++v+i+  ++i N  igd ++i    ++++  i       +eiG +  V   ++ii+    +k  a    +
  gi|488601466|ref|YP_007907937.1| 274 PYTTIGDNVSIEALTIISNSIIGDNCMIGSGANIKDSVID----RFTEIGCNftVLGGEGIIEIDGILKANA---GA 343
                                       5779*******************************98775....5566776522555566665544444333...46 PP

                           DUF4954 247 fvGqavklkkqfsaed.sllfaNcqge 272
                                       f+G++++++++  ++  +++++ c +e
  gi|488601466|ref|YP_007907937.1| 344 FIGENCRIGNNIVVKPlTVIGNECMIE 370
                                       888888888877665424455556555 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.1   0.00028       0.5      17      91 ..     222     293 ..     216     308 .. 0.84
   2 ?    1.7   1.2      0.18   3.3e+02      24      57 ..     332     365 ..     299     382 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                        Bactofilin  17 gdlridGkveGdieakgklvvgeggkvegnikaeevvvaGtvkGnveaeekvelkktakveGdikaksleieega 91 
                                       ++ +i+Gkve +++ kg++++geg+ +++    e  v+ G+   n+e+  +  lk+ +++  +++ + l+i ++ 
  gi|488601466|ref|YP_007907937.1| 222 DGKVIAGKVEKNVTVKGNVIIGEGSIIKAGTYIEGPVIIGE---NCEIGPNTVLKPYTTIGDNVSIEALTIISNS 293
                                       56789*********************999999988888787...7888888888888888888888888876655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                        Bactofilin  24 kveGdieakgklvvgeggkvegnikaeevvvaGt 57 
                                       +++G ++a++   +ge+ ++  ni ++ ++v G+
  gi|488601466|ref|YP_007907937.1| 332 EIDGILKANAGAFIGENCRIGNNIVVKPLTVIGN 365
                                       4567777777888999999999999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2254.24
//
Query:       gi|488601467|ref|YP_007907938.1|  [L=402]
Description: UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-39  134.4   0.1    6.5e-39  134.0   0.1    1.2  1  NTP_transferase  Nucleotidyl transferase
    2.1e-24   84.3  36.4    8.4e-09   34.8   4.3    4.6  4  Hexapep          Bacterial transferase hexapeptide (six repea
    6.8e-14   52.5   0.0    9.7e-14   52.0   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    2.2e-13   49.7  31.4      2e-07   30.7   3.7    5.1  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    7.8e-05   21.0   6.2    0.00092   17.5   5.8    2.5  2  DUF4954          Domain of unknown function (DUF4954)
    0.00011   22.0   0.0    0.00017   21.4   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.012   15.9   3.5      0.012   15.9   3.5    2.2  2  Bactofilin       Polymer-forming cytoskeletal
      0.057   12.4   1.2       0.35    9.7   0.7    2.1  2  Fucokinase       L-fucokinase
       0.15   12.3   0.9         22    5.3   0.3    2.9  3  CART             Cocaine and amphetamine regulated transcript


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 !  134.0   0.1   3.3e-42   6.5e-39       2     244 ..       3     224 ..       2     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 134.0 bits;  conditional E-value: 3.3e-42
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       avIL+ G+GtR++PLt t++k ++ v++k +++ + +++l + g++e+i+v+  + ++ v+e++++++  gv+++++
  gi|488601467|ref|YP_007907938.1|   3 AVILSAGEGTRMRPLTYTRPKVMIEVANK-PILAHLIEELKKVGVDEVILVVG-YYQEKVREYFGKTW-NGVRLKYS 76 
                                       8****************************.*****************777776.77889********9.79****** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       +++++ gtAdA++ a+ ++ed++     l+L+gD +++  ++++++    e++    +t+g+  v+++++yGv+ ++
  gi|488601467|ref|YP_007907938.1|  77 TQTKQLGTADALRSAEHYIEDDF-----LMLNGDTIVDAeDLKRII----ENE----MTIGVNTVDDPENYGVVVVK 140
                                       ********************887.....9*********65555555....444....59*****************9 PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       + g ve+++EKP+++  ++++++GiY f++++++++ +   ++ rge eitd+++ a+++g +   +  +   +W D
  gi|488601467|ref|YP_007907938.1| 141 D-GFVEEIIEKPEKPV-ANTINAGIYHFTRDIFDYI-RITPKSVRGEYEITDTINLAIKDGVRFSTAKIS---GWID 211
                                       9.79************.89*****************.8899999****************9777554444...5999 PP

                                       XSSHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanek 244
                                          + +ll++ne 
  gi|488601467|ref|YP_007907938.1| 212 ASYPWDLLKINEL 224
                                       8888888888765 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   2.8   1.5e-07    0.0003      10      36 .]     237     263 ..     234     263 .. 0.92
   2 !   34.8   4.3   4.2e-12   8.4e-09       2      35 ..     265     298 ..     264     299 .. 0.93
   3 !   16.2   2.0   3.1e-06    0.0061       2      35 ..     300     332 ..     299     333 .. 0.87
   4 !   30.6   4.3   9.2e-11   1.8e-07       1      35 [.     358     392 ..     358     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                                       E-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                       + ++++i gnV+IG++++I ag++i g
  gi|488601467|ref|YP_007907938.1| 237 VEKNVTIKGNVVIGEGSIIKAGTYIEG 263
                                       678*********************975 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 4.2e-12
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +vIG+n+ Igp+++i++++ IG+++kIga v ++
  gi|488601467|ref|YP_007907938.1| 265 VVIGKNCEIGPNCYIRAHTSIGNGCKIGAAVEVK 298
                                       89***************************88776 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 3.1e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++ ++++I +  +i g+ +IG+n+  gag+ ++
  gi|488601467|ref|YP_007907938.1| 300 SIVMNGTKIPHHNYI-GDSVIGENCNFGAGTKVA 332
                                       67899**********.5555***********987 PP

  == domain 4  score: 30.6 bits;  conditional E-value: 9.2e-11
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +++IG+nv+ g +a i +++ IG+n+ I++++++ 
  gi|488601467|ref|YP_007907938.1| 358 GAIIGDNVKTGINASINAGAMIGNNCFIAPNAYVD 392
                                       589*****************************996 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   4.9e-17   9.7e-14       1     110 [.       3     119 ..       3     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 4.9e-17
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC..TS-EEE-TTS CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarl..gvrvvededp 68 
                                       aviL +G+++Rm      ++K ++++++kp+l+++++ l+++gvdev++v+g+  e+v++++ ++  gvr+ + ++ 
  gi|488601467|ref|YP_007907938.1|   3 AVILSAGEGTRMRpltytRPKVMIEVANKPILAHLIEELKKVGVDEVILVVGYyqEKVREYFGKTwnGVRLKYSTQT 79 
                                       79**********7554436********************************99877888877666666777555444 PP

                                       .S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHC CS
                      NTP_transf_3  69 .gkgplaslaaalraaadadavlvlacDmPlltpelverllaa 110
                                        + g++ +l++a + +  +d +l+l +D++ +++e ++r++++
  gi|488601467|ref|YP_007907938.1|  80 kQLGTADALRSAEHYI--EDDFLMLNGDTI-VDAEDLKRIIEN 119
                                       279**********998..6**********6.6*****999986 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.1   4.2e+03       3      15 ..     116     128 ..     116     138 .. 0.71
   2 !   10.1   0.8   0.00026      0.53      13      32 ..     240     261 ..     237     262 .. 0.89
   3 !   30.7   3.7   9.9e-11     2e-07       1      28 [.     264     293 ..     264     297 .. 0.94
   4 !    8.3   0.3   0.00097       1.9       4      13 ..     319     328 ..     318     331 .. 0.89
   5 !   16.4   4.2   2.9e-06    0.0057       3      33 ..     360     392 ..     358     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.1
                                       EE-TT-EE-TT-E CS
                         Hexapep_2   3 iIGdnCliGanag 15 
                                       iI++   iG+n +
  gi|488601467|ref|YP_007907938.1| 116 IIENEMTIGVNTV 128
                                       5777777888865 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00026
                                       T-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2  13 nagi.G.vslGdncvvgaGvvi 32 
                                       n +i G v +G+++++ aG +i
  gi|488601467|ref|YP_007907938.1| 240 NVTIkGnVVIGEGSIIKAGTYI 261
                                       7778888**************9 PP

  == domain 3  score: 30.7 bits;  conditional E-value: 9.9e-11
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvga 28 
                                       pv IG+nC iG+n++i   +s+G++c++ga
  gi|488601467|ref|YP_007907938.1| 264 PVVIGKNCEIGPNCYIraHTSIGNGCKIGA 293
                                       8**************9988**********9 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.00097
                                       E-TT-EE-TT CS
                         Hexapep_2   4 IGdnCliGan 13 
                                       IG+nC++Ga 
  gi|488601467|ref|YP_007907938.1| 319 IGENCNFGAG 328
                                       ********96 PP

  == domain 5  score: 16.4 bits;  conditional E-value: 2.9e-06
                                       EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                         Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                       iIGdn+  G na i  G  +G+nc ++++ +++
  gi|488601467|ref|YP_007907938.1| 360 IIGDNVKTGINASInaGAMIGNNCFIAPNAYVD 392
                                       9************999***************96 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   5.8   4.6e-07   0.00092     146     260 ..     217     331 ..     210     338 .. 0.69
   2 ?    0.3   0.0     0.071   1.4e+02     235     285 ..     348     399 ..     340     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.6e-07
                           DUF4954 146 alyRhdkelteklkelidkyaeekksevGe..igekvkilnaglikN.vkigdyatiegasklengtinSskeapve 219
                                        l + ++ + +++++ id ++e++ + +G+  ige + i+  ++i+  v ig+ ++i     ++  t +    +  +
  gi|488601467|ref|YP_007907938.1| 217 DLLKINELMLSNIDTEIDGVVEKNVTIKGNvvIGEGSIIKAGTYIEGpVVIGKNCEIGPNCYIRAHTSI---GNGCK 290
                                       555666667777777777777777777774226777777777777633677777777666666555433...34578 PP

                           DUF4954 220 iGegViledfiissGskikdgavisrcfvGqavklkkqfsa 260
                                       iG  V+++++i+++G+ki +   i ++++G++++++ + ++
  gi|488601467|ref|YP_007907938.1| 291 IGAAVEVKNSIVMNGTKIPHHNYIGDSVIGENCNFGAGTKV 331
                                       99999999999999999999999999999999988876655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.071
                           DUF4954 235 skikdgavisrcfvGqavklkkqfsaed.sllfaNcqgengEavaifagPyt 285
                                        +ik g +   +++G +vk + ++s++  +++++Nc +     v  ++ Pyt
  gi|488601467|ref|YP_007907938.1| 348 KRIKTGRKKLGAIIGDNVKTGINASINAgAMIGNNCFIAPNAYVDGWIDPYT 399
                                       6788899999999******999999875278899999998888888888887 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 !   21.4   0.0   8.8e-08   0.00017       1      60 [.       1      61 [.       1     126 [. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.8e-08
                                      EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHH CS
                              IspD  1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefe 60
                                      + +vi  AG+G+Rm+     +pK  +e++++++l+h ++ l +   vd++++vv  ++ e+++
  gi|488601467|ref|YP_007907938.1|  1 MQAVILSAGEGTRMRpltYTRPKVMIEVANKPILAHLIEELKK-VGVDEVILVVGYYQ-EKVR 61
                                      5799*********97333689*******************998.77899999987776.4444 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   3.5   5.8e-06     0.012      16      92 ..     228     307 ..     219     310 .. 0.87
   2 ?   -1.8   0.0         2   3.9e+03      32      56 ..     368     393 ..     347     396 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                        Bactofilin  16 egdlridGkveGdieakgklvvgeggkvegnikaeevvvaGt...vkGnveaeekvelkktakveGdikaksleiee 89 
                                       + d +idG ve +++ kg++v+geg+ +++    e  vv G+   +  n++++++ ++ + +k+ + +++k+  + +
  gi|488601467|ref|YP_007907938.1| 228 NIDTEIDGVVEKNVTIKGNVVIGEGSIIKAGTYIEGPVVIGKnceIGPNCYIRAHTSIGNGCKIGAAVEVKNSIVMN 304
                                       56889*****************************99999999543445**********************9888888 PP

                        Bactofilin  90 gav 92 
                                       g +
  gi|488601467|ref|YP_007907938.1| 305 GTK 307
                                       766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                        Bactofilin  32 kgklvvgeggkvegn.ikaeevvvaG 56 
                                       + +  ++ g+ +  n   a +++v+G
  gi|488601467|ref|YP_007907938.1| 368 GINASINAGAMIGNNcFIAPNAYVDG 393
                                       33333444444433333334444444 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.7   0.00018      0.35     274     337 ..     236     310 ..     211     313 .. 0.65
   2 ?    4.4   0.1    0.0073        15     273     319 ..     294     340 ..     284     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00018
                        Fucokinase 274 avvinSvlessvsvgegsviehs.slkgnvsigsnsiv.sglelessee.........slelpddtilqtlslkl 337
                                       +v  n  ++++v +gegs+i+    ++g+v ig+n+ +  +++++++++          +e+++ ++++++++ +
  gi|488601467|ref|YP_007907938.1| 236 VVEKNVTIKGNVVIGEGSIIKAGtYIEGPVVIGKNCEIgPNCYIRAHTSigngckigaAVEVKNSIVMNGTKIPH 310
                                       444566788888999999998441344666666666552355555554455556777778899999999888765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0073
                        Fucokinase 273 savvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesse 319
                                        + v nS++ ++ ++  + +i +s +++n++ g+++ v +l+l+++e
  gi|488601467|ref|YP_007907938.1| 294 AVEVKNSIVMNGTKIPHHNYIGDSVIGENCNFGAGTKVANLKLDEKE 340
                                       566889**********************************9999873 PP

>> CART  Cocaine and amphetamine regulated transcript protein (CART)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.011        22      35      56 ..     270     291 ..     265     303 .. 0.85
   2 ?   -2.1   0.0       2.3   4.6e+03      38      50 ..     319     331 ..     310     335 .. 0.62
   3 ?    4.1   0.0     0.026        51      18      54 ..     345     383 ..     336     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                              CART  35 aCdvgerCAvrkgsRiGklCdC 56 
                                        C++g +C +r  + iG  C  
  gi|488601467|ref|YP_007907938.1| 270 NCEIGPNCYIRAHTSIGNGCKI 291
                                       6****************98865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                              CART  38 vgerCAvrkgsRi 50 
                                       +ge+C    g+++
  gi|488601467|ref|YP_007907938.1| 319 IGENCNFGAGTKV 331
                                       5666666666555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.026
                              CART  18 lqskrlpsleKklgqip..aCdvgerCAvrkgsRiGklC 54 
                                        ++kr+ + +Kklg i      +g +  +  g+ iG  C
  gi|488601467|ref|YP_007907938.1| 345 TKDKRIKTGRKKLGAIIgdNVKTGINASINAGAMIGNNC 383
                                       5899**********9962257789999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2223.52
//
Query:       gi|488601468|ref|YP_007907939.1|  [L=414]
Description: ribulose 1,5-bisphosphate carboxylase large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-99  331.8   0.6    4.8e-99  331.3   0.6    1.2  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    1.5e-33  115.5   0.0    2.6e-33  114.7   0.0    1.4  1  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai
  ------ inclusion threshold ------
      0.014   14.8   0.1      0.047   13.1   0.0    1.8  2  AP_endonuc_2     Xylose isomerase-like TIM barrel
       0.15   12.6   0.1        5.7    7.5   0.0    2.5  2  Agenet           Agenet domain


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 !  331.3   0.6  1.1e-102   4.8e-99       1     299 []     128     408 ..     128     408 .. 0.98

  Alignments for each domain:
  == domain 1  score: 331.3 bits;  conditional E-value: 1.1e-102
                                       .HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHH CS
                     RuBisCO_large   1 giaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqd 77 
                                       gi + r+++ +++rp+ +t+ KPk+G  +++ya+v y  + gg+D++KdDEnl+sqpf r+++r+++v++a +ra++
  gi|488601468|ref|YP_007907939.1| 128 GIDGVRNIMRVHDRPLTATVPKPKVGFDADEYAEVGYRSWVGGIDILKDDENLTSQPFIRFEKRLAKVMKARERAEN 204
                                       78999************************************************************************ PP

                                       HHSS--EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--S CS
                     RuBisCO_large  78 etGekklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskh 154
                                       etGekk+y +nita+  +em+rrae+v++ g e+v+vd+l++Gf+a++++r+++++ +l++H+Hra+hga+tr+++h
  gi|488601468|ref|YP_007907939.1| 205 ETGEKKGYLINITAEA-REMERRAELVADYGNEFVMVDILTAGFSAVQTVRNKCEELGLAIHAHRAMHGAFTRNEEH 280
                                       *************876.9*********************************************************** PP

                                       EE-HHHHHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS-- CS
                     RuBisCO_large 155 GisfrvlakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGih 231
                                       Gis++vl+kl+R++Gvdh+h+gt  vgk+ gd++ v+  +                ++++++++ k+v+pv sgG+h
  gi|488601468|ref|YP_007907939.1| 281 GISLKVLTKLARMAGVDHMHVGTG-VGKMAGDKAEVMELR---------------DVCRKSWHNFKPVFPVSSGGLH 341
                                       ***********************7.*********555555...............5899****************** PP

                                       TTTHHHHHHHHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                     RuBisCO_large 232 agqlpellenlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                        g +p+++e +g  dvi+qaGGG++gHpdg++ Ga alrqa+ a++eG+dle+yAk+h eLarAle w
  gi|488601468|ref|YP_007907939.1| 342 PGLIPDIIELFGV-DVIIQAGGGVHGHPDGSEKGAMALRQAISAVLEGVDLEDYAKSHSELARALERW 408
                                       *************.****************************************************99 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.0   5.8e-37   2.6e-33       1     120 []       8     118 ..       8     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 5.8e-37
                   RuBisCO_large_N   1 dyvdedyepketdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieeveeekelvki 77 
                                       d+vd +y+p+ +++++ f+v+  +++ +ee +++vA+eSS+gtwt++s   d ++k l akv++i+      e + +
  gi|488601468|ref|YP_007907939.1|   8 DFVDLSYKPE-DEIVCYFKVK--SDLPIEESSGRVASESSVGTWTTLSRLPD-RIKWLMAKVFRIDG-----ERIAV 75 
                                       699****997.58*******9..79**************************9.************65.....789** PP

                   RuBisCO_large_N  78 AYplelFeegsipqllssiaGnifgmkavkalrleDirlPkay 120
                                       AY+++lFeeg+ipq+lss+aGnifgm+a+k lr eD+++P+++
  gi|488601468|ref|YP_007907939.1|  76 AYKTDLFEEGNIPQFLSSVAGNIFGMRAIKGLRFEDFEVPASF 118
                                       ****************************************975 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 ?   13.1   0.0     1e-05     0.047      28     113 ..     248     326 ..     227     335 .. 0.68
   2 ?   -1.6   0.0      0.34   1.5e+03      79     104 ..     349     380 ..     346     409 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCC.GBCTTTSGHH CS
                      AP_endonuc_2  28 eelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGt.agagpkgsee 103
                                       ++++++r+ ++elgl i++++++ +    +e        e+   lk   +la+  G++++++++G    ag+k   e
  gi|488601468|ref|YP_007907939.1| 248 SAVQTVRNKCEELGLAIHAHRAMHGAFTRNE--------EHGISLKVLTKLARMAGVDHMHVGTGVgKMAGDKA--E 314
                                       469*************888777655544333........234678******************99332223333..2 PP

                                       ..HHHHHHHHHH CS
                      AP_endonuc_2 104 ..eawerlaesl 113
                                         e ++  ++s+
  gi|488601468|ref|YP_007907939.1| 315 vmELRDVCRKSW 326
                                       346666666666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.34
                                       HHHHTBSEEEEEBCCGBCTTTSGHH......H CS
                      AP_endonuc_2  79 aaaLGapllvlhpGtagagpkgsee......e 104
                                        + +G+++++   G+ + +p+gse+      +
  gi|488601468|ref|YP_007907939.1| 349 IELFGVDVIIQAGGGVHGHPDGSEKgamalrQ 380
                                       56677777777766543333333333332220 PP

>> Agenet  Agenet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0013       5.7      16      40 ..      59      83 ..      56      90 .. 0.84
   2 ?    2.2   0.1     0.055   2.5e+02       1      18 [.     310     327 ..     310     328 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                            Agenet 16 aWfrAtilkvkegdkylVeYdd.ldd 40
                                       W  A++ ++ +g+++ V Y++ l +
  gi|488601468|ref|YP_007907939.1| 59 KWLMAKVFRI-DGERIAVAYKTdLFE 83
                                      5*********.**********95444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.055
                            Agenet   1 GdkVEvlsdeegfrGaWf 18 
                                       Gdk Ev    + +r +W+
  gi|488601468|ref|YP_007907939.1| 310 GDKAEVMELRDVCRKSWH 327
                                       9****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.59
# Mc/sec: 2120.09
//
Query:       gi|488601469|ref|YP_007907940.1|  [L=506]
Description: Lysyl-tRNA synthetase (class II) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-72  243.5   2.0    3.6e-72  243.1   2.0    1.2  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    2.3e-17   62.7   2.5    4.3e-17   61.9   1.3    2.0  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00012   21.6   1.2    0.00089   18.8   0.1    2.4  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.1   2.0   6.1e-76   3.6e-72       2     313 ..     148     481 ..     147     482 .. 0.92

  Alignments for each domain:
  == domain 1  score: 243.1 bits;  conditional E-value: 6.1e-76
                                       CCHHHHTHHHHC.CSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2   2 eelrlknryldl.rtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtq 77 
                                        e+r+++ryld+  +e+ ++++ l ++v++++r+yl++ngfie+ tPiL+   +++ ar+F + ++  e++++ L++
  gi|488601469|ref|YP_007907940.1| 148 IETRYRQRYLDFiMNEESRETFFLINKVIHLIRNYLNDNGFIEVYTPILQPVYGGAFARPFETYHHFLEEKMY-LRI 223
                                       589*********9**************************************************9999999999.*** PP

                                       -SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  78 spqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdie 154
                                       +p+lyl++l+v+g+++v+++a++FR+Ed++  +++ EF+q+e+++++ie +++m++le++++++v ++ +++ ++ie
  gi|488601469|ref|YP_007907940.1| 224 APELYLKRLLVGGFEKVYEFAPCFRNEDVDPLHNP-EFIQLEFYWAYIELSQLMDFLEKMFEEVVLKA-TGK-TEIE 297
                                       ***********************************.*******************************9.444.4444 PP

                                       HTTTTTSEE-SSS-EEEEHHHHHHHHHTS-SS--HHHHHHHHH.......................HS--SEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxx RF
                       tRNA-synt_2 155 fvirrnskdlkkpfkrltykeaieklneigkdldkaderalvk.......................keknepvfvtd 208
                                        +   +  ++k+p+k++ +++ai+++ +i+ +  ++de ++                          ++ +p+f+t+
  gi|488601469|ref|YP_007907940.1| 298 YQG--KIVNFKRPWKKMRMVDAIKEFGGIDVEKMSDDELFNHAkelgieeerrgeiieklfdyyakDKIVNPTFITH 372
                                       444..4469****************99986666666666655577777788888888888888888999******** PP

                                       EBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHH........SSSGGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx RF
                       tRNA-synt_2 209 fPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgld........eeaeekfswyleal 277
                                       fP  ++p++++ +      +++++l+i g+E+++G +++++p e++ ++k+++           e++  +++y++al
  gi|488601469|ref|YP_007907940.1| 373 FPVDISPLAKKADGY----ADRMELYIAGMEVANGFSELNNPIEQYMRFKEEEELrkrsdkkgLETMPMDKDYIRAL 445
                                       *********999888....9******************************9998888888777788899******** PP

                                       HCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 278 eyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                       ey +pp +G+g+Gl Rl m+l +++  r+viaFP l
  gi|488601469|ref|YP_007907940.1| 446 EYAMPPASGVGIGLGRLFMILGNKRTLREVIAFPTL 481
                                       **********************************75 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 !   61.9   1.3   7.2e-21   4.3e-17       1      76 []      56     131 ..      56     131 .. 0.94
   2 ?   -1.4   0.0       0.4   2.4e+03      37      64 ..     273     300 ..     265     307 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 7.2e-21
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                       V++aGr++s+  r++g+vif+dl+D +griq+v+ +  ++ +k ++ +++Gd+++v G v ++++ge+++ v+e+++
  gi|488601469|ref|YP_007907940.1|  56 VRIAGRLMSK--RKHGGVIFADLKDSSGRIQLVFRKdfTNEFKELKLVERGDILGVDGFVIKTRRGEVSVLVKEWTV 130
                                       89********..************************7777777777788**************************98 PP

                                       E CS
                   tRNA_anti-codon  76 l 76 
                                       l
  gi|488601469|ref|YP_007907940.1| 131 L 131
                                       6 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.4
                                       HHHHHHHTTS-TTSEEEEEEEEEECTTS CS
                   tRNA_anti-codon  37 eeatklaenlkeGdvvrvtGrvkrrpgg 64 
                                       ++ ++++e+  e+ v+++tG+ +  ++g
  gi|488601469|ref|YP_007907940.1| 273 SQLMDFLEKMFEEVVLKATGKTEIEYQG 300
                                       5667788888899999999999888777 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.71   4.3e+03     147     170 ..     137     161 ..     129     193 .. 0.60
   2 !   18.8   0.1   1.5e-07   0.00089     108     171 ..     244     308 ..     237     326 .. 0.73
   3 ?    0.6   0.0     0.055   3.3e+02     211     234 ..     452     475 ..     439     479 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.71
                                       HHHHHHCTST.EEEEEEECEETTEE CS
                      tRNA-synt_2d 147 ellkklfgae.vkvrfrpsyfpfte 170
                                        l  k  g e +++r+r+ y  f  
  gi|488601469|ref|YP_007907940.1| 137 PLPDKWHGLEdIETRYRQRYLDFIM 161
                                       5555566666678888888888864 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.5e-07
                                       EEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHC....TSTEEEEEEECEETTEEE CS
                      tRNA-synt_2d 108 grvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklf....gaevkvrfrpsyfpfteP 171
                                         +fR+++vD  h +eF q+e+ ++   ++l++l+ +le++++++     g++ ++ ++ +   f  P
  gi|488601469|ref|YP_007907940.1| 244 APCFRNEDVDPLHNPEFIQLEFYWAY--IELSQLMDFLEKMFEEVVlkatGKT-EIEYQGKIVNFKRP 308
                                       569*******************9986..7777777777777766531111444.66666666666666 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.055
                                       EEEEEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 211 gfafGlGveRlamlkygieDiRel 234
                                       + + G+G+ Rl m+  +   +Re+
  gi|488601469|ref|YP_007907940.1| 452 ASGVGIGLGRLFMILGNKRTLREV 475
                                       5678**********9999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2978.08
//
Query:       gi|488601470|ref|YP_007907941.1|  [L=333]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-39  133.6   0.0    7.4e-39  132.9   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    1.2e-10   41.8   0.0    1.8e-10   41.2   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
      0.002   17.6   0.0     0.0031   17.0   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.03   14.4   0.0      0.055   13.6   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.041   14.5   0.0        0.1   13.2   0.0    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.058   14.2   0.0        0.1   13.4   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.0   2.5e-42   7.4e-39       1     121 []       3     137 ..       3     137 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 2.5e-42
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpag 77 
                                       kv++vG++Gy+G+ellrlL +hpeve+ v++s++  +Gkk+ +++k l++  dl+++++d+  ++++d+vfla+p+g
  gi|488601470|ref|YP_007907941.1|   3 KVGVVGGSGYTGSELLRLLVNHPEVEVKVVTSRKY-EGKKIWSLHKFLKGFFDLEFKSPDIRYFDDCDLVFLAVPHG 78 
                                       7**********************************.***************************************** PP

                                       HHHHHHHHHHHTTSEEEESSSTTTTST...............TSEBE-HHHHGGGGGGH CS
                    Semialdhyde_dh  78 vskelapklaeagvkviDlssdfRlkd...............davyvlpevnreaikka 121
                                        ++ +ap++++ag+kviDls+d+Rl++               +avy+lpe++r++ikka
  gi|488601470|ref|YP_007907941.1|  79 EAMRYAPEFLDAGLKVIDLSADYRLDKktfeevyekehigyrEAVYGLPEIHRDEIKKA 137
                                       ********************************************************986 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   5.9e-14   1.8e-10       2     184 .]     155     304 ..     154     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 5.9e-14
                                       HHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHH CS
                   Semialdhyde_dhC   2 kPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreel 78 
                                       +PL+++   ++rv++++++++ GaG +                 ++  +++ ++   ++py+++  +++ +e+ +el
  gi|488601470|ref|YP_007907941.1| 155 APLAEK-ELIDRVVFDSKSGITGAGVS-----------------PTDFTHYPNLHEAIVPYKVT-NHRHYWEMVQEL 212
                                       799998.779****************7.................888899999***********.************ PP

                                       HHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCSTTEEEEESSHCHHSSHHHHTT CS
                   Semialdhyde_dhC  79 kavaetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaapevkvvvneeedrPtpaavag 153
                                       +  + + ki   t+         P  rG+++ +++ l+  l+ +ev+e++e +++   ++++ ++      +  v+g
  gi|488601470|ref|YP_007907941.1| 213 GRFQGDIKISF-TP------QVFPGSRGILTNAHTFLRgeLELEEVAEIYERFYDG-CPFIRLQD---SIRLSYVRG 278
                                       ****9777655.55......358999************999999************.99999995...788899999 PP

                                       CSSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
                   Semialdhyde_dhC 154 gtnsvsVGRirkdemgdeglklvvvgDNllk 184
                                        +n+++++ + +    d+ +++ +++DNl+k
  gi|488601470|ref|YP_007907941.1| 279 -SNFCDIA-FFVGT--DR-VVVSSAIDNLVK 304
                                       .9******.44444..65.99********97 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     1e-06    0.0031       3      75 ..       6      76 ..       4      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                                      EETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                         Epimerase  3 VtGatGfiGsalvkallekg.yevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAavg 75
                                      V+G++G+ Gs l++ l ++  +ev +++++++++++    ++    + +l+++ ++   r+f+  ++d v+++  v 
  gi|488601470|ref|YP_007907941.1|  6 VVGGSGYTGSELLRLLVNHPeVEVKVVTSRKYEGKKIWSLHKflkGFFDLEFKSPD--IRYFD--DCDLVFLA--VP 76
                                      99******************888*******99999988888778888888888777..89999..79999988..33 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.8e-05     0.055       1      44 [.       2      42 ..       2      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBH CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkda 44
                                      ikv+vvG sG  G+e+++++ +++++e+  + +rk    egk++
  gi|488601470|ref|YP_007907941.1|  2 IKVGVVGGSGYTGSELLRLLVNHPEVEVKVVTSRKY---EGKKI 42
                                      79**************************99999976...56655 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 ?   13.2   0.0   3.5e-05       0.1       1      95 [.       3      98 ..       3     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.5e-05
                                      EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCC..CHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-HH CS
                     F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnpe..kaeelaeelg....vkvtavdneeaaeeadvvvlavkpe 72
                                      k+g++ G+G  g+ l++ l+++   + e+ v++sr+ e  k+ +l++ l+     + ++ +     +++d v+lav+  
  gi|488601470|ref|YP_007907941.1|  3 KVGVVgGSGYTGSELLRLLVNHP--EVEVKVVTSRKYEgkKIWSLHKFLKgffdLEFKS-PDIRYFDDCDLVFLAVPHG 78
                                      7999*9***************96..8888888999877224444444444787555555.99999************99 PP

                                      HHHHHHHHCGHHHHTTSEEEEES CS
                     F420_oxidored 73 dveevlselakdalkgklvisvl 95
                                       +   + e    +++g  vi+ +
  gi|488601470|ref|YP_007907941.1| 79 EAMRYAPEF---LDAGLKVIDLS 98
                                      998888888...66677777765 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 ?   13.4   0.0   3.4e-05       0.1       1      90 [.       2      95 ..       2      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                                      EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT....TESEEEE-S-GGG CS
                      GFO_IDH_MocA  1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladp....eidavivatpngt 74
                                      ++v+++G+ G+ gs+ lr l ++ ++ ev  + +++ e  +  + +  ++ + dle  + d     ++d+v+ a+p g+
  gi|488601470|ref|YP_007907941.1|  2 IKVGVVGGsGYTGSELLRLLVNH-PEVEVKVVTSRKYEGKKIWSLHKFLKGFFDLEFKSPDIryfdDCDLVFLAVPHGE 79
                                      6899**99788899999777777.9999998888888888877544445544443322222223338************ PP

                                      HHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA 75 heelakaaleagkhvl 90
                                       +++a ++l ag +v+
  gi|488601470|ref|YP_007907941.1| 80 AMRYAPEFLDAGLKVI 95
                                      ************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1842.14
//
Query:       gi|488601471|ref|YP_007907942.1|  [L=889]
Description: oligosaccharyl transferase, archaeosortase system-associated [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  155.9  48.4    1.9e-44  152.4  34.1    2.7  3  STT3      Oligosaccharyl transferase STT3 subunit
    5.2e-18   65.1   3.2    9.9e-18   64.2   3.2    1.5  1  AglB_L1   Archaeal glycosylation protein B long peripheral do
  ------ inclusion threshold ------
      0.041   13.7   0.0      0.086   12.7   0.0    1.4  1  TetR_C_1  Tetracyclin repressor-like, C-terminal domain
       0.11   11.4   0.2       0.15   10.9   0.2    1.1  1  Granin    Granin (chromogranin or secretogranin)


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 !  152.4  34.1   4.3e-48   1.9e-44       5     434 ..      18     430 ..      13     439 .. 0.92
   2 !   10.3   4.6   5.2e-05      0.23     337     481 ..     455     620 ..     427     624 .. 0.68
   3 ?   -2.5   0.1      0.41   1.8e+03     437     483 ..     746     806 ..     712     809 .. 0.65

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 4.3e-48
                                       HHHHHHCCCCCHCC.CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHC CS
                              STT3   5 vifalialvavasrdlFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygpliv 81 
                                       +i   i++++++++ + ++ dg    s +Dp+Y++Rl+   l+n         +++wfd ++ yP G ++++gp++v
  gi|488601471|ref|YP_007907942.1|  18 IIGLYIRIINPWNSVFVSWMDGARL-SGNDPWYYFRLIDSALHN--------SGRIWFDAFTNYPHGTYTHFGPFLV 85 
                                       4556788999999955588888877.******************........78*********************** PP

                                       CC.CHHHHHHCCHHCHHHHHHHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CC.CCCTTSTT--STCC CS
                              STT3  82 lLamlasaiinhsldvsirevclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPg.YlsrtvaGfyDtdm 157
                                       +L++la +i+  ++  ++r ++ ++pa+ gsLla+p+y l   +++++ G ++All+++ Pg +++r+v+ f+D+++
  gi|488601471|ref|YP_007907942.1|  86 YLSVLAVKITGAATLAEVRTTIAFIPAIAGSLLAVPAYILGSSIFNKRVGAASALLVVLIPGqLMARSVLSFNDHHI 162
                                       ***************************************************************************** PP

                                       CCHHHHHHHHHHHHHHHHCCS...TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-CCHHHHHH CS
                              STT3 158 feivlllfvlffflkaiktks...nkislaviaaliiflivlaWggyailiyallllfilalLiigrfelklkiavt 231
                                       +e++++l++l  f  a+k+ +   ++  ++via+l + l+ laW   +i+++++l   +la L+++    +lk    
  gi|488601471|ref|YP_007907942.1| 163 WEVFWQLSTLACFAFALKRFEdvrKHFIYPVIAGLCLGLYLLAWAPGFIIALIILGYVFLAHLTSTYLDVDLKKITY 239
                                       ***********9999999999998999*********************************************99888 PP

                                       HHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCCCHHTT.HHHHTT--GGG CS
                              STT3 232 fsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfislfqpgilsevlgligev 308
                                       +s i++ +   ++++l+++f+     ++ +++  ++++ql++++  +++   l f  ++ l   g  ++ +gl    
  gi|488601471|ref|YP_007907942.1| 240 ISAIVFLVG--ALIYLPFAFK-----YPSFSTTRYSPFQLIVLLAAAII--VLLFRGIEILKNRG-HFNKVGLKDSY 306
                                       887777766..999******9.....6**********************..99999999999999.88889999999 PP

                                       HHHHHHHHHHHHCCCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSSTTTTCCCHHHCHHCCHHCTCHHHH CS
                              STT3 309 vtalavlglialwlgilyslldleyaklkikiiilvsvwlpvgllaltkglrfliftvPlgiifvgllleflavfvk 385
                                        ++l++++++ l++g    ++    +++  ++  +v v++p+g++++++++++++ ++  +  ++ +  +f   f++
  gi|488601471|ref|YP_007907942.1| 307 AFPLSIVVIVVLFIGGVAIIS----PDFLKLLTRIVGVVQPKGGALTVAEIQPFF-SMYGEPSLTPAWRHFSITFFF 378
                                       *************99988887....9999999********************984.444555589999999999999 PP

                                       HHH...HHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHH CS
                              STT3 386 iys...vsqilfsgvvvillmltllpvlallaavkiskifstykdekeakik 434
                                       +++   + ++l+ + +    +l l++ la++aa++ +++f++y+ +++a + 
  gi|488601471|ref|YP_007907942.1| 379 AMPgmlYVAYLLIKQRDSKYLLILVWGLAMFAALAGQNRFAYYFGAVSALFA 430
                                       9999996666666666666*************************99998765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.2e-05
                                       HHHHHHHHS---S--CCHHHCCSSST..TTTCCCHH.HCHHCCHHCTCHHHHHHH.HHHHHHCCC-SCHCCCCCHHH CS
                              STT3 337 kikiiilvsvwlpvgllaltkglrfl..iftvPlgi.ifvgllleflavfvkiys.vsqilfsgvvvillmltllpv 409
                                        + ++ +++  + v  +++t +++ l  ++++P+ i i++++  +f+  + ki   +s   + +  vi ++l ++p+
  gi|488601471|ref|YP_007907942.1| 455 IHASLWVIALAILVYNYMTTMNIYVLalLALAPAVIdILINFPNSFELHVDKIRGlLSGKKVTAISVISIILIVAPA 531
                                       2333445555566677999999999886777888889999999998876655555667777888888999******* PP

                                       HHHHCCCHHH.HHHHHCCHHHHHHHHHHHHHH.......HHHHCT.TTTTHHH.TTHHHCHHH........HHHHHH CS
                              STT3 410 lallaavkis.kifstykdekeakikvaakav.......aptksnglkeslew.kantnrdsv........vitwwd 469
                                       lal++    + +++s+y +   +k ++ a +        ++  +++ +e  +     + +d +        +i+wwd
  gi|488601471|ref|YP_007907942.1| 532 LALFYPTLSDaNLYSKYSAGGINKQWYDALVWmkdntpeKELYDKFYYEMYKPpEGYKLSDRYpypdgvysIISWWD 608
                                       ******99999*********99999996655577777884445555555444444444444333333334599**** PP

                                       HHHHHHHHHHHH CS
                              STT3 470 yghilaveadrp 481
                                       ygh ++++a r 
  gi|488601471|ref|YP_007907942.1| 609 YGHWITAIAHRI 620
                                       ***999988774 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.41
                                       HHHH...........HHHHCT.TTTTHHH.TTHHHCHH..HHHHHHHHHHHHHHHHHHHHH CS
                              STT3 437 akav...........aptksnglkeslew.kantnrds..vvitwwdyghilaveadrpVt 483
                                        +++           ++ k++ ++e+l+  ++n+n  +  v +t++ y  ++ ++  ++Vt
  gi|488601471|ref|YP_007907942.1| 746 DGSGlqnyrmvyeseFEAKNQLTYEALYRiIYNSNHADhpVAVTSTGYVKVFEYVKGVKVT 806
                                       3333555555555559999999999999999998877633566666666677777766666 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 !   64.2   3.2   2.2e-21   9.9e-18       1      92 []     802     884 ..     802     884 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.2e-21
                                       -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEETTEEE CS
                           AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevtagnvta 77 
                                       G ++tG+a +g +v+++++++tnq+rtf+Y q+a+  e+G++e+++PY+++      t++ v+a ++Y++++gnvt+
  gi|488601471|ref|YP_007907942.1| 802 GVKVTGKA-SGSEVIVKANITTNQNRTFEYIQKAK-VENGHYEIVLPYAQN------TKYPVKA-SEYTIQSGNVTK 869
                                       889****9.799**********************8.89*************......9******.9*********** PP

                                       EE---HHHHHHT-EE CS
                           AglB_L1  78 eveVpEeaVlsgetv 92 
                                       +++ ++e+V++g+++
  gi|488601471|ref|YP_007907942.1| 870 TLTLSDEDVENGKII 884
                                       ************987 PP

>> TetR_C_1  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05     0.086      24      66 ..     715     757 ..     712     760 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                       HTSTTHHHHHHT-SS--HHHHHHHHHHHHHHHHTT--HHHHHH CS
                          TetR_C_1  24 lrhrdlarlfagtprlspnelrgmErlLrllrdaGlsdedavy 66 
                                       l  +++ ++ a+ +++s+n++++mE  L +l+  Gl+    vy
  gi|488601471|ref|YP_007907942.1| 715 LNIPAGSNVIATMNVPSENYFKTMEARLHILDGSGLQNYRMVY 757
                                       66788999****************************9876665 PP

>> Granin  Granin (chromogranin or secretogranin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   3.4e-05      0.15     438     494 ..     546     608 ..     540     629 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.4e-05
                                       .......XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXSXSXSTTT........T CS
                            Granin 438 dkqylGelsneyldkkqWkksdeerkeltedkfle.geeeneltlsmklsFpeynyd.....g 494
                                        k+  G   ++++d+++W+k++   kel++    e  +  +++ ls +  +p   y       
  gi|488601471|ref|YP_007907942.1| 546 SKYSAGGINKQWYDALVWMKDNTPEKELYDKFYYEmYKPPEGYKLSDRYPYPDGVYSiiswwD 608
                                       68889*************************999998778999999999999998887555551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (889 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.86u 0.39s 00:00:01.25 Elapsed: 00:00:00.56
# Mc/sec: 4773.42
//
Query:       gi|488601472|ref|YP_007907943.1|  [L=198]
Description: hypothetical protein Asulf_01984 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-55  185.8   0.0    8.5e-55  185.5   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5   0.0   4.8e-59   8.5e-55       2     196 ..       3     190 ..       2     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 4.8e-59
                                       EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--S CS
                   Methyltrn_RNA_2   2 refvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvsp 78 
                                       r f++++nka+T s+++l+dlpG agr+dv++r + ++l vshg+R+d +  +vL+g+p+  +++k++++ +k++sp
  gi|488601472|ref|YP_007907943.1|   3 RVFIIIGNKART-SEFSLNDLPG-AGRMDVICRFIAQSLLVSHGVRKDSTAIAVLLGGPQ--KSLKFKGDSIKYMSP 75 
                                       78**********.9*********.********************************9875..78************* PP

                                       SHHHHHHHHHHHHCHCCTGCCSEEEEETTEEEE---HHHHHHHHHCTSEEEEESTTSEEGGGS---SSEEEEEE-TT CS
                   Methyltrn_RNA_2  79 derniailikkalkaveeikkqekkvrpgltVrkegfealleelsekksiillkekGedisnakielnPvFilgdHi 155
                                       dern+a+li+kalka+    +++ + +pg++V+++g+ ++l+el + + i++l e+Ged +++  e +  F+lgdH+
  gi|488601472|ref|YP_007907943.1|  76 DERNVAGLIRKALKAK--ATDEWLEGSPGVYVSRKGIGEILDELEG-YRILYLREDGEDFHKVAEERDYAFVLGDHL 149
                                       *************999..999***********************99.9***************************** PP

                                       -SHHHHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHHH CS
                   Methyltrn_RNA_2 156 dlpeeeekllerlkakrvslgPlsLhadhcvtlihneldkk 196
                                       +++e+ e  + + ++  vs++P sL ad+cv++ hn ld+ 
  gi|488601472|ref|YP_007907943.1| 150 GVSENMEDEILKRADGVVSVSPISLQADQCVVILHNILDRF 190
                                       *****999988889999**********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1103.08
//
Query:       gi|488601473|ref|YP_007907944.1|  [L=188]
Description: Ribulose-5-phosphate 4-epimerase-related epimerase and aldolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  111.4   0.0    5.3e-32  111.3   0.0    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   2.9e-36   5.3e-32       4     185 ..      11     180 ..       8     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 2.9e-36
                                       HHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSC.EEEECECSSSTB-TTHHHHHH CS
                       Aldolase_II   4 aeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsg.evvegkekggkpssetplHla 79 
                                       a  +r+l++rgl +g +Gn+S + + +d+++it++gv++ +lt e++v+v++d + e++    k++++ss+ +lH +
  gi|488601473|ref|YP_007907944.1|  11 ALYGRKLYERGLIDGASGNLSFK-D-GDYVFITKTGVNLYDLTKESFVKVRIDADaEKL----KALSASSDALLHIK 81 
                                       6679*******************.4.68888*********************7333666....6789********** PP

                                       HHHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEE CS
                       Aldolase_II  80 iykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavll 156
                                       +y++ +d  +++H+H ++ v+ls++   + + p++ e++ +l  +e+ vi+     tee +e +++ ++ ++ ++++
  gi|488601473|ref|YP_007907944.1|  82 AYQK-SDYSVILHCHGTYNVVLSLI--YDKIVPVDLEGKLFL--GEIEVIDASF-MTEEYAEMVSDGIA-KKGFAVV 151
                                       ***7.8*****************76..67899******9966..7799986555.779999*****9*8.778**** PP

                                       TTTEEEEEESSHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 157 rnHGlltvGetleeAvalaetleeaaeiq 185
                                       ++HG++++G+t +e ++ +e++e+++++ 
  gi|488601473|ref|YP_007907944.1| 152 KGHGIYCAGKTFREVFNVIEYIEHSCQVL 180
                                       **************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1078.03
//
Query:       gi|488601474|ref|YP_007907945.1|  [L=287]
Description: putative permease, DMT superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-50  168.7  46.8    5.9e-26   91.3  21.1    2.0  2  EamA      EamA-like transporter family
    5.9e-05   22.6  23.2    0.00012   21.6  23.2    1.5  1  TPT       Triose-phosphate Transporter family
  ------ inclusion threshold ------
        0.6    9.0  20.3       0.21   10.5  10.0    2.1  2  CRT-like  CRT-like, chloroquine-resistance transporter-like


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 !   83.8  17.6     2e-27   1.2e-23       4     136 ..       7     136 ..       4     137 .. 0.96
   2 !   91.3  21.1   9.9e-30   5.9e-26       2     136 ..     151     286 ..     150     287 .] 0.97

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 2e-27
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       i ++   +lfw+ +f+++k+++++v+ ++ltf+rf+ia ++l +++llk+  +    ++d+  ++ lg++g++++++
  gi|488601474|ref|YP_007907945.1|   7 IAIISMTVLFWGWAFLAIKVAVKEVDAYSLTFYRFTIANVFLTAYLLLKKAVP---AKEDIPRIFALGFFGVTAYHV 80 
                                       455677899***************************************99888...9******************** PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       l++ +  ++s++ asli++l+Pvf+ ++s+ +lge +t+k++lg +++l Gv+l++
  gi|488601474|ref|YP_007907945.1|  81 LLNFGEMYISSGLASLIIALAPVFVFFFSISFLGEDFTIKKFLGSIIALSGVFLVI 136
                                       ******************************************************97 PP

  == domain 2  score: 91.3 bits;  conditional E-value: 9.9e-30
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvl 77 
                                        g+  ++++al+  +y+v+ k+l++k++pltlt++ +++a++ ll+++++  +++  ++s +   ++l+lg+++t+l
  gi|488601474|ref|YP_007907945.1| 151 VGVAAVFVSALSATFYIVYGKVLFEKYEPLTLTAYAIIFATVPLLLLIPFGVINFeFNFSAETAYSILFLGIFATFL 227
                                       588999*************************************************88899999************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++  ++y l k++as+as+++  +Pv++++ +++llgek+tl+++lg++++++Gv++++
  gi|488601474|ref|YP_007907945.1| 228 GYTGWYYVLDKMQASQASIFLQAIPVVAVFSAWFLLGEKITLLTVLGTIFVVVGVYFVN 286
                                       ********************************************************997 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  23.2   1.9e-08   0.00012      38     288 ..      40     284 ..      10     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.9e-08
                               TPT  38 qllvgsvlilvlwal..glkkrpkisseflkailplalvk.tlghvlavvslskvaVSfthtvKasePiFtvilsrl 111
                                       ++++  v++++++ l   +  +     e +  i+ l+++  t+ hvl ++    ++   +  + a++P+F   +s+ 
  gi|488601474|ref|YP_007907945.1|  40 RFTIANVFLTAYLLLkkAVPAK-----EDIPRIFALGFFGvTAYHVLLNFGEMYISSGLASLIIALAPVFVFFFSIS 111
                                       3333334433333331022222.....3455555555443134466666666677777899**************** PP

                               TPT 112 llgeklsllvylsLlpivgGvalasv..tElsFn....ligfisAlisnltfslrnifsKkllkklkdldalnlfai 182
                                       +lge ++++++l  ++ + Gv l  +   +lsF     ++g  +  +s l++++  ++ K l++k+  l+ + +  i
  gi|488601474|ref|YP_007907945.1| 112 FLGEDFTIKKFLGSIIALSGVFLVILdtSDLSFSmnesMVGVAAVFVSALSATFYIVYGKVLFEKYEPLTLTAYAII 188
                                       *********************9886522689997223358999999**************99999655777777777 PP

                               TPT 183 itilslllllPvallvegvlktpsllkstkvslkevllllllsgvlfhlynqvaymvLervspvthsvantvKrvvv 259
                                        +++ llll+P+ ++  +   + +  ++t    +++l+l + + +l +   +  y vL+++++   s+   +  vv 
  gi|488601474|ref|YP_007907945.1| 189 FATVPLLLLIPFGVINFE---F-NFSAET---AYSILFLGIFATFLGY---TGWYYVLDKMQASQASIFLQAIPVVA 255
                                       788899999999877555...2.222222...2455555555555444...567999***********99999**** PP

                               TPT 260 IvlsvlvfknpvsllnaiGtavaivGvfl 288
                                       + ++ ++++++++ll+++Gt  ++vGv+ 
  gi|488601474|ref|YP_007907945.1| 256 VFSAWFLLGEKITLLTVLGTIFVVVGVYF 284
                                       ***************************86 PP

>> CRT-like  CRT-like, chloroquine-resistance transporter-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  10.0   3.5e-05      0.21      83     195 ..      80     190 ..      33     208 .. 0.71
   2 ?    1.8   5.4     0.015        90      89     137 ..     238     284 ..     182     287 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.5e-05
                          CRT-like  83 ilvvigavstsGslqvllnqaiipitllasllllkerysliqylGAlviilgvvvvlipsllgessegnklvfnlll 159
                                       +l  +g +++s  l +l+  ++ ++ +++s+ +l e + + ++lG ++ + gv++v+  +   + s ++++v    +
  gi|488601474|ref|YP_007907945.1|  80 VLLNFGEMYISSGLASLIIALAPVFVFFFSISFLGEDFTIKKFLGSIIALSGVFLVILDTSDLSFSMNESMVGVAAV 156
                                       3445799**********************************************977665555555555555555566 PP

                          CRT-like 160 lisviPvalSnvykeiafkeveldvlyLqawvalfq 195
                                        +s + +++  vy  + f+++e   l L a+  +f 
  gi|488601474|ref|YP_007907945.1| 157 FVSALSATFYIVYGKVLFEKYE--PLTLTAYAIIFA 190
                                       6789999999999999999884..455555555555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.015
                          CRT-like  89 avstsGslqvllnqaiipitllasllllkerysliqylGAlviilgvvv 137
                                        ++ s    ++  qai ++ ++ +  ll e+  l+ +lG + +++gv  
  gi|488601474|ref|YP_007907945.1| 238 KMQAS--QASIFLQAIPVVAVFSAWFLLGEKITLLTVLGTIFVVVGVYF 284
                                       44443..34677799888899999999*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 1524.85
//
Query:       gi|488601475|ref|YP_007907946.1|  [L=272]
Description: putative permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  107.8  42.1    8.4e-18   64.9  15.2    2.0  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3  19.0     3e-17   5.3e-13       2     136 ..       6     133 ..       5     134 .. 0.95
   2 !   64.9  15.2   4.7e-22   8.4e-18       2     135 ..     141     269 ..     140     271 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 3e-17
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       lg+l ++++a+++++  ++ + +  +++ ++++f+rf++++++lli+++l+++k+   s +  + ll+++ll+++++
  gi|488601475|ref|YP_007907946.1|   6 LGVLSVIAGAIMMGSLVIFVRNI--NLNAVQTSFFRFFFGFLFLLIFSVLSRRKI---SFERPKMLLIMSLLSIMVV 77 
                                       699*******************9..******************************...6666668899999999999 PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                         +++ +++ ++a++a+l+++++Pv++l +++l  ge ++ k +++i l++ G++l+l
  gi|488601475|ref|YP_007907946.1|  78 -NFYIASIQLIPAGTAALLLYMAPVYVLPIAYLS-GEVISRKIFVSIPLSISGLYLML 133
                                       .59*******************************.********************997 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 4.7e-22
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                        gi++ l++ +++a+yf+++k++  ++ +++lt+  + i++++l + +++  +        ++ +l+ lgl++t+la
  gi|488601475|ref|YP_007907946.1| 141 AGIIFGLISGFVYALYFMVIKRIRDYMQSIELTTAYLGISSLILAPSLVIYPIGE-----VNLMWLIGLGLIPTALA 212
                                       59******************************************99999999999.....899************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       f lf+ +lk+ + s+  ++ ++eP+ + +++  l+ge++t +++ g++l+l+Gv++ 
  gi|488601475|ref|YP_007907946.1| 213 FTLFNFGLKYCKLSEGPVFALIEPISASLFGLMLFGETFTPIEITGMILVLAGVAIA 269
                                       ******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1503.16
//
Query:       gi|488601476|ref|YP_007907947.1|  [L=81]
Description: hypothetical protein Asulf_01989 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00015   21.7   0.2    0.00018   21.4   0.2    1.1  1  HTH_45       Winged helix-turn-helix
     0.0039   17.0   0.0     0.0044   16.8   0.0    1.1  1  DUF742       Protein of unknown function (DUF742)
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.021   14.6   0.0    1.3  1  FtsK_gamma   Ftsk gamma domain
       0.02   14.9   0.0       0.03   14.4   0.0    1.3  1  HemN_C       HemN C-terminal domain
      0.046   13.9   0.0      0.071   13.3   0.0    1.3  1  SelB-wing_2  Elongation factor SelB, winged helix
      0.056   13.3   0.1      0.086   12.7   0.1    1.4  1  HTH_5        Bacterial regulatory protein, arsR family
      0.085   13.2   0.1       0.11   12.9   0.1    1.4  1  Rrf2         Transcriptional regulator
        0.1   12.5   0.1        0.1   12.5   0.1    1.2  1  PTSIIA_gutA  PTS system glucitol/sorbitol-specific IIA compon


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2     8e-08   0.00018       8      72 ..      14      78 ..      10      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8e-08
                            HTH_45  8 iadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkel 72
                                      ++ IL+++++++++  +i ++     +++++ ++ L   g+++ ++++ ++Te G+e+ ++l ++
  gi|488601476|ref|YP_007907947.1| 14 MVRILKILNKKDSSIRAISKHLRVPENIAKSLIKDLEADGILSINGDNVSITEYGKEISQELTRM 78
                                      688********************************************************999876 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.9e-06    0.0044      43      92 ..      12      62 ..       4      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                            DUF742 43 pehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvrapvt 92
                                      +++ +il++ ++   s+  ++ +l++P  +++ L+ dL + g l+++   +
  gi|488601476|ref|YP_007907947.1| 12 NNMVRILKILNKkDSSIRAISKHLRVPENIAKSLIKDLEADGILSINGDNV 62
                                      6789999988887999**************************999886555 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.6e-06     0.021      14      50 ..      20      56 ..      12      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.6e-06
                        FtsK_gamma 14 vveegkaStSllQRrlriGYnRAarlidqLeeeGiVg 50
                                      +++++  S+  + ++lr+  n A +li +Le++Gi +
  gi|488601476|ref|YP_007907947.1| 20 ILNKKDSSIRAISKHLRVPENIAKSLIKDLEADGILS 56
                                      6789999****************************98 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05      0.03      36      62 ..      40      66 ..      27      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                            HemN_C 36 ellaaaleklqeqGLLeldggrlrltp 62
                                      ++ ++ +++l+++G L+++g++++ t+
  gi|488601476|ref|YP_007907947.1| 40 NIAKSLIKDLEADGILSINGDNVSITE 66
                                      556889******************997 PP

>> SelB-wing_2  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.071      28      55 ..      35      62 ..      19      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                      SSS-HCCHHHHHHHHHHTTSEEE-SSEE CS
                       SelB-wing_2 28 prlpaklfqallealvargilavegdwv 55
                                       r+p++ + +l+ +l+a+gil+++gd v
  gi|488601476|ref|YP_007907947.1| 35 LRVPENIAKSLIKDLEADGILSINGDNV 62
                                      49*********************99865 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 ?   12.7   0.1   3.8e-05     0.086       3      30 ..      13      40 ..      11      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HH CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqs 30
                                      ++++ILk+L+++  ++  ++++l++++ 
  gi|488601476|ref|YP_007907947.1| 13 NMVRILKILNKKDSSIRAISKHLRVPEN 40
                                      689********************99875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.7e-05      0.11      21      56 ..      22      56 ..       8      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +++   s+++i+++  +++++++ +++ L+  g++ 
  gi|488601476|ref|YP_007907947.1| 22 NKK-DSSIRAISKHLRVPENIAKSLIKDLEADGILS 56
                                      232.369*************************9874 PP

>> PTSIIA_gutA  PTS system glucitol/sorbitol-specific IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.6e-05       0.1      44      79 ..      44      79 ..       7      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-05
                                      .GG----TT-EEEETTEEEEEEEE-TTHHHHHHHHS CS
                       PTSIIA_gutA 44 elkeeikkgdtltigeqeykitaVGevanknLkelG 79
                                      +l ++++++  l+i++ +  it+ G++ +++L+++G
  gi|488601476|ref|YP_007907947.1| 44 SLIKDLEADGILSINGDNVSITEYGKEISQELTRMG 79
                                      578999**************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); 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: 0.53u 0.37s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 451.00
//
Query:       gi|488601477|ref|YP_007907948.1|  [L=382]
Description: putative Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   90.2   0.0    9.9e-25   87.8   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
    2.2e-05   24.6   0.0      4e-05   23.7   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
     0.0048   17.2   0.0      0.014   15.6   0.0    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 !   87.8   0.0   1.7e-28   9.9e-25       3     166 ..      90     254 ..      88     255 .. 0.93
   2 ?   -0.7   0.0      0.27   1.6e+03     108     140 ..     268     300 ..     260     307 .. 0.78

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.7e-28
                                       EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklav 75 
                                       +  gCnlrC+fC++ e   ++++ + +++++++++e +k++  ++   v++ i g gepllyp +++ll +++k++ 
  gi|488601477|ref|YP_007907948.1|  90 PITGCNLRCIFCSVDEGkkSKTRATDYIVDPDYLVEVLKQVVeFKGEgVEVHIDGQGEPLLYPYMEDLLSKISKIK- 165
                                       678**************************************9644448***************************6. PP

                                       CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                           i++ tng+l++e k+ +l e+  +r++l+l ++d ++  +l + ++ +e+v ++ e+++++  +   +  v +
  gi|488601477|ref|YP_007907948.1| 166 GVSIISMQTNGILLNESKISALEEYV-TRFNLSLSSLDRDTASRLSGIKYPVERVTRNAEMIANSKAD-LLIAPVWV 240
                                       888899******************99.*************777777799****************777.******** PP

                                       TTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       Radical_SAM 153 pGendeeleellel 166
                                       pG nd+++e+++e+
  gi|488601477|ref|YP_007907948.1| 241 PGINDRDIEKIIEF 254
                                       ************98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.27
                                       EEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 108 gleaaddekvlklmnrghtfeevlealeklrea 140
                                       g++ + + k+ +++++  tf+e+++ l+k+ e 
  gi|488601477|ref|YP_007907948.1| 268 GIQKYIPYKYGRKLKKVMTFKEFYDRLRKWEEE 300
                                       555555667889999999999999999998775 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   6.7e-09     4e-05       6     103 ..      92     189 ..      88     204 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.7e-09
                           Fer4_14   6 sgCnlsCkgCd...nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeey 78 
                                        gCnl C +C     k+++      + + + l+++lk++ + + +  ++ + G GePL+y   ++ll  ++++k   
  gi|488601477|ref|YP_007907948.1|  92 TGCNLRCIFCSvdeGKKSKTRATDYIVDPDYLVEVLKQVVEFKGEGVEVHIDGqGEPLLYPYMEDLLSKISKIKGVS 168
                                       79********9765333333344444555666666664444333344699**********76666666666666655 PP

                           Fer4_14  79 pekkiwletngtleielektpdlke 103
                                           i ++tng l  e + + +l+e
  gi|488601477|ref|YP_007907948.1| 169 ---IISMQTNGILLNESK-ISALEE 189
                                       ...99******9886655.344433 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.77   4.6e+03      44      75 ..      28      59 ..      24      68 .. 0.72
   2 !   15.6   0.0   2.4e-06     0.014      12     107 ..      91     190 ..      81     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.77
                           Fer4_12 44 iiedlkkesiegltllGGEPllpenaeallel 75
                                      + e+l k+++++ +++ GEP    n  +  el
  gi|488601477|ref|YP_007907948.1| 28 AYERLIKRKDKEYIISFGEPRKVLNHITKREL 59
                                      56778888899999999999877666555555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.4e-06
                           Fer4_12  12 vsgCnlsCkgCfnketwsfk.sgkef..tkelleeiiedlkk..esiegltllG.GEPllpenaeallelvkevkee 82 
                                       ++gCnl+C +C   e ++ k + +++  + + l e+++++ +   +  ++ + G GEPll+   e+ll+ + ++k  
  gi|488601477|ref|YP_007907948.1|  91 ITGCNLRCIFCSVDEGKKSKtRATDYivDPDYLVEVLKQVVEfkGEGVEVHIDGqGEPLLYPYMEDLLSKISKIKGV 167
                                       68*********99999988742334444556666666666541155577888999*****66666666666666655 PP

                           Fer4_12  83 kpekdiwlytgytleelskkekeel 107
                                        +    + ++g  l+e + ++ ee 
  gi|488601477|ref|YP_007907948.1| 168 SI--ISMQTNGILLNESKISALEEY 190
                                       55..789999999998876655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2183.60
//
Query:       gi|488601478|ref|YP_007907949.1|  [L=219]
Description: hypothetical protein Asulf_01991 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  105.5  15.4    5.5e-30  104.7  10.5    2.1  2  Cytochrom_C_asm  Cytochrome C assembly protein
  ------ inclusion threshold ------
        5.5    7.3  16.6        3.5    7.9   3.3    2.7  3  DUF996           Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7  10.5   6.1e-34   5.5e-30      41     208 ..       7     163 ..       1     168 [. 0.85
   2 !    3.5   0.2    0.0058        52     188     208 ..     183     203 ..     171     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 6.1e-34
                   Cytochrom_C_asm  41 aalillgfalf...lllaelqesadlnpalqspilmiHvplallsYatliigallsialliierqlkkkkklklsan 114
                                       ++li+l+++l      l +l es + +  ++++i+++H p a++s+ +++ + ++si++l                 
  gi|488601478|ref|YP_007907949.1|   7 TFLIALILMLIgsyNALLMLPESPTPQLSNNYRIIFFHLPSAITSFIAFTTTLIFSIIYL----------------- 66 
                                       33333333333333333445555566777899****************************................. PP

                   Cytochrom_C_asm 115 lkllkqldrlsyriiliGfvlltigiilGsvWaeeaWGsywsWDpketaslitWlvfaallhsri..ek.gwrgkka 188
                                       +k   ++d ++ + +++G++l+t ++i+GsvWa+ aW syw WDp+eta+li+W+v+a+++++r    + + +++++
  gi|488601478|ref|YP_007907949.1|  67 TKNDIRYDIYAVTSAKAGIFLITSALISGSVWAKVAWNSYWNWDPRETAVLILWFVYAGYFALRSsiDDiEAKARNS 143
                                       888999999******************************************************9998889******* PP

                   Cytochrom_C_asm 189 ailailgflllllayfgvrl 208
                                       a+lai+g  +++l y+++++
  gi|488601478|ref|YP_007907949.1| 144 AVLAIFGYATVPLSYLSSKI 163
                                       *****************997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0058
                   Cytochrom_C_asm 188 aailailgflllllayfgvrl 208
                                       ++ + +lgf+l+ +ay+++++
  gi|488601478|ref|YP_007907949.1| 183 TLTIMLLGFILMYIAYMFIES 203
                                       6677899**********9987 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.7    0.0025        23      29     103 ..       4      84 ..       1     108 [. 0.58
   2 ?   -1.6   0.0      0.34     3e+03      23      43 ..     134     154 ..     114     176 .. 0.58
   3 ?    7.9   3.3   0.00039       3.5     115     134 ..     179     198 ..     144     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0025
                            DUF996  29 aliafilsiialvvailalllvlgalatalelpgleeaas....lilllllvl..iiayvlliisavflkksyellg 99 
                                       +li f++++i +++     ll l ++ t   +++ + +++    +i+ ++++   +i+ ++++ ++   +++y+ ++
  gi|488601478|ref|YP_007907949.1|   4 VLITFLIALILMLIGSYNALLMLPESPTPQLSNNYRIIFFhlpsAITSFIAFTttLIFSIIYLTKNDIRYDIYAVTS 80 
                                       55555555565555555555555555555555555555554444666666555333444444444555555555555 PP

                            DUF996 100 krtg 103
                                       ++ g
  gi|488601478|ref|YP_007907949.1|  81 AKAG 84 
                                       5555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.34
                            DUF996  23 ekifsnaliafilsiialvva 43 
                                       ++i  +a  + +l+i +++ +
  gi|488601478|ref|YP_007907949.1| 134 DDIEAKARNSAVLAIFGYATV 154
                                       344444555555555555554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00039
                            DUF996 115 fiGaiLtivlvGliilliae 134
                                        +G  Lti+l G+i+++ia+
  gi|488601478|ref|YP_007907949.1| 179 NVGMTLTIMLLGFILMYIAY 198
                                       589****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); 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:                         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 0.34s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1227.06
//
Query:       gi|488601479|ref|YP_007907950.1|  [L=329]
Description: Transcription initiation factor IIB (TFIIB) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-44  148.1   1.5    1.4e-21   76.3   0.2    2.4  2  TFIIB            Transcription factor TFIIB repeat
    9.4e-20   69.9   0.4    1.6e-19   69.1   0.4    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00014   21.3   1.6     0.0034   16.9   0.3    3.2  3  Sigma70_r4       Sigma-70, region 4
     0.0012   18.7   0.3     0.0031   17.4   0.3    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0015   18.3   0.2      0.025   14.4   0.2    2.8  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.5   0.4       0.71    9.6   0.2    3.2  3  Sigma70_r4_2     Sigma-70, region 4
      0.021   14.8   0.4      0.044   13.8   0.4    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.022   15.1   0.1      0.049   14.0   0.1    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.033   14.3   2.6       0.59   10.3   0.3    2.4  2  Zn-ribbon_8      Zinc ribbon domain
      0.045   13.8   1.8        1.9    8.6   0.0    3.7  4  HTH_3            Helix-turn-helix
      0.068   12.9   0.0       0.75    9.6   0.0    2.2  2  Cyclin_N         Cyclin, N-terminal domain
      0.082   12.7   0.7       0.16   11.8   0.7    1.5  1  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        0.1   12.9   0.1          1    9.7   0.0    2.3  2  UPF0253          Uncharacterised protein family (UPF0253)
       0.12   12.4   0.0       0.42   10.7   0.0    1.9  2  RB_B             Retinoblastoma-associated protein B domain
        0.2   11.1   0.5        3.5    7.2   0.0    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.22   11.7   0.9       0.41   10.9   0.9    1.5  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.29   11.5   2.9        7.3    7.0   0.1    3.3  3  HTH_31           Helix-turn-helix domain
       0.31   10.8   1.5        1.1    9.0   1.5    1.9  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.44   10.4   3.4        1.5    8.7   0.1    3.3  3  HTH_23           Homeodomain-like domain
       0.46   10.3   3.2        6.5    6.6   3.3    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.1   7.6e-23   6.8e-20       2      71 .]     149     218 ..     148     218 .. 0.98
   2 !   76.3   0.2   1.5e-24   1.4e-21       1      71 []     242     312 ..     242     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 7.6e-23
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        r+a+al+Lp+ V++ A  ++++a++++++ Grs +g++AA+ly Acr+++v rt+ ei+  ++V  k+i
  gi|488601479|ref|YP_007907950.1| 149 DRMASALGLPKPVRETAAVVYRKAVDKNLIRGRSIEGVVAAALYAACRQAGVPRTLDEIATYSRVDRKEI 218
                                       69****************************************************************9997 PP

  == domain 2  score: 76.3 bits;  conditional E-value: 1.5e-24
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf++al+L+  ++++A e++k+a e+++++Gr p+g+aAA++yiA+ + +++rtq+e+++v+ V+e+ti
  gi|488601479|ref|YP_007907950.1| 242 VPRFCAALNLSGDIQKKAIEIIKKAEEKELTSGRGPTGVAAAAIYIASILGGERRTQREVAEVAGVTEVTI 312
                                       689******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.4   1.8e-22   1.6e-19       2      43 .]      32      73 ..      32      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.8e-22
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+Cgs++l++D+ rge++C dCGlV++d +id gpewr+f
  gi|488601479|ref|YP_007907950.1| 32 ICPECGSPRLIRDYRRGEFICQDCGLVIDDTYIDAGPEWRAF 73
                                      5***************************************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 ?   -0.4   0.0      0.94   8.4e+02      18      27 ..     199     208 ..     193     211 .. 0.81
   2 ?    0.6   0.0      0.47   4.2e+02      18      34 ..     217     233 ..     212     235 .. 0.80
   3 !   16.9   0.3   3.8e-06    0.0034      18      48 ..     293     323 ..     284     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.94
                                       TTT--HHHHH CS
                        Sigma70_r4  18 geglTleEIg 27 
                                       g ++Tl EI+
  gi|488601479|ref|YP_007907950.1| 199 GVPRTLDEIA 208
                                       6689*****9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.47
                                       TTT--HHHHHHHHTS-H CS
                        Sigma70_r4  18 geglTleEIgerlgiSr 34 
                                       + g+T+  I+++lg+ +
  gi|488601479|ref|YP_007907950.1| 217 EIGRTYRFIARELGLKL 233
                                       55899999*****9865 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 3.8e-06
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       ge +T+ E++e+ g+++ ++r + k+  +kL
  gi|488601479|ref|YP_007907950.1| 293 GERRTQREVAEVAGVTEVTIRNRYKELAEKL 323
                                       7899*********************998887 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   3.4e-06    0.0031       7      57 ..       9      60 ..       6      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
                    OrfB_Zn_ribbon  7 qleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfead 57
                                       +e k  e+ ++ +e++++ +   C+eCgs     +  + +f C++Cg+++d
  gi|488601479|ref|YP_007907950.1|  9 EVERKELEKEVERKEIEREESLDICPECGSPRLIrDYRRGEFICQDCGLVID 60
                                      578999999********************9654448999*********9987 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 ?    0.0   0.0      0.86   7.7e+02      18      29 ..     220     231 ..     220     232 .. 0.87
   2 !   14.4   0.2   2.8e-05     0.025      17      41 ..     295     319 ..     293     325 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.86
                     HTH_AsnC-type  18 isyaeLAervGl 29 
                                       ++y+ +A+++Gl
  gi|488601479|ref|YP_007907950.1| 220 RTYRFIARELGL 231
                                       57899******9 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.8e-05
                     HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                                       R++ +e+Ae  G++e t+++R++ L
  gi|488601479|ref|YP_007907950.1| 295 RRTQREVAEVAGVTEVTIRNRYKEL 319
                                       99********************988 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.47   4.3e+02      26      39 ..     219     232 ..     215     233 .. 0.86
   2 ?    9.6   0.2   0.00079      0.71      28      48 ..     297     317 ..     293     323 .. 0.88
   3 ?    1.7   0.0      0.24   2.1e+02      29      38 ..     316     325 ..     314     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.47
                                       ---HHHHHHHHT-- CS
                      Sigma70_r4_2  26 glsykEIAellgis 39 
                                       g +y+ IA++lg++
  gi|488601479|ref|YP_007907950.1| 219 GRTYRFIARELGLK 232
                                       779999******86 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00079
                                       -HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrls 48 
                                       +++E+Ae+ g++e+t+++r++
  gi|488601479|ref|YP_007907950.1| 297 TQREVAEVAGVTEVTIRNRYK 317
                                       899****************96 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.24
                                       HHHHHHHHT- CS
                      Sigma70_r4_2  29 ykEIAellgi 38 
                                       ykE Ae+lgi
  gi|488601479|ref|YP_007907950.1| 316 YKELAEKLGI 325
                                       9********8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   4.9e-05     0.044      20      44 ..      32      56 ..      28      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCr 44
                                      +CP Cgs +++r  +rg f C++C+
  gi|488601479|ref|YP_007907950.1| 32 ICPECGSPRLIRDYRRGEFICQDCG 56
                                      6*****9988888889********7 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.5e-05     0.049       3      40 ..      30      61 ..      28      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga.stpw 40
                                      L  CP Cg++  +    r+       ++C+dCg    ++
  gi|488601479|ref|YP_007907950.1| 30 LDICPECGSPRLIRDYRRG------EFICQDCGLvI-DD 61
                                      677*****98876666555......48******942.22 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00066      0.59      20      38 ..      23      43 ..      13      45 .. 0.69
   2 ?    3.8   0.1      0.07        63       5      15 ..      49      59 ..      44      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00066
                       Zn-ribbon_8 20 sis.dapltaCPeCgs.evrr 38
                                      +i  +++l  CPeCgs ++ r
  gi|488601479|ref|YP_007907950.1| 23 EIErEESLDICPECGSpRLIR 43
                                      3554566666******77765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.07
                       Zn-ribbon_8  5 eYrCeeCghef 15
                                      e+ C++Cg + 
  gi|488601479|ref|YP_007907950.1| 49 EFICQDCGLVI 59
                                      788****9765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.6   4.1e+03      39      51 ..     146     158 ..     143     159 .. 0.81
   2 ?   -0.5   0.0       1.5   1.3e+03       5      21 ..     215     231 ..     212     233 .. 0.89
   3 ?    8.6   0.0    0.0021       1.9      11      27 ..     297     313 ..     293     315 .. 0.91
   4 ?    1.3   0.0      0.42   3.8e+02      13      21 ..     317     325 ..     314     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHTSE CS
                             HTH_3  39 etlkklakaLgvs 51 
                                       + l ++a aLg++
  gi|488601479|ref|YP_007907950.1| 146 SELDRMASALGLP 158
                                       6788999999976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                                       HHHTTHHHHHHHHHHTS CS
                             HTH_3   5 RkqlglsqeeLAeklGv 21 
                                       Rk+ g + + +A++lG+
  gi|488601479|ref|YP_007907950.1| 215 RKEIGRTYRFIARELGL 231
                                       999999*******9997 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHTSSHHHHH CS
                             HTH_3  11 sqeeLAeklGvsrstis 27 
                                       +q+e+Ae++Gv+  ti+
  gi|488601479|ref|YP_007907950.1| 297 TQREVAEVAGVTEVTIR 313
                                       9*************997 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.42
                                       HHHHHHHTS CS
                             HTH_3  13 eeLAeklGv 21 
                                       +eLAeklG+
  gi|488601479|ref|YP_007907950.1| 317 KELAEKLGI 325
                                       89*****98 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00083      0.75      40     124 ..     150     231 ..     118     234 .. 0.84
   2 ?    0.9   0.0      0.39   3.5e+02      36      87 ..     240     291 ..     236     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00083
                                       HHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHH CS
                          Cyclin_N  40 evaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemEr 116
                                       ++a+ + l + +  +a++++ + + k+ ++ + ++ v+a++L+ A++   + p +l++++ ++   ++++ei +  r
  gi|488601479|ref|YP_007907950.1| 150 RMASALGLPKPVRETAAVVYRKAVDKNLIRGRSIEGVVAAALYAACRQAGV-PRTLDEIATYS--RVDRKEIGRTYR 223
                                       556667777777889999999***************************888.99******995..599999998888 PP

                                       HHHHHTTT CS
                          Cyclin_N 117 liLetLnf 124
                                        i ++L  
  gi|488601479|ref|YP_007907950.1| 224 FIARELGL 231
                                       88887765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                                       HHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHH CS
                          Cyclin_N  36 dwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKv 87 
                                       d++ + ++ ++l+ ++   a++++ +  +k+ ++ +    v+a+++++A+ +
  gi|488601479|ref|YP_007907950.1| 240 DYVPRFCAALNLSGDIQKKAIEIIKKAEEKELTSGRGPTGVAAAAIYIASIL 291
                                       56667778888888888888888888888888888889999*******9965 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00018      0.16       3      22 ..      32      51 ..      31      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                      E-SSS--EEEEEE-SSSEEE CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkrgkkGkFv 22
                                       CP+Cg++ +++  ++G+F+
  gi|488601479|ref|YP_007907950.1| 32 ICPECGSPRLIRDYRRGEFI 51
                                      6******************8 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0011         1      27      52 ..     141     166 ..     136     170 .. 0.91
   2 ?   -0.2   0.0       1.4   1.3e+03      32      45 ..     202     215 ..     187     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                           UPF0253  27 iscalktLdevaanealpeevrekAA 52 
                                       ++ al  Ld++a+   lp+ vre AA
  gi|488601479|ref|YP_007907950.1| 141 LAFALSELDRMASALGLPKPVRETAA 166
                                       6779999******************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                           UPF0253  32 ktLdevaanealpe 45 
                                       +tLde+a  +++++
  gi|488601479|ref|YP_007907950.1| 202 RTLDEIATYSRVDR 215
                                       79999999888875 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 ?   10.7   0.0   0.00047      0.42      10      94 ..     141     223 ..     132     230 .. 0.82
   2 ?   -1.9   0.0       3.5   3.1e+03      20      41 ..     245     266 ..     241     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                              RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqp 86 
                                       +  a + l ++ + L l + +re +  + ++++  +++l++ R ++ ++ +a+Y+ ++     +++ ei +  r   
  gi|488601479|ref|YP_007907950.1| 141 LAFALSELDRMASALGLPKPVRETAAVVYRKAV--DKNLIRGRSIEGVVAAALYAACRQAGVPRTLDEIATYSRVDR 215
                                       567778888899999999999888877777766..568******************************988777777 PP

                              RB_B  87 qasskvyr 94 
                                       ++  ++yr
  gi|488601479|ref|YP_007907950.1| 216 KEIGRTYR 223
                                       77777776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.5
                              RB_B  20 LcerLklsselrekiwtlfehv 41 
                                        c+ L+ls ++++k+ ++++++
  gi|488601479|ref|YP_007907950.1| 245 FCAALNLSGDIQKKAIEIIKKA 266
                                       7999999999999998888764 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0039       3.5       4      11 ..      32      39 ..      29      44 .. 0.78
   2 ?    1.8   0.1      0.19   1.7e+02      18      26 .]      51      59 ..      45      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0039
                       zf-ribbon_3  4 rCPnCGap 11
                                       CP+CG+p
  gi|488601479|ref|YP_007907950.1| 32 ICPECGSP 39
                                      58888876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                       zf-ribbon_3 18 vCpyCGtkl 26
                                      +C  CG ++
  gi|488601479|ref|YP_007907950.1| 51 ICQDCGLVI 59
                                      7*****986 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 ?   10.9   0.9   0.00045      0.41      17      40 .]      32      56 ..      30      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00045
                     Auto_anti-p27 17 tCpvCgvP.LmrdrkggkvyCvaCd 40
                                       Cp+Cg+P L rd  +g+ +C  C+
  gi|488601479|ref|YP_007907950.1| 32 ICPECGSPrLIRDYRRGEFICQDCG 56
                                      7****888356666799****9996 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.13   1.1e+02      44      61 ..     145     162 ..     123     167 .. 0.79
   2 ?   -2.1   0.1       5.6     5e+03      20      27 ..     207     214 ..     187     232 .. 0.57
   3 ?    7.0   0.1    0.0082       7.3      14      32 ..     295     313 ..     280     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                            HTH_31  44 pavlealaralgldpaer 61 
                                       ++ l+++a algl+   r
  gi|488601479|ref|YP_007907950.1| 145 LSELDRMASALGLPKPVR 162
                                       6789*********84433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.6
                            HTH_31  20 vAerlgvs 27 
                                        A  ++v 
  gi|488601479|ref|YP_007907950.1| 207 IATYSRVD 214
                                       33333332 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0082
                            HTH_31  14 GLsqeevAerlgvsestls 32 
                                       + +q+evAe +gv+e t++
  gi|488601479|ref|YP_007907950.1| 295 RRTQREVAEVAGVTEVTIR 313
                                       569***********99986 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.5    0.0012       1.1       5      31 ..      31      59 ..      27      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                           zf-RRN7  5 ppCgvCgc....rsftlddGfyyCrrChtqe 31
                                       +C++Cg+    r+++   G ++C+ C+ ++
  gi|488601479|ref|YP_007907950.1| 31 DICPECGSprliRDYRR--GEFICQDCGLVI 59
                                      58*******77777777..88******9886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.7   1.5e+03       3      16 ..     114     127 ..     112     138 .. 0.67
   2 ?   -0.3   0.0       1.1   9.8e+02      16      29 ..     217     231 ..     211     233 .. 0.77
   3 ?    8.7   0.1    0.0017       1.5      17      43 ..     295     321 ..     282     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                            HTH_23   3 sereRlrillllae 16 
                                       s+r+R++  +l + 
  gi|488601479|ref|YP_007907950.1| 114 SVRNRAQLFRLRKW 127
                                       67788888887763 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                            HTH_23  16 e.GlsvreIAreLgv 29 
                                       e G ++r IAreLg 
  gi|488601479|ref|YP_007907950.1| 217 EiGRTYRFIARELGL 231
                                       358888889999995 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0017
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlkryre 43 
                                       + ++re+A+  gv++ T+++  k  +e
  gi|488601479|ref|YP_007907950.1| 295 RRTQREVAEVAGVTEVTIRNRYKELAE 321
                                       679****************66555444 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.027        25      17      29 ..      26      38 ..      22      42 .. 0.81
   2 ?    6.6   3.3    0.0073       6.5       5      30 ..      32      58 ..      29      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.027
                     A2L_zn_ribbon 17 seqgylvCieCga 29
                                      +e +  +C+eCg+
  gi|488601479|ref|YP_007907950.1| 26 REESLDICPECGS 38
                                      6677789****96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0073
                     A2L_zn_ribbon  5 vCsvCggngiln.seqgylvCieCgas 30
                                      +C  Cg++ ++    +g+ +C++Cg++
  gi|488601479|ref|YP_007907950.1| 32 ICPECGSPRLIRdYRRGEFICQDCGLV 58
                                      7888999999955569999******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      763  (0.0425568); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 1892.88
//
Query:       gi|488601480|ref|YP_007907951.1|  [L=156]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   59.2   1.5    4.3e-16   58.2   1.5    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    3.7e-16   58.7   0.2    5.7e-16   58.1   0.2    1.3  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    2.3e-15   56.3   1.6    2.7e-15   56.1   0.5    1.7  2  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    8.3e-07   28.9   0.6    2.1e-06   27.6   0.6    1.8  1  HTH_11           HTH domain
    1.3e-06   28.1   0.1    3.3e-06   26.9   0.1    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
    2.3e-05   24.0   0.1    4.6e-05   23.1   0.1    1.5  1  HTH_23           Homeodomain-like domain
    2.9e-05   23.8   0.0    4.4e-05   23.3   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0001   22.3   0.0    0.00016   21.7   0.0    1.3  1  HTH_20           Helix-turn-helix domain
    0.00013   21.5   0.3    0.00028   20.5   0.3    1.5  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
    0.00013   21.6   0.1    0.00026   20.6   0.1    1.6  1  Sigma70_r4_2     Sigma-70, region 4
    0.00021   21.2   0.0    0.00044   20.1   0.0    1.6  1  MarR             MarR family
    0.00022   20.8   0.0    0.00049   19.7   0.0    1.7  1  HTH_50           Helix-turn-helix domain
    0.00026   21.0   0.0    0.00044   20.3   0.0    1.4  1  HTH_28           Helix-turn-helix domain
     0.0004   20.1   0.0    0.00074   19.3   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
     0.0011   18.9   0.1      0.012   15.5   0.0    2.1  2  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0021   17.8   0.1     0.0053   16.5   0.1    1.7  1  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0022   18.4   0.1     0.0083   16.6   0.1    1.9  2  HTH_40           Helix-turn-helix domain
     0.0024   17.7   0.3      0.009   15.8   0.0    1.9  2  TetR_N           Bacterial regulatory proteins, tetR family
     0.0026   17.5   0.0      0.005   16.6   0.0    1.5  1  HTH_38           Helix-turn-helix domain
      0.003   18.0   0.2      0.015   15.8   0.1    2.0  2  HTH_27           Winged helix DNA-binding domain
     0.0033   17.6   0.0       0.01   16.0   0.0    1.9  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0042   17.1   0.0      0.009   16.1   0.0    1.6  1  HTH_22           HTH domain
     0.0048   16.7   0.0      0.013   15.3   0.0    1.7  1  HTH_10           HTH DNA binding domain
     0.0064   16.3   0.0      0.014   15.2   0.0    1.5  1  MarR_2           MarR family
  ------ inclusion threshold ------
      0.012   15.1   0.1      0.022   14.3   0.1    1.5  1  Sigma70_r4       Sigma-70, region 4
      0.015   15.1   0.0      0.026   14.3   0.0    1.3  1  HTH_30           PucR C-terminal helix-turn-helix domain
      0.018   15.2   0.0        7.8    6.7   0.0    2.4  2  DUF4372          Domain of unknown function (DUF4372)
      0.018   15.4   0.1      0.062   13.7   0.0    1.9  1  Rrf2             Transcriptional regulator
      0.022   14.7   0.1      0.035   14.1   0.1    1.4  1  HTH_36           Helix-turn-helix domain
      0.024   14.9   0.2      0.092   13.0   0.0    1.9  2  UPF0122          Putative helix-turn-helix protein, YlxM / p1
      0.027   15.1   0.0       0.06   13.9   0.0    1.6  1  Mga              Mga helix-turn-helix domain
      0.044   13.9   0.5       0.43   10.8   0.1    2.3  2  AsnC_trans_reg2  AsnC-like ligand binding domain
      0.046   13.7   0.1       0.56   10.2   0.0    2.4  2  PadR             Transcriptional regulator PadR-like family
      0.047   13.2   0.0       0.09   12.3   0.0    1.5  1  GerE             Bacterial regulatory proteins, luxR family
      0.051   13.0   0.0       0.09   12.2   0.0    1.3  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.086   12.5   0.3       0.17   11.6   0.1    1.5  1  DUF4423          Domain of unknown function (DUF4423)
       0.11   11.4   0.1       0.19   10.7   0.1    1.3  1  TnsD             Tn7-like transposition protein D
       0.12   12.5   0.0       0.21   11.7   0.0    1.5  1  HTH_Tnp_1_2      Helix-turn-helix of insertion element transp
       0.14   12.2   0.0       0.27   11.3   0.0    1.4  1  HTH_29           Winged helix-turn helix
       0.14   12.4   0.0        0.4   10.9   0.0    1.8  2  HTH_17           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   1.5   9.5e-19   4.3e-16       1      48 []       5      52 ..       5      52 .. 0.99

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 9.5e-19
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld+td+kIL +Lq+++r s re+Ae+lg+  +tv  r+++L+++G+Ik
  gi|488601480|ref|YP_007907951.1|  5 LDDTDIKILIELQEDARKSLREIAEKLGVAEGTVYNRINKLKRMGIIK 52
                                      79*********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.2   1.3e-18   5.7e-16       1      42 []       5      46 ..       5      46 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.3e-18
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LD++D+kIL +LqedaR s +e+Ae++G++e tv +R+++L+
  gi|488601480|ref|YP_007907951.1|  5 LDDTDIKILIELQEDARKSLREIAEKLGVAEGTVYNRINKLK 46
                                      8***************************************95 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.2   2.8e+03       1      20 [.      12      31 ..      12      33 .. 0.70
   2 !   56.1   0.5   6.1e-18   2.7e-15       1      74 [.      71     140 ..      71     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.2
                                      EEEEE-GGGTTHHHHHHHHH CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeeal 20
                                      +l++l+ +++++l+e++e+l
  gi|488601480|ref|YP_007907951.1| 12 ILIELQEDARKSLREIAEKL 31
                                      57778855577788877775 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 6.1e-18
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       ++v+ e+g    l ++ee++a+ p V+ +y vtG++d++l +++ d e+l+rf+++ +a +++v +t t++vl+
  gi|488601480|ref|YP_007907951.1|  71 IGVTAEGGY---LVAIEEEIAKEPHVTAVYDVTGEFDMILVAKFMDRESLNRFVKK-VAGMEHVVKTYTMVVLN 140
                                       689999888...*****************************************988.***************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.6   4.7e-09   2.1e-06       4      44 ..      11      55 ..       9      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.7e-09
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.....v 44
                                      +il+ L +++   s  e+Ae+L+v + tv+++I +L+ +g     +
  gi|488601480|ref|YP_007907951.1| 11 KILIEL-QEDARKSLREIAEKLGVAEGTVYNRINKLKRMGiikkfI 55
                                      788899.777778***************************666554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   7.4e-09   3.3e-06       6      54 ..       5      53 ..       4      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 7.4e-09
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      L ++++k+ + L +  +++ +eiae+lgv + +vY+ +++L+++G++++
  gi|488601480|ref|YP_007907951.1|  5 LDDTDIKILIELQEDARKSLREIAEKLGVAEGTVYNRINKLKRMGIIKK 53
                                      6789******************************************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1     1e-07   4.6e-05      10      45 ..      12      49 ..      10      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-07
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      il  l+e  ++s reIA++Lgv + Tvy+ +++ ++ G
  gi|488601480|ref|YP_007907951.1| 12 ILIELQEdaRKSLREIAEKLGVAEGTVYNRINKLKRMG 49
                                      6667777789******************9998876666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   9.8e-08   4.4e-05       4      47 .]       9      53 ..       6      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.8e-08
                                      HHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  4 RlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                       +kIL  L+e   ++  e+ae+lg+ ++tv    +kL+ +G+++k
  gi|488601480|ref|YP_007907951.1|  9 DIKILIELQEdARKSLREIAEKLGVAEGTVYNRINKLKRMGIIKK 53
                                      5799999999777******************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.5e-07   0.00016      13      55 ..      10      52 ..       5      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.5e-07
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                       +il +L +++  ++ e+ae l+++  t+++++++L + g+++
  gi|488601480|ref|YP_007907951.1| 10 IKILIELQEDARKSLREIAEKLGVAEGTVYNRINKLKRMGIIK 52
                                      678889999999****************************996 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   6.3e-07   0.00028      11      54 ..      11      52 ..       4      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.3e-07
                      HrcA_DNA-bdg 11 qaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLve 54
                                      + Liel++  ++++  +eiAe+l+  eGtv N ++ Lk +g+++
  gi|488601480|ref|YP_007907951.1| 11 KILIELQEDARKSL--REIAEKLGVAEGTVYNRINKLKRMGIIK 52
                                      67899988888876..6************************997 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 !   20.6   0.1   5.9e-07   0.00026      27      49 ..      22      44 ..      11      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.9e-07
                                      --HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 27 lsykEIAellgisegtVksrlsR 49
                                      +s +EIAe+lg+ egtV++r+ +
  gi|488601480|ref|YP_007907951.1| 22 KSLREIAEKLGVAEGTVYNRINK 44
                                      799*****************987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   9.8e-07   0.00044       3      49 ..       7      53 ..       5      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.8e-07
                                      HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                       t ++iL  l e    s+ e+a+klgv  +tv + + +L + G i++
  gi|488601480|ref|YP_007907951.1|  7 DTDIKILIELQEDARKSLREIAEKLGVAEGTVYNRINKLKRMGIIKK 53
                                      57899***************************************987 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-06   0.00049       6      46 ..       3      44 ..       1      51 [. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                            HTH_50  6 eyveefErelikkayek.YpStRklAkrLGvShtaianklrk 46
                                      e++++++ ++++++ e   +S R +A++LGv   ++ n++ k
  gi|488601480|ref|YP_007907951.1|  3 EKLDDTDIKILIELQEDaRKSLREIAEKLGVAEGTVYNRINK 44
                                      88899998888888875379****************766443 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   0.0   9.9e-07   0.00044       4      38 ..      11      47 ..      10      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.9e-07
                            HTH_28  4 eiikllaaGh..svreaArelgisrrtvyrWikryee 38
                                      +i+ +l++    s re+A++lg+ + tvy  i+++  
  gi|488601480|ref|YP_007907951.1| 11 KILIELQEDArkSLREIAEKLGVAEGTVYNRINKLKR 47
                                      788999965336********************99865 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.7e-06   0.00074       9      49 ..      13      52 ..      10      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-06
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      L  l e ++  +l+e+A+++g++  tv++ ++ L ++G+++
  gi|488601480|ref|YP_007907951.1| 13 LIELQEDARK-SLREIAEKLGVAEGTVYNRINKLKRMGIIK 52
                                      5556777777.9**************************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.7e-05     0.012      23      53 ..      23      53 ..       7      64 .. 0.81
   2 ?    1.1   0.0      0.91   4.1e+02      34      61 ..     113     140 ..     112     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisr 53
                                      + +e+A+ lG+   tv   +++Lkr g+i++
  gi|488601480|ref|YP_007907951.1| 23 SLREIAEKLGVAEGTVYNRINKLKRMGIIKK 53
                                      668**************************94 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.91
                                       SHHHHHHHHHHHHHTTSEEETEEEEES- CS
                         HTH_Crp_2  34 tretvsrilseLkreglisrgrririld 61 
                                        re+++r  ++      + + +++++l+
  gi|488601480|ref|YP_007907951.1| 113 DRESLNRFVKKVAGMEHVVKTYTMVVLN 140
                                       69*****999987776666442366665 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 !   16.5   0.1   1.2e-05    0.0053       4      46 ..      11      53 ..       9      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +il  l+++   s+ e++e lgv+e T+ + +n+L+  g++++
  gi|488601480|ref|YP_007907951.1| 11 KILIELQEDARKSLREIAEKLGVAEGTVYNRINKLKRMGIIKK 53
                                      688889999999****************************987 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.8e-05    0.0083      12      49 ..      21      55 ..      15      92 .. 0.80
   2 ?   -0.6   0.0       4.2   1.9e+03      46      60 ..     109     123 ..      77     153 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-05
                            HTH_40 12 glsieeIAkerglkesTIegHLaelieegeeidlerlv 49
                                       +s+ eIA++ g++e+T+++ + +l + g    +++++
  gi|488601480|ref|YP_007907951.1| 21 RKSLREIAEKLGVAEGTVYNRINKLKRMGI---IKKFI 55
                                      589**********************99985...44444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.2
                            HTH_40  46 erlvseeeekeIeea 60 
                                        +++++e  ++  + 
  gi|488601480|ref|YP_007907951.1| 109 AKFMDRESLNRFVKK 123
                                       334444444444444 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 !   15.8   0.0     2e-05     0.009      18      35 ..      23      40 ..      20      41 .. 0.92
   2 ?   -1.0   0.1       3.6   1.6e+03      11      29 ..      76      94 ..      73      95 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                                      -HHHHHHHHTSSHHHHHH CS
                            TetR_N 18 tvreIAkrAGvskgalYr 35
                                      ++reIA+++Gv++g++Y 
  gi|488601480|ref|YP_007907951.1| 23 SLREIAEKLGVAEGTVYN 40
                                      79***************7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                                      HHHTTT--HHHHHHHHTSS CS
                            TetR_N 11 erGydattvreIAkrAGvs 29
                                      e Gy  +  +eIAk+ +v+
  gi|488601480|ref|YP_007907951.1| 76 EGGYLVAIEEEIAKEPHVT 94
                                      5666655557999987765 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05     0.005      19      39 ..      20      40 ..       8      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                            HTH_38 19 eGlslreIArrLgrspsTIsR 39
                                      + +slreIA +Lg++ +T+++
  gi|488601480|ref|YP_007907951.1| 20 ARKSLREIAEKLGVAEGTVYN 40
                                      459****************98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.4e-05     0.015       9      49 ..      13      52 ..       7      54 .. 0.88
   2 ?   -0.7   0.0       4.6     2e+03       5      23 ..     135     152 ..     131     155 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-05
                            HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                      L  ++ +++rk+l++++++l v   ++ + ++kL ++G ++
  gi|488601480|ref|YP_007907951.1| 13 LIELQ-EDARKSLREIAEKLGVAEGTVYNRINKLKRMGIIK 52
                                      55566.99******************************885 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.6
                            HTH_27   5 qalvLhlirhrrrrkklad 23 
                                         +vL++++ + +++ +++
  gi|488601480|ref|YP_007907951.1| 135 TMVVLNVVK-ETHGVDISE 152
                                       568999999.444444444 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 !   16.0   0.0   2.3e-05      0.01      24      52 ..      23      51 ..      10      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyv 52
                                      +  ++ae L+v+  +V   ++kL+++G +
  gi|488601480|ref|YP_007907951.1| 23 SLREIAEKLGVAEGTVYNRINKLKRMGII 51
                                      4579***********************76 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     2e-05     0.009      41      62 ..      21      42 ..      10      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                            HTH_22 41 kgavekvAekLgiSraTvYryL 62
                                      +++  ++AekLg+ + TvY+ +
  gi|488601480|ref|YP_007907951.1| 21 RKSLREIAEKLGVAEGTVYNRI 42
                                      8999****************87 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.8e-05     0.013      22      47 ..      20      45 ..      17      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-05
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrka 47
                                       r +l+e+A++lG+++ t++++++k 
  gi|488601480|ref|YP_007907951.1| 20 ARKSLREIAEKLGVAEGTVYNRINKL 45
                                      6899******************9986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.2e-05     0.014       6      52 ..       8      52 ..       4      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-05
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      ++  +L +L    + + + +e+a++lg+  ++v +++++L + G + 
  gi|488601480|ref|YP_007907951.1|  8 TDIKILIELQEDAR-K-SLREIAEKLGVAEGTVYNRINKLKRMGIIK 52
                                      66678888888875.3.9*************************9986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     5e-05     0.022      16      42 ..      16      43 ..       3      47 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-05
                                      HH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 16 rf.geglTleEIgerlgiSrerVrqiek 42
                                         +   +l EI+e+lg+ +++V  +++
  gi|488601480|ref|YP_007907951.1| 16 LQeDARKSLREIAEKLGVAEGTVYNRIN 43
                                      4447778****************77765 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 ?   14.3   0.0   5.8e-05     0.026      11      38 ..      20      47 ..      18      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-05
                                      TTT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_30 11 nggnisatAkaLhvHrnTlryRLrriee 38
                                      +  ++++ A++L+v   T+++R++++++
  gi|488601480|ref|YP_007907951.1| 20 ARKSLREIAEKLGVAEGTVYNRINKLKR 47
                                      56799********************997 PP

>> DUF4372  Domain of unknown function (DUF4372)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.017       7.8      49      69 ..      19      39 ..      10      41 .. 0.83
   2 ?    6.0   0.0     0.029        13      10      35 ..     109     135 ..     106     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.017
                           DUF4372 49 tgreSLRdieagleahaskly 69
                                        r+SLR+i ++l + ++  y
  gi|488601480|ref|YP_007907951.1| 19 DARKSLREIAEKLGVAEGTVY 39
                                      579*********999888776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.029
                           DUF4372  10 lkflprheFerlvkk.hggdkyvkkft 35 
                                        kf++r++ +r vkk  g ++ vk++t
  gi|488601480|ref|YP_007907951.1| 109 AKFMDRESLNRFVKKvAGMEHVVKTYT 135
                                       699************555666677766 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00014     0.062      12      56 ..      11      52 ..       4      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00014
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      ++l++L++ ++    s++eiae+ ++ +  +   ++kL++ g++k
  gi|488601480|ref|YP_007907951.1| 11 KILIELQEDAR---KSLREIAEKLGVAEGTVYNRINKLKRMGIIK 52
                                      56666655555...57***************************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   7.8e-05     0.035      27      55 .]      23      51 ..       5      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s + +a++lg+ + Tv++ i++L + G+i
  gi|488601480|ref|YP_007907951.1| 23 SLREIAEKLGVAEGTVYNRINKLKRMGII 51
                                      7889***********************98 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00021     0.092      33      60 ..      21      48 ..       8      54 .. 0.86
   2 ?   -0.7   0.0       3.8   1.7e+03      49      57 ..      95     103 ..      83     137 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00021
                           UPF0122 33 DlSlsEiAeefnvsrqavydnikrtekl 60
                                        Sl EiAe+  v   +vy+ i++ +++
  gi|488601480|ref|YP_007907951.1| 21 RKSLREIAEKLGVAEGTVYNRINKLKRM 48
                                      469********************99876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.8
                           UPF0122  49 avydnikrt 57 
                                       avyd     
  gi|488601480|ref|YP_007907951.1|  95 AVYDVTGEF 103
                                       555543333 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   0.00013      0.06      17      56 ..       8      47 ..       4      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                               Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                      +++++l  l e++++s+ e+a++l + e t+++ i++l+ 
  gi|488601480|ref|YP_007907951.1|  8 TDIKILIELQEDARKSLREIAEKLGVAEGTVYNRINKLKR 47
                                      6789999999***************************996 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 ?    1.2   0.0      0.91   4.1e+02      53      79 ..      17      43 ..      10      46 .. 0.74
   2 ?   10.8   0.1   0.00095      0.43      16      75 ..      77     136 ..      62     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.91
                   AsnC_trans_reg2 53 eeeveevlaeiaaatgledyevLpstr 79
                                      +e+ ++ l+eia+++g+ +  v   ++
  gi|488601480|ref|YP_007907951.1| 17 QEDARKSLREIAEKLGVAEGTVYNRIN 43
                                      68889999******9998766655555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00095
                   AsnC_trans_reg2  16 eerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevL 75 
                                          + ++ e +a++p+vt +Y    ++ +  +    ++e+++++++++a   ++ +++++
  gi|488601480|ref|YP_007907951.1|  77 GGYLVAIEEEIAKEPHVTAVYDVTGEFDMILVAKFMDRESLNRFVKKVAGMEHVVKTYTM 136
                                       444678999**************************************9987777655554 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0013      0.56      17      49 ..      22      53 ..      15      57 .. 0.83
   2 ?    0.1   0.0       1.7   7.8e+02       2      19 ..     139     154 ..     137     156 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                                      HHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEE CS
                              PadR 17 keleelsegllelseGslYpaLkrLekeglves 49
                                      k l+e  e  l + eG++Y   ++L++ g++++
  gi|488601480|ref|YP_007907951.1| 22 KSLREIAEK-LGVAEGTVYNRINKLKRMGIIKK 53
                                      556666544.6799*****************87 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.7
                                       HHHHCCS-EEHHHHHHHH CS
                              PadR   2 LalleeqpsyGyeiikel 19 
                                       L+++  ++++G++i + +
  gi|488601480|ref|YP_007907951.1| 139 LNVV--KETHGVDISELM 154
                                       5555..7889***98866 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.09      18      41 ..      22      45 ..       4      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                      S-HHHHHHHHTS-HHHHHHHHHHH CS
                              GerE 18 ksnkeIAeelniSekTVkvhksni 41
                                      ks  eIAe+l+++e TV + +  +
  gi|488601480|ref|YP_007907951.1| 22 KSLREIAEKLGVAEGTVYNRINKL 45
                                      6779*************8877655 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002      0.09      20      49 ..      12      43 ..       7      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                      HTH_Tnp_ISL3 20 ilellles..rsvkavArqlgvSwtTVwrild 49
                                      il +l+e+  +s +++A+ lgv + TV ++++
  gi|488601480|ref|YP_007907951.1| 12 ILIELQEDarKSLREIAEKLGVAEGTVYNRIN 43
                                      56666666678******************987 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00038      0.17      33      70 ..      18      53 ..      10      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                           DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkk 70
                                      +d++++ +e+a++l+  + +  v + ++ L+++g++kk
  gi|488601480|ref|YP_007907951.1| 18 EDARKSLREIAEKLG--VAEGTVYNRINKLKRMGIIKK 53
                                      3558999********..*******************98 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00042      0.19     191     225 ..      13      47 ..       9      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                              TnsD 191 lkeLveeeglslkeiAkelgvdiktVlryakklgl 225
                                       l+eL e++ +sl+eiA+ lgv  +tV+   +kl+ 
  gi|488601480|ref|YP_007907951.1|  13 LIELQEDARKSLREIAEKLGVAEGTVYNRINKLKR 47 
                                       6789999********************99999875 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 ?   11.7   0.0   0.00047      0.21      17      45 ..      11      40 ..       1      53 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00047
                                      HHHHH..HHH--S-HHHHHHHHTS-HHHHHH CS
                       HTH_Tnp_1_2 17 ellve..ndyekltldeiaeevgvsrsTlyk 45
                                      ++l+e  +d  +++l+eiae++gv++ T y+
  gi|488601480|ref|YP_007907951.1| 11 KILIElqEDA-RKSLREIAEKLGVAEGTVYN 40
                                      4454421454.99*****************7 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0006      0.27       8      36 ..      18      45 ..      11      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0006
                            HTH_29  8 laeGvstvsqiAkllglsrrtvyrwlkrf 36
                                       +    + ++iA+ lg+ + tvy+ ++  
  gi|488601480|ref|YP_007907951.1| 18 EDARK-SLREIAEKLGVAEGTVYNRINKL 45
                                      44555.59***************988765 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0009       0.4       4      26 ..      24      44 ..      23      63 .. 0.78
   2 ?   -2.1   0.0       9.9   4.5e+03      39      49 ..     113     123 ..     112     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0009
                            HTH_17  4 veEaAelLgvsrstvyrlirrge 26
                                        E+Ae Lgv + tvy+ i+  +
  gi|488601480|ref|YP_007907951.1| 24 LREIAEKLGVAEGTVYNRIN--K 44
                                      579*************9664..3 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.9
                            HTH_17  39 prsdleewlek 49 
                                       +r++l ++ +k
  gi|488601480|ref|YP_007907951.1| 113 DRESLNRFVKK 123
                                       68999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.56u 0.39s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 866.49
//
Query:       gi|488601481|ref|YP_007907952.1|  [L=71]
Description: putative RNA-binding protein, contains TRAM domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-14   52.4   2.4    4.3e-14   52.3   2.4    1.0  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   2.4   2.4e-18   4.3e-14       2      62 .]      14      70 ..      13      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2.4e-18
                                      XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM  2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62
                                      + vG   +V+ve  +  +g+gi+r+  g+vvfvp+ +    ++V+V+Itkv ++y ++e++
  gi|488601481|ref|YP_007907952.1| 14 VNVGDIRTVTVEAIG-EKGDGIARIS-GYVVFVPNVEV--DQEVTVRITKVLNKYCFAEVV 70
                                      679************.**********.********988..*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 432.02
//
Query:       gi|488601482|ref|YP_007907953.1|  [L=457]
Description: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) /cobyrinate a,c-diamide synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-39  135.1   0.0    3.2e-39  134.6   0.0    1.2  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    1.2e-20   74.2   0.4    2.4e-12   47.1   0.0    2.3  2  AAA_26    AAA domain
      1e-19   70.8   0.0      2e-19   69.9   0.0    1.5  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0024   17.2   0.0     0.0074   15.6   0.0    1.8  1  DUF1611   Domain of unknown function (DUF1611_C) P-loop domai
     0.0038   17.1   0.0     0.0077   16.1   0.0    1.5  1  SNO       SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0     9e-43   3.2e-39       3     192 ..     252     437 ..     250     441 .. 0.90

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 9e-43
                          GATase_3   3 avirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       +vi+++ +s+y+  +ld+L a++ +  ++ +l+d++l+e +d+++++Gg+++++  +l+++ +l+++i e++ ++ p
  gi|488601482|ref|YP_007907953.1| 252 GVIQDKPFSFYYedNLDALSARGIELKYIDSLNDKKLPE-IDFLYIGGGFPEVFVEELEKNDSLRKDIYEFCDDNNP 327
                                       6999*******************999999********66.************************************* PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel......aaegeevkGyEiHsGr 148
                                       v+++CGGl++LGe+i+++        e+e++g+L ++te+++ k+     + +e+        +g+++kG+E+H++r
  gi|488601482|ref|YP_007907953.1| 328 VYAECGGLMYLGESIITDG-------EYEMVGFLTFKTEMNR-KFHALGYTVCEVakdtfaFDRGDQIKGHEFHYSR 396
                                       ***************9964.......7***************.7773333333347799988889************ PP

                          GATase_3 149 tilkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfd 192
                                       +i ++k + ++kv +g++++ e dG++kk    ++l++Y H+ ++
  gi|488601482|ref|YP_007907953.1| 397 VIPSRKLDFAFKVLRGKGINgEFDGVIKK----STLACYQHLNVL 437
                                       *************88555445******99....********9776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   3.5e-09   1.2e-05       2      36 ..       5      39 ..       4      41 .. 0.94
   2 !   47.1   0.0   6.7e-16   2.4e-12      92     191 ..      72     182 ..      50     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.5e-09
                            AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                                      +i+++g+  +vGKT++s gL+ral+++g+kv+ fK
  gi|488601482|ref|YP_007907953.1|  5 RIVIAGIKSKVGKTMISIGLMRALTNRGYKVQPFK 39
                                      599***************************98777 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 6.7e-16
                            AAA_26  92 v...kelekdadivvVEGagglg.vp.itee.llnadiaknlgapvilVarggl..gtinqllltiealrqknvrvl 160
                                       +   +++ k adi ++EG  gl  ++  ++e  ++a iak l++pvilVa +++  +t +++++ ++ +  k v++ 
  gi|488601482|ref|YP_007907953.1|  72 IetfERNCKGADIAIIEGKTGLFdSHdAIDErGSTAHIAKILRSPVILVADVERmsRTAAAMIYGYKEFD-KYVNIE 147
                                       23447788899*******999985444566669*******************873245666666666665.58**** PP

                            AAA_26 161 GvilNkvrnp....envetlekksgipvlGvvPyl 191
                                       GvilN++ np    + v ++ek sg++v+G++P +
  gi|488601482|ref|YP_007907953.1| 148 GVILNRIGNPrhlkRVVLAVEKLSGVRVIGAIPRE 182
                                       **********666559*****************86 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   5.5e-23     2e-19       1     116 [.       6     183 ..       6     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 5.5e-23
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx..................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep..................... 54 
                                       i+ia+ k+ vGKT+++++L+ral +rg++V++++++p+        +                              
  gi|488601482|ref|YP_007907953.1|   6 IVIAGIKSKVGKTMISIGLMRALTNRGYKVQPFKVGPDFIDPGFhnI--------Atgrksrnidsfmmdsysiiet 74 
                                       79************************************444442332........03444456699*********** PP

                                       ...............................................CCHCCCHHHHHHCHCHHHH.....EEEEEE CS
                                       ...............................................xxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                              CbiA  55 ...............................................dlkrllellealgkkkall...lkiagvvl 81 
                                                                                      d++r++++++a+  +++ +   ++i gv+l
  gi|488601482|ref|YP_007907953.1|  75 fernckgadiaiiegktglfdshdaidergstahiakilrspvilvaDVERMSRTAAAMIYGYKEFdkyVNIEGVIL 151
                                       ********************************************************99999999999********** PP

                                       EEESS...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  82 nrvdgeneetllkealeelkqrygvpvlgviprde 116
                                       nr++++++ ++   a+e+l    gv+v+g ipr  
  gi|488601482|ref|YP_007907953.1| 152 NRIGNPRHLKRVVLAVEKLS---GVRVIGAIPREN 183
                                       ******99999999999998...*********954 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 !   15.6   0.0   2.1e-06    0.0074      11     103 ..       2      99 ..       1     116 [. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-06
                           DUF1611  11 kakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili.......agegvvldavvvdfvaGaveglvk 80 
                                       + +r+++ G  ++vGK + ++ l +al++rG+k++ +  g+  i          ++   +d+ ++d       ++++
  gi|488601482|ref|YP_007907953.1|   2 DIPRIVIAGIKSKVGKTMISIGLMRALTNRGYKVQPFKVGPDFIDPgfhniatGRKSRNIDSFMMDSY-----SIIE 73 
                                       679******************************99888887655541000010444445555555543.....4444 PP

                           DUF1611  81 kaae.eeepdlilveGQgsLt..hpa 103
                                       ++++  + +d+ ++eG ++L+  h+a
  gi|488601482|ref|YP_007907953.1|  74 TFERnCKGADIAIIEGKTGLFdsHDA 99 
                                       4444334679**********977665 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.2e-06    0.0077      28     101 ..     285     359 ..     263     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                                       GGGGCC-SEEEE-SS-H.HHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB.SS-SS--CCEEEE CS
                               SNO  28 kedlaevdaliiPGGes.tamskliertglyedllefvknsekvvlGtCaGlillskelene.lvktlellkvkvk 101
                                        ++l e+d l i GG     ++ l ++  l +d++ef  ++  +v+  C Gl++l + + ++ + + +++l  k +
  gi|488601482|ref|YP_007907953.1| 285 DKKLPEIDFLYIGGGFPeVFVEELEKNDSLRKDIYEFCDDN-NPVYAECGGLMYLGESIITDgEYEMVGFLTFKTE 359
                                       45699**********76156788999999********9987.8*************99988766777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 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:                        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: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2513.94
//
Query:       gi|488601483|ref|YP_007907954.1|  [L=304]
Description: ornithine carbamoyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  197.6   0.0    1.7e-58  197.1   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.2e-54  184.4   0.0    2.1e-54  183.6   0.0    1.4  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 !  197.1   0.0   1.9e-62   1.7e-58       2     156 ..     149     298 ..     148     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 1.9e-62
                                       C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE- CS
                            OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytd 78 
                                       ++k+++vGd+ nnv+nsli + a++g+++v+ +P g+epd+ +le+a +     ggsi++  ++eeavk+aDv+ytd
  gi|488601483|ref|YP_007907954.1| 149 KIKLVWVGDG-NNVCNSLILASAIMGIKMVYSTPAGYEPDQSILEKALEL----GGSIEYVREPEEAVKDADVIYTD 220
                                       69********.*********************************888776....9********************** PP

                                       -SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                            OTCace  79 vwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                       vw+smg+e+ere+rlk ++dyqv+ +ll+ a++d+ivlHcLPa+rgeE+tdeV++s +svv++qaeNrlh++kA+l+
  gi|488601483|ref|YP_007907954.1| 221 VWASMGQEAEREKRLKVFADYQVNTNLLSYANEDVIVLHCLPAHRGEEITDEVIESSNSVVYDQAENRLHAQKAILL 297
                                       ***************************************************************************98 PP

                                       H CS
                            OTCace 156 l 156
                                       +
  gi|488601483|ref|YP_007907954.1| 298 T 298
                                       6 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6   0.0   2.4e-58   2.1e-54       1     148 []       2     142 ..       2     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 2.4e-58
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       +hl+s++dls+eeie++ldla++lk+++ k    ++lk+k+la++Fe pStRTrvSfevA++++Gg++l+l+  +d+
  gi|488601483|ref|YP_007907954.1|   2 KHLVSISDLSREEIEKILDLADRLKSERYKGIVADYLKNKSLAMIFELPSTRTRVSFEVAMSDMGGHALYLN-WNDL 77 
                                       8***********************************************************************.77** PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       ql+     r+E+++Dtarvlsryv+ai+iR+++++ +eela+++svpviN++ ++ eHP+Q+LaDl+tire
  gi|488601483|ref|YP_007907954.1|  78 QLG-----RGEPIKDTARVLSRYVHAIMIRARNHKIIEELARHSSVPVINGL-SNLEHPCQILADLMTIRE 142
                                       ***.....78******************************************.****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1962.13
//
Query:       gi|488601484|ref|YP_007907955.1|  [L=256]
Description: NH(3)-dependent NAD(+) synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-91  306.4   0.0    1.2e-91  306.2   0.0    1.0  1  NAD_synthase   NAD synthase
      1e-08   34.4   0.1    1.8e-06   27.0   0.1    2.1  2  tRNA_Me_trans  tRNA methyl transferase
    0.00074   19.1   0.0     0.0031   17.0   0.0    1.8  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.035   13.9   0.0      0.055   13.2   0.0    1.3  1  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.2   0.0   2.7e-95   1.2e-91       3     242 .]      10     246 ..       8     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 306.2 bits;  conditional E-value: 2.7e-95
                                       HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE CS
                      NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievkt 78 
                                       +++v+f+++yv++a+a+gvvlG+SGGvDS+ va l+ kalg envl+l++P + v+ eedveda++++++ gi++k 
  gi|488601484|ref|YP_007907955.1|  10 KRIVEFIRDYVRSANAEGVVLGVSGGVDSACVAFLCSKALGGENVLGLIMPeKGVTREEDVEDAIEVCKKAGIKYKI 86 
                                       6899***********************************************999*********************** PP

                                       ---HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS- CS
                      NAD_synthase  79 idikpivrafeqelkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaell 155
                                       ++i++i++ f+   + ++ d+a +Nlk+RiRm+++y++an ln++v+gTgnksEl+vGyfTkyGDg++d++pi++l+
  gi|488601484|ref|YP_007907955.1|  87 VEISDILQKFKGISSCDR-DIALANLKPRIRMVLNYYYANCLNRIVAGTGNKSELMVGYFTKYGDGGCDFLPIGDLY 162
                                       **********98766666.9********************************************************* PP

                                       HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT--HHHHHHHHHHH CS
                      NAD_synthase 156 KtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLklvekkkspeeiikekelpaevvekieklv 232
                                       Ktev+ La++l+vPerv+kk+PsA+L+ gqtDe+e+gi+Y++lD iLk +e++++++ i +   + ++ v k+ +++
  gi|488601484|ref|YP_007907955.1| 163 KTEVFMLAEHLGVPERVIKKKPSAGLWVGQTDEDEMGISYKVLDAILKRIERGEIEKAIEE---FGKDSVDKVRDMI 236
                                       ******************************************************9999766...9************ PP

                                       HHTGGGGSSS CS
                      NAD_synthase 233 kksehKrklp 242
                                        +sehKr+lp
  gi|488601484|ref|YP_007907955.1| 237 ARSEHKRSLP 246
                                       *******998 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   4.1e-10   1.8e-06       3      72 ..      28      91 ..      26      97 .. 0.86
   2 !    5.4   0.0    0.0015       6.7     166     196 ..     156     188 ..     154     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.1e-10
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq..gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                      vv ++SgGVDS+ +a+l  ++  g +v g+++  +        + + eed++da +v++k gi++++v++++
  gi|488601484|ref|YP_007907955.1| 28 VVLGVSGGVDSACVAFLCSKAlgGENVLGLIMPEK--------GVTREEDVEDAIEVCKKAGIKYKIVEISD 91
                                      899**************998744799999999643........46789*******************99876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0015
                     tRNA_Me_trans 166 fPlgeltKeevrkiAkeagla..vaekkdSqgi 196
                                       +P+g+l K+ev  +A++ g++  v +kk S g+
  gi|488601484|ref|YP_007907955.1| 156 LPIGDLYKTEVFMLAEHLGVPerVIKKKPSAGL 188
                                       8*******************9899999999987 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     7e-07    0.0031       3      80 ..      29     109 ..      27     125 .. 0.79
   2 ?   -0.8   0.0       0.2   8.8e+02     157     176 ..     157     176 ..     155     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7e-07
                                       EEE--SSHHHHHHHHHHHHH-..SEEEEEEE.ESS-TTSHHHHHHHHHHHHT--.-EEEEE-.GGGGGGSCGGG--- CS
                              QueC   3 vvllSGGlDSttvlalakkeg..kevealtf.dYgqrhkkeleaakkiakelgveehkildl.dllkelggsaLtde 75 
                                       v+ +SGG+DS+ v++l +k+   ++v  l + + g  +++++e a +++k++g+ + ki+++ d+l++++g +  d+
  gi|488601484|ref|YP_007907955.1|  29 VLGVSGGVDSACVAFLCSKALggENVLGLIMpEKGVTREEDVEDAIEVCKKAGI-KYKIVEIsDILQKFKGISSCDR 104
                                       6779***********99997533666655442556668889999**********.9999998358999999888888 PP

                                       ----- CS
                              QueC  76 eievp 80 
                                       +i++ 
  gi|488601484|ref|YP_007907955.1| 105 DIALA 109
                                       77665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
                                       TTTT--HHHHHHHHHHTTHH CS
                              QueC 157 PlidlsKaeivklgkelgvp 176
                                       P+ dl K+e++ l+++lgvp
  gi|488601484|ref|YP_007907955.1| 157 PIGDLYKTEVFMLAEHLGVP 176
                                       9999**************87 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.055       2      79 ..      28     102 ..      27     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--HHHCTTSTCCC CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdvakkkgknlee 78 
                                       v+++vSgG+DS +   l  k     +  l +i+ + g+  e +   e   e+ckk +ik++i +++   +k k++  
  gi|488601484|ref|YP_007907955.1|  28 VVLGVSGGVDSACVAFLCSKALG-GENVLGLIMPEKGVTREEDV--EDAIEVCKKAGIKYKIVEISDILQKFKGISS 101
                                       789**********9999988855.34466777777777655444..4455899999999999998875555666655 PP

                                       H CS
                        ATP_bind_3  79 a 79 
                                        
  gi|488601484|ref|YP_007907955.1| 102 C 102
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1422.76
//
Query:       gi|488601485|ref|YP_007907956.1|  [L=271]
Description: shikimate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-10   40.6   0.2    8.5e-10   38.7   0.2    1.9  2  GHMP_kinases_N  GHMP kinases N terminal domain
    0.00063   20.1   0.0     0.0033   17.7   0.0    2.2  2  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.089   12.9   0.3        1.2    9.3   0.1    2.2  2  FtsK_alpha      FtsK alpha 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 ?   -1.4   0.0      0.47   2.8e+03      19      40 ..      11      35 ..      10      47 .. 0.68
   2 !   38.7   0.2   1.4e-13   8.5e-10       1      66 []      66     135 ..      66     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.47
                                      HHHHHHHHHHHHHTTEHHHH...HH CS
                    GHMP_kinases_N 19 AlavalvaAllallglslee...ak 40
                                      +++ a+++ +  ++g++l++   ++
  gi|488601485|ref|YP_007907956.1| 11 TIVNAVARGIGCAFGVDLRTkvlLE 35
                                      5788999999999998874334444 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 1.4e-13
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH.......HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglslee.......aklaleaerlaqggngsggDv.aasvyGg 66 
                                       ++v++s iP ++GLGSS+A+  +l++A++++ g +l+        a++al++        ++ +D+ +as++Gg
  gi|488601485|ref|YP_007907956.1|  66 RVVVESSIPKKSGLGSSSAILNSLLLAIYKFRGWELDAlkilnenADIALKSKISY----TGAFDDaSASLLGG 135
                                       589*****************************966422233433477777777544....56666659999998 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.49     3e+03      22      47 ..     100     122 ..      89     125 .. 0.63
   2 !   17.7   0.0   5.6e-07    0.0033      20      84 ..     196     254 ..     177     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.49
                    GHMP_kinases_C  22 rselkavvgilppeleellealselG 47 
                                       +   ++ ++il+++ + +l++  +++
  gi|488601485|ref|YP_007907956.1| 100 E---LDALKILNENADIALKSKISYT 122
                                       4...5666667776666666654444 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5.6e-07
                    GHMP_kinases_C  20 sqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreefe 84 
                                       +  +  ++++++l+  l+ + +a ++ G + a+lsG   Gp+ +a++  k + +++a+++r++++
  gi|488601485|ref|YP_007907956.1| 196 MLYN-SLHYCKVLNYPLKPVMDA-RDIG-IPAGLSGN--GPSYIAFG-PKKDIDELAESWRSYGK 254
                                       3333.456999999999999999.7999.********..********.99999*******99886 PP

>> FtsK_alpha  FtsK alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0002       1.2       6      43 ..      33      68 ..      29      75 .. 0.80
   2 ?    1.3   0.0     0.064   3.8e+02       6      35 ..     159     186 ..     155     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                        FtsK_alpha  6 lLeeeekekkkedeeelekkaklieetleefgieakvv 43
                                      lLee+ +   +  e++ + k++li+++l +fg++a+vv
  gi|488601485|ref|YP_007907956.1| 33 LLEESRDV--EILEKDRKIKSQLIQNVLYRFGVKARVV 68
                                      55666665..77888888899***************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.064
                        FtsK_alpha   6 lLeeeekekkkedeeelekkaklieetlee 35 
                                       lL++++k+  k+d e+++k+a+++++++ee
  gi|488601485|ref|YP_007907956.1| 159 LLSDSKKR--KVDVESVRKNAEIVDKAIEE 186
                                       45555555..9999********99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1541.00
//
Query:       gi|488601486|ref|YP_007907957.1|  [L=212]
Description: CDP-diacylglycerol--serine O-phosphatidyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   31.4   3.0    2.5e-07   31.4   3.0    3.1  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
          2    7.3   9.2        3.1    6.7   9.2    1.2  1  DUF3488          Domain of unknown function (DUF3488)


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 !   31.4   3.0   2.8e-11   2.5e-07       2      66 .]      10      70 ..       9      70 .. 0.87
   2 ?   -5.6   8.5         2   1.8e+04      41      41 ..     157     157 ..      90     200 .. 0.59

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.8e-11
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      ++++++ l+ l+++l i+++  +  + + +l+l++++++D++DG +AR   + s lG+ lDslaD
  gi|488601486|ref|YP_007907957.1| 10 IADIFSALNALFGILGIYFV--FTDVRASALFLVASAIMDGVDGAVARLE-T-SLLGENLDSLAD 70
                                      578899999********866..444689999999**************99.4.77*********9 PP

  == domain 2  score: -5.6 bits;  conditional E-value: 2
                                       T CS
                   CDP-OH_P_transf  41 D 41 
                                       D
  gi|488601486|ref|YP_007907957.1| 157 D 157
                                       1 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   9.2   0.00035       3.1      22     128 ..      92     198 ..      74     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00035
                           DUF3488  22 lwvlllaalllvwrlllarrraplpsrwlllllallav.allllsygtllgrdagvalLvlllalKllElrsrRDal 97 
                                       + +++l++++ ++rl ++ +  +++ +++ + +++ a+ +++++ +       a+v++L+ ll++  + + + RD +
  gi|488601486|ref|YP_007907957.1|  92 FSISGLFLICGMIRL-ARFNLLKIKDEFVGFPITASALiVGAMVLIDFNAVAIAFVSVLLSLLMISDIRYPKVRDKI 167
                                       456788999999885.4447788888888877776666566666666544578************************ PP

                           DUF3488  98 vllllgffllatsflfsqsllfalylllall 128
                                       vl +++++++ + f+ +   +++++++l+l+
  gi|488601486|ref|YP_007907957.1| 168 VLGVVAVVMVSVFFIPESAYILLALMVLYLF 198
                                       ****999999998888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1271.21
//
Query:       gi|488601487|ref|YP_007907958.1|  [L=113]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-39  133.3   0.0    4.9e-39  133.2   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 !  133.2   0.0   2.7e-43   4.9e-39       3     107 ..       8     112 ..       6     113 .] 0.98

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 2.7e-43
                                       HHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTEEE CS
                              DHNA   3 rerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgemldv 79 
                                       ++ A+FEagiklgal+HqfvG+Pvs e+a++le a+e++++lQPfv +++vkidre+l+e +++fgY++L+ge +++
  gi|488601487|ref|YP_007907958.1|   8 EKIACFEAGIKLGALFHQFVGAPVSLENARILEMAMESCMRLQPFVVSAEVKIDRERLKEMVSSFGYISLSGELIRA 84 
                                       678************************************************************************** PP

                                       EEEEEETTEEEEEEEEEETTTTEEEEEE CS
                              DHNA  80 eitvkyeeaevkarleyieeldYplmkv 107
                                       ++tvk++e+ ++a+l +++e++Yp+m++
  gi|488601487|ref|YP_007907958.1|  85 RVTVKVGETLARAELYWDDEKKYPMMRL 112
                                       **************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 674.65
//
Query:       gi|488601488|ref|YP_007907959.1|  [L=223]
Description: phosphoesterase, MJ0936 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  108.4   0.0    5.4e-31  108.0   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    4.4e-14   53.5   0.7    7.2e-14   52.8   0.7    1.3  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   0.0     6e-35   5.4e-31       1     164 [.       1     187 [.       1     188 [. 0.76

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 6e-35
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellelapvlaVrGNnD...........ee 64 
                                       Mk++iiSD+Hsnl ale+vle+l+++  d ii+aGD+  +   ++ + e+++ ++++ V GN+D           + 
  gi|488601488|ref|YP_007907959.1|   1 MKIGIISDIHSNLVALERVLERLEGC--DEIICAGDVvgYYPYFNEVVEIFRKERIYSVLGNHDysiitgdfselD- 74 
                                       **************************..********978777888888888888**********999986665551. PP

                     Metallophos_2  65 vveedvlreaaelgtdl........peeaelelagekvlliHgdpl..........gvkdalaellkeaeegsdvvv 123
                                           + ++ +a++ ++          e   l+l+  ++ ++Hg p             +  l e +   e + + vv
  gi|488601488|ref|YP_007907959.1|  75 ----TYGKISAGYIRKNieeknlswLENLPLKLETGRFNVYHGIPAdsldaiklhvFPTFPLIEKI--LEVEGKSVV 145
                                       ....444444444444411111111344455557778******98788887765332222222222..33555599* PP

                     Metallophos_2 124 cGHtHvpevekeggvlvvnPGsvgeprdgdpe.tyaildtde 164
                                       +GHtH++ ++++++ +vvnPGsvg+prdgd + +yai+dt+ 
  gi|488601488|ref|YP_007907959.1| 146 VGHTHIQFMKEHRNFRVVNPGSVGQPRDGDSRaCYAIYDTER 187
                                       *******************************99******986 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.7     8e-18   7.2e-14       1     169 [.       1     149 [.       1     195 [. 0.77

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 8e-18
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS.. CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe.. 75 
                                       ++i +i+D+H      +l +l+++l++l   e++d +++aGD+v   ++ +e++e +++        y +lGNH+  
  gi|488601488|ref|YP_007907959.1|   1 MKIGIISDIH-----SNLVALERVLERL---EGCDEIICAGDVVGYYPYFNEVVEIFRKERI-----YSVLGNHDys 64 
                                       89********.....**********999...8*******************99999777777.....*********9 PP

                                       ....CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC CS
                       Metallophos  76 ....gfee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg 147
                                            f+e +   k    +i +++ +++ ++++nlpl    +g  ++ ++hG  p +  sld ++  ++++ +    
  gi|488601488|ref|YP_007907959.1|  65 iitgDFSElDTYGKISAGYIRKNIEEKNLSWLENLPLKL-ETG--RFNVYHGI-PAD--SLDAIKLHVFPTFPLI-- 133
                                       9987666666666666666667777777*********98.666..77777776.444..5888888888877666.. PP

                                       HHHHHHHHHHTTCSEEEEEESS CS
                       Metallophos 148 dewlkdlekrekadwvivlgHs 169
                                       +++l+           +v+gH 
  gi|488601488|ref|YP_007907959.1| 134 EKILEV------EGKSVVVGHT 149
                                       555555......3444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      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: 0.56u 0.37s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1251.35
//
Query:       gi|488601489|ref|YP_007907960.1|  [L=325]
Description: Phosphate uptake regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-11   44.1   9.0    2.4e-08   34.3   1.5    2.7  2  PhoU            PhoU domain
    6.6e-10   38.7   0.0    2.5e-09   36.9   0.0    2.1  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0013   18.3   3.5      0.076   12.6   4.8    2.1  2  Lipoprotein_2   Borrelia lipoprotein
  ------ inclusion threshold ------
      0.054   13.8   0.1       0.15   12.4   0.1    1.8  1  DUF349          Domain of Unknown Function (DUF349)
      0.056   13.3   0.1        0.1   12.5   0.1    1.4  1  TERT_thumb      Telomerase reverse transcriptase thumb DNA bi
       0.18   12.1   2.6          7    7.0   0.6    2.5  2  DUF948          Bacterial protein of unknown function (DUF948
       0.19   12.1   4.8        1.5    9.2   0.1    3.4  3  Syntaxin_2      Syntaxin-like protein


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 !   34.3   1.5   9.6e-12   2.4e-08       1      87 [.     138     226 ..     138     228 .. 0.89
   2 !   13.4   1.1   3.1e-05      0.08       3      84 ..     240     313 ..     238     316 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 9.6e-12
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SH.HHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak.rqplae.dlrellsllriardl 75 
                                       l+rm +i+  m+d  ++ l+ kd  +++e+   + ++drl+++  r+  +++++ +  +   +lr++l+++ +++ +
  gi|488601489|ref|YP_007907960.1| 138 LKRMYQIIDAMIDGIIDGLKVKDATTLNEIKYFESDLDRLYFLALREQHRKVKElSITVKWnELRMILGARTVTKLI 214
                                       78******************************************8888999966444443356************** PP

                                       HHHHHHHHHHHH CS
                              PhoU  76 ERigDhavniae 87 
                                       E i+D  ++ ++
  gi|488601489|ref|YP_007907960.1| 215 EEIADSLREFSD 226
                                       *****9998876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHH.HHHHHHHH CS
                              PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllr.iardlERi 78 
                                       ++   v+++++++l+a++e d  + ++v      i + ek+i +  +++++++q+   ++r+ l+ l+ i +++  i
  gi|488601489|ref|YP_007907960.1| 240 KLLTDVKTIFSEVLKAYSESDLTTSEKV------IKETEKLIVEI-VRLISENQEI--NYRMSLETLKeIMKNIKSI 307
                                       56667999*************9999999......55555555444.5556555555..5666666666699999999 PP

                                       HHHHHH CS
                              PhoU  79 gDhavn 84 
                                       g  a n
  gi|488601489|ref|YP_007907960.1| 308 GEVAFN 313
                                       987765 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 !   36.9   0.0   9.7e-13   2.5e-09       1      44 [.       8      52 ..       8      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 9.7e-13
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHHS CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgd.kiilrplksl 44
                                      f +G+s++v++Pk + +++++++Gde++l v+++ +iil ++ s+
  gi|488601489|ref|YP_007907960.1|  8 FIGGSSYMVSLPKNWIRSNDLEQGDELVLNVEDEcIIILPKKISE 52
                                      789************************************999776 PP

>> Lipoprotein_2  Borrelia lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.041     1e+02      38      93 ..     112     167 ..      99     207 .. 0.86
   2 !   12.6   4.8     3e-05     0.076      33     133 ..     209     314 ..     206     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.041
                     Lipoprotein_2  38 vesvktkLnkivaelkeekkknaegteksveklvegkldkivegakkaseaalgei 93 
                                       +e +  k +kiv    ++ +   +g+ k + + +  ++d i++g k     +l+ei
  gi|488601489|ref|YP_007907960.1| 112 MEIIHAKDGKIVLRCMNTPDFDFSGVLKRMYQIIDAMIDGIIDGLKVKDATTLNEI 167
                                       6788999**********************999***********9988766666664 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3e-05
                     Lipoprotein_2  33 kvgetvesvktkLnkivaelkeekkknaegte..ksveklvegkldkivegakkaseaalgeig...dlignvaaad 104
                                       +v + +e++ + L + ++ +k++++k+++  +  ++v++  ++ l+   e+ +++se+ ++e++   ++i+   +++
  gi|488601489|ref|YP_007907960.1| 209 TVTKLIEEIADSLREFSDYVKNIEDKEEVLIKllTDVKTIFSEVLKAYSESDLTTSEKVIKETEkliVEIVRLISEN 285
                                       788899999999999999999999999986663256**************************994444455556788 PP

                     Lipoprotein_2 105 adaaagadeesvkklvkgiKgIvevvlke 133
                                       ++ +   + e +k+++k iK+I ev+ + 
  gi|488601489|ref|YP_007907960.1| 286 QEINYRMSLETLKEIMKNIKSIGEVAFNR 314
                                       99999999*****************9876 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.9e-05      0.15      12      74 ..     248     312 ..     222     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                            DUF349  12 afferrkahfeeqdaereenlekKealieeaealakstt..dwksatkrlkelqeeWkeiGpVpr 74 
                                        f e +ka+ e+     e+ +++ e+li e+  l  +++  + + + + lke+++  k+iG+V +
  gi|488601489|ref|YP_007907960.1| 248 IFSEVLKAYSESDLTTSEKVIKETEKLIVEIVRLISENQeiNYRMSLETLKEIMKNIKSIGEVAF 312
                                       57888999999999999*****************887655677889****************986 PP

>> TERT_thumb  Telomerase reverse transcriptase thumb DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     4e-05       0.1     118     184 ..     118     190 ..      99     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                                       T-----HHHHHHHHHHHHHHHHGGGHHHHH....HHHHHHHHHS---...---S-TTS-GGGGSS--HHHCSCB CS
                        TERT_thumb 118 kyrkvtfqclksiawraflavlkrrteiyk....glidriksreklt...mkfhdgevdasyfcklpekfrfvk 184
                                       k  k+ ++c+++  +  f  vlkr  +i      g+id +k ++  t   +k+++ ++d  yf  l e+ r vk
  gi|488601489|ref|YP_007907960.1| 118 KDGKIVLRCMNTPDF-DFSGVLKRMYQIIDamidGIIDGLKVKDATTlneIKYFESDLDRLYFLALREQHRKVK 190
                                       555788888887766.6999****9988651112667777888877733469*******************998 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0034       8.8      40      81 ..     208     249 ..     179     257 .. 0.77
   2 ?    7.0   0.6    0.0027         7      17      83 ..     238     310 ..     237     314 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0034
                            DUF948  40 kqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                                       + v+++++e++d l++  + ++++++k e + +l + v+++ 
  gi|488601489|ref|YP_007907960.1| 208 RTVTKLIEEIADSLREFSDYVKNIEDKEEVLIKLLTDVKTIF 249
                                       789999999999999999999999999999999999999875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0027
                            DUF948  17 livvllklkktldeaaatieele.kqvdpilkevedllakvnelledvne.....klekvdplteavadlges 83 
                                       li++l  +k +++e+ ++  e      ++++ke+e+l+ ++ +l ++ +e      le++++++++++ +ge 
  gi|488601489|ref|YP_007907960.1| 238 LIKLLTDVKTIFSEVLKAYSESDlTTSEKVIKETEKLIVEIVRLISENQEinyrmSLETLKEIMKNIKSIGEV 310
                                       677778888888888777777664344556666666666666655555555557799*************986 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.27   6.8e+02      40      64 ..      48      72 ..      39     107 .. 0.79
   2 ?    9.2   0.1    0.0006       1.5      71      98 ..     209     236 ..     182     239 .. 0.76
   3 ?    6.1   2.5    0.0057        15      74      98 ..     212     236 ..     210     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                        Syntaxin_2 40 eeinelikktnellkklsqldnsss 64
                                      ++i+e +k ++ ++k l+q+d   +
  gi|488601489|ref|YP_007907960.1| 48 KKISESSKVVKGQIKGLKQYDTDFL 72
                                      6899999999*****9999998765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0006
                        Syntaxin_2  71 qkekLkkdfkealqeFqkiqrqyaekek 98 
                                       +  kL +++ ++l+eF  +++++++ke 
  gi|488601489|ref|YP_007907960.1| 209 TVTKLIEEIADSLREFSDYVKNIEDKEE 236
                                       678**********************996 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0057
                        Syntaxin_2  74 kLkkdfkealqeFqkiqrqyaekek 98 
                                       kL +++ ++l+eF  +++++++ke 
  gi|488601489|ref|YP_007907960.1| 212 KLIEEIADSLREFSDYVKNIEDKEE 236
                                       5555666666666666666655553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1477  (0.0823805); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); 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: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 1913.78
//
Query:       gi|488601490|ref|YP_007907961.1|  [L=184]
Description: Protein involved in ribosomal biogenesis, contains PUA domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-28   97.6   1.4    6.5e-28   96.8   1.4    1.4  1  UPF0113    UPF0113 PUA domain
    9.5e-11   41.5   1.1    1.4e-10   41.0   0.3    1.7  2  PUA        PUA domain
    2.3e-07   31.3   3.5    4.1e-06   27.3   0.5    2.6  2  UPF0113_N  UPF0113 Pre-PUA domain
  ------ inclusion threshold ------
      0.055   13.3   0.1       0.12   12.3   0.1    1.5  1  PUA_3      PUA-like domain


Domain annotation for each model (and alignments):
>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   1.4   1.5e-31   6.5e-28       2      76 .]      99     177 ..      98     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 1.5e-31
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt...k.aspgkivvknlaDiGeYl 74 
                                       v+v+e++e+lFLYGrd++ es++k++es+ken+ v+V+n+ g++lGiGk+r+d+   +  +++++vv+nl+D+GeYl
  gi|488601490|ref|YP_007907961.1|  99 VYVNERGEMLFLYGRDIFSESVVKVSESIKENDIVFVCNKHGDVLGIGKSRYDGrimRsVEKDRVVVENLVDRGEYL 175
                                       89*******************************************************88****************** PP

                           UPF0113  75 Rr 76 
                                       R+
  gi|488601490|ref|YP_007907961.1| 176 RK 177
                                       *6 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.4   6.2e+03      17      24 ..      66      73 ..      59      76 .. 0.78
   2 !   41.0   0.3   3.1e-14   1.4e-10      13      68 ..     109     164 ..      97     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.4
                                      -EEEGGGE CS
                               PUA 17 asLlapGv 24
                                      +s+ ++G+
  gi|488601490|ref|YP_007907961.1| 66 KSIVCAGI 73
                                      69999998 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 3.1e-14
                                       HHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEE CS
                               PUA  13 llsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksv 68 
                                        l+g++++   vv+v ++++e+d+V ++++ g ++++G+++y++  +++++++++v
  gi|488601490|ref|YP_007907961.1| 109 FLYGRDIFSESVVKVSESIKENDIVFVCNKHGDVLGIGKSRYDGRIMRSVEKDRVV 164
                                       578************************************************98765 PP

>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.5   9.1e-10   4.1e-06       1      82 []       6      86 ..       6      86 .. 0.78
   2 ?    4.5   0.2     0.011        51      31      64 ..      87     134 ..      85     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.1e-10
                         UPF0113_N  1 RklseeetrivfekLtkyigdnvkelldrkdgtycfrlkkkrVyyvseellklae....tikpenlisaGtclGkftkt 75
                                      R+++e+e+++++++L ++   + k++l  k      + +kk+Vy++s el  +++    + + + +++aG+ lG++   
  gi|488601490|ref|YP_007907961.1|  6 RDPNEKELKTIRKALGAF---GKKDFLADKRILIAEYKNKKEVYFLSPELHDFLKeglrNGNLKSIVCAGIKLGEV--G 79
                                      899***************...77777774443334456899******888777652221678899***********..5 PP

                         UPF0113_N 76 kkFrlsi 82
                                      k+Frl++
  gi|488601490|ref|YP_007907961.1| 80 KRFRLTL 86
                                      9999986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                         UPF0113_N  31 dgtycfrlkkkrVyyvs..............eellklaetikpenlis 64 
                                       +g y++  kkkrVy+ +              e++ k++e+ik + +++
  gi|488601490|ref|YP_007907961.1|  87 EGAYYLSSKKKRVYVNErgemlflygrdifsESVVKVSESIKENDIVF 134
                                       478999999****98888888888888888888888888888777776 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.6e-05      0.12      18      49 ..     115     146 ..     114     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                             PUA_3  18 vfsneiasvegeledGdvVdvfsekgkflGtG 49 
                                       +fs+ + +v++ +++ d+V v +++g  lG G
  gi|488601490|ref|YP_007907961.1| 115 IFSESVVKVSESIKENDIVFVCNKHGDVLGIG 146
                                       8*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.32s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1148.57
//
Query:       gi|488601491|ref|YP_007907962.1|  [L=130]
Description: hypothetical protein Asulf_02004 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 742.97
//
Query:       gi|488601492|ref|YP_007907963.1|  [L=222]
Description: Uncharacterized membrane protein, possible Na+ channel or pump [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-76  255.7  23.3    3.6e-76  255.5  23.3    1.0  1  DUF554    Protein of unknown function (DUF554)
    0.00069   19.3   2.1    0.00069   19.3   2.1    2.5  2  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.22   11.7   3.9       0.13   12.4   0.9    2.1  2  YjcB      Family of unknown function


Domain annotation for each model (and alignments):
>> DUF554  Protein of unknown function (DUF554)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.5  23.3   5.9e-80   3.6e-76       1     219 [.       2     219 ..       2     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 255.5 bits;  conditional E-value: 5.9e-80
                            DUF554   1 lGtivNvlaillGsllGlllkkrlperlqktlmqalGlvvlliGismalksenvllvilslvlGaviGelldleerl 77 
                                       +Gti+N+++i+++sl+G+++++rl+ +l+++lm +lGlvv++iG++mal +++v++++ s++lG++iGe++ +e++l
  gi|488601492|ref|YP_007907963.1|   2 IGTIINSVTIVVASLFGMFIGSRLNPKLKESLMRVLGLVVVVIGLKMALLTDEVVILVGSILLGTAIGEVIGIESKL 78 
                                       7**************************************************************************** PP

                            DUF554  78 erlgealkkkvkkskrfaegfvtasllfcvGamailGslqeGltgdatlLltKslLDgvtaiilasslGigvlfsal 154
                                       e++g+ +++++++sk faegfv+++ll+cvG+ma++Gs+qeGltgd++lLltKslLDg+++i+las+lGigv+fs++
  gi|488601492|ref|YP_007907963.1|  79 ESFGRSVERRFEGSK-FAEGFVSTTLLYCVGSMAVVGSIQEGLTGDYSLLLTKSLLDGFASIALASTLGIGVMFSSI 154
                                       ***********9888.************************************************************* PP

                            DUF554 155 pvlvyqgaitllAgllapllteaviaeltavGgllilaiGlnlleikkikvanllPalllavllv 219
                                       +vlvyqg++tllAg +++l+te++iae+ta+Gg+li+aiGl+l+e+ ++k +n+lP+ll+ +++ 
  gi|488601492|ref|YP_007907963.1| 155 SVLVYQGSLTLLAGHISALMTEKIIAEITATGGVLIVAIGLRLMELIDLKPGNMLPSLLINPIIL 219
                                       ************************************************************99875 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.1   1.2e-07   0.00069     196     236 .]       9      48 ..       2      48 .. 0.91
   2 ?   -4.4  14.0       2.1   1.2e+04      92     206 ..      95     191 ..      50     214 .. 0.45

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-07
                              TauE 196 llllpgallGallGarlarrlsertlrrlfallllvlgvkl 236
                                       + +++++l+G+++G+rl+ +l+e  l r+++l+++v+g+k+
  gi|488601492|ref|YP_007907963.1|   9 VTIVVASLFGMFIGSRLNPKLKE-SLMRVLGLVVVVIGLKM 48 
                                       4589******************9.9999***********98 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 2.1
                              TauE  92 lkllfgvlllllallmllrkkrsrakgrerrptaillvliggl.vGllsGllGiGgGfllvpllllllglplkk... 164
                                        + +++  ll+ + +m++  +++++ +  +   +  ++l g++ ++ l++ lGiG+ f  + +l++   l+l     
  gi|488601492|ref|YP_007907963.1|  95 AEGFVSTTLLYCVGSMAVVGSIQEGLTGDYSLLLTKSLLDGFAsIA-LASTLGIGVMFSSISVLVYQGSLTLLAghi 170
                                       4444445555555555443332222223333333333344444333.333345555555555555544444433332 PP

                              TauE 165 .avatslllilvislagalgyalagavdwpllllllpgallGa 206
                                        a  t  +++ +++  g                      +l +
  gi|488601492|ref|YP_007907963.1| 171 sALMTEKIIAEITATGG----------------------VLIV 191
                                       33333333333333333......................3333 PP

>> YjcB  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   2.2e-05      0.13      17      53 ..      15      51 ..       2      75 .. 0.78
   2 ?   -0.8   0.1       0.3   1.8e+03      25      33 ..     143     151 ..     124     184 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                              YjcB 17 savlmflastlnirlrksdykalavvvsglGiaasCw 53
                                      s + mf+ s ln +l++s  ++l +vv  +G+ ++ +
  gi|488601492|ref|YP_007907963.1| 15 SLFGMFIGSRLNPKLKESLMRVLGLVVVVIGLKMALL 51
                                      3345****************************99865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.3
                              YjcB  25 stlnirlrk 33 
                                       stl i +  
  gi|488601492|ref|YP_007907963.1| 143 STLGIGVMF 151
                                       333222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.52
# Mc/sec: 1280.42
//
Query:       gi|488601493|ref|YP_007907964.1|  [L=378]
Description: radical SAM additional 4Fe4S-binding domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-20   72.5   0.1      9e-20   71.7   0.1    1.4  1  Radical_SAM  Radical SAM superfamily
    2.9e-09   37.3   0.0    6.1e-09   36.3   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    1.3e-06   28.5   0.0    2.4e-06   27.7   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 !   71.7   0.1   1.5e-23     9e-20       3     165 ..      92     236 ..      90     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 1.5e-23
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       vt  Cnl+C++C+ p+   +     +++   ++ee+ e+     +  ++l+ggepll+p+++ +l+ l      ++r
  gi|488601493|ref|YP_007907964.1|  92 VTLRCNLNCRHCYLPK---KQTNMDYRTFNTLIEEFSEAG----GIKLMLSGGEPLLHPEIYSFLDVLESY---DFR 158
                                       7889***********8...788888888888888888887....**************************8...*** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                        +++tngtl+de+ + ++    vd v+++++ + +    + +++++tfe+ ++al++l ++g++  v++ ++++ +n
  gi|488601493|ref|YP_007907964.1| 159 KVLITNGTLIDEKNAGKIE---VDEVQISIDGIKSH---DFIRGKGTFEKAMRALKLLIDYGVD--VSVATMVHRYN 227
                                       **********654444443...7************7...7888*********************..777788888** PP

                                       HHHHHHHHH CS
                                       xxxxxxxxx RF
                       Radical_SAM 157 deeleelle 165
                                        +e++e+ +
  gi|488601493|ref|YP_007907964.1| 228 IDEFDEMEK 236
                                       ****99865 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0     1e-12   6.1e-09       9     120 ..      90     190 ..      82     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1e-12
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                       ++ + +Cnl+C+ C+      +k++++++  + + +ie++++   ++l l+GGEPll    ++++++++ +++  + 
  gi|488601493|ref|YP_007907964.1|  90 VHVTLRCNLNCRHCY-----LPKKQTNMDYRTFNTLIEEFSEAGGIKLMLSGGEPLL---HPEIYSFLDVLESYDFR 158
                                       445679*********.....778888999999999**********************...999******99999995 PP

                           Fer4_12  86 kdiwlytgytleelskkekeellkeidvlvdGkfe 120
                                        ++++++g+ ++e ++  k e ++e+++ +dG  +
  gi|488601493|ref|YP_007907964.1| 159 -KVLITNGTLIDEKNAG-KIE-VDEVQISIDGIKS 190
                                       .79**********9865.444.7999999999655 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 !   27.7   0.0     4e-10   2.4e-06       5      92 ..      93     168 ..      89     189 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 4e-10
                           Fer4_14   5 lsgCnlsCkgCd.nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80 
                                       + +Cnl+C+ C+  k++ ++++ + +t  ++   +   ++  i  + l l+GGePL++ +  ++l++++ +  ++  
  gi|488601493|ref|YP_007907964.1|  93 TLRCNLNCRHCYlPKKQTNMDYRTFNTLIEE---F--SEAGGI--K-LMLSGGEPLLHPEIYSFLDVLESYDFRK-- 159
                                       569*********7566667777666665554...6..444555..5.99*********66666666666554444.. PP

                           Fer4_14  81 kkiwletngtle 92 
                                           l tngtl 
  gi|488601493|ref|YP_007907964.1| 160 ---VLITNGTLI 168
                                       ...455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2095.63
//
Query:       gi|488601494|ref|YP_007907965.1|  [L=60]
Description: hypothetical protein Asulf_02007 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.45u 0.34s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 367.04
//
Query:       gi|488601495|ref|YP_007907966.1|  [L=76]
Description: transcriptional regulator, AsnC family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-12   46.5   0.2      3e-12   46.3   0.2    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    4.3e-07   29.9   0.6    4.9e-07   29.7   0.6    1.1  1  NapD            NapD protein
    0.00054   19.8   0.0    0.00061   19.7   0.0    1.2  1  GYD             GYD domain
     0.0027   17.5   0.6     0.0041   17.0   0.6    1.3  1  Spt5-NGN        Early transcription elongation factor of RNA 


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 !   46.3   0.2   6.6e-16     3e-12       2      71 ..       7      72 ..       6      76 .] 0.94

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.6e-16
                                      EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
                    AsnC_trans_reg  2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                                      +v++ pg+    +++  +++e+++V+ +y+v G++d+++++ +++l  l++ +++ +++++gv++t+t +
  gi|488601495|ref|YP_007907966.1|  7 MVNVLPGK---EKTVYNEIKEMKNVRDIYHVFGEFDFVVIIEAESLSILNNTVDN-IRAIEGVTKTQTVV 72
                                      67888889...99***************************************999.************87 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.6   1.1e-10   4.9e-07       7      70 ..       7      71 ..       1      74 [. 0.94

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.1e-10
                              NapD  7 vVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVlsaslv 70
                                       V++ p++ + v ++++++++v +++++ +e   Vv+iEaes   l +t+++i+a++gV  ++ v
  gi|488601495|ref|YP_007907966.1|  7 MVNVLPGKEKTVYNEIKEMKNVrDIYHVFGEFDFVVIIEAESLSILNNTVDNIRAIEGVTKTQTV 71
                                      799******************989************************************99876 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.4e-07   0.00061      19      59 ..      12      50 ..       4      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-07
                               GYD 19 perreeakealveslGgkleslyatlGeyDvvvivEapDde 59
                                      p +++++  ++ +++  +++++y ++Ge+D+vvi+Ea+  +
  gi|488601495|ref|YP_007907966.1| 12 PGKEKTVYNEI-KEM-KNVRDIYHVFGEFDFVVIIEAESLS 50
                                      55666666777.555.3789*****************8755 PP

>> 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 !   17.0   0.6   9.1e-07    0.0041       4      74 ..       7      69 ..       5      76 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.1e-07
                          Spt5-NGN  4 avkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqgl 74
                                      +v + +g+E++v  ++ +       k+  +I+ vf   e+   +++EA++ + +++ +++i+ + gv++++
  gi|488601495|ref|YP_007907966.1|  7 MVNVLPGKEKTVYNEIKEM------KNVRDIYHVF--GEFDFVVIIEAESLSILNNTVDNIRAIEGVTKTQ 69
                                      688999**********332......3335999888..678889************************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 458.51
//
Query:       gi|488601496|ref|YP_007907967.1|  [L=605]
Description: DNA topoisomerase VI, B subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-65  218.0   0.0      1e-64  217.2   0.0    1.4  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    8.9e-19   67.7   0.0    2.1e-18   66.6   0.0    1.7  1  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
    2.1e-10   41.1   0.1    5.8e-10   39.7   0.0    1.8  2  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    4.6e-09   36.2   0.0    8.9e-09   35.3   0.0    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
     0.0045   15.8   0.6     0.0093   14.8   0.0    1.8  2  FbpA            Fibronectin-binding protein A N-terminus (Fbp
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.033   13.7   0.0    1.4  1  MS_channel      Mechanosensitive ion channel
      0.025   15.0   0.0      0.094   13.1   0.0    1.9  2  Ribosomal_S13   Ribosomal protein S13/S18
      0.047   14.3   0.1        2.9    8.5   0.0    3.3  4  PAS_10          PAS domain


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 !  217.2   0.0   4.5e-68     1e-64       1     159 []     309     472 ..     309     472 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.2 bits;  conditional E-value: 4.5e-68
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydega 77 
                                       P+tdclspige++i ++l +++ +e+ +a+trkpkvy+g+pf+vEvgi+yGGel+ ++k+++lRfaN++PL+y +g+
  gi|488601496|ref|YP_007907967.1| 309 PPTDCLSPIGEKNIMNSLISRYGVEWAHAITRKPKVYSGNPFLVEVGIGYGGELRGDDKVKLLRFANKIPLVYAQGG 385
                                       99*************************************************************************** PP

                    Topo-VIb_trans  78 dvitkavksinwkrYkleq.....pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylsk 149
                                       +++tkav+sinwk+Y+l+q     p  p+v+l+hvast++P++se+Keaia+++ei++ei+lalqe++rkLk+++++
  gi|488601496|ref|YP_007907967.1| 386 CALTKAVESINWKNYGLTQsrnelPIAPAVILIHVASTNIPYTSESKEAIASIPEIYDEIRLALQEAGRKLKEHIER 462
                                       *******************99999999************************************************** PP

                    Topo-VIb_trans 150 kekekeekek 159
                                       kek k++k+k
  gi|488601496|ref|YP_007907967.1| 463 KEKLKKKKSK 472
                                       ****999875 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 !   66.6   0.0   9.2e-22   2.1e-18       1     113 [.     492     597 ..     492     598 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 9.2e-22
                                       SSS---SHHHHHHHTT-EEEEEEE--SSS-EEEEEEE---------EEE--EES-----------EEE-SSSEEE-E CS
                           Top6b_C   1 dreepdidpvvArimgnvlvereveengdgvevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkW 77 
                                       +r+e d+++vvA+imgnv +er+++++    +v++ + N+s+ k+ f++ ei + +ie   ++ k+ + ++   + W
  gi|488601496|ref|YP_007907967.1| 492 ERDEIDVNRVVAKIMGNVYIERTIKDG----NVEIGIFNYSSAKKAFKVIEICSGKIEC--DDGKISTAGDTKTILW 562
                                       79***********************99....**************************65..469999999******* PP

                                       EE---TT-EEEE----SS-GGGS--B---------- CS
                           Top6b_C  78 elsvsageskvleYsvdseaeeelsliveGveeekv 113
                                       ++s+++ges +l+Ys++    +     veG+++e++
  gi|488601496|ref|YP_007907967.1| 563 DVSLNPGESITLSYSLNGRIINRKP-YVEGLDQEIL 597
                                       ****************998766655.9******987 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   2.6e-13   5.8e-10       4      94 ..      33     130 ..      30     178 .. 0.70
   2 ?   -2.3   0.0       2.8   6.3e+03       2      31 ..     494     524 ..     493     565 .. 0.68

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.6e-13
                                       HHHHHHHHHHHHHHHHH...HSTTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCS.TTCH...HCSTCHTST CS
                         HATPase_c   4 krLrqiisnlvdNavkf...atkageieveika.seddlvisveDnGiGipkedlkklfe.kfsq...ddstkrggg 72 
                                       k L  +++++vdN++++   a+  ++i v+i++ ++  +++ +eDnG+Gi ke+++k+f+          s +++ g
  gi|488601496|ref|YP_007907967.1|  33 KSLITCVKEAVDNSLDAcedAGILPDILVKISKvEKSIYRVVIEDNGPGIVKEQIPKIFGkL-LYgsrFHSIRQSRG 108
                                       568899**********95444455599****97433689999*****************953.44368556666667 PP

                                       SSSHHHHHHHHHHHHTTTEEEE CS
                         HATPase_c  73 gtGlGlsivkklvelmgGeiwv 94 
                                       + G+G s +  +++l  G+  v
  gi|488601496|ref|YP_007907967.1| 109 QQGIGISGAVLYAQLTTGKPAV 130
                                       7777777776666655565555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHHHHS.TTTEEEEEE CS
                         HATPase_c   2 dekrLrqiisnlvdNavkfat.kageievei 31 
                                       de+ + +++  +++N   + t k+g++e+ i
  gi|488601496|ref|YP_007907967.1| 494 DEIDVNRVVAKIMGNVYIERTiKDGNVEIGI 524
                                       6677777788888887777556666666644 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 !   35.3   0.0     4e-12   8.9e-09       6     113 ..      38     153 ..      33     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4e-12
                       HATPase_c_3   6 AlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiG 76 
                                        + e vdNsldA         + ++++k +++  ++vieD+G G+ +e++ + + +l   s+  ++ ++s+G+ GiG
  gi|488601496|ref|YP_007907967.1|  38 CVKEAVDNSLDACEDAgilpdILVKISKVEKSIYRVVIEDNGPGIVKEQIPKIFgKLLYGSRF-HSIRQSRGQQGIG 113
                                       689*********888899999666666666678*******************66489999999.578999******* PP

                       HATPase_c_3  77 lklAs....lslgkkltvitkkegesstltldvdkidkene 113
                                       +  A+    l  gk + +++k++ +s +++l++ +id +++
  gi|488601496|ref|YP_007907967.1| 114 ISGAVlyaqLTTGKPAVITSKTNPKSKAIRLKL-FIDTKKN 153
                                       765541111678999999999999998777776.4544332 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 !   14.8   0.0   4.1e-06    0.0093     182     237 ..     247     303 ..     223     309 .. 0.79
   2 ?   -3.0   0.8         1   2.3e+03     429     451 ..     449     469 ..     421     485 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-06
                                       HHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHH CS
                              FbpA 182 lsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqe 237
                                       l++ k+ +l++++ ++f  ++   aee++++agld++   +el+ e++ rly+a+++
  gi|488601496|ref|YP_007907967.1| 247 LRTtKASTLKNFMKTEFVRVGDKKAEEVIAKAGLDPNRDPRELTREEIARLYSAFSD 303
                                       22347799**********************************************986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1
                                       HHHHHHHHHHTTS----TT---- CS
                              FbpA 429 leeikeELieegylkkkkkkkkk 451
                                       l+e  ++L+  + +++k+k kkk
  gi|488601496|ref|YP_007907967.1| 449 LQEAGRKLK--EHIERKEKLKKK 469
                                       222222221..112222222222 PP

>> MS_channel  Mechanosensitive ion channel
   #    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      75     162 ..     391     478 ..     383     486 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                       EEEEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB- CS
                        MS_channel  75 tVediglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevl 151
                                       +Ve+i++  + +++  +++ + P   l+  + +N   +s  + +  si   y++++ +l+++ ++lke++++k++++
  gi|488601496|ref|YP_007907967.1| 391 AVESINWKNYGLTQSRNELPIAPAVILIHVASTNIPYTSESKEAIASIPEIYDEIRLALQEAGRKLKEHIERKEKLK 467
                                       7**************************************************************************** PP

                                       TTS-EEEEEEE CS
                        MS_channel 152 kdkellvvlde 162
                                       k+k  +vvl++
  gi|488601496|ref|YP_007907967.1| 468 KKKSKEVVLNK 478
                                       *9999999876 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.2e-05     0.094      21      59 ..     264     302 ..     255     311 .. 0.88
   2 ?   -2.8   0.1       3.5   7.9e+03       9       9 ..     468     468 ..     446     507 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-05
                     Ribosomal_S13  21 kGiGrrkakiilkkadvdedkrigelteeeiekieeive 59 
                                         +G +ka+++++ka++d +   +elt eei ++    +
  gi|488601496|ref|YP_007907967.1| 264 VRVGDKKAEEVIAKAGLDPNRDPRELTREEIARLYSAFS 302
                                       569******************************987765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.5
                     Ribosomal_S13   9 g 9  
                                       +
  gi|488601496|ref|YP_007907967.1| 468 K 468
                                       2 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    0.0013       2.9      14      57 ..      18      61 ..      13      85 .. 0.80
   2 ?    0.7   0.0      0.36   8.1e+02      11      30 ..     204     223 ..     200     232 .. 0.84
   3 ?   -1.8   0.0       2.1   4.7e+03      60      88 ..     454     482 ..     435     488 .. 0.54
   4 ?   -1.8   0.0       2.1   4.7e+03       6      35 ..     507     537 ..     499     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                            PAS_10 14 flDdnlqirrFtpaakklfklipadvGrpladihpkkavknvee 57
                                      f+ +n +i+ +++ ak+l+  +++ v ++l+++    +++++  
  gi|488601496|ref|YP_007907967.1| 18 FFEKNKHILGYSNPAKSLITCVKEAVDNSLDACEDAGILPDILV 61
                                      8899*****************************77666555433 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.36
                            PAS_10  11 eltflDdnlqirrFtpaakk 30 
                                       ++tf+D + +i  F++ +++
  gi|488601496|ref|YP_007907967.1| 204 KITFVDPDGEIFEFNRLIDE 223
                                       79*************97665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.1
                            PAS_10  60 ealrtgekdevevvvpkngkwvlvrylpy 88 
                                        +l+++ + +++ + +k++++vl ++lp+
  gi|488601496|ref|YP_007907967.1| 454 RKLKEHIERKEKLKKKKSKEVVLNKILPL 482
                                       23333333333344446677777777775 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.1
                            PAS_10   6 nstpieltflDdnlqirrFtp.aakklfkli 35 
                                        ++ ie t  D n +i  F+  +akk fk+i
  gi|488601496|ref|YP_007907967.1| 507 GNVYIERTIKDGNVEIGIFNYsSAKKAFKVI 537
                                       5677888999999999999984578888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 3660.61
//
Query:       gi|488601497|ref|YP_007907968.1|  [L=360]
Description: DNA topoisomerase VI, subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-17   62.6   0.1    7.4e-17   61.1   0.1    1.8  2  TP6A_N    Type IIB DNA topoisomerase


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.25   4.4e+03       6      22 ..      12      28 ..       9      29 .. 0.83
   2 !   61.1   0.1   4.2e-21   7.4e-17       3      62 .]      70     133 ..      68     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.25
                                      HHHHHHHHHHHHHTT-- CS
                            TP6A_N  6 llkvlelihelleegkv 22
                                      llk+ e i+e++++gk 
  gi|488601497|ref|YP_007907968.1| 12 LLKIPESIYEQMKNGKI 28
                                      6888899*****99986 PP

  == domain 2  score: 61.1 bits;  conditional E-value: 4.2e-21
                                       HHHHHHHHHHHHHHHHTT--EEHHHHHHH....GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                            TP6A_N   3 faqllkvlelihelleegkvvTkRdiYYr....dvelFksQaesdrliddievllgvsReeLnv 62 
                                       + ++ +v+ +++e+l+++k++T+R++YY     d ++F +Q esdrli+d+e +++ +Re++++
  gi|488601497|ref|YP_007907968.1|  70 LLKMAYVIGFLKEQLKTNKSSTLRELYYIsenwDIAKFNEQPESDRLIEDLEIITSFQREHFHI 133
                                       67899************************99999*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2032.70
//
Query:       gi|488601498|ref|YP_007907969.1|  [L=276]
Description: putative permease, DMT superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-24   85.2  42.8    2.4e-16   60.2  19.9    2.0  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3  14.9   1.1e-11   1.9e-07       5     136 ..       7     131 ..       3     132 .. 0.83
   2 !   60.2  19.9   1.3e-20   2.4e-16       3     135 ..     141     273 ..     139     275 .. 0.98

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.1e-11
                              EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafll 81 
                                       l++++a+l  +++ ++   +l++ + + ++f+r++i+  l++i+   ++ +    ++ ++++ ++ g ++  + f+ 
  gi|488601498|ref|YP_007907969.1|   7 LMLITAVLAVSSASIFV--VLANAPGMVVAFWRLVISIPLFIILNRSFRLPE---NRMEVIIPAVSG-FALGIHFSS 77 
                                       44555555555555555..67899**********988888877766666666...666666667777.9******** PP

                              EamA  82 ffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++ +l + s+++ + i+ +  +f+ i+s+ + ge +   q+ g++++l+Gv+l++
  gi|488601498|ref|YP_007907969.1|  78 WMESLFYASVAVSTTIVCTHSLFSGIFSSMF-GEMPRMNQITGVIVALAGVYLLS 131
                                       *******************************.********************986 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 1.3e-20
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                       gi+lal++a+f ++yf + +++  kv+  t+ ++++l+a+i+ l+ia+l++++l  +sl+ w +++ll++++++l++
  gi|488601498|ref|YP_007907969.1| 141 GIILALIGAVFGGLYFATGRYARDKVDFGTYIVFTYLFAAIVALFIAVLSGSPLTGYSLNTWMFFALLAVIPMLLGH 217
                                       9**************************************************************************** PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                        l++y+l+++++  ++  +  e + ++il++++l+++l+++ ++ i+lil+G+++ 
  gi|488601498|ref|YP_007907969.1| 218 TLLNYLLRHMEVLPVTSSVIGEAMGSAILAYIVLNQTLQVMAWVYILLILAGIAIA 273
                                       *************99999999********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.34s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1527.63
//
Query:       gi|488601499|ref|YP_007907970.1|  [L=103]
Description: hypothetical protein Asulf_02012 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-37  126.7   0.5    3.1e-37  126.5   0.5    1.0  1  DUF2103   Predicted metal-binding protein (DUF2103)


Domain annotation for each model (and alignments):
>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.5   1.7e-41   3.1e-37       4      97 ..       4      96 ..       2      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 1.7e-41
                           DUF2103  4 eklggsHstiiggreGkkllekiakhpevkkviPgvikakgsssggglrvkvtraderGnlrlllrdgssvQevfivtt 82
                                      +klgg+H+tiiggr+G+k+++ki+++++vk+++Pg+ik+ g+ssggg+r+k +r+derGnlrlllr+gs+vQe+fivtt
  gi|488601499|ref|YP_007907970.1|  4 SKLGGDHTTIIGGRRGRKIVAKISTSEKVKRIVPGIIKV-GMSSGGGFRAKFLRPDERGNLRLLLREGSTVQEIFIVTT 81
                                      79***********************************99.779************************************ PP

                           DUF2103 83 akdreegeriaeeLn 97
                                      ak+ +eg+ i++eL+
  gi|488601499|ref|YP_007907970.1| 82 AKNFKEGSDIIKELE 96
                                      **************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 577.21
//
Query:       gi|488601500|ref|YP_007907971.1|  [L=299]
Description: deoxyhypusine synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-96  321.4   0.0    5.2e-96  321.3   0.0    1.0  1  DS           Deoxyhypusine synthase
      0.005   16.5   0.0     0.0072   16.0   0.0    1.2  1  Astacin      Astacin (Peptidase family M12A)
  ------ inclusion threshold ------
       0.19   11.5   0.0       0.44   10.3   0.0    1.6  1  MafB19-deam  MafB19-like deaminase


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 !  321.3   0.0  8.8e-100   5.2e-96       2     287 ..      17     294 ..      16     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: 321.3 bits;  conditional E-value: 8.8e-100
                                DS   2 llesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikal 78 
                                       +l+++ +++f+a++l+ a++i++km+ +e+  +fl+l++++i++G+r++i+ ++k+++++++vtT+++i ++l++al
  gi|488601500|ref|YP_007907971.1|  17 ILDEMYYSAFNARRLAIAAKIFRKMV-EEDYFVFLTLSGAMIPAGMRNVISGMMKNGFINCLVTTGANIVHELVEAL 92 
                                       799**********************5.7899********************************************** PP

                                DS  79 gkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSilyw 155
                                       g  + +g++++dd eL +k+inRi++++v ++ ++++e+++++i+++le      s+ e+++ +G++i+d++S+l+ 
  gi|488601500|ref|YP_007907971.1|  93 GIGHEIGREDVDDVELASKNINRIYDVFVVQNAFEEVENFISPIISDLEGA---YSTPEFLRVVGEKIEDRNSFLRV 166
                                       ************************************************984...8********************** PP

                                DS 156 AykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlmrn 232
                                       Ay+++ipvf+p+l D+ +G++l +++    kk + +d +kDi+++ d++++++k g++i+GGGvpK+++l+a+l+++
  gi|488601500|ref|YP_007907971.1| 167 AYEKGIPVFSPTLHDSIVGLHLSIYR----KKGFYIDFMKDINQILDLCFQKRKIGVVIVGGGVPKNFTLQAMLLAD 239
                                       ********************666666....566******************************************** PP

                                DS 233 gadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                       g+d a++itt+++++G+lsgatl+Ea+Sw k+k++a++v+vy+DaTi+lPLl+a+
  gi|488601500|ref|YP_007907971.1| 240 GFDSAIQITTDSPQWGGLSGATLSEAKSWCKLKENAEEVTVYCDATIALPLLYAY 294
                                       ****************************************************986 PP

>> Astacin  Astacin (Peptidase family M12A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.2e-06    0.0072      81     118 ..      82     118 ..      38     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHTB--GGGSTTGGGTEEE-GGGB-TT-G CS
                           Astacin  81 giivHElmHalGffHeqsRtdrdeyvsinkeniekgqe 118
                                       + ivHEl+ alG+ He  R d d+ v++  +ni++ + 
  gi|488601500|ref|YP_007907971.1|  82 ANIVHELVEALGIGHEIGREDVDD-VELASKNINRIYD 118
                                       569*******************98.8999999987554 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.3e-05      0.44      87     123 ..      54      90 ..      50     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.3e-05
                       MafB19-deam  87 gaivqaglkklvygagnpkslnkLkvkekngrvelve 123
                                       ga++ ag+++++ g++++ ++n L ++  n+  elve
  gi|488601500|ref|YP_007907971.1|  54 GAMIPAGMRNVISGMMKNGFINCLVTTGANIVHELVE 90 
                                       89**************9999************99993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1738.08
//
Query:       gi|488601501|ref|YP_007907972.1|  [L=699]
Description: replicative DNA helicase Mcm [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-98  328.1   0.0    2.6e-98  327.6   0.0    1.2  1  MCM              MCM P-loop domain
    2.5e-36  124.3   0.4    4.2e-36  123.6   0.4    1.3  1  MCM_OB           MCM OB domain
    1.3e-28   99.3   4.6    1.4e-28   99.2   2.9    2.0  1  MCM_lid          MCM AAA-lid domain
    2.4e-08   34.0   0.0    1.2e-07   31.8   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
    4.5e-08   32.7   0.0    2.6e-05   23.7   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.7e-06   27.3   0.0      6e-06   26.1   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
    0.00052   19.8   0.1     0.0064   16.2   0.1    2.2  1  Sigma54_activat  Sigma-54 interaction domain
     0.0028   18.1   0.2       0.01   16.2   0.2    2.2  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.021   14.1   0.5      0.042   13.1   0.5    1.4  1  DUF2357          Domain of unknown function (DUF2357)
      0.031   13.8   0.0      0.067   12.7   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.035   14.2   0.6        0.2   11.9   0.0    2.6  2  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
      0.057   13.8   0.0        0.2   12.1   0.0    2.0  2  AAA              ATPase family associated with various cellul
      0.072   13.5   0.7         20    5.7   0.1    3.2  2  SHS2_FTSA        SHS2 domain inserted in FTSA
      0.072   13.1   0.1        0.2   11.7   0.1    1.8  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.092   12.6   1.4       0.23   11.3   0.7    2.0  2  AAA_lid_2        AAA lid domain
       0.14   12.3   0.8       0.34   11.0   0.8    1.6  1  Zn-ribbon_8      Zinc ribbon domain
       0.19   11.5   1.2       0.95    9.2   0.3    2.5  2  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 !  327.6   0.0  2.4e-101   2.6e-98       1     224 []     265     488 ..     265     488 .. 0.99

  Alignments for each domain:
  == domain 1  score: 327.6 bits;  conditional E-value: 2.4e-101
                                       HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHH CS
                               MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyv 77 
                                       ++e+i el++++d+++k+++s+ap iyg++++k ai+lqlfggv kkl+d+t++rgdi++llvgdpg+aKsq+L+yv
  gi|488601501|ref|YP_007907972.1| 265 DIEKIMELSEDPDLYKKITDSVAPVIYGYDKIKLAIALQLFGGVPKKLPDGTEIRGDIHILLVGDPGVAKSQMLRYV 341
                                       5799************************************************************************* PP

                                       HHHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEES CS
                               MCM  78 eklapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaK 154
                                       +++apr+vyt+gkg+++agLta+ +rde  g ++leaGalvladkG++++De+dkm+ edrsalhEamEqqtis+aK
  gi|488601501|ref|YP_007907972.1| 342 HRIAPRSVYTTGKGTTSAGLTATATRDEVDGRWTLEAGALVLADKGIALVDEIDKMRAEDRSALHEAMEQQTISVAK 418
                                       ***************************************************************************** PP

                                       SSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                               MCM 155 aGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                       aGi+a+L++r+++l Aanpk+gr+d   +++e+i+ls++lLsrFDlif++ D+++ ++D++laehi+++h
  gi|488601501|ref|YP_007907972.1| 419 AGINAMLRSRCALLGAANPKYGRFDLYSPLVEQIDLSPTLLSRFDLIFIMTDQPNPDHDRRLAEHILKTH 488
                                       *******************************************************************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   0.4   3.9e-39   4.2e-36       2     124 ..     102     227 ..     100     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 3.9e-39
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSE CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkleteksk 73 
                                       +Rdlrseh++k+v veGiv +++ev+pk++ka+f c +cg++v v     +l++P +C  k+C+++++f++++++s 
  gi|488601501|ref|YP_007907972.1| 102 IRDLRSEHVSKFVAVEGIVRKVTEVRPKIVKASFICLSCGNEVFVvqddnQLKQPYEC--KTCNTRGRFVFNPDNSI 176
                                       6****************************************9995699988999****..99*************** PP

                                       EEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                            MCM_OB  74 fvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                        vd q++k+QE pe++  Ge P++++v+le+dl+ k++PGdrv + Gi+ra
  gi|488601501|ref|YP_007907972.1| 177 KVDSQRIKIQEYPENLRGGEQPQTIDVFLEGDLTGKINPGDRVVINGIVRA 227
                                       ************************************************997 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   2.9   1.3e-31   1.4e-28       2      87 .]     522     604 ..     521     604 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 1.3e-31
                                       HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHH CS
                           MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedvee 78 
                                       llrkYiaya+++++P+l+++a++ + e+Yv+lR++++   ++s++it+RqLe+liRL+eA+A+lrls++vt edv++
  gi|488601501|ref|YP_007907972.1| 522 LLRKYIAYAKRTVFPVLTKDAMDRIIEYYVNLRNSSK---ESSVTITARQLEALIRLAEASARLRLSDEVTVEDVNR 595
                                       89********************************773...68*********************************** PP

                                       HHHHHHHHH CS
                           MCM_lid  79 airllkesl 87 
                                       +i+++++sl
  gi|488601501|ref|YP_007907972.1| 596 VIDVVEASL 604
                                       *****9885 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.8     4e+03      52      78 ..     202     228 ..     189     231 .. 0.79
   2 !   31.8   0.0   1.1e-10   1.2e-07       1     137 [.     323     461 ..     323     462 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                                       .....--------G-SEEEEESGGG-- CS
                             AAA_5  52 tslvdsplvraaregeilvlDEverae 78 
                                        ++ ++ l+ +++ g+ +v++++ ra+
  gi|488601501|ref|YP_007907972.1| 202 DVFLEGDLTGKINPGDRVVINGIVRAR 228
                                       567788899999999999999999997 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.1e-10
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       ++lLvG+pG++Ks++ +++ +   r+v +    ++tt++ l+     +  +g+  l+ ++lv     + i+++DE++
  gi|488601501|ref|YP_007907972.1| 323 HILLVGDPGVAKSQMLRYVHRIAPRSVYT--TGKGTTSAGLTATATRDevDGRWTLEAGALV--LADKGIALVDEID 395
                                       79****************99999555443..3445555555544443334455556999999..88999******** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..........-TT-TTHHHHTT CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.........rslnelspalrsR 137
                                       +++ e  ++L+  +e++++++++ g     ++        ++++anp +          ++ +lsp l+sR
  gi|488601501|ref|YP_007907972.1| 396 KMRAEDRSALHEAMEQQTISVAKAGINAMLRSR-----CALLGAANPKYgrfdlysplVEQIDLSPTLLSR 461
                                       ********************9888766655553.....899999999985555555555555555555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0057         6      21      49 ..     320     348 ..     316     368 .. 0.88
   2 !   23.7   0.0   2.5e-08   2.6e-05      93     158 ..     372     437 ..     359     444 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0057
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllppl 49 
                                       G  ++llvG pG  K+ + + ++ + p+ 
  gi|488601501|ref|YP_007907972.1| 320 GDIHILLVGDPGVAKSQMLRYVHRIAPRS 348
                                       7889******************9999976 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.5e-08
                      Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       g  + + G++ la +G+ ++DE+ +++++   +L e +e++++++++a  ++   +r+ l+ a+Np
  gi|488601501|ref|YP_007907972.1| 372 GRWTLEAGALVLADKGIALVDEIDKMRAEDRSALHEAMEQQTISVAKAGINAMLRSRCALLGAANP 437
                                       6668899**********************************************************9 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 !   26.1   0.0   5.7e-09     6e-06       1     112 [.     323     437 ..     323     449 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.7e-09
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqft.pdllPsdilGtevfeekekefefkkGpvf...anllladeinr 73 
                                       h+ll g PG+ak ++ + + ++   +   +  t      + ++ t   +e + ++++++G+++   + + l+dei++
  gi|488601501|ref|YP_007907972.1| 323 HILLVGDPGVAKSQMLRYVHRIAPRS---VYTTgKGTTSAGLTATATRDEVDGRWTLEAGALVladKGIALVDEIDK 396
                                       9**************99998876554...4444145678999******************976333359******** PP

                             AAA_3  74 appktqsalleameerqvtvege..thklpepflvlatqnP 112
                                         +  +sal eame+++++v+++  +  l +   +l + nP
  gi|488601501|ref|YP_007907972.1| 397 MRAEDRSALHEAMEQQTISVAKAgiNAMLRSRCALLGAANP 437
                                       *****************999865114567777777777777 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   6.1e-06    0.0064      21     142 ..     320     436 ..     315     442 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.1e-06
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEE CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtl 97 
                                        d+++l++G+ G+ K+ + r +h+  +r+   + +   + +++ l ++     ++G +t     ++G++  ad+G+ 
  gi|488601501|ref|YP_007907972.1| 320 GDIHILLVGDPGVAKSQMLRYVHRIAPRS---VYTTGKGTTSAGLTATATRDEVDGRWT----LEAGALVLADKGIA 389
                                       67899999999999999999999999865...457777888888888876667777776....678*********** PP

                                       EEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  98 fLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatn 142
                                       ++Dei ++ +e  + L ++++++++   + G ++  +  + ++ a+n
  gi|488601501|ref|YP_007907972.1| 390 LVDEIDKMRAEDRSALHEAMEQQTIsvAKAGINAMLRSRCALLGAAN 436
                                       *********************99862257787887777777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   9.7e-06      0.01      26     125 ..     323     411 ..     315     610 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.7e-06
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                        +ll+G++Gv Ks ++r ++r + ++  ++++gk + +      + l+ +++r+e+      ea +  l++   +l 
  gi|488601501|ref|YP_007907972.1| 323 HILLVGDPGVAKSQMLRYVHRIAPRS--VYTTGKGTTS------AGLTATATRDEVDGRWTLEAGALVLADKGIALV 391
                                       689*****************877777..7788888888......568888889888888888866655555555555 PP

                            AAA_16 103 ealaavpelagaeasrllellkr 125
                                       ++   +++++++++s+l+e++ +
  gi|488601501|ref|YP_007907972.1| 392 DE---IDKMRAEDRSALHEAMEQ 411
                                       54...447777777777777665 PP

>> DUF2357  Domain of unknown function (DUF2357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5     4e-05     0.042      37     138 ..     506     615 ..     496     644 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                           DUF2357  37 dykedykalldeiddeyaelifellkkteqsarkskakesselewfallrk.........lreeLeqalklIlrqph 104
                                       +y ++yk++  +id +     ++++k+t + + ++ +  +  +e ++ lr+          + +Le+ ++l +++ +
  gi|488601501|ref|YP_007907972.1| 506 EYRNEYKNIEPKIDPQLLRKYIAYAKRTVFPVLTK-DAMDRIIEYYVNLRNsskessvtiTARQLEALIRLAEASAR 581
                                       699****************************9988.7778899*******9999999999999************** PP

                           DUF2357 105 erLveeeevvradklkkldsavleellkepeklg 138
                                        rL+ e++v  ++++ ++  a l++++++pe + 
  gi|488601501|ref|YP_007907972.1| 582 LRLSDEVTVEDVNRVIDVVEASLKQIATNPETGE 615
                                       ******************************9665 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 ?   12.7   0.0   6.3e-05     0.067      32      89 ..     320     377 ..     316     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-05
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr 89 
                                        + ++llvG+ G++K+ +++ + +  +++ y++ + + sa  +a+ ++d ++ +    
  gi|488601501|ref|YP_007907972.1| 320 GDIHILLVGDPGVAKSQMLRYVHRIAPRSVYTTGKGTTSAGLTATATRDEVDGRWTLE 377
                                       5789******************************************999888766555 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.4   3.6e+03      10      32 ..     385     408 ..     381     411 .. 0.83
   2 ?   11.9   0.0   0.00019       0.2      20      49 .]     663     696 ..     656     696 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.4
                           AbiEi_4  10 qvGlfttrelea.aGispsalrrL 32 
                                       ++G++ ++e+ + +  ++sal+++
  gi|488601501|ref|YP_007907972.1| 385 DKGIALVDEIDKmRAEDRSALHEA 408
                                       579999999999999999999987 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00019
                           AbiEi_4  20 eaaGisp.sa...lrrLvrkGwLvrlrrGvYali 49 
                                        + Gi++ +a   l++L++kG+L   r+ +Y+++
  gi|488601501|ref|YP_007907972.1| 663 VEKGIDEmRAkdvLHKLREKGELYSPRPNLYRIV 696
                                       568****777*********************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 ?   12.1   0.0   0.00019       0.2       1     110 [.     324     436 ..     324     464 .. 0.69
   2 ?   -2.7   0.0       7.1   7.5e+03      44      74 ..     521     550 ..     490     580 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsell.skyvgesekkirelfkeakeka....kpsilfiDEidalak 72 
                                       +ll+G pG+ K+ + + v + + ++++++   +     +  ++ +++ + ++  ++ a    ++ i ++DEid++  
  gi|488601501|ref|YP_007907972.1| 324 ILLVGDPGVAKSQMLRYVHRIAPRSVYTTGKGTTSaGLTATATRDEVDGRWTL-EAGAlvlaDKGIALVDEIDKMRA 399
                                       69*******************97766554433333255777888888888865.5555789777***********77 PP

                                       HHTTCCCHHHHHHHHHHHHHHHHTTTS..........SSTEEEEEEES CS
                               AAA  73 srsgseseeeervvnqLlteldgvkkk..........eskvivigatn 110
                                       ++            ++L +++++++ +          +s++ ++ga+n
  gi|488601501|ref|YP_007907972.1| 400 ED-----------RSALHEAMEQQTISvakaginamlRSRCALLGAAN 436
                                       77...........33333333333333333333333435666777766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.1
                                       HHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                               AAA  44 kkirelfkeakekakpsilfiDEidalaksr 74 
                                       + +r++++ ak+     +l  D +d++++  
  gi|488601501|ref|YP_007907972.1| 521 QLLRKYIAYAKRTV-FPVLTKDAMDRIIEYY 550
                                       55566666665554.4666666666665544 PP

>> SHS2_FTSA  SHS2 domain inserted in FTSA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.041        44      17      31 ..     256     271 ..     242     281 .. 0.75
   2 ?    5.7   0.1     0.019        20      14      34 ..     583     601 ..     571     616 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.041
                                       TS-.E--HHHHHHHHH CS
                         SHS2_FTSA  17 ged.eiteedvervle 31 
                                        e+ eit+ed+e+++e
  gi|488601501|ref|YP_007907972.1| 256 YEEfEITQEDIEKIME 271
                                       3448*********998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
                                       E-TTS-E--HHHHHHHHHHH. CS
                         SHS2_FTSA  14 aisgedeiteedvervleaak 34 
                                        +s  de+t edv+rv++  +
  gi|488601501|ref|YP_007907972.1| 583 RLS--DEVTVEDVNRVIDVVE 601
                                       443..38*********88763 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   0.00019       0.2      54      95 ..     118     165 ..      51     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                       C.TTTT-EEEEEEE--EEEETTTS-EEECHH.H.HH....S-TTTSSS CS
                              HypA  54 gtvlegaeLeieevpvkvrCreCgkefelee.k.al....rCpkCgsa 95 
                                       g v + +e++ + v++++ C +Cg+e+ + + + +l    +C++C+++
  gi|488601501|ref|YP_007907972.1| 118 GIVRKVTEVRPKIVKASFICLSCGNEVFVVQdDnQLkqpyECKTCNTR 165
                                       44455567778999************99655333236677*****986 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.8   9.3e+03      37      48 ..     260     271 ..     259     272 .. 0.82
   2 ?   11.3   0.7   0.00022      0.23      21      50 ..     571     600 ..     565     603 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.8
                         AAA_lid_2  37 yVtpeDvkeaap 48 
                                       ++t+eD++++ +
  gi|488601501|ref|YP_007907972.1| 260 EITQEDIEKIME 271
                                       5799***99987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00022
                         AAA_lid_2  21 allraArAlAalegrdyVtpeDvkeaaplV 50 
                                       al+r A A A l+  d+Vt eDv +++  V
  gi|488601501|ref|YP_007907972.1| 571 ALIRLAEASARLRLSDEVTVEDVNRVIDVV 600
                                       89***********************98766 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   0.00033      0.34       6      34 ..     135     164 ..     134     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdaplta.CPeCgs 34 
                                       + C +Cg+e  v+q  ++ +++  C++C+ 
  gi|488601501|ref|YP_007907972.1| 135 FICLSCGNEVFVVQDDNQLKQPYeCKTCNT 164
                                       78************9889999999****86 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0009      0.95      35     115 ..     323     416 ..     316     434 .. 0.66
   2 ?   -2.3   0.0       3.1   3.3e+03      68     105 ..     568     605 ..     535     632 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0009
                            RuvB_N  35 hvllyGpPGlGkttlakiia....kelgvklkitsgPvl..ekagd.......laalltnleekdvlfideihrlsr 98 
                                       h+ll+G PG+ k+ + + +     + + ++ k t++  l    ++d       l a    l +k + ++dei +++ 
  gi|488601501|ref|YP_007907972.1| 323 HILLVGDPGVAKSQMLRYVHriapRSVYTTGKGTTSAGLtaTATRDevdgrwtLEAGALVLADKGIALVDEIDKMRA 399
                                       99999999999998865443000134444434333222201122221112222666667799999************ PP

                            RuvB_N  99 aveevlysamedfrldi 115
                                       +    l+ ame  ++ +
  gi|488601501|ref|YP_007907972.1| 400 EDRSALHEAMEQQTISV 416
                                       ***********999876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.1
                            RuvB_N  68 vlekagdlaalltnleekdvlfideihrlsraveevly 105
                                        le    la   ++l+ +d + ++++ r+  +ve  l 
  gi|488601501|ref|YP_007907972.1| 568 QLEALIRLAEASARLRLSDEVTVEDVNRVIDVVEASLK 605
                                       23333344555566777777777888888777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (699 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.80u 0.35s 00:00:01.14 Elapsed: 00:00:00.52
# Mc/sec: 4006.76
//
Query:       gi|488601502|ref|YP_007907973.1|  [L=94]
Description: hypothetical protein Asulf_02015 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.2   0.2       0.19   11.9   0.0    1.9  2  CDC48_N    Cell division protein 48 (CDC48), N-terminal domai
       0.16   12.1   0.1       0.35   11.0   0.0    1.6  2  AbrB-like  AbrB-like transcriptional regulator


Domain annotation for each model (and alignments):
>> 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 ?    0.3   0.0     0.089     8e+02      28      62 ..       9      44 ..       4      52 .. 0.62
   2 ?   11.9   0.0   2.1e-05      0.19      14      41 ..      63      90 ..      52      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.089
                                      TS-TTSEEEEECCCC.EEEEEEEBSTTSTTTTEEEE CS
                           CDC48_N 28 glepgdvveiegkrk.TvaivwpaepedegkgiIrm 62
                                      +l+  d+v++  k++   a v+p +   +  +iI +
  gi|488601502|ref|YP_007907973.1|  9 ELKDDDFVRVWMKKEvKSATVMPENILSDPMKIIEL 44
                                      555556666666555456777777666555666655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.1e-05
                                      TTEEEE-HHHHHHHTS-TTSEEEEECCC CS
                           CDC48_N 14 rgivridpedmeelglepgdvveiegkr 41
                                        i+ id   ++e++l+ gdvveie k+
  gi|488601502|ref|YP_007907973.1| 63 DAIITIDYTEYNEMDLKVGDVVEIEIKH 90
                                      56899*******************9776 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.83   7.5e+03      43      52 ..      48      57 ..      47      58 .. 0.79
   2 ?   11.0   0.0   3.9e-05      0.35      43      66 ..      66      91 ..      63      94 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.83
                         AbrB-like 43 iGsaYTkklg 52
                                      ++ aY k+++
  gi|488601502|ref|YP_007907973.1| 48 VSTAYLKAME 57
                                      6789999886 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.9e-05
                         AbrB-like 43 iGsaYTk..klgLkpGdefeIklgrk 66
                                      i   YT+  +++Lk Gd  eI++++ 
  gi|488601502|ref|YP_007907973.1| 66 ITIDYTEynEMDLKVGDVVEIEIKHS 91
                                      5556774338************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 559.59
//
Query:       gi|488601503|ref|YP_007907974.1|  [L=358]
Description: Glycerol dehydrogenase-related enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-64  218.1   0.1    1.9e-64  217.8   0.1    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    1.3e-19   70.2   0.2    6.4e-19   68.0   0.2    1.8  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    2.3e-09   36.8   0.6    3.7e-08   32.8   0.6    2.2  1  DHQ_synthase  3-dehydroquinate synthase
  ------ inclusion threshold ------
      0.023   14.0   0.0      0.091   12.1   0.0    1.8  2  PFK           Phosphofructokinase
       0.18   11.6   0.3       0.46   10.3   0.0    1.9  2  SinI          Anti-repressor SinI


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 !  217.8   0.1   5.2e-68   1.9e-64       3     250 .]      22     275 ..      20     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 5.2e-68
                          Fe-ADH_2   3 gegaleklgellkelelkkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlv 79 
                                       geg  + + +++ el+l+ v ++a+++ +++ag+k++e ++e    +++v    +e  ++ev+kl   l  +++d+v
  gi|488601503|ref|YP_007907974.1|  22 GEGPRKYIWDIIDELNLSSVYIIAGRTSYEVAGRKIAERINEFITGTHFV----KEGGMDEVKKLTVDLVYHDIDCV 94 
                                       566677888999****************************9996666655....58899999999999999****** PP

                          Fe-ADH_2  80 vavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllas 156
                                       +++GgG+++D+ak+ s++lnvp++svpT aS+DG+asp as+++dgk ++v +a+ P+aviaDl +l+++P rll s
  gi|488601503|ref|YP_007907974.1|  95 MGIGGGKVLDVAKVFSSELNVPFISVPTVASHDGIASPIASFKEDGKPVSV-TAKPPTAVIADLIILKHSPIRLLKS 170
                                       **************************************************9.9************************ PP

                          Fe-ADH_2 157 GvGDllgkytaladwklan........evseplaklsaamvqeaaekl.vedkk..etealeellealalsgigisr 222
                                       G+GDl+++ +a++dw+l++        e+s+++a l a+ + ++aekl  ++ +  e+ +   +l+++a+s++g+sr
  gi|488601503|ref|YP_007907974.1| 171 GYGDLISNTVAVKDWHLSKevtgedynEISASMAALPAKLMLDSAEKLdFRNLAhlEMLVRGLILSGVAISIAGSSR 247
                                       *******************66666555556688888888888888887433333114455566777778888888** PP

                          Fe-ADH_2 223 paSGsEHliSHaldmlalkqalHGeqVG 250
                                       paSGsEH +SHald+l  ++a+HGe+V+
  gi|488601503|ref|YP_007907974.1| 248 PASGSEHRFSHALDYLGYSNATHGEKVA 275
                                       ****************99********96 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.2   1.8e-22   6.4e-19       5     348 ..      20     332 ..      16     348 .. 0.80

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.8e-22
                                       EEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT. CS
                            Fe-ADH   5 vfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareeg 81 
                                         g+g  +++ + +++l++++++i++++ s+  + + +k+ e + ++ i+ t    + ++   +ev++++  +  ++
  gi|488601503|ref|YP_007907974.1|  20 ELGEGPRKYIWDIIDELNLSSVYIIAGRTSY--EVAGRKIAERI-NEFITGT---HFVKEGGMDEVKKLTVDLVYHD 90 
                                       57999999999******************99..33566666666.5555555...56689999************** PP

                                       --EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-. CS
                            Fe-ADH  82 advviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifd 158
                                       +d+v ++GGG+v+D+AK+ +  l+                  +p+i +PT+a+ +  ++p+a +   e+g+ +s++ 
  gi|488601503|ref|YP_007907974.1|  91 IDCVMGIGGGKVLDVAKVFSSELN------------------VPFISVPTVASHDGIASPIASFK--EDGKPVSVT- 146
                                       ************************..................***********************..555777777. PP

                                       .SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHH.......HHH.HT---TTSSB--HHHHHHHHHHHHHHHHH CS
                            Fe-ADH 159 pellPdlaivDpeltltlPkrvtaatglDalahalEa.......yvs.kkanplsdalaleairliaknleravadg 227
                                           P+++i D  ++ + P r++ ++ +D ++  +          v+ +  n++s  +a   ++l++++ e++    
  gi|488601503|ref|YP_007907974.1| 147 -AKPPTAVIADLIILKHSPIRLLKSGYGDLISNTVAVkdwhlskEVTgEDYNEISASMAALPAKLMLDSAEKLDFR- 221
                                       .789*****************************9998888766644447***********************7665. PP

                                       HHHHHHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC..C.GGGGGS-HHHHHHHHH..........HHHHH CS
                            Fe-ADH 228 edleareqmllastlaglafsnaglg.....avHalahalgal.f.giphglanaillpavlrfnaeaaperlaqla 297
                                        +l+  e ++ + +l+g+a+s ag +       H ++hal  l + +++hg+ +a+   +++          ++ l 
  gi|488601503|ref|YP_007907974.1| 222 -NLAHLEMLVRGLILSGVAISIAGSSrpasgSEHRFSHALDYLgYsNATHGEKVAL--GSII----------MEYLH 285
                                       .9********************9999988889999999998832334556555443..3333..........22222 PP

                                       HT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HH...HHHHHHHT- CS
                            Fe-ADH 298 ralggesdeeaaeeliealrellkelglptsLselgvdeedl...dklaeaalk 348
                                       ++          +   e++r  l+++++pt+ +e+g+++e++     la+++ +
  gi|488601503|ref|YP_007907974.1| 286 EK-------HYGNGDWERIRFSLERIQAPTTAKEVGLTKEQIleaLMLAKKIRR 332
                                       33.......556667788888889999999999999888766433555555544 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.6     1e-11   3.7e-08      32     261 ..      92     330 ..      72     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1e-11
                                       -EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGGS CS
                      DHQ_synthase  32 sllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLktL 108
                                       ++++ +GGG v+D+a   ++ +   v f+ vPt  +a  D ++    a   + gK +  +   P+av++dl +Lk  
  gi|488601503|ref|YP_007907974.1|  92 DCVMGIGGGKVLDVAKVFSSELN--VPFISVPT--VASHD-GIASPIASFKEDGKPVSVTAKPPTAVIADLIILKHS 163
                                       7899************9999886..*******9..57776.688888888899***999****************** PP

                                       -HHHHHHHHHHHHHHH.HHT-HHHHHHHHHHHHHHHC...................TTTHHHHHHHHHHHHHHHHHH CS
                      DHQ_synthase 109 perelraGlaEviKya.likdeelfelleenaeallk...................eeeeealeeliarsievkaev 165
                                       p r l++G++++i  + ++kd +l + ++ ++ + ++                    ++ ++le l++  i     +
  gi|488601503|ref|YP_007907974.1| 164 PIRLLKSGYGDLISNTvAVKDWHLSKEVTGEDYNEISasmaalpaklmldsaekldFRNLAHLEMLVRGLILSGVAI 240
                                       ************97651578989988888777776667889999999999777665445555555555555544444 PP

                                       HHHCCTTTTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---ST CS
                      DHQ_synthase 166 veeDekekglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvsl 242
                                         +     + r +    H ++Ha++ l gy++ +HGe Va+G ++  +l ek+    + + er++  l++++ p++ 
  gi|488601503|ref|YP_007907974.1| 241 SIA----GSSRPASGSEHRFSHALDYL-GYSNATHGEKVALGSIIMEYLHEKH--YGNGDWERIRFSLERIQAPTTA 310
                                       333....6778888889*******976.677************9999999777..456899**************99 PP

                                       TTT..-HHHHHHHHTTCTTX CS
                      DHQ_synthase 243 kel.leveellealkkDkkv 261
                                       ke  l+ e++leal+  kk 
  gi|488601503|ref|YP_007907974.1| 311 KEVgLTKEQILEALMLAKKI 330
                                       9988999******9999986 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.24   8.4e+02      80     108 ..      26      54 ..      17      70 .. 0.81
   2 ?   12.1   0.0   2.5e-05     0.091      78     130 ..      77     124 ..      60     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHT--EEEEEESHHHHHHHH CS
                               PFK  80 rkkaaenlkklgidaLvviGGdgslkgan 108
                                       rk + + +++l+++ + +i G  s+++a 
  gi|488601503|ref|YP_007907974.1|  26 RKYIWDIIDELNLSSVYIIAGRTSYEVAG 54 
                                       67788899999*************99984 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T....--EEEEEEET CS
                               PFK  78 egrkkaaenlkklgidaLvviGGdgslkganklseerkglleelkivgiPkTi 130
                                       +++kk+   l+ ++id+++ iGG + l++a+ +s+e  +    ++++ +P   
  gi|488601503|ref|YP_007907974.1|  77 DEVKKLTVDLVYHDIDCVMGIGGGKVLDVAKVFSSEL-N----VPFISVPTVA 124
                                       3488889999*************************98.8....8999999755 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.9   6.7e+03      23      27 ..       7      11 ..       7      12 .. 0.86
   2 ?   10.3   0.0   0.00013      0.46      12      24 ..     310     322 ..     308     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                                      HHHHH CS
                              SinI 23 ReFLe 27
                                      ReFL+
  gi|488601503|ref|YP_007907974.1|  7 REFLN 11
                                      9***8 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                                       HHHHT--SHHHHH CS
                              SinI  12 AkesGlskeEfRe 24 
                                       Ake+Gl+ke++ e
  gi|488601503|ref|YP_007907974.1| 310 AKEVGLTKEQILE 322
                                       9*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.34s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2022.33
//
Query:       gi|488601504|ref|YP_007907975.1|  [L=294]
Description: Heat shock protein, Metallo peptidase, MEROPS family M48B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-42  144.1   0.0    5.8e-42  143.7   0.0    1.2  1  Peptidase_M48    Peptidase family M48
    1.7e-09   37.3   0.1      1e-08   34.7   0.1    1.9  2  Peptidase_M56    BlaR1 peptidase M56
     0.0059   16.8   0.9        2.8    8.2   0.3    3.5  3  NAF              NAF domain


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 !  143.7   0.0   9.8e-46   5.8e-42       2     195 ..      73     287 ..      72     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 9.8e-46
                                       --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikh 77 
                                       ++++el ++v+el  +a+l  p++kv++v+ p  NAFa+g++ ++  +++t+gLl ++l+ ee++aV+GHEl+Hik+
  gi|488601504|ref|YP_007907975.1|  73 HEAPELYSMVRELSMNANL--PMPKVAIVDTPVPNAFATGRNPKNaVVAVTTGLL-RTLNYEEIKAVIGHELSHIKN 146
                                       68899**************..********************98777*********.********************* PP

                                       THHHHHHHHHHHHHHHHHHHHHHHT.....T-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  78 rhsvvslivsllasillllglalli.....sraeedaagafldalavliglliillflalSRkrEyqADeagvellk 149
                                       r+++v++i s l++++ ++ + +++     +r e+  a+a++    vl++++++ll  alSR+rEy+AD  ++ ++ 
  gi|488601504|ref|YP_007907975.1| 147 RDVAVMTIASFLSTVAWFVMRWAMFagmfgGRRENGSANAIIFGVSVLVWFISFLLIRALSRYREYSADLGSAYFTR 223
                                       ****************999988776111114666777888888888999988888888******************* PP

                                       .HHHHHHHHHHHHHHTT--S---HHHH..................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 150 rakdlvraliklakdlerqdvsaslrs..................ellstHPplleRiqalkel 195
                                       ++++l++al k++ ++e + ++ +++                    l+stHPp ++Ri++l+++
  gi|488601504|ref|YP_007907975.1| 224 NPRALISALKKISGKMELVRDEYKKEVeglnafyiipalssesilSLFSTHPPVEKRIERLEKI 287
                                       *****************988777766679999*****************************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.1   1.8e-12     1e-08     112     227 ..      41     164 ..      23     172 .. 0.73
   2 ?    0.1   0.0     0.063   3.8e+02     214     238 ..     184     206 ..     178     217 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.8e-12
                     Peptidase_M56 112 galilllyliaallvlkkr..fvrklgklraeelkeaLkeakeemqlkrnikirlsssidsPa..vlgllkp....r 180
                                       g ++++  +++a  ++  +  + ++  ++ +e++  +L ++ +e  +  n+ + + + +d+P+   ++  ++    +
  gi|488601504|ref|YP_007907975.1|  41 GLILFAGVFLFAQYYFSDKlvLYSSGARIVSEHEAPELYSMVRELSMNANLPMPKVAIVDTPVpnAFATGRNpknaV 117
                                       333333344555555555543334445566778899999999999999************99733344433222226 PP

                     Peptidase_M56 181 IvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqclfwf 227
                                       + + + +l++l+ ee++ ++ HEl+H+k++D+ v  ++ +l+ + wf
  gi|488601504|ref|YP_007907975.1| 118 VAVTTGLLRTLNYEEIKAVIGHELSHIKNRDVAVMTIASFLSTVAWF 164
                                       7788999***************************************9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.063
                     Peptidase_M56 214 vnllvavlqclfwfNPlvhlaarki 238
                                       +n++++ +++l+wf  +  l  r++
  gi|488601504|ref|YP_007907975.1| 184 ANAIIFGVSVLVWFISF--LLIRAL 206
                                       67777777777777333..333334 PP

>> NAF  NAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0071        42      25      50 ..      59      91 ..      45      95 .. 0.79
   2 ?   -2.5   0.0         1   6.1e+03      33      50 ..     224     241 ..     221     242 .. 0.76
   3 !    8.2   0.3   0.00047       2.8       4      50 ..     253     293 ..     250     294 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0071
                               NAF 25 e.......arFtskkpaeeiiskleevakklgf 50
                                      +       ar++s+++a e+ s + e+ +++++
  gi|488601504|ref|YP_007907975.1| 59 KlvlyssgARIVSEHEAPELYSMVRELSMNANL 91
                                      345555559*****************9998887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1
                               NAF  33 paeeiiskleevakklgf 50 
                                       +++++is l+++  k+++
  gi|488601504|ref|YP_007907975.1| 224 NPRALISALKKISGKMEL 241
                                       577889999999887765 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00047
                               NAF   4 lNAFdlI.SlSsgfDLsgLFeeearFtskkpaeeiiskleevakklgf 50 
                                       lNAF +I +lSs   Ls LF++      + p+e+ i++le++ ++lg+
  gi|488601504|ref|YP_007907975.1| 253 LNAFYIIpALSSESILS-LFST------HPPVEKRIERLEKISRELGL 293
                                       89999998888887665.5554......88888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1628.67
//
Query:       gi|488601505|ref|YP_007907976.1|  [L=136]
Description: hypothetical protein Asulf_02018 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   41.4   0.4    7.6e-10   39.2   0.4    1.9  1  Thioredoxin_2   Thioredoxin-like domain
    2.3e-10   40.5   0.0    3.2e-10   40.1   0.0    1.2  1  Thioredoxin_7   Thioredoxin-like
    6.8e-08   32.6   0.1    1.1e-07   32.0   0.1    1.2  1  Thioredox_DsbH  Protein of unknown function, DUF255
    2.1e-05   24.5   0.0    2.7e-05   24.1   0.0    1.2  1  Thioredoxin     Thioredoxin
      3e-05   24.0   0.0    3.4e-05   23.8   0.0    1.1  1  TraF            F plasmid transfer operon protein
    0.00013   21.9   0.0    0.00017   21.5   0.0    1.4  1  AhpC-TSA        AhpC/TSA family
    0.00088   19.4   0.1     0.0015   18.7   0.1    1.4  1  Glutaredoxin    Glutaredoxin
     0.0012   18.6   0.0      0.051   13.3   0.0    2.2  2  Redoxin         Redoxin
     0.0045   16.6   0.5     0.0077   15.8   0.4    1.5  2  SLATT_6         SMODS and SLOG-associating 2TM effector domai
  ------ inclusion threshold ------
      0.013   15.9   0.3       0.42   11.0   0.3    2.4  2  Thioredoxin_8   Thioredoxin-like
      0.019   14.6   0.3      0.034   13.8   0.3    1.4  1  DUF953          Eukaryotic protein of unknown function (DUF95
      0.049   13.8   0.4       0.98    9.6   0.7    2.0  2  Thioredoxin_4   Thioredoxin
      0.063   13.3   0.2      0.099   12.6   0.2    1.4  1  YokU            YokU-like protein, putative antitoxin
      0.089   12.6   0.1       0.18   11.5   0.1    1.6  1  DSBA            DSBA-like thioredoxin domain


Domain annotation for each model (and alignments):
>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.4   5.9e-13   7.6e-10       2     108 ..      42     131 ..      41     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 5.9e-13
                     Thioredoxin_2   2 kgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygv 78 
                                       k+n+k+v+++f++++CpyCk+ +k+l +  +v +          +e  ++ +++++        + +++ + +  + 
  gi|488601505|ref|YP_007907976.1|  42 KKNNKYVFIYFYSETCPYCKLAEKVLNDE-EVAKE---------IENRFIPVKTDE--------LMRYSHFFKDQQR 100
                                       79*******************88866555.77666.........444577776666........457999****999 PP

                     Thioredoxin_2  79 rgtPtivfldgk.eivarlpGyvpaeeleal 108
                                        gtP++++ld + + ++  +Gy+++e +++ 
  gi|488601505|ref|YP_007907976.1| 101 IGTPSFLILDSNgNAIDLRVGYMDKETFLKF 131
                                       9************999999********9986 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   2.5e-13   3.2e-10       2      82 ..      31     110 ..      30     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.5e-13
                                       --SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---...S CS
                     Thioredoxin_7   2 wlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqg...v 75 
                                       w+s +deal+  ++++k v+++f +++c++C+  e+++ ++e+ k+ + ++f+ ++ d   r  + ++ d+ +   +
  gi|488601505|ref|YP_007907976.1|  31 WKS-YDEALELSKKNNKYVFIYFYSETCPYCKLAEKVLNDEEVAKE-IENRFIPVKTDELMRYSHFFK-DQ-QrigT 103
                                       787.***************************988888877777777.************999998833.22.23459 PP

                                       SEEEEE- CS
                     Thioredoxin_7  76 Pvvafld 82 
                                       P +++ld
  gi|488601505|ref|YP_007907976.1| 104 PSFLILD 110
                                       9999998 PP

>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   8.3e-11   1.1e-07      12      80 ..      21      87 ..      18      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 8.3e-11
                    Thioredox_DsbH 12 llqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDr 80
                                      l + +++ + W+ + +eale +k+++k +++     +c +C+  +++  +deeva+ ++++f++vk D 
  gi|488601505|ref|YP_007907976.1| 21 LTSNSEDKIRWKSY-DEALELSKKNNKYVFIYFYSETCPYCKL-AEKVLNDEEVAKEIENRFIPVKTDE 87
                                      567788999**998.58************************96.67799*****************995 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.1e-08   2.7e-05      10     102 ..      34     133 ..      26     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.1e-08
                                       HHHHHTT...TSSEEEEEEE-TTSHHHHCHHHHH..HHHHHHCTTTSEEEEEE.TTTSHHHHHHTT-SSSSEEEEEE CS
                       Thioredoxin  10 Feeevak...ekklvlveFyApwCghCkalaPel..eklaeelkdkvklakvd.vdenedlakkyevegiPtlklfk 80 
                                       ++e+++    ++k v++ Fy++ C+ Ck  + +l  e++a+e+++++  +k d     ++  k+ +  g P ++++ 
  gi|488601505|ref|YP_007907976.1|  34 YDEALELskkNNKYVFIYFYSETCPYCKLAEKVLndEEVAKEIENRFIPVKTDeLMRYSHFFKDQQRIGTPSFLILD 110
                                       5555432223899***************9999984458999999988888877245667777888888999998886 PP

                                       .TTEEEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  81 .ngkevkkyegarekeklaaflk 102
                                        ng++++  +g  +ke++ +f++
  gi|488601505|ref|YP_007907976.1| 111 sNGNAIDLRVGYMDKETFLKFIS 133
                                       15557777889999999999986 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.7e-08   3.4e-05     116     172 ..      32      90 ..      20     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.7e-08
                              TraF 116 rkeekeaalkklakeygLlfFyrgkcpyceaqapilqa..fadkyglevraVsvdgrpl 172
                                       ++ +++  l+k  ++y +++Fy+++cpyc+ + ++l++  +a++++   ++V++d+ + 
  gi|488601505|ref|YP_007907976.1|  32 KSYDEALELSKKNNKYVFIYFYSETCPYCKLAEKVLNDeeVAKEIENRFIPVKTDELMR 90 
                                       455555567888899*********************75227777777788888887655 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.3e-07   0.00017      16      95 ..      36     116 ..      14     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.3e-07
                                       EEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H....SSEEEE- CS
                          AhpC-TSA  16 etvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes...lnfpllsD 89 
                                       e  +ls+ ++k+v ++fy++  cp+C+   + l+++    ke     i v +d++ +   f ++++    +  l++D
  gi|488601505|ref|YP_007907976.1|  36 EALELSKKNNKYVFIYFYSE-TCPYCKLAEKVLNDEE-VAKEIENRFIPVKTDELMRYSHFFKDQQrigTPSFLILD 110
                                       6788999999**********.********99999854.333445678999999999999999998887777777788 PP

                                       TTSHHH CS
                          AhpC-TSA  90 eegkva 95 
                                       ++g+++
  gi|488601505|ref|YP_007907976.1| 111 SNGNAI 116
                                       777665 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.2e-06    0.0015       2      44 ..      50      91 ..      48     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                                      EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHH CS
                      Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkel 44
                                      ++f + tCpyCk a ++L++  v+ +ei+    +  ++el+++
  gi|488601505|ref|YP_007907976.1| 50 IYFYSETCPYCKLAEKVLNDEEVA-KEIENRFIPVKTDELMRY 91
                                      57888*************999854.344444445555555555 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     4e-05     0.051      18      76 ..      35      91 ..      28     114 .. 0.70
   2 ?    4.7   0.0     0.018        23     110     137 ..      98     125 ..      81     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                                      EEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH..H CS
                           Redoxin 18 gnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf..v 76
                                       ++++ls+ ++k v+++f+   +cP+C+     ++ l+++  +k ++  ++ +++d++   
  gi|488601505|ref|YP_007907976.1| 35 DEALELSKKNNKYVFIYFYSE-TCPYCKLA---EKVLNDEEVAKEIENRFIPVKTDELmrY 91
                                      578899997888888888887.*****994...4667666677777777777777776543 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
                                       GGGEEE-EEEEEEETTEEEEEEESSSCH CS
                           Redoxin 110 seglrtpryavidedgkvvylevepepe 137
                                       +++++tp++ ++d +g+ + l v+ +++
  gi|488601505|ref|YP_007907976.1|  98 QQRIGTPSFLILDSNGNAIDLRVGYMDK 125
                                       3449*************99999998874 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4     6e-06    0.0077      57     141 ..       4      94 ..       1      99 [. 0.73
   2 ?   -2.3   0.0       2.3   2.9e+03       1      13 [.     123     135 ..     123     136 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6e-06
                           SLATT_6  57 tkllsalliiigiialyisayekdkekYeka..gkeltklfneLkelysevks....seeedlskleaelkeieaef 127
                                        k++++++++igi+ +++   ++dk ++++   + el k  n+   +y+  ++    +  e + + e+  keie++f
  gi|488601505|ref|YP_007907976.1|   4 AKIVALAIVVIGIVVVMLTSNSEDKIRWKSYdeALELSKKNNKYVFIYFYSETcpycKLAEKVLNDEEVAKEIENRF 80 
                                       6899*********************9998751267889999999888876654222344555666666777777777 PP

                           SLATT_6 128 kevaiskqillsdw 141
                                         v + + +  s++
  gi|488601505|ref|YP_007907976.1|  81 IPVKTDELMRYSHF 94 
                                       77766666666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.3
                           SLATT_6   1 mdkeellksiAek 13 
                                       mdke++lk i + 
  gi|488601505|ref|YP_007907976.1| 123 MDKETFLKFISQY 135
                                       99******99875 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00033      0.42       1      25 [.      45      69 ..      44     100 .. 0.75
   2 ?    3.7   0.0     0.059        76      71      94 ..      91     114 ..      68     115 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                                      .SEEEEEE--SSSHHHHHHHHHHHH CS
                     Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklke 25
                                      +k+v++yf+++ cp ck   + l++
  gi|488601505|ref|YP_007907976.1| 45 NKYVFIYFYSETCPYCKLAEKVLND 69
                                      69**************998888876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.059
                                       HHHHTT-S--TT-SEEEEE-TT-B CS
                     Thioredoxin_8  71 rnklkkkynvkaiPtlvvldknge 94 
                                        +++ k  +  + P++++ld+ng+
  gi|488601505|ref|YP_007907976.1|  91 YSHFFKDQQRIGTPSFLILDSNGN 114
                                       4567777777789*********98 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   2.7e-05     0.034       6      52 ..      32      71 ..      27      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHH..TSSSEEEEEEB--B-TTS-BSSHHHHHHHHHHHHHH CS
                            DUF953  6 eefekslkelekeskivfilFlgekdteGesWCPdCvkaepvieeal 52
                                      +  +++l+  +k++k vfi+F++e        CP+C  ae+v+++  
  gi|488601505|ref|YP_007907976.1| 32 KSYDEALELSKKNNKYVFIYFYSET-------CPYCKLAEKVLNDEE 71
                                      66788999999999********985.......**********98743 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7   0.00077      0.98      11      44 ..      43      77 ..      36      83 .. 0.84
   2 ?    3.0   0.0     0.077        98     123     154 ..      85     119 ..      63     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00077
                                      TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHH CS
                     Thioredoxin_4 11 pdApvtvieyedlrCphCakfeeeve.klleeyid 44
                                      ++ + + i + + +Cp+C+  e+ ++ + +++ i+
  gi|488601505|ref|YP_007907976.1| 43 KNNKYVFIYFYSETCPYCKLAEKVLNdEEVAKEIE 77
                                      67788999***********9999888777777776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.077
                                       HHHHHHHHHHHHHHT--SS-EEEE...TTEEE-TT CS
                     Thioredoxin_4 123 dalveaeskeakkagiestPtfii...ngekveep 154
                                        ++++++s  +k ++  +tP+f+i   ng  ++  
  gi|488601505|ref|YP_007907976.1|  85 TDELMRYSHFFKDQQRIGTPSFLIldsNGNAIDLR 119
                                       567788888888888889*****988888887644 PP

>> YokU  YokU-like protein, putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   7.7e-05     0.099      35      67 ..      57      89 ..      24     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-05
                              YokU 35 sieCseCglvyqeeevvkeiedqllLvdtkklp 67
                                      + +C+  + v ++eev keie++++ v+t +l 
  gi|488601505|ref|YP_007907976.1| 57 CPYCKLAEKVLNDEEVAKEIENRFIPVKTDELM 89
                                      3344555556689**************998875 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014      0.18       4      37 ..      51      83 ..      48     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                      EEEBTTBHHHHHHHHHHHHHHHHCCTEEEEEEE- CS
                              DSBA  4 effDvlCPyCylgkerleklaarspdvkvvlrpf 37
                                       f++  CPyC+l++++l+  + ++ +++ ++ p+
  gi|488601505|ref|YP_007907976.1| 51 YFYSETCPYCKLAEKVLNDEEVAK-EIENRFIPV 83
                                      589999**********98766555.566555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      781  (0.0435607); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 766.19
//
Query:       gi|488601506|ref|YP_007907977.1|  [L=210]
Description: hypothetical protein Asulf_02019 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.6      8e-08   32.6   0.1    2.1  2  CopD          Copper resistance protein D
     0.0014   18.8   3.8     0.0014   18.8   3.8    1.4  2  UPF0093       Uncharacterised protein family (UPF0093)
     0.0015   18.9   0.0     0.0027   18.0   0.0    1.4  1  DUF1772       Domain of unknown function (DUF1772)
  ------ inclusion threshold ------
      0.062   12.9   4.0       0.24   11.0   4.0    1.8  2  Ni_hydr_CYTB  Prokaryotic cytochrome b561
      0.079   11.8   4.8       0.49    9.2   4.8    2.1  1  MscS_TM       Mechanosensitive ion channel inner membrane dom
       0.15   12.0   0.5        0.2   11.6   0.5    1.1  1  FAM217        FAM217 family
        0.4   10.4  13.2      0.048   13.4   7.6    1.9  2  EMC3_TMCO1    Integral membrane protein EMC3/TMCO1-like


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   3.1e-11     8e-08       5      73 ..      55     126 ..      51     145 .. 0.82
   2 ?   -0.1   0.1      0.46   1.2e+03      11      23 ..     192     204 ..     170     209 .. 0.62

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.1e-11
                              CopD   5 rrFsrlalaavavvlvtGvvnallrvglagllt..tayGrlllaKlalllvllalaalnrfrlvprleaa..t 73 
                                       +r s l+++++ +++vtG++ a+   +++g+++   +y +ll +K +l+++++++  + r ++++ l+++  +
  gi|488601506|ref|YP_007907977.1|  55 KRLSMLVMVSIPILIVTGILEAWHSQSFEGFFSfeNTYSSLLSIKHILVILMIGIVIVRR-LIMRSLNREimQ 126
                                       7999*********************89****99999*******************87766.788888665441 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.46
                              CopD  11 alaavavvlvtGv 23 
                                       a++ + vv+++G+
  gi|488601506|ref|YP_007907977.1| 192 AIIGISVVILSGF 204
                                       3444445555555 PP

>> UPF0093  Uncharacterised protein family (UPF0093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.8   5.6e-07    0.0014       4     120 ..       6     129 ..       4     138 .. 0.71
   2 ?   -3.3   0.0       3.8   9.7e+03      68      68 ..     191     191 ..     171     205 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.6e-07
                           UPF0093   4 lylwikalHiiavisWmAglfyLpRlfVyhaeak..ekseekevlkimerrLlkiimtpamiltlvlGllllalae. 77 
                                       +y  +k  H +a  +W+ gl+ L  ++    +ak  +++e k +l   ++rL  ++m    il +v+G+l  +  + 
  gi|488601506|ref|YP_007907977.1|   6 VYGLVKGTHDLATAIWIGGLIQLSFVVFPAFKAKmgQGNELKPLLMDVQKRLSMLVMVSIPIL-IVTGILEAWHSQs 81 
                                       5889*******************8666544444411555777788888899988776544333.6666333333335 PP

                           UPF0093  78 .....glvalssgWlhvKlllvllllayhlvlaklrkklaagentkse 120
                                            +   + s+ l +K +lv+l++++ +v   ++++l+++  + ++
  gi|488601506|ref|YP_007907977.1|  82 fegffSFENTYSSLLSIKHILVILMIGIVIVRRLIMRSLNREIMQMQK 129
                                       6655555556677899***************99999999988766655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                           UPF0093  68 l 68 
                                        
  gi|488601506|ref|YP_007907977.1| 191 N 191
                                       1 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0027       1     109 [.      23     141 ..      23     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                           DUF1772   1 GlilafslfvvPallslpassslllkqwrrlfkrg.kavfpplallsalafayla........araasrgarllyla 68 
                                       G+++ +s++v Pa+++   + ++l ++ + + kr    v+ ++ +l++++ + ++        ++  ++ ++ll + 
  gi|488601506|ref|YP_007907977.1|  23 GGLIQLSFVVFPAFKAKMGQGNELKPLLMDVQKRLsMLVMVSIPILIVTGILEAWhsqsfegfFSFENTYSSLLSIK 99 
                                       778889*********9998877799999999999977777777777777777444679****955666666666656 PP

                           DUF1772  69 aaal.lllsivpyTllvmvPtNnkLaalkeedakekedeaev 109
                                         ++ l+++iv++  l+m+ +N+++++++++++k+  +++ +
  gi|488601506|ref|YP_007907977.1| 100 HILViLMIGIVIVRRLIMRSLNREIMQMQKMQKKKMMQAERA 141
                                       5666699*********************86666555555544 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.5    0.0012         3     101     159 ..      54     111 ..      27     112 .. 0.70
   2 ?   11.0   4.0   9.2e-05      0.24      12     122 ..      60     206 ..      59     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                                       -TTTHHHHHHHHHHHHHHHHHHHT...HHHHHHHH...HTS-THHHHHHH.HHHHHHHHHHH CS
                      Ni_hydr_CYTB 101 qklvhlllyvllvvliltGlllsf...aatagfplllddkggaqlarelHellaaallafvv 159
                                       qk + +l++v +++li+tG+l ++   +   + ++++    + +l+   H +l++++++ v+
  gi|488601506|ref|YP_007907977.1|  54 QKRLSMLVMVSIPILIVTGILEAWhsqS---FEGFFSFENTYSSLLSIKH-ILVILMIGIVI 111
                                       34478999*************9996533...3333333666666666666.88888885554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.2e-05
                                       HHHHHHHHHHHHHHHHHS------S-GGG-......HHHH.HHHHHHHHHHHHHHHHHHH...........------ CS
                      Ni_hydr_CYTB  12 lnallvvllllsgllianlhprlywgdsgk......aral.HklaGlvllalllfrllwl...........kkakkp 70 
                                       l+++++ +l+++g+ +  +h+++  g++++      ++ + H+l+ l + ++++ rl+++            ++kk+
  gi|488601506|ref|YP_007907977.1|  60 LVMVSIPILIVTGI-LEAWHSQSFEGFFSFentyssLLSIkHILVILMIGIVIVRRLIMRslnreimqmqkMQKKKM 135
                                       56789999*****8.8999999999988878987665555788876666666677777778888*999988555555 PP

                                       ------STTTSSSSS----------------TT...................THHHHHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB  71 spriifrqikrdltlllrgrkpeagknnplqkl...................vhlllyvllvvliltGlll 122
                                        +    ++  ++  +   ++kp+   + +++++                   v++  ++ + v+il+G+  
  gi|488601506|ref|YP_007907977.1| 136 MQAERAERGTKEGIKGVGENKPPKAAQGIQGQMphaqisqsikskekasmmlVFVNAIIGISVVILSGFCA 206
                                       555555555555555556666666666666666799999999*****998877777788889999999976 PP

>> MscS_TM  Mechanosensitive ion channel inner membrane domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.8   0.00019      0.49     120     193 ..      51     135 ..      12     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00019
                           MscS_TM 120 rrlrralkrlilvllplllvlilaealsdalardvlG...........rlaflllllllavflarllrpalglyank 185
                                         ++++l +l++v +p+l+v+++ ea++++ +++ ++             ++++l+++++++ + ++r+  ++  ++
  gi|488601506|ref|YP_007907977.1|  51 MDVQKRLSMLVMVSIPILIVTGILEAWHSQSFEGFFSfentyssllsiKHILVILMIGIVIVRRLIMRSLNREIMQM 127
                                       44567777777777777777777777777777777777777777777766666667776666666666666666666 PP

                           MscS_TM 186 keeeknsl 193
                                       ++++k+++
  gi|488601506|ref|YP_007907977.1| 128 QKMQKKKM 135
                                       66666554 PP

>> FAM217  FAM217 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   7.7e-05       0.2      87     150 ..     113     179 ..     109     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.7e-05
                            FAM217  87 ekyidRLlqLEwlQiqTvqkEkak.aakaRpktapgt..laalksPgsskllqsalpskklssqegl 150
                                        ++i+R l+ E +Q+q +qk k+  a +a   t  g   +++ k P+  + +q ++p++++s++ + 
  gi|488601506|ref|YP_007907977.1| 113 RRLIMRSLNREIMQMQKMQKKKMMqAERAERGTKEGIkgVGENKPPKAAQGIQGQMPHAQISQSIKS 179
                                       689******************888677766667665522689999***********99999876554 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3       0.2     5e+02      80     117 ..      50      86 ..      37     102 .. 0.73
   2 ?   13.4   7.6   1.9e-05     0.048      17     114 ..     103     202 ..      92     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                        EMC3_TMCO1  80 lmedqsemmmdqmkpmivtmipqiliffwlnsffsgfv 117
                                       lm+ q+ ++m  m + i ++i++ ++ +w ++ f+gf+
  gi|488601506|ref|YP_007907977.1|  50 LMDVQKRLSMLVMVS-IPILIVTGILEAWHSQSFEGFF 86 
                                       566666666666654.6677777777777777777775 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.9e-05
                        EMC3_TMCO1  17 vivillvgiltgllsellqkllidkkkmekeqkrekelqkrare..lqkngdklklkklekrqeelmedqsemmmdq 91 
                                       vi+++ + i++ l+++ l+   ++++km+k +++++e  +r ++   +  g+++++k+ +  q ++  +q + + ++
  gi|488601506|ref|YP_007907977.1| 103 VILMIGIVIVRRLIMRSLNREIMQMQKMQKKKMMQAERAERGTKegIKGVGENKPPKAAQGIQGQMPHAQISQSIKS 179
                                       5778888889************9999999999999998888765336669999999999999999999887774444 PP

                        EMC3_TMCO1  92 mkpmivtmipqiliffwlnsffs 114
                                         +  +++++  +i++    ++s
  gi|488601506|ref|YP_007907977.1| 180 KEKASMMLVFVNAIIGISVVILS 202
                                       33333333333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1572  (0.0876792); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); 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):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1124.95
//
Query:       gi|488601507|ref|YP_007907978.1|  [L=112]
Description: Mannose-6-phosphate isomerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-13   48.7   0.1    7.5e-13   48.0   0.0    1.4  2  Cupin_2       Cupin domain
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.021   15.2   0.0    1.2  1  Pirin_C       Pirin C-terminal cupin domain
      0.054   13.1   0.1      0.061   13.0   0.1    1.1  1  3-HAO         3-hydroxyanthranilic acid dioxygenase
      0.099   12.2   0.0       0.21   11.2   0.0    1.6  1  Cupin_1       Cupin
        0.2   11.6   0.0       0.24   11.3   0.0    1.1  1  AraC_binding  AraC-like ligand binding domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.1   7.7e+03      53      58 ..      14      19 ..       8      24 .. 0.53
   2 !   48.0   0.0   2.1e-16   7.5e-13       3      70 ..      34     100 ..      32     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                                      -EEEEE CS
                           Cupin_2 53 tpHrfr 58
                                       pH+++
  gi|488601507|ref|YP_007907978.1| 14 NPHNVE 19
                                      344443 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 2.1e-16
                                       EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                        +l+pGe  ++h+ p    +fyVleG g +++++e+  +e++ ++  pa+ pH + N++++ +r+lv+
  gi|488601507|ref|YP_007907978.1|  34 LTLKPGERLKRHVTPVD-VVFYVLEGSGIVEIGDEKRLVEKDVAIESPAKIPHCWYNESNGVLRVLVI 100
                                       689*************8.************************************************98 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   5.8e-06     0.021       2      67 ..      32      99 ..      31     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                                      EEEEE-TT-EEEEE--TT-EEEEEEEES-E..EESSTTEEE-TTEEEEE-..SSSEEEEE--SS-EEEEE CS
                           Pirin_C  2 ldltleagaelelplpegleaavyvleGel..evggerseieeeqlavlg..dgdslvvkaeekgarvlL 67
                                      ++ltl++g++l+      ++++ yvleG++  e+g+e+ ++ e+++a+ +  +  + + + ++  +rvl+
  gi|488601507|ref|YP_007907978.1| 32 IHLTLKPGERLKRH-VTPVDVVFYVLEGSGivEIGDEK-RLVEKDVAIESpaKIPHCWYNESNGVLRVLV 99
                                      689*********99.78899*********733666665.8999999988854445556555555666665 PP

>> 3-HAO  3-hydroxyanthranilic acid dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.7e-05     0.061      24     102 ..      18      94 ..       3     111 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       T-EEEEEESS.E.EEEEE-SSB--S-EEE-SS-EEEEEEES-EEEEEEETTCCC..EEEE-TTEEEEE-TT--EEEE CS
                             3-HAO  24 vcnkclhkdg.l.kvlivGGPnerkdyhleegeeffyqkkGdmvlkvldegkar..divireGeifllParvphsPq 96 
                                       v  k++++d+   ++ +   P er   h+ + + +fy ++G+ ++ + de +    d+ i+       Pa++ph   
  gi|488601507|ref|YP_007907978.1|  18 VEAKLVYDDEkAqIIHLTLKPGERLKRHVTPVDVVFYVLEGSGIVEIGDEKRLVekDVAIES------PAKIPHCWY 88 
                                       556666655313134445689**********************9999888764223777764......888888877 PP

                                       E-TT-E CS
                             3-HAO  97 rfadsv 102
                                         ++ v
  gi|488601507|ref|YP_007907978.1|  89 NESNGV 94 
                                       777766 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.9e-05      0.21      54     112 ..      49      99 ..      31     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.9e-05
                                       S-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEE CS
                           Cupin_1  54 ateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivv 112
                                          ++yvl+G+g v++  +++   + +    +  ++  Pa ++h++yn   + ++ + v
  gi|488601507|ref|YP_007907978.1|  49 VDVVFYVLEGSGIVEIGDEKR---LVE----KDVAIESPAKIPHCWYNES-NGVLRVLV 99 
                                       56799********88877774...444....4447889**********95.54444544 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 ?   11.3   0.0   6.7e-05      0.24      12      74 ..      38     100 ..      28     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.7e-05
                                       TT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEE CS
                      AraC_binding  12 pdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwl 74 
                                       p+++ ++hv +  v+ yv+eG+g+++++++   ++++  +  p   pH  + +s+  ++  ++
  gi|488601507|ref|YP_007907978.1|  38 PGERLKRHVTPVDVVFYVLEGSGIVEIGDEKRLVEKDVAIESPAKIPHCWYNESNGVLRVLVI 100
                                       7788899****99*******************9999999999999999777777765555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 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:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 600.04
//
Query:       gi|488601508|ref|YP_007907979.1|  [L=463]
Description: Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit-related amidase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.7e-129  430.4   0.0   5.1e-128  427.9   0.0    1.8  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 !  427.9   0.0  2.8e-132  5.1e-128       1     451 []      24     443 ..      24     443 .. 0.93

  Alignments for each domain:
  == domain 1  score: 427.9 bits;  conditional E-value: 2.8e-132
                                       HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B CS
                           Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenyp 77 
                                       e+veafl+ri+++n+++n ++ +++e+a ++A++l+k+ +   +++pL+G+P++vKDn+d+kg++tt+Gsk +eny+
  gi|488601508|ref|YP_007907979.1|  24 EVVEAFLERIKELNQDIN-AFVTINENAVREAKELEKASK---DDKPLYGLPVAVKDNVDTKGIRTTYGSKLYENYV 96 
                                       89****************.77789************9985...********************************** PP

                                       -SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSS CS
                           Amidase  78 aekDatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGG 154
                                       +e Da++verLk+aGa+++gkTn++e+a+   t+n++fg t+NPwd srtpGGSSGGsAAavA g+ p+a+G+D+GG
  gi|488601508|ref|YP_007907979.1|  97 PEGDAVIVERLKRAGAIVIGKTNIPELALLPITDNTLFGETKNPWDMSRTPGGSSGGSAAAVATGMIPVATGNDGGG 173
                                       ***************************************************************************** PP

                                       TTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCT CS
                           Amidase 155 SiRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeel 231
                                       SiRiP++fcgl+GlKP++grv++++  ++  +l ++G+l+r+ved+all++ i+g+d +d  s++  +e+ ++++  
  gi|488601508|ref|YP_007907979.1| 174 SIRIPSAFCGLYGLKPSFGRVPCYPSLPIFVGLNSEGVLTRCVEDTALLMDIIAGRDDRDKYSLP--DENVSYSNVI 248
                                       ***********************************************************999999..9999****** PP

                                       T---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS CS
                           Amidase 232 kkslkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvry 308
                                        +  +g+ri++  ++g+a++dpev++ v++a+ +Le+aG+ev+eve++ +    +l+++i+++ a            
  gi|488601508|ref|YP_007907979.1| 249 DEGIEGVRIAFSPNLGYATVDPEVEEIVRNAAFKLEKAGAEVEEVEVSVPRLESELVTKIVLEVAT-F--------- 315
                                       ***********************************************9999888888888885554.3......... PP

                                       ---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS CS
                           Amidase 309 erlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptp 385
                                               + ++++++ +  +   +  +   g+  l+ +     y   ++++++l++ ++++f  +D+l++Pt++ p
  gi|488601508|ref|YP_007907979.1| 316 --------MGDKFEEWKQIAYPLLLPFMELVGS--LTYRE----YVGVEARKEELWKGLRQIFSNYDFLITPTTAVP 378
                                       ........4567777766555444444444444..44443....7888888889*********************** PP

                                       --BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                           Amidase 386 aprlgekdktidsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                       +++lg+     +   +    l ++a++ p+n++g+pa s+pag+++dglPvG+qv+g++f+++ +L
  gi|488601508|ref|YP_007907979.1| 379 PFQLGNVGVS-EIAGEAVTPLGWMAFTYPFNFTGQPAASMPAGFTKDGLPVGMQVVGRRFDDAGVL 443
                                       *******866.5888888999999999***********************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); 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: 0.65u 0.38s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2541.99
//
Query:       gi|488601509|ref|YP_007907980.1|  [L=180]
Description: Acyl dehydratase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-21   75.7   0.0    3.1e-21   75.2   0.0    1.3  1  MaoC_dehydratas  MaoC like domain
    0.00081   19.7   0.2     0.0013   19.0   0.2    1.4  1  4HBT             Thioesterase superfamily
  ------ inclusion threshold ------
      0.054   13.7   0.0      0.097   12.9   0.0    1.6  1  GST_C_3          Glutathione S-transferase, C-terminal domain


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   5.1e-25   3.1e-21      12     109 ..      58     150 ..      42     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 5.1e-25
                                       EEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTTEGGGEEEEEEEE-S- CS
                   MaoC_dehydratas  12 tekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdnvvarvgeikvrFtkp 88 
                                       +  e  +t ad+ l+ l+sgD+n iH ++e+Ak ++fgg+++hG+lt++++++l+e   g      + + ++++++p
  gi|488601509|ref|YP_007907980.1|  58 F--EKRLTYADVFLFSLISGDWNVIHHSEEIAKRTKFGGRVVHGLLTTSLASALMEMLPGI---VVLLSVEFQYIRP 129
                                       3..5567799*****************************************9998877777...789999******* PP

                                       -BTTCEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  89 Vlpgdtlkvelevvgkrdvrk 109
                                       V++gdt++ +++vv+   + +
  gi|488601509|ref|YP_007907980.1| 130 VYVGDTVRGKAVVVDRLPGNR 150
                                       *************99555544 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   2.2e-07    0.0013      18      78 ..     106     165 ..      92     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-07
                                       HHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEE.EEESSEEEEEEEEEETTSCEE CS
                              4HBT  18 gaalrslggrgilvvvvelsidflrpvrlgdeltvearvl.rlgrtsavvevevrdedgrlv 78 
                                       + al++      +vv ++ + +++rpv +gd+++ +a v+ rl ++++ vev++ +e +++v
  gi|488601509|ref|YP_007907980.1| 106 ASALMEMLP--GIVVLLSVEFQYIRPVYVGDTVRGKAVVVdRLPGNRLRVEVKFINERNEVV 165
                                       455555555..79***********************98653899999999999999988765 PP

>> GST_C_3  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.6e-05     0.097      36      70 ..      46      79 ..       4      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                                      HHHHHHCHGTSSSSTTS--HHHHHHHHHHHHHHHH CS
                           GST_C_3 36 fekvlkkkgggylvgdklTyADlalfqvldgleea 70
                                       ek l+  g +  + ++lTyAD++lf++++g  ++
  gi|488601509|ref|YP_007907980.1| 46 TEKTLS-PGLEVTFEKRLTYADVFLFSLISGDWNV 79
                                      566666.455567889*************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1026.84
//
Query:       gi|488601510|ref|YP_007907981.1|  [L=469]
Description: acetyl-CoA decarbonylase/synthase gamma subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-156  521.5   0.1   1.2e-156  521.3   0.1    1.0  1  CdhD      CO dehydrogenase/acetyl-CoA synthase delta subunit
    2.9e-14   52.4   2.1    2.9e-14   52.4   0.8    1.7  2  FeS       Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.3   0.1  1.3e-160  1.2e-156       1     386 []      73     462 ..      73     462 .. 0.99

  Alignments for each domain:
  == domain 1  score: 521.3 bits;  conditional E-value: 1.3e-160
                                       EEEESSGCG-EEEE----SSTTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE....ETTEEEE--EEEEE- CS
                              CdhD   1 evvlGaeekavkiGgeevLyrfeltffnptaiaidvsDelseellkalaerieevvddwakkrvgekltldaiairl 77 
                                       evv+G+++ avkiGge+v++r+e t+fnpta+++dv+D++se   k l+e++++vv+ ++k++vg++ltld+ia+r+
  gi|488601510|ref|YP_007907981.1|  73 EVVIGVGDSAVKIGGEDVIHRHEMTYFNPTAFFYDVWDTMSE---KDLEEKCRKVVE-FRKFYVGKFLTLDGIAVRC 145
                                       8*************************************9998...8***********.******************* PP

                                       -SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEEE-.SS CS
                              CdhD  78 istdPakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvpvvllsind 154
                                       +s++P   ++ +vekva  ++ p+vl++++p++++aale v+d+rpl+yaAt+ ++ke+++lale++vpv++ + +d
  gi|488601510|ref|YP_007907981.1| 146 TSNNP-DTYKSVVEKVAS-YGKPMVLVALNPDCMRAALESVADKRPLIYAATESNWKEFLKLALEFNVPVAIRA-KD 219
                                       *****.***********6.******************************************************9.** PP

                                       HHHHHHHHHHHHCTT---EEEE---SH.....HHHHHHHHHHHHHHHHS.-TTS-S-BEEE---SSHHHHHHHHH.. CS
                              CdhD 155 leelkelarkllkagvkdivldPttaalGegleetidnvvriRraaikg.dkdlafPilslttnawlaresdeve.. 228
                                       l++lk+la ++++agvkdivldP+t++lGegl+ t+++vv++Rr+ai g dkd+afPi+ +++ awl+ e deve  
  gi|488601510|ref|YP_007907981.1| 220 LDTLKSLAVTFKEAGVKDIVLDPVTEPLGEGLKGTFERVVNLRRTAILGeDKDIAFPIMVTPISAWLI-EGDEVEka 295
                                       ********************************************************************.5999999* PP

                                       .........HHHTT-SEEEES---HHHHHHHHHHHHHHTS-SSS--B--SSEEEESS--TTS-EEEEESBHHHHHHH CS
                              CdhD 229 .........lvvrYadililrslekeellPvltlrqniYtDPrkPvavdpglyeigdrdensPvflttnfsLtyYtv 296
                                                ++v+Yadi+i+rsle ++++P++tlr+niYtDPr+Pv+vdpgl+ei+++  +sPvf+ttnf+LtyYtv
  gi|488601510|ref|YP_007907981.1| 296 ywetvlgsmFIVKYADIMIFRSLEPYSVIPTVTLRFNIYTDPRTPVQVDPGLREINNPTPDSPVFITTNFALTYYTV 372
                                       ***************************************************************************** PP

                                       HHHHHHTTS-EEEEEE-SSS--HHHHHHTTSSSHHHHHHHHHHTTHHHHSSS-EEEE-GGGGGGHHHHHHHHTSEEE CS
                              CdhD 297 egdlesdkitayLLvldteGlgvevslaggqleaekvkdlieetgieekvkhrflilPglvavlkgkiedltgwkvl 373
                                       e+dl+s +i++yLLvl+teGlgvevs+aggq++a kvk+l+eet+i+ekv+h++l++Pgl+a+l+g+ied+tgw+v+
  gi|488601510|ref|YP_007907981.1| 373 ESDLTSAGISCYLLVLNTEGLGVEVSVAGGQFTAGKVKELMEETKIAEKVNHKYLVIPGLAARLQGAIEDETGWTVK 449
                                       ***************************************************************************** PP

                                       E--SSGGGHHHHH CS
                              CdhD 374 vgprdsseivavl 386
                                       vgp+ds++i+++l
  gi|488601510|ref|YP_007907981.1| 450 VGPMDSGRIKGWL 462
                                       *********9985 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.8   3.3e-18   2.9e-14       1      33 []      13      45 ..      13      45 .. 0.99
   2 ?   -3.1   0.0      0.71   6.3e+03      12      25 ..     174     187 ..     174     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 3.3e-18
                               FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                      LP+tNCg+CG+ +Cm fA+ ++  ++++e+Cpp
  gi|488601510|ref|YP_007907981.1| 13 LPQTNCGECGFDTCMSFAAHIIDRSVKPENCPP 45
                                      9*******************************8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.71
                               FeS  12 pgCmafAealvege 25 
                                       p Cm  A   v+++
  gi|488601510|ref|YP_007907981.1| 174 PDCMRAALESVADK 187
                                       78999886666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 2502.78
//
Query:       gi|488601511|ref|YP_007907982.1|  [L=456]
Description: acetyl-CoA decarbonylase/synthase delta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-90  302.0   0.5    2.3e-83  280.0   0.0    3.2  3  CdhD          CO dehydrogenase/acetyl-CoA synthase delta subu
     0.0002   20.9   0.0    0.00032   20.2   0.0    1.2  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.032   13.9   0.2       0.47   10.1   0.2    2.1  1  Pterin_bind   Pterin binding enzyme


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.0   0.0   3.9e-87   2.3e-83       1     226 [.     132     382 ..     132     385 .. 0.97
   2 !   11.5   0.0   1.5e-05     0.087     263     292 ..     385     410 ..     383     418 .. 0.90
   3 !    7.7   0.0   0.00021       1.2     350     384 ..     419     453 ..     412     455 .. 0.87

  Alignments for each domain:
  == domain 1  score: 280.0 bits;  conditional E-value: 3.9e-87
                                       EEEESS.......GCG-EEEE----S..STTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE.......ETT CS
                              CdhD   1 evvlGa.......eekavkiGgeevL..yrfeltffnptaiaidvsDelseellkalaerieevvdd...wakkrvg 65 
                                       evvlGa       ++k v++Gge++L  y f++ ++n +aiaid++D ++++l+ka++e++e+v +d   wa+k+v+
  gi|488601511|ref|YP_007907982.1| 132 EVVLGAtkkdggtRDKVVVLGGEKSLpfYLFDADQPNLPAIAIDIFD-RKPMLAKAVREHYEDVLEDpadWARKAVK 207
                                       677887777777799**********87688*****************.7889************************* PP

                                       EEEE--EEEEE--SSST.......HHHHHHHHHHHCC--SEEEEE-S.....SHHHHHHHHTTTCCC--EEEEE-TT CS
                              CdhD  66 ekltldaiairlistdP......akkfakavekvakavkvplvlggs.....dpevlkaalevvederpllyaAtkd 131
                                       e +++d+i+++listdP      a+++ k++e+v++avk+p+++ggs     dpevl++a+ev+e+er++l++At+d
  gi|488601511|ref|YP_007907982.1| 208 E-YGADLITLHLISTDPlledtpASEAVKVLEDVLQAVKCPIIVGGSgnkekDPEVLEKAAEVAEGERIMLASATLD 283
                                       *.*************************************************************************** PP

                                       .THHHHHHHHHHTT--EEEE-.SSHHHHHHHHHHHHC.TT-..--EEEE---SH.....HHHHHHHHHHHHHHHHS- CS
                              CdhD 132 .dykeiaelaleykvpvvllsindleelkelarkllk.agv..kdivldPttaalGegleetidnvvriRraaikgd 204
                                        d+++ia++a+++++ v++++++d++++k+l+r+llk agv  +div+dPttaalG+g++++++n++riR++++kgd
  gi|488601511|ref|YP_007907982.1| 284 mDWERIANAAKNHGHVVLSWTQMDINSQKTLNRYLLKrAGVspNDIVMDPTTAALGYGIDYAFTNMERIRISGLKGD 360
                                       ************************************999************************************** PP

                                       TTS-S-BEEE---SSHHHHHHH CS
                              CdhD 205 kdlafPilslttnawlaresde 226
                                       +dlafPi+s+ttnaw+are+++
  gi|488601511|ref|YP_007907982.1| 361 SDLAFPISSGTTNAWGAREAWM 382
                                       *********************8 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.5e-05
                                       S--B--SSEEEESS--TTS-EEEEESBHHH CS
                              CdhD 263 kPvavdpglyeigdrdensPvflttnfsLt 292
                                       +P+++d ++   g+r+ ++P++++++  Lt
  gi|488601511|ref|YP_007907982.1| 385 SPIEEDSDW---GPRELRGPIWEIVT-GLT 410
                                       7********...*************9.777 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00021
                                       EEEE.-GGGGGGHHHHHHHHTSEEEE--SSGGGHHH CS
                              CdhD 350 flil.Pglvavlkgkiedltgwkvlvgprdsseiva 384
                                       f+++ Pg+vavlk+ + +l g k++  ++d + ++ 
  gi|488601511|ref|YP_007907982.1| 419 FMMMhPGAVAVLKEVMYTL-GGKISGSVADPGDWIV 453
                                       89999***********998.9999999999998876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.4e-08   0.00032       5     126 ..     173     301 ..     171     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.4e-08
                                       EEEEETTEEEEECTTCSTCEEEETTSHHHHHHHH.HHHT-SEEEEEEHHHHC....TTHHHHHHHHHHHHHH-SSEE CS
                      His_biosynth   5 alDlkdGkvVrlvkGdrfqelryagdpvelakry.eeegadelhvvDldaak....egreanldlveeiaeevfipv 76 
                                       a+D+ d k   l k +r+ ++++ +dp++ a++  +e gad +++  ++       +  ++  +++e ++++v++p+
  gi|488601511|ref|YP_007907982.1| 173 AIDIFDRKPM-LAKAVREHYEDVLEDPADWARKAvKEYGADLITLHLISTDPlledTPASEAVKVLEDVLQAVKCPI 248
                                       8*********.******************998875899999877666655545544455566799************ PP

                                       EEESSSSSHHHHHHHHHCT-S.....EEEESHHHH.H-THHHHHHHHHHCGGGEEE CS
                      His_biosynth  77 qvGGGIrsledveelleagad.....kviigtaav.knpelikelaekfgsqkivv 126
                                        vGG  ++ +d  e+le  a+     ++++++a++  ++e i ++a+++g   +v+
  gi|488601511|ref|YP_007907982.1| 249 IVGGSGNKEKD-PEVLEKAAEvaegeRIMLASATLdMDWERIANAAKNHGH--VVL 301
                                       **986555444.45555555555677*******994579999999999998..555 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   7.9e-05      0.47      22     173 ..     197     335 ..     185     354 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.9e-05
                                       HHHHHHHHHHHT.T-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S.....-HHHHHHHHHT CS
                       Pterin_bind  22 kalaqarkmvee.GAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDtt.....kaevaeaAlka 92 
                                       +  ++ark v+e GAd++ +   st P  e  ++ e+++ +  vl+     +++pi +  +     ++ev+e+A ++
  gi|488601511|ref|YP_007907982.1| 197 DPADWARKAVKEyGADLITLHLISTDPLLEDTPASEAVKVLEDVLQ----AVKCPIIVGGSgnkekDPEVLEKAAEV 269
                                       5567888888766999999999999888888888888888888888....567888887654444368999999998 PP

                                       ..TS.EEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHTT--GGG CS
                       Pterin_bind  93 ..ga.divNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeeaGvaper 166
                                         g   ++ + ++ ++ +++++ ++++   vv+  ++                  +++++ +  +  +++aGv p++
  gi|488601511|ref|YP_007907982.1| 270 aeGErIMLASATLDMDWERIANAAKNH-GHVVLSWTQ-----------------MDINSQKTLNRYLLKRAGVSPND 328
                                       886536788888888555555555555.456666555.................23445555556667889999999 PP

                                       EEEETTT CS
                       Pterin_bind 167 illDpgi 173
                                       i++Dp +
  gi|488601511|ref|YP_007907982.1| 329 IVMDPTT 335
                                       9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2531.20
//
Query:       gi|488601512|ref|YP_007907983.1|  [L=253]
Description: CO dehydrogenase maturation factor [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   66.1   0.0    4.4e-18   65.6   0.0    1.2  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.1e-12   48.3   0.0    2.1e-12   47.3   0.0    1.5  1  AAA_31           AAA domain
    4.5e-08   32.9   0.0    5.5e-05   22.7   0.0    2.1  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    1.1e-07   31.3   0.2    2.6e-07   30.1   0.2    1.9  1  ArsA_ATPase      Anion-transporting ATPase
    8.6e-05   22.1   0.1       0.31   10.4   0.0    2.3  2  ParA             NUBPL iron-transfer P-loop NTPase
    9.3e-05   22.0   0.0      0.002   17.6   0.0    2.2  1  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
     0.0028   17.4   0.0     0.0059   16.3   0.0    1.5  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.044   13.1   0.0       0.78    9.0   0.0    2.1  2  MipZ             ATPase MipZ
       0.12   12.3   0.1       0.25   11.2   0.1    1.6  1  Arg_repressor_C  Arginine repressor, C-terminal domain
       0.12   12.6   0.1       0.29   11.4   0.0    1.8  2  Toprim           Toprim domain
        0.3   10.7   1.4         14    5.2   0.1    2.5  2  SRP54            SRP54-type protein, GTPase domain
       0.37   10.2   1.6         21    4.5   0.3    2.5  2  Pox_A32          Poxvirus A32 protein


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0     3e-21   4.4e-18       3     128 .]       5     227 ..       3     227 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 3e-21
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       ++ +kGG+GKT ++a L+  l++ +++ l+vDaDp++n+   + g+ +++                           
  gi|488601512|ref|YP_007907983.1|   5 AVTGKGGTGKTIISALLIHFLSK-KYDLLAVDADPDSNLPD-ALGVTPRKTLgeirevfqvsrdemgtlnkeqwleg 79 
                                       6889*******************.***************99.455444444466666999***************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|488601512|ref|YP_007907983.1|  80 kiyseaitetddydllvmgrpegegcycfansllrgvlrklmkhydvvvidteaglehfsrgtisgadyilvvtdms 156
                                       ***************************************************************************** PP

                                       .....CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .....dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                            ++kr++el ++l+ +    +k + +v nr+ +e+  + +k++ +e+    g+++l ++p++e++++ + +g+
  gi|488601512|ref|YP_007907983.1| 157 rkglsTAKRIKELSSDLKLN----FKKIYLVGNRIMNEDGAEVIKKFADEE----GLELLELLPYSEEIVKFDIEGK 225
                                       ******************99....899***********9999888888887....******************9999 PP

                                       -H CS
                                       xx RF
                              CbiA 127 pv 128
                                       pv
  gi|488601512|ref|YP_007907983.1| 226 PV 227
                                       86 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   1.4e-15   2.1e-12       7     168 ..       6     170 ..       1     181 [. 0.73

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.4e-15
                            AAA_31   7 anqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenldl 83 
                                       +  KGG GKT  s  l  +l+k+ +  L vD+Dp +n+  +lg++ +++  ++ ev+  + +   +++k++  + ++
  gi|488601512|ref|YP_007907983.1|   6 VTGKGGTGKTIISALLIHFLSKK-YDLLAVDADPDSNLPDALGVTPRKTLGEIREVFQVSRDEMGTLNKEQWLEGKI 81 
                                       357*************9999875.789*****************999999999999853333334444455444454 PP

                            AAA_31  84 ipssidLaeaeielvelekk.........eeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaea 151
                                         s+      + +l+ + +          ++ l+ +l+k+ ++YD+++iD+   L+ + +  +  +d+++++++++ 
  gi|488601512|ref|YP_007907983.1|  82 Y-SEAITETDDYDLLVMGRPegegcycfaNSLLRGVLRKLMKHYDVVVIDTEAGLEHFSRGTISGADYILVVTDMSR 157
                                       4.4444444444554444444577777766669***************************************99855 PP

                            AAA_31 152 yaleGleqllktieevk 168
                                         l+++    k+i+e+ 
  gi|488601512|ref|YP_007907983.1| 158 KGLSTA----KRIKELS 170
                                       444443....4444444 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00086       1.3       2      40 ..       3      40 ..       2      64 .. 0.84
   2 !   22.7   0.0   3.7e-08   5.5e-05     140     245 ..     145     248 ..      98     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00086
                         Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                       ia+ GkGG Gk++ s+ l + l+++   +l v  DP +
  gi|488601512|ref|YP_007907983.1|  3 TIAVTGKGGTGKTIISALLIHFLSKK-YDLLAVDADPDS 40
                                      59***********9999888888765.457888888865 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 3.7e-08
                         Fer4_NifH 140 kaqevyivtsgelmalyaanniakgiek.yaksggvrlgG.liinsrkvddereliekfaeelgtkvlevvPrdeiv 214
                                        a+++++vt+   + l +a +i +     + + +++ l G  i+n    +d+ e+i+kfa+e g+++le +P +e++
  gi|488601512|ref|YP_007907983.1| 145 GADYILVVTDMSRKGLSTAKRIKELSSDlKLNFKKIYLVGnRIMN----EDGAEVIKKFADEEGLELLELLPYSEEI 217
                                       5899***************99976444314455666655424666....789************************* PP

                         Fer4_NifH 215 rkaelrkktvieyapeseqakeyrelarkil 245
                                        k +++ k v+  +++s+ +   +++a+k++
  gi|488601512|ref|YP_007907983.1| 218 VKFDIEGKPVVMLDDNSDYSLRVKKIAEKLV 248
                                       ******************9999999999876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2   1.7e-10   2.6e-07       3     132 ..       3     131 ..       1     248 [. 0.83

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.7e-10
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCC CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqe 79 
                                        i v+GKGG GKt +sa +   ls+ +++ l +  DP  +l D++     k+   ++e  ++   ++ +  +e++ e
  gi|488601512|ref|YP_007907983.1|   3 TIAVTGKGGTGKTIISALLIHFLSK-KYDLLAVDADPDSNLPDALGVTPRKTLGEIREVFQVSRDEMGTLNKEQWLE 78 
                                       689*************988888886.689******************999999999998888776666777889999 PP

                                       HHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHH.HHHHHH...CSSSSEEEEES CS
                       ArsA_ATPase  80 vqkeeeallgleeledvlaeelaslPGideilsfee.llkyvk...eeeydvvvlDt 132
                                        + + ea+ +++  + ++    +     +    f++ ll+ v     ++ydvvv+Dt
  gi|488601512|ref|YP_007907983.1|  79 GKIYSEAITETDDYDLLVMGRPEG----EGCYCFANsLLRGVLrklMKHYDVVVIDT 131
                                       999999888766555544443333....44444432122222223367899999998 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 !    9.9   0.0   0.00031      0.46       8      55 ..       5      50 ..       1      76 [. 0.73
   2 !   10.4   0.0   0.00021      0.31     191     245 ..     193     247 ..     121     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                              ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee 55
                                       + gKGG GK+ +++ l   L+k  ++   +DaD    ++p+ lgv+ 
  gi|488601512|ref|YP_007907983.1|  5 AVTGKGGTGKTIISALLIHFLSK-KYDLLAVDADP-DSNLPDALGVTP 50
                                      468*********99999887765.56666678884.356666666665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00021
                              ParA 191 kgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                        +  +k+a+e g++ll  +p ++ei++   egkp+v+ +++s+++  +++iaek+
  gi|488601512|ref|YP_007907983.1| 193 AEVIKKFADEEGLELLELLPYSEEIVKFDIEGKPVVMLDDNSDYSLRVKKIAEKL 247
                                       45568999********************************************997 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06     0.002       1     146 [.       1     154 [.       1     159 [. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                          CBP_BcsQ   1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlL...............rlhFnvdieqregwarae 62 
                                       m ++a++G +GG+G+t ++a L + + + ++  l++D+ pd  L               r  F+v  ++  ++ + +
  gi|488601512|ref|YP_007907983.1|   1 MVTIAVTG-KGGTGKTIISALLIH-FLSKKYDLLAVDADPDSNLpdalgvtprktlgeiREVFQVSRDEMGTLNKEQ 75 
                                       77899999.8*****988776655.5567999*******99766222222222222222335666666666666666 PP

                          CBP_BcsQ  63 ldgapwrqaaleyapgldllPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellalad 139
                                         + ++ + a+  ++++dll  G+ + e       ++ +++ l   l++l ++y+ +++D  ag ++  r +++ ad
  gi|488601512|ref|YP_007907983.1|  76 WLEGKIYSEAITETDDYDLLVMGRPEGEGC-----YCFANSLLRGVLRKLMKHYDVVVIDTEAGLEHFSRGTISGAD 147
                                       55556666778889999***9999877655.....57788999999******************************* PP

                          CBP_BcsQ 140 lvllvve 146
                                         l v+ 
  gi|488601512|ref|YP_007907983.1| 148 YILVVTD 154
                                       9999875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     4e-06    0.0059       4      78 ..       3     136 ..       1     147 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4e-06
                            AAA_24   4 kiliyGpsgiGKTtlakel......gpkplfidtekGlksldadkfpdie........swedfldevvel....... 59 
                                        i+++G+ g+GKT + + l      +++ l +d +    +l ++ +++++         ++  +de+ +l       
  gi|488601512|ref|YP_007907983.1|   3 TIAVTGKGGTGKTIISALLihflskKYDLLAVDADP-DSNLPDALGVTPRktlgeireVFQVSRDEMGTLnkeqwle 78 
                                       699*************99999999999999999999.4466666666666856655554444444444449999999 PP

                            AAA_24  60 .......................................aaeladyktlviDtidele 78 
                                                                              ++  ++y+++viDt   le
  gi|488601512|ref|YP_007907983.1|  79 gkiyseaitetddydllvmgrpegegcycfansllrgvlRKLMKHYDVVVIDTEAGLE 136
                                       99999999999*****************************************966555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.084   1.3e+02       7      28 ..       7      28 ..       1      39 [. 0.72
   2 ?    9.0   0.0   0.00052      0.78      89     126 ..     113     150 ..     102     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.084
                                      -SSTTSSHHHHHHHHHHHHHTT CS
                              MipZ  7 nekGGsGksttavhvavaLlkk 28
                                        kGG+Gk+ ++  ++  L+kk
  gi|488601512|ref|YP_007907983.1|  7 TGKGGTGKTIISALLIHFLSKK 28
                                      569*****99998877766655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00052
                                       HHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEE CS
                              MipZ  89 leelvadleaeldfividtPGsdsalsrlahsladtlv 126
                                       l+ ++++l++++d++vidt    ++ sr + s ad ++
  gi|488601512|ref|YP_007907983.1| 113 LRGVLRKLMKHYDVVVIDTEAGLEHFSRGTISGADYIL 150
                                       6678999****************************753 PP

>> Arg_repressor_C  Arginine repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00017      0.25      40      67 ..     140     167 ..     125     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                       EEEEE-SSEEEEEE-TTS-HHHHHHHHH CS
                   Arg_repressor_C  40 lGtiAGdDTilvilrseedaeelaeklk 67 
                                        Gti G D ilv++    ++ + a+++k
  gi|488601512|ref|YP_007907983.1| 140 RGTISGADYILVVTDMSRKGLSTAKRIK 167
                                       5*****************9999999997 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         5   7.4e+03      58      73 ..      24      37 ..      11      41 .. 0.51
   2 ?   11.4   0.0    0.0002      0.29      42      95 ..     123     177 ..      52     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5
                                      HHHHHHSEEEEECSSS CS
                            Toprim 58 elakradeiilatDpD 73
                                       l+k++d   la D+D
  gi|488601512|ref|YP_007907983.1| 24 FLSKKYDL--LAVDAD 37
                                      34444544..444444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0002
                                       EEE.ECTTTHHHHHHHHHHH.HHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTE CS
                            Toprim  42 vye.eiedkkkvlkalkela.kradeiilatDpDreGeaiawellevlkellenki 95 
                                       +y+ ++ d++  l+ + +   + ad+i++ tD  r G  +a+++ e+  +l  n +
  gi|488601512|ref|YP_007907983.1| 123 HYDvVVIDTEAGLEHFSRGTiSGADYILVVTDMSRKGLSTAKRIKELSSDLKLN-F 177
                                       56666666666666666666699**********************877754444.4 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.027        40       3      28 ..       3      28 ..       1      37 [. 0.79
   2 ?    5.2   0.1    0.0096        14      79     139 ..     119     202 ..     108     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.027
                                      EEEEEESTTSSHHHHHHHHHHHHHHT CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                                       i++ G  G+GKT   a L + l+k+
  gi|488601512|ref|YP_007907983.1|  3 TIAVTGKGGTGKTIISALLIHFLSKK 28
                                      58899********9999999888776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0096
                                       HHHTTSSEEEEEE.--SSTTHHHHHHHHHHHHHHH......................SSSEEEEEEETTBHTHHHHH CS
                             SRP54  79 akeekidvvlvDT.aGrlqndkelmeelkkikkvv......................kpdevllvldattgqeavkq 132
                                       +  +++dvv++DT aG  +  +  ++  + i  v+                      + ++++lv + ++ ++ ++ 
  gi|488601512|ref|YP_007907983.1| 119 KLMKHYDVVVIDTeAGLEHFSRGTISGADYILVVTdmsrkglstakrikelssdlklNFKKIYLVGNRIMNEDGAEV 195
                                       55678999999998898888888888888777777777777777777777777777777778888888888888888 PP

                                       HHHHHHH CS
                             SRP54 133 akaFkea 139
                                       +k+F+++
  gi|488601512|ref|YP_007907983.1| 196 IKKFADE 202
                                       8888766 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   0.3     0.014        21      16      41 ..       4      29 ..       1      34 [. 0.86
   2 ?    4.3   0.0     0.016        24     134     218 ..     120     203 ..     113     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                           Pox_A32 16 lalvGgsGsGktvyLlsLlrtlvkky 41
                                      +a++G+ G Gkt+    L++ l kky
  gi|488601512|ref|YP_007907983.1|  4 IAVTGKGGTGKTIISALLIHFLSKKY 29
                                      899**********9998998888888 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                           Pox_A32 134 Lcqtykhvpvngrasithlvcinvsssdienllrsmslkgskkkllkvlnilrsaeqkkrkvliiedsvfsegeari 210
                                       L++ y  v + + a + h+    +s +d  +++  ms kg      ++ ++  + + + +k++++ + ++ e+ a +
  gi|488601512|ref|YP_007907983.1| 120 LMKHYDVVVIDTEAGLEHFSRGTISGADYILVVTDMSRKGLST-AKRIKELSSDLKLNFKKIYLVGNRIMNEDGAEV 195
                                       5677778888999999999999999999999999999886544.333334555666788999999999999999999 PP

                           Pox_A32 211 CldsaDes 218
                                         ++aDe+
  gi|488601512|ref|YP_007907983.1| 196 IKKFADEE 203
                                       99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 1547.37
//
Query:       gi|488601513|ref|YP_007907984.1|  [L=520]
Description: acetyl-CoA decarbonylase/synthase beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-61  205.9   0.1    4.7e-61  205.2   0.1    1.3  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 !  205.2   0.1   2.6e-65   4.7e-61       1     154 [.      24     177 ..      24     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 2.6e-65
                              CdhC   1 ipvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkle 77 
                                       +p+++sp++eGeriRk+++yvelgg+++++fElv++ +a+eved k++v+Gpd++e+eeg+++p+a+++ vaG+++e
  gi|488601513|ref|YP_007907984.1|  24 FPFDISPMYEGERIRKKEMYVELGGTEQPGFELVMALPAEEVEDMKVTVVGPDLNEMEEGKAYPYAMIYYVAGSQVE 100
                                       699************************************************************************** PP

                              CdhC  78 edlEpvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGl.rlkhigevlyaklkeefeaivdkvevtlitdee 153
                                       +dlEpv+ERr+H+f+ny+eG+mHl+qR++iw+Ri+k a++kGl ++ +i+++ ++++k+e+ ++++k+e  +itd+e
  gi|488601513|ref|YP_007907984.1| 101 TDLEPVIERRNHDFQNYLEGYMHLNQRYDIWIRIGKGAIKKGLnSFVQIAKATMMLFKNEL-PFIEKIEAVYITDAE 176
                                       *******************************************99****************.*************98 PP

                              CdhC 154 k 154
                                        
  gi|488601513|ref|YP_007907984.1| 177 L 177
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); 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: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.52
# Mc/sec: 3030.38
//
Query:       gi|488601514|ref|YP_007907985.1|  [L=176]
Description: acetyl-CoA decarbonylase/synthase epsilon subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  205.2   0.0    6.3e-61  205.0   0.0    1.0  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
    5.7e-05   22.9   0.0    0.00057   19.6   0.0    2.1  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 !  205.0   0.0   7.1e-65   6.3e-61       2     168 .]       3     173 ..       2     173 .. 0.97

  Alignments for each domain:
  == domain 1  score: 205.0 bits;  conditional E-value: 7.1e-65
                                       XXXXXXXXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET.....HHH CS
                             CO_dh   2 klekiPfdeaaianskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata.....lke 73 
                                       k+ ++Pfd a+i+++k+atl+e++k+va+mik+akrPllivGp++ ++  +++++  ++ek +++vat+     + e
  gi|488601514|ref|YP_007907985.1|   3 KAFEQPFDAANIPGPKMATLLEKGKPVANMIKRAKRPLLIVGPDM-TDA-MFERVLRFAEKGMTIVATGsaitrFVE 77 
                                       56789****************************************.666.8************************** PP

                                       TT-G..GGSE.-HHHHHHHHHSTT--TTTSS---SEEEEES--HHHHHHHHHHHHHH-TT-EEEE-SSS--TTSSEE CS
                             CO_dh  74 aglkdyekkn.klveltkllkdpepkgfdgegeydlvlfiGviyYyasqalsslkkftdkittiaidkyyhpdAdvs 149
                                       ag k  + k+ +l+elt++l dpe+kg dg+g+ydlvl++G iyY++sq+l+++k+f+++i+++aid+yyhp+A +s
  gi|488601514|ref|YP_007907985.1|  78 AGYKGNNVKYaVLHELTQFLLDPEWKGLDGNGNYDLVLMLGTIYYHGSQMLAAIKNFAPHIRALAIDRYYHPNAAMS 154
                                       ****99999989***************************************************************** PP

                                       E---GGGHHHHHHHHHHHH CS
                             CO_dh 150 lanlskeeeeylemleell 168
                                       ++nl+k+ee+yl++l+e+l
  gi|488601514|ref|YP_007907985.1| 155 FGNLWKKEEDYLKLLDEIL 173
                                       *****************86 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.4e-08   0.00057       4      90 ..      29     123 ..      27     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.4e-08
                                       HHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTE.EEESGGGS.....CHHHHHH CS
                      TPP_enzyme_M   4 aaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhply.lgmlglhg.....skaanea 74 
                                       +a+++k+akrp+++vG  +  +   e + ++aek    v+t  +   +++   + + + ++ lh       ++  + 
  gi|488601514|ref|YP_007907985.1|  29 VANMIKRAKRPLLIVGPDMT-DAMFERVLRFAEKGMTIVATGSAITRFVEAGYKGNnVKYAVLHEltqflLDPEWKG 104
                                       89*****************9.88999*******98888887777777777655444333444433333334444444 PP

                                       HHH...-SEEEEES-SSST CS
                      TPP_enzyme_M  75 lee...aDlvlalGarfdd 90 
                                       l+     Dlvl+lG+ +  
  gi|488601514|ref|YP_007907985.1| 105 LDGngnYDLVLMLGTIYYH 123
                                       4323337888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 975.13
//
Query:       gi|488601515|ref|YP_007907986.1|  [L=800]
Description: acetyl-CoA decarbonylase/synthase alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-115  385.3   8.5     3e-113  379.2   8.5    2.0  1  Prismane  Prismane/CO dehydrogenase family
    7.3e-08   32.8  21.4    1.5e-06   28.7  12.0    3.2  2  Fer4_17   4Fe-4S dicluster domain
    7.3e-08   32.9  10.1    7.3e-08   32.9  10.1    2.1  1  Fer4_7    4Fe-4S dicluster domain
    7.5e-08   32.7  12.1    0.00017   22.0   0.0    3.2  2  Fer4_8    4Fe-4S dicluster domain
    3.4e-07   30.3  11.6    3.4e-07   30.3  11.6    2.8  2  Fer4_9    4Fe-4S dicluster domain
    5.4e-07   29.6  22.7    3.2e-06   27.2  13.1    3.1  2  Fer4_10   4Fe-4S dicluster domain
    2.4e-05   23.9  14.0    4.5e-05   23.1   2.8    3.6  2  Fer4      4Fe-4S binding domain
      5e-05   23.5  13.9      0.062   13.8   5.1    3.0  2  Fer4_4    4Fe-4S binding domain
    6.6e-05   23.0   9.8    6.6e-05   23.0   9.8    2.4  1  Fer4_21   4Fe-4S dicluster domain
    0.00042   20.5   8.3      0.096   12.9   1.3    2.6  2  Fer4_18   4Fe-4S dicluster domain
    0.00069   19.6  10.9     0.0019   18.2   1.3    3.7  2  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.021   14.9   2.7      0.021   14.9   2.7    3.1  2  Fer4_6    4Fe-4S binding domain
      0.023   15.5  13.3      0.098   13.5   2.0    2.9  2  Fer4_22   4Fe-4S dicluster domain
      0.033   15.1  18.1       0.42   11.6   3.2    3.2  3  Fer4_16   4Fe-4S double cluster binding domain
       0.91   10.1  11.4        5.2    7.7   2.9    2.9  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        7.1    7.8  34.2      0.051   14.5   4.3    4.0  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.2   8.5  2.7e-116    3e-113       2     511 .]      69     683 ..      68     683 .. 0.91

  Alignments for each domain:
  == domain 1  score: 379.2 bits;  conditional E-value: 2.7e-116
                                       EE-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHTSTTTB-SHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane   2 fCrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaahareladtliakalfktltnvnfddekklkrl 78 
                                       +C++C++g+C++t+nkrG+CG+d ++++ r ++ia+++g+a+h+ har++            l++++++  kkl+++
  gi|488601515|ref|YP_007907986.1|  69 MCCLCTMGKCDLTGNKRGACGIDLAAQTGRIVTIACAMGTACHTGHARHM------------LHDIEHMLGKKLDEI 133
                                       799***********************************************............88999999999**** PP

                                       HHHHCHHHCCSSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane  79 aealgieeelkdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlgyadeevveflaktlagle 155
                                         +lg e  +       a+va      l       ++++++++pk+l +l    +++l+ya+e++v++++++++g+e
  gi|488601515|ref|YP_007907986.1| 134 PVDLGPE--I-------AEVAP-----L-------TELITGIKPKTLADL----ERALRYAEEQIVQVMDSVHTGQE 185
                                       ****966..3.......22332.....2.......46899**********....*********************** PP

                                       STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---....--EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 156 sdpldllskalrlGlldlkgmelldeantslfGtP....eppltevnlgvldkdkvnIlvsGHdladleelleqteg 228
                                       +++ld++skal+lG++d  g e++d+a++++fG+P    ++p +ev++gvld++k ++lv+GH++  + ++++++ +
  gi|488601515|ref|YP_007907986.1| 186 GSYLDYESKALHLGMIDALGKEIADIAQICAFGFPkgesNQPYIEVGMGVLDRSKAVVLVIGHHAPPAIDIADYIDE 262
                                       *************************************99778*********************************** PP

                                       TCCCCCCCGCCCCCCHHHHHH.HHHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 229 kglnvythgemLpghcctalk.lkyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittse 304
                                       ++l ++++   L g+ccta + ++y + +++vG++ +q ka+++g++d+iv+d++Ci++++  +++k+++++i+t+e
  gi|488601515|ref|YP_007907986.1| 263 NNLGDEVD---LGGICCTAHDvTRYYQKAKIVGSLGRQLKAIRAGIADVIVIDEQCIRADILYHTKKLGIPVICTNE 336
                                       ********...****************************************************************** PP

                                       TB-...TTSEEE--CTTC..H...........HHHHHHHHHHHCCHCCTTCGG.-...................... CS
                                       xxx...xxxxxxxxxxxx..x...........xxxxxxxxxxxxxxxxxxxxxxx...................... RF
                          Prismane 305 vak...pgakhieeeeka..d...........kdaseiiekAielakareekkve...................... 343
                                       +a+   p++++ +  +k   +            d  ++ e+A+e+a+ar++ + +                      
  gi|488601515|ref|YP_007907986.1| 337 KAMhalPDMTKAD--PKDiiKylldgnpgvviLDPLKVGEVAVEVARARRKMRGDgispvlsdeefanyvksctqcg 411
                                       ***8888888887..2222414455667777799999**********998866669999999999999999999999 PP

                                       ..................................................HHH........................ CS
                                       ..................................................xxx........................ RF
                          Prismane 344 ..................................................ida........................ 346
                                                                                         i                          
  gi|488601515|ref|YP_007907986.1| 412 nctiacpqgirigdameaaengdksklehewdiciacgrceqvcpknipiI-Dvlnyaawdrlinekgkvrrsrgpv 487
                                       999888888888888777777666666666666666666555555555552.0577788888888888889999999 PP

                                       ...........HHTTSS-EEEEE-B---TTCGCCHHHHHHHHCHHTTEEEEEECHHHHHC...CCTTTTEC...GHH CS
                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx...xxx RF
                          Prismane 347 ...........iksGtIkgvvlvvGCdnakkgrdyytelakelikrdvlvltaGCakyal...nklglgti...eaa 406
                                                  i+ GtI+g++++vGC+n+++g+++ +++++e++ r+++v+t+GC+++++   ++++++t+   + +
  gi|488601515|ref|YP_007907986.1| 488 rdseirnvgapIVLGTIPGIIAIVGCSNYPNGTKDAYTIMDEFASRNYIVVTTGCMAMDAglyKDEDGLTVyekYND 564
                                       99999999999************************************************99999*****99999999 PP

                                       HHSTHCEESEEEEESCCCHHHHHHHHHHHHHHT.......TS.SGGGSSE...EEEECC-..-SHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xx.xxxxxxx...xxxxxxx..xxxxxxxxxxxxxxx RF
                          Prismane 407 elagegiPrvLdvGsCvdnyrivvialklaeal.......gv.dindLpl...aalalew..yeqKAvailltllal 470
                                       +++g g   v ++GsCv+n++i+++a+k+a+++       +  +i+d++l   +a+ ++w  y+qKA++i++++++l
  gi|488601515|ref|YP_007907986.1| 565 DFDG-G--CVANLGSCVANAHIHGAAIKVARIFakrniraNFeEIADYILnrlGACGVAWgaYSQKAASIATGVNRL 638
                                       9***.6..7******************************9888********************************** PP

                                       T-CEEECSS-TTTT-HHHHHHHHCH....HHHHHCEEEECHCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx RF
                          Prismane 471 Ginihlgptlpafgspnvlkvlved....fedriggivtveedpe 511
                                       Gi++++gp++++++++++ + ++++    ++ r+g++v++e++p+
  gi|488601515|ref|YP_007907986.1| 639 GIPVVVGPHGSKYRRAFLGRPYNDEdwmvYDVRTGKQVRIEPAPQ 683
                                       *****************************999*********9985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.8     2e-06    0.0023      37      60 ..     398     421 ..     377     422 .. 0.76
   2 !   28.7  12.0   1.3e-09   1.5e-06       2      60 ..     407     459 ..     406     460 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                           Fer4_17  37 aekeekaslCieCgeCerkCPqgl 60 
                                       +e  +++++C++Cg+C+ +CPqg+
  gi|488601515|ref|YP_007907986.1| 398 EEFANYVKSCTQCGNCTIACPQGI 421
                                       3445799***************97 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1.3e-09
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                       C+qCg C+ +Cp+++++++     ++aa++g++ +   e++++ Ci Cg+Ce++CP+++
  gi|488601515|ref|YP_007907986.1| 407 CTQCGNCTIACPQGIRIGD----AMEAAENGDKSK--LEHEWDICIACGRCEQVCPKNI 459
                                       ******************9....899988886666..599*****************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9  10.1   6.5e-11   7.3e-08       1      52 []     406     459 ..     406     459 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 6.5e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek..gtekveidpekClgCgaCvavCPtga 52 
                                       +C++Cg+C+ aCp++ +  d  e ++   + k+e++ + C+ Cg+C++vCP+++
  gi|488601515|ref|YP_007907986.1| 406 SCTQCGNCTIACPQGIRIGDAMEAAEngDKSKLEHEWDICIACGRCEQVCPKNI 459
                                       5************9888777543333115588999999*************985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.5e-07   0.00017      44      65 .]     390     421 ..     337     421 .. 0.78
   2 !   18.0   0.9   2.6e-06    0.0029      38      65 .]     432     459 ..     422     459 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.5e-07
                            Fer4_8  44 e..........eealwsCttcgaCtevCpvgi 65 
                                       +          +++++sCt+cg+Ct +Cp+gi
  gi|488601515|ref|YP_007907986.1| 390 GispvlsdeefANYVKSCTQCGNCTIACPQGI 421
                                       14444455566899***************997 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.6e-06
                            Fer4_8  38 eeqvleeeealwsCttcgaCtevCpvgi 65 
                                       + ++ + e+ ++ C +cg+C++vCp++i
  gi|488601515|ref|YP_007907986.1| 432 NGDKSKLEHEWDICIACGRCEQVCPKNI 459
                                       3333333788999*************97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   4.3       7.6   8.5e+03       2      22 ..      67      93 ..      43     113 .. 0.63
   2 !   30.3  11.6   3.1e-10   3.4e-07       2      49 ..     407     458 ..     406     460 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.6
                            Fer4_9  2 CtgCgaC.veaC.....pagvvvedaa 22
                                      C  C  C + +C     + g++  d a
  gi|488601515|ref|YP_007907986.1| 67 CDMCCLCtMGKCdltgnKRGACGIDLA 93
                                      555555533336555554444454444 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 3.1e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkg 49 
                                       Ct+Cg+C+ aCp+g+ ++da e   + ++ +     + Ci Cg+C+++Cpk+
  gi|488601515|ref|YP_007907986.1| 407 CTQCGNCTIACPQGIRIGDAMEAAENGDKSKLehewDICIACGRCEQVCPKN 458
                                       *****************999999999888777999878************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 !   27.2  13.1   2.8e-09   3.2e-06       7      56 .]     405     456 ..     401     456 .. 0.78
   2 !   16.8   2.0   4.9e-06    0.0054       5      27 ..     441     464 ..     437     487 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.8e-09
                           Fer4_10   7 dtCirCgkCvkaCPadl.tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                       ++C++Cg+C+ aCP+ +  ++  ++++++++ + +   + C++cg C ++CP
  gi|488601515|ref|YP_007907986.1| 405 KSCTQCGNCTIACPQGIrIGDAMEAAENGDKSKLEhEWDICIACGRCEQVCP 456
                                       78*************9975555555555555444438888***********9 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.9e-06
                           Fer4_10   5 dddtCirCgkCvkaCPadl.tsvg 27 
                                       + d Ci Cg+C ++CP ++   ++
  gi|488601515|ref|YP_007907986.1| 441 EWDICIACGRCEQVCPKNIpIIDV 464
                                       6689************97773333 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.5   1.2e-05     0.013       7      22 ..     406     421 ..     404     423 .. 0.90
   2 !   23.1   2.8     4e-08   4.5e-05       4      22 ..     441     459 ..     438     461 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                       TSSS-THHHHHSTTTE CS
                              Fer4   7 kCigCGaCvevCPvgA 22 
                                        C+ CG+C  +CP g 
  gi|488601515|ref|YP_007907986.1| 406 SCTQCGNCTIACPQGI 421
                                       6************985 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 4e-08
                                       ETTTSSS-THHHHHSTTTE CS
                              Fer4   4 deekCigCGaCvevCPvgA 22 
                                        ++ Ci+CG+C++vCP + 
  gi|488601515|ref|YP_007907986.1| 441 EWDICIACGRCEQVCPKNI 459
                                       5799************986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   5.1   5.5e-05     0.062       2      17 .]     405     420 ..     405     420 .. 0.92
   2 !   13.3   1.5     8e-05      0.09       3      16 ..     444     457 ..     440     464 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-05
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       ++C++Cg C++aCPqg
  gi|488601515|ref|YP_007907986.1| 405 KSCTQCGNCTIACPQG 420
                                       58************96 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        Ci Cg+C+ +CP 
  gi|488601515|ref|YP_007907986.1| 444 ICIACGRCEQVCPK 457
                                       4************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   9.8   5.9e-08   6.6e-05       7      52 ..     406     456 ..     403     462 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.9e-08
                           Fer4_21   7 kCigCgkCliaCedt.....shqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       +C +Cg+C+iaC+++     +++a e  +k++l++  d C++C  C +vCP
  gi|488601515|ref|YP_007907986.1| 406 SCTQCGNCTIACPQGirigdAMEAAENGDKSKLEHEWDICIACGRCEQVCP 456
                                       7************7522222344445556667788899************* PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.9   0.00025      0.28      51      81 ..     397     427 ..     364     432 .. 0.78
   2 !   12.9   1.3   8.6e-05     0.096      51      82 ..     435     466 ..     425     471 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                           Fer4_18  51 eerkekgagdcidcescvkvcPtgidirkGl 81 
                                       +e+ ++ +  c++c+ c   cP gi i + +
  gi|488601515|ref|YP_007907986.1| 397 DEEFANYVKSCTQCGNCTIACPQGIRIGDAM 427
                                       4445677889***************998876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.6e-05
                           Fer4_18  51 eerkekgagdcidcescvkvcPtgidirkGlq 82 
                                       +++ e++   ci+c+ c +vcP +i i + l 
  gi|488601515|ref|YP_007907986.1| 435 KSKLEHEWDICIACGRCEQVCPKNIPIIDVLN 466
                                       4445566677***************9988766 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.6   1.5e-05     0.017       9      22 .]     406     419 ..     398     419 .. 0.88
   2 !   18.2   1.3   1.7e-06    0.0019       6      21 ..     441     456 ..     437     457 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                            Fer4_2   9 rCigCgaCvsaCPa 22 
                                       +C++Cg C+ aCP+
  gi|488601515|ref|YP_007907986.1| 406 SCTQCGNCTIACPQ 419
                                       7************6 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.7e-06
                            Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                       + d+Ci+Cg C ++CP
  gi|488601515|ref|YP_007907986.1| 441 EWDICIACGRCEQVCP 456
                                       5699***********9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.7   1.8e-05     0.021       8      22 ..     406     420 ..     405     425 .. 0.91
   2 ?   13.8   5.0   4.1e-05     0.046       7      22 ..     443     458 ..     443     461 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                            Fer4_6   8 kCigCgdCvrvCPeg 22 
                                       +C++Cg+C+++CP g
  gi|488601515|ref|YP_007907986.1| 406 SCTQCGNCTIACPQG 420
                                       7************65 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.1e-05
                            Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                       d Ci Cg+C+ vCP +
  gi|488601515|ref|YP_007907986.1| 443 DICIACGRCEQVCPKN 458
                                       78************87 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.0    0.0061       6.8       2      40 ..     407     445 ..     406     445 .. 0.78
   2 ?   13.5   2.0   8.8e-05     0.098      76      96 .]     439     459 ..     427     459 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0061
                           Fer4_22   2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsC 40 
                                       C +Cg+Ct++Cp  + +    e++e+ ++++  + wd C
  gi|488601515|ref|YP_007907986.1| 407 CTQCGNCTIACPQGIRIGDAMEAAENGDKSKLEHEWDIC 445
                                       ************987665555556677888888888888 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.8e-05
                           Fer4_22  76 kfgesgCvGCgRCieacpvki 96 
                                       +++   C+ CgRC+++cp++i
  gi|488601515|ref|YP_007907986.1| 439 EHEWDICIACGRCEQVCPKNI 459
                                       567789************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 ?   -2.4   0.1       8.4   9.4e+03      53      60 ..      63      70 ..      25      74 .. 0.69
   2 ?    9.7  15.4    0.0015       1.6       2      67 .]     407     458 ..     406     458 .. 0.69
   3 ?   11.6   3.2   0.00037      0.42       2      16 ..     445     459 ..     444     492 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.4
                           Fer4_16 53 aitgCdiC 60
                                         +Cd+C
  gi|488601515|ref|YP_007907986.1| 63 YAPYCDMC 70
                                      44567777 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPan 67 
                                       C++Cg+C+ +CP++   ++    +ea e+ +     k +l+++         ++ C++C++vCP n
  gi|488601515|ref|YP_007907986.1| 407 CTQCGNCTIACPQGIRIGD---AMEAAENGD-----KSKLEHE------WDICIACGRCEQVCPKN 458
                                       ************9987777...445444422.....2222222......23478**********87 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00037
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C+ Cg+C +vCP n 
  gi|488601515|ref|YP_007907986.1| 445 CIACGRCEQVCPKNI 459
                                       999*********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 ?    6.3   1.4     0.013        14       5      18 ..     406     419 ..     404     434 .. 0.89
   2 ?    7.7   2.9    0.0047       5.2       5      18 ..     444     457 ..     441     459 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                       +C+ cg+C  ++P+
  gi|488601515|ref|YP_007907986.1| 406 SCTQCGNCTIACPQ 419
                                       7************7 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                        Ciacg C +++P+
  gi|488601515|ref|YP_007907986.1| 444 ICIACGRCEQVCPK 457
                                       6************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 ?    9.1   4.9    0.0024       2.7       1      14 [.     407     420 ..     407     421 .. 0.94
   2 ?   14.5   4.3   4.5e-05     0.051       1      14 [.     445     458 ..     445     459 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       Ct+Cg C  +CP g
  gi|488601515|ref|YP_007907986.1| 407 CTQCGNCTIACPQG 420
                                       ************98 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.5e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ Cg+C++vCP++
  gi|488601515|ref|YP_007907986.1| 445 CIACGRCEQVCPKN 458
                                       9***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (800 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.84u 0.38s 00:00:01.22 Elapsed: 00:00:00.55
# Mc/sec: 4403.54
//
Query:       gi|488601516|ref|YP_007907987.1|  [L=278]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-68  228.0   0.2      1e-67  227.7   0.2    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.7   0.2   5.6e-72     1e-67       4     204 ..      66     265 ..      63     266 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 5.6e-72
                                       --SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS-- CS
                    tRNA_deacylase   4 dvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPt 80 
                                       d+++iif+SrH+s++g++++TvHv+Gn+g+a++GGkp +la++aP ++k+++ al++  ++l+ef++tlE+tHHGP+
  gi|488601516|ref|YP_007907987.1|  66 DFNEIIFASRHRSADGRKIFTVHVSGNIGTADFGGKPYSLAKPAPITIKNYVLALNERIDQLPEFSFTLEVTHHGPS 142
                                       789************************************************************************** PP

                                       ---S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGG CS
                    tRNA_deacylase  81 elkvPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskyal 157
                                       e+k+Ps+F EiGS eeeWk+eda+++vae++++++++e+++++v++ +GG+HYapr+t+++l+t++++Gh ++ky++
  gi|488601516|ref|YP_007907987.1| 143 EIKTPSAFYEIGSGEEEWKNEDAGRIVAESIVSAINDERKSWDVAISVGGTHYAPRQTEIILNTTFTFGHSFAKYTF 219
                                       ***************************************************************************** PP

                                       GG--HHHHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 158 eelkeevikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                       ++l++e i +ale + ++d ++id+ks++s+ k ++ e+ e  g ev
  gi|488601516|ref|YP_007907987.1| 220 DHLNKEFIIKALEVT-ETDKIVIDEKSTTSKIKGMLVEVSEAVGAEV 265
                                       ***************.**************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1688.82
//
Query:       gi|488601517|ref|YP_007907988.1|  [L=290]
Description: methionine aminopeptidase, type II [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-39  136.0   0.1    1.6e-39  135.8   0.1    1.1  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.037   13.9   0.0    1.4  1  MLIP           Muscular LMNA-interacting protein


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.1   1.7e-43   1.6e-39       4     209 .]      11     283 ..       8     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 1.7e-43
                                       HHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTEEE CS
                     Peptidase_M24   4 rkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegdlv 77 
                                        +a++i + + e+v+  +kpgv+  e+a+++e++  +r+ ++++afp  + +++n++++h+tp   ++r+++egd+v
  gi|488601517|ref|YP_007907988.1|  11 IEAGKILKTVKEEVKPLVKPGVKLLEVAEFVENR--IRELGGEPAFP--CNISINSDAAHFTPkkgDTREFNEGDIV 83 
                                       589***********999***************98..778889*****..9999999999****8866777******* PP

                                       EEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSE CS
                     Peptidase_M24  78 lidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglG 154
                                       ++d+ga+++g ++D++ T+ +G  ++  ++l++a ++a+++ai+++ +Gv+++ i+++++  +++ g+ +++ +++G
  gi|488601517|ref|YP_007907988.1|  84 KLDIGAHIEGIIADTAITIDLG--DN--DDLVKASENALKRAIEEIHAGVDTAVIGRVIESEIREFGF-RPVVNLTG 155
                                       ********************99..44..67**************************************.999***** PP

                                       EEESS.SSSEEEEEESS.STTCSSB--TTBEEEEEE......EEEEETTT........................... CS
                     Peptidase_M24 155 HgvGl.evhdegpsvsr.esndgrkleeGmvftiEp......giyfapge........................... 196
                                       Hg+     h   ps+ +  + +g+kleeGmv++iEp      g      +                           
  gi|488601517|ref|YP_007907988.1| 156 HGLLPyIAHAP-PSILNyGTERGVKLEEGMVIAIEPfatdgaG------Kvgergeteifslkairpvrmkkakall 225
                                       ****9677876.9975425559**************6666442......1222344777777888888888888888 PP

                                       ............................................E.EEEEBEEEEEES CS
                     Peptidase_M24 197 ............................................g.gvriedtvlvte 209
                                                                                   g + + e+tv+v e
  gi|488601517|ref|YP_007907988.1| 226 keiekyktlpfakrwlenasdivigqlvragvlrgypvlteiakGlVSQAEHTVIVEE 283
                                       8888888888888999999999999999999999999999999988999999999975 PP

>> MLIP  Muscular LMNA-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-06     0.037     215     252 .]     212     251 ..     202     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-06
                              MLIP 215 virpvlvk.griaqqkeevyqpnpfkk.yleeisdqdieq 252
                                        irpv +k ++++++  e y+  pf k +le+ sd  i q
  gi|488601517|ref|YP_007907988.1| 212 AIRPVRMKkAKALLKEIEKYKTLPFAKrWLENASDIVIGQ 251
                                       69***987255566667********6549******98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1540.39
//
Query:       gi|488601518|ref|YP_007907989.1|  [L=467]
Description: Acetyl-CoA hydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-57  194.0   0.0    4.2e-57  193.3   0.0    1.3  1  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    9.1e-57  191.3   0.0    1.5e-56  190.6   0.0    1.4  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    0.00079   18.9   0.5       0.37   10.2   0.2    2.5  2  CoA_trans        Coenzyme A transferase
     0.0056   15.6   0.0      0.015   14.2   0.0    1.6  2  CitF             Citrate lyase, alpha subunit (CitF)
  ------ inclusion threshold ------
      0.079   12.9   0.0        6.6    6.7   0.0    2.9  3  DeoRC            DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> 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 !  193.3   0.0   1.2e-60   4.2e-57       1     198 []       2     192 ..       2     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 1.2e-60
                   AcetylCoA_hydro   1 rqeeyekklkepeeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevle 77 
                                       +++ey kkl+++eeaa lv++g++iel+g  av+ta++i+kylakrk+e  +vk++++id+  +++l ++P  e ++
  gi|488601518|ref|YP_007907989.1|   2 YKDEYDKKLISAEEAAGLVEDGMWIELGG--AVNTALIIDKYLAKRKDEFTEVKVGTFIDISSYEMLRVDPDREIFK 76 
                                       6789*************************..********************************************** PP

                   AcetylCoA_hydro  78 ekdavlyrpapkqvgellrkainqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKvii 154
                                       + +++l  p++ ++ +l+ ++++++l+++v+ +++ev     k  + iD+ ++  t++d++Gy+n+G+++++ K+++
  gi|488601518|ref|YP_007907989.1|  77 WTSGFLLAPVRECSRNLGVCVFKPNLYHDVPRIAREVF----K--DKIDIVFLPVTPMDKNGYFNFGLTCSHLKALA 147
                                       ************************************98....3..359***************************** PP

                   AcetylCoA_hydro 155 EvaelvvivvkknpPrvng.ydelialdkvdyivvdpekvvavve 198
                                       E a++vv  vk+++P++ g yde+i++++ dyiv+d e+++++++
  gi|488601518|ref|YP_007907989.1| 148 ESAKKVVLIVKEDMPWIYGgYDEIIHISEADYIVEDKEFPTPFLP 192
                                       ******************99***********************87 PP

>> 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 !  190.6   0.0   4.2e-60   1.5e-56       1     154 []     282     442 ..     282     442 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.6 bits;  conditional E-value: 4.2e-60
                                       S-HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECT.......TCCTCGGTTHHHHH CS
                   AcetylCoA_hyd_C   1 GskklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslg.......grvvsGvGgqldFv 70 
                                       G+k+ly++ld+np+++++pv+y+ndp++i+q++k++sin a+++dl+Gqvnse++g         +vsG+GgqldFv
  gi|488601518|ref|YP_007907989.1| 282 GTKNLYEYLDRNPSVATYPVDYTNDPFIISQQPKMFSINGAAQIDLMGQVNSEQMGlrtptckLFQVSGTGGQLDFV 358
                                       99*****************************************************96666655559*********** PP

                                       HHHHHSTT..-EEEEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHTTS-HH CS
                   AcetylCoA_hyd_C  71 rgaalskg..gksiialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealikiAhpd 145
                                       +g+  s++  gksi+ l+St+ kg+ SrI+p+l++ga+vt++r++++yvvTE+G+a+Lrg s++era ali++Ahpd
  gi|488601518|ref|YP_007907989.1| 359 MGCLFSRDrkGKSILGLYSTY-KGD-SRILPVLDKGAAVTVPRSMTQYVVTEWGVAYLRGYSVKERALALIRLAHPD 433
                                       ******7777***********.555.9************************************************** PP

                                       HHHHHHHHH CS
                   AcetylCoA_hyd_C 146 freeLleea 154
                                       +r++L+eea
  gi|488601518|ref|YP_007907989.1| 434 HRDWLVEEA 442
                                       ******997 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0015       5.3       3      56 ..      12      60 ..      10      70 .. 0.76
   2 !   10.2   0.2    0.0001      0.37      11      63 ..     213     261 ..     203     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0015
                                      HHHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEEEEESTTTE.ECC CS
                         CoA_trans  3 taaeavakeikdGmtvavGGFgligiPealiaalarsgvkdltviiseagv.lgl 56
                                      +a+ea+   ++dGm + +G  g+++++  +i++++ +  +++ +   + g+ +++
  gi|488601518|ref|YP_007907989.1| 12 SAEEAAG-LVEDGMWIELG--GAVNTA-LIIDKYLAK--RKDEFTEVKVGTfIDI 60
                                      6788888.***********..788888.999999998..5555555555554555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0001
                                       T--TTEEEEE-SBTTBT.HHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTT CS
                         CoA_trans  11 eikdGmtvavGGFglig.iPealiaalarsgvkdltviiseagvlglgplllng 63 
                                        ++dGmtv vG    ig +P + ++ + +sgvkdl + + + g  g+  l+ +g
  gi|488601518|ref|YP_007907989.1| 213 LLEDGMTVQVG----IGgMPDSVVKIMKESGVKDLGIHTEMMGD-GILELINEG 261
                                       699********....666**999999999999998666655555.666666555 PP

>> CitF  Citrate lyase, alpha subunit (CitF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.2e-06     0.015     117     260 ..     117     249 ..     111     273 .. 0.72
   2 ?   -2.7   0.0      0.55     2e+03     375     403 ..     384     412 ..     380     415 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-06
                              CitF 117 kidvaflGvpsadefGnanGlkGkakcGslGyalvdaeyadkvvllteelveypntpisikqdqvdlvvkvdavGdp 193
                                       kid+ fl v   d+ G  n      +c  l   +  ae a+kvvl+ +e +++         d++  + + d + + 
  gi|488601518|ref|YP_007907989.1| 117 KIDIVFLPVTPMDKNGYFNFGL---TCSHL---KALAESAKKVVLIVKEDMPWIY----GGYDEIIHISEADYIVED 183
                                       5778888777777777666322...23333...3448999999999888776533....234555555555555566 PP

                              CitF 194 kkigagatrltknpkelliakkaaevivnsgyfkeGfslqtGtGGaslavtrflrekmike.nikasf 260
                                       k+  +    +t  p+e    k++ae i+++g +++G+++q G GG   +v ++++e+ +k+  i++++
  gi|488601518|ref|YP_007907989.1| 184 KEFPTPFLPFTMPPNEE--DKMIAENIFEAGLLEDGMTVQVGIGGMPDSVVKIMKESGVKDlGIHTEM 249
                                       77777788999999996..6999********************************9866531455555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.55
                              CitF 375 riptvveevttvitpGesvdvlvtdvGia 403
                                       ri  v+++  +v  p +  + +vt+ G+a
  gi|488601518|ref|YP_007907989.1| 384 RILPVLDKGAAVTVPRSMTQYVVTEWGVA 412
                                       88889999999999*9999*******998 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0018       6.6       3      42 ..       6      46 ..       4      75 .. 0.76
   2 ?    2.3   0.0     0.039   1.4e+02      92     159 ..     117     183 ..     108     184 .. 0.72
   3 ?   -0.5   0.0      0.29     1e+03      14      42 ..     211     239 ..     198     251 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0018
                             DeoRC  3 aeeKrrIAkaAaeliedgdtifldaGt.TtlelaraLaekk 42
                                      +++K   A++Aa l+edg+ i l++   T+l + ++La++k
  gi|488601518|ref|YP_007907989.1|  6 YDKKLISAEEAAGLVEDGMWIELGGAVnTALIIDKYLAKRK 46
                                      56677779***************987615555556777776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.039
                             DeoRC  92 nvdkaflgangidaegglttsdeeeaevkralieaarrvillaDss.KfgkrafvriaaleeidalitD 159
                                       ++d++fl ++ +d+ +g +++ +    +k al+e+a++v+l++ ++  +   +  +i++++e d+++ D
  gi|488601518|ref|YP_007907989.1| 117 KIDIVFLPVTPMDK-NGYFNFGLTCSHLK-ALAESAKKVVLIVKEDmPWIYGGYDEIIHISEADYIVED 183
                                       68999999999998.69999999777765.788999999988765413445555556666666666665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.29
                             DeoRC  14 aeliedgdtifldaGtTtlelaraLaekk 42 
                                       a l+edg+t+ +++G     +++ ++e+ 
  gi|488601518|ref|YP_007907989.1| 211 AGLLEDGMTVQVGIGGMPDSVVKIMKESG 239
                                       6799***********99999998888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2715.72
//
Query:       gi|488601519|ref|YP_007907990.1|  [L=477]
Description: hypothetical protein Asulf_02033 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-169  562.4   0.1   7.9e-169  562.2   0.1    1.1  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 !  562.2   0.1  4.4e-173  7.9e-169       1     412 []      46     477 .]      46     477 .] 0.99

  Alignments for each domain:
  == domain 1  score: 562.2 bits;  conditional E-value: 4.4e-173
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       q++nva++pgi+ ++++mPDvH+G+g+piG+V+ ++   gv++P++VG+DI CGvr+l+ nlt +e+++k+kel++e
  gi|488601519|ref|YP_007907990.1|  46 QAANVATMPGIQYASLVMPDVHVGYGFPIGGVAGFDaeeGVVSPGGVGFDInCGVRVLRSNLTVDEVRPKIKELIDE 122
                                       89*************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       l+ avp+g+gs+++++++++el+e++ +ga+wav++g+g++edl+++ee+g+l++ + + vskkak+r+++qlGtlG
  gi|488601519|ref|YP_007907990.1| 123 LFVAVPSGVGSEGRLRVTDDELDEIFVKGAEWAVRNGFGTKEDLKHCEENGCLEGGRGDVVSKKAKNRGKPQLGTLG 199
                                       ***************************************************************************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagse 227
                                       sGNHF+Evq+ve+i++eeaak +gleeg+v+vm+H+GSRglGhq+++d l+++++a++k++i+lpd++La++p++s+
  gi|488601519|ref|YP_007907990.1| 200 SGNHFLEVQYVEKIYNEEAAKVMGLEEGMVTVMIHCGSRGLGHQVCTDSLEVLNRAVRKYHISLPDKQLACAPIKSR 276
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxx RF
                              RtcB 228 egqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAt 300
                                       eg++Y++ m+a+anyA+aNRq+it+++re++ek+++   +dl+++l++dvaHNiak+Eeh+ +   +k+++hRKGAt
  gi|488601519|ref|YP_007907990.1| 277 EGEDYFAGMAASANYAWANRQIITHWTRETFEKIFG---SDLGMDLIYDVAHNIAKFEEHYvNgekMKLCIHRKGAT 350
                                       ***********************************7...5899*****************99457899********* PP

                                       E-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCC CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 301 rA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeq 362
                                       rA             k+gqpv+ipGsmgt+Syi+ G+++a+  +fgSt+HG+GR+msRa ak+k+++++vk++l+++
  gi|488601519|ref|YP_007907990.1| 351 RAfgrnskelpedytKIGQPVLIPGSMGTASYILLGTEKAMkeTFGSTCHGSGRVMSRAMAKRKLRGSRVKDELARK 427
                                       ***************************************************************************** PP

                                       T-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 363 gigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       gi+v+a++ + ++eEap+aYK  d Vv+++++ag++  varl+p++v+kg
  gi|488601519|ref|YP_007907990.1| 428 GIYVRATHGAILAEEAPQAYKLSDVVVDVVHNAGISLLVARLRPIGVAKG 477
                                       ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2641.22
//
Query:       gi|488601520|ref|YP_007907991.1|  [L=159]
Description: hypothetical protein Asulf_02034 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.8   2.1      0.031   13.8   2.1    2.8  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.12   12.9   2.7       0.38   11.3   0.2    2.2  2  zf-CHY          CHY zinc finger
       0.26   11.3   6.4       0.95    9.5   1.2    2.9  2  DZR             Double zinc ribbon
       0.53   10.2   5.0        1.7    8.6   1.4    2.8  3  HalOD2          Halobacterial output domain 2
        0.7   10.0   9.6        1.5    9.0   0.2    3.3  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.85    9.5   8.5       0.93    9.4   1.7    2.8  2  zinc_ribbon_12  Probable zinc-ribbon domain
        1.2    9.2   0.0        1.2    9.2   0.0    3.4  4  zf-BED          BED zinc finger
        6.5    6.8  13.4        1.1    9.2   0.3    3.4  3  DUF1610         Domain of unknown function (DUF1610)
        6.8    6.6  11.0       0.78    9.5   0.2    3.5  4  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.1   1.5e-05     0.031       2      32 ..       4      33 ..       3      36 .. 0.91
   2 ?   -0.3   4.4       0.4   7.9e+02       2      29 ..     115     148 ..     114     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                                      EETTTTCEECHEETSTTCE.EESSSSBEEEEC CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergel.vCtdCGlVledn 32
                                       C +Cg++  v+D    e+ +C++C+ V++d 
  gi|488601520|ref|YP_007907991.1|  4 NCVVCGGK--VVDGRYIEFgICGECERVIDDI 33
                                      6******9..***999*************985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.4
                                       EETTTTCEEC....HEETSTTCEE..ESSSSBEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnl....veDpergelv..CtdCGlVl 29 
                                       kC  Cg + +    v++  +g ++  C +CG V+
  gi|488601520|ref|YP_007907991.1| 115 KCNSCGKELIpgsvVVEQVNGSFIvkCNSCGDVI 148
                                       6777776656777777777777744599999886 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.17   3.3e+02      56      73 ..       4      27 ..       1      38 [. 0.55
   2 ?   11.3   0.2   0.00019      0.38      14      62 ..     107     156 ..      97     159 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                            zf-CHY 56 lCkkCkk..efaey....fCpiCk 73
                                      +C  C+     ++y     C  C+
  gi|488601520|ref|YP_007907991.1|  4 NCVVCGGkvVDGRYiefgICGECE 27
                                      566665423223344444466664 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00019
                            zf-CHY  14 pcCkkly.aCreCHeeledhelerlevkevlcllCeteqekavlCkkCkk 62 
                                       +  +k++ +C++C +el   ++   +v+   +++C++  ++ v C  Ck+
  gi|488601520|ref|YP_007907991.1| 107 KIGEKFFaKCNSCGKELIPGSVVVEQVNGSFIVKCNSCGDVIVSCIVCKR 156
                                       556777746*******999999999999999*****************86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3     0.043        85      15      36 ..       5      28 ..       2      32 .. 0.48
   2 ?    9.5   1.2   0.00048      0.95      14      37 ..     115     147 ..     106     159 .] 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.043
                               DZR 15 CseCgtklkavaa...edrCpsCge 36
                                      C  Cg k+    +      C +C++
  gi|488601520|ref|YP_007907991.1|  5 CVVCGGKVVD-GRyieFGICGECER 28
                                      5555555432.11344555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00048
                               DZR  14 fCseCgtklkavaa..........edrCpsCgek 37 
                                        C+ Cg++l +  +            +C sCg  
  gi|488601520|ref|YP_007907991.1| 115 KCNSCGKELIPG-SvvveqvngsfIVKCNSCGDV 147
                                       599999999844.358999999998999999865 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       3.8   7.6e+03      34      38 ..      23      27 ..      22      30 .. 0.61
   2 ?    2.4   0.1     0.072   1.4e+02      30      41 ..     112     123 ..     104     134 .. 0.70
   3 ?    8.6   1.4   0.00086       1.7      28      43 ..     135     150 ..     114     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.8
                            HalOD2 34 CtrCG 38
                                      C++C 
  gi|488601520|ref|YP_007907991.1| 23 CGECE 27
                                      66664 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.072
                            HalOD2  30 yvWkCtrCGevq 41 
                                       +  kC  CG+ +
  gi|488601520|ref|YP_007907991.1| 112 FFAKCNSCGKEL 123
                                       456999999866 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00086
                            HalOD2  28 GayvWkCtrCGevqaa 43 
                                       G+++ kC  CG+v  +
  gi|488601520|ref|YP_007907991.1| 135 GSFIVKCNSCGDVIVS 150
                                       9***********9876 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 ?   -2.1   0.4       2.1   4.2e+03       4      10 ..      23      29 ..      23      30 .. 0.71
   2 ?    6.1   0.3     0.006        12       3       9 ..     115     121 ..     113     123 .. 0.81
   3 ?    9.0   0.2   0.00076       1.5       2      11 ..     139     148 ..     139     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                            zf-ACC  4 CpsCgem 10
                                      C +C+ +
  gi|488601520|ref|YP_007907991.1| 23 CGECERV 29
                                      8889865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.006
                            zf-ACC   3 KCpsCge 9  
                                       KC+sCg 
  gi|488601520|ref|YP_007907991.1| 115 KCNSCGK 121
                                       9****96 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00076
                            zf-ACC   2 tKCpsCgeml 11 
                                       +KC+sCg ++
  gi|488601520|ref|YP_007907991.1| 139 VKCNSCGDVI 148
                                       7******987 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3     0.031        62      34      41 ..      23      30 ..      22      31 .. 0.90
   2 ?    9.4   1.7   0.00047      0.93       6      41 ..     113     148 ..     112     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.031
                    zinc_ribbon_12 34 CGaCsevl 41
                                      CG+C+ v+
  gi|488601520|ref|YP_007907991.1| 23 CGECERVI 30
                                      ******98 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00047
                    zinc_ribbon_12   6 FvvCsnCfelLqlP.kkflllkkkqqklrCGaCsevl 41 
                                       F  C++C + L +P + ++   +    ++C +C  v+
  gi|488601520|ref|YP_007907991.1| 113 FAKCNSCGKEL-IPgSVVVEQVNGSFIVKCNSCGDVI 148
                                       889******99.78466666777999********998 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       6.7   1.3e+04      19      24 ..       5      10 ..       4      15 .. 0.67
   2 ?   -2.0   0.0       1.9   3.7e+03      18      27 ..      22      31 ..      20      32 .. 0.80
   3 ?    9.2   0.0   0.00061       1.2      11      26 ..     106     123 ..      92     128 .. 0.77
   4 ?    2.2   2.3     0.094   1.9e+02      15      27 ..     137     149 ..     130     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.7
                                      ETTTTE CS
                            zf-BED 19 CryCgk 24
                                      C  Cg 
  gi|488601520|ref|YP_007907991.1|  5 CVVCGG 10
                                      777875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                                      EETTTTEE-- CS
                            zf-BED 18 vCryCgkils 27
                                      +C  C+++++
  gi|488601520|ref|YP_007907991.1| 22 ICGECERVID 31
                                      6999999885 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00061
                                       -..GGSS--EETTTTEE- CS
                            zf-BED  11 s..lkeqkavCryCgkil 26 
                                       +   ++ +a+C+ Cgk+l
  gi|488601520|ref|YP_007907991.1| 106 KkiGEKFFAKCNSCGKEL 123
                                       2567899*********87 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.094
                                       S--EETTTTEE-- CS
                            zf-BED  15 qkavCryCgkils 27 
                                         ++C+ Cg ++ 
  gi|488601520|ref|YP_007907991.1| 137 FIVKCNSCGDVIV 149
                                       5799*****9986 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.7      0.12   2.4e+02       1      17 [.       5      20 ..       5      26 .. 0.75
   2 ?    9.2   0.3   0.00057       1.1       1      11 [.     116     126 ..     116     130 .. 0.91
   3 ?    3.2   1.0     0.044        88       1       9 [.     141     149 ..     141     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                           DUF1610  1 CtSCGaelaprEravvF 17
                                      C+ CG+  +++  + +F
  gi|488601520|ref|YP_007907991.1|  5 CVVCGGKVVDGR-YIEF 20
                                      999**9999875.8777 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00057
                           DUF1610   1 CtSCGaelapr 11 
                                       C SCG+el+p+
  gi|488601520|ref|YP_007907991.1| 116 CNSCGKELIPG 126
                                       99*******97 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.044
                           DUF1610   1 CtSCGaela 9  
                                       C SCG +++
  gi|488601520|ref|YP_007907991.1| 141 CNSCGDVIV 149
                                       99****997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       1.2   2.3e+03       2       6 ..       5       9 ..       5      15 .. 0.56
   2 ?   -1.4   0.1       1.1   2.1e+03       2       7 ..      23      28 ..      22      32 .. 0.58
   3 ?    9.5   0.2   0.00039      0.78       1      13 [.     115     127 ..     115     129 .. 0.85
   4 ?    2.8   0.1     0.052     1e+02       1       6 [.     140     145 ..     140     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                     zinc_ribbon_2 2 CpnCG 6
                                     C  CG
  gi|488601520|ref|YP_007907991.1| 5 CVVCG 9
                                     55566 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C +C +
  gi|488601520|ref|YP_007907991.1| 23 CGECER 28
                                      666655 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00039
                     zinc_ribbon_2   1 fCpnCGaelqdna 13 
                                       +C +CG+el +++
  gi|488601520|ref|YP_007907991.1| 115 KCNSCGKELIPGS 127
                                       8*******97776 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.052
                     zinc_ribbon_2   1 fCpnCG 6  
                                       +C +CG
  gi|488601520|ref|YP_007907991.1| 140 KCNSCG 145
                                       799999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 856.26
//
Query:       gi|488601521|ref|YP_007907992.1|  [L=122]
Description: DNA ligase D, 3-phosphoesterase domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-34  116.3   0.0    8.4e-34  116.0   0.0    1.1  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 !  116.0   0.0   4.7e-38   8.4e-34       1     104 [.       6     103 ..       6     104 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 4.7e-38
                                       EEEESSSEEEEEEEEETTEEEEEEETT---SSTTSEEEEEEEEEE-GGGGGEEEEE-TTSTT-EEEEEEEEEEEEE. CS
                            LigD_N   1 qeHdaprlHYDlrLeidevlsswavpkglpedpnskrlAvetedhpleyadfegliekgeygaGsvliwDtGtyeve 77 
                                       qeH a+++HYD+rLe+++v +swavpkg+p +  ++rlA+++edh+++y+dfeg+i++g ygaG+v iwD+G+y+  
  gi|488601521|ref|YP_007907992.1|   6 QEHFAKKHHYDFRLEMNGVAKSWAVPKGMPLKRGERRLAIQVEDHDVDYMDFEGEIPDG-YGAGTVRIWDRGEYDL- 80 
                                       79*******************************************************99.7**************9. PP

                                       .-HHHHHHHTEEEEEEECSSSEEEEEE CS
                            LigD_N  78 eklaealkkrkiklrLhGeklkgkyvl 104
                                            + ++++ik+rL+G+kl+g yvl
  gi|488601521|ref|YP_007907992.1|  81 ----LKRSDNEIKVRLRGNKLNGVYVL 103
                                       ....578899***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        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 0.32s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 718.09
//
Query:       gi|488601522|ref|YP_007907993.1|  [L=60]
Description: hypothetical protein Asulf_02036 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00043   20.6   0.4    0.00047   20.5   0.4    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0014   18.1   5.3     0.0035   16.8   5.3    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0021   18.1   0.2     0.0021   18.1   0.2    1.2  1  Elf1             Transcription elongation factor Elf1 like
     0.0028   17.7   1.2       0.81    9.9   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
      0.004   16.8   6.3       0.15   11.8   6.3    2.2  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0063   16.5   0.9     0.0098   15.9   0.9    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0092   15.9   0.7      0.012   15.5   0.7    1.2  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.056   13.2   0.6      0.059   13.2   0.6    1.1  1  PRKCSH-like      Glucosidase II beta subunit-like
      0.075   13.0   0.9       0.11   12.5   0.9    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.11   12.6   2.1        2.3    8.3   0.1    2.4  2  Rubredoxin       Rubredoxin
       0.12   12.9   2.9        7.5    7.2   0.3    2.2  2  zf-H2C2_2        Zinc-finger double domain
       0.23   11.3   2.4          9    6.2   0.3    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.33   10.4   5.4        5.9    6.5   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.81    9.5   7.6       0.63    9.8   1.6    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


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 !   20.5   0.4   3.7e-07   0.00047       3      43 ..       4      40 ..       2      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.7e-07
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCgastpwfki 43
                                       + CP C++++v   +++ +       +C++Cg+ ++ +  
  gi|488601522|ref|YP_007907993.1|  4 FLVCPVCNSKDVEPDTGGYTG----KYHCKNCGYIGSFILK 40
                                      678****************99....89*******3333333 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   5.3   2.8e-06    0.0035       2      27 ..       6      33 ..       5      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                                      EETTTTCEECHEETS..TTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpe..rgelvCtdCGl 27
                                      +CP+C+s++++ D+   +g + C++CG+
  gi|488601522|ref|YP_007907993.1|  6 VCPVCNSKDVEPDTGgyTGKYHCKNCGY 33
                                      8*******988885444899*******8 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   1.6e-06    0.0021      20      53 ..       3      33 ..       1      57 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                              Elf1 20 tkFdCpfCnheksvevkldkkekiaevsCkvCge 53
                                      +   Cp+Cn++   +v+ d+   +++ +Ck+Cg 
  gi|488601522|ref|YP_007907993.1|  3 KFLVCPVCNSK---DVEPDTGGYTGKYHCKNCGY 33
                                      5568*******...9*****************97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0046       5.9      28      37 ..       6      16 ..       1      17 [. 0.81
   2 !    9.9   0.1   0.00063      0.81       6      22 ..      26      42 ..      25      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0046
                       Zn-ribbon_8 28 aCPeCgs.evr 37
                                      +CP C+s +v+
  gi|488601522|ref|YP_007907993.1|  6 VCPVCNSkDVE 16
                                      6******8875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00063
                       Zn-ribbon_8  6 YrCeeCghefevlqsis 22
                                      Y+C++Cg     + +++
  gi|488601522|ref|YP_007907993.1| 26 YHCKNCGYIGSFILKMD 42
                                      *******8877666666 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 !   11.8   6.3   0.00012      0.15       6      23 ..       6      23 ..       5      33 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                           zf-RRN7  6 pCgvCgcrsftlddGfyy 23
                                      +C+vC+++++ +d G y 
  gi|488601522|ref|YP_007907993.1|  6 VCPVCNSKDVEPDTGGYT 23
                                      8************98774 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 !   15.9   0.9   7.6e-06    0.0098      20      45 ..       6      33 ..       2      34 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.6e-06
                     Zn_Tnp_IS1595 20 vCPhCgsrkayrikt..rglfqCkeCrk 45
                                      vCP C s+ +   ++   g+++Ck C++
  gi|488601522|ref|YP_007907993.1|  6 VCPVCNSKDVEPDTGgyTGKYHCKNCGY 33
                                      8*******55555555678*******97 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 !   15.5   0.7   9.4e-06     0.012      85     116 ..       2      33 ..       1      34 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.4e-06
                                       HHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  85 eeyVlCkeCkspetelekeerllvlkCkaCga 116
                                       +++++C+ C+s+++e  + + +   +Ck+Cg 
  gi|488601522|ref|YP_007907993.1|   2 KKFLVCPVCNSKDVEPDTGGYTGKYHCKNCGY 33 
                                       89****************9999999*****95 PP

>> PRKCSH-like  Glucosidase II beta subunit-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   4.6e-05     0.059      65      90 ..      15      39 ..       3      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                       PRKCSH-like 65 dePGtsacengkfycaneGyisgyie 90
                                       eP t   + gk++c+n Gyi ++i 
  gi|488601522|ref|YP_007907993.1| 15 VEPDTG-GYTGKYHCKNCGYIGSFIL 39
                                      477765.588**************95 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 ?   12.5   0.9   8.4e-05      0.11      31      54 ..       7      33 ..       5      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                    OrfB_Zn_ribbon 31 CseCgsknke...alsgrtfkCpnCgf 54
                                      C++C sk+ e      + +++C+nCg+
  gi|488601522|ref|YP_007907993.1|  7 CPVCNSKDVEpdtGGYTGKYHCKNCGY 33
                                      **********88888889********8 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.032        41      36      43 ..       6      13 ..       3      19 .. 0.81
   2 ?    8.3   0.1    0.0018       2.3       1      10 [.      25      34 ..      25      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.032
                                      BBTTTB-B CS
                        Rubredoxin 36 vCPdCgve 43
                                      vCP+C+ +
  gi|488601522|ref|YP_007907993.1|  6 VCPVCNSK 13
                                      79**9865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0018
                                      EEEETTT-BE CS
                        Rubredoxin  1 kyeCkvCgyv 10
                                      ky+Ck Cgy+
  gi|488601522|ref|YP_007907993.1| 25 KYHCKNCGYI 34
                                      79*******8 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 ?    7.2   0.3    0.0059       7.5      12      22 ..       2      12 ..       1      13 [. 0.83
   2 ?    6.3   0.1     0.011        14      14      22 ..      25      33 ..      19      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0059
                         zf-H2C2_2 12 ekpyeCplCdk 22
                                      +k++ Cp+C+ 
  gi|488601522|ref|YP_007907993.1|  2 KKFLVCPVCNS 12
                                      6889*****96 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                         zf-H2C2_2 14 pyeCplCdk 22
                                      +y+C+ C++
  gi|488601522|ref|YP_007907993.1| 25 KYHCKNCGY 33
                                      59*****98 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 ?    5.1   0.1     0.016        20       2       9 ..       6      13 ..       1      17 [. 0.59
   2 ?    6.2   0.3    0.0071         9      26      36 ..      23      33 ..      20      34 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                           TFIIS_C  2 kCpkCgsr 9 
                                       Cp C+s+
  gi|488601522|ref|YP_007907993.1|  6 VCPVCNSK 13
                                      35555555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0071
                           TFIIS_C 26 tvfykCtkCgh 36
                                      t  y C++Cg+
  gi|488601522|ref|YP_007907993.1| 23 TGKYHCKNCGY 33
                                      55799****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 ?    6.5   0.1    0.0046       5.9       5      15 ..       7      18 ..       4      19 .. 0.79
   2 ?    5.8   1.5    0.0073       9.4      18      24 ..      27      33 ..      23      33 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0046
                       zf-ribbon_3  5 CPnCGap.lssd 15
                                      CP C+++ +++d
  gi|488601522|ref|YP_007907993.1|  7 CPVCNSKdVEPD 18
                                      *****9657776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0073
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C++CG+
  gi|488601522|ref|YP_007907993.1| 27 HCKNCGY 33
                                      7999996 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.4     0.061        78      17      22 ..       7      12 ..       6      12 .. 0.85
   2 ?    9.8   1.6    0.0005      0.63       1       8 [.      26      33 ..      26      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.061
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp C+s
  gi|488601522|ref|YP_007907993.1|  7 CPVCNS 12
                                      ****96 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0005
                      Rubredoxin_2  1 YvCsqCGf 8 
                                      Y+C++CG+
  gi|488601522|ref|YP_007907993.1| 26 YHCKNCGY 33
                                      9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 362.92
//
Query:       gi|488601523|ref|YP_007907994.1|  [L=373]
Description: GTP cyclohydrolase II /3,4-dihydroxy-2-butanone 4-phosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-65  218.8   0.0    4.5e-65  218.2   0.0    1.2  1  GTP_cyclohydro2  GTP cyclohydrolase II
    3.6e-28   98.4   0.0    7.1e-28   97.4   0.0    1.4  1  DHBP_synthase    3,4-dihydroxy-2-butanone 4-phosphate synthas


Domain annotation for each model (and alignments):
>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.2   0.0     5e-69   4.5e-65       2     160 ..     181     342 ..     180     344 .. 0.97

  Alignments for each domain:
  == domain 1  score: 218.2 bits;  conditional E-value: 5e-69
                                       XEEEEEEEETT.EEEEEEEE--.....EEEEEE-........EEEEEE--HHHHHS-B--TTTTTHHHHHHHHHHHH CS
                   GTP_cyclohydro2   2 rvaeaklptrf.gefrliayedkvdgkehlalvkgdi...pvlvRvHsecltgDvlgslrcdcgeqldealeliaee 74 
                                       rv++a+lpt+f g+f++++y+  +   e +alvkg++   +v+vR+HsecltgDv++slrcdcg+ql++al++i+++
  gi|488601523|ref|YP_007907994.1| 181 RVVTATLPTKFyGTFKAVGYKTPIG--EIVALVKGNVtegEVMVRIHSECLTGDVFHSLRCDCGDQLENALKRIDSA 255
                                       7779******99********88877..*************9*********************************88* PP

                                       -.EEEEEE-.-TTTTTHHHHHHHHHHHHHCT--HHHHHHHHT--S-----HHHHHHHHHTT--EEEEE-S-HHHHHH CS
                   GTP_cyclohydro2  75 grGvlvylr.qegrgigllnklkayalqdeglDTveanlalglpadardygiaaqILkdlgvkkirLlTnnpekvea 150
                                       g+Gvl+y+r +egrgigl+nkl+ay+lq+eg DTveanl+lg+p+d+r+ygi aqIL dlgvkki L+Tnnp k+e+
  gi|488601523|ref|YP_007907994.1| 256 GKGVLIYMRgHEGRGIGLINKLMAYKLQEEGKDTVEANLELGFPPDMRSYGISAQILMDLGVKKILLMTNNPLKIEE 332
                                       ***************************************************************************** PP

                                       HCTT....SE CS
                   GTP_cyclohydro2 151 Legfgievve 160
                                       L+++g ev++
  gi|488601523|ref|YP_007907994.1| 333 LRKYGFEVKR 342
                                       *******985 PP

>> 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 !   97.4   0.0   7.9e-32   7.1e-28      11     190 ..       4     169 ..       2     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 7.9e-32
                                       --EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-SSTT---BB--EEESS CS
                     DHBP_synthase  11 kfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveenedkhktaftvsvdaae 87 
                                       k+ +vvD+    n + +  +Ae vt +++afm+++++  + val+ e +++L+L+            + ++ +d + 
  gi|488601523|ref|YP_007907994.1|   4 KPCVVVDK----NKAVVSHPAEIVTSKEIAFMMKNCDE-LRVALPWETISQLGLNKFK------FFGENSIPIDFK- 68 
                                       67788886....7799999****************998.79*************8887......445568*****9. PP

                                       T-SSS-SHHHHHHHHHHHH-TT--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TTS CS
                     DHBP_synthase  88 gttTGIsaaDRalTirkladpkakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpaavicellnddg 164
                                         t G sa+++a+ ir+l+++k + e++  PG++f+ +a+++gvl++ + +Ea++d+ar+ g  pa+v++ l++ dg
  gi|488601523|ref|YP_007907994.1|  69 --TNGSSAEEKAEFIRNLVKNKVSREEIIYPGRIFIEVAKKEGVLDKPAFAEACLDIARMDGYIPASVFSYLMTPDG 143
                                       ..9************************************************************************** PP

                                       CB-BHHHHHHHHHHHT-EEEEHHHHH CS
                     DHBP_synthase 165 tmarrdeleefakkhglkiitiedli 190
                                       + a+++ +++fa++hgl + +i++li
  gi|488601523|ref|YP_007907994.1| 144 KLANEKYARKFAEEHGLRLFSIQELI 169
                                       ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2197.55
//
Query:       gi|488601524|ref|YP_007907995.1|  [L=194]
Description: hypothetical protein Asulf_02039 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1114.28
//
Query:       gi|488601525|ref|YP_007907996.1|  [L=80]
Description: hypothetical protein Asulf_02040 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       469  (0.0261587); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 470.83
//
Query:       gi|488601526|ref|YP_007907997.1|  [L=61]
Description: hypothetical protein Asulf_02041 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0095   15.4   0.4       0.01   15.3   0.4    1.0  1  Glycoprotein_B  Herpesvirus Glycoprotein B ectodomain


Domain annotation for each model (and alignments):
>> Glycoprotein_B  Herpesvirus Glycoprotein B ectodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   5.7e-07      0.01     160     207 ..      10      58 ..       6      61 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.7e-07
                                       EETTTS---.--------------------SS-HHHHHTT-SS-HHHHH CS
                    Glycoprotein_B 160 veledietl.dtfieLnltlledidfkvlelYsreelrdsnvldleevl 207
                                       +++e ie+  +++i++nl+l+e+++ +  e+ + +e++d + ld + v 
  gi|488601526|ref|YP_007907997.1|  10 TKVERIEKFlQALIDVNLDLIEEVEPEDWEIQTVKERKDNEFLDWKSVE 58 
                                       5677787655**********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 354.69
//
Query:       gi|488601527|ref|YP_007907998.1|  [L=342]
Description: hypothetical protein Asulf_02042 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-106  354.3   0.4   6.7e-106  354.0   0.4    1.0  1  DUF917    Protein of unknown function (DUF917)


Domain annotation for each model (and alignments):
>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.0   0.4  3.8e-110  6.7e-106       3     343 ..       9     340 ..       7     342 .] 0.98

  Alignments for each domain:
  == domain 1  score: 354.0 bits;  conditional E-value: 3.8e-110
                                       HHHHHHHHHHTTTT-SS-HHHHHHHHTT-SBTT--EEEE-GGG--SEE..EEEEEEE-HHHHTT-SS-HH....HHH CS
                            DUF917   3 lealatGaavLGtGGGGspysgylllrqaleegksvrvvsldelpddalvvvvgamGsptvieeklpsgdelleave 79 
                                       ++ +a+Ga vLG+GGGG++y + l++ q+l+eg++  +++++e+pddal++ v++mGsp +++eklp+g+e++++++
  gi|488601527|ref|YP_007907998.1|   9 VRRIAKGAEVLGSGGGGQAYVSELMALQLLKEGRTTYLIDPEEVPDDALILSVALMGSPLILKEKLPNGKEAITVLR 85 
                                       678******************************889***************************************** PP

                                       HHHHHHT--EEEEE-SSSSCCHHHHHHHHHHHHT-EEESB-SSSS--SSGGGSHHHHTT----SEEEE-SSS-EEEE CS
                            DUF917  80 alekllgrkidavislEiGGlNglvallaaaklglpvvDaDgmGRAfPelqqttfavagisltPlaladekgnvvll 156
                                        le+++g++  a++++E +GlN+l++++a+ ++++p+vDaDgmGRAfPelq+ttf+++gis+tP+a++dekgn++ +
  gi|488601527|ref|YP_007907998.1|  86 MLENYFGEETYAIVPVEGAGLNSLTPIVAGLNSDIPIVDADGMGRAFPELQMTTFHLHGISITPMAISDEKGNTIFV 162
                                       ***************************************************************************** PP

                                       EE.---HHHHHHHHHHCTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--..-SHHHHHHHHHH-EE CS
                            DUF917 157 kkaqsdkavErllRaalvemgsfagvaaypmtgaelkraavpgtlslalriGravaeareakdvveailealgggak 233
                                       ++  +++  E ++R ++  mg++++++ y mtg+elk++a+++t+++++ iG+ + +  ++++ + +i+e++g g+ 
  gi|488601527|ref|YP_007907998.1| 163 DS-IDSVYGEWFARGITRLMGGYSWISFYAMTGRELKKSAIRHTITKSVMIGEILMSDMSNESKIMEICEITG-GSL 237
                                       **.77779***************************************************999***********.677 PP

                                       EEEEEEE--------------EEEET.......EEEEEEESSSEEEEE..ET-SEETTSEEEEEHHB-SSSSB-TTT CS
                            DUF917 234 vlfkGkivdverrteggfdvgevtiegldedegrelkiefqNEnllaeedgevlatvPDlIsvldaetgepigteel 310
                                        l +Gk+++++r+  + f  g+v++       ++++ ++fqNE+l+ae +g   +tvPD+I+++d ++ +pi+tee+
  gi|488601527|ref|YP_007907998.1| 238 -LGEGKVAGISRMRFNRFYGGQVEVV-----GDKKISLIFQNEYLVAE-NGVERVTVPDIITLMDVDSLRPITTEEI 307
                                       .************************9.....5799*************.99************************** PP

                                       T.TS-EEEEEE---GGGS..SHHHH-S-....- CS
                            DUF917 311 ryGlrVtVlalpasekwrteeglelvgPkaFGy 343
                                       r G++V+V+ +p +ekw+te+gl++vgP+ FG+
  gi|488601527|ref|YP_007907998.1| 308 RCGMNVYVVTMPSDEKWKTEKGLQVVGPEVFGL 340
                                       ********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1885.79
//
Query:       gi|488601528|ref|YP_007907999.1|  [L=147]
Description: Transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-16   60.6   0.2    1.8e-16   59.9   0.2    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    3.4e-15   55.3   1.1    5.6e-15   54.6   1.1    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.8e-14   53.3   1.1    2.9e-14   52.6   1.1    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    6.9e-09   35.5   1.1    1.7e-08   34.2   0.2    2.0  2  HTH_11          HTH domain
    1.6e-06   27.9   0.1    3.5e-06   26.8   0.1    1.6  1  MarR            MarR family
    1.2e-05   25.2   1.0    2.6e-05   24.1   0.1    1.9  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      3e-05   23.7   0.4    5.5e-05   22.8   0.4    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    4.5e-05   23.2   0.0    6.7e-05   22.6   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
    0.00048   19.6   0.1    0.00097   18.6   0.1    1.5  1  Sigma70_r4      Sigma-70, region 4
    0.00064   19.5   0.2     0.0013   18.5   0.2    1.5  1  FtsK_gamma      Ftsk gamma domain
    0.00073   19.7   0.0     0.0018   18.4   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00099   19.1   0.0     0.0014   18.6   0.0    1.3  1  HTH_20          Helix-turn-helix domain
     0.0049   16.7   0.0     0.0088   15.9   0.0    1.4  1  MarR_2          MarR family
     0.0057   16.7   0.2      0.017   15.1   0.0    1.9  2  NapD            NapD protein
     0.0074   16.9   0.8      0.053   14.1   0.3    2.5  3  ACT_4           ACT domain
     0.0083   15.8   0.2      0.014   15.0   0.1    1.4  2  E3_UFM1_ligase  E3 UFM1-protein ligase 1
     0.0094   15.6   0.0      0.018   14.7   0.0    1.5  1  Sigma70_r4_2    Sigma-70, region 4
  ------ inclusion threshold ------
      0.011   15.5   0.0       0.02   14.7   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
      0.014   14.8   0.0      0.022   14.2   0.0    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.02   14.7   0.0      0.044   13.6   0.0    1.5  1  HTH_23          Homeodomain-like domain
      0.024   14.9   0.1      0.039   14.2   0.1    1.3  1  HTH_Tnp_Tc3_2   Transposase
      0.038   14.1   0.0      0.085   12.9   0.0    1.6  1  HTH_7           Helix-turn-helix domain of resolvase
      0.045   13.5   0.2      0.072   12.9   0.2    1.3  1  HTH_38          Helix-turn-helix domain
      0.049   13.2   0.1      0.083   12.5   0.1    1.4  1  HTH_47          winged helix-turn-helix
      0.062   13.2   0.1       0.12   12.3   0.1    1.5  1  RuvB_C          RuvB C-terminal winged helix domain
      0.072   13.1   0.0       0.11   12.5   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.092   12.7   0.0       0.17   11.9   0.0    1.4  1  HTH_6           Helix-turn-helix domain, rpiR family
      0.099   12.5   0.0       0.21   11.4   0.0    1.5  1  HTH_30          PucR C-terminal helix-turn-helix domain
       0.16   12.0   1.8        4.5    7.4   0.4    2.9  2  HTH_19          Helix-turn-helix domain
       0.17   12.0   0.8        1.7    8.9   0.1    2.4  2  Trp_repressor   Trp repressor 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 !   59.9   0.2     3e-19   1.8e-16       1      75 []      68     138 ..      68     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 3e-19
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       +++++ p+     +e+ ++l  ++e++e+y vtGd+d+++k vv d++++ r++++ +++++gv +t++ iv +t
  gi|488601528|ref|YP_007907999.1|  68 IEIKTMPNY---EDEILDKLSSFDEITEVYWVTGDFDLIVKLVVGDIKEFTRVIKK-IREMNGVIDTKSAIVVKT 138
                                       577778777...9*****************************************99.***************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 !   54.6   1.1   9.3e-18   5.6e-15       1      48 []       2      49 ..       2      49 .. 0.99

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 9.3e-18
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      lde+d++IL+lLq++++is +e+A rl + ++tv+rr++r++ +G+Ik
  gi|488601528|ref|YP_007907999.1|  2 LDEIDKDILRLLQEDGNISLSEIANRLSVGVATVHRRIQRMKMDGIIK 49
                                      7**********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   1.1   4.8e-17   2.9e-14       1      42 []       2      43 ..       2      43 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 4.8e-17
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LDeiD+ IL++Lqed+ is +e+A r+ +  +tv+rR++r++
  gi|488601528|ref|YP_007907999.1|  2 LDEIDKDILRLLQEDGNISLSEIANRLSVGVATVHRRIQRMK 43
                                      8***************************************95 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.2   2.9e-11   1.7e-08       3      44 ..       7      47 ..       6      59 .. 0.89
   2 ?   -0.7   0.1       2.3   1.4e+03      34      47 ..     116     129 ..     115     141 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.9e-11
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ++il+lL +++g+is +e+A +L+v  +tv+r+I+++++ g+
  gi|488601528|ref|YP_007907999.1|  7 KDILRLL-QEDGNISLSEIANRLSVGVATVHRRIQRMKMDGI 47
                                      5899999.*********************************2 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.3
                            HTH_11  34 rdIkaLeelgvpIe 47 
                                       r Ik+++e+   I+
  gi|488601528|ref|YP_007907999.1| 116 RVIKKIREMNGVID 129
                                       67999998873333 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   5.9e-09   3.5e-06       7      50 ..       8      51 ..       7      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.9e-09
                                      HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      +iLr+l e g++s+se+a++l+v  +tv r + r+  +G i+++
  gi|488601528|ref|YP_007907999.1|  8 DILRLLQEDGNISLSEIANRLSVGVATVHRRIQRMKMDGIIKKK 51
                                      59***************************************975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   4.3e-08   2.6e-05      21      64 ..      18      59 ..       6      62 .. 0.88
   2 ?   -1.0   0.1       2.9   1.7e+03      39      59 ..     115     136 ..     111     140 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.3e-08
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHH CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririldlea 64
                                      +++  e+A++l +   tv r ++++k +g+i+++  i++ d+e+
  gi|488601528|ref|YP_007907999.1| 18 NISLSEIANRLSVGVATVHRRIQRMKMDGIIKKK--IVVVDPEK 59
                                      67889***************************65..******97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                                       HHHHHHHHH.TTSEEET.EEEEE CS
                         HTH_Crp_2  39 srilseLkr.eglisrg.rriri 59 
                                       +r++++ ++  g+i+++   i++
  gi|488601528|ref|YP_007907999.1| 115 TRVIKKIREmNGVIDTKsA-IVV 136
                                       7777777772477885414.776 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.4   9.2e-08   5.5e-05       3      46 ..       7      50 ..       6      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.2e-08
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      + il ll+++g +s+ e++++l v  aT+ R ++ ++ +g++++
  gi|488601528|ref|YP_007907999.1|  7 KDILRLLQEDGNISLSEIANRLSVGVATVHRRIQRMKMDGIIKK 50
                                      679*************************************9987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.1e-07   6.7e-05       7      50 ..       8      50 ..       8      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-07
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +iL++l e +   +lse+A+r+ +  +tvhR +q +   G++++
  gi|488601528|ref|YP_007907999.1|  8 DILRLLQEDGN-ISLSEIANRLSVGVATVHRRIQRMKMDGIIKK 50
                                      69*****9999.8**********************999998875 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.6e-06   0.00097       5      43 ..       2      41 ..       1      44 [. 0.95

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                                      S-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  5 Lpererevlelrf.geglTleEIgerlgiSrerVrqiekr 43
                                      L+e ++++l+l   + + +l+EI++rl +   +V++++ r
  gi|488601528|ref|YP_007907999.1|  2 LDEIDKDILRLLQeDGNISLSEIANRLSVGVATVHRRIQR 41
                                      89999*********99********************9987 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   2.2e-06    0.0013       4      51 ..       3      50 ..       1      53 [. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                        FtsK_gamma  4 DelfeeavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgp 51
                                      De+ +++++l  e+g++S S +  rl++G +   r i +++ +Gi+ +
  gi|488601528|ref|YP_007907999.1|  3 DEIDKDILRLLQEDGNISLSEIANRLSVGVATVHRRIQRMKMDGIIKK 50
                                      77778999**************************************86 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     3e-06    0.0018      12      53 ..       8      49 ..       7      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3e-06
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                       I++l  e + ++ +++a rL v  ++V   +++++ dG ++
  gi|488601528|ref|YP_007907999.1|  8 DILRLLQEDGNISLSEIANRLSVGVATVHRRIQRMKMDGIIK 49
                                      6999999*******************************9775 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.4e-06    0.0014      12      55 ..       6      49 ..       1      51 [. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                        +ilr+L +++  ++se+a rl++  +t++++++ +   g+++
  gi|488601528|ref|YP_007907999.1|  6 DKDILRLLQEDGNISLSEIANRLSVGVATVHRRIQRMKMDGIIK 49
                                      579*******************************9997788775 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.5e-05    0.0088      10      53 ..       9      50 ..       6      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +L  L   +   ++ +e+a rl +  ++v+r+++r+   G + +
  gi|488601528|ref|YP_007907999.1|  9 ILRLLQEDGN--ISLSEIANRLSVGVATVHRRIQRMKMDGIIKK 50
                                      5666655555..9***********************99999876 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1         7   4.2e+03      37      42 ..      50      55 ..      32      60 .. 0.65
   2 !   15.1   0.0   2.9e-05     0.017       8      67 ..      70     130 ..      62     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7
                              NapD 37 gklVvv 42
                                       k+Vvv
  gi|488601528|ref|YP_007907999.1| 50 KKIVVV 55
                                      455554 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.9e-05
                              NapD   8 Vqarperlaavkaalaalpg.vEvhasdeegklVvviEaesedeladtieaiealpgVlsa 67 
                                       ++++p+  ++++++l ++++ +Ev+ ++++  l+v +   + +e ++ i++i++++gV+++
  gi|488601528|ref|YP_007907999.1|  70 IKTMPNYEDEILDKLSSFDEiTEVYWVTGDFDLIVKLVVGDIKEFTRVIKKIREMNGVIDT 130
                                       899***************8847*************************************98 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       5.4   3.2e+03      33      38 ..      20      25 ..       7      46 .. 0.52
   2 ?    0.0   0.0       2.2   1.3e+03      64      79 ..      79      94 ..      63      95 .. 0.85
   3 !   14.1   0.3   8.9e-05     0.053      48      77 ..     100     129 ..      89     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.4
                             ACT_4 33 nivsvn 38
                                      +++++ 
  gi|488601528|ref|YP_007907999.1| 20 SLSEIA 25
                                      333322 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.2
                             ACT_4 64 rviakLraipgVisVe 79
                                      ++++kL + +++++V+
  gi|488601528|ref|YP_007907999.1| 79 EILDKLSSFDEITEVY 94
                                      68999*9999999996 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 8.9e-05
                             ACT_4  48 aeikitveVkdvehLsrviakLraipgVis 77 
                                       +++ +++ V d+++ +rvi+k+r+++gVi+
  gi|488601528|ref|YP_007907999.1| 100 FDLIVKLVVGDIKEFTRVIKKIREMNGVID 129
                                       788899**********************98 PP

>> E3_UFM1_ligase  E3 UFM1-protein ligase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.3e-05     0.014     114     163 ..       2      52 ..       1      66 [. 0.88
   2 ?   -2.5   0.0         5     3e+03     138     155 ..      98     115 ..      76     139 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                    E3_UFM1_ligase 114 ldsiaeeineklqeagqvsiaelakqydlpvdflke.llekrlgkiikgrl 163
                                       ld+i ++i   lqe g++s++e+a++++++v  +++ +++ +++ iik ++
  gi|488601528|ref|YP_007907999.1|   2 LDEIDKDILRLLQEDGNISLSEIANRLSVGVATVHRrIQRMKMDGIIKKKI 52 
                                       6899999***************************99777799988988764 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5
                    E3_UFM1_ligase 138 kqydlpvdflkellekrl 155
                                        ++dl v+++   +++  
  gi|488601528|ref|YP_007907999.1|  98 GDFDLIVKLVVGDIKEFT 115
                                       444444444444443322 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-05     0.018      11      49 ..       2      41 ..       1      44 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                                      S-HHHHHHHHHHHTS-.--HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 11 Lperqreifllryleg.lsykEIAellgisegtVksrlsR 49
                                      L e+++ i+ l +++g  s  EIA +l + ++tV +r++R
  gi|488601528|ref|YP_007907999.1|  2 LDEIDKDILRLLQEDGnISLSEIANRLSVGVATVHRRIQR 41
                                      889999999999888768*********************9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.4e-05      0.02       6      47 .]       8      50 ..       3      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +IL+lL+e g+ + +e+a+ l +  +tv +   +++  G+++k
  gi|488601528|ref|YP_007907999.1|  8 DILRLLQEdGNISLSEIANRLSVGVATVHRRIQRMKMDGIIKK 50
                                      6*****************************9999999999986 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 ?   14.2   0.0   3.7e-05     0.022      19      50 ..       8      41 ..       4      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                      HTH_Tnp_ISL3 19 yilellles..rsvkavArqlgvSwtTVwrildr 50
                                       il+ll+e+  +s +++A++l v+  TV+r++ r
  gi|488601528|ref|YP_007907999.1|  8 DILRLLQEDgnISLSEIANRLSVGVATVHRRIQR 41
                                      6999*****9*********************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.4e-05     0.044      10      40 ..       9      41 ..       8      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-05
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkr 40
                                      il+ll+e   +s +eIA +L v   Tv r ++r
  gi|488601528|ref|YP_007907999.1|  9 ILRLLQEdgNISLSEIANRLSVGVATVHRRIQR 41
                                      89999999*********************9999 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   6.5e-05     0.039       2      59 ..       7      59 ..       6      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.5e-05
                     HTH_Tnp_Tc3_2  2 rrIvrlvrkdPritlreLanelkeeGksvsreTirrrLrkaglkkrkprkkplLskkn 59
                                        I+rl ++d  i+l e+an+l     sv  +T+ rr+++ ++ +   +k +++ ++ 
  gi|488601528|ref|YP_007907999.1|  7 KDILRLLQEDGNISLSEIANRL-----SVGVATVHRRIQRMKMDGIIKKKIVVVDPEK 59
                                      579*******************.....9****************99999988877665 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 ?   12.9   0.0   0.00014     0.085      14      40 ..      10      37 ..       3      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                      GGSSTTTT.--STTTSSSS---SSSS-- CS
                             HTH_7 14 vvkLleeG.isiskIAkevnisRsTvYR 40
                                      ++ L e+G is s+IA ++ ++++Tv R
  gi|488601528|ref|YP_007907999.1| 10 LRLLQEDGnISLSEIANRLSVGVATVHR 37
                                      45677899******************87 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00012     0.072      13      43 ..       9      41 ..       7      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            HTH_38 13 Ierlla.eG.lslreIArrLgrspsTIsRElkR 43
                                      I rll+  G  sl+eIA rL +   T++R ++R
  gi|488601528|ref|YP_007907999.1|  9 ILRLLQeDGnISLSEIANRLSVGVATVHRRIQR 41
                                      88998625589999***************9988 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00014     0.083      43      77 ..      15      49 ..       3      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                      -EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 43 aDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                       DG+ sL +iA+r+ +++++v   +++++  g+++
  gi|488601528|ref|YP_007907999.1| 15 EDGNISLSEIANRLSVGVATVHRRIQRMKMDGIIK 49
                                      5*****************************99997 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 ?   12.3   0.1   0.00019      0.12       4      44 ..       2      39 ..       2      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTT CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedvi 44
                                      Lde+d+++L+ll+   ++g ++l+ +a+ l++   t+   i
  gi|488601528|ref|YP_007907999.1|  2 LDEIDKDILRLLQ---EDGNISLSEIANRLSVGVATVHRRI 39
                                      89**********9...79**************999998776 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018      0.11       4      41 ..       9      47 ..       7      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                            HTH_29  4 allllaeGvs.tvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      +l+ll e +  + s+iA +l +   tv r + r+ ++G+
  gi|488601528|ref|YP_007907999.1|  9 ILRLLQEDGNiSLSEIANRLSVGVATVHRRIQRMKMDGI 47
                                      7788888766889*************************7 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.17      25      62 ..       9      46 ..       3      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                                      HHH-S---TT--HHHHHHHTT--HHHHHHHH---S-SS CS
                             HTH_6 25 ilaspdkaielsikalAkaaavSeativrfakkLGfkG 62
                                      il+  ++  ++s++++A+ ++v+ at+ r  + + + G
  gi|488601528|ref|YP_007907999.1|  9 ILRLLQEDGNISLSEIANRLSVGVATVHRRIQRMKMDG 46
                                      55556666689******************999998887 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 ?   11.4   0.0   0.00035      0.21      12      37 ..      18      43 ..      11      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                      TT-HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_30 12 ggnisatAkaLhvHrnTlryRLrrie 37
                                      + ++s+ A++L v + T++ R++r +
  gi|488601528|ref|YP_007907999.1| 18 NISLSEIANRLSVGVATVHRRIQRMK 43
                                      55789******************975 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0075       4.5       4      25 ..      10      31 ..       8      99 .. 0.83
   2 ?    2.9   0.0      0.19   1.2e+02       2      13 ..     116     127 ..     115     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0075
                            HTH_19  4 LkeaReelgltqeelaerlgis 25
                                      L+ + e  ++++ e+a+rl++ 
  gi|488601528|ref|YP_007907999.1| 10 LRLLQEDGNISLSEIANRLSVG 31
                                      8999*************99875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                            HTH_19   2 erLkeaReelgl 13 
                                       + +k++Re++g 
  gi|488601528|ref|YP_007907999.1| 116 RVIKKIREMNGV 127
                                       569******996 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0028       1.7      43      74 ..      11      43 ..       7      53 .. 0.76
   2 ?    1.1   0.0      0.74   4.4e+02      12      35 ..      70      93 ..      62      95 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0028
                     Trp_repressor 43 keLLk..eelsqreIaeelgvSiAtItRvsrsLk 74
                                      + LL+  ++ s +eIa+ l v++At+ R  + +k
  gi|488601528|ref|YP_007907999.1| 11 R-LLQedGNISLSEIANRLSVGVATVHRRIQRMK 43
                                      5.5541157899**************99776666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.74
                     Trp_repressor 12 kleneeeleellelllTpdEreal 35
                                           +  +e+l+ l ++dE++ +
  gi|488601528|ref|YP_007907999.1| 70 IKTMPNYEDEILDKLSSFDEITEV 93
                                      444555667899999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 822.45
//
Query:       gi|488601529|ref|YP_007908000.1|  [L=353]
Description: L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.4e-56  189.4   0.0    9.2e-56  188.9   0.0    1.1  1  MR_MLE_C   Enolase C-terminal domain-like
    1.7e-12   47.6   0.0    3.4e-12   46.6   0.0    1.5  1  MR_MLE_N   Mandelate racemase / muconate lactonizing enzyme, 
    1.7e-08   34.0   0.3    5.8e-08   32.2   0.2    1.9  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus
    0.00047   19.5   0.0    0.00072   18.9   0.0    1.2  1  Enolase_C  Enolase, C-terminal TIM barrel domain
  ------ inclusion threshold ------
       0.18   12.3   0.9       0.47   11.0   0.1    2.1  3  OsmC       OsmC-like protein


Domain annotation for each model (and alignments):
>> 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 !  188.9   0.0   2.6e-59   9.2e-56       3     214 ..     141     344 ..     139     348 .. 0.92

  Alignments for each domain:
  == domain 1  score: 188.9 bits;  conditional E-value: 2.6e-59
                                       HHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEES CS
                          MR_MLE_C   3 aeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEE 79 
                                       +++a e+  ++g+r++K+kv gd v++d +r++a+ +    ++  ++++Danq+++++tA+r++r+++e+d++++E+
  gi|488601529|ref|YP_007908000.1| 141 RKKALEA-ISRGYRILKIKVEGD-VERDFKRIEAISDL---EV--RIRIDANQGFTPKTAVRFIRRVREFDVEFIEQ 210
                                       5566564.457********8886.*********88876...45..******************************** PP

                                       SSSTTTHHHHHHHHHHHHSSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS CS
                          MR_MLE_C  80 PvppeddleglaelrarasipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs 156
                                       Pvp + d++gl+ +++r++ipi+a+Es++s+ d+ ++++++avd ++++++++gGi+ a++++++ae +g+p+++++
  gi|488601529|ref|YP_007908000.1| 211 PVPYW-DIDGLRYVKERSDIPIIADESVHSARDALNVVKCDAVDGINIKLMKCGGISDAVRIVHIAESAGIPCMVGC 286
                                       ****5.6********555*********************************************************** PP

                                       CS.SHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSS CS
                          MR_MLE_C 157 gs.gglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGv 214
                                       +  + ++l a++hla a +n+++++ +     l+e+ + + +e+ +G++t+p++pGlG+
  gi|488601529|ref|YP_007908000.1| 287 MLeSRISLTAAAHLALAFKNIKYVDLDSHLF-LKEDPVVGGMEIVEGMMTLPEKPGLGI 344
                                       9659***************999999888665.9*************************8 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   9.6e-16   3.4e-12      12     117 .]      14     120 ..       5     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 9.6e-16
                                       EEC.EEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-...STT.GHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHH CS
                          MR_MLE_N  12 klr.PvqlavttvqkqslvlvkietseGvvGigeats...vgg.raetikaelddhlapllvgkdaanisdlaqllk 83 
                                        l+ P+++a++t+   s +lvki  se   Gige+++   ++g  +e   + ++  + pll+g++++ +  l +++ 
  gi|488601529|ref|YP_007908000.1|  14 SLKePFRIALGTMTSSSNILVKIF-SEEHFGIGEGSPtlmITGdNQEGCLSFIES-ISPLLIGEELNLE-VLYEKI- 86 
                                       3444********************.777889999865112344478888888876.*******998653.333333. PP

                                       HHCSSCHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  84 ravlgnmsAkaaidmAlwDlkakalnlpladLlG 117
                                           g+ +Akaa+d+Al+Dl +k++  p+++LlG
  gi|488601529|ref|YP_007908000.1|  87 NSFRGMPAAKAALDIALYDLIGKQQSKPVYKLLG 120
                                       34566999*************************9 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.52   1.8e+03      56      91 ..      81     117 ..      78     161 .. 0.73
   2 !   32.2   0.2   1.6e-11   5.8e-08     136     220 ..     225     308 ..     219     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.52
                            MAAL_C  56 wlkeRiekl.gseeykptlhiDvygtlgkvfdddeer 91 
                                       +l e+i++  g +  k  l i +y  +gk  ++ + +
  gi|488601529|ref|YP_007908000.1|  81 VLYEKINSFrGMPAAKAALDIALYDLIGKQQSKPVYK 117
                                       5667777766888888889999999999876655444 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 1.6e-11
                            MAAL_C 136 kgikvelvaDeWcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhv 212
                                       + +++ ++aDe   +  d  + v  +a+d + ik    Ggi++++  v ++++ g+ +++G    e  +s  +++h+
  gi|488601529|ref|YP_007908000.1| 225 ERSDIPIIADESVHSARDALNVVKCDAVDGINIKLMKCGGISDAVRIVHIAESAGIPCMVG-CMLESRISLTAAAHL 300
                                       567999**************************************************99987.5679*********** PP

                            MAAL_C 213 alatrpaq 220
                                       ala++  +
  gi|488601529|ref|YP_007908000.1| 301 ALAFKNIK 308
                                       ***98765 PP

>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     2e-07   0.00072      76     234 ..     134     285 ..     125     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-07
                                       -SSHHHHHHHHHHHHHHCT-TC.TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-E CS
                         Enolase_C  76 lqsnkealdliveaiekaGykg.kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPi 151
                                       +++++e  +   eai++ Gy+  k+k+  dv   + +k+ +   dl+++  + d ++ +t +  + + +  v+++ +
  gi|488601529|ref|YP_007908000.1| 134 IDTPEEVRKKALEAISR-GYRIlKIKVEGDVER-D-FKRIEAISDLEVRI-RIDANQGFTPKTAVRFIRR-VREFDV 205
                                       67777777778888876.787769999999864.4.567789999*9999.8999999999999998876.789*** PP

                                       EEEES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT CS
                         Enolase_C 152 vsiedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeag 228
                                         ie p+   d ++ ++++e+ +  + i+ d+  v  ++   + ++ +a + + +k+ + G +++++  v++a++ag
  gi|488601529|ref|YP_007908000.1| 206 EFIEQPVPYWDIDGLRYVKERSD--IPIIADES-VHSARDALNVVKCDAVDGINIKLMKCGGISDAVRIVHIAESAG 279
                                       ***********************..****9986.56666666899******************************** PP

                                       -EEEEE CS
                         Enolase_C 229 ygvvvs 234
                                          +v 
  gi|488601529|ref|YP_007908000.1| 280 IPCMVG 285
                                       999985 PP

>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.5   1.8e+03      55      81 ..     124     148 ..     115     151 .. 0.70
   2 ?   11.0   0.1   0.00013      0.47      28      82 ..     147     201 ..     143     203 .. 0.88
   3 ?   -2.7   0.0       2.3   8.4e+03      72      97 ..     269     294 ..     249     296 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.5
                                       EEEEEEEEEE-SS-H..HHHHHHHHHH CS
                              OsmC  55 teirlkvevkipgadseeklkklleka 81 
                                       ++i+ ++++ i+  + ee  kk+le++
  gi|488601529|ref|YP_007908000.1| 124 EKIETDITIGIDT-P-EEVRKKALEAI 148
                                       5777777775554.3.48888888766 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                                       TCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHHHHHH CS
                              OsmC  28 akkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkkllekae 82 
                                       a  +g+++ +++ve ++erd ++ + i+++++++++++    +++++ +++++++
  gi|488601529|ref|YP_007908000.1| 147 AISRGYRILKIKVEGDVERDFKRIEAISDLEVRIRIDANQGFTPKTAVRFIRRVR 201
                                       66789999999999999**999888999999********99999**999999886 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHSHHHHHHCT-SSS CS
                              OsmC  72 eklkkllekaekrCpvsntlkngvkv 97 
                                        ++  ++e a   C+v  +l++ +++
  gi|488601529|ref|YP_007908000.1| 269 VRIVHIAESAGIPCMVGCMLESRISL 294
                                       45555556666668888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2089.10
//
Query:       gi|488601530|ref|YP_007908001.1|  [L=96]
Description: hypothetical protein Asulf_02045 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   13.3   0.0      0.098   12.8   0.0    1.2  1  Cass2     Integron-associated effector binding protein
      0.082   13.0   0.0       0.11   12.6   0.0    1.2  1  LPD1      Large polyvalent protein-associated domain 1


Domain annotation for each model (and alignments):
>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.098      85     117 ..      62      94 ..      57      96 .] 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                       EEE--EEEEEEEEESSSTT-HHHHHHHHHHCHC CS
                             Cass2  85 keiPggkYavftiegdfeedlaeaweaiygell 117
                                       k+i++gkY v+++e++f+e l+++++ +++el 
  gi|488601530|ref|YP_007908001.1|  62 KKIDEGKYSVMESEEKFKEFLDRIIQDFAEELK 94 
                                       89**************************99986 PP

>> LPD1  Large polyvalent protein-associated domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05      0.11      26      76 ..      44      91 ..      40      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                              LPD1 26 edkleekgirndyLvsgtkeseeakaglYpkgeerkainkafdklfktlke 76
                                      +  le++gi  d+L+   +e ++ ++g+Y   e  ++ ++ +d+++++  e
  gi|488601530|ref|YP_007908001.1| 44 ISILEKHGIADDFLA---EERKKIDEGKYSVMESEEKFKEFLDRIIQDFAE 91
                                      55689**********...33457899******************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); 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 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 604.65
//
Query:       gi|488601531|ref|YP_007908002.1|  [L=171]
Description: Nitroreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-32  112.4   1.5    1.8e-18   67.2   0.1    2.1  2  Nitroreductase  Nitroreductase family
    1.6e-12   47.5   0.5    1.6e-05   24.6   0.1    3.0  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.1     2e-22   1.8e-18       1      54 [.       8      61 ..       8      64 .. 0.96
   2 !   44.9   0.2   1.4e-15   1.2e-11      86     170 .]      66     145 ..      61     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2e-22
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelrykla 54
                                      i+kRrSiRkF+d+ v++++++ki+ea+ +aPsagn+qpw fvvv++k+ ++k++
  gi|488601531|ref|YP_007908002.1|  8 ILKRRSIRKFRDQEVEEDKIRKIVEAGIWAPSAGNMQPWVFVVVRNKKNIEKIK 61
                                      789*********************************************999986 PP

  == domain 2  score: 44.9 bits;  conditional E-value: 1.4e-15
                                       HHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEE CS
                    Nitroreductase  86 alagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeei 162
                                        +++ p++i++     +    a++ +++ +++d+++aaqn+lL+A +lGlg+cp+  f+++a  v+ ll+lp  e+i
  gi|488601531|ref|YP_007908002.1|  66 GMFDLPAVIIA---VCRDMGLAGNFEENISIFDVAMAAQNMLLMACDLGLGACPVRSFNQKA--VQVLLDLP--EHI 135
                                       57777777777...677777788888999*********************************..********..666 PP

                                       E..EEEEEE- CS
                    Nitroreductase 163 v..vliavGy 170
                                       v  +l+++Gy
  gi|488601531|ref|YP_007908002.1| 136 VpeLLVTLGY 145
                                       666******9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.4   1.3e-05      0.12       3      27 ..       5      29 ..       3      30 .. 0.89
   2 !   24.6   0.1   1.8e-09   1.6e-05     158     191 ..      25      57 ..      23      78 .. 0.79
   3 !   11.1   0.0   2.4e-05      0.22      89     143 ..     101     157 ..      97     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                                      HHHHHH--B---B--S---HHHHHH CS
                    TM1586_NiRdase  3 yeaiekRhsvRkYkdealeeellee 27
                                      +e i kR+s+Rk++d+++ee+++ +
  gi|488601531|ref|YP_007908002.1|  5 FEVILKRRSIRKFRDQEVEEDKIRK 29
                                      799*****************98876 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHHHTS--GGG----EEE.E-SSEE.. CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdddeiki 191
                                       +++++i+ea + APsA N qpw f ++ ++  +i
  gi|488601531|ref|YP_007908002.1|  25 DKIRKIVEAGIWAPSAGNMQPWVFVVVRNK-KNI 57 
                                       789**********************88864.333 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS----..---- CS
                    TM1586_NiRdase  89 eqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktklv.eakrk 143
                                       ++++L ++ lGlg c v++  +k +++ ++l++     ++++lGy++++   +++rk
  gi|488601531|ref|YP_007908002.1| 101 QNMLLMACDLGLGACPVRSFNQKaVQVLLDLPEHIVPELLVTLGYPDESPSpPERRK 157
                                       789**************987777688888888888889********99987444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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 0.32s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1067.61
//
Query:       gi|488601532|ref|YP_007908003.1|  [L=240]
Description: Hydantoin racemase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   52.4   0.1      8e-14   52.0   0.1    1.2  1  Asp_Glu_race     Asp/Glu/Hydantoin racemase
     0.0024   17.7   2.2      0.016   15.1   0.0    2.9  3  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.038   13.9   0.2       0.14   12.1   0.0    1.9  2  AAA_31           AAA domain


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.1   1.3e-17     8e-14      43     221 ..      42     213 ..      15     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.3e-17
                                       HHHHHCH..T..THH.HHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEECHHHHHHHHHH..HSS-EEE CS
                      Asp_Glu_race  43 teaieee.sgddpvl.klleaakkLekagadaiviaCnTahavadelqkkikiPvlgiveataealka..tgvkkvg 115
                                       t++ie+e +++  ++  +l+ + + ek g d ++i C+    ++++ ++ ++iPv+g +e+++  +++  ++ + v 
  gi|488601532|ref|YP_007908003.1|  42 TASIESEfDEA-LAApDILNKVIEAEKKGFDGVIIDCFGD-PAVKAAREVVDIPVVGAAEPSMLLACSlgQRFSVVT 116
                                       45565563444.444499999999****************.*********************998888789999999 PP

                                       EEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCCHC.HHHH.TT-TTSHHHHHHHHHHHHHHTTT-SEEEE- CS
                      Asp_Glu_race 116 lLgTrgtlksglyqkeleanqgievvvpseelqssvnqaiy.eelk.aGevteearrailkllerlaergadaviLG 190
                                       +L + + + +++ +       ++       + ++svn  i+  el  +++++++ ++++lk+++   e++a ++iLG
  gi|488601532|ref|YP_007908003.1| 117 VLENVIPMIENIAKVLGVY-EKL-------ASVRSVN--IPvLELHdKDTLKNALFEEMLKAIK---EDKAHVLILG 180
                                       9999999998887666444.355.......8888998..553367789999999**********...********** PP

                                       STTHHHHHHHHHHCC-TT...SEEEEHHHHHHH CS
                      Asp_Glu_race 191 CTelplllekaealekek..svpvidptdilar 221
                                       CT +  + +++++   ++  +vpvidp+++ +r
  gi|488601532|ref|YP_007908003.1| 181 CTGMMGVADDLHEMLAKEgyDVPVIDPAAASIR 213
                                       *****999998877776679*******998775 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.59   3.6e+03      40      55 ..       5      20 ..       2      62 .. 0.55
   2 ?    0.3   0.0       0.1   6.1e+02      29      57 ..     136     160 ..     124     166 .. 0.78
   3 !   15.1   0.0   2.6e-06     0.016       5      44 ..     169     208 ..     165     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.59
                                      EEE-SEEESHHHHHHH CS
                   Transketolase_C 40 VvdlrtvkplDketil 55
                                      V+ ++ v+ +D+e  +
  gi|488601532|ref|YP_007908003.1|  5 VIVPIIVDIFDEEVKK 20
                                      5555555555555433 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.1
                                       HHHHTTTTCEEEEE-SEEESHHHHHHHHH CS
                   Transketolase_C  29 eeLekegisaeVvdlrtvkplDketiles 57 
                                       e+L     s++ v+++ ++  Dk+t++++
  gi|488601532|ref|YP_007908003.1| 136 EKL----ASVRSVNIPVLELHDKDTLKNA 160
                                       444....48899999*********99965 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.6e-06
                                       EEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-S CS
                   Transketolase_C   5 ilregkdvtlvayGsmveealeAaeeLekegisaeVvdlr 44 
                                       i+ ++ +v++++   m+ +a +  e+L+keg+++ V+d+ 
  gi|488601532|ref|YP_007908003.1| 169 IKEDKAHVLILGCTGMMGVADDLHEMLAKEGYDVPVIDPA 208
                                       566799********************************85 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05      0.14      76     126 ..      28      78 ..       6      87 .. 0.81
   2 ?   -1.2   0.0      0.28   1.7e+03     105     118 ..     160     173 ..     116     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                            AAA_31  76 tkvenldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcp 126
                                       ++ve+++++  +   a++e e+ e+    +il++++e+ k+ +D +iiDc 
  gi|488601532|ref|YP_007908003.1|  28 SEVEEIEVVHLDKGTASIESEFDEALAAPDILNKVIEAEKKGFDGVIIDCF 78 
                                       446666777777788999999*99999***********************5 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.28
                            AAA_31 105 eilkellekvkdeY 118
                                         ++e+l+++k++ 
  gi|488601532|ref|YP_007908003.1| 160 ALFEEMLKAIKEDK 173
                                       22355555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1358.75
//
Query:       gi|488601533|ref|YP_007908004.1|  [L=442]
Description: Purine-cytosine permease-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-27   94.8  37.2    6.3e-27   94.4  37.2    1.2  1  Transp_cyt_pur  Permease for cytosine/purines, uracil, thiami
  ------ inclusion threshold ------
      0.019   13.3  17.9      0.019   13.3   3.4    2.6  3  DUF2070         Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> Transp_cyt_pur  Permease for cytosine/purines, uracil, thiamine, allantoin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4  37.2     7e-31   6.3e-27       1     385 [.      17     372 ..      17     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 7e-31
                    Transp_cyt_pur   1 pvpeeeRtwktlnlfsiWlganlnintwvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpils 77 
                                       pvp e R+ ++l++  +W+g  ++++++++g+    +gL+++++ ++i++g+l+++i+ +l +++Ga +Gl+++++ 
  gi|488601533|ref|YP_007908004.1|  17 PVPMELRK-NWLEMGLVWIGIGMCLAALMLGGVV-GFGLDLKSAAAAIVLGSLVLTIVNSLCSIVGADTGLSTAMIG 91 
                                       56666665.699999****************987.****************************************** PP

                    Transp_cyt_pur  78 RasfGirgsllplllrvviaivwfgvqawiGsealllmlgkifgkwleiggailgtsltelvtffifwvvslvivll 154
                                       R+ fG +g  + + ++++   +wf+vq  + +e+ +  ++ i g           + +   + ++i ++++l++ + 
  gi|488601533|ref|YP_007908004.1|  92 RFAFGDIGVYVTAAVLAMGCYGWFAVQLGLFGETAAKGIDLIAG-----------VPVSTQLLIVIGGILMLATAIY 157
                                       ***************999999***************99999977...........5688888999************ PP

                    Transp_cyt_pur 155 gvskirkffviaallvpvaafgfliwalvkaegGpvldkavklgkselflsavagvlagfatlilnapDFtryaktk 231
                                       g   i+ ++++a++l+ ++ f+ li +l +  +G+++ ++    ++  f +a   ++++f+  ++  pD tryak  
  gi|488601533|ref|YP_007908004.1| 158 GYRGIATLSKVAVPLMVIILFASLIQILNQHPWGQLIVEPPPGDPL-PFGVAASIIAGSFMVGAVIGPDITRYAKDR 233
                                       **************************************77433333.56666666778888888888********** PP

                    Transp_cyt_pur 232 kssvkiqlvavpllftlllligilvaaaakaayganawspldilakfdetagvllililvalaqlgvnisanllsag 308
                                       k++v  +++++ ++f+l++ +g + a a    ++++++ +l          g  li+i+v++   ++++++nl+sa+
  gi|488601533|ref|YP_007908004.1| 234 KHAVGAAILGFLIGFSLMVYLGSILAHAVGEWDAVKIMIGL----------GWGLIAIVVLILAQWTTNDNNLYSAA 300
                                       **********************9999999999999999999..........5567888888888999********** PP

                    Transp_cyt_pur 309 ldlaallPkkinikrgsliaavialvivpwkllssssklftaflsllavflspvagviiadyfvvrrgylklaalyt 385
                                       l l+ ++  + +    +l+a v++++i++   ++ +    +++l +l++ + p+ gv + dyf   r  +k ++l +
  gi|488601533|ref|YP_007908004.1| 301 LNLSVIFR-TWPKWKLTLVAGVLGIIIALSGIYGRF----IQWLMVLSATIPPIGGVYVTDYFLFHRDMYKYENLDR 372
                                       ****9988.778888899999999999999999875....559*********************9999888887755 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   4.1     0.056     5e+02      37     122 ..      85     178 ..      44     188 .. 0.48
   2 ?   10.6   1.0   1.4e-05      0.12       5     131 ..     159     300 ..     157     305 .. 0.75
   3 ?   13.3   3.4   2.1e-06     0.019       6     114 ..     304     425 ..     301     435 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.056
                           DUF2070  37 k...lfgillfglp..alvaflltlpvlrilggr...ltykrslflalltelivviisllaillsallqalvllalv 105
                                           ++g ++fg    +++a++l   +  ++  +   +    +  + l++ ++v+  +l+ i   ++l++ ++ +  
  gi|488601533|ref|YP_007908004.1|  85 LstaMIGRFAFGDIgvYVTAAVLAMGCYGWFAVQlglFGETAAKGIDLIAGVPVSTQLLIVIGGILMLATAIYGYRG 161
                                       15555555555544446666666666666666665543333334455555555554444444433333333333333 PP

                           DUF2070 106 lslalvfalrllvlvav 122
                                       ++  + +a++l+v++++
  gi|488601533|ref|YP_007908004.1| 162 IATLSKVAVPLMVIILF 178
                                       33333333333333322 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 1.4e-05
                           DUF2070   5 skyifrlPswkvsllliillalligllaflssk............lfgillfglp..alvaflltlpvlrilggrlt 67 
                                       ++ i +l ++ v l++iil+a li++l+   +              fg+ + ++   ++v +++   + r+++ r +
  gi|488601533|ref|YP_007908004.1| 159 YRGIATLSKVAVPLMVIILFASLIQILNQHPWGqlivepppgdplPFGVAASIIAgsFMVGAVIGPDITRYAKDRKH 235
                                       666778888888888888889999998877777************77777777766699999999999999977755 PP

                           DUF2070  68 ykrslflalltelivviisllaillsall..qalvllalvlslalvfalrllvl.vavsdesllkav 131
                                          +++l +l+ + +++  +l+++l++ +  ++ v  ++ l++ l+++++l++  +++ d++l  a+
  gi|488601533|ref|YP_007908004.1| 236 AVGAAILGFLIGFSLMV--YLGSILAHAVgeWDAVKIMIGLGWGLIAIVVLILAqWTTNDNNLYSAA 300
                                       55557777777776666..666666666668999999999999999888776651555555555544 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 2.1e-06
                           DUF2070   6 kyifr.lPswk.vsllliillalligllaflssklfgillfglp.....alvaflltlpvlrilggr...ltykrsl 72 
                                       ++ifr  P+wk + ++ ++ ++++++ ++ +++++  +l  ++p     +++  +l+++ +  ++     ++++  +
  gi|488601533|ref|YP_007908004.1| 304 SVIFRtWPKWKlTLVAGVLGIIIALSGIYGRFIQWLMVLSATIPpiggvYVTDYFLFHRDMYKYENLdriPKWRPLM 380
                                       5678879****77777788888888888888888*********999999999999999999888777888******* PP

                           DUF2070  73 flalltelivviisllaillsall...qalvllalvlslalvfal 114
                                       f+a ++  iv++ ++ +   + l+   +   ++a+++++++ ++l
  gi|488601533|ref|YP_007908004.1| 381 FVAWAAGSIVAFCTTPPPNGFGLFtltTVPAVDAFIVAVVVQAVL 425
                                       ***999999999888887777766565444444555543333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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):               2  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.55
# Mc/sec: 2415.94
//
Query:       gi|488601534|ref|YP_007908005.1|  [L=517]
Description: N-methylhydantoinase A/acetone carboxylase, beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  162.5   8.2    1.2e-46  158.7   0.4    3.2  3  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    4.9e-40  137.6   9.8    4.2e-37  128.0   3.2    3.3  3  Hydantoinase_A  Hydantoinase/oxoprolinase
    9.3e-09   35.2   0.4    7.8e-05   22.3   0.3    2.9  3  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
    3.8e-06   25.8   1.7      0.005   15.5   0.1    2.4  2  MutL            MutL protein
      0.001   18.4   1.2          1    8.5   0.0    2.8  3  StbA            StbA protein
     0.0085   15.6   2.3      0.009   15.5   0.1    2.2  3  ROK             ROK family
  ------ inclusion threshold ------
      0.046   13.6   0.1      0.086   12.7   0.1    1.4  1  DEDD_Tnp_IS110  Transposase
       0.06   13.7   0.8        0.9    9.9   0.1    2.8  3  Radical_SAM     Radical SAM superfamily
      0.087   13.3  12.3        1.3    9.5   2.0    3.9  2  FtsA            Cell division protein FtsA
      0.099   12.6   0.7        0.3   11.0   0.0    2.2  3  DUF3783         Domain of unknown function (DUF3783)
       0.53   10.2   6.7        3.1    7.8   0.3    3.5  3  GA-like         GA-like domain


Domain annotation for each model (and alignments):
>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   0.4   7.2e-50   1.2e-46       1     177 [.       4     174 ..       4     175 .. 0.91
   2 !    7.4   0.2     0.002       3.3       2      16 ..     272     286 ..     271     299 .. 0.84
   3 ?   -1.6   0.1       1.2   1.9e+03     114     144 ..     452     480 ..     435     488 .. 0.74

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 7.2e-50
                        Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg. 76 
                                       r+gIDvGGT+TDav+ld++++ va++K+ +t ++v++gi++al+ vl+ s  ++s+i++ ++GTT++tNa++erk+ 
  gi|488601534|ref|YP_007908005.1|   4 RLGIDVGGTNTDAVILDKNDQPVAKIKVATT-EDVTTGILNALDGVLKDSSVDPSEIKYAMLGTTHCTNAIVERKNl 79 
                                       68*****************************.********************************************9 PP

                        Hydant_A_N  77 ervaLittkgfrd.lleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagves 152
                                       +rv++i + +     ++   ++ +dl        +++   ++ v++++e+dg++l pldeeev++a+k+lk++gves
  gi|488601534|ref|YP_007908005.1|  80 ARVGIIRIGRPATlSIKPLISWPEDL-------VEAIGGYTHIVHGGHEYDGRELAPLDEEEVKRAVKDLKEKGVES 149
                                       88888877554431345555666666.......5677888999********************************** PP

                        Hydant_A_N 153 iavvllhSylnpehElrvaeiarei 177
                                       +a++ ++S++n+ehElrvaei+rei
  gi|488601534|ref|YP_007908005.1| 150 VAISAVFSPVNNEHELRVAEIVREI 174
                                       ***********************98 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.002
                        Hydant_A_N   2 igIDvGGTfTDaval 16 
                                       + +DvGGT TD+ +l
  gi|488601534|ref|YP_007908005.1| 272 VVVDVGGTTTDIGVL 286
                                       78*********9665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.2
                        Hydant_A_N 114 eevvevderveadgevlkpldeeevrealka 144
                                       ++v+ ++er +   +vlk+ +e +v+ea+ka
  gi|488601534|ref|YP_007908005.1| 452 DKVFSLEERSRE--DVLKEAKEIAVKEAIKA 480
                                       667777777766..48888888888888876 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.052        85      83      98 ..       6      21 ..       3      41 .. 0.81
   2 !  128.0   3.2   2.6e-40   4.2e-37       1     200 [.     194     386 ..     194     388 .. 0.94
   3 !   12.7   0.0   3.3e-05     0.054     209     288 ..     372     448 ..     366     451 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.052
                    Hydantoinase_A 83 tfDmGGTstDvslikd 98
                                      ++D+GGT tD+  +++
  gi|488601534|ref|YP_007908005.1|  6 GIDVGGTNTDAVILDK 21
                                      68********998875 PP

  == domain 2  score: 128.0 bits;  conditional E-value: 2.6e-40
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       r ++a++nA++  + +  ++s+e++l+k+g+ a+l++ q dG l+sa++a k pv ti+SGPa ++ g      l g
  gi|488601534|ref|YP_007908005.1| 194 RENAAILNAAVVKVAEIAVKSFENALKKKGIDAQLYITQNDGTLMSAEYALKYPVLTIASGPANSLRGGTF---LSG 267
                                       7899*****************************************************************99...999 PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgev.evsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgp 153
                                        k+++++D+GGT+tD+ ++ +g + e s + ei+gv++++++ d+ ++g+gGgsi+    +g ++vgp+s+g++ + 
  gi|488601534|ref|YP_007908005.1| 268 LKNAVVVDVGGTTTDIGVLVNGFPrESSVAVEIGGVRTNFRMPDLISIGLGGGSIV-EEVNGDVKVGPRSVGYRLEK 343
                                       999*******************98345678999***********************.9999**************** PP

                    Hydantoinase_A 154 acyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafe 200
                                        +   Gg++lt+TD+++ LGr++  d    p+  ++ld+ l+++a+ 
  gi|488601534|ref|YP_007908005.1| 344 EALVFGGNTLTTTDIAVSLGRIKLGD----PSKVENLDKTLVEKAAG 386
                                       **********************9986....46777888888888765 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 3.3e-05
                    Hydantoinase_A 209 kveevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalA 285
                                       kve++ ++++++a  +++  v++ + + +  p+ + ++ +GG++ ++  +l    g ++vi pp+ +v++a+G+a+A
  gi|488601534|ref|YP_007908005.1| 372 KVENLDKTLVEKAAGKIKTMVEEAIDRMKTSPEPVPVILVGGGSIIIPDEL---RGASEVIKPPHFEVANAIGAAIA 445
                                       688888999*********************************999999998...899******************** PP

                    Hydantoinase_A 286 dvr 288
                                       +v+
  gi|488601534|ref|YP_007908005.1| 446 QVS 448
                                       986 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 !   22.3   0.3   4.8e-08   7.8e-05       1      78 [.       5      75 ..       5      86 .. 0.85
   2 ?   -2.4   0.0       1.6   2.6e+03     174     208 ..     154     188 ..     110     232 .. 0.53
   3 !    9.4   0.0    0.0004      0.65       3      69 ..     274     413 ..     272     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.8e-08
                                      EEEEE-SSEEEEEEEETTTE.EEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTC CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmdekge.vlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlp 78
                                      +GiD+G+T t av++d++ + v++  +++++ ++ ++       + +al+ +l+ +  ++++i++ +l++t    a ++
  gi|488601534|ref|YP_007908005.1|  5 LGIDVGGTNTDAVILDKNDQpVAKIKVATTEDVT-TG-------ILNALDGVLKDSSVDPSEIKYAMLGTTHCTNAIVE 75
                                      8*******************77777777666666.55.......889*********************99987776665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHH CS
                       BcrAD_BadFG 174 avfaeaelrdalsggekaedIlaglhraialrvia 208
                                       avf++   ++ l   e+ ++I+ ++  ++   + +
  gi|488601534|ref|YP_007908005.1| 154 AVFSPVNNEHELRVAEIVREIMGDVPISLSHEIGS 188
                                       45555555555544444444444444444444333 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0004
                                       EEE-SSEEEE.EEEE...TTTEEEEEEEE--.............................................. CS
                       BcrAD_BadFG   3 iDgGsTttka.vlmd...ekgevlgrgitns.............................................. 29 
                                       +D+G+Ttt   vl++   + ++ ++  i +                                               
  gi|488601534|ref|YP_007908005.1| 274 VDVGGTTTDIgVLVNgfpR-ESSVAVEIGGVrtnfrmpdlisiglgggsiveevngdvkvgprsvgyrlekealvfg 349
                                       8999999985266667742.333333443335667899999999999999999999999999999999999999999 PP

                                       ........................TTS-HHH.........HHHHHHHHHHT--GGGECEE..EE CS
                       BcrAD_BadFG  30 ........................anlesvrfeaaekvleealtealerageeeadieetylvg 69 
                                                               +nl+++ +e+a++ +++ ++ea++r++++++ ++ + ++g
  gi|488601534|ref|YP_007908005.1| 350 gntltttdiavslgriklgdpskvENLDKTLVEKAAGKIKTMVEEAIDRMKTSPEPVPVILVGG 413
                                       999999999999*********999999*9***************************99886654 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2   0.00026      0.42       2      54 ..       5      51 ..       4      72 .. 0.81
   2 !   15.5   0.1   3.1e-06     0.005     232     277 ..     259     299 ..     243     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00026
                              MutL  2 lviDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleek 54
                                      l iD+G t T ++++d+++   + +++ +  Tt    dv++G+ +al+ + + 
  gi|488601534|ref|YP_007908005.1|  5 LGIDVGGTNTDAVILDKND---QPVAKIKVATTE---DVTTGILNALDGVLKD 51
                                      569**************76...777777777775...9********9988766 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.1e-06
                              MutL 232 lkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekekvllk 277
                                       l++  +l+      l +++vvDvGG+TTd+   ++g p++++v+++
  gi|488601534|ref|YP_007908005.1| 259 LRGGTFLSG-----LKNAVVVDVGGTTTDIGVLVNGFPRESSVAVE 299
                                       555555555.....6699*************999999999999876 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.9   3.2e+03     168     191 ..       7      30 ..       4      59 .. 0.66
   2 !    7.7   0.0    0.0011       1.8     159     181 ..     265     287 ..     251     300 .. 0.80
   3 !    8.5   0.0   0.00062         1     250     296 ..     380     429 ..     362     443 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                              StbA 168 iDlGGttLDvakvrgklegiskvk 191
                                       iD+GGt  D   +  + + ++k+k
  gi|488601534|ref|YP_007908005.1|   7 IDVGGTNTDAVILDKNDQPVAKIK 30 
                                       899999888665555555555554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
                              StbA 159 ldeleslLiiDlGGttLDvakvr 181
                                       l+ l + +++D+GGtt D++ + 
  gi|488601534|ref|YP_007908005.1| 265 LSGLKNAVVVDVGGTTTDIGVLV 287
                                       7889999************9765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00062
                              StbA 250 vinekvkkLkerviravsefsgyth...vmvvGGGaeliaeaikkatevs 296
                                        ++++  k+k  v +a+ +++  +    v++vGGG+ +i + ++ a ev 
  gi|488601534|ref|YP_007908005.1| 380 LVEKAAGKIKTMVEEAIDRMKTSPEpvpVILVGGGSIIIPDELRGASEVI 429
                                       35666778888899999888877766669**************9998875 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.5e-06     0.009       2      52 ..       5      54 ..       4      79 .. 0.80
   2 ?   -3.5   0.1       3.4   5.5e+03       4     142 ..     274     289 ..     267     308 .. 0.56
   3 ?   -1.9   0.0       1.2   1.9e+03      27      84 ..     380     437 ..     368     465 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.5e-06
                                      EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHC CS
                               ROK  2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaer 52
                                      +gid+Ggt++ + ++d++ + +a+ kv  +te++  ++ +a++ ++++   
  gi|488601534|ref|YP_007908005.1|  5 LGIDVGGTNTDAVILDKNDQPVAKIKV-ATTEDVTTGILNALDGVLKDSSV 54
                                      79*************************.66666666777888777666544 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.4
                                       EEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEBSSGGC CS
                               ROK   4 idiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeliavgigspGlisdksgkivstpn 80 
                                       +d+Ggt + +                                                                   
  gi|488601534|ref|YP_007908005.1| 274 VDVGGTTTDI------------------------------------------------------------------- 283
                                       4555555544................................................................... PP

                                       GCCCCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETT CS
                               ROK  81 itwenfdlvekleerlnvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviing 142
                                                                                               Gv++ng
  gi|488601534|ref|YP_007908005.1| 284 --------------------------------------------------------GVLVNG 289
                                       ........................................................444444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.2
                                       EEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEE.EEEEEESSEEETTCCEBSSGGCGCCC CS
                               ROK  27 kvetptetteetlvdaiaelvdeaerkadeli.avgigspGlisdksgkivstpnitwe 84 
                                        ve+ + +++ ++++ai+ ++++ e     l+ + +i++p  + ++ + ++++p+ +++
  gi|488601534|ref|YP_007908005.1| 380 LVEKAAGKIKTMVEEAIDRMKTSPEPVPVILVgGGSIIIPDEL-RGASEVIKPPHFEVA 437
                                       4455555555555555555555555444322222334444444.666666677666654 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.3e-05     0.086       1      58 [.       5      69 ..       5      79 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
                    DEDD_Tnp_IS110  1 vGiDvakdkhdacvidaegkvllservpndee.......glealleklaakagevlvvveatghy 58
                                      +GiDv+ ++ da+++d++ + +++ +v+++e+       +l+ +l++ + + +e++ ++  t+h 
  gi|488601534|ref|YP_007908005.1|  5 LGIDVGGTNTDAVILDKNDQPVAKIKVATTEDvttgilnALDGVLKDSSVDPSEIKYAMLGTTHC 69
                                      5****************************996333222244444444444456666666666665 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00055       0.9     112     160 ..     119     165 ..      67     224 .. 0.63
   2 ?   -2.2   0.0       2.9   4.7e+03      33      55 ..     391     414 ..     343     423 .. 0.63
   3 ?    1.0   0.0       0.3   4.9e+02      27      58 ..     458     485 ..     452     511 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00055
                                       SSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 112 addekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeel 160
                                       +++ + ++l  +  + eev++a++ l+e+g+++v +  v  p  n++el
  gi|488601534|ref|YP_007908005.1| 119 GHEYDGRELA-P-LDEEEVKRAVKDLKEKGVESVAISAVFSPVNNEHEL 165
                                       4444322333.2.456777777777777777755555555554444443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHTT.SEEEEEESS CS
                                       xxxxxxxxxxxxxx.xxxxxxxxx RF
                       Radical_SAM  33 eileevkelkaekg.vkevilggg 55 
                                       +++e ++++k ++  v ++++ggg
  gi|488601534|ref|YP_007908005.1| 391 MVEEAIDRMKTSPEpVPVILVGGG 414
                                       233333444422232555555555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHHTTSEEEEEESSTGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  27 rslsveeileevkelkaekgvkevilgggepl 58 
                                       +++s e++l+e+ke++    vke i  g +p+
  gi|488601534|ref|YP_007908005.1| 458 EERSREDVLKEAKEIA----VKEAIKAGADPN 485
                                       6789999999999998....666666666665 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.9    0.0049         8       2      42 ..       6      46 ..       5     246 .. 0.83
   2 ?    9.5   2.0    0.0008       1.3       1      25 [.     272     296 ..     272     493 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0049
                                      EEEE-SSSEEEEEEETTEEEEEEEES-.-HHHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                              FtsA  2 lvDiGagktdvavaedgalvhlrvigv.ggngitkdiakalr 42
                                      ++D+G++ td+++++++  + ++ i+v   + +t +i +al 
  gi|488601534|ref|YP_007908005.1|  6 GIDVGGTNTDAVILDKND-QPVAKIKVaTTEDVTTGILNALD 46
                                      79*************964.23555555566778888766664 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0008
                                       EEEEE-SSSEEEEEEETTEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA   1 alvDiGagktdvavaedgalvhlrv 25 
                                       ++vD+G+++td+ v+ +g ++ ++v
  gi|488601534|ref|YP_007908005.1| 272 VVVDVGGTTTDIGVLVNGFPRESSV 296
                                       79***************99988443 PP

>> DUF3783  Domain of unknown function (DUF3783)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019       0.3       8      41 ..     130     164 ..     127     177 .. 0.81
   2 ?   -3.5   0.0       6.6   1.1e+04      15      26 ..     214     225 ..     212     228 .. 0.75
   3 ?   -2.7   0.1       3.6   5.9e+03      16      31 ..     465     480 ..     460     482 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                           DUF3783   8 fsseeldklldalkkaglp.iplkAvlTptNinWt 41 
                                       +++ee++++++ lk++g++ +++ Av  p N +  
  gi|488601534|ref|YP_007908005.1| 130 LDEEEVKRAVKDLKEKGVEsVAISAVFSPVNNEHE 164
                                       799***********************999997654 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.6
                           DUF3783  15 klldalkkaglp 26 
                                        + +alkk+g++
  gi|488601534|ref|YP_007908005.1| 214 SFENALKKKGID 225
                                       567899**9996 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.6
                           DUF3783  16 lldalkkaglpiplkA 31 
                                       +l++ k+  +++++kA
  gi|488601534|ref|YP_007908005.1| 465 VLKEAKEIAVKEAIKA 480
                                       7889999999999998 PP

>> GA-like  GA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.13   2.1e+02      13      26 ..     136     149 ..     132     151 .. 0.85
   2 ?    2.1   0.1      0.12   1.9e+02      18      32 ..     218     232 ..     213     235 .. 0.88
   3 ?    7.8   0.3    0.0019       3.1       4      26 ..     462     483 ..     459     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.13
                           GA-like  13 eaAkaeLkaaGits 26 
                                       + A+++Lk+ G++s
  gi|488601534|ref|YP_007908005.1| 136 KRAVKDLKEKGVES 149
                                       46999*******76 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                           GA-like  18 eLkaaGitsdfyiek 32 
                                       +Lk+ Gi+  +yi++
  gi|488601534|ref|YP_007908005.1| 218 ALKKKGIDAQLYITQ 232
                                       7***********975 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0019
                           GA-like   4 kkeaLkeAKeaAkaeLkaaGits 26 
                                        ++ LkeAKe A++e  +aG+ +
  gi|488601534|ref|YP_007908005.1| 462 REDVLKEAKEIAVKEAIKAGA-D 483
                                       5678***********999999.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.76u 0.39s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 2842.02
//
Query:       gi|488601535|ref|YP_007908006.1|  [L=362]
Description: hypothetical protein Asulf_02050 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-140  465.4   0.4     1e-139  465.2   0.4    1.0  1  DUF917    Protein of unknown function (DUF917)


Domain annotation for each model (and alignments):
>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.2   0.4  5.8e-144    1e-139       1     350 []       7     354 ..       7     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 465.2 bits;  conditional E-value: 5.8e-144
                                       GGHHHHHHHHHHTTTT-SS-HHHHHHHHTT-SBTT--EEEE-GGG--SEE..EEEEEEE-HHHHTT-SS-HH....H CS
                            DUF917   1 edlealatGaavLGtGGGGspysgylllrqaleegksvrvvsldelpddalvvvvgamGsptvieeklpsgdellea 77 
                                       ed+e+la Gaa+LGtGGGG+py g+l++ qal+eg +++vv+++e+pddalv++ + mGsptvi+ek+p+g+e+++a
  gi|488601535|ref|YP_007908006.1|   7 EDIENLAVGAAILGTGGGGDPYLGKLTAIQALDEGYEINVVDVKEVPDDALVIPSAGMGSPTVIVEKIPKGTEIINA 83 
                                       69*********************************67**************************************** PP

                                       HHHHHHHHT--EEEEE-SSSSCCHHHHHHHHHHHHT-EEESB-SSSS--SSGGGSHHHHTT----SEEEE-SSS-EE CS
                            DUF917  78 vealekllgrkidavislEiGGlNglvallaaaklglpvvDaDgmGRAfPelqqttfavagisltPlaladekgnvv 154
                                       +++l+++lgr++ a++++E+GGlN++ +l+++ak+g+p+vDaDgmGRAfPelq+ttf+++g+++tP+alade++n+v
  gi|488601535|ref|YP_007908006.1|  84 FKTLSEYLGREVYATMPIEAGGLNSTFPLAVGAKMGIPIVDADGMGRAFPELQMTTFHINGVTVTPMALADERDNTV 160
                                       ***************************************************************************** PP

                                       EEEE.---HHHHHHHHHHCTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--...-SHHHHHHHHHH CS
                            DUF917 155 llkkaqsdkavErllRaalvemgsfagvaaypmtgaelkraavpgtlslalriGravaeareak.dvveailealgg 230
                                       llk++++  ++E ++R++++++g+ a++a ypmtg+elk+aa+pgt+ la ++G av+e +e+k ++++a+l++++ 
  gi|488601535|ref|YP_007908006.1| 161 LLKTCDNY-WAEWIARDITIRFGGTAWIALYPMTGKELKKAAIPGTMGLAEKLGAAVRETKESKgNPIDAVLDVSN- 235
                                       ****5555.****************************************************9856***********. PP

                                       -EEEEEEEEE--------------EEEET.......EEEEEEESSSEEEEE..ET-SEETTSEEEEEHHB-SSSSB- CS
                            DUF917 231 gakvlfkGkivdverrteggfdvgevtiegldedegrelkiefqNEnllaeedgevlatvPDlIsvldaetgepigt 307
                                       g++ lfkGkivdv rrt+ggf++ge++ieg+de++g++l ++fqNEnl+a++dgev+a+vPDlI++ld et+ pi+t
  gi|488601535|ref|YP_007908006.1| 236 GFE-LFKGKIVDVVRRTTGGFARGEIKIEGIDEYKGQNLLVHFQNENLVAIKDGEVIASVPDLITLLDLETAMPITT 311
                                       899.************************************************************************* PP

                                       TTTT.TS-EEEEEE---GGGS..SHHHH-S-....-....--- CS
                            DUF917 308 eelryGlrVtVlalpasekwrteeglelvgPkaFGydleykpl 350
                                       e ++yG r++V+++p+se wrte+gle++gPk+FGyd+eykp+
  gi|488601535|ref|YP_007908006.1| 312 EAVKYGYRCFVIGIPCSEMWRTEKGLEVAGPKYFGYDVEYKPI 354
                                       *****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2012.42
//
Query:       gi|488601536|ref|YP_007908007.1|  [L=33]
Description: hypothetical protein Asulf_02052 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); 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: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 193.83
//
Query:       gi|488601537|ref|YP_007908008.1|  [L=90]
Description: hypothetical protein Asulf_02053 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 506.38
//
Query:       gi|488601538|ref|YP_007908009.1|  [L=329]
Description: Outer membrane lipoprotein-sorting protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-12   45.4   4.4    2.8e-11   43.5   1.7    2.4  2  LolA_like  Outer membrane lipoprotein-sorting protein
    2.1e-10   40.5   0.0    3.6e-10   39.7   0.0    1.4  1  MucB_RseB  MucB/RseB N-terminal domain
    1.9e-09   37.4   0.4    1.1e-08   34.9   0.1    2.1  2  LolA       Outer membrane lipoprotein carrier protein LolA
    6.9e-09   35.4   0.1    2.5e-05   23.7   0.0    2.3  2  DUF2092    Predicted periplasmic protein (DUF2092)
      4e-08   33.7   1.2      4e-08   33.7   1.2    2.5  2  DUF4367    Domain of unknown function (DUF4367)
    2.4e-05   24.2   0.8    5.4e-05   23.1   0.8    1.6  1  DUF4412    Domain of unknown function (DUF4412)
  ------ inclusion threshold ------
       0.16   11.9   1.1        2.8    8.0   0.2    2.5  2  DUF3787    Domain of unknown function (DUF3787)


Domain annotation for each model (and alignments):
>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   1.7   1.1e-14   2.8e-11       8     118 ..      65     171 ..      61     173 .. 0.83
   2 ?    1.7   0.0     0.075   1.9e+02     157     177 ..     178     198 ..     174     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.1e-14
                                       EEEESTTT....TT-EEEEESSSTTEEEEEETTTTCEEEE-GGGTTSECCTTC.EHHHHC--SCCCEEEEEEEEEEE CS
                         LolA_like   8 vftePadv....kGtafLtlkekdddlWlYlPalkrvrrisssdksqsfmGsdfsyeDlssrevedythellgeeev 80 
                                       vf++P +v    k +++L + ++++++W+Y+ + ++v  +     + + ++ d  y+ l ++ ++ y++++lg+e+v
  gi|488601538|ref|YP_007908009.1|  65 VFKKPNKVrmhnKEMGTLIV-SNGEKMWIYDEKKNEVFVMD--VGQYNQVNPD--YGELVKDMLKRYDVKILGSEKV 136
                                       56666665222246666766.899*********99999998..4455556777..********************** PP

                                       TTEEEEEEEEEESS.TTSSECEEEEEEETTT--EEEEE CS
                         LolA_like  81 ggkdcyvleltpkdaadvsYskivlwvdketylplkve 118
                                        g+dcyv++ltpkd+   +  + ++wvdke ++plk+e
  gi|488601538|ref|YP_007908009.1| 137 SGRDCYVVQLTPKDN---ESIEAKMWVDKEYWYPLKIE 171
                                       **************5...556899************98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.075
                                       EEEEEEEEEEE--.--GGGCS CS
                         LolA_like 157 kTvleisevefdkglpdklFt 177
                                       k+++e+ +vef++g++d+ F+
  gi|488601538|ref|YP_007908009.1| 178 KSTVEYINVEFNTGVSDDEFQ 198
                                       8999*************9996 PP

>> MucB_RseB  MucB/RseB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   1.4e-13   3.6e-10      58     146 ..      83     171 ..      77     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.4e-13
                         MucB_RseB  58 virrndevscfepeskavsvesrkikdslpallpadlealeehYefrllGreRvAgreaqvvrilPkDqlRYgyrlw 134
                                       ++ +++++ ++ +++++v v +    +++     +  +++ + Y++++lG+e+v+gr++ vv+++PkD+   + ++w
  gi|488601538|ref|YP_007908009.1|  83 IVSNGEKMWIYDEKKNEVFVMDVGQYNQVNPDYGELVKDMLKRYDVKILGSEKVSGRDCYVVQLTPKDNESIEAKMW 159
                                       56778888888777777666666555999999999999*************************************** PP

                         MucB_RseB 135 iDeetgLlLksd 146
                                       +D+e   +Lk++
  gi|488601538|ref|YP_007908009.1| 160 VDKEYWYPLKIE 171
                                       **********87 PP

>> LolA  Outer membrane lipoprotein carrier protein LolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   4.4e-12   1.1e-08      31     165 .]      66     200 ..      52     200 .. 0.78
   2 ?    0.0   0.0      0.24   6.1e+02      97     129 ..     221     254 ..     209     286 .. 0.67

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4.4e-12
                                       EETTTEEEEEE-TTS-EEEEEETTEEEEEETTTTEEEEEEHHHHTTT-GGG.GGGS-HHHHTTTEEEE.EEEE.... CS
                              LolA  31 ikrPgkfrweytsPdeqlivsdgktvwlydpdleqvtieslkqalsktplv.lLledkaklskdynvs.vkke.... 101
                                       +k+P+k+r++ ++    livs+g+++w+yd + ++v ++++ q  + +p    L+   +++ k+y+v+   +e    
  gi|488601538|ref|YP_007908009.1|  66 FKKPNKVRMHNKE-MGTLIVSNGEKMWIYDEKKNEVFVMDVGQYNQVNPDYgELV---KDMLKRYDVKiLGSEkvsg 138
                                       89********887.99***********************9887777776441333...5666666666544431111 PP

                                       TTEEEEEEEESSS-SSECEEEEEE.ETTEEEEEEEEET.T--EEEEEEEEEEES----GGGG--- CS
                              LolA 102 qdldtltlkpkakdanlsritigfdkkgllkqlkvvda.qGqrttitfsnvkenakladdlFkft 165
                                        d  +++l+pk  d+   ++++++dk+     lk+  +  G ++t++  nv+ n  ++dd F+ft
  gi|488601538|ref|YP_007908009.1| 139 RDCYVVQLTPK--DNESIEAKMWVDKEY-WYPLKIEHSiGGIKSTVEYINVEFNTGVSDDEFQFT 200
                                       56778999999..8888899****7777.666666555167899*******************97 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.24
                                       EEEEETTEEEEEEEES.SS-SSECEEEEEE.ETT CS
                              LolA  97 svkkeqdldtltlkpk.akdanlsritigfdkkg 129
                                        ++ ++ +d   lkp  ++   l++++++f+  +
  gi|488601538|ref|YP_007908009.1| 221 VEEAQKHVDFRILKPAyTAGYELKEVSLMFNSVS 254
                                       4344444444456777777777888888887654 PP

>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00015      0.39      29      88 ..      49     106 ..      45     129 .. 0.76
   2 !   23.7   0.0   9.9e-09   2.5e-05     126     207 ..     127     206 ..     111     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                           DUF2092  29 vlasgqklqfsasrevkvqrPdklrvdtsgdekdrefyyDGktftlydkaenvYaqapap 88 
                                       v+a+g+  +++ + e   ++P+k+r++ +  e  + ++++G+++ +yd+++n + +++++
  gi|488601538|ref|YP_007908009.1|  49 VTAEGKSGKMVMEYEYVFKKPNKVRMHNK--EMGTLIVSNGEKMWIYDEKKNEVFVMDVG 106
                                       778888888899999999*******9986..56678999999999999999987776654 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 9.9e-09
                           DUF2092 126 sakyvgtskvngqecehlafr...nkdvdwqlWIsqgdkpLprkivityktdpgapqytaefsdWnldpeipedtFr 199
                                       ++k++g++kv g +c++++++   n+ ++  +W+ ++++  p+ki     +  g  ++t+e+ + ++++ +++d F+
  gi|488601538|ref|YP_007908009.1| 127 DVKILGSEKVSGRDCYVVQLTpkdNESIEAKMWV-DKEYWYPLKI----EHSIGGIKSTVEYINVEFNTGVSDDEFQ 198
                                       6899**************7652227779******.6667789998....57789999******************** PP

                           DUF2092 200 ftpPkgAr 207
                                       ftpP+gA+
  gi|488601538|ref|YP_007908009.1| 199 FTPPEGAK 206
                                       ******98 PP

>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.2      0.97   2.5e+03      18      38 ..      83     102 ..      27     130 .. 0.60
   2 !   33.7   1.2   1.6e-11     4e-08      21     110 .]     249     328 ..     233     328 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.97
                           DUF4367  18 isedsesalleYkdengelis 38 
                                       i+ + e++++ Y ++++e ++
  gi|488601538|ref|YP_007908009.1|  83 IVSNGEKMWI-YDEKKNEVFV 102
                                       2333333333.2223333333 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.6e-11
                           DUF4367  21 dsesalleYkdengelisfsiskqskeesqklsidteda.......evekieingikatyyekedgeyvlvwedegv 90 
                                        ++s++l Y  ++++ ++++                ++        + e++++   ++ y e+ +   +l++++++v
  gi|488601538|ref|YP_007908009.1| 249 MFNSVSLMYA-KKDKMLMIT---------------EAKGeelpkmqNAENVKVEDSEGLYAEIYGS-SMLMFKKGDV 308
                                       4444444442.333333333...............11113335555779**************999.9********* PP

                           DUF4367  91 vytlsgniskeelikiaesi 110
                                       v+t++g iskeelikiaes+
  gi|488601538|ref|YP_007908009.1| 309 VVTMTGMISKEELIKIAESM 328
                                       *******************8 PP

>> DUF4412  Domain of unknown function (DUF4412)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.8   2.1e-08   5.4e-05       1     121 [.      43     163 ..      43     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.1e-08
                           DUF4412   1 FeGvlemkltapkges..emtyflgk.ekqRmemsvqlkkipeklkttvltkakkpdelyilnekaktYseidlkea 74 
                                       F+G+l+++    +g++  e +y+++k +k+Rm  + +   i ++ + + + ++kk +e+ ++  + + Y++++    
  gi|488601538|ref|YP_007908009.1|  43 FKGILRVTAEGKSGKMvmEYEYVFKKpNKVRMHNKEMGTLIVSNGEKMWIYDEKK-NEVFVM--DVGQYNQVNP--- 113
                                       8999999998887776336678887647899988877776666666455666655.666655..4567999998... PP

                           DUF4412  75 aesaalldadsdytveklGketikGYsCehvritskee...tlelWvtkd 121
                                       + ++ ++d  + y+v+ lG e++ G +C  v++t k++   +  +Wv k+
  gi|488601538|ref|YP_007908009.1| 114 DYGELVKDMLKRYDVKILGSEKVSGRDCYVVQLTPKDNesiEAKMWVDKE 163
                                       7889999999************************4444336789**9886 PP

>> DUF3787  Domain of unknown function (DUF3787)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0011       2.8      35      49 ..     148     162 ..     144     164 .. 0.91
   2 ?    2.0   0.0      0.08     2e+02      26      48 ..     207     229 ..     203     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                           DUF3787  35 PseeeVenAKewVDn 49 
                                       P+++e ++AK wVD+
  gi|488601538|ref|YP_007908009.1| 148 PKDNESIEAKMWVDK 162
                                       999***********7 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.08
                           DUF3787  26 lkpeskVsiPseeeVenAKewVD 48 
                                        k+e    i + ++Ve+A ++VD
  gi|488601538|ref|YP_007908009.1| 207 IKTEEDLGIKKFNSVEEAQKHVD 229
                                       56666666667789********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 1850.93
//
Query:       gi|488601539|ref|YP_007908010.1|  [L=267]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    2.8e-10   40.2   0.0    1.4  1  DUF1724   Domain of unknown function (DUF1724)
      8e-06   25.8   0.0    1.4e-05   25.0   0.0    1.4  1  HTH_20    Helix-turn-helix domain
      3e-05   23.9   0.0    7.7e-05   22.6   0.0    1.6  1  HTH_45    Winged helix-turn-helix
      0.001   18.9   0.0     0.0022   17.8   0.0    1.6  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0011   18.8   0.0     0.0021   17.9   0.0    1.4  1  MarR_2    MarR family
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.019   14.8   0.0    1.4  1  RuvB_C    RuvB C-terminal winged helix domain
      0.021   14.7   0.0       0.04   13.9   0.0    1.4  1  MarR      MarR family
      0.022   14.8   0.0      0.043   13.9   0.0    1.4  1  HemN_C    HemN C-terminal domain
      0.047   13.6   0.0      0.084   12.8   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.047   13.3   0.0      0.091   12.3   0.0    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
       0.06   13.2   0.0       0.11   12.3   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain
      0.087   12.8   0.0       0.17   11.8   0.0    1.5  1  HTH_11    HTH domain
       0.12   12.0   0.0        0.2   11.3   0.0    1.2  1  RP-C      Replication protein C N-terminal domain
       0.16   12.0   0.0       0.29   11.2   0.0    1.4  1  HTH_29    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.2e-13   2.8e-10       2      62 .]     193     251 ..     192     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.2e-13
                           DUF1724   2 klyvydeeikplsltvtDkflslslfdkdgkydhk.dlisfdesAlkWGeeLFeyYlkrSep 62 
                                       +++v+++   +++++v++k ++++l+  d  yd +   ++++++A++WG +LF+ + +rS++
  gi|488601539|ref|YP_007908010.1| 193 EMRVCSDA--KVAFVVAEKGFAMGLYVGD-AYDANhIFVCTSDEAVRWGFKLFNNFYSRSRK 251
                                       68999984..9******************.5****8899*********************85 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.1e-08   1.4e-05       9      60 ..      14      63 ..       8      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.1e-08
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                       P  ++il  L  + ++  s la+ ld+s+ t+  H+r  +eagLve+ +eg
  gi|488601539|ref|YP_007908010.1| 14 TPLKLKILEGL--ENPAGISSLARSLDVSRDTVKPHIRNFVEAGLVERCGEG 63
                                      49999******..***********************************9998 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     6e-08   7.7e-05      10      75 ..      19      83 ..      13      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6e-08
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                       ILe + e+ a  +++  + + s ++++  +   ve gl++  +e Y+lT+ G+ +lek  e+e+l
  gi|488601539|ref|YP_007908010.1| 19 KILEGL-ENPAGISSLARSLDVSRDTVKPHIRNFVEAGLVERCGEGYRLTALGRIILEKAVEVEKL 83
                                      799999.99***************************************************999987 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 !   17.8   0.0   1.7e-06    0.0022       2      46 ..      15      58 ..      14      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      p +lkIL  L e+++ ++ la+ l++s+ tv  H +   eaGLVe
  gi|488601539|ref|YP_007908010.1| 15 PLKLKILEGL-ENPAGISSLARSLDVSRDTVKPHIRNFVEAGLVE 58
                                      5566666666.589******************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.6e-06    0.0021      25      54 ..      31      60 ..      14      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 25 gelarrlglsksavsrilkrLvaaGLverr 54
                                      + lar l++s+ +v  +++ +v+aGLver+
  gi|488601539|ref|YP_007908010.1| 31 SSLARSLDVSRDTVKPHIRNFVEAGLVERC 60
                                      679*************************98 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 ?   14.8   0.0   1.5e-05     0.019      13      71 ..      19      74 ..      14      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                      HHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-HHHHHHH CS
                            RuvB_C 13 kllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTkkglkyl 71
                                      k+l     ++p+g+++la  l+++++t+   i   +++ gl+er   G +lT  g  +l
  gi|488601539|ref|YP_007908010.1| 19 KILEG--LENPAGISSLARSLDVSRDTVKPHI-RNFVEAGLVERCGEGYRLTALGRIIL 74
                                      55544..579*******************999.678****************9997766 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.1e-05      0.04      16      49 ..      26      59 ..      14      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +p+ +s La+ l vs+ tv   ++  +++Gl+eR
  gi|488601539|ref|YP_007908010.1| 26 NPAGISSLARSLDVSRDTVKPHIRNFVEAGLVER 59
                                      46899****************************9 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-05     0.043      35      65 ..      41      71 ..      27      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                            HemN_C 35 eellaaaleklqeqGLLeldggrlrltprGr 65
                                      ++++++ ++ + e+GL+e  g+++rlt  Gr
  gi|488601539|ref|YP_007908010.1| 41 RDTVKPHIRNFVEAGLVERCGEGYRLTALGR 71
                                      4566999**********************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.5e-05     0.084      20      57 ..      25      62 ..      18      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.5e-05
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      + pa ++ +a+ l+v+r +v   +r+ +++GlVer  +
  gi|488601539|ref|YP_007908010.1| 25 ENPAGISSLARSLDVSRDTVKPHIRNFVEAGLVERCGE 62
                                      56888999**************************9755 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   7.1e-05     0.091      21      48 .]      31      58 ..      16      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + LA+ l++S+ tv+ ++++++e+Gl++
  gi|488601539|ref|YP_007908010.1| 31 SSLARSLDVSRDTVKPHIRNFVEAGLVE 58
                                      67************************96 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.5e-05      0.11       9      50 ..      18      59 ..      18      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.5e-05
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      L++l+    + ++s lAr +++++ tv  +++ +ve G+ve+
  gi|488601539|ref|YP_007908010.1| 18 LKILEGLENPAGISSLARSLDVSRDTVKPHIRNFVEAGLVER 59
                                      67888889999*****************************97 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   0.00014      0.17       7      38 ..      19      50 ..      16      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                            HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIka 38
                                      ++L   ++p  ++ LA+ L+vSr tv  +I+ 
  gi|488601539|ref|YP_007908010.1| 19 KILEGLENPAGISSLARSLDVSRDTVKPHIRN 50
                                      45544455577889**************9986 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016       0.2      76     102 ..      32      58 ..      30      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                              RP-C  76 qLsralglsestlrrhlaaLveaGlii 102
                                        L+r+l++s+ t++ h+++ veaGl+ 
  gi|488601539|ref|YP_007908010.1|  32 SLARSLDVSRDTVKPHIRNFVEAGLVE 58 
                                       5899*********************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.29      14      41 ..      29      56 ..      18      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGl 41
                                       +s +A+ l++sr+tv  +++ f+e Gl
  gi|488601539|ref|YP_007908010.1| 29 GISSLARSLDVSRDTVKPHIRNFVEAGL 56
                                      4899********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1468.68
//
Query:       gi|488601540|ref|YP_007908011.1|  [L=288]
Description: hypothetical protein Asulf_02058 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1599.06
//
Query:       gi|488601541|ref|YP_007908012.1|  [L=350]
Description: Glycosyltransferase, probably involved in cell wall biogenesis [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-13   48.7   0.0    6.9e-12   45.7   0.0    1.9  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.1e-11   43.0   0.6    7.3e-11   42.2   0.6    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
    7.2e-08   32.6  15.4    5.9e-07   29.6  15.4    2.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
       0.12   12.5   0.1       0.24   11.6   0.1    1.4  1  CSD2             Cold shock domain
       0.14   10.8   7.7       0.23   10.0   7.7    1.2  1  Chitin_synth_2   Chitin synthase
       0.29   11.5   2.3       0.52   10.7   2.3    1.4  1  CRCB             CrcB-like protein, Camphor Resistance (CrcB)


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 !   45.7   0.0   2.3e-15   6.9e-12       4     230 .]       2     202 ..       1     202 [. 0.82

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.3e-15
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       l+v++++++++ +++e +  l    +++ e+++ +de d e  e +    +++     ++  n+r    +gk raln
  gi|488601541|ref|YP_007908012.1|   2 LSVIITAYKNAGYIEENIKKL----NHNAEIIIAADEPDSEIKEIV----DKYNLK--HTFSNKR----RGKWRALN 64 
                                       89********88887777766....568************955555....567653..4555544....7******* PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralgv 157
                                       +al+ v++d +l++D+Dt++ +   + l ++       +v  +++  n stl+ +l ++ +   +l   + ++ ++ 
  gi|488601541|ref|YP_007908012.1|  65 DALKLVEGDKILFLDSDTRIVDFDPEILDHY------SVVEIRKEI-NSSTLMERLVNIDYFNMFLTAKLSSKLGTC 134
                                       ********************88774444344......466666665.578999999999999999988888888889 PP

                   Glyco_tranf_2_3 158 ltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                       l lnGs +lir +v + +   +++  +++D++lg+r+  ag  + +v g+   +  p slk+   qr+Rw+ g
  gi|488601541|ref|YP_007908012.1| 135 LGLNGSAFLIRKDVIEKF---RFRRRIVEDADLGVRVGIAG-ESFFVDGR-ALTKAPNSLKKWLIQRERWALG 202
                                       ******************...44669*************98.67888888.6788888************975 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.6   2.4e-14   7.3e-11       1      91 [.       3      83 ..       3     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.4e-14
                                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH-- CS
                   Glycos_transf_2  1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraat 79
                                      sv+i++y  + +++e ++ l  +      eii++ D    e +ei++++     +++    ++++Gk +aln +l+ + 
  gi|488601541|ref|YP_007908012.1|  3 SVIITAYKNAGYIEENIKKLNHN-----AEIIIAADEPDSEIKEIVDKY-----NLKHTFSNKRRGKWRALNDALKLVE 71
                                      8*****************88886.....*********************.....9************************ PP

                                      SSEEEEEESSEE CS
                   Glycos_transf_2 80 gdyilflDaDde 91
                                      gd ilflD+D+ 
  gi|488601541|ref|YP_007908012.1| 72 GDKILFLDSDTR 83
                                      **********86 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  15.4     2e-10   5.9e-07       2     191 ..      75     300 ..      74     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2e-10
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvm.....nvanwleelaalffaedhgkdilvrealgrvvpsv 73 
                                       il+lD+Dt++   +  ei+++++           +v+     n+++++e+l  + + ++++ + l+ ++lg ++ + 
  gi|488601541|ref|YP_007908012.1|  75 ILFLDSDTRIVD-FDPEILDHYS-----------VVEirkeiNSSTLMERLVNIDYFNMFLTAKLS-SKLGTCLGLN 138
                                       566666666654.3333434442...........22111346788999999999988899999888.69******** PP

                   Glyco_trans_2_3  74 GsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc...... 144
                                       Gs +++r +++++  +++   + + ED d+g+r   +G   +fv+++   +k p++l+ +l Qr+Rwa+G       
  gi|488601541|ref|YP_007908012.1| 139 GSAFLIRKDVIEKF-RFR---RRIVEDADLGVRVGIAG-ESFFVDGR-ALTKAPNSLKKWLIQRERWALGGaeivme 209
                                       **************.666...5899************7.67899999.79********************8754433 PP

                   Glyco_trans_2_3 145 .eleklil................................................lvrllgylgsllwsalplhla 172
                                        +                                                       v+ + ++ + ++s l+++ +
  gi|488601541|ref|YP_007908012.1| 210 fL-----WdlikkpvnilpvlflfypaiigflldlilpdylllkamylilppihhlPVNIVSLTLLAIFSMLSFRNL 281
                                       30.....1444566666777778888888999999989988877777777766664222223344444444555555 PP

                   Glyco_trans_2_3 173 llllfsllalalvllllll 191
                                       ++ l+s++ +al+++ll l
  gi|488601541|ref|YP_007908012.1| 282 VASLTSFAVWALAMILLSL 300
                                       5566666656666665554 PP

>> CSD2  Cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.9e-05      0.24      48      74 .]      27      53 ..      24      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.9e-05
                              CSD2 48 evLGkkgdpgveilsilakhglpeeFP 74
                                      e++  +++p+ ei+ i+ k++l++ F+
  gi|488601541|ref|YP_007908012.1| 27 EIIIAADEPDSEIKEIVDKYNLKHTFS 53
                                      788899********************7 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.7   7.7e-05      0.23     346     482 ..     175     317 ..     171     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.7e-05
                    Chitin_synth_2 346 fvpqakcktvaPdtfkvllsqrrrwinstvhnllelv....l..vrdlcGtfcfsmrfvvfieligtvvlPvaiaf. 415
                                       f  + ++ t aP++ k  l qr rw       ++e++    +  v+ l   f+f       i ++  ++lP  +++ 
  gi|488601541|ref|YP_007908012.1| 175 FFVDGRALTKAPNSLKKWLIQRERWALGGAEIVMEFLwdliKkpVNILPVLFLFYPA---IIGFLLDLILPDYLLLk 248
                                       7778999******************98887777776522112223344444444333...34445567899887762 PP

                    Chitin_synth_2 416 tlylivasilksklvpviplvllai..vlGlpailivltarkleyvawllvyllalPifnf.vlPlyafw 482
                                        +yli+  i +  +v++++l llai  +l ++ ++  lt+  +  +a +l+ l +    +f +lP+y f+
  gi|488601541|ref|YP_007908012.1| 249 AMYLILPPIHH-LPVNIVSLTLLAIfsMLSFRNLVASLTSFAVWALAMILLSLTTNYRIEFrLLPIYYFF 317
                                       56777776665.9***********9445677889999998777777777777766555555368999886 PP

>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.3   0.00017      0.52       7      92 ..     231     328 ..     225     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHH.HHHHBE.......BHHHHHHHHHHHHHHHHHHHHHTTTHHHHHS-SHHHHHHHHHHHHHT-HHHH CS
                              CRCB   7 galGallRyllssllnkr.......plgtlavNvlGsfllglllallttGflGglTTfStfvlelvslleegellaa 76 
                                       +++G ll ++l ++l+ +       p+  l vN++   ll+++ +l    ++ +lT f+ ++l ++ l  + ++   
  gi|488601541|ref|YP_007908012.1| 231 AIIGFLLDLILPDYLLLKamylilpPIHHLPVNIVSLTLLAIFSMLSFRNLVASLTSFAVWALAMILLSLTTNYRIE 307
                                       6666666666666665556777777789999**************999****************9999855544444 PP

                                       H.....HHHHHHHHHHHHHHH CS
                              CRCB  77 l.....lyvllsvvlgllavv 92 
                                       +      y++ s +++++++v
  gi|488601541|ref|YP_007908012.1| 308 FrllpiYYFFYSPLWAMICFV 328
                                       447786666778777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 1916.28
//
Query:       gi|488601542|ref|YP_007908013.1|  [L=215]
Description: LSU ribosomal protein L1P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  155.3   3.7      2e-45  155.1   3.7    1.1  1  Ribosomal_L1   Ribosomal protein L1p/L10e family
  ------ inclusion threshold ------
      0.083   12.8   0.3       0.57   10.1   0.0    2.2  2  MtrG           Tetrahydromethanopterin S-methyltransferase, s
       0.28   11.5   5.2          3    8.1   0.3    2.3  2  Ribosomal_L22  Ribosomal protein L22p/L17e


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 !  155.1   3.7   3.3e-49     2e-45       2     204 .]      17     210 ..       8     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 3.3e-49
                                       HHHS-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHH CS
                      Ribosomal_L1   2 lkhakkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklk 78 
                                       +k + ++f e+ve+a+nl+++++kk+++r+   ++Lp+++gk+ k+ +++k+++a    +akeag  + v + +++ 
  gi|488601542|ref|YP_007908013.1|  17 KKSKDRNFLETVEVAVNLKNLDMKKPENRIDALVTLPNGTGKDRKVGVFAKGDTAL---KAKEAG-ADVVFSAEDID 89 
                                       566677899***********************************************...******.667789***** PP

                                       HHHT-HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC...CT.BTS-HHHHHHHHCTTEEEEE-TTT CS
                      Ribosomal_L1  79 kkyksfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipv.ltkgtvkedvkkevekalkstvvvrldkg 154
                                       +  k++++ rk+++e d+f+a+  +mp+++k LG+++g+r+k+P p+         d k  +++++k +v++r++++
  gi|488601542|ref|YP_007908013.1|  90 ELAKDKRKLRKIANEMDFFIAEAPLMPEIGKKLGPILGPRGKIPQPIpPL-----SDPKPVIDRLKK-SVKIRTRDK 160
                                       ***********************************************433.....389*********.********* PP

                                       SEEEEEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 155 tclsvkvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                        +++++vG+ +++++e+ eNi +++k +++k ++  +n+ks+y+kttm+p
  gi|488601542|ref|YP_007908013.1| 161 MTFHAPVGTKNMSPDEISENILEILKVVENKYENAVNNVKSVYVKTTMGP 210
                                       *************************************************8 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   9.6e-05      0.57       8      42 ..      87     123 ..      80     127 .. 0.76
   2 ?   -0.1   0.1      0.15   8.9e+02       9      33 ..     174     199 ..     169     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.6e-05
                              MtrG   8 dpddfnevkkrLdeieekvefvnsE..iaqriGkkvG 42 
                                       d d+  + k++L +i + ++f+ +E  ++  iGkk+G
  gi|488601542|ref|YP_007908013.1|  87 DIDELAKDKRKLRKIANEMDFFIAEapLMPEIGKKLG 123
                                       4455556678*************99445789****99 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.15
                              MtrG   9 pddf.nevkkrLdeieekvefvnsEi 33 
                                       pd++ +++ + L  +e+k e++   +
  gi|488601542|ref|YP_007908013.1| 174 PDEIsENILEILKVVENKYENAVNNV 199
                                       55551458888888999988876654 PP

>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5     0.004        24      44      72 ..       5      33 ..       3      45 .. 0.88
   2 ?    8.1   0.3   0.00051         3      34      68 ..     171     206 ..     149     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.004
                                      HHHHHHHHHHHH..HT-GGGEEEEEEEEE CS
                     Ribosomal_L22 44 lklLknaeanaelkgldvdslvIeeiqvn 72
                                      ++++k+a+++a++k +d + l  +e+ vn
  gi|488601542|ref|YP_007908013.1|  5 KEVVKKAVEEAIKKSKDRNFLETVEVAVN 33
                                      589*******************9999998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00051
                                       T.-SSTTHHHHHHHHHHHHHHHH..HT-GGGEEEEE CS
                     Ribosomal_L22  34 f.skkkaakfvlklLknaeanaelkgldvdslvIee 68 
                                       + s+ + ++ +l++Lk +e++ e+  ++v+s+++++
  gi|488601542|ref|YP_007908013.1| 171 NmSPDEISENILEILKVVENKYENAVNNVKSVYVKT 206
                                       447788999*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1201.78
//
Query:       gi|488601543|ref|YP_007908014.1|  [L=337]
Description: LSU ribosomal protein L10P [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-28   96.9   1.8    1.6e-27   95.6   1.8    1.8  1  Ribosomal_L10  Ribosomal protein L10
    1.6e-15   56.8   0.3    4.5e-15   55.4   0.1    1.8  2  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
  ------ inclusion threshold ------
      0.022   14.6   0.2       0.11   12.4   0.2    2.2  2  DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
       0.82    9.9  11.9        0.4   10.9   9.1    1.9  2  DUF3886        Protein of unknown function (DUF3886)


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 !   95.6   1.8   3.5e-31   1.6e-27       3      98 ..       9     103 ..       7     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 3.5e-31
                                       CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.SSCGCCSSSE CS
                     Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeeklkellkgpv 79 
                                       +++K + v+elkel+k+y+++ +v+++g+++ q+q++R++lr++ +++kvvKntl+++A+ee++e e+lke+l  +v
  gi|488601543|ref|YP_007908014.1|   9 PQWKLKDVEELKELMKNYQTIGIVSFRGVPAGQMQKIRRELRDK-VKIKVVKNTLIEKAIEEAEEFESLKEFLGDQV 84 
                                       79*****************************************9.*******************9989********* PP

                                       EEEEESS-TCHHHHCCCCC CS
                     Ribosomal_L10  80 alvftnedpvalakvleef 98 
                                       a+v ++++p++l k le++
  gi|488601543|ref|YP_007908014.1|  85 AFVASDMNPFKLFKELEKT 103
                                       ***************9987 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 !   55.4   0.1   9.9e-19   4.5e-15       2      71 .]     110     179 ..     110     179 .. 0.98
   2 ?   -3.2   0.0         2   9.1e+03      31      44 ..     183     198 ..     183     205 .. 0.59

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 9.9e-19
                      RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       +++++++ dv++++gp++  Pg++   L+  glp+ ++kGkiv++  ++v+++Ge++++e a+ L+lL+i
  gi|488601543|ref|YP_007908014.1| 110 KPNQVSPVDVVVEKGPTSFPPGPVLGDLQMGGLPAAIEKGKIVIKDTVTVVRAGEVVKPEVAKALSLLEI 179
                                       7899****************************************************************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2
                      RL10P_insert  31 klglptkl..kkGkiv 44 
                                       klgl t++  +kG ++
  gi|488601543|ref|YP_007908014.1| 183 KLGLDTRVlmEKGIVF 198
                                       5777777422566555 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 ?   12.4   0.2   2.5e-05      0.11      43      70 ..     145     173 ..     143     178 .. 0.87
   2 ?   -3.5   0.0       2.2     1e+04      62      70 ..     260     268 ..     245     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                                       XXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
                     DNA_ligase_OB  43 eierkdirigdtVvvekaGdvI.Pevvgv 70 
                                        ie+  i i+dtV+v +aG+v+ Pev ++
  gi|488601543|ref|YP_007908014.1| 145 AIEKGKIVIKDTVTVVRAGEVVkPEVAKA 173
                                       588899**************998999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
                                       XXXXXXXXX CS
                     DNA_ligase_OB  62 dvIPevvgv 70 
                                       + IPe++g 
  gi|488601543|ref|YP_007908014.1| 260 EAIPEILGK 268
                                       679999876 PP

>> DUF3886  Protein of unknown function (DUF3886)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   7.7e+03       6      16 ..      74      84 ..      64      85 .. 0.61
   2 ?   10.9   9.1     9e-05       0.4       9      51 ..     282     328 ..     277     333 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                           DUF3886  6 vtLkDlLnedv 16
                                       +Lk+ L ++v
  gi|488601543|ref|YP_007908014.1| 74 ESLKEFLGDQV 84
                                      35666666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9e-05
                           DUF3886   9 kDlLnedvlekLk....akkkeLkeeeekrkeeekarreeerkarek 51 
                                       +++L+ed+l+k k    +k +    eeek++eee+ + eee k++e 
  gi|488601543|ref|YP_007908014.1| 282 EEALDEDLLAKVKsvevQKVETVSVEEEKKEEEEEVEEEEESKEEEA 328
                                       689*********9444446678999*******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2003  (0.111718); expected 358.6 (0.02)
Passed bias filter:                     1036  (0.0577835); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
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: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 1966.43
//
Query:       gi|488601544|ref|YP_007908015.1|  [L=105]
Description: LSU ribosomal protein L12AE [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-21   74.9  22.5    6.7e-21   74.7  22.5    1.1  1  Ribosomal_60s    60s Acidic ribosomal protein
     0.0067   16.5   1.5       0.18   11.9   0.1    2.4  2  VIGSSK           Helicase-associated putative binding domain,
  ------ inclusion threshold ------
        0.1   12.1   0.7       0.12   11.9   0.7    1.0  1  DUF2868          Protein of unknown function (DUF2868)
       0.22   10.5   4.3       0.25   10.3   4.3    1.0  1  Paf1             Paf1
       0.85    9.5   7.0        0.9    9.4   7.0    1.1  1  Spore_coat_CotO  Spore coat protein CotO


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 !   74.7  22.5   1.9e-24   6.7e-21       1      88 []      16     104 ..      16     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.9e-24
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaakla.aaaaaaaaaaaaaaaaaaaeekkkeeeee 76 
                                       e+t++ ik++l+aagvev++arvk+lv+ale+++iee++++++ ++a a aaa+aaa a++a+++++ee+++eee+ 
  gi|488601544|ref|YP_007908015.1|  16 EITEDGIKAILEAAGVEVNEARVKALVSALEDVNIEEAIEKASFAVApAPAAAPAAAPAEGAEEEKKEEEEEEEEK- 91 
                                       69****************************************9888844444444444444444444444444444. PP

                                       XX--SS--.STTT CS
                     Ribosomal_60s  77 EeedddmG.fgLF 88 
                                        ee+  +G ++LF
  gi|488601544|ref|YP_007908015.1|  92 KEEEAIEGlGALF 104
                                       5899999999999 PP

>> VIGSSK  Helicase-associated putative binding domain, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   5.1e-05      0.18      23      39 ..      16      32 ..       8      34 .. 0.85
   2 ?    3.4   0.2     0.023        83      10      30 ..      78      98 ..      69     101 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                            VIGSSK 23 kkksDaiqAILasaGVe 39
                                      +  +D i+AIL++aGVe
  gi|488601544|ref|YP_007908015.1| 16 EITEDGIKAILEAAGVE 32
                                      55689***********8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.023
                            VIGSSK 10 eakekkkeakkstkkksDaiq 30
                                      e+++k++e+++++kk ++ai+
  gi|488601544|ref|YP_007908015.1| 78 EEEKKEEEEEEEEKKEEEAIE 98
                                      333344444444777777775 PP

>> DUF2868  Protein of unknown function (DUF2868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   3.3e-05      0.12     149     211 ..      29      91 ..      22     103 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                           DUF2868 149 lpldlslpgyqaLlarlqtpsletgvnda.aapePeaapepkaeaepepasepadvlelelder 211
                                       + ++++ ++++aL++ l+   +e ++++a  a +P++a++p a++++++ +e++   e+e++e+
  gi|488601544|ref|YP_007908015.1|  29 AGVEVNEARVKALVSALEDVNIEEAIEKAsFAVAPAPAAAPAAAPAEGAEEEKK-EEEEEEEEK 91 
                                       45556699*********9999999999998445555555555555555444422.112222222 PP

>> Paf1  Paf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.3   7.1e-05      0.25     330     388 ..      36      94 ..      23     100 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.1e-05
                              Paf1 330 skkdklvvklrelneeelkarekresefdpleee......keeeeeeeeeeeeekseeeeekeee 388
                                        +++ lv  l+++n ee+ ++ ++   + p  ++      +       eee++e++eeeeek+ee
  gi|488601544|ref|YP_007908015.1|  36 ARVKALVSALEDVNIEEAIEKASFAVAPAPAAAPaaapaeG------AEEEKKEEEEEEEEKKEE 94 
                                       56778888899999999999999999998888885544332......333333311112222222 PP

>> Spore_coat_CotO  Spore coat protein CotO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.0   0.00025       0.9      49      98 ..      46      96 ..      15     102 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00025
                   Spore_coat_CotO 49 eekkpekaveeeveqekkkeaaePaeqeeeekaeeee.kkeeeeqkeeeee 98
                                      e+ + e+a+e+  +  + ++aa Pa +  e ++ee++ ++eeee+k+eee+
  gi|488601544|ref|YP_007908015.1| 46 EDVNIEEAIEKASFAVAPAPAAAPAAAPAEGAEEEKKeEEEEEEEKKEEEA 96
                                      444555555555444555555555554443333332202233333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1504  (0.0838864); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.36s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 605.48
//
Query:       gi|488601545|ref|YP_007908016.1|  [L=515]
Description: pyruvate carboxylase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-71  238.9   0.0    6.2e-71  238.3   0.0    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.5e-46  156.8   0.1    4.7e-46  155.9   0.1    1.5  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    1.1e-41  141.3   0.0    2.8e-41  140.0   0.0    1.7  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    2.9e-12   46.6   0.0      1e-11   44.8   0.0    1.9  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.2e-06   28.3   0.0    4.2e-06   26.5   0.0    1.8  1  RimK             RimK-like ATP-grasp domain
    1.2e-05   24.9   0.0    3.1e-05   23.6   0.0    1.7  2  ATP-grasp        ATP-grasp domain
    3.3e-05   23.7   0.0      7e-05   22.7   0.0    1.6  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    3.5e-05   23.9   0.1    9.1e-05   22.6   0.0    1.8  2  ATP-grasp_3      ATP-grasp domain
     0.0015   18.0   0.0      0.003   17.0   0.0    1.4  1  ATP-grasp_5      ATP-grasp domain
  ------ inclusion threshold ------
      0.041   13.4   0.4       0.09   12.3   0.4    1.5  1  ATP-grasp_2      ATP-grasp domain
      0.043   12.5   0.2       0.17   10.6   0.1    2.0  3  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
      0.096   12.5   0.1         11    5.8   0.0    2.3  2  SKA2             Spindle and kinetochore-associated protein 2


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 !  238.3   0.0   4.1e-74   6.2e-71       2     209 ..     116     319 ..     115     320 .. 0.98

  Alignments for each domain:
  == domain 1  score: 238.3 bits;  conditional E-value: 4.1e-74
                                       HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                       k++a++++++++vpv+p+s+a +etleea a+a++igyPv +ka+ g+GG G  +a+ne el+ ++k++ +  ++ f
  gi|488601545|ref|YP_007908016.1| 116 KVNARKLMRNAGVPVIPGSDA-IETLEEAKAFAEKIGYPVAVKASGGGGGIGINIANNEGELERAFKRSKKLGESYF 191
                                       7899****************9.******************************************************* PP

                                       STS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-E CS
                       CPSase_L_D2  79 gnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvv 155
                                        +++v++ek+l +p++iE+++l+D  +nv++++ere+s+q+r+qk+ie+APs++ ++e r++ ++ avk ++ +g++
  gi|488601545|ref|YP_007908016.1| 192 KDPSVYIEKYLPKPRHIEFQILADD-ENVVHLGERECSIQRRHQKLIEEAPSPVFDEEMREKFGRLAVKGAKYIGYR 267
                                       ************************6.79************************************************* PP

                                       EEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 156 gagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       +agt+efl++  ++e y++E+NtRl+ve++++e++TG+d+vke+++ia+g+ L+
  gi|488601545|ref|YP_007908016.1| 268 NAGTMEFLYQ--DGELYFLEMNTRLQVEHTVTEMVTGIDIVKEQIRIASGMGLS 319
                                       *********9..6*************************************9885 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 !  155.9   0.1   3.1e-49   4.7e-46       1     110 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 155.9 bits;  conditional E-value: 3.1e-49
                                       ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SE CS
                     Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgada 77 
                                       +++k+l+anrGe+Avr++ra++e+gi+tvavys++d+++ h  +a+e + +g++++++sYln++ki+++ak+s+++a
  gi|488601545|ref|YP_007908016.1|   1 MFSKILVANRGEVAVRVMRACKEMGIKTVAVYSDADRKAFHRVYANECYYIGDSDPKKSYLNMDKIIDVAKKSDSEA 77 
                                       689************************************************************************** PP

                                       EE--SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                     Biotin_carb_N  78 vhpGyGflsEnaefaeaveeagivfiGPsaeal 110
                                       +hpGyGflsEnaefa+++ee+givfiGP+++++
  gi|488601545|ref|YP_007908016.1|  78 IHPGYGFLSENAEFAKRCEEEGIVFIGPPSKVI 110
                                       *****************************9986 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 !  140.0   0.0   1.8e-44   2.8e-41       1     108 []     333     439 ..     333     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 1.8e-44
                                       EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EE CS
                     Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelri 77 
                                       e+RinaEdp + flp sG +t+++ p+g+g+Rvdsgv++g+e++pyyDs+++Kl ++g+tre a+a+++raL e+ i
  gi|488601545|ref|YP_007908016.1| 333 ECRINAEDPVN-FLPRSGVITHYRSPGGTGIRVDSGVHQGYEIPPYYDSMISKLLAWGRTREGAIAKMKRALYEYII 408
                                       8********99.***************************************************************** PP

                                       ESS-BSHHHHHHHHH-HHHHHT---TTTCCC CS
                     Biotin_carb_C  78 eGvktnieflrailedeefakgeldtkflee 108
                                       +Gv+tni+f+  +l+d++f++g+++tkf++e
  gi|488601545|ref|YP_007908016.1| 409 DGVETNIPFHMVVLDDPDFVSGNIHTKFVDE 439
                                       ****************************985 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 !   44.8   0.0   6.9e-15     1e-11      25     174 ..     140     288 ..     122     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6.9e-15
                                       -HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT......T-SCEEEEE--.ESEEEEEEEEETS CS
                   Dala_Dala_lig_C  25 kellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk......ydekvlvEeai.egreievavlgne 94 
                                        e  ++  e++gypv VK++  G  +G++ +++e el++a++++ k      +d +v +E+++ + r ie  +l  +
  gi|488601545|ref|YP_007908016.1| 140 LEEAKAFAEKIGYPVAVKASGGGGGIGINIANNEGELERAFKRSKKlgesyfKDPSVYIEKYLpKPRHIEFQILA-D 215
                                       355678999*******************************998776444443699********************.6 PP

                                       SCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEE CS
                   Dala_Dala_lig_C  95 klevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnE 171
                                       + +v ++ge+  +  + + ++k ++++ +       ++e++ek   la+k  k ++ r  + + f+++ +ge+++ E
  gi|488601545|ref|YP_007908016.1| 216 DENVVHLGERECS--IQRRHQKLIEEAPSP----VFDEEMREKFGRLAVKGAKYIGYRNAGTMEFLYQ-DGELYFLE 285
                                       6777788887665..556778887433332....3588999************************998.9******* PP

                                       EES CS
                   Dala_Dala_lig_C 172 vNt 174
                                       +Nt
  gi|488601545|ref|YP_007908016.1| 286 MNT 288
                                       **9 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.8e-09   4.2e-06       4     185 ..     116     310 ..     114     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.8e-09
                                       HHHHHHHHHHTT---.--EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH........ CS
                              RimK   4 KlkslklLakakikv.pntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea........ 71 
                                       K+ + kl+  a+++v p +  ++  e+a+++ eki  + Pv vK + g  Gi++ +a++e +l+  ++         
  gi|488601545|ref|YP_007908016.1| 116 KVNARKLMRNAGVPViPGSDAIETLEEAKAFAEKI--GYPVAVKASGGGGGIGINIANNEGELERAFKRskklgesy 190
                                       6666777777777643788889999**********..69*************************9998767755555 PP

                                       .GGG--EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE-..---HHHHHHHHHHHHHCT-S CS
                              RimK  72 .lkeailvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaekl..qlseeekelAikaakamelv 145
                                         + ++ + +y+ +    +  +l  d++vv   +r +        l   + + ++  ++ e+  +lA+k ak ++  
  gi|488601545|ref|YP_007908016.1| 191 fKDPSVYIEKYLPKPRHIEFQILADDENVVHLGERECSIQRRHQKLIEEAPSPVFdeEMREKFGRLAVKGAKYIGYR 267
                                       55556699**********************98888866523333344433333221155666668************ PP

                                       EEEEE.EEEETTEEEEEEEESS--SHH..HHHHHT--HHHHHH CS
                              RimK 146 vaGvD.llrakrgllvlEvnsspglek..iektlgidiakkli 185
                                        aG    l ++ +l++lE+n+  ++e+   e+ +gidi k+ i
  gi|488601545|ref|YP_007908016.1| 268 NAGTMeFLYQDGELYFLEMNTRLQVEHtvTEMVTGIDIVKEQI 310
                                       ***765***************998875226999****998866 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.7     7e+03     124     151 ..      12      43 ..       8      47 .. 0.66
   2 !   23.6   0.0   2.1e-08   3.1e-05       5     159 ..     127     289 ..     123     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHTSSEEEEEEEEEETTCT....E CS
                         ATP-grasp 124 eiakkiveeLggvGvfavElFvledge....l 151
                                       e+a +++++   +G+ +v ++  +d +    +
  gi|488601545|ref|YP_007908016.1|  12 EVAVRVMRACKEMGIKTVAVYSDADRKafhrV 43 
                                       56778888888888888877776665544455 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 2.1e-08
                                       T--B.-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE-- CS
                         ATP-grasp   5 glpv.prflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefv 72 
                                       g+pv p   a+e+ ee++++ae++g+pv vK + +g  G G  + ++e +le+a++          k+ +v++E++ 
  gi|488601545|ref|YP_007908016.1| 127 GVPViPGSDAIETLEEAKAFAEKIGYPVAVK-ASGGGGGIGINIANNEGELERAFKRSkklgesyfKDPSVYIEKYL 202
                                       55542677899********************.89999******************999999*999999********* PP

                                       --SEEEEEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-.SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETT CS
                         ATP-grasp  73 pfekElsvlvvrsaeGetafypvvetvqedgilrlsvapaev.sekaqkkaeeiakkiveeLggvGvfavElFvled 148
                                       p  + +   +  + e  ++  +    +q++    +  ap++v +e+  +k  ++a k ++ +g+    ++E+ ++ d
  gi|488601545|ref|YP_007908016.1| 203 PKPRHIEFQILADDENVVHLGERECSIQRRHQKLIEEAPSPVfDEEMREKFGRLAVKGAKYIGYRNAGTMEFLYQ-D 278
                                       *99999988888888878888888888887777777777776155578888899999999999999999997766.9 PP

                                       CTEEEEEEESS CS
                         ATP-grasp 149 gellvnElapR 159
                                       gel++ E+  R
  gi|488601545|ref|YP_007908016.1| 279 GELYFLEMNTR 289
                                       99999888777 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 !   22.7   0.0   4.7e-08     7e-05       1     108 [.     114     222 ..     114     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.7e-08
                                       HBHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TT CS
                            GARS_A   1 asKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkf 76 
                                       +sK  a++l+++ag+p     +a++  eeak++ e+ + ++  vKa+g  +g g+ +a++e e  +a k     kk 
  gi|488601545|ref|YP_007908016.1| 114 GSKVNARKLMRNAGVPVIpGSDAIETLEEAKAFAEKIGYPV-AVKASGGGGGIGINIANNEGELERAFKRS---KKL 186
                                       69999***********7549999******************.9***************9999988887753...445 PP

                                       CCC...CSSEEEEE--.-SEEEEEEEEECTTEEEE- CS
                            GARS_A  77 Gea...gekvviEell.eGeEvsllalvdgktvkpl 108
                                       Ge+     +v iE++l +   + ++ l d ++v++l
  gi|488601545|ref|YP_007908016.1| 187 GESyfkDPSVYIEKYLpKPRHIEFQILADDENVVHL 222
                                       554222678999999943567888888888888776 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.1e-08   9.1e-05       3     159 ..     115     291 ..     113     293 .. 0.85
   2 ?   -3.2   0.0       5.1   7.6e+03     113     139 ..     467     493 ..     462     498 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.1e-08
                                       SHHHHHHHHTTT.S--.-.........-EESS--..SSSEEEEESS-------B--SS--TTE.............. CS
                       ATP-grasp_3   3 dKlktykkLkeagvkv.P.....tkleaeeleee..ekklvvKprdGaggesvrvveekeeaeaaieeve....... 64 
                                       +K++  k +++agv+v P     ++le++++  e   +++ vK + G+gg ++ +++++ e+e+a++  +       
  gi|488601545|ref|YP_007908016.1| 115 SKVNARKLMRNAGVPViPgsdaiETLEEAKAFAEkiGYPVAVKASGGGGGIGINIANNEGELERAFKRSKklgesyf 191
                                       5777778888888875368877755555554333459*****************************99999****** PP

                                       .....EEEE--.-SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT-- CS
                       ATP-grasp_3  65 .....lvqefi.eGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevveklegla 135
                                             + +++ + +++  ++l+d e+v+ l   +  i++++++++    +  ++ e++e++ +la +  + + g +
  gi|488601545|ref|YP_007908016.1| 192 kdpsvYIEKYLpKPRHIEFQILADDENVVHLGERECSIQRRHQKLIEEAPSPVFDEEMREKFGRLAVKGAKYI-GYR 267
                                       ****95556662689***********************99888887777777788888***************.*** PP

                                       EEEEEEEEESS.SEEEEEEESS-- CS
                       ATP-grasp_3 136 GyvGvDlvlkdeepyviEvNPRlt 159
                                            +++++d+e+y++E N Rl+
  gi|488601545|ref|YP_007908016.1| 268 NAGTMEFLYQDGELYFLEMNTRLQ 291
                                       9999******************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                                       ---HHHHHHHHHHHHHTTSTT--EEEE CS
                       ATP-grasp_3 113 etelkeevvelaeevvekleglaGyvG 139
                                       e e +e+++++a +++++ + l +  G
  gi|488601545|ref|YP_007908016.1| 467 EEEINEKIIAIAISAINAYKRLESEIG 493
                                       445589999999999988877777666 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     2e-06     0.003      13      53 ..     117     158 ..     112     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                       ATP-grasp_5  13 aeakelleaygipvvetrl.assaeeaveaaeeigypvvlKi 53 
                                        +a++l++  g+pv++    +++ eea + ae+igypv++K 
  gi|488601545|ref|YP_007908016.1| 117 VNARKLMRNAGVPVIPGSDaIETLEEAKAFAEKIGYPVAVKA 158
                                       6899**********99654399*******************7 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4     6e-05      0.09       6      72 ..     118     180 ..     116     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6e-05
                                       HHHHHHHCTT----SEE.EESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHH CS
                       ATP-grasp_2   6 qakeilakygvkvpege.vaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaa 72 
                                       +a++++++ gv+v  g    e+ eea++ a+k+g  + +vKa     G G + G+++++++ e+++a 
  gi|488601545|ref|YP_007908016.1| 118 NARKLMRNAGVPVIPGSdAIETLEEAKAFAEKIGYPV-AVKA----SGGGGGIGINIANNEGELERAF 180
                                       589*********97765166899************99.7776....4556688999999999888765 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 ?   10.6   0.1   0.00011      0.17     274     313 ..       4      55 ..       3     147 .. 0.69
   2 ?   -2.0   0.0      0.75   1.1e+03     144     182 ..     124     161 ..     107     164 .. 0.69
   3 ?   -2.1   0.0      0.83   1.2e+03     325     359 ..     407     441 ..     389     447 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                       EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHH............H CS
                    Oxidored_nitro 274 rvaiygdpdrvvalarllkelGmevvaagtetahrddee............r 313
                                       +++++  ++ +v ++r++ke+G+++va+ +   +++++             +
  gi|488601545|ref|YP_007908016.1|   4 KILVANRGEVAVRVMRACKEMGIKTVAVYSDADRKAFHRvyanecyyigdsD 55 
                                       78899999************************99999953444444444440 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.75
                                       -SSEEEEEEETTCGHGHHHHHHHHHHHHTEEEEEEECTS CS
                    Oxidored_nitro 144 eprkvnilgeynlgpgdlrelkelleklGlevnavftgg 182
                                       ++  v +++++  + + l+e k   ek+G+ v + ++gg
  gi|488601545|ref|YP_007908016.1| 124 RNAGVPVIPGS-DAIETLEEAKAFAEKIGYPVAVKASGG 161
                                       44467788888.444888899999999998888777776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.83
                                       EEES.CHHHHHHHHHHHT-SEEEE-CCHHHHHHHT CS
                    Oxidored_nitro 325 viddadleeleelikelkpdlllggskeryiaekl 359
                                       +id+++     +++    pd++ g+++++++ ek 
  gi|488601545|ref|YP_007908016.1| 407 IIDGVETNIPFHMVVLDDPDFVSGNIHTKFVDEKD 441
                                       55555555555666677899*******99998885 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 ?    4.2   0.0     0.023        35      30      60 ..     211     239 ..     206     242 .. 0.82
   2 ?    5.8   0.0    0.0076        11      47     101 ..     446     501 ..     440     510 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.023
                              SKA2  30 qqsypdnaeNpvkLlerlkkvkeelqaLkeq 60 
                                       q +++d+ eN+v L er   +++++q+L e+
  gi|488601545|ref|YP_007908016.1| 211 Q-ILADD-ENVVHLGERECSIQRRHQKLIEE 239
                                       4.45555.5******************9876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0076
                              SKA2  47 lkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasaelppls.ee 101
                                       +k+    + +Lk++++e+ ++ +e+ +ki +  ++  +  ++L+ +++l   + +e
  gi|488601545|ref|YP_007908016.1| 446 VKEAMPSIVNLKKRLDEIFNKEEEINEKIIAIAISAINAYKRLESEIGLVDVNtSE 501
                                       4444556779***********************************99654443144 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 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:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 2972.37
//
Query:       gi|488601546|ref|YP_007908017.1|  [L=93]
Description: transcriptional regulator, ArsR family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-12   46.7   0.1      3e-12   46.2   0.1    1.2  1  HTH_5          Bacterial regulatory protein, arsR family
    2.9e-09   36.3   0.2    3.9e-09   35.9   0.2    1.2  1  HTH_24         Winged helix-turn-helix DNA-binding
      2e-08   34.2   0.0    2.7e-08   33.8   0.0    1.2  1  HTH_20         Helix-turn-helix domain
    2.6e-07   30.5   0.0    4.2e-07   29.8   0.0    1.3  1  MarR           MarR family
    5.7e-07   29.3   0.0    7.9e-07   28.9   0.0    1.2  1  MarR_2         MarR family
    1.7e-05   24.6   0.0    2.4e-05   24.2   0.0    1.3  1  HTH_11         HTH domain
    5.8e-05   22.8   0.1    0.00013   21.8   0.0    1.6  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    0.00011   22.0   0.0    0.00018   21.3   0.0    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00016   21.3   0.0    0.00024   20.8   0.0    1.2  1  HTH_DeoR       DeoR-like helix-turn-helix domain
    0.00021   21.2   0.0    0.00026   20.9   0.0    1.2  1  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0015   19.0   0.0     0.0019   18.6   0.0    1.3  1  HTH_40         Helix-turn-helix domain
     0.0018   18.0   0.3     0.0033   17.2   0.3    1.4  1  HTH_23         Homeodomain-like domain
     0.0038   16.9   0.2     0.0064   16.2   0.2    1.4  1  HTH_psq        helix-turn-helix, Psq domain
     0.0078   16.2   0.1      0.012   15.6   0.1    1.3  1  HTH_36         Helix-turn-helix domain
     0.0093   15.9   0.0       0.01   15.8   0.0    1.1  1  DUF977         Bacterial protein of unknown function (DUF977)
     0.0099   15.6   0.2      0.017   14.8   0.2    1.4  1  HTH_38         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.019   14.7   0.0    1.3  1  HTH_IclR       IclR helix-turn-helix domain
      0.014   15.5   0.0      0.025   14.7   0.0    1.6  1  HTH_22         HTH domain
      0.014   15.2   0.2      0.031   14.1   0.0    1.8  1  IF2_N          Translation initiation factor IF-2, N-terminal
       0.02   14.4   0.1       0.04   13.4   0.1    1.5  1  Sigma70_r4     Sigma-70, region 4
      0.022   14.5   0.0      0.043   13.6   0.0    1.4  1  HTH_10         HTH DNA binding domain
      0.032   13.9   0.1       0.05   13.2   0.1    1.3  1  GntR           Bacterial regulatory proteins, gntR family
      0.042   13.7   0.1      0.061   13.2   0.1    1.5  1  TFIIE_alpha    TFIIE alpha subunit
      0.078   12.6   0.0       0.14   11.8   0.0    1.4  1  Crp            Bacterial regulatory proteins, crp family
      0.083   13.3   0.0      0.095   13.1   0.0    1.3  1  Rrf2           Transcriptional regulator
        0.1   12.6   0.0       0.13   12.3   0.0    1.2  1  Replic_Relax   Replication-relaxation
       0.11   12.9   0.4       0.16   12.4   0.1    1.5  1  DUF4093        Domain of unknown function (DUF4093)


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 !   46.2   0.1   4.5e-15     3e-12       3      46 ..      14      58 ..      12      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 4.5e-15
                                      HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       R++IL+  ++ g+++v+++a++lg+++ t S+HLk+L+++G+V+
  gi|488601546|ref|YP_007908017.1| 14 IRRQILCEISRnGKMSVHQIAKKLGVTEYTASRHLKILYDLGIVD 58
                                      7******************************************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.2   5.9e-12   3.9e-09       3      47 ..      13      57 ..      11      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.9e-12
                            HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      +++r+IL+++ +n+++s  ++A++lg++  t +r+lk L + G++
  gi|488601546|ref|YP_007908017.1| 13 KIRRQILCEISRNGKMSVHQIAKKLGVTEYTASRHLKILYDLGIV 57
                                      799**************************************9998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0     4e-11   2.7e-08       2      55 ..       5      58 ..       4      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4e-11
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++a+AL  + Rr il +++r++ +++ ++a+ l+++  t+s+HL++L + g+v+
  gi|488601546|ref|YP_007908017.1|  5 KLARALRAKIRRQILCEISRNGKMSVHQIAKKLGVTEYTASRHLKILYDLGIVD 58
                                      5799***********************************************995 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   6.3e-10   4.2e-07       8      50 ..      18      60 ..      16      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 6.3e-10
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      iL+ ++++g +sv+++akklgv+  t++r l+ L++ G ++ +
  gi|488601546|ref|YP_007908017.1| 18 ILCEISRNGKMSVHQIAKKLGVTEYTASRHLKILYDLGIVDFE 60
                                      8*************************************99875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.2e-09   7.9e-07       8      54 ..      16      60 ..      14      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.2e-09
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +++L ++ r++   ++v ++a++lg++  ++sr+lk L + G v  +
  gi|488601546|ref|YP_007908017.1| 16 RQILCEISRNGK--MSVHQIAKKLGVTEYTASRHLKILYDLGIVDFE 60
                                      79*********9..*****************************9877 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.6e-08   2.4e-05       2      45 ..      15      58 ..      14      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.6e-08
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vp 45
                                      ++qil  + + +g++s  ++A++L+v++ t  r++k+L +lg v+
  gi|488601546|ref|YP_007908017.1| 15 RRQILCEI-SRNGKMSVHQIAKKLGVTEYTASRHLKILYDLGiVD 58
                                      57888889.55556************************9999554 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.7   3.8e+03      20      27 ..       3      10 ..       1      12 [. 0.60
   2 !   21.8   0.0   1.9e-07   0.00013       6      36 ..      16      46 ..      13      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.7
                     HTH_AsnC-type 20 yaeLAerv 27
                                       ++LA+++
  gi|488601546|ref|YP_007908017.1|  3 DEKLARAL 10
                                      45666665 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.9e-07
                     HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlr 36
                                      r+IL ++ +++++s++++A+++G++e t+ r
  gi|488601546|ref|YP_007908017.1| 16 RQILCEISRNGKMSVHQIAKKLGVTEYTASR 46
                                      89************************99877 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.7e-07   0.00018      19      66 ..      24      71 ..      17      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.7e-07
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                      ++g++++ +ia++lgv + ++ + L+ L d G+V+ e + p +Y  + 
  gi|488601546|ref|YP_007908017.1| 24 RNGKMSVHQIAKKLGVTEYTASRHLKILYDLGIVDFEMRPPEKYYFIR 71
                                      689*****************************************9875 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.6e-07   0.00024       3      43 ..      16      56 ..      15      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.6e-07
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgl 43
                                       qil  + + gk+sv +++  lgv+e T+ R L++L   g+
  gi|488601546|ref|YP_007908017.1| 16 RQILCEISRNGKMSVHQIAKKLGVTEYTASRHLKILYDLGI 56
                                      5999******************************9988877 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 !   20.9   0.0   3.9e-07   0.00026       2      66 ..       5      79 ..       4      81 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.9e-07
                                      HHHHHHHHHHCTTT...C.EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE...E..TEE..EEES-HHHHH CS
                         HTH_Crp_2  2 RlArfLlrlaerag...g.eielpltqeelAsmlGltretvsrilseLkreglis...r..grr..irildleaLr 66
                                      +lAr L     r++   + + + +++  ++A  lG+t  t sr l+ L + g+++   r  ++   ir+++ ++L 
  gi|488601546|ref|YP_007908017.1|  5 KLARALRA-KIRRQilcEiSRNGKMSVHQIAKKLGVTEYTASRHLKILYDLGIVDfemRppEKYyfIRLKSFKKLL 79
                                      67777733.233222222333559*******************************854233222478888888875 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.9e-06    0.0019      11      65 ..      26      86 ..       8      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.9e-06
                            HTH_40 11 eglsieeIAkerglkesTIegHLaelieegeeidl.....erl..vseeeekeIeeaiekvg 65
                                       ++s+++IAk+ g++e T  +HL  l+  g  +d+     e++  +  + +k++ +++e+v 
  gi|488601546|ref|YP_007908017.1| 26 GKMSVHQIAKKLGVTEYTASRHLKILYDLGI-VDFemrppEKYyfIRLKSFKKLLDVYEEVT 86
                                      579**************************95.666335553322256677777777777765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3     5e-06    0.0033       3      39 ..      11      49 ..       7      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5e-06
                            HTH_23  3 sereRlrillllae..GlsvreIAreLgvsrrTvyrwlk 39
                                      ++++R +il    +  ++sv++IA++Lgv++ T +r lk
  gi|488601546|ref|YP_007908017.1| 11 RAKIRRQILCEISRngKMSVHQIAKKLGVTEYTASRHLK 49
                                      56677777777777899*****************99776 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 !   16.2   0.2   9.6e-06    0.0064       2      38 ..       3      49 ..       2      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.6e-06
                           HTH_psq  2 pealaaAleavv..........nGkmSirkAArkYgiPrsTLwrrkr 38
                                      +e+la+Al+a +          nGkmS+++ A+k g+   T +r+++
  gi|488601546|ref|YP_007908017.1|  3 DEKLARALRAKIrrqilceisrNGKMSVHQIAKKLGVTEYTASRHLK 49
                                      5899999999666999999999**************98888888776 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.8e-05     0.012      14      55 .]      19      57 ..      17      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                            HTH_36 14 lasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      l+  + ++     s+  +ak+lg+ + T+sr++k L +lG++
  gi|488601546|ref|YP_007908017.1| 19 LCEISRNGKM---SVHQIAKKLGVTEYTASRHLKILYDLGIV 57
                                      6666655555...9999**********************985 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-05      0.01       9      54 ..      10      55 ..       4      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                            DUF977  9 ereelkeriiGlvkkneritisdleritGvgrtsvrkylvdvlerG 54
                                       r +++ +i+  + +n+++ + ++ + +Gv   ++ + l++  + G
  gi|488601546|ref|YP_007908017.1| 10 LRAKIRRQILCEISRNGKMSVHQIAKKLGVTEYTASRHLKILYDLG 55
                                      588999**********************************988776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   2.6e-05     0.017      13      42 ..      20      49 ..      15      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                            HTH_38 13 IerllaeGlslreIArrLgrspsTIsRElk 42
                                      +e+ ++ ++s+ +IA++Lg+   T sR+lk
  gi|488601546|ref|YP_007908017.1| 20 CEISRNGKMSVHQIAKKLGVTEYTASRHLK 49
                                      56677788*******************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 ?   14.7   0.0   2.9e-05     0.019      15      49 ..      24      58 ..      17      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                                      TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +++ +++ ++A+++g++  t++R+L+ L  lG+v 
  gi|488601546|ref|YP_007908017.1| 24 RNGKMSVHQIAKKLGVTEYTASRHLKILYDLGIVD 58
                                      4667****************************996 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.7e-05     0.025      41      63 .]      27      49 ..       4      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                            HTH_22 41 kgavekvAekLgiSraTvYryLr 63
                                      k +v ++A+kLg++++T  r+L+
  gi|488601546|ref|YP_007908017.1| 27 KMSVHQIAKKLGVTEYTASRHLK 49
                                      88***************988885 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 ?   14.1   0.0   4.7e-05     0.031       2      16 ..      26      40 ..      25      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                             IF2_N  2 skirVyeLAkeLgvk 16
                                       k++V+++Ak+Lgv+
  gi|488601546|ref|YP_007908017.1| 26 GKMSVHQIAKKLGVT 40
                                      69***********86 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     6e-05      0.04      10      42 ..      16      49 ..      13      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-05
                                      HHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 10 revlelrf.geglTleEIgerlgiSrerVrqiek 42
                                      r++l+      +++ ++I+++lg+++ ++++++k
  gi|488601546|ref|YP_007908017.1| 16 RQILCEISrNGKMSVHQIAKKLGVTEYTASRHLK 49
                                      6677666668899***************999875 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.4e-05     0.043      24      45 ..      28      49 ..      24      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-05
                            HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                      +++ ++Ak+lG+++ t+s hL+
  gi|488601546|ref|YP_007908017.1| 28 MSVHQIAKKLGVTEYTASRHLK 49
                                      57899****************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 ?   13.2   0.1   7.6e-05      0.05       2      54 ..       7      57 ..       3      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.6e-05
                                      HHHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR  2 yeqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                      ++++ +++r++Il  e++ + k+ s+ ++a+++gV+  t  + L+ L   g+v
  gi|488601546|ref|YP_007908017.1|  7 ARALRAKIRRQILC-EISRNGKM-SVHQIAKKLGVTEYTASRHLKILYDLGIV 57
                                      45667788888887.889999**.***************99999999999888 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.2e-05     0.061      17      63 ..      17      63 ..       4      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-05
                                      HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEE CS
                       TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrr 63
                                      ++l  + ++g+++  ++ak+l++      + L  Ly+ ++v++ +r 
  gi|488601546|ref|YP_007908017.1| 17 QILCEISRNGKMSVHQIAKKLGVTEYTASRHLKILYDLGIVDFEMRP 63
                                      6888899************************************9985 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.14       2      25 ..      27      50 ..      27      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                      E--HHHHHHHHTS-HHHHHHHHHH CS
                               Crp  2 pmSRqdIAdylGlTrETVSRlLtr 25
                                      +mS  +IA+ lG T  T+SR L+ 
  gi|488601546|ref|YP_007908017.1| 27 KMSVHQIAKKLGVTEYTASRHLKI 50
                                      6999****************9985 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00014     0.095      15      56 ..      20      58 ..       5      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      ++++++    ++s+++ia++ ++ +  +++ l+ L   g+v 
  gi|488601546|ref|YP_007908017.1| 20 CEISRNG---KMSVHQIAKKLGVTEYTASRHLKILYDLGIVD 58
                                      4444444...49***************************997 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    0.0002      0.13       8      46 ..      26      64 ..      19      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                      Replic_Relax  8 rvlTtrqiarllfashratarrrLarLrelgllsr.lrkr 46
                                      + ++ +qia+ l  ++ + a+r L++L++lg+++  +r+ 
  gi|488601546|ref|YP_007908017.1| 26 GKMSVHQIAKKLGVTEYT-ASRHLKILYDLGIVDFeMRPP 64
                                      56899*************.***************988876 PP

>> DUF4093  Domain of unknown function (DUF4093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00024      0.16      38      78 ..       6      46 ..       1      51 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                           DUF4093 38 LvggadskkrReklgekLgigyangkqllkrLnmfkitkee 78
                                      L  +  +k rR+ l+e  + g+++  q+ k+L + ++t   
  gi|488601546|ref|YP_007908017.1|  6 LARALRAKIRRQILCEISRNGKMSVHQIAKKLGVTEYTASR 46
                                      66777899************************999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 547.71
//
Query:       gi|488601547|ref|YP_007908018.1|  [L=328]
Description: Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-44  150.8   0.0    6.1e-44  150.5   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    5.8e-09   35.3   1.6    6.2e-06   25.7   0.3    2.7  2  Hexapep          Bacterial transferase hexapeptide (six repea
    1.6e-06   28.6   0.0    1.9e-06   28.3   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0076   16.0   0.3      0.021   14.6   0.3    1.8  1  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.044   12.7   0.0        2.3    7.1   0.0    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 !  150.5   0.0   1.7e-47   6.1e-44       5     245 ..       1     229 [.       1     231 [. 0.89

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 1.7e-47
                                       E--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                   NTP_transferase   5 LaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                       +aGG+ tRLwP+t+t +k+l+p ++k ++i+  ++++ +  +  +i+v+t+++ +   +++++ ++++   li+ e+
  gi|488601547|ref|YP_007908018.1|   1 MAGGYATRLWPITKTKPKPLLPLGKK-TIIDLIYEKIRK--FGYPIYVSTNKRFENDFKKWAKDKDAR---LIIEET 71 
                                       8*************************.**********96..88899*******999999999999888...333333 PP

                                       S--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTS CS
                   NTP_transferase  82 egk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeeg 157
                                        ++ +  +Av+   e+++d ++   ++v++gD l++ ++e+++k+ + k++++t+++ + +ve a++yGv+e+d+ +
  gi|488601547|ref|YP_007908018.1|  72 LKEeEKLGAVRALGEIAKDLDD--ELFVIAGDNLFSFNLEDMLKFYKTKKSAITALYDVGDVELAKRYGVAEIDN-D 145
                                       3333445555555555555553..579***********************************************9.6 PP

                                       BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSS CS
                   NTP_transferase 158 rverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGt 234
                                       r+ rf EKP++++ s+l+  GiY+ n+e++++l++ ++++ +++d+++d+l++++++++v  + + ++  +W DvG+
  gi|488601547|ref|YP_007908018.1| 146 RIVRFYEKPEKPP-STLVGIGIYILNREAVDYLVE-YTDSGEKRDNLGDFLSYLCQKTEVYGYPFTNG--NWYDVGN 218
                                       9************.*******************98.99999*****************9999988888..5****** PP

                                       HHHHHHHHHHH CS
                   NTP_transferase 235 ldslleanekl 245
                                        ds++ea +++
  gi|488601547|ref|YP_007908018.1| 219 ADSYIEALKFY 229
                                       ******98876 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.3   1.7e-09   6.2e-06       2      30 ..     249     277 ..     248     278 .. 0.96
   2 !    8.2   0.0   0.00059       2.1       2      24 ..     299     325 ..     298     326 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
                                       EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                       +vI+++++I+  ++ig+ + IG+n++I++
  gi|488601547|ref|YP_007908018.1| 249 VVIEDGCVIRGRSMIGPYAYIGKNCYIEN 277
                                       89*************************98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00059
                                       EEEETTEEE-T....TEEEETTEEE-T CS
                           Hexapep   2 tvIGsnvlIgp....faviggnVkIGd 24 
                                       ++I +++ I++    +++igg++kI +
  gi|488601547|ref|YP_007908018.1| 299 SIIDEKCEIRNlelsGSIIGGHAKIQR 325
                                       57999*******************976 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.3e-10   1.9e-06       4      98 ..       1     104 [.       1     187 [. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.3e-10
                                       EEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCTS-EEE-TTS.S-S CS
                      NTP_transf_3   4 LAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd...eevlaalarlgvrvvededp.gkg 71 
                                       +AGG ++R+      ++K+llplg+k++++ +++++r+ g  +++v+++    ++ ++ ++++++r++ +e   ++ 
  gi|488601547|ref|YP_007908018.1|   1 MAGGYATRLwpitkTKPKPLLPLGKKTIIDLIYEKIRKFG-YPIYVSTNKrfeNDFKKWAKDKDARLIIEETLkEEE 76 
                                       59*******7776335***********************8.7******995544889999999**998776553677 PP

                                       HHHHHHHHHHHH..SSSCEEEEETT-TT CS
                      NTP_transf_3  72 plaslaaalraaa.dadavlvlacDmPl 98 
                                        l++++a  + a+  +d ++v+a+D  +
  gi|488601547|ref|YP_007908018.1|  77 KLGAVRALGEIAKdLDDELFVIAGDNLF 104
                                       777777776665546899*******877 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   5.8e-06     0.021       1      28 [.     248     277 ..     248     277 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.8e-06
                                       .EEE-TT-EE-TT-EES..EEE-TT-EE-T CS
                         Hexapep_2   1 pviIGdnCliGanagiG..vslGdncvvga 28 
                                       pv I+d C+i  ++ iG    +G+nc +++
  gi|488601547|ref|YP_007908018.1| 248 PVVIEDGCVIRGRSMIGpyAYIGKNCYIEN 277
                                       8***************99**********97 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0074        27      46      98 ..      89     145 ..      80     162 .. 0.79
   2 ?    7.1   0.0   0.00064       2.3     283     318 ..     247     283 ..     191     306 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0074
                        Fucokinase  46 krmkpGvlvtssDvlllf....dseeisfdkagvtalavpstldigtnHGVfvlddq 98 
                                       k +   ++v+++D l  f      ++++ +k+ +tal   ++++ ++  GV  +d++
  gi|488601547|ref|YP_007908018.1|  89 KDLDDELFVIAGDNLFSFnledMLKFYKTKKSAITALYDVGDVELAKRYGVAEIDND 145
                                       5566789********988766555666777779999*9*************999988 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00064
                        Fucokinase 283 ssvsvgegsvie.hsslkgnvsigsnsivsgleless 318
                                       + v +++g+vi   s +++   ig+n+++ + ++++s
  gi|488601547|ref|YP_007908018.1| 247 PPVVIEDGCVIRgRSMIGPYAYIGKNCYIENSDVSES 283
                                       3445555555554444445555666666666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 1739.24
//
Query:       gi|488601548|ref|YP_007908019.1|  [L=232]
Description: hypothetical protein Asulf_02066 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  155.1   0.0      3e-45  154.9   0.0    1.0  1  ATP_bind_1       Conserved hypothetical ATP binding protein
    0.00018   21.1   0.0     0.0055   16.3   0.0    2.3  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    0.00064   19.0   0.0     0.0013   18.0   0.0    1.6  2  G-alpha          G-protein alpha subunit
    0.00082   19.8   0.0     0.0012   19.2   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.001   19.1   0.0      0.002   18.2   0.0    1.5  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0023   17.9   0.0     0.0048   16.9   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.003   18.1   0.0      0.011   16.2   0.0    1.9  2  ABC_tran         ABC transporter
     0.0038   16.9   0.1     0.0078   15.9   0.1    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0047   15.9   0.0      0.047   12.7   0.0    2.0  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0054   16.3   0.1      0.017   14.7   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
      0.006   16.9   0.0     0.0092   16.3   0.0    1.4  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.014   15.3   0.8        1.3    8.9   0.6    2.9  2  RsgA_GTPase      RsgA GTPase
      0.017   15.1   0.1       0.46   10.4   0.0    2.2  2  NTPase_1         NTPase
      0.022   14.7   0.0      0.048   13.6   0.0    1.5  1  NACHT            NACHT domain
      0.032   14.0   0.0      0.046   13.5   0.0    1.4  1  AAA_24           AAA domain
      0.054   13.2   0.0      0.074   12.8   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.058   13.5   0.0      0.079   13.0   0.0    1.4  1  DUF87            Helicase HerA, central domain
       0.11   12.7   0.0       0.16   12.1   0.0    1.3  1  AAA_33           AAA domain
       0.12   13.0   0.1       0.18   12.3   0.1    1.4  1  AAA_18           AAA domain
       0.12   11.7   0.1       0.22   10.8   0.1    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.13   12.7   0.0        3.1    8.2   0.2    2.3  3  AAA_23           AAA domain
       0.15   12.3   0.0       0.29   11.3   0.0    1.6  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.22   10.6   0.0       0.32   10.1   0.0    1.2  1  DUF815           Protein of unknown function (DUF815)
       0.24   11.1   0.0       0.43   10.3   0.0    1.3  1  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.9   0.0     4e-48     3e-45       1     239 [.       5     225 ..       5     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 4e-48
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflre 77 
                                       ++G+aGsGK+t+v+++se+l+ + +sv++vNLDPA+    Y a++d r+++ +ed+m++ +lg ngal+ ++e+l++
  gi|488601548|ref|YP_007908019.1|   5 ILGHAGSGKSTLVKNFSEFLRGS-YSVKTVNLDPAST-PCYTASIDSRKFVRTEDIMKRFNLGINGALMKSMEMLKD 79 
                                       68*******************99.***********98.89************************************* PP

                        ATP_bind_1  78 sldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlr 154
                                        +d+l       +dd +l+DtPGQ+elf + + +  + e+L +   + +++L+Ds  +++p k++s+++++  + lr
  gi|488601548|ref|YP_007908019.1|  80 YIDHLI-----VKDDIVLYDTPGQLELFLFTDFGEVFSERLGK--DTTAIFLIDSGLCRSPEKYLSAIFQSAVISLR 149
                                       *96554.....45699*************************98..899***************************** PP

                        ATP_bind_1 155 lelPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedl 231
                                       +++ +++++nk+D+ +          + +e++ + +e+ee+   +l + i  + e+++l  r +++s+++++++++l
  gi|488601548|ref|YP_007908019.1| 150 TGVETITIFNKADISS---------PPKFEEVVEYIEQEEGVLPELLKGILPFRELTSLRFREMVISARNGTGFDEL 217
                                       **************66.........33444455566677799999******************************** PP

                        ATP_bind_1 232 lslideal 239
                                       + +i+e+ 
  gi|488601548|ref|YP_007908019.1| 218 IGMINEIH 225
                                       ****9875 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 !   16.3   0.0   7.4e-06    0.0055       4     190 ..       1     223 [.       1     226 [. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.4e-06
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST......HCHSHHHHHHTSCSSCEEEEEE....... CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv......lDtlkeErergiTiksaaisle....... 64 
                                       +n+ i+gh  +GK+TL+ +  + +    + ++++      ++      +D++k  r   i                 
  gi|488601548|ref|YP_007908019.1|   1 MNLLILGHAGSGKSTLVKNFSEFLRGSYSVKTVNldpA--STpcytasIDSRKFVRTEDI---------Mkrfnlgi 66 
                                       5999****************999999888777775331..33455555443333333322.........01112222 PP

                                       ................TTCSSEEEEEEEESSS......GGGHHHHHHHHHT-SEEEEEEETT.....TBSTHHHHHH CS
                          GTP_EFTU  65 ................ketkkylinliDtPGH......vdFskevirglrvlDgavlvvdav.....eGvepqteev 114
                                                       +   k  i l DtPG        dF +  ++ l +   a++++d+      e   +   + 
  gi|488601548|ref|YP_007908019.1|  67 ngalmksmemlkdyidHLIVKDDIVLYDTPGQlelflfTDFGEVFSERLGKDTTAIFLIDSGlcrspEKYLSAIFQS 143
                                       233444557777777668888899999****8433333578888888899999999999987554444456666666 PP

                                       HHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHH...HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHH CS
                          GTP_EFTU 115 lrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrk...eeklekygekgekevpvvfgSalkgegvktllea 187
                                       + + l+ gv++i++ NK+D     +++e+ve ++q+        + +  + e ++  +  + +Sa +g g+++l+ +
  gi|488601548|ref|YP_007908019.1| 144 AVISLRTGVETITIFNKADISsPPKFEEVVEYIEQEEGVLpelLKGILPFRELTSLRFREMVISARNGTGFDELIGM 220
                                       6777889999*********9986777777777776654443333333333333336778899999999999999998 PP

                                       HHH CS
                          GTP_EFTU 188 lve 190
                                       + e
  gi|488601548|ref|YP_007908019.1| 221 INE 223
                                       865 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.8e-06    0.0013      24      52 ..       1      29 [.       1      85 [. 0.90
   2 ?   -2.2   0.0       2.3   1.7e+03     270     281 ..     152     163 ..     132     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                                      EEEEEEESTTSSHHHHHHHHHHHCS---- CS
                           G-alpha 24 vkllllGqseSGKsTilkqlkllykkgfs 52
                                      ++ll+lG+++SGKsT++k++  + ++++s
  gi|488601548|ref|YP_007908019.1|  1 MNLLILGHAGSGKSTLVKNFSEFLRGSYS 29
                                      69******************988877766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                                       SEEEEEEE-HHH CS
                           G-alpha 270 tpiiLflnKlDi 281
                                       ++ i ++nK Di
  gi|488601548|ref|YP_007908019.1| 152 VETITIFNKADI 163
                                       445666666665 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   1.6e-06    0.0012      26      52 ..       2      28 ..       1      68 [. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                            AAA_16 26 lvllsGesGvGKsslvrellralekdg 52
                                      ++l+ G++G+GKs+lv+ + + l++++
  gi|488601548|ref|YP_007908019.1|  2 NLLILGHAGSGKSTLVKNFSEFLRGSY 28
                                      689*****************9999883 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.7e-06     0.002       2      87 ..       3     133 ..       2     160 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                                       EEEEESTTSSHHHHHHHHHT.........S.TEEESSSTTSSSSEEEEEEE.ETTEE.................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.........e.kaivsdkpgtTrdinegrvk.lkgke.................... 47 
                                        +i+G+  +GKStL++  ++         + +   +++p  T  i  +++  +   e                    
  gi|488601548|ref|YP_007908019.1|   3 LLILGHAGSGKSTLVKNFSEflrgsysvkTvNLDPASTPCYTASIDSRKFVrT---Edimkrfnlgingalmksmem 76 
                                       579***************97666666553233455677777777766666521...123344455555555556666 PP

                                       .............EEEEECGGCSSHHHHHH..HHHHHHHHHHC.TSEEEEEEETT....T CS
                          MMR_HSR1  48 .............ielvDtpGliegaseek..glgkaflalee.adlillvvdas....e 87 
                                                    i+l+DtpG +e        ++g+ f +       +++++d+      
  gi|488601548|ref|YP_007908019.1|  77 lkdyidhlivkddIVLYDTPGQLE-LF--LftDFGEVFSERLGkDTTAIFLIDSGlcrsP 133
                                       6666666666666********654.22..1336777777644413557888884444441 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.4e-06    0.0048       1      33 [.       2      36 ..       2      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.4e-06
                                      EEEEE--SSSSHHHHHHHGGGGB..S--EEEEE-- CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal..nreveyvqlt 33
                                      ++l++G  G+gKs+l++ ++++l    +v +v+l 
  gi|488601548|ref|YP_007908019.1|  2 NLLILGHAGSGKSTLVKNFSEFLrgSYSVKTVNLD 36
                                      689********************655556666555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.5e-05     0.011      14      36 ..       3      25 ..       1      69 [. 0.84
   2 ?   -0.8   0.0       2.6     2e+03      44      74 ..     158     186 ..     138     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                                      EEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllk 36
                                      + i+G+ G+GKStL+k +++ l+
  gi|488601548|ref|YP_007908019.1|  3 LLILGHAGSGKSTLVKNFSEFLR 25
                                      579*************9988765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.6
                                       ETTCEGGGB-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  44 ldgkdlkeqeleslrkeigvlpqepqlfpel 74 
                                       ++++d+++   +++++ +++++qe+ + pel
  gi|488601548|ref|YP_007908019.1| 158 FNKADISS--PPKFEEVVEYIEQEEGVLPEL 186
                                       44666666..778888999999998887775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     1e-05    0.0078      25      42 ..       3      20 ..       1      34 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                            AAA_29 25 tlltGpsGsGKSTllDAi 42
                                       l+ G+ GsGKSTl+  +
  gi|488601548|ref|YP_007908019.1|  3 LLILGHAGSGKSTLVKNF 20
                                      79************9655 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   0.0   6.2e-05     0.047      34      70 ..       5      40 ..       2      58 .. 0.85
   2 ?    0.9   0.0      0.24   1.8e+02     171     227 ..     155     223 ..     148     228 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      + G  G+Gkstlv+++ + lr   + v  + +DP+s+
  gi|488601548|ref|YP_007908019.1|  5 ILGHAGSGKSTLVKNFSEFLR-GSYSVKTVNLDPAST 40
                                      56999***********98775.5689********996 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.24
                                       EEEEE---...HHHHHHHHHHHHHHHHHCST.........TBTTB--EEEEEBCCCTBSHHHHHHHHHH CS
                              MeaB 171 iivvnkaD...kkeaekaarelraaleleee.........kekeWrpkvlktsavegeGidelvdaiee 227
                                       i++ nkaD   +++ e++ +++++   ++ e         + ++ r + + +sa +g G del+  i+e
  gi|488601548|ref|YP_007908019.1| 155 ITIFNKADissPPKFEEVVEYIEQEEGVLPEllkgilpfrELTSLRFREMVISARNGTGFDELIGMINE 223
                                       566677774333333333333333333332255555554433444555566799999999999998877 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 !   14.7   0.0   2.3e-05     0.017      35      77 ..       2      43 ..       1      58 [. 0.86
   2 ?   -0.8   0.0       1.3   9.6e+02      65     107 ..      64     106 ..      44     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                                      ++l+ G++G+GK++++k++ + l   +y+++t+n+    ++  
  gi|488601548|ref|YP_007908019.1|  2 NLLILGHAGSGKSTLVKNFSEFLR-GSYSVKTVNLDPASTPCY 43
                                      6899****************9999.*********988777655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                             AAA_7  65 ltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvD 107
                                       l in   + s ++l+d i+  + k    +y  pg+ +l +F D
  gi|488601548|ref|YP_007908019.1|  64 LGINGALMKSMEMLKDYIDHLIVKDDIVLYDTPGQLELFLFTD 106
                                       5566666778888999999999999999999999999988877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0092       8      38 ..       3      36 ..       1      93 [. 0.67

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee...e 38
                                      l++ G++G+GK+tl++++ e l   ++ ++    
  gi|488601548|ref|YP_007908019.1|  3 LLILGHAGSGKSTLVKNFSEFLRGSYSVKTvnlD 36
                                      7899****************99665555555552 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.6    0.0018       1.3     103     121 ..       4      22 ..       2     103 .. 0.77
   2 ?    3.6   0.0     0.076        57      34      73 ..     139     177 ..     119     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                                       EEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase 103 vlvGqSGvGKStLinallp 121
                                       +++G+ G GKStL++++ +
  gi|488601548|ref|YP_007908019.1|   4 LILGHAGSGKSTLVKNFSE 22 
                                       689***********98765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.076
                                       HHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHH CS
                       RsgA_GTPase  34 lldrfLvlaeekgiepvivlnKiDlleeeeeleelkeele 73 
                                        + +  v+  ++g+e + ++nK+D+ +  + +ee+ e +e
  gi|488601548|ref|YP_007908019.1| 139 AIFQSAVISLRTGVETITIFNKADISSPPK-FEEVVEYIE 177
                                       5556667778899************99999.776666555 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   0.00062      0.46       2      26 ..       3      27 ..       2      35 .. 0.84
   2 ?    2.8   0.0      0.13        99      84     133 ..      76     126 ..      45     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
                                      EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                                      ++i G+ G+GK+Tlvk+ +e l+ s
  gi|488601548|ref|YP_007908019.1|  3 LLILGHAGSGKSTLVKNFSEFLRGS 27
                                      6789****************99765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHH-EEEE---STTGGG-.HHHHHHHHHHHTTTSEEEEE-- CS
                          NTPase_1  84 lalealrkalseadviviDEiGkmElks.kkfkeaveevLksekpvlavih 133
                                       +  + +++ + + d+++ D  G++El+    f e   e L +++  ++ i 
  gi|488601548|ref|YP_007908019.1|  76 MLKDYIDHLIVKDDIVLYDTPGQLELFLfTDFGEVFSERLGKDTTAIFLID 126
                                       3466778888999************99636788888888888888777765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.5e-05     0.048       3      26 ..       3      26 ..       2      37 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawae 26
                                      +++ G aGsGK+tL++ + + ++ 
  gi|488601548|ref|YP_007908019.1|  3 LLILGHAGSGKSTLVKNFSEFLRG 26
                                      6899************99876665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.1e-05     0.046       4      33 ..       2      37 ..       1     127 [. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel......gpkplfidtek 33
                                      ++li G +g+GK+tl+k++       +++  ++++ 
  gi|488601548|ref|YP_007908019.1|  2 NLLILGHAGSGKSTLVKNFseflrgSYSVKTVNLDP 37
                                      689****************55555534444444444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.9e-05     0.074       2      21 ..       4      23 ..       3      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.9e-05
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                      ++ G +G+GKStl++++ + 
  gi|488601548|ref|YP_007908019.1|  4 LILGHAGSGKSTLVKNFSEF 23
                                      799************99877 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.079      26      60 ..       3      37 ..       1      80 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                             DUF87 26 lAilgsTGsGKSntvavLleellekkgatililDp 60
                                      l+ilg +GsGKS++v+   e l  + +++++ lDp
  gi|488601548|ref|YP_007908019.1|  3 LLILGHAGSGKSTLVKNFSEFLRGSYSVKTVNLDP 37
                                      68*************98777666566666666665 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   0.00021      0.16       3      22 ..       4      23 ..       3      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                            AAA_33  3 llvGlpGsGKstlaerllkk 22
                                      l+ G++GsGKstl+++  + 
  gi|488601548|ref|YP_007908019.1|  4 LILGHAGSGKSTLVKNFSEF 23
                                      678************97655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00025      0.18       2      42 ..       4      46 ..       3     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00025
                            AAA_18  2 lltGtpGvGKttlakeLskrl.gf.gvnlrdvakenglllevd 42
                                      l+ G +G+GK+tl k+ s+ l g+ +v+   + + + ++++  
  gi|488601548|ref|YP_007908019.1|  4 LILGHAGSGKSTLVKNFSEFLrGSySVKTVNLDPASTPCYTAS 46
                                      689**************99886667433333333333333333 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0003      0.22      41      58 ..       2      19 ..       1      24 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                      SEEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE 41 hllvaGatgsGKStalnt 58
                                      +ll++G  gsGKSt +++
  gi|488601548|ref|YP_007908019.1|  2 NLLILGHAGSGKSTLVKN 19
                                      89************9987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0042       3.1      23      36 ..       4      17 ..       2      26 .. 0.92
   2 ?    2.1   0.0      0.31   2.3e+02     114     143 ..      73     111 ..      21     188 .. 0.64
   3 ?   -2.6   0.0       8.8   6.6e+03       4      31 ..     187     213 ..     186     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0042
                            AAA_23 23 lItGpNGaGKTTil 36
                                      lI G+ G+GK+T++
  gi|488601548|ref|YP_007908019.1|  4 LILGHAGSGKSTLV 17
                                      8***********97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.31
                            AAA_23 114 i.deleqfisellgskki.......ilnlilflgqer.f 143
                                         + l+++i++l+ +++i       +l+l+lf + ++ f
  gi|488601548|ref|YP_007908019.1|  73 SmEMLKDYIDHLIVKDDIvlydtpgQLELFLFTDFGEvF 111
                                       257789999999999999999999999999998888742 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 8.8
                            AAA_23   4 ienfrsfrdqe.idFskgltlItGpNGaG 31 
                                       ++++ +fr+ + + F     +I+  NG+G
  gi|488601548|ref|YP_007908019.1| 187 LKGILPFRELTsLRFR--EMVISARNGTG 213
                                       6888899886668886..35688888887 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 ?   11.3   0.0   0.00039      0.29       2      38 ..       3      39 ..       2      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                                      EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEE CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdflt 38
                                      ++++G +g+GK++l+k+f e    + + +t+ +d ++
  gi|488601548|ref|YP_007908019.1|  3 LLILGHAGSGKSTLVKNFSEFLRGSYSVKTVNLDPAS 39
                                      789***************9876666666676666555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00043      0.32      55      75 ..       2      22 ..       1      41 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                            DUF815 55 nvLLwGarGtGKSslvkalln 75
                                      n+L+ G+ G+GKS+lvk   +
  gi|488601548|ref|YP_007908019.1|  2 NLLILGHAGSGKSTLVKNFSE 22
                                      89***************8765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00058      0.43      22      44 ..       4      26 ..       2      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00058
                            AAA_30 22 vltGpAGtGKttalkalreawea 44
                                      ++ G AG+GK+t++k   e ++ 
  gi|488601548|ref|YP_007908019.1|  4 LILGHAGSGKSTLVKNFSEFLRG 26
                                      688************99998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 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:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1293.74
//
Query:       gi|488601549|ref|YP_007908020.1|  [L=714]
Description: Superfamily II helicase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-25   89.9   0.0    7.2e-25   87.8   0.0    2.0  2  DEAD             DEAD/DEAH box helicase
      2e-11   44.2   0.0    2.6e-10   40.6   0.0    2.8  2  Helicase_C       Helicase conserved C-terminal domain
    1.3e-08   35.3   0.4    5.9e-08   33.2   0.4    2.2  1  HHH_5            Helix-hairpin-helix domain
    1.3e-08   35.0   0.0    2.8e-08   34.0   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
      7e-06   25.8   0.0    2.1e-05   24.2   0.0    1.8  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.036   13.2   0.0      0.054   12.6   0.0    1.2  1  Sec63            Sec63 Brl domain
      0.085   12.8   0.1       0.34   10.9   0.0    2.2  2  HHH              Helix-hairpin-helix motif
       0.11   11.5   0.0        0.2   10.7   0.0    1.3  1  T2SSE            Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   3.2e-28   7.2e-25       2     171 ..      28     185 ..      27     189 .. 0.89
   2 ?   -1.2   0.0      0.67   1.5e+03     128     136 ..     275     283 ..     235     339 .. 0.54

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 3.2e-28
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       + Q+e+i+l l + ++++++++T+sGKTl++ ++++++++     +g k+l+++P+r+La + +++++ + k i+++
  gi|488601549|ref|YP_007908020.1|  28 PPQKEVIELGLfSRKNFVISIPTASGKTLIAELAMVREIM-----EGGKCLYIVPLRALASEKFEEFSIWEK-IGIK 98 
                                       67*********8889*********************9996.....588*******************99988.7888 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       +   +g  +++++ + l  ++di+++t ++ d++l++    +++++++V+DE++ + + ++++ ++ +++++++i+ 
  gi|488601549|ref|YP_007908020.1|  99 TGYSVG--DYESKDEWL-GECDIIITTSEKADSFLRNSASWIKKISCIVVDEIHLIDSFKRGPVLEILIAKMRKINP 172
                                       875556..566667778.88***************777777*******************************99988 PP

                                       TSTTTSEEEEEESSBSH CS
                                       xxxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlpk 171
                                       d +    +i lSAT+p+
  gi|488601549|ref|YP_007908020.1| 173 DIR----IIGLSATIPN 185
                                       876....********93 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.67
                                       ETHHHHHHT CS
                                       xxxxxxxxx RF
                              DEAD 128 DEadrlldq 136
                                       DE+d++ + 
  gi|488601549|ref|YP_007908020.1| 275 DEVDEIANA 283
                                       333333322 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 ?   -2.3   0.0       2.4   5.4e+03      15      50 ..      68     106 ..      56     135 .. 0.54
   2 !   40.6   0.0   1.2e-13   2.6e-10      13     111 .]     242     381 ..     233     381 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                                       TTSEEEEEESSHHHHHH.HHHH..HHHTTSTEEEESTTS CS
                        Helicase_C  15 eggkilifvntidrlek.vkll..lekkgikvavlhgel 50 
                                       eggk+l +v+ +  +++ ++ +   ek gik+ +  g+ 
  gi|488601549|ref|YP_007908020.1|  68 EGGKCLYIVPLRALASEkFEEFsiWEKIGIKTGYSVGDY 106
                                       667777777777633312222211122244444444433 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 1.2e-13
                                       TTTTSEEEEEESSHHHHHH........HHHH...................HHHT.......TSTEEEESTTSTHHHH CS
                        Helicase_C  13 eeeggkilifvntidrlek........vkll...................lekk.......gikvavlhgelpqner 55 
                                        e+gg++l+f  t++++e+        +k +                      +       +  +a +h+ l +++r
  gi|488601549|ref|YP_007908020.1| 242 LEDGGQVLVFDSTRRNAEStavkiskiTKKFvgdevdeianavleendgdM--SkklseciKKGSAFHHAGLLNSQR 316
                                       377888888888888553333232223222245555555555543333331..03344556888999999******* PP

                                       HHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSH.........HHHHHHHTTSSSTT CS
                        Helicase_C  56 eeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnv.........tsyiqriGRtgRag 111
                                       + + ++f+++ ++vL+at  ++ G+++p  +++i     +++          +y+q++GR+gR g
  gi|488601549|ref|YP_007908020.1| 317 KTVEDAFKSNLIKVLVATPTLSAGVNLPARRVIIKSYHRFEPnlgnvpikvLEYKQMAGRAGRPG 381
                                       ****************************88888854444333334445555************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 !   33.2   0.4   2.6e-11   5.9e-08       3      54 ..     658     706 ..     656     708 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.6e-11
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriile 54 
                                       +L++v+GiG+++A++l++ Gi+s edl++ ++++++++  iGkk Aerii e
  gi|488601549|ref|YP_007908020.1| 658 DLIEVKGIGRARARKLYNYGIRSKEDLLE-NRAKVSEL--IGKKWAERIIGE 706
                                       8*************************999.69******..*********955 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.2e-11   2.8e-08       5     170 ..      27     184 ..      23     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.2e-11
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflse 80 
                                        + Q+e+ie  l       +k+++i ++T +GKTl+a +++++++++ g+  k+l +vp ++l +   eef+ + + 
  gi|488601549|ref|YP_007908020.1|  27 FPPQKEVIELGL-----FSRKNFVISIPTASGKTLIAeLAMVREIME-GG--KCLYIVPLRALASEKFEEFSIWEKI 95 
                                       566666666555.....35789***************9999999998.45..8**********99999999888777 PP

                                       ....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T......... CS
                            ResIII  81 aykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk......... 148
                                            ++ +s   +++k +   +++i++tt +++d+ +      +     +++ +i++DE H + + k         
  gi|488601549|ref|YP_007908020.1|  96 GI---KTGYSVGDYESKDEWLGECDIIITTSEKADSFL-----RNSASWIKKISCIVVDEIHLIDSFKrgpvleili 164
                                       74...44444444444356779****************.....77888899999********999974555555544 PP

                                       .TTHHHHHT---SEEEEEESS-S CS
                            ResIII 149 .swreilekfkeavllglTATpe 170
                                        ++r+i   +++  ++gl+AT++
  gi|488601549|ref|YP_007908020.1| 165 aKMRKI---NPDIRIIGLSATIP 184
                                       455555...45578*******86 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   9.4e-09   2.1e-05       5      36 ..     661     692 ..     658     696 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.4e-09
                   DNA_pol_lambd_f   5 kvyGVGpktAkkwyakGirtledlrakrakLt 36 
                                       +v G+G+++A+k+y+ Gir+ edl+++rak++
  gi|488601549|ref|YP_007908020.1| 661 EVKGIGRARARKLYNYGIRSKEDLLENRAKVS 692
                                       799***********************888876 PP

>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.054       1      68 [.     497     565 ..     497     601 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                       ECHHHHHHHHHT--HHHHHHHHHHS-..TT--HHHHHHHHHTSGGGGGS---TTHHHHHHHHHHTSSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             Sec63   1 ptelGriaShYyisyetiklfneslk..pnttlkdlLeilssasEFeeipvReeEkkelkkLlekvpikv 68 
                                       ptelG+++S+ yi   t  +f ++l+   + ++  +L+ l++  + e + +R+ ++  +++L++k++ ++
  gi|488601549|ref|YP_007908020.1| 497 PTELGKLVSKLYIDPLTGFIFYDTLEkfDDLSEVAILHTLCRTPDMETLYIRKYDD-WVEELADKFRNEL 565
                                       89***********************9555679999*****************9975.6788888854443 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.34      10      30 .]     656     676 ..     647     676 .. 0.83
   2 ?   -3.2   0.0       4.4   9.8e+03      19      28 ..     695     704 ..     695     705 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                       HHHHHTSTT-SHHHHHHHHHH CS
                               HHH  10 reeLlalPGVGpktAeaIlsy 30 
                                       + +L +++G+G+++A++ ++y
  gi|488601549|ref|YP_007908020.1| 656 LIDLIEVKGIGRARARKLYNY 676
                                       679*************99876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                                       -SHHHHHHHH CS
                               HHH  19 VGpktAeaIl 28 
                                       +G+k Ae+I+
  gi|488601549|ref|YP_007908020.1| 695 IGKKWAERII 704
                                       89**9**996 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.7e-05       0.2     118     160 ..      30      73 ..      11      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.7e-05
                             T2SSE 118 iaevlrkavrerglilvsGgTgsGKttll.yallkeinksderi 160
                                       ++ev++  + +r+++++s +T sGKt ++  a++ ei +  +++
  gi|488601549|ref|YP_007908020.1|  30 QKEVIELGLFSRKNFVISIPTASGKTLIAeLAMVREIMEGGKCL 73 
                                       6789999999****************998557778887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.76u 0.35s 00:00:01.10 Elapsed: 00:00:00.56
# Mc/sec: 3872.26
//
Query:       gi|488601550|ref|YP_007908021.1|  [L=274]
Description: putative transcriptional regulator [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   72.2   0.1    5.3e-20   71.1   0.1    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0003   20.5   0.0    0.00057   19.6   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    0.00047   19.4   0.1     0.0053   16.0   0.1    2.2  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0006   19.6   0.6     0.0012   18.6   0.1    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0029   17.7   0.0     0.0061   16.6   0.0    1.6  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.005   16.7   0.0      0.011   15.7   0.0    1.6  1  MarR            MarR family
     0.0069   16.3   0.0       0.02   14.8   0.0    1.7  2  PLDc_2          PLD-like domain
  ------ inclusion threshold ------
      0.034   14.0   0.0      0.069   13.1   0.0    1.5  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 !   71.1   0.1   2.4e-23   5.3e-20       1      67 [.       7      73 ..       7      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.4e-23
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L+klGLs+y ak+ + Llk g+a+a+ei+e +gvpr+k+YevL +L d GlV+++++rp ++r+ +p
  gi|488601550|ref|YP_007908021.1|  7 LEKLGLSSYQAKALISLLKCGEAKASEISELSGVPRAKIYEVLDQLADLGLVDKIPSRPVKFRVREP 73
                                      89************************************************************98776 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 !   19.6   0.0   2.6e-07   0.00057      16      50 ..      27      60 ..      18      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.6e-07
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++  + se+++ +g+p+++ +  L  L  lG+v +
  gi|488601550|ref|YP_007908021.1| 27 GE-AKASEISELSGVPRAKIYEVLDQLADLGLVDK 60
                                      44.499***************************86 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.3e-06    0.0053      17      80 ..     136     200 ..     120     208 .. 0.84
   2 ?    1.3   0.0     0.074   1.7e+02     178     206 ..     208     236 ..     201     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-06
                                       HHHHH-SSEE.EEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S--- CS
                    Regulator_TrmB  17 elIesAenel.ivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvrrsg 80 
                                        + ++Ae+e+ ivs   e+ +++r+el +a +rgv++ +l+ ++++ +e+ ++ +  ++++++s 
  gi|488601550|ref|YP_007908021.1| 136 LMYREAEKEInIVSRCFEYYPKVRKELVDAFNRGVKIKILLLGRKFIDERGMKVQNEVLKMIKSD 200
                                       56689*****5568889**************************9999999888888888877765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.074
                                       T--EEEEEEEEEEEEEETTTTEEEEEEEE CS
                    Regulator_TrmB 178 tgeevtieGrvveatlnstpgvaslvvet 206
                                       ++++  ++G +v+ ++++ +g+a +vve 
  gi|488601550|ref|YP_007908021.1| 208 SRTPLPLRGSIVDPSYEYKTGKAIFVVED 236
                                       6778889********************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 ?   -3.5   0.0       4.6     1e+04      38      44 ..       6      12 ..       4      13 .. 0.75
   2 !   18.6   0.1   5.5e-07    0.0012       8      47 .]      21      60 ..      16      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.6
                                      HHHHTTS CS
                             HTH_5 38 kLreaGL 44
                                      +L+++GL
  gi|488601550|ref|YP_007908021.1|  6 ILEKLGL 12
                                      7888887 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5.5e-07
                                      HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  8 LklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      ++lL  ge++++e++e  g++++++ + L +L ++GLV+k
  gi|488601550|ref|YP_007908021.1| 21 ISLLKCGEAKASEISELSGVPRAKIYEVLDQLADLGLVDK 60
                                      455555********************************87 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06    0.0061      23      69 ..      29      75 ..       4      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                           DUF2250 23 dYaksiakeleipleevrellkkLeelGLlervegktikrteaklKk 69
                                        a  i++   +p+ ++ e+l++L +lGL+++  ++ +k++ ++ K+
  gi|488601550|ref|YP_007908021.1| 29 AKASEISELSGVPRAKIYEVLDQLADLGLVDKIPSRPVKFRVREPKE 75
                                      4577899999******************************9998875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.9e-06     0.011       1      52 [.      12      63 ..      12      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.9e-06
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      l+  q ++L +l   g+++ se+ + +gv ++ + +vld+L + Gl+++ +s
  gi|488601550|ref|YP_007908021.1| 12 LSSYQAKALISLLKCGEAKASEISELSGVPRAKIYEVLDQLADLGLVDKIPS 63
                                      56678999***************************************99775 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   8.8e-06      0.02       6      49 ..     139     185 ..     137     221 .. 0.75
   2 ?   -2.3   0.0       1.7   3.7e+03     115     133 .]     248     266 ..     246     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.8e-06
                            PLDc_2   6 ksAkksidiatyyfvsdreildallkaakrgvkvrilldskkd...d 49 
                                       ++A+k+i i++  f+  +++ ++l++a +rgvk++ill  +k     
  gi|488601550|ref|YP_007908021.1| 139 REAEKEINIVSRCFEYYPKVRKELVDAFNRGVKIKILLLGRKFideR 185
                                       589***********99999******************9873324331 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                            PLDc_2 115 viedkelakeleeeFerlw 133
                                       v++++ l++ ++++F+ +w
  gi|488601550|ref|YP_007908021.1| 248 VTDNPSLVAGMKKYFDLIW 266
                                       788999999*******998 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   3.1e-05     0.069       2      56 ..      11      63 ..      10      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      gl+  qa +L  L   ++    ++e+ +  g++++ +  +l+ L + GLv + p+
  gi|488601550|ref|YP_007908021.1| 11 GLSSYQAKALISLLKCGE--AKASEISELSGVPRAKIYEVLDQLADLGLVDKIPS 63
                                      777778888888777777..8*****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1540.84
//
Query:       gi|488601551|ref|YP_007908022.1|  [L=384]
Description: UDP-sulfoquinovose synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-18   66.5   0.0    3.9e-18   65.8   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.2e-18   65.1   0.0    3.7e-16   59.5   0.0    2.2  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.7e-08   34.0   0.0    0.00085   18.5   0.0    2.4  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0042   16.3   0.0     0.0076   15.4   0.0    1.4  1  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.022   13.9   0.0      0.079   12.0   0.0    1.9  2  RmlD_sub_bind    RmlD substrate binding 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 !   65.8   0.0   1.1e-21   3.9e-18       1     228 [.       3     280 ..       3     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.1e-21
                                       EEEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC.........................EEEE--T CS
                         Epimerase   1 ilVtGatGfiGsalvkallekg..yevigldrlssasntarledl.........................elveldl 50 
                                       +lVtGa G++G  ++ +l+e     ++ig+d+   a++++ +e +                         +++++dl
  gi|488601551|ref|YP_007908022.1|   3 VLVTGADGYVGWCVLLRLAETMpdERIIGVDNF--ARRRWVEE-VgsrslipilspekrkeiveeeygkvSFINGDL 76 
                                       79************999999987566*******..33333333.34689**************************** PP

                                       T-HHHHHHHHHHHT-SEEEE--S.---H..HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT..EEEEEEEGGGGTSC CS
                         Epimerase  51 tdrsalerlfkeeqpdavihlAa.vggv..aassedpadfieknlqgtlnlleaarkagvk..rllflsSsevYGkd 122
                                       t ++ ++ +++ +qpd++ihlAa  + +  + s+e++ +++++n + tlnll  ++++g+    ++ + ++ vYG +
  gi|488601551|ref|YP_007908022.1|  77 TSQEFVNTMLRVYQPDTIIHLAAqPSAPysQISWEKAVYTMYNNNVSTLNLLWGLKENGMLntHFISATTTGVYGSP 153
                                       ***********************544432256799***********************887679999999*****88 PP

                                       SS.SS.........BSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTT..S-TTS.TTSHH CS
                         Epimerase 123 ae.qp.........keettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGpr..ngege.vsrvi 186
                                       +  +p            ++   p    s Y ++K    + ++ +++q gln+  +r+  + G+   + +ge  +r+ 
  gi|488601551|ref|YP_007908022.1| 154 EYpIPegfyeveykGGRDVVPHPHMAGSFYHMSKCNDINHMWLANKQWGLNISDVRVGIVTGATteEAKGElSTRFD 230
                                       88667888744433222332334467899***********************************8866666666665 PP

                                       HHHHHHHHT.........TSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 187 palirkile.........gkqevtllgdgtalRdflyveDvaeaillvleh 228
                                       + +   + +         g  ++t++g+g +  +f+  eD+++ ++ ++ +
  gi|488601551|ref|YP_007908022.1| 231 FDFYFGVVThrfcaqamiGY-PITVYGKGLQGKPFVTLEDCVKSFVELAIK 280
                                       55555555533332222255.*********************998866655 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 !   59.5   0.0     1e-19   3.7e-16       1     137 [.       4     154 ..       4     188 .. 0.78
   2 ?    3.3   0.0     0.012        43     199     282 ..     241     324 ..     222     355 .. 0.68

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1e-19
                                       EEETTTSHHHHHHHHHHHHC..T-CCEEEEEEESS-TTHHHH...........HCTTT...TTGCCEEEEE--TT-H CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlek..gyevhgivrrsssfntgrie...........hlakdpkeeleenlklhkgDltDs 64 
                                       L+TG  G++G  ++ +L e   + +++g+++ +    ++++            + ++   ee  +++++++gDlt +
  gi|488601551|ref|YP_007908022.1|   4 LVTGADGYVGWCVLLRLAETmpDERIIGVDNFARRRWVEEVGsrslipilspeKRKEIV-EEEYGKVSFINGDLTSQ 79 
                                       89********9999999998555677777776555544433322222222111222222.2234599********** PP

                                       HHHHHHHHHHT-SEEEE--S---...HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S CS
                     GDP_Man_Dehyd  65 sslerllaevqpdevynLAAqsh...VdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq 137
                                       + ++ +l+ +qpd++++LAAq      + s+ek+ yt+ +n + tl+LL   ++ g+  +++f+ a t  vYG+++
  gi|488601551|ref|YP_007908022.1|  80 EFVNTMLRVYQPDTIIHLAAQPSapySQISWEKAVYTMYNNNVSTLNLLWGLKENGML-NTHFISATTTGVYGSPE 154
                                       *********************651224668**************************96.79************986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.012
                                       HHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHH.HHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH. CS
                     GDP_Man_Dehyd 199 ravarialgkqevlylGnldakRdwghvkDyveamwl.mlqqdkpedyviatgethsvrefvelaflelgktieweg 274
                                       r+ a++  g  +++++G++ + + +   +D v+ ++  +++ ++  +++ +t   +++ e++e+  +++ ++i  e 
  gi|488601551|ref|YP_007908022.1| 241 RFCAQAMIGY-PITVYGKGLQGKPFVTLEDCVKSFVElAIKGGEGYKVYNQTVGAVKIVELAEIIREAAMEEIGLEV 316
                                       6778888887.8899*****************996651667777777777777777777777776666665555544 PP

                                       ........ CS
                     GDP_Man_Dehyd 275 kgeeevgr 282
                                       + ++  + 
  gi|488601551|ref|YP_007908022.1| 317 EIKHVPNP 324
                                       32222222 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-07   0.00085       1     126 [.       3     142 ..       3     149 .. 0.68
   2 !   12.8   0.1   1.3e-05     0.047     176     283 ..     236     342 ..     235     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-07
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH...................-TTEEEE....E--TT CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeieke.............leeelkkkklkveivpvigdvr 64 
                                       vlvtGa G +G  ++ +++++ p + i+   d ++  +  +e             +++e+ ++++  ++  + gd++
  gi|488601551|ref|YP_007908022.1|   3 VLVTGADGYVGWCVLLRLAETMPDERII-GVDNFARRRWVEEvgsrslipilspeKRKEIVEEEY-GKVSFINGDLT 77 
                                       7999999999999999999997766443.333333222222223335555533334444444444.4556777**** PP

                                       -HHHHHHHTT..T-SEEEE------HHHHHHSHHHHH...HHHHHHHHHHHHHHHHTT-SEEEEE CS
                   Polysacc_synt_2  65 dkerlekaleelkvdvvfhaAAlKhVPlveenpleai...ktNvlgtenvieaaieagvkkvvli 126
                                        +e ++++l+ +++d+++h AA    P  +  + +a+    +N ++t n++   +e+g+ +  +i
  gi|488601551|ref|YP_007908022.1|  78 SQEFVNTMLRVYQPDTIIHLAAQPSAPYSQISWEKAVytmYNNNVSTLNLLWGLKENGMLNTHFI 142
                                       ***************************99988887762224688888888877777766555555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.3e-05
                                       TSSHHHHHHHHHTTSSEEES-TT-E.EEEE-HHHHHH.HHHHHHHH--SS-EEEE--.-EEEHHHHHHHH....... CS
                   Polysacc_synt_2 176 GSviplFkkqikeggpvtvTdpemt.Ryfmtieeavq.LvlqalalakggeifvldmGepvkivdlakalielsgle 250
                                       G v   F +q   g p+tv  + +  + f+t+e+ v+ +v  a++ ++g +++ + +  +vkiv+la+ + e +  e
  gi|488601551|ref|YP_007908022.1| 236 GVVTHRFCAQAMIGYPITVYGKGLQgKPFVTLEDCVKsFVELAIKGGEGYKVYNQTV-GAVKIVELAEIIREAAMEE 311
                                       6677889999999999999999986478*******9658999***************.69*******9986666544 PP

                                       ...SSSS-EEE----TT--SS-EEE-GGGGGGE CS
                   Polysacc_synt_2 251 ekkeedieikitGlRpGEklyEeLlieeesvee 283
                                            ++eik +     Ek   e+++e+++ ++
  gi|488601551|ref|YP_007908022.1| 312 I--GLEVEIKHVPNPRVEKEDHEMIMENDNFRK 342
                                       4..469999999999999999999999988765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.1e-06    0.0076       1     210 [.       5     220 ..       5     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEE...E-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGG CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyll...vRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprl 74 
                                       +TGa G++G ++l +L +t p+ +i+ +   +R +  e++  R    + + e  +++ +e   ++++++GDl+ +++
  gi|488601551|ref|YP_007908022.1|   5 VTGADGYVGWCVLLRLAETMPDERIIGVdnfARRRWVEEVGSRSLIPILSPEKRKEIVEEEYGKVSFINGDLTSQEF 81 
                                       7*******************998666542337777777777776666666666666666999**************8 PP

                                       G--HHHHHHHHHH--EEEE--SS.......-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-T CS
                     NAD_binding_4  75 GLseedlqelaeevdviihsaAt.......vnfdepykellrvNveGtrevlelakklkklkvllhvSTayvngere 144
                                          ++ l+  + + d iih aA+       +++++ + ++++ Nv     +  l +++  + +++   T  v+g  e
  gi|488601551|ref|YP_007908022.1|  82 V--NTMLR--VYQPDTIIHLAAQpsapysqISWEKAVYTMYNNNVSTLNLLWGLKENGMLNTHFISATTTGVYGSPE 154
                                       4..33333..4689*******954444444899999999*****998888889988877775666666688888888 PP

                                       TT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-...-S CS
                     NAD_binding_4 145 geveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg...es 210
                                         + e +ye +    k   d   + +     Y  sK    + +  a+++ gl+++ vR++i+tg   e 
  gi|488601551|ref|YP_007908022.1| 155 YPIPEGFYEVE---YKGGRDVVPHPHMAGSFYHMSKCNDINHMWLANKQWGLNISDVRVGIVTGattEE 220
                                       89999999844...44444445555555567*****98888888888889*************954433 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 ?   12.0   0.0   2.2e-05     0.079       1      60 [.       1      99 [.       1     103 [. 0.89
   2 ?   -3.4   0.0       1.1   3.9e+03     220     281 ..     297     357 ..     276     361 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                                      EEEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT.....................................T--TTSH CS
                     RmlD_sub_bind  1 mkilvtGanGqlGseLakqlae..eglevlaltre.....................................eldltda 40
                                      m++lvtGa+G +G+ +  +lae   +  ++++++                                      + dlt +
  gi|488601551|ref|YP_007908022.1|  1 MTVLVTGADGYVGWCVLLRLAEtmPDERIIGVDNFarrrwveevgsrslipilspekrkeiveeeygkvsfiNGDLTSQ 79
                                      899***********98877776445667777755467799*************************************** PP

                                      HHHHHHHHHH--SEEEE--- CS
                     RmlD_sub_bind 41 eavaellkeakpdvvvnaAA 60
                                      e v+++l+  +pd ++++AA
  gi|488601551|ref|YP_007908022.1| 80 EFVNTMLRVYQPDTIIHLAA 99
                                      *******************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHH CS
                     RmlD_sub_bind 220 wlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkev 281
                                        +e+A+ i ++a ++      i++  +p+  k+ ++  ++++++++    k+++ ++a+k++
  gi|488601551|ref|YP_007908022.1| 297 IVELAEIIREAAMEEIGLEVEIKHVPNPRVEKEDHEMIMENDNFRKL-VGKPQDLKDAIKDI 357
                                       55666555555444443334566666666667777777777777776.44455666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 2052.21
//
Query:       gi|488601552|ref|YP_007908023.1|  [L=306]
Description: Nucleoside-diphosphate-sugar epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-51  174.3   0.0    3.8e-51  173.9   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      4e-34  118.5   0.0    4.9e-34  118.2   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      1e-21   77.2   0.0    1.2e-21   76.9   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.2e-17   62.2   0.0    5.1e-17   61.9   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    8.9e-12   44.7   0.1    8.9e-11   41.4   0.1    2.4  1  NAD_binding_4    Male sterility protein
    1.8e-11   43.7   0.0    5.7e-11   42.1   0.0    1.7  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.5e-09   36.8   0.0    4.4e-09   36.5   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    0.00047   19.8   0.0     0.0036   16.9   0.0    2.0  2  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.022   14.7   0.1       0.37   10.7   0.1    2.2  1  KR               KR domain
      0.027   13.9   0.0      0.052   13.0   0.0    1.6  1  adh_short        short chain dehydrogenase
      0.081   13.1   0.0       0.21   11.8   0.0    1.6  2  Spore_GerAC      Spore germination B3/ GerAC like, C-terminal


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 !  173.9   0.0   2.3e-54   3.8e-51       1     241 []       2     233 ..       2     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 2.3e-54
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S. CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAa. 73 
                                       il+tG++G+iG  + + l++++ e  +ld+ s +s+ + l      e++ +d++++++++++f+  ++davihlAa 
  gi|488601552|ref|YP_007908023.1|   2 ILITGGNGYIGIEISELLADRNEEFRVLDNFSGSSPLNMLFVNgkaEFIWGDVRKPEEMKEAFR--DVDAVIHLAAk 76 
                                       8******************************999999998888999******************..89********* PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHH CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlage 150
                                         + +  ++++ d+ ++n +gt+n+le ark+++  ++f+s++ vYG + +   +e++   + kp + Ya +Kl +e
  gi|488601552|ref|YP_007908023.1|  77 LPTAPGMVDEAGDVNDTNYRGTVNVLELARKSDA-SMIFASTCNVYGVGMN--MDESS---EPKPLNSYAESKLKAE 147
                                       **********************************.************9998..56777...899************* PP

                                       HHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHH CS
                         Epimerase 151 klveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvle 227
                                       + + +y+++ygl++ ilrl ++yG   +  + + v+ ++  ++ +g  ++t++gdg+++R+f++v+Dva+a+l+++e
  gi|488601552|ref|YP_007908023.1| 148 RACIEYHEKYGLDVKILRLASVYGYS-PGVRFNLVVNYFTLRAVTGY-PLTVFGDGSNWRPFVHVRDVAKAFLFFIE 222
                                       *************************9.33447789999999*****9.***************************** PP

                                       HHTT-STTEEEEES CS
                         Epimerase 228 hvdagdkgeiyniG 241
                                       +   g++geiyniG
  gi|488601552|ref|YP_007908023.1| 223 N---GKSGEIYNIG 233
                                       *...999******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 !  118.2   0.0     3e-37   4.9e-34       1     272 [.       3     256 ..       3     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 3e-37
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       LiTG++G+iG  + elL +++ e+ ++++ s s     ++ l       ++++ +++ gD++  +++++++++v  d
  gi|488601552|ref|YP_007908023.1|   3 LITGGNGYIGIEISELLADRNEEFRVLDNFSGSSP---LNMLF------VNGKAEFIWGDVRKPEEMKEAFRDV--D 68 
                                       9*************************999998855...55555......356789******************9..9 PP

                                       EEEE--S---.HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqsh.VdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPY 153
                                       +v++LAA+    +  ++++  + ++n  Gt+++Le++r+     ++ +++aSt  vYG      ++E+   +P + Y
  gi|488601552|ref|YP_007908023.1|  69 AVIHLAAKLPtAPGMVDEAGDVNDTNYRGTVNVLELARKS----DASMIFASTCNVYGVG--MNMDESSEPKPLNSY 139
                                       *******9661567789*********************96....57899*********86..5789*********** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       a +Kl a+  +++y+e+ygl + + +l   ++   g +f    +  +  r+  g  + +++G++++ R + hv+D++
  gi|488601552|ref|YP_007908023.1| 140 AESKLKAERACIEYHEKYGLDVKILRLASVYGYSPGVRFN-LVVNYFTLRAVTGY-PLTVFGDGSNWRPFVHVRDVA 214
                                       ******************************9999999875.45555666666666.99999**************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHH CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiew 272
                                       +a+  +++++k+ +++    e++ +r+++e+   e+  +i+ 
  gi|488601552|ref|YP_007908023.1| 215 KAFLFFIENGKSGEIYNIGRENYMIRDVAEIVKREVNPSIDI 256
                                       *******************************99999865543 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0   7.5e-25   1.2e-21       1     226 [.       3     218 ..       3     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 7.5e-25
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       ++tGg G++G ++ + L +++e  e rvlD   +++ l+ l+  + +++i gDv++ ++++ea ++vd+vihla+  
  gi|488601552|ref|YP_007908023.1|   3 LITGGNGYIGIEISELLADRNE--EFRVLDNFSGSSPLNMLFVNGKAEFIWGDVRKPEEMKEAFRDVDAVIHLAAKL 77 
                                       69**********9999998885..*************99999999999**************************998 PP

                         3Beta_HSD  78 dvag..kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKal 152
                                       + a   +++ + + + n++GT nvle ++k++   +++ S+++v g    g ++    E+   e+++ + y+esK  
  gi|488601552|ref|YP_007908023.1|  78 PTAPgmVDEAGDVNDTNYRGTVNVLELARKSDA-SMIFASTCNVYGV---GMNMD---ES--SEPKPLNSYAESKLK 145
                                       877545678889******************996.689*******999...55555...44..46778889******* PP

                         3Beta_HSD 153 aEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlak....lglalfkigdeevlsdrvYvgNvawah 225
                                       aE++ ++  +   k g  l    LR a +yG    + ++l++++      +g+ l   gd ++   +v v  va+a 
  gi|488601552|ref|YP_007908023.1| 146 AERACIEYHE---KYG--LDVKILRLASVYGYSPGVRFNLVVNYFTlravTGYPLTVFGDGSNWRPFVHVRDVAKAF 217
                                       *******999...777..8888999999999877777777777655111156788999***************9997 PP

                         3Beta_HSD 226 i 226
                                       +
  gi|488601552|ref|YP_007908023.1| 218 L 218
                                       5 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 !   61.9   0.0   3.1e-20   5.1e-17       3     202 ..       2     226 ..       1     265 [. 0.82

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 3.1e-20
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE---- CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAAy 61 
                                       il+tG+nG +G e+ ++la ++ e+  l++                     d++++e+++e++++   d+v+++AA 
  gi|488601552|ref|YP_007908023.1|   2 ILITGGNGYIGIEISELLADRNEEFRVLDNFsgssplnmlfvngkaefiWGDVRKPEEMKEAFRD--VDAVIHLAAK 76 
                                       9*********************999999766789************99889**************..789*****97 PP

                                       ..--HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHH CS
                     RmlD_sub_bind  62 ..tavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqav 136
                                         ta   +  e    +  n +++ ++ e+a++ +a +i+ St  V+     ++  e++e++Pln Y+++Kl+ E+a 
  gi|488601552|ref|YP_007908023.1|  77 lpTAPGMVD-EAGDVNDTNYRGTVNVLELARKSDASMIFASTCNVYGVG--MNMDESSEPKPLNSYAESKLKAERAC 150
                                       335544444.3444567899**************************866..5569*********************9 PP

                                       HH....H-SSEEEEEE-SEESS...SSS-HHHHHHHHH.HH-SEEEEESS-EE.--.EEHHHHHHHHHHHHHHCHH CS
                     RmlD_sub_bind 137 la....agkkalivRtswvyge...kgknfvktmlrla.kereelkvvaDqlg.sP.TsardlAevllqllekaae 202
                                        +    +g ++ i+R + vyg     + n+v + + l   +  +l+v+ D    +P  ++rd+A++ l  +e+ ++
  gi|488601552|ref|YP_007908023.1| 151 IEyhekYGLDVKILRLASVYGYspgVRFNLVVNYFTLRaVTGYPLTVFGDGSNwRPfVHVRDVAKAFLFFIENGKS 226
                                       993333445679*********9555455776666665437888999999865325636788888888888877665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   5.5e-14   8.9e-11      58     210 ..      43     173 ..       4     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.5e-14
                                       HTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.ST....TSSEEHHHHHHHHHHHHHHHTSSS--.- CS
                     NAD_binding_4  58 laerikvveGDlseprlGLseedlqelaeevdviihsaAtvnfde....pykellrvNveGtrevlelakklkklkv 130
                                       +  + +++ GD+ +p      e+++e  + vd++ih aA++        +  ++ ++N +Gt++vlela+k  +   
  gi|488601552|ref|YP_007908023.1|  43 VNGKAEFIWGDVRKP------EEMKEAFRDVDAVIHLAAKLPTAPgmvdEAGDVNDTNYRGTVNVLELARKSDAS-- 111
                                       666666777777665......699****************975442222788899***************77655.. PP

                                       EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE CS
                     NAD_binding_4 131 llhvSTayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiit 207
                                       +++ ST  v+g   +                  ++++++ +  n Y  sK  aE+ + e++++ gl v i+R+  ++
  gi|488601552|ref|YP_007908023.1| 112 MIFASTCNVYGVGMN------------------MDESSEPKPLNSYAESKLKAERACIEYHEKYGLDVKILRLASVY 170
                                       ******888887773..................45566777889********************************9 PP

                                       --S CS
                     NAD_binding_4 208 ges 210
                                       g s
  gi|488601552|ref|YP_007908023.1| 171 GYS 173
                                       943 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   3.5e-14   5.7e-11       1     265 [.       2     262 ..       2     267 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.5e-14
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +l+tG+ G iG e+ + +l+ + ++ ++l++   +   +++ +     + k +     + gdvr+ e++++a++  +
  gi|488601552|ref|YP_007908023.1|   2 ILITGGNGYIGIEISE-LLADRNEEFRVLDNFSGS-SPLNMLF----VNGKAE----FIWGDVRKPEEMKEAFR--D 66 
                                       89***********865.666677888888875432.3344433....232333....469**************..* PP

                                       -SEEEE---.---HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE..........GGGS..S--SHHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAA.lKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt..........DKAv..nPtnvmGat 141
                                       vd+v+h AA l   P +  ++ ++ +tN  gt nv+e a +++ + +++ St          D     +P n +  +
  gi|488601552|ref|YP_007908023.1|  67 VDAVIHLAAkLPTAPGMVDEAGDVNDTNYRGTVNVLELARKSDAS-MIFASTcnvygvgmnmDESSepKPLNSYAES 142
                                       ******998457899999999999*****************9975.6666764444444444666633579****** PP

                                       HHHHHHHHHHGGG--SSS--EEEEEEE-EETT.GTTS....SHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHHHH CS
                   Polysacc_synt_2 142 KrlaekllqalakeseekktkfvvvRfGNVlg.SrGS....viplFkkqikeggpvtv.TdpemtRyfmtieeavqL 212
                                       K+ ae  +++++++       + + R   V g S G     v+  F+ +  +g p+tv  d +  R f+ +++ ++ 
  gi|488601552|ref|YP_007908023.1| 143 KLKAERACIEYHEKY---GLDVKILRLASVYGySPGVrfnlVVNYFTLRAVTGYPLTVfGDGSNWRPFVHVRDVAKA 216
                                       ***********9998...55666666666665333433334899*************95588999************ PP

                                       HHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE---- CS
                   Polysacc_synt_2 213 vlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlR 265
                                        l  ++++k+gei+     e + i+d+a+ + +        +++i+i +tG +
  gi|488601552|ref|YP_007908023.1| 217 FLFFIENGKSGEIYNIGR-ENYMIRDVAEIVKRE------VNPSIDILFTGKK 262
                                       **************9999.9********999333......3577888888866 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   2.7e-12   4.4e-09       1     146 [.       6     169 ..       6     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.7e-12
                                       TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-........ CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal........ 68 
                                       G++G +G ++ + l++r+ +++v      ++ l+ l  + ++e + gdv ++e+++ea++++daV+  +        
  gi|488601552|ref|YP_007908023.1|   6 GGNGYIGIEISELLADRNeEFRVLDNFSGSSPLNMLFVNGKAEFIWGDVRKPEEMKEAFRDVDAVIHLAaklptapg 82 
                                       99*********9999997445444446668899999999**************************999967776444 PP

                                       ....--TCCHHHH.........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHH CS
                    NAD_binding_10  69 ....ggggkdeeg.........aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellr 132
                                           +       g         ++n+++ a++++   +++ s+ +v+   ++  ++   + l++y++ k +ae+   
  gi|488601552|ref|YP_007908023.1|  83 mvdeA-------GdvndtnyrgTVNVLELARKSDA-SMIFASTCNVYGVGMNMDESSEPKPLNSYAESKLKAERACI 151
                                       44432.......2333344466***********99.68899999999877777777777999999999999999854 PP

                                       H....SSSEEEEEEE-CE CS
                    NAD_binding_10 133 a....sgldwTivrpggL 146
                                       +     gld  i+r +  
  gi|488601552|ref|YP_007908023.1| 152 EyhekYGLDVKILRLASV 169
                                       434437999999998765 PP

>> NmrA  NmrA-like 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       1      71 [.       2      73 ..       2      84 .. 0.88
   2 ?    0.7   0.0      0.19   3.1e+02     166     227 ..     194     252 ..     140     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHST.TEEEES-TT-HHHHHHHHTT-SEEEE- CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaG.velvkgdlddkeslvealkgvdvvfsv 71
                                      Il++G+ G++G  + + l++++ + r+l   + s  ++ l  +G +e++ gd+   e ++ea+++vd+v+  
  gi|488601552|ref|YP_007908023.1|  2 ILITGGNGYIGIEISELLADRNEEFRVLDNFSGSSPLNMLFVNGkAEFIWGDVRKPEEMKEAFRDVDAVIHL 73
                                      89*************************98888666666666555489**********************976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.19
                                       -EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS CS
                              NmrA 166 kvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigk 227
                                        +t+ g+g+ + +++++++D++++ +  +++ +  +g+++++  + +   +++e+ +++++ 
  gi|488601552|ref|YP_007908023.1| 194 PLTVFGDGS-NWRPFVHVRDVAKAFLFFIENGK--SGEIYNIGRENYMIRDVAEIVKREVNP 252
                                       578899999.55555699999999998888765..688888889999999999999988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00023      0.37       3     144 ..       2     124 ..       1     150 [. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        litGG G +G e+++ la++ ++  vl   s  +     + ++ l  +  + e++  Dv +++++++++++++   
  gi|488601552|ref|YP_007908023.1|   2 ILITGGNGYIGIEISELLADRNEEFRVLDNFS-GS-----SPLNMLFVN-GKAEFIWGDVRKPEEMKEAFRDVD--- 68 
                                       59*****************9986655554444.21.....233333333.366788888888888888877775... PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsa 144
                                            vih A  l +++ +    ++   v     +G+ n+ el +  + d  ++f+S  +++g  
  gi|488601552|ref|YP_007908023.1|  69 ----AVIHLAAKLPTAPGM---VDEAGDVNDTNYRGTVNVLELAR--KSDASMIFASTCNVYGVG 124
                                       ....788888777666544...44455555666777777777776..467777777777777765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.2e-05     0.052       3      73 ..       2      69 ..       1     110 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavk 73
                                      +l+tG+ + IG +i++ la ++ +  v+d+ +      ++    +  + ka +i +Dv++ ee++++++++ +
  gi|488601552|ref|YP_007908023.1|  2 ILITGGNGYIGIEISELLADRNEEFRVLDNFSGSS--PLNM---LfvNGKAEFIWGDVRKPEEMKEAFRDVDA 69
                                      89***********************9988775544..3333...333678*****************998854 PP

>> Spore_GerAC  Spore germination B3/ GerAC like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         3   4.9e+03      85     121 ..     126     161 ..     114     162 .. 0.75
   2 ?   11.8   0.0   0.00013      0.21      21      81 ..     215     280 ..     210     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3
                                       -.-----HHHHHHHHHHHHHHHHHHHHHHHHTT---- CS
                       Spore_GerAC  85 nlleeeelkelekalekeiekeieealkklqeyksDi 121
                                       n++e+ e k l++ +e +++ e  + ++   +y+ D+
  gi|488601552|ref|YP_007908023.1| 126 NMDESSEPKPLNSYAESKLKAE-RACIEYHEKYGLDV 161
                                       5566666778888889999988.77788888888885 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                                       HHHHHHTT-----EEEEE.ETTEEEE......EEEEEEE.EEEEEEE-SSSEEEEEEEEEEEEEE...- CS
                       Spore_GerAC  21 rgllllrgkvksgvitiplpkgkdek.....vsveissskskikvkiengkpsfdikiklegdie...e 81 
                                       +++l++ ++ ksg i+ +++ ++  +      ++++++++ +i++ ++++kp+f++++++e +i+   e
  gi|488601552|ref|YP_007908023.1| 215 KAFLFFIENGKSGEIY-NIGREN--YmirdvAEIVKREVNPSIDILFTGKKPEFSYHVSFEKSIQagfE 280
                                       5666777777776653.222233..24578999******************************994332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1935.39
//
Query:       gi|488601553|ref|YP_007908024.1|  [L=301]
Description: UDP-glucose 4-epimerase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  151.9   0.0    2.7e-44  151.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.4e-32  111.0   0.0    1.8e-31  109.7   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.2e-24   86.1   0.0    2.4e-24   85.9   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.6e-20   73.3   0.1    2.2e-20   72.9   0.1    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.9e-19   68.6   0.4    9.2e-18   64.4   0.4    2.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.3e-10   39.2   0.0    1.9e-07   30.5   0.0    2.5  2  NAD_binding_4    Male sterility protein
    4.4e-05   23.4   0.0    7.3e-05   22.7   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.028   14.5   0.1      0.067   13.3   0.1    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   0.0   1.2e-47   2.7e-44       2     236 ..       4     226 ..       3     232 .. 0.95

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 1.2e-47
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                        VtGa G++G+ l+ +l+ek +ev+ ld+  ++ + +++  ++++ +d++dr+++e l++  ++d+++hlAa++gva
  gi|488601553|ref|YP_007908024.1|   4 GVTGAGGYVGAGLCSKLMEK-HEVVMLDNF-YKAQIGSIGGKKIIWADIRDRAEMESLLR--DCDVIVHLAAISGVA 76 
                                       59****************86.8********.88999999999******************..8************** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                       +  e p++ ++ n++gt n++  +rk+g+  ++f sS +v G++ e+p +      p +p + Y+ +K   e+ ++a
  gi|488601553|ref|YP_007908024.1|  77 ECDEMPERAYDVNIIGTENICWICRKYGI-DMIFPSSMAVVGNPVEIPITPRH---PRNPLNMYGFTKWVNEENIRA 149
                                       *****************************.*****************988888...99******************* PP

                                       HHHHHT-EEEEEEESEEESTT..S-TTS.TTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHH CS
                         Epimerase 156 yaaqyglnaiilrlfnlyGpr..ngege.vsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehv 229
                                       + +   +na+i++ +nlyG++  +g++   + vi  +++k+++++ ++t+ + gt+ Rdf++v Dv++a+ll++e+ 
  gi|488601553|ref|YP_007908024.1| 150 FSKNS-FNALIFMKTNLYGEYevDGNRIsKNTVINIFANKAKRNE-NLTVHKPGTQTRDFIHVLDVIDAYLLAIENM 224
                                       *8888.****************99999999**************9.*****************************93 PP

                                       TT-STTE CS
                         Epimerase 230 dagdkge 236
                                             e
  gi|488601553|ref|YP_007908024.1| 225 P-----E 226
                                       3.....3 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 !  109.7   0.0   8.2e-35   1.8e-31       2     330 ..       5     296 ..       5     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 8.2e-35
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       +TG  G++G+ l+ +L+ek +ev+ ++    +f+ ++i ++  +         k++ +D++D++++e+ll+++  d 
  gi|488601553|ref|YP_007908024.1|   5 VTGAGGYVGAGLCSKLMEK-HEVVMLD----NFYKAQIGSIGGK---------KIIWADIRDRAEMESLLRDC--DV 65 
                                       8*****************9.7777764....5677778777642.........589***************98..9* PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaa 155
                                       +++LAA s V++  e+Pe+ ++vn++Gt ++  ++r++g+     +++ S+  v G++ e+p+t ++p +P + Y+ 
  gi|488601553|ref|YP_007908024.1|  66 IVHLAAISGVAECDEMPERAYDVNIIGTENICWICRKYGI----DMIFPSSMAVVGNPVEIPITPRHPRNPLNMYGF 138
                                       **************************************96....6999***************************** PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS..-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprr..getfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       +K + +  ++++ ++  + a++    n ++ +   g+++ +++++++ a+ a+ +++ ++   + ++Rd+ hv D++
  gi|488601553|ref|YP_007908024.1| 139 TKWVNEENIRAFSKN-SFNALIFMKTNLYGEYEvdGNRISKNTVINIFANKAKRNENLTVHKPGTQTRDFIHVLDVI 214
                                       ************985.4555555555555555411789999********999999999999**************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       +a+ l++++  pe ++i t    +  +++++a+l  +++              ++ g ++ve  p + +++++ +  
  gi|488601553|ref|YP_007908024.1| 215 DAYLLAIENM-PEGFNIVTLAGGECLSVLDIANL--VQK-------------YSDVGIDLVEN-P-RKKETHAPNFE 273
                                       *****99975.77777665444444333333322..221.............12233333332.2.23356666677 PP

                                       B-THHHHHHH----SS-HHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvr 330
                                        d+s +ke +g++ k ++ee vr
  gi|488601553|ref|YP_007908024.1| 274 VDTSEIKELIGFESKRKVEEEVR 296
                                       77777777777777777777666 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 !   85.9   0.0   1.1e-27   2.4e-24       1     233 [.       1     254 [.       1     297 [. 0.83

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.1e-27
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..............T--TTSHHHHHHHHHHH--SEEEE------ CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre..............eldltdaeavaellkeakpdvvvnaAAyta 63 
                                       m+i vtGa+G +G  L  +l e++ ev+ l++                +d++d++++++ll++  +dv+v++AA   
  gi|488601553|ref|YP_007908024.1|   1 MRIGVTGAGGYVGAGLCSKLMEKH-EVVMLDNFykaqigsiggkkiiWADIRDRAEMESLLRD--CDVIVHLAAISG 74 
                                       8999*****************998.888887667899*********999**************..9*********** PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH.. CS
                     RmlD_sub_bind  64 vDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla.. 138
                                       v ++ + +e+ay vn  ++e++   ++++g+ +i+ S+  V     + p ++ ++ +Pln+YG tK+  E+ ++a  
  gi|488601553|ref|YP_007908024.1|  75 VAECDEMPERAYDVNIIGTENICWICRKYGIDMIFPSSMAVVGNPVEIPITPRHPRNPLNMYGFTKWVNEENIRAfs 151
                                       ******************************************999*****************************966 PP

                                       .H-SSEEEEEE-SEESS........SSS-HHHHHHHHHHH-SEEEEES..S-EE--EEHHHHHHHHHHHHHHCHH.G CS
                     RmlD_sub_bind 139 .agkkalivRtswvyge........kgknfvktmlrlakereelkvva..DqlgsPTsardlAevllqllekaaeek 204
                                        ++ +ali+  + +yge        +++  ++ + ++ak++e+l+v +   q++   ++ d+ ++ l ++e++ e  
  gi|488601553|ref|YP_007908024.1| 152 kNSFNALIFMKTNLYGEyevdgnriSKNTVINIFANKAKRNENLTVHKpgTQTRDFIHVLDVIDAYLLAIENMPE-- 226
                                       566699***********8887777444445555678889999999976223555555555555555555554443.. PP

                                       GG-EEEE---BS-EEHHHHHHHHHHHHCH CS
                     RmlD_sub_bind 205 elagvyHlanegetswlefArailkeaga 233
                                         + +  la+ + +s l++A+ + k +++
  gi|488601553|ref|YP_007908024.1| 227 -GFNIVTLAGGECLSVLDIANLVQKYSDV 254
                                       .4667777777777777777777666655 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.1   9.6e-24   2.2e-20       2     235 ..       5     227 ..       4     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 9.6e-24
                         3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvd 78 
                                       vtG++G++G+ l+++L++ +   ev +lD   + ++     +++ kk+i +D++d +++e  l++ dv++hla+++ 
  gi|488601553|ref|YP_007908024.1|   5 VTGAGGYVGAGLCSKLMEKH---EVVMLDNFYKAQI----GSIGGKKIIWADIRDRAEMESLLRDCDVIVHLAAISG 74 
                                       9***************9877...7999998777776....8899999****************************** PP

                         3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaE 154
                                       va      ++ ++vn+ GT+n+   c+k g+  +++ Ss+ vvg+   + +i     + +++ ++ ++y  +K + E
  gi|488601553|ref|YP_007908024.1|  75 VAEcDEMPERAYDVNIIGTENICWICRKYGID-MIFPSSMAVVGN-PVEIPI-----TPRHPRNPLNMYGFTKWVNE 144
                                       **97778999*********************8.68*********9.444444.....4899999************* PP

                         3Beta_HSD 155 klvlkaNgrtlknggrlyTcaLRpagiyGeg..dkllvpllkqlaklglalfkigdeevlsdrvYvgNvawahilAa 229
                                       + + +   + ++    + T       + G++  ++++ + + + ak +++l       ++ d++ v  v +a++lA 
  gi|488601553|ref|YP_007908024.1| 145 ENIRAFSKNSFNALIFMKTNLYGEYEVDGNRisKNTVINIFANKAKRNENLTVHKPGTQTRDFIHVLDVIDAYLLAI 221
                                       **98876645555545666555555666654323445566667777777888888889999**************** PP

                         3Beta_HSD 230 ralqdp 235
                                        ++ + 
  gi|488601553|ref|YP_007908024.1| 222 ENMPEG 227
                                       999775 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.4   4.1e-21   9.2e-18       3     249 ..       5     254 ..       3     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 4.1e-21
                                       EETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-S CS
                   Polysacc_synt_2   3 vtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvd 79 
                                       vtGagG +G  l++++++k  +++++l++     y+ +      +  kk+      + +d+rd++++e++l+  ++d
  gi|488601553|ref|YP_007908024.1|   5 VTGAGGYVGAGLCSKLMEK--HEVVMLDNF----YKAQIGS---IGGKKI------IWADIRDRAEMESLLR--DCD 64 
                                       9**************9976..588888864....3333322...344455......579*************..*** PP

                                       EEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEE.............EEEEEGGGSS--SHHHHHHH CS
                   Polysacc_synt_2  80 vvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkv.............vliStDKAvnPtnvmGatKr 143
                                       v++h AA+  V  ++e p  a + N++gten++ ++ ++g++ +             + i      nP n++G tK 
  gi|488601553|ref|YP_007908024.1|  65 VIVHLAAISGVAECDEMPERAYDVNIIGTENICWICRKYGIDMIfpssmavvgnpveIPITPRHPRNPLNMYGFTKW 141
                                       *****************************************8652222221111111223334556899******** PP

                                       HHHHHHHHGGG--SSS--EEEEEEE-E..ETT...GTTSSHHHHHHHHHTTSSEEES-T.T-EEEEE-HHHHHHHHH CS
                   Polysacc_synt_2 144 laekllqalakeseekktkfvvvRfGN..Vlg...SrGSviplFkkqikeggpvtvTdp.emtRyfmtieeavqLvl 214
                                       + e  + a++k+s ++   + +  +G   V g   S+  vi +F ++ k+++++tv  p + tR f+ + + ++  l
  gi|488601553|ref|YP_007908024.1| 142 VNEENIRAFSKNSFNALIFMKTNLYGEyeVDGnriSKNTVINIFANKAKRNENLTVHKPgTQTRDFIHVLDVIDAYL 218
                                       ************966655555556875334442237788******************994569***********999 PP

                                       HHHHH--SS.-EEEE--.-EEEHHHHHHHH...... CS
                   Polysacc_synt_2 215 qalalakgg.eifvldmGepvkivdlakalielsgl 249
                                        a++++ +g +i  l  Ge ++++d+a+ + ++s++
  gi|488601553|ref|YP_007908024.1| 219 LAIENMPEGfNIVTLAGGECLSVLDIANLVQKYSDV 254
                                       99987766637999999**********998887765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0029       6.6       1      22 [.       5      26 ..       5      33 .. 0.89
   2 !   30.5   0.0   8.6e-11   1.9e-07      79     208 ..      54     167 ..      52     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0029
                                      EE-TTSHHHHHHHHHHHHHS-. CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpe 22
                                      +TGa G++G+ L  kL+++++ 
  gi|488601553|ref|YP_007908024.1|  5 VTGAGGYVGAGLCSKLMEKHEV 26
                                      7*****************9973 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 8.6e-11
                                       HHHHHHHHH--EEEE--SS...-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS CS
                     NAD_binding_4  79 edlqelaeevdviihsaAt...vnfdepykellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekv 151
                                       ++++ l + +dvi+h aA     + de  +++++vN+ Gt++++ +++k      +++ S+ a+v +  e       
  gi|488601553|ref|YP_007908024.1|  54 AEMESLLRDCDVIVHLAAIsgvAECDEMPERAYDVNIIGTENICWICRKYGID--MIFPSSmAVVGNPVEI------ 122
                                       678999***********97221455667788*****************98777..8999996777766664...... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                                    ++++ ++  n Y ++K++ E+ +r+ +++  ++++i+  ++++g
  gi|488601553|ref|YP_007908024.1| 123 -----------PITPRHPRNPLNMYGFTKWVNEENIRAFSKN-SFNALIFMKTNLYG 167
                                       ...........46999************************77.99999987777776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.2e-08   7.3e-05       1     106 [.       7     121 ..       7     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.2e-08
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                       GA G vG  l+++l ++  hev+ +  n  k++ + +  g +++ +d+ d +++++ l+++d++v  ++ +g     
  gi|488601553|ref|YP_007908024.1|   7 GAGGYVGAGLCSKLMEK--HEVV-MLDNFYKAQ-IGSIGGKKIIWADIRDRAEMESLLRDCDVIVHLAAISGVaecd 79 
                                       9***************9..8986.568877766.6666899*********************876555444443554 PP

                                       HHHH...........HHHHHHHHHHCT--EEEEEEETTTTSGCG CS
                    NAD_binding_10  74 deeg...........aknivdaakeagvkRfvlvsaigvgdevp 106
                                       +  +           ++ni+  +++ g+  +   s + vg+ v+
  gi|488601553|ref|YP_007908024.1|  80 E--MperaydvniigTENICWICRKYGIDMIFPSSMAVVGNPVE 121
                                       0..345557778899*************9888888888887554 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     3e-05     0.067       1      85 [.       1      80 [.       1      96 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS..--S-BEBSSHHHHHHH-SEEEE-S-H CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg..klgvavtddleevlekadvliDFTtp 77
                                      ++++v+Ga G +G  +++ + e+ ++ +   + + +       +g++ g++    ++   +++e++l+++dv++ + + 
  gi|488601553|ref|YP_007908024.1|  1 MRIGVTGAGGYVGAGLCSKLMEKHEVVMLDNFYKAQ-------IGSIGGKKiiWADIRDRAEMESLLRDCDVIVHLAAI 72
                                      89***************9999977777777776665.......77777777224455556999***********99988 PP

                                      HHHHHHHH CS
                            DapB_N 78 eavlenlk 85
                                      ++v e+ +
  gi|488601553|ref|YP_007908024.1| 73 SGVAECDE 80
                                      88877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1863.90
//
Query:       gi|488601554|ref|YP_007908025.1|  [L=637]
Description: thioredoxin domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-62  208.9   0.0    7.1e-62  208.2   0.0    1.3  1  Thioredox_DsbH  Protein of unknown function, DUF255
    2.8e-12   46.7   0.0    5.8e-12   45.6   0.0    1.5  1  Thioredoxin_7   Thioredoxin-like
    0.00056   19.9   0.2     0.0013   18.6   0.2    1.6  1  Thioredoxin     Thioredoxin
     0.0027   18.2   0.0     0.0072   16.8   0.0    1.8  2  Thioredoxin_2   Thioredoxin-like domain
     0.0036   17.1   0.1       0.14   12.0   0.0    2.9  3  HTH_10          HTH DNA binding domain
  ------ inclusion threshold ------
      0.011   15.9   0.3       0.12   12.5   0.0    2.6  2  Mrr_N           Mrr N-terminal domain
      0.011   15.8   0.0      0.033   14.3   0.0    1.8  1  Sigma70_r3      Sigma-70 region 3


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 !  208.2   0.0   2.8e-65   7.1e-62       6     162 ..      12     168 ..       9     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 2.8e-65
                    Thioredox_DsbH   6 eekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDree 82 
                                       +++s+Yl++  ++pv Wyp+++e ++ a++edkpil++iG s+chWChvm++es++d+e+a++lne+f++vkvDr+e
  gi|488601554|ref|YP_007908025.1|  12 KSSSAYLKEALNQPVRWYPYTKEVFKMAEKEDKPILIDIGASWCHWCHVMDEESYSDPEIARFLNENFICVKVDRDE 88 
                                       689************************************************************************** PP

                    Thioredox_DsbH  83 rPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaeell 159
                                        P++d+ y+ea++altg+ggWPl+vf  p++++f+ggtYfpkee+ g+p f++vl+++ + +++ere+ e+ aee+ 
  gi|488601554|ref|YP_007908025.1|  89 MPNIDRKYQEAISALTGEGGWPLTVFALPNGEAFYGGTYFPKEEKFGKPAFMKVLKAVLDSFKKEREKTEAIAEEIK 165
                                       ***************************************************************************99 PP

                    Thioredox_DsbH 160 eal 162
                                       ++l
  gi|488601554|ref|YP_007908025.1| 166 KNL 168
                                       987 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   2.3e-15   5.8e-12       2      64 ..      28      90 ..      27     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.3e-15
                                      --SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S- CS
                     Thioredoxin_7  2 wlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterd 64
                                      w+    e +  a+++ kp+l+++gaswc+ C++++++  sd+e+++ l+e+f++++vd +e  
  gi|488601554|ref|YP_007908025.1| 28 WYPYTKEVFKMAEKEDKPILIDIGASWCHWCHVMDEESYSDPEIARFLNENFICVKVDRDEMP 90
                                      666666777889**********************************999*********96654 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   5.2e-07    0.0013       8      68 ..      34      96 ..      28     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.2e-07
                                      HHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHH...HHHHHCTTTSEEEEEETTTSHHHHHHT CS
                       Thioredoxin  8 enFeeevakekklvlveFyApwCghCkalaPele...klaeelkdkvklakvdvdenedlakky 68
                                      e F+ + +ke+k++l++  A+wC  C  +  e     ++a+ l++++  +kvd de +++ +ky
  gi|488601554|ref|YP_007908025.1| 34 EVFKMA-EKEDKPILIDIGASWCHWCHVMDEESYsdpEIARFLNENFICVKVDRDEMPNIDRKY 96
                                      445444.456*******************9875323479999999***********99988877 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.8e-06    0.0072       1      72 [.      39      98 ..      39     135 .. 0.74
   2 ?   -3.7   0.0       6.6   1.7e+04      43      56 ..     154     167 ..     139     192 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                     Thioredoxin_2  1 akgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvel 72
                                      a+++ kp+l+++ +++C  C+ + +e  +++++  +     l+++  ++ v++++++ ++     i+++++ 
  gi|488601554|ref|YP_007908025.1| 39 AEKEDKPILIDIGASWCHWCHVMDEESYSDPEIARF-----LNEN--FICVKVDRDEMPN-----IDRKYQE 98
                                      68999*******************************.....9988..9999999998887.....5444443 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.6
                     Thioredoxin_2  43 kpsfepkavaiwca 56 
                                       +++ e++a++i+++
  gi|488601554|ref|YP_007908025.1| 154 REKTEAIAEEIKKN 167
                                       33333333333332 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   5.5e-05      0.14      24      51 ..     367     394 ..     366     396 .. 0.89
   2 ?   -3.6   0.0       4.1   1.1e+04      37      49 ..     431     443 ..     429     445 .. 0.80
   3 ?    1.5   0.0       0.1   2.6e+02      14      37 ..     503     526 ..     502     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.5e-05
                            HTH_10  24 vtlkeLAkelGIskstlsehLrkaeskl 51 
                                       ++++ +A+e+GIs ++l+e+L++  +kl
  gi|488601554|ref|YP_007908025.1| 367 ASVDTVAEEMGISVQDLEEILSSGREKL 394
                                       67899****************9988887 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.1
                            HTH_10  37 kstlsehLrkaes 49 
                                       ++++++ +++ae+
  gi|488601554|ref|YP_007908025.1| 431 ENDTEYAIKNAEK 443
                                       5788999999997 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.1
                            HTH_10  14 emGYFdyPRrvtlkeLAkelGIsk 37 
                                       ++G++d +  +++++L+ +  +s+
  gi|488601554|ref|YP_007908025.1| 503 NNGFYDGDDPASINDLSHRSAVSQ 526
                                       68***************9998886 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.48   1.2e+03       4      31 ..     142     168 ..     139     176 .. 0.70
   2 ?   12.5   0.0   4.8e-05      0.12      20      54 ..     365     401 ..     356     405 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.48
                             Mrr_N   4 lmlplLealadgsehrlkeirervaerf 31 
                                       +++++L  +++++e++ + i e++++++
  gi|488601554|ref|YP_007908025.1| 142 VLKAVLDSFKKEREKT-EAIAEEIKKNL 168
                                       5667777777777776.77888877765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.8e-05
                             Mrr_N  20 lkeirervaerfglseeeraellpsgkq..trfknrv 54 
                                       ++  +++vae++g+s ++++e l+sg++  +r+++r+
  gi|488601554|ref|YP_007908025.1| 365 IDASVDTVAEEMGISVQDLEEILSSGREklRRYRYRL 401
                                       566789*********************9777777775 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.033      16      46 ..     362     392 ..     360     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                       HHSSXXXHHHHHHHHTXXHHHHHHHHHHHXX CS
                        Sigma70_r3  16 elgrePtpeEiAeeLglseekVrevleaare 46 
                                       +l  +++++ +Aee+g+s+++++e+l   re
  gi|488601554|ref|YP_007908025.1| 362 HLRIDASVDTVAEEMGISVQDLEEILSSGRE 392
                                       68899*********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 4000.39
//
Query:       gi|488601555|ref|YP_007908026.1|  [L=178]
Description: hypothetical protein Asulf_02073 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-09   36.9   0.3    2.1e-09   36.9   0.3    1.7  2  RHH_1         Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.012   15.6   1.1      0.019   14.9   1.1    1.3  1  DUF386        YhcH/YjgK/YiaL
      0.026   14.3   0.1       0.42   10.5   0.0    2.6  3  Castor1_N     Cytosolic arginine sensor for mTORC1 subunit 1 
        2.9    8.7   7.2       0.74   10.6   2.7    2.3  3  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.3   4.8e-13   2.1e-09       1      36 [.       6      41 ..       6      41 .. 0.98
   2 ?   -3.2   0.2       2.1   9.5e+03       8      15 ..     112     119 ..     112     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 4.8e-13
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlrey 36
                                      r+++ ldee ++ L++l+r++g S+Se++R Al++y
  gi|488601555|ref|YP_007908026.1|  6 RITVALDEESYRILEKLKRESGLSQSEIMRNALKFY 41
                                      8********************************987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.1
                                       HHHHHHHH CS
                             RHH_1   8 eellerLd 15 
                                       +++lerL+
  gi|488601555|ref|YP_007908026.1| 112 DDILERLE 119
                                       68888887 PP

>> DUF386  YhcH/YjgK/YiaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.1   4.3e-06     0.019       2      71 ..      40     102 ..      33     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-06
                                       EEEETTSTTTT--HHHHHHHHHHHTS-GCC--SEEEE-..SSS-EEEEE--B-B-GGGS-EEE-SSEEEEE CS
                            DUF386   2 IidnlenlkrylkpklkkaleylketdlenlpeGkyei.dgdklfvnvqeyetkpaeeakfEsHrkyiDiq 71 
                                       ++d++++l++y   kl+++  y+     e l+eG++ i d +++++ +   e++p++e+++E+H+k +  +
  gi|488601555|ref|YP_007908026.1|  40 FYDQYKDLQKY---KLERIKTYA-----EMLAEGEHVIlDINHWIAFLRFIESHPEKEKFWEIHKKIANMH 102
                                       46777777777...455555666.....788999999967789***********************98766 PP

>> Castor1_N  Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.14   6.2e+02      44      55 ..       8      19 ..       4      23 .. 0.86
   2 ?   -2.2   0.0      0.83   3.7e+03      22      34 ..      76      92 ..      75      96 .. 0.76
   3 ?   10.5   0.0   9.5e-05      0.42      27      50 ..     117     140 ..     113     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                         Castor1_N 44 TiivdeegfkeL 55
                                      T+ +dee ++ L
  gi|488601555|ref|YP_007908026.1|  8 TVALDEESYRIL 19
                                      999******977 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.83
                         Castor1_N 22 LafL....sektrckFf 34
                                      +afL    s++ + kF+
  gi|488601555|ref|YP_007908026.1| 76 IAFLrfieSHPEKEKFW 92
                                      57777777889999996 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 9.5e-05
                         Castor1_N  27 ektrckFfsLTetpedYTiivdee 50 
                                       +   c+Ff + e + +YT+++++e
  gi|488601555|ref|YP_007908026.1| 117 RLEACNFFRINERRGEYTLVLNNE 140
                                       5678****************9987 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.7   0.00017      0.74       2      50 ..       8      63 ..       7      74 .. 0.77
   2 ?   -1.2   0.1       0.8   3.6e+03      43      67 ..      79     104 ..      76     106 .. 0.71
   3 ?   -3.9   0.0         4   1.8e+04      24      30 ..     112     118 ..     108     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                      VAPB_antitox  2 tIsIsdevYekLkklKr.egeSFsdvIerLle......kkkkgkkkellelfgils 50
                                      t+ +++e Y+ L+klKr  g S s++ ++ l+        +k k ++++ ++++l 
  gi|488601555|ref|YP_007908026.1|  8 TVALDEESYRILEKLKReSGLSQSEIMRNALKfydqykDLQKYKLERIKTYAEMLA 63
                                      7899*************5589*****999998766655445556666777766665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.8
                      VAPB_antitox  43 lelfgilseeea.deiekaskelrke 67 
                                       l+++++ +e+e   ei k++ +++ e
  gi|488601555|ref|YP_007908026.1|  79 LRFIESHPEKEKfWEIHKKIANMHAE 104
                                       56677776766668888888888765 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 4
                      VAPB_antitox  24 sdvIerL 30 
                                       +d++erL
  gi|488601555|ref|YP_007908026.1| 112 DDILERL 118
                                       4666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1057.16
//
Query:       gi|488601556|ref|YP_007908027.1|  [L=395]
Description: ammonium transporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-134  447.3  43.4   4.3e-134  447.2  43.4    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.2  43.4  2.4e-138  4.3e-134       1     399 []      14     394 ..      14     394 .. 0.98

  Alignments for each domain:
  == domain 1  score: 447.2 bits;  conditional E-value: 2.4e-138
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-TTTTSCCG CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfignlglsaagv 77 
                                       a+ll s+alv++m++g++l+++g+v +knvl+++ ++++ +avv++++vl+Gy++afg++  +sg+ g   l++ g+
  gi|488601556|ref|YP_007908027.1|  14 AWLLTSTALVMLMTPGLGLFYGGMVGKKNVLSMISMSFITFAVVSIQWVLLGYTMAFGRD--ISGLLGG--LEHIGL 86 
                                       7**********************************************************9..****999..677899 PP

                                       CCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.-SSSTT CS
                   Ammonium_transp  78 qdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliDfAgst 154
                                       +d +++d++f++fql+faa++++i+++a+aer+kfsa++lf++l++++vy p+ahwvwg +gwlaklg+l DfAg+t
  gi|488601556|ref|YP_007908027.1|  87 KDLKMIDYAFVAFQLVFAAITLAIITSAMAERVKFSAFILFAVLWTSIVYDPLAHWVWG-NGWLAKLGAL-DFAGGT 161
                                       9999*******************************************************.**********.****** PP

                                       TTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHH CS
                   Ammonium_transp 155 vVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAa 231
                                       vVH+ +g+++La+a+v+gkr+g +   e+++++hn+p+++lG++lLwfgWfgFNaGsal+an+ a++ a+++T++Aa
  gi|488601556|ref|YP_007908027.1| 162 VVHISSGFSALALAFVVGKRRGFG---EYSMEPHNIPMTLLGAALLWFGWFGFNAGSALAANDLAAN-AFIVTNTAA 234
                                       **********************99...9***************************************.********* PP

                                       HHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHH CS
                   Ammonium_transp 232 aagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidDsldvv 308
                                       +aga+ +l++s++k gk+  lg+++G++AGlVAiT+a+++v+p++A+iiG+vAgv++++++ +++   +id+sld++
  gi|488601556|ref|YP_007908027.1| 235 SAGAISWLIVSWIK-GKPGSLGIVSGAIAGLVAITPAAGFVDPLSAIIIGVVAGVICYYAM-LFRISKGIDESLDAW 309
                                       **************.**********************************************.6************** PP

                                       HHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB--HHHH CS
                   Ammonium_transp 309 avHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLrvseeee 385
                                       a+HgvgG+wG++a+gifa         ++gll g+  qlv+q+ig++ +++yafv+tli+++ +++++gLrvs+eee
  gi|488601556|ref|YP_007908027.1| 310 AIHGVGGFWGAIATGIFASVG------ATGLLLGNVGQLVAQIIGAVSAALYAFVLTLIIAKFVDMTIGLRVSNEEE 380
                                       *******************97......5689999999**************************************** PP

                                       HHSHHHHHHSSSSB CS
                   Ammonium_transp 386 evglDvaehgetay 399
                                       +vglDv++hge ay
  gi|488601556|ref|YP_007908027.1| 381 YVGLDVSQHGEVAY 394
                                       ************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.68s 00:00:01.24 Elapsed: 00:00:00.73
# Mc/sec: 1629.02
//
Query:       gi|488601557|ref|YP_007908028.1|  [L=109]
Description: nitrogen regulatory protein P-II family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-39  133.2   2.7      5e-39  133.0   2.7    1.0  1  P-II      Nitrogen regulatory protein P-II
  ------ inclusion threshold ------
      0.078   13.2   0.0      0.092   13.0   0.0    1.2  1  DUF5091   Domain of unknown function (DUF5091)


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 !  133.0   2.7   5.6e-43     5e-39       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 5.6e-43
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       ieaiirpekle vk+aLe+ g+ ++t+tevkGrG+qkg +  +rg+ + v++lpk+k+eiv++dedve+++++ii++
  gi|488601557|ref|YP_007908028.1|   4 IEAIIRPEKLECVKKALEESGYVAMTITEVKGRGEQKGIKLQFRGRIMDVDMLPKIKIEIVADDEDVEEIINTIIQN 80 
                                       89*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tg++GDGkiFvlpve+ irirtg
  gi|488601557|ref|YP_007908028.1|  81 ARTGKYGDGKIFVLPVERSIRIRTG 105
                                       ************************8 PP

>> DUF5091  Domain of unknown function (DUF5091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.092      34     100 ..       8      73 ..       4     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                           DUF5091  34 isPislkhlkaklenlglvsweltenglkFifknfilkFkGsltitvkedkifsieidfdpeidsev 100
                                       i P +l+ +k+ le+ g v +++te       k  +l+F+G +  + +  ki +iei +d e  +e+
  gi|488601557|ref|YP_007908028.1|   8 IRPEKLECVKKALEESGYVAMTITEVKGRGEQKGIKLQFRGRIMDVDMLPKI-KIEIVADDEDVEEI 73 
                                       8999**********************99*************87655554344.45555444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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 0.71s 00:00:01.22 Elapsed: 00:00:00.68
# Mc/sec: 484.44
//
Query:       gi|488601558|ref|YP_007908029.1|  [L=399]
Description: ammonium transporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-131  438.1  42.9   2.7e-131  437.9  42.9    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.9  42.9  1.5e-135  2.7e-131       1     399 []       7     398 ..       7     398 .. 0.98

  Alignments for each domain:
  == domain 1  score: 437.9 bits;  conditional E-value: 1.5e-135
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-......TT CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign......lg 71 
                                       a++l+s+alv++m++g++l++ag+vr+kn++n++  +++ l+vv++++v++ yslafg++  v gf+g        +
  gi|488601558|ref|YP_007908029.1|   7 AWILVSTALVMLMTPGVGLFYAGMVRKKNAVNMIALSFVCLVVVSIIWVAYAYSLAFGSD--VAGFTGDlsyaflEK 81 
                                       7**********************************************************9..999999999999888 PP

                                       TTSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--. CS
                   Ammonium_transp  72 lsaagvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvli 148
                                       ++   ++  t+++++f+++q++fa+++++i ++avaer+k+s++++f++l++tlvy+p+ahw wg +gwlaklg+l 
  gi|488601558|ref|YP_007908029.1|  82 VGFDPLDGMTIPHLVFVIYQMMFAVITLAILTSAVAERVKLSSFIIFGILWITLVYAPFAHWLWG-NGWLAKLGAL- 156
                                       888999999********************************************************.**********. PP

                                       -SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHH CS
                   Ammonium_transp 149 DfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaav 225
                                       DfAg++vVH+ +g+a+La+a+v+gkr g +   e++i++hn+p+++lG++lLwfgWfgFN+Gsal+an+ a++ a+v
  gi|488601558|ref|YP_007908029.1| 157 DFAGGMVVHISSGFAALALAFVVGKRGGFG---EYNIEPHNIPMTLLGAALLWFGWFGFNGGSALAANGLAAN-AIV 229
                                       ****************************99...9***************************************.*** PP

                                       HHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC- CS
                   Ammonium_transp 226 tTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkid 302
                                       +T+++aa+++ ++++i ++k gk+  lg+++G++AGl+AiT+a+++v++ gA+iiGlv+g++++l+++ ++ k +id
  gi|488601558|ref|YP_007908029.1| 230 VTNTSAAVAGAVWMIIGWIK-GKPGSLGIVSGAIAGLAAITPAAGFVDVKGAIIIGLVSGIICYLAMD-FRIKKQID 304
                                       ********************.**********************************************8.******** PP

                                       CTTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB CS
                   Ammonium_transp 303 DsldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLr 379
                                       +sld++a+Hg+gG+wG+lavgifa+++ +   + +gl++g+ ++l +q+i+++++++yafvv+++l++++++++gLr
  gi|488601558|ref|YP_007908029.1| 305 ESLDAWAIHGIGGLWGSLAVGIFATTSIN---EFAGLINGSVSLLKAQIIAVIATVIYAFVVSYVLAKIVDAVFGLR 378
                                       **************************955...8888***************************************** PP

                                       --HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 380 vseeeeevglDvaehgetay 399
                                       vs+eee+vglDv++h+e ay
  gi|488601558|ref|YP_007908029.1| 379 VSNEEEYVGLDVSQHEEVAY 398
                                       ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.64u 0.38s 00:00:01.02 Elapsed: 00:00:01.01
# Mc/sec: 1194.04
//
Query:       gi|488601559|ref|YP_007908030.1|  [L=110]
Description: nitrogen regulatory protein P-II family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-38  130.2   3.1    4.3e-38  130.0   3.1    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 !  130.0   3.1   2.4e-42   4.3e-38       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 2.4e-42
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       ieaiirpekle vk+aLe+ g+ ++tvtevkGrG+qkg +  +rg+e+ v++l+k+k+eiv++d+dv++++++i+++
  gi|488601559|ref|YP_007908030.1|   4 IEAIIRPEKLECVKKALEESGYVAMTVTEVKGRGEQKGIKLQFRGREVDVDFLQKTKIEIVAEDKDVDRIIDIITSS 80 
                                       89*************************************************************************** PP

                                       H-SSSTTSEEEEEEEESEEEETTTT CS
                              P-II  78 aktgeiGDGkiFvlpveevirirtg 102
                                       a+tg++GDG+iFvlpve+ ++irtg
  gi|488601559|ref|YP_007908030.1|  81 ARTGKYGDGRIFVLPVEKSVKIRTG 105
                                       ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.35s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 643.70
//
Query:       gi|488601560|ref|YP_007908031.1|  [L=225]
Description: CTP-dependent riboflavin kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-49  165.2   0.0      1e-48  164.4   0.0    1.4  1  CTP-dep_RFKase   Domain of unknown function DUF120
    4.1e-06   26.3   1.4    5.9e-06   25.7   0.0    2.1  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00017   21.4   0.7    0.00025   20.9   0.1    1.6  1  MarR             MarR family
    0.00019   21.1   1.0    0.00027   20.6   1.0    1.2  1  DDRGK            DDRGK domain
    0.00022   21.2   0.1     0.0004   20.3   0.1    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00073   19.4   0.2     0.0014   18.5   0.2    1.5  1  HTH_11           HTH domain
     0.0033   17.6   1.0      0.011   16.0   0.0    2.1  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0035   17.2   0.0      0.013   15.3   0.0    1.8  2  MarR_2           MarR family
  ------ inclusion threshold ------
      0.011   15.7   1.2      0.022   14.7   1.2    1.7  1  HTH_45           Winged helix-turn-helix
      0.022   15.0   0.2      0.051   13.9   0.2    1.6  1  Glyco_hydro_67N  Glycosyl hydrolase family 67 N-terminus
      0.028   14.2   0.1       0.05   13.3   0.1    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.034   14.1   0.1       0.06   13.3   0.1    1.4  1  HTH_36           Helix-turn-helix domain
      0.046   14.1   0.1      0.075   13.4   0.1    1.3  1  Rrf2             Transcriptional regulator
      0.061   13.5   0.3       0.34   11.1   0.4    2.1  2  HTH_34           Winged helix DNA-binding domain
      0.072   12.9   0.1       0.13   12.1   0.1    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
       0.11   12.4   0.1       0.19   11.6   0.1    1.5  1  DUF3116          Protein of unknown function (DUF3116)
       0.11   12.2   0.0        0.2   11.3   0.0    1.5  1  Crp              Bacterial regulatory proteins, crp family
       0.12   12.4   0.0       0.25   11.4   0.0    1.5  1  HTH_20           Helix-turn-helix domain
       0.13   12.2   0.0       0.28   11.2   0.0    1.5  1  DUF2766          Protein of unknown function (DUF2766)


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 !  164.4   0.0   1.1e-51     1e-48       1     121 []     103     223 ..     103     223 .. 0.99

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 1.1e-51
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       V+sG+geG+yyvsl+gy++qf+eklgf+pypGTLN+kl +e+  lr+++++ +gi+i+gf++e+rtfg+vk++++ki
  gi|488601560|ref|YP_007908031.1| 103 VMSGIGEGRYYVSLDGYRKQFREKLGFDPYPGTLNLKLPKEQAYLRRRIDEEDGIIIHGFKTEDRTFGEVKAFKCKI 179
                                       89*************************************************************************** PP

                                       CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                    CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                        ++++a+v+p+rthy++d+lE+iap+kLR+kl+lkdgd vevev
  gi|488601560|ref|YP_007908031.1| 180 GDYEGAIVLPQRTHYPKDILEVIAPVKLRDKLGLKDGDFVEVEV 223
                                       ******************************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.5       8.1   7.6e+03       3      12 ..       9      18 ..       7      20 .. 0.70
   2 !   25.7   0.0   6.2e-09   5.9e-06      18      47 ..      30      59 ..      28      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.1
                            HTH_24  3 etdrkILelL 12
                                       + ++IL+lL
  gi|488601560|ref|YP_007908031.1|  9 LKMIEILKLL 18
                                      5567899887 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 6.2e-09
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      is +eLA+++g S +t  r lk+Lee+G+I
  gi|488601560|ref|YP_007908031.1| 30 ISSKELADKIGQSFQTAARKLKELEENGYI 59
                                      99***************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   2.7e-07   0.00025      18      53 ..      30      65 ..       7      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.7e-07
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                      +s +eLa+k+g s  t+ r l++Le++G+i R+ ++
  gi|488601560|ref|YP_007908031.1| 30 ISSKELADKIGQSFQTAARKLKELEENGYILRTIDK 65
                                      5667****************************9886 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.0   2.9e-07   0.00027     111     159 ..      25      75 ..      10      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.9e-07
                                       -SEE-H..HHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---X CS
                             DDRGK 111 kKvvll..eelavkfklktqevierikeLeeqgsltGvlDdrGkyiyitde 159
                                       k+vv++  +ela k++ + q ++ ++keLee+g +   +D  G+yi it++
  gi|488601560|ref|YP_007908031.1|  25 KRVVKIssKELADKIGQSFQTAARKLKELEENGYILRTIDKDGQYIVITEN 75 
                                       5567764469***************************************87 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   4.2e-07    0.0004       7      59 ..      17      72 ..      14      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.2e-07
                                      HHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..T.EE.EEE CS
                         HTH_Crp_2  7 LlrlaeraggeielpltqeelAsmlGltretvsrilseLkreglis.r..g.rr.iri 59
                                      Ll l +  + ++ ++++ +elA+ +G + +t  r l+eL++ g+i  +  + ++ i+i
  gi|488601560|ref|YP_007908031.1| 17 LLALMDAHK-RV-VKISSKELADKIGQSFQTAARKLKELEENGYILrTidKdGQyIVI 72
                                      555655422.45.89*****************************98523322234665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.5e-06    0.0014      16      46 ..      30      60 ..      12      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                            HTH_11 16 isgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      is++eLA++++ S +t  r +k+Lee g+ +
  gi|488601560|ref|YP_007908031.1| 30 ISSKELADKIGQSFQTAARKLKELEENGYIL 60
                                      9***************************765 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 !   16.0   0.0   1.1e-05     0.011      15      52 ..      22      59 ..      16      65 .. 0.89
   2 ?   -0.6   0.1       1.7   1.6e+03      44      56 ..      77      89 ..      72      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                                      HHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 15 tlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      ++ +  ++++ k+la  +++s  ++   lk+Le++Gy+
  gi|488601560|ref|YP_007908031.1| 22 DAHKRVVKISSKELADKIGQSFQTAARKLKELEENGYI 59
                                      667778899****************************7 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                      HHHHHTTSEEEET CS
                    Fe_dep_repress 44 kkLekdGyveyek 56
                                      +kL  ++y++y+k
  gi|488601560|ref|YP_007908031.1| 77 EKLLYKEYLDYKK 89
                                      6888999****97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.4e-05     0.013      11      54 ..      17      62 ..       8      68 .. 0.81
   2 ?   -1.0   0.0       1.8   1.7e+03      30      60 ..     126     156 ..     121     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                                      HHHHHCTTTS..EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 11 LaaLgrrpgr..dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      L+aL ++  r  +++ +ela++ g s +++ r lk+L++ G++ r+
  gi|488601560|ref|YP_007908031.1| 17 LLALMDAHKRvvKISSKELADKIGQSFQTAARKLKELEENGYILRT 62
                                      445555555557889****************************987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                                       HHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                            MarR_2  30 rlglsksavsrilkrLvaaGLverrpgpeDk 60 
                                       +lg ++   +  lk   ++ +++rr ++eD+
  gi|488601560|ref|YP_007908031.1| 126 KLGFDPYPGTLNLKLPKEQAYLRRRIDEEDG 156
                                       5666666666666666788899999999886 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.2   2.3e-05     0.022      32      68 ..      42      82 ..      10      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                            HTH_45 32 sykllnkYLdmLvekgli....kkskekYvlTekGlellek 68
                                      s++++ + L+ L e+g+i    +k+++  v+Te G++ll k
  gi|488601560|ref|YP_007908031.1| 42 SFQTAARKLKELEENGYIlrtiDKDGQYIVITENGEKLLYK 82
                                      89999************8888677777789*******9853 PP

>> Glyco_hydro_67N  Glycosyl hydrolase family 67 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   5.4e-05     0.051      79     117 ..      45      81 ..      22      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                                       --THHHHTTTTT-EEEEEEEETTEEEEEEEESSHHHHHH CS
                   Glyco_hydro_67N  79 alpeeleelgeeGfllktveveekksvvivgqterGvLY 117
                                       +  ++l+el+e+G++l+t  ++++++ +++ ++ + +LY
  gi|488601560|ref|YP_007908031.1|  45 TAARKLKELEENGYILRT--IDKDGQYIVITENGEKLLY 81 
                                       34466899**********..8999999999999999999 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.3e-05      0.05      14      47 ..      29      62 ..      13      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.3e-05
                          HTH_DeoR 14 klsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      k+s +el++  g S +T+ R L+eLee g + Rt
  gi|488601560|ref|YP_007908031.1| 29 KISSKELADKIGQSFQTAARKLKELEENGYILRT 62
                                      78899***************************97 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.3e-05      0.06      27      55 .]      31      59 ..       8      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s + la + g s +T+ r +keLe+ Gyi
  gi|488601560|ref|YP_007908031.1| 31 SSKELADKIGQSFQTAARKLKELEENGYI 59
                                      66899***********************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.9e-05     0.075      11      55 ..      15      59 ..       7      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-05
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglv 55
                                      l++l+ + ++++  ++ss+e+a++ + s + +++ l++L+++g++
  gi|488601560|ref|YP_007908031.1| 15 LKLLALMDAHKRVVKISSKELADKIGQSFQTAARKLKELEENGYI 59
                                      678999999999999****************************98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00036      0.34      10      69 ..      25      80 ..      14      94 .. 0.79
   2 ?   -1.3   0.0       2.8   2.6e+03      16      30 ..     203     217 ..     200     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                            HTH_34 10 asvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreaf 69
                                        v +++ +el ++++ +    + +lk Le++gYi ++++++g+     + iT++G +  
  gi|488601560|ref|YP_007908031.1| 25 KRVVKISSKELADKIGQSFQTAARKLKELEENGYILRTIDKDGQ----YIVITENGEKLL 80
                                      446677888999999999999999*****************999....788999997653 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.8
                            HTH_34  16 dfvelkealeatdgn 30 
                                        +v+l+++l++ dg 
  gi|488601560|ref|YP_007908031.1| 203 APVKLRDKLGLKDGD 217
                                       5789*******9995 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 ?   12.1   0.1   0.00014      0.13       8      42 .]      17      54 ..      14      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                     HTH_AsnC-type  8 ILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                                      +L+++ +     +is +eLA+++G S +t++r ++ Le
  gi|488601560|ref|YP_007908031.1| 17 LLALMDAHkrvVKISSKELADKIGQSFQTAARKLKELE 54
                                      5555555577789**********************998 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    0.0002      0.19      51      81 ..      53      81 ..      10      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                           DUF3116 51 LElkgyilRkeekannkkrYelTekGellyk 81
                                      LE++gyilR     ++ ++  +Te+Ge+l+ 
  gi|488601560|ref|YP_007908031.1| 53 LEENGYILRTID--KDGQYIVITENGEKLLY 81
                                      9*********99..5788889*****98764 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021       0.2       2      32 .]      29      59 ..      28      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                      E--HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                               Crp  2 pmSRqdIAdylGlTrETVSRlLtrLrekGLI 32
                                      + S  ++Ad +G +  T+ R L+ L+e+G I
  gi|488601560|ref|YP_007908031.1| 29 KISSKELADKIGQSFQTAARKLKELEENGYI 59
                                      56889***********************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 ?   11.4   0.0   0.00026      0.25      24      56 ..      29      61 ..      12      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                      TB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 24 gltaselaerldlskntlsyHLrvLeeagLvev 56
                                        + +ela+ ++ s +t+ + L++Lee g++ +
  gi|488601560|ref|YP_007908031.1| 29 KISSKELADKIGQSFQTAARKLKELEENGYILR 61
                                      56899************************9865 PP

>> DUF2766  Protein of unknown function (DUF2766)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.28      27      50 ..     197     218 ..     193     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                           DUF2766  27 dvieviaPaevrekmsaqlksidf 50 
                                       d++eviaP+ +r+k+   lk+ df
  gi|488601560|ref|YP_007908031.1| 197 DILEVIAPVKLRDKLG--LKDGDF 218
                                       99************86..666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.44s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 1208.05
//
Query:       gi|488601561|ref|YP_007908032.1|  [L=234]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-57  194.5   0.1    1.5e-57  194.3   0.1    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase


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 !  194.3   0.1   8.2e-62   1.5e-57       2     192 .]       4     221 ..       3     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 194.3 bits;  conditional E-value: 8.2e-62
                                       HHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S...... CS
                     DHBP_synthase   2 eaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene...... 72 
                                       ea++a+++G++v+++D ++re+e+d+ i+A +v+ ++va+m+ +++Glicva+++  ad+L++p+m++         
  gi|488601561|ref|YP_007908032.1|   4 EALKAFRRGEPVLIYDFDHREGETDIAIPAVNVSHQDVAMMRIDGGGLICVAIHPIAADKLQIPFMHD--Vlaaage 78 
                                       89****************************************************************95..4457788 PP

                                       ..............STT---BB--EEESST-SSS-SHHHHHHHHHHHH-T..........T--GGGEEEEEEEEEEE CS
                     DHBP_synthase  73 ..............dkhktaftvsvdaaegttTGIsaaDRalTirkladp..........kakpedfrrPGhvfplr 125
                                                       ++++f+v+v+++ +t+TGI++ DRalTir++ +           +  +++fr+PGhv +lr
  gi|488601561|ref|YP_007908032.1|  79 kmpyllslsrndikYDSRSSFAVWVNHR-DTFTGITDIDRALTIRRVGEVvdmvmtngefD-FASEFRSPGHVALLR 153
                                       899999999999984568**********.9*****************99556888888752.579************ PP

                                       E-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TT.SCB-BHHHHHHHHHHHT-EEEEHHHHHHH CS
                     DHBP_synthase 126 areggvleRrghTEaavdLarlaglkpaavicellndd.gtmarrdeleefakkhglkiitiedliey 192
                                       a+ + + +R g+TE++v+La++ag++pa +ice+l+ + g+++++++++e+a++ g++++++++++ey
  gi|488601561|ref|YP_007908032.1| 154 AAVNLTYDRVGQTELSVALAEMAGISPAVAICEMLDAEtGKALSKEKAIEYAEERGIPFVEGDEIVEY 221
                                       ************************************87799*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 1394.70
//
Query:       gi|488601562|ref|YP_007908033.1|  [L=399]
Description: hypothetical protein Asulf_02080 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.53u 0.76s 00:00:01.29 Elapsed: 00:00:00.70
# Mc/sec: 1713.17
//
Query:       gi|488601563|ref|YP_007908034.1|  [L=449]
Description: TBP-interacting protein TIP49 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-151  504.2   0.3   2.4e-151  503.9   0.3    1.1  1  TIP49            TIP49 P-loop domain
    2.5e-24   85.2   0.3    5.2e-24   84.2   0.3    1.6  1  TIP49_C          TIP49 AAA-lid domain
    2.7e-12   47.3   0.9    9.6e-09   35.8   0.1    2.6  2  AAA              ATPase family associated with various cellul
    1.3e-09   37.9   0.6    6.3e-07   29.3   0.1    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00014   22.3   0.2    0.00099   19.5   0.2    2.3  1  AAA_16           AAA ATPase domain
     0.0005   20.4   0.1       0.85    9.9   0.0    2.4  2  AAA_22           AAA domain
    0.00058   20.4   0.1     0.0079   16.7   0.0    2.5  2  AAA_18           AAA domain
    0.00099   18.5   0.2     0.0025   17.2   0.0    1.7  2  DnaB_C           DnaB-like helicase C terminal domain
     0.0014   18.1   1.1     0.0096   15.3   0.2    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0043   17.3   2.4       0.02   15.1   0.1    2.7  3  AAA_28           AAA domain
      0.006   16.3   0.2       0.24   11.1   0.1    2.5  2  Sigma54_activat  Sigma-54 interaction domain
     0.0064   16.5   0.2      0.042   13.9   0.0    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0067   15.7   0.1       0.02   14.2   0.0    1.7  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0088   15.8   0.0      0.022   14.5   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.013   14.8   0.2      0.037   13.3   0.1    1.8  2  Zeta_toxin       Zeta toxin
      0.021   13.9   0.4       0.74    8.8   0.1    2.3  2  T2SSE            Type II/IV secretion system protein
      0.027   14.3   0.0      0.058   13.2   0.0    1.5  1  AAA_11           AAA domain
      0.027   14.8   0.0       0.06   13.7   0.0    1.6  1  RNA_helicase     RNA helicase
      0.031   13.8   0.0      0.059   12.9   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.032   14.6   1.4       0.12   12.8   0.0    2.5  3  AAA_17           AAA domain
      0.043   13.8   0.3        2.9    7.9   0.1    2.3  2  ResIII           Type III restriction enzyme, res subunit
      0.059   12.9   0.3       0.28   10.7   0.1    2.1  2  AAA_25           AAA domain
      0.087   12.7   0.0        2.4    8.1   0.0    2.3  2  NACHT            NACHT domain
      0.091   12.9   0.0       0.25   11.5   0.0    1.8  1  AAA_33           AAA domain
       0.12   12.7   3.7        1.2    9.5   3.7    2.3  1  AAA_19           AAA domain
       0.16   11.9   0.0       0.31   10.9   0.0    1.4  1  Rad17            Rad17 P-loop domain
       0.69    9.6   4.1        2.7    7.6   0.1    2.9  3  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  503.9   0.3  3.6e-154  2.4e-151       1     350 [.      14     360 ..      14     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 503.9 bits;  conditional E-value: 3.6e-154
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49   1 rislhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelged 77 
                                       r+++hshi+gLGld++++a++++eglvGqkkareaagviv+lik++k+aGr++L+aGp+gtGkta+a+aiskelg+d
  gi|488601563|ref|YP_007908034.1|  14 RVGAHSHIRGLGLDDNLRAKDVAEGLVGQKKAREAAGVIVRLIKSGKMAGRGILMAGPPGTGKTAIAVAISKELGKD 90 
                                       789************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-...TTS--EEEEEE-SS-E CS
                             TIP49  78 vpfvalsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenpls.kekkikevkitlktakee 153
                                       +pfv+ s+se+ys+e+kkte+l+q +rk+igvri+e+++vleGev+ l+++++ np++ ++k  +++++tl t++e+
  gi|488601563|ref|YP_007908034.1|  91 IPFVQTSASEFYSAEMKKTEALIQSMRKAIGVRIRETRTVLEGEVTGLDYNMVPNPYNpTQKIPESATLTLSTKDET 167
                                       **********************************************************8889999************ PP

                                       EEEEE-HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS------S--------S---S----XXXXXXXXXXX CS
                             TIP49 154 kklklgskiaeellkekvkegDviviekesGkvkklGrsearakefDiekdefvelPkGevekkkevvqevtLhdlD 230
                                       ++++++ ++a ++l+  +++gDvi+i+ke+G++  +Grse+ +k++D+  + +ve+P+G+vek++e++  vtLhdlD
  gi|488601563|ref|YP_007908034.1| 168 RTFSVSGRMALQFLQYGIQVGDVIMIDKETGRISIIGRSEKASKKYDLGGSDVVEVPSGKVEKEREFTYVVTLHDLD 244
                                       ***************************************************************************** PP

                                       XXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 231 vanarpqdllslllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnralesela 307
                                        anar+++++sl+    +s+++ei++++re ++++v+k+veeg+ae+vpGvlfiDe+h++Die f+++nra+ese+a
  gi|488601563|ref|YP_007908034.1| 245 EANARRTSIFSLF----TSQSREIDSEVREAVDEQVKKWVEEGRAELVPGVLFIDETHLMDIELFAFMNRAMESEMA 317
                                       *************....99********************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 308 PivilatnrgiakirGtdiisphGipvDlldrlliiktekytk 350
                                       Pi+ila+nrg++kirGtd+++phGip+Dlldrllii+te+y++
  gi|488601563|ref|YP_007908034.1| 318 PIIILASNRGFSKIRGTDLVAPHGIPLDLLDRLLIITTEPYKR 360
                                       *****************************************97 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.3   7.8e-27   5.2e-24       1      66 []     366     431 ..     366     431 .. 0.99

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 7.8e-27
                           TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                       Il+iRa+e+g++l+++Al++L++ig e S+RYa+qLl+pa+ +ak+r++k+vevedve+++e+F+D
  gi|488601563|ref|YP_007908034.1| 366 ILEIRAAESGIMLSDDALEKLTDIGAENSMRYAVQLLAPAHEFAKLREAKKVEVEDVERAAEIFAD 431
                                       9***************************************************************99 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1   1.5e-11   9.6e-09       1      52 [.      66     119 ..      66     131 .. 0.85
   2 !    9.6   0.1    0.0018       1.2      26     111 ..     256     326 ..     240     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.5e-11
                                       EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfke 52 
                                       +l+ GppGtGKT++a a+ kelg  ++f+++s+se+ s  ++++e+ i+ + k+
  gi|488601563|ref|YP_007908034.1|  66 ILMAGPPGTGKTAIAVAISKELGkdIPFVQTSASEFYSAEMKKTEALIQSMRKA 119
                                       699*******************7679***********88788887777776554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                                       EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSST CS
                               AAA  26 fleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkesk 102
                                       +++ +  e+ s++ ++  +++++ ++e +++  p +lfiDE + +   +          + + + ++++ +      
  gi|488601563|ref|YP_007908034.1| 256 LFTSQSREIDSEVREAVDEQVKKWVEEGRAELVPGVLFIDETHLMD-IE----------LFAFMNRAMESEMA---- 317
                                       5555666677888899999999999999888889********9882.22..........34444444444444.... PP

                                       EEEEEEESS CS
                               AAA 103 vivigatnr 111
                                        i+i+a+nr
  gi|488601563|ref|YP_007908034.1| 318 PIIILASNR 326
                                       466777776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   9.4e-10   6.3e-07       7      63 ..      37      93 ..      30     119 .. 0.85
   2 !    6.7   0.1    0.0082       5.4      87     117 ..     291     321 ..     285     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 9.4e-10
                            RuvB_N  7 eeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklki 63
                                      e  +gq+k +e   ++++  k+ + a   +l++GpPG Gkt++a  i+kelg ++  
  gi|488601563|ref|YP_007908034.1| 37 EGLVGQKKAREAAGVIVRLIKSGKMAGRGILMAGPPGTGKTAIAVAISKELGKDIPF 93
                                      4589***********************************************998754 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0082
                            RuvB_N  87 vlfideihrlsraveevlysamedfrldivi 117
                                       vlfide h ++ ++  ++  ame  +  i+i
  gi|488601563|ref|YP_007908034.1| 291 VLFIDETHLMDIELFAFMNRAMESEMAPIII 321
                                       9**********************99888887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.5e-06   0.00099      24     148 ..      61     301 ..      39     322 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                            AAA_16  24 p..elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr 98 
                                          + +l  G++G+GK++++ ++ ++l kd + f+++ + ++     y   a++ ++e l++ +  +a     ++ r
  gi|488601563|ref|YP_007908034.1|  61 MagRGILMAGPPGTGKTAIAVAISKELGKD-IPFVQTSASEF-----Y--SAEMKKTEALIQSMR-KAIGVRIRETR 128
                                       34589*************************.89999999999.....4..444444434444443.33444555566 PP

                            AAA_16  99 ekleeala..................................................................... 106
                                       + le++++                                                                     
  gi|488601563|ref|YP_007908034.1| 129 TVLEGEVTgldynmvpnpynptqkipesatltlstkdetrtfsvsgrmalqflqygiqvgdvimidketgrisiigr 205
                                       66666666666666677776666666666666666666666666666666666666666666666666666666666 PP

                            AAA_16 107 ......................................................avpelagaeasrllellkrllal 129
                                                                                             +++e++++ ++++ e++k+ ++ 
  gi|488601563|ref|YP_007908034.1| 206 sekaskkydlggsdvvevpsgkvekereftyvvtlhdldeanarrtsifslftsQSREIDSEVREAVDEQVKKWVEE 282
                                       66666666666666666666666666666666666666555555555555555555555555555555555555544 PP

                            AAA_16 130 lsrderplvlvlDdlqwad 148
                                        + +  p vl++D+ +  d
  gi|488601563|ref|YP_007908034.1| 283 GRAELVPGVLFIDETHLMD 301
                                       4443456666666666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0047       3.1       8      30 ..      66      88 ..      61     136 .. 0.71
   2 !    9.9   0.0    0.0013      0.85      38     126 ..     231     320 ..     207     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0047
                            AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                      ++  G++GtGKT  +  + ++l 
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKELG 88
                                      5668**********999998884 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                            AAA_22  38 erpevvfvtlpsstsskdllrellralglelka.erlsseellealeqalrarav...ielliiDEaqhlrseeale 110
                                       er  ++ vtl  + +    ++ +++ ++++  +     +e++ e++ + +++ ++   +++l iDE + +   e++ 
  gi|488601563|ref|YP_007908034.1| 231 EREFTYVVTLHDLDEANARRTSIFSLFTSQSREiDSEVREAVDEQVKKWVEEGRAelvPGVLFIDETHLM-DIELFA 306
                                       67788899999999999999999999998888843333344447777777777779999***********.777777 PP

                            AAA_22 111 eLrsllnlsrkgvqli 126
                                       +  + ++  +   ++i
  gi|488601563|ref|YP_007908034.1| 307 FMNRAME--SEMAPII 320
                                       7765555..4444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.2e-05    0.0079       1      23 [.      66      88 ..      66     133 .. 0.80
   2 ?    0.6   0.0       1.1   7.5e+02      45      76 ..     257     285 ..     211     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlg 23
                                      Il +G+pG+GKt +a ++sk+lg
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKELG 88
                                      8899****************983 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                            AAA_18  45 aldeskrldedkldklldaleenssaleegkn 76 
                                        +++s+++d ++++++ ++++++ +   eg  
  gi|488601563|ref|YP_007908034.1| 257 FTSQSREIDSEVREAVDEQVKKWVE---EGRA 285
                                       5678999999999999999999965...3333 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 !   17.2   0.0   3.8e-06    0.0025      15      81 ..      59     129 ..      55     195 .. 0.78
   2 ?   -2.2   0.0       3.2   2.1e+03      87     126 ..     274     314 ..     246     322 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.8e-06
                                       SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHH....CSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  15 GlqkgdliiiAarpsmGktalalniaenaav....keklpvavfslemsaeqlvqRllsseaeidskklrt 81 
                                       G   g  i++A+ p++Gkta+a+ i ++  +     ++    ++s em++++ + + + +  +++ ++ rt
  gi|488601563|ref|YP_007908034.1|  59 GKMAGRGILMAGPPGTGKTAIAVAISKELGKdipfVQTSASEFYSAEMKKTEALIQSMRKAIGVRIRETRT 129
                                       556677799*****************9987644444455699*******9998888888777777666654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                                       HHHHHHHHH.HHHHHHSEEEEEEXSSXCHHHHHHHHHHHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  87 edwekltea.ieelseaklfiddtpaltvseirskarrlkk 126
                                       e+++k  e+  +el    lfid+t  + ++      r +++
  gi|488601563|ref|YP_007908034.1| 274 EQVKKWVEEgRAELVPGVLFIDETHLMDIELFAFMNRAMES 314
                                       34444444325566666777877777777666665555544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.4e-05    0.0096       6      48 ..      40      89 ..      35     120 .. 0.65
   2 ?    0.9   0.0      0.39   2.6e+02     108     134 ..     290     316 ..     282     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                      Mg_chelatase  6 kGqeeakraleiaa....aG...gHnlllvGppGsGKtmlakrlpsllpp 48
                                      +Gq++a++a  + +    +G   g  +l++GppG+GKt +a ++++ l +
  gi|488601563|ref|YP_007908034.1| 40 VGQKKAREAAGVIVrlikSGkmaGRGILMAGPPGTGKTAIAVAISKELGK 89
                                      566666666544322222331114679**************999876655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledge 134
                                       GvLf+DE+  ++ + +  + + +e++ 
  gi|488601563|ref|YP_007908034.1| 290 GVLFIDETHLMDIELFAFMNRAMESEM 316
                                       9*******9999999999888888775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.1e-05      0.02       2      54 ..      66     121 ..      65     138 .. 0.82
   2 ?   -2.0   0.0       5.6   3.7e+03     126     150 ..     261     285 ..     254     292 .. 0.79
   3 ?    0.2   0.1       1.2   7.9e+02      98     141 ..     384     429 ..     343     440 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpwvedlla 54 
                                       i + G+++tGKT ++ a++++   ++p v+ +a e+++ +++k+e  +++ ++++ 
  gi|488601563|ref|YP_007908034.1|  66 ILMAGPPGTGKTAIAVAISKElgkDIPFVQTSASEFYSAEMKKTEALIQSMRKAIG 121
                                       6789***************888889****************999986665544444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.6
                            AAA_28 126 eRredleereaiderlrealrelgi 150
                                        R+ d e rea+de+++++++e + 
  gi|488601563|ref|YP_007908034.1| 261 SREIDSEVREAVDEQVKKWVEEGRA 285
                                       6778888999999999999887655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.2
                            AAA_28  98 aelea..aarekrydlvfllppapei...dddgeRredleereaiderl 141
                                       ++l++  a++++ry+  +l p  +++   +  ++  ed+e++++i   +
  gi|488601563|ref|YP_007908034.1| 384 EKLTDigAENSMRYAVQLLAPAHEFAklrEAKKVEVEDVERAAEI---F 429
                                       456655566688888888887766553344444444555555444...3 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00037      0.24      14      59 ..      55      99 ..      40     115 .. 0.75
   2 ?    2.5   0.0      0.16   1.1e+02      95     119 ..     290     314 ..     277     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                                      HHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETT CS
                   Sigma54_activat 14 qikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavnca 59
                                       ik+       +l+ G  GtGK+ +a ai ++   k+ pfv+   +
  gi|488601563|ref|YP_007908034.1| 55 LIKSGKMAGRGILMAGPPGTGKTAIAVAISKELG-KDIPFVQTSAS 99
                                      444455555789*****************88765.67888887665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.16
                                       SEEEEETGGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqe 119
                                       G+lf+De + +++el + + r++++
  gi|488601563|ref|YP_007908034.1| 290 GVLFIDETHLMDIELFAFMNRAMES 314
                                       9************998888888776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   6.3e-05     0.042       2      34 ..      66      98 ..      65     139 .. 0.81
   2 ?   -0.4   0.0       1.5     1e+03      44      90 ..     261     313 ..     236     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.3e-05
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--T CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltr 34
                                      +l+ GppGtgK+ +a  +++ l++ +  vq ++
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKELGKDIPFVQTSA 98
                                      799*****************9977666666554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                                       -B--.........--------......G-SEEEEESGGG--HHHHHHHHHHHH CS
                             AAA_5  44 rreikngttslvdsplvraar......egeilvlDEveraesevlnsLlslle 90 
                                       +rei+++ ++ vd  +++ ++       + +l++DE + ++ e ++ +++ +e
  gi|488601563|ref|YP_007908034.1| 261 SREIDSEVREAVDEQVKKWVEegraelVPGVLFIDETHLMDIELFAFMNRAME 313
                                       56666666666666666666555566666778888877777776666666665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     3e-05      0.02       4      55 ..      66     124 ..      64     138 .. 0.88
   2 ?   -1.9   0.0       2.3   1.6e+03     163     182 ..     263     282 ..     230     312 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                           DUF2075   4 vlVtGvaGtGKtvvllnllael.......eddeeertavylsvNhplvlvlrealakke 55 
                                       +l  G +GtGKt +++++  el       +++++e +++ + + ++l++ +r+a+  + 
  gi|488601563|ref|YP_007908034.1|  66 ILMAGPPGTGKTAIAVAISKELgkdipfvQTSASEFYSAEMKKTEALIQSMRKAIGVRI 124
                                       5778******************9999999999999999999999999999999997655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.3
                           DUF2075 163 hLksqfRvaaseaviewvda 182
                                       + +s +R a +e+v +wv++
  gi|488601563|ref|YP_007908034.1| 263 EIDSEVREAVDEQVKKWVEE 282
                                       56677777777777777765 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 !   14.5   0.0   3.4e-05     0.022      48      71 ..      64      87 ..      42     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                         IstB_IS21 48 enivllGpsGvGKshlaialgvea 71
                                       +i++ Gp+G+GK+ +a+a+++e 
  gi|488601563|ref|YP_007908034.1| 64 RGILMAGPPGTGKTAIAVAISKEL 87
                                      5799****************9864 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.6e-05     0.037      19      48 ..      66      95 ..      62     107 .. 0.87
   2 ?   -3.6   0.0       8.2   5.4e+03     117     142 ..     390     415 ..     377     432 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvr 48
                                      il++G pG GK+++a ++ +el+++  +v+
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKELGKDIPFVQ 95
                                      89*******************987766666 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.2
                        Zeta_toxin 117 lkkaGYevevvvvavkkelSrlgvld 142
                                        +++  +  v ++a   e++ l+ ++
  gi|488601563|ref|YP_007908034.1| 390 GAENSMRYAVQLLAPAHEFAKLREAK 415
                                       44444444444444444444433333 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 ?    8.8   0.1    0.0011      0.74     129     156 ..      63      90 ..      36      97 .. 0.80
   2 ?    2.9   0.0      0.07        46      37      91 ..      99     151 ..      92     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                             T2SSE 129 rglilvsGgTgsGKttllyallkeinks 156
                                          il++G+ g+GKt ++ a+ ke+ k+
  gi|488601563|ref|YP_007908034.1|  63 GRGILMAGPPGTGKTAIAVAISKELGKD 90 
                                       4569******************999876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.07
                             T2SSE  37 reveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvage 91 
                                       +e  + e +++e+li+ +  + + +i e r +++++++  g + ++v  P   ++
  gi|488601563|ref|YP_007908034.1|  99 SEFYSAEMKKTEALIQSMRKAIGVRIRETRTVLEGEVT--GLDYNMVPNPYNPTQ 151
                                       56677888999**************************9..777777666655443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.7e-05     0.058      20      44 ..      66      90 ..      52     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-05
                            AAA_11 20 tliqGPPGtgKTktivellsqllsr 44
                                       l+ GPPGtgKT   v++ ++l + 
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKELGKD 90
                                      599*************999999533 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   9.1e-05      0.06       1      40 [.      66     108 ..      66     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.1e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..klkkkdsvys.rnpe 40 
                                       i++ Gp+g+GK+ +a  ++k+l k++   +++++++ys   ++
  gi|488601563|ref|YP_007908034.1|  66 ILMAGPPGTGKTAIAVAISKELGKDIpfVQTSASEFYSaEMKK 108
                                       6789********************9988677778999855544 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   8.9e-05     0.059      32      75 ..      62     104 ..      51     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.9e-05
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsa 75 
                                       +++ +l+ Gp GtGKt+i+  + k+l  +++ +++ + s   sa
  gi|488601563|ref|YP_007908034.1|  62 AGRGILMAGPPGTGKTAIAVAISKELG-KDIPFVQTSASEFYSA 104
                                       67889******************9999.5555555555544444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       7.6   5.1e+03      29      69 ..       4      44 ..       1      55 [. 0.70
   2 ?   12.8   0.0   0.00018      0.12       2      55 ..      70     128 ..      69     136 .. 0.71
   3 ?   -1.2   0.0       3.9   2.6e+03      46      70 ..     257     281 ..     232     317 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.6
                                      HHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17 29 llreeakrgglakardemrklpleekkelqkeaaekiaeea 69
                                       +re a+r + + a++++r l l+++ +  + a+  + +++
  gi|488601563|ref|YP_007908034.1|  4 EIREIAQRFERVGAHSHIRGLGLDDNLRAKDVAEGLVGQKK 44
                                      67888888888888899998888888887777777776665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00018
                                       E-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklveky....gfthlsaGdllreeakrggl.akardemrklpleekk 55 
                                       G+PG GK+ ++  + +++     f   sa++   +e+k+ ++ +++  +   + ++e++
  gi|488601563|ref|YP_007908034.1|  70 GPPGTGKTAIAVAISKELgkdiPFVQTSASEFYSAEMKKTEAlIQSMRKAIGVRIRETR 128
                                       9**************99866334556688999999999998634444444444555544 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.9
                                       HCTSHHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17  46 mrklpleekkelqkeaaekiaeeak 70 
                                       +   + e++ e+++ + e++++  +
  gi|488601563|ref|YP_007908034.1| 257 FTSQSREIDSEVREAVDEQVKKWVE 281
                                       4455566666666666666665433 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 ?    7.9   0.1    0.0043       2.9      25      50 ..      64      89 ..      38      97 .. 0.79
   2 ?    3.8   0.0      0.08        53     106     146 ..     235     302 ..     197     323 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0043
                                      SEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII 25 krglikmaTGtGKTlvaaklierllk 50
                                      + +l++ + GtGKT +a+++ ++l k
  gi|488601563|ref|YP_007908034.1| 64 RGILMAGPPGTGKTAIAVAISKELGK 89
                                      45678999***********9998865 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.08
                                       EEEEEHHHHHHTH...............................HHHTTT-S........EEEEETGGGTTS CS
                            ResIII 106 ilvttiqsldadseee.......................eeeseellrdrfd........viiiDEaHrlga 146
                                        +v+t + ld+++ ++                       e+ ++  +    +        v++iDE H +  
  gi|488601563|ref|YP_007908034.1| 235 TYVVTLHDLDEANARRtsifslftsqsreidsevreavdEQVKKWVE----EgraelvpgVLFIDETHLMDI 302
                                       44444444444443334444444444433433344445433333333....244558999********7655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.7   1.8e+03      85     110 ..       7      37 ..       3      58 .. 0.72
   2 ?   10.7   0.1   0.00042      0.28      32      57 ..      62      87 ..      52     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.7
                            AAA_25  85 elrrRlravgeal.....rddarllvldlag 110
                                       e+++R+++vg++       +d++l++ d+a+
  gi|488601563|ref|YP_007908034.1|   7 EIAQRFERVGAHShirglGLDDNLRAKDVAE 37 
                                       6899999999887778888888888887765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00042
                            AAA_25 32 agelallaGapgtGKttlaldlalav 57
                                      ag  +l aG+pgtGKt++a+ ++ ++
  gi|488601563|ref|YP_007908034.1| 62 AGRGILMAGPPGTGKTAIAVAISKEL 87
                                      6777899************9887655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0036       2.4       3      32 ..      66      95 ..      64     124 .. 0.82
   2 ?    2.1   0.0      0.24   1.6e+02      26      72 ..     225     274 ..     220     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0036
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklpqg 32
                                      +++ G++G GKT+ +  +  ++ ++ ++ +
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKELGKDIPFVQ 95
                                      7899***************99998876655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.24
                                       TS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C...C CS
                             NACHT  26 egklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse...v 72 
                                       +gk ++++ ++ ++++l++l + ++  +s+  l +sq  e+ ++v+e    
  gi|488601563|ref|YP_007908034.1| 225 SGKVEKER-EFTYVVTLHDLDEANARrTSIFSLFTSQSREIDSEVREavdE 274
                                       67888876.9999*******99988899***************99994440 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   0.00037      0.25       2      28 ..      66      94 ..      66     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                            AAA_33  2 vllvGlpGsGKstlaerllkklg..avll 28
                                      +l+ G+pG+GK+  a  + k+lg    ++
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKELGkdIPFV 94
                                      68**************9999999773333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.7    0.0017       1.2       9      78 ..      62     262 ..      54     323 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelg.gvkp...........eeillvaftgrAakelrerlaalgae..... 68 
                                       + + +l+ ++pGtGKT + ++i ++l +    v+            +       t+   + +r+++ +   +     
  gi|488601563|ref|YP_007908034.1|  62 AGRGILMAGPPGTGKTAIAVAISKELGKDIpFVQTsasefysaemkK-------TEALIQSMRKAIGV---Riretr 128
                                       5566888999*********9999988654302222333322222221.......22222222222211...122222 PP

                            AAA_19  69 .............atTiHrlal....................................................... 77 
                                                            +                                                       
  gi|488601563|ref|YP_007908034.1| 129 tvlegevtgldynM-------Vpnpynptqkipesatltlstkdetrtfsvsgrmalqflqygiqvgdvimidketg 198
                                       22222233333330.......03333333333333333333344444444444455555555555555555555555 PP

                            AAA_19  78 ...............................................................l 78 
                                                                                                       
  gi|488601563|ref|YP_007908034.1| 199 risiigrsekaskkydlggsdvvevpsgkvekereftyvvtlhdldeanarrtsifslftsqsR 262
                                       5555555555555555555555555555555555555555555555566666666655555551 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00047      0.31      48      74 ..      66      92 ..      52     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                             Rad17 48 LLisGPsGCgkstvvkvLskelgiklr 74
                                      +L++GP+G gk+ +   +skelg ++ 
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKELGKDIP 92
                                      799*******************98764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0041       2.7      21      41 ..      66      86 ..      51     135 .. 0.78
   2 ?    2.0   0.1      0.23   1.5e+02      74     120 ..     277     320 ..     237     326 .. 0.70
   3 ?   -1.2   0.1       2.2   1.4e+03      46      76 ..     396     425 ..     382     444 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0041
                            AAA_30 21 avltGpAGtGKttalkalrea 41
                                       ++ Gp+GtGKt +  a+ + 
  gi|488601563|ref|YP_007908034.1| 66 ILMAGPPGTGKTAIAVAISKE 86
                                      5789********998887554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.23
                            AAA_30  74 akllkrlk.grarlepgtllivDEagmvdtkqlaallkaaekagakvi 120
                                       +k++   + gra+l p  +l +DE+ ++d++ +a + +a+e++ a +i
  gi|488601563|ref|YP_007908034.1| 277 KKWV---EeGRAELVP-GVLFIDETHLMDIELFAFMNRAMESEMAPII 320
                                       3333...133333333.5899**********99999999888777666 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.2
                            AAA_30  46 ggrviglAptgkaAkvLaeelgieastiakl 76 
                                        + v +lAp ++ Ak L+e+  +e + +++ 
  gi|488601563|ref|YP_007908034.1| 396 RYAVQLLAPAHEFAK-LREAKKVEVEDVERA 425
                                       478888888888875.555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.68u 0.68s 00:00:01.36 Elapsed: 00:00:00.63
# Mc/sec: 2137.16
//
Query:       gi|488601564|ref|YP_007908035.1|  [L=114]
Description: hypothetical protein Asulf_02082 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-19   67.5   0.0    1.1e-18   67.3   0.0    1.0  1  DUF498        Protein of unknown function (DUF498/DUF598)
  ------ inclusion threshold ------
      0.059   13.2   0.8      0.084   12.8   0.8    1.2  1  YajC          Preprotein translocase subunit
      0.071   13.1   0.4        4.5    7.3   0.1    2.1  2  HU-DNA_bdg    DNA-binding domain
      0.085   12.6   0.2       0.11   12.3   0.2    1.1  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> DUF498  Protein of unknown function (DUF498/DUF598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   2.4e-22   1.1e-18       3     109 .]       4     111 ..       3     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.4e-22
                                       EEESSEEEETTEEESSEEEE-SSSE..EE-THCSTTCEECHHHHHHCT..T..SEEEEE-TTS.-----HHHHHHHH CS
                            DUF498   3 aygeggfelngvkysgsllvlpeea..fawdvakaedlteeslellellepkpellilGtGkr.qlplspevrealn 76 
                                       ay++g++ ++++ y+++l+++ e++   +w+ ++++++++e+++ +  l+++ +++i+GtG + ++++++ev++ ++
  gi|488601564|ref|YP_007908035.1|   4 AYDFGKLYIDKKLYTSDLILGREGIinKRWWRKEGHRVQKEDIDDI--LNRNSDIVIFGTGYHgVVKIDEEVINLIK 78 
                                       799*********************9877899655************..89*************************** PP

                                       CCTSEEEEE-HHHHHHHHHHHHHHT--EEEEEE CS
                            DUF498  77 elgigvevmdtraAartyNllaaegrrVaaaLi 109
                                       ++g +vev ++r A++ +   ++eg++ ++a++
  gi|488601564|ref|YP_007908035.1|  79 QKGSEVEVAKSRVAVEIFKKALSEGKNAILAIH 111
                                       **************************9999986 PP

>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   1.9e-05     0.084      35      79 ..      50      92 ..      34      93 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                              YajC 35 LkkGdeVvtig.GivGkvvkvdddevtveigesagvkikversaia 79
                                      L++++ +v  g G +G v k+d++ v + + +++g +++v +s +a
  gi|488601564|ref|YP_007908035.1| 50 LNRNSDIVIFGtGYHGVV-KIDEE-V-INLIKQKGSEVEVAKSRVA 92
                                      666655555553888877.9**86.4.44445579*******9997 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0078        35      40      62 ..      36      58 ..      22      62 .. 0.86
   2 ?    7.3   0.1     0.001       4.5      31      63 ..      70     102 ..      58     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0078
                                      HH-TTS-HHHHHHHHHHHHHHHH CS
                        HU-DNA_bdg 40 kegtevrketienilnlykrevs 62
                                      keg  v+ke+i +iln+  + v+
  gi|488601564|ref|YP_007908035.1| 36 KEGHRVQKEDIDDILNRNSDIVI 58
                                      899************99877665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHH CS
                        HU-DNA_bdg  31 ledIidemvkegtevrketienilnlykrevse 63 
                                        e++i+ ++++g+ev+ +    +++++k+ +se
  gi|488601564|ref|YP_007908035.1|  70 DEEVINLIKQKGSEVEVAKSRVAVEIFKKALSE 102
                                       479*************************99876 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.4e-05      0.11       3      56 ..      56     107 ..      54     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                                       EEEEE-SSCGGGCH.HHHHHHHHHTTEEEEEEESCHHHHCCHHGGS....TCSSH CS
                      Flavoprotein   3 illgiTGsvaaika.lellekLkkegievqvvltkaAkkfiskeklklaaredpi 56 
                                       i++  TG ++++k+  e+++ +k++g ev+v  ++ A ++++k    l++ ++ i
  gi|488601564|ref|YP_007908035.1|  56 IVIFGTGYHGVVKIdEEVINLIKQKGSEVEVAKSRVAVEIFKKA---LSEGKNAI 107
                                       89999*********9999999999******************76...33334445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.39s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 721.82
//
Query:       gi|488601565|ref|YP_007908036.1|  [L=425]
Description: serine hydroxymethyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-80  268.4   0.0      1e-79  268.1   0.0    1.1  1  SHMT             Serine hydroxymethyltransferase
    1.7e-08   34.0   0.0    7.1e-08   32.0   0.0    1.8  2  Aminotran_1_2    Aminotransferase class I and II
    6.7e-06   25.3   0.0    2.2e-05   23.6   0.0    1.9  1  SelA             L-seryl-tRNA selenium transferase
    0.00012   21.5   0.0    0.00038   19.8   0.0    1.7  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.017   14.1   0.0      0.025   13.5   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
      0.098   11.2   0.0       0.34    9.4   0.0    1.9  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.1   0.0   3.3e-83     1e-79       7     398 ..      13     385 ..       8     386 .. 0.94

  Alignments for each domain:
  == domain 1  score: 268.1 bits;  conditional E-value: 3.3e-83
                                       HHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-ST CS
                              SHMT   7 evaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldp 83 
                                       +v +i++k +e  ++++ +iasen+ts+ v     s l  +yaeG   +r+y Gc ++de+ee+a++ +k+lf+++ 
  gi|488601565|ref|YP_007908036.1|  13 RVEDIVRKHHEFFRNSLPMIASENLTSSFVRRYYTSDLGHRYAEGKVNERFYQGCAYIDEIEEMAIKLTKKLFDAE- 88 
                                       678999999*******************************************************************. PP

                                       TTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHH.HSEEEEE-B-TTTSSB-HH CS
                              SHMT  84 akwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassk.lfesveykvdketglidyd 159
                                          ++nvqp sG  an+a + al +pgd i++l+++ GGh++h +      isa+++   ++++y  ++e+  id d
  gi|488601565|ref|YP_007908036.1|  89 ---HANVQPISGVTANIAGFFALTNPGDLIMSLSVPCGGHISHDT------ISAAGIrGLDVIHYPFNNEEMEIDVD 156
                                       ...****************************************75......44555415899*************** PP

                                       HHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCC.TSSEEEEESSSTT- CS
                              SHMT 160 elekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfe.yadvvtttthktlr 235
                                       e +k a e kP+l v G+s        + + e+a e+ a ++ d +h+ Gl+a++ + +P++  ad+vt  thkt+ 
  gi|488601565|ref|YP_007908036.1| 157 ETRKLAMEKKPRLFVLGSSLILFPQPVKEISELASEISAKVMFDASHVLGLIAGKKFQDPLReGADIVTGSTHKTFF 233
                                       ********************9999999*********************************96269************ PP

                                       S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHH CS
                              SHMT 236 GprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakal 312
                                       Gp+ ++il+r              +el++k+++avfPg+    +  ++a+  va+ e le   k+y+++v++nak+l
  gi|488601565|ref|YP_007908036.1| 234 GPQRAIILSR--------------KELADKVDKAVFPGVVSNHHLNTLAGYVVAVIEMLEF-GKEYARDVVRNAKKL 295
                                       **********..............68*****************************998764.49************* PP

                                       HHHHHHTT-EEGG...GS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS..STTTT-SEEEEESHHHHH CS
                              SHMT 313 aealkekgyklvs...gGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd..ksalvtsGlrlGtpalts 384
                                       ae l + g+++v    g t++h v vd+++ g  G+++ + le++ni  nkn +P d  +++  +sG+rlG   lt+
  gi|488601565|ref|YP_007908036.1| 296 AESLYNYGFDVVGanrGFTESHQVAVDVSKIG-GGEKVARELERINIVLNKNLLPWDsmEKTSNPSGIRLGVQELTR 371
                                       ************7333569********98877.7999********************999999************** PP

                                       TT--HHHHHHHHHH CS
                              SHMT 385 rgfkeedlekvakf 398
                                        g+ke+++e++a++
  gi|488601565|ref|YP_007908036.1| 372 LGMKENEMEEIADI 385
                                       ***********986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.4e-11   7.1e-08      38     306 ..      62     313 ..      53     316 .. 0.86
   2 ?   -3.1   0.0       1.1   3.4e+03     158     200 ..     357     397 ..     354     411 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.4e-11
                                       TST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEES...S-THHHHH.. CS
                     Aminotran_1_2  38 neygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdp...tyasykni.. 109
                                        +y+ +   +e ee  +k+ +  +  + ++ a+v+ +sG +a+i+ +++l++  pgd i + +     + s+++i  
  gi|488601565|ref|YP_007908036.1|  62 RFYQGCAYIDEIEEMAIKLTK--KLFDAEH-ANVQPISGVTANIAGFFALTN--PGDLIMSLSVpcgGHISHDTIsa 133
                                       678899999999999999999..4444555.5****************9996..*****975542338888876522 PP

                                       HHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEE CS
                     Aminotran_1_2 110 lrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfv 186
                                       + ++g+ v+ yp++  e++++d+++  ++  e      k++++++ s       ++ ++ ++++ +la +  + +++
  gi|488601565|ref|YP_007908036.1| 134 AGIRGLDVIHYPFN-NEEMEIDVDETRKLAMEK-----KPRLFVLGS-----SLILFPQPVKEISELASEISAKVMF 199
                                       7789********77.8999*******9977763.....556666665.....47999999***************** PP

                                       EETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHH CS
                     Aminotran_1_2 187 DeaYagfvfgsldavatranveeepnllivgslsKaf.GlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaa 262
                                       D  +  +    +++      + e+ + +++gs  K f G      ++il+ +++++ + k++ p+ +s++    +a 
  gi|488601565|ref|YP_007908036.1| 200 DASHVLGLIAGKKF---QDPLREGAD-IVTGSTHKTFfGPQR---AIILSRKELADKVDKAVFPGVVSNHHLNTLAG 269
                                       ********999887...668888878.999999999879999...******************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                     Aminotran_1_2 263 alsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                        + ++ ++ ++ +e ++ + +++k+l ++L + g++v++ + g+
  gi|488601565|ref|YP_007908036.1| 270 YVVAVIEMLEFGKEYARDVVRNAKKLAESLYNYGFDVVGANRGF 313
                                       ******999*********************999*****999887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHT CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYagfvfgslda 200
                                       +NP+G  +  +el+ l   +k++++  + D  Y +++ +++da
  gi|488601565|ref|YP_007908036.1| 357 SNPSGIRLGVQELTRL--GMKENEMEEIADIFYLKLMKDESDA 397
                                       7888888888888888..6777777777777777777766665 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   7.3e-09   2.2e-05     188     237 ..     205     254 ..     182     357 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.3e-09
                                       GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHHST CS
                              SelA 188 yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklkknp 237
                                        gl    ++q+ l+eG+d+v+ s  k + gpq  ii+ +kel +k++k  
  gi|488601565|ref|YP_007908036.1| 205 LGLIAGKKFQDPLREGADIVTGSTHKTFFGPQRAIILSRKELADKVDKAV 254
                                       578888899************************************98865 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.3e-07   0.00038      42     276 ..      82     342 ..      32     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-07
                                       HHHTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT...-HHHHSSTTHHHHC.C--EEEEE-EBTTTBE-HHH CS
                   Beta_elim_lyase  42 aelfgkeaalfvp.qGtaAnsillkillqrgeevivtep...ahihfdetgaiael.agvklrdlknkeaGkmdlek 113
                                       ++lf++e+a   p +G  An   + +l+++g+ ++  +    +hi  d+  a+     +v   +++n+e  ++d+++
  gi|488601565|ref|YP_007908036.1|  82 KKLFDAEHANVQPiSGVTANIAGFFALTNPGDLIMSLSVpcgGHISHDTISAAGIRgLDVIHYPFNNEE-MEIDVDE 157
                                       447777765544438999999999999988887765554677899999988776664566666666766.8888888 PP

                                       HHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSS CS
                   Beta_elim_lyase 114 leaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvD 190
                                        +++  e     +k++l +l           + ++ ++e++++a +   ++++D+  ++    + +     + +++D
  gi|488601565|ref|YP_007908036.1| 158 TRKLAME-----KKPRLFVLGSSLI------LFPQPVKEISELASEISAKVMFDASHVLGLI-AGKKFQDPLREGAD 222
                                       8887766.....4678888776665......688999*******************999765.444444455579** PP

                                       EEEEESSSTT--SS-EEEEE-HH......................................HHHHHHHHHHHHT--- CS
                   Beta_elim_lyase 191 svtmslkKdllanvGgvlafrddel..................................edylaerveqrkylgggl 233
                                       +vt s  K  + +  ++++ r++ +                                  ++y +  v+ +k+l++ l
  gi|488601565|ref|YP_007908036.1| 223 IVTGSTHKTFFGPQRAIILSRKELAdkvdkavfpgvvsnhhlntlagyvvaviemlefgKEYARDVVRNAKKLAESL 299
                                       **********************988**************************************************** PP

                                       SSTHHHHH..HHHHHHHHSSTTHHHHHHH..HHHHHHHHHHCT-- CS
                   Beta_elim_lyase 234 rqagvlaaleagiraleeglaslerdhkt..aeqlaeklelvrla 276
                                       +++g+ ++   + r  +e  + + +  k   +e+ a++le ++++
  gi|488601565|ref|YP_007908036.1| 300 YNYGFDVV--GANRGFTESHQVAVDVSKIggGEKVARELERINIV 342
                                       ****9988..55555555433333333333356666666666555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.5e-06     0.025     111     228 ..     136     257 ..      52     271 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.5e-06
                                       HHTEEEEEEEB.ETTSCBEGGGHHHH--.TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTT....T CS
                       Aminotran_5 111 rtgakvkvipl.deegeldldeleklln.ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqav....g 181
                                        +g++v ++p+ +ee e+d+de +kl   +k++l      s+ +   qpv+ei +la +  a v+ Da+  +    g
  gi|488601565|ref|YP_007908036.1| 136 IRGLDVIHYPFnNEEMEIDVDETRKLAMeKKPRLFV--LGSSLILFPQPVKEISELASEISAKVMFDASHVLgliaG 210
                                       456666555541567789999997765415555544..356666689**********************98622225 PP

                                       TS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.ST CS
                       Aminotran_5 182 hipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllgg 228
                                       ++  d  + g+D+++ s+hK ++gP+   ++  rkel  k+ ++ ++g
  gi|488601565|ref|YP_007908036.1| 211 KKFQDPLREGADIVTGSTHKtFFGPQR-AIILSRKELADKVDKAVFPG 257
                                       67789999************999**95.45555666777777777666 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00011      0.34     156     205 ..     183     237 ..      73     252 .. 0.72
   2 ?   -1.1   0.0      0.18   5.4e+02     271     314 ..     248     294 ..     237     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHTT-EEEEEGTTTHTT.....TS-GGGGT-SEEEEETTTTTTCSSS CS
                   Cys_Met_Meta_PP 156 iekiaklakkagvlvvvDntfaspl.....lqrplklgaDivvhSaTKylgGhsd 205
                                       +++i++la + ++ v+ D++ + +l     +q pl+ gaDiv+ S+ K   G ++
  gi|488601565|ref|YP_007908036.1| 183 VKEISELASEISAKVMFDASHVLGLiagkkFQDPLREGADIVTGSTHKTFFGPQR 237
                                       789***************99765532222289*************9997766655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.18
                                       TTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHH...HHHHH CS
                   Cys_Met_Meta_PP 271 pkvekvyYpglpshpqhelakkqlkgaggvlsFelksee...ekakk 314
                                       +kv k  +pg+ s+++ ++ + ++  +  +l F  +  +   ++akk
  gi|488601565|ref|YP_007908036.1| 248 DKVDKAVFPGVVSNHHLNTLAGYVVAVIEMLEFGKEYARdvvRNAKK 294
                                       7999999****999999999999999988999976655433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2713.99
//
Query:       gi|488601566|ref|YP_007908037.1|  [L=199]
Description: Orotate phosphoribosyltransferase-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-18   64.6   0.2      1e-17   64.1   0.2    1.3  1  Pribosyltran     Phosphoribosyl transferase domain
    0.00065   19.2   0.3     0.0032   17.0   0.1    2.1  2  Sigma70_r4       Sigma-70, region 4
    0.00078   19.3   0.2     0.0019   18.1   0.2    1.8  1  HTH_11           HTH domain
     0.0012   18.8   0.3     0.0051   16.8   0.0    2.1  2  HTH_7            Helix-turn-helix domain of resolvase
     0.0027   17.4   0.1     0.0092   15.8   0.0    1.9  2  HTH_23           Homeodomain-like domain
     0.0051   16.5   0.4       0.13   12.0   0.1    3.0  3  HTH_38           Helix-turn-helix domain
     0.0066   16.5   0.0      0.019   15.1   0.0    1.7  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.012   15.1   0.1       0.43   10.0   0.1    2.1  1  PRTase_2         Phosphoribosyl transferase
      0.023   14.2   0.1      0.091   12.3   0.0    2.0  2  GerE             Bacterial regulatory proteins, luxR family
      0.027   14.3   0.0      0.081   12.7   0.0    1.8  1  HTH_10           HTH DNA binding domain
      0.042   13.4   0.0       0.11   12.1   0.0    1.8  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.047   14.1   0.0       0.15   12.5   0.0    1.9  2  HTH_40           Helix-turn-helix domain
      0.069   12.8   0.1       0.64    9.7   0.0    2.5  2  Sigma70_r4_2     Sigma-70, region 4
      0.069   13.4   0.0       0.17   12.1   0.0    1.7  2  Acetyltransf_1   Acetyltransferase (GNAT) family
      0.087   12.9   0.0       0.15   12.1   0.0    1.3  1  NUC202           NUC202 domain
        0.1   12.8   0.3       0.41   10.9   0.1    2.0  2  HTH_17           Helix-turn-helix domain
       0.14   11.7   0.0       0.17   11.4   0.0    1.2  1  DUF1403          Protein of unknown function (DUF1403)


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.2   9.8e-21     1e-17       5     129 ..      59     182 ..      55     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 9.8e-21
                                       TTT---EEEEEEETTEEEEEE.--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........E CS
                      Pribosyltran   5 llenpaildavarlaaeilee.yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesr 80 
                                       + + p  ++++a+ + + + + ++ ++ vv+gia+ G+p+a+ +a eL++ la  + +k   ++ e  + g   e  
  gi|488601566|ref|YP_007908037.1|  59 FVKSPYRMRNIAKSLVDMVLDvIEDEIEVVIGIATSGIPIATMIAEELNADLALYYPRKLKWENEEREIAGTLSE-- 133
                                       5666666777777777777778999***********************999995555555555555555454444.. PP

                                       E----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHH CS
                      Pribosyltran  81 lledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpat 129
                                       + ++++ k ++ +DDi++tG+Tl++++e + +k+ + + ++v++dk+  
  gi|488601566|ref|YP_007908037.1| 134 NYAKVDRKNCIAIDDIITTGSTLREVAEYVSKKEGKLLCACVVIDKRGL 182
                                       99**********************************9999999999865 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     3e-06    0.0032      17      37 ..      13      35 ..       4      45 .. 0.83
   2 ?   -1.1   0.0       1.3   1.4e+03      20      29 ..     153     162 ..     151     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                                      H..TTT--HHHHHHHHTS-HHHH CS
                        Sigma70_r4 17 f..geglTleEIgerlgiSrerV 37
                                      +  ++glT  EI+++l++Sre++
  gi|488601566|ref|YP_007908037.1| 13 RlkEKGLTTGEIADELNVSRETA 35
                                      35689****************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                       T--HHHHHHH CS
                        Sigma70_r4  20 glTleEIger 29 
                                       g Tl E++e 
  gi|488601566|ref|YP_007908037.1| 153 GSTLREVAEY 162
                                       679****996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   1.8e-06    0.0019       2      31 ..       4      34 ..       3      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                            HTH_11  2 llqilelLleargp.isgeeLAeeLnvSrrt 31
                                       ++++e  ++ +++ ++  e+A+eLnvSr t
  gi|488601566|ref|YP_007908037.1|  4 IESLIEKARRLKEKgLTTGEIADELNVSRET 34
                                      567777777777777**************99 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 !   16.8   0.0   4.9e-06    0.0051      11      37 ..       8      34 ..       4      36 .. 0.93
   2 ?   -1.8   0.0       3.2   3.3e+03      19      32 ..      93     107 ..      82     107 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.9e-06
                                      HGGGGSSTTTT--STTTSSSS---SSS CS
                             HTH_7 11 inrvvkLleeGisiskIAkevnisRsT 37
                                      i+ +++L e+G +  +IA+e+n+sR+T
  gi|488601566|ref|YP_007908037.1|  8 IEKARRLKEKGLTTGEIADELNVSRET 34
                                      67899*********************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.2
                                       TTT--STT.TSSSS- CS
                             HTH_7  19 eeGisisk.IAkevn 32 
                                        +Gi+i++ IA+e+n
  gi|488601566|ref|YP_007908037.1|  93 TSGIPIATmIAEELN 107
                                       568777543888876 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   8.7e-06    0.0092      13      33 ..      13      34 ..       6      38 .. 0.86
   2 ?   -3.1   0.0       7.4   7.8e+03      17      25 ..     153     161 ..     145     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.7e-06
                            HTH_23 13 llae.GlsvreIAreLgvsrrT 33
                                       l+e Gl++ eIA+eL+vsr T
  gi|488601566|ref|YP_007908037.1| 13 RLKEkGLTTGEIADELNVSRET 34
                                      55667***************99 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.4
                            HTH_23  17 GlsvreIAr 25 
                                       G + re+A+
  gi|488601566|ref|YP_007908037.1| 153 GSTLREVAE 161
                                       778899997 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00013      0.13      14      36 ..      12      34 ..       6      34 .. 0.90
   2 ?   -2.2   0.0       3.4   3.6e+03      22      30 ..      65      73 ..      62      73 .. 0.81
   3 ?    0.8   0.0      0.39   4.1e+02      13      32 ..     146     165 ..     144     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                            HTH_38 14 erllaeGlslreIArrLgrspsT 36
                                       rl ++Gl+  eIA +L++s+ T
  gi|488601566|ref|YP_007908037.1| 12 RRLKEKGLTTGEIADELNVSRET 34
                                      68999****************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                            HTH_38 22 slreIArrL 30
                                       +r IA+ L
  gi|488601566|ref|YP_007908037.1| 65 RMRNIAKSL 73
                                      689999976 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.39
                            HTH_38  13 IerllaeGlslreIArrLgr 32 
                                       I + +  G +lre+A ++ +
  gi|488601566|ref|YP_007908037.1| 146 IDDIITTGSTLREVAEYVSK 165
                                       566677899******98876 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-05     0.019      22      56 ..      50      84 ..      39      90 .. 0.87
   2 ?   -2.9   0.0       7.2   7.6e+03      52      69 ..     148     165 ..     145     174 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                   Acetyltransf_CG 22 egvldfthTeVpeelrGkGiAkkLvkaalddaree 56
                                      ++v++ + T+V+  +r ++iAk Lv+ +ld +++e
  gi|488601566|ref|YP_007908037.1| 50 SDVYIEWRTFVKSPYRMRNIAKSLVDMVLDVIEDE 84
                                      56888899**********************99876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.2
                   Acetyltransf_CG  52 dareeglkvvptCsyvaa 69 
                                       d+  +g + + + +yv++
  gi|488601566|ref|YP_007908037.1| 148 DIITTGSTLREVAEYVSK 165
                                       555555555555555554 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00041      0.43     120     148 ..     139     167 ..      57     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                          PRTase_2 120 aakelvLvDDEistGktalnliralqekl 148
                                       ++k+ + +DD i+tG+t+ ++++ +++k 
  gi|488601566|ref|YP_007908037.1| 139 DRKNCIAIDDIITTGSTLREVAEYVSKKE 167
                                       45678999**********99999887764 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.6e-05     0.091      15      33 ..      16      34 ..      13      35 .. 0.90
   2 ?   -3.7   0.0       8.7   9.2e+03      22      28 ..     101     107 ..     100     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-05
                                      CTTS-HHHHHHHHTS-HHH CS
                              GerE 15 aeGksnkeIAeelniSekT 33
                                       +G+++ eIA+eln+S +T
  gi|488601566|ref|YP_007908037.1| 16 EKGLTTGEIADELNVSRET 34
                                      58**************998 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.7
                                       HHHHHHT CS
                              GerE  22 eIAeeln 28 
                                       +IAeeln
  gi|488601566|ref|YP_007908037.1| 101 MIAEELN 107
                                       6999997 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.7e-05     0.081      22      51 ..      17      46 ..      15      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-05
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrkaeskl 51
                                      +  t+ e+A+el++s+ t++  L ka++ +
  gi|488601566|ref|YP_007908037.1| 17 KGLTTGEIADELNVSRETALWLLTKATEDI 46
                                      567899*******************99865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.11      14      43 ..      15      44 ..      12      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLee 43
                                      k+ +++  e+A++l++S+ t ++ l + +e
  gi|488601566|ref|YP_007908037.1| 15 KEKGLTTGEIADELNVSRETALWLLTKATE 44
                                      56799****************999887766 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.15       4      60 ..      10      72 ..       8     113 .. 0.82
   2 ?   -0.8   0.0       2.1   2.2e+03      45      49 ..     146     150 ..      91     171 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                            HTH_40  4 etlelleeglsieeIAkerglkesTIegHLaelieeg......eeidlerlvse.eeekeIeea 60
                                      ++ +l e+gl+  eIA+e ++++ T    L+++ e+       + i+++ +v++  + ++I++ 
  gi|488601566|ref|YP_007908037.1| 10 KARRLKEKGLTTGEIADELNVSRETALWLLTKATEDIsppsdvY-IEWRTFVKSpYRMRNIAKS 72
                                      677889**************************999944444435.8899998554888887765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                            HTH_40  45 lerlv 49 
                                       +++++
  gi|488601566|ref|YP_007908037.1| 146 IDDII 150
                                       33333 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 ?    9.7   0.0    0.0006      0.64      24      42 ..      16      34 ..       4      41 .. 0.93
   2 ?   -0.6   0.0         1   1.1e+03      26      40 ..     153     167 ..     152     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0006
                                      TS---HHHHHHHHT--HHH CS
                      Sigma70_r4_2 24 leglsykEIAellgisegt 42
                                      ++gl++ EIA +l++s  t
  gi|488601566|ref|YP_007908037.1| 16 EKGLTTGEIADELNVSRET 34
                                      78**************877 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                       ---HHHHHHHHT--H CS
                      Sigma70_r4_2  26 glsykEIAellgise 40 
                                       g++ +E+Ae+   +e
  gi|488601566|ref|YP_007908037.1| 153 GSTLREVAEYVSKKE 167
                                       78999****987666 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.17      55      94 ..      44      85 ..       8      95 .. 0.83
   2 ?   -2.8   0.0       6.8   7.2e+03      42      65 ..     125     148 ..     112     152 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      T...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                    Acetyltransf_1 55 d...ekggvayieslaVspeyrgkGlGsaLlealeerareegi 94
                                      +   +  +v++ ++ +V++ yr +++++ L++ +++  ++e i
  gi|488601566|ref|YP_007908037.1| 44 EdisPPSDVYIEWRTFVKSPYRMRNIAKSLVDMVLDVIEDE-I 85
                                      345567899*************************9955544.4 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.8
                                       TEEEEEEEEEEEETTSTTEEEEEE CS
                    Acetyltransf_1  42 geliGfisllkipdekggvayies 65 
                                        e++G++s +     ++++++i++
  gi|488601566|ref|YP_007908037.1| 125 REIAGTLSENYAKVDRKNCIAIDD 148
                                       336666643333334566666665 PP

>> NUC202  NUC202 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.15      19      57 ..      20      59 ..      12      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            NUC202 19 tCGasegsLqvsafsseaLltaLlsdivPpada.lklrsl 57
                                      t G  ++ L+vs+  +  Llt+ + di+Pp+d  +  r++
  gi|488601566|ref|YP_007908037.1| 20 TTGEIADELNVSRETALWLLTKATEDISPPSDVyIEWRTF 59
                                      568999*******999999***********9963566665 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00039      0.41       2      21 ..      19      38 ..      19      45 .. 0.90
   2 ?   -1.5   0.0       2.8   2.9e+03       3      10 ..     155     162 ..     155     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                            HTH_17  2 ltveEaAelLgvsrstvyrl 21
                                      lt+ E+A+ L+vsr t+  l
  gi|488601566|ref|YP_007908037.1| 19 LTTGEIADELNVSRETALWL 38
                                      8***************9776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                            HTH_17   3 tveEaAel 10 
                                       t  E+Ae+
  gi|488601566|ref|YP_007908037.1| 155 TLREVAEY 162
                                       67899998 PP

>> DUF1403  Protein of unknown function (DUF1403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.17      83     126 ..      37      80 ..      21     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                           DUF1403  83 vlLtkpgddpgPaGklllawrrlaarpa...kltaaelaavldllgl 126
                                       +lLtk+ +d +P  +++  wr++++ p    ++ +  +  v   l++
  gi|488601566|ref|YP_007908037.1|  37 WLLTKATEDISPPSDVYIEWRTFVKSPYrmrNIAKSLVDMV---LDV 80 
                                       89************************994433333333333...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1271.98
//
Query:       gi|488601567|ref|YP_007908038.1|  [L=308]
Description: glycosyltransferase, TIGR04182 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.1    1.1e-21   77.3   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    2.1e-07   31.1   0.0    2.6e-07   30.8   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00029   21.3   0.0    0.00049   20.5   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.028   14.9   0.1      0.053   14.0   0.1    1.4  1  YflT             Heat induced stress protein YflT
      0.036   13.7   0.2      0.074   12.7   0.2    1.5  1  DAGK_cat         Diacylglycerol kinase catalytic domain
       0.11   12.5   2.1        0.2   11.6   2.1    1.3  1  LrgA             LrgA 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 !   77.3   0.1   3.8e-25   1.1e-21       1     168 [.       7     162 ..       7     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 3.8e-25
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       +v+ipt Nee+ +  t++  ++        i+v+D +StD+t+ei+++      + +v  ++  +Gk+ a+ ++++ 
  gi|488601567|ref|YP_007908038.1|   7 CVIIPTLNEEEAIGHTIDEFKKE---GFNNIFVIDGNSTDRTREIARKK-----GAKVEVQSG-KGKGQAVAEAFKL 74 
                                       79****************99999...777788888889***********.....899999995.5************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       +++d+i+++D D +++ ++ +kl++++ kd ad v+g+r ++  +  + + n++    +++ +++ + +++ +l ++
  gi|488601567|ref|YP_007908038.1|  75 VDSDVIILVDGDGTYPAKDAKKLLDPIFKDVADHVVGNRLKNYEKGAFTRLNLF---GNKIINFIFRLFYGVELYDI 148
                                       ****************************************************95...9******************* PP

                                       STCCCEEEEHHHHH CS
                   Glycos_transf_2 155 igsaallrrealee 168
                                        +++++lr+e++++
  gi|488601567|ref|YP_007908038.1| 149 LSGYRALRKELYKS 162
                                       **********9876 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 !   30.8   0.0   8.6e-11   2.6e-07       3     132 ..       5     121 ..       4     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 8.6e-11
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       ++ v++pt+nee+ +g +++++ +  ++   ++v++ +s++ t+e a+      ++++v v  +    g +gk +a+
  gi|488601567|ref|YP_007908038.1|   5 RVCVIIPTLNEEEAIGHTIDEFKK--EGFNNIFVIDGNSTDRTREIARK-----KGAKVEV--Q---SG-KGKGQAV 68 
                                       489********************9..66688999999999999998886.....5557774..3...25.59***** PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfllnrstl 132
                                       +ea++ v+sd+++lvD+D     +d+ k+ll  ++ + +++v ++++ ++++ +
  gi|488601567|ref|YP_007908038.1|  69 AEAFKLVDSDVIILVDGDGTYpAKDA-KKLLDPIFKDVADHVVGNRLKNYEKGA 121
                                       ******************77646666.444444435566676666666655555 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 !   20.5   0.0   1.7e-07   0.00049       2      47 ..      14      60 ..      13      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkel.pevkllh 47
                                      ne+++++++++  ++ gf++i+v+d +stD+tr+i ++  ++v++  
  gi|488601567|ref|YP_007908038.1| 14 NEEEAIGHTIDEFKKEGFNNIFVIDGNSTDRTREIARKKgAKVEVQS 60
                                      99**********************************88646677654 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.8e-05     0.053       5      68 ..      14      76 ..      10      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                              YflT  5 eneeellsaieelkaeGyneddiyvva.kdkdrlerlaentdaetettseeglwdsiknlfrskg 68
                                      + ee   + i+e+k+eG+n  +i+v+  +  dr++++a++++a++e  s +g +++++++f+  +
  gi|488601567|ref|YP_007908038.1| 14 NEEEAIGHTIDEFKKEGFN--NIFVIDgNSTDRTREIARKKGAKVEVQSGKGKGQAVAEAFKLVD 76
                                      566667799*********8..58888538899*****************************8755 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.5e-05     0.074      20      68 ..      43      89 ..      38      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                                      HHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHH CS
                          DAGK_cat 20 rkvrelleeagvelelieteepgdakelakeakeegvdlivvaGGDGtv 68
                                      ++ re+ +++g ++e++  +++g+a + a ++ ++  d+i+ + GDGt 
  gi|488601567|ref|YP_007908038.1| 43 DRTREIARKKGAKVEVQSGKGKGQAVAEAFKLVDS--DVIILVDGDGTY 89
                                      67789999**********99999888888777776..**********95 PP

>> LrgA  LrgA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.1   6.8e-05       0.2      21      62 ..     233     275 ..     231     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.8e-05
                              LrgA  21 GlllLlllLltki.vklekveeaadfllkhlallFvPagvgvm 62 
                                       Gl++L+l ++t+i v  e+  ++++ ll++l+ l++ ag++v+
  gi|488601567|ref|YP_007908038.1| 233 GLIMLFLGFITGIyVVYEWFHRITHSLLAILTTLLIIAGIQVI 275
                                       9*********998356799*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
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: 0.53u 0.36s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1850.15
//
Query:       gi|488601568|ref|YP_007908039.1|  [L=425]
Description: 3-hydroxy-3-methylglutaryl-coenzyme A reductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-116  387.9   3.1   5.2e-116  387.7   3.1    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.7   3.1  2.9e-120  5.2e-116       2     367 .]      17     381 ..      16     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 387.7 bits;  conditional E-value: 2.9e-120
                                       HHHHHHHHHH...S-HHHHHHH.TT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHH CS
                       HMG-CoA_red   2 veeRrkllee...lteeeleel.keesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsas 74 
                                       +e+R+k + e   l++ee e l k++sl+ ++ad+miEnviG+++lP+G+a+++li+gk+yl+Pm++eE+s+vA+as
  gi|488601568|ref|YP_007908039.1|  17 IEKRLKKVVEfsgLSDEEAELLkKTGSLSIDIADRMIENVIGTFELPIGIATNFLIDGKDYLIPMVIEEPSVVAAAS 93 
                                       57888888777889999999996669999************************************************ PP

                                       HHHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-. CS
                       HMG-CoA_red  75 rgakainesgGvkttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla. 146
                                       ++ak+++ +gG+  t+++  ++++qv+++ ++ +++ ++ ++ ++k+e++e an+ +++  s ggg+kdie+ v++ 
  gi|488601568|ref|YP_007908039.1|  94 NAAKMARVKGGF-WTSSTGPLMIGQVQVT-NLPNPNYARLQVlAHKDEIIEKANEQDPMlvSLGGGCKDIEArVIDt 168
                                       ************.7777778*********.********99999*****************************88889 PP

                                       ..SSEEEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHH CS
                       HMG-CoA_red 147 ..grlvvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatige 221
                                         g++++++l vd++DAmGaN+vn+++ea+a+lie+++g++++l+i sNl+ +++a+a + ++++++        ge
  gi|488601568|ref|YP_007908039.1| 169 mkGKMLIIHLIVDVRDAMGANAVNTMAEAVAPLIEKITGGRVYLRIISNLAVYRLARAYAIFDKDAI-------GGE 238
                                       99************************************************************99999.......9** PP

                                       HHHHHHHHHHHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT......SEEE...T CS
                       HMG-CoA_red 222 evvekilkasaealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa......leev...e 289
                                       evve i++a+a+al+d++r   +t+nkGi       +Ngi+Av+lAtG+D++a+e+++ha+a+      l+++   +
  gi|488601568|ref|YP_007908039.1| 239 EVVEGIMNAYAFALADPFRC--ATHNKGI-------MNGISAVVLATGNDFRAIEAGAHAYASlngykpLTTYevnS 306
                                       ********************..*******.......***************************99999966667668 PP

                                       TTEEEEEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHH CS
                       HMG-CoA_red 290 dgdlygsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmkl 365
                                       +gdl+g++++P ++VG++GG+t+++p a+++ k+lgvk+a+   eL++iiaavgLAq+++alrALa+eg+q+gHm+l
  gi|488601568|ref|YP_007908039.1| 307 KGDLVGTIEVP-VAVGVIGGSTSVNPLAKINlKILGVKSAD---ELSRIIAAVGLAQNFAALRALATEGIQRGHMSL 379
                                       888********.*****************************...********************************* PP

                                       HH CS
                       HMG-CoA_red 366 hr 367
                                       h+
  gi|488601568|ref|YP_007908039.1| 380 HA 381
                                       96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2660.39
//
Query:       gi|488601569|ref|YP_007908040.1|  [L=95]
Description: hypothetical protein Asulf_02088 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   25.9   4.0    2.2e-05   24.9   4.0    1.5  1  OAD_gamma        Oxaloacetate decarboxylase, gamma chain
    0.00037   20.5   0.0    0.00045   20.2   0.0    1.2  1  Sdh_cyt          Succinate dehydrogenase/Fumarate reductase t
  ------ inclusion threshold ------
      0.013   15.4   0.4      0.022   14.7   0.4    1.3  1  TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane p
      0.027   13.4   0.0      0.027   13.4   0.0    1.0  1  MFS_1            Major Facilitator Superfamily
      0.085   13.2   2.3        3.4    8.1   1.8    2.2  2  Spore_SspJ       Small spore protein J (Spore_SspJ)


Domain annotation for each model (and alignments):
>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   4.0   6.2e-09   2.2e-05       2      54 ..       5      57 ..       4      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.2e-09
                         OAD_gamma  2 egllltllGmgvVFvvLilLslvislfskiikkkakkkkkkakaaaaaaaaaa 54
                                      ++l ++  G++ VF+vL lL l+i l+++++  k++k ++++ka+++ +++++
  gi|488601569|ref|YP_007908040.1|  5 QALAISAEGISGVFIVLGLLALFIWLMGFFNFEKTEKVEENQKAQEKFSEKEK 57
                                      78889999**********************98888888888888877776544 PP

>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.3e-07   0.00045      28     107 ..      14      88 ..       4      95 .] 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                           Sdh_cyt  28 itGvallvglllllvwlllalslsspesfarv..vallaspiklilllllllallyHllnGiRhllwDlglgleles 102
                                       i+Gv++++gll l++wl+       +e +++v      a+  ++ ++  +++a++yHl  G R +++D+   + +++
  gi|488601569|ref|YP_007908040.1|  14 ISGVFIVLGLLALFIWLMGFF---NFEKTEKVeeN-QKAQEKFSEKEKFAIIAAIYHLEEGGREMVVDV---MAPSE 83 
                                       9*******9999999*66555...77888888642.22234455556788899999************7...34455 PP

                           Sdh_cyt 103 arksa 107
                                        +k+a
  gi|488601569|ref|YP_007908040.1|  84 WKKTA 88 
                                       55544 PP

>> TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   6.2e-06     0.022       8      46 ..      17      56 ..      14      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.2e-06
                   TMEMspv1-c74-12  8 iFSvvivLgiFly.iGLsiyqKikqirgkkkDKKeierke 46
                                      +F v+ +L++F++ +G   + K  +++ ++k + +  +ke
  gi|488601569|ref|YP_007908040.1| 17 VFIVLGLLALFIWlMGFFNFEKTEKVEENQKAQEKFSEKE 56
                                      788999999****55********************99998 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.5e-06     0.027     143     195 ..       6      59 ..       1      92 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.5e-06
                             MFS_1 143 lla.sslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpap 195
                                       +la s+ g ++vf++l++++l+  +++++ +  +++ +++++ +e+ + +++++
  gi|488601569|ref|YP_007908040.1|   6 ALAiSAEGISGVFIVLGLLALFIWLMGFFNFEKTEKVEENQKAQEKFSEKEKFA 59 
                                       555588899**************9997777777777777766666643333333 PP

>> Spore_SspJ  Small spore protein J (Spore_SspJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.8   0.00095       3.4       1      18 [.      31      48 ..      31      51 .. 0.93
   2 ?    5.5   0.1     0.006        22       5      31 ..      46      75 ..      46      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00095
                        Spore_SspJ  1 mgFFnKDkgkksEKdkna 18
                                      mgFFn  k +k E +++a
  gi|488601569|ref|YP_007908040.1| 31 MGFFNFEKTEKVEENQKA 48
                                      9************99986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.006
                        Spore_SspJ  5 nKDkgkksEKdknavdga...LEdAgkaLk 31
                                      +K + k sEK+k a+  a   LE+ g+++ 
  gi|488601569|ref|YP_007908040.1| 46 QKAQEKFSEKEKFAIIAAiyhLEEGGREMV 75
                                      6778899*****999887566899998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1507  (0.0840538); expected 358.6 (0.02)
Passed bias filter:                      832  (0.0464053); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.35s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 585.31
//
Query:       gi|488601570|ref|YP_007908041.1|  [L=138]
Description: hypothetical protein Asulf_02089 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-22   78.1   2.5    6.4e-22   77.2   2.5    1.5  1  Biotin_lipoyl    Biotin-requiring enzyme
      1e-16   60.5   1.7    9.1e-08   31.8   0.2    2.7  3  Biotin_lipoyl_2  Biotin-lipoyl like
    1.6e-06   28.8   0.9     0.0022   18.7   0.1    2.7  3  HlyD_3           HlyD family secretion protein
    3.8e-06   26.3   0.9     0.0092   15.2   0.0    2.5  3  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    8.4e-05   22.5   3.0    0.00045   20.1   0.4    2.1  2  GCV_H            Glycine cleavage H-protein
    0.00022   21.2   0.3       0.16   12.1   0.0    2.5  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
    0.00027   20.5   0.9     0.0007   19.1   0.8    1.8  1  NQRA             Na(+)-translocating NADH-quinone reductase s
     0.0004   20.3   0.3     0.0021   18.0   0.3    2.2  1  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0007   19.3   2.8      0.021   14.6   1.2    2.7  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
     0.0021   18.3   0.1     0.0053   16.9   0.1    1.8  2  Peptidase_M23    Peptidase family M23
     0.0091   15.6   0.7        2.1    8.1   0.2    2.5  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
  ------ inclusion threshold ------
       0.04   13.9   7.4        1.1    9.2   4.6    2.1  2  DUF2118          Uncharacterized protein conserved in archaea
       0.11   12.7   0.0       0.15   12.3   0.0    1.3  1  DUF695           Family of unknown function (DUF695)
       0.23   11.4   2.0        4.6    7.2   0.0    2.8  3  PASTA            PASTA domain


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   2.5     5e-25   6.4e-22       5      73 .]      74     137 ..      70     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 5e-25
                                       ESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl   5 sPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                       s  +G++++     +lvk+GdkV+ag +++++eamKme+ei++p +G+vkei vk+Gd v++gd+l++i
  gi|488601570|ref|YP_007908041.1|  74 SMLPGTVMK-----ILVKEGDKVNAGNTVLILEAMKMENEITSPFDGIVKEIRVKSGDRVDTGDVLVVI 137
                                       444556666.....****************************************************997 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    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      33      45 ..       8      20 ..       6      30 .. 0.57
   2 !   28.4   0.0   8.2e-10     1e-06       4      41 ..      71     108 ..      62     110 .. 0.90
   3 !   31.8   0.2   7.1e-11   9.1e-08       4      33 ..     108     137 ..     106     138 .] 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.5
                   Biotin_lipoyl_2 33 lDsralqlalaqa 45
                                      +D++++++ + ++
  gi|488601570|ref|YP_007908041.1|  8 IDDEEFDVFVEKL 20
                                      6666666555543 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 8.2e-10
                   Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqla 41 
                                       +I++ ++G+V +++Vk+G+ V+aG++ ++l+  + +++
  gi|488601570|ref|YP_007908041.1|  71 EIKSMLPGTVMKILVKEGDKVNAGNTVLILEAMKMENE 108
                                       69999*************************99888876 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 7.1e-11
                   Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                       +I++p++G V++++Vk G+rV +GdvL+++
  gi|488601570|ref|YP_007908041.1| 108 EITSPFDGIVKEIRVKSGDRVDTGDVLVVI 137
                                       599************************998 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.6   3.4e+03      13      26 ..      27      41 ..      13      59 .. 0.57
   2 !    7.8   0.0    0.0041       5.2       2      28 ..      72      98 ..      71     104 .. 0.90
   3 !   18.7   0.1   1.7e-06    0.0022       2      30 ..     109     137 ..     108     138 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.6
                            HlyD_3 13 lnv.eegevvqagde 26
                                      +++  +  vv+ +d 
  gi|488601570|ref|YP_007908041.1| 27 VQInDKTAVVSIRDD 41
                                      333333334444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0041
                            HlyD_3  2 lrApvdGvvvelnveegevvqagdell 28
                                      +++   G+v ++ v+eg+ v+ag ++l
  gi|488601570|ref|YP_007908041.1| 72 IKSMLPGTVMKILVKEGDKVNAGNTVL 98
                                      789999******************997 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.7e-06
                            HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                       +++p+dG+v+e+ v+ g+ v  gd+l+ i
  gi|488601570|ref|YP_007908041.1| 109 ITSPFDGIVKEIRVKSGDRVDTGDVLVVI 137
                                       89************************988 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 ?   -1.2   0.0      0.75   9.5e+02      13      49 ..       7      43 ..       5      71 .. 0.58
   2 !    9.7   0.1   0.00035      0.44     107     139 ..      69     100 ..      49     105 .. 0.70
   3 !   15.2   0.0   7.2e-06    0.0092     108     139 ..     106     137 ..     101     138 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.75
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 13 ayderrlarvsarveGwveklyvnatgdkVkkGqpLa 49
                                      a+d++++ +   +++  v k+++n     V+  + ++
  gi|488601570|ref|YP_007908041.1|  7 AIDDEEFDVFVEKLDDNVYKVQINDKTAVVSIRDDII 43
                                      5555555555555555555555555555555444444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00035
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 107 ktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                       +  ++k+ + G+V++  v eG+ v++g+t++ +
  gi|488601570|ref|YP_007908041.1|  69 R-REIKSMLPGTVMKILVKEGDKVNAGNTVLIL 100
                                       3.4788888899999999999999988887755 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 7.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                       + ++++p++G+V e +v  G++v++gd+l+ i
  gi|488601570|ref|YP_007908041.1| 106 ENEITSPFDGIVKEIRVKSGDRVDTGDVLVVI 137
                                       56899**********************99987 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.6     0.009        12       9      73 ..      16      82 ..       7      86 .. 0.84
   2 !   20.1   0.4   3.5e-07   0.00045      20      75 ..      67     121 ..      58     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.009
                                      EEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EE..EEE-SSSEEEEE CS
                             GCV_H  9 wvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaas..evyapvsGevve 73
                                      +v++ +d+v++v i d ++    +   +e ++  + v  +e+  +vE  K ++  e+ + + G+v++
  gi|488601570|ref|YP_007908041.1| 16 FVEKLDDNVYKVQINDKTAVVSIRDDIIEFKDSEAIVVREEKARSVEVKKDVGrrEIKSMLPGTVMK 82
                                      7888888899999998888877777889***********************9866799999999986 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.5e-07
                                       EEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE- CS
                             GCV_H  20 vGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevN 75 
                                       vG  ++     g v+ + ++ +g+kv++g+++ ++E+ K+  e+ +p++G v e+ 
  gi|488601570|ref|YP_007908041.1|  67 VGRREIKSMLPGTVMKILVK-EGDKVNAGNTVLILEAMKMENEITSPFDGIVKEIR 121
                                       66666666667778877665.69*****************************9986 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00012      0.16      39      69 ..      72     102 ..      48     105 .. 0.89
   2 !    7.3   0.1    0.0038       4.8      44      68 ..     114     138 .]     103     138 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                       HHHHHTTTEEEESS-TT-EEETTEEEEEEEE CS
                         QRPTase_N  39 vfellpglevellvkDGervekgdvlleieG 69 
                                       + ++lpg+ +++lvk+G++v++g+++l +e+
  gi|488601570|ref|YP_007908041.1|  72 IKSMLPGTVMKILVKEGDKVNAGNTVLILEA 102
                                       445569999*****************99886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0038
                                       TTTEEEESS-TT-EEETTEEEEEEE CS
                         QRPTase_N  44 pglevellvkDGervekgdvlleie 68 
                                       +g+  e+ vk+G+rv  gdvl+ ie
  gi|488601570|ref|YP_007908041.1| 114 DGIVKEIRVKSGDRVDTGDVLVVIE 138
                                       57777899*************9885 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.8   5.4e-07    0.0007      38      84 ..      78     127 ..      54     138 .] 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.4e-07
                              NQRA  38 glkpklkvkegdkVkkGqvlf.edKknpgvlftspasGevvein..rGek 84 
                                       g  +k++vkegdkV++G++++  +  + +  +tsp +G v+ei+   G++
  gi|488601570|ref|YP_007908041.1|  78 GTVMKILVKEGDKVNAGNTVLiLEAMKMENEITSPFDGIVKEIRvkSGDR 127
                                       566899***********876515666778999*********985115655 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   1.6e-06    0.0021      39      84 ..      78     124 ..      49     138 .] 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                            RnfC_N  39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrl 84 
                                       G+  k+lvk+gdkV+ G+ +   e+  +  ++ ++  G Vk+i+   
  gi|488601570|ref|YP_007908041.1|  78 GTVMKILVKEGDKVNAGNTVLILEAmKMENEITSPFDGIVKEIRVKS 124
                                       77789************9876655544599************98655 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.2   1.7e-05     0.021      21     112 ..      15     109 ..       1     119 [. 0.68
   2 ?    4.0   0.0     0.031        40      85     102 ..     119     136 ..     110     138 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                                       HHHT-TTSEEEEEEE-SSEEEES--EEEEE--SSSSEEEEESSSS..-EEEEE-SSSTTT..TTTTTEEES----SE CS
                        PTS_EIIA_1  21 vfaekmlGdGvaiepsegkvvapvdGkvekvfptkHaigiktddg..vevlihiGidtvk..lkgegFellvkegdk 93 
                                       vf ek+  + + ++ ++++ v  +   +  + +   ai++++++   vev   +G   +k  l g++ ++lvkegdk
  gi|488601570|ref|YP_007908041.1|  15 VFVEKLDDNVYKVQINDKTAVVSIRDDIIEF-KDSEAIVVREEKArsVEVKKDVGRREIKsmLPGTVMKILVKEGDK 90 
                                       5666666666666666554444444444444.446788887765422666667787766522599************ PP

                                       E-SEEEEEEE-HHHHGGGS CS
                        PTS_EIIA_1  94 Vkagdklvevdleaikkag 112
                                       V+ag++++ ++  +++++ 
  gi|488601570|ref|YP_007908041.1|  91 VNAGNTVLILEAMKMENEI 109
                                       *******999988888765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.031
                                       EES----SEE-SEEEEEE CS
                        PTS_EIIA_1  85 ellvkegdkVkagdklve 102
                                       e+ vk+gd+V +gd lv 
  gi|488601570|ref|YP_007908041.1| 119 EIRVKSGDRVDTGDVLVV 136
                                       7889**********9985 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0063         8      52      69 ..      80      97 ..      25      97 .. 0.75
   2 !   16.9   0.1   4.1e-06    0.0053      14      69 ..      70     134 ..      56     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0063
                                      ESEESS-TTEEE-TTCEE CS
                     Peptidase_M23 52 lskisvkegqkVkaGqvI 69
                                      + ki vkeg+kV+aG+++
  gi|488601570|ref|YP_007908041.1| 80 VMKILVKEGDKVNAGNTV 97
                                      56789*********9875 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.1e-06
                                       -EEEESSSEEE....EEEEEETTTEEEEEEEE....CTCEEEEEEE.ESEESS-TTEEE-TTCEE CS
                     Peptidase_M23  14 tpVlAaadGtV....vfagkkegyGnvviidh....gdgystlyah.lskisvkegqkVkaGqvI 69 
                                        +++++  GtV    v+ g+k ++Gn+v+i      ++++++ +   +++i+vk g++V++G+v+
  gi|488601570|ref|YP_007908041.1|  70 REIKSMLPGTVmkilVKEGDKVNAGNTVLILEamkmENEITSPFDGiVKEIRVKSGDRVDTGDVL 134
                                       379********6654455555588****999955555666666666567799**********986 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 !    5.6   0.0    0.0098        13      36      53 ..      83     100 ..      74     111 .. 0.85
   2 !    8.1   0.2    0.0016       2.1      36      53 ..     120     137 ..     115     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0098
                                       ES--TT-EEBTTSEEEEE CS
                            PYNP_C  36 lhkklGdkVkkGeplati 53 
                                       + +k GdkV++G +++ +
  gi|488601570|ref|YP_007908041.1|  83 ILVKEGDKVNAGNTVLIL 100
                                       67899********99876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                                       ES--TT-EEBTTSEEEEE CS
                            PYNP_C  36 lhkklGdkVkkGeplati 53 
                                       + +k Gd+V++G++l++i
  gi|488601570|ref|YP_007908041.1| 120 IRVKSGDRVDTGDVLVVI 137
                                       67899**********987 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 ?    9.2   4.6   0.00083       1.1      23     130 ..       9     117 ..       2     121 .. 0.79
   2 ?    8.1   0.1    0.0019       2.4      87     111 ..     112     136 ..     107     138 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00083
                           DUF2118  23 eeeevekfadkveekklkgkvvYeelldeivdvleekvtrdviivlpderklillkk..Gdklklipvegvkvtliv 97 
                                       + ee   f +k++++  k +   ++++ +i d + e    + i+v +++ + + +kk  G +  +  + g +  + v
  gi|488601570|ref|YP_007908041.1|   9 DDEEFDVFVEKLDDNVYKVQINDKTAVVSIRDDIIEFKDSEAIVVREEKARSVEVKKdvGRREIKSMLPGTVMKILV 85 
                                       567788888899988888777778888889886666666777777788888888888557776677789******** PP

                           DUF2118  98 dvGdrveegdtlaavttrkgevrylrapvegvV 130
                                       ++Gd+v+ g+t+  + + k e   + +p +g+V
  gi|488601570|ref|YP_007908041.1|  86 KEGDKVNAGNTVLILEAMKME-NEITSPFDGIV 117
                                       ***********9999999998.46778888887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0019
                           DUF2118  87 pvegvkvtlivdvGdrveegdtlaa 111
                                       p +g+++ + v+ Gdrv +gd+l  
  gi|488601570|ref|YP_007908041.1| 112 PFDGIVKEIRVKSGDRVDTGDVLVV 136
                                       67899****************9965 PP

>> DUF695  Family of unknown function (DUF695)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.15       5      34 ..      24      53 ..      23      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            DUF695  5 vyranlddkpaiirvnldlaefapsekykh 34
                                      vy  +++dk+a++++++d+ ef++se   +
  gi|488601570|ref|YP_007908041.1| 24 VYKVQINDKTAVVSIRDDIIEFKDSEAIVV 53
                                      799*********************998755 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.91   1.2e+03      22      52 ..       3      37 ..       2      44 .. 0.69
   2 ?    7.2   0.0    0.0036       4.6      31      58 ..      71      98 ..      55     102 .. 0.79
   3 ?    2.8   0.1     0.083   1.1e+02      36      59 ..     113     136 ..      98     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.91
                                      T--CCCEEE...ECTCCGTTBEEEECS-TTSEE.C CS
                             PASTA 22 Glkiktvee...tsddvpeGtVisQsPeaGtev.s 52
                                      G+ki ++ e   + +++ ++ V+++ ++  t v s
  gi|488601570|ref|YP_007908041.1|  3 GFKIAIDDEefdVFVEKLDDNVYKVQINDKTAVvS 37
                                      78888888877777777777788877777666645 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0036
                                      ECTCCGTTBEEEECS-TTSEECTTS-EE CS
                             PASTA 31 tsddvpeGtVisQsPeaGtevskgskvt 58
                                      + ++  +GtV +  +++G +v++g +v 
  gi|488601570|ref|YP_007908041.1| 71 EIKSMLPGTVMKILVKEGDKVNAGNTVL 98
                                      5567789****************99985 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.083
                                       GTTBEEEECS-TTSEECTTS-EEE CS
                             PASTA  36 peGtVisQsPeaGtevskgskvtl 59 
                                        +G V +  +++G +v+ g+ +++
  gi|488601570|ref|YP_007908041.1| 113 FDGIVKEIRVKSGDRVDTGDVLVV 136
                                       4788999999******99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); 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:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.46u 0.34s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 881.90
//
Query:       gi|488601571|ref|YP_007908042.1|  [L=369]
Description: sodium ion-translocating decarboxylase, beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-157  523.0  32.4   3.5e-157  522.8  32.4    1.0  1  OAD_beta  Na+-transporting oxaloacetate decarboxylase beta su


Domain annotation for each model (and alignments):
>> OAD_beta  Na+-transporting oxaloacetate decarboxylase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  522.8  32.4    2e-161  3.5e-157       2     348 ..      16     367 ..      15     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 522.8 bits;  conditional E-value: 2e-161
                          OAD_beta   2 nlvmiliglvllyLaikkkleplllvpigfgallvNlpeaglle.....gllellyegavksellplliFlgiGalt 73 
                                       n+v+iligl+l+yL+ikk++eplllvpig+ga+l+N+p+ g+++     g+l ++ +  +++e++plliFlgiGalt
  gi|488601571|ref|YP_007908042.1|  16 NAVLILIGLALIYLGIKKEMEPLLLVPIGIGAILANIPKGGIADiegygGILGIFLKYLISTEIVPLLIFLGIGALT 92 
                                       689************************************9999899999**************************** PP

                          OAD_beta  74 DfgpllanpkslllgaaaqlGifvtllvalllgftlkeaasigiiGgaDGptaifvasklapellgaiavaaYsYma 150
                                       Dfgpl+anpk++llgaaaq+Gif+++++a+ll+ft++e+asigiiGgaDGpt+i++++ lap++l+a a+aaYsYm+
  gi|488601571|ref|YP_007908042.1|  93 DFGPLIANPKTFLLGAAAQIGIFCAFIMAMLLNFTPQESASIGIIGGADGPTTIYTTTILAPHMLAATAIAAYSYMS 169
                                       ***************************************************************************** PP

                          OAD_beta 151 LvpiiqppiikllttkkerkikmeklrkvskkekilfpivvtivvallvpsaapLigmlmlGnllresgvverlskt 227
                                       Lvp+iqppiik+lttk+er+i+m++lrkvs++eki+fpi+++i+++llvp+a+pLigmlm Gn++resgv+erl+k 
  gi|488601571|ref|YP_007908042.1| 170 LVPLIQPPIIKALTTKEERRIRMKTLRKVSRTEKIIFPIATMIITGLLVPAALPLIGMLMAGNIFRESGVTERLAKG 246
                                       ***************************************************************************** PP

                          OAD_beta 228 aqnellnivtillgltvgatmeaekflkletllilvlGlvafvlstagGvllaklmnllskkkiNPliGaaGvsavP 304
                                       a++ellni+ti+lgltvg+tm+ae+fl+++t+lil+lG++af+++tagGvllaklmnl+ k+k+NP+iGaaGvsavP
  gi|488601571|ref|YP_007908042.1| 247 ASEELLNIMTIILGLTVGSTMKAESFLTVKTILILLLGVFAFATATAGGVLLAKLMNLFVKEKVNPMIGAAGVSAVP 323
                                       ***************************************************************************** PP

                          OAD_beta 305 maarvvqkvgqkedpsnflLmhamgpnvaGvigsavaagvllal 348
                                       m+arvvqk++++ed++n+lLmhamgpnvaGvigsa aag+l++l
  gi|488601571|ref|YP_007908042.1| 324 MSARVVQKLALEEDKENHLLMHAMGPNVAGVIGSATAAGILIHL 367
                                       *****************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); 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: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2244.44
//
Query:       gi|488601572|ref|YP_007908043.1|  [L=213]
Description: hypothetical protein Asulf_02091 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   0.5    6.1e-18   65.1   0.5    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 !   65.1   0.5   3.4e-22   6.1e-18      72     208 ..      54     187 ..      52     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 3.4e-22
                                       EEEEES-H.HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHH CS
                       RNase_P_p30  72 lvvsdpsklqrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinysp 148
                                       ++++d ++l++  + ++k  ++av+  +  ++r a++  +vD+i   +      +++   +++++e++va+Ei    
  gi|488601572|ref|YP_007908043.1|  54 IECDDTNSLKKELRKASKSWIVAVKSNNVSVIREAISRKKVDLIVDSFH-----VMDYISLKLCAEKNVAVEIPMYR 125
                                       78999999955556666667************************88885.....5999******************* PP

                                       HHHS-HHHHHHHHHHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHH CS
                       RNase_P_p30 149 llrdsglaRrnfisnarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedra 208
                                        ++++g++R+++i+ + ++++++++  +++v+SSgA    e+R+++++ ++ + +G +++r+
  gi|488601572|ref|YP_007908043.1| 126 FIHSRGYRRARLIESMINVIKIAKKhsTNLVLSSGAGEFCEMRHIKQLKTFFTYFGADFSRS 187
                                       ********************************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 1259.84
//
Query:       gi|488601573|ref|YP_007908044.1|  [L=147]
Description: putative exosome subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-36  122.7   0.0    1.1e-35  122.5   0.0    1.1  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.5   0.0     6e-40   1.1e-35       2     118 ..       9     124 ..       8     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 6e-40
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHHHH CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeeikeLl 77 
                                       i + a vh+TEd ekV+ a+snl+p e +ei+ ++aeGh+gnp+ +le+e+++k++ k+++++++++l +++ ++Ll
  gi|488601573|ref|YP_007908044.1|   9 IGFYATVHSTEDHEKVAYAISNLIPFE-FEIQASDAEGHFGNPMMFLEVEIKNKRKiKELWNYIMDRLGDQK-EYLL 83 
                                       67889********************88.89**************************************9886.**** PP

                                       HCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEE CS
                       RNA_binding  78 keleervdekgklylrldKQaaylgklslvegddvIkvkik 118
                                       +el+ r+d++g+ly+r+dKQaa+l++++l  ++d I +k k
  gi|488601573|ref|YP_007908044.1|  84 DELDLRIDDDGTLYMRFDKQAAFLDEVKLIPRGDGIIMKTK 124
                                       ************************************99977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 902.73
//
Query:       gi|488601574|ref|YP_007908045.1|  [L=191]
Description: LSU ribosomal protein L15E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-82  276.5  10.8    1.2e-82  276.3  10.8    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 !  276.3  10.8   6.6e-87   1.2e-82       1     191 []       3     188 ..       3     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 276.3 bits;  conditional E-value: 6.6e-87
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++y+y+re+wk+++ ++++el+++rl+++r++pavvrverptrldrAr+LGYkak+Gi+vvrvrvrrGgr+   +++
  gi|488601574|ref|YP_007908045.1|   3 SCYAYIREAWKNPKGSYVAELMWVRLQKWRRDPAVVRVERPTRLDRARTLGYKAKRGIIVVRVRVRRGGRHI--TRF 77 
                                       68********************************************************************99..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                       ++grk+k++ vnk +p+kslq+iaeer++rk++n++vLnSYwvgeDg+yk++EvilvD+ ++ i+ dk+++wic  +
  gi|488601574|ref|YP_007908045.1|  78 RKGRKTKNMLVNKRTPKKSLQRIAEERAARKYRNMEVLNSYWVGEDGKYKWFEVILVDRDSPDIKADKDLSWIC--R 152
                                       **************************************************************************..5 PP

                                       GTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-TGGG CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkglkgaekirgsrran 191
                                       +k+R++rGltsagkk+RGlr++g +gaek+r+s ran
  gi|488601574|ref|YP_007908045.1| 153 QKGRAFRGLTSAGKKGRGLRNRG-RGAEKVRPSLRAN 188
                                       79*********************.**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1231.11
//
Query:       gi|488601575|ref|YP_007908046.1|  [L=254]
Description: Exodeoxyribonuclease III [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-24   87.4   0.1    1.2e-24   87.1   0.1    1.1  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
  ------ inclusion threshold ------
      0.032   14.1   0.2       0.11   12.3   0.1    1.9  2  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 !   87.1   0.1   1.4e-28   1.2e-24       1     233 []       5     245 ..       5     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.4e-28
                                       EEEEESTGCHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCHECSSSTTSSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos   1 ltwNvngqaspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllalggflgasstsptgggggggnggav 77 
                                       +t+Nvn+  ++      r   +  +++++++D+l+LQE++  + ++++    + g++        + g +g+ng+a+
  gi|488601575|ref|YP_007908046.1|   5 ATFNVNSI-RS------RLHIVIPWIREHKPDILCLQETKVADKNFPESEFHRIGYHVV------FSGSKGRNGVAI 68 
                                       7******8.44......7999**********************9887777766444444......4678******** PP

                                       EECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE..CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  78 lsrfpltslfrrtfiefndlvaalrreplaakleqlni..ashrdhdlvrdlqllalllqvealnadrgapvivaGD 152
                                       +s+  + ++  ++  + nd++  lr   ++ ++ + +    ++ d +  r    ++   ++   n++ + +++++GD
  gi|488601575|ref|YP_007908046.1|  69 VSKKEPEEF--DSGLDGNDRDRLLRAVIDGITVINIYApqGQSLDSPMFRYKLDWYKRFKNYLENLNLSNHILICGD 143
                                       ******999..44444444444444444444444444489999********************************** PP

                                       -SSSTSGGGBSCGHHHHHHCTTTH..........H..............SSCESCETTTTTTTTTTTEB-BEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..........x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 153 fNarpsdddsrvlrtrglalapap..........v..............glyllgggptptyvtraggsrlDrilas 205
                                       fN++p + d++++    ++ +             +                y+++  ++ ++v ++ g+r+D+ila+
  gi|488601575|ref|YP_007908046.1| 144 FNVAPEEIDVHNPKRLKNHVCFHEdvrkafkeilSlgfvdifrkhhpddRQYTFFDYRVRNAVEKGLGWRVDHILAT 220
                                       ************99999998888887777666550566778899999****************************** PP

                                       CHHHCCEEEEEEECCHHEECTSSCSSSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 206 palalfrsgvlppplalvrrealtlSDH 233
                                        +la +++  +++  ++ r   +++SDH
  gi|488601575|ref|YP_007908046.1| 221 ESLAERSVDCYIDMNSRLR---EKPSDH 245
                                       *999999999999988887...8****9 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.2e-05      0.11       1      41 [.      97     146 ..      97     162 .. 0.75
   2 ?   -1.7   0.0      0.28   2.5e+03      25     115 ..     238     245 ..     211     252 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                   Exo_endo_phos_2   1 lliisvYippsd............elenlestlekllselksp.kiiilGDfNa 41 
                                       +++i++Y p+ +            + +     ++++l++l+ + +i+i+GDfN+
  gi|488601575|ref|YP_007908046.1|  97 ITVINIYAPQGQsldspmfrykldWYK----RFKNYLENLNLSnHILICGDFNV 146
                                       578999999999999998875444444....45555555555558********7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                   Exo_endo_phos_2  25 lselkspkiiilGDfNakhplWgsedtdssargeeLiefleehslsllnllksgptfkssngsstiDltltsdnlal 101
                                       l+                                                                           
  gi|488601575|ref|YP_007908046.1| 238 LR--------------------------------------------------------------------------- 239
                                       22........................................................................... PP

                   Exo_endo_phos_2 102 skleleeedlgSDH 115
                                               +  SDH
  gi|488601575|ref|YP_007908046.1| 240 --------EKPSDH 245
                                       ........223333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.31s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1646.22
//
Query:       gi|488601576|ref|YP_007908047.1|  [L=566]
Description: glycyl-tRNA synthetase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   85.1   0.1    8.1e-24   83.6   0.1    1.9  1  HGTP_anticodon   Anticodon binding domain
    3.1e-09   37.0   1.1    1.7e-08   34.6   0.1    2.5  3  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
  ------ inclusion threshold ------
       0.18   11.6   0.1       0.46   10.3   0.1    1.6  1  Glutaredoxin2_C  Glutaredoxin 2, C terminal domain


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.1   1.3e-27   8.1e-24       1      93 [.     459     549 ..     459     550 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1.3e-27
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       qv+v+pl + +e ++  a++l ++L++agi +e d +++sig+++r++d++g+pf+v+++ +++e+ t+t+rdrdt+
  gi|488601576|ref|YP_007908047.1| 459 QVAVLPLLS-REPFTSKAEELTAKLKEAGIFTEKD-DSGSIGRRYRRYDEIGTPFCVTIDHQTFEDSTITIRDRDTT 533
                                       8********.666*****************99997.79*************************************** PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                       +q+rv++++lv++lke
  gi|488601576|ref|YP_007908047.1| 534 KQIRVEVEKLVDVLKE 549
                                       **************98 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.1   6.7e+03     130     149 ..      87     106 ..      38     120 .. 0.59
   2 !   34.6   0.1   2.9e-12   1.7e-08      12      78 ..     153     220 ..     147     256 .. 0.79
   3 ?    0.0   0.0      0.12   7.2e+02      57      89 ..     323     356 ..     315     506 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.1
                                       EEEEEEEEETHHHHHTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 130 eigtiqklgtrlserlgatv 149
                                       ++g i+  + +  e+lg+++
  gi|488601576|ref|YP_007908047.1|  87 NCGKIFRADHYIKEKLGIEA 106
                                       34455555445555555544 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 2.9e-12
                                       EE-SSSHHHHHHHHHHHEE..EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHH CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  12 iLkPtneetfvelirdevl..rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasldd 78 
                                       +L+P+  +++   ++      r+k LP+ + qi++ yR+E s  +G++R+reF+q + + f+++++ + 
  gi|488601576|ref|YP_007908047.1| 153 YLRPETAQGMFINFKRLADyfRNK-LPFGVCQIGRAYRNEISPRQGVIRLREFNQAELEYFVHPKEKKH 220
                                       789988888776666443343555.****************9566*****************9654443 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.12
                                       TB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  57 lRvreFhqkdgyvfha.easlddslrdlikaisr 89 
                                        R r + ++d  vf+  ++ ++ ++r li  +++
  gi|488601576|ref|YP_007908047.1| 323 SRHRRYSKEDLSVFVYyDEPVKVKVRRLIPNMKK 356
                                       5667777777777766556666666655555544 PP

>> Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   7.7e-05      0.46       9      65 ..     184     239 ..     181     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.7e-05
                   Glutaredoxin2_C   9 vsellkrLllPRfvkaplpEFatqsAreyftkkkeksigdfeellaktpeliaelna 65 
                                       +++++++ + PR   + l EF++++  eyf++ kek+  df++  + t +l+ ++++
  gi|488601576|ref|YP_007908047.1| 184 IGRAYRNEISPRQGVIRLREFNQAE-LEYFVHPKEKKHPDFDKYRNFTVTLVDKFDQ 239
                                       5566777789***********9776.89***************99999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3666.25
//
Query:       gi|488601577|ref|YP_007908048.1|  [L=310]
Description: nucleoside ABC transporter membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  128.5  30.8    3.2e-37  128.2  30.8    1.1  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
      0.036   14.4   0.8      0.085   13.2   0.8    1.5  1  Corona_3      Coronavirus ORF3 protein
        3.1    7.4  11.5       0.29   10.8   1.1    2.9  3  PRA1          PRA1 family protein


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2  30.8   5.3e-41   3.2e-37       2     268 .]      11     283 ..      10     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 5.3e-41
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       i+  ++ +++l++a lG  ++  ++Gv+nlg +g+m++Ga++ ++++   ++ ++l++l++ l+g++++ + ++ ++
  gi|488601577|ref|YP_007908048.1|  11 IAASMRAGTPLLFATLGEIITE-RSGVLNLGLEGIMIMGAMTGFYVSLVTGN-PWLGILIGGLAGLLLAIIHAFFTV 85 
                                       66789999**************.****************************9.************************ PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagal.lsflsaviv......llalllvlavlll 148
                                        lkvd+ +++l+l+++ +glt  +l  ++  v ++++  +++++++ + +++l+ +++      +l ++lv +++++
  gi|488601577|ref|YP_007908048.1|  86 TLKVDQAVTGLMLVLLGLGLTG-FL--GKDFVGTVAEYITPMEIPYLSdIPYLGTALFshdpfvYLGIALVPVIWFI 159
                                       *********************9.33..3334444444444444444331334444444577777************* PP

                      BPD_transp_2 149 lrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGg 224
                                       +++tr+G+ l+avgen+eaa+ +Gi+v+rv++++++i+g+l g+aGa l+l ++ +++     g g+  +a v+  g
  gi|488601577|ref|YP_007908048.1| 160 MNKTRYGMELFAVGENPEAADTMGIPVDRVRFIAVLIGGFLVGVAGAYLSLAYAKVWTeGLTAGRGWICLALVIFSG 236
                                       ***************************************************************************** PP

                      BPD_transp_2 225 agsllgtviGaliigvvksllltllgi.....ptelarvllgallilvl 268
                                       + ++  +++Ga+++g ++  l++ l++     +  + r++ ++  ilvl
  gi|488601577|ref|YP_007908048.1| 237 W-TPHRAIFGAYLFGGLDV-LSFKLQAlglgvSYHFMRMVPYVFTILVL 283
                                       *.*****************.55555555777766666777776666664 PP

>> Corona_3  Coronavirus ORF3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.8   1.4e-05     0.085      20      51 ..      80     112 ..      73     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                          Corona_3  20 rayfavtlkvef.ktGkllvciGfGdtlleakd 51 
                                        a+f+vtlkv+   tG +lv +G+G t +  kd
  gi|488601577|ref|YP_007908048.1|  80 HAFFTVTLKVDQaVTGLMLVLLGLGLTGFLGKD 112
                                       69********86269**********98766665 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.1   4.8e-05      0.29      92     134 ..      33      85 ..       4      92 .. 0.73
   2 ?    3.1   0.1     0.011        66      56     117 ..     142     212 ..     133     222 .. 0.69
   3 ?   -1.1   0.6      0.22   1.3e+03      84      97 ..     264     278 ..     226     294 .. 0.42

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.8e-05
                              PRA1  92 r..........vvlivllvvsvlllfltgavlvllwalliglllvllHAsfrk 134
                                       r          +++++ ++  ++ l++ +++l +l++ l+glll ++HA f +
  gi|488601577|ref|YP_007908048.1|  33 RsgvlnlglegIMIMGAMTGFYVSLVTGNPWLGILIGGLAGLLLAIIHAFFTV 85 
                                       34555555544566677778888888889********************9976 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.011
                              PRA1  56 tnplslivllllvlawlflyflr..seplvl.fgrelsdr......vvlivllvvsvlllfltgavlvllw 117
                                         p+  + ++l+ ++w++++++r   e + +  ++e +d        v ++ +++  +l+ ++ga+l l +
  gi|488601577|ref|YP_007908048.1| 142 HDPFVYLGIALVPVIWFIMNKTRygMELFAVgENPEAADTmgipvdRVRFIAVLIGGFLVGVAGAYLSLAY 212
                                       468888889999999****9999954444453334444547888886666666666777777777766655 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.22
                              PRA1  84 l.fgrelsdrvvliv 97 
                                       l +++++ ++v +++
  gi|488601577|ref|YP_007908048.1| 264 LgVSYHFMRMVPYVF 278
                                       223444433322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2004.46
//
Query:       gi|488601578|ref|YP_007908049.1|  [L=351]
Description: nucleoside ABC transporter membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-38  132.4  32.8    1.7e-38  132.4  32.8    1.4  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
      0.081   13.4   0.5      0.081   13.4   0.5    4.0  5  Sigma_M_inh   Sigma-M inhibitor


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2      0.46   4.1e+03     231     246 ..      21      36 ..      16      50 .. 0.53
   2 !  132.4  32.8   1.9e-42   1.7e-38       4     267 ..      60     334 ..      57     335 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.46
                      BPD_transp_2 231 tviGaliigvvkslll 246
                                        ++++l ++ v   ++
  gi|488601578|ref|YP_007908049.1|  21 SILASLFFVGVLLAII 36 
                                       4444444443333333 PP

  == domain 2  score: 132.4 bits;  conditional E-value: 1.9e-42
                      BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl.....lllallvallvgaavglllgl 75 
                                       +l +++a++++++l++++   +aG++n+g++g++ +Ga++a +++ +l+ +     ++l++++a  +g++++ + ++
  gi|488601578|ref|YP_007908049.1|  60 ELFVKTAPIILTGLAVSIPL-RAGLWNIGAEGQLYMGAFAASVIALYLPIHtsavvIPLMIIFAAFFGMVWASIPAF 135
                                       677899**************.**************************9999************************** PP

                      BPD_transp_2  76 lvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv....llalllvlavlll 148
                                       l++++ ++e+i+tlll++v+++ + +l+ g+ +g +  + +   l+ ++a+l++ ++  +    ++a++++++++ll
  gi|488601578|ref|YP_007908049.1| 136 LKAKFDLNEIISTLLLNYVAIYWVEYLVYGPMKGKYVYNFPYSDLFGDYAILPRFFGTRFhlgvIIAFVVAILIYLL 212
                                       ********************************************************99999**************** PP

                      BPD_transp_2 149 lrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGg 224
                                       + +t++G+ +r  g+n++ a+++Gi+  +v + t++++g++AglaG++ +  l+     n+++g+g+++i +++l+ 
  gi|488601578|ref|YP_007908049.1| 213 MMKTSYGFSVRIFGSNPRSAEYAGIKRSWVVVSTMLLAGMIAGLAGMIEVSGLHMRLRaNVSPGYGYTGIPVALLAR 289
                                       *****************************************************999888****************** PP

                      BPD_transp_2 225 agsllgtviGaliigvvksllltllgi....ptelarvllgallilv 267
                                         ++l +++ a+++g ++  ++++++     p +  +v++ ++++++
  gi|488601578|ref|YP_007908049.1| 290 G-NPLFVILSAFLFGWLYV-GGSAMQTtfgiPVAIVDVFQALVVLFI 334
                                       9.*****************.666666668889*********999987 PP

>> Sigma_M_inh  Sigma-M inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5     9e-06     0.081      11      65 ..      12      68 ..       3      86 .. 0.80
   2 ?   -3.1   0.2       1.2   1.1e+04      22      28 ..     145     151 ..     117     164 .. 0.53
   3 ?   -1.0   0.2      0.27   2.4e+03      69      85 ..     196     212 ..     184     220 .. 0.77
   4 ?   -0.5   0.1       0.2   1.8e+03      14      36 ..     240     262 ..     236     288 .. 0.81
   5 ?    0.9   0.2     0.069   6.2e+02      12      33 ..     301     323 ..     292     338 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9e-06
                       Sigma_M_inh 11 nvfgwvsvgtavlslllln..lailsdviaysykmlpfamaavplgvvelfikkgrt 65
                                       ++ +++ g+ + sl+ +   lai+    + +y  + +   a  +gv elf+k    
  gi|488601578|ref|YP_007908049.1| 12 RIYLYITAGSILASLFFVGvlLAIIGVNPVDAYSTMMYRAFATKFGVTELFVKTAPI 68
                                      6788999***999*99864338999988888888888999999*********98654 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                       Sigma_M_inh  22 vlsllll 28 
                                       ++s lll
  gi|488601578|ref|YP_007908049.1| 145 IISTLLL 151
                                       3333333 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.27
                       Sigma_M_inh  69 llgvvlnlfvlvcvyti 85 
                                        lgv++ ++v + +y +
  gi|488601578|ref|YP_007908049.1| 196 HLGVIIAFVVAILIYLL 212
                                       48889888888888865 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.2
                       Sigma_M_inh  14 gwvsvgtavlsllllnlailsdv 36 
                                        wv v t +l+ ++  la + +v
  gi|488601578|ref|YP_007908049.1| 240 SWVVVSTMLLAGMIAGLAGMIEV 262
                                       59999999999888888866655 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.069
                       Sigma_M_inh  12 vfgwvsvg.tavlsllllnlail 33 
                                       +fgw+ vg +a+ + + + +ai+
  gi|488601578|ref|YP_007908049.1| 301 LFGWLYVGgSAMQTTFGIPVAIV 323
                                       68888886245556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1987.10
//
Query:       gi|488601579|ref|YP_007908050.1|  [L=502]
Description: nucleoside ABC transporter ATP-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-51  174.7   0.1    1.9e-32  112.6   0.0    2.3  2  ABC_tran      ABC transporter
    3.2e-08   33.7   1.3     0.0015   18.4   0.1    2.4  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0077   16.7   0.1      0.015   15.8   0.1    1.7  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.029   14.3   2.6       0.21   11.5   0.1    3.2  3  GTP_EFTU_D4   Elongation factor Tu domain 4
      0.035   13.8   0.0       0.13   12.0   0.0    2.0  1  AAA_29        P-loop containing region of AAA domain
      0.057   13.8   0.3       0.61   10.5   0.1    2.6  2  Ribosomal_L5  Ribosomal protein L5
      0.072   12.5   0.0       0.91    8.9   0.0    2.4  1  SMC_N         RecF/RecN/SMC N terminal domain
       0.16   11.7   0.1        2.2    8.0   0.0    2.5  3  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 !  112.6   0.0   8.5e-36   1.9e-32       2     137 .]      22     170 ..      21     170 .. 0.97
   2 !   60.0   0.0   1.5e-19   3.5e-16       1     136 [.     274     428 ..     274     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 8.5e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++v+lk+++ge+++++GenGaGK+tL+++l+gl+kp++Gei +d +k + + ++   ++ ig+++q+ +l +++t+ 
  gi|488601579|ref|YP_007908050.1|  22 DRVNLKVRKGEIHGLLGENGAGKTTLMSILYGLYKPDSGEIIFDgKKRVFNSPKDAIEAGIGMVHQHFKLVNKMTAL 98 
                                       689*****************************************77777779************************* PP

                                       HH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +n                +++e+i+++++k +++ + d++v     ++S G+ qrv++ ++l+++ kll+lDEpt+
  gi|488601579|ref|YP_007908050.1|  99 DNiilgyktpndplvdygWARERIKEIMEKSKIDVDLDEIV----VNMSVGEEQRVEILKSLMRDVKLLILDEPTS 170
                                       *****************************************....*****************************96 PP

  == domain 2  score: 60.0 bits;  conditional E-value: 1.5e-19
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpe 73 
                                       lk ++l+++ege+++i G +G G   L +++ g  + + G i +dgk +++    e+ +  i+++p++   + l   
  gi|488601579|ref|YP_007908050.1| 274 LKGINLSVREGEILGIAGVSGNGQRELEEIIVGVRDIERGAIYFDGKRIDSaGVYERIQLGISCIPEDrinSGLALS 350
                                       789***********************************************98899*************999999999 PP

                                       SBHHHH..................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                       xxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                       lt+++n                  + ++++e++++++++k      v+  +s+LSgG  qr+ +ar + ++p+ll++
  gi|488601579|ref|YP_007908050.1| 351 LTIADNlvlrdyrkfcrkgiidfsNIEAHAERLVKEYDIKT---PSVHALASTLSGGNMQRLIIAREFSRNPRLLIA 424
                                       9*********9999999999877777777777777777666...4455568*************************9 PP

                                       ESTT CS
                                       xxxx RF
                          ABC_tran 133 DEpt 136
                                         pt
  gi|488601579|ref|YP_007908050.1| 425 SQPT 428
                                       8887 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   6.8e-07    0.0015       2      57 ..      34      77 ..      33      88 .. 0.67
   2 !   13.8   0.1   1.7e-05     0.038     244     297 ..     150     199 ..     117     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.8e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeip 57
                                       +l G Ng+GK++L+ +l++l              +++g+i+ + ++  +++p+ +
  gi|488601579|ref|YP_007908050.1| 34 HGLLGENGAGKTTLMSILYGLYK------------PDSGEIIFDGKKRVFNSPKDA 77
                                      689******************64............444444444444444444444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.7e-05
                            AAA_21 244 llalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +  +l +l r+    +ll++DEp + L P+ +++l+  lk+ +++g  v++ TH
  gi|488601579|ref|YP_007908050.1| 150 V-EILKSLMRDV---KLLILDEPTSVLTPSETEKLFVALKSMKEKGLTVLFITH 199
                                       4.6777788877...99************************************* 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   6.6e-06     0.015      22      64 ..      34      69 ..       6     248 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.6e-06
                            AAA_23 22 tlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve 64
                                        + G+NGaGKTT++  i ++Ly   ++      + +++++ +
  gi|488601579|ref|YP_007908050.1| 34 HGLLGENGAGKTTLM-SILYGLYKPDSG------EIIFDGKKR 69
                                      5689*********98.588999874332......223333333 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   9.4e-05      0.21      38      79 ..     214     257 ..     206     264 .. 0.87
   2 ?    1.2   0.1      0.16   3.5e+02      13      41 ..     297     326 ..     288     360 .. 0.81
   3 ?   -2.4   0.1       2.1   4.7e+03      56      56 ..     459     459 ..     433     483 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.4e-05
                                       ETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-..TTTS- CS
                       GTP_EFTU_D4  38 kedGrevGeilqiqdkgkkleeakaGqevaisiegki..vGrqi 79 
                                        ++Gr+vG+i+  ++++k+l ++  G+e+ +  + ++   Gr++
  gi|488601579|ref|YP_007908050.1| 214 LRKGRNVGTIVTSETNEKELAKMMVGREIKMEFRKSVrnYGRDV 257
                                       469****************************9999987667765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.16
                                       EETCCCEEEEEE.EEEEEEETT-EEEETTE CS
                       GTP_EFTU_D4  13 frrsdpaivGve.vlgGvikpgvklikedG 41 
                                        r+ +++ivGv+ +  G i+ + k i++ G
  gi|488601579|ref|YP_007908050.1| 297 QRELEEIIVGVRdIERGAIYFDGKRIDSAG 326
                                       578899*****6588899987666666555 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.1
                                       E CS
                       GTP_EFTU_D4  56 k 56 
                                        
  gi|488601579|ref|YP_007908050.1| 459 D 459
                                       1 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.9e-05      0.13      16      39 ..      25      48 ..      18      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-05
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                       ++++  g ++ l G++G+GK+Tl+
  gi|488601579|ref|YP_007908050.1| 25 NLKVRK-GeIHGLLGENGAGKTTLM 48
                                      556664.44889************8 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00027      0.61       7      35 ..     134     161 ..     131     171 .. 0.78
   2 ?   -0.2   0.0      0.56   1.3e+03       4      23 ..     483     502 .]     481     502 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                                       EEEEEEEEEE-SSSSSCHHHHHCCHHHHC CS
                      Ribosomal_L5   7 rleKivinmgvGeagedkkllekaakeLa 35 
                                        l++iv+nm vGe  +  ++l++ +++ +
  gi|488601579|ref|YP_007908050.1| 134 DLDEIVVNMSVGEEQR-VEILKSLMRDVK 161
                                       699*********7664.478888777765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.56
                                       TS-EEEEEEEEEE-SSSSSC CS
                      Ribosomal_L5   4 qvPrleKivinmgvGeaged 23 
                                       ++P  eKi i m  Ge  ed
  gi|488601579|ref|YP_007908050.1| 483 EEPDMEKIGILMSGGEINED 502
                                       89********9999987765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00041      0.91      25     141 ..      32     146 ..      19     499 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00041
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       ++  ++G+NG+GK+ l+ +il+ L + ++ ++  +  +++ ++ k+  ++  + v+ +f+  +k   +  +++ +  
  gi|488601579|ref|YP_007908050.1|  32 EIHGLLGENGAGKTTLM-SILYGLYKPDSGEIIFDGKKRVFNSPKDAIEAGIGMVHQHFKLVNKM--TALDNIILGY 105
                                       467899********998.56688887777777777777777777777777777777777766666..3333333333 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske......lLSgGe 141
                                       +  ++        +    ++ ++e++e+++i+ +      ++S Ge
  gi|488601579|ref|YP_007908050.1| 106 KTPNDPLV-----DYGWARERIKEIMEKSKIDVDldeivvNMSVGE 146
                                       33333332.....233344455666666666666556666444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00097       2.2      19      48 ..      32      61 ..      24      72 .. 0.81
   2 ?   -0.8   0.1      0.49   1.1e+03      87     121 ..     157     196 ..     119     220 .. 0.75
   3 ?   -0.8   0.0      0.47     1e+03      52      82 ..     373     405 ..     358     423 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00097
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggr 48
                                       ++ l G  G+GKtt+++ l  +++ + g+
  gi|488601579|ref|YP_007908050.1| 32 EIHGLLGENGAGKTTLMSILYGLYKPDSGE 61
                                      477899************998888876545 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.49
                            AAA_30  87 epg.tllivDEagmv....dtkqlaallkaaekagakvil 121
                                        ++ +lli DE   v     t++l   lk+++++g +v++
  gi|488601579|ref|YP_007908050.1| 157 MRDvKLLILDEPTSVltpsETEKLFVALKSMKEKGLTVLF 196
                                       4444899999977665555555555556666666777666 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.47
                            AAA_30  52 lAptgkaAkvLaeelgieastiakllkrlk..g 82 
                                       ++  ++ A++L +e +i++ +++ l ++l   +
  gi|488601579|ref|YP_007908050.1| 373 FSNIEAHAERLVKEYDIKTPSVHALASTLSggN 405
                                       5566788999999*********99998887541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 2909.13
//
Query:       gi|488601580|ref|YP_007908051.1|  [L=198]
Description: putative phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   84.3   0.0      9e-24   83.8   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00089   18.8   0.0     0.0011   18.4   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.084   12.4   0.1       0.17   11.4   0.1    1.4  2  PRTase_2      Phosphoribosyl transferase
       0.12   11.4   0.0       0.15   11.1   0.0    1.1  1  NO_synthase   Nitric oxide synthase, oxygenase domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.0     2e-27     9e-24       9     135 ..      11     134 ..       6     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 2e-27
                                       --EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS......TT-EE-EEEEEE-TTT--EE........ CS
                      Pribosyltran   9 paildavarlaaeileeyngkpdvvvgiargGvpfakiladeL......evplayvrkvkyrpdgseeaargssdes 79 
                                         i++ +  +a++ +++ ++kpd++v++ rgG+++a i++d L       v+  y ++   r+d   ++++++    
  gi|488601580|ref|YP_007908051.1|  11 DHIYRVCFTIAKDVRKS-GFKPDAIVAVGRGGWIPARIISDFLnirelySVKAEYWDVAESRDDAVITQPINV---- 82 
                                       45556666777777777.*************************888888888889999999999999998655.... PP

                                       EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHH CS
                      Pribosyltran  80 rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdk 135
                                           d  gkkVl+VDD+ dtG+Tl+ ++ +L+++g+ e+++avl +k+++e+ +d+
  gi|488601580|ref|YP_007908051.1|  83 ----DMSGKKVLLVDDVADTGKTLNVVVSHLRKAGAREIKTAVLQYKKTSEFIPDF 134
                                       ....9*********************************************999987 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.5e-07    0.0011     105     157 ..      70     122 ..      20     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-07
                           UPRTase 105 tlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                       + +   + + +  +++ ++vll+D v  TG+++  ++++L+++g++e k  vl
  gi|488601580|ref|YP_007908051.1|  70 SRDDAVITQPINVDMSGKKVLLVDDVADTGKTLNVVVSHLRKAGAREIKTAVL 122
                                       44445666677788899*************************99988776665 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.8e-05      0.17     120     150 ..      85     115 ..      71     128 .. 0.82
   2 ?   -3.9   0.0       1.9   8.4e+03      59      69 ..     150     160 ..     148     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr 150
                                       + k+++LvDD + tGkt+  ++++l+++  r
  gi|488601580|ref|YP_007908051.1|  85 SGKKVLLVDDVADTGKTLNVVVSHLRKAGAR 115
                                       45889**************999999988666 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.9
                          PRTase_2  59 gfAEtAtaLgh 69 
                                       g+ EtA++  +
  gi|488601580|ref|YP_007908051.1| 150 GLTETAIGFLK 160
                                       78899988654 PP

>> NO_synthase  Nitric oxide synthase, oxygenase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.2e-05      0.15     260     352 ..      76     169 ..      62     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.2e-05
                                       HHHHTT--TT-GGGTHHHHHH...HHHHHHHHHHHHHCT--EE-HHHHHHHHHHHHHHHHCCT---B--HHHCS-SS CS
                       NO_synthase 260 vakklgldtskesslwkDral...velnvavlhSfqkakvtivDhhtaaesFlkfeeneeklrrevpadwvwlvppl 333
                                       +++ +++d+s ++ l  D ++     lnv v h  +ka+      +ta  +++k  e   +  +e+ ++wvw+v p 
  gi|488601580|ref|YP_007908051.1|  76 ITQPINVDMSGKKVLLVDDVAdtgKTLNVVVSHL-RKAGA--REIKTAVLQYKKTSEFIPDFSGEIFSRWVWIVYPW 149
                                       5666777777777666655442223567666664.33333..344899***************************** PP

                                       SGGGSCG.GGS--B----SS CS
                       NO_synthase 334 sgsltpv.fhqemenyilkp 352
                                       + + t + f ++++ny+ k 
  gi|488601580|ref|YP_007908051.1| 150 GLTETAIgFLKKIDNYKEKS 169
                                       99888877999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 1211.01
//
Query:       gi|488601581|ref|YP_007908052.1|  [L=105]
Description: hypothetical protein Asulf_02101 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   12.4   0.5      0.053   12.2   0.5    1.1  1  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 ?   12.2   0.5     3e-06     0.053     348     383 ..      33      68 ..       7      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-06
                               SNF 348 svlFFlmlillgldsqfgtvegiitavvDefkvllr 383
                                       sv+FF  l++l+l++ f  +e  +  +++ef++++r
  gi|488601581|ref|YP_007908052.1|  33 SVIFFAFLLTLSLGALFISMELRMKKIMEEFENTKR 68 
                                       89*****************************99554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 657.83
//
Query:       gi|488601582|ref|YP_007908053.1|  [L=337]
Description: flap endonuclease 1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-26   91.2   0.0    1.2e-25   89.7   0.0    1.8  2  XPG_I       XPG I-region
      1e-18   67.7   0.0      3e-18   66.2   0.0    1.7  2  XPG_N       XPG N-terminal domain
    1.6e-06   28.6   0.1    1.6e-06   28.6   0.1    1.9  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
     0.0049   16.9   0.1      0.017   15.2   0.0    1.9  2  HHH_2       Helix-hairpin-helix motif
  ------ inclusion threshold ------
        1.3    9.0   0.0        1.3    9.0   0.0    3.0  4  Prefoldin   Prefoldin subunit


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 !   89.7   0.0   3.4e-29   1.2e-25       2      94 .]     140     235 ..     139     235 .. 0.93
   2 ?   -3.0   0.0       2.7   9.7e+03      43      76 ..     298     330 ..     296     335 .. 0.49

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 3.4e-29
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       +mgip+++Ap+E+EAq+ay++ kg+ d++ s+D+D+llFG+pk+ rnl+ ++k+k      +++ k+e+i+l+k l+
  gi|488601582|ref|YP_007908053.1| 140 MMGIPCIDAPSEGEAQAAYITLKGDSDFTGSQDYDSLLFGSPKLARNLTiTGKRKLPgkYVYVDIKPEIINLSKNLR 216
                                       59**********************************************97555555576788999************ PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                       +l++treql+d+ail+g+D
  gi|488601582|ref|YP_007908053.1| 217 RLEITREQLVDIAILVGTD 235
                                       ******************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.7
                                       SEEEESTT.ECECTT..EEECEEEEEEHHHHHHH CS
                             XPG_I  43 pkvlrnlskkkskkkkekekkkvevidlekvlke 76 
                                       +k+++ l+ ++ + ++++++k ve+++    +++
  gi|488601582|ref|YP_007908053.1| 298 EKIVEFLC-EEHDFSRDRVEKAVEKLTAGLKTSQ 330
                                       56666666.3333333555555665555444444 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   8.3e-22     3e-18      18     100 ..      13     100 ..       6     101 .. 0.95
   2 ?   -2.7   0.0       2.3   8.2e+03      16      35 ..     111     130 ..     105     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 8.3e-22
                                       EEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHH CS
                             XPG_N  18 svsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkke 89 
                                       +v++  ++g k+ iDa   +y+fl  +r+++g+ l+      tshl gl++r+  +++ g kPi+VFdg++p++k++
  gi|488601582|ref|YP_007908053.1|  13 KVELDYFSGYKISIDAFNTIYQFLSIIRQPDGTPLKDsqgriTSHLSGLLYRTANMVEVGLKPIYVFDGQPPEFKRK 89 
                                       688999*****************************9999************************************** PP

                                       HHHHHHHHHHH CS
                             XPG_N  90 elekrserrqe 100
                                       e+e r++r+ e
  gi|488601582|ref|YP_007908053.1|  90 EIEERKKRKME 100
                                       *******9976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                                       EEEEEGGGGTTEEEEEEHHH CS
                             XPG_N  16 irsvsiealegkklaiDasl 35 
                                       +++ +++++ + +  +D ++
  gi|488601582|ref|YP_007908053.1| 111 MGEKDLKKYAQATARVDEYI 130
                                       34788889988888888776 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 ?   -3.2   0.3       3.8   1.4e+04      55      64 ..     100     109 ..      87     125 .. 0.52
   2 !   28.6   0.1   4.5e-10   1.6e-06       3      50 ..     222     267 ..     220     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.8
                        5_3_exonuc  55 klkekLeenk 64 
                                       +++ekLe ++
  gi|488601582|ref|YP_007908053.1| 100 EMEEKLEIAR 109
                                       2333333333 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 4.5e-10
                        5_3_exonuc   3 PeqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenlde 50 
                                        eq++d++ LvG   D   G++g+G+k+A +L+k+yg+ +++l+++ +
  gi|488601582|ref|YP_007908053.1| 222 REQLVDIAILVGT--DYNDGIKGVGPKKAYNLIKKYGDGDKVLKAIGK 267
                                       589*********5..56679************************8863 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.7e-06     0.017       7      43 ..     239     275 ..     237     278 .. 0.87
   2 ?   -3.2   0.0       2.6   9.4e+03      48      59 ..     297     308 ..     297     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddi 43 
                                       GI+ VG k A +L k++++ d+  ka  + + ++++i
  gi|488601582|ref|YP_007908053.1| 239 GIKGVGPKKAYNLIKKYGDGDKVLKAIGKSIENLEEI 275
                                       9***********************9977777666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.6
                             HHH_2  48 AqsivefFenek 59 
                                       A++ivef+ +e+
  gi|488601582|ref|YP_007908053.1| 297 AEKIVEFLCEEH 308
                                       899****98876 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.7      0.16   5.7e+02       9      34 ..      88     113 ..      85     133 .. 0.70
   2 ?   -2.3   0.1       1.1     4e+03      21      36 ..     207     221 ..     204     231 .. 0.49
   3 ?   -2.3   0.0       1.1     4e+03      86     101 ..     262     277 ..     259     280 .. 0.59
   4 ?    9.0   0.0   0.00036       1.3      67     116 ..     286     335 ..     283     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         Prefoldin   9 qaelaqlkeaieelektletlktlkk 34 
                                       ++e+++ k++++e e+ le+ +++ +
  gi|488601582|ref|YP_007908053.1|  88 RKEIEERKKRKMEMEEKLEIAREMGE 113
                                       67777778888888877777777666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHTT.- CS
                         Prefoldin  21 elektletlktlkked 36 
                                       e+ ++ ++l++l+  +
  gi|488601582|ref|YP_007908053.1| 207 EIINLSKNLRRLEI-T 221
                                       45555555555544.2 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHH CS
                         Prefoldin  86 leelekqlekleeele 101
                                       l+ + k++e+lee  e
  gi|488601582|ref|YP_007908053.1| 262 LKAIGKSIENLEEIRE 277
                                       5556666666666554 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00036
                                       TTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  67 agyyveksleeAiellkkkleelekqlekleeeleklkdqittleanlaq 116
                                        +y +++s+ +A+++++  +ee + +++ +e+++ekl++ ++t ++nl++
  gi|488601582|ref|YP_007908053.1| 286 DDYEIKFSKPDAEKIVEFLCEEHDFSRDRVEKAVEKLTAGLKTSQMNLSR 335
                                       689999*****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.54
# Mc/sec: 1880.23
//
Query:       gi|488601583|ref|YP_007908054.1|  [L=171]
Description: molybdopterin adenylyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-28   98.4   0.0    3.3e-28   98.2   0.0    1.1  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 !   98.2   0.0   1.8e-32   3.3e-28       2     142 ..      14     160 ..      13     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.8e-32
                                       EEEE-HHHH........TTSS....GBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS- CS
                     MoCF_biosynth   2 vitvGdell........sgki....eDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGt 66 
                                       ++tv+++++                +D +g  + e++k+l     +y++v+Dd e+ik+++ + l+e d++i+ GGt
  gi|488601583|ref|YP_007908054.1|  14 IVTVSTSRFekygnlrgI--DkipeDDGSGREIFEAFKDLAT---DYALVADDVEAIKNTVSEMLKECDAVIVNGGT 85 
                                       777777777554444331..0445578888888888887654...789*************9999************ PP

                                       SSSTT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE....TTE.EEEE-SSHHHHHHHHHHHH CS
                     MoCF_biosynth  67 GptpdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav....gkt.iigLPGspkavkealeeil 138
                                       G+ p+Dvt ea+++l+ek+++gf+e+fr +s+k+     v++ ailsra+    +++ +++LPGs +av+ +l++i 
  gi|488601583|ref|YP_007908054.1|  86 GLNPKDVTIEAIEPLLEKKIDGFGEIFRYLSYKE-----VGTSAILSRATagivNSKaVFCLPGSRNAVELGLRIIR 157
                                       *********************************9.....99*************6566**************99986 PP

                                       HGGH CS
                     MoCF_biosynth 139 lpal 142
                                        + l
  gi|488601583|ref|YP_007908054.1| 158 -ESL 160
                                       .665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.40s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 943.72
//
Query:       gi|488601584|ref|YP_007908055.1|  [L=369]
Description: ORC complex protein Cdc6/Orc1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   43.0   0.1    5.3e-10   39.9   0.1    2.3  1  AAA_16           AAA ATPase domain
    2.6e-07   31.0   0.0    5.4e-07   30.0   0.0    1.5  1  AAA_22           AAA domain
    2.7e-06   27.8   0.1    6.9e-06   26.5   0.0    1.7  2  AAA              ATPase family associated with various cellul
    0.00054   20.1   0.1     0.0012   19.0   0.1    1.6  1  TIP49_C          TIP49 AAA-lid domain
    0.00077   19.0   0.0      0.006   16.1   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0025   18.2   0.0     0.0063   16.8   0.0    2.0  1  AAA_19           AAA domain
     0.0062   16.3   0.0       0.11   12.3   0.0    2.0  2  AAA_11           AAA domain
     0.0096   15.1   0.0      0.027   13.6   0.0    1.7  2  DUF815           Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.015   15.1   0.3         12    5.5   0.0    3.1  3  IstB_IS21        IstB-like ATP binding protein
      0.015   15.6   0.2      0.052   13.9   0.0    1.9  2  AAA_assoc_2      AAA C-terminal domain
       0.02   14.9   0.2      0.059   13.4   0.2    1.8  1  Cdc6_C           CDC6, C terminal winged helix domain
      0.057   13.1   0.0      0.098   12.4   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.067   12.9   0.1        0.5   10.1   0.0    2.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.081   12.1   0.0        0.2   10.8   0.0    1.6  1  KAP_NTPase       KAP family P-loop domain
      0.091   12.2   0.0       0.96    8.8   0.0    2.3  2  TniB             Bacterial TniB protein
       0.12   12.1   0.0        0.4   10.4   0.0    1.7  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.1   4.8e-13   5.3e-10       1      74 [.      25     100 ..      25     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 4.8e-13
                            AAA_16   1 rlvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laq 74 
                                       +l+ R+ +l+++ + l+ ++r+ +p ++l+ G++G+GK+s ++ ++r+le+ ++i ++++c+ l+s+ +    + +
  gi|488601584|ref|YP_007908055.1|  25 KLYFRDSQLRRISANLKpAIRKTQPVNMLCLGPPGTGKTSAIKLIFRELEDFDVIPVYANCQLLGSKQAVFGkIFE 100
                                       699**************78888888*************************999999*******9666333222332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   4.8e-10   5.4e-07       8     135 ..      52     180 ..      45     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.8e-10
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka.erlsseellea 81 
                                       +++ G++GtGKT  ++ ++++l+        + +v+  + +++ ++s + ++ ++++al   +   ++     l++ 
  gi|488601584|ref|YP_007908055.1|  52 MLCLGPPGTGKTSAIKLIFRELE--------DFDVIpvYANCQLLGSKQAVFGKIFEALYGYKPPsYGIPFAKLYAS 120
                                       789*******************6........9999999********************9965555566777777755 PP

                            AAA_22  82 leqalraravielliiDEaqh.lrseealeeL.rsllnl....srkgvqliLvGtp.elrk 135
                                       + + + + +++ ++ +D++   l ++++++++   +l+     +  ++ +i +Gt  +l+ 
  gi|488601584|ref|YP_007908055.1| 121 ILNKVLEIDKVLVVALDDINLlL-NDTQINDVlYAILKAyeevDGVKTGVIAIGTDlKLNA 180
                                       555555555589*********55.6777776643443334445688888888888766665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   6.2e-09   6.9e-06       1     108 [.      52     174 ..      52     190 .. 0.80
   2 ?   -3.2   0.0       9.5   1.1e+04      61      64 ..     276     279 ..     247     306 .. 0.54

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.2e-09
                                       EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg...vefleisgsellsk..................yvgesekkirelfkeakek 56 
                                       +l  GppGtGKT+++k + +el+   v  +  ++  l sk                  y    +k  + +++++ e 
  gi|488601584|ref|YP_007908055.1|  52 MLCLGPPGTGKTSAIKLIFRELEdfdVIPVYANCQLLGSKqavfgkifealygykppsYGIPFAKLYASILNKVLEI 128
                                       7889*****************95533445666777777778889999999999999998888888888888887666 PP

                                       STSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEE CS
                               AAA  57 akpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskviviga 108
                                        k  ++ +D+i  l ++       + ++v+ ++l++ ++v+  +  vi ig+
  gi|488601584|ref|YP_007908055.1| 129 DKVLVVALDDINLLLNDT------QINDVLYAILKAYEEVDGVKTGVIAIGT 174
                                       6569**********9998......7788888888888888887666777665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.5
                                       EEEE CS
                               AAA  61 ilfi 64 
                                       ++++
  gi|488601584|ref|YP_007908055.1| 276 VVLL 279
                                       2322 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.1e-06    0.0012      13      61 ..     222     271 ..     208     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                           TIP49_C  13 ldeeAldlLakigtetS.LRYaiqLltpasilakkrkkkevevedveeve 61 
                                       +++  +++ a++  et+ LR  + Ll++a i a+ r+++++++edve++ 
  gi|488601584|ref|YP_007908055.1| 222 ISDAVIERVAELTYETGdLRVGLYLLKMAGISAEERGSRKISIEDVEKAF 271
                                       788889999999999977*****************************985 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.3e-06     0.006      33      70 ..      49      86 ..      25     116 .. 0.82
   2 ?   -0.4   0.1      0.62     7e+02     100     128 ..     130     158 ..     127     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                             AAA_7 33 kkpvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                        ++l+ Gp GtGKt+ ik ++++l++ +++++  n++
  gi|488601584|ref|YP_007908055.1| 49 PVNMLCLGPPGTGKTSAIKLIFRELEDFDVIPVYANCQ 86
                                      35689*********************999998888876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.62
                             AAA_7 100 kklvvFvDDlnmpakekygaqppiellRq 128
                                       k lvv +DD+n+   ++  +    ++l+ 
  gi|488601584|ref|YP_007908055.1| 130 KVLVVALDDINLLLNDTQINDVLYAILKA 158
                                       789999*****999988777766666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.7e-06    0.0063       4      42 ..      43      81 ..      41     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.7e-06
                            AAA_19  4 avealkekvllvtaGpGtGKTrvlkhivallvelggvkp 42
                                      a+++++  ++l +++pGtGKT  +k i ++l++   +++
  gi|488601584|ref|YP_007908055.1| 43 AIRKTQPVNMLCLGPPGTGKTSAIKLIFRELEDFDVIPV 81
                                      6667788899*******************9998876665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   9.6e-05      0.11      18      41 ..      48      73 ..      28     110 .. 0.73
   2 ?    2.0   0.0      0.13   1.5e+02      54     148 ..     210     305 ..     205     352 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.6e-05
                            AAA_11 18 e..itliqGPPGtgKTktivellsql 41
                                      +    l  GPPGtgKT++i  ++++l
  gi|488601584|ref|YP_007908055.1| 48 QpvNMLCLGPPGTGKTSAIKLIFREL 73
                                      24445778***********9999888 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                            AAA_11  54 kpriLvCapSNaAvDellerllr...glldsegekykpkivRvgneeeriseavksvsleekvekrlekee...kaq 124
                                       k+r Lv    N+  D ++er+++   +  d ++  y +k++ + +ee    +  +++s  e vek  +k++     +
  gi|488601584|ref|YP_007908055.1| 210 KNRCLVGFYRNVISDAVIERVAEltyETGDLRVGLYLLKMAGISAEE----RGSRKIS-IEDVEKAFSKSKvvlLKK 281
                                       67777777788889999999999655555555666777777777777....3333333.233444444443111333 PP

                            AAA_11 125 lakeiskeleklakelrafeeeee 148
                                       + + +++e++++ k++ ++++ ++
  gi|488601584|ref|YP_007908055.1| 282 CISMLNQEEREILKQIYQQDDIST 305
                                       333344444444444433333333 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   0.0   2.4e-05     0.027      29      79 ..      25      75 ..       8      97 .. 0.90
   2 ?   -2.9   0.2       2.7     3e+03      98     122 ..     121     145 ..     116     156 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                            DUF815 29 dLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyae 79
                                      +L   d+q +++ +n +  +++++  n+L  G  GtGK s +k +++e+++
  gi|488601584|ref|YP_007908055.1| 25 KLYFRDSQLRRISANLKPAIRKTQPVNMLCLGPPGTGKTSAIKLIFRELED 75
                                      5666789999**********************************9998765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.7
                            DUF815  98 lvellrerperfilfvDDLsFeeee 122
                                       +++++ e ++ +++ +DD+    ++
  gi|488601584|ref|YP_007908055.1| 121 ILNKVLEIDKVLVVALDDINLLLND 145
                                       4455555555555555555443333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.011        12      48      61 ..      50      63 ..      26      70 .. 0.84
   2 ?    5.2   0.1     0.014        15      99     139 ..     121     160 ..     113     174 .. 0.81
   3 ?   -0.2   0.0      0.62     7e+02      70      94 ..     310     334 ..     306     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                         IstB_IS21 48 enivllGpsGvGKs 61
                                       n++ lGp+G+GK+
  gi|488601584|ref|YP_007908055.1| 50 VNMLCLGPPGTGKT 63
                                      58999********9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                         IstB_IS21  99 laralkrllkvdllilDdlgllpldqaeaellfeviekrye 139
                                       + +++ ++ kv ++ lDd+ ll  d + + +l+ ++++ ye
  gi|488601584|ref|YP_007908055.1| 121 ILNKVLEIDKVLVVALDDINLLLNDTQINDVLYAILKA-YE 160
                                       555666788889999************99999999965.44 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.62
                         IstB_IS21  70 eavraglsvlfvrvedLveelkrar 94 
                                       + vr+++++ +++  +++++l+  r
  gi|488601584|ref|YP_007908055.1| 310 KKVRKDHKIGYTKFYNIISKLENLR 334
                                       6799999999999999999998655 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.6e-05     0.052       7      60 ..     222     276 ..     218     282 .. 0.82
   2 ?   -1.4   0.0       2.7     3e+03      66      74 ..     320     328 ..     284     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                                       XXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   7 leddalealaela..dGDaRkaLnlLElaaeaaeakegkieitledleealqrkal 60 
                                       ++d ++e +ael    GD R+ L lL +a  +ae+ +g+++i+ ed+e+a++++ +
  gi|488601584|ref|YP_007908055.1| 222 ISDAVIERVAELTyeTGDLRVGLYLLKMAGISAEE-RGSRKISIEDVEKAFSKSKV 276
                                       5666777777665337*************999987.9*************988765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                                       XXXHHHHHH CS
                       AAA_assoc_2  66 gdehYdliS 74 
                                         ++Y++iS
  gi|488601584|ref|YP_007908055.1| 320 YTKFYNIIS 328
                                       346899998 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   5.2e-05     0.059      36      72 ..     317     351 ..     299     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                                       ---HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEE CS
                            Cdc6_C  36 pltqrevsdllseLemlgileleksskGrregrtrki 72 
                                       ++  + +++++s+Le l++++l   ++G+  grtr i
  gi|488601584|ref|YP_007908055.1| 317 KIGYTKFYNIISKLENLRLIDLSYLKRGK--GRTRSI 351
                                       45889*****************9776765..888877 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.8e-05     0.098       5      63 ..      30      91 ..      26     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.8e-05
                                      SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS.-T CS
                   Sigma54_activat  5 sealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskrkekpfvavncaai.pe 63
                                      +++l+++ +++k +++++  +++l +G  GtGK+   ++i+++ +  +   v  nc  + ++
  gi|488601584|ref|YP_007908055.1| 30 DSQLRRISANLKPAIRKTqpVNMLCLGPPGTGKTSAIKLIFRELEDFDVIPVYANCQLLgSK 91
                                      56677777777777755445999********************9999999999999865333 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 ?   10.1   0.0   0.00045       0.5      29      58 ..      45      74 ..      26      79 .. 0.80
   2 ?   -0.1   0.2       0.6   6.7e+02      82     112 ..     128     160 ..     114     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00045
                            RuvB_N 29 reealdhvllyGpPGlGkttlakiiakelg 58
                                      r+++   +l  GpPG Gkt+  k+i +el+
  gi|488601584|ref|YP_007908055.1| 45 RKTQPVNMLCLGPPGTGKTSAIKLIFRELE 74
                                      55555678999*************999986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.6
                            RuvB_N  82 leekdvlfideihrl..sraveevlysamedfr 112
                                       +++  v+ +d+i  l  ++++++vly+ +  ++
  gi|488601584|ref|YP_007908055.1| 128 IDKVLVVALDDINLLlnDTQINDVLYAILKAYE 160
                                       333335567888877333578899998887775 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018       0.2      28     101 ..      57     126 ..      34     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                        KAP_NTPase  28 kWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkllrakklkal 101
                                       + G+GK+s ++++ +el++f    +++ +++n  +  ++++++ ++++aL+   + +yg+   kl++    k l
  gi|488601584|ref|YP_007908055.1|  57 PPGTGKTSAIKLIFRELEDF----DVIPVYANCQLLGSKQAVFGKIFEALYGYKPPSYGIPFAKLYASILNKVL 126
                                       559*****************....5555555555555568**********999888888887777776555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00086      0.96      27     164 ..      41     176 ..      20     195 .. 0.63
   2 ?    0.6   0.0      0.28   3.2e+02       4      26 ..     311     333 ..     309     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00086
                              TniB  27 leypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara. 102
                                         + +++++ n+l +G++ +GKt+ ++   r+      ed + +pv ++++    ++++ + +i+eal+    ++  
  gi|488601584|ref|YP_007908055.1|  41 KPAIRKTQPVNMLCLGPPGTGKTSAIKLIFREL-----EDFDVIPV-YANCQLLGSKQAVFGKIFEALYGYKPPSYg 111
                                       34456788899**************99766543.....34456665.677777888888888888888765555542 PP

                              TniB 103 .rvskleqqvl.rllrelkvrvLiiDEihnllagsarkqreflnalksLg..nelkipivlvGtee 164
                                          +kl++ +l ++l+  kv v+ +D i+ ll+ + +    + ++lk     + +k  ++++Gt+ 
  gi|488601584|ref|YP_007908055.1| 112 iPFAKLYASILnKVLEIDKVLVVALDDINLLLNDT-QINDVLYAILKAYEevDGVKTGVIAIGTDL 176
                                       25567766665245555567777778887777322.233344455555441134556666666655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                              TniB   4 yiradrwigyprakeilerLeeL 26 
                                       ++r+d+ igy++  +i+++Le+L
  gi|488601584|ref|YP_007908055.1| 311 KVRKDHKIGYTKFYNIISKLENL 333
                                       6899999**************98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00036       0.4      21      40 ..      52      71 ..      39      83 .. 0.80
   2 ?   -1.8   0.0         2   2.2e+03     149     174 ..     292     317 ..     278     327 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                            AAA_30 21 avltGpAGtGKttalkalre 40
                                      ++  Gp+GtGKt a+k + +
  gi|488601584|ref|YP_007908055.1| 52 MLCLGPPGTGKTSAIKLIFR 71
                                      5778***********99843 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                            AAA_30 149 aeLtevvRqkeseeraaalalregda 174
                                         L++++ q++ +  ++ +++r+++ 
  gi|488601584|ref|YP_007908055.1| 292 EILKQIYQQDDISTGEMYKKVRKDHK 317
                                       45777888877777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2039.70
//
Query:       gi|488601585|ref|YP_007908056.1|  [L=334]
Description: hypothetical protein Asulf_02105 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-10   38.8   0.0    1.1e-09   38.3   0.0    1.3  1  Methyltransf_28  Putative S-adenosyl-L-methionine-dependent m
  ------ inclusion threshold ------
      0.032   13.3   0.0       0.06   12.4   0.0    1.4  1  Mtc              Tricarboxylate carrier


Domain annotation for each model (and alignments):
>> Methyltransf_28  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   1.3e-13   1.1e-09      97     261 ..     109     255 ..      70     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.3e-13
                   Methyltransf_28  97 keipeetgfilanEffDaLPihqfertedgwrellveltpekkakekefrltlspsetdplsevlpklskrlkalee 173
                                       +e+++ +g+il   ++ aLP h++ ++    ++++v+++      +++f+ ++++  + +   ++ ++s  l+++ +
  gi|488601585|ref|YP_007908056.1| 109 DEVESCEGVILISRILSALPSHILLSN----KQVFVDFK------NGRFEEKIEDIDK-S---LFDEFSDVLEKIDP 171
                                       444456799999999**********33....479****9......7889999877776.3...44444444444559 PP

                   Methyltransf_28 174 gsrieispeaeallediaerlakegGaaLiiDYgesssepngtLrairkhklv.dpleepGevDltadvDFtalaea 249
                                       ++++++s ea +l++++ ++l+   G++ i DY    +e  + ++++ +     dp+++pG++    + +   +a++
  gi|488601585|ref|YP_007908056.1| 172 SKKVYLSIEALKLIQQLCKKLST--GFMVITDYMS--EELCDAITCYDETVHThDPYASPGKMRMRIPLNIPIVANV 244
                                       9**********************..********97..589******976544459********************** PP

                   Methyltransf_28 250 aeeasglevlgp 261
                                       a++  glev+g 
  gi|488601585|ref|YP_007908056.1| 245 ARKM-GLEVFGL 255
                                       *777.9999986 PP

>> Mtc  Tricarboxylate carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.7e-06      0.06      16      91 ..     168     243 ..     159     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-06
                               Mtc  16 vtdpr.tlllseaeleeakelvekykkgk.lppelteeelwkakklvdSavHPdtgekillpfRmsafvpvnllitg 90 
                                        +dp+  + ls + l+  ++l++k  +g  + +++ +eel +a + +d +vH  t ++   p++m + +p n++i++
  gi|488601585|ref|YP_007908056.1| 168 KIDPSkKVYLSIEALKLIQQLCKKLSTGFmVITDYMSEELCDAITCYDETVH--THDPYASPGKMRMRIPLNIPIVA 242
                                       5666524678999999**********99863445555***************..78*******************98 PP

                               Mtc  91 g 91 
                                        
  gi|488601585|ref|YP_007908056.1| 243 N 243
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1822.01
//
Query:       gi|488601586|ref|YP_007908057.1|  [L=258]
Description: Enoyl-CoA hydratase/carnithine racemase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-55  188.4   0.0    1.5e-55  188.3   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.6e-33  116.6   0.1    2.5e-30  106.1   0.0    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   0.0   1.6e-59   1.5e-55       2     249 ..      12     257 ..      11     258 .] 0.96

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 1.6e-59
                                       EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHH CS
                             ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevl 78 
                                       +++ +  i+lnrPe+ Nals  ll+El    ++l  +++v++v++ G +k+F++G dl+e++++ + + ++l  + +
  gi|488601586|ref|YP_007908057.1|  12 EKDRIGIITLNRPEKRNALSYDLLDELESLVNDLAAERKVKVVIIKGAGKIFSSGHDLNEILNH-PIEVEKLFRKCF 87 
                                       5778999********************************************************7.555555556778 PP

                                       HHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHH CS
                             ECH_1  79 elwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilll 155
                                       + + ++++ p   ia v G a+++G++l++acD+++a +na f+l+ +k+Gl+  +  + ++ r+vG+++A e++++
  gi|488601586|ref|YP_007908057.1|  88 SVMLAIRNAPQTYIAQVHGMAAAAGCQLVSACDLAVAEENALFSLPGVKIGLFC-STPVVFVSRAVGRKRAYEMAIT 163
                                       8999*************************************************9.7888899*************** PP

                                       T-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHH CS
                             ECH_1 156 gkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskdd 232
                                       g+ i+a+ a ++Gl +k+vp e+l++ ++ela+kl   s +al+  k  + ++++++   +le   ++ +   s++d
  gi|488601586|ref|YP_007908057.1| 164 GEFITAKQAYEWGLLNKIVPVEELESATMELARKLSGYSFTALESGKRMFYRQIQMEDFLALEYATEVISLQSSSED 240
                                       ***************************************************************************** PP

                                       HHHHHHHHHTCSH---- CS
                             ECH_1 233 ikeGlqaflEkrkpefe 249
                                         eG++aflEkr+p+++
  gi|488601586|ref|YP_007908057.1| 241 AVEGIKAFLEKREPRWK 257
                                       ****************8 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.0   2.8e-34   2.5e-30       1     187 [.      16     197 ..      16     210 .. 0.93
   2 !    9.1   0.0   8.9e-05       0.8     275     319 ..     215     258 .]     196     258 .] 0.74

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 2.8e-34
                                       .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHH CS
                             ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeY 77 
                                       +g+itLnrp++ NaLs++++++l++ +++ +++ +vk+v++kgag k f++G D++++ ++  e     e++fr+ +
  gi|488601586|ref|YP_007908057.1|  16 IGIITLNRPEKRNALSYDLLDELESLVNDLAAERKVKVVIIKGAG-KIFSSGHDLNEILNHPIEV----EKLFRKCF 87 
                                       589****************************************99.************9988773....359***** PP

                                       HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH- CS
                             ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTG 154
                                       ++  +i + p++++a ++G++   G+ l   + + v+ e+++f+ P ++IGlf+   + ++   +  + +  +a+TG
  gi|488601586|ref|YP_007908057.1|  88 SVMLAIRNAPQTYIAQVHGMAAAAGCQLVSACDLAVAEENALFSLPGVKIGLFCSTPVVFVSRAVGRKRAYEMAITG 164
                                       ******************************************************998877665566688888***** PP

                                       --B-HHHHHHTTS--EE--GGGHHHHHHHHHTT CS
                             ECH_2 155 arlkgadalaaglathyvpseklealeeaLael 187
                                       + +++++a++ gl +++vp e+le+ + +La+ 
  gi|488601586|ref|YP_007908057.1| 165 EFITAKQAYEWGLLNKIVPVEELESATMELARK 197
                                       ************************999999874 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 8.9e-05
                                       TTT--HHHHHHHHHHHHHHHHHH..SSHHHHHHHHTTS-------SS CS
                             ECH_2 275 rklsslaevlrmElrlalrllae..kDfveGvrallvdkdkkPkWkp 319
                                       r+  ++++ l+ E++  +  l++  +D veG++a l +  ++P+Wk+
  gi|488601586|ref|YP_007908057.1| 215 RQI-QMEDFLALEYATEVISLQSssEDAVEGIKAFLEK--REPRWKY 258
                                       333.47899*****99998888667*********9955..68***85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1569.51
//
Query:       gi|488601587|ref|YP_007908058.1|  [L=197]
Description: methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-14   52.5   0.0    6.2e-14   51.9   0.0    1.2  1  MTS              Methyltransferase small domain
    1.6e-12   48.0   0.1    3.1e-12   47.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    6.2e-11   42.3   0.0    6.4e-11   42.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.4e-10   41.0   0.2    1.9e-10   40.6   0.2    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.9e-09   36.7   0.2    3.9e-08   33.8   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
    3.5e-06   26.7   0.0    4.9e-06   26.2   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    5.7e-06   26.1   0.1    1.3e-05   24.9   0.1    1.6  1  UPF0020          Putative RNA methylase family UPF0020
    5.9e-05   22.5   0.0    8.8e-05   22.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00012   22.7   0.0    0.00021   22.0   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    0.00012   21.3   0.2    0.00031   20.0   0.0    1.6  2  DUF43            Branched-chain polyamine synthase A C-termin
    0.00026   20.7   0.0    0.00035   20.3   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00039   20.3   0.0     0.0006   19.7   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0018   18.1   0.1     0.0082   15.9   0.0    1.9  2  N6_N4_Mtase      DNA methylase
     0.0032   16.5   0.0     0.0041   16.2   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0035   17.0   0.1     0.0052   16.4   0.1    1.2  1  NodS             Nodulation protein S (NodS)
     0.0043   16.5   0.0     0.0067   15.9   0.0    1.3  1  TehB             Tellurite resistance protein TehB
     0.0081   16.2   0.0      0.011   15.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.031   14.2   0.1      0.073   13.0   0.1    1.6  2  Methyltransf_18  Methyltransferase domain
      0.035   13.8   0.1      0.051   13.3   0.1    1.2  1  Methyltransf_16  Lysine methyltransferase
      0.036   13.4   0.2       0.15   11.3   0.0    1.8  2  CMAS             Mycolic acid cyclopropane synthetase
      0.056   13.2   0.0      0.072   12.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.094   12.7   0.1       0.16   12.0   0.1    1.6  1  ADH_zinc_N       Zinc-binding dehydrogenase


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 !   51.9   0.0   7.7e-17   6.2e-14      34     112 ..      47     123 ..      35     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 7.7e-17
                                       EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTT CS
                               MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhag 110
                                       +vlDlGcG+G++++a+   s +  v+ vd+d+ Al++ak+n+e+ +++++++  d+ + + +k+  + ++NPPf  +
  gi|488601587|ref|YP_007908058.1|  47 DVLDLGCGTGMISIACSLLSAR--VVGVDIDMSALKIAKKNAEKFGVDIDLIRADIKSLWLKKRDFTTIMNPPFGIQ 121
                                       59***************99888..9**********************************9955555679*****877 PP

                                       CH CS
                               MTS 111 ka 112
                                       + 
  gi|488601587|ref|YP_007908058.1| 122 RR 123
                                       65 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   3.8e-15   3.1e-12       1      69 [.      48     114 ..      48     134 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 3.8e-15
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvv 69 
                                       vLdlGcGtG +++a++    +a+v+gvDi+ ++l++a+++ae+ g++++++++d+++l ++++ f  ++
  gi|488601587|ref|YP_007908058.1|  48 VLDLGCGTGMISIACSLL--SARVVGVDIDMSALKIAKKNAEKFGVDIDLIRADIKSLWLKKRDFTTIM 114
                                       9**************977..4**************************************9999998886 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   7.9e-14   6.4e-11       5      73 ..      46     108 ..      42     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 7.9e-14
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekllede 73 
                                       + vlDlGCGtG ++++   +l   a+vvG+Di+  a++ A++na+k g+d + + ++di +l   l+++
  gi|488601587|ref|YP_007908058.1|  46 VDVLDLGCGTGMISIACS-LL--SARVVGVDIDMSALKIAKKNAEKFGVD-IDLIRADIKSLW--LKKR 108
                                       78*************999.44..69************************8.********9976..4444 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.2   2.4e-13   1.9e-10     164     211 ..      47      93 ..      32     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.4e-13
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea 211
                                        vlD+G+G+G+++ia ++L a +vv+vDiD  A+k+ak+Nae+ +v+ 
  gi|488601587|ref|YP_007908058.1|  47 DVLDLGCGTGMISIACSLLSA-RVVGVDIDMSALKIAKKNAEKFGVDI 93 
                                       79***************9987.699****************9877765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   4.8e-11   3.9e-08       1      64 [.      49     112 ..      49     115 .. 0.93
   2 ?    0.6   0.1       1.1   9.1e+02      72      89 ..     179     196 ..     173     197 .] 0.91

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.8e-11
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDl 64 
                                       Ld+GcGtG ++ a+    arvvgvD++  +lk+ak++a++ g+ +++++ad+++l +++  f  
  gi|488601587|ref|YP_007908058.1|  49 LDLGCGTGMISIACSLLSARVVGVDIDMSALKIAKKNAEKFGVDIDLIRADIKSLWLKKRDFTT 112
                                       8**************999************************9***********9998877765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                                       CC-CCHHHHHHHHHHHEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLk 89 
                                       +hv++ +++  e++R++k
  gi|488601587|ref|YP_007908058.1| 179 FHVKEYKQIAVEVYRLVK 196
                                       5999***********998 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0     6e-09   4.9e-06       4      66 ..      48     108 ..      46     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6e-09
                   Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklk 66 
                                       +lDl +G+G  +i+  l   +v++++i+++ l++a++Nae +gv+  i+l+ +d+++l  k +
  gi|488601587|ref|YP_007908058.1|  48 VLDLGCGTGMISIACSLLSARVVGVDIDMSALKIAKKNAEKFGVD--IDLIRADIKSLWLKKR 108
                                       79****************************************985..9999999998543322 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.6e-08   1.3e-05      77     135 ..      67     122 ..      44     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.6e-08
                                       --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-------- CS
                           UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerl 135
                                       ++++g+D+d ++++ a++Naek gv+  i++  ad+++L lk+ ++ + + npP+G+  
  gi|488601587|ref|YP_007908058.1|  67 ARVVGVDIDMSALKIAKKNAEKFGVD--IDLIRADIKSLWLKKRDF-TTIMNPPFGIQR 122
                                       4588******************9986..99999*******888788.7788*****865 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.1e-07   8.8e-05      50     136 ..      47     131 ..      33     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                                       EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-.T-EEEEEEES- CS
                   Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed.dsfDvvtvsfG 125
                                       +vlD+ +Gtg ++++ s     + +vv++Di+ + Lk+++k +++ g+ +i+++ a+ + L  ++ d   ++   fG
  gi|488601587|ref|YP_007908058.1|  47 DVLDLGCGTGMISIACSLL---SARVVGVDIDMSALKIAKKNAEKFGV-DIDLIRADIKSLWLKKrDFTTIMNPPFG 119
                                       79*********99988754...678*****************999986.9***********9998344445566799 PP

                                       G.GG-S-HHHHH CS
                   Ubie_methyltran 126 l.rnvtDklkaL 136
                                       + r  +D+   L
  gi|488601587|ref|YP_007908058.1| 120 IqRRHADRYFIL 131
                                       855566666555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.6e-07   0.00021       1      43 [.      49      89 ..      49     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-07
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakr 43
                                      L++GcGtG ++ a+      ++++gvDi+ sa++ ak+   k 
  gi|488601587|ref|YP_007908058.1| 49 LDLGCGTGMISIACSLL--SARVVGVDIDMSALKIAKKNAEKF 89
                                      8*************999..**************6666655544 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 !   20.0   0.0   3.8e-07   0.00031      24     117 ..      25     114 ..      16     132 .. 0.77
   2 ?   -1.5   0.0       1.5   1.2e+03      81      96 ..     150     165 ..     149     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.8e-07
                                       -B-HHHHHHHHHHHHH.TT-STT-EEEEES.-TT-HHHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--EEEE- CS
                             DUF43  24 fvtpettvaRvallye.rGDLegkeilvlG.dDDLtslalaLtglpkkvvvvDiDeRlikfiervakelglkieaiv 98 
                                       +vtp +  + +a+     GDL   ++l lG    ++s+a +L  l+ +vv vDiD   +k+ ++ a++ g++i+ i 
  gi|488601587|ref|YP_007908058.1|  25 YVTPPSLASFIAINARlMGDLV--DVLDLGcGTGMISIACSL--LSARVVGVDIDMSALKIAKKNAEKFGVDIDLIR 97 
                                       7777777776666433268886..578888667788888777..789****************************** PP

                                       --TTS---TTTSS-BSEEE CS
                             DUF43  99 yDlrkplpeelkekFdvfi 117
                                        D++  + +  k+ F +++
  gi|488601587|ref|YP_007908058.1|  98 ADIKSLWLK--KRDFTTIM 114
                                       ***987654..45565554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHT--EEE CS
                             DUF43  81 kfiervakelglkiea 96 
                                       +fi +v++e+g+ki  
  gi|488601587|ref|YP_007908058.1| 150 RFIRKVSEEKGFKITH 165
                                       6999999999999753 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   4.3e-07   0.00035      40     126 ..      43     121 ..      31     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.3e-07
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                       ++   vLDl +G+G +++ A S   +++v v+ d +a+ki k+n e+++++  ++ ++ d ++ +lk+    + f  
  gi|488601587|ref|YP_007908058.1|  43 GDLVDVLDLGCGTGMISI-ACSLLSARVVGVDIDMSALKIAKKNAEKFGVD--IDLIRADIKSLWLKK----RDFTT 112
                                       455689***********9.899999************************77..89*****99999888....56887 PP

                                       EEE--SSSTT CS
                     Cons_hypoth95 117 vflDPPyake 126
                                       + ++PP+  +
  gi|488601587|ref|YP_007908058.1| 113 I-MNPPFGIQ 121
                                       7.68999755 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.4e-07    0.0006      25      70 ..      47      90 ..      23     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.4e-07
                   Methyltransf_23 25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdq 70
                                       vLd+GcGtG  +  ++   + v+gvD++  a +ia+  k+a+k  
  gi|488601587|ref|YP_007908058.1| 47 DVLDLGCGTGMISIACSLLSARVVGVDIDMSALKIAK--KNAEKFG 90
                                      79********999999************998888874..3333333 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-05    0.0082     177     231 .]      28      84 ..       9      84 .. 0.81
   2 ?    0.0   0.0       0.7   5.7e+02       7      44 ..     115     193 ..     103     196 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                       -HHHHHHHHHHHS-TT-E..EEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       N6_N4_Mtase 177 PvallerlIklstkkgdi..vlDpFaGSGtTavaakelgrkfiGieieeeyvelaek 231
                                       P  l+ ++      +gd+  vlD  +G+G + +a+  l+ + +G++i+ +++++a+k
  gi|488601587|ref|YP_007908058.1|  28 PPSLASFIAINARLMGDLvdVLDLGCGTGMISIACSLLSARVVGVDIDMSALKIAKK 84 
                                       555555555555566777336********************************9986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.7
                                       --SSSSSCS..............................................GCCGCCHHHHHHHHHHHHHHHH CS
                       N6_N4_Mtase   7 dpPYntgkdy.........................................endeqyeeedsyeeyleflekvlkev 42 
                                        pP+++++++                                          +++++  + +ye  ++  ++++ ev
  gi|488601587|ref|YP_007908058.1| 115 NPPFGIQRRHadryfilkafelseviysihsagserfirkvseekgfkithLWRFEIPLKRTYEFHVKEYKQIAVEV 191
                                       56666666655555555555555555555555555555555555555554444555555555555555555555555 PP

                                       HH CS
                       N6_N4_Mtase  43 rr 44 
                                       +r
  gi|488601587|ref|YP_007908058.1| 192 YR 193
                                       55 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     5e-06    0.0041     203     256 ..      46      98 ..      32     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                   tRNA_U5-meth_tr 203 gdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirl 256
                                        d+l+l cG G  s+a +    +v+  +i  s+++ a++n ++  +d +++ir 
  gi|488601587|ref|YP_007908058.1|  46 VDVLDLGCGTGMISIACSLLSARVVGVDIDMSALKIAKKNAEKFGVD-IDLIRA 98 
                                       489***************************************99987.777775 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.4e-06    0.0052      41     106 ..      42     108 ..      32     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-06
                              NodS  41 qgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkes.shiswivsdvqqfstdek 106
                                        g++ d+l++Gc +G ++   + ++ r+  vd+  +a++ a++  ++   +i  i +d++ + ++++
  gi|488601587|ref|YP_007908058.1|  42 MGDLVDVLDLGCGTGMISIACSLLSARVVGVDIDMSALKIAKKNAEKFgVDIDLIRADIKSLWLKKR 108
                                       68999***********************************99999886369********99876654 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.3e-06    0.0067      33      95 ..      47     108 ..      32     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.3e-06
                                       EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S- CS
                              TehB  33 kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklder 95 
                                        vldlgcg g  s+  sll   v  +d + ++++  ++ +ek  ++ i+    di ++ l++r
  gi|488601587|ref|YP_007908058.1|  47 DVLDLGCGTGMISIACSLLSARVVGVDIDMSALKIAKKNAEKFGVD-IDLIRADIKSLWLKKR 108
                                       69************************************99999999.9999999998887654 PP

>> Methyltransf_32  Methyltransferase 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     0.011      25      76 ..      44      91 ..      29     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                   Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgk 76
                                      + ++v+D+G+G g  s + +l    ++ +vvg+d+  +  + a+k aek+g 
  gi|488601587|ref|YP_007908058.1| 44 DLVDVLDLGCGTGMISIACSL----LSARVVGVDIDMSALKIAKKNAEKFGV 91
                                      45789*************999....69**********************993 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     9e-05     0.073      17      67 ..      47      93 ..      35     114 .. 0.83
   2 ?   -2.0   0.0       3.9   3.1e+03     117     136 ..     145     164 ..     131     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-05
                   Methyltransf_18 17 rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledki 67
                                       v+D G+  g+++i+        +v+ +Di  ++l+ ak+n+ek g++  i
  gi|488601587|ref|YP_007908058.1| 47 DVLDLGCGTGMISIACS--LLSARVVGVDIDMSALKIAKKNAEKFGVD--I 93
                                      699**********9987..56789********************9984..4 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                   Methyltransf_18 117 pnseaeelRkylvengfkie 136
                                       +  +++ +Rk+  e+gfki+
  gi|488601587|ref|YP_007908058.1| 145 SAGSERFIRKVSEEKGFKIT 164
                                       55567778999999999986 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.2e-05     0.051      48      91 ..      46      88 ..      31     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-05
                   Methyltransf_16 48 lsvlELGsGtGlvGlavaellpeakviltDlee.llellkkniel 91
                                      + vl+LG GtG++ +a  +l  +a+v+  D++  +l++ kkn e 
  gi|488601587|ref|YP_007908058.1| 46 VDVLDLGCGTGMISIACSLL--SARVVGVDIDMsALKIAKKNAEK 88
                                      689***************99..99999999997789999999876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.15      65     110 ..      47      91 ..      40     102 .. 0.86
   2 ?   -0.3   0.0      0.64   5.3e+02     198     233 ..     149     184 ..     132     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                                       EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-S CS
                              CMAS  65 tlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldl 110
                                        +Ld+GcG G + + a +   ++vvg+ +     k akk+ ++ ++
  gi|488601587|ref|YP_007908058.1|  47 DVLDLGCGTGMISI-ACSLLSARVVGVDIDMSALKIAKKNAEKFGV 91 
                                       58*******97765.66777*******************9998875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHH CS
                              CMAS 198 ieeieeeiseagftvvdveslrahYakTLkaWaeal 233
                                        + i + ++e gf++++  ++++  ++T +   +++
  gi|488601587|ref|YP_007908058.1| 149 ERFIRKVSEEKGFKITHLWRFEIPLKRTYEFHVKEY 184
                                       566788889999999999998888888876655555 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 ?   12.8   0.0   8.9e-05     0.072      50     124 ..      20      92 ..      10     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                                       EETTEEE--HHHHHHHHHHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC CS
                              PCMT  50 igynatiSaphmvalalelle.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle 124
                                       i  ++++  p++ +++    + + +   vL++G+G+G  +   + l   ++rvv+++   +  + ak+n +k +++
  gi|488601587|ref|YP_007908058.1|  20 IHLEQYVTPPSLASFIAINARlMGDLVDVLDLGCGTGMISIACSLL---SARVVGVDIDMSALKIAKKNAEKFGVD 92 
                                       6677788778777766655564667789*********987666554...56789***9999999*****9998876 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00019      0.16       3      54 ..      54     104 ..      52     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                       HHHHHHHHH.HTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHT CS
                        ADH_zinc_N   3 GlaavqlAk.alGaeviavdsseeklelakklGadevinykeadlverikelt 54 
                                       G+  + +A   l a+v++vd++ + l++akk+  ++ ++  +  + ++ik+l+
  gi|488601587|ref|YP_007908058.1|  54 GTGMISIACsLLSARVVGVDIDMSALKIAKKNAEKFGVDI-D-LIRADIKSLW 104
                                       66666665548899*****************988877777.2.2555565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 1103.95
//
Query:       gi|488601588|ref|YP_007908059.1|  [L=383]
Description: putative adenylylsulfate reductase-associated electron transfer protein QmoC [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-08   32.9   5.7    1.1e-07   32.2   5.7    1.4  1  Fer4_17          4Fe-4S dicluster domain
    1.7e-06   28.0   7.0    2.8e-06   27.4   7.0    1.3  1  Fer4_9           4Fe-4S dicluster domain
    3.4e-06   27.4   6.7    6.9e-06   26.4   6.7    1.5  1  Fer4_8           4Fe-4S dicluster domain
    2.9e-05   24.1   4.3      0.047   13.8   0.5    2.2  2  Fer4_10          4Fe-4S dicluster domain
     0.0012   18.4   8.2       0.44   10.1   4.5    2.3  2  Nitrate_red_gam  Nitrate reductase gamma subunit
     0.0089   16.9   6.9       0.75   10.8   0.6    2.3  2  Fer4_16          4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.011   16.3  10.9       0.04   14.5  11.1    1.8  2  Fer4_7           4Fe-4S dicluster domain
      0.023   14.8   7.6       0.34   11.1   0.9    2.2  2  Fer4_21          4Fe-4S dicluster domain
      0.071   13.0  11.3        1.2    9.0   2.1    2.3  2  Fer4             4Fe-4S binding domain
       0.15   12.2  13.6       0.13   12.4   3.0    2.3  2  Fer4_6           4Fe-4S binding domain
        1.2    9.8   9.4       0.63   10.7   2.2    2.2  2  Fer4_4           4Fe-4S binding domain
        2.4    8.4  11.1        2.6    8.3   3.0    2.4  2  Fer4_2           4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   5.7   7.6e-11   1.1e-07       1      59 [.      23      81 ..      23      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.6e-11
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                      +C qC+ C  +Cp   + + +p+k +  a++gl+++  k++ + lC++C+ C+  CP g
  gi|488601588|ref|YP_007908059.1| 23 KCFQCATCSVVCPLSPDDNPYPRKEMIWAQWGLKDKLLKDPDIWLCHQCNDCSINCPRG 81
                                      6****************999999999999****************************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 !   27.4   7.0   1.9e-09   2.8e-06       1      50 [.      23      82 ..      23      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.9e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkga 50
                                      kC +C +C  +Cp     +   ++++   +++           + C++C++C   Cp+ga
  gi|488601588|ref|YP_007908059.1| 23 KCFQCATCSVVCPLSPDDNPYPRKEMIWAQWGLkdkllkdpdiWLCHQCNDCSINCPRGA 82
                                      7***********9888888888888888777778999999******************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 !   26.4   6.7   4.6e-09   6.9e-06       2      64 ..      21      81 ..      20      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.6e-09
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      l+kC +C  C   Cp+  + +  + +     a+    +++l ++  +w C++c+ C+ +Cp g
  gi|488601588|ref|YP_007908059.1| 21 LKKCFQCATCSVVCPLSPDDNPYPRKEMIW-AQ-WGLKDKLLKDPDIWLCHQCNDCSINCPRG 81
                                      689************988876443333333.22.233333334778***************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 !   13.8   0.5   3.1e-05     0.047       6      25 ..      21      38 ..      18      56 .. 0.80
   2 !   11.6   0.2   0.00015      0.23       8      23 ..      67      82 ..      58     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                           Fer4_10  6 ddtCirCgkCvkaCPadlts 25
                                       ++C +C++C  +CP   + 
  gi|488601588|ref|YP_007908059.1| 21 LKKCFQCATCSVVCPL--SP 38
                                      589************9..44 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00015
                           Fer4_10  8 tCirCgkCvkaCPadl 23
                                       C +C++C   CP  +
  gi|488601588|ref|YP_007908059.1| 67 LCHQCNDCSINCPRGA 82
                                      39***********933 PP

>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00033      0.49      89     144 ..     275     330 ..     251     339 .. 0.86
   2 !   10.1   4.5   0.00029      0.44     177     210 ..     340     373 ..     328     380 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                   Nitrate_red_gam  89 vaGliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvs 144
                                       ++G i  +l++ G++ +++ Rl+n+    + s +D+++++ L+l+i++G+l+ ++ 
  gi|488601588|ref|YP_007908059.1| 275 IIGNIGFLLIFGGMTWIVYTRLANSDRAGKPSYQDWFFITDLYLVIITGILMEILR 330
                                       456666677888999***********************************998775 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00029
                   Nitrate_red_gam 177 lifklHvllglllfalfPFtrLvHvlsapleYll 210
                                        ++ +H++l ++l+a  P++++ H++   l+Y+ 
  gi|488601588|ref|YP_007908059.1| 340 PLYMVHLVLVFMLLAYAPYSKFAHLMYRGLAYMH 373
                                       4789****************************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 !    9.2   0.9    0.0016       2.4      52      65 ..      22      35 ..      10      37 .. 0.78
   2 !   10.8   0.6    0.0005      0.75       2      16 ..      68      82 ..      67     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                           Fer4_16 52 eaitgCdiCqdvCP 65
                                      ++++ C++C  vCP
  gi|488601588|ref|YP_007908059.1| 22 KKCFQCATCSVVCP 35
                                      57888888888888 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0005
                           Fer4_16  2 CgtCgkCaevCPtna 16
                                      C++C+ C   CP +a
  gi|488601588|ref|YP_007908059.1| 68 CHQCNDCSINCPRGA 82
                                      ************998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.8    0.0031       4.7      37      49 ..      23      35 ..      14      38 .. 0.71
   2 ?   14.5  11.1   2.7e-05      0.04       1      52 []      23      82 ..      23      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0031
                            Fer4_7 37 kClgCgaCvavCP 49
                                      kC +C  C  vCP
  gi|488601588|ref|YP_007908059.1| 23 KCFQCATCSVVCP 35
                                      6777777777776 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.7e-05
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekv...........eidpekClgCgaCvavCPtga 52
                                      +C +C  C ++Cp   ++ d+  ++++ + +           + d + C +C+ C   CP ga
  gi|488601588|ref|YP_007908059.1| 23 KCFQCATCSVVCP---LSPDDNPYPRKEMIWaqwglkdkllkDPDIWLCHQCNDCSINCPRGA 82
                                      7************...55555555554433355566666666667789************997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   0.00023      0.34      39      53 ..      22      36 ..       9      39 .. 0.85
   2 ?    7.2   0.9    0.0037       5.6       8      20 ..      68      80 ..      63      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                           Fer4_21 39 deCvGCnlCssvCPv 53
                                      ++C  C+ Cs vCP+
  gi|488601588|ref|YP_007908059.1| 22 KKCFQCATCSVVCPL 36
                                      589999999999996 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0037
                           Fer4_21  8 CigCgkCliaCed 20
                                      C +C+ C i C+ 
  gi|488601588|ref|YP_007908059.1| 68 CHQCNDCSINCPR 80
                                      6677777777765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.0   0.00095       1.4       7      19 ..      23      35 ..      20      36 .. 0.93
   2 ?    9.0   2.1   0.00082       1.2       7      22 ..      67      82 ..      67      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00095
                                      TSSS-THHHHHST CS
                              Fer4  7 kCigCGaCvevCP 19
                                      kC  C +C  vCP
  gi|488601588|ref|YP_007908059.1| 23 KCFQCATCSVVCP 35
                                      9************ PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00082
                                      TSSS-THHHHHSTTTE CS
                              Fer4  7 kCigCGaCvevCPvgA 22
                                      +C  C+ C   CP gA
  gi|488601588|ref|YP_007908059.1| 67 LCHQCNDCSINCPRGA 82
                                      6*************99 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   3.0     0.021        32       8      20 ..      23      35 ..      22      40 .. 0.92
   2 ?   12.4   3.0   8.6e-05      0.13       8      23 ..      67      82 ..      67      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.021
                            Fer4_6  8 kCigCgdCvrvCP 20
                                      kC +C  C +vCP
  gi|488601588|ref|YP_007908059.1| 23 KCFQCATCSVVCP 35
                                      6889********9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.6e-05
                            Fer4_6  8 kCigCgdCvrvCPega 23
                                      +C +C+dC ++CP ga
  gi|488601588|ref|YP_007908059.1| 67 LCHQCNDCSINCPRGA 82
                                      6************876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.2   0.00042      0.63       2      15 ..      22      35 ..      21      44 .. 0.91
   2 ?    3.2   0.8      0.11   1.6e+02       4      16 ..      68      80 ..      57      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++C++C  C  +CP
  gi|488601588|ref|YP_007908059.1| 22 KKCFQCATCSVVCP 35
                                      79***********9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C +C  C + CP 
  gi|488601588|ref|YP_007908059.1| 68 CHQCNDCSINCPR 80
                                      999999*999996 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.0    0.0018       2.6       9      21 ..      23      35 ..      20      36 .. 0.92
   2 ?    4.7   1.2     0.024        36       9      21 ..      67      79 ..      58      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      +C +C +C  +CP
  gi|488601588|ref|YP_007908059.1| 23 KCFQCATCSVVCP 35
                                      8***********9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                            Fer4_2  9 rCigCgaCvsaCP 21
                                       C +C+ C  +CP
  gi|488601588|ref|YP_007908059.1| 67 LCHQCNDCSINCP 79
                                      6889****999*9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.41s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 2013.00
//
Query:       gi|488601589|ref|YP_007908060.1|  [L=749]
Description: putative adenylylsulfate reductase-associated electron transfer protein QmoB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  149.1   0.0      3e-42  143.5   0.0    2.8  2  FlpD            Methyl-viologen-reducing hydrogenase, delta s
    2.2e-14   53.4   5.5    3.2e-11   43.0   0.9    3.1  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-09   38.3   0.2    1.1e-06   28.4   0.0    2.6  3  DAO             FAD dependent oxidoreductase
    4.8e-08   32.5  16.9      8e-05   22.3   0.4    3.2  3  Fer4            4Fe-4S binding domain
    5.2e-08   32.4   0.9    2.3e-07   30.2   1.4    1.8  2  FAD_binding_2   FAD binding domain
    1.2e-07   31.4   0.0    2.4e-07   30.4   0.0    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    1.7e-07   31.4   0.0    3.4e-07   30.4   0.0    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.3e-07   31.1  12.4     0.0017   19.2   2.8    3.5  3  Fer4_16         4Fe-4S double cluster binding domain
    5.1e-07   29.8  12.3    5.1e-07   29.8  12.3    2.0  1  Fer4_9          4Fe-4S dicluster domain
    6.4e-07   28.9   5.4    7.6e-05   22.1   2.4    3.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    7.9e-07   29.4   6.7    0.00098   19.5   0.1    3.2  2  Fer4_8          4Fe-4S dicluster domain
    3.2e-06   27.1  26.2    6.8e-05   22.9  15.8    2.7  2  Fer4_10         4Fe-4S dicluster domain
    1.3e-05   25.0  19.1    8.5e-05   22.5   0.3    3.2  2  Fer4_6          4Fe-4S binding domain
    3.1e-05   22.8   1.8    0.00018   20.4   0.5    2.5  3  HI0933_like     HI0933-like protein
    9.4e-05   22.9  14.5    9.4e-05   22.9  14.5    2.9  3  Fer4_7          4Fe-4S dicluster domain
    0.00016   20.9   8.3     0.0012   18.0   1.0    3.3  4  GIDA            Glucose inhibited division protein A
    0.00017   22.1   6.9      0.003   18.1   1.4    3.2  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00018   20.9   2.0     0.0034   16.7   1.1    2.1  2  FAD_binding_3   FAD binding domain
    0.00023   21.0  19.9      0.016   15.2   1.5    3.3  3  Fer4_2          4Fe-4S binding domain
    0.00086   18.3   2.4       0.13   11.1   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
     0.0022   17.2   0.1       0.11   11.6   0.0    2.6  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0038   16.6   0.0     0.0088   15.4   0.0    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0064   16.9   0.1       0.08   13.4   0.0    2.6  2  NAD_binding_7   Putative NAD(P)-binding
     0.0079   16.3   5.6     0.0079   16.3   5.6    2.6  2  Fer4_21         4Fe-4S dicluster domain
     0.0092   16.4   2.0     0.0092   16.4   2.0    3.6  3  Fer4_4          4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   16.2  16.8       0.25   11.9   3.9    3.0  3  Fer4_17         4Fe-4S dicluster domain
      0.025   13.8   0.1       0.06   12.6   0.1    1.5  1  Thi4            Thi4 family
      0.028   14.4   1.3        2.1    8.3   0.0    3.0  3  NAD_binding_9   FAD-NAD(P)-binding
      0.028   14.3   0.0      0.059   13.2   0.0    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.051   12.9   0.1       0.14   11.5   0.0    1.7  2  Amino_oxidase   Flavin containing amine oxidoreductase
      0.073   12.6   0.0       0.15   11.6   0.0    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.3   1.7e+02      40      62 ..      51      73 ..      26      79 .. 0.87
   2 !  143.5   0.0   5.2e-45     3e-42       2     120 ..     617     738 ..     616     739 .. 0.99

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.3
                              FlpD 40 dpefilkalekGadgVlvlgChp 62
                                       +e+i k +e+G++ +++++C p
  gi|488601589|ref|YP_007908060.1| 51 GVELIKKDIEEGVNTIIIAACSP 73
                                      568999***************87 PP

  == domain 2  score: 143.5 bits;  conditional E-value: 5.2e-45
                              FlpD   2 laFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgd...ChyvkGnekae 75 
                                       laF+C+++ay+a+d+a+++r+++ p+vrii+v+C+g+ ++ ++++al++G+dgV+++gC++gd   Ch++kG+e a+
  gi|488601589|ref|YP_007908060.1| 617 LAFVCENDAYPAFDMAALNRMEWHPDVRIIPVRCLGSFNVVWVADALSRGIDGVILIGCKYGDdyqCHFIKGSELAN 693
                                       79*************************************************************************** PP

                              FlpD  76 rrveklkelleelgiepeRvrleevsaaegekfaevikefvekik 120
                                       rr+e+++e+l++l +e eRv+++++ ++e++k++++i+efve+i+
  gi|488601589|ref|YP_007908060.1| 694 RRMENVQETLQRLALEAERVQVVQLPISEYDKIPQIIQEFVERIE 738
                                       *******************************************97 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 !   43.0   0.9   5.5e-14   3.2e-11     142     248 ..     126     262 ..      97     268 .. 0.76
   2 !   10.2   0.1   0.00054      0.31     182     256 ..     348     424 ..     314     438 .. 0.73
   3 ?   -3.7   0.0       9.2   5.3e+03     265     279 ..     480     494 ..     473     507 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5.5e-14
                                       T..........SEEEEES-SHHHHHHHHHHHHHT-EEE.................EEESSSSSSTTS-HHHHHHHHH CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 142 p..........krivvvGgGyiGvElAaalaklgkevt.................lveardrllraldkelsaalee 191
                                       +          k ++v+GgG++G+  A+++a++g++v+                 +    + + ++ ++++ + +++
  gi|488601589|ref|YP_007908060.1| 126 EfpepykeeitKTVLVIGGGVTGLTSAIEAANAGYDVVlvekeaelggwvkkfakITPNEPPFREPREPDIDEKIKQ 202
                                       3334444566689**********************8775666666666555555566666666677889******** PP

                                       HHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCE..EEESEEEE-S-EEES-HHCSHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 192 alekeGvevklgtsvkeidgngekle.vvledgee..idadlvvvavGvrpstelleekl 248
                                       ++e++ ++v++ + v++i g++   + v++++g++  + +  +vvavG +p ++++ e+l
  gi|488601589|ref|YP_007908060.1| 203 VMENDRIKVYTSAYVEKISGQPGLFDvVINQNGNQeeVRVGSIVVAVGWEPYDATKLENL 262
                                       **********************9444555555555559999**********987743555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00054
                                       -HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 182 dkelsaaleealekeGvevklgtsvkeidgnge....kle.vvledgeeidadlvvvavGvrpstelleeklgleld 253
                                       + e +++++++ e+ Gv + ++ ++k i++ ++    ++  + l++  e+++dlvv+a+G+  + + +  ++ le +
  gi|488601589|ref|YP_007908060.1| 348 PGEYEDFYKRVQEDPGV-FLTKGEIKSITKTDNgmlvEVAnTLLGEDIEVEVDLVVLATGMVSRLKKI--ADMLEAK 421
                                       56788999999999999.5558899999999999976444799999999***********98876654..4555555 PP

                                       ETT CS
                                       xxx RF
                       Pyr_redox_2 254 erg 256
                                       e g
  gi|488601589|ref|YP_007908060.1| 422 EEG 424
                                       555 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9.2
                                       BESSTTEEE-GGGCT CS
                                       xxxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtnvpgiyaiGDvag 279
                                       +t+ + iya+G + +
  gi|488601589|ref|YP_007908060.1| 480 ETQRTAIYAAGPFRQ 494
                                       788999*****8873 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     2e-09   1.1e-06       2      36 ..     139     174 ..     138     192 .. 0.90
   2 ?   -2.8   0.0       6.1   3.5e+03     156     201 ..     204     250 ..     199     259 .. 0.64
   3 !    7.2   0.0    0.0057       3.3     153     210 ..     355     418 ..     331     548 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2e-09
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36 
                                       v++iGGG++Gl+ A e+a +g  V+l+ek+ ++g g 
  gi|488601589|ref|YP_007908060.1| 139 VLVIGGGVTGLTSAIEAANAGydVVLVEKEAELG-GW 174
                                       99****************************9999.75 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.1
                                       HHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEE..EEE--G CS
                               DAO 156 aealGveilegtevtgleeedgkvwgve.rttp.gendaada..vVnaaG 201
                                       +e+  +++++ + v++++ + g +  v  +  + g++++++   +V+a G
  gi|488601589|ref|YP_007908060.1| 204 MENDRIKVYTSAYVEKISGQPG-LFDVViN--QnGNQEEVRVgsIVVAVG 250
                                       6667788888888888855433.3444342..335544456666***999 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0057
                                       HHHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECT.EEE.E.EEEEEEE--GGGHH..HH.HTT CS
                               DAO 153 araaealGveilegtevtgleeed.gkvwgverttp.gen.d.aadavVnaaGawsd..ll.gll 210
                                       ++++++  + +l++ e++++ ++d g +++v  +t  ge  + ++d vV+a+G  s+  ++ ++l
  gi|488601589|ref|YP_007908060.1| 355 YKRVQEDPGVFLTKGEIKSITKTDnGMLVEV-ANTLlGEDiEvEVDLVVLATGMVSRlkKIaDML 418
                                       456667777777777****976554666666.666677774247788******999866554555 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   0.8       7.3   4.2e+03       8      12 ..      14      18 ..      12      19 .. 0.84
   2 !   22.3   0.4   1.4e-07     8e-05       6      23 ..     540     557 ..     535     558 .. 0.88
   3 !   19.7   3.2   8.8e-07   0.00051       2      23 ..     566     587 ..     565     588 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.3
                                      SSS-T CS
                              Fer4  8 CigCG 12
                                      C+gC 
  gi|488601589|ref|YP_007908060.1| 14 CTGCD 18
                                      ****5 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.4e-07
                                       TTSSS-THHHHHSTTTEE CS
                              Fer4   6 ekCigCGaCvevCPvgAI 23 
                                        +C+ C++C e CP+gA+
  gi|488601589|ref|YP_007908060.1| 540 QRCTQCKRCTEECPFGAL 557
                                       69***************8 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 8.8e-07
                                       EEETTTSSS-THHHHHSTTTEE CS
                              Fer4   2 videekCigCGaCvevCPvgAI 23 
                                       + ++++C +CG C+ +CP   I
  gi|488601589|ref|YP_007908060.1| 566 KPNPNRCRRCGVCMGACPERII 587
                                       569***************9988 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   1.4     4e-10   2.3e-07       2      36 ..     139     173 ..     138     179 .. 0.94
   2 ?   -2.6   0.0       3.8   2.2e+03     227     254 ..     678     705 ..     675     712 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4e-10
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                       v+ViG+G+ GL++A+eaa+aG +v++veke e gg
  gi|488601589|ref|YP_007908060.1| 139 VLVIGGGVTGLTSAIEAANAGYDVVLVEKEAELGG 173
                                       9******************************9987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
                                       -HHHHHHHCTTSSEES..TT-EEEEEEE CS
                     FAD_binding_2 227 GdglalalragaalnddrmeevqfhPts 254
                                       Gd+ + ++ +g +l+++rme+vq+  + 
  gi|488601589|ref|YP_007908060.1| 678 GDDYQCHFIKGSELANRRMENVQETLQR 705
                                       89999999999999999******97665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   4.2e-10   2.4e-07       2      37 ..     139     174 ..     138     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.2e-10
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGl 37 
                                       v+V+GGg+ G++ Ai Aa+aG  v+Lve++  lGG 
  gi|488601589|ref|YP_007908060.1| 139 VLVIGGGVTGLTSAIEAANAGYDVVLVEKEAELGGW 174
                                       99*********************************6 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 !   30.4   0.0   5.9e-10   3.4e-07       1      38 [.     141     178 ..     141     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 5.9e-10
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38 
                                       ++G+G++Gl+ A ++a+ag+dv+l+ek   lGG+++ +
  gi|488601589|ref|YP_007908060.1| 141 VIGGGVTGLTSAIEAANAGYDVVLVEKEAELGGWVKKF 178
                                       8*********************************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 ?   -0.8   0.1       5.3   3.1e+03      44      59 ..       4      19 ..       1      21 [. 0.76
   2 !   19.2   2.8     3e-06    0.0017       1      24 [.     541     564 ..     541     570 .. 0.84
   3 !   16.6   0.3     2e-05     0.012       1      26 [.     571     595 ..     571     623 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.3
                           Fer4_16 44 deekckkqeaitgCdi 59
                                      + ek+++ + +tgCdi
  gi|488601589|ref|YP_007908060.1|  4 EFEKNYMLYICTGCDI 19
                                      5567778899999996 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 3e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkeke 24 
                                       rC++C++C+e CP +a++e+++ +
  gi|488601589|ref|YP_007908060.1| 541 RCTQCKRCTEECPFGALDEDEKGT 564
                                       6******************96655 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 2e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                       rC +Cg C+ +CP++ i+ k +++++
  gi|488601589|ref|YP_007908060.1| 571 RCRRCGVCMGACPERIISFK-NYNVD 595
                                       6*****************99.44444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8  12.3   8.8e-10   5.1e-07       1      50 [.     541     586 ..     541     587 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 8.8e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       +Ct+C++C+e Cp+g+  ed++++   + +    +C  Cg C+ aCp+ +
  gi|488601589|ref|YP_007908060.1| 541 RCTQCKRCTEECPFGALDEDEKGTPKPNPN----RCRRCGVCMGACPERI 586
                                       6****************9999999988765....6************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 !   22.1   2.4   1.3e-07   7.6e-05     164     276 ..     136     261 ..     124     279 .. 0.75
   2 ?    3.8   0.1     0.048        28     231     287 ..     367     426 ..     348     441 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsysl..........kpdienrleelvkeekikvl 230
                                       ++ v+ViGg+ ++   A+e +++g +V +v +++e+  + +++              +pdi +++++++++++ikv+
  gi|488601589|ref|YP_007908060.1| 136 TKTVLVIGGGVTGLTSAIEAANAGYDVVLVEKEAELGGWVKKFAKITpneppfreprEPDIDEKIKQVMENDRIKVY 212
                                       689******************************998887765543212222222222799***************** PP

                       Pyr_redox_3 231 fnaevkeikekeeeykvk.tedgkkvev.kddvvlatGykp.dlsflkk 276
                                       + a v++i+ +   ++v   ++g++ ev    +v+a+G++p d++ l++
  gi|488601589|ref|YP_007908060.1| 213 TSAYVEKISGQPGLFDVViNQNGNQEEVrVGSIVVAVGWEPyDATKLEN 261
                                       **********999886653566666665235667789999834555655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.048
                       Pyr_redox_3 231 fnaevkeikekeeeykvkted...gkkvevkdd.vvlatGykpdlsflkkslfeldedgrp 287
                                       ++ e+k+i+++++ + v+ ++   g+ +ev+ d vvlatG  + l+ ++  ++e +e+g+ 
  gi|488601589|ref|YP_007908060.1| 367 TKGEIKSITKTDNGMLVEVANtllGEDIEVEVDlVVLATGMVSRLKKIA-DMLEAKEEGEA 426
                                       45689999999999988865533378888865516777********999.55555566554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.7e-06   0.00098      45      64 ..     536     555 ..     488     556 .. 0.72
   2 !   12.0   0.7   0.00037      0.22       3      17 ..     570     588 ..     568     623 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-06
                            Fer4_8  45 eealwsCttcgaCtevCpvg 64 
                                       e  l++Ct+c++Cte+Cp g
  gi|488601589|ref|YP_007908060.1| 536 EFFLQRCTQCKRCTEECPFG 555
                                       66799*************75 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00037
                            Fer4_8   3 ekCieCgaCqsaCp....v 17 
                                       ++C +Cg C+ aCp    +
  gi|488601589|ref|YP_007908060.1| 570 NRCRRCGVCMGACPeriiS 588
                                       58***********965553 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9  15.8   1.2e-07   6.8e-05       7      56 .]     540     583 ..     536     583 .. 0.92
   2 !   18.7   2.6   2.5e-06    0.0014       5      37 ..     568     600 ..     564     609 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.2e-07
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++C++C++C++ CP+      +   ++e+++ + ++ +C +cg C+ aCP
  gi|488601589|ref|YP_007908060.1| 540 QRCTQCKRCTEECPF------GALDEDEKGTPKPNPNRCRRCGVCMGACP 583
                                       79*************......8888888888899***************9 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.5e-06
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeea 37 
                                       ++++C rCg C+ aCP  + s ++++ ++++++
  gi|488601589|ref|YP_007908060.1| 568 NPNRCRRCGVCMGACPERIISFKNYNVDMIGSM 600
                                       799**************8877777776666655 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   0.3   1.5e-07   8.5e-05       2      24 .]     535     557 ..     534     557 .. 0.93
   2 !   12.9   4.7   0.00016     0.092       5      24 .]     568     587 ..     568     587 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.5e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       +e+  ++C++C +C+  CP+ga+
  gi|488601589|ref|YP_007908060.1| 535 PEFFLQRCTQCKRCTEECPFGAL 557
                                       789999***************97 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00016
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       +p++C  Cg C+ +CPe +i
  gi|488601589|ref|YP_007908060.1| 568 NPNRCRRCGVCMGACPERII 587
                                       79**************9876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.5     3e-07   0.00018       2      36 ..     138     172 ..     137     179 .. 0.92
   2 ?    0.1   0.0      0.45   2.6e+02     115     163 ..     200     250 ..     194     257 .. 0.78
   3 ?   -1.8   0.0       1.7   9.7e+02     120     166 ..     359     409 ..     352     411 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3e-07
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +v+viGgG  Gl  Ai+aa++g +V+l+ek+ +lg
  gi|488601589|ref|YP_007908060.1| 138 TVLVIGGGVTGLTSAIEAANAGYDVVLVEKEAELG 172
                                       699****************************9998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.45
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE--- CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvkt.k..seeeleadklvlAtG 163
                                       +++ +++ ++k++++  v++++ +  g f v + +  ++ee++  ++v+A+G
  gi|488601589|ref|YP_007908060.1| 200 IKQVMENDRIKVYTSAYVEKISGQP-GLFDVVInQngNQEEVRVGSIVVAVG 250
                                       567789999************7655.5577777334578899********99 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.7
                                       HHHT-EEE-S--EEEEECETTE.EEEEE......TTEEEEESEEEE----SS CS
                       HI0933_like 120 keagvklrletevksvekeedgkfrvktk.....seeeleadklvlAtGGlS 166
                                       +e    + ++ e+ks++k+++g + v++      ++ e+e d +vlAtG  S
  gi|488601589|ref|YP_007908060.1| 359 QEDPGVFLTKGEIKSITKTDNG-MLVEVAntllgEDIEVEVDLVVLATGMVS 409
                                       5555566788899999998888.77777324555667999999*****9765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   3.8   9.5e-05     0.055      33      52 .]     537     556 ..     523     556 .. 0.85
   2 !   22.9  14.5   1.6e-07   9.4e-05       1      50 [.     541     584 ..     541     586 .. 0.90
   3 !   11.7   4.9   0.00052       0.3       1      25 [.     571     595 ..     571     655 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.5e-05
                            Fer4_7  33 idpekClgCgaCvavCPtga 52 
                                       +  ++C++C++C ++CP+ga
  gi|488601589|ref|YP_007908060.1| 537 FFLQRCTQCKRCTEECPFGA 556
                                       55689*************97 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.6e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       rC++C++C++ Cp +a++ de+    g  +++ +p++C  Cg+C+ +CP 
  gi|488601589|ref|YP_007908060.1| 541 RCTQCKRCTEECPFGALDEDEK----G--TPKPNPNRCRRCGVCMGACPE 584
                                       8*****************9886....4..55668***************6 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00052
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeene 25 
                                       rC  Cg C+ aCp + i++++++++
  gi|488601589|ref|YP_007908060.1| 571 RCRRCGVCMGACPERIISFKNYNVD 595
                                       7*****************9987554 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.95   5.5e+02     188     217 ..      65      95 ..      38     126 .. 0.70
   2 !   18.0   1.0     2e-06    0.0012       2      31 ..     139     168 ..     138     182 .. 0.85
   3 ?   -3.3   0.1       6.1   3.5e+03      99     149 ..     198     250 ..     194     292 .. 0.66
   4 ?    5.4   0.2     0.014       8.2     102     184 ..     355     449 ..     348     455 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.95
                                       EEEEEEE--EEEGGGS-TTTSEEE---.SS- CS
                              GIDA 188 lrlktgtppridkesidfskleeqsgd.keg 217
                                         +  +++pr++ ++ df +++ +  + +e+
  gi|488601589|ref|YP_007908060.1|  65 TIIIAACSPRVNYDTFDFPNVIVERVNlREH 95 
                                       4567899***********9999888774443 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2e-06
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithk 31 
                                       v ViGgG  G+  A++aa++G++v+L+ ++
  gi|488601589|ref|YP_007908060.1| 139 VLVIGGGVTGLTSAIEAANAGYDVVLVEKE 168
                                       99************************9443 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.1
                                       HHHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-..EEEECEEEE--T CS
                              GIDA  99 kevteklenepnleiiee.eveeliveekkvkgvvtedge..tikakavviatG 149
                                       +++++++en + +++ +   ve+++ + +   +v+ ++g+  +++  ++v+a G
  gi|488601589|ref|YP_007908060.1| 198 EKIKQVMEN-DRIKVYTSaYVEKISGQPGLFDVVINQNGNqeEVRVGSIVVAVG 250
                                       566666666.77888654156777777777778877776511455558888888 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.014
                                       HHHHHTSTTEEEEES-EEEEEECT....TEEEEEEETTS-EEEECEEEE--TT.........-BT-EEEETTEEEES CS
                              GIDA 102 teklenepnleiieeeveelivee....kkvkgvvtedgetikakavviatGt.........flkgkihigekelsa 165
                                        +++++ p + + ++e++++  ++     +v+  ++ ++ +++ + vv+atG           l++k     ke +a
  gi|488601589|ref|YP_007908060.1| 355 YKRVQEDPGVFLTKGEIKSITKTDngmlVEVANTLLGEDIEVEVDLVVLATGMvsrlkkiadMLEAKEEGEAKEGEA 431
                                       57889999************8877776656666777777788888*******9555444444444443333333333 PP

                                       SCTTC--B-THHHHHHHTT CS
                              GIDA 166 Grlgeltseglseslkelg 184
                                       G ++  + e+l+e+++e+g
  gi|488601589|ref|YP_007908060.1| 432 GETE-EAEEKLAEAIEEVG 449
                                       4333.56666666666655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.4   5.1e-06     0.003       2      35 ..     139     172 ..     138     182 .. 0.92
   2 ?    5.7   0.0     0.038        22      39      71 ..     193     225 ..     177     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.1e-06
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       v+v+GgG++gl  A ++a+ g +V +ve + +l 
  gi|488601589|ref|YP_007908060.1| 139 VLVIGGGVTGLTSAIEAANAGYDVVLVEKEAELG 172
                                       89**************************999886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.038
                                       SHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  39 Deeaskilqeklekngievllntkveeiegsed 71 
                                       ++++ + +++ +e+  i+v++++ ve+i g++ 
  gi|488601589|ref|YP_007908060.1| 193 EPDIDEKIKQVMENDRIKVYTSAYVEKISGQPG 225
                                       68899999999******************9875 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.1   5.8e-06    0.0034       3      35 ..     138     170 ..     136     173 .. 0.94
   2 ?    2.7   0.0       0.1        59     116     175 ..     359     418 ..     352     504 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.8e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                       +Vl++G+G +Gl++a + ++aG +vvlvek ++
  gi|488601589|ref|YP_007908060.1| 138 TVLVIGGGVTGLTSAIEAANAGYDVVLVEKEAE 170
                                       69****************************875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.1
                                       HHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGG CS
                     FAD_binding_3 116 eerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgie 175
                                       +e +  +  k e++s++++++g   ev +   ge+ +v+ + +v a G+ S+  k +++ 
  gi|488601589|ref|YP_007908060.1| 359 QEDPGVFLTKGEIKSITKTDNGMLVEVANTLLGEDIEVEVDLVVLATGMVSRLKKIADML 418
                                       566666778899***************************************988766654 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       4.5   2.6e+03       9      13 ..      13      17 ..      11      19 .. 0.83
   2 !   15.2   1.5   2.8e-05     0.016       5      21 ..     537     553 ..     533     554 .. 0.84
   3 !   14.1   5.9   6.6e-05     0.038       6      22 .]     568     584 ..     565     584 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.5
                            Fer4_2  9 rCigC 13
                                      +C+gC
  gi|488601589|ref|YP_007908060.1| 13 ICTGC 17
                                      6**** PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.8e-05
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       +  +rC++C+ C+  CP
  gi|488601589|ref|YP_007908060.1| 537 FFLQRCTQCKRCTEECP 553
                                       55689************ PP

  == domain 3  score: 14.1 bits;  conditional E-value: 6.6e-05
                            Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                       +++rC +Cg C  aCP+
  gi|488601589|ref|YP_007908060.1| 568 NPNRCRRCGVCMGACPE 584
                                       89**************5 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   1.2     0.007         4       2      34 ..     139     168 ..     138     172 .. 0.93
   2 !   11.1   0.0   0.00022      0.13     154     214 ..     349     412 ..     310     423 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.007
                                       EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlvese 34 
                                       ++++GGG  G ++A+  a+a+   ++v lve+e
  gi|488601589|ref|YP_007908060.1| 139 VLVIGGGVTGLTSAIEAANAG---YDVVLVEKE 168
                                       89**************99999...99*****98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
                                       HHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-III CS
                    Trp_halogenase 154 alyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrglli 214
                                       ++y++f +rv e+ Gv  ++g++++++  ++g   ++  +    + eve+dl++ ++G+ ++l 
  gi|488601589|ref|YP_007908060.1| 349 GEYEDFYKRVQEDPGVFLTKGEIKSITKTDNGMLVEVANTLlgeDIEVEVDLVVLATGMVSRLK 412
                                       579***************************997666654433228899***********99985 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.5   1.4e+03     191     204 ..     136     149 ..     121     171 .. 0.73
   2 ?    2.4   0.0      0.12        71     131     161 ..     225     254 ..     200     301 .. 0.78
   3 !   11.6   0.0    0.0002      0.11     281     339 ..     351     406 ..     349     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.5
                       K_oxygenase 191 kkriaVvGsGqSaa 204
                                        k+++V+G+G ++ 
  gi|488601589|ref|YP_007908060.1| 136 TKTVLVIGGGVTGL 149
                                       68899999998764 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                       K_oxygenase 131 elltveskdaegeeeelearnlvlgvGtepk 161
                                        l++v   +++g++ee++  ++v++vG ep+
  gi|488601589|ref|YP_007908060.1| 225 GLFDVVI-NQNGNQEEVRVGSIVVAVGWEPY 254
                                       5788887.68999999999999999999998 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0002
                       K_oxygenase 281 yeelyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                       ye++y++ v +e++  +l++ e++s++++ + ++ +++ n+  ge+ ++evd vvlATG
  gi|488601589|ref|YP_007908060.1| 351 YEDFYKR-V-QEDPGVFLTKGEIKSITKTDN-GMLVEVANTLLGEDIEVEVDLVVLATG 406
                                       5555544.3.3566778999*********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 !   15.4   0.0   1.5e-05    0.0088      30      67 ..     138     175 ..     133     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleql 67 
                                       +vlviGgGv Gl ++  a++ g +V++++++++    +
  gi|488601589|ref|YP_007908060.1| 138 TVLVIGGGVTGLTSAIEAANAGYDVVLVEKEAELGGWV 175
                                       69*************************99988765555 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 !   13.4   0.0   0.00014      0.08       8      41 ..     137     176 ..     135     243 .. 0.71
   2 ?   -0.3   0.0       2.5   1.5e+03      47      83 ..     382     419 ..     354     424 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev......k 41 
                                       k+vlv+GgG  +++ +   ++ag +v++v +e       k
  gi|488601589|ref|YP_007908060.1| 137 KTVLVIGGGVTGLTSAIEAANAGYDVVLVEKEAelggwvK 176
                                       89****************************9954433332 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.5
                     NAD_binding_7  47 lvklaeeelekdle.gadlviaatddrelneriaeaak 83 
                                       lv++a++ l +d+e ++dlv+ at   +  ++ia++ +
  gi|488601589|ref|YP_007908060.1| 382 LVEVANTLLGEDIEvEVDLVVLATGMVSRLKKIADMLE 419
                                       5556666666676647999**99999888888888665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       5.9   3.4e+03      41      46 ..      14      19 ..       7      23 .. 0.81
   2 !   16.3   5.6   1.4e-05    0.0079       6      56 ..     540     586 ..     537     589 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.9
                           Fer4_21 41 CvGCnl 46
                                      C+GC++
  gi|488601589|ref|YP_007908060.1| 14 CTGCDI 19
                                      9***87 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.4e-05
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedc 56 
                                       ++C +C++C+  C+     a++ d+k + k   ++C  C +C+  CP e  
  gi|488601589|ref|YP_007908060.1| 540 QRCTQCKRCTEECP---FGALDEDEKGTPKPNPNRCRRCGVCMGACP-ERI 586
                                       58************...899999*9999999****************.455 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   0.1       6.8   3.9e+03       4       8 ..      14      18 ..       8      18 .. 0.90
   2 !   13.5   4.8   0.00013     0.077       2      17 .]     540     555 ..     539     555 .. 0.92
   3 !   16.4   2.0   1.6e-05    0.0092       1      16 [.     569     584 ..     569     593 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6.8
                            Fer4_4  4 CigCg 8 
                                      C+gC+
  gi|488601589|ref|YP_007908060.1| 14 CTGCD 18
                                      ****6 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00013
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                       +rC++C++C+  CP+g
  gi|488601589|ref|YP_007908060.1| 540 QRCTQCKRCTEECPFG 555
                                       8*************86 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.6e-05
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       ++rC +Cg+C+ aCP 
  gi|488601589|ref|YP_007908060.1| 569 PNRCRRCGVCMGACPE 584
                                       69*************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 ?   11.9   3.9   0.00043      0.25      43      58 ..     539     554 ..     518     557 .. 0.82
   2 ?   10.5   4.7    0.0012       0.7       1      20 [.     541     560 ..     541     571 .. 0.72
   3 ?   11.1   2.0    0.0008      0.46       1      18 [.     571     589 ..     571     612 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00043
                           Fer4_17  43 aslCieCgeCerkCPq 58 
                                        ++C++C++C+++CP 
  gi|488601589|ref|YP_007908060.1| 539 LQRCTQCKRCTEECPF 554
                                       6789999999999996 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                           Fer4_17   1 rCiqCgyClpeCpsyeaydn 20 
                                       rC+qC+ C++eCp+++  ++
  gi|488601589|ref|YP_007908060.1| 541 RCTQCKRCTEECPFGALDED 560
                                       58888888888887776555 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0008
                           Fer4_17   1 rCiqCgyClpeCpsyea.y 18 
                                       rC++Cg C+ +Cp  ++  
  gi|488601589|ref|YP_007908060.1| 571 RCRRCGVCMGACPERIIsF 589
                                       7************755433 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1    0.0001      0.06      17      55 ..     136     173 ..     122     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                       EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55 
                                          v+++G+G +GLt+a   a++ +  v+++e++  +GG
  gi|488601589|ref|YP_007908060.1| 136 TKTVLVIGGGVTGLTSAIEAANA-GYDVVLVEKEAELGG 173
                                       56799**************9999.**********99999 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2      0.16        95       2      40 ..     141     174 ..     140     179 .. 0.79
   2 ?   -0.2   0.0       1.5   8.6e+02     110     154 ..     202     250 ..     196     252 .. 0.69
   3 ?    8.3   0.0    0.0036       2.1     106     155 ..     353     407 ..     350     408 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.16
                     NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdp.sepgagr 40 
                                       ++G+G++Gl+ + + ++        ++ l+++ +e+g g+
  gi|488601589|ref|YP_007908060.1| 141 VIGGGVTGLTSAIEAANA-----GYDVVLVEKeAELG-GW 174
                                       8*********99987766.....68999999955556.65 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.5
                     NAD_binding_9 110 rlpegvtvevhra.evvdleeradgqavll.adg..aslaadaVvLAlG 154
                                       ++ e+ +++v+++  v++++ +++ + v+  ++g  +++++ ++v+A+G
  gi|488601589|ref|YP_007908060.1| 202 QVMENDRIKVYTSaYVEKISGQPGLFDVVInQNGnqEEVRVGSIVVAVG 250
                                       5555667888754378899999999855552455225689*******99 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0036
                     NAD_binding_9 106 ellarlpegvtvevhraevvdleeradgqavll.....adgaslaadaVvLAlGh 155
                                       ++ +r++e+  v + ++e+ +++++++g+ v        ++ ++++d VvLA+G+
  gi|488601589|ref|YP_007908060.1| 353 DFYKRVQEDPGVFLTKGEIKSITKTDNGMLVEVantllGEDIEVEVDLVVLATGM 407
                                       5667777888899999************7554411111455679**********7 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.059       1      33 [.     138     170 ..     138     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdisee 33 
                                       +v viG G+ G   a  +a+ag++Vvlv+ ++e
  gi|488601589|ref|YP_007908060.1| 138 TVLVIGGGVTGLTSAIEAANAGYDVVLVEKEAE 170
                                       588*************************98765 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.14       2      33 ..     147     178 ..     146     180 .. 0.93
   2 ?   -2.2   0.0       3.3   1.9e+03     212     261 ..     354     406 ..     323     413 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EE CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtv 33 
                                       +GL+ A + ++aG+dV+++E +  +GG++  +
  gi|488601589|ref|YP_007908060.1| 147 TGLTSAIEAANAGYDVVLVEKEAELGGWVKKF 178
                                       8***************************9866 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
                                       HHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEET...TSTEE..EESEEEE-S- CS
                     Amino_oxidase 212 lpealaeelrgldirlntrVkeikregdgvtvtle...dgevv..eaDaVvvTvp 261
                                         ++++e   ++ +++  + k+i++ ++g  v++     ge++  e+D Vv+++ 
  gi|488601589|ref|YP_007908060.1| 354 FYKRVQE--DPGVFLTKGEIKSITKTDNGMLVEVAntlLGEDIevEVDLVVLATG 406
                                       5555555..5666667778999999888844444422234444679999999975 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 ?   11.6   0.0   0.00026      0.15       2      69 ..     138     214 ..     137     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-H......HHHHHHCTTS-SS--...TTHHHHHHHHCHTTTEEEES- CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDide......ekvdklnsgkipiye...pgLeelvkkavesgrlsfttd 69 
                                       ++ viG G  Gl++a+  a++g +v++v +++      +k +k+  ++ p+ e   p+++e +k+++e++r++  t+
  gi|488601589|ref|YP_007908060.1| 138 TVLVIGGGVTGLTSAIEAANAGYDVVLVEKEAelggwvKKFAKITPNEPPFREprePDIDEKIKQVMENDRIKVYTS 214
                                       688***************************97333333588889999999975222689999999999999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (749 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.84u 0.36s 00:00:01.20 Elapsed: 00:00:00.58
# Mc/sec: 3900.60
//
Query:       gi|488601590|ref|YP_007908061.1|  [L=422]
Description: putative adenylylsulfate reductase-associated electron transfer protein QmoA [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-17   61.2   2.2    1.6e-14   53.9   2.2    3.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.8e-10   39.9   1.2    1.1e-06   28.5   0.9    2.4  2  DAO             FAD dependent oxidoreductase
    7.7e-09   35.1   0.5    1.6e-08   34.1   0.5    1.5  1  FAD_binding_2   FAD binding domain
    2.1e-08   34.3   0.1    4.1e-08   33.3   0.1    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.1e-08   34.0   0.1    4.4e-08   32.9   0.1    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    4.1e-07   30.5  10.7    0.00014   22.4   1.0    3.0  3  Fer4_7          4Fe-4S dicluster domain
    5.6e-07   30.0   0.1      3e-05   24.5   0.1    2.7  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.2e-06   28.0   0.6     0.0032   16.8   0.1    3.2  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.9e-06   27.4  17.0    1.2e-05   25.0   4.5    2.8  2  Fer4            4Fe-4S binding domain
    1.5e-05   24.2   0.8    0.00046   19.4   0.0    2.6  3  GIDA            Glucose inhibited division protein A
    2.1e-05   24.5   0.2      0.069   13.1   0.0    2.5  2  NAD_binding_9   FAD-NAD(P)-binding
    2.3e-05   25.2   6.4       0.03   15.3   0.7    2.6  2  Fer4_16         4Fe-4S double cluster binding domain
    2.5e-05   23.7   0.0    5.2e-05   22.6   0.0    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    5.1e-05   23.3  17.1    0.00026   21.0   1.0    2.8  2  Fer4_10         4Fe-4S dicluster domain
    6.6e-05   21.8   2.6    9.3e-05   21.3   0.3    2.3  3  HI0933_like     HI0933-like protein
    0.00027   20.4   0.3    0.00056   19.3   0.0    1.6  2  Amino_oxidase   Flavin containing amine oxidoreductase
    0.00047   20.2  12.0       0.01   15.9   1.9    2.6  2  Fer4_21         4Fe-4S dicluster domain
    0.00049   20.0   4.3    0.00049   20.0   4.3    2.7  2  Fer4_6          4Fe-4S binding domain
    0.00053   19.9  12.8      0.005   16.9   3.7    2.5  2  Fer4_2          4Fe-4S binding domain
     0.0012   18.1   0.2     0.0019   17.5   0.2    1.2  1  FAD_binding_3   FAD binding domain
     0.0023   16.8   0.2        1.6    7.5   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
     0.0071   15.5   0.2       0.13   11.4   0.0    2.6  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
       0.01   14.9   0.7       0.13   11.2   0.2    2.1  2  Lycopene_cycl   Lycopene cyclase protein
       0.01   15.9   2.3       0.01   15.9   2.3    2.6  3  Fer4_9          4Fe-4S dicluster domain
      0.023   13.9   0.1      0.071   12.3   0.1    1.8  1  Thi4            Thi4 family
       0.04   14.4   3.2       0.04   14.4   3.2    2.4  2  Fer4_8          4Fe-4S dicluster domain
      0.092   13.3  11.2      0.052   14.1   2.9    2.5  3  Fer4_17         4Fe-4S dicluster domain
       0.59   10.3   6.6       0.25   11.5   0.5    2.4  2  Fer4_18         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   2.2   2.5e-17   1.6e-14       2     292 ..      13     407 ..      12     409 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 2.5e-17
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHHHCHHHHHHHHHHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcllskallgvaedaeias.......... 57 
                                       +++viGgG+AGl+aal++++ag++v++ve           l           +k + +   ++  ++          
  gi|488601590|ref|YP_007908061.1|  13 NILVIGGGIAGLSAALEASEAGYDVYVVErnpylggrvaqL-----------YKYFPKLCPPYCGLEilfrrirtnp 78 
                                       799*************************6445544444442...........3333333333333334444444455 PP

                                       ..................................................................HHHHCHHHHCC CS
                                       ..................................................................xxxxxxxxxxx RF
                       Pyr_redox_2  58 ..................................................................evvkklnqgie 68 
                                                                                                          +   l   ++
  gi|488601590|ref|YP_007908061.1|  79 kikfltmsevvdvsgspgnfdvtvrikpryvdiskctacgecakvcpverdndfnygmdktkaiylPH--DLAFPMK 153
                                       55569999999999999999999999999999999999999999999976666555555555554422..3333344 PP

                                       CCHCCTCEEEEESCEEEEETEEEC.......TCEEEEEESEEEE---EEE-BC.TCTTC.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxx.xxxxx.................. RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklekkke.......gdeekiaydklvlAtGssprdl.gipGv.................. 119
                                       ++ + +v k d+ +k+v   k  +       +++ +i+++++++AtG +p d  ++  +                  
  gi|488601590|ref|YP_007908061.1| 154 YVIDDSVCKKDECAKCVSACKY-DaidfsmeEKTINIKAESIIVATGWKPYDAtKLTNLgfgkypnvitnvmmerla 229
                                       4444666666666666655443.259999999999****************9986664455889999********** PP

                                       ....TTBEECCSECHHHHHHCCSS-T.......SEE....EEES-SHHHHHHHHHHHHHT-......EEEEEESSSS CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxx.......xxx....xxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxx RF
                       Pyr_redox_2 120 ...aenvgklvrtldsaealklkllp.......kri....vvvGgGyiGvElAaalaklgk......evtlveardr 176
                                          +++ gk vr++d +e+   + ++       +++    +++   + ++  A ++           +v++ +   r
  gi|488601590|ref|YP_007908061.1| 230 synGPTKGKIVRPSDGKEPNTIAFVQcagsrdeNHLpycsAICC--LASMKQATYI----ReqypdaKVYIFYIDIR 300
                                       ***9**********************999988766633334442..4444444444....13444447887777444 PP

                                       SSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.....EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 177 llraldkelsaaleealekeGvevklgtsvkeidgnge.....kle.vvledgeeidadlvvvavGvrpstelleek 247
                                            + +++++++ + e+e++ ++ g+++ +i++ ++      +e + ++++++ ++++vv+a+G++p+       
  gi|488601590|ref|YP_007908061.1| 301 A----PGRFEDFYATVSEDENIVFVKGKVA-KIEEGENgnlivVAEnTLTGEKTRTEVEMVVLATGMQPEL------ 366
                                       4....689*****************77777.77766666888544489999999***************95...... PP

                                       CT-EEEETTEEE--TTS.BESSTTEEE-GGGCTECCSS--HHHHHH CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 248 lglelderggivvdefl.rtnvpgiyaiGDvaggkggpelaqaAvq 292
                                       +g++l +   ++ d+++ + + pgiy++G va   ++p  + +Av+
  gi|488601590|ref|YP_007908061.1| 367 SGVNL-PIKELKLDSYGfALSSPGIYVAG-VA---KKPSDVATAVE 407
                                       57788.88*********7789********.67...68888887776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.9   1.7e-09   1.1e-06       2      33 ..      14      47 ..      13      52 .. 0.93
   2 !    9.2   0.0    0.0012      0.79     145     218 ..     302     374 ..     281     399 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.7e-09
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      +++iGGGi+Gls+A+e++++g  V ++e+++ +g
  gi|488601590|ref|YP_007908061.1| 14 ILVIGGGIAGLSAALEASEAGydVYVVERNPYLG 47
                                      99****************************8887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHTT-EEEESECEEEEEE.EETCEEEEE.EECT.EEE.E.EEEEEEE--GGGHHHHHTTCTTTSE CS
                               DAO 145 pakltaalaraaealGveilegtevtglee.edgkvwgve.rttp.gen.d.aadavVnaaGawsdllgllkeldlp 216
                                       p ++  ++a   e+  + +++g +v ++ee e+g +  v  + t  ge+ + +++ vV+a+G +  l+     ++lp
  gi|488601590|ref|YP_007908061.1| 302 PGRFEDFYATVSEDENIVFVKG-KVAKIEEgENGNLIVVAeN-TLtGEKtRtEVEMVVLATGMQPELS----GVNLP 372
                                       777778888888999999****.*****88444666666553.4447663324455******996544....22234 PP

                                       EE CS
                               DAO 217 is 218
                                       i+
  gi|488601590|ref|YP_007908061.1| 373 IK 374
                                       43 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.5   2.5e-11   1.6e-08       2      37 ..      14      49 ..      13      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.5e-11
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      ++ViG+G+AGL+AAlea+eaG +v vve  ++ gg 
  gi|488601590|ref|YP_007908061.1| 14 ILVIGGGIAGLSAALEASEAGYDVYVVERNPYLGGR 49
                                      79*****************************99985 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1   6.5e-11   4.1e-08       1      36 [.      16      51 ..      16      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 6.5e-11
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      ++G+G++Gl+aA ++++ag+dv ++e++++lGGr+a
  gi|488601590|ref|YP_007908061.1| 16 VIGGGIAGLSAALEASEAGYDVYVVERNPYLGGRVA 51
                                      8*********************************86 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   6.8e-11   4.4e-08       2      39 ..      14      51 ..      13      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 6.8e-11
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                      ++V+GGg+aG+ AA+ A +aG  v +ve++++lGG ++
  gi|488601590|ref|YP_007908061.1| 14 ILVIGGGIAGLSAALEASEAGYDVYVVERNPYLGGRVA 51
                                      89*********************************865 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.0   2.1e-07   0.00014      31      50 ..     100     126 ..      59     127 .. 0.52
   2 !   13.4   0.4   0.00014     0.087       4      23 ..     165     184 ..     161     210 .. 0.84
   3 ?   -0.9   0.1       4.1   2.7e+03       7      15 ..     267     279 ..     254     317 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.1e-07
                            Fer4_7  31 v.......eidpekClgCgaCvavCPt 50 
                                       v       ++d +kC+ Cg+C++vCP+
  gi|488601590|ref|YP_007908061.1| 100 VtvrikprYVDISKCTACGECAKVCPV 126
                                       133344448899**************8 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00014
                            Fer4_7   4 gCgaCvaaCpvkaieldeee 23 
                                       +C +Cv+aC+++ai++  ee
  gi|488601590|ref|YP_007908061.1| 165 ECAKCVSACKYDAIDFSMEE 184
                                       7**************97653 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.1
                            Fer4_7   7 aCvaaC....pvk 15 
                                       +C a C    + +
  gi|488601590|ref|YP_007908061.1| 267 YCSAICclasMKQ 279
                                       7999984443222 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   4.6e-08     3e-05       1      71 [.      13      96 ..      13     110 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.6e-08
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS...TTSSHHHHHHH.........HHHHHHT.TEEEECSEEEEEE CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll...rllDeeaskil.........qeklekn.gievllntkveei 66
                                      +++v+GgG  gl +A +++e g +V+vver++ l     +l + + k++          ++++ n +i++l+ ++v+ +
  gi|488601590|ref|YP_007908061.1| 13 NILVIGGGIAGLSAALEASEAGYDVYVVERNPYLGgrvAQLYKYFPKLCppycgleilFRRIRTNpKIKFLTMSEVVDV 91
                                      589*****************************99864433333333222222222223566666666666666666666 PP

                                      EEETT CS
                         Pyr_redox 67 egsed 71
                                       gs+ 
  gi|488601590|ref|YP_007908061.1| 92 SGSPG 96
                                      66665 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 !   16.8   0.1     5e-06    0.0032       1      30 [.      15      43 ..      15      59 .. 0.84
   2 ?    4.0   0.0      0.04        25     108     137 ..     174     205 ..     165     233 .. 0.74
   3 ?    4.0   0.0     0.039        25     234     276 ..     324     371 ..     301     394 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      ++iG+G aGl+aa+e+ +ag  d+ ++E++
  gi|488601590|ref|YP_007908061.1| 15 LVIGGGIAGLSAALEASEAGY-DVYVVERN 43
                                      69*******************.789***97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.04
                       Pyr_redox_3 108 kkedegfevetsketyeAkkviiAtGe..fdk 137
                                       k ++  f+ e ++ +++A+++i+AtG   +d 
  gi|488601590|ref|YP_007908061.1| 174 KYDAIDFSMEEKTINIKAESIIVATGWkpYDA 205
                                       556667888999999***********522554 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.039
                       Pyr_redox_3 234 evkeikekeeeykvk....tedgkkvev.kddvvlatGykpdlsflkk 276
                                       +v +i+e e+   +     t +g+k+++  + vvlatG +p+ls ++ 
  gi|488601590|ref|YP_007908061.1| 324 KVAKIEEGENGNLIVvaenTLTGEKTRTeVEMVVLATGMQPELSGVNL 371
                                       455555443332221112233455555424566778999999987764 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   4.5   1.8e-08   1.2e-05       2      21 ..     108     127 ..     107     127 .. 0.93
   2 !   11.3   0.8   0.00037      0.24      11      24 .]     166     179 ..     164     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.8e-08
                                       EEETTTSSS-THHHHHSTTT CS
                              Fer4   2 videekCigCGaCvevCPvg 21 
                                       ++d +kC++CG+C++vCPv+
  gi|488601590|ref|YP_007908061.1| 108 YVDISKCTACGECAKVCPVE 127
                                       7999**************95 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00037
                                       -THHHHHSTTTEEE CS
                              Fer4  11 CGaCvevCPvgAIt 24 
                                       C +Cv++C ++AI+
  gi|488601590|ref|YP_007908061.1| 166 CAKCVSACKYDAID 179
                                       99**********95 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.1e-07   0.00046       2      29 ..      14      41 ..      13      66 .. 0.86
   2 ?   -1.1   0.0       1.2   7.4e+02     134     150 ..     184     200 ..     169     288 .. 0.74
   3 ?    2.0   0.1      0.14        90     103     150 ..     310     362 ..     304     376 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.1e-07
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLit 29
                                      + ViGgG AG+ AAl+a+++G++v  + 
  gi|488601590|ref|YP_007908061.1| 14 ILVIGGGIAGLSAALEASEAGYDVYVVE 41
                                      79**********************9883 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                       TTS-EEEECEEEE--TT CS
                              GIDA 134 edgetikakavviatGt 150
                                       e+   ika+++++atG 
  gi|488601590|ref|YP_007908061.1| 184 EKTINIKAESIIVATGW 200
                                       56667889999999995 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.14
                                       HHHHTSTTEEEEES-EEEEEECT.TEEEEEE..ETTS-EEEEC..EEEE--TT CS
                              GIDA 103 eklenepnleiieeeveelivee.kkvkgvv..tedgetikak..avviatGt 150
                                       +++++ +n+  ++++v++++  e +++ +v   t +ge+ +++   vv+atG 
  gi|488601590|ref|YP_007908061.1| 310 ATVSEDENIVFVKGKVAKIEEGEnGNLIVVAenTLTGEKTRTEveMVVLATGM 362
                                       5788899999999999999664442222222112233333333559*****95 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 !    8.9   0.1    0.0021       1.4       2      43 ..      16      52 ..      15      56 .. 0.86
   2 !   13.1   0.0   0.00011     0.069     103     155 ..     304     362 ..     279     363 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwr 43
                                      ++G+G++Gl+++ +  +        ++ +++++++ g grv++
  gi|488601590|ref|YP_007908061.1| 16 VIGGGIAGLSAALEASEA-----GYDVYVVERNPYlG-GRVAQ 52
                                      8*********99876666.....7**********956.99975 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                     NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradg.....qavll.adgaslaadaVvLAlGh 155
                                       +fe++ a+++e+ ++ +++++v ++ee ++g     ++ +l  ++++++++ VvLA+G+
  gi|488601590|ref|YP_007908061.1| 304 RFEDFYATVSEDENIVFVKGKVAKIEEGENGnlivvAENTLtGEKTRTEVEMVVLATGM 362
                                       689999999999*****************9944332122221344678**********8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.7   4.6e-05      0.03       1      14 [.     113     126 ..     103     141 .. 0.85
   2 !   12.3   0.6    0.0004      0.26       4      30 ..     165     192 ..     160     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-05
                           Fer4_16   1 rCgtCgkCaevCPt 14 
                                       +C+ Cg+Ca+vCP+
  gi|488601590|ref|YP_007908061.1| 113 KCTACGECAKVCPV 126
                                       48888888888886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0004
                           Fer4_16   4 tCgkCaevCPtnaikek.kekeiearec 30 
                                       +C kC+++C  +ai+   +ek+i+++++
  gi|488601590|ref|YP_007908061.1| 165 ECAKCVSACKYDAIDFSmEEKTINIKAE 192
                                       6**************8845555665544 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   8.1e-08   5.2e-05      28      65 ..      11      48 ..       4      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.1e-08
                                      --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHH CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparle 65
                                       +++lviGgG+aGl+A+  a++ g +V+v++ +p    
  gi|488601590|ref|YP_007908061.1| 11 SGNILVIGGGIAGLSAALEASEAGYDVYVVERNPYLGG 48
                                      589****************************9986655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.0   4.1e-07   0.00026       4      23 ..     109     128 ..     107     143 .. 0.72
   2 !   12.2   3.0   0.00023      0.15       2      43 ..     154     192 ..     153     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.1e-07
                           Fer4_10   4 idddtCirCgkCvkaCPadl 23 
                                       +d ++C+ Cg+C k+CP+  
  gi|488601590|ref|YP_007908061.1| 109 VDISKCTACGECAKVCPVER 128
                                       57789************933 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00023
                           Fer4_10   2 vvidddtC..irCgkCvkaCPadltsvgakgeaseeeavrkkve 43 
                                        vidd+ C   +C+kCv+aC     +++a+++ +ee+++++k e
  gi|488601590|ref|YP_007908061.1| 154 YVIDDSVCkkDECAKCVSAC-----KYDAIDFSMEEKTINIKAE 192
                                       689*****5559********.....6899999999999998876 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   0.3   1.5e-07   9.3e-05       2      38 ..      13      49 ..      12      52 .. 0.92
   2 ?   -0.9   0.0      0.77   4.9e+02     143     165 ..     180     201 ..     164     211 .. 0.73
   3 ?   -3.6   0.1       5.4   3.4e+03     131     163 ..     324     361 ..     315     363 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      +++viGgG AGl aA++a+++g +V ++e+++ lg +
  gi|488601590|ref|YP_007908061.1| 13 NILVIGGGIAGLSAALEASEAGYDVYVVERNPYLGGR 49
                                      589****************************999866 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.77
                                       EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 143 frvktkseeeleadklvlAtGGl 165
                                       f+++  ++ +++a+++++AtG +
  gi|488601590|ref|YP_007908061.1| 180 FSMEE-KTINIKAESIIVATGWK 201
                                       44444.67799*********966 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.4
                                       -EEEEECETTE.EEEEE......TTEEEEESEEEE--- CS
                       HI0933_like 131 evksvekeedgkfrvktk.....seeeleadklvlAtG 163
                                       +v+++e+ e+g++ v ++     ++++ e + +vlAtG
  gi|488601590|ref|YP_007908061.1| 324 KVAKIEEGENGNLIVVAEntltgEKTRTEVEMVVLATG 361
                                       66667666666666555324444567788888999988 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.7e-07   0.00056       1      32 [.      21      52 ..      21      56 .. 0.94
   2 ?   -2.3   0.1       3.2   2.1e+03     230     261 ..     324     361 ..     314     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.7e-07
                                      HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-E CS
                     Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrvGGRirt 32
                                      +aGL+aA + ++aG+dV v+E ++ +GGR++ 
  gi|488601590|ref|YP_007908061.1| 21 IAGLSAALEASEAGYDVYVVERNPYLGGRVAQ 52
                                      8****************************975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                       EEEEEEEETTC....EEEEETTSTEE..EESEEEE-S- CS
                     Amino_oxidase 230 rVkeikregdg....vtvtledgevv..eaDaVvvTvp 261
                                       +V +i+ +++g    v+ ++ +ge++  e+  Vv+++ 
  gi|488601590|ref|YP_007908061.1| 324 KVAKIEEGENGnlivVAENTLTGEKTrtEVEMVVLATG 361
                                       79999998888889999999999999999999999986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.9   1.6e-05      0.01      37      54 ..     110     127 ..      99     129 .. 0.84
   2 !    8.7   2.8    0.0028       1.8       3      33 ..     156     185 ..     154     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                           Fer4_21  37 vedeCvGCnlCssvCPve 54 
                                         ++C++C  C++vCPve
  gi|488601590|ref|YP_007908061.1| 110 DISKCTACGECAKVCPVE 127
                                       4589************95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                           Fer4_21   3 idedkCi..gCgkCliaCedtshqaieidaktv 33 
                                       id++ C   +C kC+ aC+   ++ai+++ +++
  gi|488601590|ref|YP_007908061.1| 156 IDDSVCKkdECAKCVSACK---YDAIDFSMEEK 185
                                       7778886336*********...89998875544 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   4.3   7.7e-07   0.00049       4      21 ..     109     126 ..     108     131 .. 0.92
   2 !   11.2   4.5   0.00047       0.3       3      24 .]     155     178 ..     155     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.7e-07
                            Fer4_6   4 idpdkCigCgdCvrvCPe 21 
                                       +d +kC+ Cg+C++vCP 
  gi|488601590|ref|YP_007908061.1| 109 VDISKCTACGECAKVCPV 126
                                       899**************6 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00047
                            Fer4_6   3 eidpdkCi..gCgdCvrvCPegai 24 
                                       +id++ C    C +Cv++C ++ai
  gi|488601590|ref|YP_007908061.1| 155 VIDDSVCKkdECAKCVSACKYDAI 178
                                       689999*9555***********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 !   16.9   3.7   7.8e-06     0.005       4      21 ..     108     125 ..     105     126 .. 0.89
   2 !    7.9   1.7    0.0054       3.5       3      21 ..     154     174 ..     152     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.8e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                       +vd  +C++Cg C ++CP
  gi|488601590|ref|YP_007908061.1| 108 YVDISKCTACGECAKVCP 125
                                       78999************* PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0054
                            Fer4_2   3 vvvdtdrCig..CgaCvsaCP 21 
                                       +v+d   C    C +CvsaC 
  gi|488601590|ref|YP_007908061.1| 154 YVIDDSVCKKdeCAKCVSACK 174
                                       678888995445********5 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2     3e-06    0.0019       4      33 ..      14      43 ..      12      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3e-06
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      +l++G+G aGl++al+ seaG +v +ve+ 
  gi|488601590|ref|YP_007908061.1| 14 ILVIGGGIAGLSAALEASEAGYDVYVVERN 43
                                      79**************************96 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0027       1.7       1      33 [.      13      42 ..      13      47 .. 0.90
   2 !    7.5   0.0    0.0025       1.6     144     214 ..     290     367 ..     249     376 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0027
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      +i+++GGG+aG  aA   ++a+   ++v +ve 
  gi|488601590|ref|YP_007908061.1| 13 NILVIGGGIAGLSAALEASEAG---YDVYVVER 42
                                      599************9999999...89999986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                                       -S--EEEE-H...HHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT....S-EEE-SEEEE-SGGG-II CS
                    Trp_halogenase 144 alsyAyhlda...alyakfLrrvaearGvtrvegkvvevqldedgrveslrled....greveadlfiDcsGfrgll 213
                                       a  y + +d    +++++f  +v+e++++  v+gkv++++  e+g+   +  ++     ++ e+++++ ++G++  l
  gi|488601590|ref|YP_007908061.1| 290 AKVYIFYIDIrapGRFEDFYATVSEDENIVFVKGKVAKIEEGENGNLIVVAENTltgeKTRTEVEMVVLATGMQPEL 366
                                       444555555322268****************************9997666655555445678999***9*9998777 PP

                                       I CS
                    Trp_halogenase 214 i 214
                                        
  gi|488601590|ref|YP_007908061.1| 367 S 367
                                       6 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.1   6.8e+02     192     207 ..      12      27 ..       3      46 .. 0.57
   2 ?    0.0   0.0      0.58   3.7e+02     141     160 ..     183     202 ..     169     215 .. 0.72
   3 !   11.4   0.0    0.0002      0.13     299     341 ..     321     363 ..     305     364 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                       K_oxygenase 192 kriaVvGsGqSaaeif 207
                                        +i+V+G+G  +   +
  gi|488601590|ref|YP_007908061.1|  12 GNILVIGGGIAGLSAA 27 
                                       5677777776554333 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.58
                       K_oxygenase 141 egeeeelearnlvlgvGtep 160
                                       e+++ +++a+++++++G +p
  gi|488601590|ref|YP_007908061.1| 183 EEKTINIKAESIIVATGWKP 202
                                       44555666677777777666 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0002
                       K_oxygenase 299 pnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                                        + +v ++e+ ++g++ +  +n+ +ge++++ev++vvlATG +
  gi|488601590|ref|YP_007908061.1| 321 VKGKVAKIEEGENGNLIVVAENTLTGEKTRTEVEMVVLATGMQ 363
                                       4568999****999***************************75 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00021      0.13       2      34 ..      14      44 ..      13      50 .. 0.86
   2 ?    1.8   0.0      0.15        99     100     140 ..     316     361 ..     304     375 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasp 34
                                      ++viG+G Agls A +   +++g  v ++e  p
  gi|488601590|ref|YP_007908061.1| 14 ILVIGGGIAGLSAALEA--SEAGYDVYVVERNP 44
                                      79***************..88888888888766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                     Lycopene_cycl 100 ngvklleakvesveeeeageslvvleggr.....kirarlvvdarg 140
                                       +++ ++++kv+++ee e+g+  vv e+       + +  +vv a+g
  gi|488601590|ref|YP_007908061.1| 316 ENIVFVKGKVAKIEEGENGNLIVVAENTLtgektRTEVEMVVLATG 361
                                       567899************9999987753222234556667777777 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   2.3   1.6e-05      0.01      33      48 ..     108     126 ..      85     129 .. 0.74
   2 ?   13.1  14.4   0.00013      0.08       1      51 []     113     178 ..     113     178 .. 0.77
   3 ?    6.8   3.3     0.012       7.6       4      17 ..     165     178 ..     161     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                            Fer4_9  33 e...eaCigCgaCveaCpk 48 
                                       +   ++C+ Cg+C+++Cp 
  gi|488601590|ref|YP_007908061.1| 108 YvdiSKCTACGECAKVCPV 126
                                       144578***********96 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00013
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.............eaC..igCgaCveaCpkgai 51 
                                       kCt Cg+C ++Cp +  ++ + +      ++               + C   +C +Cv aC+ +ai
  gi|488601590|ref|YP_007908061.1| 113 KCTACGECAKVCPVERDNDFNYGMDKTKAIYLPhdlafpmkyviddSVCkkDECAKCVSACKYDAI 178
                                       7***********88877666655554443333366789999999998897677*********9987 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.012
                            Fer4_9   4 gCgaCveaCpagvv 17 
                                       +C +Cv+aC+++++
  gi|488601590|ref|YP_007908061.1| 165 ECAKCVSACKYDAI 178
                                       46666666666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011     0.071      19      57 ..      13      50 ..       9      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                      +++++G+G +GL+aa   +++ +  v ++er+  +GG +
  gi|488601590|ref|YP_007908061.1| 13 NILVIGGGIAGLSAALEASEA-GYDVYVVERNPYLGGRV 50
                                      699**************9999.*********99999865 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   3.2   6.3e-05      0.04      47      63 ..     110     126 ..      84     128 .. 0.83
   2 ?    9.9  11.1    0.0016         1       2      62 ..     111     174 ..     110     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.3e-05
                            Fer4_8  47 alwsCttcgaCtevCpv 63 
                                        + +Ct+cg+C++vCpv
  gi|488601590|ref|YP_007908061.1| 110 DISKCTACGECAKVCPV 126
                                       57899999999999998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0016
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtk.khlldargeaae.........dvqeeqvleeeealwsCttcgaCtevCp 62 
                                       ++kC+ Cg C + Cpv r+ + +  +d+ +             +v        ++++ +  +c +C+++C+
  gi|488601590|ref|YP_007908061.1| 111 ISKCTACGECAKVCPVERDNDfNYGMDKTKAIYLphdlafpmkYVI-------DDSVCKKDECAKCVSACK 174
                                       689999*****99*99999986666665555555554444443333.......333444466777777776 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.9   8.1e-05     0.052      42      58 ..     110     126 ..      59     129 .. 0.75
   2 ?    8.3  12.1    0.0052       3.3       1      58 [.     113     175 ..     113     177 .. 0.62
   3 ?    2.4   1.9      0.37   2.4e+02       4      15 ..     165     176 ..     160     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.1e-05
                           Fer4_17  42 kaslCieCgeCerkCPq 58 
                                        +s+C+ CgeC+++CP 
  gi|488601590|ref|YP_007908061.1| 110 DISKCTACGECAKVCPV 126
                                       6899***********96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0052
                           Fer4_17   1 rCiqCgyClpeCpsyeaydne.pkkllraakl.....glleeaeke..ekaslCieCgeCerkCPq 58 
                                       +C+ Cg C+++Cp  +++d++  +   +a++l       +++++++  +k +   eC +C+++C +
  gi|488601590|ref|YP_007908061.1| 113 KCTACGECAKVCPVERDNDFNyGMDKTKAIYLphdlaFPMKYVIDDsvCKKD---ECAKCVSACKY 175
                                       6****************88742334444444454443245666666233444...55666667665 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.37
                           Fer4_17   4 qCgyClpeCpsy 15 
                                       +C+ C+ +C + 
  gi|488601590|ref|YP_007908061.1| 165 ECAKCVSACKYD 176
                                       455566666553 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5    0.0004      0.25      57      76 ..     110     129 ..      98     138 .. 0.84
   2 ?    1.1   0.9      0.69   4.4e+02      87      96 ..     165     174 ..     156     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                           Fer4_18  57 gagdcidcescvkvcPtgid 76 
                                       + ++c++c+ c kvcP++ d
  gi|488601590|ref|YP_007908061.1| 110 DISKCTACGECAKVCPVERD 129
                                       5679************9765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.69
                           Fer4_18  87 scllcidacd 96 
                                       +c++c+ ac+
  gi|488601590|ref|YP_007908061.1| 165 ECAKCVSACK 174
                                       5888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2312.98
//
Query:       gi|488601591|ref|YP_007908062.1|  [L=638]
Description: dissimilatory adenylylsulfate reductase alpha subunit precursor [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   48.6   0.7    2.1e-12   46.8   0.1    2.1  2  FAD_binding_2   FAD binding domain
    3.6e-07   30.2   0.0    7.7e-07   29.1   0.0    1.5  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
     0.0014   18.2   0.1     0.0036   16.9   0.1    1.7  1  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.072   12.3   1.1       0.68    9.1   0.2    2.6  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.072   12.4   0.2       0.14   11.4   0.2    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.076   12.4   2.6      0.046   13.1   0.7    1.6  2  FAD_oxidored    FAD dependent oxidoreductase
      0.092   11.8   3.9        0.7    8.9   1.3    2.2  2  GIDA            Glucose inhibited division protein A
      0.097   13.1   0.0       0.22   12.0   0.0    1.5  1  DUF3140         Protein of unknown function (DUF3140)
       0.18   11.0   1.3       0.34   10.1   0.5    1.8  2  Thi4            Thi4 family


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.1   1.1e-15   2.1e-12       1     242 [.      13     246 ..      13     257 .. 0.85
   2 ?   -3.0   0.1       1.4   2.9e+03     387     408 ..     422     443 ..     418     447 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.1e-15
                                       SEEEE--SHHHHHHHHHH...HH.TTT-EEEEESSSGGGS.GGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHH CS
                     FAD_binding_2   1 DviViGsGlAGLaAAlea...ae.aGlkvavvekeqefgg.atawsqGgidavlspeqkkagikdspelhrtdtlka 72 
                                       Dv++ G+G++G+ AA+ea   a+  G kv++v+k+   ++ a a+    i+ +l    +++ ++ +pe+ ++++++ 
  gi|488601591|ref|YP_007908062.1|  13 DVLILGGGMSGCGAAVEAcywAKpLGMKVVLVDKAAIDRSgAVAMGLSAINTYLGMSGRASYGQWTPEDFVKYVRTD 89 
                                       9***************98444334899********99888799***********6666777777899********** PP

                                       TTT-S-HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHH CS
                     FAD_binding_2  73 ldeladqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlve 149
                                       l +   ++lv  +++++   v+ +e++g+p+ +++dg++   + G     ++++  ++        + + ++a  ++
  gi|488601591|ref|YP_007908062.1|  90 LMGIVREDLVYDVARHVDSSVHLFEKWGLPIWKDKDGKYV--REGP----WQVMI-NGE-------SYKVIVAEAAK 152
                                       *******************************996776554..3343....34445.555.......57788888888 PP

                                       HHHTCTEEEEESEEEEEEEECTT...EEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGT CS
                     FAD_binding_2 150 sarkagvdfqerteadeLivedg...rvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnap 223
                                       s+++ +  ++er  +++L+++d+   rv Gav    ++ +   ++akav++a gG+ +  ++++    +   +  +p
  gi|488601591|ref|YP_007908062.1| 153 SVLD-PENIYERVMITHLLTDDNdpnRVCGAVGFSVREDKFYVFKAKAVICAMGGAVH-VFRPRSTGEGLGRAWYPP 227
                                       8855.489************988899*****999778888889**************6.8989988889999999** PP

                                       T-S-HHHHHHHCTTSSEES CS
                     FAD_binding_2 224 avtGdglalalragaalnd 242
                                       ++ G   al +++ga+l+ 
  gi|488601591|ref|YP_007908062.1| 228 WNAGSTYALMAQVGAELTC 246
                                       ***************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                       TEEESSBTEEE-STCEESSSST CS
                     FAD_binding_2 387 adgqpipGLYAaGevaaggvhg 408
                                       +  +++ GL+ +G  a+++ h 
  gi|488601591|ref|YP_007908062.1| 422 NRMTTVMGLFTCGDGAGASGHK 443
                                       5567999******999777665 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.9e-10   7.7e-07       3     114 ..     517     630 ..     516     635 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.9e-10
                                       HHHHHHHHHSS.....SSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH- CS
                    Succ_DH_flav_C   3 eLgkimqkkvg.....vfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaR 74 
                                       +L+kim+++vg        +e+ ++++lk l+ l+e+ ++++ +d +     el +++e  + + +Aea a+  laR
  gi|488601591|ref|YP_007908062.1| 517 RLQKIMDEYVGgistyYTTSEKMIEQGLKLLQFLKEDSEKLAAEDLH-----ELQRVWENIHRMWVAEAHARTILAR 588
                                       58999999997322222345777899999999999999999888864.....7899999999999************ PP

                                       -S-B..TTBEBTTS-SEETTT-SEEEEE...TT-SS-EEEEE CS
                    Succ_DH_flav_C  75 kESr..GaHaredfperdDenwlkhtlasldaakeeveleye 114
                                       kE r  G ++r d+pe dD+nw+k   + ++++++e e+  +
  gi|488601591|ref|YP_007908062.1| 589 KETRypGYYYRADYPELDDANWRKFVNVRYNPQTDEWEVIER 630
                                       ****8899********************99999998887655 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.8e-06    0.0036       1      36 [.      13      54 ..      13     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                                      EEEEECTSHHHHHHHHHH...HHT.T..EEEEESSSSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeL...arr.g..Vtllekgdiagsga 36
                                      dv+i GGG+ G+++A e+   a+  g  V+l++k+ i  sga
  gi|488601591|ref|YP_007908062.1| 13 DVLILGGGMSGCGAAVEAcywAKPlGmkVVLVDKAAIDRSGA 54
                                      8*****************664443559*******96655454 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00034      0.68       2      42 ..      13      61 ..      12     218 .. 0.80
   2 ?   -2.1   0.0      0.86   1.7e+03     266     278 ..     425     437 ..     421     446 .. 0.80
   3 ?   -0.0   0.0       0.2   4.1e+02      10      99 ..     454     558 ..     452     562 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00034
                                      SEEEE--SHHHHHHHHHHHH....HTS-EEEEE....TTHCHHHCSHHH CS
                                      xxxxxxxxxxxxxxxxxxxx....xxxxxxxxx....xxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaq....agakvtlve....legtclnggcll 42
                                      dv+++GgG+ G+ aa ++       g+kv+lv+    ++   +  g + 
  gi|488601591|ref|YP_007908062.1| 13 DVLILGGGMSGCGAAVEACYwakpLGMKVVLVDkaaiDRSGAVAMGLSA 61
                                      89999***99999999987776667999999976666555555555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.86
                                       ESSTTEEE-GGGC CS
                                       xxxxxxxxxxxxx RF
                       Pyr_redox_2 266 tnvpgiyaiGDva 278
                                       t+v g++ +GD a
  gi|488601591|ref|YP_007908062.1| 425 TTVMGLFTCGDGA 437
                                       7899*******99 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHH.HTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH.............HHHHCHHHHCC CS
                                       xxxxxxxxxxxx.xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxx RF
                       Pyr_redox_2  10 pAGlaaaltlaq.agakvtlve....legtclnggcllskallgvaedaeias.............evvkklnqgie 68 
                                       +AG aa ++++  + +  ++ e    + ++++++   l++ +  +  ++ei               + ++++  gi 
  gi|488601591|ref|YP_007908062.1| 454 IAGKAAVKFARDhKDYTPAVSEerikKLKEIVYRPLNLYEQYKDATTRPEINPnyirpkmfmfrlqKIMDEYVGGIS 530
                                       689999999999447777777678877788999999999999999999998889999********999999999999 PP

                                       CCHCCTCEEEEESCEEEEETEEECTCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklekkkegdeekia 99 
                                       ++++++   i++g k ++  k   +d ek+a
  gi|488601591|ref|YP_007908062.1| 531 TYYTTSEKMIEQGLKLLQFLK---EDSEKLA 558
                                       999988888877776666643...3344555 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 ?   11.4   0.2     7e-05      0.14      28      61 ..      11      48 ..       4      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7e-05
                                      --EEEEESTSHHHHHHH....HHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqAi....atakglgakVtvlDvrp 61
                                      +a vl++GgG+ G  A+      ak lg kV+++D+ +
  gi|488601591|ref|YP_007908062.1| 11 EADVLILGGGMSGCGAAveacYWAKPLGMKVVLVDKAA 48
                                      599********998666111156899*******99875 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7   2.3e-05     0.046       1      30 [.      13      46 ..      13      49 .. 0.82
   2 ?   -3.5   0.0       2.4   4.7e+03     205     229 ..     545     571 ..     470     612 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAa....raGakvlLvee 30
                                      Dv++ GGg++G+ AA+ A+      G kv+Lv++
  gi|488601591|ref|YP_007908062.1| 13 DVLILGGGMSGCGAAVEACywakPLGMKVVLVDK 46
                                      9***************975222268999999987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.4
                      FAD_oxidored 205 nrvpfe.kkpegydparyel.arvfea 229
                                       + ++f  +  e+++ ++ +  +rv+e+
  gi|488601591|ref|YP_007908062.1| 545 KLLQFLkEDSEKLAAEDLHElQRVWEN 571
                                       222222122222222222223333333 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.3   0.00035       0.7       1      29 [.      13      46 ..      13      73 .. 0.75
   2 ?    3.2   0.1     0.019        38     350     389 ..     424     464 ..     413     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00035
                                      CEEEE-SSHHHHHHHHHH....HHTT--EEEE.E CS
                              GIDA  1 dviViGgGhAGceAAlaa....arlGakvlLi.t 29
                                      dv ++GgG++Gc AA++a    + lG+kv+L+  
  gi|488601591|ref|YP_007908062.1| 13 DVLILGGGMSGCGAAVEAcywaKPLGMKVVLVdK 46
                                      799********97776642221779999999952 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.019
                                       SBBSSSBTEEE-CGGGTB-SHHHHHH...HHHHHHHHHHHHHC CS
                              GIDA 350 LetkkvkgLflAGqinGteGYeEaaa...qGllAGinaarkak 389
                                       +   +v gLf++G+  G +G+  + +    G +AG  a++ a+
  gi|488601591|ref|YP_007908062.1| 424 M--TTVMGLFTCGDGAGASGHKFSSGsftEGRIAGKAAVKFAR 464
                                       4..4579*************9988776779*****99988766 PP

>> DUF3140  Protein of unknown function (DUF3140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.22      37      78 ..     540     581 ..     530     594 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                           DUF3140  37 hesGrkiveilrkkkadltdddlehmrkVvgyvkrhlaqeep 78 
                                        e+G k ++ l+ ++++l ++dl+ +++V + ++r    e +
  gi|488601591|ref|YP_007908062.1| 540 IEQGLKLLQFLKEDSEKLAAEDLHELQRVWENIHRMWVAEAH 581
                                       57899******************************9865454 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00017      0.34      13      50 ..       7      47 ..       3      62 .. 0.78
   2 ?   -3.8   0.0       3.1   6.2e+03     141     163 ..     144     166 ..     137     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                                      HHHTEEEEEEE--SHHHHHHHH...HHHHCTTS-EEEEESS CS
                              Thi4 13 lkyaesDvvivGaGssGLtaay...ylakkpdlkvailers 50
                                      +k +e+Dv+i G+G sG  aa    y ak  ++kv+++++ 
  gi|488601591|ref|YP_007908062.1|  7 IKEVEADVLILGGGMSGCGAAVeacYWAKPLGMKVVLVDKA 47
                                      56689*************9975222778889****999875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.1
                                       HHHTCTTTSS.-B-EEEEEEEEE CS
                              Thi4 141 lvelahdtqscvDPlvirakvvv 163
                                        v +a   +s++DP  i  +v++
  gi|488601591|ref|YP_007908062.1| 144 KVIVAEAAKSVLDPENIYERVMI 166
                                       45555566788888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); 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: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 3649.86
//
Query:       gi|488601592|ref|YP_007908063.1|  [L=147]
Description: dissimilatory adenylylsulfate reductase beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-35  119.0   0.0    9.9e-35  118.6   0.0    1.2  1  APS-reductase_C  Adenosine-5'-phosphosulfate reductase beta s
      2e-10   40.7  10.8    2.9e-10   40.1  10.8    1.3  1  Fer4_9           4Fe-4S dicluster domain
    3.3e-09   36.2  12.5    3.7e-06   26.5   2.9    3.3  3  Fer4             4Fe-4S binding domain
    1.7e-08   34.9  10.4    2.9e-08   34.2  10.4    1.4  1  Fer4_7           4Fe-4S dicluster domain
    4.9e-05   23.2  11.7     0.0052   16.8   2.4    2.4  2  Fer4_2           4Fe-4S binding domain
    8.7e-05   22.7  11.8      0.066   13.8   3.8    2.4  2  Fer4_4           4Fe-4S binding domain
    0.00015   21.7  14.7     0.0099   15.9   2.9    2.6  2  Fer4_6           4Fe-4S binding domain
    0.00019   22.2  12.9      0.011   16.6   3.8    2.4  2  Fer4_3           4Fe-4S binding domain
    0.00053   20.1  14.9      0.014   15.5   4.2    2.0  2  Fer4_10          4Fe-4S dicluster domain
     0.0087   17.0  11.0      0.024   15.5   2.4    2.5  2  Fer4_16          4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.011   15.8  10.2      0.031   14.4  10.2    1.7  1  Fer4_21          4Fe-4S dicluster domain
      0.016   15.4   0.7      0.016   15.4   0.7    1.9  2  Fer4_18          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> APS-reductase_C  Adenosine-5'-phosphosulfate reductase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.0   6.6e-38   9.9e-35       1      79 [.      64     141 ..      64     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 6.6e-38
                                       E---TTT--TT-EEEEEE-SSEEEEEEE-TTS-EEEEEEE--SS-TT---TTTT-----HHHHTSS--TTTTGGGTS CS
                   APS-reductase_C   1 vRgYaDfvPlGasvvplrgeekimWtvkfRnGkvkrfkfpirTtpeGsaqpladvaepskedldselLftepkslrl 77 
                                       vR YaDf+PlGa v+plrg+++imWtv+fRnG+vkrfkfpirTtpeGs+++ ++++e + edldselLf ep++l++
  gi|488601592|ref|YP_007908063.1|  64 VRCYADFAPLGARVTPLRGSDSIMWTVQFRNGTVKRFKFPIRTTPEGSIKAHDGFPEAKPEDLDSELLFSEPDTLEV 140
                                       8************************************************************************9998 PP

                                       SS CS
                   APS-reductase_C  78 de 79 
                                        e
  gi|488601592|ref|YP_007908063.1| 141 -E 141
                                       .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 !   40.1  10.8     2e-13   2.9e-10       1      51 []       9      62 ..       9      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2e-13
                            Fer4_9  1 kCtgCga.....CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC gC+a     C++ Cp++++v d+ ++ka +r+ ++  C++C  Cv++Cp+gai
  gi|488601592|ref|YP_007908063.1|  9 KCDGCKAldktaCQYICPNDLMVLDKEKEKAYNREPEM--CWECYNCVKICPQGAI 62
                                      7****7666667*********************99876..**************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   0.00012      0.18       2      13 ..       4      15 ..       3      15 .. 0.90
   2 ?    3.6   0.1     0.042        63      13      21 ..      20      28 ..      19      30 .. 0.90
   3 !   26.5   2.9   2.5e-09   3.7e-06       5      24 .]      44      63 ..      40      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                      EEETTTSSS-TH CS
                              Fer4  2 videekCigCGa 13
                                      ++++ekC gC+a
  gi|488601592|ref|YP_007908063.1|  4 YVNPEKCDGCKA 15
                                      79********86 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.042
                                      HHHHHSTTT CS
                              Fer4 13 aCvevCPvg 21
                                      aC  +CP++
  gi|488601592|ref|YP_007908063.1| 20 ACQYICPND 28
                                      7******97 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 2.5e-09
                                      TTTSSS-THHHHHSTTTEEE CS
                              Fer4  5 eekCigCGaCvevCPvgAIt 24
                                      +e+C  C +Cv++CP gAI+
  gi|488601592|ref|YP_007908063.1| 44 PEMCWECYNCVKICPQGAIE 63
                                      9******************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 !   34.2  10.4   1.9e-11   2.9e-08       1      52 []       9      61 ..       9      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.9e-11
                            Fer4_7  1 rCigCg.....aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C gC+     aC+  Cp++ + ld+e+     + ++ +pe+C+ C++Cv+ CP ga
  gi|488601592|ref|YP_007908063.1|  9 KCDGCKaldktACQYICPNDLMVLDKEK----EKAYNREPEMCWECYNCVKICPQGA 61
                                      7****777777*************9983....355899****************997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.4   3.5e-06    0.0052       4      22 .]       4      27 ..       2      27 .. 0.90
   2 !   11.4   2.0   0.00019      0.28       6      22 .]      43      59 ..      39      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.5e-06
                            Fer4_2  4 vvdtdrCigCg.....aCvsaCPa 22
                                      +v++++C gC+     aC+  CP+
  gi|488601592|ref|YP_007908063.1|  4 YVNPEKCDGCKaldktACQYICPN 27
                                      79********888889*******5 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00019
                            Fer4_2  6 dtdrCigCgaCvsaCPa 22
                                      ++++C +C  Cv+ CP+
  gi|488601592|ref|YP_007908063.1| 43 EPEMCWECYNCVKICPQ 59
                                      5789************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 !   13.5   1.0   5.3e-05     0.079       1      15 [.       7      26 ..       7      37 .. 0.86
   2 !   13.8   3.8   4.4e-05     0.066       1      17 []      44      60 ..      44      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-05
                            Fer4_4  1 qerCigCgs.....CvaaCP 15
                                      +e+C gC++     C ++CP
  gi|488601592|ref|YP_007908063.1|  7 PEKCDGCKAldktaCQYICP 26
                                      69******667777****** PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.4e-05
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      +e C +C  Cv +CPqg
  gi|488601592|ref|YP_007908063.1| 44 PEMCWECYNCVKICPQG 60
                                      589************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 !   10.9   4.1   0.00026      0.38       3      20 ..       4      26 ..       2      32 .. 0.89
   2 !   15.9   2.9   6.6e-06    0.0099       6      24 .]      44      62 ..      42      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                            Fer4_6  3 eidpdkCigCgd.....CvrvCP 20
                                       ++p+kC+gC +     C  +CP
  gi|488601592|ref|YP_007908063.1|  4 YVNPEKCDGCKAldktaCQYICP 26
                                      69********9999999999999 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.6e-06
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                      p+ C  C++Cv++CP gai
  gi|488601592|ref|YP_007908063.1| 44 PEMCWECYNCVKICPQGAI 62
                                      778889*********9998 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   1.7   0.00058      0.87       1      13 [.      10      27 ..      10      28 .. 0.88
   2 !   16.6   3.8   7.3e-06     0.011       1      15 []      47      61 ..      47      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00058
                            Fer4_3  1 CtgCg.....aCvevCPv 13
                                      C+gC      aC   CP+
  gi|488601592|ref|YP_007908063.1| 10 CDGCKaldktACQYICPN 27
                                      ****8788889******7 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7.3e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C+ Cv+ CP gA
  gi|488601592|ref|YP_007908063.1| 47 CWECYNCVKICPQGA 61
                                      9************99 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   3.4   0.00089       1.3      40      56 .]       5      26 ..       2      26 .. 0.81
   2 !   15.5   4.2   9.2e-06     0.014       4      23 ..      42      61 ..      39      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00089
                           Fer4_10 40 kkvekCtgc.....gaCveaCP 56
                                      +++ekC+gc     +aC+ +CP
  gi|488601592|ref|YP_007908063.1|  5 VNPEKCDGCkaldkTACQYICP 26
                                      57899****666666******9 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9.2e-06
                           Fer4_10  4 idddtCirCgkCvkaCPadl 23
                                      ++++ C +C +Cvk CP+ +
  gi|488601592|ref|YP_007908063.1| 42 REPEMCWECYNCVKICPQGA 61
                                      67899************955 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.5     0.017        26       6      29 ..      19      42 ..       9      45 .. 0.68
   2 !   15.5   2.4   1.6e-05     0.024       2      20 ..      47      65 ..      46      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                           Fer4_16  6 gkCaevCPtnaikekkekeieare 29
                                      ++C  +CP + +  +keke ++++
  gi|488601592|ref|YP_007908063.1| 19 TACQYICPNDLMVLDKEKEKAYNR 42
                                      469999999999988777665555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C +C +C+++CP++ai+ +
  gi|488601592|ref|YP_007908063.1| 47 CWECYNCVKICPQGAIEVR 65
                                      99**************976 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4  10.2   2.1e-05     0.031       3      58 ..       5      63 ..       3      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                           Fer4_21  3 idedkCigC.....gkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      ++++kC gC     + C   C++     +++++++ ++   + C  C  C+++CP +++ie
  gi|488601592|ref|YP_007908063.1|  5 VNPEKCDGCkaldkTACQYICPN-DLMVLDKEKEKAYNREPEMCWECYNCVKICP-QGAIE 63
                                      78889988844444479999994.444556666666677789*************.79997 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.87   1.3e+03       4      12 ..      19      27 ..      16      31 .. 0.74
   2 ?   15.4   0.7     1e-05     0.016      47      78 ..      33      65 ..      27      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.87
                           Fer4_18  4 dvcvyvcPy 12
                                        c y+cP 
  gi|488601592|ref|YP_007908063.1| 19 TACQYICPN 27
                                      568888884 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1e-05
                           Fer4_18 47 lkekeerkekgagdcidcescvkvcPtg.idir 78
                                       keke+  +++   c +c  cvk+cP g i++r
  gi|488601592|ref|YP_007908063.1| 33 DKEKEKAYNREPEMCWECYNCVKICPQGaIEVR 65
                                      57788888888899************9746776 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:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 908.28
//
Query:       gi|488601593|ref|YP_007908064.1|  [L=121]
Description: hypothetical protein Asulf_02113 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   13.5   0.2      0.036   13.5   0.2    2.2  2  UBM       Ubiquitin binding region


Domain annotation for each model (and alignments):
>> UBM  Ubiquitin binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2     2e-06     0.036       4      28 ..      54      78 ..      42      81 .. 0.86
   2 ?   -0.1   0.2      0.04   7.1e+02       3      12 ..     111     119 ..     109     121 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-06
                               UBM  4 pppegiDp.sFLaaLPpdLReEVLaq 28
                                      p++  iD  sFL+ LP + R++  ++
  gi|488601593|ref|YP_007908064.1| 54 PNAR-IDSrSFLEDLPVAFRRALFQE 78
                                      4455.****************98876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.04
                               UBM   3 apppegiDps 12 
                                       +ppp+ iD+s
  gi|488601593|ref|YP_007908064.1| 111 IPPPD-IDTS 119
                                       56777.9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 669.17
//
Query:       gi|488601594|ref|YP_007908065.1|  [L=454]
Description: sulfate adenylyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-73  245.3   0.0    5.7e-73  244.9   0.0    1.2  1  ATP-sulfurylase  ATP-sulfurylase
    9.8e-33  113.1   0.0    1.5e-32  112.5   0.0    1.3  1  PUA_2            PUA-like domain
  ------ inclusion threshold ------
      0.066   12.9   0.0       0.14   11.9   0.0    1.5  1  DUF309           Domain of unknown function (DUF309)
      0.098   12.6   0.1        0.2   11.7   0.1    1.5  1  DUF1610          Domain of unknown function (DUF1610)
       0.18   11.4   0.0       0.33   10.6   0.0    1.3  1  DUF4105          Domain of unknown function (DUF4105)


Domain annotation for each model (and alignments):
>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.9   0.0   1.6e-76   5.7e-73       2     212 .]     193     421 ..     192     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: 244.9 bits;  conditional E-value: 1.6e-76
                                       CCB.-HHHHHHHHHHTT-SSEEEEEESS---HHHHHHHHHHHHH.TSE...EEEEEEB-SB-STTSTTHHHHHHHHH CS
                   ATP-sulfurylase   2 eyrltPaevreefkekgwdkVvAfqtrnplHraHeellkralee.ead...glllhplvgptkpgdvpaevrvraye 74 
                                       ++++ Pa++reefk+kgw++ +A+qtrn++H +He+l+k+a+ + +++   g+l+++++g+++ gd+p+e++++ ++
  gi|488601594|ref|YP_007908065.1| 193 KFWFPPAKCREEFKKKGWRTAIAHQTRNVPHVGHEALMKNAAYTgDVEpcrGILVNAIIGAKRRGDYPDEAILEGHA 269
                                       799****************************************874444446************************* PP

                                       HHHHH.HS-GGGEEE-BB-SB---SCHHHHHHHHHHHHHTT-SEEEE-TTTT-STCSS-TTHHHHHHHHCHHH.... CS
                   ATP-sulfurylase  75 aliee.ylpkdrvvlallplamryaGprEallhaiirknyGcthfivGrdhagvgdfYgpydaqellakvage.... 146
                                       a+++  y++++r++++++ ++mry++p E+llh iir+n+Gcth+++Grdha+vg++Y+ y++q l++k  ++    
  gi|488601594|ref|YP_007908065.1| 270 AVNRFgYIKPERHMVTFTLWDMRYGNPIESLLHGIIRQNMGCTHHMFGRDHAAVGEYYDMYATQILWTKGIPSfgfe 346
                                       ********************************************************************999999*** PP

                                       .........CTSEEEE---EEEETTTTEEEECCCCGCCGGEEE--HHHHHCCHHTT----TTTS-HHHHHHHHHH CS
                   ATP-sulfurylase 147 .........lgiepvkfeeavYckkegevasektchkkeevesisgtelrkllregeeipewfsrpevlkvLrea 212
                                                l+i p ++ e++Yc+k+ge+a+++tc + ++ +++sg+ +r +++eg  +p++++rpev+k ++++
  gi|488601594|ref|YP_007908065.1| 347 appnevdygLKIIPQNMAEFWYCPKCGEMAYSETCGHVDQKQKLSGSFIRGMVAEGIFPPNIIMRPEVYKAIVKW 421
                                       **********************************************************************99875 PP

>> PUA_2  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.0   4.1e-36   1.5e-32       2     158 ..       8     183 ..       7     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 4.1e-36
                                       S-TTSS----B--CHHHHHHHHHHHTS-EEE--HHHH.........HHHHHHHTTTTTT-SCC--HHHHHHHHHHSE CS
                             PUA_2   2 kphggkLvelvvedeekeellkeakelpsielskrel.........qdlellaeGgfsPLegFmreedyesvleemr 69 
                                       +phgg+Lv++vv++ ++++++++   + +++++++ l         ++++++ +G+fsP+eg m ++++e+vlee+r
  gi|488601594|ref|YP_007908065.1|   8 PPHGGNLVDRVVRNPDRAKKMAD--GCVTYDIKPTMLdgvpirnvyREIMSICYGFFSPVEGSMVRNEVERVLEERR 82 
                                       7*************999877765..67999999999999************************************** PP

                                       ETTS-E-SS---EEEECCHCHH..HTT-SEEEEEETTTEEEEEEEEEEEEE-HHHHHHHHHHS---TT......... CS
                             PUA_2  70 LadgllwsiPivLdvseedakk..lkegdrvaLkdkegellAileveeiyeldkeeeaekvfgttdea......... 135
                                       L ++++++ P+v+d+seed k+  + egdr++L+ k g+++A+l+++eiy++d  + a+++fgt +++         
  gi|488601594|ref|YP_007908065.1|  83 LLNEWVFPYPLVFDISEEDYKNlgVGEGDRLLLRLK-GQPFAVLDIDEIYKIDPVDIATRTFGTPERNpevvkvpfd 158
                                       *********************988899*********.******************************999******* PP

                                       ..SHHHHHHC.TS-SEEEEEEEEE-S CS
                             PUA_2 136 ..HPgvkkvl.eqgevlvgGkvevle 158
                                         HPg  +++ +++ v+++Gk ++++
  gi|488601594|ref|YP_007908065.1| 159 kkHPGY-MIYrSMNPVVLAGKYTIVN 183
                                       ******.6766**********99887 PP

>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.9e-05      0.14      23      57 ..     288     323 ..     282     324 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                            DUF309  23 lW.keageperkllqglIqlAvAlyhlrrgnvrgak 57 
                                       lW +++g+p ++ll+g+I+  ++++h+  g+ ++a+
  gi|488601594|ref|YP_007908065.1| 288 LWdMRYGNPIESLLHGIIRQNMGCTHHMFGRDHAAV 323
                                       8*99***9***********************99986 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.5e-05       0.2       7      24 .]     357     374 ..     355     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                           DUF1610   7 elaprEravvFpCPNCGE 24 
                                        ++p + a   +CP+CGE
  gi|488601594|ref|YP_007908065.1| 357 KIIPQNMAEFWYCPKCGE 374
                                       68888877778******9 PP

>> DUF4105  Domain of unknown function (DUF4105)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.3e-05      0.33      56     106 ..      47      96 ..      38     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.3e-05
                           DUF4105  56 vrkeenelfyalkglfggyegsfvvapyrdkireytnvekrdvweyrLnlt 106
                                       +r+   e++++  g+f   egs+v ++++++++e+ ++ ++ v  y+L ++
  gi|488601594|ref|YP_007908065.1|  47 IRNVYREIMSICYGFFSPVEGSMVRNEVERVLEER-RLLNEWVFPYPLVFD 96 
                                       6777899****************************.************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 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:                        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: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2558.05
//
Query:       gi|488601595|ref|YP_007908066.1|  [L=347]
Description: Uncharacterized protein conserved in archaea [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-81  272.9   0.0    2.6e-81  272.7   0.0    1.1  1  DUF1786   Putative pyruvate format-lyase activating enzyme (D
  ------ inclusion threshold ------
      0.085   13.5   0.2       0.81   10.4   0.0    2.3  2  SnoaL_2   SnoaL-like domain
       0.25   10.1   0.5       0.56    9.0   0.0    1.7  2  MreB_Mbl  MreB/Mbl protein


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 !  272.7   0.0   4.3e-85   2.6e-81       1     251 [.      60     312 ..      60     313 .. 0.96

  Alignments for each domain:
  == domain 1  score: 272.7 bits;  conditional E-value: 4.3e-85
                           DUF1786   1 MGGGavtkavkehlkaGlkvvateeaAltlrddlekvkemGieiveeapeeaekielkDvdlealkealeafglelp 77 
                                       MGGG++t+  ++h+++Gl+++a ++ Alt++ddl+kv+emG+eive+++e+ae+ie++D  + +++++++++++++p
  gi|488601595|ref|YP_007908066.1|  60 MGGGPCTRYARKHIERGLRIFAFPKPALTFNDDLQKVREMGVEIVESEMEDAERIEMRDAFMPEFEAFFKNLSVSIP 136
                                       ***************************************************************************** PP

                           DUF1786  78 ekvavavqDHGyspgesnrkfRfelleelleeggkleelvfeeevpeeftRlkavaeslkeeg.......kvvvmDt 147
                                       +k++++vqDHG+sp++snrkfRf+++e++  ++g+++++++++  pe+f+R+++v es++++g       +v+++Dt
  gi|488601595|ref|YP_007908066.1| 137 DKIFFSVQDHGFSPDMSNRKFRFMVFERTA-RKGSIYSFFYRDV-PEYFNRMRSVVESIEDYGrsvgrefEVFIIDT 211
                                       ****************************98.5689******988.***************99999************ PP

                           DUF1786 148 gaaavlGalldpeveklsgalvvnvGngHtlaalvke.grivgvfEhHTsaltke...kleelieklaegeltneev 220
                                        ++av+Ga++d +++   +al+vn+Gn+Ht++a+v+e g+i+++fEhHT a++++    ++++ie++++ge++ne+v
  gi|488601595|ref|YP_007908066.1| 212 VFSAVIGAMVDCKEF---PALIVNFGNSHTIGAVVDEdGTIYSLFEHHTFAMKQKgleGINRFIERFVRGEISNEDV 285
                                       **************9...9*****************99****************944456799************** PP

                           DUF1786 221 fedgGHGvlaaaekeeaeevekvvvtGPrre 251
                                       f++gGHG    a+++e+ +v++ v+tGP+ +
  gi|488601595|ref|YP_007908066.1| 286 FNEGGHG----AYVDEVVDVKDRVCTGPNSH 312
                                       *******....66667899*********987 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.16   9.6e+02      28      53 ..     108     131 ..      86     167 .. 0.76
   2 ?   10.4   0.0   0.00014      0.81      11      68 ..     234     293 ..     225     324 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.16
                                       ET.TSEEESHHHHHHHHHHHHHHEEEE CS
                           SnoaL_2  28 dp.ggelrGreairaffralfaafpdl 53 
                                          + +++ r+a++  f+a+f+    l
  gi|488601595|ref|YP_007908066.1| 108 MEdAERIEMRDAFMPEFEAFFK---NL 131
                                       4434448889999999999986...33 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                                       TCHHHHHHTEEEEEEEE.....ET.TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEE CS
                           SnoaL_2  11 gdldalaalfapdvvwe.....dp.ggelrGreairaffralfaafpdlrfeihdvvadgdrva 68 
                                       g+  ++ a++++d + +     ++ +++++G e+i +f++++     + +++ +dv+ +g + a
  gi|488601595|ref|YP_007908066.1| 234 GNSHTIGAVVDEDGTIYslfehHTfAMKQKGLEGINRFIERF----VRGEISNEDVFNEGGHGA 293
                                       5667788999999998855553344444**************....578999999999987765 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.27   1.6e+03     239     280 ..      21      61 ..       6      75 .. 0.62
   2 ?    9.0   0.0   9.4e-05      0.56     111     169 ..     192     250 ..     185     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEE CS
                          MreB_Mbl 239 seevrealkepvsaiveavkevLektppeLaadivdrgivlt 280
                                       s+++r++lk  + + ++ v+e ++ +  e  ++i+  g ++ 
  gi|488601595|ref|YP_007908066.1|  21 SKNIRNCLKMILPSPTKVVAERIRVC-TESGKNIMLTGYTMG 61 
                                       45566666666666666666555444.455666666666664 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 9.4e-05
                                       HHHHHHHHTT-S.EEEEEEHHHHHHHHTT--TTSSS-EEEEEE-SS-EEEEEEETTEEEE CS
                          MreB_Mbl 111 AvkeaakkaGar.evllieeplaAAiGaglpveepsgnmvvdiGggttevavislggivt 169
                                        +++  +++G + ev++i++++ A iGa ++ +e    ++v+ G   t  av+   g ++
  gi|488601595|ref|YP_007908066.1| 192 SIEDYGRSVGREfEVFIIDTVFSAVIGAMVDCKEFP-ALIVNFGNSHTIGAVVDEDGTIY 250
                                       57788888887658*****************99865.699*****999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1933.82
//
Query:       gi|488601596|ref|YP_007908067.1|  [L=332]
Description: FO synthase subunit 1 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-11   44.3   0.0    2.6e-10   40.9   0.0    2.1  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   1.4e-14   2.6e-10       2     157 ..      17     173 ..      16     183 .. 0.90
   2 ?    1.1   0.0     0.026   4.6e+02     120     149 ..     211     239 ..     178     241 .. 0.70

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.4e-14
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.............TTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.............pdfve 65 
                                       + t +C++rC++C +++     + ++ + + e++e++ ++ ++  + e +++ ge  +              +dfv+
  gi|488601596|ref|YP_007908067.1|  17 PLTTACRNRCHYCGFRS-----DNPELMGISEVKELLNKA-KN--ASEALFTFGEKADEvkgvrerlksmgfSDFVD 85 
                                       6899************6.....8**************999.56..88999998888888889999999999988888 PP

                                       HHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  66 llerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                       ++ ++ +la    +    tn++ ++   l+rl++++   + l le a + +++    +g+ +e ++++++ + ++ i
  gi|488601596|ref|YP_007908067.1|  86 YVVEMNRLA-ISKSKLPHTNAGILSYSELKRLKPYN-ASMGLMLEQAVELDCHSES-PGKKPEVRIKTIKDAGKLKI 159
                                       888888886.667778889999999***********.*************9*****.******************** PP

                                       ETEEEEEEEBTTTSH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 143 krvvdrivglpGend 157
                                       +  +++i+++ Ge++
  gi|488601596|ref|YP_007908067.1| 160 P-FTTGILVGIGESF 173
                                       *.**********986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.026
                                       HHTCTSHHHHHHHHHHHHHHTTSET.EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                       Radical_SAM 120 lmnrghtfeevlealeklreagikr.vvdri 149
                                       +m   ++ ++ l+ ++ +re  +++ +++ i
  gi|488601596|ref|YP_007908067.1| 211 RM-ESPSADRMLKIVKEAREI-LPDdITIQI 239
                                       33.446669999999999999.887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1991.49
//
Query:       gi|488601597|ref|YP_007908068.1|  [L=338]
Description: FO synthase subunit 2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   62.7   0.5      2e-16   60.8   0.4    1.8  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 !   60.8   0.4   1.1e-20     2e-16       1     160 [.      39     202 ..      39     208 .. 0.87
   2 ?   -1.0   0.0      0.11     2e+03      24      40 ..     303     319 ..     288     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1.1e-20
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavp 76 
                                       +++t  C +rC+fC+++     +++   ls e+i+++v+e+ +e g ++++i+gg    ++ df+  ++++++  ++
  gi|488601597|ref|YP_007908068.1|  39 INFTDLCVNRCKFCSFR-----NRKRFLLSREDIKRKVEEA-VEYGcTEVCIQGGLLEGADIDFYIGILQAVRDVSE 109
                                       68999************.....7******************.89999*******99999999999999999999999 PP

                                       TEEEEEEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagi 142
                                       +i+i+  ++  ++          e++l++l+++g        +e++dd  +++ ++  +   +e++e +++++++gi
  gi|488601597|ref|YP_007908068.1| 110 KIHIHAFSPMEVLHasrnsnmhyEDVLRELKKAGlDSMPGTAAEILDDG-IRNEICpEKLKTKEWIEIIKAAHRNGI 185
                                       999999999999999*******************445555666666666.******999999*************** PP

                                       ETEEEEEEEBTTTSHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 143 krvvdrivglpGendeel 160
                                       + ++ +++ ++  +++++
  gi|488601597|ref|YP_007908068.1| 186 P-TTATMMYGHIDSWDDR 202
                                       *.6666666665666664 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                       Radical_SAM  24 grgrslsveeileevke 40 
                                         g++++veeil +++ 
  gi|488601597|ref|YP_007908068.1| 303 TSGEFMDVEEILTLIRM 319
                                       56789999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1883.59
//
Query:       gi|488601598|ref|YP_007908069.1|  [L=389]
Description: putative Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.7e-25   88.4   0.2    2.7e-24   86.4   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
    3.3e-11   43.6   0.3    8.8e-11   42.2   0.0    1.8  2  Fer4_12      4Fe-4S single cluster domain
    8.6e-10   38.8   0.1    1.9e-09   37.7   0.1    1.6  1  Fer4_14      4Fe-4S single cluster domain
    8.3e-05   23.0   0.4    0.00021   21.7   0.4    1.6  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 !   86.4   0.0   5.9e-28   2.7e-24       2     165 ..      45     197 ..      44     199 .. 0.87
   2 ?   -1.1   0.0      0.48   2.2e+03     144     166 ..     257     282 ..     206     285 .. 0.54

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 5.9e-28
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       + tr CnlrC++C+      +   +++l++eei++ ++ l ae+ + +++++ggepl ++d+ el+e +  +   gi
  gi|488601598|ref|YP_007908069.1|  45 NLTRKCNLRCVHCYADA---SSHSSKELTTEEIKAVIDDL-AEMKIPVLLFSGGEPLIRKDIFELAEYANDK---GI 114
                                       679*************8...7*******************.7999*****************9999999998...** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpG 154
                                       +++++tngtl++ee+++ l+   + +v ++l+ + d  v ++++   ++fe+ l++l ++r+agi  + +r ++ + 
  gi|488601598|ref|YP_007908069.1| 115 NCSLSTNGTLITEEIADMLKS-CFIYVGVSLDGLKD--VNDRFRgVEGSFERALQGLINARDAGIM-TGIRFTVTR- 186
                                       ***********6666666666.66************..6666666********************9.777766666. PP

                                       TSHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 155 endeeleelle 165
                                       +n  +++ +++
  gi|488601598|ref|YP_007908069.1| 187 YNQNDIDPIIN 197
                                       66666666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
                                       T...EEEEEEEBTTTSHHHHHHHHHH CS
                                       x...xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 144 r...vvdrivglpGendeeleellel 166
                                       +    v+ ++ ++ en +  e++le+
  gi|488601598|ref|YP_007908069.1| 257 NpvdGVFAYLKMRDENPDYAEKILEF 282
                                       13345555566666666666666655 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0     2e-14   8.8e-11      11     121 ..      46     146 ..      37     160 .. 0.81
   2 ?   -3.7   0.0         3   1.3e+04      34      53 ..     222     241 ..     218     245 .. 0.66

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2e-14
                           Fer4_12  11 fvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekd 87 
                                       ++  Cnl+C  C++    s +s+ke t+e ++ +i+dl++ +i+ l ++GGEPl    ++++ el+++   ++++  
  gi|488601598|ref|YP_007908069.1|  46 LTRKCNLRCVHCYAD--ASSHSSKELTTEEIKAVIDDLAEMKIPVLLFSGGEPLI---RKDIFELAEYANDKGIN-C 116
                                       5789*********55..56788999999999************************...9***************6.6 PP

                           Fer4_12  88 iwlytgytleelskkekeellkeidvlvdGkfee 121
                                        ++++g+ + e       ++lk + + v + ++ 
  gi|488601598|ref|YP_007908069.1| 117 SLSTNGTLITEEI----ADMLKSCFIYVGVSLDG 146
                                       7888888776665....47888888888777663 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                           Fer4_12  34 keftkelleeiiedlkkesi 53 
                                       ++++ke  ++iie l+ +s+
  gi|488601598|ref|YP_007908069.1| 222 DDISKEERRKIIEYLMRKSV 241
                                       56667777777777766655 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 !   37.7   0.1   4.3e-13   1.9e-09       5     106 ..      47     138 ..      43     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 4.3e-13
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       + +Cnl C+ C+  +  +s++ k+ t e+++++++dl + +i    l ++GGePL+    k++++l ++  +++  +
  gi|488601598|ref|YP_007908069.1|  47 TRKCNLRCVHCYADA--SSHSSKELTTEEIKAVIDDLAEMKI--PVLLFSGGEPLIR---KDIFELAEYANDKG--I 114
                                       679*********988..67777888888899***88888888..669********66...9*************..* PP

                           Fer4_14  82 kiwletngtleielektpdlkekle 106
                                       +  l tngtl  e   ++ lk+++ 
  gi|488601598|ref|YP_007908069.1| 115 NCSLSTNGTLITEEI-ADMLKSCFI 138
                                       ********9975533.455555555 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.4   4.8e-08   0.00021       6      68 .]     294     352 ..     291     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.8e-08
                             SPASM   6 rslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse..eyqefrkskkfplielCrnCp 68 
                                       r + I+  G+V+p     + +  +++ Gn++e +++eIw ++   + ++r +k++ l   C  C+
  gi|488601598|ref|YP_007908069.1| 294 RIANIDMYGYVHPN----QFW-WDYSCGNVKERKFSEIWLNPneLLIKLR-NKEKYLRGKCGMCN 352
                                       6789**********....333.37***************55543778899.67777778898885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.37s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2148.97
//
Query:       gi|488601599|ref|YP_007908070.1|  [L=213]
Description: Zn-dependent hydrolase, including glyoxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  105.8   0.5    3.4e-30  105.5   0.5    1.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    9.8e-08   31.8   0.0    1.3e-07   31.3   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.037   13.9   0.0      0.054   13.4   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   0.5   5.6e-34   3.4e-30       3     197 .]      14     190 ..      12     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 5.6e-34
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                       p+ +n+yli   +   LiDtG+++++        +++++pkd+ +++lTH+H+DH++++ +++  +    ++ +e +
  gi|488601599|ref|YP_007908070.1|  14 PLAANVYLI-LSEVPALIDTGGDAAYLVDE---VRRYINPKDIAYIFLTHSHFDHASAVSDWKGWFEDTRVVIHESE 86 
                                       778899999.899999************96...9******************************************* PP

                                       HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SH CS
                       Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.ag 155
                                        al +  + +  ++       ++++ pd++  +++ +++g+ +l+++++pgh++g+++++ +++k+lf+GD+++  g
  gi|488601599|ref|YP_007908070.1|  87 MALVRSQVSFFGVK-------FRPFEPDIVVRGGERFDLGDIELEIIHTPGHSPGSICLYEKEKKWLFSGDTVFaHG 156
                                       ********888887.......89***************************************************555 PP

                                       HCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 156 etgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       + gr+dl        ++++a ++++s++kl +l++  l+pgH
  gi|488601599|ref|YP_007908070.1| 157 SFGRVDL--------PGGSAYELIESIKKLSNLDVRNLYPGH 190
                                       6666666........*************************** PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   2.2e-11   1.3e-07       4     149 ..      29     157 ..      28     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.2e-11
                                       EES--TT...HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHH CS
                     Lactamase_B_2   4 LiDagpd...lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyl 77 
                                       LiD+g d   l+   +r+        ++++i+ ++lth+H+DH   + + +  + ++ +++ +++ +a ++++ +++
  gi|488601599|ref|YP_007908070.1|  29 LIDTGGDaayLVDEVRRY-------INPKDIAYIFLTHSHFDHASAVSDWKG-WFEDTRVVIHESEMALVRSQVSFF 97 
                                       788888844333333444.......46789**************99999999.555578999***********9998 PP

                                       HCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH CS
                     Lactamase_B_2  78 aleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee 149
                                         +  p+++   +  ge+f+lgd  +e++++  ++ s+           + ++ +++k+ +++gDt + +++
  gi|488601599|ref|YP_007908070.1|  98 GVKFRPFEPDIVVRGGERFDLGD--IELEIIHTPGHSPG----------SICLYEKEKKWLFSGDTVFAHGS 157
                                       888888888899999******95..77888888899998..........88999999999999999876655 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 ?   13.4   0.0     9e-06     0.054      11     112 ..      29     129 ..       9     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9e-06
                     Lactamase_B_3  11 lletag.arilvDPfkanlgyeppaeeaDlvlisqaledHahl.etlkqlaenvkvleegeslevg..gleiravat 83 
                                       l++t+g a  lvD ++     +++++++  + +++++ dHa +    k+ +e+++v+ +++++++   ++++ +v+ 
  gi|488601599|ref|YP_007908070.1|  29 LIDTGGdAAYLVDEVR----RYINPKDIAYIFLTHSHFDHASAvSDWKGWFEDTRVVIHESEMALVrsQVSFFGVKF 101
                                       5556543666777555....678889**************9861556788888888888777665312444444443 PP

                     Lactamase_B_3  84 shdavggs.ergenngflleqdgltiyhlG 112
                                            ++  + +++  f l + +l+i+h +
  gi|488601599|ref|YP_007908070.1| 102 RP--FEPDiVVRGGERFDLGDIELEIIHTP 129
                                       33..32222333344455555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1183.04
//
Query:       gi|488601600|ref|YP_007908071.1|  [L=105]
Description: hypothetical protein Asulf_02122 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-13   49.9   5.5    3.2e-13   49.7   5.5    1.1  1  AzlD             Branched-chain amino acid transport protein 
  ------ inclusion threshold ------
      0.046   13.9   2.7       0.15   12.2   2.7    1.9  1  NiFe_hyd_3_EhaA  NiFe-hydrogenase-type-3 Eha complex subunit 


Domain annotation for each model (and alignments):
>> AzlD  Branched-chain amino acid transport protein (AzlD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   5.5   3.6e-17   3.2e-13       2      98 ..       3      95 ..       2      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.6e-17
                              AzlD  2 llaillmalvtyltRylplllfrrlklppwlqrllryvPiavLaaliapellaetgklsaslglarllaalvavlvall 80
                                      llai+l+a++tyltR+lp+ +++ +  +++++++l y ++a+++al+++++++ +  +    +   l+a+l++++ + +
  gi|488601600|ref|YP_007908071.1|  3 LLAIVLVAAGTYLTRFLPMKFGKIR--SERFEEFLAYSSTALISALFVTSFISFPIVFR--DLGVGLVAILFVFVTYRR 77
                                      79******************99955..5************************9988755..477788999999999999 PP

                              AzlD 81 trnlllsilvGmavyall 98
                                        nl++s+l+G+++ +ll
  gi|488601600|ref|YP_007908071.1| 78 WENLGISVLAGVLTHLLL 95
                                      99***********98887 PP

>> NiFe_hyd_3_EhaA  NiFe-hydrogenase-type-3 Eha complex subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.7   1.7e-05      0.15      46      93 ..      52     102 ..       4     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                   NiFe_hyd_3_EhaA  46 vifPtav..lalGllalvfklgve.iydGlllaiiiGvlsalfskyllekv 93 
                                       + fP ++  l +Gl+a++f + ++  ++ l +++++Gvl+ l+   +++ +
  gi|488601600|ref|YP_007908071.1|  52 ISFPIVFrdLGVGLVAILFVFVTYrRWENLGISVLAGVLTHLLLSLSVQAI 102
                                       34777764467899***999666659****************988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 694.65
//
Query:       gi|488601601|ref|YP_007908072.1|  [L=210]
Description: putative branched-chain amino acid permease (azaleucine resistance) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  119.6   6.3    1.2e-34  119.6   6.3    1.7  2  AzlC      AzlC protein


Domain annotation for each model (and alignments):
>> AzlC  AzlC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.6   6.3     7e-39   1.2e-34       1     136 []      11     141 ..      11     141 .. 0.95
   2 ?   -0.8   0.2      0.11   1.9e+03      91     134 ..     153     198 ..     144     200 .. 0.54

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 7e-39
                              AzlC   1 PillgylpvgiafGvlavqaglsvweavlmSllvfAGsaqfaavgllaagasllaivlttllvNlRhllyglslapk 77 
                                       Pi++gy+pv+++fG++a + g+s +e++l+S+lvfAG++qfa+++l+    s++++v++ +++NlRh++yg  +++ 
  gi|488601601|ref|YP_007908072.1|  11 PIVIGYVPVAMTFGIIALALGFSKVETLLTSALVFAGASQFALISLM--PYSFVNAVFIPIFLNLRHIVYGYIVSQN 85 
                                       9**********************************************..589************************* PP

                              AzlC  78 lkklsrlkrlllaflltDetfalasarklsrayflglglllylawvlgtllGallgsll 136
                                       +   + +k  + af+ltDe+fa + +   ++++++gl+l +y+awvlgt++G++ g++l
  gi|488601601|ref|YP_007908072.1|  86 F---EIKKPCITAFGLTDEVFARSLTAPRDERFLWGLELGSYSAWVLGTAIGIVGGAFL 141
                                       *...456777888***********766668************************99986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.11
                              AzlC  91 flltDetfalasar..klsrayflglglllylawvlgtllGallgs 134
                                       f lt    +l++ +  k + + ++g  ++l++ + + + +G+ll+ 
  gi|488601601|ref|YP_007908072.1| 153 FSLTALFLVLLIPNlkKYRLSAIMGGLIALIFHYFGYSSIGILLAG 198
                                       4444444444442233334555555556666666667777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1155.15
//
Query:       gi|488601602|ref|YP_007908073.1|  [L=466]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-14   54.7   0.4    2.2e-14   53.7   0.4    1.4  1  OrfB_IS605      Probable transposase
     0.0041   17.0   0.0      0.008   16.1   0.0    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.17   12.4   0.1        5.3    7.7   0.0    2.7  2  PC_rep          Proteasome/cyclosome repeat


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 !   53.7   0.4   3.7e-18   2.2e-14       3     116 ..     187     302 ..     184     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 3.7e-18
                        OrfB_IS605   3 pvevevelpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkkskn...ykkasr 75 
                                        ve+e ++++p++++  +iD++ +n+a+ v ed  + ++++gr l s ++++ k+i +lqs+ +  k    ++k  +
  gi|488601602|ref|YP_007908073.1| 187 SVEQE-QTQQPEKERLMSIDFNTSNFAVIVIEDHPTsYIIDGRGLMSLLRKYLKKISRLQSRRDNLKEglpHHKLNE 262
                                       45544.399999999******************8667*************************99998899******* PP

                        OrfB_IS605  76 klarlhrkrsrrrkhllhklathliktlkevgvetLnvgnm 116
                                       ++a+l++++++ ++++ h +++ li +l +++v  +++gn 
  gi|488601602|ref|YP_007908073.1| 263 RIAKLWKRVRNLLRDFSHRVSN-LIVELARRQVTRIVIGNV 302
                                       ******************9766.556788999999999986 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 !   16.1   0.0   1.3e-06     0.008       4      69 .]     328     394 ..     325     394 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                    OrfB_Zn_ribbon   4 lkeqleykakeyGikveevnpay.TSktCseCgsknke.....alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       + + l+yk      +v+e++++y +  ++ ++ + +ke     ++ +r +  +     +++Dvn+a+Nilk+
  gi|488601602|ref|YP_007908073.1| 328 VVKHLQYKFG----NVIEISEEYtSGVDSVKHEHPSKEhyeprKRVKRGLFKS-VIGIINADVNSARNILKK 394
                                       5555666655....799999999455788899999999988874445555444.57779***********96 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.077   4.6e+02      14      28 ..     227     240 ..     226     244 .. 0.85
   2 ?    7.7   0.0   0.00089       5.3       6      28 ..     378     398 ..     378     400 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.077
                                       TCHHHHHHHHHHHHH CS
                            PC_rep  14 gneeaislLkpylsd 28 
                                       g++ ++slL++yl++
  gi|488601602|ref|YP_007908073.1| 227 GRG-LMSLLRKYLKK 240
                                       677.99*******86 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00089
                                       HHHHCTTSTCHHHHHHHHHHHHH CS
                            PC_rep   6 LGlihaGsgneeaislLkpylsd 28 
                                       +G+i+a   n+ a+++Lk+yl++
  gi|488601602|ref|YP_007908073.1| 378 IGIINAD-VNS-ARNILKKYLYE 398
                                       7******.999.*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.33s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2596.41
//
Query:       gi|488601603|ref|YP_007908074.1|  [L=185]
Description: hypothetical protein Asulf_02125 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-06   28.0   3.2    1.5e-06   28.0   3.2    2.0  2  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.13   12.7   1.8       0.24   11.9   0.4    2.1  2  RuvA_C    RuvA, C-terminal domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   3.2   1.6e-10   1.5e-06       1      38 [.      13      50 ..      13      51 .. 0.98
   2 ?   -2.4   0.0      0.59   5.3e+03      12      19 ..      85      92 ..      83      94 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.6e-10
                                      EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                      r+si ld+e+ + ++ lar+++r+ Se IReA+++y+e
  gi|488601603|ref|YP_007908074.1| 13 RLSIALDAETEKMVELLAREEDRNASETIREAIKAYYE 50
                                      89**********************************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.59
                                      HHHHHHHH CS
                             RHH_1 12 erLdelar 19
                                      + Ldel +
  gi|488601603|ref|YP_007908074.1| 85 KILDELNK 92
                                      56777755 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   2.7e-05      0.24      18      45 ..      20      47 ..      19      48 .. 0.93
   2 ?   -1.2   0.0      0.34     3e+03      39      46 ..      51      58 ..      50      72 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHHHHC-TTS-HHHHHHHHHCC CS
                            RuvA_C 18 keaekAvakvlanpgasveelIraALkl 45
                                      +e ek+v+ ++++++ +++e Ir+A+k+
  gi|488601603|ref|YP_007908074.1| 20 AETEKMVELLAREEDRNASETIREAIKA 47
                                      6899******99**************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.34
                                      HHHHHCCT CS
                            RuvA_C 39 IraALklL 46
                                      I++A++ L
  gi|488601603|ref|YP_007908074.1| 51 IKKAIRYL 58
                                      55565554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.36s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1010.48
//
Query:       gi|488601604|ref|YP_007908075.1|  [L=173]
Description: hypothetical protein Asulf_02126 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.3   0.6    0.00043   20.3   0.6    1.5  1  DUF1634         Protein of unknown function (DUF1634)
  ------ inclusion threshold ------
      0.014   15.1   0.1        2.7    7.8   0.0    2.5  2  Form-deh_trans  Formate dehydrogenase N, transmembrane
      0.024   14.8   1.3          2    8.7   0.0    2.2  2  Pox_A14         Poxvirus virion envelope protein A14


Domain annotation for each model (and alignments):
>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.6   7.2e-08   0.00043       2      92 ..      49     156 ..      48     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.2e-08
                           DUF1634   2 gklLriGvllsaavvllGlilllvkhgs.....se...........senseltslseileglle.lkglaiiqlGll 61 
                                       g ++ri   + +av++++ ++++v  +      +e            ++ + t++++  + l++ +++++i+ lG+ 
  gi|488601604|ref|YP_007908075.1|  49 GDVMRILCNVGLAVIIIASVFYFVGISPkdnpsNEaarwnepavafWKDVKGTEINGYSWFLSDlMDPENIVILGIT 125
                                       678999999999*********999888655565115555556666644555555555555555514699******** PP

                           DUF1634  62 vLiatPvlrVvlsliaFlkekdilyviitli 92 
                                       +L +tP++  ++++ +   +  +l+viit+ 
  gi|488601604|ref|YP_007908075.1| 126 ILALTPLVGFLFAIPKAHGALRVLLVIITIE 156
                                       ***************9999999999999984 PP

>> Form-deh_trans  Formate dehydrogenase N, transmembrane
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00046       2.7      10      38 ..      50      78 ..      41      83 .. 0.90
   2 ?    4.8   0.1    0.0041        24       3      11 ..      90      98 ..      89      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00046
                                      TTHHHHHHHHHHHHHHHHHHHHHHH--B- CS
                    Form-deh_trans 10 GvlKplgalgmaatalagffHYitvGPne 38
                                      +v++ l  +g+a+ ++a++f ++++ P++
  gi|488601604|ref|YP_007908075.1| 50 DVMRILCNVGLAVIIIASVFYFVGISPKD 78
                                      79999*******************99987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0041
                                      HHHHHHHTT CS
                    Form-deh_trans  3 plVelWKGv 11
                                      p+V++WK+v
  gi|488601604|ref|YP_007908075.1| 90 PAVAFWKDV 98
                                      89******8 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00033         2      15      44 ..      56      85 ..      44      94 .. 0.82
   2 ?    5.0   0.4    0.0046        28      12      58 ..     117     163 ..     111     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00033
                           Pox_A14 15 liaGiiLLilacifafvdfskststtdkaw 44
                                        +G++++i+a +f fv +s + +++++a 
  gi|488601604|ref|YP_007908075.1| 56 CNVGLAVIIIASVFYFVGISPKDNPSNEAA 85
                                      458*****************9998887664 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0046
                           Pox_A14  12 stvliaGiiLLilacifafv.dfskststtdkawralsivsFilgivi 58 
                                        +++i Gi +L+l+ ++ f+  + k+   + +++ ++  + F+ +i+ 
  gi|488601604|ref|YP_007908075.1| 117 ENIVILGITILALTPLVGFLfAIPKAHG-ALRVLLVIITIEFVYAILR 163
                                       689**********999999613444444.5556667777778777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1005.58
//
Query:       gi|488601605|ref|YP_007908076.1|  [L=73]
Description: hypothetical protein Asulf_02127 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 433.73
//
Query:       gi|488601606|ref|YP_007908077.1|  [L=332]
Description: putative permease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  116.7  32.5    1.2e-33  116.7  32.5    1.9  2  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.8     0.034   6.1e+02     124     149 ..      15      39 ..       1      46 [. 0.46
   2 !  116.7  32.5   6.6e-38   1.2e-33       1     234 [.      51     317 ..      50     318 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.034
                              TauE 124 taillvligglvGllsGllGiGgGfl 149
                                        ++++ +i +++G+l+ ++  G G++
  gi|488601606|ref|YP_007908077.1|  15 VLAAISAIILIAGILAWFFLQG-GAM 39 
                                       2222222224455555555444.343 PP

  == domain 2  score: 116.7 bits;  conditional E-value: 6.6e-38
                              TauE   1 lllagllaGfvagllGiGggliavPlLll.l.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsli 75 
                                       l+l+ +++G+++ + G+Ggg+i+v l ++ l ++   + ++ l+a+++t+ls+a  + ++g  +++++ +l+++s i
  gi|488601606|ref|YP_007908077.1|  51 LFLFTFVIGILGPMSGVGGGVIFVGLGMAiLpFHVDFIRGAGLVAALTTALSSAPHFTKKGLANFKVAAPLVVVSTI 127
                                       58999********************99994545555588**********************9999998888887776 PP

                              TauE  76 GallGallllllpsel......lkllfgvlllllallmllrkkr..........................srakgre 120
                                        ++ G+++ l++++++      +k+ +gv+l ++ + ++++k+                           +  + +e
  gi|488601606|ref|YP_007908077.1| 128 FSIMGSVFGLWISNAFpqgssyVKVSLGVVLFIMLAALATSKNVeypetkkqdrlskmlniygewyeptlN--RVVE 202
                                       6666666666666553444444*********9999999987777899999999999998888887766432..2567 PP

                              TauE 121 rrptaillvliggl.vGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwplll 196
                                       +r + + ++l+ ++ vG+++G++G G+G   vp+l l++g+plk avats+++ +++  a++++y++ gav + +++
  gi|488601606|ref|YP_007908077.1| 203 YRVGNLPIGLLFFAgVGFVAGMFGLGAGWANVPVLNLIMGVPLKAAVATSMVILAINDSASLWVYLSKGAVLPLIVV 279
                                       888888888888888*********************************************************99999 PP

                              TauE 197 lllpgallGallGarlarrlsertlrrlfallllvlgv 234
                                       + ++g+ +G+ +G+r+a r ++++++ l+++l+ ++++
  gi|488601606|ref|YP_007908077.1| 280 PTVLGIGIGSRIGSRIAVRTKPKVIKYLVIGLIGLSAI 317
                                       9*******************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.37s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 1789.17
//
Query:       gi|488601607|ref|YP_007908078.1|  [L=99]
Description: hypothetical protein Asulf_02129 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.35s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 570.80
//
Query:       gi|488601608|ref|YP_007908079.1|  [L=613]
Description: Aldehyde:ferredoxin oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-148  493.5   0.1   4.9e-148  493.2   0.1    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    3.7e-77  258.7   0.1    6.7e-77  257.8   0.1    1.4  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.2   0.1  5.5e-152  4.9e-148       3     382 .]     231     611 ..     229     611 .. 0.98

  Alignments for each domain:
  == domain 1  score: 493.2 bits;  conditional E-value: 5.5e-152
                                       HHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EE CS
                            AFOR_C   3 gkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgr 79 
                                        kk++++ik++p + ++l+kyGTa lvn++n++g lp kn+q+g+ ++a+kisge+l+ekyl+kn+gC++C+i Cgr
  gi|488601608|ref|YP_007908079.1| 231 SKKANDKIKQNPLTGEGLTKYGTAILVNVINNAGSLPFKNWQTGYNPEADKISGETLAEKYLIKNHGCWGCTITCGR 307
                                       5899********7777*************************************************99********** PP

                                       EEE.......ET.EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS CS
                            AFOR_C  80 evkveegkk.vk.vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdg 154
                                       ++kve+g++ +  +egpeye++++lG+++g++dleai+k+n+ cde+GlDtis+G+tia+amelyekG + +e ++g
  gi|488601608|ref|YP_007908079.1| 308 VTKVESGPYqILySEGPEYESIWSLGNATGVTDLEAIIKANHFCDEYGLDTISMGSTIACAMELYEKGSIPEEYLQG 384
                                       ********97669**************************************************************** PP

                                       ----TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-S CS
                            AFOR_C 155 lelefgdaeallellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacH 231
                                       ++l+fg+  al+e++ ++A + g+g+ lA G+krlae +g++el+m+vkGle+paydprg+kg++l+Yat+nrG+cH
  gi|488601608|ref|YP_007908079.1| 385 VDLSFGNSSALVEMVWRTAFKAGFGKYLALGSKRLAEMFGHPELSMSVKGLEMPAYDPRGIKGIGLTYATANRGGCH 461
                                       ***************************************************************************** PP

                                       GGG-THHHH.....S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHH CS
                            AFOR_C 232 lrayliale.....ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeel 303
                                       + +y++a+e     ek dpl++egka++vk fqd+t++v+s + C+ft+     +  e++a +lsavtG+d++ eel
  gi|488601608|ref|YP_007908079.1| 462 VTGYTVAPEiaglpEKIDPLTEEGKAQWVKAFQDFTCVVNSTVNCLFTT---FAIGAEDFAPMLSAVTGWDFSVEEL 535
                                       ********************99***************************...5778999****************** PP

                                       HHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHHC CS
                            AFOR_C 304 lkaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkrL 380
                                       +k+GeRiynleR++ ++ G+++kddtlp+rll+e+l+eg akg+v+  +l++m++eyYe+rGW  +GvPt+e+lk+L
  gi|488601608|ref|YP_007908079.1| 536 MKIGERIYNLERVIINKFGFDAKDDTLPPRLLKEALPEGAAKGHVV--DLDKMKKEYYEIRGWV-DGVPTEEKLKEL 609
                                       *********************************************9..8***************.************ PP

                                       T- CS
                            AFOR_C 381 gL 382
                                       ++
  gi|488601608|ref|YP_007908079.1| 610 EI 611
                                       86 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.8   0.1   7.5e-81   6.7e-77       1     197 [.       6     215 ..       6     216 .. 0.96

  Alignments for each domain:
  == domain 1  score: 257.8 bits;  conditional E-value: 7.5e-81
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS.........-TTS-TTSTTS-EEEEE-TTTTSS.ST CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldev.........ppgvdplspenplvfatGpltgtp.ap 67 
                                       gkilrvdLs+g++++e+++ee+a+kylGg+g+a++++++++         p+++dpl++ n l+fatGp tg++ +p
  gi|488601608|ref|YP_007908079.1|   6 GKILRVDLSSGTTKIEPISEEIARKYLGGKGYATYMIYQKLkslekegiyPADIDPLGEFNDLIFATGPATGIAgFP 82 
                                       79*************************************776777777779************************** PP

                                       TB-EEEEEE.E-TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHH CS
                            AFOR_N  68 gsgrlvvva.ksPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettea 143
                                         gr++v++ +sPltg++g++n+Gg+fg+++k+aG+d iv+eGk++kpvyl++ d+++ei+da+dlwg ++++tt+ 
  gi|488601608|ref|YP_007908079.1|  83 EPGRYHVMTvRSPLTGSIGSANSGGKFGPYMKFAGFDIIVVEGKSDKPVYLEVVDGSAEIKDASDLWGRNVFDTTRI 159
                                       ********989****************************************************************** PP

                                       HHHHHTS..EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                            AFOR_N 144 lkeelgd..kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                       l++++g+  +va+iGpaGenlv fA+i+ d++raagr+G+GavmgsK+lkaiv+ g
  gi|488601608|ref|YP_007908079.1| 160 LSDRVGRrcSVACIGPAGENLVLFANIMNDEHRAAGRTGVGAVMGSKKLKAIVCAG 215
                                       *******99999***************666999********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 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:                        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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3722.04
//
Query:       gi|488601609|ref|YP_007908080.1|  [L=172]
Description: Nitroreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  102.1   0.4    7.1e-17   62.0   0.1    2.1  2  Nitroreductase  Nitroreductase family
    2.1e-14   53.6   0.3    3.7e-07   29.9   0.0    3.1  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.1   7.9e-21   7.1e-17       1      55 [.       7      61 ..       7      64 .. 0.96
   2 !   38.8   0.0     1e-13   9.3e-10     115     170 .]      92     149 ..      62     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 7.9e-21
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHH CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklae 55
                                      i +RrSiRk++ +++++ ++ekil+aa+ aPsagn qpw+f+vv+dke ++klae
  gi|488601609|ref|YP_007908080.1|  7 IYTRRSIRKYSGRKIKDVKIEKILKAAMLAPSAGNEQPWHFIVVRDKERLKKLAE 61
                                      568******************************************9999999987 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 1e-13
                                       HHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHH..HHHHHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 115 alldagaaaqnllLaAtalGlgscpiggfdeaae..evrkllglpdeeeivvliavGy 170
                                        ++d++aa qn+lL+A++lG+gs+++g +  +++   +++ll++pd+  ++ l+++Gy
  gi|488601609|ref|YP_007908080.1|  92 WVQDCSAATQNILLSARMLGIGSVWLGVYPVEDRmkSIAELLEVPDGVVVFSLVSLGY 149
                                       3689**************************7777778********988888******9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.5   2.3e-05      0.21       2      27 ..       3      28 ..       2      29 .. 0.88
   2 !   29.9   0.0   4.1e-11   3.7e-07     159     191 ..      25      56 ..      22      80 .. 0.79
   3 !   11.6   0.0   1.7e-05      0.15      88     136 ..     100     153 ..      82     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                                      HHHHHHH--B---B--S---HHHHHH CS
                    TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeellee 27
                                       +e+i +R+s+RkY+ +++++ ++e+
  gi|488601609|ref|YP_007908080.1|  3 CLEMIYTRRSIRKYSGRKIKDVKIEK 28
                                      689****************9988876 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 4.1e-11
                                       HHHHHHHHHHTS--GGG----EEE.E-SSEE.. CS
                    TM1586_NiRdase 159 wfkeileaarlAPsAlNqqpwrfelkdddeiki 191
                                       ++++il+aa+lAPsA N+qpw+f ++ d+  ++
  gi|488601609|ref|YP_007908080.1|  25 KIEKILKAAMLAPSAGNEQPWHFIVVRDK-ERL 56 
                                       689*********************88864.444 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHTT-EEEEES--SST................T-S-EEEEE-BS-- CS
                    TM1586_NiRdase  88 geqlvLkltalGlgtcWvggtykkkkak.....velkkgeklvivIalGyaktk 136
                                        ++++L +  lG+g+ W+g    ++++k     +e+++g  ++ +++lGy++++
  gi|488601609|ref|YP_007908080.1| 100 TQNILLSARMLGIGSVWLGVYPVEDRMKsiaelLEVPDGVVVFSLVSLGYPESD 153
                                       6899***************9877755441112257788999999999**99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 960.37
//
Query:       gi|488601610|ref|YP_007908081.1|  [L=430]
Description: hypothetical protein Asulf_02132 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   88.9   0.0      1e-16   60.9   0.0    2.2  2  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 !   26.1   0.0   2.3e-10   4.2e-06     113     220 ..      78     180 ..      49     199 .. 0.88
   2 !   60.9   0.0   5.8e-21     1e-16      91     226 ..     290     422 ..     220     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.3e-10
                                       HHHHHHHHHSTT-ST-EEE---GGGGGGSSS--SEEEEEEEE..SEETEEEEEEEEEEEETTTHHHHHHHHHHHHHH CS
                   Thymidylat_synt 113 akvidqlkenpdsRriivsawnpaeldkmaLppChvlfqfyvkdkkegkLslqlyqRSaDvflGvpFNiasyalLth 189
                                       + + +++k++p+ Rr+ + +w p++  +   pp  + + +       ++L+++ y RS D    +  N     + + 
  gi|488601610|ref|YP_007908081.1|  78 DICAEKIKSSPYTRRVSIPIWMPKDH-HCRNPPAITEISLLP----VKELHATAYIRSLDAYNFFMHNADFITFVLD 149
                                       345679*******************5.889999999988887....246**************************** PP

                                       HHHHHHT-EEEEEEEEEEEEEEEGGGHHHHH CS
                   Thymidylat_synt 190 mlaqvtglkpgelihtigdaHiYsnhveqvk 220
                                        +a+  g+++g+  +  +  HiY + +++++
  gi|488601610|ref|YP_007908081.1| 150 YVAEKAGFDVGSAGFIASIPHIYLRDLKHID 180
                                       ***********************99988876 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 5.8e-21
                                       SSSHHHHHHH.BTSTTTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGGSSS--SEEEEEEEE..SEETEEEEEE CS
                   Thymidylat_synt  91 gpvYGkqwrk.fkaeegkkidqlakvidqlkenpdsRriivsawnpaeldkmaLppChvlfqfyvkdkkegkLslql 166
                                       g+ Y +  r  + ++++  +dql +vi++lk++ + R   v +    +l k   ppC   +qf  +++   +L+  +
  gi|488601610|ref|YP_007908081.1| 290 GETYTYAERArYCERDDLIVDQLYTVIEKLKQDRYRRDCYVGISRIWDL-KSDEPPCLRGYQFVGDHD---HLKGIF 362
                                       5556665554244568889**********************99999999.8899*********99444...6***** PP

                                       EEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGGHHHHHHHHTS- CS
                   Thymidylat_synt 167 yqRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnhveqvkeqlere 226
                                       y RS+D+  ++  N  ++++Lt+ +a+ tg++ ++++h   daHiY + +++vke le e
  gi|488601610|ref|YP_007908081.1| 363 YMRSNDIYGAMHANAYAFSTLTQYVAELTGFQRHKYYHFAVDAHIYGEFLKAVKEILEPE 422
                                       *******************************************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2585.75
//
Query:       gi|488601611|ref|YP_007908082.1|  [L=178]
Description: putative HD superfamily hydrolase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-18   64.6   4.3    1.7e-17   63.8   4.3    1.4  1  HD        HD domain
     0.0041   17.0   0.1     0.0069   16.3   0.1    1.4  1  DUF4202   Domain of unknown function (DUF4202)


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 !   63.8   4.3   1.9e-21   1.7e-17       3     122 .]      13     109 ..      12     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.9e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH.. CS
                                HD   3 eHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld.. 77 
                                       eH  +V++la  +ae++g   d  ++++aa lHDi+ ++++               H+++ga+i+re++k +g+d  
  gi|488601611|ref|YP_007908082.1|  13 EHVKRVLNLALYIAEREG--GDIAIVKKAAELHDIARDKEN---------------HAVEGAKIAREILKEEGFDre 72 
                                       8*****************..*******************66...............8******************** PP

                                       .HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHHH CS
                                HD  78 .ledvaklirehheswegkkrprglaerqlslearivklaDrlaam 122
                                        ++ va+ i++h++s+ ++         +++lea+i+++aD+l+am
  gi|488601611|ref|YP_007908082.1|  73 fIDRVAHCIEAHSFSSGIE---------PKTLEAKILSDADKLDAM 109
                                       ****************866.........****************98 PP

>> DUF4202  Domain of unknown function (DUF4202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   7.7e-07    0.0069      82     128 ..      50      96 ..      33     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.7e-07
                           DUF4202  82 telkkrqAelaaelleeagydeeeiervaalvrkeelkrdeetqlLE 128
                                       ++++   A++a+e+l+e g+d+e i+rva+ ++ +++++  e ++LE
  gi|488601611|ref|YP_007908082.1|  50 ENHAVEGAKIAREILKEEGFDREFIDRVAHCIEAHSFSSGIEPKTLE 96 
                                       5667778*****************************99854444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 1.49s 00:00:02.02 Elapsed: 00:00:00.79
# Mc/sec: 681.99
//
Query:       gi|488601612|ref|YP_007908083.1|  [L=556]
Description: putative NAD(FAD)-dependent dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  223.6   1.3    4.2e-66  223.2   1.3    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.7e-22   78.7   8.6    8.8e-18   64.7   1.0    3.5  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.7e-17   62.6   0.0      1e-16   61.2   0.0    1.8  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    8.8e-13   48.2   3.7    1.1e-08   34.7   0.7    2.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    9.8e-13   48.4   5.6     0.0023   17.6   0.3    4.1  4  DAO             FAD dependent oxidoreductase
    4.7e-12   46.0   0.1    2.2e-05   24.6   0.1    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.1e-12   45.4   0.0    6.2e-11   42.8   0.0    2.3  2  Rhodanese       Rhodanese-like domain
    2.8e-10   39.5   2.0    0.00064   18.5   0.1    4.1  4  HI0933_like     HI0933-like protein
    1.5e-07   30.9   5.9    0.00064   18.9   0.3    3.5  3  FAD_binding_2   FAD binding domain
    1.6e-07   30.5   0.9     0.0015   17.4   0.0    3.1  3  Trp_halogenase  Tryptophan halogenase
      7e-07   28.6   2.2      0.032   13.3   0.1    3.1  3  Lycopene_cycl   Lycopene cyclase protein
    1.4e-06   27.7   0.6       0.02   14.2   0.1    2.7  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    2.4e-05   23.9   5.2      0.077   12.3   0.1    2.8  3  FAD_oxidored    FAD dependent oxidoreductase
    6.4e-05   23.0   0.5       0.65   10.0   0.0    3.4  3  NAD_binding_9   FAD-NAD(P)-binding
    0.00012   22.4   1.4       0.84   10.1   0.0    3.1  3  NAD_binding_7   Putative NAD(P)-binding
    0.00033   19.9   5.6       0.18   10.9   0.2    3.6  4  GIDA            Glucose inhibited division protein A
    0.00038   19.8   5.5       0.53    9.5   0.1    3.2  3  Thi4            Thi4 family
      0.001   19.3   0.5        1.2    9.4   0.1    3.1  2  TrkA_N          TrkA-N domain
      0.003   16.8   1.0       0.13   11.4   0.0    2.9  4  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
       0.03   13.5   0.7        3.9    6.5   0.0    2.7  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
       0.15   11.4   0.9         16    4.8   0.1    2.6  3  GMC_oxred_N     GMC 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 !  223.2   1.3   4.9e-69   4.2e-66       2     279 ..       4     296 ..       3     315 .. 0.93

  Alignments for each domain:
  == domain 1  score: 223.2 bits;  conditional E-value: 4.9e-69
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgi 67 
                                       ++vv+GgG+AGl+aa ++++   +a++t++e++++  +g+c l++ ++g+ +d + +          e+  k  ++i
  gi|488601612|ref|YP_007908083.1|   4 EIVVVGGGAAGLKAASRARRrdEEAEITVIEKGEYPSLGRCGLPYYVEGFVHDISNLMetlsgdvrdEEYFKKVKNI 80 
                                       69******************877*******************************98889********777777889* PP

                                       CCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2  68 elllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.. 142
                                        +l+++e+++id+++k vk++  ++g   ++ yd+lvlAtG++p +l ++Gv  ++++++ + ++a ++ + +++  
  gi|488601612|ref|YP_007908083.1|  81 NVLTKTEALSIDRKRKAVKIS--RNGRDDELNYDYLVLATGAKPVRLSVKGVDADGIFSLTSAEDALKITEMWMNes 155
                                       ********************5..4467779*********************************************77 PP

                                       .SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 .krivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngekle 217
                                        +++v++GgG+iG+E+A al +l  +vt+ve  ++ll +++d e+++ +++ + +eGv+v + t+v+e++ ++ k++
  gi|488601612|ref|YP_007908083.1| 156 iESAVIIGGGLIGLETAEALERLDIDVTIVELKNQLLwNSFDFEMAELVRKCIIREGVKVLTSTTVQEFITEDGKVK 232
                                       7777*********************************************************************99** PP

                                       EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC...T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                       Pyr_redox_2 218 vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva...g 279
                                        v  +++ ++a+lv++++Gv+p+tel+ e++glel+e+g+i+v+e+l+t++p iya GD++   +
  gi|488601612|ref|YP_007908083.1| 233 AVRVNEKILPAELVIISIGVEPRTELA-ESAGLELTEKGAIKVNEYLQTSDPFIYAGGDCVeniN 296
                                       ***************************.********************************94440 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   0.1   9.3e-05      0.08       2      32 ..       5      37 ..       4      43 .. 0.85
   2 ?    3.6   0.1      0.11        97      48      78 ..      72     100 ..      55     106 .. 0.81
   3 !   64.7   1.0     1e-20   8.8e-18       2      79 ..     159     237 ..     158     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.3e-05
                                      EEEECSSHHHHHHHHHHHHTT..SEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvversd 32
                                      +vvvGgG  gl +A+ +++    +++tv+e ++
  gi|488601612|ref|YP_007908083.1|  5 IVVVGGGAAGLKAASRARRRDeeAEITVIEKGE 37
                                      8****************776544899***9876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                                       HHHHHT.TEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  48 eklekn.gievllntkveeiegsedgvesvkl 78 
                                       e+++k  +i+vl++t++ +i+ + +    vk+
  gi|488601612|ref|YP_007908083.1|  72 EYFKKVkNINVLTKTEALSIDRKRKA---VKI 100
                                       45555459*************88876...554 PP

  == domain 3  score: 64.7 bits;  conditional E-value: 1e-20
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +v++GgG+iglE A+al +l  +Vt+ve +++ll + +D e+++++++ + ++g++vl++t+v+e+ +++ +v++v+
  gi|488601612|ref|YP_007908083.1| 159 AVIIGGGLIGLETAEALERLDIDVTIVELKNQLLwNSFDFEMAELVRKCIIREGVKVLTSTTVQEFITEDGKVKAVR 235
                                       79*****************************************************************99988****9 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       ++
  gi|488601612|ref|YP_007908083.1| 236 VN 237
                                       96 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 !   61.2   0.0   1.2e-19     1e-16       6     107 ..     340     442 ..     335     445 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.2e-19
                                       ESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEECTTHHH.HHHHHH CS
                     Pyr_redox_dim   6 ftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivGpgage.liqela 80 
                                       +++  ++ +Glte++A++ag + +++ +p    +ra++y+  + + +Kl+ad++t+kvlGa+ +G g+ + +i+ +a
  gi|488601612|ref|YP_007908083.1| 340 VFNADAGRTGLTEKQAREAGFDPVIAISP--GPDRAHYYPGfKPIRLKLIADRRTRKVLGAQAFGLGVIDkRIDVIA 414
                                       5667889*************776665555..58999999999***********************998777****** PP

                                       HHHHTTSBHH.HHHTSBSSSSSTGGGGH CS
                     Pyr_redox_dim  81 vaikagltve.dladtihihPtlsealk 107
                                       +ai+ g+tv+ ++  +++++P++s al+
  gi|488601612|ref|YP_007908083.1| 415 MAIHRGATVDdLAEVDLAYAPPFSAALD 442
                                       **********447789********8876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   3.3e-05     0.028       1      31 [.       6      37 ..       6      42 .. 0.88
   2 !   34.7   0.7   1.3e-11   1.1e-08      89     292 ..      76     277 ..      69     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl.edylilEkgn 31
                                      +++G+G+aGl+aa  +++ +   +++++Ekg+
  gi|488601612|ref|YP_007908083.1|  6 VVVGGGAAGLKAASRARRRDEeAEITVIEKGE 37
                                      79**************9987735799****97 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1.3e-11
                       Pyr_redox_3  89 evaksfelpiklfeeVesvkkedegfevetske..tyeAkkviiAtGefdkPnklnipGeek...lvkhyskv.... 156
                                       +    +++++ +++e  s++++++  +++ + +  +++ +++++AtG   kP +l+++G +     +  ++++    
  gi|488601612|ref|YP_007908083.1|  76 K---VKNINVLTKTEALSIDRKRKAVKISRNGRddELNYDYLVLATGA--KPVRLSVKGVDAdgiFSLTSAEDalki 147
                                       3...48999*******************99875559***********9..*********996332222222222333 PP

                       Pyr_redox_3 157 .kefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfn 232
                                        + +++ + +  v+iGg+  + ++A  l r + +Vt+v  ++++  ++ d++      + + +++++ +e +kvl+ 
  gi|488601612|ref|YP_007908083.1| 148 tEMWMNESIESAVIIGGGLIGLETAEALERLDIDVTIVELKNQLLWNSFDFE------MAELVRKCIIREGVKVLTS 218
                                       35788888999*****************************998777654444......4566666666677****** PP

                       Pyr_redox_3 233 aevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvltee 292
                                       ++v+e  +++ ++k    + +k+   + v++ +G +p +++ +++++el+e+g ++++e 
  gi|488601612|ref|YP_007908083.1| 219 TTVQEFITEDGKVKAVRVN-EKILPAELVIISIGVEPRTELAESAGLELTEKGAIKVNEY 277
                                       *****99999999887777.677778999999************************9985 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   2.7e-06    0.0023       2      33 ..       5      40 ..       4      45 .. 0.88
   2 !    5.9   0.0    0.0094         8     161     203 ..      80     121 ..      51     137 .. 0.71
   3 !   14.0   0.1   3.2e-05     0.028       2      27 ..     159     186 ..     158     194 .. 0.88
   4 !   10.8   0.0   0.00031      0.27     151     207 ..     202     258 ..     198     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                                      EEEECTSHHHHHHHHHHHHTT....EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarrg....Vtllekgdiag 33
                                      +v++GGG +Gl +A  + rr     +t++ekg+ ++
  gi|488601612|ref|YP_007908083.1|  5 IVVVGGGAAGLKAASRARRRDeeaeITVIEKGEYPS 40
                                      9****************8876789********7776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0094
                                       -EEEESECEEEEEEEETCEEEEE.EECTEEEE..EEEEEEE--GGG CS
                               DAO 161 veilegtevtgleeedgkvwgve.rttpgend..aadavVnaaGaw 203
                                       +++l++te+ ++++++ k++++  +   g+ d   +d++V+a+Ga 
  gi|488601612|ref|YP_007908083.1|  80 INVLTKTEALSIDRKR-KAVKISrN---GRDDelNYDYLVLATGAK 121
                                       567888******8764.44555343...4332234799******86 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.2e-05
                                       EEEECTSHHHHHHHHHHHHTT..EEEEE CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtlle 27 
                                        viiGGG iGl tA +L r    Vt++e
  gi|488601612|ref|YP_007908083.1| 159 AVIIGGGLIGLETAEALERLDidVTIVE 186
                                       59***************666789****9 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00031
                                       HHHHH.HHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGGHH.HH CS
                               DAO 151 alara.aealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaaGawsd.ll 207
                                        l r+ + + Gv++l+ t+v+++  edgkv+ v+ +   + +  a+ v+++ G+  + +l
  gi|488601612|ref|YP_007908083.1| 202 ELVRKcIIREGVKVLTSTTVQEFITEDGKVKAVRvN---EKILPAELVIISIGVEPRtEL 258
                                       5666746899************98999******432...33335699****998876644 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 !   24.6   0.1   2.5e-08   2.2e-05       1      35 [.       7      44 ..       7      59 .. 0.85
   2 !   18.7   0.0   1.7e-06    0.0015       1      39 [.     161     199 ..     161     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.5e-08
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSSSSS.GGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdrlG.Gra 35
                                      +vG+G++Gl aA++++++   ++++++ek+++++ Gr+
  gi|488601612|ref|YP_007908083.1|  7 VVGGGAAGLKAASRARRRdeEAEITVIEKGEYPSlGRC 44
                                      8***************986799********99887766 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.7e-06
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39 
                                       I+G+Gl Gl +A +L + ++dv+++e  ++l  ++ ++e
  gi|488601612|ref|YP_007908083.1| 161 IIGGGLIGLETAEALERLDIDVTIVELKNQLLWNSFDFE 199
                                       9*************************9998855555555 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.2   2.8e+03      46     100 ..      76     129 ..      51     132 .. 0.56
   2 !   42.8   0.0   7.3e-14   6.2e-11       1     104 [.     463     554 ..     463     555 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.2
                         Rhodanese  46 kseapllelpeellelgidnkktvvvycdgggraaaa.aallkklGykn.vsvldGG 100
                                       k+++    + +e+l   id+k++ v + ++g + +    +l+ + G  + v++   G
  gi|488601612|ref|YP_007908083.1|  76 KVKNINVLTKTEAL--SIDRKRKAVKISRNGRDDELNyDYLVLATG-AKpVRLSVKG 129
                                       33333333333333..347777777777777773333244555566.4446665555 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 7.3e-14
                         Rhodanese   1 sakelkellekgkva.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgg 76 
                                       ++ elk++l++g+   llDvR++ e+e+ +I+g              ++ pl el  +l el   ++k++v++c+ g
  gi|488601612|ref|YP_007908083.1| 463 TPVELKRRLDAGEDLyLLDVRSQKEFEARRIEGYEV-----------HNIPLSELRNRLDEL--PKDKEIVTICAIG 526
                                       5789*****9998669***************98543...........477***********9..************* PP

                         Rhodanese  77 graaaaaallkklGyknvsvldGGfkaw 104
                                        r+ +aa+ll   G+++v++ldG +  w
  gi|488601612|ref|YP_007908083.1| 527 TRSYEAARLLMNKGFEKVRFLDGALATW 554
                                       ********9999**999******99988 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   7.5e-07   0.00064       2      33 ..       4      37 ..       3      43 .. 0.84
   2 ?    3.7   0.0     0.024        21     122     165 ..      78     121 ..      72     150 .. 0.82
   3 !    6.0   0.0    0.0049       4.2       3      35 ..     159     191 ..     157     193 .. 0.92
   4 !    7.9   0.0    0.0012       1.1     117     189 ..     206     276 ..     199     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.5e-07
                                      SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVlllekak 33
                                      +++v+GgGaAGl aA +a  ++++++++++ek++
  gi|488601612|ref|YP_007908083.1|  4 EIVVVGGGAAGLKAASRArrRDEEAEITVIEKGE 37
                                      69****************55566788999**986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.024
                                       HT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE----S CS
                       HI0933_like 122 agvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGGl 165
                                       +++++ ++te  s++++++  ++++    ++el+ d+lvlAtG +
  gi|488601612|ref|YP_007908083.1|  78 KNINVLTKTEALSIDRKRKA-VKISRnGRDDELNYDYLVLATGAK 121
                                       688999999999**887777.6666646889************87 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0049
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                        ++iGgG  Gl +A+++++ + +V+++e +++l
  gi|488601612|ref|YP_007908083.1| 159 AVIIGGGLIGLETAEALERLDIDVTIVELKNQL 191
                                       79**************************98876 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0012
                                       HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT--SHHHHHHHHTT--EEE CS
                       HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGstgkgyklaeqfghtivp 189
                                       k + ++gvk+ ++t+v+++ +e++++  v++ +e+ l a+ +++++G +   +l ++ +g +l e+  +++ +
  gi|488601612|ref|YP_007908083.1| 206 KCIIREGVKVLTSTTVQEFITEDGKVKAVRV-NEKILPAELVIISIGVEPRTEL-AESAGLELTEKGAIKVNE 276
                                       445679*************************.9************998766666.566666776666666655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   7.5e-07   0.00064       2      33 ..       5      38 ..       4      42 .. 0.88
   2 !    7.0   0.1    0.0032       2.7       2      33 ..     159     190 ..     158     196 .. 0.91
   3 !    6.3   0.1    0.0049       4.2     146     190 ..     203     247 ..     192     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.5e-07
                                      EEEE--SHHHHHHHHHHHHTTT..-EEEEESSSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGl..kvavvekeqe 33
                                      ++V+G+G+AGL AA +a+++    +++v+ek+++
  gi|488601612|ref|YP_007908083.1|  5 IVVVGGGAAGLKAASRARRRDEeaEITVIEKGEY 38
                                      89****************9665559******986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0032
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                       +++iG+Gl GL  A ++ +   +v++ve +++
  gi|488601612|ref|YP_007908083.1| 159 AVIIGGGLIGLETAEALERLDIDVTIVELKNQ 190
                                       69**************************8876 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0049
                                       HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEE CS
                     FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevri 190
                                        + + + + gv+++++t ++e+i+edg+v  + v+++  + e  i
  gi|488601612|ref|YP_007908083.1| 203 LVRKCIIREGVKVLTSTTVQEFITEDGKVKAVRVNEKILPAELVI 247
                                       4444445667************************98765555555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06    0.0015       1      40 [.       4      42 ..       4      80 .. 0.76
   2 ?    4.3   0.1     0.017        15       3      33 ..     160     187 ..     158     191 .. 0.91
   3 !    5.9   0.0    0.0058         5     156     207 ..     200     250 ..     194     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvg 40
                                      +iv+vGGG aG  aA+  ++   +++e+t++e+ e + +g
  gi|488601612|ref|YP_007908083.1|  4 EIVVVGGGAAGLKAASRARRRD-EEAEITVIEKGEYPSLG 42
                                      59**************999988.66********9998775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                                       EEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlves 33 
                                       vi+GGG  G  +A al++     ++vt+ve 
  gi|488601612|ref|YP_007908083.1| 160 VIIGGGLIGLETAEALERLD---IDVTIVEL 187
                                       9*****************98...99999995 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-S CS
                    Trp_halogenase 156 yakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcs 207
                                       +a++ r+   ++Gv+++  + v+  + edg+v+++r+ +++ + a+l+i   
  gi|488601612|ref|YP_007908083.1| 200 MAELVRKCIIREGVKVLTSTTVQEFITEDGKVKAVRV-NEKILPAELVIISI 250
                                       68999*******************************9.67779999988555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   3.7e-05     0.032       2      35 ..       5      38 ..       4      44 .. 0.91
   2 !   11.3   0.0   0.00015      0.13       3      39 ..     160     194 ..     159     199 .. 0.94
   3 ?    2.5   0.1     0.071        61      91     143 ..     201     253 ..     194     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasps 35
                                      +vv+G+G+Agl+ A r  +   + ++++ie ++ 
  gi|488601612|ref|YP_007908083.1|  5 IVVVGGGAAGLKAASRARRRDEEAEITVIEKGEY 38
                                      8****************99999*******99976 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsllfp 39 
                                       v+iG+G+ gl  A+ l  ++ ++ v+++e  ++ll+ 
  gi|488601612|ref|YP_007908083.1| 160 VIIGGGLIGLETAEAL--ERLDIDVTIVELKNQLLWN 194
                                       8***************..***********99999985 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.071
                     Lycopene_cycl  91 eellerlv.engvklleakvesveeeeageslvvleggrkirarlvvdarglas 143
                                       +el ++++  +gvk l ++  +    e+g++ +v  +++ ++a lv+ + g+ +
  gi|488601612|ref|YP_007908083.1| 201 AELVRKCIiREGVKVLTSTTVQEFITEDGKVKAVRVNEKILPAELVIISIGV-E 253
                                       467777777999999888766655566669******************9994.3 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 !   10.9   0.1   0.00024       0.2      30      53 ..       4      27 ..       2      41 .. 0.79
   2 !   14.2   0.1   2.3e-05      0.02      31      95 ..     159     246 ..     153     271 .. 0.70
   3 ?   -3.0   0.0       4.3   3.7e+03      52     111 ..     475     537 ..     469     543 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                      EEEEESTSHHHHHHHHHHHHTT-E CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgak 53
                                      +++v+GgG aGl+A++ a++ + +
  gi|488601612|ref|YP_007908083.1|  4 EIVVVGGGAAGLKAASRARRRDEE 27
                                      589***************986533 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.3e-05
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE.........................HCHHH CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev.........................lksqe 82 
                                        ++iGgG  Gl+ +++  +l+ +Vt+++++ + l +  +++    e+                          k ++
  gi|488601612|ref|YP_007908083.1| 159 AVIIGGGLIGLETAEALERLDIDVTIVELKNQLLWNSFDFEMA--ELvrkciiregvkvltsttvqefitedGKVKA 233
                                       69**************************999887665554332..11123555556555555555555555544455 PP

                                       HHHHHHHHH-SEE CS
                       AlaDh_PNT_C  83 ellaeavkeadvv 95 
                                         ++e++  a++v
  gi|488601612|ref|YP_007908083.1| 234 VRVNEKILPAELV 246
                                       5555555555555 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.3
                                       -EEEEEESSHHHHHHHHHTTTCECEE..HCHHHHHHHHHHHH-SEE.EE---BTTSS---SC- CS
                       AlaDh_PNT_C  52 akVtvlDvrparleqleslgakfvev..lksqeellaeavkeadvv.igtvlipGkkaPkLvt 111
                                        + ++lDvr+++  + + +++  v+   l++ ++ l+e  k+ ++v i+++     +a++L+ 
  gi|488601612|ref|YP_007908083.1| 475 EDLYLLDVRSQKEFEARRIEGYEVHNipLSELRNRLDELPKDKEIVtICAIGTRSYEAARLLM 537
                                       566778888888877777777766654555566777777777776657887777777777765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.3     9e-05     0.077       1      24 [.       4      27 ..       4      42 .. 0.79
   2 ?    1.4   0.1      0.19   1.6e+02       3      32 ..     160     189 ..     158     192 .. 0.91
   3 !   12.3   0.1     9e-05     0.077      75     128 ..     187     239 ..     172     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGak 24
                                      ++vVvGGg+aG+ AA  A r++ +
  gi|488601612|ref|YP_007908083.1|  4 EIVVVGGGAAGLKAASRARRRDEE 27
                                      59******************8753 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.19
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                       v++GGg+ G+  A a  r +  v +ve ++
  gi|488601612|ref|YP_007908083.1| 160 VIIGGGLIGLETAEALERLDIDVTIVELKN 189
                                       8*************************9655 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 9e-05
                      FAD_oxidored  75 lkkrskwntfepevakavleemlaeagvtvllntrlvevekegkriesvtvesk 128
                                       lk++  wn+f+ e+a+ v + +++e gv+vl+ t+++e ++e++++++v+v++k
  gi|488601612|ref|YP_007908083.1| 187 LKNQLLWNSFDFEMAELVRKCIIRE-GVKVLTSTTVQEFITEDGKVKAVRVNEK 239
                                       446677899**************99.****************99*******643 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00076      0.65       1      34 [.       6      37 ..       6      51 .. 0.84
   2 ?    4.7   0.0     0.032        27     117     155 ..      80     120 ..      71     121 .. 0.76
   3 ?    4.5   0.1     0.036        31       1      33 [.     160     187 ..     160     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00076
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.s 34
                                      ++vG+G++Gl ++ r  +r   +++ eit++++ +
  gi|488601612|ref|YP_007908083.1|  6 VVVGGGAAGLKAASRARRR---DEEAEITVIEKgE 37
                                      69*************9999...7*********952 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.032
                     NAD_binding_9 117 vevh.raevvdleeradgqavlladg.aslaadaVvLAlGh 155
                                       ++v+ ++e+++++++++ +++  ++  ++l +d++vLA+G 
  gi|488601612|ref|YP_007908083.1|  80 INVLtKTEALSIDRKRKAVKISRNGRdDELNYDYLVLATGA 120
                                       4444278999***99999987665443789*********95 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.036
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp 33 
                                       +i+G+G  Gl ++e+L +      ++++t+++ 
  gi|488601612|ref|YP_007908083.1| 160 VIIGGGLIGLETAEALERL-----DIDVTIVEL 187
                                       7**************9888.....588888775 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 !   10.1   0.0   0.00099      0.84       7      45 ..       2      39 ..       1     124 [. 0.66
   2 !   10.0   0.1    0.0011      0.91       9      41 ..     158     194 ..     151     263 .. 0.68
   3 ?   -1.4   0.0       3.9   3.3e+03      19      78 ..     388     445 ..     386     454 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00099
                     NAD_binding_7  7 gkkvlvvGgGevAarkvrklleag..akvtvvapevkeele 45
                                      g++++vvGgG  +++ +++  + +  a++tv+ +    e +
  gi|488601612|ref|YP_007908083.1|  2 GREIVVVGGGAAGLKAASRARRRDeeAEITVIEKG---EYP 39
                                      689********998777766653333******998...433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev....k 41 
                                       + +++GgG ++++ ++ l + + +vt+v  +     +
  gi|488601612|ref|YP_007908083.1| 158 SAVIIGGGLIGLETAEALERLDIDVTIVELKNqllwN 194
                                       689*************************988534431 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.9
                     NAD_binding_7  19 Aarkvrklleaga.kvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneri 78 
                                       A r+ rk+l a+a  + v++++   +    + +++    +dl+++dl++a +  ++l + i
  gi|488601612|ref|YP_007908083.1| 388 ADRRTRKVLGAQAfGLGVIDKR---IDVIAMAIHRGATVDDLAEVDLAYAPPFSAALDHVI 445
                                       6677777777665246666666...222223344555568888888888877777777666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   0.00021      0.18       2      24 ..       5      27 ..       4      45 .. 0.84
   2 ?   -0.3   0.0       0.5   4.3e+02     105     150 ..      74     120 ..      68     142 .. 0.75
   3 !    8.4   0.0    0.0012         1       3      31 ..     160     188 ..     158     197 .. 0.86
   4 ?   -0.3   0.1      0.51   4.3e+02     113     150 ..     216     252 ..     194     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                      EEEE-SSHHHHHHHHHHHHTT-- CS
                              GIDA  2 viViGgGhAGceAAlaaarlGak 24
                                      ++V+GgG AG+ AA  a r+  +
  gi|488601612|ref|YP_007908083.1|  5 IVVVGGGAAGLKAASRARRRDEE 27
                                      89**************9998655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.5
                                       HHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 105 lenepnleiiee.eveeliveekkvkgvvtedgetikakavviatGt 150
                                        ++ +n++++++ e+ +++ + k vk  +  ++ +++ +  v+atG+
  gi|488601612|ref|YP_007908083.1|  74 FKKVKNINVLTKtEALSIDRKRKAVKISRNGRDDELNYDYLVLATGA 120
                                       56677888765415666666667777777778899999999999998 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0012
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLithk 31 
                                       ++iGgG+ G+e A a+ rl ++v+++  k
  gi|488601612|ref|YP_007908083.1| 160 VIIGGGLIGLETAEALERLDIDVTIVELK 188
                                       89**********************99555 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.51
                                       EEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 113 iieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                       + + +v+e i+e++kvk+v+ + ++++ a+ v+i+ G 
  gi|488601612|ref|YP_007908083.1| 216 LTSTTVQEFITEDGKVKAVRVN-EKILPAELVIISIGV 252
                                       3467899999999***999875.578899999999996 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00063      0.53      19      49 ..       4      35 ..       1      45 [. 0.87
   2 !    6.5   0.2    0.0051       4.4      10      49 ..     149     187 ..     143     192 .. 0.83
   3 ?    5.1   0.2     0.013        11     100     139 ..     200     238 ..     191     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00063
                                      EEEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                              Thi4 19 DvvivGaGssGLtaayylakk.pdlkvailer 49
                                      ++v+vG+G++GL aa    ++  + +++++e+
  gi|488601612|ref|YP_007908083.1|  4 EIVVVGGGAAGLKAASRARRRdEEAEITVIEK 35
                                      79*************99888878899999997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0051
                                       HHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  10 edllkyaesDvvivGaGssGLtaayylakkpdlkvailer 49 
                                       e++++      vi+G+G  GL +a  l +  d+ v+i+e 
  gi|488601612|ref|YP_007908083.1| 149 EMWMNESIESAVIIGGGLIGLETAEALERL-DIDVTIVEL 187
                                       566666666678899************999.****99996 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.013
                                       HHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEE CS
                              Thi4 100 tstllskvlqlanvkllnavaveDlivregegvaGvvinw 139
                                       +++l+ k + + +vk+l++++v + i+ +  +v+ v +n 
  gi|488601612|ref|YP_007908083.1| 200 MAELVRKCIIREGVKVLTSTTVQEFITED-GKVKAVRVNE 238
                                       68899999999****************99.6777776665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0086       7.3       1      31 [.       5      37 ..       5      77 .. 0.83
   2 !    9.4   0.1    0.0014       1.2       2      30 ..     160     188 ..     159     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0086
                                      EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkde 31
                                      i+++G G  G + a + ++ ++  +++vi+k e
  gi|488601612|ref|YP_007908083.1|  5 IVVVGGGAAGLKAASRARRrDEeAEITVIEKGE 37
                                      89*****************555866*****965 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESS CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkd 30 
                                       +iiG G +G + ae L++  +dv++++ +
  gi|488601612|ref|YP_007908083.1| 160 VIIGGGLIGLETAEALERLDIDVTIVELK 188
                                       8*****************6668****975 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.073        62       3      18 ..       4      19 ..       3      37 .. 0.86
   2 ?   -1.8   0.0       1.7   1.5e+03     124     168 ..      84     123 ..      76     142 .. 0.71
   3 !   11.4   0.0   0.00016      0.13       4      34 ..     159     189 ..     157     195 .. 0.90
   4 ?   -4.0   0.0       7.8   6.6e+03     117     144 ..     210     237 ..     203     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.073
                                      EEEEE--SHHHHHHHH CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlal 18
                                      ++++VG+G aGl +a+
  gi|488601612|ref|YP_007908083.1|  4 EIVVVGGGAAGLKAAS 19
                                      579*********9996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                                       CSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HH CS
                     FAD_binding_3 124 fktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStv 168
                                        kte +s+ +  +     v+ +++g++ +++ +Ylv a G++  v
  gi|488601612|ref|YP_007908083.1|  84 TKTEALSIDRKRKA----VKISRNGRDDELNYDYLVLATGAKP-V 123
                                       55555555544444....4556678888999999999999885.4 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00016
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                        +I+G+G+ Gl +a  L +  ++v++ve  +
  gi|488601612|ref|YP_007908083.1| 159 AVIIGGGLIGLETAEALERLDIDVTIVELKN 189
                                       57*************************9665 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 7.8
                                       HHTEEETCSEEEECCEECCCCCCCEEEE CS
                     FAD_binding_3 117 erglqvrfktevesleqdeegvtaevrd 144
                                       ++g++v  +t v+ +  ++ +v+a+  +
  gi|488601612|ref|YP_007908083.1| 210 REGVKVLTSTTVQEFITEDGKVKAVRVN 237
                                       5789999999999999999999998765 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 ?    4.3   0.1     0.022        19     192     224 ..       3      35 ..       1      40 [. 0.90
   2 ?    6.5   0.0    0.0045       3.9     283     339 ..      67     119 ..      56     122 .. 0.69
   3 ?   -1.7   0.0       1.5   1.2e+03     189     212 ..     154     177 ..     137     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.022
                       K_oxygenase 192 kriaVvGsGqSaaeifedllrrqkkvelklvtr 224
                                       ++i+VvG+G  +   +  + rr +++e++++ +
  gi|488601612|ref|YP_007908083.1|   3 REIVVVGGGAAGLKAASRARRRDEEAEITVIEK 35 
                                       79*************************999876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0045
                       K_oxygenase 283 elyeqkvk.geerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                       +++++++  + +++++l+++e  s++++ k +v++    + +g++++l++d++vlATG
  gi|488601612|ref|YP_007908083.1|  67 DVRDEEYFkKVKNINVLTKTEALSIDRKRK-AVKI----SRNGRDDELNYDYLVLATG 119
                                       444443330346789999999999999986.4444....4478999************ PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.5
                       K_oxygenase 189 lakkriaVvGsGqSaaeifedllr 212
                                       ++ ++ +++G+G  + e +e l r
  gi|488601612|ref|YP_007908083.1| 154 ESIESAVIIGGGLIGLETAEALER 177
                                       556778999999999888877655 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.022        18       3      35 ..       5      38 ..       3      57 .. 0.86
   2 ?   -3.3   0.0       5.3   4.6e+03       4      27 ..     160     182 ..     158     190 .. 0.71
   3 ?    4.8   0.1     0.018        16     201     234 ..     206     237 ..     196     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.022
                       GMC_oxred_N  3 elveggGsagsvvAaRLse.dpstsvlvleaggr 35
                                       +v+ggG+ag   A+R    d++++++v+e g +
  gi|488601612|ref|YP_007908083.1|  5 IVVVGGGAAGLKAASRARRrDEEAEITVIEKGEY 38
                                      689*************975267789*****9975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.3
                       GMC_oxred_N   4 lveggGsagsvvAaRLsedpstsv 27 
                                       +++ggG++g  +A+ L   + + v
  gi|488601612|ref|YP_007908083.1| 160 VIIGGGLIGLETAEALERLD-IDV 182
                                       79999999999998875543.444 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.018
                       GMC_oxred_N 201 palerpnleiltgakaekiilegrkkravGVeas 234
                                       + + r+++++lt+++++ +i e  ++++ +V+++
  gi|488601612|ref|YP_007908083.1| 206 KCIIREGVKVLTSTTVQEFITE--DGKVKAVRVN 237
                                       445688*************999..7777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.74u 0.34s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 3157.65
//
Query:       gi|488601613|ref|YP_007908084.1|  [L=162]
Description: hypothetical protein Asulf_02135 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 899.88
//
Query:       gi|488601614|ref|YP_007908085.1|  [L=383]
Description: NADH dehydrogenase, FAD-containing subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-22   77.8   0.0    2.9e-13   49.7   0.0    2.1  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    2.1e-06   26.9   0.0    8.6e-06   24.9   0.0    1.8  2  Trp_halogenase   Tryptophan halogenase
    2.8e-06   27.4   0.0      0.015   15.3   0.0    2.3  2  NAD_binding_9    FAD-NAD(P)-binding
    4.9e-05   23.1   0.1      0.016   14.9   0.0    2.3  2  DAO              FAD dependent oxidoreductase
      0.003   16.9   0.0      0.034   13.4   0.0    2.1  2  FAD_binding_3    FAD binding domain
     0.0034   17.9   0.0      0.047   14.2   0.0    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0037   17.5   0.1     0.0086   16.3   0.1    1.6  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
     0.0037   16.0   0.0      0.061   12.0   0.1    2.3  3  HI0933_like      HI0933-like protein
     0.0058   15.9   0.1      0.016   14.5   0.1    1.8  1  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
       0.08   13.2   0.0       0.17   12.2   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.082   11.9   0.0       0.19   10.7   0.0    1.6  2  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 !   49.7   0.0   1.8e-16   2.9e-13       2     126 ..       3     124 ..       2     153 .. 0.84
   2 !   26.3   0.0   2.4e-09   3.8e-06     167     294 .]     186     307 ..     168     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.8e-16
                                       SEEEE--SHHHHHHHHHHHH....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCT CS
                                       xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq....agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgee 74 
                                       +++++GgG AG+ +a +l++     +a++t+v ++   ++ ++ ++ +  g +e ++ ++   + + +g  ++ + e
  gi|488601614|ref|YP_007908085.1|   3 RILIVGGGSAGIMTAARLRNalsmDEAEITIV-DRSDKHYYQPGYTLIPFGLEEVENLIKPMKDVIPAGCNFIQD-E 77 
                                       799*****************98877*******.9999**********999999999999955566999*999999.* PP

                                       CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  75 vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgkl 126
                                       vv++ +++  v+      + +++++yd+lvlAtG++     i+G+aen +k+
  gi|488601614|ref|YP_007908085.1|  78 VVSFNFDNNYVET-----KGGKRLEYDYLVLATGAKLVMEEIEGLAENLYKN 124
                                       ********77777.....45669***********999999*****6665543 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 2.4e-09
                                       EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 167 evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstel 243
                                       ++t+  a++ +     +  +  l + ++++++++k g ++ eid++++   v   +g+e+ +dl+vv     p+   
  gi|488601614|ref|YP_007908085.1| 186 NITITSALPAIF--SREPYASKLDAMFRDRNINTKSGFTPSEIDPEEK--VVRSWEGDELHYDLLVVVP---PNEGE 255
                                       677777777777..347778889999*********************8..6778899*********965...44433 PP

                                       CS.HCCT-EEEETTEEE--TTS.BES.STTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xx.xxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 244 le.eklglelderggivvdefl.rtn.vpgiyaiGDvaggkggpelaqaAvqqG 294
                                          e  g++ d ++++  d++  + +  p++++iGD+a +  + ++a  A +q+
  gi|488601614|ref|YP_007908085.1| 256 SIyEGTGIA-DATNFVMADKHKlQLEkYPNVFVIGDCA-NYPTSKTASGARKQA 307
                                       335999997.69999988876548877***********.778888888888876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   5.3e-09   8.6e-06       1      47 [.       3      50 ..       3      62 .. 0.93
   2 ?   -0.7   0.0      0.31     5e+02     168     210 ..      70     108 ..      63     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.3e-09
                                      EEEEE--SHHHHHHHHHHHHHTTTS.SEEEEEE-SSS---SS-EE--T CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgk.levtlveseeigtvgvGeatip 47
                                      +i+ivGGG+aG ++Aa l++al+ + +e+t+v+ ++   ++ G  +ip
  gi|488601614|ref|YP_007908085.1|  3 RILIVGGGSAGIMTAARLRNALSMDeAEITIVDRSDKHYYQPGYTLIP 50
                                      69********************9999**********999999999998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.31
                                       T-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
                    Trp_halogenase 168 GvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfr 210
                                       G + ++++vv+ + d+    + ++++ g+++e+d  + ++G +
  gi|488601614|ref|YP_007908085.1|  70 GCNFIQDEVVSFNFDN----NYVETKGGKRLEYDYLVLATGAK 108
                                       5666666666666665....468999**************986 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.3e-06     0.015       2      35 ..       6      38 ..       5      46 .. 0.89
   2 !   10.0   0.0    0.0004      0.65     117     155 ..      71     107 ..      56     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.3e-06
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpse 35
                                      ivG+G +G+++++rL +   + ++ eit++d+s 
  gi|488601614|ref|YP_007908085.1|  6 IVGGGSAGIMTAARLRNAL-SMDEAEITIVDRSD 38
                                      9**************9997.99*********964 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0004
                     NAD_binding_9 117 vevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                        +++++evv+ + +++  +v +++g++l++d++vLA+G 
  gi|488601614|ref|YP_007908085.1|  71 CNFIQDEVVSFNFDNN--YVETKGGKRLEYDYLVLATGA 107
                                       5789999999998876..6999***************95 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.5e-06     0.016       2      30 ..       4      38 ..       3      42 .. 0.83
   2 !    6.0   0.0    0.0048       7.8     159     204 ..      69     109 ..      63     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.5e-06
                                      EEEECTSHHHHHHHHHHHHT.T.....EEEEESSS CS
                               DAO  2 vviiGGGiiGlstAyeLarr.g.....Vtllekgd 30
                                      ++i+GGG +G+ tA  L  +       +t+++++d
  gi|488601614|ref|YP_007908085.1|  4 ILIVGGGSAGIMTAARLRNAlSmdeaeITIVDRSD 38
                                      99***************4334256789*****984 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0048
                                       TT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGH CS
                               DAO 159 lGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaws 204
                                       +G+++++  ev++++ +      v  +t+ g + ++d++V+a+Ga  
  gi|488601614|ref|YP_007908085.1|  69 AGCNFIQD-EVVSFNFD---NNYV--ETKgGKRLEYDYLVLATGAKL 109
                                       78999999.99999554...4677..7776776567********983 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.1e-05     0.034       3      40 ..       3      44 ..       1      47 [. 0.84
   2 ?    1.1   0.0      0.11   1.9e+02     280     327 ..     278     323 ..     255     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                      EEEEE--SHHHHHHHHHHHHTTHH.....EEEEESSSSSCCSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvr.....vvlvekrsttvvlp 40
                                       +lIVG+G aG+m+a  L++a  +      ++v++ ++ +++p
  gi|488601614|ref|YP_007908085.1|  3 RILIVGGGSAGIMTAARLRNA-LSmdeaeITIVDRSDKHYYQP 44
                                      589************988887.656666699999999988875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                                       SSEET.TEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTSS- CS
                     FAD_binding_3 280 kyrkg.rvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGeAk 327
                                       +++k  +vf++GD a   + +++ G   a + a  L++ L av+kGe  
  gi|488601614|ref|YP_007908085.1| 278 QLEKYpNVFVIGDCANYPTSKTASG---ARKQAEVLVKNLLAVMKGEEP 323
                                       4555448**********99999999...567888899999999998765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.9e-05     0.047       1      33 [.       3      39 ..       3      45 .. 0.88
   2 ?    0.7   0.0      0.47   7.7e+02      43      71 ..     203     231 ..     174     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                                      EEEEECSSHHHHHHHHHHHH.TT...SEEEEEESSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalae.lg...kkVtvversdk 33
                                      ++++vGgG  g++ A+ l++ l    +++t+v+rsdk
  gi|488601614|ref|YP_007908085.1|  3 RILIVGGGSAGIMTAARLRNaLSmdeAEITIVDRSDK 39
                                      79****************885557778********98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.47
                                       HHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  43 skilqeklekngievllntkveeiegsed 71 
                                       ++ l   +++++i+   + ++ ei+ +e+
  gi|488601614|ref|YP_007908085.1| 203 ASKLDAMFRDRNINTKSGFTPSEIDPEEK 231
                                       5667888999**************99887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   5.3e-06    0.0086       1      29 [.       6      38 ..       6      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.3e-06
                                      EE--SHHHHHHHHHHHCC....TEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka....gfdvlllekrd 29
                                      IvG+G +G  +A++L++a     +++++++++d
  gi|488601614|ref|YP_007908085.1|  6 IVGGGSAGIMTAARLRNAlsmdEAEITIVDRSD 38
                                      9***************966666889*****987 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   3.8e-05     0.061       2      33 ..       3      38 ..       2      41 .. 0.78
   2 ?    1.1   0.0     0.075   1.2e+02     143     165 ..      86     108 ..      72     112 .. 0.81
   3 ?   -3.7   0.0       2.2   3.6e+03     367     384 ..     274     291 ..     272     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                                      SEEEE--SHHHHHHHHHH....HHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisa....akrgkrVlllekak 33
                                      +++++GgG AG+m+A+++    +  +++++++++ +
  gi|488601614|ref|YP_007908085.1|  3 RILIVGGGSAGIMTAARLrnalSMDEAEITIVDRSD 38
                                      589************998554556677888887765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.075
                                       EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 143 frvktkseeeleadklvlAtGGl 165
                                         v+tk++++le d+lvlAtG +
  gi|488601614|ref|YP_007908085.1|  86 NYVETKGGKRLEYDYLVLATGAK 108
                                       4689999**************86 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.2
                                       TTT-BBTTSTTEEE-GGG CS
                       HI0933_like 367 sktmeskkvpgLffaGEv 384
                                       ++ ++ +k p++f++G +
  gi|488601614|ref|YP_007908085.1| 274 KHKLQLEKYPNVFVIGDC 291
                                       56789999*******975 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 !   14.5   0.1   9.8e-06     0.016     166     275 ..       3     115 ..       1     133 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.8e-06
                       Pyr_redox_3 166 kvvViGgknSavDaAlelvrk....gaeVtvvtrgseiekeesdpsyslkpdienrleelvke..ekikvlfnaevk 236
                                       +++++Gg+  ++ +A  l ++    +ae+t+v+r++   k+ ++p y+l p   +++e+l+k   +    +  a  +
  gi|488601614|ref|YP_007908085.1|   3 RILIVGGGSAGIMTAARLRNAlsmdEAEITIVDRSD---KHYYQPGYTLIPFGLEEVENLIKPmkD----VIPAGCN 72 
                                       799************99987777779********97...67889****************996542....3333333 PP

                       Pyr_redox_3 237 eikekeeey.....kvktedgkkvevkddvvlatGykpdlsflk 275
                                        i+++ +++      v+t+ gk++ ++d  vlatG k  ++ ++
  gi|488601614|ref|YP_007908085.1|  73 FIQDEVVSFnfdnnYVETKGGKRL-EYDYLVLATGAKLVMEEIE 115
                                       333333333111114677777775.57999*****998777766 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.17       1      36 [.       4      40 ..       4      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                      EEEE--SHHHHHHHHHHHCTCCT-G.EEEEEESSHHH CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvda.eitvadrskek 36
                                      +li+G+Gs G  +a  l +  ++d+ eit++drs+++
  gi|488601614|ref|YP_007908085.1|  4 ILIVGGGSAGIMTAARLRNALSMDEaEITIVDRSDKH 40
                                      89**********************9*********986 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   0.0   0.00012      0.19       2      43 ..       4      47 ..       3      61 .. 0.83
   2 ?   -2.0   0.0      0.88   1.4e+03     104     143 ..      73     109 ..      50     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                     Lycopene_cycl  2 vvviGaGpAglslAarl..teakpglkvvlieaspsllfpnnyv 43
                                      ++++G+G Ag+  Aarl  + +  + ++++++ s++  + + y+
  gi|488601614|ref|YP_007908085.1|  4 ILIVGGGSAGIMTAARLrnALSMDEAEITIVDRSDKHYYQPGYT 47
                                      78***************544456677899999999988777665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.88
                     Lycopene_cycl 104 lleakvesveeeeageslvvleggrkirarlvvdarglas 143
                                       + +  v s + ++    +v ++gg++++    v a+g+  
  gi|488601614|ref|YP_007908085.1|  73 FIQDEVVSFNFDN---NYVETKGGKRLEYDYLVLATGAKL 109
                                       5555555555444...499999999999999999999543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.38s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2117.57
//
Query:       gi|488601615|ref|YP_007908086.1|  [L=278]
Description: hypothetical protein Asulf_02137 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-16   58.7   0.1    7.3e-16   57.8   0.1    1.5  1  DUF1641         Protein of unknown function (DUF1641)
    0.00054   20.3   2.8        5.6    7.4   0.0    3.7  4  Syntaxin_2      Syntaxin-like protein
     0.0027   16.8   3.0       0.83    8.7   0.2    2.7  3  MCR_C           Methyl-coenzyme M reductase operon protein C
     0.0093   16.0   2.4        2.7    8.1   0.1    2.8  3  LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
  ------ inclusion threshold ------
      0.011   15.5   0.2        3.8    7.3   0.0    2.4  2  Flavi_capsid    Flavivirus capsid protein C
      0.027   14.3   1.3          4    7.3   0.1    3.2  2  Sec34           Sec34-like family
      0.031   14.7   3.0        7.7    7.0   0.1    3.1  4  TBCC_N          Tubulin-specific chaperone C N-terminal domai
      0.037   13.6   7.4      0.084   12.4   0.7    2.7  3  4HB_MCP_1       Four helix bundle sensory module for signal t
      0.077   13.5   7.7          1    9.9   0.9    3.0  3  EF-G-binding_N  Elongation factor G-binding protein, N-termin
       0.11   13.1   2.2         24    5.7   0.1    3.4  4  DNA_repr_REX1B  DNA repair REX1-B
       0.16   12.1   4.8        1.9    8.6   0.2    2.9  4  Spore_III_AB    Stage III sporulation protein AB (spore_III_A
        0.2   11.8   1.6          7    6.7   0.1    3.4  4  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
       0.57   10.5   9.0        1.4    9.2   0.7    3.3  4  GAT             GAT domain
        3.7    6.4   6.2        6.3    5.7   1.5    2.3  2  Ran-binding     RanGTP-binding protein


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.1   5.7e-19   7.3e-16       2      39 .]     238     275 ..     237     275 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 5.7e-19
                           DUF1641   2 gleepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                       ++ee k+v++fg+l+a+rD+DVqrG+G ++++LKalG+
  gi|488601615|ref|YP_007908086.1| 238 DEEEIKKVSTFGILSAMRDEDVQRGIGAVFTILKALGR 275
                                       689**********************************8 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.049        63      25      53 ..      20      49 ..       4      56 .. 0.57
   2 !    7.0   0.0    0.0059       7.5       5      54 ..      58     108 ..      54     114 .. 0.85
   3 !    7.4   0.0    0.0044       5.6       5      45 ..     116     161 ..     112     174 .. 0.73
   4 ?   -1.4   0.0       2.3     3e+03      58      64 ..     216     222 ..     200     248 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.049
                        Syntaxin_2 25 kkd.teelreklhelieeinelikktnell 53
                                       kd  +el  kl+el eei+ l+++  +++
  gi|488601615|ref|YP_007908086.1| 20 TKDlIQELLPKLKELSEEITPLLTEFRKNV 49
                                      333344555555555555555555544444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0059
                        Syntaxin_2   5 lqkinsnvstleklvkqLgtkkd.teelreklhelieeinelikktnellk 54 
                                       l+k+++n+ t+ kl++  +  +d  ee   +++el eei+ l+++  +++ 
  gi|488601615|ref|YP_007908086.1|  58 LTKLTENIDTMLKLINLMEAGRDfLEEGIPNFKELSEEITPLLTEFRKNVD 108
                                       89*********************8777778888888888888888888775 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0044
                        Syntaxin_2   5 lqkinsnvstleklvkqLgtkkd.....teelreklhelieeinel 45 
                                       l+k+++n+ t+ kl++  +  +d      ++++e  +e++ +in+l
  gi|488601615|ref|YP_007908086.1| 116 LTKLTENIDTMLKLINLMEAGRDfleegIPNFKELSEEITPKINRL 161
                                       89********************996666555555555555555554 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.3
                        Syntaxin_2  58 qldnsss 64 
                                       ++ ++ s
  gi|488601615|ref|YP_007908086.1| 216 TIVKQPS 222
                                       3322222 PP

>> 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 !    8.7   0.2   0.00065      0.83     195     240 ..      28      73 ..      18      79 .. 0.90
   2 !    7.7   0.1    0.0013       1.6     193     240 ..      84     131 ..      76     137 .. 0.90
   3 ?   -1.7   0.0      0.94   1.2e+03     193     221 ..     142     170 ..     133     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00065
                             MCR_C 195 iealdelveeveevldkkreelakDpllvsparvkkeieeqveeie 240
                                       + +l+el+ee++ +l + r+++++D  ++  +++ ++i++ ++ i+
  gi|488601615|ref|YP_007908086.1|  28 LPKLKELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLIN 73 
                                       6799**********************************99988776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0013
                             MCR_C 193 eeiealdelveeveevldkkreelakDpllvsparvkkeieeqveeie 240
                                       e i +++el+ee++ +l + r+++++D  ++  +++ ++i++ ++ i+
  gi|488601615|ref|YP_007908086.1|  84 EGIPNFKELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLIN 131
                                       6788999*********************************99988776 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.94
                             MCR_C 193 eeiealdelveeveevldkkreelakDpl 221
                                       e i +++el+ee++  +++ r+ l++D  
  gi|488601615|ref|YP_007908086.1| 142 EGIPNFKELSEEITPKINRLRTLLDDDET 170
                                       56778899999999999999999988864 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0021       2.7      31      83 ..      32      81 ..      12      88 .. 0.77
   2 !    7.3   0.1    0.0039         5      49      82 ..     105     138 ..      84     144 .. 0.76
   3 ?   -3.0   0.0       6.1   7.8e+03      13      29 ..     197     213 ..     187     230 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                    LAGLIDADG_WhiA 31 eelaeqlqkllnefeleakilerrkkyvvylKkaeqIvdlLkiigahesllkf 83
                                      +el e+++ ll ef+   k ++r + +++ +K  e+I ++Lk+i+ +e+ ++f
  gi|488601615|ref|YP_007908086.1| 32 KELSEEITPLLTEFR---KNVDRDETVILLTKLTENIDTMLKLINLMEAGRDF 81
                                      455555555555554...667889999999**************999886655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0039
                    LAGLIDADG_WhiA  49 kilerrkkyvvylKkaeqIvdlLkiigahesllk 82 
                                       k ++r + +++ +K  e+I ++Lk+i+ +e+ ++
  gi|488601615|ref|YP_007908086.1| 105 KNVDRDETVILLTKLTENIDTMLKLINLMEAGRD 138
                                       667889999999**************99988665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.1
                    LAGLIDADG_WhiA  13 GsindpekkyhLEivsp 29 
                                       Gsin  + +  +E+ s+
  gi|488601615|ref|YP_007908086.1| 197 GSINLDSIEKTFEMLSE 213
                                       44444433333333333 PP

>> Flavi_capsid  Flavivirus capsid protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.003       3.8      40      90 ..      23      73 ..      17      82 .. 0.89
   2 ?    5.9   0.0    0.0078        10      51      90 ..      92     131 ..      81     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.003
                      Flavi_capsid 40 lvlallaffrftaiaptpallkrWrtvkkkqAlkvLkkfkkevgtlldsln 90
                                      l++ ll  ++ ++ + tp l ++ + v+  + +  L+k+  ++ t+l+ +n
  gi|488601615|ref|YP_007908086.1| 23 LIQELLPKLKELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLIN 73
                                      6677777777888899********************************998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0078
                      Flavi_capsid  51 taiaptpallkrWrtvkkkqAlkvLkkfkkevgtlldsln 90 
                                       ++ + tp l ++ + v+  + +  L+k+  ++ t+l+ +n
  gi|488601615|ref|YP_007908086.1|  92 LSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLIN 131
                                       566789*******************************998 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.065        84      13      51 ..      59      97 ..      51     113 .. 0.67
   2 ?    7.3   0.1    0.0031         4      12      63 ..     116     167 ..     110     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.065
                             Sec34 13 delleqtdealeqLeeleekfksvsektsslheaceqll 51
                                      ++l e++d++l++++ +e   ++ +e   +++e +e+++
  gi|488601615|ref|YP_007908086.1| 59 TKLTENIDTMLKLINLMEAGRDFLEEGIPNFKELSEEIT 97
                                      566777777777777777777777776666666666543 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0031
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                       +++l e++d++l++++ +e   ++ +e   +++e +e+++ + +rl++l ++
  gi|488601615|ref|YP_007908086.1| 116 LTKLTENIDTMLKLINLMEAGRDFLEEGIPNFKELSEEITPKINRLRTLLDD 167
                                       578999**************************************99998876 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.006       7.7      27      80 ..      20      73 ..      15      77 .. 0.89
   2 ?    6.7   0.1    0.0076       9.7      37      80 ..      88     131 ..      80     135 .. 0.94
   3 ?   -2.0   0.0       3.8   4.8e+03      41      79 ..     150     165 ..     143     177 .. 0.55
   4 ?   -2.0   0.0       3.8   4.9e+03      64      79 ..     200     215 ..     187     239 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.006
                            TBCC_N 27 eeekvdsFlkaFteekaaieellesveesadksklkqkldeitaeiqeLqklla 80
                                      +++ +++ l +++e +++i  ll++++++ d+++    l ++t++i+++ kl++
  gi|488601615|ref|YP_007908086.1| 20 TKDLIQELLPKLKELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLIN 73
                                      566778889999999************9********************999876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0076
                            TBCC_N  37 aFteekaaieellesveesadksklkqkldeitaeiqeLqklla 80 
                                       +F+e +++i  ll++++++ d+++    l ++t++i+++ kl++
  gi|488601615|ref|YP_007908086.1|  88 NFKELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLIN 131
                                       79*************************************99887 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.8
                            TBCC_N  41 ekaaieellesveesadksklkqkldeitaeiqeLqkll 79 
                                        ++                       eit +i++L+ ll
  gi|488601615|ref|YP_007908086.1| 150 LSE-----------------------EITPKINRLRTLL 165
                                       333.......................4444444444443 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.8
                            TBCC_N  64 kldeitaeiqeLqkll 79 
                                       +ld i++ ++ L +l+
  gi|488601615|ref|YP_007908086.1| 200 NLDSIEKTFEMLSELA 215
                                       4555555555554443 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   6.6e-05     0.084      68     125 ..      15      72 ..      12      79 .. 0.90
   2 ?    4.8   0.2     0.014        18      82     125 ..      87     130 ..      74     155 .. 0.89
   3 ?   -2.2   0.0         2   2.6e+03     101     127 ..     190     217 ..     184     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                         4HB_MCP_1  68 liltkdkaekdellkdieeleaeidkllekyektilteeEkelleefkeqlnaYrevr 125
                                       + ++ +k+  +ell +++el++ei  ll +++k    +e   ll+++ e++++  +++
  gi|488601615|ref|YP_007908086.1|  15 YTIEATKDLIQELLPKLKELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLI 72 
                                       457789999*****************************************99987665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.014
                         4HB_MCP_1  82 kdieeleaeidkllekyektilteeEkelleefkeqlnaYrevr 125
                                        + +el++ei  ll +++k    +e   ll+++ e++++  +++
  gi|488601615|ref|YP_007908086.1|  87 PNFKELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLI 130
                                       57899***************99999999********99987665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2
                         4HB_MCP_1 101 tilteeE.kelleefkeqlnaYrevrkk 127
                                       +++ +eE +  l+++++ +++ +e+   
  gi|488601615|ref|YP_007908086.1| 190 SMMVDEEgSINLDSIEKTFEMLSELATI 217
                                       4444444244666666666655555444 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.9   0.00081         1      29      80 ..      16      66 ..      10      68 .. 0.87
   2 ?    6.6   0.1    0.0087        11      31      80 ..      76     124 ..      72     126 .. 0.84
   3 ?   -2.2   0.0         5   6.4e+03      79      79 ..     218     218 ..     201     245 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00081
                    EF-G-binding_N 29 vveavkalaaekIlelfpelseeqkelLeqiddiktkekaeklLeeLkeyVi 80
                                      ++ea+k+l++e + + ++elsee + lL+++ +  ++ +   lL++L e + 
  gi|488601615|ref|YP_007908086.1| 16 TIEATKDLIQELLPK-LKELSEEITPLLTEFRKNVDRDETVILLTKLTENID 66
                                      788899888877666.799****************************99875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0087
                    EF-G-binding_N  31 eavkalaaekIlelfpelseeqkelLeqiddiktkekaeklLeeLkeyVi 80 
                                       ea ++ ++e I + f+elsee + lL+++ +  ++ +   lL++L e + 
  gi|488601615|ref|YP_007908086.1|  76 EAGRDFLEEGIPN-FKELSEEITPLLTEFRKNVDRDETVILLTKLTENID 124
                                       5566666777777.89*****************************99875 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5
                    EF-G-binding_N  79 V 79 
                                       V
  gi|488601615|ref|YP_007908086.1| 218 V 218
                                       1 PP

>> DNA_repr_REX1B  DNA repair REX1-B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.019        24      37      80 ..      21      64 ..      15      79 .. 0.86
   2 ?    4.8   0.1     0.035        45      46      80 ..      88     122 ..      60     137 .. 0.84
   3 ?    0.2   0.0      0.94   1.2e+03      35      61 ..     146     161 ..     130     175 .. 0.65
   4 ?   -1.9   0.0       4.2   5.4e+03      60      77 ..     213     230 ..     202     248 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                    DNA_repr_REX1B 37 kqlvkevTeefseiSkevleieaaLreeasredlaelirkvqek 80
                                      k l++e+  +++e+S+e+  + +++r++ +r++   l+ k+ e+
  gi|488601615|ref|YP_007908086.1| 21 KDLIQELLPKLKELSEEITPLLTEFRKNVDRDETVILLTKLTEN 64
                                      6788999999******************9**9999999998776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.035
                    DNA_repr_REX1B  46 efseiSkevleieaaLreeasredlaelirkvqek 80 
                                       +f+e+S+e+  + +++r++ +r++   l+ k+ e+
  gi|488601615|ref|YP_007908086.1|  88 NFKELSEEITPLLTEFRKNVDRDETVILLTKLTEN 122
                                       7999**************99999999999888776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.94
                    DNA_repr_REX1B  35 eykqlvkevTeefseiSkevleieaaL 61 
                                       ++k+l +e+T ++++           L
  gi|488601615|ref|YP_007908086.1| 146 NFKELSEEITPKINR-----------L 161
                                       355555555555544...........3 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.2
                    DNA_repr_REX1B  60 aLreeasredlaelirkv 77 
                                       +L +  ++++l ++i+ v
  gi|488601615|ref|YP_007908086.1| 213 ELATIVKQPSLQKMIEGV 230
                                       444444455555555444 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0015       1.9      36     112 ..       5      84 ..       3      95 .. 0.80
   2 ?    5.4   0.3     0.014        17      27     117 ..      62     147 ..      58     167 .. 0.80
   3 ?    0.3   0.8      0.53   6.7e+02      29      69 ..     122     161 ..     112     244 .. 0.60
   4 ?    2.8   0.1     0.087   1.1e+02      65     121 ..     203     256 ..     174     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHH-SS-....HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHHHH CS
                      Spore_III_AB  36 alellegeirygatp....LpealeklaeksesplseffeevaerleekegesfeeaweeavekllkklaLkkedke 108
                                        l  l gei y+ +     ++e+l kl+ + ++++  ++ e++++++++e   + + + e+++  lk  +L ++ ++
  gi|488601615|ref|YP_007908086.1|   5 TLGSLDGEIVYTIEAtkdlIQELLPKLK-ELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLINLMEAGRD 80 
                                       5778999999988883344455555555.66668*************************************999999 PP

                                       HHHH CS
                      Spore_III_AB 109 ilke 112
                                        l e
  gi|488601615|ref|YP_007908086.1|  81 FLEE 84 
                                       8887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS--- CS
                      Spore_III_AB  27 lkeleelkralellegeirygatpLpealeklaeksesplseffeevaerleekegesfeeaweeavekllkklaLk 103
                                        +++  ++++++l+e+   +  + +p+ +++l+    +++  ++ e++++++++e   + + + e+++  lk  +L 
  gi|488601615|ref|YP_007908086.1|  62 TENIDTMLKLINLMEAGRDFLEEGIPN-FKELS----EEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLINLM 133
                                       466777888888888888888888888.88888....5566688888999998999999999********9999999 PP

                                       HHHHHHHHHHHHHH CS
                      Spore_III_AB 104 kedkeilkelgesl 117
                                       ++ ++ l e   ++
  gi|488601615|ref|YP_007908086.1| 134 EAGRDFLEEGIPNF 147
                                       99999988766555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHH CS
                      Spore_III_AB  29 eleelkralellegeirygatpLpealeklaeksesplsef 69 
                                       ++  ++++++l+e+   +  + +p+ +++l+e+++++++++
  gi|488601615|ref|YP_007908086.1| 122 NIDTMLKLINLMEAGRDFLEEGIPN-FKELSEEITPKINRL 161
                                       5556666666666666666666666.666666666655554 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.087
                                       THHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHHHHHHHHHHHHHT--S CS
                      Spore_III_AB  65 plseffeevaerleekegesfeeaweeavekllkklaLkkedkeilkelgeslgysd 121
                                       ++++ fe+++e     ++ s+++++e  ve      +L++e+++ ++++g      d
  gi|488601615|ref|YP_007908086.1| 203 SIEKTFEMLSELATIVKQPSLQKMIEGVVEGF---KKLDEEEIKKVSTFGILSAMRD 256
                                       67777888888766679999999999999998...8899999999999996555555 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 ?    6.7   0.1    0.0055         7      37      69 ..      19      51 ..      12      67 .. 0.87
   2 ?    0.8   0.0      0.36   4.6e+02      47      69 ..      87     109 ..      73     114 .. 0.81
   3 ?    1.0   0.1      0.31     4e+02      53      69 ..      93     109 ..      88     170 .. 0.58
   4 ?   -0.5   0.0      0.96   1.2e+03      91      98 ..     222     229 ..     201     273 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0055
                         ApoLp-III 37 qlkqvikslqeelkkksdeleealkevkkkiee 69
                                        k++i++l ++lk+ s+e++++l+e++k++ +
  gi|488601615|ref|YP_007908086.1| 19 ATKDLIQELLPKLKELSEEITPLLTEFRKNVDR 51
                                      56789999999******************9975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.36
                         ApoLp-III  47 eelkkksdeleealkevkkkiee 69 
                                       ++ k+ s+e++++l+e++k++ +
  gi|488601615|ref|YP_007908086.1|  87 PNFKELSEEITPLLTEFRKNVDR 109
                                       56788899999999999999865 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.31
                         ApoLp-III  53 sdeleealkevkkkiee 69 
                                       s+e++++l+e++k++ +
  gi|488601615|ref|YP_007908086.1|  93 SEEITPLLTEFRKNVDR 109
                                       55555555555555543 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.96
                         ApoLp-III  91 kvQsgvqs 98 
                                       ++Q+ ++ 
  gi|488601615|ref|YP_007908086.1| 222 SLQKMIEG 229
                                       22222222 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.7    0.0011       1.4      22      70 ..      20      71 ..       8      78 .. 0.79
   2 ?   -0.8   0.2       1.5     2e+03      53      68 ..     112     127 ..      80     136 .. 0.51
   3 ?   -1.7   0.1       2.8   3.6e+03       7      43 ..     126     161 ..     120     174 .. 0.48
   4 ?    5.0   0.1     0.023        30      23      47 ..     208     230 ..     186     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                               GAT 22 enellkeLyetckamqpriqklieet...adeedllaelLqlNDeLnnvler 70
                                       ++l++eL  ++k++++ i+ l++e     d+++++  l +l +++ ++l+ 
  gi|488601615|ref|YP_007908086.1| 20 TKDLIQELLPKLKELSEEITPLLTEFrknVDRDETVILLTKLTENIDTMLKL 71
                                      58***********************876666666888888888888777665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                               GAT  53 llaelLqlNDeLnnvl 68 
                                       ++  l +l +++ ++l
  gi|488601615|ref|YP_007908086.1| 112 TVILLTKLTENIDTML 127
                                       3444444444443333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.8
                               GAT   7 LsemLsstepdeellenellkeLyetckamqpriqkl 43 
                                       +  +++ +e+++++  +e +  + e  +++ p+i +l
  gi|488601615|ref|YP_007908086.1| 126 MLKLINLMEAGRDF-LEEGIPNFKELSEEITPKINRL 161
                                       44444444444222.2344444444444555555554 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.023
                               GAT  23 nellkeLyetckamqpriqklieet 47 
                                        e+l eL++ +k  qp++qk+ie +
  gi|488601615|ref|YP_007908086.1| 208 FEMLSELATIVK--QPSLQKMIEGV 230
                                       69999****999..********975 PP

>> Ran-binding  RanGTP-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.5    0.0049       6.3      80     137 ..      16      73 ..       8      77 .. 0.91
   2 ?    2.9   0.2     0.035        45      49     110 ..     112     169 ..      94     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0049
                       Ran-binding  80 sLesaveLtksLkkeieelgerleeaaekeekskkkeeekeelkkviedikeLLkrie 137
                                       ++e++ +L+++L  +++el+e+++ + ++ +k+ +++e+   l+k++e+i+++Lk i+
  gi|488601615|ref|YP_007908086.1|  16 TIEATKDLIQELLPKLKELSEEITPLLTEFRKNVDRDETVILLTKLTENIDTMLKLIN 73 
                                       57999***********************999888899999999999999999999887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.035
                       Ran-binding  49 leklqkkLeskikiispaidLieliaarGntsLesaveLtksLkkeieelgerleeaaekee 110
                                          l +kL + i+ +   + Li+l+ a G  +Le+ ++  k+L +ei+   +rl+++ ++ e
  gi|488601615|ref|YP_007908086.1| 112 TVILLTKLTENIDTM---LKLINLMEA-GRDFLEEGIPNFKELSEEITPKINRLRTLLDDDE 169
                                       333444444444433...345555443.6667777777777777777666666655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.66
# Mc/sec: 1277.94
//
Query:       gi|488601616|ref|YP_007908087.1|  [L=221]
Description: Nitrate reductase gamma subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-07   29.0   8.5    7.3e-06   25.7   1.8    2.3  2  Nitrate_red_gam  Nitrate reductase gamma subunit
  ------ inclusion threshold ------
       0.17   11.9   1.0       0.32   11.0   0.1    2.0  2  LRR19-TM         Leucine-rich repeat family 19 TM domain
       0.99    8.7   2.9        1.7    7.9   2.9    1.4  1  DUF4191          Domain of unknown function (DUF4191)


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 !    7.3   0.3   0.00052       3.1       3      24 ..       7      28 ..       5      39 .. 0.82
   2 !   25.7   1.8   1.2e-09   7.3e-06      88     203 ..     101     206 ..      92     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00052
                   Nitrate_red_gam  3 llfvvlPYvalavlvvgsllry 24
                                      ++ vv+PY+a++++v++ +++ 
  gi|488601616|ref|YP_007908087.1|  7 FVGVVMPYIAMSIFVIAAIYKV 28
                                      56689***********999865 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.2e-09
                   Nitrate_red_gam  88 lvaGliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsaldygseretispwlrsllt 164
                                        ++G++ +v +l+G +lL+l Rl+n+++++ ++a+ ++ lllL+++  l l++ +++   +     +i +++ s+lt
  gi|488601616|ref|YP_007908087.1| 101 YYLGVLGAVGVLIGSVLLFLTRLSNSEMKMISNATQYINLLLLMITSGLALYADFFN---F-----KIRDYFLSILT 169
                                       5789999999**************************999988888777777766664...3.....79********* PP

                   Nitrate_red_gam 165 lqpdaellaevplifklHvllglllfalfPFtrLvHvls 203
                                        +p+ ++  + +++  l ++  ++l   +P + +vH ++
  gi|488601616|ref|YP_007908087.1| 170 GSPNYQIFDKPEFFLALFFVEIFVL--YLPLSSMVHFFA 206
                                       ********99998888877766655..68*******986 PP

>> LRR19-TM  Leucine-rich repeat family 19 TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.4e-05      0.32      14      36 ..       3      25 ..       1      48 [. 0.85
   2 ?   -2.5   0.1      0.87   5.2e+03      17      44 ..     187     214 ..     186     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.4e-05
                          LRR19-TM 14 sWaylvgvvvlalvtsllillai 36
                                       W+y+vgvv+  + +s++++ ai
  gi|488601616|ref|YP_007908087.1|  3 GWEYFVGVVMPYIAMSIFVIAAI 25
                                      6***************9988877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.87
                          LRR19-TM  17 ylvgvvvlalvtsllillaikckllykf 44 
                                       ++v + vl l +s ++   +k  ++ k+
  gi|488601616|ref|YP_007908087.1| 187 FFVEIFVLYLPLSSMVHFFAKYYTWDKI 214
                                       7888889999999999999999998875 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.9   0.00029       1.7       7      83 ..      56     133 ..      50     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00029
                           DUF4191   7 rlkqiaqvfkltrkedkk.llwlllaaflvvvvvfvvlglllgslilllilgillgllvalivltrraekaayaqie 82 
                                       +l++i+  +++ + + k  +  lll   l ++ + +vl+++  ++++l +lg +  l+  ++++  r++++ ++ i 
  gi|488601616|ref|YP_007908087.1|  56 MLREIIVLYQVYNYNRKIwFQSLLLHYGLYALGLWLVLTVIGVNVYYLGVLGAVGVLIGSVLLFLTRLSNSEMKMIS 132
                                       56666666666554444325555666666666666666666556889999998888888888888888888888776 PP

                           DUF4191  83 g 83 
                                       +
  gi|488601616|ref|YP_007908087.1| 133 N 133
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1255.71
//
Query:       gi|488601617|ref|YP_007908088.1|  [L=464]
Description: Fe-S oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-17   62.2   0.6      4e-17   62.2   0.6    2.1  2  CCG       Cysteine-rich domain
    2.2e-10   40.9   1.7    2.2e-10   40.9   1.7    1.9  2  Fer4_8    4Fe-4S dicluster domain
    1.9e-07   31.5   3.3    1.9e-07   31.5   3.3    3.1  3  Fer4_17   4Fe-4S dicluster domain
      7e-07   29.7   5.1      7e-07   29.7   5.1    2.2  2  Fer4_7    4Fe-4S dicluster domain
    1.3e-06   28.0  12.2    0.00019   21.1   1.5    2.8  2  Fer4      4Fe-4S binding domain
    0.00039   20.4  13.9     0.0087   16.1   2.2    2.7  2  Fer4_6    4Fe-4S binding domain
    0.00049   20.2  14.7     0.0039   17.3  12.0    2.9  3  Fer4_10   4Fe-4S dicluster domain
     0.0013   18.9   8.4      0.095   12.9   0.2    2.7  2  Fer4_21   4Fe-4S dicluster domain
      0.002   18.3  13.4      0.025   14.7  11.8    2.8  4  Fer4_9    4Fe-4S dicluster domain
     0.0027   17.9   2.5       0.21   11.8   0.1    2.5  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   16.3  15.4      0.016   16.1  12.2    2.7  2  Fer4_16   4Fe-4S double cluster binding domain
       0.02   15.2   0.0        0.1   12.9   0.0    2.2  1  DED       Death effector domain
      0.048   13.8  17.5      0.086   13.0   2.3    3.2  3  Fer4_2    4Fe-4S binding domain
        2.7    8.7  16.4       0.75   10.5   1.7    2.9  2  Fer4_4    4Fe-4S binding domain
          7    7.6  11.1        9.6    7.1   0.0    3.4  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       9.7   1.2e+04      56      75 ..     274     293 ..     267     298 .. 0.64
   2 !   62.2   0.6   3.3e-20     4e-17       1      85 []     346     438 ..     346     438 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.7
                               CCG  56 alakrnvetaeetgadaivt 75 
                                       +++k ++e +++++++ +v+
  gi|488601617|ref|YP_007908088.1| 274 DIGKLHLEVVKKLKPKTVVV 293
                                       67777778888877666555 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 3.3e-20
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee......laealakrnvetaeet 68 
                                       v+y+d+C+l+r    y+e+r++lk++ ++++ e++++ e + CCG ggg++++++      ++e+++k ++++++et
  gi|488601617|ref|YP_007908088.1| 346 VTYHDPCKLGRLGglYEEPRRILKAV-CKDFREMQPNrEMSVCCGGGGGFAIMHKddfmtfRMETYGKIKANQIKET 421
                                       89*********999************.**************************87778777778************* PP

                               CCG  69 gadaivtacpgCllqlk 85 
                                       ga++++ ac++C++q++
  gi|488601617|ref|YP_007908088.1| 422 GAEVLALACSNCKGQFR 438
                                       **************986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   1.7   1.8e-13   2.2e-10       3      65 .]      56     142 ..      54     142 .. 0.77
   2 ?   -2.1   0.1       4.5   5.4e+03      46      55 ..     425     434 ..     385     435 .. 0.62

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.8e-13
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae........................dvqeeqvleeeealwsCttcg 55 
                                       + C++C  C +aCp++ +++k + + +  +++                        dv ee+ +  +e++++C+ c+
  gi|488601617|ref|YP_007908088.1|  56 DLCVKCNTCAEACPFYTASGKKPIYHPVYRSDmlrriykkyftlsgkifgglvgarDVTEEDINALAESAYRCSVCR 132
                                       67******************6666666666665888888888888888888666654444444444*********** PP

                            Fer4_8  56 aCtevCpvgi 65 
                                       +C+ vCp+g+
  gi|488601617|ref|YP_007908088.1| 133 RCAYVCPIGV 142
                                       *******986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.5
                            Fer4_8  46 ealwsCttcg 55 
                                         + +C++c+
  gi|488601617|ref|YP_007908088.1| 425 VLALACSNCK 434
                                       3455677665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   3.3   1.6e-10   1.9e-07       2      61 .]      58     143 ..      57     143 .. 0.75
   2 ?   -1.0   0.1       2.2   2.6e+03      22      48 ..     364     389 ..     351     392 .. 0.70
   3 ?    0.2   0.1      0.93   1.1e+03      24      50 ..     408     434 ..     396     435 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.6e-10
                           Fer4_17   2 CiqCgyClpeCpsyea.......ydnepkkllraakl.................glleeaeke...ekaslCieCge 51 
                                       C +C  C+++Cp+y a       ++ ++  +lr+++                    +ee + +   e a +C+ C++
  gi|488601617|ref|YP_007908088.1|  58 CVKCNTCAEACPFYTAsgkkpiyHPVYRSDMLRRIYKkyftlsgkifgglvgarDVTEEDI-NalaESAYRCSVCRR 133
                                       ****************555555444466677777765788999999998887632333333.25778********** PP

                           Fer4_17  52 CerkCPqgld 61 
                                       C+++CP g+d
  gi|488601617|ref|YP_007908088.1| 134 CAYVCPIGVD 143
                                       ******9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                           Fer4_17  22 pkkllraaklglleeaekeekaslCie 48 
                                       p+++l+a  +++++e++ ++++s C++
  gi|488601617|ref|YP_007908088.1| 364 PRRILKA-VCKDFREMQPNREMSVCCG 389
                                       4444444.4478899999999999986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.93
                           Fer4_17  24 kllraaklglleeaekeekaslCieCg 50 
                                       ++  ++k+++++e+ +e  a  C++C+
  gi|488601617|ref|YP_007908088.1| 408 ETYGKIKANQIKETGAEVLALACSNCK 434
                                       555667777777776777899999997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   5.1   5.9e-10     7e-07       2      52 .]      58     142 ..      57     142 .. 0.72
   2 ?   -2.8   0.0       8.6     1e+04      37      41 ..     429     433 ..     403     434 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.9e-10
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek.............................gtekv........eidpekClgC 41 
                                       C++C+ C++aCp ++ + ++  +++                                 v        + ++ +C+ C
  gi|488601617|ref|YP_007908088.1|  58 CVKCNTCAEACPFYTASGKKPIYHPvyrsdmlrriykkyftlsgkifgglvgarD---VteedinalAESAYRCSVC 131
                                       ************9999999877777666777766666666666666655554430...144444444667789**** PP

                            Fer4_7  42 gaCvavCPtga 52 
                                       ++C+ vCP g+
  gi|488601617|ref|YP_007908088.1| 132 RRCAYVCPIGV 142
                                       ********886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.6
                            Fer4_7  37 kClgC 41 
                                        C++C
  gi|488601617|ref|YP_007908088.1| 429 ACSNC 433
                                       45554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.5   1.6e-07   0.00019       6      20 ..      56      70 ..      53      72 .. 0.92
   2 !   11.0   3.4   0.00024      0.29       7      21 ..     127     141 ..     124     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                                      TTSSS-THHHHHSTT CS
                              Fer4  6 ekCigCGaCvevCPv 20
                                      ++C++C++C+e+CP+
  gi|488601617|ref|YP_007908088.1| 56 DLCVKCNTCAEACPF 70
                                      99************7 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                                       TSSS-THHHHHSTTT CS
                              Fer4   7 kCigCGaCvevCPvg 21 
                                       +C  C +C+ vCP g
  gi|488601617|ref|YP_007908088.1| 127 RCSVCRRCAYVCPIG 141
                                       8************88 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   2.2   7.3e-06    0.0087       7      21 ..      56      70 ..      54      73 .. 0.92
   2 !    8.8   4.2    0.0015       1.8       8      22 ..     127     141 ..     125     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.3e-06
                            Fer4_6  7 dkCigCgdCvrvCPe 21
                                      d+C+ C+ C+ +CP+
  gi|488601617|ref|YP_007908088.1| 56 DLCVKCNTCAEACPF 70
                                      89************7 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                            Fer4_6   8 kCigCgdCvrvCPeg 22 
                                       +C  C++C+ vCP g
  gi|488601617|ref|YP_007908088.1| 127 RCSVCRRCAYVCPIG 141
                                       7************65 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  12.0   3.2e-06    0.0039       6      56 .]      55     139 ..      51     139 .. 0.85
   2 !   10.8   1.9   0.00035      0.42       8      23 ..     127     142 ..     120     168 .. 0.75
   3 ?   -1.5   0.1       2.4   2.9e+03      36      48 ..     420     433 ..     384     436 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadl.................................tsvgakgeas.eeeavrkkvekCtgc 48 
                                        d C++C++C +aCP++                                    vga++ ++ +++a  +  ++C  c
  gi|488601617|ref|YP_007908088.1|  55 LDLCVKCNTCAEACPFYTasgkkpiyhpvyrsdmlrriykkyftlsgkifgGLVGARDVTEeDINALAESAYRCSVC 131
                                       689*************99*******************************99445544444404455555899***** PP

                           Fer4_10  49 gaCveaCP 56 
                                         C+ +CP
  gi|488601617|ref|YP_007908088.1| 132 RRCAYVCP 139
                                       *******9 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00035
                           Fer4_10   8 tCirCgkCvkaCPadl 23 
                                       +C  C++C  +CP  +
  gi|488601617|ref|YP_007908088.1| 127 RCSVCRRCAYVCPIGV 142
                                       7************933 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.4
                           Fer4_10  36 eavrk.kvekCtgc 48 
                                       e+  +    +C +c
  gi|488601617|ref|YP_007908088.1| 420 ETGAEvLALACSNC 433
                                       33333344555555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   7.9e-05     0.095      39      53 ..      56      70 ..      38      74 .. 0.81
   2 !   10.6   0.5    0.0004      0.48      38      53 ..     125     140 ..     110     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                           Fer4_21 39 deCvGCnlCssvCPv 53
                                      d Cv Cn C++ CP 
  gi|488601617|ref|YP_007908088.1| 56 DLCVKCNTCAEACPF 70
                                      678888888888884 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0004
                           Fer4_21  38 edeCvGCnlCssvCPv 53 
                                       + +C  C  C+ vCP+
  gi|488601617|ref|YP_007908088.1| 125 AYRCSVCRRCAYVCPI 140
                                       458************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 !   13.2   2.9   6.4e-05     0.077      33      47 ..      45      69 ..      20      73 .. 0.71
   2 !   14.7  11.8   2.1e-05     0.025       2      48 ..      58     140 ..      57     143 .. 0.93
   3 !    8.7   2.4    0.0016       1.9       1      18 [.     127     144 ..     127     154 .. 0.84
   4 ?   -2.1   0.0       3.9   4.7e+03      35      39 ..     429     433 ..     405     435 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                            Fer4_9 33 e..........eaCigCgaCveaCp 47
                                      +          + C++C++C+eaCp
  gi|488601617|ref|YP_007908088.1| 45 WtfwlplltslDLCVKCNTCAEACP 69
                                      2555666666678999999999998 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....................................eaCigCgaC 42 
                                       C++C++C eaCp+ ++++++  +   +r +                                       +C  C++C
  gi|488601617|ref|YP_007908088.1|  58 CVKCNTCAEACPFYTASGKKPIYHPVYRSDMLrriykkyftlsgkifgglvgardvteedinalaesaYRCSVCRRC 134
                                       ****************999999998887665599**********************************99******* PP

                            Fer4_9  43 veaCpk 48 
                                       + +Cp 
  gi|488601617|ref|YP_007908088.1| 135 AYVCPI 140
                                       ****96 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0016
                            Fer4_9   1 kCtgCgaCveaCpagvvv 18 
                                       +C  C++C ++Cp gv +
  gi|488601617|ref|YP_007908088.1| 127 RCSVCRRCAYVCPIGVDN 144
                                       5999********998865 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.9
                            Fer4_9  35 aCigC 39 
                                       aC  C
  gi|488601617|ref|YP_007908088.1| 429 ACSNC 433
                                       34444 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.6     0.021        25      61      73 ..      58      70 ..      51      76 .. 0.81
   2 !   11.8   0.1   0.00017      0.21      53      76 ..     120     143 ..      95     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
                           Fer4_18 61 cidcescvkvcPt 73
                                      c++c++c + cP 
  gi|488601617|ref|YP_007908088.1| 58 CVKCNTCAEACPF 70
                                      8888888888885 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
                           Fer4_18  53 rkekgagdcidcescvkvcPtgid 76 
                                         +++a  c  c+ c  vcP+g+d
  gi|488601617|ref|YP_007908088.1| 120 ALAESAYRCSVCRRCAYVCPIGVD 143
                                       44567779***************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1  12.2   1.4e-05     0.016       2      66 ..      58     140 ..      57     141 .. 0.65
   2 ?   -2.2   0.1         7   8.4e+03      46      61 ..     418     434 ..     398     435 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek...kekeieare..cisy.............ntaekkdlaedeekck..kqeaitgCd 58 
                                       C++C+ Cae+CP    ++k    ++++++++                      + +d++e+  +    +++++  C+
  gi|488601617|ref|YP_007908088.1|  58 CVKCNTCAEACPFYTASGKkpiYHPVYRSDMlrR--IykkyftlsgkifgGLVGARDVTEEDINALaeSAYRCSVCR 132
                                       ************9998877333233333333332..1446789999999944455555544444332346899**** PP

                           Fer4_16  59 iCqdvCPa 66 
                                       +C+ vCP+
  gi|488601617|ref|YP_007908088.1| 133 RCAYVCPI 140
                                       *******7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7
                           Fer4_16  46 ekckkqeai..tgCdiCq 61 
                                        k++ +e +    C +C+
  gi|488601617|ref|YP_007908088.1| 418 IKETGAE-VlaLACSNCK 434
                                       3333222.2246777775 PP

>> DED  Death effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.8e-05       0.1      18      53 ..     301     336 ..     299     342 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.8e-05
                                       HHHHHHCCGCSTTS--TT.S.HHHHHHHHHHCTSSS CS
                               DED  18 esLkfLlkdelpkrklekiksglelfleLekrglls 53 
                                       e++kfL kd  p++k  ++ s  elf eL + g+++
  gi|488601617|ref|YP_007908088.1| 301 EAMKFLYKDIFPEWKNVRVISIIELFDELIRTGKIK 336
                                       79*************9889***************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 ?   13.0   2.3   7.2e-05     0.086       8      21 ..      56      69 ..      50      70 .. 0.90
   2 ?    8.1   3.4    0.0026       3.2       9      21 ..     127     139 ..     120     139 .. 0.90
   3 ?   -0.5   0.1       1.4   1.7e+03       8      13 ..     428     433 ..     423     435 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                            Fer4_2  8 drCigCgaCvsaCP 21
                                      d C+ C++C  aCP
  gi|488601617|ref|YP_007908088.1| 56 DLCVKCNTCAEACP 69
                                      89************ PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0026
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                       rC  C+ C  +CP
  gi|488601617|ref|YP_007908088.1| 127 RCSVCRRCAYVCP 139
                                       8***********9 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.4
                            Fer4_2   8 drCigC 13 
                                        +C +C
  gi|488601617|ref|YP_007908088.1| 428 LACSNC 433
                                       578888 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.7   0.00063      0.75       2      16 ..      56      70 ..      55      75 .. 0.91
   2 ?    8.1   1.4    0.0035       4.2       3      15 ..     127     139 ..     125     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00063
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      + C+ C  C  aCP+
  gi|488601617|ref|YP_007908088.1| 56 DLCVKCNTCAEACPF 70
                                      78************6 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0035
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                       rC  C++C ++CP
  gi|488601617|ref|YP_007908088.1| 127 RCSVCRRCAYVCP 139
                                       8999********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 ?    7.1   0.0     0.008       9.6      79      93 ..      55      69 ..       8      74 .. 0.70
   2 ?    5.1   1.2     0.034        40       1      13 [.     127     139 ..     117     142 .. 0.69
   3 ?   -0.1   0.3       1.5   1.7e+03      60      86 ..     365     391 ..     360     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.008
                           Fer4_22 79 esgCvGCgRCieacp 93
                                         Cv C+ C eacp
  gi|488601617|ref|YP_007908088.1| 55 LDLCVKCNTCAEACP 69
                                      556777777777776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.034
                           Fer4_22   1 rClsCgaCtlvCp 13 
                                       rC  C +C++vCp
  gi|488601617|ref|YP_007908088.1| 127 RCSVCRRCAYVCP 139
                                       4666666666665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.5
                           Fer4_22  60 erlrqrllhklsefkekfgesgCvGCg 86 
                                       +r+ + +++ ++e++ + ++s+C+G g
  gi|488601617|ref|YP_007908088.1| 365 RRILKAVCKDFREMQPNREMSVCCGGG 391
                                       577788899999999999999999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 2613.29
//
Query:       gi|488601618|ref|YP_007908089.1|  [L=308]
Description: transposase, IS605 OrfB family, central region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   88.9   0.2    4.7e-25   88.1   0.2    1.3  1  OrfB_IS605      Probable transposase
    0.00012   21.9   0.0    0.00028   20.8   0.0    1.6  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 !   88.1   0.2   5.2e-29   4.7e-25      10     117 ..      97     201 ..      78     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 5.2e-29
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsr 86 
                                       +p ++++k++giD+G++ +++  +++    + ++ ++ +++k+ ++ ++ l++k+k+skn++k++ kla+ ++k+ +
  gi|488601618|ref|YP_007908089.1|  97 KPLAPTGKVVGIDVGVRYFLADTDGR---QVENPCFYEKTLKRIKRLQRDLSRKQKGSKNWEKCRIKLAKAYEKLVN 170
                                       78899*********************...************************************************ PP

                        OrfB_IS605  87 rrkhllhklathliktlkevgvetLnvgnmk 117
                                       +r+++lhkl++  +++++ ++ve+L ++nm+
  gi|488601618|ref|YP_007908089.1| 171 QRNDFLHKLSRFYVDNYDVIAVEDLRIQNMV 201
                                       ******************************8 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.1e-08   0.00028       1      29 [.     216     244 ..     216     245 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.1e-08
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSk 29 
                                       ++k+++ l+yka+++G+ v+ v+p  TS 
  gi|488601618|ref|YP_007908089.1| 216 WGKFIQLLSYKAERAGRRVVRVSPKGTSE 244
                                       99*************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.75
# Mc/sec: 1236.22
//
Query:       gi|488601619|ref|YP_007908090.1|  [L=75]
Description: hypothetical protein Asulf_02142 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-12   44.6   0.4    1.3e-11   43.8   0.4    1.4  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   14.9   0.2      0.013   14.9   0.2    1.0  1  Tam41_Mmp37     Phosphatidate cytidylyltransferase, mitochond


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 !   43.8   0.4   1.5e-15   1.3e-11       1      47 []       1      46 [.       1      46 [. 0.97

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.5e-15
                    HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                      M l +yk+r+yP ++ ++ l++ ++ +R+ YN+ L+e ++a +e++k
  gi|488601619|ref|YP_007908090.1|  1 M-LISYKFRIYPSKTVQNILEEQLELCRWLYNRLLEEVNKARKEGRK 46
                                      8.99***************************************9976 PP

>> Tam41_Mmp37  Phosphatidate cytidylyltransferase, mitochondrial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   1.5e-06     0.013     187     234 ..      13      64 ..       3      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-06
                       Tam41_Mmp37 187 nKvkniVekqleefrelYkplleelenvellekekekeee....kkleqdls 234
                                       + v+ni e+qle  r lY++llee+++ +    + +++++     kl+q+ +
  gi|488601619|ref|YP_007908090.1|  13 KTVQNILEEQLELCRWLYNRLLEEVNKARKEGRKIKRTDTqaliIKLKQEEK 64 
                                       569*********************9998776655544444344444445443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 421.54
//
Query:       gi|488601620|ref|YP_007908091.1|  [L=138]
Description: Transposase-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-40  137.7   1.7    2.2e-40  137.5   1.7    1.0  1  Y1_Tnp    Transposase IS200 like
  ------ inclusion threshold ------
      0.057   13.3   0.9        4.6    7.2   0.1    2.2  2  DUF559    Protein of unknown function (DUF559)


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 !  137.5   1.7   2.4e-44   2.2e-40       1     121 []      12     132 ..      12     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 2.4e-44
                            Y1_Tnp   1 vsnlkyhivlvtkyRrkvltge.veerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgass 76 
                                       v++l+yh+++v+kyRrkv+t++ + ++lk+ i+ei+e++ev++l++e++ DHvH+l++++p+l+i+k+++alk  +s
  gi|488601620|ref|YP_007908091.1|  12 VYSLHYHLIFVIKYRRKVFTNDeIIDFLKQKIHEISETFEVEVLAIECDVDHVHILFKAKPTLNIPKYINALKTITS 88 
                                       689*****************999****************************************************** PP

                            Y1_Tnp  77 rlinkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                       r i+++fpe+kkk l+++ +W+++Yf++t+g+++l+++krY+e+q
  gi|488601620|ref|YP_007908091.1|  89 REIRRNFPEVKKK-LWRNVFWSPSYFLATTGQVTLDVLKRYVESQ 132
                                       *********9977.677**************************98 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0029        26      28      56 ..      18      46 ..      10      53 .. 0.81
   2 ?    7.2   0.1   0.00051       4.6       5      25 ..      86     106 ..      82     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0029
                                      GTTTT--EEEEEEETTEEEEEEETTTTEE CS
                            DUF559 28 rrlsglkfrRqkpigsYivDfvclkakli 56
                                      + +  +k+rR++  ++ i+Df+ +k + i
  gi|488601620|ref|YP_007908091.1| 18 HLIFVIKYRRKVFTNDEIIDFLKQKIHEI 46
                                      566679***************98876655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00051
                                       XXXXXXXXXX-HHHHHHHHHH CS
                            DUF559   5 anarklRreqteaekkLWqll 25 
                                        ++r++Rr+ +e  kkLW+ +
  gi|488601620|ref|YP_007908091.1|  86 ITSREIRRNFPEVKKKLWRNV 106
                                       579***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 779.63
//
Query:       gi|488601621|ref|YP_007908092.1|  [L=65]
Description: hypothetical protein Asulf_02144 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 369.30
//
Query:       gi|488601622|ref|YP_007908093.1|  [L=84]
Description: hypothetical protein Asulf_02145 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 483.33
//
Query:       gi|488601623|ref|YP_007908094.1|  [L=311]
Description: ABC-type metal ion transport system, periplasmic component/surface adhesin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   80.5   0.0    1.5e-22   80.2   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 !   80.2   0.0   8.6e-27   1.5e-22       1     251 [.      25     280 ..      25     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 8.6e-27
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvev 77 
                                       +v+t +  +++v+++a d +ev++L+p+g dpH++++t++d+  l++Adl+v +  el ++  k+ ++ +++t  ++
  gi|488601623|ref|YP_007908094.1|  25 IVCTNPDFAQIVKEIAED-AEVESLMPSGSDPHTFSVTKEDMLLLESADLIVLTNSELLNFEVKIKEQYGDKTL-DF 99 
                                       899*************98.8********************************9998888777788888874333.44 PP

                                       EETTT.TCCSEBCSS..EST.GGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS CS
                                       xxxxx.xxxxxxxxx..xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  78 idlse.gveeeeeee..DpH.iWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeip 150
                                        d  e g +    ++  + H  Wl ++na a++++i+d+L  ++p+  dty+ n++a+++++  l++     ++  +
  gi|488601623|ref|YP_007908094.1| 100 EDYREyGAKLLYFDDykNLHgYWLYLDNALAIAKAIEDRLEILKPELRDTYRINLKAFEREILSLKEV-SG-IS--K 172
                                       4433343222222225599989****************************************999654.33.33..4 PP

                                       GTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS.....HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                              ZnuA 151 eekrklvtthdafgylarayglevagiagiste.....aaqiaalieeikeagvkaifveplaspklaetlae.... 218
                                       e++   v   + + y  ++ g++  +i  +++       ++ ++++ ++k+++ k+i+v  +++++ a ++a     
  gi|488601623|ref|YP_007908094.1| 173 ERDMRCVAVIPGVTYIMKNAGVDTGAI-LLEEGsgfvsGKEYSDIQSKLKSSEFKCIVVPASMKDSKAGEIALqlsr 248
                                       677789*****************9877.44444689999********************999988887777762222 PP

                                       HHT-EEEEE-STSSSTSTT.S.TTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxx RF
                              ZnuA 219 eagvkvatlysldslgdeg.s.aetYidmmranle 251
                                       ++g  v  +y  + ++ ++   a++  ++m+ n+e
  gi|488601623|ref|YP_007908094.1| 249 DTGKPV--VYV-KFVSGDSsFlAQHIYNLMQFNIE 280
                                       555333..222.22222221234455666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1912.44
//
Query:       gi|488601624|ref|YP_007908095.1|  [L=264]
Description: ABC-type Mn/Zn transport systems, ATPase component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-33  115.5   0.0    3.1e-33  115.2   0.0    1.1  1  ABC_tran     ABC transporter
    4.4e-12   46.4   1.8    2.5e-05   24.2   0.6    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.2e-05   25.0   1.3    3.1e-05   24.6   1.3    1.4  1  AAA_23       AAA domain
    0.00012   21.8   0.1    0.00025   20.7   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0003   20.9   0.0     0.0094   16.2   0.0    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
    0.00038   20.0   0.2     0.0082   15.6   0.2    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00094   16.8   0.1     0.0013   16.4   0.1    1.1  1  DUF3584      Protein of unknown function (DUF3584)
      0.003   17.3   0.1      0.008   15.9   0.1    1.7  2  AAA_15       AAA ATPase domain
     0.0045   16.7   0.0     0.0071   16.1   0.0    1.2  1  AAA_30       AAA domain
     0.0058   17.0   0.1     0.0079   16.6   0.1    1.4  1  AAA_16       AAA ATPase domain
     0.0065   16.4   0.1     0.0099   15.8   0.1    1.4  1  ATPase_2     ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.013   15.4   0.0       0.02   14.8   0.0    1.4  1  NACHT        NACHT domain
      0.019   14.0   0.1      0.027   13.5   0.1    1.2  1  T2SSE        Type II/IV secretion system protein
      0.019   14.9   0.8      0.032   14.1   0.2    1.7  1  NTPase_1     NTPase
       0.02   15.2   0.2      0.052   13.8   0.1    1.7  2  AAA_22       AAA domain
      0.027   14.7   0.4      0.053   13.8   0.4    1.5  1  AAA_28       AAA domain
      0.031   14.3   0.1      0.074   13.1   0.0    1.7  2  AAA_14       AAA domain
      0.034   14.6   0.1        1.8    9.0   0.0    2.4  2  AAA          ATPase family associated with various cellular a
      0.049   14.0   0.5       0.12   12.7   0.5    1.8  1  AAA_19       AAA domain
      0.062   12.9   0.1      0.099   12.2   0.1    1.3  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.078   11.8   0.1       0.11   11.4   0.1    1.1  1  DLIC         Dynein light intermediate chain (DLIC)
      0.079   12.7   0.0       0.13   12.0   0.0    1.4  1  PRK          Phosphoribulokinase / Uridine kinase family
      0.079   12.9   0.0       0.15   12.0   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.09   12.3   0.1       0.18   11.3   0.1    1.5  1  AAA_25       AAA domain
       0.11   11.7   0.1       0.18   10.9   0.1    1.3  1  PIF1         PIF1-like helicase
       0.11   12.6   2.6       0.75    9.8   2.6    2.0  1  DUF87        Helicase HerA, central domain
       0.11   11.7   0.0       0.17   11.2   0.0    1.2  1  Zeta_toxin   Zeta toxin
       0.13   12.8   0.1       0.21   12.1   0.1    1.5  1  AAA_18       AAA domain
       0.14   11.1   0.0       0.21   10.5   0.0    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.15   11.3   0.1       0.25   10.5   0.1    1.3  1  NB-ARC       NB-ARC domain
       0.17   10.5   0.1       0.25    9.9   0.1    1.2  1  AAA_13       AAA domain
       0.21   11.7   0.6       0.51   10.4   0.5    1.7  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 !  115.2   0.0   5.6e-36   3.1e-33       1     137 []      25     174 ..      25     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 5.6e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.. 75 
                                       l++v++++++ge vai+G nG+GK+tLl+l++g lkp +G+il+ g d+++  +e+++k ig +pq++++ ++    
  gi|488601624|ref|YP_007908095.1|  25 LSDVNFEIEKGEFVAITGANGSGKTTLLRLITGILKPIKGKILVFGVDTND--RERVQKYIGLMPQKEHISSNFPls 99 
                                       689*********************************************999..**************8888887522 PP

                                       HHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       v++                s+e+ie a ++l+l++  ++ ++++ ++LSgGq+qrv laral+ kp++lllDEp++
  gi|488601624|ref|YP_007908095.1| 100 VKDVvlmglsarkgverkLSREDIELAKENLRLVG-LESLWDRRFNELSGGQRQRVLLARALAVKPEILLLDEPFN 174
                                       5555*****99999888644444555555555555.444555555*****************************86 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 !   24.2   0.6   4.5e-08   2.5e-05       1      83 [.      37     103 ..      37     133 .. 0.59
   2 !   21.9   0.1   2.4e-07   0.00013     232     297 ..     141     203 ..     111     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.5e-08
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       + +++G+NgsGK++LL+++ ++            +       +ki  +   ++++++++  i  +  q+  ++ ++ 
  gi|488601624|ref|YP_007908095.1|  37 FVAITGANGSGKTTLLRLITGILKP---------I------KGKILVFGVDTNDRERVQKYIG-LMPQKEHISSNFP 97 
                                       679****************999632.........2......2333333333344455555555.5556666666666 PP

                            AAA_21  78 lersqv 83 
                                       l  ++v
  gi|488601624|ref|YP_007908095.1|  98 LSVKDV 103
                                       666666 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.4e-07
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       + ++elS G+++   l+ al+  +    +ll+DEp ng +   + r+++l+ el+r g   i++ H
  gi|488601624|ref|YP_007908095.1| 141 RRFNELSGGQRQRVLLARALAVKP---EILLLDEPFNGVDVPSQNRIIDLIYELTRDGLTAIMVVH 203
                                       568899999999966666666655...9***************************98888877666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   1.3   5.6e-08   3.1e-05      12      43 ..      27      59 ..      19     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.6e-08
                            AAA_23 12 dqeidFsk.gltlItGpNGaGKTTildAiklaL 43
                                      d++++ +k  +++ItG NG+GKTT+l+ i+ +L
  gi|488601624|ref|YP_007908095.1| 27 DVNFEIEKgEFVAITGANGSGKTTLLRLITGIL 59
                                      4555555526889****************9887 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 !   20.7   0.1   4.5e-07   0.00025      15      48 ..      28      61 ..      22      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.5e-07
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                        +ei+  +++ +tG++GsGK+Tll  i+ +L p
  gi|488601624|ref|YP_007908095.1| 28 VNFEIEKGEFVAITGANGSGKTTLLRLITGILKP 61
                                      678888555***************9666666655 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 !   16.2   0.0   1.7e-05    0.0094      23      88 ..     136     188 ..     111     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                           SbcCD_C  23 ekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       e+ ++r++++lSGG++q +    la al            ++++++LDE F+++D  s++++++l+
  gi|488601624|ref|YP_007908095.1| 136 ESLWDRRFNELSGGQRQRV---LLARAL----AV------KPEILLLDEPFNGVDVPSQNRIIDLI 188
                                       5567899999999999543...333222....23......5899*****************99986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.5e-05    0.0082      24     186 ..      35     191 ..      19     221 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEE..SSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkk..lkiekeev 97 
                                        +f ai+G+NGSGK+ ll  i    G      l+  k + l++    + ++  + ++ ++ ++e  +  ++ + ++v
  gi|488601624|ref|YP_007908095.1|  35 GEFVAITGANGSGKTTLLRLI---TG-----ILKPIKGKILVFGvDTNDRERVQKYIGLMPQKEHISsnFPLSVKDV 103
                                       4699************99888...33.....2444445555555322333333334444433332223355555555 PP

                                       EEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtk.kevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                       +++    rkg  e k+ +++++  ke  +l+  + +     ++LSgG+++ v la  +A++   p+ + llDe    
  gi|488601624|ref|YP_007908095.1| 104 VLMGLSARKGV-ERKLSREDIELaKENLRLVGLESLwdrRFNELSGGQRQRVLLARALAVK---PE-ILLLDEPFNG 175
                                       55544444444.4444444444422222222222221112346777776666666555543...33.4455666566 PP

                                       S-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkek 186
                                        D    +++ +l+ e 
  gi|488601624|ref|YP_007908095.1| 176 VDVPSQNRIIDLIYEL 191
                                       6666666666665555 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.2e-06    0.0013      13      37 ..      31      55 ..      27      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.2e-06
                           DUF3584 13 eldldghtnieGtNaaGKTtLlrLi 37
                                      e++  + + i G+N++GKTtLlrLi
  gi|488601624|ref|YP_007908095.1| 31 EIEKGEFVAITGANGSGKTTLLRLI 55
                                      556667799***************8 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   0.1   1.4e-05     0.008      16      50 ..      29      62 ..      25     132 .. 0.77
   2 ?   -1.3   0.0       2.4   1.3e+03     323     355 ..     163     195 ..     143     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                            AAA_15 16 dveidlseeltvliGkNnsGKSsilealdlFlnnk 50
                                      ++ei+  e +  + G+N+sGK+++l+++  +l+  
  gi|488601624|ref|YP_007908095.1| 29 NFEIEKGE-FVAITGANGSGKTTLLRLITGILKPI 62
                                      35666555.*******************9888765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandn 355
                                       k+ ill++EP +      q+ +i+l++el +d+
  gi|488601624|ref|YP_007908095.1| 163 KPEILLLDEPFNGVDVPSQNRIIDLIYELTRDG 195
                                       578899999999999999999999999998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-05    0.0071      19      66 ..      36      83 ..      29      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeel 66
                                       ++++tG+ G+GKtt+l+ ++ +++  +g+++++    +  +++++ +
  gi|488601624|ref|YP_007908095.1| 36 EFVAITGANGSGKTTLLRLITGILKPIKGKILVFGVDTNDRERVQKYI 83
                                      5899********************999889988877776666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.4e-05    0.0079      24      56 ..      35      62 ..      21     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-05
                            AAA_16 24 pelvllsGesGvGKsslvrellralekdggifl 56
                                      +e v ++G+ G+GK++l+r +   + k     +
  gi|488601624|ref|YP_007908095.1| 35 GEFVAITGANGSGKTTLLRLITG-ILKP----I 62
                                      3789**************99884.4444....3 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.8e-05    0.0099      17      91 ..      32     105 ..      25     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                          ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkael 91 
                                        e+ e++ i+G  gsGKt+Ll+ i   l+   k +i ++ + + + ++++++i+   +k+ ++  +   v+ + l
  gi|488601624|ref|YP_007908095.1|  32 IEKGEFVAITGANGSGKTTLLRLITGILKPI-KGKILVFGVDTNDRERVQKYIGLMPQKEHISSNFPLSVKDVVL 105
                                       5678999***************999988664.4678888888888888888888555555556555333333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.6e-05      0.02       3      22 ..      38      57 ..      36      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-05
                                      EEEEC-TTTCHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklal 22
                                      v+++G++GsGKTtLl+ +  
  gi|488601624|ref|YP_007908095.1| 38 VAITGANGSGKTTLLRLITG 57
                                      89*************98765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.9e-05     0.027     123     161 ..      29      67 ..       6      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-05
                             T2SSE 123 rkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                       +  +++   + ++G+ gsGKttll  +  +++  + +i+
  gi|488601624|ref|YP_007908095.1|  29 NFEIEKGEFVAITGANGSGKTTLLRLITGILKPIKGKIL 67 
                                       55566667788**************99999999888876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   5.8e-05     0.032       2      25 ..      38      61 ..      37      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-05
                                      EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellks 25
                                      v+iTG  G+GKtTl++ ++  lk 
  gi|488601624|ref|YP_007908095.1| 38 VAITGANGSGKTTLLRLITGILKP 61
                                      78***************9999974 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   9.2e-05     0.052       4      26 ..      34      56 ..      31      81 .. 0.89
   2 ?   -1.7   0.0       5.9   3.3e+03      86      99 ..     155     171 ..     114     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.2e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                      +  ++++tG  G+GKTtllr ++
  gi|488601624|ref|YP_007908095.1| 34 KGEFVAITGANGSGKTTLLRLIT 56
                                      56799**************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.9
                            AAA_22  86 lrarav...ielliiDE 99 
                                       l ara    +e+l++DE
  gi|488601624|ref|YP_007908095.1| 155 LLARALavkPEILLLDE 171
                                       33333345556666666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   9.4e-05     0.053       2      18 ..      38      54 ..      37      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.4e-05
                            AAA_28  2 ivitGgestGKTtllea 18
                                      ++itG+ ++GKTtll+ 
  gi|488601624|ref|YP_007908095.1| 38 VAITGANGSGKTTLLRL 54
                                      89************986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.074       3      46 ..      36      79 ..      34     101 .. 0.76
   2 ?   -2.2   0.0       7.1     4e+03      39      72 ..     136     171 ..     117     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkl 46
                                      + ++itGa  +GKTtll+ +   l   k +il + +d+++ ++ 
  gi|488601624|ref|YP_007908095.1| 36 EFVAITGANGSGKTTLLRLITGILKPIKGKILVFGVDTNDRERV 79
                                      6799************9877654444467788888877666554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.1
                            AAA_14  39 dderdkkladpe..kllelilek.lkeekktylflDE 72 
                                       ++  d+++++ +  +  +++l++ l + k ++l+lDE
  gi|488601624|ref|YP_007908095.1| 136 ESLWDRRFNELSggQRQRVLLARaL-AVKPEILLLDE 171
                                       4444444443333334455555523.23667888888 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 ?    9.0   0.0    0.0033       1.8       2      43 ..      39      87 ..      38     105 .. 0.74
   2 ?    3.3   0.0      0.18     1e+02      36      66 ..     140     171 ..     119     225 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0033
                                      EEESSTTSSHHHHHHHHHHHHT.......HEEEEEETTTCSSSSTTHHH CS
                               AAA  2 llyGppGtGKTllakavakelg.......vefleisgsellskyvgese 43
                                       ++G  G GKT+l + +   l+       v  + ++  e ++ky+g ++
  gi|488601624|ref|YP_007908095.1| 39 AITGANGSGKTTLLRLITGILKpikgkilVFGVDTNDRERVQKYIGLMP 87
                                      578**************99986544444333356666666677777655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.18
                                       SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  36 skyvgesekkirelfkeakeka.kpsilfiDE 66 
                                       +  + e +   r+ +  a++ a kp il++DE
  gi|488601624|ref|YP_007908095.1| 140 DRRFNELSGGQRQRVLLARALAvKPEILLLDE 171
                                       5556666666777777788888889*****99 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   0.00021      0.12       9      39 ..      34      64 ..      28     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelgg 39
                                      k + +++t+  G+GKT++l+ i  +l+ ++g
  gi|488601624|ref|YP_007908095.1| 34 KGEFVAITGANGSGKTTLLRLITGILKPIKG 64
                                      567899***************9999998884 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 ?   12.2   0.1   0.00018     0.099       3      21 ..      38      56 ..      36      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      + +tG  GsGKTtLl+ ++
  gi|488601624|ref|YP_007908095.1| 38 VAITGANGSGKTTLLRLIT 56
                                      679************9776 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00019      0.11      25      59 ..      35      69 ..      22      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                              DLIC 25 gksvlvlGedgsGkttliaklqGveeekkGrGley 59
                                      g  v + G +gsGkttl+  + G+ ++ kG+ l +
  gi|488601624|ref|YP_007908095.1| 35 GEFVAITGANGSGKTTLLRLITGILKPIKGKILVF 69
                                      6678999***********************97754 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   0.00023      0.13       2      24 ..      38      60 ..      37      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                               PRK  2 IgvagsSGaGkttvarklekifg 24
                                      ++++g+ G+Gktt+ r ++ i++
  gi|488601624|ref|YP_007908095.1| 38 VAITGANGSGKTTLLRLITGILK 60
                                      89*****************9998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00026      0.15      79     121 ..      14      57 ..       3      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                                       EEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  79 vllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        ++   +tk+ l++++ ++++ +++++ G  G GK+tL+  +++
  gi|488601624|ref|YP_007908095.1|  14 DVTFAYDTKTVLSDVNFEIEKgEFVAITGANGSGKTTLLRLITG 57 
                                       4556677889999999999998*****************99876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00033      0.18      30      50 ..      32      52 ..      28      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      + +ge+++++Ga g+GKttl+
  gi|488601624|ref|YP_007908095.1| 32 IEKGEFVAITGANGSGKTTLL 52
                                      579****************97 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00032      0.18      10      54 ..      25      67 ..      17      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                                      HHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEE CS
                              PIF1 10 fdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivl 54
                                      +  +      ekg+++ +tG  G+gKt l++ ++ +l++ + ++l
  gi|488601624|ref|YP_007908095.1| 25 LSDV--NFEIEKGEFVAITGANGSGKTTLLRLITGILKPIKGKIL 67
                                      4444..344589*************************99554444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.6    0.0013      0.75      26      60 ..      38      71 ..      26     220 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                             DUF87 26 lAilgsTGsGKSntvavLleellekkgatililDp 60
                                      +Ai g  GsGK+++ +++   l    +++il++ +
  gi|488601624|ref|YP_007908095.1| 38 VAITGANGSGKTTLLRLITGILK-PIKGKILVFGV 71
                                      79************998765555.9999****955 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.17      17      66 ..      36      87 ..      22     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                        Zeta_toxin 17 klillgGqpGAGKselaellkdele.rqgnvvrldpDdl.RelhPeyeeilk 66
                                        + + G+ G+GK++l++l++  l+  +g+++++  D+  Re+  +y +++ 
  gi|488601624|ref|YP_007908095.1| 36 EFVAITGANGSGKTTLLRLITGILKpIKGKILVFGVDTNdRERVQKYIGLMP 87
                                      568899**************99998778888888777533666666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00038      0.21       1      18 [.      38      55 ..      38     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00038
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      +++tG+ G+GKttl + +
  gi|488601624|ref|YP_007908095.1| 38 VAITGANGSGKTTLLRLI 55
                                      78************9987 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   0.00038      0.21      14      66 ..      20      72 ..       5      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                                      HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                      ++k++l+ +  +  + + v +tG  G+Gk tl+  ++  l+    ++ v  vD
  gi|488601624|ref|YP_007908095.1| 20 DTKTVLSDVNFEIEKGEFVAITGANGSGKTTLLRLITGILKPIKGKILVFGVD 72
                                      6788999999999999*****************99988888877788888887 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00044      0.25      21      41 ..      36      56 ..      21      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                                      EEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqil 41
                                       +va+ G  G+GKttl++ i 
  gi|488601624|ref|YP_007908095.1| 36 EFVAITGANGSGKTTLLRLIT 56
                                      499*************98775 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00045      0.25      21      39 ..      40      58 ..      34      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00045
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G+NG+GKTtL rl+  +
  gi|488601624|ref|YP_007908095.1| 40 ITGANGSGKTTLLRLITGI 58
                                      66*************9875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00091      0.51       2      28 ..      38      65 ..      37     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00091
                                      EEEEESTTSSHHHHHHHHHTS.TEEESS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsd 28
                                      vai G   +GK+tL++ +tg  k i ++
  gi|488601624|ref|YP_007908095.1| 38 VAITGANGSGKTTLLRLITGIlKPIKGK 65
                                      89*****************954444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 1519.15
//
Query:       gi|488601625|ref|YP_007908096.1|  [L=264]
Description: ABC-type Mn2+/Zn2+ transport systems, permease component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-53  181.8  34.5    2.1e-53  181.5  34.5    1.0  1  ABC-3     ABC 3 transport family
    2.6e-11   43.1  35.4    3.8e-11   42.6  35.4    1.3  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 !  181.5  34.5   2.3e-57   2.1e-53       3     257 ..       8     262 ..       7     263 .. 0.97

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 2.3e-57
                             ABC-3   3 eflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvn.lllgailvgliaavalellkrkt 78 
                                       +f++ral+a +++++++++ gsf+v+r +s+l ++ sH+al+G al +ll+   + l   + +++ a+a+++l+ ++
  gi|488601625|ref|YP_007908096.1|   8 PFVVRALIAILIIAINASIAGSFTVFRNVSFLIAGASHSALAGYALLILLSGYgIHLNPYFGSIAFALAIAYLAGRS 84 
                                       5899**********************************************9887888999999999********999 PP

                             ABC-3  79 klkedtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfde 155
                                       k +++taigi ++++++l+++++s++k+++++++ +L G++  ++++d++l++ ++++++++  + ++ +l+i+fd+
  gi|488601625|ref|YP_007908096.1|  85 K-ETNTAIGIAFAMSMSLAILFISMTKEYASKVWTILVGDLFLLTNQDIYLMILMTILIVIASAIYYRAFLFISFDP 160
                                       8.579************************************************************************ PP

                             ABC-3 156 elAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllS 232
                                       e A++ g++vkl++++ll +i+l+  + l+ vG+iLv+a+l++P+a A +++r++++++++++l++l s+++ l++S
  gi|488601625|ref|YP_007908096.1| 161 EGAEAFGINVKLYNYILLSMISLSTIILLKGVGAILVFAMLVAPSASANLIARNIREVFVCSFLIALTSMLFSLIIS 237
                                       ***************************************************************************** PP

                             ABC-3 233 yyldlatGavivlvatllfllallv 257
                                       ++++l+++a+  l+a++++++a++ 
  gi|488601625|ref|YP_007908096.1| 238 FFIELSPSALASLIASTAYFIASFR 262
                                       *********************9875 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6  35.4   4.2e-15   3.8e-11      74     307 ..      38     258 ..       5     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 4.2e-15
                             FecCD  74 PsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsl 150
                                         i G s+ a +g +l++ll     s +++ l   +g+++ +l +  la    g s+++   +Gia+++ +s l+ l
  gi|488601625|ref|YP_007908096.1|  38 FLIAGASHSALAGYALLILL-----SGYGIHLNPYFGSIAFALAIAYLA----GRSKETNTAIGIAFAMSMS-LAIL 104
                                       55677777777777776666.....678888888999999999999999....4444444457999976665.5555 PP

                             FecCD 151 lllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllll 227
                                       ++ + ++e ++++ ++l+G+l   + ++++l++++++l+++++++++r +  ++++ e A+++G+nv+ ++++ll +
  gi|488601625|ref|YP_007908096.1| 105 FISM-TKEYASKVWTILVGDLFLLTNQDIYLMILMTILIVIASAIYYRAFLFISFDPEGAEAFGINVKLYNYILLSM 180
                                       5555.799********************************************************************* PP

                             FecCD 228 valltavavalvGpi.gFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliG. 302
                                       ++l t +    vG i  F  L++P+    l+ ++ r + ++s+l++ + +l++ +++ ++    el+ +++ +li  
  gi|488601625|ref|YP_007908096.1| 181 ISLSTIILLKGVGAIlVFAMLVAPSASANLIARNIREVFVCSFLIALTSMLFSLIISFFI----ELSPSALASLIAs 253
                                       *************87479999*********************************999877....5555555555541 PP

                             FecCD 303 apffi 307
                                       + +fi
  gi|488601625|ref|YP_007908096.1| 254 TAYFI 258
                                       45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1229  (0.0685482); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1628.48
//
Query:       gi|488601626|ref|YP_007908097.1|  [L=479]
Description: phosphoribosylamine--glycine ligase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-72  241.8   0.0    7.7e-72  241.1   0.0    1.3  1  GARS_A         Phosphoribosylglycinamide synthetase, ATP-gras
    3.6e-26   91.8   0.1    6.6e-26   90.9   0.1    1.5  1  GARS_N         Phosphoribosylglycinamide synthetase, N domain
    5.1e-17   61.9   0.0    1.2e-16   60.8   0.0    1.6  1  GARS_C         Phosphoribosylglycinamide synthetase, C domain
     0.0012   18.5   0.0     0.0021   17.7   0.0    1.4  1  ATP-grasp      ATP-grasp domain
     0.0018   18.1   0.0     0.0055   16.5   0.0    1.8  1  DUF448         Protein of unknown function (DUF448)
  ------ inclusion threshold ------
      0.033   13.7   0.0      0.086   12.4   0.0    1.6  2  ATP-grasp_2    ATP-grasp domain
      0.081   12.2   0.0       0.16   11.2   0.0    1.4  1  ATPgrasp_ST    Sugar-transfer associated ATP-grasp
       0.11   12.5   0.0       0.27   11.3   0.0    1.8  1  ATP-grasp_3    ATP-grasp domain
       0.11   12.1   0.1         11    5.8   0.0    2.9  3  Baculo_LEF5_C  Baculoviridae late expression factor 5 C-termi


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 !  241.1   0.0   3.9e-75   7.7e-72       1     194 []     109     342 ..     109     342 .. 0.97

  Alignments for each domain:
  == domain 1  score: 241.1 bits;  conditional E-value: 3.9e-75
                                       HBHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSE....EEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS CS
                            GARS_A   1 asKsfakdllkkagiptaeyeaftdpeeakeyieeataka....lVvKadglaagKgvivakseeealkavkeilek 73 
                                       asK++akd+++k+g+p++ey +f+d+e+ake+++e+  ++    lVvKadglaagKgv+v++s++e lka++ei+ +
  gi|488601626|ref|YP_007908097.1| 109 ASKCWAKDFMRKIGVPIPEYWNFDDAESAKEFVKEFYRENpdknLVVKADGLAAGKGVYVCDSVDECLKAIDEIMIE 185
                                       79******************************9998766555669******************************** PP

                                       -TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCE............................ CS
                            GARS_A  74 kkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDk............................ 122
                                       kkfG+ag+k+ iEe+l G+Ev+++al+dgk+ + + +a+d+kr+++ D+                            
  gi|488601626|ref|YP_007908097.1| 186 KKFGSAGNKICIEERLYGIEVAFTALSDGKNAVCFGHAKDYKRAFDPDDleglrnfyigynkkfisldaakklfeeg 262
                                       ***************************************************************************** PP

                                       ...EEEECECEEEES-TTS-HHHHHHHHHHTHHHHHHHHHC.TT---EEEEEEEEEEETTE....EEEEEEESS--T CS
                            GARS_A 123 ...gpnTGGmGayspapvvteellekikeeileptveglkk.egipfkGvLyaglmlvedg....pkvlefnvRfgD 191
                                          +pnTGGmGa+sp+p++ eel+++i++e+++p++ ++++ eg +f+GvLy+++mlv++g    pkvle+nvR++D
  gi|488601626|ref|YP_007908097.1| 263 kllNPNTGGMGAVSPHPFLNEELESRIMDEVVNPIIRKFRElEGKEFRGVLYPVIMLVREGdefvPKVLEINVRDCD 339
                                       ***************************************986899**************999*************** PP

                                       TCH CS
                            GARS_A 192 pet 194
                                       p++
  gi|488601626|ref|YP_007908097.1| 340 PGA 342
                                       *86 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.1   3.3e-29   6.6e-26       1      90 []       1     108 [.       1     108 [. 0.93

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 3.3e-29
                                       EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG...................TTHHHHHHHHHHCTESEEEE- CS
                            GARS_N   1 mkvLvvGsGGRehalawklaqspkvekvyvapgNagt...................edlealvefakeekidlvvvG 58 
                                       m+vLvv  GGR +a+a+++++s++v++vyvapgN+g                      ++++vefak+ ++dlv+vG
  gi|488601626|ref|YP_007908097.1|   1 MRVLVVDAGGRGNAIAHAFSRSETVKEVYVAPGNGGSeffdkcriaelngkkipsiRAVDEIVEFAKKSEVDLVFVG 77 
                                       9************************************999999988888877776655668**************** PP

                                       SHHHHHTTHHHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  59 peapLvaGvadaleeekgikvfGpskeaAqlE 90 
                                       pe+pL  G++d+leee gi+++Gp+k+   lE
  gi|488601626|ref|YP_007908097.1|  78 PEEPLSLGLVDRLEEE-GINAVGPRKQETILE 108
                                       *************777.**********99988 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   5.9e-20   1.2e-16       9      79 ..     395     475 ..     393     476 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 5.9e-20
                                       TTTTSS--ST-EEBS......TTEEEEESSEE....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE--S CS
                            GARS_C   9 kGYPgsyekgkeitg......egvkvfhagtk....lvtsGGRvlavvavgetleeArakayeavkkikfeglfyRk 75 
                                        GYP++  ++++itg      e++ ++ +g +    + t+GGRvl+v++++++leeAr+k+y+a++ki+f+g+ yRk
  gi|488601626|ref|YP_007908097.1| 395 PGYPSDHYTNQPITGietamsEDTFIYANGISkangYQTTGGRVLTVSSLADSLEEARKKSYDALSKISFPGMRYRK 471
                                       59******************97788888997788899**************************************** PP

                                       TTTH CS
                            GARS_C  76 DIGa 79 
                                        IG 
  gi|488601626|ref|YP_007908097.1| 472 TIGM 475
                                       *995 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-06    0.0021       2      71 ..     119     200 ..     118     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                                       HTTT--B-EEEEECCHHHHHHHHHHH.....-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTC CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeel.....glpvvvKarrlgydGkGqsvvrseedleqaleal........keek 65 
                                       +k g+p+p+++  +++e+++e+++e+     +  +vvK + +   GkG +v+ s ++  +a++++        +++k
  gi|488601626|ref|YP_007908097.1| 119 RKIGVPIPEYWNFDDAESAKEFVKEFyrenpDKNLVVK-ADGLAAGKGVYVCDSVDECLKAIDEImiekkfgsAGNK 194
                                       6789**********************99999999****.566668************99999998788777776777 PP

                                       EEEEE- CS
                         ATP-grasp  66 vivEef 71 
                                       + +Ee+
  gi|488601626|ref|YP_007908097.1| 195 ICIEER 200
                                       777776 PP

>> DUF448  Protein of unknown function (DUF448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.8e-06    0.0055      21      62 ..     148     189 ..     134     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.8e-06
                            DUF448  21 tpegevvlDltgklpGRGaYvcpseeclekaikkkaleralk 62 
                                       +p++++v+  +g + G+G+Yvc s +   kai +  +e+++ 
  gi|488601626|ref|YP_007908097.1| 148 NPDKNLVVKADGLAAGKGVYVCDSVDECLKAIDEIMIEKKFG 189
                                       37788999999*************777778999989988887 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.8   5.6e+03      48      56 ..       6      14 ..       6      31 .. 0.61
   2 ?   12.4   0.0   4.3e-05     0.086       7      79 ..     114     186 ..     111     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                                      -SSSTCCCT CS
                       ATP-grasp_2 48 vlaGGRGKa 56
                                      v aGGRG a
  gi|488601626|ref|YP_007908097.1|  6 VDAGGRGNA 14
                                      568999887 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.3e-05
                                       HHHHHHCTT----SEEEESSHHHHHHHHHHHTS....SSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSE CS
                       ATP-grasp_2   7 akeilakygvkvpegevaesaeeaeeaakklge....kelvvKaQvlaGGRGKagGvklvkskeeakeaakellgke 79 
                                       ak+ ++k gv++pe    ++ae+a+e +k++ +    k+lvvKa  la G+    Gv +++s++e  +a++e++ ++
  gi|488601626|ref|YP_007908097.1| 114 AKDFMRKIGVPIPEYWNFDDAESAKEFVKEFYRenpdKNLVVKADGLAAGK----GVYVCDSVDECLKAIDEIMIEK 186
                                       899********************9999999965222267899998888765....79********999999986544 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     8e-05      0.16      20      96 ..     109     184 ..      93     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8e-05
                       ATPgrasp_ST  20 ddKlkfkelalraglkvpkllgvikeqaeisel.eafvkeleeg.vviKpakgsgGkGilviteredqdylkssgks 94 
                                       ++K   k+++ + g+++p+ +  ++  ++++e+ ++f +e ++  +v+K+    +GkG+ v+ +   ++ lk+ ++ 
  gi|488601626|ref|YP_007908097.1| 109 ASKCWAKDFMRKIGVPIPE-YWNFDDAESAKEFvKEFYRENPDKnLVVKADGLAAGKGVYVCDS--VDECLKAIDEI 182
                                       47889999***********.7777777666665267777775549*****************66..34444555555 PP

                       ATPgrasp_ST  95 al 96 
                                       + 
  gi|488601626|ref|YP_007908097.1| 183 MI 184
                                       55 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.27       4      95 ..     111     226 ..     109     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       HHHHHHHHTTT.S---..........-EESS--............SSSEEEEESS-------B--SS--TTE..... CS
                       ATP-grasp_3   4 KlktykkLkeagvkvP......tkleaeeleee............ekklvvKprdGaggesvrvveekeeaeaaiee 62 
                                       K    +++++ gv++P      +      +e++            +k+lvvK    a+g++v v +  +e  +ai+e
  gi|488601626|ref|YP_007908097.1| 111 KCWAKDFMRKIGVPIPeywnfdD------AESAkefvkefyrenpDKNLVVKADGLAAGKGVYVCDSVDECLKAIDE 181
                                       555566778889999*6654442......33333355568888999*******999****************99999 PP

                                       ..............EEEE---SEEEEEEEEE.SSSEEEEEEEEEE CS
                       ATP-grasp_3  63 ve............lvqefieGkplSvsllsdgekvlvlavnrql 95 
                                       +              + e + G ++  ++lsdg++++++   + +
  gi|488601626|ref|YP_007908097.1| 182 IMiekkfgsagnkiCIEERLYGIEVAFTALSDGKNAVCFGHAKDY 226
                                       999999*******999******************99998776655 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.044        87      25      34 ..      57      66 ..      55      69 .. 0.87
   2 ?    5.8   0.0    0.0055        11      15      33 ..     278     297 ..     275     302 .. 0.84
   3 ?   -3.9   0.0         6   1.2e+04      25      31 ..     321     327 ..     321     336 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.044
                     Baculo_LEF5_C 25 RagDEivsfv 34
                                      Ra DEiv f 
  gi|488601626|ref|YP_007908097.1| 57 RAVDEIVEFA 66
                                      9******996 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0055
                     Baculo_LEF5_C  15 HdfvtiEiQnRagDEivs.f 33 
                                       H f  +E   R +DE+v+ +
  gi|488601626|ref|YP_007908097.1| 278 HPFLNEELESRIMDEVVNpI 297
                                       77888999*********944 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 6
                     Baculo_LEF5_C  25 RagDEiv 31 
                                       R gDE v
  gi|488601626|ref|YP_007908097.1| 321 REGDEFV 327
                                       6688876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.58
# Mc/sec: 2491.09
//
Query:       gi|488601627|ref|YP_007908098.1|  [L=625]
Description: NADH:flavin oxidoreductase, Old Yellow Enzyme family [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-71  241.0   0.0    3.9e-71  240.1   0.0    1.5  1  Oxidored_FMN     NADH:flavin oxidoreductase / NADH oxidase fa
    2.4e-32  112.4   5.5    5.5e-32  111.2   5.4    1.7  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    2.3e-21   76.1   5.5      8e-15   55.2   0.9    2.9  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    8.3e-14   51.5   1.6    3.9e-09   36.2   0.2    2.5  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    1.9e-13   50.5   0.4    2.4e-05   24.5   0.0    2.8  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    2.1e-12   47.3  10.4    1.9e-05   24.4   1.4    3.6  3  DAO              FAD dependent oxidoreductase
    4.6e-10   38.8  12.0    3.4e-05   22.7   0.5    3.5  4  HI0933_like      HI0933-like protein
    9.4e-10   38.3   1.3    0.00071   18.9   0.1    2.3  2  FAD_binding_3    FAD binding domain
    1.8e-09   37.2   6.3    6.6e-05   22.2   0.3    2.4  2  FAD_binding_2    FAD binding domain
    4.1e-09   36.3   4.7    2.6e-05   23.8   0.0    3.1  3  FAD_oxidored     FAD dependent oxidoreductase
    1.5e-08   34.4   1.7    0.00012   21.7   0.4    3.1  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    4.6e-07   29.3   0.5     0.0011   18.3   0.0    2.3  2  Thi4             Thi4 family
    3.2e-06   26.9   6.0     0.0056   16.3   2.1    3.3  2  ApbA             Ketopantoate reductase PanE/ApbA
    3.5e-06   27.4   2.9      0.031   14.7   0.2    2.8  2  NAD_binding_7    Putative NAD(P)-binding
    1.1e-05   24.7  10.2     0.0001   21.5   0.3    3.1  3  GIDA             Glucose inhibited division protein A
    3.8e-05   22.9   2.6      0.029   13.4   0.0    2.9  3  Lycopene_cycl    Lycopene cyclase protein
    0.00015   21.2   4.1      0.096   12.0   0.2    2.6  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    0.00015   20.8   3.6      0.017   14.0   0.1    2.2  2  Trp_halogenase   Tryptophan halogenase
    0.00017   21.9   2.4       0.35   11.1   0.2    3.1  2  TrkA_N           TrkA-N domain
    0.00023   21.2   2.8        1.2    9.2   0.2    4.5  5  B12-binding      B12 binding domain
    0.00026   20.9   0.2       0.95    9.3   0.0    2.6  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00037   20.5   0.1        1.1    9.2   0.1    2.5  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0013   18.2   0.0          1    8.7   0.0    3.0  3  AP_endonuc_2     Xylose isomerase-like TIM barrel
     0.0022   18.0   5.6      0.045   13.7   0.0    3.5  3  NAD_binding_9    FAD-NAD(P)-binding
     0.0029   17.0   0.1         11    5.1   0.0    3.2  3  Amino_oxidase    Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
       0.02   14.0   0.0      0.059   12.4   0.0    1.7  1  Dus              Dihydrouridine synthase (Dus)
      0.023   14.6   0.0        3.7    7.4   0.0    2.5  2  MCR_D            Methyl-coenzyme M reductase operon protein D
       0.03   14.4   3.0        2.1    8.4   0.1    2.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.035   13.2   2.3        6.5    5.8   0.1    3.0  3  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
      0.052   12.9   6.1        2.1    7.7   0.1    2.7  3  ThiF             ThiF family
       0.17   12.1   0.8        3.1    8.1   0.3    2.6  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
        2.1    9.0   7.1         27    5.4   0.4    3.6  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


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 !  240.1   0.0     7e-74   3.9e-71       1     341 [.       2     328 ..       2     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: 240.1 bits;  conditional E-value: 7e-74
                                       CCCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-SCTTSEE-SSGG CS
                      Oxidored_FMN   1 kLFkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksggfdnapgiwdee 77 
                                       kL +P+++g m++knRivm+++     + +g v++  ++e+y++ra+ +v+ ++++ a ++p+   f +  +i+d+ 
  gi|488601627|ref|YP_007908098.1|   2 KLLEPVEVGGMEIKNRIVMPAVGSNFWTVDGAVTK-KLIEFYRERAMNGVGYVVVGVAKIEPQ---FFGGLAIHDDR 74 
                                       689*******************9999999996666.9*************************8...8889******* PP

                                       GHHHHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHH CS
                      Oxidored_FMN  78 qieewrklteavhengskvvvqlwhlGreakseyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqef 154
                                        i +++kl++  he++ k +vqlwh Gr+  s ++ ++   s+s   +++ ++++  +   +k+ltk+ei ++ +ef
  gi|488601627|ref|YP_007908098.1|  75 YIDGLKKLADVFHEYDVKCAVQLWHPGRYEISLSDSQPV--SAS---DIPPPIFTRRK---PKALTKDEILKIEDEF 143
                                       ****************************99655555555..777...88999883333...57************** PP

                                       HHHHHHHHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--S CS
                      Oxidored_FMN 155 veAAkraieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeervgyRlSpedvv 231
                                       +eAA ra++AgfD Ve   + GYL+ qFlsp +nkrtDeygGslenRarF++e+++ +ke+ g+  vg R+S ++ v
  gi|488601627|ref|YP_007908098.1| 144 AEAALRAKKAGFDAVELICSAGYLISQFLSPATNKRTDEYGGSLENRARFAVEIIERIKEKCGNFPVGCRISGDEFV 220
                                       ****************************************************************99*********** PP

                                       TTS--HHHH...HHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHHCCTTHHHHHHCCCHSSEEEE-SS--SHH CS
                      Oxidored_FMN 232 ekgldfaet...aqkivllkelekrlkdgkklalvhaaeprkrgagsvrteqekntefvkevwkkplitvgriadee 305
                                       e g++  ++   a+ ++ ++    ++ +g++++   +++      +  r      +e +k+ +++p+i+ +ri+ +e
  gi|488601627|ref|YP_007908098.1| 221 EGGNTLEDMkkiAKILESAGSAYFNVTAGWHESKRPLIT-----MFVPRGGFVYLAEGIKSAVDVPVIASNRINTPE 292
                                       **9999999443334444444445555566665554444.....3444444334568******************** PP

                                       HHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTCG CS
                      Oxidored_FMN 306 kaaeivaegeadLvamgRefladpdlveklkkglpl 341
                                        a++i++eg+ad+v+m R++ladp+l++k+ +g+ +
  gi|488601627|ref|YP_007908098.1| 293 LAEKILQEGKADMVSMMRALLADPELPRKVMEGRMD 328
                                       *********************************987 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 !  111.2   5.4   9.9e-35   5.5e-32       1     252 [.     373     599 ..     373     611 .. 0.84

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 9.9e-35
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvk 77 
                                       k++vv+GgGpAG++aa+ la++g++v+l+  e+  l+g+ + + +    +e+   + e        +e++l +  v+
  gi|488601627|ref|YP_007908098.1| 373 KRIVVVGGGPAGCKAAEMLAEKGHEVILF--EKKRLGGQLIFAAKSPYGREFSA-IPEY-------FERVLPKREVQ 439
                                       589**************************..77779999998666555555553.4444.......77778877888 PP

                                       EEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  78 idpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiG 154
                                       i +++++ +          ++  d++++A G++p +++ipGv en+      ++  e l  +++ +r+v++GgG +G
  gi|488601627|ref|YP_007908098.1| 440 IRYEEATAEK-------VLELNPDAVIVAVGAEPIIPQIPGV-ENA------ITAFEVLDGAEVGDRAVIIGGGGVG 502
                                       8777744443.......357999*******************.777......566888888888999********** PP

                                       HHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCE..EEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                       Pyr_redox_2 155 vElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgee..idad 229
                                       + +Aa+la+ gk+vt+ve ++++ +  + + +  +  +l+++Gv++ ++t+++ei++n+    vv+++ge+  +++d
  gi|488601627|ref|YP_007908098.1| 503 CSTAAMLAENGKDVTIVEMLPKIGNDIGISTRWNVLLYLREKGVKMLTNTKAVEIKKNSV---VVESQGERkeLECD 576
                                       ************************9999999999*************************9...5555555555**** PP

                                       EEEE-S-EEES-HHCSHCCT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 230 lvvvavGvrpstelleeklglel 252
                                       + ++avG +p + l++e   +e+
  gi|488601627|ref|YP_007908098.1| 577 TAIIAVGTKPADGLYDELKDVEV 599
                                       ***********999866556666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3     3e-07   0.00017       1      31 [.     374     404 ..     374     409 .. 0.94
   2 !   55.2   0.9   1.4e-17     8e-15       1      71 [.     492     562 ..     492     569 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3e-07
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvvers 31 
                                       ++vvvGgG  g+ +A++lae g++V ++e +
  gi|488601627|ref|YP_007908098.1| 374 RIVVVGGGPAGCKAAEMLAEKGHEVILFEKK 404
                                       79*************************9976 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 1.4e-17
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                       ++v++GgG +g+  A++lae gk+Vt+ve+ +k+ + ++  ++ ++  +l+++g+++l+ntk++ei++++ 
  gi|488601627|ref|YP_007908098.1| 492 RAVIIGGGGVGCSTAAMLAENGKDVTIVEMLPKIGNDIGISTRWNVLLYLREKGVKMLTNTKAVEIKKNSV 562
                                       68*********************************99999999999*********************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 !   14.0   0.1   3.9e-05     0.022       1      33 [.     376     407 ..     363     412 .. 0.88
   2 !   36.2   0.2     7e-12   3.9e-09     122     270 ..     452     587 ..     427     600 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnig 33 
                                       +++G+GPaG +aa  l ++g  +++  Ek+++g
  gi|488601627|ref|YP_007908098.1| 376 VVVGGGPAGCKAAEMLAEKGH-EVILFEKKRLG 407
                                       689999999999999999999.68899999887 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 7e-12
                       Pyr_redox_3 122 tyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                                       +++ + vi+A G    P  ++ipG e +++   +v + +++ g++ v+iGg+  ++ +A  l+++g++Vt+v    +
  gi|488601627|ref|YP_007908098.1| 452 ELNPDAVIVAVGA--EPIIPQIPGVE-NAITAFEVLDGAEV-GDRAVIIGGGGVGCSTAAMLAENGKDVTIVEMLPK 524
                                       566789******9..**********9.99999999999666.89999***************************998 PP

                       Pyr_redox_3 199 iekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpd 270
                                       i ++   +   ++ + +  l  +++e+ +k+l+n+++ eik++++ ++ + e+ k++e  d  ++a+G kp 
  gi|488601627|ref|YP_007908098.1| 525 IGND---I--GISTRWNVLL--YLREKGVKMLTNTKAVEIKKNSVVVESQGER-KELE-CDTAIIAVGTKPA 587
                                       8875...3..4444433333..344455*************986665555555.4555.5777999999885 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 !   24.5   0.0   4.3e-08   2.4e-05       1      35 [.     377     410 ..     377     430 .. 0.94
   2 !   23.3   0.1     1e-07   5.7e-05       1      33 [.     495     527 ..     495     547 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.3e-08
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35 
                                       +vG+G +G+ aA  La++g++v l+ek  rlGG++
  gi|488601627|ref|YP_007908098.1| 377 VVGGGPAGCKAAEMLAEKGHEVILFEKK-RLGGQL 410
                                       8**************************7.999985 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1e-07
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33 
                                       I+G+G  G+++A+ La++g+dv+++e+ +++G 
  gi|488601627|ref|YP_007908098.1| 495 IIGGGGVGCSTAAMLAENGKDVTIVEMLPKIGN 527
                                       9******************************94 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.5e-06   0.00087       1      35 [.     374     408 ..     374     415 .. 0.91
   2 !   24.4   1.4   3.4e-08   1.9e-05       2      33 ..     493     526 ..     492     536 .. 0.88
   3 !    8.4   0.1    0.0025       1.4     155     203 ..     540     585 ..     531     610 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                       ++v++GGG +G+ +A  La++g  V+l+ek+ ++g g
  gi|488601627|ref|YP_007908098.1| 374 RIVVVGGGPAGCKAAEMLAEKGheVILFEKK-RLG-G 408
                                       59*******************99*******9.666.5 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 3.4e-08
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                        viiGGG +G+stA  La+ g  Vt++e+ + +g
  gi|488601627|ref|YP_007908098.1| 493 AVIIGGGGVGCSTAAMLAENGkdVTIVEMLPKIG 526
                                       69******************99******866555 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0025
                                       HHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.E.EEEEEEE--GGG CS
                               DAO 155 aaealGveilegtevtgleeedgkvwgverttpgen.d.aadavVnaaGaw 203
                                        ++++Gv++l++t++++++++    + v  +++ge+ + ++d+ ++a G  
  gi|488601627|ref|YP_007908098.1| 540 YLREKGVKMLTNTKAVEIKKN---SVVV--ESQGERkElECDTAIIAVGTK 585
                                       4799**************653...3444..4445553356799*****965 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       7.3   4.1e+03      29      51 ..     226     248 ..     225     264 .. 0.84
   2 !   22.7   0.5     6e-08   3.4e-05       2      35 ..     374     407 ..     373     414 .. 0.88
   3 !   14.0   1.4   2.6e-05     0.015       3      42 ..     493     532 ..     491     537 .. 0.94
   4 !    7.7   0.3    0.0022       1.3     119     165 ..     541     585 ..     536     590 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.3
                                       E-SSSSS-HHHHHCGGGT-EEEE CS
                       HI0933_like  29 lekakklgrKilisGgGrcNvTn 51 
                                       le +kk+++ +  +G    NvT 
  gi|488601627|ref|YP_007908098.1| 226 LEDMKKIAKILESAGSAYFNVTA 248
                                       68999999999999999999996 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 6e-08
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       +++v+GgG+AG  aA+ +a++g++V+l+ek++  
  gi|488601627|ref|YP_007908098.1| 374 RIVVVGGGPAGCKAAEMLAEKGHEVILFEKKRLG 407
                                       69****************************9644 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 2.6e-05
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakklgrKilis 42 
                                        ++iGgG  G  +A+ +a++gk+V+++e  +k+g+ i is
  gi|488601627|ref|YP_007908098.1| 493 AVIIGGGGVGCSTAAMLAENGKDVTIVEMLPKIGNDIGIS 532
                                       79*********************************99988 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0022
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE----S CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGGl 165
                                       l+e+gvk+ ++t+  +++k  ++ + v+   +++ele+d+ ++A+G +
  gi|488601627|ref|YP_007908098.1| 541 LREKGVKMLTNTKAVEIKK--NS-VVVESqGERKELECDTAIIAVGTK 585
                                       7899*********999955..33.4455534899************86 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.3e-06   0.00071       4      33 ..     375     404 ..     372     408 .. 0.93
   2 !   18.1   0.1   2.2e-06    0.0012       5      33 ..     494     522 ..     492     577 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       +++VG+GpaG  +a +L+e+G +v+l ek 
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEKGHEVILFEKK 404
                                       78*************************997 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.2e-06
                                       EEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                       +I+G+G +G ++a +L+e G +v++ve  
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENGKDVTIVEML 522
                                       7*************************965 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   1.2e-07   6.6e-05       2      41 ..     375     413 ..     374     415 .. 0.90
   2 !   17.4   1.0   3.2e-06    0.0018       2      35 ..     493     526 ..     492     535 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG- CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggataws 41 
                                       ++V+G+G AG+ AA  +ae+G++v++ ek+   gg++ ++
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEKGHEVILFEKKRL-GGQLIFA 413
                                       79***************************985.7777665 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.2e-06
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                       +++iG+G+ G++ A+ +ae+G++v++ve  ++ g
  gi|488601627|ref|YP_007908098.1| 493 AVIIGGGGVGCSTAAMLAENGKDVTIVEMLPKIG 526
                                       69**************************988766 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   4.6e-08   2.6e-05       2      42 ..     375     414 ..     374     447 .. 0.90
   2 !    9.4   1.0     0.001      0.59       3      35 ..     494     526 ..     493     534 .. 0.91
   3 ?    3.0   0.1     0.094        52      97     140 ..     541     579 ..     530     583 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.6e-08
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42 
                                       +vVvGGgpaG+ AA   a++G +v+L e++ +lGG+l  ++
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEKGHEVILFEKK-RLGGQLIFAA 414
                                       8**************************985.79**987665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.001
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergvlG 35 
                                       v++GGg  G+  A   a++G+ v +ve  + +G
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENGKDVTIVEMLPKIG 526
                                       7999999999999999***********998887 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.094
                      FAD_oxidored  97 laeagvtvllntrlvevekegkriesvtveskegrktirAkvfi 140
                                       l+e+gv++l+nt++ve++k+     sv+ves+ +rk+++++  i
  gi|488601627|ref|YP_007908098.1| 541 LREKGVKMLTNTKAVEIKKN-----SVVVESQGERKELECDTAI 579
                                       599***************98.....7999766579988887665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.6   8.7e+02     152     172 ..     216     236 ..     193     240 .. 0.82
   2 !    9.8   0.0   0.00094      0.52       2      29 ..     374     401 ..     373     405 .. 0.92
   3 !   21.7   0.4   2.2e-07   0.00012       3      90 ..     493     588 ..     491     602 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                                       ------TTSHHHHHHS-S-EE CS
                    UDPG_MGDP_dh_N 152 nPEflregsavkdllnpdrvv 172
                                         Ef++ g++++d+ +  +++
  gi|488601627|ref|YP_007908098.1| 216 GDEFVEGGNTLEDMKKIAKIL 236
                                       569***********9999986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00094
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigv 29 
                                       +i+v+G G  G   a +lae+ghevi+ 
  gi|488601627|ref|YP_007908098.1| 374 RIVVVGGGPAGCKAAEMLAEKGHEVILF 401
                                       8************************975 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2.2e-07
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S.....-HHHHHHHCTTS-SS--TTHHHHHHHHC...HTTTEEEES-HH CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDi.....deekvdklnsgkipiyepgLeelvkkav...esgrlsfttdve 71 
                                        ++iG G vG  taa+lae g++v++v +     ++  +++  +  +++ e+g ++l ++++   +++ +  +++ e
  gi|488601627|ref|YP_007908098.1| 493 AVIIGGGGVGCSTAAMLAENGKDVTIVEMlpkigNDIGISTRWNVLLYLREKGVKMLTNTKAveiKKNSVVVESQGE 569
                                       579*************************8555556667887778889999*****9987653111344556778888 PP

                                       HHHHC-SEEEE-----B-T CS
                    UDPG_MGDP_dh_N  72 kaveeadvifiaVgTPskk 90 
                                       ++  e+d  +iaVgT   +
  gi|488601627|ref|YP_007908098.1| 570 RKELECDTAIIAVGTKPAD 588
                                       9999***********5444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.9e-06    0.0011       8      54 ..     363     407 ..     359     457 .. 0.79
   2 !    8.6   0.4    0.0018      0.99      20      79 ..     493     551 ..     477     571 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-06
                                       HHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4   8 yfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspG 54 
                                        f++l   ++  +v+vG+G++G  aa +la+k + +v+++e++  +G
  gi|488601627|ref|YP_007908098.1| 363 EFRNLKADVKKRIVVVGGGPAGCKAAEMLAEK-GHEVILFEKKR-LG 407
                                       677788888999********************.********974.34 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0018
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHH CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLde 79 
                                        vi+G+G  G ++a +la++ +  v+i+e    +G  ++   +    + +r+++ ++L +
  gi|488601627|ref|YP_007908098.1| 493 AVIIGGGGVGCSTAAMLAEN-GKDVTIVEMLPKIGNDIGISTRWNVLLYLREKGVKMLTN 551
                                       589999**************.999999998877777766666655555666666666655 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0032       1.8       1      30 [.     375     404 ..     375     410 .. 0.92
   2 !   16.3   2.1     1e-05    0.0056       2      82 ..     494     588 ..     493     597 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0032
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SC CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrs 30 
                                       i+++G G  G+  a +La++g++v+l  ++
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEKGHEVILFEKK 404
                                       89***********************98766 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1e-05
                                       EEES-SHHHHHHHHHHHHHTHC.............EEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCH.SCC CS
                              ApbA   2 ailGaGaiGsllaakLakagad.............vtlilrsrrlealkknGlrltseggeeilrppealsae.eks 64 
                                       +i+G G++G+  aa+La++g d             + + +r++ l  l+++G+++ ++++ + ++++ ++ ++  ++
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENGKDvtivemlpkigndIGISTRWNVLLYLREKGVKMLTNTKAVEIKKNSVVVESqGER 570
                                       69********************6776666666666667778886666888888888888444444444444443556 PP

                                       CCS-ESEEEE-SSGGGHH CS
                              ApbA  65 elepidlvivtvKayqte 82 
                                       +  ++d  i++v + +++
  gi|488601627|ref|YP_007908098.1| 571 KELECDTAIIAVGTKPAD 588
                                       667788888887666655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00037      0.21       7      40 ..     372     405 ..     369     466 .. 0.77
   2 !   14.7   0.2   5.6e-05     0.031       8      37 ..     491     520 ..     489     585 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00037
                     NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                       +k+++vvGgG+ + + ++ l+e+g +v++  ++ 
  gi|488601627|ref|YP_007908098.1| 372 KKRIVVVGGGPAGCKAAEMLAEKGHEVILFEKKR 405
                                       589*************************998883 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.6e-05
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvva 37 
                                        + +++GgG v+ + +  l+e+g++vt+v 
  gi|488601627|ref|YP_007908098.1| 491 DRAVIIGGGGVGCSTAAMLAENGKDVTIVE 520
                                       6899************************85 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.3   1.8e-07    0.0001       2      31 ..     375     404 ..     374     415 .. 0.90
   2 !    7.6   1.4    0.0032       1.8       3      28 ..     494     519 ..     492     537 .. 0.86
   3 ?   -0.5   0.1      0.91   5.1e+02     115     150 ..     543     584 ..     529     604 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithk 31 
                                       ++V+GgG AGc AA  +a++G++v+L+ +k
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEKGHEVILFEKK 404
                                       89************************9554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0032
                                       EEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLi 28 
                                       ++iGgG  Gc  A+ +a+ G +v+++
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENGKDVTIV 519
                                       89*********************998 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.91
                                       ES-EEEEEECT....TEEEEEEETTS..-EEEECEEEE--TT CS
                              GIDA 115 eeeveelivee....kkvkgvvtedg..etikakavviatGt 150
                                       e+ v+ l  ++    kk ++vv ++g  +++++++ +ia Gt
  gi|488601627|ref|YP_007908098.1| 543 EKGVKMLTNTKaveiKKNSVVVESQGerKELECDTAIIAVGT 584
                                       5555555433355444455555555511678899*******9 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   5.2e-05     0.029       2      32 ..     375     403 ..     374     450 .. 0.82
   2 !    7.9   0.6    0.0025       1.4       3      36 ..     494     525 ..     493     536 .. 0.86
   3 ?   -1.0   0.0       1.3   7.2e+02      99     141 ..     543     584 ..     533     595 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvliea 32 
                                       +vv+G+GpAg++ A+ l  a++g +v+l e 
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEML--AEKGHEVILFEK 403
                                       79***************..999999999885 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       v+iG+G  g+s Aa l  a+ g  v+++e  p++
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAML--AENGKDVTIVEMLPKI 525
                                       8***************..8888888888877665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.3
                     Lycopene_cycl  99 engvkl.leakvesveeeeageslvvleggr.kirarlvvdargl 141
                                       e+gvk+ ++ k+ +++++++   +v  +g+r ++++ +++ a g 
  gi|488601627|ref|YP_007908098.1| 543 EKGVKMlTNTKAVEIKKNSV---VVESQGERkELECDTAIIAVGT 584
                                       55665414566666666666...7778888789******999993 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 !   12.0   0.2   0.00017     0.096      29      60 ..     373     404 ..     366     462 .. 0.91
   2 !    9.8   0.6    0.0008      0.45      30      61 ..     492     523 ..     473     565 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvr 60 
                                        +++v+GgG aG +A+++ ++ g +V +++++
  gi|488601627|ref|YP_007908098.1| 373 KRIVVVGGGPAGCKAAEMLAEKGHEVILFEKK 404
                                       589***********************999875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0008
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61 
                                       + ++iGgG +G + +a+ ++ g +Vt++++ p
  gi|488601627|ref|YP_007908098.1| 492 RAVIIGGGGVGCSTAAMLAENGKDVTIVEMLP 523
                                       679************************99866 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1     3e-05     0.017       1      37 [.     374     407 ..     374     416 .. 0.93
   2 !    7.4   0.7     0.003       1.7       3      33 ..     494     521 ..     492     533 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37 
                                       +iv+vGGG+aG  aA +la+ +   +ev l e++ +g
  gi|488601627|ref|YP_007908098.1| 374 RIVVVGGGPAGCKAAEMLAEKG---HEVILFEKKRLG 407
                                       69******************99...89***9999876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.003
                                       EEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlves 33 
                                       vi+GGG  G  +Aa+la+ +    +vt+ve 
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENG---KDVTIVEM 521
                                       9*****************99...56888885 PP

>> TrkA_N  TrkA-N domain
   #    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       1      30 [.     375     404 ..     375     406 .. 0.89
   2 !   11.1   0.2   0.00063      0.35       2      31 ..     494     523 ..     493     529 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30 
                                       i+++G G  G + ae L e g+ +v++ +k+
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEkGH-EVILFEKK 404
                                       89*****************556.6**99985 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00063
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkde 31 
                                       +iiG G vG s a  L e+gkdv++++  +
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENGKDVTIVEMLP 523
                                       8*****************8889****9755 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.9   1.1e+03      61      97 ..      28      64 ..      19      76 .. 0.73
   2 ?   -1.0   0.0         3   1.7e+03      64     102 ..     225     263 ..     222     281 .. 0.79
   3 ?    0.1   0.0       1.4   7.9e+02      14      57 ..     264     308 ..     257     315 .. 0.75
   4 ?    6.8   0.0     0.012       6.5      58     109 ..     351     399 ..     349     407 .. 0.69
   5 !    9.2   0.2    0.0021       1.2      41     108 ..     444     517 ..     425     521 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.9
                       B12-binding 61 ltsqleavkelvel.lkrirprvkvvvGGahpsldpee 97
                                      +t   + +k+l+e+ ++r+ ++v  vv G+ + + p++
  gi|488601627|ref|YP_007908098.1| 28 WTVDGAVTKKLIEFyRERAMNGVGYVVVGV-AKIEPQF 64
                                      566666778899998888888999999886.4777766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                       B12-binding  64 qleavkelvellkrirprvkvvvGGahpsldpeetleak 102
                                       +le++k++++ l+++++    v+ G h s  p  t+   
  gi|488601627|ref|YP_007908098.1| 225 TLEDMKKIAKILESAGSAYFNVTAGWHESKRPLITMFVP 263
                                       7899*******9999999999999999888888777654 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.4
                       B12-binding  14 plGlavlaaalrdagfeVqllganven.edivaairae.kpdvvgl 57 
                                         G+ +la+ ++ a ++V ++  n  n ++++++i +e k+d+v +
  gi|488601627|ref|YP_007908098.1| 264 RGGFVYLAEGIKSA-VDVPVIASNRINtPELAEKILQEgKADMVSM 308
                                       55777888888884.777766555544699999998888****976 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.012
                       B12-binding  58 SalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvv 109
                                       ++l++  +   ke  +l++ +++r+ vv GG+ +   ++e+l++  g   v+
  gi|488601627|ref|YP_007908098.1| 351 TCLVNPAVGREKEFRNLKADVKKRIVVVGGGP-AGCKAAEMLAE-KG-HEVI 399
                                       67788888888999999999999976666665.56666666766.55.4444 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0021
                       B12-binding  41 edivaairaekpdvvglSal...ltsqleavkelvel.....lkrirprvkvvvGGahpsldpeetleaklgiddv 108
                                       e++++++ +++pd+v + +    +  q+++v++ + +      +++++r+ ++ GG ++    + +l++ +g d+ 
  gi|488601627|ref|YP_007908098.1| 444 EATAEKVLELNPDAVIVAVGaepIIPQIPGVENAITAfevldGAEVGDRAVIIGGG-GVGCSTAAMLAE-NGKDVT 517
                                       88999*********99977788899********99999**9877788886666555.555655555666.773443 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 !    9.3   0.0    0.0017      0.95       2      31 ..     375     404 ..     374     450 .. 0.93
   2 !    9.1   0.1     0.002       1.1       3      33 ..     494     524 ..     492     577 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdis 31 
                                       + v+G G  G + a+++a++g+eV l++ +
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEKGHEVILFEKK 404
                                       78***********************99875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.002
                                       EEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdisee 33 
                                        +iG G +G + aa++a++g +V++v++ ++
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENGKDVTIVEMLPK 524
                                       69************************98665 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0024       1.3       2      32 ..     375     405 ..     374     474 .. 0.80
   2 !    9.2   0.1     0.002       1.1       3      38 ..     494     529 ..     492     564 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-H CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree 32 
                                       i v+G+G  G   A +lae+ghev l+ +++
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEKGHEVILFEKKR 405
                                       89************************98876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                                       EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHH CS
                    NAD_Gly3P_dh_N   3 avlGaGswGtalAkvlaenghevrlwvreeelieei 38 
                                        ++G+G  G + A++laeng++v++  + ++  ++i
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENGKDVTIVEMLPKIGNDI 529
                                       59**********************999888777766 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0019         1     103     135 ..      69     101 ..      18     110 .. 0.83
   2 ?    5.9   0.0     0.014       7.8       3      92 ..     149     249 ..     148     280 .. 0.69
   3 ?   -2.0   0.0       3.5     2e+03      81     120 ..     572     622 ..     571     624 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTT CS
                      AP_endonuc_2 103 eeawerlaeslneladyaekegvklalEtlags 135
                                       +   +r++++l++lad++++++vk a++ +++ 
  gi|488601627|ref|YP_007908098.1|  69 AIHDDRYIDGLKKLADVFHEYDVKCAVQLWHPG 101
                                       55679**********************998875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                                       HHHHCT-SEEEEECCTCSHHHHC...............HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC..HTT CS
                      AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvsel...............sdeelrelrkaldelglriaslslftrfgypded..ere 62 
                                       +a++aGfd+vEl ++ ++ +s+                 + ++r   +++++   +  + +++ +   ++++  e+ 
  gi|488601627|ref|YP_007908098.1| 149 RAKKAGFDAVELICSAGYLISQFlspatnkrtdeyggsLENRARFAVEIIERIKEK--CGNFPVGCRISGDEfvEGG 223
                                       589***************99977777766666666666555555555555555555..4444444444333333444 PP

                                       CSHHHHHHHHHHHHHHHHHHTBSEEEEEBC CS
                      AP_endonuc_2  63 arreesvdalkraielaaaLGapllvlhpG 92 
                                             ++++k+ +++ +  G  + ++ +G
  gi|488601627|ref|YP_007908098.1| 224 NT----LEDMKKIAKILESAGSAYFNVTAG 249
                                       44....777777777777777777777777 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.5
                                       HHTBSEEEEEBCC...........GBCTTTSGHHHHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  81 aLGapllvlhpGt...........agagpkgseeeawerlaeslneladya 120
                                       +L +++ ++ +Gt           +   ++ ++ e+ +++ ++++++ad a
  gi|488601627|ref|YP_007908098.1| 572 ELECDTAIIAVGTkpadglydelkDVEVYRIGDCECPAKALDAIRQAADLA 622
                                       677777777777555555444444334444444477777777777777765 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   8.1e-05     0.045       1      47 [.     376     416 ..     376     421 .. 0.83
   2 ?    3.6   0.4      0.11        59       1      29 [.     494     517 ..     494     530 .. 0.81
   3 ?    0.9   0.0      0.73   4.1e+02     123     155 ..     553     584 ..     534     585 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.1e-05
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdqs 47 
                                       ++vG+Gp+G  ++e L+++      +e+ lf+++ +g g+   +++s
  gi|488601627|ref|YP_007908098.1| 376 VVVGGGPAGCKAAEMLAEK-----GHEVILFEKKRLG-GQLIFAAKS 416
                                       69***************99.....59**********9.555444444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleit 29 
                                       +i+G+G  G ++++ L+++       ++t
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENG-----KDVT 517
                                       7****************995.....3333 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.73
                     NAD_binding_9 123 evvdleeradgqavlladg..aslaadaVvLAlGh 155
                                       ++v+++  ++++ v++++g  ++l++d  ++A+G 
  gi|488601627|ref|YP_007908098.1| 553 KAVEIK--KNSV-VVESQGerKELECDTAIIAVGT 584
                                       333333..4444.45555523568*********96 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.02        11       2      28 ..     383     408 ..     382     412 .. 0.87
   2 ?    3.9   0.0     0.049        27       5      27 ..     504     526 ..     502     527 .. 0.91
   3 ?    4.0   0.1     0.044        25     220     261 ..     543     583 ..     536     598 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                       aG  aA  L+++G++V+++E + r+GG
  gi|488601627|ref|YP_007908098.1| 383 AGCKAAEMLAEKGHEVILFEKK-RLGG 408
                                       7889****************64.7777 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.049
                                       HHHHHHHHTTEEEEEEESSSSSB CS
                     Amino_oxidase   5 aaArqLlsaGfdVtvlEardrvG 27 
                                       ++A  L+++G dVt++E  + +G
  gi|488601627|ref|YP_007908098.1| 504 STAAMLAENGKDVTIVEMLPKIG 526
                                       89***************988887 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.044
                                       TTTEEEETSEEEEEEEEETTCEEEEETTSTEE.EESEEEE-S- CS
                     Amino_oxidase 220 lrgldirlntrVkeikregdgvtvtledgevv.eaDaVvvTvp 261
                                       ++g++ ++nt+  eik+  + v v+ +  ++  e+D  +++v 
  gi|488601627|ref|YP_007908098.1| 543 EKGVKMLTNTKAVEIKK--NSVVVESQGERKElECDTAIIAVG 583
                                       489*************9..44444444444445********96 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011     0.059      96     233 ..     180     326 ..     173     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                       TEEEGGGGGGSHHHHHHHHHHHHCCSS.S-EEEEEESESS......TTTC.HHHHHHHHHHCT-SEEEEESS..... CS
                               Dus  96 rggaGaaLlrkpdlvaqivkavvkave.iPvtvkirigid......deeenalelakiveaaGaqaltvHgR..... 160
                                         ++G +L + ++ + +i++ ++++ + +Pv  +i+   d      ++ e++ ++aki+e aG + + v +      
  gi|488601627|ref|YP_007908098.1| 180 TDEYGGSLENRARFAVEIIERIKEKCGnFPVGCRISG--DefveggNTLEDMKKIAKILESAGSAYFNVTAGwhesk 254
                                       5566777777777777777777777776777665543..22354666777777788888888888888877755533 PP

                                       ....ECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHHHHHHHHSC CS
                               Dus 161 ....traqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfaestavktge 233
                                           t    + g ++++  + +k av +pvia   I ++e a++il+e  ad v + r+ l +P l +   +v +g+
  gi|488601627|ref|YP_007908098.1| 255 rpliTMFVPRGGFVYLA--EGIKSAVDVPVIASNRINTPELAEKILQEGKADMVSMMRALLADPELPR---KVMEGR 326
                                       33322222222222222..469**************************99***************998...555554 PP

>> 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 ?    4.4   0.0     0.056        31      84     123 ..     196     234 ..     187     242 .. 0.85
   2 ?    7.4   0.0    0.0066       3.7       4      49 ..     283     329 ..     280     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.056
                             MCR_D  84 eviekieeiceevlpfsyeikegkfirkkktvsDyakyGe 123
                                       e+ie+i+e c  ++p++++i+ ++f++  +t+ D+ k ++
  gi|488601627|ref|YP_007908098.1| 196 EIIERIKEKCG-NFPVGCRISGDEFVEGGNTLEDMKKIAK 234
                                       57788888886.59********************999865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0066
                             MCR_D   4 ifpeRlLkpetteklLnel.velegikrvvihGprLPkkvpygpakG 49 
                                       i ++R+ +pe +ek+L+e  +++ ++ r+++  p+LP+kv  g  ++
  gi|488601627|ref|YP_007908098.1| 283 IASNRINTPELAEKILQEGkADMVSMMRALLADPELPRKVMEGRMDE 329
                                       7889************985267899***************9997665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0038       2.1      12      39 ..     372     399 ..     361     408 .. 0.84
   2 ?    5.0   0.4     0.042        23      13      42 ..     491     519 ..     475     521 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0038
                                       T-EEEEES-SHHHHHHHHHHHCCT-CEE CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkv 39 
                                       +k+++++G G  + ++a++L++kg + +
  gi|488601627|ref|YP_007908098.1| 372 KKRIVVVGGGPAGCKAAEMLAEKGHEVI 399
                                       799********************99854 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.042
                                       -EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkvvva 42 
                                        ++++iG G ++  +a +L+++g + v+++
  gi|488601627|ref|YP_007908098.1| 491 DRAVIIGGGGVGCSTAAMLAENGKD-VTIV 519
                                       689****************998876.8886 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 ?    5.4   0.0     0.015       8.6     188     217 ..     369     398 ..     355     451 .. 0.74
   2 ?    5.8   0.1     0.012       6.5     135     217 ..     440     516 ..     412     524 .. 0.74
   3 ?    0.4   0.1      0.49   2.8e+02     133     160 ..     562     586 ..     543     588 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                       K_oxygenase 188 llakkriaVvGsGqSaaeifedllrrqkkv 217
                                          kkri+VvG+G  +   +e l+++ ++v
  gi|488601627|ref|YP_007908098.1| 369 ADVKKRIVVVGGGPAGCKAAEMLAEKGHEV 398
                                       56799***********99999999987754 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                       K_oxygenase 135 veskd.aegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedl 210
                                       ++ ++ ++++  el+  +++++vG ep iP++       e+ + + e+l      + ++r +++G+G  +   +  l
  gi|488601627|ref|YP_007908098.1| 440 IRYEEaTAEKVLELNPDAVIVAVGAEPIIPQIPG----VENAITAFEVLDGA---EVGDRAVIIGGGGVGCSTAAML 509
                                       444443455666788899************9765....35677777887776...6788889999998888877777 PP

                       K_oxygenase 211 lrrqkkv 217
                                       +++ k+v
  gi|488601627|ref|YP_007908098.1| 510 AENGKDV 516
                                       7776654 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.49
                       K_oxygenase 133 ltveskdaegeeeelearnlvlgvGtep 160
                                       + v   +++ge++ele+ + +++vGt+p
  gi|488601627|ref|YP_007908098.1| 562 VVV---ESQGERKELECDTAIIAVGTKP 586
                                       333...369999*************999 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0037       2.1      18      41 ..     369     395 ..     353     401 .. 0.80
   2 ?   -3.2   0.0       7.5   4.2e+03      75      93 ..     444     462 ..     438     466 .. 0.88
   3 ?    7.4   0.9    0.0045       2.5      20      41 ..     492     513 ..     484     521 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0037
                                       T...SEEEEE--SHHHHHHHHHHHHHT CS
                                       x...xxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  18 d...skvllvGaGglGsellknLalsG 41 
                                       +   +++++vG G  G+ ++++La  G
  gi|488601627|ref|YP_007908098.1| 369 AdvkKRIVVVGGGPAGCKAAEMLAEKG 395
                                       34449*******************877 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.5
                                       HHHHHHHHHT-TTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              ThiF  75 evaaealqeinpdveveav 93 
                                       e+ ae++ e+npd+ ++av
  gi|488601627|ref|YP_007908098.1| 444 EATAEKVLELNPDAVIVAV 462
                                       788999*******999987 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0045
                                       EEEEE--SHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  20 kvllvGaGglGsellknLalsG 41 
                                       + +++G Gg+G+  + +La  G
  gi|488601627|ref|YP_007908098.1| 492 RAVIIGGGGVGCSTAAMLAENG 513
                                       679****************988 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 ?    1.5   0.0       0.6   3.4e+02       1      45 [.     375     418 ..     375     460 .. 0.81
   2 ?    8.1   0.3    0.0055       3.1       2      30 ..     494     519 ..     493     527 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.6
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..T CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..l 45 
                                       ++++G+G  G  +ae+la++++   e+++ ++++ + + ++a++   
  gi|488601627|ref|YP_007908098.1| 375 IVVVGGGPAGCKAAEMLAEKGH---EVILFEKKRLGGQLIFAAKspY 418
                                       89*****************997...5999888888888887766552 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0055
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEE CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitva 30 
                                       +iiG+G+vG ++a +la++++    +t++
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENGKD---VTIV 519
                                       89*****************975...7776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4     0.048        27       1      70 [.     374     463 ..     374     477 .. 0.70
   2 ?    4.2   1.3      0.12        66       3      31 ..     494     519 ..     492     598 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.048
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......................-EEECEC CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......................vkvtavd 54 
                                       +i ++G+G  g   a+ l+++g   he+++  +++    + + ++ +                       ++ ++ +
  gi|488601627|ref|YP_007908098.1| 374 RIVVVGGGPAGCKAAEMLAEKG---HEVILF-EKKRLGGQLIFAAKSpygrefsaipeyfervlpkrevqIRYEEAT 446
                                       68999*****************...***977.544444333333333344777777777777777777666666667 PP

                                       HHHHHH.H-SEEEE-S- CS
                     F420_oxidored  55 neeaae.eadvvvlavk 70 
                                       +e+++e + d v++av 
  gi|488601627|ref|YP_007908098.1| 447 AEKVLElNPDAVIVAVG 463
                                       77777777777777775 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.12
                                       EEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                     F420_oxidored   3 giiGaGnmgealasgllaagaqpheivva 31 
                                        iiG+G +g + a  l+++g   ++++++
  gi|488601627|ref|YP_007908098.1| 494 VIIGGGGVGCSTAAMLAENG---KDVTIV 519
                                       589*****************...999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.91u 0.39s 00:00:01.30 Elapsed: 00:00:00.58
# Mc/sec: 3252.49
//
Query:       gi|488601628|ref|YP_007908099.1|  [L=205]
Description: hypothetical protein Asulf_02151 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-12   45.2   0.1    8.9e-12   44.7   0.1    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    8.6e-09   35.3   0.1    1.9e-08   34.3   0.1    1.5  1  HTH_20           Helix-turn-helix domain
    3.5e-08   33.8   0.2    7.1e-08   32.8   0.2    1.6  1  HTH_27           Winged helix DNA-binding domain
    1.1e-07   31.3   0.0      2e-07   30.4   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    3.9e-06   26.6   0.0    7.7e-06   25.7   0.0    1.4  1  MarR_2           MarR family
    1.6e-05   24.6   1.0    4.8e-05   23.1   0.1    2.1  2  HTH_IclR         IclR helix-turn-helix domain
    5.9e-05   22.9   0.1    0.00012   21.9   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00014   21.7   0.2    0.00041   20.2   0.1    1.9  1  MarR             MarR family
    0.00064   20.1   0.1    0.00097   19.5   0.1    1.3  1  Penicillinase_R  Penicillinase repressor
    0.00085   19.5   0.1     0.0013   18.9   0.1    1.3  1  HTH_34           Winged helix DNA-binding domain
    0.00086   19.1   0.4     0.0016   18.3   0.4    1.3  1  HxlR             HxlR-like helix-turn-helix
     0.0016   18.2   0.1      0.037   13.8   0.1    2.3  1  DUF1495          Winged helix DNA-binding domain (DUF1495)
     0.0047   16.9   0.2     0.0074   16.3   0.2    1.4  1  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.026   14.5   0.0    1.5  1  HTH_11           HTH domain
      0.013   15.4   0.1      0.021   14.8   0.1    1.2  1  HTH_45           Winged helix-turn-helix
      0.016   15.3   1.2        1.6    8.9   0.1    2.3  2  DUF2250          Uncharacterized protein conserved in archaea
      0.019   15.0   0.1      0.028   14.5   0.1    1.3  1  MerR_1           MerR HTH family regulatory protein
      0.022   15.0   0.0      0.034   14.4   0.0    1.2  1  DUF2513          Hypothetical protein (DUF2513)
      0.023   14.7   0.2      0.094   12.7   0.1    2.1  2  BLACT_WH         Beta-lactamase associated winged helix domai
      0.026   14.3   0.0      0.044   13.6   0.0    1.4  1  HTH_10           HTH DNA binding domain
      0.029   14.3   0.3      0.062   13.3   0.3    1.7  1  HTH_12           Ribonuclease R winged-helix domain
      0.049   13.7   0.1      0.083   12.9   0.1    1.3  1  HTH_35           Winged helix-turn-helix DNA-binding
      0.068   13.5   0.0       0.11   12.8   0.0    1.3  1  Rrf2             Transcriptional regulator
       0.11   10.8   0.1       0.15   10.4   0.1    1.2  1  DUF505           Protein of unknown function (DUF505)
       0.14   12.0   3.1       0.23   11.2   3.1    1.3  1  MCPVI            Minor capsid protein VI
       0.14   12.4   0.0       0.26   11.5   0.0    1.4  1  PaaX             PaaX-like protein
       0.42    8.2  11.7       0.52    7.9  11.7    1.1  1  TALPID3          Hedgehog signalling target


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 !   44.7   0.1   1.3e-14   8.9e-12       3      46 ..      11      54 ..       9      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.3e-14
                                      HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                       R++IL  L+e++++++el++++g s+st+ +H  kL+e+G+V+
  gi|488601628|ref|YP_007908099.1| 11 SRSRILTKLEERPHTISELSKKTGYSKSTLAYHMEKLMEMGVVR 54
                                      69****************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   2.8e-11   1.9e-08      12      61 .]      12      60 ..      10      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.8e-11
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      R ril  L +++++t sel +  + sk+tl yH+++L e g v++v+ gr
  gi|488601628|ref|YP_007908099.1| 12 RSRILTKL-EERPHTISELSKKTGYSKSTLAYHMEKLMEMGVVRRVEDGR 60
                                      99******.*************************************9987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.2   1.1e-10   7.1e-08       6      68 .]      13      71 ..       8      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.1e-10
                            HTH_27  6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      + +L  ++  +r+ ++++l++++ +++s+ +y ++kL e+G+v r +d   r+ + ++lTd+G
  gi|488601628|ref|YP_007908099.1| 13 SRILTKLE--ERPHTISELSKKTGYSKSTLAYHMEKLMEMGVVRRVEDG--RKWVYYELTDEG 71
                                      55777777..999******************************999776..777********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 !   30.4   0.0     3e-10     2e-07      17      48 .]      23      54 ..      14      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3e-10
                            HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                        +++eL++++g S+st+ +++++L+e+G+++
  gi|488601628|ref|YP_007908099.1| 23 PHTISELSKKTGYSKSTLAYHMEKLMEMGVVR 54
                                      489***************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.2e-08   7.7e-06       3      61 ..       8      60 ..       7      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.2e-08
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      +t +  r+L  L  rp    t++el +++g+sks++ ++ ++L + G v+r++   D+R
  gi|488601628|ref|YP_007908099.1|  8 FTTSRSRILTKLEERPH---TISELSKKTGYSKSTLAYHMEKLMEMGVVRRVE---DGR 60
                                      5788899*********5...*******************************96...555 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 !   23.1   0.1   7.2e-08   4.8e-05      16      51 ..      21      56 ..      13      57 .. 0.86
   2 ?   -0.7   0.1         2   1.3e+03      34      43 ..      96     105 ..      96     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.2e-08
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                       ++ t+sel+++tg +kSt   ++  L+e+G v++ 
  gi|488601628|ref|YP_007908099.1| 21 ERPHTISELSKKTGYSKSTLAYHMEKLMEMGVVRRV 56
                                      34568****************************985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                                       HHHHHHHHHH CS
                          HTH_IclR  34 tvhRlLqtLv 43 
                                       +++RlL+ ++
  gi|488601628|ref|YP_007908099.1|  96 SAFRLLHRMQ 105
                                       799***9987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.8e-07   0.00012      18      62 ..      19      64 ..      14      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.8e-07
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT.EE CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk.lY 62
                                      l++ p t++e+++++g ++s+    +++L+++G+V+r++  +k +Y
  gi|488601628|ref|YP_007908099.1| 19 LEERPHTISELSKKTGYSKSTLAYHMEKLMEMGVVRRVEDGRKwVY 64
                                      68999*********************************96654355 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   6.1e-07   0.00041       5      51 ..      12      57 ..       8      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.1e-07
                                      HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      + +iL++l+e+ p+++seL kk g skst+     +L + G ++R  
  gi|488601628|ref|YP_007908099.1| 12 RSRILTKLEER-PHTISELSKKTGYSKSTLAYHMEKLMEMGVVRRVE 57
                                      56788888775.7********************************76 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.5e-06   0.00097      24      81 ..      26      84 ..      21     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                                      HHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----X.XXXXXXXXXXXXX CS
                   Penicillinase_R 24 veeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvse.eeavasavkqlld 81
                                      ++el++++  ++sT +  +++L++ g+++r ++gr+ +Y+ l++e +++v++ + ++ +
  gi|488601628|ref|YP_007908099.1| 26 ISELSKKTGYSKSTLAYHMEKLMEMGVVRRVEDGRKWVYYELTDEgRKLVRRDMIKMAS 84
                                      6899************************************9998834566666666555 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 !   18.9   0.1   1.9e-06    0.0013      15      79 ..      24      85 ..      12      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                            HTH_34 15 adfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksl 79
                                       + +el+++++ +++ L+ h++kL + g +     ++++++   +++T+eGr+   + +  + sl
  gi|488601628|ref|YP_007908099.1| 24 HTISELSKKTGYSKSTLAYHMEKLMEMGVVR--R-VEDGRKWVYYELTDEGRKLVRRDMIKMASL 85
                                      57899***********************664..3.44455899**********999988888776 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4   2.3e-06    0.0016       9      73 ..      14      75 ..      11      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.3e-06
                                      HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGH CS
                              HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsle 73
                                       il++l + ++  sel+++  + s+++La ++ +L + g++ r++     + v Y+lt++Gr+l 
  gi|488601628|ref|YP_007908099.1| 14 RILTKLEERPHTISELSKKT-GYSKSTLAYHMEKLMEMGVVRRVE--DGRKWVYYELTDEGRKLV 75
                                      699****************9.89******************9975..4456689********985 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 !   13.8   0.1   5.6e-05     0.037      54      88 ..      43      76 ..       8      77 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                           DUF1495 54 nsessLielGLveeeeeseglklYklteeGieive 88
                                      +  + L+e+G+v+++e+ +   +Y+lt+eG+++v 
  gi|488601628|ref|YP_007908099.1| 43 HM-EKLMEMGVVRRVEDGRKWVYYELTDEGRKLVR 76
                                      33.459*******999999999**********986 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.1e-05    0.0074       8      50 ..      13      55 ..       6      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                    Sulfolobus_pRN  8 ekillilsrrcatleeleektGiekeellvyltrlykrGlisr 50
                                       +il  l  r  t+ el  ktG  k +l  ++ +l + G++ r
  gi|488601628|ref|YP_007908099.1| 13 SRILTKLEERPHTISELSKKTGYSKSTLAYHMEKLMEMGVVRR 55
                                      589*************************************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.9e-05     0.026       3      44 ..      13      52 ..      11      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      + il+ L e+r+  +++eL+++++ S++t   ++++L e+gv
  gi|488601628|ref|YP_007908099.1| 13 SRILTKL-EERP-HTISELSKKTGYSKSTLAYHMEKLMEMGV 52
                                      5788999.7776.8*************************994 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.1e-05     0.021      10      67 ..      14      76 ..      12      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli.....kkskekYvlTekGlelle 67
                                       IL +++e   + +++ +k   s ++l   +++L+e g++       +   Y+lT++G++l++
  gi|488601628|ref|YP_007908099.1| 14 RILTKLEERPHTISELSKKTGYSKSTLAYHMEKLMEMGVVrrvedGRKWVYYELTDEGRKLVR 76
                                      69999*9********************************9887555566789********987 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.024        16      28      56 ..      29      57 ..      13      60 .. 0.87
   2 ?    8.9   0.1    0.0025       1.6      75      92 ..      60      77 ..      57      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.024
                           DUF2250 28 iakeleipleevrellkkLeelGLlerve 56
                                      ++k++  +++     ++kL+e+G + rve
  gi|488601628|ref|YP_007908099.1| 29 LSKKTGYSKSTLAYHMEKLMEMGVVRRVE 57
                                      578888999999999************98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0025
                           DUF2250 75 khHtYYrltreGelllre 92
                                      ++  YY+lt+eG  l+r+
  gi|488601628|ref|YP_007908099.1| 60 RKWVYYELTDEGRKLVRR 77
                                      6789************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 ?   14.5   0.1   4.2e-05     0.028       2      38 ..      25      65 ..      24      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                                      EHHHHHHHHTS-HHHHHHHHHHTT.-S-EE...-TTS-EEE CS
                            MerR_1  2 sigevakilgvtthtlrywekegl.lkpkr...teggrryY 38
                                      +i+e++k++g +++tl y+ ++   +   r   +++   yY
  gi|488601628|ref|YP_007908099.1| 25 TISELSKKTGYSKSTLAYHMEKLMeMGVVRrveDGRKWVYY 65
                                      8*********************9998777774444444666 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.2e-05     0.034      10      78 ..      15      71 ..       3      83 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-05
                           DUF2513 10 iLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweG 78
                                      iL +lee + +        ++ls+ +gysk +++yh+++l+e g ++ +++ +k+      +++Lt eG
  gi|488601628|ref|YP_007908099.1| 15 ILTKLEERPHTI-------SELSKKTGYSKSTLAYHMEKLMEMGVVRRVEDGRKWV-----YYELTDEG 71
                                      444444444444.......4445679********************9988877665.....66666666 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       5.6   3.7e+03      28      35 ..      15      22 ..      14      27 .. 0.87
   2 ?   12.7   0.1   0.00014     0.094      26      47 .]      41      62 ..      37      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.6
                          BLACT_WH 28 hLeKLeee 35
                                      +L KLee+
  gi|488601628|ref|YP_007908099.1| 15 ILTKLEER 22
                                      799**985 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                          BLACT_WH 26 lahLeKLeeeGkVkregdkgkW 47
                                        h+eKL+e G V+r++d +kW
  gi|488601628|ref|YP_007908099.1| 41 AYHMEKLMEMGVVRRVEDGRKW 62
                                      56*************9998999 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.6e-05     0.044      22      46 ..      22      46 ..      20      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-05
                            HTH_10 22 RrvtlkeLAkelGIskstlsehLrk 46
                                      R  t++eL+k+ G skstl +h++k
  gi|488601628|ref|YP_007908099.1| 22 RPHTISELSKKTGYSKSTLAYHMEK 46
                                      66799*****************988 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   9.3e-05     0.062      21      64 ..      27      73 ..      10      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.3e-05
                            HTH_12 21 eeLkkr.gydigeravRyrLrkleergltrrvgya....greltEkGle 64
                                      +eL k+ gy     ++ y++ kl e+g +rrv  +      elt+ G +
  gi|488601628|ref|YP_007908099.1| 27 SELSKKtGYSK--STLAYHMEKLMEMGVVRRVEDGrkwvYYELTDEGRK 73
                                      45666669877..8999***************88754555577777765 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00012     0.083       6      37 ..      14      45 ..      11      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            HTH_35  6 dIiAaLrkrgttLaalsreaglssstlsnalt 37
                                       I  +L++r  t+++ls++ g+s+stl+  ++
  gi|488601628|ref|YP_007908099.1| 14 RILTKLEERPHTISELSKKTGYSKSTLAYHME 45
                                      6999***********************87665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017      0.11      20      58 ..      19      56 ..      12      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                      SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                        ee+p +++e++++++ s+s l+  ++kL + g+v+ v
  gi|488601628|ref|YP_007908099.1| 19 L-EERPHTISELSKKTGYSKSTLAYHMEKLMEMGVVRRV 56
                                      3.45679*****************************865 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00023      0.15     369     422 ..      43      96 ..       9     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                            DUF505 369 aLysLesfeLieseveekgkevyvlTeyGekvledqekklrevsaeavkaitit 422
                                        + +L  ++ +++ ++     +y+lT++G+k++ +   k+++   ++v++i+ +
  gi|488601628|ref|YP_007908099.1|  43 HMEKLMEMGVVRRVEDGRKWVYYELTDEGRKLVRRDMIKMASLLVTGVMSIIFS 96 
                                       445555556666664444456899**********99999************976 PP

>> MCPVI  Minor capsid protein VI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.1   0.00035      0.23      35     179 ..      13     162 ..       8     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                                       ...XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                             MCPVI  35 ssitsglkniGsfikntgskivns.stfqqlkqglkesnvlenvadlagetlsalvDigrlkvqkdleklkrk.alG 109
                                       s+i   l++   +i+  ++k + s st     ++l e +v+++v d+       l+D gr+ v++d+ k+    + G
  gi|488601628|ref|YP_007908099.1|  13 SRILTKLEERPHTISELSKKTGYSkSTLAYHMEKLMEMGVVRRVEDGRKWVYYELTDEGRKLVRRDMIKMASLlVTG 89 
                                       57777788888999999***998834678889**********************************98887651555 PP

                                       XXXXXXXXX.XXXXXXXX...XXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             MCPVI 110 eerpatqeeleaLiaald...pkdeea..vkqgeptvePiaPeaksvlvPvtldlpesvdevkkPvlssesavvv 179
                                           +  +    L+  ++   +  e++  v +  + v  + P+a+++ +Pv  + p +     +P +s++   +v
  gi|488601628|ref|YP_007908099.1|  90 VMSIIFSAF--RLLHRMQrpsAAPEMVtpVVREVEKVPTAVPAATPTPTPVPTPTPTPTPAPTPPPTSTPMPSPV 162
                                       555555444..6777777744333443223334444445567777777777777666666666666655543333 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00039      0.26      28      70 .]      28      71 ..      21      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                              PaaX 28 rllaelGiseslvRaalsRlakaGwlvrekegr.rsfYrLsdkg 70
                                      +l ++ G s s++   +  l + G ++r ++gr  ++Y+L+d+g
  gi|488601628|ref|YP_007908099.1| 28 ELSKKTGYSKSTLAYHMEKLMEMGVVRRVEDGRkWVYYELTDEG 71
                                      677888999999999999***************779******86 PP

>> TALPID3  Hedgehog signalling target
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  11.7   0.00079      0.52     942     981 ..     121     161 ..      87     177 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00079
                           TALPID3 942 vskketllp..tPvptPqptppqsPpssekelspvktPdsSp 981
                                       v+k  t +p  tP ptP ptp ++P++ +  + p +tP  Sp
  gi|488601628|ref|YP_007908099.1| 121 VEKVPTAVPaaTPTPTPVPTPTPTPTP-APTPPPTSTPMPSP 161
                                       333333333443333333333333321.22233333443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); 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):              27  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 1204.67
//
Query:       gi|488601629|ref|YP_007908100.1|  [L=370]
Description: Sep-tRNA:Cys-tRNA synthase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-59  202.2   0.0    2.4e-59  201.0   0.0    1.6  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
    4.1e-12   45.8   0.0    6.4e-12   45.1   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
      2e-11   43.7   0.0    2.5e-11   43.4   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    7.9e-05   22.1   0.0    0.00027   20.4   0.0    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.069   12.4   0.0       0.11   11.7   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
      0.075   12.1   0.0       0.27   10.3   0.0    1.8  2  Dus              Dihydrouridine synthase (Dus)


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 !  201.0   0.0   8.1e-63   2.4e-59       2     389 .]      35     366 ..      34     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 8.1e-63
                                       BGGGSSS.----SS-S---S-HHHHHCCCCHHCTBSBTTBTTS-CCCCCCCCCHCCCCCHHHHHHHHHTTHCCHHEE CS
                           SepSecS   2 Dtdkdvd.tvgiGerearvlselkeesvfdfiHgvGrsGnlvdvqPKalGasvlakltNklvkdilkllGlrevkna 77 
                                       D+++++d  +g        l+++k++++++f+H          + P +lG++v a++tN          G+re k  
  gi|488601629|ref|YP_007908100.1|  35 DGYSVCDfCTGT-------LDSIKTPPIYKFVHE---------ILPEFLGCDV-ARITN----------GAREGK-- 82 
                                       777888844444.......9*************9.........78********.*****..........***666.. PP

                                       CCCSS-HHHHHHHHHHHHHHHCC--CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHHHCCTCC CS
                           SepSecS  78 fvvPlatGlslaLClsalrkrskakkviwvridekSslkavelaGleialvekvlegDelitdvedveeiiekkree 154
                                       f++           + a+    k+ ++i    ++ Ss++++e+aGl+++  ++  ++++++t  +d e++i+   ++
  gi|488601629|ref|YP_007908100.1|  83 FAI-----------MHAFS-GCKGGEIIMDENAHYSSYVSAERAGLKVIFAKNSGYPEYIVTA-DDYETAIDS-AKN 145
                                       999...........55555.66899*********************************99885.678999977.456 PP

                                       CEEEEEECSSTTTTB----HHHHHHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCH CS
                           SepSecS 155 vilavlstlsffaprspDdvkeiakiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGg 231
                                        +la++++++++++++p  +k+iak+C+   +P++vNgAYai               GR+d  +k ++ +++v++G+
  gi|488601629|ref|YP_007908100.1| 146 PVLALVTYPDGNYGNLPN-IKRIAKVCESNSIPLIVNGAYAI---------------GRMDFKLKRMGGDFIVGSGH 206
                                       69***************9.***********************...............******************** PP

                                       CCCCESSCHCCCCCHCCCHCHCTSCHCCCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC......... CS
                           SepSecS 232 aiiaasdesfikeiskeypgrasaapskdvlisllllGskaykkllkeqkesfkllreklkklaeeve......... 299
                                       +++a+ ++ ++ ++++ y+++++++++k +++++++lG++a++ ++ ++ +sf+++ e++k+++eev          
  gi|488601629|ref|YP_007908100.1| 207 KSMASAGPVGVLGMKEDYADIVLKKSEKFKVKEIEMLGCTARGVVVMTLIASFPHIVERIKRWDEEVRkaryfaerf 283
                                       *******************************************************************99******** PP

                                       .....EEESSSTT-SSEEEEE-CCCHCCCC...THHHHHHHHHHHTTECSSE.EE-SSTCECTTSSS-SSSEEEEEE CS
                           SepSecS 300 .....ekllevpeNpissaltletldeikk...karldlaseLfsrkvtGargvrasdsklTshlkeyhsrYlkias 368
                                             +l+e+p+N++++++  ++l+ei+k    +r++l++eL+++k++G++      ++lT        + +k+ s
  gi|488601629|ref|YP_007908100.1| 284 eelgiIQLGEKPHNHDLMFFESKVLYEISKkakSGRFFLYKELKKKKIHGIK------PGLT--------KHFKL-S 345
                                       **9999**********************99676689****************......****........899**.* PP

                                       -TT--HHHHHHHHHHHHHHHH CS
                           SepSecS 369 aiGlkdedvdkvlerldeile 389
                                       ++ l++e++++++++++ei+e
  gi|488601629|ref|YP_007908100.1| 346 TYMLSEEEIEYIIRAFEEIIE 366
                                       ******************986 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   2.1e-15   6.4e-12      67     218 ..      75     225 ..      59     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 2.1e-15
                                       ESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBE..TTSCBEGGGHHHH--..TT CS
                       Aminotran_5  67 tsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipld..eegeldldeleklln..ek 139
                                       t G+ e+  ++++++  s  +g ei++ e+ h +  v ++++    g+kv +++    +e  ++ d++e++++  ++
  gi|488601629|ref|YP_007908100.1|  75 TNGAREGKFAIMHAF--SGCKGGEIIMDENAHYSSYVSAERA----GLKVIFAKNSgyPEYIVTADDYETAIDsaKN 145
                                       566667777888888..45799**************776666....6888777765114555679*******65599 PP

                                       EEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT.-EEEEEEH CS
                       Aminotran_5 140 tklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtG.iGvlyvrk 215
                                       + l  +t      G++  +++i+k++  + + ++v +a a+g + +++k++g Df++ sghK ++ +G +Gvl +++
  gi|488601629|ref|YP_007908100.1| 146 PVLALVTYPDGNYGNLPNIKRIAKVCESNSIPLIVNGAYAIGRMDFKLKRMGGDFIVGSGHKSMASAGpVGVLGMKE 222
                                       99999*********************************************************9999988****9999 PP

                                       HHH CS
                       Aminotran_5 216 ell 218
                                       ++ 
  gi|488601629|ref|YP_007908100.1| 223 DYA 225
                                       875 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   8.4e-15   2.5e-11      74     362 ..      75     360 ..      55     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 8.4e-15
                                       ESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEE CS
                     Aminotran_1_2  74 gsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktk 150
                                       ++Ga ++  a++ +++  +g ei++++  + s    ++ +g++v+  + +  +++ ++++++e+a+++a  +n+   
  gi|488601629|ref|YP_007908100.1|  75 TNGAREGKFAIMHAFSGCKGGEIIMDENAHYSSYVSAERAGLKVIFAKNSGYPEYIVTADDYETAIDSA--KNP--V 147
                                       79999999***9999999******************************7777***************96..455..3 PP

                                       EEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGG CS
                     Aminotran_1_2 151 vilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaG 227
                                       + lv+    P+G   +l+ ++ ++++++++ + l+v  aYa++ ++        +++++   ++ivgs  K++++aG
  gi|488601629|ref|YP_007908100.1| 148 LALVTY---PDGNYGNLPNIKRIAKVCESNSIPLIVNGAYAIGRMD--------FKLKRMGGDFIVGSGHKSMASAG 213
                                       445555...55555555556666666*******************9........99999999*************** PP

                                       G-EEEEEEEHHHHHHHHHHHHHHTS.......SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHH CS
                     Aminotran_1_2 228 eRvGyilgnaavvsqlrklsrpfls.......ssllqaavaaalsdallkqseleemrqrlq...krrkelrdeLae 294
                                         vG +  ++++++ + k s  f +       +++   +v++ +  ++     + e+ +r     ++++++ ++++e
  gi|488601629|ref|YP_007908100.1| 214 -PVGVLGMKEDYADIVLKKSEKFKVkeiemlgCTARGVVVMTLIASFPH----IVERIKRWDeevRKARYFAERFEE 285
                                       .*********999999999999999888773333333344444444443....333333333111467899999999 PP

                                       STEEEECCSCSSEEEEEETHHCHHHHHHH.......HHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 295 lglkvlasqsgmflltdlsaetakelskk.......LleevgvyvtpgtsftvpgrlRitvAglteeeleelvea 362
                                       lg++ l+++ +   l+ ++ +   e+skk       L +e +   ++g  ++++++++++   l+eee+e++++a
  gi|488601629|ref|YP_007908100.1| 286 LGIIQLGEKPHNHDLMFFESKVLYEISKKaksgrffLYKELKKKKIHGIKPGLTKHFKLSTYMLSEEEIEYIIRA 360
                                       999888888777777777777455555555566677666655555566668888888888878888888888876 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 !   20.4   0.0   9.1e-08   0.00027      33     159 ..      64     197 ..      45     208 .. 0.84
   2 ?   -1.4   0.0      0.39   1.2e+03     246     302 ..     274     331 ..     261     335 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.1e-08
                                       HHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG- CS
                   DegT_DnrJ_EryC1  33 aaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaai 108
                                        ++lg + a  ++ + ++   +++a++  +g e+I+  +   ++  ++ ++g+k++f+       y +++++ e ai
  gi|488601629|ref|YP_007908100.1|  64 PEFLGCDVARITNGAREGKFAIMHAFSGCKGGEIIMDENAHYSSYVSAERAGLKVIFAKNSgYPEYIVTADDYETAI 140
                                       5788888888888888999999***88888****************************7652689************ PP

                                       -TTEEEEEEB-G.....GGB---HHHHHHHHHHCT-EEEEE-TT-TT.-EETTEECC CS
                   DegT_DnrJ_EryC1 109 tertkaIlpVhl.....yGqvadmdalkaiaakhglkvieDaAhAlG.atykgkkvG 159
                                        +    +l+  +     yG+  +++++ +++++  +++i   A A+G   +k k++G
  gi|488601629|ref|YP_007908100.1| 141 DSAKNPVLALVTypdgnYGNLPNIKRIAKVCESNSIPLIVNGAYAIGrMDFKLKRMG 197
                                       ***9777654331434489999999999******************95455555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHC..HHHHHHHHHHCCE CS
                   DegT_DnrJ_EryC1 246 eiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevk..rdelvealkeegi 302
                                       + a ++ e+++el+ ++  + p++++   ++   vl e ++++k  r  l ++lk+++i
  gi|488601629|ref|YP_007908100.1| 274 RKARYFAERFEELGIIQLGEKPHNHD-LMFFESKVLYEISKKAKsgRFFLYKELKKKKI 331
                                       45789999999999875555555555.67777777766665533246677788888777 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.8e-05      0.11      70     240 ..      93     290 ..      71     367 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                                       TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB--- CS
                   Beta_elim_lyase  70 rgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvs 146
                                       +g e+i++e+ah+  +     a l+ + +++   +e   +++++ e ai+   a   k +++ l vT     G+   
  gi|488601629|ref|YP_007908100.1|  93 KGGEIIMDENAHYSSYVSAERAGLKVIFAKNSGYPE-YIVTADDYETAIDS--A---KNPVLAL-VTYPD--GNYGN 160
                                       677888888888888888777777777777777777.78889999999999..3...4454444.44444..88999 PP

                                       HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-..EEEEE-HH........ CS
                   Beta_elim_lyase 147 leelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG..gvlafrddel...... 215
                                       l +++++a++++++ ipl++ gA    a   ++ ++k+m  + D ++ s+ K + a  G  gvl +++d +      
  gi|488601629|ref|YP_007908100.1| 161 LPNIKRIAKVCESNSIPLIVNGAY---AIGRMDFKLKRM--GGDFIVGSGHKSM-ASAGpvGVLGMKEDYAdivlkk 231
                                       **********************85...556678888888..6899999999994.5577778999999955777777 PP

                                       .....................................HHHHHHHHHHHHT---SSTHHHH CS
                   Beta_elim_lyase 216 ...................................edylaerveqrkylggglrqagvla 240
                                                                          +   +e v+ ++y ++++++ g++ 
  gi|488601629|ref|YP_007908100.1| 232 sekfkvkeiemlgctargvvvmtliasfphiveriKRW-DEEVRKARYFAERFEELGIIQ 290
                                       76666666666666666666666666666665553222.555556666666666666654 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.9e-05      0.27     169     191 ..     161     183 ..     154     199 .. 0.87
   2 ?   -1.3   0.0      0.31   9.3e+02     123     152 ..     259     288 ..     248     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.9e-05
                                       G--CHHHHHHHHH-SS-EEEESS CS
                               Dus 169 tadweaIkevkqavsipviaNGd 191
                                         ++++I++v++++sip+i+NG+
  gi|488601629|ref|YP_007908100.1| 161 LPNIKRIAKVCESNSIPLIVNGA 183
                                       56899*****************6 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.31
                                       S-EEEEEESESSTTTC.HHHHHHHHHHCT- CS
                               Dus 123 iPvtvkirigiddeeenalelakiveaaGa 152
                                       +P+ v+   ++d+e ++a  +a++ e+ G+
  gi|488601629|ref|YP_007908100.1| 259 FPHIVERIKRWDEEVRKARYFAERFEELGI 288
                                       7888888889**************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2101.85
//
Query:       gi|488601630|ref|YP_007908101.1|  [L=281]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-43  146.8  48.4    2.9e-23   82.6  21.2    2.0  2  EamA      EamA-like transporter family
     0.0048   17.2   0.1        1.1    9.6   0.0    2.4  2  UXS1_N    UDP-glucuronate decarboxylase N-terminal


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6  19.2   1.6e-23   1.4e-19       1     136 [.       2     139 ..       2     140 .. 0.97
   2 !   82.6  21.2   3.2e-27   2.9e-23       2     137 .]     148     280 ..     147     280 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.6e-23
                              EamA   1 llgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllg 74 
                                       ++g+++a+l+a+fwai++ + k++l++++ ++ + +r+ + ++ ++i+++l+++ +   + l+l+ +++l++ ++++
  gi|488601630|ref|YP_007908101.1|   2 HIGEIFAFLSAIFWAIGAGFYKKGLETTDVWSGNLMRTGFTSLGFIIFMVLNDSLIesiNALTLELVFWLIFSAFFA 78 
                                       589****************************************************99999999999*********** PP

                              EamA  75 tvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++l+ +l++ ++k+ ++++a++i+s+ P+f+ ++s+ll+g kl+l+ l+g++li++++ li+
  gi|488601630|ref|YP_007908101.1|  79 FFLGDVLYLASIKECGVAKAVPISSTYPIFVSVWSFLLFG-KLSLYVLFGAILIVMAIKLIS 139
                                       **************************************76.8***************98875 PP

  == domain 2  score: 82.6 bits;  conditional E-value: 3.2e-27
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +gi+la+ a+++w++++++   l +++++ +++++rf+ia+++l +i + ++ ++   s++++l++ + g + +vl+
  gi|488601630|ref|YP_007908101.1| 148 KGIFLAISASISWSLSITVLELLTSYLPSEAVAGFRFIIAFMFLNLIVAKNGFNF---SWNSLLWMGVGGMFVMVLG 221
                                       8*******************************************99999999999...******************* PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllill 137
                                       +++f+ a+k ++++++s+i+++ P+++++++  +l+ek+tl+ ++g++l+++Gvll+l+
  gi|488601630|ref|YP_007908101.1| 222 NYVFVEAIKLIGSAKVSPISAVYPILSAVFAGTVLREKITLRIIAGTLLSFAGVLLVLT 280
                                       ********************************************************986 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 !    9.6   0.0   0.00013       1.1       6      47 ..      56      97 ..      53     104 .. 0.92
   2 !    5.0   0.0    0.0036        32      30      50 ..     219     238 ..     211     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                            UXS1_N  6 litavnrrrmklLlalaliaYvasvwGtfvnmrsiqenGdvK 47
                                      li ++n   ++l++ l + a+ a   G+  ++ si+e G  K
  gi|488601630|ref|YP_007908101.1| 56 LIESINALTLELVFWLIFSAFFAFFLGDVLYLASIKECGVAK 97
                                      7999**********************************9877 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0036
                            UXS1_N  30 vwGtfvnmrsiqenGdvKvek 50 
                                       v G++v++ +i+  G  Kv +
  gi|488601630|ref|YP_007908101.1| 219 VLGNYVFVEAIKLIGSAKV-S 238
                                       67****************9.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1611.23
//
Query:       gi|488601631|ref|YP_007908102.1|  [L=149]
Description: hypothetical protein Asulf_02155 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-43  147.9   0.4    1.3e-43  147.8   0.4    1.0  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   0.4     7e-48   1.3e-43      13     127 ..      20     133 ..       6     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 7e-48
                                       EEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEEEEEEEEEE CS
                       DNase-RNase  13 spvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledgtfyAelvlrk 89 
                                       s+vv+Lr e+gr +lpI+ig++ea+ai+ al++++++RP+thDLl+++l++l +kv r++I+dl d+tfyA++vl++
  gi|488601631|ref|YP_007908102.1|  20 SSVVVLRAEDGR-YLPIYIGNTEAMAIHSALRNKTMSRPMTHDLLTEILKKLRTKVVRIIIDDLVDNTFYARIVLSQ 95 
                                       89*********9.***************************************************************9 PP

                                       T---EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH-EE CS
                       DNase-RNase  90 eeeeleidaRpSDaiaLAlrtgapIyveeevleeasie 127
                                       +++e+e+daRpSD+ia+A+r+ +pIyv+e+vl+ea+ +
  gi|488601631|ref|YP_007908102.1|  96 NNHEIELDARPSDSIAIAVRMASPIYVDEKVLDEAGQD 133
                                       8667*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 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:                        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: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 835.01
//
Query:       gi|488601632|ref|YP_007908103.1|  [L=344]
Description: Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase-related flavin-dependent oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-56  191.2   0.0    5.3e-56  190.3   0.0    1.3  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
       0.11   11.6   0.0        4.4    6.3   0.0    2.3  2  GHL10           Glycosyl hydrolase-like 10


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 !  190.3   0.0   5.9e-60   5.3e-56      20     314 .]      14     314 ..       4     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 5.9e-60
                    Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpgga..ldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLd 94 
                                       ++++++ +l++++E++ fd++w+++h ++  +   +d +t+++al+  T ++r+g+avt++ +rhP + Aq++at+d
  gi|488601632|ref|YP_007908103.1|  14 EPIERIFRLVERVEKYPFDSIWFPDHTLMYPKGfcPDVWTVISALSTKT-KLRMGSAVTCPHRRHPSIFAQMIATID 89 
                                       5899************************86666*************999.6************************** PP

                    Bac_luciferase  95 hlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyv 171
                                       hls G +++g+g+g++++  + fG++++++++ +rEf+ev+r lw ge+vd++Geff+++ga+l+ rp+   iP+y+
  gi|488601632|ref|YP_007908103.1|  90 HLSAG-ISVGIGAGESMNL-DPFGIEWRKPVKKMREFIEVCRLLWGGEKVDYDGEFFKLRGAYLQIRPKRY-IPIYI 163
                                       *****.*************.*************************88999******************888.***** PP

                    Bac_luciferase 172 aaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagl 248
                                       +a + +++el++++adg+++  e+p+ +++ +e++ + a++a rd  +++ ++++ +++ d ee+    +  ++  +
  gi|488601632|ref|YP_007908103.1| 164 GANGRKTRELTGEIADGWIPICESPKTYKKNAEEVISSARKAKRD--KPEMALQIYTAISDREEDLNFVR--MYPVV 236
                                       ********************************************7..99999999999999999987666..44445 PP

                    Bac_luciferase 249 d..fyaldsegagreaeaa..........eiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                       +   +  + ++ag++ + +           i+ e+  n+  +    +p e+ + + + G+ e+++e+++a+ +agv+
  gi|488601632|ref|YP_007908103.1| 237 MllGSLKKIREAGYDVDIDeigdefyfkeLIPGESMENKLYELIPKIPVEVSNDFSIMGNREECIEKIEAFIKAGVE 313
                                       556333444444444444422223333333455666677777788889999999999******************98 PP

                    Bac_luciferase 314 e 314
                                       +
  gi|488601632|ref|YP_007908103.1| 314 H 314
                                       7 PP

>> GHL10  Glycosyl hydrolase-like 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0   0.00049       4.4     146     170 ..      22      47 ..       6     117 .. 0.84
   2 ?    3.0   0.0    0.0049        44     153     231 ..     250     324 ..     242     333 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00049
                             GHL10 146 vvevvkrYdvDgvqlDDyfy.lpesf 170
                                       +ve v++Y+ D++ + D++  +p+ f
  gi|488601632|ref|YP_007908103.1|  22 LVERVEKYPFDSIWFPDHTLmYPKGF 47 
                                       56889*************86144545 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0049
                             GHL10 153 YdvDgvqlDDyfylpesfGydlidvalYrqetkkealsnkeddlwidWRrdkisqlvkklnatika.vkPnvkisvs 228
                                       YdvD  ++ D fy++e    + ++++lY+   k  ++ + +d         + ++ ++k+ a ika v   + i + 
  gi|488601632|ref|YP_007908103.1| 250 YDVDIDEIGDEFYFKELIPGESMENKLYELIPK-IPVEVSNDFSI----MGNREECIEKIEAFIKAgVEHFILINIG 321
                                       9***99*********99999999******9996.89999888333....3455667788888888756777777777 PP

                             GHL10 229 Pag 231
                                       P +
  gi|488601632|ref|YP_007908103.1| 322 PDP 324
                                       766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2096.88
//
Query:       gi|488601633|ref|YP_007908104.1|  [L=308]
Description: birA, biotin-(acetyl-CoA-carboxylase) ligase region [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    1.6e-16   60.4   0.0    1.3  1  BPL_LplA_LipB    Biotin/lipoate A/B protein ligase family
      1e-15   57.4   0.1    1.9e-15   56.5   0.1    1.4  1  HTH_11           HTH domain
      2e-07   30.8   0.0    3.7e-07   29.9   0.0    1.5  1  BPL_C            Biotin protein ligase C terminal domain
    2.9e-06   26.7   0.1    5.5e-06   25.9   0.1    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
      2e-05   24.7   0.0    3.8e-05   23.8   0.0    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00015   21.5   0.2    0.00028   20.6   0.2    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0012   18.6   0.0      0.005   16.7   0.0    2.1  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0052   17.1   0.0       0.01   16.2   0.0    1.6  1  Rrf2             Transcriptional regulator
     0.0076   15.8   0.0      0.011   15.3   0.0    1.3  1  BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.044   13.7   0.0    1.6  1  HTH_1            Bacterial regulatory helix-turn-helix protei
      0.018   15.5   0.0      0.048   14.2   0.0    1.7  1  HTH_27           Winged helix DNA-binding domain
      0.018   14.6   0.3       0.11   12.1   0.0    2.4  4  HTH_50           Helix-turn-helix domain
      0.029   14.2   0.0       0.06   13.2   0.0    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
      0.041   14.1   0.1       0.32   11.2   0.0    2.2  2  UPF0122          Putative helix-turn-helix protein, YlxM / p1
      0.041   13.7   0.1        0.1   12.4   0.1    1.7  1  HTH_8            Bacterial regulatory protein, Fis family
      0.049   13.5   0.0       0.12   12.2   0.0    1.6  1  MarR_2           MarR family
      0.054   13.5   0.0       0.12   12.3   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.096   12.6   0.1       0.42   10.5   0.0    2.1  2  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
        0.1   12.4   0.0        1.1    9.2   0.1    2.4  2  HTH_23           Homeodomain-like domain
       0.11   12.7   0.0       0.21   11.7   0.0    1.4  1  OSCP             ATP synthase delta (OSCP) subunit
       0.15   12.0   0.0        0.3   11.1   0.0    1.4  1  MarR             MarR family
       0.25    9.5   0.0       0.36    9.0   0.0    1.1  1  COG6             Conserved oligomeric complex COG6


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 !   60.4   0.0   1.9e-19   1.6e-16      17     131 .]      99     205 ..      89     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.9e-19
                                       CGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT CS
                     BPL_LplA_LipB  17 nsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgie 89 
                                       + +el+  +lv++++q  G+    + w+s kg+l++s++l+pe   +   +++ +++++ +av++al         e
  gi|488601633|ref|YP_007908104.1|  99 KARELPENSLVIAEEQIMGKgrlgRKWFSKKGGLYFSIALKPE---MNLEDIPKLTLTSGVAVARAL---------E 163
                                       46788999**********9999*******************77...59999****************.........7 PP

                                       -TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  90 gipvfikwpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                       + +++ kwpnD+++ng+K+ Gi+ + + + + + +++g+g+n
  gi|488601633|ref|YP_007908104.1| 164 EYQARLKWPNDVLINGKKVCGILSEIVGEIENFKVIVGIGIN 205
                                       8899999*********************************99 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.1   2.4e-18   1.9e-15      13      55 .]      21      63 ..      12      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.4e-18
                            HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGYr 55
                                      +g +sgeeLA++LnvSr++v++ Ik+L+ +g+ Ie+ +g+GYr
  gi|488601633|ref|YP_007908104.1| 21 KGWVSGEELARKLNVSRTAVWKKIKRLRNMGYVIEGAKGKGYR 63
                                      4559**************************************8 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   4.5e-10   3.7e-07       1      46 [.     262     306 ..     262     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.5e-10
                                       STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEE CS
                             BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdis 46 
                                       ++G+ V ++ ++++++G+a + d dG L+++t++g ++++ sGd++
  gi|488601633|ref|YP_007908104.1| 262 TIGKFVEVKAGNRTYRGKAIDMDYDGGLIVETEEG-TEKVFSGDCF 306
                                       69999******************************.*********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 !   25.9   0.1   6.7e-09   5.5e-06      22      47 ..      28      53 ..      24      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.7e-09
                            HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlI 47
                                      eLA++l++S+++v++ +krL ++G++
  gi|488601633|ref|YP_007908104.1| 28 ELARKLNVSRTAVWKKIKRLRNMGYV 53
                                      9************************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   4.7e-08   3.8e-05      15      53 ..      15      54 ..      11      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.7e-08
                                      HHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 15 tlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      ++se  k+ v+  +la+ Lnvs   V + +k+L+++Gyv+
  gi|488601633|ref|YP_007908104.1| 15 EISElLKGWVSGEELARKLNVSRTAVWKKIKRLRNMGYVI 54
                                      567778999******************************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 !   20.6   0.2   3.5e-07   0.00028      21      42 .]      27      48 ..      24      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.5e-07
                     HTH_AsnC-type 21 aeLAervGlSestvlrRvrrLe 42
                                      +eLA+++++S+++v++ ++rL+
  gi|488601633|ref|YP_007908104.1| 27 EELARKLNVSRTAVWKKIKRLR 48
                                      79*******************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 !   16.7   0.0   6.1e-06     0.005      23      54 ..      24      55 ..      18      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.1e-06
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVer 54
                                       + +e+a++l+v+r+ v + +++L ++G+V  
  gi|488601633|ref|YP_007908104.1| 24 VSGEELARKLNVSRTAVWKKIKRLRNMGYVIE 55
                                      6779*************************975 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05      0.01      23      72 ..      22      69 ..       1      81 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE.EEETTT-TCEEESSHCC CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglv.ksvrGkgGGyrLakppe 72
                                      +  vs ee+a++ n+s++ + k +++Lr+ g+v +  +Gk  Gyr+  +p+
  gi|488601633|ref|YP_007908104.1| 22 G-WVSGEELARKLNVSRTAVWKKIKRLRNMGYViEGAKGK--GYRIVSEPK 69
                                      3.4999*************************972566676..999888876 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 !   15.3   0.0   1.4e-05     0.011      39     101 ..     129     187 ..     102     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                   BPL_LplA_LipB_2  39 adlleaAlvlaPevplakAaamlpvlmvalqdAlgalaPPevavhlewpgtilvngar.vGgvr 101
                                       +  l +++ l+Pe +l++  ++  + +va++ Al+ +       +l+wp+++l+ng + +G ++
  gi|488601633|ref|YP_007908104.1| 129 KGGLYFSIALKPEMNLEDIPKLTLTSGVAVARALEEYQ-----ARLKWPNDVLINGKKvCGILS 187
                                       5567899***************************9775.....5***********976155444 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-05     0.044      20      39 ..      30      49 ..      29      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                                      HHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEe 39
                                      A++L++s  av++ ikrL++
  gi|488601633|ref|YP_007908104.1| 30 ARKLNVSRTAVWKKIKRLRN 49
                                      9*****************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.8e-05     0.048      22      55 ..      27      58 ..      22      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-05
                            HTH_27 22 adlcgrlnvedshisyslkkLtekGLvertgdea 55
                                      ++l+++lnv+ +++ + +k+L ++G+v   + ++
  gi|488601633|ref|YP_007908104.1| 27 EELARKLNVSRTAVWKKIKRLRNMGYV--IEGAK 58
                                      79*************************..33333 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.11      18      46 ..      18      46 ..      15      47 .. 0.84
   2 ?   -3.2   0.0       8.5   6.9e+03      39      47 ..     157     165 ..     153     166 .. 0.56
   3 ?   -2.2   0.0         4   3.3e+03       4      12 ..     186     194 ..     184     195 .. 0.88
   4 ?   -3.1   0.1       7.8   6.4e+03      13      21 ..     231     239 ..     226     242 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            HTH_50 18 kayekYpStRklAkrLGvShtaianklrk 46
                                      ++++ + S   lA++L vS ta+ +k+++
  gi|488601633|ref|YP_007908104.1| 18 ELLKGWVSGEELARKLNVSRTAVWKKIKR 46
                                      566667777789***************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.5
                            HTH_50  39 aianklrkY 47 
                                       a+a+ l  Y
  gi|488601633|ref|YP_007908104.1| 157 AVARALEEY 165
                                       666666555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4
                            HTH_50   4 LkeyveefE 12 
                                       L+e+v+e+E
  gi|488601633|ref|YP_007908104.1| 186 LSEIVGEIE 194
                                       89*****99 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 7.8
                            HTH_50  13 relikkaye 21 
                                       +++i+++ +
  gi|488601633|ref|YP_007908104.1| 231 KDVIEQFTK 239
                                       444555544 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.4e-05      0.06      20      46 ..      28      54 ..      16      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.4e-05
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 20 elaeelglsqstvShHLkkLreaGLVe 46
                                      ela++l++s+ +v    k+Lr++G+V 
  gi|488601633|ref|YP_007908104.1| 28 ELARKLNVSRTAVWKKIKRLRNMGYVI 54
                                      9************************95 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 ?   11.2   0.0   0.00039      0.32      35      60 ..      25      50 ..      12      56 .. 0.89
   2 ?   -0.1   0.0       1.4   1.1e+03      57      89 ..     206     238 ..     186     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                           UPF0122 35 SlsEiAeefnvsrqavydnikrtekl 60
                                      S +E+A + nvsr+av+ +ikr +++
  gi|488601633|ref|YP_007908104.1| 25 SGEELARKLNVSRTAVWKKIKRLRNM 50
                                      6689******************9876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                           UPF0122  57 tekllekyEekLkllekykkreellekikdkll 89 
                                       +e+ + +y + Lk l+   +r e+l+++ ++ +
  gi|488601633|ref|YP_007908104.1| 206 VENAVPDYATNLKNLNSEVNRAEILKDVIEQFT 238
                                       567778899999999999999999988877655 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012       0.1      24      42 .]      29      47 ..      27      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                      HHHHHTS-HHHHHHHHHHT CS
                             HTH_8 24 AArlLGisRrtLyrKLkkY 42
                                       Ar L++sR+ +++K+k++
  gi|488601633|ref|YP_007908104.1| 29 LARKLNVSRTAVWKKIKRL 47
                                      69***************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.12      23      53 ..      25      55 ..      15      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLver 53
                                      +  elar+l++s+ av + +krL   G+v +
  gi|488601633|ref|YP_007908104.1| 25 SGEELARKLNVSRTAVWKKIKRLRNMGYVIE 55
                                      5579************************975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.12      23      60 ..      25      65 ..      15      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE...ETEEEEES CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis...rgrriril 60
                                      + eelA+ l+++r  v + +++L++ g++    +g++ ri 
  gi|488601633|ref|YP_007908104.1| 25 SGEELARKLNVSRTAVWKKIKRLRNMGYVIegaKGKGYRIV 65
                                      779************************97634334336665 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 ?   10.5   0.0   0.00051      0.42       9      30 ..      24      45 ..      16      55 .. 0.75
   2 ?   -1.8   0.0       3.7     3e+03      44      63 ..     218     236 ..     209     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00051
                    YdaS_antitoxin  9 GgqkaLAealgvsqqaVsqWlk 30
                                       +  +LA++l+vs+ aV++ +k
  gi|488601633|ref|YP_007908104.1| 24 VSGEELARKLNVSRTAVWKKIK 45
                                      56689*************9875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                    YdaS_antitoxin  44 ekatnGeVtreeLRpDvdws 63 
                                        ++ + eV r e+ +Dv  +
  gi|488601633|ref|YP_007908104.1| 218 KNLNS-EVNRAEILKDVIEQ 236
                                       55555.89999999998655 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0013       1.1      21      45 ..      27      51 ..      24      58 .. 0.81
   2 ?   -0.2   0.0       1.1   9.2e+02       3      16 ..     222     235 ..     221     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                            HTH_23 21 reIAreLgvsrrTvyrwlkryreeG 45
                                      +e Ar+L+vsr  v++ +kr r+ G
  gi|488601633|ref|YP_007908104.1| 27 EELARKLNVSRTAVWKKIKRLRNMG 51
                                      799************8888877666 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                            HTH_23   3 sereRlrillllae 16 
                                       se++R++il+ + e
  gi|488601633|ref|YP_007908104.1| 222 SEVNRAEILKDVIE 235
                                       799******98765 PP

>> OSCP  ATP synthase delta (OSCP) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00025      0.21      18      97 ..     161     242 ..     153     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                              OSCP  18 aleeveeelealeavlaedkklaellsnpavsaeekkdlleelfke.......klseavknflkllaenkRlalLpe 87 
                                       alee+++ l+  ++vl + kk+  +ls+   + e+ k ++     +       ++ ++ +n+ +l +e +R ++L++
  gi|488601633|ref|YP_007908104.1| 161 ALEEYQARLKWPNDVLINGKKVCGILSEIVGEIENFKVIV-----GiginvenAVPDYATNLKNLNSEVNRAEILKD 232
                                       4556666666666666666666666655555555544444.....0333345599********************** PP

                              OSCP  88 iaeefeella 97 
                                       ++e+f ++++
  gi|488601633|ref|YP_007908104.1| 233 VIEQFTKYYK 242
                                       ******9986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00036       0.3      21      47 ..      27      53 ..      21      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 21 seLakklgvskstvtrvldrLekkGli 47
                                       eLa+kl+vs+++v + ++rL   G++
  gi|488601633|ref|YP_007908104.1| 27 EELARKLNVSRTAVWKKIKRLRNMGYV 53
                                      49*******************999987 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00045      0.36     560     598 ..     206     244 ..     204     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00045
                              COG6 560 LpsaltdalenlekLqspklrseiteeaaeklveaYekl 598
                                       +++a  d+  nl++L+s   r ei + + e++++ Y+ l
  gi|488601633|ref|YP_007908104.1| 206 VENAVPDYATNLKNLNSEVNRAEILKDVIEQFTKYYKML 244
                                       6789999*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1845.19
//
Query:       gi|488601634|ref|YP_007908105.1|  [L=230]
Description: KaiC domain protein, AF_0351 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-56  191.5   1.2    1.5e-56  191.4   1.2    1.0  1  ATPase           KaiC
    2.2e-09   37.2   0.0    3.4e-09   36.6   0.0    1.3  1  AAA_25           AAA domain
    2.4e-09   37.0   0.0    4.4e-09   36.2   0.0    1.4  1  RecA             recA bacterial DNA recombination protein
    4.5e-08   32.6   2.3    0.00013   21.2   0.2    2.1  2  PAXNEB           PAXNEB protein
    1.7e-07   30.8   0.0    3.1e-07   29.9   0.0    1.3  1  Rad51            Rad51
    1.3e-06   27.3   1.1    2.2e-06   26.6   0.9    1.4  1  GvpD             GvpD gas vesicle protein
    2.9e-05   24.1   0.2    4.1e-05   23.6   0.2    1.3  1  AAA_14           AAA domain
    3.2e-05   23.4   0.2    0.00099   18.5   0.2    2.2  1  DnaB_C           DnaB-like helicase C terminal domain
    0.00026   20.8   0.3    0.00046   20.0   0.3    1.5  1  AAA_24           AAA domain
    0.00086   19.3   0.1     0.0012   18.8   0.1    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.016   15.1   0.7        0.2   11.5   0.7    2.0  1  NACHT            NACHT domain
      0.024   13.9   0.0      0.029   13.6   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.067   13.7   0.0       0.11   13.0   0.0    1.3  1  ABC_tran         ABC transporter
      0.081   12.3   0.5       0.21   11.0   0.5    1.6  1  TniB             Bacterial TniB protein
      0.095   12.4   0.0        1.1    8.9   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
       0.13   12.6   0.0       0.17   12.2   0.0    1.2  1  HET              Heterokaryon incompatibility protein (HET)
       0.16   11.8   0.0       0.25   11.2   0.0    1.3  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.4   1.2   1.4e-59   1.5e-56       2     229 ..       8     226 ..       7     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 1.4e-59
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       +tgIeglD i+ gGipeg++v ++G++GtGKt+f+l+F+++g+++ +e+ vf++++e++ ++ e+aks+G+dle ++
  gi|488601634|ref|YP_007908105.1|   8 STGIEGLDSIIGGGIPEGHTVVVYGSYGTGKTTFGLHFIYEGLKN-NEKSVFISLDEDEDSILESAKSFGMDLEPFN 83 
                                       7*****************************************999.******************************* PP

                            ATPase  79 eegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaR.eilrqlvrvlkkl 154
                                       ++ +++ +d+++          ke+le++++el ++ k+++++r+viDs++ l ++  +++ R   +  l  ++k+ 
  gi|488601634|ref|YP_007908105.1|  84 DKLEIIRLDVVMV---------KESLEKVTNELLNVFKRMNVRRIVIDSLSIL-ESLFDEKERwLAISSLRDIIKQS 150
                                       **88888888777.........468****************************.66666665516799999999*** PP

                            ATPase 155 gvTailvsekssseeaaggygveefivdgvivLdlkeiee..elvRtleivkmRgtkhskkehpfeIteegikvlee 229
                                       g Tail+se s+++++ ++yg+ e+++dg+i L+  +++   e v  le+vkmR+ +hs+k +p+ It++gi+v+e 
  gi|488601634|ref|YP_007908105.1| 151 GATAILTSE-SDKSGESTKYGIMEYMSDGAINLKIIRKHPleEPVLALEVVKMRRIRHSRKPVPYMITDRGITVMEG 226
                                       *********.6667999****************977766577********************************986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   3.2e-12   3.4e-09      18     193 ..      10     164 ..       4     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.2e-12
                            AAA_25  18 pppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg 94 
                                        ++ ++ +++g +p+g++++++G  gtGKtt+ l+  ++ ++             k +++s++++ed + + ++  g
  gi|488601634|ref|YP_007908105.1|  10 GIEGLDSIIGGGIPEGHTVVVYGSYGTGKTTFGLHFIYEGLKNN----------EKSVFISLDEDEDSILESAKSFG 76 
                                       5677899****************************999998755..........499******************** PP

                            AAA_25  95 eal.rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg.densnsdvgalv 169
                                        +l +++++l ++ l+ v    ++      + l+ ++++l ++ +++ +vr +viD+ls + +  de+   +   ++
  gi|488601634|ref|YP_007908105.1|  77 MDLePFNDKLEIIRLDVV----MV-----KESLEKVTNELLNVFKRM-NVRRIVIDSLSILESLfDEK---ERWLAI 140
                                       ***8889******98444....43.....3457888899*******6.6*********9888776666...667889 PP

                            AAA_25 170 ealeriarrtgaavllvhHvgKes 193
                                       + l++i ++ ga+ +l+  + K++
  gi|488601634|ref|YP_007908105.1| 141 SSLRDIIKQSGATAILTSESDKSG 164
                                       999999999999999998888876 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   4.2e-12   4.4e-09      33     106 ..       6      80 ..       3     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 4.2e-12
                                       EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----H..HHHHHTT--GG CS
                              RecA  33 tissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldp..kyakklGvdid 106
                                       ++s+G  +ld+ +G GG+p+G  + +yG+  +Gktt+ lh i e  k++  ++fi  +   d+  + ak +G+d++
  gi|488601634|ref|YP_007908105.1|   6 MLSTGIEGLDSIIG-GGIPEGHTVVVYGSYGTGKTTFGLHFIYEGLKNNEKSVFISLDEDEDSilESAKSFGMDLE 80 
                                       589***********.****************************************988888862256899999986 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   1.2e-07   0.00013      18      83 ..       6      70 ..       4      73 .. 0.89
   2 !   11.4   0.2   0.00012      0.13     202     286 ..     110     187 ..      82     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.2e-07
                            PAXNEB 18 ltStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlr 83
                                      + StG++ LD+++gGG+p G+ +++  + + + +++    F+ eG+ ++ + +++sld+d++++l+
  gi|488601634|ref|YP_007908105.1|  6 MLSTGIEGLDSIIGGGIPEGHTVVVYGS-YGTGKTTFGLHFIYEGLKNNEKSVFISLDEDEDSILE 70
                                      78***********************977.66667777789******************99999876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00012
                            PAXNEB 202 aptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtv 278
                                         +  nv Rivi sL            +++e+ l  + sLr ++++s ++a+ t  ++    +s+    +e ++D++
  gi|488601634|ref|YP_007908105.1| 110 VFKRMNVRRIVIDSLSILES-----LFDEKERWL-AISSLRDIIKQSGATAILTSESDKS-GESTKYGIMEYMSDGA 179
                                       2223679******9954333.....123344444.489******************9999.7888899********* PP

                            PAXNEB 279 ieLesfag 286
                                       i+L+ + +
  gi|488601634|ref|YP_007908105.1| 180 INLKIIRK 187
                                       ***87655 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0     3e-10   3.1e-07      18     141 ..       6     124 ..       3     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3e-10
                                       EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHH CS
                             Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaer 94 
                                       +l+tG + lD+++gGGi+ g    ++G +++Gkt +   +        e    ++k v+i+ +     + ++e a+ 
  gi|488601634|ref|YP_007908105.1|   6 MLSTGIEGLDSIIGGGIPEGHTVVVYGSYGTGKTTFGLHFIY------EGLKNNEKSVFISLDE--DEDSILESAKS 74 
                                       589*******************************99987643......33347899*****997..5778******* PP

                                       TT--HHHHGGG...EEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETT CS
                             Rad51  95 ykldkeevlen...vayaRaytiehqeellqqaaallaedkfallivDsv 141
                                       +++d e   ++   +  + +   e+ e++ +++ + +++ +++ +++Ds+
  gi|488601634|ref|YP_007908105.1|  75 FGMDLEPFNDKleiIRLDVVMVKESLEKVTNELLNVFKRMNVRRIVIDSL 124
                                       ****8766555111556667888*************************97 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.9   2.1e-09   2.2e-06      10     207 ..      25     218 ..      21     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.1e-09
                              GvpD  10 GktllikGaPGtGktlftlrgl.dvlrresdvlyvstrvddetvseayfsgeaeldktalldllkdplel.dldvdv 84 
                                       G+t+++ G  GtGkt+f l+++ + l+++++ +++s   d++++ e   s          l+ ++d le+  ldv++
  gi|488601634|ref|YP_007908105.1|  25 GHTVVVYGSYGTGKTTFGLHFIyEGLKNNEKSVFISLDEDEDSILESAKSFG------MDLEPFNDKLEIiRLDVVM 95 
                                       99******************97478*******************99654433......3356678888761444444 PP

                              GvpD  85 Piekldlesll.efvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaans 160
                                          k  le +  e ++ + +  +   i +ds   ++e l  + +    i  ++ d   + ++sg+  +l +e+ +  
  gi|488601634|ref|YP_007908105.1|  96 V--KESLEKVTnELLN-VFKRMNVRRIVIDS-LSILESLFDEKERWLAISSLR-D---IIKQSGATAILTSESDKSG 164
                                       3..4444444313333.33344444577999.446677766666666666665.3...4489999999988876542 PP

                              GvpD 161 r......leyivdGvvtlnv.keddrgrlrrdlrleklrGvrignrlqPftlad 207
                                       +      +ey+ dG + l++ ++      +  l + k+r +r   +  P+ ++d
  gi|488601634|ref|YP_007908105.1| 165 EstkygiMEYMSDGAINLKIiRKHPLEEPVLALEVVKMRRIRHSRKPVPYMITD 218
                                       21234449**********76145555666777778899*999999888888877 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   3.9e-08   4.1e-05       3     104 ..      26     127 ..      24     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.9e-08
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek..lkeekktylflDEiqevp 77 
                                       + +v+ G   +GKTt+  ++i+e l ++e+ ++i+ld+++d+ l+  +   ++ +++  ++ +k +++ lD +   +
  gi|488601634|ref|YP_007908105.1|  26 HTVVVYGSYGTGKTTFGLHFIYEGLKNNEKSVFISLDEDEDSILESAK---SFGMDLepFN-DKLEIIRLDVVMVKE 98 
                                       6799*********************9************9997666542...3333332244.47889*******99* PP

                            AAA_14  78 ewekalkslvd..egknldvivtGSnskl 104
                                       ++ek+ ++l++  ++ n++ iv  S+s l
  gi|488601634|ref|YP_007908105.1|  99 SLEKVTNELLNvfKRMNVRRIVIDSLSIL 127
                                       *********99655568888999998876 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 !   18.5   0.2   9.4e-07   0.00099       2      66 ..       7      71 ..       7     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.4e-07
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR 66
                                      lstg + LD++++ G+ +g+ +++ +  ++Gkt++ l+++ +  + ++ + +++sl+ +++++++ 
  gi|488601634|ref|YP_007908105.1|  7 LSTGIEGLDSIIGgGIPEGHTVVVYGSYGTGKTTFGLHFIYEGLK-NNEKSVFISLDEDEDSILES 71
                                      689******998626999**********************99886.56678899**9999988764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   4.4e-07   0.00046       4      82 ..      27     132 ..      24     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.4e-07
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtek...Glksldadkfpdieswedfldevvel........... 59 
                                        +++yG+ g+GKTt+ +++        +k +fi +++   +  +     + d+e ++d l+ +  +           
  gi|488601634|ref|YP_007908105.1|  27 TVVVYGSYGTGKTTFGLHFiyeglknNEKSVFISLDEdedSILESAKSFGMDLEPFNDKLEIIRLDvvmvkeslekv 103
                                       699**********************9999999977661112222222222222233333333332255556666666 PP

                            AAA_24  60 ......aaeladyktlviDtideleelcl 82 
                                               +  + + +viD+++ le+l +
  gi|488601634|ref|YP_007908105.1| 104 tnellnVFKRMNVRRIVIDSLSILESLFD 132
                                       76677766677788999999999988765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.2e-06    0.0012      21     124 ..      26     121 ..      11     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilk. 96 
                                       + +++YG+ g GKt++  ++i + ++ +++ ++++ l e++ s l++     ++     ++++++++  +l+ ++  
  gi|488601634|ref|YP_007908105.1|  26 HTVVVYGSYGTGKTTFGLHFIYEGLKNNEKSVFIS-LDEDEDSILESA----KSFGMDLEPFNDKLEIIRLDVVMVk 97 
                                       578******************99988888888764.444444444444....2222224444555555555554444 PP

                          ATPase_2  97 eksklvfkaielllekikkkgkkiiiii 124
                                       e  ++v++ + ++++ ++ ++    i+i
  gi|488601634|ref|YP_007908105.1|  98 ESLEKVTNELLNVFKRMNVRR----IVI 121
                                       566666666666666666552....334 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7   0.00019       0.2       1     134 [.      26     165 ..      26     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                       SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.............-HCHHHCCCCTS--S CS
                             NACHT   1 rlvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..........rsladllfsqlpepaa 67 
                                       ++v++ G  G GKTt+  +++ +  +++ +    ++++ l   e+s  + a              ++++ +    ++
  gi|488601634|ref|YP_007908105.1|  26 HTVVVYGSYGTGKTTFGLHFIYEGLKNNEK----SVFISLDEDEDSILESAksfgmdlepfNDKLEIIRLDVVMVKE 98 
                                       589*************77776655444422....4455555555444444455555554443333455555555555 PP

                                       SS-CCHHHHCCSCCCEE...EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH CS
                             NACHT  68 pvsevwavllelperlL...lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd 134
                                         ++v ++ll +++r+    +++D+l  l++ +++ke+  +   L+++i++   ++a+ +lt+ ++++ +
  gi|488601634|ref|YP_007908105.1|  99 SLEKVTNELLNVFKRMNvrrIVIDSLSILESLFDEKERWLAISSLRDIIKQ---SGATAILTSESDKSGE 165
                                       555566667776666668999999999999999998888899999999999...8899999998888755 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   2.7e-05     0.029       2      49 ..      26      71 ..      25     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlre 49
                                      + v+V G  GtGKt  +l++++e    ++++++v++s  +++  +l++
  gi|488601634|ref|YP_007908105.1| 26 HTVVVYGSYGTGKTTFGLHFIYEG--LKNNEKSVFISLDEDEDSILES 71
                                      579********************9..9999999999988888777765 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   0.00011      0.11       7      67 ..      21      99 ..      17     179 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                      EEETTSEEEEEESTTSSHHHH.HHHHTTSS--SEEEE..........EETTCEGGG..............B-HHHCCHC CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx..........xxxxxxxxx..............xxxxxxxxx RF
                          ABC_tran  7 klkegekvaivGenGaGKStL.lkllagllkpteGei..........lldgkdlke..............qeleslrke 60
                                       + eg++v++ G+ G+GK+t+ l  +++ lk++e ++                                 ++le+ r  
  gi|488601634|ref|YP_007908105.1| 21 GIPEGHTVVVYGSYGTGKTTFgLHFIYEGLKNNEKSVfisldededsI-------LesaksfgmdlepfnDKLEIIRLD 92
                                      5899****************9789999999998888844444444431.......033333443333344344444444 PP

                                      EEEE-SS CS
                                      xxxxxxx RF
                          ABC_tran 61 igvlpqe 67
                                      + ++++ 
  gi|488601634|ref|YP_007908105.1| 93 VVMVKES 99
                                      4444444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5    0.0002      0.21      37     134 ..      27     130 ..      22     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                              TniB  37 nlllvGdsnnGKtmivekFarlhppekd......edaekvpvlvvqappkpdekrlyaaiLealgap.lkararvsk 106
                                        ++++G + +GKt+   +F  +  ++++       d+++  +l        d + + ++ Le ++ + +  +++++k
  gi|488601634|ref|YP_007908105.1|  27 TVVVYGSYGTGKTTFGLHFIYEGLKNNEksvfisLDEDEDSILESAKSFGMDLEPFNDK-LEIIRLDvVMVKESLEK 102
                                       57788888888888888887555444331122225555656666666666666666655.45554442458999*** PP

                              TniB 107 leqqvlrllrelkvrvLiiDEihnllag 134
                                        +++ l+++++++vr ++iD +  l++ 
  gi|488601634|ref|YP_007908105.1| 103 VTNELLNVFKRMNVRRIVIDSLSILESL 130
                                       ********************98766543 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.001       1.1      22      68 ..      25      71 ..       8      84 .. 0.68
   2 ?    0.9   0.0      0.31   3.2e+02      82     123 ..     165     206 ..     161     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                                      SS-EEEECSTTSSHHHHH.HHHHHHSTTTTS-EEEEETTTS-TTCHHH CS
                   Sigma54_activat 22 dlsvlitGesGtGKella.raiheaskrkekpfvavncaaipeelles 68
                                        +v++ G  GtGK+++  + i+e   +++++ v +   + ++++les
  gi|488601634|ref|YP_007908105.1| 25 GHTVVVYGSYGTGKTTFGlHFIYE-GLKNNEKSVFISLDEDEDSILES 71
                                      5799************98245565.33444444444444555555554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.31
                                       SS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEE CS
                   Sigma54_activat  82 ekekkGlfekadgGtlfLDeigelplelQekLlrvlqegeve 123
                                       e++k G +e  ++G + L  i + ple  +  l+v++ ++++
  gi|488601634|ref|YP_007908105.1| 165 ESTKYGIMEYMSDGAINLKIIRKHPLEEPVLALEVVKMRRIR 206
                                       56788*******************999988888888877765 PP

>> HET  Heterokaryon incompatibility protein (HET)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.17      24      95 ..      98     171 ..      71     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                               HET  24 leltenledalqvlrklgerylWiDaiCInQd..ddkekskqvqlmadIYsnAelvivalgsesedsgllalea 95 
                                        +l++  +++l+v+++ ++r + iD++ I  +  d+ke+   +++++dI +++ ++ + +++++++   +++  
  gi|488601634|ref|YP_007908105.1|  98 ESLEKVTNELLNVFKRMNVRRIVIDSLSILESlfDEKERWLAISSLRDIIKQSGATAILTSESDKSGESTKYGI 171
                                       46677778899999999*************9833555777799*****************99997664444444 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 ?   11.2   0.0   0.00023      0.25      18      75 ..      43      98 ..      25     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                              MEDS 18 vpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrg 75
                                      + fi +gl+++ek + +  ++++d ++e  ++ g+d++   ++++lei++ + +++++
  gi|488601634|ref|YP_007908105.1| 43 LHFIYEGLKNNEKSVFISLDEDEDSILESAKSFGMDLEP--FNDKLEIIRLDVVMVKE 98
                                      579*********88888888**********999999999..77888999988776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 1309.58
//
Query:       gi|488601635|ref|YP_007908106.1|  [L=259]
Description: hypothetical protein Asulf_02159 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   12.5   1.9       0.66    9.3   1.9    2.0  1  ATPase    KaiC
      0.098   12.2   0.0       0.15   11.7   0.0    1.3  1  MP        Viral movement protein (MP)
       0.17   11.0   0.3        8.5    5.4   0.1    2.1  2  PAXNEB    PAXNEB protein


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.9   0.00011      0.66       2     205 ..       8     225 ..       7     230 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00011
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGwdlekl 77 
                                       ktgI  +D  + gG+p+g + l+  e G+G   fal+ l+k a++  e+  + ++ ++  +++++ + ++    +++
  gi|488601635|ref|YP_007908106.1|   8 KTGIDVFDSQI-GGLPSGLIFLLE-EVGAGGREFALTTLMKLAKSGFENLYYFAISSTVDEIKRELTlTFPKSGNEW 82 
                                       89999999998.999999988886.7788888889888888888855666666666666666655544444444444 PP

                            ATPase  78 eeegklaiidasesaeesaee..........kdkedleelieelaeaikeika.krvviDsitglayee.....kea 138
                                        ++  + i   s++   ++             +  +   l+++l +  ++++  + ++iDs   l +++     +e 
  gi|488601635|ref|YP_007908106.1|  83 IDK--IDIKSFSKDFFAKTVVplswldvevgLSALKKGDLLRNLFDGFEKVGDnSVLLIDSFIDLVRKTdvlggNEL 157
                                       444..333333333333222234456555443344445677777788888877567778886666222211111344 PP

                            ATPase 139 vaRei...lrqlvrvl..kklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkm 205
                                         R+    +  l +++  k++ v  +++ ++ +  ++a++ ++   ++dgviv +    +e ++R++ i+k+
  gi|488601635|ref|YP_007908106.1| 158 SWRDLvdfVTGLRKFIikKNMLVYCLMTKDV-V--GKAKEEELIS-SSDGVIVFEFLHGKEMVKRSMFIRKL 225
                                       4565411145677777634444555666663.3..3445555555.599****99999999999***99996 PP

>> MP  Viral movement protein (MP)
   #    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      22      53 ..     165     196 ..     146     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                                MP  22 lfkklkklfirknevlfkVstkeligdkdslv 53 
                                       + + l+k++i+kn ++++++tk+++g ++++ 
  gi|488601635|ref|YP_007908106.1| 165 FVTGLRKFIIKKNMLVYCLMTKDVVGKAKEEE 196
                                       556789******************88877654 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0014       8.5      21      46 ..       9      33 ..       7      48 .. 0.89
   2 ?    3.7   0.0    0.0048        29     232     291 ..     160     217 ..     150     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0014
                            PAXNEB 21 tGtpsLDklLgGGLplGsillieEdg 46
                                      tG++ +D+ + GGLp G i+l+eE g
  gi|488601635|ref|YP_007908106.1|  9 TGIDVFDSQI-GGLPSGLIFLLEEVG 33
                                      9*********.99**********976 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0048
                            PAXNEB 232 edllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieLesfagseket 291
                                       +dl+ F+++Lr ++ ++n+ + + +  +++   ++  +++ + +D+vi  e + g+e  +
  gi|488601635|ref|YP_007908106.1| 160 RDLVDFVTGLRKFIIKKNMLVYCLMTKDVV--GKAKEEELISSSDGVIVFEFLHGKEMVK 217
                                       789************999999999999999..7777788888889988888777765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1494.34
//
Query:       gi|488601636|ref|YP_007908107.1|  [L=191]
Description: hypothetical protein Asulf_02160 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   20.6   0.3    0.00046   19.9   0.3    1.5  1  DUF835    Protein of unknown function (DUF835)
     0.0012   18.3   0.2     0.0017   17.8   0.2    1.3  1  ATPase    KaiC
  ------ inclusion threshold ------
      0.059   13.7   0.0       0.76   10.1   0.1    2.1  2  DUF243    Domain of unknown function (DUF243)
      0.082   12.1   0.0       0.11   11.6   0.0    1.2  1  ALAD      Delta-aminolevulinic acid dehydratase


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 !   19.9   0.3     1e-07   0.00046      57     112 ..     106     160 ..      38     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-07
                            DUF835  57 sPtnlekltetivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkn 112
                                       +Pt +++  e   + ++ ++  ++++D+l  + l+++Fe+ lkf+ ++   + +k+
  gi|488601636|ref|YP_007908107.1| 106 DPTLMQVSIERAMDLIRTEN-RFIYLDSLSTISLYKSFETLLKFIRYITAKIRVKG 160
                                       45555554555555555555.4***********************99987776665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   3.8e-07    0.0017      49     168 ..      51     174 ..      40     191 .] 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-07
                            ATPase  49 epgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaee......kdkedleelieelaeaikeik 119
                                        +g++vt++ p  ++++ +++ G+dl+kl   ++++     e+      +       ++ d+  +  ++++a++ i+
  gi|488601636|ref|YP_007908107.1|  51 AEGIYVTLNRPYASMKKIMQKEGIDLNKLIFIDSITRQTGGEEI-----DtdrciyINSPDPTLMQVSIERAMDLIR 122
                                       679***********************998655444444333333.....2335667778889999999999999888 PP

                            ATPase 120 a..krvviDsitglayeekeavaReilrqlvrvlkklgv.Tailvsekssse 168
                                          + + +Ds+++++ +++ +++ + +r ++  ++ +g   a++  ek+ +e
  gi|488601636|ref|YP_007908107.1| 123 TenRFIYLDSLSTISLYKSFETLLKFIRYITAKIRVKGFfGALFSVEKELDE 174
                                       85467889******77777777777888888888666641566666654444 PP

>> DUF243  Domain of unknown function (DUF243)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00017      0.76      13      74 ..       4      64 ..       1      78 [. 0.71
   2 ?    1.4   0.0     0.089     4e+02      33      65 ..      97     129 ..      85     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                            DUF243 13 eeeeeeekeleqlakalkknykvvFikaPenkaleaaalalakqqaeekTviYVLskkadea 74
                                      e+++++++ +e+l++a+     v+ ikaP++k l+ ++  ++    ++   iYV  +++ ++
  gi|488601636|ref|YP_007908107.1|  4 ETTATSTNLIEELESAIASGAEVILIKAPAKKYLNVSLEITK-YLCQKAEGIYVTLNRPYAS 64
                                      45666777788899999999************9887766555.3333334599976666554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.089
                            DUF243  33 ykvvFikaPenkaleaaalalakqqaeekTviY 65 
                                        + ++i +P+++ ++ ++  ++   + e+  iY
  gi|488601636|ref|YP_007908107.1|  97 DRCIYINSPDPTLMQVSIERAMDLIRTENRFIY 129
                                       5889*******9999999888877777777777 PP

>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.5e-05      0.11     222     292 ..       8      81 ..       3      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                                       -HHHHHHHHHHHHHTT-SBEEEE.S-TTGHHHHHHHHTT-.SS-EEEE.E-HHHHHHHHHHHHTTSS-HHHHHH CS
                              ALAD 222 nsrealreveldleeGADivmvK.PalaylDiirevkeef.dlpvaay.qvSGEYamikaaaengwldekkvvl 292
                                        s++ ++e+e  ++ GA ++++K Pa  yl +  e+ + + +    +y      Ya +k+ ++++ +d +k+++
  gi|488601636|ref|YP_007908107.1|   8 TSTNLIEELESAIASGAEVILIKaPAKKYLNVSLEITKYLcQKAEGIYvTLNRPYASMKKIMQKEGIDLNKLIF 81 
                                       566678999*************99********999998875555555525678899999999999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 1059.87
//
Query:       gi|488601637|ref|YP_007908108.1|  [L=236]
Description: RecA-superfamily ATPases implicated in signal transduction [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-24   86.8   0.0    1.8e-24   86.4   0.0    1.1  1  ATPase     KaiC
    8.6e-07   28.7   1.7    6.2e-06   25.9   1.7    2.0  1  AAA_25     AAA domain
    0.00017   21.0   0.0    0.00029   20.3   0.0    1.5  1  DnaB_C     DnaB-like helicase C terminal domain
    0.00086   19.1   0.1     0.0015   18.3   0.1    1.5  1  IstB_IS21  IstB-like ATP binding protein
     0.0062   16.9   0.1     0.0098   16.3   0.1    1.4  1  AAA_16     AAA ATPase domain
  ------ inclusion threshold ------
      0.018   14.8   1.5      0.064   13.0   1.5    1.8  1  AAA_24     AAA domain
      0.018   14.9   0.0      0.027   14.4   0.0    1.3  1  ATPase_2   ATPase domain predominantly from Archaea
        0.1   12.5   0.5       0.27   11.1   0.5    1.6  1  NTPase_1   NTPase
       0.11   12.8   0.0       0.15   12.4   0.0    1.3  1  AAA_19     AAA domain
       0.12   11.8   0.6        1.1    8.6   0.6    2.1  1  RecA       recA bacterial DNA recombination protein
       0.15   11.5   0.6       0.35   10.3   0.6    1.8  1  PhoH       PhoH-like protein
       0.16   11.8   0.1       0.26   11.2   0.1    1.4  1  NACHT      NACHT domain
       0.17   12.4   0.2       0.59   10.6   0.1    2.0  2  AAA        ATPase family associated with various cellular act
       0.22   10.8   0.4       0.39    9.9   0.1    1.6  2  Rad51      Rad51
       0.24   11.1   1.2       0.38   10.4   0.6    1.6  2  AAA_30     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 !   86.4   0.0   1.5e-27   1.8e-24       2     227 ..       4     220 ..       3     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 1.5e-27
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       k g + lD+ + gG+ e++v l+tG +G GKti+a +++ +ga++ g  + + ++   +++     k++   +e++ 
  gi|488601637|ref|YP_007908108.1|   4 KFGLKRLDDAIGGGLDENTVNLVTGRSGIGKTILASHWAAEGAKN-GMGVAYLATTLVKRSCETYLKKFRF-MEDVY 78 
                                       568999**************************************9.**********999999999999876.67777 PP

                            ATPase  79 eegklaiidasesaeesaeekdkedl.eelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkk 153
                                       ++ ++ +i + ++        ++e + +++i++++  +k   +  +v D++t l +  +++ ++R+ ++ ++    k
  gi|488601637|ref|YP_007908108.1|  79 DKIHWRFIRVDAKYMMP---VTRERIeQAVITTIK--MKPEDVDMIVFDTVTDLdKALADPVLFRRVIKYMADLCYK 150
                                       77777777666665441...223333033444443..34445589*********9999******************* PP

                            ATPase 154 lgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvl 227
                                       +++Ta++++e+++  +  ++ +++e     vi Ldl   e+  +R ++i+k  +++h  + +p++It+egi+  
  gi|488601637|ref|YP_007908108.1| 151 NDITALFIEEAPMMGDWSETKNLSE----SVIFLDLLHTENGYERAMRILKKYRSSHPLEWIPYDITDEGIVFK 220
                                       *************999999999999....9*********************999*****************976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.7   5.2e-09   6.2e-06      19     157 ..       7     130 ..       2     159 .. 0.62

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.2e-09
                            AAA_25  19 ppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg 94 
                                       ++++++ ++g l +++++l++G++g GKt la+++a++ a  G             V y+++       +  l++ +
  gi|488601637|ref|YP_007908108.1|   7 LKRLDDAIGGGLDENTVNLVTGRSGIGKTILASHWAAEGAkNGM-----------GVAYLATTLVKRSCETYLKKFR 72 
                                       567889999999****************************5444...........4555554433333333333222 PP

                            AAA_25  95 ..ealrddarllvldlagveslpLfakdrggtlltadvdaleaaieeveg.vrlvviDplsralgg 157
                                         e++ d+ +++++ ++ +  +p++      ++++++   ++ +i+  ++ v+++v+D+++ +  +
  gi|488601637|ref|YP_007908108.1|  73 fmEDVYDKIHWRFIRVDAKYMMPVT-----RERIEQA---VITTIKMKPEdVDMIVFDTVTDLDKA 130
                                       2244444444445544333222221.....2234444...67777776445999999999987655 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.4e-07   0.00029       3      55 ..       4      56 ..       3     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.4e-07
                                      XSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEE CS
                                      xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  3 stgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfs 55
                                      + g+k+LD+++ +Gl ++++ ++ +r+++Gkt la + a++ a+ + ++va+  
  gi|488601637|ref|YP_007908108.1|  4 KFGLKRLDDAIgGGLDENTVNLVTGRSGIGKTILASHWAAEGAK-NGMGVAYLA 56
                                      78999**97762689************************99885.566777654 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 !   18.3   0.1   1.3e-06    0.0015      48     117 ..      22      91 ..      16     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdl 117
                                          +++G sG+GK+ la   + e++++g+ v ++ ++ + ++ ++  ++ ++ + +   ++ + + +D  
  gi|488601637|ref|YP_007908108.1|  22 TVNLVTGRSGIGKTILASHWAAEGAKNGMGVAYLATTLVKRSCETYLKKFRFMEDVYDKIHWRFIRVDAK 91 
                                       445799****************************998887777777777777776666666666666655 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   8.2e-06    0.0098      11      60 ..       9      57 ..       6     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.2e-06
                            AAA_16 11 qLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkc 60
                                      +L +a++   +    + l++G sG+GK+ l+ +++ +  k+g+ +++  +
  gi|488601637|ref|YP_007908108.1|  9 RLDDAIGGGLDEN-TVNLVTGRSGIGKTILASHWAAEGAKNGMGVAYLAT 57
                                      5666666555444.5668*****************988888766644333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.5   5.3e-05     0.064       6      78 ..      25     128 ..      20     137 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                            AAA_24   6 liyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel................ 59 
                                       l++G sgiGKT la++        g  ++++ t   +k+   + +++ + +ed++d++                   
  gi|488601637|ref|YP_007908108.1|  25 LVTGRSGIGKTILASHWaaegaknGMGVAYLATTL-VKRSCETYLKKFRFMEDVYDKIHWRfirvdakymmpvtrer 100
                                       899**************777666644444443332.22222222222223333333333336666666668888888 PP

                            AAA_24  60 .........aaeladyktlviDtidele 78 
                                                + +++d + +v+Dt+++l 
  gi|488601637|ref|YP_007908108.1| 101 ieqavittiKMKPEDVDMIVFDTVTDLD 128
                                       88889999*****************985 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.2e-05     0.027      19     118 ..      20     132 ..       7     159 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyia.l.reesiskldefie.eeeekkklekal.......... 82 
                                       +n++ +++G+ g+GKt L  + + +  + +  v y+   l +++ +++l++f +  e++ +k+   +          
  gi|488601637|ref|YP_007908108.1|  20 ENTVNLVTGRSGIGKTILASHWAAEGAKNGMGVAYLATtLvKRSCETYLKKF-RfMEDVYDKIHWRFirvdakymmp 95 
                                       6899*******************************86424144444555554.443333333333334455566555 PP

                          ATPase_2  83 ..giavpkaeleeilkeksklvfkaielllekikkkgk 118
                                          +++++a + + +k k ++v+  + +   ++ k   
  gi|488601637|ref|YP_007908108.1|  96 vtRERIEQAVI-TTIKMKPEDVDMIVFDTVTDLDKALA 132
                                       54444444444.23345555555555555555555544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00022      0.27       3     104 ..      25     124 ..      23     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-----..--EEE.EEET.T--EEEEEETT---SSEETTEEE CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggr..rigFk.ivdlasgeegiLarveakreprvgkyvv 76 
                                       ++TG++G+GKt l +  + + +++g+ v+ + t  v++  +     F+ + d+ ++ +  + rv+ak  +      v
  gi|488601637|ref|YP_007908108.1|  25 LVTGRSGIGKTILASHWAAEGAKNGMGVAYLATTLVKRSCEtyLKKFRfMEDVYDKIHWRFIRVDAKYMM-----PV 96 
                                       69*******************9******999999998544311233331556766667777777722222.....23 PP

                                       -HHHHHHHHHHHHHHHHHHH-EEEE--- CS
                          NTPase_1  77 dvesfeelalealrkalseadviviDEi 104
                                       + e++e+ ++  ++ + ++ d+iv D +
  gi|488601637|ref|YP_007908108.1|  97 TRERIEQAVITTIKMKPEDVDMIVFDTV 124
                                       3356788888888877788888888866 PP

>> AAA_19  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      0.15      10     118 ..      21     132 ..      12     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiH.rlalldfddllt 85 
                                       ++v lvt+  G GKT +  h  a+  ++g      +l+ ++ +r+++   ++ + ++   + iH r+  + +d + +
  gi|488601637|ref|YP_007908108.1|  21 NTVNLVTGRSGIGKTILASHWAAEGAKNGMG--VAYLATTLVKRSCETYLKKFRFMEDVYDKIHwRF--IRVDAKYM 93 
                                       67889*****************999999965..8999***********9999999999999999777..55555554 PP

                            AAA_19  86 ealelle.......eaeeekklqeeellivDEfqdvd.elq 118
                                       ++++  e        + + k+  + ++++ D + d+d  l+
  gi|488601637|ref|YP_007908108.1|  94 MPVTR-ErieqaviTTIKMKPE-DVDMIVFDTVTDLDkALA 132
                                       44333.1344655422222333.455888888888885444 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6   0.00096       1.1      37      88 ..       6      56 ..       2     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00096
                                      S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                              RecA 37 GslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafid 88
                                      G   ld a+G GGl +  +  + G    Gkt la h  ae  k+g  +a++ 
  gi|488601637|ref|YP_007908108.1|  6 GLKRLDDAIG-GGLDENTVNLVTGRSGIGKTILASHWAAEGAKNGMGVAYLA 56
                                      5567999***.********************************998888764 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   0.00029      0.35      16      46 ..      18      48 ..       9     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                                      HHH-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 16 lkkndivfaiGpaGtGKtylavalavealkk 46
                                      l++n++  ++G++G GKt la   a+e  k+
  gi|488601637|ref|YP_007908108.1| 18 LDENTVNLVTGRSGIGKTILASHWAAEGAKN 48
                                      5689999****************99987776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00022      0.26       4      26 ..      25      47 ..      22      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      EEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  4 ilqGeaGsGKTtLlqklalawae 26
                                      +++G++G+GKT+L+ + a + a+
  gi|488601637|ref|YP_007908108.1| 25 LVTGRSGIGKTILASHWAAEGAK 47
                                      799**********9987766555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00049      0.59       2      38 ..      25      73 ..      24     133 .. 0.63
   2 ?   -1.6   0.0       2.8   3.3e+03      54      68 ..     171     184 ..     150     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00049
                                      EEESSTTSSHHHHHHHHHHH..........HTHEEEEEETTTCSSS..S CS
                               AAA  2 llyGppGtGKTllakavake..........lgvefleisgsellsk..y 38
                                      l++G  G+GKT+la+  a e          l +++++ s+ + l+k  +
  gi|488601637|ref|YP_007908108.1| 25 LVTGRSGIGKTILASHWAAEgakngmgvayLATTLVKRSCETYLKKfrF 73
                                      789***************9976666444332355666666666655552 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                                       HHTSTSEEEEEETGG CS
                               AAA  54 kekakpsilfiDEid 68 
                                       k+  + s++f+D ++
  gi|488601637|ref|YP_007908108.1| 171 KNL-SESVIFLDLLH 184
                                       333.46899998655 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00033      0.39      18      55 ..       2      39 ..       1      52 [. 0.91
   2 ?   -3.1   0.0       3.1   3.7e+03     124     142 ..     107     125 ..      79     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlch 55
                                      +l  G k+lD+ +gGG++  ++  + G ++ Gkt l+ 
  gi|488601637|ref|YP_007908108.1|  2 KLKFGLKRLDDAIGGGLDENTVNLVTGRSGIGKTILAS 39
                                      677899****************************9875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.1
                                       THHHHHHS-EEEEEEETTT CS
                             Rad51 124 aaallaedkfallivDsvt 142
                                       ++++++ + + +++ D+vt
  gi|488601637|ref|YP_007908108.1| 107 TTIKMKPEDVDMIVFDTVT 125
                                       4567888888888888887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00032      0.38      17      55 ..      20      58 ..      12      63 .. 0.90
   2 ?   -2.2   0.0       2.4   2.9e+03      88     103 ..     151     167 ..     121     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrviglApt 55
                                      ++ v ++tG+ G GKt + ++ ++  +++g+ v+ lA t
  gi|488601637|ref|YP_007908108.1| 20 ENTVNLVTGRSGIGKTILASHWAAEGAKNGMGVAYLATT 58
                                      56799*****************99999999******998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.4
                            AAA_30  88 pg.tllivDEagmvdtk 103
                                       ++ t l + Ea m++ +
  gi|488601637|ref|YP_007908108.1| 151 NDiTALFIEEAPMMGDW 167
                                       34478899999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.63u 0.41s 00:00:01.04 Elapsed: 00:00:00.57
# Mc/sec: 1250.31
//
Query:       gi|488601638|ref|YP_007908109.1|  [L=151]
Description: Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-39  135.3   0.1    1.3e-39  135.2   0.1    1.0  1  AIRC      AIR carboxylase
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.54   10.0   0.0    1.9  2  CobS_N    Cobaltochelatase CobS subunit N terminal


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 !  135.2   0.1   1.4e-43   1.3e-39       3     146 ..       4     143 ..       2     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 1.4e-43
                                       EEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS- CS
                              AIRC   3 giimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlP 79 
                                       ++imGS+ D++++kk+a+ l+ +g+++e++v+Sah+tp ++le+++e e+++  v++++AG++++L+g+v ++tt P
  gi|488601638|ref|YP_007908109.1|   4 ILIMGSKADINFCKKIADKLAFFGIDCEMKVASAHKTPMRVLEIIREFENED-VVFVTVAGRSNALSGFVDANTTKP 79 
                                       68**********************************************9975.7*********************** PP

                                       EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHH CS
                              AIRC  80 VigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelk 146
                                       Vi++P+ s+++ g+d +lS+++mPsgv+ + v   +++n+al+ a+i+++k+e++++k+ ey+ ++k
  gi|488601638|ref|YP_007908109.1|  80 VIACPPVSESFAGMD-ILSSLRMPSGVAPMVVL--EPENCALAVAKIFGIKNENIRKKILEYQVNKK 143
                                       ********9999997.7899***********99..***************************98876 PP

>> CobS_N  Cobaltochelatase CobS subunit N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   6.1e-05      0.54      15      24 ..      25      34 ..      24      36 .. 0.89
   2 ?   -1.0   0.0      0.16   1.5e+03      11      18 ..     119     126 ..     116     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.1e-05
                            CobS_N 15 vFGIDsDmeV 24
                                       FGID++m+V
  gi|488601638|ref|YP_007908109.1| 25 FFGIDCEMKV 34
                                      5********9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.16
                            CobS_N  11 svRevFGI 18 
                                        v + FGI
  gi|488601638|ref|YP_007908109.1| 119 AVAKIFGI 126
                                       58899**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 822.81
//
Query:       gi|488601639|ref|YP_007908110.1|  [L=60]
Description: hypothetical protein Asulf_02163 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-27   93.5   6.7    8.9e-27   93.3   6.7    1.0  1  DUF5350   Family of unknown function (DUF5350)


Domain annotation for each model (and alignments):
>> DUF5350  Family of unknown function (DUF5350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   6.7     5e-31   8.9e-27       1      56 [.       1      56 [.       1      57 [. 0.98

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 5e-31
                           DUF5350  1 MGKTGsveWvkvKgrkgqirlVpkkegekkkpGPnQrfkssgkkrrikrrsakaiv 56
                                      MGKTG+++W+++Kgrk+q+rlVp k++++k +GPnQ+++s+g++rr+ +rs+k+i+
  gi|488601639|ref|YP_007908110.1|  1 MGKTGTTTWIRIKGRKDQVRLVPGKWQHYKPTGPNQKYDSKGRRRRRLKRSQKSIL 56
                                      *****************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.33s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 350.95
//
Query:       gi|488601640|ref|YP_007908111.1|  [L=113]
Description: hypothetical protein Asulf_02164 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-15   55.2   0.0    5.4e-15   54.9   0.0    1.1  1  Cupin_2          Cupin domain
    1.1e-08   34.8   0.0    1.6e-08   34.3   0.0    1.2  1  Cupin_1          Cupin
    4.1e-08   33.2   0.0    4.8e-08   33.0   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
    3.1e-05   24.1   0.1      4e-05   23.7   0.1    1.3  1  CENP-C_C         Mif2/CENP-C like
    0.00033   20.6   0.1    0.00038   20.4   0.1    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
     0.0026   17.6   0.1     0.0037   17.1   0.1    1.3  1  Cupin_7          ChrR Cupin-like domain
     0.0029   17.3   0.2     0.0066   16.1   0.1    1.8  1  Cupin_3          Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.023   14.6   0.2       0.17   11.8   0.2    2.0  1  DUF386           YhcH/YjgK/YiaL
      0.047   14.0   0.0      0.063   13.6   0.0    1.1  1  Pirin_C          Pirin C-terminal cupin domain
      0.051   13.3   0.1      0.075   12.8   0.1    1.2  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 !   54.9   0.0     3e-18   5.4e-15       2      69 ..      32      99 ..      31     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3e-18
                                      EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                           Cupin_2  2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllv 69
                                      +ve+p G++ + h+H+ ++e+fy+l+Ge++l +++ e++ ++Gd++++++   H+++N ++  +++lv
  gi|488601640|ref|YP_007908111.1| 32 MVEIPAGATVKKHYHRKQTEVFYILKGEAKLGIEDTEYDAKEGDIFLCKPESIHWVVNSSQNSFKVLV 99
                                      799**********************************************************9999997 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0     9e-12   1.6e-08      34     121 ..      29     108 ..      14     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 9e-12
                                       EEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEE CS
                           Cupin_1  34 saarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavai 110
                                       ++ +v + +g+ +  hyh + te++y+l+Ge+ +g+  ++        + +eGd+f   +  +h+++ns  ++ + +
  gi|488601640|ref|YP_007908111.1|  29 FVQMVEIPAGATVKKHYHRKQTEVFYILKGEAKLGIEDTEY-------DAKEGDIFLCKPESIHWVVNSS-QNSFKV 97 
                                       34556669*************************99988886.......799******************7.999*** PP

                                       EEEESSSTT-E CS
                           Cupin_1 111 vvfdtnnpgnq 121
                                        vf+ n ++n 
  gi|488601640|ref|YP_007908111.1|  98 LVFKYNWEEND 108
                                       ***98877765 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 !   33.0   0.0   2.7e-11   4.8e-08      16      78 ..      41     104 ..      35     113 .] 0.87

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.7e-11
                                       EEEETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE-- CS
                      AraC_binding  16 fpphvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfeg 78 
                                       +++h h  + ++ y+++G+++l +++ +yd+++Gd+fL +p+ +H    +s+++++  +++++ 
  gi|488601640|ref|YP_007908111.1|  41 VKKHYHRkQTEVFYILKGEAKLGIEDTEYDAKEGDIFLCKPESIHWVVNSSQNSFKVLVFKYNW 104
                                       578999989************************************9999999888888777665 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 !   23.7   0.1   2.2e-08     4e-05      16      73 ..      32      89 ..      18     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.2e-08
                                      EEEE-TCCCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE CS
                          CENP-C_C 16 ilkLppgaeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieN 73
                                      ++++p+ga+ kk+  +k+t vFy+++G+ +  +++t++ + +g++F+    +   + N
  gi|488601640|ref|YP_007908111.1| 32 MVEIPAGATVKKHYHRKQTEVFYILKGEAKLGIEDTEYDAKEGDIFLCKPESIHWVVN 89
                                      89****999999999999****************************875555555555 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.1e-07   0.00038      55     133 ..      20      98 ..       7     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                   MannoseP_isomer  55 evldegeryqvkritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiple 131
                                       +v d +e+  v+++++  g+++  + h+ ++e + ++kG ak+ ++d+++  ke +    + ++ih + n  + +++
  gi|488601640|ref|YP_007908111.1|  20 RVFDISETSFVQMVEIPAGATVKKHYHRKQTEVFYILKGEAKLGIEDTEYDAKEGDIFLCKPESIHWVVNSSQNSFK 96 
                                       45677777778888887777665555555579999********************9999999*******99988777 PP

                   MannoseP_isomer 132 li 133
                                       ++
  gi|488601640|ref|YP_007908111.1|  97 VL 98 
                                       65 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.1e-06    0.0037      21      79 ..      25      88 ..       9     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                                      SS-EEEEEEEE-TTEE---EE-TT.-EEEEEEEEE..EEETTEEE..ETTEEEEE-TT-EE--E CS
                           Cupin_7 21 ekaratslvryapgsafsahkHpg.geeilVLeGv..fsdeegdy..paGsylrnppgsshapv 79
                                      ++++ +++v++ +g+  ++h H + +e +++L+G+  +  e+ +y  ++G+ ++  p+s h  v
  gi|488601640|ref|YP_007908111.1| 25 SETSFVQMVEIPAGATVKKHYHRKqTEVFYILKGEakLGIEDTEYdaKEGDIFLCKPESIHWVV 88
                                      345699****************75277788****733557888887789999999999999776 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.7e-06    0.0066      20      60 ..      44      83 ..      25     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.7e-06
                                      EECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                           Cupin_3 20 rltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgl 60
                                      + + +++E +yil+Ge k+   +  ++  ++GD++ +++ +
  gi|488601640|ref|YP_007908111.1| 44 HYHRKQTEVFYILKGEAKLGI-EDTEYDAKEGDIFLCKPES 83
                                      6667889**************.9999***********9976 PP

>> DUF386  YhcH/YjgK/YiaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   9.5e-05      0.17      89     146 ..      39     101 ..       7     103 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.5e-05
                                       GGGS---BTTTTBEEE......S--TTEEEEEE-TTEEEEE-TT--EEE.....B--B-EEEEEE CS
                            DUF386  89 eelkeeydeekDiafy......aegeeessvtlkpgdfaiffPedaHrp.eaekekekvkKvVvK 146
                                        ++k+ y+ ++  +fy      + g e++  ++k+gd++++ Pe +H + +  +++++ k +V+K
  gi|488601640|ref|YP_007908111.1|  39 ATVKKHYHRKQTEVFYilkgeaKLGIEDTEYDAKEGDIFLCKPESIHWVvN--SSQNSFKVLVFK 101
                                       444444444444444444333333345666666666666666666666632..344456666666 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.5e-05     0.063       4      68 ..      33     100 ..      30     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                                       EEE-TT-EEEEE--TT-EEEEEEEES-EEESSTTEEE-TTEEEEE-...SSSEEEEE--SS-EEEEEE CS
                           Pirin_C   4 ltleagaelelplpegleaavyvleGelevggerseieeeqlavlg...dgdslvvkaeekgarvlLl 68 
                                       ++++aga+++     + + + y+l+Ge+++g e++e ++++  ++    ++ + vv++++++ +vl++
  gi|488601640|ref|YP_007908111.1|  33 VEIPAGATVKKHYHRKQTEVFYILKGEAKLGIEDTEYDAKEGDIFLckpESIHWVVNSSQNSFKVLVF 100
                                       6899***********************99988886555555544444366666666666688888876 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.2e-05     0.075      96     151 ..      50     105 ..      37     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                              EutQ  96 deidyvieGrldvlidGrkvvaeaGdviliPkgskiefsvtde.akflyvayPadwq 151
                                        e+ y++ G+ ++ i+  +  a+ Gd+ ++ k  +i++ v ++   f  +++  +w+
  gi|488601640|ref|YP_007908111.1|  50 TEVFYILKGEAKLGIEDTEYDAKEGDI-FLCKPESIHWVVNSSqNSFKVLVFKYNWE 105
                                       6999**********************7.56788899999876515688889999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 625.60
//
Query:       gi|488601641|ref|YP_007908112.1|  [L=233]
Description: putative phosphoesterase, SbcD/Mre11-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-06   28.6   0.0    2.1e-06   28.0   0.0    1.3  1  Metallophos_2   Calcineurin-like phosphoesterase superfamily 
    3.3e-05   24.5   2.6    4.3e-05   24.1   0.2    1.8  2  Metallophos     Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
       0.05   13.9   0.0      0.087   13.1   0.0    1.3  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f


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 !   28.0   0.0   3.5e-10   2.1e-06       4     110 ..      21     158 ..      19     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.5e-10
                     Metallophos_2   4 aiiSDlH..............snldaleavlealkevgvdaiihaGDleeeep...........e.vleellelapv 54 
                                       a+i+DlH              +  + +++v +++++ gv ++i+aGD+ + e+           + ++ee+ +l ++
  gi|488601641|ref|YP_007908112.1|  21 AVIADLHlgieqtaygviprlQIDEVVDRVRDIFERYGVKRLIVAGDM-KHEFsknmpyewddvTyFIEEISKLGEL 96 
                                       799999999999999999887666778899*****************6.33333445666654434777777777** PP

                     Metallophos_2  55 laVrGNnDeevveedvlreaaelgtdl.....peeaelel.agekvlliHgdpl.gvkdalae 110
                                       ++VrGN+D +++   +++   +l++++       +  +e+ +g+k+ + H++p  + ++++a+
  gi|488601641|ref|YP_007908112.1|  97 RVVRGNHD-NYLLAILAKYDIPLEREIrigewVIAHGHEImDGRKIIIGHEHPViRIRQDFAQ 158
                                       ********.333333333333333333223221222222246888888888876766666555 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   7.3e-09   4.3e-05       4      78 ..      21     106 ..      20     125 .. 0.72
   2 ?    0.1   0.2      0.16   9.5e+02     161     177 ..     126     143 ..     110     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7.3e-09
                                       EEEESBTB.....TTCCTHHHHHHHHHHHH...HHHTTESEEEEESTSSSSS......HHHHHHHHHHHHHHHHTSE CS
                       Metallophos   4 lvigDlHl.....algggqlddllkllddl...lreekpdlvllaGDlvdrg......dlekellellaalvkypip 66 
                                       +vi+DlHl     a+g+ +  ++++++d++    ++ ++  +++aGD  ++       +++  + +++++  k+   
  gi|488601641|ref|YP_007908112.1|  21 AVIADLHLgieqtAYGVIPRLQIDEVVDRVrdiFERYGVKRLIVAGDMKHEFsknmpyEWDD-VTYFIEEISKL-GE 95 
                                       79*********996666666666666655522266699999******999988999996666.66666666665.44 PP

                                       EEEEC-TTSCHH CS
                       Metallophos  67 vylllGNHegfe 78 
                                       + +++GNH+  +
  gi|488601641|ref|YP_007908112.1|  96 LRVVRGNHD-NY 106
                                       8********.33 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                                       SEEEEEESSESS.CSSSC CS
                       Metallophos 161 dwvivlgHsply.rgsgy 177
                                       +wvi++gH  +  r++  
  gi|488601641|ref|YP_007908112.1| 126 EWVIAHGHEIMDgRKIII 143
                                       677888877776433333 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.087      73     112 ..      43      80 ..      40      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                    baeRF_family10  73 lkevAellaklleergverlvlgGdeeetaalldrlpkal 112
                                       ++ev++ +++++e+ gv+rl+++Gd  +++++ +++p ++
  gi|488601641|ref|YP_007908112.1|  43 IDEVVDRVRDIFERYGVKRLIVAGD--MKHEFSKNMPYEW 80 
                                       689*********************8..4456666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1331.72
//
Query:       gi|488601642|ref|YP_007908113.1|  [L=874]
Description: ATP dependent helicase, Lhr family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  188.4   0.0    1.9e-55  187.6   0.0    1.4  1  DEAD_assoc  DEAD/H associated
    1.4e-29  103.1   0.5    5.2e-28   98.0   0.0    3.1  3  DEAD        DEAD/DEAH box helicase
    2.8e-18   66.3   0.2      4e-17   62.6   0.1    2.7  2  Helicase_C  Helicase conserved C-terminal domain
    7.3e-11   42.4   0.1    2.1e-10   40.9   0.0    1.8  2  ResIII      Type III restriction enzyme, res subunit
     0.0067   15.5   0.0      0.014   14.5   0.0    1.4  1  T2SSE       Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.034   13.3   0.1      0.071   12.3   0.1    1.5  1  TIP49       TIP49 P-loop domain
      0.038   13.8   0.1       0.15   11.8   0.0    1.9  2  AAA_11      AAA domain
      0.047   13.9   1.6        0.7   10.1   0.2    2.9  2  E2_bind     E2 binding domain
      0.052   13.9   0.0       0.51   10.7   0.0    2.4  2  AAA_19      AAA domain
      0.067   12.6   0.0       0.17   11.3   0.0    1.6  1  PhoH        PhoH-like protein
      0.096   12.5   2.3        8.3    6.2   0.0    3.1  4  Bac_DnaA    Bacterial dnaA  protein
        0.1   12.7   0.5         14    5.9   0.0    3.6  4  DUF4327     Domain of unknown function (DUF4327)
       0.13   12.2   0.0        5.7    6.9   0.0    2.5  2  SPA         Stabilization of polarity axis
       0.31   11.3   1.3        7.3    6.9   0.1    3.5  3  AAA_22      AAA domain


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.0   1.5e-58   1.9e-55       1     191 []     651     838 ..     651     838 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 1.5e-58
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +Ptdr++l+E+f+de g+  +v+hs+ Grr+n a++++la+r   + +++v++a+nD+g++l lp +++l  ++de+
  gi|488601642|ref|YP_007908113.1| 651 IPTDRRFLIENFQDE-GNECYVFHSLIGRRANSAISRVLAYRAGLKKNCSVKIAVNDNGFMLKLPRRKVL--SFDEI 724
                                       8***********996.5899******************************************99988886..59*** PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvar.eyp.dfpllleav 152
                                       lel++ +++eedl +al+++e+++rrFr+vA r+l+++r+y g++k++w+q+l+a+ Ll+ ++ ++  +fp+l+e++
  gi|488601642|ref|YP_007908113.1| 725 LELMNVENFEEDLIKALDRTEILRRRFRHVAVRSLMVLRNYLGREKSVWRQQLSADSLLRLIKkKFGrNFPVLKETY 801
                                       *************************************************************8736779********* PP

                        DEAD_assoc 153 revledqlDlerlaellrriaageirvvevetprpSpfA 191
                                       re++ed +Dl ++ ++l++++++ei++++   p pSpfA
  gi|488601642|ref|YP_007908113.1| 802 REIMEDSMDLGNAIDFLTKLEKKEIKLTR--IPFPSPFA 838
                                       *****************************..*******9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   4.1e-31   5.2e-28       1     170 [.      43     227 ..      43     235 .. 0.84
   2 ?    1.1   0.0      0.22   2.8e+02      38     103 ..     280     351 ..     274     424 .. 0.77
   3 ?   -0.8   0.0      0.88   1.1e+03     122     152 ..     839     869 ..     822     872 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 4.1e-31
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       t+ Q++ai ++l+ +++l++ +TGsGKTla++++ ++ +++     + +++  +l+v+P+++L +++ +nl++ +k+
  gi|488601642|ref|YP_007908113.1|  43 TPPQKHAIVEALNRNNILISSPTGSGKTLAAFLASISMLIDLaeknRLEDKVYTLYVSPLKALNNDIRKNLEEPLKE 119
                                       788*********************************99998899888999**************************6 PP

                                       ST............SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHT CS
                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                              DEAD  74 id............lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldq 136
                                       i             +r+ + +g+++ ++ ++++++ ++i+++tp+ l  +l + k++  ls++ fl++DE++ + ++
  gi|488601642|ref|YP_007908113.1| 120 IYeiaeskglklqkIRIGVRTGDTDPSERQRQVRKPPHILITTPETLSIILVSPKFSkhLSNLDFLIVDEIHAIAEN 196
                                       444667778555445555556677777777788788*************7744444445****************** PP

                                       TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 137 gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +++ +++  +++l++i++  +     i lSAT++
  gi|488601642|ref|YP_007908113.1| 197 KRGTHLSLSIERLQEIQEG-R--MVRIGLSATIH 227
                                       *************666544.4..348*******9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.22
                                       HHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEE.EEETTSSHHHHHHHHHTT.CSEEEE CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
                              DEAD  38 ivyet...kgktgpkalivePtreLaeqtlnnlkkfkky.idlrvl.liiggvaardqlskldng.vdivvg 103
                                       ++y+t     k+ + +li + tr+ +e ++ nlkk +     ++++ + ++++ + +  ++l+ng +++vv+
  gi|488601642|ref|YP_007908113.1| 280 KLYNTladLVKSSKTTLIFTNTRSATERVVYNLKKKLGSdFPIKAHhSSLSKNVRLEVEDELKNGeLRCVVS 351
                                       555556654567778999999******999999888774333455435555555556666666666666665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.88
                                       EEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 122 vrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                       ++++Vl E d +l +++++ i+++ +++ q 
  gi|488601642|ref|YP_007908113.1| 839 LNIFVLGEEDIVLMEDRKKVIQSLYEKITQV 869
                                       6789*******************99999765 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.7     9e+02      36      62 ..     129     155 ..      78     172 .. 0.76
   2 !   62.6   0.1   3.1e-20     4e-17       4     108 ..     279     387 ..     276     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.7
                                       HHHTTSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  36 lekkgikvavlhgelpqnereeileqf 62 
                                       l+ ++i++ v +g++  +er++ +++ 
  gi|488601642|ref|YP_007908113.1| 129 LKLQKIRIGVRTGDTDPSERQRQVRKP 155
                                       34558****************998876 PP

  == domain 2  score: 62.6 bits;  conditional E-value: 3.1e-20
                                       HHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                        Helicase_C   4 eallell.kleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                       e+l++ l +l ++ +++lif+nt++  e+v + l+kk   ++ + ++h++l++n r+e+ ++ ++ge +++++++ +
  gi|488601642|ref|YP_007908113.1| 279 EKLYNTLaDLVKSSKTTLIFTNTRSATERVVYNLKKKlgsDFPIKAHHSSLSKNVRLEVEDELKNGELRCVVSSTSL 355
                                       567788778899*************8887555566667888************************************ PP

                                       TSSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                       e Gidi  ++lV+ ++ p+++ ++ qriGR g
  gi|488601642|ref|YP_007908113.1| 356 ELGIDIGYIDLVVLLGSPKSINRALQRIGRSG 387
                                       ******************************87 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   1.7e-13   2.1e-10       5     169 ..      43     226 ..      38     228 .. 0.74
   2 ?   -3.4   0.1       6.5   8.4e+03      99     118 ..     289     308 ..     263     334 .. 0.57

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.7e-13
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHG CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleef 74 
                                        + Q++ai + l      +++++li  +TG+GKTl a ++ i  l   ++++       +l + p k+l +  ++++
  gi|488601642|ref|YP_007908113.1|  43 TPPQKHAIVEAL------NRNNILISSPTGSGKTLAAfLASISMLIDLAEKNrledkvYTLYVSPLKALNNDIRKNL 113
                                       566777666665......5789**************965555555554444478899999***************** PP

                                       GGGTGG...............GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEE CS
                            ResIII  75 kkflseayke...........igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviii 138
                                       ++ l+e y+              ++ +gd++ +  +++ ++  +il+tt ++l+ ++    + + ++  ++ d++i+
  gi|488601642|ref|YP_007908113.1| 114 EEPLKEIYEIaeskglklqkiRIGVRTGDTDPSerQRQVRKPPHILITTPETLSIIL---VSPKFSKHLSNLDFLIV 187
                                       9999999866444344433332222555555448888889999**************...5566666666777**** PP

                                       ETGGGTTS.T.......TTHHHHHT---..SEEEEEESS- CS
                            ResIII 139 DEaHrlgakk.......swreilekfke..avllglTATp 169
                                       DE H ++++k       s+++ l+ ++e   v++gl+AT+
  gi|488601642|ref|YP_007908113.1| 188 DEIHAIAENKrgthlslSIER-LQEIQEgrMVRIGLSATI 226
                                       ********9655555555555.455555669********7 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.5
                                       .....-SEEEEEHHHHHHTH CS
                            ResIII  99 kdstnkkilvttiqsldads 118
                                        +s+++ +++t++ s++++ 
  gi|488601642|ref|YP_007908113.1| 289 VKSSKTTLIFTNTRSATERV 308
                                       25555556666555555444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.1e-05     0.014     113     147 ..      41      74 ..      36      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                             T2SSE 113 alkekiaevlrkavrerglilvsGgTgsGKttlly 147
                                       ++++ +++++ +a  +r +il+s +TgsGKt  + 
  gi|488601642|ref|YP_007908113.1|  41 SFTPPQKHAIVEA-LNRNNILISSPTGSGKTLAAF 74 
                                       5566677777777.6899*************8653 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.6e-05     0.071      51     167 ..      57     180 ..      50     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrksigvrikeekevleGevvelev 127
                                         +L++ p+g+Gkt  a   s ++  d+        +vy+l v+   +l + +rk +   +ke+ e+ e +  +l+ 
  gi|488601642|ref|YP_007908113.1|  57 NNILISSPTGSGKTLAAFLASISMLIDLAEKNRLEDKVYTLYVSPLKALNNDIRKNLEEPLKEIYEIAESKGLKLQK 133
                                       579***********99988887777777777778899********************************99887765 PP

                                       ........-SSS-....TTS--EEEEEE-SS-EEEEEE-HHHHHHHH CS
                             TIP49 128 ee.....aenpls..kekkikevkitlktakeekklklgskiaeell 167
                                        +      +++ s  +++  k  +i + t ++ + + +++k  ++l+
  gi|488601642|ref|YP_007908113.1| 134 IRigvrtGDTDPSerQRQVRKPPHILITTPETLSIILVSPKFSKHLS 180
                                       54111112222222234444555666666666666666666666665 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   0.00012      0.15       5      97 ..      45     140 ..      41     165 .. 0.59
   2 ?   -0.5   0.0      0.69   8.8e+02     190     225 ..     150     189 ..     103     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                            AAA_11   5 sqreaiksalseseitliqGPPGtgKT.ktivellsqll...srrkseeeksakpriLvCapSNaAvDellerllr. 76 
                                        q++ai +al++++  li+ P G+gKT  + ++ +s+l+   +    +++ + k   L+ +p  a  +++ + l + 
  gi|488601642|ref|YP_007908113.1|  45 PQKHAIVEALNRNN-ILISSPTGSGKTlAAFLASISMLIdlaE----KNRLEDKVYTLYVSPLKALNNDIRKNLEEp 116
                                       69************.7***********8677777777763330....455555555555555554444444444443 PP

                            AAA_11  77 ...glldsegekykpkivRvgnee 97 
                                              +e +  k++ +R+g   
  gi|488601642|ref|YP_007908113.1| 117 lkeIYEIAESKGLKLQKIRIGVRT 140
                                       321112223333344444444444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.69
                            AAA_11 190 eevldeaeivltT...lsga.gsklleklakkfdvviIDE 225
                                       ++v +  +i +tT   ls++  s++++k   + d +i+DE
  gi|488601642|ref|YP_007908113.1| 150 RQVRKPPHILITTpetLSIIlVSPKFSKHLSNLDFLIVDE 189
                                       556666666666522255444688999999999******9 PP

>> E2_bind  E2 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00055       0.7      28      59 ..      90     121 ..      69     134 .. 0.80
   2 ?    1.3   0.1       0.3   3.8e+02      29      55 ..     290     316 ..     272     338 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00055
                           E2_bind  28 lstegktLymqappsLeeatrpNLekkLkeLv 59 
                                       l+++  tLy++  ++L++  r+NLe +Lke+ 
  gi|488601642|ref|YP_007908113.1|  90 LEDKVYTLYVSPLKALNNDIRKNLEEPLKEIY 121
                                       5667779***********************83 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                           E2_bind  29 stegktLymqappsLeeatrpNLekkL 55 
                                       +++++tL + +  s  e+   NL+kkL
  gi|488601642|ref|YP_007908113.1| 290 KSSKTTLIFTNTRSATERVVYNLKKKL 316
                                       446677777777777777777777777 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0004      0.51       1     114 [.      46     193 ..      46     199 .. 0.60
   2 ?   -0.2   0.0      0.89   1.1e+03      42      75 ..     292     328 ..     276     496 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrv.....lkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatT 71 
                                       q++a+  al+++++l+  + G+GKT       + + + l+++++ ++    l v++ +   + +r++l   +++ + 
  gi|488601642|ref|YP_007908113.1|  46 QKHAIVeALNRNNILISSPTGSGKTLAaflasISMLIDLAEKNRLEDKVYTLYVSPLKALNNDIRKNL---EEPLKE 119
                                       6777755******************6421111444444444444444456666777766677777777...455555 PP

                            AAA_19  72 iHrlal..................................ldfddlltealelle..........eaeeekklqeee 104
                                       i ++a+                                  +                        + + +k+l + +
  gi|488601642|ref|YP_007908113.1| 120 IYEIAEskglklqkirigvrtgdtdpserqrqvrkpphilI-------------TtpetlsiilvSPKFSKHLSNLD 183
                                       55554445577777777777777777666666665555421.............02222223333456777786666 PP

                            AAA_19 105 llivDEfqdv 114
                                        livDE+  +
  gi|488601642|ref|YP_007908113.1| 184 FLIVDEIHAI 193
                                       8888888766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.89
                            AAA_19  42 peeillvaftgrAakelrerlaalgae...atTiHrl 75 
                                        ++ l+ + t+ A++++  +l++ +++   ++  H+ 
  gi|488601642|ref|YP_007908113.1| 292 SKTTLIFTNTRSATERVVYNLKKKLGSdfpIKAHHSS 328
                                       4678888999999888877775433334556666643 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.17       9      46 ..      47      83 ..      40      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      HHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH  9 QkeylealkkndivfaiGpaGtGKtylavalavealkk 46
                                       ++++eal++n+i++   p+G+GKt+ a  + +++l +
  gi|488601642|ref|YP_007908113.1| 47 KHAIVEALNRNNILI-SSPTGSGKTLAAFLASISMLID 83
                                      345788999988865.68*************9999865 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.8   3.6e+03      34      58 ..      56      82 ..      46     121 .. 0.66
   2 ?    6.2   0.0    0.0065       8.3      90     114 ..     174     198 ..     171     220 .. 0.85
   3 ?    4.5   0.1     0.021        27      95     155 ..     255     320 ..     245     338 .. 0.77
   4 ?   -3.7   0.0       6.8   8.7e+03      70      97 ..     728     753 ..     725     757 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.8
                                      S--EEEE-SSSSSHH..HHHHHHHHHH CS
                          Bac_DnaA 34 ynPlfiygevGlGkt..HLlkaignev 58
                                       n ++i +++G Gkt    l +i+  +
  gi|488601642|ref|YP_007908113.1| 56 RNNILISSPTGSGKTlaAFLASISMLI 82
                                      588999999999999333566666543 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0065
                                       HHHHHHTT-SEEEEE-GGGGTT-HH CS
                          Bac_DnaA  90 efkeklrkvDvLliDDiqflagkek 114
                                       +f ++l ++D L++D+i+ +a+ ++
  gi|488601642|ref|YP_007908113.1| 174 KFSKHLSNLDFLIVDEIHAIAENKR 198
                                       7999***************997654 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.021
                                       HTT-SEEEEE-GGGG..TT-HHHHHHHHHHHHHHHTTT-E.EEEEESS-TTT..-SS--HHHHHHH CS
                          Bac_DnaA  95 lrkvDvLliDDiqfl..agkektqeelfhtfnalleegkq.vvlssDrsPke..leeledrlrsrf 155
                                       l+ +D+ +i  ++++  ++ e++ e+l+ t+  l++++k  ++++  rs +e  + +l+++l s f
  gi|488601642|ref|YP_007908113.1| 255 LKPIDIKVISPVKDFfrESSEQISEKLYNTLADLVKSSKTtLIFTNTRSATErvVYNLKKKLGSDF 320
                                       567899999999855224568999***********9988537888888765533566777766665 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 6.8
                                       EEHHHHHHHHHHHHHTT-HHHHHHHHTT CS
                          Bac_DnaA  70 ltaeeFlnelvkalrdkkaeefkeklrk 97 
                                       ++ e+F ++l+kal  +++  +++++r+
  gi|488601642|ref|YP_007908113.1| 728 MNVENFEEDLIKALDRTEI--LRRRFRH 753
                                       6779999999999976654..5555555 PP

>> DUF4327  Domain of unknown function (DUF4327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.1   1.3e+03      40      57 ..     175     192 ..     173     197 .. 0.83
   2 ?    5.9   0.0     0.011        14       3      31 ..     599     627 ..     597     633 .. 0.88
   3 ?    2.0   0.0      0.18   2.4e+02      47      67 .]     716     736 ..     707     736 .. 0.82
   4 ?   -3.4   0.0       8.7   1.1e+04      24      44 ..     758     777 ..     756     780 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.1
                           DUF4327  40 vekeLeendfllrDriad 57 
                                       + k L + dfl+ D+i  
  gi|488601642|ref|YP_007908113.1| 175 FSKHLSNLDFLIVDEIHA 192
                                       56889**********975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                           DUF4327   3 iekiqeevrsLvekglvsrqqpiyklaky 31 
                                       i+ +++ev++L+ ++l++ +++++ l k 
  gi|488601642|ref|YP_007908113.1| 599 IQRFRREVEELLGSELLEFEDAVWYLRKK 627
                                       789*********************99764 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.18
                           DUF4327  47 ndfllrDriadLlgvEeWded 67 
                                          l  D+i +L++vE+ +ed
  gi|488601642|ref|YP_007908113.1| 716 RKVLSFDEILELMNVENFEED 736
                                       556667***********9998 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 8.7
                           DUF4327  24 piyklakyipareWaavekeL 44 
                                       ++++l +y++  e +++ ++L
  gi|488601642|ref|YP_007908113.1| 758 SLMVLRNYLGR-EKSVWRQQL 777
                                       56777777776.777777777 PP

>> SPA  Stabilization of polarity axis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0045       5.7       9      57 ..      40      89 ..      37     113 .. 0.81
   2 ?    2.2   0.0      0.13   1.6e+02      36      87 ..     430     480 ..     425     486 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0045
                               SPA  9 ekftpeiillinalltskriivlstkasadevsefvLalsnlisp.agdv 57
                                      + ftp+  + i + l++  i++ s + s ++++ f  ++s+li   ++++
  gi|488601642|ref|YP_007908113.1| 40 RSFTPPQKHAIVEALNRNNILISSPTGSGKTLAAFLASISMLIDLaEKNR 89
                                      57899999999999*****************************9832222 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                               SPA  36 sadevsefvLalsnlispagdvlrgfknnsfPyvdlseldalekvpgyIvGv 87 
                                       + d ++++v  + +  +   d   ++ ++s+Py +l + d++ +v  y++G 
  gi|488601642|ref|YP_007908113.1| 430 PLDVLCQHVVGMAIERKWGIDEALKVIRRSYPYRNLTK-DEFLEVLRYLAGY 480
                                       566677777766666555344444566788********.9*********995 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0057       7.3       5     105 ..      56     198 ..      53     226 .. 0.62
   2 ?    0.1   0.0      0.71   9.1e+02     103     135 ..     277     306 ..     268     308 .. 0.80
   3 ?   -3.6   0.0       9.6   1.2e+04      62      83 ..     731     752 ..     712     760 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0057
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka......... 70 
                                       ++ +++  ++G+GKT+ +     +    ++ +e + ++    +tl +s  +k l +++ ++l+++lk+         
  gi|488601642|ref|YP_007908113.1|  56 RNNILISSPTGSGKTLAAFLASISM--LIDLAE-KNRLEdkVYTLYVSP-LKALNNDIRKNLEEPLKEiyeiaeskg 128
                                       6678999999999998653222222..122222.222224133333333.678888999999998888888888888 PP

                            AAA_22  71 ..................................erlsseell.ealeqalraravielliiDEaqhlr...s 105
                                                                         ++  s  l+  ++ ++l++     +li+DE++ +    +
  gi|488601642|ref|YP_007908113.1| 129 lklqkirigvrtgdtdpserqrqvrkpphilittPETLSIILVsPKFSKHLSNL---DFLIVDEIHAIAenkR 198
                                       888888888888888888777777776666665422222233335555555555...5699999998865432 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.71
                            AAA_22 103 lrseealeeLrsllnlsrkgvqliLvGtpelrk 135
                                       + se+++++L +l++  +++++li+  t+++ +
  gi|488601642|ref|YP_007908113.1| 277 I-SEKLYNTLADLVK--SSKTTLIFTNTRSATE 306
                                       4.6899999999999..9999999988887766 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 9.6
                            AAA_22  62 ralglelkaerlsseelleale 83 
                                       ++++++l ++ +++e l+++++
  gi|488601642|ref|YP_007908113.1| 731 ENFEEDLIKALDRTEILRRRFR 752
                                       2222222224445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (874 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.81u 0.36s 00:00:01.17 Elapsed: 00:00:00.55
# Mc/sec: 4813.69
//
Query:       gi|488601643|ref|YP_007908114.1|  [L=527]
Description: Na+/panthothenate symporter [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-52  176.5  37.0    1.1e-51  176.0  37.0    1.2  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
       0.13   11.9   0.1       0.45   10.2   0.1    1.9  1  DUF3172   Protein of unknown function (DUF3172)


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0  37.0   1.2e-55   1.1e-51       1     406 []      34     455 ..      34     455 .. 0.89

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 1.2e-55
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvlle.lgalllvlllllllaerlr....nagalTlp 72 
                                       y +agr++ +  ++ls +a  is + +vG  G++ + G+  ++l  l++l+++ +++ ++++r r    ++galT+p
  gi|488601643|ref|YP_007908114.1|  34 YLVAGRKINPAIMALSYGAAFISTSAIVGFGGVAGLFGMPLLWLTfLNILVGIFIAYAVVGKRVRrfgmKTGALTFP 110
                                       89*****************************************983599999************9999********* PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdti 149
                                       ++l k ++++  l +++ l+++l++ l+  v l+g+ +++e +l+++y++a+l++a+++a+Y+v GGl+Av+ytd  
  gi|488601643|ref|YP_007908114.1| 111 ELLGKMYGSRF-LQVFAGLVVFLFMPLYAGVVLIGASRFMEVSLSIDYNMALLIMAVIIAVYVVYGGLIAVIYTDAF 186
                                       *********99.8999************************************************************* PP

                               SSF 150 qavlmlvgalilliivllevGgleslveklkeaapkvvdl...........ltpdslkllrdpltalslwlglvlGv 215
                                       q+ +mlv  ++lli +   +Gg+  + e+l++ +   v++               +l  +   + + sl lg+++Gv
  gi|488601643|ref|YP_007908114.1| 187 QGGIMLVSMIFLLISTYAFFGGVIPAHETLTSYNDLAVEIfsskipghngwTAFPTLGSVAWWVLVSSLILGVGIGV 263
                                       **********************9999999998888777777777788777522333345777888889999****** PP

                               SSF 216 aglphilvRflaakdakailkgvlkltivlilvligmisiilfaikla.gavp.kavgtevgvsniaypeLvvkllp 290
                                         +p  +vR++++ + + + ++v ++  ++ +++   ++++  +++++   v+   +  + g+ + ++p  ++  +p
  gi|488601643|ref|YP_007908114.1| 264 LAQPQLAVRLMTVGSDRDLDRAVPIGAFFIFIMVGTSFIVGALSNAYFlETVGkPSIAVAGGNVDKIIPAFINSFMP 340
                                       ***********************999876666555556666555555514566434444556789************ PP

                               SSF 291 nllaGlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvl 367
                                       +++  l+l   lAa mstl+s++    sa+ +D++++ + k+   ek ++ + ri++ + i+ +i+la   +   ++
  gi|488601643|ref|YP_007908114.1| 341 DWFVVLFLVTLLAAAMSTLSSQFHTIGSALGRDVFQAGLMKGRYDEKTIL-ITRIAIAIGIVFSIFLAYILPPGVIA 416
                                       *************************************9999977776654.67888888888888888888877799 PP

                               SSF 368 klvelafaglasavlavillalfwkrvneqGAlagliiG 406
                                          ++ fa  as +l+  l +l+w+++ ++GA+ ++++G
  gi|488601643|ref|YP_007908114.1| 417 RGTAIFFALCASSFLPAYLGGLYWSKASREGAITSILAG 455
                                       999999*****************************9988 PP

>> DUF3172  Protein of unknown function (DUF3172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1     5e-05      0.45       6      47 ..     249     290 ..     245     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5e-05
                           DUF3172   6 ailagvlvlGigiGvalsstanldpenvasreaidraaPnae 47 
                                        +l + l+lG+giGv  + + ++    v s + +dra+P   
  gi|488601643|ref|YP_007908114.1| 249 WVLVSSLILGVGIGVLAQPQLAVRLMTVGSDRDLDRAVPIGA 290
                                       5788899*******************************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.79u 0.36s 00:00:01.14 Elapsed: 00:00:00.58
# Mc/sec: 2752.83
//
Query:       gi|488601644|ref|YP_007908115.1|  [L=33]
Description: hypothetical protein Asulf_02168 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.52
# Mc/sec: 191.67
//
Query:       gi|488601645|ref|YP_007908116.1|  [L=78]
Description: hypothetical protein Asulf_02169 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 445.44
//
Query:       gi|488601646|ref|YP_007908117.1|  [L=131]
Description: hypothetical protein Asulf_02170 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-05   24.2   9.2    3.3e-05   24.2   9.2    1.7  2  PsiE      Phosphate-starvation-inducible E


Domain annotation for each model (and alignments):
>> PsiE  Phosphate-starvation-inducible E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3      0.21   3.7e+03      32      39 ..      16      23 ..       8      28 .. 0.58
   2 !   24.2   9.2   1.8e-09   3.3e-05       4      62 ..      55     113 ..      52     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.21
                              PsiE 32 ieaaiiav 39
                                      i+a iia+
  gi|488601646|ref|YP_007908117.1| 16 ILALIIAF 23
                                      44444443 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1.8e-09
                              PsiE   4 iLllLillEllrtivaylkehriavrlvieaaiiavaRklIildlkdggyltllglaaa 62 
                                       +++ LillEll+  +  l ++ i   l++ ++++a+ R++Iildlk+ +y ++++l+++
  gi|488601646|ref|YP_007908117.1|  55 VMVSLILLELLALTLRFLIHDIIDPNLLLITVLTALGREIIILDLKEVDYTKIIALGLV 113
                                       6788************************************************9999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); 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:                         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 0.34s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 779.09
//
Query:       gi|488601647|ref|YP_007908118.1|  [L=178]
Description: hypothetical protein Asulf_02172 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00082   19.4   8.1     0.0024   17.9   8.1    1.8  1  bZIP_1          bZIP transcription factor
     0.0034   17.5   3.1     0.0097   16.1   3.1    1.7  1  JIP_LZII        JNK-interacting protein  leucine zipper II
     0.0062   16.7   3.2      0.067   13.3   3.2    2.3  1  Baculo_FP       Baculovirus FP protein
  ------ inclusion threshold ------
      0.014   15.2   2.9      0.014   15.2   2.9    1.8  2  DivIC           Septum formation initiator
      0.015   15.4   1.4      0.023   14.8   1.4    1.3  1  ADIP            Afadin- and alpha -actinin-Binding
       0.02   15.5   1.0      0.041   14.4   1.0    1.6  1  Syntaxin-6_N    Syntaxin 6, N-terminal
      0.024   14.4   4.0      0.049   13.5   4.0    1.5  1  CCDC66          Coiled-coil domain-containing protein 66
      0.035   14.0   0.1        0.1   12.5   0.1    1.8  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
      0.042   14.3   6.4      0.058   13.9   6.0    1.6  1  ZapB            Cell division protein ZapB
      0.047   13.6   4.0      0.093   12.7   3.6    1.6  1  Wtap            WTAP/Mum2p family
      0.065   13.6   2.0      0.065   13.6   2.0    2.1  2  TSC22           TSC-22/dip/bun family
       0.12   12.4   4.6       0.29   11.1   4.6    1.8  1  DUF2205         Short coiled-coil protein
       0.17   11.2   3.2       0.07   12.4   0.9    1.5  2  DUF3450         Protein of unknown function (DUF3450)
       0.26   11.2   2.7        1.4    8.9   1.2    2.5  2  MerR_2          MerR HTH family regulatory protein
       0.45   11.2   3.8       0.63   10.7   3.4    1.6  1  YabA            Initiation control protein YabA
        1.1    9.5   6.2       0.41   10.8   2.8    2.2  2  NYD-SP28_assoc  Sperm tail C-terminal domain


Domain annotation for each model (and alignments):
>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   8.1   2.2e-06    0.0024      29      63 ..      64      98 ..      62      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 29 eeLerrvkaLekeNksLkseleelkkevekLkskv 63
                                      +eL +rvk+Le eNk+L++e+  lk+ v+kL +++
  gi|488601647|ref|YP_007908118.1| 64 KELLDRVKKLEDENKELRKENRMLKNLVDKLDEEL 98
                                      7999**************************98876 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 !   16.1   3.1   8.7e-06    0.0097      26      64 ..      61      99 ..      59     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.7e-06
                          JIP_LZII 26 vvkddLIarvdeLtsereiLreEleslqkakerlesrik 64
                                      v +++L+ rv +L  e++ Lr+E+++l++  ++l +++k
  gi|488601647|ref|YP_007908118.1| 61 VSRKELLDRVKKLEDENKELRKENRMLKNLVDKLDEELK 99
                                      5799******************************99987 PP

>> Baculo_FP  Baculovirus FP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   3.2   5.9e-05     0.067      49      87 ..      10      48 ..       6     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                         Baculo_FP 49 ktvkrnfilvkLvDekkvkeWeaksrekrLkssdlvsnv 87
                                      +tvk+  i v L  e+ ++eW++ ++e+++  s +v + 
  gi|488601647|ref|YP_007908118.1| 10 ETVKKRAIYVYLPSEEMAEEWKRIAKERNISISKFVVEC 48
                                      79****************************999985443 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.9   1.2e-05     0.014      16      53 ..      60      96 ..      57     104 .. 0.86
   2 ?   -2.7   0.0       4.6   5.1e+03      45      62 ..     156     172 ..     149     172 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                      XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                             DivIC 16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksd 53
                                      ++++k+l   +++l++e+++l++en+ L+  v++L ++
  gi|488601647|ref|YP_007908118.1| 60 FVSRKELLDRVKKLEDENKELRKENRMLKNLVDKL-DE 96
                                      6778899999*************************.44 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.6
                                       HHHCC-XXXXXXXXXXXX CS
                             DivIC  45 aevkdLksdedyieerAR 62 
                                       ++++ L  ++  ie  AR
  gi|488601647|ref|YP_007908118.1| 156 RQIEAL-EQYGLIESTAR 172
                                       455666.46666666665 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.4     2e-05     0.023      37      95 ..      45     103 ..      22     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                              ADIP  37 iinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqa 95 
                                       ++ ++ + l + ++d   r++l ++++kle e++ l+++ + lk+ + +l+ el+ + a
  gi|488601647|ref|YP_007908118.1|  45 VVECVQESLSKDESDFVSRKELLDRVKKLEDENKELRKENRMLKNLVDKLDEELKIYRA 103
                                       79999999******************************************999987765 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 ?   14.4   1.0   3.7e-05     0.041       6      71 ..      45     105 ..      43     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                      Syntaxin-6_N   6 vkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknp 71 
                                       v e Vq+sl+k es + + ++ll+       ++l++ ++eLrk+ r +++ ++ L+e  +i +++p
  gi|488601647|ref|YP_007908118.1|  45 VVECVQESLSKDESDFVSRKELLDR-----VKKLEDENKELRKENRMLKNLVDKLDEELKIYRAKP 105
                                       5689*****************9988.....678999999999999999999999999999988754 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 ?   13.5   4.0   4.4e-05     0.049      80     144 ..      24      90 ..      11      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                            CCDC66  80 eeqlee.erlrRereeeqerleeer.rkqkekeeaekkktqalldaiakAqeaAqkekqkkRkrela 144
                                       ee+ ee +r+++er+    ++ +e  ++ + k+e      ++lld ++k + + ++ ++++R+ +  
  gi|488601647|ref|YP_007908118.1|  24 EEMAEEwKRIAKERNISISKFVVECvQESLSKDESDFVSRKELLDRVKKLEDENKELRKENRMLKNL 90 
                                       56555548***************96256799*******************************97665 PP

>> 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 ?   12.5   0.1   9.1e-05       0.1       4      41 ..      17      55 ..      15      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                             RHH_5  4 vnvtLP.eelleeLeewAdeegRsvSnlaafLvekalre 41
                                      ++v+LP ee  ee ++ A+e+  s+S ++  +v+++l++
  gi|488601647|ref|YP_007908118.1| 17 IYVYLPsEEMAEEWKRIAKERNISISKFVVECVQESLSK 55
                                      78999955799*************************976 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   6.0   5.1e-05     0.058      15      52 ..      65     102 ..      62     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                              ZapB  15 kaidtitlLqmeieeLkeeneelkeenreleeeneqlk 52 
                                       +++d++++L  e++eL++en+ lk+  ++l ee++  +
  gi|488601647|ref|YP_007908118.1|  65 ELLDRVKKLEDENKELRKENRMLKNLVDKLDEELKIYR 102
                                       799****************************9998766 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.6   8.3e-05     0.093      86     122 ..      61      99 ..      42     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                              Wtap  86 qtGkrLmakcrvLeqENeELgkvle..egrvakLesela 122
                                       ++ k+L+ ++++Le+EN+EL k ++  ++ v kL +el+
  gi|488601647|ref|YP_007908118.1|  61 VSRKELLDRVKKLEDENKELRKENRmlKNLVDKLDEELK 99 
                                       56699***************9988733456777777766 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.0   5.8e-05     0.065      19      44 ..      66      91 ..      64     104 .. 0.81
   2 ?   -2.9   0.0       7.8   8.7e+03      24      40 ..     122     138 ..     119     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.8e-05
                             TSC22 19 LkekIkeLeernseleeENslLkala 44
                                      L +++k Le++n+el++EN++Lk+l+
  gi|488601647|ref|YP_007908118.1| 66 LLDRVKKLEDENKELRKENRMLKNLV 91
                                      55788999999999999999999876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.8
                             TSC22  24 keLeernseleeENslL 40 
                                        +L +r + +e+E  +L
  gi|488601647|ref|YP_007908118.1| 122 IDLFKRRKYVEYEELYL 138
                                       57888888888876555 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.6   0.00026      0.29      33      63 ..      64      94 ..      23     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                           DUF2205 33 qaLaervdeVkeehdKLesenrfLqqYIgdL 63
                                      ++L++rv +   e++ L+ enr+L + +++L
  gi|488601647|ref|YP_007908118.1| 64 KELLDRVKKLEDENKELRKENRMLKNLVDKL 94
                                      78**********************9988887 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   6.3e-05      0.07      45      82 ..      62      99 ..      45     104 .. 0.88
   2 ?   -3.3   0.1         4   4.5e+03     143     157 ..     148     162 ..     131     167 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                           DUF3450 45 ekqellaeyralkeeleslevyneqlerlvasqeqeia 82
                                       ++ell+++++l++e+++l+++n+ l++lv+++++e++
  gi|488601647|ref|YP_007908118.1| 62 SRKELLDRVKKLEDENKELRKENRMLKNLVDKLDEELK 99
                                      6899*******************************997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4
                           DUF3450 143 aekyrrvleayqiEa 157
                                       +e +r  l  ++   
  gi|488601647|ref|YP_007908118.1| 148 QELVRSYLRQIEALE 162
                                       333333333333333 PP

>> MerR_2  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.2    0.0012       1.4      67      84 .]      65      82 ..      63      82 .. 0.94
   2 ?    0.7   0.0      0.43   4.8e+02      17      32 ..     158     173 ..     148     178 .] 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                            MerR_2 67 dLLdrieqLqrelesLrn 84
                                      +LLdr+++L+ e+++Lr+
  gi|488601647|ref|YP_007908118.1| 65 ELLDRVKKLEDENKELRK 82
                                      7***************97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.43
                            MerR_2  17 lieLvelgliepeiee 32 
                                       ++ L+++glie +  +
  gi|488601647|ref|YP_007908118.1| 158 IEALEQYGLIESTARG 173
                                       6778899999876655 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.4   0.00056      0.63      25      57 ..      64      96 ..      42     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXX CS
                              YabA 25 eelkeelaelleenaeLeleneklrerleeeek 57
                                      +el +++++l +en+eL+ en+ l++++++ ++
  gi|488601647|ref|YP_007908118.1| 64 KELLDRVKKLEDENKELRKENRMLKNLVDKLDE 96
                                      678889999999999999999999999854433 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 ?   10.8   2.8   0.00037      0.41      35      54 ..      63      82 ..      60      94 .. 0.70
   2 ?   -3.2   0.1       8.7   9.8e+03      42      47 ..     158     163 ..     152     164 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                    NYD-SP28_assoc 35 RaklieetesLekqNeeLrn 54
                                      R++l++++++Le +N+eLr+
  gi|488601647|ref|YP_007908118.1| 63 RKELLDRVKKLEDENKELRK 82
                                      77777777777777777764 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.7
                    NYD-SP28_assoc  42 tesLek 47 
                                       +e+Le+
  gi|488601647|ref|YP_007908118.1| 158 IEALEQ 163
                                       444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1624  (0.0905795); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.59
# Mc/sec: 911.01
//
Query:       gi|488601648|ref|YP_007908119.1|  [L=308]
Description: Site-specific recombinase XerD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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    4.3e-28   98.2   0.0    1.3  1  Phage_integrase  Phage integrase family
    1.3e-12   48.0   0.0      3e-12   46.8   0.0    1.6  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    2.3e-12   47.0   0.1    5.7e-12   45.8   0.1    1.7  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    2.6e-08   34.1   0.2    1.2e-07   32.0   0.1    2.1  2  Phage_int_SAM_5  Phage integrase SAM-like domain
     0.0098   14.5   0.0      0.085   11.4   0.0    2.0  2  Sfi1             Sfi1 spindle body protein
  ------ inclusion threshold ------
       0.01   15.9   0.1      0.019   15.0   0.1    1.4  1  Phage_int_SAM_6  Phage integrase 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 !   98.2   0.0   1.4e-31   4.3e-28       2     171 ..     119     291 ..     118     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.4e-31
                                       HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHH CS
                   Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseeale 78 
                                       vlt +e++ l++ +++   irdk+++ ll++tG+R +El+s++v+d+++e++ il+  + + ++ +r+v + +e  +
  gi|488601648|ref|YP_007908119.1| 119 VLTVEEASLLVNSIPY---IRDKAIVLLLLKTGIRRGELISIDVQDINWEEQSILL--KPKAKRSNRVVFFDDETGR 190
                                       8999************...*************************************..5555666799999****** PP

                                       HHHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S........SC--TTHHHHHHHHHHHHHCTS CS
                   Phage_integrase  79 llkellskaleeaeksellfaskrgkplsrqtvrkafkraveeagie........kpltpHtlRhsfataLleagvd 147
                                        lk++++++ + ++k+++lf+++rg++l r+ v++a+ +++   g          +++tpHt Rh f ++L ++g+ 
  gi|488601648|ref|YP_007908119.1| 191 ILKKWMKVREKLNPKTDALFVNERGERLRRNGVYGAVTKWASMLGFHnpesdnpmDHFTPHTCRHCFTMWLRKSGMR 267
                                       *******************************************999999999************************* PP

                                       HHHHHHHHT-SSCCHHHHHHCCCH CS
                   Phage_integrase 148 lrvvqkllGHssisttqiYthvak 171
                                        +++++l G s  + + iY h +k
  gi|488601648|ref|YP_007908119.1| 268 REFIKELRGDSRREAIDIYDHIDK 291
                                       *******************99875 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 !   46.8   0.0     1e-15     3e-12       1      82 [.       9      91 ..       9      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1e-15
                   Phage_int_SAM_4  1 LlerfrealrlaglserTiksYlsaikrflrflkkk..apeeltkedieaYlnyLanerklsastqknalnalsffykk 77
                                      +le+fre + ++g++ ++i+ Y+s ++ fl++l+++   ++ ++k  ++++l+yL+ ++ l+ +t  n+++a+s+fy  
  gi|488601648|ref|YP_007908119.1|  9 FLEAFREDCISRGMTSESIRRYISCLRIFLKWLDERnvDVKGVDKFVLRDFLSYLR-SKGLKQKTLENYFSAISSFYDF 86
                                      699******************************988446688889999********.*********************9 PP

                   Phage_int_SAM_4 78 vlere 82
                                      +l + 
  gi|488601648|ref|YP_007908119.1| 87 LLYEG 91
                                      99865 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 !   45.8   0.1   1.9e-15   5.7e-12       2      84 .]      11      91 ..      10      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.9e-15
                                      HHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHH CS
                   Phage_int_SAM_1  2 eqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqfl 80
                                      e+f+e+  + rg++  ++r Y   Lr flk+l+e +  ++  ++   +r+fl +l+++gl++++l +++sa+ sF++fl
  gi|488601648|ref|YP_007908119.1| 11 EAFREDC-ISRGMTSESIRRYISCLRIFLKWLDE-RNVDVKGVDKFVLRDFLSYLRSKGLKQKTLENYFSAISSFYDFL 87
                                      5665554.49************************.******************************************** PP

                                      HHTT CS
                   Phage_int_SAM_1 81 vreg 84
                                      + eg
  gi|488601648|ref|YP_007908119.1| 88 LYEG 91
                                      9997 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 !   32.0   0.1   3.9e-11   1.2e-07       2      94 ..       9      98 ..       7     114 .. 0.86
   2 ?   -1.2   0.0       0.9   2.7e+03      37      65 ..     239     267 ..     210     273 .. 0.60

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.9e-11
                                      HHHHHHHHTHHHHTTS-HHHHHHHHHHHHHTTTS-..S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5  2 fldyfkeyiekkkkkgskgtlrnykstlkhlkkFlkkkditfeeidkefleeFedYLkkkkglsentiskyfkklkavl 80
                                      fl+ f+e +  +  ++   ++r+y s+l+ + k+l + ++ ++ +dk  l++F  YL ++kgl++ t  +yf+ +  ++
  gi|488601648|ref|YP_007908119.1|  9 FLEAFREDCISRGMTS--ESIRRYISCLRIFLKWLDERNVDVKGVDKFVLRDFLSYL-RSKGLKQKTLENYFSAISSFY 84
                                      5555555555554444..889999999999999999999******************.9******************** PP

                                      HHHHHTTS--S-HH CS
                   Phage_int_SAM_5 81 nkAikegilkknpy 94
                                           eg++k np+
  gi|488601648|ref|YP_007908119.1| 85 DFLLYEGVVKGNPV 98
                                      99999999999985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.9
                                       ..S---TTT--HHHHHH.HHHHHHHTS--- CS
                   Phage_int_SAM_5  37 kkkditfeeidkeflee.FedYLkkkkgls 65 
                                        ++d +++ +++  +++ F  +L +k+g+ 
  gi|488601648|ref|YP_007908119.1| 239 PESDNPMDHFTPHTCRHcFTMWL-RKSGMR 267
                                       34667777777777765588888.666655 PP

>> Sfi1  Sfi1 spindle body protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   2.8e-05     0.085      51     103 ..      26      78 ..      22      82 .. 0.90
   2 ?    0.7   0.0     0.049   1.5e+02     169     211 ..     226     268 ..     187     288 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                              Sfi1  51 aarrhiLrkkyfnaWreltavnelKaqrfalkkplkkWkartkeieereekav 103
                                         rr i + ++f +W +  +v+ + + +f+l+ +l+ ++++  +++++e+ + 
  gi|488601648|ref|YP_007908119.1|  26 SIRRYISCLRIFLKWLDERNVDVKGVDKFVLRDFLSYLRSKGLKQKTLENYFS 78 
                                       568999999************************************99998765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.049
                              Sfi1 169 alqiwserseevqaaeaeadsllrqkllrrvleewrkqarlep 211
                                       a+ +w+++   ++ ++ +  +++  + +r++++ w +++ +++
  gi|488601648|ref|YP_007908119.1| 226 AVTKWASMLGFHNPESDNPMDHFTPHTCRHCFTMWLRKSGMRR 268
                                       5555655555555555555566666666666666665554444 PP

>> Phage_int_SAM_6  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   6.4e-06     0.019      66     128 ..      25      87 ..       3      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.4e-06
                   Phage_int_SAM_6  66 iGintyanPllklyeyliklelaslkeideellseflaie.taslsdAskknyrialinfFgfi 128
                                         i  y++ l  + + l + ++ ++k +d+ +l++fl+   + +l + +  ny  a+ +f++f+
  gi|488601648|ref|YP_007908119.1|  25 ESIRRYISCLRIFLKWLDERNV-DVKGVDKFVLRDFLSYLrSKGLKQKTLENYFSAISSFYDFL 87 
                                       3689999999999999988776.79************9761568******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 1632.44
//
Query:       gi|488601649|ref|YP_007908120.1|  [L=359]
Description: hypothetical protein Asulf_02174 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.3   0.0      0.072   12.7   0.0    1.7  1  FAM124    FAM124 family
      0.057   12.9   0.0       0.15   11.5   0.0    1.6  1  DUF1248   Protein of unknown function (DUF1248)


Domain annotation for each model (and alignments):
>> FAM124  FAM124 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     8e-06     0.072     102     143 ..     204     246 ..     184     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8e-06
                            FAM124 102 lasqdfyslaeemPlwav.rqvhyGkeivRvtlyvseenyeda 143
                                       ++ +  +sl ++ P+wa+ ++v+y++e +++ + +++ +y+d 
  gi|488601649|ref|YP_007908120.1| 204 MKGKAIMSLIDSPPIWAIlSTVKYSHEALKFFVLCNQGKYSDE 246
                                       5556678889999****8579*******************985 PP

>> DUF1248  Protein of unknown function (DUF1248)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.6e-05      0.15       4      62 ..      99     157 ..      97     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.6e-05
                           DUF1248   4 vdvvinpdeklvdafmkvhGneRldfkkeDiakwkesfkddYrlklvllkgterviats 62 
                                       v+v  n + ++v+ +    Gn  +df k +++k+k++f d+ r  l+l   t++     
  gi|488601649|ref|YP_007908120.1|  99 VEVFENYKGDYVELMHTDFGNLVIDFLKAELDKLKNAFSDEIRRLLILSSSTKKTYLER 157
                                       78999************************************999999888888766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2099.89
//
Query:       gi|488601650|ref|YP_007908121.1|  [L=101]
Description: hypothetical protein Asulf_02175 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.37s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 564.54
//
Query:       gi|488601651|ref|YP_007908122.1|  [L=149]
Description: hypothetical protein Asulf_02176 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-15   56.9   0.1    2.5e-15   56.6   0.1    1.1  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
       0.03   14.4   0.9      0.042   14.0   0.0    1.7  2  ProRS-C_2     Prolyl-tRNA synthetase, C-terminal


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 !   56.6   0.1   2.8e-19   2.5e-15       1     111 [.      12     128 ..      12     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 2.8e-19
                                       EEEESSSHHHHHHHHHHHH.....HTTEEEEE.EESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTT CS
                      Response_reg   1 vlivdDdplvrellrqlle.....eegyeeva.eaedgkealellkeekvdlillDinmpgmdGlellkeireedpe 71 
                                       +li+dD+++++e++++++        ++++v  ++++gkea++++ e k++l ++D+ m + +G+el++ei  + ++
  gi|488601651|ref|YP_007908122.1|  12 ILIADDEKALVEIIEKMIVhffnqYPNFNVVVyKTTSGKEAFQKYAEVKPHLSFIDLVMRDKHGMELIDEITSNFQN 88 
                                       8**************999767656677887778******************************************** PP

                                       SEEEEEESSTSHHHHHHHHHCTESE.EEESSG-HHHHHHHH CS
                      Response_reg  72 lpviiltahseeedavealkagadd.flsKpfdpeeLlkal 111
                                        ++i+l+  se + + e+ k+g d  +l+Kpf++++L +a+
  gi|488601651|ref|YP_007908122.1|  89 SKIIVLSPFSE-SIIREVKKLGKDTtVLTKPFRIRDLYTAI 128
                                       *******9997.899999***99862789********9997 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 ?   -2.6   0.2      0.69   6.2e+03       2      19 ..      11      28 ..      10      31 .. 0.58
   2 ?   14.0   0.0   4.7e-06     0.042      10      41 ..      76     107 ..      68     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.69
                                      EE-SS--....HHHHHHH CS
                         ProRS-C_2  2 tiLeaenvnlllenikek 19
                                      +iL a + ++l+e i ++
  gi|488601651|ref|YP_007908122.1| 11 KILIADDEKALVEIIEKM 28
                                      566555656777766554 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.7e-06
                                       ...HHHHHHHCTTT-SEEEEE--GGG-SHHHH CS
                         ProRS-C_2  10 nlllenikeklsekkGvvLvPfneeiYneefe 41 
                                         l ++i   +++ k +vL Pf e+i  e   
  gi|488601651|ref|YP_007908122.1|  76 MELIDEITSNFQNSKIIVLSPFSESIIREVKK 107
                                       6799**********************988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 860.28
//
Query:       gi|488601652|ref|YP_007908123.1|  [L=380]
Description: RNA ligase, Pab1020 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-41  141.5   1.9    2.6e-41  140.5   1.9    1.5  1  Lig_C           Ligase Pab1020 C-terminal region
    2.1e-17   63.9   0.1    3.7e-17   63.1   0.1    1.4  1  RNA_ligase      RNA ligase
    5.3e-06   26.2   0.1     0.0026   17.4   0.0    2.4  2  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.5   1.9   4.4e-45   2.6e-41       2     125 .]     255     378 ..     254     378 .. 0.99

  Alignments for each domain:
  == domain 1  score: 140.5 bits;  conditional E-value: 4.4e-45
                                       HCCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHH CS
                             Lig_C   2 afsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeenie 78 
                                       af+y++++g+dF++sR++Reafq++ef+e+e +++er++++G++iLe+m++++ +v+ +++v+e++r+rf + e +e
  gi|488601652|ref|YP_007908123.1| 255 AFRYFNDYGKDFMLSRLVREAFQSFEFNENESKFKERCERIGKAILESMIKSVIDVSCGREVSEHHRLRFSSLEVLE 331
                                       9**************************************************************************** PP

                                       HHHHHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHHHHHHHTT- CS
                             Lig_C  79 ellehLrrlgvkaeveekekedgelvvkfkkiaqsttdkikslLeGg 125
                                        ++ hL r+gv+++++++ ++++++v++f++i++sttdki+++L+G+
  gi|488601652|ref|YP_007908123.1| 332 LFKVHLIRMGVDVRFSDPYHDGEKYVLEFRRIMRSTTDKISHHLKGN 378
                                       **********************************************7 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.1   6.2e-21   3.7e-17       1     159 [.      88     241 ..      88     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 6.2e-21
                                       SEEEEEEE-SSEEEEEEEE.TTEEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH........ECCEEEEEEEES CS
                        RNA_ligase   1 eevvvtEKlDGtnfriylv.kevgvasRsqil.pfgeekfkefkrwaaalrkklkekla......neelilyGElig 69 
                                       +evvv+EK++G+n+ri+    ++++++R++++ p          +  ++ r+ +    +       +el+l++E++g
  gi|488601652|ref|YP_007908123.1|  88 DEVVVEEKMNGYNVRIVNFgSNLYAITRRGFIcP----------YTTEKAREMI----DssffrhYPELMLCCEVVG 150
                                       59**************877644**********54..........2222222222....2222345667********* PP

                                       ....SS......TTSS.EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SS.HHHHHCCC..HHHH CS
                        RNA_ligase  70 ...hsi....kygglpkefyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkfl.aaeellel.llskg 135
                                          +       yg  + +fy Fd+    +k+++r ls d+  ++a+++g   +p+l++ +++ a+e ++++ +   +
  gi|488601652|ref|YP_007908123.1| 151 kesP-FvvkdIYGT-DLDFYIFDVR---EKRSNRSLSIDNKMKIAEEYGfkLAPILERCDTNvAHEVCRDIiERIGN 222
                                       7542.256644444.6699999999...677**********99999999*********9999888888888522466 PP

                                       TC--EEEEEESSSSBETTEBSEEE CS
                        RNA_ligase 136 nkrEGlVikpeselyknkgraifK 159
                                       + rEG+V+k++++       + +K
  gi|488601652|ref|YP_007908123.1| 223 EGREGIVLKDPEMK-----INPIK 241
                                       79*******88773.....55555 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 !   17.4   0.0   4.4e-07    0.0026      11      82 ..      79     150 ..      72     193 .. 0.87
   2 !    6.6   0.0   0.00089       5.3     166     192 ..     212     238 ..     163     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.4e-07
                                       HHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEE CS
                    DNA_ligase_A_M  11 ekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElva 82 
                                       + ++kk+ +++++vE+K++G+ +++ + g++ + ++Rr+   +++ ++  +++++ f+ +  +++l +E+v 
  gi|488601652|ref|YP_007908123.1|  79 HPTIKKHFRDEVVVEEKMNGYNVRIVNFGSNLYAITRRGFICPYTTEKAREMIDSSFFRHYPELMLCCEVVG 150
                                       556777779999**********************************************************96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00089
                                       HHHHHHHHHHHTTECEEEEEETT-CC- CS
                    DNA_ligase_A_M 166 eleelleeaiseglEGlvvKnpdskYe 192
                                         ++++e+  +eg EG+v+K+p+ k +
  gi|488601652|ref|YP_007908123.1| 212 VCRDIIERIGNEGREGIVLKDPEMKIN 238
                                       34778999999**********997755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2150.43
//
Query:       gi|488601653|ref|YP_007908124.1|  [L=307]
Description: CBS domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  180.1   8.9    5.7e-14   52.3   0.1    4.2  4  CBS       CBS domain
  ------ inclusion threshold ------
       0.18   11.8   0.0       0.42   10.6   0.0    1.6  1  RL        RL domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   2.8e-14   2.6e-10       3      54 ..      26      78 ..      22      81 .. 0.85
   2 !   50.0   0.5   3.3e-17     3e-13       1      56 [.     104     159 ..     104     160 .. 0.95
   3 !   52.3   0.1   6.4e-18   5.7e-14       1      55 [.     168     221 ..     168     223 .. 0.95
   4 !   40.3   0.0   3.6e-14   3.3e-10       7      55 ..     256     303 ..     250     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.8e-14
                                      HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
                               CBS  3 dimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllra 54
                                      d++t+ vvt+pp++t+  a++ m +++++r+P+  ++ ++l Gi+t +D++++
  gi|488601653|ref|YP_007908124.1| 26 DYCTKSVVTIPPTSTIMSAVKSMMKYNFRRMPIAdPGTKRLEGIITVTDIINF 78
                                      67*************888888866*********9444449***********98 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 3.3e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V++im  dv++++ +++le+a+elm +k+v++ PVVd d+ ++Gi+t++D+l++l+
  gi|488601653|ref|YP_007908124.1| 104 VEAIMEGDVISIDFTSSLEDAIELMLKKRVGGCPVVDRDNIILGIITEKDVLSYLS 159
                                       7889999******************************999899***********97 PP

  == domain 3  score: 52.3 bits;  conditional E-value: 6.4e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+ +mt+ v+t++pdtt+eea++lm++++ +rlPV+  dg +vG+vt r +lr+ 
  gi|488601653|ref|YP_007908124.1| 168 VRNYMTKGVITASPDTTVEEAMKLMISRKMRRLPVI-RDGIFVGLVTAREILRYF 221
                                       7889*********************99999******.8***************95 PP

  == domain 4  score: 40.3 bits;  conditional E-value: 3.6e-14
                                       SSCEEEETTSBHHHHHHHHHHHTSS.EEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   7 rdvvtvppdttleealelmrekgvs.rlPVVdedgklvGivtlrDllral 55 
                                       ++++ vppd+ ++++++lm+ +g++ + +VV ++g+l Gi+t+rDl+r+l
  gi|488601653|ref|YP_007908124.1| 256 KEPLLVPPDERISDLVKLMKGSGYGvA-LVV-NNGNLEGIITERDLIRFL 303
                                       57889**************65558524.5**.5999************98 PP

>> RL  RL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.6e-05      0.42      25      51 ..     149     176 ..     146     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.6e-05
                                RL  25 isekkllkylsqhGkinkhF.fYeskgv 51 
                                       i+ek++l yls+ G+i+ +   Y +kgv
  gi|488601653|ref|YP_007908124.1| 149 ITEKDVLSYLSENGEIDGFVrNYMTKGV 176
                                       79***************98634777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1728.92
//
Query:       gi|488601654|ref|YP_007908125.1|  [L=182]
Description: hypothetical protein Asulf_02179 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-29   99.8   4.4    4.7e-17   62.2   0.5    2.1  2  CBS           CBS domain
  ------ inclusion threshold ------
       0.12   12.5   1.9        0.2   11.8   1.9    1.3  1  Arv1          Arv1-like family
       0.18   11.7   2.1         14    5.8   0.5    2.5  2  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.2     1e-13   6.2e-10       1      55 [.       7      60 ..       7      62 .. 0.90
   2 !   62.2   0.5   7.9e-21   4.7e-17       2      55 ..      73     125 ..      72     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1e-13
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V++imtr+v t++ +++l  a ++m e gv+++ VV ++g++vGivt++D+l+++
  gi|488601654|ref|YP_007908125.1|  7 VKEIMTREVCTASLEDSLLNASRKMLECGVGSI-VVLDNGNPVGIVTEKDILEKV 60
                                      89***********************765599**.6536**************987 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 7.9e-21
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +dimt+++++++p t+l+ea+++m +kg++rlP+V+ +++lvGi+t+ D+l++ 
  gi|488601654|ref|YP_007908125.1|  73 KDIMTTPLIVINPMTSLREAAQIMLKKGIRRLPIVN-ENRLVGIITDNDILSVS 125
                                       79*********************************7.666***********975 PP

>> Arv1  Arv1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.9   3.4e-05       0.2      10      42 ..     138     170 ..     133     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                              Arv1  10 ksLytkYskgnirltkCknCkkvaDkYvEfdnv 42 
                                       k L ++ + + +r  kC++C+k+ D+ vE++ +
  gi|488601654|ref|YP_007908125.1| 138 KMLLRESEYEDVRFGKCEKCGKFYDNLVEYNGL 170
                                       567777778899******************866 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5    0.0023        14       3      11 ..     151     159 ..     150     160 .. 0.89
   2 ?    4.9   0.0    0.0043        26      20      32 ..     166     178 ..     164     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0023
                      zf-dskA_traR   3 ygsCeeCGE 11 
                                       +g+Ce+CG+
  gi|488601654|ref|YP_007908125.1| 151 FGKCEKCGK 159
                                       899*****5 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0043
                      zf-dskA_traR  20 alPgarlCveCqe 32 
                                        + g +lC +C+e
  gi|488601654|ref|YP_007908125.1| 166 EYNGLKLCEDCAE 178
                                       567999*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1019.94
//
Query:       gi|488601655|ref|YP_007908126.1|  [L=270]
Description: hypothetical protein Asulf_02180 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-09   35.7   2.5    9.3e-09   35.7   2.5    2.0  2  Cohesin   Cohesin domain
  ------ inclusion threshold ------
        1.2    8.9   5.6        1.5    8.5   5.6    1.1  1  DUF1387   Protein of unknown function (DUF1387)
        9.9    5.4  12.8         13    5.0  12.8    1.1  1  CDC27     DNA polymerase subunit Cdc27


Domain annotation for each model (and alignments):
>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   2.5   1.6e-12   9.3e-09       7     139 .]      26     144 ..      20     144 .. 0.80
   2 ?   -1.6   1.0      0.48   2.9e+03      86     114 ..     189     217 ..     145     242 .. 0.58

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.6e-12
                                       EEEE-TTSEEEEEEEEESECTTEEEEEEEEEE.TTTEEEEEEEE-TTS.SSGGHCEEEEEECGTTEEEEEEE.TTSS CS
                           Cohesin   7 kvsakvGdtvtvpvtvsnvskkvaaaqftikYDpavlevvsvkaGsiv.knssvnfgsnlleepgkikflfldlasl 82 
                                       + ++k G++++v+v  s  ++ +a+++++i++Dp+v ++++++aG+ + k  + n   n+++++g  +++   +   
  gi|488601655|ref|YP_007908126.1|  26 TQTVKEGENFKVKVYGSYFDS-IAGIDLNIQFDPSVIKLNGISAGKNFsKCFKFN---NINNTRGFGRVA---II-C 94 
                                       34459****************.*************************95444443...667799999999...44.5 PP

                                       STTCBEESSEEEEEEEEEESTTS-TCEEEEEEEEEEEEEETTSEBE-EEEECEEEEE CS
                           Cohesin  83 gssgiaekdgvlatitfkvkskaaegttaikisdtlsfgdgeekeiskvtvdgtinv 139
                                       g+   + k+  +a   f++++ +    t  +++ t+s++ ++ k + + tvdg+++v
  gi|488601655|ref|YP_007908126.1|  95 GDAR-TFKNDLIAIYSFTALKGE----T--HLHITASLSTSDFKTVYPETVDGSVKV 144
                                       6654.4589999999*******9....4..45555555555559999999****987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.48
                                       CBEESSEEEEEEEEEESTTS-TCEEEEEE CS
                           Cohesin  86 giaekdgvlatitfkvkskaaegttaiki 114
                                       +++++++ +a+ t k ks ++++t++   
  gi|488601655|ref|YP_007908126.1| 189 PAKTEQTPIAEQTQKPKSQTEQKTSSPAS 217
                                       44445666666666677766665333333 PP

>> DUF1387  Protein of unknown function (DUF1387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.6   0.00025       1.5      63     165 ..     143     245 ..     121     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00025
                           DUF1387  63 ekldtasldakeleseesasaeteekeselelqkaevelepklvaksesseaqq.ksakkqqkneskpksrtssess 138
                                       + l   s d  + ++  s  +++ +++++    + +v+  ++ v+++++ +++q + a+++qk +s+++++tss  s
  gi|488601655|ref|YP_007908126.1| 143 KVLTKGSPDTGSASTGSSGLTDPANNAQN--GVQPTVQPTQQPVNTVQPAKTEQtPIAEQTQKPKSQTEQKTSSPAS 217
                                       55555555555444444444444333333..3455677777788887776665514555666888899999999999 PP

                           DUF1387 139 vkasskkevktddvqessagkkl.gsni 165
                                       +++ +   ++t+ +++s++++kl  +ni
  gi|488601655|ref|YP_007908126.1| 218 HTTPTAIPTTTEIATKSTTEEKLnLKNI 245
                                       9999999999999999999655404555 PP

>> CDC27  DNA polymerase subunit Cdc27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  12.8    0.0022        13     132     207 ..     168     243 ..     154     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0022
                             CDC27 132 aeelgrpplaapaseakektangkkpkaakekaaketssakseskkksaekskdaskettkekaekaasskaaslk 207
                                       +++ g +p  +p++++ +++ ++k++++++ ++ ++ +s+ +++++ +a+ +++++  tt+e a+k +++++ +lk
  gi|488601655|ref|YP_007908126.1| 168 NAQNGVQPTVQPTQQPVNTVQPAKTEQTPIAEQTQKPKSQTEQKTSSPASHTTPTAIPTTTEIATKSTTEEKLNLK 243
                                       3334889*******************99888888888888889999999999999999999988888888887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1536.80
//
Query:       gi|488601656|ref|YP_007908127.1|  [L=233]
Description: hypothetical protein Asulf_02181 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-05   23.8   0.0    6.9e-05   22.8   0.0    1.6  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.3   0.2      0.038   13.9   0.2    1.9  1  HTH_12    Ribonuclease R winged-helix domain
      0.023   15.2   0.1      0.051   14.1   0.1    1.6  1  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-08   6.9e-05      38      61 .]     191     215 ..     164     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-08
                                       HHH.HHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  38 knt.lsyHLrvLeeagLvevvregr 61 
                                       +   +syHL+ Lee gL+e +reg+
  gi|488601656|ref|YP_007908127.1| 191 QRArMSYHLKGLEEDGLIEMRREGK 215
                                       5555*******************96 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   6.4e-06     0.038      35      62 ..     195     225 ..     155     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-06
                            HTH_12  35 vRyrLrkleerglt..rrvgya.greltEkG 62 
                                       + y+L+ lee+gl+  rr g++ +  lt+ G
  gi|488601656|ref|YP_007908127.1| 195 MSYHLKGLEEDGLIemRREGKNvKIILTDLG 225
                                       56**********9833577776677888887 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.5e-06     0.051      28      68 .]     188     225 ..     185     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.5e-06
                            HTH_27  28 lnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       ++ + + +sy lk L+e GL+e+    ++++++ + lTd G
  gi|488601656|ref|YP_007908127.1| 188 YMAQRARMSYHLKGLEEDGLIEMR---REGKNVKIILTDLG 225
                                       66778899*************777...66899999999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1324.57
//
Query:       gi|488601657|ref|YP_007908128.1|  [L=597]
Description: Aldehyde:ferredoxin oxidoreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.1e-112  374.0   0.0   9.9e-112  373.7   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    2.4e-72  243.0   0.1    3.9e-72  242.3   0.1    1.3  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.7   0.0  1.1e-115  9.9e-112       5     382 .]     224     592 ..     220     592 .. 0.97

  Alignments for each domain:
  == domain 1  score: 373.7 bits;  conditional E-value: 1.1e-115
                                       HHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEE CS
                            AFOR_C   5 kiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrev 81 
                                        ++++i ++  + + +r+ GT+++v++++  g lp+k+f++gtfeka++isg +++e+yl++ +gCf+C ++Cg++v
  gi|488601657|ref|YP_007908128.1| 224 ALNERIDNNF-TCNMFREIGTSGYVETSEMFGDLPVKYFTQGTFEKASDISGTKMAEEYLKRSDGCFGCRVRCGTVV 299
                                       5678888888.777*************************************************99************ PP

                                       E......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS---- CS
                            AFOR_C  82 kveegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglele 158
                                       +++  +    +gpeyet+a++Gs   +ddl++ +++n+l+++ GlDtisaG tiafam l+ +G+ +      ++++
  gi|488601657|ref|YP_007908128.1| 300 EIDGRS---IHGPEYETIASFGSLQLVDDLKSLIEINYLANDFGLDTISAGVTIAFAMFLTDNGVYD------FSIR 367
                                       *97776...79*******************************************************6......599* PP

                                       TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG- CS
                            AFOR_C 159 fgdaeallellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlray 235
                                       +gdae + +l+e+iA r++ g++lAeG++ + +k+  e+la++vkGle+p++dpr+  ++a aYa+ nrGacHl + 
  gi|488601657|ref|YP_007908128.1| 368 WGDAEGVKKLIEEIAFRKNRGEILAEGTRFIGNKFSVENLAANVKGLEIPMHDPRAFASLAAAYAMHNRGACHLPHQ 444
                                       ***************************************************************************** PP

                                       THHHH..........S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHH CS
                            AFOR_C 236 liale..........ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteee 302
                                       ++++e           + d+++ e+k+ +++ +q++t+l++++++C f+      ++++++a+ll+  tG+d++ + 
  gi|488601657|ref|YP_007908128.1| 445 MYNIEmglkvkeygiVSDDRFSSENKGVITARMQNYTELYNCVTMCAFMP-----VKPAQMANLLKYSTGFDFDVNS 516
                                       *999999*******988999*99**************************9.....7899****************** PP

                                       HHHHHHHHHHHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHH CS
                            AFOR_C 303 llkaGeRiynleRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkr 379
                                       ++ aGeRiynl+R+fn+++G+t++ddtlpe ++ +pl eg ++g+v+  ++e  ++eyY +rGWd++GvP++e+lk 
  gi|488601657|ref|YP_007908128.1| 517 IYLAGERIYNLKRMFNVKCGITARDDTLPEIVM-KPL-EGGSEGNVP--DFELQKKEYYIERGWDDNGVPKPEKLKA 589
                                       *********************************.799.799999**9..8*************************** PP

                                       CT- CS
                            AFOR_C 380 LgL 382
                                       LgL
  gi|488601657|ref|YP_007908128.1| 590 LGL 592
                                       **8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.3   0.1   4.3e-76   3.9e-72       1     195 [.       6     203 ..       6     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 242.3 bits;  conditional E-value: 4.3e-76
                                       SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                            AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                       g+il+v+L++g++ev +l+e++a++y+Gg+g++a++l++    +++p+s +n+l +  Gpl+gt ap+++rl+++ak
  gi|488601657|ref|YP_007908128.1|   6 GRILKVNLEKGSAEVMDLDEDVAKNYIGGSGFGAYFLYRMKVYDAEPFSDSNVLGIFNGPLSGTIAPSTSRLEFCAK 82 
                                       69*************************************877*********************************** PP

                                       -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS...E CS
                            AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd...k 151
                                       sPltg +gesn+Gg+f+a lk+aG+d+i+ieGk+ekpvyl i+ d++ei++a+ +wgl++y+ ++++++e+g+   +
  gi|488601657|ref|YP_007908128.1|  83 SPLTGIWGESNSGGKFSAFLKFAGWDGIIIEGKSEKPVYLLINPDTAEIRSADGIWGLGCYDSQKEIEKEVGEsriS 159
                                       **********************************************************************9999888 PP

                                       EEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEE CS
                            AFOR_N 152 vaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivv 195
                                       +aviG+aGenlvr+A++++d++r+agr+G+GavmgsK+lk i+v
  gi|488601657|ref|YP_007908128.1| 160 TAVIGQAGENLVRYACVQLDNSRHAGRTGMGAVMGSKKLKGIAV 203
                                       88****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 3429.36
//
Query:       gi|488601658|ref|YP_007908129.1|  [L=380]
Description: Alcohol dehydrogenase, class IV [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-99  330.6   0.0    1.1e-98  330.4   0.0    1.0  1  Fe-ADH          Iron-containing alcohol dehydrogenase
    6.7e-20   71.8   1.6    5.2e-11   42.7   0.5    2.1  2  Fe-ADH_2        Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
       0.18   11.4   0.0        0.3   10.6   0.0    1.3  1  DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase dom


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.4   0.0  1.9e-102   1.1e-98       3     364 .]       8     365 ..       6     365 .. 0.92

  Alignments for each domain:
  == domain 1  score: 330.4 bits;  conditional E-value: 1.9e-102
                                       EEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-T CS
                            Fe-ADH   3 rivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalare 79 
                                       +i fg+++l+     l+ l   +a+ivtd++++ ksg++dkv++ l   ++e++vfd+vep+p+ e v+e++++a+ 
  gi|488601658|ref|YP_007908129.1|   8 KIAFGEDSLD----FLETLD-GKAMIVTDENLV-KSGVVDKVTKRL---NLEYEVFDKVEPDPSFEIVMEGVEFAKR 75 
                                       8899999995....555555.4*********99.************...**************************** PP

                                       T.--EEEEEESHHHHHHHHHHHHHTT.....................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  80 egadvviavGGGsviDtAKaialllanpe..vedylgegkakkkka.lpliaiPTtaGtGsevtplavitdeeegek 153
                                        ++d++i+vGGGs++DtAK+i+l+++np+  +e++     ++ k++ ++li iPT +G+Gse +++ v+t+++eg+k
  gi|488601658|ref|YP_007908129.1|  76 VKPDYIIGVGGGSSLDTAKGIRLIYENPDldPEEVS--PWTDVKSGeVKLILIPTASGSGSEGSNAIVLTKKDEGRK 150
                                       ***************************975444444..333344445****************************** PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedl 230
                                       ++  +p +++d+aivDpe++  lP +v+++tglDal+ha++ayvs  +n+++d+l+ +a++l++k+l+ra++d +d 
  gi|488601658|ref|YP_007908129.1| 151 IASIHPAVMADYAIVDPEMVRELPEKVAVFTGLDALSHAMDAYVSAWKNDFTDGLCIQACKLLFKYLPRACRDRSDS 227
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT.......T CS
                            Fe-ADH 231 eareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralggesdee 307
                                       ea e++++a+tlagla+++++ g++H+++h+lga f+iphg+a++++lp+ ++++ +  +e++ +la  +g     +
  gi|488601658|ref|YP_007908129.1| 228 EAVEKVHNAATLAGLAIGSSQAGLSHSIGHSLGAVFHIPHGFACGVALPYTTQYYSKFVREQYDELAYHIG----FR 300
                                       *********************************************************99**********95....67 PP

                                       --HHHHHHHHHHHHHTT---SHHHH....T-TT-HH....HHHHHHHT-TSGGGGSSS---HHHH CS
                            Fe-ADH 308 aaeeliealrellkelglptsLsel....gvdeedl....dklaeaalkdrslannpreltaedv 364
                                         eeli++ +ell++l+ p s ++l    g++e+++    d+l+ +a +d+++ +   ++++ed+
  gi|488601658|ref|YP_007908129.1| 301 DCEELIDKTKELLASLNTPLSYKDLleeyGISEKEFlerlDELVYKASTDNTIVTLEEAPDEEDL 365
                                       99*****************9988855555*9997555555*******999999999999998885 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.5e-10   1.5e-06      21      93 ..      25      95 ..      13      99 .. 0.85
   2 !   42.7   0.5   8.6e-15   5.2e-11      99     250 .]     120     272 ..     117     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.5e-10
                          Fe-ADH_2 21 kvllvaden.tkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiaky 93
                                      k+++v+den +k+ + +kv++ l+   ++ ev+++ve+++++e v++ ve ++  + d +++vGgG+ +D+ak 
  gi|488601658|ref|YP_007908129.1| 25 KAMIVTDENlVKSGVVDKVTKRLN---LEYEVFDKVEPDPSFEIVMEGVEFAKRVKPDYIIGVGGGSSLDTAKG 95
                                      678999999445559999999995...5577799**************************************96 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 8.6e-15
                          Fe-ADH_2  99 nvpyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwk 172
                                       +v+++ +pTa    +  s  + l+++  g+k+   ++a ++   i+D ++++e P++       D+l+  +  + + 
  gi|488601658|ref|YP_007908129.1| 120 EVKLILIPTASGSGSEGSNAIVLTKKdeGRKIASiHPAVMADYAIVDPEMVRELPEKVAVFTGLDALSHAMDAYVSA 196
                                       57899*****99998999999999877899988779**999999************99776556************* PP

                          Fe-ADH_2 173 lanevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalHGeqV 249
                                        +n++++ l+ ++ + +++ + ++ +d  + ea+e++ +a +l+g++i ++  G  H i H l +++  +  HG  +
  gi|488601658|ref|YP_007908129.1| 197 WKNDFTDGLCIQACKLLFKYLPRACRDRSDSEAVEKVHNAATLAGLAIGSSQAGLSHSIGHSLGAVF--HIPHGFAC 271
                                       *******************************************************************..9****999 PP

                          Fe-ADH_2 250 G 250
                                       G
  gi|488601658|ref|YP_007908129.1| 272 G 272
                                       8 PP

>> DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase domain
   #    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      15      67 ..      35      89 ..      20      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5e-05
                                      STT---TTHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHH..HTT--B-S--GGG CS
                    DNA_pol3_alpha 15 lkeelpeevkerlekElevIekmgfadyflivadlvkaak..kkgilvGpgRGSa 67
                                      +k+++ ++v +rl+ E+ev +k++ +  f iv++ v++ak  k ++ +G g GS 
  gi|488601658|ref|YP_007908129.1| 35 VKSGVVDKVTKRLNLEYEVFDKVEPDPSFEIVMEGVEFAKrvKPDYIIGVGGGSS 89
                                      4677899********************************9445789****99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2158.14
//
Query:       gi|488601659|ref|YP_007908130.1|  [L=133]
Description: Putative sterol carrier protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   43.8   0.0    3.4e-11   43.5   0.0    1.1  1  SCP2      SCP-2 sterol transfer family


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   1.9e-15   3.4e-11       5     100 ..      14     119 ..      10     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.9e-15
                                       HHHHHHH.HHHHHHCCH-EEEEEEECTC.T.....EEEEEETTSTEEE....SSCTTBS-SEEEEEEHHHHHHHHCT CS
                              SCP2   5 lerlkdp.ekkealkklagvlrfdltdlkg.....sltldlkegqldv....aakdegkadvtlslsledllelaeg 71 
                                        e l+ + e+++a+k+++g + f +++ ++     + ++dl +g+ +      +++e  +  ++s++ +++++l++g
  gi|488601659|ref|YP_007908130.1|  14 MEVLNTSkEYENAAKDWEGDFLFVIEPDDEldspkYAYIDLYHGKARKgfvvNDPSEVNPAYVFSGKFSNWKKLLNG 90 
                                       55554455***********999***9998899*********97755545555777779******************* PP

                                       SS-HHHHHHTTSSEEEC-HHHHHHHHHHH CS
                              SCP2  72 klnpqkafmqgkLkieGDielaqkleall 100
                                       +++p k + ++k +++G++++++++++++
  gi|488601659|ref|YP_007908130.1|  91 EIDPIKGLITRKFTLKGNMAKVMRYAKAA 119
                                       *************************9886 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:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 741.52
//
Query:       gi|488601660|ref|YP_007908131.1|  [L=228]
Description: putative membrane protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-50  170.5  11.2    5.2e-50  169.8  11.2    1.3  1  DUF1614   Protein of unknown function (DUF1614)


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.8  11.2   2.9e-54   5.2e-50       1     170 []      54     223 ..      54     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 169.8 bits;  conditional E-value: 2.9e-54
                           DUF1614   1 llgslinipvaelkskeelvevkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavsllaallavli 77 
                                       ++gs+inip+ e + ke ++e++++gi y+v +     +k++vavN+GG++ P l+++ lll+l+  l+++++a+++
  gi|488601660|ref|YP_007908131.1|  54 VIGSFINIPLVEKEGKEVVREYNFFGIIYQVRQR----SKMTVAVNLGGCIFPSLIAVKLLLSLP--LTPWIIAFIL 124
                                       69*************887889*********9943....4599***********************..9********* PP

                           DUF1614  78 vaavvyllarpvpgvGivvpllipplvaalaa.lllaeeea.....aavaYisgvlGtLiGadllnlkkieklgapv 148
                                       +++++y+ a+pv+gvGi+vp+++ppl+++l++ ++++         +++aY+ gvl++L+Gad+l+lk++ek+g+ v
  gi|488601660|ref|YP_007908131.1| 125 TSIIIYFNAKPVRGVGIAVPMFLPPLISVLTSyFIISFFGLdmyllPKFAYAVGVLAVLFGADILHLKDLEKIGSGV 201
                                       ********************************7666666558999******************************** PP

                           DUF1614 149 vsIGGaGtFdGifltgilavll 170
                                       +sIGGaGtFdGifltgi++v+l
  gi|488601660|ref|YP_007908131.1| 202 ISIGGAGTFDGIFLTGIFSVIL 223
                                       ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1254.75
//
Query:       gi|488601661|ref|YP_007908132.1|  [L=81]
Description: hypothetical protein Asulf_02186 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   41.5   0.1    1.1e-10   41.4   0.1    1.0  1  PRC       PRC-barrel domain
      0.003   17.8   0.3      0.014   15.7   0.3    1.8  1  DUF2171   Uncharacterized protein conserved in bacteria (DUF2


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 !   41.4   0.1   1.3e-14   1.1e-10       5      77 ..       3      78 ..       1      80 [. 0.92

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.3e-14
                                      CS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.........-EEEEEGG.CEECCCTEEEETTS-G CS
                               PRC  5 rasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi....gekevliPfdlavkigkdriivdapke 77
                                       a  l  k V  +dG+++G V++v  d k+g++  l+v+ g ++ +    ++++++iPf+ avk++++++++d  k 
  gi|488601661|ref|YP_007908132.1|  3 LAKTLSKKMVLMSDGTEVGMVYNVTADLKTGMLIDLIVKPGQKPLPdlekTDNYYIIPFE-AVKSISHYVVLDKKKL 78
                                      677889999********************************98766**************.***********98765 PP

>> DUF2171  Uncharacterized protein conserved in bacteria (DUF2171)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.5e-06     0.014       7      61 ..      12      77 ..       8      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-06
                           DUF2171  7 VvgsdGehvGtVDhv.....egdrikLtkddseeg.......gqhhyiplswVasvdddkVhLskta 61
                                      V+ sdG++vG V  v      g  i L  +  ++        ++ ++ip+++V+s+    V+L+k++
  gi|488601661|ref|YP_007908132.1| 12 VLMSDGTEVGMVYNVtadlkTGMLIDLIVKPGQKPlpdlektDNYYIIPFEAVKSIS-HYVVLDKKK 77
                                      8899***********88887778899988888666888888788899**********.*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 466.38
//
Query:       gi|488601662|ref|YP_007908133.1|  [L=809]
Description: AAA family ATPase, CDC48 subfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  330.1   0.0    1.7e-49  167.6   0.0    3.3  3  AAA              ATPase family associated with various cellul
    2.2e-32  110.6   3.6    5.7e-19   67.7   1.0    3.1  2  AAA_lid_3        AAA+ lid domain
    6.8e-32  109.5   0.7    1.8e-31  108.1   0.1    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      3e-16   59.7   0.2    1.6e-06   28.2   0.1    3.6  2  AAA_5            AAA domain (dynein-related subfamily)
    2.5e-15   57.3   0.7    4.1e-07   30.5   0.0    3.8  3  AAA_16           AAA ATPase domain
    3.4e-15   56.2   0.0      1e-07   31.8   0.0    3.4  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.6e-15   55.9   0.0    1.1e-06   28.8   0.0    3.3  3  AAA_2            AAA domain (Cdc48 subfamily)
    6.7e-15   54.6   0.0    5.3e-14   51.7   0.0    2.3  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    9.8e-14   51.3   0.1    5.5e-05   22.5   0.0    3.6  3  TIP49            TIP49 P-loop domain
    6.1e-11   42.5   0.0    0.00097   19.2   0.0    3.5  4  AAA_14           AAA domain
    1.3e-09   38.4   1.9      0.007   16.7   0.2    4.5  2  AAA_22           AAA domain
    1.9e-09   37.8   0.0    0.00011   22.3   0.0    2.7  2  AAA_33           AAA domain
    7.5e-09   35.5   0.8    0.00041   20.3   0.0    2.8  2  Vps4_C           Vps4 C terminal oligomerisation domain
    5.5e-08   33.4   0.0      0.012   16.2   0.0    3.0  2  AAA_18           AAA domain
    5.3e-07   29.5   0.0      0.025   14.3   0.0    2.7  2  IstB_IS21        IstB-like ATP binding protein
      1e-06   28.4   0.0      0.039   13.5   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    1.1e-06   28.5   0.1      0.086   12.5   0.0    3.4  2  Sigma54_activat  Sigma-54 interaction domain
    1.6e-06   28.4   0.0      0.066   13.6   0.0    2.6  2  RNA_helicase     RNA helicase
      2e-06   27.3   0.1      0.049   13.0   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.7e-06   28.0   0.0     0.0038   17.7   0.0    2.8  2  ABC_tran         ABC transporter
      3e-06   27.1   0.0       0.47   10.1   0.0    3.5  3  AAA_30           AAA domain
    5.1e-06   26.4   0.0      0.057   13.3   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    9.8e-06   25.0   0.1      0.061   12.6   0.0    2.8  3  DUF2075          Uncharacterized conserved protein (DUF2075)
    1.1e-05   24.8   0.1      0.084   12.1   0.0    2.8  2  Zeta_toxin       Zeta toxin
    1.2e-05   25.1   0.0       0.14   11.9   0.0    3.4  3  AAA_24           AAA domain
    1.3e-05   25.5   0.2       0.14   12.4   0.0    3.0  2  AAA_28           AAA domain
    1.7e-05   24.9   0.1       0.15   12.0   0.0    2.9  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    3.5e-05   23.7   0.4       0.19   11.5   0.0    2.9  3  AAA_11           AAA domain
    7.4e-05   22.7   1.0        4.1    7.2   0.0    3.6  3  Bac_DnaA         Bacterial dnaA  protein
    9.7e-05   21.6   0.1       0.13   11.3   0.0    2.4  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00013   22.1   0.1       0.77    9.9   0.0    3.2  3  Sigma54_activ_2  Sigma-54 interaction domain
    0.00014   21.1   0.0      0.074   12.2   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    0.00016   22.1   0.0       0.56   10.6   0.0    3.7  2  AAA_17           AAA domain
    0.00017   21.1   0.3       0.54    9.7   0.0    2.7  2  PhoH             PhoH-like protein
    0.00019   21.1   2.3        1.5    8.4   0.3    4.0  3  AAA_25           AAA domain
    0.00026   21.0   0.3       0.69    9.8   0.0    3.8  3  NACHT            NACHT domain
    0.00031   20.8   0.0       0.82    9.6   0.0    3.1  2  ResIII           Type III restriction enzyme, res subunit
    0.00059   19.1   0.0          1    8.5   0.0    2.6  2  NB-ARC           NB-ARC domain
    0.00099   18.5   8.3        2.1    7.6   0.0    4.9  5  ATPase           KaiC
     0.0015   18.5   2.6          3    7.7   0.0    4.2  4  NTPase_1         NTPase
     0.0017   18.5   0.5       0.49   10.5   0.0    2.9  2  Cytidylate_kin2  Cytidylate kinase-like family
     0.0023   18.3   4.8        1.1    9.6   0.0    3.4  2  AAA_19           AAA domain
     0.0024   18.0   0.1        1.6    8.8   0.0    2.8  2  SKI              Shikimate kinase
     0.0039   16.9   0.1        2.2    8.0   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
     0.0048   16.7   1.2         21    4.8   0.0    4.4  4  DEAD             DEAD/DEAH box helicase
     0.0059   16.9   0.0        1.3    9.3   0.0    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like domain
  ------ inclusion threshold ------
      0.015   15.0   0.2         43    3.7   0.0    4.0  4  Guanylate_kin    Guanylate kinase
      0.017   14.6   0.1        8.5    5.7   0.0    3.5  3  TniB             Bacterial TniB protein
      0.021   13.8   0.1        5.6    5.8   0.0    3.0  3  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.024   14.5   0.0        5.9    6.7   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.032   14.2   0.0         18    5.1   0.0    3.1  3  Rad17            Rad17 P-loop domain
      0.033   13.1   0.0        5.5    5.8   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
      0.034   14.2   0.0        4.1    7.5   0.0    2.5  2  Torsin           Torsin
      0.036   13.7   0.0        1.8    8.2   0.0    2.8  2  Zot              Zonular occludens toxin (Zot)
      0.039   14.1   0.3      0.098   12.8   0.3    1.7  1  CtsR_C           CtsR C-terminal dimerization domain
      0.061   12.4   0.0        2.7    7.0   0.0    2.7  2  MCM              MCM P-loop domain
      0.065   13.0   0.0         15    5.3   0.0    2.7  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.065   13.0   0.0         10    6.0   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.068   12.2   0.0         12    4.8   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
      0.081   12.3   0.3        5.4    6.3   0.0    2.4  2  IPT              Isopentenyl transferase
       0.11   12.9   0.0        3.5    8.0   0.0    2.8  2  Antiterm         Antitermination protein
        2.3    8.7   9.1         35    4.8   0.0    3.6  2  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       3.9   1.1e+03      49      74 ..     152     176 ..     119     188 .. 0.72
   2 !  167.6   0.0   5.9e-52   1.7e-49       1     131 [.     230     359 ..     230     360 .. 0.98
   3 !  158.0   0.0   5.7e-49   1.7e-46       1     130 [.     570     699 ..     570     701 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.9
                                       HHHHHHHTSTS.EEEEEETGGGHHHHH CS
                               AAA  49 lfkeakekakp.silfiDEidalaksr 74 
                                       +f ++k+   p  +++iDE  +++ ++
  gi|488601662|ref|YP_007908133.1| 152 VFVAVKTD--PkDVVIIDETTKVVYRE 176
                                       34444444..559******98877655 PP

  == domain 2  score: 167.6 bits;  conditional E-value: 5.9e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKTl+a+ava+e+g++f++i+g+e++sk+ gese+++re+f+eake++ psi+fiDEida+a++r++ 
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYTINGPEIMSKFYGESEQRLREIFEEAKENS-PSIIFIDEIDAIAPRRDEV 305
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt +dg++++ ++vivi+atnr+d +dpal+r gRfdr+iei+
  gi|488601662|ref|YP_007908133.1| 306 TGEVERRVVAQLLTLMDGLEER-GQVIVIAATNRVDAVDPALRRpGRFDREIEIG 359
                                       *********************7.56***************************996 PP

  == domain 3  score: 158.0 bits;  conditional E-value: 5.7e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       vllyGppGtGKTl+akava+e++++f++++gsellsk++gesek +r++f++a++ a p+i+f+DEida+a+ r  +
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFITVKGSELLSKWLGESEKAVRKIFRKARQVA-PCIIFFDEIDAIAQMRgLD 645
                                       79******************************************************9.****************988 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       + s+  ervvnq+lte+dg+++ e+ viv+gatnrpd ldpallr gRfdr +++
  gi|488601662|ref|YP_007908133.1| 646 EGSRAVERVVNQILTEMDGLEELEE-VIVLGATNRPDILDPALLRpGRFDRLVYV 699
                                       89999*****************866.*************************9987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   2.3e-13   6.6e-11       4      39 ..     452     487 ..     450     510 .. 0.79
   2 !   67.7   1.0     2e-21   5.7e-19       1      45 []     723     769 ..     723     769 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.3e-13
                         AAA_lid_3   4 lkeLAerTeGySGADlaalcreAallAlrrgikeit 39 
                                       lk+LA +T+G++GAD++al +eAa+ Alr  +++i+
  gi|488601662|ref|YP_007908133.1| 452 LKQLADQTHGFVGADIEALSKEAAMKALRKYLPQID 487
                                       89***************************9655543 PP

  == domain 2  score: 67.7 bits;  conditional E-value: 2e-21
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.e.itmedfee 45 
                                       dvdl+eLA +TeGy+GAD++a+creA++lAlr+++  e ++m++f e
  gi|488601662|ref|YP_007908133.1| 723 DVDLEELADLTEGYVGADIEAVCREAVMLALREDLNaEvVEMRHFLE 769
                                       9**********************************9658*****975 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 !  108.1   0.1   6.3e-34   1.8e-31       1      84 [.       4      87 ..       4      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 6.3e-34
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVt 79
                                      +L+V++a+++d+grgi+r+dp++m +l+++pgd++ei+g+r Tva+vw+a + d+gkgiIr+d+++R+n gv+iGd+V+
  gi|488601662|ref|YP_007908133.1|  4 TLKVNQAYPSDSGRGIARLDPDTMLKLKISPGDIIEIKGRRATVAKVWRAPKRDWGKGIIRVDRFIRENSGVGIGDSVE 82
                                      69***************************************************************************** PP

                                      EEEE- CS
                           CDC48_N 80 Vrkae 84
                                      Vrk++
  gi|488601662|ref|YP_007908133.1| 83 VRKVD 87
                                      ***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 !   28.2   0.1   5.5e-09   1.6e-06       1     136 [.     229     348 ..     229     349 .. 0.80
   2 !   27.1   0.0   1.1e-08   3.3e-06       1     135 [.     569     688 ..     569     691 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 5.5e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ +a  +++++ ++++++ +++  + g+ e        +  ++ ++a+  +++i+++DE++
  gi|488601662|ref|YP_007908133.1| 229 GVLLHGPPGTGKTLIARAVANEIGASFYTINGPEIMSK--FYGESE-------QRLREIFEEAKenSPSIIFIDEID 296
                                       59********************************8875..555555.......34567777777889********** PP

                                       G--...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 rae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        +    +ev++++ +    + l l++g e+ +         + via++n++d     ++palr+
  gi|488601662|ref|YP_007908133.1| 297 AIAprrDEVTGEVERRVVAQLLTLMDGLEERGQ--------VIVIAATNRVD----AVDPALRR 348
                                       987334577787766666666666666666644........99********9....77888886 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.1e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ +a+ +++++ +v +++      l+ ++   ++ ++ v +++  +ar   ++i+++DE++
  gi|488601662|ref|YP_007908133.1| 569 GVLLYGPPGTGKTLIAKAVAHETEANFITVKGSE------LLSKWL--GESEKAVRKIFR-KARqvAPCIIFFDEID 636
                                       59****************************9987......999999..455555555555.555599********** PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---.........-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddller...frviatanpldrslnelspalr 135
                                            ++ + ++ l+e  + +e   +++  + d+ le+   + v++++n++d     l+pal+
  gi|488601662|ref|YP_007908133.1| 637 -----AI-AQMRGLDEGSRAVERVVNQILTEMDG-LEEleeVIVLGATNRPD----ILDPALL 688
                                       .....33.44578899999999999999888876.33335599999999998....6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.4e-09   4.1e-07      21     141 ..     224     333 ..     217     346 .. 0.73
   2 !   19.3   0.0   4.2e-06    0.0012      24      60 ..     567     600 ..     559     611 .. 0.79
   3 ?    2.4   0.0      0.62   1.8e+02     122     146 ..     614     643 ..     612     674 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.4e-09
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesaelea 96 
                                        + p  vll+G++G+GK+ ++r++++++ ++ +++++g    +        +      e+ lr++ +e +e++    
  gi|488601662|ref|YP_007908133.1| 224 IDPPKGVLLHGPPGTGKTLIARAVANEIGAS-FYTINGPEIMS-------KFYGES--EQRLREIFEEaKENSPSII 290
                                       555699************************9.77777777666.......322222..3444444444144455566 PP

                            AAA_16  97 wrekleealaavpelagaeasrllellkrllallsrderplvlvl 141
                                       + +++++ +   +e++g+ ++r+ ++l  l++ l+++++  v+v+
  gi|488601662|ref|YP_007908133.1| 291 FIDEIDAIAPRRDEVTGEVERRVVAQLLTLMDGLEERGQ--VIVI 333
                                       66677777779999999999***********99999777..4444 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 4.2e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkc 60 
                                       p  vll+G++G+GK+ ++++++++ e++   f++ k 
  gi|488601662|ref|YP_007908133.1| 567 PKGVLLYGPPGTGKTLIAKAVAHETEAN---FITVKG 600
                                       589*******************877776...444444 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.62
                            AAA_16 122 llkrllallsrderplvlvlDdlq......w 146
                                       +++++++++++   p ++++D+++       
  gi|488601662|ref|YP_007908133.1| 614 AVRKIFRKARQ-VAPCIIFFDEIDaiaqmrG 643
                                       56788899999.778*********5555544 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       3.8   1.1e+03      70      95 ..     146     171 ..     136     175 .. 0.84
   2 !   31.8   0.0   3.6e-10     1e-07      35     103 ..     229     305 ..     211     347 .. 0.87
   3 !   19.8   0.0   1.8e-06   0.00051      35      69 ..     569     603 ..     560     689 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.8
                            RuvB_N  70 ekagdlaalltnleekdvlfideihr 95 
                                       +++g l+ + ++ ++kdv+ ide  +
  gi|488601662|ref|YP_007908133.1| 146 QNQGALVFVAVKTDPKDVVIIDETTK 171
                                       6788899999999**********765 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 3.6e-10
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                        vll+GpPG Gkt +a+ +a+e+g+++ +  gP +      e ++ l  ++ + +e+   ++fidei  +++  +ev
  gi|488601662|ref|YP_007908133.1| 229 GVLLHGPPGTGKTLIARAVANEIGASFYTINGPEImskfygESEQRLREIFEEAKENspSIIFIDEIDAIAPRRDEV 305
                                       69*******************************994444434567799999988876336********999988887 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 1.8e-06
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                        vllyGpPG Gkt +ak +a+e ++++ +  g  l
  gi|488601662|ref|YP_007908133.1| 569 GVLLYGPPGTGKTLIAKAVAHETEANFITVKGSEL 603
                                       69***********************9988777654 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         7     2e+03      70      83 ..     149     175 ..     138     191 .. 0.68
   2 !   28.8   0.0   3.9e-09   1.1e-06       6     105 ..     230     323 ..     225     330 .. 0.91
   3 !   22.8   0.0   2.8e-07     8e-05       6     103 ..     570     659 ..     565     665 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 7
                                       S.............EEEEETGGG---- CS
                             AAA_2  70 G.............ivllDEidKihpk 83 
                                       G             +v +DE  K+  +
  gi|488601662|ref|YP_007908133.1| 149 GalvfvavktdpkdVVIIDETTKVVYR 175
                                       34666666666667******9999875 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 3.9e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++a+a+a+ + +    ++ +++  e++     + + ++++  ++   +a+e+   i+++DEid i
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGA----SFYTINGPEIMS----KFYGESEQRLREIFEEAKENSpsIIFIDEIDAI 298
                                       6899******************96....************....99999999999*99999999999********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +p+ ++ + +v r  V+  LL +++g
  gi|488601662|ref|YP_007908133.1| 299 APRrDEVTGEVERR-VVAQLLTLMDG 323
                                       **988888888886.66678889887 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 2.8e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++aka+a   ++    ++i++  sell     + l ++++  ++   +a +    i+++DEid i
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEA----NFITVKGSELLS----KWLGESEKAVRKIFRKARQVApcIIFFDEIDAI 638
                                       6899***************99985....************....77777777777777777777789********** PP

                                       ------------HHHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSregVqrdLLqil 103
                                       ++    g d  +  V r+  qil
  gi|488601662|ref|YP_007908133.1| 639 AQ--MRGLDEGSRAVERVVNQIL 659
                                       **..4444444444444444443 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 ?   -0.2   0.0         3   8.7e+02      34      61 ..       3      34 ..       1      43 [. 0.76
   2 !   51.7   0.0   1.8e-16   5.3e-14       5      63 ..     110     180 ..     105     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3
                                      EEEEEEEECCCC....SCEEECTSCCEEESTT CS
                           CDC48_2 34 iklvVvstePkg....pvgitetTeielgtkp 61
                                      ++l+V    P++    +++ +++T+ +l   p
  gi|488601662|ref|YP_007908133.1|  3 LTLKVNQAYPSDsgrgIARLDPDTMLKLKISP 34
                                      78888888899888888888888887777666 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 1.8e-16
                                       CCCH.HHHCCCTTEEE-TTEEEEECCT............CCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                           CDC48_2   5 dema.ylkrqFlgrpvtkGdlvvfefk............gqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                       d +  ylk+q+l+rp+++Gdl++                 +++ +v+v+t+Pk++v+i+etT++ ++++p++
  gi|488601662|ref|YP_007908133.1| 110 D-IGdYLKHQLLKRPLVEGDLIPLVGApaltgfgkyaqnQGALVFVAVKTDPKDVVIIDETTKVVYRERPAK 180
                                       4.555*****************652223335567888889******************************98 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.23        67     164     195 ..      25      56 ..      18      74 .. 0.87
   2 !   21.5   0.0   3.8e-07   0.00011      51      96 ..     228     271 ..     224     295 .. 0.88
   3 !   22.5   0.0   1.9e-07   5.5e-05      51     107 ..     568     623 ..     560     626 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
                                       HHHHHHT--TT-EEEEETTT--EEE-SSS-SS CS
                             TIP49 164 eellkekvkegDviviekesGkvkklGrsear 195
                                       +++lk k++ gD+i i+ ++ +v k+ r+ +r
  gi|488601662|ref|YP_007908133.1|  25 DTMLKLKISPGDIIEIKGRRATVAKVWRAPKR 56 
                                       568899*******************9998765 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.8e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt 96 
                                       ++vLl Gp+gtGkt +a a+++e+g    f +++g e+ s     +
  gi|488601662|ref|YP_007908133.1| 228 KGVLLHGPPGTGKTLIARAVANEIG--ASFYTINGPEIMSKFYGES 271
                                       89***********************..679********99755555 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1.9e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksi 107
                                       ++vLl Gp+gtGkt +a a+++e      f++++gse+ s  +  +e ++ + +rk+ 
  gi|488601662|ref|YP_007908133.1| 568 KGVLLYGPPGTGKTLIAKAVAHETE--ANFITVKGSELLSKWLGESEkAVRKIFRKAR 623
                                       89********************965..89************99998845677889985 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       6.9     2e+03      62      76 ..     158     172 ..     143     190 .. 0.72
   2 !   19.2   0.0   3.3e-06   0.00097       5      88 ..     230     310 ..     227     351 .. 0.77
   3 ?   -1.6   0.1         9   2.6e+03      63     101 ..     428     466 ..     387     488 .. 0.56
   4 !   18.3   0.0   6.3e-06    0.0018       5      77 ..     570     649 ..     567     678 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6.9
                            AAA_14  62 eekktylflDEiqev 76 
                                       ++ k ++++DE  +v
  gi|488601662|ref|YP_007908133.1| 158 TDPKDVVIIDETTKV 172
                                       346899*****9988 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 3.3e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81 
                                       +++ G+  +GKT +++ +++e      s+  in  +   k + ++e+ l++i+e++ke+  +++f+DEi  +   ++
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIG---ASFYTINGPEIMSKFYGESEQRLREIFEEAKENSPSIIFIDEIDAIAPRRD 303
                                       7899**************98888...99*****9998887777766566666666667799********99955444 PP

                            AAA_14  82 alkslvd 88 
                                        + + v+
  gi|488601662|ref|YP_007908133.1| 304 EVTGEVE 310
                                       4444443 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 9
                            AAA_14  63 ekktylflDEiqevpewekalkslvdegknldvivtGSn 101
                                       ++  y ++DE   ++  ++++k+++++  +    + G  
  gi|488601662|ref|YP_007908133.1| 428 KDLIYSLFDETIIAELEREIIKNMLKQLADQTHGFVGAD 466
                                       345566777766665555555555554433344444555 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 6.3e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT ++k +++e      +++ ++  +   k l ++ek  + i++k+++    ++f+DEi  +     
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETE---ANFITVKGSELLSKWLGESEKAVRKIFRKARQVAPCIIFFDEIDAIaqmrg 643
                                       7899**************98888...9******999999888888777777777755557899******99955555 PP

                            AAA_14  77 .....p 77 
                                            +
  gi|488601662|ref|YP_007908133.1| 644 ldegsR 649
                                       544444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   2.4e-05     0.007       8      51 ..     230     264 ..     225     341 .. 0.67
   2 !   14.8   0.1   8.8e-05     0.025       8      40 ..     570     593 ..     565     668 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.4e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                       ++++G++GtGKT+ +r ++++          ++++++++ p+ +
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEI---------GASFYTINGPEIM 264
                                       689*****************98.........5555555444433 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.8e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                       ++++G++GtGKT+ ++ ++++ +         +
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETE---------A 593
                                       689*****************983.........3 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.9e-07   0.00011       2      79 ..     230     337 ..     230     363 .. 0.72
   2 !   12.7   0.0   0.00036      0.11       2      33 ..     570     603 ..     570     703 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.9e-07
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll+G+pG+GK+  a+ ++++ g  +++++ ++++++ +g+ +q+++                              
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGasFYTINGPEIMSKFYGESEQRLReifeeakenspsiifideidaiaprrdeVT 306
                                       799*************************************8888888666666666667777777776666554322 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatn 79 
                                        +v+ r+ ++l  l +   ++g+ +++ atn
  gi|488601662|ref|YP_007908133.1| 307 GEVERRVVAQLLTLMDGLEERGQVIVIAATN 337
                                       3355555556655555444444445556665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00036
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtl 33 
                                       vll G+pG+GK+  a+ ++ ++   ++++   +l
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEanFITVKGSEL 603
                                       7899**************9998866666665554 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 !   12.7   0.2   0.00034     0.099      15      44 ..     489     518 ..     484     534 .. 0.85
   2 !   20.3   0.0   1.4e-06   0.00041      22      58 ..     755     791 ..     742     793 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00034
                            Vps4_C  15 twmdipsdkllePpvtlkDflkalkkarpt 44 
                                       +  +ip++ l   ++t++Df++alk+  p+
  gi|488601662|ref|YP_007908133.1| 489 NKDEIPAEVLESIKITIDDFKEALKEIEPS 518
                                       5578999989999**************998 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.4e-06
                            Vps4_C  22 dkllePpvtlkDflkalkkarptVskeDLekheeFTk 58 
                                       ++l +  v++++fl+alkk++p+V+++ L  +e+F +
  gi|488601662|ref|YP_007908133.1| 755 EDLNAEVVEMRHFLEALKKVKPSVTDSMLSFYERFEE 791
                                       56777789*************************9965 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00021     0.062       1      79 [.     230     333 ..     230     342 .. 0.63
   2 !   16.2   0.0   4.1e-05     0.012       1      68 [.     570     666 ..     570     700 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00021
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......aldes 49 
                                       +ll G+pG+GKt +a++++++ g                       +++ + aken +++ + +e         + +
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGAsfytingpeimskfygeseqrLREIFEEAKENSPSIIFIDEidaiaprRDEVT 306
                                       7899**************99974447888888667667777755555555555555555555555665444433344 PP

                            AAA_18  50 krldedkldklldaleenssaleegknlvi 79 
                                        ++++ ++++ll+++++    +e g+++vi
  gi|488601662|ref|YP_007908133.1| 307 GEVERRVVAQLLTLMDGL---EERGQVIVI 333
                                       445555555555555554...345555555 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.1e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe........alde 48 
                                       +ll G+pG+GKt +ak+++ ++ ++                    ++++   a++  +++ +++e         lde
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETeANfitvkgsellskwlgesekaVRKIFRKARQVAPCIIFFDEidaiaqmrGLDE 646
                                       799***************88875446988888888888888877733333333333344444444555588888888 PP

                            AAA_18  49 skrldedkldklldaleens 68 
                                         r++e +++++l+++++  
  gi|488601662|ref|YP_007908133.1| 647 GSRAVERVVNQILTEMDGLE 666
                                       88888888888888888864 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00041      0.12      47      70 ..     227     250 ..     215     299 .. 0.87
   2 !   14.3   0.0   8.8e-05     0.025      48      71 ..     568     591 ..     560     635 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00041
                         IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                        ++++l Gp+G+GK+ +a a++ e
  gi|488601662|ref|YP_007908133.1| 227 PKGVLLHGPPGTGKTLIARAVANE 250
                                       57899***************9876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.8e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       ++++l Gp+G+GK+ +a a+++e+
  gi|488601662|ref|YP_007908133.1| 568 KGVLLYGPPGTGKTLIAKAVAHET 591
                                       6899****************9986 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00035       0.1      33      65 ..     227     259 ..     216     301 .. 0.82
   2 !   13.5   0.0   0.00013     0.039      30      62 ..     564     595 ..     557     636 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00035
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekylsl 65 
                                        k vll Gp GtGKt+i++ + +++  + y+++
  gi|488601662|ref|YP_007908133.1| 227 PKGVLLHGPPGTGKTLIARAVANEIGASFYTIN 259
                                       5789****************9999986666655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00013
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkeky 62 
                                       +k  k vll+Gp GtGKt+i+k + ++ +  ++
  gi|488601662|ref|YP_007908133.1| 564 IKPPKGVLLYGPPGTGKTLIAKAVAHETE-ANF 595
                                       566789*****************999888.444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00075      0.22      23      57 ..     228     259 ..     219     341 .. 0.81
   2 !   12.5   0.0    0.0003     0.086      21      57 ..     566     599 ..     553     613 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00075
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavn 57 
                                         vl++G  GtGK+l+ara+ ++     ++f ++n
  gi|488601662|ref|YP_007908133.1| 228 KGVLLHGPPGTGKTLIARAVANEIG---ASFYTIN 259
                                       569****************987554...5566665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0003
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavn 57 
                                        +  vl+ G  GtGK+l+a+a+ +++   e++f++v 
  gi|488601662|ref|YP_007908133.1| 566 PPKGVLLYGPPGTGKTLIAKAVAHET---EANFITVK 599
                                       45789***************996554...35666665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00023     0.066       1      36 [.     230     265 ..     230     337 .. 0.82
   2 !   12.2   0.0   0.00062      0.18       1      26 [.     570     595 ..     570     635 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00023
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++l+Gp+g+GK+++a+ +a+++  ++ +++ ++++s
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYTINGPEIMS 265
                                       689*******************98885555554443 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00062
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++lyGp+g+GK+++ak +a++ + ++
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANF 595
                                       689**************999887665 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   0.00043      0.12      25      43 ..     230     248 ..     227     255 .. 0.89
   2 !   13.0   0.0   0.00017     0.049      25      43 ..     570     588 ..     565     624 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00043
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKt++a++++
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVA 248
                                       79*************9875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00017
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt++ak+++
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVA 588
                                       89*************9875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.028       8.1       8      49 ..     224     263 ..     221     342 .. 0.75
   2 !   17.7   0.0   1.3e-05    0.0038       5      80 ..     561     646 ..     559     676 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.028
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdl 49 
                                       + + + v + G+ G+GK+ +++++a++      +i  +g ++
  gi|488601662|ref|YP_007908133.1| 224 IDPPKGVLLHGPPGTGKTLIARAVANEIGASFYTI--NGPEI 263
                                       566677899**************999876544444..55555 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.3e-05
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx. RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren. 79 
                                       ++++k+ + v + G+ G+GK+ ++k++a++++  +  i+++g +l ++ l +++k ++ ++ +  q+ p +   ++ 
  gi|488601662|ref|YP_007908133.1| 561 KFSIKPPKGVLLYGPPGTGKTLIAKAVAHETE--ANFITVKGSELLSKWLGESEKAVRKIFRKaRQVAPCIIFFDEi 635
                                       589999999********************986..789999*******9**********9999966777766655555 PP

                                       ..........H CS
                                       ..........x RF
                          ABC_tran  80 ..........e 80 
                                                 e
  gi|488601662|ref|YP_007908133.1| 636 daiaqmrgldE 646
                                       66655555551 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.41   1.2e+02      82     100 ..     154     172 ..     123     181 .. 0.81
   2 !   10.1   0.0    0.0016      0.47      21      44 ..     230     253 ..     218     261 .. 0.83
   3 !   10.1   0.0    0.0016      0.48      21      48 ..     570     597 ..     559     670 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.41
                            AAA_30  82 grarlepgtllivDEagmv 100
                                        +++ +p++++i+DE+  v
  gi|488601662|ref|YP_007908133.1| 154 VAVKTDPKDVVIIDETTKV 172
                                       4578899********9876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0016
                            AAA_30  21 avltGpAGtGKttalkalreawea 44 
                                       ++l+Gp+GtGKt + +a+++ + a
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGA 253
                                       689**************9876655 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0016
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggr 48 
                                       ++l Gp+GtGKt + ka+++  ea+  +
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFIT 597
                                       6789*************99888876555 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 !   13.3   0.0    0.0002     0.057       2      31 ..     230     259 ..     229     341 .. 0.82
   2 !   10.5   0.0    0.0014      0.41       2      31 ..     570     599 ..     569     671 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0002
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll+g PG++ktl+++a+a+ ++++f  i 
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYTIN 259
                                       89***********************99885 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll g PG++ktl++ka+a+  +++f  ++
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFITVK 599
                                       7999*******************9997765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       9.2   2.7e+03      86     104 ..     158     176 ..     154     183 .. 0.75
   2 !   12.6   0.0   0.00021     0.061       4      55 ..     230     275 ..     227     310 .. 0.67
   3 !    9.4   0.0    0.0019      0.54       4      25 ..     570     591 ..     567     626 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.2
                           DUF2075  86 epkedvvivDEAhrlltks 104
                                        ++ dvvi+DE  ++  ++
  gi|488601662|ref|YP_007908133.1| 158 TDPKDVVIIDETTKVVYRE 176
                                       56789******88776655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00021
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhpl.vlvlrealakke 55 
                                       vl +G +GtGKt+++ ++++e+        a + + N+p+ + + + + +++ 
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEI-------GASFYTINGPEiMSKFYGESEQRL 275
                                       6889******************.......333333333331345555555544 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0019
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl  G +GtGKt+++ ++++e 
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHET 591
                                       6789*************99998 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0019      0.55      15      44 ..     226     253 ..     218     268 .. 0.86
   2 !   12.1   0.0   0.00029     0.084      14      51 ..     565     600 ..     556     605 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqg 44 
                                        Pk +ll G pG GK+ +a+++++e+  + 
  gi|488601662|ref|YP_007908133.1| 226 PPKGVLLHGPPGTGKTLIARAVANEI--GA 253
                                       5999********************98..44 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00029
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       + Pk +ll G pG GK+ +a++++ e+  + n++++++
  gi|488601662|ref|YP_007908133.1| 565 KPPKGVLLYGPPGTGKTLIAKAVAHET--EANFITVKG 600
                                       779***********************9..899998876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0047       1.4       5      76 ..     230     297 ..     227     306 .. 0.62
   2 ?   -1.0   0.0       4.1   1.2e+03     149     177 ..     420     450 ..     408     467 .. 0.76
   3 !   11.9   0.0   0.00048      0.14       5      23 ..     570     590 ..     567     647 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0047
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie......swedfldevvelaaeladyktlviDtid 75 
                                       +l+ Gp+g+GKT +a+           e G+ s + +++p+i       s + +++ ++e +++ +  ++++iD id
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAV-------ANEIGA-SFYTINGPEIMskfygeSEQRLREIFEEAKENSP--SIIFIDEID 296
                                       799**********99988.......222233.3344444444333344455555555555555554..777777777 PP

                            AAA_24  76 e 76 
                                        
  gi|488601662|ref|YP_007908133.1| 297 A 297
                                       6 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.1
                            AAA_24 149 epklgkktanelkeevDlvlranlkred..k 177
                                       +++ +++ ++++ + +D+ + a+l+re+  +
  gi|488601662|ref|YP_007908133.1| 420 KLETKEQIKDLIYSLFDETIIAELEREIikN 450
                                       6677888899***********9999877651 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00048
                            AAA_24   5 iliyGpsgiGKTtlakel..g 23 
                                       +l+yGp+g+GKT +ak    +
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVahE 590
                                       89*************988542 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0    0.0005      0.14       2      47 ..     230     280 ..     229     317 .. 0.76
   2 !   10.1   0.0    0.0024      0.71       2      30 ..     570     599 ..     569     640 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0005
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalp 47 
                                       + + G+++tGKT +++a a++    + ++  pE++ +++ e  ++ +++ +
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEigaSFYTIngPEIMSKFYGESEQRLREIFE 280
                                       6799***************88844333445788877777666655555444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0024
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEa 30 
                                       + + G+++tGKT +++a a +   ++ +v   
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHEteaNFITV--K 599
                                       6799***************5443344444..3 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00053      0.15      20      51 ..     228     261 ..     199     274 .. 0.80
   2 ?   -0.4   0.0       3.8   1.1e+03      80     105 ..     532     557 ..     528     568 .. 0.68
   3 !    8.9   0.0     0.005       1.4      20      46 ..     568     594 ..     553     601 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00053
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + +lL+G+ G+GKT ++r++a+++g +  +++ P
  gi|488601662|ref|YP_007908133.1| 228 KGVLLHGPPGTGKTLIARAVANEIGASfyTINGP 261
                                       459*********************9987777766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.8
                                       HHHCTTCCCCSTSCEEEEETGGGGCC CS
                              TsaE  80 leelgleeyleeeavvlvEWpeklee 105
                                       +e++g  e +++e v +vEWp k+ e
  gi|488601662|ref|YP_007908133.1| 532 WEDVGGLEEIKREIVEAVEWPLKYPE 557
                                       5666655666666799*****98544 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.005
                                       EEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve 46 
                                       + +lL+G+ G+GKT +++++a++ + +
  gi|488601662|ref|YP_007908133.1| 568 KGVLLYGPPGTGKTLIAKAVAHETEAN 594
                                       459******************998766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       8.6   2.5e+03     218     228 ..     161     171 ..     156     173 .. 0.80
   2 !   11.5   0.0   0.00067      0.19      20      41 ..     230     251 ..     220     289 .. 0.79
   3 !    9.0   0.0    0.0037       1.1      18      41 ..     568     591 ..     557     626 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.6
                            AAA_11 218 fdvviIDEAaq 228
                                        dvviIDE ++
  gi|488601662|ref|YP_007908133.1| 161 KDVVIIDETTK 171
                                       59******875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00067
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                       +l++GPPGtgKT    ++ +++
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEI 251
                                       79**********8888887776 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0037
                            AAA_11  18 eitliqGPPGtgKTktivellsql 41 
                                       + +l+ GPPGtgKT    ++ ++ 
  gi|488601662|ref|YP_007908133.1| 568 KGVLLYGPPGTGKTLIAKAVAHET 591
                                       45799*********7777766665 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.038        11      37     175 ..     230     370 ..     225     382 .. 0.57
   2 ?    3.9   2.3      0.14        42      94     200 ..     407     507 ..     382     526 .. 0.62
   3 ?    7.2   0.0     0.014       4.1      37      66 ..     570     599 ..     560     714 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.038
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       ++++g+ G Gkt + +a++ne+ +++       +++ e ++++    +++  e f e    +  ++ iD+i  +a +
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYT-----INGPEIMSKFYGESEQRLREIFEEAKEnSPSIIFIDEIDAIAPR 301
                                       799*****************99877644.....55666666666665555555555544424456667777777644 PP

                                       H.........HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHH..HHHSSEEEE-----HHHHHHHH CS
                          Bac_DnaA 113 e.........ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrs..rfeaGlvvdieppdletrlail 175
                                                 ++  +l+++++ l e g+ +v+++     +++ ++  lr   rf++   ++i  pd+e r +il
  gi|488601662|ref|YP_007908133.1| 302 RdevtgeverRVVAQLLTLMDGLEERGQVIVIAATN---RVDAVDPALRRpgRFDR--EIEIGVPDREGRFEIL 370
                                       211111111123334555555555555555555543...34444444443114443..4455556666666666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.14
                                       HHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHH CS
                          Bac_DnaA  94 klrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdlet 170
                                        +r++D   i+ +  l++ke++++ ++ +f    +e   ++  ++ + + ++++ ++l  + +  + +die   +e 
  gi|488601662|ref|YP_007908133.1| 407 LIREIDF-AIEGVSKLETKEQIKDLIYSLF----DE--TII--AELEREIIKNMLKQLADQTHGFVGADIEALSKEA 474
                                       3344443.3455555555555555555554....44..344..455557889999999999999999********** PP

                                       HHHHHHHHHHHTT--...--TTHHHHHHHH--S CS
                          Bac_DnaA 171 rlailkkkieaekle...vpeevlefiaervtd 200
                                       +++ l+k + + +l+   +p evle i  +++d
  gi|488601662|ref|YP_007908133.1| 475 AMKALRKYLPQIDLNkdeIPAEVLESIKITIDD 507
                                       *******87765555555******998755543 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.014
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                       +++yg+ G Gkt + ka+++e+++n+   +
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFITVK 599
                                       79*******************999987665 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0058       1.7     117     137 ..     230     250 ..     224     254 .. 0.90
   2 !   11.3   0.0   0.00047      0.13     117     137 ..     570     590 ..     563     595 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0058
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v+++Gp+ tGkt +a+a a+ 
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANE 250
                                       899**************9985 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00047
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp+ tGkt +a+a a+ 
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHE 590
                                       89****************996 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    0.0094       2.7      24      47 ..     230     253 ..     225     303 .. 0.62
   2 ?   -1.2   0.1         7     2e+03      62      96 ..     449     486 ..     422     502 .. 0.69
   3 !    9.9   0.0    0.0027      0.77      23      49 ..     569     595 ..     558     642 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0094
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       v+l G++G+gk+l+Ar+ +++ g 
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGA 253
                                       9****************9987655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 7
                                       HHHHHHT..TTSEEEEEE-TT--HHH.HHHHHHHHHHH CS
                   Sigma54_activ_2  62 ldlleqa..kggtLylkdiadlskae.qkeLlellaka 96 
                                       +++l+q+  +   ++  di+ lsk++  k L ++l++ 
  gi|488601662|ref|YP_007908133.1| 449 KNMLKQLadQTHGFVGADIEALSKEAaMKALRKYLPQI 486
                                       55566642334457778888888865156677777765 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0027
                                       -EEEEEETT--HHHHHHCC--TTS-EE CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwl 49 
                                        v+l G++G+gk+l+A++ +++ + + 
  gi|488601662|ref|YP_007908133.1| 569 GVLLYGPPGTGKTLIAKAVAHETEANF 595
                                       59*****************99887743 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.016       4.7      53      81 ..     227     255 ..     218     342 .. 0.69
   2 !   12.2   0.0   0.00026     0.074      24     115 ..     529     634 ..     512     641 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                            DUF815  53 annvLLwGarGtGKSslvkallneyaeeg 81 
                                        + vLL G  GtGK  + +a+ ne+ ++ 
  gi|488601662|ref|YP_007908133.1| 227 PKGVLLHGPPGTGKTLIARAVANEIGASF 255
                                       5679*******************998776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00026
                            DUF815  24 evklddLvgidkqkealvente.......qf..leglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievek 89 
                                       +v+++d+ g+++ k+++ve +e       +f   + +p + vLL+G  GtGK  + ka+ +e++++   ++  e+  
  gi|488601662|ref|YP_007908133.1| 529 KVTWEDVGGLEEIKREIVEAVEwplkypeKFkkFSIKPPKGVLLYGPPGTGKTLIAKAVAHETEANFitVKGSELLS 605
                                       56666666666666666666542221221331123468899********************9999873344456666 PP

                            DUF815  90 edlkelpklvellrerper...filfvDD 115
                                       + l e +k v+++ +++++   +i+f D 
  gi|488601662|ref|YP_007908133.1| 606 KWLGESEKAVRKIFRKARQvapCIIFFDE 634
                                       66666666666554333321226777775 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.026       7.5       2      25 ..     234     257 ..     233     311 .. 0.82
   2 !   10.6   0.0    0.0019      0.56       1      53 [.     573     626 ..     573     672 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.026
                                       E-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthls 25 
                                       G+PG GK+ +++ ++ ++g ++++
  gi|488601662|ref|YP_007908133.1| 234 GPPGTGKTLIARAVANEIGASFYT 257
                                       9****************9987765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0019
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemrklplee 53 
                                       +G+PG GK+ +++ ++++   +f  +  ++ll +   +++    r+ +rk+ ++ 
  gi|488601662|ref|YP_007908133.1| 573 YGPPGTGKTLIAKAVAHETeaNFITVKGSELLSKWLGESEK-AVRKIFRKARQVA 626
                                       7***********99998764478888878888776655543.3456666665555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0042       1.2      22      41 ..     230     249 ..     223     254 .. 0.87
   2 !    9.7   0.0    0.0019      0.54      22      42 ..     570     590 ..     559     598 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0042
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt++a a+a 
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVAN 249
                                       6788***********99985 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0019
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp GtGKt++a a+a e
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHE 590
                                       7789***********999865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.028       8.2      36      53 ..     230     247 ..     225     253 .. 0.86
   2 ?    3.4   0.0      0.17        50     128     176 ..     273     321 ..     258     336 .. 0.80
   3 !    8.4   0.3    0.0051       1.5      36      55 ..     570     589 ..     564     673 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.028
                            AAA_25  36 allaGapgtGKttlaldl 53 
                                       +ll G+pgtGKt +a  +
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAV 247
                                       689**********98665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.17
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                       + ++++ ++++e + +  + iD ++++ +   +   +v +++v++l  + 
  gi|488601662|ref|YP_007908133.1| 273 QRLREIFEEAKE-NSPSIIFIDEIDAIAPRRDEVTGEVeRRVVAQLLTLM 321
                                       557889999999.88************99955555555599998887664 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0051
                            AAA_25  36 allaGapgtGKttlaldlal 55 
                                       +ll+G+pgtGKt +a  +a+
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAH 589
                                       69***********9988776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0024      0.69       3      92 ..     230     326 ..     228     339 .. 0.59
   2 ?   -1.8   0.0       9.1   2.6e+03     101     163 ..     423     483 ..     390     485 .. 0.57
   3 ?    6.7   0.0     0.021       6.1       3      24 ..     570     591 ..     568     670 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0024
                                       EEEEC-TTTCHHHHHHHHHHHHCTS..-SCCCC-SEEEEEETTTTTTS-.......-HCHHHCCCCTS--SSS-CCH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaeg..klpqgafklvFflslrelsrsgna....rsladllfsqlpepaapvsevw 73 
                                       v+l+G++G GKT  ++ +a ++ ++  + ++ +    F+ ++ ++ r+  +     s+  +  ++ +++a + +ev 
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASfyTINGPEIMSKFYGESEQRLREIFEeakeNSPSIIFIDEIDAIAPRRDEVT 306
                                       79*****************9998762223333344444444333333222233445555555566666666666655 PP

                                       HHHCCSC.CCEEEEEE-STT CS
                             NACHT  74 avllelp.erlLlilDglDe 92 
                                        ++ ++   +lL ++Dgl+e
  gi|488601662|ref|YP_007908133.1| 307 GEVERRVvAQLLTLMDGLEE 326
                                       55544331344455566665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.1
                                       ........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE......EEEE--TCCHHHHHHHHCT CS
                             NACHT 101 ekqpvrtlLselirkkllpeasllltvrpralrdleeqleea....ivlevegfsesrrkqlvrkyf 163
                                       +k+++++l+ +l+ ++++ e         +  +++ +ql+++      + +e++s++ + + +rky+
  gi|488601662|ref|YP_007908133.1| 423 TKEQIKDLIYSLFDETIIAELE------REIIKNMLKQLADQthgfVGADIEALSKEAAMKALRKYL 483
                                       3444556666666654444333......333333333333333333566777777777777777765 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.021
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                       v+l G++G GKT  ++ +a++ 
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHET 591
                                       789*************999875 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 ?    7.4   0.0     0.014         4      22      49 ..     225     252 ..     195     286 .. 0.80
   2 !    9.6   0.0    0.0028      0.82      17      74 ..     557     611 ..     511     646 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.014
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierll 49 
                                       +  k +l++ + GtGKTl+a +++ ++ 
  gi|488601662|ref|YP_007908133.1| 225 DPPKGVLLHGPPGTGKTLIARAVANEIG 252
                                       6678899*************88887765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0028
                                       .........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG CS
                            ResIII  17 eklks...krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef 74 
                                       ek+k+   k  k +l+  + GtGKTl+a +++ +   +      ++ v + +ll+++l e 
  gi|488601662|ref|YP_007908133.1| 557 EKFKKfsiKPPKGVLLYGPPGTGKTLIAKAVAHETEAN------FITVKGSELLSKWLGES 611
                                       33333555999999*************98888877764......34567777777777554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0036         1      23      43 ..     230     250 ..     216     259 .. 0.83
   2 !    7.7   0.0    0.0064       1.8      23      43 ..     570     590 ..     560     598 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l+G +G GKt +a+ + n+
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANE 250
                                       789**************9998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0064
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l+G +G GKt +ak + ++
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHE 590
                                       779**************9998 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0076       2.2      15      37 ..     223     245 ..     214     251 .. 0.83
   2 ?    2.2   0.1      0.33        97     109     154 ..     273     324 ..     262     341 .. 0.69
   3 ?   -1.6   0.2       4.9   1.4e+03      70      84 ..     463     477 ..     391     520 .. 0.53
   4 !    7.6   0.0    0.0073       2.1      21      38 ..     569     586 ..     560     599 .. 0.86
   5 ?    1.6   0.1       0.5   1.5e+02      99     144 ..     752     797 ..     723     803 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0076
                            ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                       Gi   + vl+ G pGtGKt++a 
  gi|488601662|ref|YP_007908133.1| 223 GIDPPKGVLLHGPPGTGKTLIAR 245
                                       77777889************985 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.33
                            ATPase 109 eelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                       ++l+e+ +e k+   + + iD i+++     e + +v R+ + ql++ + +l
  gi|488601662|ref|YP_007908133.1| 273 QRLREIFEEAKEnspSIIFIDEIDAIaprRDEVTGEVERRVVAQLLTLMDGL 324
                                       5556665555554448899999999943233445567899999999998654 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.9
                            ATPase  70 lGwdlekleeegkla 84 
                                       +G d+e+l +e  + 
  gi|488601662|ref|YP_007908133.1| 463 VGADIEALSKEAAMK 477
                                       244444444443333 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0073
                            ATPase  21 vvlitGepGtGKtifalq 38 
                                        vl++G pGtGKt++a+ 
  gi|488601662|ref|YP_007908133.1| 569 GVLLYGPPGTGKTLIAKA 586
                                       589***********9975 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.5
                            ATPase  99 kdkedleelieelaeaikeika.krvviDsitglayeekeavaReil 144
                                         +edl++ + e+++ ++++k  k  v Ds  ++ ye  e++aR++ 
  gi|488601662|ref|YP_007908133.1| 752 ALREDLNAEVVEMRHFLEALKKvKPSVTDSMLSF-YERFEEKARQER 797
                                       6789999999999999999887699*********.*********975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       5.6   1.6e+03      93     104 ..     158     169 ..     140     177 .. 0.75
   2 ?    7.7   0.0      0.01         3       2      32 ..     230     260 ..     229     276 .. 0.85
   3 ?    0.3   0.1       1.9   5.6e+02      81     105 ..     271     296 ..     265     320 .. 0.78
   4 ?    6.8   0.1     0.021         6       2      32 ..     570     600 ..     569     604 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.6
                                       HHHH-EEEE--- CS
                          NTPase_1  93 lseadviviDEi 104
                                          +dv++iDE 
  gi|488601662|ref|YP_007908133.1| 158 TDPKDVVIIDET 169
                                       46789*****95 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.01
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + + v++++  s ++++G
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYTING 260
                                       6789******************998888888 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHH.HHH-EEEE---S CS
                          NTPase_1  81 feelalealrkal.seadviviDEiG 105
                                        e+   e++++a  +++ +i iDEi 
  gi|488601662|ref|YP_007908133.1| 271 SEQRLREIFEEAKeNSPSIIFIDEID 296
                                       567777888888756677******95 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.021
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + k v+++ + + ++v+G
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFITVKG 600
                                       6788**************9999888888887 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0017      0.49       8      63 ..     236     295 ..     232     334 .. 0.70
   2 ?    4.8   0.0     0.094        27       8      54 ..     576     623 ..     572     675 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0017
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde...rsrlssflskl 63 
                                        G+g++ i++a+A++ g  fy  + +e ++k  g se+ + e ++e   +s++  f++++
  gi|488601662|ref|YP_007908133.1| 236 PGTGKTLIARAVANEIGASFYTINGPEIMSKFYGESEQRLrEIFEEakeNSPSIIFIDEI 295
                                       69*******************998888888888888888865555542244444444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.094
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde.rs 54 
                                        G+g++ i++a+A++ + +f+  +  e ++k lg se+ v+++   ++
  gi|488601662|ref|YP_007908133.1| 576 PGTGKTLIAKAVAHETEANFITVKGSELLSKWLGESEKAVRKIFRkAR 623
                                       59********************************99999955444143 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.6    0.0071         2      12      36 ..     229     253 ..     224     466 .. 0.77
   2 !    9.6   0.0    0.0039       1.1      11      34 ..     568     591 ..     562     618 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0071
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallve 36 
                                        +l+ ++pGtGKT + +++ +++ +
  gi|488601662|ref|YP_007908133.1| 229 GVLLHGPPGTGKTLIARAVANEIGA 253
                                       6899*********999988776655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0039
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivall 34 
                                       k +l+ ++pGtGKT + k++ ++ 
  gi|488601662|ref|YP_007908133.1| 568 KGVLLYGPPGTGKTLIAKAVAHET 591
                                       56899*********8877765544 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0055       1.6       1      44 [.     236     284 ..     236     286 .. 0.72
   2 ?    6.2   0.0     0.036        10       1      23 [.     576     598 ..     576     624 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0055
                                       TTSSHHHHHHHHHHHHTSEEEEHHH..HHHHHHT...S-HHHHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDe..liekrtg...ksiaeifeeege 44 
                                       +G+GK+ +++++A+++g +f+ +    +++k  g   ++ +eifee  e
  gi|488601662|ref|YP_007908133.1| 236 PGTGKTLIARAVANEIGASFYTINGpeIMSKFYGeseQRLREIFEEAKE 284
                                       69******************98864315555554333567777777766 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.036
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A++ + +fi +
  gi|488601662|ref|YP_007908133.1| 576 PGTGKTLIAKAVAHETEANFITV 598
                                       69******************976 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0075       2.2       3      26 ..     232     255 ..     230     260 .. 0.90
   2 ?    6.3   0.0     0.024         7       4      27 ..     573     596 ..     570     600 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0075
                                       EE-STTSSHHHHHHHHHHHHT-EE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglky 26 
                                       + GP g+GK  +ara+a+++g+++
  gi|488601662|ref|YP_007908133.1| 232 LHGPPGTGKTLIARAVANEIGASF 255
                                       68******************9987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.024
                                       E-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                        GP g+GK  +a+a+a++ +++++
  gi|488601662|ref|YP_007908133.1| 573 YGPPGTGKTLIAKAVAHETEANFI 596
                                       6*****************999987 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.38   1.1e+02      15      34 ..     228     247 ..     215     264 .. 0.83
   2 ?    2.6   0.0      0.34        98     106     170 ..     273     338 ..     252     344 .. 0.77
   3 ?    1.2   0.1      0.97   2.8e+02      15      33 ..     568     586 ..     561     604 .. 0.83
   4 ?    4.8   0.0     0.072        21     125     170 ..     630     679 ..     608     684 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.38
                                       CEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflip 34 
                                       + vl++++ G+GKTl++   
  gi|488601662|ref|YP_007908133.1| 228 KGVLLHGPPGTGKTLIARAV 247
                                       6799***********98655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.34
                                       HHHHHHHHCTSSHCTTEEEEEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 106 grlddllstgklnlsqvrflVlDEadrlldq...gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +rl +++++ k   ++ +++ +DE+d +        ++  +r+++ql +  +  ++  qviv+ AT  
  gi|488601662|ref|YP_007908133.1| 273 QRLREIFEEAK--ENSPSIIFIDEIDAIAPRrdeVTGEVERRVVAQLLTLMDGLEERGQVIVIAATNR 338
                                       56777776555..67788999******98665547788888899999766666668888******976 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.97
                                       CEEEEEESTTSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlafli 33 
                                       + vl+ ++ G+GKTl++  
  gi|488601662|ref|YP_007908133.1| 568 KGVLLYGPPGTGKTLIAKA 586
                                       5699999*******99755 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.072
                                       EEEETHHHHHHT....TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 125 lVlDEadrlldq....gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       + +DE+d + ++    + s+ ++r++nq+ +  +  ++ ++vivl AT  
  gi|488601662|ref|YP_007908133.1| 630 IFFDEIDAIAQMrgldEGSRAVERVVNQILTEMDGLEELEEVIVLGATNR 679
                                       558********9988778899999****9655555555557******976 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0044       1.3       2      31 ..     230     259 ..     229     284 .. 0.90
   2 ?    5.3   0.1     0.072        21       2      30 ..     570     598 ..     569     603 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0044
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                       +++hG+P +GKt +a ++a + +a++ ti 
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYTIN 259
                                       689**********************99996 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.072
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       +++ G+P +GKt +a ++a++ ea ++t+
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFITV 598
                                       5789********************99998 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.5   4.3e+02       4      30 ..     229     255 ..     227     260 .. 0.84
   2 ?    1.5   0.0      0.74   2.1e+02      75      96 ..     264     288 ..     257     304 .. 0.79
   3 ?    3.7   0.0      0.15        43       4      30 ..     569     595 ..     567     602 .. 0.87
   4 ?    3.2   0.0      0.22        63      75     109 ..     604     642 ..     593     651 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.5
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        v l gp g+Gk  +  a+ +e   +f
  gi|488601662|ref|YP_007908133.1| 229 GVLLHGPPGTGKTLIARAVANEIGASF 255
                                       68899**********999988877776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.74
                                       TTEEEEEEHHHHHHHHHTTSE...E CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki...v 96 
                                        ++ yg+s +  +e++e++k+    
  gi|488601662|ref|YP_007908133.1| 264 MSKFYGESEQRLREIFEEAKEnspS 288
                                       6789**************9975552 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.15
                                       EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                        v l gp g+Gk  + ka+ +e + +f
  gi|488601662|ref|YP_007908133.1| 569 GVLLYGPPGTGKTLIAKAVAHETEANF 595
                                       6899***************99998888 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.22
                                       TTEEEEEEHHHHHHHHHTTSE...EEEE--.CHHHHHHH CS
                     Guanylate_kin  75 sgnlygtsveaieevlekgki...viLDvd.iqavkqlr 109
                                        ++ +g+s +a+++++ k+++   +i+  d i+a++q+r
  gi|488601662|ref|YP_007908133.1| 604 LSKWLGESEKAVRKIFRKARQvapCIIFFDeIDAIAQMR 642
                                       56889***************9778777666677777766 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.091        26      33      56 ..     225     248 ..     210     257 .. 0.82
   2 ?    5.7   0.0     0.029       8.5      35      59 ..     567     591 ..     541     601 .. 0.75
   3 ?   -2.2   0.0       8.2   2.4e+03     107     133 ..     614     640 ..     609     658 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.091
                              TniB  33 krmpnlllvGdsnnGKtmivekFa 56 
                                       + ++ +ll+G++ +GKt i++  a
  gi|488601662|ref|YP_007908133.1| 225 DPPKGVLLHGPPGTGKTLIARAVA 248
                                       556889*************98765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.029
                              TniB  35 mpnlllvGdsnnGKtmivekFarlh 59 
                                       ++ +ll+G++ +GKt i++  a++ 
  gi|488601662|ref|YP_007908133.1| 567 PKGVLLYGPPGTGKTLIAKAVAHET 591
                                       5789*************99877665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 8.2
                              TniB 107 leqqvlrllrelkvrvLiiDEihnlla 133
                                       + +++ r  r++ + ++ +DEi+ + +
  gi|488601662|ref|YP_007908133.1| 614 AVRKIFRKARQVAPCIIFFDEIDAIAQ 640
                                       4556667778999999******99875 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 ?    5.8   0.0     0.019       5.6      36      68 ..     231     263 ..     223     269 .. 0.87
   2 ?   -0.9   0.0       2.1   6.1e+02     153     202 ..     390     438 ..     379     461 .. 0.67
   3 ?    3.8   0.0     0.078        23      35      69 ..     570     604 ..     563     645 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.019
                             AAA_6  36 apaGpagtGKtEtvkdLakalakqvvvfncsdq 68 
                                        ++Gp gtGKt   + +a++++  ++ +n  + 
  gi|488601662|ref|YP_007908133.1| 231 LLHGPPGTGKTLIARAVANEIGASFYTINGPEI 263
                                       679**********************99997665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                             AAA_6 153 dnLkalfRpvammvPdlelIaeimLfseGfkeakelakklvtlykllseq 202
                                       + Lk+l ++ am   d +lI ei ++ eG ++ ++  +    +y+l++e 
  gi|488601662|ref|YP_007908133.1| 390 EALKSLKKSYAM-DGDEDLIREIDFAIEGVSKLETKEQIKDLIYSLFDET 438
                                       566666666654.5677788888888887777666555555556655554 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.078
                             AAA_6  35 gapaGpagtGKtEtvkdLakalakqvvvfncsdql 69 
                                         ++Gp gtGKt   k +a++    ++ ++ s+ l
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFITVKGSELL 604
                                       5679***************9998888888877765 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.02       5.9       4      36 ..     230     262 ..     228     317 .. 0.84
   2 ?    5.1   0.0     0.062        18       4      36 ..     570     602 ..     568     659 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.02
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDa 36 
                                       +lL+G + +GK+ +ara+ + + ++++ ++  +
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYTINGPE 262
                                       89****************999999998876555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.062
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDa 36 
                                       +lL G + +GK+ +a+a+ + +++ ++ ++  +
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFITVKGSE 602
                                       89**********************999886555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.064        18      48      75 ..     230     257 ..     219     274 .. 0.81
   2 ?   -0.1   0.0       2.6   7.6e+02     140     177 ..     262     297 ..     257     304 .. 0.77
   3 ?    4.5   0.0     0.098        28      48      75 ..     570     597 ..     553     649 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.064
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklre 75 
                                       +L+ GP+G gk+ + + ++ e g ++  
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYT 257
                                       689******************9998754 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.6
                             Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteies 177
                                       ++ +kfy++s ++lre+  ++   s +   i+ i ei+ 
  gi|488601662|ref|YP_007908133.1| 262 EIMSKFYGESeQRLREIFEEAKENSPS---IIFIDEIDA 297
                                       677999999989999999887655544...666777775 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.098
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklre 75 
                                       +L+ GP+G gk+ + k ++ e   +++ 
  gi|488601662|ref|YP_007908133.1| 570 VLLYGPPGTGKTLIAKAVAHETEANFIT 597
                                       6899************999998777665 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     0.045        13      59      78 ..     224     243 ..     198     258 .. 0.87
   2 ?    5.8   0.0     0.019       5.5      55      78 ..     560     583 ..     537     592 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.045
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtyl 78 
                                         p++g+ l+G+ G GKt +
  gi|488601662|ref|YP_007908133.1| 224 IDPPKGVLLHGPPGTGKTLI 243
                                       579***************76 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                       AFG1_ATPase  55 krksvepvrglYlwGgvGrGKtyl 78 
                                       k+ s +p++g+ l+G+ G GKt +
  gi|488601662|ref|YP_007908133.1| 560 KKFSIKPPKGVLLYGPPGTGKTLI 583
                                       334789****************86 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.014       4.1      57      77 ..     231     251 ..     224     257 .. 0.88
   2 ?    3.8   0.0       0.2        56      55      77 ..     569     591 ..     536     608 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                                       EEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  57 sfhGwtGtGknfvaeiiaenl 77 
                                        +hG +GtGk  +a+ +a+++
  gi|488601662|ref|YP_007908133.1| 231 LLHGPPGTGKTLIARAVANEI 251
                                       58***************9976 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.2
                                       EEEEEE-TTSSHHHHHHHHHHHH CS
                            Torsin  55 vlsfhGwtGtGknfvaeiiaenl 77 
                                        + ++G +GtGk  +a+ +a+++
  gi|488601662|ref|YP_007908133.1| 569 GVLLYGPPGTGKTLIAKAVAHET 591
                                       45689************999865 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0061       1.8       4      62 ..     231     294 ..     230     314 .. 0.84
   2 ?    2.0   0.0      0.49   1.4e+02       4      59 ..     571     631 ..     570     651 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0061
                               Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarliridn 62 
                                       l +G+pG+gKt+  +av +++       +g +i+ +  G   +r++ +++e+++ ++ +i+id+
  gi|488601662|ref|YP_007908133.1| 231 LLHGPPGTGKTLiaRAVANEIGASFYtiNGPEIMSKFYGESEQRLREIFEEAKEnSPSIIFIDE 294
                                       789********733689999998555347**********************9999999***993 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.49
                               Zot   4 lvtGapGsgKtsga..vkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarlir 59 
                                       l +G+pG+gKt+ a  v  +       ++g ++  +  G   ++++++++++ + ++ +i+
  gi|488601662|ref|YP_007908133.1| 571 LLYGPPGTGKTLIAkaVAHETEAnfITVKGSELLSKWLGESEKAVRKIFRKARQvAPCIIF 631
                                       679********86511544433332223566666666666666666666666555555555 PP

>> CtsR_C  CtsR C-terminal dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00034     0.098      18      48 ..     423     453 ..     404     462 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00034
                            CtsR_C  18 seqdaeaiiqrLleegliterEakLmkaals 48 
                                       + ++++++i+ L++e +i e E++++k++l 
  gi|488601662|ref|YP_007908133.1| 423 TKEQIKDLIYSLFDETIIAELEREIIKNMLK 453
                                       67889************************97 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.31        90      60      87 ..     230     257 ..     226     262 .. 0.91
   2 ?    7.0   0.0    0.0094       2.7      18      92 ..     527     601 ..     509     605 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.31
                                       EEEEESSTSTHHHHHHHHHHHSSSEEEE CS
                               MCM  60 vllvgdpgtaKsqlLkyveklapravyt 87 
                                       vll g pgt+K+ + ++v++ +  + yt
  gi|488601662|ref|YP_007908133.1| 230 VLLHGPPGTGKTLIARAVANEIGASFYT 257
                                       89*****************999999998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0094
                                       HHHHSSTTSSS-HHHHHHHHHHHH---EB.BBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSS CS
                               MCM  18 lvksiapsiyghedvkkaillqlfggvkk.kledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkgs 92 
                                       + k   + + g e++k+ i+ ++  + k  ++ +k +++    vll g pgt+K+ + k+v++   +a++++ kgs
  gi|488601662|ref|YP_007908133.1| 527 IPKVTWEDVGGLEEIKREIVEAVEWPLKYpEKFKKFSIKPPKGVLLYGPPGTGKTLIAKAVAH-ETEANFITVKGS 601
                                       5555666677777777777655554444312234567888889****************9995.556777777776 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 ?   -2.0   0.0       8.5   2.5e+03      61      74 ..     159     172 ..     153     175 .. 0.79
   2 ?    4.4   0.0     0.091        26       2      71 ..     231     295 ..     230     300 .. 0.57
   3 ?    5.3   0.0      0.05        15       5      71 ..     574     635 ..     570     641 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.5
                   Viral_helicase1  61 tkgkililDEylll 74 
                                         ++++i+DE +++
  gi|488601662|ref|YP_007908133.1| 159 DPKDVVIIDETTKV 172
                                       3489******9986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.091
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       + hG pG GK+ + r ++++   ++ +++   e+ +   ++ + ++ r  + f++a+ +s    i+++DE+
  gi|488601662|ref|YP_007908133.1| 231 LLHGPPGTGKTLIARAVANEIgASFYTING-PEIMS---KFYGESEQRLREIFEEAKENS--PSIIFIDEI 295
                                       67**********999999994422222222.23333...333333344333344444333..457777776 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.05
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ + + ++++   ++ +++   ell++++ ++++   + ++++ + +  ++   i+++DE+
  gi|488601662|ref|YP_007908133.1| 574 GPPGTGKTLIAKAVAHETeANFITVKG-SELLSKWLGESEKAVRKIFRKARQVA--PC---IIFFDEI 635
                                       78******9999999888977777777.8*******888888777777665543..34...8999997 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 ?    4.4   0.0      0.11        31      21      38 ..     227     243 ..     218     249 .. 0.75
   2 ?    6.0   0.0     0.035        10      16      38 ..     561     583 ..     548     589 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.11
                            AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                       +kg +ll Gp G+GK+ +
  gi|488601662|ref|YP_007908133.1| 227 PKG-VLLHGPPGTGKTLI 243
                                       355.9**********755 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.035
                            AAA_29  16 tieidlkgatlltGpsGsGKSTl 38 
                                       +++i++   +ll Gp G+GK+ +
  gi|488601662|ref|YP_007908133.1| 561 KFSIKPPKGVLLYGPPGTGKTLI 583
                                       445554445***********866 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.047        13     131     156 ..     229     254 ..     203     262 .. 0.88
   2 ?    4.8   0.0     0.042        12     124     156 ..     565     594 ..     497     602 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.047
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks 156
                                        +l+ G+ g+GKt ++ a+ +ei +s
  gi|488601662|ref|YP_007908133.1| 229 GVLLHGPPGTGKTLIARAVANEIGAS 254
                                       5899***************9999876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.042
                             T2SSE 124 kavrerglilvsGgTgsGKttllyallkeinks 156
                                       k+    + +l+ G+ g+GKt ++ a+ +e +++
  gi|488601662|ref|YP_007908133.1| 565 KP---PKGVLLYGPPGTGKTLIAKAVAHETEAN 594
                                       33...678999************9999886654 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.15        44       5      28 ..     231     254 ..     228     259 .. 0.90
   2 ?    6.3   0.0     0.019       5.4       5      31 ..     571     597 ..     568     606 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.15
                               IPT   5 lifGatttGKtaeaiklaketgap 28 
                                       l++G+ +tGKt  a ++a+e ga+
  gi|488601662|ref|YP_007908133.1| 231 LLHGPPGTGKTLIARAVANEIGAS 254
                                       899*****************9987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++G+ +tGKt  a ++a+et a  i+
  gi|488601662|ref|YP_007908133.1| 571 LLYGPPGTGKTLIAKAVAHETEANFIT 597
                                       89*******************988775 PP

>> Antiterm  Antitermination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.012       3.5      34      80 ..     416     460 ..     407     461 .. 0.85
   2 ?    1.4   0.0       1.5   4.2e+02      33      57 ..     464     488 ..     462     500 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.012
                                       XXBXSTTHHHHHHHHHCCCCCHGHHH.HHTSHHHHCHHHHHHHHHHHH CS
                          Antiterm  34 rGysrldsteaiealtklapaltekt.lrklwerkvkpflelLvtkaf 80 
                                       +G+s+l++    e++++l+ +l ++t +++l++++ k++l++L+++ +
  gi|488601662|ref|YP_007908133.1| 416 EGVSKLET---KEQIKDLIYSLFDETiIAELEREIIKNMLKQLADQTH 460
                                       67777776...7889999999999999*****************9865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.5
                                       TXXBXSTTHHHHHHHHHCCCCCHGH CS
                          Antiterm  33 krGysrldsteaiealtklapalte 57 
                                       ++ ++ l ++ a++al+k++p++  
  gi|488601662|ref|YP_007908133.1| 464 GADIEALSKEAAMKALRKYLPQIDL 488
                                       7889999**************9875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   6.9       4.9   1.4e+03      16      45 ..     225     253 ..     217     526 .. 0.42
   2 ?    4.8   0.0      0.12        35      10      39 ..     559     587 ..     557     588 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 4.9
                            AAA_23  16 dFskgltlItGpNGaGKTTildAiklaLyg 45 
                                       d  kg+ l++Gp G+GKT i +A+    + 
  gi|488601662|ref|YP_007908133.1| 225 DPPKGV-LLHGPPGTGKTLIARAVANEIGA 253
                                       555555.88888888888888887644443 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.12
                            AAA_23  10 frdqeidFskgltlItGpNGaGKTTildAi 39 
                                       f++++i   kg+ l++Gp G+GKT i  A+
  gi|488601662|ref|YP_007908133.1| 559 FKKFSIKPPKGV-LLYGPPGTGKTLIAKAV 587
                                       778888888888.9**********999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (809 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        63  (0.00351386); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              62  [number of targets reported over threshold]
# CPU time: 1.03u 0.39s 00:00:01.42 Elapsed: 00:00:00.56
# Mc/sec: 4330.24
//
Query:       gi|488601663|ref|YP_007908134.1|  [L=393]
Description: TIGR00299 family protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-105  352.1   0.0   4.2e-105  351.9   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 !  351.9   0.0  2.4e-109  4.2e-105       2     373 .]       5     380 ..       4     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: 351.9 bits;  conditional E-value: 2.4e-109
                            DUF111   2 yldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdveeeehehehrslaeieeii 78 
                                       ++dc+ G+sGDm++++Ll +  +++ l +  + l+l ++e+++++v+k+gisa+ vdv +   +++ r++++++++i
  gi|488601663|ref|YP_007908134.1|   5 IVDCFNGASGDMIIASLLGISLSESDLDRIAKLLDL-NIEFSVKTVNKKGISAKMVDVLD---RNTDRKFSDVKNLI 77 
                                       68*************************999999999.8********************66...8999********** PP

                            DUF111  79 eaaslsekvkek...alaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgv..ekvvasplalG 150
                                       ++++ ++++ke      +if++laeAea+vhg+++ee+ fhEvG+ Dai+d+v+ al++++L     +++++p++lG
  gi|488601663|ref|YP_007908134.1|  78 KKLKKDQELKEIyqpTYEIFRILAEAEARVHGKDIEEIVFHEVGSDDAIFDVVSSALGFSRLISrgYEIFTTPINLG 154
                                       ****99988875222789********************************************664478********* PP

                            DUF111 151 sGtvrcahGilPvPaPAvlellkelklkl...gevegElvTPTGaAilaalaeefgslpamkvekiGyGaGkrdlee 224
                                        G+++++hG++PvPaPAv+e+lk++kl++   +  ++El TPT  Ail+++++ + + p ++v++++yGaGk+d+ +
  gi|488601663|ref|YP_007908134.1| 155 YGEIEMHHGRYPVPAPAVVEILKNSKLEVyfgRIGDEELFTPTASAILSYFSNGCLKHP-FTVDDVSYGAGKKDT-D 229
                                       **************************99999766789**************99999886.***************.9 PP

                            DUF111 225 ipnvlRvlleeeeeelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedae 301
                                        pnvlR++l+   ++  +++++++etniDD+s+e++g++++ L++  ++D++++p++ KK+Rp+++l+++c+ ++ae
  gi|488601663|ref|YP_007908134.1| 230 KPNVLRIMLG---RASVHDSIAIVETNIDDVSGEIMGNAMNILTKI-CHDISAIPVFGKKNRPGYILKAICDFSKAE 302
                                       *********6...67789***********************99888.9***************************** PP

                            DUF111 302 eleellfretttlGvRese.verlvlereietvetelg....evrvKva.eevvkvkpEyedvkkiAeetglplkev 372
                                       e+++++++et++lGvR  +  +r+ +er++++v+++++    +vr+Kv+  ++  +kpE+edv++i+ee g pl ev
  gi|488601663|ref|YP_007908134.1| 303 EVARVMMHETGSLGVRIIPvYHRMLAERHFREVKINVHgkefTVRFKVSyPDQKIAKPEFEDVRRISEEIGKPLPEV 379
                                       *******************99****************999*********7568899*******************99 PP

                            DUF111 373 l 373
                                       +
  gi|488601663|ref|YP_007908134.1| 380 Y 380
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.35s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2199.20
//
Query:       gi|488601664|ref|YP_007908135.1|  [L=219]
Description: DNA repair and recombination protein RadB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-35  122.1   0.3    2.6e-35  121.9   0.3    1.0  1  Rad51            Rad51
    2.6e-16   59.9   0.0    3.1e-16   59.6   0.0    1.2  1  RecA             recA bacterial DNA recombination protein
    8.9e-11   41.7   0.0    1.3e-10   41.2   0.0    1.2  1  AAA_25           AAA domain
    3.7e-10   39.5   5.3    1.5e-08   34.3   5.3    2.1  1  ATPase           KaiC
    6.7e-10   38.9   0.1      8e-10   38.7   0.1    1.0  1  Zot              Zonular occludens toxin (Zot)
    2.4e-08   33.9   0.1    3.4e-08   33.5   0.1    1.2  1  AAA_24           AAA domain
    3.8e-06   26.4   2.5     0.0072   15.7   1.4    2.1  2  DnaB_C           DnaB-like helicase C terminal domain
    0.00014   22.2   0.4    0.00031   21.2   0.4    1.6  1  AAA              ATPase family associated with various cellul
    0.00096   19.7   0.0     0.0015   19.1   0.0    1.4  1  AAA_18           AAA domain
     0.0012   19.4   0.4     0.0021   18.6   0.4    1.5  1  ABC_tran         ABC transporter
     0.0015   18.5   0.5     0.0024   17.9   0.5    1.4  1  AAA_14           AAA domain
     0.0044   16.9   0.2     0.0064   16.4   0.2    1.2  1  AAA_31           AAA domain
     0.0091   15.6   0.4      0.038   13.5   0.4    1.9  1  CobU             Cobinamide kinase / cobinamide phosphate gua
  ------ inclusion threshold ------
      0.011   15.4   0.1       0.37   10.5   0.0    2.3  2  IstB_IS21        IstB-like ATP binding protein
      0.015   15.3   0.1      0.026   14.6   0.1    1.6  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
      0.033   14.5   0.1      0.054   13.8   0.1    1.4  1  AAA_22           AAA domain
      0.034   13.1   0.1      0.082   11.8   0.1    1.7  2  AAA_10           AAA-like domain
      0.034   14.0   0.3      0.051   13.5   0.3    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.044   13.6   0.2       0.32   10.8   0.0    2.1  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.046   12.5   0.1       0.16   10.8   0.0    1.8  2  AAA_35           AAA-like domain
      0.069   12.4   0.1      0.097   11.9   0.1    1.2  1  V_cholerae_RfbT  Vibrio cholerae RfbT protein


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.3     3e-38   2.6e-35      18     253 ..       2     218 ..       1     219 [] 0.93

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 3e-38
                                       EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHH CS
                             Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaer 94 
                                       +l tGs  lD+lLgGG+e g it i+G + +Gkt +c  l+ t+ ++      egk++yidteg +  er+ +i   
  gi|488601664|ref|YP_007908135.1|   2 NLPTGSDCLDRLLGGGVEKGIITQIYGPSATGKTSICLMLTYTTAMN------EGKVIYIDTEG-LSRERVNQIF-- 69 
                                       689**********************************9999998876......9*********8.7779999995.. PP

                                       TT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHH CS
                             Rad51  95 ykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrk 171
                                          + +e+l+nv    + +  +q++ +++a++l  ++k+ l++vDs+talyR++ ++ ++  k +++l+  l+ L  
  gi|488601664|ref|YP_007908135.1|  70 ---EIKEALNNVFLYEVMNFRQQSSAIREASKLCRSEKIDLIVVDSITALYRSELENDEKQIKIKRELTSQLTFLLG 143
                                       ...46899***********************************************99999999999*********** PP

                                       HHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-E.EEEEE CS
                             Rad51 172 ladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpele.avfai 247
                                       la ++++avv+tnq+  +v          + kP gG  l h s+t + l k  ++eRi+ +++  + +e e + f i
  gi|488601664|ref|YP_007908135.1| 144 LARKYNLAVVVTNQMFTDVRS-------GEIKPLGGPSLDHLSKTIVGLEKV-NRERIATLIKHRSKAEGErCSFII 212
                                       ****************99988.......5789*****************997.578999999999998876589*** PP

                                       ETTEEE CS
                             Rad51 248 geeGie 253
                                       +++G+e
  gi|488601664|ref|YP_007908135.1| 213 TDKGVE 218
                                       ****95 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   3.6e-19   3.1e-16      34     192 ..       3     161 ..       1     211 [. 0.83

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 3.6e-19
                                       E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--..GGG- CS
                              RecA  34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvd..idel 108
                                       +++Gs  ld  lG GG+ kG i++iyGp ++Gkt+++l +   +  + g + +id+e     +  + + ++  ++++
  gi|488601664|ref|YP_007908135.1|   3 LPTGSDCLDRLLG-GGVEKGIITQIYGPSATGKTSICLMLTYTTAMNEGKVIYIDTEGLSRERVNQIFEIKeaLNNV 78 
                                       78***********.*******************************************76665555555553226777 PP

                                       EEE--...SSHHHHHHHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--E CS
                              RecA 109 lvsqp...dtGeqaleiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntv 182
                                       ++ +     +  +a+  a +l rs  idlivvds++al  ++e+e +  ++++ ++  l sq l  l g  +k n +
  gi|488601664|ref|YP_007908135.1|  79 FLYEVmnfRQQSSAIREASKLCRSEKIDLIVVDSITALY-RSELEND--EKQIKIKRELTSQ-LTFLLGLARKYNLA 151
                                       76554100455567777889*****************96.8999987..5566666667776.88999********* PP

                                       EEEEEE---- CS
                              RecA 183 vifinqirek 192
                                       v+  nq+ + 
  gi|488601664|ref|YP_007908135.1| 152 VVVTNQMFTD 161
                                       ******8665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   1.5e-13   1.3e-10      21     186 ..       9     155 ..       2     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.5e-13
                            AAA_25  21 prrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                       +++ l++g + +g ++ ++G+++tGKt ++l l +++a             gkV+y+++E+     r+R+ +++e  
  gi|488601664|ref|YP_007908135.1|   9 CLDRLLGGGVEKGIITQIYGPSATGKTSICLMLTYTTAMN----------EGKVIYIDTEGLS---RERVNQIFEIK 72 
                                       6778889888*********************999999964..........58**********9...88999888777 PP

                            AAA_25  98 rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg.densnsd......vga 167
                                       ++  +++++ ++++          +++   +++++  + +++ e+++l+v+D+++++++   en++++       ++
  gi|488601664|ref|YP_007908135.1|  73 EALNNVFLYEVMNF----------RQQS--SAIREASKLCRS-EKIDLIVVDSITALYRSeLENDEKQikikreLTS 136
                                       77799999999876..........3333..788888999999.99***************88888888665543355 PP

                            AAA_25 168 lvealeriarrtgaavllv 186
                                        ++ l  +ar+++ av+++
  gi|488601664|ref|YP_007908135.1| 137 QLTFLLGLARKYNLAVVVT 155
                                       6666677899999999886 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   5.3   1.7e-11   1.5e-08       2     225 ..       4     218 ..       3     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.7e-11
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       +tg   lD++l gG+ +g ++ i+G + tGKt ++l  +++ a++ + +++++ +e  +++   +++++  ++++  
  gi|488601664|ref|YP_007908135.1|   4 PTGSDCLDRLLGGGVEKGIITQIYGPSATGKTSICLMLTYTTAMN-EGKVIYIDTEGLSRE---RVNQI-FEIKEAL 75 
                                       89999****************************************.899****99877643...44443.5677777 PP

                            ATPase  79 eegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl..ayeekeav....aReilrqlvr 149
                                       ++  +++ ++++ +++          ++ i+e  +  ++ k+  +v+Dsit+l  ++ e++++     Re   ql+ 
  gi|488601664|ref|YP_007908135.1|  76 NN--VFLYEVMNFRQQ----------SSAIREASKLCRSEKIDLIVVDSITALyrSELENDEKqikiKRELTSQLTF 140
                                       77..555555555443..........445667788999**************9643333332222325666667776 PP

                            ATPase 150 vl...kklgvTailvsekss.....seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfe 218
                                        l   +k+++  + ++++ +     + +  gg+ + + +++ ++ L++     +++R+   +k R++  + ++  f 
  gi|488601664|ref|YP_007908135.1| 141 LLglaRKYNLAVVVTNQMFTdvrsgEIKPLGGPSLDH-LSKTIVGLEK----VNRERIATLIKHRSK-AEGERCSFI 211
                                       666667888888888887667777777899*******.9999999994....356788889999975.56788999* PP

                            ATPase 219 Iteegik 225
                                       It++g++
  gi|488601664|ref|YP_007908135.1| 212 ITDKGVE 218
                                       ***9985 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   9.4e-13     8e-10       5     173 ..      26     204 ..      22     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 9.4e-13
                               Zot   5 vtGapGsgKtsgavkkdllpalkegRkiitnidGlrlerieqvlgekvstar..lirid.npegaetlkefakwati 78 
                                        +G+  +gKts  +      a+ eg++i+ + +Gl  er++q+++ k   ++  l ++   +++ + + e+ k ++ 
  gi|488601664|ref|YP_007908135.1|  26 IYGPSATGKTSICLMLTYTTAMNEGKVIYIDTEGLSRERVNQIFEIKEALNNvfLYEVMnFRQQSSAIREASKLCRS 102
                                       5899**************************************99988885553333333566777777888888888 PP

                               Zot  79 dkgallviDEcqeifpvrakegrkd........pevinaftehRhlgwDivlltqdiskihk.evralaekavklkr 146
                                       +k  l+v+D    ++  + ++++k+         +    +  +R+++  +v + q ++ +++ e++ l +    +  
  gi|488601664|ref|YP_007908135.1| 103 EKIDLIVVDSITALYRSELENDEKQikikreltSQLTFLLGLARKYNLAVVVTNQMFTDVRSgEIKPLGGPSLDHLS 179
                                       8999****************98888999988844444666789*****************9769************* PP

                               Zot 147 kaaigikgryrltraleddhaktekvt 173
                                       k+ +g+++ +r   a+   ++ ++k++
  gi|488601664|ref|YP_007908135.1| 180 KTIVGLEKVNRERIATL--IKHRSKAE 204
                                       ********998776553..44555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1     4e-11   3.4e-08       5      88 ..      24     127 ..      20     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4e-11
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.........swedfldevvel.....a 60 
                                        +iyGps +GKT+++++l       + k+++idte+ l +  ++++ +i+          + +f+++  ++      
  gi|488601664|ref|YP_007908135.1|  24 TQIYGPSATGKTSICLMLtyttamnEGKVIYIDTEG-LSRERVNQIFEIKealnnvflyEVMNFRQQSSAIreaskL 99 
                                       68*********************************9.7677777777777888888888777777777777888887 PP

                            AAA_24  61 aeladyktlviDtideleelclaevirq 88 
                                       +  ++++ +v+D+i+ l++  l++  +q
  gi|488601664|ref|YP_007908135.1| 100 CRSEKIDLIVVDSITALYRSELENDEKQ 127
                                       88899*************9776655554 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00013      0.11       2      66 ..       3      67 ..       2      77 .. 0.80
   2 !   15.7   1.4   8.5e-06    0.0072      83     183 ..      59     163 ..      53     178 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR 66
                                      l+tg + LD+l++ G++kg ++ i + +++Gkt+++l +  ++a++e  +v+++  e  +++ v++
  gi|488601664|ref|YP_007908135.1|  3 LPTGSDCLDRLLGgGVEKGIITQIYGPSATGKTSICLMLTYTTAMNEG-KVIYIDTEGLSRERVNQ 67
                                      6899999**99862689999999******************9998555.78888877666655555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 8.5e-06
                                       TSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTS.CSSSCCCHHHH.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xx RF
                            DnaB_C  83 klkeedweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlmegs.eekenreqevs.ei 157
                                        l++e ++++ e  e l+++ l+   + + + s ir+   +l ++++++liv+D +  +  s  e+++++ ++  e+
  gi|488601664|ref|YP_007908135.1|  59 GLSRERVNQIFEIKEALNNVFLYEVMNFRQQSSAIREA-SKLCRSEKIDLIVVDSITALYRSeLENDEKQIKIKrEL 134
                                       56777788888888888887777777777788888875.5566779**********999865333444444442244 PP

                                       HHH...HHHHHHHCTSXEEEEEEXSGGGC CS
                                       xxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 158 srs...LkalakelnvpvialsqLsrave 183
                                       + +   L  la+  n+ v++  q+  +v 
  gi|488601664|ref|YP_007908135.1| 135 TSQltfLLGLARKYNLAVVVTNQMFTDVR 163
                                       5441115689*************977665 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 !   21.2   0.4   3.7e-07   0.00031       3     110 ..      26     156 ..      24     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.7e-07
                                       EESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS.....................STTHHHHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel...gvefleisgsellsk.....................yvgesekkirelfkeake 55 
                                       +yGp  tGKT+++  +  ++   + +++ i+   l  +                      + ++++ ire  k +++
  gi|488601664|ref|YP_007908135.1|  26 IYGPSATGKTSICLMLTYTTamnEGKVIYIDTEGLSRErvnqifeikealnnvflyevmNFRQQSSAIREASKLCRS 102
                                       79**************9997344355677776666644577788888888888888888888999999999999998 PP

                                       TSTSEEEEEETGGGHHHHH...TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
                               AAA  56 kakpsilfiDEidalaksr...sgseseeeervvnqLlteldgvkkkeskvivigatn 110
                                       ++    +++D i al +s+   ++++ + ++++ +qL   l   +k+ +  + +++tn
  gi|488601664|ref|YP_007908135.1| 103 EK-IDLIVVDSITALYRSElenDEKQIKIKRELTSQLTFLLGLARKY-N--LAVVVTN 156
                                       87.9***************5433333444444444444444333332.3..4555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.8e-06    0.0015       3      93 ..      26     124 ..      25     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenss......... 69 
                                       + G++++GKt+++  L   +++   +++ + +e+ +++ v++    e k++  ++  + + +++++ss         
  gi|488601664|ref|YP_007908135.1|  26 IYGPSATGKTSICLMLTYTTAMnEGKVIYIDTEGLSRERVNQI--FEIKEALNNVFLYEVMNFRQQSSaireasklc 100
                                       78**************776655577777777776666666666..55555555555555555555555555555555 PP

                            AAA_18  70 aleegknlvidghlaeleseaakd 93 
                                       ++e+ + +v+d++ a ++se   d
  gi|488601664|ref|YP_007908135.1| 101 RSEKIDLIVVDSITALYRSELEND 124
                                       69*************999987666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.4   2.4e-06    0.0021       7      52 ..      17      67 ..      14     158 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-06
                                      EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.....B CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                          ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.....q 52
                                       +++g +++i G++ +GK++++ +l+  +  +eG++ + +++  +     q
  gi|488601664|ref|YP_007908135.1| 17 GVEKGIITQIYGPSATGKTSICLMLTYTTAMNEGKVIYIDTEGLSrervnQ 67
                                      589999*****************************9544333222122220 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   2.8e-06    0.0024       4     110 ..      23     122 ..      20     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                       i  i G+  +GKT ++  l ++  +++ +++yi+ +  + ++ ++      +i+e l++     +fl E+ + ++ +
  gi|488601664|ref|YP_007908135.1|  23 ITQIYGPSATGKTSICLMLTYTTAMNEGKVIYIDTEGLSRERVNQI----FEIKEALNN-----VFLYEVMNFRQQS 90 
                                       66799**************999999***********9888655533....345555444.....9************ PP

                            AAA_14  81 kalkslvd..egknldvivtGSnskllskeia 110
                                       +a+++  +  +++++d+iv  S   l  +e++
  gi|488601664|ref|YP_007908135.1|  91 SAIREASKlcRSEKIDLIVVDSITALYRSELE 122
                                       *9999998776679999999998888777665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   7.5e-06    0.0064      13     109 ..      32     133 ..      23     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.5e-06
                            AAA_31  13 vGKTTtsvnlaaalaklgkkvLlvDlDpQanatt..glgiekneiektlyevl...ieeknikeaiiktkvenldli 84 
                                        GKT  +++l ++ a ++ kv+ +D    +   +   ++i++   +  lyev+    +++ i+ea +  ++e++dli
  gi|488601664|ref|YP_007908135.1|  32 TGKTSICLMLTYTTAMNEGKVIYIDTEGLSRERVnqIFEIKEALNNVFLYEVMnfrQQSSAIREASKLCRSEKIDLI 108
                                       59************************976555441155555555777889998653477889999988889999999 PP

                            AAA_31  85 pssidLaeaeielvelekkeeilke 109
                                       + +   a +  el + ek+ +i +e
  gi|488601664|ref|YP_007908135.1| 109 VVDSITALYRSELENDEKQIKIKRE 133
                                       9988888888888776666444333 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.4   4.5e-05     0.038      64     129 ..      96     161 ..      24     167 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-05
                              CobU  64 aealkeeekkevvLvDcltlwltnllleeeaek.veekleeeveellealkelkatvvlVsnEvglg 129
                                       a++l ++ek + ++vD++t +  + l ++e++  ++++l+++++ ll  +++ +   v+V+n +  +
  gi|488601664|ref|YP_007908135.1|  96 ASKLCRSEKIDLIVVDSITALYRSELENDEKQIkIKRELTSQLTFLLGLARKYNL-AVVVTNQMFTD 161
                                       22333344469****************9875546788888888888888888775.56788887665 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   0.00043      0.37      52      88 ..      26      62 ..      18      84 .. 0.87
   2 ?    2.7   0.0      0.11        93      91     122 ..      87     118 ..      78     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00043
                         IstB_IS21 52 llGpsGvGKshlaialgveavraglsvlfvrvedLve 88
                                      + Gps +GK+ +   l + ++ ++ +v+++ +e L +
  gi|488601664|ref|YP_007908135.1| 26 IYGPSATGKTSICLMLTYTTAMNEGKVIYIDTEGLSR 62
                                      89****************************9998865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                         IstB_IS21  91 krarrdgklaralkrllkvdllilDdlgllpl 122
                                       +++ +  + a++l r  k+dl+++D +  l  
  gi|488601664|ref|YP_007908135.1|  87 RQQSSAIREASKLCRSEKIDLIVVDSITALYR 118
                                       4444445556677778889******9987654 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.1e-05     0.026       7      63 ..      31      88 ..      25     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                                      -SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-E.EEEEE-SCH CS
                       PAPS_reduct  7 sgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglr.lkvyepeee 63
                                      + Gk s+ l+  ++ a+++++v+++dt+   +e ++ + e++e ++   l  + + ++
  gi|488601664|ref|YP_007908135.1| 31 ATGKTSICLMLTYTTAMNEGKVIYIDTEGLSRERVNQIFEIKEALNNVfLYEVMNFRQ 88
                                      68******************************************94332333333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.4e-05     0.054       7     104 ..      23     117 ..      18     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlssee 77 
                                       i+ ++G+s tGKT  + +l+++       ++++ +v++++  +++  ++  ++++++ +  ++       +  +++ 
  gi|488601664|ref|YP_007908135.1|  23 ITQIYGPSATGKTSICLMLTYTT------AMNEGKVIYIDTEGLS--RERVNQIFEIKEALNNVflyevmNFRQQSS 91 
                                       5669*****************98......4568999999999999..555555555555333335654543344444 PP

                            AAA_22  78 llealeqalraravielliiDEaqhlr 104
                                        ++   + +r+ +   l+++D +  l 
  gi|488601664|ref|YP_007908135.1|  92 AIREASKLCRSEKI-DLIVVDSITALY 117
                                       44444555555555.999999887775 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.6e-05     0.082      16      80 ..      16      80 ..      10     139 .. 0.82
   2 ?   -1.2   0.0      0.88   7.5e+02     270     292 ..     146     168 ..     129     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.6e-05
                            AAA_10 16 gsktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiakkinvvtL 80
                                      g +++   + i G+   GK  +  +l +  ++ +gk+++iD     ++ ++++ ei++ +n v L
  gi|488601664|ref|YP_007908135.1| 16 GGVEKGIITQIYGPSATGKTSICLMLTYTTAMNEGKVIYIDTEGLSRERVNQIFEIKEALNNVFL 80
                                      556666677899******************************99989999999998888888776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.88
                            AAA_10 270 RsynaavylvtqsadDvlkeelk 292
                                       R+yn av+   q + Dv   e+k
  gi|488601664|ref|YP_007908135.1| 146 RKYNLAVVVTNQMFTDVRSGEIK 168
                                       999*9***999****99877765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3     6e-05     0.051      21     105 ..      22     108 ..      17     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..eeeekkklekalgiavpkaeleeil 95 
                                        i  iYGp   GKt++   +       ++ ++ yi+ ++ s +++++ +e  e  ++ +l ++++ + ++ ++ e +
  gi|488601664|ref|YP_007908135.1|  22 IITQIYGPSATGKTSICLMLTYTTAM-NEGKVIYIDTEGLSRERVNQIFEikEALNNVFLYEVMNFRQQSSAIREAS 97 
                                       5778***********99888777755.55555566788888888888877766666666666665555555555555 PP

                          ATPase_2  96 k.eksklvfka 105
                                       k  +s++++  
  gi|488601664|ref|YP_007908135.1|  98 KlCRSEKIDLI 108
                                       44333333333 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00037      0.32       1      30 [.      28      57 ..      28      59 .. 0.95
   2 ?    0.4   0.0      0.58   4.9e+02     121     148 ..     100     127 ..      69     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDl 30
                                      Gp+ +GK++++ +L  + + ++ k++y+D+
  gi|488601664|ref|YP_007908135.1| 28 GPSATGKTSICLMLTYTTAMNEGKVIYIDT 57
                                      8999*************************7 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.58
                            CLP1_P 121 llleliealepdvvvvldqeellnelkr 148
                                       +  e+i+++ +d + +l ++el+n+ k+
  gi|488601664|ref|YP_007908135.1| 100 CRSEKIDLIVVDSITALYRSELENDEKQ 127
                                       4567778888888888888777776665 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.16      29      76 ..      19      66 ..       7      82 .. 0.87
   2 ?   -0.3   0.0      0.43   3.7e+02     162     183 ..      98     119 ..      59     152 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                            AAA_35 29 kpGalirikapkkmGKtSLlarilakakqqgyktvsldlqladkeils 76
                                      ++G + +i +p+ +GKtS+   +  +++ ++ k++++d + + +e ++
  gi|488601664|ref|YP_007908135.1| 19 EKGIITQIYGPSATGKTSICLMLTYTTAMNEGKVIYIDTEGLSRERVN 66
                                      578999********************************9988776554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.43
                            AAA_35 162 nkeiwqkLrLvvvhstevyipl 183
                                       +    +k++L+vv s  +  ++
  gi|488601664|ref|YP_007908135.1|  98 KLCRSEKIDLIVVDSITALYRS 119
                                       4445567777777775554444 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00011     0.097     191     229 ..      49      87 ..      35     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                   V_cholerae_RfbT 191 nsvvikidaegaeieilnqiyeftekhngieyyicfefa 229
                                       +  vi id+eg   e +nqi+e+ e  n +  y +++f 
  gi|488601664|ref|YP_007908135.1|  49 EGKVIYIDTEGLSRERVNQIFEIKEALNNVFLYEVMNFR 87 
                                       4579*************************9999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 1238.76
//
Query:       gi|488601665|ref|YP_007908136.1|  [L=63]
Description: hypothetical protein Asulf_02190 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 362.07
//
Query:       gi|488601666|ref|YP_007908137.1|  [L=209]
Description: H(+)-transporting ATP synthase, vacuolar type, subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-57  194.2  14.0    2.3e-57  194.0  14.0    1.0  1  ATP-synt_D   ATP synthase subunit D
     0.0036   17.3   0.7      0.053   13.5   0.2    2.1  2  PTPS         6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
      0.095   13.1   6.3       0.51   10.7   0.7    2.4  2  HrpB7        Bacterial type III secretion protein (HrpB7)
      0.099   12.4   0.0        0.2   11.4   0.0    1.5  1  CCDC92       Coiled-coil domain of unknown function
       0.23   11.7   4.7         17    5.7   1.4    3.4  2  DUF2508      Protein of unknown function (DUF2508)
       0.26   11.7   2.6       0.65   10.4   0.6    2.1  2  Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C te
       0.78    9.7   6.3       0.86    9.6   0.5    2.5  2  Prefoldin_2  Prefoldin subunit


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 !  194.0  14.0   8.9e-61   2.3e-57       1     196 []      10     203 ..      10     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 194.0 bits;  conditional E-value: 8.9e-61
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       eLi+l++r+kl +rgh lLk+Krd Li efr++l+++ke   +l +++++a+++la+a+a++g  +i+s++l+  k 
  gi|488601666|ref|YP_007908137.1|  10 ELIKLRRRIKLSKRGHALLKMKRDGLIVEFRDMLEQAKEVISRLVDRYEKAEEKLALAMAVEGVVAIKSMALSCSK- 85 
                                       79**********************************************************************8877. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikk 153
                                         + + ++k++n++GV vpv++ e+  k  +++ yg+++t+a++de+v+a++e++++++e+a++et+l++L eei k
  gi|488601666|ref|YP_007908137.1|  86 --EPQFSIKKKNIMGVVVPVVKREKVrKPIHEREYGVIGTTARIDEVVSAYEEVVDAVLEVAEIETTLKRLLEEIDK 160
                                       ..588****************8766674455667******************************************* PP

                                       HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 154 tnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                       t+rRvNaLe+ vIP++e++ +yI+ +L+E++re+++rlkk+k+
  gi|488601666|ref|YP_007908137.1| 161 TKRRVNALEYRVIPEMENAARYISFRLEEMDRENIVRLKKIKA 203
                                       *****************************************95 PP

>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.059   1.5e+02      40      67 ..      30      57 ..      15      81 .. 0.81
   2 !   13.5   0.2   2.1e-05     0.053      40     109 ..     135     202 ..     106     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.059
                                      STCTTBSS-HHHHHHHHHHHHHCTTTEE CS
                              PTPS 40 ldetgmvvdfgelkealkeileelDhkf 67
                                       +++g +v f+++ e  ke++++l  ++
  gi|488601666|ref|YP_007908137.1| 30 MKRDGLIVEFRDMLEQAKEVISRLVDRY 57
                                      57899**************998876555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.1e-05
                                       STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCCS.--HHHHHHHHHHHHHHHHGCCCGCEEEEE CS
                              PTPS  40 ldetgmvvdfgelkealkeileelDhkflnaddpeleellspTaEnlaklifeelkerlqekevklskvr 109
                                       ++  + v+  +e+++ lk++lee+D +   ++  e++  + p +En a++i  +l+e  +e+ v+l+k++
  gi|488601666|ref|YP_007908137.1| 135 EEVVDAVLEVAEIETTLKRLLEEIDKTKRRVNALEYR--VIPEMENAARYISFRLEEMDRENIVRLKKIK 202
                                       66778999******************99886666665..45**************999889999999887 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5      0.01        26     116     155 ..      36      75 ..      10      78 .. 0.77
   2 ?   10.7   0.7    0.0002      0.51      94     136 ..     129     171 ..     122     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.01
                             HrpB7 116 iaRndaqidacrerierlrraaeraredaadEEaeEavLA 155
                                       i+  + ++++ +e i rl + +e+a+e+ a   a+E+v+A
  gi|488601666|ref|YP_007908137.1|  36 IVEFRDMLEQAKEVISRLVDRYEKAEEKLALAMAVEGVVA 75 
                                       5556677888888888888888888888888888888887 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                             HrpB7  94 elaaarqaldaaedavaatarkiaRndaqidacrerierlrra 136
                                       e++ a +++ +a  +va+ ++++ R++ +id++++r+++l+  
  gi|488601666|ref|YP_007908137.1| 129 EVVSAYEEVVDAVLEVAEIETTLKRLLEEIDKTKRRVNALEYR 171
                                       56778889999999***********************999865 PP

>> CCDC92  Coiled-coil domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.9e-05       0.2      19      44 ..     148     173 ..     145     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.9e-05
                            CCDC92  19 aatLkgLHkEIekLqkenkdLtfkli 44 
                                       ++tLk L +EI+k ++++  L++ +i
  gi|488601666|ref|YP_007908137.1| 148 ETTLKRLLEEIDKTKRRVNALEYRVI 173
                                       68*********************997 PP

>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.083   2.1e+02      22      52 ..      36      66 ..      12      70 .. 0.75
   2 ?    5.7   1.4    0.0066        17      16      31 ..     152     167 ..     146     205 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.083
                           DUF2508 22 IektkeelesakslfensvDlsdeliyqlkl 52
                                      I + ++ le+ak+ +   vD  ++ + +l+l
  gi|488601666|ref|YP_007908137.1| 36 IVEFRDMLEQAKEVISRLVDRYEKAEEKLAL 66
                                      7788999999999999999955655555555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0066
                           DUF2508  16 eeLleeIektkeeles 31 
                                       ++LleeI+ktk+  ++
  gi|488601666|ref|YP_007908137.1| 152 KRLLEEIDKTKRRVNA 167
                                       6788888888875443 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 ?    1.1   0.1      0.19     5e+02      13      39 ..      39      65 ..      29      93 .. 0.74
   2 ?   10.4   0.6   0.00025      0.65       9      70 ..     143     207 ..     139     209 .] 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                       Uso1_p115_C 13 lkdeneklkaelqslskalesleqkea 39
                                      ++d+ e++k  ++ l +++e++e+k a
  gi|488601666|ref|YP_007908137.1| 39 FRDMLEQAKEVISRLVDRYEKAEEKLA 65
                                      567778888888888888888888833 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00025
                       Uso1_p115_C   9 eaaslkdeneklkaelqslskalesleqk...eakkaaesqakeleaenkklekeleklraelke 70 
                                       e+a++++  ++l  e+++++++++ le     e ++aa++ + +le++  +   +l+k++a++++
  gi|488601666|ref|YP_007908137.1| 143 EVAEIETTLKRLLEEIDKTKRRVNALEYRvipEMENAARYISFRLEEMDRENIVRLKKIKAKMAA 207
                                       578889999999999999999999999999999999***************99*********987 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5   0.00034      0.86      52      92 ..      24      64 ..       3      67 .. 0.90
   2 ?    2.6   0.6     0.049   1.2e+02      73      94 ..     146     167 ..     132     179 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                                      TTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2 52 GdvlvkqdkeevkeeLeerketlekeiktlekqleklekel 92
                                      G +l+k++++ ++ e  +++e+++++i++l +++ek e++l
  gi|488601666|ref|YP_007908137.1| 24 GHALLKMKRDGLIVEFRDMLEQAKEVISRLVDRYEKAEEKL 64
                                      89999********9**********************99998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.049
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  73 tlekeiktlekqleklekelee 94 
                                       ++e+ +k+l ++++k +++++ 
  gi|488601666|ref|YP_007908137.1| 146 EIETTLKRLLEEIDKTKRRVNA 167
                                       3444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1580  (0.0881254); expected 358.6 (0.02)
Passed bias filter:                      761  (0.0424452); 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: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1199.61
//
Query:       gi|488601667|ref|YP_007908138.1|  [L=467]
Description: ATP synthase archaeal, B subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-66  221.6   0.0    1.2e-65  221.2   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    1.4e-13   51.1   1.1    1.4e-13   51.1   1.1    1.8  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
    0.00064   19.8   0.3     0.0022   18.1   0.3    2.0  1  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.2   0.0   1.9e-69   1.2e-65       1     213 []     129     347 ..     129     347 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.2 bits;  conditional E-value: 1.9e-69
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D + ++v+Gq++ i++++g++++ i+ ++++q++ +    + a+i++++G  ++e+ +++++f+++++++r 
  gi|488601667|ref|YP_007908138.1| 129 GISAIDGMNTLVRGQKLPIFSGSGLPHNDIALQVARQAKVRgsgeEfAVIFAAMGITNEEAYQFMKDFERTGALERA 205
                                       89***********************************9888999868****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       v+++n +++p+++r++++++++t+AE++++  + ++l+i++++++++eAlreis++ +e+p+++gyp+y++++la++
  gi|488601667|ref|YP_007908138.1| 206 VVFLNLADDPAIERLLTPRMALTAAEFLAYeYDLHILVILTDMTNYCEALREISAAREEVPGRRGYPGYMYTDLATI 282
                                       *****************************98899******************************************* PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag+++ r+G++t++++++++g+D+++p+++ t +it+g++vL+++l++++++P+i+vl S+S
  gi|488601667|ref|YP_007908138.1| 283 YERAGRIQGRKGTITQMPILTMPGDDITHPIPDLTGYITEGQVVLSRELHAKGIYPPIDVLPSLS 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 !   51.1   1.1   2.4e-17   1.4e-13       1      69 []       7      72 ..       7      72 .. 0.90
   2 ?   -3.7   0.0         3   1.8e+04      49      64 ..     129     144 ..     128     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 2.4e-17
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i+qv Gp++ ve+ + + +g+++ ++    + g+  +g++l  + d+V+v+v+++t+G++  + V++TG
  gi|488601667|ref|YP_007908138.1|  7 ISQVAGPLIFVEKTEPVGYGELVNITLA--D-GSTKRGQVLDTSKDVVVVQVFEGTRGIDTSSAVRFTG 72
                                      89**************556666555555..9.************************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                                       EEEESS-STTBBTTSE CS
                     ATP-synt_ab_N  49 rvivmgstdGlsrGte 64 
                                       ++ +++++  l+rG++
  gi|488601667|ref|YP_007908138.1| 129 GISAIDGMNTLVRGQK 144
                                       5778889999999975 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.3   3.7e-07    0.0022       4      83 ..       3      67 ..       1      88 [. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-07
                        HAS-barrel  4 vigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalated 81
                                      ++ + ++  +++++ve +++v++Ge+V i l dg+   G+v+d ++                       d +v++++e+
  gi|488601667|ref|YP_007908138.1|  3 EYKTISQvAGPLIFVEKTEPVGYGELVNITLADGSTKRGQVLDTSK-----------------------DVVVVQVFEG 58
                                      56666666999***********************************.......................9999999999 PP

                        HAS-barrel 82 t.......g 83
                                      t        
  gi|488601667|ref|YP_007908138.1| 59 TrgidtssA 67
                                      985555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2631.71
//
Query:       gi|488601668|ref|YP_007908139.1|  [L=575]
Description: ATP synthase archaeal, A subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  317.6   0.0    5.1e-95  317.1   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.6e-43  147.4   0.0    2.8e-43  146.6   0.0    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    2.8e-14   53.4   2.9      1e-13   51.6   2.9    2.1  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
     0.0027   17.9   0.1       0.31   11.3   0.0    2.6  2  Peptidase_M23    Peptidase family M23
  ------ inclusion threshold ------
      0.016   15.5   0.0      0.035   14.4   0.0    1.5  1  AAA_22           AAA domain
      0.057   13.4   0.3       0.22   11.5   0.1    2.0  2  RnfC_N           RnfC Barrel sandwich hybrid 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 !  317.1   0.0   1.7e-98   5.1e-95       1     213 []     209     430 ..     209     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 317.1 bits;  conditional E-value: 1.7e-98
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+r+lD++fp+++G++ +ipg fg Gktv +++l+k+s+++ +++yvg+Gergne++evleefpe      g+ +m+
  gi|488601668|ref|YP_007908139.1| 209 GQRILDTFFPVAKGGTAAIPGPFGSGKTVTQHQLAKWSDTE-IVVYVGCGERGNEMTEVLEEFPElidpksGKpLME 284
                                       9************************************9877.*************************9987337*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       rtvl+antsn+pvaareas+ytgit+AEyfrd+g+nv + ads+srwaeA+reis+rl+emp+++gypayl+++la+
  gi|488601668|ref|YP_007908139.1| 285 RTVLIANTSNMPVAAREASVYTGITIAEYFRDMGYNVAVQADSTSRWAEAMREISGRLEEMPGEEGYPAYLASRLAE 361
                                       ***************************************************************************** PP

                                       HHTTSEEE...TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka...pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yERag++     + Gsvt+v avsp+ggDfs+pvt++tl+i+++f+ Ld kla+r+hfPain+l+S+S
  gi|488601668|ref|YP_007908139.1| 362 FYERAGRVktlGGNVGSVTVVGAVSPPGGDFSEPVTQNTLRIVKVFWALDAKLAARRHFPAINWLQSYS 430
                                       ********7776679*****************************************************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 !  146.6   0.0   9.4e-47   2.8e-43       1     121 []      85     200 ..      85     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 9.4e-47
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvke 77 
                                       yDGiqrpL +++e+sg+fi+rG+++p l+r+  wefkp+vk+gdkv++g+i+Gtvqete++eh+i+vpp+v g ++e
  gi|488601668|ref|YP_007908139.1|  85 YDGIQRPLPALKESSGDFISRGIQAPGLSRDAVWEFKPTVKKGDKVNPGEIIGTVQETEIVEHRILVPPNVGGVITE 161
                                       9**************************************************************************** PP

                                       E--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                   ATP-synt_ab_Xtn  78 iaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                       i  eg+++v+d++a++++++    el+l++kwPvr++rp++ekl
  gi|488601668|ref|YP_007908139.1| 162 IY-EGKFKVDDVVAVLDNGT----ELKLYHKWPVREARPYQEKL 200
                                       *9.**************766....8*****************97 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   2.9   3.4e-17     1e-13       1      69 []       8      69 ..       8      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.4e-17
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      +++v+Gp+v +  gi   p +y++++v+  e  ++l+g++++l++ k +++v+++t+G+++G+ V++TG
  gi|488601668|ref|YP_007908139.1|  8 VYRVSGPLVVA-EGIK--PRMYDVCRVG--E--EGLMGEVVGLQGAKTLIQVYEDTSGVKPGDVVINTG 69
                                      689********.9999..**********..8..***********************************9 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.028        85      24      63 ..      28      65 ..      25      73 .. 0.84
   2 !   11.3   0.0    0.0001      0.31      56      76 ..     123     143 ..     118     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.028
                                      EEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE CS
                     Peptidase_M23 24 VvfagkkegyGnvviidhgdgystlyahlskisvkegqkV 63
                                      V  +g+++ +G+vv ++ ++ ++++y   s   vk+g+ V
  gi|488601668|ref|YP_007908139.1| 28 VCRVGEEGLMGEVVGLQGAKTLIQVYEDTSG--VKPGDVV 65
                                      5667887666*****************9999..9999987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                                       SS-TTEEE-TTCEEEEEBSTS CS
                     Peptidase_M23  56 svkegqkVkaGqvIGtvgstg 76 
                                       +vk+g+kV+ G++IGtv +t+
  gi|488601668|ref|YP_007908139.1| 123 TVKKGDKVNPGEIIGTVQETE 143
                                       59***************9886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.035       6      69 ..     223     279 ..     220     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelk 69 
                                       g  ++ G+ G+GKT++  +l+++ d           vv+v + + + + +++l+e+ + ++ +  
  gi|488601668|ref|YP_007908139.1| 223 GTAAIPGPFGSGKTVTQHQLAKWSD--------TEIVVYVGCGERGnEMTEVLEEFPELIDPKSG 279
                                       66799******************97........67777**9999998999999999999885444 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 ?   -1.9   0.0       1.1   3.3e+03      46      75 ..      29      58 ..      24      60 .. 0.86
   2 ?   11.5   0.1   7.4e-05      0.22      41      80 ..     119     162 ..     111     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                            RnfC_N 46 vkvgdkVlkGqkiaeaegfvsapvhasvsG 75
                                        vg++ l+G++++ +++ +  +v+  +sG
  gi|488601668|ref|YP_007908139.1| 29 CRVGEEGLMGEVVGLQGAKTLIQVYEDTSG 58
                                      578999999*****9999779999999999 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.4e-05
                            RnfC_N  41 pakplvkvgdkVlkGqkiaeaeg..fvsapvhas..vsGtVkai 80 
                                       + kp vk+gdkV+ G++i++ ++  +v   +  +  v G +++i
  gi|488601668|ref|YP_007908139.1| 119 EFKPTVKKGDKVNPGEIIGTVQEteIVEHRILVPpnVGGVITEI 162
                                       5689***************9876446666666543366666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 3327.10
//
Query:       gi|488601669|ref|YP_007908140.1|  [L=100]
Description: Archaeal/vacuolar-type H+-ATPase subunit F [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-11   42.6   0.7    6.7e-11   42.4   0.7    1.1  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
     0.0096   15.7   0.1        2.6    7.9   0.0    2.2  2  ACT         ACT domain
  ------ inclusion threshold ------
      0.097   13.2   0.0       0.15   12.5   0.0    1.3  1  DUF668      Protein of unknown function (DUF668)


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 !   42.4   0.7   1.1e-14   6.7e-11       2      90 ..       5      92 ..       4      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.1e-14
                                      EEEESHHHHHHHHHTTCEEEE.CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHH.HCTCSSSSEEEEESCSCC CS
                        ATP-synt_F  2 avIGdedtvtgfrlaGvgeve.vtdeeeieealkelleredigiilitekiaeeirelid.eykeealPaileIPskeg 78
                                      +vIGd d+ +gfrl G+++++ vtde e+ ++++e+l  ++ gi++i+ ++++ ++ +++ +++e+  P+++++ +++g
  gi|488601669|ref|YP_007908140.1|  5 MVIGDPDFNIGFRLSGIRNIVdVTDETELPKIVEEAL--QKKGIVVIKYDLYKSLPIQLKlRIEESIEPTFVKVGGEGG 81
                                      69*****************998999************..6669*************6665166666********77777 PP

                                      GGSHHCHHHHHH CS
                        ATP-synt_F 79 pydeekdsvrkk 90
                                       ++e k+++rk 
  gi|488601669|ref|YP_007908140.1| 82 -VEEIKEKIRKA 92
                                      .54558888876 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00044       2.6      41      61 ..      19      39 ..       7      45 .. 0.89
   2 !    6.1   0.0    0.0016       9.6      43      66 ..      70      93 ..      63      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00044
                                      CEEEEEEEEEEHHHHHHHHHH CS
                               ACT 41 agivfvvivvdeedleevlea 61
                                       gi ++v+v+de +l++++e+
  gi|488601669|ref|YP_007908140.1| 19 SGIRNIVDVTDETELPKIVEE 39
                                      57999**************98 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0016
                                      EEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT 43 ivfvvivvdeedleevlealkkle 66
                                      + ++v v++e ++ee++e+++k +
  gi|488601669|ref|YP_007908140.1| 70 EPTFVKVGGEGGVEEIKEKIRKAI 93
                                      568999***************975 PP

>> DUF668  Protein of unknown function (DUF668)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05      0.15      33      76 ..      50      92 ..      35      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                            DUF668 33 rdeLYqmLpasvrsalrakLrslekkeavdellaaeikeeveki 76
                                      + +LY++Lp +++  +++ ++ +++k +  e  ++eike+++k 
  gi|488601669|ref|YP_007908140.1| 50 KYDLYKSLPIQLKLRIEESIEPTFVKVG-GEGGVEEIKEKIRKA 92
                                      569***********************65.677889999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 590.57
//
Query:       gi|488601670|ref|YP_007908141.1|  [L=349]
Description: ATP synthase A1, C subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-69  232.5   8.1      1e-68  232.4   8.1    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 !  232.4   8.1   5.6e-73     1e-68       2     335 ..      20     343 ..      19     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 5.6e-73
                                       HHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--......SSSHHHHHHHHHHHHHHHTTTGGGGS-H CS
                    vATP-synt_AC39   2 eArvramrsglLteedyenLlqcesledvkryLketdYgnfladel.seplsrsdiekalreklarefnklreqapg 77 
                                       + rvr+m+++l++ ++y++L++ ++l++++ryL+e++Y+++ +del  ++ + + i++a + +l r++nkl + ++g
  gi|488601670|ref|YP_007908141.1|  20 VSRVRVMSRKLIPGDEYNKLVN-MDLDEIIRYLEESEYKKE-IDELgFKYHGLTLIDYAFSLNLSRTYNKLIRVSKG 94 
                                       68******************55.5*****************.5555588**************************** PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHH..T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHH CS
                    vATP-synt_AC39  78 psrefldyllyrydidNvklllrgklsg.dldleeleeklhplgelsaldldklieaksveelyeallgtpyakyle 153
                                        +r++++++l+rydi N+++++rgk+ + ++  ee+e+ ++p+ge++++ ++ l+ ++s+ee+ ++++gt+++++le
  gi|488601670|ref|YP_007908141.1|  95 VPRDLISAYLRRYDIYNIINIIRGKMFNfPV--EEVEATIIPAGEYDMEFFKSLMMKESIEEIAKVFEGTQFYPALE 169
                                       *99************************7666..******************************************** PP

                                       HHHCC...--SHHHHHHHHHHHHHHHHHHH.HHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...- CS
                    vATP-synt_AC39 154 ealdeleetgdleiienaLdkayledllkf.ckklggetaeilreilgfeiDlrniniilrskkygelskedrkkll 229
                                       +++ +       +++e  L+k y++ l  + +++l+ +    + +++++e+D++ni++ilr+kk g    e +   +
  gi|488601670|ref|YP_007908141.1| 170 KLVRVCPM----SEFEDDLYKIYYNTLAGIkAESLDMKY---FIDFIKMEVDIKNIKTILRMKKEGGTADE-IMTKI 238
                                       *9999999....******************555566666...**********************9976666.66667 PP

                                       -SS-.S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHH CS
                    vATP-synt_AC39 230 ipgg.slypeglealaeaedveellaalkyteygelleealeeagslksledaldealvkllkk.afrqqfsvgvfy 304
                                       ip g ++++++ ++la+  +++el++ l+ + ++e +++ +e+  +l+++e ald+  vk+  + ++ +++s+ +++
  gi|488601670|ref|YP_007908141.1| 239 IPRGlQIHEAEARKLAAL-ELDELMKSLEGYWFWEGMKDQVES--ELSKIEAALDRIWVKKVLSkSHSYPLSILPVM 312
                                       77777***********99.7********999999988866553..3***************9999************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 305 aYlklkeqEirnlrwIaegiaqglpkekIre 335
                                       a+++lk+ Ei+nlr+Ia+g+a gl++e I+e
  gi|488601670|ref|YP_007908141.1| 313 AFILLKKIEIDNLRIIARGKAVGLDNESIKE 343
                                       *****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1977.42
//
Query:       gi|488601671|ref|YP_007908142.1|  [L=183]
Description: Archaeal/vacuolar-type H+-ATPase subunit E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-28   99.5  31.8    2.6e-27   95.5  31.8    1.9  1  vATP-synt_E     ATP synthase (E/31 kDa) subunit
      0.001   18.5  25.0     0.0014   18.1  25.0    1.1  1  DUF3552         Domain of unknown function (DUF3552)
     0.0081   16.3   9.4     0.0081   16.3   9.4    2.2  2  DivIVA          DivIVA protein
     0.0082   15.7   7.5      0.011   15.4   7.5    1.1  1  Exonuc_VII_L    Exonuclease VII, large subunit
  ------ inclusion threshold ------
      0.016   15.7  21.6      0.016   15.7  21.6    1.9  1  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
      0.023   15.2  11.7       0.52   10.9   1.5    2.9  3  EF-G-binding_N  Elongation factor G-binding protein, N-termin
      0.026   14.4   3.3      0.035   14.0   3.3    1.2  1  HrpE            HrpE/YscL/FliH and V-type ATPase subunit E
        0.4   10.7  19.1        0.5   10.4   9.4    2.3  2  Phasin          Poly(hydroxyalcanoate) granule associated pro
       0.52    8.2  11.4       0.59    8.0  11.4    1.0  1  V_ATPase_I      V-type ATPase 116kDa subunit family
        1.2    9.5   9.7        7.7    7.0   2.2    2.6  2  Asp23           Asp23 family, cell envelope-related function
        1.4    9.0  18.5       0.24   11.5  14.0    2.0  2  ATP-synt_B      ATP synthase B/B' CF(0)
        1.9    8.3  16.5      0.083   12.7   6.2    2.3  2  Peptidase_M41   Peptidase family M41
        1.9    8.3   4.7         12    5.7   0.7    2.5  2  RNA_pol_L_2     RNA polymerase Rpb3/Rpb11 dimerisation domain
        2.4    8.7  25.6        8.2    7.0  10.4    3.2  3  FadA            Adhesion protein FadA
        4.8    7.9  12.1         73    4.1  10.2    2.5  2  DUF883          Bacterial protein of unknown function (DUF883
        5.2    5.1  17.7        7.4    4.6  17.7    1.2  1  HSP70           Hsp70 protein
        5.6    7.7   8.4         24    5.7   1.0    3.4  3  Zn_ribbon_2     Putative zinc ribbon domain
          7    6.6  21.2         13    5.7  20.3    1.9  1  RRF             Ribosome recycling factor


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 !   95.5  31.8   2.6e-30   2.6e-27       2     199 .]      10     182 ..       9     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 2.6e-30
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   2 IrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevf 78 
                                       I +++++++ eIk++ae+e+e+++ +++e+++e +++a++ +e ++e+ +k++iS++ ++++++ L+ r+evle+v 
  gi|488601671|ref|YP_007908142.1|  10 IVKKGQQRVSEIKSEAEKEVEKIVVEAEEKAKEILKKARDTAENEVERLRKQEISSINLEMKREELNRRKEVLEAVY 86 
                                       8899************************************************************************* PP

                                       HHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESS CS
                       vATP-synt_E  79 eeaekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeed 155
                                       e++ +k++ +++++       kkL+ + l ++e +   v+++keD+e+v+++    + ey++            +  
  gi|488601671|ref|YP_007908142.1|  87 EKLVEKVKSMDKEE------KKKLMEKLLKANEKEGYRVYSNKEDEEIVKSI---SKMEYAG------------N-- 140
                                       ***********999......6677777777899999***************5...2333444............4.. PP

                                       EBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 156 fledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                         ++++GGvvle+adg+ ++n T++++L++++e++++e+++ LF
  gi|488601671|ref|YP_007908142.1| 141 --IECIGGVVLESADGQFRINLTFDEMLSTLFESKMKEVSEILF 182
                                       ..68***************************************9 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  25.0   1.4e-06    0.0014      25     131 ..       7     113 ..       3     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-06
                           DUF3552  25 aekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelke.rrnelqrlekRllqkeetLdrkees 100
                                        e+ +++ +++ ++i +eA+ke e++  ea  +ake ++k+r+ +e+e+++ r++e+++++  l+ k e+L+r++e 
  gi|488601671|ref|YP_007908142.1|   7 IEEIVKKGQQRVSEIKSEAEKEVEKIVVEAEEKAKEILKKARDTAENEVERlRKQEISSIN--LEMKREELNRRKEV 81 
                                       67889999****************************************9654888999885..8999999******* PP

                           DUF3552 101 lekkeesleekekelkqke.qsleekeeelee 131
                                       le   e+l ek k+++++e ++l ek  +++e
  gi|488601671|ref|YP_007908142.1|  82 LEAVYEKLVEKVKSMDKEEkKKLMEKLLKANE 113
                                       ****9999999999876541344444444433 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   9.4   8.1e-06    0.0081      71     122 ..      13      61 ..       3      71 .. 0.83
   2 ?    0.9   7.3      0.44   4.3e+02      35      92 ..      73     130 ..      67     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.1e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  71 vaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrq 122
                                         q+   e+k++a+ke e i+ eAe+ka++i+++a++ a   ++e+e+l++q
  gi|488601671|ref|YP_007908142.1|  13 KGQQRVSEIKSEAEKEVEKIVVEAEEKAKEILKKARDTA---ENEVERLRKQ 61 
                                       569999**************************9888765...5667777766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHHCCCCTXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  35 eallkeneelkekvkeleeklkeykele.etLkktlvvaqetaeevkanakkeaeliik 92 
                                       e+l +++e l++  ++l ek+k++++ e ++L + l+ a e  e  +  ++ke e i+k
  gi|488601671|ref|YP_007908142.1|  73 EELNRRKEVLEAVYEKLVEKVKSMDKEEkKKLMEKLLKANE-KEGYRVYSNKEDEEIVK 130
                                       89999******************987652689999999976.56777777777777766 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 !   15.4   7.5   1.1e-05     0.011     159     293 ..       6     142 ..       2     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                      Exonuc_VII_L 159 aikrlleekkqrleklasrlk.speellerkrqrldeleerleralkkqlkk.krerleelkerl.kekleekkerl 232
                                        i++ +++ +qr+++++s+ + + e+++ +++++ +e+ ++ + + ++++++ +++++++++ ++ +e+l+++ke l
  gi|488601671|ref|YP_007908142.1|   6 VIEEIVKKGQQRVSEIKSEAEkEVEKIVVEAEEKAKEILKKARDTAENEVERlRKQEISSINLEMkREELNRRKEVL 82 
                                       56777888888888888888547777777788888887777777666665541445566666445345555555555 PP

                      Exonuc_VII_L 233 kklkerlelleekkerleeleeklealsplkvLkrGyaivrk.edgkvvtsakdlkkgdele 293
                                       +++ e+l  +e+ k++ +e ++kl     ++  k Gy + ++ ed+++v+s+++++   ++e
  gi|488601671|ref|YP_007908142.1|  83 EAVYEKL--VEKVKSMDKEEKKKLMEKLLKANEKEGYRVYSNkEDEEIVKSISKMEYAGNIE 142
                                       4443333..34444444444444555555555679******999********9998776665 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7  21.6   1.6e-05     0.016      11      99 ..      24     110 ..      15     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHH CS
                        V-ATPase_G  11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefk.ekeaeklgseeelekkieketeekikelkesv 86 
                                       +AEke ++iv eA ++ ++ lk+A+++Ae+E+e+ r+++   ++ e++ e+l +++e+ + + ++  ek+k++++  
  gi|488601671|ref|YP_007908142.1|  24 EAEKEVEKIVVEAEEKAKEILKKARDTAENEVERLRKQEISSINlEMKREELNRRKEVLEAVYEKLVEKVKSMDK-- 98 
                                       7************************************99998873455566666777766666666666666655.. PP

                                       HHHHHHHHHHHHH CS
                        V-ATPase_G  87 kknkeavvkellk 99 
                                        ++k++ +++llk
  gi|488601671|ref|YP_007908142.1|  99 -EEKKKLMEKLLK 110
                                       .566677777776 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0    0.0018       1.8      31      65 ..      19      53 ..      14      64 .. 0.83
   2 ?   10.9   1.5   0.00052      0.52      27      68 ..      79     117 ..      77     123 .. 0.86
   3 ?   -1.6   0.0         4     4e+03      49      63 ..     122     136 ..     119     142 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                    EF-G-binding_N 31 eavkalaaekIlelfpelseeqkelLeqiddiktk 65
                                      + +k++a+++++++++e++e++ke+L++  d+ ++
  gi|488601671|ref|YP_007908142.1| 19 SEIKSEAEKEVEKIVVEAEEKAKEILKKARDTAEN 53
                                      66899*********************887776543 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00052
                    EF-G-binding_N  27 kkvveavkalaaekIlelfpelseeqkelLeqiddiktkeka 68 
                                       k+v+eav++ + ek++ +    +ee+k+l+e++ + ++ke  
  gi|488601671|ref|YP_007908142.1|  79 KEVLEAVYEKLVEKVKSM---DKEEKKKLMEKLLKANEKEGY 117
                                       6799*************9...67889*********9988865 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4
                    EF-G-binding_N  49 seeqkelLeqiddik 63 
                                       ++e++e++++i++ +
  gi|488601671|ref|YP_007908142.1| 122 NKEDEEIVKSISKME 136
                                       456677887777765 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.3   3.5e-05     0.035      28     131 ..      14     116 ..       3     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                              HrpE  28 eslrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrglqqeRealeeqlltaveqLLsdala 104
                                        ++r  e+  eA +  e+++ +a+eka+e+l++a + Ae++  +      +++     +++++ l + +++L+   +
  gi|488601671|ref|YP_007908142.1|  14 GQQRVSEIKSEAEKEVEKIVVEAEEKAKEILKKARDTAENEVERLRK---QEISSINLEMKREELNRRKEVLEAVYE 87 
                                       468999**************************999999987655444...455555666778888888888888888 PP

                              HrpE 105 rlLdetpla..eRasALlRqLlksqqgea 131
                                       +l+++++    e  + L+ +Llk  + e+
  gi|488601671|ref|YP_007908142.1|  88 KLVEKVKSMdkEEKKKLMEKLLKANEKEG 116
                                       88888875411456778888888777765 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 ?   10.4   9.4    0.0005       0.5      36     106 ..       6      80 ..       4      84 .. 0.69
   2 ?    5.3   3.0     0.019        18      35      70 ..      84     119 ..      75     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0005
                            Phasin  36 lfeaLvkeGeklekktkkvaeekleevresvkskveevkekaeeqwd.klekafdervaka...Lsrlgvpsred 106
                                       ++e++vk+G++  ++ k++ae+++e++  ++++k++e+ +ka ++ + ++e++ ++ ++++   ++r ++ +r++
  gi|488601671|ref|YP_007908142.1|   6 VIEEIVKKGQQRVSEIKSEAEKEVEKIVVEAEEKAKEILKKARDTAEnEVERLRKQEISSInleMKREELNRRKE 80 
                                       789********9999999999999999988888888887777665533666666555544211155555555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                            Phasin  35 klfeaLvkeGeklekktkkvaeekleevresvkskv 70 
                                        ++e+Lv++ ++++k+ kk+  ekl +++e+   +v
  gi|488601671|ref|YP_007908142.1|  84 AVYEKLVEKVKSMDKEEKKKLMEKLLKANEKEGYRV 119
                                       689********************9999997654444 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  11.4   0.00059      0.59      43     171 ..      18     154 ..       6     182 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00059
                        V_ATPase_I  43 eeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee 119
                                        +ei++++++++++   + + e++ ++ l++  ++ e+  e+l++++ ++ +l+ +++el   k+vle + e l e+
  gi|488601671|ref|YP_007908142.1|  18 VSEIKSEAEKEVEKI--VVEAEEKAKEILKKARDTAENEVERLRKQEISSINLEMKREELNRRKEVLEAVYEKLVEK 92 
                                       344444333333332..45566667777888888999999999999999999***************9998888777 PP

                        V_ATPase_I 120 .eeeeeeeeseeeeee...keeeeeeeseeeeeeelleeeee.............lsfvaGvikrekve 171
                                        +++++ee+++ +e+    +e+e  +  +++e+e       e             ++ + Gv+ ++   
  gi|488601671|ref|YP_007908142.1|  93 vKSMDKEEKKKLMEKLlkaNEKEGYRVYSNKEDE-------EivksiskmeyagnIECIGGVVLESADG 154
                                       5555555444444333332111111222222222.......1223344566666666677777666554 PP

>> Asp23  Asp23 family, cell envelope-related function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.2    0.0078       7.7      65     103 ..      31      69 ..       5      72 .. 0.78
   2 ?    6.7   0.9    0.0096       9.6      23      75 ..      90     142 ..      71     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0078
                             Asp23  65 yvvveYGvkipevaenvqekVkeaveemtglevseVnvh 103
                                       ++vve + k +e+ ++ ++  +++ve++   e+s++n++
  gi|488601671|ref|YP_007908142.1|  31 KIVVEAEEKAKEILKKARDTAENEVERLRKQEISSINLE 69 
                                       799*********************************986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0096
                             Asp23  23 veGvvgmagklkdglaellgkenltkgvkvevgeekqvavdlyvvveYGvkip 75 
                                       ve v +m+++ k++l e+l k+n ++g +v  ++e++  v+    +eY  +i+
  gi|488601671|ref|YP_007908142.1|  90 VEKVKSMDKEEKKKLMEKLLKANEKEGYRVYSNKEDEEIVKSISKMEYAGNIE 142
                                       5667899999999*****************98887777777666677766665 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 ?   11.5  14.0   0.00024      0.24      57     120 ..      19      82 ..       7      94 .. 0.76
   2 ?   -0.7   0.6       1.4   1.4e+03      43      57 ..      99     113 ..      76     130 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                        ATP-synt_B  57 eqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvv 120
                                        + + eA++e ++i+ +A+++a+++ +++++ ae+e+erl+++    I+ e +r + + r++v 
  gi|488601671|ref|YP_007908142.1|  19 SEIKSEAEKEVEKIVVEAEEKAKEILKKARDTAENEVERLRKQEISSINLEMKREELNRRKEVL 82 
                                       4556788888889999999999999999999999999999999988888888876666666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                        ATP-synt_B  43 eerrkeaaallaeae 57 
                                       ee++k +++ll++ e
  gi|488601671|ref|YP_007908142.1|  99 EEKKKLMEKLLKANE 113
                                       444455555555444 PP

>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.2   8.3e-05     0.083     132     182 ..      13      63 ..       4      72 .. 0.86
   2 ?    1.0   2.7      0.33   3.3e+02     149     180 ..      79     111 ..      65     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                                       ---SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSE CS
                     Peptidase_M41 132 kekelseetaeeideevkelveeayerakeileekreelealaeaLlekEt 182
                                       k ++  +e+++e ++ev+++v ea e+akeil++ r++ e+ +e+L ++E+
  gi|488601671|ref|YP_007908142.1|  13 KGQQRVSEIKSEAEKEVEKIVVEAEEKAKEILKKARDTAENEVERLRKQEI 63 
                                       4555667899********************************999999886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHHHHH.THHHHHHHHHHHHHH CS
                     Peptidase_M41 149 kelveeayerakeilee.kreelealaeaLlek 180
                                       ke++e+ ye+ +e +++  +ee ++l e+Ll+ 
  gi|488601671|ref|YP_007908142.1|  79 KEVLEAVYEKLVEKVKSmDKEEKKKLMEKLLKA 111
                                       678888888888777762466777888888875 PP

>> 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 ?    5.7   0.7     0.012        12      45      74 ..      33      60 ..       6      61 .. 0.79
   2 ?    4.2   0.3     0.038        38      39      74 ..      63      98 ..      59      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                                      EEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2 45 riqtkssnnpleaLkkalkdlldicdelee 74
                                       ++   +++++e+Lkka ++ +++++ l++
  gi|488601671|ref|YP_007908142.1| 33 VVEA--EEKAKEILKKARDTAENEVERLRK 60
                                      2332..579***************999986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.038
                                      TSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2 39 epkmnlriqtkssnnpleaLkkalkdlldicdelee 74
                                      ++++nl ++ ++ n+ +e+L+   ++l ++++++ +
  gi|488601671|ref|YP_007908142.1| 63 ISSINLEMKREELNRRKEVLEAVYEKLVEKVKSMDK 98
                                      58999****99999**************99998875 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   8.1     0.017        17       5      61 ..       3      59 ..       2      61 .. 0.76
   2 ?    7.0  10.4    0.0083       8.2      14      76 ..      36      98 ..      33      99 .. 0.84
   3 ?    4.1   9.4     0.063        63      15      70 ..      70     131 ..      66     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                              FadA  5 LeaelqkLekkeeqrykkekakaeaaaaklakk.kelkakieeklakleadsevrfyk 61
                                      Le  +++++kk +qr ++ k +ae++++k+  + +e  ++i +k ++ +a++ev+  +
  gi|488601671|ref|YP_007908142.1|  3 LEPVIEEIVKKGQQRVSEIKSEAEKEVEKIVVEaEEKAKEILKKARD-TAENEVERLR 59
                                      566789999*****************999765505555678888888.7777776655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0083
                              FadA 14 kkeeqr..ykkekakaeaaaaklakkkelkakieeklakleadsevrfykdeYkellkeyksllk 76
                                       +e+++  +kk +++ae+++++l k++ +  ++e k ++l  ++  ++ +  Y++l++++ks+ k
  gi|488601671|ref|YP_007908142.1| 36 AEEKAKeiLKKARDTAENEVERLRKQEISSINLEMKREEL--NRRKEVLEAVYEKLVEKVKSMDK 98
                                      45555688**************************999996..555666899********999866 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.063
                              FadA  15 keeqrykkekakaeaaaaklakk.....kelkakieeklakleadsevrfykde.Ykellke 70 
                                       +  ++++++k+ +ea  +kl +k     ke k+k+ ekl k+++++ +r+y+++  +e++k+
  gi|488601671|ref|YP_007908142.1|  70 MKREELNRRKEVLEAVYEKLVEKvksmdKEEKKKLMEKLLKANEKEGYRVYSNKeDEEIVKS 131
                                       55667999******99999998733333567899*****************86514455555 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 ?    4.1  10.2     0.073        73      12      46 ..      27      61 ..      15     102 .. 0.52
   2 ?    2.1   0.9       0.3   2.9e+02      42      63 ..      77      98 ..      69     126 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.073
                            DUF883 12 adleellkeaadeageeaeelRerleerlerarer 46
                                      +++e+++ ea+++a+e ++++R+ +e+++er+r++
  gi|488601671|ref|YP_007908142.1| 27 KEVEKIVVEAEEKAKEILKKARDTAENEVERLRKQ 61
                                      44444444444444444444444444444444443 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.3
                            DUF883 42 rarerlrdaeeavaerakeaae 63
                                      r +e l++++e+++e++k++ +
  gi|488601671|ref|YP_007908142.1| 77 RRKEVLEAVYEKLVEKVKSMDK 98
                                      4444444444444444444332 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  17.7    0.0075       7.4     490     598 ..      12     120 ..       6     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0075
                                       CEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.GGGSTHHHHHHHHHHHH CS
                             HSP70 490 keeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleee.aekvseaekekvesaie 565
                                       k+ + ++++ ++  e+e+ek+v +aee a+e   kk++  a+ne+e+l ++  ++++ e + +  + +ke +e+  e
  gi|488601671|ref|YP_007908142.1|  12 KKGQQRVSEIKSEAEKEVEKIVVEAEEKAKE-ILKKARDTAENEVERLRKQEISSINLEmKREELNRRKEVLEAVYE 87 
                                       455667778888899*********9997765.555555578999999999988888877544444577899****** PP

                                       HHHCHTTSSCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 566 eLkeeleeeekeeieakteelkkvvekiaekly 598
                                       +L e++++ +kee ++ +e+l k+ ek + ++y
  gi|488601671|ref|YP_007908142.1|  88 KLVEKVKSMDKEEKKKLMEKLLKANEKEGYRVY 120
                                       *********************999998877765 PP

>> Zn_ribbon_2  Putative zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.5      0.71   7.1e+02      48      54 ..      29      35 ..       3      72 .. 0.54
   2 ?    5.7   1.0     0.024        24      45      76 ..      79     110 ..      67     114 .. 0.85
   3 ?    3.8   0.0     0.094        94      33      57 ..     152     176 ..     151     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.71
                       Zn_ribbon_2 48 iekcvkk 54
                                      +ek+v +
  gi|488601671|ref|YP_007908142.1| 29 VEKIVVE 35
                                      2222222 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
                       Zn_ribbon_2  45 eemiekcvkklaeenkelteeearkllkkllp 76 
                                       +e++e + +kl e+ k++++ee +kl++kll+
  gi|488601671|ref|YP_007908142.1|  79 KEVLEAVYEKLVEKVKSMDKEEKKKLMEKLLK 110
                                       68889999999999999***********9997 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.094
                       Zn_ribbon_2  33 kdGeftepdltmeemiekcvk.klae 57 
                                       +dG+f   +lt++em++ + + k++e
  gi|488601671|ref|YP_007908142.1| 152 ADGQFRI-NLTFDEMLSTLFEsKMKE 176
                                       59***98.********9998845554 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  20.3     0.013        13      87     162 .]      22     105 ..      15     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.C.......S-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               RRF  87 TeErrkelvkeakkaaekakvairniRrdankklkklek.k.......iseDdvkkaekeiqkltdkyikeidellk 155
                                         E  ke+ k + +a ekak+ ++++R  a++++++l+k +       ++++++++ ++ ++ + +k +++++++ k
  gi|488601671|ref|YP_007908142.1|  22 KSEAEKEVEKIVVEAEEKAKEILKKARDTAENEVERLRKqEissinleMKREELNRRKEVLEAVYEKLVEKVKSMDK 98 
                                       578999*****************************9999559999998889************************** PP

                                       HHHHHHT CS
                               RRF 156 akekell 162
                                       + +k+l+
  gi|488601671|ref|YP_007908142.1|  99 EEKKKLM 105
                                       ****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3865  (0.215573); expected 358.6 (0.02)
Passed bias filter:                      912  (0.0508673); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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):              18  [number of targets reported over threshold]
# CPU time: 0.79u 0.39s 00:00:01.18 Elapsed: 00:00:00.58
# Mc/sec: 957.39
//
Query:       gi|488601672|ref|YP_007908143.1|  [L=71]
Description: F0F1-type ATP synthase, subunit c/Archaeal/vacuolar-type H+-ATPase, subunit K [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-17   62.8  11.1    3.3e-17   62.6  11.1    1.1  1  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 !   62.6  11.1   1.8e-21   3.3e-17       1      60 []       9      68 ..       9      68 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.8e-21
                                      HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                      +gaglavGl+++g+G+g   +g+a+++a+a++p+ f++ l++ +++e+i ++gL+++++l
  gi|488601672|ref|YP_007908143.1|  9 IGAGLAVGLAGIGAGLGEQGIGAAAVGAMAEDPDFFGRGLLMTVIPETIVIFGLVISFLL 68
                                      7*********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 439.38
//
Query:       gi|488601673|ref|YP_007908144.1|  [L=642]
Description: Archaeal/vacuolar-type H+-ATPase subunit I [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  126.0  20.3    1.1e-23   83.2   0.0    3.9  4  V_ATPase_I       V-type ATPase 116kDa subunit family
    0.00053   20.1   0.8    0.00053   20.1   0.8    2.1  2  DUF1640          Protein of unknown function (DUF1640)
     0.0021   18.6   8.8       0.13   12.7   1.4    2.2  2  APG6_N           Apg6 coiled-coil region
     0.0077   15.6   1.9     0.0077   15.6   1.9    2.1  2  CASP_C           CASP C terminal
     0.0089   15.9   6.2       0.07   13.0   1.6    2.5  2  Shugoshin_N      Shugoshin N-terminal coiled-coil region
  ------ inclusion threshold ------
      0.016   14.7   0.2      0.027   13.9   0.2    1.4  1  Acetyltransf_15  Putative acetyl-transferase
      0.017   14.7   2.0       0.97    9.0   0.2    2.2  2  DUF4795          Domain of unknown function (DUF4795)
      0.018   15.6   4.2       0.29   11.8   0.3    2.4  2  YabA             Initiation control protein YabA
      0.024   15.1   2.8        1.1    9.8   0.3    2.4  2  DUF16            Protein of unknown function DUF16
      0.031   14.7   2.3        4.5    7.8   0.5    2.3  2  DUF4140          N-terminal domain of unknown function (DUF41
      0.035   14.1  12.2       0.14   12.2   4.7    2.3  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.043   14.0   8.1        1.3    9.3   0.5    2.4  2  Spc24            Spc24 subunit of Ndc80
      0.047   13.8   1.5       0.69   10.0   0.0    2.4  2  Med9             RNA polymerase II transcription mediator com
      0.052   13.5   9.7        0.2   11.6   0.5    2.6  2  Prefoldin_2      Prefoldin subunit
      0.071   13.0   5.0          2    8.4   1.3    2.4  2  Prefoldin        Prefoldin subunit
      0.098   13.1   3.8        2.3    8.6   0.5    2.2  2  Fez1             Fez1
       0.13   12.6   3.5        5.6    7.3   0.6    2.3  2  DUF641           Plant protein of unknown function (DUF641)
       0.14   10.8   9.4       0.45    9.2   2.0    2.1  2  Tektin           Tektin family
       0.21   11.7   8.0        2.5    8.1   0.7    2.7  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.22   11.7   1.1         13    6.0   0.1    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.23   10.3   6.2        1.7    7.5   0.8    2.1  2  DUF812           Protein of unknown function (DUF812)
       0.28   11.1   6.3       0.43   10.5   0.6    2.2  2  Ax_dynein_light  Axonemal dynein light chain
       0.37   10.9   4.5        0.9    9.7   0.4    2.2  2  MRP-L28          Mitochondrial ribosomal protein L28
       0.38   10.8   7.7       0.62   10.1   1.1    2.2  2  ADIP             Afadin- and alpha -actinin-Binding
       0.39    9.3   3.5        4.6    5.7   0.3    2.2  2  FapA             Flagellar Assembly Protein A
       0.45   10.8   3.4         10    6.5   0.1    2.2  2  DUF5082          Domain of unknown function (DUF5082)
        0.5    9.0   9.2        1.6    7.4   9.3    1.6  1  MAP65_ASE1       Microtubule associated protein (MAP65/ASE1 f
       0.53   10.0   1.5        7.9    6.2   0.3    2.1  2  HDV_ag           Hepatitis delta virus delta antigen
          1    9.9   9.4       0.76   10.3   1.4    2.5  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        1.1    9.5  10.4       0.66   10.2   2.4    2.3  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.1    9.4  10.5        1.8    8.7   1.8    2.4  2  BRE1             BRE1 E3 ubiquitin ligase
        1.2    9.2   6.0         15    5.7   1.0    2.5  2  COG2             COG (conserved oligomeric Golgi) complex com
        1.4    9.6   3.8        6.9    7.4   0.3    2.3  2  SlyX             SlyX
        1.7    9.0   9.4       0.83   10.0   2.1    2.3  2  DUF4164          Domain of unknown function (DUF4164)
        1.9    7.6   8.3        6.7    5.9   1.9    2.8  3  MPS2             Monopolar spindle protein 2
        2.1    8.5  10.9        4.7    7.4   1.6    2.1  2  ATG16            Autophagy protein 16 (ATG16)
        2.2    8.3   9.7        4.5    7.4   1.5    2.2  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        2.4    8.6   9.7        4.5    7.7   2.7    2.2  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        2.8    8.4  13.9        2.2    8.7   3.0    2.6  2  FlaC_arch        Flagella accessory protein C (FlaC)
          3    7.7  10.6          3    7.7   0.8    2.6  2  DivIC            Septum formation initiator
        3.5    7.8  15.4          4    7.6   3.8    2.4  2  bZIP_1           bZIP transcription factor
        5.2    6.3   5.8        8.3    5.6   0.5    2.1  2  DUF3450          Protein of unknown function (DUF3450)
        5.3    7.2   8.3         21    5.3   1.4    2.6  2  Swi5             Swi5
        8.8    6.8   7.6         10    6.6   1.2    2.3  2  CENP-H           Centromere protein H (CENP-H)


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 ?    0.4   0.5      0.28   1.2e+02      60     102 ..      84     126 ..      51     138 .. 0.58
   2 !   83.2   0.0   2.6e-26   1.1e-23     204     460 ..     173     412 ..     144     427 .. 0.77
   3 !    6.6   3.7    0.0037       1.5     515     565 ..     447     498 ..     444     512 .. 0.86
   4 !   45.3   0.7   7.5e-15   3.1e-12     710     811 ..     538     632 ..     529     633 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.28
                        V_ATPase_I  60 eesleapeekeldeleeelekleeelkelnenleklkkelnel 102
                                        ++l++  ek+++ele+e++   ee+++ +e+ +kl++e++ l
  gi|488601673|ref|YP_007908144.1|  84 ISELDSVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVL 126
                                       3334444445555555555555555555555555555554444 PP

  == domain 2  score: 83.2 bits;  conditional E-value: 2.6e-26
                        V_ATPase_I 204 kveksvfiiffqgeqlkekikkicesfgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakel 280
                                       + ek++   +f  ++  + + k+++ fg + +++p+ e +++e+l+e+e++ ++l++ +++ +++++++ +e  + +
  gi|488601673|ref|YP_007908144.1| 173 EYEKEFVGAIFVKNEHAQDVFKVIQEFGYREIPVPDFEGSYDERLSEIERETSELKSKIKSLRTEMESLEKENLDLM 249
                                       3445555556666777889*************************************999888777766554443333 PP

                        V_ATPase_I 281 eewk..lkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyf 355
                                        +++  l+++ ek   + L l    v+k  ++  g+vpke+ + +++ +++at     + + ++++++ + +pPT  
  gi|488601673|ref|YP_007908144.1| 250 LAMEehLTIELEK---SELPLR-AAVSKYAFVLAGYVPKEKFDLVKNEVTSAT-----NGKVVVEKLDDELKPPTAL 317
                                       3333002333333...345554.57889999******************9988.....3458999999999****** PP

                        V_ATPase_I 356 rtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkkkkdeileml 432
                                       +  +f + f  +  +Y +++Y+Ev p+ ++ i FP +F+ M GDiG G+++l++ l+l   +kk+++   +++++  
  gi|488601673|ref|YP_007908144.1| 318 KNPRFAKPFELLTMTYTTPKYHEVDPTTLMAIVFPLMFGFMLGDIGYGICILALCLWL---KKKFRTPGWQDLFN-- 389
                                       ***************************************************9998887...55666554334444.. PP

                        V_ATPase_I 433 fsgRYiillmGlfsiYtGliYNdifsks 460
                                            i++  ++  i  G+iY ++f+  
  gi|488601673|ref|YP_007908144.1| 390 -----ILIYSSVSTIVFGFIYGELFGFE 412
                                       .....45556677777788888887754 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0037
                        V_ATPase_I 515 lsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsi.fgYlvll 565
                                       l + +Gvi+M +g+++ ++N   ++ + + ++e +  ll l+si f+ + ++
  gi|488601673|ref|YP_007908144.1| 447 LTIAIGVIHMAIGYIFGILNVAKEHGWKHAVYEKLNWLLALISIaFIIMGFI 498
                                       5799*******************************99999998834444444 PP

  == domain 4  score: 45.3 bits;  conditional E-value: 7.5e-15
                        V_ATPase_I 710 IEfvLgciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafL 786
                                       IE+ L  +SnT SY RL A+ LA    +  +  mvl++ +    +++g+i    +++vf +l  ++ ll+ +l+  L
  gi|488601673|ref|YP_007908144.1| 538 IEY-LTLLSNTISYARLLAVGLASVGFAIAFNYMVLEMLF--PAGIVGII---AGIIVF-LLGHFINLLLGVLDPGL 607
                                       777.899*****************************9955..34555544...455554.56677888999****** PP

                        V_ATPase_I 787 HaLRLhWVEfqsKFykgdGykFepf 811
                                        +LRLh VE   KF++g G+k++pf
  gi|488601673|ref|YP_007908144.1| 608 QSLRLHYVEHFVKFFEGGGIKYNPF 632
                                       ************************9 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.3       6.6   2.7e+03     120     149 ..      87     116 ..      79     124 .. 0.62
   2 !   20.1   0.8   1.3e-06   0.00053      46     101 ..     218     273 ..     216     288 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.6
                           DUF1640 120 elakleakiqelnnkidrevsalrteiEsv 149
                                         + le+k++el+  i+  ++++r++ E++
  gi|488601673|ref|YP_007908144.1|  87 LDSVLEKKVSELESEITARLEEIRKAEEQI 116
                                       444556666666666666666666555554 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.3e-06
                           DUF1640  46 selekseylqkaalselrkevqisersefaalrseteklqreleklkqkLreeidk 101
                                       se+e+++ + k+++++lr+e++++e++   ++ +  e+l +elek +  Lr  ++k
  gi|488601673|ref|YP_007908144.1| 218 SEIERETSELKSKIKSLRTEMESLEKENLDLMLAMEEHLTIELEKSELPLRAAVSK 273
                                       689******************************************99988887776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   1.0    0.0024      0.98      45      79 ..      91     125 ..      51     131 .. 0.69
   2 !   12.7   1.4   0.00033      0.13      47     107 ..     215     254 ..     184     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0024
                            APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekeree 79 
                                        ++++ ele e+ +  +e ++++e++++le+e++ 
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKKV 125
                                       44566666666666666666666666666666654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00033
                            APG6_N  47 eeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne 107
                                       e                      L e+e+e +el++++++l+ e e le+e+   +    e
  gi|488601673|ref|YP_007908144.1| 215 ER---------------------LSEIERETSELKSKIKSLRTEMESLEKENLDLMLAMEE 254
                                       44.....................45555555555555555555555555555444444444 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.4      0.57   2.3e+02      98     126 ..      93     121 ..      91     128 .. 0.78
   2 !   15.6   1.9   1.9e-05    0.0077      98     131 ..     215     248 ..     213     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.57
                            CASP_C  98 krnaeLEeelrkqeetvsslraeiaslqk 126
                                       k+++eLE+e+    e++++  ++i +l+ 
  gi|488601673|ref|YP_007908144.1|  93 KKVSELESEITARLEEIRKAEEQIRKLED 121
                                       67888888888888888888888888865 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.9e-05
                            CASP_C  98 krnaeLEeelrkqeetvsslraeiaslqkDNlkL 131
                                       +r +e+E+e ++ +++++slr+e++sl+k+Nl+L
  gi|488601673|ref|YP_007908144.1| 215 ERLSEIERETSELKSKIKSLRTEMESLEKENLDL 248
                                       799*****************************99 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.076        31      25      37 ..      90     102 ..      89     106 .. 0.84
   2 !   13.0   1.6   0.00017      0.07      10      40 ..     218     248 ..     213     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.076
                       Shugoshin_N  25 elekevseLlsEN 37 
                                        lek+vseL sE+
  gi|488601673|ref|YP_007908144.1|  90 VLEKKVSELESEI 102
                                       6999999999995 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00017
                       Shugoshin_N  10 reLAKsNsalslkirelekevseLlsENlnL 40 
                                       +e+ +  s l+ ki++l++e+++L +ENl+L
  gi|488601673|ref|YP_007908144.1| 218 SEIERETSELKSKIKSLRTEMESLEKENLDL 248
                                       566677789********************98 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   6.7e-05     0.027      13      64 ..     145     194 ..     105     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-05
                   Acetyltransf_15  13 lkevkkeFrnkrdeeeaitknenkydivqykkkeeLvasvfivkkkyyslvs 64 
                                       lk    +F ++  e  +i++++++++i+ +++++e+v+ +f+++++  ++++
  gi|488601673|ref|YP_007908144.1| 145 LKVFVGYFTANPME--KIMEVTKEFEIIFSEYEKEFVGAIFVKNEHAQDVFK 194
                                       56666778887777..9*****************************999998 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0024      0.97      18      59 ..      83     124 ..      20     134 .. 0.81
   2 ?    5.4   0.1     0.031        13      28      60 ..     215     247 ..     189     299 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                           DUF4795  18 klqeelekleekvkelekrledkekklealkkqieelekvka 59 
                                        ++e  + le+kv+ele+++ ++ +++   ++qi++le++k+
  gi|488601673|ref|YP_007908144.1|  83 SISELDSVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       55544455899***************************9995 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.031
                           DUF4795  28 ekvkelekrledkekklealkkqieelekvkad 60 
                                       e+ +e+e + +++++k+++l+ ++e lek++ d
  gi|488601673|ref|YP_007908144.1| 215 ERLSEIERETSELKSKIKSLRTEMESLEKENLD 247
                                       455566666666666666666666666666655 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3       0.1        41       6      41 ..      91     126 ..      87     135 .. 0.89
   2 ?   11.8   0.3   0.00072      0.29       8      50 ..     215     258 ..     211     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeL 41 
                                       l +k++ele+++++ lee+++ +e++ +l +e + L
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVL 126
                                       567899**********************99998877 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00072
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHH CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLele.neklre 50 
                                       ++l+e+e++++el++++++l++e+++l +en +L l   e+l  
  gi|488601673|ref|YP_007908144.1| 215 ERLSEIERETSELKSKIKSLRTEMESLEKENLDLMLAmEEHLTI 258
                                       56788888888888888888888888888888776542344444 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3    0.0027       1.1      39      74 ..      91     126 ..      82     145 .. 0.85
   2 ?    5.1   0.2     0.076        31      27      63 ..     208     244 ..     187     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0027
                                       HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  39 ieakvdklgeqinkleqkvekqgekikelkveqkaq 74 
                                       +e+kv+ l+ +i +  ++++k +e+i++l+ e k  
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVL 126
                                       58999999999999999***********99998865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.076
                                       HB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHH CS
                             DUF16  27 efkdsnkqrLkkieakvdklgeqinkleqkvekqgek 63 
                                       +f  s ++rL +ie + + l+ +i+ l  ++e ++++
  gi|488601673|ref|YP_007908144.1| 208 DFEGSYDERLSEIERETSELKSKIKSLRTEMESLEKE 244
                                       5778889999999999999999999999998888765 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.5     0.011       4.5      66      98 .]      94     126 ..      67     127 .. 0.71
   2 ?    6.1   0.0     0.036        15      65      94 ..     212     244 ..     183     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                           DUF4140  66 elkalraeleeledelaaledelaaaearlafl 98 
                                       ++++l++e+++  +e++++e++++ +e+++++l
  gi|488601673|ref|YP_007908144.1|  94 KVSELESEITARLEEIRKAEEQIRKLEDEKKVL 126
                                       477888888888888888888888888777765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.036
                           DUF4140  65 e...elkalraeleeledelaaledelaaaear 94 
                                       +   +l+++++e  el+ +++ l+ e++++e++
  gi|488601673|ref|YP_007908144.1| 212 SydeRLSEIERETSELKSKIKSLRTEMESLEKE 244
                                       244347777777777777777777777777764 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.8     0.025        10      94     125 ..      93     124 ..      61     133 .. 0.71
   2 ?   12.2   4.7   0.00034      0.14       9      50 ..     214     255 ..     211     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.025
                    CENP-F_leu_zip  94 ervseLeslnsslenlleekEqekvqmkeesk 125
                                       ++vseLes      + ++++E++ +++++e k
  gi|488601673|ref|YP_007908144.1|  93 KKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       45666666666666666666666666666554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00034
                    CENP-F_leu_zip   9 lekLKeserkadsLkdkvenLerelemseenqekvileaEts 50 
                                        e+L e+er+ + Lk k+++L  e+e +e+++ +++l +E+ 
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEMESLEKENLDLMLAMEEH 255
                                       5899****************************9999999976 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5    0.0032       1.3       9      81 ..      91     189 ..      83     199 .. 0.67
   2 ?    7.9   1.9    0.0087       3.5      11      43 ..     215     247 ..     212     274 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0032
                             Spc24   9 iakelsdleselesleselaelkeeleeleeeseekeser...ve.detllklklYrsLGiel.............. 67 
                                       + k++s+lese+++  +e ++ +e++++le+e++     +   ++ +  +  lk Y++L++ +              
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKKV----LaplKAlNIPVNLLKGYKNLKVFVgyftanpmekimev 163
                                       67889999999999999999999999999988877....22324446666888889999888777766666666666 PP

                             Spc24  68 ...........ekd.vnkvlirnkek 81 
                                                  ek+ v  + ++n++ 
  gi|488601673|ref|YP_007908144.1| 164 tkefeiifseyEKEfVGAIFVKNEHA 189
                                       66555555533222455555555555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0087
                             Spc24  11 kelsdleselesleselaelkeeleeleeesee 43 
                                       + ls++e+e+++l+s+ ++l++e+e le+e+ +
  gi|488601673|ref|YP_007908144.1| 215 ERLSEIERETSELKSKIKSLRTEMESLEKENLD 247
                                       457788888888888888888888888877655 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5      0.58   2.4e+02      46      69 ..      96     119 ..      81     129 .. 0.61
   2 ?   10.0   0.0    0.0017      0.69      21      47 ..     217     243 ..     191     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.58
                              Med9  46 pgidrsveeqeaeieeleeqlakK 69 
                                       ++++  +  +++ei++ eeq++k 
  gi|488601673|ref|YP_007908144.1|  96 SELESEITARLEEIRKAEEQIRKL 119
                                       334444445555555555555554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                              Med9  21 skdletktgelrhkLkkarelirelpg 47 
                                         ++e +t+el+ k+k+ r+ +++l+ 
  gi|488601673|ref|YP_007908144.1| 217 LSEIERETSELKSKIKSLRTEMESLEK 243
                                       568999****************99985 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.0     0.058        24      67      98 ..      91     122 ..      83     130 .. 0.53
   2 ?   11.6   0.5   0.00049       0.2      60      99 ..     206     245 ..     202     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  67 Leerketlekeiktlekqleklekeleelkee 98 
                                       Le++  +le ei++  ++++k e+++++l++e
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDE 122
                                       55555555555555555555555555555443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                       +++ +   +er+ ++e e ++l++++++l++e+e l++e+
  gi|488601673|ref|YP_007908144.1| 206 VPDFEGSYDERLSEIERETSELKSKIKSLRTEMESLEKEN 245
                                       6677777899**************************9986 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.3    0.0048         2      76     113 ..      85     122 ..      81     128 .. 0.87
   2 ?    5.7   0.1     0.032        13      82     112 ..     213     243 ..     203     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0048
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  76 eeAiellkkkleelekqlekleeeleklkdqittlean 113
                                        e   +l+kk++ele+ ++   ee++k+ +qi +le++
  gi|488601673|ref|YP_007908144.1|  85 SELDSVLEKKVSELESEITARLEEIRKAEEQIRKLEDE 122
                                       5556789***************************9987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittlea 112
                                       ++++l+e+e+   +l+ +++ l++++++le+
  gi|488601673|ref|YP_007908144.1| 213 YDERLSEIERETSELKSKIKSLRTEMESLEK 243
                                       6778888888888888888888888887776 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.059        24      50      92 ..      91     132 ..      83     163 .. 0.82
   2 ?    8.6   0.5    0.0056       2.3      31      78 ..     222     270 ..     208     320 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.059
                              Fez1  50 keeeikeleesleektlelevcenelqrkkseaellrekvekl 92 
                                        e++++ele++++ + +e+ + e+++++ ++e+++l   +++l
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVLAP-LKAL 132
                                       58899999999999999999999999999999988865.5555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0056
                              Fez1  31 seivalkaqlrelrakleekeeeikeleesleek.tlelevcenelqrk 78 
                                        e  +lk++++ lr+++e+ e+e+ +l  ++ee+ t ele+ e  l+ +
  gi|488601673|ref|YP_007908144.1| 222 RETSELKSKIKSLRTEMESLEKENLDLMLAMEEHlTIELEKSELPLRAA 270
                                       4667899999999999999999999988887765356777777666655 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 ?    7.3   0.6     0.014       5.6      88     123 ..      89     124 ..      69     127 .. 0.86
   2 ?    5.7   0.1     0.043        18      89     123 ..     212     246 ..     183     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.014
                            DUF641  88 ktyeitvkkleaelkakdseieeLkekLeeaeksnk 123
                                        ++e+ v++le+e++a+ +ei + +e+++++e ++k
  gi|488601673|ref|YP_007908144.1|  89 SVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       56799999******************9999998876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.043
                            DUF641  89 tyeitvkkleaelkakdseieeLkekLeeaeksnk 123
                                       +y+ +++++e+e+++ +s+i++L+ ++e++ek+n 
  gi|488601673|ref|YP_007908144.1| 212 SYDERLSEIERETSELKSKIKSLRTEMESLEKENL 246
                                       57888899999999999999999999999998886 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.9     0.011       4.4     251     296 ..      79     124 ..      71     127 .. 0.54
   2 ?    9.2   2.0    0.0011      0.45      48      89 ..     213     254 ..     208     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                            Tektin 251 krieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplk 296
                                       kr++ + +  + le++ ++++ ei++  ++i++ e++ir+ e+  k
  gi|488601673|ref|YP_007908144.1|  79 KRVYSISELDSVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       4555555555555555555555555555555555555555554444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                            Tektin  48 LeeRiediefwkeeLekeleelkeeieaLeeekrrlekalea 89 
                                        +eR+++ie+  +eL+ +++ l++e+e+Le+e   l  a+e+
  gi|488601673|ref|YP_007908144.1| 213 YDERLSEIERETSELKSKIKSLRTEMESLEKENLDLMLAMEE 254
                                       579***************************999988888875 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0098         4      75     122 ..      82     126 ..      56     137 .. 0.82
   2 ?    8.1   0.7    0.0062       2.5      87     128 ..     213     254 ..     161     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0098
                           UPF0242  75 aklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqL 122
                                         ++eld   ++ e+++ el++e   + ee+ + ee++++l+ e++ L
  gi|488601673|ref|YP_007908144.1|  82 YSISELD---SVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVL 126
                                       5677888...88899999999999999999999999999999998866 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0062
                           UPF0242  87 keealeelqeeeeeLkeeldakeeelerlkeenqqLqeklea 128
                                        +e l e + e+ eLk ++++  +e+e l++en  L   +e+
  gi|488601673|ref|YP_007908144.1| 213 YDERLSEIERETSELKSKIKSLRTEMESLEKENLDLMLAMEE 254
                                       467899999999999999999999999999999887765554 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.032        13      72     115 ..      77     120 ..      50     129 .. 0.59
   2 ?    4.2   0.1      0.11        46      93     124 ..     213     244 ..     187     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHH CS
                         Fib_alpha  72 kkdndnvikksskeleeeilrlketidaqesnirvLqnvlesne 115
                                       +++    i+++ + le+++++l+ +i+a  ++ir+  + ++++e
  gi|488601673|ref|YP_007908144.1|  77 EPKRVYSISELDSVLEKKVSELESEITARLEEIRKAEEQIRKLE 120
                                       44444455555556666666666666666666655555555544 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                                       HHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  93 lketidaqesnirvLqnvlesneqkiqkLeqd 124
                                       ++e++++ e++  +L++ ++s++ +++ Le++
  gi|488601673|ref|YP_007908144.1| 213 YDERLSEIERETSELKSKIKSLRTEMESLEKE 244
                                       55666666777778888888888888888775 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.8    0.0041       1.7     413     466 ..      70     124 ..      56     131 .. 0.83
   2 ?    5.7   0.4     0.014       5.8     329     365 ..     214     250 ..     159     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0041
                            DUF812 413 velakqWekhRvplieeyre.lkesksekekeaerkleeikklrekmkevaeelr 466
                                       +++   +e++Rv  i e+ + l+++ se e+e+  +leei+k +e+++++++e +
  gi|488601673|ref|YP_007908144.1|  70 IKVDPAYEPKRVYSISELDSvLEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       5666678999999999998746777788999999999999999999999988765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                            DUF812 329 eeeleelqeqieeleskieeleeeikklessikqvee 365
                                       +e l+e++++ +el+ski++l+ e+++le++   ++ 
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEMESLEKENLDLML 250
                                       4556666666666666666666666666665544443 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.7      0.18        72     122     156 ..      89     123 ..      71     131 .. 0.66
   2 ?   10.5   0.6    0.0011      0.43     125     165 ..     214     254 ..     188     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.18
                   Ax_dynein_light 122 selekkikeLeeekeelekqvaelkaklealekre 156
                                       s lekk++eLe+e     +++ + ++++++le ++
  gi|488601673|ref|YP_007908144.1|  89 SVLEKKVSELESEITARLEEIRKAEEQIRKLEDEK 123
                                       55666666666666666666666666666665554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0011
                   Ax_dynein_light 125 ekkikeLeeekeelekqvaelkaklealekrekerrqeeek 165
                                       +++++e+e+e +el++++++l++++e+lek++ + + + e+
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEMESLEKENLDLMLAMEE 254
                                       56666667777777777777777777776666555444444 PP

>> MRP-L28  Mitochondrial ribosomal protein L28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4    0.0022       0.9       7      57 ..      93     141 ..      87     149 .. 0.80
   2 ?    2.6   0.3      0.34   1.4e+02      86     140 ..     215     274 ..     212     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0022
                                       XXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXSXSXXTTSSTT CS
                           MRP-L28   7 kkkkkvdpqvvkrreerakkrlekqirkleksakelkPveelivplksvds 57 
                                       kk   ++ +++ r ee +  + e+qirkle ++k l P++ l +p+++++ 
  gi|488601673|ref|YP_007908144.1|  93 KKVSELESEITARLEEIR--KAEEQIRKLEDEKKVLAPLKALNIPVNLLKG 141
                                       555566677777777665..56899*********************99875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTTCTT.....CS-XXTTSTTXXXXXXBS CS
                           MRP-L28  86 yrqqekekdeqlirqqleaqeealeeLkkvseeLYea.....AvkrdegllPlelkgpte 140
                                       +r  e e+++ +++  +++++  +e L+k++  L  a      ++ ++++lPl + +  +
  gi|488601673|ref|YP_007908144.1| 215 ERLSEIERETSELKSKIKSLRTEMESLEKENLDLMLAmeehlTIELEKSELPLRAAVSKY 274
                                       57788899999*******************999874422233566677788888777665 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.8      0.11        44      79     112 ..      91     124 ..      85     128 .. 0.79
   2 ?   10.1   1.1    0.0015      0.62      56     107 ..     211     263 ..     208     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                              ADIP  79 lktqleqlerelalvqakerqlekklktleqklk 112
                                       l++++++le+e+++  ++ r++e ++++le+  k
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       7788888888888888888888888888887655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0015
                              ADIP  56 eslnetirkleaeierlqskierlktqleqlerela.lvqakerqlekklktl 107
                                        s+ e+++++e e + l+ski++l t+ e+le+e+  l  a e +l+ +l++ 
  gi|488601673|ref|YP_007908144.1| 211 GSYDERLSEIERETSELKSKIKSLRTEMESLEKENLdLMLAMEEHLTIELEKS 263
                                       578899***************************98779999999999888765 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.029        12     329     368 ..      86     124 ..      74     187 .. 0.81
   2 ?    5.7   0.3     0.011       4.6     336     396 ..     214     262 ..     202     306 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.029
                              FapA 329 gldepelkeklkeleeeleeleeeleklkkkikklpklka 368
                                       +ld   l +k++ele e+ +  ee++k +++i+kl+++k+
  gi|488601673|ref|YP_007908144.1|  86 ELD-SVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       555.667788899999999999999999999999998554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                              FapA 336 keklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeelee 396
                                       +e+l+e+e+e  el+++++ l+ ++++l+k            e l+ +l   e+l+ ele+
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEMESLEK------------ENLDLMLAMEEHLTIELEK 262
                                       444444444444444444444444444444............5555555555555555554 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.8     0.095        39       2      33 ..      92     123 ..      81     131 .. 0.74
   2 ?    6.5   0.1     0.024        10      83     116 ..     210     243 ..     197     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.095
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeak 33 
                                        +k s+l+++i    +ei++ ee+I++L+  k
  gi|488601673|ref|YP_007908144.1|  92 EKKVSELESEITARLEEIRKAEEQIRKLEDEK 123
                                       45667777777777778888888888887655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.024
                           DUF5082  83 vdkldelidaieeEIerLenqiseaqgvldtlqs 116
                                       +   de  ++ie+E+++L+++i+++ + +++l++
  gi|488601673|ref|YP_007908144.1| 210 EGSYDERLSEIERETSELKSKIKSLRTEMESLEK 243
                                       5566777889999999999999999888877765 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   9.3    0.0038       1.6      44     171 ..      62     252 ..      50     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0038
                                       HHHHHST-----....-SS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS....---SS--TS CS
                        MAP65_ASE1  44 glksiLheepvdvpqsekkelsLlqkkkkldtaleelrkekaerlaeflelleqlqklceelge....eplsllids 116
                                       +l+s+L+  +vd   ++k   s+ +  + l++++ el  e + rl+e+ +  eq +kl +e +     + l+++ + 
  gi|488601673|ref|YP_007908144.1|  62 TLRSMLSYIKVDPAYEPKRVYSISELDSVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVlaplKALNIPVNL 138
                                       689999999999889999999************************************99986665444444444444 PP

                                       S--HHH........HHHHHHHHHHHHH.................................................. CS
                        MAP65_ASE1 117 lpklee........leslrkhleelke.................................................. 135
                                       l+  ++        +           +                                                  
  gi|488601673|ref|YP_007908144.1| 139 LKGYKNlkvfvgyfT-----------Anpmekimevtkefeiifseyekefvgaifvknehaqdvfkviqefgyrei 204
                                       444444555555552...........12334455555578889999999**************************** PP

                                       .......HHHHHHHHHHHHHHHHHHHHHHHT----SHHHHHH.....H CS
                        MAP65_ASE1 136 .......ekerRleeikelkkqIkslmeeLglepktsieedl.....l 171
                                               +++Rl ei+   +++ks ++ L++e++   +e+l     +
  gi|488601673|ref|YP_007908144.1| 205 pvpdfegSYDERLSEIERETSELKSKIKSLRTEMESLEKENLdlmlaM 252
                                       **********************************99999988655440 PP

>> HDV_ag  Hepatitis delta virus delta antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.019       7.9      15      56 ..      89     131 ..      81     135 .. 0.75
   2 ?    2.6   0.1      0.25     1e+02      24      49 ..     214     239 ..     199     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
                            HDV_ag  15 evleqwvsgrk.kleelerdlrkvkkkikkledehpwlgnikg 56 
                                        vle+ vs  + ++     ++rk +++i+klede+  l  +k 
  gi|488601673|ref|YP_007908144.1|  89 SVLEKKVSELEsEITARLEEIRKAEEQIRKLEDEKKVLAPLKA 131
                                       567777765431344444579**************99988876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.25
                            HDV_ag  24 rkkleelerdlrkvkkkikkledehp 49 
                                        ++l e+er+  ++k kik l  e  
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEME 239
                                       57899***************998865 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 ?    3.5   1.4      0.25     1e+02      34      71 ..      89     126 ..      81     132 .. 0.89
   2 ?   10.3   1.4    0.0019      0.76      32      74 ..     209     251 ..     207     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.25
                       Fungal_TACC  34 akyqkkldklelenkslkqeieqLkkqleaerkEKqeL 71 
                                       +  +kk+++le e  +  +ei + ++q+   + EK+ L
  gi|488601673|ref|YP_007908144.1|  89 SVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVL 126
                                       557899*****************************977 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0019
                       Fungal_TACC  32 yeakyqkkldklelenkslkqeieqLkkqleaerkEKqeLlkl 74 
                                       +e  y ++l+++e e ++lk+ i++L+ ++e+ +kE  +L+  
  gi|488601673|ref|YP_007908144.1| 209 FEGSYDERLSEIERETSELKSKIKSLRTEMESLEKENLDLMLA 251
                                       8999************************999999998877655 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.2      0.18        74      14      41 ..      95     122 ..      82     129 .. 0.52
   2 ?   10.2   2.4    0.0016      0.66      20      69 ..     216     265 ..     211     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.18
                       TMF_TATA_bd  14 verlsseirrlEgElaslkeelerleae 41 
                                       v++l+sei  +  E+++++e++ +le e
  gi|488601673|ref|YP_007908144.1|  95 VSELESEITARLEEIRKAEEQIRKLEDE 122
                                       3344444444444444444444444444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0016
                       TMF_TATA_bd  20 eirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleel 69 
                                       ++ + E E ++lk+++++l +e +++++e ++lm  +ee  + + e +el
  gi|488601673|ref|YP_007908144.1| 216 RLSEIERETSELKSKIKSLRTEMESLEKENLDLMLAMEEHLTIELEKSEL 265
                                       67789*****************************9999887776666555 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.8    0.0044       1.8      28      64 ..      90     126 ..      84     131 .. 0.83
   2 ?    5.0   1.8     0.061        25      30      65 ..     214     249 ..     211     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0044
                              BRE1  28 ileekklrleaekakadqkyfaamrskdalenelkkL 64 
                                        le+k++ le+e++   +++  a+ ++++le e k L
  gi|488601673|ref|YP_007908144.1|  90 VLEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVL 126
                                       6889999999999999999999999999999998887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.061
                              BRE1  30 eekklrleaekakadqkyfaamrskdalenelkkLn 65 
                                        e+++ +e e ++ + k+++++ ++++le+e+  L 
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEMESLEKENLDLM 249
                                       577788888888888888888888888888887664 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 ?    5.7   1.0     0.036        15      80     120 ..      90     130 ..      79     140 .. 0.80
   2 ?    5.5   0.3     0.043        18      66      98 ..     212     244 ..     211     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.036
                              COG2  80 aarkkvesvreklsereeeveskleeakeleekrellklll 120
                                        + kkv+++++++ +r ee+++  e+ ++le+++++l  l 
  gi|488601673|ref|YP_007908144.1|  90 VLEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVLAPLK 130
                                       56789999999999999999999999999999998877665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.043
                              COG2  66 glqeeleevesplaaarkkvesvreklsereee 98 
                                       +++e+l+e+e + +++++k++s+r +++  e+e
  gi|488601673|ref|YP_007908144.1| 212 SYDERLSEIERETSELKSKIKSLRTEMESLEKE 244
                                       579999999999999999999999988877654 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3     0.017       6.9      15      48 ..      91     124 ..      82     132 .. 0.87
   2 ?    2.8   0.3      0.46   1.9e+02      27      53 ..     218     244 ..     213     255 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                              SlyX  15 qedtieeLndvvaeqqqqidrlqrqlrllaerlk 48 
                                       +e+ + eL  ++++  ++i + ++q+r+l+++ k
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       799999**********************998765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  27 aeqqqqidrlqrqlrllaerlkelees 53 
                                        e +++ ++l+ +++ l+ ++++le++
  gi|488601673|ref|YP_007908144.1| 218 SEIERETSELKSKIKSLRTEMESLEKE 244
                                       444555555555555555555555554 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.1     0.002      0.83       5      52 ..      83     127 ..      80     129 .. 0.84
   2 ?    2.9   0.8      0.34   1.4e+02      21      54 ..     210     244 ..     206     263 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.002
                           DUF4164   5 eleaaltrLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLa 52 
                                       ++++  + Le+++ +LE+ +++rle+ r   ++e++i++l+++++ La
  gi|488601673|ref|YP_007908144.1|  83 SISELDSVLEKKVSELESEITARLEEIR---KAEEQIRKLEDEKKVLA 127
                                       67777788***************98766...57889999999998776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.34
                           DUF4164  21 Ekavdrrlea.erkrdeleaeiealgedrsRLaee 54 
                                       E++ d+rl++ er+++el+++i+ l+ + + L++e
  gi|488601673|ref|YP_007908144.1| 210 EGSYDERLSEiERETSELKSKIKSLRTEMESLEKE 244
                                       66677777542566688888888888777777654 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.3   1.4e+03      43      70 ..      19      46 ..       7      49 .. 0.83
   2 ?    5.9   1.9     0.016       6.7     143     191 ..      72     120 ..      44     127 .. 0.83
   3 ?    4.3   0.3     0.051        21     178     207 ..     215     244 ..     211     315 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.3
                              MPS2 43 yelrlpllselgkdllrtFakekeffki 70
                                      +e  +++l +l+   ++ Fa+e e+f+i
  gi|488601673|ref|YP_007908144.1| 19 FEKTAEVLHKLNLLHIEDFAEEGEYFRI 46
                                      5667888899999999**********98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                              MPS2 143 lkkqesPeklrrsnrklkaLevrveslkdELeakdevlrekeRelleLk 191
                                        ++  +P+++ ++ ++   Le +v +l+ E++a+ e +r+ e ++ +L+
  gi|488601673|ref|YP_007908144.1|  72 VDPAYEPKRVYSISELDSVLEKKVSELESEITARLEEIRKAEEQIRKLE 120
                                       456789************************************9999886 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.051
                              MPS2 178 evlrekeRelleLkkrlseykekYellqre 207
                                       e l e eRe +eLk++++ ++   e+l++e
  gi|488601673|ref|YP_007908144.1| 215 ERLSEIERETSELKSKIKSLRTEMESLEKE 244
                                       556666677777777777666666666654 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.6     0.011       4.7     107     140 ..      91     124 ..      84     129 .. 0.59
   2 ?    5.9   2.2     0.032        13     101     140 ..     214     253 ..     210     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                             ATG16 107 lneelqkleeklkedeerlaeleaeraaletklk 140
                                       l++++++le++++++ e+++++e+++++le++ k
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       4555555555555555555555555555555543 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.032
                             ATG16 101 aqrllelneelqkleeklkedeerlaeleaeraaletklk 140
                                        +rl e + e ++l++k+k+ ++++++le+e+ +l  +++
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEMESLEKENLDLMLAME 253
                                       5677777777777777777777777777777776665554 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 ?    5.3   1.5     0.048        19       2      30 ..      94     122 ..      93     128 .. 0.90
   2 ?    7.4   1.5     0.011       4.5      58      88 ..     216     246 ..     212     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.048
                        TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqed 30 
                                       ++++le+ei++ +ee+ +ae++++kl+++
  gi|488601673|ref|YP_007908144.1|  94 KVSELESEITARLEEIRKAEEQIRKLEDE 122
                                       7899**********************987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                        TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaele 88 
                                        l+++  e +elk++i++l++e es+++e+ 
  gi|488601673|ref|YP_007908144.1| 216 RLSEIERETSELKSKIKSLRTEMESLEKENL 246
                                       6888889999999999999999999888765 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.7     0.082        33       6      54 ..      91     123 ..      79     135 .. 0.58
   2 ?    7.7   2.7     0.011       4.5       7      50 ..     214     249 ..     210     275 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.082
                       Uso1_p115_C   6 leseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaen 54 
                                       le+++++l++e ++   e++++++++++le +                +
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDE----------------K 123
                                       45555555555555555555555555555544................2 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.011
                       Uso1_p115_C   7 eseaaslkdeneklkaelqslskalesleqk.eakkaaesqakel 50 
                                        ++ +++++e ++lk++++sl++++esle++           + +
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEMESLEKEnL---------DLM 249
                                       567788888888888888888888888888831.........222 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 ?    4.4   3.3      0.12        48       5      36 ..      91     122 ..      89     127 .. 0.84
   2 ?    8.7   3.0    0.0054       2.2       1      30 [.     216     245 ..     216     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.12
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksveelken 36 
                                       lE+k+s+l++e++   +e+ + ++++ +l+++
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDE 122
                                       89********9998888888888888888875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0054
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksv 30 
                                       r+ e+E + s+l+++++++++e+e+l+k+ 
  gi|488601673|ref|YP_007908144.1| 216 RLSEIERETSELKSKIKSLRTEMESLEKEN 245
                                       7899*********************99975 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.1      0.12        50      23      54 ..      92     122 ..      84     127 .. 0.67
   2 ?    7.7   0.8    0.0073         3      18      46 ..     216     244 ..     214     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                             DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                       ++++ +l+ e+ +  +e+++ e+++++L+ de
  gi|488601673|ref|YP_007908144.1|  92 EKKVSELESEITARLEEIRKAEEQIRKLE-DE 122
                                       66677777777777777777777777774.43 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0073
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeae 46 
                                       +++++++e  +l+ ++++l+ e e+Le+e
  gi|488601673|ref|YP_007908144.1| 216 RLSEIERETSELKSKIKSLRTEMESLEKE 244
                                       57889999999999999999999999998 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.8     0.045        18      31      63 ..      91     123 ..      88     124 .. 0.94
   2 ?    7.6   3.8    0.0099         4      31      56 ..     220     245 ..     214     254 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  31 LerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       Le++v++Le+e ++  +e+ + ++++ kL++++
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEK 123
                                       9****************************9987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  31 LerrvkaLekeNksLkseleelkkev 56 
                                        er+ ++L+++ ksL+ e+e+l+ke+
  gi|488601673|ref|YP_007908144.1| 220 IERETSELKSKIKSLRTEMESLEKEN 245
                                       44444444444444444444444443 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5      0.13        52      33      68 ..      89     124 ..      79     131 .. 0.71
   2 ?    5.6   0.5      0.02       8.3      36      70 ..     214     248 ..     210     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.13
                           DUF3450  33 aqsqkkidklddekqellaeyralkeeleslevyne 68 
                                       +  +kk+++l+ e +  l+e+r+++e++ +le +++
  gi|488601673|ref|YP_007908144.1|  89 SVLEKKVSELESEITARLEEIRKAEEQIRKLEDEKK 124
                                       455678888888888888888888888877776555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
                           DUF3450  36 qkkidklddekqellaeyralkeeleslevyneql 70 
                                        ++ +++++e++el++++++l++e esle++n  l
  gi|488601673|ref|YP_007908144.1| 214 DERLSEIERETSELKSKIKSLRTEMESLEKENLDL 248
                                       56778899999999999999999999999988665 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.4     0.052        21       2      37 ..      92     133 ..      91     147 .. 0.66
   2 ?    5.2   0.8     0.055        22       3      30 ..     215     242 ..     213     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHH CS
                              Swi5   2 eaeikeleeqleelekelaelkeelkekk......dpeetvk 37 
                                       e++++ele+++++  +e+ +++e+ ++ +      +p + ++
  gi|488601673|ref|YP_007908144.1|  92 EKKVSELESEITARLEEIRKAEEQIRKLEdekkvlAPLKALN 133
                                       789999998888888888888888876663334444555555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Swi5   3 aeikeleeqleelekelaelkeelkekk 30 
                                       ++++e+e++++el++++++l+ e+++ +
  gi|488601673|ref|YP_007908144.1| 215 ERLSEIERETSELKSKIKSLRTEMESLE 242
                                       6778888888888888888888887654 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.7      0.24     1e+02      11      46 ..      91     126 ..      84     129 .. 0.76
   2 ?    6.6   1.2     0.025        10      28      61 ..     216     249 ..     212     276 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.24
                            CENP-H  11 lssellklsqelrelqeeltevekenlrlkrknrel 46 
                                       l +++ +l++e+++ +ee+ ++e+++++l+ +++ l
  gi|488601673|ref|YP_007908144.1|  91 LEKKVSELESEITARLEEIRKAEEQIRKLEDEKKVL 126
                                       556778888888888888888888888887776655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.025
                            CENP-H  28 eltevekenlrlkrknrelaaellelakekesek 61 
                                       +l+e+e+e+ +lk k ++l +e++ l+ke+    
  gi|488601673|ref|YP_007908144.1| 216 RLSEIERETSELKSKIKSLRTEMESLEKENLDLM 249
                                       4555555555555555555555533333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1823  (0.101679); expected 358.6 (0.02)
Passed bias filter:                     1018  (0.0567795); expected 358.6 (0.02)
Passed Vit filter:                       174  (0.00970495); expected 17.9 (0.001)
Passed Fwd filter:                        61  (0.00340231); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 1.03u 0.41s 00:00:01.44 Elapsed: 00:00:00.60
# Mc/sec: 3220.27
//
Query:       gi|488601674|ref|YP_007908145.1|  [L=106]
Description: ATP synthase archaeal, H subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-08   34.8  16.5    1.9e-08   34.6  16.5    1.0  1  V-ATPase_G_2     Vacuolar (H+)-ATPase G subunit
    9.3e-06   25.8  21.0    2.4e-05   24.4  21.1    1.6  1  ATP-synt_B       ATP synthase B/B' CF(0)
     0.0026   17.2  18.9     0.0026   17.2  18.9    2.0  2  DUF3552          Domain of unknown function (DUF3552)
     0.0099   15.3  18.4     0.0099   15.3  18.4    2.1  2  vATP-synt_E      ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
      0.011   16.3   7.1      0.015   15.9   6.7    1.3  1  DUF883           Bacterial protein of unknown function (DUF88
      0.049   13.9   1.6      0.054   13.8   1.6    1.1  1  FANCI_S2         FANCI solenoid 2
       0.12   12.1   3.8       0.14   12.0   3.8    1.1  1  REF              Rubber elongation factor protein (REF)
       0.17   12.0  18.4       0.24   11.5  18.4    1.4  1  DivIVA           DivIVA protein
       0.26   10.3   9.5       0.32   10.0   9.5    1.1  1  RapA_C           RNA polymerase recycling family C-terminal
       0.28   11.7  11.4        4.1    8.0  11.4    2.0  1  PRESAN           Plasmodium RESA N-terminal
       0.36    9.3   5.6       0.39    9.2   5.6    1.0  1  Aldedh           Aldehyde dehydrogenase family
       0.39   11.0  13.0       0.45   10.8  13.0    1.1  1  zf-C4H2          Zinc finger-containing protein
       0.88    9.4   9.3        1.3    8.8   9.3    1.2  1  NACHT_N          N-terminal domain of NWD NACHT-NTPase
          1    7.4  14.9        1.1    7.4  14.9    1.0  1  HSP70            Hsp70 protein
          2    8.9  14.0        2.6    8.5  14.0    1.2  1  CENP-H           Centromere protein H (CENP-H)
        4.6    5.8   6.1        5.2    5.7   6.1    1.0  1  CENP-I           Mis6
        5.9    6.0   9.6        6.6    5.9   9.6    1.1  1  TMPIT            TMPIT-like protein
        6.2    6.6  12.1        4.7    7.0  10.2    1.7  2  Peptidase_M41    Peptidase family M41
        6.7    6.8   9.8        7.8    6.6   9.8    1.2  1  PTPlike_phytase  Inositol hexakisphosphate
        6.9    6.7  15.8        8.5    6.4  15.8    1.3  1  Clathrin_lg_ch   Clathrin light chain
        7.5    5.7  16.4          9    5.4  16.4    1.1  1  ISG65-75         Invariant surface glycoprotein
        9.9    5.9  13.3        1.7    8.4   8.5    1.8  2  PRKCSH-like      Glucosidase II beta subunit-like


Domain annotation for each model (and alignments):
>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6  16.5   2.3e-11   1.9e-08       1      99 [.       1      99 [.       1     103 [. 0.96

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.3e-11
                                      XXXXHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2  1 dessrllkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeae 79
                                      +e+  +l++++e E++ ++ +  A +e ++ + +A+  A+ i+++Ae++a+++++e  ++ + e+++++e +r++  +e
  gi|488601674|ref|YP_007908145.1|  1 MEKTEILSKIKEVEQKVEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIREKRLKE 79
                                      67889************************************************************************** PP

                                      HHHHHHHHHCSHHHHHHHHH CS
                      V-ATPase_G_2 80 aqavrkraearlqqAvelil 99
                                       ++v  +++ r+++Av+   
  gi|488601674|ref|YP_007908145.1| 80 INDVVSKGKSRIDEAVDFLY 99
                                      ****************8765 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 !   24.4  21.1     3e-08   2.4e-05      34     102 ..       5      74 ..       3      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3e-08
                        ATP-synt_B  34 kIadeiaeAeer.rkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaa 102
                                       +I ++i+e e++  ++ + +++e+++   eA+ +A+eii nA+keaek+k+ei+++a+ e+e+ kes ++
  gi|488601674|ref|YP_007908145.1|   5 EILSKIKEVEQKvEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIRE 74 
                                       799999**9977367899999999**************************************99998655 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   6.6    0.0048       3.9      33      63 ..      10      40 ..       1      41 [. 0.80
   2 !   17.2  18.9   3.2e-06    0.0026      24      88 ..      27      92 ..      23      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0048
                           DUF3552 33 eeeAkkiieeAkkeAeakkkealleakeeih 63
                                       +e ++ +ee  k+Ae+ k++ +leake+++
  gi|488601674|ref|YP_007908145.1| 10 IKEVEQKVEEDIKSAEEEKRKVILEAKEKAR 40
                                      456677799999****************976 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.2e-06
                           DUF3552 24 iaekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreel.ekelkerrnelqrlekRll 88
                                       ++k i eA+e+A++ii++A+keAe++k e++ +ak ei k +e + ek lke ++ +++   R+ 
  gi|488601674|ref|YP_007908145.1| 27 EKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIrEKRLKEINDVVSKGKSRID 92
                                      5667899************************************99757778888877777777765 PP

>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   2.9       0.7   5.7e+02      26      45 ..      11      30 ..       2      33 .. 0.47
   2 !   15.3  18.4   1.2e-05    0.0099       5      44 ..      34      73 ..      30      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.7
                                      HHHHHHHHHCHHHHHHHHHH CS
                       vATP-synt_E 26 aklveeeeekieeayekkeK 45
                                      ++++++ ee i++a e+k+K
  gi|488601674|ref|YP_007908145.1| 11 KEVEQKVEEDIKSAEEEKRK 30
                                      33334444444444444444 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH CS
                       vATP-synt_E  5 eAeekAeeIkakaeeefeiekaklveeeeekieeayekke 44
                                      eA+ekA+eI+++ae+e+e++k+++ e+++ +ie+++e+ +
  gi|488601674|ref|YP_007908145.1| 34 EAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIR 73
                                      9****************************99999988743 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 ?   15.9   6.7   1.8e-05     0.015       2      73 ..       5      76 ..       4      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                            DUF883  2 eleaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVrenP 73
                                      e+ + ++++ +++ee +k+a++e ++ + e++e+++e +++a +++++ ++++ e+ak  +e+ ++ +re+ 
  gi|488601674|ref|YP_007908145.1|  5 EILSKIKEVEQKVEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIREKR 76
                                      567899********************************************************9999999975 PP

>> FANCI_S2  FANCI solenoid 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.6   6.7e-05     0.054      26      93 ..      20      87 ..       3     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-05
                          FANCI_S2 26 saeasaaksktvaqaaaklgsqiLlelfkvhesarseiieqllsriitkseeevsqyiklLselvksa 93
                                       ++++++++++v+ +a++ +++i++++ k  e++++eiie+ + +i +++e+  ++ +k + + v + 
  gi|488601674|ref|YP_007908145.1| 20 DIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIREKRLKEINDVVSKG 87
                                      2333367789***********************************99999987777666666666555 PP

>> REF  Rubber elongation factor protein (REF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.8   0.00017      0.14      71     124 ..      13      66 ..       5      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                               REF  71 vDrKvdesvtkldkrvpsvvKevssqalavaqkapeaarevasevqraGvveaa 124
                                       v++Kv+e +++ +++  +v+ e+ ++a +++ +a ++a+++ +e+ ++  ve  
  gi|488601674|ref|YP_007908145.1|  13 VEQKVEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIE 66 
                                       778888888888888888888888888888888888888888888777666655 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  18.4   0.00029      0.24      52     121 ..       4      74 ..       1      97 [. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                                       CCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                            DivIVA  52 eeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeak.kiaeeieelkr 121
                                       +e l++ ke+e+++++ + +a+e   +v  +ak++a+ ii++Aek+aeki +e  e+ak +i++e e++++
  gi|488601674|ref|YP_007908145.1|   4 TEILSKIKEVEQKVEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKvEIEKEKESIRE 74 
                                       45566777777777777777777777777777777777777777777776654333332233333333333 PP

>> RapA_C  RNA polymerase recycling family C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   9.5   0.00039      0.32     256     328 ..      17      86 ..       2      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                                       TT-------STTSSTTSSS-SHHHHTTTTTTTTSSSHHHHHHHHHHHHHHHHHHHHHTHHHHTHHHH--S--S CS
                            RapA_C 256 lnkqlkkvkkklarklvkakrkeiekllkkaeklaeeqaeelieeakaraeqelsaEleRLeaLkavNpnird 328
                                       +++ +k+  ++  rk++  ++++ ++++++aek ae+ ++e+ie+ak ++e+  ++E  R ++Lk++N+ +++
  gi|488601674|ref|YP_007908145.1|  17 VEEDIKS-AEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEK--EKESIREKRLKEINDVVSK 86 
                                       3444444.455678899999999***********************999987..5888999999999998875 PP

>> PRESAN  Plasmodium RESA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  11.4     0.005       4.1      54     108 ..      45      99 ..       2     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.005
                                       HHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-SEEEHHHHHHHHH CS
                            PRESAN  54 kkynipeeykkklwkeckneitkelkklekeynknfynllkkkklsidefkefin 108
                                       +  +  e++k+++ +++k ei+ke +++ ++  k +++ + k+k  ide ++f++
  gi|488601674|ref|YP_007908145.1|  45 NAEKEAEKIKNEIIEKAKVEIEKEKESIREKRLKEINDVVSKGKSRIDEAVDFLY 99 
                                       4445578999999999999999999999999999999999999999999999997 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   5.6   0.00048      0.39       8      97 ..       9      98 ..       1     104 [. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00048
                                      EEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHH CS
                            Aldedh  8 tievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaea 86
                                      +i+ ++   +e i ++++ +++ + +a ++A+e  ++ +k   + + ei++ka   +e++ke + e   +e+   +++ 
  gi|488601674|ref|YP_007908145.1|  9 KIKEVEQKVEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIREKRLKEINDVVSKG 87
                                      566677777888889999999999999999999999999999999********************************** PP

                                      HHHHHHHHHHH CS
                            Aldedh 87 raeveeaidvl 97
                                      +  ++ea+d+l
  gi|488601674|ref|YP_007908145.1| 88 KSRIDEAVDFL 98
                                      *********97 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  13.0   0.00055      0.45      49     128 ..       2      81 ..       1     100 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00055
                           zf-C4H2  49 aHveeLrlIhaDinalEsvikeaeeekekslekakklyeey.kklkeevnelrselglekledleeeeeellkeeif 124
                                       +  e L +I++  +++E+ ik+aeeek+k + +ak++ +e+ ++  +e +++++e ++ek +   e+e+e ++e+++
  gi|488601674|ref|YP_007908145.1|   2 EKTEILSKIKEVEQKVEEDIKSAEEEKRKVILEAKEKAREIiSNAEKEAEKIKNE-IIEKAKVEIEKEKESIREKRL 77 
                                       56799999***9******************9999999887626667777777777.567777778888888999997 PP

                           zf-C4H2 125 ekqk 128
                                       ++ +
  gi|488601674|ref|YP_007908145.1|  78 KEIN 81 
                                       7754 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 ?    8.8   9.3    0.0016       1.3      24      97 ..      15      96 ..       3     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                           NACHT_N 24 kils......eeeekesskkeeeseekeeeseeekrqeqlkrlvekglkrvekkk..kakegiaeaaevvlavkdlide 94
                                      + ++      eee+++ + + +e++ +++++ e++ ++  ++++ek+   +ek+k    +++++e+ +vv + k+ ide
  gi|488601674|ref|YP_007908145.1| 15 QKVEediksaEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKesIREKRLKEINDVVSKGKSRIDE 93
                                      333333335445555555666666667777777777777789*******9999986456678999************** PP

                           NACHT_N 95 avk 97
                                      av 
  gi|488601674|ref|YP_007908145.1| 94 AVD 96
                                      *96 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  14.9    0.0014       1.1     505     592 ..      11      97 ..       1     103 [. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHH CS
                             HSP70 505 eeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeiea 581
                                       +e+e+ v++  +sa e++k+k   eak++a e++ ++ek+ e+ ++++ e++k ++e+++e+++e+  +e ++ +++
  gi|488601674|ref|YP_007908145.1|  11 KEVEQKVEEDIKSA-EEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIREKRLKEINDVVSK 86 
                                       55666565555555.556677788*****************************************998888888888 PP

                                       HHHHHHHHHHH CS
                             HSP70 582 kteelkkvvek 592
                                        +++++++v  
  gi|488601674|ref|YP_007908145.1|  87 GKSRIDEAVDF 97 
                                       88888887765 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  14.0    0.0032       2.6      17      77 ..       9      74 ..       2      86 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                            CENP-H 17 klsqelrelqeeltevekenlrlkrknrelaaell.elakekesek....eklkeelekleaelkk 77
                                      k+++  ++++e++ ++e+e +++  + +e+a+e+    +ke+e+ k    ek+k e+ek ++ +++
  gi|488601674|ref|YP_007908145.1|  9 KIKEVEQKVEEDIKSAEEEKRKVILEAKEKAREIIsNAEKEAEKIKneiiEKAKVEIEKEKESIRE 74
                                      4555567899************************51444444444455554455555554444444 PP

>> CENP-I  Mis6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.1    0.0064       5.2      28     105 ..      16      97 ..       2     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0064
                            CENP-I  28 kvdss.ksvleekss..eedsesaddqkkdseedslkkalryfekvqkkvslkknevlekhlktvenvalk.kGlap 100
                                       kv+++ ks++eek++  +e +e+a +   ++e+++ k+  + +ek++ ++ ++k+++ ek lk +++v  k k    
  gi|488601674|ref|YP_007908145.1|  16 KVEEDiKSAEEEKRKviLEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIREKRLKEINDVVSKgKSRID 92 
                                       333222455433332226788888888899999999999999*********************99998765234445 PP

                            CENP-I 101 eaidi 105
                                       ea+d 
  gi|488601674|ref|YP_007908145.1|  93 EAVDF 97 
                                       66665 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   9.6    0.0081       6.6       5      89 ..      15      98 ..       2     105 .. 0.43

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0081
                             TMPIT  5 eelekefkeleetakey.kqkleelsklqskcskeikkqkkrl.kelksslkklkksvkeeeeeeveelkeelkerkkv 81
                                      +++e+++k+ ee+++++  +  e+  + +s+  ke++k k+++ ++ k ++   +k++++ +e++++e+++ +++ k+ 
  gi|488601674|ref|YP_007908145.1| 15 QKVEEDIKSAEEEKRKViLEAKEKAREIISNAEKEAEKIKNEIiEKAKVEI---EKEKESIREKRLKEINDVVSKGKSR 90
                                      233444444444332220222333333333333333333333201222222...2223345566666666666666666 PP

                             TMPIT 82 lkevesll 89
                                      ++e  ++l
  gi|488601674|ref|YP_007908145.1| 91 IDEAVDFL 98
                                      66665555 PP

>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.2    0.0058       4.7     131     186 ..      11      66 ..       1      72 [. 0.76
   2 ?    1.5   0.2      0.29   2.3e+02     141     177 ..      62      98 ..      59     103 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0058
                                       ----SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEE-HH CS
                     Peptidase_M41 131 kkekelseetaeeideevkelveeayerakeileekreelealaeaLlekEtldae 186
                                       k+ ++  ee  +  +ee ++++ ea e+a+ei+++ ++e e++ ++++ek  ++ e
  gi|488601674|ref|YP_007908145.1|  11 KEVEQKVEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIE 66 
                                       333333344445568999*******************************9887755 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHH CS
                     Peptidase_M41 141 aeeideevkelveeayerakeileekreelealaeaL 177
                                       + ei++e +++ e++ ++ ++++++ + ++++ ++ L
  gi|488601674|ref|YP_007908145.1|  62 KVEIEKEKESIREKRLKEINDVVSKGKSRIDEAVDFL 98 
                                       5567777777777777777777777777777666554 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   9.8    0.0096       7.8      21      90 ..       3      72 ..       1      95 [. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0096
                                      GGG-TTTT--.HHHHHHHHHHHHHHHHT-SEEEEEEEHHHHHTT-CCG-EE.E-S-................EE- CS
                   PTPlike_phytase 21 kedllenlkeytgisaeeleklearlkeevlaeakksegrvlvhdeteegk.dvktlqevweeve....tpeevy 90
                                      k + l+++ke++++ +e++++ e++ k+ v+ eak+++ +++++ e+e +k + +   e+ e+++    +++e +
  gi|488601674|ref|YP_007908145.1|  3 KTEILSKIKEVEQKVEEDIKSAEEE-KRKVILEAKEKAREIISNAEKEAEKiK-N---EIIEKAKveieKEKESI 72
                                      667778899999999********99.999999***********9999999732.2...33333332232333333 PP

>> Clathrin_lg_ch  Clathrin light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  15.8      0.01       8.5     103     171 ..      16      84 ..       1     101 [. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.01
                    Clathrin_lg_ch 103 eesssaeeeeeeepesirkWReerkkeieerdeasekkkeetkekAkkeiddfyenynekkektkaqnr 171
                                       + +++ +++eee+ ++i + +e+ ++ i++ ++++ek k+e++ekAk ei++  e+  ek+ k+++++ 
  gi|488601674|ref|YP_007908145.1|  16 KVEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNEIIEKAKVEIEKEKESIREKRLKEINDVV 84 
                                       222266778899999************************************999999999999888765 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  16.4     0.011         9      52     141 ..       3      95 ..       1      96 [. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                          ISG65-75  52 adyllketkdklayienakekvdyyvekle.slleeakekgtltesdaekl.kkaceeAkaknkkareka.kkalek 125
                                       ++++l+++k+ ++ +e+++++ ++++ k+  + +e+a+e  +  e++aek+ ++++e+Ak +++k++e   +k l++
  gi|488601674|ref|YP_007908145.1|   3 KTEILSKIKEVEQKVEEDIKSAEEEKRKVIlEAKEKAREIISNAEKEAEKIkNEIIEKAKVEIEKEKESIrEKRLKE 79 
                                       678999****************998888732666667776777788888885678999**99998887762667899 PP

                          ISG65-75 126 aekaskkakeaakkAl 141
                                       ++++++k k+   +A+
  gi|488601674|ref|YP_007908145.1|  80 INDVVSKGKSRIDEAV 95 
                                       *****99999888875 PP

>> PRKCSH-like  Glucosidase II beta subunit-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.5    0.0021       1.7     121     172 ..       5      56 ..       2      64 .. 0.89
   2 ?    1.0   2.6      0.41   3.3e+02     135     171 ..      51      86 ..      44      95 .. 0.42

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                       PRKCSH-like 121 eiarkfeelleeankkvkkglkikeelllaakkkldelkkklkeledslkak 172
                                       ei  k++e+++++++++k++ + k++++l+ak+k +e++ + ++  +++k++
  gi|488601674|ref|YP_007908145.1|   5 EILSKIKEVEQKVEEDIKSAEEEKRKVILEAKEKAREIISNAEKEAEKIKNE 56 
                                       77889999*******************************9999999888876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.41
                       PRKCSH-like 135 kkvkkglkikeelllaakkkldel.kkklkeledslka 171
                                       +k+k+ +  k ++  + +k ++ + +k+lke++d + +
  gi|488601674|ref|YP_007908145.1|  51 EKIKNEIIEKAKV--EIEKEKESIrEKRLKEINDVVSK 86 
                                       3333333333222..22223333313455555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3448  (0.192314); expected 358.6 (0.02)
Passed bias filter:                      884  (0.0493056); expected 358.6 (0.02)
Passed Vit filter:                       154  (0.00858944); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.73u 0.39s 00:00:01.12 Elapsed: 00:00:00.60
# Mc/sec: 534.60
//
Query:       gi|488601675|ref|YP_007908146.1|  [L=356]
Description: Molybdopterin biosynthesis enzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-21   75.7   0.0    4.3e-21   75.1   0.0    1.2  1  MoCF_biosynth  Probable molybdopterin binding domain
    1.4e-18   67.1   0.0    2.3e-18   66.4   0.0    1.4  1  MoeA_N         MoeA N-terminal region (domain I and II)


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 !   75.1   0.0   4.8e-25   4.3e-21       1     138 [.     151     271 ..     151     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 4.8e-25
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpea 77 
                                       avi +Gdel +  i  tng +++ell+  g+ev++ + ++Dd + i+e++++  ++ d+i+t+GGt+++++D+++++
  gi|488601675|ref|YP_007908146.1| 151 AVIPTGDELNKI-IIETNGLMISELLSGWGCEVERFEPLKDDFNLISEEIESL-DH-DLIVTSGGTSIGRRDIVRKV 224
                                       799*****9887.9************************************555.77.******************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHH CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeil 138
                                       +++ +e       ++f + + kpg+   ++ + +++     +i++L G ++a+  +l +++
  gi|488601675|ref|YP_007908146.1| 225 VERKGE-------IIFSKSKIKPGR---TTIFGMIQT----PIFCLAGMQSACLSGLLFYV 271
                                       ******.......9***********...666656663....6***********99988777 PP

>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   2.6e-22   2.3e-18       2     157 .]       3     138 ..       2     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 2.6e-22
                                       -HHHHHHHHHHH-.HH-EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...........-S- CS
                            MoeA_N   2 sveealaiilaal.eleeeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeepsaageeper 77 
                                       s++eal+ i++ +  + +e+vp+ ++++grv+ ed++A  d+Pp+d S  DGYA++  +  +              +
  gi|488601675|ref|YP_007908146.1|   3 SYNEALSSIKRFVpDIGKEKVPV-EDSVGRVVYEDIRAIADYPPHDISLFDGYALKNYELGKI-------------E 65 
                                       899*********97777777***.99*****************************65544444.............5 PP

                                       --TT-EEEE-TTSB--TT--EEEEGGGE...E.......EETTES--STTTTEE-TTSSB-TTSEEE-TTBB--CCC CS
                            MoeA_N  78 llpggavrimTGaplPegadaVvpvEdte..eee...aketvevkavkpgenvrraGedikaGevllragtrltpae 149
                                       +  ++  +++TG+ + ++   Vv+vEd+e  + +   a +    ++ +      ++Ge++++ ev+l++gt++t  +
  gi|488601675|ref|YP_007908146.1|  66 SGIKNYRWVNTGDIVEDE--VVVKVEDAEitS-DgliA-H----SVFQ----PAKKGEEYRKEEVILKKGTKITLNH 130
                                       55566999*******866..8******96522.12221.1....3333....479********************** PP

                                       HHHHHHCT CS
                            MoeA_N 150 igllasvG 157
                                       + ++  +G
  gi|488601675|ref|YP_007908146.1| 131 VIAMKNCG 138
                                       *9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1900.17
//
Query:       gi|488601676|ref|YP_007908147.1|  [L=88]
Description: MoaD family protein, archaeal [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-20   74.0   0.1    1.3e-20   73.8   0.1    1.0  1  ThiS      ThiS family
     0.0076   16.6   0.0     0.0086   16.4   0.0    1.0  1  Urm1      Urm1 (Ubiquitin related modifier)
  ------ inclusion threshold ------
      0.013   15.8   0.1      0.031   14.6   0.1    1.7  1  Desmo_N   Viral Desmoplakin N-terminus
      0.094   12.8   0.0       0.14   12.3   0.0    1.3  1  TGS       TGS domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.1   2.9e-24   1.3e-20       1      77 []       4      88 .]       4      88 .] 0.98

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 2.9e-24
                                      EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEE CS
                              ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypela........lerrvavavNgeivpr.lwldtelkdgDevai 70
                                      v+lfa+ re+a+ +++++ e++t++ell+ L +++++l+        l++ v ++vNg+++++ ++ dtelk+ D+vai
  gi|488601676|ref|YP_007908147.1|  4 VKLFANFREAAN-TKEVEVEAKTIKELLQTLTTKFEKLKpliyegdrLRDYVHIMVNGRHIRSlNGIDTELKEEDVVAI 81
                                      89*********8.9999999***************************99**************88************** PP

                                      EESTTC- CS
                              ThiS 71 lppVaGG 77
                                      +ppV+GG
  gi|488601676|ref|YP_007908147.1| 82 FPPVSGG 88
                                      ******9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.9e-06    0.0086      20      96 .]      13      88 .]       4      88 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                                      EEEEE-SSSSS-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                              Urm1 20 hkveleieseevnleeliayikknlikerkevFlekdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                       + + e+e e  +++el++ +++++  + k +  e+d++r  + +++n   +  l+  d+elk++D++     + GG
  gi|488601676|ref|YP_007908147.1| 13 AANTKEVEVEAKTIKELLQTLTTKFE-KLKPLIYEGDRLRDYVHIMVNGRHIRSLNGIDTELKEEDVVAIFPPVSGG 88
                                      44444556678899******999875.57788899********************************9987777666 PP

>> Desmo_N  Viral Desmoplakin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   6.9e-06     0.031       3      44 ..      17      58 ..      15      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.9e-06
                           Desmo_N  3 kGvdvttrtvndllktintssakiktledyeeklreihkvvl 44
                                      k v+v+++t+++ll+t+ t   k+k l    ++lr+  ++++
  gi|488601676|ref|YP_007908147.1| 17 KEVEVEAKTIKELLQTLTTKFEKLKPLIYEGDRLRDYVHIMV 58
                                      6799**********************9877799999855544 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     3e-05      0.14      39      59 ..      58      82 ..      50      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                      ECS....EEEETTSBB-SSEEEEEE CS
                               TGS 39 VnG....qrvgldhvLedgdvveIv 59
                                      VnG     + g+d++L+++dvv I+
  gi|488601676|ref|YP_007908147.1| 58 VNGrhirSLNGIDTELKEEDVVAIF 82
                                      8888888899************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      836  (0.0466284); 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: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 546.93
//
Query:       gi|488601677|ref|YP_007908148.1|  [L=347]
Description: hypothetical protein Asulf_02202 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0012   18.7   0.4     0.0083   16.0   0.1    2.1  2  CdhC           CO dehydrogenase/acetyl-CoA synthase complex b
  ------ inclusion threshold ------
      0.022   15.2   0.3      0.042   14.3   0.3    1.5  1  Baculo_LEF-11  Baculovirus LEF-11 protein


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 ?    0.6   0.0     0.052   4.7e+02       4      34 ..      21      54 ..      19      63 .. 0.63
   2 !   16.0   0.1   9.2e-07    0.0083      76     154 ..      70     141 ..      49     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.052
                              CdhC  4 evspafeGeriRkedly.velgg..kktkafElv 34
                                      e s a++Ger++  ++   el +   k++++El+
  gi|488601677|ref|YP_007908148.1| 21 EHSLAYQGERVKGVEIRgFELVTtnPKRDGIELL 54
                                      6789999**9998777434544433445566665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.2e-07
                              CdhC  76 leedlEpvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGlrlkhigevlyaklkeefeaivdkvevtlitde 152
                                         e+  + lE  i e++n ++Gv  l+ ++++ +R+ k  +  G +++ i++++y  +    ++ivd+vev li d+
  gi|488601677|ref|YP_007908148.1|  70 CSEESASALEALIGEVVNRLKGVEYLNRKENVVLRVEKLNT--G-TFECIAQIIYFSF----KKIVDRVEVILILDR 139
                                       4566778899999***********************99655..5.5999999999875....5799********998 PP

                              CdhC 153 ek 154
                                       ++
  gi|488601677|ref|YP_007908148.1| 140 DE 141
                                       75 PP

>> Baculo_LEF-11  Baculovirus LEF-11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   4.7e-06     0.042       5      54 ..      76     130 ..      74     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-06
                     Baculo_LEF-11   5 seiialvrevintlkst...ndtedvta..hhldtdsFetirefirehadvivrk 54 
                                       s + al+ ev+n lk     n  e+v++  ++l+t  Fe+i + i    ++iv++
  gi|488601677|ref|YP_007908148.1|  76 SALEALIGEVVNRLKGVeylNRKENVVLrvEKLNTGTFECIAQIIYFSFKKIVDR 130
                                       7789***********7522256677765227899999********9999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1959.06
//
Query:       gi|488601678|ref|YP_007908149.1|  [L=273]
Description: ATPases involved in chromosome partitioning [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-101  337.1   0.0   6.4e-101  336.9   0.0    1.0  1  ParA          NUBPL iron-transfer P-loop NTPase
      8e-17   61.5   0.0    8.2e-16   58.2   0.0    2.2  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      1e-13   51.6   2.1    5.6e-12   45.9   2.1    2.2  1  AAA_31        AAA domain
    1.7e-08   34.1   1.4    1.3e-07   31.2   0.9    2.1  2  ArsA_ATPase   Anion-transporting ATPase
    7.8e-08   31.9   0.2    1.7e-07   30.8   0.2    1.7  1  MipZ          ATPase MipZ
    8.3e-07   28.7   0.1    2.8e-05   23.7   0.3    2.2  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    1.2e-05   25.3   0.9      0.073   12.9   0.3    2.2  2  AAA_26        AAA domain
    0.00011   22.1   0.1    0.00017   21.5   0.1    1.3  1  APS_kinase    Adenylylsulphate kinase
     0.0003   20.7   0.0    0.00048   20.0   0.0    1.3  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
    0.00037   19.6   0.1      0.001   18.1   0.2    1.7  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
    0.00045   19.9   0.1    0.00082   19.1   0.1    1.4  1  SRP54         SRP54-type protein, GTPase domain
     0.0036   17.2   2.1      0.018   14.9   0.5    2.1  2  RsgA_GTPase   RsgA GTPase
     0.0037   17.2   0.2     0.0071   16.3   0.2    1.5  1  DUF1610       Domain of unknown function (DUF1610)
     0.0043   16.7   0.1     0.0073   15.9   0.1    1.3  1  AAA_25        AAA domain
     0.0079   16.1   0.2      0.015   15.2   0.2    1.4  1  NTPase_1      NTPase
     0.0087   15.4   0.0      0.015   14.6   0.0    1.3  1  VirC1         VirC1 protein
  ------ inclusion threshold ------
      0.016   14.4   0.7      0.022   14.0   0.7    1.2  1  NB-ARC        NB-ARC domain
      0.016   14.7   0.1      0.023   14.1   0.1    1.2  1  KTI12         Chromatin associated protein KTI12
      0.024   14.1   0.2       0.17   11.3   0.1    1.9  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
      0.031   14.8   0.0      0.056   14.0   0.0    1.4  1  AAA_18        AAA domain
      0.031   14.0   0.2      0.059   13.1   0.2    1.4  1  IstB_IS21     IstB-like ATP binding protein
      0.037   13.9   0.1      0.068   13.1   0.1    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.051   13.0   0.4      0.084   12.3   0.4    1.2  1  PhoH          PhoH-like protein
      0.088   13.0   0.2       0.16   12.1   0.2    1.4  1  AAA_33        AAA domain
      0.093   12.0   0.2       0.15   11.3   0.2    1.2  1  Zeta_toxin    Zeta toxin
       0.11   12.9   0.1       0.19   12.1   0.1    1.3  1  AAA_16        AAA ATPase domain
       0.13   12.7   0.1       0.21   12.0   0.1    1.3  1  RNA_helicase  RNA helicase
       0.15   12.2   0.5       0.27   11.4   0.5    1.3  1  Zn-ribbon_8   Zinc ribbon domain
       0.17   11.4   0.1        0.3   10.6   0.1    1.3  1  AAA_7         P-loop containing dynein motor region
       0.18   11.1   0.2        1.1    8.5   0.0    1.9  2  DnaB_C        DnaB-like helicase C terminal domain
       0.27   10.8   1.2       0.48   10.0   1.2    1.4  1  TF_Zn_Ribbon  TFIIB zinc-binding
        0.3   10.8   0.5       0.53   10.0   0.5    1.3  1  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.9   0.0  1.1e-103  6.4e-101       2     245 ..      10     255 ..       9     256 .. 0.99

  Alignments for each domain:
  == domain 1  score: 336.9 bits;  conditional E-value: 1.1e-103
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmS 77 
                                       +k++i+v+SgKGGVGKStvavnlA++L++kg+kvgllD Di+Gps+p++lgve+++  + ++++ Pv    ++kv+S
  gi|488601678|ref|YP_007908149.1|  10 IKHKIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIHGPSVPKMLGVEGARFPVFDETIEPVIIpPSLKVVS 86 
                                       89*****************************************************9999999******999****** PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladv 153
                                       i+fll+++d++v+wrGpmk ++ kq+l++v+wg+lDyLiiDlPPGtgDe+l +a+ + +++gaviV+tpq+val  v
  gi|488601678|ref|YP_007908149.1|  87 IAFLLPESDTPVIWRGPMKFSITKQFLEKVDWGDLDYLIIDLPPGTGDEALNIAHLIaSIDGAVIVSTPQDVALLSV 163
                                       ********************************************************9999***************** PP

                              ParA 154 kkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkep 230
                                       +k+i+++kk++++v+G++eNmsgf+cp+cg++ ++fgkg++e++++e+++++lg ip+dp+++e++d g+p+v+k p
  gi|488601678|ref|YP_007908149.1| 164 RKSINFAKKLNIPVIGLIENMSGFACPNCGKEFNVFGKGNVERVCKEMDLRFLGYIPIDPAVAESGDYGEPFVVKYP 240
                                       ***************************************************************************** PP

                              ParA 231 eseaakaleeiaekv 245
                                       es+ +ka++ i++kv
  gi|488601678|ref|YP_007908149.1| 241 ESASSKAFDGIVDKV 255
                                       ************998 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   1.5e-18   8.2e-16       1     127 [.      14     234 ..      14     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.5e-18
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+++s+kGGvGK+t+a+nLa+ l+++g++V l+D+D  +++     g+e+ + p                       
  gi|488601678|ref|YP_007908149.1|  14 IVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIHGPSVPKMLGVEGARFPvfdetiepviippslkvvsiafl 90 
                                       799**************************************99888888888889********************** PP

                                       .......................................................................CCHCCC CS
                                       .......................................................................xxxxxx RF
                              CbiA  55 .......................................................................dlkrll 60 
                                                                                                              ++ + +
  gi|488601678|ref|YP_007908149.1|  91 lpesdtpviwrgpmkfsitkqflekvdwgdldyliidlppgtgdealniahliasidgavivstpqdvallSVRKSI 167
                                       **************************************************************999977666555555 PP

                                       HHHHHHCHCHHHH...EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  61 ellealgkkkall.lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                       +++++l +++  l  ++ g+     ++e  +   k ++e++++++ +++lg ip d avae+   gep
  gi|488601678|ref|YP_007908149.1| 168 NFAKKLNIPVIGLiENMSGFACPNCGKE-FNVFGKGNVERVCKEMDLRFLGYIPIDPAVAESGDYGEP 234
                                       5566666553222444444444444444.2334456799999999*****************999988 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   2.1   9.9e-15   5.6e-12       3     167 ..      13     173 ..      11     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 9.9e-15
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyevlieeknikeaiiktkv 78 
                                        I+++  KGGvGK+T +vnlaa l+++g+kv l D+D  + +    lg+e        + v   +++i+ +ii    
  gi|488601678|ref|YP_007908149.1|  13 KIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIHGPSVPkMLGVE-----GARFPV--FDETIEPVII---P 79 
                                       689999********************************997765144432.....222333..3567888999...5 PP

                            AAA_31  79 enldlipssidLaeaeielvelekkeeil.kellekvk.deYDyiiiDcpPsLg..lltenaLvas.dsviipvqae 150
                                        +l+++     L e ++ ++     +  + k++lekv+  + Dy iiD pP  g   l++  L+as d  +i+  ++
  gi|488601678|ref|YP_007908149.1|  80 PSLKVVSIAFLLPESDTPVIWRGPMKFSItKQFLEKVDwGDLDYLIIDLPPGTGdeALNIAHLIASiDGAVIVSTPQ 156
                                       66888888888999999888777776665599*****9457**********997335666678888799******** PP

                            AAA_31 151 ayaleGleqllktieev 167
                                       + al  +++ +++ +++
  gi|488601678|ref|YP_007908149.1| 157 DVALLSVRKSINFAKKL 173
                                       *******9999998876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.9   2.3e-10   1.3e-07       1      38 [.      12      49 ..      12      52 .. 0.92
   2 ?    1.0   0.0      0.34   1.9e+02     114     137 ..     110     134 ..     105     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.3e-10
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +k+++++GKGGVGK+tv+  +a+kls+kg+kv l+  D
  gi|488601678|ref|YP_007908149.1| 12 HKIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCD 49
                                      589****************************9887665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.34
                                       HHHHHHHHCSSSSEEEEESBS.CCH CS
                       ArsA_ATPase 114 eellkyvkeeeydvvvlDtaP.TGh 137
                                       +++l+ v+  + d++++D +P TG+
  gi|488601678|ref|YP_007908149.1| 110 KQFLEKVDWGDLDYLIIDLPPgTGD 134
                                       577888899999******9996663 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.2     3e-10   1.7e-07       1      48 [.      12      59 ..      12     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3e-10
                                      EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH CS
                              MipZ  1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl 48
                                      h iv+   kGG Gkst+av +a  L++kG +v+ +d d+   ++ + l
  gi|488601678|ref|YP_007908149.1| 12 HKIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIHGPSVPKML 59
                                      789***********************************9887776665 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 !   23.7   0.3     5e-08   2.8e-05       2      42 ..      14      54 ..      13      66 .. 0.87
   2 ?    2.6   0.0      0.13        75     190     249 ..     201     260 ..     148     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5e-08
                         Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDs 42
                                       + + GkGG+Gkst + nl+a l+++g kv ++ CD    s
  gi|488601678|ref|YP_007908149.1| 14 IVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIHGPS 54
                                      57789*******************************76655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                         Fer4_NifH 190 reliekfaeelgtkvlevvPrdeivrkae.lrkktvieyapeseqakeyrelarkilenkk 249
                                       ++ +e+  +e++++ l  +P d  v ++    +  v++y +++  +k +  + +k+le  +
  gi|488601678|ref|YP_007908149.1| 201 KGNVERVCKEMDLRFLGYIPIDPAVAESGdYGEPFVVKYPESA-SSKAFDGIVDKVLEFVE 260
                                       56688899999999********999887515555666665555.59999999999988655 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.3   0.00013     0.073       2      33 ..      13      44 ..      12      47 .. 0.93
   2 !   10.9   0.0   0.00053       0.3     132     194 ..     150     225 ..     131     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                            AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                      +i+v +   gvGK++v+  L+++l++kg+kvg
  gi|488601678|ref|YP_007908149.1| 13 KIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVG 44
                                      79999999***********************8 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00053
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk..vrnpe...........nvetlekksgipvlGvvPylpdl 194
                                       ++V ++++ ++  +  +i+++++ n++v+G+i N   ++ p+           nve ++k   ++ lG +P +p +
  gi|488601678|ref|YP_007908149.1| 150 VIVSTPQDVALLSVRKSINFAKKLNIPVIGLIENMsgFACPNcgkefnvfgkgNVERVCKEMDLRFLGYIPIDPAV 225
                                       66788888888888899***************997443333244557777778******************99876 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   3.1e-07   0.00017       3      40 ..      13      50 ..      11      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.1e-07
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                       +v ++G  g GKst+a++l+ kL +kg++v lLd d 
  gi|488601678|ref|YP_007908149.1| 13 KIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDI 50
                                      57999******************************985 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 !   20.0   0.0   8.5e-07   0.00048       1      35 [.      19      53 ..      19      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.5e-07
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqs 35
                                      G+  +GKST+a +L+ ++ +kg+k+ ++D+D+  +
  gi|488601678|ref|YP_007908149.1| 19 GKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIHGP 53
                                      66789**************************9655 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 !   18.1   0.2   1.8e-06     0.001      29      66 ..      12      49 ..       1      61 [. 0.83
   2 ?   -2.3   0.0         3   1.7e+03     214     237 ..     244     267 ..     230     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                                      SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                       + v + G  G+Gkst+  +l+++l ++G++v++l  D
  gi|488601678|ref|YP_007908149.1| 12 HKIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCD 49
                                      4567789***************************9988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                                       CTBSHHHHHHHHHHHHHHHHHTTH CS
                              MeaB 214 egeGidelvdaieehrevlkktGl 237
                                         +  d +vd++ e+ e+++++ +
  gi|488601678|ref|YP_007908149.1| 244 SSKAFDGIVDKVLEFVEAVNESNE 267
                                       456788999999999999988755 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.5e-06   0.00082       2      40 ..      13      51 ..      12      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                      +++++ G  G+GK t +  Laa+l+++g+kv l  +D+ 
  gi|488601678|ref|YP_007908149.1| 13 KIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIH 51
                                      6899******************************99985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.5   3.2e-05     0.018      97     126 ..      10      39 ..       2      44 .. 0.84
   2 ?    1.5   0.0      0.44   2.5e+02      13      50 ..     143     178 ..     124     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-05
                                       CTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpelelk 126
                                       +k+k++v+ G+ GvGKSt+  +l+ +l++k
  gi|488601678|ref|YP_007908149.1|  10 IKHKIVVMSGKGGVGKSTVAVNLAAKLSQK 39 
                                       788****************99999887776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.44
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEE CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepv 50 
                                       +a +d ++iv++ +  ++ l  + + + +a++ +i+++
  gi|488601678|ref|YP_007908149.1| 143 IASIDGAVIVSTPQ--DVALLSVRKSINFAKKLNIPVI 178
                                       899****9998887..8999999999999999999876 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.3e-05    0.0071      12      24 .]     182     194 ..     178     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                           DUF1610  12 EravvFpCPNCGE 24 
                                       E+ + F+CPNCG+
  gi|488601678|ref|YP_007908149.1| 182 ENMSGFACPNCGK 194
                                       55688*******8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.3e-05    0.0073      32      59 ..      11      38 ..       6      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                            AAA_25 32 agelallaGapgtGKttlaldlalavat 59
                                      ++++++  G +g+GK+t+a++la+++++
  gi|488601678|ref|YP_007908149.1| 11 KHKIVVMSGKGGVGKSTVAVNLAAKLSQ 38
                                      688999******************9884 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   2.7e-05     0.015       2      31 ..      15      44 ..      14      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                      v+++G+ GvGK+T+  +++ +l+++g+kvg
  gi|488601678|ref|YP_007908149.1| 15 VVMSGKGGVGKSTVAVNLAAKLSQKGYKVG 44
                                      6889************************96 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.7e-05     0.015       4      40 ..      14      50 ..      12      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeade 40
                                      i + s kGG Gk+t  + l + l ++g +v+l+++d 
  gi|488601678|ref|YP_007908149.1| 14 IVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDI 50
                                      667899****************************996 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.7   3.9e-05     0.022      11      46 ..       4      38 ..       1      43 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
                                      HHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC 11 kLlekdelqslvvalvGmgGvGKttlakqilnksde 46
                                      kL   ++++  +v ++G+gGvGK+t+a +   k+++
  gi|488601678|ref|YP_007908149.1|  4 KLE-LKGIKHKIVVMSGKGGVGKSTVAVNLAAKLSQ 38
                                      555.6788889****************999888665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.2e-05     0.023       3      37 ..      14      48 ..      13      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                                      EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-T CS
                             KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvvidd 37
                                      +vv++G   +GKst+a +La +l++++++v ++d 
  gi|488601678|ref|YP_007908149.1| 14 IVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDC 48
                                      599**************************988875 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00031      0.17       3      38 ..      14      48 ..      12      52 .. 0.88
   2 ?    0.4   0.0      0.66   3.7e+02     107     147 ..     111     155 ..     104     170 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesvlviDl 38
                                      +++++G +GGvG++++++ La  l + g++v ++D 
  gi|488601678|ref|YP_007908149.1| 14 IVVMSG-KGGVGKSTVAVNLAAKLSQKGYKVGLLDC 48
                                      556666.8***********************99985 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.66
                          CBP_BcsQ 107 aalkelk.eqyrwillDlpagasaltre...llaladlvllvvep 147
                                       ++l+++  ++ +++++Dlp g+ + + +   l+a  d  + v +p
  gi|488601678|ref|YP_007908149.1| 111 QFLEKVDwGDLDYLIIDLPPGTGDEALNiahLIASIDGAVIVSTP 155
                                       667777778899*******98776554400144445555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0    0.0001     0.056       2      22 ..      16      36 ..      15      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                            AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                      + +G+ GvGK+t+a +L+ +l
  gi|488601678|ref|YP_007908149.1| 16 VMSGKGGVGKSTVAVNLAAKL 36
                                      668999***********9997 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   0.00011     0.059      46      78 ..      11      43 ..       9      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                         IstB_IS21 46 kkenivllGpsGvGKshlaialgveavraglsv 78
                                      k++ +v+ G  GvGKs +a+ l+ +  ++g++v
  gi|488601678|ref|YP_007908149.1| 11 KHKIVVMSGKGGVGKSTVAVNLAAKLSQKGYKV 43
                                      5778999************************99 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00012     0.068       1      39 [.      14      52 ..      14      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                              MobB  1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhg 39
                                      ++ + gk g GK t   +l ++l+++g++vg++  + hg
  gi|488601678|ref|YP_007908149.1| 14 IVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIHG 52
                                      5678899*************************9888887 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00015     0.084      18      46 ..      11      39 ..       2      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                      H-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 18 kndivfaiGpaGtGKtylavalavealkk 46
                                      k++iv++ G+ G GK+ +av la+++ +k
  gi|488601678|ref|YP_007908149.1| 11 KHKIVVMSGKGGVGKSTVAVNLAAKLSQK 39
                                      899*********************98876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00029      0.16       1      24 [.      14      37 ..      14      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00029
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg 24
                                      +v++ G  G+GKst+a +l++kl 
  gi|488601678|ref|YP_007908149.1| 14 IVVMSGKGGVGKSTVAVNLAAKLS 37
                                      599****************99986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00027      0.15      14      44 ..      10      40 ..       2      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                        Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqg 44
                                       + k+++++G  G GKs++a  l+++l ++g
  gi|488601678|ref|YP_007908149.1| 10 IKHKIVVMSGKGGVGKSTVAVNLAAKLSQKG 40
                                      56799******************99997544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00033      0.19      25      63 ..      13      51 ..       6      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00033
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                       +v+ sG  GvGKs+++  l+  l+++g  +   +cd +
  gi|488601678|ref|YP_007908149.1| 13 KIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVGLLDCDIH 51
                                      68999************9999999999766666666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00038      0.21       1      25 [.      15      39 ..      15      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00038
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      ++++G+ g+GKSt+a +La++l++k
  gi|488601678|ref|YP_007908149.1| 15 VVMSGKGGVGKSTVAVNLAAKLSQK 39
                                      6899*****************9976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00048      0.27       6      29 ..     187     208 ..     186     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00048
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaC 29 
                                       + C +Cg+ef+v+ + +   + +C
  gi|488601678|ref|YP_007908149.1| 187 FACPNCGKEFNVFGKGN--VERVC 208
                                       78**********99866..23346 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00053       0.3      32      65 ..      11      44 ..       5      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00053
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsl 65
                                      ++k v++ G+ G+GK++++ +l  kl+++ y++ 
  gi|488601678|ref|YP_007908149.1| 11 KHKIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVG 44
                                      4677999********************9999875 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 ?    8.5   0.0     0.002       1.1      19      52 ..      12      44 ..       6      59 .. 0.79
   2 ?    0.1   0.0      0.74   4.1e+02     160     176 ..     165     181 ..     142     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                                      TXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 19 gdliiiAarpsmGktalalniaenaavkeklpva 52
                                       +++++ ++ ++Gk+++a+n+a++  + +  +v 
  gi|488601678|ref|YP_007908149.1| 12 HKIVVMSGKGGVGKSTVAVNLAAKLSQ-KGYKVG 44
                                      4589******************99886.344555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.74
                                       HHHHHHHHCTSXEEEEE CS
                                       xxxxxxxxxxxxxxxxx RF
                            DnaB_C 160 sLkalakelnvpvials 176
                                       +  ++ak ln+pvi l 
  gi|488601678|ref|YP_007908149.1| 165 KSINFAKKLNIPVIGLI 181
                                       44578*********875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.2   0.00086      0.48       1      24 [.     187     210 ..     187     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00086
                                       EEETTTTCEECHEETSTTCEEESS CS
                      TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtd 24 
                                       + CPnCg ++ v+   + e vC++
  gi|488601678|ref|YP_007908149.1| 187 FACPNCGKEFNVFGKGNVERVCKE 210
                                       57******9999999999999985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00095      0.53      18      50 ..      12      44 ..       6      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00095
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                      ++++v+ G  G GK+t+   l++ + ++g++v 
  gi|488601678|ref|YP_007908149.1| 12 HKIVVMSGKGGVGKSTVAVNLAAKLSQKGYKVG 44
                                      6799**************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                       163  (0.00909142); 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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 1604.21
//
Query:       gi|488601679|ref|YP_007908150.1|  [L=129]
Description: putative DNA-binding protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-23   81.3   0.2    7.1e-23   81.0   0.2    1.1  1  DUF134        Protein of unknown function  DUF134
      6e-07   29.0   0.1    9.5e-07   28.4   0.1    1.3  1  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.021   14.6   0.1    1.4  1  HTH_23        Homeodomain-like domain
      0.013   15.0   0.2      0.021   14.3   0.2    1.3  1  Sigma70_r4    Sigma-70, region 4
      0.014   15.3   0.7      0.014   15.3   0.7    1.6  2  Prok-RING_1   Prokaryotic RING finger family 1
       0.02   14.8   0.1      0.024   14.5   0.1    1.1  1  Sigma70_ECF   ECF sigma factor
      0.053   13.3   0.2       0.13   12.1   0.0    1.7  2  HTH_10        HTH DNA binding domain
      0.099   11.8   0.0       0.12   11.6   0.0    1.1  1  FANCF         Fanconi anemia group F protein (FANCF)


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 !   81.0   0.2   3.2e-26   7.1e-23       5      96 ..       2      97 ..       1      99 [. 0.91

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 3.2e-26
                            DUF134  5 grprklrdileePkvrifkPea.veetg...kvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkia 79
                                      gr +  r+i  + kv+ f+P+  ++  +   k+ ++ +e+ea+rlvd   +++eea+ +mG+s++++wr l+ ar+k+ 
  gi|488601679|ref|YP_007908150.1|  2 GRRKSARRICYKTKVKGFIPKFeDSRPElgdKILLTHEEIEALRLVDLLGMTHEEASIVMGVSRKAFWRDLKRARRKLV 80
                                      79999***************964443334469*********************************************** PP

                            DUF134 80 kalveGraiilkGGeyk 96
                                       alveG+ai ++ Gey 
  gi|488601679|ref|YP_007908150.1| 81 TALVEGKAIEIEEGEYV 97
                                      ***************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   4.3e-10   9.5e-07      17      54 .]      42      79 ..      36      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.3e-10
                                      HHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2 17 eifllryleglsykEIAellgisegtVksrlsRArkkL 54
                                      e++ l +l g++++E++ ++g+s ++  + l+RAr+kL
  gi|488601679|ref|YP_007908150.1| 42 EALRLVDLLGMTHEEASIVMGVSRKAFWRDLKRARRKL 79
                                      7999*********************************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.4e-06     0.021       8      41 ..      41      75 ..      38      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                            HTH_23  8 lrillllae.GlsvreIAreLgvsrrTvyrwlkry 41
                                      +++l+l++  G++ +e++  +gvsr   +r lkr 
  gi|488601679|ref|YP_007908150.1| 41 IEALRLVDLlGMTHEEASIVMGVSRKAFWRDLKRA 75
                                      6899999999*****************99977765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   9.5e-06     0.021       5      48 ..      36      79 ..      35      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.5e-06
                                      S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48
                                      L+ +e e l+l+ + g+T+eE + ++g+Sr +  + +krA+rkL
  gi|488601679|ref|YP_007908150.1| 36 LTHEEIEALRLVDLLGMTHEEASIVMGVSRKAFWRDLKRARRKL 79
                                      78899999**********************99888888888887 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       3.5   7.8e+03      32      37 ..       9      14 ..       7      17 .. 0.73
   2 ?   15.3   0.7   6.1e-06     0.014       6      30 ..     105     127 ..     101     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.5
                       Prok-RING_1 32 raCyek 37
                                      r Cy++
  gi|488601679|ref|YP_007908150.1|  9 RICYKT 14
                                      668876 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.1e-06
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgtpy 30 
                                       kC  C++ ++e   iV Cp+Cg  y
  gi|488601679|ref|YP_007908150.1| 105 KCRGCEHDISEL--IVLCPTCGRGY 127
                                       8**********9..********766 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.1e-05     0.024     139     182 ..      39      82 ..      22      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                       Sigma70_ECF 139 eqarlvelrkleGlsveEiAeklgvskrtverrlalaRawlere 182
                                       e  + + l  l G++ eE++ ++gvs+++  r+l+ aR +l  +
  gi|488601679|ref|YP_007908150.1|  39 EEIEALRLVDLLGMTHEEASIVMGVSRKAFWRDLKRARRKLVTA 82 
                                       555666777789**************************998766 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.5   3.4e+03       1      10 [.      36      45 ..      36      46 .. 0.88
   2 ?   12.1   0.0   5.9e-05      0.13      32      53 .]      60      81 ..      52      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                            HTH_10  1 LTdkqlevlk 10
                                      LT  ++e+l+
  gi|488601679|ref|YP_007908150.1| 36 LTHEEIEALR 45
                                      8999999998 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.9e-05
                            HTH_10 32 elGIskstlsehLrkaesklie 53
                                       +G+s+ +++  L++a +kl++
  gi|488601679|ref|YP_007908150.1| 60 VMGVSRKAFWRDLKRARRKLVT 81
                                      59*****************985 PP

>> FANCF  Fanconi anemia group F protein (FANCF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.12      62     126 ..      50     115 ..      36     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                             FANCF  62 LrntnkresealknlaklsfkaLgrcdelLvlaLLenpalssaalkalleals.pipgageedeee 126
                                       L  t+++ s +++ ++k   ++L+r++  Lv aL e +a++ +  ++++e+++ p +   e+d +e
  gi|488601679|ref|YP_007908150.1|  50 LGMTHEEASIVMGVSRKAFWRDLKRARRKLVTALVEGKAIEIEEGEYVFEKIRlPKCRGCEHDISE 115
                                       55566666666777778899********************************98777777777555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 735.12
//
Query:       gi|488601680|ref|YP_007908151.1|  [L=218]
Description: hypothetical protein Asulf_02205 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  100.4  12.0    1.1e-28  100.1  12.0    1.1  1  Yip1             Yip1 domain
    5.7e-09   36.0   8.4    7.2e-09   35.6   8.4    1.1  1  DUF1282          Protein of unknown function (DUF1282)
  ------ inclusion threshold ------
        3.1    7.4  19.3       0.19   11.3   8.7    2.4  2  TauE             Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1  12.0   1.9e-32   1.1e-28       1     170 [.       3     204 ..       3     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 1.9e-32
                              Yip1   1 llldPrevfrrlkkeppilrapdlallllalltlllgllaslnlgqtlasgeevqgltlssllga...iiggylgll 74 
                                       l+++P+e+f++l +e    + p  +++ +a++  ++ +l++  l+q+++s+     l+++ ++ga   iig+++g++
  gi|488601680|ref|YP_007908151.1|   3 LITNPNEFFQELSREDVRIQKPMTIVVAIAAIISAYQYLLAAKLSQVIPSD-----LAGFFVVGAyigIIGSFIGIF 74 
                                       689**************4444444444444444444444445777777777.....4444444444559******** PP

                              Yip1  75 lgllllalllhliakllg.gkgsfkqtlsvvgyallPlilgaliaillllllgt....................... 127
                                       + +l+l++ +h ++ ll  gkgsf++t++++gy++lP+++g+l++i+++ ++                         
  gi|488601680|ref|YP_007908151.1|  75 AVWLILTVMMHGLSSLLFnGKGSFRRTFEFTGYGFLPSLVGSLVTIPMSAYYVLnakvpkisieqlqqnpeivksvl 151
                                       ************9998888***************************99887777*********************** PP

                              Yip1 128 ..........llllvgllaliWslvllylglkaahnlskkkallaalilllll 170
                                                   l++ l++++Wsl l+++++k+a nl++k+a++ ali+ +l+
  gi|488601680|ref|YP_007908151.1| 152 lsilprdlvySNLIINLAITVWSLTLWTFAIKHARNLTTKRAFVSALIPTMLF 204
                                       ************************************************99886 PP

>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   8.4   1.2e-12   7.2e-09       1     165 [.       3     203 ..       3     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.2e-12
                           DUF1282   1 lltsPaeefeeikkreetgkvlyivlillllliglvvfiystfqvlseiltkqankltlassliisvvfylal...g 74 
                                       l+t P e f+e++++  +++ +++++++++++i  +++ y ++  ls++    +    +++++ i++++++++    
  gi|488601680|ref|YP_007908151.1|   3 LITNPNEFFQELSREDVRIQKPMTIVVAIAAII--SAYQYLLAAKLSQVIPS-DLAGFFVVGAYIGIIGSFIGifaV 76 
                                       799************************999996..77777777799999998.446667889999999999998888 PP

                           DUF1282  75 vlvlayliklmgrtyd.sqhsyskifafaayalvplflgglalglsllllva......................... 125
                                       +l+l+ +++  ++ ++ ++ s+  +f f++y + p   g l+++ ++   v                          
  gi|488601680|ref|YP_007908151.1|  77 WLILTVMMHGLSSLLFnGKGSFRRTFEFTGYGFLPSLVGSLVTIPMSAYYVLnakvpkisieqlqqnpeivksvlls 153
                                       999999999999999999********************9999998887777789*********************** PP

                           DUF1282 126 ...........lvslllllyvvvLlylGvptlmnirekdraiviallvlvv 165
                                                  ++ l++ ++++ L   +++   n+  ++ra+v al + ++
  gi|488601680|ref|YP_007908151.1| 154 ilprdlvysnlIINLAITVWSLTLWTFAIKHARNL-TTKRAFVSALIPTML 203
                                       **********98999999******999********.99*****99997665 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   8.7   3.2e-05      0.19      92     156 ..      25      85 ..      10      98 .. 0.80
   2 ?    1.4   3.0     0.035   2.1e+02      26      77 ..     150     205 ..     104     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.2e-05
                              TauE  92 lkllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpllll 156
                                       ++++++++ +++a++ ll +k s    +  ++++++++++g+ +G++++++Gi +  l++ +++ 
  gi|488601680|ref|YP_007908151.1|  25 MTIVVAIAAIISAYQYLLAAKLS----QVIPSDLAGFFVVGAYIGIIGSFIGIFAVWLILTVMMH 85 
                                       68899999999999999877633....4679999999999999***********87777777664 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.035
                              TauE  26 lLllllppavavatsllavvatslsgalah...rrr.gnvdw.rlllllllgsliGa 77 
                                       +Ll +  p+  v ++l++++a +++++  +   +++ +n+   r+++  l+++++ +
  gi|488601680|ref|YP_007908151.1| 150 VLLSI-LPRDLVYSNLIINLAITVWSLTLWtfaIKHaRNLTTkRAFVSALIPTMLFG 205
                                       44553.367777788888888888874444333333233433133333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); 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:                         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 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1285.46
//
Query:       gi|488601681|ref|YP_007908152.1|  [L=96]
Description: hypothetical protein Asulf_02206 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 592.78
//
Query:       gi|488601682|ref|YP_007908153.1|  [L=183]
Description: hypothetical protein Asulf_02207 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   86.4  16.2    2.5e-24   86.1  16.2    1.1  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
      0.024   14.3   2.7      0.024   14.3   2.7    2.7  3  EpuA      DNA-directed RNA polymerase subunit beta


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 !   86.1  16.2   2.8e-28   2.5e-24       2     155 ..      13     172 ..       8     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 2.8e-28
                            SpoIIM   2 lllflvgillgallaasnfaeqis..seskensalslflaifan.NlrvalllfllGllllgiptilvllinGfvlG 75 
                                       +ll+++gi+lg+ l ++  ++++    ++++ns l+++ ++++  Nl + +l++llG   +g++t + l++nG++l 
  gi|488601682|ref|YP_007908153.1|  13 ALLYIFGIILGYGLLNDLTDHSLAikVKYNNNSLLQFSYQSIIAtNLNL-ILILLLG---FGVVTSINLVFNGANLA 85 
                                       7899************333333335577777888888877666658888.9999***...5**************** PP

                            SpoIIM  76 ..avaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal......rsrrkalkeakrellklllllvpll 144
                                         ++ +l      l+ fl+l lPhgi+e+paiiiagaag+++ +++      +++   +ke  +e+l+l+l++++l+
  gi|488601682|ref|YP_007908153.1|  86 flYIESLRRG-MDLWNFLILTLPHGIFEIPAIIIAGAAGFKIPYEIirylvgKKETILTKEDVKEYLTLALISIILI 161
                                       5444444444.45*********************************9999987777788889*************** PP

                            SpoIIM 145 liAaliEafvt 155
                                       +iAa iEa +t
  gi|488601682|ref|YP_007908153.1| 162 VIAAWIEANIT 172
                                       *********98 PP

>> EpuA  DNA-directed RNA polymerase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.7   2.7e-06     0.024       1      24 [.       5      28 ..       5      38 .. 0.89
   2 ?   -1.8   0.6      0.28   2.5e+03      16      22 ..      65      71 ..      59      73 .. 0.49
   3 ?   -3.5   2.4      0.98   8.8e+03       2      11 ..     156     165 ..     155     167 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-06
                              EpuA  1 iiiVivLavlalaiGlmiGYgviG 24
                                      +ii i+L +l+++ G+++GYg++ 
  gi|488601682|ref|YP_007908153.1|  5 VIILILLSALLYIFGIILGYGLLN 28
                                      7999*****************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.28
                              EpuA 16 lmiGYgv 22
                                      l++G+gv
  gi|488601682|ref|YP_007908153.1| 65 LLLGFGV 71
                                      3344444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.98
                              EpuA   2 iiVivLavla 11 
                                       i +i+++++a
  gi|488601682|ref|YP_007908153.1| 156 ISIILIVIAA 165
                                       5566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); 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:                         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 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1108.14
//
Query:       gi|488601683|ref|YP_007908154.1|  [L=94]
Description: hypothetical protein Asulf_02208 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00021   20.9  18.5    0.00021   20.9  18.5    1.9  2  Gly-zipper_YMGG  YMGG-like Gly-zipper
  ------ inclusion threshold ------
      0.035   13.9  19.5      0.069   12.9  19.5    1.5  1  Gly-zipper_OmpA  Glycine-zipper domain
      0.095   12.7  25.8       0.68   10.0  24.2    2.6  2  Gly-zipper_Omp   Glycine zipper
       0.69    9.8  25.9        4.7    7.2  25.9    2.4  1  Rick_17kDa_Anti  Glycine zipper 2TM domain
        2.4    8.1   0.1        2.4    8.1   0.1    3.2  2  TAT_signal       TAT (twin-arginine translocation) pathway si
        8.2    6.7   6.9         16    5.8   2.5    2.3  2  XhlA             Haemolysin XhlA


Domain annotation for each model (and alignments):
>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       0.6   1.8e+03      33      40 ..      24      31 ..      18      40 .. 0.59
   2 !   20.9  18.5   7.2e-08   0.00021       8      45 ..      58      93 ..      52      94 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.6
                                      XXXXXXXX CS
                   Gly-zipper_YMGG 33 AaaGalaG 40
                                      A +G ++ 
  gi|488601683|ref|YP_007908154.1| 24 AMVGMVVT 31
                                      44444444 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 7.2e-08
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                   Gly-zipper_YMGG  8 aiGAaaGAvvGaliGsgggkGAaiGAaaGalaGgaiGa 45
                                      + G+a+GA +Ga+iG  g  G + GA++G + Gg+ Ga
  gi|488601683|ref|YP_007908154.1| 58 LWGTAVGATIGAVIG--GLAGGVAGAGIGLTLGGMWGA 93
                                      568888888888888..77788*************998 PP

>> Gly-zipper_OmpA  Glycine-zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  19.5   2.3e-05     0.069       6      42 ..      59      90 ..      55      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                   Gly-zipper_OmpA  6 vGAalGAaaGAavGaitGsaGtGAaiGAasGavaGll 42
                                       G+a+GA+ GA++G+ +     G  +GA++G++ G++
  gi|488601683|ref|YP_007908154.1| 59 WGTAVGATIGAVIGGLA-----GGVAGAGIGLTLGGM 90
                                      59**************9.....999*******99986 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  16.3   0.00031      0.92      19      40 ..      60      81 ..      18      81 .. 0.77
   2 ?   10.0  24.2   0.00023      0.68       2      41 ..      60      94 .]      60      94 .] 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00031
                    Gly-zipper_Omp 19 grgtGaliGAavGaavGgliGa 40
                                      g+++Ga iGA++G+++Gg+ Ga
  gi|488601683|ref|YP_007908154.1| 60 GTAVGATIGAVIGGLAGGVAGA 81
                                      4588888888888888888875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00023
                    Gly-zipper_Omp  2 GaaiGAaaGaliGgavggrgtGaliGAavGaavGgliGaa 41
                                      G+a+GA +Ga+iGg +gg     ++GA++G ++Gg++Gaa
  gi|488601683|ref|YP_007908154.1| 60 GTAVGATIGAVIGGLAGG-----VAGAGIGLTLGGMWGAA 94
                                      778888888888888776.....89*************85 PP

>> Rick_17kDa_Anti  Glycine zipper 2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  25.9    0.0016       4.7       4      42 .]      58      92 ..      55      94 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0016
                   Rick_17kDa_Anti  4 liGAaaGgvaGaaigggggrvlGavvGAaaGavaGnaig 42
                                      l+G a+G+ +Ga igg    ++G+v+GA++G  +G+++g
  gi|488601683|ref|YP_007908154.1| 58 LWGTAVGATIGAVIGG----LAGGVAGAGIGLTLGGMWG 92
                                      6788888888888866....7777777777777777775 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00081       2.4       7      25 ..      13      31 ..      12      32 .. 0.88
   2 ?   -8.6  15.2         6   1.8e+04      10      20 ..      75      85 ..      58      93 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00081
                        TAT_signal  7 FLKgsAAaaAAaalggcaa 25
                                       +K+ A+++ +a++g++++
  gi|488601683|ref|YP_007908154.1| 13 VIKWLAVGMVLAMVGMVVT 31
                                      68*************9876 PP

  == domain 2  score: -8.6 bits;  conditional E-value: 6
                        TAT_signal 10 gsAAaaAAaal 20
                                      ++++a+A+ +l
  gi|488601683|ref|YP_007908154.1| 75 AGGVAGAGIGL 85
                                      34555555444 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.046   1.4e+02      47      65 ..      13      31 ..      10      33 .. 0.84
   2 ?    5.8   2.5    0.0053        16      51      66 ..      58      73 ..      57      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.046
                              XhlA 47 nqkWlirtiiGalisaviy 65
                                       +kWl   ++ a++++v++
  gi|488601683|ref|YP_007908154.1| 13 VIKWLAVGMVLAMVGMVVT 31
                                      6899999999999999987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0053
                              XhlA 51 lirtiiGalisaviyl 66
                                      l++t +Ga i+avi++
  gi|488601683|ref|YP_007908154.1| 58 LWGTAVGATIGAVIGG 73
                                      7************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 566.66
//
Query:       gi|488601684|ref|YP_007908155.1|  [L=62]
Description: hypothetical protein Asulf_02209 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.8   0.1      0.019   14.6   0.1    1.0  1  Ilm1      Increased loss of mitochondrial DNA protein 1


Domain annotation for each model (and alignments):
>> Ilm1  Increased loss of mitochondrial DNA protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.1e-06     0.019      55     111 ..       6      58 ..       1      61 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-06
                              Ilm1  55 plAflgvlLlvlalvDlvllslneelavaeywgrqaplRlllffivslyiYlssess 111
                                        lA+l++lL++++l  + l++++e++  a  w+++     +l++++s y+Y+ s+++
  gi|488601684|ref|YP_007908155.1|   6 NLAVLAILLFAFGLL-IWLITMEEDMYEAILWRDSF---WCLSAALSGYAYAISKKE 58 
                                       68************6.56679*****9999999987...7999********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 398.19
//
Query:       gi|488601685|ref|YP_007908156.1|  [L=88]
Description: hypothetical protein Asulf_02210 [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-16   59.1   1.5    5.2e-16   59.1   1.5    1.0  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   1.5   2.9e-20   5.2e-16      60     140 ..       2      86 ..       1      88 [] 0.77

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.9e-20
                            SpoIIM  60 giptilvllinGfvlGav.aalvaefgglllflllilPhgilelpaiiiagaaglrlgkal......rsrrkalke. 128
                                       g  t++ l +nG++lGa+    +++  +l  flll++Phgi+e+paiiiagaag+++ +++      +      ke 
  gi|488601685|ref|YP_007908156.1|   2 GSSTMINLSFNGILLGALlKKSITNSISLQNFLLLVIPHGIFEIPAIIIAGAAGFKIPYEIvrylvgK------KEt 72 
                                       55689999********665777777788*********************************8765442......222 PP

                            SpoIIM 129 ..akrellklllll 140
                                          k++ +++l l 
  gi|488601685|ref|YP_007908156.1|  73 ilTKEDTKEYLTLA 86 
                                       23555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 524.22
//
Query:       gi|488601686|ref|YP_007908157.1|  [L=287]
Description: Periplasmic serine proteases (ClpP class) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-150  500.0   1.0   1.8e-150  499.7   1.0    1.0  1  SDH_sah        Serine dehydrogenase proteinase
    2.7e-07   30.6   0.2    1.1e-06   28.7   0.0    1.9  2  CLP_protease   Clp protease
     0.0028   17.6   0.0     0.0054   16.7   0.0    1.4  1  Peptidase_S49  Peptidase family S49
  ------ inclusion threshold ------
       0.09   12.8   0.1       0.25   11.4   0.1    1.7  1  Dimerisation   Dimerisation domain
       0.15   12.7   0.0       0.27   11.8   0.0    1.4  1  AntA           AntA/AntB antirepressor


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 !  499.7   1.0    5e-154  1.8e-150       3     282 ..       2     282 ..       1     285 [. 0.99

  Alignments for each domain:
  == domain 1  score: 499.7 bits;  conditional E-value: 5e-154
                           SDH_sah   3 ksdplsslssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedse 79 
                                       ++dp  s+++l+wfl+++yl+l pq+k++ql+ +r+ ++ k++ krks+vitmihrqesig++Gip y+fi++edse
  gi|488601686|ref|YP_007908157.1|   2 VYDPTGSFFNLIWFLFLFYLILGPQIKHRQLVNTRKALMEKMSAKRKSNVITMIHRQESIGLFGIPFYRFINVEDSE 78 
                                       58999************************************************************************ PP

                           SDH_sah  80 evlrairltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvd 156
                                       +vlrair+tpkd+pidl+ihtpGGlvlaa qiakalk+h+akt vivphyamsGGtlialaadeii+d++avlGpvd
  gi|488601686|ref|YP_007908157.1|  79 QVLRAIRTTPKDQPIDLVIHTPGGLVLAASQIAKALKSHPAKTSVIVPHYAMSGGTLIALAADEIIMDPHAVLGPVD 155
                                       ***************************************************************************** PP

                           SDH_sah 157 pqlgqypaasilkvvekkeakdiddktliladiakkaikqveefvyellkdkydeekakeiakklteGrwthdyplt 233
                                       pql++ypa+si+k+v kk++kd++dktlilad+a+kai+qv+ fvyell+dk+++ekake+ak+lteG+wthdyp+t
  gi|488601686|ref|YP_007908157.1| 156 PQLMNYPAPSIVKAVSKKDPKDVEDKTLILADLAEKAINQVRSFVYELLRDKMGDEKAKEVAKILTEGKWTHDYPIT 232
                                       ***************************************************************************** PP

                           SDH_sah 234 veelkelGlevntnvpeevyellelyeqplgqrps.veyipvpvkkkeqe 282
                                       ve +kelGl+v t+vpeevy l+ely+qp++qr + ve+ p+p k+ e+e
  gi|488601686|ref|YP_007908157.1| 233 VEVAKELGLNVRTDVPEEVYMLMELYPQPMMQRYPnVEFYPMPRKRGESE 282
                                       *********************************999*********88877 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0     3e-10   1.1e-06      37      98 ..      81     142 ..      32     151 .. 0.86
   2 ?   -0.6   0.0       0.3   1.1e+03     130     174 ..     191     241 ..     185     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3e-10
                                       HHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-T CS
                      CLP_protease  37 LllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagek 98 
                                       L ++ ++ +d++i l+i++pGG v a+  I+ +++ + ++ s+i+   a+S g+l+++a+++
  gi|488601686|ref|YP_007908157.1|  81 LRAIRTTPKDQPIDLVIHTPGGLVLAASQIAKALKSHPAKTSVIVPHYAMSGGTLIALAADE 142
                                       4456677899*************************************************986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHHTS-.HHHHHH.....HHCSTEEEEHHHHHHHTS CS
                      CLP_protease 130 eellkikerlneilakhtgqs.lekiek.....dldrdtflsaeeAveyGL 174
                                       + ++++++ + e+l ++ g + +++++k     + + d+ +++e A+e GL
  gi|488601686|ref|YP_007908157.1| 191 KAINQVRSFVYELLRDKMGDEkAKEVAKiltegKWTHDYPITVEVAKELGL 241
                                       668888888888888777754145566655566778888888899999887 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0054       8      40 ..     120     152 ..     113     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                                       -EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49   8 PvvasaenvaaSggYylasaadkivanpstivg 40 
                                       +  +++  +a Sgg ++a aad+i+++p+++ g
  gi|488601686|ref|YP_007908157.1| 120 KTSVIVPHYAMSGGTLIALAADEIIMDPHAVLG 152
                                       55678899**********************987 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   6.9e-05      0.25      14      43 ..      96     124 ..      94     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                      Dimerisation  14 iiakaggkplspsEiaskLptknpeapvll 43 
                                       +i++ gg  l++s+ia++L+ ++p +++++
  gi|488601686|ref|YP_007908157.1|  96 VIHTPGGLVLAASQIAKALK-SHPAKTSVI 124
                                       699999**************.***998765 PP

>> AntA  AntA/AntB antirepressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.6e-05      0.27      44      65 ..     221     242 ..     201     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                              AntA  44 gggrpskdYaltldmAKelaMv 65 
                                       ++g+ + dY +t+++AKel++ 
  gi|488601686|ref|YP_007908157.1| 221 TEGKWTHDYPITVEVAKELGLN 242
                                       4558899************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1562.59
//
Query:       gi|488601687|ref|YP_007908158.1|  [L=849]
Description: PAS domain S-box [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-78  258.0   0.0    2.3e-17   63.0   0.1    6.5  6  PAS              PAS fold
    9.2e-72  238.3   0.0    2.2e-14   53.7   0.0    5.6  5  PAS_4            PAS fold
    3.2e-66  220.1   2.6    9.3e-15   54.8   0.0    6.6  7  PAS_9            PAS domain
    1.5e-48  163.0   1.8    1.4e-18   66.9   0.0    5.1  5  PAS_3            PAS fold
    9.1e-41  137.3   0.1    1.9e-09   37.3   0.0    5.6  5  PAS_8            PAS domain
      3e-11   43.4   0.0    0.00095   19.3   0.0    3.9  3  PAS_11           PAS domain
    2.2e-10   41.0   0.0    7.5e-10   39.2   0.0    2.0  1  GAF_2            GAF domain
    4.4e-09   36.9   0.1    0.00082   19.9   0.1    4.2  3  PAS_10           PAS domain
    2.2e-08   34.3   0.4      0.042   14.0   0.0    5.2  4  PAS_7            PAS fold
    6.2e-07   29.8   0.0      2e-06   28.2   0.0    1.9  2  GAF_3            GAF domain
    1.6e-06   28.8   0.0      4e-06   27.5   0.0    1.8  1  GAF              GAF domain
    1.6e-05   24.8   0.5    1.6e-05   24.8   0.5    3.6  3  HisKA            His Kinase A (phospho-acceptor) domain
    0.00021   21.2   0.7       0.04   13.8   0.1    2.7  2  MEKHLA           MEKHLA domain
     0.0097   16.0   0.0         37    4.4   0.0    3.6  3  MLTR_LBD         MmyB-like transcription regulator ligand bin
  ------ inclusion threshold ------
      0.015   15.1   0.0        2.9    7.8   0.0    3.2  3  PAS_6            YheO-like PAS domain
      0.092   12.6   0.2       0.79    9.6   0.2    2.7  1  FAM165           FAM165 family
       0.12   12.2   0.0       0.37   10.6   0.0    1.8  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


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 !   59.3   0.0   3.2e-19   3.4e-16       2     113 .]       9     116 ..       8     116 .. 0.94
   2 !   38.8   0.0   6.9e-13   7.3e-10       2     113 .]     128     234 ..     127     234 .. 0.88
   3 !   61.5   0.0   6.3e-20   6.6e-17       1     106 [.     249     352 ..     249     359 .. 0.92
   4 !   63.0   0.1   2.2e-20   2.3e-17       2      92 ..     382     472 ..     381     492 .. 0.90
   5 !   23.2   0.0     5e-08   5.3e-05       2      90 ..     509     590 ..     508     606 .. 0.75
   6 ?    3.4   0.0     0.071        75      45      92 ..     624     671 ..     614     673 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 3.2e-19
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++++i+e +pdp+ ++D +g+il+vN+aae+ +G+s+ee+l  ++  l++  d+ ++ e+l+q++e+g      ++ 
  gi|488601687|ref|YP_007908158.1|   9 KFKEIFEVIPDPVYILDLNGNILEVNSAAEKTTGYSEEELLEMNVRQLLSDYDPKKVDERLKQVMEDGYAVVELKR- 84 
                                       578999*****************************************************************99666. PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                       +++ dg+ +++ev+a+ +  ++++   +++v rdi
  gi|488601687|ref|YP_007908158.1|  85 ERK-DGTCYYAEVHARLIDYESKK--AIFCVERDI 116
                                       666.9**************99998..999999997 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 6.9e-13
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                        +r+i+ ++ d+i ++D+dg+ ++ N+a +ellG+s +e+ gk+  + + ee    + +++ + ++ +   r++ ++
  gi|488601687|ref|YP_007908158.1| 128 LYREIFTNSNDGIAIIDADGNYVEQNQAHRELLGYSDDELKGKTPAIHMGEE----QFSKIYEEISKKGWYRGEIKC 200
                                       699*******************************************988776....556666666666666666666 PP

                                       EECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                               PAS  79 fklrdgrpihlevraspvrdaggeilgflgvlrdi 113
                                        ++ dg+pi++e+ a  + d +g +++++g+ rdi
  gi|488601687|ref|YP_007908158.1| 201 YRK-DGSPIYVELSAFALKDDKGDVICYVGIKRDI 234
                                       666.**************************99998 PP

  == domain 3  score: 61.5 bits;  conditional E-value: 6.3e-20
                                       HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCE CS
                               PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesragei 77 
                                       e++r i+e+++d i+ vDe+g+ +yv+++ e+ lG+++e+++gk++++++h++d + +++++ ++ e++++++++ +
  gi|488601687|ref|YP_007908158.1| 249 EKYRLIVENSRDIIVTVDENGIRTYVSPSVESVLGYKPEDLVGKPVFEQVHPDDLDAVRAEFFRAVETKRPGKIVHR 325
                                       579************************************************************************** PP

                                       EEECTTSSEEEEEEEEEEEEETTEEEEEE CS
                               PAS  78 sfklrdgrpihlevraspvrdaggeilgf 106
                                        +++ dg+ i+le   sp++  ++ + g 
  gi|488601687|ref|YP_007908158.1| 326 YRRK-DGKWIWLESKGSPMFINDSFV-GG 352
                                       9999.*************98777633.44 PP

  == domain 4  score: 63.0 bits;  conditional E-value: 2.2e-20
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda.elaelleqlleqgeesragei 77 
                                        l+++++ +p++i+++D + r++++N++ae+++ +++eev+g+ l++l++ e+++  ++e +e+++++ge++ +++ 
  gi|488601687|ref|YP_007908158.1| 382 LLQRMIDVAPAAIIGWDLNFRVNLWNKTAEKMFEWKAEEVMGRDLIELMISESEReRVREVIEEVMKTGESKINVNE 458
                                       689*************************************************9999999****************** PP

                                       EEECTTSSEEEEEEE CS
                               PAS  78 sfklrdgrpihlevr 92 
                                       ++ + +gr+  +e  
  gi|488601687|ref|YP_007908158.1| 459 NIAK-NGRKLMVEWY 472
                                       ****.***9998865 PP

  == domain 5  score: 23.2 bits;  conditional E-value: 5e-08
                                       HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEE CS
                               PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageis 78 
                                       ++r i+e++p  i ++D+dg+++++N+a+ +  G   ++ +gksl++l++ e  + + ell+++l + +  +++++ 
  gi|488601687|ref|YP_007908158.1| 509 KFRKIFENSPYSIAILDKDGVFVEANPATIKSIG---KDPVGKSLFELFPKEVAERRMELLTKVLDEDRLVTTEDV- 581
                                       799****************************999...688*********876433444444444444444444444. PP

                                       EECTTSSEEEEE CS
                               PAS  79 fklrdgrpihle 90 
                                          rdgr++ + 
  gi|488601687|ref|YP_007908158.1| 582 ---RDGRYFSVS 590
                                       ...677777654 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.071
                                       BGGGGBSTTHHH.HHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEE CS
                               PAS  45 slldliheedda.elaelleqlleqgeesrageisfklrdgrpihlevr 92 
                                       +++ li++e+d  +l e+ ++ l++ e+ ++   ++ + dg +i++ v 
  gi|488601687|ref|YP_007908158.1| 624 NINKLIVHEKDKqKLLERASEELASLEDYSIATLCLVK-DGAIIPVAVS 671
                                       6777888887777*************************.*****99886 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.1e-11   1.1e-08       1     110 []      14     121 ..      14     121 .. 0.94
   2 !   49.8   0.0   3.2e-16   3.4e-13       1     109 [.     133     238 ..     133     239 .. 0.92
   3 !   44.9   0.0   1.1e-14   1.1e-11       1     109 [.     255     363 ..     255     364 .. 0.94
   4 !   47.7   0.0   1.5e-15   1.6e-12       2     109 ..     388     497 ..     387     498 .. 0.95
   5 !   53.7   0.0     2e-17   2.2e-14       1     109 [.     514     613 ..     514     614 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.1e-11
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++ +pd++++ld +g++l +N aa++  g++ eell + +++ll++ d   +++ l++v+e + ++ +l   + +g 
  gi|488601687|ref|YP_007908158.1|  14 FEVIPDPVYILDLNGNILEVNSAAEKTTGYSEEELLEMNVRQLLSDYDPKKVDERLKQVMEDGYAVVELKRERKDGT 90 
                                       6899***********************************************************888888877779** PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerrr 110
                                         + e++++ ++ es +  +++++ rDiT r++
  gi|488601687|ref|YP_007908158.1|  91 CYYAEVHARLIDYESKK--AIFCVERDITKRKE 121
                                       ***********888888..9*********9985 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 3.2e-16
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpeedaarleralrrvlegeepiefleelllpg 76 
                                       +++++d++a++d+dg+++  N+a +el+g++++el Gkt+a  +      ++++ ++++  + +    +  +++ +g
  gi|488601687|ref|YP_007908158.1| 133 FTNSNDGIAIIDADGNYVEQNQAHRELLGYSDDELKGKTPAiHM----GEEQFSKIYEEISKKGWYRGEIKCYRKDG 205
                                       689**************************************666....668999999999888877778888888** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++ ++el+++ l+d++G+vi +++i rDiT+r+
  gi|488601687|ref|YP_007908158.1| 206 SPIYVELSAFALKDDKGDVICYVGIKRDITQRK 238
                                       *******************************98 PP

  == domain 3  score: 44.9 bits;  conditional E-value: 1.1e-14
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll.pg 76 
                                       ++++ d+++ +d++g  +y++++ ++++g+ pe+l+Gk+++e + ++d +++++   r++e+++p + ++ +++ +g
  gi|488601687|ref|YP_007908158.1| 255 VENSRDIIVTVDENGIRTYVSPSVESVLGYKPEDLVGKPVFEQVHPDDLDAVRAEFFRAVETKRPGKIVHRYRRkDG 331
                                       689**************************************755555****************************** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       ++ ++e   +P++  +   +g ++i+rD+Ter 
  gi|488601687|ref|YP_007908158.1| 332 KWIWLESKGSPMF-INDSFVGGVIIARDVTERI 363
                                       ************9.566779999********95 PP

  == domain 4  score: 47.7 bits;  conditional E-value: 1.5e-15
                             PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlae.llpeedaarleralrrvlegeepiefleelll.pg 76 
                                       d  p+a++ +d ++rv  +N++a+++f + +ee++G+ l e + +e+ ++r+++ +++v++++e+ + + e    +g
  gi|488601687|ref|YP_007908158.1| 388 DVAPAAIIGWDLNFRVNLWNKTAEKMFEWKAEEVMGRDLIElMISESERERVREVIEEVMKTGESKINVNENIAkNG 464
                                       568999**********************************9677777*****************99999998889** PP

                             PAS_4  77 eerhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +   +e+  + ++d++G+++g+  i++D+Ter 
  gi|488601687|ref|YP_007908158.1| 465 RKLMVEWYNFAIKDAEGKTVGAASIGVDLTERI 497
                                       *******************************95 PP

  == domain 5  score: 53.7 bits;  conditional E-value: 2e-17
                             PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpge 77 
                                       ++++p  +a+ld+dg+++ aN+a    ++  +++ +Gk+l+el+p+e+a+r ++ l++vl++++ +++++     ++
  gi|488601687|ref|YP_007908158.1| 514 FENSPYSIAILDKDGVFVEANPA---TIKSIGKDPVGKSLFELFPKEVAERRMELLTKVLDEDRLVTTED----VRD 583
                                       79*********************...455678889********************************999....666 PP

                             PAS_4  78 erhyelrllPlrdesGevigvlvisrDiTerr 109
                                       +r+++++l+P++ ++G+   +l+++ +iT+++
  gi|488601687|ref|YP_007908158.1| 584 GRYFSVSLVPVDLPDGK--YCLILAKEITDLV 613
                                       7****************..9999999999986 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   4.3e-17   4.6e-14       1     104 []      18     118 ..      18     118 .. 0.93
   2 !   54.8   0.0   8.8e-18   9.3e-15       2     104 .]     138     236 ..     137     236 .. 0.91
   3 !   47.9   0.0   1.2e-15   1.2e-12       2     104 .]     260     361 ..     259     361 .. 0.91
   4 !   34.9   0.1   1.4e-11   1.5e-08       4     104 .]     394     495 ..     391     495 .. 0.86
   5 !   22.8   0.0   8.1e-08   8.5e-05       1     104 []     518     611 ..     518     611 .. 0.90
   6 ?    0.6   0.0      0.62   6.6e+02      36      82 ..     625     672 ..     607     674 .. 0.80
   7 ?   -2.6   0.0       6.2   6.5e+03      30      59 ..     807     833 ..     795     846 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 4.3e-17
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                       pd++ i + +g+il +N aa++ +Gys+ee+l  ++++l+  +++++ +erl++++e+g      ve+   rk+g+ 
  gi|488601687|ref|YP_007908158.1|  18 PDPVYILDLNGNILEVNSAAEKTTGYSEEELLEMNVRQLLsdYDPKKVDERLKQVMEDGY---AVVELKRERKDGTC 91 
                                       68899999********************************88888888888888888888...999*********** PP

                             PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                       ++++++a+ +  ++++ ++  ++ rDit+
  gi|488601687|ref|YP_007908158.1|  92 YYAEVHARLIDYESKKAIF--CVERDITK 118
                                       **********999989888..******95 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 8.8e-18
                             PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwv 78 
                                       dgi+i++ dg+ +  N+a ++llGys +e+ gk     +   +e  +++ + +  +    +++e+ ++rk+g++++v
  gi|488601687|ref|YP_007908158.1| 138 DGIAIIDADGNYVEQNQAHRELLGYSDDELKGKTPAIHM--GEEQFSKIYEEISKKG--WYRGEIKCYRKDGSPIYV 210
                                       89***99********************************..6666666666666666..9***************** PP

                             PAS_9  79 lltaspvkdddgelvgiivilrDite 104
                                       +l+a+++kdd+g ++ +++i rDit+
  gi|488601687|ref|YP_007908158.1| 211 ELSAFALKDDKGDVICYVGIKRDITQ 236
                                       **********999999*********7 PP

  == domain 3  score: 47.9 bits;  conditional E-value: 1.2e-15
                             PAS_9   2 dgilidnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirkngetf 76 
                                       d i+ ++++g i  y++++++ +lGy+pe+++gk++++ + ++++ +   ++++++ ++  +      ++rk+g+ +
  gi|488601687|ref|YP_007908158.1| 260 DIIVTVDENG-IRtYVSPSVESVLGYKPEDLVGKPVFEQV-HPDDLDAVRAEFFRAVETkRPGKIVHRYRRKDGKWI 334
                                       5677799***.777**************************.8999999999999999988799999999******** PP

                             PAS_9  77 wvlltaspvkdddgelvgiivilrDite 104
                                       w + + sp++ + + +vg ++i rD+te
  gi|488601687|ref|YP_007908158.1| 335 WLESKGSPMFIN-DSFVGGVIIARDVTE 361
                                       *********876.579999********8 PP

  == domain 4  score: 34.9 bits;  conditional E-value: 1.4e-11
                             PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlf...vtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       i+  + ++r+  +N++a++++  ++eev+g+++ +l+   ++ ++ +e +++++++g+   +   +++i kng++++
  gi|488601687|ref|YP_007908158.1| 394 IIGWDLNFRVNLWNKTAEKMFEWKAEEVMGRDLIELMiseSERERVREVIEEVMKTGE--SKINVNENIAKNGRKLM 468
                                       454347888889********************99999666666666666677777777..9**************** PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                       v+   +++kd++g+ vg+++i +D+te
  gi|488601687|ref|YP_007908158.1| 469 VEWYNFAIKDAEGKTVGAASIGVDLTE 495
                                       **************************8 PP

  == domain 5  score: 22.8 bits;  conditional E-value: 8.1e-08
                             PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       p +i+i ++dg  + aN+a ++ +G   ++ +gks+++lf +++ a++r++ + + ++  e +  +++  ++g++f 
  gi|488601687|ref|YP_007908158.1| 518 PYSIAILDKDGVFVEANPATIKSIG---KDPVGKSLFELF-PKEVAERRMELLTKVLD--EDRLVTTEDVRDGRYFS 588
                                       56899999***666**********9...889*********.99999999999999999..99999999999999888 PP

                             PAS_9  78 vlltaspvkdddgelvgiivilrDite 104
                                         ++++pv   dg++++  ++ + it+
  gi|488601687|ref|YP_007908158.1| 589 --VSLVPVDLPDGKYCL--ILAKEITD 611
                                       ..******888****99..88888885 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.62
                             PAS_9  36 itdlfvtdpeanerlraaleqgrk.kerevevvlirkngetfwvllta 82 
                                       i  l+v++++ ++ l++a e++ + + ++  + +  k+g  ++v +++
  gi|488601687|ref|YP_007908158.1| 625 INKLIVHEKDKQKLLERASEELASlEDYSIATLCLVKDGAIIPVAVSV 672
                                       344558889999999999999998999999*************99886 PP

  == domain 7  score: -2.6 bits;  conditional E-value: 6.2
                             PAS_9  30 evlgksitdlfvtdpeanerlraaleqgrk 59 
                                       e+  +++++l+    + +er+++++++++k
  gi|488601687|ref|YP_007908158.1| 807 EIKDRKLSELI---IQQAERIEDIIKRLDK 833
                                       78889999999...7888888888888775 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   5.2e-10   5.5e-07       2      84 ..      31     110 ..      30     113 .. 0.92
   2 !   36.2   0.1   5.4e-12   5.7e-09       4      88 ..     152     230 ..     149     231 .. 0.85
   3 !   66.9   0.0   1.4e-21   1.4e-18       2      78 ..     272     346 ..     271     355 .. 0.93
   4 !   24.8   0.1   1.8e-08   1.9e-05       4      85 ..     406     486 ..     403     489 .. 0.92
   5 ?   -1.0   0.0       2.1   2.2e+03      29      69 ..     629     669 ..     626     672 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5.2e-10
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       + v+ + e+++Gys+eell+   ++++l+   D ++v e l++++++g +  +e ++ rkdG+ ++ e +ar i +e
  gi|488601687|ref|YP_007908158.1|  31 LEVNSAAEKTTGYSEEELLEM--NVRQLLSDYDPKKVDERLKQVMEDGYA-VVELKRERKDGTCYYAEVHARLIDYE 104
                                       6899*****************..**********************99995.69*********************888 PP

                             PAS_3  79 ngkpvr 84 
                                       + k ++
  gi|488601687|ref|YP_007908158.1| 105 SKKAIF 110
                                       877665 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 5.4e-12
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                        +++ +e+lGys++el+gk      ++h  + e++ + ++e+ kkg  y ge+++ rkdG+ ++ve +a++++d++g
  gi|488601687|ref|YP_007908158.1| 152 QNQAHRELLGYSDDELKGK----TPAIHMGE-EQFSKIYEEISKKGW-YRGEIKCYRKDGSPIYVELSAFALKDDKG 222
                                       6899***************....66666665.555555555557788.***************************** PP

                             PAS_3  81 kpvrvigv 88 
                                        +++++g+
  gi|488601687|ref|YP_007908158.1| 223 DVICYVGI 230
                                       ******97 PP

  == domain 3  score: 66.9 bits;  conditional E-value: 1.4e-21
                             PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirde 78 
                                       +yvs++ve +lGy pe+l gk   + + vhp+D++ vr+++ +a+++++p ++ +R+rrkdG+++w+e+++++++ +
  gi|488601687|ref|YP_007908158.1| 272 TYVSPSVESVLGYKPEDLVGK--PVFEQVHPDDLDAVRAEFFRAVETKRPGKIVHRYRRKDGKWIWLESKGSPMFIN 346
                                       79*******************..*************************************************99544 PP

  == domain 4  score: 24.8 bits;  conditional E-value: 1.8e-08
                             PAS_3   4 vserveeilGyspeellgkveswldlvhpeD.rervrealqealkkgepyegeyRirrkdGeyrwveararvirden 79 
                                       ++++ e+++ + +ee++g+  ++++l+  e  rervre ++e++k+ge+       + k+G    ve++ ++i+d +
  gi|488601687|ref|YP_007908158.1| 406 WNKTAEKMFEWKAEEVMGR--DLIELMISESeRERVREVIEEVMKTGESKINVNENIAKNGRKLMVEWYNFAIKDAE 480
                                       9******************..99999999988****************6667799********************** PP

                             PAS_3  80 gkpvrv 85 
                                       gk v  
  gi|488601687|ref|YP_007908158.1| 481 GKTVGA 486
                                       **8865 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 2.1
                             PAS_3  29 lvhpeDrervrealqealkkgepyegeyRirrkdGeyrwve 69 
                                       +vh  D +++ e   e l++ e+y++   ++ kdG ++ v 
  gi|488601687|ref|YP_007908158.1| 629 IVHEKDKQKLLERASEELASLEDYSIATLCLVKDGAIIPVA 669
                                       79****99999988888899999999999999999998876 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   1.8e-12   1.9e-09       2      58 ..       9      68 ..       8      77 .. 0.89
   2 !   32.6   0.0   5.3e-11   5.6e-08       2      44 ..     128     171 ..     127     186 .. 0.89
   3 !   17.4   0.0   3.1e-06    0.0033       1      53 [.     249     304 ..     249     318 .. 0.73
   4 !   17.7   0.1   2.5e-06    0.0026       1      48 [.     381     429 ..     381     447 .. 0.75
   5 !   24.8   0.0   1.6e-08   1.7e-05       1      51 [.     508     556 ..     508     574 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.8e-12
                             PAS_8  2 rlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgellgqllpvlrplle..d 58
                                      +++ +fe +pd++ ++d +g+ i++vN aa++ +Gys ++l+++ ++qll + +p ++  +
  gi|488601687|ref|YP_007908158.1|  9 KFKEIFEVIPDPVYILDlNGN-ILEVNSAAEKTTGYSeEELLEMNVRQLLSDYDPKKVdeR 68
                                      6899*************7777.*****************************9999998544 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 5.3e-11
                             PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgel 44 
                                        +r +f +s+dgia++d++++ v+ Nqa  ellGys ++lkg++
  gi|488601687|ref|YP_007908158.1| 128 LYREIFTNSNDGIAIIDADGNYVEQNQAHRELLGYSdDELKGKT 171
                                       69***************6666***************88888864 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.1e-06
                             PAS_8   1 erlralfesspdgiavvdlgdrivd.vNqaalellGys.adlkgell..gqllpvlr 53 
                                       e++r ++e+s+d i+ vd+++ i+  v ++ +  lGy+ +dl g+++  ++ +++l+
  gi|488601687|ref|YP_007908158.1| 249 EKYRLIVENSRDIIVTVDENG-IRTyVSPSVESVLGYKpEDLVGKPVfeQVHPDDLD 304
                                       79****************777.6555************8888888874323333332 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 2.5e-06
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgql 48 
                                       e l+ +++ +p +i+ +dl+ r+  +N++a++++ ++ +++ g +l +l
  gi|488601687|ref|YP_007908158.1| 381 ELLQRMIDVAPAAIIGWDLNFRVNLWNKTAEKMFEWKaEEVMGRDLIEL 429
                                       6799**************5557*************99777777777432 PP

  == domain 5  score: 24.8 bits;  conditional E-value: 1.6e-08
                             PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGysadlkgellgqllpv 51 
                                       e++r +fe+sp +ia++d ++ +v++N+a+++  G + d  g+ l +l+p 
  gi|488601687|ref|YP_007908158.1| 508 EKFRKIFENSPYSIAILDKDGVFVEANPATIKSIG-K-DPVGKSLFELFPK 556
                                       79****************6666*********9999.3.3333333344444 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     9e-07   0.00095       7      88 ..      23      99 ..      21     112 .. 0.82
   2 !   18.2   0.0   1.9e-06     0.002      23      90 ..     277     343 ..     245     358 .. 0.83
   3 ?    0.4   0.0      0.66     7e+02      29      68 ..     415     454 ..     409     465 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9e-07
                            PAS_11  7 rldidgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvkt 85
                                      +ld++g+I++v++    a+ ++g+++eel+++ + +L++  d++++++ l++v+ + g a   l R r  ++++ ++  
  gi|488601687|ref|YP_007908158.1| 23 ILDLNGNILEVNS---AAEKTTGYSEEELLEMNVRQLLSDYDPKKVDERLKQVM-EDGYAVVELKRERK-DGTCYYAEV 96
                                      689**********...**************************************.77776666655444.555555555 PP

                            PAS_11 86 ksk 88
                                       ++
  gi|488601687|ref|YP_007908158.1| 97 HAR 99
                                      555 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.9e-06
                            PAS_11  23 rasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklf 90 
                                       + + +lg++ e+lvg+ +++ +hp+dl  ++  +   + ++++ ++ + R r +++k++++  k+   
  gi|488601687|ref|YP_007908158.1| 277 SVESVLGYKPEDLVGKPVFEQVHPDDLDAVRAEFFRAV-ETKRPGKIVHRYRRKDGKWIWLESKGSPM 343
                                       4566789*******************************.9*********************9998765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.66
                            PAS_11  29 glekeelvgrsiydLchpqd.lstlkshlrevissngeats 68 
                                        ++ ee++gr + +L+  +  ++++++  +ev+ ++ge+++
  gi|488601687|ref|YP_007908158.1| 415 EWKAEEVMGRDLIELMISESeRERVREVIEEVM-KTGESKI 454
                                       588899****999999988868899999*****.8888765 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   7.1e-13   7.5e-10       2     137 ..     633     763 ..     632     764 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 7.1e-13
                                       HHHHHHHHHHHHHHHHS.S..EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TT.HHHHHHHHTS-EEES-GGG CS
                             GAF_2   2 adleelldlvldelvel.gaalgyillvdddgglrlaawgeaeeefgaaldrplgeg.lvgealrtgrpvilndlee 76 
                                       +d + ll+++ +el+ l + +++ + lv d+  + +a++ + +e ++  l+ + +e+ ++ +a+++ +++ + d   
  gi|488601687|ref|YP_007908158.1| 633 KDKQKLLERASEELASLeDYSIATLCLVKDGAIIPVAVSVGGDEILDNLLR-KHRECeIIKKAIES-KSITIRD--- 704
                                       67899************8899999999886555545555555555555553.446666********.7888877... PP

                                       -S-HHHHHHHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHHHHH CS
                             GAF_2  77 dpdkkglpaghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqiaiai 137
                                           +    g  g++s +++P++ +g+v Gv++ly +  ++ ++++lelL ++ae++a+ai
  gi|488601687|ref|YP_007908158.1| 705 --GGICVGCGLTGIKSVISIPMVVDGEVKGVITLYLTTSREISDDELELLGTMAEDLAFAI 763
                                       ..2222334889***********************9************************9 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0045       4.7      12     102 ..     262     356 ..     253     360 .. 0.70
   2 !   19.9   0.1   7.8e-07   0.00082       1     106 []     383     494 ..     383     494 .. 0.83
   3 ?    3.8   0.0     0.084        88       6      95 ..     515     601 ..     511     602 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0045
                            PAS_10  12 ltflDdnlqirrFtpaakklfklipad.vGrpladihpkkavknv.eeviealrtgek.devevvvpkngkwvlvry 85 
                                       ++ +D+n   ++ +p+ ++++ ++p+d vG p+ + ++++ ++ v  e++ a+ t++  + v+ ++ k+gkw+ ++ 
  gi|488601687|ref|YP_007908158.1| 262 IVTVDENGIRTYVSPSVESVLGYKPEDlVGKPVFEQVHPDDLDAVrAEFFRAVETKRPgKIVHRYRRKDGKWIWLES 338
                                       56789888888889999*******99967****8766666666662667888888887444555566****987654 PP

                            PAS_10  86 ..lpyrdedgeiaGvvetf 102
                                         +p+  +d  + G v++ 
  gi|488601687|ref|YP_007908158.1| 339 kgSPMFINDSFV-GGVIIA 356
                                       115777555444.444444 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 7.8e-07
                            PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipadv.Grpladih.pkkavknveeviealrtgekdevevvvp 75 
                                       l+ +++ +p +++  D n ++  ++++a+k+f+ ++++v Gr+l ++  ++++ ++v+evie++ ++ + + +v  +
  gi|488601687|ref|YP_007908158.1| 383 LQRMIDVAPAAIIGWDLNFRVNLWNKTAEKMFEWKAEEVmGRDLIELMiSESERERVREVIEEVMKTGESKINVNEN 459
                                       6789999999***********************9987755***999962669999******9999888877776665 PP

                            PAS_10  76 ..kngkwvlv..rylpyrdedgeiaGvvetfvDit 106
                                         kng+  +v  + ++++d +g++ G+  + vD+t
  gi|488601687|ref|YP_007908158.1| 460 iaKNGRKLMVewYNFAIKDAEGKTVGAASIGVDLT 494
                                       558877655511678************99999875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.084
                            PAS_10   6 nstpieltflDdnlqirrFtpaakklfklipadvGrpladihpkkavknveeviealrtgekdevevvvpkngkwvl 82 
                                       ++ p ++  lD++  +   +pa  ++ ++ ++ vG +l ++ pk+  ++  e++ ++ ++ + +  ++  ++g+++ 
  gi|488601687|ref|YP_007908158.1| 515 ENSPYSIAILDKDGVFVEANPA--TIKSIGKDPVGKSLFELFPKEVAERRMELLTKVLDEDRLVT-TEDVRDGRYFS 588
                                       5666666667777776666666..56667778899999999999888777777777777666443.344479***** PP

                            PAS_10  83 vrylpyrdedgei 95 
                                       v   p+   dg++
  gi|488601687|ref|YP_007908158.1| 589 VSLVPVDLPDGKY 601
                                       ******9999987 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.22   2.3e+02      37     112 ..      41     121 ..      22     124 .. 0.62
   2 !   14.0   0.0   3.9e-05     0.042       2      40 ..     134     172 ..     133     242 .. 0.86
   3 ?    4.0   0.0     0.052        55      62     114 ..     306     366 ..     292     367 .. 0.63
   4 !    7.7   0.0    0.0036       3.8       7      65 ..     393     445 ..     387     501 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.22
                             PAS_7  37 vgvpleellrynaer..gefgagdveaeverrlaaaragkphsfererpdgr..vievrgnpl...pdgGfVttytD 106
                                       +g + eell++n+++   ++++++v++ ++++++   a     ++rer+dg+    ev+++ +    ++ +  +  D
  gi|488601687|ref|YP_007908158.1|  41 TGYSEEELLEMNVRQllSDYDPKKVDERLKQVMEDGYAVV--ELKRERKDGTcyYAEVHARLIdyeSKKAIFCVERD 115
                                       5777889999997772244557777777777776555544..44555556551145666666644334555555667 PP

                             PAS_7 107 iTerrr 112
                                       iT+r++
  gi|488601687|ref|YP_007908158.1| 116 ITKRKE 121
                                       777776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.9e-05
                             PAS_7   2 enmsqGisvfDadlrLvawNrrylelldlpeelvqvgvp 40 
                                        n ++Gi+++Dad++ v  N+  +ell+++++ ++  +p
  gi|488601687|ref|YP_007908158.1| 134 TNSNDGIAIIDADGNYVEQNQAHRELLGYSDDELKGKTP 172
                                       57799**************************98866555 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.052
                             PAS_7  62 everrlaaaragkphs..fererpdgrvi..evrgnpl....pdgGfVttytDiTerrrae 114
                                         +++++a+++++p +     +r+dg++i  e +g+p+       G V++  D+Ter++ e
  gi|488601687|ref|YP_007908158.1| 306 VRAEFFRAVETKRPGKivHRYRRKDGKWIwlESKGSPMfindSFVGGVIIARDVTERIELE 366
                                       44444444444443330034456777765227788899886555899**********9865 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0036
                             PAS_7   7 GisvfDadlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaever 65 
                                       +i+  D + r+ +wN+   +++++ +e v +g+ l el+   +er+ ++     + +e+
  gi|488601687|ref|YP_007908158.1| 393 AIIGWDLNFRVNLWNKTAEKMFEWKAEEV-MGRDLIELMISESERERVR-----EVIEE 445
                                       566678899******************99.9999888888888888777.....33333 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.8   7.1e+03      47      71 ..     556     580 ..     511     604 .. 0.52
   2 !   28.2   0.0   1.9e-09     2e-06       2     127 ..     635     763 ..     634     765 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.8
                             GAF_3  47 sesldedsalarralssgevvseps 71 
                                       +e+ ++++ l   +l+++  v++ +
  gi|488601687|ref|YP_007908158.1| 556 KEVAERRMELLTKVLDEDRLVTTED 580
                                       2233455555555555555555555 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.9e-09
                             GAF_3   2 ldellekllkllvkllgaevgalllldedgnklqvaagwdgkpalsesld...edsalarralssgevvsepsfaee 75 
                                        ++lle + ++l++l + +++ l+l+  dg  + ++a + g++ +  +l    +++  ++ a++s+ + +  ++ + 
  gi|488601687|ref|YP_007908158.1| 635 KQKLLERASEELASLEDYSIATLCLVK-DGAII-PVAVSVGGDEILDNLLrkhRECEIIKKAIESKSITIRDGGICV 709
                                       5899***********************.55555.66666466666666644889999999*************9997 PP

                             GAF_3  76 dg..lpdraalavPLvagr.qviGvlalastkprafdaedlelleslArqiatai 127
                                        +  +   +++ +P+v+ + +v Gv+ l+ t  r++++++lell ++A  +a ai
  gi|488601687|ref|YP_007908158.1| 710 GCglTGIKSVISIPMVV-DgEVKGVITLYLTTSREISDDELELLGTMAEDLAFAI 763
                                       555477888899*****.66*********************************99 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   3.8e-09     4e-06       4     133 .]     637     763 ..     634     763 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.8e-09
                                       HHHHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC........EEEETTSH.HHHHHHHHSSSEEESTGGTST CS
                               GAF   4 elldtvveelrellgadrvalylpdydGlhydipqasrw........lfmkngrg.icgqvlatgqplvipdstpdp 71 
                                       +ll+++ eel++l ++  ++l l   dG    ip a +         l +k  ++ i+ ++++  ++++i d     
  gi|488601687|ref|YP_007908158.1| 637 KLLERASEELASLEDYSIATLCL-VKDG-AI-IPVAVSVggdeildnLLRKHRECeIIKKAIE-SKSITIRD--GGI 707
                                       67777777777777777777766.4566.33.4444444444444434444433335555555.77777775..444 PP

                                       THHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHHHHH CS
                               GAF  72 rfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqvaval 133
                                       +          + +gi+s++++P+v+dge+ G+++l+ ++  + +++elell ++a+ +a a+
  gi|488601687|ref|YP_007908158.1| 708 CVGC-------GLTGIKSVISIPMVVDGEVKGVITLYLTTSrEISDDELELLGTMAEDLAFAI 763
                                       4333.......457************************555589*************999887 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 ?   -0.6   0.0       1.3   1.4e+03      36      58 ..     422     446 ..     409     452 .. 0.75
   2 ?   -3.2   0.1       8.4   8.8e+03      17      47 ..     619     645 ..     614     651 .. 0.44
   3 !   24.8   0.5   1.6e-08   1.6e-05       5      65 ..     785     837 ..     766     839 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                                       SCHHHHHHHHHHHH..HHHHHHHHH CS
                             HisKA  36 elkeyletiesear..rldhlvedl 58 
                                       + ++++e ++se++  r+++++e++
  gi|488601687|ref|YP_007908158.1| 422 MGRDLIELMISESEreRVREVIEEV 446
                                       5567788888888877888888887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.4
                                       HHHHHHHHHHH...HC..T-HSSCHHHHHHHHHH CS
                             HisKA  17 LsailgnaeaL...kregklteelkeyletiese 47 
                                       L+ai+   +++   k       + +++le++ +e
  gi|488601687|ref|YP_007908158.1| 619 LNAIYNINKLIvheK-------DKQKLLERASEE 645
                                       666666666654322.......223333333333 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 1.6e-08
                                       HHHHHHHHHHHHHHHHHHHHHH.HHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                             HisKA   5 flagvaHELrtPLsailgnaea.LkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                                        +a +   +r+PL+ai++ ae+ +k+        +++ e i+++a+r+++++++l d +++e
  gi|488601687|ref|YP_007908158.1| 785 QFAILVDHIRNPLAAIILLAELeIKD--------RKLSELIIQQAERIEDIIKRL-DKGWLE 837
                                       67889999**************5566........89*****************98.766666 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.022        24      55      99 ..      34      78 ..      32      90 .. 0.89
   2 !   13.8   0.1   3.8e-05      0.04      36     136 ..     390     488 ..     365     494 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.022
                            MEKHLA 55 NqaaldllettweeltdlpsrksaepeekeeRealLekvaeqgfv 99
                                      N aa +   ++ eel ++ +r+ +++ + ++ ++ L++v+e+g++
  gi|488601687|ref|YP_007908158.1| 34 NSAAEKTTGYSEEELLEMNVRQLLSDYDPKKVDERLKQVMEDGYA 78
                                      788888899999*************99967779**********97 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.8e-05
                            MEKHLA  36 apfavlshslkadpvfnyaNqaaldllettweeltdlps.rksaepeekeeRealLekvaeqgfvenysGvrisstG 111
                                       ap a++  +l+     n  N++a +++e + ee++   + +++++++e+e  ++ +e+v+++g  +      i+++G
  gi|488601687|ref|YP_007908158.1| 390 APAAIIGWDLN--FRVNLWNKTAEKMFEWKAEEVMGRDLiELMISESERERVREVIEEVMKTGESKINVNENIAKNG 464
                                       66666666655..345667**************99987625555555566667788********************* PP

                            MEKHLA 112 rrfsienavvWkvldeegkahGqAa 136
                                       r++++e    + + d+egk++G A 
  gi|488601687|ref|YP_007908158.1| 465 RKLMVEW-YNFAIKDAEGKTVGAAS 488
                                       ***9985.67899999999999986 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 ?    4.4   0.0     0.036        37      15      39 ..      19      43 ..      15     100 .. 0.86
   2 ?    3.5   0.0     0.064        67      18      42 ..     141     165 ..     138     176 .. 0.84
   3 ?    3.3   0.0     0.074        78       9      61 ..     383     437 ..     377     451 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.036
                          MLTR_LBD 15 vPAlVldrrwdvlaaNraaraLlgd 39
                                       P+++ld + ++l  N aa++  g 
  gi|488601687|ref|YP_007908158.1| 19 DPVYILDLNGNILEVNSAAEKTTGY 43
                                      59******************99998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.064
                          MLTR_LBD  18 lVldrrwdvlaaNraaraLlgdpaa 42 
                                       +++d++ + + +N+a r Llg  ++
  gi|488601687|ref|YP_007908158.1| 141 AIIDADGNYVEQNQAHRELLGYSDD 165
                                       699******************9544 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.074
                          MLTR_LBD   9 Ldal.epvPAlVl..drrwdvlaaNraaraLlgdpaalpeperNllrlvfldpglr 61 
                                       L+++ + +PA+++  d ++ v  +N+ a+++++  +a +  +r l+ l+  + +  
  gi|488601687|ref|YP_007908158.1| 383 LQRMiDVAPAAIIgwDLNFRVNLWNKTAEKMFEW-KAEEVMGRDLIELMISESERE 437
                                       44441346888872255667899**********9.777788888888888765433 PP

>> PAS_6  YheO-like PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         4   4.2e+03      97     112 ..     107     122 ..      97     124 .. 0.77
   2 ?    3.5   0.0      0.06        63      83     113 ..     211     241 ..     178     243 .. 0.82
   3 ?    7.8   0.0    0.0027       2.9      56     112 ..     441     499 ..     430     502 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4
                             PAS_6  97 iglLCiNldlskleaa 112
                                        +++C+  d++k +++
  gi|488601687|ref|YP_007908158.1| 107 KAIFCVERDITKRKEL 122
                                       5789999999987665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.06
                             PAS_6  83 ksstifirdekgkliglLCiNldlskleaae 113
                                         s + ++d+kg++i   +i  d+++ +++e
  gi|488601687|ref|YP_007908158.1| 211 ELSAFALKDDKGDVICYVGIKRDITQRKKLE 241
                                       568999*******************987765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0027
                             PAS_6  56 ellkeeeeeeedvlvnyktktkdgkil..ksstifirdekgkliglLCiNldlskleaa 112
                                       e+++e  ++ e+++   ++ +k+g++l      + i+d++gk++g+ +i +dl++  ++
  gi|488601687|ref|YP_007908158.1| 441 EVIEEVMKTGESKINVNENIAKNGRKLmvEWYNFAIKDAEGKTVGAASIGVDLTERIEM 499
                                       5555555556666777778888898872245799*******************987766 PP

>> FAM165  FAM165 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00075      0.79      26      45 ..     229     250 ..     224     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00075
                            FAM165  26 GvK..iyQrKklEaklkkkeee 45 
                                       G+K  i QrKklE++l+k+ee+
  gi|488601687|ref|YP_007908158.1| 229 GIKrdITQRKKLEEELRKNEEK 250
                                       6655588**********99875 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 ?   10.6   0.0   0.00035      0.37      13      66 ..     375     432 ..     368     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                   Exo_endo_phos_2  13 elenlestlekllselkspkiiilGDfNakhplWgsedtds......sargeeLieflee 66 
                                       + +++ + l+++++ ++    ii+ D+N +  lW+++ ++       +  g++Lie++ +
  gi|488601687|ref|YP_007908158.1| 375 KYRETAELLQRMIDVAP--AAIIGWDLNFRVNLWNKTAEKMfewkaeEVMGRDLIELMIS 432
                                       67889999********9..89***************766658887777778888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (849 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1367  (0.0762452); expected 358.6 (0.02)
Passed bias filter:                      781  (0.0435607); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.94u 0.35s 00:00:01.29 Elapsed: 00:00:00.55
# Mc/sec: 4675.99
//
Query:       gi|488601688|ref|YP_007908159.1|  [L=120]
Description: hypothetical protein Asulf_02213 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   65.0   0.1    9.3e-18   64.7   0.1    1.1  1  DrsE      DsrE/DsrF-like family
      0.004   17.0   0.0     0.0045   16.9   0.0    1.2  1  DrsE_2    DsrE/DsrF/DrsH-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 !   64.7   0.1     1e-21   9.3e-18       1     117 []       8     120 .]       5     120 .] 0.89

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1e-21
                                       -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT......-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT CS
                              DrsE   1 kkvfilvtggpygseaarealelalaaaalg......hevsvffygdGvllllkgqtanpadeknlaellkalkeyg 71 
                                       k+vf+l+     ++   +  l la++ ++l+       ++++   g +v+l++k   a       + e+l++l+++g
  gi|488601688|ref|YP_007908159.1|   8 KVVFHLDF----DDT-PTFELSLANITNFLNdvgaetVDIALLANGFAVKLFVK-ASA-----MKFREKLEELHKQG 73 
                                       56777777....666.79999*********************************.334.....46************ PP

                                       -EEEEEHHHHHHTT--GGGE-.T-.-EEEE-HHHHHHHHHH-SEEEE- CS
                              DrsE  72 vklyvCgqaakargldededl.gv.gvevsglgelaelqnegdrvitf 117
                                       vk+yvC +a++ ++++++ d+ ++ +v+++g++ l+elq eg+++i++
  gi|488601688|ref|YP_007908159.1|  74 VKFYVCNNALNVHNISKE-DIfELcEVVPAGITKLVELQREGYAYIKP 120
                                       ****************65.554446*********************86 PP

>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     5e-07    0.0045      91     135 ..      55      99 ..       5     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-07
                                       HHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-EE CS
                            DrsE_2  91 kekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgvei 135
                                        ++ +++ +e le+ +++gvk++ C+ ++++ +++ke++++  e+
  gi|488601688|ref|YP_007908159.1|  55 VKASAMKFREKLEELHKQGVKFYVCNNALNVHNISKEDIFELCEV 99 
                                       67788999999***************************9986544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.55u 0.39s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 642.54
//
Query:       gi|488601689|ref|YP_007908160.1|  [L=257]
Description: putative metal-dependent hydrolases with the TIM-barrel fold [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-15   56.6   0.3    8.3e-15   54.8   0.3    1.9  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
      0.041   13.2   0.3       0.12   11.6   0.3    1.7  1  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.3   9.3e-19   8.3e-15      44     161 ..      59     174 ..       8     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 9.3e-19
                                       HHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHH CS
                        TatD_DNase  44 vlelakkypnkvyavlGiHPnevdeasedlleelkelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlA 120
                                         +  +++ ++ ++ +GiHP     + ++ll  ++++  ++ sk+v+iGe+GLD + +     +  eev+ eql++A
  gi|488601689|ref|YP_007908160.1|  59 HCKRLEEFGINAHIFVGIHPRCTPPEWKKLLPVIENY--IESSKAVGIGEVGLDSM-S-----KTEEEVLSEQLKIA 127
                                       344455689999********88887777888888888..****************4.3.....3689********** PP

                                       HHTTEEEEEEEES.....-HHHHHHHHHHCG.GCCSEEEETT--S-H CS
                        TatD_DNase 121 kelklplviHlrk.....aeedlleilkeaa.eakakvvlHsfsgsa 161
                                       +e++ p+++H        a e++++i+k+ + + +  v+ H  s ++
  gi|488601689|ref|YP_007908160.1| 128 REYDVPVIVHIPMverikAVEKVISIAKSIEmDFGKLVIDHTSSDTI 174
                                       ***********9988999999********987777455556544444 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   1.4e-05      0.12       6     164 ..       7     152 ..       6     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                                       EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH....HHHHHHHHHHTSSSEEE CS
                      Amidohydro_1   6 lIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst....giealleaaeelplglr 78 
                                       l+D+H+H++   +         +p+ +++ +    i+  +   + + a++++t ++      +   + +ee  ++ +
  gi|488601689|ref|YP_007908160.1|   7 LVDSHTHAY---M---------LPKKDLELMGLAKIVDVVLCSFVPLAKHIETLIDhfeeLYSIHCKRLEEFGINAH 71 
                                       577777775...2.........4555555555555555555555555555555555333333333345555555888 PP

                                       EEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE.. CS
                      Amidohydro_1  79 ilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa.. 152
                                       i++g        + + + +++kl++ +++ i   ++++v   +++  +   +++e l+e lk a+++d+pv +H+  
  gi|488601689|ref|YP_007908160.1|  72 IFVG------IHPRCTPPEWKKLLPVIENYIE--SSKAVGiGEVGLDSMSKTEEEVLSEQLKIAREYDVPVIVHIpm 140
                                       8888......8899999999***999988887..77788878999999999999********************988 PP

                                       TSSCHHHHHHHH CS
                      Amidohydro_1 153 letkgevedaea 164
                                        e  ++ve ++ 
  gi|488601689|ref|YP_007908160.1| 141 VERIKAVEKVIS 152
                                       888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1432.30
//
Query:       gi|488601690|ref|YP_007908161.1|  [L=117]
Description: hypothetical protein Asulf_02215 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-07   31.0   1.7    1.8e-06   28.0   1.7    2.0  1  DUF2250   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   1.7     1e-10   1.8e-06       5      89 ..       9     107 ..       5     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1e-10
                           DUF2250   5 eedelalkvlkhlkkanvdYaksiake.....leipleevrellkkLeelGLlervegk.........tikrteakl 67 
                                       + +el+ kv+ h+ + ++d +k+++++     ++++l+  ++ + kL e GL+++  gk         +ik + + +
  gi|488601690|ref|YP_007908161.1|   9 NLSELQKKVILHFLTFGPDTPKLMSRRllgvkTHVDLQILEKDCLKLCEKGLIKKIAGKkvpkrvptsSIKPHIKIR 85 
                                       56778899****************9863333379999999*************976654111222222677777767 PP

                           DUF2250  68 KkksevhkhHtYYrltreGell 89 
                                        k++e ++h +Y++lt +G+++
  gi|488601690|ref|YP_007908161.1|  86 AKSKEIRRHGQYFELTHRGKQV 107
                                       779****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 00:00:00.53
# Mc/sec: 665.70
//
Query:       gi|488601691|ref|YP_007908162.1|  [L=382]
Description: succinyl-CoA synthetase (ADP-forming) beta subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  229.4   5.3    4.5e-68  228.8   5.3    1.3  1  ATP-grasp_2  ATP-grasp domain
    8.9e-20   71.1   0.2      2e-19   69.9   0.2    1.6  1  Ligase_CoA   CoA-ligase
    7.9e-16   58.2   0.3    1.4e-15   57.4   0.3    1.4  1  ATP-grasp_5  ATP-grasp domain
    1.8e-07   31.1   1.7    4.5e-07   29.8   1.7    1.6  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
    7.8e-05   22.3   1.5    0.00094   18.8   0.5    2.2  2  ATP-grasp    ATP-grasp domain
    0.00015   21.3   0.2    0.00025   20.6   0.2    1.3  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
  ------ inclusion threshold ------
        0.2   11.6   1.7       0.88    9.6   0.2    2.7  3  Mistic       Membrane-integrating protein Mistic


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.8   5.3   1.8e-71   4.5e-68       1     202 []       2     194 ..       2     194 .. 0.99

  Alignments for each domain:
  == domain 1  score: 228.8 bits;  conditional E-value: 1.8e-71
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellg 77 
                                       +l+Eyqake ++k+g+k+p++++a++ +e+ee+ak+lg+  +v+K+Qvl+GGRGKagG+  +++++ea e+akel+g
  gi|488601691|ref|YP_007908162.1|   2 KLYEYQAKEFFSKHGIKIPKSKLATDVNEVEEIAKELGK--VVLKSQVLVGGRGKAGGILKAQDVSEAVEKAKELFG 76 
                                       69***********************************96..57********************************** PP

                                       SEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB- CS
                       ATP-grasp_2  78 kelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl 154
                                       k+++       G +vek+lvee+ldi++E+Y++i+lDra+k++v+i+Ss GG+diEe+a k+P+ki k ++ p++gl
  gi|488601691|ref|YP_007908162.1|  77 KDIK-------GFRVEKILVEEMLDIEREMYVGITLDRANKGIVIILSSVGGMDIEEIAIKHPDKISKKVVSPVWGL 146
                                       ****.......****************************************************************** PP

                                       -HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEE CS
                       ATP-grasp_2 155 keeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLvv 202
                                       +++q+re++ + g++ke++k++++iikkly++fv+++a+l EiNPLvv
  gi|488601691|ref|YP_007908162.1| 147 RDYQIRELLYESGMPKEYFKEVSSIIKKLYEIFVKYEAELTEINPLVV 194
                                       **********************************************96 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.2   7.8e-23     2e-19       2     152 ..     253     375 ..     252     376 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 7.8e-23
                                       ESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEE CS
                        Ligase_CoA   2 vnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvil 78 
                                        nG+++++ +mdli ++              g+++++++d+G++a            + + + ++ +++dp+v+v++
  gi|488601691|ref|YP_007908162.1| 253 ANGAGMSMSTMDLIYLE--------------GGKPANFLDIGGGAS----------AELVETSINLITSDPSVRVVF 305
                                       69***************..............***************..........7******************** PP

                                       EEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHHH CS
                        Ligase_CoA  79 ldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraaka 152
                                       ++i++G+ +++ +a++l+ka++++k    ++pvv r+aGt+++  + +  a+ ++++ v+++  ++ ++ a+ka
  gi|488601691|ref|YP_007908162.1| 306 INIFGGITRCDVVAEGLIKAFNKIK---IDIPVVLRLAGTNEE-EGKEMIAEFMKSSDVKLYMVDTMEEGAKKA 375
                                       *************************...***************.555667778888888888777777666665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.3   5.5e-19   1.4e-15      10     222 .]       3     209 ..       1     209 [. 0.86

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 5.5e-19
                       ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeile 86 
                                       L+e++ake ++  gi++++++la++++e+ e+a+e+g +vvlK ++  +  + ++gG+      a++v +a+e+ +e
  gi|488601691|ref|YP_007908162.1|   3 LYEYQAKEFFSKHGIKIPKSKLATDVNEVEEIAKELG-KVVLKSQVL-VGGRGKAGGILK----AQDVSEAVEKAKE 73 
                                       99**********************************9.9****9864.778999999877....8888888888888 PP

                       ATP-grasp_5  87 rvkekspeariegvlVqemakrggrElivgvteDp.vFGpvilfGl.GGtavevlkdvavalpplnstlareliert 161
                                        + +  ++ r+e++lV+em +  +rE+ vg+t D    G vi++   GG+ +e     a+++p   s+++ + +  +
  gi|488601691|ref|YP_007908162.1|  74 LFGKDIKGFRVEKILVEEMLD-IEREMYVGITLDRaNKGIVIILSSvGGMDIEE---IAIKHPDKISKKVVSPVWGL 146
                                       88888899***********99.89**********72569998776549999996...56888888888888877777 PP

                       ATP-grasp_5 162 kaskllkg..vrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeeg.vvalDarirl 222
                                       + +++ +    +g +k   +++++++ +l ++ v++ e +  +inPl+v+++g ++a+D+r+++
  gi|488601691|ref|YP_007908162.1| 147 RDYQIRELlyESGMPKEYFKEVSSIIKKLYEIFVKY-EAELTEINPLVVTRSGeILAADGRLNI 209
                                       777776655346777899*****************5.668889********988*******986 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 !   29.8   1.7   1.8e-10   4.5e-07       6      90 ..       8      94 ..       5     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.8e-10
                                      HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-....EEEESSHHHHHHHHHHHCTS-TTCCCC CS
                            GARS_A  6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKg....vivakseeealkavkeilekkkfGeag 80
                                      ak++++k+gi++++ +  td++e++e+ +e+++ + V+K++ l +g+g    +  a++++ea++ +ke++ k   G   
  gi|488601691|ref|YP_007908162.1|  8 AKEFFSKHGIKIPKSKLATDVNEVEEIAKELGK-V-VLKSQVLVGGRGkaggILKAQDVSEAVEKAKELFGKDIKGFRV 84
                                      79************************9999886.4.7******999852222566799********************* PP

                                      SSEEEEE--- CS
                            GARS_A 81 ekvviEelle 90
                                      ek+++Ee+l+
  gi|488601691|ref|YP_007908162.1| 85 EKILVEEMLD 94
                                      ********97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.5   3.7e-07   0.00094       2     104 ..      13     127 ..      12     141 .. 0.78
   2 ?    2.2   0.0     0.047   1.2e+02      66     106 ..     174     216 ..     157     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.7e-07
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEE.EECTCCGHHCHHHHC...........GTTCE CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqs.vvrseedleqaleal...........keekv 66 
                                       +k+g+++p+  ++++ +e+ee+a+elg  vv+K++ +   G+G+   + +++d+++a+e +           + ek+
  gi|488601691|ref|YP_007908162.1|  13 SKHGIKIPKSKLATDVNEVEEIAKELGK-VVLKSQ-VLVGGRGKAgGILKAQDVSEAVEKAkelfgkdikgfRVEKI 87 
                                       689***********************96.688854.44566666533556667777777666889***9999999** PP

                                       EEEE----SEEEEE..EEEEETTC-EEE--EEEEEEETTE CS
                         ATP-grasp  67 ivEefvpfekElsv..lvvrsaeGetafypvvetvqedgi 104
                                       +vEe+ + e+E+ v     r+ +G + ++  v+ +  ++i
  gi|488601691|ref|YP_007908162.1|  88 LVEEMLDIEREMYVgiTLDRANKGIVIILSSVGGMDIEEI 127
                                       ***********86521444788888888888877776665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.047
                                       EEEEE----SEEEEEE..EEEETTC-EEE--EEEEEEETTEEE CS
                         ATP-grasp  66 vivEefvpfekElsvl..vvrsaeGetafypvvetvqedgilr 106
                                        + E fv++e El+ +   v +++Ge+ + +   ++ ++  +r
  gi|488601691|ref|YP_007908162.1| 174 KLYEIFVKYEAELTEInpLVVTRSGEILAADGRLNIDDNALYR 216
                                       56799*********99444668888887777777776666665 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 !   20.6   0.2   9.7e-08   0.00025       4     110 ..       7     114 ..       5     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.7e-08
                                       HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTE..EE..ESSHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   4 sakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGm..rv..arneeelaelvkkalaeaka 76 
                                       +ake  +k ++++ +s+ a  ++++e+ +iake+g  v++k+ + +GG+G   ++  a++ +e +e +k+ + +   
  gi|488601691|ref|YP_007908162.1|   7 QAKEFFSKHGIKIPKSKLA--TDVNEVEEIAKELGK-VVLKSQVLVGGRGKagGIlkAQDVSEAVEKAKELFGKDIK 80 
                                       578888999999*999999..9*************5.999********99532442234444555555555666778 PP

                                       HHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEE CS
                       CPSase_L_D2  77 afgnkqvlvekslkgpkeiEvevlrDakgnvitv 110
                                        f  +++lve++l+  +e+ v +  D+++  i++
  gi|488601691|ref|YP_007908162.1|  81 GFRVEKILVEEMLDIEREMYVGITLDRANKGIVI 114
                                       9********************9999987665543 PP

>> Mistic  Membrane-integrating protein Mistic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00034      0.88      37      69 ..      62      95 ..      57      99 .. 0.85
   2 ?   -0.9   0.0      0.64   1.6e+03      17      33 ..     320     336 ..     315     353 .. 0.81
   3 ?   -2.6   0.0       2.1   5.5e+03       9      22 ..     365     378 ..     364     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                                      HHHHHHHHHHHHHTSSSS-HHHHHHH.HHHHHHT CS
                            Mistic 37 eevleaiekAkekYGeevvnkKiNti.vkevLsf 69
                                      ++v ea+ekAke +G+++   ++ +i v+e+L +
  gi|488601691|ref|YP_007908162.1| 62 QDVSEAVEKAKELFGKDIKGFRVEKIlVEEMLDI 95
                                      799***************9999998746788875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.64
                                       HHHHHH--SSS-SS-SS CS
                            Mistic  17 dafieLYNeseedkpli 33 
                                       + +i+ +N+ + d p++
  gi|488601691|ref|YP_007908162.1| 320 EGLIKAFNKIKIDIPVV 336
                                       55799999999999986 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
                                       HHTTTHHHHHHHHH CS
                            Mistic   9 iDkmnegldafieL 22 
                                       +D+m+eg    +eL
  gi|488601691|ref|YP_007908162.1| 365 VDTMEEGAKKAVEL 378
                                       799***99887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2194.47
//
Query:       gi|488601692|ref|YP_007908163.1|  [L=290]
Description: succinyl-CoA synthetase (ADP-forming) alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  106.1   1.6    1.1e-30  106.1   1.6    1.9  2  CoA_binding    CoA binding domain
      3e-17   62.9   0.6    5.4e-17   62.0   0.6    1.4  1  Ligase_CoA     CoA-ligase
    1.8e-08   34.3   0.2    4.4e-08   33.0   0.1    1.7  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    2.8e-06   27.8   0.0    9.3e-06   26.1   0.0    1.9  2  CoA_binding_2  CoA binding domain
     0.0081   15.7   0.1      0.015   14.9   0.1    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   1.6   3.1e-34   1.1e-30       1      96 []       6      99 ..       6      99 .. 0.99
   2 ?   -1.6   0.1       1.3   4.6e+03      32      39 ..     174     181 ..     144     208 .. 0.62

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 3.1e-34
                                      CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding  1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeav 79
                                      d++tk iv+G++g   +g +h k++l+yg+++v+gv+p+k+g ev+g+pv+++v+e++e+t ++++vi+vP+++a +av
  gi|488601692|ref|YP_007908163.1|  6 DENTKAIVQGITGY--QGSFHAKRMLDYGTNIVGGVTPGKGGMEVHGIPVFNTVKEAVEETSANASVIFVPPAFASDAV 82
                                      689***********..*************************************************************** PP

                                      HHHHHTT-SEEEEESST CS
                       CoA_binding 80 delveagikgiviiteg 96
                                       e+v+ gi+++v+iteg
  gi|488601692|ref|YP_007908163.1| 83 FEAVDSGIEVVVCITEG 99
                                      ***************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                       EEEEC-TT CS
                       CoA_binding  32 avfgvnpr 39 
                                        v+g++++
  gi|488601692|ref|YP_007908163.1| 174 TVVGIGGD 181
                                       44444433 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.6   1.5e-20   5.4e-17       1     152 [.     151     271 ..     151     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 1.5e-20
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++++GtL+y  ++ +++               g +q++++++G+d+           ++++i+ lkk+ +d++++++
  gi|488601692|ref|YP_007908163.1| 151 VSRSGTLTYQIAYNLTNF--------------GIGQSTVVGIGGDRII---------GSDFIDILKKFEKDDQTEIV 204
                                       689***************..............***************8.........******************** PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraaka 152
                                       +l +++G ga e+ aae+++   e+      +pvv ++aG +a+p++++++a+a+ e+g  +a+sk +al+ a++
  gi|488601692|ref|YP_007908163.1| 205 VLVGEIG-GADEENAAEFIAS--EMS-----KPVVGYIAGITAPPGKRMGHAGAIIEGGKGTAESKIKALEKAGV 271
                                       *******.*********9964..333.....6*************************************999875 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         1   3.6e+03      51      66 ..      86     101 ..      81     112 .. 0.82
   2 !   33.0   0.1   1.2e-11   4.4e-08       2     106 ..     146     251 ..     145     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                      Succ_CoA_lig  51 edpetkvillylEsir 66 
                                        d+ ++v+++  E+i 
  gi|488601692|ref|YP_007908163.1|  86 VDSGIEVVVCITEGIP 101
                                       5889999999999996 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 1.2e-11
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsirdgrkflsaar 76 
                                       G+++++s SG+l  +++  +++ g+g s+vv +G    +  d+ d+l+ +++d++t++++l+ E  +  ++ ++   
  gi|488601692|ref|YP_007908163.1| 146 GSVGIVSRSGTLTYQIAYNLTNFGIGQSTVVGIGGdrIIGSDFIDILKKFEKDDQTEIVVLVGEIGGADEENAAEFI 222
                                       99********************************833466799*******************998877777666666 PP

                      Succ_CoA_lig  77 raarkkpvvvlksGrseagaraaashtgal 106
                                       +   +kpvv + +G ++   +  + h ga+
  gi|488601692|ref|YP_007908163.1| 223 ASEMSKPVVGYIAGITAPPGKR-MGHAGAI 251
                                       66667****9999986544333.3455554 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.6e-09   9.3e-06      25     114 ..      30     128 ..      18     130 .. 0.83
   2 ?   -2.9   0.0       2.5   9.1e+03      59      65 ..     271     277 ..     244     288 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.6e-09
                                       HHT--EE.EESSS-..SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---H CS
                     CoA_binding_2  25 ehglpvv.pVnpke..eeilgekvyaslaed..pepvdlvdvftppeatpeivkealalgakavwlqpg....sede 92 
                                       + g ++v  V+p +   e++g +v+ +++e+  ++   + ++f+pp+ + + v ea++ g+++v++  +      + 
  gi|488601692|ref|YP_007908163.1|  30 DYGTNIVgGVTPGKggMEVHGIPVFNTVKEAveETSANASVIFVPPAFASDAVFEAVDSGIEVVVCITEgipvHDEL 106
                                       55555442488888778************8446788889****************************9999766666 PP

                                       HHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  93 eaaelaeeagirvvgdrCilve 114
                                       +++ +++e++  ++g++C++++
  gi|488601692|ref|YP_007908163.1| 107 KLYWKVREKNAVLIGPNCPGII 128
                                       78888999***********997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                                       EEE-S-H CS
                     CoA_binding_2  59 vdvftpp 65 
                                       v v + p
  gi|488601692|ref|YP_007908163.1| 271 VRVGRTP 277
                                       3444444 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 !   14.9   0.1   4.1e-06     0.015      12     121 ..      17     126 ..       4     131 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.1e-06
                                       -SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT..-SEEEE-S-HHHHHHHHHHHTGGG-- CS
                              IlvN  12 yGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkk..advvmiliPDelqkevyeeeiepnlk 86 
                                        G qG  +a+ + d g ++v g+  g+  ++      f++  v+eav++  a+  +i +P  + ++ + e++   ++
  gi|488601692|ref|YP_007908163.1|  17 TGYQGSFHAKRMLDYGTNIVGGVTPGKGGMEVHGIPVFNT--VKEAVEEtsANASVIFVPPAFASDAVFEAVDSGIE 91 
                                       489************************7776655555544..45555432255556666766666555588988886 PP

                                       TT-EEEESSSHHHHTT..SS---TTSEEEEEEESS-S CS
                              IlvN  87 egkalafahGfnihfg..likppkdvdvvlvAPkgpG 121
                                          ++  + G  +h +  l    ++ + vl+ P +pG
  gi|488601692|ref|YP_007908163.1|  92 V--VVCITEGIPVHDElkLYWKVREKNAVLIGPNCPG 126
                                       5..5566778888765113444556678889999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1630.08
//
Query:       gi|488601693|ref|YP_007908164.1|  [L=562]
Description: succinate dehydrogenase subunit A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-116  388.7   0.1   4.5e-116  388.4   0.1    1.1  1  FAD_binding_2   FAD binding domain
    4.6e-44  149.5   0.0    8.2e-44  148.7   0.0    1.4  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    8.6e-09   35.0   0.9    5.1e-05   22.7   0.8    3.0  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.9e-06   26.6   1.4      0.013   14.6   1.4    2.3  2  GIDA            Glucose inhibited division protein A
    1.1e-05   25.0   1.9      0.041   13.2   2.3    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
      0.008   15.8   0.9       0.27   10.8   0.1    2.7  2  DAO             FAD dependent oxidoreductase
     0.0089   15.3   0.8      0.095   11.9   0.2    2.6  3  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.074   12.1   0.4       0.11   11.5   0.4    1.2  1  Lycopene_cycl   Lycopene cyclase protein
       0.12   12.7   2.1        0.2   12.0   0.7    1.9  2  DUF5517         Family of unknown function (DUF5517)
       0.13   10.9   6.1       0.16   10.6   0.8    3.0  4  HI0933_like     HI0933-like protein
       0.38   10.0   3.3        3.1    7.0   0.5    3.0  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.45    9.8   2.3        0.5    9.6   0.5    1.9  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.4   0.1    3e-119  4.5e-116       1     416 [.       6     384 ..       6     385 .. 0.99

  Alignments for each domain:
  == domain 1  score: 388.4 bits;  conditional E-value: 3e-119
                                       SEEEE--SHHHHHHHHHHHH..TTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaae..aGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkalde 75 
                                       D++++G+GlAG++AA++aae  + l++a+v+k+ + ++++++++Gg +av        +++ds +lh++dt+k++d 
  gi|488601693|ref|YP_007908164.1|   6 DIVIVGAGLAGMRAAIAAAEvsKQLSIAIVSKTYPIRCHSVCAEGGTAAVM-------REGDSFDLHAWDTVKGADF 75 
                                       99******************86666**************************.......457**************** PP

                                       -S-HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHH CS
                     FAD_binding_2  76 ladqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesar 152
                                       ladq++ve+fv+++p+++  L ++g+p+srtedg++++r++Gg+s + rt++ aad+      tg++ +++l+e+++
  gi|488601693|ref|YP_007908164.1|  76 LADQDAVEFFVKEMPREILLLDNWGCPWSRTEDGKIAQRPFGGHSFN-RTVF-AADR------TGFHEVHTLYERML 144
                                       ***********************************************.****.****......************** PP

                                       TCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-H CS
                     FAD_binding_2 153 kag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGd 228
                                       +++ ++ ++++++++L++e+++v G+++ +++s++ v ++akav++atgG+gr           +  tt  ++vtGd
  gi|488601693|ref|YP_007908164.1| 145 SYPnITRFDEYFMTNLVIENNEVKGITAIELKSSELVLFEAKAVIIATGGAGR----------LFGFTTYSHTVTGD 211
                                       *****************************************************..........************** PP

                                       HHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHHH CS
                     FAD_binding_2 229 glalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsra 298
                                       gla+a+rag++l+d  me++qfhPt+l+    +sgiL+tea+rgeGg+l++++G+rFm       +ela+rdvv+r+
  gi|488601693|ref|YP_007908164.1| 212 GLAVAYRAGVPLKD--MEFFQFHPTGLI----PSGILMTEACRGEGGYLLNSKGERFMeryaperMELAPRDVVARS 282
                                       **************..************....********************************************* PP

                                       HH.HHHHTTTS.....CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEE CS
                     FAD_binding_2 299 ilekeiaeggs.....eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqh 370
                                       ++ +ei eg++     ++++ ld++h l++e+++++l+ i+++a+++++      +dp ++pip       v+p +h
  gi|488601693|ref|YP_007908164.1| 283 MW-TEILEGRGlkspyGDYIALDLTH-LGEEKINERLPLIRDAAIKFAG------VDPVEEPIP-------VKPVAH 344
                                       **.999999999****9*********.**********************......*********.......****** PP

                                       EES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHH CS
                     FAD_binding_2 371 ytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGns 416
                                       ytmgG++t+  +++      p+ GLYAaGe+ ++++hganrlg+ns
  gi|488601693|ref|YP_007908164.1| 345 YTMGGIHTNMYCET------PVRGLYAAGEAGCVSIHGANRLGSNS 384
                                       **************......*************************8 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   0.0   5.5e-47   8.2e-44       2     128 .]     438     562 .]     437     562 .] 0.98

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 5.5e-47
                                       HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-B CS
                    Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESr 78 
                                       +eL+k+m+++  +fR+e+g+ +a+k++kel+er+knv+v+d++k +N++l+ a+e+  +l+lAe++a +Al+RkESr
  gi|488601693|ref|YP_007908164.1| 438 TELNKTMDENLWIFRDEQGIMNAIKKIKELKERYKNVGVSDRGKSFNTDLTYAIEVGYMLDLAEVVAIGALNRKESR 514
                                       69*************************************************************************** PP

                                       TTBEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                    Succ_DH_flav_C  79 GaHaredfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                       GaH+r+d+p+rdDenwlkhtla+++++   +++ey pv++++ +p eR+Y
  gi|488601693|ref|YP_007908164.1| 515 GAHFRTDYPKRDDENWLKHTLAYYTPE--GPKFEYIPVTITKWEPVERKY 562
                                       **********************88866..9*******************9 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.8   3.4e-08   5.1e-05       2     115 ..       6     200 ..       5     218 .. 0.65
   2 !    7.8   0.0    0.0011       1.7     233     276 ..     326     368 ..     294     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.4e-08
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHH..HCHHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcll..skallgvaedaeias................. 57 
                                       d+v++G+G AG++aa+ +a+  +++ +++v   +t + +  ++      ++v+++++ +                  
  gi|488601693|ref|YP_007908164.1|   6 DIVIVGAGLAGMRAAIAAAEvsKQLSIAIV--SKTYPIRCHSVcaEGGTAAVMREGDSFDlhawdtvkgadfladqd 80 
                                       89******************999*******..444444422221133444444444444477788888888888888 PP

                                       ........................................................................HHHHC CS
                                       ........................................................................xxxxx RF
                       Pyr_redox_2  58 ........................................................................evvkk 62 
                                                                                                               +    
  gi|488601693|ref|YP_007908164.1|  81 aveffvkempreillldnwgcpwsrtedgkiaqrpfgghsfnrtvfaadrtgfhevhtlyermlsypnitrfD---- 153
                                       8888889999999999999999999999999999998888888888888877766665554444442221111.... PP

                                       HHHHCCCCHCCTCEEEEESCEEEEETEEEC..........TCEEEEEESEEEE---EEE-BCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  63 lnqgielllgeevvkidpgkkkvklekkke..........gdeekiaydklvlAtGssprdlg 115
                                         + +        +++  ++ +                  ++   ++++++++AtG+  r++g
  gi|488601693|ref|YP_007908164.1| 154 --EYF-------MTNLVIENNE-------VkgitaielksSELVLFEAKAVIIATGGAGRLFG 200
                                       ..111.......1111111111.......1122222233255556788999999998888775 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                                       E-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 233 vavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGD 276
                                         +Gv p  e ++    ++    ggi ++ +++t v g+ya+G 
  gi|488601693|ref|YP_007908164.1| 326 KFAGVDPVEEPIP-VKPVAHYTMGGIHTNMYCETPVRGLYAAGE 368
                                       5667777777764.334555568********************7 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.4   8.6e-06     0.013       1      24 [.       6      29 ..       6      61 .. 0.83
   2 !    9.7   0.0   0.00027       0.4      84     150 ..     120     194 ..     110     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.6e-06
                                      CEEEE-SSHHHHHHHHHHHHTT-- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGak 24
                                      d++++G+G+AG+ AA+aaa+   +
  gi|488601693|ref|YP_007908164.1|  6 DIVIVGAGLAGMRAAIAAAEVSKQ 29
                                      79*****************97655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00027
                                       CC-EEEEEE-HHHHHH..HHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEE...ETTS-..EEEECEEEE--TT CS
                              GIDA  84 avralraqvdrelysk..evteklenepnleiiee.eveeliveekkvkgvv...tedge..tikakavviatGt 150
                                       + + +  ++dr  +++  ++ e++ ++pn++ + e  +++l++e+++vkg++   +++ e   ++akav+iatG 
  gi|488601693|ref|YP_007908164.1| 120 SFNRTVFAADRTGFHEvhTLYERMLSYPNITRFDEyFMTNLVIENNEVKGITaieLKSSElvLFEAKAVIIATGG 194
                                       5566667889999886224457788889999876626899*****9999976222333331157899*******8 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.3   2.7e-05     0.041       1      23 [.       6      28 ..       6      38 .. 0.86
   2 !    9.2   0.0   0.00046      0.68      89     145 ..     136     194 ..     105     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.7e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGa 23
                                      D+v+vG+g+aG+ AAiaAa+  +
  gi|488601693|ref|YP_007908164.1|  6 DIVIVGAGLAGMRAAIAAAEVSK 28
                                      9******************8655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00046
                      FAD_oxidored  89 akavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATgd 145
                                       + +++e ml+ +++t + + ++++ + e+++++++t+ + +      ++Ak +i ATg 
  gi|488601693|ref|YP_007908164.1| 136 VHTLYERMLSYPNITRFDEYFMTNLVIENNEVKGITAIELKsSeLVLFEAKAVIIATGG 194
                                       56899*********************998776666555444334************974 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00018      0.27       1      29 [.       6      38 ..       6     101 .. 0.85
   2 ?    3.2   0.1     0.037        55     163     207 ..     161     199 ..     155     377 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                      EEEEECTSHHHHHHHHHHHHTT....EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg....Vtllekg 29
                                      d+vi+G+G +G+ +A ++a+      ++++ k 
  gi|488601693|ref|YP_007908164.1|  6 DIVIVGAGLAGMRAAIAAAEVSkqlsIAIVSKT 38
                                      9*****************886446889999887 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.037
                                       EEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHHHH CS
                               DAO 163 ilegtevtgleeedgkvwgverttp.gen.daadavVnaaGawsdll 207
                                       ++e+ ev+g+      + ++   ++ + + ++a+av++a+G   +l+
  gi|488601693|ref|YP_007908164.1| 161 VIENNEVKGIT-----AIEL---KSsELVlFEAKAVIIATGGAGRLF 199
                                       45666777762.....2223...333666668899****99764444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2   6.4e-05     0.095      17      49 ..       4      37 ..       2      52 .. 0.88
   2 ?   -0.4   0.0      0.38   5.7e+02     102     142 ..     138     173 ..     125     206 .. 0.68
   3 ?   -1.1   0.0       0.6   8.9e+02     212     233 ..     360     382 ..     355     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                                      EEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakk.pdlkvailer 49
                                        D+vivGaG +G+ aa   a+   +l +ai+ +
  gi|488601693|ref|YP_007908164.1|  4 RNDIVIVGAGLAGMRAAIAAAEVsKQLSIAIVSK 37
                                      57***************99998878899999865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.38
                                       HHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHH CS
                              Thi4 102 tllskvlqlanvkllnavaveDlivregegvaGvvinwtlv 142
                                       tl  ++l  +n+  ++   + +l++ + ++v+G+     ++
  gi|488601693|ref|YP_007908164.1| 138 TLYERMLSYPNITRFDEYFMTNLVIEN-NEVKGIT----AI 173
                                       777888888888888888888888888.7777763....33 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.6
                                       ETTEEE-THH.HHHHHT-EB--S CS
                              Thi4 212 vpnlyvaGme.vaevdganRmGp 233
                                       v +ly+aG +    ++ganR+G+
  gi|488601693|ref|YP_007908164.1| 360 VRGLYAAGEAgCVSIHGANRLGS 382
                                       7899***98735689******96 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   7.6e-05      0.11       1      30 [.       6      35 ..       6      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.6e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                      D+v++GaG+Ag++ A   +e  ++l++ ++
  gi|488601693|ref|YP_007908164.1|  6 DIVIVGAGLAGMRAAIAAAEVSKQLSIAIV 35
                                      9**************999999999999999 PP

>> DUF5517  Family of unknown function (DUF5517)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         2     3e+03      27      47 ..     294     314 ..     287     320 .. 0.79
   2 ?   12.0   0.7   0.00013       0.2      24      86 ..     424     486 ..     412     497 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2
                                       EETTEEEEEEEEEETTTEEEE CS
                           DUF5517  27 rkpygsylhikieldedekle 47 
                                       + pyg y+ + +    +ek++
  gi|488601693|ref|YP_007908164.1| 294 KSPYGDYIALDLTHLGEEKIN 314
                                       469****99998777777765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00013
                                       EEEEETTEEEEEEEEEETTTEEEEEEEESTT--HHHHHHHHHHHHHHHTT--STTHHHHHHHH CS
                           DUF5517  24 tlgrkpygsylhikieldedeklekeiyadniklenelrqlkrlyevyqsveiddaqkaiqke 86 
                                       +l r    s  +ik el++    +  i+ d+  + n ++++k l e y+ v + d  k+ + +
  gi|488601693|ref|YP_007908164.1| 424 SLFREGDESVYQIKTELNKTMDENLWIFRDEQGIMNAIKKIKELKERYKNVGVSDRGKSFNTD 486
                                       456777789999******98888889*****************************99987765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   0.00011      0.16       2      26 ..       6      30 ..       5      39 .. 0.84
   2 ?    1.2   0.0      0.08   1.2e+02     143     165 ..     173     195 ..     153     203 .. 0.71
   3 ?   -2.0   0.0      0.76   1.1e+03     353     383 ..     343     368 ..     282     397 .. 0.75
   4 ?   -1.6   0.1      0.57   8.6e+02     287     328 ..     430     470 ..     412     474 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                      SEEEE--SHHHHHHHHHHHHTT--E CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrV 26
                                      d++++G+G AG+ aAi+aa+  k+ 
  gi|488601693|ref|YP_007908164.1|  6 DIVIVGAGLAGMRAAIAAAEVSKQL 30
                                      89****************8876654 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.08
                                       EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 143 frvktkseeeleadklvlAtGGl 165
                                       +++k ++   +ea+++++AtGG+
  gi|488601693|ref|YP_007908164.1| 173 IELKSSELVLFEAKAVIIATGGA 195
                                       333333444689**********7 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.76
                                       -SEEEEEE-GGGB-TTT-BBTTSTTEEE-GG CS
                       HI0933_like 353 aevTaGGVdlkevssktmeskkvpgLffaGE 383
                                       a  T+GG++++   +       v gL+ aGE
  gi|488601693|ref|YP_007908164.1| 343 AHYTMGGIHTNMYCE-----TPVRGLYAAGE 368
                                       566888887764333.....34689999998 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.57
                                       HTTTSBHHHHHTTTS-HHHHHHHHHC..TTT-TTBGGG--HH CS
                       HI0933_like 287 keskkslknalaellpkrlvevlleealieeedkklaqlskk 328
                                       +es  ++k+ l++++ ++l+ +  e+ +i ++ kk+++l+++
  gi|488601693|ref|YP_007908164.1| 430 DESVYQIKTELNKTMDENLWIFRDEQ-GIMNAIKKIKELKER 470
                                       45567999************999888.555887889888765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5    0.0021       3.1       1      21 [.       8      28 ..       8      40 .. 0.80
   2 ?    0.9   0.0      0.15   2.2e+02     122     133 ..     182     193 ..     123     206 .. 0.70
   3 ?    0.1   0.0      0.26   3.9e+02     195     276 ..     427     504 ..     409     521 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0021
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl 21
                                      +I+GaG aG+ aai++ ++  
  gi|488601693|ref|YP_007908164.1|  8 VIVGAGLAGMRAAIAAAEVSK 28
                                      7**************998754 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.15
                       Pyr_redox_3 122 tyeAkkviiAtG 133
                                        +eAk viiAtG
  gi|488601693|ref|YP_007908164.1| 182 LFEAKAVIIATG 193
                                       457777777777 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.26
                       Pyr_redox_3 195 rgseiekeesdpsyslkpdienrleelvke.ekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpd 270
                                       r+   +++ ++++ +l+ ++ ++l+   +e +   +   +++ke+ke+ +++ v +++gk+++++  + + +Gy  d
  gi|488601693|ref|YP_007908164.1| 427 REG--DESVYQIKTELNKTMDENLWIFRDEqG--IMNAIKKIKELKERYKNVGV-SDRGKSFNTDLTYAIEVGYMLD 498
                                       543..455667777777777777776665533..22333346666665555555.4456777776666666899888 PP

                       Pyr_redox_3 271 lsflkk 276
                                       l  + +
  gi|488601693|ref|YP_007908164.1| 499 LAEVVA 504
                                       765554 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   0.5   0.00034       0.5      30      56 ..       6      32 ..       3      52 .. 0.86
   2 ?   -1.5   0.1      0.83   1.2e+03       3      30 ..     374     401 ..     366     405 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                                      EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtv 56
                                       ++++G+G aG+ A+ +a+++  +  +
  gi|488601693|ref|YP_007908164.1|  6 DIVIVGAGLAGMRAAIAAAEVSKQLSI 32
                                      689*************99998877665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.83
                                       HHHHHHCSCGCTSEEETTCEETCB---E CS
                       AlaDh_PNT_C   3 leaakalekffggkgtlaGgvpgvepak 30 
                                       +++a+ l   ++++ ++ G+v g ++a+
  gi|488601693|ref|YP_007908164.1| 374 IHGANRLGSNSTAECLVFGRVAGERAAE 401
                                       5677777777777777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 3426.32
//
Query:       gi|488601694|ref|YP_007908165.1|  [L=238]
Description: succinate dehydrogenase subunit B [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  124.9   0.2    3.7e-36  123.4   0.0    1.8  2  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
    5.2e-08   33.2   7.4    5.2e-08   33.2   7.4    1.9  2  Fer4_8           4Fe-4S dicluster domain
    1.7e-07   31.3   8.0    1.7e-07   31.3   8.0    2.0  2  Fer4_10          4Fe-4S dicluster domain
    2.3e-07   31.3  21.1      2e-05   25.1  11.4    2.5  3  Fer4_7           4Fe-4S dicluster domain
    3.2e-07   29.9   1.8    3.2e-07   29.9   1.8    3.7  4  Fer4             4Fe-4S binding domain
    9.5e-07   28.6   1.7    9.5e-07   28.6   1.7    3.9  4  Fer4_6           4Fe-4S binding domain
    4.2e-06   27.6   8.6    4.2e-06   27.6   8.6    2.2  2  Fer4_16          4Fe-4S double cluster binding domain
    1.1e-05   25.5   9.4    1.1e-05   25.5   9.4    2.6  3  Fer4_9           4Fe-4S dicluster domain
    1.6e-05   25.3  17.8    0.00048   20.6   9.6    2.4  3  Fer4_17          4Fe-4S dicluster domain
    3.5e-05   23.6   1.1    3.5e-05   23.6   1.1    3.7  3  Fer4_2           4Fe-4S binding domain
    0.00012   21.9   0.1    0.00012   21.9   0.1    2.0  2  Fer2             2Fe-2S iron-sulfur cluster binding domain
     0.0012   19.1   1.2     0.0012   19.1   1.2    3.5  3  Fer4_4           4Fe-4S binding domain
     0.0066   16.6   0.1     0.0066   16.6   0.1    2.9  3  Fer4_21          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.024   14.4   0.9        0.2   11.4   0.1    2.3  2  HydF_tetramer    Hydrogen maturase F tetramerization domain
      0.029   14.9   0.5      0.029   14.9   0.5    2.7  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
      0.037   14.8   3.0       0.18   12.6   0.1    2.8  2  Fer4_15          4Fe-4S single cluster domain
      0.042   14.7   1.2      0.042   14.7   1.2    2.6  2  Fer4_22          4Fe-4S dicluster domain
       0.14   12.4   6.3       0.22   11.7   0.0    2.6  2  Fer4_18          4Fe-4S dicluster domain
        3.3    7.5   8.8          4    7.2   1.4    2.6  3  Fer4_20          Dihydroprymidine dehydrogenase domain II, 4F


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   0.0     4e-39   3.7e-36       2     108 ..       5     105 ..       4     106 .. 0.96
   2 ?   -2.5   0.2       5.5   5.2e+03      57      78 ..     195     216 ..     185     233 .. 0.63

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 4e-39
                            Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikd 78 
                                       +++kRfd     +k+ + ey v+ae+++tvl+ L +ike++d +lafrasCr giCGsca++i+G+p+laC+++i +
  gi|488601694|ref|YP_007908165.1|   5 FRIKRFDG----EKSSWAEYVVPAEKGMTVLEGLYYIKENYDGSLAFRASCRMGICGSCAMKIDGTPKLACETQILS 77 
                                       68999999....6899************************************************************* PP

                            Fer2_3  79 lakqkseieleplpkfpvirDLvvDideml 108
                                       l k+k  i++epl++f+vi+DLv+D d+++
  gi|488601694|ref|YP_007908165.1|  78 LGKSK--ITIEPLDNFKVIKDLVADFDSFF 105
                                       *9986..********************997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.5
                            Fer2_3  57 CGscavainGkptlaCtatikd 78 
                                       CG      n +   +C ++i+ 
  gi|488601694|ref|YP_007908165.1| 195 CGVWRCHFNAECSEVCPKNINP 216
                                       4443445566666666666554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.5       5.2   4.9e+03      54      58 ..      56      60 ..      49      79 .. 0.76
   2 !   33.2   7.4   5.5e-11   5.2e-08       4      65 .]     143     214 ..     140     214 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.2
                            Fer4_8 54 cgaCt 58
                                      cg+C+
  gi|488601694|ref|YP_007908165.1| 56 CGSCA 60
                                      55553 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 5.5e-11
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvlee...........eealwsCttcgaCtevCpvgi 65 
                                        Ci+CgaC s Cp+  ++ ++ l +  +aa++  +++ ++e           + ++w+C+   +C+evCp++i
  gi|488601694|ref|YP_007908165.1| 143 LCIKCGACYSVCPASATR-EDYLGPAAMAAAYRFNTDSRDEgkdirmdivcsDCGVWRCHFNAECSEVCPKNI 214
                                       6***********944443.333333333344233333322233344556666899****************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 ?   -2.4   0.7       5.6   5.3e+03      47      51 ..      53      59 ..      46      62 .. 0.59
   2 !   31.3   8.0   1.8e-10   1.7e-07       4      56 .]     139     211 ..     137     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.6
                           Fer4_10 47 g..cgaC 51
                                      +  cg+C
  gi|488601694|ref|YP_007908165.1| 53 MgiCGSC 59
                                      4445555 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 1.8e-10
                           Fer4_10   4 idddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d + Ci+Cg+C ++CPa++                    +++++k++++++   + +v++C++  +C e+CP
  gi|488601694|ref|YP_007908165.1| 139 YDYSLCIKCGACYSVCPASAtredylgpaamaaayrfntdSRDEGKDIRMDIVCSDCGVWRCHFNAECSEVCP 211
                                       78999*************99******************9777777777777777777***************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 ?   -0.8   0.1       2.6   2.4e+03      41      45 ..      56      60 ..      38      87 .. 0.75
   2 !   18.8   2.1   1.9e-06    0.0018      29      52 .]     135     158 ..     105     158 .. 0.72
   3 !   25.1  11.4   2.1e-08     2e-05       2      52 .]     144     214 ..     143     214 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.6
                            Fer4_7 41 CgaCv 45
                                      Cg+C+
  gi|488601694|ref|YP_007908165.1| 56 CGSCA 60
                                      44443 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.9e-06
                            Fer4_7  29 ekveidpekClgCgaCvavCPtga 52 
                                        + ++d++ C+ CgaC +vCP+ a
  gi|488601694|ref|YP_007908165.1| 135 LYEYYDYSLCIKCGACYSVCPASA 158
                                       334778899999999999999865 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 2.1e-08
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek.............gtekveidpekClgCg........aCvavCPtga 52 
                                       Ci+CgaC ++Cp++a + d+   ++             + +++++d   C++Cg        +C +vCP+++
  gi|488601694|ref|YP_007908165.1| 144 CIKCGACYSVCPASATREDYLGPAAmaaayrfntdsrdEGKDIRMDI-VCSDCGvwrchfnaECSEVCPKNI 214
                                       ***********999999775322221111111111212223333322.355553333333338******985 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   0.5      0.61   5.7e+02      11      16 ..      56      61 ..      55      62 .. 0.88
   2 !   29.9   1.8   3.4e-10   3.2e-07       2      22 ..     138     158 ..     137     159 .. 0.92
   3 ?   -2.3   0.5       4.9   4.7e+03       8      12 ..     192     196 ..     191     197 .. 0.82
   4 ?    5.7   0.5     0.015        14      13      21 ..     205     213 ..     204     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.61
                                      -THHHH CS
                              Fer4 11 CGaCve 16
                                      CG C++
  gi|488601694|ref|YP_007908165.1| 56 CGSCAM 61
                                      ****96 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 3.4e-10
                                       EEETTTSSS-THHHHHSTTTE CS
                              Fer4   2 videekCigCGaCvevCPvgA 22 
                                       ++d+++Ci+CGaC++vCP  A
  gi|488601694|ref|YP_007908165.1| 138 YYDYSLCIKCGACYSVCPASA 158
                                       78****************866 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.9
                                       SSS-T CS
                              Fer4   8 CigCG 12 
                                       C  CG
  gi|488601694|ref|YP_007908165.1| 192 CSDCG 196
                                       99999 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.015
                                       HHHHHSTTT CS
                              Fer4  13 aCvevCPvg 21 
                                       +C evCP +
  gi|488601694|ref|YP_007908165.1| 205 ECSEVCPKN 213
                                       6******87 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.7         2   1.9e+03       7      16 ..      49      60 ..      46      62 .. 0.71
   2 ?   -2.7   0.0       7.8   7.4e+03      18      24 .]      70      76 ..      69      76 .. 0.77
   3 !   28.6   1.7     1e-09   9.5e-07       4      23 ..     139     158 ..     138     159 .. 0.93
   4 ?   -2.0   6.6       4.7   4.5e+03      14      22 ..     205     213 ..     190     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2
                            Fer4_6  7 dkCig..CgdCv 16
                                       +C    Cg C+
  gi|488601694|ref|YP_007908165.1| 49 ASCRMgiCGSCA 60
                                      677755799996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.8
                            Fer4_6 18 vCPegai 24
                                      +C ++++
  gi|488601694|ref|YP_007908165.1| 70 ACETQIL 76
                                      7999875 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 1e-09
                            Fer4_6   4 idpdkCigCgdCvrvCPega 23 
                                       +d+++Ci Cg+C++vCP+ a
  gi|488601694|ref|YP_007908165.1| 139 YDYSLCIKCGACYSVCPASA 158
                                       799**************987 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.7
                            Fer4_6  14 dCvrvCPeg 22 
                                       +C  vCP +
  gi|488601694|ref|YP_007908165.1| 205 ECSEVCPKN 213
                                       59999*976 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.8       8.9   8.4e+03       5       9 ..      56      60 ..      48      63 .. 0.66
   2 !   27.6   8.6   4.5e-09   4.2e-06       2      67 .]     144     213 ..     143     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.9
                           Fer4_16  5 CgkCa 9 
                                      Cg Ca
  gi|488601694|ref|YP_007908165.1| 56 CGSCA 60
                                      55554 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 4.5e-09
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy.....ntaekkdlaedeekck.kqeaitgCdiCqdvCPan 67 
                                       C++Cg+C +vCP++a +e+  +   a +  +y     + +e kd++ d+   +   +++++ + C +vCP n
  gi|488601694|ref|YP_007908165.1| 144 CIKCGACYSVCPASATRED--YLGPAAMAAAYrfntdSRDEGKDIRMDIVCSDcGVWRCHFNAECSEVCPKN 213
                                       *****************99..3333333333333334666778888777554434699************88 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   1.4       2.8   2.6e+03      36      43 ..      51      60 ..      32      76 .. 0.72
   2 ?   -2.3   1.8       5.6   5.3e+03      39      43 ..      56      60 ..      48      84 .. 0.71
   3 !   25.5   9.4   1.1e-08   1.1e-05       2      49 ..     144     213 ..     143     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.8
                            Fer4_9 36 Cig..CgaCv 43
                                      C +  Cg+C+
  gi|488601694|ref|YP_007908165.1| 51 CRMgiCGSCA 60
                                      4333466664 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.6
                            Fer4_9 39 CgaCv 43
                                      Cg+C+
  gi|488601694|ref|YP_007908165.1| 56 CGSCA 60
                                      44443 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 1.1e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                                       C++CgaC ++Cpa +++ed  +  a   a++                       ++C++  +C e+Cpk+
  gi|488601694|ref|YP_007908165.1| 144 CIKCGACYSVCPASATREDYLGPAAMAAAYRFntdsrdegkdirmdivcsdcgvWRCHFNAECSEVCPKN 213
                                       *********************9999998888899************7666666666666666******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 ?   -1.9   0.7       5.3     5e+03      49      53 ..      56      60 ..      46      74 .. 0.71
   2 !   16.9   1.1   7.6e-06    0.0071      32      58 ..     130     156 ..     108     159 .. 0.76
   3 !   20.6   9.6   5.1e-07   0.00048       2      61 .]     144     215 ..     143     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.3
                           Fer4_17 49 CgeCe 53
                                      Cg C+
  gi|488601694|ref|YP_007908165.1| 56 CGSCA 60
                                      44443 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 7.6e-06
                           Fer4_17  32 glleeaekeekaslCieCgeCerkCPq 58 
                                       ++ ee  +    slCi+Cg C ++CP+
  gi|488601694|ref|YP_007908165.1| 130 QKPEELYEYYDYSLCIKCGACYSVCPA 156
                                       455666667889**************7 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 5.1e-07
                           Fer4_17   2 CiqCgyClpeCpsyeaydne..pkkllraakl....glleeaeke......ekaslCieCgeCerkCPqgld 61 
                                       Ci+Cg+C  +Cp  + ++++  p+ +++a+++     + ++ +++      + + +C+   eC+++CP++++
  gi|488601694|ref|YP_007908165.1| 144 CIKCGACYSVCPASATREDYlgPAAMAAAYRFntdsRDEGKDIRMdivcsdCGVWRCHFNAECSEVCPKNIN 215
                                       ************9998777544666665555544542233334446777768999**************985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.9      0.53     5e+02       9      17 ..      50      60 ..      46      62 .. 0.71
   2 !   23.6   1.1   3.7e-08   3.5e-05       4      22 .]     138     156 ..     135     156 .. 0.93
   3 ?    0.4   5.2      0.93   8.8e+02      10      21 ..     192     211 ..     187     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.53
                            Fer4_2  9 rCig..CgaCv 17
                                      +C    Cg+C 
  gi|488601694|ref|YP_007908165.1| 50 SCRMgiCGSCA 60
                                      67433799995 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 3.7e-08
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                       ++d   Ci CgaC+s+CPa
  gi|488601694|ref|YP_007908165.1| 138 YYDYSLCIKCGACYSVCPA 156
                                       7999**************8 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.93
                            Fer4_2  10 CigCg........aCvsaCP 21 
                                       C  Cg         C  +CP
  gi|488601694|ref|YP_007908165.1| 192 CSDCGvwrchfnaECSEVCP 211
                                       88887776778888999999 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 !   21.9   0.1   1.3e-07   0.00012      10      75 ..      22      73 ..      14      76 .. 0.74
   2 ?   -2.4   0.6       4.9   4.7e+03      39      44 ..     146     151 ..     143     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                                      EEEETTTHBHHHHHH....H.TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGS CS
                              Fer2 10 vevadgettlldaae....e.nggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqt 75
                                      v++++g t +l+ +     + +g +++++sC++g Cg+C+ +++            g ++      laC t
  gi|488601694|ref|YP_007908165.1| 22 VPAEKGMT-VLEGLYyikeNyDGSLAFRASCRMGICGSCAMKID------------GTPK------LACET 73
                                      55656666.776666666566789*****************988............5553......56655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.9
                                       SSSTTE CS
                              Fer2  39 gCgtCl 44 
                                       +Cg+C 
  gi|488601694|ref|YP_007908165.1| 146 KCGACY 151
                                       499996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.7       3.2     3e+03       7      10 ..      56      59 ..      56      61 .. 0.86
   2 !   19.1   1.2   1.3e-06    0.0012       3      16 ..     143     156 ..     140     167 .. 0.90
   3 ?    2.1   2.6      0.38   3.6e+02       4      15 ..     192     211 ..     187     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.2
                            Fer4_4  7 CgsC 10
                                      CgsC
  gi|488601694|ref|YP_007908165.1| 56 CGSC 59
                                      **** PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.3e-06
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        Ci Cg+C+++CP 
  gi|488601694|ref|YP_007908165.1| 143 LCIKCGACYSVCPA 156
                                       6************4 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.38
                            Fer4_4   4 CigCgs........CvaaCP 15 
                                       C +Cg+        C  +CP
  gi|488601694|ref|YP_007908165.1| 192 CSDCGVwrchfnaeCSEVCP 211
                                       99***888777777888888 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       5.1   4.8e+03      11      17 ..      56      62 ..      52      76 .. 0.74
   2 !   16.6   0.1     7e-06    0.0066       5      22 ..     141     158 ..     123     171 .. 0.77
   3 ?   -0.7   4.0       1.7   1.6e+03      45      52 ..     204     211 ..     184     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.1
                           Fer4_21 11 CgkClia 17
                                      Cg+C++ 
  gi|488601694|ref|YP_007908165.1| 56 CGSCAMK 62
                                      7777765 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7e-06
                           Fer4_21   5 edkCigCgkCliaCedts 22 
                                        + Ci+Cg C+ +C+ ++
  gi|488601694|ref|YP_007908165.1| 141 YSLCIKCGACYSVCPASA 158
                                       456777777777777554 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.7
                           Fer4_21  45 nlCssvCP 52 
                                       + Cs+vCP
  gi|488601694|ref|YP_007908165.1| 204 AECSEVCP 211
                                       5699***9 PP

>> HydF_tetramer  Hydrogen maturase F tetramerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00021       0.2      40      78 ..     113     151 ..     109     161 .. 0.89
   2 ?    0.9   0.1      0.39   3.7e+02      53      91 ..     171     209 ..     161     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                       HHHHHHHH----EEEEE--SS--HHHTT-SEEEE-TT-- CS
                     HydF_tetramer  40 PkllkkktgkelefevaagrefpeeleeyklvihCggCm 78 
                                       P l++kk   e  +e+ ++ e   e  +y+l+i+Cg+C+
  gi|488601694|ref|YP_007908165.1| 113 PYLIRKKEDYENPVELIQKPEELYEYYDYSLCIKCGACY 151
                                       78899999999999999999999999************8 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                                       EEEE--SS--HHHTT-SEEEE-TT----HHHHHHHHHHH CS
                     HydF_tetramer  53 fevaagrefpeeleeyklvihCggCmitrkellaRikel 91 
                                         ++++++  +e +++++ i C+ C + r + +a ++e+
  gi|488601694|ref|YP_007908165.1| 171 AAYRFNTDSRDEGKDIRMDIVCSDCGVWRCHFNAECSEV 209
                                       556677888899999**********99888877766655 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.5   3.1e-05     0.029       4      18 ..     142     156 ..     140     184 .. 0.86
   2 ?   -0.0   0.6       1.4   1.3e+03       6      18 ..     200     212 ..     198     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       + Ci cgaC++++P 
  gi|488601694|ref|YP_007908165.1| 142 SLCIKCGACYSVCPA 156
                                       67************7 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.4
                           Fer4_13   6 CiacgaCvelaPd 18 
                                       C   + C e++P+
  gi|488601694|ref|YP_007908165.1| 200 CHFNAECSEVCPK 212
                                       666788*****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 ?   12.6   0.1   0.00019      0.18       3      27 ..     139     163 ..     138     189 .. 0.77
   2 ?    1.6   0.1       0.5   4.7e+02       6      23 ..     198     215 ..     197     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                           Fer4_15   3 vDrdaCigcglCvaeapevfelded 27 
                                       +D ++Ci cg+C+ ++p   + +++
  gi|488601694|ref|YP_007908165.1| 139 YDYSLCIKCGACYSVCPASATREDY 163
                                       799*************987776664 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.5
                           Fer4_15   6 daCigcglCvaeapevfe 23 
                                       ++C   + C +++p+ + 
  gi|488601694|ref|YP_007908165.1| 198 WRCHFNAECSEVCPKNIN 215
                                       58************9875 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.2   4.5e-05     0.042      53      94 ..     115     156 ..      49     158 .. 0.80
   2 ?   -2.2   2.9       8.2   7.7e+03      82      94 ..     200     212 ..     184     214 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-05
                           Fer4_22  53 nvrkekkerlrqrllhklsefkekfgesgCvGCgRCieacpv 94 
                                        +rk++       l++k +e+ e ++ s C+ Cg C ++cp+
  gi|488601694|ref|YP_007908165.1| 115 LIRKKEDYENPVELIQKPEELYEYYDYSLCIKCGACYSVCPA 156
                                       456666666677889999999999****************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.2
                           Fer4_22  82 CvGCgRCieacpv 94 
                                       C     C+e+cp+
  gi|488601694|ref|YP_007908165.1| 200 CHFNAECSEVCPK 212
                                       3333345555554 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.22      45      74 ..     128     157 ..      96     164 .. 0.79
   2 ?    4.0   0.3      0.06        56      60      82 ..     199     221 ..     170     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                           Fer4_18  45 kalkekeerkekgagdcidcescvkvcPtg 74 
                                         +k +e+ +  + + ci+c++c +vcP  
  gi|488601694|ref|YP_007908165.1| 128 LIQKPEELYEYYDYSLCIKCGACYSVCPAS 157
                                       4556666777778889************75 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.06
                           Fer4_18  60 dcidcescvkvcPtgidirkGlq 82 
                                        c     c +vcP +i+  k +q
  gi|488601694|ref|YP_007908165.1| 199 RCHFNAECSEVCPKNINPAKAVQ 221
                                       3444568*******998777666 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       4.9   4.6e+03      81     103 ..      71      91 ..      50      95 .. 0.60
   2 ?    4.8   0.1     0.024        22      23      46 ..     143     164 ..     119     182 .. 0.83
   3 ?    7.2   1.4    0.0043         4      26      58 ..     199     232 ..     189     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.9
                                       GCCS-GGGTTB.----HHHHHHH CS
                           Fer4_20  81 CegaCvlekkgkepvaigklerf 103
                                       Ce++      gk++++i+ l+ f
  gi|488601694|ref|YP_007908165.1|  71 CETQILS--LGKSKITIEPLDNF 91 
                                       4443333..34456677666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.024
                                       T----TT-HHHHCSTT---HHHHH CS
                           Fer4_20  23 RClqCkkapcvkgCPveidipefi 46 
                                        C++C    c + CP++ + ++++
  gi|488601694|ref|YP_007908165.1| 143 LCIKC--GACYSVCPASATREDYL 164
                                       59999..789999**999888876 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0043
                                       --T.T-HHHHCSTT---HHHHHHHHHTT-HHHHH CS
                           Fer4_20  26 qCk.kapcvkgCPveidipefikkiaegnleeaa 58 
                                       +C+ +a+c++ CP +i+  + ++k++ +    ++
  gi|488601694|ref|YP_007908165.1| 199 RCHfNAECSEVCPKNINPAKAVQKLRFQTAIYSI 232
                                       4666899**********99988888766655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1353.47
//
Query:       gi|488601695|ref|YP_007908166.1|  [L=124]
Description: succinate dehydrogenase subunit C [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-12   45.7   8.8    7.2e-12   45.4   8.8    1.1  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr
     0.0075   16.4   5.6      0.017   15.2   5.6    1.7  1  Fumarate_red_C  Fumarate reductase subunit C
  ------ inclusion threshold ------
      0.022   14.9   6.1      0.036   14.2   6.1    1.5  1  Ferric_reduct   Ferric reductase like transmembrane component
      0.065   13.3   5.5       0.72   10.0   0.1    2.5  2  AA_permease_C   C-terminus of AA_permease


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   8.8   1.6e-15   7.2e-12      20     115 ..      16     111 ..       5     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.6e-15
                           Sdh_cyt  20 awlsilhritGvallvglllllvwlllalslsspesfarvvallaspiklilllllllallyHllnGiRhllwD..l 94 
                                       ++ + +hr+tGv+l++ +ll+++   l+++++++e+++ +++    p +l+  lll+la +yH++nG+R+++    l
  gi|488601695|ref|YP_007908166.1|  16 SISYSFHRLTGVVLAI-YLLMHLG-YLTSIRLGKEVYDIFISTTVTPTFLAFDLLLVLAGVYHGINGVRLIIHEfaL 90 
                                       67789***********.6666665.45777899******95444456666666*********************433 PP

                           Sdh_cyt  95 glglelesarksalavlalav 115
                                       g+ l+++  + + ++vl++ +
  gi|488601695|ref|YP_007908166.1|  91 GYELRKSLLYLTYILVLIVWL 111
                                       443333333444444444443 PP

>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   5.6   3.9e-06     0.017      19      83 ..      14      78 ..       3     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.9e-06
                    Fumarate_red_C 19 pfYrfYmlrEatavlvalfalvlllgllaLaqgeaayeafleflqnPlvlllniiaLaaallhav 83
                                       f + Y ++ +t v++a++ l+ l  l+++  g++ y+ f+++   P +l++++++++a ++h +
  gi|488601695|ref|YP_007908166.1| 14 LFSISYSFHRLTGVVLAIYLLMHLGYLTSIRLGKEVYDIFISTTVTPTFLAFDLLLVLAGVYHGI 78
                                      5667899********************************************************76 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 ?   14.2   6.1     8e-06     0.036      25      94 ..       9      72 ..       2     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8e-06
                     Ferric_reduct 25 ltglsldklll.fHkwlgvlafllallHvilyllnflrfsaldeerlldsllkkpynllGvlalllliila 94
                                      ++g sl +  + fH+++gv++++++l+H  + +   l +       ++++++ ++ ++  +la+ ll++la
  gi|488601695|ref|YP_007908166.1|  9 IRGKSLFSISYsFHRLTGVVLAIYLLMHLGYLTSIRLGK-------EVYDIFISTTVTPTFLAFDLLLVLA 72
                                      556666665556*****************9999888854.......4555555555555555555555554 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 ?   10.0   0.1   0.00016      0.72      13      33 ..      26      46 ..      24      49 .. 0.88
   2 ?    3.8   2.4     0.014        62      23      44 ..      97     119 ..      90     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                     AA_permease_C 13 sIlvNiyLmlqLdsltwirfg 33
                                      ++++ iyL+++L++lt ir g
  gi|488601695|ref|YP_007908166.1| 26 GVVLAIYLLMHLGYLTSIRLG 46
                                      67889*************975 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
                     AA_permease_C  23 qLdsltwirf.gvwmliglliYf 44 
                                       +L +lt+i++ +vw+ + +++Y 
  gi|488601695|ref|YP_007908166.1|  97 SLLYLTYILVlIVWLYASYVMYR 119
                                       68899999973579999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 693.23
//
Query:       gi|488601696|ref|YP_007908167.1|  [L=120]
Description: succinate dehydrogenase subunit D [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-16   58.8   3.0    6.1e-16   58.6   3.0    1.1  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr
     0.0088   16.1   2.1      0.014   15.5   2.1    1.3  1  Fumarate_red_D  Fumarate reductase subunit D
  ------ inclusion threshold ------
      0.013   15.0   1.1      0.018   14.6   1.1    1.3  1  NnrU            NnrU protein
      0.091   13.1   0.0       0.24   11.7   0.0    1.7  1  CCDC-167        Coiled-coil domain-containing protein 167
       0.12   12.0   0.9       0.31   10.7   0.9    1.7  2  CybS            CybS, succinate dehydrogenase cytochrome B sm
       0.34   11.4   1.3       0.41   11.1   0.3    1.7  2  SIT             SHP2-interacting transmembrane adaptor protei
       0.61   10.1   3.7        1.4    8.9   1.4    2.2  2  SK_channel      Calcium-activated SK potassium channel


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   3.0   2.4e-19   6.1e-16      21     115 ..      17     110 ..       5     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.4e-19
                           Sdh_cyt  21 wlsilhritGvallv.glllllvwlllalslsspesfarvvallaspiklilllllllallyHllnGiRhllwDlgl 96 
                                       + ++l+ itG++l++ ++++++     + + +++ +f++vv+ l+s ++++ ++llll + +H++nGiR +++D+ +
  gi|488601696|ref|YP_007908167.1|  17 LGWLLQLITGILLVIlVTFHFIET---HMISHDALDFEKVVERLSSGGYKAFYALLLLTVSFHAYNGIRAIILDTEF 90 
                                       67*************777777743...77778**************66666669********************977 PP

                           Sdh_cyt  97 gl.elesarksalavlalav 115
                                       g  ++++++   ++v+++a+
  gi|488601696|ref|YP_007908167.1|  91 GReNRKAVNIAMAIVIIGAF 110
                                       66333444444444444444 PP

>> Fumarate_red_D  Fumarate reductase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.1   5.3e-06     0.014      28     106 ..      30     107 ..       9     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.3e-06
                    Fumarate_red_D  28 lililglllplGlldsdalsyekvlafaqswigklvllvviilplwhalhrihhglhdlkihvkkaaklifYglAal 104
                                       +il++   +   ++++dal++ekv++ ++s   k++ ++++  + +ha + i+ ++ d ++ ++ + k++  ++A++
  gi|488601696|ref|YP_007908167.1|  30 VILVTFHFIETHMISHDALDFEKVVERLSSGGYKAFYALLLLTVSFHAYNGIRAIILDTEFGRE-NRKAVNIAMAIV 105
                                       344444567778899***********************************************99.788888888877 PP

                    Fumarate_red_D 105 ls 106
                                       + 
  gi|488601696|ref|YP_007908167.1| 106 II 107
                                       64 PP

>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.1     7e-06     0.018       3      82 ..      31     107 ..      27     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7e-06
                              NnrU   3 ilglllFlgaHsvra.apalRarliarlGergykilyslvsllglvlliigfgaaryevllWeppawlrhlalllml 78 
                                       il ++ F+ +H+++  a ++  ++++rl   gyk++y+l+ l   ++ + +++  r+++l  e+    r +++++m+
  gi|488601696|ref|YP_007908167.1|  31 ILVTFHFIETHMISHdALDFE-KVVERLSSGGYKAFYALLLL---TVSFHAYNGIRAIILDTEFGRENRKAVNIAMA 103
                                       677888999****99777776.999************98765...55666666666664334455666666666666 PP

                              NnrU  79 vafi 82 
                                       +++i
  gi|488601696|ref|YP_007908167.1| 104 IVII 107
                                       6655 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 ?   11.7   0.0   9.5e-05      0.24      63      83 ..      92     112 ..      88     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
                          CCDC-167  63 keNrksmllsvalllvlaLvY 83 
                                       +eNrk + +++a++++ a+vY
  gi|488601696|ref|YP_007908167.1|  92 RENRKAVNIAMAIVIIGAFVY 112
                                       7******************** PP

>> CybS  CybS, succinate dehydrogenase cytochrome B small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.52   1.3e+03     101     118 ..      19      36 ..       9      44 .. 0.71
   2 ?   10.7   0.9   0.00012      0.31      62     111 ..      64     113 ..      19     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.52
                              CybS 101 ylLalgtvlslvGlYele 118
                                       +lL+l+t++ lv l ++ 
  gi|488601696|ref|YP_007908167.1|  19 WLLQLITGILLVILVTFH 36 
                                       777778877777665554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                              CybS  62 vlDavlavlllihshlgfesciiDYipkrvygklhklahylLalgtvlsl 111
                                       +  a+l +++ +h++ g+ ++i+D    r  +k+ ++a+ ++ +g ++ +
  gi|488601696|ref|YP_007908167.1|  64 AFYALLLLTVSFHAYNGIRAIILDTEFGRENRKAVNIAMAIVIIGAFVYG 113
                                       55578889999*************99999999********9999988754 PP

>> SIT  SHP2-interacting transmembrane adaptor protein, SIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00016      0.41       1      24 [.      19      42 ..      19      58 .. 0.87
   2 ?   -2.5   0.0       2.6   6.7e+03      12      20 ..      68      76 ..      63      80 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                               SIT  1 wllllilallLlllviasllawrm 24
                                      wll li+++lL++lv++ ++   m
  gi|488601696|ref|YP_007908167.1| 19 WLLQLITGILLVILVTFHFIETHM 42
                                      9***************99887666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                               SIT 12 lllviasll 20
                                      lll+++s+ 
  gi|488601696|ref|YP_007908167.1| 68 LLLLTVSFH 76
                                      344555555 PP

>> SK_channel  Calcium-activated SK potassium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.4   0.00055       1.4      52      82 ..      17      47 ..       2      73 .. 0.82
   2 ?    1.0   0.1      0.15   3.9e+02      22      41 ..      76      95 ..      70     119 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00055
                        SK_channel 52 lkvlislsTviLLvlivlyhaaeiqlflidn 82
                                      l  l  l T iLLv++v++h++e ++  +d+
  gi|488601696|ref|YP_007908167.1| 17 LGWLLQLITGILLVILVTFHFIETHMISHDA 47
                                      56678889***************99988876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                        SK_channel 22 lalfGivlmvvetEllalav 41
                                       a  Gi  ++++tE+   + 
  gi|488601696|ref|YP_007908167.1| 76 HAYNGIRAIILDTEFGRENR 95
                                      56778888888888755333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.36s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 671.25
//
Query:       gi|488601697|ref|YP_007908168.1|  [L=326]
Description: K+ transport systems, NAD-binding component [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-30  105.1   0.6      5e-30  104.2   0.6    1.5  1  TrkA_N           TrkA-N domain
    2.3e-13   49.8   0.1    5.3e-13   48.6   0.1    1.6  1  TrkA_C           TrkA-C domain
    3.3e-12   46.2  15.0    5.6e-12   45.4  15.0    1.4  1  Ion_trans_2      Ion channel
    0.00029   21.4   2.0     0.0036   17.8   0.1    2.9  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00086   19.6   0.4     0.0015   18.7   0.4    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0046   16.0   0.1     0.0061   15.6   0.1    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0052   16.1   7.3     0.0095   15.2   7.3    1.4  1  Ion_trans        Ion transport protein
  ------ inclusion threshold ------
      0.015   14.8   2.0       0.24   10.8   0.4    2.3  2  DUF3798          Protein of unknown function (DUF3798)
      0.016   15.4   0.6       0.06   13.5   0.4    1.9  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.019   14.9   0.3        1.1    9.3   0.0    2.5  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.025   14.1   0.1      0.055   13.0   0.1    1.5  1  MTS              Methyltransferase small domain
      0.037   13.9   0.2      0.083   12.8   0.2    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.096   12.2   0.2       0.24   10.9   0.1    1.6  2  NmrA             NmrA-like family
      0.098   12.5   0.1       0.22   11.3   0.1    1.5  1  Methyltransf_31  Methyltransferase domain
        1.3    7.7   5.9          2    7.1   3.8    1.9  2  DUF2207          Predicted membrane protein (DUF2207)


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 !  104.2   0.6   4.1e-33     5e-30       1     116 []     105     221 ..     105     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 4.1e-33
                                       EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddea 75 
                                       +ii+G+G +Gr++a+eL +  + +++v+id + e+v  +re+g+ +++gd  +e+vLe+a i++a+a+ia++ +d +
  gi|488601697|ref|YP_007908168.1| 105 YIICGYGVMGREIAQELVKvTNkDKIVIIDENMEKVSLARENGYIAIQGDSVEEDVLERARIKHAKALIACM-NDSS 180
                                       79*****************977777**********************************************9.99** PP

                                       HHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                            TrkA_N  76 nilavllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                       n++a+++ake+np+++++a a++p+ +++ k++gad+v+sp
  gi|488601697|ref|YP_007908168.1| 181 NAFAIMSAKEMNPNIYTMAVARTPSGVKNTKRAGADYVLSP 221
                                       **************************************998 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   4.4e-16   5.3e-13       8      62 ..     260     315 ..     257     318 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 4.4e-16
                                       --GGGTTSBHHHHTHHHH.S-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHH CS
                            TrkA_C   8 agsplvGktlkelnlrar.gvlvvairRggeliipsgdtvLeeGDvllvvgspsdl 62 
                                       ++  l+Gk++k+l+lr++ g+++va+ R+g+++ip+ d+ L+ GD l+++gs ++l
  gi|488601697|ref|YP_007908168.1| 260 SNKNLDGKKIKDLDLRRKtGATIVAVERKGDILIPDADLSLKFGDNLYLMGSEDQL 315
                                       6889************************************************9986 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4  15.0   4.7e-15   5.6e-12       1      77 [.      13      86 ..      13      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 4.7e-15
                                      HHHHHTCHHHHHHHHT....T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  1 ivlllvlifgaviysleegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvl 77
                                      i+ll+++++g++ +++    e+ws++d++Y++++t+tT GY +++  +  gr+++i+++++G+++f++ +++++  +
  gi|488601697|ref|YP_007908168.1| 13 ILLLITIAIGTIGFTV---IEGWSLFDSFYMTVITITTTGYKEVYDLSYNGRFLAIFLMFFGIGVFFYSINLIIPTI 86
                                      57999***********...9999************************8888********************998765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.7   4.4e+03       5      19 ..      19      33 ..      17      49 .. 0.81
   2 !   17.8   0.1     3e-06    0.0036       4      57 ..     106     158 ..     105     177 .. 0.87
   3 ?    1.8   0.0      0.32   3.8e+02      25      67 ..     193     234 ..     180     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.7
                                      ETTSHHHHHHHHHHH CS
                     F420_oxidored  5 iGaGnmgealasgll 19
                                      i+ G +g+++++g++
  gi|488601697|ref|YP_007908168.1| 19 IAIGTIGFTVIEGWS 33
                                      78999****999997 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3e-06
                                       EE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHH CS
                     F420_oxidored   4 ii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdnee 57 
                                       ii G+G mg+ +a+ l++   ++ +iv++ + n ek+  ++e+ ++ +++ + ee
  gi|488601697|ref|YP_007908168.1| 106 IIcGYGVMGREIAQELVKVT-NKDKIVII-DENMEKVSLARENGYIAIQGDSVEE 158
                                       677***************97.99****89.*******999999999999876655 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.32
                                       GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE CS
                     F420_oxidored  25 pheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvl 67 
                                       p+  ++a  r+p+ ++ ++++ g++   ++++++a++a v++ 
  gi|488601697|ref|YP_007908168.1| 193 PNIYTMAVARTPSGVKNTKRA-GADYVLSPYSDTAKKAMVILS 234
                                       444455778999999998777.567777799999997777664 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 !   18.7   0.4   1.3e-06    0.0015       2      91 ..     106     190 ..     105     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-S CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnls 77 
                                       +i G+G +G+ +a++l++  + d +i+++d + ek+  +    ++   +ai+ d  +++  L+++ +k++++++ ++
  gi|488601697|ref|YP_007908168.1| 106 IICGYGVMGREIAQELVKVTNKD-KIVIIDENMEKVSLA----RENGYIAIQGDSVEEDV-LERArIKHAKALIACM 176
                                       688****************9986.***********4333....56667777777766665.7777799999999999 PP

                                       SGGGHHHHHHHHHH CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCie 91 
                                        + s++  +  + e
  gi|488601697|ref|YP_007908168.1| 177 NDSSNAFAIMSAKE 190
                                       99988755555555 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 !   15.6   0.1   5.1e-06    0.0061       2      81 ..     106     181 ..     105     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-06
                         3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleea.legvdvvihlaslv 77 
                                       ++ g G +Gr++ +eLv++ ++ ++ ++D + ++     +++ + +  i+gD  ++d le+a ++ ++++i  a+++
  gi|488601697|ref|YP_007908168.1| 106 IICGYGVMGREIAQELVKVTNKDKIVIIDENMEKVS--LARENGYI-AIQGDSVEEDVLERArIKHAKALI--ACMN 177
                                       67899***********************97766554..55666666.678888888888777445555544..4555 PP

                         3Beta_HSD  78 dvag 81 
                                       d+ +
  gi|488601697|ref|YP_007908168.1| 178 DSSN 181
                                       5544 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   7.3     8e-06    0.0095     178     234 ..      33      87 ..       2      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                                       SHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 178 nfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNlliavia 234
                                       ++f++++ ++ ++tt g+ ++++  ++++  +  i+++ f i + f+ +Nl+i+ i+
  gi|488601697|ref|YP_007908168.1|  33 SLFDSFYMTVITITTTGYKEVYDLSYNGR--FLAIFLMFFGIGVFFYSINLIIPTIV 87 
                                       47899************************..66666666666667788999998886 PP

>> DUF3798  Protein of unknown function (DUF3798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.031        37      62     113 ..     105     156 ..      96     160 .. 0.87
   2 ?   10.8   0.4    0.0002      0.24      51     122 ..     160     235 ..     149     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.031
                                       EEEEE-SS---HHHHHHHHHH-TTSEEEESS--S-HHHHHHHSSEEEE--HH CS
                           DUF3798  62 aivvaqavpgtleAirkvkekrpdilliagepeedpavlssaaDlvleadaa 113
                                       +i++  +v g   A + vk +++d ++i  e  e +++  +   ++++ d++
  gi|488601697|ref|YP_007908168.1| 105 YIICGYGVMGREIAQELVKVTNKDKIVIIDENMEKVSLARENGYIAIQGDSV 156
                                       79999**************************999998888777777776665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
                                       HHGGGG-TTEEEEEEE-SS---HHHHHHHHHH-TTSEEEESS..--S-HHHHHHHSSEEEE..--HHHHHHHHHHH CS
                           DUF3798  51 ivslAdDpkvkaivvaqavpgtleAirkvkekrpdilliage..peedpavlssaaDlvle..adaakrgkliiek 122
                                       +++ A  ++ ka++ + + +  + Ai  +ke++p+i ++a +  p+  +++  + aD vl+   d+ak++ +i ++
  gi|488601697|ref|YP_007908168.1| 160 VLERARIKHAKALIACMNDSSNAFAIMSAKEMNPNIYTMAVArtPSGVKNTKRAGADYVLSpySDTAKKAMVILSR 235
                                       6666777899**************************9987641155667777778888886336777777777654 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 ?   13.5   0.4     5e-05      0.06       5      68 ..     108     181 ..     104     213 .. 0.78
   2 ?   -0.3   0.0      0.89   1.1e+03      24      75 ..     196     247 ..     184     272 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                       E--SHHHHHHHHHH..HHTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHC.....SEEEE-SSSHHH CS
                     NAD_binding_2   5 iGlGvMGsnmalnl..lkagykvavynrtkekveelvaeg...akaaesieelvasl.....dvvitmvkagka 68 
                                        G GvMG+++a++l  + ++ k+++++ + ekv  + ++g   +++ +  e++++++     ++ i +++++++
  gi|488601697|ref|YP_007908168.1| 108 CGYGVMGREIAQELvkVTNKDKIVIIDENMEKVSLARENGyiaIQGDSVEEDVLERArikhaKALIACMNDSSN 181
                                       69************5557999****************9998854444444577777766666666666666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.89
                                       EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS CS
                     NAD_binding_2  24 kvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg 75 
                                        ++++ rt++ v++   +ga+ + s+ + +a+  +vi+  ++ ++  e+i++
  gi|488601697|ref|YP_007908168.1| 196 YTMAVARTPSGVKNTKRAGADYVLSPYSDTAKKAMVILSRQSAADFLEIISK 247
                                       4566678888889998888888888776555556666666666666666665 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.066        78      16      37 ..     129     150 ..     111     181 .. 0.69
   2 ?    9.3   0.0    0.0009       1.1       5      48 ..     183     228 ..     181     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.066
                                       EEEEEESSHHHHHHHHHTTESE CS
                        ADH_zinc_N  16 eviavdsseeklelakklGade 37 
                                       +++ +d + ek+ la+++G  +
  gi|488601697|ref|YP_007908168.1| 129 KIVIIDENMEKVSLARENGYIA 150
                                       8999**************9433 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0009
                                       HHHHHHHHTT-..EEEEEESSHHHHHHHHHTTESEEEET.....TTCHHHH CS
                        ADH_zinc_N   5 aavqlAkalGa..eviavdsseeklelakklGadeviny.....keadlve 48 
                                       +a++ Ak ++    ++av+++++ ++  k+ Gad+v+ +     k     +
  gi|488601697|ref|YP_007908168.1| 183 FAIMSAKEMNPniYTMAVARTPSGVKNTKRAGADYVLSPysdtaK-----K 228
                                       78999998888668888*********************9433330.....2 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.6e-05     0.055      39      94 ..     107     165 ..      91     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                                       T-TTSHHHHHHHHH....TTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST CS
                               MTS  39 GcGaGvlgaalake....speaevtlvdvdarAlesakenleanklevevvasdvleeve 94 
                                        cG+Gv+g ++a+e    +++ +++++d++++ + +a+en    +++++ v++dvle + 
  gi|488601697|ref|YP_007908168.1| 107 ICGYGVMGREIAQElvkvTNKDKIVIIDENMEKVSLARENGY-IAIQGDSVEEDVLERAR 165
                                       6******9998876221145567****************964.45567777777777665 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 ?   12.8   0.2   6.9e-05     0.083       4      75 ..     107     181 ..     105     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-05
                                       EE--SCCHHHHHHHHHHT..T-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTTSS-HHHHCCCHHCEEEES-HHH CS
                           3HCDH_N   4 viGaGtmGagiaavfasa..gleVvlvdiseealekalekiek.sleklvekgklkeeeveaalarisfttdlee 75 
                                       ++G G+mG++ia+ +++   + ++v++d + e++  a+e+         ve+  l+++ +++a a i   +d ++
  gi|488601697|ref|YP_007908168.1| 107 ICGYGVMGREIAQELVKVtnKDKIVIIDENMEKVSLARENGYIaIQGDSVEEDVLERARIKHAKALIACMNDSSN 181
                                       79***********8877544889******9999998887654413445667777777777777777777666655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0002      0.24       3      74 ..     106     178 ..     105     191 .. 0.91
   2 ?   -1.8   0.0       1.5   1.8e+03     143     226 ..     195     279 ..     190     283 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                       ESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE---G CS
                              NmrA   3 viGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtgf 74 
                                       +i + G +G+ +++ l+k+ +k ++++ d++ e++    e+G   ++gd  ++++l++a +k +++ ++ ++ 
  gi|488601697|ref|YP_007908168.1| 106 IICGYGVMGREIAQELVKVTNKDKIVIIDENMEKVSLARENGYIAIQGDSVEEDVLERArIKHAKALIACMND 178
                                       6778899*************************************************99879999999998884 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                       EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE..-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHH CS
                              NmrA 143 ffmenflsllaqlkvgdtappedkvtllgpgnpkavll..daeeDiGafvikilkdprklkgkriklagntlsgnei 217
                                       +++  +++++    v++t+  +  ++l+  +++  + +   + +  + f   i k  + +  + ++l+++ l g++i
  gi|488601697|ref|YP_007908168.1| 195 IYTMAVARTPSG--VKNTKRAGADYVLSPYSDTAKKAMviLSRQSAADFLEIISKVGKRFLLEKVQLSNKNLDGKKI 269
                                       555555555555..444444444455554444433333324444444444444444555577888888888887777 PP

                                       HHH.HHHHHT CS
                              NmrA 218 vel.fekkig 226
                                        +l + +k+g
  gi|488601697|ref|YP_007908168.1| 270 KDLdLRRKTG 279
                                       6664455555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00018      0.22      12      47 ..     108     146 ..     103     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                   Methyltransf_31  12 CGtGeltfelae...elgpkaevvGiDiseeaielAren 47 
                                       CG G  + e+a+   ++  k ++v iD + e ++lAren
  gi|488601697|ref|YP_007908168.1| 108 CGYGVMGREIAQelvKVTNKDKIVIIDENMEKVSLAREN 146
                                       ************6666666888***************97 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.8    0.0017         2     382     448 ..       6     101 ..       2     103 .. 0.65
   2 ?    0.2   0.0       0.2   2.4e+02     276     367 ..     117     217 ..     104     237 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0017
                           DUF2207 382 klsalglgliilglilillallllvll.............................lvfllilllillliaiivlll 429
                                       + +a+ ++l+++ ++++++++ ++ ++                             +  ++++++++++++  + l+
  gi|488601697|ref|YP_007908168.1|   6 RAIAITIILLLITIAIGTIGFTVIEGWslfdsfymtvititttgykevydlsyngrFLAIFLMFFGIGVFFYSINLI 82 
                                       556666666666666666665555555999********************966655333333333333333333333 PP

                           DUF2207 430 fsrllgrrteeGaellakw 448
                                       + ++++rr e +++ll+k+
  gi|488601697|ref|YP_007908168.1|  83 IPTIVQRRLERWRKLLEKI 101
                                       3359999999999999886 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.2
                           DUF2207 276 ltAtlldLavkgyitieeekkkkkkgkd...tltilkkndeeldpyEkalldlLfdkseeg.ks....lkeikkyak 344
                                       ++  l+   +k +i i +e+++k    +   +  i ++     d+ E+++l+    k ++  +     +      + 
  gi|488601697|ref|YP_007908168.1| 117 IAQELVKVTNKDKIVIIDENMEKVSLARengY--IAIQG----DSVEEDVLERARIKHAKAlIAcmndS---SNAFA 184
                                       55567788899999999999998654445332..33333....67777777766633333333364222...22222 PP

                           DUF2207 345 kskk...kakkfkkalkkwksavkk.......k 367
                                         ++   +++ +  a+++  s+vk+        
  gi|488601697|ref|YP_007908168.1| 185 IMSAkemNPNIYTMAVARTPSGVKNtkragadY 217
                                       222234488888888888888888866555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); 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):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 1857.83
//
Query:       gi|488601698|ref|YP_007908169.1|  [L=208]
Description: haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-13   49.1   0.0    1.6e-12   47.8   0.0    1.6  1  HAD_2           Haloacid dehalogenase-like hydrolase
    2.8e-10   40.9   0.0    6.2e-09   36.5   0.0    2.0  1  Hydrolase       haloacid dehalogenase-like hydrolase
     0.0006   19.8   0.0     0.0017   18.4   0.0    1.7  2  Hydrolase_like  HAD-hyrolase-like
     0.0027   18.1   0.1     0.0045   17.4   0.1    1.5  1  HAD             haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   3.7e-16   1.6e-12       3     176 ..       8     185 ..       6     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 3.7e-16
                             HAD_2   3 FDlDgTlldteeliiqafnelleey.....gls.elseeelrklig.lslrellrklgeseeeeekieellrkynee 72 
                                       FD+DgT++d   ++ +++ne++ +      gls +  +  +++ +    +++l ++l +   ++ ++   ++++ ++
  gi|488601698|ref|YP_007908169.1|   8 FDVDGTIVDA-GFMDKFWNEVVPRLyaerhGLSyDEALGIVKREYDaVGDKDLRWYLPDYWFKKFDLGVDWKDVLKS 83 
                                       *********6.355555555554442222322211112222222220233333333333333333777777777777 PP

                             HAD_2  73 kkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklk 149
                                         + e+++y+++ e+L+ L +++y++  +T+  re +e +++++  + + ++  + +d++    +pe++e+++e  +
  gi|488601698|ref|YP_007908169.1|  84 FSN-ELRFYPDAMEVLNLL-SKKYRIVAITNAVREILEFEIDRIS-HLFWKKFSCPSDFGDIRRKPEIFERVCEVCG 157
                                       777.***************.99*********************99.5778999999999998888************ PP

                             HAD_2 150 lkkeeviyvGDsp.tDieaakkagikvi 176
                                       +k+eev+ vGD+p +D e  k+agi ++
  gi|488601698|ref|YP_007908169.1| 158 VKPEEVVHVGDHPfFDYEVPKRAGIMAF 185
                                       ************************9765 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.4e-12   6.2e-09       1     210 []       3     181 ..       3     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.4e-12
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE..HHHHTHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg..ayaigkpe 75 
                                       ik + fD+dGT+++      ++++++            ++ ++++        + ++++   +  r   a+     +
  gi|488601698|ref|YP_007908169.1|   3 IKMLTFDVDGTIVDAG-FMDKFWNEV-----------VPRLYAERH-------GLSYDEALGIVKREydAVGDKDLR 60 
                                       789999*******777.556677777...........222233333.......333333333333331134444444 PP

                                       HHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                         Hydrolase  76 wltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae.ra 151
                                       w              +   + +  v ++  ++l  f  +  l+ +p+a e+++ L  +++++v +t+  +e  e ++
  gi|488601698|ref|YP_007908169.1|  61 WYLPD----------YWFKKFDLGVDWK--DVLKSFSNE--LRFYPDAMEVLNLLS-KKYRIVAITNAVREILEfEI 122
                                       44444..........6666688888899..666666555..55***********99.5699*************888 PP

                                       HHHTTGGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 152 anqlGddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                        +      f +   + ++ +    +pe+++++++ +++kpeev++VGD +  D +  ++Ag
  gi|488601698|ref|YP_007908169.1| 123 DRISH--LFwKKFSCPSDFGDIRRKPEIFERVCEVCGVKPEEVVHVGDHPFfDYEVPKRAG 181
                                       88877..676667777777777779***********************9888877777765 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.5   6.6e+03      15      30 ..      42      57 ..      36      58 .. 0.71
   2 !   18.4   0.0   3.8e-07    0.0017       3      49 ..     144     188 ..     142     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.5
                                      HHH---GGGEEEEES- CS
                    Hydrolase_like 15 evlgsdpeevlmiGDr 30
                                      e+lg+ ++e  ++GD+
  gi|488601698|ref|YP_007908169.1| 42 EALGIVKREYDAVGDK 57
                                      4556677888888986 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.8e-07
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEES CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVl 49 
                                       +KPe  ++++  ev+g++peev+ +GD +  D +  ++aG++  L+ 
  gi|488601698|ref|YP_007908169.1| 144 RKPE--IFERVCEVCGVKPEEVVHVGDHPFFDYEVPKRAGIMAFLID 188
                                       5666..***********************************999975 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     1e-06    0.0045       2     116 ..       7     119 ..       6     171 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-06
                               HAD   2 lfDfDgTLldgdslelllrfllrrgaprlwralrek.lllalfrellrldraglaellea......llagls.eela 70 
                                        fD+DgT++d   ++ ++  ++ r    l+++ +   +++al   + +++++++     +       ++ ++ + + 
  gi|488601698|ref|YP_007908169.1|   7 TFDVDGTIVDAGFMDKFWNEVVPR----LYAERHGLsYDEAL--GIVKREYDAVGDKDLRwylpdyWFKKFDlGVDW 77 
                                       6**********7666555534433....33333333222222..333333333333333344555566777777777 PP

                               HAD  71 aelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplve 116
                                       +++ + +  + r   ++p+a+e+l+  +++ +r+v ++++ r+++e
  gi|488601698|ref|YP_007908169.1|  78 KDVLKSFSNELR---FYPDAMEVLN-LLSKKYRIVAITNAVREILE 119
                                       777777743333...77********.77999***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1179.13
//
Query:       gi|488601699|ref|YP_007908170.1|  [L=129]
Description: ribonuclease P protein subunit Rpp14 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-18   65.2   0.1    6.1e-18   65.0   0.1    1.0  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.1   3.4e-22   6.1e-18       1     102 [.      13     115 ..      13     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3.4e-22
                                       EEEEEEEEESS..........-....HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHH CS
                     RNase_P_Rpp14   1 RYllveilypde....eeelte....ksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlv 69 
                                       RY++++i+  ++    + +  +    k++++ ++e++ +lfG++gl + +  +++ y+++  + +iiRcs+es ++v
  gi|488601699|ref|YP_007908170.1|  13 RYIAFRIIGLRTsdrtS-D--QseniKKVAHKLMENLISLFGEVGLTNSS--VWIEYMEN--EYGIIRCSNESLDKV 82 
                                       9******9998644331.1..13357******************976655..5*******..89************* PP

                                       HHHHHT--EETTEEEEEEEEEEESSHHHHHHHT CS
                     RNase_P_Rpp14  70 waaLtlitkiegrpvvfrvvrvsGTikkaeeea 102
                                       + a++li++i+g +v+  +++vsGTik+++ ++
  gi|488601699|ref|YP_007908170.1|  83 MIAFSLISEIDGVKVLPITLGVSGTIKRCKMKY 115
                                       *****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 718.70
//
Query:       gi|488601700|ref|YP_007908171.1|  [L=247]
Description: proteasome endopeptidase complex, archaeal, alpha subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-64  214.3   0.6    1.4e-63  213.8   0.6    1.2  1  Proteasome      Proteasome subunit
    1.8e-14   53.1   0.1    3.6e-14   52.1   0.1    1.5  1  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
      0.078   13.1   0.1        0.7   10.0   0.0    2.4  2  IgG_binding_B   B domain


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.8   0.6   2.3e-67   1.4e-63       1     190 []      31     214 ..      31     214 .. 0.97

  Alignments for each domain:
  == domain 1  score: 213.8 bits;  conditional E-value: 2.3e-67
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vk+G t++Gik+k+gv++ ad+r+   skll+ +t+eK++kid+hi++a++Gl+aDar+l++rar eaq  rl+y++
  gi|488601700|ref|YP_007908171.1|  31 VKRGATAIGIKTKEGVIILADRRVA--SKLLEADTIEKVYKIDEHICIATSGLVADARVLIDRARIEAQISRLTYDE 105
                                       79***********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       pi+++ l++++++ +q+ytq++g+rpfgvslliagvd  ++p+Ly++dpsG+++e+k a+aiG g++a+ +++ekey
  gi|488601700|ref|YP_007908171.1| 106 PISIKDLTRKICDFKQQYTQYGGVRPFGVSLLIAGVD--EKPRLYETDPSGALLEYK-ATAIGAGRNAVVEYFEKEY 179
                                       *************************************..459**************8.******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                       ++dltleea+ + + a+ +a+e  +++ ++i+ ++i
  gi|488601700|ref|YP_007908171.1| 180 RDDLTLEEAIIMGIVAMGKAIE-SEVTTDGIDTGII 214
                                       **********************.5699999998876 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.1   6.1e-18   3.6e-14       1      23 []       8      30 ..       8      30 .. 0.99

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 6.1e-18
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr++t+FSPdGRLfQVEYA +A
  gi|488601700|ref|YP_007908171.1|  8 YDRAITIFSPDGRLFQVEYAREA 30
                                      *********************99 PP

>> IgG_binding_B  B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.22   1.3e+03      16      30 ..      55      69 ..      52      71 .. 0.87
   2 ?   10.0   0.0   0.00012       0.7       5      34 ..     194     226 ..     191     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                                      EEEESSHHHHHHHHH CS
                     IgG_binding_B 16 ttkavDaataekaFk 30
                                      + k ++a+t ek +k
  gi|488601700|ref|YP_007908171.1| 55 ASKLLEADTIEKVYK 69
                                      678999******987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00012
                                       EEE-SSEEEEEEEEESSH...HHHHHHHHHHHH CS
                     IgG_binding_B   5 vikGktlsGetttkavDa...ataekaFkqYan 34 
                                       v  Gk ++ e tt  +D      a+k+Fkq+ +
  gi|488601700|ref|YP_007908171.1| 194 VAMGKAIESEVTTDGIDTgiiSVADKKFKQFSE 226
                                       6789*************844468*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1398.84
//
Query:       gi|488601701|ref|YP_007908172.1|  [L=235]
Description: rRNA metabolism protein, SBDS family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-24   84.6   1.8    7.1e-24   83.7   1.8    1.5  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    7.5e-22   77.5   0.2    1.6e-21   76.5   0.0    1.6  2  SBDS_C    SBDS protein C-terminal domain
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.029   14.5   0.1    1.3  1  UPF0262   Uncharacterised protein family (UPF0262)
      0.028   14.4   0.0       0.11   12.6   0.0    1.9  2  EFG_C     Elongation factor G C-terminus
      0.052   13.6   0.0      0.071   13.1   0.0    1.3  1  DUF2278   Uncharacterized conserved protein (DUF2278)
       0.12   13.0   0.2       0.28   11.7   0.2    1.7  1  HD_assoc  Phosphohydrolase-associated domain


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   1.8   2.4e-27   7.1e-24       2      88 .]       7      93 ..       6      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 2.4e-27
                                      -EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEE CS
                              SBDS  2 vsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGei 80
                                      ++i+r++k++++Fe +v++  + + +egke++ ++ +++e+++++++kGe+as +el+k+fgt++ +eiikeI+++Ge+
  gi|488601701|ref|YP_007908172.1|  7 AVIARLRKHGENFEALVDPYLARDLKEGKEVNFDDLVAVEEVYKDSKKGERASIEELKKVFGTSNIQEIIKEIIREGEV 85
                                      6899*************************************************************************** PP

                                      E--HHHHH CS
                              SBDS 81 qvsaeerk 88
                                      q +ae+rk
  gi|488601701|ref|YP_007908172.1| 86 QITAEQRK 93
                                      *****997 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.1   6.3e+03      49      61 ..      73      85 ..      62      94 .. 0.59
   2 !   76.5   0.0   5.4e-25   1.6e-21       2     113 ..     100     215 ..      99     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.1
                                      HHHHHHHTTTS-- CS
                            SBDS_C 49 levikaLiqeipi 61
                                      +e+ik++i+e ++
  gi|488601701|ref|YP_007908172.1| 73 QEIIKEIIREGEV 85
                                      4455555544444 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 5.4e-25
                                       HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CC CS
                            SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikd 78 
                                       +k+ii+++++++v+p+t++p+++++Ie+al+e+++++++ k+ ++Q+ ++ikaL+ ++pi+ ++++++i++p +   
  gi|488601701|ref|YP_007908172.1| 100 RKQIIDYISKNTVDPRTGTPHPPSRIERALEEARVHIDIFKKIEAQIKDIIKALKPILPIRVEEVEIAIKIPPEY-- 174
                                       79**********************************************************************555.. PP

                                       CHHHHHHHH.HH.....S.EE......EEEEEEGGGHHHHHH CS
                            SBDS_C  79 kilklieqv.esqkvaekewe......vvvliePgaykelee 113
                                        + k i+ + +  ++ ++ew+      +v+ i++g+  +l +
  gi|488601701|ref|YP_007908172.1| 175 -AGKSISALySFGNIIQEEWQkdgswiCVIRIPAGLKGDLLD 215
                                       .44444444333223333433333332777799998777765 PP

>> UPF0262  Uncharacterised protein family (UPF0262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   9.8e-06     0.029      16      81 ..      90     156 ..      74     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.8e-06
                           UPF0262  16 rasaeveqerkvAifDlleensfaleg.eeegpyklklsleekrlvldireeeeeelaelilsltpf 81 
                                       ++++e+ ++++  i+D + +n+  + + + + p +++ +lee r+++di ++ e++++ +i +l+p+
  gi|488601701|ref|YP_007908172.1|  90 EQRKEMLEQKRKQIIDYISKNTVDPRTgTPHPPSRIERALEEARVHIDIFKKIEAQIKDIIKALKPI 156
                                       333444445566799**********987899*****************************9999986 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 ?   -1.7   0.1         1   3.1e+03      18      25 ..      72      79 ..      45     106 .. 0.61
   2 ?   12.6   0.0   3.7e-05      0.11       8      70 ..     165     226 ..     162     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                                      CCCHHHHH CS
                             EFG_C 18 vgkvisdl 25
                                      ++++i+++
  gi|488601701|ref|YP_007908172.1| 72 IQEIIKEI 79
                                      33333333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.7e-05
                                       EEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-E CS
                             EFG_C   8 kveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegs 70 
                                       ++ i++p ey gk is l s   +i++  q+ +g  i   +iP+    ++ + L  lT+Ge+ 
  gi|488601701|ref|YP_007908172.1| 165 EIAIKIPPEYAGKSISALYSFGNIIQEEWQK-DGSWICVIRIPAGLKGDLLDLLARLTQGEAL 226
                                       6889*****************9999999999.555556689**99999************995 PP

>> DUF2278  Uncharacterized conserved protein (DUF2278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.4e-05     0.071      83     146 ..      95     191 ..      50     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                           DUF2278  83 lesepkglaLDyirsklldlkkgrvlphd..................kpgedndildklepilkkaieek....... 134
                                       + ++++++ +Dyi ++ +d+++g+++p +                  ++ + +di++ l+pil   +ee        
  gi|488601701|ref|YP_007908172.1|  95 MLEQKRKQIIDYISKNTVDPRTGTPHPPSrieraleearvhidifkkIEAQIKDIIKALKPILPIRVEEVeiaikip 171
                                       335778889******************999******88888888888888888888888888888877778899999 PP

                           DUF2278 135 ........atvyvFGekfed 146
                                                 +y FG+  ++
  gi|488601701|ref|YP_007908172.1| 172 peyagksiSALYSFGNIIQE 191
                                       99999998889999976655 PP

>> HD_assoc  Phosphohydrolase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   9.3e-05      0.28       4      79 ..      24     108 ..      21     111 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.3e-05
                          HD_assoc   4 seevaaeiaeLkkflfenvyrhpevqreeekarri.ireLfealle.dperllpeefrarl.....eaaedd..ara 71 
                                       ++ +a+ ++e k++ f+ ++  +ev ++ +k++r  i+eL +++ + + ++ ++e +r+       e++++   +++
  gi|488601701|ref|YP_007908172.1|  24 DPYLARDLKEGKEVNFDDLVAVEEVYKDSKKGERAsIEELKKVFGTsNIQEIIKEIIREGEvqitaEQRKEMleQKR 100
                                       56677888899999***********99999987644********552444455554444333333244444498999 PP

                          HD_assoc  72 RvVcDyiA 79 
                                       ++++Dyi+
  gi|488601701|ref|YP_007908172.1| 101 KQIIDYIS 108
                                       9******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1358  (0.0757432); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1466.20
//
Query:       gi|488601702|ref|YP_007908173.1|  [L=223]
Description: ribosomal RNA-processing protein RRP4 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-07   30.4   0.0    4.5e-07   29.6   0.0    1.5  1  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region
    3.3e-06   26.8   0.4    9.1e-06   25.4   0.4    1.7  1  KH_1      KH domain
    5.1e-06   26.2   4.3    6.8e-06   25.8   1.6    2.5  2  KH_2      KH domain
    2.7e-05   24.4   0.2    5.6e-05   23.4   0.2    1.6  1  KH_6      KH domain
  ------ inclusion threshold ------
      0.018   15.4   0.2      0.087   13.2   0.1    2.2  2  S1        S1 RNA binding domain
       0.12   12.2   0.0        0.4   10.5   0.0    1.8  2  PapC_C    PapC C-terminal 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 !   29.6   0.0   1.5e-10   4.5e-07       1      37 [.       5      40 ..       5      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.5e-10
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                      iV+PG+ + t +  ++G GT+v++g++yA ++G v +
  gi|488601702|ref|YP_007908173.1|  5 IVLPGDLVSTNP-KLAGYGTFVENGKVYAKIMGLVDR 40
                                      9*******5555.589******************986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.4   3.1e-09   9.1e-06       6      64 ..     141     192 ..     137     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.1e-09
                                       EGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                              KH_1   6 vPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                       ++   v+r+IGk+Gs+Ik +++e g +  v  ++     +  + +sG++ +v+ A+e+i
  gi|488601702|ref|YP_007908173.1| 141 INPTRVPRVIGKKGSMIKLLKSELGIQTIV--GQ-----NGLIWLSGDRRKVDIAEEAI 192
                                       66667*****************88*99554..43.....469*****9999*****998 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   1.6   2.3e-09   6.8e-06      16      68 ..     128     178 ..     108     186 .. 0.88
   2 ?   -0.2   0.1      0.31   9.2e+02      16      35 ..     183     200 ..     179     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.3e-09
                                       EEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                              KH_2  16 skveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                                       + ++I r   + i+ i   +  +vIGk+Gs+ik +++el+ ++ + +++ ++l
  gi|488601702|ref|YP_007908173.1| 128 KICRIIR--FGRIVAINPTRVPRVIGKKGSMIKLLKSELGIQTIVGQNGLIWL 178
                                       5577767..889*******************************9999999987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.31
                                       EEEEEECCSCEEEEEEEESC CS
                              KH_2  16 skveIertanrviiviresq 35 
                                       +kv+I  +++++ i++re++
  gi|488601702|ref|YP_007908173.1| 183 RKVDI--AEEAIYIIEREAH 200
                                       57788..4589999999987 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   1.9e-08   5.6e-05       1      42 [.     136     180 ..     136     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.9e-08
                              KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvks 42 
                                       G ++ + +  v+R++     +++ L+ +++++++vG+NG iW+++
  gi|488601702|ref|YP_007908173.1| 136 GRIVAINPTRVPRVIgkkGSMIKLLKSELGIQTIVGQNGLIWLSG 180
                                       6678999********555333355556688************987 PP

>> S1  S1 RNA binding domain
   #    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      37 ..      21      43 ..      16      48 .. 0.73
   2 ?   13.2   0.1   2.9e-05     0.087       3      68 ..      57     120 ..      55     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.94
                                      TEEEEEET...TTEEEEEEGGGS CS
                                S1 18 gGafVelg...ngvegfvpasel 37
                                      +G fVe g   +++ g+v +se 
  gi|488601702|ref|YP_007908173.1| 21 YGTFVENGkvyAKIMGLVDRSET 43
                                      67788877766777788888875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.9e-05
                                       TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTT CS
                                S1   3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrr 68 
                                         g+vv G+V +++  G  V++  + ++f+p  e +    +  ++  +  +d + +kv  +d + +
  gi|488601702|ref|YP_007908173.1|  57 SNGDVVIGVVREIVSNGYNVDINSPYSAFLPSTEKPEI--KGRRNSDIELDDAIIAKVVAIDPKMK 120
                                       679****************************8887754..6669999999********99998766 PP

>> PapC_C  PapC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.4   4.1e+03      30      40 ..      25      35 ..      16      42 .. 0.76
   2 ?   10.5   0.0   0.00013       0.4      15      41 ..     154     182 ..     152     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                                      -CCCEEEEECE CS
                            PapC_C 30 gqgGqvylrgl 40
                                       ++G+vy+  +
  gi|488601702|ref|YP_007908173.1| 25 VENGKVYAKIM 35
                                      67899998655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                                       T-EEEETTSSS..-EEB-CCCEEEEECE- CS
                            PapC_C  15 GAevtdeengk..vgiVgqgGqvylrglp 41 
                                       G+++ + +++   ++iVgq+G ++l+g  
  gi|488601702|ref|YP_007908173.1| 154 GSMIKLLKSELgiQTIVGQNGLIWLSGDR 182
                                       78888886666856************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); 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:                         6  (0.000334653); expected 0.2 (1e-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 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1290.99
//
Query:       gi|488601703|ref|YP_007908174.1|  [L=247]
Description: ribosomal RNA-processing protein RRP41/SKI6 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-37  129.4   0.0    1.7e-37  128.9   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    1.8e-12   47.1   0.1    3.6e-12   46.1   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 !  128.9   0.0   1.9e-41   1.7e-37       1     132 []      21     150 ..      21     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 1.9e-41
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeie 77 
                                       elR+++ie g+l++a+GS+y+e+G++kv+a+v+gp+e++p+  +d+++ ++  ++++apf+ +er+r   p+++++e
  gi|488601703|ref|YP_007908174.1|  21 ELRPIKIEAGILKRADGSCYIEMGKNKVVAAVYGPREVHPRHLQDPSKAVVRYRYNMAPFSVEERKR-PGPDRRSVE 96 
                                       79************************************88888777777799999999*******87.56******* PP

                                       HHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  78 lsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       +s++  +a++p+i+ e +p+s idi+++vl++d  ++  a+inaa++AL+dagip
  gi|488601703|ref|YP_007908174.1|  97 ISKVSREAFEPVIMKELFPRSGIDIFVEVLQADA-GTRTACINAATVALVDAGIP 150
                                       **********************************.*******************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 !   46.1   0.1     4e-16   3.6e-12       2      67 .]     154     221 ..     153     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4e-16
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEE...ETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlav...agtkevvtlmkeggsqldeetlleaielAkkg 67 
                                       ++ +v+v+k d+ +vlDp keE++++e+d+++a    +g+ e+++l++++g  l++e+l++a  +Ak+g
  gi|488601703|ref|YP_007908174.1| 154 LITSVAVAKADGVLVLDPMKEEDNYGEADVPFAFlirNGKIESIALLQMDGR-LSAEELKKATQMAKEG 221
                                       6779************************************************.*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 1343.88
//
Query:       gi|488601704|ref|YP_007908175.1|  [L=259]
Description: ribosomal RNA-processing protein RRP42 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-29  103.6   0.0    1.5e-29  103.1   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    2.1e-11   43.7   0.1    3.8e-11   42.8   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 !  103.1   0.0   1.7e-33   1.5e-29       1     132 []      31     166 ..      31     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 1.7e-33
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeei 76 
                                       e+R+++iet+++s+a+GSa+++lGdt+v++++++++ e p++++ d  +g + ++ e+ p+as++++  g p++++i
  gi|488601704|ref|YP_007908175.1|  31 EVRKIQIETNIISKAEGSALVKLGDTQVMVGIKMQVGE-PFPDTpD--KGIIITNAELVPLASPTFEA-GPPDETSI 103
                                       78**********************************99.8888744..578***************55.9******* PP

                                       HHHHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  77 elsrlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       el+r+++r +r+s  +        e+++ + + idi+ l++dg +l da+ +aa+ AL+++ +p
  gi|488601704|ref|YP_007908175.1| 104 ELARIVDRGIRESEAVdlhklcieEGEKVWIVFIDIHALDDDG-NLVDASALAAISALLNTTVP 166
                                       ***************88888899999999**************.*****************998 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 !   42.8   0.1   4.3e-15   3.8e-11       1      64 [.     182     245 ..     182     248 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 4.3e-15
                                       S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHH CS
                        RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielA 64 
                                       ++++avt  +v+d++++Dp+ +E ++++  lt++ ++++++v+++k+g+  ldee++ e i+++
  gi|488601704|ref|YP_007908175.1| 182 DLPVAVTSLVVGDKYLVDPNRDEMSVGNKLLTITTDKDDNIVAIQKSGSYLLDEEKFYELIDVS 245
                                       589**********************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.37s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1366.68
//
Query:       gi|488601705|ref|YP_007908176.1|  [L=88]
Description: LSU ribosomal protein L37AE [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-33  114.6   5.3    1.9e-33  114.4   5.3    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
     0.0012   18.7   5.5     0.0025   17.8   5.6    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0057   16.3   4.4        0.8    9.5   0.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
     0.0077   16.3   0.5        1.2    9.3   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
     0.0089   15.8   0.8      0.011   15.5   0.8    1.1  1  Rep_fac-A_C      Replication factor-A C terminal domain
  ------ inclusion threshold ------
       0.04   13.8   4.3      0.071   13.0   4.3    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.089   12.6   2.2      0.089   12.6   2.2    1.9  2  zf-CCHC_2        Zinc knuckle
        0.1   12.5   2.6       0.14   12.1   2.6    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
       0.17   11.8   3.7        3.3    7.7   0.2    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.25   11.7   2.6       0.43   10.9   2.5    1.4  1  C1_2             C1 domain
       0.26   11.8   5.5       0.46   11.0   0.7    2.2  2  zf-H2C2_2        Zinc-finger double domain
       0.61    9.6   4.5          7    6.2   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.87    9.0   5.5        1.8    8.0   0.9    2.1  2  zf-RanBP         Zn-finger in Ran binding protein and others
        1.1    9.2   5.7        9.6    6.2   4.4    2.2  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        2.3    8.2   6.1          3    7.8   4.1    1.9  2  HalOD2           Halobacterial output domain 2
        2.3    8.3   6.8        6.8    6.8   1.4    2.2  2  zf-BED           BED zinc finger


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 !  114.4   5.3   1.7e-36   1.9e-33       1      78 [.       3      80 ..       3      85 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.7e-36
                                      XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH CS
                   Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvks 78
                                      rtkkv+iaG++g rYG+++rk++ kie++q++ky C++cgk++vkR+++giw+Ck+cg+++aGg+y+p t+s k + +
  gi|488601705|ref|YP_007908176.1|  3 RTKKVKIAGRFGSRYGVRVRKNIIKIEQEQRRKYVCNRCGKKRVKRVGTGIWECKSCGYKFAGGTYIPVTPSVKLIDK 80
                                      79**********************************************************************998876 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 !   17.8   5.6   2.2e-06    0.0025      19      45 ..      36      61 ..      30      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                       vC +Cg++++ r+ t g ++Ck+C++
  gi|488601705|ref|YP_007908176.1| 36 YVCNRCGKKRVKRVGT-GIWECKSCGY 61
                                      69**************.********98 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2   0.00071       0.8       1      12 [.      36      47 ..      36      51 .. 0.78
   2 !    8.5   0.6    0.0014       1.6       1      10 [.      54      63 ..      54      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00071
                      Rubredoxin_2  1 YvCsqCGfesak 12
                                      YvC++CG +  k
  gi|488601705|ref|YP_007908176.1| 36 YVCNRCGKKRVK 47
                                      9******87665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0014
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      ++C++CG+++
  gi|488601705|ref|YP_007908176.1| 54 WECKSCGYKF 63
                                      79*****986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1     0.001       1.2      25      39 ..      33      49 ..      21      50 .. 0.72
   2 ?    5.5   0.0     0.016        18       7      15 ..      55      63 ..      53      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                       Zn-ribbon_8 25 plta.CPeCgs.evrrv 39
                                        +  C +Cg+ +v+rv
  gi|488601705|ref|YP_007908176.1| 33 RRKYvCNRCGKkRVKRV 49
                                      44555999999888886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                       Zn-ribbon_8  7 rCeeCghef 15
                                      +C++Cg +f
  gi|488601705|ref|YP_007908176.1| 55 ECKSCGYKF 63
                                      7*****998 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 !   15.5   0.8   9.5e-06     0.011       5      49 ..      22      65 ..      19      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.5e-06
                                      EEEEEEEETTTTEEEB--STT---B-EEE.TTTEEEETTTTEEESS CS
                       Rep_fac-A_C  5 katvsfikkdnlvYkACpsedCnkKvvee.edgewrCekCdkevee 49
                                      +  + +i++++     C+   C kK v++ + g w C+ C  +++ 
  gi|488601705|ref|YP_007908176.1| 22 RKNIIKIEQEQRRKYVCN--RCGKKRVKRvGTGIWECKSCGYKFAG 65
                                      556778888877777899..*****9999889********988765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.3   6.3e-05     0.071      30      56 ..      37      63 ..      15      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                       C++Cg+k  +++ +  ++C++Cg+++
  gi|488601705|ref|YP_007908176.1| 37 VCNRCGKKRVKRVGTGIWECKSCGYKF 63
                                      5**********9************985 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.2   7.9e-05     0.089       2      12 ..      34      44 ..      33      44 .. 0.89
   2 ?   -0.7   0.2       1.2   1.3e+03       6      10 ..      56      60 ..      53      62 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.9e-05
                         zf-CCHC_2  2 pgYvChiCgkk 12
                                      + YvC++Cgkk
  gi|488601705|ref|YP_007908176.1| 34 RKYVCNRCGKK 44
                                      57*******98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                         zf-CCHC_2  6 ChiCg 10
                                      C+ Cg
  gi|488601705|ref|YP_007908176.1| 56 CKSCG 60
                                      77776 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 ?   12.1   2.6   0.00013      0.14       9      38 ..      33      63 ..      27      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      SS--B-TTT-SB--S.SSS-EEEETTT--EE CS
                              C1_1  9 kqptfCkhCgeflwg.kekqglkCswCkllv 38
                                      +++  C+ Cg+   +  ++ ++ C+ C++++
  gi|488601705|ref|YP_007908176.1| 33 RRKYVCNRCGKKRVKrVGTGIWECKSCGYKF 63
                                      67789*****998777************975 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0029       3.3      25      37 ..      32      44 ..      27      45 .. 0.84
   2 ?    5.3   0.5     0.016        18      29      38 ..      54      63 ..      51      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0029
                           TFIIS_C 25 mtvfykCtkCghr 37
                                      + + y+C+ Cg++
  gi|488601705|ref|YP_007908176.1| 32 QRRKYVCNRCGKK 44
                                      67889*****986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                           TFIIS_C 29 ykCtkCghrW 38
                                       +C++Cg+++
  gi|488601705|ref|YP_007908176.1| 54 WECKSCGYKF 63
                                      58999*9998 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.5   0.00039      0.43      13      41 ..      30      62 ..      21      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                              C1_2 13 edssesfnCsaCgrk....idgff...YsCseCdfs 41
                                      +++  ++ C+ Cg+k    +        +C+ C ++
  gi|488601705|ref|YP_007908176.1| 30 QEQRRKYVCNRCGKKrvkrV---GtgiWECKSCGYK 62
                                      5667889********95533...4558***99*886 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.6      0.11   1.2e+02      12      23 ..      33      44 ..      26      47 .. 0.80
   2 ?   11.0   0.7   0.00041      0.46      14      25 ..      53      64 ..      44      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                         zf-H2C2_2 12 ekpyeCplCdka 23
                                       ++y C  C+k+
  gi|488601705|ref|YP_007908176.1| 33 RRKYVCNRCGKK 44
                                      467*******96 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00041
                         zf-H2C2_2 14 pyeCplCdkaFk 25
                                      ++eC++C+++F+
  gi|488601705|ref|YP_007908176.1| 53 IWECKSCGYKFA 64
                                      79*********6 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0062         7       2      11 ..      35      44 ..      34      48 .. 0.77
   2 ?    4.7   1.0     0.018        20      19      26 .]      56      63 ..      56      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0062
                       zf-ribbon_3  2 tvrCPnCGap 11
                                      ++ C++CG++
  gi|488601705|ref|YP_007908176.1| 35 KYVCNRCGKK 44
                                      578*****95 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
                       zf-ribbon_3 19 CpyCGtkl 26
                                      C++CG+k+
  gi|488601705|ref|YP_007908176.1| 56 CKSCGYKF 63
                                      *****985 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 ?    3.4   0.3     0.042        48      20      25 ..      37      42 ..      33      45 .. 0.83
   2 ?    8.0   0.9    0.0016       1.8       3      13 ..      52      62 ..      51      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.042
                                      B-TTT- CS
                          zf-RanBP 20 kCvaCq 25
                                      +C++C+
  gi|488601705|ref|YP_007908176.1| 37 VCNRCG 42
                                      7****7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                                      SSEE-SSS--E CS
                          zf-RanBP  3 gdWdCskClvq 13
                                      g W+C++C+++
  gi|488601705|ref|YP_007908176.1| 52 GIWECKSCGYK 62
                                      55******985 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.1      0.23   2.5e+02      16      28 ..      29      42 ..      25      46 .. 0.77
   2 ?    6.2   4.4    0.0085       9.6      20      31 ..      51      63 ..      38      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                                      CSCCCE.EEESSSS CS
                    RNA_POL_M_15KD 16 dkegkn.feCrqCg 28
                                       +e ++ + C  Cg
  gi|488601705|ref|YP_007908176.1| 29 EQEQRRkYVCNRCG 42
                                      577777899**998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0085
                                      CE.EEESSSS-EE CS
                    RNA_POL_M_15KD 20 kn.feCrqCgYee 31
                                      +   eC +CgY++
  gi|488601705|ref|YP_007908176.1| 51 TGiWECKSCGYKF 63
                                      44589******97 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.39   4.4e+02      34      39 ..      38      43 ..      34      47 .. 0.80
   2 ?    7.8   4.1    0.0027         3      22      42 ..      43      64 ..      39      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.39
                            HalOD2 34 CtrCGe 39
                                      C rCG+
  gi|488601705|ref|YP_007908176.1| 38 CNRCGK 43
                                      999997 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0027
                            HalOD2 22 e.GyrqLGayvWkCtrCGevqa 42
                                      +  +++ G+ +W C  CG   a
  gi|488601705|ref|YP_007908176.1| 43 KkRVKRVGTGIWECKSCGYKFA 64
                                      546899************7655 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.4     0.006       6.8      12      29 ..      31      48 ..      25      53 .. 0.78
   2 ?    5.0   0.4     0.021        24      15      29 ..      52      66 ..      46      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.006
                                      GGSS--EETTTTEE---- CS
                            zf-BED 12 lkeqkavCryCgkilsrg 29
                                      +++ k vC+ Cgk+   +
  gi|488601705|ref|YP_007908176.1| 31 EQRRKYVCNRCGKKRVKR 48
                                      78999********86665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.021
                                      S--EETTTTEE---- CS
                            zf-BED 15 qkavCryCgkilsrg 29
                                      + ++C+ Cg ++++g
  gi|488601705|ref|YP_007908176.1| 52 GIWECKSCGYKFAGG 66
                                      679******999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 545.53
//
Query:       gi|488601706|ref|YP_007908177.1|  [L=46]
Description: DNA-directed RNA polymerase, subunit P [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-08   33.0   1.1    5.3e-08   32.4   1.1    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
     0.0012   18.0   0.4     0.0012   18.0   0.4    1.0  1  Tmemb_55A       Transmembrane protein 55A
     0.0044   16.9   2.0     0.0057   16.5   2.0    1.1  1  PHD             PHD-finger
     0.0048   16.8   0.4          2    8.4   0.1    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0073   15.8   0.6     0.0089   15.5   0.6    1.1  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.025   14.2   1.9        1.8    8.2   0.2    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.025   14.3   2.4      0.035   13.8   2.4    1.2  1  A2L_zn_ribbon   A2L zinc ribbon domain
      0.028   14.3   1.2      0.035   14.0   1.2    1.1  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.032   14.3   0.1       0.05   13.7   0.1    1.3  1  Zn-ribbon_8     Zinc ribbon domain
      0.033   14.2   0.2      0.036   14.1   0.2    1.2  1  Elf1            Transcription elongation factor Elf1 like
       0.04   13.9   0.1      0.046   13.6   0.1    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.07   13.0   1.5      0.074   13.0   0.2    1.7  2  DUF951          Bacterial protein of unknown function (DUF951
      0.095   12.7   0.4       0.12   12.4   0.4    1.1  1  DUF1451         Zinc-ribbon containing domain
       0.13   12.3   0.2       0.21   11.6   0.2    1.5  1  zf-C3HC         C3HC zinc finger-like
       0.39   10.5   3.3          4    7.3   3.3    2.0  1  zf-HYPF         HypF finger


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   1.1   4.5e-11   5.3e-08       1      32 []       3      35 ..       3      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 4.5e-11
                                      -B-SSS--B--.--SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCGhRilYKkR 32
                                      YiC  C++e   +  +  i+C++CG Ril K+R
  gi|488601706|ref|YP_007908177.1|  3 YICLVCQSEIDvDLDRNLIQCTKCGNRILLKPR 35
                                      ******99877644555**************99 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.4   9.8e-07    0.0012      61     100 ..       5      43 ..       1      46 [] 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.8e-07
                         Tmemb_55A  61 CrvCqslidvegkleqhvvkCevCneatpikn.apagkkyv 100
                                       C vCqs idv+   ++  ++C++C +   +k+ +pa kk v
  gi|488601706|ref|YP_007908177.1|   5 CLVCQSEIDVDL--DRNLIQCTKCGNRILLKPrPPALKKRV 43 
                                       9********985..6679***********997255667766 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.0   4.8e-06    0.0057       1      23 [.       4      28 ..       4      30 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.8e-06
                                      SBTTTTS..TTSTTSCEEEETTTSC CS
                               PHD  1 rCavCkk..ksdeeeelvqCdgCkr 23
                                      +C vC++  + d +++l+qC +C++
  gi|488601706|ref|YP_007908177.1|  4 ICLVCQSeiDVDLDRNLIQCTKCGN 28
                                      6******999999**********97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0045       5.4       5      15 ..       3      13 ..       2      16 .. 0.80
   2 !    8.4   0.1    0.0017         2       6      22 ..      22      36 ..      22      40 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0045
                    Zn_ribbon_SprT  5 YrCtgCgreyt 15
                                      Y C  C++e++
  gi|488601706|ref|YP_007908177.1|  3 YICLVCQSEID 13
                                      89999998865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
                    Zn_ribbon_SprT  6 rCtgCgreythhlsi.rr 22
                                      +Ct Cg   +++l + r+
  gi|488601706|ref|YP_007908177.1| 22 QCTKCG---NRILLKpRP 36
                                      7*****...777766565 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   7.4e-06    0.0089       1      27 [.       3      28 ..       3      30 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.4e-06
                                      EEETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                      y+C +C s+ + +D +r+ + Ct+CG+
  gi|488601706|ref|YP_007908177.1|  3 YICLVCQSE-IDVDLDRNLIQCTKCGN 28
                                      79*****97.99**************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 ?    6.4   0.1    0.0058       6.9       2      16 ..       2      17 ..       1      20 [. 0.86
   2 ?    8.2   0.2    0.0015       1.8       3      13 ..      21      31 ..      19      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0058
                            zf_UBZ  2 tylCerCgkeipes.e 16
                                      +y+C  C++ei ++ +
  gi|488601706|ref|YP_007908177.1|  2 SYICLVCQSEIDVDlD 17
                                      69*********99855 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                            zf_UBZ  3 ylCerCgkeip 13
                                      ++C +Cg +i+
  gi|488601706|ref|YP_007908177.1| 21 IQCTKCGNRIL 31
                                      78*******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 ?   13.8   2.4   2.9e-05     0.035       4      29 ..       3      28 ..       2      29 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                     A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCga 29
                                      ++C vC ++ ++  +++  +C +Cg+
  gi|488601706|ref|YP_007908177.1|  3 YICLVCQSEIDVDLDRNLIQCTKCGN 28
                                      79***********************7 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.2   2.9e-05     0.035       5      27 ..       3      27 ..       1      29 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                       Prok-RING_1  5 kkCpvCgkelkee..dDiVvCpeCg 27
                                       +C vC+ e++ +    +++C++Cg
  gi|488601706|ref|YP_007908177.1|  3 YICLVCQSEIDVDldRNLIQCTKCG 27
                                      58********99844669******9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.2e-05      0.05       6      34 ..       3      28 ..       2      31 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsis.dapltaCPeCgs 34
                                      Y C  C++e +v    + d++l++C +Cg 
  gi|488601706|ref|YP_007908177.1|  3 YICLVCQSEIDV----DlDRNLIQCTKCGN 28
                                      99*****99994....44788*******97 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2     3e-05     0.036      22      56 ..       3      31 ..       1      45 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                              Elf1 22 FdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                      + C++C++e  ++v+ld++     ++C++Cg ++ 
  gi|488601706|ref|YP_007908177.1|  3 YICLVCQSE--IDVDLDRN----LIQCTKCGNRIL 31
                                      56*******..99999998....9*******9765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.8e-05     0.046      28      55 ..       2      29 ..       1      31 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                    OrfB_Zn_ribbon 28 SktCseCgsknkealsgrtfkCpnCgfe 55
                                      S  C +C s+ + +l++++ +C++Cg +
  gi|488601706|ref|YP_007908177.1|  2 SYICLVCQSEIDVDLDRNLIQCTKCGNR 29
                                      778***********************86 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 ?   -0.5   0.1         1   1.2e+03      33      41 ..       5      13 ..       3      22 .. 0.71
   2 ?   13.0   0.2   6.2e-05     0.074      31      53 ..      21      45 ..      16      46 .] 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1
                            DUF951 33 Clgcgrevm 41
                                      Cl c+ e+ 
  gi|488601706|ref|YP_007908177.1|  5 CLVCQSEID 13
                                      888888774 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.2e-05
                            DUF951 31 lkClgcgrevml.pRs.kfekkikk 53
                                      ++C++cg+ ++l pR   ++k++k 
  gi|488601706|ref|YP_007908177.1| 21 IQCTKCGNRILLkPRPpALKKRVKA 45
                                      89********972554256777776 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   9.7e-05      0.12     116     140 ..       4      28 ..       2      31 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.7e-05
                           DUF1451 116 vCekCgkelalkkteeippCpkCga 140
                                       +C  C+ e++++  +++ +C kCg+
  gi|488601706|ref|YP_007908177.1|   4 ICLVCQSEIDVDLDRNLIQCTKCGN 28 
                                       7**********************98 PP

>> zf-C3HC  C3HC zinc finger-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00018      0.21      40      65 ..      17      40 ..       4      45 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                           zf-C3HC 40 skdrlkCevCgaslvlklksseeesd 65
                                      +++ ++C+ Cg++++lk  + + +++
  gi|488601706|ref|YP_007908177.1| 17 DRNLIQCTKCGNRILLK--PRPPALK 40
                                      599************99..5555544 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.3    0.0034         4       1      30 [.       4      29 ..       4      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0034
                                      --HHHHHHHC-TTSTTTT-TT---TTTS-- CS
                           zf-HYPF  1 lCedClrEykdpldRRfhaqfisCtnCGPr 30
                                      +C  C+ E++  ldR      i Ct+CG r
  gi|488601706|ref|YP_007908177.1|  4 ICLVCQSEIDVDLDR----NLIQCTKCGNR 29
                                      577888888888888....6799****977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 261.33
//
Query:       gi|488601707|ref|YP_007908178.1|  [L=54]
Description: Rubredoxin [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-25   89.4   4.2    1.2e-25   89.2   4.2    1.0  1  Rubredoxin      Rubredoxin
    0.00026   20.4   1.9       0.18   11.4   0.3    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.015   15.4   2.3      0.041   14.0   2.2    1.8  1  Zn-ribbon_8     Zinc ribbon domain
      0.016   15.6   1.5       0.76   10.3   0.2    2.1  2  zf-H2C2_2       Zinc-finger double domain
      0.021   14.5   1.3        2.3    8.0   0.0    2.2  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.028   14.1   0.3      0.028   14.1   0.3    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
      0.028   13.7   2.4       0.06   12.7   0.2    2.1  2  zf-RanBP        Zn-finger in Ran binding protein and others
       0.03   13.7   0.4       0.15   11.5   0.1    2.0  2  Vps36-NZF-N     Vacuolar protein sorting 36 NZF-N zinc-finger
      0.034   14.2   0.1      0.036   14.1   0.1    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.035   13.8   0.9        2.8    7.8   0.0    2.1  2  A2L_zn_ribbon   A2L zinc ribbon domain
       0.04   14.2   0.6        2.4    8.5   0.0    2.1  2  zf-nanos        Nanos RNA binding domain
      0.045   13.4   0.3        2.6    7.8   0.0    2.1  2  zf_C2H2_ZHX     Zinc-fingers and homeoboxes C2H2 finger domai
      0.049   13.5   1.0         11    6.0   0.1    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.075   12.8   1.4        3.8    7.3   0.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.081   12.9   0.9        2.7    8.1   0.5    2.0  2  ADK_lid         Adenylate kinase, active site lid
       0.09   13.7   0.6         19    6.4   0.1    2.2  2  zf-C2H2_4       C2H2-type zinc finger
      0.093   12.8   5.2        3.9    7.6   5.5    2.1  1  PHD_4           PHD-finger
       0.15   11.6   0.1        6.3    6.4   0.1    2.2  2  zf-C2H2_12      Zinc-finger C2H2-type
       0.17   11.8   2.4        1.1    9.2   0.3    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.24   11.2   7.6        3.4    7.5   0.8    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
        0.3   11.4   2.0         19    5.7   0.0    2.1  2  C1_2            C1 domain
       0.53   10.9   3.0        7.7    7.2   0.4    2.2  2  zf-C2H2         Zinc finger, C2H2 type
       0.54   10.1   4.4        2.1    8.2   0.7    2.1  2  Cys_rich_CPCC   Cysteine-rich CPCC
        0.6   10.1   5.7        3.1    7.8   0.2    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        0.8    9.7   4.9        8.4    6.4   4.9    2.0  1  Prok-RING_1     Prokaryotic RING finger family 1


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 !   89.2   4.2   1.7e-28   1.2e-25       1      47 []       3      49 ..       3      49 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 1.7e-28
                                      EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                      ky+C vCgyvYd+++Gdp++++ +gTk+edlPddWvCP+Cg++k++F
  gi|488601707|ref|YP_007908178.1|  3 KYQCMVCGYVYDEDEGDPESNVLAGTKWEDLPDDWVCPVCGASKDEF 49
                                      7********************************************99 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   0.00025      0.18      20      38 ..       4      22 ..       2      23 .. 0.87
   2 !    8.7   0.1    0.0016       1.2       2      13 ..      38      49 ..      37      54 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                      EEESSSSBEEEECCCCCCC CS
                      TF_Zn_Ribbon 20 lvCtdCGlVlednsidegp 38
                                      + C  CG+V +++  d+++
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVYDEDEGDPES 22
                                      569***********99985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                                      EETTTTCEECHE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlve 13
                                      +CP+Cg +++++
  gi|488601707|ref|YP_007908178.1| 38 VCPVCGASKDEF 49
                                      799999977655 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.2   5.7e-05     0.041       6      34 ..       4      44 ..       3      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-05
                       Zn-ribbon_8  6 YrCeeCghefe.........vlqsis..daplta.CPeCgs 34
                                      Y+C  Cg +++         vl+  +  d p+   CP Cg+
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVYDedegdpesnVLAGTKweDLPDDWvCPVCGA 44
                                      9******************9888888767778888*****8 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2    0.0011      0.76      14      24 ..       3      13 ..       2      15 .. 0.88
   2 ?    4.8   0.1     0.059        42      15      21 ..      37      43 ..      31      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                         zf-H2C2_2 14 pyeCplCdkaF 24
                                      +y+C++C++++
  gi|488601707|ref|YP_007908178.1|  3 KYQCMVCGYVY 13
                                      59*******98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.059
                         zf-H2C2_2 15 yeCplCd 21
                                      + Cp+C+
  gi|488601707|ref|YP_007908178.1| 37 WVCPVCG 43
                                      68****8 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.7     0.018        13      44      52 ..       3      11 ..       1      13 [. 0.86
   2 ?    8.0   0.0    0.0032       2.3      39      52 ..      29      44 ..      20      46 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.018
                    zinc_ribbon_10 44 kyrCpkCga 52
                                      ky+C+ Cg 
  gi|488601707|ref|YP_007908178.1|  3 KYQCMVCGY 11
                                      8******97 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                    zinc_ribbon_10 39 eleev..kyrCpkCga 52
                                      ++e++   ++Cp Cga
  gi|488601707|ref|YP_007908178.1| 29 KWEDLpdDWVCPVCGA 44
                                      55555558******97 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.4       1.4     1e+03       8      20 ..       7      18 ..       4      18 .. 0.57
   2 ?   14.1   0.3   3.9e-05     0.028       4      19 ..      36      54 .]      34      54 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                           zf-RRN7  8 gvCgcrsftlddG 20
                                       vCg + +++d+G
  gi|488601707|ref|YP_007908178.1|  7 MVCG-YVYDEDEG 18
                                      5555.35666666 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.9e-05
                           zf-RRN7  4 gppCgvCgc..rsftl.dd 19
                                       ++C+vCg+  ++f   +d
  gi|488601707|ref|YP_007908178.1| 36 DWVCPVCGAskDEFEKlED 54
                                      589*******889998777 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 ?    0.8   0.1      0.44   3.2e+02       6      12 ..       5      11 ..       5      12 .. 0.77
   2 ?   12.7   0.2   8.3e-05      0.06       3      12 ..      35      44 ..      33      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.44
                                      E-SSS-- CS
                          zf-RanBP  6 dCskClv 12
                                      +C +C++
  gi|488601707|ref|YP_007908178.1|  5 QCMVCGY 11
                                      7888986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.3e-05
                                      SSEE-SSS-- CS
                          zf-RanBP  3 gdWdCskClv 12
                                      +dW C++C++
  gi|488601707|ref|YP_007908178.1| 35 DDWVCPVCGA 44
                                      89******96 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.46   3.3e+02      35      40 ..       5      10 ..       1      16 [. 0.69
   2 ?   11.5   0.1   0.00021      0.15       8      18 ..      35      45 ..      28      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.46
                       Vps36-NZF-N 35 pClaCG 40
                                       C  CG
  gi|488601707|ref|YP_007908178.1|  5 QCMVCG 10
                                      466666 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00021
                       Vps36-NZF-N  8 atWvCpICsfs 18
                                       +WvCp+C  s
  gi|488601707|ref|YP_007908178.1| 35 DDWVCPVCGAS 45
                                      68******876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     5e-05     0.036      69      99 ..       2      49 ..       1      54 [] 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                                      -EEEETTTS-EEECHH.H.HH...............S-TTTSSS-EEE CS
                              HypA 69 vkvrCreCgkefelee.k.al...............rCpkCgsadvei 99
                                      +k++C +Cg+ ++++e + +                 Cp Cg+++ e+
  gi|488601707|ref|YP_007908178.1|  2 AKYQCMVCGYVYDEDEgDpESnvlagtkwedlpddwVCPVCGASKDEF 49
                                      5789*********88754433789******************987665 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.032        23      22      31 ..       4      13 ..       2      14 .. 0.85
   2 ?    7.8   0.0    0.0039       2.8      21      30 ..      36      45 ..      34      47 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.032
                     A2L_zn_ribbon 22 lvCieCgasf 31
                                      ++C  Cg+++
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVY 13
                                      89999*9986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0039
                     A2L_zn_ribbon 21 ylvCieCgas 30
                                      + vC+ Cgas
  gi|488601707|ref|YP_007908178.1| 36 DWVCPVCGAS 45
                                      5577777776 PP

>> zf-nanos  Nanos RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.061        44      32      41 ..       2      11 ..       1      17 [. 0.82
   2 ?    8.5   0.0    0.0033       2.4      34      45 ..      37      48 ..      35      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.061
                          zf-nanos 32 rkyvCpiCga 41
                                       ky+C +Cg 
  gi|488601707|ref|YP_007908178.1|  2 AKYQCMVCGY 11
                                      69******96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0033
                          zf-nanos 34 yvCpiCgatgdk 45
                                       vCp+Cga++d+
  gi|488601707|ref|YP_007908178.1| 37 WVCPVCGASKDE 48
                                      59******9985 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.055        39       4      13 ..       3      12 ..       2      18 .. 0.79
   2 ?    7.8   0.0    0.0036       2.6       5      21 ..      37      53 ..      35      54 .] 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.055
                       zf_C2H2_ZHX  4 sFvCveCsfs 13
                                       + C+ C++ 
  gi|488601707|ref|YP_007908178.1|  3 KYQCMVCGYV 12
                                      599****986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0036
                       zf_C2H2_ZHX  5 FvCveCsfsakkfegLa 21
                                      +vC  C+ s  +fe+L+
  gi|488601707|ref|YP_007908178.1| 37 WVCPVCGASKDEFEKLE 53
                                      79*************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 ?    6.0   0.1     0.016        11      46      59 ..       3      16 ..       1      18 [. 0.83
   2 ?    5.4   0.1     0.025        18      31      39 ..      39      47 ..      36      52 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                    OrfB_Zn_ribbon 46 tfkCpnCgfeadrD 59
                                      +++C  Cg+++d D
  gi|488601707|ref|YP_007908178.1|  3 KYQCMVCGYVYDED 16
                                      68899999999977 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.025
                    OrfB_Zn_ribbon 31 CseCgsknk 39
                                      C++Cg+ ++
  gi|488601707|ref|YP_007908178.1| 39 CPVCGASKD 47
                                      666665554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.038        28      14      21 ..       3      11 ..       2      16 .. 0.79
   2 ?    7.3   0.1    0.0053       3.8       2       7 ..      39      44 ..      38      51 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.038
                     zinc_ribbon_2 14 kF.CpyCGt 21
                                      k+ C  CG+
  gi|488601707|ref|YP_007908178.1|  3 KYqCMVCGY 11
                                      566999997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0053
                     zinc_ribbon_2  2 CpnCGa 7 
                                      Cp CGa
  gi|488601707|ref|YP_007908178.1| 39 CPVCGA 44
                                      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 ?    3.8   0.0     0.082        59       4      12 ..       6      14 ..       4      36 .. 0.80
   2 ?    8.1   0.5    0.0037       2.7       2      10 ..      37      45 ..      37      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.082
                                      -TTT--EEE CS
                           ADK_lid  4 CpkCGrsYh 12
                                      C  CG +Y 
  gi|488601707|ref|YP_007908178.1|  6 CMVCGYVYD 14
                                      999**9997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0037
                                      EE-TTT--E CS
                           ADK_lid  2 rvCpkCGrs 10
                                      +vCp CG+s
  gi|488601707|ref|YP_007908178.1| 37 WVCPVCGAS 45
                                      9******97 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.036        25       1      11 [.       4      14 ..       4      18 .. 0.83
   2 ?    6.4   0.1     0.026        19       2       9 ..      38      45 ..      37      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.036
                         zf-C2H2_4  1 fkCpiCgksFs 11
                                      ++C +Cg ++ 
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVYD 14
                                      89****99884 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.026
                         zf-C2H2_4  2 kCpiCgks 9 
                                       Cp+Cg+s
  gi|488601707|ref|YP_007908178.1| 38 VCPVCGAS 45
                                      7****987 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.5    0.0055       3.9      51      67 ..      26      42 ..       5      43 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0055
                             PHD_4 51 egvvnedlpnsWeCpkC 67
                                       g+  edlp +W Cp C
  gi|488601707|ref|YP_007908178.1| 26 AGTKWEDLPDDWVCPVC 42
                                      577889**********9 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 ?    6.4   0.1    0.0088       6.3      24      31 ..       5      12 ..       2      16 .. 0.82
   2 ?    3.4   0.0     0.079        57      23      32 ..      37      46 ..      30      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0088
                        zf-C2H2_12 24 vCmvCges 31
                                       CmvCg +
  gi|488601707|ref|YP_007908178.1|  5 QCMVCGYV 12
                                      6****986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.079
                        zf-C2H2_12 23 lvCmvCgesl 32
                                       vC vCg s 
  gi|488601707|ref|YP_007908178.1| 37 WVCPVCGASK 46
                                      69*****875 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0016       1.1      22      34 ..       4      16 ..       1      18 [. 0.83
   2 ?    2.9   0.1      0.14     1e+02      16      30 ..      35      45 ..      34      51 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                                      EEESSSS-EEESS CS
                    RNA_POL_M_15KD 22 feCrqCgYeepad 34
                                      + C  CgY++  d
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVYDED 16
                                      78*******9766 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                                      CSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD 16 dkegknfeCrqCgYe 30
                                      d+++    C  Cg+ 
  gi|488601707|ref|YP_007908178.1| 35 DDWV----CPVCGAS 45
                                      5677....8888875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.0    0.0051       3.6       1      10 [.       4      13 ..       4      15 .. 0.91
   2 ?    7.5   0.8    0.0048       3.4      15      22 ..      37      44 ..      37      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0051
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      Y+C  CG+++
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVY 13
                                      9*******87 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0048
                      Rubredoxin_2 15 GrCpsCgs 22
                                      + Cp Cg+
  gi|488601707|ref|YP_007908178.1| 37 WVCPVCGA 44
                                      99****97 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6     0.027        19      33      44 ..       4      15 ..       1      16 [. 0.79
   2 ?    5.7   0.0     0.027        19      16      31 ..      34      49 ..      25      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.027
                              C1_2 33 YsCseCdfslhv 44
                                      Y C  C ++ ++
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVYDE 15
                                      999889999887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                              C1_2 16 sesfnCsaCgrkidgf 31
                                       +++ C +Cg + d+f
  gi|488601707|ref|YP_007908178.1| 34 PDDWVCPVCGASKDEF 49
                                      67899*****998776 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4     0.011       7.7       1      10 [.       4      13 ..       4      15 .. 0.91
   2 ?    4.2   0.1     0.095        68       2       8 ..      38      44 ..      37      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                                      EEETTTTEEE CS
                           zf-C2H2  1 ykCpdCgksF 10
                                      y+C +Cg+++
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVY 13
                                      9******998 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.095
                                      EETTTTE CS
                           zf-C2H2  2 kCpdCgk 8 
                                      +Cp+Cg 
  gi|488601707|ref|YP_007908178.1| 38 VCPVCGA 44
                                      7****95 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.7     0.003       2.1       1      27 [.       4      31 ..       4      38 .. 0.69
   2 ?    4.3   0.4     0.048        35      20      31 ..      38      49 ..      31      54 .] 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.003
                     Cys_rich_CPCC  1 yqCpcCgyltleeee.gsydiCpvCfWe 27
                                      yqC +Cgy+  e+e   + ++ +   We
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVYDEDEGdPESNVLAGTKWE 31
                                      79******87765543555666666666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.048
                     Cys_rich_CPCC 20 iCpvCfWedDlv 31
                                      +CpvC   +D++
  gi|488601707|ref|YP_007908178.1| 38 VCPVCGASKDEF 49
                                      677777666665 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   1.4     0.043        30       4      12 ..       3      11 ..       3      14 .. 0.82
   2 ?    7.8   0.2    0.0043       3.1       4      11 ..      36      43 ..      34      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.043
                    Zn_ribbon_SprT  4 vYrCtgCgr 12
                                      +Y+C  Cg 
  gi|488601707|ref|YP_007908178.1|  3 KYQCMVCGY 11
                                      7*******4 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0043
                    Zn_ribbon_SprT  4 vYrCtgCg 11
                                       ++C+ Cg
  gi|488601707|ref|YP_007908178.1| 36 DWVCPVCG 43
                                      59*****9 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.9     0.012       8.4       5      29 ..       4      45 ..       1      48 [. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                       Prok-RING_1  5 kkCpvCgkelkee..................dDiVvCpeCgtp 29
                                       +C vCg   +e+                  d   vCp+Cg++
  gi|488601707|ref|YP_007908178.1|  4 YQCMVCGYVYDEDegdpesnvlagtkwedlpD-DWVCPVCGAS 45
                                      56777777666666667777777777766634.458*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 329.08
//
Query:       gi|488601708|ref|YP_007908179.1|  [L=81]
Description: putative nucleic-acid-binding protein containing a Zn-ribbon domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-24   84.6   1.1    4.4e-24   84.4   1.1    1.0  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
     0.0043   17.4   1.7       0.19   12.1   0.2    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0083   15.8   3.1       0.36   10.6   0.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
  ------ inclusion threshold ------
      0.011   15.2   0.1      0.012   15.2   0.1    1.1  1  Peptidase_C98    Ubiquitin-specific peptidase-like, SUMO isop
      0.015   15.1   2.1      0.066   13.0   0.2    2.1  2  zf-HYPF          HypF finger
      0.017   15.3   1.7      0.021   15.0   0.2    1.8  2  DUF2387          Probable metal-binding protein (DUF2387)
      0.026   15.3   0.5      0.032   15.0   0.5    1.2  1  zinc_ribbon_15   zinc-ribbon family
      0.037   13.9   0.3        6.7    6.7   0.1    2.2  2  ADD_ATRX         Cysteine Rich ADD domain
       0.05   13.4   0.3       0.51   10.2   0.1    2.0  2  zf-ZPR1          ZPR1 zinc-finger domain
      0.056   13.5   0.1        8.5    6.4   0.0    2.0  2  CpXC             CpXC protein
      0.061   13.0   1.5        6.3    6.6   0.1    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.09   13.0   0.0         15    5.9   0.0    2.1  2  Ribosomal_L32p   Ribosomal L32p protein family
      0.092   12.8   2.3       0.46   10.6   2.3    1.9  1  Elf1             Transcription elongation factor Elf1 like
      0.094   12.7   3.1        4.1    7.5   0.1    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.095   12.8   1.4        5.3    7.2   0.0    2.2  2  Zn-ribbon_8      Zinc ribbon domain
       0.23   11.0   4.7        4.5    6.9   0.7    2.2  2  zn-ribbon_14     Zinc-ribbon
       0.23   11.3   4.8        4.8    7.1   0.6    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.64    9.8   5.3        5.1    6.9   0.3    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.67    9.9   5.1        2.2    8.2   0.4    2.6  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        1.8    8.8   6.0        2.3    8.4   0.8    2.2  2  Ribosomal_L37e   Ribosomal protein L37e


Domain annotation for each model (and alignments):
>> 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 !   84.4   1.1   4.9e-27   4.4e-24       1      62 [.      12      79 ..      12      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 4.9e-27
                    zinc_ribbon_13  1 kCpKCgnteaevkevaatG.sglskifdvqnkkfitvsCknCgYtelYkaetsegk.....nilDlll 62
                                      kC+KCg ++a++k++a+tG s++++++d+q++++++vsC+nCgY+e+Y+ae++egk     ++lDl++
  gi|488601708|ref|YP_007908179.1| 12 KCQKCGVQTARIKKLAITGaSFFDRWTDWQRNTYYFVSCTNCGYMEVYDAEVLEGKkdkltEVLDLIF 79
                                      7******************999**********************************9*********98 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 ?    5.4   0.1     0.026        23      28      38 ..      10      20 ..       1      37 [. 0.71
   2 !   12.1   0.2   0.00021      0.19      19      54 ..      41      71 ..      29      75 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                   Lar_restr_allev 28 cvyCadCgast 38
                                       + C++Cg+ t
  gi|488601708|ref|YP_007908179.1| 10 HFKCQKCGVQT 20
                                      789*****933 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00021
                   Lar_restr_allev 19 qrvvaeigqcvyCadCgastpwfkiaedeaeaekea 54
                                      qr+++   ++v+C++Cg+   +++ ae  + +++++
  gi|488601708|ref|YP_007908179.1| 41 QRNTY---YFVSCTNCGY--MEVYDAEVLEGKKDKL 71
                                      33444...4*********..6666666666666665 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2    0.0004      0.36       1      12 [.      11      22 ..      11      23 .. 0.90
   2 ?    5.8   0.3     0.012        11       3       9 ..      50      56 ..      49      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                      Rubredoxin_2  1 YvCsqCGfesak 12
                                      + C++CG ++a+
  gi|488601708|ref|YP_007908179.1| 11 FKCQKCGVQTAR 22
                                      89*******987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                      Rubredoxin_2  3 CsqCGfe 9 
                                      C +CG+ 
  gi|488601708|ref|YP_007908179.1| 50 CTNCGYM 56
                                      *****96 PP

>> Peptidase_C98  Ubiquitin-specific peptidase-like, SUMO isopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.3e-05     0.012     132     186 ..      10      65 ..       3      81 .] 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                     Peptidase_C98 132 efeCseCgvkkkervektltt...ftnvvpdwhplnAvhlapCnkCkkkeqrrkmvle 186
                                       +f+C++Cgv+++ r++k   t   f +  +dw+  n  ++ +C++C   e     vle
  gi|488601708|ref|YP_007908179.1|  10 HFKCQKCGVQTA-RIKKLAITgasFFDRWTDWQ-RNTYYFVSCTNCGYMEVYDAEVLE 65 
                                       7*******9876.56666555111555556665.588999******987766666654 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.26   2.3e+02      24      29 ..      13      18 ..      10      21 .. 0.81
   2 ?   13.0   0.2   7.3e-05     0.066      16      28 ..      42      54 ..      35      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.26
                                      -TTTS- CS
                           zf-HYPF 24 CtnCGP 29
                                      C +CG 
  gi|488601708|ref|YP_007908179.1| 13 CQKCGV 18
                                      999995 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.3e-05
                                      TTT-TT---TTTS CS
                           zf-HYPF 16 RfhaqfisCtnCG 28
                                      R  + f+sCtnCG
  gi|488601708|ref|YP_007908179.1| 42 RNTYYFVSCTNCG 54
                                      77899*******9 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.4   1.3e+03      29      40 ..       9      20 ..       3      30 .. 0.69
   2 ?   15.0   0.2   2.4e-05     0.021      18      57 ..      35      74 ..      24      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                           DUF2387 29 eyrECvsCgftd 40
                                       +  C +Cg   
  gi|488601708|ref|YP_007908179.1|  9 SHFKCQKCGVQT 20
                                      567788888654 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.4e-05
                           DUF2387 18 DkirmweedeveyrECvsCgftdelsekgqsvakelktrv 57
                                      D+   w+ +   ++ C++Cg+++  ++++ + +k+  t v
  gi|488601708|ref|YP_007908179.1| 35 DRWTDWQRNTYYFVSCTNCGYMEVYDAEVLEGKKDKLTEV 74
                                      77788********************999888888776665 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   3.6e-05     0.032       2      52 ..      12      62 ..      11      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-05
                    zinc_ribbon_15  2 lCpkCgklskaelvkkkkvlklffipvfkwkkkkpy.lacskCkslleaske 52
                                      +C+kCg +++a+++k   +   ff    +w+++++y + c++C+++   + e
  gi|488601708|ref|YP_007908179.1| 12 KCQKCG-VQTARIKKLAITGASFFDRWTDWQRNTYYfVSCTNCGYMEVYDAE 62
                                      7*****.6888888888888899999999*998765378****987555554 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0075       6.7       5      28 ..       4      27 ..       1      30 [. 0.79
   2 ?    5.6   0.0     0.016        14      10      18 ..      46      54 ..      39      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0075
                          ADD_ATRX  5 dkeleeivsCtaCgqqvnhfqkds 28
                                      +++  + ++C  Cg q  +++k  
  gi|488601708|ref|YP_007908179.1|  4 EDRILSHFKCQKCGVQTARIKKLA 27
                                      55666789********99998865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.016
                          ADD_ATRX 10 eivsCtaCg 18
                                        vsCt Cg
  gi|488601708|ref|YP_007908179.1| 46 YFVSCTNCG 54
                                      569*****9 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00057      0.51      24      46 ..       4      26 ..       1      32 [. 0.85
   2 ?    1.8   0.0      0.21   1.9e+02      31      40 ..      48      57 ..      40      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                           zf-ZPR1 24 keviimsfeCehCgyknnevksa 46
                                      ++ i++ f+C++Cg ++  +k +
  gi|488601708|ref|YP_007908179.1|  4 EDRILSHFKCQKCGVQTARIKKL 26
                                      567999***********999865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.21
                           zf-ZPR1 31 feCehCgykn 40
                                      ++C +Cgy +
  gi|488601708|ref|YP_007908179.1| 48 VSCTNCGYME 57
                                      6899999864 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0095       8.5      31      48 ..       4      21 ..       1      34 [. 0.76
   2 ?    5.7   0.0     0.017        15      33      54 ..      43      64 ..      38      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0095
                              CpXC 31 ldgslfeatCpkCgatak 48
                                       d  l  ++C+kCg +++
  gi|488601708|ref|YP_007908179.1|  4 EDRILSHFKCQKCGVQTA 21
                                      5666889*******8876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                              CpXC 33 gslfeatCpkCgatakleapll 54
                                      +++  + C +Cg+   ++a++l
  gi|488601708|ref|YP_007908179.1| 43 NTYYFVSCTNCGYMEVYDAEVL 64
                                      5667789******999999887 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.013        12      19      25 ..      12      18 ..       2      25 .. 0.81
   2 ?    6.6   0.1     0.007       6.3      18      27 ..      48      57 ..      46      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                                      --SSS-- CS
                    DNA_RNApol_7kD 19 RCkeCGh 25
                                      +C++CG 
  gi|488601708|ref|YP_007908179.1| 12 KCQKCGV 18
                                      8999996 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.007
                                      ---SSS---- CS
                    DNA_RNApol_7kD 18 iRCkeCGhRi 27
                                      + C++CG+  
  gi|488601708|ref|YP_007908179.1| 48 VSCTNCGYME 57
                                      67*****965 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.027        25      36      49 ..       7      22 ..       3      27 .. 0.75
   2 ?    5.9   0.0     0.017        15      17      35 ..      38      56 ..      35      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                                      ECTTC-BTTTT..BSS CS
                    Ribosomal_L32p 36 klpHrvcpscG..yYk 49
                                      +l+H  c +cG  + +
  gi|488601708|ref|YP_007908179.1|  7 ILSHFKCQKCGvqTAR 22
                                      799*******944444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.017
                                      GGT------EEEETTTCCE CS
                    Ribosomal_L32p 17 ahwklkapnlvecpncgel 35
                                      + w++++  +v c+ncg +
  gi|488601708|ref|YP_007908179.1| 38 TDWQRNTYYFVSCTNCGYM 56
                                      6678888889999999976 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.3   0.00052      0.46      14      74 ..       3      76 ..       1      80 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                              Elf1 14 kkkklptkFdCpfCnheksvevkldkkek..............iaevsCkvCgesfetkvnalsepvDvYskwiD 74
                                        +++ ++F+C  C+ + + ++k    ++                 vsC++Cg    ++++ l+ + D  ++++D
  gi|488601708|ref|YP_007908179.1|  3 VEDRILSHFKCQKCGVQ-TARIKKLAITGasffdrwtdwqrntYYFVSCTNCGYMEVYDAEVLEGKKDKLTEVLD 76
                                      5567999*********9.666665555557899999999999889999****98777777777766666665555 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.8     0.016        14      18      27 ..      10      19 ..       5      37 .. 0.74
   2 ?    7.5   0.1    0.0045       4.1      18      31 ..      43      60 ..      35      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
                     Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                      +f C +Cg++
  gi|488601708|ref|YP_007908179.1| 10 HFKCQKCGVQ 19
                                      5677777776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0045
                     Zn_Tnp_IS1595 18 g...fv.CPhCgsrkayr 31
                                      +   fv C +Cg++++y 
  gi|488601708|ref|YP_007908179.1| 43 NtyyFVsCTNCGYMEVYD 60
                                      3677677*******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 ?    7.2   0.0    0.0059       5.3       6      18 ..      11      23 ..      10      31 .. 0.74
   2 ?    4.8   0.3     0.035        32       5      16 ..      46      57 ..      44      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0059
                       Zn-ribbon_8  6 YrCeeCghefevl 18
                                      ++C++Cg +  ++
  gi|488601708|ref|YP_007908179.1| 11 FKCQKCGVQTARI 23
                                      8999999665554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.035
                       Zn-ribbon_8  5 eYr.CeeCghefe 16
                                       +  C++Cg   e
  gi|488601708|ref|YP_007908179.1| 46 YFVsCTNCG-YME 57
                                      4444****9.555 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   0.2    0.0089         8       2       9 ..      12      19 ..      11      22 .. 0.85
   2 ?    6.9   0.7     0.005       4.5       3       9 ..      50      56 ..      48      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0089
                      zn-ribbon_14  2 kCerCGyl 9 
                                      kC++CG  
  gi|488601708|ref|YP_007908179.1| 12 KCQKCGVQ 19
                                      8*****86 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.005
                      zn-ribbon_14  3 CerCGyl 9 
                                      C+ CGy+
  gi|488601708|ref|YP_007908179.1| 50 CTNCGYM 56
                                      ******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 ?    6.1   0.2     0.011        10       1      11 [.      11      21 ..      10      26 .. 0.76
   2 ?    7.1   0.6    0.0053       4.8      27      36 ..      46      55 ..      43      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                           TFIIS_C  1 akCpkCgsrea 11
                                      +kC+kCg + a
  gi|488601708|ref|YP_007908179.1| 11 FKCQKCGVQTA 21
                                      57888887665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0053
                           TFIIS_C 27 vfykCtkCgh 36
                                       f+ Ct+Cg+
  gi|488601708|ref|YP_007908179.1| 46 YFVSCTNCGY 55
                                      5999999996 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.7     0.024        22       1       6 [.      12      17 ..      12      19 .. 0.80
   2 ?    6.9   0.3    0.0057       5.1      16      21 ..      50      55 ..      43      56 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.024
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +C +CG
  gi|488601708|ref|YP_007908179.1| 12 KCQKCG 17
                                      799999 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0057
                     zinc_ribbon_2 16 CpyCGt 21
                                      C++CG+
  gi|488601708|ref|YP_007908179.1| 50 CTNCGY 55
                                      666664 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 ?    3.5   0.1     0.073        65      22      28 ..      11      17 ..       2      19 .. 0.68
   2 ?    8.2   0.4    0.0025       2.2      19      31 ..      43      57 ..      38      62 .. 0.77
   3 ?   -2.0   0.0       3.8   3.4e+03      11      21 ..      64      74 ..      63      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.073
                                      EEESSSS CS
                    RNA_POL_M_15KD 22 feCrqCg 28
                                      f C +Cg
  gi|488601708|ref|YP_007908179.1| 11 FKCQKCG 17
                                      6777775 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                                      CCE..EEESSSS-EE CS
                    RNA_POL_M_15KD 19 gkn..feCrqCgYee 31
                                      +++  + C +CgY e
  gi|488601708|ref|YP_007908179.1| 43 NTYyfVSCTNCGYME 57
                                      5556899******86 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.8
                                      EEEEECSCCCE CS
                    RNA_POL_M_15KD 11 Llpkedkegkn 21
                                      L+ k+dk++ +
  gi|488601708|ref|YP_007908179.1| 64 LEGKKDKLTEV 74
                                      67789999865 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8    0.0026       2.3      15      31 ..       9      25 ..       4      43 .. 0.77
   2 ?    3.1   0.5      0.12   1.1e+02      33      39 ..      49      55 ..      42      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0026
                    Ribosomal_L37e 15 tHilCrrCgkrsyhvqk 31
                                      +H +C++Cg ++  ++k
  gi|488601708|ref|YP_007908179.1|  9 SHFKCQKCGVQTARIKK 25
                                      78899999887766666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                    Ribosomal_L37e 33 tCascGy 39
                                      +C +cGy
  gi|488601708|ref|YP_007908179.1| 49 SCTNCGY 55
                                      6888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 463.36
//
Query:       gi|488601709|ref|YP_007908180.1|  [L=252]
Description: hypothetical protein Asulf_02234 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-69  231.6   0.0    9.9e-69  231.4   0.0    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.4   0.0   5.5e-73   9.9e-69       1     232 [.       4     246 ..       4     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 231.4 bits;  conditional E-value: 5.5e-73
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       itLlTDFG  + y+g+mkgvil+++pd++ivDitH+++p++  +aaflL++  ++f  +++h+avVDpgvg+er+al
  gi|488601709|ref|YP_007908180.1|   4 ITLLTDFG--EFYPGVMKGVILRLCPDVTIVDITHSVDPQNTLQAAFLLNSYHRFFE-NAIHVAVVDPGVGSEREAL 77 
                                       9*******..***************************************99999998.79***************** PP

                                       EEEETTSEEEEESSSTTHHHH.SEEEEEEGSSCC.......--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGGS CS
                   SAM_adeno_trans  78 vveakggyfvgPDNGlltlal.lleeaveieeee.......ssatFhgrDvFapvaarlaagvsleelgeeldpeel 146
                                       +ve ++ +f++P+NG+lt++l +  ++++i+e++        s+tFhgrDvFap+aa  a +  +ee++e+++  ++
  gi|488601709|ref|YP_007908180.1|  78 IVERGN-IFIAPNNGILTPVLdSKCKIWKIDESKasrfvgtLSSTFHGRDVFAPAAALAALN-MIEEIAEPFEG-RV 151
                                       ***877.**************73379*****998999999977***********99966665.589****9986.88 PP

                                       -SSS....E..CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE.....EEEEESSGGGSTTTSEEEEE-TTSE CS
                   SAM_adeno_trans 147 vrle....e..derlegevlyvDrFGNvitniskelleelekerkva.....klkkvetyaevaegellalvnssgl 212
                                       vrl+    e  ++r++ +v y+DrFGN++t +++e++++l+ + + +      +  ve+ya+v+ +e+l l++s ++
  gi|488601709|ref|YP_007908180.1| 152 VRLDlfnpEiiENRIKCNVAYIDRFGNIVTDLRREAVRKLNPK-G-FylkdtYFPLVEKYADVDLNEPLSLIGSFDT 226
                                       99999987467999*******************9999877443.3.24567533456******************** PP

                                       EEEEETTC-HHHHHT--TT- CS
                   SAM_adeno_trans 213 leiavnkgsaaellglkvgd 232
                                       le+++++g+a+++lg+ +g+
  gi|488601709|ref|YP_007908180.1| 227 LEFSIRNGNASKVLGIGYGK 246
                                       ****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1388.76
//
Query:       gi|488601710|ref|YP_007908181.1|  [L=467]
Description: adenosylcobyric acid synthase (glutamine-hydrolysing) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  168.6   0.0    1.9e-49  167.9   0.0    1.3  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    2.4e-18   66.4   0.0    4.6e-18   65.5   0.0    1.4  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    4.3e-13   49.5   0.0    2.3e-12   47.2   0.0    2.1  2  AAA_26    AAA domain
    0.00072   19.4   0.0     0.0012   18.7   0.0    1.3  1  GATase    Glutamine amidotransferase class-I
     0.0081   16.0   0.0      0.014   15.3   0.0    1.3  1  SNO       SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   0.0   5.3e-53   1.9e-49       1     194 [.     246     425 ..     246     427 .. 0.94

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 5.3e-53
                          GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       +i+v+rlp+isn+td++pL+ ++   vrf++l+++++  d+d++i+pG+kdti+dl++l+++g+de ik++a  ++p
  gi|488601710|ref|YP_007908181.1| 246 EICVLRLPRISNFTDFEPLRFAG---VRFADLNEKDF--DCDILIIPGTKDTIADLKALKDTGMDERIKKLAG-KIP 316
                                       59******************988...9999999****..5******************************886.9** PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeageveglglLdietefek.ekltgqvegevel......aaegeevkGyEiHsG 147
                                       ++giCGG+q+LG+e++d+ gve+ + + +glglLd+ t+f   +k+t+qv+++v          +g+ v GyEiH+G
  gi|488601710|ref|YP_007908181.1| 317 IIGICGGYQILGKELIDK-GVEHGVIRTKGLGLLDAVTVFDVyRKTTRQVRKRVTGdavildRIKGNYVWGYEIHKG 392
                                       *****************5.9*********************98999999999977799*9998899*********** PP

                          GATase_3 148 rtilkekakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnr 194
                                       r+i++   kp+++          dG v  s dg v+GtYlHglf+n+
  gi|488601710|ref|YP_007908181.1| 393 RSISR---KPIFED---------DGTV--SDDGMVWGTYLHGLFWND 425
                                       99964...688866.........****..77*************996 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   1.3e-21   4.6e-18       1     115 [.       4     226 ..       4     234 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.3e-21
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep...................... 54 
                                       i+i +t++ +GK+ ++a+L++++++ g+rV++++a++++ n++i   g+e+ i++                      
  gi|488601710|ref|YP_007908181.1|   4 IFIGATSSHAGKSLITASLCKIISKMGYRVAPFKAQNMSLNSFItRNGKEIAIAQafqaqsagiepdermnpillkp 80 
                                       67889**************************************999999999999********************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|488601710|ref|YP_007908181.1|  81 kgnfisqlvvmgeavgdisskeyyrkvpelfevvkscyeslaeeyeiiviegaggmaeinlydrdianigtirmanp 157
                                       ***************************************************************************** PP

                                       ......CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE-- CS
                                       ......xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ......dlkrllellealgkkkall.....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprd 115
                                             d++r ++++++++++++ll      +++g+++n+ +g   e  l++++++++ ++g++++g++p+ 
  gi|488601710|ref|YP_007908181.1| 158 dvyivgDIER-GGVFSSVYGTYSLLpsdvrDRVKGFIINKLRGY--EDVLESGIKQIESMTGLKCIGILPFM 226
                                       **********.*******************************98..*************99********986 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   6.4e-16   2.3e-12       2     190 ..       3     225 ..       2     227 .. 0.80
   2 ?   -2.9   0.0       1.4   4.8e+03     132     147 ..     283     298 ..     276     315 .. 0.64

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 6.4e-16
                            AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie....ededselikellgldq....tyelpeplals 70 
                                       +if+ +t+ ++GK+++++ L++++++ g++v+ fK  +  ++    ++++   i++++++++    + e ++p++l+
  gi|488601710|ref|YP_007908181.1|   3 SIFIGATSSHAGKSLITASLCKIISKMGYRVAPFKAQNMSLNsfitRNGKEIAIAQAFQAQSagiePDERMNPILLK 79 
                                       69*********************************877776677766665555666555554111123357888887 PP

                            AAA_26  71 ap...lspelaarqegedidlekiv..............kelekdadivvVEGagglgvpitee..llnadiaknlg 128
                                            +s+ + + +   di  +++               ++l+++++i+v+EGagg+ +  +++    n+  +++ +
  gi|488601710|ref|YP_007908181.1|  80 PKgnfISQLVVMGEAVGDISSKEYYrkvpelfevvkscyESLAEEYEIIVIEGAGGMAEINLYDrdIANIGTIRMAN 156
                                       432225777777777777776666678888888889**888*****************88666644678889***** PP

                            AAA_26 129 apvilVarggl.gtinqllltiealr.qknvrvlGvilNkvrnpe.....nvetlekksgipvlGvvPy 190
                                        +v +V+ +++ g +  ++ t+++l  +   rv+G i+Nk+r  e      ++++e+++g++ +G++P 
  gi|488601710|ref|YP_007908181.1| 157 PDVYIVGDIERgGVFSSVYGTYSLLPsDVRDRVKGFIINKLRGYEdvlesGIKQIESMTGLKCIGILPF 225
                                       *********99458899999**9997245779**********99667777******************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                            AAA_26 132 ilVargglgtinqlll 147
                                       il+++g+++ti++l +
  gi|488601710|ref|YP_007908181.1| 283 ILIIPGTKDTIADLKA 298
                                       4556666666666655 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.3e-07    0.0012      46      90 ..     283     333 ..     268     382 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.3e-07
                                       EEEEEESSCTT.......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT CS
                            GATase  46 ilvsgGpgspg.......vegkieaikearenkiPiLGICLGmQllaiefgr 90 
                                       il+ +G  +          +g+ e ik++++ kiPi+GIC G Q+l++e+  
  gi|488601710|ref|YP_007908181.1| 283 ILIIPGTKDTIadlkalkDTGMDERIKKLAG-KIPIIGICGGYQILGKELID 333
                                       4444444444336666667899999******.***************99866 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.8e-06     0.014      33      97 ..     280     350 ..     269     406 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.8e-06
                                       C-SEEEE-SS-HHHHH.HHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB.......SS-SS--CC CS
                               SNO  33 evdaliiPGGestams.kliertglyedllefvknsekvvlGtCaGlillskelene.......lvktlellk 97 
                                       ++d liiPG   t    k ++ tg +++  ++++ ++ +++G C G  +l kel  +         k l+ll+
  gi|488601710|ref|YP_007908181.1| 280 DCDILIIPGTKDTIADlKALKDTG-MDERIKKLA-GKIPIIGICGGYQILGKELIDKgvehgviRTKGLGLLD 350
                                       7*********99976625567778.555555554.448*************9997763334444445566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2638.78
//
Query:       gi|488601711|ref|YP_007908182.1|  [L=208]
Description: putative ATPases of PP-loop superfamily [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-50  169.5   0.2    8.1e-50  169.3   0.2    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
       0.18   11.3   0.0       0.31   10.6   0.0    1.4  1  ThiI             Thiamine biosynthesis protein (ThiI)


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 !  169.3   0.2     9e-54   8.1e-50       4     213 ..       3     206 ..       1     208 [] 0.94

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 9e-54
                   Diphthami_syn_2   4 avlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkg 79 
                                       ++++sGGkDs+la+++ l++  ev+ L+++++e+++s ++h+     +e +  ++ i+ +  + +  +e +  ++k 
  gi|488601711|ref|YP_007908182.1|   3 VAMWSGGKDSCLAVHRMLRNgNEVSKLICMLDEDNQS-RAHGFYKIALERQLKALQIDGVFGNSS--WEGYKSEFKR 76 
                                       79*****************999**********99995.78888888889999******9999988..********** PP

                   Diphthami_syn_2  80 tlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrri 156
                                        ++ l++e+vv+G+i +e+++ ++e+vC e+ + +v+PLWk+d+e+l+ e+++e++ +++v+v++    +++LGr++
  gi|488601711|ref|YP_007908182.1|  77 LMNGLKAEKVVFGDIFLEEHRVWLEQVCDEVNVEPVFPLWKEDTEKLAREFLSEGYTAYIVSVRKDLGLDEYLGRKF 153
                                       ***************************************************************99766689****** PP

                   Diphthami_syn_2 157 dkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyld 213
                                         ++idel +l    g+d++ge Ge++t+v D+P+f k +e +  +  + e++  ++
  gi|488601711|ref|YP_007908182.1| 154 SDEIIDELMSL----GVDPCGELGEFHTFVTDGPMFVKPVEFEFGNVVEREKYKQIQ 206
                                       ***********....*************************99988888888776665 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.5e-05      0.31       7      34 ..       3      30 ..       1      57 [. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.5e-05
                              ThiI  7 laLlSgGiDSpVaaylllkRGcrvvlvh 34
                                      +a+ SgG DS  a +++l+ G +v  + 
  gi|488601711|ref|YP_007908182.1|  3 VAMWSGGKDSCLAVHRMLRNGNEVSKLI 30
                                      8999*******************97543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1215.55
//
Query:       gi|488601712|ref|YP_007908183.1|  [L=218]
Description: cobalamin biosynthesis protein CbiM [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-54  184.8  18.5    1.9e-54  184.7  18.5    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi
  ------ inclusion threshold ------
        2.1    6.9  13.9        4.6    5.8  11.8    1.9  2  EMP70     Endomembrane protein 70


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 !  184.7  18.5   2.1e-58   1.9e-54       1     207 []       2     212 ..       2     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 2.1e-58
                              CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldear..vpllallaafifaaqminipipggtslHllgavlaai 75 
                                       Hi++g+L+p +++++ya +l++++++++r++ke++++     lla++a fif+++ ++ip  +g+++H++g+++a +
  gi|488601712|ref|YP_007908183.1|   2 HIMEGFLPPFWAAVWYAFSLPIVGYGTYRAKKEIEKNPknKSLLAVAAGFIFVLSALKIPSVTGSCSHPTGTGIAVV 78 
                                       *********************************8855457************************************* PP

                              CbiM  76 LlGpwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvla 152
                                       L+Gp+++++  ++vll qall+++GG+t+LGaN+ +m+++g+++++l+yr++    ++k+++++++f+aa+++ +++
  gi|488601712|ref|YP_007908183.1|  79 LFGPAITAFLSIIVLLYQALLLAHGGLTTLGANTASMGIVGPFVGWLIYRAI----KGKTSIKVSTFVAAAVADWVT 151
                                       **************************************************99....45689**************** PP

                              CbiM 153 allvalelalsgleas......lsltaalaamllvhlpvgilEgviTaaivkalkkvrpel 207
                                       +++++++lal+  ++       +s t++la++ ++++p++i+Eg++ a+++ +l ++r +l
  gi|488601712|ref|YP_007908183.1| 152 YVVTSIQLALAFPAGAgvagviASATKFLAVFSVTQIPLAIIEGIVAALLMGYLVQIRDDL 212
                                       ***********766668****************************************9886 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.024   2.1e+02     374     399 ..      14      38 ..      11      48 .. 0.71
   2 ?    5.8  11.8   0.00051       4.6     268     391 ..      71     198 ..      56     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.024
                             EMP70 374 llwflisvPlvliGsllgfkkkai.eh 399
                                       ++w+  s+P+v  G++ ++k+  i ++
  gi|488601712|ref|YP_007908183.1|  14 AVWYAFSLPIVGYGTYRAKKE--IeKN 38 
                                       789999999999999999884..3233 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00051
                             EMP70 268 vGsGvqlllma.lvtlllallgfls...psnrgslltvalllyvllgliaGYvsarlyktfgge.kwkkntlltall 339
                                        G+G+ ++l    +t +l+++ +l+      +g+l t++    + +g+++ +v+  +y+ ++g+ ++k +t++ a +
  gi|488601712|ref|YP_007908183.1|  71 TGTGIAVVLFGpAITAFLSIIVLLYqalLLAHGGLTTLG-ANTASMGIVGPFVGWLIYRAIKGKtSIKVSTFVAAAV 146
                                       566655544321233333333333322234456666655.567899***************9995666666666666 PP

                             EMP70 340 lpgllflvffllnlilwakessgalpfgtlvlllllwflisvPlvliGsllg 391
                                          ++ +v+ +   +++  ++  a  + + + +l+++ + ++Pl +i ++++
  gi|488601712|ref|YP_007908183.1| 147 ADWVTYVVTSIQLALAFPAGAGVAGVIASATKFLAVFSVTQIPLAIIEGIVA 198
                                       66666666666666777788888889999*****************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1234.84
//
Query:       gi|488601713|ref|YP_007908184.1|  [L=89]
Description: cobalt transport protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   94.8   1.3    2.7e-27   94.6   1.3    1.1  1  CbiN      Cobalt transport protein component CbiN
  ------ inclusion threshold ------
      0.066   13.5   0.0          3    8.2   0.0    2.0  2  Orf78     Orf78 (ac78)


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 !   94.6   1.3     3e-31   2.7e-27       7      67 .]       5      67 ..       1      67 [. 0.86

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 3e-31
                              CbiN  7 lvvllavvplflv..kgaeFgGaDdqaeevIeeiapdyepwfeplweppsGEiESlLFalQAA 67
                                      ++vll+++ +f+     +e++GaD++aeevI +iapdyepwf+p++eppsGEiESlLF+lQAA
  gi|488601713|ref|YP_007908184.1|  5 VIVLLTAIFFFVTiaAAEEWAGADEKAEEVIGDIAPDYEPWFSPIFEPPSGEIESLLFSLQAA 67
                                      4555555555555766777*******************************************8 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00033         3      74      92 ..       3      21 ..       1      35 [. 0.81
   2 ?    3.9   0.0    0.0074        66      62      86 ..      56      80 ..      41      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00033
                             Orf78 74 vcvlvllyviyYfvilrer 92
                                      + v+vll +i++fv +   
  gi|488601713|ref|YP_007908184.1|  3 LKVIVLLTAIFFFVTIAAA 21
                                      569***********87665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0074
                             Orf78 62 alnillisllavvcvlvllyviyYf 86
                                      + + ll+sl a +  l++ y+i Y+
  gi|488601713|ref|YP_007908184.1| 56 EIESLLFSLQAAIGSLIIGYIIGYY 80
                                      5678999***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 561.67
//
Query:       gi|488601714|ref|YP_007908185.1|  [L=241]
Description: cobalt ABC transporter, permease protein CbiQ [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-41  140.2  10.6    9.7e-41  139.8  10.6    1.1  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8  10.6   5.4e-45   9.7e-41       5     211 ..      13     212 ..       9     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 5.4e-45
                                       CCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE.......E CS
                              CbiQ   5 lhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlittege 81 
                                       +++ld  +k  +++llll++v + ++ ++ + +++++ +l l++  +++ ++l +p  fl+ g++i+l+ +i  +g+
  gi|488601714|ref|YP_007908185.1|  13 RKVLDGSLKIHFCLLLLLFVVTSGKVSVY-LAAFAIFSCLSLYAAGWYYIRILKVPVYFLISGIIIILL-FI--PGK 85 
                                       55666666666666666655555555555.8888999999999999********************999.45..9** PP

                                       ECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHH CS
                              CbiQ  82 fvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevq 158
                                       + ++    ++i +eG+ ++++++lR l++ls++++++lTT+++el+s+++rl+ P  ++++ lL+yR i++Ll+e+ 
  gi|488601714|ref|YP_007908185.1|  86 TAYQLYF-LKISEEGIDTAINTTLRALASLSIMSFMILTTTIPELFSTFKRLRLPGFIVEMCLLVYRVIQILLDEAA 161
                                       *******.********************************************************************* PP

                                       HHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 159 rikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       +++ + ++Rlg++  + +  +++++ l  +lflr+lkr+e++  Am+aR+Y+g
  gi|488601714|ref|YP_007908185.1| 162 KLDMSASSRLGYA--SKKVFVNTTALLSYSLFLRSLKRSEKLDRAMDARCYSG 212
                                       *************..7777788******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.31s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1360.73
//
Query:       gi|488601715|ref|YP_007908186.1|  [L=341]
Description: cobalt transport protein ATP-binding subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-30  104.5   0.0    9.5e-30  103.9   0.0    1.3  1  ABC_tran     ABC transporter
    2.6e-09   37.3   0.0     0.0014   18.5   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      5e-06   26.1   0.0     0.0027   17.2   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00035   20.4   0.0     0.0021   17.8   0.0    2.1  3  AAA_15       AAA ATPase domain
     0.0013   18.4   0.0     0.0028   17.4   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0014   19.2   0.0     0.0025   18.4   0.0    1.4  1  AAA_23       AAA domain
     0.0036   17.2   0.2      0.059   13.3   0.1    2.2  2  NACHT        NACHT domain
     0.0039   15.9   0.0       0.67    8.5   0.0    2.1  2  AAA_13       AAA domain
     0.0049   16.5   0.0      0.013   15.1   0.0    1.7  1  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.024   14.5   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.018   14.8   0.0      0.045   13.5   0.0    1.6  2  AAA_30       AAA domain
       0.03   13.9   0.0       0.14   11.8   0.0    2.0  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.042   14.2   0.0       0.12   12.7   0.0    1.8  1  AAA_16       AAA ATPase domain
      0.085   12.4   0.1       0.16   11.5   0.1    1.4  1  AAA_27       AAA domain
       0.11   11.3   0.0       0.18   10.6   0.0    1.3  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 !  103.9   0.0   7.9e-33   9.5e-30       1     137 []      17     161 ..      17     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 7.9e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpe 73 
                                       lk v++  ++ge++ ++G+nGaGK+tLl+ l gllkp  Ge+++dg  +k+  ++l ++rk++g+++q+  +q+   
  gi|488601715|ref|YP_007908186.1|  17 LKGVNFRANKGEVTILLGRNGAGKTTLLMHLNGLLKPSRGEVWIDGVRVKYdrKSLIEVRKKVGFVFQNpdDQIIAP 93 
                                       799************************************************8899999***********64333333 PP

                                       SBHHHH........HHHTC....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx........xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren........esdee....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + v +                  +e+a+++lglk+ +++ +    +sLSgG+k+rva+a +l+ +p+ +++DEpta
  gi|488601715|ref|YP_007908186.1|  94 T-VWQDvvfgpkniG---MgyefAEEAIKSLGLKGYEERLC----NSLSGGEKRRVAIAGVLAMNPDYIIMDEPTA 161
                                       3.6666677766553...044479*****************....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2     4e-06    0.0048       1      23 [.      29      51 ..      29      92 .. 0.81
   2 !   18.5   0.0   1.1e-06    0.0014     230     299 ..     126     192 ..      70     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      +++l G+Ng+GK++LL  l +l 
  gi|488601715|ref|YP_007908186.1| 29 VTILLGRNGAGKTTLLMHLNGLL 51
                                      69**************9999885 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.1e-06
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        e+  ++lS G kr  a++  l+  +   + ++ DEp +gL+   l+  +e++++l++ g  ++++TH+ 
  gi|488601715|ref|YP_007908186.1| 126 EERLCNSLSGGEKRRVAIAGVLAMNP---DYIIMDEPTAGLDGFGLKNMIEIIENLRDSGKTFVISTHDL 192
                                       55666789****************99...67*************************************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 !    6.8   0.0    0.0033       3.9      24      41 ..      27      44 ..      17      51 .. 0.85
   2 !   17.2   0.0   2.2e-06    0.0027     136     199 ..     132     191 ..      50     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0033
                                      SSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnll 41
                                       ++t+++G+NG+GK+ ll
  gi|488601715|ref|YP_007908186.1| 27 GEVTILLGRNGAGKTTLL 44
                                      46899**********986 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2.2e-06
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                       +LSgGek  va+a ++A++   p    ++De  a LD    k++ e++++ +++   +vis ++
  gi|488601715|ref|YP_007908186.1| 132 SLSGGEKRRVAIAGVLAMN---PD-YIIMDEPTAGLDGFGLKNMIEIIENLRDSGKTFVISTHD 191
                                       8**************9975...43.468*************************98888888655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.8e-06    0.0021      10      50 ..      21      54 ..      19     127 .. 0.81
   2 ?   -0.1   0.0       0.5   5.9e+02     327     367 ..     154     193 ..     130     195 .. 0.79
   3 ?   -3.5   0.0       5.2   6.3e+03     235     269 ..     303     337 ..     259     338 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                            AAA_15 10 NFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnk 50
                                      NFR+ k       e +t+l G+N++GK+++l+ l+ +l+ +
  gi|488601715|ref|YP_007908186.1| 21 NFRANKG------E-VTILLGRNGAGKTTLLMHLNGLLKPS 54
                                      6666663......5.********************999988 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.5
                            AAA_15 327 lliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       ++++EP a L     k +i+ + +l +++k   +i+TH   
  gi|488601715|ref|YP_007908186.1| 154 IIMDEPTAGLDGFGLKNMIEIIENLRDSGK-TFVISTHDLD 193
                                       666666666666677889999999999998.8999***865 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.2
                            AAA_15 235 eeelteklkeiqeklkeidkklaeelkkilkkkid 269
                                        e+  ek++ ++e l+ +d   a ++ +i+++ i+
  gi|488601715|ref|YP_007908186.1| 303 VEREAEKFPVFLEILDGFDHLAAVNTDSIFDSTIK 337
                                       34566777777777777777777777777776665 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   2.3e-06    0.0028      16      49 ..      21      54 ..      15      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49
                                       ++ +  g +t+l G++G+GK+Tll  ++ lL p+
  gi|488601715|ref|YP_007908186.1| 21 NFRANK-GeVTILLGRNGAGKTTLLMHLNGLLKPS 54
                                      566664.45***************97777777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.1e-06    0.0025      15      39 ..      20      47 ..       8      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                      ++F   +  +t++ G NGaGKTT+l  +
  gi|488601715|ref|YP_007908186.1| 20 VNFranKGEVTILLGRNGAGKTTLLMHL 47
                                      5666644469**************9766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   4.9e-05     0.059       2      25 ..      29      52 ..      28      57 .. 0.85
   2 ?    1.8   0.0      0.17   2.1e+02      82      99 ..     312     329 ..     278     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      + il G++G GKTtLl +l  +++
  gi|488601715|ref|YP_007908186.1| 29 VTILLGRNGAGKTTLLMHLNGLLK 52
                                      689***************976665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.17
                                       CEEEEEE-STT-SS-TCH CS
                             NACHT  82 rlLlilDglDelvtdlgq 99 
                                         L ilDg+D l++ +  
  gi|488601715|ref|YP_007908186.1| 312 VFLEILDGFDHLAAVNTD 329
                                       45669*******997765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00056      0.67      20      39 ..      31      50 ..      21      76 .. 0.84
   2 !    5.3   0.0    0.0053       6.3     529     582 ..     153     203 ..     130     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00056
                            AAA_13 20 liYGwNGaGKTtLSrllrsl 39
                                      ++ G+NGaGKTtL + l+ l
  gi|488601715|ref|YP_007908186.1| 31 ILLGRNGAGKTTLLMHLNGL 50
                                      678**********9888876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0053
                            AAA_13 529 ivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntk 582
                                        +++D P   LD   l   +  i++     ++ k + i+TH l+f +ev +++ 
  gi|488601715|ref|YP_007908186.1| 153 YIIMDEPTAGLDGFGLKNMIEIIENLR---DSGKTFVISTHDLDFAREVGERFV 203
                                       578899999999999999999999996...99999*************988775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05     0.013      31      53 ..      25      47 ..      14      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                            AAA_25 31 pagelallaGapgtGKttlaldl 53
                                       +ge+++l G+ g+GKttl+++l
  gi|488601715|ref|YP_007908186.1| 25 NKGEVTILLGRNGAGKTTLLMHL 47
                                      68******************998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     2e-05     0.024      96     125 ..      23      53 ..       3      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelel 125
                                       + ++ ++++l+G  G+GK+tL+ +l++ l+ 
  gi|488601715|ref|YP_007908186.1|  23 RANKgEVTILLGRNGAGKTTLLMHLNGLLKP 53 
                                       444449*****************99986655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.7e-05     0.045      15      49 ..      24      58 ..      19      64 .. 0.83
   2 ?   -3.8   0.0       7.3   8.7e+03      29      37 ..     181     189 ..     168     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                      +++  v++l G+ G+GKtt+l +l+ +++ + g+v
  gi|488601715|ref|YP_007908186.1| 24 ANKGEVTILLGRNGAGKTTLLMHLNGLLKPSRGEV 58
                                      55667******************999888775555 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.3
                            AAA_30  29 tGKttalka 37 
                                       +GKt+++++
  gi|488601715|ref|YP_007908186.1| 181 SGKTFVIST 189
                                       788888764 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 ?   11.8   0.0   0.00011      0.14       2      21 ..      29      48 ..      28      78 .. 0.84
   2 ?   -0.9   0.0      0.92   1.1e+03      40      65 ..     189     215 ..     180     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      vt+l G  G+GKTtLl hl 
  gi|488601715|ref|YP_007908186.1| 29 VTILLGRNGAGKTTLLMHLN 48
                                      899*************9985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.92
                                       HCCCCCCHCCCT.EEEETTTTECCH.C CS
                              cobW  40 siDaellretgveivelenGciCct.l 65 
                                        +D ++ re g+  v + nG i +   
  gi|488601715|ref|YP_007908186.1| 189 THDLDFAREVGERFVYMDNGEIVHEsD 215
                                       578888888899999999999988744 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001      0.12      21      58 ..      24      62 ..      14      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif.lrg 58
                                      ++ +e+++l G  G GK++l+ +l   l+ ++g + + g
  gi|488601715|ref|YP_007908186.1| 24 ANKGEVTILLGRNGAGKTTLLMHLNGLLKPSRGEVwIDG 62
                                      4455899**************999987777743333333 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013      0.16      19      50 ..      20      51 ..      10      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      ++f+a++ ++++++G N AGK+t+l  ++ ll
  gi|488601715|ref|YP_007908186.1| 20 VNFRANKGEVTILLGRNGAGKTTLLMHLNGLL 51
                                      789999******************98877765 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.18      22      54 ..      24      56 ..       3      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                              DLIC 22 lPsgksvlvlGedgsGkttliaklqGveeekkG 54
                                         g   ++lG +g+Gkttl+  l G+ ++ +G
  gi|488601715|ref|YP_007908186.1| 24 ANKGEVTILLGRNGAGKTTLLMHLNGLLKPSRG 56
                                      445667799*****************9988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 1731.86
//
Query:       gi|488601716|ref|YP_007908187.1|  [L=124]
Description: hypothetical protein Asulf_02241 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 775.94
//
Query:       gi|488601717|ref|YP_007908188.1|  [L=38]
Description: hypothetical protein Asulf_02242 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.016   15.3   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 ?   15.3   0.0     9e-07     0.016     102     121 .]      16      35 ..       4      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9e-07
                            Y1_Tnp 102 fvstvgeasletvkrYIenq 121
                                       f+s+vg+++le+vkrYIe+q
  gi|488601717|ref|YP_007908188.1|  16 FISSVGTVTLEVVKRYIEEQ 35 
                                       6789**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 243.01
//
Query:       gi|488601718|ref|YP_007908189.1|  [L=417]
Description: Transposase-like protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   84.8   2.8    1.5e-23   82.5   1.2    2.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.5e-22   80.1   1.1      4e-22   78.7   0.0    2.2  2  OrfB_IS605      Probable transposase
     0.0045   16.9   3.0      0.012   15.6   3.0    1.7  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.6   1.2      0.025   14.5   1.2    1.5  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.12   12.4   0.5       0.22   11.5   0.5    1.4  1  PhnA_Zn_Ribbon  PhnA 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 ?    0.8   0.0      0.13   4.6e+02      10      30 ..     219     239 ..     216     254 .. 0.88
   2 !   82.5   1.2   4.2e-27   1.5e-23       2      66 ..     303     366 ..     302     368 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                    OrfB_Zn_ribbon  10 ykakeyGikveevnpayTSkt 30 
                                        k  +y  k++ vn  +TSk+
  gi|488601718|ref|YP_007908189.1| 219 KKIAKYQSKLKRVNNKHTSKR 239
                                       57888999***********96 PP

  == domain 2  score: 82.5 bits;  conditional E-value: 4.2e-27
                    OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNi 66 
                                       + l++++++ka+eyG+kv++v+++yTS++C++Cgs++ + +++r+fkC nCg+ea+rD ++++Ni
  gi|488601718|ref|YP_007908189.1| 303 DYLIQRIKEKAEEYGMKVTQVDESYTSSRCPRCGSVKVY-KHKRLFKCLNCGLEAHRDAVGCVNI 366
                                       6799***********************************.************************9 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3      0.53   1.9e+03      39      73 ..       5      38 ..       2      41 .. 0.72
   2 !   78.7   0.0   1.1e-25     4e-22       2     119 ..     168     282 ..     167     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.53
                        OrfB_IS605 39 flykgrrlksdykylakeiaelqsklkksknykka 73
                                       ++k +++k+++k+l +   +++++ ++ + yk++
  gi|488601718|ref|YP_007908189.1|  5 NVFKLKPTKEQEKRLFELANNCSRLWNEIN-YKRR 38
                                      567778888888888888888888877774.5554 PP

  == domain 2  score: 78.7 bits;  conditional E-value: 1.1e-25
                        OrfB_IS605   2 ipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrkla 78 
                                       +pveve+ l +p g k+a  DlG+++L+  +  + + f y+++rl sd  y++k+ia+ qsklk+ +n k +s++l+
  gi|488601718|ref|YP_007908189.1| 168 QPVEVEP-LHQPIGYKKAYCDLGVRVLIMAAIDN-EVFGYSSNRLLSDWWYWSKKIAKYQSKLKRVNN-KHTSKRLR 241
                                       699*997.*******************9988888.89*****************************99.******** PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                        l+rkr+rr +h+++ ++++ i+ ++e+gv+++++g++k i
  gi|488601718|ref|YP_007908189.1| 242 QLYRKRKRRFRHFVNTIVNRFIRLCYERGVSEIVIGDLKGI 282
                                       *************************************9976 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   3.0   3.4e-06     0.012      20      44 ..     331     353 ..     327     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.4e-06
                     Zn_Tnp_IS1595  20 vCPhCgsrkayriktrglfqCkeCr 44 
                                       +CP+Cgs k+y+ k+  lf+C  C+
  gi|488601718|ref|YP_007908189.1| 331 RCPRCGSVKVYKHKR--LFKCLNCG 353
                                       7*****99***9997..*******7 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.2   6.9e-06     0.025       9      44 ..     327     365 ..     321     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-06
                                       SS--B-TTT-SB--SSSS-EEEETTT--EE-CC...CCT CS
                              C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllvHkk...Che 44 
                                       + +++C  Cg+    k k+ +kC +C+l +H +   C++
  gi|488601718|ref|YP_007908189.1| 327 YTSSRCPRCGSVKVYKHKRLFKCLNCGLEAHRDavgCVN 365
                                       67899*****99966****************98777765 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   6.1e-05      0.22       3      27 ..     330     354 ..     325     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.1e-05
                    PhnA_Zn_Ribbon   3 pkCplCaSeytYedgallvCpeCah 27 
                                       + Cp C+S  +Y  + l+ C +C+ 
  gi|488601718|ref|YP_007908189.1| 330 SRCPRCGSVKVYKHKRLFKCLNCGL 354
                                       89*********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1377  (0.0768029); expected 358.6 (0.02)
Passed bias filter:                      781  (0.0435607); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2294.02
//
Query:       gi|488601719|ref|YP_007908190.1|  [L=89]
Description: hypothetical protein Asulf_02244 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.075   12.8   0.3       0.16   11.7   0.1    1.7  2  Form-deh_trans  Formate dehydrogenase N, transmembrane


Domain annotation for each model (and alignments):
>> Form-deh_trans  Formate dehydrogenase N, transmembrane
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.28   5.1e+03      18      24 ..      36      42 ..      32      50 .. 0.54
   2 ?   11.7   0.1   9.1e-06      0.16      18      40 ..      66      88 ..      65      89 .] 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.28
                                      HHHHHHH CS
                    Form-deh_trans 18 lgmaata 24
                                      ++++ ++
  gi|488601719|ref|YP_007908190.1| 36 ATIVTVV 42
                                      4444333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.1e-06
                                      HHHHHHHHHHHHHHHHH--B-S- CS
                    Form-deh_trans 18 lgmaatalagffHYitvGPneve 40
                                      +g++++a++++ H i + P++v+
  gi|488601719|ref|YP_007908190.1| 66 AGLIIAAVGAITHIIEIKPKRVT 88
                                      89******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); 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: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 510.21
//
Query:       gi|488601720|ref|YP_007908191.1|  [L=162]
Description: Precorrin-6B methylase 2 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-09   34.7   0.0      1e-08   34.6   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    1.1e-08   35.7   0.0      2e-08   34.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    6.5e-08   33.1   0.0    1.1e-07   32.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.6e-07   29.9   0.0    1.9e-06   27.5   0.0    1.8  2  MTS              Methyltransferase small domain
    1.6e-06   28.1   0.0    1.9e-06   27.9   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
    5.1e-05   23.1   0.1    6.1e-05   22.9   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
    6.7e-05   22.7   0.0    9.1e-05   22.3   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0004   20.0   0.0    0.00079   19.0   0.0    1.4  2  Methyltransf_5   MraW methylase family
    0.00059   19.5   0.0    0.00089   18.9   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0012   19.6   0.0     0.0021   18.8   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
     0.0012   18.7   0.0     0.0013   18.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0012   18.0   0.0     0.0017   17.5   0.0    1.2  1  DREV             DREV methyltransferase
     0.0015   18.0   0.0     0.0027   17.2   0.0    1.4  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.031   13.8   0.0      0.034   13.7   0.0    1.2  1  DOT1             Histone methylation protein DOT1
      0.035   14.7   0.0       0.22   12.1   0.0    2.0  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.041   13.2   0.0      0.074   12.4   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.043   13.4   0.0        0.1   12.2   0.0    1.5  2  NodS             Nodulation protein S (NodS)
      0.073   12.5   0.0       0.13   11.6   0.0    1.4  1  TehB             Tellurite resistance protein TehB
       0.11   12.0   0.0       0.22   11.1   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


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 !   34.6   0.0   1.1e-11     1e-08      16      88 ..       6      77 ..       3     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.1e-11
                                      HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGH CS
                            RrnaAD 16 kkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkf 88
                                      + +i   + kl++++k+   +ig G G+ +e +  ++ +v ++E de+++++ +++l+ +++++++  D+++f
  gi|488601720|ref|YP_007908191.1|  6 PEIIGVLFAKLKPNKKDVFADIGCGSGAVSEFFSRYVSKVYAVERDESMLQIAKERLK-GNNIELILSDGYDF 77
                                      5667777899*********************************************998.************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   2.1e-11     2e-08       3      70 ..      26      88 ..      24     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.1e-11
                                      EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25  3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70
                                      d+GcG+G +++ +++ +  +kv++v+ +e+ml++a+er+  +g n+e++  d  d+  e + +D+ + 
  gi|488601720|ref|YP_007908191.1| 26 DIGCGSGAVSEFFSRYV--SKVYAVERDESMLQIAKERL--KGNNIELILSDGYDFLKE-HDCDIAFF 88
                                      9***************9..9*******************..5679*******9997543.35776665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   1.2e-10   1.1e-07       2      67 ..      26      88 ..      25     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.2e-10
                                      EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11  2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvs 67
                                      d+GcG+G+++e + +++++v++v+ ++ ml++ake+ ++++  +e++ +d  ++ ++++ +D+ + 
  gi|488601720|ref|YP_007908191.1| 26 DIGCGSGAVSEFFSRYVSKVYAVERDESMLQIAKERLKGNN--IELILSDGYDF-LKEHDCDIAFF 88
                                      9*************999**********************98..99999999994.77788888776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0     2e-09   1.9e-06      22     100 ..      11      85 ..       9      88 .. 0.92
   2 ?    0.1   0.0      0.54     5e+02      57      78 ..      97     118 ..      90     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2e-09
                                       HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-E CS
                               MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkf 98 
                                       +L  +l+ ++++  +D+GcG G+++  + +  ++  v +v+ d   l++ake l+ n+  +e++ sd+++ ++e+++
  gi|488601720|ref|YP_007908191.1|  11 VLFAKLKPNKKDVFADIGCGSGAVSEFFSRYVSK--VYAVERDESMLQIAKERLKGNN--IELILSDGYDFLKEHDC 83 
                                       6888999999999****************99888..9********************9..589999****9999999 PP

                                       EE CS
                               MTS  99 dl 100
                                       d+
  gi|488601720|ref|YP_007908191.1|  84 DI 85 
                                       86 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.54
                                       EEEEEESBHHHHHHHHHHHHHT CS
                               MTS  57 evtlvdvdarAlesakenlean 78 
                                        ++++d++  A+++a+  ++ +
  gi|488601720|ref|YP_007908191.1|  97 MLEVCDAERIAVNAARIEVAVE 118
                                       5889999999999999887654 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.1e-09   1.9e-06      14     103 ..      20     101 ..      12     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.1e-09
                   Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvviaG 90 
                                       k++++aDiG+  g ++ +    + ++kv+a++  e+ l+ ake ++ +    +ie++lsdG + lke+++d++   G
  gi|488601720|ref|YP_007908191.1|  20 KKDVFADIGCGSGAVSEFFS--RYVSKVYAVERDESMLQIAKERLKGN----NIELILSDGYDFLKEHDCDIAFFGG 90 
                                       56699**********98886..799********************985....689***********99999877665 PP

                   Methyltransf_18  91 mGgelileILeea 103
                                         ++ i ++Le +
  gi|488601720|ref|YP_007908191.1|  91 --TKGIERMLEVC 101
                                       ..34455555544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   6.5e-08   6.1e-05       2      77 ..      19      85 ..      18     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.5e-08
                   Methyltransf_31  2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDl 77
                                      +k+ ++ D+GCG+G+ +  + + +   ++v+ ++++e +++ A+e+   l+ +n+e+  +d  + l+++  d   D+
  gi|488601720|ref|YP_007908191.1| 19 NKKDVFADIGCGSGAVSEFFSRYV---SKVYAVERDESMLQIAKER---LKGNNIELILSDGYDfLKEH--D--CDI 85
                                      5677889*********99999665...78****************7...55678888888888866643..3..555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   9.7e-08   9.1e-05      67     165 ..      14     125 ..       3     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.7e-08
                                       HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.............SEEEEE CS
                              PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.............nvivvv 130
                                         l+ +k++   ++G+GsG  +  ++r+v ++    ++er +++ + ak++lk +++e             +  + +
  gi|488601720|ref|YP_007908191.1|  14 AKLKPNKKDVFADIGCGSGAVSEFFSRYVSKVY---AVERDESMLQIAKERLKGNNIElilsdgydflkehDCDIAF 87 
                                       445555566677*****************9888...****************9988877777777776666555666 PP

                                       S-GGGTTG...GG-SEEEEEESSBBSS--HHHHHTEEE CS
                              PCMT 131 gDGrkGye...ekaPYdaihvgaaapeiPealidQLke 165
                                         G+kG e   e    ++i v aa  e+  + ++++k+
  gi|488601720|ref|YP_007908191.1|  88 FGGTKGIErmlEVCDAERIAVNAARIEVAVEVTKKMKS 125
                                       66666665222345556666666666666666666665 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   8.4e-07   0.00079      13      83 ..      13      80 ..       5      95 .. 0.80
   2 ?   -2.2   0.0       2.4   2.3e+03     205     220 ..     101     116 ..      85     133 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.4e-07
                                      HHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---EEEEES-GGGHHH CS
                    Methyltransf_5 13 vellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekrltlvkgnfkelke 83
                                      +  l+p+++ v+ D   G+g  se + + +   ++++++rD+s+l++akerLk  + +l ++++ +++lke
  gi|488601720|ref|YP_007908191.1| 13 FAKLKPNKKDVFADIGCGSGAVSEFFSRYV--SKVYAVERDESMLQIAKERLKGNNIEL-ILSDGYDFLKE 80
                                      567999***************999885554..4689****************9765443.33455566655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.4
                                       HHHHHHHHHTHHHHHH CS
                    Methyltransf_5 205 FQAlRIavNdEleele 220
                                         A RIavN    e+ 
  gi|488601720|ref|YP_007908191.1| 101 CDAERIAVNAARIEVA 116
                                       5566777775433333 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.5e-07   0.00089      32      89 ..      12      67 ..       3      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.5e-07
                                      HHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT- CS
                     Cons_hypoth95 32 lFnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkl 89
                                      lF  l+++ ++  + D+ +GsGa++ E  SR+++k+++ve+d+++++i ke l+  ++
  gi|488601720|ref|YP_007908191.1| 12 LFAKLKPNKKDV-FADIGCGSGAVS-EFFSRYVSKVYAVERDESMLQIAKERLKGNNI 67
                                      566666665555.89999*****97.***********************999887664 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.2e-06    0.0021       2      44 ..      26      66 ..      25      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-06
                   Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakre 44
                                      +iGcG+G++++ + ++   +++++v+ ++s+++ ake+l+ ++
  gi|488601720|ref|YP_007908191.1| 26 DIGCGSGAVSEFFSRY--VSKVYAVERDESMLQIAKERLKGNN 66
                                      9***************..*********************9876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.3e-06    0.0013      21      62 ..      19      72 ..       4     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                   Methyltransf_23 21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae............k 62
                                      +++    diGcG+G ++e +++++ +v++v+ ++ + +ia+            +
  gi|488601720|ref|YP_007908191.1| 19 NKKDVFADIGCGSGAVSEFFSRYVSKVYAVERDESMLQIAKerlkgnnielilS 72
                                      4555677*****************************999986666655555550 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.8e-06    0.0017      95     131 ..      21      57 ..      10      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                              DREV  95 dkklldlGaGdGeitkrvaptfeevyatelsetmrdr 131
                                       +    d+G G G +++  + ++++vya e  e m + 
  gi|488601720|ref|YP_007908191.1|  21 KDVFADIGCGSGAVSEFFSRYVSKVYAVERDESMLQI 57 
                                       44567**************************999653 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.9e-06    0.0027     162     213 ..      20      71 ..       9      87 .. 0.80
   2 ?   -2.8   0.0       3.5   3.3e+03     191     206 ..     102     117 ..      95     135 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                              PrmA 162 geevl.DvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakl 213
                                       ++ v+ D+G+GSG  +   ++   +kv+av  De  +++ake ++ N++e  l
  gi|488601720|ref|YP_007908191.1|  20 KKDVFaDIGCGSGAVSEFFSRY-VSKVYAVERDESMLQIAKERLKGNNIELIL 71 
                                       445655*******999877775.789**********************98765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.5
                              PrmA 191 DiDevAvkvakeNael 206
                                       D + +Av++a+  +++
  gi|488601720|ref|YP_007908191.1| 102 DAERIAVNAARIEVAV 117
                                       5555555555544433 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.034      25      85 ..       3      61 ..       2     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                                      -B-HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHH CS
                              DOT1 25 EllpeflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekq 85
                                      E++pe++  ++ k++ +k+dvF D+G G G v  + + +v   + + vE  ++  ++a+++
  gi|488601720|ref|YP_007908191.1|  3 ETKPEIIGVLFAKLKPNKKDVFADIGCGSGAVSEFFSRYVS--KVYAVERDESMLQIAKER 61
                                      89999***************************999998865..457788877777777765 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   0.00024      0.22      15      60 ..      35      72 ..      27      83 .. 0.90
   2 ?   -0.1   0.0       1.5   1.4e+03      41      55 ..     114     128 ..     100     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                      HHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECS CS
                         Pyr_redox 15 AgalaelgkkVtvversdkllrllDeeaskilqeklekngievlln 60
                                       ++++++ +kV+ ver + +l        +i +e+l+ n+ie++l+
  gi|488601720|ref|YP_007908191.1| 35 SEFFSRYVSKVYAVERDESML--------QIAKERLKGNNIELILS 72
                                      6899*****************........999***********997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHTTE CS
                         Pyr_redox  41 easkilqeklekngi 55 
                                       e++ ++++k++ +gi
  gi|488601720|ref|YP_007908191.1| 114 EVAVEVTKKMKSMGI 128
                                       567778888888887 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.9e-05     0.074      48     109 ..      21      76 ..       8      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                                       TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT CS
                   Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaee 109
                                          + D+ +G+g ++  +s+ v    kv  ++ +e+mL++++++lk +   nie++ +++ +
  gi|488601720|ref|YP_007908191.1|  21 KDVFADIGCGSGAVSEFFSRYVS---KVYAVERDESMLQIAKERLKGN---NIELILSDGYD 76 
                                       34689**********99999986...67888999***********975...66777666655 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011       0.1      49     108 ..      26      84 ..      13      91 .. 0.89
   2 ?   -2.3   0.0       2.9   2.8e+03      33      53 ..      96     116 ..      90     129 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                              NodS  49 evGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfd 108
                                       ++Gc +Ga++e ++ y  ++  v+  e+ ++ a+er+k  ++i  i sd   f +++  d
  gi|488601720|ref|YP_007908191.1|  26 DIGCGSGAVSEFFSRYVSKVYAVERDESMLQIAKERLKG-NNIELILSDGYDFLKEHDCD 84 
                                       79************************************9.99999999988777666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.9
                              NodS  33 qilrlslaqgsiadalevGca 53 
                                       ++l+++ a++ + +a  +  a
  gi|488601720|ref|YP_007908191.1|  96 RMLEVCDAERIAVNAARIEVA 116
                                       566666666666555555444 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.13      34      86 ..      24      76 ..       4      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                      EEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE-- CS
                              TehB 34 vldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalyd 86
                                        d+gcg+g  s ++s    +v a++++e+ ++  +e  + +n++ i +  yd
  gi|488601720|ref|YP_007908191.1| 24 FADIGCGSGAVSEFFSRYVSKVYAVERDESMLQIAKERLKGNNIELILSDGYD 76
                                      369**************************999999999888998888777777 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.22       4      53 ..      24      69 ..      21      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                   Methyltransf_15  4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitl 53
                                        D+ +G+G  +  f ++ +kv+a+e +++ l++a++  +      +i l
  gi|488601720|ref|YP_007908191.1| 24 FADIGCGSGAVSEFFSRYVSKVYAVERDESMLQIAKERLKGN----NIEL 69
                                      56999****99999*******************999877643....4555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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 0.32s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 935.36
//
Query:       gi|488601721|ref|YP_007908192.1|  [L=195]
Description: cobalt-factor II C20-methyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-33  114.4   0.0    1.9e-32  113.0   0.0    1.6  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.062   13.7   0.1       0.11   12.9   0.1    1.4  1  Radical_SAM   Radical SAM superfamily
        0.1   12.2   0.0        1.3    8.6   0.0    2.1  2  DAGK_cat      Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0   3.1e-36   1.9e-32       1     207 [.       1     180 [.       1     182 [. 0.86

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 3.1e-36
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal.aeal 76 
                                       +ly+VG+GpGd +llT+rA++++k++d v+ +++ a+e+++d+ ++ + +e+pm        ++ ee+a+ l +e  
  gi|488601721|ref|YP_007908192.1|   1 MLYGVGLGPGDKKLLTLRAVEIIKEVDEVIVPGKMAYELIKDIREP-RIVEFPM--------GKSEEVARSLaREIS 68 
                                       79*******************************78*****885332.2444444........446999999977777 PP

                      TP_methylase  77 ragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeere 153
                                       +++ d ++ ++GDP +y+t+ ++ve+l a +++ eveviPGvss+++a a++++ ++    ++++l       +++ 
  gi|488601721|ref|YP_007908192.1|  69 ERDDDTAFCCIGDPIFYSTFHHIVEELLAINPEAEVEVIPGVSSINSALAKTRTFIN----NSMLL----T--TQDF 135
                                       77888************************************************9999....55555....2..2345 PP

                      TP_methylase 154 leallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrg 207
                                       ++      d  v+lka r  +e++e Lke+  + + + +++er+ +++e+v+++
  gi|488601721|ref|YP_007908192.1| 136 FDV-----DVAVVLKAKR-SKEVVEKLKER--GFN-EFILIERMFMDGEKVYES 180
                                       555.....999***8887.***********..645.9**************975 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.8e-05      0.11      30     154 ..      56     174 ..      44     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  30 sveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvs 106
                                       s e    +++e++ e++ ++ +   g+p++y+ f+ ++e+l ++  p+ ++ v+     +    l++ +    + + 
  gi|488601721|ref|YP_007908192.1|  56 SEEVARSLAREIS-ERDDDTAFCCIGDPIFYSTFHHIVEELLAIN-PEAEVEVIPGVSSI-NSALAKTRTFINNSML 129
                                       6667777788886.555999999999******************4.55555555555555.7777888888888888 PP

                                       EEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                       Radical_SAM 107 lgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpG 154
                                       l+ + + d +v   +      ++ +e++ekl+e+g+++ + +  + + G
  gi|488601721|ref|YP_007908192.1| 130 LTTQDFFDVDVAVVL----KAKRSKEVVEKLKERGFNEfILIERMFMDG 174
                                       888888887666666....378888889999999998766665555555 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00022       1.3      37      89 ..      53     108 ..      32     119 .. 0.73
   2 ?    1.5   0.0     0.035   2.1e+02      20      57 ..     125     163 ..     110     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00022
                                       E--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT...HHCTTSEEEEEE CS
                          DAGK_cat  37 eteepgdakelakeakeegvdlivvaGGDGtvsevlnglle...elatkpplgiiP 89 
                                         ++++ a++la+e++e++ d+ +++ GD ++   ++ ++e   + + + ++ +iP
  gi|488601721|ref|YP_007908192.1|  53 MGKSEEVARSLAREISERDDDTAFCCIGDPIFYSTFHHIVEellAINPEAEVEVIP 108
                                       34556899*********************877666666666555477777777777 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.035
                                       HHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-.S CS
                          DAGK_cat  20 rkvrelleeagvelelieteepgdakelakeakeegv.d 57 
                                       ++   l ++  +++++  + +++  ke+++++ke+g+ +
  gi|488601721|ref|YP_007908192.1| 125 NNSMLLTTQDFFDVDVAVVLKAKRSKEVVEKLKERGFnE 163
                                       544555566777999999999999********9998744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1159.32
//
Query:       gi|488601722|ref|YP_007908193.1|  [L=477]
Description: 3-octaprenyl-4hydroxybenzoate decarboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-167  557.6   0.4   1.7e-167  557.4   0.4    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 !  557.4   0.4  9.4e-172  1.7e-167       1     405 [.      10     415 ..      10     416 .. 0.96

  Alignments for each domain:
  == domain 1  score: 557.4 bits;  conditional E-value: 9.4e-172
                                       HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHH CS
                              UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeile 77 
                                       + +le+++el ri+ee++pelE++ ia++++++gg+allFe++kg+  ++pvl+n+fgt++r+++al+++ leei+e
  gi|488601722|ref|YP_007908193.1|  10 IHKLEEENELARIREEISPELEMTVIAEKAVKNGGKALLFEKPKGY--DIPVLMNAFGTEKRMKMALEVERLEEIGE 84 
                                       679****************************************866..8**************************** PP

                                       HHHHHHHS..-.................---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEE CS
                              UbiD  78 klaellepkpp.................ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvi 137
                                       +l  l++ kp                  + pk+v+  k++c+ ev+   +++dLsk+P+l++wpgD+G++it ++vi
  gi|488601722|ref|YP_007908193.1|  85 RLIGLTKIKPSglidglknisvlkdamsFIPKKVR--KGACK-EVI---TEPDLSKFPILKCWPGDAGRFITFPVVI 155
                                       *******9886799**************99****6..599**.663...37************************** PP

                                       EE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHH CS
                              UbiD 138 trdpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsEle 214
                                       t+dpetg+ n+g+yRmqv+d++++g+hwqihk+gaeh+rk +  g  ++++avaiGvdPa+++a++aplP+g++E++
  gi|488601722|ref|YP_007908193.1| 156 TKDPETGELNAGMYRMQVFDEKTTGMHWQIHKHGAEHFRKSE--G--KIEAAVAIGVDPAVLYASTAPLPTGMDEFM 228
                                       ************************************999876..4..689*************************** PP

                                       HHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE CS
                              UbiD 215 faGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypt 291
                                       faG++r e+v+lv+cetvdl+vpadAEivleG+++ +  + EGPfgdhtGyy ++ +++pvf+VtaithR++piy++
  gi|488601722|ref|YP_007908193.1| 229 FAGFIRRERVKLVDCETVDLMVPADAEIVLEGYVEGE--RIEGPFGDHTGYY-TPPEKYPVFHVTAITHRENPIYHA 302
                                       ***********************************96..8************.56677******************9 PP

                                       -SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SE CS
                              UbiD 292 tvvgkppeedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltK 368
                                       tvvgkpp+eda+lgka+e++flp+l++ +pe++d++lp eg+fh+la+vsi+k+ypghakkvm+alw+++  lsltK
  gi|488601722|ref|YP_007908193.1| 303 TVVGKPPMEDAWLGKATERIFLPVLRMLFPEIVDINLPIEGTFHNLAIVSIDKKYPGHAKKVMFALWGIGM-LSLTK 378
                                       99*******************************************************************99.***** PP

                                       EEEEEETTS-TTSHHHHHHHHHHC--CCCCEEEECCC CS
                              UbiD 369 lvivvDedvdvrdlkevlwaiatrvdpdrDlviiegt 405
                                       +vivvD dv+v++l+evlwa++ r+dp+rD+v+ie++
  gi|488601722|ref|YP_007908193.1| 379 IVIVVDSDVNVQNLSEVLWAVTSRFDPARDIVVIENA 415
                                       ***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2624.42
//
Query:       gi|488601723|ref|YP_007908194.1|  [L=151]
Description: hydrogenase maturation protease [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   98.6   0.3    2.6e-28   98.4   0.3    1.0  1  HycI      Hydrogenase maturation protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.3   1.5e-32   2.6e-28       1     130 []      20     147 ..      20     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 1.5e-32
                                       HHHHHHHHHHEC--TTEEEEEECT-SGGGHHHHCC-SEEEEEEE--SSS-TT-EEEEECCHHHHHHTTC.CGCCCHC CS
                              HycI   1 vrvvekLkrryefkenvtviDgGtqglelvgtleeadkliivDavdfglepGevkiikddevpkklkakkmsaHqlp 77 
                                       vrvve+L + +e +++v+v Dg t g  l+++l + dk +ivDav +g++pG ++++   e+      + +saH+++
  gi|488601723|ref|YP_007908194.1|  20 VRVVEELRK-LELPDYVEVYDGATLGIALLNLLSDSDKAVIVDAVFGGGKPGDIYRFSLYEILDTPLKNLISAHDID 95 
                                       89*****99.9*****************************************************999999******* PP

                                       HHHHHHHHHHCCS--SEEEEEEE--S-BST.CCS--HHHHCCHHHHHHHCCCH CS
                              HycI  78 laevlklleekgeipkevillgvqpesledvgielseevkkavekavelilee 130
                                       ++ + k+ ++  ++p++++++g++p+++e+ g+els+evkka++ka+e+ilee
  gi|488601723|ref|YP_007908194.1|  96 FVTAFKMGKDLLNLPQNIVVVGIEPKTIEE-GMELSDEVKKAIPKAIEIILEE 147
                                       ******************************.*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 849.11
//
Query:       gi|488601724|ref|YP_007908195.1|  [L=215]
Description: hypothetical protein Asulf_02249 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-21   74.2  21.5    1.5e-20   73.6  21.5    1.3  1  Ni_hydr_CYTB  Prokaryotic cytochrome b561
    0.00018   22.0  11.3    0.00018   22.0  11.3    2.4  2  DUF4405       Domain of unknown function (DUF4405)
  ------ inclusion threshold ------
       0.24   11.3   1.4         14    5.6   0.0    2.6  2  UPF0139       Uncharacterised protein family (UPF0139)


Domain annotation for each model (and alignments):
>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6  21.5   2.5e-24   1.5e-20       1     182 []       8     207 ..       8     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 2.5e-24
                                       -----TTHHHHHHHHHHHHHHHHHHHHHS------S-GGG-HHHHHHHHHHHHHHHHHHHHHHH......------- CS
                      Ni_hydr_CYTB   1 ryslvarllHWlnallvvllllsgllianlhprlywgdsgkaralHklaGlvllalllfrllwl......kkakkps 71 
                                       r+sl++r++HW ++++ ++l ++gl i   +  + +gd +     H ++Glv+ +l++++ +++      +   ++ 
  gi|488601724|ref|YP_007908195.1|   8 RHSLFTRVVHWSIVITGIILGFTGLEIGGHYGIRFLGDNV--TSTHVYVGLVFGVLWVMFTYYMltkewkWISLSRI 82 
                                       79************************************99..999************99999996666655555555 PP

                                       -----STTTSSSSS----------------TT...........THHHHHHHHHHHHHHHHHHHTHHHHHHHH..... CS
                      Ni_hydr_CYTB  72 priifrqikrdltlllrgrkpeagknnplqkl...........vhlllyvllvvliltGlllsfaatagfpll.... 133
                                         + ++ + +  +++   +  +++ ++p++             v + ++vl v++ +tGl++  a   +f++     
  gi|488601724|ref|YP_007908195.1|  83 IYSLKFLLAETRAWFGGPHIEDPRAYDPKKGEyvekivptqvmVWWGYFVLAVIIGFTGLAM--AFKDFFSWVfaig 157
                                       5555555555555555555666666666666699999*************************..5557777778888 PP

                                       ........HTS-THHHHHHH.HHHHHHH.HHHHHHHHHHHHHHH---XXXXXXXXX CS
                      Ni_hydr_CYTB 134 ......lddkggaqlarelHellaaall.afvvlHiaaallhgpvkkdtlrrMitg 182
                                                + g +++r +H ll++ l+  ++++Hi+a+++ g     +l++M+tg
  gi|488601724|ref|YP_007908195.1| 158 daigpiFGAESGYAFVRAVH-LLFMYLFaTVMIVHIYAVIIFG-----VLKSMFTG 207
                                       888888999***********.77777776************99.....57899997 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   5.3    0.0052        31      13      58 ..      20      62 ..      10      66 .. 0.74
   2 !   22.0  11.3     3e-08   0.00018       4      64 ..     128     194 ..     125     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0052
                           DUF4405 13 laiSGillsfavlpsgrgaywa.flglskhqwrdiHeilgllflilv 58
                                      ++i+Gi+l f+ l+ ++g+y++ f     + ++  H ++gl+f +l 
  gi|488601724|ref|YP_007908195.1| 20 IVITGIILGFTGLE-IGGHYGIrF---LGDNVTSTHVYVGLVFGVLW 62
                                      67899999988665.344444453...5788************8875 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 3e-08
                           DUF4405   4 lllllsflvlaiSGillsfavlpsgrgaywa....flgl..skhqwrdiHeilgllflilvvlHlgl 64 
                                       ++ +++ +++ ++G+ + f  + s+  a +     ++g   ++ ++r++H ++++lf  ++++H++ 
  gi|488601724|ref|YP_007908195.1| 128 WGYFVLAVIIGFTGLAMAFKDFFSWVFAIGDaigpIFGAesGYAFVRAVHLLFMYLFATVMIVHIYA 194
                                       5679*************9885555555444479997788999***********************96 PP

>> UPF0139  Uncharacterised protein family (UPF0139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4    0.0084        50      33      62 ..      57      86 ..      43      94 .. 0.66
   2 ?    5.6   0.0    0.0024        14      32      53 ..     131     153 ..     102     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0084
                           UPF0139 33 llgmifsllglmlklkwcaWvalvcslisf 62
                                      ++g++  ++   + +k   W++l  ++ s+
  gi|488601724|ref|YP_007908195.1| 57 VFGVLWVMFTYYMLTKEWKWISLSRIIYSL 86
                                      344444455555666888899997777665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0024
                           UPF0139  32 nllgmifsllglmlklk.wcaWv 53 
                                        +l++i++++gl + +k   +Wv
  gi|488601724|ref|YP_007908195.1| 131 FVLAVIIGFTGLAMAFKdFFSWV 153
                                       489************99446776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 1197.40
//
Query:       gi|488601725|ref|YP_007908196.1|  [L=568]
Description: Ni,Fe-hydrogenase I large subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-103  345.9   0.0    1.9e-69  234.9   0.0    3.1  3  NiFeSe_Hases  Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   8.4e-30   1.5e-25       1      74 [.      46     119 ..      46     122 .. 0.98
   2 !  234.9   0.0   1.1e-73   1.9e-69     151     486 ..     149     497 ..     141     500 .. 0.87
   3 !   17.2   0.0     1e-07    0.0018     489     505 .]     548     564 ..     533     564 .. 0.81

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 8.4e-30
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLh 74 
                                       RG+E+ilkgrdprda +++qRiCGVC+  H  ++++a+++A+g+++p  a l+rn++++a+++ dh++h Y L 
  gi|488601725|ref|YP_007908196.1|  46 RGWEIILKGRDPRDAFFITQRICGVCPAPHGETAIQALDHAYGVTPPPAAVLMRNILHGAYYVYDHMIHTYLLI 119
                                       9**********************************************************************985 PP

  == domain 2  score: 234.9 bits;  conditional E-value: 1.1e-73
                                       HHHHHHHHHHHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTG CS
                      NiFeSe_Hases 151 ahYLeaLelqrkaakivaifggknPhpqslvvGGvtcaidllnaerlaevkslikevkefveevylpDvlaiakaYk 227
                                       + Y   +e+qrk++++va++ggk Ph +s   GG+t++   ++ +r+a+  s ++e+ +fv +v++pD++ai +   
  gi|488601725|ref|YP_007908196.1| 149 SSYAACIEMQRKVNRVVALWGGKFPHHTSEYPGGMTVK---PTLDRIANTLSAMTELWDFVVNVMVPDLMAIVSKND 222
                                       679999********************************...9******************************99987 PP

                                       GGGCS.............--GGGGT-EEEEEEEESSTT-STT.GGE......EEEEEEESTTETT.SEBEE-TTTEE CS
                      NiFeSe_Hases 228 dwaki.............gkglgkknflsvgefpeekseelk.esl......llpsGvilngdls.kveevdeekit 283
                                       + a++             + g +++nfls+g fp+ +  ++  + +      + ++++i  g ++ + +++ ++ki+
  gi|488601725|ref|YP_007908196.1| 223 HIAETvsslldidfnglqDLGQTYGNFLSFGLFPDYNDYDKWvR-VqdgeegYRENALIRAGAWDgSPKKFTHKKIR 298
                                       6665556677778877776677788********88655433221.133344477888887777766788999***** PP

                                       EE-TTSSBS..TS-B-GGG---EB---EEE--TTSB-BSS-EEEETTB--BESHHHHHHHHHHTT.-HHHHHHHHHH CS
                      NiFeSe_Hases 284 EevkhswYk..ekslhplegetepkytleeldeegkYswikaPrykgkamevGplarvlvayakg.keevkelvdkl 357
                                       E+vk+s Y+  +++lhp eg t+p       d+ g+Y+w+kaPry+gk++evGplar++ ++  + k +v++ v+  
  gi|488601725|ref|YP_007908196.1| 299 EYVKYSRYDdsATGLHPSEGVTKP-----VKDKPGAYAWMKAPRYDGKVYEVGPLARMINTFGLKwKIDVTNPVNGK 370
                                       *********87777**********.....46899**************************99876578899999977 PP

                                       HHHHT-HGGGGS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTE CS
                      NiFeSe_Hases 358 lkklglkvealf.stlGRtaaRaleakliaellkewldelvenikkgdtetaneekldkkevpkeakGvglveapRG 433
                                         +++ +v + + s++ R aaR  ++ l+a++++ew  el++ ++     ++n +  d + vp++a+G+gl++apRG
  gi|488601725|ref|YP_007908196.1| 371 SFTFEWNVLNPKgSVIDRVAARVAQTLLFATKTMEWAIELKQFMHDD---IVNAKIPDYSYVPDNAEGMGLWDAPRG 444
                                       6666665544446***************************9999884...777777799999*99************ PP

                                       EEEEEEEEETTEEEEEEEE-HHHHHH--S-TT----HHHHHHTT-B-SSTTS- CS
                      NiFeSe_Hases 434 aLsHwikikdgkienYqavvPsTWnasPrdakgqkgayEaaLigtpvadpekP 486
                                       aL H+ ki+++ki+nYq++vPsTWn++Prd+ +q+g++E+aL gt + + + P
  gi|488601725|ref|YP_007908196.1| 445 ALLHYTKIRNKKIDNYQCIVPSTWNLGPRDDMDQPGPVEKALEGTWLPKLDVP 497
                                       ********************************************998877766 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1e-07
                                       HHHHHHHT--BHHHHH- CS
                      NiFeSe_Hases 489 ilrtihSfDPClACavH 505
                                       ++ +++SfDPC+AC vH
  gi|488601725|ref|YP_007908196.1| 548 AITIVRSFDPCIACGVH 564
                                       5779************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 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:                        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: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 3036.76
//
Query:       gi|488601726|ref|YP_007908197.1|  [L=354]
Description: methanophenazine-reducing hydrogenase, small subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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  102.6   0.2    2.1e-29  102.0   0.2    1.3  1  Oxidored_q6     NADH ubiquinone oxidoreductase, 20 Kd subunit
    1.7e-26   92.4   6.5    7.7e-26   90.3   4.0    2.2  2  NiFe_hyd_SSU_C  NiFe/NiFeSe hydrogenase small subunit C-termi
    0.00034   20.3   0.7    0.00034   20.3   0.7    3.0  3  TAT_signal      TAT (twin-arginine translocation) pathway sig


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 !  102.0   0.2   3.6e-33   2.1e-29       1     130 [.      53     209 ..      53     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 3.6e-33
                                       -SHHHHHH.T-TTTTHHHHH.HTEE.........EEEETTT-S--HHH.......HHHTHTTTSEEEEEESBE...E CS
                       Oxidored_q6   1 CtGcsisl.laleedlldll.elie.........lryhetlladskee.......eieakekeadvlvveGavtrkp 59 
                                       CtGc+is+ +a+e+dl+++l e+            +y+et++ +s++        +++++  +  vl+veGav+++ 
  gi|488601726|ref|YP_007908197.1|  53 CTGCTISFaQASEPDLVQILtEITVgtsglpialPDYMETIHPASGSLaerlkdeRWAQGTPGRRVLIVEGAVQEEG 129
                                       ********************6654489999999989999999999977999**999999**************5444 PP

                                       ......EEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-T..EE-HHHHHHHC.....S-E.EEE-SSS--HHHH CS
                       Oxidored_q6  60 ......kealellkelaekakaviavGtCAafGGipaaannp..svgeevgellev....vpvdinipGCPphpeai 124
                                             k+++++lke+ e a+aviavG+CA++GGipaa++np  ++g  v+e+ ++    +pv inip CP+hp+++
  gi|488601726|ref|YP_007908197.1| 130 yctiagKDFRDHLKEAGEVADAVIAVGQCATYGGIPAAKPNPtgAMG--VSEFFKEvginKPV-INIPLCPVHPDHL 203
                                       ******************************************88777..33444444556***.************* PP

                                       HHHHHH CS
                       Oxidored_q6 125 letlla 130
                                       + t++a
  gi|488601726|ref|YP_007908197.1| 204 VLTIAA 209
                                       **9987 PP

>> NiFe_hyd_SSU_C  NiFe/NiFeSe hydrogenase small subunit C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.039   2.3e+02      60      69 ..      49      58 ..      24      66 .. 0.78
   2 !   90.3   4.0   1.3e-29   7.7e-26       1      80 []     228     306 ..     228     306 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.039
                                      TTS----TTS CS
                    NiFe_hyd_SSU_C 60 agapCigCte 69
                                       ga+C+gCt 
  gi|488601726|ref|YP_007908197.1| 49 NGAACTGCTI 58
                                      699*****94 PP

  == domain 2  score: 90.3 bits;  conditional E-value: 1.3e-29
                                       HSSBCGGC.-TTHHHHHHT-B-SSTTSHTSBSGGGT--GGG-BSSTTTC-BTTTTB-TTTTTS----TTSTTGGGGS CS
                    NiFe_hyd_SSU_C   1 ygktihdn.CerreyfdagefaeefgdeegClyklGCkGpvtyadcpkrkwnegvswpvkagapCigCtepgfpdkk 76 
                                       +gk++hd+ C++r+y+d+g+f++++g+ egC y +GCkGp+t++dc+ rkwn + s++v++++ CigC+epg+pdk+
  gi|488601726|ref|YP_007908197.1| 228 FGKNMHDEiCPYRPYYDRGIFTRRPGE-EGCRYVMGCKGPITKTDCALRKWNMHISYCVETNM-CIGCSEPGWPDKF 302
                                       7999**999******************.********************************887.************* PP

                                       SSTT CS
                    NiFe_hyd_SSU_C  77 spfy 80 
                                       spfy
  gi|488601726|ref|YP_007908197.1| 303 SPFY 306
                                       **97 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.7   5.7e-08   0.00034       1      21 [.       6      26 ..       6      28 .. 0.92
   2 ?   -3.6   0.2       2.1   1.2e+04      16      22 ..     208     214 ..     206     216 .. 0.64
   3 ?    0.0   1.0      0.15   8.8e+02      12      16 ..     329     333 ..     326     339 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.7e-08
                        TAT_signal  1 klSRRdFLKgsAAaaAAaalg 21
                                      kl+RR+F+K +A+ +A a l 
  gi|488601726|ref|YP_007908197.1|  6 KLTRRNFMKLAAMMGATAFLT 26
                                      68****************985 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.1
                        TAT_signal  16 AAaalgg 22 
                                       AA++ g+
  gi|488601726|ref|YP_007908197.1| 208 AAVMIGA 214
                                       6776665 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.15
                        TAT_signal  12 AAaaA 16 
                                       +AaaA
  gi|488601726|ref|YP_007908197.1| 329 GAAAA 333
                                       23333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2084.92
//
Query:       gi|488601727|ref|YP_007908198.1|  [L=246]
Description: hypothetical protein Asulf_02252 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 1358.37
//
Query:       gi|488601728|ref|YP_007908199.1|  [L=1042]
Description: Reverse gyrase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-68  229.4   0.2    3.1e-67  227.4   0.2    2.0  1  Topoisom_bac   DNA topoisomerase
    7.6e-21   74.3   1.8    2.7e-20   72.5   0.0    2.9  4  Toprim         Toprim domain
    1.8e-11   44.1   0.0    4.9e-11   42.7   0.0    1.7  1  DEAD           DEAD/DEAH box helicase
    1.2e-09   38.4   0.1    4.5e-09   36.6   0.1    1.9  1  ResIII         Type III restriction enzyme, res subunit
    1.3e-06   28.8   0.5      0.035   14.4   0.1    3.5  2  Helicase_C     Helicase conserved C-terminal domain
     0.0023   17.3   0.7       0.25   10.7   0.2    2.5  2  zf_Rg          Reverse gyrase zinc finger
  ------ inclusion threshold ------
       0.03   14.1   0.0      0.088   12.5   0.0    1.8  1  IstB_IS21      IstB-like ATP binding protein
      0.045   13.3   0.0      0.092   12.3   0.0    1.5  1  AAA_25         AAA domain
      0.051   13.7   5.0        0.5   10.5   0.4    2.3  2  DUF1272        Protein of unknown function (DUF1272)
       0.14   12.0   0.0       0.29   11.0   0.0    1.5  1  Helicase_RecD  Helicase
          6    6.8  11.4        5.2    7.0   0.1    4.8  4  Rad50_zn_hook  Rad50 zinc hook motif


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 !  227.4   0.2   1.9e-70   3.1e-67       2     411 ..     654    1030 ..     653    1032 .. 0.78

  Alignments for each domain:
  == domain 1  score: 227.4 bits;  conditional E-value: 1.9e-70
                      Topoisom_bac    2 inenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76  
                                        ++enlv+a++ Rr+ D++iG++ls+ l+k ++++++lsaGR qtp+L++i++R ++ ++ +     e  + + ++
  gi|488601728|ref|YP_007908199.1|  654 VDENLVKAQMFRRIEDRWIGFSLSEKLWK-IFNNRNLSAGRAQTPVLGWIIDRFEKSKRKKDVAIIEDFGIFVDD 727 
                                        689*************************7.8889*********************99999655544444443222 PP

                      Topoisom_bac   77 kkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsia 151 
                                        ++      k  k+++k+k+++          ++++e+++++ +++  p p++t +L+ +a r+l++ a +++s+a
  gi|488601728|ref|YP_007908199.1|  728 SEI----IKLLKSKLKNKKKV----------KVRIEKIDERVEERVLP-PYTTESLLIDAGRILKIPAREAMSLA 787 
                                        222....23334434433333..........46777778888888889.9************************* PP

                      Topoisom_bac  152 qkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteel 226 
                                        q+L+e+ glitY+RTdstr+s++  l+ ++e+l ++    ++         ++++    +++ +aHe+IrPt+  
  gi|488601728|ref|YP_007908199.1|  788 QDLFEN-GLITYHRTDSTRVSDDG-LRVAKEYLGED----FR---------GRHW----SSE-GAHECIRPTKPF 842 
                                        *****7.****************9.88888888875....23.........3445....566.9********998 PP

                      Topoisom_bac  227 pkl..kels............ddekklYelIvrrflaslmk.dakyeettvkl..eveeeefkasgktilekGfk 284 
                                        +k+   +l+            ++   lY+lI+rrf+as+++ + ++e+ ++ l  ++ e+e+ +s +        
  gi|488601728|ref|YP_007908199.1|  843 DKNtvMRLIeegilyaekltfRHF-ALYDLIFRRFMASQSTaEIRFERYSISLngKIIEHEIPVSARGRSY---- 912 
                                        843233333777888888885555.5*************86245677777777333344444444444444.... PP

                      Topoisom_bac  285 kvykeekkeeeeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYv 359 
                                        ++yk+   +e    lp+ + + +v  k       k    k++t+a+++ +m +++iG+p+T+a+ii+kl+ r+Y+
  gi|488601728|ref|YP_007908199.1|  913 ELYKSVLLRE---PLPRGEAEVSV--KT-----IKIAEAKPLTQAEVVGLMRERKIGRPSTYATIIDKLFLRRYI 977 
                                        4554444443...26665555554..44.....34566789********************************** PP

                      Topoisom_bac  360 erkkkslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkadakev 411 
                                         +k++ l+p++lG+ + + l +++ ++vs++ T+eleek++eI++g +d+ + 
  gi|488601728|ref|YP_007908199.1|  978 FEKNGFLIPSRLGMDVFSYLsKNYGKFVSEHRTRELEEKMEEIEKGIQDYYQA 1030
                                        **99****************7777**********************9998765 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.3     1e+04      31      60 ..     247     271 ..     226     290 .. 0.67
   2 !   72.5   0.0   1.7e-23   2.7e-20       2     103 .]     490     639 ..     489     639 .. 0.95
   3 ?   -1.3   0.1       1.6   2.6e+03      20      53 ..     712     745 ..     679     760 .. 0.56
   4 ?   -3.6   0.1       8.3   1.4e+04      39      65 ..    1013    1040 ..     996    1041 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.3
                                       SSEEEHSTTEEEEEECTTTHHHHHHHHHHH CS
                            Toprim  31 hildletefkpvyeeiedkkkvlkalkela 60 
                                       h++++e+     + +++d++++lk + +++
  gi|488601728|ref|YP_007908199.1| 247 HVRNIED-----FVIMHDEIEALKNIMREL 271
                                       6666666.....556666666666655444 PP

  == domain 2  score: 72.5 bits;  conditional E-value: 1.7e-23
                                       EEEESSHHHHHHHHHTHT..................STEEEEEEESSSSEEEHS...........TTEEEEE..... CS
                            Toprim   2 lvivEgpsdaktiakalg..................sgfqavtaslGhildlet...........efkpvye..... 44 
                                       l +vE+p++a++i++++g                  +  + +tas+Gh++dl+t           +f pvy      
  gi|488601728|ref|YP_007908199.1| 490 LLVVESPTKARQISRFFGkpsvkildgvpvyevameDYVLFITASIGHLTDLVTdrgfhgvevgqDFIPVYAsikrc 566
                                       89*********************************************************************9***** PP

                                       .................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESSS CS
                            Toprim  45 .................eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefsei 103
                                                        e +d k+ + al++la +   +i+ tDpD+eGe+iaw++ ++l       +i+r+ef+e+
  gi|488601728|ref|YP_007908199.1| 567 kscgyqftsgscpkckgEFDDSKQRILALRKLAYDTGFVIVGTDPDTEGEKIAWDIKNLLA----CgEIRRAEFHEV 639
                                       *********************************************************5444....446*******95 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.6
                                       STEEEEEEESSSSEEEHSTTEEEEE.ECTTTHHHH CS
                            Toprim  20 sgfqavtaslGhildletefkpvye.eiedkkkvl 53 
                                       ++++a++   G  +d  + + + ++ ++++kkkv 
  gi|488601728|ref|YP_007908199.1| 712 KKDVAIIEDFGIFVDDSE-IIKLLKsKLKNKKKVK 745
                                       345555555555555555.3333333333333333 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 8.3
                                        TEEEEE.ECTTTHHHHHHHHHHHHHHSE CS
                            Toprim   39 fkpvye.eiedkkkvlkalkelakrade 65  
                                        +++++e + ++++++ +alkel ++ +e
  gi|488601728|ref|YP_007908199.1| 1013 LEEKMEeIEKGIQDYYQALKELYEEIKE 1040
                                        3334444555666666667777666666 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0     3e-14   4.9e-11       4     170 ..      58     226 ..      55     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 3e-14
                                       HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                              DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl. 79 
                                       Q    + +l+++++++  +TGsGKT+  l   +  ++    k+g+k+ ++ Pt+ L+ q +++++++++ ++l+++ 
  gi|488601728|ref|YP_007908199.1|  58 QLLWAKRVLRNESFCITSPTGSGKTAFGLAMSI--FL---AKKGKKCYLIFPTTVLVVQAFERINSMLESLKLNLKv 129
                                       56667789999**************76554444..54...59999************************98766663 PP

                                       EEETTSSHHHHHHHHHTT...CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS...H CS
                                       xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                              DEAD  80 liiggvaardqlskldng...vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql...p 150
                                         ++g+ ++++++++ ++    +i+++  + l + ++   l+  ++ f+ +D +d +l+   s+ ++ril+ l   p
  gi|488601728|ref|YP_007908199.1| 130 GYYHGKLKKEEKEDFMKNignFNIIITSSQFLSKNFD--VLKNYRFDFIFVDDVDAILKA--SRNVERILTLLglnP 202
                                       3456777777777665445679*******99999775..444667778***********8..666777666551113 PP

                                       HHCTTSTTTSE....EEEEESSBS CS
                                       xxxxxxxxxxx....xxxxxxxxx RF
                              DEAD 151 qitcdgklqrq....vivlSATlp 170
                                       +   + +++++    ++v +AT++
  gi|488601728|ref|YP_007908199.1| 203 ELDGKNPAENKgigcLVVSTATAK 226
                                       333333322224555666667765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   2.7e-12   4.5e-09      22     140 ..      66     180 ..      28     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.7e-12
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG..........GEEEESSS CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke......igkkvsgd 92 
                                        r++ ++i  +TG+GKT   +++   l+kkgk  k+ ++ p++ l+ q+ e+++++l++ + +      +gk ++++
  gi|488601728|ref|YP_007908199.1|  66 LRNESFCITSPTGSGKTAFGLAMSIFLAKKGK--KCYLIFPTTVLVVQAFERINSMLESLKLNlkvgyyHGKLKKEE 140
                                       57899************999999888888877..***********************99998899999778888888 PP

                                       -B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEET CS
                            ResIII  93 kkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDE 140
                                       k+++ +k++ n +i++t+ q l+++        + l++ rfd+i++D 
  gi|488601728|ref|YP_007908199.1| 141 KEDF-MKNIGNFNIIITSSQFLSKNF-------DVLKNYRFDFIFVDD 180
                                       8887.********************9.......888889999999996 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 !   14.4   0.1   2.1e-05     0.035      18      74 ..     105     158 ..      86     183 .. 0.71
   2 !   10.0   0.0   0.00052      0.85      40     109 ..     293     420 ..     259     421 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                                       EEEEEESSHHHHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                        Helicase_C  18 kilifvntidrlekvklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                       +++++v+  +r++  ++l++ k ++kv ++hg+l+++e+e+ +++   g+++++i+++
  gi|488601728|ref|YP_007908199.1| 105 TTVLVVQAFERIN--SMLESLKlNLKVGYYHGKLKKEEKEDFMKNI--GNFNIIITSS 158
                                       3344444444554..444332359**********************..99**777654 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00052
                                       TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG....GTSSSTST.TESEEEESSSS....SSH.......... CS
                        Helicase_C  40 gikvavlhgelpqnereeileqfnkgesdvLiatdv....aerGidip.kvnlVinfdlp....rnv.......... 97 
                                       ++++ v+++      ++  +e f++ge+d+Li t      + rG+d+p k+++ i++++p    + v          
  gi|488601728|ref|YP_007908199.1| 293 EFRIGVVTS------KKNDFEMFKAGEVDYLIGTAHyygsLVRGLDLPeKIRYAIFVGFPvfkmK-Vedidsasenq 362
                                       566655555......5566999************998888999****9789*******9985540.25567778888 PP

                                       ..............................................HHHHHHHTTSSS CS
                        Helicase_C  98 ..............................................tsyiqriGRtgR 109
                                                                                     ++yiq++GRt R
  gi|488601728|ref|YP_007908199.1| 363 lriiarilginandaklkekikeamkkerivsdvvvkdntitfpdlRTYIQASGRTSR 420
                                       9999999999999999999999999999999999999999999999999999999988 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00016      0.25       3      20 ..       2      19 ..       1      26 [. 0.85
   2 ?    4.3   0.0     0.016        25       7      19 ..     575     587 ..     571     593 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                             zf_Rg  3 kavfeklCPNCgGdisde 20
                                      + ++e lCP C+Gd+s +
  gi|488601728|ref|YP_007908199.1|  2 QVIYEGLCPVCDGDLSLN 19
                                      579***********9865 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                             zf_Rg   7 eklCPNCgGdisd 19 
                                       + +CP C+G+  d
  gi|488601728|ref|YP_007908199.1| 575 SGSCPKCKGEFDD 587
                                       579******9876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.4e-05     0.088      39      80 ..      60     101 ..      24     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-05
                         IstB_IS21  39 atlsfiekkenivllGpsGvGKshlaialgveavraglsvlf 80 
                                          + + ++e+++++ p+G GK+ +  a++   +++g++ + 
  gi|488601728|ref|YP_007908199.1|  60 LWAKRVLRNESFCITSPTGSGKTAFGLAMSIFLAKKGKKCYL 101
                                       334446789*************************99998753 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.6e-05     0.092      12      79 ..      47     112 ..      36     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                            AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsa 79 
                                       ++    ++++++ l+   + ++e   ++ ++g+GKt++ l +++ +a +Gk+   ++   + +Vl+v+a
  gi|488601728|ref|YP_007908199.1|  47 FNSCVGRIRKLQLLWAKRVLRNESFCITSPTGSGKTAFGLAMSIFLAkKGKKCYLIF---PTTVLVVQA 112
                                       555567899999999998899**************************9999776655...668888775 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.018        30       8      25 ..       9      26 ..       3      36 .. 0.84
   2 ?   10.5   0.4   0.00031       0.5      32      52 ..     566     586 ..     560     591 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.018
                           DUF1272  8 CecCdkdlppdseearic 25
                                      C  Cd dl+ ++ ea+ic
  gi|488601728|ref|YP_007908199.1|  9 CPVCDGDLSLNEIEATIC 26
                                      888999999999999998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00031
                           DUF1272  32 CaeCaeevlenvCPncgGelv 52 
                                       C++C  +  ++ CP c Ge+ 
  gi|488601728|ref|YP_007908199.1| 566 CKSCGYQFTSGSCPKCKGEFD 586
                                       *******************95 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.29       2     101 ..      73     183 ..      72     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke..........eekkkkaekae 68 
                                       +t+  G GK+a  Gla++ ++a++ +++++  p+   v + fe++++ le+l+l+           +   +++e+ +
  gi|488601728|ref|YP_007908199.1|  73 ITSPTGSGKTA-FGLAMSIFLAKKGKKCYLIFPTTVLVVQAFERINSMLESLKLNLkvgyyhgklkK---EEKEDFM 145
                                       89999****75.7***************************************999888998774431...2222222 PP

                     Helicase_RecD  69 lrvr.......kqrieyiapdellklkeqadllvvDEAAa 101
                                          +        ++ ++++ +  + ++ + d+++vD   a
  gi|488601728|ref|YP_007908199.1| 146 K--NignfniiITSSQFLSKNFDVLKNYRFDFIFVDDVDA 183
                                       2..2234456566677777776555566778888887655 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.036        59      21      30 ..       8      17 ..       5      25 .. 0.80
   2 ?    7.0   0.1    0.0032       5.2      20      33 ..     576     589 ..     574     596 .. 0.83
   3 ?   -1.2   0.7       1.1   1.9e+03      35      50 ..     728     743 ..     726     744 .. 0.87
   4 ?   -1.7   0.2       1.6   2.6e+03       5      16 ..    1010    1021 ..    1007    1024 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.036
                                      E-TTT--EE- CS
                     Rad50_zn_hook 21 cCPlCgReld 30
                                       CP+C+ +l+
  gi|488601728|ref|YP_007908199.1|  8 LCPVCDGDLS 17
                                      5*****9997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0032
                                       EE-TTT--EE-HHH CS
                     Rad50_zn_hook  20 gcCPlCgReldeeh 33 
                                       g+CP C+ e+d+ +
  gi|488601728|ref|YP_007908199.1| 576 GSCPKCKGEFDDSK 589
                                       59*********977 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHH. CS
                     Rad50_zn_hook  35 seLikelqsklerlpe 50 
                                       se+ik l+skl+++++
  gi|488601728|ref|YP_007908199.1| 728 SEIIKLLKSKLKNKKK 743
                                       799999*****99875 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.6
                                        HHHHHHHHHHHT CS
                     Rad50_zn_hook    5 teelnkkieelk 16  
                                        t el++k+ee++
  gi|488601728|ref|YP_007908199.1| 1010 TRELEEKMEEIE 1021
                                        556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1042 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1513  (0.0843884); expected 358.6 (0.02)
Passed bias filter:                     1063  (0.0592894); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); 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: 1.10u 0.37s 00:00:01.47 Elapsed: 00:00:00.56
# Mc/sec: 5564.87
//
Query:       gi|488601729|ref|YP_007908200.1|  [L=288]
Description: KaiC domain protein, AF_0795 family [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-64  217.0   0.4    2.5e-64  216.8   0.4    1.0  1  ATPase      KaiC
    2.9e-05   23.9   0.0    7.1e-05   22.6   0.0    1.7  1  IstB_IS21   IstB-like ATP binding protein
     0.0011   18.5   0.0     0.0019   17.8   0.0    1.3  1  AAA_25      AAA domain
     0.0016   18.2   0.1     0.0031   17.3   0.1    1.4  1  AAA_24      AAA domain
     0.0042   17.1   0.4      0.016   15.2   0.4    1.9  1  AAA_14      AAA domain
      0.006   15.6   0.0      0.012   14.7   0.0    1.4  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.038   13.2   0.1      0.057   12.7   0.1    1.3  1  Rad51       Rad51
      0.051   13.0   0.0      0.082   12.3   0.0    1.4  1  KTI12       Chromatin associated protein KTI12
      0.078   12.9   0.2        6.1    6.7   0.1    2.2  2  APS_kinase  Adenylylsulphate kinase
       0.15    9.7   0.0       0.19    9.4   0.0    1.0  1  TALPID3     Hedgehog signalling target


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 !  216.8   0.4   1.4e-67   2.5e-64       3     230 ..      23     274 ..      21     275 .. 0.96

  Alignments for each domain:
  == domain 1  score: 216.8 bits;  conditional E-value: 1.4e-67
                            ATPase   3 tgIeglDeilk..............gGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa....e 61 
                                       t ++ lDe+++              +G+p+ +v++itG p+tGK+i+a+qF+i++a+  g++++fvtve+pa     
  gi|488601729|ref|YP_007908200.1|  23 TWTK-LDEMFYrieregdkfvrkplNGLPHLAVINITGIPDTGKSILAEQFAITQANL-GYKVLFVTVESPAeflyL 97 
                                       5555.89999778999999999999******************************998.*************88888 PP

                            ATPase  62 dlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekea 138
                                       +l+e+  +lG ++ek+e++  +++idas++++       +e+++ l++++a+aike++ +++viDsitgl ye+ke 
  gi|488601729|ref|YP_007908200.1|  98 ALKEKSLALGYNFEKIEKN--IVVIDASQDDDL------REEPKTLLDTMAYAIKEKRTNNTVIDSITGL-YEHKEV 165
                                       999****************..*********998......99*****************************.****** PP

                            ATPase 139 vaReilrqlvrvlkklgvTailvsekss.....seeaaggygveefivdgvivLdlkeiee............elvR 198
                                       +aR+i+r+++++lkk+++Ta+lvs+k+s     s+eaagg +v++ ivdg+iv+d+k ie+            ++ R
  gi|488601729|ref|YP_007908200.1| 166 MARQIVRKFFNFLKKYRQTALLVSQKRSaqaseSAEAAGGLAVAH-IVDGTIVMDKKIIETkwdvnlykkpigSVIR 241
                                       ***************************99**9999**********.******************************* PP

                            ATPase 199 tleivkmRgtkhskkehpfeIte.egikvleek 230
                                       t++i+++R t+h++++++feIte ++i++l+++
  gi|488601729|ref|YP_007908200.1| 242 TIRIDGCRLTAHDSRTWVFEITEhGTINILKPL 274
                                       ***********************99****9876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     4e-08   7.1e-05      48     158 ..      53     166 ..      17     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4e-08
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralk.rllkvdllilDdlgllpld 123
                                       + i ++G + +GKs la  ++   ++ g++vlfv+ve   e l +a ++ +la   + + ++ +++++D     +l 
  gi|488601729|ref|YP_007908200.1|  53 AVINITGIPDTGKSILAEQFAITQANLGYKVLFVTVESPAEFLYLALKEKSLALGYNfEKIEKNIVVIDASQDDDLR 129
                                       45789********************************9999998888888877654313344578888877777776 PP

                         IstB_IS21 124 qaeaellfeviekryerr..siiitsnlpfaewdevl 158
                                       ++ ++ll  +  +  e+r   ++i s   + e++ev+
  gi|488601729|ref|YP_007908200.1| 130 EEPKTLLDTMAYAIKEKRtnNTVIDSITGLYEHKEVM 166
                                       6555544433333334331146666666666666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     1e-06    0.0019      31     186 ..      50     188 ..      42     196 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-06
                            AAA_25  31 pagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.....rdda 101
                                       p  +++ ++G p+tGK+ la + a++ a +G            kVl+v  E +++ l   l++   al     +  +
  gi|488601729|ref|YP_007908200.1|  50 PHLAVINITGIPDTGKSILAEQFAITQAnLGY-----------KVLFVTVESPAEFLYLALKEKSLALgynfeKIEK 115
                                       677899**********************5555...........6777777777654444444433333333333345 PP

                            AAA_25 102 rllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                       +  v+d+ ++ ++l         +  +  +d ++ ai+e ++    viD+++ ++++ e  ++++ +++++ l++  
  gi|488601729|ref|YP_007908200.1| 116 NIVVIDA-SQdDDL--------REEPKTLLDTMAYAIKE-KRTNNTVIDSITGLYEHKEVMARQIvRKFFNFLKK-- 180
                                       5566664.332222........22245667889******.99*************99998776655666655554.. PP

                            AAA_25 177 rrtgaavllv 186
                                         ++ + llv
  gi|488601729|ref|YP_007908200.1| 181 --YRQTALLV 188
                                       ..55555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.7e-06    0.0031       5      87 ..      55     169 ..      52     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfi.........................dtekGlksldadkfpdie.s 48 
                                       i i+G + +GK+ la ++       g+k+lf+                          +ek    +da + +d++  
  gi|488601729|ref|YP_007908200.1|  55 INITGIPDTGKSILAEQFaitqanlGYKVLFVtvespaeflylalkekslalgynfeKIEKNIVVIDASQDDDLReE 131
                                       779*****************************999999999999888888888855555555555555555555555 PP

                            AAA_24  49 wedfldevvelaaeladyktlviDtideleelclaevir 87 
                                        +++ld++++  +e++  +  viD+i+ l+e++  ++++
  gi|488601729|ref|YP_007908200.1| 132 PKTLLDTMAYAIKEKR-TNNTVIDSITGLYEHKEVMARQ 169
                                       5555555555555555.66678*********98877665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   9.1e-06     0.016       4      76 ..      54     126 ..      52     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.1e-06
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe...kllelileklkeekktylflDEiqev 76 
                                       ++ itG+  +GK+ l++q++ ++     ++l+++++++ +  +   +     l + +ek+   +k+++++D  q  
  gi|488601729|ref|YP_007908200.1|  54 VINITGIPDTGKSILAEQFAITQANLGYKVLFVTVESPAEFLYLALKeksLALGYNFEKI---EKNIVVIDASQDD 126
                                       6789***************98887667888999999888844332221112223333333...6788888877765 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   6.5e-06     0.012      30      66 ..      53      89 ..      39      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.5e-06
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                       v+ +tG+P +Gks l e+++++ ++ G++v  + v+
  gi|488601729|ref|YP_007908200.1| 53 AVINITGIPDTGKSILAEQFAITQANLGYKVLFVTVE 89
                                      5899***************************999987 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.2e-05     0.057      33     148 ..      48     163 ..      35     253 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                                       SEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGG....HHHH..HHT.T--HHHH CS
                             Rad51  33 GietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperl....veia..ery.kldkeev 102
                                       G++  ++ +i G   +Gk+ l+ ++++t q          k++++  e+  +   l     ++a    + k++k+ v
  gi|488601729|ref|YP_007908200.1|  48 GLPHLAVINITGIPDTGKSILAEQFAIT-QA-----NLGYKVLFVTVESPAEFLYLalkeKSLAlgYNFeKIEKNIV 118
                                       6888889999999999999999999986.33.....33468888888886543322111133442244455555555 PP

                                       GGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH- CS
                             Rad51 103 lenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtd 148
                                       +++ + +     e+ + ll+++a  ++e++ +  ++Ds+t ly   
  gi|488601729|ref|YP_007908200.1| 119 VIDASQDDDLR-EEPKTLLDTMAYAIKEKRTNNTVIDSITGLYEHK 163
                                       55555555544.66789*************************9654 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.6e-05     0.082       3      81 ..      54     141 ..      52     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-05
                                       EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.......TTSS....S--GGGHHHHHHHHHHHHHHHHT CS
                             KTI12   3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslg......iekds....ykdsakekalRsslrsavkrdLs 69 
                                        + +tG+P +GKs +a+++a + ++ +++v  +  es        ++++s    y+ ++ ek++   + ++ + dL 
  gi|488601729|ref|YP_007908200.1|  54 VINITGIPDTGKSILAEQFAITQANLGYKVLFVTVESPAeflylaLKEKSlalgYNFEKIEKNIV-VIDASQDDDLR 129
                                       5779******************9999999998887765545566555555566666666666663.34445556666 PP

                                       T.SEEEE-S--- CS
                             KTI12  70 kekvVIvDslny 81 
                                       +e  + +D ++y
  gi|488601729|ref|YP_007908200.1| 130 EEPKTLLDTMAY 141
                                       666666666666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.021        38       3      33 ..      53      83 ..      51      89 .. 0.84
   2 ?    6.7   0.1    0.0034       6.1      72     120 ..     147     195 ..     112     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.021
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisv 33
                                      +v+ +tG+  +GKs +a++++ +  + g++v
  gi|488601729|ref|YP_007908200.1| 53 AVINITGIPDTGKSILAEQFAITQANLGYKV 83
                                      5899**************9988777777766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0034
                                       HTT-EEEEE----SHHHHHHHHHHHHCHTEEEEEEEE--HHHHHHHTTT CS
                        APS_kinase  72 daglivlvafisPyreeReaarelleealkfievfvdtplevceerDpk 120
                                       +++  v+ ++   y+++  +ar+++++  +f++ + +t l v+++r  +
  gi|488601729|ref|YP_007908200.1| 147 RTNNTVIDSITGLYEHKEVMARQIVRKFFNFLKKYRQTALLVSQKRSAQ 195
                                       5677899999999*************99***************999766 PP

>> TALPID3  Hedgehog signalling target
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0001      0.19     820     908 ..     132     224 ..     128     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0001
                           TALPID3 820 aqptadildkvierretlENkLvdWV.....EqeimariisglfPlqaqaapdvsvsesEeseavtsdiVeaagggg 891
                                       ++ + d +   i+ + t  N ++d +      +e+mar i + f    ++  +++  +s +  a +s+  eaagg +
  gi|488601729|ref|YP_007908200.1| 132 PKTLLDTMAYAIKEKRT-NNTVIDSItglyeHKEVMARQIVRKFFNFLKKYRQTALLVSQKRSAQASESAEAAGGLA 207
                                       55666777777877776.577777553333259*****99998888877778888999******************* PP

                           TALPID3 892 lqlfvdagVPVdSelir 908
                                       +  +vd  +  d ++i+
  gi|488601729|ref|YP_007908200.1| 208 VAHIVDGTIVMDKKIIE 224
                                       *******9999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1695.34
//
Query:       gi|488601730|ref|YP_007908201.1|  [L=119]
Description: putative regulatory domain protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-06   28.0   1.0    1.3e-06   27.8   0.1    1.6  2  Sigma70_r4       Sigma-70, region 4
    2.6e-06   27.0   0.0    4.5e-06   26.3   0.0    1.4  1  HTH_23           Homeodomain-like domain
    3.2e-06   26.7   0.1    6.2e-06   25.8   0.1    1.4  1  Sigma70_r4_2     Sigma-70, region 4
    7.6e-05   22.6   0.2    0.00017   21.5   0.0    1.8  1  HTH_29           Winged helix-turn helix
    0.00022   21.3   0.0    0.00057   19.9   0.0    1.7  1  HTH_28           Helix-turn-helix domain
     0.0007   19.1   0.1      0.002   17.6   0.0    1.7  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00074   18.9   0.0      0.001   18.4   0.0    1.2  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
    0.00091   19.2   0.1     0.0016   18.4   0.1    1.4  1  HTH_3            Helix-turn-helix
    0.00092   19.0   0.0     0.0019   18.0   0.0    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0014   18.4   0.1     0.0026   17.5   0.1    1.4  1  HTH_38           Helix-turn-helix domain
     0.0036   17.3   0.0      0.006   16.6   0.0    1.4  1  Phage_terminase  Phage terminase small subunit
     0.0042   17.1   0.0     0.0096   16.0   0.0    1.6  1  HTH_7            Helix-turn-helix domain of resolvase
     0.0044   16.6   0.3      0.013   15.1   0.0    1.8  2  CENP-B_N         CENP-B N-terminal DNA-binding domain
     0.0048   16.8   0.1     0.0075   16.1   0.1    1.3  1  Terminase_5      Putative ATPase subunit of terminase (gpP-li
     0.0057   16.5   0.2      0.015   15.1   0.1    1.7  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0069   15.9   0.1      0.015   14.8   0.1    1.5  1  GerE             Bacterial regulatory proteins, luxR family
     0.0079   16.3   0.4      0.017   15.2   0.2    1.6  1  Sigma70_r3       Sigma-70 region 3
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.024   14.6   0.0    1.5  1  HTH_11           HTH domain
      0.016   15.0   0.0       0.04   13.7   0.0    1.6  1  HTH_10           HTH DNA binding domain
      0.018   14.9   0.1       0.15   12.0   0.0    2.4  3  YdaS_antitoxin   Putative antitoxin of bacterial toxin-antito
       0.02   14.6   0.0      0.041   13.6   0.0    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.032   14.3   0.0      0.057   13.4   0.0    1.5  1  HTH_Mga          M protein trans-acting positive regulator (M
      0.046   13.7   2.0      0.083   12.9   0.6    2.2  2  HTH_19           Helix-turn-helix domain
      0.046   13.9   0.0      0.096   12.9   0.0    1.6  1  HTH_17           Helix-turn-helix domain
       0.07   13.2   0.2       0.14   12.3   0.2    1.6  1  SpoIIID          Stage III sporulation protein D
      0.085   12.8   0.0       0.13   12.1   0.0    1.2  1  MarR_2           MarR family
       0.12   12.8   0.0       0.22   12.0   0.0    1.5  1  HTH_26           Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1     2e-09   1.3e-06      11      41 ..      49      79 ..      45      81 .. 0.92
   2 ?   -3.0   0.1       8.5   5.6e+03      42      50 .]     107     115 ..     105     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2e-09
                                      HHHHHHHTTT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4 11 evlelrfgeglTleEIgerlgiSrerVrqie 41
                                       v++lr +   T+ EI+e+lgi++ +Vr i 
  gi|488601730|ref|YP_007908201.1| 49 YVIVLRNEGMKTYREIAEELGITENTVRNIV 79
                                      59**************************996 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.5
                                       HHHHHHHHH CS
                        Sigma70_r4  42 krAlrkLRk 50 
                                       k A +kL++
  gi|488601730|ref|YP_007908201.1| 107 KLAYKKLKQ 115
                                       678999985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   6.8e-09   4.5e-06      10      40 ..      50      81 ..      42      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.8e-09
                            HTH_23 10 illllae.GlsvreIAreLgvsrrTvyrwlkr 40
                                      ++ l  e  +++reIA+eLg++++Tv++++++
  gi|488601730|ref|YP_007908201.1| 50 VIVLRNEgMKTYREIAEELGITENTVRNIVNA 81
                                      5666666779*******************986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   9.4e-09   6.2e-06      18      45 ..      50      77 ..      45      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.4e-09
                                      HHHHHHTS---HHHHHHHHT--HHHHHH CS
                      Sigma70_r4_2 18 ifllryleglsykEIAellgisegtVks 45
                                      +++lr +  ++y+EIAe+lgi+e+tV++
  gi|488601730|ref|YP_007908201.1| 50 VIVLRNEGMKTYREIAEELGITENTVRN 77
                                      899999999*****************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 !   21.5   0.0   2.5e-07   0.00017       4      35 ..      50      81 ..      48     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-07
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkr 35
                                      ++ l +eG++t ++iA+ lg+++ tv++++++
  gi|488601730|ref|YP_007908201.1| 50 VIVLRNEGMKTYREIAEELGITENTVRNIVNA 81
                                      677899***********************997 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.6e-07   0.00057      11      34 ..      56      80 ..      50      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.6e-07
                            HTH_28 11 aGh.svreaArelgisrrtvyrWik 34
                                      +G+ ++re+A+elgi++ tv+  ++
  gi|488601730|ref|YP_007908201.1| 56 EGMkTYREIAEELGITENTVRNIVN 80
                                      7999*****************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 ?   -2.2   0.0       4.9   3.3e+03      22      31 ..      13      22 ..      11      34 .. 0.63
   2 !   17.6   0.0     3e-06     0.002      16      39 ..      56      80 ..      51      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.9
                            HTH_24 22 eLAerlglSp 31
                                      e Ae++ + +
  gi|488601730|ref|YP_007908201.1| 13 EMAEKVFMNS 22
                                      6677776654 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3e-06
                            HTH_24 16 pr.isqreLAerlglSpstvnrrlk 39
                                       +  ++re+Ae+lg++ +tv+  ++
  gi|488601730|ref|YP_007908201.1| 56 EGmKTYREIAEELGITENTVRNIVN 80
                                      44479***************98886 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 !   18.4   0.0   1.6e-06     0.001      20      49 ..      51      80 ..      35      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                      HTH_Tnp_ISL3 20 ilelllesrsvkavArqlgvSwtTVwrild 49
                                      i+ +   +++ +++A++lg++++TV++i++
  gi|488601730|ref|YP_007908201.1| 51 IVLRNEGMKTYREIAEELGITENTVRNIVN 80
                                      5555556799******************97 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   0.1   2.5e-06    0.0016       4      32 ..      53      81 ..      52      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-06
                                      HHHHTTHHHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnG 32
                                      lR++ + + +e+Ae+lG++ +t+++i n 
  gi|488601730|ref|YP_007908201.1| 53 LRNEGMKTYREIAEELGITENTVRNIVNA 81
                                      6999***********************98 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.8e-06    0.0019      12      35 ..      53      76 ..      51      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.8e-06
                     HTH_AsnC-type 12 LqedaRisyaeLAervGlSestvl 35
                                      L+  +  +y+e+Ae++G++e+tv+
  gi|488601730|ref|YP_007908201.1| 53 LRNEGMKTYREIAEELGITENTVR 76
                                      6777899****************8 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.9e-06    0.0026      16      41 ..      53      79 ..      45      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.9e-06
                            HTH_38 16 llaeG.lslreIArrLgrspsTIsREl 41
                                      l++eG +++reIA +Lg   +T+ + +
  gi|488601730|ref|YP_007908201.1| 53 LRNEGmKTYREIAEELGITENTVRNIV 79
                                      89*********************9976 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     9e-06     0.006      12      46 ..      48      82 ..      45      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9e-06
                   Phage_terminase 12 AyelykEsggtlklkdIAkvLdvsestvrkWKakD 46
                                      Ay + + + g +  ++IA++L++ e+tvr+    D
  gi|488601730|ref|YP_007908201.1| 48 AYVIVLRNEGMKTYREIAEELGITENTVRNIVNAD 82
                                      788888899999*****************966555 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 !   16.0   0.0   1.4e-05    0.0096      10      40 ..      46      77 ..      41      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                                      HHGGGGSSTTTT.--STTTSSSS---SSSS-- CS
                             HTH_7 10 dinrvvkLleeG.isiskIAkevnisRsTvYR 40
                                      + ++v+ L++eG  + ++IA+e++i+  Tv  
  gi|488601730|ref|YP_007908201.1| 46 EAAYVIVLRNEGmKTYREIAEELGITENTVRN 77
                                      4699********999**************965 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 ?   -1.3   0.1       2.6   1.7e+03      13      22 ..       1      10 [.       1      11 [. 0.86
   2 !   15.1   0.0     2e-05     0.013      15      48 ..      50      84 ..      43      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.6
                                      HHHHHHHHCT CS
                          CENP-B_N 13 ievIqrleeg 22
                                      +e+I++++ g
  gi|488601730|ref|YP_007908201.1|  1 MEIIKKVDSG 10
                                      79***99976 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2e-05
                                      HHHHHHCTT.-HHHHHHHHT--CCHHHHHHHCHHH CS
                          CENP-B_N 15 vIqrleege.SkaelarrfnvpestlsdilknKkk 48
                                      vI +  eg+   +e+a ++++ e t+++i+++ +k
  gi|488601730|ref|YP_007908201.1| 50 VIVLRNEGMkTYREIAEELGITENTVRNIVNADEK 84
                                      677778999999******************99775 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.1e-05    0.0075      16      40 ..      61      85 ..      60     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                       Terminase_5 16 vaeIAeelglkeatVysWkkrdewd 40
                                       +eIAeelg+ e+tV + +++de++
  gi|488601730|ref|YP_007908201.1| 61 YREIAEELGITENTVRNIVNADEKE 85
                                      58********************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 !   15.1   0.1   2.3e-05     0.015      13      44 ..      48      80 ..      44      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                                      HCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHH CS
                              TrmB 13 vYlaLl.klgpatadeiaeelgvprskvYevLr 44
                                      +Y+ +l ++g +t +eiaeelg+ +++v ++++
  gi|488601730|ref|YP_007908201.1| 48 AYVIVLrNEGMKTYREIAEELGITENTVRNIVN 80
                                      79999978889999**************99986 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.2e-05     0.015      18      36 ..      59      77 ..      55      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
                                      S-HHHHHHHHTS-HHHHHH CS
                              GerE 18 ksnkeIAeelniSekTVkv 36
                                      k+  eIAeel+i e+TV++
  gi|488601730|ref|YP_007908201.1| 59 KTYREIAEELGITENTVRN 77
                                      5678*************86 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   2.5e-05     0.017      24      45 ..      62      83 ..      60      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                                      HHHHHHHTXXHHHHHHHHHHHX CS
                        Sigma70_r3 24 eEiAeeLglseekVrevleaar 45
                                       EiAeeLg++e+ Vr++++a +
  gi|488601730|ref|YP_007908201.1| 62 REIAEELGITENTVRNIVNADE 83
                                      7****************98865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.5e-05     0.024       9      34 ..      52      77 ..      45      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
                            HTH_11  9 LleargpisgeeLAeeLnvSrrtvrr 34
                                      +l+++g  +  e+AeeL++++ tvr+
  gi|488601730|ref|YP_007908201.1| 52 VLRNEGMKTYREIAEELGITENTVRN 77
                                      45788888999**************8 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.1e-05      0.04      25      49 ..      60      84 ..      58      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
                            HTH_10 25 tlkeLAkelGIskstlsehLrkaes 49
                                      t +e+A+elGI+++t+ +++++ e+
  gi|488601730|ref|YP_007908201.1| 60 TYREIAEELGITENTVRNIVNADEK 84
                                      679*************999877655 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 ?   -1.0   0.0       2.5   1.7e+03       4      14 ..      22      32 ..      19      33 .. 0.86
   2 ?   12.0   0.0   0.00022      0.15      12      44 ..      62      95 ..      56     101 .. 0.76
   3 ?   -0.9   0.0       2.3   1.5e+03       7      15 ..     101     109 ..      94     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.5
                    YdaS_antitoxin  4 aieivGgqkaL 14
                                       i+i+Gg ++L
  gi|488601730|ref|YP_007908201.1| 22 SIKILGGLRKL 32
                                      79*****9988 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
                    YdaS_antitoxin 12 kaLAealgvsqqaVsqWlk.gkkqvpaervpeIe 44
                                      ++ Ae+lg+++ +V++ ++ ++k+v      eIe
  gi|488601730|ref|YP_007908201.1| 62 REIAEELGITENTVRNIVNaDEKEVEMYIKGEIE 95
                                      689***************9444546655555555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.3
                    YdaS_antitoxin   7 ivGgqkaLA 15 
                                       ++Gg ++LA
  gi|488601730|ref|YP_007908201.1| 101 VAGGIAKLA 109
                                       78999**99 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.2e-05     0.041       8      33 ..      52      77 ..      47      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.2e-05
                          HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRR 33
                                       l+++g  +  e++e+lg++e+T+R+
  gi|488601730|ref|YP_007908201.1| 52 VLRNEGMKTYREIAEELGITENTVRN 77
                                      58889999999**************7 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.6e-05     0.057      15      42 ..      53      80 ..      50      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-05
                           HTH_Mga 15 teneksltldelakeLglseltlqsdis 42
                                      + ne+  t+ e+a+eLg++e t++++++
  gi|488601730|ref|YP_007908201.1| 53 LRNEGMKTYREIAEELGITENTVRNIVN 80
                                      5555555889**************9986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.7   1.1e+03      31      45 ..      24      38 ..       2      47 .. 0.61
   2 ?   12.9   0.6   0.00013     0.083      10      37 ..      55      83 ..      52     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                            HTH_19 31 aiEngkkdvpsaell 45
                                      +i +g ++ +++++l
  gi|488601730|ref|YP_007908201.1| 24 KILGGLRKLIDYRNL 38
                                      566664446666555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00013
                            HTH_19 10 elgl.tqeelaerlgisrskisaiEngkk 37
                                      + g+ t +e+ae+lgi+ +  ++i n   
  gi|488601730|ref|YP_007908201.1| 55 NEGMkTYREIAEELGITENTVRNIVNADE 83
                                      445559***************99999733 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014     0.096       4      24 ..      61      81 ..      60      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                            HTH_17  4 veEaAelLgvsrstvyrlirr 24
                                        E+Ae Lg+ ++tv++ +++
  gi|488601730|ref|YP_007908201.1| 61 YREIAEELGITENTVRNIVNA 81
                                      579**************9964 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00021      0.14      17      73 ..      56     106 ..      43     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                           SpoIIID  17 eskatvRkaakvfgvskstvhkDvterLkkinkklakqvkevLeknkaeRhiRGGea 73 
                                       e  +t R++a+++g+   tv + v    k++++ +  ++ +v      + h+ GG a
  gi|488601730|ref|YP_007908201.1|  56 EGMKTYREIAEELGITENTVRNIVNADEKEVEMYIKGEIEKV------DEHVAGGIA 106
                                       44589*********************99***99999988766......557777766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.13       5      43 ..      44      80 ..      41      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHHH CS
                            MarR_2  5 paqarvLaaLgrrpgrdl.tvgelarrlglsksavsrilk 43
                                      +a+a    +L++++   + t +e+a++lg++  +v +i++
  gi|488601730|ref|YP_007908201.1| 44 LAEAAYVIVLRNEG---MkTYREIAEELGITENTVRNIVN 80
                                      67777777787777...55******************998 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 ?   12.0   0.0   0.00034      0.22       5      34 ..      52      82 ..      51      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00034
                            HTH_26  5 lmadrgi.tkseLargtgisaatlsrlvkgk 34
                                      +++  g+ t+ e a+ +gi+++t+ ++v+  
  gi|488601730|ref|YP_007908201.1| 52 VLRNEGMkTYREIAEELGITENTVRNIVNAD 82
                                      578889*********************9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 640.62
//
Query:       gi|488601731|ref|YP_007908202.1|  [L=120]
Description: LSU ribosomal protein L7AE [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  100.7   0.5    3.2e-29  100.5   0.5    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    1.9e-05   24.4   0.0    2.7e-05   24.0   0.0    1.3  1  PELOTA_1        PELOTA RNA binding domain
     0.0011   19.0   0.0     0.0012   18.9   0.0    1.1  1  RNase_P_pop3    RNase P subunit Pop3


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.5   5.3e-33   3.2e-29       5      93 ..      18     106 ..      14     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 5.3e-33
                                       HHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECS CS
                    Ribosomal_L7Ae   5 evlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvs 81 
                                        +l+k +++g++++G++e+tk +erg+aklv +A dvep+e++++l+ lc+ek+vpy+++ksk  LG+++g+++ ++
  gi|488601731|ref|YP_007908202.1|  18 ALLEKFRETGRIKKGTNETTKVVERGQAKLVYIATDVEPPEIVAHLPLLCEEKNVPYIYIKSKSSLGQAAGLQVNCA 94 
                                       5789999********************************************************************** PP

                                       EEEEEESTTTHH CS
                    Ribosomal_L7Ae  82 alaikdegdskd 93 
                                       a+a++deg++k+
  gi|488601731|ref|YP_007908202.1|  95 AVAVVDEGEAKK 106
                                       ********9986 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   4.5e-09   2.7e-05      17      70 ..      24      79 ..      12      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.5e-09
                          PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpd 70
                                      +++ +iK g  E+T+v+ R + + v ++ + e  + +ahl lL++ek+vp+  +++
  gi|488601731|ref|YP_007908202.1| 24 RETGRIKKGTNETTKVVERGQAKLVYIATDVEppEIVAHLPLLCEEKNVPYIYIKS 79
                                      56789**********************9987765679*************987765 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     2e-07    0.0012      49     150 ..      22     117 ..       8     120 .] 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-07
                      RNase_P_pop3  49 keneeseltvglneivelLecsesddvvllvcnkDtPsvLlsqlpllvavanltvklvqlpksaqakldeklGlska 125
                                       k  e   +  g ne  ++ e  ++++ v ++ + + P  ++ +lpll++ +n  v+ + +  +    l ++ Gl+ +
  gi|488601731|ref|YP_007908202.1|  22 KFRETGRIKKGTNETTKVVE-RGQAKLVYIATDVE-PPEIVAHLPLLCEEKN--VPYIYIKSK--SSLGQAAGLQVN 92 
                                       45556678899999999999.66666666666555.9999************..888887655..557777777655 PP

                      RNase_P_pop3 126 .gmllvrkdasldkklaklvskkvee 150
                                         +++v ++ + +k+l +lv+k ++ 
  gi|488601731|ref|YP_007908202.1|  93 cAAVAVVDEGEAKKELRDLVTK-IDG 117
                                       48899999999999*****998.875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        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 0.50s 00:00:01.01 Elapsed: 00:00:00.67
# Mc/sec: 542.19
//
Query:       gi|488601732|ref|YP_007908203.1|  [L=71]
Description: SSU ribosomal protein S28E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  107.5   2.1    2.6e-31  107.4   2.1    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   2.1   1.5e-35   2.6e-31       1      64 []       5      68 ..       5      68 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 1.5e-35
                                      ---EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  1 eeaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                      e++++AeVi+++grtG++Ge+tqV+v++l+g++kgrii+RnV GPvr+GD+L+++Et+rEA++L
  gi|488601732|ref|YP_007908203.1|  5 EDIQPAEVIEIIGRTGMHGEATQVKVRVLGGENKGRIITRNVFGPVRVGDVLMIKETAREAKKL 68
                                      579***********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 410.95
//
Query:       gi|488601733|ref|YP_007908204.1|  [L=59]
Description: LSU ribosomal protein L24E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-25   89.1   4.2    1.7e-25   89.0   4.2    1.0  1  Ribosomal_L24e   Ribosomal protein L24e
    5.2e-05   23.3   0.8    7.1e-05   22.8   0.8    1.4  1  YHS              YHS domain
     0.0013   18.6   2.4     0.0023   17.8   2.4    1.4  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
     0.0048   17.2   3.1     0.0082   16.5   3.1    1.4  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
      0.014   15.7   0.5      0.015   15.7   0.5    1.1  1  DUF3268          zinc-finger-containing domain


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   4.2   4.6e-29   1.7e-25       1      57 [.       1      58 [.       1      59 [] 0.95

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 4.6e-29
                                      XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT-X CS
                    Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkayRr 57
                                      m+t+ CsF+gy+i+ G+Gk++vr+Dg+vf F+s Kc +++ k krnPrklkWTk+y +
  gi|488601733|ref|YP_007908204.1|  1 METHVCSFCGYEIEVGTGKMYVRRDGRVFYFCSGKCeKNMLKLKRNPRKLKWTKKYAK 58
                                      89**********************************778899************9965 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.8     2e-08   7.1e-05       6      35 ..       9      38 ..       4      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2e-08
                               YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkd 35
                                      cg  ++ ++ + +++++G+ +yFcS +C+ 
  gi|488601733|ref|YP_007908204.1|  9 CGYEIEVGTGKMYVRRDGRVFYFCSGKCEK 38
                                      9999999*********************85 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 !   17.8   2.4   6.4e-07    0.0023       6      37 ..       6      36 ..       3      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.4e-07
                            zf-FCS  6 CwfCkkyikgkpeftyvlendgvvgqFCStsC 37
                                      C+fC+ +i++++    ++ +dg v +FCS  C
  gi|488601733|ref|YP_007908204.1|  6 CSFCGYEIEVGT-GKMYVRRDGRVFYFCSGKC 36
                                      ********9999.689*************888 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.1   2.3e-06    0.0082       1      35 [.       6      42 ..       6      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-06
                   Arc_trans_TRASH  1 CDYCGkei.vgePivy.klknkvYyvCCktCkselkk 35
                                      C +CG ei vg+  +y +   +v+y+C   C++++ k
  gi|488601733|ref|YP_007908204.1|  6 CSFCGYEIeVGTGKMYvRRDGRVFYFCSGKCEKNMLK 42
                                      99******6677666525667***********99877 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.5   4.1e-06     0.015       2      38 ..       3      38 ..       2      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.1e-06
                           DUF3268  2 ttrCpyCGekvilvsaseiYkerskgkllylC.pkCda 38
                                      t++C++CG ++ + +  ++Y  r+ g+++y C  kC+ 
  gi|488601733|ref|YP_007908204.1|  3 THVCSFCGYEIEVGT-GKMY-VRRDGRVFYFCsGKCEK 38
                                      679******988665.6789.899999*****889985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.54
# Mc/sec: 328.03
//
Query:       gi|488601734|ref|YP_007908205.1|  [L=149]
Description: nucleoside diphosphate kinase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-63  210.5   0.1    8.7e-63  210.3   0.1    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 !  210.3   0.1   4.8e-67   8.7e-63       1     135 []       2     136 ..       2     136 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 4.8e-67
                                       EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEEST CS
                               NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlege 77 
                                       ert+v+iKPd+v+rg+ige+isr+e+kglkiva+km+r++ee+a++hYaehk+kpff +l++++ts+pvva+v+eg+
  gi|488601734|ref|YP_007908205.1|   2 ERTFVMIKPDGVERGVIGEVISRIERKGLKIVAMKMMRISEELAQKHYAEHKEKPFFGALISYITSSPVVAMVVEGK 78 
                                       89*************************************************************************** PP

                                       THHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGGS CS
                               NDK  78 daiekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeeei 135
                                       +ai++vr+++Gatnpaea+pgtiR+dfg+++g+N++H+Sds+esa+rei+lfF++eei
  gi|488601734|ref|YP_007908205.1|  79 NAIRVVRTIVGATNPAEANPGTIRGDFGMDVGRNIIHASDSPESAKREINLFFSPEEI 136
                                       *******************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 836.37
//
Query:       gi|488601735|ref|YP_007908206.1|  [L=597]
Description: translation initiation factor eaIF-5B [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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  116.5   0.0      8e-33  113.6   0.0    2.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.4e-26   92.2   4.6    1.7e-26   91.9   0.3    2.8  3  GTP_EFTU_D4  Elongation factor Tu domain 4
    8.4e-22   77.3   1.4    2.4e-21   75.8   1.4    1.8  1  IF-2         Translation-initiation factor 2
    1.1e-08   35.2   0.9    1.2e-07   31.8   0.0    2.8  2  MMR_HSR1     50S ribosome-binding GTPase
    2.3e-08   34.3   3.9    1.2e-05   25.5   0.2    2.9  2  GTP_EFTU_D2  Elongation factor Tu domain 2
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.032   14.4   0.0    1.5  1  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.18   11.8   0.6        4.7    7.2   0.0    3.0  3  Dynamin_N    Dynamin family
       0.74   10.2   4.0        2.5    8.5   1.0    3.2  3  DUF1947      Domain of unknown function (DUF1947)


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 !  113.6   0.0   3.6e-36     8e-33       4     191 ..      16     222 ..      13     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 3.6e-36
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                         ++++ghvDhGKtTL+d++ +   + +++g  ++ +      + E  + i  ++   ++e       + +iDtPGH
  gi|488601735|ref|YP_007908206.1|  16 PIVSVLGHVDHGKTTLLDKIRKGRVTAKEAGGITQ-HIGATEIPIEMIKNICKDIWRKEVE----LPGLLFIDTPGH 87 
                                       5689*****************77666666554443.4456666666666666666655555....9999******** PP

                                       GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHH CS
                          GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveev 146
                                       + F++   rg + +D+a+l+vd++eG +pqtee l ++++ ++p++v+ NK+D++            ++++++ + +
  gi|488601735|ref|YP_007908206.1|  88 KAFTNLRRRGGALADLAILIVDINEGFKPQTEEALSILRTFRTPFVVAANKIDKIpawqspgfvpfLKSYSMQEDIA 164
                                       *************************************************************9999878888888888 PP

                                       HHHHHHH....HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 147 kqklsrk....eeklekygekge.........kevpvvfgSalkgegvktllealvel 191
                                       k++l++k     +kl ++g++++         ++v ++++Sal+gegv +ll +lv l
  gi|488601735|ref|YP_007908206.1| 165 KNRLDNKiyelIGKLYEFGFSADrfdritdftRNVAIIPISALTGEGVPELLLVLVGL 222
                                       8888666777755666666665588888888899******************998865 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 ?    1.1   0.1      0.17   3.8e+02      60      75 ..     265     281 ..     231     287 .. 0.79
   2 ?   -3.8   0.0       5.8   1.3e+04      47      64 ..     376     393 ..     374     394 .. 0.76
   3 !   91.9   0.3   7.6e-30   1.7e-26       1      86 []     469     554 ..     469     554 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.17
                                       EETT-EEEEEEESS-.T CS
                       GTP_EFTU_D4  60 akaGqevaisiegki.v 75 
                                        k G+++ai++++ + v
  gi|488601735|ref|YP_007908206.1| 265 LKVGDRIAIAMRDGVkV 281
                                       57899999999998844 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.8
                                       EEEEEETTEEESEEETT- CS
                       GTP_EFTU_D4  47 ilqiqdkgkkleeakaGq 64 
                                       i +++d g k++ a+ G+
  gi|488601735|ref|YP_007908206.1| 376 INELKDAGIKIKNAEVGD 393
                                       667788888888888885 PP

  == domain 3  score: 91.9 bits;  conditional E-value: 7.6e-30
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr 77 
                                       +P kik+l++++frrs+pa+vG++vl+G +k + klik+dG+  G+++++q++g+++ +ak+G+e+aisi+g ++Gr
  gi|488601735|ref|YP_007908206.1| 469 KPCKIKLLKEYIFRRSKPAVVGIRVLAGELKRDAKLIKADGSPAGSVRSMQKEGENVPVAKEGEELAISIDGVTIGR 545
                                       79*************************************************************************** PP

                                       S--TT-EEE CS
                       GTP_EFTU_D4  78 qikegdily 86 
                                       q++ +++ly
  gi|488601735|ref|YP_007908206.1| 546 QLNGDEVLY 554
                                       ********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 !   75.8   1.4   1.1e-24   2.4e-21       2     104 ..     347     448 ..     346     449 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.1e-24
                                       CCHHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH....STEEEEEESS CS
                              IF-2   2 eelfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa....snaiiigFnv 74 
                                       e+++eei+ +++e +v++k+D+ GsleAl + L++       +k+ +++vG++ ++Dv  asa     n +ii+F v
  gi|488601735|ref|YP_007908206.1| 347 EKEYEEIEIRTDEEGVVLKTDTLGSLEALINELKDA-----GIKIKNAEVGDVDKRDVIEASAnrdeLNRVIIAFSV 418
                                       7889999*999************************8.....5*********************554335******** PP

                                       SCTHHHHHCCCCCTSEEEEESSHHHHHHHH CS
                              IF-2  75 kvskkakklaekegvkirlynvIYkliddv 104
                                       k+ + ++++aek gv+++  ++IY lid +
  gi|488601735|ref|YP_007908206.1| 419 KLLPGVEEEAEKYGVRVFRDEIIYSLIDSF 448
                                       ***************************975 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   5.3e-11   1.2e-07       2     114 .]      18     138 ..      17     138 .. 0.79
   2 ?    1.0   0.2      0.19   4.3e+02      63     103 ..     295     345 ..     246     475 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 5.3e-11
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE...............EEEEECGGCSSHHHHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke...............ielvDtpGliegasee 63 
                                       v ++G+   GK+tL+ ++ + ++ +++  g T++i   ++ ++  +               + ++DtpG  +     
  gi|488601735|ref|YP_007908206.1|  18 VSVLGHVDHGKTTLLDKIRKGRVTAKEAGGITQHIGATEIPIEMIKnickdiwrkevelpgLLFIDTPG-HK----- 88 
                                       7899*******************************888887443222444455555566669*******.33..... PP

                                       HHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  64 kglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                         +++  ++    adl++l+vd++ e++kp+ ee  ++l+  + p+++++nk
  gi|488601735|ref|YP_007908206.1|  89 -AFTNLRRRGGAlADLAILIVDIN-EGFKPQTEEALSILRTFRTPFVVAANK 138
                                       .3333333333348********99.88************9999999999998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHC..TSEEEEEEETT..........TTCSHHHHHHHHHHHHH CS
                          MMR_HSR1  63 ekglgkaflalee..adlillvvdas..........eeklkpldeeleellee 103
                                       e +l+ +f+++++  a + + ++ a           e    + ++++ee++++
  gi|488601735|ref|YP_007908206.1| 295 EMRLESKFRSVKSvvAAAGVKLIAADlegvlagsefE--AIESEKDIEEFRKR 345
                                       4455555555444332222222222222444432211..11222334433333 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 !   25.5   0.2   5.6e-09   1.2e-05       3      71 ..     255     328 ..     253     330 .. 0.84
   2 !    8.8   0.5   0.00094       2.1       3      70 ..     488     549 ..     487     553 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.6e-09
                                       EEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE..........ETTSEEEEEEEESSCCSGSS CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea..........vaganaGvivaikgledaii 68 
                                       ++++++y+Gtlk+Gd++ i   ++      vt +++++++  + +e+           + a+aGv++ + +le  ++
  gi|488601735|ref|YP_007908206.1| 255 TCDVILYDGTLKVGDRIAIAMrDG--V--KVTHVKGILKP-RPSQEMrleskfrsvkSVVAAAGVKLIAADLEG-VL 325
                                       789****************65444..4..48*********.558888899*****9988899999998889998.88 PP

                                       TTC CS
                       GTP_EFTU_D2  69 vGd 71 
                                       +G+
  gi|488601735|ref|YP_007908206.1| 326 AGS 328
                                       885 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00094
                                       EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTT CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivG 70 
                                       v+++rv  G+lk++ ++     d s     + ++s++++ e++  a +g+   + + ++ +    + G
  gi|488601735|ref|YP_007908206.1| 488 VVGIRVLAGELKRDAKLIK--ADGSPA---GSVRSMQKEGENVPVAKEGEELAISIDGVTIGRQ-LNG 549
                                       89***************99..664444...99**************999998888888777664.555 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 ?   14.4   0.0   1.4e-05     0.032       3     119 ..      19     140 ..      18     141 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                                       EEESSTTSSHHHHHHCHCT-CCC-EEE....TTTTEEEEEEECGGSGGCTTBTTTTCEEE...EEEEE-SGGCTTTT CS
                               Roc   3 vlvGdsgvGKtsllkrfvedkfsekek....stigvdfltkevtkikgvendkkvkkvkl...niWDtaGqerfrsl 72 
                                        ++G    GKt+ll+++ +++++ ke     + ig++ +  e   ik++ +d   k+v+l    + Dt G++ f +l
  gi|488601735|ref|YP_007908206.1|  19 SVLGHVDHGKTTLLDKIRKGRVTAKEAggitQHIGATEIPIE--MIKNICKDIWRKEVELpglLFIDTPGHKAFTNL 93 
                                       689*******************99986221144444444333..3555555544566665443899*********** PP

                                       -HHHHCTSCEEEEEEEGHH.HH.CHHHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  73 hplylreaalailvydsrs.se.nlkeWlkelkkvagkspvilvgnkiD 119
                                       ++     a+lail++d ++ ++ + +e l+ l++   ++p+++ +nkiD
  gi|488601735|ref|YP_007908206.1|  94 RRRGGALADLAILIVDINEgFKpQTEEALSILRTF--RTPFVVAANKID 140
                                       ***************96651332455566666554..578999999999 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0021       4.7       1      34 [.      18      51 ..      18      64 .. 0.91
   2 ?    0.3   0.0      0.28   6.3e+02      97     112 ..      73      88 ..      56      96 .. 0.81
   3 ?   -0.6   0.1      0.56   1.2e+03      59      81 ..     333     355 ..     322     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0021
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                      + v+G++ +GK+++l+++ + ++  ++++ +T+ 
  gi|488601735|ref|YP_007908206.1| 18 VSVLGHVDHGKTTLLDKIRKGRVTAKEAGGITQH 51
                                      689****************999999999998875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.28
                                       ETTS-SEEEEE---B- CS
                         Dynamin_N  97 sllvkgltlvDlPGld 112
                                       +   +gl ++D+PG +
  gi|488601735|ref|YP_007908206.1|  73 EVELPGLLFIDTPGHK 88 
                                       56778999******76 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.56
                                       T-EB--CHHHHHHHHHHHHHHHT CS
                         Dynamin_N  59 ekkledfsevreeieketekiag 81 
                                        + ++d++e+r+ +eke e+i+ 
  gi|488601735|ref|YP_007908206.1| 333 IESEKDIEEFRKRLEKEYEEIEI 355
                                       56788999999999999999883 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.0    0.0011       2.5       6      29 ..     335     358 ..     335     364 .. 0.93
   2 ?   -2.6   0.1       3.2   7.2e+03      13      27 ..     375     389 ..     373     399 .. 0.72
   3 ?   -0.4   0.0      0.64   1.4e+03      26      47 ..     520     541 ..     512     549 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                                       -HHHHHHHHHHHHTTT---TT--. CS
                           DUF1947   6 SkKeakeileklkekyisislesd 29 
                                       S+K+++e+ ++l+++y++i++ +d
  gi|488601735|ref|YP_007908206.1| 335 SEKDIEEFRKRLEKEYEEIEIRTD 358
                                       89******************9887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                                       HHHHHHTTT---TT- CS
                           DUF1947  13 ileklkekyisisle 27 
                                       ++++lk+ +i+i++ 
  gi|488601735|ref|YP_007908206.1| 375 LINELKDAGIKIKNA 389
                                       789999999777653 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.64
                                       T--..-EEEE-SS-EEEEETTE CS
                           DUF1947  26 lesdkiEieeekkeklYlingv 47 
                                        e++++ +++e +e ++ i+gv
  gi|488601735|ref|YP_007908206.1| 520 KEGENVPVAKEGEELAISIDGV 541
                                       5777899999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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):               8  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.52
# Mc/sec: 3433.98
//
Query:       gi|488601736|ref|YP_007908207.1|  [L=126]
Description: SSU ribosomal protein S6E [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-39  132.8   0.0    6.7e-39  132.7   0.0    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   0.0   3.8e-43   6.7e-39       1     122 [.       3     122 ..       3     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 3.8e-43
                                       -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEE CS
                     Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLls 77 
                                       +k++isdp+tg +++  v+++++++ligk+ig+ ++g+++    ++y lkitggsdk+Gfpm+++++++ r+rlLl+
  gi|488601736|ref|YP_007908207.1|   3 FKVVISDPSTGMAYQKVVSGANANRLIGKKIGDVINGTLVE-LPPDYELKITGGSDKDGFPMRKDLPGNVRRRLLLA 78 
                                       79*************************************99.558******************************** PP

                                       TTSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TT CS
                     Ribosomal_S6e  78 kggvgyrprrkGerkrksvrGcivsadisqlnlvivkkgekdieg 122
                                       + gvgy+p+++G r++k+vrG+++s+di+q+nl++ k+g+ ++++
  gi|488601736|ref|YP_007908207.1|  79 G-GVGYNPNERGLRRKKMVRGNVISRDIVQINLKVEKAGKIPLAE 122
                                       9.*************************************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 768.64
//
Query:       gi|488601737|ref|YP_007908208.1|  [L=206]
Description: Methylase involved in ubiquinone/menaquinone biosynthesis [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-20   74.1   0.0    1.5e-20   73.7   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.4e-20   73.7   0.0    2.3e-20   73.1   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    2.6e-17   63.0   0.0      6e-15   55.2   0.0    2.0  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      3e-15   56.3   0.0    3.9e-15   56.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.7e-12   46.8   0.0    5.5e-12   46.3   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    3.4e-10   40.0   0.0    4.7e-10   39.6   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.3e-07   31.6   0.0    2.3e-07   30.8   0.0    1.4  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0001   21.8   0.0    0.00089   18.8   0.0    2.1  2  Methyltransf_4   Putative methyltransferase
    0.00028   20.5   0.0    0.00035   20.2   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00072   18.6   0.0     0.0011   18.0   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0024   17.0   0.0     0.0033   16.5   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0056   16.0   0.0     0.0082   15.5   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.1   0.0       0.02   14.5   0.0    1.3  1  NodS             Nodulation protein S (NodS)
      0.015   14.8   0.0      0.027   14.0   0.0    1.4  1  MTS              Methyltransferase small domain
      0.021   15.1   0.0       0.24   11.7   0.0    2.3  2  TrkA_N           TrkA-N domain
      0.023   14.0   0.0      0.038   13.3   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
      0.035   13.8   0.0      0.056   13.2   0.0    1.3  1  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
      0.054   14.5   0.0       0.08   14.0   0.0    1.3  1  Methyltransf_24  Methyltransferase domain
      0.064   12.4   0.0      0.097   11.8   0.0    1.2  1  Methyltransf_3   O-methyltransferase
       0.07   12.1   0.0      0.089   11.8   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
       0.22   11.5   0.0       0.31   11.0   0.0    1.2  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 !   73.7   0.0   1.7e-23   1.5e-20       1      96 []      50     143 ..      50     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.7e-23
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       L+vGcGtG  ++ +a+++  + +v+vDl++e++   ++++++ +  v+++++dae+lpf+dn+fD  +s  ++++++
  gi|488601737|ref|YP_007908208.1|  50 LEVGCGTGFTTAGIASKVpqSGIVAVDLTPEQM---RKAIQKLPY-VNYIRGDAENLPFKDNTFDSAISAGSIEYWP 122
                                       89*************8888999***********...666666665.88***************************** PP

                                       CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                       +p+k ++e+aRv k gG++v+
  gi|488601737|ref|YP_007908208.1| 123 NPKKGIAEMARVTKEGGKVVV 143
                                       *****************9986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0   2.7e-23   2.3e-20       1      97 []      49     139 ..      49     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2.7e-23
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vL++GcGtG +t+ +a +++++ +++vD+++e++++a +++    + v++++gdae+lpf+d++fD  +s+g+++++
  gi|488601737|ref|YP_007908208.1|  49 VLEVGCGTGFTTAGIASKVPQSGIVAVDLTPEQMRKAIQKL----PYVNYIRGDAENLPFKDNTFDSAISAGSIEYW 121
                                       9******************99********************....9************************999***8 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +++  +k ++e+arv+k+gG
  gi|488601737|ref|YP_007908208.1| 122 PNP--KKGIAEMARVTKEGG 139
                                       855..599***********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 !   55.2   0.0   7.1e-18     6e-15       9     162 ..      10     154 ..       2     158 .. 0.85
   2 !    6.3   0.0    0.0063       5.4     191     221 ..     157     187 ..     153     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 7.1e-18
                                       XXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHH CS
                   Ubie_methyltran   9 vkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmL 85 
                                        ++ +   ++ yD +n ++ +  h l  ++v+++    +   vl+v +Gtg  ++ ++++v ++g +v +D+ ++ +
  gi|488601737|ref|YP_007908208.1|  10 ARNFYRHFSKIYDRINPIF-YADHML--EKVIEMAEIEERDLVLEVGCGTGFTTAGIASKVPQSG-IVAVDLTPEQM 82 
                                       456778889999***9986.566776..56778888888899*******************9998.66789999888 PP

                                       HHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHH CS
                   Ubie_methyltran  86 kvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpll 162
                                       + + +kl       ++++ ++ae+Lpf+d++fD+   +  +   ++ +k++ e+ rv k GG++vvl   k+ + l+
  gi|488601737|ref|YP_007908208.1|  83 RKAIQKLP-----YVNYIRGDAENLPFKDNTFDSAISAGSIEYWPNPKKGIAEMARVTKEGGKVVVLAPRKPDNLLV 154
                                       87777764.....699*****************9876677999************************9988887665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0063
                                       HHHHHHHS--HHHHHHHHHHTTEEEEEEEEE CS
                   Ubie_methyltran 191 LvesirafPdqetlkeliedaGfksveyesl 221
                                       ++esi  fP +++  + +e aG+k++++ + 
  gi|488601737|ref|YP_007908208.1| 157 FAESIMLFPSTQQCVAWFEAAGLKNIRFVET 187
                                       589***********************99765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   4.6e-18   3.9e-15       7     114 ..      49     148 ..      43     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 4.6e-18
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                       vl++GCGtG+ t  +a++  p++ +v +D ++e  ++A +   kl +  v+  +gd+e+l+  ++d++fD  +s + 
  gi|488601737|ref|YP_007908208.1|  49 VLEVGCGTGFTTAGIASK-VPQSGIVAVDLTPEQMRKAIQ---KLPY--VNYIRGDAENLP--FKDNTFDSAISAGS 117
                                       9***************65.689****************99...5666..8899********..************** PP

                   Methyltransf_31  84 lnaladpdkileeiervlkpggilliedprl 114
                                       + + ++p+k + e+ rv k+gg +++  pr 
  gi|488601737|ref|YP_007908208.1| 118 IEYWPNPKKGIAEMARVTKEGGKVVVLAPRK 148
                                       **************************99993 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   6.4e-15   5.5e-12       1      98 [.      50     140 ..      50     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.4e-15
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       Le+GcGtG +++ ++ k p++ +++vD+ p+++ +a +kl       +n ++ +a++l  +d   +fD  ++++ ++
  gi|488601737|ref|YP_007908208.1|  50 LEVGCGTGFTTAGIASKVPQSGIVAVDLTPEQMRKAIQKLPY-----VNYIRGDAENLPFKDN--TFDSAISAGSIE 119
                                       8********************************444444444.....4468888888776665..************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       +++++++ +++++++ k gG+
  gi|488601737|ref|YP_007908208.1| 120 YWPNPKKGIAEMARVTKEGGK 140
                                       ********************8 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   5.5e-13   4.7e-10      15     152 ..      39     180 ..      25     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 5.5e-13
                   Methyltransf_23  15 rllpklraggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiaekakkaqkdqf...deqeaaepqgkfdlI 86 
                                       ++++  +++  vL++GcGtG +++ ++++ +   +++vDl pe+  +a  ++k + +++   d+++ ++++++fd +
  gi|488601737|ref|YP_007908208.1|  39 EMAE-IEERDLVLEVGCGTGfTTAGIASKVPQsGIVAVDLTPEQMRKA--IQKLPYVNYirgDAENLPFKDNTFDSA 112
                                       4443.678888*********5555555665444799******998887..555555555111455666699****** PP

                   Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllseplaslk.edrllldwlylvpag.rhisffsarslk 152
                                       ++  ++e  p+p + ++ +a+ +k+gG ++++ p +++    r++ +  +l+p   + + +f a  lk
  gi|488601737|ref|YP_007908208.1| 113 ISAGSIEYWPNPKKGIAEMARVTKEGGKVVVLAPRKPDNlLVRKFAESIMLFPSTqQCVAWFEAAGLK 180
                                       *********************************99888535555666544444442444666665555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.7e-10   2.3e-07      58     118 ..      30      89 ..      16     105 .. 0.92
   2 ?   -3.5   0.0       8.5   7.2e+03     164     171 ..     136     143 ..     129     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.7e-10
                                       -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHH CS
                              PCMT  58 aphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnl 118
                                       a hm  +++e+ e+++ + vLevG+G+G+ ta +a  v ++g +v+++ ++e +++a ++l
  gi|488601737|ref|YP_007908208.1|  30 ADHMLEKVIEMAEIEERDLVLEVGCGTGFTTAGIASKVPQSG-IVAVDLTPEQMRKAIQKL 89 
                                       679***************************************.*********999998877 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.5
                                       EEEEEEEE CS
                              PCMT 164 keGGrlvv 171
                                       keGG++vv
  gi|488601737|ref|YP_007908208.1| 136 KEGGKVVV 143
                                       67887776 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     1e-06   0.00089       3      46 ..      47      90 ..      45     113 .. 0.86
   2 ?    0.4   0.0      0.46   3.9e+02      13      57 ..     138     186 ..     135     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                                      EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHH CS
                    Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkie 46
                                       +vle+GcG G  +  +A k P+  ++++++  + ++k+++k  
  gi|488601737|ref|YP_007908208.1| 47 DLVLEVGCGTGFTTAGIASKVPQSGIVAVDLTPEQMRKAIQKLP 90
                                      689***********************************999864 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.46
                                       SHHHHHHHHHSTTSEEE...EEE.S-HHHHHHHHHHHHHCTTSSEEEEE CS
                    Methyltransf_4  13 GeflvalAkknPdknfl...GiE.irvkvvakvlkkiealelkNlrilr 57 
                                       G+ +v lA+++Pd++++   +   + +++++++++  ea +lkN+r ++
  gi|488601737|ref|YP_007908208.1| 138 GGKVVVLAPRKPDNLLVrkfAESiMLFPSTQQCVAWFEAAGLKNIRFVE 186
                                       5566666777776655422121212357788888888999999998876 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.1e-07   0.00035      10     104 ..      42     137 ..      31     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.1e-07
                              MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGl...eldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsq 83 
                                        i+++  vl++GcG G     ++   +v   G+   +l  e + ++++k  +v     d +   f+d++fd ++ + 
  gi|488601737|ref|YP_007908208.1|  42 EIEERDLVLEVGCGTGFTTAGIAS--KVPQSGIvavDLTPEQMRKAIQKLPYVNYIRGDAENLPFKDNTFDSAISAG 116
                                       3788999*********99888866..4555554222788999*******866655444555568************* PP

                              MetW  84 tlqatrnpkevldellrigrr 104
                                       ++    npk+ + e+ r++++
  gi|488601737|ref|YP_007908208.1| 117 SIEYWPNPKKGIAEMARVTKE 137
                                       ******************875 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 !   18.0   0.0   1.3e-06    0.0011     112     268 ..      41     187 ..      23     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-06
                                       .--TT-.EEEEET-TTSHHHHHHHHCT-SE.EEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEE CS
                    Methyltransf_9 112 sdlkgr.tildvGcgnGyhlwrmvgegakl.vvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdt 185
                                       +++++r  +l+vGcg+G+    ++++ +++ +v +d +   +   +a++kl      ++ +    e+lp   ++fd 
  gi|488601737|ref|YP_007908208.1|  41 AEIEERdLVLEVGCGTGFTTAGIASKVPQSgIVAVDLTPEQM--RKAIQKLP----YVNYIRGDAENLPFkDNTFDS 111
                                       556665369***********9999998876355666554433..36777776....677777788****86899*** PP

                                       EEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS-TT-EE--SS-BTTBSS---EEBHHHHHHHHHHTT-EE CS
                    Methyltransf_9 186 vfsmGvlyhrrsPldhllqlkdqlvkgGelvletlvieGdenavlvPedryakmrnvyfiPsaaalkvWlekvgfvd 262
                                         s G + +   P   + ++    ++gG++v+     +   +++lv   ++a  +++ ++Ps++    W+e +g+++
  gi|488601737|ref|YP_007908208.1| 112 AISAGSIEYWPNPKKGIAEMARVTKEGGKVVVL---APRKPDNLLVR--KFA--ESIMLFPSTQQCVAWFEAAGLKN 181
                                       *****************************9964...34555566664..566..57899****************** PP

                                       EEEEEE CS
                    Methyltransf_9 263 vrivde 268
                                       +r v++
  gi|488601737|ref|YP_007908208.1| 182 IRFVET 187
                                       **9975 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.9e-06    0.0033      18      52 ..      33      67 ..      28     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-06
                                      HHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC- CS
                            RrnaAD 18 vineIldklnleekltvleigpGkGilTeeLakra 52
                                      +++++++ +++ee + vle+g G+G++T+ +a  +
  gi|488601737|ref|YP_007908208.1| 33 MLEKVIEMAEIEERDLVLEVGCGTGFTTAGIASKV 67
                                      67899***********************9997766 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.6e-06    0.0082      51     131 ..      34     108 ..       5     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.6e-06
                                       HHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTTS--- CS
                    Methyltransf_2  51 akkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehlsageeervefvgGdffkdslP 126
                                        +kv+e  ++e+   +++vG GtG + + i+s+ P+  ++  Dl pe +++A ++      + v+++ Gd    +lP
  gi|488601737|ref|YP_007908208.1|  34 LEKVIEMAEIEERDLVLEVGCGTGFTTAGIASKVPQSGIVAVDLtPEQMRKAIQK-----LPYVNYIRGDAE--NLP 103
                                       5789999999**9******************************967888888887.....688888888865..777 PP

                                       --SEE CS
                    Methyltransf_2 127 eaDai 131
                                         D  
  gi|488601737|ref|YP_007908208.1| 104 FKDNT 108
                                       66554 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.3e-05      0.02      32     118 ..      35     120 ..      21     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                              NodS  32 aqilrlslaqgsiadalevGcaaGalterlapyckrltv..vdvveeaiararervkesshiswivsdvqqfs.tde 105
                                       +++++++  + +   +levGc +G  t  +a    +  +  vd+ +   ++ r+ +++ + +++i  d +++  +d+
  gi|488601737|ref|YP_007908208.1|  35 EKVIEMAEIEER-DLVLEVGCGTGFTTAGIASKVPQSGIvaVDLTP---EQMRKAIQKLPYVNYIRGDAENLPfKDN 107
                                       555555544332.349*************99887665550155555...566777888999********99973577 PP

                              NodS 106 kfdlivvaevlyy 118
                                        fd  + a  + y
  gi|488601737|ref|YP_007908208.1| 108 TFDSAISAGSIEY 120
                                       8999998876655 PP

>> 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-05     0.027      31      65 ..      45      79 ..      27      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                                      TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBH CS
                               MTS 31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvda 65
                                      +++ vl +GcG+G+ +a +a++ p+  +++vd   
  gi|488601737|ref|YP_007908208.1| 45 ERDLVLEVGCGTGFTTAGIASKVPQSGIVAVDLTP 79
                                      45569*********************9***99765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.74   6.3e+02      42      67 ..      25      50 ..      11      53 .. 0.84
   2 ?   11.7   0.0   0.00028      0.24       4      51 ..      54     101 ..      52     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.74
                                      SEEEES-TTSHHHHHHTTGGGESEEE CS
                            TrkA_N 42 levvvgdatdeevLeeagiekadavi 67
                                       +++++d   e+v+e a+ie+ d+v+
  gi|488601737|ref|YP_007908208.1| 25 NPIFYADHMLEKVIEMAEIEERDLVL 50
                                      4689999999***********99986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00028
                                       ES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT..SEEEES-TTS CS
                            TrkA_N   4 iGlGrvGrslaeeLseggkdvvvidkdeerveelreeg..levvvgdatd 51 
                                       +G G ++  +a ++ ++g  +v++d  +e+++++ ++   ++++ gda +
  gi|488601737|ref|YP_007908208.1|  54 CGTGFTTAGIASKVPQSG--IVAVDLTPEQMRKAIQKLpyVNYIRGDAEN 101
                                       899999**********99..9****************98888*****975 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.038      52     139 ..      35     120 ..      29     155 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---- CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldek 127
                                       + ++e +e+++ + +L++GcG G ++   +++  +  +v++ l  eq+++a +++  ++  r  + + l ++d  + 
  gi|488601737|ref|YP_007908208.1|  35 EKVIEMAEIEERDLVLEVGCGTGFTTAGIASKVpQSGIVAVDLTPEQMRKAIQKLPYVNYIR-GDAENLPFKD--NT 108
                                       5667888999*************999988887525678999999999988888777666443.3334444443..56 PP

                                       -SEEEEES-GGG CS
                              CMAS 128 vdrvvsvgafeh 139
                                       +d+ +s g +e 
  gi|488601737|ref|YP_007908208.1| 109 FDSAISAGSIEY 120
                                       777777777765 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 ?   13.2   0.0   6.5e-05     0.056      74     121 ..      42      87 ..      27     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                                       HHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC- CS
                      TPP_enzyme_M  74 aleeaDlvlalGarfddirttgsepefapeakiihididpaeigknyq 121
                                        +ee Dlvl +G+   + +t+g  ++  p++ i+ +d  p+++ k+ q
  gi|488601737|ref|YP_007908208.1|  42 EIEERDLVLEVGCGTGF-TTAGIASK-VPQSGIVAVDLTPEQMRKAIQ 87 
                                       5799********99888.55664445.56779*************985 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.4e-05      0.08       1     101 [.      50     141 ..      50     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.4e-05
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddrvrlikadseealaslaagsiDllfiDg 77 
                                       +E+G+  G++t+ +++ + + g   +vavd  p  e+ ++ +++     +v+ i++d+e++   +++ ++D ++  g
  gi|488601737|ref|YP_007908208.1|  50 LEVGCGTGFTTAGIASKVPQSG---IVAVDLTP--EQMRKAIQK---LPYVNYIRGDAENL--PFKDNTFDSAISAG 116
                                       79******************99...7*******..677888887...67888888998888..44445788877777 PP

                   Methyltransf_24  78 ghaa.eavledleallprlapggvv 101
                                       + ++    ++ +  + ++ ++gg v
  gi|488601737|ref|YP_007908208.1| 117 SIEYwPNPKKGIAEMARVTKEGGKV 141
                                       7777545566666666666666655 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011     0.097      45      93 ..      43      87 ..      29     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                      HHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHH CS
                    Methyltransf_3 45 lvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiq 93
                                      + +   vle+G  tG++   +a ++P+ G i+a+d  +e++  a   iq
  gi|488601737|ref|YP_007908208.1| 43 IEERDLVLEVGCGTGFTTAGIASKVPQSG-IVAVDLTPEQMRKA---IQ 87
                                      4455669********************99.89****99987533...44 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001     0.089     172     236 ..      14      82 ..       5     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                   tRNA_U5-meth_tr 172 yrqvensftqPnaa.vnekmleWalevtqeskgdl.lelycGnGnfslalarnfek..vlateiakssv 236
                                       yr+  + + + n    + +mle ++e+++ +++dl le+ cG G  +  +a ++ +  ++a +++  ++
  gi|488601737|ref|YP_007908208.1|  14 YRHFSKIYDRINPIfYADHMLEKVIEMAEIEERDLvLEVGCGTGFTTAGIASKVPQsgIVAVDLTPEQM 82 
                                       6666666666665414789**************9868*******9998898877543355555554444 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00036      0.31      14      69 ..      35      87 ..      28     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                   Methyltransf_32 14 akllkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaek 69
                                      +k+++  a+ +++  v++vG+G g+ +  +a+   +  +  +v++d+  e ++ka +
  gi|488601737|ref|YP_007908208.1| 35 EKVIEM-AEIEERDLVLEVGCGTGFTTAGIAS---KvPQSGIVAVDLTPEQMRKAIQ 87
                                      444444.445778899****************...436899******9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1165.06
//
Query:       gi|488601738|ref|YP_007908209.1|  [L=214]
Description: putative RNA-binding protein containing a C-terminal EMAP domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-10   39.5   1.3    1.4e-09   38.2   1.3    1.7  1  Alpha_Helical  Alpha helical domain
     0.0015   18.6   0.0     0.0047   17.0   0.0    1.8  2  tRNA_bind      Putative tRNA binding domain
  ------ inclusion threshold ------
       0.15   12.3   1.5        1.2    9.5   0.1    2.6  3  DUF4709        Domain of unknown function (DUF4709)


Domain annotation for each model (and alignments):
>> Alpha_Helical  Alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   1.3   2.3e-13   1.4e-09       2      78 ..       4      77 ..       3     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.3e-13
                     Alpha_Helical  2 wDtskDYRllvaekavelferivegaklrgkwnkkkalelakemeselqslkysylepedLakseevkklkekaeei 78
                                      +DtskD+R+l+aeka+  +e++ +  kl+   ++k+ ++ +k++ s++q+lkysy+ p+ +   ++ k++  ++++ 
  gi|488601738|ref|YP_007908209.1|  4 FDTSKDFRILMAEKAIVELEKLFNVLKLQ---KRKEYVRKMKDLYSKVQNLKYSYVAPDGIKALDDFKEIVTSTKKF 77
                                      6**********************998887...468899999********************9999999998877765 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.83   4.9e+03      31      51 ..      68      88 ..      64      95 .. 0.68
   2 !   17.0   0.0   7.9e-07    0.0047      11      79 ..     128     188 ..     124     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.83
                                      EEEEESCTTTSTHHHHTTEEE CS
                         tRNA_bind 31 rqivsgaknvyepeelvakkv 51
                                      ++iv+  k++ e+   ++++ 
  gi|488601738|ref|YP_007908209.1| 68 KEIVTSTKKFKEDVRKLDRDA 88
                                      678888888888555555555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.9e-07
                                       EETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCES CS
                         tRNA_bind  11 ehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeelde 79 
                                        +++ d+L  + vd G +   +i+++ +++ +      +  +vva l p+++   +SeGM++ + ++++
  gi|488601738|ref|YP_007908209.1| 128 SIKELDRLWLCGVDCGFKL--NIITNSEKFKQ------GSYAVVAYLPPREFGKYTSEGMFVDLLDGEK 188
                                       567889**********988..***********......**********************976665444 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.086   5.1e+02      23      39 ..      35      51 ..      13      57 .. 0.60
   2 ?    9.5   0.1    0.0002       1.2      27      65 ..      65     103 ..      60     108 .. 0.89
   3 ?   -2.7   0.0       1.2     7e+03      23      32 ..     123     132 ..     117     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.086
                           DUF4709 23 vsEilelkeltevtqkL 39
                                      ++ + ++k+l +++q+L
  gi|488601738|ref|YP_007908209.1| 35 KEYVRKMKDLYSKVQNL 51
                                      33344555555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0002
                           DUF4709  27 lelkeltevtqkLvkevkslkrdfeflkqllqakyeekl 65 
                                        + ke++++t+k++++v++l rd+++ k l  ++y e l
  gi|488601738|ref|YP_007908209.1|  65 DDFKEIVTSTKKFKEDVRKLDRDAQVIKALYWLEYLESL 103
                                       578**************************9999997776 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.2
                           DUF4709  23 vsEilelkel 32 
                                         Ei+++kel
  gi|488601738|ref|YP_007908209.1| 123 RGEIVSIKEL 132
                                       5799999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1186.59
//
Query:       gi|488601739|ref|YP_007908210.1|  [L=353]
Description: BioD-like N-terminal domain of phosphotransacetylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-28   98.9   0.0    1.3e-27   96.9   0.0    1.8  2  AAA_26        AAA domain
      2e-26   91.8   0.0    4.3e-26   90.8   0.0    1.6  1  DRTGG         DRTGG domain
    5.8e-06   26.4   0.0    2.3e-05   24.4   0.0    1.9  2  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      0.003   17.6   0.0     0.0076   16.3   0.0    1.7  1  Hpr_kinase_N  HPr Serine kinase N terminus


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   2.9e-31   1.3e-27       1     191 [.       2     203 ..       2     208 .. 0.90
   2 ?   -0.9   0.0      0.28   1.3e+03     120     142 ..     291     313 ..     283     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 2.9e-31
                            AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie......ededselikellgldqtyelpeplalsa 71 
                                       ++i+v++++ ++GK++ + + +++l +kg++vgyfKP++t  e       d+d+  +++++g+++++++++p++l+a
  gi|488601739|ref|YP_007908210.1|   2 QGIMVSSVEGDAGKSSMIIAMASYLLDKGYSVGYFKPLGTSPEyhdgklVDGDALNTSKMIGVEDEIDDICPIVLNA 78 
                                       68***************************************996666666669999999****************** PP

                            AAA_26  72 plspelaarqegedidlekiv....kelekdadivvVEGagglgvpiteellnadiaknlgapvilVargglg.tin 143
                                       p+++++  ++ +   +l+k+v    +++++++d+v+VEG+  +  +++ el ++ + k l+++ +l+a + ++  ++
  gi|488601739|ref|YP_007908210.1|  79 PYAEFINIADPN---ELKKVVsasfDRIKEEKDFVFVEGSIDYKIGSAVELGDISVSKLLDLKALLIAGYSEDfVLD 152
                                       ******988766...4555555557*********************************************9974789 PP

                            AAA_26 144 qllltiealrqknvrvlGvilNkvrnpe......nvetlekksgipvlGvvPyl 191
                                       ++l++ +++ +   r+++vi+Nk++  +         +l + + +++lG++P +
  gi|488601739|ref|YP_007908210.1| 153 RILTAKSVFGE---RLKAVIFNKLTGYKrsyiegVAGSLLQRNDLEILGIIPRD 203
                                       99999999999...8*********9995566667999***************86 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.28
                            AAA_26 120 nadiaknlgapvilVargglgti 142
                                       + d a++ g+pv+lV   +l t 
  gi|488601739|ref|YP_007908210.1| 291 ILDRAESKGVPVLLVSEDTLTTT 313
                                       667789999******98877765 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   9.5e-30   4.3e-26       1     105 []     213     319 ..     213     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 9.5e-30
                                       HHHHHTT-EEEE--..SS--E-EEEE-SS-HHHHHHHHHT..SEEEEEETT-HHHHHHHTT-T.EEEEEEETT---- CS
                             DRTGG   1 eiaealgaevlnggeeelrrvekvvvgamsvenmlerlke..gdlvivpGDRediqlaaleag.iaalilTggleps 74 
                                       ei + l+ae+l++ + e   ve+++vgams+++++e++++  +++++++GDR+d+q+ ale   i+++ilTg+l+ps
  gi|488601739|ref|YP_007908210.1| 213 EIKDYLKAEYLVEPR-EDMIVENIIVGAMSPNSAIEYFRRakNAALVTGGDRADLQVVALEIPnIKLIILTGNLRPS 288
                                       68899*********6.4446********************99********************99************* PP

                                       HHHHHHHHHHT--EEE-SS-HHHHHHHHHTT CS
                             DRTGG  75 eevlklaeeaglpvlsveldtfttakrinql 105
                                       + +l++ae +g+pvl v++dt+tt++r++++
  gi|488601739|ref|YP_007908210.1| 289 KFILDRAESKGVPVLLVSEDTLTTTERLEKM 319
                                       ***************************9975 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   5.1e-09   2.3e-05       1     118 [.       4     206 ..       4     208 .. 0.86
   2 ?   -1.7   0.0      0.64   2.9e+03      54      65 ..     306     340 ..     238     348 .. 0.55

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.1e-09
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i++ s  G++GK+++ +++a +l ++g+ V  ++  p +++ ++ +g+  d +                        
  gi|488601739|ref|YP_007908210.1|   4 IMVSSVEGDAGKSSMIIAMASYLLDKGYSVGYFK--PLGTSPEYHDGKLVDGDAlntskmigvedeiddicpivlna 78 
                                       789999****************************..44444555588888888789999****************** PP

                                       .......................................................................CCHCCC CS
                                       .......................................................................xxxxxx RF
                              CbiA  55 .......................................................................dlkrll 60 
                                                                                                                    
  gi|488601739|ref|YP_007908210.1|  79 pyaefiniadpnelkkvvsasfdrikeekdfvfvegsidykigsavelgdisvsklldlkalliagysedfV----- 150
                                       *********************************************************998888874444443..... PP

                                       HHHHHHCHCHHHH...EEEEEEEEESS...-TTCHHHHH.HHHHHCTS-EEEEEE--CCH CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                              CbiA  61 ellealgkkkall.lkiagvvlnrvdgeneetllkeale.elkqrygvpvlgviprdeav 118
                                         l ++ + k+++  +++ v++n+  g   +++ +e+++  l+qr  +++lg+iprd+ v
  gi|488601739|ref|YP_007908210.1| 151 --LDRILTAKSVFgERLKAVIFNKLTGY--KRSYIEGVAgSLLQRNDLEILGIIPRDVIV 206
                                       ..4444444444467799*******998..9999999882455555**********9865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.64
                                       H.......................CCHCCCHHHHH CS
                                       x.......................xxxxxxxxxxx RF
                              CbiA  54 p.......................dlkrllellea 65 
                                                                lkr+ el+e+
  gi|488601739|ref|YP_007908210.1| 306 SedtlttterlekmfgksrikseiKLKRMRELFES 340
                                       03333322222222222233333355666666655 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.7e-06    0.0076      80     123 ..     275     318 ..     267     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-06
                                       --S-EEEETTT---HHHHHHHHHH---EEEESS-HHHHHTTHHH CS
                      Hpr_kinase_N  80 kipciiltrgleppeellelaeeygvpllrtklstsefiaelir 123
                                       +i +iilt +l+p + +l+ ae +gvp+l  ++ t +++++l +
  gi|488601739|ref|YP_007908210.1| 275 NIKLIILTGNLRPSKFILDRAESKGVPVLLVSEDTLTTTERLEK 318
                                       6789*****************************99999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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 0.35s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1945.54
//
Query:       gi|488601740|ref|YP_007908211.1|  [L=170]
Description: hypothetical protein Asulf_02265 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   8.4      0.035   13.8   8.4    1.1  1  Yip1             Yip1 domain
       0.22   10.2   3.1       0.25   10.1   3.1    1.2  1  DUF2207          Predicted membrane protein (DUF2207)
        1.5    9.2   6.7          4    7.8   4.3    2.1  2  DUF3040          Protein of unknown function (DUF3040)
        2.1    7.7   8.0       0.85    9.0   1.1    2.1  2  DUF5305          Family of unknown function (DUF5305)
        4.3    7.4  12.1      0.092   12.7   1.4    2.6  2  DUF4083          Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   8.4   9.8e-06     0.035      13      82 ..      51     118 ..      39     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.8e-06
                              Yip1  13 kkeppilrapdlallllalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylglllgllllal 82 
                                       kk+  + r++++a++ll+l++ll +++a ++++    +++ + ++  +   + +i+g+++l+l++l+ ++
  gi|488601740|ref|YP_007908211.1|  51 KKN--PKRNYLVAGILLILIGLLIVVFAKQIISALKINDGLITSFVIFNGGALVIVGIILLILWWLVRSF 118
                                       344..459*********************88888888884444444444444455555555555555444 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.1     7e-05      0.25     367     431 ..      45     116 ..       5     144 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7e-05
                           DUF2207 367 kergyfdkkgkkklkklsalglgliilglilillallllvll..........lvfllilllillliaiivlllfs 431
                                        ++  ++k++k+++   ++l++++++l+++++  ++ +   l          ++f +  l+i+++i++i+++l +
  gi|488601740|ref|YP_007908211.1|  45 ISSMTLKKNPKRNYLVAGILLILIGLLIVVFAKQIISA---LkindglitsfVIFNGGALVIVGIILLILWWLVR 116
                                       55556677777777555555555555555554444443...156699*766533333333334444333333333 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.3    0.0011         4      27      70 ..      46      95 ..      42     109 .. 0.65
   2 ?    1.3   2.5      0.12   4.2e+02      46      72 ..      96     115 ..      84     126 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                           DUF3040 27 aalrggaararrrslrrlavlavllfvaGllllvlG.vaaaa..........vvl 70
                                      +++     + ++   r+++v+++ll+++Gll++v+   + +a           v+
  gi|488601740|ref|YP_007908211.1| 46 SSM-----TLKKNPKRNYLVAGILLILIGLLIVVFAkQIISAlkindglitsFVI 95
                                      555.....3344456899****************998666655777776664333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                           DUF3040  46 vlavllfvaGllllvlGvaaaavvlgv 72 
                                       + + +l+++G++ll+l          v
  gi|488601740|ref|YP_007908211.1|  96 FNGGALVIVGIILLILW-------WLV 115
                                       33445555555555554.......333 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.1   0.00024      0.85      76     135 ..      18      77 ..       8      92 .. 0.69
   2 ?    2.8   1.0     0.019        68     116     163 ..      98     147 ..      89     159 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00024
                           DUF5305  76 srlpiplteqtyeikkdetd.eengeitetvtvkespslaegilliilgllaliglvvlir 135
                                        + ++++t++  +ik+++++     +   + t k++p+  +++++i+l+l++l+++v++ +
  gi|488601740|ref|YP_007908211.1|  18 ASSTVEITQNQLRIKSKNSEeIIFIDFISSMTLKKNPKRNYLVAGILLILIGLLIVVFA-K 77 
                                       56678888888899887776555666667777777777777777777777777776665.3 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.019
                           DUF5305 116 gilliilgllaliglvvlirriiftssk...aekyelelekilkeYdewIv 163
                                       g++l+i+g++ li  ++++ + i ++++   +    +++ek l+   e I+
  gi|488601740|ref|YP_007908211.1|  98 GGALVIVGIILLILWWLVRSF-ILIINQlsnTVLLSNRTEKPLRTIYEKII 147
                                       778899998887776666555.43333312255555666666665555555 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   3.5      0.58   2.1e+03      10      22 ..      63      75 ..      58      83 .. 0.56
   2 ?   12.7   1.4   2.6e-05     0.092       3      52 ..      99     148 ..      97     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.58
                           DUF4083 10 ivivLilllvfsf 22
                                      i+++Li+ll++ f
  gi|488601740|ref|YP_007908211.1| 63 ILLILIGLLIVVF 75
                                      3444444444433 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.6e-05
                           DUF4083   3 gdliyliivivLilllvfsftlfiRrvvsrsaakkkkskeleqKLDkiIe 52 
                                       g+l++  i+++++  lv sf+l+i +++     ++  +k+l     kiIe
  gi|488601740|ref|YP_007908211.1|  99 GALVIVGIILLILWWLVRSFILIINQLSNTVLLSNRTEKPLRTIYEKIIE 148
                                       7788888999999999************9999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 927.14
//
Query:       gi|488601741|ref|YP_007908212.1|  [L=83]
Description: hypothetical protein Asulf_02266 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   18.8   0.0     0.0016   18.4   0.0    1.2  1  HTH_36    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.8e-08    0.0016       2      55 .]       2      56 ..       1      56 [. 0.96

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.8e-08
                            HTH_36  2 rLspsaklllgslasfanknggcfpsqetlakrlgls.knTvsraikeLeqlGyi 55
                                      +L+  +k++++++ + ++k   + +  e ++k + ++    + + +k+L++lGy+
  gi|488601741|ref|YP_007908212.1|  2 ELTELDKAIIVTIYKRSGKSKKAHFPIEFICKGYPKHlHGMIKSRVKKLVKLGYL 56
                                      69999************99999***************8889*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 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:                        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 0.34s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 470.77
//
Query:       gi|488601742|ref|YP_007908213.1|  [L=82]
Description: hypothetical protein Asulf_02267 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   35.5   0.1    8.9e-09   35.1   0.1    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    4.1e-07   29.5   0.0    5.4e-07   29.1   0.0    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
      3e-06   27.1   0.1    4.7e-06   26.5   0.1    1.5  1  PadR            Transcriptional regulator PadR-like family
    8.2e-06   25.5   0.0    1.1e-05   25.2   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
    9.4e-06   25.5   0.0    1.1e-05   25.2   0.0    1.1  1  HTH_11          HTH domain
    1.7e-05   24.6   0.0      2e-05   24.4   0.0    1.1  1  MarR_2          MarR family
    4.7e-05   23.1   0.0    6.8e-05   22.5   0.0    1.4  1  HTH_23          Homeodomain-like domain
      9e-05   22.3   0.0    0.00012   21.9   0.0    1.2  1  MarR            MarR family
    0.00026   20.6   0.0    0.00028   20.5   0.0    1.1  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
    0.00072   19.4   0.0    0.00096   19.0   0.0    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0011   18.6   0.0     0.0014   18.3   0.0    1.1  1  PheRS_DBD1      PheRS DNA binding domain 1
     0.0015   18.6   0.0     0.0019   18.2   0.0    1.1  1  HTH_20          Helix-turn-helix domain
     0.0026   17.6   0.1     0.0052   16.6   0.1    1.5  1  IF2_N           Translation initiation factor IF-2, N-termina
     0.0032   18.1   0.0      0.004   17.8   0.0    1.1  1  RPA_C           Replication protein A C terminal
     0.0038   17.7   0.0     0.0048   17.4   0.0    1.1  1  HTH_27          Winged helix DNA-binding domain
     0.0045   17.0   0.0     0.0068   16.4   0.0    1.3  1  HTH_29          Winged helix-turn helix
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.021   14.5   0.0    1.7  1  Sigma70_r4_2    Sigma-70, region 4
      0.016   15.4   0.0      0.019   15.1   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.017   15.1   0.0      0.022   14.7   0.0    1.3  1  HTH_36          Helix-turn-helix domain
      0.022   15.0   0.1       0.03   14.5   0.1    1.2  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.025   14.6   0.0      0.031   14.3   0.0    1.2  1  FeoC            FeoC like transcriptional regulator
      0.031   14.6   0.0      0.035   14.4   0.0    1.1  1  Rrf2            Transcriptional regulator
       0.05   13.3   0.0      0.056   13.1   0.0    1.1  1  DUF4423         Domain of unknown function (DUF4423)
       0.05   13.0   0.1      0.055   12.8   0.1    1.0  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
      0.051   13.3   0.1      0.084   12.6   0.1    1.3  1  HTH_41          Helix-turn-helix domain
      0.059   13.5   0.0      0.063   13.4   0.0    1.2  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.078   13.3   0.1       0.09   13.1   0.1    1.2  1  HTH_Tnp_1       Transposase
      0.087   12.9   0.0       0.12   12.4   0.0    1.4  1  DUF3489         Protein of unknown function (DUF3489)
      0.098   12.6   0.0       0.11   12.5   0.0    1.3  1  Cdc6_C          CDC6, C terminal winged helix domain
      0.099   11.6   0.0      0.099   11.6   0.0    1.0  1  TnsD            Tn7-like transposition protein D
       0.12   12.2   0.0       0.19   11.5   0.0    1.4  1  HTH_38          Helix-turn-helix domain
       0.16   11.6   0.0       0.22   11.1   0.0    1.2  1  HTH_47          winged helix-turn-helix
       0.18   11.8   0.0        0.2   11.7   0.0    1.1  1  HTH_Crp_2       Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   1.6e-11   8.9e-09      13      59 ..      13      64 ..       4      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.6e-11
                                      HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....T CS
                              TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....p 59
                                      vY  + k+  ++++eia++lg +  kvY++++sLe++GlV+++ +      +
  gi|488601742|ref|YP_007908213.1| 13 VYEFVNKHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKTSLEVeggraK 64
                                      77777899********************************987654455553 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   9.9e-10   5.4e-07      10      48 .]      15      53 ..      13      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.9e-10
                            HTH_24 10 elLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      e + k++++s  e+A++lg S++ v   +k Lee+Gl+k
  gi|488601742|ref|YP_007908213.1| 15 EFVNKHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVK 53
                                      5677999******************************97 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   8.7e-09   4.7e-06      29      64 ..      34      69 ..       2      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.7e-09
                                      TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEE CS
                              PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyYr 64
                                       s G++Y + k+Le+ glv+++ e +g + +rk+Y 
  gi|488601742|ref|YP_007908213.1| 34 WSSGKVYNIIKSLEEMGLVKTSLEVEGGRAKRKVYP 69
                                      579********************************6 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0     2e-08   1.1e-05      17      50 ..      21      54 ..      15      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2e-08
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       +l++ e+A+++g++  +v++++++L+e+G+v++
  gi|488601742|ref|YP_007908213.1| 21 SGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKT 54
                                      5699****************************96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.1e-08   1.1e-05       5      44 ..      13      56 ..       9      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.1e-08
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.....v 44
                                      ++e++ ++++ +s  e+A++L+ S   v++ Ik+Lee+g     +
  gi|488601742|ref|YP_007908213.1| 13 VYEFV-NKHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGlvktsL 56
                                      55666.67777****************************766444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.8e-08     2e-05      14      61 ..      17      62 ..      13      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.8e-08
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      +  + g  l+v e+a++lg s + v +i+k L++ GLv ++   e +R
  gi|488601742|ref|YP_007908213.1| 17 VNKHSG--LSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKTSLEVEGGR 62
                                      556777..9*****************************9994444444 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.2e-07   6.8e-05      15      46 ..      17      51 ..       1      54 [. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-07
                            HTH_23 15 ae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                       +   Glsv eIA++Lg+s   vy+++k  +e Gl
  gi|488601742|ref|YP_007908213.1| 17 VNkhsGLSVYEIAKKLGWSSGKVYNIIKSLEEMGL 51
                                      43456***********************9988886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.2e-07   0.00012      14      48 ..      19      53 ..      16      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.2e-07
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                       + +lsv e+akklg s++ v ++++ Le+ Gl++
  gi|488601742|ref|YP_007908213.1| 19 KHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVK 53
                                      57899****************************96 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   5.1e-07   0.00028      10      62 ..       9      61 ..       1      66 [. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.1e-07
                      HrcA_DNA-bdg 10 lqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGG 62
                                       ++ +  + +k++ +   eiA++l+  +G v N+++sL  +gLv++    +GG
  gi|488601742|ref|YP_007908213.1|  9 AEEFVYEFVNKHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKTSLEVEGG 61
                                      556666666777788889**************************987666666 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 !   19.0   0.0   1.8e-06   0.00096      16      46 ..      23      53 ..      15      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      l+v e+a++lg s ++v    k L+e+GLV+
  gi|488601742|ref|YP_007908213.1| 23 LSVYEIAKKLGWSSGKVYNIIKSLEEMGLVK 53
                                      89****************************8 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 !   18.3   0.0   2.7e-06    0.0014       5      53 ..       9      56 ..       5      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                        PheRS_DBD1  5 laeqlLqrLekkgevdslelAaelgvdHqkvVGavKSLqalgelIkaeq 53
                                      ++e + + ++k+ ++  +e+A++lg++  kv  ++KSL+ +g l+k+  
  gi|488601742|ref|YP_007908213.1|  9 AEEFVYEFVNKHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMG-LVKTSL 56
                                      578888999*********************************.***975 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.5e-06    0.0019      22      56 ..      20      54 ..       9      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.5e-06
                                      CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 22 aegltaselaerldlskntlsyHLrvLeeagLvev 56
                                        gl++ e+a+ l++s   +++ ++ Lee gLv++
  gi|488601742|ref|YP_007908213.1| 20 HSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKT 54
                                      57999****************************97 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 !   16.6   0.1   9.6e-06    0.0052       2      33 ..      21      53 ..      20      56 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.6e-06
                             IF2_N  2 skirVyeLAkeLg...vkskevikkLfkelGievk 33
                                      s ++Vye+Ak+Lg    k+  +ik L +e+G   k
  gi|488601742|ref|YP_007908213.1| 21 SGLSVYEIAKKLGwssGKVYNIIKSL-EEMGLV-K 53
                                      5789*********4444445578888.668987.5 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 !   17.8   0.0   7.4e-06     0.004      62      97 ..      17      52 ..       5      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.4e-06
                                      SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 62 peseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                      +++  G++v eia+kl+ s  +v +++++L++ G++
  gi|488601742|ref|YP_007908213.1| 17 VNKHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLV 52
                                      56699****************************987 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 !   17.4   0.0   8.9e-06    0.0048      22      61 ..      26      65 ..      12      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.9e-06
                            HTH_27 22 adlcgrlnvedshisyslkkLtekGLvertgdeadrrekr 61
                                       +++++l  ++  + +++k L+e+GLv+++   + +r+kr
  gi|488601742|ref|YP_007908213.1| 26 YEIAKKLGWSSGKVYNIIKSLEEMGLVKTSLEVEGGRAKR 65
                                      58999**********************9999888888876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05    0.0068      11      55 ..      22      65 ..      19      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                            HTH_29 11 GvstvsqiAkllglsrrtvyrwlkrfeegGlaa.lldrrrsgrprn 55
                                      G+s v +iAk lg s  +vy+++k  ee Gl +  l   ++gr ++
  gi|488601742|ref|YP_007908213.1| 22 GLS-VYEIAKKLGWSSGKVYNIIKSLEEMGLVKtSL-EVEGGRAKR 65
                                      786.99************************876322.455666655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.9e-05     0.021      26      45 ..      22      41 ..       1      44 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-05
                                      ---HHHHHHHHT--HHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVks 45
                                      gls  EIA++lg s+g V++
  gi|488601742|ref|YP_007908213.1| 22 GLSVYEIAKKLGWSSGKVYN 41
                                      9****************987 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.5e-05     0.019      15      49 ..      19      53 ..      17      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-05
                    B-block_TFIIIC 15 RysGitqsdLakeskqdprslfyrlksLekkgLIv 49
                                      ++sG+   ++ak ++ ++ +++ ++ksLe+ gL++
  gi|488601742|ref|YP_007908213.1| 19 KHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVK 53
                                      789******************************97 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.1e-05     0.022      27      55 .]      24      52 ..       7      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s+  +ak+lg s  +v+++ik+Le+ G++
  gi|488601742|ref|YP_007908213.1| 24 SVYEIAKKLGWSSGKVYNIIKSLEEMGLV 52
                                      6678***********************85 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   5.5e-05      0.03      12      54 ..      12      54 ..       8      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.5e-05
                                      HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                    Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54
                                       +Y+  ++++  ++ ++a+ L+ s   V   +k Le++G+v++
  gi|488601742|ref|YP_007908213.1| 12 FVYEFVNKHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKT 54
                                      5788888899999****************************97 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.8e-05     0.031       6      48 ..      14      56 ..      11      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-05
                              FeoC  6 keyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekva 48
                                       e+++++   s+ e+++++  s+  +  ++  ++ +G v+   
  gi|488601742|ref|YP_007908213.1| 14 YEFVNKHSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKTSL 56
                                      58999*********************************99765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.5e-05     0.035      19      64 ..      18      61 ..       1      63 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.5e-05
                                      HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TC CS
                              Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGG 64
                                      ++++ + +s+ eia++ + s   +  i++ L++ glvk+   ++GG
  gi|488601742|ref|YP_007908213.1| 18 NKHS-G-LSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKTSLEVEGG 61
                                      3333.3.89*****************************97655555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.056      30      71 ..      17      55 ..      11      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                           DUF4423 30 lplkdfkadpeelakrlrpkisaeevekalefLlklgllkkd 71
                                      ++ + +  ++ e+ak+l+   s  +v ++++ L+++gl+k +
  gi|488601742|ref|YP_007908213.1| 17 VNKHSG-LSVYEIAKKLG--WSSGKVYNIIKSLEEMGLVKTS 55
                                      555556.7788*******..*******************976 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1    0.0001     0.055      88     146 ..      10      68 ..       5      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSS..SSSXEEE CS
                     RNA_pol_Rpc34  88 eslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvk..aptkkiY 146
                                       e+ Vy+++++   +G    +i +kl+     v +++ksLe  +++k    v+    ++k+Y
  gi|488601742|ref|YP_007908213.1|  10 EEFVYEFVNK--HSGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKTSLEVEggRAKRKVY 68 
                                       7899999987..68********************************999888334566776 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00015     0.084       8      39 ..      24      55 ..      23      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                            HTH_41  8 tIeelakeleLSvGlvQkALklLeddkaisle 39
                                      ++ e+ak+l+ S G v   +k+Le+++ ++++
  gi|488601742|ref|YP_007908213.1| 24 SVYEIAKKLGWSSGKVYNIIKSLEEMGLVKTS 55
                                      57899************************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 ?   13.4   0.0   0.00012     0.063      27      54 ..      27      54 ..       3      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                           DUF2250 27 siakeleipleevrellkkLeelGLler 54
                                       iak+l  +  +v +++k+Lee+GL++ 
  gi|488601742|ref|YP_007908213.1| 27 EIAKKLGWSSGKVYNIIKSLEEMGLVKT 54
                                      5899999*******************85 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00017      0.09       5      51 ..       6      49 ..       3      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                         HTH_Tnp_1  5 rrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyrege 51
                                      +r+ +ef  ++V+    +g sv e+A+++g s    y+ ++  + ++
  gi|488601742|ref|YP_007908213.1|  6 KRYAEEFVYEFVNKH--SGLSVYEIAKKLGWSSGKVYNIIKSLE-EM 49
                                      89************9..***************999999988885.33 PP

>> DUF3489  Protein of unknown function (DUF3489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00023      0.12      10      35 ..      11      36 ..       5      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                           DUF3489 10 arlialLrrpeGatiaeimeatgWqa 35
                                      + + + +++ +G ++ ei++++gW +
  gi|488601742|ref|YP_007908213.1| 11 EFVYEFVNKHSGLSVYEIAKKLGWSS 36
                                      56789999****************87 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0002      0.11      38      68 ..      35      65 ..      14      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                                      -HHHHHHHHHHHHHTTSEEEEEEE-CC.C-E CS
                            Cdc6_C 38 tqrevsdllseLemlgileleksskGrregr 68
                                      ++  v+++++ Le +g++++  + +G r +r
  gi|488601742|ref|YP_007908213.1| 35 SSGKVYNIIKSLEEMGLVKTSLEVEGGRAKR 65
                                      6788****************97777766444 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018     0.099     193     227 ..      11      50 ..       4      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                              TnsD 193 eLvee.....eglslkeiAkelgvdiktVlryakklgllk 227
                                       e+v+e     +gls+ eiAk lg + ++V+ + k+l++  
  gi|488601742|ref|YP_007908213.1|  11 EFVYEfvnkhSGLSVYEIAKKLGWSSGKVYNIIKSLEEMG 50 
                                       45555555579***********************987654 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00036      0.19      19      42 ..      21      44 ..      19      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                            HTH_38 19 eGlslreIArrLgrspsTIsRElk 42
                                       Gls++eIA++Lg s + +++ +k
  gi|488601742|ref|YP_007908213.1| 21 SGLSVYEIAKKLGWSSGKVYNIIK 44
                                      59***********99887777765 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0004      0.22      48      77 ..      24      53 ..      20      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                                      EHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 48 sLldiAeriglpfdrvaaiaraLaeaglla 77
                                      s+ +iA+++g +  +v++i+++L+e gl++
  gi|488601742|ref|YP_007908213.1| 24 SVYEIAKKLGWSSGKVYNIIKSLEEMGLVK 53
                                      7889************************96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036       0.2      20      53 ..      21      54 ..       1      62 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisr 53
                                        l+  e+A  lG +   v  i++ L++ gl+++
  gi|488601742|ref|YP_007908213.1| 21 SGLSVYEIAKKLGWSSGKVYNIIKSLEEMGLVKT 54
                                      468999*************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 468.53
//
Query:       gi|488601743|ref|YP_007908214.1|  [L=401]
Description: Site-specific recombinase XerD [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-09   37.1   0.0    5.9e-09   35.9   0.0    1.6  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.047   13.7   1.2       0.39   10.7   0.1    2.8  3  COX5A            Cytochrome c oxidase subunit Va
      0.048   13.7   0.3      0.094   12.8   0.3    1.4  1  DZR              Double zinc ribbon
       0.13   11.7   0.8       0.27   10.7   0.8    1.5  1  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   1.3e-12   5.9e-09       3     136 ..     146     280 ..     144     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.3e-12
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSE.EEEECT.HHHH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgske.ravpls.eeal 77 
                                       +t+d+  +ll+a+++   +rd +l+++ y+ G R  Ell+L++k+++ ++  i+v+++++K+ +    +++s   +l
  gi|488601743|ref|YP_007908214.1| 146 ITADDFFKLLKACRR---VRDSALIAMHYDLGCRPEELLTLQLKHIRRDDLGIKVNIHQSKTFTRaPRLTFSiPYVL 219
                                       68899999*******...*************************************8888777443233444434444 PP

                                       HHHHHHHHHHCHCCTTTSBSSBET....TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHH CS
                   Phage_integrase  78 ellkellskaleeaeksellfask....rgkplsrqtvrkafkraveeagiekpltpHtlRhs 136
                                       e+l+   ++     +   ++ +++    + k++++++++++++r++e+ag++k++    +Rh+
  gi|488601743|ref|YP_007908214.1| 220 EWLEAHPARD--DPDAPLWIDLNAhragKIKHITEEAYYQILQRLKERAGLKKRIFHYLFRHT 280
                                       4444444444..344444666666899*************************99988889998 PP

>> COX5A  Cytochrome c oxidase subunit Va
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.79   3.5e+03      12      12 ..      41      41 ..       8      91 .. 0.58
   2 ?   10.7   0.1   8.7e-05      0.39      18      60 ..     123     166 ..     106     172 .. 0.74
   3 ?   -0.2   0.0      0.22   9.6e+02      64      86 ..     258     280 ..     248     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.79
                             COX5A 12 y 12
                                      y
  gi|488601743|ref|YP_007908214.1| 41 Y 41
                                      3 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.7e-05
                             COX5A  18 rediDl.felrrgl.nnlfayDlvPepkvieaalracrrvndfal 60 
                                       +e++ + f++r ++ n+l+a Dl+ + +   + l+acrrv d al
  gi|488601743|ref|YP_007908214.1| 123 KEELNKyFKVRDKVdNELTADDLITADDFF-KLLKACRRVRDSAL 166
                                       555543267887773668899999998876.68*********997 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.22
                             COX5A  64 ilEavkekvenkkqiYeyllqel 86 
                                       il  +ke+++ kk+i++yl  ++
  gi|488601743|ref|YP_007908214.1| 258 ILQRLKERAGLKKRIFHYLFRHT 280
                                       67778888888888888887654 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   2.1e-05     0.094      30      49 .]     343     362 ..     325     368 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                               DZR  30 rCpsCgekvdpearfCpeCG 49 
                                       +C +Cg  + ++a  C  CG
  gi|488601743|ref|YP_007908214.1| 343 QCYNCGMVNRADAVRCRWCG 362
                                       55555555555555555555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8     6e-05      0.27       4      23 ..     343     362 ..     342     365 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6e-05
                       zf-ribbon_3   4 rCPnCGa.plssddnvCpyCG 23 
                                       +C nCG  + ++d++ C +CG
  gi|488601743|ref|YP_007908214.1| 343 QCYNCGMvN-RADAVRCRWCG 362
                                       799****99.*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); 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: 0.66u 0.38s 00:00:01.04 Elapsed: 00:00:00.59
# Mc/sec: 2042.72
//
Query:       gi|488601744|ref|YP_007908215.1|  [L=201]
Description: Molybdopterin-guanine dinucleotide biosynthesis protein A [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-26   91.7   0.0    7.4e-26   91.4   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
    0.00087   18.5   0.0     0.0061   15.8   0.0    1.9  1  CofC          Guanylyl transferase CofC like
     0.0022   17.8   0.0      0.033   13.9   0.0    2.2  2  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr
  ------ inclusion threshold ------
       0.03   14.2   0.0        0.1   12.5   0.0    1.8  1  CTP_transf_3  Cytidylyltransferase
      0.058   13.8   0.8       0.11   12.9   0.8    1.4  1  NBD94         Nucleotide-Binding Domain 94 of RH


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 !   91.4   0.0   2.1e-29   7.4e-26       1     154 [.       3     150 ..       3     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 2.1e-29
                                       EEEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHH CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplasl 76 
                                       aviLAGG ++R+g  +K l+++ggkp++  ++d+l++    e++++++de+ ++ ++r+g +vv+d  ++ gpl+++
  gi|488601744|ref|YP_007908215.1|   3 AVILAGGYGRRLGYtEKGLIEIGGKPIISKIIDSLTKF---EIIISCRDENQAEKYERFG-EVVVDILKDFGPLSGI 75 
                                       79***********66*********************99...9*********999999999.889999999******* PP

                                       HHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..EEEGGGHHHHHHHCTHTTHH CS
                      NTP_transf_3  77 aaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpl..lfrarllsalaallgdqgar 151
                                       ++al+++   ++++++++DmP++++e+ e++ ++++  g+d+++p ++++  +p   +++ ++ ++++++ + +  r
  gi|488601744|ref|YP_007908215.1|  76 HSALKKI--GERAVFISADMPFVKQEICEAIYRECE--GYDAAIPIWNDGKLEPTlsAYSPAVTEKIEQCYR-KNIR 147
                                       ******9..79************************7..99***************77778888899999875.5666 PP

                                       HCH CS
                      NTP_transf_3 152 rll 154
                                       ++l
  gi|488601744|ref|YP_007908215.1| 148 KVL 150
                                       665 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-06    0.0061      33     126 ..      29     121 ..      23     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
                              CofC  33 mlldvidalkrldvlvvsedeevle.yal.delgvevvkek..ekdlntavekafeeieekeviiipsdiPlikked 105
                                       ++  +id+l + ++++  +de+  e y++  e  v+++k+    +++ +a++k+      ++ + i +d+P++k+e 
  gi|488601744|ref|YP_007908215.1|  29 IISKIIDSLTKFEIIISCRDENQAEkYERfGEVVVDILKDFgpLSGIHSALKKI----G-ERAVFISADMPFVKQEI 100
                                       56789**************99877623321345556666654445555555555....4.4667889********** PP

                              CofC 106 vkdllelekradvviaPargG 126
                                        + ++   + +d  i   ++G
  gi|488601744|ref|YP_007908215.1| 101 CEAIYRECEGYDAAIPIWNDG 121
                                       *****9999999888665555 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 !   13.9   0.0   9.1e-06     0.033       1      42 [.       1      41 [.       1      68 [. 0.83
   2 ?    1.5   0.0     0.057     2e+02     204     220 ..     178     194 ..     172     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.1e-06
                                      EEEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTT CS
                              IspD  1 vvvvipAAGsGkRmkaglpKqflelkgqtllehtvdallask 42
                                      + +vi A G G+R++  ++K ++e+ g++++++ +d+l + +
  gi|488601744|ref|YP_007908215.1|  1 MYAVILAGGYGRRLGY-TEKGLIEIGGKPIISKIIDSLTKFE 41
                                      579***********97.579***************9998844 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.057
                                       ----SHHHHHHHHHHHH CS
                              IspD 204 lKittpeDlalAeailr 220
                                       + i tpeDl  Ae+il+
  gi|488601744|ref|YP_007908215.1| 178 MNINTPEDLRKAEIILK 194
                                       5799***********97 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05       0.1      15      63 ..      18      62 ..      13     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                      TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEE CS
                      CTP_transf_3 15 gKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasv 63
                                      +K l+++ggkp+i  +++ + k   f ++i+++ +e+ ++  + fg  v
  gi|488601744|ref|YP_007908215.1| 18 EKGLIEIGGKPIISKIIDSLTK---F-EIIISCRDENQAEKYERFGEVV 62
                                      799*******************...4.57********999999997433 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8     3e-05      0.11      11      74 ..     135     196 ..     132     201 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                             NBD94  11 idkkkkiy.eniekllnEleeiekek.tsleevknielsYgrsLikllvqkIdeekkkaenlieei 74 
                                       ++k+++ y +ni+k+l  ++ +ek k +++e++k    +Y+r Li ++  +  e+ +kae++++++
  gi|488601744|ref|YP_007908215.1| 135 TEKIEQCYrKNIRKVLCAIHGLEKVKyIPIENLK----QYDRKLISFMNINTPEDLRKAEIILKTV 196
                                       56788888569***********996648898888....6************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1133.18
//
Query:       gi|488601745|ref|YP_007908216.1|  [L=305]
Description: cyclic pyranopterin monophosphate synthase subunit MoaA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-31  109.4   0.1    5.3e-31  108.2   0.0    1.6  2  Radical_SAM  Radical SAM superfamily
    1.5e-17   63.7   0.1    2.6e-17   63.0   0.1    1.4  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    5.9e-07   29.8   0.4      2e-06   28.1   0.0    2.1  3  Fer4_12      4Fe-4S single cluster domain
    2.6e-06   27.5   0.0    6.2e-06   26.3   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.0   1.2e-34   5.3e-31       1     166 [.      15     172 ..      15     173 .. 0.93
   2 ?   -1.9   0.0      0.87   3.9e+03      66      86 ..     206     252 ..     180     272 .. 0.57

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 1.2e-34
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       ++vt +Cnl+C +C+      ++  + +lsve+i+e+ k++ +e g+k v ++ggepll++d+ +++  +       
  gi|488601745|ref|YP_007908216.1|  15 ISVTDACNLNCFYCHKEGYCVKGSSPDVLSVEDIAEITKAF-YELGIKKVKITGGEPLLRKDILDIISVMPD----F 86 
                                       6899*************99999*******************.8******************99666666655....6 PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpG 154
                                        +i+++tngtl+ ++++ +l+++g++rv+++l+++++e+++k++  g+++e+vl +le + +ag+ +v+ ++v+++ 
  gi|488601745|ref|YP_007908216.1|  87 EEISMTTNGTLL-DKYAYELKDAGLNRVNISLDSLNPETYKKIT--GGELERVLSGLESAVNAGLTPVKLNMVVMKE 160
                                       9***********.*************************555555..69***************************** PP

                                       TSHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                       Radical_SAM 155 endeeleellel 166
                                       +n++e++++le+
  gi|488601745|ref|YP_007908216.1| 161 VNEDEIDDMLEF 172
                                       *********998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.87
                                       HHHHHHHTC..........................CCTEEEEEEECS CS
                                       xxxxxxxxx..........................xxxxxxxxxxxx RF
                       Radical_SAM  66 llerlakla..........................vpgiritvetng 86 
                                       + er+ak+a                          v++ ++++ +n 
  gi|488601745|ref|YP_007908216.1| 206 IEERIAKKAinfrirsmqkrkqyhlgssvvefvkpVDNTEFCYNCNR 252
                                       33333333344444444444444455555555544455555555555 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 !   63.0   0.1   5.7e-21   2.6e-17       3     126 ..     185     297 ..     183     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 5.7e-21
                                       EEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--EE CS
                       Mob_synth_C   3 lrfIElmpvgegeewrekkvvsadeilerieerlalleakketkgpakrykikdgkgeiglIapvsep.FCasCnRl 78 
                                       l++IEl ++ e e+     ++  ++i eri+++    ++  ++++++k+y++ +    +++++pv+++ FC +CnR+
  gi|488601745|ref|YP_007908216.1| 185 LQIIELLKLPELED----YYMDISSIEERIAKKAINFRI--RSMQKRKQYHLGSS--VVEFVKPVDNTeFCYNCNRI 253
                                       66677777776653....356666666666555555554..55999999999555..5*********99******** PP

                                       EE-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHHT----H CS
                       Mob_synth_C  79 RltadGklktCLfaeee.idlrdllregaseeeLkelikealarkkekh 126
                                       R+t dGk+k+CL+++++ +d+r l +      +Lke i +a++ +++++
  gi|488601745|ref|YP_007908216.1| 254 RITKDGKIKPCLMRNDNlVDVRGL-KGY----ALKEKIFQAVNMREPYF 297
                                       *****************9999975.333....48899999998888876 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 !   28.1   0.0   4.5e-10     2e-06      13     113 ..      19     115 ..      10     135 .. 0.74
   2 ?   -2.9   0.0       1.6   7.3e+03      76      97 ..     158     178 ..     151     191 .. 0.56
   3 ?   -2.2   0.0       1.1   4.7e+03      87     118 ..     244     275 ..     232     288 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.5e-10
                           Fer4_12  13 sgCnlsCkgCfnketwsfksgkef.tkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                         Cnl+C +C+ +      s+ ++ + e ++ei + + +  i+++ ++GGEPll++   ++++++  ++e       
  gi|488601745|ref|YP_007908216.1|  19 DACNLNCFYCHKEGYCVKGSSPDVlSVEDIAEITKAFYELGIKKVKITGGEPLLRKDILDIISVMPDFEEI-----S 90 
                                       57*********7766666666555479**********9****************55555555555555544.....4 PP

                           Fer4_12  89 wlytgytleelskkekeellkeidv 113
                                       + ++g+ l++   + k+  l+ +++
  gi|488601745|ref|YP_007908216.1|  91 MTTNGTLLDKYAYELKDAGLNRVNI 115
                                       5677777777665555555555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.6
                           Fer4_12  76 vkevkeekpekdiwlytgytle 97 
                                       +kev e  ++ d++++t   +e
  gi|488601745|ref|YP_007908216.1| 158 MKEVNEDEID-DMLEFTSKYNE 178
                                       4444444442.44444444433 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                           Fer4_12  87 diwlytgytleelskkekeellkeidvlvdGk 118
                                       + ++y+   +   ++ + ++ l   d lvd++
  gi|488601745|ref|YP_007908216.1| 244 TEFCYNCNRIRITKDGKIKPCLMRNDNLVDVR 275
                                       44566666666666556677777777777765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.4e-09   6.2e-06       5      94 ..      18      99 ..      15     120 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.4e-09
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpq..teelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81
                                      +  Cnl+C  C ++  +  +   p+  + e++ +i+k +++    i+++ +tGGePL+    k++l++++ + +     
  gi|488601745|ref|YP_007908216.1| 18 TDACNLNCFYCHKEG-YCVKGSSPDvlSVEDIAEITKAFYELG--IKKVKITGGEPLLR---KDILDIISVMPDFE--- 87
                                      568********9877.555555554116667777775555555..588*********55...88999998666554... PP

                           Fer4_14 82 kiwletngtleie 94
                                      +i + tngtl  +
  gi|488601745|ref|YP_007908216.1| 88 EISMTTNGTLL-D 99
                                      99999999987.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1663.84
//
Query:       gi|488601746|ref|YP_007908217.1|  [L=54]
Description: hypothetical protein Asulf_02272 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 342.94
//
Query:       gi|488601747|ref|YP_007908218.1|  [L=358]
Description: histidinol phosphate aminotransferase apoenzyme [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-48  164.5   0.0    4.6e-48  164.2   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
    2.8e-08   33.1   0.0    4.9e-06   25.7   0.0    2.2  2  Alliinase_C    Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2   0.0   5.1e-52   4.6e-48       2     361 ..      34     348 ..      33     349 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 5.1e-52
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                        v++L+sne++++     +p++++  ++    +  ++ y+p +   el e++ +++g      ++ + ++v + G +
  gi|488601747|ref|YP_007908218.1|  34 RVVKLASNENPYG----ASPKTIESFQK----FTAFHVYPPKQ-PEELIEKISEYIG------VDSN-RIVICAGID 94 
                                       689**********....88988888776....***********.*************......8888.********* PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                        ++e l+ ++ +++gd + +  pt++ y+  + +sg++ v+ +         d + +++  +e        k+ +v+
  gi|488601747|ref|YP_007908218.1|  95 GVLECLFKIF-IERGDSVAIAPPTFPYYHILADISGAKKVYLK--------RDQNFMIAEKDE------NAKLTIVC 156
                                       **********.***************************99999........577777777777......568***** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGy 232
                                       sp+NPtG    +e ++++   ++  + ++f+DeaYa+f  ++       +++ ee n+++++++sKafGla++R+Gy
  gi|488601747|ref|YP_007908218.1| 157 SPNNPTGNTEREEIVREI---VDG-RGIVFIDEAYAEFSDDD------MVDFTEEENVVLARTFSKAFGLANLRIGY 223
                                       ******************...886.99**************6......6777888899******************* PP

                                       EEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEE CS
                     Aminotran_1_2 233 ilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfll 309
                                       +++ ++++++   + +pf +s+++  a+  al+d +    ++ ++++++ ++r++++ eL++ g++v++sq++++ +
  gi|488601747|ref|YP_007908218.1| 224 AVVPEWMKKYFMMVNTPFPISTPAINAAISALEDID----YMRDTVEKIRDERDRVYRELKNVGVEVYPSQANFLFF 296
                                       **********************************99....*********************************9988 PP

                                       EEETHH.CHHHHHHHHHHTCTEEEEEGGGG.TS.TTEEEEECTTS-HHHHHHHHH CS
                     Aminotran_1_2 310 tdlsae.takelskkLleevgvyvtpgtsf.tv.pgrlRitvAglteeeleelve 361
                                       ++      a++ +++L ++ gv+v+ ++sf ++ + ++R+++  + +e+++ +++
  gi|488601747|ref|YP_007908218.1| 297 SLKQFNlPASQYCEELMKR-GVIVRDCSSFiGCdEYSVRVSI--GRKEDNDVFLD 348
                                       877766679999999****.9999999988355999******..88888887776 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   5.4e-10   4.9e-06     102     210 ..     114     228 ..      72     242 .. 0.80
   2 !    5.3   0.0   0.00085       7.6     312     358 ..     304     349 ..     281     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.4e-10
                                       -SS--THHHHHTTTT-BTTEEEEEESTT-.--S..S-EEEEEESS-TTT---.-----...-TT-EEEEEE-TT-.S CS
                       Alliinase_C 102 avPyysvykeqtslldsklykweGdaaayvkkknpeefielvtsPnnPdgll.reavv...kgseakviyDlayY.W 173
                                       a P ++ y+  +++   k+   + d +  + +k+ +  + +v sPnnP g+  re++v    + +++v  D ay  +
  gi|488601747|ref|YP_007908218.1| 114 APPTFPYYHILADISGAKKVYLKRDQNFMIAEKDENAKLTIVCSPNNPTGNTeREEIVreiVDGRGIVFIDEAYAeF 190
                                       45667777777777777777778887777788889999***********9863677775554567778899999535 PP

                                       TTTS---S-B--SEEEE.EHHHHHS-GGG-EEEEEES- CS
                       Alliinase_C 174 PhytpitskadedimLf.tlskltGhaGsrlGWalvkd 210
                                        +   +   ++e+++L  t+sk  G a  r+G+a+v +
  gi|488601747|ref|YP_007908218.1| 191 SDDDMVDFTEEENVVLArTFSKAFGLANLRIGYAVVPE 228
                                       6667789999999999659****************965 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.00085
                                       SS..-HHHHHHTTTEEEEEGGGGTS-TTEEEEESSS-HHHHHHHHHH CS
                       Alliinase_C 312 eededcaevlrekkiltrsGevfeaesryvrlsllkrdddfdvller 358
                                       + ++ c+e+++++ i+    + +++++  vr+s+  r++d dv+l+ 
  gi|488601747|ref|YP_007908218.1| 304 PASQYCEELMKRGVIVRDCSSFIGCDEYSVRVSIG-RKEDNDVFLDA 349
                                       56678999999999999999999**********75.55566888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 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:                        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 0.34s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2069.30
//
Query:       gi|488601748|ref|YP_007908219.1|  [L=182]
Description: putative nucleotide kinase (related to CMP and AMP kinases) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   86.4   0.1    3.7e-24   85.7   0.1    1.2  1  AAA_18           AAA domain
    1.5e-06   28.3   0.3      0.056   13.3   0.1    2.3  2  dNK              Deoxynucleoside kinase
    7.7e-05   23.1   0.6      0.043   14.2   0.0    2.6  2  AAA_17           AAA domain
    0.00028   21.2   0.0    0.00073   19.8   0.0    1.7  2  AAA_28           AAA domain
    0.00039   20.1   0.2      0.056   13.1   0.1    2.1  2  Thymidylate_kin  Thymidylate kinase
    0.00061   19.8   0.0      0.059   13.4   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0013   19.0   0.0     0.0019   18.5   0.0    1.6  1  AAA_22           AAA domain
     0.0021   18.2   0.1      0.015   15.4   0.1    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0022   18.4   1.3     0.0082   16.6   1.3    2.1  1  AAA              ATPase family associated with various cellul
     0.0039   16.9   0.1      0.006   16.3   0.1    1.5  1  AAA_24           AAA domain
     0.0091   16.1   0.3        1.5    8.9   0.3    2.7  2  ADK              Adenylate kinase
  ------ inclusion threshold ------
       0.01   16.0   0.4        4.4    7.5   0.1    2.2  2  AAA_33           AAA domain
      0.024   14.5   1.1        1.4    8.8   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
       0.03   14.0   2.5       0.33   10.6   0.1    2.6  3  CoaE             Dephospho-CoA kinase
       0.03   14.7   0.0      0.045   14.1   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.032   14.0   0.0      0.075   12.8   0.0    1.6  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.033   14.3   0.1        4.6    7.3   0.0    2.3  2  SKI              Shikimate kinase
       0.04   13.8   2.2        3.9    7.4   0.4    2.2  2  NACHT            NACHT domain
      0.063   12.7   0.0       0.11   11.9   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
        0.1   12.3   0.0       0.14   11.9   0.0    1.4  1  AAA_30           AAA domain
        0.1   13.1   0.0       0.13   12.8   0.0    1.5  1  ABC_tran         ABC transporter
       0.15   12.4   0.0       0.33   11.3   0.0    1.6  1  AAA_19           AAA domain
       0.19   11.0   0.9        1.1    8.5   0.1    2.3  2  Zeta_toxin       Zeta toxin


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 !   85.7   0.1   4.7e-27   3.7e-24       3     130 .]       5     115 ..       4     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 4.7e-27
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlv 78 
                                       ltGtpG+GKt++a+ Ls+   + ++ ++++a en++ ++v+++    s+++d+d l ++++++++         ++v
  gi|488601748|ref|YP_007908219.1|   5 LTGTPGTGKTSVARMLSDI--YdVRSVKEIAEENDCIIDVEDD----SLVIDIDSLSEIVRQFRQL--------DIV 67 
                                       9***************998..8899******************....******************7........58* PP

                            AAA_18  79 idghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                       i+ghl++l+s++ +    +vL+++p++l+eRl +R+++e ki+en eae ld
  gi|488601748|ref|YP_007908219.1|  68 IEGHLSHLLSPDVV----IVLRCNPKVLKERLLNRNWSEEKIRENLEAEVLD 115
                                       ***********999....*******************************985 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   8.6e-05     0.067       3      34 ..       5      36 ..       3      51 .. 0.90
   2 !   13.3   0.1   7.1e-05     0.056     113     150 ..      68     108 ..      55     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-05
                                      EEESTTSSHHHHHHHHHCCSTCEEEE-HHHHC CS
                               dNK  3 veGnIgaGKstlvklLskklgvkvfeEpvdkw 34
                                      + G+ g GK++++ +Ls+ ++v  ++E+ +++
  gi|488601748|ref|YP_007908219.1|  5 LTGTPGTGKTSVARMLSDIYDVRSVKEIAEEN 36
                                      67999**********************99998 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCT...T CS
                               dNK 113 ldnlleelakpdlliYLkasletclerikkRgreeek...k 150
                                        +  l++l +pd++i L++++++++er+ +R+ +eek   +
  gi|488601748|ref|YP_007908219.1|  68 IEGHLSHLLSPDVVIVLRCNPKVLKERLLNRNWSEEKireN 108
                                       5555677778************************9986553 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0077         6       1      21 [.       6      26 ..       6      32 .. 0.86
   2 !   14.2   0.0   5.5e-05     0.043      96     126 ..      72     103 ..      25     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0077
                                      EE-TTSSHHHHHHHHHHHHTE CS
                            AAA_17  1 lGgPGsGKgtqceklvekygf 21
                                      +G PG GK+ +++ l + y++
  gi|488601748|ref|YP_007908219.1|  6 TGTPGTGKTSVARMLSDIYDV 26
                                      69**********999988876 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-05
                                       HHHHH..SEEEEEE--HHHHHHHHHHH.TTST CS
                            AAA_17  96 vleelkpdaiilleadpeeilerrlkd.rtrg 126
                                         + l+pd++i+l ++p+++ er+l++  +++
  gi|488601748|ref|YP_007908219.1|  72 LSHLLSPDVVIVLRCNPKVLKERLLNRnWSEE 103
                                       345679********************953333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.3e-07   0.00073       2      33 ..       3      35 ..       2      63 .. 0.93
   2 ?   -1.4   0.0       3.2   2.5e+03     136     153 ..     100     117 ..      85     156 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.3e-07
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvvpEaare 33
                                      +++tG+++tGKT++++ L++  +++ v+E+a e
  gi|488601748|ref|YP_007908219.1|  3 FALTGTPGTGKTSVARMLSDIyDVRSVKEIAEE 35
                                      689****************96699999999875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                            AAA_28 136 aiderlrealrelgipvi 153
                                       +++e++re l++   +vi
  gi|488601748|ref|YP_007908219.1| 100 WSEEKIRENLEAEVLDVI 117
                                       444444444433333333 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.017        14       3      26 ..       7      30 ..       5      41 .. 0.80
   2 !   13.1   0.1   7.2e-05     0.056     115     181 ..      75     141 ..      58     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                                      ESTTSSHHHHHHHHHHHHHHTTE. CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik 26
                                      G  G+GKt++a++l + ++ +  k
  gi|488601748|ref|YP_007908219.1|  7 GTPGTGKTSVARMLSDIYDVRSVK 30
                                      777************999877654 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.2e-05
                                       TSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-.HHHH CS
                   Thymidylate_kin 115 llkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakederiliidasks.ieev 181
                                       ll+Pd+++ l + p+v  +Rl  r+ ++e++ e+l+  + +   + e ++e +r++ id+++  +e+v
  gi|488601748|ref|YP_007908219.1|  75 LLSPDVVIVLRCNPKVLKERLLNRNWSEEKIRENLE-AEVLDVILVESIEEVDRVYEIDTTDRsVEDV 141
                                       349***********************8888888888.5555666666677888888888887657776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   7.5e-05     0.059       4      27 ..       5      29 ..       2      39 .. 0.82
   2 ?    4.5   0.1     0.041        32      27      99 ..      91     159 ..      68     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.5e-05
                                      EE--SSSSHHHHHHHGGGGB.S--E CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nrev 27
                                      L G pGtgK+++a+ l+  +  r+v
  gi|488601748|ref|YP_007908219.1|  5 LTGTPGTGKTSVARMLSDIYdVRSV 29
                                      99***************99865554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.041
                                       EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-S CS
                             AAA_5  27 veyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraesevlnsLlslleerrllleeg 99 
                                       + + +l+r+++ee+++  +e     ++  d +lv++++   +++ +D  +r   +v++++  ++e +++ +e  
  gi|488601748|ref|YP_007908219.1|  91 LKERLLNRNWSEEKIRENLE-----AEVLDVILVESIEeVDRVYEIDTTDRSVEDVAKIVVEIIEFEKRGIEAK 159
                                       55667888888888888888.....6999999999999557888899999999999999999999888877665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-06    0.0019       7      51 ..       2      48 ..       1     154 [. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsst 51
                                      i ++tG +GtGKT ++r+l + +d ++  e   e++ ++ v+  s+ 
  gi|488601748|ref|YP_007908219.1|  2 IFALTGTPGTGKTSVARMLSDIYDVRSVKEIaeENDCIIDVEDDSLV 48
                                      5789******************9876544446555555555544444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     2e-05     0.015       6     104 ..       3     150 ..       1     153 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                                       EEEE--TTSSHHHHHHHHHHHTT-..................-EEEEEGGG-------THHHHHHHHHTTT-HHHHT CS
                             AAA_2   6 illlgptgvGktelakalaellfv..............kkekkliradaselleeeevehlvsrligappgyvgaee 68 
                                       + l+g+ g+Gkt +a++l+++ +v              + e+   ++d  +l e      +v ++ +    + g+  
  gi|488601748|ref|YP_007908219.1|   3 FALTGTPGTGKTSVARMLSDIYDVrsvkeiaeendciiDVEDDSLVIDIDSLSE------IVRQFRQLDIVIEGHLS 73 
                                       778999*****************9888887765555555555555555555555......55555555555555544 PP

                                       TS........................................EEEEETGGG----.---------HHHHHHHHHHHH CS
                             AAA_2  69 gG........................................ivllDEidKihpk.essgadvSregVqrdLLqile 104
                                       +                                         ++l++ i+ + +  e  + d S e+V ++   i+e
  gi|488601748|ref|YP_007908219.1|  74 HLlspdvvivlrcnpkvlkerllnrnwseekirenleaevldVILVESIEEVDRVyEIDTTDRSVEDVAKIVVEIIE 150
                                       4477788888888889999999999999999999999999**99999999999988899*************99998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.3   1.1e-05    0.0082       3      25 ..       5      27 ..       3     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                                      EESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  3 lyGppGtGKTllakavakelgve 25
                                      l+G+pGtGKT++a+ +    +v+
  gi|488601748|ref|YP_007908219.1|  5 LTGTPGTGKTSVARMLSDIYDVR 27
                                      89*************99887655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   7.8e-06     0.006       5      75 ..       3     123 ..       1     143 [. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.8e-06
                            AAA_24   5 iliyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdieswedfldevvel......... 59 
                                       ++++G +g+GKT++a++l             +++  +id+e+ +  +d d + +i      + ++ +l         
  gi|488601748|ref|YP_007908219.1|   3 FALTGTPGTGKTSVARMLsdiydvrsvkeiaEENDCIIDVEDDSLVIDIDSLSEI------VRQFRQLdivieghls 73 
                                       589********************999999999999999****8888888877755......3333333344455555 PP

                            AAA_24  60 ..................................aaeladyktlviDtid 75 
                                                                         + e + ++++ + +i+
  gi|488601748|ref|YP_007908219.1|  74 hllspdvvivlrcnpkvlkerllnrnwseekireNLEAEVLDVILVESIE 123
                                       55555555566666666666666666666555554444455555555555 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.049        38       1      23 [.       5      27 ..       5      32 .. 0.87
   2 !    8.9   0.3    0.0019       1.5      99     134 ..      74     111 ..      51     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.049
                                      EEESTTSSHHHHHHHHHHHHTSE CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkygla 23
                                      l G+Pg+GK  +a+ l + y + 
  gi|488601748|ref|YP_007908219.1|  5 LTGTPGTGKTSVARMLSDIYDVR 27
                                      67************999988775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0019
                                       HTSEESEEEEEE--HHHHHHHHHT..GSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                               ADK  99 ekvkldlvleldvpeevlveRltg..DneetvkkRlet 134
                                       +  + d+v+ l+++ +vl+eRl++   +ee++++ le+
  gi|488601748|ref|YP_007908219.1|  74 HLLSPDVVIVLRCNPKVLKERLLNrnWSEEKIRENLEA 111
                                       345789****************9966456666666653 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0057       4.4       4      19 ..       5      20 ..       2      47 .. 0.88
   2 ?    7.1   0.0     0.007       5.5      94     134 ..      74     115 ..      27     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0057
                            AAA_33  4 lvGlpGsGKstlaerl 19
                                      l G pG+GK+ +a+ l
  gi|488601748|ref|YP_007908219.1|  5 LTGTPGTGKTSVARML 20
                                      78**********9976 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.007
                            AAA_33  94 rlgvpvrivvvetdeetlkeRlakRaang.ddrsevpeeald 134
                                       +l +p+ ++v+++ +++lkeRl  R+ ++ + r +++ e+ld
  gi|488601748|ref|YP_007908219.1|  74 HLLSPDVVIVLRCNPKVLKERLLNRNWSEeKIRENLEAEVLD 115
                                       444579*******************99873445566666665 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0017       1.4       3      26 ..       2      25 ..       1      30 [. 0.89
   2 ?    3.9   0.4     0.053        42     116     171 ..      84     147 ..      57     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                                      EEEEEE-TTSSHHHHHHHHHHHSS CS
                               CPT  3 iilLnGgsssGKsslaralqevld 26
                                      i  L G++ +GK+s+ar l ++ d
  gi|488601748|ref|YP_007908219.1|  2 IFALTGTPGTGKTSVARMLSDIYD 25
                                      56799**************99876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.053
                                       EE--HHHHHHHHHHHTS.....SSTTHHHH.HTTGGGTT---S..EEEETTSS-HHHHHHHHHT CS
                               CPT 116 vrcplevlerRelergd.....RepGlaal.qaeavHagaeyD..levDtsaktpeecAraire 171
                                       +rc+ +vl++R l+r       Re   a++ +   v + +e D  +e+Dt+   +e++A+ + e
  gi|488601748|ref|YP_007908219.1|  84 LRCNPKVLKERLLNRNWseekiRENLEAEVlDVILVESIEEVDrvYEIDTTDRSVEDVAKIVVE 147
                                       5666666666666655433333332222211222333333444337999999999999987765 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00043      0.33       1      27 [.       1      28 [.       1      73 [. 0.82
   2 ?    3.0   0.1     0.089        69     112     157 ..      66     112 ..      51     116 .. 0.76
   3 ?   -0.4   0.2         1   8.1e+02     127     163 ..     116     154 ..     102     160 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                                      EEEEEEESTTSSHHHHHHHHHH.TT-EE CS
                              CoaE  1 livgltGgiasGKstvanlfad.lgvpi 27
                                      +i +ltG  ++GK+ va++++d + v  
  gi|488601748|ref|YP_007908219.1|  1 MIFALTGTPGTGKTSVARMLSDiYDVRS 28
                                      5789*****************9777665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.089
                                       TTTTTTGGGGS..SEEEEEE--HHHHHHHHHHCCTSTHHHHHHHHHHS CS
                              CoaE 112 LLvEkqlekli..ervlvvdvelelqveRlvardgvseeevkaiiaaQ 157
                                       + +E +l++l+  ++v+v+ ++++   eRl++r+  see++++ ++a 
  gi|488601748|ref|YP_007908219.1|  66 IVIEGHLSHLLspDVVIVLRCNPKVLKERLLNRN-WSEEKIRENLEAE 112
                                       5678888887733578888999999999999985.7888888877765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1
                                       EEE--HHHHHHHHHHCC..TSTHHHHHHHHHHS--HHHH CS
                              CoaE 127 vvdvelelqveRlvard..gvseeevkaiiaaQlseeer 163
                                       v+ ve  ++v+R+ + d  + s e+v++i+   ++ e+r
  gi|488601748|ref|YP_007908219.1| 116 VILVESIEEVDRVYEIDttDRSVEDVAKIVVEIIEFEKR 154
                                       555667778888877663356668888888777766666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.8e-05     0.045      27      48 ..       3      24 ..       1     113 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-05
                            AAA_16 27 vllsGesGvGKsslvrellral 48
                                        l+G +G+GK+s++r+l + +
  gi|488601748|ref|YP_007908219.1|  3 FALTGTPGTGKTSVARMLSDIY 24
                                      579*************998755 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.6e-05     0.075       1      39 [.       2      40 ..       2      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsfl 39
                                      + +++g  G Gkt+var l +i    +vk    e d ++
  gi|488601748|ref|YP_007908219.1|  2 IFALTGTPGTGKTSVARMLSDIYDVRSVKEIAEENDCII 40
                                      5689********************999986655665554 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0059       4.6       1      19 [.       9      27 ..       9      36 .. 0.88
   2 ?    4.9   0.2     0.033        26      80     155 ..      73     147 ..      65     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0059
                                      TTSSHHHHHHHHHHHHTSE CS
                               SKI  1 mGaGKstvGkllAkklgle 19
                                      +G+GK++v+++l++ ++++
  gi|488601748|ref|YP_007908219.1|  9 PGTGKTSVARMLSDIYDVR 27
                                      69***********987765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.033
                                       HHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSC.EEEECTSSHHHHHHHHHH CS
                               SKI  80 ellkekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaad.vvvdeseeskeevaeeil 154
                                       ++l +  +vi L++++++l erl +++     +ek +e+ + e l     ++ ee++  + +d++++s e va+ ++
  gi|488601748|ref|YP_007908219.1|  73 SHLLSPDVVIVLRCNPKVLKERLLNRNW---SEEKIRENLEAEVLDvILVESIEEVDRvYEIDTTDRSVEDVAKIVV 146
                                       45555899**************977766...4666666666666666667778887662567777777655555544 PP

                                       H CS
                               SKI 155 e 155
                                       e
  gi|488601748|ref|YP_007908219.1| 147 E 147
                                       4 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0094       7.3       4      22 ..       4      22 ..       1      34 [. 0.85
   2 ?    7.4   0.4     0.005       3.9      80     137 ..      43      98 ..      27     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0094
                                      EEEC-TTTCHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklal 22
                                      +l+G +G GKT  ++ l +
  gi|488601748|ref|YP_007908219.1|  4 ALTGTPGTGKTSVARMLSD 22
                                      799*********9998865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.005
                                       CCCEEEE.EE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH..HCT CS
                             NACHT  80 perlLli.lDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd..lee 137
                                       ++  L i +D+l e+v++++q     ++ ++++ ++  l p + ++l + p+ l++  l +
  gi|488601748|ref|YP_007908219.1|  43 EDDSLVIdIDSLSEIVRQFRQ-----LDIVIEGHLSHLLSPDVVIVLRCNPKVLKErlLNR 98 
                                       444444449************.....99999999999999999999999999987666333 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   0.00014      0.11      27      58 ..       5      36 ..       2      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplseeealeva 58
                                      l+G+pG+GKt +a+ l+ +    s +e+ e +
  gi|488601748|ref|YP_007908219.1|  5 LTGTPGTGKTSVARMLSDIYDVRSVKEIAEEN 36
                                      89*****************9988888887755 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      44 ..       3      26 ..       1      83 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            AAA_30 21 avltGpAGtGKttalkalreawea 44
                                       +ltG +GtGKt + + l ++++ 
  gi|488601748|ref|YP_007908219.1|  3 FALTGTPGTGKTSVARMLSDIYDV 26
                                      579*************99999875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017      0.13      14      39 ..       3      28 ..       1     158 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                      EEEEESTTSSHHHHHHHHTTSS--SE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkpte 39
                                       a++G  G+GK++++++l+  ++  +
  gi|488601748|ref|YP_007908219.1|  3 FALTGTPGTGKTSVARMLSDIYDVRS 28
                                      699*****************999733 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00043      0.33      13      33 ..       3      23 ..       1      41 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                            AAA_19 13 llvtaGpGtGKTrvlkhival 33
                                      +++t+ pGtGKT v ++   +
  gi|488601748|ref|YP_007908219.1|  3 FALTGTPGTGKTSVARMLSDI 23
                                      679*********998876555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0014       1.1      20      39 ..       4      23 ..       1      83 [. 0.90
   2 ?    1.0   0.1      0.27   2.1e+02     126     175 ..      81     130 ..      78     154 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                        Zeta_toxin 20 llgGqpGAGKselaellkde 39
                                       l G pG GK+++a++l d 
  gi|488601748|ref|YP_007908219.1|  4 ALTGTPGTGKTSVARMLSDI 23
                                      589************99875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.27
                        Zeta_toxin 126 vvvvavkkelSrlgvldRyeee..vaegRlvpkeehdeafeglresvealee 175
                                       v+v+ +++++  +++l+R + e  + e  + + e+ d +  +  e+v+++ e
  gi|488601748|ref|YP_007908219.1|  81 VIVLRCNPKVLKERLLNRNWSEekIRE--NLEAEVLDVILVESIEEVDRVYE 130
                                       678888888888899999888833222..33333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.57u 0.38s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1085.22
//
Query:       gi|488601749|ref|YP_007908220.1|  [L=193]
Description: Nitroreductase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  141.0   0.0    4.3e-41  140.8   0.0    1.0  1  Nitroreductase  Nitroreductase family
    8.7e-17   61.4   1.5      2e-07   30.8   0.1    2.9  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.0   4.7e-45   4.3e-41       2     170 .]      12     172 ..      11     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 4.7e-45
                                       HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG. CS
                    Nitroreductase   2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke. 77 
                                       ++RrS+R++ d+ v++e++e++le a++aPsa+n+q+w fvvv ++e++++l+e + ++++++  ++e  ++++ + 
  gi|488601749|ref|YP_007908220.1|  12 MERRSHRFYLDKEVEREKIEELLELAMWAPSAMNRQQWYFVVV-SGEKLKELQETIEKSFDYILGRLERFFKETPKv 87 
                                       79*****************************************.9**********************9999988779 PP

                                       .HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHH CS
                    Nitroreductase  78 .elklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkl 153
                                        +l++   k l++apv+i++        ++++ +++  ++++++aa+qn+lLaA+a+Glg+c+++g+  +++e++ +
  gi|488601749|ref|YP_007908220.1|  88 iALTKQFFKTLGNAPVMIFA--------YYTPTGDDYSDVQSVSAAIQNMLLAAHAMGLGTCWMTGPVHVEDEINSF 156
                                       99******************........77777777778999*********************************** PP

                                       HT-S..SEEEEEEEEE- CS
                    Nitroreductase 154 lglpdeeeivvliavGy 170
                                       lg+++ +++v++i++Gy
  gi|488601749|ref|YP_007908220.1| 157 LGVEG-KKLVAVITLGY 172
                                       ****7.**********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0002       1.8       3      29 ..       8      34 ..       7      35 .. 0.91
   2 !   30.8   0.1   2.2e-11     2e-07     155     193 ..      25      63 ..      21      73 .. 0.81
   3 !   26.4   0.0   4.8e-10   4.3e-06      89     137 ..     127     177 ..     113     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0002
                                      HHHHHH--B---B--S---HHHHHHHH CS
                    TM1586_NiRdase  3 yeaiekRhsvRkYkdealeeelleelk 29
                                      ++ + +R+s R Y d+++e e++eel 
  gi|488601749|ref|YP_007908220.1|  8 KKVMMERRSHRFYLDKEVEREKIEELL 34
                                      6899******************99985 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 2.2e-11
                                       GS-HHHHHHHHHHHTS--GGG----EEE.E-SSEE.... CS
                    TM1586_NiRdase 155 elpewfkeileaarlAPsAlNqqpwrfelkdddeikika 193
                                         +e+++e+le+a+ APsA+N+q+w+f +++ +++k ++
  gi|488601749|ref|YP_007908220.1|  25 VEREKIEELLELAMWAPSAMNRQQWYFVVVSGEKLKELQ 63 
                                       4589************************99988777655 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 4.8e-10
                                       HHHHHHHHHTT-EEEEES--SST.............T-S-EEEEE-BS--- CS
                    TM1586_NiRdase  89 eqlvLkltalGlgtcWvggtykkkka..kvelkkgeklvivIalGyaktkl 137
                                       ++++L + a GlgtcW+ g  + +++   +   +g+klv+vI+lGy++++ 
  gi|488601749|ref|YP_007908220.1| 127 QNMLLAAHAMGLGTCWMTGPVHVEDEinSFLGVEGKKLVAVITLGYPAKTP 177
                                       789***************98877544113445689************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1062.06
//
Query:       gi|488601750|ref|YP_007908221.1|  [L=403]
Description: dihydroorotase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-14   51.6   0.0      2e-13   50.4   0.0    1.6  1  Amidohydro_1  Amidohydrolase family
    6.3e-07   29.2   0.0    1.8e-05   24.4   0.0    2.2  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   2.2e-17     2e-13       2     322 ..      42     368 ..      41     385 .. 0.71

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.2e-17
                                       EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH......HHHHHHHHHHT CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst......giealleaaee 72 
                                       +lP++ID+HvH++             + +e  +e++e+g   al +G+  v d ++t++       +++++  a ++
  gi|488601750|ref|YP_007908221.1|  42 ILPAGIDVHVHFR-------------DFDEREKETIETGSLSALYGGICLVVDQPNTRPVidnpetYFKRMEIAEKD 105
                                       89**********9.............99****************************976699888777776655555 PP

                                       SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEE CS
                      Amidohydro_1  73 lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpv 148
                                         +++ + ++   l++++a+  ++ ++++    +e+ +++a g v+  + +  e  +++ +++k +    ++  + +
  gi|488601750|ref|YP_007908221.1| 106 SYIDYFLNIA---LTNSNADRIIDYIKEI----EEKYRIPAIGEVFlQHDD--ENMQIGFDAIKTLR---DATSKLI 170
                                       5455555555...3335555555555555....555599998888833333..45666668998888...67799** PP

                                       EEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE..HH.........HHHHHHHHHHHHC CS
                      Amidohydro_1 149 aiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt..pt.........eaellkerlkeag 214
                                       ++Ha e+++ v    ++ g  +e   + e  e  ++ + +kl   h +h++  ++         ++e          
  gi|488601750|ref|YP_007908221.1| 171 TVHA-EQPELV----KGLG--HEL-RPPEA-EIKAVENCLKLGNFHFCHIStyDSamkisdsdsTFE---------- 228
                                       ****.888887....4444..233.23333.333445556788999999998644222222222223.......... PP

                                       EE....HHHHHHHHSEHHHHHHHHHHHHTSC...........EEEEEECT.......TSSCCGGHHHHHHHHHHHHH CS
                      Amidohydro_1 215 va....hcpfsnsilrsgrealrkaldeGvk...........vglgtDga.......asgnslnlleelrlalklqr 269
                                        +     +   +++ ++g +++++ l++ v             ++++D+a        +g+ +  + ++   +    
  gi|488601750|ref|YP_007908221.1| 229 -VaphhFILNYEDYFKPGFMNVNPPLRSKVEaelmfnslpvaDMIASDHAphtiedkKHGKPG--FPGVETTY---- 298
                                       .14665788999999999999999999999899999999999******999999998555555..34444444.... PP

                                       HCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC....CT.............C CS
                      Amidohydro_1 270 gllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl....di.............l 322
                                       +ll +  ++g +s+ +++++   n+A+++g++   G+ievG +A+l+v++l    +i             +
  gi|488601750|ref|YP_007908221.1| 299 PLLVSmMKKGLVSVRRVVDLIAVNPARIFGFE-GYGAIEVGNYANLAVFNLkrvrKIkaeklhtkaewtpY 368
                                       44444457999********************5.****************9976653355555555554444 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.7   0.0    0.0076        68       9      20 ..      41      52 ..      39      70 .. 0.87
   2 !   24.4   0.0     2e-09   1.8e-05     404     469 ..     306     383 ..     257     387 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0076
                      Amidohydro_3  9 lvlPGFvDsHtH 20
                                      l lP+++D+H H
  gi|488601750|ref|YP_007908221.1| 41 LILPAGIDVHVH 52
                                      789********* PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2e-09
                      Amidohydro_3 404 pdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear............vrltvv 467
                                        +  +s++ +++l+  +pA+++g e   G +evG +A+l+v++ +   ++++++l+++             ++ ++ 
  gi|488601750|ref|YP_007908221.1| 306 KKGLVSVRRVVDLIAVNPARIFGFEGY-GAIEVGNYANLAVFNlKRVRKIKAEKLHTKAewtpyenfeaifPERVYL 381
                                       56789*********************9.***************5555556666666554555555555555555555 PP

                      Amidohydro_3 468 dG 469
                                       +G
  gi|488601750|ref|YP_007908221.1| 382 KG 383
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2282.16
//
Query:       gi|488601751|ref|YP_007908222.1|  [L=364]
Description: cell division protein FtsZ [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-43  148.9   0.1    3.1e-43  148.3   0.1    1.3  1  Tubulin         Tubulin/FtsZ family, GTPase domain
    1.5e-37  127.8   0.7    3.4e-37  126.6   0.7    1.6  1  FtsZ_C          FtsZ family, C-terminal domain
     0.0082   16.1   0.1      0.021   14.7   0.1    1.7  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.051   11.9   0.4        1.2    7.4   0.0    2.0  2  PhageP22-tail   Salmonella phage P22 tail-spike
        4.3    6.4   9.8        7.8    5.6   3.4    2.6  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 !  148.3   0.1   8.7e-47   3.1e-43       2     196 ..      41     200 ..      40     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 8.7e-47
                                       EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE- CS
                           Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklll 78 
                                       i+vigvG++G++++++++e      gi             +g ++++    a++td q+l  +ka+      +++l+
  gi|488601751|ref|YP_007908222.1|  41 IKVIGVGGSGCNTVSRMFE-----TGI-------------EG-ADLY----AVNTDVQHLYYTKAH------KRILI 88 
                                       89*****************.....6**.............88.8888....9**************......***** PP

                                       -CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEE CS
                           Tubulin  79 gkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvv 155
                                       gk+ ++++gag+ p+vg+eaa+e++eei+k ve++d+   +fit +lgGGTG+G++pvi+e+ +e   +al+++vv+
  gi|488601751|ref|YP_007908222.1|  89 GKKRTRGLGAGSLPQVGEEAARENEEEIKKLVEGADL---VFITCGLGGGTGTGAAPVIAEASQEA--GALTIAVVT 160
                                       *************************************...**************************..********* PP

                                       E--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                           Tubulin 156 lPsefsevvvepynailalkelieesdavividNdaLlkil 196
                                       +P++  e+ ++ +na+ +l++l+e  d+vivi+Nd+Ll+++
  gi|488601751|ref|YP_007908222.1| 161 FPFSA-EGAIRRQNAEAGLERLREVTDTVIVIPNDRLLEVV 200
                                       ***99.*******************************9986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.7   9.4e-41   3.4e-37       1      94 [.     248     341 ..     248     342 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 9.4e-41
                                       EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE CS
                            FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavi 77 
                                       GvAm+g+Geasged+a+e++++a++spLL+vd+sgA+++lvn+tgg+d+t++E+e+v+e+i++++d++a++i+Ga++
  gi|488601751|ref|YP_007908222.1| 248 GVAMIGLGEASGEDKASESVRKALKSPLLEVDISGARSALVNVTGGPDMTIEEAESVVEEIYSKIDPDARIIWGAMV 324
                                       99*************************************************************************** PP

                                       -TT--SEEEEEEEEES- CS
                            FtsZ_C  78 deeledeirvtvvatgl 94 
                                       d+ le+++++ v++tg+
  gi|488601751|ref|YP_007908222.1| 325 DPALENTMQTLVIVTGV 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 !   14.7   0.1   5.9e-06     0.021      49      98 ..     111     161 ..     103     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.9e-06
                                       T-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEEE CS
                    NAD_binding_10  49 tdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvsa 98 
                                       +++e++++ ++gad V+++ g gg++ +g a  i++a +eag   + +v+ 
  gi|488601751|ref|YP_007908222.1| 111 ENEEEIKKLVEGADLVFITCGLGGGTGTGaAPVIAEASQEAGALTIAVVTF 161
                                       789*************99998777766663777778999999999999886 PP

>> PhageP22-tail  Salmonella phage P22 tail-spike
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1    0.0088        31     409     476 ..      74     142 ..      46     160 .. 0.82
   2 ?    7.4   0.0   0.00034       1.2     384     434 ..     280     331 ..     275     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0088
                                       EEEEESS--GGGEEEEEEEETTE-SEEEEESSSSEE.EEEEEETTT-SSS-SEEEEEEESSSTTSS-EE CS
                     PhageP22-tail 409 lsgivgnvdpdrilvanlleevlgnirinsfnsdsa.elklrihklsktldsgalrstlnggagsgsay 476
                                       +  +  +   +ril+++    +lg   +   + ++a e +  i+kl    d   +   l gg+g+g+a 
  gi|488601751|ref|YP_007908222.1|  74 VQHLYYTKAHKRILIGKKRTRGLGAGSLPQVGEEAArENEEEIKKLVEGADLVFITCGLGGGTGTGAAP 142
                                       555555566789999999999999999999999988346679************************984 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00034
                                       EEEEEE-SSSSTTSSSESEEEEEEEEEEEESS--GG.GEEEEEEEETTE-SE CS
                     PhageP22-tail 384 vnglrligikstdskgliidapnstlsgivgnvdpd.rilvanlleevlgni 434
                                       + g r + ++ t +  ++i+  +s +  i  ++dpd ri  + +++++l n+
  gi|488601751|ref|YP_007908222.1| 280 ISGARSALVNVTGGPDMTIEEAESVVEEIYSKIDPDaRIIWGAMVDPALENT 331
                                       67999999999************************879**********9987 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.5    0.0065        23       2      16 ..      43      57 ..      43      66 .. 0.91
   2 ?    5.6   3.4    0.0022       7.8     157     174 ..     125     142 ..      79     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0065
                         Tubulin_2  2 viGLGGtGgkvlael 16
                                      viG+GG+G+++++++
  gi|488601751|ref|YP_007908222.1| 43 VIGVGGSGCNTVSRM 57
                                      7***********998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0022
                         Tubulin_2 157 nvfVvgSLaGGTGSGifl 174
                                        vf+ ++L GGTG G + 
  gi|488601751|ref|YP_007908222.1| 125 LVFITCGLGGGTGTGAAP 142
                                       49************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2041.70
//
Query:       gi|488601752|ref|YP_007908223.1|  [L=210]
Description: putative metal-dependent phosphoesterases (PHP family) [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   49.1   0.1    1.1e-12   47.5   0.1    1.9  2  PHP_C     PHP-associated
    3.5e-10   40.5   0.0    5.1e-10   39.9   0.0    1.3  1  PHP       PHP domain
  ------ inclusion threshold ------
       0.14   11.4   0.0       0.23   10.7   0.0    1.3  1  IMPa_N_2  Immunomodulating metalloprotease N-terminal domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.75   4.5e+03       6      16 ..      47      57 ..      46      60 .. 0.85
   2 !   47.5   0.1   1.9e-16   1.1e-12       4      56 .]     140     191 ..     137     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.75
                             PHP_C  6 rArrfAeklgl 16
                                      +A++f e++gl
  gi|488601752|ref|YP_007908223.1| 47 KALEFVERNGL 57
                                      89999999997 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 1.9e-16
                             PHP_C   4 NrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegrt 56 
                                        ++A ++A+ +g+ +++GSDAH+++ +G ++T++++++ ++ +++eair+g+t
  gi|488601752|ref|YP_007908223.1| 140 TKKAVSLAKNHGKGFVAGSDAHSCRAIGYGVTVVKSKN-SVRSIIEAIRRGET 191
                                       589*******************************6654.59**********97 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   8.5e-14   5.1e-10       1     127 [.       5     158 ..       4     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 8.5e-14
                                       EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE........... CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                               PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse... 73 
                                       +lH+H+  s +  +++  e++v+ a+e++l+ ia+TDh+ l g +++ + + +++  +i+++ G+e++ ++++    
  gi|488601752|ref|YP_007908223.1|   5 ELHSHSCLSdGI-DTV--EDMVRCAIEKKLDVIAVTDHDSLEGSLKALEFV-ERNGLDITVLPGYELSAKEGHFliy 77 
                                       577777777555.566..************************999999888.555699********76666654666 PP

                                       .......................................E....EHHHHHHHHHHHHH..........HHHHHHS.. CS
                                       .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  74 .............................kerpshltllaknqeGyknllkllskaylegfyrkpridkellekhse 121
                                                                     +++   ++ ak + ++ + ++ +  + ++g  +k+    +l ++h +
  gi|488601752|ref|YP_007908223.1|  78 gderklevldkgtsirevdrnwlivmahpYQFYRSGVIRAKKYVEFVDAVEVFNSRTISGIFTKKA--VSLAKNHGK 152
                                       666666666666666655555555555554444444444444444333333333333333222221..444444666 PP

                                       ...... CS
                                       xxxxxx RF
                               PHP 122 gLivls 127
                                       g++++s
  gi|488601752|ref|YP_007908223.1| 153 GFVAGS 158
                                       666655 PP

>> IMPa_N_2  Immunomodulating metalloprotease N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.9e-05      0.23      19      63 ..     132     175 ..     124     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
                                       ---EEESSTTTEEEEEE-TTS-EEEEEE-GGG--EEEESS-GGGS CS
                          IMPa_N_2  19 SqliqlaeadsalplitgdkGrvlaalsekqggRalAyGtdilas 63 
                                       S++i+    ++a++ +  ++G++++a s+++  Ra++yG  ++ s
  gi|488601752|ref|YP_007908223.1| 132 SRTISGIFTKKAVS-LAKNHGKGFVAGSDAHSCRAIGYGVTVVKS 175
                                       55555555555554.578**********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1218.21
//
Query:       gi|488601753|ref|YP_007908224.1|  [L=482]
Description: dihydropteroate synthase-related protein [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   40.9   0.1    6.5e-10   39.1   0.0    2.0  2  DUF4346      Domain of unknown function (DUF4346)
    5.7e-05   22.9   0.1    9.6e-05   22.2   0.1    1.3  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.55     5e+03      57      74 ..     337     354 ..     326     379 .. 0.54
   2 !   39.1   0.0   7.2e-14   6.5e-10      65     118 .]     417     467 ..     386     467 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.55
                           DUF4346  57 kgkkkreaekvyrgrtak 74 
                                       +g+ ++ + + y +++ak
  gi|488601753|ref|YP_007908224.1| 337 TGSIRELKIASYMAKAAK 354
                                       444444444444444444 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 7.2e-14
                           DUF4346  65 ekvyrgrtakelcvkileeeeelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                       ++v  grtake+  + +       +++ldha YlGRel +ae+aL+ gk+Y qD
  gi|488601753|ref|YP_007908224.1| 417 RAVIVGRTAKEIYDAAVK---MGLLSRLDHACYLGRELAKAEIALKLGKNYTQD 467
                                       567889****98766554...3679****************************9 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   1.1e-08   9.6e-05      30     121 ..     162     241 ..     149     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-08
                                       HHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEEEEETTTTSSS CS
                       Pterin_bind  30 mveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadivNdvsgeerd 106
                                         ee Adi+D+g           ++ ee+er v++ ++++   ++p+siDt++ + +eaA+++  d+v ++s ++  
  gi|488601753|ref|YP_007908224.1| 162 YYEEHADIIDLGIPLD-------EKPEEVERTVEFAKKIT---RLPLSIDTFDERLIEAAINKRIDMVMSISSKN-- 226
                                       5677899999999877.......8999********99554...67***************************999.. PP

                                       TTHHHHHHHHT-EEE CS
                       Pterin_bind 107 pkmlelvaeagaavv 121
                                          l  + +  + vv
  gi|488601753|ref|YP_007908224.1| 227 LSALDYIDDQAVVVV 241
                                       555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2756.69
//
Query:       gi|488601754|ref|YP_007908225.1|  [L=272]
Description: methylenetetrahydromethanopterin dehydrogenase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-133  443.7   7.3   2.6e-133  443.5   7.3    1.0  1  MTD          methylene-5,6,7,8-tetrahydromethanopterin dehydr
  ------ inclusion threshold ------
      0.038   14.0   0.0       0.27   11.3   0.0    2.2  2  DUF218       DUF218 domain
       0.09   12.8   0.0       0.19   11.8   0.0    1.6  1  B12-binding  B12 binding domain
       0.12   12.1   0.1          2    8.1   0.0    2.4  3  Redoxin      Redoxin


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 !  443.5   7.3  5.8e-137  2.6e-133       1     273 [.       2     271 ..       2     272 .] 1.00

  Alignments for each domain:
  == domain 1  score: 443.5 bits;  conditional E-value: 5.8e-137
                                       EEEEEEEES--HHHHHTTGGGSTTS--SSEEEEEEEEET--SHHHHHHHHHHHHHH--SEEEEE-S-TTSHHHHHHH CS
                               MTD   1 vkigiiklGnigtslvidlllDeradRedievrvvgsgaklkkeeveevveklkefdpdlvivisPnaaapgptkar 77 
                                       vk+g++k+G+igt+l++++llDeradRedi+vrvv+sgak+++ee+e +vek+kefdpdlviv+sPnaa+pgp++ar
  gi|488601754|ref|YP_007908225.1|   2 VKVGVVKMGAIGTALLVEYLLDERADREDITVRVVTSGAKMQPEEAE-IVEKMKEFDPDLVIVVSPNAALPGPKAAR 77 
                                       79********************************************9.9**************************** PP

                                       HHHHHSSS-EEEEEEGGGGGGHHHHHHTT-EEEEETTS------TTT--HHHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                               MTD  78 ellsekdvpaivisDapgkkekdeleeeglGYiivkaDpliGarrefLDptemalfnadvlkvLaatGavRlvqeel 154
                                       e++  +++p+ivisDap+kk+k+e+ee+g+GYi+v+aD++iGarrefLDptemalfn+dv+kvLaatGa+Rlvqee+
  gi|488601754|ref|YP_007908225.1|  78 EAF--EGKPVIVISDAPAKKAKEEFEEKGFGYILVNADSMIGARREFLDPTEMALFNSDVVKVLAATGAFRLVQEEI 152
                                       ***..9*********************************************************************** PP

                                       HHHHHHHTTT-GGGS-EEEESGGGGGGSS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT---HHHHHHHHHHHHHH CS
                               MTD 155 dkviekvkagkeielPkividaekaveaaefsnPYakakalaayeiaekvadidvkaCfmekelekyilivasahel 231
                                       dkvie++k+gk++elPkiv++aekav+a +f+nPYakaka+aay+iaekvadidvk+Cf+e++ ekyi++va+ahe+
  gi|488601754|ref|YP_007908225.1| 153 DKVIEALKEGKTPELPKIVVTAEKAVKAGNFKNPYAKAKAMAAYYIAEKVADIDVKGCFIERDPEKYIPLVAAAHEM 229
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHTT---B--B-TTSSB--BSSTTS-- CS
                               MTD 232 lraaakLadeaReieksndtvlRkphakdGkvlsktkllekP 273
                                       +r+aa  ad aReiek+ d+v+R+phakdGk+lskt+l+ekP
  gi|488601754|ref|YP_007908225.1| 230 MRVAAIEADRAREIEKGGDSVYRNPHAKDGKILSKTSLMEKP 271
                                       *****************************************9 PP

>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.3   1.4e+03      28      47 ..      34      51 ..      14      70 .. 0.65
   2 ?   11.3   0.0     6e-05      0.27       2      56 ..     135     203 ..     134     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.3
                            DUF218 28 kiivsGggadedvseaeama 47
                                      ++++sG +   +++eae+++
  gi|488601754|ref|YP_007908225.1| 34 RVVTSGAK--MQPEEAEIVE 51
                                      46777752..3555666544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6e-05
                            DUF218   2 aivVLGaal..pllaeRldeaaelyrag......kiivsGg......gadedvseaeamaeylrelgvp 56 
                                       ++ VL a+   +l +e +d+ +e +++g      ki+v+        + ++++ +a+ama+y ++  v 
  gi|488601754|ref|YP_007908225.1| 135 VVKVLAATGafRLVQEEIDKVIEALKEGktpelpKIVVTAEkavkagNFKNPYAKAKAMAAYYIAEKVA 203
                                       6667763334688999************88776559999777888776669************999887 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   4.2e-05      0.19      29      74 ..      33      79 ..       6     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.2e-05
                       B12-binding 29 feVqllganven..edivaairaekpdvvglSalltsqleavkelvel 74
                                      ++V+  ga+ ++  ++iv+++++++pd+v + + +++ l++ k+  e+
  gi|488601754|ref|YP_007908225.1| 33 VRVVTSGAKMQPeeAEIVEKMKEFDPDLVIVVS-PNAALPGPKAAREA 79
                                      35666677777788**************98866.77777776666665 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00044         2      48      96 ..      42      94 ..      35      99 .. 0.84
   2 ?    1.7   0.0     0.043   1.9e+02      52      72 ..      94     114 ..      93     123 .. 0.89
   3 ?   -1.5   0.0      0.42   1.9e+03      63      96 ..     133     178 ..     113     220 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00044
                                      HH.HHHTHHHHHHCSTTTEEEEEESSSHH..HHHHHHH.TT-TSEEEE-TTSH CS
                           Redoxin 48 hp.yleklaellkekgvdvvavvadndaf..vkefwgk.eglkfpvlsDgsaa 96
                                      +  +++++ e+ ke + d v+vv+ n a+   k++ ++ eg++++v+sD+ a+
  gi|488601754|ref|YP_007908225.1| 42 MQpEEAEIVEKMKEFDPDLVIVVSPNAALpgPKAAREAfEGKPVIVISDAPAK 94
                                      555888999999*****************8777777779999*******7665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.043
                                       HTHHHHHHCSTTTEEEEEESS CS
                           Redoxin  52 eklaellkekgvdvvavvadn 72 
                                       +k +e+++ekg+  + v+ad+
  gi|488601754|ref|YP_007908225.1|  94 KKAKEEFEEKGFGYILVNADS 114
                                       578999************997 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.42
                                       TTEEEEEESSSHH..HHHHHHH..........TT-TSEEEE-TTSH CS
                           Redoxin  63 vdvvavvadndaf..vkefwgk..........eglkfpvlsDgsaa 96 
                                        dvv v a++ af  v+e ++k           +l+ +v++ ++a 
  gi|488601754|ref|YP_007908225.1| 133 SDVVKVLAATGAFrlVQEEIDKviealkegktPELPKIVVTAEKAV 178
                                       5566666666666664444444443343355533333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1513.07
//
Query:       gi|488601755|ref|YP_007908226.1|  [L=120]
Description: hypothetical protein Asulf_02281 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   81.0   0.5    5.4e-23   80.7   0.5    1.1  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    0.00065   19.0   0.3     0.0034   16.8   0.3    2.0  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
     0.0049   17.2   1.0       0.02   15.2   0.7    1.9  2  C1_2             C1 domain
  ------ inclusion threshold ------
      0.014   15.2   2.2      0.028   14.3   2.2    1.4  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.048   14.0   0.1      0.063   13.6   0.1    1.2  1  zf-C2H2_8        C2H2-type zinc ribbon
        0.2   12.5   4.1       0.34   11.7   4.1    1.4  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
       0.28   11.2   3.2       0.63   10.1   0.9    2.4  2  ADD_DNMT3        Cysteine rich ADD domain in DNMT3
       0.98    9.2   4.1         12    5.7   0.4    2.4  2  zf-C2H2_11       zinc-finger C2H2-type


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 !   80.7   0.5   2.4e-26   5.4e-23       1      68 [.       8      74 ..       8      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 2.4e-26
                    OrfB_Zn_ribbon  1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilk 68
                                      fr +  +l+  a+++Gikv++vn+ayTS++C  Cgskn + +++r+fkC nCg++a+rD+++++Ni++
  gi|488601755|ref|YP_007908226.1|  8 FRYVVDRLKITAENFGIKVKLVNEAYTSSRCLWCGSKNVK-KHKRLFKCLNCGVKAHRDIVGVLNIAR 74
                                      788999**********************************.*************************97 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.19   4.2e+02      28      40 ..      30      42 ..      18      45 .. 0.71
   2 !   16.8   0.3   1.5e-06    0.0034      27      48 ..      46      67 ..      30      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.19
                       Vps36-NZF-N 28 nastplPpClaCG 40
                                      n+  +   Cl CG
  gi|488601755|ref|YP_007908226.1| 30 NEAYTSSRCLWCG 42
                                      5556667899999 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.5e-06
                       Vps36-NZF-N 27 pnastplPpClaCGvkpdleli 48
                                      +++++ l +Cl+CGvk+ ++++
  gi|488601755|ref|YP_007908226.1| 46 VKKHKRLFKCLNCGVKAHRDIV 67
                                      36799999***********997 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.7   8.8e-06      0.02      13      44 ..      30      64 ..      21      65 .. 0.81
   2 ?   -0.3   0.0      0.63   1.4e+03       5      11 ..      86      95 ..      84     103 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.8e-06
                              C1_2 13 edssesfnCsaCgrk..idgff..YsCseCdfslhv 44
                                      ++ + s +C +Cg k    + +  ++C  C ++ h 
  gi|488601755|ref|YP_007908226.1| 30 NEAYTSSRCLWCGSKnvK-KHKrlFKCLNCGVKAHR 64
                                      5678899********953.44459*******99995 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.63
                              C1_2  5 HpLtls...k 11
                                      HpL l     
  gi|488601755|ref|YP_007908226.1| 86 HPLFLRvddA 95
                                      9999995432 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   2.2   1.2e-05     0.028       9      40 ..      33      64 ..      25      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                      SS--B-TTT-SB--SSSS-EEEETTT--EE-C CS
                              C1_1  9 kqptfCkhCgeflwgkekqglkCswCkllvHk 40
                                      + +++C  Cg+   +k k+ +kC +C++++H 
  gi|488601755|ref|YP_007908226.1| 33 YTSSRCLWCGSKNVKKHKRLFKCLNCGVKAHR 64
                                      67899*******989****************7 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.8e-05     0.063      34      86 ..      20      70 ..       8      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                         zf-C2H2_8 34 klfrcstascaetfpsmqelvahtklhykpnryfkcencllrfrthrslfkhl 86
                                        f    + + e++ s + l + +k   k +r fkc nc +  ++hr +   l
  gi|488601755|ref|YP_007908226.1| 20 ENFGIKVKLVNEAYTSSRCLWCGSKNVKKHKRLFKCLNCGV--KAHRDIVGVL 70
                                      566677777899***************************76..5777766555 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   4.1   0.00015      0.34       2      24 ..      37      60 ..      36      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                   Tnp_zf-ribbon_2  2 RCkvClkkkikkeTr.iiCqeCdv 24
                                      RC++C +k++kk  r + C  C+v
  gi|488601755|ref|YP_007908226.1| 37 RCLWCGSKNVKKHKRlFKCLNCGV 60
                                      9******99999755256888875 PP

>> ADD_DNMT3  Cysteine rich ADD domain in DNMT3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.9   0.00028      0.63      18      43 ..      36      58 ..      23      64 .. 0.83
   2 ?    0.4   0.1       0.3   6.8e+02      30      35 ..      84      89 ..      79      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00028
                         ADD_DNMT3 18 diClsCGslevetqHPLFeGglClkC 43
                                        Cl CGs++v+    LF+   Cl+C
  gi|488601755|ref|YP_007908226.1| 36 SRCLWCGSKNVKKHKRLFK---CLNC 58
                                      57****************9...6666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.3
                         ADD_DNMT3 30 tqHPLF 35
                                      + HPLF
  gi|488601755|ref|YP_007908226.1| 84 LAHPLF 89
                                      68***9 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 ?    4.4   0.2     0.014        32       3      12 ..      34      43 ..      33      44 .. 0.84
   2 ?    5.7   0.4    0.0056        12       5      13 ..      53      61 ..      52      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
                        zf-C2H2_11  3 stcqCleCGl 12
                                      ++ +Cl CG 
  gi|488601755|ref|YP_007908226.1| 34 TSSRCLWCGS 43
                                      689*****96 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0056
                        zf-C2H2_11  5 cqCleCGlc 13
                                      ++Cl CG++
  gi|488601755|ref|YP_007908226.1| 53 FKCLNCGVK 61
                                      59*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 655.91
//
Query:       gi|488601756|ref|YP_007908227.1|  [L=162]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   38.9   2.0    1.8e-09   38.1   2.0    1.4  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.014   15.6   0.5        1.4    9.3   0.1    2.5  2  PIN_4     PIN domain
      0.016   14.7   1.8        1.3    8.4   0.0    2.2  2  PIN_5     PINc domain ribonuclease
      0.019   14.9   0.0      0.038   13.9   0.0    1.5  1  SCAB-ABD  Actin-binding domain of plant-specific actin-bindin
       0.04   14.2   0.5       0.15   12.4   0.3    2.0  2  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 !   38.1   2.0   5.1e-13   1.8e-09       1     120 [.       4     137 ..       4     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.1e-13
                                       EEE-HHHHHHHH.............TTSHHHHHHHHHHHTS......SEEEEEHHHHHHHHHHHHSSCHCHHHHHHH CS
                               PIN   1 ivlDTsvliall.............rgeekaeaarklleel......eelvtsalvlaEllyvlarrkskrekaael 58 
                                       +v+DTsv+++ +             r+ e ++++r+++  l       +++++++ + E+++v +r    ++++ + 
  gi|488601756|ref|YP_007908227.1|   4 VVFDTSVIVKSIfkpmkslsneiykRELETHKKCREIIRMLeevdadVDVYIPKICIVETAAVTKR---LSGRDLAM 77 
                                       689******9999************8888888888888777888**********************...66777777 PP

                                       HHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  59 velllllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       + ++ +l++ ++++  a ++  a++ia   g++ +D + +A+A+  ++ li t D  ++  a
  gi|488601756|ref|YP_007908227.1|  78 KISKAILDSYEVVD-EAVLFNSAWKIAIDTGCSGFDSYFIALARIKNAVLI-TDDAGMHSHA 137
                                       78888999******.*********************************999.***9887655 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00042       1.5       2      58 ..       5      87 ..       4     113 .. 0.71
   2 ?    9.3   0.1   0.00038       1.4      14     125 ..      43     142 ..      28     148 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00042
                             PIN_4  2 VlDTnvlLhdp.ealksf.........................keehdvviPitVleELdklKkgsserelarlarqan 54
                                      V+DT+v+ +++ + +ks+                         + + dv+iP + + E  ++ k+ s r+la ++++a+
  gi|488601756|ref|YP_007908227.1|  5 VFDTSVIVKSIfKPMKSLsneiykrelethkkcreiirmleevDADVDVYIPKICIVETAAVTKRLSGRDLAMKISKAI 83
                                      677777776651223333666777777777777777777777799****************999999888888888776 PP

                             PIN_4 55 rlld 58
                                         +
  gi|488601756|ref|YP_007908227.1| 84 LDSY 87
                                      4444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00038
                             PIN_4  14 alksfkeehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsaeelpee.eseseknDn 89 
                                       +l++++ + dv+iP + + E  ++ k+ s                           ++ +a ++++      e  D+
  gi|488601756|ref|YP_007908227.1|  43 MLEEVDADVDVYIPKICIVETAAVTKRLS---------------------------GRDLAMKISKAiLDSYEVVDE 92 
                                       33333444444444444444444444444...........................444444444332211233333 PP

                             PIN_4  90 rIl.avalelkeekp.............drkvvLvskDinlrikAkalgi 125
                                       ++l + a +++  +               ++ vL+++D  +   Ak  ++
  gi|488601756|ref|YP_007908227.1|  93 AVLfNSAWKIAIDTGcsgfdsyfialarIKNAVLITDDAGMHSHAKEVEV 142
                                       33322233333222255555555555555666666666666666666665 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4    0.0021       7.6       3      62 ..       5      70 ..       3      98 .. 0.61
   2 ?    8.4   0.0   0.00037       1.3     163     193 ..     116     146 ..     103     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0021
                             PIN_5  3 vlDTsaltdp......evreklgeeeleeavkklldliae.arlklgiscyippsvykElkeflkre 62
                                      v DTs+++++      ++ +++ ++el e+ kk  ++i+   +++ ++++yip+    E   ++kr 
  gi|488601756|ref|YP_007908227.1|  5 VFDTSVIVKSifkpmkSLSNEIYKREL-ETHKKCREIIRMlEEVDADVDVYIPKICIVETAAVTKRL 70
                                      778888776422111134444545555.444444455443234667889****99888887776654 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00037
                             PIN_5 163 llLAkELdaavvssDeGikkwaeklGlrlve 193
                                       + LA+  +a+++++D+G+++ a+++ ++ v 
  gi|488601756|ref|YP_007908227.1| 116 IALARIKNAVLITDDAGMHSHAKEVEVNSVL 146
                                       67899999****************9998764 PP

>> SCAB-ABD  Actin-binding domain of plant-specific actin-binding 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     0.038      16      31 ..      67      82 ..      62      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                          SCAB-ABD 16 hkRLSVRDLasKFekg 31
                                       kRLS RDLa+K  k 
  gi|488601756|ref|YP_007908227.1| 67 TKRLSGRDLAMKISKA 82
                                      59**********8875 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.54   1.9e+03      31      65 ..       9      43 ..       4      52 .. 0.60
   2 ?   12.4   0.3   4.1e-05      0.15      18     115 ..      40     149 ..      31     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.54
                             PIN_9 31 lvvpkavleELerlakagkgkertaakvalsLaer 65
                                       v+ k++++ +++l+++  ++e +  k  +++ + 
  gi|488601756|ref|YP_007908227.1|  9 SVIVKSIFKPMKSLSNEIYKRELETHKKCREIIRM 43
                                      56777777777777776666665555555555544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.1e-05
                             PIN_9  18 ifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveae..............eekaDdai 80 
                                       i+  le++  +v++ +pk  + E ++++k+ +g++  a+k+++++ + +e+v+                 +  D   
  gi|488601756|ref|YP_007908227.1|  40 IIRMLEEVDADVDVYIPKICIVETAAVTKRLSGRD-LAMKISKAILDSYEVVDEAvlfnsawkiaidtgCSGFDSYF 115
                                       55556666678999*************99988876.799*************99999999999998876667899** PP

                             PIN_9  81 lelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                       ++la+  + avl+T D+++  +++e +++ +l+R+
  gi|488601756|ref|YP_007908227.1| 116 IALARIKN-AVLITDDAGMHSHAKEVEVNSVLVRE 149
                                       ****9666.7777************9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.39s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 876.12
//
Query:       gi|488601757|ref|YP_007908228.1|  [L=64]
Description: hypothetical protein Asulf_02283 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-13   48.9   2.4    7.9e-13   48.6   2.4    1.2  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 !   48.6   2.4   4.4e-17   7.9e-13       5      53 ..       3      52 ..       1      58 [. 0.81

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 4.4e-17
                            DUF104  5 IeavYEnGvLKPLekvdLkEGeevkikIee.akeilkklkgilkeadeee 53
                                      ++a+YEnGvLK ++k+dL+E++ev ++I+   +++l++l +i  ++d ++
  gi|488601757|ref|YP_007908228.1|  3 VKAIYENGVLKLMKKLDLPEKTEVSVIIKGsFSKLLDELGEIEAKEDVNT 52
                                      89****************************77777777766555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.55
# Mc/sec: 348.77
//
Query:       gi|488601758|ref|YP_007908229.1|  [L=309]
Description: L-threonine O-3-phosphate decarboxylase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-32  110.9   0.0      1e-31  110.5   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
       0.22    9.6   0.0       0.53    8.4   0.0    1.5  2  RHD3           Root hair defective 3 GTP-binding protein (RHD


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 !  110.5   0.0   1.1e-35     1e-31      48     357 ..      44     298 ..      11     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1.1e-35
                                       HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEE CS
                     Aminotran_1_2  48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplys 124
                                        le++l ++++            v v+ Ga+++i ++   + l   + +++p+pty++y++i+r  g+ vv++pl+ 
  gi|488601758|ref|YP_007908229.1|  44 HLEQKLSELVK----------NDVSVTAGATEAIYLIGIHF-LRELESVVIPKPTYSEYERIARFFGCRVVEVPLS- 108
                                       45555555555..........479***************99.99******************************55. PP

                                       TTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTH CS
                     Aminotran_1_2 125 eedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldav 201
                                             +le++ + l++    +     i++++p+NPtG  ++++el+ l+d ++  + + f+Dea+ +fv g     
  gi|488601758|ref|YP_007908229.1| 109 ------NLESIGDRLSS----S---SAIFFCNPNNPTGRYYSPKELKPLVDAVEDSRSIMFLDEAFMDFVEG----- 167
                                       ......99999999997....3...48*********************************************..... PP

                                       HHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 202 atranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemr 278
                                         +  v+ e n++  +++ K++Gl+G+RvGy++  ++v+++      p+ + s++ a++ + ++d+     +l+++ 
  gi|488601758|ref|YP_007908229.1| 168 --YRSVDSE-NVVKIRTFTKSYGLPGIRVGYVINFEEVKEY----RMPWSIGSVGYAFLEKLIEDKFS---FLKQSM 234
                                       ..7788876.77*********************98888776....55655669999999999988775...9***** PP

                                       HHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHH CS
                     Aminotran_1_2 279 qrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglteee 355
                                        +++++ +++ ++L       ++ ++++fl+    a        + l+ +g+yv+ ++sf++ g++R+++    +ee
  gi|488601758|ref|YP_007908229.1| 235 PKIWREKRKFESKL------GVKGDANFFLMYMPGAV-------EFLKSKGIYVRDCSSFGLDGHIRFSI--RLPEE 296
                                       **************......45667888888777666.......456666********************..55555 PP

                                       HH CS
                     Aminotran_1_2 356 le 357
                                       ++
  gi|488601758|ref|YP_007908229.1| 297 ND 298
                                       55 PP

>> RHD3  Root hair defective 3 GTP-binding protein (RHD3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.1   9.4e+02     350     400 ..      41      91 ..      12     102 .. 0.57
   2 ?    8.4   0.0   5.9e-05      0.53     519     545 ..     220     246 ..     211     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.1
                                       HHHHHHHHHH.HCT.TTTHHHHHHHHHHHHHHHHHHHH.HTTSTTTTS--. CS
                              RHD3 350 llekfkeavekalkagedFaesvkekkkklvekfdeeaeslvveqakwdas 400
                                        +e++++++++ +k++ + +  ++e +  +  +f +e es+v+++ +++++
  gi|488601758|ref|YP_007908229.1|  41 YWEHLEQKLSELVKNDVSVTAGATEAIYLIGIHFLRELESVVIPKPTYSEY 91 
                                       345555555555555555555555555555555555555555555555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 5.9e-05
                                       HHHHHHHHTBBSSTBB----SHHHHCC CS
                              RHD3 519 rdrFedvFryDedgvPrlwkkkediea 545
                                        +  ed+F++ ++++P++w++k + e 
  gi|488601758|ref|YP_007908229.1| 220 EKLIEDKFSFLKQSMPKIWREKRKFES 246
                                       56679****************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1762.19
//
Query:       gi|488601759|ref|YP_007908230.1|  [L=333]
Description: NaMN:DMB phosphoribosyltransferase [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   15.3   0.0      0.014   14.7   0.0    1.3  1  DBI_PRT   Phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.6e-07     0.014     139     235 ..     118     214 ..      77     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-07
                                       HHHHHHHHHHCTTECEEEEEEE-TTCHHHHHHHHHHHHT--HHHH---TTT--HHHHHHHHHHHHHHHHCH....-. CS
                           DBI_PRT 139 aGieladeladagadllalGemGigNttaaaallaallglepeevvGrGtglddeglarKiavieqalarh....a. 210
                                        ++    ++ ++ +d l++Ge   g tt+a a+l al  +  +  +       ++  + K +vi++ ++r       
  gi|488601759|ref|YP_007908230.1| 118 NARMFG-QELRKFVDELVIGESTPGGTTTAQAVLWALGYRAKTSSA-----SPSNPHQLKEEVIKEGFRRIdadiGc 188
                                       444333.444667899*****************9998776555444.....34566677778888888887543313 PP

                                       .TT.HHHHHHHHS-HHHHHHHHHHHH CS
                           DBI_PRT 211 .ekdplevLakvGGleiaalaGailg 235
                                        +++p ++L+++G   +a++aG++lg
  gi|488601759|ref|YP_007908230.1| 189 fADEPYKALQEFGDPMLATVAGICLG 214
                                       2459********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1806.29
//
Query:       gi|488601760|ref|YP_007908231.1|  [L=63]
Description: hypothetical protein Asulf_02286 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   43.7  24.5    8.7e-07   28.5   5.2    2.5  3  Fer4      4Fe-4S binding domain
    1.1e-10   41.5  15.2    1.6e-10   41.0  15.2    1.2  1  Fer4_10   4Fe-4S dicluster domain
    4.2e-09   36.9  14.1    6.5e-09   36.3  14.1    1.4  1  Fer4_7    4Fe-4S dicluster domain
    2.3e-08   34.1  13.1    3.3e-08   33.6  13.1    1.3  1  Fer4_9    4Fe-4S dicluster domain
      5e-08   32.7  22.4    6.3e-08   32.4   3.7    2.6  3  Fer4_6    4Fe-4S binding domain
      5e-07   29.8  15.9    8.8e-07   29.0  15.9    1.4  1  Fer4_21   4Fe-4S dicluster domain
    6.9e-07   29.0  24.5      4e-06   26.6   3.1    2.5  3  Fer4_2    4Fe-4S binding domain
    6.8e-06   26.9  16.4      0.001   20.0   0.6    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    3.7e-05   24.2  21.4     0.0014   19.1  21.4    2.2  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    6.4e-05   23.3  13.4     0.0079   16.6   3.1    2.1  2  Fer4_8    4Fe-4S dicluster domain
    9.7e-05   23.0  18.2     0.0063   17.2  18.2    2.2  1  Fer4_15   4Fe-4S single cluster domain
    0.00065   20.0   2.1    0.00065   20.0   2.1    2.7  3  Fer4_4    4Fe-4S binding domain
     0.0015   19.0  17.4      0.086   13.4   6.3    2.1  2  Fer4_17   4Fe-4S dicluster domain
     0.0018   19.1  25.7     0.0096   16.8   4.3    2.6  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.029   14.5  18.2      0.097   12.9   7.5    2.2  2  Fer4_18   4Fe-4S dicluster domain
      0.037   14.9   1.6      0.037   14.9   1.6    2.1  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   5.2   7.8e-10   8.7e-07       1      20 [.       4      23 ..       4      27 .. 0.91
   2 !   25.3   6.9   7.9e-09   8.8e-06       2      24 .]      36      58 ..      35      58 .. 0.93
   3 ?   -2.3   0.1       4.2   4.7e+03      15      18 ..      59      62 ..      59      63 .] 0.60

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 7.8e-10
                                      EEEETTTSSS-THHHHHSTT CS
                              Fer4  1 vvideekCigCGaCvevCPv 20
                                      +v+d+e C gCG+C++vCP 
  gi|488601760|ref|YP_007908231.1|  4 IVVDKETCDGCGECISVCPE 23
                                      69*****************7 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 7.9e-09
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       +++++C  C  CvevCP+g It
  gi|488601760|ref|YP_007908231.1| 36 PVNMDDCSECCSCVEVCPTGSIT 58
                                      599*****************996 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.2
                                      HHHS CS
                              Fer4 15 vevC 18
                                      v++C
  gi|488601760|ref|YP_007908231.1| 59 VDAC 62
                                      5666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0  15.2   1.4e-13   1.6e-10       2      56 .]       4      53 ..       3      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.4e-13
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v+d++tC +Cg+C ++CP      ++++++++++ + +++++C +c +Cve+CP
  gi|488601760|ref|YP_007908231.1|  4 IVVDKETCDGCGECISVCPE-----SVYEFDDDGKSEPVNMDDCSECCSCVEVCP 53
                                      799*****************.....*****************************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 !   36.3  14.1   5.8e-12   6.5e-09       1      51 [.      10      55 ..       6      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5.8e-12
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                      +C gCg C ++Cp ++ e+d++      ++  +++++C+ C +Cv+vCPtg
  gi|488601760|ref|YP_007908231.1| 10 TCDGCGECISVCPESVYEFDDDG-----KSEPVNMDDCSECCSCVEVCPTG 55
                                      6******************9983.....445699****************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 !   33.6  13.1     3e-11   3.3e-08       2      50 ..      11      56 ..      10      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3e-11
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      C gCg+C+++Cp  v++ d+ ++   ++++   +C +C +Cve+Cp+g 
  gi|488601760|ref|YP_007908231.1| 11 CDGCGECISVCPESVYEFDDDGKSEPVNMD---DCSECCSCVEVCPTGS 56
                                      **********************99999886...7************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 !   32.4   3.7   5.7e-11   6.3e-08       2      23 ..       4      25 ..       3      26 .. 0.93
   2 !    9.3   7.2    0.0011       1.2       4      24 .]      37      57 ..      37      57 .. 0.84
   3 ?   -2.7   0.1       6.9   7.8e+03      17      19 ..      60      62 ..      59      63 .] 0.52

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5.7e-11
                            Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                      +++d++ C+gCg+C++vCPe +
  gi|488601760|ref|YP_007908231.1|  4 IVVDKETCDGCGECISVCPESV 25
                                      79*****************987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      ++ d C  C  Cv vCP+g i
  gi|488601760|ref|YP_007908231.1| 37 VNMDDCSECCSCVEVCPTGSI 57
                                      57788999999*******965 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.9
                            Fer4_6 17 rvC 19
                                      ++C
  gi|488601760|ref|YP_007908231.1| 60 DAC 62
                                      455 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0  15.9   7.9e-10   8.8e-07       2      58 ..       5      58 ..       2      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.9e-10
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      ++d+++C gCg+C+ +C+++ ++  + d  +  +v  d+C  C  C++vCP+ + i+
  gi|488601760|ref|YP_007908231.1|  5 VVDKETCDGCGECISVCPESVYE-FDDD-GKSEPVNMDDCSECCSCVEVCPT-GSIT 58
                                      589***************85444.3333.3556999***************6.8887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   3.1   3.6e-09     4e-06       3      22 .]       4      23 ..       2      23 .. 0.92
   2 !   12.0   9.4   0.00016      0.18       5      22 .]      37      54 ..      36      54 .. 0.93
   3 ?   -3.0   0.1       9.6   1.1e+04      18      20 ..      60      62 ..      59      62 .. 0.52

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.6e-09
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +vvd ++C gCg C+s+CP+
  gi|488601760|ref|YP_007908231.1|  4 IVVDKETCDGCGECISVCPE 23
                                      89*****************5 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                      v+ d C +C +Cv +CP+
  gi|488601760|ref|YP_007908231.1| 37 VNMDDCSECCSCVEVCPT 54
                                      68899************7 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.6
                            Fer4_2 18 saC 20
                                      +aC
  gi|488601760|ref|YP_007908231.1| 60 DAC 62
                                      556 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 !   20.0   0.6   8.9e-07     0.001       1      21 [.      10      30 ..      10      39 .. 0.82
   2 !   11.9   9.2    0.0003      0.33       2      20 ..      42      60 ..      41      63 .] 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.9e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                      +C +Cg+C++vCP+++ + + 
  gi|488601760|ref|YP_007908231.1| 10 TCDGCGECISVCPESVYEFDD 30
                                      5*************9987764 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0003
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C +C  C+evCPt+ i+ +
  gi|488601760|ref|YP_007908231.1| 42 CSECCSCVEVCPTGSITVD 60
                                      ****************976 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  21.4   1.3e-06    0.0014       1      58 []       6      59 ..       6      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                           Fer4_13  1 VDrdtCiacgaCvelaPd.vFeeddeggasvvaeqptseeekadaeeAadaCPvesIgv 58
                                      VD++tC +cg C +++P+ v+e dd+ g+s    +p++ ++ +++ + ++ CP+ sI+v
  gi|488601760|ref|YP_007908231.1|  6 VDKETCDGCGECISVCPEsVYEFDDD-GKS----EPVNMDDCSECCSCVEVCPTGSITV 59
                                      9****************868999998.554....7999999999*************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 !   12.5   2.7   0.00014      0.15      49      65 .]       9      25 ..       6      25 .. 0.86
   2 !   16.6   3.1     7e-06    0.0079      45      64 ..      36      55 ..      26      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                            Fer4_8 49 wsCttcgaCtevCpvgi 65
                                      ++C +cg+C +vCp+++
  gi|488601760|ref|YP_007908231.1|  9 ETCDGCGECISVCPESV 25
                                      57999999999999975 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7e-06
                            Fer4_8 45 eealwsCttcgaCtevCpvg 64
                                        +++ C++c +C+evCp+g
  gi|488601760|ref|YP_007908231.1| 36 PVNMDDCSECCSCVEVCPTG 55
                                      45799*************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 !   17.2  18.2   5.6e-06    0.0063       1      66 []       4      59 ..       4      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.6e-06
                           Fer4_15  1 VvvDrdaCigcglCvaeape.vfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                      +vvD+++C+gcg C+ ++pe v e+d+dg++           ++v+ d+  +    +++CP++ I+v
  gi|488601760|ref|YP_007908231.1|  4 IVVDKETCDGCGECISVCPEsVYEFDDDGKS-----------EPVNMDDCSECCSCVEVCPTGSITV 59
                                      89****************7637899999998...........6889999999999999999999986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   2.1   5.8e-07   0.00065       1      15 [.       8      22 ..       8      32 .. 0.89
   2 !    6.8   8.4    0.0099        11       2      17 .]      40      55 ..      39      55 .. 0.90
   3 ?   -1.0   0.0       3.2   3.6e+03      11      15 ..      59      63 .]      59      63 .] 0.65

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.8e-07
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +e+C gCg C+++CP
  gi|488601760|ref|YP_007908231.1|  8 KETCDGCGECISVCP 22
                                      699************ PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0099
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      + C +C sCv +CP+g
  gi|488601760|ref|YP_007908231.1| 40 DDCSECCSCVEVCPTG 55
                                      77************86 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.2
                            Fer4_4 11 vaaCP 15
                                      v+aC+
  gi|488601760|ref|YP_007908231.1| 59 VDACE 63
                                      57785 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   3.3   0.00027      0.31      45      60 ..      10      25 ..       6      26 .. 0.76
   2 !   13.4   6.3   7.6e-05     0.086      40      59 ..      36      55 ..      26      56 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                           Fer4_17 45 lCieCgeCerkCPqgl 60
                                      +C +CgeC ++CP+++
  gi|488601760|ref|YP_007908231.1| 10 TCDGCGECISVCPESV 25
                                      6888888888888765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.6e-05
                           Fer4_17 40 eekaslCieCgeCerkCPqg 59
                                        ++++C+eC  C+++CP g
  gi|488601760|ref|YP_007908231.1| 36 PVNMDDCSECCSCVEVCPTG 55
                                      349***************75 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.3   8.5e-06    0.0096       1      13 [.      11      23 ..      11      25 .. 0.94
   2 !   11.6   9.4   0.00039      0.43       1      14 [.      42      55 ..      42      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.5e-06
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+gCg C  vCP+
  gi|488601760|ref|YP_007908231.1| 11 CDGCGECISVCPE 23
                                      ************6 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00039
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C  C  CvevCP+g
  gi|488601760|ref|YP_007908231.1| 42 CSECCSCVEVCPTG 55
                                      999999******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 ?    8.0   3.1    0.0029       3.3      58      75 ..       8      25 ..       3      31 .. 0.85
   2 ?   12.9   7.5   8.6e-05     0.097      54      74 ..      35      55 ..      25      63 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                           Fer4_18 58 agdcidcescvkvcPtgi 75
                                      +  c  c+ c++vcP  +
  gi|488601760|ref|YP_007908231.1|  8 KETCDGCGECISVCPESV 25
                                      567999*********876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.6e-05
                           Fer4_18 54 kekgagdcidcescvkvcPtg 74
                                      +  ++ dc +c scv+vcPtg
  gi|488601760|ref|YP_007908231.1| 35 EPVNMDDCSECCSCVEVCPTG 55
                                      556789*************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 ?   14.9   1.6   3.3e-05     0.037      77      95 ..       6      24 ..       1      25 [. 0.86
   2 ?    5.1   6.5     0.038        43       2      15 ..      42      55 ..      41      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      +++++C GCg Ci++cp++
  gi|488601760|ref|YP_007908231.1|  6 VDKETCDGCGECISVCPES 24
                                      57899***********986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.038
                           Fer4_22  2 ClsCgaCtlvCptC 15
                                      C +C +C  vCpt 
  gi|488601760|ref|YP_007908231.1| 42 CSECCSCVEVCPTG 55
                                      9***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.46u 0.35s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 371.14
//
Query:       gi|488601761|ref|YP_007908232.1|  [L=130]
Description: putative sulfite reductase-associated electron transfer protein DsrJ [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score 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   14.3   6.9       0.12   12.8   3.0    2.3  2  Cytochrom_c3_2  Cytochrome c3
       0.11   12.5   9.9       0.99    9.5   9.9    2.2  1  Cytochrome_C7   Cytochrome c7 and related cytochrome c
       0.83    9.3  10.3        6.6    6.4  10.5    2.5  2  Cytochrom_NNT   NapC/NirT cytochrome c family, N-terminal reg


Domain annotation for each model (and alignments):
>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.0   2.1e-05      0.12      55      80 .]      85     107 ..      41     107 .. 0.73
   2 ?    3.5   0.1     0.017        99      28      39 ..     114     125 ..     109     130 .] 0.53

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                                       CTSSS-GGGTS-TTTSBT-GGGGT-S CS
                    Cytochrom_c3_2  55 hekeleCteCHkeHkksekvCaeCHe 80 
                                       + ++ +C eCH   +++ ++C++CHe
  gi|488601761|ref|YP_007908232.1|  85 YISTYTCFECH---QSKAEFCDKCHE 107
                                       34566666666...56778******6 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.017
                                       HHHHHH--HHHC CS
                    Cytochrom_c3_2  28 kClsCHgkleel 39 
                                       +C  CH + e l
  gi|488601761|ref|YP_007908232.1| 114 NCWDCHITPELL 125
                                       455555544444 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   9.9   0.00017      0.99      42      72 ..      83     119 ..      56     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                     Cytochrome_C7  42 kaevesltCgaCHdgknaf......svakkaeCakCH 72 
                                       k  ++++tC +CH++k +f       v  k +C +CH
  gi|488601761|ref|YP_007908232.1|  83 KYYISTYTCFECHQSKAEFcdkcheYVGVKPNCWDCH 119
                                       3334448899999999999777776445578888888 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.016        94     157     165 ..      88      96 ..      72      99 .. 0.68
   2 ?    6.4  10.5    0.0011       6.6      39      78 ..      91     125 ..      83     130 .] 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.016
                     Cytochrom_NNT 157 ektCidCHk 165
                                       + tC +CH+
  gi|488601761|ref|YP_007908232.1|  88 TYTCFECHQ 96 
                                       456777776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0011
                     Cytochrom_NNT  39 CvsCHemednveeykesiHysnrsgvraeCsdCHvPkelv 78 
                                       C+ CH   +  +e+ +  H     gv+ +C dCH+  el+
  gi|488601761|ref|YP_007908232.1|  91 CFECH---QSKAEFCDKCHE--YVGVKPNCWDCHITPELL 125
                                       88888...567899999998..89***********88776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); 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: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 756.86
//
Query:       gi|488601762|ref|YP_007908233.1|  [L=546]
Description: putative sulfite reductase-associated electron transfer protein DsrK [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   38.3   1.9    3.5e-09   37.0   1.9    1.7  1  Fer4_8    4Fe-4S dicluster domain
    1.5e-09   38.2   2.3    4.1e-09   36.9   2.3    1.8  1  Fer4_17   4Fe-4S dicluster domain
    4.2e-07   30.4   1.4    1.5e-06   28.7   1.4    2.0  1  Fer4_7    4Fe-4S dicluster domain
    2.4e-06   27.6   1.4       0.02   15.0   0.1    2.6  2  Fer4_10   4Fe-4S dicluster domain
    0.00018   21.2  11.1      0.039   13.8   3.8    2.5  2  Fer4      4Fe-4S binding domain
     0.0008   19.5   8.5      0.049   13.8  10.1    2.4  3  Fer4_9    4Fe-4S dicluster domain
      0.001   19.0   9.7       0.11   12.6   1.7    2.6  2  Fer4_2    4Fe-4S binding domain
     0.0018   18.5   0.3      0.031   14.5   0.2    2.5  2  CCG       Cysteine-rich domain
  ------ inclusion threshold ------
      0.021   15.3  11.7       0.87   10.3   2.3    2.6  2  Fer4_4    4Fe-4S binding domain
      0.034   14.3   3.3        4.8    7.4   0.2    2.6  2  Fer4_21   4Fe-4S dicluster domain
      0.034   14.2  12.2       0.31   11.2   2.1    2.5  2  Fer4_6    4Fe-4S binding domain
       0.04   14.1   0.7        3.1    8.0   0.0    2.4  2  Fer4_18   4Fe-4S dicluster domain
       0.19   12.6   6.4        1.9    9.4   0.2    3.0  2  Fer4_22   4Fe-4S dicluster domain
        1.6    9.7  13.2        9.7    7.2   2.8    2.7  2  Fer4_16   4Fe-4S double cluster binding domain
        6.7    7.9  13.8          3    9.0   2.6    2.7  2  Fer4_3    4Fe-4S binding 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 !   37.0   1.9   2.9e-12   3.5e-09       3      65 .]      94     179 ..      93     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.9e-12
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae......................dvqeeqvlee.........eeal 48 
                                       + C++CgaC ++C+ +  t++ ++ +  +a+                       +        e         + + 
  gi|488601762|ref|YP_007908233.1|  94 DICVRCGACADKCHYYIGTGDPKNMPVVRAELlrsiyrkyftktgkvfgeyagaR--------EltedvikewYIYY 162
                                       56***********977777766666666655556555555555555555644442........0333355568999* PP

                            Fer4_8  49 wsCttcgaCtevCpvgi 65 
                                       ++C++c++C++ Cp gi
  gi|488601762|ref|YP_007908233.1| 163 FQCSECRRCSVFCPYGI 179
                                       **************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 !   36.9   2.3   3.4e-12   4.1e-09       2      61 .]      96     180 ..      95     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3.4e-12
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraakl.......................glleeaeke..ekaslCieCgeCe 53 
                                       C +Cg+C+++C +y+ +++ +++++ +a+l                       +l+e+++ke   +  +C+eC++C+
  gi|488601762|ref|YP_007908233.1|  96 CVRCGACADKCHYYIGTGDPKNMPVVRAELlrsiyrkyftktgkvfgeyagarELTEDVIKEwyIYYFQCSECRRCS 172
                                       ****************999888888888878878889999998888888777555666666665699********** PP

                           Fer4_17  54 rkCPqgld 61 
                                         CP+g+d
  gi|488601762|ref|YP_007908233.1| 173 VFCPYGID 180
                                       ******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 !   28.7   1.4   1.2e-09   1.5e-06       2      52 .]      96     179 ..      95     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.2e-09
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek.................................gtekveidpekClgCgaCv 45 
                                       C+ CgaC++ C ++  + d+++ +                                   +++++i + +C+ C++C 
  gi|488601762|ref|YP_007908233.1|  96 CVRCGACADKCHYYIGTGDPKNMPVvraellrsiyrkyftktgkvfgeyagareltedVIKEWYIYYFQCSECRRCS 172
                                       ***********8888887775444455555555555566555555555554444333344889************** PP

                            Fer4_7  46 avCPtga 52 
                                         CP+g+
  gi|488601762|ref|YP_007908233.1| 173 VFCPYGI 179
                                       ****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 !   11.0   0.2   0.00031      0.37       7      19 ..      94     106 ..      89     139 .. 0.79
   2 !   15.0   0.1   1.7e-05      0.02       3      23 ..     159     179 ..     157     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                           Fer4_10   7 dtCirCgkCvkaC 19 
                                       d C+rCg+C + C
  gi|488601762|ref|YP_007908233.1|  94 DICVRCGACADKC 106
                                       7899999999999 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.7e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadl 23 
                                       +i   +C +C++C  +CP+ +
  gi|488601762|ref|YP_007908233.1| 159 YIYYFQCSECRRCSVFCPYGI 179
                                       566789************966 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   3.8   3.2e-05     0.039       3      18 ..      91     106 ..      89     106 .. 0.90
   2 !   11.4   0.7   0.00018      0.22       3      21 ..     160     178 ..     158     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                                       EETTTSSS-THHHHHS CS
                              Fer4   3 ideekCigCGaCvevC 18 
                                       + ++ C++CGaC++ C
  gi|488601762|ref|YP_007908233.1|  91 VFMDICVRCGACADKC 106
                                       77899**********9 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00018
                                       EETTTSSS-THHHHHSTTT CS
                              Fer4   3 ideekCigCGaCvevCPvg 21 
                                       i +  C  C +C   CP+g
  gi|488601762|ref|YP_007908233.1| 160 IYYFQCSECRRCSVFCPYG 178
                                       55667************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 !   10.1   2.2   0.00058      0.69      33      47 ..      89     107 ..      70     110 .. 0.66
   2 !   13.8  10.1   4.1e-05     0.049       2      49 ..      96     178 ..      95     180 .. 0.72
   3 !    9.4   2.4   0.00096       1.1       1      16 [.     164     179 ..     164     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00058
                            Fer4_9  33 e....eaCigCgaCveaCp 47 
                                            + C+ CgaC+++C 
  gi|488601762|ref|YP_007908233.1|  89 FqvfmDICVRCGACADKCH 107
                                       0334457*********997 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.1e-05
                            Fer4_9   2 CtgCgaCveaC........pagvvvedaaerkarlraase..................................... 33 
                                       C++CgaC ++C        p        ++  +   +                                        
  gi|488601762|ref|YP_007908233.1|  96 CVRCGACADKChyyigtgdP--------KNMPVVRAE--Llrsiyrkyftktgkvfgeyagareltedvikewyiyy 162
                                       ***********655555552........333333221..112345555556788888888888888899999***** PP

                            Fer4_9  34 eaCigCgaCveaCpkg 49 
                                        +C +C++C   Cp g
  gi|488601762|ref|YP_007908233.1| 163 FQCSECRRCSVFCPYG 178
                                       9*************98 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00096
                            Fer4_9   1 kCtgCgaCveaCpagv 16 
                                       +C +C++C   Cp+g+
  gi|488601762|ref|YP_007908233.1| 164 QCSECRRCSVFCPYGI 179
                                       6999999999999886 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   1.7   9.3e-05      0.11       6      20 ..      92     106 ..      87     108 .. 0.83
   2 !   10.4   1.3   0.00046      0.55      10      22 .]     165     177 ..     159     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.3e-05
                            Fer4_2   6 dtdrCigCgaCvsaC 20 
                                         d+C++CgaC + C
  gi|488601762|ref|YP_007908233.1|  92 FMDICVRCGACADKC 106
                                       569*********999 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00046
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       C +C+ C   CP+
  gi|488601762|ref|YP_007908233.1| 165 CSECRRCSVFCPY 177
                                       *******888**5 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.46   5.5e+02      42      74 ..     295     326 ..     294     332 .. 0.82
   2 !   14.5   0.2   2.6e-05     0.031       1      52 [.     404     459 ..     404     491 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.46
                               CCG  42 Gagggrsgkeelaealakrnvetaeetgadaiv 74 
                                       G+ g+++++e +a++++++ +++a+++g++ i+
  gi|488601762|ref|YP_007908233.1| 295 GNFGFFHSFE-VAKKINQKIYKEAKRLGVKWIL 326
                                       5566777777.9***************999886 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.6e-05
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel..ekesCCGagggrsgkee 52 
                                       v+ +d+C+++r++   +e+r ++k + +      ++   ek++CCG+g+g    e 
  gi|488601762|ref|YP_007908233.1| 404 VTHHDSCNIARGMglFEEPRYVIKSVCNYYYDMPDHSirEKSYCCGSGAGLLADEL 459
                                       789***********************665555555447799*******99777764 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.3   0.00072      0.87       2      16 ..      94     108 ..      93     112 .. 0.88
   2 ?    9.4   2.2    0.0014       1.7       4      17 .]     165     178 ..     156     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00072
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C++Cg+C + C +
  gi|488601762|ref|YP_007908233.1|  94 DICVRCGACADKCHY 108
                                       56***********75 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C +C++C  +CP+g
  gi|488601762|ref|YP_007908233.1| 165 CSECRRCSVFCPYG 178
                                       ************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 ?    7.4   0.2     0.004       4.8       6      19 ..      94     107 ..      78     123 .. 0.73
   2 ?    6.8   0.3    0.0062       7.4      40      52 ..     164     176 ..     155     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.004
                           Fer4_21   6 dkCigCgkCliaCe 19 
                                       d C+ Cg C+  C+
  gi|488601762|ref|YP_007908233.1|  94 DICVRCGACADKCH 107
                                       45666666666664 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0062
                           Fer4_21  40 eCvGCnlCssvCP 52 
                                       +C  C  Cs  CP
  gi|488601762|ref|YP_007908233.1| 164 QCSECRRCSVFCP 176
                                       4666666666666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.1   0.00026      0.31       4      22 ..      91     109 ..      88     110 .. 0.86
   2 ?    7.8   2.8     0.003       3.6       9      22 ..     165     178 ..     164     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                            Fer4_6   4 idpdkCigCgdCvrvCPeg 22 
                                       +  d C+ Cg+C++ C ++
  gi|488601762|ref|YP_007908233.1|  91 VFMDICVRCGACADKCHYY 109
                                       7789**********99875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.003
                            Fer4_6   9 CigCgdCvrvCPeg 22 
                                       C  C++C + CP+g
  gi|488601762|ref|YP_007908233.1| 165 CSECRRCSVFCPYG 178
                                       999*********98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.047        57      85      97 ..      96     108 ..      81     119 .. 0.82
   2 ?    8.0   0.0    0.0026       3.1      60      77 ..     164     181 ..     133     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.047
                           Fer4_18  85 ciscllcidacdk 97 
                                       c+ c+ c d c+ 
  gi|488601762|ref|YP_007908233.1|  96 CVRCGACADKCHY 108
                                       9999999999975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0026
                           Fer4_18  60 dcidcescvkvcPtgidi 77 
                                       +c +c+ c   cP gid 
  gi|488601762|ref|YP_007908233.1| 164 QCSECRRCSVFCPYGIDT 181
                                       7***************96 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2    0.0016       1.9      66      95 ..      75     109 ..      67     110 .. 0.68
   2 ?    5.5   0.3     0.026        32      81      94 ..     164     177 ..     151     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                           Fer4_22  66 llhklsefkekf.....gesgCvGCgRCieacpvk 95 
                                       +++k+ e+++k+      +  Cv Cg C ++c+  
  gi|488601762|ref|YP_007908233.1|  75 IINKMDELRKKYrsfqvFMDICVRCGACADKCHYY 109
                                       555555555555433335789***********875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.026
                           Fer4_22  81 gCvGCgRCieacpv 94 
                                       +C  C RC+  cp 
  gi|488601762|ref|YP_007908233.1| 164 QCSECRRCSVFCPY 177
                                       56667777777765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  13.6     0.047        56       2      66 ..      96     177 ..      95     178 .. 0.69
   2 ?    7.2   2.8    0.0081       9.7       1      15 [.     164     178 ..     164     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.047
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare....cisy.............ntaekkdlaedeekck..kqeaitgCdi 59 
                                       C++Cg+Ca+ C     +++ +++   r+    +                + a+ ++l+ed  k+    + ++  C++
  gi|488601762|ref|YP_007908233.1|  96 CVRCGACADKCHYYIGTGDPKNMPVVRAellrS--IyrkyftktgkvfgEYAGARELTEDVIKEWyiYYFQCSECRR 170
                                       ***********9999887755544444423432..14566777888888777777777776554422347789**** PP

                           Fer4_16  60 CqdvCPa 66 
                                       C   CP+
  gi|488601762|ref|YP_007908233.1| 171 CSVFCPY 177
                                       ******8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0081
                           Fer4_16   1 rCgtCgkCaevCPtn 15 
                                       +C +C++C   CP +
  gi|488601762|ref|YP_007908233.1| 164 QCSECRRCSVFCPYG 178
                                       5************87 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.5      0.12   1.4e+02       1      12 [.      96     107 ..      96     110 .. 0.89
   2 ?    9.0   2.6    0.0025         3       1      14 [.     165     178 ..     165     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                            Fer4_3   1 CtgCgaCvevCP 12 
                                       C+ CgaC + C 
  gi|488601762|ref|YP_007908233.1|  96 CVRCGACADKCH 107
                                       99******9996 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0025
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C  C++C + CP+g
  gi|488601762|ref|YP_007908233.1| 165 CSECRRCSVFCPYG 178
                                       999*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 3101.72
//
Query:       gi|488601763|ref|YP_007908234.1|  [L=320]
Description: Nitrate reductase gamma subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-16   60.7  16.7    1.9e-15   57.0  10.1    2.2  2  Nitrate_red_gam  Nitrate reductase gamma subunit


Domain annotation for each model (and alignments):
>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.5   0.00013       2.3       6      25 ..      10      29 ..       6      54 .. 0.80
   2 !   57.0  10.1   1.1e-19   1.9e-15      27     201 ..      86     261 ..      67     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00013
                   Nitrate_red_gam  6 vvlPYvalavlvvgsllryr 25
                                      v +PY+a  ++vvg l+r  
  gi|488601763|ref|YP_007908234.1| 10 VYIPYIAAFIFVVGVLYRVF 29
                                      578**************964 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 1.1e-19
                   Nitrate_red_gam  27 dqftwtskSsqllekklLrlgsplFHvGilvvllgHlvGlliPksvteal.....gvseelyqll..alvaGliagv 96 
                                       ++++++  + + +++k+L +   +FH+ +l+vl+ H+  +l P  ++ ++     g  e  + ++   ++  li+g+
  gi|488601763|ref|YP_007908234.1|  86 KNVRYELPAQKAVSTKWLWVFGLVFHWSLLIVLIRHFRFFLEPVPWFVSTlmkldGFFEVHMDWFqpHMTHILITGL 162
                                       5555566666778899999999*******************9987765441111133344444442346667899** PP

                   Nitrate_red_gam  97 lalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsaldygseretispwlrslltlqpdaella 173
                                       ++lv ll+Ll+RRl+ ++ r+ +  sD++ l+lLl + ++Gll+ +v+ +d+    ++++  +++ll ++p a+   
  gi|488601763|ref|YP_007908234.1| 163 TLLVALLYLLYRRLAFPKERTFSLPSDYIALILLLGVATTGLLMRYVYPVDV----SEVKALAQGLLSFHPPAN--P 233
                                       ************************************************9988....999***********9987..6 PP

                   Nitrate_red_gam 174 evplifklHvllglllfalfPFtrLvHv 201
                                       +++l+f lH+l+  +l+a fPF++L+H 
  gi|488601763|ref|YP_007908234.1| 234 DLDLMFMLHLLFVSTLLAYFPFSKLMHS 261
                                       99*************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1867.70
//
Query:       gi|488601764|ref|YP_007908235.1|  [L=455]
Description: putative sulfite reductase-associated electron transfer protein DsrP [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-43  150.1  20.7    2.1e-43  149.2  20.7    1.5  1  NrfD             Polysulphide reductase, NrfD
     0.0071   15.6   5.7       0.01   15.0   5.7    1.1  1  Actin_micro      Putative actin-like family
  ------ inclusion threshold ------
       0.13   12.5   6.6       0.21   11.8   6.6    1.2  1  MTCP1            Mature-T-Cell Proliferation I type
       0.36   11.8   2.0       0.76   10.8   2.0    1.6  1  zf-C2H2_4        C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> NrfD  Polysulphide reductase, NrfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2  20.7   4.7e-47   2.1e-43       2     309 ..      40     341 ..      39     343 .. 0.82

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 4.7e-47
                              NrfD   2 vpehsnsvvWglliavylFligisAgalilaillklfkkkegkslkliirtgallaalavlagllilvldlgrperf 78 
                                       v+++s++v+Wgl+ia++ Fl+g++A a+i+ + ++l      k++k++ + g +l+a av++ +l++++dlgrp+r 
  gi|488601764|ref|YP_007908235.1|  40 VTGMSKEVSWGLYIANFTFLVGVAASAVIVVLPAYLYDY---KKFKNLTSIGEFLGASAVIMCILFILVDLGRPDRV 113
                                       899*****************************9977755...568889999************************** PP

                              NrfD  79 lklllyynfsSimswgvlllslyivvlvlyllvifekdlaakglpalgilaklislaervakilaiialilavllgs 155
                                       ++++l+++++S+m  + ++ls+y+++ +++ ++++ ++ ++kg+             +   kil  ia+++a+++++
  gi|488601764|ref|YP_007908235.1| 114 MNVVLNPRPNSVMLYDFIVLSGYFLLNIVIAWSVLAAKEKNKGY-------------ATWLKILIYIAIPWAISIHT 177
                                       ****************************9999997766666662.............23456788999********* PP

                              NrfD 156 ytgfllsavlsrplwnspllpvlFlasaiasGlavlllasllaarfekesedagllkklellvilteagllvilfvg 232
                                       +t+fl++ ++ rp+wn++l++++Fla a+asG+++l++a l++ +f+k+++ ++ lkk+  + ++   ++l+++ v 
  gi|488601764|ref|YP_007908235.1| 178 VTAFLYGGLVGRPFWNTALMAPRFLAGAFASGPSLLIVAGLVIRKFTKFDPGMDALKKIAEIAAFAMVANLFMIGVE 254
                                       ***********************************************************999999999999996553 PP

                              NrfD 233 ....laleggekiealeaalsggflt..........vlFwlgvvllglaiplllslavprlrenvavvviasilalv 295
                                           ++ +   ++e ++ +++g  l+           + w   ++lg++++l+l  + p++r   + +  a+++  +
  gi|488601764|ref|YP_007908235.1| 255 lfttYYSGHPHHLEHFNYLFFG--LQedghvynklvPWIWT-SLALGVISVLML--IYPKTRTTPKYLAAACVMIFA 326
                                       2332666666778888887666..53345555565333333.567777777775..666678888888888876666 PP

                              NrfD 296 gvll.lrfllliagq 309
                                        v + ++  l+i+g+
  gi|488601764|ref|YP_007908235.1| 327 SVWIdKGMGLIIPGY 341
                                       554413455666665 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   5.7   2.3e-06      0.01     205     252 ..     395     443 ..     380     452 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-06
                       Actin_micro 205 adeedfvdefrkleelkekkefsCkvCdvkfev.ekiseHllkkHiike 252
                                        +ee++ +e + +ee+ e+ke++C++Cd+ f   ++  eH +k+H+i++
  gi|488601764|ref|YP_007908235.1| 395 EEEEEVEEEVEVVEEVVEEKEYKCELCDAVFRNlDECCEHAEKEHKISK 443
                                       5788999999***********************9***********9965 PP

>> MTCP1  Mature-T-Cell Proliferation I type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.6   4.7e-05      0.21      14      52 ..     412     448 ..     406     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                             MTCP1  14 qknnYneskCekvieaLyeCCkkfykengedaksvsCpk 52 
                                       ++++Y+ + C +v ++L eCC++ +ke+  + +  sC+ 
  gi|488601764|ref|YP_007908235.1| 412 EEKEYKCELCDAVFRNLDECCEHAEKEH--KISKASCDM 448
                                       6789*********************996..666666664 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 ?   10.8   2.0   0.00017      0.76       1      24 []     416     439 ..     416     439 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                         zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                       +kC++C+++F++ ++ + H ++ H
  gi|488601764|ref|YP_007908235.1| 416 YKCELCDAVFRNLDECCEHAEKEH 439
                                       89*****************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1293  (0.0721178); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 2642.02
//
Query:       gi|488601765|ref|YP_007908236.1|  [L=252]
Description: putative sulfite reductase-associated electron transfer protein DsrO [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.2e-20   70.8  10.9    5.4e-13   48.9   5.5    2.2  2  Fer4_11     4Fe-4S dicluster domain
    5.1e-11   43.0  12.1      7e-07   29.7   5.2    2.4  2  Fer4_7      4Fe-4S dicluster domain
    5.6e-11   42.4  25.8    2.5e-07   30.7   4.1    2.4  2  Fer4_10     4Fe-4S dicluster domain
    1.9e-08   34.3  23.1      3e-05   24.1  11.3    2.4  3  Fer4_9      4Fe-4S dicluster domain
    3.4e-08   33.2  19.8    1.2e-06   28.4   2.1    3.0  3  Fer4_6      4Fe-4S binding domain
    1.5e-06   28.6   7.3    0.00014   22.2   2.3    2.4  2  Fer4_8      4Fe-4S dicluster domain
    1.7e-06   28.5   7.3    0.00023   21.6   3.2    2.5  2  Fer4_17     4Fe-4S dicluster domain
    2.7e-06   26.9  19.9    3.4e-06   26.6   1.2    4.1  4  Fer4        4Fe-4S binding domain
    4.2e-05   24.2  25.1     0.0099   16.8   6.5    3.3  3  Fer4_3      4Fe-4S binding domain
    7.4e-05   22.6  18.0     0.0015   18.5   2.0    3.0  3  Fer4_2      4Fe-4S binding domain
     0.0015   18.9   3.1     0.0015   18.9   3.1    2.9  2  Fer4_4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.012   15.8   4.1      0.012   15.8   4.1    1.8  2  Fer4_18     4Fe-4S dicluster domain
      0.057   14.4  17.8        2.2    9.3   6.5    3.1  2  Fer4_16     4Fe-4S double cluster binding domain
      0.079   12.3   1.2       0.14   11.6   0.5    1.8  2  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T
       0.18   11.5  13.0        1.2    8.9   3.4    2.5  2  Fer4_20     Dihydroprymidine dehydrogenase domain II, 4Fe-4S 
       0.23   12.2   0.6       0.23   12.2   0.6    2.4  2  Fer4_15     4Fe-4S single cluster domain
       0.26   11.4  15.4       0.22   11.7  12.2    2.5  2  Fer4_21     4Fe-4S dicluster 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 !   48.9   5.5   5.1e-16   5.4e-13       2      64 ..     107     167 ..     106     175 .. 0.94
   2 !   24.9   0.2   1.6e-08   1.7e-05      58      92 ..     178     212 ..     175     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 5.1e-16
                           Fer4_11   2 ewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrknee 64 
                                       +wl +p  C+hC+++pCv+++p++a  +++ +G+V +d +++  ++r ++ acPy +   n++
  gi|488601765|ref|YP_007908236.1| 107 KWLEVPILCNHCENAPCVKVCPTNATWQRD-DGIVTMDYHRCI-GCRYCMAACPYGMRSFNWK 167
                                       68889***********************99.***********7.*************999997 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.6e-08
                           Fer4_11  58 ivrkneetgkvekCdmcldrveaGllpacvescpt 92 
                                         ++++++g+vekC++c+ r e+G++pacve+  +
  gi|488601765|ref|YP_007908236.1| 178 TEYETRTKGVVEKCTFCVRRLESGKEPACVEASEG 212
                                       567788999*********************98765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.6   4.3e-06    0.0046      30      52 .]     107     131 ..      64     131 .. 0.81
   2 !   29.7   5.2   6.6e-10     7e-07       1      45 [.     146     207 ..     146     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.3e-06
                            Fer4_7  30 kveidpekClgCga..CvavCPtga 52 
                                       k+  +p  C +C++  Cv+vCPt+a
  gi|488601765|ref|YP_007908236.1| 107 KWLEVPILCNHCENapCVKVCPTNA 131
                                       55667889*****99********97 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 6.6e-10
                            Fer4_7   1 rCigCgaCvaaCpvkaield........eeenekgtekveidpekClgC.........gaCv 45 
                                       rCigC++C+aaCp++ ++++        ++ n +   +++++ ekC++C          aCv
  gi|488601765|ref|YP_007908236.1| 146 RCIGCRYCMAACPYGMRSFNwkdprpfiKKLNTEYETRTKGVVEKCTFCvrrlesgkePACV 207
                                       8*****************994444443323333344778999*******5555444333465 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7  13.9   1.7e-08   1.8e-05       6      56 .]     112     158 ..     107     158 .. 0.91
   2 !   30.7   4.1   2.4e-10   2.5e-07       3      54 ..     141     209 ..     139     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.7e-08
                           Fer4_10   6 ddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +  C +C+   Cvk+CP+      +   + +++ v  ++ +C+gc +C++aCP
  gi|488601765|ref|YP_007908236.1| 112 PILCNHCEnaPCVKVCPT------NATWQRDDGIVTMDYHRCIGCRYCMAACP 158
                                       567*****889*******......9999999999999***************9 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 2.4e-10
                           Fer4_10   3 vidddtCirCgkCvkaCPadl........tsvgakgeaseeeavrkkvekCtgc......g...aCvea 54 
                                         d  +Ci+C+ C++aCP+ +        +   +k  +++e + +++vekCt+c      g   aCvea
  gi|488601765|ref|YP_007908236.1| 141 TMDYHRCIGCRYCMAACPYGMrsfnwkdpRPFIKKLNTEYETRTKGVVEKCTFCvrrlesGkepACVEA 209
                                       67889**************99******9988899999999999999********777766255699985 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   3.5   0.00067      0.71      33      50 ..     101     131 ..      63     132 .. 0.68
   2 !   24.1  11.3   2.9e-08     3e-05       2      49 ..     115     160 ..     114     162 .. 0.83
   3 !   23.3   3.9   5.1e-08   5.3e-05       1      44 [.     146     208 ..     146     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00067
                            Fer4_9  33 e...........eaCigCga..CveaCpkga 50 
                                       +             C +C+   Cv++Cp++a
  gi|488601765|ref|YP_007908236.1| 101 YleehlkwlevpILCNHCENapCVKVCPTNA 131
                                       0455555566667899999999999999875 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.9e-08
                            Fer4_9   2 CtgCga..CveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C+ C +  Cv++Cp++++ ++d++  ++ ++     +CigC+ C++aCp g
  gi|488601765|ref|YP_007908236.1| 115 CNHCENapCVKVCPTNATwQRDDGIVTMDYH-----RCIGCRYCMAACPYG 160
                                       ****9888********985666666666664.....5************87 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 5.1e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCga.........Cve 44 
                                       +C+gC++C++aCp+g+ +  ++     +++ +           e+C++C +         Cve
  gi|488601765|ref|YP_007908236.1| 146 RCIGCRYCMAACPYGMRSFNWKDPRPFIKKLNTeyetrtkgvvEKCTFCVRrlesgkepaCVE 208
                                       6************9999777777777777766677999***********87777777777766 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   4.1     2e-05     0.021       8      23 ..     114     131 ..     114     132 .. 0.92
   2 !   28.4   2.1   1.1e-09   1.2e-06       1      23 [.     139     161 ..     139     161 .. 0.94
   3 ?   -2.0   0.3       4.4   4.6e+03      12      17 ..     191     196 ..     189     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                            Fer4_6   8 kCigCgd..CvrvCPega 23 
                                       +C++C++  Cv+vCP++a
  gi|488601765|ref|YP_007908236.1| 114 LCNHCENapCVKVCPTNA 131
                                       6****888********98 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.1e-09
                            Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                                       +v+ d+ +CigC+ C+++CP+g+
  gi|488601765|ref|YP_007908236.1| 139 IVTMDYHRCIGCRYCMAACPYGM 161
                                       699*****************985 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.4
                            Fer4_6  12 CgdCvr 17 
                                       C  Cvr
  gi|488601765|ref|YP_007908236.1| 191 CTFCVR 196
                                       889986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2    0.0017       1.7      45      64 ..     109     130 ..      48     131 .. 0.79
   2 !   22.2   2.3   1.4e-07   0.00014       3      54 ..     145     194 ..     143     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                            Fer4_8  45 eealwsCttcga..CtevCpvg 64 
                                        e    C++c++  C++vCp++
  gi|488601765|ref|YP_007908236.1| 109 LEVPILCNHCENapCVKVCPTN 130
                                       456678*****99*******87 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.4e-07
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttc 54 
                                       ++Ci+C +C++aCp   r+ ++ +d+r   ++   +e ++ ++  +++Ct c
  gi|488601765|ref|YP_007908236.1| 145 HRCIGCRYCMAACPYGMRSFNW-KDPRPFIKK-LNTEYETRTKGVVEKCTFC 194
                                       79************88887666.444444455.4555555567789999998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0032       3.4       2      16 ..     115     131 ..      87     141 .. 0.83
   2 !   21.6   3.2   2.2e-07   0.00023       1      49 [.     146     194 ..     146     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0032
                           Fer4_17   2 CiqCgy..ClpeCpsye 16 
                                       C++C+   C+++Cp+++
  gi|488601765|ref|YP_007908236.1| 115 CNHCENapCVKVCPTNA 131
                                       88888667888888765 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.2e-07
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydne.pkkllraaklglleeaekeekaslCieC 49 
                                       rCi+C+yC+++Cp++++  +++ p+ ++++++     e+ ++ ++++C+ C
  gi|488601765|ref|YP_007908236.1| 146 RCIGCRYCMAACPYGMRsFNWKdPRPFIKKLNT--EYETRTKGVVEKCTFC 194
                                       7*************9986555515555555443..2333456799999988 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.5   1.6e+03      10      16 ..     114     120 ..     113     121 .. 0.60
   2 !    9.8   1.6   0.00066       0.7      14      22 ..     123     131 ..     122     132 .. 0.97
   3 !   26.6   1.2   3.2e-09   3.4e-06       3      22 ..     142     161 ..     140     163 .. 0.88
   4 ?    1.5   0.3      0.28     3e+02       6      11 ..     189     194 ..     187     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
                                       S-THHHH CS
                              Fer4  10 gCGaCve 16 
                                        C+ C++
  gi|488601765|ref|YP_007908236.1| 114 LCNHCEN 120
                                       6777765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00066
                                       HHHHSTTTE CS
                              Fer4  14 CvevCPvgA 22 
                                       Cv+vCP++A
  gi|488601765|ref|YP_007908236.1| 123 CVKVCPTNA 131
                                       ********9 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 3.2e-09
                                       EETTTSSS-THHHHHSTTTE CS
                              Fer4   3 ideekCigCGaCvevCPvgA 22 
                                        d+ +CigC +C+ +CP+g 
  gi|488601765|ref|YP_007908236.1| 142 MDYHRCIGCRYCMAACPYGM 161
                                       6899**************95 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.28
                                       TTSSS- CS
                              Fer4   6 ekCigC 11 
                                       ekC++C
  gi|488601765|ref|YP_007908236.1| 189 EKCTFC 194
                                       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 !   16.8   6.5   9.4e-06    0.0099       1      15 []     115     131 ..     115     131 .. 0.92
   2 !   14.5   4.4   4.9e-05     0.052       1      14 [.     147     160 ..     147     160 .. 0.96
   3 ?    3.1   0.4      0.22   2.4e+02       1      10 [.     191     209 ..     191     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.4e-06
                            Fer4_3   1 CtgCg..aCvevCPvgA 15 
                                       C++C+  +Cv+vCP++A
  gi|488601765|ref|YP_007908236.1| 115 CNHCEnaPCVKVCPTNA 131
                                       ****8778*******98 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.9e-05
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gC+ C+ +CP+g
  gi|488601765|ref|YP_007908236.1| 147 CIGCRYCMAACPYG 160
                                       ****99******98 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.22
                            Fer4_3   1 CtgCg.........aCvev 10 
                                       Ct C          aCve+
  gi|488601765|ref|YP_007908236.1| 191 CTFCVrrlesgkepACVEA 209
                                       999955788889999*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 !   13.7   3.0   4.8e-05     0.051       9      22 .]     114     129 ..     108     129 .. 0.90
   2 !   18.5   2.0   1.4e-06    0.0015       4      22 .]     141     159 ..     138     159 .. 0.86
   3 ?   -2.6   0.2       7.3   7.7e+03      13      16 ..     191     194 ..     188     196 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                            Fer4_2   9 rCigCg..aCvsaCPa 22 
                                        C++C+  +Cv++CP+
  gi|488601765|ref|YP_007908236.1| 114 LCNHCEnaPCVKVCPT 129
                                       5****889*******7 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.4e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                         d  rCigC+ C  aCP+
  gi|488601765|ref|YP_007908236.1| 141 TMDYHRCIGCRYCMAACPY 159
                                       567789************5 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.3
                            Fer4_2  13 CgaC 16 
                                       C  C
  gi|488601765|ref|YP_007908236.1| 191 CTFC 194
                                       3334 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   1.2   0.00095         1       4      17 .]     115     130 ..     107     132 .. 0.91
   2 !   18.9   3.1   1.4e-06    0.0015       2      17 .]     145     160 ..     144     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00095
                            Fer4_4   4 CigCgs..CvaaCPqg 17 
                                       C++C    Cv +CP++
  gi|488601765|ref|YP_007908236.1| 115 CNHCENapCVKVCPTN 130
                                       *****889******85 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.4e-06
                            Fer4_4   2 erCigCgsCvaaCPqg 17 
                                        rCigC+ C+aaCP+g
  gi|488601765|ref|YP_007908236.1| 145 HRCIGCRYCMAACPYG 160
                                       79************86 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   4.1   1.2e-05     0.012      61     105 ..     115     167 ..     102     174 .. 0.76
   2 ?   -2.0   0.0       3.7   3.9e+03      55      68 ..     182     195 ..     167     200 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                           Fer4_18  61 cidces..cvkvcPtgidir..kGlql....eciscllcidacdkvmeklgkp 105
                                       c +ce   cvkvcPt+   +  +G+       ci c  c+ ac   m +++++
  gi|488601765|ref|YP_007908236.1| 115 CNHCENapCVKVCPTNATWQrdDGIVTmdyhRCIGCRYCMAACPYGMRSFNWK 167
                                       77787555*******98653225653222237***********9999998775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                           Fer4_18  55 ekgagdcidcescv 68 
                                       ++++g   +c +cv
  gi|488601765|ref|YP_007908236.1| 182 TRTKGVVEKCTFCV 195
                                       33344444566666 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 ?    9.2   3.4    0.0022       2.3       2      18 ..     115     133 ..     114     145 .. 0.85
   2 ?    9.3   6.5    0.0021       2.2       1      20 [.     146     165 ..     146     197 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                           Fer4_16   2 CgtCgk..CaevCPtnaik 18 
                                       C  C++  C++vCPtna  
  gi|488601765|ref|YP_007908236.1| 115 CNHCENapCVKVCPTNATW 133
                                       999*9999********965 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       rC++C+ C+ +CP +  + +
  gi|488601765|ref|YP_007908236.1| 146 RCIGCRYCMAACPYGMRSFN 165
                                       699**********9875544 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00013      0.14      10      27 ..       3      20 ..       1      23 [. 0.88
   2 ?   -3.5   0.0       6.8   7.2e+03      33      39 ..     171     177 ..     171     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                        UCR_Fe-S_N 10 tRRDFLyiATgavgaVGa 27
                                      tRR+FL++A +a+ a  a
  gi|488601765|ref|YP_007908236.1|  3 TRRRFLIMAGSAITALTA 20
                                      9***********999776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.8
                        UCR_Fe-S_N  33 Pfidqmn 39 
                                       Pfi+ +n
  gi|488601765|ref|YP_007908236.1| 171 PFIKKLN 177
                                       9**9998 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 ?    8.9   3.4    0.0011       1.2      24      40 ..     115     131 ..      94     135 .. 0.90
   2 ?    8.1   1.6    0.0021       2.2      20      42 ..     143     163 ..     136     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                       ----TT-HHHHCSTT-- CS
                           Fer4_20  24 ClqCkkapcvkgCPvei 40 
                                       C +C++apcvk CP++ 
  gi|488601765|ref|YP_007908236.1| 115 CNHCENAPCVKVCPTNA 131
                                       99************986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                                       HHTT----TT-HHHHCSTT---H CS
                           Fer4_20  20 eAsRClqCkkapcvkgCPveidi 42 
                                       + +RC+ C  ++c+++CP  ++ 
  gi|488601765|ref|YP_007908236.1| 143 DYHRCIGC--RYCMAACPYGMRS 163
                                       568*****..89******98754 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 ?   -1.1   0.5         3   3.2e+03      13      22 ..     122     131 ..     114     139 .. 0.63
   2 ?   12.2   0.6   0.00022      0.23       1      19 [.     140     158 ..     140     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3
                           Fer4_15  13 lCvaeapevf 22 
                                        Cv+++p+  
  gi|488601765|ref|YP_007908236.1| 122 PCVKVCPTNA 131
                                       5777776544 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V+ D  +Cigc  C+a++p
  gi|488601765|ref|YP_007908236.1| 140 VTMDYHRCIGCRYCMAACP 158
                                       899***************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 ?   11.7  12.2   0.00021      0.22       8      52 ..     115     158 ..     110     163 .. 0.81
   2 ?   -1.2   0.1       2.1   2.3e+03      34      44 ..     184     194 ..     173     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                           Fer4_21   8 CigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       C +C++  C+++C+   ++a    ++ ++++  ++C+GC  C++ CP
  gi|488601765|ref|YP_007908236.1| 115 CNHCENapCVKVCP---TNATWQRDDGIVTMDYHRCIGCRYCMAACP 158
                                       66775444899999...477777788899999*************** PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                           Fer4_21  34 lkvvedeCvGC 44 
                                       +k v ++C+ C
  gi|488601765|ref|YP_007908236.1| 184 TKGVVEKCTFC 194
                                       45556677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1442.40
//
Query:       gi|488601766|ref|YP_007908237.1|  [L=116]
Description: Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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-45  152.7   0.0    4.6e-45  152.5   0.0    1.0  1  DsrC            DsrC like protein
  ------ inclusion threshold ------
      0.096   12.5   0.0       0.14   12.0   0.0    1.2  1  LexA_DNA_bind   LexA DNA binding domain
       0.11   11.1   0.0       0.12   11.0   0.0    1.1  1  Staph_opine_DH  Staphylopine dehydrogenase


Domain annotation for each model (and alignments):
>> DsrC  DsrC like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.5   0.0   7.7e-49   4.6e-45       1     107 []       5     116 .]       5     116 .] 0.98

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 7.7e-49
                              DsrC   1 evngkeieldeegfLkdledwseevaealake.....egieLteehwevikflreyyeeygvapairklvkalkkel 72 
                                       ev+g+++ lde+gfL+d+e+w+e+va+ala++      ++eLt+ehwe+i+flr+yye+ygvap ir lvk++kk++
  gi|488601766|ref|YP_007908237.1|   5 EVKGRKLLLDEDGFLQDWEEWDEDVAKALAADdrwtgAKVELTDEHWEIIRFLRSYYEKYGVAPPIRILVKEVKKAF 81 
                                       689****************************988888899************************************* PP

                              DsrC  73 geekgnskelyelFpkgpakqackiAGlpkPtgCv 107
                                       g+ekgn k+ly+lFp+gpak+ac+iAGlpkPtgCv
  gi|488601766|ref|YP_007908237.1|  82 GPEKGNLKYLYKLFPQGPAKDACRIAGLPKPTGCV 116
                                       **********************************8 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.3e-05      0.14       3      35 ..      45      77 ..      43      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                                      ---HHHHHHHHHHHHHHHHHSS---HHHHHHHH CS
                     LexA_DNA_bind  3 kLTerQrevldlikasieetgypPsireiaral 35
                                      +LT+   e++++++++ e+ g +P ir + +++
  gi|488601766|ref|YP_007908237.1| 45 ELTDEHWEIIRFLRSYYEKYGVAPPIRILVKEV 77
                                      699999********************9777766 PP

>> Staph_opine_DH  Staphylopine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     2e-05      0.12     215     246 ..      68     100 ..      40     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2e-05
                                       HHHHSSHHHHHHHT-SS.S---BTTSBTTTSSB CS
                    Staph_opine_DH 215 pplflnelsLkavfeee.kakkyvYklfPeGPi 246
                                       pp+ +    +k+ f +e  + ky+YklfP GP 
  gi|488601766|ref|YP_007908237.1|  68 PPIRILVKEVKKAFGPEkGNLKYLYKLFPQGPA 100
                                       555555555566666551578***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 683.31
//
Query:       gi|488601767|ref|YP_007908238.1|  [L=341]
Description: putative Fe-S protein PflX [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-14   55.3   0.5      1e-13   52.0   0.1    2.3  2  Radical_SAM  Radical SAM superfamily
    2.7e-06   27.7   0.0    6.2e-06   26.5   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain
    8.9e-06   25.8   0.0    2.3e-05   24.5   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.1   1.7e-17     1e-13       2     153 ..     134     275 ..     133     288 .. 0.89
   2 ?    0.9   0.0     0.091   5.4e+02      94     141 ..     290     337 ..     277     340 .. 0.67

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.7e-17
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlaklavpg 77 
                                       ++++ C++rC+fC++       +++ + +v+ei+    + + +++g ++v ++gg+p+ +++ +  +++ ++    +
  gi|488601767|ref|YP_007908238.1| 134 IFFNRCTFRCVFCQNFD----IVYSDNYPVDEIELARSIDRrYRQGSRNVNFVGGNPDQHAHTILRILQHVES---N 203
                                       6899************6....7999999999997777666679999*****************9999999997...* PP

                                       EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglp 153
                                       i ++  +n ++  ee +e + +  vd+   + + ++d++ lk+ + ++ +  v ++++++ ++ ++   +r++++p
  gi|488601767|ref|YP_007908238.1| 204 IAVVWNSNMYHS-EELAEIIED-VVDVWLGDFKYGNDRCALKYSKAKNYWRVVTRNFRRAENN-GE-LLIRHLVMP 275
                                       ***********8.888888888.56********************99************9999.56.688888887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.091
                                       HHHHHHTT-SEEEEEEBSSSHH...HHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  94 lerllelgvdrvslgleaadde...kvlklmnrghtfeevlealeklreag 141
                                       +e+l++ g +r++l  + +  +   ++ ++  r+ ++ee+ +al+++++++
  gi|488601767|ref|YP_007908238.1| 290 AEELKP-G-TRFNLMFQYYPTFrayEYPEIS-RRLNREEIQRALDIAKRYR 337
                                       555566.5.7888888888888777555555.5566677777777776654 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0     1e-09   6.2e-06       9     101 ..     133     220 ..     126     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1e-09
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                       ++f+++C+++C +C n ++     + ++++  l++ i++   +  + + ++GG P    +a ++l+++++v+++   
  gi|488601767|ref|YP_007908238.1| 133 TIFFNRCTFRCVFCQNFDIVYS-DNYPVDEIELARSIDRRYRQGSRNVNFVGGNPDQ--HAHTILRILQHVESNIA- 205
                                       79***********998877643.3455667777777777778888**********99..************99998. PP

                           Fer4_12  86 kdiwlytgytleelsk 101
                                        ++w ++ y  eel +
  gi|488601767|ref|YP_007908238.1| 206 -VVWNSNMYHSEELAE 220
                                       .9*********99974 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 !   24.5   0.0   3.8e-09   2.3e-05       2      89 ..     135     212 ..     134     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.8e-09
                           Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                       f  +++C++ C++C n +    + + p +e +l + ++  + + +  +++ ++GG+P ++   +++l++++++  ++
  gi|488601767|ref|YP_007908238.1| 135 F--FNRCTFRCVFCQNFDIV-YSDNYPVDEIELARSIDRRYRQGS--RNVNFVGGNPDQH--AHTILRILQHVESNI 204
                                       4..49**********99954.555667778888899955554444..55********955..9**********9999 PP

                           Fer4_14  79 pekkiwletng 89 
                                           +w ++n 
  gi|488601767|ref|YP_007908238.1| 205 --AVVW-NSNM 212
                                       ..4444.4443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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 0.33s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1909.35
//
Query:       gi|488601768|ref|YP_007908239.1|  [L=98]
Description: hypothetical protein Asulf_02294 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (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   40.8   0.0    1.7e-10   40.4   0.0    1.4  1  UPF0175        Uncharacterised protein family (UPF0175)
    3.5e-08   33.1   1.6    4.1e-07   29.7   0.5    2.6  3  RHH_1          Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.019   14.5   0.0        2.6    7.7   0.0    2.3  2  HTH_24         Winged helix-turn-helix DNA-binding
      0.027   14.4   0.1       0.23   11.4   0.1    1.9  2  RelB           RelB antitoxin
      0.036   13.9   0.0       0.89    9.4   0.0    2.2  2  TetR_N         Bacterial regulatory proteins, tetR family
      0.037   13.8   0.0        3.6    7.5   0.0    2.3  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.088   12.6   0.0          5    7.1   0.0    2.3  2  HTH_23         Homeodomain-like domain
       0.12   12.2   0.0        4.5    7.2   0.0    2.2  2  HTH_IclR       IclR helix-turn-helix domain
       0.22   11.4   1.5       0.96    9.4   0.0    2.3  2  RHH_5          CopG-like RHH_1 or ribbon-helix-helix 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 !   40.4   0.0   8.6e-14   1.7e-10      21      74 ..      44      96 ..      18      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 8.6e-14
                           UPF0175 21 rialAvklYeegrlSlgkAaelaglsrveflelLarrgiplinydeeeleeDle 74
                                      +i+  +k Ye+g+++l ++ae +gls +e+ ++ ++r+i  + y+ e+l+eDle
  gi|488601768|ref|YP_007908239.1| 44 LIERSLKDYEDGKVTLWQVAERCGLSLWEVVNEVKKREIH-VPYTLEDLKEDLE 96
                                      56666788********************************.6**********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 !   29.7   0.5   2.1e-10   4.1e-07       5      37 ..       8      40 ..       5      42 .. 0.91
   2 ?    1.7   0.0      0.13   2.7e+02      25      37 ..      41      53 ..      41      54 .. 0.85
   3 ?   -2.5   0.0         3   5.9e+03      18      24 ..      63      69 ..      61      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.1e-10
                                      EEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                             RHH_1  5 rldeellerLdelarrrgrSrSelIReAlreyl 37
                                      r+d+el++++de+a+++g+ rS ++R+ l  ++
  gi|488601768|ref|YP_007908239.1|  8 RVDDELAKLIDEIAAKEGMDRSTVMRRFLSKAV 40
                                      8**************************887765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHHH CS
                             RHH_1 25 rSelIReAlreyl 37
                                      r +lI++ l++y 
  gi|488601768|ref|YP_007908239.1| 41 RDWLIERSLKDYE 53
                                      569******9995 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3
                                      HHHHTSS CS
                             RHH_1 18 arrrgrS 24
                                      a+r+g S
  gi|488601768|ref|YP_007908239.1| 63 AERCGLS 69
                                      7899988 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0013       2.6      21      37 ..      18      34 ..      17      35 .. 0.93
   2 ?    4.6   0.0     0.012        24      14      31 ..      53      70 ..      49      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                            HTH_24 21 reLAerlglSpstvnrr 37
                                       e+A + g+ +stv rr
  gi|488601768|ref|YP_007908239.1| 18 DEIAAKEGMDRSTVMRR 34
                                      59*************99 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.012
                            HTH_24 14 knprisqreLAerlglSp 31
                                      ++++ +  ++Aer+glS+
  gi|488601768|ref|YP_007908239.1| 53 EDGKVTLWQVAERCGLSL 70
                                      677888889*******95 PP

>> RelB  RelB antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.23       3      40 ..       4      41 ..       3      45 .. 0.92
   2 ?    0.7   0.0      0.27   5.3e+02      11      32 ..      54      75 ..      48      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      EEEEEEEHHHHHHHHHHHHCCT--HHHHHHHHHHHHHH CS
                              RelB  3 sislRidedlKaeatdvlekmGltiSqairlfLekiak 40
                                      ++ +R+d++l    +++ +k G+  S+++r fL k ++
  gi|488601768|ref|YP_007908239.1|  4 TLTTRVDDELAKLIDEIAAKEGMDRSTVMRRFLSKAVR 41
                                      6889*****************************98766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
                                      HHHHHHHHHHHCCT--HHHHHH CS
                              RelB 11 dlKaeatdvlekmGltiSqair 32
                                      d K    +v e+ Gl+  ++++
  gi|488601768|ref|YP_007908239.1| 54 DGKVTLWQVAERCGLSLWEVVN 75
                                      5577788999999999988876 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 ?    9.4   0.0   0.00045      0.89      19      41 ..      17      39 ..      14      40 .. 0.94
   2 ?    2.2   0.0      0.08   1.6e+02      16      29 ..      56      69 ..      54      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00045
                                      HHHHHHHHTSSHHHHHHHTSSHH CS
                            TetR_N 19 vreIAkrAGvskgalYryFpsKe 41
                                      ++eIA++ G+ ++++ r+F sK+
  gi|488601768|ref|YP_007908239.1| 17 IDEIAAKEGMDRSTVMRRFLSKA 39
                                      68*******************96 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.08
                                      T--HHHHHHHHTSS CS
                            TetR_N 16 attvreIAkrAGvs 29
                                      ++t+ ++A+r+G+s
  gi|488601768|ref|YP_007908239.1| 56 KVTLWQVAERCGLS 69
                                      588999******87 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 ?    7.5   0.0    0.0018       3.6      22      37 ..      19      34 ..      17      36 .. 0.93
   2 ?    4.3   0.0     0.018        37      14      30 ..      53      69 ..      52      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                     HTH_AsnC-type 22 eLAervGlSestvlrR 37
                                      e+A++ G+++stv+rR
  gi|488601768|ref|YP_007908239.1| 19 EIAAKEGMDRSTVMRR 34
                                      99************** PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                     HTH_AsnC-type 14 edaRisyaeLAervGlS 30
                                      ed++ +  ++Aer+GlS
  gi|488601768|ref|YP_007908239.1| 53 EDGKVTLWQVAERCGLS 69
                                      688888999*******9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0025         5      20      36 ..      17      33 ..      10      46 .. 0.86
   2 ?    3.6   0.0     0.031        63      12      30 ..      50      69 ..      44      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                            HTH_23 20 vreIAreLgvsrrTvyr 36
                                      + eIA++ g+ r+Tv r
  gi|488601768|ref|YP_007908239.1| 17 IDEIAAKEGMDRSTVMR 33
                                      679************85 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.031
                            HTH_23 12 lllae.GlsvreIAreLgvs 30
                                      + + + + +  ++A+++g s
  gi|488601768|ref|YP_007908239.1| 50 KDYEDgKVTLWQVAERCGLS 69
                                      55666788999*******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 ?    7.2   0.0    0.0022       4.5      23      37 ..      19      33 ..      13      37 .. 0.90
   2 ?    2.9   0.0     0.049        98      16      31 ..      54      69 ..      49      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0022
                                      HHHHHHTS-HHHHHH CS
                          HTH_IclR 23 elArrtglpkStvhR 37
                                      e+A++ g+ +Stv R
  gi|488601768|ref|YP_007908239.1| 19 EIAAKEGMDRSTVMR 33
                                      9************87 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.049
                                      BSS-BHHHHHHHHTS- CS
                          HTH_IclR 16 pqeltlselArrtglp 31
                                      ++ +tl ++A+r+gl+
  gi|488601768|ref|YP_007908239.1| 54 DGKVTLWQVAERCGLS 69
                                      5678999*******97 PP

>> 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 ?    9.4   0.0   0.00048      0.96      10      40 ..      11      41 ..       8      42 .. 0.95
   2 ?    0.6   0.3      0.27   5.5e+02      10      18 ..      89      97 ..      88      98 .] 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00048
                             RHH_5 10 eelleeLeewAdeegRsvSnlaafLvekalr 40
                                      +el + ++e A++eg ++S ++  ++ ka+r
  gi|488601768|ref|YP_007908239.1| 11 DELAKLIDEIAAKEGMDRSTVMRRFLSKAVR 41
                                      789999***********************98 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.27
                             RHH_5 10 eelleeLee 18
                                      e+l+e+Le 
  gi|488601768|ref|YP_007908239.1| 89 EDLKEDLEG 97
                                      79*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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 0.37s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 521.57
//
Query:       gi|488601769|ref|YP_007908240.1|  [L=167]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   39.8   1.5    7.2e-10   38.5   0.1    2.3  2  DUF3368     Domain of unknown function (DUF3368)
  ------ inclusion threshold ------
      0.027   14.4   0.2       0.19   11.7   0.0    2.3  2  Vps23_core  Vps23 core domain
      0.046   13.3   0.2       0.11   12.1   0.2    1.7  1  EF-hand_1   EF hand
      0.069   13.1   0.1       0.18   11.8   0.1    1.7  1  EF-hand_6   EF-hand domain
        0.1   12.7   0.0       0.21   11.8   0.0    1.5  1  HTH_28      Helix-turn-helix domain


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 ?   -0.7   0.2      0.36   1.3e+03       7      16 ..      82      91 ..      81      93 .. 0.87
   2 !   38.5   0.1     2e-13   7.2e-10       2      46 .]     113     159 ..     113     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.36
                           DUF3368  7 iLllAKqrGl 16
                                      +L lAK+ G+
  gi|488601769|ref|YP_007908240.1| 82 VLSLAKKLGV 91
                                      899****995 PP

  == domain 2  score: 38.5 bits;  conditional E-value: 2e-13
                           DUF3368   2 tGTLGiLllAKqrGlIps..vkplldaLiqaGfrispklyaevLrla 46 
                                       +GT+ +Ll+A ++G I+     ++l ++i +Gfr+ ++++ e++r+a
  gi|488601769|ref|YP_007908240.1| 113 RGTIFVLLRALKNGEIDLdeFLDILSKMIGHGFRLKEEIFVEAIREA 159
                                       6*******************************************986 PP

>> Vps23_core  Vps23 core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.26   9.4e+02      16      25 ..      49      58 ..      41      97 .. 0.63
   2 ?   11.7   0.0   5.3e-05      0.19      26      45 ..     115     134 ..     113     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.26
                        Vps23_core 16 lvaedkAieD 25
                                      ++a +kAi +
  gi|488601769|ref|YP_007908240.1| 49 AYAVEKAIHE 58
                                      5555555543 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.3e-05
                        Vps23_core  26 tiylLdkaldrgkidldtfl 45 
                                       ti +L +al++g idld+fl
  gi|488601769|ref|YP_007908240.1| 115 TIFVLLRALKNGEIDLDEFL 134
                                       899****************8 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2     3e-05      0.11      13      29 .]     124     140 ..     124     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                                       SSSEEEHHHHHHHHHHH CS
                         EF-hand_1  13 gdGkIdfeEfkellkkl 29 
                                       ++G Id++Ef+++l+k+
  gi|488601769|ref|YP_007908240.1| 124 KNGEIDLDEFLDILSKM 140
                                       79************986 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.1e-05      0.18      13      28 ..     124     139 ..     122     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                         EF-hand_6  13 gdGkidaeElrkalrk 28 
                                       ++G+id +E+ ++l+k
  gi|488601769|ref|YP_007908240.1| 124 KNGEIDLDEFLDILSK 139
                                       79************97 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.7e-05      0.21       6      41 ..      91     128 ..      85     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                            HTH_28   6 iklla.aGhsvreaArelgi.srrtvyrWikryeegGi 41 
                                       +k+++ +  s+r+aAr+lg+  r t+ ++++++  g i
  gi|488601769|ref|YP_007908240.1|  91 VKEVLvDETSARAAARLLGLkPRGTIFVLLRALKNGEI 128
                                       567666888***********888999999998887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 893.02
//
Query:       gi|488601770|ref|YP_007908241.1|  [L=99]
Description: hypothetical protein Asulf_02296 [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   53.7   0.8    1.7e-14   53.2   0.8    1.2  1  UPF0175   Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
      0.024   13.3   0.2      0.024   13.3   0.2    1.0  1  INTS5_C   Integrator complex subunit 5 C-terminus
      0.038   14.0   0.3       0.23   11.5   0.2    2.0  2  KorB      KorB domain
      0.076   13.0   0.3      0.076   13.0   0.3    2.3  3  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 !   53.2   0.8   3.9e-18   1.7e-14      19      74 ..      41      95 ..      30      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3.9e-18
                           UPF0175 19 elrialAvklYeegrlSlgkAaelaglsrveflelLarrgiplinydeeeleeDle 74
                                      e ++  A++lY e+++Sl+kAae+a++s  ++lel +++g++ +n ++e+l++D+e
  gi|488601770|ref|YP_007908241.1| 41 EELKKFALMLYVERKVSLAKAAEIAEISVRDMLELIKEKGVS-LNITVEDLKRDFE 95
                                      446789************************************.7**********97 PP

>> INTS5_C  Integrator complex subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   5.3e-06     0.024     284     342 ..      14      64 ..       2      92 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.3e-06
                           INTS5_C 284 qnlatllkweksskeetlvskqiskavskhLeklssllkknedievaeaivsllsslel 342
                                       + ++ l+++eks+k+  +v+k i + ++++L+k++ +l  ++ +++a+a+       e+
  gi|488601770|ref|YP_007908241.1|  14 RKIKKLMEFEKSDKSS-IVRKAIERGINEELKKFALMLYVERKVSLAKAA-------EI 64 
                                       67899********999.*********************555555554443.......33 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.071   3.2e+02      61      86 ..      15      42 ..       6      46 .. 0.63
   2 ?   11.5   0.2   5.1e-05      0.23      48      83 ..      55      90 ..      25      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.071
                              KorB 61 evrafv..aengeagltrsavrrflksl 86
                                      ++++++  +++ ++ + r+a++r ++++
  gi|488601770|ref|YP_007908241.1| 15 KIKKLMefEKSDKSSIVRKAIERGINEE 42
                                      5555555556666777777777766654 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.1e-05
                              KorB 48 LyeLrraaekhpaevrafvaengeagltrsavrrfl 83
                                       ++L++aae+ +  vr++++  +e+g++++   + l
  gi|488601770|ref|YP_007908241.1| 55 KVSLAKAAEIAEISVRDMLELIKEKGVSLNITVEDL 90
                                      479************************998665555 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.7e-05     0.076       2      36 ..       4      38 ..       3      41 .. 0.93
   2 ?   -3.0   0.1       1.9   8.3e+03      32      39 .]      47      54 ..      47      54 .. 0.84
   3 ?   -1.3   0.0      0.53   2.4e+03       9      16 ..      71      78 ..      67      82 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlrey 36
                                      +s+r   +l +++ +l + +++ +S ++R A+++ 
  gi|488601770|ref|YP_007908241.1|  4 ISVRATPDLERKIKKLMEFEKSDKSSIVRKAIERG 38
                                      8*******************************975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                                      HHHHHHHH CS
                             RHH_1 32 Alreyler 39
                                      Al+ y+er
  gi|488601770|ref|YP_007908241.1| 47 ALMLYVER 54
                                      88999997 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.53
                                      HHHHHHHH CS
                             RHH_1  9 ellerLde 16
                                      ++le++ e
  gi|488601770|ref|YP_007908241.1| 71 DMLELIKE 78
                                      56666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.36s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 557.82
//
Query:       gi|488601771|ref|YP_007908242.1|  [L=168]
Description: putative nucleic acid-binding protein, contains PIN domain [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   59.6   1.0    5.5e-14   51.7   0.1    2.9  3  DUF3368   Domain of unknown function (DUF3368)


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 !    5.5   0.0   0.00082        15       7      24 ..      38      57 ..      38      60 .. 0.84
   2 ?   -0.9   0.1     0.079   1.4e+03      13      25 ..      58      74 ..      52      78 .. 0.56
   3 !   51.7   0.1   3.1e-18   5.5e-14       1      45 [.     115     161 ..     115     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00082
                           DUF3368  7 iLllAKqrGlIps..vkpll 24
                                      ++++ K+rG I++  v +l+
  gi|488601771|ref|YP_007908242.1| 38 VVVKGKERGDIDAfiVEDLI 57
                                      789*********98877776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.079
                           DUF3368 13 qrGlIps....vkplld 25
                                      ++G+I      v  ll 
  gi|488601771|ref|YP_007908242.1| 58 KKGVIKVidveVEGLLR 74
                                      66777663334444444 PP

  == domain 3  score: 51.7 bits;  conditional E-value: 3.1e-18
                           DUF3368   1 vtGTLGiLllAKqrGlIps..vkplldaLiqaGfrispklyaevLrl 45 
                                       v+G+L++++l+ ++G+I++  +k  ++++i++Gfr+s+++y+e+Lrl
  gi|488601771|ref|YP_007908242.1| 115 VHGSLYLVFLMLKKGKIDKktAKSKVEEMIRKGFRLSAEVYSEFLRL 161
                                       8********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 951.35
//
Query:       gi|488601772|ref|YP_007908243.1|  [L=197]
Description: indolepyruvate ferredoxin oxidoreductase, subunit iorB [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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  147.5   0.7    4.8e-43  147.3   0.7    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
      0.078   12.5   0.1       0.11   12.1   0.1    1.1  1  ComR_TPR  ComR tetratricopeptide


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 !  147.3   0.7   5.3e-47   4.8e-43       1     177 []      13     194 ..      13     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 5.3e-47
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv+t ++i+a+aa+r+G++v++++++g+++rGg++++hvri+d  ++p i+ g ad+++al++ ++ +++++++
  gi|488601772|ref|YP_007908243.1|  13 GGQGVLTSSNIIARAAMRKGMNVLTSETHGMAQRGGSVEVHVRIGDV-HSPLIPFGSADIVIALEPVEALRYAHYMN 88 
                                       9********************************************97.89****************9999******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH......T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H. CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl......gvrvygvdatkiakeiggneraaNtvmlGalaallglpl. 147
                                       +++ ii+ns ++kp++++  + e++e +e          ++ +vda++ia++ ++   a+N+v+lG+la++l   + 
  gi|488601772|ref|YP_007908243.1|  89 ENTMIILNSRKIKPTTVNVGLAEYPEIEEIIerlktvTEKIKVVDASAIAEKVAR-VQATNVVVLGMLAKVLEGRFl 164
                                       *******************99999988777799****999999***********9.****************95555 PP

                                       ..HHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 148 ..ealeeaikkrfpkkkeviekNlkafragye 177
                                         e+le ++++ +p++  ++e Nlka++agye
  gi|488601772|ref|YP_007908243.1| 165 tlEDLEYGVRAFLPER--LVEINLKALKAGYE 194
                                       66************96..*************7 PP

>> ComR_TPR  ComR tetratricopeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.2e-05      0.11     121     175 ..      80     134 ..      70     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                                       HHHHTTTS-GGGHHHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHT--TT CS
                          ComR_TPR 121 llnqeesleeedlfllrdvllsaltvllklkeyeklekllkvlnkimektqdfqk 175
                                        l + ++++e+ +++l++  ++  tv + l+ey ++e+++++l+++ ek++ +  
  gi|488601772|ref|YP_007908243.1|  80 ALRYAHYMNENTMIILNSRKIKPTTVNVGLAEYPEIEEIIERLKTVTEKIKVVDA 134
                                       5778899*****************************************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1097.07
//
Query:       gi|488601773|ref|YP_007908244.1|  [L=621]
Description: indolepyruvate ferredoxin oxidoreductase, subunit iorA [Archaeoglobus sulfaticallidus PM70-1]
Scores for complete 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   99.0   0.3    3.6e-28   98.3   0.3    1.4  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    1.4e-11   44.6   0.0    2.4e-11   43.8   0.0    1.3  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    0.00022   21.2   4.8    0.00022   21.2   4.8    3.1  2  Fer4_6           4Fe-4S binding domain
    0.00024   20.8   5.8    0.00024   20.8   5.8    2.8  2  Fer4             4Fe-4S binding domain
    0.00085   19.6   0.0     0.0023   18.2   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0012   19.0  10.9     0.0043   17.2  11.1    1.9  1  Fer4_9           4Fe-4S dicluster domain
     0.0013   19.3   9.1      0.019   15.6   1.3    2.6  2  Fer4_7           4Fe-4S dicluster domain
     0.0019   18.3  11.1     0.0046   17.1  11.1    1.7  1  Fer4_21          4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.02   15.8  10.3      0.036   15.0   3.2    2.6  2  Fer4_16          4Fe-4S double cluster binding domain
      0.021   14.9  15.1      0.022   14.8   2.6    3.1  2  Fer4_2           4Fe-4S binding domain
      0.044   13.9  13.5       0.07   13.2   2.5    2.6  2  Fer4_10          4Fe-4S dicluster domain
      0.054   14.0   5.9        1.4    9.5   0.8    2.5  2  Fer4_17          4Fe-4S dicluster domain
       0.13   12.1   0.1       0.55   10.1   0.0    2.0  2  Transketolase_C  Transketolase, C-terminal domain
       0.31   11.5   6.7        6.8    7.2   1.5    2.5  2  Fer4_8           4Fe-4S dicluster domain
        0.5   11.0  13.1       0.11   13.1   3.4    2.7  2  Fer4_4           4Fe-4S binding domain
          3    8.5  13.8        2.3    8.8   4.1    2.6  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I


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 !   98.3   0.3   3.2e-31   3.6e-28       1     151 [.     401     540 ..     401     542 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 3.2e-31
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc+tl      ++++p + ++  ++ +mG + ++A G++    d ++va++GD++f++  ++ la+av++nl+ t
  gi|488601773|ref|YP_007908244.1| 401 DIGCYTL------GINKPLEAVD--TTICMGASAGVANGLSYFV-DGKIVATIGDSTFFHAgMPPLANAVYNNLNYT 468
                                       8******......**********..9***************943.569***************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpali 151
                                       +++++N+++gmtg+q++p +g r  g+    ++ v+++ ++++lG++ + +v++++v +l e +++a+e++g+a++
  gi|488601773|ref|YP_007908244.1| 469 LIIMDNSTTGMTGHQPHPGTGIRACGE----GRRVSLEDVVKGLGVEfVEVVNSYNVRKLIESIRRAIEHDGVAVV 540
                                       *********************999885....6899************888************************99 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   2.1e-14   2.4e-11       2     168 ..      24     189 ..      23     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.1e-14
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEE.E.-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevv.q.mesEigaisaviGAaaaGaraaTaTSgqGllLmi 76 
                                       +ai+ g+d+++ YP TPssei ++la++    +  +++++ +   +E  a+++ iGA++aG ra+++    Gl  + 
  gi|488601773|ref|YP_007908244.1|  24 GAIESGIDIVSCYPGTPSSEITDTLAQACSHLRG-KMDYFvEySTNEKVAFETGIGASLAGKRALVTMKHVGLNVAA 99 
                                       8999*************************99996.45544142578******************************* PP

                                       CCHHHHH..HTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEE CS
                             POR_N  77 enlglaa..geelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPviv 151
                                       ++l+  a  g++  +v+v +    p+   s +++q    +    +l vl ++ v ea +l+ vAf l+e++ +P+i 
  gi|488601773|ref|YP_007908244.1| 100 DSLFSFAyvGARGGFVVVTAD--DPTM-HSSQNEQDNRWYGKSAKLPVLEPSGVNEAKELVKVAFDLSERFGLPMIF 173
                                       ***987622666666666654..4555.78999*****************************************875 PP

                                       EEEHHHH.HEEEEEEC- CS
                             POR_N 152 lfDgfllshevekvelp 168
                                           ++lsh+   v+l 
  gi|488601773|ref|YP_007908244.1| 174 R-TYTRLSHSSGIVDLG 189
                                       5.567788998887765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   3.2    0.0085       9.6       7      21 ..     568     584 ..     566     585 .. 0.86
   2 !   21.2   4.8   1.9e-07   0.00022       1      24 []     591     614 ..     591     614 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0085
                            Fer4_6   7 dkCigCgdCvrv..CPe 21 
                                       ++C+ C++C++   CP+
  gi|488601773|ref|YP_007908244.1| 568 ENCTVCMKCITDftCPA 584
                                       89*******99888886 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.9e-07
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +v id+ +C+gC  C+++CPe+ai
  gi|488601773|ref|YP_007908244.1| 591 KVGIDAALCVGCAVCASICPEKAI 614
                                       5789******************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.5     0.086        97       5      15 ..     567     577 ..     565     578 .. 0.88
   2 !   20.8   5.8   2.1e-07   0.00024       3      24 .]     594     615 ..     592     615 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.086
                                       TTTSSS-THHH CS
                              Fer4   5 eekCigCGaCv 15 
                                        e C+ C++C+
  gi|488601773|ref|YP_007908244.1| 567 AENCTVCMKCI 577
                                       589*******7 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.1e-07
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       id  +C+gC  C+++CP  AI+
  gi|488601773|ref|YP_007908244.1| 594 IDAALCVGCAVCASICPEKAIK 615
                                       999*****************96 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.1e-06    0.0023       2      61 ..     247     308 ..     246     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-06
                                       SEEEEE-STHHHHHHHHHHHHHHTT-..-EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegi..kvGllrlrtlrPFPeeelkellkkvkkvvvldrn 61 
                                       ++ i+a G + + +k+a+++lR +    +  +l+l ++ P Pe+ ++++++++kkv+v++  
  gi|488601773|ref|YP_007908244.1| 247 DTGIIACGLSYSYVKEAIENLRSKNDfdSPPVLKLSSMHPVPEKLIERFTDGLKKVLVVEEV 308
                                       6679******************9864226789***************************975 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  11.1   3.8e-06    0.0043       1      51 []     569     614 ..     569     614 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.8e-06
                            Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       +Ct C +C++   Cpa  v + +++  a+l       C+gC  C+ +Cp++ai
  gi|488601773|ref|YP_007908244.1| 569 NCTVCMKCITDftCPAIFVDDGKVGIDAAL-------CVGCAVCASICPEKAI 614
                                       5*******87667*************9997.......*************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 !    7.2   1.3    0.0067       7.5      20      49 ..     551     583 ..     537     585 .. 0.73
   2 !   15.6   1.3   1.7e-05     0.019       2      18 ..     599     615 ..     590     620 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0067
                            Fer4_7  20 deeenekgtekvei.dpekClgCgaCva..vCP 49 
                                       + e + kg+e  ++ ++e+C+ C +C++  +CP
  gi|488601773|ref|YP_007908244.1| 551 TRERKRKGIEVRAFeVAENCTVCMKCITdfTCP 583
                                       444455565555552589*********977888 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.7e-05
                            Fer4_7   2 CigCgaCvaaCpvkaie 18 
                                       C+gC  C++ Cp kai+
  gi|488601773|ref|YP_007908244.1| 599 CVGCAVCASICPEKAIK 615
                                       88888888888888776 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1  11.1   4.1e-06    0.0046       7      57 ..     569     614 ..     563     616 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.1e-06
                           Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       +   C+ C++   d +  ai +d+ +v  + +  CvGC++C+s+CP e++i
  gi|488601773|ref|YP_007908244.1| 569 N---CTVCMKCITDFTCPAIFVDDGKV-GIDAALCVGCAVCASICP-EKAI 614
                                       4...55555555666677999986665.899***************.6887 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.7      0.06        67      30      65 ..     546     583 ..     529     585 .. 0.58
   2 ?   15.0   3.2   3.2e-05     0.036       2      20 ..     599     617 ..     598     620 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.06
                           Fer4_16  30 cisyntaekkdlaedeekckkqeaitgCdiCqd..vCP 65 
                                       c    t+e+k+  ++ ++ + +e++t C +C +  +CP
  gi|488601773|ref|YP_007908244.1| 546 CAILWTRERKRKGIEVRAFEVAENCTVCMKCITdfTCP 583
                                       44444555555555555555668889998885322666 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.2e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                       C++C  Ca++CP++aik k
  gi|488601773|ref|YP_007908244.1| 599 CVGCAVCASICPEKAIKPK 617
                                       ****************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 ?    6.4   2.9    0.0097        11       6      22 .]     566     584 ..     561     584 .. 0.77
   2 ?   14.8   2.6     2e-05     0.022       2      22 .]     591     611 ..     590     611 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0097
                            Fer4_2   6 dtdrCigCgaCv.sa.CPa 22 
                                       ++++C+ C +C+ +  CPa
  gi|488601773|ref|YP_007908244.1| 566 VAENCTVCMKCItDFtCPA 584
                                       5799*******64446**8 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2e-05
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                       +v +d++ C+gC  C s CP+
  gi|488601773|ref|YP_007908244.1| 591 KVGIDAALCVGCAVCASICPE 611
                                       5779****************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 ?    7.3  13.8    0.0045         5       6      56 .]     567     610 ..     562     610 .. 0.89
   2 ?   13.2   2.5   6.3e-05      0.07       2      22 ..     592     612 ..     591     620 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0045
                           Fer4_10   6 ddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       ++ C+ C kC +   CPa         +  ++++v ++   C gc  C+++CP
  gi|488601773|ref|YP_007908244.1| 567 AENCTVCMKCITdfTCPA---------IFVDDGKVGIDAALCVGCAVCASICP 610
                                       578********9767***.........88888889999**************9 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.3e-05
                           Fer4_10   2 vvidddtCirCgkCvkaCPad 22 
                                       v id+  C++C+ C + CP +
  gi|488601773|ref|YP_007908244.1| 592 VGIDAALCVGCAVCASICPEK 612
                                       7799***************93 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.4     0.011        13      40      57 ..     562     583 ..     531     586 .. 0.74
   2 ?    9.5   0.8    0.0013       1.4      43      58 ..     596     611 ..     588     613 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                           Fer4_17  40 e..ekaslCieCgeCe..rkCP 57 
                                       +  e+a++C+ C +C     CP
  gi|488601773|ref|YP_007908244.1| 562 RafEVAENCTVCMKCItdFTCP 583
                                       144899*********7456787 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                           Fer4_17  43 aslCieCgeCerkCPq 58 
                                       a lC++C  C++ CP+
  gi|488601773|ref|YP_007908244.1| 596 AALCVGCAVCASICPE 611
                                       789999****999997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00049      0.55      11      71 ..     247     309 ..     241     322 .. 0.90
   2 ?   -3.1   0.0         6   6.7e+03      62      86 ..     496     518 ..     495     532 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00049
                                       SEEEEEETTHHHHHHHHHHHHHTT..TTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEE CS
                   Transketolase_C  11 dvtlvayGsmveealeAaeeLeke..gisaeVvdlrtvkplDketilesvkktgrlvvveeav 71 
                                       d  ++a G   + + eA+e+L+++    s  V+ l ++ p+ +++i+      ++++vvee  
  gi|488601773|ref|YP_007908244.1| 247 DTGIIACGLSYSYVKEAIENLRSKndFDSPPVLKLSSMHPVPEKLIERFTDGLKKVLVVEEVD 309
                                       6679******************996446899*****************************975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6
                                       SEEEEEEEEESTTSHHHHHHHHHHH CS
                   Transketolase_C  62 grlvvveeavkrgGigsevaaalae 86 
                                       gr v +e+ vk  G+g e++++++ 
  gi|488601773|ref|YP_007908244.1| 496 GRRVSLEDVVK--GLGVEFVEVVNS 518
                                       56677788777..888899998888 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3    0.0099        11      46      59 ..     565     578 ..     530     589 .. 0.75
   2 ?    7.2   1.5    0.0061       6.8       4      16 ..     598     610 ..     594     616 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0099
                            Fer4_8  46 ealwsCttcgaCte 59 
                                       e +++Ct c++C +
  gi|488601773|ref|YP_007908244.1| 565 EVAENCTVCMKCIT 578
                                       56888999999965 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0061
                            Fer4_8   4 kCieCgaCqsaCp 16 
                                        C++C  C s Cp
  gi|488601773|ref|YP_007908244.1| 598 LCVGCAVCASICP 610
                                       4666666666666 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   2.2      0.26   2.9e+02       2      11 ..     568     577 ..     567     585 .. 0.81
   2 ?   13.1   3.4   9.8e-05      0.11       4      16 ..     599     611 ..     596     612 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.26
                            Fer4_4   2 erCigCgsCv 11 
                                       e+C+ C++C+
  gi|488601773|ref|YP_007908244.1| 568 ENCTVCMKCI 577
                                       89*******7 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.8e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C+gC +C ++CP 
  gi|488601773|ref|YP_007908244.1| 599 CVGCAVCASICPE 611
                                       ************5 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.2     0.046        52       4      25 ..     568     591 ..     566     593 .. 0.85
   2 ?    8.8   4.1    0.0021       2.3       1      18 [.     594     611 ..     594     612 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.046
                           Fer4_13   4 dtCiacgaCve..laPdvFeedde 25 
                                       ++C+ c++C    ++P +F  d +
  gi|488601773|ref|YP_007908244.1| 568 ENCTVCMKCITdfTCPAIFVDDGK 591
                                       79*******97779*****98865 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0021
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       +D   C++c++C++++P+
  gi|488601773|ref|YP_007908244.1| 594 IDAALCVGCAVCASICPE 611
                                       78899************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 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:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 3424.29
//
Query:       gi|488601774|ref|YP_007908245.1|  [L=370]
Description: Archaeal fructose 1,6-bisphosphatase [Archaeoglobus sulfaticallidus PM70-1]
Scores for 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-183  610.5   0.0   1.2e-183  610.3   0.0    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.3   0.0  6.4e-188  1.2e-183       1     361 []       4     368 ..       4     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 610.3 bits;  conditional E-value: 6.4e-188
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       k+t+s+ikaDvG+l+Gh+ v +e++e ++++leeak++g +id++v + GDD++limth++gvd++++h++aw++f+
  gi|488601774|ref|YP_007908245.1|   4 KITVSIIKADVGGLPGHVLVPDEIIEVAKQSLEEAKQSGDIIDYRVLNAGDDLDLIMTHREGVDSTKIHRIAWETFE 80 
                                       89*************************************************************************** PP

                          FBPase_3  78 eatevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGl 154
                                       +ate akelklygaGqDlL+dafsGnv+G+GPgvae+ef+eR+sepv+ f++Dktepgafnlp++++fadpfntaGl
  gi|488601774|ref|YP_007908245.1|  81 KATEKAKELKLYGAGQDLLADAFSGNVRGMGPGVAEMEFTERESEPVLAFLMDKTEPGAFNLPIFRMFADPFNTAGL 157
                                       ***************************************************************************** PP

                          FBPase_3 155 vidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvysk....kdeeiaavvsterlsliaGkY 227
                                       vidp++h+Gf fe++D++e+k++ +++pee+yd+lal+g k+r+vikrvy k      +e++av+ste+l +iaG+Y
  gi|488601774|ref|YP_007908245.1| 158 VIDPSMHNGFVFEIWDIYESKRVFMKTPEEIYDILALIGGKSRFVIKRVYPKegklPADEPVAVISTEKLYKIAGEY 234
                                       ****************************************************77766889***************** PP

                          FBPase_3 228 vGkDDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvg 304
                                       vGkDDPva+vRaqsglPavgev+e+fa+phlv+GwmrGshngp+mPv+++ +k+trfdgpprv+a gfql++gklvg
  gi|488601774|ref|YP_007908245.1| 235 VGKDDPVALVRAQSGLPAVGEVIEAFAFPHLVSGWMRGSHNGPIMPVPFRYSKCTRFDGPPRVIAAGFQLANGKLVG 311
                                       ***************************************************************************** PP

                          FBPase_3 305 pvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerfe 361
                                       pvDlfddpafd++R+ka+e+a+++Rr+Gpfephrlp+e++eYttlp vl+klkerfe
  gi|488601774|ref|YP_007908245.1| 312 PVDLFDDPAFDYTRQKAMEVAEYMRRHGPFEPHRLPSEDMEYTTLPGVLKKLKERFE 368
                                       *******************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 2007.85
//
[ok]
